#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
NCOA3	8202	hgsc.bcm.edu	37	20	46279815	46279823	+	In_Frame_Del	DEL	GCAGCAGCA	GCAGCAGCA	-	rs3830810		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	GCAGCAGCA	GCAGCAGCA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:46279815_46279823delGCAGCAGCA	ENST00000371998.3	+	20	3932_3940	c.3741_3749delGCAGCAGCA	c.(3739-3750)atgcagcagcag>atg	p.QQQ1272del	NCOA3_ENST00000341724.6_In_Frame_Del_p.QQQ1198del|NCOA3_ENST00000372004.3_In_Frame_Del_p.QQQ1268del|NCOA3_ENST00000371997.3_In_Frame_Del_p.QQQ1263del			Q9Y6Q9	NCOA3_HUMAN	nuclear receptor coactivator 3	1272	Acetyltransferase.|Poly-Gln.				androgen receptor signaling pathway (GO:0030521)|developmental growth (GO:0048589)|histone acetylation (GO:0016573)|labyrinthine layer morphogenesis (GO:0060713)|mammary gland branching involved in thelarche (GO:0060744)|multicellular organism growth (GO:0035264)|positive regulation of gene expression (GO:0010628)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|receptor transactivation (GO:0035624)|regulation of RNA biosynthetic process (GO:2001141)|transcription, DNA-templated (GO:0006351)|vagina development (GO:0060068)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)|protein N-terminus binding (GO:0047485)|signal transducer activity (GO:0004871)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)			breast(3)|endometrium(3)|kidney(4)|large_intestine(12)|lung(19)|ovary(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	52						CTATGATGATgcagcagcagcagcagcag	0.545																																					p.1247_1250del		Pindel,Atlas-Indel	.											.	NCOA3	156	.	0			c.3740_3748del						PASS	.																																			SO:0001651	inframe_deletion	8202	exon20			.	AF012108	CCDS13406.1, CCDS13407.1, CCDS54472.1	20q12	2011-07-01			ENSG00000124151	ENSG00000124151		"""Chromatin-modifying enzymes / K-acetyltransferases"", ""Basic helix-loop-helix proteins"""	7670	protein-coding gene	gene with protein product	"""receptor-associated coactivator 3"", ""thyroid hormone receptor activator molecule 1"""	601937				9252329, 9346901	Standard	NM_181659		Approved	RAC3, AIB1, ACTR, p/CIP, TRAM-1, CAGH16, TNRC16, KAT13B, bHLHe42, SRC-3, SRC3	uc002xtk.3	Q9Y6Q9	OTTHUMG00000033061	ENST00000371998.3:c.3741_3749delGCAGCAGCA	20.37:g.46279824_46279832delGCAGCAGCA	ENSP00000361066:p.Gln1272_Gln1274del	Somatic	107	.	.		WXS	Illumina HiSeq	Phase_I	92	16	0.174	NM_181659	A4LAZ5|Q0VF45|Q5JYD9|Q5JYE0|Q9BR49|Q9UPC9|Q9UPG4|Q9UPG7	In_Frame_Del	DEL	ENST00000371998.3	37	CCDS13407.1																																																																																			.	.	none		0.545	NCOA3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080405.1	NM_006534	
FAM90A1	55138	hgsc.bcm.edu	37	12	8374781	8374782	+	In_Frame_Ins	INS	-	-	ACG	rs71265055		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:8374781_8374782insACG	ENST00000538603.1	-	7	1589_1590	c.1031_1032insCGT	c.(1030-1032)acg>acCGTg	p.344_345insV	FAM90A1_ENST00000307435.6_In_Frame_Ins_p.344_345insV	NM_018088.3	NP_060558.3	Q86YD7	F90A1_HUMAN	family with sequence similarity 90, member A1	344				T -> TV (in Ref. 1; BAA91593). {ECO:0000305}.			nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(4)|lung(11)|ovary(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	25				Kidney(36;0.0866)		TCTGGGGTGACGTACGTGGTCC	0.673														2167	0.432708	0.0802	0.5101	5008	,	,		16505	0.5764		0.6968	False		,,,				2504	0.4346				p.T344delinsTV		Pindel,Atlas-Indel	.											.	FAM90A1	68	.	0			c.1032_1033insCGT						PASS	.			758,3506		60,638,1434						0.0	0.0		dbSNP_130	26	5796,2428		1994,1808,310	no	coding	FAM90A1	NM_018088.3		2054,2446,1744	A1A1,A1R,RR		29.5233,17.7767,47.5176				6554,5934				SO:0001652	inframe_insertion	55138	exon7			.	AK001270	CCDS31738.1	12p13.31	2011-08-31		2005-11-20	ENSG00000171847	ENSG00000171847			25526	protein-coding gene	gene with protein product		613041					Standard	NM_018088		Approved	FLJ10408	uc001qui.2	Q86YD7	OTTHUMG00000168641	ENST00000538603.1:c.1031_1032insCGT	12.37:g.8374781_8374782insACG	ENSP00000445418:p.Thr344_Ser345insVal	Somatic	91	.	.		WXS	Illumina HiSeq	Phase_I	83	20	0.241	NM_018088	D3DUU9|Q9NVZ6	In_Frame_Ins	INS	ENST00000538603.1	37	CCDS31738.1																																																																																			-|0.250;ACG|0.750	0.750	strong		0.673	FAM90A1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400468.1	NM_018088	
C9orf43	257169	hgsc.bcm.edu	37	9	116187645	116187646	+	In_Frame_Ins	INS	-	-	GCA	rs374165893|rs527300639|rs371732185		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:116187645_116187646insGCA	ENST00000288462.4	+	10	1333_1334	c.887_888insGCA	c.(886-891)cggcag>cgGCAgcag	p.304_305insQ	C9orf43_ENST00000374165.1_In_Frame_Ins_p.304_305insQ	NM_152786.1	NP_689999.1	Q8TAL5	CI043_HUMAN	chromosome 9 open reading frame 43	304	Gln-rich.									breast(2)|large_intestine(6)|lung(2)|ovary(1)|pancreas(1)|prostate(3)	15						cagcagcagcggcagcagcagc	0.55																																					p.R296delinsRQ		Pindel,Atlas-Indel	.											C9orf43,colon,carcinoma,0,1	C9orf43	49	1	0			c.887_888insGCA						PASS	.																																			SO:0001652	inframe_insertion	257169	exon10			.	BC026884	CCDS6796.1	9q33.1	2012-03-15			ENSG00000157653	ENSG00000157653			23570	protein-coding gene	gene with protein product						12477932	Standard	NM_152786		Approved	MGC17358	uc004bhp.3	Q8TAL5	OTTHUMG00000020526	ENST00000288462.4:c.906_908dupGCA	9.37:g.116187652_116187654dupGCA	ENSP00000288462:p.Gln304_Gln304dup	Somatic	79	.	.		WXS	Illumina HiSeq	Phase_I	61	22	0.361	NM_152786		In_Frame_Ins	INS	ENST00000288462.4	37	CCDS6796.1																																																																																			.	.	weak		0.550	C9orf43-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053739.1	NM_152786	
PCSK9	255738	hgsc.bcm.edu	37	1	55505552	55505553	+	In_Frame_Ins	INS	-	-	CTG	rs35574083|rs371488778|rs113330492|rs45454392|rs67610340	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:55505552_55505553insCTG	ENST00000302118.5	+	1	332_333	c.42_43insCTG	c.(43-45)ctg>CTGctg	p.15_15L>LL	PCSK9_ENST00000543384.1_5'Flank|PCSK9_ENST00000452118.2_In_Frame_Ins_p.15_15L>LL	NM_174936.3	NP_777596.2	Q8NBP7	PCSK9_HUMAN	proprotein convertase subtilisin/kexin type 9	15					apoptotic process (GO:0006915)|cellular response to insulin stimulus (GO:0032869)|cellular response to starvation (GO:0009267)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|kidney development (GO:0001822)|lipoprotein metabolic process (GO:0042157)|liver development (GO:0001889)|low-density lipoprotein particle receptor catabolic process (GO:0032802)|lysosomal transport (GO:0007041)|negative regulation of low-density lipoprotein particle clearance (GO:0010989)|negative regulation of receptor recycling (GO:0001920)|neurogenesis (GO:0022008)|neuron differentiation (GO:0030182)|phospholipid metabolic process (GO:0006644)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of receptor internalization (GO:0002092)|protein autoprocessing (GO:0016540)|proteolysis (GO:0006508)|regulation of low-density lipoprotein particle receptor catabolic process (GO:0032803)|regulation of neuron apoptotic process (GO:0043523)|regulation of receptor activity (GO:0010469)|triglyceride metabolic process (GO:0006641)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle (GO:0030134)|extracellular space (GO:0005615)|extrinsic component of external side of plasma membrane (GO:0031232)|Golgi apparatus (GO:0005794)|late endosome (GO:0005770)|lysosome (GO:0005764)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|rough endoplasmic reticulum (GO:0005791)	apolipoprotein binding (GO:0034185)|apolipoprotein receptor binding (GO:0034190)|low-density lipoprotein particle binding (GO:0030169)|low-density lipoprotein particle receptor binding (GO:0050750)|poly(A) RNA binding (GO:0044822)|protein self-association (GO:0043621)|serine-type endopeptidase activity (GO:0004252)|sodium channel inhibitor activity (GO:0019871)|very-low-density lipoprotein particle binding (GO:0034189)|very-low-density lipoprotein particle receptor binding (GO:0070326)	p.P14_L15insL(2)		NS(2)|breast(2)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(1)|liver(2)|lung(4)|ovary(3)|prostate(3)|skin(1)|urinary_tract(1)	32						Ggccgctgccactgctgctgct	0.703																																					p.P14delinsPL	Pancreas(137;1454 1827 5886 22361 42375)	Pindel,Atlas-Indel	.											.	PCSK9	76	.	2	Insertion - In frame(2)	breast(1)|central_nervous_system(1)	c.42_43insCTG						PASS	.																																			SO:0001652	inframe_insertion	255738	exon1			.	AX207686	CCDS603.1	1p34.1-p32	2014-09-17	2003-05-13		ENSG00000169174	ENSG00000169174			20001	protein-coding gene	gene with protein product		607786	"""hypercholesterolemia, autosomal dominant 3"""	HCHOLA3		12552133, 12730697	Standard	NM_174936		Approved	NARC-1, FH3	uc001cyf.2	Q8NBP7	OTTHUMG00000008136	ENST00000302118.5:c.61_63dupCTG	1.37:g.55505559_55505561dupCTG	ENSP00000303208:p.Leu23dup	Somatic	65	.	.		WXS	Illumina HiSeq	Phase_I	97	20	0.206	NM_174936	A8T640|C0JYY9|Q5PSM5|Q5SZQ2	In_Frame_Ins	INS	ENST00000302118.5	37	CCDS603.1																																																																																			.	.	none		0.703	PCSK9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022280.1	NM_174936	
POLI	11201	hgsc.bcm.edu	37	18	51795958	51795960	+	In_Frame_Del	DEL	CGA	CGA	-	rs78943519|rs10584411|rs3729509	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	CGA	CGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:51795958_51795960delCGA	ENST00000579534.1	+	1	185_187	c.42_44delCGA	c.(40-45)ggcgac>ggc	p.D17del	POLI_ENST00000579434.1_5'UTR|POLI_ENST00000217800.5_5'Flank|POLI_ENST00000406285.3_In_Frame_Del_p.D17del	NM_007195.2	NP_009126.2	Q9UNA4	POLI_HUMAN	polymerase (DNA directed) iota	17					DNA repair (GO:0006281)|DNA-dependent DNA replication (GO:0006261)	intracellular (GO:0005622)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	damaged DNA binding (GO:0003684)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)	p.D17delD(1)		breast(1)|endometrium(4)|kidney(2)|large_intestine(10)|lung(5)|ovary(3)|urinary_tract(1)	26				Colorectal(16;0.0234)|READ - Rectum adenocarcinoma(59;0.197)		AAGGCGGCGGCGACGACGACGAG	0.729								DNA polymerases (catalytic subunits)						3926	0.783946	0.9705	0.6427	5008	,	,		12312	0.7054		0.7078	False		,,,				2504	0.7914				p.14_15del		Pindel,Atlas-Indel	.											.	POLI	132	.	1	Deletion - In frame(1)	large_intestine(1)	c.41_43del						PASS	.			3523,343		1644,235,54						1.5	0.0		dbSNP_119	14	5235,2405		1985,1265,570	no	coding	POLI	NM_007195.2		3629,1500,624	A1A1,A1R,RR		31.4791,8.8722,23.8832				8758,2748				SO:0001651	inframe_deletion	11201	exon1			.		CCDS11954.2	18q21.1	2012-05-18			ENSG00000101751	ENSG00000101751		"""DNA polymerases"""	9182	protein-coding gene	gene with protein product		605252		RAD3OB, RAD30B		17609217	Standard	NM_007195		Approved		uc002lfj.4	Q9UNA4	OTTHUMG00000132704	ENST00000579534.1:c.42_44delCGA	18.37:g.51795967_51795969delCGA	ENSP00000462664:p.Asp17del	Somatic	72	.	.		WXS	Illumina HiSeq	Phase_I	63	31	0.492	NM_007195	Q8N590|Q9H0S1|Q9NYH6	In_Frame_Del	DEL	ENST00000579534.1	37	CCDS11954.2																																																																																			CGA|0.254;-|0.746	0.746	strong		0.729	POLI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256002.3	NM_007195	
VWA3A	146177	hgsc.bcm.edu	37	16	22144375	22144375	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:22144375delC	ENST00000389398.5	+	20	2123	c.2027delC	c.(2026-2028)accfs	p.T676fs	VWA3A_ENST00000389397.4_5'UTR	NM_173615.3	NP_775886.3	A6NCI4	VWA3A_HUMAN	von Willebrand factor A domain containing 3A	676	VWFA 1. {ECO:0000255|PROSITE- ProRule:PRU00219}.					extracellular region (GO:0005576)				haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(1)|skin(1)	7				GBM - Glioblastoma multiforme(48;0.0439)		AAGGAGGTCACCCGGGCTGCA	0.577																																					p.T676fs		Atlas-Indel	.											.	VWA3A	115	.	0			c.2026delA						PASS	.						38.0	42.0	41.0					16																	22144375		2053	4186	6239	SO:0001589	frameshift_variant	146177	exon20			.	AK128606, AK098260	CCDS45441.1	16p12.1	2008-02-05				ENSG00000175267			27088	protein-coding gene	gene with protein product						12477932	Standard	XM_006721021		Approved	FLJ46765, FLJ40941	uc010vbq.2	A6NCI4		ENST00000389398.5:c.2027delC	16.37:g.22144375delC	ENSP00000374049:p.Thr676fs	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	69	27	0.391304	NM_173615	A4QMU8|A6NNC0|Q6UTX4|Q6ZQZ9|Q8IUY6|Q8N9W1	Frame_Shift_Del	DEL	ENST00000389398.5	37	CCDS45441.1																																																																																			.	.	none		0.577	VWA3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430052.1		
DAAM2	23500	hgsc.bcm.edu	37	6	39869657	39869659	+	In_Frame_Del	DEL	GGA	GGA	-			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	GGA	GGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:39869657_39869659delGGA	ENST00000398904.2	+	25	3233_3235	c.3051_3053delGGA	c.(3049-3054)ctggag>ctg	p.E1019del	DAAM2_ENST00000538976.1_In_Frame_Del_p.E1018del|RP11-61I13.3_ENST00000437947.1_RNA|DAAM2_ENST00000274867.4_In_Frame_Del_p.E1019del			Q86T65	DAAM2_HUMAN	dishevelled associated activator of morphogenesis 2	1019	DAD. {ECO:0000255|PROSITE- ProRule:PRU00577}.				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)					GCAGCTCGCTGGAGGAGGGAGGA	0.65																																					p.1017_1018del		Pindel,Atlas-Indel	.											.	DAAM2	101	.	0			c.3050_3052del						PASS	.																																			SO:0001651	inframe_deletion	23500	exon25			.	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.3051_3053delGGA	6.37:g.39869660_39869662delGGA	ENSP00000381876:p.Glu1019del	Somatic	57	.	.		WXS	Illumina HiSeq	Phase_I	45	22	0.489	NM_001201427	G5EA45|Q5T4T8|Q5T4U0|Q9NQI5|Q9Y4G0	In_Frame_Del	DEL	ENST00000398904.2	37	CCDS56426.1																																																																																			.	.	none		0.650	DAAM2-003	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000280648.1		
ACOT4	122970	hgsc.bcm.edu	37	14	74060511	74060512	+	Frame_Shift_Ins	INS	-	-	TCAA	rs79684878|rs373880503	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:74060511_74060512insTCAA	ENST00000326303.4	+	2	817_818	c.563_564insTCAA	c.(562-567)ctagctfs	p.A189fs		NM_152331.3	NP_689544.3	Q8N9L9	ACOT4_HUMAN	acyl-CoA thioesterase 4	189				ALAY -> DLQS (in Ref. 1; BAC04313). {ECO:0000305}.	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)		ACGTTGGCTCTAGCTTATTATA	0.495														6	0.00119808	0.0	0.0	5008	,	,		16663	0.0		0.006	False		,,,				2504	0.0				p.L188fs		Atlas-Indel	.											.	ACOT4	25	.	0			c.563_564insTCAA						PASS	.																																			SO:0001589	frameshift_variant	122970	exon2			.	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	Exception_encountered	14.37:g.74060511_74060512insTCAA	ENSP00000323071:p.Ala189fs	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	82	12	0.146341	NM_152331	Q17RF4|Q5BKT6|Q86TX0|Q86TX1|Q96N88	Frame_Shift_Ins	INS	ENST00000326303.4	37	CCDS9817.1																																																																																			.	.	weak		0.495	ACOT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404298.2	NM_152331	
CNKSR1	10256	hgsc.bcm.edu	37	1	26510311	26510311	+	Frame_Shift_Del	DEL	C	C	-	rs201305445	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:26510311delC	ENST00000374253.5	+	9	905	c.866delC	c.(865-867)accfs	p.T289fs	CNKSR1_ENST00000531191.1_Frame_Shift_Del_p.T24fs|CNKSR1_ENST00000361530.6_Frame_Shift_Del_p.T282fs	NM_006314.2	NP_006305.2	Q969H4	CNKR1_HUMAN	connector enhancer of kinase suppressor of Ras 1	289	Pro-rich.				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)			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)		ATACCGGAGACCCCCCCACAG	0.667														59	0.0117812	0.0008	0.0202	5008	,	,		6575	0.001		0.0348	False		,,,				2504	0.0082				p.T282fs	NSCLC(180;1396 2109 28270 30756 34275)	Pindel,Atlas-Indel	.											.	CNKSR1	66	.	0			c.844delA						PASS	.			5,37,4224		0,0,5,0,37,2091	44.0	46.0	45.0			-0.5	0.0	1		47	1,431,7822		0,0,1,13,405,3708	no	codingComplex	CNKSR1	NM_006314.2		0,0,6,13,442,5799	A1A1,A1A2,A1R,A2A2,A2R,RR		5.2338,0.9845,3.7859			26510311	6,468,12046	2203	4300	6503	SO:0001589	frameshift_variant	10256	exon9			.	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.866delC	1.37:g.26510311delC	ENSP00000363371:p.Thr289fs	Somatic	77	.	.		WXS	Illumina HiSeq	Phase_I	92	25	0.272	NM_006314	B1AMW9|O95381	Frame_Shift_Del	DEL	ENST00000374253.5	37																																																																																				C|0.980;-|0.020	0.020	strong		0.667	CNKSR1-007	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000089943.2	NM_006314	
RP1L1	94137	hgsc.bcm.edu	37	8	10467681	10467686	+	In_Frame_Del	DEL	TCCTTC	TCCTTC	-	rs386722181		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	TCCTTC	TCCTTC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:10467681_10467686delTCCTTC	ENST00000382483.3	-	4	4145_4150	c.3922_3927delGAAGGA	c.(3922-3927)gaaggadel	p.EG1308del		NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	1326	8 X 16 AA approximate tandem repeats of T-E-E-G-L-Q-E-E-G-V-Q-L-E-E-T-K.				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)		ctccttctgttccttcttTAGTTTCC	0.485																																					p.1308_1310del		Atlas-Indel	.											.	RP1L1	453	.	0			c.3923_3928del						PASS	.			43,79,3686		3,0,37,3,73,1788						-0.4	0.0			135	362,29,7561		4,0,354,0,29,3589	no	codingComplex	RP1L1	NM_178857.5		7,0,391,3,102,5377	A1A1,A1A2,A1R,A2A2,A2R,RR		4.917,3.2038,4.3622				405,108,11247				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.3922_3927delGAAGGA	8.37:g.10467681_10467686delTCCTTC	ENSP00000371923:p.Glu1308_Gly1309del	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	78	18	0.230769	NM_178857	Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	In_Frame_Del	DEL	ENST00000382483.3	37	CCDS43708.1																																																																																			.	.	none		0.485	RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375673.1		
SLC28A1	9154	hgsc.bcm.edu	37	15	85438311	85438312	+	In_Frame_Ins	INS	-	-	TTG	rs17215836|rs151038463	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:85438311_85438312insTTG	ENST00000286749.3	+	5	508_509	c.418_419insTTG	c.(418-420)ctc>cTTGtc	p.140_141insV	SLC28A1_ENST00000538177.1_In_Frame_Ins_p.140_141insV|SLC28A1_ENST00000537624.1_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_ENST00000394573.1_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,Atlas-Indel	.											.	SLC28A1	118	.	2	Insertion - In frame(2)	lung(2)	c.418_419insTTG						PASS	.		,	1267,2997		209,849,1074					,	-2.5	0.0		dbSNP_126	46	2510,5742		383,1744,1999	no	coding,coding	SLC28A1	NM_201651.1,NM_004213.3	,	592,2593,3073	A1A1,A1R,RR		30.4169,29.7139,30.1774	,	,		3777,8739				SO:0001652	inframe_insertion	9154	exon6			.	U62967	CCDS10334.1, CCDS10335.1, CCDS73777.1	15q25.3	2013-07-17	2013-07-17		ENSG00000156222	ENSG00000156222		"""Solute carriers"""	11001	protein-coding gene	gene with protein product		606207	"""solute carrier family 28 (sodium-coupled nucleoside transporter), member 1"""			9124315	Standard	NM_004213		Approved	CNT1	uc002blg.3	O00337	OTTHUMG00000148668	Exception_encountered	15.37:g.85438311_85438312insTTG	ENSP00000286749:p.Leu140_Lys141insVal	Somatic	67	.	.		WXS	Illumina HiSeq	Phase_I	89	33	0.371	NM_004213	A0AV42|A8K7I2|O00335|O00336|Q5U5S6|Q5U648|Q9UEZ9	In_Frame_Ins	INS	ENST00000286749.3	37	CCDS10334.1																																																																																			-|0.732;TTG|0.268	0.268	strong		0.639	SLC28A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000308998.2		
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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	TGCAACCCCTGCAGCCCCTGCAACCCG	TGCAACCCCTGCAGCCCCTGCAACCCG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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		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	130	0	0		WXS	Illumina HiSeq	Phase_I	103	19	0.184466	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		
KRTAP10-2	386679	hgsc.bcm.edu	37	21	45970760	45970774	+	In_Frame_Del	DEL	CTTGCAGCAGACAGG	CTTGCAGCAGACAGG	-	rs113146284|rs371219783|rs200215960|rs67692969|rs76536096|rs76021731|rs71199610	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	CTTGCAGCAGACAGG	CTTGCAGCAGACAGG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:45970760_45970774delCTTGCAGCAGACAGG	ENST00000391621.1	-	1	614_628	c.568_582delCCTGTCTGCTGCAAG	c.(568-582)cctgtctgctgcaagdel	p.PVCCK190del	TSPEAR_ENST00000397916.1_Intron|TSPEAR_ENST00000323084.4_Intron|KRTAP10-2_ENST00000498210.1_Intron	NM_198693.2	NP_941966.1	P60368	KR102_HUMAN	keratin associated protein 10-2	190	22 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				large_intestine(1)|lung(4)|skin(1)	6						AGCAGATGGACTTGCAGCAGACAGGCTTGCAGCAG	0.609														1066	0.212859	0.1664	0.1513	5008	,	,		23256	0.3661		0.2058	False		,,,				2504	0.1687				p.190_195del		Atlas-Indel	.											.	KRTAP10-2	21	.	0			c.569_583del						PASS	.		,	649,3615		35,579,1518					,	0.6	0.0		dbSNP_130	134	1460,6792		93,1274,2759	no	coding,intron	TSPEAR,KRTAP10-2	NM_198693.2,NM_144991.2	,	128,1853,4277	A1A1,A1R,RR		17.6927,15.2205,16.8504	,	,		2109,10407				SO:0001651	inframe_deletion	386679	exon1			.	AJ566381	CCDS42955.1	21q22.3	2007-10-05			ENSG00000205445	ENSG00000205445		"""Keratin associated proteins"""	22967	protein-coding gene	gene with protein product				KRTAP18-2			Standard	NM_198693		Approved	KAP10.2, KAP18.2	uc002zfi.1	P60368	OTTHUMG00000057625	ENST00000391621.1:c.568_582delCCTGTCTGCTGCAAG	21.37:g.45970760_45970774delCTTGCAGCAGACAGG	ENSP00000375479:p.Pro190_Lys194del	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	103	21	0.203883	NM_198693	Q70LJ5	In_Frame_Del	DEL	ENST00000391621.1	37	CCDS42955.1																																																																																			CTTGCAGCAGACAGG|0.758;-|0.242	0.242	strong		0.609	KRTAP10-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128027.1		
ANKRD36	375248	hgsc.bcm.edu	37	2	97779488	97779488	+	Frame_Shift_Del	DEL	C	C	-	rs141447363	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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,Atlas-Indel	.											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	129	.	.		WXS	Illumina HiSeq	Phase_I	118	38	0.322	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		
AKAP3	10566	hgsc.bcm.edu	37	12	4735970	4735970	+	Frame_Shift_Del	DEL	A	A	-	rs527978551|rs370203105|rs71441828|rs67512580|rs2041290	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:4735970delA	ENST00000545990.2	-	5	2622	c.2098delT	c.(2098-2100)tctfs	p.S700fs	AKAP3_ENST00000228850.1_Frame_Shift_Del_p.S700fs|RP11-500M8.7_ENST00000536588.1_Intron	NM_001278309.1	NP_001265238.1	O75969	AKAP3_HUMAN	A kinase (PRKA) anchor protein 3	700			S -> F (in dbSNP:rs2041291).|S -> P (in dbSNP:rs2041290).	S -> L (in Ref. 2; AAC35854). {ECO:0000305}.	acrosome reaction (GO:0007340)|cellular component movement (GO:0006928)|protein localization (GO:0008104)|single fertilization (GO:0007338)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	acrosomal vesicle (GO:0001669)|nucleus (GO:0005634)|sperm fibrous sheath (GO:0035686)|sperm principal piece (GO:0097228)	protein kinase A binding (GO:0051018)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(13)|liver(1)|lung(17)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	51						GCATCTCCAGACTTGTCATCT	0.502																																					p.S700fs		Atlas-Indel	.											.	AKAP3	212	.	0			c.2099delC						PASS	.			579,3685		38,503,1591	76.0	65.0	69.0			0.4	0.8	12	dbSNP_94	71	1072,7176		68,936,3120	no	frameshift	AKAP3	NM_006422.2		106,1439,4711	A1A1,A1R,RR		12.9971,13.5788,13.1953			4735970	1651,10861	2203	4300	6503	SO:0001589	frameshift_variant	10566	exon4			.	U85715	CCDS8531.1	12p13.3	2009-03-12				ENSG00000111254		"""A-kinase anchor proteins"""	373	protein-coding gene	gene with protein product	"""Fibrous Sheath Protein of 95 kDa"", ""cancer/testis antigen 82"""	604689				10334916, 10319321	Standard	NM_001278309		Approved	FSP95, SOB1, AKAP110, CT82	uc001qnb.4	O75969		ENST00000545990.2:c.2098delT	12.37:g.4735970delA	ENSP00000440994:p.Ser700fs	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	78	11	0.141026	NM_006422	O75945|Q86X01|Q9UM61	Frame_Shift_Del	DEL	ENST00000545990.2	37	CCDS8531.1																																																																																			A|0.868;-|0.132	0.132	strong		0.502	AKAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398911.2	NM_006422	
CELA1	1990	hgsc.bcm.edu	37	12	51740413	51740414	+	Frame_Shift_Ins	INS	-	-	C	rs573952082|rs386762976|rs377599213|rs370927847	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	154	0	0		WXS	Illumina HiSeq	Phase_I	92	15	0.163043	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	
CDCP2	200008	hgsc.bcm.edu	37	1	54605318	54605319	+	Frame_Shift_Ins	INS	-	-	GG	rs77544356|rs36013100|rs66537746|rs76608277|rs549857682|rs3841798	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:54605318_54605319insGG	ENST00000371330.1	-	4	2071_2072	c.1224_1225insCC	c.(1222-1227)cccatgfs	p.M409fs	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	409						extracellular region (GO:0005576)		p.M409fs*>42(1)		kidney(1)|large_intestine(6)|lung(13)|ovary(1)|prostate(2)|stomach(1)	24						AGACCATTCATGGGGGGGGCAG	0.594																																					p.M409fs		Pindel,Atlas-Indel	.											.	CDCP2	52	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.1225_1226insCC						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_1224dupCC	1.37:g.54605325_54605326dupGG	ENSP00000360381:p.Met409fs	Somatic	86	.	.		WXS	Illumina HiSeq	Phase_I	70	13	0.186	NM_201546	Q6ZWJ3	Frame_Shift_Ins	INS	ENST00000371330.1	37	CCDS588.2																																																																																			-|0.500;GG|0.500	0.500	strong		0.594	CDCP2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000022209.2	NM_201546	
SYT14	255928	hgsc.bcm.edu	37	1	210267894	210267896	+	In_Frame_Del	DEL	GAA	GAA	-	rs144713062|rs200839898|rs2307890	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	GAA	GAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:210267894_210267896delGAA	ENST00000472886.1	+	5	684_686	c.670_672delGAA	c.(670-672)gaadel	p.E225del	SYT14_ENST00000534859.1_In_Frame_Del_p.E225del|SYT14_ENST00000367019.1_In_Frame_Del_p.E225del|SYT14_ENST00000367015.1_In_Frame_Del_p.E187del|SYT14_ENST00000399639.2_In_Frame_Del_p.E225del|SYT14_ENST00000271745.7_3'UTR|SYT14_ENST00000537238.1_In_Frame_Del_p.E187del|SYT14_ENST00000422431.1_In_Frame_Del_p.E270del			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	181	.	.		WXS	Illumina HiSeq	Phase_I	120	40	0.333	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	
TMPRSS3	64699	hgsc.bcm.edu	37	21	43803308	43803309	+	Splice_Site	INS	-	-	TA	rs34966432|rs56283966	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:43803308_43803309insTA	ENST00000291532.3	-	8	1572		c.e8-1		TMPRSS3_ENST00000433957.2_Splice_Site|TMPRSS3_ENST00000398405.1_Splice_Site|TMPRSS3_ENST00000380399.1_Splice_Site|TMPRSS3_ENST00000398397.3_Splice_Site|TMPRSS3_ENST00000474596.1_Splice_Site	NM_032404.2	NP_115780.1	P57727	TMPS3_HUMAN	transmembrane protease, serine 3						cellular sodium ion homeostasis (GO:0006883)|proteolysis (GO:0006508)|sensory perception of sound (GO:0007605)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)|sodium channel regulator activity (GO:0017080)	p.?(2)		breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(2)|ovary(4)|skin(1)	13						TGACCACAGGCTATGGAGGGGA	0.599														870	0.173722	0.118	0.0865	5008	,	,		22290	0.3145		0.0865	False		,,,				2504	0.2556				.		Pindel,Atlas-Indel	.											TMPRSS3,NS,carcinoma,0,2	TMPRSS3	40	2	2	Unknown(2)	ovary(2)	c.617-1->TA						PASS	.		,	532,3732		34,464,1634				http://www.ncbi.nlm.nih.gov/sites/varvu?gene	,	4.8	0.9		dbSNP_129	68	605,7649		19,567,3541	no	splice-3,splice-3	TMPRSS3	NM_032405.1,NM_024022.2	,	53,1031,5175	A1A1,A1R,RR		7.3298,12.4765,9.0829	,	,		1137,11381				SO:0001630	splice_region_variant	64699	exon9			.	AF201380	CCDS13686.1, CCDS42939.1, CCDS58790.1	21q22.3	2010-04-13			ENSG00000160183	ENSG00000160183		"""Serine peptidases / Transmembrane"""	11877	protein-coding gene	gene with protein product		605511		DFNB10, DFNB8		11462234, 11907649	Standard	NM_032405		Approved		uc002zbc.3	P57727	OTTHUMG00000086796	ENST00000291532.3:c.617-1->TA	21.37:g.43803309_43803310dupTA		Somatic	65	.	.		WXS	Illumina HiSeq	Phase_I	88	29	0.330	NM_024022	D3DSJ6|Q5USC7|Q6ZMC3	Splice_Site	INS	ENST00000291532.3	37	CCDS13686.1																																																																																			-|0.840;TA|0.160	0.160	strong		0.599	TMPRSS3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000195347.1		Intron
SKA3	221150	hgsc.bcm.edu	37	13	21746601	21746601	+	Frame_Shift_Del	DEL	G	G	-	rs151272242	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:21746601delG	ENST00000314759.5	-	3	332	c.208delC	c.(208-210)caafs	p.Q70fs	SKA3_ENST00000400018.3_Frame_Shift_Del_p.Q70fs	NM_145061.5	NP_659498.4	Q8IX90	SKA3_HUMAN	spindle and kinetochore associated complex subunit 3	70					chromosome segregation (GO:0007059)|mitotic nuclear division (GO:0007067)|regulation of microtubule polymerization or depolymerization (GO:0031110)	condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|spindle microtubule (GO:0005876)				breast(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	19						ATGCCTTCTTGATTTTCCAAT	0.259													G|G|-|deletion	696	0.138978	0.0295	0.134	5008	,	,		19850	0.2391		0.1412	False		,,,				2504	0.1851				p.Q70fs		Atlas-Indel	.											.	SKA3	76	.	0			c.209delA						PASS	.		,	159,4085		0,159,1963	42.0	43.0	42.0		,	3.0	0.9	13	dbSNP_134	45	930,7300		2,926,3187	no	frameshift,frameshift	SKA3	NM_145061.5,NM_001166017.1	,	2,1085,5150	A1A1,A1R,RR		11.3001,3.7465,8.7302	,	,	21746601	1089,11385	2195	4287	6482	SO:0001589	frameshift_variant	221150	exon3			.	AF361358	CCDS31946.1, CCDS53856.1	13q11	2013-01-17	2009-08-19	2009-08-19	ENSG00000165480	ENSG00000165480			20262	protein-coding gene	gene with protein product			"""chromosome 13 open reading frame 3"""	C13orf3		19387489, 19289083, 19646878, 19360002	Standard	NM_145061		Approved	MGC4832, RAMA1	uc001unt.3	Q8IX90	OTTHUMG00000016539	ENST00000314759.5:c.208delC	13.37:g.21746601delG	ENSP00000319417:p.Gln70fs	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	137	14	0.10219	NM_145061	A2A330|A2A331|B2RBY2|Q5VZV5|Q86WR2|Q8NBG1|Q96D22	Frame_Shift_Del	DEL	ENST00000314759.5	37	CCDS31946.1																																																																																			.	.	strong		0.259	SKA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000272912.1	NM_145061	
OR51F1	256892	hgsc.bcm.edu	37	11	4790874	4790874	+	Frame_Shift_Del	DEL	G	G	-	rs563980182|rs34672924	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:4790874delG	ENST00000380383.1	-	1	294	c.295delC	c.(295-297)cgtfs	p.R99fs	OR51F1_ENST00000343430.3_Frame_Shift_Del_p.R92fs|MMP26_ENST00000477339.1_Intron|MMP26_ENST00000380390.1_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		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	106	0	0		WXS	Illumina HiSeq	Phase_I	109	24	0.220183	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	
TAF1L	138474	hgsc.bcm.edu	37	9	32633583	32633584	+	Frame_Shift_Ins	INS	-	-	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:32633583_32633584insT	ENST00000242310.4	-	1	2083_2084	c.1994_1995insA	c.(1993-1995)aagfs	p.K665fs	RP11-555J4.4_ENST00000430787.1_RNA	NM_153809.2	NP_722516.1	Q8IZX4	TAF1L_HUMAN	TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 210kDa-like	665					DNA-templated transcription, initiation (GO:0006352)|histone acetylation (GO:0016573)|male meiosis (GO:0007140)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	transcription factor TFIID complex (GO:0005669)	DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|lysine-acetylated histone binding (GO:0070577)|protein serine/threonine kinase activity (GO:0004674)|TBP-class protein binding (GO:0017025)	p.K665fs*4(2)		breast(6)|central_nervous_system(4)|endometrium(14)|kidney(11)|large_intestine(32)|liver(2)|lung(68)|ovary(2)|pancreas(2)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(1)	159			LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.00301)		TCATCTTGGCCTTTTTTTTGAT	0.48																																					p.K665fs		Atlas-Indel	.											.	TAF1L	382	.	2	Deletion - Frameshift(2)	large_intestine(2)	c.1995_1996insA						PASS	.			1,4261		0,1,2130						0.6	1.0			147	0,8252		0,0,4126	no	frameshift	TAF1L	NM_153809.2		0,1,6256	A1A1,A1R,RR		0.0,0.0235,0.0080				1,12513				SO:0001589	frameshift_variant	138474	exon1			.	AF390562	CCDS35003.1	9p12	2007-07-27	2007-07-27		ENSG00000122728	ENSG00000122728			18056	protein-coding gene	gene with protein product		607798	"""TAF1-like RNA polymerase II, TATA box binding protein (TBP)-associated factor, 210kDa"""			12217962	Standard	NM_153809		Approved		uc003zrg.1	Q8IZX4	OTTHUMG00000019747	ENST00000242310.4:c.1995dupA	9.37:g.32633591_32633591dupT	ENSP00000418379:p.Lys665fs	Somatic	377	0	0		WXS	Illumina HiSeq	Phase_I	234	16	0.0683761	NM_153809	Q0VG57	Frame_Shift_Ins	INS	ENST00000242310.4	37	CCDS35003.1																																																																																			.	.	none		0.480	TAF1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052012.2		
ERICH3	127254	hgsc.bcm.edu	37	1	75037858	75037860	+	In_Frame_Del	DEL	CCT	CCT	-	rs10539747	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	CCT	CCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:75037858_75037860delCCT	ENST00000326665.5	-	14	3752_3754	c.3534_3536delAGG	c.(3532-3537)ggaggg>ggg	p.1178_1179GG>G	C1orf173_ENST00000433746.2_5'UTR	NM_001002912.4	NP_001002912.4	Q5RHP9	ERIC3_HUMAN		1178	Glu-rich.							p.G1178G(1)|p.G1179V(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(23)|lung(123)|ovary(3)|prostate(10)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)	184						CAGTCTTTCCCCTCCTCCTTCTT	0.493														619	0.123602	0.053	0.1484	5008	,	,		21479	0.2212		0.1034	False		,,,				2504	0.1217				p.1179_1179del		Pindel,Atlas-Indel	.											C1orf173,NS,carcinoma,-1,1	C1orf173	380	1	2	Substitution - Missense(1)|Substitution - coding silent(1)	lung(2)	c.3535_3537del						PASS	.			239,4027		6,227,1900						-1.3	0.0		dbSNP_119	131	781,7473		37,707,3383	no	coding	C1orf173	NM_001002912.4		43,934,5283	A1A1,A1R,RR		9.4621,5.6024,8.147				1020,11500				SO:0001651	inframe_deletion	127254	exon14			.																												ENST00000326665.5:c.3534_3536delAGG	1.37:g.75037864_75037866delCCT	ENSP00000322609:p.Gly1179del	Somatic	128	.	.		WXS	Illumina HiSeq	Phase_I	147	50	0.340	NM_001002912	Q68DL8|Q6GMR8|Q6ZSF9|Q8ND41	In_Frame_Del	DEL	ENST00000326665.5	37	CCDS30755.1																																																																																			CCT|0.871;-|0.129	0.129	strong		0.493	C1orf173-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026516.1		
DNAH8	1769	hgsc.bcm.edu	37	6	38840427	38840428	+	Frame_Shift_Del	DEL	AT	AT	-			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	AT	AT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:38840427_38840428delAT	ENST00000359357.3	+	48	6709_6710	c.6455_6456delAT	c.(6454-6456)catfs	p.H2152fs	DNAH8_ENST00000441566.1_Frame_Shift_Del_p.H2116fs|DNAH8_ENST00000449981.2_Frame_Shift_Del_p.H2369fs			Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy chain 8	2152	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(7)|breast(9)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(16)|large_intestine(44)|liver(4)|lung(101)|ovary(7)|pancreas(2)|prostate(8)|skin(28)|stomach(4)|upper_aerodigestive_tract(6)|urinary_tract(4)	260						GGAAGGCCTCATAGAGAAATGC	0.47																																					p.2369_2369del		Pindel,Atlas-Indel	.											.	DNAH8	1239	.	0			c.7105_7106del						PASS	.																																			SO:0001589	frameshift_variant	1769	exon50			.	Z83806	CCDS75447.1	6p21.2	2012-04-19	2006-09-04		ENSG00000124721	ENSG00000124721		"""Axonemal dyneins"""	2952	protein-coding gene	gene with protein product		603337	"""dynein, axonemal, heavy polypeptide 8"""			9373155	Standard	NM_001206927		Approved	hdhc9	uc021yzh.1	Q96JB1	OTTHUMG00000016253	ENST00000359357.3:c.6455_6456delAT	6.37:g.38840427_38840428delAT	ENSP00000352312:p.His2152fs	Somatic	117	.	.		WXS	Illumina HiSeq	Phase_I	128	43	0.336	NM_001206927	O00438|Q5JYI2|Q5T2M3|Q5T2M4|Q5TG00|Q9UEM4	Frame_Shift_Del	DEL	ENST00000359357.3	37																																																																																				.	.	none		0.470	DNAH8-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000043574.1	NM_001206927	
AOC1	26	hgsc.bcm.edu	37	7	150558156	150558156	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:150558156delC	ENST00000493429.1	+	7	2699	c.2115delC	c.(2113-2115)gacfs	p.D705fs	AOC1_ENST00000360937.4_Frame_Shift_Del_p.D705fs|AOC1_ENST00000416793.2_Frame_Shift_Del_p.D724fs|AOC1_ENST00000467291.1_Frame_Shift_Del_p.D705fs|AOC1_ENST00000480582.1_3'UTR			P19801	AOC1_HUMAN	amine oxidase, copper containing 1	705					amine metabolic process (GO:0009308)|cellular response to azide (GO:0097185)|cellular response to copper ion (GO:0071280)|cellular response to copper ion starvation (GO:0035874)|cellular response to heparin (GO:0071504)|cellular response to histamine (GO:0071420)|oxidation-reduction process (GO:0055114)|response to antibiotic (GO:0046677)|response to drug (GO:0042493)|sodium ion transmembrane transport (GO:0035725)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|peroxisome (GO:0005777)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	calcium ion binding (GO:0005509)|cation channel activity (GO:0005261)|copper ion binding (GO:0005507)|diamine oxidase activity (GO:0052597)|drug binding (GO:0008144)|heparin binding (GO:0008201)|histamine oxidase activity (GO:0052598)|methylputrescine oxidase activity (GO:0052599)|primary amine oxidase activity (GO:0008131)|propane-1,3-diamine oxidase activity (GO:0052600)|protein complex binding (GO:0032403)|protein homodimerization activity (GO:0042803)|quinone binding (GO:0048038)|receptor activity (GO:0004872)|sodium channel activity (GO:0005272)|zinc ion binding (GO:0008270)									Amiloride(DB00594)	TCCCAGAGGACCCCTCCCTGG	0.617																																					p.D724fs		Pindel,Atlas-Indel	.											.	ABP1	92	.	0			c.2171delA						PASS	.						63.0	74.0	70.0					7																	150558156		2045	4197	6242	SO:0001589	frameshift_variant	26	exon5			.	AK092514	CCDS43679.1, CCDS64797.1	7q36.1	2013-06-19	2013-06-19	2013-06-19	ENSG00000002726	ENSG00000002726	1.4.3.22		80	protein-coding gene	gene with protein product	"""diamine oxidase"""	104610	"""amiloride binding protein 1 (amine oxidase (copper-containing))"""	ABP1		8182053	Standard	NM_001091		Approved	DAO	uc003wia.2	P19801	OTTHUMG00000158306	ENST00000493429.1:c.2115delC	7.37:g.150558156delC	ENSP00000418614:p.Asp705fs	Somatic	95	.	.		WXS	Illumina HiSeq	Phase_I	81	17	0.210	NM_001272072	C9J690|Q16683|Q16684|Q56II4|Q6GU42	Frame_Shift_Del	DEL	ENST00000493429.1	37	CCDS43679.1																																																																																			.	.	none		0.617	AOC1-009	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350628.1	NM_001091	
CIB1	10519	hgsc.bcm.edu	37	15	90774448	90774451	+	Intron	DEL	AGAG	AGAG	-	rs199557034|rs71715019|rs201909717|rs34604050	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	AGAG	AGAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:90774448_90774451delAGAG	ENST00000328649.6	-	5	508				GDPGP1_ENST00000558017.1_5'Flank	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)			ATCAAAGTCTAGAGAGCAGACACA	0.588														2970	0.593051	0.4198	0.6138	5008	,	,		19737	0.8016		0.5169	False		,,,				2504	0.6759				.		Pindel,Atlas-Indel	.											.	CIB1	8	.	0			.						PASS	.																																			SO:0001627	intron_variant	10519	.			.	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	ENST00000328649.6:c.347-3CTCT>-	15.37:g.90774448_90774451delAGAG		Somatic	60	.	.		WXS	Illumina HiSeq	Phase_I	59	27	0.458	.	B5BU40|H6WJF3|O00693|O00735|Q6IB49|Q96J54|Q99971	Splice_Site	DEL	ENST00000328649.6	37	CCDS10360.1																																																																																			AGAG|0.433;-|0.567	0.567	strong		0.588	CIB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313419.1		
ZNF880	400713	hgsc.bcm.edu	37	19	52887146	52887146	+	Frame_Shift_Del	DEL	A	A	-	rs398101268|rs34470614		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:52887146delA	ENST00000422689.2	+	4	328	c.313delA	c.(313-315)aaafs	p.K105fs	ZNF880_ENST00000424032.2_3'UTR	NM_001145434.1	NP_001138906.1	Q6PDB4	ZN880_HUMAN	zinc finger protein 880	105					regulation of transcription, DNA-templated (GO:0006355)	intracellular (GO:0005622)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(2)|skin(1)	10						CAAGTCTCTTAAAAATCAACT	0.368																																					p.L104fs		Pindel,Atlas-Indel	.											.	ZNF880	45	.	0			c.312delT						PASS	.			1094,2682		234,626,1028	61.0	45.0	50.0			-2.8	0.0	19	dbSNP_126	72	3080,4810		677,1726,1542	no	frameshift	ZNF880	NM_001145434.1		911,2352,2570	A1A1,A1R,RR		39.0368,28.9725,35.7792			52887146	4174,7492	690	1569	2259	SO:0001589	frameshift_variant	400713	exon4			.	BC058819	CCDS46164.1	19q13.41	2013-01-08			ENSG00000221923	ENSG00000221923		"""Zinc fingers, C2H2-type"", ""-"""	37249	protein-coding gene	gene with protein product							Standard	NM_001145434		Approved		uc002pzc.3	Q6PDB4	OTTHUMG00000167972	ENST00000422689.2:c.313delA	19.37:g.52887146delA	ENSP00000406318:p.Lys105fs	Somatic	118	.	.		WXS	Illumina HiSeq	Phase_I	74	47	0.635	NM_001145434	B4DNA6	Frame_Shift_Del	DEL	ENST00000422689.2	37	CCDS46164.1																																																																																			A|0.672;-|0.328	0.328	strong		0.368	ZNF880-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397374.1	NM_001145434	
PLAC9	219348	hgsc.bcm.edu	37	10	81904097	81904098	+	In_Frame_Ins	INS	-	-	AGA	rs368889684|rs149506488|rs71482765	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:81904097_81904098insAGA	ENST00000372263.3	+	3	323_324	c.281_282insAGA	c.(280-285)ggagat>ggAGAagat	p.94_95GD>GED	PLAC9_ENST00000372270.2_In_Frame_Ins_p.52_53GD>GED|PLAC9_ENST00000372267.2_Intron	NM_001012973.1	NP_001012991.1	Q5JTB6	PLAC9_HUMAN	placenta-specific 9	94						extracellular region (GO:0005576)				kidney(1)|ovary(1)	2	Prostate(51;0.0095)|all_epithelial(25;0.175)		Colorectal(32;0.109)			GACCTTCTCGGAGGTGAGCAGT	0.678											OREG0020321	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)		103	0.0205671	0.0227	0.0173	5008	,	,		12770	0.0		0.0338	False		,,,				2504	0.0276				p.G94delinsGE		Pindel,Atlas-Indel	.											.	PLAC9	9	.	0			c.281_282insAGA						PASS	.			91,4169		2,87,2041						0.8	0.0		dbSNP_130	18	352,7896		6,340,3778	no	coding-near-splice	PLAC9	NM_001012973.1		8,427,5819	A1A1,A1R,RR		4.2677,2.1362,3.5417				443,12065				SO:0001652	inframe_insertion	219348	exon3			.		CCDS31232.1	10q23.2	2008-02-04			ENSG00000189129	ENSG00000189129			19255	protein-coding gene	gene with protein product		612857					Standard	NM_001012973		Approved		uc001kbp.1	Q5JTB6	OTTHUMG00000018596	ENST00000372263.3:c.282_284dupAGA	10.37:g.81904097_81904098insAGA	ENSP00000361337:p.Gly94_Asp95insGlu	Somatic	23	.	.	1209	WXS	Illumina HiSeq	Phase_I	25	11	0.440	NM_001012973		In_Frame_Ins	INS	ENST00000372263.3	37	CCDS31232.1																																																																																			.	.	strong		0.678	PLAC9-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049019.1	NM_001012973	
CYP4B1	1580	hgsc.bcm.edu	37	1	47280747	47280748	+	Splice_Site	DEL	AT	AT	-	rs55835239|rs397687617|rs3215983	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	AT	AT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:47280747_47280748delAT	ENST00000271153.4	+	8	917_918	c.881_882delAT	c.(880-882)gat>g	p.D294fs	CYP4B1_ENST00000371919.4_Splice_Site_p.D280fs|CYP4B1_ENST00000452782.2_Splice_Site_p.D132fs|CYP4B1_ENST00000371923.4_Splice_Site_p.D295fs			P13584	CP4B1_HUMAN	cytochrome P450, family 4, subfamily B, polypeptide 1	294					biphenyl metabolic process (GO:0018879)|exogenous drug catabolic process (GO:0042738)|fluorene metabolic process (GO:0018917)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	aromatase activity (GO:0070330)|drug binding (GO:0008144)|fluorene oxygenase activity (GO:0018585)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxygen binding (GO:0019825)			NS(2)|breast(1)|endometrium(2)|kidney(1)|large_intestine(12)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	36	Acute lymphoblastic leukemia(166;0.155)				Midazolam(DB00683)|Phenobarbital(DB01174)|Thiamine(DB00152)	CTAACCCAGGATGAAGATGACA	0.485														678	0.135383	0.0386	0.1816	5008	,	,		24735	0.255		0.1302	False		,,,				2504	0.1155				p.295_295del		Pindel,Atlas-Indel	.											.	CYP4B1	81	.	0			c.883_884del	GRCh37	CD025487	CYP4B1	D	rs3215983	PASS	.		,	243,4023		8,227,1898					,	5.8	1.0		dbSNP_106	78	1188,7066		82,1024,3021	yes	frameshift-near-splice,frameshift-near-splice	CYP4B1	NM_001099772.1,NM_000779.3	,	90,1251,4919	A1A1,A1R,RR		14.393,5.6962,11.4297	,	,		1431,11089				SO:0001630	splice_region_variant	1580	exon8			.	BC017758	CCDS542.1, CCDS41328.1	1p33	2013-11-11	2003-01-14		ENSG00000142973	ENSG00000142973		"""Cytochrome P450s"""	2644	protein-coding gene	gene with protein product		124075	"""cytochrome P450, subfamily IVB, polypeptide 1"""				Standard	NM_000779		Approved		uc001cqn.4	P13584	OTTHUMG00000007984	ENST00000271153.4:c.880-1AT>-	1.37:g.47280747_47280748delAT		Somatic	108	.	.		WXS	Illumina HiSeq	Phase_I	58	24	0.414	NM_001099772	Q1HBI2|Q8TD85|Q8WWF2|Q8WWU9|Q8WWV0	Frame_Shift_Del	DEL	ENST00000271153.4	37	CCDS542.1																																																																																			AT|0.822;-|0.178	0.178	strong		0.485	CYP4B1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000021911.1	NM_000779	Frame_Shift_Del
GPR112	139378	hgsc.bcm.edu	37	X	135474445	135474447	+	In_Frame_Del	DEL	GAT	GAT	-	rs563570937|rs112397171|rs199977689|rs200712981|rs34255702|rs397895612	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	GAT	GAT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:135474445_135474447delGAT	ENST00000394143.1	+	17	8257_8259	c.7966_7968delGAT	c.(7966-7968)gatdel	p.D2657del	GPR112_ENST00000412101.1_In_Frame_Del_p.D2452del|GPR112_ENST00000370652.1_In_Frame_Del_p.D2657del|GPR112_ENST00000287534.4_In_Frame_Del_p.D2410del|GPR112_ENST00000394141.1_In_Frame_Del_p.D2452del	NM_153834.3	NP_722576.3	Q8IZF6	GP112_HUMAN	G protein-coupled receptor 112	2657					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(13)|central_nervous_system(2)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(33)|lung(97)|ovary(5)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(2)	199	Acute lymphoblastic leukemia(192;0.000127)					CAGCATTTCAGATGATATGTTCA	0.374														2783	0.737219	0.5242	0.5879	3775	,	,		15064	0.7014		0.4801	False		,,,				2504	0.5031				p.2655_2656del		Pindel,Atlas-Indel	.											.	GPR112	459	.	0			c.7965_7967del						PASS	.			2546,1175		745,681,375,166,162						1.2	0.3		dbSNP_126	112	3935,2549		867,1130,1071,360,699	no	coding	GPR112	NM_153834.3		1612,1811,1446,526,861	A1A1,A1R,A1,RR,R		39.3122,31.5775,36.4919				6481,3724				SO:0001651	inframe_deletion	139378	exon17			.	AY140954	CCDS35409.1	Xq26.3	2014-08-08			ENSG00000156920	ENSG00000156920		"""-"", ""GPCR / Class B : Orphans"""	18992	protein-coding gene	gene with protein product						12435584	Standard	XM_005262367		Approved	RP1-299I16, PGR17	uc004ezu.1	Q8IZF6	OTTHUMG00000022508	ENST00000394143.1:c.7966_7968delGAT	X.37:g.135474448_135474450delGAT	ENSP00000377699:p.Asp2657del	Somatic	356	.	.		WXS	Illumina HiSeq	Phase_I	198	102	0.515	NM_153834	A2A2J1|A2A2J2|Q5EGP2|Q86SM6	In_Frame_Del	DEL	ENST00000394143.1	37	CCDS35409.1																																																																																			GAT|0.500;-|0.500	0.500	strong		0.374	GPR112-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000286639.1		
KRTAP10-11	386678	hgsc.bcm.edu	37	21	46067225	46067226	+	Frame_Shift_Ins	INS	-	-	G	rs77998434|rs148239295	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:46067225_46067226insG	ENST00000334670.8	+	1	895_896	c.850_851insG	c.(850-852)cgcfs	p.R284fs	TSPEAR_ENST00000323084.4_Intron	NM_198692.2	NP_941965.2	P60412	KR10B_HUMAN	keratin associated protein 10-11	284						keratin filament (GO:0045095)				NS(1)|endometrium(1)|large_intestine(1)|lung(6)|ovary(2)|prostate(1)	12						CGCAAGCTCCCGCCTGGCCTGC	0.649													G|G|GG|insertion	12	0.00239617	0.0091	0.0	5008	,	,		19715	0.0		0.0	False		,,,				2504	0.0				p.R284fs		Atlas-Indel	.											.	KRTAP10-11	36	.	0			c.850_851insG						PASS	.		,	42,4180		1,40,2070					,	1.5	0.0		dbSNP_131	40	0,8174		0,0,4087	no	frameshift,intron	TSPEAR,KRTAP10-11	NM_198692.2,NM_144991.2	,	1,40,6157	A1A1,A1R,RR		0.0,0.9948,0.3388	,	,		42,12354				SO:0001589	frameshift_variant	386678	exon1			.	AB076359	CCDS42962.1	21q22.3	2006-03-13	2004-07-12	2004-07-14	ENSG00000243489	ENSG00000243489		"""Keratin associated proteins"""	20528	protein-coding gene	gene with protein product			"""keratin associated protein 10-11"""	KRTAP18-11			Standard	NM_198692		Approved	KRTAP18.11, KAP18.11, KAP10.11	uc002zfr.4	P60412	OTTHUMG00000057626	ENST00000334670.8:c.851dupG	21.37:g.46067226_46067226dupG	ENSP00000334197:p.Arg284fs	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	132	14	0.106061	NM_198692	A2RRF9	Frame_Shift_Ins	INS	ENST00000334670.8	37	CCDS42962.1																																																																																			.	.	strong		0.649	KRTAP10-11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128029.1	NM_198692	
ZFHX3	463	hgsc.bcm.edu	37	16	72822564	72822569	+	In_Frame_Del	DEL	TGCTGC	TGCTGC	-	rs139466756	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	TGCTGC	TGCTGC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:72822564_72822569delTGCTGC	ENST00000268489.5	-	10	10278_10283	c.9606_9611delGCAGCA	c.(9604-9612)cagcagcaa>caa	p.3202_3204QQQ>Q	ZFHX3_ENST00000397992.5_In_Frame_Del_p.2288_2290QQQ>Q|RP5-991G20.4_ENST00000569195.1_RNA|RP5-991G20.1_ENST00000563328.2_RNA|AC004943.1_ENST00000584072.1_RNA	NM_006885.3	NP_008816.3	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3	3202	Poly-Gln.				brain development (GO:0007420)|cell cycle arrest (GO:0007050)|muscle organ development (GO:0007517)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of myoblast differentiation (GO:0045663)|regulation of neuron differentiation (GO:0045664)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	enzyme binding (GO:0019899)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			NS(3)|breast(7)|cervix(2)|endometrium(18)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(22)|liver(1)|lung(46)|ovary(5)|pancreas(1)|prostate(15)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(11)	153		Ovarian(137;0.13)				cacctgtggttgctgctgctgctgct	0.646																																					p.3203_3204del		Pindel,Atlas-Indel	.											.	ZFHX3	404	.	0			c.9607_9612del						PASS	.																																			SO:0001651	inframe_deletion	463	exon10			.	D10250	CCDS10908.1, CCDS54035.1	16q22.3	2012-03-09	2007-08-09	2007-08-09	ENSG00000140836	ENSG00000140836		"""Zinc fingers, C2H2-type"", ""Homeoboxes / ZF class"""	777	protein-coding gene	gene with protein product		104155	"""AT-binding transcription factor 1"""	ATBF1		1719379, 7592926	Standard	NM_006885		Approved	ZNF927	uc002fck.3	Q15911	OTTHUMG00000137599	ENST00000268489.5:c.9606_9611delGCAGCA	16.37:g.72822570_72822575delTGCTGC	ENSP00000268489:p.Gln3202_Gln3203del	Somatic	106	.	.		WXS	Illumina HiSeq	Phase_I	105	24	0.229	NM_006885	D3DWS8|O15101|Q13719	In_Frame_Del	DEL	ENST00000268489.5	37	CCDS10908.1																																																																																			.	.	alt		0.646	ZFHX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269008.1	NM_006885	
SYNJ1	8867	hgsc.bcm.edu	37	21	34003928	34003929	+	In_Frame_Ins	INS	-	-	AGTATT	rs57257560|rs71640263	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:34003928_34003929insAGTATT	ENST00000322229.7	-	31	4097_4098	c.4098_4099insAATACT	c.(4096-4101)gttttg>gttAATACTttg	p.1366_1367VL>VNTL	SYNJ1_ENST00000357345.3_3'UTR|SYNJ1_ENST00000433931.2_In_Frame_Ins_p.1405_1406VL>VNTL|SYNJ1_ENST00000382499.2_3'UTR|SYNJ1_ENST00000382491.3_In_Frame_Ins_p.1319_1320VL>VNTL			O43426	SYNJ1_HUMAN	synaptojanin 1	1366	Pro-rich.		V -> A (in dbSNP:rs9980589).	V -> VNT (in Ref. 1; AAC51922). {ECO:0000305}.	cell death (GO:0008219)|inositol phosphate metabolic process (GO:0043647)|phosphate-containing compound metabolic process (GO:0006796)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|positive regulation of synaptic vesicle uncoating (GO:1903390)|regulation of synaptic vesicle membrane organization (GO:1901632)|small molecule metabolic process (GO:0044281)|synaptic vesicle endocytosis (GO:0048488)	cytosol (GO:0005829)	inositol-polyphosphate 5-phosphatase activity (GO:0004445)|nucleotide binding (GO:0000166)|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity (GO:0004439)|RNA binding (GO:0003723)			breast(1)|cervix(1)|endometrium(13)|kidney(5)|large_intestine(13)|lung(11)|ovary(4)|pancreas(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	57						ACAGAACTCAAAACATTACTTT	0.45														2860	0.571086	0.7269	0.4755	5008	,	,		21036	0.4712		0.5268	False		,,,				2504	0.5767				p.L1406delinsNTL		Pindel,Atlas-Indel	.											.	SYNJ1	253	.	0			c.4216_4217insAATACT						PASS	.		,,,	2849,1415		970,909,253					,,,	-0.8	0.3		dbSNP_130	73	4172,4082		1048,2076,1003	no	utr-3,coding,coding,utr-3	SYNJ1	NM_203446.2,NM_003895.3,NM_001160306.1,NM_001160302.1	,,,	2018,2985,1256	A1A1,A1R,RR		49.4548,33.1848,43.9128	,,,	,,,		7021,5497				SO:0001652	inframe_insertion	8867	exon32			.	AF009040	CCDS33539.1, CCDS33540.1, CCDS33539.2, CCDS33540.2, CCDS54483.1	21q22.2	2008-06-23			ENSG00000159082	ENSG00000159082			11503	protein-coding gene	gene with protein product		604297				9428629, 10773674	Standard	NM_203446		Approved	INPP5G	uc002yqh.2	O43426	OTTHUMG00000064926	ENST00000322229.7:c.4098_4099insAATACT	21.37:g.34003928_34003929insAGTATT	ENSP00000322234:p.Val1366_Leu1367insAsnThr	Somatic	174	.	.		WXS	Illumina HiSeq	Phase_I	151	31	0.205	NM_003895	O43425|O94984|Q4KMR1	In_Frame_Ins	INS	ENST00000322229.7	37	CCDS54484.1																																																																																			-|0.489;AGTATT|0.511	0.511	strong		0.450	SYNJ1-201	KNOWN	basic|CCDS	protein_coding	protein_coding			
L1TD1	54596	hgsc.bcm.edu	37	1	62672389	62672390	+	In_Frame_Ins	INS	-	-	AACAGA	rs374688773|rs150799576	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:62672389_62672390insAACAGA	ENST00000498273.1	+	3	384_385	c.89_90insAACAGA	c.(88-93)ttaaca>ttAACAGAaaca	p.33_34insET		NM_001164835.1|NM_019079.4	NP_001158307.1|NP_061952.3	Q5T7N2	LITD1_HUMAN	LINE-1 type transposase domain containing 1	33										breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(12)|ovary(2)|prostate(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	35						agagagcagttaacagaaactg	0.327														173	0.0345447	0.084	0.0159	5008	,	,		18275	0.001		0.0258	False		,,,				2504	0.0245				p.L30delinsLTE		Pindel,Atlas-Indel	.											.	L1TD1	114	.	0			c.89_90insAACAGA						PASS	.		,	271,3517		14,243,1637					,	1.0	0.0		dbSNP_134	24	117,7287		5,107,3590	no	coding,coding	L1TD1	NM_019079.4,NM_001164835.1	,	19,350,5227	A1A1,A1R,RR		1.5802,7.1542,3.4668	,	,		388,10804				SO:0001652	inframe_insertion	54596	exon4			.	BC060808	CCDS619.1	1p31.3	2009-01-12			ENSG00000240563	ENSG00000240563			25595	protein-coding gene	gene with protein product						12477932	Standard	NM_001164835		Approved	FLJ10884, ECAT11	uc001dae.4	Q5T7N2	OTTHUMG00000008914	ENST00000498273.1:c.90_95dupAACAGA	1.37:g.62672390_62672395dupAACAGA	ENSP00000419901:p.Glu32_Thr33dup	Somatic	215	.	.		WXS	Illumina HiSeq	Phase_I	127	38	0.299	NM_001164835	Q8NDA1|Q9NUV8|Q9NV78	In_Frame_Ins	INS	ENST00000498273.1	37	CCDS619.1																																																																																			-|0.971;AACAGA|0.029	0.029	strong		0.327	L1TD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024688.1	NM_019079	
ANKRD20A3	441425	hgsc.bcm.edu	37	9	43121655	43121658	+	Frame_Shift_Del	DEL	TAAG	TAAG	-			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	TAAG	TAAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:43121655_43121658delTAAG	ENST00000254835.2	-	6	886_889	c.775_778delCTTA	c.(775-780)cttaaafs	p.LK259fs	RNU6-538P_ENST00000459237.1_RNA	NM_001012419.1	NP_001012419.1	Q5VUR7	A20A3_HUMAN	ankyrin repeat domain 20 family, member A3	259																	TTCTCCTTTTTAAGTATCTTCTTT	0.26																																					p.259_260del		Atlas-Indel	.											.	.	.	.	0			c.776_779del						PASS	.																																			SO:0001589	frameshift_variant	441425	exon6			.		CCDS35029.1	9q12	2014-05-06			ENSG00000132498	ENSG00000276203		"""Ankyrin repeat domain containing"""	31981	protein-coding gene	gene with protein product							Standard	NM_001012419		Approved		uc004acd.3	Q5VUR7	OTTHUMG00000188432	ENST00000254835.2:c.775_778delCTTA	9.37:g.43121655_43121658delTAAG	ENSP00000254835:p.Leu259fs	Somatic	352	0	0		WXS	Illumina HiSeq	Phase_I	359	25	0.0696379	NM_001012419		Frame_Shift_Del	DEL	ENST00000254835.2	37	CCDS35029.1																																																																																			.	.	none		0.260	ANKRD20A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000037047.1		
DOC2A	8448	hgsc.bcm.edu	37	16	30018351	30018353	+	Splice_Site	DEL	CCT	CCT	-			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	CCT	CCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:30018351_30018353delCCT	ENST00000350119.4	-	7	903_905	c.713_715delAGG	c.(712-717)gaggtg>gtg	p.E238del	DOC2A_ENST00000564944.1_Splice_Site_p.E238del|DOC2A_ENST00000564979.1_Splice_Site_p.E238del	NM_001282062.1|NM_001282063.1|NM_001282068.1|NM_003586.2	NP_001268991.1|NP_001268992.1|NP_001268997.1|NP_003577.2	Q14183	DOC2A_HUMAN	double C2-like domains, alpha	238	Interaction with UNC13D.			E -> D (in Ref. 1; BAA06695). {ECO:0000305}.	nervous system development (GO:0007399)|regulation of calcium ion-dependent exocytosis (GO:0017158)|synaptic transmission (GO:0007268)|synaptic vesicle exocytosis (GO:0016079)	cell junction (GO:0030054)|lysosome (GO:0005764)|membrane (GO:0016020)|neuron projection (GO:0043005)|synaptic vesicle (GO:0008021)	calcium-dependent phospholipid binding (GO:0005544)|transporter activity (GO:0005215)			central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(2)|ovary(2)	9						AGGTGCCTCACCTCCTTCAGATA	0.65																																					p.238_238del		Pindel,Atlas-Indel	.											.	DOC2A	40	.	0			c.714_714del						PASS	.																																			SO:0001630	splice_region_variant	8448	exon7			.	D31897	CCDS10666.1	16p11.2	2014-07-02			ENSG00000149927	ENSG00000149927		"""Synaptotagmins"""	2985	protein-coding gene	gene with protein product		604567				7826360, 9736751	Standard	NM_003586		Approved		uc002dvn.3	Q14183	OTTHUMG00000132109	ENST00000350119.4:c.714+1AGG>-	16.37:g.30018354_30018356delCCT		Somatic	139	.	.		WXS	Illumina HiSeq	Phase_I	184	32	0.174	NM_003586	B4DEJ2|H3BNH6|Q6P4G4|Q7Z5G0|Q8IVX0	Frame_Shift_Del	DEL	ENST00000350119.4	37	CCDS10666.1																																																																																			.	.	none		0.650	DOC2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255148.2	NM_003586	In_Frame_Del
CLCA4	22802	hgsc.bcm.edu	37	1	87045897	87045902	+	In_Frame_Del	DEL	CCTACA	CCTACA	-	rs1932809|rs4001061|rs77067122|rs56040873|rs574759485|rs368263974|rs201606404	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	CCTACA	CCTACA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:87045897_87045902delCCTACA	ENST00000370563.3	+	14	2671_2676	c.2629_2634delCCTACA	c.(2629-2634)cctacadel	p.PT885del	RP4-651E10.4_ENST00000456587.1_RNA	NM_012128.3	NP_036260.2	Q14CN2	CLCA4_HUMAN	chloride channel accessory 4	885					chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	chloride channel activity (GO:0005254)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(7)|liver(2)|lung(21)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	44		Lung NSC(277;0.238)		all cancers(265;0.0202)|Epithelial(280;0.0404)		TGACATTGAtcctacacctactccta	0.354														3541	0.707069	0.5363	0.7925	5008	,	,		17981	0.7282		0.7207	False		,,,				2504	0.8415				p.876_878del		Pindel,Atlas-Indel	.											.	CLCA4	131	.	0			c.2628_2633del						PASS	.																																			SO:0001651	inframe_deletion	22802	exon14			.	AF127035	CCDS41355.1	1p31-p22	2012-02-26	2009-01-29		ENSG00000016602	ENSG00000016602			2018	protein-coding gene	gene with protein product			"""chloride channel, calcium activated, family member 4"", ""chloride channel regulator 4"""			10437792	Standard	NM_012128		Approved	CaCC2	uc009wcs.3	Q14CN2	OTTHUMG00000010260	ENST00000370563.3:c.2629_2634delCCTACA	1.37:g.87045897_87045902delCCTACA	ENSP00000359594:p.Pro885_Thr886del	Somatic	226	.	.		WXS	Illumina HiSeq	Phase_I	169	40	0.237	NM_012128	A8MQC9|B7Z1Q5|Q6UX81|Q9UNF7	In_Frame_Del	DEL	ENST00000370563.3	37	CCDS41355.1																																																																																			CCTACA|0.284;-|0.716	0.716	strong		0.354	CLCA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028292.1	NM_012128	
NUTM2F	54754	hgsc.bcm.edu	37	9	97080945	97080947	+	In_Frame_Del	DEL	AGA	AGA	-	rs150455117|rs112857574	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	AGA	AGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:97080945_97080947delAGA	ENST00000253262.4	-	7	2091_2093	c.2071_2073delTCT	c.(2071-2073)tctdel	p.S691del	NUTM2F_ENST00000335456.7_Intron|NUTM2F_ENST00000341207.4_In_Frame_Del_p.S676del	NM_017561.1	NP_060031.1	A1L443	NTM2F_HUMAN	NUT family member 2F	691				Missing (in Ref. 2; AAI30391 and 3; CAB61394). {ECO:0000305}.				p.S557delS(1)									TGCTGGCAGGAGAAGGTGATGGG	0.611														3777	0.754193	0.6051	0.8084	5008	,	,		15297	0.8869		0.7227	False		,,,				2504	0.8129				p.691_692del		Pindel,Atlas-Indel	.											.	FAM22F	72	.	1	Deletion - In frame(1)	central_nervous_system(1)	c.2072_2074del						PASS	.			2288,1260		619,1050,105						-3.0	0.0		dbSNP_134	20	5646,2060		2048,1550,255	no	coding	FAM22F	NM_017561.1		2667,2600,360	A1A1,A1R,RR		26.7324,35.513,29.5006				7934,3320				SO:0001651	inframe_deletion	54754	exon7			.		CCDS47994.1	9q22.32	2013-05-02	2013-03-14	2013-05-02	ENSG00000130950	ENSG00000130950			23450	protein-coding gene	gene with protein product			"""family with sequence similarity 22, member F"""	FAM22F			Standard	NM_017561		Approved	DKFZp434I1117		A1L443	OTTHUMG00000020260	ENST00000253262.4:c.2071_2073delTCT	9.37:g.97080945_97080947delAGA	ENSP00000253262:p.Ser691del	Somatic	411	.	.		WXS	Illumina HiSeq	Phase_I	270	51	0.189	NM_017561	B6ZDF0|Q5SR58|Q5SR59|Q9UFB1	In_Frame_Del	DEL	ENST00000253262.4	37	CCDS47994.1																																																																																			.	.	strong		0.611	NUTM2F-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053173.2	NM_017561	
CPS1	1373	hgsc.bcm.edu	37	2	211421452	211421453	+	5'UTR	INS	-	-	TCT	rs61509952|rs3835047|rs34778124|rs201874641	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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		Pindel,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	169	.	.		WXS	Illumina HiSeq	Phase_I	123	35	0.285	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		
ZNF527	84503	hgsc.bcm.edu	37	19	37879852	37879853	+	Frame_Shift_Ins	INS	-	-	TGTG	rs2385182|rs376931538|rs386809049	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:37879852_37879853insTGTG	ENST00000436120.2	+	5	1008_1009	c.901_902insTGTG	c.(901-903)ccafs	p.P301fs	ZNF527_ENST00000587349.1_Intron	NM_032453.1	NP_115829.1	Q8NB42	ZN527_HUMAN	zinc finger protein 527	301					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(14)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	33			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			TGGAGAAAAACCATATGCATGC	0.391																																					p.P301fs		Atlas-Indel	.											.	ZNF527	78	.	0			c.901_902insTGTG						PASS	.			75,3965		3,69,1948						-1.5	0.3		dbSNP_126	99	898,7198		92,714,3242	no	frameshift	ZNF527	NM_032453.1		95,783,5190	A1A1,A1R,RR		11.0919,1.8564,8.0175				973,11163				SO:0001589	frameshift_variant	84503	exon5			.	AB058732, AK091585	CCDS42559.1	19q13.1	2013-01-08			ENSG00000189164	ENSG00000189164		"""Zinc fingers, C2H2-type"", ""-"""	29385	protein-coding gene	gene with protein product						11347906	Standard	NM_032453		Approved	KIAA1829	uc010efk.1	Q8NB42	OTTHUMG00000048173	Exception_encountered	19.37:g.37879852_37879853insTGTG	ENSP00000390179:p.Pro301fs	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	92	35	0.380435	NM_032453	B4DVL5	Frame_Shift_Ins	INS	ENST00000436120.2	37	CCDS42559.1																																																																																			.	.	weak		0.391	ZNF527-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458434.1	NM_032453	
GRAMD1A	57655	hgsc.bcm.edu	37	19	35505282	35505282	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:35505282delG	ENST00000317991.5	+	10	1252	c.1060delG	c.(1060-1062)gggfs	p.G354fs	CTD-2527I21.14_ENST00000605640.1_RNA|GRAMD1A_ENST00000599564.1_Frame_Shift_Del_p.G441fs|GRAMD1A_ENST00000504615.2_Frame_Shift_Del_p.G120fs|GRAMD1A_ENST00000411896.2_Frame_Shift_Del_p.G347fs	NM_020895.3	NP_065946.2	Q96CP6	GRM1A_HUMAN	GRAM domain containing 1A	354						integral component of membrane (GO:0016021)				NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(10)|prostate(1)|upper_aerodigestive_tract(1)	19	all_lung(56;2.66e-08)|Lung NSC(56;4.13e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0849)			TTCATCCACTGGGGAGGAAGG	0.607																																					p.T353fs		Pindel,Atlas-Indel	.											.	GRAMD1A	39	.	0			c.1059delT						PASS	.						38.0	43.0	41.0					19																	35505282		1972	4145	6117	SO:0001589	frameshift_variant	57655	exon10			.	AK074864	CCDS42546.1, CCDS46046.1	19q13.13	2008-02-05	2005-11-02	2005-11-02		ENSG00000089351			29305	protein-coding gene	gene with protein product			"""KIAA1533"""	KIAA1533		10819331	Standard	NM_020895		Approved	FLJ90346	uc010xse.1	Q96CP6		ENST00000317991.5:c.1060delG	19.37:g.35505282delG	ENSP00000441032:p.Gly354fs	Somatic	158	.	.		WXS	Illumina HiSeq	Phase_I	143	43	0.301	NM_020895	A6NKY7|Q8NC77|Q9P1Z5	Frame_Shift_Del	DEL	ENST00000317991.5	37	CCDS42546.1																																																																																			.	.	none		0.607	GRAMD1A-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000461557.1	NM_020895	
SCN3A	6328	hgsc.bcm.edu	37	2	166032776	166032778	+	In_Frame_Del	DEL	ATT	ATT	-	rs34236036|rs72471101	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	ATT	ATT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:166032776_166032778delATT	ENST00000360093.3	-	3	618_620	c.127_129delAAT	c.(127-129)aatdel	p.N43del	SCN3A_ENST00000409101.3_In_Frame_Del_p.N43del|SCN3A_ENST00000283254.7_In_Frame_Del_p.N43del	NM_001081677.1	NP_001075146.1	Q9NY46	SCN3A_HUMAN	sodium channel, voltage-gated, type III, alpha subunit	43			Missing. {ECO:0000269|PubMed:12610651}.		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)	TCTCATCATCATTATCTTGTTCC	0.433														257	0.0513179	0.0424	0.0245	5008	,	,		17721	0.002		0.0934	False		,,,				2504	0.09				p.43_44del		Pindel,Atlas-Indel	.											.	SCN3A	544	.	0			c.128_130del						PASS	.		,,	238,4028		8,222,1903					,,	5.3	1.0		dbSNP_130	217	824,7430		45,734,3348	no	coding,coding,coding	SCN3A	NM_006922.3,NM_001081677.1,NM_001081676.1	,,	53,956,5251	A1A1,A1R,RR		9.983,5.579,8.4824	,,	,,		1062,11458				SO:0001651	inframe_deletion	6328	exon3			.	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.127_129delAAT	2.37:g.166032776_166032778delATT	ENSP00000353206:p.Asn43del	Somatic	227	.	.		WXS	Illumina HiSeq	Phase_I	229	49	0.214	NM_001081677	Q16142|Q53SX0|Q9BZB3|Q9C006|Q9NYK2|Q9P2J1|Q9UPD1|Q9Y6P4	In_Frame_Del	DEL	ENST00000360093.3	37																																																																																				ATT|0.949;-|0.051	0.051	strong		0.433	SCN3A-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_006922	
FBXW10	10517	hgsc.bcm.edu	37	17	18682351	18682352	+	Frame_Shift_Del	DEL	AA	AA	-			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	AA	AA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:18682351_18682352delAA	ENST00000395665.4	+	14	3120_3121	c.2899_2900delAA	c.(2899-2901)aaafs	p.K967fs	FBXW10_ENST00000308799.4_Frame_Shift_Del_p.K976fs|TVP23B_ENST00000476139.1_5'Flank|FBXW10_ENST00000395667.1_Frame_Shift_Del_p.K966fs|TVP23B_ENST00000574226.1_5'Flank|FBXW10_ENST00000301938.4_Frame_Shift_Del_p.K914fs|TVP23B_ENST00000307767.8_5'Flank			Q5XX13	FBW10_HUMAN	F-box and WD repeat domain containing 10	967								p.K966fs*10(1)		NS(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(13)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	42						GTCTCTTAAGAAAGAACGGCCT	0.53																																					p.966_967del		Atlas-Indel	.											.	FBXW10	82	.	1	Deletion - Frameshift(1)	skin(1)	c.2898_2899del						PASS	.			6,4034		2,2,2016						1.3	0.5			20	27,7731		6,15,3858	no	frameshift	FBXW10	NM_031456.3		8,17,5874	A1A1,A1R,RR		0.348,0.1485,0.2797				33,11765				SO:0001589	frameshift_variant	10517	exon14			.	BC028364	CCDS11199.2, CCDS11199.3, CCDS58524.1	17p11	2013-01-09	2007-02-08	2004-07-21	ENSG00000171931	ENSG00000171931		"""F-boxes / WD-40 domains"", ""WD repeat domain containing"""	1211	protein-coding gene	gene with protein product		611679	"""chromosome 17 open reading frame 1A"", ""F-box and WD-40 domain protein 10"""	C17orf1, C17orf1A		9787083, 7586531	Standard	NM_001267585		Approved	SM2SH2, HREP, Fbw10	uc002guk.3	Q5XX13	OTTHUMG00000059048	ENST00000395665.4:c.2899_2900delAA	17.37:g.18682351_18682352delAA	ENSP00000379025:p.Lys967fs	Somatic	343	0	0		WXS	Illumina HiSeq	Phase_I	153	43	0.281046	NM_001267585	C9JRY8|C9JZD7|Q8TC00|Q9H0F0	Frame_Shift_Del	DEL	ENST00000395665.4	37	CCDS11199.3																																																																																			.	.	none		0.530	FBXW10-003	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313531.2	NM_031456	
ZNF527	84503	hgsc.bcm.edu	37	19	37879855	37879855	+	Frame_Shift_Del	DEL	T	T	-	rs373623156|rs200420244|rs386809049|rs200343305|rs3081552		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:37879855delT	ENST00000436120.2	+	5	1011	c.904delT	c.(904-906)tatfs	p.Y302fs	ZNF527_ENST00000587349.1_Intron	NM_032453.1	NP_115829.1	Q8NB42	ZN527_HUMAN	zinc finger protein 527	302					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(14)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	33			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			AGAAAAACCATATGCATGCAA	0.393																																					p.P301fs		Atlas-Indel	.											.	ZNF527	78	.	0			c.903delA						PASS	.			51,3991		2,47,1972	104.0	92.0	96.0			-2.3	0.1	19	dbSNP_102	97	580,7526		48,484,3521	no	frameshift	ZNF527	NM_032453.1		50,531,5493	A1A1,A1R,RR		7.1552,1.2618,5.1943			37879855	631,11517	2092	4235	6327	SO:0001589	frameshift_variant	84503	exon5			.	AB058732, AK091585	CCDS42559.1	19q13.1	2013-01-08			ENSG00000189164	ENSG00000189164		"""Zinc fingers, C2H2-type"", ""-"""	29385	protein-coding gene	gene with protein product						11347906	Standard	NM_032453		Approved	KIAA1829	uc010efk.1	Q8NB42	OTTHUMG00000048173	ENST00000436120.2:c.904delT	19.37:g.37879855delT	ENSP00000390179:p.Tyr302fs	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	83	35	0.421687	NM_032453	B4DVL5	Frame_Shift_Del	DEL	ENST00000436120.2	37	CCDS42559.1																																																																																			T|0.910;-|0.090	0.090	strong		0.393	ZNF527-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458434.1	NM_032453	
MSI2	124540	hgsc.bcm.edu	37	17	55693404	55693405	+	Frame_Shift_Ins	INS	-	-	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:55693404_55693405insT	ENST00000284073.2	+	9	820_821	c.611_612insT	c.(610-615)ccttacfs	p.Y205fs	MSI2_ENST00000579505.1_3'UTR|MSI2_ENST00000442934.2_Frame_Shift_Ins_p.Y144fs|MSI2_ENST00000322684.3_Frame_Shift_Ins_p.Y201fs|RN7SL449P_ENST00000464937.2_RNA|MSI2_ENST00000416426.2_Frame_Shift_Ins_p.Y183fs|MSI2_ENST00000579180.1_Frame_Shift_Ins_p.Y101fs	NM_138962.2	NP_620412.1	Q96DH6	MSI2H_HUMAN	musashi RNA-binding protein 2	205						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)		CGGGGACTGCCTTACACCATGG	0.559			T	HOXA9	CML																																p.P204fs		Pindel,Atlas-Indel	.		Dom	yes		17	17q23.2	124540	musashi homolog 2 (Drosophila)		L	.	MSI2	52	.	0			c.611_612insT						PASS	.																																			SO:0001589	frameshift_variant	124540	exon9			.	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.613dupT	17.37:g.55693406_55693406dupT	ENSP00000284073:p.Tyr205fs	Somatic	52	.	.		WXS	Illumina HiSeq	Phase_I	51	11	0.216	NM_138962	Q7Z6M7|Q8N9T4	Frame_Shift_Ins	INS	ENST00000284073.2	37	CCDS11596.1																																																																																			.	.	none		0.559	MSI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441813.1		
GPRIN1	114787	hgsc.bcm.edu	37	5	176026136	176026146	+	Frame_Shift_Del	DEL	CCTCCTTCCTC	CCTCCTTCCTC	-	rs79403503|rs386695335|rs550332435|rs77245696|rs142779818|rs371149640|rs201635586	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	CCTCCTTCCTC	CCTCCTTCCTC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:176026136_176026146delCCTCCTTCCTC	ENST00000303991.4	-	2	867_877	c.690_700delGAGGAAGGAGG	c.(688-702)ccgaggaaggaggatfs	p.RKED231fs		NM_052899.2	NP_443131.2	Q7Z2K8	GRIN1_HUMAN	G protein regulated inducer of neurite outgrowth 1	231				Missing (in Ref. 4; CAD38868). {ECO:0000305}.	neuron projection development (GO:0031175)	cell projection (GO:0042995)|plasma membrane (GO:0005886)				NS(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(3)|liver(1)|lung(15)|ovary(2)|prostate(5)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	35	all_cancers(89;0.00263)|Renal(175;0.000269)|Lung NSC(126;0.00902)|all_lung(126;0.0142)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			GACCCAGGATCCTCCTTCCTCGGTGACACTG	0.498																																					p.231_234del		Atlas-Indel	.											.	GPRIN1	77	.	0			c.691_701del						PASS	.			563,3699		9,545,1577						-2.4	0.0		dbSNP_134	89	851,7393		18,815,3289	no	frameshift	GPRIN1	NM_052899.2		27,1360,4866	A1A1,A1R,RR		10.3227,13.2098,11.3066				1414,11092				SO:0001589	frameshift_variant	114787	exon2			.	AB067480	CCDS4405.1	5q35.2	2008-02-05			ENSG00000169258	ENSG00000169258			24835	protein-coding gene	gene with protein product		611239				11572484	Standard	NM_052899		Approved	GRIN1, KIAA1893	uc003meo.1	Q7Z2K8	OTTHUMG00000130659	ENST00000303991.4:c.690_700delGAGGAAGGAGG	5.37:g.176026136_176026146delCCTCCTTCCTC	ENSP00000305839:p.Arg231fs	Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	140	20	0.142857	NM_052899	C9JM70|Q8ND74|Q96PZ4	Frame_Shift_Del	DEL	ENST00000303991.4	37	CCDS4405.1																																																																																			.	.	none		0.498	GPRIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253149.1	NM_052899	
RPGR	6103	hgsc.bcm.edu	37	X	38145805	38145805	+	Intron	DEL	C	C	-			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:38145805delC	ENST00000339363.3	-	14	2688				RPGR_ENST00000342811.3_Intron|TM4SF2_ENST00000465127.1_Intron|RPGR_ENST00000318842.7_Intron|RPGR_ENST00000378505.2_Frame_Shift_Del_p.G817fs|RPGR_ENST00000309513.3_Intron|RPGR_ENST00000338898.3_Intron			Q92834	RPGR_HUMAN	retinitis pigmentosa GTPase regulator						cilium assembly (GO:0042384)|eye photoreceptor cell development (GO:0042462)|intracellular protein transport (GO:0006886)|intraciliary transport (GO:0042073)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|Golgi apparatus (GO:0005794)|photoreceptor outer segment (GO:0001750)|sperm flagellum (GO:0036126)	guanyl-nucleotide exchange factor activity (GO:0005085)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	25						tacttcccctccctctacttc	0.597																																					p.G816fs		Atlas-Indel	.											.	RPGR	175	.	0			c.2448delA						PASS	.						159.0	119.0	133.0					X																	38145805		1802	3474	5276	SO:0001627	intron_variant	6103	exon15			.	U57629	CCDS14246.1, CCDS35229.1	Xp11.4	2013-06-06	2004-02-13		ENSG00000156313	ENSG00000156313			10295	protein-coding gene	gene with protein product		312610	"""retinitis pigmentosa 15"", ""cone dystrophy 1 (X-linked)"""	CRD, RP3, RP15, COD1		8673101, 8817343	Standard	XM_005272633		Approved	CORDX1	uc004ded.1	Q92834	OTTHUMG00000021361	ENST00000339363.3:c.2520+541G>-	X.37:g.38145805delC		Somatic	209	0	0		WXS	Illumina HiSeq	Phase_I	38	17	0.447368	NM_001034853	B1ARN3|E9PE28|O00702|O00737|Q3KN84|Q8N5T6|Q93039|Q9HD29|Q9UMR1	Frame_Shift_Del	DEL	ENST00000339363.3	37																																																																																				.	.	none		0.597	RPGR-203	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_000328	
ADRA2B	151	hgsc.bcm.edu	37	2	96780986	96780987	+	In_Frame_Ins	INS	-	-	TCCTCCTCT	rs4426564|rs60083507|rs28365031|rs34667759|rs29000568	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:96780986_96780987insTCCTCCTCT	ENST00000409345.3	-	1	997_998	c.902_903insAGAGGAGGA	c.(901-903)gag>gaAGAGGAGGAg	p.301_301E>EEEE		NM_000682.5	NP_000673	P18089	ADA2B_HUMAN	adrenoceptor alpha 2B	301	Asp/Glu-rich (acidic).				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)	cctcctcctcctcctcctcttc	0.658														2357	0.470647	0.5151	0.4625	5008	,	,		17797	0.4067		0.4652	False		,,,				2504	0.4877				p.E301delinsEEEE		Pindel,Atlas-Indel	.											.	ADRA2B	115	.	0			c.903_904insAGAGGAGGA						PASS	.			3210,27,22,767		1369,23,7,442,1,0,2,7,1,161						-1.6	0.6		dbSNP_130	13	5261,50,21,2686		1819,45,7,1571,1,0,3,4,6,553	no	codingComplex	ADRA2B	NM_000682.5		3188,68,14,2013,2,0,5,11,7,714	A1A1,A1A2,A1A3,A1R,A2A2,A2A3,A2R,A3A3,A3R,RR		34.3851,20.2683,29.6662				8471,77,43,3453				SO:0001652	inframe_insertion	151	exon1			.	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.894_902dupAGAGGAGGA	2.37:g.96780987_96780995dupTCCTCCTCT	ENSP00000387281:p.GluGluGlu304dup	Somatic	121	.	.		WXS	Illumina HiSeq	Phase_I	87	38	0.437	NM_000682	Q4TUH9|Q53RF2|Q9BZK0	In_Frame_Ins	INS	ENST00000409345.3	37	CCDS56129.1																																																																																			-|0.500;TCCTCCTCT|0.500	0.500	strong		0.658	ADRA2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334990.1		
TDG	6996	hgsc.bcm.edu	37	12	104373728	104373729	+	Frame_Shift_Ins	INS	-	-	A	rs151041931	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:104373728_104373729insA	ENST00000392872.3	+	3	520_521	c.286_287insA	c.(286-288)gaafs	p.E96fs	TDG_ENST00000544861.1_5'UTR|TDG_ENST00000542036.1_5'Flank|TDG_ENST00000266775.9_Frame_Shift_Ins_p.E92fs	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	114	0	0		WXS	Illumina HiSeq	Phase_I	194	73	0.376289	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		
MUC4	4585	hgsc.bcm.edu	37	3	195512373	195512374	+	In_Frame_Ins	INS	-	-	GAT	rs112774151|rs63118461		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195512373_195512374insGAT	ENST00000463781.3	-	2	6536_6537	c.6077_6078insATC	c.(6076-6078)tcc>tcATCc	p.2026_2026S>SS	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_In_Frame_Ins_p.2026_2026S>SS	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.S2026_T2027insS(3)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		TGTCACCAGTGGATGCTGAGGA	0.579																																					p.S2026delinsSS		Atlas-Indel	.											.	MUC4	1505	.	3	Insertion - In frame(3)	large_intestine(2)|breast(1)	c.6078_6079insATC						PASS	.		,,	1110,2296		177,756,770					,,		0.0		dbSNP_130	24	1888,5346		82,1724,1811	no	intron,coding,intron	MUC4	NM_138297.4,NM_018406.6,NM_004532.5	,,	259,2480,2581	A1A1,A1R,RR		26.099,32.5895,28.1767	,,	,,		2998,7642				SO:0001652	inframe_insertion	4585	exon2			.	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.6075_6077dupATC	3.37:g.195512374_195512376dupGAT	ENSP00000417498:p.Ser2026dup	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	104	21	0.201923	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	In_Frame_Ins	INS	ENST00000463781.3	37	CCDS54700.1																																																																																			-|0.500;GAT|0.500	0.500	strong		0.579	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
USP2	9099	hgsc.bcm.edu	37	11	119228548	119228549	+	Intron	DEL	GA	GA	-	rs397897488|rs45619639	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	GA	GA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:119228548_119228549delGA	ENST00000260187.2	-	10	1717				USP2_ENST00000525735.1_Intron|USP2_ENST00000455332.2_Intron	NM_004205.4	NP_004196.4	O75604	UBP2_HUMAN	ubiquitin specific peptidase 2						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)		CAGCATGTCTGAGAGACAAGAC	0.5														162	0.0323482	0.0076	0.049	5008	,	,		19728	0.002		0.0964	False		,,,				2504	0.0194				.		Pindel,Atlas-Indel	.											.	USP2	71	.	0			.						PASS	.		,	123,4141		1,121,2010					,	5.8	1.0		dbSNP_127	182	826,7424		46,734,3345	no	intron,intron	USP2	NM_171997.2,NM_004205.4	,	47,855,5355	A1A1,A1R,RR		10.0121,2.8846,7.5835	,	,		949,11565				SO:0001627	intron_variant	9099	.			.	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.1423-3TC>-	11.37:g.119228552_119228553delGA		Somatic	113	.	.		WXS	Illumina HiSeq	Phase_I	81	39	0.481	.	B0YJB8|E9PPM2|Q8IUM2|Q8IW04|Q96MB9|Q9BQ21	Splice_Site	DEL	ENST00000260187.2	37	CCDS8422.1																																																																																			GA|0.963;-|0.037	0.037	strong		0.500	USP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388361.2	NM_171997	
TRIOBP	11078	hgsc.bcm.edu	37	22	38120176	38120178	+	In_Frame_Del	DEL	CCT	CCT	-	rs529080937|rs36219868	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	CCT	CCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:38120176_38120178delCCT	ENST00000406386.3	+	7	1868_1870	c.1613_1615delCCT	c.(1612-1617)gcctcc>gcc	p.S540del		NM_001039141.2	NP_001034230.1	Q9H2D6	TARA_HUMAN	TRIO and F-actin binding protein	540					actin modification (GO:0030047)|barbed-end actin filament capping (GO:0051016)|mitotic nuclear division (GO:0007067)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	actin filament binding (GO:0051015)|GTP-Rho binding (GO:0017049)|myosin II binding (GO:0045159)|ubiquitin protein ligase binding (GO:0031625)	p.S540delS(1)		central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	12	Melanoma(58;0.0574)					AATCCCAGAGCCTCCTCTCCCAA	0.606														1254	0.250399	0.1362	0.2277	5008	,	,		30273	0.3651		0.2932	False		,,,				2504	0.2587				p.538_538del		Atlas-Indel	.											.	TRIOBP	262	.	1	Deletion - In frame(1)	ovary(1)	c.1612_1614del						PASS	.			598,3166		11,576,1295						-6.6	0.0		dbSNP_126	143	2675,5301		8,2659,1321	no	coding	TRIOBP	NM_001039141.2		19,3235,2616	A1A1,A1R,RR		33.5381,15.8874,27.879				3273,8467				SO:0001651	inframe_deletion	11078	exon7			.	AB051449	CCDS33644.1, CCDS43015.1, CCDS43016.1	22q13.1	2014-06-03			ENSG00000100106	ENSG00000100106		"""Pleckstrin homology (PH) domain containing"""	17009	protein-coding gene	gene with protein product		609761		DFNB28		11148140, 16385457, 16385458	Standard	NM_001039141		Approved	HRIHFB2122, KIAA1662, Tara, TAP68	uc003atr.3	Q9H2D6	OTTHUMG00000150657	ENST00000406386.3:c.1613_1615delCCT	22.37:g.38120179_38120181delCCT	ENSP00000384312:p.Ser540del	Somatic	355	0	0		WXS	Illumina HiSeq	Phase_I	305	47	0.154098	NM_001039141	B1AHD4|B1AHD7|F2Z2W0|F8W6V6|O94797|Q2PZW8|Q2Q3Z9|Q2Q400|Q5R3M6|Q96DW1|Q9BT77|Q9BTL7|Q9BY98|Q9Y3L4	In_Frame_Del	DEL	ENST00000406386.3	37	CCDS43015.1																																																																																			.	.	strong		0.606	TRIOBP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319439.2		
KRTAP4-5	85289	hgsc.bcm.edu	37	17	39305775	39305776	+	In_Frame_Ins	INS	-	-	GGCAGCAGCTGGGGC	rs535144703|rs141265645|rs58117746|rs146438235	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	48	0	0		WXS	Illumina HiSeq	Phase_I	47	10	0.212766	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		
TSPYL6	388951	hgsc.bcm.edu	37	2	54482704	54482709	+	In_Frame_Del	DEL	GGGCCC	GGGCCC	-	rs76397255|rs398060196	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	GGGCCC	GGGCCC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:54482704_54482709delGGGCCC	ENST00000317802.7	-	1	700_705	c.580_585delGGGCCC	c.(580-585)gggcccdel	p.GP194del	ACYP2_ENST00000606865.1_Intron|ACYP2_ENST00000607452.1_Intron|ACYP2_ENST00000394666.3_Intron|ACYP2_ENST00000303536.4_Intron	NM_001003937.2	NP_001003937.2	Q8N831	TSYL6_HUMAN	TSPY-like 6	194					nucleosome assembly (GO:0006334)	nucleus (GO:0005634)				NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(1)|ovary(1)|skin(1)|stomach(2)	20						CCACGTTCAGGGGCCCGGGCCCGGGC	0.626														798	0.159345	0.1921	0.111	5008	,	,		19038	0.1865		0.1143	False		,,,				2504	0.1677				p.194_196del		Pindel,Atlas-Indel	.											.	TSPYL6	54	.	0			c.581_586del						PASS	.		,	65,738,2585		2,12,49,141,444,1046					,	0.3	0.0		dbSNP_134	31	3,1183,6334		0,1,2,162,858,2737	no	intron,codingComplex	ACYP2,TSPYL6	NM_138448.3,NM_001003937.2	,	2,13,51,303,1302,3783	A1A1,A1A2,A1R,A2A2,A2R,RR		15.7713,23.7013,18.2343	,	,		68,1921,8919				SO:0001651	inframe_deletion	388951	exon1			.	AK097417	CCDS42682.1	2p16.3	2007-10-22			ENSG00000178021	ENSG00000178021			14521	protein-coding gene	gene with protein product							Standard	NM_001003937		Approved		uc002rxr.2	Q8N831	OTTHUMG00000151823	ENST00000317802.7:c.580_585delGGGCCC	2.37:g.54482710_54482715delGGGCCC	ENSP00000417919:p.Gly194_Pro195del	Somatic	68	.	.		WXS	Illumina HiSeq	Phase_I	131	51	0.389	NM_001003937	Q6NUJ3	In_Frame_Del	DEL	ENST00000317802.7	37	CCDS42682.1																																																																																			GGGCCC|0.831;-|0.169	0.169	strong		0.626	TSPYL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324069.3	XM_371494	
GEN1	348654	hgsc.bcm.edu	37	2	17962994	17962998	+	Frame_Shift_Del	DEL	AAGTT	AAGTT	-	rs113873109|rs149936944	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	AAGTT	AAGTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:17962994_17962998delAAGTT	ENST00000381254.2	+	14	2729_2733	c.2515_2519delAAGTT	c.(2515-2520)aagttgfs	p.KL839fs	SMC6_ENST00000402989.1_Intron|GEN1_ENST00000317402.7_Frame_Shift_Del_p.KL839fs	NM_001130009.1	NP_001123481.1	Q17RS7	GEN_HUMAN	GEN1 Holliday junction 5' flap endonuclease	839					DNA catabolic process, endonucleolytic (GO:0000737)|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)|resolution of recombination intermediates (GO:0071139)	centrosome (GO:0005813)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	crossover junction endodeoxyribonuclease activity (GO:0008821)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(6)|central_nervous_system(1)|kidney(1)|large_intestine(3)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	16	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)					TGGCCATAACAAGTTGAGTAGCCCT	0.371								Homologous recombination						297	0.0593051	0.0076	0.0548	5008	,	,		20614	0.1081		0.0905	False		,,,				2504	0.0501				p.838_840del		Pindel,Atlas-Indel	.											.	GEN1	79	.	0			c.2514_2518del						PASS	.		,	107,4159		0,107,2026					,	3.6	0.0		dbSNP_131	57	906,7340		48,810,3265	no	frameshift,frameshift	GEN1	NM_182625.3,NM_001130009.1	,	48,917,5291	A1A1,A1R,RR		10.9871,2.5082,8.0962	,	,		1013,11499				SO:0001589	frameshift_variant	348654	exon14			.	AK098188	CCDS1691.1	2p24.2	2013-06-04	2013-06-04		ENSG00000178295	ENSG00000178295			26881	protein-coding gene	gene with protein product	"""Holliday junction resolvase"""	612449	"""Gen endonuclease homolog 1 (Drosophila)"""			15576351	Standard	NM_182625		Approved	FLJ40869, Gen	uc002rct.2	Q17RS7	OTTHUMG00000121173	ENST00000381254.2:c.2515_2519delAAGTT	2.37:g.17962994_17962998delAAGTT	ENSP00000370653:p.Lys839fs	Somatic	83	.	.		WXS	Illumina HiSeq	Phase_I	101	43	0.426	NM_182625	Q17RS9|Q6ZN37	Frame_Shift_Del	DEL	ENST00000381254.2	37	CCDS1691.1																																																																																			AAGTT|0.926;-|0.074	0.074	strong		0.371	GEN1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241661.2	NM_182625	
WDR60	55112	hgsc.bcm.edu	37	7	158664075	158664077	+	In_Frame_Del	DEL	GAA	GAA	-	rs3833679|rs145233696	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	GAA	GAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:158664075_158664077delGAA	ENST00000407559.3	+	3	470_472	c.312_314delGAA	c.(310-315)ctgaag>ctg	p.K105del		NM_018051.4	NP_060521.4	Q8WVS4	WDR60_HUMAN	WD repeat domain 60	105					cell projection organization (GO:0030030)	cilium (GO:0005929)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)		p.K105delK(1)		NS(3)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(3)|kidney(1)|large_intestine(2)|liver(4)|lung(16)|ovary(2)	35	Ovarian(565;0.152)	all_cancers(7;1.25e-09)|all_epithelial(9;0.000894)|all_hematologic(28;0.00603)	OV - Ovarian serous cystadenocarcinoma(82;0.00174)	UCEC - Uterine corpus endometrioid carcinoma (81;0.19)|STAD - Stomach adenocarcinoma(7;0.18)		aagaaaagctgaaggagaaacat	0.542														583	0.116414	0.0908	0.0965	5008	,	,		19368	0.0556		0.1889	False		,,,				2504	0.1534				p.104_105del		Pindel,Atlas-Indel	.											.	WDR60	94	.	1	Deletion - In frame(1)	central_nervous_system(1)	c.311_313del						PASS	.			346,3112		52,242,1435						-8.3	0.0		dbSNP_107	66	1313,5999		217,879,2560	no	coding	WDR60	NM_018051.4		269,1121,3995	A1A1,A1R,RR		17.9568,10.0058,15.4039				1659,9111				SO:0001651	inframe_deletion	55112	exon3			.		CCDS47757.1	7q36.3	2013-11-15			ENSG00000126870	ENSG00000126870		"""WD repeat domain containing"""	21862	protein-coding gene	gene with protein product		615462				23910462	Standard	NM_018051		Approved	FLJ10300, FAP163	uc003woe.4	Q8WVS4	OTTHUMG00000151443	ENST00000407559.3:c.312_314delGAA	7.37:g.158664075_158664077delGAA	ENSP00000384290:p.Lys105del	Somatic	44	.	.		WXS	Illumina HiSeq	Phase_I	33	13	0.394	NM_018051	Q9NW58	In_Frame_Del	DEL	ENST00000407559.3	37	CCDS47757.1																																																																																			GAA|0.880;-|0.120	0.120	strong		0.542	WDR60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322668.1	NM_018051	
PRSS16	10279	hgsc.bcm.edu	37	6	27223065	27223079	+	In_Frame_Del	DEL	AAGGAGAGCCAGATT	AAGGAGAGCCAGATT	-	rs199705677|rs201493618|rs144604424|rs140280737|rs371606222|rs147170589|rs143492910|rs200987021|rs141138864|rs142712601	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	AAGGAGAGCCAGATT	AAGGAGAGCCAGATT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:27223065_27223079delAAGGAGAGCCAGATT	ENST00000230582.3	+	12	1531_1545	c.1516_1530delAAGGAGAGCCAGATT	c.(1516-1530)aaggagagccagattdel	p.KESQI506del	PRSS16_ENST00000377456.2_3'UTR|PRSS16_ENST00000421826.2_In_Frame_Del_p.KESQI249del	NM_005865.3	NP_005856.1	Q9NQE7	TSSP_HUMAN	protease, serine, 16 (thymus)	506					protein catabolic process (GO:0030163)	cytoplasmic vesicle (GO:0031410)|endosome (GO:0005768)|lysosome (GO:0005764)	serine-type peptidase activity (GO:0008236)	p.K506_I510delKESQI(1)		central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(5)|lung(9)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	26						CAAGCTGGCAAAGGAGAGCCAGATTAAGGGTGAAG	0.479														511	0.102037	0.1135	0.1124	5008	,	,		20927	0.0139		0.174	False		,,,				2504	0.0961				p.505_510del	NSCLC(178;1118 2105 17078 23587 44429)	Pindel,Atlas-Indel	.											.	PRSS16	66	.	1	Deletion - In frame(1)	ovary(1)	c.1515_1529del						PASS	.			514,3748		27,460,1644						-5.7	0.0		dbSNP_113	73	1519,6735		166,1187,2774	no	coding	PRSS16	NM_005865.3		193,1647,4418	A1A1,A1R,RR		18.4032,12.0601,16.2432				2033,10483				SO:0001651	inframe_deletion	10279	exon12			.	AF052514	CCDS4623.1	6p21	2010-05-07			ENSG00000112812	ENSG00000112812		"""Serine peptidases / Serine peptidases"""	9480	protein-coding gene	gene with protein product		607169				10527559	Standard	NM_005865		Approved	TSSP	uc003nja.3	Q9NQE7	OTTHUMG00000016167	ENST00000230582.3:c.1516_1530delAAGGAGAGCCAGATT	6.37:g.27223065_27223079delAAGGAGAGCCAGATT	ENSP00000230582:p.Lys506_Ile510del	Somatic	100	.	.		WXS	Illumina HiSeq	Phase_I	55	44	0.800	NM_005865	O75416	In_Frame_Del	DEL	ENST00000230582.3	37	CCDS4623.1																																																																																			AAGGAGAGCCAGATT|0.883;-|0.117	0.117	strong		0.479	PRSS16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043418.2		
AGAP1	116987	hgsc.bcm.edu	37	2	236761414	236761415	+	Intron	INS	-	-	CAGG	rs142341634|rs370965020	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:236761414_236761415insCAGG	ENST00000304032.8	+	10	1630				AGAP1_ENST00000409457.1_Frame_Shift_Ins_p.-380fs|AGAP1_ENST00000409538.1_Intron|AGAP1_ENST00000428334.2_Intron|AGAP1_ENST00000336665.5_Intron	NM_001037131.2	NP_001032208.1	Q9UPQ3	AGAP1_HUMAN	ArfGAP with GTPase domain, ankyrin repeat and PH domain 1						protein transport (GO:0015031)|regulation of ARF GTPase activity (GO:0032312)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	ARF GTPase activator activity (GO:0008060)|GTP binding (GO:0005525)|phospholipid binding (GO:0005543)|zinc ion binding (GO:0008270)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(12)|lung(11)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	41						CTCCCCCTGGCCAGGGCCGAGG	0.619														719	0.14357	0.0257	0.1268	5008	,	,		15083	0.1677		0.1978	False		,,,				2504	0.2342				p.P379fs		Pindel,Atlas-Indel	.											.	AGAP1	95	.	0			c.1135_1136insCAGG						PASS	.																																			SO:0001627	intron_variant	116987	exon10			.	AF413078	CCDS2514.1, CCDS33408.1, CCDS58756.1	2q37	2013-01-10	2008-09-22	2008-09-22	ENSG00000157985	ENSG00000157985		"""ADP-ribosylation factor GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"", ""Ankyrin repeat domain containing"""	16922	protein-coding gene	gene with protein product		608651	"""centaurin, gamma 2"""	CENTG2			Standard	NM_001037131		Approved	KIAA1099, GGAP1	uc002vvs.3	Q9UPQ3	OTTHUMG00000133293	ENST00000304032.8:c.1051-30574->CAGG	2.37:g.236761415_236761418dupCAGG		Somatic	319	.	.		WXS	Illumina HiSeq	Phase_I	269	66	0.245	NM_001244888	B2RTX7|Q541S5|Q6P9D7|Q9NV93	Frame_Shift_Ins	INS	ENST00000304032.8	37	CCDS33408.1																																																																																			-|0.857;CAGG|0.143	0.143	strong		0.619	AGAP1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000257076.2	NM_014914	
ZFYVE19	84936	hgsc.bcm.edu	37	15	41099899	41099900	+	Frame_Shift_Ins	INS	-	-	GGGGC	rs371684343|rs200042011|rs142730574|rs369585041	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:41099899_41099900insGGGGC	ENST00000355341.4	+	1	613_614	c.112_113insGGGGC	c.(112-114)tggfs	p.-40fs	DNAJC17_ENST00000220496.4_5'Flank|ZFYVE19_ENST00000563530.1_3'UTR|ZFYVE19_ENST00000564258.1_Intron|ZFYVE19_ENST00000336455.5_Intron|ZFYVE19_ENST00000299173.10_Frame_Shift_Ins_p.-40fs|ZFYVE19_ENST00000570108.1_Intron	NM_001077268.1	NP_001070736.1	Q96K21	ANCHR_HUMAN	zinc finger, FYVE domain containing 19						abscission (GO:0009838)|cell division (GO:0051301)|cytokinesis checkpoint (GO:0031565)|negative regulation of cytokinesis (GO:0032466)	centrosome (GO:0005813)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|midbody (GO:0030496)	phosphatidylinositol-3-phosphate binding (GO:0032266)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(1)|large_intestine(1)|lung(4)|skin(1)	9		all_cancers(109;3.31e-18)|all_epithelial(112;2.33e-15)|Lung NSC(122;5.34e-11)|all_lung(180;1.33e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946)		GBM - Glioblastoma multiforme(113;2.76e-05)|COAD - Colon adenocarcinoma(120;0.151)|BRCA - Breast invasive adenocarcinoma(123;0.164)		AGTGGGCGTGTGgggcggggca	0.718														1685	0.336462	0.3411	0.3112	5008	,	,		13821	0.2252		0.3777	False		,,,				2504	0.4202				p.W38fs		Atlas-Indel	.											.	ZFYVE19	31	.	0			c.112_113insGGGGC						PASS	.			1226,2460		247,732,864						2.0	0.3		dbSNP_130	17	2598,5206		494,1610,1798	no	frameshift	ZFYVE19	NM_001077268.1		741,2342,2662	A1A1,A1R,RR		33.2906,33.261,33.2811				3824,7666				SO:0001589	frameshift_variant	84936	exon1			.	AK027746	CCDS42025.1, CCDS58353.1, CCDS58354.1, CCDS58355.1	15q14	2008-05-02				ENSG00000166140		"""Zinc fingers, FYVE domain containing"""	20758	protein-coding gene	gene with protein product							Standard	NM_001077268		Approved	FLJ14840	uc031qrk.1	Q96K21		ENST00000355341.4:c.118_122dupGGGGC	15.37:g.41099905_41099909dupGGGGC	ENSP00000347498:p.Gly40fs	Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	95	23	0.242105	NM_001077268	B3KVB2|C9JNF4|H3BUF9|Q86WC2|Q8WU96	Frame_Shift_Ins	INS	ENST00000355341.4	37	CCDS42025.1																																																																																			-|0.663;GGGGC|0.337	0.337	strong		0.718	ZFYVE19-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000418996.1	NM_032850	
HCG17	414778	hgsc.bcm.edu	37	6	30229034	30229035	+	lincRNA	INS	-	-	T	rs11393606|rs568184983	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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,Atlas-Indel	.											.	.	.	.	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	129	.	.		WXS	Illumina HiSeq	Phase_I	130	24	0.185	.		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	
WWC1	23286	hgsc.bcm.edu	37	5	167881030	167881032	+	In_Frame_Del	DEL	GGA	GGA	-	rs111457550|rs28429769|rs28421695|rs376909223	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	GGA	GGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:167881030_167881032delGGA	ENST00000265293.4	+	18	3085_3087	c.2583_2585delGGA	c.(2581-2586)gtggag>gtg	p.E865del	WWC1_ENST00000521089.1_In_Frame_Del_p.E865del|WWC1_ENST00000522140.1_3'UTR	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	865	Glu-rich.|Interaction with histone H3.			Missing (in Ref. 6; AAO73817). {ECO:0000305}.	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)		aggaggaggtggaggaggaggag	0.547																																					p.861_862del		Pindel,Atlas-Indel	.											WWC1,colon,carcinoma,0,1	WWC1	98	1	0			c.2582_2584del						PASS	.		,,	2323,1941		637,1049,446					,,	-0.6	0.1		dbSNP_132	92	1828,6426		217,1394,2516	no	coding,coding,coding	WWC1	NM_015238.2,NM_001161662.1,NM_001161661.1	,,	854,2443,2962	A1A1,A1R,RR		22.1468,45.5206,33.1602	,,	,,		4151,8367				SO:0001651	inframe_deletion	23286	exon18			.	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.2583_2585delGGA	5.37:g.167881039_167881041delGGA	ENSP00000265293:p.Glu865del	Somatic	139	.	.		WXS	Illumina HiSeq	Phase_I	194	41	0.211	NM_015238	B4DK05|O94946|Q6MZX4|Q6Y2F8|Q7Z4G8|Q8WVM4|Q9BT29	In_Frame_Del	DEL	ENST00000265293.4	37	CCDS4366.1																																																																																			GGA|0.612;-|0.388	0.388	strong		0.547	WWC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252791.2	NM_015238	
PRR25	388199	hgsc.bcm.edu	37	16	855518	855523	+	In_Frame_Del	DEL	GCAGCT	GCAGCT	-	rs137876084|rs368672563	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	GCAGCT	GCAGCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:855518_855523delGCAGCT	ENST00000301698.1	+	1	76_81	c.76_81delGCAGCT	c.(76-81)gcagctdel	p.AA26del		NM_001013638.1	NP_001013660.1	Q96S07	PRR25_HUMAN	proline rich 25	26										large_intestine(1)|lung(1)|skin(1)	3						CACGGGTGGGGCAGCTGCACACCCCA	0.631														493	0.0984425	0.0023	0.1052	5008	,	,		18662	0.1855		0.0338	False		,,,				2504	0.2004				p.25_27del		Pindel,Atlas-Indel	.											.	PRR25	27	.	0			c.75_80del						PASS	.			59,3833		7,45,1894						-1.3	0.0		dbSNP_134	27	309,7635		6,297,3669	no	coding	PRR25	NM_001013638.1		13,342,5563	A1A1,A1R,RR		3.8897,1.5159,3.1092				368,11468				SO:0001651	inframe_deletion	388199	exon1			.	BC156145	CCDS45372.1	16p13.3	2009-09-11			ENSG00000167945	ENSG00000167945			37230	protein-coding gene	gene with protein product						11157797	Standard	NM_001013638		Approved	gs64	uc010uut.2	Q96S07		ENST00000301698.1:c.76_81delGCAGCT	16.37:g.855518_855523delGCAGCT	ENSP00000301698:p.Ala26_Ala27del	Somatic	45	.	.		WXS	Illumina HiSeq	Phase_I	25	11	0.440	NM_001013638		In_Frame_Del	DEL	ENST00000301698.1	37	CCDS45372.1																																																																																			GCAGCT|0.922;-|0.078	0.078	strong		0.631	PRR25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440563.1	NM_001013638	
PIEZO1	9780	hgsc.bcm.edu	37	16	88780635	88780640	+	IGR	DEL	GGTGTG	GGTGTG	-	rs397761749|rs149847195|rs571090098|rs562672342|rs11278302	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	GGTGTG	GGTGTG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:88780635_88780640delGGTGTG	ENST00000301015.9	-	0	8072				MIR4722_ENST00000578292.1_RNA|CTU2_ENST00000312060.5_Splice_Site_p.R366del|CTU2_ENST00000453996.2_Splice_Site_p.R366del|CTU2_ENST00000378384.3_Splice_Site_p.R279del|CTU2_ENST00000567949.1_Splice_Site_p.R437del	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						ACtgtgtacaggtgtgggtgtgtgtg	0.646														3875	0.773762	0.5923	0.7997	5008	,	,		15812	0.9385		0.7644	False		,,,				2504	0.8405				p.366_366del		Pindel,Atlas-Indel	.											.	CTU2	66	.	0			c.1096_1097del						PASS	.																																			SO:0001628	intergenic_variant	348180	exon10			.	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.88780641_88780646delGGTGTG		Somatic	102	.	.		WXS	Illumina HiSeq	Phase_I	105	46	0.438	NM_001012759	A6NHT9|A7E2B7|Q0KKZ9	Frame_Shift_Del	DEL	ENST00000301015.9	37	CCDS54058.1																																																																																			GGTGTG|0.183;-|0.817	0.817	strong		0.646	PIEZO1-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000345699.4	NM_014745	
CTAGE5	4253	hgsc.bcm.edu	37	14	39784005	39784006	+	Splice_Site	DEL	TA	TA	-	rs577313725|rs548723883|rs75318507|rs201697727	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	TA	TA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:39784005_39784006delTA	ENST00000280083.3	+	15	1670		c.e15+2		CTAGE5_ENST00000557038.1_Splice_Site|CTAGE5_ENST00000341502.5_Splice_Site|CTAGE5_ENST00000553352.1_Splice_Site|CTAGE5_ENST00000348007.3_Splice_Site|RP11-407N17.3_ENST00000553728.1_Splice_Site|CTAGE5_ENST00000341749.3_Splice_Site|CTAGE5_ENST00000556148.1_Splice_Site|RP11-407N17.3_ENST00000603904.1_Splice_Site|CTAGE5_ENST00000396158.2_Splice_Site|CTAGE5_ENST00000396165.4_Splice_Site			O15320	CTGE5_HUMAN	CTAGE family, member 5						positive regulation of catalytic activity (GO:0043085)	membrane (GO:0016020)	enzyme activator activity (GO:0008047)	p.?(1)	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)		CAAGGGCAGGTATATATATAtg	0.297																																					.		Atlas-Indel	.											.	CTAGE5	75	.	1	Unknown(1)	haematopoietic_and_lymphoid_tissue(1)	.						PASS	.																																			SO:0001630	splice_region_variant	4253	.			.	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.1356+2TA>-	14.37:g.39784013_39784014delTA		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	125	77	0.616	.	B3KRA6|B4DQS6|D3DSA6|G3XAC5|O00169|Q6MZN2|Q6P2R8|Q86TF6|Q8IX92|Q8IX93	Splice_Site	DEL	ENST00000280083.3	37	CCDS9674.1																																																																																			.	.	strong		0.297	CTAGE5-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000276771.2	NM_005930	Intron
TRIM13	10206	hgsc.bcm.edu	37	13	50590292	50590293	+	3'UTR	INS	-	-	CTC	rs59774589|rs201003919|rs10675754	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:50590292_50590293insCTC	ENST00000378182.3	+	0	4954_4955				KCNRG_ENST00000312942.1_Intron|TRIM13_ENST00000478111.1_Intron|KCNRG_ENST00000360473.4_Intron	NM_001007278.1|NM_005798.3|NM_052811.2|NM_213590.1	NP_001007279.1|NP_005789.2|NP_434698.1|NP_998755.1	O60858	TRI13_HUMAN	tripartite motif containing 13						anatomical structure morphogenesis (GO:0009653)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|innate immune response (GO:0045087)|negative regulation of viral release from host cell (GO:1902187)|negative regulation of viral transcription (GO:0032897)|positive regulation of cell death (GO:0010942)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of macroautophagy (GO:0016239)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein autoubiquitination (GO:0051865)|response to gamma radiation (GO:0010332)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|perinuclear endoplasmic reticulum (GO:0097038)	ligase activity (GO:0016874)|signal transducer activity (GO:0004871)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			large_intestine(5)|lung(2)|ovary(2)|upper_aerodigestive_tract(1)	10		Acute lymphoblastic leukemia(7;3.41e-06)|Lung NSC(96;3.08e-05)|Breast(56;9.7e-05)|Prostate(109;0.00174)|Hepatocellular(98;0.0207)|Myeloproliferative disorder(33;0.163)|Lung SC(185;0.187)|all_neural(104;0.19)		GBM - Glioblastoma multiforme(99;1.53e-10)|COAD - Colon adenocarcinoma(199;0.205)		GCCTGTAACTTCTGGAAAAGAT	0.351														830	0.165735	0.3033	0.1297	5008	,	,		20068	0.0298		0.168	False		,,,				2504	0.1431				.		Pindel,Atlas-Indel	.											.	TRIM13	30	.	0			.						PASS	.																																			SO:0001624	3_prime_UTR_variant	10206	.			.	AF220127	CCDS9423.1, CCDS41888.1	13q14	2013-01-09	2011-01-25	2006-09-26	ENSG00000204977	ENSG00000204977		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	9976	protein-coding gene	gene with protein product		605661	"""ret finger protein 2"", ""tripartite motif-containing 13"""	RFP2		9599022	Standard	NM_213590		Approved	Leu5, RNF77, DLEU5	uc001vdp.1	O60858	OTTHUMG00000016926	ENST00000378182.3:c.*2993->CTC	13.37:g.50590292_50590293insCTC		Somatic	136	.	.		WXS	Illumina HiSeq	Phase_I	116	34	0.293	.	B2RB49|Q5UBW0|Q5W0U8|Q5W0U9|Q9BQ47|Q9C021	RNA	INS	ENST00000378182.3	37	CCDS9423.1																																																																																			-|0.500;CTC|0.500	0.500	strong		0.351	TRIM13-005	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000354875.1	NM_001007278	
APLF	200558	hgsc.bcm.edu	37	2	68805143	68805143	+	Frame_Shift_Del	DEL	A	A	-	rs149897324	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:68805143delA	ENST00000303795.4	+	10	1696	c.1525delA	c.(1525-1527)aaafs	p.K509fs	APLF_ENST00000471727.1_Intron	NM_173545.2	NP_775816.1	Q8IW19	APLF_HUMAN	aprataxin and PNKP like factor	509					cellular response to DNA damage stimulus (GO:0006974)|DNA catabolic process, endonucleolytic (GO:0000737)|double-strand break repair (GO:0006302)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|positive regulation of DNA ligation (GO:0051106)|regulation of isotype switching (GO:0045191)|single strand break repair (GO:0000012)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|site of double-strand break (GO:0035861)	3'-5' exonuclease activity (GO:0008408)|DNA-(apurinic or apyrimidinic site) lyase activity (GO:0003906)|endodeoxyribonuclease activity (GO:0004520)|metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)			autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|liver(2)|lung(9)|ovary(3)|prostate(1)|skin(1)	25						AAGGTTTATGAAAAGAAAATA	0.358													AAAA|AAAA|AAA|deletion	23	0.00459265	0.0008	0.0058	5008	,	,		20808	0.0		0.0119	False		,,,				2504	0.0061				p.M508fs		Pindel,Atlas-Indel	.											.	APLF	69	.	0			c.1524delG						PASS	.			15,4251		0,15,2118	68.0	74.0	72.0			2.8	1.0	2	dbSNP_134	73	121,8127		3,115,4006	no	frameshift	APLF	NM_173545.2		3,130,6124	A1A1,A1R,RR		1.467,0.3516,1.0868			68805143	136,12378	2203	4299	6502	SO:0001589	frameshift_variant	200558	exon10			.	BC030711	CCDS1888.1	2p14	2014-02-20	2008-10-01	2008-10-01	ENSG00000169621	ENSG00000169621			28724	protein-coding gene	gene with protein product	"""XRCC1-interacting protein 1"", ""zinc finger, CX5CX6HX5H motif containing 1"""	611035	"""chromosome 2 open reading frame 13"""	C2orf13		18474613, 18077224, 17353262	Standard	NM_173545		Approved	MGC47799, Xip1, ZCCHH1	uc002sep.3	Q8IW19	OTTHUMG00000129566	ENST00000303795.4:c.1525delA	2.37:g.68805143delA	ENSP00000307004:p.Lys509fs	Somatic	79	.	.		WXS	Illumina HiSeq	Phase_I	50	20	0.400	NM_173545	A8K476|Q53P47|Q53PB9|Q53QU0	Frame_Shift_Del	DEL	ENST00000303795.4	37	CCDS1888.1																																																																																			A|0.991;-|0.009	0.009	strong		0.358	APLF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251759.1	NM_173545	
ERICH6B	220081	hgsc.bcm.edu	37	13	46170720	46170737	+	In_Frame_Del	DEL	CCAGATACTCTTCCTCCT	CCAGATACTCTTCCTCCT	-	rs373081063|rs117004691|rs28548352|rs142875900|rs28460344|rs45625342|rs375947127	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	CCAGATACTCTTCCTCCT	CCAGATACTCTTCCTCCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:46170720_46170737delCCAGATACTCTTCCTCCT	ENST00000298738.2	-	3	568_585	c.404_421delAGGAGGAAGAGTATCTGG	c.(403-423)gaggaggaagagtatctgggg>ggg	p.EEEEYL135del		NM_182542.2	NP_872348.2	Q5W0A0	ERI6B_HUMAN		135	Glu-rich.									breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)	5						CCTTCCTTCCCCAGATActcttcctcctccagatgctc	0.486														1379	0.275359	0.1362	0.4308	5008	,	,		23489	0.1607		0.493	False		,,,				2504	0.2474				p.135_141del		Pindel,Atlas-Indel	.											.	FAM194B	42	.	0			c.405_422del						PASS	.			414,2088		68,278,905						-4.5	0.0		dbSNP_134	119	2412,2596		704,1004,796	no	coding	FAM194B	NM_182542.2		772,1282,1701	A1A1,A1R,RR		48.1629,16.5468,37.6298				2826,4684				SO:0001651	inframe_deletion	220081	exon3			.																												ENST00000298738.2:c.404_421delAGGAGGAAGAGTATCTGG	13.37:g.46170720_46170737delCCAGATACTCTTCCTCCT	ENSP00000298738:p.Glu135_Leu140del	Somatic	88	.	.		WXS	Illumina HiSeq	Phase_I	79	14	0.177	NM_182542	Q96MB5	In_Frame_Del	DEL	ENST00000298738.2	37	CCDS45045.1																																																																																			.	.	strong		0.486	FAM194B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044781.3		
CELA1	1990	hgsc.bcm.edu	37	12	51740415	51740416	+	Frame_Shift_Del	DEL	AC	AC	-	rs370927847|rs386762976|rs61761206|rs55827519|rs148235680	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	AC	AC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	152	0	0		WXS	Illumina HiSeq	Phase_I	92	15	0.163043	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	
TTN	7273	hgsc.bcm.edu	37	2	179514942	179514959	+	In_Frame_Del	DEL	TTTCCTCTTCAGGAGCAA	TTTCCTCTTCAGGAGCAA	-	rs374976705|rs139512154	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	TTTCCTCTTCAGGAGCAA	TTTCCTCTTCAGGAGCAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:179514942_179514959delTTTCCTCTTCAGGAGCAA	ENST00000591111.1	-	165	35452_35469	c.35228_35245delTTGCTCCTGAAGAGGAAA	c.(35227-35247)attgctcctgaagaggaaaag>aag	p.IAPEEE11743del	TTN_ENST00000359218.5_Intron|TTN-AS1_ENST00000589830.1_RNA|TTN-AS1_ENST00000589487.1_RNA|TTN_ENST00000342992.6_In_Frame_Del_p.IAPEEE10816del|TTN_ENST00000460472.2_Intron|TTN_ENST00000589042.1_In_Frame_Del_p.IAPEEE13250del|TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000431752.1_RNA			Q8WZ42	TITIN_HUMAN	titin	11743	Glu-rich.|Pro-rich.				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)			GGAACTGGCTTTTCCTCTTCAGGAGCAATTTCCTCTTC	0.381														166	0.033147	0.084	0.0173	5008	,	,		20291	0.0119		0.0139	False		,,,				2504	0.0174				p.13250_13256del		Pindel,Atlas-Indel	.											.	TTN	18412	.	0			c.39750_39767del						PASS	.		,,,	109,3367		6,97,1635					,,,	1.6	1.0		dbSNP_134	28	38,7756		1,36,3860	no	intron,intron,coding,intron	TTN	NM_133437.3,NM_133432.3,NM_133378.4,NM_003319.4	,,,	7,133,5495	A1A1,A1R,RR		0.4876,3.1358,1.3043	,,,	,,,		147,11123				SO:0001651	inframe_deletion	7273	exon210			.	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.35228_35245delTTGCTCCTGAAGAGGAAA	2.37:g.179514942_179514959delTTTCCTCTTCAGGAGCAA	ENSP00000465570:p.Ile11743_Glu11748del	Somatic	230	.	.		WXS	Illumina HiSeq	Phase_I	159	34	0.214	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	In_Frame_Del	DEL	ENST00000591111.1	37																																																																																				TTTCCTCTTCAGGAGCAA|0.972;-|0.028	0.028	strong		0.381	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
OR8J1	219477	hgsc.bcm.edu	37	11	56128673	56128674	+	Stop_Codon_Ins	INS	-	-	T	rs56266017|rs372964103|rs34649252	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:56128673_56128674insT	ENST00000303039.3	+	0	983_984					NM_001005205.2	NP_001005205.2	Q8NGP2	OR8J1_HUMAN	olfactory receptor, family 8, subfamily J, member 1							integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(30)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	47	Esophageal squamous(21;0.00448)					AAACAATGTAATTTTAAACAGT	0.361													TTTT|TTTT|TTTTT|insertion	345	0.0688898	0.0431	0.0317	5008	,	,		18925	0.0933		0.0934	False		,,,				2504	0.0798				p.X317delinsX		Pindel,Atlas-Indel	.											.	OR8J1	87	.	0			c.951_952insT						PASS	.			204,4056		4,196,1930						1.4	0.0		dbSNP_126	35	720,7518		32,656,3431	no	frameshift	OR8J1	NM_001005205.2		36,852,5361	A1A1,A1R,RR		8.74,4.7887,7.3932				924,11574				SO:0001567	stop_retained_variant	219477	exon1			.	AB065748	CCDS31529.1	11q11	2012-08-09			ENSG00000172487	ENSG00000172487		"""GPCR / Class A : Olfactory receptors"""	14855	protein-coding gene	gene with protein product							Standard	NM_001005205		Approved		uc010rjh.2	Q8NGP2	OTTHUMG00000166859	ENST00000303039.3:c.952dupT	11.37:g.56128677_56128677dupT		Somatic	68	.	.		WXS	Illumina HiSeq	Phase_I	50	23	0.460	NM_001005205	B2RNQ6|B9EH63|Q6IFC2|Q96RC3	Frame_Shift_Ins	INS	ENST00000303039.3	37	CCDS31529.1																																																																																			-|0.931;T|0.069	0.069	strong		0.361	OR8J1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391606.2	NM_001005205	
MYO7A	4647	hgsc.bcm.edu	37	11	76895771	76895792	+	Intron	DEL	GGAGGCGGGGACACCAGGGCCT	GGAGGCGGGGACACCAGGGCCT	-	rs111906251|rs143953991|rs78509218|rs111033223|rs369969967|rs12291062	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	GGAGGCGGGGACACCAGGGCCT	GGAGGCGGGGACACCAGGGCCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:76895771_76895792delGGAGGCGGGGACACCAGGGCCT	ENST00000409709.3	+	27	3775				MYO7A_ENST00000458637.2_Intron|MYO7A_ENST00000409893.1_Stop_Codon_Del|MYO7A_ENST00000409619.2_Intron	NM_000260.3	NP_000251.3	Q13402	MYO7A_HUMAN	myosin VIIA						actin filament-based movement (GO:0030048)|auditory receptor cell stereocilium organization (GO:0060088)|equilibrioception (GO:0050957)|eye photoreceptor cell development (GO:0042462)|intracellular protein transport (GO:0006886)|lysosome organization (GO:0007040)|metabolic process (GO:0008152)|phagolysosome assembly (GO:0001845)|pigment granule transport (GO:0051904)|post-embryonic organ morphogenesis (GO:0048563)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|lysosomal membrane (GO:0005765)|melanosome (GO:0042470)|myosin VII complex (GO:0031477)|photoreceptor connecting cilium (GO:0032391)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|stereocilium (GO:0032420)|synapse (GO:0045202)	actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|spectrin binding (GO:0030507)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(10)|lung(32)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	64						GTCAGTGCCGGGAGGCGGGGACACCAGGGCCTGAAAGTCTTT	0.599														2033	0.40595	0.466	0.4712	5008	,	,		20094	0.3194		0.4901	False		,,,				2504	0.2812				p.1171_1178del		Pindel,Atlas-Indel	.											.	MYO7A	164	.	0			c.3513_3534del						PASS	.		,,	1379,2453		340,699,877					,,	-8.4	0.0		dbSNP_126	18	3099,4701		776,1547,1577	no	intron,frameshift,intron	MYO7A	NM_001127180.1,NM_001127179.2,NM_000260.3	,,	1116,2246,2454	A1A1,A1R,RR		39.7308,35.9864,38.4972	,,	,,		4478,7154				SO:0001627	intron_variant	4647	exon27			.	U39226	CCDS53683.1, CCDS53684.1, CCDS53685.1	11q13.5	2013-01-08	2005-09-12		ENSG00000137474	ENSG00000137474		"""A-kinase anchor proteins"", ""Myosins / Myosin superfamily : Class VII"""	7606	protein-coding gene	gene with protein product		276903	"""myosin VIIA (Usher syndrome 1B (autosomal recessive, severe))"""	USH1B, DFNB2, DFNA11		8884266	Standard	NM_000260		Approved	NSRD2	uc001oyb.2	Q13402	OTTHUMG00000152822	ENST00000409709.3:c.3503+11GGAGGCGGGGACACCAGGGCCT>-	11.37:g.76895771_76895792delGGAGGCGGGGACACCAGGGCCT		Somatic	132	.	.		WXS	Illumina HiSeq	Phase_I	98	75	0.765	NM_001127179	B9A011|F8VUN5|P78427|Q13321|Q14785|Q92821|Q92822	Frame_Shift_Del	DEL	ENST00000409709.3	37	CCDS53683.1																																																																																			GGAGGCGGGGACACCAGGGCCT|0.573;-|0.427	0.427	strong		0.599	MYO7A-001	KNOWN	non_canonical_conserved|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000328133.1	NM_000260	
CCDC71	64925	hgsc.bcm.edu	37	3	49200611	49200616	+	In_Frame_Del	DEL	GCCTTG	GCCTTG	-			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	GCCTTG	GCCTTG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:49200611_49200616delGCCTTG	ENST00000321895.6	-	2	1132_1137	c.1026_1031delCAAGGC	c.(1024-1032)gccaaggct>gct	p.342_344AKA>A		NM_022903.3	NP_075054.3	Q8IV32	CCD71_HUMAN	coiled-coil domain containing 71	342										endometrium(1)|large_intestine(4)|lung(3)|ovary(1)|prostate(1)	10				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00217)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)		cttggctttagccttggccttggccc	0.617																																					p.343_344del		Pindel,Atlas-Indel	.											.	CCDC71	33	.	0			c.1027_1032del						PASS	.																																			SO:0001651	inframe_deletion	64925	exon2			.	AK022862	CCDS2790.1	3p21.31	2014-02-12			ENSG00000177352	ENSG00000177352			25760	protein-coding gene	gene with protein product						12477932	Standard	NM_022903		Approved	FLJ12800	uc003cwg.4	Q8IV32	OTTHUMG00000156815	ENST00000321895.6:c.1026_1031delCAAGGC	3.37:g.49200617_49200622delGCCTTG	ENSP00000319006:p.Ala346_Lys347del	Somatic	69	.	.		WXS	Illumina HiSeq	Phase_I	86	21	0.244	NM_022903	Q6IPE2|Q9H8H4|Q9H9F1	In_Frame_Del	DEL	ENST00000321895.6	37	CCDS2790.1																																																																																			.	.	none		0.617	CCDC71-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345980.1	NM_022903	
TBCK	93627	hgsc.bcm.edu	37	4	107171638	107171642	+	Intron	DEL	AAATA	AAATA	-	rs139991421	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	AAATA	AAATA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:107171638_107171642delAAATA	ENST00000273980.5	-	8	1045				TBCK_ENST00000394706.3_Intron|TBCK_ENST00000394708.2_Intron|TBCK_ENST00000432496.2_Intron|TBCK_ENST00000361687.4_Intron					TBC1 domain containing kinase											NS(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(9)|ovary(1)|pancreas(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(1)	25						TTTCTTCCCTAAATAAAATGAGAAA	0.273														684	0.136581	0.0076	0.1167	5008	,	,		15823	0.1468		0.1789	False		,,,				2504	0.271				.		Pindel,Atlas-Indel	.											.	TBCK	89	.	0			.						PASS	.		,,,	130,3952		3,124,1914					,,,	5.8	1.0		dbSNP_106	22	1346,6704		147,1052,2826	no	intron,intron,intron,intron	TBCK	NM_033115.3,NM_001163437.1,NM_001163436.1,NM_001163435.1	,,,	150,1176,4740	A1A1,A1R,RR		16.7205,3.1847,12.1662	,,,	,,,		1476,10656				SO:0001627	intron_variant	93627	.			.		CCDS3673.1, CCDS54788.1, CCDS54789.1	4q24	2014-09-17			ENSG00000145348	ENSG00000145348			28261	protein-coding gene	gene with protein product						12471243	Standard	XR_427553		Approved	MGC16169, HSPC302	uc010ilv.2	Q8TEA7	OTTHUMG00000131214	ENST00000273980.5:c.598-3TATTT>-	4.37:g.107171638_107171642delAAATA		Somatic	66	.	.		WXS	Illumina HiSeq	Phase_I	49	22	0.449	.		Splice_Site	DEL	ENST00000273980.5	37	CCDS54788.1																																																																																			AAATA|0.864;-|0.136	0.136	strong		0.273	TBCK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253953.4	NM_033115	
HOMEZ	57594	hgsc.bcm.edu	37	14	23744827	23744829	+	In_Frame_Del	DEL	TCC	TCC	-	rs79723196|rs35076736|rs67447855	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	TCC	TCC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:23744827_23744829delTCC	ENST00000357460.5	-	2	1772_1774	c.1608_1610delGGA	c.(1606-1611)gaggaa>gaa	p.536_537EE>E	HOMEZ_ENST00000561013.1_In_Frame_Del_p.538_539EE>E|HOMEZ_ENST00000431326.2_In_Frame_Del_p.538_539EE>E	NM_020834.2	NP_065885.2	Q8IX15	HOMEZ_HUMAN	homeobox and leucine zipper encoding	536	Glu-rich.|Poly-Asp.				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)		atcatcatcttcctcctcctcct	0.483														1763	0.352037	0.3949	0.3386	5008	,	,		20301	0.1974		0.3738	False		,,,				2504	0.4407				p.537_537del		Pindel,Atlas-Indel	.											.	HOMEZ	80	.	0			c.1609_1611del						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.1608_1610delGGA	14.37:g.23744836_23744838delTCC	ENSP00000350049:p.Glu537del	Somatic	102	.	.		WXS	Illumina HiSeq	Phase_I	81	13	0.160	NM_020834	A1L445|B4DZ80|F8WCA3|Q6P049|Q86XB6|Q9P2A5	In_Frame_Del	DEL	ENST00000357460.5	37	CCDS45085.1																																																																																			TCC|0.500;-|0.500	0.500	weak		0.483	HOMEZ-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000416939.2	NM_020834	
HAVCR1	26762	hgsc.bcm.edu	37	5	156479558	156479572	+	In_Frame_Del	DEL	TTGGAACAGTCGTCA	TTGGAACAGTCGTCA	-	rs386693994|rs139041445|rs6149307|rs10068551|rs141023871|rs77147640|rs376729615|rs183130208|rs2862716	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	TTGGAACAGTCGTCA	TTGGAACAGTCGTCA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:156479558_156479572delTTGGAACAGTCGTCA	ENST00000339252.3	-	3	1005_1019	c.473_487delTGACGACTGTTCCAA	c.(472-489)atgacgactgttccaacg>acg	p.MTTVP158del	HAVCR1_ENST00000425854.1_In_Frame_Del_p.MTTVP158del|HAVCR1_ENST00000523175.1_In_Frame_Del_p.MTTVP158del|HAVCR1_ENST00000544197.1_In_Frame_Del_p.MTTVP158del|HAVCR1_ENST00000522693.1_In_Frame_Del_p.MTTVP158del	NM_012206.2	NP_036338.2	Q96D42	HAVR1_HUMAN	hepatitis A virus cellular receptor 1	0	11 X 6 AA approximate tandem repeats of V-P-T-T-T-T].|Thr-rich.				viral process (GO:0016032)	integral component of membrane (GO:0016021)	virus receptor activity (GO:0001618)	p.T160_V161insT(1)		endometrium(3)|large_intestine(2)|lung(17)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	28	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.0999)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			ACAGTTGTCGTTGGAACAGTCGTCATTGGAACAGT	0.488														2916	0.582268	0.2579	0.6787	5008	,	,		26558	0.7629		0.6282	False		,,,				2504	0.7188				p.158_163del		Pindel,Atlas-Indel	.											.	HAVCR1	84	.	1	Insertion - In frame(1)	ovary(1)	c.474_488del						PASS	.		,,	1966,2046		278,1410,318					,,	-1.5	0.0		dbSNP_127	595	4901,3081		1333,2235,423	no	coding,coding,coding	HAVCR1	NM_012206.2,NM_001173393.1,NM_001099414.1	,,	1611,3645,741	A1A1,A1R,RR		38.5993,49.003,42.7464	,,	,,		6867,5127				SO:0001651	inframe_deletion	26762	exon4			.	AF043724	CCDS43392.1	5q33.2	2014-01-14			ENSG00000113249	ENSG00000113249		"""Immunoglobulin superfamily / V-set domain containing"""	17866	protein-coding gene	gene with protein product	"""T-cell immunoglobulin mucin family member 1"""	606518				9658108, 11725301	Standard	NM_012206		Approved	HAVCR-1, TIM-1, TIM1, HAVCR, TIMD1	uc021ygj.1	Q96D42	OTTHUMG00000163466	ENST00000339252.3:c.473_487delTGACGACTGTTCCAA	5.37:g.156479558_156479572delTTGGAACAGTCGTCA	ENSP00000344844:p.Met158_Pro162del	Somatic	428	.	.		WXS	Illumina HiSeq	Phase_I	228	82	0.360	NM_001099414	O43656	In_Frame_Del	DEL	ENST00000339252.3	37	CCDS43392.1																																																																																			.	.	strong		0.488	HAVCR1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373698.1		
ATAD5	79915	hgsc.bcm.edu	37	17	29161956	29161961	+	In_Frame_Del	DEL	CAATGT	CAATGT	-	rs60663953|rs80170526|rs398102309|rs72427574	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	CAATGT	CAATGT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:29161956_29161961delCAATGT	ENST00000321990.4	+	2	1235_1240	c.857_862delCAATGT	c.(856-864)acaatgtca>aca	p.MS287del	CTD-2349P21.11_ENST00000580873.1_RNA	NM_024857.3	NP_079133.3	Q96QE3	ATAD5_HUMAN	ATPase family, AAA domain containing 5	287					cellular response to DNA damage stimulus (GO:0006974)	nucleus (GO:0005634)	ATP binding (GO:0005524)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(3)|large_intestine(18)|lung(13)|ovary(3)|pancreas(1)	51		all_hematologic(16;0.0202)|Acute lymphoblastic leukemia(14;0.0238)|Myeloproliferative disorder(56;0.0393)				CCAGACTCTACAATGTCAATTTGTGT	0.354														721	0.14397	0.0703	0.1859	5008	,	,		20341	0.1359		0.1074	False		,,,				2504	0.2597				p.286_287del		Pindel,Atlas-Indel	.											ATAD5,NS,carcinoma,0,1	ATAD5	150	1	0			c.856_861del						PASS	.			276,3982		14,248,1867						0.7	0.0		dbSNP_130	43	796,7436		29,738,3349	no	coding	ATAD5	NM_024857.3		43,986,5216	A1A1,A1R,RR		9.6696,6.4819,8.5829				1072,11418				SO:0001651	inframe_deletion	79915	exon2			.		CCDS11260.1	17q11.2	2010-04-21	2007-02-08	2007-02-08	ENSG00000176208	ENSG00000176208		"""ATPases / AAA-type"""	25752	protein-coding gene	gene with protein product	"""enhanced level of genomic instability 1 homolog (S. cerevisiae)"""	609534	"""chromosome 17 open reading frame 41"""	C17orf41		15983387, 11468690, 19755857	Standard	NM_024857		Approved	FLJ12735, FRAG1, ELG1	uc002hfs.1	Q96QE3	OTTHUMG00000132794	ENST00000321990.4:c.857_862delCAATGT	17.37:g.29161956_29161961delCAATGT	ENSP00000313171:p.Met287_Ser288del	Somatic	135	.	.		WXS	Illumina HiSeq	Phase_I	97	30	0.309	NM_024857	Q05DH0|Q69YR6|Q9H9I1	In_Frame_Del	DEL	ENST00000321990.4	37	CCDS11260.1																																																																																			CAATGT|0.874;-|0.126	0.126	strong		0.354	ATAD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256206.2	NM_024857	
ANKRD20A4	728747	hgsc.bcm.edu	37	9	69393857	69393860	+	Frame_Shift_Del	DEL	TACT	TACT	-			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	TACT	TACT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:69393857_69393860delTACT	ENST00000357336.3	+	6	1054_1057	c.773_776delTACT	c.(772-777)atacttfs	p.IL258fs	RNU6-1193P_ENST00000459461.1_RNA	NM_001098805.1	NP_001092275.1	Q4UJ75	A20A4_HUMAN	ankyrin repeat domain 20 family, member A4	258										breast(1)|large_intestine(1)|liver(1)|lung(9)|pancreas(2)|skin(2)	16						AAAAAGAAGATACTTAAAAAGGAG	0.25																																					p.258_259del		Atlas-Indel	.											.	ANKRD20A4	38	.	0			c.772_775del						PASS	.																																			SO:0001589	frameshift_variant	728747	exon6			.		CCDS43828.1	9q21.11	2013-01-10			ENSG00000172014	ENSG00000172014		"""Ankyrin repeat domain containing"""	31982	protein-coding gene	gene with protein product							Standard	NM_001098805		Approved	OTTHUMG00000066855	uc004afn.3	Q4UJ75	OTTHUMG00000066855	ENST00000357336.3:c.773_776delTACT	9.37:g.69393857_69393860delTACT	ENSP00000349891:p.Ile258fs	Somatic	321	0	0		WXS	Illumina HiSeq	Phase_I	363	22	0.0606061	NM_001098805		Frame_Shift_Del	DEL	ENST00000357336.3	37	CCDS43828.1																																																																																			.	.	none		0.250	ANKRD20A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143287.3	NM_001098805	
RFPL1	5988	hgsc.bcm.edu	37	22	29837567	29837569	+	In_Frame_Del	DEL	TCC	TCC	-	rs397745673|rs79401928|rs71324764|rs3842466	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	TCC	TCC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:29837567_29837569delTCC	ENST00000354373.2	+	2	619_621	c.410_412delTCC	c.(409-414)ttcctc>ttc	p.L139del	RFPL1S_ENST00000461286.3_RNA|RFPL1S_ENST00000539579.1_RNA	NM_021026.2	NP_066306.2	O75677	RFPL1_HUMAN	ret finger protein-like 1	139	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.		Missing (in RFPL1S).				zinc ion binding (GO:0008270)			endometrium(3)|large_intestine(1)|lung(6)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	16						GCCAACAACTTCCTCCTCATTTC	0.502														1336	0.266773	0.149	0.4193	5008	,	,		21601	0.1131		0.4503	False		,,,				2504	0.2873				p.137_137del		Pindel,Atlas-Indel	.											.	RFPL1	43	.	0			c.409_411del						PASS	.			779,3485		64,651,1417						-2.2	0.0		dbSNP_130	107	3633,4621		805,2023,1299	no	coding	RFPL1	NM_021026.2		869,2674,2716	A1A1,A1R,RR		44.015,18.2692,35.2452				4412,8106				SO:0001651	inframe_deletion	5988	exon2			.	AJ010228	CCDS13857.2	22q12	2006-04-25			ENSG00000128250	ENSG00000128250		"""RING-type (C3HC4) zinc fingers"""	9977	protein-coding gene	gene with protein product		605968				10508838	Standard	NM_021026		Approved	RNF78	uc003afn.3	O75677	OTTHUMG00000150516	ENST00000354373.2:c.410_412delTCC	22.37:g.29837570_29837572delTCC	ENSP00000346342:p.Leu139del	Somatic	286	.	.		WXS	Illumina HiSeq	Phase_I	190	54	0.284	NM_021026	Q6IC06|Q9UJ97	In_Frame_Del	DEL	ENST00000354373.2	37	CCDS13857.2																																																																																			TCC|0.697;-|0.303	0.303	strong		0.502	RFPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318719.1	NM_021026	
PI4KAP2	375133	hgsc.bcm.edu	37	22	21841122	21841126	+	RNA	DEL	TCTTA	TCTTA	-	rs200598591		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	TCTTA	TCTTA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:21841122_21841126delTCTTA	ENST00000450651.1	-	0	866_870							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						GTCAGGTACTTCTTATCTGAGAACA	0.537																																					.		Atlas-Indel	.											.	PI4KAP2	11	.	0			.						PASS	.																																					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.21841122_21841126delTCTTA		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	109	14	0.12844	.	Q6ICJ0|Q6ZT68|Q8WUK7	RNA	DEL	ENST00000450651.1	37																																																																																				TCTTA|0.738;-|0.262	0.262	strong		0.537	PI4KAP2-005	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000334908.1		
DNAH5	1767	hgsc.bcm.edu	37	5	13883045	13883045	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:13883045delC	ENST00000265104.4	-	20	3246	c.3142delG	c.(3142-3144)gtcfs	p.V1048fs	CTB-51A17.1_ENST00000503244.1_RNA	NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	1048	Stem. {ECO:0000250}.				cilium movement (GO:0003341)|lateral ventricle development (GO:0021670)|left/right axis specification (GO:0070986)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(6)|breast(14)|central_nervous_system(4)|cervix(2)|endometrium(23)|haematopoietic_and_lymphoid_tissue(8)|kidney(11)|large_intestine(85)|liver(1)|lung(129)|ovary(16)|pancreas(2)|prostate(5)|skin(48)|stomach(5)|upper_aerodigestive_tract(11)|urinary_tract(8)	378	Lung NSC(4;0.00476)					CACTGTCTGACCCCCTTAGGG	0.507									Kartagener syndrome																												p.V1048fs		Atlas-Indel	.											.	DNAH5	868	.	0			c.3143delT						PASS	.						167.0	149.0	155.0					5																	13883045		2203	4300	6503	SO:0001589	frameshift_variant	1767	exon20	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	.	AJ132090	CCDS3882.1	5p15.2	2008-07-18	2006-09-04		ENSG00000039139	ENSG00000039139		"""Axonemal dyneins"""	2950	protein-coding gene	gene with protein product	"""dynein heavy chain 5"""	603335	"""dynein, axonemal, heavy polypeptide 5"""			9256245, 11788826	Standard	NM_001369		Approved	Dnahc5, HL1, PCD, CILD3, KTGNR	uc003jfd.2	Q8TE73	OTTHUMG00000090533	ENST00000265104.4:c.3142delG	5.37:g.13883045delC	ENSP00000265104:p.Val1048fs	Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	164	26	0.158537	NM_001369	Q92860|Q96L74|Q9H5S7|Q9HCG9	Frame_Shift_Del	DEL	ENST00000265104.4	37	CCDS3882.1																																																																																			.	.	none		0.507	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369	
BAIAP2L2	80115	hgsc.bcm.edu	37	22	38483174	38483175	+	In_Frame_Ins	INS	-	-	CATGGAGGT	rs374089121|rs200930717|rs78489217	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:38483174_38483175insCATGGAGGT	ENST00000381669.3	-	11	1359_1360	c.1215_1216insACCTCCATG	c.(1213-1218)atgtcc>atgACCTCCATGtcc	p.404_405insMTS	CTA-228A9.3_ENST00000609162.1_lincRNA	NM_025045.4	NP_079321.3	Q6UXY1	BI2L2_HUMAN	BAI1-associated protein 2-like 2	404					filopodium assembly (GO:0046847)|membrane organization (GO:0061024)|regulation of actin cytoskeleton organization (GO:0032956)|signal transduction (GO:0007165)	cell-cell contact zone (GO:0044291)|cytoplasmic vesicle (GO:0031410)|plasma membrane (GO:0005886)|vesicle membrane (GO:0012506)	phospholipid binding (GO:0005543)	p.M405_S406insTSM(1)		large_intestine(2)|lung(1)|ovary(2)|pancreas(1)|prostate(1)|stomach(1)	8	Melanoma(58;0.045)					gtcatgggggacatggaggtca	0.653																																					p.S406delinsTSMS		Pindel,Atlas-Indel	.											.	BAIAP2L2	39	.	1	Insertion - In frame(1)	ovary(1)	c.1216_1217insACCTCCATG						PASS	.																																			SO:0001652	inframe_insertion	80115	exon11			.	BC015619	CCDS43018.1	22q13.1	2005-02-09			ENSG00000128298	ENSG00000128298			26203	protein-coding gene	gene with protein product							Standard	NM_025045		Approved	FLJ22582	uc003auw.3	Q6UXY1	OTTHUMG00000151197	ENST00000381669.3:c.1207_1215dupACCTCCATG	22.37:g.38483175_38483183dupCATGGAGGT	ENSP00000371085:p.Met402_Ser404dup	Somatic	49	.	.		WXS	Illumina HiSeq	Phase_I	39	13	0.333	NM_025045	B0QYE2|Q96BG7	In_Frame_Ins	INS	ENST00000381669.3	37	CCDS43018.1																																																																																			-|0.896;CATGGAGGT|0.104	0.104	strong		0.653	BAIAP2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321727.1	NM_025045	
ANKRD30B	374860	hgsc.bcm.edu	37	18	14851887	14851888	+	Frame_Shift_Ins	INS	-	-	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:14851887_14851888insA	ENST00000358984.4	+	36	3767_3768	c.3587_3588insA	c.(3586-3591)agaaaafs	p.RK1196fs		NM_001145029.1	NP_001138501.1	Q9BXX2	AN30B_HUMAN	ankyrin repeat domain 30B	1196										breast(3)|endometrium(4)|kidney(3)|lung(8)|ovary(1)|prostate(2)|skin(1)	22						GTCACATCAAGAAAAAACCAAG	0.381																																					p.R1196fs		Atlas-Indel	.											.	ANKRD30B	237	.	0			c.3587_3588insA						PASS	.																																			SO:0001589	frameshift_variant	374860	exon36			.	BC028407	CCDS54182.1	18p11.21	2013-01-10			ENSG00000180777	ENSG00000180777		"""Ankyrin repeat domain containing"""	24165	protein-coding gene	gene with protein product						11280766	Standard	NM_001145029		Approved	NY-BR-1.1	uc010dlo.2	Q9BXX2		ENST00000358984.4:c.3593dupA	18.37:g.14851893_14851893dupA	ENSP00000351875:p.Arg1196fs	Somatic	230	0	0		WXS	Illumina HiSeq	Phase_I	192	13	0.0677083	NM_001145029	B4DGP1|F8WAG3|Q4G175	Frame_Shift_Ins	INS	ENST00000358984.4	37	CCDS54182.1																																																																																			.	.	none		0.381	ANKRD30B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000443557.1	NM_001145029	
AGAP6	414189	hgsc.bcm.edu	37	10	51768675	51768676	+	Frame_Shift_Del	DEL	AA	AA	-	rs141217862|rs200646112	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	AA	AA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:51768675_51768676delAA	ENST00000374056.4	+	7	1119_1120	c.721_722delAA	c.(721-723)aaafs	p.K241fs	AGAP6_ENST00000412531.3_Frame_Shift_Del_p.K264fs			Q5VW22	AGAP6_HUMAN	ArfGAP with GTPase domain, ankyrin repeat and PH domain 6	241					regulation of ARF GTPase activity (GO:0032312)		ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)			NS(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|liver(1)|lung(8)|prostate(3)|skin(1)|stomach(2)	29						TGACCCAGACAAAGAGAGGAAA	0.55														591	0.118011	0.0356	0.1542	5008	,	,		18267	0.0327		0.2694	False		,,,				2504	0.136				p.263_264del		Pindel,Atlas-Indel	.											.	AGAP6	53	.	0			c.789_790del						PASS	.																																			SO:0001589	frameshift_variant	414189	exon8			.		CCDS44397.1	10q11.23	2013-01-10	2008-09-22	2008-09-22	ENSG00000204149	ENSG00000204149		"""ADP-ribosylation factor GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"", ""Ankyrin repeat domain containing"""	23466	protein-coding gene	gene with protein product			"""centaurin, gamma-like family, member 3"""	CTGLF3			Standard	NM_001077665		Approved	bA324H6.1	uc001jix.4	Q5VW22	OTTHUMG00000018220	ENST00000374056.4:c.721_722delAA	10.37:g.51768675_51768676delAA	ENSP00000363168:p.Lys241fs	Somatic	71	.	.		WXS	Illumina HiSeq	Phase_I	55	36	0.655	NM_001077665		Frame_Shift_Del	DEL	ENST00000374056.4	37																																																																																				AA|0.500;-|0.500	0.500	weak		0.550	AGAP6-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_001077665	
FAM90A1	55138	hgsc.bcm.edu	37	12	8377368	8377368	+	Frame_Shift_Del	DEL	G	G	-	rs553658866		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:8377368delG	ENST00000538603.1	-	4	619	c.61delC	c.(61-63)cagfs	p.Q21fs	FAM90A1_ENST00000307435.6_Frame_Shift_Del_p.Q21fs	NM_018088.3	NP_060558.3	Q86YD7	F90A1_HUMAN	family with sequence similarity 90, member A1	21							nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(4)|lung(11)|ovary(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	25				Kidney(36;0.0866)		CGCTGCTTCTGGAGGGTCTGG	0.607													|||unknown(NO_COVERAGE)	41	0.0081869	0.0	0.0072	5008	,	,		13918	0.0		0.0179	False		,,,				2504	0.0184				p.Q21fs		Pindel,Atlas-Indel	.											.	FAM90A1	68	.	0			c.62delA						PASS	.			12,4248		0,12,2118	23.0	28.0	27.0			-0.6	0.0	12		26	132,8118		1,130,3994	no	frameshift	FAM90A1	NM_018088.3		1,142,6112	A1A1,A1R,RR		1.6,0.2817,1.1511			8377368	144,12366	2203	4295	6498	SO:0001589	frameshift_variant	55138	exon4			.	AK001270	CCDS31738.1	12p13.31	2011-08-31		2005-11-20	ENSG00000171847	ENSG00000171847			25526	protein-coding gene	gene with protein product		613041					Standard	NM_018088		Approved	FLJ10408	uc001qui.2	Q86YD7	OTTHUMG00000168641	ENST00000538603.1:c.61delC	12.37:g.8377368delG	ENSP00000445418:p.Gln21fs	Somatic	11	.	.		WXS	Illumina HiSeq	Phase_I	24	13	0.542	NM_018088	D3DUU9|Q9NVZ6	Frame_Shift_Del	DEL	ENST00000538603.1	37	CCDS31738.1																																																																																			.	.	none		0.607	FAM90A1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400468.1	NM_018088	
CCR8	1237	hgsc.bcm.edu	37	3	39374514	39374516	+	In_Frame_Del	DEL	ACA	ACA	-			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	ACA	ACA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:39374514_39374516delACA	ENST00000326306.4	+	2	830_832	c.692_694delACA	c.(691-696)cacaac>cac	p.N232del	CCR8_ENST00000545843.1_In_Frame_Del_p.N149del|CCR8_ENST00000414803.1_3'UTR	NM_005201.3	NP_005192.1	P51685	CCR8_HUMAN	chemokine (C-C motif) receptor 8	232					cell adhesion (GO:0007155)|chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|positive regulation of cytosolic calcium ion concentration (GO:0007204)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	C-C chemokine receptor activity (GO:0016493)|chemokine receptor activity (GO:0004950)|coreceptor activity (GO:0015026)			NS(3)|breast(1)|endometrium(3)|large_intestine(5)|lung(7)|ovary(1)|skin(1)	21				KIRC - Kidney renal clear cell carcinoma(284;0.0504)|Kidney(284;0.0635)		TGTCAAAACCACAACAAGACCAA	0.429																																					p.231_231del		Pindel,Atlas-Indel	.											.	CCR8	34	.	0			c.691_693del						PASS	.			1,4265		0,1,2132						3.9	1.0			109	0,8248		0,0,4124	no	coding	CCR8	NM_005201.3		0,1,6256	A1A1,A1R,RR		0.0,0.0234,0.0080				1,12513				SO:0001651	inframe_deletion	1237	exon2			.	D49919	CCDS2684.1	3p22	2012-08-08			ENSG00000179934	ENSG00000179934		"""GPCR / Class A : Chemokine receptors : C-C motif"", ""CD molecules"""	1609	protein-coding gene	gene with protein product		601834		CMKBRL2, CMKBR8		8816377, 8886020	Standard	NM_005201		Approved	CY6, TER1, CKR-L1, GPR-CY6, CDw198	uc010hhr.2	P51685	OTTHUMG00000131290	ENST00000326306.4:c.692_694delACA	3.37:g.39374517_39374519delACA	ENSP00000326432:p.Asn232del	Somatic	372	.	.		WXS	Illumina HiSeq	Phase_I	296	57	0.193	NM_005201	B2RC64|Q3KNQ8|Q3KNR3|Q9BYX5	In_Frame_Del	DEL	ENST00000326306.4	37	CCDS2684.1																																																																																			.	.	none		0.429	CCR8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254058.2	NM_005201	
CARD8	22900	hgsc.bcm.edu	37	19	48735017	48735018	+	Frame_Shift_Ins	INS	-	-	TT	rs146319637|rs140826611	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:48735017_48735018insTT	ENST00000359009.4	-	4	438_439	c.126_127insAA	c.(124-129)aaagtcfs	p.V43fs	ZNF114_ENST00000597695.1_Intron|CARD8_ENST00000391898.3_Frame_Shift_Ins_p.V148fs|CARD8_ENST00000519940.1_Frame_Shift_Ins_p.V148fs|CARD8_ENST00000357778.5_5'UTR|CARD8_ENST00000447740.2_Frame_Shift_Ins_p.V98fs|CARD8_ENST00000521613.1_Frame_Shift_Ins_p.V98fs|CARD8_ENST00000520753.1_Frame_Shift_Ins_p.V148fs|CARD8_ENST00000520153.1_Frame_Shift_Ins_p.V98fs|CARD8_ENST00000520015.1_Frame_Shift_Ins_p.V148fs			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	84	.	.		WXS	Illumina HiSeq	Phase_I	84	24	0.286	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	
KRTAP10-10	353333	hgsc.bcm.edu	37	21	46057613	46057627	+	In_Frame_Del	DEL	CTGCTGTGTGCCTGT	CTGCTGTGTGCCTGT	-	rs66931310|rs375198526|rs56249559|rs55677560|rs77286437	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	CTGCTGTGTGCCTGT	CTGCTGTGTGCCTGT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:46057613_46057627delCTGCTGTGTGCCTGT	ENST00000380095.1	+	1	341_355	c.279_293delCTGCTGTGTGCCTGT	c.(277-294)gcctgctgtgtgcctgtc>gcc	p.CCVPV104del	TSPEAR_ENST00000323084.4_Intron	NM_181688.1	NP_859016.1	P60014	KR10A_HUMAN	keratin associated protein 10-10	104	15 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				NS(1)|endometrium(2)|kidney(1)|lung(6)|prostate(1)|skin(2)	13						gccagcaggcctgctgtgtgcctgtctgctgtgtg	0.628														2493	0.497804	0.5575	0.6153	5008	,	,		22046	0.37		0.5736	False		,,,				2504	0.3875				p.93_98del		Pindel,Atlas-Indel	.											.	KRTAP10-10	37	.	0			c.278_292del						PASS	.		,	2335,1929		615,1105,412					,	-1.6	0.0		dbSNP_130	113	4575,3679		1191,2193,743	no	coding,intron	TSPEAR,KRTAP10-10	NM_181688.1,NM_144991.2	,	1806,3298,1155	A1A1,A1R,RR		44.5723,45.2392,44.7995	,	,		6910,5608				SO:0001651	inframe_deletion	353333	exon1			.	AJ566387	CCDS33585.1	21q22.3	2006-03-13			ENSG00000221859	ENSG00000221859		"""Keratin associated proteins"""	22972	protein-coding gene	gene with protein product							Standard	NM_181688		Approved	KAP10.10, KAP18.10, KRTAP18-10	uc002zfq.3	P60014	OTTHUMG00000057631	ENST00000380095.1:c.279_293delCTGCTGTGTGCCTGT	21.37:g.46057613_46057627delCTGCTGTGTGCCTGT	ENSP00000369438:p.Cys104_Val108del	Somatic	155	.	.		WXS	Illumina HiSeq	Phase_I	103	50	0.485	NM_181688		In_Frame_Del	DEL	ENST00000380095.1	37	CCDS33585.1																																																																																			CTGCTGTGTGCCTGT|0.469;-|0.531	0.531	strong		0.628	KRTAP10-10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128034.1	NM_181688	
AXDND1	126859	hgsc.bcm.edu	37	1	179504026	179504028	+	In_Frame_Del	DEL	AAG	AAG	-	rs551573109|rs141228272	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	AAG	AAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:179504026_179504028delAAG	ENST00000367618.3	+	25	3347_3349	c.2960_2962delAAG	c.(2959-2964)aaagaa>aaa	p.E991del		NM_144696.4	NP_653297.3	Q5T1B0	AXDN1_HUMAN	axonemal dynein light chain domain containing 1	991	Glu-rich.		E -> Q (in dbSNP:rs6425573).							NS(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(27)|ovary(1)|pancreas(1)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)	59						agagaagtaaaagaagaagaaga	0.325																																					p.987_987del		Pindel,Atlas-Indel	.											.	AXDND1	142	.	0			c.2959_2961del						PASS	.																																			SO:0001651	inframe_deletion	126859	exon25			.	BX647935	CCDS30948.1	1q25.2	2011-02-18	2011-02-18	2011-02-18	ENSG00000162779	ENSG00000162779			26564	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 125"""	C1orf125		14702039	Standard	NM_144696		Approved	FLJ32940	uc001gmo.3	Q5T1B0	OTTHUMG00000035266	ENST00000367618.3:c.2960_2962delAAG	1.37:g.179504035_179504037delAAG	ENSP00000356590:p.Glu991del	Somatic	212	.	.		WXS	Illumina HiSeq	Phase_I	162	40	0.247	NM_144696	Q6AWB2|Q96LJ3|Q96M01	In_Frame_Del	DEL	ENST00000367618.3	37	CCDS30948.1																																																																																			AAG|0.640;-|0.360	0.360	strong		0.325	AXDND1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085312.1	NM_144696	
PDE4DIP	9659	hgsc.bcm.edu	37	1	144873963	144873963	+	Frame_Shift_Del	DEL	T	T	-	rs11341221	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:144873963delT	ENST00000369354.3	-	31	5183	c.4994delA	c.(4993-4995)cagfs	p.Q1665fs	PDE4DIP_ENST00000369359.4_Frame_Shift_Del_p.Q1801fs|PDE4DIP_ENST00000313382.9_Frame_Shift_Del_p.Q1621fs|RP4-791M13.5_ENST00000531288.1_RNA|PDE4DIP_ENST00000369356.4_Frame_Shift_Del_p.Q1665fs|PDE4DIP_ENST00000530740.1_Intron|PDE4DIP_ENST00000524974.1_5'UTR			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	1665					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)		CTTAGCCCCCTGAGATGCACT	0.478			T	PDGFRB	MPD								|||unknown(NO_COVERAGE)	1448	0.289137	0.4614	0.2695	5008	,	,		41973	0.0704		0.3569	False		,,,				2504	0.226				p.Q1665fs		Pindel,Atlas-Indel	.		Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	.	PDE4DIP	817	.	0			c.4995delG						PASS	.		,,	1906,2360		0,1906,227	287.0	329.0	314.0		,,	0.8	1.0	1	dbSNP_120	422	2987,5261		0,2987,1137	no	frameshift,frameshift,frameshift	PDE4DIP	NM_014644.4,NM_001198834.2,NM_001198832.1	,,	0,4893,1364	A1A1,A1R,RR		36.2148,44.6789,39.1002	,,	,,	144873963	4893,7621	2203	4297	6500	SO:0001589	frameshift_variant	9659	exon31			.	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.4994delA	1.37:g.144873963delT	ENSP00000358360:p.Gln1665fs	Somatic	272	.	.		WXS	Illumina HiSeq	Phase_I	305	49	0.161	NM_014644	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																																																																																			-|0.272;A|0.364	0.272	strong		0.478	PDE4DIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000038858.2	NM_022359	
SYT15	83849	hgsc.bcm.edu	37	10	46965887	46965888	+	Splice_Site	INS	-	-	G	rs368272154|rs112965082		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:46965887_46965888insG	ENST00000374321.4	-	5	718		c.e5-2		SYT15_ENST00000374325.3_Splice_Site|SYT15_ENST00000503753.1_Splice_Site|RP11-38L15.3_ENST00000506914.1_RNA|SYT15_ENST00000374323.4_Splice_Site	NM_031912.4	NP_114118.2	Q9BQS2	SYT15_HUMAN	synaptotagmin XV							integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				cervix(1)|endometrium(5)|kidney(2)|lung(5)	13						GCTGGACACCTGGGGGGGACAA	0.604																																					.	Ovarian(57;1152 1428 19651 37745)	Pindel,Atlas-Indel	.											.	SYT15	165	.	0			c.652-2->C						PASS	.																																			SO:0001630	splice_region_variant	83849	exon6			.	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.652-2->C	10.37:g.46965894_46965894dupG		Somatic	45	.	.		WXS	Illumina HiSeq	Phase_I	49	10	0.204	NM_181519	A5D6W8|Q5VY53|Q5VY55|Q7Z439|Q7Z440	Splice_Site	INS	ENST00000374321.4	37	CCDS44376.1																																																																																			-|0.500;G|0.500	0.500	weak		0.604	SYT15-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367008.1	NM_031912	Intron
HSP90B1	7184	hgsc.bcm.edu	37	12	104341188	104341190	+	In_Frame_Del	DEL	GAA	GAA	-	rs5800607|rs201427769	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	GAA	GAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:104341188_104341190delGAA	ENST00000299767.5	+	17	2544_2546	c.2362_2364delGAA	c.(2362-2364)gaadel	p.E791del	C12orf73_ENST00000543740.2_5'Flank	NM_003299.2	NP_003290.1	P14625	ENPL_HUMAN	heat shock protein 90kDa beta (Grp94), member 1	791					actin rod assembly (GO:0031247)|activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|cellular response to ATP (GO:0071318)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|innate immune response (GO:0045087)|negative regulation of apoptotic process (GO:0043066)|protein folding (GO:0006457)|protein transport (GO:0015031)|regulation of phosphoprotein phosphatase activity (GO:0043666)|response to hypoxia (GO:0001666)|sequestering of calcium ion (GO:0051208)|toll-like receptor signaling pathway (GO:0002224)	cytosol (GO:0005829)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|midbody (GO:0030496)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|low-density lipoprotein particle receptor binding (GO:0050750)|protein phosphatase binding (GO:0019903)|RNA binding (GO:0003723)|virion binding (GO:0046790)			central_nervous_system(1)|kidney(5)|large_intestine(7)|lung(8)|ovary(2)|prostate(1)|skin(1)|urinary_tract(4)	29					Rifabutin(DB00615)	gggaacagatgaagaagaagaaA	0.424														600	0.119808	0.0053	0.111	5008	,	,		20608	0.3254		0.0954	False		,,,				2504	0.0941				p.787_788del		Pindel,Atlas-Indel	.											.	HSP90B1	72	.	0			c.2361_2363del						PASS	.			250,4012		72,106,1953						-7.4	0.4		dbSNP_114	222	1075,7179		156,763,3208	no	coding	HSP90B1	NM_003299.1		228,869,5161	A1A1,A1R,RR		13.024,5.8658,10.5864				1325,11191				SO:0001651	inframe_deletion	7184	exon17			.	AY040226	CCDS9094.1	12q24.2-q24.3	2011-09-02	2006-02-24	2006-02-24		ENSG00000166598		"""Heat shock proteins / HSPC"""	12028	protein-coding gene	gene with protein product		191175	"""tumor rejection antigen (gp96) 1"""	TRA1		16269234	Standard	NM_003299		Approved	GP96, GRP94	uc001tkb.2	P14625	OTTHUMG00000170118	ENST00000299767.5:c.2362_2364delGAA	12.37:g.104341197_104341199delGAA	ENSP00000299767:p.Glu791del	Somatic	142	.	.		WXS	Illumina HiSeq	Phase_I	142	41	0.289	NM_003299	Q96A97	In_Frame_Del	DEL	ENST00000299767.5	37	CCDS9094.1																																																																																			GAA|0.865;-|0.135	0.135	strong		0.424	HSP90B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407349.1	NM_003299	
GTF3C1	2975	hgsc.bcm.edu	37	16	27499956	27499956	+	Splice_Site	DEL	C	C	-	rs560536443		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:27499956delC	ENST00000356183.4	-	22	3445	c.3430delG	c.(3430-3432)gag>ag	p.E1144fs	GTF3C1_ENST00000561623.1_Splice_Site_p.E1144fs	NM_001520.3	NP_001511.2	Q12789	TF3C1_HUMAN	general transcription factor IIIC, polypeptide 1, alpha 220kDa	1144					5S class rRNA transcription from RNA polymerase III type 1 promoter (GO:0042791)|gene expression (GO:0010467)|rRNA transcription (GO:0009303)|transcription from RNA polymerase III promoter (GO:0006383)|transcription, DNA-templated (GO:0006351)|tRNA transcription (GO:0009304)|tRNA transcription from RNA polymerase III promoter (GO:0042797)	membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|transcription factor TFIIIC complex (GO:0000127)	DNA binding (GO:0003677)			breast(2)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(14)|liver(3)|lung(28)|ovary(2)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)	80						GCAGTGTTCTCCTGTGAGACA	0.557																																					p.E1144fs		Pindel,Atlas-Indel	.											.	GTF3C1	210	.	0			c.3431delA						PASS	.						97.0	90.0	92.0					16																	27499956		2197	4300	6497	SO:0001630	splice_region_variant	2975	exon22			.	U06485	CCDS32414.1, CCDS66988.1	16p12	2010-03-23	2002-08-29			ENSG00000077235		"""General transcription factors"""	4664	protein-coding gene	gene with protein product		603246	"""general transcription factor IIIC, polypeptide 1 (alpha subunit, 220kD )"""			8164661, 8127861	Standard	NM_001520		Approved	TFIIIC220	uc002dov.2	Q12789		ENST00000356183.4:c.3430-1G>-	16.37:g.27499956delC		Somatic	44	.	.		WXS	Illumina HiSeq	Phase_I	46	13	0.283	NM_001520	B2RP21|Q12838|Q6DKN9|Q9Y4W9	Frame_Shift_Del	DEL	ENST00000356183.4	37	CCDS32414.1																																																																																			.	.	none		0.557	GTF3C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433856.1	NM_001520	Frame_Shift_Del
CCDC9	26093	hgsc.bcm.edu	37	19	47774666	47774668	+	In_Frame_Del	DEL	GAG	GAG	-	rs138370983|rs79550409|rs373093080	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	GAG	GAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:47774666_47774668delGAG	ENST00000221922.6	+	12	1549_1551	c.1327_1329delGAG	c.(1327-1329)gagdel	p.E445del		NM_015603.2	NP_056418.1	Q9Y3X0	CCDC9_HUMAN	coiled-coil domain containing 9	445	Glu-rich.						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)		agaaggtgatgaggaggaACCAG	0.606														552	0.110224	0.034	0.1844	5008	,	,		16057	0.0903		0.0895	False		,,,				2504	0.2025				p.442_443del		Pindel,Atlas-Indel	.											.	CCDC9	37	.	0			c.1326_1328del						PASS	.			208,4056		4,200,1928						-8.6	0.0		dbSNP_134	113	947,7301		59,829,3236	no	coding	CCDC9	NM_015603.2		63,1029,5164	A1A1,A1R,RR		11.4816,4.878,9.2311				1155,11357				SO:0001651	inframe_deletion	26093	exon12			.	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.1327_1329delGAG	19.37:g.47774669_47774671delGAG	ENSP00000221922:p.Glu445del	Somatic	47	.	.		WXS	Illumina HiSeq	Phase_I	51	15	0.294	NM_015603		In_Frame_Del	DEL	ENST00000221922.6	37	CCDS12698.1																																																																																			GAG|0.916;-|0.084	0.084	strong		0.606	CCDC9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466917.1	NM_015603	
MUC6	4588	hgsc.bcm.edu	37	11	1031058	1031059	+	Splice_Site	INS	-	-	G	rs71464128	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:1031058_1031059insG	ENST00000421673.2	-	6	625		c.e6-2			NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming						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)		GGAACTTGCCTGGGGTGCAGAA	0.703													GGGGG|GGGG|GGGGG|deletion	644	0.128594	0.348	0.0879	5008	,	,		7216	0.002		0.0895	False		,,,				2504	0.0317				.		Pindel,Atlas-Indel	.											.	MUC6	408	.	0			c.575-2->C						PASS	.			1070,2502		189,692,905						2.3	0.8		dbSNP_130	29	606,7194		45,516,3339	no	splice-3	MUC6	NM_005961.2		234,1208,4244	A1A1,A1R,RR		7.7692,29.9552,14.738				1676,9696				SO:0001630	splice_region_variant	4588	exon7			.	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.575-2->C	11.37:g.1031062_1031062dupG		Somatic	135	.	.		WXS	Illumina HiSeq	Phase_I	160	65	0.406	NM_005961	O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	Splice_Site	INS	ENST00000421673.2	37	CCDS44513.1																																																																																			-|0.878;G|0.122	0.122	strong		0.703	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382120.2	XM_290540	Intron
ALPK2	115701	hgsc.bcm.edu	37	18	56203253	56203255	+	In_Frame_Del	DEL	AAG	AAG	-	rs141586980	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	AAG	AAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:56203253_56203255delAAG	ENST00000361673.3	-	5	4377_4379	c.4164_4166delCTT	c.(4162-4167)ttcttt>ttt	p.1388_1389FF>F	RP11-1151B14.4_ENST00000591360.1_RNA	NM_052947.3	NP_443179.3	Q86TB3	ALPK2_HUMAN	alpha-kinase 2	1388						nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.F750delF(1)|p.F1389delF(1)		NS(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(33)|ovary(7)|prostate(1)|skin(10)|upper_aerodigestive_tract(2)	84						AAACTTTTTAAAGAAGGCAGTGT	0.443														361	0.0720847	0.0424	0.0706	5008	,	,		21127	0.0119		0.1272	False		,,,				2504	0.1186				p.1389_1389del		Pindel,Atlas-Indel	.											.	ALPK2	487	.	2	Deletion - In frame(2)	lung(2)	c.4165_4167del						PASS	.			296,3968		16,264,1852						-2.9	0.0		dbSNP_132	97	1141,7113		79,983,3065	no	coding	ALPK2	NM_052947.3		95,1247,4917	A1A1,A1R,RR		13.8236,6.9418,11.4795				1437,11081				SO:0001651	inframe_deletion	115701	exon5			.	AY044450	CCDS11966.2	18q21.31	2013-01-11			ENSG00000198796	ENSG00000198796		"""Immunoglobulin superfamily / I-set domain containing"""	20565	protein-coding gene	gene with protein product	"""heart alpha-kinase"""					10021370	Standard	NM_052947		Approved	HAK	uc002lhj.4	Q86TB3	OTTHUMG00000132755	ENST00000361673.3:c.4164_4166delCTT	18.37:g.56203256_56203258delAAG	ENSP00000354991:p.Phe1389del	Somatic	148	.	.		WXS	Illumina HiSeq	Phase_I	79	30	0.380	NM_052947	Q6ZUX0|Q8NAT5|Q96L95	In_Frame_Del	DEL	ENST00000361673.3	37	CCDS11966.2																																																																																			AAG|0.927;-|0.073	0.073	strong		0.443	ALPK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256126.1	NM_052947	
ETFB	2109	hgsc.bcm.edu	37	19	51857614	51857615	+	Intron	INS	-	-	G	rs55874945|rs141529162|rs74357706	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:51857614_51857615insG	ENST00000309244.4	-	2	149				ETFB_ENST00000354232.4_Frame_Shift_Ins_p.P93fs|CTD-2616J11.9_ENST00000600974.1_RNA|CTD-2616J11.11_ENST00000600067.1_Intron	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		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	43	0	0		WXS	Illumina HiSeq	Phase_I	36	14	0.388889	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		
CELA1	1990	hgsc.bcm.edu	37	12	51723598	51723599	+	Frame_Shift_Ins	INS	-	-	G	rs398102298|rs76813052|rs17860363|rs75442020	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	48	.	.		WXS	Illumina HiSeq	Phase_I	61	18	0.295	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	
CFTR	1080	hgsc.bcm.edu	37	7	117199645	117199647	+	In_Frame_Del	DEL	TCT	TCT	-	rs121909001|rs199826652|rs113993960	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	TCT	TCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:117199645_117199647delTCT	ENST00000003084.6	+	11	1652_1654	c.1520_1522delTCT	c.(1519-1524)atcttt>att	p.F508del	CFTR_ENST00000454343.1_In_Frame_Del_p.F447del|AC000111.3_ENST00000441019.1_RNA	NM_000492.3	NP_000483.3	P13569	CFTR_HUMAN	cystic fibrosis transmembrane conductance regulator (ATP-binding cassette sub-family C, member 7)	508	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.		F -> C (in dbSNP:rs1800093).|Missing (in CF and CBAVD; most common mutation; 72% of the population; CFTR fails to be properly delivered to plasma membrane).		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)	GAAAATATCATCTTTGGTGTTTC	0.365									Cystic Fibrosis					20	0.00399361	0.0	0.0101	5008	,	,		18625	0.0		0.0089	False		,,,				2504	0.0041				p.507_507del		Pindel,Atlas-Indel	.											.	CFTR	171	.	0			c.1519_1521del	GRCh37	CD890142|CI075604	CFTR	D|I	rs1800093	PASS	.			13,4251		0,13,2119				http://www.ncbi.nlm.nih.gov/sites/varvu?gene		1.9	1.0		dbSNP_133	89	809,7445		317,175,3635	no	coding	CFTR	NM_000492.3		317,188,5754	A1A1,A1R,RR		9.8013,0.3049,6.5665				822,11696				SO:0001651	inframe_deletion	1080	exon11	Familial Cancer Database	CF	.	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.1520_1522delTCT	7.37:g.117199645_117199647delTCT	ENSP00000003084:p.Phe508del	Somatic	81	.	.		WXS	Illumina HiSeq	Phase_I	49	17	0.347	NM_000492	Q20BG8|Q20BH2|Q2I0A1|Q2I102	In_Frame_Del	DEL	ENST00000003084.6	37	CCDS5773.1																																																																																			TCT|0.994;-|0.006	0.006	strong		0.365	CFTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059397.3	NM_000492	
PSORS1C1	170679	hgsc.bcm.edu	37	6	31084943	31084945	+	Intron	DEL	CTT	CTT	-	rs57244323|rs540877039	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	CTT	CTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:31084943_31084945delCTT	ENST00000259881.9	+	1	61				PSORS1C1_ENST00000467107.1_3'UTR|CDSN_ENST00000376288.2_In_Frame_Del_p.S153del	NM_014068.2	NP_054787.2	Q9UIG5	PS1C1_HUMAN	psoriasis susceptibility 1 candidate 1											kidney(1)|ovary(2)|prostate(1)|skin(1)	5						AGAGCTGCTGCTTCCCGAGTGAG	0.571														939	0.1875	0.2065	0.1527	5008	,	,		17220	0.1637		0.1869	False		,,,				2504	0.2117				p.150_150del		Pindel,Atlas-Indel	.											.	CDSN	48	.	0			c.448_450del						PASS	.		,	950,3314		87,776,1269					,	2.5	0.2		dbSNP_126	37	1846,6398		222,1402,2498	no	intron,coding	CDSN,PSORS1C1	NM_014068.2,NM_001264.4	,	309,2178,3767	A1A1,A1R,RR		22.392,22.2795,22.3537	,	,		2796,9712				SO:0001627	intron_variant	1041	exon2			.	AB031479	CCDS34390.1	6p21.3	2014-01-28	2003-06-12		ENSG00000204540	ENSG00000204540			17202	protein-coding gene	gene with protein product		613525	"""chromosome 6 open reading frame 16"""	C6orf16			Standard	NM_014068		Approved	SEEK1	uc003nsl.2	Q9UIG5	OTTHUMG00000031077	ENST00000259881.9:c.-229+2275CTT>-	6.37:g.31084943_31084945delCTT		Somatic	46	.	.		WXS	Illumina HiSeq	Phase_I	50	20	0.400	NM_001264	B0V083|Q5ST21|Q86WJ8|Q86WJ9|Q96QC3	In_Frame_Del	DEL	ENST00000259881.9	37	CCDS34390.1																																																																																			CTT|0.500;-|0.500	0.500	strong		0.571	PSORS1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076110.3	NM_014068	
RNH1	6050	hgsc.bcm.edu	37	11	502130	502144	+	In_Frame_Del	DEL	CTGGATGTCCAGGCT	CTGGATGTCCAGGCT	-	rs71462090|rs71022920	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	CTGGATGTCCAGGCT	CTGGATGTCCAGGCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:502130_502144delCTGGATGTCCAGGCT	ENST00000534797.1	-	1	1426_1440	c.19_33delAGCCTGGACATCCAG	c.(19-33)agcctggacatccagdel	p.SLDIQ7del	RNH1_ENST00000354420.2_In_Frame_Del_p.SLDIQ7del|RNH1_ENST00000533592.1_5'UTR|RNH1_ENST00000438658.2_In_Frame_Del_p.SLDIQ7del|RNH1_ENST00000397615.2_In_Frame_Del_p.SLDIQ7del|RNH1_ENST00000533410.1_In_Frame_Del_p.SLDIQ7del|RNH1_ENST00000397614.1_In_Frame_Del_p.SLDIQ7del|RNH1_ENST00000356187.5_In_Frame_Del_p.SLDIQ7del|RNH1_ENST00000397604.3_In_Frame_Del_p.SLDIQ7del			O60930	RNH1_HUMAN	ribonuclease/angiogenin inhibitor 1	0					mitochondrial DNA replication (GO:0006264)|RNA catabolic process (GO:0006401)|RNA phosphodiester bond hydrolysis (GO:0090501)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	magnesium ion binding (GO:0000287)|nucleic acid binding (GO:0003676)|ribonuclease activity (GO:0004540)|RNA binding (GO:0003723)|RNA-DNA hybrid ribonuclease activity (GO:0004523)			endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)	10		all_cancers(49;3.02e-09)|all_epithelial(84;2.09e-06)|Breast(177;0.000162)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.0538)|all_lung(207;0.0713)		all cancers(45;1.26e-26)|Epithelial(43;1.34e-25)|OV - Ovarian serous cystadenocarcinoma(40;5.31e-20)|BRCA - Breast invasive adenocarcinoma(625;8.01e-05)|Lung(200;0.0378)|LUSC - Lung squamous cell carcinoma(625;0.0703)		GCTCCTCACACTGGATGTCCAGGCTCTGGATGTCC	0.633														278	0.0555112	0.0061	0.2118	5008	,	,		19876	0.002		0.0974	False		,,,				2504	0.0235				p.7_12del		Pindel,Atlas-Indel	.											.	RNH1	24	.	0			c.20_34del						PASS	.		,,,,,,,	104,4158		3,98,2030					,,,,,,,	2.4	0.7		dbSNP_130	66	994,7260		61,872,3194	no	coding,coding,coding,coding,coding,coding,coding,coding	RNH1	NM_203389.1,NM_203388.1,NM_203387.1,NM_203386.1,NM_203385.1,NM_203384.1,NM_203383.1,NM_002939.3	,,,,,,,	64,970,5224	A1A1,A1R,RR		12.0426,2.4402,8.7728	,,,,,,,	,,,,,,,		1098,11418				SO:0001651	inframe_deletion	6050	exon3			.		CCDS7697.1	11p15.5	2008-02-05	2005-06-01	2005-06-01	ENSG00000023191	ENSG00000023191			10074	protein-coding gene	gene with protein product		173320	"""ribonuclease/angiogenin inhibitor"""	RNH			Standard	NM_203386		Approved	RAI	uc001lpo.1	P13489	OTTHUMG00000119086	ENST00000534797.1:c.19_33delAGCCTGGACATCCAG	11.37:g.502130_502144delCTGGATGTCCAGGCT	ENSP00000433999:p.Ser7_Gln11del	Somatic	47	.	.		WXS	Illumina HiSeq	Phase_I	45	21	0.467	NM_203386	B3KQU4|O60523|O60857|Q57Z93|Q5U0C1|Q6FHD4	In_Frame_Del	DEL	ENST00000534797.1	37	CCDS7697.1																																																																																			CTGGATGTCCAGGCT|0.938;-|0.062	0.062	strong		0.633	RNH1-009	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384301.1	NM_203389	
GFM2	84340	hgsc.bcm.edu	37	5	74021847	74021852	+	In_Frame_Del	DEL	ACTCAA	ACTCAA	-	rs5868753|rs76339998	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	ACTCAA	ACTCAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:74021847_74021852delACTCAA	ENST00000296805.3	-	18	2283_2288	c.1826_1831delTTGAGT	c.(1825-1833)tttgagtat>tat	p.FE609del	GFM2_ENST00000345239.2_In_Frame_Del_p.FE562del|GFM2_ENST00000515125.1_5'UTR|RNU6-658P_ENST00000384606.1_RNA|GFM2_ENST00000509430.1_In_Frame_Del_p.FE609del	NM_032380.3	NP_115756.2			G elongation factor, mitochondrial 2									p.F609Y(1)		breast(2)|endometrium(2)|large_intestine(4)|lung(5)|prostate(1)	14		all_lung(232;0.00101)|Lung NSC(167;0.00278)|Ovarian(174;0.0129)|Breast(144;0.231)		OV - Ovarian serous cystadenocarcinoma(47;1.86e-56)		CTTTCAGCATACTCAAACTCAATCAC	0.413														1915	0.382388	0.7572	0.3372	5008	,	,		20860	0.1974		0.2425	False		,,,				2504	0.2423				p.609_611del		Pindel,Atlas-Indel	.											.	GFM2	38	.	1	Substitution - Missense(1)	lung(1)	c.1827_1832del						PASS	.																																			SO:0001651	inframe_deletion	84340	exon18			.	AF111808	CCDS4023.1, CCDS4024.1, CCDS47232.1	5q13	2008-02-05			ENSG00000164347	ENSG00000164347			29682	protein-coding gene	gene with protein product		606544				11735030	Standard	NM_001281302		Approved	EFG2, FLJ21661	uc003kdh.1	Q969S9	OTTHUMG00000102058	ENST00000296805.3:c.1826_1831delTTGAGT	5.37:g.74021853_74021858delACTCAA	ENSP00000296805:p.Phe609_Glu610del	Somatic	113	.	.		WXS	Illumina HiSeq	Phase_I	105	42	0.400	NM_032380		In_Frame_Del	DEL	ENST00000296805.3	37	CCDS4023.1																																																																																			ACTCAA|0.643;-|0.357	0.357	strong		0.413	GFM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219860.2	NM_032380	
ZNF568	374900	hgsc.bcm.edu	37	19	37440852	37440852	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:37440852delT	ENST00000333987.7	+	7	1303	c.797delT	c.(796-798)attfs	p.I266fs	ZNF568_ENST00000427117.1_Intron|ZNF568_ENST00000455427.2_Intron|ZNF568_ENST00000415168.1_Frame_Shift_Del_p.I202fs	NM_001204835.1|NM_198539.3	NP_001191764.1|NP_940941.2	Q3ZCX4	ZN568_HUMAN	zinc finger protein 568	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)			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)			GAAAATCTTATTACACATCAG	0.353																																					p.I266fs		Atlas-Indel	.											.	ZNF568	106	.	0			c.796delA						PASS	.						39.0	43.0	41.0					19																	37440852		2118	4251	6369	SO:0001589	frameshift_variant	374900	exon7			.	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	ENST00000333987.7:c.797delT	19.37:g.37440852delT	ENSP00000334685:p.Ile266fs	Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	45	11	0.244444	NM_198539	B4DS92|E7ER33|Q6N060|Q8NA64	Frame_Shift_Del	DEL	ENST00000333987.7	37	CCDS42558.1																																																																																			.	.	none		0.353	ZNF568-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109572.2	NM_198539	
OR13A1	79290	hgsc.bcm.edu	37	10	45799065	45799066	+	Frame_Shift_Ins	INS	-	-	A	rs35302355|rs376671137	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:45799065_45799066insA	ENST00000553795.1	-	4	1113_1114	c.805_806insT	c.(805-807)tatfs	p.Y269fs	OR13A1_ENST00000374401.2_Frame_Shift_Ins_p.Y269fs|OR13A1_ENST00000536058.1_Frame_Shift_Ins_p.Y269fs	NM_001004297.2	NP_001004297.2	Q8NGR1	O13A1_HUMAN	olfactory receptor, family 13, subfamily A, member 1	269						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|kidney(1)|large_intestine(5)|lung(9)|skin(2)|urinary_tract(1)	19						AGCGGTGTAATACATGCACACC	0.569													A|A|AA|insertion	125	0.0249601	0.0484	0.0231	5008	,	,		20385	0.001		0.0358	False		,,,				2504	0.0082				p.Y269fs		Pindel,Atlas-Indel	.											.	OR13A1	49	.	0			c.806_807insT						PASS	.			257,4007		8,241,1883						3.4	0.7		dbSNP_126	89	341,7913		9,323,3795	no	frameshift	OR13A1	NM_001004297.2		17,564,5678	A1A1,A1R,RR		4.1313,6.0272,4.7771				598,11920				SO:0001589	frameshift_variant	79290	exon4			.	AB065728	CCDS31188.1	10q11.21	2012-10-03			ENSG00000256574	ENSG00000256574		"""GPCR / Class A : Olfactory receptors"""	14772	protein-coding gene	gene with protein product							Standard	NM_001004297		Approved		uc001jcc.1	Q8NGR1	OTTHUMG00000018080	ENST00000553795.1:c.806dupT	10.37:g.45799066_45799066dupA	ENSP00000451950:p.Tyr269fs	Somatic	81	.	.		WXS	Illumina HiSeq	Phase_I	52	19	0.365	NM_001004297	Q2M3M4|Q5VV57|Q6IFH5|Q6ZMN6	Frame_Shift_Ins	INS	ENST00000553795.1	37	CCDS31188.1																																																																																			.	.	none		0.569	OR13A1-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047779.2	NM_001004297	
NFKBIE	4794	hgsc.bcm.edu	37	6	44232739	44232742	+	Frame_Shift_Del	DEL	GTAA	GTAA	-	rs375669043		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	GTAA	GTAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:44232739_44232742delGTAA	ENST00000275015.5	-	1	758_761	c.759_762delTTAC	c.(757-762)acttacfs	p.TY253fs		NM_004556.2	NP_004547.2	O00221	IKBE_HUMAN	nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, epsilon	253					cytoplasmic sequestering of transcription factor (GO:0042994)|D-serine transport (GO:0042942)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|perinuclear region of cytoplasm (GO:0048471)				breast(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(3)|urinary_tract(1)	10	all_cancers(18;2e-05)|all_lung(25;0.00747)|Hepatocellular(11;0.00908)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			CCTCGGAGATGTAAGTGAGTGCTT	0.676																																					p.254_255del		Atlas-Indel	.											.	NFKBIE	31	.	0			c.760_763del						PASS	.																																			SO:0001589	frameshift_variant	4794	exon1			.	U91616	CCDS34463.1	6p21.1	2013-01-10			ENSG00000146232	ENSG00000146232		"""Ankyrin repeat domain containing"""	7799	protein-coding gene	gene with protein product		604548				9135156	Standard	NM_004556		Approved	IKBE	uc003oxe.1	O00221	OTTHUMG00000014762	ENST00000275015.5:c.759_762delTTAC	6.37:g.44232739_44232742delGTAA	ENSP00000275015:p.Thr253fs	Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	35	11	0.314286	NM_004556	Q5T9V9	Frame_Shift_Del	DEL	ENST00000275015.5	37	CCDS34463.1																																																																																			.	.	none		0.676	NFKBIE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040733.2		
CASP8AP2	9994	hgsc.bcm.edu	37	6	90577712	90577728	+	RNA	DEL	CTTTGCCCAGACATGGA	CTTTGCCCAGACATGGA	-	rs202101805|rs202111256|rs201189413|rs199515704|rs202116886|rs200213073|rs537929246|rs200862023|rs199694900|rs201534830	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	CTTTGCCCAGACATGGA	CTTTGCCCAGACATGGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	74	0	0		WXS	Illumina HiSeq	Phase_I	49	18	0.367347	NM_012115		Frame_Shift_Del	DEL	ENST00000551025.1	37																																																																																				.	.	none		0.378	CASP8AP2-202	KNOWN	basic	processed_transcript	processed_transcript		NM_001137667	
TRMT2A	27037	hgsc.bcm.edu	37	22	20100166	20100167	+	Frame_Shift_Ins	INS	-	-	C	rs554627514	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:20100166_20100167insC	ENST00000252136.7	-	12	2185_2186	c.1797_1798insG	c.(1795-1800)gggcccfs	p.P600fs	TRMT2A_ENST00000439169.2_Frame_Shift_Ins_p.P618fs|TRMT2A_ENST00000492988.1_5'Flank|TRMT2A_ENST00000403707.3_Frame_Shift_Ins_p.P600fs|TRMT2A_ENST00000404751.3_3'UTR|AC006547.8_ENST00000412713.1_RNA	NM_001257994.1|NM_022727.5|NM_182984.4	NP_001244923.1|NP_073564.3|NP_892029.2	Q8IZ69	TRM2A_HUMAN	tRNA methyltransferase 2 homolog A (S. cerevisiae)	600					RNA processing (GO:0006396)		nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA methyltransferase activity (GO:0008173)			breast(2)|endometrium(2)|lung(5)	9						GGGCTGTGGGGCCCCAAGACCC	0.609													CCCC|CCCC|CCCCC|insertion	25	0.00499201	0.0008	0.0043	5008	,	,		17006	0.0		0.004	False		,,,				2504	0.0174				p.P600fs		Pindel,Atlas-Indel	.											.	TRMT2A	34	.	0			c.1798_1799insG						PASS	.		,	8,4256		0,8,2124					,	3.2	0.0			60	78,8176		0,78,4049	no	frameshift,frameshift	TRMT2A	NM_182984.3,NM_022727.4	,	0,86,6173	A1A1,A1R,RR		0.945,0.1876,0.687	,	,		86,12432				SO:0001589	frameshift_variant	27037	exon12			.	BC017184	CCDS13774.1, CCDS58793.1	22q11.21	2014-02-12	2012-06-12		ENSG00000099899	ENSG00000099899			24974	protein-coding gene	gene with protein product	"""HpaII tiny fragments locus 9C"""	611151				9417108, 18075473	Standard	NM_022727		Approved	HTF9C	uc002zrl.2	Q8IZ69	OTTHUMG00000150454	ENST00000252136.7:c.1798dupG	22.37:g.20100170_20100170dupC	ENSP00000252136:p.Pro600fs	Somatic	387	.	.		WXS	Illumina HiSeq	Phase_I	367	87	0.237	NM_022727	D3DX25|Q32P57|Q96ME6|Q9H732	Frame_Shift_Ins	INS	ENST00000252136.7	37	CCDS13774.1																																																																																			.	.	none		0.609	TRMT2A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318168.3	NM_022727	
FASTKD1	79675	hgsc.bcm.edu	37	2	170387132	170387133	+	Frame_Shift_Ins	INS	-	-	T	rs148187838|rs566862006	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:170387132_170387133insT	ENST00000453153.2	-	14	2752_2753	c.2406_2407insA	c.(2404-2409)aaacgafs	p.R803fs	FASTKD1_ENST00000453929.2_Frame_Shift_Ins_p.R760fs|FASTKD1_ENST00000495505.1_5'UTR	NM_024622.3	NP_078898.3	Q53R41	FAKD1_HUMAN	FAST kinase domains 1	803	RAP. {ECO:0000255|PROSITE- ProRule:PRU00619}.				cellular respiration (GO:0045333)	mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(5)|large_intestine(10)|lung(9)|ovary(4)|prostate(3)	37						TCCAAATGTCGTTTTTTCATAG	0.342													TTTTTT|TTTTTT|TTTTTTT|insertion	18	0.00359425	0.0008	0.0029	5008	,	,		15503	0.0		0.007	False		,,,				2504	0.0082				p.R803fs		Pindel,Atlas-Indel	.											.	FASTKD1	86	.	0			c.2407_2408insA						PASS	.			8,4258		0,8,2125						3.3	1.0			159	99,8155		1,97,4029	no	frameshift	FASTKD1	NM_024622.3		1,105,6154	A1A1,A1R,RR		1.1994,0.1875,0.8546				107,12413				SO:0001589	frameshift_variant	79675	exon14			.	AL832058	CCDS33318.1, CCDS63051.1	2q31.1	2008-02-05			ENSG00000138399	ENSG00000138399			26150	protein-coding gene	gene with protein product						11347906	Standard	NM_024622		Approved	FLJ21901	uc002uev.4	Q53R41	OTTHUMG00000154953	ENST00000453153.2:c.2407dupA	2.37:g.170387138_170387138dupT	ENSP00000400513:p.Arg803fs	Somatic	213	.	.		WXS	Illumina HiSeq	Phase_I	206	69	0.335	NM_024622	Q8N583|Q8TEA9|Q96JM5|Q96N71|Q9H6T4	Frame_Shift_Ins	INS	ENST00000453153.2	37	CCDS33318.1																																																																																			.	.	none		0.342	FASTKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337788.2	NM_024622	
KRTAP19-6	337973	hgsc.bcm.edu	37	21	31913982	31913982	+	Frame_Shift_Del	DEL	G	G	-	rs5843453|rs201420116|rs570064399	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:31913982delG	ENST00000334046.5	-	1	201	c.171delC	c.(169-171)ttcfs	p.F57fs		NM_181612.2	NP_853643.1	Q3LI70	KR196_HUMAN	keratin associated protein 19-6	57						intermediate filament (GO:0005882)				breast(1)|large_intestine(2)|lung(5)|upper_aerodigestive_tract(1)	9						TTTTTTAGTAGAATCCAGAGA	0.463													?|G|-|unsure	3942	0.787141	0.9266	0.7421	5008	,	,		17489	0.7034		0.7127	False		,,,				2504	0.7935				p.Y58fs		Pindel,Atlas-Indel	.											.	KRTAP19-6	16	.	0			c.172delT						PASS	.						33.0	58.0	51.0					21																	31913982		1069	2843	3912	SO:0001589	frameshift_variant	337973	exon1			.	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.171delC	21.37:g.31913982delG	ENSP00000375107:p.Phe57fs	Somatic	66	.	.		WXS	Illumina HiSeq	Phase_I	58	17	0.293	NM_181612	Q3LI71	Frame_Shift_Del	DEL	ENST00000334046.5	37	CCDS13598.1																																																																																			-|0.758;G|0.242	0.758	strong		0.463	KRTAP19-6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128231.4		
COL12A1	1303	hgsc.bcm.edu	37	6	75887427	75887436	+	Frame_Shift_Del	DEL	AATATTCAGG	AATATTCAGG	-			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	AATATTCAGG	AATATTCAGG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:75887427_75887436delAATATTCAGG	ENST00000322507.8	-	12	2689_2698	c.2380_2389delCCTGAATATT	c.(2380-2391)cctgaatatttcfs	p.PEYF794fs	COL12A1_ENST00000345356.6_Intron|COL12A1_ENST00000416123.2_Frame_Shift_Del_p.PEYF794fs|COL12A1_ENST00000483888.2_Frame_Shift_Del_p.PEYF794fs	NM_004370.5	NP_004361.3	Q99715	COCA1_HUMAN	collagen, type XII, alpha 1	794	Fibronectin type-III 4. {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						GGTCCTGAGAAATATTCAGGAATTACAGAT	0.438																																					p.794_797del		Atlas-Indel	.											.	COL12A1	385	.	0			c.2381_2390del						PASS	.																																			SO:0001589	frameshift_variant	1303	exon12			.	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.2380_2389delCCTGAATATT	6.37:g.75887427_75887436delAATATTCAGG	ENSP00000325146:p.Pro794fs	Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	155	16	0.103226	NM_004370	O43853|Q15955|Q5VYK1|Q5VYK2|Q71UR3|Q99716	Frame_Shift_Del	DEL	ENST00000322507.8	37	CCDS43482.1																																																																																			.	.	none		0.438	COL12A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041249.3	NM_004370	
GPRIN1	114787	hgsc.bcm.edu	37	5	176026122	176026134	+	Frame_Shift_Del	DEL	CAAAGACCCAGGA	CAAAGACCCAGGA	-	rs3797464|rs200519605|rs386695335|rs550332435|rs142779818|rs371149640|rs199714570|rs373697082	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	CAAAGACCCAGGA	CAAAGACCCAGGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:176026122_176026134delCAAAGACCCAGGA	ENST00000303991.4	-	2	879_891	c.702_714delTCCTGGGTCTTTG	c.(700-714)gatcctgggtctttgfs	p.DPGSL234fs		NM_052899.2	NP_443131.2	Q7Z2K8	GRIN1_HUMAN	G protein regulated inducer of neurite outgrowth 1	234				Missing (in Ref. 4; CAD38868). {ECO:0000305}.	neuron projection development (GO:0031175)	cell projection (GO:0042995)|plasma membrane (GO:0005886)		p.L238L(1)		NS(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(3)|liver(1)|lung(15)|ovary(2)|prostate(5)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	35	all_cancers(89;0.00263)|Renal(175;0.000269)|Lung NSC(126;0.00902)|all_lung(126;0.0142)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CCACCTTTCTCAAAGACCCAGGATCCTCCTTCC	0.488																																					p.235_239del		Atlas-Indel	.											.	GPRIN1	77	.	1	Substitution - coding silent(1)	lung(1)	c.703_715del						PASS	.			721,3495		76,569,1463						-0.3	0.0		dbSNP_107	106	1092,7070		103,886,3092	no	frameshift	GPRIN1	NM_052899.2		179,1455,4555	A1A1,A1R,RR		13.3791,17.1015,14.647				1813,10565				SO:0001589	frameshift_variant	114787	exon2			.	AB067480	CCDS4405.1	5q35.2	2008-02-05			ENSG00000169258	ENSG00000169258			24835	protein-coding gene	gene with protein product		611239				11572484	Standard	NM_052899		Approved	GRIN1, KIAA1893	uc003meo.1	Q7Z2K8	OTTHUMG00000130659	ENST00000303991.4:c.702_714delTCCTGGGTCTTTG	5.37:g.176026122_176026134delCAAAGACCCAGGA	ENSP00000305839:p.Asp234fs	Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	125	20	0.16	NM_052899	C9JM70|Q8ND74|Q96PZ4	Frame_Shift_Del	DEL	ENST00000303991.4	37	CCDS4405.1																																																																																			.	.	none		0.488	GPRIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253149.1	NM_052899	
NR1H2	7376	hgsc.bcm.edu	37	19	50881820	50881821	+	In_Frame_Ins	INS	-	-	AAC	rs57917904|rs397738863|rs78398331|rs55652650	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:50881820_50881821insAAC	ENST00000253727.5	+	6	749_750	c.514_515insAAC	c.(514-516)aaa>aAACaa	p.175_176insQ	NR1H2_ENST00000593926.1_In_Frame_Ins_p.175_176insQ|NR1H2_ENST00000599105.1_In_Frame_Ins_p.175_176insQ|NR1H2_ENST00000598168.1_In_Frame_Ins_p.175_176insQ|NR1H2_ENST00000542413.1_5'UTR|NR1H2_ENST00000411902.2_In_Frame_Ins_p.78_79insQ	NM_007121.5	NP_009052	P55055	NR1H2_HUMAN	nuclear receptor subfamily 1, group H, member 2	175				Q -> QQ (in Ref. 1; AAA61783, 2; BAF83544/BAG60288, 4; AAH07790/AAH33500/ AAH47750/AAH74500 and 5; AAA58594). {ECO:0000305}.	cellular lipid metabolic process (GO:0044255)|gene expression (GO:0010467)|negative regulation of cholesterol storage (GO:0010887)|negative regulation of interferon-gamma-mediated signaling pathway (GO:0060336)|negative regulation of lipid transport (GO:0032369)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|negative regulation of pinocytosis (GO:0048550)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of cholesterol transport (GO:0032376)|positive regulation of fatty acid biosynthetic process (GO:0045723)|positive regulation of lipoprotein lipase activity (GO:0051006)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of triglyceride biosynthetic process (GO:0010867)|regulation of cholesterol homeostasis (GO:2000188)|retinoic acid receptor signaling pathway (GO:0048384)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	apolipoprotein A-I receptor binding (GO:0034191)|ATPase binding (GO:0051117)|DNA binding (GO:0003677)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|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 transcription regulatory region DNA binding RNA polymerase II transcription factor recruiting transcription factor activity (GO:0001133)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(1)|lung(3)|upper_aerodigestive_tract(2)	8		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.00757)|GBM - Glioblastoma multiforme(134;0.0186)		GAAGATTCGGAAACAGCAGCAG	0.639														2745	0.548123	0.3434	0.5259	5008	,	,		18006	0.7857		0.5994	False		,,,				2504	0.5429				p.K172delinsKQ		Pindel,Atlas-Indel	.											.	NR1H2	47	.	0			c.514_515insAAC						PASS	.			3058,1042		1021,1016,13						3.4	0.8		dbSNP_129	42	6607,1515		2573,1461,27	no	coding	NR1H2	NM_007121.4		3594,2477,40	A1A1,A1R,RR		18.653,25.4146,20.9213				9665,2557				SO:0001652	inframe_insertion	7376	exon6			.	U14534	CCDS42593.1, CCDS58673.1	19q13.3	2013-01-16				ENSG00000131408		"""Nuclear hormone receptors"""	7965	protein-coding gene	gene with protein product	"""liver X receptor-beta"""	600380	"""ubiquitously-expressed nuclear receptor"""	UNR		7782080, 7971966	Standard	NM_007121		Approved	NER, NER-I, RIP15, LXR-b	uc010enw.4	P55055		ENST00000253727.5:c.515_517dupAAC	19.37:g.50881821_50881823dupAAC	ENSP00000253727:p.Gln175_Gln175dup	Somatic	96	.	.		WXS	Illumina HiSeq	Phase_I	81	46	0.568	NM_007121	A8K490|B4DNM6|E7EWA6|Q12970|Q5I0Y1	In_Frame_Ins	INS	ENST00000253727.5	37	CCDS42593.1																																																																																			-|0.132;AAC|0.868	0.868	strong		0.639	NR1H2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464724.2		
TAF1	6872	hgsc.bcm.edu	37	X	70612454	70612455	+	In_Frame_Ins	INS	-	-	ATT			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:70612454_70612455insATT	ENST00000373790.4	+	19	2865_2866	c.2814_2815insATT	c.(2815-2817)att>ATTatt	p.939_939I>II	TAF1_ENST00000449580.1_In_Frame_Ins_p.939_939I>II|TAF1_ENST00000423759.1_In_Frame_Ins_p.960_960I>II|TAF1_ENST00000276072.3_In_Frame_Ins_p.960_960I>II	NM_004606.3|NM_138923.2	NP_004597.2|NP_620278.1	P21675	TAF1_HUMAN	TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa	939	Histone acetyltransferase (HAT).				cellular response to DNA damage stimulus (GO:0006974)|DNA-templated transcription, initiation (GO:0006352)|gene expression (GO:0010467)|histone acetylation (GO:0016573)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|protein autophosphorylation (GO:0046777)|regulation of transcription involved in G2/M transition of mitotic cell cycle (GO:0000117)|RNA polymerase II transcriptional preinitiation complex assembly (GO:0051123)|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)	MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)	ATP binding (GO:0005524)|histone acetyltransferase activity (GO:0004402)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)|protein serine/threonine kinase activity (GO:0004674)|sequence-specific DNA binding (GO:0043565)|TBP-class protein binding (GO:0017025)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)			breast(13)|central_nervous_system(6)|cervix(1)|endometrium(25)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(16)|lung(34)|ovary(9)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(3)	124	Renal(35;0.156)	all_lung(315;0.000321)				CAAGGGCCTTCATTGCTGCCAT	0.49																																					p.F959delinsFI		Pindel,Atlas-Indel	.											.	TAF1	439	.	0			c.2877_2878insATT						PASS	.																																			SO:0001652	inframe_insertion	6872	exon19			.		CCDS14412.1, CCDS35325.1, CCDS69783.1	Xq13.1	2011-07-01	2002-08-29	2001-12-07	ENSG00000147133	ENSG00000147133		"""Chromatin-modifying enzymes / K-acetyltransferases"""	11535	protein-coding gene	gene with protein product		313650	"""TATA box binding protein (TBP)-associated factor, RNA polymerase II, A, 250kD"", ""dystonia 3 (with Parkinsonism)"""	TAF2A, BA2R, CCG1, CCGS, DYT3		3556424, 12928496, 17952504	Standard	XM_005262295		Approved	NSCL2, TAFII250, KAT4, DYT3/TAF1	uc004dzt.4	P21675	OTTHUMG00000022723	ENST00000373790.4:c.2815_2817dupATT	X.37:g.70612455_70612457dupATT	ENSP00000362895:p.Ile939dup	Somatic	127	.	.		WXS	Illumina HiSeq	Phase_I	118	27	0.229	NM_004606	A5CVC8|A5CVC9|A5CVD0|A5CVD1|B1Q2X3|Q59FZ3|Q6IUZ1|Q70Q86|Q70Q87|Q70T00|Q70T01|Q70T02|Q70T03	In_Frame_Ins	INS	ENST00000373790.4	37	CCDS35325.1																																																																																			.	.	none		0.490	TAF1-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000058995.2	NM_004606	
KANK3	256949	hgsc.bcm.edu	37	19	8389893	8389895	+	In_Frame_Del	DEL	TCC	TCC	-	rs367746100|rs111905975	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	TCC	TCC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	79	.	.		WXS	Illumina HiSeq	Phase_I	84	26	0.310	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	
OR6Q1	219952	hgsc.bcm.edu	37	11	57799109	57799109	+	Frame_Shift_Del	DEL	C	C	-	rs34846253	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:57799109delC	ENST00000302622.3	+	1	708	c.685delC	c.(685-687)ctgfs	p.L230fs	OR9Q1_ENST00000335397.3_Intron	NM_001005186.2	NP_001005186.2	Q8NGQ2	OR6Q1_HUMAN	olfactory receptor, family 6, subfamily Q, member 1	230						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)				CGTCTGGACACTGCTGCACAT	0.532													C|C|-|deletion	594	0.11861	0.1225	0.1153	5008	,	,		22097	0.0218		0.2048	False		,,,				2504	0.1268				p.T228fs		Pindel,Atlas-Indel	.											.	OR6Q1	58	.	0			c.684delA	GRCh37	CD035873	OR6Q1	D	rs34846253	PASS	.			656,3608		57,542,1533	155.0	121.0	133.0			-7.0	0.1	11	dbSNP_126	158	1588,6664		147,1294,2685	no	frameshift	OR6Q1	NM_001005186.2		204,1836,4218	A1A1,A1R,RR		19.2438,15.3846,17.9291			57799109	2244,10272	2161	4187	6348	SO:0001589	frameshift_variant	219952	exon1			.	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.685delC	11.37:g.57799109delC	ENSP00000307734:p.Leu230fs	Somatic	204	.	.		WXS	Illumina HiSeq	Phase_I	167	73	0.437	NM_001005186	B9EKW1|Q6IFH1|Q96R34	Frame_Shift_Del	DEL	ENST00000302622.3	37	CCDS31541.1																																																																																			C|0.867;-|0.133	0.133	strong		0.532	OR6Q1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401257.1	NM_001005186	
CD200R1L	344807	hgsc.bcm.edu	37	3	112545911	112545911	+	Frame_Shift_Del	DEL	T	T	-	rs58161637|rs200703227	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	134	.	.		WXS	Illumina HiSeq	Phase_I	110	37	0.336	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	
GNRH2	2797	hgsc.bcm.edu	37	20	3026345	3026346	+	Frame_Shift_Ins	INS	-	-	GCCCC	rs544846287|rs67749149|rs16996832|rs377041343	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:3026345_3026346insGCCCC	ENST00000245983.2	+	4	377_378	c.326_327insGCCCC	c.(325-330)gagcccfs	p.-111fs	GNRH2_ENST00000359100.2_Frame_Shift_Ins_p.-104fs|GNRH2_ENST00000380347.2_Frame_Shift_Ins_p.-104fs|MRPS26_ENST00000380325.3_5'Flank|GNRH2_ENST00000359987.1_Frame_Shift_Ins_p.-103fs|GNRH2_ENST00000380346.2_Frame_Shift_Ins_p.-103fs	NM_001501.1	NP_001492.1	O43555	GON2_HUMAN	gonadotropin-releasing hormone 2						multicellular organismal development (GO:0007275)|signal transduction (GO:0007165)	extracellular region (GO:0005576)	hormone activity (GO:0005179)			ovary(1)|upper_aerodigestive_tract(1)	2						GCAGCCCGAGAGCCCCGCCCCG	0.634														729	0.145567	0.0295	0.1571	5008	,	,		10164	0.2391		0.1014	False		,,,				2504	0.2434				p.E109fs		Pindel,Atlas-Indel	.											.	GNRH2	15	.	0			c.326_327insGCCCC						PASS	.																																			SO:0001589	frameshift_variant	2797	exon4			.	AF036329	CCDS13040.1, CCDS13041.1, CCDS13042.1	20p13	2013-02-26			ENSG00000125787	ENSG00000125787		"""Endogenous ligands"""	4420	protein-coding gene	gene with protein product		602352				9419371, 12447356	Standard	NM_178331		Approved		uc002whr.1	O43555	OTTHUMG00000031723	ENST00000245983.2:c.337_341dupGCCCC	20.37:g.3026351_3026355dupGCCCC	ENSP00000245983:p.Arg111fs	Somatic	100	.	.		WXS	Illumina HiSeq	Phase_I	61	11	0.180	NM_001501	Q14C68|Q14C69|Q9BYN9|Q9BYP0	Frame_Shift_Ins	INS	ENST00000245983.2	37	CCDS13040.1																																																																																			-|0.814;GCCCC|0.186	0.186	strong		0.634	GNRH2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077694.2	NM_001501	
DUSP18	150290	hgsc.bcm.edu	37	22	31059499	31059500	+	Frame_Shift_Del	DEL	CA	CA	-	rs538206035	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	CA	CA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:31059499_31059500delCA	ENST00000334679.3	-	2	996_997	c.491_492delTG	c.(490-492)gtgfs	p.V164fs	DUSP18_ENST00000403268.1_3'UTR|DUSP18_ENST00000461301.1_Intron|DUSP18_ENST00000404885.1_Frame_Shift_Del_p.V164fs|DUSP18_ENST00000407308.1_Frame_Shift_Del_p.V164fs	NM_152511.3	NP_689724.3	Q8NEJ0	DUS18_HUMAN	dual specificity phosphatase 18	164					peptidyl-tyrosine dephosphorylation (GO:0035335)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	MAP kinase tyrosine/serine/threonine phosphatase activity (GO:0017017)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			large_intestine(1)|lung(1)|prostate(1)|skin(1)	4						TGACCATGTGCACAGTGTTCTT	0.535														9	0.00179712	0.0	0.0	5008	,	,		20452	0.0		0.0089	False		,,,				2504	0.0				p.164_165del		Pindel,Atlas-Indel	.											.	DUSP18	10	.	0			c.492_493del						PASS	.			3,4261		0,3,2129						5.3	0.9		dbSNP_130	115	32,8222		0,32,4095	no	frameshift	DUSP18	NM_152511.3		0,35,6224	A1A1,A1R,RR		0.3877,0.0704,0.2796				35,12483				SO:0001589	frameshift_variant	150290	exon2			.	AF461689	CCDS13883.1	22q12.1	2011-06-09				ENSG00000167065		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Atypical dual specificity phosphatases"""	18484	protein-coding gene	gene with protein product		611446				12408986	Standard	NM_152511		Approved	DUSP20	uc003aiw.1	Q8NEJ0		ENST00000334679.3:c.491_492delTG	22.37:g.31059501_31059502delCA	ENSP00000333917:p.Val164fs	Somatic	128	.	.		WXS	Illumina HiSeq	Phase_I	119	32	0.269	NM_152511	B3KPA4	Frame_Shift_Del	DEL	ENST00000334679.3	37	CCDS13883.1																																																																																			.	.	weak		0.535	DUSP18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321400.1		
KCNN3	3782	hgsc.bcm.edu	37	1	154842199	154842200	+	In_Frame_Ins	INS	-	-	GCTGCTGCTGCTGCT	rs56352724|rs3831942|rs367921715|rs58327065		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:154842199_154842200insGCTGCTGCTGCTGCT	ENST00000271915.4	-	1	556_557	c.241_242insAGCAGCAGCAGCAGC	c.(241-243)cca>cAGCAGCAGCAGCAGCca	p.80_81insQQQQQ	KCNN3_ENST00000358505.2_5'Flank	NM_001204087.1|NM_002249.5	NP_001191016.1|NP_002240.3	Q9UGI6	KCNN3_HUMAN	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 3	80	Gln-rich.		Missing.		potassium ion transmembrane transport (GO:0071805)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	calmodulin binding (GO:0005516)|small conductance calcium-activated potassium channel activity (GO:0016286)	p.Q80_P81insQQ(2)		cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(11)|prostate(4)|skin(1)	28	all_lung(78;2.29e-27)|all_hematologic(923;0.088)|Hepatocellular(266;0.108)|all_neural(408;0.245)		BRCA - Breast invasive adenocarcinoma(34;0.00819)		Miconazole(DB01110)|Procaine(DB00721)	GGGATGCGGTGgctgctgctgc	0.698																																					p.P81delinsQQQQQP		Atlas-Indel	.											KCNN3,colon,carcinoma,0,1	KCNN3	141	1	2	Insertion - In frame(2)	prostate(2)	c.242_243insAGCAGCAGCAGCAGC						PASS	.																																			SO:0001652	inframe_insertion	3782	exon1			.	AF031815	CCDS1072.1, CCDS30880.1, CCDS72928.1	1q21.3	2012-07-05			ENSG00000143603	ENSG00000143603		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, calcium-activated"""	6292	protein-coding gene	gene with protein product		602983				9491810, 16382103	Standard	NM_002249		Approved	KCa2.3, hSK3, SKCA3	uc021pah.1	Q9UGI6	OTTHUMG00000037260	ENST00000271915.4:c.227_241dupAGCAGCAGCAGCAGC	1.37:g.154842199_154842200insGCTGCTGCTGCTGCT	ENSP00000271915:p.Gln76_Gln80dup	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	58	11	0.189655	NM_001204087	B1ANX0|O43517|Q86VF9|Q8WXG7	In_Frame_Ins	INS	ENST00000271915.4	37	CCDS30880.1																																																																																			.	.	alt		0.698	KCNN3-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090688.3	NM_002249	
FAM157A	728262	hgsc.bcm.edu	37	3	197880131	197880133	+	lincRNA	DEL	GCA	GCA	-	rs56683636		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	GCA	GCA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:197880131_197880133delGCA	ENST00000437428.2	+	0	11_13							C9JC47	F157A_HUMAN	family with sequence similarity 157, member A											NS(1)|skin(1)	2						ACAAGAACTGgcagcagcagcag	0.537																																					p.70_71del		Atlas-Indel	.											.	FAM157A	4	.	0			c.209_211del						PASS	.																																					728262	exon2			.			3q29	2013-01-30			ENSG00000236438	ENSG00000236438			34079	other	unknown							Standard	NM_001145248		Approved		uc011bup.1	C9JC47			3.37:g.197880140_197880142delGCA		Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	362	22	0.0607735	NM_001145248		In_Frame_Del	DEL	ENST00000437428.2	37																																																																																				.	.	weak		0.537	FAM157A-001	KNOWN	not_best_in_genome_evidence|mRNA_end_NF|basic	lincRNA	lincRNA	OTTHUMT00000340078.2	NM_001145248	
SCN9A	6335	hgsc.bcm.edu	37	2	167144980	167144980	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:167144980delT	ENST00000409435.1	-	9	1280	c.1281delA	c.(1279-1281)ttafs	p.L427fs	AC010127.3_ENST00000447809.2_RNA|SCN9A_ENST00000303354.6_Frame_Shift_Del_p.L428fs|SCN9A_ENST00000375387.4_Frame_Shift_Del_p.L428fs|SCN9A_ENST00000409672.1_Frame_Shift_Del_p.L427fs			Q15858	SCN9A_HUMAN	sodium channel, voltage-gated, type IX, alpha subunit	427					behavioral response to pain (GO:0048266)|inflammatory response (GO:0006954)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|post-embryonic development (GO:0009791)|response to toxic substance (GO:0009636)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	sodium ion binding (GO:0031402)|voltage-gated sodium channel activity (GO:0005248)			NS(1)|breast(5)|central_nervous_system(6)|endometrium(6)|kidney(3)|large_intestine(27)|lung(38)|ovary(6)|prostate(8)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	108					Lacosamide(DB06218)|Lidocaine(DB00281)|Ranolazine(DB00243)|Rufinamide(DB06201)|Valproic Acid(DB00313)|Zonisamide(DB00909)	TAAGACGGTCTAACATCTGTT	0.383																																					p.D428fs		Atlas-Indel	.											.	SCN9A	296	.	0			c.1282delG						PASS	.						146.0	154.0	151.0					2																	167144980		1841	4092	5933	SO:0001589	frameshift_variant	6335	exon10			.	X82835	CCDS46441.1	2q24	2014-09-17	2007-01-23		ENSG00000169432	ENSG00000169432		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10597	protein-coding gene	gene with protein product		603415	"""sodium channel, voltage-gated, type IX, alpha polypeptide"""			7720699, 10198179, 16382098	Standard	NM_002977		Approved	Nav1.7, PN1, NE-NA, NENA, ETHA	uc010fpl.3	Q15858	OTTHUMG00000154044	ENST00000409435.1:c.1281delA	2.37:g.167144980delT	ENSP00000386330:p.Leu427fs	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	79	12	0.151899	NM_002977	A1BUH5|Q6B4R9|Q6B4S0|Q6B4S1|Q70HX1|Q70HX2|Q8WTU1|Q8WWN4	Frame_Shift_Del	DEL	ENST00000409435.1	37	CCDS46441.1																																																																																			.	.	none		0.383	SCN9A-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333639.1	NM_002977	
IST1	9798	hgsc.bcm.edu	37	16	71956512	71956517	+	In_Frame_Del	DEL	ATGCCC	ATGCCC	-	rs549750934|rs372825060	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	ATGCCC	ATGCCC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:71956512_71956517delATGCCC	ENST00000378799.6	+	7	1044_1049	c.688_693delATGCCC	c.(688-693)atgcccdel	p.MP238del	IST1_ENST00000329908.8_In_Frame_Del_p.MP238del|IST1_ENST00000538565.1_3'UTR|IST1_ENST00000541571.2_In_Frame_Del_p.MP238del|RP11-498D10.5_ENST00000567146.1_RNA|IST1_ENST00000535424.1_In_Frame_Del_p.MP251del|IST1_ENST00000544564.1_In_Frame_Del_p.MP238del|IST1_ENST00000538850.1_In_Frame_Del_p.MP90del|IST1_ENST00000606369.1_In_Frame_Del_p.MP90del|IST1_ENST00000378798.5_In_Frame_Del_p.MP238del			P53990	IST1_HUMAN	increased sodium tolerance 1 homolog (yeast)	236	Interaction with VPS37B.|Interaction with VTA1.				abscission (GO:0009838)|cell division (GO:0051301)|cytokinesis (GO:0000910)|establishment of protein localization (GO:0045184)|positive regulation of collateral sprouting (GO:0048672)|positive regulation of proteolysis (GO:0045862)|protein localization (GO:0008104)|viral capsid secondary envelopment (GO:0046745)|viral release from host cell (GO:0019076)	centrosome (GO:0005813)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular vesicular exosome (GO:0070062)|Flemming body (GO:0090543)|midbody (GO:0030496)	MIT domain binding (GO:0090541)|protein complex binding (GO:0032403)|protein domain specific binding (GO:0019904)										AACGGtgccaatgcccatgcccatgc	0.495														1400	0.279553	0.1725	0.2507	5008	,	,		22310	0.2649		0.341	False		,,,				2504	0.3967				p.242_244del		Pindel,Atlas-Indel	.											.	.	.	.	0			c.726_731del						PASS	.																																			SO:0001651	inframe_deletion	9798	exon8			.	BC004359	CCDS10905.1, CCDS59271.1, CCDS59272.1, CCDS59273.1, CCDS59274.1	16q22.2	2011-08-18	2011-08-18	2011-08-18	ENSG00000182149	ENSG00000182149			28977	protein-coding gene	gene with protein product			"""KIAA0174"""	KIAA0174		8724849, 19129480	Standard	NM_001270975		Approved		uc002fbm.2	P53990	OTTHUMG00000137597	ENST00000378799.6:c.688_693delATGCCC	16.37:g.71956518_71956523delATGCCC	ENSP00000368076:p.Met238_Pro239del	Somatic	90	.	.		WXS	Illumina HiSeq	Phase_I	112	17	0.152	NM_001270976	A8KAH5|J3QLU7|Q3SYM4|Q9BQ81|Q9BWN2	In_Frame_Del	DEL	ENST00000378799.6	37	CCDS59272.1																																																																																			.	.	strong		0.495	IST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269005.2	NM_014761	
PITRM1	10531	hgsc.bcm.edu	37	10	3193558	3193570	+	Intron	DEL	AAAAAAGAAACAA	AAAAAAGAAACAA	-	rs60985673|rs79011862	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	AAAAAAGAAACAA	AAAAAAGAAACAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:3193558_3193570delAAAAAAGAAACAA	ENST00000224949.4	-	15	1656				PITRM1-AS1_ENST00000601046.1_RNA|PITRM1_ENST00000380994.1_Intron|PITRM1_ENST00000380989.2_Intron|PITRM1_ENST00000451104.2_Intron|PITRM1-AS1_ENST00000598280.1_RNA|PITRM1_ENST00000464395.1_5'Flank			Q5JRX3	PREP_HUMAN	pitrilysin metallopeptidase 1						positive regulation of catalytic activity (GO:0043085)|proteolysis (GO:0006508)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	enzyme activator activity (GO:0008047)|metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			breast(2)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(5)|liver(1)|lung(5)|ovary(1)|pancreas(1)|prostate(4)|skin(1)|stomach(2)|urinary_tract(3)	33						TTCTAGACCTAAAAAAGAAACAAGAAAAAGGAA	0.408														931	0.185903	0.084	0.1859	5008	,	,		21309	0.3006		0.16	False		,,,				2504	0.2321				.		Atlas-Indel	.											.	PITRM1	109	.	0			.						PASS	.		,,	322,3302		18,286,1508					,,	5.7	0.7		dbSNP_129	43	1062,6812		64,934,2939	no	intron,intron,intron	PITRM1	NM_014889.3,NM_001242309.1,NM_001242307.1	,,	82,1220,4447	A1A1,A1R,RR		13.4874,8.8852,12.0369	,,	,,		1384,10114				SO:0001627	intron_variant	10531	.			.	AB029027	CCDS55699.1, CCDS55700.1, CCDS59208.1	10p15.2	2008-07-30	2005-08-17		ENSG00000107959	ENSG00000107959			17663	protein-coding gene	gene with protein product	"""PreP peptidasome"""		"""pitrilysin metalloproteinase 1"""			1036083, 10470851, 16849325	Standard	NM_014889		Approved	MP1, KIAA1104, hMP1, PreP	uc009xhv.2	Q5JRX3	OTTHUMG00000017557	ENST00000224949.4:c.1622-3TTGTTTCTTTTTT>-	10.37:g.3193558_3193570delAAAAAAGAAACAA		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	38	13	0.342105	.	B3KMJ6|B4E0J8|C9JSL2|E7ES23|O95204|Q2M2G6|Q4VBR1|Q5JRW7|Q7L5Z7|Q9BSI6|Q9BVJ5|Q9UPP8	Splice_Site	DEL	ENST00000224949.4	37	CCDS59208.1																																																																																			AAAAAAGAAACAA|0.500;-|0.500	0.500	strong		0.408	PITRM1-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000046469.2		
CCDC87	55231	hgsc.bcm.edu	37	11	66358631	66358633	+	In_Frame_Del	DEL	TCT	TCT	-	rs535066162		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	TCT	TCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:66358631_66358633delTCT	ENST00000333861.3	-	1	1921_1923	c.1854_1856delAGA	c.(1852-1857)gaagag>gag	p.618_619EE>E	CCS_ENST00000310190.4_5'Flank|CCS_ENST00000533244.1_5'Flank	NM_018219.2	NP_060689.2	Q9NVE4	CCD87_HUMAN	coiled-coil domain containing 87	618					cytokinesis (GO:0000910)|microtubule cytoskeleton organization (GO:0000226)					central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(12)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	28						CACAGGAACCTCTTCTTCATGCA	0.473																																					p.619_619del		Pindel,Atlas-Indel	.											.	CCDC87	83	.	0			c.1855_1857del						PASS	.			3,4259		0,3,2128						-1.9	0.2			112	18,8232		0,18,4107	no	coding	CCDC87	NM_018219.2		0,21,6235	A1A1,A1R,RR		0.2182,0.0704,0.1678				21,12491				SO:0001651	inframe_deletion	55231	exon1			.	BC034469	CCDS8145.1	11q13.2	2006-03-15			ENSG00000182791	ENSG00000182791			25579	protein-coding gene	gene with protein product						12477932	Standard	NM_018219		Approved	FLJ10786	uc001oiq.4	Q9NVE4	OTTHUMG00000167237	ENST00000333861.3:c.1854_1856delAGA	11.37:g.66358634_66358636delTCT	ENSP00000328487:p.Glu619del	Somatic	229	.	.		WXS	Illumina HiSeq	Phase_I	180	78	0.433	NM_018219	Q8NE76	In_Frame_Del	DEL	ENST00000333861.3	37	CCDS8145.1																																																																																			.	.	none		0.473	CCDC87-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393825.1	NM_018219	
NLGN4Y	22829	hgsc.bcm.edu	37	Y	16952663	16952663	+	3'UTR	DEL	C	C	-			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrY:16952663delC	ENST00000476359.1	+	0	2517							Q8NFZ3	NLGNY_HUMAN	neuroligin 4, Y-linked						learning (GO:0007612)|neuron cell-cell adhesion (GO:0007158)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|vocalization behavior (GO:0071625)	cell junction (GO:0030054)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|neurexin family protein binding (GO:0042043)|receptor activity (GO:0004872)			large_intestine(3)|lung(7)|prostate(2)|skin(2)	14						CAAAACAGGGCCCGAGGACAC	0.532																																					p.G657fs		Pindel,Atlas-Indel	.											.	NLGN4Y	44	.	0			c.1971delG						PASS	.																																			SO:0001624	3_prime_UTR_variant	22829	exon6			.		CCDS14788.1, CCDS55553.1, CCDS56619.1	Yq11.221	2013-09-20	2004-05-21		ENSG00000165246	ENSG00000165246			15529	protein-coding gene	gene with protein product		400028	"""neuroligin 4, Y linked"""			10231032	Standard	NM_014893		Approved	KIAA0951	uc004ftg.2	Q8NFZ3	OTTHUMG00000036618	ENST00000476359.1:c.*2514C>-	Y.37:g.16952663delC		Somatic	3	.	.		WXS	Illumina HiSeq	Phase_I	79	41	0.519	NM_014893	F5H6W0|Q14D08|Q7Z3T5|Q8N5B6|Q9Y2F8	Frame_Shift_Del	DEL	ENST00000476359.1	37																																																																																				.	.	none		0.532	NLGN4Y-004	KNOWN	basic	processed_transcript	protein_coding	OTTHUMT00000089064.2	NM_014893	
TRIOBP	11078	hgsc.bcm.edu	37	22	38119755	38119757	+	In_Frame_Del	DEL	CAA	CAA	-	rs201160789|rs71322688|rs55745992|rs67890459|rs77530465|rs199535040	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	CAA	CAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:38119755_38119757delCAA	ENST00000406386.3	+	7	1447_1449	c.1192_1194delCAA	c.(1192-1194)caadel	p.Q398del		NM_001039141.2	NP_001034230.1	Q9H2D6	TARA_HUMAN	TRIO and F-actin binding protein	398					actin modification (GO:0030047)|barbed-end actin filament capping (GO:0051016)|mitotic nuclear division (GO:0007067)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	actin filament binding (GO:0051015)|GTP-Rho binding (GO:0017049)|myosin II binding (GO:0045159)|ubiquitin protein ligase binding (GO:0031625)	p.Q398R(1)		central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	12	Melanoma(58;0.0574)					CAGAACCACTCAACGAGAGAATT	0.552														1684	0.336262	0.1536	0.2853	5008	,	,		18750	0.5863		0.3877	False		,,,				2504	0.3088				p.397_398del		Pindel,Atlas-Indel	.											.	TRIOBP	262	.	1	Substitution - Missense(1)	lung(1)	c.1191_1193del						PASS	.			658,3014		76,506,1254						-4.9	0.1		dbSNP_132	129	3439,4489		755,1929,1280	no	coding	TRIOBP	NM_001039141.2		831,2435,2534	A1A1,A1R,RR		43.3779,17.9194,35.319				4097,7503				SO:0001651	inframe_deletion	11078	exon7			.	AB051449	CCDS33644.1, CCDS43015.1, CCDS43016.1	22q13.1	2014-06-03			ENSG00000100106	ENSG00000100106		"""Pleckstrin homology (PH) domain containing"""	17009	protein-coding gene	gene with protein product		609761		DFNB28		11148140, 16385457, 16385458	Standard	NM_001039141		Approved	HRIHFB2122, KIAA1662, Tara, TAP68	uc003atr.3	Q9H2D6	OTTHUMG00000150657	ENST00000406386.3:c.1192_1194delCAA	22.37:g.38119755_38119757delCAA	ENSP00000384312:p.Gln398del	Somatic	103	.	.		WXS	Illumina HiSeq	Phase_I	69	28	0.406	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		
HTR3E	285242	hgsc.bcm.edu	37	3	183818222	183818222	+	Intron	DEL	G	G	-	rs5855015|rs397897677	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:183818222delG	ENST00000415389.2	+	2	533				HTR3E_ENST00000335304.2_Frame_Shift_Del_p.R21fs|HTR3E_ENST00000440596.2_Frame_Shift_Del_p.R21fs|HTR3E_ENST00000436361.2_Frame_Shift_Del_p.R21fs|HTR3E_ENST00000425359.2_Intron|HTR3E-AS1_ENST00000431427.1_RNA	NM_001256613.1|NM_198313.2	NP_001243542.1|NP_938055.1	A5X5Y0	5HT3E_HUMAN	5-hydroxytryptamine (serotonin) receptor 3E, ionotropic						ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	extracellular ligand-gated ion channel activity (GO:0005230)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(8)|lung(20)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	40	all_cancers(143;1.46e-10)|Ovarian(172;0.0303)		Epithelial(37;7.06e-36)|OV - Ovarian serous cystadenocarcinoma(80;3.11e-22)		Ergoloid mesylate(DB01049)	CTCTCATATAGGGAGCACAGG	0.527													GGG|GGG|GG|deletion	178	0.0355431	0.0023	0.0764	5008	,	,		17512	0.0		0.1113	False		,,,				2504	0.0102				p.R21fs	Melanoma(7;227 727 6634 44770)	Pindel,Atlas-Indel	.											.	HTR3E	65	.	0			c.61delA						PASS	.			99,4167		3,93,2037	157.0	143.0	147.0			2.5	0.0	3	dbSNP_114	156	829,7423		36,757,3333	yes	frameshift	HTR3E	NM_182589.2		39,850,5370	A1A1,A1R,RR		10.046,2.3207,7.4133			183818222	928,11590	2202	4293	6495	SO:0001627	intron_variant	285242	exon1			.	AY159813	CCDS3251.1, CCDS58868.1, CCDS58869.1, CCDS58870.1, CCDS58871.1	3q27	2012-05-22	2012-02-03		ENSG00000186038	ENSG00000186038		"""5-HT (serotonin) receptors"", ""Ligand-gated ion channels / 5-HT (serotonin) receptors, ionotropic"""	24005	protein-coding gene	gene with protein product		610123	"""5-hydroxytryptamine (serotonin) receptor 3, family member E"""			12801637, 15157181	Standard	NM_001256613		Approved		uc010hxr.3	A5X5Y0	OTTHUMG00000156857	ENST00000415389.2:c.68-51G>-	3.37:g.183818222delG		Somatic	107	.	.		WXS	Illumina HiSeq	Phase_I	68	18	0.265	NM_182589	A8IKD7|E9PGF1|Q495G1|Q495G3|Q6V706|Q6V707|Q7Z6B2	Frame_Shift_Del	DEL	ENST00000415389.2	37	CCDS58868.1																																																																																			G|0.951;-|0.049	0.049	strong		0.527	HTR3E-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000346284.1	NM_182589	
CFAP74	85452	hgsc.bcm.edu	37	1	1900106	1900107	+	IGR	INS	-	-	CTC	rs61233860|rs145742571|rs72634902	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	183	.	.		WXS	Illumina HiSeq	Phase_I	114	30	0.263	NM_001080484		In_Frame_Ins	INS		37																																																																																				.	.	strong	0	0.569								
M6PR	4074	hgsc.bcm.edu	37	12	9098995	9098996	+	In_Frame_Ins	INS	-	-	AAC	rs3217106|rs373924445|rs149871778		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:9098995_9098996insAAC	ENST00000000412.3	-	2	473_474	c.5_6insGTT	c.(4-6)ttc>ttGTTc	p.1_2insL		NM_002355.3	NP_002346.1	P20645	MPRD_HUMAN	mannose-6-phosphate receptor (cation dependent)	1					endosome to lysosome transport (GO:0008333)|receptor-mediated endocytosis (GO:0006898)|signal transduction (GO:0007165)	endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)	mannose binding (GO:0005537)|mannose transmembrane transporter activity (GO:0015578)|transmembrane signaling receptor activity (GO:0004888)			cervix(1)|endometrium(6)|kidney(1)|large_intestine(2)|lung(1)	11		Hepatocellular(102;0.137)		BRCA - Breast invasive adenocarcinoma(232;0.0146)	Alglucosidase alfa(DB01272)	TGTAGAAAGGGAACATCCTTTG	0.475														687	0.137181	0.0038	0.0576	5008	,	,		18966	0.3075		0.1123	False		,,,				2504	0.2239				p.F2delinsLF		Pindel,Atlas-Indel	.											M6PR,NS,carcinoma,0,1	M6PR	33	1	0			c.6_7insGTT						PASS	.		,	106,4158		1,104,2027					,	2.9	0.3		dbSNP_106	77	857,7397		49,759,3319	no	coding,coding	M6PR	NM_002355.3,NM_001207024.1	,	50,863,5346	A1A1,A1R,RR		10.3828,2.4859,7.6929	,	,		963,11555				SO:0001652	inframe_insertion	4074	exon2			.		CCDS8598.1, CCDS73440.1	12p13.31	2013-09-20			ENSG00000003056	ENSG00000003056			6752	protein-coding gene	gene with protein product		154540					Standard	NM_002355		Approved		uc001qvf.3	P20645	OTTHUMG00000168276	ENST00000000412.3:c.3_5dupGTT	12.37:g.9098996_9098998dupAAC	ENSP00000000412:p.Met1_Phe2insLeu	Somatic	124	.	.		WXS	Illumina HiSeq	Phase_I	87	52	0.598	NM_001207024	A8K528|D3DUV5	In_Frame_Ins	INS	ENST00000000412.3	37	CCDS8598.1																																																																																			-|0.877;AAC|0.123	0.123	strong		0.475	M6PR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399130.1		
AKAP3	10566	hgsc.bcm.edu	37	12	4735965	4735966	+	Frame_Shift_Ins	INS	-	-	C	rs200178782|rs397849865		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:4735965_4735966insC	ENST00000545990.2	-	5	2626_2627	c.2102_2103insG	c.(2101-2103)ggafs	p.G701fs	AKAP3_ENST00000228850.1_Frame_Shift_Ins_p.G701fs|RP11-500M8.7_ENST00000536588.1_Intron	NM_001278309.1	NP_001265238.1	O75969	AKAP3_HUMAN	A kinase (PRKA) anchor protein 3	701					acrosome reaction (GO:0007340)|cellular component movement (GO:0006928)|protein localization (GO:0008104)|single fertilization (GO:0007338)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	acrosomal vesicle (GO:0001669)|nucleus (GO:0005634)|sperm fibrous sheath (GO:0035686)|sperm principal piece (GO:0097228)	protein kinase A binding (GO:0051018)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(13)|liver(1)|lung(17)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	51						TACTGGCATCTCCAGACTTGTC	0.495																																					p.G701fs		Atlas-Indel	.											.	AKAP3	212	.	0			c.2103_2104insG						PASS	.			552,3712		38,476,1618						-2.2	1.0		dbSNP_126	70	1069,7179		68,933,3123	no	frameshift	AKAP3	NM_006422.2		106,1409,4741	A1A1,A1R,RR		12.9607,12.9456,12.9556				1621,10891				SO:0001589	frameshift_variant	10566	exon4			.	U85715	CCDS8531.1	12p13.3	2009-03-12				ENSG00000111254		"""A-kinase anchor proteins"""	373	protein-coding gene	gene with protein product	"""Fibrous Sheath Protein of 95 kDa"", ""cancer/testis antigen 82"""	604689				10334916, 10319321	Standard	NM_001278309		Approved	FSP95, SOB1, AKAP110, CT82	uc001qnb.4	O75969		ENST00000545990.2:c.2103dupG	12.37:g.4735967_4735967dupC	ENSP00000440994:p.Gly701fs	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	82	11	0.134146	NM_006422	O75945|Q86X01|Q9UM61	Frame_Shift_Ins	INS	ENST00000545990.2	37	CCDS8531.1																																																																																			-|0.868;C|0.132	0.132	strong		0.495	AKAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398911.2	NM_006422	
RYR3	6263	hgsc.bcm.edu	37	15	34137080	34137082	+	In_Frame_Del	DEL	AGA	AGA	-	rs3217346|rs397840365	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	AGA	AGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:34137080_34137082delAGA	ENST00000389232.4	+	93	13384_13386	c.13314_13316delAGA	c.(13312-13317)ttagaa>tta	p.E4441del	RYR3_ENST00000415757.3_In_Frame_Del_p.E4436del	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	4441					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)	p.E4440delE(1)		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)		AAGAACCTTTAGAAGAAGAGACA	0.419														372	0.0742812	0.0424	0.1124	5008	,	,		20594	0.0069		0.1491	False		,,,				2504	0.0828				p.4438_4439del		Pindel,Atlas-Indel	.											.	RYR3	760	.	1	Deletion - In frame(1)	ovary(1)	c.13313_13315del						PASS	.			177,3473		13,151,1661						3.8	1.0		dbSNP_134	95	1380,6492		115,1150,2671	no	coding	RYR3	NM_001036.3		128,1301,4332	A1A1,A1R,RR		17.5305,4.8493,13.5133				1557,9965				SO:0001651	inframe_deletion	6263	exon93			.		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.13314_13316delAGA	15.37:g.34137086_34137088delAGA	ENSP00000373884:p.Glu4441del	Somatic	108	.	.		WXS	Illumina HiSeq	Phase_I	114	48	0.421	NM_001036	O15175|Q15412	In_Frame_Del	DEL	ENST00000389232.4	37	CCDS45210.1																																																																																			AGA|0.918;-|0.082	0.082	strong		0.419	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1		
ACOT4	122970	hgsc.bcm.edu	37	14	74060514	74060517	+	Frame_Shift_Del	DEL	CTTA	CTTA	-	rs74553611|rs562751690|rs77261428|rs77814755|rs375801976|rs77408762	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	CTTA	CTTA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:74060514_74060517delCTTA	ENST00000326303.4	+	2	820_823	c.566_569delCTTA	c.(565-570)gcttatfs	p.AY189fs		NM_152331.3	NP_689544.3	Q8N9L9	ACOT4_HUMAN	acyl-CoA thioesterase 4	189				ALAY -> DLQS (in Ref. 1; BAC04313). {ECO:0000305}.	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)	p.A189fs*32(2)		endometrium(1)|large_intestine(3)|lung(4)	8				BRCA - Breast invasive adenocarcinoma(234;0.00331)		TTGGCTCTAGCTTATTATAACTTT	0.495																																					p.189_190del		Atlas-Indel	.											.	ACOT4	25	.	2	Deletion - Frameshift(2)	large_intestine(2)	c.565_568del						PASS	.			103,4159		3,97,2031						4.3	1.0			126	861,7311		130,601,3355	no	frameshift	ACOT4	NM_152331.3		133,698,5386	A1A1,A1R,RR		10.536,2.4167,7.7529				964,11470				SO:0001589	frameshift_variant	122970	exon2			.	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.566_569delCTTA	14.37:g.74060514_74060517delCTTA	ENSP00000323071:p.Ala189fs	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	74	12	0.162162	NM_152331	Q17RF4|Q5BKT6|Q86TX0|Q86TX1|Q96N88	Frame_Shift_Del	DEL	ENST00000326303.4	37	CCDS9817.1																																																																																			.	.	weak		0.495	ACOT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404298.2	NM_152331	
HLA-C	3107	hgsc.bcm.edu	37	6	31238973	31238986	+	Frame_Shift_Del	DEL	TCTGAGCCGCGGTG	TCTGAGCCGCGGTG	-	rs45578735|rs2308584|rs200155513|rs45622747|rs2308585|rs200892438|rs41541313|rs281860498|rs45505091|rs281860496|rs281860497|rs281860495	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	TCTGAGCCGCGGTG	TCTGAGCCGCGGTG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:31238973_31238986delTCTGAGCCGCGGTG	ENST00000376228.5	-	3	497_510	c.483_496delCACCGCGGCTCAGA	c.(481-498)gacaccgcggctcagatcfs	p.TAAQI162fs	HLA-C_ENST00000383329.3_Frame_Shift_Del_p.TAAQI162fs	NM_002117.5	NP_002108.4	Q95604	1C17_HUMAN	major histocompatibility complex, class I, C	162	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						CGCTGGGTGATCTGAGCCGCGGTGTCCGCGGCGG	0.692																																					p.162_166del		Atlas-Indel	.											.	HLA-C	92	.	0			c.484_497del						PASS	.																																			SO:0001589	frameshift_variant	3107	exon3			.	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.483_496delCACCGCGGCTCAGA	6.37:g.31238973_31238986delTCTGAGCCGCGGTG	ENSP00000365402:p.Thr162fs	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	151	29	0.192053	NM_002117	O02864|O02958|Q29643|Q9MY30	Frame_Shift_Del	DEL	ENST00000376228.5	37	CCDS34393.1																																																																																			.	.	none		0.692	HLA-C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076281.3	NM_002117	
ALMS1	7840	hgsc.bcm.edu	37	2	73613032	73613037	+	In_Frame_Del	DEL	GGAGGA	GGAGGA	-	rs61156725|rs70965731|rs72319667|rs3074417	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	GGAGGA	GGAGGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:73613032_73613037delGGAGGA	ENST00000264448.6	+	1	147_152	c.36_41delGGAGGA	c.(34-42)ctggaggag>ctg	p.EE27del	ALMS1_ENST00000409009.1_In_Frame_Del_p.EE27del|ALMS1_ENST00000377715.1_In_Frame_Del_p.EE27del	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	27	Glu-rich.				endosomal transport (GO:0016197)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of stress fiber assembly (GO:0051492)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)		p.E27_E28delEE(1)|p.E28_A29insE(1)		breast(4)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(31)|lung(68)|ovary(4)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	147						CGGGCGAGCTggaggaggaggaggag	0.694														3836	0.765974	0.9183	0.7176	5008	,	,		6363	0.7024		0.6819	False		,,,				2504	0.7464				p.12_14del		Atlas-Indel	.											.	ALMS1	384	.	2	Insertion - In frame(1)|Deletion - In frame(1)	ovary(1)|breast(1)	c.35_40del						PASS	.																																			SO:0001651	inframe_deletion	7840	exon1			.	AB002326	CCDS42697.1	2p13.1	2014-09-17			ENSG00000116127	ENSG00000116127			428	protein-coding gene	gene with protein product		606844				9063741	Standard	NM_015120		Approved	KIAA0328	uc002sje.1	Q8TCU4	OTTHUMG00000152812	ENST00000264448.6:c.36_41delGGAGGA	2.37:g.73613038_73613043delGGAGGA	ENSP00000264448:p.Glu27_Glu28del	Somatic	11	0	0		WXS	Illumina HiSeq	Phase_I	21	10	0.47619	NM_015120	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	In_Frame_Del	DEL	ENST00000264448.6	37	CCDS42697.1																																																																																			-|0.500;GGAGGA|0.500	0.500	weak		0.694	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120	
SRSF2	6427	hgsc.bcm.edu	37	17	74732390	74732395	+	In_Frame_Del	DEL	GGACTT	GGACTT	-			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	GGACTT	GGACTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:74732390_74732395delGGACTT	ENST00000392485.2	-	2	686_691	c.514_519delAAGTCC	c.(514-519)aagtccdel	p.KS172del	SRSF2_ENST00000508921.3_In_Frame_Del_p.KS160del|MFSD11_ENST00000593181.1_5'Flank|MFSD11_ENST00000336509.4_5'Flank|RP11-318A15.7_ENST00000587459.1_Intron|MFSD11_ENST00000590393.1_5'Flank|SRSF2_ENST00000359995.5_In_Frame_Del_p.KS172del|MFSD11_ENST00000588460.1_5'UTR|MFSD11_ENST00000586622.1_5'UTR|MFSD11_ENST00000591864.1_5'Flank|MFSD11_ENST00000590514.1_5'Flank|MFSD11_ENST00000355954.3_5'Flank|MIR636_ENST00000384825.1_RNA	NM_003016.4	NP_003007.2	Q01130	SRSF2_HUMAN	serine/arginine-rich splicing factor 2	172	Arg/Ser-rich (RS domain).				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)|regulation of RNA biosynthetic process (GO:2001141)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	extracellular vesicular exosome (GO:0070062)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|transcription corepressor activity (GO:0003714)			haematopoietic_and_lymphoid_tissue(320)|kidney(2)|large_intestine(1)|lung(4)|prostate(2)	329						AGACCGACGAGGACTTGGACTTGGAC	0.617			Mis		"""MDS, CLL"""																																p.172_174del		Pindel,Atlas-Indel	.		Dom	yes		17	17q25	6427	serine/arginine-rich splicing factor 2		L	.	SRSF2	544	.	0			c.515_520del						PASS	.																																			SO:0001651	inframe_deletion	6427	exon2			.	M90104	CCDS11749.1	17q25.2	2014-09-17	2010-06-22	2010-06-22	ENSG00000161547	ENSG00000161547		"""Serine/arginine-rich splicing factors"", ""RNA binding motif (RRM) containing"""	10783	protein-coding gene	gene with protein product	"""SR splicing factor 2"""	600813	"""splicing factor, arginine/serine-rich 2"""	SFRS2		8530103, 20516191	Standard	NM_003016		Approved	SC-35, SC35, PR264, SFRS2A	uc002jsv.3	Q01130		ENST00000392485.2:c.514_519delAAGTCC	17.37:g.74732396_74732401delGGACTT	ENSP00000376276:p.Lys172_Ser173del	Somatic	72	.	.		WXS	Illumina HiSeq	Phase_I	67	14	0.209	NM_001195427	B3KWD5|B4DN89|H0YG49	In_Frame_Del	DEL	ENST00000392485.2	37	CCDS11749.1																																																																																			.	.	none		0.617	SRSF2-003	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437489.1	NM_003016	
PTCHD3	374308	hgsc.bcm.edu	37	10	27702256	27702257	+	Frame_Shift_Ins	INS	-	-	C	rs369926016|rs112067123|rs75297921|rs377312318	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:27702256_27702257insC	ENST00000438700.3	-	1	1040_1041	c.923_924insG	c.(922-924)ggcfs	p.G308fs		NM_001034842.3	NP_001030014.2	Q3KNS1	PTHD3_HUMAN	patched domain containing 3	308					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						TTCCTAGGCTGCCCCCCAAGAT	0.589													CCCCCC|CCCCCC|CCCCCCC|insertion	1387	0.276957	0.2693	0.304	5008	,	,		18563	0.1806		0.3449	False		,,,				2504	0.2975				p.G308fs		Pindel,Atlas-Indel	.											.	PTCHD3	140	.	0			c.924_925insG						PASS	.																																			SO:0001589	frameshift_variant	374308	exon1			.	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.924dupG	10.37:g.27702262_27702262dupC	ENSP00000417658:p.Gly308fs	Somatic	85	.	.		WXS	Illumina HiSeq	Phase_I	78	46	0.590	NM_001034842	I3L499|Q6ZU28	Frame_Shift_Ins	INS	ENST00000438700.3	37	CCDS31173.1																																																																																			-|0.732;C|0.268	0.268	strong		0.589	PTCHD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047325.3	XM_370541	
HK3	3101	hgsc.bcm.edu	37	5	176314086	176314086	+	Frame_Shift_Del	DEL	G	G	-	rs534008020	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:176314086delG	ENST00000292432.5	-	13	1865	c.1774delC	c.(1774-1776)cagfs	p.Q593fs		NM_002115.2	NP_002106.2	P52790	HXK3_HUMAN	hexokinase 3 (white cell)	593	Catalytic.|Hexokinase type-1 2.				carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|cellular glucose homeostasis (GO:0001678)|glucose 6-phosphate metabolic process (GO:0051156)|glucose transport (GO:0015758)|glycolytic process (GO:0006096)|hexose metabolic process (GO:0019318)|hexose transport (GO:0008645)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|protein complex (GO:0043234)	ATP binding (GO:0005524)|fructokinase activity (GO:0008865)|glucokinase activity (GO:0004340)|hexokinase activity (GO:0004396)|hormone binding (GO:0042562)|mannokinase activity (GO:0019158)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(21)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	47	all_cancers(89;0.000104)|Renal(175;0.000269)|Lung NSC(126;0.00696)|all_lung(126;0.0115)	Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			TGCTTCTGCTGGAAGTCCACG	0.602																																					p.Q592fs		Pindel,Atlas-Indel	.											.	HK3	210	.	0			c.1775delA						PASS	.						84.0	76.0	79.0					5																	176314086		2203	4300	6503	SO:0001589	frameshift_variant	3101	exon13			.		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.1774delC	5.37:g.176314086delG	ENSP00000292432:p.Gln593fs	Somatic	86	.	.		WXS	Illumina HiSeq	Phase_I	121	41	0.339	NM_002115	Q8N1E7	Frame_Shift_Del	DEL	ENST00000292432.5	37	CCDS4407.1																																																																																			.	.	none		0.602	HK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253428.1		
ANKRD30B	374860	hgsc.bcm.edu	37	18	14837637	14837637	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:14837637delG	ENST00000358984.4	+	30	2773	c.2593delG	c.(2593-2595)ggafs	p.G865fs		NM_001145029.1	NP_001138501.1	Q9BXX2	AN30B_HUMAN	ankyrin repeat domain 30B	865										breast(3)|endometrium(4)|kidney(3)|lung(8)|ovary(1)|prostate(2)|skin(1)	22						ATCAGAATTAGGAAGAAAAGA	0.264																																					p.L864fs		Atlas-Indel	.											.	ANKRD30B	237	.	0			c.2592delA						PASS	.						19.0	24.0	23.0					18																	14837637		690	1579	2269	SO:0001589	frameshift_variant	374860	exon30			.	BC028407	CCDS54182.1	18p11.21	2013-01-10			ENSG00000180777	ENSG00000180777		"""Ankyrin repeat domain containing"""	24165	protein-coding gene	gene with protein product						11280766	Standard	NM_001145029		Approved	NY-BR-1.1	uc010dlo.2	Q9BXX2		ENST00000358984.4:c.2593delG	18.37:g.14837637delG	ENSP00000351875:p.Gly865fs	Somatic	694	0	0		WXS	Illumina HiSeq	Phase_I	736	142	0.192935	NM_001145029	B4DGP1|F8WAG3|Q4G175	Frame_Shift_Del	DEL	ENST00000358984.4	37	CCDS54182.1																																																																																			.	.	none		0.264	ANKRD30B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000443557.1	NM_001145029	
TRIM52	84851	hgsc.bcm.edu	37	5	180687429	180687431	+	In_Frame_Del	DEL	TCT	TCT	-	rs200454506|rs78075294|rs3073543|rs33972170	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	TCT	TCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:180687429_180687431delTCT	ENST00000327767.4	-	1	688_690	c.384_386delAGA	c.(382-387)gaagag>gag	p.128_129EE>E	TRIM52-AS1_ENST00000509252.1_RNA|TRIM52_ENST00000514805.1_5'UTR|TRIM52-AS1_ENST00000507434.1_RNA|CTC-338M12.4_ENST00000417281.2_RNA|CTC-338M12.4_ENST00000505151.1_RNA|CTC-338M12.4_ENST00000511331.1_RNA|TRIM52-AS1_ENST00000514146.1_RNA	NM_032765.2	NP_116154.1	Q96A61	TRI52_HUMAN	tripartite motif containing 52	128	Glu-rich.				positive regulation of NF-kappaB transcription factor activity (GO:0051092)	intracellular (GO:0005622)	zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(2)|lung(3)|skin(1)|stomach(1)	8	all_cancers(89;8.79e-06)|all_epithelial(37;1.13e-06)|Renal(175;0.000159)|Lung NSC(126;0.00354)|all_lung(126;0.00609)|Breast(19;0.0654)	all_cancers(40;0.0106)|Medulloblastoma(196;0.0392)|all_neural(177;0.0529)|all_hematologic(541;0.0588)|all_lung(500;0.149)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.232)		CTGATCTTCCTCTTCTTCTTCTT	0.453														2462	0.491613	0.916	0.304	5008	,	,		21160	0.3393		0.2773	False		,,,				2504	0.4284				p.129_129del		Pindel,Atlas-Indel	.											.	TRIM52	20	.	0			c.385_387del						PASS	.																																			SO:0001651	inframe_deletion	84851	exon1			.		CCDS4467.1	5q35.3	2013-01-09	2011-01-25		ENSG00000183718	ENSG00000183718		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	19024	protein-coding gene	gene with protein product			"""tripartite motif-containing 52"""				Standard	NM_032765		Approved	RNF102	uc003mnp.3	Q96A61	OTTHUMG00000130964	ENST00000327767.4:c.384_386delAGA	5.37:g.180687438_180687440delTCT	ENSP00000332152:p.Glu130del	Somatic	136	.	.		WXS	Illumina HiSeq	Phase_I	157	50	0.318	NM_032765		In_Frame_Del	DEL	ENST00000327767.4	37	CCDS4467.1																																																																																			TCT|0.580;-|0.420	0.420	strong		0.453	TRIM52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253572.3	NM_032765	
CRIPAK	285464	hgsc.bcm.edu	37	4	1388375	1388376	+	Frame_Shift_Ins	INS	-	-	CA	rs533172496|rs530731346|rs373032956	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	124	0	0		WXS	Illumina HiSeq	Phase_I	95	19	0.2	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	
VSIG10	54621	hgsc.bcm.edu	37	12	118506328	118506333	+	In_Frame_Del	DEL	TCCTCC	TCCTCC	-	rs67582641|rs199991783|rs72125532	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	TCCTCC	TCCTCC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	269	0	0		WXS	Illumina HiSeq	Phase_I	207	56	0.270531	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	
TTBK1	84630	hgsc.bcm.edu	37	6	43250726	43250728	+	In_Frame_Del	DEL	GAA	GAA	-	rs373093693|rs113160341	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	GAA	GAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:43250726_43250728delGAA	ENST00000259750.4	+	14	2331_2333	c.2248_2250delGAA	c.(2248-2250)gaadel	p.E771del		NM_032538.1	NP_115927.1	Q5TCY1	TTBK1_HUMAN	tau tubulin kinase 1	771	Glu-rich.				substantia nigra development (GO:0021762)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(10)|liver(1)|lung(21)|ovary(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	53			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0125)|OV - Ovarian serous cystadenocarcinoma(102;0.0399)			agaggatgaggaagaagaagagg	0.596														1066	0.212859	0.3041	0.1988	5008	,	,		16464	0.1131		0.172	False		,,,				2504	0.2444				p.749_750del		Atlas-Indel	.											TTBK1,NS,carcinoma,0,1	TTBK1	124	1	0			c.2247_2249del						PASS	.			1250,3010		180,890,1060						2.3	0.3		dbSNP_132	18	1640,6596		164,1312,2642	no	coding	TTBK1	NM_032538.1		344,2202,3702	A1A1,A1R,RR		19.9126,29.3427,23.1274				2890,9606				SO:0001651	inframe_deletion	84630	exon14			.	AB058758	CCDS34455.1	6p21.1	2008-02-05			ENSG00000146216	ENSG00000146216			19140	protein-coding gene	gene with protein product						11347906	Standard	XM_006715229		Approved	KIAA1855	uc003ouq.1	Q5TCY1	OTTHUMG00000014725	ENST00000259750.4:c.2248_2250delGAA	6.37:g.43250732_43250734delGAA	ENSP00000259750:p.Glu771del	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	55	18	0.327273	NM_032538	A2A2U5|Q2L6C6|Q6ZNH0|Q8N444|Q96JH2	In_Frame_Del	DEL	ENST00000259750.4	37	CCDS34455.1																																																																																			GAA|0.806;-|0.194	0.194	strong		0.596	TTBK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040584.3		
NINL	22981	hgsc.bcm.edu	37	20	25457050	25457055	+	In_Frame_Del	DEL	CTCCCA	CTCCCA	-	rs68078266|rs146288604|rs200097181|rs34410422|rs201074890	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	CTCCCA	CTCCCA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:25457050_25457055delCTCCCA	ENST00000278886.6	-	17	2945_2950	c.2872_2877delTGGGAG	c.(2872-2877)tgggagdel	p.WE958del	NINL_ENST00000422516.1_Intron	NM_025176.4	NP_079452.3	Q9Y2I6	NINL_HUMAN	ninein-like	958				Missing (in Ref. 4; AAH36380). {ECO:0000305}.	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						TCAGGGGTGGCTCCCACATCCGTGGC	0.689														2791	0.557308	0.5356	0.3559	5008	,	,		14584	0.9067		0.4304	False		,,,				2504	0.5				p.958_960del		Pindel,Atlas-Indel	.											.	NINL	148	.	0			c.2873_2878del						PASS	.			1921,2191		513,895,648						0.3	0.0		dbSNP_130	17	3184,4816		750,1684,1566	no	coding	NINL	NM_025176.4		1263,2579,2214	A1A1,A1R,RR		39.8,46.7169,42.1483				5105,7007				SO:0001651	inframe_deletion	22981	exon17			.		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.2872_2877delTGGGAG	20.37:g.25457050_25457055delCTCCCA	ENSP00000278886:p.Trp958_Glu959del	Somatic	95	.	.		WXS	Illumina HiSeq	Phase_I	59	14	0.237	NM_025176	A6NJN0|B3V9H6|B7Z1V8|Q5JYP0|Q8NE38|Q9NQE3	In_Frame_Del	DEL	ENST00000278886.6	37	CCDS33452.1																																																																																			CTCCCA|0.450;-|0.550	0.550	strong		0.689	NINL-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078445.3	NM_025176	
GLT6D1	360203	hgsc.bcm.edu	37	9	138516347	138516347	+	Frame_Shift_Del	DEL	A	A	-	rs34217442	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:138516347delA	ENST00000371763.1	-	5	680	c.427delT	c.(427-429)tggfs	p.W143fs		NM_182974.2	NP_892019.2	Q7Z4J2	GL6D1_HUMAN	glycosyltransferase 6 domain containing 1	143					carbohydrate metabolic process (GO:0005975)	integral component of membrane (GO:0016021)	transferase activity, transferring hexosyl groups (GO:0016758)			endometrium(2)|large_intestine(5)|lung(3)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(1)	15		Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;4.3e-07)|Epithelial(140;1.58e-06)|all cancers(34;5.36e-05)		CCATCGAGCCACCACCTCTCG	0.552													A|A|-|deletion	860	0.171725	0.09	0.1888	5008	,	,		16603	0.2103		0.1839	False		,,,				2504	0.2178				p.W143fs		Pindel,Atlas-Indel	.											.	GLT6D1	56	.	0			c.428delG						PASS	.			334,3488		26,282,1603	39.0	36.0	37.0			-1.0	0.0	9	dbSNP_126	43	1598,6358		173,1252,2553	yes	frameshift	GLT6D1	NM_182974.2		199,1534,4156	A1A1,A1R,RR		20.0855,8.7389,16.4035			138516347	1932,9846	1961	4021	5982	SO:0001589	frameshift_variant	360203	exon5			.	AY336054	CCDS43900.1	9q34.3	2013-02-22	2004-09-16	2004-09-17	ENSG00000204007	ENSG00000204007		"""Glycosyltransferase family 6 domain containing"""	23671	protein-coding gene	gene with protein product		613699	"""galactosyltransferase family 6 domain containing 1"""	GLTDC1			Standard	NM_182974		Approved		uc010nbd.1	Q7Z4J2	OTTHUMG00000020911	ENST00000371763.1:c.427delT	9.37:g.138516347delA	ENSP00000360829:p.Trp143fs	Somatic	104	.	.		WXS	Illumina HiSeq	Phase_I	77	24	0.312	NM_182974		Frame_Shift_Del	DEL	ENST00000371763.1	37	CCDS43900.1																																																																																			A|0.829;-|0.171	0.171	strong		0.552	GLT6D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055005.2	NM_182974	
CASP8AP2	9994	hgsc.bcm.edu	37	6	90577707	90577707	+	RNA	DEL	G	G	-	rs527250207|rs202116886	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	79	0	0		WXS	Illumina HiSeq	Phase_I	66	33	0.5	NM_012115		Frame_Shift_Del	DEL	ENST00000551025.1	37																																																																																				.	.	alt		0.378	CASP8AP2-202	KNOWN	basic	processed_transcript	processed_transcript		NM_001137667	
ZNF880	400713	hgsc.bcm.edu	37	19	52887246	52887247	+	In_Frame_Ins	INS	-	-	CAA	rs398071206|rs71836013|rs34678014		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:52887246_52887247insCAA	ENST00000422689.2	+	4	428_429	c.413_414insCAA	c.(412-417)atcaac>atCAAcaac	p.140_141insN		NM_001145434.1	NP_001138906.1	Q6PDB4	ZN880_HUMAN	zinc finger protein 880	140					regulation of transcription, DNA-templated (GO:0006355)	intracellular (GO:0005622)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(2)|skin(1)	10						GAAAAACCTATCAACAATTCCT	0.312																																					p.I138delinsIN		Pindel,Atlas-Indel	.											.	ZNF880	45	.	0			c.413_414insCAA						PASS	.			958,2510		225,508,1001						-0.9	0.0		dbSNP_126	61	2771,4597		695,1381,1608	no	coding	ZNF880	NM_001145434.1		920,1889,2609	A1A1,A1R,RR		37.6086,27.624,34.4131				3729,7107				SO:0001652	inframe_insertion	400713	exon4			.	BC058819	CCDS46164.1	19q13.41	2013-01-08			ENSG00000221923	ENSG00000221923		"""Zinc fingers, C2H2-type"", ""-"""	37249	protein-coding gene	gene with protein product							Standard	NM_001145434		Approved		uc002pzc.3	Q6PDB4	OTTHUMG00000167972	ENST00000422689.2:c.417_419dupCAA	19.37:g.52887250_52887252dupCAA	ENSP00000406318:p.Asn140_Asn140dup	Somatic	168	.	.		WXS	Illumina HiSeq	Phase_I	102	73	0.716	NM_001145434	B4DNA6	In_Frame_Ins	INS	ENST00000422689.2	37	CCDS46164.1																																																																																			-|0.657;CAA|0.343	0.343	strong		0.312	ZNF880-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397374.1	NM_001145434	
THAP2	83591	hgsc.bcm.edu	37	12	72070506	72070508	+	In_Frame_Del	DEL	GTT	GTT	-	rs140783391	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	GTT	GTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	114	.	.		WXS	Illumina HiSeq	Phase_I	95	30	0.316	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	10467579	10467581	+	In_Frame_Del	DEL	TTC	TTC	-	rs143686100		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	TTC	TTC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:10467579_10467581delTTC	ENST00000382483.3	-	4	4250_4252	c.4027_4029delGAA	c.(4027-4029)gaadel	p.E1343del		NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	1359	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)		ctccttctgtttctttagtttcc	0.488																																					p.1343_1344del		Atlas-Indel	.											.	RP1L1	453	.	0			c.4028_4030del						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.4027_4029delGAA	8.37:g.10467579_10467581delTTC	ENSP00000371923:p.Glu1343del	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	120	21	0.175	NM_178857	Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	In_Frame_Del	DEL	ENST00000382483.3	37	CCDS43708.1																																																																																			.	.	strong		0.488	RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375673.1		
C18orf25	147339	hgsc.bcm.edu	37	18	43833701	43833702	+	In_Frame_Ins	INS	-	-	CTG	rs34068795|rs148874606|rs397790301|rs77850739	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:43833701_43833702insCTG	ENST00000282059.6	+	4	1311_1312	c.937_938insCTG	c.(937-939)tct>tCTGct	p.313_314insA	C18orf25_ENST00000321319.6_In_Frame_Ins_p.252_253insA	NM_145055.3	NP_659492	Q96B23	CR025_HUMAN	chromosome 18 open reading frame 25	313			S -> SA. {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005, ECO:0000269|Ref.4}.					p.S313A(1)		central_nervous_system(2)|endometrium(2)|large_intestine(1)|lung(4)|pancreas(1)|prostate(1)	11						TGACAAAACATCTGGCAATGCG	0.406														3469	0.692692	0.7383	0.7147	5008	,	,		19132	0.6022		0.7485	False		,,,				2504	0.6513				p.S313delinsSA		Pindel,Atlas-Indel	.											C18orf25,NS,carcinoma,0,1	C18orf25	27	1	1	Substitution - Missense(1)	pancreas(1)	c.937_938insCTG						PASS	.																																			SO:0001652	inframe_insertion	147339	exon4			.	AL713661	CCDS42430.1, CCDS42431.1	18q21.1	2014-01-03			ENSG00000152242	ENSG00000152242			28172	protein-coding gene	gene with protein product	"""ARKadia-like 1"""					15722956	Standard	NM_001008239		Approved	MGC12909, ARKL1, RNF111L1	uc002lbw.3	Q96B23		ENST00000282059.6:c.938_940dupCTG	18.37:g.43833702_43833704dupCTG	ENSP00000282059:p.Ser313_Gly314insAla	Somatic	134	.	.		WXS	Illumina HiSeq	Phase_I	126	35	0.278	NM_145055	A8K123|A8KAB6|Q5XG78|Q6N058|Q86TB5|Q8TCQ5	In_Frame_Ins	INS	ENST00000282059.6	37	CCDS42430.1																																																																																			-|0.306;CTG|0.694	0.694	strong		0.406	C18orf25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445242.1	NM_145055	
KRTAP4-8	728224	hgsc.bcm.edu	37	17	39254335	39254336	+	Start_Codon_Ins	INS	-	-	T	rs201764113	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:39254335_39254336insT	ENST00000333822.4	-	0	57_58					NM_031960.2	NP_114166.1	Q9BYQ9	KRA48_HUMAN	keratin associated protein 4-8						aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)				endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(1)|prostate(1)	11						GGAGTTGACCATGGTGTCAGAG	0.55													T|T|TT|insertion	2826	0.564297	0.6543	0.6124	5008	,	,		18816	0.4147		0.6183	False		,,,				2504	0.5072				p.M1fs		Atlas-Indel	.											.	KRTAP4-8	57	.	0			c.2_3insA						PASS	.			2669,1587		858,953,317						3.6	1.0			26	5156,3084		1626,1904,590	no	frameshift	KRTAP4-8	NM_031960.2		2484,2857,907	A1A1,A1R,RR		37.4272,37.2885,37.38				7825,4671				SO:0001582	initiator_codon_variant	728224	exon1			.	AJ406940	CCDS45674.1	17q21.2	2013-06-25			ENSG00000204880	ENSG00000204880		"""Keratin associated proteins"""	17230	protein-coding gene	gene with protein product						11279113	Standard	NM_031960		Approved	KAP4.8	uc010wfo.2	Q9BYQ9	OTTHUMG00000133580	ENST00000333822.4:c.2dupA	17.37:g.39254336_39254336dupT		Somatic	253	0	0		WXS	Illumina HiSeq	Phase_I	169	52	0.307692	NM_031960	A8MSH3	Frame_Shift_Ins	INS	ENST00000333822.4	37	CCDS45674.1																																																																																			-|0.420;T|0.580	0.580	strong		0.550	KRTAP4-8-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257684.1	NM_031960	
HIST1H4J	8363	hgsc.bcm.edu	37	6	27792127	27792128	+	Frame_Shift_Ins	INS	-	-	CACGC			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:27792127_27792128insCACGC	ENST00000355057.1	+	1	244_245	c.225_226insCACGC	c.(226-228)cacfs	p.-77fs		NM_021968.3	NP_068803.1	P62805	H4_HUMAN	histone cluster 1, H4j						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(1)|pancreas(1)	4						CCTATACAGAGCACGCCAAGCG	0.624																																					p.E75fs		Atlas-Indel	.											HIST1H4J,NS,carcinoma,+2,1	HIST1H4J	11	1	0			c.225_226insCACGC						PASS	.																																			SO:0001589	frameshift_variant	8363	exon1			.	J00188	CCDS4630.1	6p22.1	2011-01-27	2006-10-11	2003-02-14	ENSG00000197238	ENSG00000197238		"""Histones / Replication-dependent"""	4785	protein-coding gene	gene with protein product		602826	"""H4 histone family, member E"", ""histone 1, H4j"""	H4FE		6265100, 9439656, 12408966	Standard	NM_021968		Approved	H4/e, H4F2iv	uc003njp.3	P62805	OTTHUMG00000014487	ENST00000355057.1:c.226_230dupCACGC	6.37:g.27792128_27792132dupCACGC	ENSP00000347168:p.Ala77fs	Somatic	242	0	0		WXS	Illumina HiSeq	Phase_I	199	13	0.0653266	NM_021968	A2VCL0|P02304|P02305|Q6DRA9|Q6FGB8|Q6NWP7	Frame_Shift_Ins	INS	ENST00000355057.1	37	CCDS4630.1																																																																																			.	.	none		0.624	HIST1H4J-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040155.1	NM_021968	
VWA3A	146177	hgsc.bcm.edu	37	16	22144376	22144378	+	In_Frame_Del	DEL	CCG	CCG	-	rs200086497|rs371670962		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	CCG	CCG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:22144376_22144378delCCG	ENST00000389398.5	+	20	2124_2126	c.2028_2030delCCG	c.(2026-2031)acccgg>acg	p.R677del	VWA3A_ENST00000389397.4_5'UTR	NM_173615.3	NP_775886.3	A6NCI4	VWA3A_HUMAN	von Willebrand factor A domain containing 3A	677	VWFA 1. {ECO:0000255|PROSITE- ProRule:PRU00219}.					extracellular region (GO:0005576)				haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(1)|skin(1)	7				GBM - Glioblastoma multiforme(48;0.0439)		AGGAGGTCACCCGGGCTGCAGGT	0.576																																					p.676_677del		Pindel	.											.	VWA3A	115	.	0			c.2027_2029del						PASS	.																																			SO:0001651	inframe_deletion	146177	exon20			.	AK128606, AK098260	CCDS45441.1	16p12.1	2008-02-05				ENSG00000175267			27088	protein-coding gene	gene with protein product						12477932	Standard	XM_006721021		Approved	FLJ46765, FLJ40941	uc010vbq.2	A6NCI4		ENST00000389398.5:c.2028_2030delCCG	16.37:g.22144376_22144378delCCG	ENSP00000374049:p.Arg677del	Somatic	90	.	.		WXS	Illumina HiSeq	Phase_I	71	21	0.296	NM_173615	A4QMU8|A6NNC0|Q6UTX4|Q6ZQZ9|Q8IUY6|Q8N9W1	In_Frame_Del	DEL	ENST00000389398.5	37	CCDS45441.1																																																																																			.	.	none		0.576	VWA3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430052.1		
DSPP	1834	hgsc.bcm.edu	37	4	88535832	88535833	+	In_Frame_Ins	INS	-	-	TAGCAGTGACAGCAGCAG	rs201553143|rs142316753		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:88535832_88535833insTAGCAGTGACAGCAGCAG	ENST00000282478.7	+	4	2051_2052	c.2018_2019insTAGCAGTGACAGCAGCAG	c.(2017-2022)gatagc>gaTAGCAGTGACAGCAGCAGtagc	p.680_681insSDSSSS	RP11-742B18.1_ENST00000506480.1_RNA|DSPP_ENST00000399271.1_In_Frame_Ins_p.680_681insSDSSSS			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	680	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)		gacagcagtgatagcagtgaca	0.485																																					p.D673delinsDSSDSSS		Pindel	.											.	DSPP	174	.	0			c.2018_2019insTAGCAGTGACAGCAGCAG						PASS	.																																			SO:0001652	inframe_insertion	1834	exon5			.	AF163151	CCDS43248.1	4q21.3	2008-02-05			ENSG00000152591	ENSG00000152591			3054	protein-coding gene	gene with protein product		125485		DFNA39, DGI1		8995371, 9533027	Standard	NM_014208		Approved	DMP3	uc003hqu.3	Q9NZW4	OTTHUMG00000161061	ENST00000282478.7:c.2019_2036dupTAGCAGTGACAGCAGCAG	4.37:g.88535832_88535833insTAGCAGTGACAGCAGCAG	ENSP00000282478:p.Ser675_Ser680dup	Somatic	117	.	.		WXS	Illumina HiSeq	Phase_I	109	21	0.193	NM_014208	A8MUI0|O95815	In_Frame_Ins	INS	ENST00000282478.7	37	CCDS43248.1																																																																																			.	.	alt		0.485	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208	
ACOT4	122970	hgsc.bcm.edu	37	14	74060512	74060517	+	In_Frame_Del	DEL	AGCTTA	AGCTTA	-	rs74553611|rs80196271|rs562751690|rs79684878|rs77261428|rs77814755|rs375801976|rs77408762	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	AGCTTA	AGCTTA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:74060512_74060517delAGCTTA	ENST00000326303.4	+	2	818_823	c.564_569delAGCTTA	c.(562-570)ctagcttat>ctt	p.AY189del		NM_152331.3	NP_689544.3	Q8N9L9	ACOT4_HUMAN	acyl-CoA thioesterase 4	189				ALAY -> DLQS (in Ref. 1; BAC04313). {ECO:0000305}.	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)	p.A189fs*32(2)		endometrium(1)|large_intestine(3)|lung(4)	8				BRCA - Breast invasive adenocarcinoma(234;0.00331)		CGTTGGCTCTAGCTTATTATAACTTT	0.495																																					p.188_190del		Pindel	.											.	ACOT4	25	.	2	Deletion - Frameshift(2)	large_intestine(2)	c.563_568del						PASS	.																																			SO:0001651	inframe_deletion	122970	exon2			.	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.564_569delAGCTTA	14.37:g.74060512_74060517delAGCTTA	ENSP00000323071:p.Ala189_Tyr190del	Somatic	97	.	.		WXS	Illumina HiSeq	Phase_I	85	16	0.188	NM_152331	Q17RF4|Q5BKT6|Q86TX0|Q86TX1|Q96N88	In_Frame_Del	DEL	ENST00000326303.4	37	CCDS9817.1																																																																																			.	.	alt		0.495	ACOT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404298.2	NM_152331	
RPGR	6103	hgsc.bcm.edu	37	X	38145791	38145805	+	Intron	DEL	CCTCTACTTCCCCTC	CCTCTACTTCCCCTC	-			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	CCTCTACTTCCCCTC	CCTCTACTTCCCCTC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:38145791_38145805delCCTCTACTTCCCCTC	ENST00000339363.3	-	14	2688				RPGR_ENST00000342811.3_Intron|TM4SF2_ENST00000465127.1_Intron|RPGR_ENST00000318842.7_Intron|RPGR_ENST00000378505.2_In_Frame_Del_p.GGEVE816del|RPGR_ENST00000309513.3_Intron|RPGR_ENST00000338898.3_Intron			Q92834	RPGR_HUMAN	retinitis pigmentosa GTPase regulator						cilium assembly (GO:0042384)|eye photoreceptor cell development (GO:0042462)|intracellular protein transport (GO:0006886)|intraciliary transport (GO:0042073)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|Golgi apparatus (GO:0005794)|photoreceptor outer segment (GO:0001750)|sperm flagellum (GO:0036126)	guanyl-nucleotide exchange factor activity (GO:0005085)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	25						cctttcccctcctctacttcccctccctctacttc	0.595														2	0.000529801	0.0	0.0	3775	,	,		7341	0.0		0.002	False		,,,				2504	0.0				p.816_821del		Pindel	.											.	RPGR	175	.	0			c.2448_2462del	GRCh37	CD020354	orf15	D		PASS	.		,	16,2991		1,13,1,1344,290					,	1.2	0.0			113	16,4996		3,7,3,1902,1185	no	coding,intron	RPGR	NM_001034853.1,NM_000328.2	,	4,20,4,3246,1475	A1A1,A1R,A1,RR,R		0.3192,0.5321,0.3991	,	,		32,7987				SO:0001627	intron_variant	6103	exon15			.	U57629	CCDS14246.1, CCDS35229.1	Xp11.4	2013-06-06	2004-02-13		ENSG00000156313	ENSG00000156313			10295	protein-coding gene	gene with protein product		312610	"""retinitis pigmentosa 15"", ""cone dystrophy 1 (X-linked)"""	CRD, RP3, RP15, COD1		8673101, 8817343	Standard	XM_005272633		Approved	CORDX1	uc004ded.1	Q92834	OTTHUMG00000021361	ENST00000339363.3:c.2520+541GAGGGGAAGTAGAGG>-	X.37:g.38145791_38145805delCCTCTACTTCCCCTC		Somatic	197	.	.		WXS	Illumina HiSeq	Phase_I	33	18	0.545	NM_001034853	B1ARN3|E9PE28|O00702|O00737|Q3KN84|Q8N5T6|Q93039|Q9HD29|Q9UMR1	In_Frame_Del	DEL	ENST00000339363.3	37																																																																																				.	.	none		0.595	RPGR-203	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_000328	
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-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	CTGGACCATATCCACTTACCATAAAGGAC	CTGGACCATATCCACTTACCATAAAGGAC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	157	.	.		WXS	Illumina HiSeq	Phase_I	93	19	0.204	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
SELPLG	6404	hgsc.bcm.edu	37	12	109017651	109017680	+	In_Frame_Del	DEL	GAGTGGTCTGTGCCTCCGTGGGCACTGGTT	GAGTGGTCTGTGCCTCCGTGGGCACTGGTT	-	rs200527674|rs540144714|rs368721402|rs63748999|rs372173288|rs201851784|rs377406736|rs200694582|rs200732108|rs199985195|rs558357966	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	GAGTGGTCTGTGCCTCCGTGGGCACTGGTT	GAGTGGTCTGTGCCTCCGTGGGCACTGGTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:109017651_109017680delGAGTGGTCTGTGCCTCCGTGGGCACTGGTT	ENST00000550948.1	-	2	628_657	c.404_433delAACCAGTGCCCACGGAGGCACAGACCACTC	c.(403-435)caaccagtgcccacggaggcacagaccactcca>cca	p.QPVPTEAQTT135del	SELPLG_ENST00000228463.6_In_Frame_Del_p.QPVPTEAQTT151del|SELPLG_ENST00000388962.3_Splice_Site_p.NQCPR131del			Q14242	SELPL_HUMAN	selectin P ligand	135	12 X 10 AA tandem repeats.		Missing (in short form; not an alternative splicing; dbSNP:rs63748999). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:7505206}.		blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cellular response to interleukin-6 (GO:0071354)|leukocyte adhesive activation (GO:0050902)|leukocyte migration (GO:0050900)|leukocyte tethering or rolling (GO:0050901)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)	p.Q135P(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(3)|prostate(3)|skin(1)	12						GCTGCCAGTGGAGTGGTCTGTGCCTCCGTGGGCACTGGTTGAGTGGTCTG	0.617														558	0.111422	0.0817	0.0879	5008	,	,		27757	0.13		0.0835	False		,,,				2504	0.1779				p.151_161del		Pindel	.											.	SELPLG	138	.	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.453_482del						PASS	.		,	500,3762		33,434,1664					,	-2.0	0.0		dbSNP_129	146	1398,6854		132,1134,2860	no	coding,coding	SELPLG	NM_003006.4,NM_001206609.1	,	165,1568,4524	A1A1,A1R,RR		16.9413,11.7316,15.167	,	,		1898,10616				SO:0001651	inframe_deletion	6404	exon2			.		CCDS31895.1, CCDS31895.2, CCDS55881.1	12q24	2014-01-30						"""CD molecules"", ""Endogenous ligands"""	10722	protein-coding gene	gene with protein product		600738				7505206	Standard	NM_003006		Approved	PSGL-1, CD162	uc010sxe.2	Q14242		ENST00000550948.1:c.404_433delAACCAGTGCCCACGGAGGCACAGACCACTC	12.37:g.109017651_109017680delGAGTGGTCTGTGCCTCCGTGGGCACTGGTT	ENSP00000447752:p.Gln135_Thr144del	Somatic	127	.	.		WXS	Illumina HiSeq	Phase_I	107	17	0.159	NM_001206609	A8K2Y0|B4DQC3|B7Z5C7|J3KMX6|Q12775|Q6GTW7|Q8N7J7	In_Frame_Del	DEL	ENST00000550948.1	37	CCDS31895.2																																																																																			.	.	none		0.617	SELPLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403904.1		
TMIE	259236	hgsc.bcm.edu	37	3	46751074	46751076	+	In_Frame_Del	DEL	AAG	AAG	-	rs552239745|rs397817178|rs10578999|rs372639803|rs544504092|rs538183178|rs71619660|rs75020261	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	AAG	AAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:46751074_46751076delAAG	ENST00000326431.3	+	4	522_524	c.367_369delAAG	c.(367-369)aagdel	p.K131del		NM_147196.2	NP_671729.2	Q8NEW7	TMIE_HUMAN	transmembrane inner ear	131	Lys-rich.			Missing (in Ref. 1; AAL89820 and 4; AAI26259/AAI26261). {ECO:0000305}.	inner ear morphogenesis (GO:0042472)|sensory perception of sound (GO:0007605)	integral component of membrane (GO:0016021)				endometrium(1)|lung(1)|skin(1)	3				BRCA - Breast invasive adenocarcinoma(193;0.000688)|KIRC - Kidney renal clear cell carcinoma(197;0.0177)|Kidney(197;0.0208)		CACAGAGGATaagaagaagaaga	0.502																																					p.122_123del		Pindel	.											.	TMIE	16	.	0			c.366_368del						PASS	.																																			SO:0001651	inframe_deletion	259236	exon4			.	AY081842	CCDS43081.1	3p21	2010-01-06	2004-05-19		ENSG00000181585	ENSG00000181585			30800	protein-coding gene	gene with protein product		607237	"""deafness, autosomal recessive 6"""	DFNB6		12140191, 12145746	Standard	NM_147196		Approved		uc010hjk.1	Q8NEW7	OTTHUMG00000149909	ENST00000326431.3:c.367_369delAAG	3.37:g.46751083_46751085delAAG	ENSP00000324775:p.Lys131del	Somatic	156	.	.		WXS	Illumina HiSeq	Phase_I	177	51	0.288	NM_147196	A0AV93|A8K0R0	In_Frame_Del	DEL	ENST00000326431.3	37	CCDS43081.1																																																																																			.	.	strong		0.502	TMIE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313853.1	NM_147196	
SOX2	6657	hgsc.bcm.edu	37	3	181431226	181431227	+	3'UTR	INS	-	-	A	rs201307121|rs201617684	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:181431226_181431227insA	ENST00000325404.1	+	0	1505_1506					NM_003106.3	NP_003097.1	P48431	SOX2_HUMAN	SRY (sex determining region Y)-box 2						adenohypophysis development (GO:0021984)|cell cycle arrest (GO:0007050)|cerebral cortex development (GO:0021987)|chromatin organization (GO:0006325)|detection of mechanical stimulus involved in equilibrioception (GO:0050973)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|diencephalon morphogenesis (GO:0048852)|endodermal cell fate specification (GO:0001714)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|eye development (GO:0001654)|forebrain development (GO:0030900)|forebrain neuron differentiation (GO:0021879)|glial cell fate commitment (GO:0021781)|inner ear development (GO:0048839)|inner ear morphogenesis (GO:0042472)|lens induction in camera-type eye (GO:0060235)|lung alveolus development (GO:0048286)|male genitalia development (GO:0030539)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron fate commitment (GO:0048663)|neuronal stem cell maintenance (GO:0097150)|olfactory placode formation (GO:0030910)|osteoblast differentiation (GO:0001649)|pigment biosynthetic process (GO:0046148)|pituitary gland development (GO:0021983)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of gene expression (GO:0010468)|regulation of transcription, DNA-templated (GO:0006355)|response to growth factor (GO:0070848)|response to retinoic acid (GO:0032526)|response to wounding (GO:0009611)|retina morphogenesis in camera-type eye (GO:0060042)|somatic stem cell maintenance (GO:0035019)|tongue development (GO:0043586)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear transcription factor complex (GO:0044798)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|miRNA binding (GO:0035198)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(1)|skin(1)	10	all_cancers(143;1.22e-16)|Ovarian(172;0.0283)		all cancers(12;1.82e-48)|Epithelial(37;9.85e-40)|OV - Ovarian serous cystadenocarcinoma(80;7.37e-23)|Lung(8;2.01e-21)|GBM - Glioblastoma multiforme(1;2.13e-08)			AAAGAAAAAGGAAAAAAAAAAA	0.436			A		"""NSCLC, oesophageal squamous carcinoma"""		MICROPHTHALMIA AND ESOPHAGEAL ATRESIA SYNDROME						|||unknown(HR)	501	0.10004	0.118	0.0231	5008	,	,		13728	0.246		0.0348	False		,,,				2504	0.047				.		Pindel	.		Dom	yes		3	3q26.3-q27	6657	SRY (sex determining region Y)-box 2	yes	E	.	SOX2	28	.	0			.						PASS	.																																			SO:0001624	3_prime_UTR_variant	6657	.			.	BC013923	CCDS3239.1	3q26.3-q27	2014-09-17						"""SRY (sex determining region Y)-boxes"""	11195	protein-coding gene	gene with protein product		184429				7849401	Standard	NM_003106		Approved		uc003fkx.3	P48431		ENST00000325404.1:c.*125->A	3.37:g.181431237_181431237dupA		Somatic	43	.	.		WXS	Illumina HiSeq	Phase_I	42	10	0.238	.	Q14537	RNA	INS	ENST00000325404.1	37	CCDS3239.1																																																																																			.	.	weak		0.436	SOX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350419.1	NM_003106	
OR5P2	120065	hgsc.bcm.edu	37	11	7818383	7818384	+	In_Frame_Ins	INS	-	-	ATATGGTTACCAGGTAGATGC	rs138967151	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:7818383_7818384insATATGGTTACCAGGTAGATGC	ENST00000329434.2	-	1	136_137	c.106_107insGCATCTACCTGGTAACCATAT	c.(106-108)tct>tGCATCTACCTGGTAACCATATct	p.35_36insCIYLVTI	RP11-35J10.5_ENST00000527565.1_lincRNA	NM_153444.1	NP_703145.1	Q8WZ92	OR5P2_HUMAN	olfactory receptor, family 5, subfamily P, member 2	35						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(4)	22				Epithelial(150;8.62e-08)|BRCA - Breast invasive adenocarcinoma(625;0.189)		GAGATTACCAGATAGGATGATC	0.436														1170	0.233626	0.3404	0.2896	5008	,	,		17899	0.128		0.2763	False		,,,				2504	0.1145				p.S36delinsCIYLVTIS		Pindel	.											.	OR5P2	68	.	0			c.107_108insGCATCTACCTGGTAACCATAT						PASS	.																																			SO:0001652	inframe_insertion	120065	exon1			.	AF173006	CCDS7782.1	11p15.4	2012-08-09			ENSG00000183303	ENSG00000183303		"""GPCR / Class A : Olfactory receptors"""	14783	protein-coding gene	gene with protein product							Standard	NM_153444		Approved	JCG3	uc001mfp.1	Q8WZ92	OTTHUMG00000165668	ENST00000329434.2:c.106_107insGCATCTACCTGGTAACCATAT	11.37:g.7818383_7818384insATATGGTTACCAGGTAGATGC	ENSP00000331823:p.Leu35_Ser36insCysIleTyrLeuValThrIle	Somatic	48	.	.		WXS	Illumina HiSeq	Phase_I	47	18	0.383	NM_153444	Q3MIS8	In_Frame_Ins	INS	ENST00000329434.2	37	CCDS7782.1																																																																																			.	.	strong		0.436	OR5P2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385696.1	NM_153444	
YEATS2	55689	hgsc.bcm.edu	37	3	183493744	183493746	+	In_Frame_Del	DEL	GGA	GGA	-	rs146705467|rs560342307|rs559825021	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	GGA	GGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:183493744_183493746delGGA	ENST00000305135.5	+	18	2605_2607	c.2410_2412delGGA	c.(2410-2412)ggadel	p.G814del		NM_018023.4	NP_060493.3	Q9ULM3	YETS2_HUMAN	YEATS domain containing 2	814	Gly-rich.				chromatin organization (GO:0006325)|histone H3 acetylation (GO:0043966)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)	Ada2/Gcn5/Ada3 transcription activator complex (GO:0005671)|mitotic spindle (GO:0072686)	TBP-class protein binding (GO:0017025)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(24)|ovary(3)|prostate(2)|skin(3)	49	all_cancers(143;6.55e-10)|Ovarian(172;0.0303)		all cancers(12;2.38e-42)|Epithelial(37;1.9e-36)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)			GAGTGGTGCCggaggaggaggag	0.542																																					p.803_804del		Pindel	.											YEATS2,NS,carcinoma,+2,1	YEATS2	111	1	0			c.2409_2411del						PASS	.																																			SO:0001651	inframe_deletion	55689	exon18			.	AB033023	CCDS43175.1	3q27.3	2004-08-18			ENSG00000163872	ENSG00000163872			25489	protein-coding gene	gene with protein product		613373				10574462	Standard	NM_018023		Approved	FLJ10201, FLJ12841, FLJ13308, KIAA1197	uc003fly.2	Q9ULM3	OTTHUMG00000156898	ENST00000305135.5:c.2410_2412delGGA	3.37:g.183493753_183493755delGGA	ENSP00000306983:p.Gly814del	Somatic	97	.	.		WXS	Illumina HiSeq	Phase_I	86	14	0.163	NM_018023	A7E2B9|D3DNS9|Q641P6|Q9NW96	In_Frame_Del	DEL	ENST00000305135.5	37	CCDS43175.1																																																																																			.	.	strong		0.542	YEATS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346507.2	NM_018023	
TCHH	7062	hgsc.bcm.edu	37	1	152084175	152084176	+	In_Frame_Ins	INS	-	-	TGCTGCTCGCGCCTCTCC			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:152084175_152084176insTGCTGCTCGCGCCTCTCC	ENST00000368804.1	-	2	1516_1517	c.1517_1518insGGAGAGGCGCGAGCAGCA	c.(1516-1518)caa>caGGAGAGGCGCGAGCAGCAa	p.506_506Q>QERREQQ		NM_007113.2	NP_009044.2	Q07283	TRHY_HUMAN	trichohyalin	506	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)			CCCGCCTTAGTTGCTGCTCGCG	0.644																																					p.Q506delinsQERREQQ		Pindel	.											.	TCHH	275	.	0			c.1518_1519insGGAGAGGCGCGAGCAGCA						PASS	.																																			SO:0001652	inframe_insertion	7062	exon3			.	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.1500_1517dupGGAGAGGCGCGAGCAGCA	1.37:g.152084175_152084176insTGCTGCTCGCGCCTCTCC	ENSP00000357794:p.GluArgArgGluGlnGln506dup	Somatic	123	.	.		WXS	Illumina HiSeq	Phase_I	103	19	0.184	NM_007113	Q5VUI3	In_Frame_Ins	INS	ENST00000368804.1	37	CCDS41396.1																																																																																			.	.	none		0.644	TCHH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036671.2	NM_007113	
OR51T1	401665	hgsc.bcm.edu	37	11	4903673	4903674	+	Frame_Shift_Ins	INS	-	-	ACCACCCC	rs564566592|rs137974659	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:4903673_4903674insACCACCCC	ENST00000322049.1	+	1	544_545	c.544_545insACCACCCC	c.(544-546)tacfs	p.-184fs	MMP26_ENST00000477339.1_Intron|OR51T1_ENST00000380378.1_Frame_Shift_Ins_p.-211fs|MMP26_ENST00000380390.1_Intron			Q8NGJ9	O51T1_HUMAN	olfactory receptor, family 51, subfamily T, member 1							integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(16)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	34		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;4.77e-12)|BRCA - Breast invasive adenocarcinoma(625;0.00435)|LUSC - Lung squamous cell carcinoma(625;0.19)		TCCATTTTGCTACCACCCAGAA	0.441														11	0.00219649	0.0	0.0058	5008	,	,		21558	0.0		0.007	False		,,,				2504	0.0				p.Y209fs		Pindel	.											.	OR51T1	92	.	0			c.625_626insACCACCCC						PASS	.			11,4253		0,11,2121						4.8	1.0			170	81,8171		0,81,4045	no	frameshift	OR51T1	NM_001004759.1		0,92,6166	A1A1,A1R,RR		0.9816,0.258,0.7351				92,12424				SO:0001589	frameshift_variant	401665	exon1			.	BK004283	CCDS31363.1	11p15.4	2012-08-09			ENSG00000176900	ENSG00000176900		"""GPCR / Class A : Olfactory receptors"""	15205	protein-coding gene	gene with protein product							Standard	NM_001004759		Approved		uc010qyp.2	Q8NGJ9	OTTHUMG00000066507	Exception_encountered	11.37:g.4903673_4903674insACCACCCC	ENSP00000322679:p.Pro184fs	Somatic	238	.	.		WXS	Illumina HiSeq	Phase_I	139	59	0.424	NM_001004759	Q6IFH9	Frame_Shift_Ins	INS	ENST00000322049.1	37																																																																																				.	.	none		0.441	OR51T1-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000142180.1	NM_001004759	
ZNF527	84503	hgsc.bcm.edu	37	19	37879853	37879855	+	In_Frame_Del	DEL	CAT	CAT	-	rs200420244|rs373623156|rs2385182|rs3081552|rs386809049|rs200343305|rs2891700	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	CAT	CAT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:37879853_37879855delCAT	ENST00000436120.2	+	5	1009_1011	c.902_904delCAT	c.(901-906)ccatat>cat	p.301_302PY>H	ZNF527_ENST00000587349.1_Intron	NM_032453.1	NP_115829.1	Q8NB42	ZN527_HUMAN	zinc finger protein 527	301					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(14)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	33			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			GGAGAAAAACCATATGCATGCAA	0.394																																					p.301_301del		Pindel	.											.	ZNF527	78	.	0			c.901_903del						PASS	.																																			SO:0001651	inframe_deletion	84503	exon5			.	AB058732, AK091585	CCDS42559.1	19q13.1	2013-01-08			ENSG00000189164	ENSG00000189164		"""Zinc fingers, C2H2-type"", ""-"""	29385	protein-coding gene	gene with protein product						11347906	Standard	NM_032453		Approved	KIAA1829	uc010efk.1	Q8NB42	OTTHUMG00000048173	ENST00000436120.2:c.902_904delCAT	19.37:g.37879853_37879855delCAT	ENSP00000390179:p.Pro301_Tyr302delinsHis	Somatic	119	.	.		WXS	Illumina HiSeq	Phase_I	89	24	0.270	NM_032453	B4DVL5	In_Frame_Del	DEL	ENST00000436120.2	37	CCDS42559.1																																																																																			.	.	alt		0.394	ZNF527-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458434.1	NM_032453	
CEP68	23177	hgsc.bcm.edu	37	2	65298647	65298649	+	In_Frame_Del	DEL	AAC	AAC	-	rs199636840|rs147392467	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	AAC	AAC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:65298647_65298649delAAC	ENST00000377990.2	+	3	620_622	c.417_419delAAC	c.(415-420)agaaca>aga	p.T142del	CEP68_ENST00000260569.4_In_Frame_Del_p.T142del|RAB1A_ENST00000494188.1_Intron|CEP68_ENST00000537589.1_5'UTR|CEP68_ENST00000546106.1_In_Frame_Del_p.T142del|CEP68_ENST00000497039.1_3'UTR	NM_015147.2	NP_055962.2	Q76N32	CEP68_HUMAN	centrosomal protein 68kDa	142					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						GCCTTCCCAGAACAACAACTATT	0.502														371	0.0740815	0.0681	0.0749	5008	,	,		23192	0.0		0.1233	False		,,,				2504	0.1074				p.139_140del		Pindel	.											.	CEP68	69	.	0			c.416_418del						PASS	.			372,3894		14,344,1775						1.5	0.0		dbSNP_132	95	1019,7235		59,901,3167	no	coding	CEP68	NM_015147.2		73,1245,4942	A1A1,A1R,RR		12.3455,8.7201,11.1102				1391,11129				SO:0001651	inframe_deletion	23177	exon3			.	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.417_419delAAC	2.37:g.65298653_65298655delAAC	ENSP00000367229:p.Thr142del	Somatic	207	.	.		WXS	Illumina HiSeq	Phase_I	401	137	0.342	NM_015147	B4DRQ1|D6W5F1|D6W5F2|O60326|Q9BQ18|Q9UDM9	In_Frame_Del	DEL	ENST00000377990.2	37	CCDS1880.2																																																																																			AAC|0.932;-|0.068	0.068	strong		0.502	CEP68-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251727.2	NM_015147	
PLEKHG5	57449	hgsc.bcm.edu	37	1	6529183	6529185	+	In_Frame_Del	DEL	TCC	TCC	-	rs113541584|rs375111412	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	TCC	TCC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:6529183_6529185delTCC	ENST00000400915.3	-	20	2400_2402	c.2334_2336delGGA	c.(2332-2337)gaggaa>gaa	p.778_779EE>E	PLEKHG5_ENST00000377728.3_In_Frame_Del_p.722_723EE>E|PLEKHG5_ENST00000535355.1_In_Frame_Del_p.791_792EE>E|TNFRSF25_ENST00000356876.3_5'Flank|PLEKHG5_ENST00000544978.1_In_Frame_Del_p.722_723EE>E|TNFRSF25_ENST00000351959.5_5'Flank|PLEKHG5_ENST00000400913.1_In_Frame_Del_p.722_723EE>E|TNFRSF25_ENST00000377782.3_5'Flank|PLEKHG5_ENST00000537245.1_In_Frame_Del_p.801_802EE>E|PLEKHG5_ENST00000377725.1_In_Frame_Del_p.722_723EE>E|PLEKHG5_ENST00000340850.5_In_Frame_Del_p.722_723EE>E|PLEKHG5_ENST00000377740.3_In_Frame_Del_p.799_800EE>E|PLEKHG5_ENST00000377732.1_In_Frame_Del_p.759_760EE>E|PLEKHG5_ENST00000377748.1_In_Frame_Del_p.799_800EE>E|PLEKHG5_ENST00000377737.2_In_Frame_Del_p.722_723EE>E	NM_001042663.1	NP_001036128.1	O94827	PKHG5_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 5	778	Glu-rich.			Missing (in Ref. 6; BAC77354). {ECO:0000305}.	apoptotic signaling pathway (GO:0097190)|endothelial cell chemotaxis (GO:0035767)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)|signal transducer activity (GO:0004871)			liver(1)	1	Ovarian(185;0.02)|all_lung(157;0.154)	all_cancers(23;1.7e-35)|all_epithelial(116;2.78e-22)|all_lung(118;7.57e-07)|Lung NSC(185;4.26e-06)|Colorectal(325;4.47e-05)|all_hematologic(16;0.00014)|Breast(487;0.000688)|Renal(390;0.0007)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0448)		Epithelial(90;5.51e-35)|GBM - Glioblastoma multiforme(13;3.57e-27)|Colorectal(212;6.23e-08)|COAD - Colon adenocarcinoma(227;1.33e-05)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000894)|BRCA - Breast invasive adenocarcinoma(365;0.00107)|STAD - Stomach adenocarcinoma(132;0.00159)|READ - Rectum adenocarcinoma(331;0.0419)		Gtcctcgccttcctcctcctcct	0.631														487	0.0972444	0.1906	0.0663	5008	,	,		23598	0.004		0.0646	False		,,,				2504	0.1227				p.802_802del		Pindel	.											.	PLEKHG5	66	.	0			c.2404_2406del						PASS	.																																			SO:0001651	inframe_deletion	57449	exon20			.	AK024676	CCDS79.1, CCDS41240.1, CCDS41241.1, CCDS57967.1, CCDS57968.1, CCDS57969.1	1p36.31	2014-09-17		2005-08-09	ENSG00000171680	ENSG00000171680		"""Pleckstrin homology (PH) domain containing"""	29105	protein-coding gene	gene with protein product	"""synectin-binding guanine exchange factor"""	611101				17564964	Standard	NM_001042663		Approved	KIAA0720, Syx, GEF720, Tech	uc010nzr.1	O94827	OTTHUMG00000000905	ENST00000400915.3:c.2334_2336delGGA	1.37:g.6529192_6529194delTCC	ENSP00000383706:p.Glu779del	Somatic	72	.	.		WXS	Illumina HiSeq	Phase_I	79	15	0.190	NM_001265592	B3KU07|B7Z2M3|B7Z5X2|F5GZ21|F5H1I0|Q5SY17|Q5T8W5|Q5T8W9|Q6ZNM0|Q7Z436|Q86YD8|Q96BS1	In_Frame_Del	DEL	ENST00000400915.3	37	CCDS41241.1																																																																																			TCC|0.500;-|0.500	0.500	strong		0.631	PLEKHG5-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000002631.1	NM_020631	
LOXHD1	125336	hgsc.bcm.edu	37	18	44140280	44140282	+	In_Frame_Del	DEL	TCT	TCT	-	rs142960762		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	TCT	TCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:44140280_44140282delTCT	ENST00000398722.4	-	12	1990_1992	c.1991_1993delAGA	c.(1990-1995)aagagg>agg	p.K664del	LOXHD1_ENST00000300591.6_5'Flank|LOXHD1_ENST00000441551.2_Intron|LOXHD1_ENST00000536736.1_In_Frame_Del_p.K942del|LOXHD1_ENST00000582408.1_5'Flank|LOXHD1_ENST00000441893.2_5'Flank			Q8IVV2	LOXH1_HUMAN	lipoxygenase homology domains 1	664					calcium ion transmembrane transport (GO:0070588)|detection of mechanical stimulus (GO:0050982)|sensory perception of sound (GO:0007605)	membrane (GO:0016020)|stereocilium (GO:0032420)	calcium channel activity (GO:0005262)			NS(3)|autonomic_ganglia(1)|breast(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|lung(2)|pancreas(1)|prostate(4)|skin(4)|stomach(1)	36						ctgcccttcctcttcttcttctt	0.591																																					p.942_943del		Pindel	.											.	LOXHD1	367	.	0			c.2826_2828del						PASS	.			51,3765		11,29,1868						1.2	0.6		dbSNP_134	90	184,6944		23,138,3403	no	coding	LOXHD1	NM_144612.6		34,167,5271	A1A1,A1R,RR		2.5814,1.3365,2.1473				235,10709				SO:0001651	inframe_deletion	125336	exon19			.	AK057232	CCDS45861.1, CCDS45862.1, CCDS54184.1	18q21.1	2009-09-11			ENSG00000167210	ENSG00000167210			26521	protein-coding gene	gene with protein product		613072	"""deafness, autosomal recessive 77"""	DFNB77		19732867	Standard	NM_144612		Approved	FLJ32670, LH2D1	uc010xcw.1	Q8IVV2	OTTHUMG00000132644	ENST00000398722.4:c.1991_1993delAGA	18.37:g.44140289_44140291delTCT	ENSP00000381707:p.Lys664del	Somatic	96	.	.		WXS	Illumina HiSeq	Phase_I	91	27	0.297	NM_144612	B7WNN3|B7WNT1|B7WPI9|Q6ZRY7|Q86WW9|Q96DL7	In_Frame_Del	DEL	ENST00000398722.4	37																																																																																				TCT|0.982;-|0.018	0.018	strong		0.591	LOXHD1-201	KNOWN	basic	protein_coding	protein_coding		NM_144612	
CASP8AP2	9994	hgsc.bcm.edu	37	6	90577707	90577728	+	RNA	DEL	GACATCTTTGCCCAGACATGGA	GACATCTTTGCCCAGACATGGA	-	rs202101805|rs202111256|rs201189413|rs199515704|rs202116886|rs539529375|rs200213073|rs537929246|rs527250207|rs200862023|rs199694900|rs201534830	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	GACATCTTTGCCCAGACATGGA	GACATCTTTGCCCAGACATGGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	76	.	.		WXS	Illumina HiSeq	Phase_I	59	25	0.424	NM_012115		Frame_Shift_Del	DEL	ENST00000551025.1	37																																																																																				.	.	alt		0.374	CASP8AP2-202	KNOWN	basic	processed_transcript	processed_transcript		NM_001137667	
RPTN	126638	hgsc.bcm.edu	37	1	152129066	152129101	+	In_Frame_Del	DEL	TGGTGGGAATCTCTGTCTTGTTTCTCAGACTGACCA	TGGTGGGAATCTCTGTCTTGTTTCTCAGACTGACCA	-	rs369805852|rs78544048|rs375710188|rs368770198|rs200003389|rs117596468|rs76015112|rs199889562	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	TGGTGGGAATCTCTGTCTTGTTTCTCAGACTGACCA	TGGTGGGAATCTCTGTCTTGTTTCTCAGACTGACCA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:152129066_152129101delTGGTGGGAATCTCTGTCTTGTTTCTCAGACTGACCA	ENST00000316073.3	-	3	538_573	c.474_509delTGGTCAGTCTGAGAAACAAGACAGAGATTCCCACCA	c.(472-510)catggtcagtctgagaaacaagacagagattcccaccac>cac	p.158_170HGQSEKQDRDSHH>H		NM_001122965.1	NP_001116437.1	Q6XPR3	RPTN_HUMAN	repetin	158	Gln-rich.					cornified envelope (GO:0001533)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)	p.G159_H170delGQSEKQDRDSHH(1)|p.S168>?(1)		breast(2)|central_nervous_system(1)|endometrium(14)|kidney(2)|large_intestine(1)|lung(32)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	59						AGGCTGACTGTGGTGGGAATCTCTGTCTTGTTTCTCAGACTGACCATGGTGGGAAT	0.492																																					p.159_170del		Pindel	.											.	RPTN	123	.	2	Complex(1)|Deletion - In frame(1)	stomach(1)|skin(1)	c.475_510del						PASS	.																																			SO:0001651	inframe_deletion	126638	exon3			.	AK096436	CCDS41397.1	1q21.3	2013-01-10			ENSG00000215853	ENSG00000215853		"""EF-hand domain containing"""	26809	protein-coding gene	gene with protein product		613259				15854042	Standard	NM_001122965		Approved	FLJ39117	uc001ezs.1	Q6XPR3	OTTHUMG00000154095	ENST00000316073.3:c.474_509delTGGTCAGTCTGAGAAACAAGACAGAGATTCCCACCA	1.37:g.152129066_152129101delTGGTGGGAATCTCTGTCTTGTTTCTCAGACTGACCA	ENSP00000317895:p.His158_His169del	Somatic	285	.	.		WXS	Illumina HiSeq	Phase_I	192	36	0.188	NM_001122965	B7ZBZ3	In_Frame_Del	DEL	ENST00000316073.3	37	CCDS41397.1																																																																																			.	.	none		0.492	RPTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333867.1	XM_371312	
SPRR1B	6699	hgsc.bcm.edu	37	1	153004942	153005013	+	In_Frame_Del	DEL	TGCCACCCCAAGGTGCCTGAGCCCTGCCACCCCAAAGTGCCCGAGCCCTGCCAGCCCAAGGTTCCAGAGCCA	TGCCACCCCAAGGTGCCTGAGCCCTGCCACCCCAAAGTGCCCGAGCCCTGCCAGCCCAAGGTTCCAGAGCCA	-	rs2339500|rs145337134|rs201925274|rs367847286|rs12195|rs368848590|rs200829544|rs551505658	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	TGCCACCCCAAGGTGCCTGAGCCCTGCCACCCCAAAGTGCCCGAGCCCTGCCAGCCCAAGGTTCCAGAGCCA	TGCCACCCCAAGGTGCCTGAGCCCTGCCACCCCAAAGTGCCCGAGCCCTGCCAGCCCAAGGTTCCAGAGCCA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:153004942_153005013delTGCCACCCCAAGGTGCCTGAGCCCTGCCACCCCAAAGTGCCCGAGCCCTGCCAGCCCAAGGTTCCAGAGCCA	ENST00000307098.4	+	2	186_257	c.121_192delTGCCACCCCAAGGTGCCTGAGCCCTGCCACCCCAAAGTGCCCGAGCCCTGCCAGCCCAAGGTTCCAGAGCCA	c.(121-192)tgccaccccaaggtgcctgagccctgccaccccaaagtgcccgagccctgccagcccaaggttccagagccadel	p.CHPKVPEPCHPKVPEPCQPKVPEP41del	SPRR1B_ENST00000392661.3_Splice_Site_p.CHPKVPEPCHPK41del	NM_003125.2	NP_003116.2	P22528	SPR1B_HUMAN	small proline-rich protein 1B	41	6 X 8 AA approximate tandem repeats.				epidermis development (GO:0008544)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	protein binding, bridging (GO:0030674)|structural molecule activity (GO:0005198)	p.C41_P64delCHPKVPEPCHPKVPEPCQPKVPEP(1)|p.P43A(1)		breast(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|ovary(2)|skin(2)	9	Lung NSC(65;1.49e-28)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			CAAGGAGCCCTGCCACCCCAAGGTGCCTGAGCCCTGCCACCCCAAAGTGCCCGAGCCCTGCCAGCCCAAGGTTCCAGAGCCATGCCACCCCA	0.621																																					p.40_64del		Pindel	.											.	SPRR1B	18	.	2	Substitution - Missense(1)|Deletion - In frame(1)	ovary(1)|haematopoietic_and_lymphoid_tissue(1)	c.120_191del						PASS	.																																			SO:0001651	inframe_deletion	6699	exon2			.	M84757	CCDS30863.1	1q21-q22	2010-06-25	2010-06-25		ENSG00000169469	ENSG00000169469			11260	protein-coding gene	gene with protein product	"""cornifin"""	182266		SPRR1		8325635, 1438308	Standard	NM_003125		Approved	GADD33	uc001fba.3	P22528	OTTHUMG00000013869	ENST00000307098.4:c.121_192delTGCCACCCCAAGGTGCCTGAGCCCTGCCACCCCAAAGTGCCCGAGCCCTGCCAGCCCAAGGTTCCAGAGCCA	1.37:g.153004942_153005013delTGCCACCCCAAGGTGCCTGAGCCCTGCCACCCCAAAGTGCCCGAGCCCTGCCAGCCCAAGGTTCCAGAGCCA	ENSP00000306461:p.Cys41_Pro64del	Somatic	104	.	.		WXS	Illumina HiSeq	Phase_I	78	23	0.295	NM_003125	B2R5H7|P22529|P22530|Q5T524	In_Frame_Del	DEL	ENST00000307098.4	37	CCDS30863.1																																																																																			.	.	none		0.621	SPRR1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038906.1	NM_003125	
ASPN	54829	hgsc.bcm.edu	37	9	95237025	95237027	+	In_Frame_Del	DEL	TCA	TCA	-	rs200538582|rs397840756|rs557103556|rs3078372|rs397838876		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	TCA	TCA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:95237025_95237027delTCA	ENST00000375544.3	-	2	396_398	c.153_155delTGA	c.(151-156)gatgag>gag	p.D51del	CENPP_ENST00000375587.3_Intron|ASPN_ENST00000450139.2_In_Frame_Del_p.D23del|ASPN_ENST00000395538.3_In_Frame_Del_p.D51del|ASPN_ENST00000375543.1_In_Frame_Del_p.D51del	NM_017680.4	NP_060150	Q9BXN1	ASPN_HUMAN	asporin	51	Poly-Asp.				bone mineralization (GO:0030282)|negative regulation of tooth mineralization (GO:0070171)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)	proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(1)|skin(1)	9						AGAGTTGTCCtcatcatcatcat	0.394																																					p.52_52del		Pindel	.											.	ASPN	52	.	0			c.154_156del						PASS	.																																			SO:0001651	inframe_deletion	54829	exon2			.	AF316824		9q22.31	2008-05-14	2007-02-15		ENSG00000106819	ENSG00000106819		"""Proteoglycans / Extracellular Matrix : Small leucine-rich repeats"""	14872	protein-coding gene	gene with protein product	"""asporin proteoglycan"""	608135	"""asporin (LRR class 1)"""				Standard	NM_017680		Approved	FLJ20129, SLRR1C, PLAP1	uc004ase.2	Q9BXN1	OTTHUMG00000020227	ENST00000375544.3:c.153_155delTGA	9.37:g.95237034_95237036delTCA	ENSP00000364694:p.Asp51del	Somatic	135	.	.		WXS	Illumina HiSeq	Phase_I	100	31	0.310	NM_001193335	Q5TBF3|Q96K79|Q96LD0|Q9NXP3	In_Frame_Del	DEL	ENST00000375544.3	37																																																																																				TCA|0.500;-|0.500	0.500	strong		0.394	ASPN-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000053094.1	NM_017680	
SH3BGR	6450	hgsc.bcm.edu	37	21	40883671	40883672	+	In_Frame_Ins	INS	-	-	AGA	rs111921581|rs397694871|rs3831201|rs77389080	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:40883671_40883672insAGA	ENST00000333634.4	+	6	767_768	c.689_690insAGA	c.(688-693)ggagaa>ggAGAagaa	p.232_233insE	SH3BGR_ENST00000380631.1_In_Frame_Ins_p.121_122insE|SH3BGR_ENST00000380634.1_In_Frame_Ins_p.121_122insE|SH3BGR_ENST00000458295.1_In_Frame_Ins_p.90_91insE|SH3BGR_ENST00000380637.3_In_Frame_Ins_p.121_122insE	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	.											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	81	.	.		WXS	Illumina HiSeq	Phase_I	82	55	0.671	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	
MAML2	84441	hgsc.bcm.edu	37	11	95825375	95825383	+	In_Frame_Del	DEL	TGCTGCTGC	TGCTGCTGC	-	rs539857207|rs113349418|rs543548810|rs572830140|rs141671766|rs60727839	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	TGCTGCTGC	TGCTGCTGC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:95825375_95825383delTGCTGCTGC	ENST00000524717.1	-	2	3096_3104	c.1812_1820delGCAGCAGCA	c.(1810-1821)cagcagcagcaa>caa	p.604_607QQQQ>Q		NM_032427.1	NP_115803.1	Q8IZL2	MAML2_HUMAN	mastermind-like 2 (Drosophila)	604					gene expression (GO:0010467)|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)	Golgi apparatus (GO:0005794)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)		CRTC3/MAML2(26)|CRTC1/MAML2(516)	breast(2)|cervix(1)|endometrium(11)|kidney(4)|large_intestine(8)|lung(12)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	43		Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837)				ctgctgctgttgctgctgctgctgctgct	0.531			T	"""MECT1, CRTC3"""	salivary gland mucoepidermoid									4203	0.839257	0.7542	0.8862	5008	,	,		16018	0.8829		0.8151	False		,,,				2504	0.9008				p.605_607del		Pindel	.		Dom	yes		11	11q22-q23	84441	mastermind-like 2 (Drosophila)		E	MAML2,NS,carcinoma,0,1	MAML2	94	1	0			c.1813_1821del						PASS	.																																			SO:0001651	inframe_deletion	84441	exon2			.	AB058722	CCDS44714.1	11q	2008-02-05	2001-11-28		ENSG00000184384	ENSG00000184384			16259	protein-coding gene	gene with protein product		607537	"""mastermind (Drosophila)-like 2"""			12370315, 12386158	Standard	NM_032427		Approved	KIAA1819, MAM3	uc001pfw.1	Q8IZL2	OTTHUMG00000167677	ENST00000524717.1:c.1812_1820delGCAGCAGCA	11.37:g.95825384_95825392delTGCTGCTGC	ENSP00000434552:p.Gln619_Gln621del	Somatic	114	.	.		WXS	Illumina HiSeq	Phase_I	95	19	0.200	NM_032427	A7MD26|Q6AI23|Q6Y3A3|Q8IUL3|Q96JK6	In_Frame_Del	DEL	ENST00000524717.1	37	CCDS44714.1																																																																																			.	.	strong		0.531	MAML2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395540.1		
GPRIN1	114787	hgsc.bcm.edu	37	5	176026115	176026138	+	In_Frame_Del	DEL	CCTTTCTCAAAGACCCAGGATCCT	CCTTTCTCAAAGACCCAGGATCCT	-	rs3797464|rs200519605|rs386695335|rs550332435|rs142779818|rs371149640|rs199714570|rs373697082|rs201635586	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	CCTTTCTCAAAGACCCAGGATCCT	CCTTTCTCAAAGACCCAGGATCCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:176026115_176026138delCCTTTCTCAAAGACCCAGGATCCT	ENST00000303991.4	-	2	875_898	c.698_721delAGGATCCTGGGTCTTTGAGAAAGG	c.(697-723)gaggatcctgggtctttgagaaaggtg>gtg	p.EDPGSLRK233del		NM_052899.2	NP_443131.2	Q7Z2K8	GRIN1_HUMAN	G protein regulated inducer of neurite outgrowth 1	233				Missing (in Ref. 4; CAD38868). {ECO:0000305}.	neuron projection development (GO:0031175)	cell projection (GO:0042995)|plasma membrane (GO:0005886)		p.L238L(1)		NS(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(3)|liver(1)|lung(15)|ovary(2)|prostate(5)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	35	all_cancers(89;0.00263)|Renal(175;0.000269)|Lung NSC(126;0.00902)|all_lung(126;0.0142)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			ACAGGATCCACCTTTCTCAAAGACCCAGGATCCTCCTTCCTCGG	0.496																																					p.233_241del		Pindel	.											.	GPRIN1	77	.	1	Substitution - coding silent(1)	lung(1)	c.699_722del						PASS	.																																			SO:0001651	inframe_deletion	114787	exon2			.	AB067480	CCDS4405.1	5q35.2	2008-02-05			ENSG00000169258	ENSG00000169258			24835	protein-coding gene	gene with protein product		611239				11572484	Standard	NM_052899		Approved	GRIN1, KIAA1893	uc003meo.1	Q7Z2K8	OTTHUMG00000130659	ENST00000303991.4:c.698_721delAGGATCCTGGGTCTTTGAGAAAGG	5.37:g.176026115_176026138delCCTTTCTCAAAGACCCAGGATCCT	ENSP00000305839:p.Glu233_Lys240del	Somatic	168	.	.		WXS	Illumina HiSeq	Phase_I	168	48	0.286	NM_052899	C9JM70|Q8ND74|Q96PZ4	In_Frame_Del	DEL	ENST00000303991.4	37	CCDS4405.1																																																																																			.	.	none		0.496	GPRIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253149.1	NM_052899	
LCE1F	353137	hgsc.bcm.edu	37	1	152749008	152749009	+	In_Frame_Ins	INS	-	-	CAGCTCTGGGGGCTGCTG	rs544759833|rs200931119	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:152749008_152749009insCAGCTCTGGGGGCTGCTG	ENST00000334371.2	+	1	161_162	c.161_162insCAGCTCTGGGGGCTGCTG	c.(160-165)tccagc>tcCAGCTCTGGGGGCTGCTGcagc	p.61_62insSGGCCS		NM_178354.2	NP_848131.1	Q5T754	LCE1F_HUMAN	late cornified envelope 1F	61					keratinization (GO:0031424)					kidney(1)|large_intestine(2)|lung(7)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	15	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)			TGCTGTGGCTCCAGCTCTGGGG	0.683																																					p.S54delinsSSSGGCC		Pindel	.											LCE1F,colon,carcinoma,0,2	LCE1F	42	2	0			c.161_162insCAGCTCTGGGGGCTGCTG						PASS	.																																			SO:0001652	inframe_insertion	353137	exon1			.		CCDS1023.1	1q21.3	2008-02-05			ENSG00000240386	ENSG00000240386		"""Late cornified envelopes"""	29467	protein-coding gene	gene with protein product		612608				11698679	Standard	NM_178354		Approved	LEP6	uc010pdv.2	Q5T754	OTTHUMG00000012403	ENST00000334371.2:c.162_179dupCAGCTCTGGGGGCTGCTG	1.37:g.152749008_152749009insCAGCTCTGGGGGCTGCTG	ENSP00000334187:p.Ser56_Ser61dup	Somatic	88	.	.		WXS	Illumina HiSeq	Phase_I	100	17	0.170	NM_178354		In_Frame_Ins	INS	ENST00000334371.2	37	CCDS1023.1																																																																																			.	.	none		0.683	LCE1F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034523.2	NM_178354	
TEKT4	150483	hgsc.bcm.edu	37	2	95537380	95537381	+	Frame_Shift_Ins	INS	-	-	T	rs150741943|rs79003945		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:95537380_95537381insT	ENST00000295201.4	+	1	193_194	c.56_57insT	c.(55-60)cgtaacfs	p.N20fs	TEKT4_ENST00000427593.2_Frame_Shift_Ins_p.N20fs|AC097374.2_ENST00000568768.1_RNA	NM_144705.2	NP_653306.1	Q8WW24	TEKT4_HUMAN	tektin 4	20					cell projection organization (GO:0030030)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|motile cilium (GO:0031514)|nucleus (GO:0005634)				NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(15)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	28						GACGTGGCCCGTAACACGGGCG	0.663																																					p.R19fs		Pindel	.											.	TEKT4	72	.	0			c.56_57insT						PASS	.			0,4178		0,0,2089						1.9	0.8			20	2,8078		0,2,4038	no	frameshift	TEKT4	NM_144705.2		0,2,6127	A1A1,A1R,RR		0.0248,0.0,0.0163				2,12256				SO:0001589	frameshift_variant	150483	exon1			.	AK097438	CCDS2005.1	2q11.2	2008-02-05			ENSG00000163060	ENSG00000163060			31012	protein-coding gene	gene with protein product							Standard	XM_005263876		Approved	MGC27019	uc002stw.1	Q8WW24	OTTHUMG00000130396	ENST00000295201.4:c.57dupT	2.37:g.95537381_95537381dupT	ENSP00000295201:p.Asn20fs	Somatic	112	.	.		WXS	Illumina HiSeq	Phase_I	85	21	0.247	NM_144705		Frame_Shift_Ins	INS	ENST00000295201.4	37	CCDS2005.1																																																																																			.	.	none		0.663	TEKT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252777.1	NM_144705	
TMEM255B	348013	hgsc.bcm.edu	37	13	114503876	114503957	+	Splice_Site	DEL	CCTGCGGGAGGTGAGGGGCACCGGGGACCCCCATATCTACACCTGCGGGAGGTGAGGGGCGCTGGGGACCCCCGTATCTACA	CCTGCGGGAGGTGAGGGGCACCGGGGACCCCCATATCTACACCTGCGGGAGGTGAGGGGCGCTGGGGACCCCCGTATCTACA	-	rs9577890|rs76163514|rs111667140|rs41284484|rs41284485|rs144347748|rs9577889|rs79620376|rs114746443|rs41284483|rs66696122|rs371072437|rs553476183|rs148763547|rs371342802|rs115620789|rs550352190|rs575880631|rs386775130|rs372249488	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	CCTGCGGGAGGTGAGGGGCACCGGGGACCCCCATATCTACACCTGCGGGAGGTGAGGGGCGCTGGGGACCCCCGTATCTACA	CCTGCGGGAGGTGAGGGGCACCGGGGACCCCCATATCTACACCTGCGGGAGGTGAGGGGCGCTGGGGACCCCCGTATCTACA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:114503876_114503957delCCTGCGGGAGGTGAGGGGCACCGGGGACCCCCATATCTACACCTGCGGGAGGTGAGGGGCGCTGGGGACCCCCGTATCTACA	ENST00000375353.3	+	6	527_536	c.500_509delCCTGCGGGAGGTGAGGGGCACCGGGGACCCCCATATCTACACCTGCGGGAGGTGAGGGGCGCTGGGGACCCCCGTATCTACA	c.(499-510)gcctgcgggagg>gg	p.ACGR167fs		NM_182614.2	NP_872420.1	Q8WV15	T255B_HUMAN	transmembrane protein 255B	167						integral component of membrane (GO:0016021)											GACCTCTATGCCTGCGGGAGGTGAGGGGCACCGGGGACCCCCATATCTACACCTGCGGGAGGTGAGGGGCGCTGGGGACCCCCGTATCTACACCTGCGGGAG	0.652																																					p.167_170del		Pindel	.											.	.	.	.	0			c.499_509del						PASS	.			409,860,2993		20,66,303,99,596,1047						-3.0	0.0		dbSNP_130	62	1222,24,7006		90,3,1039,0,21,2973	no	codingComplex	FAM70B	NM_182614.2		110,69,1342,99,617,4020	A1A1,A1A2,A1R,A2A2,A2R,RR		15.0994,29.7748,20.0975				1631,884,9999				SO:0001630	splice_region_variant	348013	exon6			.	BC018995	CCDS45071.1	13q34	2012-11-30	2012-11-30	2012-11-30	ENSG00000184497	ENSG00000184497			28297	protein-coding gene	gene with protein product			"""family with sequence similarity 70, member B"""	FAM70B		12477932	Standard	NM_182614		Approved	MGC20579	uc001vuh.3	Q8WV15	OTTHUMG00000017398	ENST00000375353.3:c.509+1CCTGCGGGAGGTGAGGGGCACCGGGGACCCCCATATCTACACCTGCGGGAGGTGAGGGGCGCTGGGGACCCCCGTATCTACA>-	13.37:g.114503876_114503957delCCTGCGGGAGGTGAGGGGCACCGGGGACCCCCATATCTACACCTGCGGGAGGTGAGGGGCGCTGGGGACCCCCGTATCTACA		Somatic	117	.	.		WXS	Illumina HiSeq	Phase_I	98	25	0.255	NM_182614		Frame_Shift_Del	DEL	ENST00000375353.3	37	CCDS45071.1																																																																																			.	.	none		0.652	TMEM255B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045953.4	NM_182614	Frame_Shift_Del
SIPA1	6494	hgsc.bcm.edu	37	11	65412467	65412467	+	Silent	SNP	G	G	A	rs2306364	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:65412467G>A	ENST00000394224.3	+	5	1322	c.1026G>A	c.(1024-1026)gcG>gcA	p.A342A	SIPA1_ENST00000534313.1_Silent_p.A342A|SIPA1_ENST00000394227.3_Silent_p.A342A|SIPA1_ENST00000527525.1_Silent_p.A342A	NM_153253.29	NP_694985.29	Q96FS4	SIPA1_HUMAN	signal-induced proliferation-associated 1	342	Rap-GAP. {ECO:0000255|PROSITE- ProRule:PRU00165}.				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						ACTGCCGGGCGGGCCAGGGCT	0.632													G|||	1770	0.353435	0.3321	0.2579	5008	,	,		17424	0.251		0.4364	False		,,,				2504	0.4703				p.A342A		Atlas-SNP	.											.	SIPA1	45	.	0			c.G1026A						PASS	.	G	,	1478,2924	475.5+/-357.3	251,976,974	92.0	93.0	93.0		1026,1026	-9.6	0.4	11	dbSNP_100	93	3605,4989	520.5+/-379.7	749,2107,1441	no	coding-synonymous,coding-synonymous	SIPA1	NM_006747.3,NM_153253.29	,	1000,3083,2415	AA,AG,GG		41.9479,33.5756,39.112	,	342/1043,342/1043	65412467	5083,7913	2201	4297	6498	SO:0001819	synonymous_variant	6494	exon5			CCGGGCGGGCCAG	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.1026G>A	11.37:g.65412467G>A		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	110	24	0.218182	NM_006747	O14518|O60484|O60618|Q2YD83	Silent	SNP	ENST00000394224.3	37	CCDS8108.1																																																																																			G|0.637;A|0.363	0.363	strong		0.632	SIPA1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390356.1	NM_006747	
MUC16	94025	hgsc.bcm.edu	37	19	8999044	8999044	+	Silent	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:8999044G>A	ENST00000397910.4	-	57	41003	c.40800C>T	c.(40798-40800)agC>agT	p.S13600S	MUC16_ENST00000380951.5_Silent_p.S241S	NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	13602				Missing (in Ref. 3; AAK74120). {ECO:0000305}.	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						TGGGCACAGAGCTCCGCTGTG	0.547																																					p.S13600S		Atlas-SNP	.											.	MUC16	4315	.	0			c.C40800T						PASS	.						71.0	71.0	71.0					19																	8999044		1988	4149	6137	SO:0001819	synonymous_variant	94025	exon57			CACAGAGCTCCGC	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.40800C>T	19.37:g.8999044G>A		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	100	22	0.22	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	37	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	.	1.631	-0.518888	0.04171	.	.	ENSG00000181143	ENST00000542240	.	.	.	1.04	1.04	0.20106	.	.	.	.	.	T	0.37348	0.1000	.	.	.	.	.	.	.	.	.	.	.	.	T	0.43523	-0.9386	3	.	.	.	.	5.4159	0.16374	0.0:0.0:1.0:0.0	.	.	.	.	V	440	.	.	A	-	2	0	MUC16	8860044	0.000000	0.05858	0.001000	0.08648	0.003000	0.03518	-1.186000	0.03070	0.865000	0.35603	0.455000	0.32223	GCT	.	.	none		0.547	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
VILL	50853	hgsc.bcm.edu	37	3	38038982	38038982	+	Silent	SNP	T	T	C	rs6809649	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:38038982T>C	ENST00000283713.6	+	7	836	c.570T>C	c.(568-570)gcT>gcC	p.A190A	VILL_ENST00000383759.2_Silent_p.A190A|VILL_ENST00000465644.1_Intron			O15195	VILL_HUMAN	villin-like	190					actin filament capping (GO:0051693)|cytoskeleton organization (GO:0007010)	actin cytoskeleton (GO:0015629)	structural constituent of cytoskeleton (GO:0005200)			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)		AGGGGCTGGCTTTGACCTACA	0.607													C|||	1182	0.236022	0.4304	0.1398	5008	,	,		18461	0.0863		0.1441	False		,,,				2504	0.2904				p.A190A		Atlas-SNP	.											.	VILL	61	.	0			c.T570C						PASS	.	C		1760,2646	641.1+/-397.4	346,1068,789	62.0	61.0	61.0		570	3.5	0.7	3	dbSNP_116	61	1488,7112	747.8+/-407.3	125,1238,2937	no	coding-synonymous	VILL	NM_015873.3		471,2306,3726	CC,CT,TT		17.3023,39.9455,24.9731		190/857	38038982	3248,9758	2203	4300	6503	SO:0001819	synonymous_variant	50853	exon6			GCTGGCTTTGACC		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.570T>C	3.37:g.38038982T>C		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	65	65	1	NM_015873	A8MZP1|Q9BT80|Q9BWH7	Silent	SNP	ENST00000283713.6	37	CCDS2670.2																																																																																			T|0.768;C|0.232	0.232	strong		0.607	VILL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253360.3	NM_015873	
TNFRSF10A	8797	hgsc.bcm.edu	37	8	23059324	23059324	+	Missense_Mutation	SNP	C	C	G	rs20575	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:23059324C>G	ENST00000221132.3	-	4	690	c.626G>C	c.(625-627)aGa>aCa	p.R209T		NM_003844.3	NP_003835.3	O00220	TR10A_HUMAN	tumor necrosis factor receptor superfamily, member 10a	209			R -> T (in dbSNP:rs20575). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:9082980}.		activation of NF-kappaB-inducing kinase activity (GO:0007250)|apoptotic process (GO:0006915)|cellular response to mechanical stimulus (GO:0071260)|extrinsic apoptotic signaling pathway (GO:0097191)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|signal transduction (GO:0007165)|TRAIL-activated apoptotic signaling pathway (GO:0036462)	integral component of membrane (GO:0016021)	death receptor activity (GO:0005035)|protease binding (GO:0002020)|receptor activity (GO:0004872)|TRAIL binding (GO:0045569)|transcription factor binding (GO:0008134)			NS(2)|central_nervous_system(3)|endometrium(2)|large_intestine(3)|lung(1)|ovary(3)|prostate(1)|skin(1)	16		Prostate(55;0.0421)|Breast(100;0.14)		Colorectal(74;0.016)|COAD - Colon adenocarcinoma(73;0.0646)		GTCTCACCCTCTGCTGCACTT	0.532													G|||	2902	0.579473	0.2769	0.6138	5008	,	,		17637	0.9732		0.4553	False		,,,				2504	0.6861				p.R209T		Atlas-SNP	.											.	TNFRSF10A	40	.	0			c.G626C						PASS	.	G	THR/ARG	1393,3013	689.0+/-405.1	205,983,1015	90.0	71.0	77.0		626	0.2	0.0	8	dbSNP_67	77	3944,4656	602.3+/-394.5	924,2096,1280	yes	missense	TNFRSF10A	NM_003844.3	71	1129,3079,2295	GG,GC,CC		45.8605,31.616,41.0349	benign	209/469	23059324	5337,7669	2203	4300	6503	SO:0001583	missense	8797	exon4			CACCCTCTGCTGC	U90875	CCDS6039.1	8p21	2006-02-22			ENSG00000104689	ENSG00000104689		"""Tumor necrosis factor receptor superfamily"", ""CD molecules"""	11904	protein-coding gene	gene with protein product		603611				9311998, 9082980	Standard	NM_003844		Approved	DR4, Apo2, TRAILR-1, CD261	uc003xda.3	O00220	OTTHUMG00000097843	ENST00000221132.3:c.626G>C	8.37:g.23059324C>G	ENSP00000221132:p.Arg209Thr	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	73	19	0.260274	NM_003844	A8K5I4|Q53Y72|Q96E62	Missense_Mutation	SNP	ENST00000221132.3	37	CCDS6039.1	1249	0.5718864468864469	129	0.2621951219512195	210	0.580110497237569	561	0.9807692307692307	349	0.4604221635883905	G	0.019	-1.462074	0.01062	0.31616	0.458605	ENSG00000104689	ENST00000221132;ENST00000524158	D;T	0.90620	-2.7;1.75	4.2	0.222	0.15288	TNFR/CD27/30/40/95 cysteine-rich region (4);	0.747139	0.11590	N	0.548796	T	0.00012	0.0000	N	0.00043	-2.47	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.38499	-0.9658	9	0.02654	T	1	.	4.4761	0.11745	0.2821:0.3084:0.4095:0.0	rs20575;rs4871857;rs11550539;rs17398665;rs17759966;rs52835905;rs60716604;rs4871857	209	O00220	TR10A_HUMAN	T	209;7	ENSP00000221132:R209T;ENSP00000428884:R7T	ENSP00000221132:R209T	R	-	2	0	TNFRSF10A	23115269	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.139000	0.10358	-0.547000	0.06207	-0.738000	0.03535	AGA	C|0.521;G|0.478	0.478	strong		0.532	TNFRSF10A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215133.2	NM_003844	
NUDCD3	23386	hgsc.bcm.edu	37	7	44530193	44530193	+	Missense_Mutation	SNP	T	T	G	rs307007	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:44530193T>G	ENST00000355451.7	-	1	286	c.7A>C	c.(7-9)Aca>Cca	p.T3P		NM_015332.3	NP_056147.2	Q8IVD9	NUDC3_HUMAN	NudC domain containing 3	3			T -> P (in dbSNP:rs307007). {ECO:0000269|PubMed:15489334}.							endometrium(2)|large_intestine(1)|lung(3)|skin(1)	7						GCCGCCCCTGTCTCCATGTCG	0.657													G|||	822	0.164137	0.3041	0.1427	5008	,	,		14436	0.005		0.1928	False		,,,				2504	0.1247				p.T3P		Atlas-SNP	.											.	NUDCD3	20	.	0			c.A7C						PASS	.	G	PRO/THR	1182,3014		177,828,1093	21.0	27.0	25.0		7	4.4	1.0	7	dbSNP_79	25	1822,6632		209,1404,2614	yes	missense	NUDCD3	NM_015332.3	38	386,2232,3707	GG,GT,TT		21.5519,28.1697,23.747	benign	3/362	44530193	3004,9646	2098	4227	6325	SO:0001583	missense	23386	exon1			CCCCTGTCTCCAT	BC003691	CCDS5490.2	7p13-p12	2005-03-18			ENSG00000015676	ENSG00000015676			22208	protein-coding gene	gene with protein product		610296					Standard	NM_015332		Approved	KIAA1068	uc003tkz.3	Q8IVD9	OTTHUMG00000129174	ENST00000355451.7:c.7A>C	7.37:g.44530193T>G	ENSP00000347626:p.Thr3Pro	Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	42	34	0.809524	NM_015332	Q9BTI3|Q9H7W9|Q9UPT4	Missense_Mutation	SNP	ENST00000355451.7	37	CCDS5490.2	359	0.16437728937728938	154	0.3130081300813008	62	0.1712707182320442	4	0.006993006993006993	139	0.18337730870712401	G	0.066	-1.213676	0.01555	0.281697	0.215519	ENSG00000015676	ENST00000355451	T	0.54071	0.59	4.44	4.44	0.53790	.	0.163924	0.42172	N	0.000747	T	0.00012	0.0000	N	0.02011	-0.69	0.52501	P	4.599999999999049E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.26643	-1.0097	9	0.07175	T	0.84	-0.2123	7.8815	0.29624	0.0:0.178:0.6377:0.1843	rs307007;rs1656050	3	Q8IVD9	NUDC3_HUMAN	P	3	ENSP00000347626:T3P	ENSP00000347626:T3P	T	-	1	0	NUDCD3	44496718	1.000000	0.71417	0.969000	0.41365	0.003000	0.03518	1.408000	0.34668	1.208000	0.43306	-0.215000	0.12644	ACA	C|0.000;G|0.171;T|0.828	0.171	strong		0.657	NUDCD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251248.3	NM_015332	
TTC39B	158219	hgsc.bcm.edu	37	9	15189791	15189791	+	Splice_Site	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:15189791C>T	ENST00000512701.2	-	12	1142		c.e12-1		TTC39B_ENST00000380850.4_Splice_Site|TTC39B_ENST00000355694.2_Splice_Site|TTC39B_ENST00000297615.5_Splice_Site|TTC39B_ENST00000507285.1_Splice_Site|TTC39B_ENST00000507993.1_Splice_Site			Q5VTQ0	TT39B_HUMAN	tetratricopeptide repeat domain 39B											NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(7)|ovary(2)|prostate(1)	21						TCTCCTGTACCTAGAAATTTA	0.408																																					.		Atlas-SNP	.											.	TTC39B	83	.	0			c.1100-1G>A						PASS	.						52.0	48.0	49.0					9																	15189791		2203	4300	6503	SO:0001630	splice_region_variant	158219	exon13			CTGTACCTAGAAA	AK091187	CCDS6477.1, CCDS6477.2, CCDS55294.1, CCDS55295.1, CCDS55296.1	9p22.2	2013-01-11	2008-06-23	2008-06-23	ENSG00000155158	ENSG00000155158		"""Tetratricopeptide (TTC) repeat domain containing"""	23704	protein-coding gene	gene with protein product		613574	"""chromosome 9 open reading frame 52"""	C9orf52			Standard	NM_001168339		Approved	FLJ33868	uc003zlr.2	Q5VTQ0	OTTHUMG00000019581	ENST00000512701.2:c.1106-1G>A	9.37:g.15189791C>T		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	57	11	0.192982	NM_001168339	A5PLN1|B4DQ10|B4DQX4|B4DW93|Q8IVR7|Q8IXZ6|Q8N267	Splice_Site	SNP	ENST00000512701.2	37	CCDS6477.2	.	.	.	.	.	.	.	.	.	.	C	27.7	4.859434	0.91433	.	.	ENSG00000155158	ENST00000380850;ENST00000297615;ENST00000355694;ENST00000512701;ENST00000507285;ENST00000507993	.	.	.	5.72	5.72	0.89469	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.8823	0.96903	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	TTC39B	15179791	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.261000	0.78400	2.693000	0.91896	0.585000	0.79938	.	.	.	none		0.408	TTC39B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051758.3	NM_152574	Intron
ABCA7	10347	hgsc.bcm.edu	37	19	1044712	1044712	+	Missense_Mutation	SNP	A	A	G	rs567222111|rs3764647	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:1044712A>G	ENST00000263094.6	+	11	1415	c.1184A>G	c.(1183-1185)cAc>cGc	p.H395R	ABCA7_ENST00000435683.2_Missense_Mutation_p.H257R|ABCA7_ENST00000433129.1_Missense_Mutation_p.H395R	NM_019112.3	NP_061985.2	Q8IZY2	ABCA7_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 7	395			H -> R (in dbSNP:rs3764647). {ECO:0000269|PubMed:12111378}.		apolipoprotein A-I-mediated signaling pathway (GO:0038027)|ATP catabolic process (GO:0006200)|cholesterol efflux (GO:0033344)|high-density lipoprotein particle assembly (GO:0034380)|memory (GO:0007613)|negative regulation of amyloid precursor protein biosynthetic process (GO:0042985)|negative regulation of ATPase activity (GO:0032780)|negative regulation of beta-amyloid formation (GO:1902430)|peptide cross-linking (GO:0018149)|phagocytosis (GO:0006909)|phospholipid efflux (GO:0033700)|phospholipid scrambling (GO:0017121)|positive regulation of ATPase activity (GO:0032781)|positive regulation of beta-amyloid clearance (GO:1900223)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of engulfment of apoptotic cell (GO:1901076)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of phagocytosis (GO:0050766)|positive regulation of phospholipid efflux (GO:1902995)|protein localization to nucleus (GO:0034504)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|ATP-binding cassette (ABC) transporter complex (GO:0043190)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|phagocytic cup (GO:0001891)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	apolipoprotein A-I receptor activity (GO:0034188)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|phospholipid transporter activity (GO:0005548)|transporter activity (GO:0005215)			NS(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(7)|lung(22)|ovary(1)|pancreas(7)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	65		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GATGTGGGGCACCTGGTGGGC	0.677													G|||	545	0.108826	0.2572	0.0259	5008	,	,		14078	0.0923		0.0358	False		,,,				2504	0.0593				p.H395R		Atlas-SNP	.											.	ABCA7	174	.	0			c.A1184G						PASS	.	G	ARG/HIS	1054,3344	689.3+/-405.1	126,802,1271	39.0	39.0	39.0		1184	-4.4	0.0	19	dbSNP_107	39	348,8248	775.2+/-407.7	4,340,3954	yes	missense	ABCA7	NM_019112.3	29	130,1142,5225	GG,GA,AA		4.0484,23.9654,10.7896	benign	395/2147	1044712	1402,11592	2199	4298	6497	SO:0001583	missense	10347	exon11			TGGGGCACCTGGT	AF328787	CCDS12055.1	19p13.3	2012-03-14			ENSG00000064687	ENSG00000064687		"""ATP binding cassette transporters / subfamily A"""	37	protein-coding gene	gene with protein product		605414					Standard	NM_019112		Approved	ABCX	uc002lqw.4	Q8IZY2	OTTHUMG00000167547	ENST00000263094.6:c.1184A>G	19.37:g.1044712A>G	ENSP00000263094:p.His395Arg	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	73	33	0.452055	NM_019112	Q96S58|Q9BZC4|Q9NR73|Q9UKP8	Missense_Mutation	SNP	ENST00000263094.6	37	CCDS12055.1	212	0.09706959706959707	128	0.2601626016260163	10	0.027624309392265192	47	0.08216783216783216	27	0.03562005277044855	G	2.961	-0.214544	0.06101	0.239654	0.040484	ENSG00000064687	ENST00000263094;ENST00000433129	D;D	0.85556	-2.0;-2.0	4.1	-4.44	0.03557	.	.	.	.	.	T	0.00012	0.0000	N	0.02751	-0.505	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.0	T	0.02431	-1.1160	8	0.07030	T	0.85	.	3.7456	0.08547	0.4253:0.0:0.1756:0.3991	rs3764647;rs3764647	257;395	Q8IZY2-2;Q8IZY2	.;ABCA7_HUMAN	R	395	ENSP00000263094:H395R;ENSP00000414062:H395R	ENSP00000263094:H395R	H	+	2	0	ABCA7	995712	0.000000	0.05858	0.000000	0.03702	0.177000	0.22998	-2.738000	0.00800	-1.146000	0.02854	-0.374000	0.07098	CAC	A|0.886;G|0.114	0.114	strong		0.677	ABCA7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000394993.1	NM_019112	
PHOX2B	8929	hgsc.bcm.edu	37	4	41747899	41747899	+	Silent	SNP	G	G	T	rs17885864	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:41747899G>T	ENST00000226382.2	-	3	1229	c.870C>A	c.(868-870)ccC>ccA	p.P290P	RP11-227F19.1_ENST00000508038.1_RNA	NM_003924.3	NP_003915.2	Q99453	PHX2B_HUMAN	paired-like homeobox 2b	290					autonomic nervous system development (GO:0048483)|brainstem development (GO:0003360)|cell differentiation in hindbrain (GO:0021533)|cellular response to BMP stimulus (GO:0071773)|dopaminergic neuron differentiation (GO:0071542)|efferent axon development in a lateral line nerve (GO:0048894)|enteric nervous system development (GO:0048484)|glial cell differentiation (GO:0010001)|hindbrain tangential cell migration (GO:0021934)|inner ear development (GO:0048839)|medullary reticular formation development (GO:0021723)|negative regulation of cell cycle arrest (GO:0071157)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron differentiation (GO:0045665)|neural crest cell migration involved in autonomic nervous system development (GO:1901166)|neuron migration (GO:0001764)|noradrenergic neuron development (GO:0003358)|noradrenergic neuron differentiation (GO:0003357)|parasympathetic nervous system development (GO:0048486)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of gene expression (GO:0010468)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|respiratory system development (GO:0060541)|retrotrapezoid nucleus neuron differentiation (GO:0061452)|skeletal muscle cell differentiation (GO:0035914)|sympathetic ganglion development (GO:0061549)|sympathetic nervous system development (GO:0048485)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)			autonomic_ganglia(7)|central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(11)|ovary(2)|skin(1)|urinary_tract(1)	30						CGCTGGCGAAGGGACCCCCAA	0.677			"""Mis, F"""		neuroblastoma	neuroblastoma	congenital central hypoventilation syndrome		Neuroblastoma, Familial Clustering of;Congenital Central Hypoventilation Syndrome				G|||	129	0.0257588	0.0537	0.0375	5008	,	,		6089	0.0		0.0169	False		,,,				2504	0.0153				p.P290P		Atlas-SNP	.	yes	Rec	yes	familial neuroblastoma	4	4p12	8929	paired-like homeobox 2b	yes	O	.	PHOX2B	53	.	0			c.C870A						PASS	.	G		246,4160	129.0+/-165.8	6,234,1963	24.0	32.0	29.0		870	3.1	1.0	4	dbSNP_124	29	164,8436	73.8+/-136.5	1,162,4137	no	coding-synonymous	PHOX2B	NM_003924.3		7,396,6100	TT,TG,GG		1.907,5.5833,3.1524		290/315	41747899	410,12596	2203	4300	6503	SO:0001819	synonymous_variant	8929	exon3	Familial Cancer Database	Familial Neuroblastoma;CCHS, Ondine Curse, incl. Ondine-Hirschsprung Disease	GGCGAAGGGACCC	D82344	CCDS3463.1	4p13	2014-09-17	2003-02-10	2003-02-14	ENSG00000109132	ENSG00000109132		"""Homeoboxes / PRD class"""	9143	protein-coding gene	gene with protein product		603851	"""paired mesoderm homeobox 2b"""	PMX2B		9039501, 10395798	Standard	NM_003924		Approved	Phox2b, NBPhox	uc003gwf.4	Q99453	OTTHUMG00000099379	ENST00000226382.2:c.870C>A	4.37:g.41747899G>T		Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	45	21	0.466667	NM_003924	Q6PJD9	Silent	SNP	ENST00000226382.2	37	CCDS3463.1																																																																																			G|0.972;T|0.028	0.028	strong		0.677	PHOX2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216832.2		
MYO1H	283446	hgsc.bcm.edu	37	12	109835590	109835590	+	Silent	SNP	A	A	G	rs11611358	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:109835590A>G	ENST00000431443.2	+	4	495	c.495A>G	c.(493-495)aaA>aaG	p.K165K	MYO1H_ENST00000310903.5_Silent_p.K165K	NM_001101421.3	NP_001094891.3	Q8N1T3	MYO1H_HUMAN	myosin IH	165	Myosin motor.					myosin complex (GO:0016459)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(17)|prostate(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	47						GATTTGGGAAATACATGGATA	0.453													A|||	1264	0.252396	0.0651	0.4524	5008	,	,		18134	0.3552		0.3052	False		,,,				2504	0.2035				p.K165K		Atlas-SNP	.											MYO1H,colon,carcinoma,0,1	MYO1H	98	1	0			c.A495G						PASS	.	A		411,3381		29,353,1514	79.0	74.0	76.0		495	-0.5	1.0	12	dbSNP_120	76	2477,5837		351,1775,2031	no	coding-synonymous	MYO1H	NM_001101421.3		380,2128,3545	GG,GA,AA		29.7931,10.8386,23.8559		165/1023	109835590	2888,9218	1896	4157	6053	SO:0001819	synonymous_variant	283446	exon4			TGGGAAATACATG		CCDS53826.1	12q24.11	2011-09-27			ENSG00000174527	ENSG00000174527		"""Myosins / Myosin superfamily : Class I"""	13879	protein-coding gene	gene with protein product		614636					Standard	NM_001101421		Approved	FLJ37587	uc010sxn.1	Q8N1T3	OTTHUMG00000169252	ENST00000431443.2:c.495A>G	12.37:g.109835590A>G		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	81	41	0.506173	NM_001101421	F5H3C6	Silent	SNP	ENST00000431443.2	37																																																																																				A|0.742;G|0.258	0.258	strong		0.453	MYO1H-201	KNOWN	basic	protein_coding	protein_coding		NM_173597	
RGPD4	285190	hgsc.bcm.edu	37	2	108475928	108475928	+	Missense_Mutation	SNP	C	C	T	rs143215949	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:108475928C>T	ENST00000408999.3	+	11	1629	c.1552C>T	c.(1552-1554)Ctt>Ttt	p.L518F	RGPD4_ENST00000354986.4_Missense_Mutation_p.L518F	NM_182588.2	NP_872394.2	Q7Z3J3	RGPD4_HUMAN	RANBP2-like and GRIP domain containing 4	518					protein targeting to Golgi (GO:0000042)			p.L518F(1)		breast(1)|endometrium(7)|kidney(4)|lung(23)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(3)	43						ATGCCTGCCCCTTCCTGTATG	0.393																																					p.L518F		Atlas-SNP	.											RGPD4,extremity,malignant_melanoma,0,1	RGPD4	112	1	1	Substitution - Missense(1)	skin(1)	c.C1552T						scavenged	.	C	PHE/LEU	20,1364		0,20,672	115.0	99.0	104.0		1552	1.7	1.0	2	dbSNP_134	104	15,3167		0,15,1576	no	missense	RGPD4	NM_182588.2	22	0,35,2248	TT,TC,CC		0.4714,1.4451,0.7665	probably-damaging	518/1759	108475928	35,4531	692	1591	2283	SO:0001583	missense	285190	exon11			CTGCCCCTTCCTG	BX537861	CCDS46381.1	2q12.3	2013-01-10			ENSG00000196862	ENSG00000196862		"""Tetratricopeptide (TTC) repeat domain containing"""	32417	protein-coding gene	gene with protein product		612707				15710750, 15815621	Standard	NM_182588		Approved	RGP4, DKFZp686P0288	uc010ywk.2	Q7Z3J3	OTTHUMG00000153208	ENST00000408999.3:c.1552C>T	2.37:g.108475928C>T	ENSP00000386810:p.Leu518Phe	Somatic	198	0	0		WXS	Illumina HiSeq	Phase_I	262	91	0.347328	NM_182588	B9A029	Missense_Mutation	SNP	ENST00000408999.3	37	CCDS46381.1	.	.	.	.	.	.	.	.	.	.	-	5.511	0.279200	0.10458	0.014451	0.004714	ENSG00000196862	ENST00000354986;ENST00000408999;ENST00000439322	T;T	0.50548	0.74;0.74	2.6	1.7	0.24286	.	.	.	.	.	T	0.34803	0.0910	M	0.69823	2.125	0.27171	N	0.960928	B	0.06786	0.001	B	0.06405	0.002	T	0.33317	-0.9873	9	0.38643	T	0.18	-11.7549	6.3947	0.21605	0.0:0.7319:0.0:0.2681	.	518	Q7Z3J3	RGPD4_HUMAN	F	518;518;276	ENSP00000347081:L518F;ENSP00000386810:L518F	ENSP00000347081:L518F	L	+	1	0	RGPD4	107842360	0.830000	0.29337	0.968000	0.41197	0.263000	0.26337	1.503000	0.35715	0.308000	0.22923	0.152000	0.16155	CTT	.	.	weak		0.393	RGPD4-001	NOVEL	not_best_in_genome_evidence|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330096.2	XM_496581	
DSC1	1823	hgsc.bcm.edu	37	18	28710619	28710619	+	Missense_Mutation	SNP	C	C	A	rs985861	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:28710619C>A	ENST00000257198.5	-	16	2804	c.2543G>T	c.(2542-2544)tGt>tTt	p.C848F	DSC1_ENST00000257197.3_3'UTR|RP11-408H20.2_ENST00000581836.1_RNA|RP11-408H20.3_ENST00000582307.1_RNA	NM_024421.2	NP_077739.1	Q08554	DSC1_HUMAN	desmocollin 1	848			C -> F (in dbSNP:rs985861). {ECO:0000269|PubMed:8507556}.		homophilic cell adhesion (GO:0007156)	desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|gap junction (GO:0005921)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(20)|ovary(3)|skin(10)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	53			OV - Ovarian serous cystadenocarcinoma(10;0.00778)			GTTATACGAACAAACGTAGTC	0.413													C|||	467	0.0932508	0.2549	0.0533	5008	,	,		17746	0.0		0.0477	False		,,,				2504	0.046				p.C848F		Atlas-SNP	.											.	DSC1	240	.	0			c.G2543T						PASS	.	C	,PHE/CYS	885,3521	340.5+/-306.2	88,709,1406	132.0	133.0	132.0		,2543	2.0	0.2	18	dbSNP_86	132	344,8256	117.4+/-177.0	6,332,3962	yes	utr-3,missense	DSC1	NM_004948.3,NM_024421.2	,205	94,1041,5368	AA,AC,CC		4.0,20.0862,9.4495	,benign	,848/895	28710619	1229,11777	2203	4300	6503	SO:0001583	missense	1823	exon16			TACGAACAAACGT	AF293358	CCDS11894.1, CCDS11895.1	18q12.1	2010-01-26			ENSG00000134765	ENSG00000134765		"""Cadherins / Major cadherins"""	3035	protein-coding gene	gene with protein product		125643				8486729	Standard	NM_024421		Approved	CDHF1	uc002kwn.3	Q08554	OTTHUMG00000131982	ENST00000257198.5:c.2543G>T	18.37:g.28710619C>A	ENSP00000257198:p.Cys848Phe	Somatic	240	0	0		WXS	Illumina HiSeq	Phase_I	198	85	0.429293	NM_024421	Q9HB01	Missense_Mutation	SNP	ENST00000257198.5	37	CCDS11894.1	180	0.08241758241758242	125	0.2540650406504065	21	0.058011049723756904	0	0.0	34	0.044854881266490766	C	10.91	1.485333	0.26598	0.200862	0.04	ENSG00000134765	ENST00000257198	T	0.76060	-0.99	6.17	2.05	0.26809	Cadherin, cytoplasmic domain (1);	0.127555	0.35615	N	0.003081	T	0.00012	0.0000	N	0.08118	0	0.58432	P	1.999999999946489E-6	B	0.06786	0.001	B	0.01281	0.0	T	0.05937	-1.0855	9	0.72032	D	0.01	.	6.2715	0.20956	0.4608:0.3859:0.0:0.1532	rs985861;rs52820787;rs985861	848	Q08554	DSC1_HUMAN	F	848	ENSP00000257198:C848F	ENSP00000257198:C848F	C	-	2	0	DSC1	26964617	0.682000	0.27624	0.197000	0.23402	0.663000	0.39108	1.525000	0.35953	0.485000	0.27652	0.655000	0.94253	TGT	C|0.914;A|0.086	0.086	strong		0.413	DSC1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254946.1	NM_004948, NM_024421	
EIF4ENIF1	56478	hgsc.bcm.edu	37	22	31838085	31838085	+	Silent	SNP	G	G	A	rs5997988	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:31838085G>A	ENST00000397525.1	-	17	2449	c.2226C>T	c.(2224-2226)agC>agT	p.S742S	EIF4ENIF1_ENST00000397523.1_Silent_p.S718S|EIF4ENIF1_ENST00000441289.1_5'Flank|EIF4ENIF1_ENST00000330125.5_Silent_p.S742S|EIF4ENIF1_ENST00000382180.2_Silent_p.S397S|EIF4ENIF1_ENST00000344710.5_Silent_p.S568S	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	170	0	0		WXS	Illumina HiSeq	Phase_I	133	57	0.428571	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	
PPL	5493	hgsc.bcm.edu	37	16	4934777	4934777	+	Silent	SNP	C	C	T	rs61744951	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:4934777C>T	ENST00000345988.2	-	22	3968	c.3879G>A	c.(3877-3879)caG>caA	p.Q1293Q	PPL_ENST00000590782.2_Silent_p.Q1291Q	NM_002705.4	NP_002696	O60437	PEPL_HUMAN	periplakin	1293					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						GGAGGATCTCCTGGACCACCT	0.507													C|||	286	0.0571086	0.1135	0.0317	5008	,	,		18685	0.006		0.0775	False		,,,				2504	0.0307				p.Q1293Q		Atlas-SNP	.											.	PPL	168	.	0			c.G3879A						PASS	.	C		499,3895	230.4+/-244.6	17,465,1715	170.0	169.0	169.0		3879	2.2	1.0	16	dbSNP_129	169	657,7943	166.1+/-218.1	29,599,3672	no	coding-synonymous	PPL	NM_002705.4		46,1064,5387	TT,TC,CC		7.6395,11.3564,8.8964		1293/1757	4934777	1156,11838	2197	4300	6497	SO:0001819	synonymous_variant	5493	exon22			GATCTCCTGGACC	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.3879G>A	16.37:g.4934777C>T		Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	136	100	0.735294	NM_002705	O60314|O60454|Q14C98	Silent	SNP	ENST00000345988.2	37	CCDS10526.1																																																																																			C|0.918;T|0.082	0.082	strong		0.507	PPL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251715.1	NM_002705	
HLTF	6596	hgsc.bcm.edu	37	3	148759325	148759325	+	Silent	SNP	T	T	C	rs2290725	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:148759325T>C	ENST00000310053.5	-	20	2521	c.2328A>G	c.(2326-2328)gcA>gcG	p.A776A	HLTF_ENST00000494055.1_Silent_p.A776A|HLTF_ENST00000465259.1_Silent_p.A775A|HLTF_ENST00000392912.2_Silent_p.A776A	NM_003071.3|NM_139048.2	NP_003062.2|NP_620636.1	Q14527	HLTF_HUMAN	helicase-like transcription factor	776					chromatin modification (GO:0016568)|protein ubiquitination (GO:0016567)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.A776A(1)		breast(2)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(18)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	47			LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)			AAAATACATGTGCACAATGTG	0.378													T|||	1581	0.315695	0.32	0.3098	5008	,	,		17556	0.3353		0.337	False		,,,				2504	0.272				p.A776A		Atlas-SNP	.											.	HLTF	87	.	1	Substitution - coding silent(1)	lung(1)	c.A2328G						PASS	.	T	,	1331,3075	447.5+/-348.4	219,893,1091	134.0	129.0	131.0		2328,2328	3.7	1.0	3	dbSNP_100	131	2639,5961	427.5+/-355.6	404,1831,2065	no	coding-synonymous,coding-synonymous	HLTF	NM_003071.3,NM_139048.2	,	623,2724,3156	CC,CT,TT		30.686,30.2088,30.5244	,	776/1010,776/1010	148759325	3970,9036	2203	4300	6503	SO:0001819	synonymous_variant	6596	exon20			TACATGTGCACAA	L34673	CCDS33875.1	3q25.1-q26.1	2006-11-09	2006-11-09	2006-11-09	ENSG00000071794	ENSG00000071794		"""RING-type (C3HC4) zinc fingers"""	11099	protein-coding gene	gene with protein product		603257	"""SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 3"""	SNF2L3, SMARCA3		7558014	Standard	NM_139048		Approved	HIP116A, HLTF1, RNF80	uc003ewr.1	Q14527	OTTHUMG00000159534	ENST00000310053.5:c.2328A>G	3.37:g.148759325T>C		Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	126	60	0.47619	NM_139048	D3DNH3|Q14536|Q16051|Q7KYJ6|Q86YA5|Q92652|Q96KM9	Silent	SNP	ENST00000310053.5	37	CCDS33875.1																																																																																			T|0.692;C|0.308	0.308	strong		0.378	HLTF-003	KNOWN	alternative_3_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356064.1		
STT3A	3703	hgsc.bcm.edu	37	11	125476252	125476252	+	Silent	SNP	C	C	G	rs34964592	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:125476252C>G	ENST00000529196.1	+	9	878	c.672C>G	c.(670-672)ctC>ctG	p.L224L	STT3A_ENST00000392708.4_Silent_p.L224L|STT3A_ENST00000531491.1_Silent_p.L132L			P46977	STT3A_HUMAN	STT3A, subunit of the oligosaccharyltransferase complex (catalytic)	224					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)		TCCACGTCCTCGTGCTGATGC	0.473													G|||	519	0.103634	0.2436	0.0605	5008	,	,		17944	0.0308		0.0716	False		,,,				2504	0.0532				p.L224L		Atlas-SNP	.											.	STT3A	52	.	0			c.C672G						PASS	.	G		917,3485	738.5+/-411.0	88,741,1372	371.0	316.0	335.0		672	2.2	1.0	11	dbSNP_126	335	578,8020	793.3+/-407.5	18,542,3739	no	coding-synonymous	STT3A	NM_152713.3		106,1283,5111	GG,GC,CC		6.7225,20.8314,11.5		224/706	125476252	1495,11505	2201	4299	6500	SO:0001819	synonymous_variant	3703	exon8			CGTCCTCGTGCTG	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.672C>G	11.37:g.125476252C>G		Somatic	193	0	0		WXS	Illumina HiSeq	Phase_I	191	154	0.806283	NM_152713	B4DJ24|E9PNQ1|Q86XU9|Q8TE35|Q8WUB4	Silent	SNP	ENST00000529196.1	37	CCDS8458.1																																																																																			C|0.891;G|0.109	0.109	strong		0.473	STT3A-002	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000386691.1	NM_152713	
SUPT16H	11198	hgsc.bcm.edu	37	14	21831419	21831419	+	Silent	SNP	C	C	T	rs61746713	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	81	0	0		WXS	Illumina HiSeq	Phase_I	64	35	0.546875	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		
APOBEC2	10930	hgsc.bcm.edu	37	6	41029342	41029342	+	Missense_Mutation	SNP	T	T	C	rs2076472	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	110	0	0		WXS	Illumina HiSeq	Phase_I	98	46	0.469388	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	
PER3	8863	hgsc.bcm.edu	37	1	7887248	7887248	+	Silent	SNP	G	G	A	rs2859387	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:7887248G>A	ENST00000361923.2	+	17	2410	c.2235G>A	c.(2233-2235)ccG>ccA	p.P745P	RP3-467L1.4_ENST00000451646.1_RNA|PER3_ENST00000377532.3_Silent_p.P753P	NM_016831.1	NP_058515.1	P56645	PER3_HUMAN	period circadian clock 3	745	CSNK1E binding domain. {ECO:0000250}.				circadian regulation of gene expression (GO:0032922)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of circadian sleep/wake cycle, sleep (GO:0045187)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	signal transducer activity (GO:0004871)			breast(4)|central_nervous_system(3)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(9)|lung(8)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	39	Ovarian(185;0.0634)|all_lung(157;0.178)	all_epithelial(116;9.35e-21)|all_lung(118;7.57e-07)|Lung NSC(185;4.52e-06)|Renal(390;0.000147)|Breast(487;0.00086)|Colorectal(325;0.000959)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0234)|all cancers(8;8.58e-70)|GBM - Glioblastoma multiforme(8;1.81e-35)|Colorectal(212;2.06e-07)|COAD - Colon adenocarcinoma(227;1.92e-05)|Kidney(185;7.18e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000472)|STAD - Stomach adenocarcinoma(132;0.00118)|KIRC - Kidney renal clear cell carcinoma(229;0.00122)|READ - Rectum adenocarcinoma(331;0.0649)		AGAAGCTGCCGGAGCCGCCAG	0.632													G|||	2588	0.516773	0.5333	0.4597	5008	,	,		14514	0.8026		0.3718	False		,,,				2504	0.3896				p.P745P		Atlas-SNP	.											PER3,NS,carcinoma,+1,1	PER3	95	1	0			c.G2235A						PASS	.	G		2207,2153		589,1029,562	21.0	26.0	24.0		2235	-8.8	0.0	1	dbSNP_100	24	3035,5501		587,1861,1820	no	coding-synonymous	PER3	NM_016831.1		1176,2890,2382	AA,AG,GG		35.5553,49.3807,40.6483		745/1202	7887248	5242,7654	2180	4268	6448	SO:0001819	synonymous_variant	8863	exon17			GCTGCCGGAGCCG	BC026102	CCDS89.1, CCDS72695.1	1p36.23	2012-12-13	2012-12-13		ENSG00000049246	ENSG00000049246			8847	protein-coding gene	gene with protein product		603427	"""period (Drosophila) homolog 3"", ""period homolog 3 (Drosophila)"""			9427249	Standard	XM_005263520		Approved		uc001aoo.3	P56645	OTTHUMG00000001216	ENST00000361923.2:c.2235G>A	1.37:g.7887248G>A		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	73	72	0.986301	NM_016831	Q5H8X4|Q5H8X5|Q969K6|Q96S77|Q96S78|Q9C0J3|Q9NSP9|Q9UGU8	Silent	SNP	ENST00000361923.2	37	CCDS89.1																																																																																			G|0.567;A|0.433	0.433	strong		0.632	PER3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000003607.1	NM_016831	
GAS8	2622	hgsc.bcm.edu	37	16	90095561	90095561	+	Intron	SNP	C	C	T	rs3785183	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:90095561C>T	ENST00000268699.4	+	2	212				GAS8_ENST00000540721.1_Intron|GAS8_ENST00000536122.1_Intron|C16orf3_ENST00000408886.2_Missense_Mutation_p.V64I	NM_001481.2	NP_001472.1	O95995	GAS8_HUMAN	growth arrest-specific 8						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)		p.V64I(1)		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)		gggcagcctacggggcaggct	0.672													N|||	1658	0.33107	0.3638	0.3127	5008	,	,		16091	0.1687		0.335	False		,,,				2504	0.4632				p.V64I		Atlas-SNP	.											C16orf3,NS,carcinoma,0,1	C16orf3	14	1	1	Substitution - Missense(1)	prostate(1)	c.G190A						PASS	.						23.0	19.0	21.0					16																	90095561		2193	4300	6493	SO:0001627	intron_variant	750	exon1			AGCCTACGGGGCA	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.90+1431C>T	16.37:g.90095561C>T		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	121	48	0.396694	NM_001214	B2RCT1|B7Z4U1|G3V1L5|Q2M234	Missense_Mutation	SNP	ENST00000268699.4	37	CCDS10992.1	638	0.29212454212454214	196	0.3983739837398374	106	0.292817679558011	103	0.18006993006993008	233	0.3073878627968338	N	2.174	-0.389260	0.04932	.	.	ENSG00000221819	ENST00000408886	T	0.55052	0.54	1.41	0.438	0.16560	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.25609	0.13	B	0.08055	0.003	T	0.46091	-0.9216	7	.	.	.	.	5.5547	0.17109	0.0:0.6469:0.3531:0.0	rs3785183;rs57727995;rs3785183	72	O95177	CP003_HUMAN	I	64	ENSP00000386218:V64I	.	V	-	1	0	C16orf3	88623062	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.385000	0.07379	0.197000	0.20387	-0.486000	0.04755	GTA	C|0.676;T|0.324	0.324	strong		0.672	GAS8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000272877.2		
PREP	5550	hgsc.bcm.edu	37	6	105776866	105776866	+	Missense_Mutation	SNP	A	A	C	rs12192054	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:105776866A>C	ENST00000369110.3	-	9	1243	c.1051T>G	c.(1051-1053)Tta>Gta	p.L351V		NM_002726.4	NP_002717.3	P48147	PPCE_HUMAN	prolyl endopeptidase	351			L -> V (in dbSNP:rs12192054).		proteolysis (GO:0006508)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	serine-type endopeptidase activity (GO:0004252)|serine-type exopeptidase activity (GO:0070008)|serine-type peptidase activity (GO:0008236)			breast(1)|endometrium(2)|large_intestine(7)|lung(12)|ovary(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	29		all_cancers(87;0.000128)|Acute lymphoblastic leukemia(125;1.9e-08)|all_hematologic(75;9.25e-07)|all_epithelial(87;0.0344)|Lung NSC(302;0.191)|Colorectal(196;0.202)			Oxytocin(DB00107)	AGGTAGCATAAGACCAAGAAG	0.413													A|||	582	0.116214	0.1142	0.1009	5008	,	,		17957	0.0198		0.1412	False		,,,				2504	0.2035				p.L351V		Atlas-SNP	.											.	PREP	65	.	0			c.T1051G						PASS	.	A	VAL/LEU	466,3940	220.0+/-237.6	23,420,1760	82.0	84.0	84.0		1051	1.5	0.9	6	dbSNP_120	84	1289,7311	254.4+/-279.7	94,1101,3105	yes	missense	PREP	NM_002726.4	32	117,1521,4865	CC,CA,AA		14.9884,10.5765,13.4938	benign	351/711	105776866	1755,11251	2203	4300	6503	SO:0001583	missense	5550	exon9			AGCATAAGACCAA		CCDS5053.1	6q22	2008-02-05			ENSG00000085377	ENSG00000085377	3.4.21.26		9358	protein-coding gene	gene with protein product		600400				7959018	Standard	NM_002726		Approved		uc003prc.3	P48147	OTTHUMG00000015297	ENST00000369110.3:c.1051T>G	6.37:g.105776866A>C	ENSP00000358106:p.Leu351Val	Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	80	39	0.4875	NM_002726	Q8N6D4	Missense_Mutation	SNP	ENST00000369110.3	37	CCDS5053.1	221	0.10119047619047619	56	0.11382113821138211	40	0.11049723756906077	8	0.013986013986013986	117	0.15435356200527706	A	2.908	-0.226019	0.06022	0.105765	0.149884	ENSG00000085377	ENST00000369110	T	0.38401	1.14	5.48	1.51	0.23008	Peptidase S9A, oligopeptidase, N-terminal (1);Peptidase S9A/B/C, oligopeptidase, N-terminal beta-propeller (2);	0.066231	0.64402	D	0.000011	T	0.03390	0.0098	N	0.02697	-0.525	0.23416	P	0.99772027	B	0.06786	0.001	B	0.12837	0.008	T	0.43475	-0.9389	9	0.02654	T	1	-13.2179	8.5806	0.33626	0.7461:0.0:0.2539:0.0	rs12192054;rs52795757;rs58933780;rs12192054	351	P48147	PPCE_HUMAN	V	351	ENSP00000358106:L351V	ENSP00000358106:L351V	L	-	1	2	PREP	105883559	0.331000	0.24713	0.908000	0.35775	0.985000	0.73830	0.874000	0.28065	0.068000	0.16574	0.459000	0.35465	TTA	A|0.879;C|0.121	0.121	strong		0.413	PREP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041658.1		
HMGXB3	22993	hgsc.bcm.edu	37	5	149390148	149390148	+	Missense_Mutation	SNP	G	G	A	rs2241698	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:149390148G>A	ENST00000502717.1	+	4	1251	c.787G>A	c.(787-789)Gta>Ata	p.V263I	HMGXB3_ENST00000503427.1_Missense_Mutation_p.V263I	NM_014983.2	NP_055798	Q12766	HMGX3_HUMAN	HMG box domain containing 3	509					phosphorylation (GO:0016310)	nucleus (GO:0005634)	DNA binding (GO:0003677)|kinase activity (GO:0016301)			central_nervous_system(1)|endometrium(3)|kidney(3)|skin(2)	9						TGGGGAGAGTGTATCAGTGGT	0.512													G|||	572	0.114217	0.09	0.2579	5008	,	,		21250	0.1002		0.1292	False		,,,				2504	0.044				p.V263I		Atlas-SNP	.											.	HMGXB3	31	.	0			c.G787A						PASS	.	G	ILE/VAL	117,1267		4,109,579	10.0	11.0	11.0		787	1.7	0.9	5	dbSNP_98	11	360,2820		18,324,1248	yes	missense	HMGXB3	NM_014983.2	29	22,433,1827	AA,AG,GG		11.3208,8.4538,10.4514	benign	263/1293	149390148	477,4087	692	1590	2282	SO:0001583	missense	22993	exon4			GAGAGTGTATCAG	D83778	CCDS54935.1	5q33.1	2011-07-01		2009-01-05	ENSG00000113716	ENSG00000113716		"""High mobility group / Non-canonical"""	28982	protein-coding gene	gene with protein product				HMGX3		8724849	Standard	NM_014983		Approved	SMF, KIAA0194	uc003lrk.4	Q12766	OTTHUMG00000163493	ENST00000502717.1:c.787G>A	5.37:g.149390148G>A	ENSP00000421917:p.Val263Ile	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	56	27	0.482143	NM_014983	G5E9Y4|Q86UG3|Q9UMF4	Missense_Mutation	SNP	ENST00000502717.1	37	CCDS54935.1	295	0.13507326007326007	52	0.10569105691056911	80	0.22099447513812154	69	0.12062937062937062	94	0.12401055408970976	G	11.69	1.714490	0.30413	0.084538	0.113208	ENSG00000113716	ENST00000503427;ENST00000502717	.	.	.	5.91	1.74	0.24563	.	0.581569	0.19816	N	0.105425	T	0.00012	0.0000	L	0.44542	1.39	0.50467	P	1.2500000000004174E-4	B	0.13594	0.008	B	0.08055	0.003	T	0.13683	-1.0500	8	0.87932	D	0	-4.5868	1.4062	0.02281	0.1925:0.1287:0.403:0.2759	rs2241698;rs61145259;rs2241698	509	Q12766	HMGX3_HUMAN	I	263	.	ENSP00000421917:V263I	V	+	1	0	HMGXB3	149370341	0.352000	0.24895	0.888000	0.34837	0.974000	0.67602	0.359000	0.20233	0.017000	0.15025	0.655000	0.94253	GTA	G|0.869;A|0.131	0.131	strong		0.512	HMGXB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373771.1	XM_001717202	
GFPT2	9945	hgsc.bcm.edu	37	5	179740827	179740827	+	Missense_Mutation	SNP	T	T	C	rs2303007	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:179740827T>C	ENST00000253778.8	-	14	1580	c.1411A>G	c.(1411-1413)Atc>Gtc	p.I471V	GFPT2_ENST00000520165.1_5'Flank	NM_005110.2	NP_005101.1	O94808	GFPT2_HUMAN	glutamine-fructose-6-phosphate transaminase 2	471	SIS 1. {ECO:0000255|PROSITE- ProRule:PRU00797}.		I -> V (in dbSNP:rs2303007). {ECO:0000269|Ref.2}.		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)			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)	GCCACGCCGATCTCCGGCCCT	0.711													T|||	1174	0.234425	0.062	0.2176	5008	,	,		8734	0.4028		0.2256	False		,,,				2504	0.3149				p.I471V		Atlas-SNP	.											GFPT2,NS,carcinoma,0,1	GFPT2	74	1	0			c.A1411G	GRCh37	CM040423	GFPT2	M	rs2303007	PASS	.	T	VAL/ILE	320,4048		14,292,1878	12.0	15.0	14.0		1411	2.2	1.0	5	dbSNP_100	14	1641,6917		163,1315,2801	yes	missense	GFPT2	NM_005110.2	29	177,1607,4679	CC,CT,TT		19.175,7.326,15.171	benign	471/683	179740827	1961,10965	2184	4279	6463	SO:0001583	missense	9945	exon14			CGCCGATCTCCGG	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.1411A>G	5.37:g.179740827T>C	ENSP00000253778:p.Ile471Val	Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	57	16	0.280702	NM_005110	Q53XM2|Q9BWS4	Missense_Mutation	SNP	ENST00000253778.8	37	CCDS43411.1	497	0.22756410256410256	26	0.052845528455284556	75	0.20718232044198895	218	0.3811188811188811	178	0.23482849604221637	T	12.31	1.900188	0.33535	0.07326	0.19175	ENSG00000131459	ENST00000253778	T	0.62788	-0.0	5.8	2.15	0.27550	Sugar isomerase (SIS) (2);	0.139878	0.64402	N	0.000007	T	0.00012	0.0000	L	0.42744	1.35	0.20703	P	0.999866909	B	0.06786	0.001	B	0.13407	0.009	T	0.36529	-0.9744	8	.	.	.	-20.4654	11.429	0.50029	0.0:0.1875:0.0:0.8125	rs2303007;rs17855340;rs2303007	471	O94808	GFPT2_HUMAN	V	471	ENSP00000253778:I471V	.	I	-	1	0	GFPT2	179673433	1.000000	0.71417	0.983000	0.44433	0.689000	0.40095	3.092000	0.50207	-0.084000	0.12595	-1.162000	0.01777	ATC	T|0.789;C|0.211	0.211	strong		0.711	GFPT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373444.4	NM_005110	
PRIMPOL	201973	hgsc.bcm.edu	37	4	185599489	185599489	+	Silent	SNP	G	G	A	rs34985821	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:185599489G>A	ENST00000314970.6	+	8	1381	c.948G>A	c.(946-948)caG>caA	p.Q316Q	PRIMPOL_ENST00000512834.1_Silent_p.Q316Q|PRIMPOL_ENST00000515774.1_Silent_p.Q187Q|PRIMPOL_ENST00000503752.1_Silent_p.Q316Q	NM_152683.2	NP_689896	Q96LW4	PRIPO_HUMAN	primase and polymerase (DNA-directed)	316					mitochondrial DNA replication (GO:0006264)|replication fork processing (GO:0031297)|response to UV (GO:0009411)|translesion synthesis (GO:0019985)	mitochondrial matrix (GO:0005759)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA primase activity (GO:0003896)|DNA-directed DNA polymerase activity (GO:0003887)|manganese ion binding (GO:0030145)										TTCCTATACAGTCAAAAGATG	0.318													G|||	307	0.0613019	0.0272	0.1066	5008	,	,		13541	0.001		0.1243	False		,,,				2504	0.0726				p.Q316Q		Atlas-SNP	.											.	CCDC111	43	.	0			c.G948A						PASS	.	G		175,4227	111.6+/-149.8	4,167,2030	50.0	52.0	52.0		948	-1.9	0.0	4	dbSNP_126	52	1186,7404	238.3+/-269.8	93,1000,3202	no	coding-synonymous	CCDC111	NM_152683.2		97,1167,5232	AA,AG,GG		13.8068,3.9755,10.4757		316/561	185599489	1361,11631	2201	4295	6496	SO:0001819	synonymous_variant	201973	exon8			TATACAGTCAAAA	AK057729	CCDS3837.1, CCDS75211.1, CCDS75212.1	4q35.1	2013-09-27	2013-09-27	2013-09-27	ENSG00000164306	ENSG00000164306			26575	protein-coding gene	gene with protein product		615421	"""coiled-coil domain containing 111"""	CCDC111		12477932	Standard	XM_005262814		Approved	FLJ33167	uc003iwk.2	Q96LW4	OTTHUMG00000160495	ENST00000314970.6:c.948G>A	4.37:g.185599489G>A		Somatic	427	0	0		WXS	Illumina HiSeq	Phase_I	356	183	0.514045	NM_152683	D3DP55|D6RDM1|Q5HYJ9	Silent	SNP	ENST00000314970.6	37	CCDS3837.1	144	0.06593406593406594	15	0.03048780487804878	41	0.1132596685082873	0	0.0	88	0.11609498680738786	G	7.626	0.677847	0.14841	0.039755	0.138068	ENSG00000164306	ENST00000508001	.	.	.	5.95	-1.91	0.07641	.	.	.	.	.	T	0.00178	0.0005	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.28267	-1.0049	4	0.14656	T	0.56	-6.382	6.4791	0.22053	0.5647:0.0:0.178:0.2573	rs34985821	.	.	.	N	20	.	ENSP00000424639:S20N	S	+	2	0	CCDC111	185836483	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.522000	0.06237	-0.186000	0.10533	0.655000	0.94253	AGT	G|0.904;A|0.096	0.096	strong		0.318	PRIMPOL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000360827.1	NM_152683	
OR51S1	119692	hgsc.bcm.edu	37	11	4870284	4870284	+	Missense_Mutation	SNP	G	G	C	rs35918613	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:4870284G>C	ENST00000322101.2	-	1	230	c.155C>G	c.(154-156)aCc>aGc	p.T52S	MMP26_ENST00000477339.1_Intron|MMP26_ENST00000380390.1_Intron	NM_001004758.1	NP_001004758.1	Q8NGJ8	O51S1_HUMAN	olfactory receptor, family 51, subfamily S, member 1	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	187	0	0		WXS	Illumina HiSeq	Phase_I	255	59	0.231373	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	
PPP1R32	220004	hgsc.bcm.edu	37	11	61253841	61253841	+	Missense_Mutation	SNP	C	C	A	rs11230707	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:61253841C>A	ENST00000338608.2	+	8	838	c.713C>A	c.(712-714)aCc>aAc	p.T238N	PPP1R32_ENST00000432063.2_Intron|PPP1R32_ENST00000538185.1_5'Flank|PPP1R32_ENST00000366212.4_5'Flank	NM_145017.2	NP_659454.2	Q7Z5V6	PPR32_HUMAN	protein phosphatase 1, regulatory subunit 32	238			T -> N (in dbSNP:rs11230707).				phosphatase binding (GO:0019902)										CAGAGTGTCACCAAGTCAGAC	0.637													C|||	206	0.0411342	0.1392	0.0058	5008	,	,		19286	0.001		0.008	False		,,,				2504	0.0092				p.T238N		Atlas-SNP	.											.	.	.	.	0			c.C713A						PASS	.	C	,ASN/THR	512,3892	233.3+/-246.5	36,440,1726	48.0	47.0	47.0		,713	3.4	1.0	11	dbSNP_120	47	62,8536	38.3+/-94.2	0,62,4237	yes	intron,missense	C11orf66	NM_001170753.1,NM_145017.2	,65	36,502,5963	AA,AC,CC		0.7211,11.6258,4.4147	,possibly-damaging	,238/426	61253841	574,12428	2202	4299	6501	SO:0001583	missense	220004	exon8			GTGTCACCAAGTC	AK057333	CCDS8008.1, CCDS53641.1	11q12.2	2012-04-17	2011-10-11	2011-10-11	ENSG00000162148	ENSG00000162148		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	28869	protein-coding gene	gene with protein product			"""chromosome 11 open reading frame 66"""	C11orf66		12477932	Standard	NM_145017		Approved	IIIG9, FLJ32771	uc001nru.2	Q7Z5V6	OTTHUMG00000168176	ENST00000338608.2:c.713C>A	11.37:g.61253841C>A	ENSP00000344140:p.Thr238Asn	Somatic	194	0	0		WXS	Illumina HiSeq	Phase_I	143	107	0.748252	NM_145017	Q4G0P4|Q96M77	Missense_Mutation	SNP	ENST00000338608.2	37	CCDS8008.1	89	0.04075091575091575	79	0.16056910569105692	2	0.0055248618784530384	0	0.0	8	0.010554089709762533	C	17.86	3.492963	0.64074	0.116258	0.007211	ENSG00000162148	ENST00000338608;ENST00000542951;ENST00000535545	T;T;T	0.44881	1.39;0.91;1.3	4.37	3.39	0.38822	.	0.338132	0.23748	N	0.044945	T	0.00384	0.0012	M	0.73598	2.24	0.09310	P	0.9999999999999436	D	0.67145	0.996	D	0.66847	0.947	T	0.13899	-1.0492	9	0.56958	D	0.05	-0.1502	12.184	0.54227	0.0:0.8279:0.1721:0.0	rs11230707;rs11230707	238	Q7Z5V6	PPR32_HUMAN	N	238;18;5	ENSP00000344140:T238N;ENSP00000441053:T18N;ENSP00000437511:T5N	ENSP00000344140:T238N	T	+	2	0	C11orf66	61010417	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	1.646000	0.37249	2.153000	0.67306	0.650000	0.86243	ACC	C|0.955;A|0.045	0.045	strong		0.637	PPP1R32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398621.1	NM_145017	
T	6862	hgsc.bcm.edu	37	6	166580188	166580188	+	Silent	SNP	G	G	A	rs1056048	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:166580188G>A	ENST00000296946.2	-	3	831	c.363C>T	c.(361-363)agC>agT	p.S121S	T_ENST00000366871.3_Silent_p.S121S	NM_003181.3	NP_003172.1	O15178	BRAC_HUMAN	T, brachyury homolog (mouse)	121					anterior/posterior axis specification, embryo (GO:0008595)|BMP signaling pathway (GO:0030509)|bone morphogenesis (GO:0060349)|canonical Wnt signaling pathway (GO:0060070)|determination of heart left/right asymmetry (GO:0061371)|embryonic skeletal system development (GO:0048706)|heart morphogenesis (GO:0003007)|mesoderm development (GO:0007498)|mesoderm migration involved in gastrulation (GO:0007509)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural plate morphogenesis (GO:0001839)|neural tube closure (GO:0001843)|notochord formation (GO:0014028)|penetration of zona pellucida (GO:0007341)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation (GO:0003257)|post-anal tail morphogenesis (GO:0036342)|primitive streak formation (GO:0090009)|signal transduction (GO:0007165)|signal transduction involved in regulation of gene expression (GO:0023019)|SMAD protein signal transduction (GO:0060395)|somitogenesis (GO:0001756)|transcription from RNA polymerase II promoter (GO:0006366)|vasculogenesis (GO:0001570)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)			autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(23)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	39		Prostate(117;4.48e-07)|Ovarian(120;1.78e-06)|Breast(66;2.54e-06)|Lung SC(201;0.0225)|Esophageal squamous(34;0.0559)		OV - Ovarian serous cystadenocarcinoma(33;1.09e-113)|GBM - Glioblastoma multiforme(31;1.51e-108)|BRCA - Breast invasive adenocarcinoma(81;8.45e-09)|LUAD - Lung adenocarcinoma(999;0.0407)		TGTAGACGCAGCTGGGCGCCT	0.642									Chordoma, Familial Clustering of				G|||	1063	0.21226	0.3737	0.2176	5008	,	,		14789	0.0437		0.2137	False		,,,				2504	0.1626				p.S121S		Atlas-SNP	.											.	T	77	.	0			c.C363T						PASS	.	G		1535,2871	474.6+/-357.0	253,1029,921	49.0	54.0	52.0		363	3.8	1.0	6	dbSNP_86	52	1805,6795	318.6+/-313.7	192,1421,2687	no	coding-synonymous	T	NM_003181.2		445,2450,3608	AA,AG,GG		20.9884,34.8389,25.6805		121/436	166580188	3340,9666	2203	4300	6503	SO:0001819	synonymous_variant	6862	exon3	Familial Cancer Database		GACGCAGCTGGGC	AJ001699	CCDS5290.1, CCDS59045.1	6q27	2011-06-13	2001-11-28		ENSG00000164458	ENSG00000164458		"""T-boxes"""	11515	protein-coding gene	gene with protein product		601397	"""T brachyury (mouse) homolog"""			8963900	Standard	NM_003181		Approved		uc003quu.2	O15178	OTTHUMG00000015991	ENST00000296946.2:c.363C>T	6.37:g.166580188G>A		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	74	19	0.256757	NM_003181	E7ERD6|Q4KMP4	Silent	SNP	ENST00000296946.2	37	CCDS5290.1																																																																																			G|0.749;A|0.251	0.251	strong		0.642	T-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043037.2	NM_003181	
SEMA6B	10501	hgsc.bcm.edu	37	19	4558431	4558431	+	Silent	SNP	C	C	G	rs2304213	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:4558431C>G	ENST00000586582.1	-	2	349	c.39G>C	c.(37-39)ctG>ctC	p.L13L	SEMA6B_ENST00000301293.3_Silent_p.L13L|SEMA6B_ENST00000586965.1_Silent_p.L13L	NM_032108.3	NP_115484.2	Q9H3T3	SEM6B_HUMAN	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6B	13					cell differentiation (GO:0030154)|nervous system development (GO:0007399)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			breast(1)|central_nervous_system(2)|large_intestine(4)|lung(11)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0149)|STAD - Stomach adenocarcinoma(1328;0.18)		GCAGAAGCAGCAGGGCCGGGC	0.736											OREG0025169	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	2336	0.466454	0.3707	0.4841	5008	,	,		9439	0.5952		0.4543	False		,,,				2504	0.4632				p.L13L		Atlas-SNP	.											SEMA6B,NS,carcinoma,0,2	SEMA6B	51	2	0			c.G39C						PASS	.	C		1228,2490		275,678,906	3.0	5.0	4.0		39	-1.8	0.5	19	dbSNP_100	4	2974,4598		716,1542,1528	no	coding-synonymous	SEMA6B	NM_032108.3		991,2220,2434	GG,GC,CC		39.2763,33.0285,37.2188		13/889	4558431	4202,7088	1859	3786	5645	SO:0001819	synonymous_variant	10501	exon2			AAGCAGCAGGGCC	AB022433	CCDS12131.1	19p13.3	2008-07-22				ENSG00000167680		"""Semaphorins"""	10739	protein-coding gene	gene with protein product	"""Sema VIb"", ""semaphorin Z"", ""semaphorin VIB"""	608873		SEMAN		9361278	Standard	NM_032108		Approved	semaZ, SEMA-VIB, SEM-SEMA-Y	uc010dud.2	Q9H3T3		ENST00000586582.1:c.39G>C	19.37:g.4558431C>G		Somatic	15	0	0	619	WXS	Illumina HiSeq	Phase_I	20	12	0.6	NM_032108	A5PKU4|F6IB19|Q9NRK9	Silent	SNP	ENST00000586582.1	37	CCDS12131.1																																																																																			C|0.510;G|0.490	0.490	strong		0.736	SEMA6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458656.2	NM_032108	
KRT32	3882	hgsc.bcm.edu	37	17	39623363	39623363	+	Missense_Mutation	SNP	T	T	C	rs3744786	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	103	0	0		WXS	Illumina HiSeq	Phase_I	65	65	1	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	
IGSF1	3547	hgsc.bcm.edu	37	X	130408745	130408745	+	Silent	SNP	G	G	A	rs6529473	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:130408745G>A	ENST00000361420.3	-	18	3658	c.3579C>T	c.(3577-3579)gtC>gtT	p.V1193V	IGSF1_ENST00000370903.3_Silent_p.V1198V|IGSF1_ENST00000467244.1_5'Flank|IGSF1_ENST00000370910.1_Silent_p.V1184V|IGSF1_ENST00000370904.1_Silent_p.V1184V			Q8N6C5	IGSF1_HUMAN	immunoglobulin superfamily, member 1	1193	Ig-like C2-type 12.				regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	coreceptor activity (GO:0015026)|inhibin binding (GO:0034711)|receptor activity (GO:0004872)			breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(15)|liver(1)|lung(37)|ovary(4)|skin(3)|upper_aerodigestive_tract(2)	78						CATGTTCTAGGACAAATTCAA	0.502													G|||	1759	0.46596	0.2806	0.3545	3775	,	,		14720	0.6101		0.1769	False		,,,				2504	0.3569				p.V1198V		Atlas-SNP	.											.	IGSF1	231	.	0			c.C3594T						PASS	.	G	,,	1354,2481		201,750,202,681,369	167.0	163.0	165.0		3594,3552,3579	-1.1	1.0	X	dbSNP_116	165	1486,5242		122,844,398,1462,1474	no	coding-synonymous,coding-synonymous,coding-synonymous	IGSF1	NM_001170961.1,NM_001170962.1,NM_001555.4	,,	323,1594,600,2143,1843	AA,AG,A,GG,G		22.0868,35.3064,26.8863	,,	1198/1342,1184/1328,1193/1337	130408745	2840,7723	2203	4300	6503	SO:0001819	synonymous_variant	3547	exon18			TTCTAGGACAAAT	AF034198	CCDS14629.1, CCDS14630.1, CCDS55490.1, CCDS55491.1	Xq25	2013-01-11			ENSG00000147255	ENSG00000147255		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5948	protein-coding gene	gene with protein product		300137				9521868, 9729118	Standard	NM_001555		Approved	KIAA0364, IGDC1, IGCD1, INHBP, MGC75490, PGSF2	uc004ewe.4	Q8N6C5	OTTHUMG00000022406	ENST00000361420.3:c.3579C>T	X.37:g.130408745G>A		Somatic	233	0	0		WXS	Illumina HiSeq	Phase_I	169	167	0.988166	NM_001170961	B5MEG2|H9KV64|O15070|Q9NTC8	Silent	SNP	ENST00000361420.3	37	CCDS14629.1																																																																																			0|0.003;A|0.363	0.363	strong		0.502	IGSF1-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000058288.1		
UNC13D	201294	hgsc.bcm.edu	37	17	73836162	73836162	+	Silent	SNP	C	C	G	rs7223416	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:73836162C>G	ENST00000207549.4	-	11	1267	c.888G>C	c.(886-888)ccG>ccC	p.P296P	UNC13D_ENST00000587504.1_5'UTR|UNC13D_ENST00000412096.2_Silent_p.P296P	NM_199242.2	NP_954712.1	Q70J99	UN13D_HUMAN	unc-13 homolog D (C. elegans)	296	Interaction with RAB27A.				defense response to virus (GO:0051607)|germinal center formation (GO:0002467)|granuloma formation (GO:0002432)|natural killer cell degranulation (GO:0043320)|phagocytosis (GO:0006909)|positive regulation of exocytosis (GO:0045921)|regulation of mast cell degranulation (GO:0043304)	endosome (GO:0005768)|exocytic vesicle (GO:0070382)|lysosome (GO:0005764)|membrane (GO:0016020)				central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(9)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29			all cancers(21;2.11e-06)|Epithelial(20;2.32e-06)|BRCA - Breast invasive adenocarcinoma(9;0.000618)|LUSC - Lung squamous cell carcinoma(166;0.154)			CGGTGTAGCTCGGCTGCGAGC	0.682									Familial Hemophagocytic Lymphohistiocytosis				G|||	2455	0.490216	0.8608	0.2954	5008	,	,		14710	0.4246		0.339	False		,,,				2504	0.3507				p.P296P		Atlas-SNP	.											.	UNC13D	68	.	0			c.G888C						PASS	.	G		3440,966	349.0+/-310.2	1354,732,117	28.0	33.0	32.0		888	4.3	1.0	17	dbSNP_116	32	2855,5743	658.1+/-401.5	475,1905,1919	no	coding-synonymous	UNC13D	NM_199242.2		1829,2637,2036	GG,GC,CC		33.2054,21.9246,48.4082		296/1091	73836162	6295,6709	2203	4299	6502	SO:0001819	synonymous_variant	201294	exon11	Familial Cancer Database	FHLH, FHL, Familial Hemophagocytic Reticulosis, FHR	GTAGCTCGGCTGC	AK024474	CCDS11730.1	17q25.3	2014-09-17				ENSG00000092929			23147	protein-coding gene	gene with protein product		608897					Standard	NM_199242		Approved	Munc13-4	uc002jpp.3	Q70J99		ENST00000207549.4:c.888G>C	17.37:g.73836162C>G		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	69	39	0.565217	NM_199242	B4DWG9|Q9H7K5	Silent	SNP	ENST00000207549.4	37	CCDS11730.1																																																																																			C|0.507;G|0.493	0.493	strong		0.682	UNC13D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448847.2	XM_113950	
TMEM184A	202915	hgsc.bcm.edu	37	7	1595068	1595068	+	Missense_Mutation	SNP	G	G	A	rs17852421	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:1595068G>A	ENST00000297477.5	-	2	369	c.53C>T	c.(52-54)gCg>gTg	p.A18V		NM_001097620.1	NP_001091089.1	Q6ZMB5	T184A_HUMAN	transmembrane protein 184A	18			A -> V (in dbSNP:rs17852421). {ECO:0000269|PubMed:15489334}.		germ-line sex determination (GO:0018992)|regulation of protein localization (GO:0032880)|regulation of secretion (GO:0051046)	early endosome membrane (GO:0031901)|integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(1)|lung(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	12		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0178)|OV - Ovarian serous cystadenocarcinoma(56;5.88e-15)		CGGCCAGTTCGCTGACACCAG	0.667													G|||	1112	0.222045	0.1936	0.3631	5008	,	,		15201	0.1915		0.2455	False		,,,				2504	0.1677				p.A18V		Atlas-SNP	.											.	TMEM184A	35	.	0			c.C53T						PASS	.		VAL/ALA	775,3333		93,589,1372	25.0	32.0	30.0		53	-2.5	0.0	7	dbSNP_123	30	1905,6493		246,1413,2540	yes	missense	TMEM184A	NM_001097620.1	64	339,2002,3912	AA,AG,GG		22.684,18.8656,21.4297	benign	18/414	1595068	2680,9826	2054	4199	6253	SO:0001583	missense	202915	exon2			CAGTTCGCTGACA		CCDS43537.1	7p22.3	2008-05-02			ENSG00000164855	ENSG00000164855			28797	protein-coding gene	gene with protein product						12477932	Standard	NM_001097620		Approved	MGC9712	uc003skv.4	Q6ZMB5	OTTHUMG00000119025	ENST00000297477.5:c.53C>T	7.37:g.1595068G>A	ENSP00000297477:p.Ala18Val	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	90	21	0.233333	NM_001097620	Q8TBQ6	Missense_Mutation	SNP	ENST00000297477.5	37	CCDS43537.1	520	0.23809523809523808	100	0.2032520325203252	121	0.3342541436464088	105	0.18356643356643357	194	0.2559366754617414	G	5.573	0.290622	0.10567	0.188656	0.22684	ENSG00000164855	ENST00000297477;ENST00000319010;ENST00000414730;ENST00000441933;ENST00000431208	T;T;T;T;T	0.50813	1.42;0.73;0.82;0.81;0.82	4.27	-2.47	0.06442	.	1.185970	0.06584	U	0.750848	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	0.37150	-0.9718	9	0.25106	T	0.35	-22.5353	6.1542	0.20328	0.4139:0.1304:0.4557:0.0	rs17852421;rs60268535	18	Q6ZMB5	T184A_HUMAN	V	18	ENSP00000297477:A18V;ENSP00000325945:A18V;ENSP00000398382:A18V;ENSP00000389092:A18V;ENSP00000403499:A18V	ENSP00000297477:A18V	A	-	2	0	TMEM184A	1561594	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.512000	0.06313	-0.333000	0.08476	-0.369000	0.07265	GCG	G|0.778;A|0.222	0.222	strong		0.667	TMEM184A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239229.4	NM_152689	
ITIH1	3697	hgsc.bcm.edu	37	3	52820981	52820981	+	Missense_Mutation	SNP	A	A	T	rs678	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:52820981A>T	ENST00000273283.2	+	14	1778	c.1754A>T	c.(1753-1755)gAg>gTg	p.E585V	ITIH1_ENST00000542827.1_Missense_Mutation_p.E585V|ITIH1_ENST00000540715.1_Missense_Mutation_p.E443V|ITIH1_ENST00000405128.3_5'Flank|ITIH1_ENST00000537050.1_Missense_Mutation_p.E297V	NM_002215.3	NP_002206.2	P19827	ITIH1_HUMAN	inter-alpha-trypsin inhibitor heavy chain 1	585	Hyaluronan-binding.		E -> V (in allele ITIH1*2; dbSNP:rs678). {ECO:0000269|PubMed:1380832, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:7535743}.		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)		GACAGGGAGGAGAGGGCCAAC	0.572													A|||	1437	0.286941	0.1293	0.4452	5008	,	,		17837	0.3621		0.3936	False		,,,				2504	0.2004				p.E585V		Atlas-SNP	.											.	ITIH1	108	.	0			c.A1754T						PASS	.	A	VAL/GLU,VAL/GLU,VAL/GLU,VAL/GLU	646,3760	276.6+/-273.2	53,540,1610	84.0	77.0	79.0		1328,890,890,1754	5.3	1.0	3	dbSNP_36	79	3261,5339	488.0+/-372.2	652,1957,1691	yes	missense,missense,missense,missense	ITIH1	NM_001166434.1,NM_001166435.1,NM_001166436.1,NM_002215.2	121,121,121,121	705,2497,3301	TT,TA,AA		37.9186,14.6618,30.04	probably-damaging,probably-damaging,probably-damaging,probably-damaging	443/770,297/624,297/624,585/912	52820981	3907,9099	2203	4300	6503	SO:0001583	missense	3697	exon14			GGGAGGAGAGGGC		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.1754A>T	3.37:g.52820981A>T	ENSP00000273283:p.Glu585Val	Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	126	113	0.896825	NM_002215	A8K9N5|B2RAH9|B7Z558|B7Z8C0|F5H165|F5H7Y8|P78455|Q01746|Q562G1	Missense_Mutation	SNP	ENST00000273283.2	37	CCDS2864.1	779	0.3566849816849817	70	0.14227642276422764	165	0.4558011049723757	242	0.4230769230769231	302	0.39841688654353563	A	17.23	3.337296	0.60963	0.146618	0.379186	ENSG00000055957	ENST00000542827;ENST00000273283;ENST00000540715;ENST00000537050;ENST00000428133	T;T;T;T;T	0.40225	1.04;1.04;1.04;1.04;1.04	5.31	5.31	0.75309	.	0.095165	0.64402	D	0.000001	T	0.00012	0.0000	M	0.84846	2.72	0.22858	P	0.99864774	D;D;D	0.89917	0.989;0.997;1.0	D;D;D	0.85130	0.928;0.938;0.997	T	0.46091	-0.9216	9	0.62326	D	0.03	-40.9172	13.6481	0.62294	1.0:0.0:0.0:0.0	rs678;rs1126898;rs3177009;rs3182233;rs17418916;rs52793076;rs678	443;186;585	F5H165;Q9P1C5;P19827	.;.;ITIH1_HUMAN	V	585;585;443;297;138	ENSP00000442584:E585V;ENSP00000273283:E585V;ENSP00000443973:E443V;ENSP00000443847:E297V;ENSP00000395836:E138V	ENSP00000273283:E585V	E	+	2	0	ITIH1	52796021	1.000000	0.71417	0.983000	0.44433	0.153000	0.21895	5.954000	0.70298	2.234000	0.73211	0.459000	0.35465	GAG	A|0.681;T|0.319	0.319	strong		0.572	ITIH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317522.1	NM_002215	
KRT73	319101	hgsc.bcm.edu	37	12	53012053	53012053	+	Missense_Mutation	SNP	A	A	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:53012053A>C	ENST00000305748.3	-	1	290	c.256T>G	c.(256-258)Ttt>Gtt	p.F86V	RP11-641A6.2_ENST00000552364.1_RNA	NM_175068.2	NP_778238.1	Q86Y46	K2C73_HUMAN	keratin 73	86	Gly-rich.|Head.					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)		ACACTGCCAAACATGCTGCCA	0.637																																					p.F86V		Atlas-SNP	.											.	KRT73	101	.	0			c.T256G						PASS	.						107.0	119.0	115.0					12																	53012053		2203	4300	6503	SO:0001583	missense	319101	exon1			TGCCAAACATGCT	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.256T>G	12.37:g.53012053A>C	ENSP00000307014:p.Phe86Val	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	118	69	0.584746	NM_175068	Q32MB2	Missense_Mutation	SNP	ENST00000305748.3	37	CCDS8834.1	.	.	.	.	.	.	.	.	.	.	A	12.73	2.025490	0.35701	.	.	ENSG00000186049	ENST00000305748	D	0.91351	-2.83	4.64	3.5	0.40072	.	0.114168	0.38959	N	0.001513	D	0.91372	0.7278	M	0.89534	3.04	0.28878	N	0.894598	P	0.38455	0.632	B	0.43155	0.41	D	0.84270	0.0488	10	0.23302	T	0.38	.	6.9916	0.24758	0.7232:0.1908:0.086:0.0	.	86	Q86Y46	K2C73_HUMAN	V	86	ENSP00000307014:F86V	ENSP00000307014:F86V	F	-	1	0	KRT73	51298320	0.193000	0.23313	1.000000	0.80357	0.888000	0.51559	3.442000	0.52900	0.887000	0.36136	0.533000	0.62120	TTT	.	.	none		0.637	KRT73-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405700.1	NM_175068	
MAGEB3	4114	hgsc.bcm.edu	37	X	30254530	30254530	+	Silent	SNP	A	A	G	rs2071310	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:30254530A>G	ENST00000361644.2	+	5	1226	c.489A>G	c.(487-489)gtA>gtG	p.V163V		NM_002365.4	NP_002356.2	O15480	MAGB3_HUMAN	melanoma antigen family B, 3	163	MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.							p.V163V(1)		NS(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(12)|prostate(2)|skin(2)	25						TGGAGGTGGTATTTGGTGTTG	0.408													A|||	1761	0.46649	0.2474	0.3746	3775	,	,		15794	0.4008		0.3648	False		,,,				2504	0.4121				p.V163V		Atlas-SNP	.											.	MAGEB3	54	.	1	Substitution - coding silent(1)	prostate(1)	c.A489G						PASS	.	A		1297,2536		173,753,198,705,373	92.0	85.0	88.0		489	-7.2	0.1	X	dbSNP_96	88	3010,3718		470,1217,853,741,1019	no	coding-synonymous	MAGEB3	NM_002365.4		643,1970,1051,1446,1392	GG,GA,G,AA,A		44.7384,33.8377,40.7821		163/347	30254530	4307,6254	2202	4300	6502	SO:0001819	synonymous_variant	4114	exon5			GGTGGTATTTGGT	AK057441	CCDS14220.1	Xp21.3	2009-03-17			ENSG00000198798	ENSG00000198798			6810	protein-coding gene	gene with protein product	"""cancer/testis antigen family 3, member 5"""	300152				9441743	Standard	NM_002365		Approved	CT3.5	uc004dca.2	O15480	OTTHUMG00000021320	ENST00000361644.2:c.489A>G	X.37:g.30254530A>G		Somatic	402	0	0		WXS	Illumina HiSeq	Phase_I	240	238	0.991667	NM_002365	A0AVE4|B3KQ52|O75861	Silent	SNP	ENST00000361644.2	37	CCDS14220.1																																																																																			A|0.567;0|0.003	.	strong		0.408	MAGEB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056158.2	NM_002365	
SPTLC3	55304	hgsc.bcm.edu	37	20	13134768	13134768	+	Silent	SNP	T	T	C	rs6078938	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:13134768T>C	ENST00000399002.2	+	10	1672	c.1398T>C	c.(1396-1398)taT>taC	p.Y466Y	SPTLC3_ENST00000378194.4_3'UTR	NM_018327.2	NP_060797.2	Q9NUV7	SPTC3_HUMAN	serine palmitoyltransferase, long chain base subunit 3	466					small molecule metabolic process (GO:0044281)|sphingoid biosynthetic process (GO:0046520)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|serine C-palmitoyltransferase complex (GO:0017059)	pyridoxal phosphate binding (GO:0030170)|serine C-palmitoyltransferase activity (GO:0004758)			breast(1)|endometrium(1)|large_intestine(7)|lung(14)|skin(1)|urinary_tract(1)	25						TGCTTCTTTATATGCCTGGTA	0.413													T|||	764	0.152556	0.146	0.2219	5008	,	,		23284	0.2262		0.1282	False		,,,				2504	0.0613				p.Y466Y		Atlas-SNP	.											.	SPTLC3	78	.	0			c.T1398C						PASS	.	T		545,3323		40,465,1429	148.0	138.0	141.0		1398	-3.3	1.0	20	dbSNP_114	141	1155,7143		81,993,3075	no	coding-synonymous	SPTLC3	NM_018327.2		121,1458,4504	CC,CT,TT		13.919,14.09,13.9734		466/553	13134768	1700,10466	1934	4149	6083	SO:0001819	synonymous_variant	55304	exon10			TCTTTATATGCCT	AL109983	CCDS13115.2	20p12.1	2011-07-05	2006-12-21	2006-12-21	ENSG00000172296	ENSG00000172296	2.3.1.50		16253	protein-coding gene	gene with protein product		611120	"""chromosome 20 open reading frame 38"", ""serine palmitoyltransferase, long chain base subunit 2-like (aminotransferase 2)"""	C20orf38, SPTLC2L		17023427	Standard	NM_018327		Approved	LCB2B, FLJ11112, hLCB2b	uc002wod.1	Q9NUV7	OTTHUMG00000031899	ENST00000399002.2:c.1398T>C	20.37:g.13134768T>C		Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	141	50	0.35461	NM_018327	A2A2I4|B9EK64|Q05DQ8|Q5T1U4|Q9H1L1|Q9H1Z0	Silent	SNP	ENST00000399002.2	37	CCDS13115.2	410	0.18772893772893773	95	0.19308943089430894	78	0.2154696132596685	134	0.23426573426573427	103	0.1358839050131926	T	4.123	0.021081	0.08006	0.1409	0.13919	ENSG00000172296	ENST00000431275	.	.	.	5.91	-3.3	0.05003	.	.	.	.	.	T	0.00039	0.0001	.	.	.	0.09310	P	0.9999999999999999	.	.	.	.	.	.	T	0.29274	-1.0017	3	.	.	.	-15.7123	14.1581	0.65430	0.0:0.4471:0.0:0.5529	rs6078938;rs60355870;rs6078938	.	.	.	T	64	.	.	I	+	2	0	SPTLC3	13082768	0.997000	0.39634	0.979000	0.43373	0.565000	0.35776	0.543000	0.23237	-0.392000	0.07751	-1.033000	0.02402	ATA	T|0.826;C|0.174	0.174	strong		0.413	SPTLC3-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254544.1	NM_018327	
CD101	9398	hgsc.bcm.edu	37	1	117554247	117554247	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:117554247C>T	ENST00000256652.4	+	3	558	c.500C>T	c.(499-501)aCc>aTc	p.T167I	CD101_ENST00000369470.1_Missense_Mutation_p.T167I	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	167	Ig-like C2-type 2.				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						TTAGCCCTCACCTGTGAGGCA	0.483																																					p.T167I		Atlas-SNP	.											.	CD101	95	.	0			c.C500T						PASS	.						107.0	93.0	98.0					1																	117554247		2203	4300	6503	SO:0001583	missense	9398	exon3			CCCTCACCTGTGA	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.500C>T	1.37:g.117554247C>T	ENSP00000256652:p.Thr167Ile	Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	141	60	0.425532	NM_001256109	Q15856	Missense_Mutation	SNP	ENST00000256652.4	37	CCDS891.1	.	.	.	.	.	.	.	.	.	.	C	12.64	1.999464	0.35320	.	.	ENSG00000134256	ENST00000256652;ENST00000369470	T;T	0.67171	-0.25;-0.25	5.33	4.41	0.53225	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.565464	0.18042	N	0.153594	T	0.73729	0.3624	M	0.82823	2.61	0.33375	D	0.574133	D	0.89917	1.0	D	0.80764	0.994	T	0.76672	-0.2873	10	0.72032	D	0.01	-9.8961	7.5864	0.27995	0.0:0.7445:0.1664:0.0891	.	167	Q93033	IGSF2_HUMAN	I	167	ENSP00000256652:T167I;ENSP00000358482:T167I	ENSP00000256652:T167I	T	+	2	0	CD101	117355770	0.104000	0.21937	0.653000	0.29593	0.026000	0.11368	0.930000	0.28858	1.254000	0.44035	0.650000	0.86243	ACC	.	.	none		0.483	CD101-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033274.1	NM_004258	
GALNT8	26290	hgsc.bcm.edu	37	12	4835882	4835882	+	Silent	SNP	T	T	G	rs2286578	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:4835882T>G	ENST00000252318.2	+	2	733	c.396T>G	c.(394-396)ctT>ctG	p.L132L	RP11-234B24.6_ENST00000544741.2_3'UTR	NM_017417.1	NP_059113.1	Q9NY28	GALT8_HUMAN	polypeptide N-acetylgalactosaminyltransferase 8	132					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)			central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(13)|ovary(2)|pancreas(1)|prostate(4)|skin(2)|urinary_tract(1)	35						GCGAGGATCTTTCTGAGGCCC	0.522													T|||	1568	0.313099	0.1838	0.4179	5008	,	,		16829	0.3601		0.4274	False		,,,				2504	0.2474				p.L132L	Colon(108;631 1558 7270 20097 39846)	Atlas-SNP	.											.	GALNT8	89	.	0			c.T396G						PASS	.	T		1049,3357	385.8+/-325.9	140,769,1294	64.0	60.0	61.0		396	-6.1	0.0	12	dbSNP_100	61	3571,5029	517.6+/-379.1	741,2089,1470	no	coding-synonymous	GALNT8	NM_017417.1		881,2858,2764	GG,GT,TT		41.5233,23.8084,35.5221		132/638	4835882	4620,8386	2203	4300	6503	SO:0001819	synonymous_variant	26290	exon2			GGATCTTTCTGAG	AJ271385	CCDS8533.1	12p13.32	2014-03-13	2014-03-13		ENSG00000130035	ENSG00000130035	2.4.1.41	"""Glycosyltransferase family 2 domain containing"""	4130	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase 8"""	606250	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 8 (GalNAc-T8)"""			10767557	Standard	NM_017417		Approved	GALNAC-T8	uc001qne.1	Q9NY28	OTTHUMG00000166188	ENST00000252318.2:c.396T>G	12.37:g.4835882T>G		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	57	29	0.508772	NM_017417	B2RU02	Silent	SNP	ENST00000252318.2	37	CCDS8533.1																																																																																			T|0.649;G|0.351	0.351	strong		0.522	GALNT8-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388277.2	NM_017417	
FAM200B	285550	hgsc.bcm.edu	37	4	15689632	15689632	+	Silent	SNP	G	G	A	rs11729955	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:15689632G>A	ENST00000422728.2	+	2	1870	c.1032G>A	c.(1030-1032)gaG>gaA	p.E344E	FAM200B_ENST00000504137.1_Intron	NM_001145191.1	NP_001138663.1	P0CF97	F200B_HUMAN	family with sequence similarity 200, member B	344							nucleic acid binding (GO:0003676)	p.E344E(2)		endometrium(1)|kidney(1)	2						atctcatggaggtattgaaaa	0.328													A|||	1502	0.29992	0.3858	0.3098	5008	,	,		17540	0.1379		0.4056	False		,,,				2504	0.2352				p.E344E		Atlas-SNP	.											FAM200B_ENST00000422728,NS,carcinoma,0,2	FAM200B	56	2	2	Substitution - coding silent(2)	kidney(2)	c.G1032A						PASS	.	A		529,855		110,309,273	52.0	48.0	49.0		1032	2.6	1.0	4	dbSNP_120	49	1257,1925		249,759,583	no	coding-synonymous	FAM200B	NM_001145191.1		359,1068,856	AA,AG,GG		39.5035,38.2225,39.1152		344/658	15689632	1786,2780	692	1591	2283	SO:0001819	synonymous_variant	285550	exon2			CATGGAGGTATTG	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.1032G>A	4.37:g.15689632G>A		Somatic	218	0	0		WXS	Illumina HiSeq	Phase_I	191	93	0.486911	NM_001145191		Silent	SNP	ENST00000422728.2	37	CCDS47028.1																																																																																			G|0.683;A|0.317	0.317	strong		0.328	FAM200B-005	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360100.1	NM_001145191	
ERICH3	127254	hgsc.bcm.edu	37	1	75055419	75055419	+	Missense_Mutation	SNP	T	T	C	rs2305549	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:75055419T>C	ENST00000326665.5	-	12	2290	c.2072A>G	c.(2071-2073)cAt>cGt	p.H691R	RP4-612J11.1_ENST00000416017.1_RNA|C1orf173_ENST00000420661.2_Missense_Mutation_p.H494R	NM_001002912.4	NP_001002912.4	Q5RHP9	ERIC3_HUMAN		691	Glu-rich.		H -> R (in dbSNP:rs2305549).							NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(23)|lung(123)|ovary(3)|prostate(10)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)	184						TGCAGAAACATGTTTCCCGGA	0.453													T|||	589	0.117612	0.0461	0.1455	5008	,	,		21440	0.2252		0.0964	False		,,,				2504	0.1053				p.H691R		Atlas-SNP	.											.	C1orf173	380	.	0			c.A2072G						PASS	.	T	ARG/HIS	192,4214	121.7+/-159.2	2,188,2013	177.0	173.0	174.0		2072	-1.8	0.0	1	dbSNP_100	174	745,7855	180.0+/-229.1	32,681,3587	yes	missense	C1orf173	NM_001002912.4	29	34,869,5600	CC,CT,TT		8.6628,4.3577,7.2044	benign	691/1531	75055419	937,12069	2203	4300	6503	SO:0001583	missense	127254	exon12			GAAACATGTTTCC																												ENST00000326665.5:c.2072A>G	1.37:g.75055419T>C	ENSP00000322609:p.His691Arg	Somatic	265	0	0		WXS	Illumina HiSeq	Phase_I	240	107	0.445833	NM_001002912	Q68DL8|Q6GMR8|Q6ZSF9|Q8ND41	Missense_Mutation	SNP	ENST00000326665.5	37	CCDS30755.1	278	0.12728937728937728	25	0.0508130081300813	53	0.1464088397790055	119	0.20804195804195805	81	0.10686015831134564	T	9.430	1.085260	0.20390	0.043577	0.086628	ENSG00000178965	ENST00000326665;ENST00000420661	T;T	0.16743	2.73;2.32	5.44	-1.84	0.07809	.	.	.	.	.	T	0.03011	0.0089	L	0.39898	1.24	0.80722	P	0.0	B;P	0.39216	0.062;0.664	B;B	0.37239	0.101;0.244	T	0.37663	-0.9696	8	0.16420	T	0.52	0.0943	3.3231	0.07057	0.3447:0.2397:0.0:0.4156	rs2305549;rs52830994;rs57246811;rs2305549	494;691	Q5RHP9-3;Q5RHP9	.;CA173_HUMAN	R	691;494	ENSP00000322609:H691R;ENSP00000398581:H494R	ENSP00000322609:H691R	H	-	2	0	C1orf173	74828007	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-0.564000	0.05936	-0.662000	0.05338	-0.317000	0.08691	CAT	T|0.909;C|0.091	0.091	strong		0.453	C1orf173-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026516.1		
PIGG	54872	hgsc.bcm.edu	37	4	527677	527677	+	Missense_Mutation	SNP	T	T	C	rs34623004	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:527677T>C	ENST00000453061.2	+	12	2748	c.2642T>C	c.(2641-2643)aTc>aCc	p.I881T	PIGG_ENST00000383028.4_Missense_Mutation_p.I748T|PIGG_ENST00000296306.7_3'UTR|PIGG_ENST00000504346.1_Missense_Mutation_p.I792T|PIGG_ENST00000310340.5_Missense_Mutation_p.I873T	NM_001127178.1	NP_001120650.1	Q5H8A4	PIGG_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class G	881			I -> T (in dbSNP:rs34623004).		C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|GPI anchor biosynthetic process (GO:0006506)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	CP2 mannose-ethanolamine phosphotransferase activity (GO:0051267)|phosphotransferase activity, for other substituted phosphate groups (GO:0016780)	p.I873T(1)		breast(1)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(5)|lung(16)|ovary(3)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	39						TACGTGGAAATCCCAGCCGTG	0.582													T|||	1041	0.207867	0.3593	0.098	5008	,	,		18246	0.2212		0.1262	False		,,,				2504	0.1513				p.I881T		Atlas-SNP	.											PIGG,colon,carcinoma,0,5	PIGG	86	5	1	Substitution - Missense(1)	central_nervous_system(1)	c.T2642C						PASS	.	T	THR/ILE,THR/ILE	1418,2988	462.6+/-353.3	227,964,1012	120.0	100.0	107.0		2642,2618	3.3	0.7	4	dbSNP_126	107	1087,7513	227.1+/-262.6	73,941,3286	yes	missense,missense	PIGG	NM_001127178.1,NM_017733.3	89,89	300,1905,4298	CC,CT,TT		12.6395,32.1834,19.2603	benign,benign	881/984,873/976	527677	2505,10501	2203	4300	6503	SO:0001583	missense	54872	exon12			TGGAAATCCCAGC		CCDS3336.1, CCDS46992.1, CCDS75080.1, CCDS75081.1, CCDS75082.1, CCDS75083.1	4p16.3	2013-02-26	2006-06-28		ENSG00000174227	ENSG00000174227		"""Phosphatidylinositol glycan anchor biosynthesis"""	25985	protein-coding gene	gene with protein product			"""phosphatidylinositol glycan, class G"""			15632136	Standard	XM_005272287		Approved	FLJ20265, GPI7, LAS21	uc003gak.4	Q5H8A4	OTTHUMG00000112457	ENST00000453061.2:c.2642T>C	4.37:g.527677T>C	ENSP00000415203:p.Ile881Thr	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	125	60	0.48	NM_001127178	B4DKC7|Q2TAK5|Q6UX31|Q7L5Y4|Q8N866|Q8NCC9|Q96SY9|Q9BVT7|Q9NXG5	Missense_Mutation	SNP	ENST00000453061.2	37	CCDS46992.1	452	0.20695970695970695	181	0.3678861788617886	40	0.11049723756906077	139	0.243006993006993	92	0.12137203166226913	T	13.76	2.332370	0.41297	0.321834	0.126395	ENSG00000174227	ENST00000310340;ENST00000453061;ENST00000504346;ENST00000383028;ENST00000453065	T;T;T;T	0.30714	1.52;1.52;1.52;1.52	5.78	3.28	0.37604	.	0.832250	0.11531	N	0.554683	T	0.00012	0.0000	L	0.36672	1.1	0.27728	P	0.9448951	B;B;B	0.15473	0.013;0.004;0.007	B;B;B	0.14578	0.007;0.005;0.011	T	0.42682	-0.9437	9	0.31617	T	0.26	-3.3367	6.3218	0.21223	0.0:0.0893:0.1585:0.7522	rs34623004;rs58102883	748;881;873	Q5H8A4-3;Q5H8A4;Q5H8A4-2	.;PIGG_HUMAN;.	T	873;881;792;748;37	ENSP00000311750:I873T;ENSP00000415203:I881T;ENSP00000424800:I792T;ENSP00000372494:I748T	ENSP00000311750:I873T	I	+	2	0	PIGG	517677	0.623000	0.27094	0.683000	0.30040	0.922000	0.55478	2.837000	0.48191	0.505000	0.28104	0.533000	0.62120	ATC	T|0.799;C|0.201	0.201	strong		0.582	PIGG-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000357494.1	NM_017733	
EXOC1	55763	hgsc.bcm.edu	37	4	56756531	56756531	+	Silent	SNP	T	T	C	rs2290016	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:56756531T>C	ENST00000381295.2	+	12	1866	c.1518T>C	c.(1516-1518)gcT>gcC	p.A506A	EXOC1_ENST00000349598.6_Silent_p.A491A|EXOC1_ENST00000346134.7_Silent_p.A506A	NM_001024924.1	NP_001020095.1	Q9NV70	EXOC1_HUMAN	exocyst complex component 1	506					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)					TCGATGTTGCTGACAGGACCA	0.388													C|||	1632	0.325879	0.2617	0.281	5008	,	,		18688	0.5278		0.2843	False		,,,				2504	0.2791				p.A506A		Atlas-SNP	.											.	EXOC1	103	.	0			c.T1518C						PASS	.	C	,,	1235,3171	704.5+/-407.1	169,897,1137	130.0	115.0	120.0		1518,1518,1473	-10.9	0.1	4	dbSNP_100	120	2500,6100	695.2+/-404.8	371,1758,2171	no	coding-synonymous,coding-synonymous,coding-synonymous	EXOC1	NM_001024924.1,NM_018261.3,NM_178237.2	,,	540,2655,3308	CC,CT,TT		29.0698,28.03,28.7175	,,	506/895,506/895,491/880	56756531	3735,9271	2203	4300	6503	SO:0001819	synonymous_variant	55763	exon12			TGTTGCTGACAGG	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.1518T>C	4.37:g.56756531T>C		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	71	70	0.985915	NM_018261	Q504V4|Q8WUE7|Q96T15|Q9NZE4	Silent	SNP	ENST00000381295.2	37	CCDS3502.1																																																																																			T|0.688;C|0.312	0.312	strong		0.388	EXOC1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361799.1	NM_018261	
COASY	80347	hgsc.bcm.edu	37	17	40714804	40714804	+	Missense_Mutation	SNP	C	C	A	rs615942	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:40714804C>A	ENST00000393818.2	+	1	620	c.164C>A	c.(163-165)tCc>tAc	p.S55Y	RP11-400F19.8_ENST00000585572.1_RNA|COASY_ENST00000590958.1_Missense_Mutation_p.S84Y|COASY_ENST00000421097.2_Missense_Mutation_p.S55Y|COASY_ENST00000449624.1_Intron|COASY_ENST00000420359.1_Missense_Mutation_p.S55Y	NM_025233.6	NP_079509.5	Q13057	COASY_HUMAN	CoA synthase	55			S -> Y (in dbSNP:rs615942). {ECO:0000269|PubMed:11923312, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.6}.		cell death (GO:0008219)|coenzyme A biosynthetic process (GO:0015937)|coenzyme biosynthetic process (GO:0009108)|pantothenate metabolic process (GO:0015939)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrial outer membrane (GO:0005741)|nucleus (GO:0005634)	ATP binding (GO:0005524)|dephospho-CoA kinase activity (GO:0004140)|pantetheine-phosphate adenylyltransferase activity (GO:0004595)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(3)|large_intestine(2)|lung(7)|ovary(1)|prostate(1)	21		all_cancers(22;1.06e-05)|Breast(137;0.000153)|all_epithelial(22;0.000344)		BRCA - Breast invasive adenocarcinoma(366;0.13)		CAGCCCCAGTCCAGCCCCGTG	0.627													C|||	2539	0.506989	0.4289	0.487	5008	,	,		16531	0.4524		0.5239	False		,,,				2504	0.6656				p.S84Y		Atlas-SNP	.											COASY,colon,carcinoma,0,1	COASY	45	1	0			c.C251A						PASS	.	C	TYR/SER,TYR/SER,,TYR/SER,TYR/SER	1897,2505		400,1097,704	48.0	59.0	55.0		164,164,,251,164	5.7	1.0	17	dbSNP_83	55	4667,3929		1289,2089,920	yes	missense,missense,intron,missense,missense	COASY	NM_001042529.1,NM_001042530.1,NM_001042531.1,NM_001042532.2,NM_025233.5	144,144,,144,144	1689,3186,1624	AA,AC,CC		45.7073,43.094,49.4999	benign,benign,,benign,benign	55/565,55/565,,84/594,55/565	40714804	6564,6434	2201	4298	6499	SO:0001583	missense	80347	exon3			CCCAGTCCAGCCC	AF453478	CCDS11429.1, CCDS45685.1	17q12-q21	2010-04-30	2010-04-30			ENSG00000068120	2.7.7.3		29932	protein-coding gene	gene with protein product		609855	"""Coenzyme A synthase"""			11923312, 11980892	Standard	NM_025233		Approved	DPCK, NBP, CoASY, PPAT	uc010cyj.4	Q13057		ENST00000393818.2:c.164C>A	17.37:g.40714804C>A	ENSP00000377406:p.Ser55Tyr	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	76	30	0.394737	NM_001042532	B2RA78|B4DLU0|Q6GS23|Q8NBM7|Q8NEW1|Q8WXD4|Q9NRM3	Missense_Mutation	SNP	ENST00000393818.2	37	CCDS11429.1	1035	0.4739010989010989	222	0.45121951219512196	158	0.43646408839779005	256	0.44755244755244755	399	0.5263852242744064	C	19.53	3.845183	0.71603	0.43094	0.542927	ENSG00000068120	ENST00000421097;ENST00000420359;ENST00000393818;ENST00000426807	T;T	0.32515	1.45;1.45	5.69	5.69	0.88448	.	0.237138	0.43919	D	0.000516	T	0.00012	0.0000	N	0.24115	0.695	0.09310	P	1.0	P;P	0.51351	0.944;0.802	P;B	0.51135	0.66;0.176	T	0.48490	-0.9031	9	0.72032	D	0.01	-2.8551	17.2983	0.87175	0.0:1.0:0.0:0.0	rs615942;rs3198732;rs17738735;rs57211394;rs615942	84;55	Q13057-2;Q13057	.;COASY_HUMAN	Y	84;55;55;55	ENSP00000413338:S55Y;ENSP00000377406:S55Y	ENSP00000377406:S55Y	S	+	2	0	COASY	37968330	1.000000	0.71417	0.993000	0.49108	0.942000	0.58702	5.153000	0.64888	2.693000	0.91896	0.561000	0.74099	TCC	C|0.512;A|0.488	0.488	strong		0.627	COASY-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450409.1	NM_025233	
LRRC14	9684	hgsc.bcm.edu	37	8	145742879	145742879	+	5'Flank	SNP	T	T	C	rs2306386	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:145742879T>C	ENST00000292524.1	+	0	0				RECQL4_ENST00000532237.1_5'UTR|LRRC14_ENST00000529022.1_5'Flank|RECQL4_ENST00000428558.2_Silent_p.E44E	NM_001272036.1|NM_014665.2	NP_001258965.1|NP_055480.1	Q15048	LRC14_HUMAN	leucine rich repeat containing 14											endometrium(1)|lung(3)|prostate(1)	5	all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055)			GAGTGCGGTATTCCCGGTAGA	0.786													C|||	2880	0.57508	0.618	0.6282	5008	,	,		8649	0.5238		0.4891	False		,,,				2504	0.6207				p.E44E		Atlas-SNP	.											.	RECQL4	75	.	0			c.A132G						PASS	.	C		2027,1165		681,665,250	5.0	7.0	6.0		132	1.0	0.6	8	dbSNP_100	6	3861,3639		1088,1685,977	no	coding-synonymous	RECQL4	NM_004260.3		1769,2350,1227	CC,CT,TT		48.52,36.4975,44.9308		44/1209	145742879	5888,4804	1596	3750	5346	SO:0001631	upstream_gene_variant	9401	exon3			GCGGTATTCCCGG	BC011377	CCDS6432.1	8q24.3	2012-08-20			ENSG00000160959	ENSG00000160959			20419	protein-coding gene	gene with protein product						7584026	Standard	NM_001272036		Approved	KIAA0014, LRRC14A	uc003zdk.3	Q15048	OTTHUMG00000165179		8.37:g.145742879T>C	Exception_encountered	Somatic	4	0	0		WXS	Illumina HiSeq	Phase_I	10	10	1	NM_004260	A8K0A8|D3DWM8	Silent	SNP	ENST00000292524.1	37	CCDS6432.1																																																																																			T|0.468;C|0.532	0.532	strong		0.786	LRRC14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382494.1	NM_014665	
MUC5B	727897	hgsc.bcm.edu	37	11	1264767	1264767	+	Silent	SNP	G	G	A	rs2943501	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:1264767G>A	ENST00000529681.1	+	31	6715	c.6657G>A	c.(6655-6657)tcG>tcA	p.S2219S	MUC5B_ENST00000447027.1_Silent_p.S2222S|RP11-532E4.2_ENST00000532061.2_RNA	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	213	1	0.00469484		WXS	Illumina HiSeq	Phase_I	306	7	0.0228758	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	
ASIC4	55515	hgsc.bcm.edu	37	2	220402671	220402671	+	Missense_Mutation	SNP	G	G	T	rs11689281	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:220402671G>T	ENST00000347842.3	+	9	1861	c.1847G>T	c.(1846-1848)cGg>cTg	p.R616L	ASIC4_ENST00000358078.4_Missense_Mutation_p.R635L	NM_182847.2	NP_878267.2	Q96FT7	ASIC4_HUMAN	acid-sensing (proton-gated) ion channel family member 4	616			R -> L (in dbSNP:rs11689281). {ECO:0000269|PubMed:10852210, ECO:0000269|PubMed:11571555, ECO:0000269|PubMed:15489334}.		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)										TGCCCGAGCCGGGGCCGAGTG	0.627													G|||	2715	0.542133	0.3177	0.451	5008	,	,		15586	0.6706		0.5427	False		,,,				2504	0.7771				p.R616L		Atlas-SNP	.											.	.	.	.	0			c.G1847T						PASS	.	G	LEU/ARG,LEU/ARG	1469,2931		262,945,993	22.0	24.0	23.0		1904,1847	3.0	0.6	2	dbSNP_120	23	4544,4056		1224,2096,980	yes	missense,missense	ACCN4	NM_018674.4,NM_182847.2	102,102	1486,3041,1973	TT,TG,GG		47.1628,33.3864,46.2538	possibly-damaging,possibly-damaging	635/667,616/648	220402671	6013,6987	2200	4300	6500	SO:0001583	missense	55515	exon9			CGAGCCGGGGCCG	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.1847G>T	2.37:g.220402671G>T	ENSP00000326627:p.Arg616Leu	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	62	37	0.596774	NM_182847	Q53SB7|Q6GMS1|Q6PIN9|Q9NQA4	Missense_Mutation	SNP	ENST00000347842.3	37	CCDS2442.1	1142	0.5228937728937729	170	0.34552845528455284	183	0.505524861878453	381	0.666083916083916	408	0.5382585751978892	G	8.626	0.892657	0.17613	0.333864	0.528372	ENSG00000072182	ENST00000347842;ENST00000358078	T;T	0.62364	0.03;0.05	4.77	2.96	0.34315	.	0.196293	0.25526	N	0.030072	T	0.00012	0.0000	L	0.43923	1.385	0.25181	P	0.99020138	B;B	0.09022	0.001;0.002	B;B	0.10450	0.002;0.005	T	0.41945	-0.9480	9	0.33141	T	0.24	-6.4063	6.6013	0.22703	0.1619:0.0:0.6858:0.1523	rs11689281;rs17845259;rs17858088;rs11689281	616;635	Q96FT7;Q96FT7-4	ACCN4_HUMAN;.	L	616;635	ENSP00000326627:R616L;ENSP00000350786:R635L	ENSP00000326627:R616L	R	+	2	0	ACCN4	220110915	0.939000	0.31865	0.574000	0.28523	0.124000	0.20399	2.375000	0.44283	0.737000	0.32582	0.655000	0.94253	CGG	G|0.523;T|0.477	0.477	strong		0.627	ASIC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000130263.1	NM_018674	
ACAN	176	hgsc.bcm.edu	37	15	89400339	89400339	+	Missense_Mutation	SNP	A	A	C	rs2882676	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:89400339A>C	ENST00000561243.1	+	11	4523	c.4523A>C	c.(4522-4524)gAa>gCa	p.E1508A	ACAN_ENST00000439576.2_Missense_Mutation_p.E1508A|ACAN_ENST00000559004.1_Missense_Mutation_p.E1508A|ACAN_ENST00000352105.7_Missense_Mutation_p.E1508A			P16112	PGCA_HUMAN	aggrecan	1509	CS-2.				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|proteolysis (GO:0006508)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)	carbohydrate binding (GO:0030246)|extracellular matrix structural constituent (GO:0005201)|hyaluronic acid binding (GO:0005540)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(4)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(15)|liver(2)|lung(40)|ovary(2)|prostate(5)|skin(5)|stomach(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	93	Lung NSC(78;0.0392)|all_lung(78;0.077)		BRCA - Breast invasive adenocarcinoma(143;0.146)			GATGTCAGTGAACTTCCTTCA	0.493													A|||	2124	0.424121	0.3396	0.3804	5008	,	,		18797	0.25		0.6521	False		,,,				2504	0.5143				p.E1508A		Atlas-SNP	.											.	ACAN	220	.	0			c.A4523C	GRCh37	CM071536	ACAN	M	rs2882676	PASS	.	A	ALA/GLU,ALA/GLU	1469,2269		281,907,681	68.0	69.0	69.0		4523,4523	-2.1	0.0	15	dbSNP_101	69	5322,2876		1716,1890,493	yes	missense,missense	ACAN	NM_013227.3,NM_001135.3	107,107	1997,2797,1174	CC,CA,AA		35.0817,39.2991,43.1049	benign,benign	1508/2531,1508/2432	89400339	6791,5145	1869	4099	5968	SO:0001583	missense	176	exon12			TCAGTGAACTTCC	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.4523A>C	15.37:g.89400339A>C	ENSP00000453342:p.Glu1508Ala	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	95	95	1	NM_001135	Q13650|Q9UCD3|Q9UCP4|Q9UCP5|Q9UDE0	Missense_Mutation	SNP	ENST00000561243.1	37	CCDS53970.1	948	0.4340659340659341	157	0.31910569105691056	166	0.4585635359116022	120	0.2097902097902098	505	0.6662269129287599	A	2.232	-0.375823	0.05034	0.392991	0.649183	ENSG00000157766	ENST00000439576;ENST00000352105;ENST00000268134	D;D	0.94758	-3.51;-3.51	2.9	-2.06	0.07298	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	P;B	0.37061	0.58;0.425	B;B	0.39590	0.304;0.242	T	0.31308	-0.9948	7	0.25106	T	0.35	.	5.4084	0.16335	0.1053:0.0:0.4459:0.4488	rs2882676;rs3825995;rs52814625;rs59974113;rs2882676	1508;1508	E7ENV9;E7EX88	.;.	A	1508;1508;1394	ENSP00000387356:E1508A;ENSP00000341615:E1508A	ENSP00000268134:E1394A	E	+	2	0	ACAN	87201343	0.029000	0.19370	0.002000	0.10522	0.950000	0.60333	0.825000	0.27393	-0.544000	0.06232	0.260000	0.18958	GAA	A|0.565;C|0.435	0.435	strong		0.493	ACAN-006	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416267.2	NM_001135	
UNC5CL	222643	hgsc.bcm.edu	37	6	40998141	40998141	+	Silent	SNP	G	G	A	rs736795	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:40998141G>A	ENST00000373164.1	-	7	1380	c.1320C>T	c.(1318-1320)tgC>tgT	p.C440C	UNC5CL_ENST00000470102.1_5'UTR|UNC5CL_ENST00000244565.3_Silent_p.C440C			Q8IV45	UN5CL_HUMAN	unc-5 homolog C (C. elegans)-like	440	Death. {ECO:0000255|PROSITE- ProRule:PRU00064}.				positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of JNK cascade (GO:0046330)|proteolysis (GO:0006508)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	peptidase activity (GO:0008233)			endometrium(1)|kidney(3)|large_intestine(3)|lung(3)|ovary(2)|upper_aerodigestive_tract(1)	13	Ovarian(28;0.0418)|Colorectal(47;0.196)					TCTTCATGCCGCAAAGCCCCA	0.597													G|||	1385	0.276558	0.2368	0.268	5008	,	,		19416	0.2778		0.2038	False		,,,				2504	0.41				p.C440C		Atlas-SNP	.											.	UNC5CL	52	.	0			c.C1320T						PASS	.	G		1033,3373	380.9+/-323.9	131,771,1301	82.0	74.0	76.0		1320	-5.8	0.9	6	dbSNP_86	76	2098,6502	363.7+/-333.3	254,1590,2456	no	coding-synonymous	UNC5CL	NM_173561.2		385,2361,3757	AA,AG,GG		24.3953,23.4453,24.0735		440/519	40998141	3131,9875	2203	4300	6503	SO:0001819	synonymous_variant	222643	exon8			CATGCCGCAAAGC	BC035284	CCDS4847.1	6p21.1	2013-10-15			ENSG00000124602	ENSG00000124602			21203	protein-coding gene	gene with protein product	"""ZU5 and death domain containing"""					14769797	Standard	NM_173561		Approved	MGC34763, ZUD	uc003opi.3	Q8IV45	OTTHUMG00000014665	ENST00000373164.1:c.1320C>T	6.37:g.40998141G>A		Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	125	50	0.4	NM_173561	Q5TGU1	Silent	SNP	ENST00000373164.1	37	CCDS4847.1																																																																																			G|0.767;A|0.233	0.233	strong		0.597	UNC5CL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040491.1	NM_173561	
AHNAK2	113146	hgsc.bcm.edu	37	14	105416254	105416254	+	Missense_Mutation	SNP	G	G	A	rs386781100|rs201136817	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:105416254G>A	ENST00000333244.5	-	7	5653	c.5534C>T	c.(5533-5535)tCg>tTg	p.S1845L	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	1845						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)			CACATCCACCGAGGCCTCGAT	0.602													.|||	21	0.00419329	0.0136	0.0014	5008	,	,		19151	0.001		0.001	False		,,,				2504	0.0				p.S1845L		Atlas-SNP	.											AHNAK2_ENST00000333244,colon,carcinoma,+1,1	AHNAK2	719	1	0			c.C5534T						scavenged	.						178.0	216.0	203.0					14																	105416254		1935	4101	6036	SO:0001583	missense	113146	exon7			TCCACCGAGGCCT	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.5534C>T	14.37:g.105416254G>A	ENSP00000353114:p.Ser1845Leu	Somatic	196	1	0.00510204		WXS	Illumina HiSeq	Phase_I	182	8	0.043956	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	17	0.007783882783882784	17	0.034552845528455285	0	0.0	0	0.0	0	0.0	g	13.31	2.199950	0.38905	.	.	ENSG00000185567	ENST00000333244	T	0.00940	5.52	4.12	4.12	0.48240	.	.	.	.	.	T	0.00875	0.0029	M	0.88377	2.95	0.09310	N	1	P	0.39022	0.655	B	0.36719	0.231	T	0.19582	-1.0301	9	0.52906	T	0.07	-10.2489	13.9709	0.64240	0.0:0.0:1.0:0.0	.	1845	Q8IVF2	AHNK2_HUMAN	L	1845	ENSP00000353114:S1845L	ENSP00000353114:S1845L	S	-	2	0	AHNAK2	104487299	0.001000	0.12720	0.003000	0.11579	0.009000	0.06853	0.540000	0.23191	2.157000	0.67596	0.556000	0.70494	TCG	G|0.992;A|0.008	0.008	strong		0.602	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
CCDC168	643677	hgsc.bcm.edu	37	13	103388015	103388015	+	Missense_Mutation	SNP	C	C	G	rs17507841	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:103388015C>G	ENST00000322527.2	-	1	1144	c.1145G>C	c.(1144-1146)gGa>gCa	p.G382A		NM_001146197.1	NP_001139669.1	Q8NDH2	CC168_HUMAN	coiled-coil domain containing 168	382			G -> A (in dbSNP:rs17507841).														TTTCTCTTCTCCCTGTGCTGT	0.408													C|||	98	0.0195687	0.0023	0.0202	5008	,	,		22051	0.001		0.0328	False		,,,				2504	0.0481				p.G5011A		Atlas-SNP	.											.	.	.	.	0			c.G15032C						PASS	.	C	ALA/GLY	4,1380		0,4,688	205.0	161.0	174.0		15032	1.3	0.1	13	dbSNP_123	174	91,3091		3,85,1503	yes	missense	CCDC168	NM_001146197.1	60	3,89,2191	GG,GC,CC		2.8598,0.289,2.0806	benign	5011/7082	103388015	95,4471	692	1591	2283	SO:0001583	missense	643677	exon4			TCTTCTCCCTGTG		CCDS73596.1	13q33.1	2014-06-17	2011-08-09	2011-08-09	ENSG00000175820	ENSG00000175820			26851	protein-coding gene	gene with protein product			"""chromosome 13 open reading frame 40"""	C13orf40			Standard	NM_001146197		Approved	FLJ40176	uc001vpm.3	Q8NDH2	OTTHUMG00000187287	ENST00000322527.2:c.1145G>C	13.37:g.103388015C>G	ENSP00000320232:p.Gly382Ala	Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	180	93	0.516667	NM_001146197	Q8N800	Missense_Mutation	SNP	ENST00000322527.2	37		36	0.016483516483516484	3	0.006097560975609756	8	0.022099447513812154	0	0.0	25	0.032981530343007916	C	3.488	-0.104389	0.06967	0.00289	0.028598	ENSG00000175820	ENST00000322527	T	0.03635	3.86	2.53	1.28	0.21552	.	.	.	.	.	T	0.00637	0.0021	N	0.08118	0	0.09310	N	1	B	0.15930	0.015	B	0.09377	0.004	T	0.49560	-0.8927	9	0.19147	T	0.46	.	4.3333	0.11075	0.0:0.1678:0.0:0.8322	rs17507841;rs52799978;rs17507841	382	Q8NDH2	CC168_HUMAN	A	382	ENSP00000320232:G382A	ENSP00000320232:G382A	G	-	2	0	CCDC168	102186016	0.000000	0.05858	0.065000	0.19835	0.080000	0.17528	-0.038000	0.12144	0.384000	0.24942	-0.624000	0.04008	GGA	C|0.984;G|0.016	0.016	strong		0.408	CCDC168-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001146197	
IQGAP2	10788	hgsc.bcm.edu	37	5	75932869	75932869	+	Silent	SNP	C	C	T	rs2910819	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:75932869C>T	ENST00000274364.6	+	16	2088	c.1791C>T	c.(1789-1791)gaC>gaT	p.D597D	IQGAP2_ENST00000502745.1_Silent_p.D150D|IQGAP2_ENST00000396234.3_Silent_p.D150D|IQGAP2_ENST00000379730.3_Silent_p.D156D	NM_006633.2	NP_006624	Q13576	IQGA2_HUMAN	IQ motif containing GTPase activating protein 2	597	WW. {ECO:0000255|PROSITE- ProRule:PRU00224}.				negative regulation of catalytic activity (GO:0043086)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|microvillus (GO:0005902)	actin binding (GO:0003779)|GTPase inhibitor activity (GO:0005095)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|Ras GTPase activator activity (GO:0005099)	p.D597D(1)		NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(15)|lung(23)|ovary(6)|prostate(1)|skin(3)|stomach(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	68		all_lung(232;0.000514)|Lung NSC(167;0.00135)|Prostate(461;0.00838)|Ovarian(174;0.0149)		all cancers(79;1.38e-36)		TGTCTAGTGACGGTTCATGGC	0.328													C|||	2757	0.550519	0.5424	0.4942	5008	,	,		18779	0.4722		0.6083	False		,,,				2504	0.6227				p.D597D		Atlas-SNP	.											IQGAP2,NS,carcinoma,0,1	IQGAP2	186	1	1	Substitution - coding silent(1)	stomach(1)	c.C1791T						PASS	.	C		2418,1988	615.3+/-392.5	637,1144,422	106.0	101.0	103.0		1791	0.5	1.0	5	dbSNP_101	103	5083,3517	630.8+/-398.4	1480,2123,697	no	coding-synonymous	IQGAP2	NM_006633.2		2117,3267,1119	TT,TC,CC		40.8953,45.1203,42.3266		597/1576	75932869	7501,5505	2203	4300	6503	SO:0001819	synonymous_variant	10788	exon16			TAGTGACGGTTCA	U51903	CCDS34188.1, CCDS68897.1, CCDS68898.1, CCDS75262.1	5q	2008-07-18			ENSG00000145703	ENSG00000145703			6111	protein-coding gene	gene with protein product		605401				8756646	Standard	XM_005248409		Approved		uc003kek.3	Q13576	OTTHUMG00000162432	ENST00000274364.6:c.1791C>T	5.37:g.75932869C>T		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	120	119	0.991667	NM_006633	A8K4V1|B7Z8A4|J3KR91	Silent	SNP	ENST00000274364.6	37	CCDS34188.1	1181	0.5407509157509157	250	0.508130081300813	184	0.5082872928176796	293	0.5122377622377622	454	0.5989445910290238	C	21.2	4.113915	0.77210	0.548797	0.591047	ENSG00000145703	ENST00000509074	T	0.37915	1.17	5.82	0.504	0.16946	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999969292	.	.	.	.	.	.	T	0.44251	-0.9340	5	0.66056	D	0.02	-12.9495	6.1782	0.20455	0.451:0.1424:0.0:0.4066	rs2910819;rs3797459;rs17681358;rs2910819	.	.	.	M	148	ENSP00000425351:T148M	ENSP00000425351:T148M	T	+	2	0	IQGAP2	75968625	1.000000	0.71417	0.962000	0.40283	0.671000	0.39405	1.248000	0.32827	-0.127000	0.11661	-1.006000	0.02489	ACG	C|0.441;T|0.559	0.559	strong		0.328	IQGAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368877.1	NM_006633	
PRKCQ	5588	hgsc.bcm.edu	37	10	6553071	6553071	+	Silent	SNP	T	T	C	rs17555072	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:6553071T>C	ENST00000263125.5	-	3	303	c.204A>G	c.(202-204)agA>agG	p.R68R	PRKCQ_ENST00000397176.2_Silent_p.R68R|PRKCQ_ENST00000539722.1_5'UTR	NM_001282644.1|NM_006257.3	NP_001269573.1|NP_006248.1	Q04759	KPCT_HUMAN	protein kinase C, theta	68	C2.				apoptotic process (GO:0006915)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|Fc-epsilon receptor signaling pathway (GO:0038095)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|membrane protein ectodomain proteolysis (GO:0006509)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of T cell apoptotic process (GO:0070233)|phototransduction, visible light (GO:0007603)|platelet activation (GO:0030168)|positive regulation of interleukin-17 production (GO:0032740)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of interleukin-4 production (GO:0032753)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of T-helper 17 type immune response (GO:2000318)|positive regulation of T-helper 2 cell activation (GO:2000570)|protein ubiquitination (GO:0016567)|regulation of cell growth (GO:0001558)|regulation of platelet aggregation (GO:0090330)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|regulation of transcription, DNA-templated (GO:0006355)|rhodopsin mediated signaling pathway (GO:0016056)|T cell receptor signaling pathway (GO:0050852)	cytosol (GO:0005829)|immunological synapse (GO:0001772)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)|ubiquitin-protein transferase activity (GO:0004842)			NS(1)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|liver(1)|lung(13)|ovary(4)|prostate(1)|skin(4)|stomach(2)	45					Tamoxifen(DB00675)	TCTGCATGACTCTTCCCTTGT	0.498													T|||	121	0.0241613	0.003	0.0259	5008	,	,		20101	0.0		0.0616	False		,,,				2504	0.0378				p.R68R	Ovarian(50;572 1126 10530 25349 30594)	Atlas-SNP	.											.	PRKCQ	113	.	0			c.A204G						PASS	.	T	,	65,4341	62.3+/-99.4	0,65,2138	228.0	191.0	204.0		204,204	0.7	0.9	10	dbSNP_123	204	628,7972	162.5+/-215.2	21,586,3693	no	coding-synonymous,coding-synonymous	PRKCQ	NM_001242413.1,NM_006257.3	,	21,651,5831	CC,CT,TT		7.3023,1.4753,5.3283	,	68/644,68/707	6553071	693,12313	2203	4300	6503	SO:0001819	synonymous_variant	5588	exon3			CATGACTCTTCCC	L07032	CCDS7079.1, CCDS55701.1, CCDS60482.1	10p15	2009-07-10			ENSG00000065675	ENSG00000065675	2.7.11.1		9410	protein-coding gene	gene with protein product		600448				8444877	Standard	NM_001282645		Approved		uc001ijj.2	Q04759	OTTHUMG00000017623	ENST00000263125.5:c.204A>G	10.37:g.6553071T>C		Somatic	268	0	0		WXS	Illumina HiSeq	Phase_I	252	125	0.496032	NM_006257	B4DF52|Q14DH6|Q3MJF1|Q64FY5|Q9H508|Q9H549	Silent	SNP	ENST00000263125.5	37	CCDS7079.1																																																																																			T|0.958;C|0.042	0.042	strong		0.498	PRKCQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046665.1	NM_006257	
NUP214	8021	hgsc.bcm.edu	37	9	134021630	134021630	+	Silent	SNP	A	A	G	rs2296710	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:134021630A>G	ENST00000359428.5	+	13	2028	c.1884A>G	c.(1882-1884)acA>acG	p.T628T	RP11-544A12.4_ENST00000590461.1_RNA|RP11-544A12.4_ENST00000589667.1_RNA|RP11-544A12.4_ENST00000415391.2_RNA|RP11-544A12.4_ENST00000589540.1_RNA|NUP214_ENST00000451030.1_Silent_p.T628T|RP11-544A12.4_ENST00000587408.1_RNA|RP11-544A12.4_ENST00000588378.1_RNA|RP11-544A12.4_ENST00000587264.1_RNA|NUP214_ENST00000411637.2_Silent_p.T617T|RP11-544A12.4_ENST00000586290.1_RNA			P35658	NU214_HUMAN	nucleoporin 214kDa	628	11 X 5 AA approximate repeats.				carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|gene expression (GO:0010467)|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)|mRNA metabolic process (GO:0016071)|protein export from nucleus (GO:0006611)|protein import into nucleus (GO:0006606)|regulation of cell cycle (GO:0051726)|regulation of glucose transport (GO:0010827)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|focal adhesion (GO:0005925)|intracellular membrane-bounded organelle (GO:0043231)|nuclear pore (GO:0005643)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleocytoplasmic transporter activity (GO:0005487)|transporter activity (GO:0005215)	p.T628T(1)		NS(1)|breast(9)|central_nervous_system(3)|endometrium(13)|kidney(2)|large_intestine(9)|liver(2)|lung(29)|ovary(2)|prostate(3)|skin(7)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	86	all_hematologic(7;0.0028)	Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;3.42e-05)|Epithelial(140;0.000256)		GCCACCCCACACCTCTCTCAG	0.552			T	"""DEK, SET, ABL1"""	"""AML, T-ALL"""								g|||	1735	0.346446	0.2821	0.2277	5008	,	,		18493	0.4276		0.3191	False		,,,				2504	0.4622				p.T628T	Pancreas(4;24 48 25510 30394 32571)	Atlas-SNP	.		Dom	yes		9	9q34.1	8021	nucleoporin 214kDa (CAN)		L	NUP214,NS,carcinoma,0,1	NUP214	166	1	1	Substitution - coding silent(1)	stomach(1)	c.A1884G						PASS	.			1195,3211	709.5+/-407.8	166,863,1174	357.0	314.0	328.0		1884	-1.5	0.0	9	dbSNP_100	328	2735,5865	681.0+/-403.7	446,1843,2011	no	coding-synonymous	NUP214	NM_005085.2		612,2706,3185	GG,GA,AA		31.8023,27.1221,30.2168		628/2091	134021630	3930,9076	2203	4300	6503	SO:0001819	synonymous_variant	8021	exon13			CCCCACACCTCTC	X64228	CCDS6940.1	9q34	2008-07-21	2002-08-29		ENSG00000126883	ENSG00000126883			8064	protein-coding gene	gene with protein product	"""nuclear pore complex protein Nup214"", ""CAN protein, putative oncogene"""	114350	"""nucleoporin 214kD (CAIN)"""			8108440, 2370860	Standard	NM_005085		Approved	CAIN, CAN, D9S46E, N214	uc004cag.3	P35658	OTTHUMG00000020816	ENST00000359428.5:c.1884A>G	9.37:g.134021630A>G		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	113	54	0.477876	NM_005085	A6NFQ0|Q15010|Q3KQZ0|Q5JUP7|Q75R47|Q86XD3	Silent	SNP	ENST00000359428.5	37	CCDS6940.1																																																																																			T|0.000;G|0.312;A|0.687	0.312	strong		0.552	NUP214-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000054694.2	NM_005085	
RCOR3	55758	hgsc.bcm.edu	37	1	211451467	211451467	+	Silent	SNP	T	T	C	rs11577985	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:211451467T>C	ENST00000367005.4	+	5	492	c.351T>C	c.(349-351)gaT>gaC	p.D117D	RCOR3_ENST00000452621.2_Silent_p.D175D|RCOR3_ENST00000367006.4_Silent_p.D175D|RCOR3_ENST00000419091.2_Silent_p.D175D	NM_018254.3	NP_060724.1	Q9P2K3	RCOR3_HUMAN	REST corepressor 3	117	SANT 1. {ECO:0000255|PROSITE- ProRule:PRU00624}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)	p.D117D(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(6)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	21				OV - Ovarian serous cystadenocarcinoma(81;0.00961)|all cancers(67;0.0999)|Epithelial(68;0.171)		AGCTTCCAGATAAGACAATTG	0.299													T|||	870	0.173722	0.3003	0.1643	5008	,	,		17065	0.0655		0.1421	False		,,,				2504	0.1534				p.D175D		Atlas-SNP	.											RCOR3,NS,carcinoma,0,1	RCOR3	51	1	1	Substitution - coding silent(1)	stomach(1)	c.T525C						PASS	.	T	,,,	1198,3208	394.0+/-329.1	179,840,1184	48.0	49.0	49.0		525,525,525,351	4.5	1.0	1	dbSNP_120	49	1268,7332	249.7+/-276.9	98,1072,3130	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	RCOR3	NM_001136223.1,NM_001136224.2,NM_001136225.1,NM_018254.3	,,,	277,1912,4314	CC,CT,TT		14.7442,27.1902,18.9605	,,,	175/554,175/437,175/450,117/496	211451467	2466,10540	2203	4300	6503	SO:0001819	synonymous_variant	55758	exon6			TCCAGATAAGACA	AK001738	CCDS31016.1, CCDS44312.1, CCDS44313.1, CCDS44314.1	1q32.3	2008-02-05			ENSG00000117625	ENSG00000117625			25594	protein-coding gene	gene with protein product						10718198	Standard	NM_018254		Approved	FLJ10876	uc010psw.2	Q9P2K3	OTTHUMG00000036996	ENST00000367005.4:c.351T>C	1.37:g.211451467T>C		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	59	59	1	NM_001136223	B3KYA2|B4DYY7|Q5VT47|Q7L9I5|Q8N5U3|Q9NV83	Silent	SNP	ENST00000367005.4	37	CCDS31016.1																																																																																			T|0.830;C|0.170	0.170	strong		0.299	RCOR3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000089821.1	NM_018254	
FAM179A	165186	hgsc.bcm.edu	37	2	29240673	29240673	+	Missense_Mutation	SNP	G	G	A	rs35166194	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:29240673G>A	ENST00000379558.4	+	10	1562	c.1211G>A	c.(1210-1212)cGg>cAg	p.R404Q	FAM179A_ENST00000403861.2_Intron|FAM179A_ENST00000465300.1_Intron	NM_199280.2	NP_954974.2	Q6ZUX3	F179A_HUMAN	family with sequence similarity 179, member A	404										breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(5)|lung(9)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	26						CTTCCCCTCCGGGGCAGCGGG	0.612													G|||	1030	0.205671	0.2413	0.1859	5008	,	,		20368	0.1567		0.2485	False		,,,				2504	0.1779				p.R404Q		Atlas-SNP	.											.	FAM179A	106	.	0			c.G1211A						PASS	.	G	GLN/ARG	858,3198		92,674,1262	27.0	31.0	30.0		1211	3.3	1.0	2	dbSNP_126	30	1952,6390		240,1472,2459	yes	missense	FAM179A	NM_199280.2	43	332,2146,3721	AA,AG,GG		23.3997,21.1538,22.6649	probably-damaging	404/1020	29240673	2810,9588	2028	4171	6199	SO:0001583	missense	165186	exon10			CCCTCCGGGGCAG	AK125239, AK125744	CCDS1769.2	2p23.2	2008-10-30			ENSG00000189350	ENSG00000189350			33715	protein-coding gene	gene with protein product						16344560	Standard	NM_199280		Approved	FLJ43249, LOC165186	uc010ezl.3	Q6ZUX3	OTTHUMG00000128432	ENST00000379558.4:c.1211G>A	2.37:g.29240673G>A	ENSP00000368876:p.Arg404Gln	Somatic	232	0	0		WXS	Illumina HiSeq	Phase_I	242	111	0.458678	NM_199280	Q6ZUF5	Missense_Mutation	SNP	ENST00000379558.4	37	CCDS1769.2	454	0.2078754578754579	114	0.23170731707317074	70	0.19337016574585636	80	0.13986013986013987	190	0.25065963060686014	G	9.972	1.225871	0.22542	0.211538	0.233997	ENSG00000189350	ENST00000379558	T	0.09538	2.97	4.18	3.29	0.37713	.	.	.	.	.	T	0.00012	0.0000	L	0.29908	0.895	0.53688	P	2.8999999999945736E-5	P	0.47253	0.892	B	0.35182	0.197	T	0.48163	-0.9059	8	0.39692	T	0.17	.	3.4568	0.07518	0.1891:0.2611:0.5498:0.0	rs35166194	404	Q6ZUX3	F179A_HUMAN	Q	404	ENSP00000368876:R404Q	ENSP00000368876:R404Q	R	+	2	0	FAM179A	29094177	0.258000	0.24033	0.956000	0.39512	0.038000	0.13279	1.692000	0.37731	2.312000	0.78011	0.563000	0.77884	CGG	G|0.779;A|0.221	0.221	strong		0.612	FAM179A-003	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317848.4	NM_199280	
NUP88	4927	hgsc.bcm.edu	37	17	5289580	5289580	+	Silent	SNP	A	A	G	rs11209	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:5289580A>G	ENST00000573584.1	-	17	2681	c.2172T>C	c.(2170-2172)caT>caC	p.H724H	NUP88_ENST00000573169.1_5'Flank	NM_002532.4	NP_002523.2	Q99567	NUP88_HUMAN	nucleoporin 88kDa	724					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)	cytosol (GO:0005829)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	transporter activity (GO:0005215)			endometrium(4)|kidney(4)|large_intestine(4)|lung(3)	15						TTTCCCTTATATGTTCACCCC	0.358													G|||	2887	0.576478	0.5061	0.4308	5008	,	,		17870	0.8244		0.4165	False		,,,				2504	0.684				p.H724H		Atlas-SNP	.											.	NUP88	47	.	0			c.T2172C						PASS	.	G		2220,2186	586.2+/-386.4	558,1104,541	224.0	208.0	214.0		2172	4.0	1.0	17	dbSNP_52	214	3248,5352	649.5+/-400.6	606,2036,1658	no	coding-synonymous	NUP88	NM_002532.4		1164,3140,2199	GG,GA,AA		37.7674,49.6142,42.0421		724/742	5289580	5468,7538	2203	4300	6503	SO:0001819	synonymous_variant	4927	exon17			CCTTATATGTTCA	Y08612	CCDS11070.1	17p13	2004-02-18	2002-08-29		ENSG00000108559	ENSG00000108559			8067	protein-coding gene	gene with protein product		602552	"""nucleoporin 88kD"""			9049309	Standard	NM_002532		Approved	MGC8530	uc002gbo.2	Q99567	OTTHUMG00000099453	ENST00000573584.1:c.2172T>C	17.37:g.5289580A>G		Somatic	229	0	0		WXS	Illumina HiSeq	Phase_I	214	96	0.448598	NM_002532	D3DTM2|Q9BWE5	Silent	SNP	ENST00000573584.1	37	CCDS11070.1																																																																																			A|0.526;G|0.474	0.474	strong		0.358	NUP88-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216918.3	NM_002532	
AK9	221264	hgsc.bcm.edu	37	6	109886005	109886005	+	Silent	SNP	T	T	C	rs7757895	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:109886005T>C	ENST00000424296.2	-	22	2464	c.2388A>G	c.(2386-2388)ccA>ccG	p.P796P	AK9_ENST00000341338.6_5'UTR	NM_001145128.2	NP_001138600.2	Q5TCS8	KAD9_HUMAN	adenylate kinase 9	796					ADP phosphorylation (GO:0006757)|AMP phosphorylation (GO:0006756)|CDP phosphorylation (GO:0061508)|CMP phosphorylation (GO:0061566)|dADP phosphorylation (GO:0006174)|dAMP phosphorylation (GO:0061565)|dCDP phosphorylation (GO:0061570)|dCMP phosphorylation (GO:0061567)|dGDP phosphorylation (GO:0006186)|GDP phosphorylation (GO:0061568)|TDP phosphorylation (GO:0061571)|UDP phosphorylation (GO:0061569)	cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|nucleoside diphosphate kinase activity (GO:0004550)|nucleoside phosphate kinase activity (GO:0050145)										TGGATCCTTTTGGGATTTCTG	0.313													T|||	1110	0.221645	0.0295	0.2723	5008	,	,		16903	0.3433		0.2197	False		,,,				2504	0.3221				p.P796P		Atlas-SNP	.											.	AKD1	223	.	0			c.A2388G						PASS	.	T		83,1301		3,77,612	233.0	190.0	203.0		2388	0.7	0.4	6	dbSNP_116	203	751,2431		87,577,927	no	coding-synonymous	AKD1	NM_001145128.2		90,654,1539	CC,CT,TT		23.6015,5.9971,18.2654		796/1912	109886005	834,3732	692	1591	2283	SO:0001819	synonymous_variant	221264	exon22			TCCTTTTGGGATT	AK131244, BC146443, BC087860	CCDS5077.1, CCDS55048.1	6q21	2013-04-29	2013-04-29	2013-04-29			2.7.4.3		33814	protein-coding gene	gene with protein product		615358	"""chromosome 6 open reading frame 224"", ""adenylate kinase domain containing 2"", ""chromosome 6 open reading frame 199"", ""adenylate kinase domain containing 1"""	C6orf224, AKD2, C6orf199, AKD1		23416111	Standard	NM_145025		Approved	FLJ42177, FLJ25791, dJ70A9.1, MGC26954		Q5TCS8		ENST00000424296.2:c.2388A>G	6.37:g.109886005T>C		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	102	102	1	NM_001145128	A6NL75|B2RDJ0|B6ZDM7|Q3MIS4|Q5I0W8|Q6ZNF1|Q6ZVR7|Q8N7C6|Q8WW00|Q96NF4	Silent	SNP	ENST00000424296.2	37	CCDS55048.1																																																																																			T|0.802;C|0.198	0.198	strong		0.313	AK9-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001145128	
FRMPD4	9758	hgsc.bcm.edu	37	X	12725701	12725701	+	Silent	SNP	C	C	G	rs6641078	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:12725701C>G	ENST00000380682.1	+	13	1907	c.1401C>G	c.(1399-1401)gtC>gtG	p.V467V		NM_014728.3	NP_055543.2	Q14CM0	FRPD4_HUMAN	FERM and PDZ domain containing 4	467	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)			breast(1)|central_nervous_system(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(1)|ovary(3)|pancreas(1)|skin(3)	22						TTAGCCACGTCAACAGGATCG	0.517													C|||	918	0.243179	0.0106	0.2046	3775	,	,		13918	0.5308		0.0785	False		,,,				2504	0.1513				p.V467V		Atlas-SNP	.											.	FRMPD4	214	.	0			c.C1401G						PASS	.	C		140,3695		0,118,22,1514,549	139.0	116.0	124.0		1401	1.6	1.0	X	dbSNP_116	124	804,5924		38,508,220,1882,1652	no	coding-synonymous	FRMPD4	NM_014728.3		38,626,242,3396,2201	GG,GC,G,CC,C		11.9501,3.6506,8.9369		467/1323	12725701	944,9619	2203	4300	6503	SO:0001819	synonymous_variant	9758	exon13			CCACGTCAACAGG	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.1401C>G	X.37:g.12725701C>G		Somatic	236	1	0.00423729		WXS	Illumina HiSeq	Phase_I	173	173	1	NM_014728	A8K0X9|O15032	Silent	SNP	ENST00000380682.1	37	CCDS35201.1																																																																																			C|0.852;G|0.148	0.148	strong		0.517	FRMPD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055771.1	XM_045712	
ZSCAN29	146050	hgsc.bcm.edu	37	15	43661802	43661802	+	Missense_Mutation	SNP	T	T	C	rs3809482	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:43661802T>C	ENST00000396976.2	-	1	444	c.310A>G	c.(310-312)Aga>Gga	p.R104G	ZSCAN29_ENST00000396972.1_Missense_Mutation_p.R104G|TUBGCP4_ENST00000570081.1_3'UTR|ZSCAN29_ENST00000563508.1_5'Flank|ZSCAN29_ENST00000562072.1_Missense_Mutation_p.R103G|ZSCAN29_ENST00000568898.1_Missense_Mutation_p.R103G|TUBGCP4_ENST00000564079.1_5'Flank|TUBGCP4_ENST00000260383.7_5'Flank	NM_152455.3	NP_689668.3	Q8IWY8	ZSC29_HUMAN	zinc finger and SCAN domain containing 29	104			R -> G (in dbSNP:rs3809482). {ECO:0000269|PubMed:14702039}.		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)			cervix(1)|endometrium(2)|kidney(3)|large_intestine(9)|lung(7)|skin(2)	24		all_cancers(109;2.12e-14)|all_epithelial(112;1.99e-12)|Lung NSC(122;2.46e-08)|all_lung(180;2.75e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;8.97e-07)		ACCGAAGATCTAGGTCTTCCA	0.463													C|||	2734	0.545927	0.9728	0.3357	5008	,	,		20870	0.4692		0.3082	False		,,,				2504	0.4417				p.R104G		Atlas-SNP	.											.	ZSCAN29	57	.	0			c.A310G						PASS	.	C	GLY/ARG	3743,659	281.1+/-275.7	1596,551,54	96.0	107.0	103.0		310	3.9	1.0	15	dbSNP_107	103	2625,5973	686.6+/-404.1	393,1839,2067	yes	missense	ZSCAN29	NM_152455.3	125	1989,2390,2121	CC,CT,TT		30.5304,14.9705,48.9846	benign	104/853	43661802	6368,6632	2201	4299	6500	SO:0001583	missense	146050	exon1			AAGATCTAGGTCT	AF525399	CCDS10095.2	15q15.3	2013-01-08	2007-03-08	2007-03-08	ENSG00000140265	ENSG00000140265		"""-"", ""Zinc fingers, C2H2-type"""	26673	protein-coding gene	gene with protein product			"""zinc finger protein 690"""	ZNF690		12434312	Standard	NM_152455		Approved	FLJ35867, Zfp690	uc001zrk.1	Q8IWY8	OTTHUMG00000130767	ENST00000396976.2:c.310A>G	15.37:g.43661802T>C	ENSP00000380174:p.Arg104Gly	Somatic	188	0	0		WXS	Illumina HiSeq	Phase_I	192	65	0.338542	NM_152455	B3KVB9|Q32M75|Q32M76|Q8NA40	Missense_Mutation	SNP	ENST00000396976.2	37	CCDS10095.2	1120	0.5128205128205128	473	0.9613821138211383	126	0.34806629834254144	287	0.5017482517482518	234	0.3087071240105541	C	12.58	1.979660	0.34942	0.850295	0.305304	ENSG00000140265	ENST00000396976;ENST00000396972	T;T	0.04049	3.72;3.72	4.79	3.87	0.44632	Retrovirus capsid, C-terminal (1);Transcription regulator SCAN (2);	0.138436	0.33161	N	0.005210	T	0.00012	0.0000	N	0.13140	0.3	0.09310	P	0.999999999179701	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.06405	0.0;0.002;0.001;0.0	T	0.42189	-0.9466	9	0.02654	T	1	-9.2469	9.3264	0.37995	0.0:0.8239:0.0:0.1761	rs3809482;rs52793500;rs61337793;rs3809482	104;103;104;104	Q8IWY8-4;C9K0J8;Q8IWY8-3;Q8IWY8	.;.;.;ZSC29_HUMAN	G	104	ENSP00000380174:R104G;ENSP00000380170:R104G	ENSP00000380170:R104G	R	-	1	2	ZSCAN29	41449094	0.933000	0.31639	0.995000	0.50966	0.861000	0.49209	1.320000	0.33666	0.739000	0.32628	-0.119000	0.15052	AGA	T|0.485;C|0.515	0.515	strong		0.463	ZSCAN29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253278.1	NM_152455	
OR5P2	120065	hgsc.bcm.edu	37	11	7818190	7818190	+	Silent	SNP	C	C	T	rs73406607	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:7818190C>T	ENST00000329434.2	-	1	330	c.300G>A	c.(298-300)gcG>gcA	p.A100A	RP11-35J10.5_ENST00000527565.1_lincRNA	NM_153444.1	NP_703145.1	Q8WZ92	OR5P2_HUMAN	olfactory receptor, family 5, subfamily P, member 2	100						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(4)	22				Epithelial(150;8.62e-08)|BRCA - Breast invasive adenocarcinoma(625;0.189)		CAAAGAAAGCCGCTGAACCAA	0.483													C|||	1185	0.236621	0.348	0.2911	5008	,	,		18298	0.128		0.2763	False		,,,				2504	0.1186				p.A100A		Atlas-SNP	.											OR5P2,brain,glioma,0,2	OR5P2	68	2	0			c.G300A						PASS	.	C		1370,2838		401,568,1135	98.0	116.0	110.0		300	-7.1	0.0	11	dbSNP_130	110	2424,6160		392,1640,2260	no	coding-synonymous	OR5P2	NM_153444.1		793,2208,3395	TT,TC,CC		28.2386,32.557,29.6592		100/323	7818190	3794,8998	2104	4292	6396	SO:0001819	synonymous_variant	120065	exon1			GAAAGCCGCTGAA	AF173006	CCDS7782.1	11p15.4	2012-08-09			ENSG00000183303	ENSG00000183303		"""GPCR / Class A : Olfactory receptors"""	14783	protein-coding gene	gene with protein product							Standard	NM_153444		Approved	JCG3	uc001mfp.1	Q8WZ92	OTTHUMG00000165668	ENST00000329434.2:c.300G>A	11.37:g.7818190C>T		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	44	34	0.772727	NM_153444	Q3MIS8	Silent	SNP	ENST00000329434.2	37	CCDS7782.1																																																																																			C|0.738;T|0.262	0.262	strong		0.483	OR5P2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385696.1	NM_153444	
FHAD1	114827	hgsc.bcm.edu	37	1	15653563	15653563	+	Silent	SNP	C	C	T	rs3765357	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:15653563C>T	ENST00000375998.4	+	11	1482	c.1482C>T	c.(1480-1482)caC>caT	p.H494H	FHAD1_ENST00000375999.3_Silent_p.H494H|RP3-467K16.2_ENST00000428747.1_RNA|FHAD1_ENST00000358897.4_Silent_p.H494H|FHAD1_ENST00000401090.2_Silent_p.H164H|FHAD1_ENST00000417793.1_Silent_p.H494H|FHAD1_ENST00000375995.3_Silent_p.H99H			B1AJZ9	FHAD1_HUMAN	forkhead-associated (FHA) phosphopeptide binding domain 1	494										skin(1)|stomach(1)	2						AGCTGGAGCACTTCAGAAGTC	0.632													C|||	1107	0.221046	0.1293	0.3228	5008	,	,		15223	0.0486		0.329	False		,,,				2504	0.3395				p.H494H		Atlas-SNP	.											.	FHAD1	78	.	0			c.C1482T						PASS	.	C		219,1165		18,183,491	41.0	43.0	42.0		1482	-4.2	1.0	1	dbSNP_107	42	944,2238		142,660,789	no	coding-synonymous	FHAD1	NM_052929.1		160,843,1280	TT,TC,CC		29.6669,15.8237,25.4709		494/1413	15653563	1163,3403	692	1591	2283	SO:0001819	synonymous_variant	114827	exon12			GGAGCACTTCAGA	AK093300		1p36.21	2012-04-19			ENSG00000142621	ENSG00000142621			29408	protein-coding gene	gene with protein product						11572484	Standard	NM_052929		Approved	KIAA1937	uc001awb.2	B1AJZ9	OTTHUMG00000002088	ENST00000375998.4:c.1482C>T	1.37:g.15653563C>T		Somatic	248	0	0		WXS	Illumina HiSeq	Phase_I	212	98	0.462264	NM_052929	Q0P6F5|Q8N8D3|Q8N9T6|Q8NA05	Silent	SNP	ENST00000375998.4	37		456	0.2087912087912088	60	0.12195121951219512	111	0.30662983425414364	26	0.045454545454545456	259	0.341688654353562	C	11.36	1.616153	0.28801	0.158237	0.296669	ENSG00000142621	ENST00000375997	.	.	.	5.38	-4.2	0.03823	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.999999999804148	.	.	.	.	.	.	T	0.43669	-0.9377	3	.	.	.	-5.6922	2.1205	0.03724	0.1237:0.3211:0.1261:0.4291	rs3765357;rs60818774;rs3765357	.	.	.	F	173	.	.	L	+	1	0	FHAD1	15526150	0.688000	0.27680	0.969000	0.41365	0.717000	0.41224	-0.664000	0.05292	-0.649000	0.05430	-0.258000	0.10820	CTT	C|0.799;T|0.201	0.201	strong		0.632	FHAD1-026	PUTATIVE	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000393400.2	NM_052929	
SLC5A8	160728	hgsc.bcm.edu	37	12	101560328	101560328	+	Missense_Mutation	SNP	C	C	A	rs164365	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	138	0	0		WXS	Illumina HiSeq	Phase_I	118	63	0.533898	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	
SRD5A1	6715	hgsc.bcm.edu	37	5	6656210	6656210	+	Silent	SNP	G	G	A	rs3736316	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:6656210G>A	ENST00000274192.5	+	3	714	c.480G>A	c.(478-480)acG>acA	p.T160T	SRD5A1_ENST00000537411.1_3'UTR|SRD5A1_ENST00000538824.1_Silent_p.T113T	NM_001047.2	NP_001038.1	P18405	S5A1_HUMAN	steroid-5-alpha-reductase, alpha polypeptide 1 (3-oxo-5 alpha-steroid delta 4-dehydrogenase alpha 1)	160					androgen biosynthetic process (GO:0006702)|cell differentiation (GO:0030154)|sex determination (GO:0007530)|sex differentiation (GO:0007548)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	3-oxo-5-alpha-steroid 4-dehydrogenase activity (GO:0003865)|cholestenone 5-alpha-reductase activity (GO:0047751)|electron carrier activity (GO:0009055)	p.T160T(1)		endometrium(3)|kidney(1)|large_intestine(1)|lung(8)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	19					Dutasteride(DB01126)|Finasteride(DB01216)|Levonorgestrel(DB00367)|Spironolactone(DB00421)	TGTGGTTAACGGGCATGTTGA	0.388													G|||	1447	0.288938	0.3298	0.3919	5008	,	,		19956	0.1587		0.3897	False		,,,				2504	0.1912				p.T160T		Atlas-SNP	.											SRD5A1,NS,carcinoma,0,1	SRD5A1	31	1	1	Substitution - coding silent(1)	stomach(1)	c.G480A						PASS	.	G		1452,2954	468.7+/-355.2	244,964,995	116.0	110.0	112.0		480	-1.3	0.0	5	dbSNP_107	112	3218,5382	484.5+/-371.4	611,1996,1693	no	coding-synonymous	SRD5A1	NM_001047.2		855,2960,2688	AA,AG,GG		37.4186,32.9551,35.9065		160/260	6656210	4670,8336	2203	4300	6503	SO:0001819	synonymous_variant	6715	exon3			GTTAACGGGCATG	M32313	CCDS3870.1	5p15.31	2008-02-05			ENSG00000145545	ENSG00000145545	1.3.99.5		11284	protein-coding gene	gene with protein product		184753				1686016	Standard	XR_427663		Approved		uc003jdw.3	P18405	OTTHUMG00000090456	ENST00000274192.5:c.480G>A	5.37:g.6656210G>A		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	133	77	0.578947	NM_001047	B2R7Q1|Q9UHY4|Q9UP36|Q9UP37	Silent	SNP	ENST00000274192.5	37	CCDS3870.1																																																																																			.	.	weak		0.388	SRD5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206903.1	NM_001047	
DDX4	54514	hgsc.bcm.edu	37	5	55082474	55082474	+	Silent	SNP	C	C	T	rs957459	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:55082474C>T	ENST00000505374.1	+	14	1085	c.993C>T	c.(991-993)tgC>tgT	p.C331C	DDX4_ENST00000354991.5_Silent_p.C297C|DDX4_ENST00000511853.1_Silent_p.C182C|DDX4_ENST00000353507.5_Silent_p.C297C|DDX4_ENST00000514278.2_Silent_p.C311C	NM_024415.2	NP_077726.1	Q9NQI0	DDX4_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 4	331	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				male meiosis I (GO:0007141)|multicellular organismal development (GO:0007275)|regulation of protein localization (GO:0032880)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)	chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|pi-body (GO:0071546)|piP-body (GO:0071547)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|nucleic acid binding (GO:0003676)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(8)|ovary(1)|skin(3)|upper_aerodigestive_tract(2)	24		Lung NSC(810;6.93e-05)|all_neural(839;0.00409)|Prostate(74;0.0107)|Breast(144;0.0544)|Ovarian(174;0.223)				TGATGGCTTGCGCTCAAACAG	0.403													T|||	2329	0.465056	0.6339	0.5519	5008	,	,		18821	0.497		0.3091	False		,,,				2504	0.3027				p.C331C		Atlas-SNP	.											.	DDX4	194	.	0			c.C993T						PASS	.	T	,,,	2583,1823	532.6+/-373.5	754,1075,374	112.0	106.0	108.0		891,933,546,993	3.9	1.0	5	dbSNP_86	108	2721,5879	680.3+/-403.6	430,1861,2009	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	DDX4	NM_001142549.1,NM_001166533.1,NM_001166534.1,NM_024415.2	,,,	1184,2936,2383	TT,TC,CC		31.6395,41.3754,40.7812	,,,	297/691,311/705,182/576,331/725	55082474	5304,7702	2203	4300	6503	SO:0001819	synonymous_variant	54514	exon14			GGCTTGCGCTCAA	AF262962	CCDS3969.1, CCDS47208.1, CCDS54854.1, CCDS54855.1	5p15.2-p13.1	2008-02-05	2003-06-13		ENSG00000152670	ENSG00000152670		"""DEAD-boxes"""	18700	protein-coding gene	gene with protein product		605281	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 4"""			10920202, 11850529	Standard	NM_001142549		Approved	VASA	uc003jqg.4	Q9NQI0	OTTHUMG00000097044	ENST00000505374.1:c.993C>T	5.37:g.55082474C>T		Somatic	201	0	0		WXS	Illumina HiSeq	Phase_I	230	75	0.326087	NM_024415	A8K8Q2|B3KSF4|D6RDK4|E9PCD8|Q5M7Z3|Q86VX0|Q9NT92|Q9NYB1	Silent	SNP	ENST00000505374.1	37	CCDS3969.1																																																																																			C|0.565;T|0.435	0.435	strong		0.403	DDX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214147.2	NM_024415	
ASCC3	10973	hgsc.bcm.edu	37	6	101049748	101049748	+	Silent	SNP	C	C	T	rs61746540	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:101049748C>T	ENST00000369162.2	-	34	5585	c.5241G>A	c.(5239-5241)aaG>aaA	p.K1747K		NM_006828.2	NP_006819.2	Q8N3C0	ASCC3_HUMAN	activating signal cointegrator 1 complex subunit 3	1747					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)		ATGCATCTTGCTTAGATGTAA	0.403													C|||	174	0.0347444	0.0741	0.0101	5008	,	,		15178	0.0437		0.0159	False		,,,				2504	0.0092				p.K1747K		Atlas-SNP	.											.	ASCC3	205	.	0			c.G5241A						PASS	.	C		208,4198	128.2+/-165.1	4,200,1999	151.0	146.0	148.0		5241	5.1	1.0	6	dbSNP_129	148	170,8430	78.6+/-141.3	4,162,4134	no	coding-synonymous	ASCC3	NM_006828.2		8,362,6133	TT,TC,CC		1.9767,4.7208,2.9064		1747/2203	101049748	378,12628	2203	4300	6503	SO:0001819	synonymous_variant	10973	exon34			ATCTTGCTTAGAT	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.5241G>A	6.37:g.101049748C>T		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	75	44	0.586667	NM_006828	E7EW23|O43738|Q4G1A0|Q5VTN2|Q9H1I9|Q9H5A2|Q9NTR0	Silent	SNP	ENST00000369162.2	37	CCDS5046.1																																																																																			C|0.969;T|0.031	0.031	strong		0.403	ASCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041632.2	NM_006828	
POM121L12	285877	hgsc.bcm.edu	37	7	53103571	53103571	+	Silent	SNP	G	G	A	rs11238248	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:53103571G>A	ENST00000408890.4	+	1	223	c.207G>A	c.(205-207)ggG>ggA	p.G69G		NM_182595.3	NP_872401.3	Q8N7R1	P1L12_HUMAN	POM121 transmembrane nucleoporin-like 12	69										endometrium(5)|kidney(1)|large_intestine(5)|lung(44)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	61						TCCAGTGGGGGCGCCCGGTGC	0.706													g|||	1646	0.328674	0.1725	0.4308	5008	,	,		11528	0.3026		0.4861	False		,,,				2504	0.3323				p.G69G		Atlas-SNP	.											.	POM121L12	146	.	0			c.G207A						PASS	.	A		812,3026		96,620,1203	23.0	28.0	26.0		207	-1.0	0.0	7	dbSNP_120	26	4179,4089		1058,2063,1013	no	coding-synonymous	POM121L12	NM_182595.3		1154,2683,2216	AA,AG,GG		49.4557,21.1569,41.2275		69/297	53103571	4991,7115	1919	4134	6053	SO:0001819	synonymous_variant	285877	exon1			GTGGGGGCGCCCG		CCDS43584.1	7p12.1	2012-03-13	2012-03-13		ENSG00000221900	ENSG00000221900			25369	protein-coding gene	gene with protein product			"""POM121 membrane glycoprotein-like 12"""				Standard	NM_182595		Approved	DKFZp564N2472	uc003tpz.3	Q8N7R1	OTTHUMG00000155995	ENST00000408890.4:c.207G>A	7.37:g.53103571G>A		Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	43	22	0.511628	NM_182595	Q8NDI9	Silent	SNP	ENST00000408890.4	37	CCDS43584.1																																																																																			G|0.585;A|0.415	0.415	strong		0.706	POM121L12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342656.1	NM_182595	
FASTKD1	79675	hgsc.bcm.edu	37	2	170403106	170403106	+	Silent	SNP	G	G	A	rs16857030	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:170403106G>A	ENST00000453153.2	-	8	1669	c.1323C>T	c.(1321-1323)gcC>gcT	p.A441A	FASTKD1_ENST00000453929.2_Silent_p.A441A	NM_024622.3	NP_078898.3	Q53R41	FAKD1_HUMAN	FAST kinase domains 1	441					cellular respiration (GO:0045333)	mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(5)|large_intestine(10)|lung(9)|ovary(4)|prostate(3)	37						GTGGTAAAACGGCTTCAATTC	0.428													G|||	494	0.0986422	0.2496	0.0764	5008	,	,		19180	0.003		0.0636	False		,,,				2504	0.045				p.A441A		Atlas-SNP	.											.	FASTKD1	86	.	0			c.C1323T						PASS	.	G		878,3528	338.9+/-305.5	90,698,1415	70.0	72.0	72.0		1323	-1.6	0.9	2	dbSNP_123	72	483,8117	139.5+/-196.2	10,463,3827	no	coding-synonymous	FASTKD1	NM_024622.3		100,1161,5242	AA,AG,GG		5.6163,19.9274,10.4644		441/848	170403106	1361,11645	2203	4300	6503	SO:0001819	synonymous_variant	79675	exon8			TAAAACGGCTTCA	AL832058	CCDS33318.1, CCDS63051.1	2q31.1	2008-02-05			ENSG00000138399	ENSG00000138399			26150	protein-coding gene	gene with protein product						11347906	Standard	NM_024622		Approved	FLJ21901	uc002uev.4	Q53R41	OTTHUMG00000154953	ENST00000453153.2:c.1323C>T	2.37:g.170403106G>A		Somatic	225	0	0		WXS	Illumina HiSeq	Phase_I	220	92	0.418182	NM_024622	Q8N583|Q8TEA9|Q96JM5|Q96N71|Q9H6T4	Silent	SNP	ENST00000453153.2	37	CCDS33318.1																																																																																			G|0.902;A|0.098	0.098	strong		0.428	FASTKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337788.2	NM_024622	
ZPLD1	131368	hgsc.bcm.edu	37	3	102181131	102181131	+	Missense_Mutation	SNP	A	A	G	rs12054046	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:102181131A>G	ENST00000491959.1	+	13	1471	c.589A>G	c.(589-591)Acc>Gcc	p.T197A	ZPLD1_ENST00000306176.1_Missense_Mutation_p.T213A|ZPLD1_ENST00000466937.1_Missense_Mutation_p.T197A			Q8TCW7	ZPLD1_HUMAN	zona pellucida-like domain containing 1	197	ZP. {ECO:0000255|PROSITE- ProRule:PRU00375}.		T -> A (in dbSNP:rs12054046).			integral component of membrane (GO:0016021)				central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(18)|ovary(2)|skin(3)	35						TTAGGATTCAACCTACAACCA	0.343													A|||	481	0.0960463	0.0893	0.1585	5008	,	,		16495	0.0357		0.1372	False		,,,				2504	0.0808				p.T213A		Atlas-SNP	.											.	ZPLD1	82	.	0			c.A637G						PASS	.	A	ALA/THR	404,4002	200.4+/-223.7	18,368,1817	76.0	77.0	77.0		637	4.1	1.0	3	dbSNP_120	77	1328,7270	259.5+/-282.7	95,1138,3066	yes	missense	ZPLD1	NM_175056.1	58	113,1506,4883	GG,GA,AA		15.4455,9.1693,13.319	benign	213/432	102181131	1732,11272	2203	4299	6502	SO:0001583	missense	131368	exon6			GATTCAACCTACA	AY090780	CCDS2947.1	3q12.3	2009-03-25			ENSG00000170044	ENSG00000170044			27022	protein-coding gene	gene with protein product		615915				18632209	Standard	NM_175056		Approved		uc003dvt.1	Q8TCW7	OTTHUMG00000159229	ENST00000491959.1:c.589A>G	3.37:g.102181131A>G	ENSP00000420265:p.Thr197Ala	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	91	45	0.494505	NM_175056	Q49AS1|Q8WU36	Missense_Mutation	SNP	ENST00000491959.1	37		219	0.10027472527472528	40	0.08130081300813008	58	0.16022099447513813	16	0.027972027972027972	105	0.13852242744063326	A	11.67	1.707151	0.30232	0.091693	0.154455	ENSG00000170044	ENST00000491959;ENST00000306176;ENST00000466937	D;D;D	0.81996	-1.56;-1.56;-1.56	5.28	4.09	0.47781	Zona pellucida sperm-binding protein (3);	0.157465	0.56097	D	0.000021	T	0.00552	0.0018	N	0.16130	0.375	0.23260	P	0.99802135	B;B	0.19583	0.037;0.007	B;B	0.19666	0.022;0.026	T	0.17561	-1.0365	9	0.35671	T	0.21	4.2278	11.3184	0.49405	0.8635:0.0:0.0:0.1365	rs12054046;rs52822606;rs60979721;rs12054046	213;197	Q8TCW7-2;Q8TCW7	.;ZPLD1_HUMAN	A	197;213;197	ENSP00000420265:T197A;ENSP00000307801:T213A;ENSP00000418253:T197A	ENSP00000307801:T213A	T	+	1	0	ZPLD1	103663821	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	2.357000	0.44125	0.797000	0.33971	0.482000	0.46254	ACC	A|0.884;G|0.116	0.116	strong		0.343	ZPLD1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000353984.1	NM_175056	
BCKDHA	593	hgsc.bcm.edu	37	19	41928927	41928927	+	Silent	SNP	C	C	T	rs548045051		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:41928927C>T	ENST00000269980.2	+	8	1388	c.1020C>T	c.(1018-1020)gaC>gaT	p.D340D	CTC-435M10.6_ENST00000598887.1_RNA|BCKDHA_ENST00000595085.1_Silent_p.D374D|CTC-435M10.3_ENST00000540732.1_Silent_p.D374D|BCKDHA_ENST00000457836.2_Silent_p.D343D	NM_000709.3|NM_001164783.1	NP_000700.1|NP_001158255.1	P12694	ODBA_HUMAN	branched chain keto acid dehydrogenase E1, alpha polypeptide	340					branched-chain amino acid catabolic process (GO:0009083)|cellular nitrogen compound metabolic process (GO:0034641)|response to cAMP (GO:0051591)|response to glucocorticoid (GO:0051384)|response to nutrient (GO:0007584)|small molecule metabolic process (GO:0044281)	mitochondrial alpha-ketoglutarate dehydrogenase complex (GO:0005947)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) activity (GO:0003863)|alpha-ketoacid dehydrogenase activity (GO:0003826)|carboxy-lyase activity (GO:0016831)|metal ion binding (GO:0046872)			central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(4)|prostate(1)	10						GCACCAGTGACGACAGTTCAG	0.627													C|||	1	0.000199681	0.0008	0.0	5008	,	,		19107	0.0		0.0	False		,,,				2504	0.0				p.D340D		Atlas-SNP	.											BCKDHA,NS,carcinoma,0,1	BCKDHA	36	1	0			c.C1020T						scavenged	.						57.0	44.0	49.0					19																	41928927		2203	4300	6503	SO:0001819	synonymous_variant	593	exon8			CAGTGACGACAGT	J04474	CCDS12581.1	19q13.1-q13.2	2008-07-09	2005-11-29		ENSG00000248098	ENSG00000248098			986	protein-coding gene	gene with protein product	"""maple syrup urine disease"""	608348	"""branched chain keto acid dehydrogenase E1, alpha polypeptide (maple syrup urine disease)"", ""2-oxoisovalerate dehydrogenase (lipoamide)"""	OVD1A			Standard	NM_000709		Approved	MSU	uc002oqq.3	P12694	OTTHUMG00000168128	ENST00000269980.2:c.1020C>T	19.37:g.41928927C>T		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	108	2	0.0185185	NM_000709	B4DP47|E7EW46|Q16034|Q16472	Silent	SNP	ENST00000269980.2	37	CCDS12581.1																																																																																			.	.	none		0.627	BCKDHA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398313.3	NM_000709	
ANKRD36	375248	hgsc.bcm.edu	37	2	97790211	97790211	+	Missense_Mutation	SNP	A	A	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:97790211A>T	ENST00000461153.2	+	5	852	c.608A>T	c.(607-609)cAt>cTt	p.H203L	ANKRD36_ENST00000420699.2_Missense_Mutation_p.H203L			A6QL64	AN36A_HUMAN	ankyrin repeat domain 36	203								p.H203L(2)		endometrium(9)|kidney(5)|liver(1)|lung(3)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	23						GCCCTCATACATGCTGTTACT	0.323																																					p.H203L		Atlas-SNP	.											ANKRD36_ENST00000420699,extremity,malignant_melanoma,0,2	ANKRD36	170	2	2	Substitution - Missense(2)	NS(1)|skin(1)	c.A608T						scavenged	.						79.0	60.0	65.0					2																	97790211		692	1589	2281	SO:0001583	missense	375248	exon5			TCATACATGCTGT	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.608A>T	2.37:g.97790211A>T	ENSP00000419530:p.His203Leu	Somatic	200	2	0.01		WXS	Illumina HiSeq	Phase_I	198	13	0.0656566	NM_001164315	B4E3I8|Q6UX02|Q86X62|Q9HCD1	Missense_Mutation	SNP	ENST00000461153.2	37	CCDS54379.1	.	.	.	.	.	.	.	.	.	.	A	0.010	-1.781271	0.00634	.	.	ENSG00000135976	ENST00000461153;ENST00000420699;ENST00000393513;ENST00000455519	T;T	0.60920	0.15;0.15	0.946	-0.341	0.12639	Ankyrin repeat-containing domain (4);	.	.	.	.	T	0.16642	0.0400	N	0.00855	-1.145	0.47511	D	0.999447	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.37384	-0.9708	9	0.02654	T	1	.	3.0347	0.06118	0.3942:0.0:0.0:0.6058	.	203;203	A6QL64;F2Z332	AN36A_HUMAN;.	L	203	ENSP00000419530:H203L;ENSP00000391950:H203L	ENSP00000377149:H203L	H	+	2	0	ANKRD36	97153938	0.990000	0.36364	0.731000	0.30826	0.427000	0.31564	0.125000	0.15749	-0.131000	0.11578	-1.495000	0.00966	CAT	.	.	none		0.323	ANKRD36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339154.5		
C11orf21	29125	hgsc.bcm.edu	37	11	2323022	2323022	+	Missense_Mutation	SNP	C	C	T	rs12276847	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:2323022C>T	ENST00000381153.3	-	1	268	c.17G>A	c.(16-18)tGt>tAt	p.C6Y	TSPAN32_ENST00000381121.3_5'Flank|TSPAN32_ENST00000182290.4_5'Flank|TSPAN32_ENST00000451520.2_5'Flank|C11orf21_ENST00000470369.1_5'UTR			Q9P2W6	CK021_HUMAN	chromosome 11 open reading frame 21	6						cytoplasm (GO:0005737)											CCACATCCCACACCAGGTCCT	0.642											OREG0003773	type=REGULATORY REGION|Gene=TSPAN32|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	C|||	1052	0.210064	0.0802	0.2637	5008	,	,		16273	0.1399		0.3588	False		,,,				2504	0.2669				p.V24M		Atlas-SNP	.											.	C11orf21	11	.	0			c.G70A						PASS	.	C	MET/VAL	171,1213		16,139,537	90.0	99.0	96.0		70	-0.9	0.0	11	dbSNP_120	96	1092,2090		192,708,691	yes	missense	C11orf21	NM_001142946.1	21	208,847,1228	TT,TC,CC		34.318,12.3555,27.661	benign	24/179	2323022	1263,3303	692	1591	2283	SO:0001583	missense	29125	exon1			ATCCCACACCAGG	AB029488	CCDS44518.1	11p15.5	2012-08-09			ENSG00000110665	ENSG00000110665			13231	protein-coding gene	gene with protein product		611033				11054561	Standard	NM_001142946		Approved		uc009ydj.2	Q9P2W6	OTTHUMG00000009759	ENST00000381153.3:c.17G>A	11.37:g.2323022C>T	ENSP00000370545:p.Cys6Tyr	Somatic	69	0	0	602	WXS	Illumina HiSeq	Phase_I	80	16	0.2	NM_001142946		Missense_Mutation	SNP	ENST00000381153.3	37		521|521	0.23855311355311357|0.23855311355311357	45|45	0.09146341463414634|0.09146341463414634	117|117	0.32320441988950277|0.32320441988950277	81|81	0.14160839160839161|0.14160839160839161	278|278	0.36675461741424803|0.36675461741424803	C|C	2.389|2.389	-0.340270|-0.340270	0.05243|0.05243	0.123555|0.123555	0.34318|0.34318	ENSG00000110665|ENSG00000110665	ENST00000381153|ENST00000456145	.|.	.|.	.|.	1.85|1.85	-0.933|-0.933	0.10431|0.10431	.|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.08118|0.08118	0|0	0.80722|0.80722	P|P	0.0|0.0	B|B	0.02656|0.02656	0.0|0.0	B|B	0.01281|0.04013	0.0|0.001	T|T	0.41770|0.41770	-0.9490|-0.9490	7|7	0.02654|0.87932	T|D	1|0	.|.	4.636|4.636	0.12525|0.12525	0.0:0.4842:0.0:0.5158|0.0:0.4842:0.0:0.5158	rs12276847|rs12276847	6|24	Q9P2W6|E9PAM5	CK021_HUMAN|.	Y|M	6|24	.|.	ENSP00000370545:C6Y|ENSP00000406541:V24M	C|V	-|-	2|1	0|0	C11orf21|C11orf21	2279598|2279598	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.001000|0.001000	0.01503|0.01503	-0.563000|-0.563000	0.05943|0.05943	-0.238000|-0.238000	0.09724|0.09724	-0.521000|-0.521000	0.04368|0.04368	TGT|GTG	C|0.750;T|0.250	0.250	strong		0.642	C11orf21-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000026908.2	NM_001142946	
MYO7A	4647	hgsc.bcm.edu	37	11	76910766	76910766	+	Silent	SNP	C	C	T	rs7927472	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:76910766C>T	ENST00000409709.3	+	35	5027	c.4755C>T	c.(4753-4755)agC>agT	p.S1585S	MYO7A_ENST00000458637.2_Silent_p.S1547S|MYO7A_ENST00000409619.2_Silent_p.S1536S	NM_000260.3	NP_000251.3	Q13402	MYO7A_HUMAN	myosin VIIA	1585	FERM 1. {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						TCACCTCCAGCAATGCTGAGG	0.597													C|||	2166	0.432508	0.3185	0.5937	5008	,	,		20140	0.4494		0.5527	False		,,,				2504	0.3313				p.S1585S		Atlas-SNP	.											.	MYO7A	164	.	0			c.C4755T						PASS	.	C	,	1319,2745		228,863,941	39.0	43.0	42.0		4755,4641	4.0	1.0	11	dbSNP_116	42	4381,4019		1147,2087,966	no	coding-synonymous,coding-synonymous	MYO7A	NM_000260.3,NM_001127180.1	,	1375,2950,1907	TT,TC,CC		47.8452,32.4557,45.7317	,	1585/2216,1547/2176	76910766	5700,6764	2032	4200	6232	SO:0001819	synonymous_variant	4647	exon35			CTCCAGCAATGCT	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.4755C>T	11.37:g.76910766C>T		Somatic	106	1	0.00943396		WXS	Illumina HiSeq	Phase_I	92	92	1	NM_000260	B9A011|F8VUN5|P78427|Q13321|Q14785|Q92821|Q92822	Silent	SNP	ENST00000409709.3	37	CCDS53683.1																																																																																			C|0.511;T|0.489	0.489	strong		0.597	MYO7A-001	KNOWN	non_canonical_conserved|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000328133.1	NM_000260	
ZSCAN5B	342933	hgsc.bcm.edu	37	19	56703286	56703286	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:56703286G>A	ENST00000586855.2	-	3	834	c.521C>T	c.(520-522)cCg>cTg	p.P174L	ZSCAN5B_ENST00000358992.3_Missense_Mutation_p.P174L			A6NJL1	ZSA5B_HUMAN	zinc finger and SCAN domain containing 5B	174					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						GCCTGTCCCCGGATGCATCTG	0.632																																					p.P174L		Atlas-SNP	.											.	ZSCAN5B	160	.	0			c.C521T						PASS	.						33.0	35.0	34.0					19																	56703286		2203	4300	6503	SO:0001583	missense	342933	exon2			GTCCCCGGATGCA		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.521C>T	19.37:g.56703286G>A	ENSP00000466072:p.Pro174Leu	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	87	33	0.37931	NM_001080456		Missense_Mutation	SNP	ENST00000586855.2	37	CCDS46203.1	.	.	.	.	.	.	.	.	.	.	G	6.658	0.489887	0.12702	.	.	ENSG00000197213	ENST00000358992	T	0.05580	3.42	1.9	0.827	0.18835	.	.	.	.	.	T	0.08358	0.0208	M	0.78049	2.395	0.09310	N	1	B	0.09022	0.002	B	0.06405	0.002	T	0.33085	-0.9882	9	0.34782	T	0.22	.	3.7907	0.08719	0.2493:0.0:0.7507:0.0	.	174	A6NJL1	ZSA5B_HUMAN	L	174	ENSP00000351883:P174L	ENSP00000351883:P174L	P	-	2	0	ZSCAN5B	61395098	0.002000	0.14202	0.001000	0.08648	0.001000	0.01503	0.329000	0.19698	0.345000	0.23873	0.306000	0.20318	CCG	.	.	none		0.632	ZSCAN5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457834.2	NM_001080456	
FSIP2	401024	hgsc.bcm.edu	37	2	186672527	186672527	+	Missense_Mutation	SNP	T	T	A	rs72900086	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:186672527T>A	ENST00000424728.1	+	17	18494	c.18494T>A	c.(18493-18495)cTa>cAa	p.L6165Q	FSIP2_ENST00000343098.5_Missense_Mutation_p.L6254Q			Q5CZC0	FSIP2_HUMAN	fibrous sheath interacting protein 2	6165				L -> Q (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						GATGTGCCCCTACCTAAACCT	0.338													T|||	706	0.140974	0.0666	0.2363	5008	,	,		17708	0.0377		0.2207	False		,,,				2504	0.1984				p.L6254Q		Atlas-SNP	.											.	FSIP2	251	.	0			c.T18761A						PASS	.	T	GLN/LEU	428,3200		23,382,1409	75.0	64.0	67.0		18761	0.3	0.0	2	dbSNP_130	67	1958,6208		223,1512,2348	yes	missense	FSIP2	NM_173651.2	113	246,1894,3757	AA,AT,TT		23.9775,11.7971,20.2306	benign	6254/6997	186672527	2386,9408	1814	4083	5897	SO:0001583	missense	401024	exon17			TGCCCCTACCTAA	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.18494T>A	2.37:g.186672527T>A	ENSP00000401306:p.Leu6165Gln	Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	107	59	0.551402	NM_173651	Q53TL3|Q53TN5|Q5HYH2|Q6ZTZ5|Q6ZU14|Q6ZU21	Missense_Mutation	SNP	ENST00000424728.1	37		289	0.13232600732600733	36	0.07317073170731707	80	0.22099447513812154	15	0.026223776223776224	158	0.20844327176781002	T	0.071	-1.201616	0.01581	0.117971	0.239775	ENSG00000188738	ENST00000343098;ENST00000424728	T;T	0.39406	1.08;1.08	4.97	0.32	0.15878	.	0.838313	0.10284	N	0.693125	T	0.00012	0.0000	N	0.04090	-0.28	0.80722	P	0.0	.	.	.	.	.	.	T	0.32640	-0.9899	7	0.09338	T	0.73	.	2.5587	0.04766	0.2659:0.4882:0.1186:0.1273	.	.	.	.	Q	6254;6165	ENSP00000344403:L6254Q;ENSP00000401306:L6165Q	ENSP00000344403:L6254Q	L	+	2	0	FSIP2	186380772	0.000000	0.05858	0.001000	0.08648	0.010000	0.07245	0.003000	0.13083	0.157000	0.19338	-0.415000	0.06103	CTA	T|0.836;A|0.164	0.164	strong		0.338	FSIP2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000332778.3	NM_173651	
PGLYRP2	114770	hgsc.bcm.edu	37	19	15586672	15586672	+	Missense_Mutation	SNP	A	A	T	rs892145	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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						PASS	.	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	60	0	0		WXS	Illumina HiSeq	Phase_I	62	30	0.483871	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	
LIPI	149998	hgsc.bcm.edu	37	21	15516948	15516948	+	Missense_Mutation	SNP	C	C	T	rs2822432	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:15516948C>T	ENST00000536861.1	-	9	1290	c.1291G>A	c.(1291-1293)Gaa>Aaa	p.E431K	LIPI_ENST00000344577.2_Missense_Mutation_p.E452K|AP001347.6_ENST00000432621.1_RNA|AP001347.6_ENST00000428809.1_RNA			Q6XZB0	LIPI_HUMAN	lipase, member I	431			E -> K (in dbSNP:rs2822432). {ECO:0000269|PubMed:12719377}.		lipid catabolic process (GO:0016042)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|plasma membrane (GO:0005886)	heparin binding (GO:0008201)|phospholipase activity (GO:0004620)			endometrium(1)|kidney(13)|large_intestine(9)|liver(3)|lung(24)|ovary(3)|urinary_tract(1)	54				Epithelial(23;0.000155)|COAD - Colon adenocarcinoma(22;0.0015)|Colorectal(24;0.00693)|Lung(58;0.166)		TCTTACCTTTCTGGGTATGTA	0.294													C|||	1589	0.317292	0.5537	0.4006	5008	,	,		15349	0.0526		0.33	False		,,,				2504	0.1984				p.E452K		Atlas-SNP	.											.	LIPI	95	.	0			c.G1354A						PASS	.	C	LYS/GLU	2345,2055	557.1+/-379.7	637,1071,492	56.0	60.0	59.0		1354	5.3	1.0	21	dbSNP_100	59	2904,5690	428.6+/-355.9	490,1924,1883	yes	missense	LIPI	NM_198996.2	56	1127,2995,2375	TT,TC,CC		33.791,46.7045,40.3956	benign	452/482	15516948	5249,7745	2200	4297	6497	SO:0001583	missense	149998	exon9			ACCTTTCTGGGTA	BC028732	CCDS13564.1	21q11.2	2012-07-31			ENSG00000188992	ENSG00000188992			18821	protein-coding gene	gene with protein product	"""membrane-associated phospholipase A1 beta"", ""cancer/testis antigen 17"""	609252				12719377	Standard	XM_005260924		Approved	PRED5, LPDL, CT17, mPA-PLA1beta, PLA1C	uc002yjm.3	Q6XZB0	OTTHUMG00000074258	ENST00000536861.1:c.1291G>A	21.37:g.15516948C>T	ENSP00000440381:p.Glu431Lys	Somatic	237	0	0		WXS	Illumina HiSeq	Phase_I	145	144	0.993103	NM_198996	G1JSG3|G1JSG4|G1JSG5|G1JSG6|G1JSG7|G1JSG8|G1JSG9	Missense_Mutation	SNP	ENST00000536861.1	37		697	0.3191391941391941	265	0.5386178861788617	144	0.39779005524861877	33	0.057692307692307696	255	0.33641160949868076	C	23.2	4.387982	0.82902	0.532955	0.33791	ENSG00000188992	ENST00000344577;ENST00000536861	D;D	0.88975	-2.45;-2.44	5.34	5.34	0.76211	.	0.684752	0.12545	U	0.459591	T	0.00012	0.0000	L	0.61218	1.895	0.37979	P	0.06645599999999996	B	0.31274	0.317	B	0.36666	0.23	T	0.35325	-0.9793	9	0.13470	T	0.59	.	14.9043	0.70706	0.0:1.0:0.0:0.0	rs2822432;rs60846610;rs2822432	452	Q6XZB0-2	.	K	452;431	ENSP00000343331:E452K;ENSP00000440381:E431K	ENSP00000343331:E452K	E	-	1	0	LIPI	14438819	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	1.230000	0.32612	2.654000	0.90174	0.650000	0.86243	GAA	C|0.629;T|0.371	0.371	strong		0.294	LIPI-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_198996	
CDRT1	374286	hgsc.bcm.edu	37	17	15496727	15496727	+	Missense_Mutation	SNP	T	T	G	rs79385100	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:15496727T>G	ENST00000395906.3	-	11	1929	c.1930A>C	c.(1930-1932)Aat>Cat	p.N644H	CDRT1_ENST00000583965.1_Intron|CDRT1_ENST00000354433.3_Missense_Mutation_p.N144H|RP11-385D13.1_ENST00000455584.2_Intron	NM_006382.3	NP_006373.2	O95170	CDRT1_HUMAN	CMT1A duplicated region transcript 1	644				N -> H (in Ref. 1; AAC52034/AAD10830). {ECO:0000305}.						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)		CAGTTCCCATTGAAGAAATTG	0.512													.|||	987	0.197085	0.1936	0.281	5008	,	,		17558	0.2331		0.1213	False		,,,				2504	0.183				p.N644H		Atlas-SNP	.											.	CDRT1	83	.	0			c.A1930C						PASS	.	T	HIS/ASN	830,3576	318.5+/-295.7	75,680,1448	229.0	240.0	236.0		1930	3.6	1.0	17	dbSNP_131	236	1103,7497	221.0+/-258.6	72,959,3269	yes	missense	CDRT1	NM_006382.3	68	147,1639,4717	GG,GT,TT		12.8256,18.8379,14.8624	probably-damaging	644/753	15496727	1933,11073	2203	4300	6503	SO:0001583	missense	374286	exon11			TCCCATTGAAGAA	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.1930A>C	17.37:g.15496727T>G	ENSP00000379242:p.Asn644His	Somatic	227	0	0		WXS	Illumina HiSeq	Phase_I	211	209	0.990521	NM_006382	O43848|O95611	Missense_Mutation	SNP	ENST00000395906.3	37	CCDS45619.1	398	0.18223443223443223	82	0.16666666666666666	94	0.2596685082872928	126	0.2202797202797203	96	0.1266490765171504	t	17.55	3.416430	0.62511	0.188379	0.128256	ENSG00000241322;ENSG00000251537;ENSG00000251537	ENST00000354433;ENST00000261644;ENST00000395906	T;T	0.19669	2.13;2.13	4.74	3.61	0.41365	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	.	.	.	.	T	0.00012	0.0000	M	0.61703	1.905	0.09310	P	0.9999999999999785	D	0.65815	0.995	P	0.62885	0.908	T	0.15521	-1.0434	7	.	.	.	.	9.886	0.41262	0.1521:0.0:0.0:0.8479	.	644	O95170	CDRT1_HUMAN	H	144;674;644	ENSP00000346416:N144H;ENSP00000379242:N644H	.	N	-	1	0	CDRT1;RP11-385D13.1	15437452	0.999000	0.42202	0.988000	0.46212	0.915000	0.54546	4.784000	0.62411	1.781000	0.52344	0.528000	0.53228	AAT	T|0.825;G|0.175	0.175	strong		0.512	CDRT1-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448127.1	NM_006382	
LIMD2	80774	hgsc.bcm.edu	37	17	61775992	61775992	+	Missense_Mutation	SNP	A	A	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:61775992A>T	ENST00000259006.3	-	5	462	c.304T>A	c.(304-306)Tac>Aac	p.Y102N	LIMD2_ENST00000583211.1_Missense_Mutation_p.Y53N|LIMD2_ENST00000582055.1_Missense_Mutation_p.Y53N|LIMD2_ENST00000578402.1_Missense_Mutation_p.Y102N|LIMD2_ENST00000578993.1_Missense_Mutation_p.Y62N|LIMD2_ENST00000578061.1_Missense_Mutation_p.Y102N	NM_030576.3	NP_085053.1	Q9BT23	LIMD2_HUMAN	LIM domain containing 2	102							zinc ion binding (GO:0008270)			kidney(1)|lung(2)	3						CCCTCGTCGTAGTTGCCTTTG	0.617																																					p.Y102N		Atlas-SNP	.											.	LIMD2	6	.	0			c.T304A						PASS	.						73.0	58.0	63.0					17																	61775992		2203	4300	6503	SO:0001583	missense	80774	exon5			CGTCGTAGTTGCC	AK092301	CCDS11641.1	17q23.3	2006-02-03				ENSG00000136490			28142	protein-coding gene	gene with protein product						12477932	Standard	NM_030576		Approved	MGC10986	uc002jbj.4	Q9BT23		ENST00000259006.3:c.304T>A	17.37:g.61775992A>T	ENSP00000259006:p.Tyr102Asn	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	102	27	0.264706	NM_030576	D3DU16|Q96S91	Missense_Mutation	SNP	ENST00000259006.3	37	CCDS11641.1	.	.	.	.	.	.	.	.	.	.	A	23.0	4.358147	0.82243	.	.	ENSG00000136490	ENST00000259006	T	0.79845	-1.31	5.0	5.0	0.66597	.	0.000000	0.85682	D	0.000000	D	0.90212	0.6940	M	0.86268	2.805	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	D	0.91871	0.5507	10	0.87932	D	0	-26.4471	14.5766	0.68252	1.0:0.0:0.0:0.0	.	102	Q9BT23	LIMD2_HUMAN	N	102	ENSP00000259006:Y102N	ENSP00000259006:Y102N	Y	-	1	0	LIMD2	59129724	1.000000	0.71417	1.000000	0.80357	0.480000	0.33159	9.313000	0.96297	2.100000	0.63781	0.533000	0.62120	TAC	.	.	none		0.617	LIMD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443877.1	NM_030576	
KANK4	163782	hgsc.bcm.edu	37	1	62713246	62713246	+	Silent	SNP	G	G	A	rs10889315	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:62713246G>A	ENST00000371153.4	-	9	3159	c.2781C>T	c.(2779-2781)caC>caT	p.H927H	KANK4_ENST00000354381.3_Silent_p.H299H|KANK4_ENST00000317477.4_Silent_p.H65H|KANK4_ENST00000371150.1_Silent_p.H283H	NM_181712.4	NP_859063.3	Q5T7N3	KANK4_HUMAN	KN motif and ankyrin repeat domains 4	927						cytoplasm (GO:0005737)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(49)|ovary(3)|prostate(4)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)	81						AGGATCCATCGTGGTCCTGCA	0.627													G|||	1597	0.31889	0.3026	0.3444	5008	,	,		20100	0.1429		0.4195	False		,,,				2504	0.4008				p.H927H		Atlas-SNP	.											KANK4,NS,carcinoma,0,1	KANK4	135	1	0			c.C2781T						PASS	.	G		1464,2942	472.6+/-356.4	242,980,981	100.0	82.0	88.0		2781	-4.0	0.2	1	dbSNP_120	88	3620,4980	522.0+/-380.0	769,2082,1449	no	coding-synonymous	KANK4	NM_181712.4		1011,3062,2430	AA,AG,GG		42.093,33.2274,39.0897		927/996	62713246	5084,7922	2203	4300	6503	SO:0001819	synonymous_variant	163782	exon9			TCCATCGTGGTCC	AK096259	CCDS620.1	1p31.3	2013-10-11	2008-01-29	2008-01-29	ENSG00000132854	ENSG00000132854		"""KN motif and ankyrin repeat domain containing"", ""Ankyrin repeat domain containing"""	27263	protein-coding gene	gene with protein product		614612	"""ankyrin repeat domain 38"""	ANKRD38		17996375, 19554261	Standard	NM_181712		Approved	KIAA0172	uc001dah.4	Q5T7N3	OTTHUMG00000008971	ENST00000371153.4:c.2781C>T	1.37:g.62713246G>A		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	121	60	0.495868	NM_181712	B1ALP7|Q6P9A0|Q86T71|Q86VE6|Q8NAX3	Silent	SNP	ENST00000371153.4	37	CCDS620.1																																																																																			G|0.637;A|0.363	0.363	strong		0.627	KANK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024877.1	NM_181712	
MYO6	4646	hgsc.bcm.edu	37	6	76576290	76576290	+	Silent	SNP	C	C	T	rs11756446	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:76576290C>T	ENST00000369977.3	+	17	1861	c.1722C>T	c.(1720-1722)gaC>gaT	p.D574D	RNA5SP209_ENST00000411237.1_RNA|MYO6_ENST00000369981.3_Silent_p.D574D|MYO6_ENST00000369975.1_Silent_p.D574D|snoU13_ENST00000459013.1_RNA|MYO6_ENST00000369985.4_Silent_p.D574D	NM_004999.3	NP_004990.3	Q9UM54	MYO6_HUMAN	myosin VI	574	Myosin motor.				actin filament-based movement (GO:0030048)|auditory receptor cell differentiation (GO:0042491)|cellular response to electrical stimulus (GO:0071257)|dendrite development (GO:0016358)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|endocytosis (GO:0006897)|glutamate secretion (GO:0014047)|inner ear morphogenesis (GO:0042472)|intracellular protein transport (GO:0006886)|locomotory behavior (GO:0007626)|membrane organization (GO:0061024)|metabolic process (GO:0008152)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein targeting (GO:0006605)|regulation of secretion (GO:0051046)|regulation of synaptic plasticity (GO:0048167)|response to drug (GO:0042493)|sensory perception of sound (GO:0007605)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	apical part of cell (GO:0045177)|axon (GO:0030424)|cell cortex (GO:0005938)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|DNA-directed RNA polymerase II, holoenzyme (GO:0016591)|endocytic vesicle (GO:0030139)|extracellular vesicular exosome (GO:0070062)|filamentous actin (GO:0031941)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|microvillus (GO:0005902)|neuronal cell body (GO:0043025)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|ruffle membrane (GO:0032587)|unconventional myosin complex (GO:0016461)|vesicle membrane (GO:0012506)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|minus-end directed microfilament motor activity (GO:0060001)|motor activity (GO:0003774)			breast(2)|central_nervous_system(1)|endometrium(7)|kidney(5)|large_intestine(16)|lung(19)|ovary(1)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	58		all_hematologic(105;0.189)		BRCA - Breast invasive adenocarcinoma(397;0.223)		TCAGAGACGACGAAGGCTTCA	0.353													c|||	145	0.0289537	0.0023	0.0331	5008	,	,		17803	0.0129		0.0577	False		,,,				2504	0.0491				p.D574D		Atlas-SNP	.											MYO6,NS,carcinoma,+2,1	MYO6	124	1	0			c.C1722T						PASS	.	C		42,4364	44.6+/-78.6	0,42,2161	102.0	101.0	101.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1722	-9.0	0.8	6	dbSNP_120	101	524,8076	147.3+/-202.7	14,496,3790	no	coding-synonymous	MYO6	NM_004999.3		14,538,5951	TT,TC,CC		6.093,0.9532,4.3518		574/1286	76576290	566,12440	2203	4300	6503	SO:0001819	synonymous_variant	4646	exon17			AGACGACGAAGGC	U90236, AB002387	CCDS34487.1, CCDS75481.1	6q14.1	2014-09-17	2004-05-19		ENSG00000196586	ENSG00000196586		"""Myosins / Myosin superfamily : Class VI"""	7605	protein-coding gene	gene with protein product		600970	"""deafness, autosomal recessive 37"""	DFNA22, DFNB37		9259267, 11468689	Standard	XM_005248719		Approved	KIAA0389	uc003pih.1	Q9UM54	OTTHUMG00000015061	ENST00000369977.3:c.1722C>T	6.37:g.76576290C>T		Somatic	208	0	0		WXS	Illumina HiSeq	Phase_I	175	88	0.502857	NM_004999	A6H8V4|E1P540|Q5TEM5|Q5TEM6|Q5TEM7|Q9BZZ7|Q9UEG2	Silent	SNP	ENST00000369977.3	37	CCDS34487.1																																																																																			C|0.959;T|0.041	0.041	strong		0.353	MYO6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041279.2	NM_004999	
TMEM231	79583	hgsc.bcm.edu	37	16	75574030	75574030	+	Silent	SNP	C	C	T	rs2242406	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:75574030C>T	ENST00000258173.6	-	7	889	c.813G>A	c.(811-813)gtG>gtA	p.V271V	RP11-77K12.8_ENST00000564489.1_RNA|RP11-77K12.7_ENST00000460606.1_Intron|TMEM231_ENST00000568377.1_Silent_p.V300V|TMEM231_ENST00000569294.1_5'UTR|TMEM231_ENST00000565067.1_Silent_p.V223V	NM_001077418.1	NP_001070886.1	Q9H6L2	TM231_HUMAN	transmembrane protein 231	271					cilium assembly (GO:0042384)|smoothened signaling pathway (GO:0007224)	ciliary membrane (GO:0060170)|ciliary transition zone (GO:0035869)|integral component of membrane (GO:0016021)|TCTN-B9D complex (GO:0036038)				endometrium(1)|kidney(1)|large_intestine(2)|lung(1)	5						TGACATACTGCACCCAGGCGA	0.453													C|||	1353	0.270168	0.0068	0.3429	5008	,	,		22674	0.7034		0.0437	False		,,,				2504	0.3609				p.V324V		Atlas-SNP	.											.	TMEM231	13	.	0			c.G972A						PASS	.	C	,,	86,3786		1,84,1851	64.0	58.0	60.0		900,813,465	3.3	1.0	16	dbSNP_98	60	444,7804		11,422,3691	no	coding-synonymous,coding-synonymous,coding-synonymous	TMEM231	NM_001077416.1,NM_001077418.1,NM_001077419.1	,,	12,506,5542	TT,TC,CC		5.3831,2.2211,4.3729	,,	300/346,271/317,155/201	75574030	530,11590	1936	4124	6060	SO:0001819	synonymous_variant	79583	exon6			ATACTGCACCCAG		CCDS45530.1	16q23.1	2014-01-28			ENSG00000205084	ENSG00000205084			37234	protein-coding gene	gene with protein product		614949				23012439	Standard	NM_001077416		Approved	FLJ22167, ALYE870, PRO1886, JBTS20, MKS11	uc002fek.4	Q9H6L2		ENST00000258173.6:c.813G>A	16.37:g.75574030C>T		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	70	28	0.4	NM_001077416	A0JLU1|A6NDZ6|B3KU85|G5E9E3|Q6P450|Q6UWW5	Silent	SNP	ENST00000258173.6	37	CCDS45530.1																																																																																			C|0.752;T|0.248	0.248	strong		0.453	TMEM231-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435481.2	NM_001077416	
PCDHGA9	56107	hgsc.bcm.edu	37	5	140784895	140784895	+	Silent	SNP	C	C	T	rs4912606	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:140784895C>T	ENST00000573521.1	+	1	2376	c.2376C>T	c.(2374-2376)tgC>tgT	p.C792C	PCDHGA3_ENST00000253812.6_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGB6_ENST00000520790.1_5'Flank|PCDHGA4_ENST00000571252.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA8_ENST00000398604.2_Intron	NM_018921.2|NM_032089.1	NP_061744.1|NP_114478.1	Q9Y5G4	PCDG9_HUMAN	protocadherin gamma subfamily A, 9	792					homophilic cell adhesion (GO:0007156)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(1)|lung(3)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AGCCTTTGTGCGTCTCTGTTG	0.428													.|||	79	0.0157748	0.0008	0.0216	5008	,	,		20897	0.0		0.0586	False		,,,				2504	0.0041				p.C792C		Atlas-SNP	.											.	PCDHGA9	110	.	0			c.C2376T						PASS	.	C	,,,,,,,,,,,,,,	40,4344		0,40,2152	72.0	80.0	77.0		,,,,,,,,2376,,,,,,2376	-6.7	0.0	5	dbSNP_111	77	341,8255		5,331,3962	no	intron,intron,intron,intron,intron,intron,intron,intron,coding-synonymous,intron,intron,intron,intron,intron,coding-synonymous	PCDHGB4,PCDHGA8,PCDHGB5,PCDHGB3,PCDHGB2,PCDHGB1,PCDHGA9,PCDHGA7,PCDHGA6,PCDHGA5,PCDHGA4,PCDHGA3,PCDHGA2,PCDHGA1	NM_003736.2,NM_018912.2,NM_018915.2,NM_018916.3,NM_018917.2,NM_018918.2,NM_018919.2,NM_018920.2,NM_018921.2,NM_018922.2,NM_018923.2,NM_018924.2,NM_018925.2,NM_032088.1,NM_032089.1	,,,,,,,,,,,,,,	5,371,6114	TT,TC,CC		3.967,0.9124,2.9353	,,,,,,,,,,,,,,	,,,,,,,,792/933,,,,,,792/829	140784895	381,12599	2192	4298	6490	SO:0001819	synonymous_variant	56107	exon1			TTTGTGCGTCTCT	AF152516	CCDS58981.1, CCDS75341.1	5q31	2010-01-26						"""Cadherins / Protocadherins : Clustered"""	8707	other	protocadherin		606296				10380929	Standard	NM_018921		Approved	PCDH-GAMMA-A9		Q9Y5G4		ENST00000573521.1:c.2376C>T	5.37:g.140784895C>T		Somatic	190	0	0		WXS	Illumina HiSeq	Phase_I	151	73	0.483444	NM_032089	A2RU65|Q9Y5C9	Silent	SNP	ENST00000573521.1	37	CCDS58981.1																																																																																			C|0.975;T|0.025	0.025	strong		0.428	PCDHGA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437105.1	NM_018921	
PXDNL	137902	hgsc.bcm.edu	37	8	52233408	52233408	+	Missense_Mutation	SNP	C	C	T	rs7827446	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:52233408C>T	ENST00000356297.4	-	22	4296	c.4196G>A	c.(4195-4197)aGa>aAa	p.R1399K	PXDNL_ENST00000543296.1_Silent_p.*1317*|RP11-401H2.1_ENST00000521294.1_RNA	NM_144651.4	NP_653252	A1KZ92	PXDNL_HUMAN	peroxidasin homolog (Drosophila)-like	1399	VWFC. {ECO:0000255|PROSITE- ProRule:PRU00220}.		R -> K (in dbSNP:rs7827446). {ECO:0000269|Ref.2}.		hydrogen peroxide catabolic process (GO:0042744)|oxidation-reduction process (GO:0055114)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	endonuclease activity (GO:0004519)|heme binding (GO:0020037)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)			NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(6)|lung(25)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	48		all_cancers(86;0.107)|Lung NSC(129;0.00641)|all_epithelial(80;0.00716)|all_lung(136;0.015)				TGGAACCCCTCTAACATCTGT	0.517													T|||	1609	0.321286	0.6346	0.2291	5008	,	,		16120	0.1429		0.2396	False		,,,				2504	0.2311				p.R1399K		Atlas-SNP	.											PXDNL_ENST00000356297,caecum,carcinoma,0,1	PXDNL	414	1	0			c.G4196A						PASS	.	T	LYS/ARG	2105,1793		579,947,423	149.0	162.0	158.0		4196	0.6	0.4	8	dbSNP_116	158	2170,6112		296,1578,2267	yes	missense	PXDNL	NM_144651.4	26	875,2525,2690	TT,TC,CC		26.2014,45.9979,35.0985	benign	1399/1464	52233408	4275,7905	1949	4141	6090	SO:0001583	missense	137902	exon22			ACCCCTCTAACAT		CCDS47855.1	8q11.21-q11.22	2013-02-18	2007-01-12		ENSG00000147485	ENSG00000147485		"""Immunoglobulin superfamily / I-set domain containing"""	26359	protein-coding gene	gene with protein product	"""polysomal ribonuclease 1 homolog (Xenopus)"""	615904	"""peroxidasin homolog-like (Drosophila)"""			22543864	Standard	NM_144651		Approved	FLJ25471, PMR1	uc003xqu.4	A1KZ92	OTTHUMG00000164244	ENST00000356297.4:c.4196G>A	8.37:g.52233408C>T	ENSP00000348645:p.Arg1399Lys	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	82	12	0.146341	NM_144651	B5ME43|B6CGZ3|H0YBM9|Q6ZMR2|Q96LH9	Missense_Mutation	SNP	ENST00000356297.4	37	CCDS47855.1	670|670	0.3067765567765568|0.3067765567765568	308|308	0.6260162601626016|0.6260162601626016	94|94	0.2596685082872928|0.2596685082872928	85|85	0.1486013986013986|0.1486013986013986	183|183	0.24142480211081793|0.24142480211081793	T|T	1.339|1.339	-0.594680|-0.594680	0.03771|0.03771	0.540021|0.540021	0.262014|0.262014	ENSG00000147485|ENSG00000147485	ENST00000522933|ENST00000356297	.|T	.|0.64085	.|-0.08	4.49|4.49	0.646|0.646	0.17789|0.17789	.|von Willebrand factor, type C (3);	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.02129|0.02129	-0.67|-0.67	0.23689|0.23689	P|P	0.99710698|0.99710698	.|B	.|0.02656	.|0.0	.|B	.|0.04013	.|0.001	T|T	0.42832|0.42832	-0.9428|-0.9428	4|8	.|0.02654	.|T	.|1	.|.	4.1727|4.1727	0.10337|0.10337	0.0:0.3128:0.1769:0.5103|0.0:0.3128:0.1769:0.5103	rs7827446;rs52800611;rs58970495;rs7827446|rs7827446;rs52800611;rs58970495;rs7827446	.|1399	.|A1KZ92	.|PXDNL_HUMAN	K|K	473|1399	.|ENSP00000348645:R1399K	.|ENSP00000348645:R1399K	E|R	-|-	1|2	0|0	PXDNL|PXDNL	52395961|52395961	0.000000|0.000000	0.05858|0.05858	0.403000|0.403000	0.26384|0.26384	0.001000|0.001000	0.01503|0.01503	-0.062000|-0.062000	0.11674|0.11674	-0.466000|-0.466000	0.06943|0.06943	-2.070000|-2.070000	0.00385|0.00385	GAG|AGA	C|0.679;T|0.321	0.321	strong		0.517	PXDNL-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377905.1	NM_144651	
OBSCN	84033	hgsc.bcm.edu	37	1	228469870	228469870	+	Missense_Mutation	SNP	C	C	T	rs3795785	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:228469870C>T	ENST00000422127.1	+	31	8478	c.8434C>T	c.(8434-8436)Cgg>Tgg	p.R2812W	OBSCN_ENST00000284548.11_Missense_Mutation_p.R2812W|OBSCN_ENST00000359599.6_Missense_Mutation_p.R1659W|OBSCN_ENST00000570156.2_Missense_Mutation_p.R3241W|OBSCN_ENST00000366709.4_5'UTR|OBSCN_ENST00000366707.4_5'UTR	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	2812	Ig-like 27.		R -> W (in dbSNP:rs3795785).		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)				CTTCTCTGTGCGGGGCCTCAC	0.652													C|||	437	0.0872604	0.0439	0.013	5008	,	,		16137	0.2808		0.0249	False		,,,				2504	0.0634				p.R3241W		Atlas-SNP	.											.	OBSCN	2142	.	0			c.C9721T						PASS	.	C	TRP/ARG,TRP/ARG	187,3787		6,175,1806	31.0	36.0	35.0		8434,8434	-0.2	0.0	1	dbSNP_107	35	148,8144		0,148,3998	yes	missense,missense	OBSCN	NM_001098623.1,NM_052843.2	101,101	6,323,5804	TT,TC,CC		1.7849,4.7056,2.7311	benign,benign	2812/7969,2812/6621	228469870	335,11931	1987	4146	6133	SO:0001583	missense	84033	exon36			TCTGTGCGGGGCC	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.8434C>T	1.37:g.228469870C>T	ENSP00000409493:p.Arg2812Trp	Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	187	94	0.502674	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	217	0.09935897435897435	18	0.036585365853658534	5	0.013812154696132596	170	0.2972027972027972	24	0.0316622691292876	C	9.047	0.991227	0.18966	0.047056	0.017849	ENSG00000154358	ENST00000284548;ENST00000422127;ENST00000359599;ENST00000366706;ENST00000366704	T;T;T	0.41400	1.0;1.0;1.0	4.21	-0.154	0.13399	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like fold (1);	1.005240	0.08013	N	0.990625	T	0.00012	0.0000	M	0.70275	2.135	0.28160	P	0.9290387	B;B;B	0.21606	0.058;0.035;0.048	B;B;B	0.20577	0.011;0.001;0.03	T	0.25467	-1.0131	9	0.66056	D	0.02	.	10.1616	0.42855	0.0:0.5157:0.4097:0.0746	rs3795785;rs61099141;rs3795785	2812;2812;2812	Q5VST9;Q5VST9-2;Q5VST9-3	OBSCN_HUMAN;.;.	W	2812;2812;1659;511;218	ENSP00000284548:R2812W;ENSP00000409493:R2812W;ENSP00000352613:R1659W	ENSP00000284548:R2812W	R	+	1	2	OBSCN	226536493	0.004000	0.15560	0.026000	0.17262	0.140000	0.21249	0.994000	0.29693	-0.239000	0.09710	-1.520000	0.00934	CGG	C|0.882;T|0.118	0.118	strong		0.652	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
MUC4	4585	hgsc.bcm.edu	37	3	195508418	195508418	+	Missense_Mutation	SNP	C	C	G	rs548345415	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195508418C>G	ENST00000463781.3	-	2	10492	c.10033G>C	c.(10033-10035)Gtg>Ctg	p.V3345L	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.V3345L	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)		GTGACAGGCACAGGGGTGGTG	0.597													.|||	1317	0.262979	0.3646	0.2075	5008	,	,		12766	0.2976		0.2336	False		,,,				2504	0.1595				p.V3345L		Atlas-SNP	.											MUC4_ENST00000463781,rectum,carcinoma,+2,1	MUC4	1505	1	0			c.G10033C						scavenged	.						31.0	24.0	26.0					3																	195508418		666	1575	2241	SO:0001583	missense	4585	exon2			CAGGCACAGGGGT	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.10033G>C	3.37:g.195508418C>G	ENSP00000417498:p.Val3345Leu	Somatic	92	2	0.0217391		WXS	Illumina HiSeq	Phase_I	73	4	0.0547945	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	0.014	-1.600585	0.00849	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.37584	1.26;1.19	1.03	-2.05	0.07321	.	.	.	.	.	T	0.10680	0.0261	N	0.02539	-0.55	0.09310	N	1	B	0.09022	0.002	B	0.01281	0.0	T	0.08411	-1.0723	8	.	.	.	.	0.4737	0.00536	0.1854:0.3006:0.1852:0.3288	.	3217	E7ESK3	.	L	3345	ENSP00000417498:V3345L;ENSP00000420243:V3345L	.	V	-	1	0	MUC4	196993197	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-5.422000	0.00123	-4.572000	0.00041	-4.097000	0.00011	GTG	.	.	none		0.597	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
TRMT12	55039	hgsc.bcm.edu	37	8	125463250	125463250	+	Missense_Mutation	SNP	T	T	C	rs3812475	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:125463250T>C	ENST00000328599.3	+	1	203	c.82T>C	c.(82-84)Tgg>Cgg	p.W28R	TRMT12_ENST00000521443.1_3'UTR	NM_017956.3	NP_060426.2	Q53H54	TYW2_HUMAN	tRNA methyltransferase 12 homolog (S. cerevisiae)	28			W -> R (in dbSNP:rs3812475). {ECO:0000269|PubMed:15489334}.		tRNA processing (GO:0008033)		transferase activity (GO:0016740)			breast(2)|endometrium(1)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	15	Ovarian(258;0.00438)|all_neural(195;0.0779)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.00288)			GACTGAGCCTTGGTTTACCCA	0.517													C|||	2860	0.571086	0.7814	0.4798	5008	,	,		18795	0.4415		0.495	False		,,,				2504	0.5634				p.W28R		Atlas-SNP	.											.	TRMT12	28	.	0			c.T82C						PASS	.	C	ARG/TRP	3061,1345	447.5+/-348.4	1073,915,215	123.0	128.0	126.0		82	5.2	0.9	8	dbSNP_107	126	4059,4541	595.1+/-393.4	942,2175,1183	yes	missense	TRMT12	NM_017956.3	101	2015,3090,1398	CC,CT,TT		47.1977,30.5266,45.256	benign	28/449	125463250	7120,5886	2203	4300	6503	SO:0001583	missense	55039	exon1			GAGCCTTGGTTTA	AF313041	CCDS6349.1	8q24.13	2011-05-09	2006-11-16		ENSG00000183665	ENSG00000183665			26091	protein-coding gene	gene with protein product	"""tRNA-yW synthesizing protein 2"""	611244	"""tRNA methyltranferase 12 homolog (S. cerevisiae)"""			16005430, 17150819	Standard	NM_017956		Approved	FLJ20772, Trm12, TYW2	uc003yra.4	Q53H54	OTTHUMG00000165022	ENST00000328599.3:c.82T>C	8.37:g.125463250T>C	ENSP00000329858:p.Trp28Arg	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	85	85	1	NM_017956	Q6PKB9|Q96F21|Q9NWK6	Missense_Mutation	SNP	ENST00000328599.3	37	CCDS6349.1	1205	0.5517399267399268	394	0.8008130081300813	189	0.5220994475138122	242	0.4230769230769231	380	0.5013192612137203	C	0.456	-0.891521	0.02491	0.694734	0.471977	ENSG00000183665	ENST00000328599	T	0.38560	1.13	5.15	5.15	0.70609	.	0.426796	0.26563	N	0.023680	T	0.00012	0.0000	N	0.00128	-2.045	0.58432	P	9.99999999995449E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.39099	-0.9630	9	0.02654	T	1	-11.5588	10.5383	0.45018	0.0:0.9086:0.0:0.0914	rs3812475;rs17856366;rs52807988;rs59731176;rs3812475	28	Q53H54	TYW2_HUMAN	R	28	ENSP00000329858:W28R	ENSP00000329858:W28R	W	+	1	0	TRMT12	125532431	0.468000	0.25839	0.923000	0.36655	0.456000	0.32438	0.518000	0.22847	1.515000	0.48885	-0.215000	0.12644	TGG	T|0.442;C|0.558	0.558	strong		0.517	TRMT12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381465.1	NM_017956	
SYNE1	23345	hgsc.bcm.edu	37	6	152746593	152746593	+	Missense_Mutation	SNP	A	A	T	rs111250109	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:152746593A>T	ENST00000367255.5	-	39	5791	c.5190T>A	c.(5188-5190)gaT>gaA	p.D1730E	SYNE1_ENST00000265368.4_Missense_Mutation_p.D1730E|SYNE1_ENST00000448038.1_Missense_Mutation_p.D1737E|SYNE1_ENST00000423061.1_Missense_Mutation_p.D1737E|SYNE1_ENST00000341594.5_Missense_Mutation_p.D1767E	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	1730					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)		TTTTCACATCATCTTTGGAGG	0.363										HNSCC(10;0.0054)			A|||	164	0.0327476	0.0287	0.0288	5008	,	,		18407	0.005		0.0577	False		,,,				2504	0.044				p.D1737E		Atlas-SNP	.											.	SYNE1	3227	.	0			c.T5211A						PASS	.	A	GLU/ASP,GLU/ASP	183,4223	118.8+/-156.5	5,173,2025	153.0	143.0	147.0		5211,5190	-6.3	0.8	6	dbSNP_132	147	444,8156	134.3+/-191.7	18,408,3874	yes	missense,missense	SYNE1	NM_033071.3,NM_182961.3	45,45	23,581,5899	TT,TA,AA		5.1628,4.1534,4.8209	benign,benign	1737/8750,1730/8798	152746593	627,12379	2203	4300	6503	SO:0001583	missense	23345	exon39			CACATCATCTTTG	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.5190T>A	6.37:g.152746593A>T	ENSP00000356224:p.Asp1730Glu	Somatic	230	0	0		WXS	Illumina HiSeq	Phase_I	142	95	0.669014	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	68	0.031135531135531136	14	0.028455284552845527	10	0.027624309392265192	2	0.0034965034965034965	42	0.055408970976253295	A	12.76	2.033458	0.35893	0.041534	0.051628	ENSG00000131018	ENST00000367255;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594	T;T;T;T;T	0.30714	1.52;1.52;1.52;1.52;1.52	5.71	-6.32	0.01995	.	0.397222	0.23999	N	0.042496	T	0.02230	0.0069	N	0.04959	-0.14	0.80722	D	1	B;B;B;B	0.06786	0.001;0.0;0.0;0.0	B;B;B;B	0.04013	0.001;0.0;0.0;0.001	T	0.36744	-0.9735	10	0.02654	T	1	.	5.6049	0.17374	0.1571:0.5244:0.1775:0.141	.	1713;1730;1730;1737	B3W695;Q8NF91;E7EQI5;Q8NF91-4	.;SYNE1_HUMAN;.;.	E	1730;1737;1730;1737;1767	ENSP00000356224:D1730E;ENSP00000396024:D1737E;ENSP00000265368:D1730E;ENSP00000390975:D1737E;ENSP00000341887:D1767E	ENSP00000265368:D1730E	D	-	3	2	SYNE1	152788286	0.003000	0.15002	0.784000	0.31847	0.973000	0.67179	-2.103000	0.01341	-1.475000	0.01876	-0.314000	0.08810	GAT	A|0.951;T|0.049	0.049	strong		0.363	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961	
ERCC2	2068	hgsc.bcm.edu	37	19	45855478	45855478	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:45855478G>A	ENST00000391945.4	-	22	2256	c.2179C>T	c.(2179-2181)Ccc>Tcc	p.P727S	ERCC2_ENST00000391944.3_Missense_Mutation_p.P649S	NM_000400.3	NP_000391.1	P18074	ERCC2_HUMAN	excision repair cross-complementation group 2	727			Missing (in XP-D and TTDP). {ECO:0000269|PubMed:9195225}.		7-methylguanosine mRNA capping (GO:0006370)|aging (GO:0007568)|apoptotic process (GO:0006915)|ATP catabolic process (GO:0006200)|bone mineralization (GO:0030282)|cell proliferation (GO:0008283)|central nervous system myelin formation (GO:0032289)|chromosome segregation (GO:0007059)|DNA duplex unwinding (GO:0032508)|DNA repair (GO:0006281)|embryonic cleavage (GO:0040016)|erythrocyte maturation (GO:0043249)|extracellular matrix organization (GO:0030198)|gene expression (GO:0010467)|hair cell differentiation (GO:0035315)|hair follicle maturation (GO:0048820)|hematopoietic stem cell differentiation (GO:0060218)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|nucleotide-excision repair, DNA incision (GO:0033683)|positive regulation of DNA binding (GO:0043388)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of viral transcription (GO:0050434)|post-embryonic development (GO:0009791)|protein phosphorylation (GO:0006468)|regulation of mitotic cell cycle phase transition (GO:1901990)|response to hypoxia (GO:0001666)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)|spinal cord development (GO:0021510)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|UV protection (GO:0009650)|viral process (GO:0016032)	cytoplasm (GO:0005737)|holo TFIIH complex (GO:0005675)|MMXD complex (GO:0071817)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	4 iron, 4 sulfur cluster binding (GO:0051539)|5'-3' DNA helicase activity (GO:0043139)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)|protein N-terminus binding (GO:0047485)			large_intestine(4)|lung(2)|ovary(1)|pancreas(1)|stomach(1)	9		Ovarian(192;0.0728)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.0226)		CGGTGGAAGGGCTGTGCCATC	0.652			"""Mis, N, F, S"""			"""skin basal cell, skin squamous cell, melanoma"""		Nucleotide excision repair (NER)	Xeroderma Pigmentosum																												p.P727S		Atlas-SNP	.	yes	Rec		Xeroderma pigmentosum (D)	19	19q13.2-q13.3	2068	"""excision repair cross-complementing rodent repair deficiency, complementation group 2 (xeroderma pigmentosum D)"""		E	.	ERCC2	78	.	0			c.C2179T						PASS	.						73.0	55.0	61.0					19																	45855478		2203	4300	6503	SO:0001583	missense	2068	exon22	Familial Cancer Database	incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV	GGAAGGGCTGTGC		CCDS33049.1, CCDS46112.1	19q13.3	2014-09-17	2014-03-07		ENSG00000104884	ENSG00000104884	3.6.4.12	"""General transcription factor IIH complex subunits"""	3434	protein-coding gene	gene with protein product	"""excision repair cross-complementing rodent repair deficiency, complementation group 2 protein"", ""TFIIH basal transcription factor complex helicase XPB subunit"""	126340	"""xeroderma pigmentosum complementary group D"", ""excision repair cross-complementing rodent repair deficiency, complementation group 2"""	XPD		8413672, 2184031	Standard	NM_000400		Approved	MAG, EM9, MGC102762, MGC126218, MGC126219, TFIIH	uc002pbj.2	P18074	OTTHUMG00000048190	ENST00000391945.4:c.2179C>T	19.37:g.45855478G>A	ENSP00000375809:p.Pro727Ser	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	114	30	0.263158	NM_000400	Q2TB78|Q2YDY2|Q7KZU6|Q8N721	Missense_Mutation	SNP	ENST00000391945.4	37	CCDS33049.1	.	.	.	.	.	.	.	.	.	.	G	21.5	4.159589	0.78226	.	.	ENSG00000104884	ENST00000391941;ENST00000391942;ENST00000391945;ENST00000391944	T;D	0.82984	-1.41;-1.67	5.27	5.27	0.74061	.	0.126130	0.52532	D	0.000065	D	0.87815	0.6272	M	0.91663	3.23	0.80722	D	1	P;P;P	0.46987	0.762;0.756;0.888	B;B;B	0.43194	0.411;0.391;0.343	D	0.90746	0.4653	10	0.66056	D	0.02	-31.7778	16.3902	0.83532	0.0:0.0:1.0:0.0	.	649;727;420	E7EVE9;P18074;Q6ZNQ5	.;ERCC2_HUMAN;.	S	677;703;727;649	ENSP00000375809:P727S;ENSP00000375808:P649S	ENSP00000375805:P677S	P	-	1	0	ERCC2	50547318	1.000000	0.71417	0.998000	0.56505	0.979000	0.70002	8.735000	0.91549	2.461000	0.83175	0.561000	0.74099	CCC	.	.	none		0.652	ERCC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109626.2	NM_000400	
ALPP	250	hgsc.bcm.edu	37	2	233245026	233245026	+	Missense_Mutation	SNP	G	G	A	rs2853378	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:233245026G>A	ENST00000392027.2	+	6	1057	c.788G>A	c.(787-789)cGc>cAc	p.R263H	AC068134.8_ENST00000439072.1_RNA|AC068134.8_ENST00000441266.1_RNA	NM_001632.3	NP_001623.3	P05187	PPB1_HUMAN	alkaline phosphatase, placental	263			R -> H (in dbSNP:rs2853378). {ECO:0000269|PubMed:3461452}.		dephosphorylation (GO:0016311)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alkaline phosphatase activity (GO:0004035)|magnesium ion binding (GO:0000287)|zinc ion binding (GO:0008270)			NS(1)|biliary_tract(1)|endometrium(1)|kidney(4)|large_intestine(2)|liver(1)|lung(10)|ovary(2)	22		all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0449)|Lung NSC(271;0.132)		Epithelial(121;4.45e-22)|Kidney(3;4.42e-11)|KIRC - Kidney renal clear cell carcinoma(3;1.9e-09)|BRCA - Breast invasive adenocarcinoma(100;0.000767)|Lung(119;0.00566)|LUSC - Lung squamous cell carcinoma(224;0.00746)|STAD - Stomach adenocarcinoma(3;0.0181)|GBM - Glioblastoma multiforme(43;0.196)		CTGGCGAAGCGCCAGGTGATG	0.662													A|||	501	0.10004	0.0507	0.0605	5008	,	,		10859	0.2242		0.1004	False		,,,				2504	0.0665				p.R263H		Atlas-SNP	.											ALPP,NS,carcinoma,+1,1	ALPP	53	1	0			c.G788A						scavenged	.						69.0	73.0	71.0					2																	233245026		2203	4300	6503	SO:0001583	missense	250	exon6			CGAAGCGCCAGGT	M14169	CCDS2490.1	2q37.1	2010-06-24	2010-06-24		ENSG00000163283	ENSG00000163283	3.1.3.1		439	protein-coding gene	gene with protein product	"""Regan isozyme"""	171800	"""alkaline phosphatase, placental (Regan isozyme)"""			3001717, 3461452	Standard	XM_005246439		Approved		uc002vsq.3	P05187	OTTHUMG00000133255	ENST00000392027.2:c.788G>A	2.37:g.233245026G>A	ENSP00000375881:p.Arg263His	Somatic	380	3	0.00789474		WXS	Illumina HiSeq	Phase_I	228	102	0.447368	NM_001632	P05188|P06861|Q53S78|Q96DB7	Missense_Mutation	SNP	ENST00000392027.2	37	CCDS2490.1	224	0.10256410256410256	21	0.042682926829268296	22	0.06077348066298342	111	0.19405594405594406	70	0.09234828496042216	.	0.012	-1.655324	0.00779	.	.	ENSG00000163283	ENST00000392027	D	0.96522	-4.04	2.31	-0.177	0.13307	Alkaline phosphatase-like, alpha/beta/alpha (1);Alkaline-phosphatase-like, core domain (1);	1.003840	0.08014	N	0.990937	T	0.00608	0.0020	N	0.02685	-0.53	0.80722	P	0.0	B	0.13145	0.007	B	0.04013	0.001	T	0.54549	-0.8277	9	0.05959	T	0.93	.	7.1392	0.25546	0.6554:0.0:0.3446:0.0	rs2853378;rs12617638;rs17838624	263	P05187	PPB1_HUMAN	H	263	ENSP00000375881:R263H	ENSP00000375881:R263H	R	+	2	0	ALPP	232953270	0.000000	0.05858	0.964000	0.40570	0.162000	0.22319	0.146000	0.16180	0.135000	0.18707	-1.054000	0.02325	CGC	G|0.500;A|0.500	0.500	weak		0.662	ALPP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257032.3	NM_001632	
FBN3	84467	hgsc.bcm.edu	37	19	8191401	8191401	+	Silent	SNP	G	G	A	rs3813778	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	65	1	0.0153846		WXS	Illumina HiSeq	Phase_I	64	64	1	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	
HSPD1	3329	hgsc.bcm.edu	37	2	198363534	198363534	+	Silent	SNP	C	C	T	rs565153254		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:198363534C>T	ENST00000388968.3	-	2	306	c.39G>A	c.(37-39)ccG>ccA	p.P13P	HSPE1_ENST00000409729.1_5'Flank|HSPD1_ENST00000345042.2_Silent_p.P13P|HSPD1_ENST00000544407.1_Silent_p.P13P|HSPE1_ENST00000409468.1_5'Flank|HSPE1_ENST00000233893.5_5'Flank|HSPE1-MOB4_ENST00000604458.1_5'Flank	NM_002156.4	NP_002147.2	P10809	CH60_HUMAN	heat shock 60kDa protein 1 (chaperonin)	13					'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)	p.P13P(1)		NS(1)|breast(3)|endometrium(2)|large_intestine(3)|lung(7)|skin(1)	17			Epithelial(96;0.225)			CCCTGGACACCGGTCTCATCT	0.502																																					p.P13P		Atlas-SNP	.											HSPD1_ENST00000426480,NS,haematopoietic_neoplasm,0,3	HSPD1	68	3	1	Substitution - coding silent(1)	breast(1)	c.G39A						scavenged	.						52.0	49.0	50.0					2																	198363534		2203	4300	6503	SO:0001819	synonymous_variant	3329	exon2			GGACACCGGTCTC	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.39G>A	2.37:g.198363534C>T		Somatic	259	1	0.003861		WXS	Illumina HiSeq	Phase_I	199	2	0.0100503	NM_002156	B2R5M6|B7Z712|Q38L19|Q9UCR6	Silent	SNP	ENST00000388968.3	37	CCDS33357.1																																																																																			.	.	none		0.502	HSPD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335324.2	NM_002156	
NOL6	65083	hgsc.bcm.edu	37	9	33464897	33464897	+	Missense_Mutation	SNP	T	T	C	rs142747625	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:33464897T>C	ENST00000379471.2	-	21	2846	c.2759A>G	c.(2758-2760)aAc>aGc	p.N920S	NOL6_ENST00000455041.2_Missense_Mutation_p.N868S|NOL6_ENST00000464829.1_Intron			Q9H6R4	NOL6_HUMAN	nucleolar protein 6 (RNA-associated)	920					rRNA processing (GO:0006364)	condensed nuclear chromosome (GO:0000794)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			endometrium(4)|kidney(4)|large_intestine(5)|lung(8)|ovary(2)|prostate(2)|skin(2)	27			LUSC - Lung squamous cell carcinoma(29;0.00788)	GBM - Glioblastoma multiforme(74;0.152)		ATTATTGAGGTTGACAAAGAG	0.478													T|||	6	0.00119808	0.0	0.0014	5008	,	,		19701	0.0		0.005	False		,,,				2504	0.0				p.N920S		Atlas-SNP	.											.	NOL6	85	.	0			c.A2759G						PASS	.	T	SER/ASN,	1,4405	2.1+/-5.4	0,1,2202	95.0	100.0	99.0		2759,	5.4	1.0	9	dbSNP_134	99	20,8580	14.6+/-50.1	0,20,4280	yes	missense,intron	NOL6	NM_022917.4,NM_139235.3	46,	0,21,6482	CC,CT,TT		0.2326,0.0227,0.1615	probably-damaging,	920/1147,	33464897	21,12985	2203	4300	6503	SO:0001583	missense	65083	exon21			TTGAGGTTGACAA	AF361079	CCDS6543.1, CCDS6544.1	9p12	2013-02-22	2013-02-22		ENSG00000165271	ENSG00000165271			19910	protein-coding gene	gene with protein product		611532	"""nucleolar protein family 6 (RNA-associated)"""			11895476, 15590835	Standard	NM_022917		Approved	bA311H10.1, Nrap, FLJ21959, MGC14896, MGC14921, MGC20838, UTP22	uc003zsz.3	Q9H6R4	OTTHUMG00000000394	ENST00000379471.2:c.2759A>G	9.37:g.33464897T>C	ENSP00000368784:p.Asn920Ser	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	77	34	0.441558	NM_022917	Q5T5M3|Q5T5M4|Q7L4G6|Q8N6I0|Q8TEY9|Q8TEZ0|Q8TEZ1|Q9H675	Missense_Mutation	SNP	ENST00000379471.2	37		5	0.0022893772893772895	0	0.0	1	0.0027624309392265192	0	0.0	4	0.005277044854881266	T	16.69	3.193496	0.58017	2.27E-4	0.002326	ENSG00000165271	ENST00000297990;ENST00000379471;ENST00000541373;ENST00000325914;ENST00000455041	T;T;T	0.47869	0.83;0.83;0.83	5.45	5.45	0.79879	.	0.000000	0.85682	D	0.000000	T	0.58807	0.2148	M	0.78049	2.395	0.80722	D	1	D;D;D;D	0.62365	0.984;0.991;0.981;0.985	P;P;P;P	0.59546	0.794;0.833;0.59;0.859	T	0.68765	-0.5322	10	0.66056	D	0.02	.	15.5171	0.75833	0.0:0.0:0.0:1.0	.	868;917;920;920	B4DF80;Q9H6R4-4;Q9H6R4-2;Q9H6R4	.;.;.;NOL6_HUMAN	S	920;920;476;920;868	ENSP00000297990:N920S;ENSP00000368784:N920S;ENSP00000395915:N868S	ENSP00000297990:N920S	N	-	2	0	NOL6	33454897	1.000000	0.71417	0.993000	0.49108	0.024000	0.10985	7.579000	0.82511	2.059000	0.61396	0.533000	0.62120	AAC	T|0.998;C|0.002	0.002	strong		0.478	NOL6-005	NOVEL	non_canonical_TEC|basic	protein_coding	protein_coding	OTTHUMT00000001019.2	NM_022917	
PKDREJ	10343	hgsc.bcm.edu	37	22	46657894	46657894	+	Silent	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:46657894C>T	ENST00000253255.5	-	1	1325	c.1326G>A	c.(1324-1326)gcG>gcA	p.A442A		NM_006071.1	NP_006062.1	Q9NTG1	PKDRE_HUMAN	polycystin (PKD) family receptor for egg jelly	442	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)		TATCAGAAAACGCTGTCCTAG	0.468																																					p.A442A		Atlas-SNP	.											.	PKDREJ	195	.	0			c.G1326A						PASS	.						110.0	103.0	105.0					22																	46657894		2203	4300	6503	SO:0001819	synonymous_variant	10343	exon1			AGAAAACGCTGTC	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.1326G>A	22.37:g.46657894C>T		Somatic	199	0	0		WXS	Illumina HiSeq	Phase_I	183	47	0.256831	NM_006071	B1AJY3|O95850	Silent	SNP	ENST00000253255.5	37	CCDS14073.1																																																																																			.	.	none		0.468	PKDREJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318466.1	NM_006071	
TCP11	6954	hgsc.bcm.edu	37	6	35108553	35108553	+	Missense_Mutation	SNP	T	T	G	rs35693439	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:35108553T>G	ENST00000512012.1	-	1	251	c.95A>C	c.(94-96)gAc>gCc	p.D32A	TCP11_ENST00000418521.2_Intron|TCP11_ENST00000444780.2_Missense_Mutation_p.D45A|TCP11_ENST00000244645.3_5'UTR|TCP11_ENST00000412155.2_Intron|TCP11_ENST00000311875.5_Missense_Mutation_p.D45A|TCP11_ENST00000510465.1_5'UTR|TCP11_ENST00000373979.2_Intron|TCP11_ENST00000373974.4_Intron			Q8WWU5	TCP11_HUMAN	t-complex 11, testis-specific	32					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)				breast(1)|kidney(5)|large_intestine(3)|lung(10)|ovary(3)|prostate(1)|skin(4)	27						GCCGCTCTTGTCTTCCTGGGG	0.652													T|||	799	0.159545	0.2814	0.1398	5008	,	,		11586	0.119		0.1521	False		,,,				2504	0.0583				p.D45A		Atlas-SNP	.											.	TCP11	94	.	0			c.A134C						PASS	.	T	ALA/ASP,	1064,2736		151,762,987	23.0	25.0	24.0		134,	-1.8	0.0	6	dbSNP_126	24	1249,6943		97,1055,2944	yes	missense,utr-5	TCP11	NM_001093728.1,NM_018679.4	126,	248,1817,3931	GG,GT,TT		15.2466,28.0,19.2879	benign,	45/517,	35108553	2313,9679	1900	4096	5996	SO:0001583	missense	6954	exon2			CTCTTGTCTTCCT		CCDS4799.1, CCDS47413.1, CCDS59015.1, CCDS59016.1, CCDS59017.1, CCDS59018.1	6p21.31	2012-09-20	2012-09-20		ENSG00000124678	ENSG00000124678			11658	protein-coding gene	gene with protein product	"""fertilization-promoting peptide receptor"""	186982	"""t-complex 11 (a murine tcp homolog)"", ""t-complex 11 homolog (mouse)"""	D6S230E		1427894, 11756566, 21597245	Standard	NM_001093728		Approved	KIAA0229, FPPR	uc003okd.2	Q8WWU5	OTTHUMG00000014560	ENST00000512012.1:c.95A>C	6.37:g.35108553T>G	ENSP00000425995:p.Asp32Ala	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	59	25	0.423729	NM_001093728	B2RCE9|B3KQ27|B7Z7B5|B7Z7G1|B7Z7H4|B7Z7S8|E7EP29|J3KNG1|Q8NF85|Q9NQZ9|Q9NR39	Missense_Mutation	SNP	ENST00000512012.1	37		363	0.1662087912087912	134	0.27235772357723576	57	0.1574585635359116	68	0.11888111888111888	104	0.13720316622691292	T	14.47	2.545732	0.45280	0.28	0.152466	ENSG00000124678	ENST00000311875;ENST00000444780;ENST00000512012	T;T;T	0.11604	2.76;2.98;2.76	3.36	-1.78	0.07957	.	1.514410	0.04407	N	0.365370	T	0.01421	0.0046	L	0.27053	0.805	0.50171	P	1.4899999999995472E-4	B;B	0.30406	0.172;0.278	B;B	0.24974	0.039;0.057	T	0.38023	-0.9680	9	0.08599	T	0.76	.	3.1198	0.06387	0.2125:0.3986:0.0:0.3889	rs35693439	45;105	B7Z7B5;Q5TB88	.;.	A	45;45;32	ENSP00000308708:D45A;ENSP00000404479:D45A;ENSP00000425995:D32A	ENSP00000308708:D45A	D	-	2	0	TCP11	35216531	0.000000	0.05858	0.000000	0.03702	0.191000	0.23601	-0.761000	0.04751	-0.350000	0.08262	0.528000	0.53228	GAC	T|0.833;G|0.167	0.167	strong		0.652	TCP11-014	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000370354.1	NM_001093728	
OPLAH	26873	hgsc.bcm.edu	37	8	145112983	145112983	+	Missense_Mutation	SNP	C	C	T	rs55916375	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:145112983C>T	ENST00000426825.1	-	8	1099	c.1018G>A	c.(1018-1020)Gtc>Atc	p.V340I	OPLAH_ENST00000534424.1_5'UTR	NM_017570.3	NP_060040.1	O14841	OPLA_HUMAN	5-oxoprolinase (ATP-hydrolysing)	340					glutathione biosynthetic process (GO:0006750)|glutathione derivative biosynthetic process (GO:1901687)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	5-oxoprolinase (ATP-hydrolyzing) activity (GO:0017168)|ATP binding (GO:0005524)			breast(1)|central_nervous_system(1)|endometrium(1)|lung(13)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	20	all_cancers(97;1.06e-10)|all_epithelial(106;1.5e-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;6.79e-41)|Epithelial(56;1.02e-39)|all cancers(56;2.24e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			TGGAGGGTGACGCCAGCTGTG	0.662													C|||	167	0.0333466	0.0174	0.0461	5008	,	,		16267	0.001		0.0835	False		,,,				2504	0.0276				p.V340I		Atlas-SNP	.											.	OPLAH	78	.	0			c.G1018A						PASS	.	C	ILE/VAL	107,4003		0,107,1948	41.0	49.0	46.0		1018	0.4	0.5	8	dbSNP_129	46	562,7804		15,532,3636	yes	missense	OPLAH	NM_017570.3	29	15,639,5584	TT,TC,CC		6.7177,2.6034,5.3623	benign	340/1289	145112983	669,11807	2055	4183	6238	SO:0001583	missense	26873	exon8			GGGTGACGCCAGC	AF024672, AB122018	CCDS75802.1	8q24.3	2010-11-23			ENSG00000178814	ENSG00000178814	3.5.2.9		8149	protein-coding gene	gene with protein product		614243				14993790	Standard	NM_017570		Approved	OPLA, 5-Opase	uc003zar.3	O14841		ENST00000426825.1:c.1018G>A	8.37:g.145112983C>T	ENSP00000475943:p.Val340Ile	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	74	73	0.986486	NM_017570	A5PKY8|Q75W65|Q9Y4Q0	Missense_Mutation	SNP	ENST00000426825.1	37		94	0.04304029304029304	12	0.024390243902439025	19	0.052486187845303865	1	0.0017482517482517483	62	0.08179419525065963	C	1.905	-0.452126	0.04540	0.026034	0.067177	ENSG00000178814	ENST00000426825	.	.	.	4.7	0.388	0.16264	.	0.121832	0.52532	D	0.000064	T	0.01353	0.0044	.	.	.	0.36301	D	0.857047	B;B	0.29766	0.143;0.256	B;B	0.29598	0.104;0.096	T	0.13602	-1.0503	7	0.15952	T	0.53	.	7.5772	0.27944	0.0:0.5138:0.0:0.4862	rs55916375	340;340	A7E261;O14841	.;OPLA_HUMAN	I	340	.	ENSP00000412071:V340I	V	-	1	0	OPLAH	145184971	0.005000	0.15991	0.508000	0.27688	0.050000	0.14768	0.061000	0.14366	0.291000	0.22468	-0.444000	0.05651	GTC	C|0.947;T|0.053	0.053	strong		0.662	OPLAH-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_017570	
CDHR5	53841	hgsc.bcm.edu	37	11	617519	617519	+	Silent	SNP	A	A	G	rs34889521	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:617519A>G	ENST00000358353.3	-	16	2692	c.2370T>C	c.(2368-2370)gcT>gcC	p.A790A	IRF7_ENST00000397562.3_5'Flank|IRF7_ENST00000397574.2_5'Flank|CDHR5_ENST00000397542.2_Silent_p.A790A|IRF7_ENST00000348655.6_5'Flank|IRF7_ENST00000397566.1_5'Flank|IRF7_ENST00000525445.1_5'Flank|IRF7_ENST00000397570.1_5'Flank|CDHR5_ENST00000349570.7_Silent_p.A596A|IRF7_ENST00000330243.5_5'Flank			Q9HBB8	CDHR5_HUMAN	cadherin-related family member 5	790					cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(7)|ovary(1)|skin(2)	23						CAAACCAGACAGCCTTGTACC	0.711													G|||	1383	0.276158	0.5847	0.3026	5008	,	,		10372	0.0208		0.2674	False		,,,				2504	0.1125				p.A790A		Atlas-SNP	.											.	CDHR5	77	.	0			c.T2370C						PASS	.	G	,,	2294,2108		590,1114,497	39.0	37.0	38.0		2352,2370,1788	-4.1	1.0	11	dbSNP_126	38	2483,6113		354,1775,2169	no	coding-synonymous,coding-synonymous,coding-synonymous	CDHR5	NM_001171968.1,NM_021924.4,NM_031264.3	,,	944,2889,2666	GG,GA,AA		28.8855,47.8873,36.7518	,,	784/840,790/846,596/652	617519	4777,8221	2201	4298	6499	SO:0001819	synonymous_variant	53841	exon15			CCAGACAGCCTTG	AF258675	CCDS7707.1, CCDS7708.1	11p15.5	2011-07-01	2010-01-25	2010-01-25	ENSG00000099834	ENSG00000099834		"""Cadherins / Cadherin-related"""	7521	protein-coding gene	gene with protein product		606839	"""mucin and cadherin-like"", ""mucin-like protocadherin"""	MUCDHL, MUPCDH		11031102, 10801787	Standard	NM_021924		Approved	FLJ20219, MU-PCDH	uc001lqj.3	Q9HBB8	OTTHUMG00000132018	ENST00000358353.3:c.2370T>C	11.37:g.617519A>G		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	71	52	0.732394	NM_021924	C9J7X1|Q9H746|Q9HAU3|Q9HBB5|Q9HBB6|Q9HBB7|Q9NX86|Q9NXI9	Silent	SNP	ENST00000358353.3	37	CCDS7707.1																																																																																			A|0.664;G|0.336	0.336	strong		0.711	CDHR5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255023.2	NM_021924	
CAMK2G	818	hgsc.bcm.edu	37	10	75574956	75574956	+	Silent	SNP	G	G	A	rs55640406	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:75574956G>A	ENST00000351293.3	-	18	1362	c.1305C>T	c.(1303-1305)caC>caT	p.H435H	CAMK2G_ENST00000322635.3_Silent_p.H467H|RP11-574K11.5_ENST00000434147.1_RNA|CAMK2G_ENST00000305762.7_Silent_p.H469H|CAMK2G_ENST00000322680.3_Silent_p.H496H|CAMK2G_ENST00000472912.1_5'UTR|CAMK2G_ENST00000423381.1_Silent_p.H528H|CAMK2G_ENST00000372765.1_Silent_p.H456H|CAMK2G_ENST00000394762.2_Silent_p.H473H	NM_001222.3|NM_172173.2	NP_001213.2|NP_751913.1	Q13555	KCC2G_HUMAN	calcium/calmodulin-dependent protein kinase II gamma	498					calcium ion transport (GO:0006816)|cell differentiation (GO:0030154)|cytokine-mediated signaling pathway (GO:0019221)|dephosphorylation (GO:0016311)|G1/S transition of mitotic cell cycle (GO:0000082)|insulin secretion (GO:0030073)|interferon-gamma-mediated signaling pathway (GO:0060333)|nervous system development (GO:0007399)|protein autophosphorylation (GO:0046777)|protein oligomerization (GO:0051259)|regulation of calcium ion transport (GO:0051924)|regulation of relaxation of cardiac muscle (GO:1901897)|regulation of skeletal muscle adaptation (GO:0014733)|synaptic transmission (GO:0007268)	calcium- and calmodulin-dependent protein kinase complex (GO:0005954)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)	ATP binding (GO:0005524)|calcium-dependent protein serine/threonine phosphatase activity (GO:0004723)|calmodulin binding (GO:0005516)|calmodulin-dependent protein kinase activity (GO:0004683)|protein homodimerization activity (GO:0042803)			kidney(2)|large_intestine(2)|lung(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	15	Prostate(51;0.0112)				Bosutinib(DB06616)	TCACGTGGACGTGTGGGTTTA	0.607													G|||	37	0.00738818	0.0	0.0144	5008	,	,		14899	0.0		0.0169	False		,,,				2504	0.0102				p.H496H		Atlas-SNP	.											.	CAMK2G	79	.	0			c.C1488T						PASS	.	G	,,,,,	25,4381	32.6+/-62.9	0,25,2178	151.0	123.0	133.0		1437,1305,1401,1374,1488,1332	-0.9	0.9	10	dbSNP_129	133	172,8428	79.2+/-141.9	3,166,4131	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CAMK2G	NM_001204492.1,NM_001222.3,NM_172169.2,NM_172170.4,NM_172171.2,NM_172173.2	,,,,,	3,191,6309	AA,AG,GG		2.0,0.5674,1.5147	,,,,,	479/540,435/496,467/528,458/519,496/557,444/505	75574956	197,12809	2203	4300	6503	SO:0001819	synonymous_variant	818	exon20			GTGGACGTGTGGG	U81554	CCDS7336.1, CCDS7337.1, CCDS7338.1, CCDS73153.1	10q22	2008-10-30	2008-10-30		ENSG00000148660	ENSG00000148660			1463	protein-coding gene	gene with protein product		602123	"""calcium/calmodulin-dependent protein kinase (CaM kinase) II gamma"""	CAMKG		8287681	Standard	NM_001204492		Approved		uc001jvm.2	Q13555	OTTHUMG00000018492	ENST00000351293.3:c.1305C>T	10.37:g.75574956G>A		Somatic	195	0	0		WXS	Illumina HiSeq	Phase_I	143	142	0.993007	NM_172171	O00561|O15378|Q13279|Q13282|Q13556|Q5SQZ3|Q5SQZ4|Q5SWX4|Q7KYX5|Q8N4I3|Q8NIA4	Silent	SNP	ENST00000351293.3	37	CCDS7336.1	18	0.008241758241758242	0	0.0	5	0.013812154696132596	0	0.0	13	0.017150395778364115	G	9.245	1.039308	0.19669	0.005674	0.02	ENSG00000148660	ENST00000441192	.	.	.	5.51	-0.849	0.10723	.	.	.	.	.	T	0.41766	0.1173	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.45716	-0.9242	4	.	.	.	.	11.3382	0.49516	0.5165:0.0:0.4835:0.0	rs55640406	.	.	.	C	275	.	.	R	-	1	0	CAMK2G	75244962	0.853000	0.29707	0.880000	0.34516	0.996000	0.88848	-0.037000	0.12164	-0.477000	0.06832	-0.137000	0.14449	CGT	G|0.988;A|0.012	0.012	strong		0.607	CAMK2G-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048715.1	NM_172169	
CDC14A	8556	hgsc.bcm.edu	37	1	100928418	100928418	+	Silent	SNP	C	C	G	rs28364884	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:100928418C>G	ENST00000336454.3	+	9	1174	c.819C>G	c.(817-819)gcC>gcG	p.A273A	CDC14A_ENST00000361544.6_Silent_p.A273A|CDC14A_ENST00000542213.1_Silent_p.A215A|CDC14A_ENST00000544534.1_Silent_p.A273A|CDC14A_ENST00000370124.3_Silent_p.A273A|CDC14A_ENST00000370125.2_3'UTR|RP5-837M10.4_ENST00000432210.1_RNA	NM_003672.3	NP_003663.2	Q9UNH5	CC14A_HUMAN	cell division cycle 14A	273	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)		CCGAAGGGGCCATCGCCGTTC	0.532													C|||	10	0.00199681	0.0008	0.0043	5008	,	,		18607	0.0		0.006	False		,,,				2504	0.0				p.A273A		Atlas-SNP	.											.	CDC14A	65	.	0			c.C819G						PASS	.	C	,,	4,4402	8.1+/-20.4	0,4,2199	61.0	52.0	55.0		819,819,819	-10.9	0.0	1	dbSNP_125	55	54,8546	33.3+/-86.6	0,54,4246	no	coding-synonymous,coding-synonymous,coding-synonymous	CDC14A	NM_003672.3,NM_033312.2,NM_033313.2	,,	0,58,6445	GG,GC,CC		0.6279,0.0908,0.4459	,,	273/595,273/624,273/384	100928418	58,12948	2203	4300	6503	SO:0001819	synonymous_variant	8556	exon9			AGGGGCCATCGCC	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.819C>G	1.37:g.100928418C>G		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	92	43	0.467391	NM_033313	A6MA65|B1AQ14|B1AQ15|O43171|O60727|O60728|Q52LH9|Q8IXX0	Silent	SNP	ENST00000336454.3	37	CCDS769.1																																																																																			C|0.997;G|0.003	0.003	strong		0.532	CDC14A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000030220.1	NM_033312	
COL18A1	80781	hgsc.bcm.edu	37	21	46896312	46896312	+	Silent	SNP	G	G	T	rs2230688	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:46896312G>T	ENST00000359759.4	+	5	2112	c.2091G>T	c.(2089-2091)acG>acT	p.T697T	COL18A1_ENST00000400337.2_Silent_p.T282T|COL18A1_ENST00000355480.5_Silent_p.T462T			P39060	COIA1_HUMAN	collagen, type XVIII, alpha 1	697	Nonhelical region 1 (NC1).				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)		CCGTCACCACGCCACCCTTGG	0.637													T|||	1141	0.227835	0.3744	0.1225	5008	,	,		16215	0.2927		0.0984	False		,,,				2504	0.1708				p.T462T		Atlas-SNP	.											.	COL18A1	129	.	0			c.G1386T						PASS	.	T	,	1253,2817		203,847,985	50.0	54.0	52.0		1386,846	0.7	0.1	21	dbSNP_98	52	801,7539		42,717,3411	no	coding-synonymous,coding-synonymous	COL18A1	NM_030582.3,NM_130445.2	,	245,1564,4396	TT,TG,GG		9.6043,30.7862,16.5512	,	462/1520,282/1340	46896312	2054,10356	2035	4170	6205	SO:0001819	synonymous_variant	80781	exon5			CACCACGCCACCC		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.2091G>T	21.37:g.46896312G>T		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	104	33	0.317308	NM_030582	A8MVI4|Q58EX6|Q6RZ39|Q6RZ40|Q6RZ41|Q8N4S4|Q8WXI5|Q96T70|Q9UK38|Q9Y6Q7|Q9Y6Q8	Silent	SNP	ENST00000359759.4	37																																																																																				A|0.000;C|0.000;G|0.800;T|0.199	0.199	strong		0.637	COL18A1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000206827.1		
AGAP6	414189	hgsc.bcm.edu	37	10	51769799	51769799	+	Silent	SNP	C	C	T	rs61848275	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:51769799C>T	ENST00000374056.4	+	7	2243	c.1845C>T	c.(1843-1845)gtC>gtT	p.V615V	AGAP6_ENST00000412531.3_Silent_p.V638V			Q5VW22	AGAP6_HUMAN	ArfGAP with GTPase domain, ankyrin repeat and PH domain 6	615					regulation of ARF GTPase activity (GO:0032312)		ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)			NS(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|liver(1)|lung(8)|prostate(3)|skin(1)|stomach(2)	29						GGAATGTGGTCCTGGCGCAGC	0.667													.|||	597	0.119209	0.0461	0.1542	5008	,	,		18357	0.0317		0.2654	False		,,,				2504	0.1329				p.V638V		Atlas-SNP	.											AGAP6,NS,carcinoma,0,1	AGAP6	53	1	0			c.C1914T						scavenged	.																																			SO:0001819	synonymous_variant	414189	exon8			TGTGGTCCTGGCG		CCDS44397.1	10q11.23	2013-01-10	2008-09-22	2008-09-22	ENSG00000204149	ENSG00000204149		"""ADP-ribosylation factor GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"", ""Ankyrin repeat domain containing"""	23466	protein-coding gene	gene with protein product			"""centaurin, gamma-like family, member 3"""	CTGLF3			Standard	NM_001077665		Approved	bA324H6.1	uc001jix.4	Q5VW22	OTTHUMG00000018220	ENST00000374056.4:c.1845C>T	10.37:g.51769799C>T		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	108	57	0.527778	NM_001077665		Silent	SNP	ENST00000374056.4	37																																																																																				C|0.500;T|0.500	0.500	weak		0.667	AGAP6-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_001077665	
IL17RD	54756	hgsc.bcm.edu	37	3	57138419	57138419	+	Missense_Mutation	SNP	G	G	A	rs6780995	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:57138419G>A	ENST00000296318.7	-	8	852	c.764C>T	c.(763-765)aCg>aTg	p.T255M	IL17RD_ENST00000463523.1_Missense_Mutation_p.T111M|IL17RD_ENST00000427856.2_Missense_Mutation_p.T231M|IL17RD_ENST00000320057.5_Missense_Mutation_p.T111M	NM_017563.3	NP_060033.3	Q8NFM7	I17RD_HUMAN	interleukin 17 receptor D	255			T -> M (in dbSNP:rs6780995). {ECO:0000269|PubMed:12958313, ECO:0000269|PubMed:12975309, ECO:0000269|PubMed:14742870, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005, ECO:0000269|Ref.3}.		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)		GCAGCTGGTCGTCTCTGTAGT	0.438													G|||	2655	0.530152	0.5741	0.5216	5008	,	,		16721	0.1369		0.7147	False		,,,				2504	0.6922				p.T255M		Atlas-SNP	.											.	IL17RD	93	.	0			c.C764T						PASS	.	G	MET/THR	2576,1830	634.6+/-396.2	751,1074,378	88.0	91.0	90.0		764	-0.5	1.0	3	dbSNP_116	90	6087,2513	689.6+/-404.4	2151,1785,364	yes	missense	IL17RD	NM_017563.3	81	2902,2859,742	AA,AG,GG		29.2209,41.5343,33.3923	benign	255/740	57138419	8663,4343	2203	4300	6503	SO:0001583	missense	54756	exon8			CTGGTCGTCTCTG	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.764C>T	3.37:g.57138419G>A	ENSP00000296318:p.Thr255Met	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	81	38	0.469136	NM_017563	Q2NKP7|Q58EZ7|Q6RVF4|Q6UWI5|Q8N113|Q8NFS0|Q9UFA0	Missense_Mutation	SNP	ENST00000296318.7	37	CCDS2880.2	1089	0.49862637362637363	262	0.532520325203252	216	0.5966850828729282	68	0.11888111888111888	543	0.716358839050132	G	12.63	1.995041	0.35226	0.584657	0.707791	ENSG00000144730	ENST00000296318;ENST00000320057;ENST00000427856;ENST00000463523	T;T;T;T	0.10288	2.89;2.9;2.89;2.9	5.65	-0.521	0.11931	.	0.558304	0.20666	N	0.087928	T	0.00012	0.0000	N	0.24115	0.695	0.35383	P	0.20989400000000002	P;P;P	0.51240	0.943;0.661;0.895	B;B;B	0.39531	0.302;0.115;0.23	T	0.07065	-1.0792	9	0.46703	T	0.11	-1.2261	10.9444	0.47292	0.5486:0.0:0.4514:0.0	rs6780995;rs13079088;rs59640451;rs6780995	111;255;231	B4DXM5;Q8NFM7;Q8NFM7-3	.;I17RD_HUMAN;.	M	255;111;231;111	ENSP00000296318:T255M;ENSP00000322250:T111M;ENSP00000399209:T231M;ENSP00000417516:T111M	ENSP00000296318:T255M	T	-	2	0	IL17RD	57113459	0.992000	0.36948	0.990000	0.47175	0.982000	0.71751	0.831000	0.27476	-0.011000	0.14247	-0.137000	0.14449	ACG	G|0.431;A|0.569	0.569	strong		0.438	IL17RD-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316680.1	NM_017563	
SLC12A3	6559	hgsc.bcm.edu	37	16	56913513	56913513	+	Silent	SNP	C	C	T	rs5801	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:56913513C>T	ENST00000563236.1	+	11	1420	c.1395C>T	c.(1393-1395)acC>acT	p.T465T	SLC12A3_ENST00000438926.2_Silent_p.T465T|SLC12A3_ENST00000566786.1_Silent_p.T464T|SLC12A3_ENST00000262502.5_Silent_p.T464T			P55017	S12A3_HUMAN	solute carrier family 12 (sodium/chloride transporter), member 3	465					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)	TCGGGGCCACCCTCTCCTCTG	0.652													C|||	699	0.139577	0.18	0.1138	5008	,	,		15730	0.0675		0.1809	False		,,,				2504	0.135				p.T465T		Atlas-SNP	.											.	SLC12A3	99	.	0			c.C1395T						PASS	.	C	,,	704,3692	292.7+/-282.2	62,580,1556	60.0	51.0	54.0		1395,1392,1395	2.4	1.0	16	dbSNP_52	54	1244,7356	247.9+/-275.8	71,1102,3127	no	coding-synonymous,coding-synonymous,coding-synonymous	SLC12A3	NM_000339.2,NM_001126107.1,NM_001126108.1	,,	133,1682,4683	TT,TC,CC		14.4651,16.0146,14.9892	,,	465/1031,464/1030,465/1022	56913513	1948,11048	2198	4300	6498	SO:0001819	synonymous_variant	6559	exon11			GGCCACCCTCTCC		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.1395C>T	16.37:g.56913513C>T		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	92	33	0.358696	NM_001126108	A8MSJ2|C9JNN9	Silent	SNP	ENST00000563236.1	37	CCDS58464.1																																																																																			C|0.858;T|0.142	0.142	strong		0.652	SLC12A3-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000432337.1		
NUSAP1	51203	hgsc.bcm.edu	37	15	41634588	41634588	+	Missense_Mutation	SNP	C	C	A	rs386783399|rs7178777	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:41634588C>A	ENST00000559596.1	+	2	185	c.98C>A	c.(97-99)aCc>aAc	p.T33N	NUSAP1_ENST00000560747.1_Missense_Mutation_p.T33N|NUSAP1_ENST00000450592.2_Intron|NUSAP1_ENST00000558123.1_3'UTR|RP11-16O9.2_ENST00000559959.1_RNA|NUSAP1_ENST00000560177.1_Missense_Mutation_p.T33N|NUSAP1_ENST00000450318.1_Missense_Mutation_p.T33N|NUSAP1_ENST00000414849.2_Missense_Mutation_p.T33N|NUSAP1_ENST00000260359.6_Missense_Mutation_p.T33N			Q9BXS6	NUSAP_HUMAN	nucleolar and spindle associated protein 1	33			T -> A (in dbSNP:rs7178634).|T -> N (in dbSNP:rs7178777).	T -> D (in Ref. 6; AL833611). {ECO:0000305}.	establishment of mitotic spindle localization (GO:0040001)|mitotic chromosome condensation (GO:0007076)|mitotic cytokinesis (GO:0000281)|mitotic sister chromatid segregation (GO:0000070)|positive regulation of mitosis (GO:0045840)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)	p.T33N(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(3)|ovary(1)|prostate(2)|urinary_tract(2)	13		all_cancers(109;5.07e-19)|all_epithelial(112;2.43e-16)|Lung NSC(122;1.81e-11)|all_lung(180;4.81e-10)|Melanoma(134;0.0179)|Colorectal(260;0.0946)|Ovarian(310;0.143)		OV - Ovarian serous cystadenocarcinoma(18;9.63e-17)|GBM - Glioblastoma multiforme(113;1.59e-06)|BRCA - Breast invasive adenocarcinoma(123;0.168)		TTGCAGGCAACCAAGTTGTTA	0.343													A|||	1714	0.342252	0.5938	0.2781	5008	,	,		23702	0.1548		0.337	False		,,,				2504	0.2464				p.T33N		Atlas-SNP	.											NUSAP1,NS,carcinoma,+1,2	NUSAP1	32	2	1	Substitution - Missense(1)	prostate(1)	c.C98A						PASS	.	A	ASN/THR,ASN/THR,ASN/THR	49,3671		8,33,1819	69.0	66.0	67.0		98,98,98	3.1	1.0	15	dbSNP_116	67	30,8164		6,18,4073	yes	missense,missense,missense	NUSAP1	NM_001129897.1,NM_016359.4,NM_018454.7	65,65,65	14,51,5892	AA,AC,CC		0.3661,1.3172,0.6631	benign,benign,benign	33/403,33/442,33/441	41634588	79,11835	1860	4097	5957	SO:0001583	missense	51203	exon2			AGGCAACCAAGTT	AF290612	CCDS45234.1, CCDS45236.1, CCDS58356.1, CCDS58357.1, CCDS58358.1, CCDS73708.1	15q14	2008-02-05				ENSG00000137804			18538	protein-coding gene	gene with protein product		612818				12963707	Standard	NM_016359		Approved	FLJ13421, LNP, ANKT, NuSAP1, SAPL, BM037, PRO0310p1, Q0310	uc001zns.4	Q9BXS6		ENST00000559596.1:c.98C>A	15.37:g.41634588C>A	ENSP00000453403:p.Thr33Asn	Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	106	42	0.396226	NM_018454	B4DDF1|E7ERR5|J3KN21|Q53GW2|Q8TBT4|Q96E58|Q96FJ1|Q9GZM9|Q9NZ85|Q9UI70	Missense_Mutation	SNP	ENST00000559596.1	37	CCDS45234.1	569	0.26053113553113555	215	0.4369918699186992	95	0.26243093922651933	73	0.12762237762237763	186	0.24538258575197888	A	10.11	1.261328	0.23051	0.013172	0.003661	ENSG00000137804	ENST00000260359;ENST00000414849;ENST00000450318	T;T;T	0.32272	1.46;1.46;1.46	5.47	3.09	0.35607	.	0.426017	0.27797	N	0.017808	T	0.00012	0.0000	N	0.02011	-0.69	0.58432	P	1.0000000000287557E-6	B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0	B;B;B;B;B	0.01281	0.0;0.0;0.0;0.0;0.0	T	0.46091	-0.9216	9	0.59425	D	0.04	.	6.8139	0.23819	0.6362:0.2882:0.0756:0.0	rs7178777;rs60176502;rs7178777	33;33;33;33;33	E9PB35;Q9BXS6-3;Q9BXS6-5;Q9BXS6;Q9BXS6-2	.;.;.;NUSAP_HUMAN;.	N	33	ENSP00000260359:T33N;ENSP00000400746:T33N;ENSP00000401351:T33N	ENSP00000260359:T33N	T	+	2	0	NUSAP1	39421880	1.000000	0.71417	0.997000	0.53966	0.243000	0.25628	1.044000	0.30329	0.105000	0.17753	-0.375000	0.07067	ACC	C|0.686;A|0.314	0.314	strong		0.343	NUSAP1-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000419427.1	NM_016359	
AKAP6	9472	hgsc.bcm.edu	37	14	33015082	33015082	+	Missense_Mutation	SNP	A	A	G	rs17099240	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:33015082A>G	ENST00000280979.4	+	4	1393	c.1223A>G	c.(1222-1224)aAt>aGt	p.N408S	AKAP6_ENST00000557272.1_Missense_Mutation_p.N408S|AKAP6_ENST00000557354.1_Missense_Mutation_p.N408S	NM_004274.4	NP_004265.3	Q13023	AKAP6_HUMAN	A kinase (PRKA) anchor protein 6	408			N -> S (in dbSNP:rs17099240).		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)		CTGAAAGGCAATGGTGGAAAG	0.428													A|||	882	0.176118	0.233	0.1859	5008	,	,		21639	0.1815		0.1014	False		,,,				2504	0.1636				p.N408S	Melanoma(49;821 1200 7288 13647 42351)	Atlas-SNP	.											.	AKAP6	308	.	0			c.A1223G						PASS	.	A	SER/ASN	878,3526	314.4+/-293.6	79,720,1403	114.0	121.0	118.0		1223	-2.4	0.0	14	dbSNP_123	118	798,7802	184.2+/-232.2	36,726,3538	yes	missense	AKAP6	NM_004274.4	46	115,1446,4941	GG,GA,AA		9.2791,19.9364,12.8883	benign	408/2320	33015082	1676,11328	2202	4300	6502	SO:0001583	missense	9472	exon4			AAGGCAATGGTGG	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.1223A>G	14.37:g.33015082A>G	ENSP00000280979:p.Asn408Ser	Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	96	94	0.979167	NM_004274	A7E242|A7E2D4|O15028	Missense_Mutation	SNP	ENST00000280979.4	37	CCDS9644.1	365	0.1671245421245421	119	0.241869918699187	62	0.1712707182320442	97	0.16958041958041958	87	0.11477572559366754	A	0.001	-2.993308	0.00045	0.199364	0.092791	ENSG00000151320	ENST00000280979;ENST00000557354;ENST00000557272;ENST00000553547	T;T;T;T	0.28895	1.59;1.59;1.59;1.59	5.74	-2.42	0.06542	.	1.268580	0.04927	N	0.456042	T	0.00012	0.0000	N	0.01705	-0.755	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.32052	-0.9921	9	0.02654	T	1	3.9669	9.3447	0.38100	0.6165:0.1331:0.2504:0.0	rs17099240;rs52790462;rs56947517;rs17099240	408;408	A7E242;Q13023	.;AKAP6_HUMAN	S	408;408;408;166	ENSP00000280979:N408S;ENSP00000450531:N408S;ENSP00000451247:N408S;ENSP00000451239:N166S	ENSP00000280979:N408S	N	+	2	0	AKAP6	32084833	0.001000	0.12720	0.000000	0.03702	0.037000	0.13140	0.358000	0.20216	-0.420000	0.07427	-0.177000	0.13119	AAT	A|0.861;G|0.139	0.139	strong		0.428	AKAP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276617.2	NM_004274	
AHNAK2	113146	hgsc.bcm.edu	37	14	105416823	105416823	+	Silent	SNP	G	G	A	rs2582504	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:105416823G>A	ENST00000333244.5	-	7	5084	c.4965C>T	c.(4963-4965)gaC>gaT	p.D1655D	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	1655						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)			TGAACTTGCTGTCTTTGGCAG	0.612													.|||	826	0.164936	0.1823	0.0836	5008	,	,		17301	0.2708		0.0507	False		,,,				2504	0.2076				p.D1655D		Atlas-SNP	.											AHNAK2_ENST00000333244,NS,carcinoma,-2,1	AHNAK2	719	1	0			c.C4965T						PASS	.	G		614,3284		98,418,1433	202.0	230.0	221.0		4965	3.1	1.0	14	dbSNP_100	221	379,7851		44,291,3780	no	coding-synonymous	AHNAK2	NM_138420.2		142,709,5213	AA,AG,GG		4.6051,15.7517,8.1877		1655/5796	105416823	993,11135	1949	4115	6064	SO:0001819	synonymous_variant	113146	exon7			CTTGCTGTCTTTG	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.4965C>T	14.37:g.105416823G>A		Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	149	74	0.496644	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Silent	SNP	ENST00000333244.5	37	CCDS45177.1																																																																																			G|0.883;A|0.117	0.117	strong		0.612	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
IDUA	3425	hgsc.bcm.edu	37	4	995305	995305	+	Silent	SNP	T	T	C	rs6815946	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	92	0	0		WXS	Illumina HiSeq	Phase_I	68	30	0.441176	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	
FSIP1	161835	hgsc.bcm.edu	37	15	39910052	39910052	+	Missense_Mutation	SNP	C	C	G	rs16969386	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:39910052C>G	ENST00000350221.3	-	11	1792	c.1583G>C	c.(1582-1584)gGc>gCc	p.G528A		NM_152597.4	NP_689810.3	Q8NA03	FSIP1_HUMAN	fibrous sheath interacting protein 1	528			G -> A (in dbSNP:rs16969386).					p.G528A(1)		NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(4)|ovary(2)|skin(4)|stomach(2)|urinary_tract(1)	23		all_cancers(109;2.66e-19)|all_epithelial(112;2.66e-16)|Lung NSC(122;1.5e-11)|all_lung(180;4.03e-10)|Melanoma(134;0.0575)|Ovarian(310;0.0827)|Colorectal(260;0.119)		GBM - Glioblastoma multiforme(113;8.22e-06)|BRCA - Breast invasive adenocarcinoma(123;0.142)		TCTCCCAATGCCAAGAGTCTT	0.408													C|||	788	0.157348	0.0333	0.1196	5008	,	,		21212	0.2907		0.1471	False		,,,				2504	0.2249				p.G528A		Atlas-SNP	.											FSIP1,NS,carcinoma,0,1	FSIP1	53	1	1	Substitution - Missense(1)	stomach(1)	c.G1583C						PASS	.	C	ALA/GLY	233,4167	136.5+/-172.5	4,225,1971	109.0	102.0	104.0		1583	4.8	1.0	15	dbSNP_123	104	1124,7470	231.9+/-265.7	65,994,3238	yes	missense	FSIP1	NM_152597.4	60	69,1219,5209	GG,GC,CC		13.0789,5.2955,10.4433	probably-damaging	528/582	39910052	1357,11637	2200	4297	6497	SO:0001583	missense	161835	exon11			CCAATGCCAAGAG	BC045191	CCDS10050.1	15q14	2012-11-19			ENSG00000150667	ENSG00000150667			21674	protein-coding gene	gene with protein product		615795				14702039	Standard	NM_152597		Approved	FLJ35989	uc001zki.3	Q8NA03	OTTHUMG00000172456	ENST00000350221.3:c.1583G>C	15.37:g.39910052C>G	ENSP00000280236:p.Gly528Ala	Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	139	62	0.446043	NM_152597	Q6X2C8|Q86Y89	Missense_Mutation	SNP	ENST00000350221.3	37	CCDS10050.1	349	0.15979853479853479	16	0.032520325203252036	48	0.13259668508287292	178	0.3111888111888112	107	0.14116094986807387	C	17.76	3.467593	0.63625	0.052955	0.130789	ENSG00000150667	ENST00000350221	T	0.14144	2.53	4.84	4.84	0.62591	.	0.168900	0.38005	N	0.001843	T	0.00012	0.0000	L	0.29908	0.895	0.35187	P	0.22696400000000005	D	0.76494	0.999	D	0.69654	0.965	T	0.46373	-0.9196	8	.	.	.	-7.1189	10.4881	0.44735	0.0:0.9018:0.0:0.0982	rs16969386;rs57363512;rs16969386	528	Q8NA03	FSIP1_HUMAN	A	528	ENSP00000280236:G528A	.	G	-	2	0	FSIP1	37697344	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	2.819000	0.48049	2.669000	0.90835	0.591000	0.81541	GGC	C|0.858;G|0.142	0.142	strong		0.408	FSIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252118.2	NM_152597	
FCGBP	8857	hgsc.bcm.edu	37	19	40368330	40368330	+	Missense_Mutation	SNP	C	C	T	rs74540349	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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						PASS	.						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	203	0	0		WXS	Illumina HiSeq	Phase_I	152	53	0.348684	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	
IL10RA	3587	hgsc.bcm.edu	37	11	117869642	117869642	+	Missense_Mutation	SNP	C	C	A	rs369418818		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:117869642C>A	ENST00000227752.3	+	7	1143	c.1023C>A	c.(1021-1023)caC>caA	p.H341Q	IL10RA_ENST00000541785.1_Missense_Mutation_p.H321Q|IL10RA_ENST00000545409.1_Missense_Mutation_p.H192Q|IL10RA_ENST00000533700.1_3'UTR	NM_001558.3	NP_001549.2	Q13651	I10R1_HUMAN	interleukin 10 receptor, alpha	341					cytokine-mediated signaling pathway (GO:0019221)|response to lipopolysaccharide (GO:0032496)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	interleukin-10 receptor activity (GO:0004920)|receptor activity (GO:0004872)|signal transducer activity (GO:0004871)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(10)|ovary(2)|prostate(1)	19	all_hematologic(175;0.0487)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;3.07e-05)|Epithelial(105;0.00108)		CTGACCCTCACCCCCAGGCTG	0.617																																					p.H341Q		Atlas-SNP	.											.	IL10RA	46	.	0			c.C1023A						PASS	.	C	GLN/HIS	0,4400		0,0,2200	59.0	54.0	56.0		1023	-2.5	0.0	11		56	4,8588	3.0+/-9.4	0,4,4292	no	missense	IL10RA	NM_001558.3	24	0,4,6492	AA,AC,CC		0.0466,0.0,0.0308	benign	341/579	117869642	4,12988	2200	4296	6496	SO:0001583	missense	3587	exon7			CCCTCACCCCCAG	U00672	CCDS8388.1	11q23	2014-09-17			ENSG00000110324	ENSG00000110324		"""Interleukins and interleukin receptors"", ""CD molecules"""	5964	protein-coding gene	gene with protein product		146933		IL10R		8120391	Standard	NR_026691		Approved	HIL-10R, CDW210A, CD210a, CD210	uc001prv.3	Q13651	OTTHUMG00000166523	ENST00000227752.3:c.1023C>A	11.37:g.117869642C>A	ENSP00000227752:p.His341Gln	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	53	43	0.811321	NM_001558	A8K6I0|B0YJ27	Missense_Mutation	SNP	ENST00000227752.3	37	CCDS8388.1	.	.	.	.	.	.	.	.	.	.	C	10.44	1.350897	0.24512	0.0	4.66E-4	ENSG00000110324	ENST00000227752;ENST00000541785;ENST00000545409;ENST00000536858	T;T;T	0.21031	2.03;2.03;2.03	5.66	-2.55	0.06288	.	1.951570	0.01920	N	0.040455	T	0.17195	0.0413	L	0.56769	1.78	0.09310	N	1	B;B	0.16802	0.019;0.011	B;B	0.15484	0.013;0.006	T	0.13926	-1.0491	10	0.12430	T	0.62	-2.9137	1.8617	0.03190	0.1108:0.3559:0.2405:0.2928	.	321;341	F5GYV8;Q13651	.;I10R1_HUMAN	Q	341;321;192;321	ENSP00000227752:H341Q;ENSP00000441397:H321Q;ENSP00000443019:H192Q	ENSP00000227752:H341Q	H	+	3	2	IL10RA	117374852	0.000000	0.05858	0.001000	0.08648	0.014000	0.08584	-0.122000	0.10627	0.058000	0.16222	0.563000	0.77884	CAC	.	.	weak		0.617	IL10RA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390167.1		
KRTAP4-8	728224	hgsc.bcm.edu	37	17	39253956	39253956	+	Silent	SNP	G	G	A	rs139720993	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:39253956G>A	ENST00000333822.4	-	1	437	c.381C>T	c.(379-381)ccC>ccT	p.P127P		NM_031960.2	NP_114166.1	Q9BYQ9	KRA48_HUMAN	keratin associated protein 4-8	127	25 X 5 AA repeats of C-C-[IKRQVHEC]- [SPRT]-[STCVQPR].				aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)		p.P127P(1)		endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(1)|prostate(1)	11						tgctgcagctggggcggcagc	0.677													G|||	1899	0.379193	0.4198	0.3934	5008	,	,		14956	0.2292		0.4553	False		,,,				2504	0.3906				p.P127P		Atlas-SNP	.											KRTAP4-8,NS,carcinoma,0,1	KRTAP4-8	57	1	1	Substitution - coding silent(1)	kidney(1)	c.C381T						scavenged	.						3.0	5.0	4.0					17																	39253956		591	1415	2006	SO:0001819	synonymous_variant	728224	exon1			GCAGCTGGGGCGG	AJ406940	CCDS45674.1	17q21.2	2013-06-25			ENSG00000204880	ENSG00000204880		"""Keratin associated proteins"""	17230	protein-coding gene	gene with protein product						11279113	Standard	NM_031960		Approved	KAP4.8	uc010wfo.2	Q9BYQ9	OTTHUMG00000133580	ENST00000333822.4:c.381C>T	17.37:g.39253956G>A		Somatic	64	1	0.015625		WXS	Illumina HiSeq	Phase_I	30	10	0.333333	NM_031960	A8MSH3	Silent	SNP	ENST00000333822.4	37	CCDS45674.1																																																																																			G|0.500;A|0.500	0.500	strong		0.677	KRTAP4-8-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257684.1	NM_031960	
MX2	4600	hgsc.bcm.edu	37	21	42771176	42771176	+	Silent	SNP	T	T	C	rs2301803	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:42771176T>C	ENST00000330714.3	+	10	1510	c.1326T>C	c.(1324-1326)gtT>gtC	p.V442V	MX2_ENST00000496774.1_3'UTR	NM_002463.1	NP_002454.1	P20592	MX2_HUMAN	MX dynamin-like GTPase 2	442					cytokine-mediated signaling pathway (GO:0019221)|defense response (GO:0006952)|defense response to virus (GO:0051607)|GTP catabolic process (GO:0006184)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of cell cycle (GO:0051726)|regulation of nucleocytoplasmic transport (GO:0046822)|response to interferon-alpha (GO:0035455)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			breast(2)|endometrium(3)|large_intestine(6)|lung(12)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)	34		Prostate(19;1.57e-07)|all_epithelial(19;0.0222)				GAGAAGAAGTTGTAAGGGAGA	0.348													T|||	393	0.0784744	0.1021	0.036	5008	,	,		21368	0.1637		0.0179	False		,,,				2504	0.0511				p.V442V		Atlas-SNP	.											.	MX2	84	.	0			c.T1326C						PASS	.	T		357,4049	182.2+/-210.1	17,323,1863	87.0	89.0	89.0		1326	-3.1	0.0	21	dbSNP_100	89	121,8479	63.1+/-125.2	2,117,4181	no	coding-synonymous	MX2	NM_002463.1		19,440,6044	CC,CT,TT		1.407,8.1026,3.6752		442/716	42771176	478,12528	2203	4300	6503	SO:0001819	synonymous_variant	4600	exon10			AGAAGTTGTAAGG		CCDS13672.1	21q22.3	2014-07-15	2014-07-15		ENSG00000183486	ENSG00000183486			7533	protein-coding gene	gene with protein product	"""interferon-regulated resistance GTP-binding protein MXB"", ""second interferon-induced protein p78"""	147890	"""myxovirus (influenza) resistance 2, homolog of murine"", ""myxovirus (influenza virus) resistance 2 (mouse)"""			2481229, 8798556	Standard	NM_002463		Approved	MXB	uc002yzf.1	P20592	OTTHUMG00000086753	ENST00000330714.3:c.1326T>C	21.37:g.42771176T>C		Somatic	212	0	0		WXS	Illumina HiSeq	Phase_I	197	117	0.593909	NM_002463	B7Z5D3|D3DSI7	Silent	SNP	ENST00000330714.3	37	CCDS13672.1																																																																																			T|0.946;C|0.054	0.054	strong		0.348	MX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195147.1	NM_002463	
HEATR3	55027	hgsc.bcm.edu	37	16	50106594	50106594	+	Silent	SNP	T	T	C	rs2287197	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:50106594T>C	ENST00000299192.7	+	5	782	c.591T>C	c.(589-591)ttT>ttC	p.F197F	HEATR3_ENST00000285767.4_Silent_p.F111F	NM_182922.2	NP_891552.1	Q7Z4Q2	HEAT3_HUMAN	HEAT repeat containing 3	197				F -> L (in Ref. 1; AAP97710). {ECO:0000305}.						cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(9)|ovary(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	28						TAAGTAGGTTTCCTACCAATG	0.343													T|||	3002	0.599441	0.3298	0.7176	5008	,	,		19578	0.6429		0.7097	False		,,,				2504	0.7219				p.F197F		Atlas-SNP	.											.	HEATR3	59	.	0			c.T591C						PASS	.	T		1695,2701	510.1+/-367.4	353,989,856	192.0	179.0	184.0		591	4.6	1.0	16	dbSNP_100	184	6124,2476	694.5+/-404.7	2189,1746,365	no	coding-synonymous	HEATR3	NM_182922.2		2542,2735,1221	CC,CT,TT		28.7907,38.5578,39.8353		197/681	50106594	7819,5177	2198	4300	6498	SO:0001819	synonymous_variant	55027	exon5			TAGGTTTCCTACC	BC018730	CCDS10739.1	16q12.1	2008-02-05			ENSG00000155393	ENSG00000155393			26087	protein-coding gene	gene with protein product		614951				12477932	Standard	XM_005256013		Approved	FLJ20718	uc002efw.3	Q7Z4Q2	OTTHUMG00000133174	ENST00000299192.7:c.591T>C	16.37:g.50106594T>C		Somatic	169	1	0.00591716		WXS	Illumina HiSeq	Phase_I	224	222	0.991071	NM_182922	A8K1N4|Q8N525|Q8WV56|Q96CC9|Q9NWN7	Silent	SNP	ENST00000299192.7	37	CCDS10739.1																																																																																			T|0.405;C|0.595	0.595	strong		0.343	HEATR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256880.2	NM_182922	
SLC14A2	8170	hgsc.bcm.edu	37	18	43252883	43252883	+	Missense_Mutation	SNP	G	G	A	rs1123617	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:43252883G>A	ENST00000255226.6	+	17	3064	c.2248G>A	c.(2248-2250)Gtt>Att	p.V750I	SLC14A2_ENST00000586448.1_Missense_Mutation_p.V750I|RP11-116O18.3_ENST00000589510.1_RNA|SLC14A2_ENST00000589658.1_Missense_Mutation_p.V227I	NM_007163.3	NP_009094.3	Q15849	UT2_HUMAN	solute carrier family 14 (urea transporter), member 2	750			V -> I (in dbSNP:rs1123617).		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)			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						AGCCATCCCCGTTGGAATTGG	0.488													G|||	853	0.170327	0.0658	0.1729	5008	,	,		20747	0.3115		0.1551	False		,,,				2504	0.18				p.V750I		Atlas-SNP	.											.	SLC14A2	121	.	0			c.G2248A	GRCh37	CM013793	SLC14A2	M	rs1123617	PASS	.	G	ILE/VAL,ILE/VAL	386,4020	193.0+/-218.2	18,350,1835	208.0	169.0	182.0		2248,2248	4.0	0.7	18	dbSNP_86	182	1305,7295	257.9+/-281.7	107,1091,3102	yes	missense,missense	SLC14A2	NM_001242692.1,NM_007163.3	29,29	125,1441,4937	AA,AG,GG		15.1744,8.7608,13.0017	benign,benign	750/921,750/921	43252883	1691,11315	2203	4300	6503	SO:0001583	missense	8170	exon18			ATCCCCGTTGGAA	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.2248G>A	18.37:g.43252883G>A	ENSP00000255226:p.Val750Ile	Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	180	86	0.477778	NM_001242692	A8K8Q7|Q2TBD6|Q96PH5	Missense_Mutation	SNP	ENST00000255226.6	37	CCDS11924.1	378	0.17307692307692307	40	0.08130081300813008	63	0.17403314917127072	165	0.28846153846153844	110	0.14511873350923482	G	16.00	2.999037	0.54147	0.087608	0.151744	ENSG00000132874	ENST00000255226	T	0.51325	0.71	5.79	4.01	0.46588	.	0.343293	0.24894	N	0.034748	T	0.00012	0.0000	M	0.64676	1.99	0.09310	P	1.0	P	0.47034	0.889	P	0.44732	0.459	T	0.11792	-1.0573	9	0.41790	T	0.15	-14.8646	11.6076	0.51041	0.1981:0.0:0.8019:0.0	rs1123617;rs2276315;rs52814222;rs59629208;rs1123617	750	Q15849	UT2_HUMAN	I	750	ENSP00000255226:V750I	ENSP00000255226:V750I	V	+	1	0	SLC14A2	41506881	1.000000	0.71417	0.723000	0.30687	0.929000	0.56500	3.901000	0.56303	0.803000	0.34113	-0.224000	0.12420	GTT	G|0.840;T|0.001	.	strong		0.488	SLC14A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255858.1		
ZNF286A	57335	hgsc.bcm.edu	37	17	15620481	15620481	+	Silent	SNP	C	C	T	rs2530064	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:15620481C>T	ENST00000464847.2	+	5	1996	c.1443C>T	c.(1441-1443)ctC>ctT	p.L481L	ZNF286A_ENST00000413242.2_Silent_p.L481L|ZNF286A_ENST00000395894.2_3'UTR|ZNF286A_ENST00000585171.1_Intron|ZNF286A_ENST00000593105.1_Silent_p.L471L|ZNF286A_ENST00000583566.1_Silent_p.L481L|ZNF286A_ENST00000421016.1_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	185	0	0		WXS	Illumina HiSeq	Phase_I	142	44	0.309859	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	
ZSCAN31	64288	hgsc.bcm.edu	37	6	28297313	28297313	+	Missense_Mutation	SNP	T	T	A	rs853678	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:28297313T>A	ENST00000414429.1	-	6	1051	c.148A>T	c.(148-150)Act>Tct	p.T50S	ZSCAN31_ENST00000439158.1_Missense_Mutation_p.T50S|ZSCAN31_ENST00000396838.2_Missense_Mutation_p.T50S|ZSCAN31_ENST00000481934.1_5'Flank|ZSCAN31_ENST00000446474.1_Intron|ZSCAN31_ENST00000344279.6_Missense_Mutation_p.T50S			Q96LW9	ZSC31_HUMAN	zinc finger and SCAN domain containing 31	50	SCAN box. {ECO:0000255|PROSITE- ProRule:PRU00187}.		T -> S (in dbSNP:rs853678).		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)										GGACCAGGAGTCTCTTGGTAA	0.522													T|||	901	0.179912	0.3585	0.1369	5008	,	,		16858	0.129		0.1193	False		,,,				2504	0.0838				p.T50S		Atlas-SNP	.											.	.	.	.	0			c.A148T						PASS	.	T	SER/THR,SER/THR,SER/THR,SER/THR	1478,2928	473.3+/-356.6	247,984,972	111.0	123.0	119.0		148,148,148,148	-1.0	0.4	6	dbSNP_86	119	1247,7353	249.2+/-276.5	92,1063,3145	yes	missense,missense,missense,missense	ZNF323	NM_001135215.1,NM_001135216.1,NM_030899.4,NM_145909.2	58,58,58,58	339,2047,4117	AA,AT,TT		14.5,33.5452,20.9519	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	50/407,50/407,50/407,50/407	28297313	2725,10281	2203	4300	6503	SO:0001583	missense	64288	exon2			CAGGAGTCTCTTG		CCDS4649.1, CCDS59001.1	6p	2013-01-09	2013-01-08	2013-01-08	ENSG00000235109	ENSG00000235109		"""-"", ""Zinc fingers, C2H2-type"""	14097	protein-coding gene	gene with protein product		610794	"""zinc finger protein 310 pseudogene"", ""zinc finger protein 323"""	ZNF310P, ZNF323			Standard	NM_001135216		Approved		uc003nla.3	Q96LW9	OTTHUMG00000014518	ENST00000414429.1:c.148A>T	6.37:g.28297313T>A	ENSP00000390076:p.Thr50Ser	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	93	49	0.526882	NM_030899	Q6P178|Q8WWS5	Missense_Mutation	SNP	ENST00000414429.1	37	CCDS4649.1	377	0.17261904761904762	162	0.32926829268292684	50	0.13812154696132597	80	0.13986013986013987	85	0.11213720316622691	T	11.25	1.582386	0.28180	0.335452	0.145	ENSG00000235109	ENST00000396838;ENST00000439158;ENST00000414429;ENST00000344279;ENST00000453745;ENST00000439636;ENST00000447021;ENST00000426756;ENST00000446222;ENST00000434036	T;T;T;T;T;T;T;T;T;T	0.04083	3.71;3.71;3.71;3.71;3.71;3.71;3.71;3.71;3.71;3.71	4.56	-1.04	0.10068	Retrovirus capsid, C-terminal (1);Transcription regulator SCAN (3);	.	.	.	.	T	0.00754	0.0025	N	0.20445	0.575	0.80722	P	0.0	B	0.20550	0.046	B	0.18263	0.021	T	0.48822	-0.9001	8	0.22109	T	0.4	.	0.5838	0.00716	0.261:0.1681:0.1338:0.437	rs853678;rs61109611;rs853678	50	Q96LW9	ZN323_HUMAN	S	50	ENSP00000380050:T50S;ENSP00000413705:T50S;ENSP00000390076:T50S;ENSP00000345339:T50S;ENSP00000389479:T50S;ENSP00000412519:T50S;ENSP00000416108:T50S;ENSP00000406376:T50S;ENSP00000411033:T50S;ENSP00000416225:T50S	ENSP00000345339:T50S	T	-	1	0	ZNF323	28405292	0.041000	0.20044	0.415000	0.26534	0.996000	0.88848	0.881000	0.28173	0.191000	0.20236	0.460000	0.39030	ACT	T|0.794;N|0.000	.	strong		0.522	ZSCAN31-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346804.1	NM_030899	
ST3GAL4	6484	hgsc.bcm.edu	37	11	126278075	126278075	+	Silent	SNP	C	C	T	rs2230279	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:126278075C>T	ENST00000526727.1	+	6	797	c.423C>T	c.(421-423)taC>taT	p.Y141Y	ST3GAL4_ENST00000392669.2_Silent_p.Y141Y|ST3GAL4_ENST00000227495.6_Silent_p.Y137Y|ST3GAL4_ENST00000534457.1_Silent_p.Y136Y|ST3GAL4_ENST00000534083.1_Silent_p.Y141Y|ST3GAL4_ENST00000532243.1_Silent_p.Y140Y|ST3GAL4_ENST00000444328.2_Silent_p.Y141Y|ST3GAL4_ENST00000530591.1_Silent_p.Y137Y|ST3GAL4_ENST00000449406.2_Silent_p.Y130Y|ST3GAL4_ENST00000356132.4_Silent_p.Y147Y|ST3GAL4_ENST00000526756.1_3'UTR			Q11206	SIA4C_HUMAN	ST3 beta-galactoside alpha-2,3-sialyltransferase 4	141					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)			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)		TCAACAAGTACGATGTGGTCA	0.582													C|||	1727	0.344848	0.3623	0.3256	5008	,	,		19286	0.5079		0.3101	False		,,,				2504	0.2025				p.Y141Y		Atlas-SNP	.											.	ST3GAL4	25	.	0			c.C423T						PASS	.	C		1546,2856	485.5+/-360.3	270,1006,925	166.0	169.0	168.0		411	2.3	1.0	11	dbSNP_98	168	2582,6014	419.5+/-353.1	365,1852,2081	no	coding-synonymous	ST3GAL4	NM_006278.1		635,2858,3006	TT,TC,CC		30.0372,35.1204,31.7587		137/330	126278075	4128,8870	2201	4298	6499	SO:0001819	synonymous_variant	6484	exon7			CAAGTACGATGTG	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.423C>T	11.37:g.126278075C>T		Somatic	205	0	0		WXS	Illumina HiSeq	Phase_I	217	155	0.714286	NM_001254757	A8K6B2|O60497|Q8N6A6|Q8NFG7|Q96QQ9	Silent	SNP	ENST00000526727.1	37	CCDS58193.1																																																																																			C|0.657;T|0.343	0.343	strong		0.582	ST3GAL4-003	PUTATIVE	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386470.1	NM_006278	
ESRRG	2104	hgsc.bcm.edu	37	1	216692669	216692669	+	Silent	SNP	C	C	T	rs945453	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:216692669C>T	ENST00000408911.3	-	6	1110	c.957G>A	c.(955-957)tcG>tcA	p.S319S	ESRRG_ENST00000361395.2_Silent_p.S296S|ESRRG_ENST00000493603.1_Silent_p.S296S|ESRRG_ENST00000359162.2_Silent_p.S296S|ESRRG_ENST00000366940.2_Silent_p.S296S|ESRRG_ENST00000366938.2_Silent_p.S296S|ESRRG_ENST00000360012.3_Silent_p.S296S|ESRRG_ENST00000493748.1_Silent_p.S296S|ESRRG_ENST00000366937.1_Silent_p.S331S|ESRRG_ENST00000361525.3_Silent_p.S296S|ESRRG_ENST00000391890.3_Silent_p.S303S|ESRRG_ENST00000487276.1_Silent_p.S296S|ESRRG_ENST00000463665.1_Silent_p.S257S	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	81	0	0		WXS	Illumina HiSeq	Phase_I	57	26	0.45614	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	
ZDHHC19	131540	hgsc.bcm.edu	37	3	195938177	195938177	+	Silent	SNP	A	A	G	rs1522394	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	65	0	0		WXS	Illumina HiSeq	Phase_I	71	31	0.43662	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	
OBSCN	84033	hgsc.bcm.edu	37	1	228528563	228528563	+	Missense_Mutation	SNP	C	C	G	rs1188710	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:228528563C>G	ENST00000422127.1	+	72	17715	c.17671C>G	c.(17671-17673)Cag>Gag	p.Q5891E	OBSCN_ENST00000284548.11_Missense_Mutation_p.Q5891E|OBSCN_ENST00000570156.2_Missense_Mutation_p.Q6848E|OBSCN_ENST00000366709.4_Missense_Mutation_p.Q3010E|OBSCN_ENST00000366707.4_Missense_Mutation_p.Q3525E	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	5891			Q -> E (in dbSNP:rs1188710).		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)				AGGCACCCTGCAGGCCCTGGG	0.677													G|||	2698	0.538738	0.6679	0.4654	5008	,	,		14531	0.5942		0.5229	False		,,,				2504	0.3753				p.Q6848E		Atlas-SNP	.											OBSCN_ENST00000570156,NS,carcinoma,0,4	OBSCN	2142	4	0			c.C20542G						PASS	.	G	GLU/GLN,GLU/GLN	2409,1553		745,919,317	13.0	14.0	14.0		17671,17671	4.1	1.0	1	dbSNP_87	14	4299,3963		1174,1951,1006	yes	missense,missense	OBSCN	NM_001098623.1,NM_052843.2	29,29	1919,2870,1323	GG,GC,CC		47.9666,39.1974,45.1243	benign,benign	5891/7969,5891/6621	228528563	6708,5516	1981	4131	6112	SO:0001583	missense	84033	exon83			ACCCTGCAGGCCC	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.17671C>G	1.37:g.228528563C>G	ENSP00000409493:p.Gln5891Glu	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	62	62	1	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	1223|1223	0.559981684981685|0.559981684981685	330|330	0.6707317073170732|0.6707317073170732	168|168	0.46408839779005523|0.46408839779005523	334|334	0.583916083916084|0.583916083916084	391|391	0.5158311345646438|0.5158311345646438	G|G	15.81|15.81	2.942720|2.942720	0.53079|0.53079	0.608026|0.608026	0.520334|0.520334	ENSG00000154358|ENSG00000154358	ENST00000441106|ENST00000284548;ENST00000422127;ENST00000366707;ENST00000366709	.|T;T;T;T	.|0.10573	.|2.86;2.86;2.86;2.86	5.04|5.04	4.12|4.12	0.48240|0.48240	.|.	.|0.149216	.|0.44097	.|N	.|0.000483	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.00268|0.00268	-1.735|-1.735	0.51482|0.51482	P|P	7.199999999996098E-5|7.199999999996098E-5	.|B;B	.|0.02656	.|0.0;0.0	.|B;B	.|0.01281	.|0.0;0.0	T|T	0.42207|0.42207	-0.9465|-0.9465	4|9	.|0.02654	.|T	.|1	.|.	14.1339|14.1339	0.65273|0.65273	0.0:0.2856:0.7144:0.0|0.0:0.2856:0.7144:0.0	rs1188710;rs1188716;rs1684871;rs60494512;rs1188710|rs1188710;rs1188716;rs1684871;rs60494512;rs1188710	.|5891;5891	.|Q5VST9;Q5VST9-3	.|OBSCN_HUMAN;.	G|E	507|5891;5891;3525;3010	.|ENSP00000284548:Q5891E;ENSP00000409493:Q5891E;ENSP00000355668:Q3525E;ENSP00000355670:Q3010E	.|ENSP00000284548:Q5891E	A|Q	+|+	2|1	0|0	OBSCN|OBSCN	226595186|226595186	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.534000|0.534000	0.34807|0.34807	5.463000|5.463000	0.66712|0.66712	0.726000|0.726000	0.32339|0.32339	-0.225000|-0.225000	0.12378|0.12378	GCA|CAG	C|0.442;G|0.558	0.558	strong		0.677	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
CACNA1H	8912	hgsc.bcm.edu	37	16	1254369	1254369	+	Missense_Mutation	SNP	C	C	T	rs3751664	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:1254369C>T	ENST00000348261.5	+	10	2610	c.2362C>T	c.(2362-2364)Cgc>Tgc	p.R788C	RP11-616M22.3_ENST00000564700.1_RNA|CACNA1H_ENST00000565831.1_Missense_Mutation_p.R788C|CACNA1H_ENST00000358590.4_Missense_Mutation_p.R788C	NM_021098.2	NP_066921.2	O95180	CAC1H_HUMAN	calcium channel, voltage-dependent, T type, alpha 1H subunit	788			R -> C (in dbSNP:rs3751664). {ECO:0000269|PubMed:12891677}.		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)	CAAGCTGCGCCGCATCGTGGA	0.672													C|||	234	0.0467252	0.0023	0.0447	5008	,	,		15609	0.1012		0.0875	False		,,,				2504	0.0102				p.R788C		Atlas-SNP	.											.	CACNA1H	317	.	0			c.C2362T	GRCh37	CM076042	CACNA1H	M	rs3751664	PASS	.	C	CYS/ARG,CYS/ARG	66,4212		0,66,2073	36.0	39.0	38.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	2362,2362	0.5	0.8	16	dbSNP_107	38	876,7610		42,792,3409	yes	missense,missense	CACNA1H	NM_001005407.1,NM_021098.2	180,180	42,858,5482	TT,TC,CC		10.3229,1.5428,7.3801	benign,benign	788/2348,788/2354	1254369	942,11822	2139	4243	6382	SO:0001583	missense	8912	exon10			CTGCGCCGCATCG	AL031703	CCDS45375.1, CCDS45376.1	16p13.3	2012-03-07	2007-02-16					"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1395	protein-coding gene	gene with protein product		607904				9670923, 16382099	Standard	NM_021098		Approved	Cav3.2	uc002cks.3	O95180		ENST00000348261.5:c.2362C>T	16.37:g.1254369C>T	ENSP00000334198:p.Arg788Cys	Somatic	207	0	0		WXS	Illumina HiSeq	Phase_I	209	156	0.746412	NM_021098	B5ME00|F8WFD1|O95802|Q8WWI6|Q96QI6|Q96RZ9|Q9NYY4|Q9NYY5	Missense_Mutation	SNP	ENST00000348261.5	37	CCDS45375.1	151	0.06913919413919414	2	0.0040650406504065045	17	0.04696132596685083	59	0.10314685314685315	73	0.09630606860158311	C	7.372	0.627044	0.14257	0.015428	0.103229	ENSG00000196557	ENST00000348261;ENST00000358590	D;D	0.96940	-4.18;-4.13	3.94	0.508	0.16972	.	0.513591	0.14982	N	0.287177	T	0.36635	0.0974	L	0.52573	1.65	0.58432	P	1.0000000000287557E-6	B;B	0.24258	0.1;0.018	B;B	0.21546	0.035;0.005	T	0.75300	-0.3366	9	0.66056	D	0.02	.	6.8165	0.23833	0.5671:0.338:0.0:0.095	rs3751664;rs56611441;rs56779145;rs3751664	788;788	O95180-2;O95180	.;CAC1H_HUMAN	C	788	ENSP00000334198:R788C;ENSP00000351401:R788C	ENSP00000334198:R788C	R	+	1	0	CACNA1H	1194370	0.000000	0.05858	0.817000	0.32601	0.217000	0.24651	-0.310000	0.08135	0.285000	0.22329	0.561000	0.74099	CGC	C|0.927;T|0.073	0.073	strong		0.672	CACNA1H-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000421601.1	NM_001005407	
AGAP7P	653268	hgsc.bcm.edu	37	10	51465366	51465366	+	Missense_Mutation	SNP	G	G	C	rs191741842	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:51465366G>C	ENST00000374095.5	-	7	1215	c.1090C>G	c.(1090-1092)Ccc>Gcc	p.P364A		NM_001077685.1	NP_001071153.1	Q5VUJ5	AGAP7_HUMAN		364	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				regulation of ARF GTPase activity (GO:0032312)		ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)			kidney(1)|large_intestine(1)|lung(7)|ovary(1)|skin(1)	11						TTGAGCTTGGGGATGGTGGTG	0.517													-|||	66	0.0131789	0.0015	0.0346	5008	,	,		17982	0.0149		0.0129	False		,,,				2504	0.0123				p.P364A		Atlas-SNP	.											.	AGAP7	33	.	0			c.C1090G						PASS	.	G	ALA/PRO	15,4385		2,11,2187	67.0	83.0	77.0		1090		0.0	10		77	153,8409		2,149,4130	no	missense	AGAP7	NM_001077685.1	27	4,160,6317	CC,CG,GG		1.787,0.3409,1.2961	probably-damaging	364/664	51465366	168,12794	2200	4281	6481	SO:0001583	missense	653268	exon7			GCTTGGGGATGGT																												ENST00000374095.5:c.1090C>G	10.37:g.51465366G>C	ENSP00000363208:p.Pro364Ala	Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	125	63	0.504	NM_001077685	A6NGH4	Missense_Mutation	SNP	ENST00000374095.5	37	CCDS41524.1	32	0.014652014652014652	1	0.0020325203252032522	11	0.03038674033149171	8	0.013986013986013986	12	0.0158311345646438	.	12.04	1.818577	0.32145	0.003409	0.01787	ENSG00000204169	ENST00000374095	T	0.54479	0.57	.	.	.	Pleckstrin homology domain (3);	0.469288	0.23662	N	0.045817	T	0.23014	0.0556	M	0.64170	1.965	0.44042	D	0.996773	B	0.20052	0.041	B	0.31869	0.137	T	0.13045	-1.0524	9	0.35671	T	0.21	.	5.9763	0.19382	6.0E-4:0.0:0.9994:0.0	.	364	Q5VUJ5	AGAP7_HUMAN	A	364	ENSP00000363208:P364A	ENSP00000363208:P364A	P	-	1	0	AGAP7	51135372	1.000000	0.71417	0.038000	0.18304	0.039000	0.13416	2.412000	0.44609	0.172000	0.19760	0.175000	0.17021	CCC	G|0.983;C|0.017	0.017	strong		0.517	AGAP7-001	KNOWN	non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048033.1		
ZIC2	7546	hgsc.bcm.edu	37	13	100635377	100635377	+	Silent	SNP	C	C	T	rs71640252|rs1831992	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:100635377C>T	ENST00000376335.3	+	1	1352	c.1059C>T	c.(1057-1059)caC>caT	p.H353H		NM_007129.3	NP_009060.2	O95409	ZIC2_HUMAN	Zic family member 2	353					brain development (GO:0007420)|developmental pigmentation (GO:0048066)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube closure (GO:0001843)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription, DNA-templated (GO:0045893)|retinal ganglion cell axon guidance (GO:0031290)|transcription, DNA-templated (GO:0006351)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			large_intestine(2)|liver(2)|lung(5)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	13	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)					TCAAGATCCACAAAAGGACCC	0.652													C|||	209	0.0417332	0.0045	0.0893	5008	,	,		15229	0.0		0.1203	False		,,,				2504	0.0204				p.H353H	Pancreas(97;119 1522 31925 44771 48764)	Atlas-SNP	.											.	ZIC2	25	.	0			c.C1059T						PASS	.	C		100,4306	75.7+/-113.9	3,94,2106	39.0	44.0	42.0		1059	4.7	1.0	13	dbSNP_92	42	970,7630	207.9+/-249.5	56,858,3386	no	coding-synonymous	ZIC2	NM_007129.3		59,952,5492	TT,TC,CC		11.2791,2.2696,8.227		353/533	100635377	1070,11936	2203	4300	6503	SO:0001819	synonymous_variant	7546	exon1			GATCCACAAAAGG	AF104902	CCDS9495.1	13q32	2013-01-08	2011-05-19		ENSG00000043355	ENSG00000043355		"""Zinc fingers, C2H2-type"""	12873	protein-coding gene	gene with protein product	"""Zinc finger protein of the cerebellum 2"""	603073	"""Zic family member 2 (odd-paired Drosophila homolog)"", ""Zic family member 2 (odd-paired homolog, Drosophila)"""			9771712	Standard	NM_007129		Approved	HPE5	uc001von.3	O95409	OTTHUMG00000017279	ENST00000376335.3:c.1059C>T	13.37:g.100635377C>T		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	54	21	0.388889	NM_007129	Q5VYA9|Q9H309	Silent	SNP	ENST00000376335.3	37	CCDS9495.1																																																																																			C|0.922;T|0.078	0.078	strong		0.652	ZIC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045618.2	NM_007129	
TTC30A	92104	hgsc.bcm.edu	37	2	178482698	178482698	+	Silent	SNP	A	A	G	rs3813256	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:178482698A>G	ENST00000355689.5	-	1	996	c.732T>C	c.(730-732)gtT>gtC	p.V244V	AC073834.3_ENST00000357045.4_RNA	NM_152275.3	NP_689488.3	Q86WT1	TT30A_HUMAN	tetratricopeptide repeat domain 30A	244					cilium assembly (GO:0042384)|intraciliary transport (GO:0042073)	cilium (GO:0005929)|intraciliary transport particle B (GO:0030992)				autonomic_ganglia(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(8)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	30			OV - Ovarian serous cystadenocarcinoma(117;0.000423)|Epithelial(96;0.00373)|all cancers(119;0.0169)			TCTGATGGAGAACTAAGGTGT	0.517													a|||	565	0.112819	0.0613	0.0447	5008	,	,		20999	0.1855		0.0875	False		,,,				2504	0.182				p.V244V		Atlas-SNP	.											.	TTC30A	60	.	0			c.T732C						PASS	.	A		317,4089	168.0+/-198.9	8,301,1894	103.0	103.0	103.0		732	-5.9	0.5	2	dbSNP_107	103	580,8020	151.9+/-206.6	19,542,3739	no	coding-synonymous	TTC30A	NM_152275.3		27,843,5633	GG,GA,AA		6.7442,7.1947,6.8968		244/666	178482698	897,12109	2203	4300	6503	SO:0001819	synonymous_variant	92104	exon1			ATGGAGAACTAAG	AK024008	CCDS2276.1	2q31.2	2013-01-11			ENSG00000197557	ENSG00000197557		"""Tetratricopeptide (TTC) repeat domain containing"""	25853	protein-coding gene	gene with protein product						12477932	Standard	NM_152275		Approved	FLJ13946	uc002ulo.3	Q86WT1	OTTHUMG00000132528	ENST00000355689.5:c.732T>C	2.37:g.178482698A>G		Somatic	214	1	0.0046729		WXS	Illumina HiSeq	Phase_I	190	106	0.557895	NM_152275	A8K8N0|Q8IVP2	Silent	SNP	ENST00000355689.5	37	CCDS2276.1																																																																																			A|0.915;G|0.085	0.085	strong		0.517	TTC30A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255728.2	NM_152275	
PSG1	5669	hgsc.bcm.edu	37	19	43372386	43372386	+	Silent	SNP	T	T	C	rs1064491	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:43372386T>C	ENST00000436291.2	-	5	1226	c.1110A>G	c.(1108-1110)gaA>gaG	p.E370E	PSG1_ENST00000403380.3_Silent_p.E277E|PSG1_ENST00000595124.1_Silent_p.E277E|PSG1_ENST00000595356.1_Silent_p.E370E|PSG1_ENST00000312439.6_Silent_p.E370E|PSG1_ENST00000244296.2_Silent_p.E370E	NM_001184825.1|NM_001184826.1	NP_001171754.1|NP_001171755.1	P11464	PSG1_HUMAN	pregnancy specific beta-1-glycoprotein 1	370	Ig-like C2-type 3.				female pregnancy (GO:0007565)	extracellular region (GO:0005576)				breast(2)|endometrium(4)|kidney(2)|large_intestine(5)|lung(9)|ovary(3)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	30		Prostate(69;0.00682)				GCTGAAACTTTTCATTAATTG	0.453													.|||	1436	0.286741	0.3139	0.1945	5008	,	,		19460	0.4167		0.1014	False		,,,				2504	0.3722				p.E370E		Atlas-SNP	.											.	PSG1	196	.	0			c.A1110G						PASS	.	C	,,	1266,3136		213,840,1148	167.0	177.0	174.0		1110,1110,1110	0.5	0.0	19	dbSNP_86	174	936,7660		68,800,3430	no	coding-synonymous,coding-synonymous,coding-synonymous	PSG1	NM_001184825.1,NM_001184826.1,NM_006905.2	,,	281,1640,4578	CC,CT,TT		10.8888,28.7597,16.9411	,,	370/420,370/418,370/427	43372386	2202,10796	2201	4298	6499	SO:0001819	synonymous_variant	5669	exon5			AAACTTTTCATTA		CCDS12612.1, CCDS54275.1, CCDS59392.1, CCDS74380.1	19q13.2	2013-01-29			ENSG00000231924	ENSG00000231924		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9514	protein-coding gene	gene with protein product		176390		PSBG1			Standard	NM_006905		Approved	PSGGA, CD66f, PBG1		P11464	OTTHUMG00000151123	ENST00000436291.2:c.1110A>G	19.37:g.43372386T>C		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	140	60	0.428571	NM_001184826	O75236|P11462|P11463|Q15231|Q15241|Q15243|Q16660|Q6ICR4|Q9P1W5|Q9UQ79	Silent	SNP	ENST00000436291.2	37	CCDS54275.1																																																																																			T|0.797;C|0.203	0.203	strong		0.453	PSG1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000321426.1		
SDC3	9672	hgsc.bcm.edu	37	1	31349647	31349647	+	Missense_Mutation	SNP	C	C	T	rs2491132	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:31349647C>T	ENST00000339394.6	-	3	796	c.622G>A	c.(622-624)Gta>Ata	p.V208I	SDC3_ENST00000336798.7_Missense_Mutation_p.V150I|SDC3_ENST00000471567.1_5'UTR	NM_014654.3	NP_055469.3	O75056	SDC3_HUMAN	syndecan 3	208	Ser/Thr-rich (mucin-like).		V -> I (in dbSNP:rs2491132).		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)		AGCCTCCGTACGCCAGTGGTC	0.677													C|||	382	0.076278	0.0091	0.1009	5008	,	,		14077	0.0347		0.2107	False		,,,				2504	0.0542				p.V208I		Atlas-SNP	.											.	SDC3	45	.	0			c.G622A	GRCh37	CM066225	SDC3	M	rs2491132	PASS	.	C	ILE/VAL	184,4222	114.6+/-152.6	7,170,2026	27.0	30.0	29.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	622	-8.7	0.0	1	dbSNP_100	29	1813,6785	315.8+/-312.4	196,1421,2682	yes	missense	SDC3	NM_014654.3	29	203,1591,4708	TT,TC,CC		21.0863,4.1761,15.3568	benign	208/443	31349647	1997,11007	2203	4299	6502	SO:0001583	missense	9672	exon3			TCCGTACGCCAGT	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.622G>A	1.37:g.31349647C>T	ENSP00000344468:p.Val208Ile	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	71	38	0.535211	NM_014654	Q5T1Z6|Q5T1Z7|Q96CT3|Q96PR8	Missense_Mutation	SNP	ENST00000339394.6	37	CCDS30661.1	221	0.10119047619047619	8	0.016260162601626018	46	0.1270718232044199	20	0.03496503496503497	147	0.19393139841688653	C	3.539	-0.094098	0.07053	0.041761	0.210863	ENSG00000162512	ENST00000336798;ENST00000339394	T;T	0.21932	1.99;1.98	4.99	-8.71	0.00848	.	0.851711	0.10100	N	0.716133	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B	0.09022	0.002;0.0	B;B	0.04013	0.001;0.0	T	0.40440	-0.9563	9	0.32370	T	0.25	-0.0407	6.0353	0.19704	0.0787:0.3723:0.0849:0.4641	rs2491132;rs17263807;rs2491132	208;150	O75056;D3DPN2	SDC3_HUMAN;.	I	150;208	ENSP00000338346:V150I;ENSP00000344468:V208I	ENSP00000338346:V150I	V	-	1	0	SDC3	31122234	0.000000	0.05858	0.003000	0.11579	0.211000	0.24417	-2.237000	0.01200	-1.210000	0.02627	-0.379000	0.06801	GTA	C|0.879;G|0.000;T|0.121	0.121	strong		0.677	SDC3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102017.1	NM_014654	
PCNT	5116	hgsc.bcm.edu	37	21	47817316	47817316	+	Missense_Mutation	SNP	G	G	A	rs143796569	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:47817316G>A	ENST00000359568.5	+	22	4461	c.4354G>A	c.(4354-4356)Ggg>Agg	p.G1452R	PCNT_ENST00000480896.1_3'UTR	NM_006031.5	NP_006022.3	O95613	PCNT_HUMAN	pericentrin	1452			G -> R (found in a patient with mental retardation, no speech, facial and limbs dysmorphisms). {ECO:0000269|PubMed:23033978}.		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)					TCAGCATCGCGGGTGTGCCAA	0.562													G|||	18	0.00359425	0.0	0.0	5008	,	,		20614	0.0		0.001	False		,,,				2504	0.0174				p.G1452R		Atlas-SNP	.											PCNT,NS,carcinoma,-2,1	PCNT	283	1	0			c.G4354A						PASS	.	G	ARG/GLY	2,4404	4.2+/-10.8	0,2,2201	70.0	68.0	69.0		4354	5.5	0.0	21	dbSNP_134	69	17,8583	12.6+/-44.7	0,17,4283	yes	missense	PCNT	NM_006031.5	125	0,19,6484	AA,AG,GG		0.1977,0.0454,0.1461	probably-damaging	1452/3337	47817316	19,12987	2203	4300	6503	SO:0001583	missense	5116	exon22			CATCGCGGGTGTG	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.4354G>A	21.37:g.47817316G>A	ENSP00000352572:p.Gly1452Arg	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	100	27	0.27	NM_006031	O43152|Q7Z7C9	Missense_Mutation	SNP	ENST00000359568.5	37	CCDS33592.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	G	15.43	2.830357	0.50845	4.54E-4	0.001977	ENSG00000160299	ENST00000359568	T	0.58506	0.33	5.46	5.46	0.80206	.	0.511594	0.14699	N	0.303674	T	0.66056	0.2751	L	0.44542	1.39	0.09310	N	0.999996	D;D	0.76494	0.999;0.998	P;P	0.57152	0.814;0.807	T	0.60182	-0.7313	10	0.51188	T	0.08	.	16.8006	0.85613	0.0:0.0:1.0:0.0	.	1334;1452	O95613-2;O95613	.;PCNT_HUMAN	R	1452	ENSP00000352572:G1452R	ENSP00000352572:G1452R	G	+	1	0	PCNT	46641744	0.968000	0.33430	0.009000	0.14445	0.009000	0.06853	4.647000	0.61418	2.560000	0.86352	0.561000	0.74099	GGG	G|0.999;A|0.001	0.001	strong		0.562	PCNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207336.1	NM_006031	
FAM228A	653140	hgsc.bcm.edu	37	2	24413298	24413298	+	Missense_Mutation	SNP	A	A	G	rs2288073	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:24413298A>G	ENST00000295150.3	+	6	505	c.419A>G	c.(418-420)tAt>tGt	p.Y140C	RP11-507M3.1_ENST00000584973.1_3'UTR	NM_001040710.1	NP_001035800.1	Q86W67	F228A_HUMAN	family with sequence similarity 228, member A	140			Y -> C (in dbSNP:rs2288073).														AAGCTCATCTATGCAGACAAG	0.408													G|||	1073	0.214257	0.1437	0.147	5008	,	,		21745	0.1478		0.3131	False		,,,				2504	0.3241				p.Y140C		Atlas-SNP	.											C2orf84,NS,carcinoma,+1,1	.	.	1	0			c.A419G						scavenged	.	G	CYS/TYR	607,3115		49,509,1303	32.0	32.0	32.0		419	-1.3	0.0	2	dbSNP_100	32	2376,5798		354,1668,2065	yes	missense	C2orf84	NM_001040710.1	194	403,2177,3368	GG,GA,AA		29.0678,16.3084,25.0757	benign	140/207	24413298	2983,8913	1861	4087	5948	SO:0001583	missense	653140	exon6			TCATCTATGCAGA		CCDS42659.1	2p23.3	2012-07-04	2012-07-04	2012-07-04	ENSG00000186453	ENSG00000186453			34418	protein-coding gene	gene with protein product			"""chromosome 2 open reading frame 84"""	C2orf84			Standard	NM_001040710		Approved	FLJ30851	uc002rfc.3	Q86W67	OTTHUMG00000151903	ENST00000295150.3:c.419A>G	2.37:g.24413298A>G	ENSP00000295150:p.Tyr140Cys	Somatic	188	1	0.00531915		WXS	Illumina HiSeq	Phase_I	221	87	0.393665	NM_001040710		Missense_Mutation	SNP	ENST00000295150.3	37	CCDS42659.1	473|473	0.21657509157509158|0.21657509157509158	83|83	0.16869918699186992|0.16869918699186992	61|61	0.1685082872928177|0.1685082872928177	82|82	0.14335664335664336|0.14335664335664336	247|247	0.3258575197889182|0.3258575197889182	G|G	0.008|0.008	-1.917424|-1.917424	0.00503|0.00503	0.163084|0.163084	0.290678|0.290678	ENSG00000186453|ENSG00000186453	ENST00000432434|ENST00000295150;ENST00000415196	.|T;T	.|0.48201	.|0.82;0.87	3.64|3.64	-1.3|-1.3	0.09259|0.09259	.|.	.|0.177091	.|0.27851	.|N	.|0.017599	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.11927|0.11927	0.2|0.2	0.80722|0.80722	P|P	0.0|0.0	.|B	.|0.02656	.|0.0	.|B	.|0.01281	.|0.0	T|T	0.35351|0.35351	-0.9792|-0.9792	4|9	.|0.56958	.|D	.|0.05	-1.3245|-1.3245	4.2867|4.2867	0.10858|0.10858	0.5053:0.0:0.3279:0.1668|0.5053:0.0:0.3279:0.1668	rs2288073;rs11545100;rs57437922;rs2288073|rs2288073;rs11545100;rs57437922;rs2288073	.|140	.|Q86W67	.|CB084_HUMAN	V|C	178|140;41	.|ENSP00000295150:Y140C;ENSP00000416595:Y41C	.|ENSP00000295150:Y140C	M|Y	+|+	1|2	0|0	C2orf84|C2orf84	24266802|24266802	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.018000|0.018000	0.09664|0.09664	-0.668000|-0.668000	0.05268|0.05268	-0.616000|-0.616000	0.05671|0.05671	-0.755000|-0.755000	0.03482|0.03482	ATG|TAT	A|0.776;G|0.224	0.224	strong		0.408	FAM228A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324342.1	NM_001040710	
HIST1H2AD	3013	hgsc.bcm.edu	37	6	26199222	26199222	+	Silent	SNP	G	G	A	rs113561314	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:26199222G>A	ENST00000341023.1	-	1	249	c.250C>T	c.(250-252)Ctg>Ttg	p.L84L	HIST1H3D_ENST00000356476.2_5'Flank|HIST1H3D_ENST00000377831.5_5'UTR|HIST1H2BF_ENST00000359985.1_5'Flank	NM_021065.2	NP_066409.1	P20671	H2A1D_HUMAN	histone cluster 1, H2ad	84						extracellular vesicular exosome (GO:0070062)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2)	6		all_hematologic(11;0.196)				GCCAGCTGCAGGTGTCGGGGG	0.607													G|||	549	0.109625	0.1467	0.0605	5008	,	,		15805	0.0585		0.1163	False		,,,				2504	0.1401				p.L84L		Atlas-SNP	.											.	HIST1H2AD	20	.	0			c.C250T						PASS	.	G	,	547,3859		35,477,1691	104.0	104.0	104.0		,250	3.9	1.0	6	dbSNP_132	104	808,7792		24,760,3516	no	utr-5,coding-synonymous	HIST1H2AD,HIST1H3D	NM_003530.3,NM_021065.2	,	59,1237,5207	AA,AG,GG		9.3953,12.4149,10.4183	,	,84/131	26199222	1355,11651	2203	4300	6503	SO:0001819	synonymous_variant	3013	exon1			GCTGCAGGTGTCG	Z80776	CCDS4591.1	6p22.1	2011-01-27	2006-10-11	2003-02-14	ENSG00000196866	ENSG00000196866		"""Histones / Replication-dependent"""	4729	protein-coding gene	gene with protein product		602792	"""H2A histone family, member G"", ""histone 1, H2ad"""	H2AFG		9119399, 12408966	Standard	NM_021065		Approved	H2A/g, H2A.3	uc003ngw.4	P20671	OTTHUMG00000014437	ENST00000341023.1:c.250C>T	6.37:g.26199222G>A		Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	165	79	0.478788	NM_021065	A0PK91|P57754|Q6FGY6	Silent	SNP	ENST00000341023.1	37	CCDS4591.1																																																																																			G|0.897;A|0.103	0.103	strong		0.607	HIST1H2AD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040100.1	NM_021065	
MYO10	4651	hgsc.bcm.edu	37	5	16794916	16794916	+	Silent	SNP	G	G	A	rs396514	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:16794916G>A	ENST00000513610.1	-	4	760	c.306C>T	c.(304-306)tcC>tcT	p.S102S		NM_012334.2	NP_036466.2	Q9HD67	MYO10_HUMAN	myosin X	102	Myosin motor.				ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cytoskeleton-dependent intracellular transport (GO:0030705)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|metabolic process (GO:0008152)|positive regulation of cell-cell adhesion (GO:0022409)|regulation of cell shape (GO:0008360)|regulation of filopodium assembly (GO:0051489)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|plus-end directed microfilament motor activity (GO:0060002)|spectrin binding (GO:0030507)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|lung(28)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	86						AGGGGTTCACGGAGGCCAGGA	0.632													G|||	1312	0.261981	0.0219	0.3458	5008	,	,		15939	0.244		0.4304	False		,,,				2504	0.3722				p.S102S		Atlas-SNP	.											.	MYO10	198	.	0			c.C306T						PASS	.	G		377,3735		20,337,1699	24.0	29.0	27.0		306	-10.4	0.2	5	dbSNP_80	27	3602,4808		787,2028,1390	no	coding-synonymous	MYO10	NM_012334.2		807,2365,3089	AA,AG,GG		42.83,9.1683,31.7761		102/2059	16794916	3979,8543	2056	4205	6261	SO:0001819	synonymous_variant	4651	exon4			GTTCACGGAGGCC	AF247457	CCDS54834.1	5p15.1-p14.3	2013-01-10				ENSG00000145555		"""Myosins / Myosin superfamily : Class X"", ""Pleckstrin homology (PH) domain containing"""	7593	protein-coding gene	gene with protein product		601481				8884266	Standard	NM_012334		Approved	KIAA0799	uc003jft.4	Q9HD67		ENST00000513610.1:c.306C>T	5.37:g.16794916G>A		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	69	35	0.507246	NM_012334	A7E2D1|O94893|Q8IVX5|Q9NYM7|Q9P110|Q9P111|Q9UHF6	Silent	SNP	ENST00000513610.1	37	CCDS54834.1																																																																																			G|0.708;A|0.292	0.292	strong		0.632	MYO10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366167.1	NM_012334	
FAM21A	387680	hgsc.bcm.edu	37	10	51853633	51853633	+	Missense_Mutation	SNP	C	C	T	rs199520696	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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_ENST00000314664.7_Missense_Mutation_p.T379M|FAM21A_ENST00000351071.6_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	701	1	0.00142653		WXS	Illumina HiSeq	Phase_I	893	144	0.161254	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	
PCDHB4	56131	hgsc.bcm.edu	37	5	140502343	140502343	+	Missense_Mutation	SNP	C	C	T	rs3733698|rs377479392	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:140502343C>T	ENST00000194152.1	+	1	763	c.763C>T	c.(763-765)Ccc>Tcc	p.P255S	AC005754.8_ENST00000606030.1_lincRNA	NM_018938.2	NP_061761.1	Q9Y5E5	PCDB4_HUMAN	protocadherin beta 4	255	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.		P -> L (in dbSNP:rs3733697).|P -> S (in dbSNP:rs3733698).		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)			GGAAAACAGCCCCCTAGACTC	0.458													C|||	743	0.148363	0.1657	0.1974	5008	,	,		19595	0.119		0.159	False		,,,				2504	0.1094				p.P255S		Atlas-SNP	.											.	PCDHB4	177	.	0			c.C763T						PASS	.	C	SER/PRO	852,3554		77,698,1428	100.0	108.0	105.0		763	3.5	0.9	5	dbSNP_107	105	1448,7152		141,1166,2993	yes	missense	PCDHB4	NM_018938.2	74	218,1864,4421	TT,TC,CC		16.8372,19.3373,17.6841	benign	255/796	140502343	2300,10706	2203	4300	6503	SO:0001583	missense	56131	exon1			AACAGCCCCCTAG	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.763C>T	5.37:g.140502343C>T	ENSP00000194152:p.Pro255Ser	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	107	51	0.476636	NM_018938	Q4V761	Missense_Mutation	SNP	ENST00000194152.1	37	CCDS4246.1	271	0.12408424908424909	67	0.13617886178861788	60	0.16574585635359115	49	0.08566433566433566	95	0.12532981530343007	C	10.02	1.237419	0.22711	0.193373	0.168372	ENSG00000081818	ENST00000194152	T	0.54279	0.58	4.41	3.53	0.40419	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.00144	0.0004	M	0.78049	2.395	0.23787	P	0.99684734	P	0.34522	0.455	B	0.41813	0.367	T	0.26916	-1.0089	8	0.59425	D	0.04	.	13.1959	0.59738	0.0:0.9181:0.0:0.0819	rs3733698;rs17844409;rs52797834;rs60589176;rs3733698	255	Q9Y5E5	PCDB4_HUMAN	S	255	ENSP00000194152:P255S	ENSP00000194152:P255S	P	+	1	0	PCDHB4	140482527	0.435000	0.25577	0.914000	0.36105	0.426000	0.31534	1.498000	0.35660	2.449000	0.82847	0.650000	0.86243	CCC	C|0.827;T|0.173	0.173	strong		0.458	PCDHB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251812.2	NM_018938	
GPR157	80045	hgsc.bcm.edu	37	1	9165685	9165685	+	Missense_Mutation	SNP	G	G	A	rs72637739	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:9165685G>A	ENST00000377411.4	-	3	794	c.652C>T	c.(652-654)Cgc>Tgc	p.R218C	GPR157_ENST00000414642.2_Intron	NM_024980.4	NP_079256.4	Q5UAW9	GP157_HUMAN	G protein-coupled receptor 157	218						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			lung(4)|prostate(1)	5	all_lung(157;0.185)	all_epithelial(116;5.02e-20)|all_lung(118;3.6e-06)|Lung NSC(185;7.93e-06)|Renal(390;0.000147)|Breast(348;0.000688)|Colorectal(325;0.00205)|Hepatocellular(190;0.00825)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.16e-07)|COAD - Colon adenocarcinoma(227;7.73e-05)|Kidney(185;0.000252)|KIRC - Kidney renal clear cell carcinoma(229;0.000917)|STAD - Stomach adenocarcinoma(132;0.00178)|BRCA - Breast invasive adenocarcinoma(304;0.00186)|READ - Rectum adenocarcinoma(331;0.0642)		GAGGAGTGGCGCAGCAGGCGG	0.642													G|||	736	0.146965	0.0113	0.2651	5008	,	,		19730	0.1905		0.2147	False		,,,				2504	0.1319				p.R218C		Atlas-SNP	.											.	GPR157	14	.	0			c.C652T						PASS	.	G	CYS/ARG	220,4186	133.7+/-170.0	2,216,1985	68.0	61.0	63.0		652	1.8	0.0	1	dbSNP_130	63	1889,6711	331.1+/-319.5	221,1447,2632	yes	missense	GPR157	NM_024980.4	180	223,1663,4617	AA,AG,GG		21.9651,4.9932,16.2156	probably-damaging	218/336	9165685	2109,10897	2203	4300	6503	SO:0001583	missense	80045	exon3			AGTGGCGCAGCAG	AK022194	CCDS100.2	1p36.22	2012-08-21			ENSG00000180758	ENSG00000180758		"""GPCR / Class B : Orphans"""	23687	protein-coding gene	gene with protein product						10574461	Standard	XM_005263496		Approved	FLJ12132	uc001apq.1	Q5UAW9	OTTHUMG00000001758	ENST00000377411.4:c.652C>T	1.37:g.9165685G>A	ENSP00000366628:p.Arg218Cys	Somatic	225	0	0		WXS	Illumina HiSeq	Phase_I	199	196	0.984925	NM_024980	A2A334|Q8WWB8|Q9HA73	Missense_Mutation	SNP	ENST00000377411.4	37	CCDS100.2	371	0.16987179487179488	9	0.018292682926829267	84	0.23204419889502761	106	0.1853146853146853	172	0.22691292875989447	G	11.42	1.632249	0.29068	0.049932	0.219651	ENSG00000180758	ENST00000377411	T	0.42513	0.97	4.82	1.77	0.24775	GPCR, family 2-like (1);	0.964959	0.08613	N	0.919723	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.22346	0.068	B	0.12837	0.008	T	0.24941	-1.0146	9	0.40728	T	0.16	-4.7394	5.8678	0.18786	0.2275:0.0:0.6312:0.1413	.	218	Q5UAW9	GP157_HUMAN	C	218	ENSP00000366628:R218C	ENSP00000366628:R218C	R	-	1	0	GPR157	9088272	0.750000	0.28316	0.000000	0.03702	0.006000	0.05464	2.540000	0.45727	0.526000	0.28541	-0.274000	0.10170	CGC	G|0.839;A|0.161	0.161	strong		0.642	GPR157-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127658.2	NM_024980	
SLC47A2	146802	hgsc.bcm.edu	37	17	19584752	19584752	+	Silent	SNP	G	G	C	rs34416664	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:19584752G>C	ENST00000325411.5	-	15	1478	c.1428C>G	c.(1426-1428)gcC>gcG	p.A476A	SLC47A2_ENST00000350657.5_Silent_p.A454A|SLC47A2_ENST00000463318.1_5'UTR	NM_152908.3	NP_690872.2	Q86VL8	S47A2_HUMAN	solute carrier family 47 (multidrug and toxin extrusion), member 2	476					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	antiporter activity (GO:0015297)|drug transmembrane transporter activity (GO:0015238)			endometrium(2)|kidney(3)|large_intestine(2)|lung(1)|ovary(1)	9	all_cancers(12;2.3e-05)|all_epithelial(12;0.0024)|Breast(13;0.245)				Aciclovir(DB00787)	GGAAGACACAGGCCAGCATGC	0.592													G|||	22	0.00439297	0.0	0.0058	5008	,	,		19756	0.0		0.0139	False		,,,				2504	0.0041				p.A476A		Atlas-SNP	.											.	SLC47A2	61	.	0			c.C1428G						PASS	.	G	,	10,4396	17.9+/-39.9	0,10,2193	57.0	48.0	51.0		1320,1428	0.9	0.0	17	dbSNP_126	51	97,8503	52.7+/-113.3	1,95,4204	no	coding-synonymous,coding-synonymous	SLC47A2	NM_001099646.1,NM_152908.3	,	1,105,6397	CC,CG,GG		1.1279,0.227,0.8227	,	440/567,476/603	19584752	107,12899	2203	4300	6503	SO:0001819	synonymous_variant	146802	exon15			GACACAGGCCAGC	AB250364	CCDS11211.1, CCDS58530.1	17p11.2	2013-07-17	2013-07-17		ENSG00000180638	ENSG00000180638		"""Solute carriers"""	26439	protein-coding gene	gene with protein product	"""multidrug and toxin extrusion 2"""	609833				16996621, 16807400	Standard	NM_152908		Approved	FLJ31196, MATE2, MATE2-K	uc002gwf.4	Q86VL8	OTTHUMG00000059464	ENST00000325411.5:c.1428C>G	17.37:g.19584752G>C		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	82	33	0.402439	NM_152908	A0JBX9|A0P8Z7|Q63HJ9|Q8IV44|Q96NA1	Silent	SNP	ENST00000325411.5	37	CCDS11211.1																																																																																			G|0.993;C|0.007	0.007	strong		0.592	SLC47A2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000132242.2	NM_152908	
ALPK2	115701	hgsc.bcm.edu	37	18	56202120	56202120	+	Missense_Mutation	SNP	G	G	A	rs7234999	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:56202120G>A	ENST00000361673.3	-	5	5512	c.5299C>T	c.(5299-5301)Cac>Tac	p.H1767Y	RP11-1151B14.4_ENST00000591360.1_RNA	NM_052947.3	NP_443179.3	Q86TB3	ALPK2_HUMAN	alpha-kinase 2	1767			H -> Y (in dbSNP:rs7234999).			nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(33)|ovary(7)|prostate(1)|skin(10)|upper_aerodigestive_tract(2)	84						TCTTCTGTGTGTGATAATGAT	0.418													G|||	361	0.0720847	0.0424	0.0706	5008	,	,		22641	0.0119		0.1272	False		,,,				2504	0.1186				p.H1767Y		Atlas-SNP	.											.	ALPK2	487	.	0			c.C5299T						PASS	.	G	TYR/HIS	304,4102	164.7+/-196.3	16,272,1915	196.0	183.0	187.0		5299	-2.3	0.0	18	dbSNP_116	187	1172,7428	239.7+/-270.7	79,1014,3207	yes	missense	ALPK2	NM_052947.3	83	95,1286,5122	AA,AG,GG		13.6279,6.8997,11.3486	benign	1767/2171	56202120	1476,11530	2203	4300	6503	SO:0001583	missense	115701	exon5			CTGTGTGTGATAA	AY044450	CCDS11966.2	18q21.31	2013-01-11			ENSG00000198796	ENSG00000198796		"""Immunoglobulin superfamily / I-set domain containing"""	20565	protein-coding gene	gene with protein product	"""heart alpha-kinase"""					10021370	Standard	NM_052947		Approved	HAK	uc002lhj.4	Q86TB3	OTTHUMG00000132755	ENST00000361673.3:c.5299C>T	18.37:g.56202120G>A	ENSP00000354991:p.His1767Tyr	Somatic	229	0	0		WXS	Illumina HiSeq	Phase_I	179	88	0.49162	NM_052947	Q6ZUX0|Q8NAT5|Q96L95	Missense_Mutation	SNP	ENST00000361673.3	37	CCDS11966.2	155	0.07097069597069597	30	0.06097560975609756	32	0.08839779005524862	8	0.013986013986013986	85	0.11213720316622691	G	3.210	-0.161853	0.06502	0.068997	0.136279	ENSG00000198796	ENST00000361673	T	0.42131	0.98	5.4	-2.26	0.06867	.	2.033870	0.01521	N	0.018366	T	0.00178	0.0005	N	0.08118	0	0.80722	P	0.0	P;P	0.41008	0.735;0.617	B;B	0.40256	0.324;0.173	T	0.09058	-1.0692	9	0.02654	T	1	5.5129	10.7369	0.46130	0.5168:0.0:0.4832:0.0	rs7234999;rs52817310;rs58659919;rs7234999	1762;1767	Q86TB3-2;Q86TB3	.;ALPK2_HUMAN	Y	1767	ENSP00000354991:H1767Y	ENSP00000354991:H1767Y	H	-	1	0	ALPK2	54353100	0.000000	0.05858	0.000000	0.03702	0.039000	0.13416	-0.893000	0.04127	-0.945000	0.03681	-0.254000	0.11334	CAC	G|0.907;A|0.093	0.093	strong		0.418	ALPK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256126.1	NM_052947	
MUC4	4585	hgsc.bcm.edu	37	3	195506499	195506499	+	Silent	SNP	G	G	A	rs542643120	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195506499G>A	ENST00000463781.3	-	2	12411	c.11952C>T	c.(11950-11952)ccC>ccT	p.P3984P	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Silent_p.P3984P	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.P3984P(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)		TGACAGGAAGGGGGGTGGCGT	0.592													.|||	1079	0.215455	0.2126	0.183	5008	,	,		8207	0.0952		0.338	False		,,,				2504	0.2403				p.P3984P		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	1	Substitution - coding silent(1)	stomach(1)	c.C11952T						scavenged	.						10.0	7.0	8.0					3																	195506499		443	903	1346	SO:0001819	synonymous_variant	4585	exon2			AGGAAGGGGGGTG	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.11952C>T	3.37:g.195506499G>A		Somatic	51	7	0.137255		WXS	Illumina HiSeq	Phase_I	42	10	0.238095	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	
SLC22A4	6583	hgsc.bcm.edu	37	5	131663062	131663062	+	Missense_Mutation	SNP	T	T	C	rs272893	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:131663062T>C	ENST00000200652.3	+	5	1091	c.917T>C	c.(916-918)aTa>aCa	p.I306T	AC034220.3_ENST00000417795.1_RNA	NM_003059.2	NP_003050.2	Q9H015	S22A4_HUMAN	solute carrier family 22 (organic cation/zwitterion transporter), member 4	306			I -> T (in dbSNP:rs272893). {ECO:0000269|PubMed:12436193, ECO:0000269|PubMed:9426230}.		body fluid secretion (GO:0007589)|carnitine metabolic process (GO:0009437)|carnitine transmembrane transport (GO:1902603)|carnitine transport (GO:0015879)|cation transmembrane transport (GO:0098655)|organic cation transport (GO:0015695)|quaternary ammonium group transport (GO:0015697)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)|triglyceride metabolic process (GO:0006641)	apical plasma membrane (GO:0016324)|integral component of plasma membrane (GO:0005887)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|carnitine transmembrane transporter activity (GO:0015226)|cation:cation antiporter activity (GO:0015491)|nucleotide binding (GO:0000166)|PDZ domain binding (GO:0030165)|quaternary ammonium group transmembrane transporter activity (GO:0015651)|secondary active organic cation transmembrane transporter activity (GO:0008513)|symporter activity (GO:0015293)			endometrium(1)|kidney(3)|large_intestine(2)|lung(8)|ovary(1)|urinary_tract(1)	16		all_cancers(142;0.0752)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)		Amiloride(DB00594)|Aminohippurate(DB00345)|Benzylpenicillin(DB01053)|Choline(DB00122)|Cimetidine(DB00501)|Clonidine(DB00575)|Desipramine(DB01151)|Guanidine(DB00536)|Imipramine(DB00458)|Ipratropium bromide(DB00332)|L-Arginine(DB00125)|L-Carnitine(DB00583)|L-Lysine(DB00123)|Levofloxacin(DB01137)|Mepyramine(DB06691)|Nicotine(DB00184)|Ofloxacin(DB01165)|Procainamide(DB01035)|Quinidine(DB00908)|Quinine(DB00468)|Spermine(DB00127)|Testosterone(DB00624)|Tiotropium(DB01409)|Verapamil(DB00661)	ATGAACAACATAGCTGTACCA	0.378													T|||	2775	0.554113	0.7731	0.6816	5008	,	,		15725	0.3512		0.5885	False		,,,				2504	0.3415				p.I306T		Atlas-SNP	.											.	SLC22A4	45	.	0			c.T917C						PASS	.	T	THR/ILE	3256,1150	713.5+/-408.2	1201,854,148	77.0	76.0	76.0		917	-1.1	0.0	5	dbSNP_79	76	5291,3309	645.5+/-400.2	1637,2017,646	yes	missense	SLC22A4	NM_003059.2	89	2838,2871,794	CC,CT,TT		38.4767,26.1008,34.2842	benign	306/552	131663062	8547,4459	2203	4300	6503	SO:0001583	missense	6583	exon5			ACAACATAGCTGT	AB007448	CCDS4153.1	5q23.3	2013-07-18	2013-07-18		ENSG00000197208	ENSG00000197208		"""Solute carriers"""	10968	protein-coding gene	gene with protein product		604190	"""solute carrier family 22 (organic cation/ergothioneine transporter), member 4"""			9426230, 15795384	Standard	NM_003059		Approved	OCTN1, MGC34546	uc003kwq.3	Q9H015	OTTHUMG00000059648	ENST00000200652.3:c.917T>C	5.37:g.131663062T>C	ENSP00000200652:p.Ile306Thr	Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	135	71	0.525926	NM_003059	O14546	Missense_Mutation	SNP	ENST00000200652.3	37	CCDS4153.1	1278	0.5851648351648352	383	0.7784552845528455	250	0.6906077348066298	203	0.3548951048951049	442	0.58311345646438	T	14.02	2.410972	0.42817	0.738992	0.615233	ENSG00000197208	ENST00000200652	T	0.73469	-0.75	5.85	-1.15	0.09709	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.788348	0.12035	N	0.505555	T	0.00012	0.0000	L	0.31371	0.925	0.80722	P	0.0	B	0.09022	0.002	B	0.15052	0.012	T	0.34551	-0.9824	9	0.54805	T	0.06	.	4.2798	0.10827	0.3127:0.1788:0.0:0.5085	rs272893;rs781674;rs52812854;rs58129057;rs272893	306	Q9H015	S22A4_HUMAN	T	306	ENSP00000200652:I306T	ENSP00000200652:I306T	I	+	2	0	SLC22A4	131690961	0.031000	0.19500	0.000000	0.03702	0.362000	0.29581	2.312000	0.43726	-0.412000	0.07519	0.533000	0.62120	ATA	T|0.373;G|0.001	.	strong		0.378	SLC22A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132661.1	NM_003059	
AK9	221264	hgsc.bcm.edu	37	6	109954518	109954518	+	Silent	SNP	T	T	C	rs9374111	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:109954518T>C	ENST00000424296.2	-	11	1018	c.942A>G	c.(940-942)ctA>ctG	p.L314L	AK9_ENST00000285397.5_Silent_p.L314L|AK9_ENST00000341338.6_5'UTR|AK9_ENST00000368948.2_Silent_p.L314L	NM_001145128.2	NP_001138600.2	Q5TCS8	KAD9_HUMAN	adenylate kinase 9	314					ADP phosphorylation (GO:0006757)|AMP phosphorylation (GO:0006756)|CDP phosphorylation (GO:0061508)|CMP phosphorylation (GO:0061566)|dADP phosphorylation (GO:0006174)|dAMP phosphorylation (GO:0061565)|dCDP phosphorylation (GO:0061570)|dCMP phosphorylation (GO:0061567)|dGDP phosphorylation (GO:0006186)|GDP phosphorylation (GO:0061568)|TDP phosphorylation (GO:0061571)|UDP phosphorylation (GO:0061569)	cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|nucleoside diphosphate kinase activity (GO:0004550)|nucleoside phosphate kinase activity (GO:0050145)	p.L314L(2)									GAGTACGAAATAGCTCATCCT	0.313													T|||	1224	0.244409	0.1097	0.2839	5008	,	,		16419	0.3433		0.2197	False		,,,				2504	0.3221				p.L314L		Atlas-SNP	.											AKD1_ENST00000424296,NS,carcinoma,0,2	AKD1	223	2	2	Substitution - coding silent(2)	stomach(2)	c.A942G						PASS	.	T	,	557,3849	237.7+/-249.4	40,477,1686	77.0	75.0	76.0		942,942	-4.4	0.0	6	dbSNP_119	76	1977,6615	342.4+/-324.5	215,1547,2534	no	coding-synonymous,coding-synonymous	AKD1	NM_001145128.2,NM_145025.4	,	255,2024,4220	CC,CT,TT		23.0098,12.6419,19.4953	,	314/1912,314/422	109954518	2534,10464	2203	4296	6499	SO:0001819	synonymous_variant	221264	exon11			ACGAAATAGCTCA	AK131244, BC146443, BC087860	CCDS5077.1, CCDS55048.1	6q21	2013-04-29	2013-04-29	2013-04-29			2.7.4.3		33814	protein-coding gene	gene with protein product		615358	"""chromosome 6 open reading frame 224"", ""adenylate kinase domain containing 2"", ""chromosome 6 open reading frame 199"", ""adenylate kinase domain containing 1"""	C6orf224, AKD2, C6orf199, AKD1		23416111	Standard	NM_145025		Approved	FLJ42177, FLJ25791, dJ70A9.1, MGC26954		Q5TCS8		ENST00000424296.2:c.942A>G	6.37:g.109954518T>C		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	38	38	1	NM_145025	A6NL75|B2RDJ0|B6ZDM7|Q3MIS4|Q5I0W8|Q6ZNF1|Q6ZVR7|Q8N7C6|Q8WW00|Q96NF4	Silent	SNP	ENST00000424296.2	37	CCDS55048.1	477	0.2184065934065934	52	0.10569105691056911	94	0.2596685082872928	163	0.28496503496503495	168	0.22163588390501318	T	3.665	-0.068715	0.07228	0.126419	0.230098	ENSG00000155085	ENST00000524674	.	.	.	5.76	-4.37	0.03633	.	.	.	.	.	T	0.06600	0.0169	.	.	.	0.19300	P	0.999979151	.	.	.	.	.	.	T	0.34179	-0.9839	3	.	.	.	-2.1874	2.143	0.03779	0.1254:0.1704:0.2628:0.4414	rs9374111;rs56417458;rs9374111	.	.	.	C	169	.	.	Y	-	2	0	AKD1	110061211	0.003000	0.15002	0.001000	0.08648	0.003000	0.03518	-0.982000	0.03762	-0.398000	0.07679	-1.064000	0.02280	TAT	C|0.211;N|0.000	0.211	strong		0.313	AK9-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001145128	
ANAPC1	64682	hgsc.bcm.edu	37	2	112592265	112592265	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:112592265T>C	ENST00000341068.3	-	19	3072	c.2300A>G	c.(2299-2301)cAc>cGc	p.H767R		NM_022662.3	NP_073153.1	Q9H1A4	APC1_HUMAN	anaphase promoting complex subunit 1	767					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)				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						ATACACAAGGTGAAGAACGAA	0.378																																					p.H767R		Atlas-SNP	.											ANAPC1,NS,carcinoma,0,1	ANAPC1	116	1	0			c.A2300G						scavenged	.						83.0	80.0	81.0					2																	112592265		2203	4300	6503	SO:0001583	missense	64682	exon19			ACAAGGTGAAGAA	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.2300A>G	2.37:g.112592265T>C	ENSP00000339109:p.His767Arg	Somatic	391	0	0		WXS	Illumina HiSeq	Phase_I	426	54	0.126761	NM_022662	Q2M3H8|Q9BSE6|Q9H8D0	Missense_Mutation	SNP	ENST00000341068.3	37	CCDS2093.1	.	.	.	.	.	.	.	.	.	.	T	23.1	4.370389	0.82573	.	.	ENSG00000153107	ENST00000341068	T	0.30448	1.53	5.16	5.16	0.70880	.	0.000000	0.46758	U	0.000266	T	0.60907	0.2305	M	0.87097	2.86	0.80722	D	1	D	0.71674	0.998	D	0.76071	0.987	T	0.68949	-0.5274	10	0.72032	D	0.01	-17.8092	15.0301	0.71698	0.0:0.0:0.0:1.0	.	767	Q9H1A4	APC1_HUMAN	R	767	ENSP00000339109:H767R	ENSP00000339109:H767R	H	-	2	0	ANAPC1	112308736	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	7.495000	0.81514	1.962000	0.57031	0.456000	0.33151	CAC	CGAAGAACG|0.500;TGAAGAACA|0.500	.	alt		0.378	ANAPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254045.2	NM_022662	
NQO2	4835	hgsc.bcm.edu	37	6	3017138	3017138	+	Silent	SNP	C	C	T	rs1130428	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:3017138C>T	ENST00000338130.2	+	9	1150	c.438C>T	c.(436-438)tcC>tcT	p.S146S	NQO2_ENST00000380455.4_Silent_p.S146S|NQO2_ENST00000380454.4_Silent_p.S108S|NQO2_ENST00000380441.1_Silent_p.S108S|NQO2_ENST00000380430.1_Silent_p.S146S			P16083	NQO2_HUMAN	NAD(P)H dehydrogenase, quinone 2	146					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)	CGCTCCTTTCCGTAACCACGG	0.552													c|||	155	0.0309505	0.0613	0.0288	5008	,	,		19744	0.0		0.0497	False		,,,				2504	0.0041				p.S146S		Atlas-SNP	.											.	NQO2	21	.	0			c.C438T						PASS	.	T		239,4167	140.4+/-175.9	5,229,1969	130.0	99.0	110.0		438	-10.8	0.0	6	dbSNP_86	110	324,8276	113.9+/-173.9	11,302,3987	no	coding-synonymous	NQO2	NM_000904.3		16,531,5956	TT,TC,CC		3.7674,5.4244,4.3288		146/232	3017138	563,12443	2203	4300	6503	SO:0001819	synonymous_variant	4835	exon6			CCTTTCCGTAACC	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.438C>T	6.37:g.3017138C>T		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	81	30	0.37037	NM_000904	B2R492|Q5TD04	Silent	SNP	ENST00000338130.2	37	CCDS4481.1																																																																																			C|0.960;T|0.040	0.040	strong		0.552	NQO2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039651.1		
OSBPL10	114884	hgsc.bcm.edu	37	3	32022622	32022622	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:32022622C>T	ENST00000396556.2	-	1	172	c.50G>A	c.(49-51)aGc>aAc	p.S17N	OSBPL10_ENST00000438237.2_Missense_Mutation_p.S17N|ZNF860_ENST00000360311.4_5'Flank	NM_017784.4	NP_060254.2	Q9BXB5	OSB10_HUMAN	oxysterol binding protein-like 10	17					lipid transport (GO:0006869)		cholesterol binding (GO:0015485)			breast(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(15)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	34				STAD - Stomach adenocarcinoma(1;0.00406)		gctgcggctgctgctgttgct	0.791																																					p.S17N		Atlas-SNP	.											.	OSBPL10	160	.	0			c.G50A						PASS	.						2.0	3.0	2.0					3																	32022622		662	1473	2135	SO:0001583	missense	114884	exon1			CGGCTGCTGCTGT	AF392451	CCDS2651.1, CCDS54559.1	3p23	2013-01-10			ENSG00000144645	ENSG00000144645		"""Oxysterol binding proteins"", ""Pleckstrin homology (PH) domain containing"""	16395	protein-coding gene	gene with protein product		606738					Standard	NM_001174060		Approved		uc021wuu.1	Q9BXB5	OTTHUMG00000130672	ENST00000396556.2:c.50G>A	3.37:g.32022622C>T	ENSP00000379804:p.Ser17Asn	Somatic	8	0	0		WXS	Illumina HiSeq	Phase_I	21	12	0.571429	NM_017784	B4E212|Q9BTU5	Missense_Mutation	SNP	ENST00000396556.2	37	CCDS2651.1	.	.	.	.	.	.	.	.	.	.	C	13.12	2.141933	0.37825	.	.	ENSG00000144645	ENST00000396556;ENST00000438237	T;T	0.26518	1.73;2.07	3.91	3.91	0.45181	.	2.901820	0.03061	N	0.155841	T	0.22898	0.0553	N	0.19112	0.55	0.26378	N	0.976786	B;B	0.27498	0.18;0.18	B;B	0.23716	0.048;0.048	T	0.23119	-1.0197	10	0.51188	T	0.08	.	13.8256	0.63348	0.0:1.0:0.0:0.0	.	17;17	B4E212;Q9BXB5	.;OSB10_HUMAN	N	17	ENSP00000379804:S17N;ENSP00000406124:S17N	ENSP00000379804:S17N	S	-	2	0	OSBPL10	31997626	1.000000	0.71417	1.000000	0.80357	0.824000	0.46624	2.460000	0.45031	2.196000	0.70406	0.298000	0.19748	AGC	.	.	none		0.791	OSBPL10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253165.2		
ZNF248	57209	hgsc.bcm.edu	37	10	38121631	38121631	+	Missense_Mutation	SNP	T	T	C	rs11011379	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:38121631T>C	ENST00000395867.3	-	6	1202	c.652A>G	c.(652-654)Aaa>Gaa	p.K218E	ZNF248_ENST00000374648.3_Intron|AL135791.1_ENST00000583461.1_RNA|ZNF248_ENST00000357328.4_Missense_Mutation_p.K218E|ZNF248_ENST00000494133.1_Intron	NM_001267605.1|NM_001267606.1|NM_001267607.1|NM_021045.2	NP_001254534.1|NP_001254535.1|NP_001254536.1|NP_066383.1	Q8NDW4	ZN248_HUMAN	zinc finger protein 248	218			K -> E (in dbSNP:rs11011379).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|endometrium(2)|large_intestine(5)|lung(9)|ovary(2)|urinary_tract(1)	20						TGTCCATTTTTACTATACTCA	0.353													T|||	38	0.00758786	0.0023	0.0202	5008	,	,		18155	0.0		0.0149	False		,,,				2504	0.0061				p.K218E		Atlas-SNP	.											.	ZNF248	61	.	0			c.A652G						PASS	.	T	GLU/LYS	17,4385	20.2+/-43.8	0,17,2184	53.0	53.0	53.0		652	1.3	0.8	10	dbSNP_120	53	185,8411	78.4+/-141.0	0,185,4113	yes	missense	ZNF248	NM_021045.1	56	0,202,6297	CC,CT,TT		2.1522,0.3862,1.5541	benign	218/580	38121631	202,12796	2201	4298	6499	SO:0001583	missense	57209	exon6			CATTTTTACTATA	AJ491695	CCDS7194.1, CCDS58077.1, CCDS73087.1	10p11.21	2013-01-08			ENSG00000198105	ENSG00000198105		"""Zinc fingers, C2H2-type"", ""-"""	13041	protein-coding gene	gene with protein product						12566394	Standard	NM_021045		Approved	bA162G10.3	uc010qeu.2	Q8NDW4	OTTHUMG00000017980	ENST00000395867.3:c.652A>G	10.37:g.38121631T>C	ENSP00000379208:p.Lys218Glu	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	56	29	0.517857	NM_001267597	Q8NDV8|Q9UMP3	Missense_Mutation	SNP	ENST00000395867.3	37	CCDS7194.1	19	0.0086996336996337	1	0.0020325203252032522	7	0.019337016574585635	0	0.0	11	0.014511873350923483	T	0.003	-2.502296	0.00157	0.003862	0.021522	ENSG00000198105	ENST00000395867;ENST00000357328	T;T	0.04194	3.68;3.68	4.3	1.32	0.21799	.	0.331549	0.22037	N	0.065510	T	0.00496	0.0016	N	0.00347	-1.61	0.21719	N	0.999574	B	0.02656	0.0	B	0.01281	0.0	T	0.44937	-0.9295	10	0.02654	T	1	.	4.193	0.10430	0.0:0.5858:0.1909:0.2233	rs11011379;rs17662331;rs11011379	218	Q8NDW4	ZN248_HUMAN	E	218	ENSP00000379208:K218E;ENSP00000349882:K218E	ENSP00000349882:K218E	K	-	1	0	ZNF248	38161637	0.935000	0.31712	0.812000	0.32479	0.150000	0.21749	-0.179000	0.09768	0.165000	0.19558	-0.468000	0.05107	AAA	T|0.986;C|0.014	0.014	strong		0.353	ZNF248-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047609.1	NM_021045	
NSMCE1	197370	hgsc.bcm.edu	37	16	27246617	27246617	+	Missense_Mutation	SNP	T	T	C	rs17856580	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:27246617T>C	ENST00000361439.4	-	3	239	c.140A>G	c.(139-141)aAt>aGt	p.N47S		NM_145080.3	NP_659547.2	Q8WV22	NSE1_HUMAN	non-SMC element 1 homolog (S. cerevisiae)	47	Interaction with NDNL2.		N -> S (in dbSNP:rs17856580). {ECO:0000269|PubMed:15489334}.		DNA recombination (GO:0006310)|DNA repair (GO:0006281)|intracellular signal transduction (GO:0035556)|positive regulation of response to DNA damage stimulus (GO:2001022)|protein ubiquitination (GO:0016567)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|Smc5-Smc6 complex (GO:0030915)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(2)|lung(3)	7						TACGGTGGCATTGCCTGGAAA	0.453											OREG0023693	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	T|||	1303	0.260184	0.1566	0.353	5008	,	,		4947	0.4256		0.2038	False		,,,				2504	0.2219				p.N47S		Atlas-SNP	.											.	NSMCE1	28	.	0			c.A140G						PASS	.	T	SER/ASN	619,3371		49,521,1425	80.0	80.0	80.0		140	0.6	0.8	16	dbSNP_123	80	1476,6884		127,1222,2831	yes	missense	NSMCE1	NM_145080.3	46	176,1743,4256	CC,CT,TT		17.6555,15.5138,16.9636	benign	47/267	27246617	2095,10255	1995	4180	6175	SO:0001583	missense	197370	exon3			GTGGCATTGCCTG	AF161451	CCDS10628.2	16p12.1	2010-03-23	2006-07-05		ENSG00000169189	ENSG00000169189			29897	protein-coding gene	gene with protein product						11927594	Standard	XM_005255163		Approved	NSE1	uc002doi.1	Q8WV22	OTTHUMG00000131674	ENST00000361439.4:c.140A>G	16.37:g.27246617T>C	ENSP00000355077:p.Asn47Ser	Somatic	49	0	0	792	WXS	Illumina HiSeq	Phase_I	46	25	0.543478	NM_145080	D3DWF6|Q9P045|Q9P049	Missense_Mutation	SNP	ENST00000361439.4	37	CCDS10628.2	598	0.27380952380952384	77	0.1565040650406504	104	0.287292817679558	248	0.43356643356643354	169	0.22295514511873352	T	11.20	1.567858	0.28003	0.155138	0.176555	ENSG00000169189	ENST00000361439	T	0.29655	1.56	5.4	0.561	0.17285	.	0.477019	0.25520	N	0.030110	T	0.00012	0.0000	N	0.05230	-0.09	0.39053	P	0.03963799999999995	B	0.09022	0.002	B	0.06405	0.002	T	0.46275	-0.9203	9	0.07990	T	0.79	.	5.6558	0.17642	0.0:0.1506:0.2878:0.5616	rs17856580;rs17856580	47	Q8WV22	NSE1_HUMAN	S	47	ENSP00000355077:N47S	ENSP00000355077:N47S	N	-	2	0	NSMCE1	27154118	0.001000	0.12720	0.798000	0.32154	0.800000	0.45204	-1.276000	0.02815	-0.108000	0.12066	0.519000	0.50382	AAT	T|0.754;C|0.246	0.246	strong		0.453	NSMCE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254577.3	NM_145080	
RAI14	26064	hgsc.bcm.edu	37	5	34811131	34811131	+	Silent	SNP	G	G	A	rs35607113	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:34811131G>A	ENST00000265109.3	+	8	752	c.465G>A	c.(463-465)ccG>ccA	p.P155P	RAI14_ENST00000515799.1_Silent_p.P158P|RAI14_ENST00000512629.1_Silent_p.P155P|RAI14_ENST00000397449.1_Silent_p.P148P|RAI14_ENST00000506376.1_Silent_p.P147P|RAI14_ENST00000507276.1_3'UTR|RAI14_ENST00000503673.1_Silent_p.P155P|RAI14_ENST00000428746.2_Silent_p.P155P	NM_001145522.1|NM_015577.2	NP_001138994.1|NP_056392.2	Q9P0K7	RAI14_HUMAN	retinoic acid induced 14	155						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)					GGAATATACCGCTGCTTCTTG	0.418													G|||	400	0.0798722	0.0091	0.1081	5008	,	,		20042	0.0109		0.162	False		,,,				2504	0.1421				p.P158P		Atlas-SNP	.											.	RAI14	100	.	0			c.G474A						PASS	.	G	,,,,,	148,4258	103.4+/-141.9	2,144,2057	290.0	282.0	285.0		465,465,465,441,474,465	-6.2	1.0	5	dbSNP_126	285	1652,6948	305.7+/-307.6	178,1296,2826	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	RAI14	NM_001145520.1,NM_001145521.1,NM_001145522.1,NM_001145523.1,NM_001145525.1,NM_015577.2	,,,,,	180,1440,4883	AA,AG,GG		19.2093,3.3591,13.8398	,,,,,	155/981,155/981,155/952,147/973,158/984,155/981	34811131	1800,11206	2203	4300	6503	SO:0001819	synonymous_variant	26064	exon10			TATACCGCTGCTT	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.465G>A	5.37:g.34811131G>A		Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	147	81	0.55102	NM_001145525	E9PED3|Q6V1W9|Q7Z5I4|Q7Z733|Q9P2L2|Q9Y3T5	Silent	SNP	ENST00000265109.3	37	CCDS34142.1																																																																																			G|0.872;A|0.128	0.128	strong		0.418	RAI14-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366786.1	NM_015577	
GOLGA6L6	727832	hgsc.bcm.edu	37	15	20740252	20740252	+	Nonsense_Mutation	SNP	C	C	A	rs199807662		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	6	0	0		WXS	Illumina HiSeq	Phase_I	33	27	0.818182	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	
TAF1L	138474	hgsc.bcm.edu	37	9	32631518	32631518	+	Missense_Mutation	SNP	C	C	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:32631518C>G	ENST00000242310.4	-	1	4149	c.4060G>C	c.(4060-4062)Gag>Cag	p.E1354Q	RP11-555J4.4_ENST00000430787.1_RNA	NM_153809.2	NP_722516.1	Q8IZX4	TAF1L_HUMAN	TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 210kDa-like	1354					DNA-templated transcription, initiation (GO:0006352)|histone acetylation (GO:0016573)|male meiosis (GO:0007140)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	transcription factor TFIID complex (GO:0005669)	DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|lysine-acetylated histone binding (GO:0070577)|protein serine/threonine kinase activity (GO:0004674)|TBP-class protein binding (GO:0017025)			breast(6)|central_nervous_system(4)|endometrium(14)|kidney(11)|large_intestine(32)|liver(2)|lung(68)|ovary(2)|pancreas(2)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(1)	159			LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.00301)		CTGCGAACCTCATGCACATTC	0.403																																					p.E1354Q		Atlas-SNP	.											.	TAF1L	382	.	0			c.G4060C						PASS	.						238.0	236.0	236.0					9																	32631518		2203	4300	6503	SO:0001583	missense	138474	exon1			GAACCTCATGCAC	AF390562	CCDS35003.1	9p12	2007-07-27	2007-07-27		ENSG00000122728	ENSG00000122728			18056	protein-coding gene	gene with protein product		607798	"""TAF1-like RNA polymerase II, TATA box binding protein (TBP)-associated factor, 210kDa"""			12217962	Standard	NM_153809		Approved		uc003zrg.1	Q8IZX4	OTTHUMG00000019747	ENST00000242310.4:c.4060G>C	9.37:g.32631518C>G	ENSP00000418379:p.Glu1354Gln	Somatic	433	1	0.00230947		WXS	Illumina HiSeq	Phase_I	338	86	0.254438	NM_153809	Q0VG57	Missense_Mutation	SNP	ENST00000242310.4	37	CCDS35003.1	.	.	.	.	.	.	.	.	.	.	C	14.20	2.465042	0.43839	.	.	ENSG00000122728	ENST00000242310	T	0.09163	3.01	0.479	0.479	0.16796	.	0.097387	0.64402	D	0.000001	T	0.13415	0.0325	L	0.47190	1.495	0.51233	D	0.999915	D	0.55605	0.972	P	0.52343	0.696	T	0.05716	-1.0868	10	0.40728	T	0.16	.	6.6915	0.23174	0.0:0.9998:0.0:2.0E-4	.	1354	Q8IZX4	TAF1L_HUMAN	Q	1354	ENSP00000418379:E1354Q	ENSP00000418379:E1354Q	E	-	1	0	TAF1L	32621518	1.000000	0.71417	0.942000	0.38095	0.559000	0.35586	4.785000	0.62418	0.507000	0.28148	0.195000	0.17529	GAG	.	.	none		0.403	TAF1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052012.2		
TMEM63A	9725	hgsc.bcm.edu	37	1	226055595	226055595	+	Silent	SNP	G	G	A	rs2292564	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	71	0	0		WXS	Illumina HiSeq	Phase_I	52	30	0.576923	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	
PDIA2	64714	hgsc.bcm.edu	37	16	334580	334580	+	Silent	SNP	G	G	C	rs432925	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:334580G>C	ENST00000219406.6	+	2	411	c.393G>C	c.(391-393)ccG>ccC	p.P131P	PDIA2_ENST00000404312.1_Silent_p.P131P	NM_006849.2	NP_006840.2	Q13087	PDIA2_HUMAN	protein disulfide isomerase family A, member 2	131	Thioredoxin 1. {ECO:0000255|PROSITE- ProRule:PRU00691}.				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)				GCACGCACCCGGAGGAGTACA	0.677													g|||	1234	0.246406	0.32	0.2089	5008	,	,		15702	0.119		0.2913	False		,,,				2504	0.2587				p.P131P		Atlas-SNP	.											.	PDIA2	51	.	0			c.G393C						PASS	.	G		1233,3005		191,851,1077	34.0	40.0	38.0		393	-8.9	0.4	16	dbSNP_80	38	2417,6025		353,1711,2157	no	coding-synonymous	PDIA2	NM_006849.2		544,2562,3234	CC,CG,GG		28.6307,29.0939,28.7855		131/526	334580	3650,9030	2119	4221	6340	SO:0001819	synonymous_variant	64714	exon2			GCACCCGGAGGAG	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.393G>C	16.37:g.334580G>C		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	75	52	0.693333	NM_006849	A6ZJ64|B4DI27|Q2WGM4|Q4TT67|Q6B010|Q96KJ6|Q9BW95	Silent	SNP	ENST00000219406.6	37	CCDS42089.1	508	0.2326007326007326	142	0.2886178861788618	81	0.22375690607734808	69	0.12062937062937062	216	0.2849604221635884	g	0.088	-1.171117	0.01660	0.290939	0.286307	ENSG00000185615	ENST00000456379	.	.	.	4.47	-8.93	0.00771	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.99999673342	.	.	.	.	.	.	T	0.20840	-1.0263	3	.	.	.	.	2.4162	0.04437	0.1433:0.1924:0.3952:0.2691	rs432925	.	.	.	P	128	.	.	R	+	2	0	PDIA2	274581	0.000000	0.05858	0.433000	0.26760	0.013000	0.08279	-1.350000	0.02624	-2.615000	0.00443	-1.077000	0.02231	CGG	G|0.756;C|0.244	0.244	strong		0.677	PDIA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139315.3	NM_006849	
TNS1	7145	hgsc.bcm.edu	37	2	218712726	218712726	+	Silent	SNP	A	A	G	rs1364642	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:218712726A>G	ENST00000171887.4	-	17	2591	c.2139T>C	c.(2137-2139)aaT>aaC	p.N713N	TNS1_ENST00000419504.1_Silent_p.N713N|TNS1_ENST00000480665.1_5'Flank|TNS1_ENST00000430930.1_Silent_p.N713N	NM_022648.4	NP_072174.3	Q9HBL0	TENS1_HUMAN	tensin 1	713					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)		GCATCAGCATATTGAGTGTTT	0.632													G|||	2182	0.435703	0.6225	0.3156	5008	,	,		16530	0.3452		0.3499	False		,,,				2504	0.4499				p.N713N		Atlas-SNP	.											.	TNS1	251	.	0			c.T2139C						PASS	.	G		2481,1925	535.8+/-374.3	702,1077,424	44.0	48.0	47.0		2139	0.4	1.0	2	dbSNP_88	47	2697,5903	674.1+/-403.1	438,1821,2041	no	coding-synonymous	TNS1	NM_022648.4		1140,2898,2465	GG,GA,AA		31.3605,43.6904,39.8124		713/1736	218712726	5178,7828	2203	4300	6503	SO:0001819	synonymous_variant	7145	exon17			CAGCATATTGAGT	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.2139T>C	2.37:g.218712726A>G		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	89	42	0.47191	NM_022648	Q4ZG71|Q6IPI5	Silent	SNP	ENST00000171887.4	37	CCDS2407.1																																																																																			A|0.591;G|0.409	0.409	strong		0.632	TNS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256672.2	NM_022648	
SLC18A2	6571	hgsc.bcm.edu	37	10	119003564	119003564	+	Silent	SNP	T	T	G	rs363387	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:119003564T>G	ENST00000298472.5	+	3	347	c.204T>G	c.(202-204)acT>acG	p.T68T	RP11-501J20.5_ENST00000425264.1_RNA|SLC18A2_ENST00000497497.1_3'UTR	NM_003054.4	NP_003045.2	Q05940	VMAT2_HUMAN	solute carrier family 18 (vesicular monoamine transporter), member 2	68					aging (GO:0007568)|cellular response to ammonium ion (GO:0071242)|cellular response to drug (GO:0035690)|death (GO:0016265)|dopamine transport (GO:0015872)|endocytic recycling (GO:0032456)|glucose homeostasis (GO:0042593)|insulin secretion (GO:0030073)|locomotory behavior (GO:0007626)|monoamine transport (GO:0015844)|negative regulation of neurotransmitter transport (GO:0051589)|neurotransmitter loading into synaptic vesicle (GO:0098700)|neurotransmitter secretion (GO:0007269)|post-embryonic development (GO:0009791)|response to amphetamine (GO:0001975)|response to cocaine (GO:0042220)|response to corticosterone (GO:0051412)|response to herbicide (GO:0009635)|response to starvation (GO:0042594)|response to zinc ion (GO:0010043)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	clathrin-sculpted monoamine transport vesicle membrane (GO:0070083)|dense core granule (GO:0031045)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)|synaptic vesicle membrane (GO:0030672)|terminal bouton (GO:0043195)	amine transmembrane transporter activity (GO:0005275)|drug binding (GO:0008144)|monoamine transmembrane transporter activity (GO:0008504)|serotonin transmembrane transporter activity (GO:0015222)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(16)	29		Colorectal(252;0.19)		all cancers(201;0.029)	Amphetamine(DB00182)|Benzphetamine(DB00865)|Deserpidine(DB01089)|Dextroamphetamine(DB01576)|Ephedra(DB01363)|Ephedrine(DB01364)|Isometheptene(DB06706)|Methamphetamine(DB01577)|Norepinephrine(DB00368)|Propylhexedrine(DB06714)|Reserpine(DB00206)|Tetrabenazine(DB04844)	CAGTGCACACTGCCTCCATCT	0.493													G|||	421	0.0840655	0.0772	0.1902	5008	,	,		20544	0.1151		0.0447	False		,,,				2504	0.0266				p.T68T		Atlas-SNP	.											.	SLC18A2	58	.	0			c.T204G						PASS	.	G		289,4117	800.0+/-415.5	11,267,1925	98.0	84.0	89.0		204	-11.6	0.0	10	dbSNP_79	89	386,8214	802.3+/-407.3	14,358,3928	no	coding-synonymous	SLC18A2	NM_003054.4		25,625,5853	GG,GT,TT		4.4884,6.5592,5.1899		68/515	119003564	675,12331	2203	4300	6503	SO:0001819	synonymous_variant	6571	exon3			GCACACTGCCTCC	L14269	CCDS7599.1	10q25	2013-07-18	2013-07-18		ENSG00000165646	ENSG00000165646		"""Solute carriers"""	10935	protein-coding gene	gene with protein product		193001		VMAT2			Standard	NM_003054		Approved	SVMT, SVAT	uc001ldd.2	Q05940	OTTHUMG00000019121	ENST00000298472.5:c.204T>G	10.37:g.119003564T>G		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	66	41	0.621212	NM_003054	B2RC96|D3DRC4|Q15876|Q4G147|Q5VW49|Q9H3P6	Silent	SNP	ENST00000298472.5	37	CCDS7599.1																																																																																			T|0.932;G|0.068	0.068	strong		0.493	SLC18A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050563.1	NM_003054	
NEFH	4744	hgsc.bcm.edu	37	22	29886043	29886043	+	Missense_Mutation	SNP	A	A	C	rs165602	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:29886043A>C	ENST00000310624.6	+	4	2447	c.2414A>C	c.(2413-2415)gAg>gCg	p.E805A		NM_021076.3	NP_066554.2	P12036	NFH_HUMAN	neurofilament, heavy polypeptide	811	30 X 6 AA repeats of K-S-P-[AEPV]-[EAK]- [AEVK].|Tail.				axon development (GO:0061564)|axonogenesis (GO:0007409)|cell death (GO:0008219)|cell projection assembly (GO:0030031)|microtubule cytoskeleton organization (GO:0000226)|neurofilament bundle assembly (GO:0033693)|peripheral nervous system neuron axonogenesis (GO:0048936)|regulation of organelle transport along microtubule (GO:1902513)	axon (GO:0030424)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|neurofibrillary tangle (GO:0097418)|neurofilament (GO:0005883)	dynein binding (GO:0045502)|kinesin binding (GO:0019894)|microtubule binding (GO:0008017)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(12)|ovary(2)|skin(3)	30						CCCCTGAAGGAGGATGCCAAG	0.552													A|||	600	0.119808	0.1135	0.1297	5008	,	,		18679	0.0526		0.1421	False		,,,				2504	0.1677				p.E805A		Atlas-SNP	.											.	NEFH	178	.	0			c.A2414C						PASS	.	A	ALA/GLU	567,3839	241.5+/-251.9	42,483,1678	41.0	44.0	43.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	2414	5.4	1.0	22	dbSNP_79	43	1313,7285	247.6+/-275.6	86,1141,3072	yes	missense	NEFH	NM_021076.3	107	128,1624,4750	CC,CA,AA		15.271,12.8688,14.4571	probably-damaging	805/1021	29886043	1880,11124	2203	4299	6502	SO:0001583	missense	4744	exon4			TGAAGGAGGATGC		CCDS13858.1	22q12.2	2013-01-16	2008-09-19		ENSG00000100285	ENSG00000100285		"""Intermediate filaments type IV"""	7737	protein-coding gene	gene with protein product		162230	"""neurofilament, heavy polypeptide 200kDa"""				Standard	NM_021076		Approved		uc003afo.3	P12036	OTTHUMG00000151155	ENST00000310624.6:c.2414A>C	22.37:g.29886043A>C	ENSP00000311997:p.Glu805Ala	Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	43	20	0.465116	NM_021076	B4DYY4|Q96HF8|Q9UJS7|Q9UQ14	Missense_Mutation	SNP	ENST00000310624.6	37	CCDS13858.1	252	0.11538461538461539	59	0.11991869918699187	54	0.14917127071823205	25	0.043706293706293704	114	0.1503957783641161	A	16.98	3.271851	0.59649	0.128688	0.15271	ENSG00000100285	ENST00000328842;ENST00000310624	D	0.86164	-2.08	5.42	5.42	0.78866	.	0.129681	0.34932	N	0.003568	T	0.03651	0.0104	L	0.55834	1.745	0.09310	P	0.999999213389	D	0.56035	0.974	P	0.50352	0.638	T	0.52208	-0.8606	9	0.87932	D	0	.	15.4256	0.75048	1.0:0.0:0.0:0.0	rs165602;rs695847;rs16987680;rs52801416;rs58898655;rs165602	811	P12036	NFH_HUMAN	A	756;805	ENSP00000311997:E805A	ENSP00000311997:E805A	E	+	2	0	NEFH	28216043	0.995000	0.38212	0.988000	0.46212	0.657000	0.38888	3.316000	0.51960	2.190000	0.69967	0.533000	0.62120	GAG	A|0.871;C|0.129	0.129	strong		0.552	NEFH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321553.2	NM_021076	
PCDHB8	56128	hgsc.bcm.edu	37	5	140559914	140559914	+	Missense_Mutation	SNP	T	T	C	rs2740583	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:140559914T>C	ENST00000239444.2	+	1	2544	c.2299T>C	c.(2299-2301)Ttc>Ctc	p.F767L	PCDHB16_ENST00000361016.2_5'Flank	NM_019120.3	NP_061993.2	Q9UN66	PCDB8_HUMAN	protocadherin beta 8	767			F -> L (in dbSNP:rs2740583). {ECO:0000269|PubMed:11322959, ECO:0000269|PubMed:15489334}.		homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(2)|breast(1)|cervix(2)|endometrium(5)|kidney(6)|large_intestine(14)|liver(1)|lung(38)|prostate(6)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	83			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			TGAGTTCCAGTTCCTGAAACC	0.502													T|||	973	0.194289	0.0197	0.2939	5008	,	,		16792	0.1171		0.3449	False		,,,				2504	0.2843				p.F767L		Atlas-SNP	.											.	PCDHB8	199	.	0			c.T2299C						PASS	.	T	LEU/PHE	301,4105	162.9+/-194.8	17,267,1919	99.0	102.0	101.0		2299	4.5	0.3	5	dbSNP_100	101	2995,5605	464.0+/-366.1	532,1931,1837	yes	missense	PCDHB8	NM_019120.3	22	549,2198,3756	CC,CT,TT		34.8256,6.8316,25.3421	benign	767/802	140559914	3296,9710	2203	4300	6503	SO:0001583	missense	56128	exon1			TTCCAGTTCCTGA	AF152501	CCDS4250.1	5q31	2010-01-26			ENSG00000120322	ENSG00000120322		"""Cadherins / Protocadherins : Clustered"""	8693	other	protocadherin		606334				10380929	Standard	NM_019120		Approved	PCDH-BETA8, PCDH3I	uc011dai.2	Q9UN66	OTTHUMG00000129621	ENST00000239444.2:c.2299T>C	5.37:g.140559914T>C	ENSP00000239444:p.Phe767Leu	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	87	46	0.528736	NM_019120	B9EGV1	Missense_Mutation	SNP	ENST00000239444.2	37	CCDS4250.1	467	0.21382783882783882	13	0.026422764227642278	121	0.3342541436464088	71	0.12412587412587413	262	0.34564643799472294	T	22.2	4.258002	0.80246	0.068316	0.348256	ENSG00000120322	ENST00000239444	T	0.18657	2.2	4.53	4.53	0.55603	.	.	.	.	.	T	0.00012	0.0000	M	0.88105	2.93	0.36688	P	0.12056599999999995	B	0.24132	0.098	B	0.29942	0.109	T	0.23190	-1.0195	8	0.66056	D	0.02	.	13.5476	0.61713	0.0:0.0:0.0:1.0	rs2740583;rs17697117;rs17844510;rs61661593;rs2740583	767	Q9UN66	PCDB8_HUMAN	L	767	ENSP00000239444:F767L	ENSP00000239444:F767L	F	+	1	0	PCDHB8	140540098	0.998000	0.40836	0.332000	0.25469	0.020000	0.10135	3.378000	0.52432	1.673000	0.50895	0.455000	0.32223	TTC	A|0.000;C|0.223;N|0.000;T|0.776	0.223	strong		0.502	PCDHB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251816.2	NM_019120	
MLC1	23209	hgsc.bcm.edu	37	22	50515843	50515843	+	Missense_Mutation	SNP	C	C	A	rs6010260	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:50515843C>A	ENST00000311597.5	-	6	1118	c.512G>T	c.(511-513)tGc>tTc	p.C171F	MLC1_ENST00000535444.1_Missense_Mutation_p.C92F|MLC1_ENST00000450140.2_Missense_Mutation_p.C119F|MLC1_ENST00000538737.1_Missense_Mutation_p.C137F|MLC1_ENST00000431262.2_Missense_Mutation_p.C141F|MLC1_ENST00000395876.2_Missense_Mutation_p.C171F	NM_015166.3	NP_055981.1	Q15049	MLC1_HUMAN	megalencephalic leukoencephalopathy with subcortical cysts 1	171			C -> F (in dbSNP:rs6010260).		caveolin-mediated endocytosis (GO:0072584)|cellular response to cholesterol (GO:0071397)|ion transport (GO:0006811)|positive regulation of intracellular transport (GO:0032388)|protein oligomerization (GO:0051259)|regulation of response to osmotic stress (GO:0047484)|transport (GO:0006810)|vesicle-mediated transport (GO:0016192)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|caveola (GO:0005901)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	protein complex binding (GO:0032403)|protein transporter activity (GO:0008565)|transporter activity (GO:0005215)			endometrium(1)|kidney(1)|large_intestine(5)|lung(7)|pancreas(1)|prostate(3)	18		all_cancers(38;7.69e-11)|all_epithelial(38;9.52e-10)|all_lung(38;3.67e-05)|Breast(42;0.000776)|Lung NSC(38;0.000946)|Ovarian(80;0.0365)|Lung SC(80;0.113)		READ - Rectum adenocarcinoma(2;0.000669)|Colorectal(2;0.00242)|LUAD - Lung adenocarcinoma(64;0.0695)|BRCA - Breast invasive adenocarcinoma(115;0.216)		CTTTTTCTTGCAGTCCTCCTC	0.632													C|||	609	0.121605	0.0514	0.1571	5008	,	,		17517	0.0913		0.1153	False		,,,				2504	0.229				p.C171F		Atlas-SNP	.											.	MLC1	48	.	0			c.G512T						PASS	.	C	PHE/CYS,PHE/CYS	312,4094	166.2+/-197.5	14,284,1905	79.0	59.0	66.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	512,512	3.3	0.2	22	dbSNP_114	66	1019,7581	218.4+/-256.8	56,907,3337	yes	missense,missense	MLC1	NM_015166.3,NM_139202.2	205,205	70,1191,5242	AA,AC,CC		11.8488,7.0813,10.2337	possibly-damaging,possibly-damaging	171/378,171/378	50515843	1331,11675	2203	4300	6503	SO:0001583	missense	23209	exon6			TTCTTGCAGTCCT	D25217	CCDS14083.1	22q13.33	2007-03-20			ENSG00000100427	ENSG00000100427			17082	protein-coding gene	gene with protein product		605908				7584026, 7584028	Standard	XR_430476		Approved	MLC, KIAA0027, LVM, VL	uc003bjg.1	Q15049	OTTHUMG00000150236	ENST00000311597.5:c.512G>T	22.37:g.50515843C>A	ENSP00000310375:p.Cys171Phe	Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	134	63	0.470149	NM_015166	B3KW61|B7Z659|Q5JZ83|Q8TAG4|Q96RP5|Q9UGY8	Missense_Mutation	SNP	ENST00000311597.5	37	CCDS14083.1	220	0.10073260073260074	32	0.06504065040650407	49	0.13535911602209943	55	0.09615384615384616	84	0.11081794195250659	C	13.23	2.175120	0.38413	0.070813	0.118488	ENSG00000100427	ENST00000395876;ENST00000311597;ENST00000538737;ENST00000431262;ENST00000535444;ENST00000450140;ENST00000442311	D;D;D;D;D;D;D	0.87412	-2.25;-2.25;-2.25;-2.25;-2.25;-2.25;-2.25	4.38	3.27	0.37495	.	0.197522	0.56097	D	0.000035	T	0.02727	0.0082	L	0.51422	1.61	0.09310	P	0.999999533183	B;B;B;B	0.30439	0.279;0.178;0.218;0.178	B;B;B;B	0.30495	0.116;0.116;0.116;0.116	T	0.60321	-0.7286	9	0.59425	D	0.04	-25.8857	10.5524	0.45097	0.1929:0.8071:0.0:0.0	rs6010260;rs52803331;rs6010260	137;141;119;171	F5H1B9;B7Z659;B7Z1X1;Q15049	.;.;.;MLC1_HUMAN	F	171;171;137;141;92;119;141	ENSP00000379216:C171F;ENSP00000310375:C171F;ENSP00000445805:C137F;ENSP00000415877:C141F;ENSP00000438910:C92F;ENSP00000412448:C119F;ENSP00000401385:C141F	ENSP00000310375:C171F	C	-	2	0	MLC1	48857970	0.967000	0.33354	0.237000	0.24090	0.736000	0.42039	2.112000	0.41892	2.124000	0.65301	0.655000	0.94253	TGC	C|0.898;A|0.102	0.102	strong		0.632	MLC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316979.2	NM_015166	
ARID4B	51742	hgsc.bcm.edu	37	1	235416122	235416122	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:235416122A>G	ENST00000264183.3	-	6	774	c.277T>C	c.(277-279)Ttt>Ctt	p.F93L	ARID4B_ENST00000366603.2_Missense_Mutation_p.F93L|ARID4B_ENST00000349213.3_Missense_Mutation_p.F93L	NM_016374.5	NP_057458.4	Q4LE39	ARI4B_HUMAN	AT rich interactive domain 4B (RBP1-like)	93					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)			CCGTCATCAAAAACTATGAGA	0.373																																					p.F93L		Atlas-SNP	.											.	ARID4B	142	.	0			c.T277C						PASS	.						63.0	63.0	63.0					1																	235416122		2203	4300	6503	SO:0001583	missense	51742	exon6			CATCAAAAACTAT	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.277T>C	1.37:g.235416122A>G	ENSP00000264183:p.Phe93Leu	Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	172	36	0.209302	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	.	.	.	.	.	.	.	.	.	.	A	32	5.147074	0.94603	.	.	ENSG00000054267	ENST00000391856;ENST00000349213;ENST00000366603;ENST00000264183;ENST00000439834;ENST00000418304	T;T;T;T	0.64618	-0.11;-0.11;-0.11;-0.11	5.73	5.73	0.89815	Tudor domain (1);	0.000000	0.85682	D	0.000000	T	0.80773	0.4687	M	0.83603	2.65	0.80722	D	1	D;D;D;D	0.71674	0.974;0.99;0.998;0.982	D;D;D;D	0.76071	0.953;0.979;0.987;0.952	D	0.83844	0.0259	10	0.87932	D	0	-14.2235	15.7063	0.77583	1.0:0.0:0.0:0.0	.	93;93;93;93	F8WB31;Q4LE39-3;Q4LE39-2;Q4LE39	.;.;.;ARI4B_HUMAN	L	93	ENSP00000264184:F93L;ENSP00000355562:F93L;ENSP00000264183:F93L;ENSP00000391497:F93L	ENSP00000264183:F93L	F	-	1	0	ARID4B	233482745	1.000000	0.71417	1.000000	0.80357	0.760000	0.43138	8.951000	0.93025	2.197000	0.70478	0.533000	0.62120	TTT	.	.	none		0.373	ARID4B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095566.3	NM_016374	
ZNF623	9831	hgsc.bcm.edu	37	8	144733176	144733176	+	Silent	SNP	C	C	T	rs141224385	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:144733176C>T	ENST00000501748.2	+	1	1223	c.1134C>T	c.(1132-1134)aaC>aaT	p.N378N	ZNF623_ENST00000526926.1_Silent_p.N338N|ZNF623_ENST00000458270.2_Silent_p.N338N	NM_014789.3	NP_055604	O75123	ZN623_HUMAN	zinc finger protein 623	378					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|kidney(3)|large_intestine(6)|lung(11)|prostate(1)|stomach(1)|urinary_tract(3)	27	all_cancers(97;3.74e-11)|all_epithelial(106;2.62e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;5.28e-40)|all cancers(56;5.23e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.146)			ATGAATGTAACGAGTGTGGGA	0.453													C|||	3	0.000599042	0.0	0.0014	5008	,	,		21487	0.0		0.0	False		,,,				2504	0.002				p.N378N		Atlas-SNP	.											ZNF623,NS,carcinoma,0,1	ZNF623	63	1	0			c.C1134T						scavenged	.	C	,	1,4405	2.1+/-5.4	0,1,2202	71.0	67.0	69.0		1014,1134	-8.1	0.0	8	dbSNP_134	69	13,8587	9.1+/-34.3	0,13,4287	no	coding-synonymous,coding-synonymous	ZNF623	NM_001082480.1,NM_014789.3	,	0,14,6489	TT,TC,CC		0.1512,0.0227,0.1076	,	338/497,378/537	144733176	14,12992	2203	4300	6503	SO:0001819	synonymous_variant	9831	exon1			ATGTAACGAGTGT	AB014528	CCDS34957.1, CCDS47931.1	8q24.3	2013-01-08				ENSG00000183309		"""Zinc fingers, C2H2-type"""	29084	protein-coding gene	gene with protein product						9734811	Standard	NM_014789		Approved	KIAA0628	uc003yzd.2	O75123		ENST00000501748.2:c.1134C>T	8.37:g.144733176C>T		Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	35	5	0.142857	NM_014789	A4FU80|B4DGP3|E7ENV5	Silent	SNP	ENST00000501748.2	37	CCDS34957.1																																																																																			C|0.999;T|0.001	0.001	strong		0.453	ZNF623-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382522.3	NM_014789	
ABCB8	11194	hgsc.bcm.edu	37	7	150739054	150739054	+	Missense_Mutation	SNP	G	G	A	rs56198402	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:150739054G>A	ENST00000297504.6	+	15	1741	c.1675G>A	c.(1675-1677)Gtc>Atc	p.V559I	ABCB8_ENST00000356058.4_3'UTR|ABCB8_ENST00000542328.1_Missense_Mutation_p.V454I|ABCB8_ENST00000498578.1_Missense_Mutation_p.V542I|ABCB8_ENST00000358849.4_Missense_Mutation_p.V542I			Q9NUT2	ABCB8_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 8	559	ABC transporter. {ECO:0000255|PROSITE- ProRule:PRU00434}.				transmembrane transport (GO:0055085)|transport (GO:0006810)	ATP-binding cassette (ABC) transporter complex (GO:0043190)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial envelope (GO:0005740)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(8)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	26			OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)	Doxorubicin(DB00997)	ACAGGAGCCCGTCCTGTTTGG	0.542													G|||	133	0.0265575	0.0008	0.0476	5008	,	,		19339	0.0208		0.0447	False		,,,				2504	0.0337				p.V542I		Atlas-SNP	.											.	ABCB8	65	.	0			c.G1624A						PASS	.	G	ILE/VAL	34,4372	37.6+/-69.7	0,34,2169	57.0	59.0	58.0		1624	3.8	1.0	7	dbSNP_129	58	348,8252	118.1+/-177.6	7,334,3959	yes	missense	ABCB8	NM_007188.3	29	7,368,6128	AA,AG,GG		4.0465,0.7717,2.9371	benign	542/719	150739054	382,12624	2203	4300	6503	SO:0001583	missense	11194	exon14			GAGCCCGTCCTGT	AF047690	CCDS5913.1, CCDS64798.1, CCDS64799.1, CCDS64800.1	7q36.1	2012-05-16			ENSG00000197150	ENSG00000197150		"""ATP binding cassette transporters / subfamily B"""	49	protein-coding gene	gene with protein product	"""mitochondrial ABC protein"""	605464				8894702	Standard	NM_001282291		Approved	EST328128, M-ABC1, MABC1	uc003wik.4	Q9NUT2	OTTHUMG00000158686	ENST00000297504.6:c.1675G>A	7.37:g.150739054G>A	ENSP00000297504:p.Val559Ile	Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	42	26	0.619048	NM_007188	A5D8W3|B2RBL8|B3KND2|B4DG02|G3XAP3|O95787|Q53GM0	Missense_Mutation	SNP	ENST00000297504.6	37		67	0.030677655677655676	0	0.0	17	0.04696132596685083	14	0.024475524475524476	36	0.047493403693931395	G	10.61	1.399063	0.25291	0.007717	0.040465	ENSG00000197150	ENST00000358849;ENST00000360651;ENST00000297504;ENST00000542328;ENST00000498578	D;D;D;D	0.90620	-2.7;-2.7;-2.7;-2.7	4.73	3.83	0.44106	ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.066008	0.64402	D	0.000013	T	0.45756	0.1358	N	0.10916	0.065	0.80722	D	1	B;B;B;B	0.24963	0.08;0.115;0.099;0.094	B;B;B;B	0.29716	0.047;0.106;0.079;0.079	T	0.65524	-0.6147	10	0.28530	T	0.3	-6.061	11.0243	0.47736	0.093:0.0:0.907:0.0	rs56198402;rs61274547;rs61734191	454;542;559;542	G3XAP3;A5D8W3;Q9NUT2;Q9NUT2-2	.;.;ABCB8_HUMAN;.	I	542;525;559;454;542	ENSP00000351717:V542I;ENSP00000297504:V559I;ENSP00000438776:V454I;ENSP00000418271:V542I	ENSP00000297504:V559I	V	+	1	0	ABCB8	150369987	1.000000	0.71417	1.000000	0.80357	0.487000	0.33371	5.412000	0.66392	2.456000	0.83038	0.462000	0.41574	GTC	G|0.969;A|0.031	0.031	strong		0.542	ABCB8-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351733.2	NM_007188	
RFX8	731220	hgsc.bcm.edu	37	2	102018908	102018908	+	Missense_Mutation	SNP	A	A	G	rs2175968|rs386648636	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:102018908A>G	ENST00000376826.2	-	14	1573	c.1574T>C	c.(1573-1575)aTg>aCg	p.M525T	RFX8_ENST00000428343.1_Missense_Mutation_p.M412T			Q6ZV50	RFX8_HUMAN	RFX family member 8, lacking RFX DNA binding domain	525				M -> T (in Ref. 1; BAG60794). {ECO:0000305}.	regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(1)|kidney(1)|stomach(1)	3						CTTATTGCCCATGGCAGTGTC	0.562													g|||	2266	0.452476	0.4569	0.3372	5008	,	,		18997	0.4861		0.5457	False		,,,				2504	0.3978				p.M412T		Atlas-SNP	.											.	RFX8	16	.	0			c.T1235C						PASS	.	G	THR/MET	647,737		156,335,201	34.0	34.0	34.0		1235	3.8	0.9	2	dbSNP_96	34	1692,1490		458,776,357	yes	missense	RFX8	NM_001145664.1	81	614,1111,558	GG,GA,AA		46.8259,46.7486,48.7735	benign	412/474	102018908	2339,2227	692	1591	2283	SO:0001583	missense	731220	exon11			TTGCCCATGGCAG	AK124976	CCDS46376.1	2q11.2	2012-11-15	2012-11-15		ENSG00000196460	ENSG00000196460			37253	protein-coding gene	gene with protein product			"""regulatory factor X, 8"", ""RFX gene family member 8, lacking RFX DNA binding domain"""				Standard	NM_001145664		Approved	FLJ42986	uc010yvx.1	Q6ZV50	OTTHUMG00000130693	ENST00000376826.2:c.1574T>C	2.37:g.102018908A>G	ENSP00000366022:p.Met525Thr	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	83	38	0.457831	NM_001145664	B4DQ32	Missense_Mutation	SNP	ENST00000376826.2	37		1054	0.4826007326007326	225	0.4573170731707317	134	0.3701657458563536	265	0.4632867132867133	430	0.5672823218997362	G	0.320	-0.962543	0.02249	0.467486	0.531741	ENSG00000196460	ENST00000376826;ENST00000428343	T;T	0.72505	-0.66;1.29	4.7	3.81	0.43845	.	0.000000	0.56097	N	0.000021	T	0.00012	0.0000	N	0.01168	-0.975	0.58432	P	5.000000000032756E-6	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.43196	-0.9406	9	0.02654	T	1	-9.8171	6.7948	0.23719	0.2067:0.0:0.7933:0.0	rs2175968;rs61081659;rs2175968	412;525	Q6ZV50-3;Q6ZV50	.;RFX8_HUMAN	T	525;412	ENSP00000366022:M525T;ENSP00000401536:M412T	ENSP00000366022:M525T	M	-	2	0	RFX8	101385340	0.815000	0.29118	0.854000	0.33618	0.936000	0.57629	0.966000	0.29331	1.354000	0.45846	-0.479000	0.04858	ATG	A|0.523;G|0.477	0.477	strong		0.562	RFX8-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001145664	
LCORL	254251	hgsc.bcm.edu	37	4	17886146	17886146	+	Missense_Mutation	SNP	A	A	G	rs17526944	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:17886146A>G	ENST00000382226.5	-	7	1114	c.1006T>C	c.(1006-1008)Tat>Cat	p.Y336H	LCORL_ENST00000539056.1_Intron|LCORL_ENST00000382224.1_Missense_Mutation_p.Y252H|LCORL_ENST00000326877.4_Intron	NM_001166139.1	NP_001159611.1	Q8N3X6	LCORL_HUMAN	ligand dependent nuclear receptor corepressor-like	336					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)			kidney(1)|large_intestine(1)|lung(1)|prostate(1)	4						CTGTCCTTATATGAATAACTA	0.388													A|||	139	0.0277556	0.0008	0.0245	5008	,	,		19488	0.0		0.0577	False		,,,				2504	0.0644				p.Y336H		Atlas-SNP	.											.	LCORL	60	.	0			c.T1006C						PASS	.	A	HIS/TYR,	14,1370		0,14,678	96.0	80.0	85.0		1006,	4.2	1.0	4	dbSNP_123	85	207,2973		8,191,1391	yes	missense,intron	LCORL	NM_001166139.1,NM_153686.7	83,	8,205,2069	GG,GA,AA		6.5094,1.0116,4.8422	,	336/603,	17886146	221,4343	692	1590	2282	SO:0001583	missense	254251	exon7			CCTTATATGAATA		CCDS3425.1, CCDS54749.1	4p15.32	2006-06-14			ENSG00000178177	ENSG00000178177			30776	protein-coding gene	gene with protein product		611799				12560079	Standard	NM_153686		Approved	MLR1, FLJ30696	uc021xmr.1	Q8N3X6	OTTHUMG00000128538	ENST00000382226.5:c.1006T>C	4.37:g.17886146A>G	ENSP00000371661:p.Tyr336His	Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	153	64	0.418301	NM_001166139	Q96NK1	Missense_Mutation	SNP	ENST00000382226.5	37	CCDS54749.1	59	0.027014652014652016	3	0.006097560975609756	14	0.03867403314917127	0	0.0	42	0.055408970976253295	A	3.788	-0.044233	0.07452	0.010116	0.065094	ENSG00000178177	ENST00000382224;ENST00000382226	.	.	.	5.34	4.16	0.48862	.	0.808427	0.11700	N	0.538015	T	0.02571	0.0078	N	0.08118	0	0.34042	D	0.655142	.	.	.	.	.	.	T	0.19647	-1.0299	7	0.25106	T	0.35	.	11.1628	0.48526	0.9277:0.0:0.0723:0.0	rs17526944;rs17526944	.	.	.	H	252;336	.	ENSP00000371659:Y252H	Y	-	1	0	LCORL	17495244	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.093000	0.50217	0.986000	0.38683	0.533000	0.62120	TAT	A|0.972;G|0.028	0.028	strong		0.388	LCORL-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_153686	
ZNF746	155061	hgsc.bcm.edu	37	7	149191460	149191460	+	Silent	SNP	G	G	A	rs112293204	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:149191460G>A	ENST00000340622.3	-	2	439	c.159C>T	c.(157-159)gcC>gcT	p.A53A	ZNF746_ENST00000458143.2_Silent_p.A53A|ZNF746_ENST00000461958.2_Silent_p.A53A			Q6NUN9	ZN746_HUMAN	zinc finger protein 746	53					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of neuron death (GO:1901216)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(4)|lung(11)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	34	Melanoma(164;0.165)		OV - Ovarian serous cystadenocarcinoma(82;0.00358)			CGAACTCCACGGCTGTCTTCT	0.622													.|||	1742	0.347843	0.2648	0.3329	5008	,	,		18600	0.5079		0.2734	False		,,,				2504	0.3824				p.A53A		Atlas-SNP	.											.	ZNF746	68	.	0			c.C159T						PASS	.	G	,	1095,3311		118,859,1226	63.0	67.0	66.0		159,159	-2.7	0.0	7	dbSNP_132	66	2519,6077		385,1749,2164	no	coding-synonymous,coding-synonymous	ZNF746	NM_001163474.1,NM_152557.4	,	503,2608,3390	AA,AG,GG		29.3043,24.8525,27.7957	,	53/646,53/645	149191460	3614,9388	2203	4298	6501	SO:0001819	synonymous_variant	155061	exon2			CTCCACGGCTGTC	AK055975	CCDS5897.1, CCDS55180.1	7q36.1	2013-01-08			ENSG00000181220	ENSG00000181220		"""Zinc fingers, C2H2-type"", ""-"""	21948	protein-coding gene	gene with protein product		613914					Standard	NM_152557		Approved	FLJ31413	uc010lpi.2	Q6NUN9	OTTHUMG00000158972	ENST00000340622.3:c.159C>T	7.37:g.149191460G>A		Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	208	97	0.466346	NM_001163474	A8K6Z9|Q6ZRF9	Silent	SNP	ENST00000340622.3	37	CCDS5897.1																																																																																			G|0.714;A|0.286	0.286	strong		0.622	ZNF746-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000352730.1	NM_152557	
FRAS1	80144	hgsc.bcm.edu	37	4	79353587	79353587	+	Missense_Mutation	SNP	C	C	G	rs35219594	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:79353587C>G	ENST00000325942.6	+	38	5486	c.5046C>G	c.(5044-5046)gaC>gaG	p.D1682E	FRAS1_ENST00000264895.6_Missense_Mutation_p.D1682E	NM_001166133.1	NP_001159605.1	Q86XX4	FRAS1_HUMAN	Fraser extracellular matrix complex subunit 1	1682					cell communication (GO:0007154)|embryonic limb morphogenesis (GO:0030326)|metanephros morphogenesis (GO:0003338)|morphogenesis of an epithelium (GO:0002009)|palate development (GO:0060021)|protein transport (GO:0015031)|skin development (GO:0043588)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sublamina densa (GO:0061618)	metal ion binding (GO:0046872)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(5)|lung(54)|prostate(7)|skin(2)|urinary_tract(4)	103						CCCGGGAAGACAGCATGGAGA	0.483													C|||	10	0.00199681	0.0008	0.0086	5008	,	,		21025	0.0		0.003	False		,,,				2504	0.0				p.D1682E		Atlas-SNP	.											FRAS1_ENST00000325942,NS,carcinoma,+2,3	FRAS1	779	3	0			c.C5046G						PASS	.	C	GLU/ASP,GLU/ASP	5,3945		0,5,1970	64.0	65.0	65.0		5046,5046	4.5	1.0	4	dbSNP_126	65	38,8276		0,38,4119	yes	missense,missense	FRAS1	NM_001166133.1,NM_025074.6	45,45	0,43,6089	GG,GC,CC		0.4571,0.1266,0.3506	probably-damaging,probably-damaging	1682/1977,1682/4013	79353587	43,12221	1975	4157	6132	SO:0001583	missense	80144	exon38			GGAAGACAGCATG	AB040933	CCDS54772.1	4q21.21	2014-06-25	2014-06-25		ENSG00000138759	ENSG00000138759			19185	protein-coding gene	gene with protein product		607830	"""Fraser syndrome 1"""			12766769, 3118036	Standard	NM_025074		Approved	FLJ22031, FLJ14927, KIAA1500	uc003hlb.2	Q86XX4	OTTHUMG00000160856	ENST00000325942.6:c.5046C>G	4.37:g.79353587C>G	ENSP00000326330:p.Asp1682Glu	Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	120	59	0.491667	NM_001166133	A2RRR8|Q86UZ4|Q8N3U9|Q8NAU7|Q96JW7|Q9H6N9|Q9P228	Missense_Mutation	SNP	ENST00000325942.6	37	CCDS54772.1	3|3	0.0013736263736263737|0.0013736263736263737	0|0	0.0|0.0	1|1	0.0027624309392265192|0.0027624309392265192	0|0	0.0|0.0	2|2	0.002638522427440633|0.002638522427440633	C|C	13.55|13.55	2.270864|2.270864	0.40194|0.40194	0.001266|0.001266	0.004571|0.004571	ENSG00000138759|ENSG00000138759	ENST00000325942;ENST00000264895;ENST00000545316|ENST00000510944	T;T|.	0.50001|.	0.76;0.76|.	6.17|6.17	4.47|4.47	0.54385|0.54385	.|.	0.048301|.	0.85682|.	D|.	0.000000|.	T|T	0.64450|0.64450	0.2599|0.2599	M|M	0.67517|0.67517	2.055|2.055	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.87578|.	0.982;0.998|.	T|T	0.62167|0.62167	-0.6911|-0.6911	10|5	0.52906|.	T|.	0.07|.	.|.	9.988|9.988	0.41854|0.41854	0.0:0.7975:0.0:0.2025|0.0:0.7975:0.0:0.2025	rs35219594|rs35219594	1682;1682|.	E9PHH6;A2RRR8|.	.;.|.	E|E	1682;1682;102|132	ENSP00000326330:D1682E;ENSP00000264895:D1682E|.	ENSP00000264895:D1682E|.	D|Q	+|+	3|1	2|0	FRAS1|FRAS1	79572611|79572611	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.004000|0.004000	0.04260|0.04260	2.301000|2.301000	0.43628|0.43628	0.954000|0.954000	0.37851|0.37851	-0.136000|-0.136000	0.14681|0.14681	GAC|CAG	C|0.998;G|0.002	0.002	strong		0.483	FRAS1-001	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000362706.2		
PRX	57716	hgsc.bcm.edu	37	19	40901614	40901614	+	Missense_Mutation	SNP	A	A	G	rs268671	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:40901614A>G	ENST00000324001.7	-	7	2915	c.2645T>C	c.(2644-2646)gTg>gCg	p.V882A	PRX_ENST00000291825.7_3'UTR	NM_181882.2	NP_870998.2	Q9BXM0	PRAX_HUMAN	periaxin	882			V -> A (in dbSNP:rs268671). {ECO:0000269|PubMed:10997877, ECO:0000269|PubMed:11133365}.		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)			AGGGCCCTCCACCCGCTCTCC	0.627													G|||	2664	0.531949	0.8427	0.4784	5008	,	,		17084	0.2401		0.506	False		,,,				2504	0.4775				p.V882A		Atlas-SNP	.											.	PRX	151	.	0			c.T2645C						PASS	.	G	,ALA/VAL	3477,929	343.1+/-307.5	1384,709,110	38.0	46.0	43.0		,2645	2.7	0.0	19	dbSNP_79	43	4453,4147	555.8+/-386.7	1152,2149,999	yes	utr-3,missense	PRX	NM_020956.2,NM_181882.2	,64	2536,2858,1109	GG,GA,AA		48.2209,21.0849,39.0281	,benign	,882/1462	40901614	7930,5076	2203	4300	6503	SO:0001583	missense	57716	exon7			CCCTCCACCCGCT	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.2645T>C	19.37:g.40901614A>G	ENSP00000326018:p.Val882Ala	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	65	21	0.323077	NM_181882	Q9BXL9|Q9HCF2	Missense_Mutation	SNP	ENST00000324001.7	37	CCDS33028.1	1082	0.49542124542124544	391	0.7947154471544715	193	0.5331491712707183	123	0.21503496503496503	375	0.4947229551451187	G	0.016	-1.538715	0.00942	0.789151	0.517791	ENSG00000105227	ENST00000324001;ENST00000341562	T	0.01113	5.32	4.88	2.7	0.31948	.	0.563419	0.14794	N	0.298050	T	0.00012	0.0000	N	0.02539	-0.55	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.01360	-1.1375	9	0.17832	T	0.49	0.0625	7.2297	0.26036	0.1619:0.1377:0.7004:0.0	rs268671;rs3745204;rs52793723;rs60720056;rs268671	882	Q9BXM0	PRAX_HUMAN	A	882	ENSP00000326018:V882A	ENSP00000326018:V882A	V	-	2	0	PRX	45593454	0.346000	0.24844	0.033000	0.17914	0.004000	0.04260	2.680000	0.46918	0.119000	0.18210	-0.900000	0.02857	GTG	A|0.446;G|0.554	0.554	strong		0.627	PRX-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000462582.1	NM_020956	
STAB1	23166	hgsc.bcm.edu	37	3	52558133	52558133	+	Silent	SNP	T	T	C	rs13621	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:52558133T>C	ENST00000321725.6	+	68	7636	c.7560T>C	c.(7558-7560)gaT>gaC	p.D2520D		NM_015136.2	NP_055951.2	Q9NY15	STAB1_HUMAN	stabilin 1	2520					cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|defense response to bacterium (GO:0042742)|inflammatory response (GO:0006954)|negative regulation of angiogenesis (GO:0016525)|oxidation-reduction process (GO:0055114)|receptor-mediated endocytosis (GO:0006898)	endocytic vesicle membrane (GO:0030666)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	hyaluronic acid binding (GO:0005540)|low-density lipoprotein particle binding (GO:0030169)|low-density lipoprotein receptor activity (GO:0005041)|protein disulfide oxidoreductase activity (GO:0015035)|scavenger receptor activity (GO:0005044)			breast(4)|central_nervous_system(3)|endometrium(7)|kidney(2)|large_intestine(13)|liver(1)|lung(27)|ovary(1)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(3)	76				BRCA - Breast invasive adenocarcinoma(193;1.73e-05)|Kidney(197;0.00182)|KIRC - Kidney renal clear cell carcinoma(197;0.00205)|OV - Ovarian serous cystadenocarcinoma(275;0.0482)		ATGATGCTGATGACGACTTCT	0.607													C|||	1958	0.390974	0.3343	0.5115	5008	,	,		18731	0.4296		0.4652	False		,,,				2504	0.2658				p.D2520D		Atlas-SNP	.											.	STAB1	178	.	0			c.T7560C						PASS	.	C		1356,3050	689.8+/-405.2	215,926,1062	168.0	154.0	159.0		7560	-11.6	0.0	3	dbSNP_52	159	4027,4573	598.1+/-393.9	980,2067,1253	no	coding-synonymous	STAB1	NM_015136.2		1195,2993,2315	CC,CT,TT		46.8256,30.7762,41.3886		2520/2571	52558133	5383,7623	2203	4300	6503	SO:0001819	synonymous_variant	23166	exon68			TGCTGATGACGAC	AJ275213	CCDS33768.1	3p21.31	2008-07-18			ENSG00000010327	ENSG00000010327			18628	protein-coding gene	gene with protein product	"""MS-1 antigen"", ""fasciclin egf-like, laminin-type egf-like, and link domain-containing scavenger receptor-1"", ""common lymphatic endothelial and vascular endothelial receptor-1"""	608560				11829752, 12077138	Standard	XM_005264973		Approved	KIAA0246, STAB-1, FEEL-1, CLEVER-1, FELE-1, FEX1	uc003dej.3	Q9NY15	OTTHUMG00000158574	ENST00000321725.6:c.7560T>C	3.37:g.52558133T>C		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	126	125	0.992063	NM_015136	A7E297|Q8IUH0|Q8IUH1|Q93072	Silent	SNP	ENST00000321725.6	37	CCDS33768.1	990	0.4532967032967033	163	0.3313008130081301	189	0.5220994475138122	282	0.493006993006993	356	0.46965699208443273	C	0.092	-1.165587	0.01673	0.307762	0.468256	ENSG00000010327	ENST00000469989	.	.	.	5.78	-11.6	0.00059	.	.	.	.	.	.	.	.	.	.	.	0.39327	P	0.03464400000000001	.	.	.	.	.	.	.	.	.	.	.	.	.	.	4.3452	0.11129	0.128:0.3704:0.2691:0.2325	rs13621;rs1131676;rs3191792;rs4687623;rs11547690;rs58635685	.	.	.	R	127	.	.	X	+	1	0	STAB1	52533173	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-4.305000	0.00256	-3.572000	0.00139	-4.178000	0.00010	TGA	A|0.000;C|0.428;G|0.000;T|0.572	0.428	strong		0.607	STAB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351380.2	NM_015136	
KRT1	3848	hgsc.bcm.edu	37	12	53070145	53070145	+	Silent	SNP	G	G	A	rs60447237|rs936958	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:53070145G>A	ENST00000252244.3	-	7	1447	c.1389C>T	c.(1387-1389)cgC>cgT	p.R463R		NM_006121.3	NP_006112.3	P04264	K2C1_HUMAN	keratin 1	463	Coil 2.|Rod.		Missing (in palmoplantar keratoderma; and mild ichthyosis largely limited to the flexural areas).	R -> C (in Ref. 9; AAA36153). {ECO:0000305}.	complement activation, lectin pathway (GO:0001867)|establishment of skin barrier (GO:0061436)|fibrinolysis (GO:0042730)|negative regulation of inflammatory response (GO:0050728)|regulation of angiogenesis (GO:0045765)|response to oxidative stress (GO:0006979)|retina homeostasis (GO:0001895)	blood microparticle (GO:0072562)|cytoskeleton (GO:0005856)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|lung(11)|ovary(1)|prostate(7)|skin(3)	39						CCTGGTAGTCGCGCAGCAGGC	0.597													a|||	2131	0.425519	0.4939	0.4424	5008	,	,		19067	0.2411		0.4523	False		,,,				2504	0.4836				p.R463R		Atlas-SNP	.											KRT1,NS,carcinoma,-2,1	KRT1	110	1	0			c.C1389T						PASS	.	A		2047,2359		466,1115,622	84.0	69.0	74.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1389	-10.1	0.5	12	dbSNP_86	74	4067,4533		964,2139,1197	no	coding-synonymous	KRT1	NM_006121.3		1430,3254,1819	AA,AG,GG		47.2907,46.4594,47.0091		463/645	53070145	6114,6892	2203	4300	6503	SO:0001819	synonymous_variant	3848	exon7			GTAGTCGCGCAGC	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.1389C>T	12.37:g.53070145G>A		Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	128	59	0.460938	NM_006121	B2RA01|P85925|P86104|Q14720|Q6GSJ0|Q9H298	Silent	SNP	ENST00000252244.3	37	CCDS8836.1																																																																																			G|0.554;A|0.446	0.446	strong		0.597	KRT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405706.1	NM_006121	
GFM2	84340	hgsc.bcm.edu	37	5	74055209	74055209	+	Missense_Mutation	SNP	T	T	C	rs957680	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:74055209T>C	ENST00000296805.3	-	4	648	c.191A>G	c.(190-192)aAt>aGt	p.N64S	GFM2_ENST00000345239.2_Missense_Mutation_p.N64S|GFM2_ENST00000427854.2_Missense_Mutation_p.N64S|GFM2_ENST00000509430.1_Missense_Mutation_p.N64S	NM_032380.3	NP_115756.2			G elongation factor, mitochondrial 2											breast(2)|endometrium(2)|large_intestine(4)|lung(5)|prostate(1)	14		all_lung(232;0.00101)|Lung NSC(167;0.00278)|Ovarian(174;0.0129)|Breast(144;0.231)		OV - Ovarian serous cystadenocarcinoma(47;1.86e-56)		TATGGGAGGATTGATGATGGA	0.303													T|||	780	0.155751	0.3427	0.1239	5008	,	,		16260	0.0208		0.1392	False		,,,				2504	0.0818				p.N64S		Atlas-SNP	.											.	GFM2	38	.	0			c.A191G						PASS	.	T	SER/ASN,SER/ASN,SER/ASN	1380,3026	455.7+/-351.1	215,950,1038	172.0	186.0	181.0		191,191,191	-4.9	0.6	5	dbSNP_86	181	1068,7532	224.7+/-261.0	65,938,3297	yes	missense,missense,missense	GFM2	NM_032380.3,NM_170681.1,NM_170691.1	46,46,46	280,1888,4335	CC,CT,TT		12.4186,31.3209,18.8221	benign,benign,benign	64/780,64/514,64/733	74055209	2448,10558	2203	4300	6503	SO:0001583	missense	84340	exon4			GGAGGATTGATGA	AF111808	CCDS4023.1, CCDS4024.1, CCDS47232.1	5q13	2008-02-05			ENSG00000164347	ENSG00000164347			29682	protein-coding gene	gene with protein product		606544				11735030	Standard	NM_001281302		Approved	EFG2, FLJ21661	uc003kdh.1	Q969S9	OTTHUMG00000102058	ENST00000296805.3:c.191A>G	5.37:g.74055209T>C	ENSP00000296805:p.Asn64Ser	Somatic	222	0	0		WXS	Illumina HiSeq	Phase_I	201	98	0.487562	NM_032380		Missense_Mutation	SNP	ENST00000296805.3	37	CCDS4023.1	336	0.15384615384615385	182	0.3699186991869919	53	0.1464088397790055	14	0.024475524475524476	87	0.11477572559366754	T	12.86	2.065030	0.36470	0.313209	0.124186	ENSG00000164347	ENST00000296805;ENST00000345239;ENST00000546082;ENST00000509430;ENST00000427854;ENST00000509097	T;T;T;T;T	0.72942	0.13;0.26;0.13;-0.7;-0.06	6.04	-4.89	0.03103	.	0.281001	0.45867	N	0.000336	T	0.00012	0.0000	N	0.11341	0.13	0.32924	P	0.48379399999999995	B;B;B;B;B	0.22604	0.072;0.001;0.004;0.003;0.0	B;B;B;B;B	0.20955	0.032;0.001;0.011;0.011;0.001	T	0.24657	-1.0154	9	0.21540	T	0.41	-6.3607	13.3358	0.60516	0.0:0.3368:0.0:0.6632	rs957680;rs52802476;rs58208552;rs957680	64;64;64;64;64	F5H687;Q969S9-3;Q969S9-5;Q969S9-2;Q969S9	.;.;.;.;RRF2M_HUMAN	S	64	ENSP00000296805:N64S;ENSP00000296804:N64S;ENSP00000427004:N64S;ENSP00000405808:N64S;ENSP00000421717:N64S	ENSP00000296805:N64S	N	-	2	0	GFM2	74090965	0.001000	0.12720	0.642000	0.29436	0.993000	0.82548	-1.041000	0.03542	-1.096000	0.03046	0.460000	0.39030	AAT	T|0.820;G|0.001	.	strong		0.303	GFM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219860.2	NM_032380	
LDLR	3949	hgsc.bcm.edu	37	19	11230881	11230881	+	Silent	SNP	T	T	C	rs5925	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:11230881T>C	ENST00000558518.1	+	13	2146	c.1959T>C	c.(1957-1959)gtT>gtC	p.V653V	LDLR_ENST00000557933.1_Silent_p.V653V|LDLR_ENST00000455727.2_Silent_p.V485V|LDLR_ENST00000558013.1_Silent_p.V653V|LDLR_ENST00000545707.1_Silent_p.V526V|LDLR_ENST00000535915.1_Silent_p.V612V	NM_000527.4|NM_001195798.1	NP_000518.1|NP_001182727.1	P01130	LDLR_HUMAN	low density lipoprotein receptor	653					cholesterol homeostasis (GO:0042632)|cholesterol import (GO:0070508)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|endocytosis (GO:0006897)|intestinal cholesterol absorption (GO:0030299)|lipid metabolic process (GO:0006629)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|low-density lipoprotein particle clearance (GO:0034383)|phospholipid transport (GO:0015914)|phototransduction, visible light (GO:0007603)|positive regulation of triglyceride biosynthetic process (GO:0010867)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol homeostasis (GO:2000188)|regulation of phosphatidylcholine catabolic process (GO:0010899)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|coated pit (GO:0005905)|early endosome (GO:0005769)|endosome membrane (GO:0010008)|external side of plasma membrane (GO:0009897)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|low-density lipoprotein particle (GO:0034362)|lysosome (GO:0005764)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|glycoprotein binding (GO:0001948)|low-density lipoprotein particle binding (GO:0030169)|low-density lipoprotein receptor activity (GO:0005041)|very-low-density lipoprotein particle receptor activity (GO:0030229)	p.?(1)		breast(2)|endometrium(2)|large_intestine(5)|lung(8)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	26		Lung NSC(9;0.000245)|Renal(1328;0.0007)|Hepatocellular(1079;0.0524)		GBM - Glioblastoma multiforme(1328;1.36e-05)|STAD - Stomach adenocarcinoma(1328;0.000766)|Lung(535;0.197)	Porfimer(DB00707)	AGGATATGGTTCTCTTCCACA	0.512													C|||	1682	0.335863	0.1498	0.5418	5008	,	,		19441	0.2163		0.4463	False		,,,				2504	0.4509				p.V653V	GBM(18;201 575 7820 21545)	Atlas-SNP	.											.	LDLR	72	.	1	Unknown(1)	lung(1)	c.T1959C	GRCh37	CM080431	LDLR	M	rs5925	PASS	.	C	,,,,,	870,3536	743.6+/-411.5	92,686,1425	101.0	75.0	84.0		1959,1959,1836,1455,1596,1578	3.2	1.0	19	dbSNP_52	84	3893,4707	606.8+/-395.1	852,2189,1259	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	LDLR	NM_000527.4,NM_001195798.1,NM_001195799.1,NM_001195800.1,NM_001195802.1,NM_001195803.1	,,,,,	944,2875,2684	CC,CT,TT		45.2674,19.7458,36.6216	,,,,,	653/861,653/859,612/820,485/693,532/740,526/683	11230881	4763,8243	2203	4300	6503	SO:0001819	synonymous_variant	3949	exon13			TATGGTTCTCTTC	AY114155	CCDS12254.1, CCDS56083.1, CCDS56084.1, CCDS56085.1, CCDS58651.1	19p13.2	2014-09-17	2008-08-01		ENSG00000130164	ENSG00000130164		"""Low density lipoprotein receptors"""	6547	protein-coding gene	gene with protein product	"""familial hypercholesterolemia"""	606945					Standard	NM_000527		Approved	LDLCQ2	uc002mqk.4	P01130		ENST00000558518.1:c.1959T>C	19.37:g.11230881T>C		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	102	57	0.558824	NM_001195798	B4DII3|B4DJZ8|B4DR00|B4DTQ3|C0JYY8|H0YLU8|H0YNT7|Q53ZD9|Q59FQ1|Q9UDH7	Silent	SNP	ENST00000558518.1	37	CCDS12254.1																																																																																			T|0.656;C|0.344	0.344	strong		0.512	LDLR-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000415973.2		
SRRM5	100170229	hgsc.bcm.edu	37	19	44118353	44118353	+	Missense_Mutation	SNP	G	G	A	rs2302421	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:44118353G>A	ENST00000607544.1	+	3	2402	c.2080G>A	c.(2080-2082)Gac>Aac	p.D694N	SRRM5_ENST00000417606.1_Missense_Mutation_p.D694N|SRRM5_ENST00000526798.1_Missense_Mutation_p.D709N|ZNF428_ENST00000300811.3_Intron			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	85	0	0		WXS	Illumina HiSeq	Phase_I	64	29	0.453125	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	
SLC9B2	133308	hgsc.bcm.edu	37	4	103964529	103964529	+	Missense_Mutation	SNP	A	A	C	rs2276976	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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_ENST00000362026.3_Missense_Mutation_p.F357C|SLC9B2_ENST00000503103.1_Missense_Mutation_p.F300C|SLC9B2_ENST00000339611.4_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	57	0	0		WXS	Illumina HiSeq	Phase_I	68	33	0.485294	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	
HLA-DPA1	3113	hgsc.bcm.edu	37	6	33037611	33037611	+	Silent	SNP	C	C	T	rs1062481	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:33037611C>T	ENST00000419277.1	-	3	282	c.153G>A	c.(151-153)ggG>ggA	p.G51G	HLA-DPA1_ENST00000428995.1_Silent_p.G51G|HLA-DPA1_ENST00000463066.1_5'UTR	NM_001242524.1|NM_001242525.1	NP_001229453.1|NP_001229454.1	P20036	DPA1_HUMAN	major histocompatibility complex, class II, DP alpha 1	51	Alpha-1.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cellular response to interferon-gamma (GO:0071346)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell proliferation (GO:0042102)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			kidney(5)|large_intestine(1)|lung(6)|prostate(1)|skin(2)	15						ACATAAACTCCCCTGTTGGTC	0.438													.|||	1016	0.202875	0.2035	0.0447	5008	,	,		20027	0.5774		0.0318	False		,,,				2504	0.1043				p.G51G		Atlas-SNP	.											.	HLA-DPA1	20	.	0			c.G153A						PASS	.	C	,,	494,2528		32,430,1049	58.0	83.0	74.0		153,153,153	-0.1	0.3	6	dbSNP_86	74	162,5254		2,158,2548	yes	coding-synonymous,coding-synonymous,coding-synonymous	HLA-DPA1	NM_001242524.1,NM_001242525.1,NM_033554.3	,,	34,588,3597	TT,TC,CC		2.9911,16.3468,7.7744	,,	51/261,51/261,51/261	33037611	656,7782	1511	2708	4219	SO:0001819	synonymous_variant	3113	exon2			AAACTCCCCTGTT	X00457	CCDS4764.1	6p21.3	2013-01-11			ENSG00000231389	ENSG00000231389		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4938	protein-coding gene	gene with protein product		142880		HLA-DP1A		6584734	Standard	NM_033554		Approved		uc003ocs.2	P20036	OTTHUMG00000031058	ENST00000419277.1:c.153G>A	6.37:g.33037611C>T		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	95	30	0.315789	NM_033554	A9YWH7|B9UKH4|O19722|O46883|P01905|P79554|Q2Q060|Q2Q061|Q5EY03|Q5STP1|Q6DQK4|Q9BCQ1|Q9TPX3|Q9XS10	Silent	SNP	ENST00000419277.1	37	CCDS4764.1																																																																																			T|0.111;G|0.000;C|0.889	0.111	strong		0.438	HLA-DPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076071.3	NM_033554	
SNX9	51429	hgsc.bcm.edu	37	6	158330765	158330765	+	Silent	SNP	G	G	A	rs3211067	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:158330765G>A	ENST00000392185.3	+	8	945	c.774G>A	c.(772-774)agG>agA	p.R258R		NM_016224.3	NP_057308.1	Q9Y5X1	SNX9_HUMAN	sorting nexin 9	258	PX. {ECO:0000255|PROSITE- ProRule:PRU00147}.				cleavage furrow formation (GO:0036089)|endocytosis (GO:0006897)|endosomal transport (GO:0016197)|intracellular protein transport (GO:0006886)|lipid tube assembly (GO:0060988)|mitotic cytokinesis (GO:0000281)|mitotic nuclear division (GO:0007067)|positive regulation of GTPase activity (GO:0043547)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|positive regulation of protein oligomerization (GO:0032461)|receptor-mediated endocytosis (GO:0006898)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoplasmic vesicle membrane (GO:0030659)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	1-phosphatidylinositol binding (GO:0005545)|protein homodimerization activity (GO:0042803)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(10)|skin(1)|upper_aerodigestive_tract(1)	20		Breast(66;0.000776)|Ovarian(120;0.0303)|Prostate(117;0.167)		OV - Ovarian serous cystadenocarcinoma(65;8.06e-18)|BRCA - Breast invasive adenocarcinoma(81;4.48e-05)		CAGATCCCAGGAAAGGCTCCA	0.408													G|||	1028	0.205272	0.2239	0.1383	5008	,	,		20959	0.1369		0.2485	False		,,,				2504	0.2536				p.R258R		Atlas-SNP	.											.	SNX9	43	.	0			c.G774A						PASS	.	G		966,3440	367.1+/-318.1	107,752,1344	170.0	166.0	167.0		774	2.8	1.0	6	dbSNP_105	167	2020,6580	352.5+/-328.7	248,1524,2528	no	coding-synonymous	SNX9	NM_016224.3		355,2276,3872	AA,AG,GG		23.4884,21.9246,22.9586		258/596	158330765	2986,10020	2203	4300	6503	SO:0001819	synonymous_variant	51429	exon8			TCCCAGGAAAGGC	AF121859	CCDS5253.1	6q25.1-q26	2008-05-22			ENSG00000130340	ENSG00000130340		"""Sorting nexins"""	14973	protein-coding gene	gene with protein product		605952				10531379, 17609109	Standard	NM_016224		Approved	SH3PX1, SDP1, SH3PXD3A	uc003qqv.1	Q9Y5X1	OTTHUMG00000015903	ENST00000392185.3:c.774G>A	6.37:g.158330765G>A		Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	88	34	0.386364	NM_016224	Q9BSI7|Q9BVM1|Q9UJH6|Q9UP20	Silent	SNP	ENST00000392185.3	37	CCDS5253.1																																																																																			G|0.778;A|0.222	0.222	strong		0.408	SNX9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042856.1		
MLLT4	4301	hgsc.bcm.edu	37	6	168352105	168352105	+	Silent	SNP	G	G	A	rs2076664	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:168352105G>A	ENST00000447894.2	+	29	4050	c.4050G>A	c.(4048-4050)ccG>ccA	p.P1350P	MLLT4_ENST00000392108.3_Silent_p.P1350P|MLLT4_ENST00000344191.4_Silent_p.P1350P|MLLT4_ENST00000351017.4_Silent_p.P1357P|MLLT4_ENST00000400822.3_Silent_p.P1349P|MLLT4_ENST00000366806.2_Silent_p.P1350P|MLLT4_ENST00000392112.1_Silent_p.P1333P			P55196	AFAD_HUMAN	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 4	1350	Pro-rich.				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)		CAGCCATACCGGCCACCCCTG	0.602			T	MLL	AL								G|||	621	0.124002	0.152	0.1124	5008	,	,		10848	0.0595		0.1899	False		,,,				2504	0.093				p.P1350P		Atlas-SNP	.		Dom	yes		6	6q27	4301	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 4 (AF6)"""		L	MLLT4,NS,carcinoma,+1,1	MLLT4	351	1	0			c.G4050A						PASS	.	G	,	632,3756		45,542,1607	46.0	64.0	58.0		4050,3999	-1.2	0.0	6	dbSNP_96	58	1419,7155		116,1187,2984	no	coding-synonymous,coding-synonymous	MLLT4	NM_001040000.2,NM_001207008.1	,	161,1729,4591	AA,AG,GG		16.55,14.4029,15.8232	,	1350/1652,1333/1744	168352105	2051,10911	2194	4287	6481	SO:0001819	synonymous_variant	4301	exon29			CATACCGGCCACC	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.4050G>A	6.37:g.168352105G>A		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	33	17	0.515152	NM_001040000	O75087|O75088|O75089|Q59FP0|Q5TIG6|Q5TIG7|Q9NSN7|Q9NU92	Silent	SNP	ENST00000447894.2	37																																																																																				G|0.852;A|0.148	0.148	strong		0.602	MLLT4-013	PUTATIVE	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000372077.1	NM_005936	
PTPRZ1	5803	hgsc.bcm.edu	37	7	121513561	121513561	+	Missense_Mutation	SNP	T	T	G	rs740965	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:121513561T>G	ENST00000393386.2	+	1	419	c.8T>G	c.(7-9)aTc>aGc	p.I3S	PTPRZ1_ENST00000449182.1_Missense_Mutation_p.I3S	NM_001206838.1|NM_002851.2	NP_001193767.1|NP_002842.2	P23471	PTPRZ_HUMAN	protein tyrosine phosphatase, receptor-type, Z polypeptide 1	3			I -> S (in dbSNP:rs740965).		axonogenesis (GO:0007409)|central nervous system development (GO:0007417)|hematopoietic progenitor cell differentiation (GO:0002244)|learning or memory (GO:0007611)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of oligodendrocyte progenitor proliferation (GO:0070445)	integral component of plasma membrane (GO:0005887)|perineuronal net (GO:0072534)|proteinaceous extracellular matrix (GO:0005578)	protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(4)|kidney(12)|large_intestine(17)|liver(1)|lung(42)|ovary(4)|prostate(5)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(2)	106						GAAATGCGAATCCTAAAGCGT	0.567													T|||	815	0.16274	0.0136	0.2305	5008	,	,		13339	0.3026		0.1243	False		,,,				2504	0.2117				p.I3S		Atlas-SNP	.											.	PTPRZ1	605	.	0			c.T8G						PASS	.	T	SER/ILE,SER/ILE,SER/ILE	192,4214	121.3+/-158.8	3,186,2014	98.0	92.0	94.0		8,8,8	-2.7	0.0	7	dbSNP_86	94	1317,7283	260.9+/-283.5	104,1109,3087	yes	missense,missense,missense	PTPRZ1	NM_001206838.1,NM_001206839.1,NM_002851.2	142,142,142	107,1295,5101	GG,GT,TT		15.314,4.3577,11.6023	probably-damaging,probably-damaging,probably-damaging	3/1456,3/1449,3/2316	121513561	1509,11497	2203	4300	6503	SO:0001583	missense	5803	exon1			TGCGAATCCTAAA	M93426	CCDS34740.1, CCDS56505.1	7q31.3	2013-02-11			ENSG00000106278	ENSG00000106278		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9685	protein-coding gene	gene with protein product		176891		PTPZ, PTPRZ		7736789, 8387522	Standard	NM_001206838		Approved	PTP18, RPTPB, phosphacan	uc003vjy.3	P23471	OTTHUMG00000157057	ENST00000393386.2:c.8T>G	7.37:g.121513561T>G	ENSP00000377047:p.Ile3Ser	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	49	22	0.44898	NM_001206838	A4D0W5|C9JFM0|O76043|Q9UDR6	Missense_Mutation	SNP	ENST00000393386.2	37	CCDS34740.1	351	0.16071428571428573	11	0.022357723577235773	74	0.20441988950276244	179	0.3129370629370629	87	0.11477572559366754	T	12.81	2.049157	0.36181	0.043577	0.15314	ENSG00000106278	ENST00000393386;ENST00000449182	T;T	0.52983	0.65;0.64	4.27	-2.66	0.06077	.	2.658710	0.02120	N	0.055569	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B;B	0.17038	0.008;0.02	B;B	0.15052	0.005;0.012	T	0.32241	-0.9914	9	0.87932	D	0	.	4.6046	0.12371	0.1552:0.3918:0.0:0.453	rs740965;rs1050503;rs3190831;rs740965	3;3	C9JFM0;P23471	.;PTPRZ_HUMAN	S	3	ENSP00000377047:I3S;ENSP00000410000:I3S	ENSP00000377047:I3S	I	+	2	0	PTPRZ1	121300797	0.001000	0.12720	0.000000	0.03702	0.005000	0.04900	0.488000	0.22371	-0.449000	0.07117	-0.516000	0.04426	ATC	T|0.868;G|0.132	0.132	strong		0.567	PTPRZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347288.1	NM_002851	
SEC14L1	6397	hgsc.bcm.edu	37	17	75190962	75190962	+	Silent	SNP	C	C	T	rs674402	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:75190962C>T	ENST00000413679.2	+	7	981	c.678C>T	c.(676-678)agC>agT	p.S226S	SEC14L1_ENST00000430767.4_Silent_p.S226S|SEC14L1_ENST00000431431.2_Silent_p.S192S|SEC14L1_ENST00000591437.1_Silent_p.S192S|SEC14L1_ENST00000392476.2_Silent_p.S226S|SEC14L1_ENST00000585618.1_Silent_p.S226S|SEC14L1_ENST00000443798.4_Silent_p.S226S|SEC14L1_ENST00000436233.4_Silent_p.S226S	NM_001143998.1|NM_001143999.1|NM_003003.3	NP_001137470|NP_001137471|NP_002994	Q92503	S14L1_HUMAN	SEC14-like 1 (S. cerevisiae)	226					transport (GO:0006810)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				NS(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(12)|ovary(3)|prostate(2)|skin(2)	31						GCAGCCCCAGCGCACCTGAGC	0.622													C|||	1794	0.358227	0.3064	0.3329	5008	,	,		15446	0.3433		0.3559	False		,,,				2504	0.4642				p.S226S		Atlas-SNP	.											.	SEC14L1	81	.	0			c.C678T						PASS	.	C	,,,,,,	1390,3016	456.7+/-351.4	232,926,1045	65.0	64.0	64.0		678,678,678,576,678,678,678	-11.2	0.0	17	dbSNP_83	64	3214,5386	476.3+/-369.4	585,2044,1671	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SEC14L1	NM_001039573.2,NM_001143998.1,NM_001143999.1,NM_001144001.1,NM_001204408.1,NM_001204410.1,NM_003003.3	,,,,,,	817,2970,2716	TT,TC,CC		37.3721,31.5479,35.399	,,,,,,	226/720,226/716,226/716,192/682,226/720,226/716,226/716	75190962	4604,8402	2203	4300	6503	SO:0001819	synonymous_variant	6397	exon9			CCCCAGCGCACCT	D67029	CCDS11752.1, CCDS42385.1, CCDS45789.1	17q25.2	2008-02-01	2001-11-28			ENSG00000129657			10698	protein-coding gene	gene with protein product		601504	"""SEC14 (S. cerevisiae)-like 1"""	SEC14L		8697811	Standard	NM_001143998		Approved	PRELID4A	uc002jto.3	Q92503		ENST00000413679.2:c.678C>T	17.37:g.75190962C>T		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	106	104	0.981132	NM_001204408	A8K4E8|B4DDI5|D5G3K1|Q99780	Silent	SNP	ENST00000413679.2	37	CCDS11752.1																																																																																			C|0.643;T|0.357	0.357	strong		0.622	SEC14L1-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000436240.1	NM_003003	
TRIO	7204	hgsc.bcm.edu	37	5	14330940	14330940	+	Silent	SNP	T	T	C	rs2277045	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:14330940T>C	ENST00000344204.4	+	10	1809	c.1785T>C	c.(1783-1785)ggT>ggC	p.G595G	TRIO_ENST00000509967.2_Silent_p.G546G|TRIO_ENST00000537187.1_Silent_p.G595G	NM_007118.2	NP_009049.2	O75962	TRIO_HUMAN	trio Rho guanine nucleotide exchange factor	595					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)					AACATACAGGTGTGGGGAAAT	0.423													T|||	200	0.0399361	0.0537	0.0476	5008	,	,		20024	0.0308		0.0368	False		,,,				2504	0.0286				p.G595G		Atlas-SNP	.											.	TRIO	305	.	0			c.T1785C						PASS	.	T		261,4145	149.5+/-183.7	8,245,1950	157.0	148.0	151.0		1785	-8.9	0.9	5	dbSNP_100	151	356,8244	120.1+/-179.3	9,338,3953	no	coding-synonymous	TRIO	NM_007118.2		17,583,5903	CC,CT,TT		4.1395,5.9237,4.744		595/3098	14330940	617,12389	2203	4300	6503	SO:0001819	synonymous_variant	7204	exon10			TACAGGTGTGGGG	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.1785T>C	5.37:g.14330940T>C		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	119	75	0.630252	NM_007118	D3DTD1|Q13458|Q59EQ7|Q6PJC9|Q6ZN05|Q8IWK8	Silent	SNP	ENST00000344204.4	37	CCDS3883.1																																																																																			T|0.952;C|0.048	0.048	strong		0.423	TRIO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253711.2	NM_007118	
CPZ	8532	hgsc.bcm.edu	37	4	8616096	8616096	+	Silent	SNP	T	T	C	rs1131140	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:8616096T>C	ENST00000360986.4	+	9	1548	c.1374T>C	c.(1372-1374)gaT>gaC	p.D458D	CPZ_ENST00000315782.6_Silent_p.D447D|CPZ_ENST00000382480.2_Silent_p.D321D|CPZ_ENST00000429646.2_Silent_p.D66D	NM_001014447.2	NP_001014447	Q66K79	CBPZ_HUMAN	carboxypeptidase Z	458					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						GCATGTCCGATTTCAACTACC	0.607													C|||	3089	0.616813	0.3782	0.6671	5008	,	,		16399	0.87		0.5517	False		,,,				2504	0.7096				p.D458D		Atlas-SNP	.											.	CPZ	95	.	0			c.T1374C						PASS	.	C	,,	1899,2507	627.0+/-394.8	397,1105,701	137.0	120.0	126.0		1374,963,1341	3.8	1.0	4	dbSNP_86	126	4569,4031	556.5+/-386.9	1196,2177,927	no	coding-synonymous,coding-synonymous,coding-synonymous	CPZ	NM_001014447.2,NM_001014448.2,NM_003652.3	,,	1593,3282,1628	CC,CT,TT		46.8721,43.1003,49.7309	,,	458/653,321/516,447/642	8616096	6468,6538	2203	4300	6503	SO:0001819	synonymous_variant	8532	exon9			GTCCGATTTCAAC	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.1374T>C	4.37:g.8616096T>C		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	107	106	0.990654	NM_001014447	O00520|Q96MX2	Silent	SNP	ENST00000360986.4	37	CCDS33953.1																																																																																			T|0.457;C|0.543	0.543	strong		0.607	CPZ-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207001.4	NM_003652	
CCR2	729230	hgsc.bcm.edu	37	3	46399798	46399798	+	Silent	SNP	T	T	C	rs1799865	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:46399798T>C	ENST00000400888.2	+	1	819	c.780T>C	c.(778-780)aaT>aaC	p.N260N	CCR2_ENST00000292301.4_Silent_p.N260N|CCR2_ENST00000465202.1_3'UTR|CCR2_ENST00000445132.2_Silent_p.N260N			P41597	CCR2_HUMAN	chemokine (C-C motif) receptor 2	260					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)		CTCCCTATAATATTGTCATTC	0.473													C|||	1645	0.328474	0.3132	0.3415	5008	,	,		21062	0.3185		0.3072	False		,,,				2504	0.3722				p.N260N		Atlas-SNP	.											.	CCR2	103	.	0			c.T780C						PASS	.	C	,	1078,2058		184,710,674	144.0	136.0	138.0		780,780	3.1	0.6	3	dbSNP_89	138	2300,4864		390,1520,1672	no	coding-synonymous,coding-synonymous	CCR2	NM_001123041.2,NM_001123396.1	,	574,2230,2346	CC,CT,TT		32.105,34.375,32.7961	,	260/375,260/361	46399798	3378,6922	1568	3582	5150	SO:0001819	synonymous_variant	729230	exon2			CTATAATATTGTC		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.780T>C	3.37:g.46399798T>C		Somatic	220	0	0		WXS	Illumina HiSeq	Phase_I	276	126	0.456522	NM_001123041	A0AVQ3|B2RMT0|Q4VBL2	Silent	SNP	ENST00000400888.2	37	CCDS43078.1																																																																																			T|0.668;C|0.332	0.332	strong		0.473	CCR2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000344292.1	NM_000647	
HLA-A	3105	hgsc.bcm.edu	37	6	29912852	29912852	+	Silent	SNP	T	T	C	rs1137296	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:29912852T>C	ENST00000396634.1	+	8	1370	c.1029T>C	c.(1027-1029)agT>agC	p.S343S	HLA-A_ENST00000376802.2_Intron|HLA-A_ENST00000376809.5_Silent_p.S343S|HLA-A_ENST00000376806.5_Silent_p.S349S			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	343					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						AAGGAGGGAGTTACACTCAGG	0.517									Osteosarcoma, Familial Clustering of;Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of;Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of	Multiple Myeloma(9;0.094)			N|||	3438	0.686502	0.73	0.7752	5008	,	,		18984	0.6885		0.6342	False		,,,				2504	0.6166				p.S343S		Atlas-SNP	.											.	HLA-A	89	.	0			c.T1029C						PASS	.						89.0	102.0	98.0					6																	29912852		1511	2709	4220	SO:0001819	synonymous_variant	3105	exon6	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	AGGGAGTTACACT	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.1029T>C	6.37:g.29912852T>C		Somatic	237	0	0		WXS	Illumina HiSeq	Phase_I	119	46	0.386555	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Silent	SNP	ENST00000396634.1	37	CCDS34373.1																																																																																			T|0.347;C|0.653	0.653	strong		0.517	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
AK9	221264	hgsc.bcm.edu	37	6	109827528	109827528	+	Splice_Site	SNP	A	A	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:109827528A>G	ENST00000424296.2	-	35	4926		c.e35+1		RP5-919F19.5_ENST00000423747.2_RNA|AL109947.2_ENST00000517228.1_RNA	NM_001145128.2	NP_001138600.2	Q5TCS8	KAD9_HUMAN	adenylate kinase 9						ADP phosphorylation (GO:0006757)|AMP phosphorylation (GO:0006756)|CDP phosphorylation (GO:0061508)|CMP phosphorylation (GO:0061566)|dADP phosphorylation (GO:0006174)|dAMP phosphorylation (GO:0061565)|dCDP phosphorylation (GO:0061570)|dCMP phosphorylation (GO:0061567)|dGDP phosphorylation (GO:0006186)|GDP phosphorylation (GO:0061568)|TDP phosphorylation (GO:0061571)|UDP phosphorylation (GO:0061569)	cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|nucleoside diphosphate kinase activity (GO:0004550)|nucleoside phosphate kinase activity (GO:0050145)										GTGCTATCTTACCTGCTTTTA	0.338																																					.		Atlas-SNP	.											C6orf224,NS,carcinoma,-2,2	AKD1	223	2	0			c.4849+2T>C						PASS	.						108.0	105.0	106.0					6																	109827528		2202	4298	6500	SO:0001630	splice_region_variant	221264	exon36			TATCTTACCTGCT	AK131244, BC146443, BC087860	CCDS5077.1, CCDS55048.1	6q21	2013-04-29	2013-04-29	2013-04-29			2.7.4.3		33814	protein-coding gene	gene with protein product		615358	"""chromosome 6 open reading frame 224"", ""adenylate kinase domain containing 2"", ""chromosome 6 open reading frame 199"", ""adenylate kinase domain containing 1"""	C6orf224, AKD2, C6orf199, AKD1		23416111	Standard	NM_145025		Approved	FLJ42177, FLJ25791, dJ70A9.1, MGC26954		Q5TCS8		ENST00000424296.2:c.4849+1T>C	6.37:g.109827528A>G		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	78	24	0.307692	NM_001145128	A6NL75|B2RDJ0|B6ZDM7|Q3MIS4|Q5I0W8|Q6ZNF1|Q6ZVR7|Q8N7C6|Q8WW00|Q96NF4	Splice_Site	SNP	ENST00000424296.2	37	CCDS55048.1	.	.	.	.	.	.	.	.	.	.	A	15.81	2.943658	0.53079	.	.	ENSG00000155085	ENST00000424296;ENST00000470564;ENST00000490722	.	.	.	5.01	5.01	0.66863	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.0182	0.71605	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	AKD1	109934221	1.000000	0.71417	0.997000	0.53966	0.685000	0.39939	8.305000	0.89960	1.995000	0.58328	0.533000	0.62120	.	.	.	none		0.338	AK9-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001145128	Intron
LILRB2	10288	hgsc.bcm.edu	37	19	54778587	54778587	+	Missense_Mutation	SNP	T	T	C	rs146683137	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:54778587T>C	ENST00000391749.4	-	14	2018	c.1747A>G	c.(1747-1749)Agg>Ggg	p.R583G	LILRB2_ENST00000434421.1_Missense_Mutation_p.R467G|LILRB2_ENST00000314446.5_Missense_Mutation_p.R582G|LILRB2_ENST00000391746.1_3'UTR|LILRB2_ENST00000391748.1_Missense_Mutation_p.R582G	NM_001278406.1	NP_001265335.1	Q8N423	LIRB2_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 2	583				R -> G (in Ref. 5; AAH36827). {ECO:0000305}.	cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|cellular defense response (GO:0006968)|cellular response to lipopolysaccharide (GO:0071222)|Fc receptor mediated inhibitory signaling pathway (GO:0002774)|heterotypic cell-cell adhesion (GO:0034113)|immune response (GO:0006955)|immune response-inhibiting cell surface receptor signaling pathway (GO:0002767)|negative regulation of antigen processing and presentation (GO:0002578)|negative regulation of calcium ion transport (GO:0051926)|negative regulation of T cell proliferation (GO:0042130)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of regulatory T cell differentiation (GO:0045591)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of T cell tolerance induction (GO:0002666)|regulation of dendritic cell differentiation (GO:2001198)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cell adhesion molecule binding (GO:0050839)|inhibitory MHC class I receptor activity (GO:0032396)|MHC class I protein binding (GO:0042288)|MHC class Ib protein binding (GO:0023029)|protein phosphatase 1 binding (GO:0008157)|receptor activity (GO:0004872)			breast(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(30)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	44	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		GGAGGTTCCCTTTCCTGGGAT	0.617													.|||	57	0.0113818	0.0015	0.0173	5008	,	,		16374	0.001		0.0318	False		,,,				2504	0.0102				p.R583G		Atlas-SNP	.											.	LILRB2	94	.	0			c.A1747G						PASS	.	C	GLY/ARG,GLY/ARG	16,4390	20.2+/-43.8	0,16,2187	142.0	123.0	129.0		1744,1747	0.2	0.0	19	dbSNP_134	129	185,8415	75.4+/-138.0	10,165,4125	no	missense,missense	LILRB2	NM_001080978.2,NM_005874.3	125,125	10,181,6312	CC,CT,TT		2.1512,0.3631,1.5454	benign,benign	582/598,583/599	54778587	201,12805	2203	4300	6503	SO:0001583	missense	10288	exon14			GTTCCCTTTCCTG	AF000574	CCDS12886.1, CCDS42612.1, CCDS62791.1, CCDS62792.1	19q13.4	2013-01-11			ENSG00000131042	ENSG00000131042		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6606	protein-coding gene	gene with protein product		604815				9151699, 9079806	Standard	XM_006722966		Approved	LIR-2, ILT4, MIR-10, LIR2, CD85d, MIR10	uc002qfb.3	Q8N423	OTTHUMG00000064896	ENST00000391749.4:c.1747A>G	19.37:g.54778587T>C	ENSP00000375629:p.Arg583Gly	Somatic	282	1	0.0035461		WXS	Illumina HiSeq	Phase_I	236	127	0.538136	NM_005874	A8MU67|C9JF29|O75017|Q8NHJ7|Q8NHJ8	Missense_Mutation	SNP	ENST00000391749.4	37	CCDS12886.1	31	0.014194139194139194	1	0.0020325203252032522	7	0.019337016574585635	0	0.0	23	0.030343007915567283	t	0.003	-2.408767	0.00193	0.003631	0.021512	ENSG00000131042	ENST00000391748;ENST00000314446;ENST00000391749;ENST00000434421	T;T;T;T	0.00487	7.15;7.15;7.15;7.05	1.31	0.206	0.15208	.	.	.	.	.	T	0.00073	0.0002	N	0.05441	-0.05	0.09310	N	1	B;B	0.06786	0.001;0.0	B;B	0.08055	0.003;0.0	T	0.35773	-0.9775	9	0.02654	T	1	.	2.9058	0.05720	0.0:0.5038:0.2939:0.2023	.	599;583	E7EVY1;Q8N423	.;LIRB2_HUMAN	G	582;582;583;467	ENSP00000375628:R582G;ENSP00000319960:R582G;ENSP00000375629:R583G;ENSP00000410117:R467G	ENSP00000319960:R582G	R	-	1	2	LILRB2	59470399	0.000000	0.05858	0.001000	0.08648	0.002000	0.02628	-1.251000	0.02882	-0.210000	0.10140	-3.158000	0.00058	AGG	T|0.983;C|0.017	0.017	strong		0.617	LILRB2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139510.1		
ANKRD20A2	441430	hgsc.bcm.edu	37	9	42368549	42368549	+	Silent	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:42368549C>T	ENST00000377601.2	+	1	247	c.135C>T	c.(133-135)gaC>gaT	p.D45D	RP11-216M21.7_ENST00000450520.1_RNA	NM_001012421.1	NP_001012421.1	Q5SQ80	A20A2_HUMAN	ankyrin repeat domain 20 family, member A2	45										large_intestine(1)|lung(1)|ovary(1)|urinary_tract(1)	4						TCAAAGGCGACGCCGCGGAGG	0.677																																					p.D45D		Atlas-SNP	.											ANKRD20A2,bladder,carcinoma,+2,2	ANKRD20A2	9	2	0			c.C135T						scavenged	.						8.0	7.0	8.0					9																	42368549		2144	4122	6266	SO:0001819	synonymous_variant	441430	exon1			AGGCGACGCCGCG		CCDS35028.1	9p12	2013-01-10			ENSG00000183148	ENSG00000183148		"""Ankyrin repeat domain containing"""	31979	protein-coding gene	gene with protein product							Standard	XM_005272519		Approved			Q5SQ80	OTTHUMG00000058641	ENST00000377601.2:c.135C>T	9.37:g.42368549C>T		Somatic	263	1	0.00380228		WXS	Illumina HiSeq	Phase_I	221	98	0.443439	NM_001012421		Silent	SNP	ENST00000377601.2	37	CCDS35028.1																																																																																			.	.	weak		0.677	ANKRD20A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129794.1	NM_001012421	
N4BP3	23138	hgsc.bcm.edu	37	5	177547336	177547336	+	Missense_Mutation	SNP	G	G	A	rs3812082	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	16	0	0		WXS	Illumina HiSeq	Phase_I	18	10	0.555556	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	
FLRT3	23767	hgsc.bcm.edu	37	20	14306896	14306896	+	Silent	SNP	G	G	A	rs6042672	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:14306896G>A	ENST00000378053.3	-	2	1513	c.1257C>T	c.(1255-1257)acC>acT	p.T419T	MACROD2_ENST00000217246.4_Intron|FLRT3_ENST00000341420.4_Silent_p.T419T|FLRT3_ENST00000462077.1_5'Flank|MACROD2_ENST00000310348.4_Intron	NM_013281.3	NP_037413.1	Q9NZU0	FLRT3_HUMAN	fibronectin leucine rich transmembrane protein 3	419	Fibronectin type-III. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|intracellular signal transduction (GO:0035556)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|proteinaceous extracellular matrix (GO:0005578)	chemorepellent activity (GO:0045499)|protein binding, bridging (GO:0030674)|receptor signaling protein activity (GO:0005057)			breast(1)|kidney(2)|large_intestine(5)|lung(5)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	17		Colorectal(1;0.0464)	COAD - Colon adenocarcinoma(2;0.129)	Colorectal(1;0.0393)		TGGTATCAGAGGTGACAGACT	0.438													G|||	1721	0.34365	0.4334	0.2089	5008	,	,		21357	0.373		0.2763	False		,,,				2504	0.3569				p.T419T		Atlas-SNP	.											.	FLRT3	67	.	0			c.C1257T						PASS	.	G	,,	1858,2548	538.7+/-375.1	404,1050,749	139.0	136.0	137.0		1257,,1257	4.0	1.0	20	dbSNP_114	137	2288,6312	385.1+/-341.3	323,1642,2335	no	coding-synonymous,intron,coding-synonymous	FLRT3,MACROD2	NM_013281.3,NM_080676.5,NM_198391.2	,,	727,2692,3084	AA,AG,GG		26.6047,42.1698,31.8776	,,	419/650,,419/650	14306896	4146,8860	2203	4300	6503	SO:0001819	synonymous_variant	23767	exon2			ATCAGAGGTGACA	AF169677	CCDS13121.1	20p11	2013-02-11			ENSG00000125848	ENSG00000125848		"""Fibronectin type III domain containing"""	3762	protein-coding gene	gene with protein product		604808				10644439	Standard	NM_198391		Approved		uc002wow.2	Q9NZU0	OTTHUMG00000031914	ENST00000378053.3:c.1257C>T	20.37:g.14306896G>A		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	108	55	0.509259	NM_013281	D3DW20|Q542Z9|Q96K39|Q96K42|Q96KB1|Q9P259	Silent	SNP	ENST00000378053.3	37	CCDS13121.1																																																																																			G|0.677;A|0.323	0.323	strong		0.438	FLRT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078075.1	NM_013281	
FZD3	7976	hgsc.bcm.edu	37	8	28384712	28384712	+	Silent	SNP	A	A	G	rs2241802	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:28384712A>G	ENST00000240093.3	+	5	913	c.435A>G	c.(433-435)ttA>ttG	p.L145L	FZD3_ENST00000537916.1_Silent_p.L145L	NM_017412.3	NP_059108.1	Q9NPG1	FZD3_HUMAN	frizzled class receptor 3	145					canonical Wnt signaling pathway (GO:0060070)|cell proliferation in midbrain (GO:0033278)|commissural neuron axon guidance (GO:0071679)|establishment of planar polarity (GO:0001736)|facial nucleus development (GO:0021754)|G-protein coupled receptor signaling pathway coupled to cGMP nucleotide second messenger (GO:0007199)|gonad development (GO:0008406)|hair follicle development (GO:0001942)|inner ear morphogenesis (GO:0042472)|neural tube closure (GO:0001843)|neuron differentiation (GO:0030182)|neuron migration (GO:0001764)|post-anal tail morphogenesis (GO:0036342)|vasculature development (GO:0001944)	apical part of cell (GO:0045177)|apical plasma membrane (GO:0016324)|axon (GO:0030424)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|lateral plasma membrane (GO:0016328)|neuron projection membrane (GO:0032589)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)	G-protein coupled receptor activity (GO:0004930)|PDZ domain binding (GO:0030165)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(14)|lung(15)|ovary(1)|prostate(1)|skin(1)	41		Ovarian(32;2.06e-05)		KIRC - Kidney renal clear cell carcinoma(542;0.109)|Kidney(114;0.13)|Colorectal(74;0.23)		ATCTGAATTTAGCTGGAGAAC	0.413													A|||	2716	0.542332	0.3949	0.598	5008	,	,		18780	0.5675		0.5944	False		,,,				2504	0.6227				p.L145L		Atlas-SNP	.											.	FZD3	65	.	0			c.A435G						PASS	.	A	,	1875,2531	541.3+/-375.7	377,1121,705	168.0	175.0	173.0		435,435	2.4	1.0	8	dbSNP_98	173	4882,3718	618.6+/-396.8	1391,2100,809	no	coding-synonymous,coding-synonymous	FZD3	NM_017412.3,NM_145866.1	,	1768,3221,1514	GG,GA,AA		43.2326,42.5556,48.0471	,	145/667,145/667	28384712	6757,6249	2203	4300	6503	SO:0001819	synonymous_variant	7976	exon5			GAATTTAGCTGGA	AJ272427	CCDS6069.1	8p21	2014-06-27	2014-01-29		ENSG00000104290	ENSG00000104290		"""GPCR / Class F : Frizzled receptors"""	4041	protein-coding gene	gene with protein product		606143	"""frizzled (Drosophila) homolog 3"", ""frizzled homolog 3 (Drosophila)"", ""frizzled 3, seven transmembrane spanning receptor"", ""frizzled family receptor 3"""			10777673, 10873558	Standard	NM_145866		Approved		uc010lvb.3	Q9NPG1	OTTHUMG00000102145	ENST00000240093.3:c.435A>G	8.37:g.28384712A>G		Somatic	316	1	0.00316456		WXS	Illumina HiSeq	Phase_I	216	214	0.990741	NM_017412	A8K615	Silent	SNP	ENST00000240093.3	37	CCDS6069.1																																																																																			A|0.459;G|0.541	0.541	strong		0.413	FZD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219986.2	NM_145866	
CD48	962	hgsc.bcm.edu	37	1	160654758	160654758	+	Missense_Mutation	SNP	C	C	G	rs2295615	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:160654758C>G	ENST00000368046.3	-	2	391	c.304G>C	c.(304-306)Gag>Cag	p.E102Q	RP11-404F10.2_ENST00000443928.2_RNA|RP11-404F10.2_ENST00000598917.2_RNA|RP11-404F10.2_ENST00000588034.1_RNA|CD48_ENST00000368045.3_Missense_Mutation_p.E102Q	NM_001778.3	NP_001769.2	P09326	CD48_HUMAN	CD48 molecule	102	Ig-like C2-type 1.		E -> Q (in dbSNP:rs2295615).		blood coagulation (GO:0007596)|defense response (GO:0006952)|leukocyte migration (GO:0050900)|mast cell activation (GO:0045576)|signal transduction (GO:0007165)|T cell activation (GO:0042110)	anchored component of plasma membrane (GO:0046658)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	antigen binding (GO:0003823)|receptor activity (GO:0004872)	p.E102Q(1)		breast(2)|endometrium(1)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)|stomach(1)	10	all_cancers(52;2.18e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.0175)			CTGTTGTCCTCTTTCTGGACC	0.453													C|||	388	0.077476	0.1089	0.0951	5008	,	,		21505	0.0198		0.1054	False		,,,				2504	0.0532				p.E102Q		Atlas-SNP	.											CD48,NS,carcinoma,0,1	CD48	31	1	1	Substitution - Missense(1)	stomach(1)	c.G304C						PASS	.	C	GLN/GLU	559,3847	251.2+/-258.0	34,491,1678	199.0	193.0	195.0		304	1.5	0.0	1	dbSNP_100	195	1176,7424	241.0+/-271.5	88,1000,3212	yes	missense	CD48	NM_001778.2	29	122,1491,4890	GG,GC,CC		13.6744,12.6872,13.34	probably-damaging	102/244	160654758	1735,11271	2203	4300	6503	SO:0001583	missense	962	exon2			TGTCCTCTTTCTG	BC016182	CCDS1208.1, CCDS72955.1	1q21.3-q22	2013-01-29	2006-03-31		ENSG00000117091	ENSG00000117091		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	1683	protein-coding gene	gene with protein product		109530	"""CD48 antigen (B-cell membrane protein)"", ""CD48 molecule """	BCM1		2828034	Standard	NM_001256030		Approved	BLAST, mCD48, hCD48, SLAMF2	uc001fwo.2	P09326	OTTHUMG00000024009	ENST00000368046.3:c.304G>C	1.37:g.160654758C>G	ENSP00000357025:p.Glu102Gln	Somatic	254	0	0		WXS	Illumina HiSeq	Phase_I	160	113	0.70625	NM_001256030	Q5U055|Q8MGR0	Missense_Mutation	SNP	ENST00000368046.3	37	CCDS1208.1	203	0.09294871794871795	80	0.16260162601626016	33	0.09116022099447514	18	0.03146853146853147	72	0.09498680738786279	C	14.22	2.470593	0.43942	0.126872	0.136744	ENSG00000117091	ENST00000368046;ENST00000368045	T;T	0.26660	1.72;1.72	3.59	1.54	0.23209	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like fold (1);	0.398328	0.27126	N	0.020819	T	0.27798	0.0684	M	0.76574	2.34	0.80722	P	0.0	D;D;D	0.76494	0.973;0.999;0.997	P;D;D	0.68943	0.831;0.961;0.958	T	0.08513	-1.0718	9	0.66056	D	0.02	0.042	3.6294	0.08126	0.2405:0.6199:0.0:0.1396	rs2295615;rs17181415;rs17378571;rs52803896;rs2295615	102;102;102	Q8MGR0;Q6IAZ2;P09326	.;.;CD48_HUMAN	Q	102	ENSP00000357025:E102Q;ENSP00000357024:E102Q	ENSP00000357024:E102Q	E	-	1	0	CD48	158921382	0.000000	0.05858	0.000000	0.03702	0.127000	0.20565	-0.538000	0.06120	0.427000	0.26145	0.462000	0.41574	GAG	C|0.882;G|0.118	0.118	strong		0.453	CD48-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060471.1	NM_001778	
AOC1	26	hgsc.bcm.edu	37	7	150557622	150557622	+	Silent	SNP	G	G	A	rs12179	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:150557622G>A	ENST00000493429.1	+	6	2474	c.1890G>A	c.(1888-1890)tcG>tcA	p.S630S	AOC1_ENST00000360937.4_Silent_p.S630S|AOC1_ENST00000416793.2_Silent_p.S649S|AOC1_ENST00000467291.1_Silent_p.S630S|AOC1_ENST00000480582.1_3'UTR			P19801	AOC1_HUMAN	amine oxidase, copper containing 1	630					amine metabolic process (GO:0009308)|cellular response to azide (GO:0097185)|cellular response to copper ion (GO:0071280)|cellular response to copper ion starvation (GO:0035874)|cellular response to heparin (GO:0071504)|cellular response to histamine (GO:0071420)|oxidation-reduction process (GO:0055114)|response to antibiotic (GO:0046677)|response to drug (GO:0042493)|sodium ion transmembrane transport (GO:0035725)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|peroxisome (GO:0005777)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	calcium ion binding (GO:0005509)|cation channel activity (GO:0005261)|copper ion binding (GO:0005507)|diamine oxidase activity (GO:0052597)|drug binding (GO:0008144)|heparin binding (GO:0008201)|histamine oxidase activity (GO:0052598)|methylputrescine oxidase activity (GO:0052599)|primary amine oxidase activity (GO:0008131)|propane-1,3-diamine oxidase activity (GO:0052600)|protein complex binding (GO:0032403)|protein homodimerization activity (GO:0042803)|quinone binding (GO:0048038)|receptor activity (GO:0004872)|sodium channel activity (GO:0005272)|zinc ion binding (GO:0008270)	p.S630S(1)								Amiloride(DB00594)	ACCGGGAGTCGGAGCTGTGCA	0.622													G|||	2270	0.453275	0.5446	0.3977	5008	,	,		17441	0.4802		0.2694	False		,,,				2504	0.5307				p.S649S		Atlas-SNP	.											ABP1,NS,carcinoma,0,1	ABP1	92	1	1	Substitution - coding silent(1)	stomach(1)	c.G1947A						PASS	.	G		2025,2247		505,1015,616	74.0	85.0	81.0		1890	-10.1	0.0	7	dbSNP_52	81	2557,5915		415,1727,2094	no	coding-synonymous	ABP1	NM_001091.2		920,2742,2710	AA,AG,GG		30.1818,47.4017,35.9542		630/752	150557622	4582,8162	2136	4236	6372	SO:0001819	synonymous_variant	26	exon4			GGAGTCGGAGCTG	AK092514	CCDS43679.1, CCDS64797.1	7q36.1	2013-06-19	2013-06-19	2013-06-19	ENSG00000002726	ENSG00000002726	1.4.3.22		80	protein-coding gene	gene with protein product	"""diamine oxidase"""	104610	"""amiloride binding protein 1 (amine oxidase (copper-containing))"""	ABP1		8182053	Standard	NM_001091		Approved	DAO	uc003wia.2	P19801	OTTHUMG00000158306	ENST00000493429.1:c.1890G>A	7.37:g.150557622G>A		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	70	33	0.471429	NM_001272072	C9J690|Q16683|Q16684|Q56II4|Q6GU42	Silent	SNP	ENST00000493429.1	37	CCDS43679.1																																																																																			G|0.580;A|0.420	0.420	strong		0.622	AOC1-009	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350628.1	NM_001091	
OR5H14	403273	hgsc.bcm.edu	37	3	97868959	97868959	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:97868959C>A	ENST00000437310.1	+	1	790	c.730C>A	c.(730-732)Cat>Aat	p.H244N	RP11-343D2.11_ENST00000508964.1_RNA	NM_001005514.1	NP_001005514.1	A6NHG9	O5H14_HUMAN	olfactory receptor, family 5, subfamily H, member 14	244						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(3)|lung(17)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	31						CTGTGGAGCTCATCTCTTATC	0.418																																					p.H244N		Atlas-SNP	.											.	OR5H14	56	.	0			c.C730A						PASS	.						57.0	55.0	56.0					3																	97868959		2203	4298	6501	SO:0001583	missense	403273	exon1			GGAGCTCATCTCT		CCDS33798.1	3q11.2	2013-09-23			ENSG00000236032	ENSG00000236032		"""GPCR / Class A : Olfactory receptors"""	31286	protein-coding gene	gene with protein product							Standard	NM_001005514		Approved		uc003dsg.1	A6NHG9	OTTHUMG00000160079	ENST00000437310.1:c.730C>A	3.37:g.97868959C>A	ENSP00000401706:p.His244Asn	Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	140	73	0.521429	NM_001005514	B9EH15	Missense_Mutation	SNP	ENST00000437310.1	37	CCDS33798.1	.	.	.	.	.	.	.	.	.	.	C	14.07	2.424491	0.43020	.	.	ENSG00000236032	ENST00000437310	T	0.00314	8.14	2.49	2.49	0.30216	GPCR, rhodopsin-like superfamily (1);	0.000000	0.48286	D	0.000194	T	0.01029	0.0034	H	0.97707	4.06	0.28760	N	0.900936	D	0.89917	1.0	D	0.97110	1.0	T	0.04178	-1.0971	10	0.87932	D	0	.	10.6214	0.45483	0.0:1.0:0.0:0.0	.	244	A6NHG9	O5H14_HUMAN	N	244	ENSP00000401706:H244N	ENSP00000401706:H244N	H	+	1	0	OR5H14	99351649	1.000000	0.71417	0.954000	0.39281	0.342000	0.28953	6.703000	0.74633	1.380000	0.46344	0.195000	0.17529	CAT	.	.	none		0.418	OR5H14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359112.1		
MUC4	4585	hgsc.bcm.edu	37	3	195511911	195511911	+	Silent	SNP	G	G	A	rs200732241		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195511911G>A	ENST00000463781.3	-	2	6999	c.6540C>T	c.(6538-6540)acC>acT	p.T2180T	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Silent_p.T2180T	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.T2180T(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)		AGGAAGTGTCGGTGACAGGAA	0.587																																					p.T2180T		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	2	Substitution - coding silent(2)	endometrium(2)	c.C6540T						scavenged	.						8.0	14.0	12.0					3																	195511911		633	1518	2151	SO:0001819	synonymous_variant	4585	exon2			AGTGTCGGTGACA	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.6540C>T	3.37:g.195511911G>A		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	94	3	0.0319149	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|0.998;A|0.002	0.002	weak		0.587	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
SLC51A	200931	hgsc.bcm.edu	37	3	195955762	195955762	+	Missense_Mutation	SNP	G	G	A	rs939885	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195955762G>A	ENST00000296327.5	+	6	813	c.604G>A	c.(604-606)Gtc>Atc	p.V202I		NM_152672.5	NP_689885.4	Q86UW1	OSTA_HUMAN	solute carrier family 51, alpha subunit	202			V -> I (in dbSNP:rs939885). {ECO:0000269|PubMed:14702039}.		bile acid and bile salt transport (GO:0015721)|transport (GO:0006810)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|transporter activity (GO:0005215)									Conjugated Estrogens(DB00286)|Digoxin(DB00390)|Dinoprostone(DB00917)	CCTGTTTCTCGTCCCCGACGG	0.522													A|||	2288	0.456869	0.1952	0.5303	5008	,	,		19510	0.7371		0.507	False		,,,				2504	0.4182				p.V202I		Atlas-SNP	.											.	.	.	.	0			c.G604A						PASS	.	A	ILE/VAL	1089,3317	722.2+/-409.3	133,823,1247	127.0	111.0	117.0		604	2.0	1.0	3	dbSNP_86	117	4108,4492	591.3+/-392.8	957,2194,1149	yes	missense	OSTalpha	NM_152672.5	29	1090,3017,2396	AA,AG,GG		47.7674,24.7163,39.9585	benign	202/341	195955762	5197,7809	2203	4300	6503	SO:0001583	missense	200931	exon6			TTTCTCGTCCCCG		CCDS3314.1	3q29	2013-05-22			ENSG00000163959	ENSG00000163959		"""Solute carriers"""	29955	protein-coding gene	gene with protein product	"""organic solute transporter, alpha subunit"""	612084				12719432, 20538072	Standard	NM_152672		Approved	OSTalpha	uc003fwd.3	Q86UW1	OTTHUMG00000155684	ENST00000296327.5:c.604G>A	3.37:g.195955762G>A	ENSP00000296327:p.Val202Ile	Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	162	67	0.41358	NM_152672	Q6ZMC7	Missense_Mutation	SNP	ENST00000296327.5	37	CCDS3314.1	1092	0.5	112	0.22764227642276422	188	0.5193370165745856	420	0.7342657342657343	372	0.49076517150395776	A	3.504	-0.101199	0.06967	0.247163	0.477674	ENSG00000163959	ENST00000296327	T	0.41758	0.99	6.07	2.01	0.26516	.	0.409491	0.20856	N	0.084434	T	0.00012	0.0000	N	0.00538	-1.39	0.35289	P	0.21799199999999996	B	0.02656	0.0	B	0.04013	0.001	T	0.34477	-0.9827	9	0.21540	T	0.41	.	0.8166	0.01103	0.3986:0.1185:0.2612:0.2217	rs939885;rs17456218;rs17856843;rs59224016;rs939885	202	Q86UW1	OSTA_HUMAN	I	202	ENSP00000296327:V202I	ENSP00000296327:V202I	V	+	1	0	AC069257.9	197440159	0.001000	0.12720	0.999000	0.59377	0.783000	0.44284	-0.095000	0.11077	0.179000	0.19938	-0.254000	0.11334	GTC	G|0.554;A|0.446	0.446	strong		0.522	SLC51A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341253.1	NM_152672	
HRAS	3265	hgsc.bcm.edu	37	11	534242	534242	+	Silent	SNP	A	A	G	rs12628	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:534242A>G	ENST00000451590.1	-	2	268	c.81T>C	c.(79-81)caT>caC	p.H27H	HRAS_ENST00000417302.1_Silent_p.H27H|HRAS_ENST00000311189.7_Silent_p.H27H|HRAS_ENST00000397594.1_Silent_p.H27H|HRAS_ENST00000468682.2_5'UTR|HRAS_ENST00000397596.2_Silent_p.H27H	NM_001130442.1|NM_005343.2	NP_001123914.1|NP_005334.1	P01112	RASH_HUMAN	Harvey rat sarcoma viral oncogene homolog	27					actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell cycle arrest (GO:0007050)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|cellular senescence (GO:0090398)|chemotaxis (GO:0006935)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|intrinsic apoptotic signaling pathway (GO:0097193)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|mitotic cell cycle checkpoint (GO:0007093)|negative regulation of cell differentiation (GO:0045596)|negative regulation of cell proliferation (GO:0008285)|negative regulation of gene expression (GO:0010629)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of Rho GTPase activity (GO:0034259)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA replication (GO:0045740)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of JNK cascade (GO:0046330)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of miRNA metabolic process (GO:2000630)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rac protein signal transduction (GO:0035022)|positive regulation of ruffle assembly (GO:1900029)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of wound healing (GO:0090303)|protein heterooligomerization (GO:0051291)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|social behavior (GO:0035176)|striated muscle cell differentiation (GO:0051146)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|protein C-terminus binding (GO:0008022)	p.H27H(26)		adrenal_gland(1)|bone(3)|breast(7)|cervix(23)|endometrium(4)|haematopoietic_and_lymphoid_tissue(12)|kidney(1)|large_intestine(2)|liver(1)|lung(16)|oesophagus(2)|penis(2)|pituitary(10)|prostate(31)|salivary_gland(24)|skin(184)|soft_tissue(38)|stomach(14)|testis(5)|thymus(1)|thyroid(173)|upper_aerodigestive_tract(122)|urinary_tract(225)	901		all_cancers(49;4.37e-09)|all_epithelial(84;2.09e-06)|Breast(177;0.000162)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.0538)|all_lung(207;0.0713)		all cancers(45;7.63e-28)|Epithelial(43;7.29e-27)|OV - Ovarian serous cystadenocarcinoma(40;7.15e-21)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0375)|LUSC - Lung squamous cell carcinoma(625;0.0703)		CGTCCACAAAATGGTTCTGGA	0.642		6	Mis		"""infrequent sarcomas, rare other types"""	"""rhadomyosarcoma, ganglioneuroblastoma, bladder"""			Costello syndrome	HNSCC(11;0.0054)			G|||	1488	0.297125	0.3729	0.3646	5008	,	,		18347	0.1726		0.3121	False		,,,				2504	0.2597				p.H27H		Atlas-SNP	.	yes	Dom	yes	Costello syndrome	11	11p15.5	3265	v-Ha-ras Harvey rat sarcoma viral oncogene homolog		"""E, L, M"""	HRAS,arm,benign_melanocytic_nevus,0,26	HRAS	1232	26	26	Substitution - coding silent(26)	urinary_tract(25)|skin(1)	c.T81C	GRCh37	CM035804	HRAS	M	rs12628	PASS	.	G	,,	1652,2754	653.2+/-399.5	309,1034,860	135.0	123.0	127.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	81,81,81	1.0	1.0	11	dbSNP_52	127	2959,5641	665.8+/-402.3	510,1939,1851	no	coding-synonymous,coding-synonymous,coding-synonymous	HRAS	NM_001130442.1,NM_005343.2,NM_176795.3	,,	819,2973,2711	GG,GA,AA		34.407,37.4943,35.4529	,,	27/190,27/190,27/171	534242	4611,8395	2203	4300	6503	SO:0001819	synonymous_variant	3265	exon2	Familial Cancer Database	incl.: Facio-Cutaneous-Skeletal syndrome	CACAAAATGGTTC	AJ437024	CCDS7698.1, CCDS7699.1	11p15.5	2014-09-17	2013-07-08		ENSG00000174775	ENSG00000174775			5173	protein-coding gene	gene with protein product		190020	"""v-Ha-ras Harvey rat sarcoma viral oncogene homolog"""	HRAS1			Standard	NM_176795		Approved		uc010qvx.2	P01112	OTTHUMG00000131919	ENST00000451590.1:c.81T>C	11.37:g.534242A>G		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	139	104	0.748201	NM_001130442	B5BUA0|Q14080|Q6FHV9|Q9BR65|Q9UCE2	Silent	SNP	ENST00000451590.1	37	CCDS7698.1																																																																																			A|0.663;G|0.337	0.337	strong		0.642	HRAS-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259403.2	NM_176795	
MRPL28	10573	hgsc.bcm.edu	37	16	419154	419154	+	Silent	SNP	G	G	A	rs1802752	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:419154G>A	ENST00000199706.8	-	3	390	c.355C>T	c.(355-357)Ctg>Ttg	p.L119L	MRPL28_ENST00000389675.2_Silent_p.L119L|MRPL28_ENST00000429738.1_Intron	NM_006428.4	NP_006419.2	Q13084	RM28_HUMAN	mitochondrial ribosomal protein L28	119					translation (GO:0006412)	cytoplasm (GO:0005737)|mitochondrial ribosome (GO:0005761)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			breast(1)|kidney(1)|lung(1)|ovary(1)|prostate(1)	5		Hepatocellular(16;0.000105)|Lung NSC(18;0.0324)|all_lung(18;0.064)				TTCTTGTCCAGGATCTCACTG	0.537													G|||	580	0.115815	0.0189	0.0865	5008	,	,		20657	0.1518		0.165	False		,,,				2504	0.18				p.L119L		Atlas-SNP	.											MRPL28,colon,carcinoma,0,1	MRPL28	15	1	0			c.C355T						PASS	.	G		179,4227	115.9+/-153.8	8,163,2032	202.0	154.0	170.0		355	1.0	1.0	16	dbSNP_89	170	1471,7129	281.6+/-295.1	114,1243,2943	no	coding-synonymous	MRPL28	NM_006428.4		122,1406,4975	AA,AG,GG		17.1047,4.0626,12.6865		119/257	419154	1650,11356	2203	4300	6503	SO:0001819	synonymous_variant	10573	exon3			TGTCCAGGATCTC	U19796	CCDS32349.1	16p13.12	2012-09-26	2002-11-13		ENSG00000086504	ENSG00000086504		"""Mitochondrial ribosomal proteins / large subunits"""	14484	protein-coding gene	gene with protein product		604853	"""melanoma-associated antigen recognised by cytotoxic T lymphocytes"""	MAAT1		11551941, 19753307	Standard	NM_006428		Approved	p15	uc002cgs.2	Q13084	OTTHUMG00000047994	ENST00000199706.8:c.355C>T	16.37:g.419154G>A		Somatic	212	0	0		WXS	Illumina HiSeq	Phase_I	167	165	0.988024	NM_006428	B2RCM4|D3DU46|Q4TT39|Q96S26|Q9BQD8|Q9BR04	Silent	SNP	ENST00000199706.8	37	CCDS32349.1																																																																																			G|0.881;A|0.119	0.119	strong		0.537	MRPL28-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139285.2		
DCLRE1A	9937	hgsc.bcm.edu	37	10	115609915	115609915	+	Missense_Mutation	SNP	C	C	G	rs3750898	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:115609915C>G	ENST00000361384.2	-	2	1866	c.949G>C	c.(949-951)Gat>Cat	p.D317H	DCLRE1A_ENST00000369305.1_Missense_Mutation_p.D317H	NM_014881.3	NP_055696.3	Q6PJP8	DCR1A_HUMAN	DNA cross-link repair 1A	317			D -> H (in dbSNP:rs3750898). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.2, ECO:0000269|Ref.4}.		mitotic nuclear division (GO:0007067)|nucleotide-excision repair (GO:0006289)	nucleus (GO:0005634)				breast(2)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(10)|lung(8)|prostate(1)|skin(2)|urinary_tract(1)	31				Epithelial(162;0.0157)|all cancers(201;0.0171)		TGTGAATCATCCGGTTTTTCA	0.388								Other identified genes with known or suspected DNA repair function					C|||	3294	0.657748	0.3086	0.817	5008	,	,		20913	0.8185		0.7942	False		,,,				2504	0.7106				p.D317H		Atlas-SNP	.											.	DCLRE1A	80	.	0			c.G949C						PASS	.	C	HIS/ASP	1693,2713	512.9+/-368.2	325,1043,835	136.0	128.0	131.0		949	4.1	1.0	10	dbSNP_107	131	6603,1997	722.4+/-406.4	2535,1533,232	yes	missense	DCLRE1A	NM_014881.3	81	2860,2576,1067	GG,GC,CC		23.2209,38.4249,36.2141	possibly-damaging	317/1041	115609915	8296,4710	2203	4300	6503	SO:0001583	missense	9937	exon2			AATCATCCGGTTT		CCDS7584.1	10q25.1	2010-06-24	2010-06-24		ENSG00000198924	ENSG00000198924			17660	protein-coding gene	gene with protein product	"""PSO2 homolog (S. cerevisiae)"""	609682	"""DNA cross-link repair 1A (PSO2 homolog, S. cerevisiae)"""			9806498, 17804464	Standard	NM_014881		Approved	SNM1, PSO2, KIAA0086, hSNM1	uc031pxf.1	Q6PJP8	OTTHUMG00000019077	ENST00000361384.2:c.949G>C	10.37:g.115609915C>G	ENSP00000355185:p.Asp317His	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	103	103	1	NM_014881	D3DRC1|Q14701|Q6P5Y3|Q6PKL4	Missense_Mutation	SNP	ENST00000361384.2	37	CCDS7584.1	1527	0.6991758241758241	170	0.34552845528455284	294	0.8121546961325967	472	0.8251748251748252	591	0.7796833773087071	C	18.82	3.704827	0.68615	0.384249	0.767791	ENSG00000198924	ENST00000361384;ENST00000369305	T;T	0.67865	-0.29;-0.29	6.02	4.13	0.48395	.	0.857054	0.10601	N	0.655643	T	0.00012	0.0000	L	0.57536	1.79	0.38063	P	0.06387799999999999	D	0.63880	0.993	P	0.53185	0.72	T	0.28839	-1.0031	9	0.52906	T	0.07	-4.0187	10.1303	0.42674	0.1343:0.7966:0.0:0.0691	rs3750898;rs17235101;rs17855758;rs52822954;rs60893685;rs3750898	317	Q6PJP8	DCR1A_HUMAN	H	317	ENSP00000355185:D317H;ENSP00000358311:D317H	ENSP00000355185:D317H	D	-	1	0	DCLRE1A	115599905	0.100000	0.21855	0.996000	0.52242	0.710000	0.40934	0.905000	0.28504	1.517000	0.48917	0.650000	0.86243	GAT	C|0.339;G|0.661	0.661	strong		0.388	DCLRE1A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050444.1	NM_014881	
GET4	51608	hgsc.bcm.edu	37	7	930689	930689	+	Silent	SNP	C	C	T	rs13171	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:930689C>T	ENST00000265857.3	+	5	685	c.591C>T	c.(589-591)gcC>gcT	p.A197A	GET4_ENST00000407192.1_Silent_p.A144A	NM_015949.2	NP_057033.2	Q7L5D6	GET4_HUMAN	golgi to ER traffic protein 4 homolog (S. cerevisiae)	197					tail-anchored membrane protein insertion into ER membrane (GO:0071816)|transport (GO:0006810)	BAT3 complex (GO:0071818)|cytosol (GO:0005829)				breast(1)|large_intestine(1)|lung(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	11						TGTTCGTGGCCCAGGCCGTGC	0.617													C|||	1007	0.201078	0.0862	0.2435	5008	,	,		17773	0.2669		0.1879	False		,,,				2504	0.272				p.A197A		Atlas-SNP	.											GET4,NS,carcinoma,0,1	GET4	17	1	0			c.C591T						PASS	.	C		437,3969	207.5+/-228.8	23,391,1789	110.0	88.0	95.0		591	-2.1	1.0	7	dbSNP_52	95	1435,7165	275.4+/-291.8	116,1203,2981	no	coding-synonymous	GET4	NM_015949.2		139,1594,4770	TT,TC,CC		16.686,9.9183,14.3934		197/328	930689	1872,11134	2203	4300	6503	SO:0001819	synonymous_variant	51608	exon5			CGTGGCCCAGGCC	AK023560	CCDS5317.1	7p22.3	2010-08-05	2010-03-24	2010-03-24	ENSG00000239857	ENSG00000239857			21690	protein-coding gene	gene with protein product	"""CGI-20 protein"", ""conserved edge protein"", ""transmembrane domain recognition complex, 35kDa"""	612056	"""chromosome 7 open reading frame 20"""	C7orf20		10810093, 20106980, 20676083	Standard	NM_015949		Approved	CGI-20, H_NH1244M04.5, CEE, TRC35	uc003sjl.1	Q7L5D6	OTTHUMG00000112459	ENST00000265857.3:c.591C>T	7.37:g.930689C>T		Somatic	313	0	0		WXS	Illumina HiSeq	Phase_I	251	71	0.282869	NM_015949	A4D2Q1|B3KNC7|Q9UFC9|Q9Y309	Silent	SNP	ENST00000265857.3	37	CCDS5317.1																																																																																			C|0.831;T|0.169	0.169	strong		0.617	GET4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000231930.1	NM_015949	
HIPK4	147746	hgsc.bcm.edu	37	19	40886993	40886993	+	Missense_Mutation	SNP	C	C	T	rs11670988	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:40886993C>T	ENST00000291823.2	-	3	1189	c.905G>A	c.(904-906)cGg>cAg	p.R302Q		NM_144685.3	NP_653286.2	Q8NE63	HIPK4_HUMAN	homeodomain interacting protein kinase 4	302	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		R -> Q (in dbSNP:rs11670988).		histone phosphorylation (GO:0016572)|peptidyl-serine phosphorylation (GO:0018105)|protein autophosphorylation (GO:0046777)|regulation of signal transduction by p53 class mediator (GO:1901796)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(5)|large_intestine(2)|lung(5)|ovary(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	20			Lung(22;4.95e-05)|LUSC - Lung squamous cell carcinoma(20;0.000292)			GAAGGTTAGCCGACTGGCCAC	0.612													C|||	371	0.0740815	0.0023	0.0403	5008	,	,		20060	0.1736		0.0905	False		,,,				2504	0.0757				p.R302Q		Atlas-SNP	.											HIPK4_ENST00000291823,larynx,carcinoma,-1,1	HIPK4	100	1	0			c.G905A						PASS	.	C	GLN/ARG	112,4286		1,110,2088	44.0	39.0	41.0		905	4.6	1.0	19	dbSNP_120	41	819,7773		34,751,3511	yes	missense	HIPK4	NM_144685.3	43	35,861,5599	TT,TC,CC		9.5321,2.5466,7.1671	possibly-damaging	302/617	40886993	931,12059	2199	4296	6495	SO:0001583	missense	147746	exon3			GTTAGCCGACTGG	BC034501	CCDS12555.1	19q13.2	2008-02-05				ENSG00000160396			19007	protein-coding gene	gene with protein product		611712					Standard	NM_144685		Approved	FLJ32818	uc002onp.3	Q8NE63		ENST00000291823.2:c.905G>A	19.37:g.40886993C>T	ENSP00000291823:p.Arg302Gln	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	62	20	0.322581	NM_144685	A8K863|Q96M54	Missense_Mutation	SNP	ENST00000291823.2	37	CCDS12555.1	188	0.08608058608058608	3	0.006097560975609756	14	0.03867403314917127	94	0.16433566433566432	77	0.10158311345646438	C	11.64	1.700119	0.30142	0.025466	0.095321	ENSG00000160396	ENST00000291823;ENST00000452139	T	0.21031	2.03	5.67	4.59	0.56863	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.154362	0.31092	N	0.008264	T	0.00073	0.0002	L	0.48260	1.515	0.30050	P	0.811871	P	0.52061	0.95	B	0.40864	0.342	T	0.14504	-1.0470	9	0.46703	T	0.11	.	5.3853	0.16215	0.0:0.7997:0.0:0.2003	rs11670988;rs59468898;rs11670988	302	Q8NE63	HIPK4_HUMAN	Q	302;267	ENSP00000291823:R302Q	ENSP00000291823:R302Q	R	-	2	0	HIPK4	45578833	0.490000	0.26012	0.998000	0.56505	0.035000	0.12851	1.035000	0.30216	2.677000	0.91161	0.561000	0.74099	CGG	C|0.921;T|0.079	0.079	strong		0.612	HIPK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462593.1	NM_144685	
KCNMB1	3779	hgsc.bcm.edu	37	5	169810796	169810796	+	Missense_Mutation	SNP	C	C	T	rs11739136	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:169810796C>T	ENST00000274629.4	-	3	635	c.193G>A	c.(193-195)Gag>Aag	p.E65K	KCNMB1_ENST00000521859.1_Missense_Mutation_p.E65K|KCNIP1_ENST00000518527.1_Intron|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	83	0	0		WXS	Illumina HiSeq	Phase_I	101	59	0.584158	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		
PTPN13	5783	hgsc.bcm.edu	37	4	87696470	87696470	+	Silent	SNP	A	A	G	rs12507034	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:87696470A>G	ENST00000411767.2	+	34	5718	c.5655A>G	c.(5653-5655)acA>acG	p.T1885T	PTPN13_ENST00000316707.6_Silent_p.T1694T|PTPN13_ENST00000436978.1_Silent_p.T1890T|PTPN13_ENST00000511467.1_Silent_p.T1890T|PTPN13_ENST00000427191.2_Silent_p.T1866T			Q12923	PTN13_HUMAN	protein tyrosine phosphatase, non-receptor type 13 (APO-1/CD95 (Fas)-associated phosphatase)	1885	PDZ 5. {ECO:0000255|PROSITE- ProRule:PRU00143}.				peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cell body (GO:0044297)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|lamellipodium (GO:0030027)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein tyrosine phosphatase activity (GO:0004725)			NS(4)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(23)|lung(24)|ovary(4)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	93		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.00082)		CGGACATAACACTAACGTGCA	0.383													A|||	353	0.0704872	0.1074	0.0677	5008	,	,		19265	0.0079		0.1143	False		,,,				2504	0.0419				p.T1890T		Atlas-SNP	.											.	PTPN13	203	.	0			c.A5670G						PASS	.	A	,,,	372,3362		19,334,1514	83.0	76.0	78.0		5598,5655,5082,5670	-0.6	0.0	4	dbSNP_120	78	996,7220		61,874,3173	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PTPN13	NM_006264.2,NM_080683.2,NM_080684.2,NM_080685.2	,,,	80,1208,4687	GG,GA,AA		12.1227,9.9625,11.4477	,,,	1866/2467,1885/2486,1694/2295,1890/2491	87696470	1368,10582	1867	4108	5975	SO:0001819	synonymous_variant	5783	exon34			CATAACACTAACG		CCDS47093.1, CCDS47094.1, CCDS47095.1, CCDS47096.1	4q21.3	2011-06-09			ENSG00000163629	ENSG00000163629		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"""	9646	protein-coding gene	gene with protein product		600267				8287977	Standard	NM_006264		Approved	PTP1E, PTP-BAS, PTPL1, PTP-BL	uc003hpy.3	Q12923	OTTHUMG00000160968	ENST00000411767.2:c.5655A>G	4.37:g.87696470A>G		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	135	53	0.392593	NM_080685	B2RTR0|Q15159|Q15263|Q15264|Q15265|Q15674|Q16826|Q8IWH7|Q9NYN9|Q9UDA8	Silent	SNP	ENST00000411767.2	37	CCDS47094.1																																																																																			A|0.906;G|0.094	0.094	strong		0.383	PTPN13-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000363191.1		
APOL6	80830	hgsc.bcm.edu	37	22	36054944	36054944	+	Silent	SNP	C	C	T	rs34527373	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:36054944C>T	ENST00000409652.4	+	3	609	c.333C>T	c.(331-333)acC>acT	p.T111T		NM_030641.3	NP_085144.1	Q9BWW8	APOL6_HUMAN	apolipoprotein L, 6	111					lipid transport (GO:0006869)|lipoprotein metabolic process (GO:0042157)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)	lipid binding (GO:0008289)			haematopoietic_and_lymphoid_tissue(1)|lung(4)	5						TGCTCTCCACCGCTGGTCAAG	0.572													C|||	106	0.0211661	0.0424	0.013	5008	,	,		17602	0.0		0.0169	False		,,,				2504	0.0245				p.T111T		Atlas-SNP	.											.	APOL6	26	.	0			c.C333T						PASS	.	C		139,4267	98.0+/-136.7	1,137,2065	62.0	59.0	60.0		333	-8.3	0.0	22	dbSNP_126	60	165,8435	77.5+/-140.1	4,157,4139	no	coding-synonymous	APOL6	NM_030641.3		5,294,6204	TT,TC,CC		1.9186,3.1548,2.3374		111/344	36054944	304,12702	2203	4300	6503	SO:0001819	synonymous_variant	80830	exon3			CTCCACCGCTGGT	AY014879	CCDS13919.1	22q12.3	2013-01-24			ENSG00000221963	ENSG00000221963		"""Apolipoproteins"""	14870	protein-coding gene	gene with protein product		607256				11374903, 15671246	Standard	NM_030641		Approved	APOL-VI, APOLVI	uc003aoe.3	Q9BWW8	OTTHUMG00000150615	ENST00000409652.4:c.333C>T	22.37:g.36054944C>T		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	69	41	0.594203	NM_030641	Q5R3S1|Q658J1|Q8IXX6|Q9UGG1	Silent	SNP	ENST00000409652.4	37	CCDS13919.1																																																																																			C|0.975;T|0.025	0.025	strong		0.572	APOL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319081.2	NM_030641	
NCAN	1463	hgsc.bcm.edu	37	19	19351431	19351431	+	Silent	SNP	G	G	A	rs2229851	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:19351431G>A	ENST00000252575.6	+	12	3528	c.3429G>A	c.(3427-3429)acG>acA	p.T1143T	NCAN_ENST00000538881.1_Silent_p.T594T	NM_004386.2	NP_004377.2	O14594	NCAN_HUMAN	neurocan	1143	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				axon guidance (GO:0007411)|carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|regulation of synapse structural plasticity (GO:0051823)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|hyaluronic acid binding (GO:0005540)			breast(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(32)|ovary(5)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	64			Epithelial(12;0.00544)		Hyaluronan(DB08818)	ATGAAAACACGTGGATCGGCC	0.642													G|||	320	0.0638978	0.0023	0.1037	5008	,	,		19510	0.1319		0.0358	False		,,,				2504	0.0777				p.T1143T		Atlas-SNP	.											.	NCAN	277	.	0			c.G3429A						PASS	.	G		49,4357	50.9+/-86.3	0,49,2154	142.0	103.0	116.0		3429	-8.0	1.0	19	dbSNP_132	116	397,8203	126.8+/-185.2	10,377,3913	no	coding-synonymous	NCAN	NM_004386.2		10,426,6067	AA,AG,GG		4.6163,1.1121,3.4292		1143/1322	19351431	446,12560	2203	4300	6503	SO:0001819	synonymous_variant	1463	exon12			AAACACGTGGATC	AF026547	CCDS12397.1	19p12	2014-01-30	2007-02-15	2007-02-15	ENSG00000130287	ENSG00000130287		"""Immunoglobulin superfamily / V-set domain containing"", ""Proteoglycans / Extracellular Matrix : Hyalectans"", ""Endogenous ligands"""	2465	protein-coding gene	gene with protein product	"""neurocan proteoglycan"""	600826	"""chondroitin sulfate proteoglycan 3"""	CSPG3		1326557, 21353194	Standard	NM_004386		Approved		uc002nlz.3	O14594		ENST00000252575.6:c.3429G>A	19.37:g.19351431G>A		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	67	36	0.537313	NM_004386	Q9UPK6	Silent	SNP	ENST00000252575.6	37	CCDS12397.1																																																																																			G|0.956;A|0.044	0.044	strong		0.642	NCAN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460111.2	NM_004386	
PIGH	5283	hgsc.bcm.edu	37	14	68060574	68060574	+	Silent	SNP	G	G	A	rs45474396	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:68060574G>A	ENST00000216452.4	-	2	359	c.276C>T	c.(274-276)atC>atT	p.I92I	PIGH_ENST00000560722.1_Silent_p.I92I|PIGH_ENST00000559581.1_Intron	NM_004569.3	NP_004560.1	Q14442	PIGH_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class H	92					C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|cellular protein modification process (GO:0006464)|GPI anchor biosynthetic process (GO:0006506)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|glycosylphosphatidylinositol-N-acetylglucosaminyltransferase (GPI-GnT) complex (GO:0000506)	catalytic activity (GO:0003824)|phosphatidylinositol N-acetylglucosaminyltransferase activity (GO:0017176)			endometrium(1)|large_intestine(1)|lung(1)|ovary(1)	4				all cancers(60;0.000592)|OV - Ovarian serous cystadenocarcinoma(108;0.00395)|BRCA - Breast invasive adenocarcinoma(234;0.00933)		GGGAATCAATGATTAACAGAG	0.418													G|||	313	0.0625	0.0794	0.0648	5008	,	,		20187	0.0288		0.1034	False		,,,				2504	0.0307				p.I92I		Atlas-SNP	.											.	PIGH	13	.	0			c.C276T						PASS	.	G		383,4023	190.5+/-216.4	19,345,1839	84.0	71.0	75.0		276	3.2	1.0	14	dbSNP_127	75	913,7687	202.7+/-245.9	49,815,3436	no	coding-synonymous	PIGH	NM_004569.3		68,1160,5275	AA,AG,GG		10.6163,8.6927,9.9646		92/189	68060574	1296,11710	2203	4300	6503	SO:0001819	synonymous_variant	5283	exon2			ATCAATGATTAAC		CCDS9784.1	14q24.1	2013-02-26	2006-06-28		ENSG00000100564	ENSG00000100564	2.4.1.198	"""Phosphatidylinositol glycan anchor biosynthesis"""	8964	protein-coding gene	gene with protein product	"""phosphatidylinositol N-acetylglucosaminyltransferase subunit"""	600154	"""phosphatidylinositol glycan, class H"""			8204896	Standard	NM_004569		Approved	GPI-H	uc001xjr.1	Q14442	OTTHUMG00000171806	ENST00000216452.4:c.276C>T	14.37:g.68060574G>A		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	125	63	0.504	NM_004569	B2RAA4	Silent	SNP	ENST00000216452.4	37	CCDS9784.1																																																																																			G|0.905;A|0.095	0.095	strong		0.418	PIGH-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000415189.2	NM_004569	
SIVA1	10572	hgsc.bcm.edu	37	14	105222988	105222988	+	Missense_Mutation	SNP	G	G	A	rs144031294	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:105222988G>A	ENST00000329967.6	+	3	463	c.361G>A	c.(361-363)Gtg>Atg	p.V121M	SIVA1_ENST00000347067.5_Missense_Mutation_p.V56M	NM_006427.3	NP_006418.2	O15304	SIVA_HUMAN	SIVA1, apoptosis-inducing factor	121	Interaction with coxsackievirus B3 VP2.				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)		CGTGCGAGCCGTGGATGGGAA	0.647																																					p.V121M		Atlas-SNP	.											.	SIVA1	12	.	0			c.G361A						PASS	.	G	MET/VAL,MET/VAL	0,4406		0,0,2203	117.0	104.0	108.0		361,166	2.9	0.0	14	dbSNP_134	108	15,8585	11.2+/-40.8	0,15,4285	yes	missense,missense	SIVA1	NM_006427.3,NM_021709.2	21,21	0,15,6488	AA,AG,GG		0.1744,0.0,0.1153	possibly-damaging,possibly-damaging	121/176,56/111	105222988	15,12991	2203	4300	6503	SO:0001583	missense	10572	exon3			CGAGCCGTGGATG	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.361G>A	14.37:g.105222988G>A	ENSP00000329213:p.Val121Met	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	135	73	0.540741	NM_006427	Q96P98|Q9UPD6	Missense_Mutation	SNP	ENST00000329967.6	37	CCDS9992.1	.	.	.	.	.	.	.	.	.	.	G	12.18	1.860882	0.32884	0.0	0.001744	ENSG00000184990	ENST00000329967;ENST00000347067;ENST00000553810	.	.	.	4.77	2.9	0.33743	.	1.203960	0.05732	N	0.599742	T	0.56001	0.1956	L	0.56769	1.78	0.09310	N	1	D;D;D	0.67145	0.994;0.996;0.994	P;P;P	0.58130	0.779;0.759;0.833	T	0.38650	-0.9651	9	0.49607	T	0.09	-10.267	9.5779	0.39470	0.1695:0.0:0.8305:0.0	.	121;56;121	B4DTY2;O15304-2;O15304	.;.;SIVA_HUMAN	M	121;56;121	.	ENSP00000329213:V121M	V	+	1	0	SIVA1	104294033	0.011000	0.17503	0.004000	0.12327	0.026000	0.11368	1.844000	0.39269	1.227000	0.43598	0.561000	0.74099	GTG	G|0.998;A|0.002	0.002	strong		0.647	SIVA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410541.1	NM_006427	
OR10H1	26539	hgsc.bcm.edu	37	19	15918654	15918654	+	Missense_Mutation	SNP	G	G	A	rs4808382	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:15918654G>A	ENST00000334920.2	-	1	282	c.194C>T	c.(193-195)gCc>gTc	p.A65V		NM_013940.2	NP_039228.1	Q9Y4A9	O10H1_HUMAN	olfactory receptor, family 10, subfamily H, member 1	65			A -> V (in dbSNP:rs4808382).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(3)|kidney(4)|large_intestine(6)|lung(8)|ovary(4)|skin(2)|urinary_tract(1)	29						GACGGAGAGGGCGCACAGGAA	0.647													.|||	767	0.153155	0.1369	0.1153	5008	,	,		20012	0.119		0.1769	False		,,,				2504	0.2127				p.A65V		Atlas-SNP	.											OR10H1,colon,carcinoma,-1,2	OR10H1	59	2	0			c.C194T						scavenged	.						114.0	99.0	104.0					19																	15918654		2203	4297	6500	SO:0001583	missense	26539	exon1			GAGAGGGCGCACA	AC004510	CCDS12335.1	19p13.1	2012-08-09				ENSG00000186723		"""GPCR / Class A : Olfactory receptors"""	8172	protein-coding gene	gene with protein product							Standard	NM_013940		Approved		uc002nbq.2	Q9Y4A9		ENST00000334920.2:c.194C>T	19.37:g.15918654G>A	ENSP00000335596:p.Ala65Val	Somatic	207	0	0		WXS	Illumina HiSeq	Phase_I	79	17	0.21519	NM_013940	Q6IFQ2|Q96R59	Missense_Mutation	SNP	ENST00000334920.2	37	CCDS12335.1	271	0.12408424908424909	53	0.10772357723577236	34	0.09392265193370165	62	0.10839160839160839	122	0.16094986807387862	g	2.686	-0.274334	0.05679	.	.	ENSG00000186723	ENST00000334920	T	0.03065	4.06	4.71	4.71	0.59529	GPCR, rhodopsin-like superfamily (1);	0.271882	0.26200	N	0.025747	T	0.00012	0.0000	N	0.01771	-0.73	0.39146	P	0.037856	B	0.11235	0.004	B	0.15052	0.012	T	0.39881	-0.9592	9	0.02654	T	1	.	15.1534	0.72720	0.0:0.0:1.0:0.0	rs4808382	65	Q9Y4A9	O10H1_HUMAN	V	65	ENSP00000335596:A65V	ENSP00000335596:A65V	A	-	2	0	OR10H1	15779654	0.589000	0.26807	0.964000	0.40570	0.471000	0.32888	1.685000	0.37659	2.169000	0.68431	0.643000	0.83706	GCC	A|1.000;|0.000	1.000	weak		0.647	OR10H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460364.1		
PCDHB1	29930	hgsc.bcm.edu	37	5	140432602	140432602	+	Missense_Mutation	SNP	C	C	T	rs116101801		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:140432602C>T	ENST00000306549.3	+	1	1624	c.1547C>T	c.(1546-1548)gCg>gTg	p.A516V		NM_013340.2	NP_037472.2	Q9Y5F3	PCDB1_HUMAN	protocadherin beta 1	516	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)			NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(16)|liver(1)|lung(13)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	53			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			AAGCTCTACGCGCTGAGAACC	0.428													C|||	1	0.000199681	0.0	0.0	5008	,	,		22962	0.0		0.001	False		,,,				2504	0.0				p.A516V		Atlas-SNP	.											PCDHB1,colon,carcinoma,+1,3	PCDHB1	148	3	0			c.C1547T						scavenged	.						71.0	72.0	72.0					5																	140432602		2203	4300	6503	SO:0001583	missense	29930	exon1			TCTACGCGCTGAG	AF152488	CCDS4243.1	5q31	2010-01-26			ENSG00000171815	ENSG00000171815		"""Cadherins / Protocadherins : Clustered"""	8680	other	protocadherin		606327				10380929	Standard	NM_013340		Approved	PCDH-BETA1	uc003lik.1	Q9Y5F3	OTTHUMG00000129627	ENST00000306549.3:c.1547C>T	5.37:g.140432602C>T	ENSP00000307234:p.Ala516Val	Somatic	122	1	0.00819672		WXS	Illumina HiSeq	Phase_I	98	2	0.0204082	NM_013340	Q2M257	Missense_Mutation	SNP	ENST00000306549.3	37	CCDS4243.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	15.14	2.745101	0.49151	.	.	ENSG00000171815	ENST00000306549	T	0.43294	0.95	6.11	6.11	0.99139	Cadherin (5);Cadherin-like (1);	0.000000	0.44483	D	0.000456	T	0.53110	0.1776	L	0.39245	1.2	0.35236	D	0.777365	D	0.76494	0.999	D	0.66084	0.941	T	0.62258	-0.6892	10	0.62326	D	0.03	.	12.783	0.57487	0.0:0.9247:0.0:0.0753	.	516	Q9Y5F3	PCDB1_HUMAN	V	516	ENSP00000307234:A516V	ENSP00000307234:A516V	A	+	2	0	PCDHB1	140412786	0.000000	0.05858	0.994000	0.49952	0.603000	0.37013	0.840000	0.27600	2.906000	0.99361	0.655000	0.94253	GCG	C|0.999;T|0.001	0.001	strong		0.428	PCDHB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251822.2	NM_013340	
RGS3	5998	hgsc.bcm.edu	37	9	116346118	116346118	+	Missense_Mutation	SNP	G	G	A	rs41305473	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:116346118G>A	ENST00000374140.2	+	21	2635	c.2426G>A	c.(2425-2427)cGg>cAg	p.R809Q	RGS3_ENST00000350696.5_Missense_Mutation_p.R809Q|RGS3_ENST00000394646.3_Intron|RGS3_ENST00000462143.1_Missense_Mutation_p.R130Q|RP11-168K11.2_ENST00000428429.1_RNA|RGS3_ENST00000342620.5_Intron|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	91	0	0		WXS	Illumina HiSeq	Phase_I	74	46	0.621622	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	
RTP4	64108	hgsc.bcm.edu	37	3	187089031	187089031	+	Missense_Mutation	SNP	C	C	A	rs1003995|rs3926263	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	36	0	0		WXS	Illumina HiSeq	Phase_I	30	20	0.666667	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	
CEP192	55125	hgsc.bcm.edu	37	18	13001523	13001523	+	5'UTR	SNP	G	G	A	rs11080618	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:13001523G>A	ENST00000325971.8	+	0	312				CEP192_ENST00000506447.1_Missense_Mutation_p.G78R			Q8TEP8	CE192_HUMAN	centrosomal protein 192kDa						centrosome duplication (GO:0051298)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|negative regulation of phosphatase activity (GO:0010923)|spindle assembly (GO:0051225)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)	phosphatase binding (GO:0019902)			NS(1)|breast(4)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(36)|ovary(4)|pancreas(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	71						GTCATCTCCCGGAAGCCAGAG	0.398													G|||	1373	0.274161	0.239	0.3991	5008	,	,		17302	0.1835		0.3688	False		,,,				2504	0.229				p.G78R		Atlas-SNP	.											.	CEP192	340	.	0			c.G232A						PASS	.						144.0	127.0	133.0					18																	13001523		692	1591	2283	SO:0001623	5_prime_UTR_variant	55125	exon3			TCTCCCGGAAGCC	AK074074	CCDS32792.1, CCDS32792.2	18p11.21	2014-02-20				ENSG00000101639		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	25515	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 62"""					11230166, 14654843	Standard	NM_032142		Approved	KIAA1569, FLJ10352, PPP1R62	uc010xac.2	Q8TEP8		ENST00000325971.8:c.-1282G>A	18.37:g.13001523G>A		Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	39	15	0.384615	NM_032142	A0A060A9S4|E9PF99|Q8WYT8|Q9H0F4|Q9NW27	Missense_Mutation	SNP	ENST00000325971.8	37		686	0.3141025641025641	143	0.29065040650406504	142	0.39226519337016574	118	0.2062937062937063	283	0.3733509234828496	G	8.885	0.952510	0.18431	.	.	ENSG00000101639	ENST00000506447	T	0.05996	3.36	4.76	-3.79	0.04320	.	.	.	.	.	T	0.00012	0.0000	N	0.14661	0.345	0.44323	P	0.002798999999999996	B	0.20887	0.049	B	0.15052	0.012	T	0.47711	-0.9096	8	0.23891	T	0.37	.	5.9309	0.19138	0.449:0.0:0.4183:0.1328	rs11080618;rs17660009;rs11080618	78	E9PF99	.	R	78	ENSP00000427550:G78R	ENSP00000427550:G78R	G	+	1	0	CEP192	12991523	0.200000	0.23398	0.561000	0.28357	0.231000	0.25187	0.303000	0.19210	-0.447000	0.07138	0.205000	0.17691	GGA	G|0.697;A|0.303	0.303	strong		0.398	CEP192-201	KNOWN	basic	protein_coding	protein_coding		NM_032142	
SPATA22	84690	hgsc.bcm.edu	37	17	3352331	3352331	+	Missense_Mutation	SNP	C	C	T	rs1488690	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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_ENST00000541913.1_Missense_Mutation_p.V132M|SPATA22_ENST00000572969.1_Missense_Mutation_p.V148M|SPATA22_ENST00000268981.5_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	273	0	0		WXS	Illumina HiSeq	Phase_I	196	112	0.571429	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	
THNSL1	79896	hgsc.bcm.edu	37	10	25314005	25314005	+	Nonsense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:25314005G>A	ENST00000524413.1	+	3	2200	c.1853G>A	c.(1852-1854)tGg>tAg	p.W618*	THNSL1_ENST00000376356.4_Nonsense_Mutation_p.W618*			Q8IYQ7	THNS1_HUMAN	threonine synthase-like 1 (S. cerevisiae)	618						cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)				NS(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|lung(5)|pancreas(1)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	28					L-Threonine(DB00156)	GTAGCTGACTGGTGCTCTGAG	0.408																																					p.W618X		Atlas-SNP	.											.	THNSL1	70	.	0			c.G1853A						PASS	.						85.0	91.0	89.0					10																	25314005		2203	4300	6503	SO:0001587	stop_gained	79896	exon3			CTGACTGGTGCTC	AK025655	CCDS7147.1	10p12.31	2008-02-05	2007-06-20		ENSG00000185875	ENSG00000185875			26160	protein-coding gene	gene with protein product		611260	"""threonine synthase-like 1 (bacterial)"""			12477932	Standard	NM_024838		Approved	FLJ22002	uc001isi.4	Q8IYQ7	OTTHUMG00000017828	ENST00000524413.1:c.1853G>A	10.37:g.25314005G>A	ENSP00000434887:p.Trp618*	Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	139	30	0.215827	NM_024838	B3KWL1|D3DRV3|Q5VV21	Nonsense_Mutation	SNP	ENST00000524413.1	37	CCDS7147.1	.	.	.	.	.	.	.	.	.	.	G	40	8.166791	0.98686	.	.	ENSG00000185875	ENST00000524413;ENST00000376356	.	.	.	5.94	5.94	0.96194	.	0.062472	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-9.9473	20.3632	0.98871	0.0:0.0:1.0:0.0	.	.	.	.	X	618	.	ENSP00000365534:W618X	W	+	2	0	THNSL1	25354011	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	8.861000	0.92277	2.826000	0.97356	0.561000	0.74099	TGG	.	.	none		0.408	THNSL1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394913.1	NM_024838	
PLEKHG2	64857	hgsc.bcm.edu	37	19	39911451	39911451	+	Missense_Mutation	SNP	C	C	G	rs34975345	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:39911451C>G	ENST00000409794.3	+	13	2208	c.1358C>G	c.(1357-1359)cCt>cGt	p.P453R	PLEKHG2_ENST00000425673.1_Missense_Mutation_p.P453R|PLEKHG2_ENST00000409797.2_Missense_Mutation_p.P453R|PLEKHG2_ENST00000458508.2_Missense_Mutation_p.P394R|PLEKHG2_ENST00000378550.1_Missense_Mutation_p.P453R	NM_022835.2	NP_073746.2	Q9H7P9	PKHG2_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 2	453					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)			TCTCCTCGACCTCGAGATGCT	0.577													C|||	87	0.0173722	0.0015	0.0259	5008	,	,		4937	0.001		0.0308	False		,,,				2504	0.0358				p.P453R		Atlas-SNP	.											.	PLEKHG2	329	.	0			c.C1358G						PASS	.	C	ARG/PRO	32,4374	36.8+/-68.6	1,30,2172	71.0	79.0	76.0		1358	2.4	1.0	19	dbSNP_126	76	282,8318	104.8+/-165.8	5,272,4023	yes	missense	PLEKHG2	NM_022835.2	103	6,302,6195	GG,GC,CC		3.2791,0.7263,2.4143	probably-damaging	453/1387	39911451	314,12692	2203	4300	6503	SO:0001583	missense	64857	exon13			CTCGACCTCGAGA	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.1358C>G	19.37:g.39911451C>G	ENSP00000386733:p.Pro453Arg	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	54	29	0.537037	NM_022835	B8ZZK6|C9J0Y4|Q6DHV6|Q96BU2|Q96D18|Q9H699	Missense_Mutation	SNP	ENST00000409794.3	37	CCDS33022.2	36|36	0.016483516483516484|0.016483516483516484	2|2	0.0040650406504065045|0.0040650406504065045	10|10	0.027624309392265192|0.027624309392265192	1|1	0.0017482517482517483|0.0017482517482517483	23|23	0.030343007915567283|0.030343007915567283	C|C	17.20|17.20	3.329691|3.329691	0.60743|0.60743	0.007263|0.007263	0.032791|0.032791	ENSG00000090924|ENSG00000090924	ENST00000205135|ENST00000409794;ENST00000425673;ENST00000378550;ENST00000458508;ENST00000409797	.|T;T;T;T;T	.|0.70869	.|-0.22;-0.19;-0.52;-0.35;-0.52	4.65|4.65	2.41|2.41	0.29592|0.29592	.|.	.|0.000000	.|0.56097	.|D	.|0.000021	T|T	0.43500|0.43500	0.1250|0.1250	L|L	0.36672|0.36672	1.1|1.1	0.33215|0.33215	D|D	0.553934|0.553934	.|P;D;P;P	.|0.60575	.|0.913;0.988;0.844;0.473	.|P;P;B;B	.|0.56916	.|0.72;0.809;0.205;0.135	T|T	0.65051|0.65051	-0.6262|-0.6262	5|10	.|0.40728	.|T	.|0.16	.|.	5.8188|5.8188	0.18516|0.18516	0.0:0.7559:0.0:0.2441|0.0:0.7559:0.0:0.2441	rs34975345|rs34975345	.|453;453;394;453	.|Q9H7P9-3;Q9H7P9;E7ESZ3;Q9H7P9-2	.|.;PKHG2_HUMAN;.;.	V|R	350|453;453;453;394;453	.|ENSP00000386733:P453R;ENSP00000392906:P453R;ENSP00000367812:P453R;ENSP00000408857:P394R;ENSP00000386492:P453R	.|ENSP00000367812:P453R	L|P	+|+	1|2	0|0	PLEKHG2|PLEKHG2	44603291|44603291	0.071000|0.071000	0.21146|0.21146	1.000000|1.000000	0.80357|0.80357	0.984000|0.984000	0.73092|0.73092	0.771000|0.771000	0.26633|0.26633	1.178000|1.178000	0.42870|0.42870	0.655000|0.655000	0.94253|0.94253	CTC|CCT	C|0.979;G|0.021	0.021	strong		0.577	PLEKHG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326802.1	NM_022835	
KRTAP10-10	353333	hgsc.bcm.edu	37	21	46057393	46057393	+	Missense_Mutation	SNP	T	T	A	rs2838602	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:46057393T>A	ENST00000380095.1	+	1	121	c.59T>A	c.(58-60)gTc>gAc	p.V20D	TSPEAR_ENST00000323084.4_Intron	NM_181688.1	NP_859016.1	P60014	KR10A_HUMAN	keratin associated protein 10-10	20			V -> D (in dbSNP:rs2838602).			keratin filament (GO:0045095)				NS(1)|endometrium(2)|kidney(1)|lung(6)|prostate(1)|skin(2)	13						TGGCGGGTAGTCGACTGCCCA	0.672													A|||	3915	0.781749	0.9183	0.745	5008	,	,		16189	0.6468		0.7694	False		,,,				2504	0.7751				p.V20D		Atlas-SNP	.											KRTAP10-10,NS,carcinoma,-1,1	KRTAP10-10	37	1	0			c.T59A						PASS	.	A	,ASP/VAL	3896,510		1748,400,55	87.0	91.0	89.0		,59	3.5	1.0	21	dbSNP_100	89	6081,2519		2262,1557,481	no	intron,missense	TSPEAR,KRTAP10-10	NM_144991.2,NM_181688.1	,152	4010,1957,536	AA,AT,TT		29.2907,11.5751,23.2893	,benign	,20/252	46057393	9977,3029	2203	4300	6503	SO:0001583	missense	353333	exon1			GGGTAGTCGACTG	AJ566387	CCDS33585.1	21q22.3	2006-03-13			ENSG00000221859	ENSG00000221859		"""Keratin associated proteins"""	22972	protein-coding gene	gene with protein product							Standard	NM_181688		Approved	KAP10.10, KAP18.10, KRTAP18-10	uc002zfq.3	P60014	OTTHUMG00000057631	ENST00000380095.1:c.59T>A	21.37:g.46057393T>A	ENSP00000369438:p.Val20Asp	Somatic	119	1	0.00840336		WXS	Illumina HiSeq	Phase_I	88	86	0.977273	NM_181688		Missense_Mutation	SNP	ENST00000380095.1	37	CCDS33585.1	1670	0.7646520146520146	454	0.9227642276422764	278	0.7679558011049724	354	0.6188811188811189	584	0.7704485488126649	a	0.006	-2.111369	0.00353	0.884249	0.707093	ENSG00000221859	ENST00000380095	T	0.02737	4.18	3.52	3.52	0.40303	.	.	.	.	.	T	0.00012	0.0000	N	0.00084	-2.21	0.34049	P	0.34411400000000003	B	0.02656	0.0	B	0.01281	0.0	T	0.17048	-1.0382	8	0.02654	T	1	.	3.1103	0.06356	0.6704:0.0:0.1185:0.2111	rs2838602;rs58907408;rs2838602	20	P60014	KR10A_HUMAN	D	20	ENSP00000369438:V20D	ENSP00000369438:V20D	V	+	2	0	KRTAP10-10	44881821	0.166000	0.22962	0.998000	0.56505	0.104000	0.19210	0.966000	0.29331	0.357000	0.24183	-0.522000	0.04353	GTC	T|0.231;A|0.769	0.769	strong		0.672	KRTAP10-10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128034.1	NM_181688	
FAM71C	196472	hgsc.bcm.edu	37	12	100042163	100042163	+	Missense_Mutation	SNP	A	A	G	rs11109969	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:100042163A>G	ENST00000324341.1	+	1	633	c.211A>G	c.(211-213)Atg>Gtg	p.M71V	ANKS1B_ENST00000547010.1_Intron|ANKS1B_ENST00000547776.2_Intron|ANKS1B_ENST00000329257.7_Intron	NM_153364.3	NP_699195.1	Q8NEG0	FA71C_HUMAN	family with sequence similarity 71, member C	71			M -> V (in dbSNP:rs11109969).							breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(8)|upper_aerodigestive_tract(1)|urinary_tract(1)	18				OV - Ovarian serous cystadenocarcinoma(2;0.00733)|Epithelial(2;0.0385)|all cancers(2;0.19)		AATGGTAACAATGGGCATCGT	0.532													G|||	1082	0.216054	0.298	0.1772	5008	,	,		19135	0.0992		0.2903	False		,,,				2504	0.1769				p.M71V		Atlas-SNP	.											.	FAM71C	48	.	0			c.A211G						PASS	.	G	,VAL/MET	1283,3123	699.8+/-406.5	165,953,1085	134.0	112.0	119.0		,211	2.0	0.2	12	dbSNP_120	119	2551,6049	691.5+/-404.5	386,1779,2135	yes	intron,missense	ANKS1B,FAM71C	NM_152788.4,NM_153364.3	,21	551,2732,3220	GG,GA,AA		29.6628,29.1194,29.4787	,benign	,71/242	100042163	3834,9172	2203	4300	6503	SO:0001583	missense	196472	exon1			GTAACAATGGGCA		CCDS9072.1	12q23.1	2006-02-03				ENSG00000180219			28594	protein-coding gene	gene with protein product						12477932	Standard	NM_153364		Approved	MGC39520	uc001tgn.3	Q8NEG0		ENST00000324341.1:c.211A>G	12.37:g.100042163A>G	ENSP00000315247:p.Met71Val	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	85	46	0.541176	NM_153364	B2R6Y6	Missense_Mutation	SNP	ENST00000324341.1	37	CCDS9072.1	514	0.23534798534798534	150	0.3048780487804878	74	0.20441988950276244	56	0.0979020979020979	234	0.3087071240105541	G	0.001	-2.909759	0.00056	0.291194	0.296628	ENSG00000180219	ENST00000324341	T	0.07688	3.17	3.85	1.97	0.26223	.	0.206665	0.29964	N	0.010752	T	0.00012	0.0000	N	0.02202	-0.64	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.48525	-0.9028	8	.	.	.	-12.1097	6.2766	0.20983	0.1027:0.3583:0.539:0.0	rs11109969;rs56567578;rs11109969	71	Q8NEG0	FA71C_HUMAN	V	71	ENSP00000315247:M71V	.	M	+	1	0	FAM71C	98566294	0.003000	0.15002	0.214000	0.23707	0.008000	0.06430	-0.136000	0.10405	0.210000	0.20664	-1.081000	0.02215	ATG	A|0.738;G|0.262	0.262	strong		0.532	FAM71C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408458.1	NM_153364	
MYH4	4622	hgsc.bcm.edu	37	17	10346781	10346781	+	Missense_Mutation	SNP	T	T	C	rs3744554	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:10346781T>C	ENST00000255381.2	-	40	5841	c.5731A>G	c.(5731-5733)Aag>Gag	p.K1911E	CTC-297N7.11_ENST00000587182.2_RNA|RP11-799N11.1_ENST00000399342.2_RNA|RP11-799N11.1_ENST00000581304.1_RNA	NM_017533.2	NP_060003.2	Q9Y623	MYH4_HUMAN	myosin, heavy chain 4, skeletal muscle	1911			K -> E (in dbSNP:rs3744554). {ECO:0000269|PubMed:10388558}.		actin filament-based movement (GO:0030048)|ATP catabolic process (GO:0006200)|membrane organization (GO:0061024)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|response to activity (GO:0014823)	muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin filament (GO:0032982)|sarcomere (GO:0030017)	ATP binding (GO:0005524)|double-stranded RNA binding (GO:0003725)|microfilament motor activity (GO:0000146)			NS(4)|breast(8)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(13)|lung(72)|ovary(10)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	149						GCCCGTTCCTTGGCCTCCTCC	0.458													C|||	2670	0.533147	0.3336	0.5245	5008	,	,		18924	0.8631		0.3698	False		,,,				2504	0.637				p.K1911E		Atlas-SNP	.											.	MYH4	349	.	0			c.A5731G						PASS	.	C	GLU/LYS	1556,2850	669.2+/-402.1	271,1014,918	135.0	124.0	128.0		5731	4.2	0.9	17	dbSNP_107	128	3586,5014	627.6+/-398.0	761,2064,1475	yes	missense	MYH4	NM_017533.2	56	1032,3078,2393	CC,CT,TT		41.6977,35.3155,39.5356	benign	1911/1940	10346781	5142,7864	2203	4300	6503	SO:0001583	missense	4622	exon40			GTTCCTTGGCCTC		CCDS11154.1	17p13.1	2013-09-19	2006-09-29		ENSG00000264424	ENSG00000264424		"""Myosins / Myosin superfamily : Class II"""	7574	protein-coding gene	gene with protein product		160742	"""myosin, heavy polypeptide 4, skeletal muscle"""			8518795	Standard	NM_017533		Approved	MYH2B, MyHC-2B, MyHC-IIb	uc002gmn.3	Q9Y623	OTTHUMG00000130365	ENST00000255381.2:c.5731A>G	17.37:g.10346781T>C	ENSP00000255381:p.Lys1911Glu	Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	173	84	0.485549	NM_017533		Missense_Mutation	SNP	ENST00000255381.2	37	CCDS11154.1	1125	0.5151098901098901	157	0.31910569105691056	186	0.5138121546961326	498	0.8706293706293706	284	0.37467018469656993	C	2.548	-0.304632	0.05495	0.353155	0.416977	ENSG00000141048	ENST00000255381	D	0.82984	-1.67	5.19	4.23	0.50019	Myosin tail (1);	0.000000	0.36101	N	0.002785	T	0.00012	0.0000	N	0.00028	-2.63	0.58432	P	5.000000000032756E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.44697	-0.9311	9	0.02654	T	1	.	12.1163	0.53868	0.0:0.8614:0.0:0.1386	rs3744554;rs3744554	1911	Q9Y623	MYH4_HUMAN	E	1911	ENSP00000255381:K1911E	ENSP00000255381:K1911E	K	-	1	0	MYH4	10287506	0.929000	0.31497	0.884000	0.34674	0.594000	0.36715	1.988000	0.40697	0.912000	0.36772	-0.119000	0.15052	AAG	T|0.573;C|0.427	0.427	strong		0.458	MYH4-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252731.1	NM_017533	
LAMC2	3918	hgsc.bcm.edu	37	1	183206573	183206573	+	Silent	SNP	G	G	A	rs1047981	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:183206573G>A	ENST00000264144.4	+	18	2753	c.2688G>A	c.(2686-2688)caG>caA	p.Q896Q	LAMC2_ENST00000493293.1_Silent_p.Q896Q	NM_005562.2	NP_005553.2	Q13753	LAMC2_HUMAN	laminin, gamma 2	896	Domain II and I.				cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	cell cortex (GO:0005938)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|laminin-2 complex (GO:0005607)|laminin-5 complex (GO:0005610)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)	heparin binding (GO:0008201)			breast(2)|endometrium(6)|kidney(8)|large_intestine(11)|lung(18)|ovary(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	55						AGCGTACACAGAAGAATCTGG	0.418													A|||	1765	0.352436	0.5401	0.3314	5008	,	,		21193	0.3333		0.1581	False		,,,				2504	0.3333				p.Q896Q		Atlas-SNP	.											LAMC2,NS,carcinoma,+2,1	LAMC2	113	1	0			c.G2688A						PASS	.	A	,	2198,2208	588.8+/-387.0	573,1052,578	99.0	104.0	102.0		2688,2688	-7.6	0.0	1	dbSNP_86	102	1527,7073	747.3+/-407.3	132,1263,2905	no	coding-synonymous,coding-synonymous	LAMC2	NM_005562.2,NM_018891.2	,	705,2315,3483	AA,AG,GG		17.7558,49.8865,28.6406	,	896/1194,896/1112	183206573	3725,9281	2203	4300	6503	SO:0001819	synonymous_variant	3918	exon18			TACACAGAAGAAT	Z15008	CCDS1352.1, CCDS44285.1	1q25-q31	2013-03-01	2002-08-29		ENSG00000058085	ENSG00000058085		"""Laminins"""	6493	protein-coding gene	gene with protein product		150292	"""laminin, gamma 2 (nicein (100kD), kalinin (105kD), BM600 (100kD), Herlitz junctional epidermolysis bullosa))"""	EBR2, LAMB2T, LAMNB2, EBR2A		1383240	Standard	NM_005562		Approved	nicein-100kDa, kalinin-105kDa, BM600-100kDa	uc001gqa.2	Q13753	OTTHUMG00000035520	ENST00000264144.4:c.2688G>A	1.37:g.183206573G>A		Somatic	362	1	0.00276243		WXS	Illumina HiSeq	Phase_I	267	150	0.561798	NM_005562	Q02536|Q02537|Q13752|Q14941|Q14DF7|Q2M1N2|Q5VYE8	Silent	SNP	ENST00000264144.4	37	CCDS1352.1																																																																																			G|0.694;A|0.306	0.306	strong		0.418	LAMC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086258.1	NM_005562	
NLGN1	22871	hgsc.bcm.edu	37	3	173997153	173997153	+	Silent	SNP	G	G	A	rs7646919	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:173997153G>A	ENST00000457714.1	+	6	1791	c.1362G>A	c.(1360-1362)aaG>aaA	p.K454K	NLGN1_ENST00000361589.4_Silent_p.K454K|NLGN1_ENST00000401917.3_Silent_p.K494K|NLGN1_ENST00000545397.1_Silent_p.K454K	NM_014932.2	NP_055747.1	Q8N2Q7	NLGN1_HUMAN	neuroligin 1	471					alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor clustering (GO:0097113)|calcium-dependent cell-cell adhesion (GO:0016339)|cytoskeletal matrix organization at active zone (GO:0048789)|establishment of protein localization (GO:0045184)|heterophilic cell-cell adhesion (GO:0007157)|N-methyl-D-aspartate receptor clustering (GO:0097114)|nervous system development (GO:0007399)|neurexin clustering (GO:0097115)|neuron cell-cell adhesion (GO:0007158)|neuronal signal transduction (GO:0023041)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of intracellular signal transduction (GO:1902533)|positive regulation of ruffle assembly (GO:1900029)|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 synaptic vesicle endocytosis (GO:1900244)|positive regulation of synaptic vesicle exocytosis (GO:2000302)|postsynaptic density protein 95 clustering (GO:0097119)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|protein heterotetramerization (GO:0051290)|protein homooligomerization (GO:0051260)|protein localization to synapse (GO:0035418)|protein targeting (GO:0006605)|receptor localization to synapse (GO:0097120)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of neuron differentiation (GO:0045664)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|synapse assembly (GO:0007416)|synaptic vesicle clustering (GO:0097091)|synaptic vesicle targeting (GO:0016080)|terminal button organization (GO:0072553)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|filopodium tip (GO:0032433)|integral component of plasma membrane (GO:0005887)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuronal postsynaptic density (GO:0097481)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|neurexin family protein binding (GO:0042043)|PDZ domain binding (GO:0030165)|protein dimerization activity (GO:0046983)|receptor activity (GO:0004872)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(9)|liver(2)|lung(54)|ovary(1)|pancreas(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	83	Ovarian(172;0.0025)		LUSC - Lung squamous cell carcinoma(14;5.36e-13)|Lung(28;9.49e-13)			CCAGAAGAAAGACATTACTGG	0.438													G|||	943	0.188299	0.2421	0.1441	5008	,	,		19105	0.0933		0.1978	False		,,,				2504	0.2352				p.K454K		Atlas-SNP	.											NLGN1,caecum,carcinoma,0,1	NLGN1	209	1	0			c.G1362A						scavenged	.	G		1052,3354	383.7+/-325.0	135,782,1286	103.0	99.0	100.0		1362	5.9	1.0	3	dbSNP_116	100	1680,6920	308.5+/-308.9	160,1360,2780	no	coding-synonymous	NLGN1	NM_014932.2		295,2142,4066	AA,AG,GG		19.5349,23.8765,21.0057		454/824	173997153	2732,10274	2203	4300	6503	SO:0001819	synonymous_variant	22871	exon6			AAGAAAGACATTA	AB028993	CCDS3222.1	3q26.32	2008-07-18			ENSG00000169760	ENSG00000169760			14291	protein-coding gene	gene with protein product		600568				10767552, 10819331	Standard	NM_014932		Approved	KIAA1070	uc003fio.1	Q8N2Q7	OTTHUMG00000157005	ENST00000457714.1:c.1362G>A	3.37:g.173997153G>A		Somatic	177	1	0.00564972		WXS	Illumina HiSeq	Phase_I	146	58	0.39726	NM_014932	Q9UPT2	Silent	SNP	ENST00000457714.1	37	CCDS3222.1																																																																																			G|0.797;A|0.203	0.203	strong		0.438	NLGN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347054.3	NM_014932	
MUC4	4585	hgsc.bcm.edu	37	3	195511238	195511238	+	Missense_Mutation	SNP	C	C	T	rs3103956		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195511238C>T	ENST00000463781.3	-	2	7672	c.7213G>A	c.(7213-7215)Gac>Aac	p.D2405N	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.D2405N	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.D2405N(3)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GAGGAAGTGTCGGTGACAGGA	0.592																																					p.D2405N		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,3	MUC4	1505	3	3	Substitution - Missense(3)	NS(2)|endometrium(1)	c.G7213A						scavenged	.						36.0	38.0	37.0					3																	195511238		689	1587	2276	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.7213G>A	3.37:g.195511238C>T	ENSP00000417498:p.Asp2405Asn	Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	133	8	0.0601504	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	7.494	0.651351	0.14516	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.30448	1.55;1.53	.	.	.	.	.	.	.	.	T	0.24967	0.0606	N	0.19112	0.55	0.09310	N	1	P	0.52577	0.954	P	0.55965	0.788	T	0.10590	-1.0623	7	.	.	.	.	2.1447	0.03784	0.0:0.3304:0.3444:0.3251	.	2405	E7ESK3	.	N	2405	ENSP00000417498:D2405N;ENSP00000420243:D2405N	.	D	-	1	0	MUC4	196995633	0.000000	0.05858	0.003000	0.11579	0.080000	0.17528	-0.920000	0.04013	-0.417000	0.07461	0.064000	0.15345	GAC	.	.	weak		0.592	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
MUC4	4585	hgsc.bcm.edu	37	3	195515141	195515141	+	Missense_Mutation	SNP	A	A	G	rs71321850		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195515141A>G	ENST00000463781.3	-	2	3769	c.3310T>C	c.(3310-3312)Tct>Cct	p.S1104P	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.S1104P	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	536					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)		ACAGGAAGAGAGGTGGCGTGA	0.577																																					p.S1104P		Atlas-SNP	.											.	MUC4	1505	.	0			c.T3310C						PASS	.						9.0	7.0	8.0					3																	195515141		652	1501	2153	SO:0001583	missense	4585	exon2			GAAGAGAGGTGGC	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.3310T>C	3.37:g.195515141A>G	ENSP00000417498:p.Ser1104Pro	Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	62	14	0.225806	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	.	.	.	.	.	.	.	.	.	.	-	2.903	-0.226978	0.06022	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.30448	1.54;1.53	0.814	-1.63	0.08345	.	.	.	.	.	T	0.14743	0.0356	N	0.19112	0.55	0.09310	N	1	B	0.18013	0.025	B	0.17979	0.02	T	0.27331	-1.0077	8	.	.	.	.	3.2893	0.06943	0.3417:0.453:0.2052:0.0	.	1104	E7ESK3	.	P	1104	ENSP00000417498:S1104P;ENSP00000420243:S1104P	.	S	-	1	0	MUC4	196999536	0.000000	0.05858	0.000000	0.03702	0.233000	0.25261	-2.301000	0.01137	-1.323000	0.02275	0.055000	0.15244	TCT	A|0.250;G|0.750	0.750	weak		0.577	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
RTN4IP1	84816	hgsc.bcm.edu	37	6	107019880	107019880	+	Silent	SNP	A	A	G	rs9486410	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:107019880A>G	ENST00000369063.3	-	9	1647	c.1182T>C	c.(1180-1182)aaT>aaC	p.N394N	RTN4IP1_ENST00000539449.1_3'UTR|RTN4IP1_ENST00000498091.1_5'UTR	NM_032730.4	NP_116119.2	Q8WWV3	RT4I1_HUMAN	reticulon 4 interacting protein 1	394						mitochondrion (GO:0005739)	oxidoreductase activity (GO:0016491)|zinc ion binding (GO:0008270)			breast(1)|kidney(3)|large_intestine(2)|lung(6)|urinary_tract(1)	13	Breast(9;0.0107)|all_epithelial(6;0.14)	all_cancers(87;9.45e-05)|Acute lymphoblastic leukemia(125;2.13e-07)|all_hematologic(75;5.28e-06)|all_epithelial(87;0.0144)	Epithelial(6;0.000873)|all cancers(7;0.00363)|BRCA - Breast invasive adenocarcinoma(8;0.00721)|OV - Ovarian serous cystadenocarcinoma(5;0.0394)	all cancers(137;0.113)|BRCA - Breast invasive adenocarcinoma(108;0.127)|Epithelial(106;0.144)		TTTAAACAACATTAATTACAG	0.383													G|||	929	0.185503	0.3011	0.1081	5008	,	,		19931	0.1696		0.1561	False		,,,				2504	0.1309				p.N394N		Atlas-SNP	.											RTN4IP1,NS,carcinoma,-2,1	RTN4IP1	31	1	0			c.T1182C						PASS	.	G		1228,3178	706.5+/-407.4	171,886,1146	111.0	105.0	107.0		1182	-0.6	0.0	6	dbSNP_119	107	981,7619	773.9+/-407.7	54,873,3373	no	coding-synonymous	RTN4IP1	NM_032730.4		225,1759,4519	GG,GA,AA		11.407,27.8711,16.9845		394/397	107019880	2209,10797	2203	4300	6503	SO:0001819	synonymous_variant	84816	exon9			AACAACATTAATT	AF336861	CCDS5056.1	6q21	2008-02-05			ENSG00000130347	ENSG00000130347			18647	protein-coding gene	gene with protein product		610502					Standard	NM_032730		Approved	NIMP	uc003prj.3	Q8WWV3	OTTHUMG00000015304	ENST00000369063.3:c.1182T>C	6.37:g.107019880A>G		Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	104	52	0.5	NM_032730	Q8N9B3|Q8WZ66|Q9BRA4	Silent	SNP	ENST00000369063.3	37	CCDS5056.1																																																																																			A|0.834;G|0.166	0.166	strong		0.383	RTN4IP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041673.1		
PARD3B	117583	hgsc.bcm.edu	37	2	206364737	206364737	+	Silent	SNP	T	T	C	rs10197347	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:206364737T>C	ENST00000406610.2	+	21	3369	c.3162T>C	c.(3160-3162)tcT>tcC	p.S1054S	PARD3B_ENST00000488622.1_3'UTR|PARD3B_ENST00000349953.3_Silent_p.S953S|PARD3B_ENST00000358768.2_Silent_p.S992S|PARD3B_ENST00000351153.1_Silent_p.S985S	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	1054					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)		CAAGGCCATCTGAGTATGACC	0.438													T|||	2246	0.448482	0.3601	0.5692	5008	,	,		21928	0.4871		0.4115	False		,,,				2504	0.4806				p.S992S		Atlas-SNP	.											.	PARD3B	314	.	0			c.T2976C						PASS	.	T	,,	1436,2416		266,904,756	216.0	198.0	203.0		2955,2976,2859	2.5	1.0	2	dbSNP_119	203	3152,5096		639,1874,1611	yes	coding-synonymous,coding-synonymous,coding-synonymous	PARD3B	NM_057177.6,NM_152526.5,NM_205863.3	,,	905,2778,2367	CC,CT,TT		38.2153,37.2793,37.9174	,,	985/1137,992/1144,953/1105	206364737	4588,7512	1926	4124	6050	SO:0001819	synonymous_variant	117583	exon20			GCCATCTGAGTAT	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.3162T>C	2.37:g.206364737T>C		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	64	36	0.5625	NM_152526	E9PE87|Q8IUC7|Q8IUC9|Q96DK9|Q96N09|Q96NX6|Q96NX7|Q96Q29	Silent	SNP	ENST00000406610.2	37																																																																																				T|0.587;C|0.413	0.413	strong		0.438	PARD3B-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000335992.1	NM_057177	
CER1	9350	hgsc.bcm.edu	37	9	14720361	14720361	+	Silent	SNP	T	T	C	rs17289263	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:14720361T>C	ENST00000380911.3	-	2	575	c.531A>G	c.(529-531)gaA>gaG	p.E177E		NM_005454.2	NP_005445.1	O95813	CER1_HUMAN	cerberus 1, DAN family BMP antagonist	177	CTCK. {ECO:0000255|PROSITE- ProRule:PRU00039}.				anterior/posterior axis specification (GO:0009948)|anterior/posterior pattern specification (GO:0009952)|BMP signaling pathway (GO:0030509)|bone mineralization (GO:0030282)|cell migration involved in gastrulation (GO:0042074)|cellular response to BMP stimulus (GO:0071773)|determination of dorsal identity (GO:0048263)|gastrulation (GO:0007369)|growth plate cartilage chondrocyte proliferation (GO:0003419)|negative regulation of activin receptor signaling pathway (GO:0032926)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of cell proliferation (GO:0008285)|negative regulation of mesoderm development (GO:2000381)|nervous system development (GO:0007399)|sequestering of BMP in extracellular matrix (GO:0035582)|signal transduction involved in regulation of gene expression (GO:0023019)|ureteric bud development (GO:0001657)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	BMP binding (GO:0036122)|morphogen activity (GO:0016015)|protein homodimerization activity (GO:0042803)			endometrium(2)|large_intestine(3)|lung(6)	11				GBM - Glioblastoma multiforme(50;3.16e-06)		CAACTACTTTTTCACAGCCTT	0.418													T|||	316	0.063099	0.056	0.0634	5008	,	,		20876	0.005		0.1203	False		,,,				2504	0.0736				p.E177E		Atlas-SNP	.											.	CER1	41	.	0			c.A531G						PASS	.	T		319,4087	166.9+/-198.0	6,307,1890	64.0	56.0	59.0		531	0.6	1.0	9	dbSNP_123	59	1048,7552	216.2+/-255.3	49,950,3301	no	coding-synonymous	CER1	NM_005454.2		55,1257,5191	CC,CT,TT		12.186,7.2401,10.5105		177/268	14720361	1367,11639	2203	4300	6503	SO:0001819	synonymous_variant	9350	exon2			TACTTTTTCACAG	AF090189	CCDS6476.1	9p23-p22	2013-02-26	2013-02-26		ENSG00000147869	ENSG00000147869			1862	protein-coding gene	gene with protein product		603777	"""cerberus 1 (Xenopus laevis) homolog (cysteine knot superfamily)"", ""cerberus 1, cysteine knot superfamily, homolog (Xenopus laevis)"""			10049596	Standard	NM_005454		Approved	DAND4	uc003zlj.3	O95813	OTTHUMG00000021022	ENST00000380911.3:c.531A>G	9.37:g.14720361T>C		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	98	44	0.44898	NM_005454	Q6ISJ1|Q6ISJ6|Q6ISQ2|Q6ISS1	Silent	SNP	ENST00000380911.3	37	CCDS6476.1																																																																																			T|0.907;C|0.093	0.093	strong		0.418	CER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055453.1	NM_005454	
LRRN3	54674	hgsc.bcm.edu	37	7	110764596	110764596	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:110764596A>G	ENST00000422987.3	+	2	2599	c.1768A>G	c.(1768-1770)Aaa>Gaa	p.K590E	IMMP2L_ENST00000450877.1_Intron|IMMP2L_ENST00000405709.2_Intron|LRRN3_ENST00000451085.1_Missense_Mutation_p.K590E|IMMP2L_ENST00000452895.1_Intron|IMMP2L_ENST00000437687.1_Intron|IMMP2L_ENST00000447215.1_Intron|IMMP2L_ENST00000415362.1_Intron|IMMP2L_ENST00000331762.3_Intron|IMMP2L_ENST00000489381.1_Intron|LRRN3_ENST00000308478.5_Missense_Mutation_p.K590E	NM_018334.4	NP_060804.3	Q9H3W5	LRRN3_HUMAN	leucine rich repeat neuronal 3	590	Fibronectin type-III. {ECO:0000255|PROSITE-ProRule:PRU00316}.				positive regulation of protein phosphorylation (GO:0001934)	clathrin adaptor complex (GO:0030131)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(15)|lung(20)|ovary(2)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	55				UCEC - Uterine corpus endometrioid carcinoma (4;0.245)|LUSC - Lung squamous cell carcinoma(290;0.0715)|Lung(3;0.0864)|STAD - Stomach adenocarcinoma(3;0.125)		AACTGAGTATAAAATTTGTAT	0.348																																					p.K590E		Atlas-SNP	.											.	LRRN3	132	.	0			c.A1768G						PASS	.						44.0	43.0	43.0					7																	110764596		2203	4300	6503	SO:0001583	missense	54674	exon2			GAGTATAAAATTT	AB060967	CCDS5754.1	7q31.1	2013-02-11			ENSG00000173114	ENSG00000173114		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	17200	protein-coding gene	gene with protein product	"""fibronectin type III, immunoglobulin and leucine rich repeat domains 5"""					11549284	Standard	NM_001099660		Approved	NLRR3, FLJ11129, FIGLER5	uc003vfs.4	Q9H3W5	OTTHUMG00000155039	ENST00000422987.3:c.1768A>G	7.37:g.110764596A>G	ENSP00000412417:p.Lys590Glu	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	69	22	0.318841	NM_018334	O43377|Q6I9V8|Q8IYQ6	Missense_Mutation	SNP	ENST00000422987.3	37	CCDS5754.1	.	.	.	.	.	.	.	.	.	.	A	0.129	-1.115378	0.01799	.	.	ENSG00000173114	ENST00000308478;ENST00000451085;ENST00000422987	T;T;T	0.55052	0.54;0.54;0.54	5.59	4.41	0.53225	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.190873	0.36303	N	0.002673	T	0.25195	0.0612	N	0.10733	0.035	0.38993	D	0.959181	B	0.10296	0.003	B	0.13407	0.009	T	0.16689	-1.0394	10	0.02654	T	1	.	7.5231	0.27639	0.7855:0.1436:0.0709:0.0	.	590	Q9H3W5	LRRN3_HUMAN	E	590	ENSP00000312001:K590E;ENSP00000397312:K590E;ENSP00000412417:K590E	ENSP00000312001:K590E	K	+	1	0	LRRN3	110551832	0.995000	0.38212	0.997000	0.53966	0.964000	0.63967	2.962000	0.49176	1.033000	0.39918	0.529000	0.55759	AAA	.	.	none		0.348	LRRN3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338171.2	NM_018334	
OR1L4	254973	hgsc.bcm.edu	37	9	125486686	125486686	+	Missense_Mutation	SNP	T	T	A	rs149895531	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:125486686T>A	ENST00000259466.1	+	1	418	c.418T>A	c.(418-420)Tgg>Agg	p.W140R		NM_001005235.1	NP_001005235.1	Q8NGR5	OR1L4_HUMAN	olfactory receptor, family 1, subfamily L, member 4	140						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(3)|lung(13)|prostate(1)|skin(1)	20						TATGAAACCATGGCATTGCCT	0.522													T|||	63	0.0125799	0.003	0.0144	5008	,	,		21978	0.0		0.0368	False		,,,				2504	0.0123				p.W140R		Atlas-SNP	.											.	OR1L4	38	.	0			c.T418A						PASS	.	T	ARG/TRP	30,4376		0,30,2173	239.0	188.0	205.0		418	-0.3	0.2	9	dbSNP_134	205	254,8346		5,244,4051	no	missense	OR1L4	NM_001005235.1	101	5,274,6224	AA,AT,TT		2.9535,0.6809,2.1836	benign	140/312	125486686	284,12722	2203	4300	6503	SO:0001583	missense	254973	exon1			AAACCATGGCATT		CCDS35129.1	9q33.2	2013-09-20			ENSG00000136939	ENSG00000136939		"""GPCR / Class A : Olfactory receptors"""	8216	protein-coding gene	gene with protein product				OR1L5			Standard	NM_001005235		Approved	OR9-E	uc004bmu.1	Q8NGR5	OTTHUMG00000020620	ENST00000259466.1:c.418T>A	9.37:g.125486686T>A	ENSP00000259466:p.Trp140Arg	Somatic	218	1	0.00458716		WXS	Illumina HiSeq	Phase_I	209	111	0.5311	NM_001005235	Q6IFN0|Q96R81	Missense_Mutation	SNP	ENST00000259466.1	37	CCDS35129.1	42	0.019230769230769232	3	0.006097560975609756	5	0.013812154696132596	0	0.0	34	0.044854881266490766	.	0.001	-3.358311	0.00016	0.006809	0.029535	ENSG00000136939	ENST00000259466	T	0.31247	1.5	4.01	-0.339	0.12647	GPCR, rhodopsin-like superfamily (1);	1.200980	0.06117	N	0.668242	T	0.01421	0.0046	N	0.00602	-1.34	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.33497	-0.9866	10	0.02654	T	1	1.6564	2.7906	0.05387	0.4926:0.2771:0.1319:0.0984	.	140	Q8NGR5	OR1L4_HUMAN	R	140	ENSP00000259466:W140R	ENSP00000259466:W140R	W	+	1	0	OR1L4	124526507	0.000000	0.05858	0.204000	0.23530	0.004000	0.04260	-0.961000	0.03845	0.326000	0.23384	-0.817000	0.03123	TGG	A|0.023;T|0.977	0.023	strong		0.522	OR1L4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053951.1		
C20orf96	140680	hgsc.bcm.edu	37	20	259969	259969	+	Silent	SNP	G	G	C	rs7271033	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:259969G>C	ENST00000360321.2	-	5	447	c.309C>G	c.(307-309)acC>acG	p.T103T	C20orf96_ENST00000400269.3_Silent_p.T45T|C20orf96_ENST00000382369.5_Silent_p.T68T	NM_080571.1|NM_153269.2	NP_542138.1|NP_695001.2	Q9NUD7	CT096_HUMAN	chromosome 20 open reading frame 96	103										endometrium(3)|large_intestine(2)|lung(4)|prostate(1)|skin(1)|urinary_tract(1)	12		all_cancers(10;0.00959)|Lung NSC(37;0.227)	OV - Ovarian serous cystadenocarcinoma(29;0.149)			TCCTGAGCGAGGTCTGCGGGC	0.716													C|||	3348	0.66853	0.8442	0.4914	5008	,	,		6030	0.7897		0.5606	False		,,,				2504	0.5429				p.T103T		Atlas-SNP	.											.	C20orf96	28	.	0			c.C309G						PASS	.	C	,	3469,937	351.6+/-311.3	1368,733,102	56.0	44.0	48.0		306,309	0.8	0.0	20	dbSNP_116	48	4816,3784	532.5+/-382.2	1353,2110,837	no	coding-synonymous,coding-synonymous	C20orf96	NM_080571.1,NM_153269.2	,	2721,2843,939	CC,CG,GG		44.0,21.2665,36.2986	,	102/363,103/364	259969	8285,4721	2203	4300	6503	SO:0001819	synonymous_variant	140680	exon5			GAGCGAGGTCTGC	AL034548	CCDS12994.1, CCDS74685.1	20p13	2012-10-30			ENSG00000196476	ENSG00000196476			16227	protein-coding gene	gene with protein product							Standard	NM_153269		Approved	dJ1103G7.2	uc002wde.2	Q9NUD7	OTTHUMG00000031626	ENST00000360321.2:c.309C>G	20.37:g.259969G>C		Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	22	12	0.545455	NM_153269	A3KPE0|B2RPH9|Q8N840|Q8NAX5	Silent	SNP	ENST00000360321.2	37	CCDS12994.1																																																																																			G|0.353;C|0.647	0.647	strong		0.716	C20orf96-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077439.2	NM_153269	
AREL1	9870	hgsc.bcm.edu	37	14	75142606	75142606	+	Silent	SNP	G	G	A	rs35864766	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:75142606G>A	ENST00000356357.4	-	8	1391	c.876C>T	c.(874-876)ggC>ggT	p.G292G	AREL1_ENST00000557401.1_5'UTR	NM_001039479.1	NP_001034568.1	O15033	AREL1_HUMAN	apoptosis resistant E3 ubiquitin protein ligase 1	292					apoptotic process (GO:0006915)|negative regulation of apoptotic process (GO:0043066)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)										AAATGCTCACGCCTGAAGTGG	0.443													G|||	35	0.00698882	0.0008	0.0101	5008	,	,		20927	0.0		0.0129	False		,,,				2504	0.0143				p.G292G		Atlas-SNP	.											.	KIAA0317	68	.	0			c.C876T						PASS	.	G		21,3991		0,21,1985	139.0	140.0	140.0		876	-1.4	1.0	14	dbSNP_126	140	193,8157		6,181,3988	no	coding-synonymous	KIAA0317	NM_001039479.1		6,202,5973	AA,AG,GG		2.3114,0.5234,1.7311		292/824	75142606	214,12148	2006	4175	6181	SO:0001819	synonymous_variant	9870	exon8			GCTCACGCCTGAA	AB002315	CCDS41971.1	14q24.2	2013-04-15	2013-04-15	2013-04-15	ENSG00000119682	ENSG00000119682			20363	protein-coding gene	gene with protein product		615380	"""KIAA0317"""	KIAA0317		9205841, 23479728	Standard	XM_006720344		Approved		uc001xqb.3	O15033	OTTHUMG00000154499	ENST00000356357.4:c.876C>T	14.37:g.75142606G>A		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	79	39	0.493671	NM_001039479	B4E2C7|Q7LDY1|Q8IYY9	Silent	SNP	ENST00000356357.4	37	CCDS41971.1	13	0.005952380952380952	1	0.0020325203252032522	4	0.011049723756906077	0	0.0	8	0.010554089709762533	G	9.535	1.111930	0.20714	0.005234	0.023114	ENSG00000119682	ENST00000490805	.	.	.	5.87	-1.44	0.08856	.	.	.	.	.	T	0.22859	0.0552	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.25847	-1.0120	4	.	.	.	.	0.1629	0.00105	0.3435:0.1631:0.1871:0.3063	rs35864766	.	.	.	V	40	.	.	A	-	2	0	KIAA0317	74212359	0.816000	0.29132	0.998000	0.56505	0.936000	0.57629	-0.124000	0.10595	-0.091000	0.12440	-0.383000	0.06682	GCG	G|0.985;A|0.015	0.015	strong		0.443	AREL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335517.2	NM_014821	
EBF4	57593	hgsc.bcm.edu	37	20	2739583	2739583	+	Silent	SNP	T	T	C	rs2073125	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:2739583T>C	ENST00000609451.1	+	16	1839	c.1767T>C	c.(1765-1767)ttT>ttC	p.F589F	EBF4_ENST00000380648.4_Silent_p.F585F|EBF4_ENST00000477287.1_3'UTR			Q9BQW3	COE4_HUMAN	early B-cell factor 4	589					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)										CTGACAAGTTTCACTCTCCAG	0.582													C|||	1929	0.385184	0.3404	0.2565	5008	,	,		17183	0.5417		0.2982	False		,,,				2504	0.4652				p.F585F		Atlas-SNP	.											.	.	.	.	0			c.T1755C						PASS	.	C		544,840		104,336,252	122.0	105.0	110.0		1755	3.8	1.0	20	dbSNP_96	110	973,2209		153,667,771	no	coding-synonymous	EBF4	NM_001110514.1		257,1003,1023	CC,CT,TT		30.5783,39.3064,33.2238		585/599	2739583	1517,3049	692	1591	2283	SO:0001819	synonymous_variant	57593	exon17			CAAGTTTCACTCT	BC019106	CCDS46573.1	20p13	2008-10-23			ENSG00000088881	ENSG00000088881			29278	protein-coding gene	gene with protein product		609935				10718198	Standard	NM_001110514		Approved	KIAA1442, COE4, RP5-860F19.3, O/E-4	uc002wgt.4	Q9BQW3	OTTHUMG00000031709	ENST00000609451.1:c.1767T>C	20.37:g.2739583T>C		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	128	58	0.453125	NM_001110514	Q1MTP7|Q5JY53|Q9NUB6|Q9P2A6	Silent	SNP	ENST00000609451.1	37																																																																																				T|0.647;C|0.353	0.353	strong		0.582	EBF4-011	PUTATIVE	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000471930.1	XM_938882	
WDR73	84942	hgsc.bcm.edu	37	15	85189464	85189464	+	Silent	SNP	T	T	G	rs2271431	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:85189464T>G	ENST00000434634.2	-	6	528	c.468A>C	c.(466-468)cgA>cgC	p.R156R	WDR73_ENST00000398528.3_5'UTR	NM_032856.2	NP_116245.2	Q6P4I2	WDR73_HUMAN	WD repeat domain 73	156										cervix(1)|large_intestine(1)|lung(1)	3						CCTGCAGACTTCGGAGCCTCG	0.602													G|||	737	0.147165	0.0287	0.1902	5008	,	,		17725	0.1379		0.2734	False		,,,				2504	0.1564				p.R156R		Atlas-SNP	.											.	WDR73	15	.	0			c.A468C						PASS	.	G		247,3761		7,233,1764	47.0	51.0	50.0		468	-2.1	0.0	15	dbSNP_100	50	2280,6066		290,1700,2183	no	coding-synonymous	WDR73	NM_032856.2		297,1933,3947	GG,GT,TT		27.3185,6.1627,20.4549		156/379	85189464	2527,9827	2004	4173	6177	SO:0001819	synonymous_variant	84942	exon6			CAGACTTCGGAGC	AK027200	CCDS45339.1	15q25.2	2013-01-09				ENSG00000177082		"""WD repeat domain containing"""	25928	protein-coding gene	gene with protein product						12477932	Standard	NM_032856		Approved	FLJ14888, HSPC264	uc002bkw.2	Q6P4I2		ENST00000434634.2:c.468A>C	15.37:g.85189464T>G		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	42	29	0.690476	NM_032856	Q96JZ1|Q9P0B7	Silent	SNP	ENST00000434634.2	37	CCDS45339.1																																																																																			T|0.830;G|0.170	0.170	strong		0.602	WDR73-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418195.1	NM_032856	
DNAH10	196385	hgsc.bcm.edu	37	12	124417889	124417889	+	Silent	SNP	C	C	T	rs4930721	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:124417889C>T	ENST00000409039.3	+	76	12979	c.12954C>T	c.(12952-12954)agC>agT	p.S4318S	RP11-380L11.3_ENST00000602292.1_RNA|DNAH10_ENST00000538983.1_3'UTR|DNAH10OS_ENST00000514254.2_Intron|CCDC92_ENST00000544798.1_Intron	NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	4318					microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	52	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)		TGACCGAGAGCGAGCCCAGCG	0.607													C|||	1305	0.260583	0.3109	0.3228	5008	,	,		16949	0.123		0.3479	False		,,,				2504	0.2004				p.S4318S		Atlas-SNP	.											.	DNAH10	888	.	0			c.C12954T						PASS	.	C		1200,2700		172,856,922	16.0	18.0	17.0		12954	-9.1	0.0	12	dbSNP_111	17	2550,5748		381,1788,1980	no	coding-synonymous	DNAH10	NM_207437.3		553,2644,2902	TT,TC,CC		30.7303,30.7692,30.7427		4318/4472	124417889	3750,8448	1950	4149	6099	SO:0001819	synonymous_variant	196385	exon76			CGAGAGCGAGCCC	AJ132089	CCDS9255.2	12q24	2008-02-05	2006-09-04		ENSG00000197653	ENSG00000197653		"""Axonemal dyneins"""	2941	protein-coding gene	gene with protein product		605884	"""dynein, axonemal, heavy polypeptide 10"""				Standard	NM_207437		Approved	FLJ43808	uc001uft.4	Q8IVF4	OTTHUMG00000154477	ENST00000409039.3:c.12954C>T	12.37:g.124417889C>T		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	59	33	0.559322	NM_207437	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Silent	SNP	ENST00000409039.3	37	CCDS9255.2																																																																																			C|0.719;T|0.281	0.281	strong		0.607	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3		
AASDH	132949	hgsc.bcm.edu	37	4	57248716	57248716	+	Missense_Mutation	SNP	G	G	C	rs34228795	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:57248716G>C	ENST00000205214.6	-	3	458	c.278C>G	c.(277-279)cCa>cGa	p.P93R	AASDH_ENST00000502617.1_Missense_Mutation_p.P93R|AASDH_ENST00000602986.1_Intron|AASDH_ENST00000451613.1_Missense_Mutation_p.P93R|AASDH_ENST00000513376.1_5'UTR|AASDH_ENST00000434343.2_5'UTR|AASDH_ENST00000510762.1_Intron	NM_181806.2	NP_861522.2	Q4L235	ACSF4_HUMAN	aminoadipate-semialdehyde dehydrogenase	93			P -> R (in dbSNP:rs34228795). {ECO:0000269|PubMed:11042152}.		fatty acid metabolic process (GO:0006631)		acid-thiol ligase activity (GO:0016878)|ATP binding (GO:0005524)			endometrium(2)|kidney(2)|large_intestine(8)|lung(17)|ovary(4)|prostate(3)|skin(2)|stomach(1)|urinary_tract(1)	40	Glioma(25;0.08)|all_neural(26;0.101)	all_hematologic(202;0.0017)				TAATGACGGTGGTGAATCTGG	0.318													G|||	324	0.0646965	0.0129	0.0231	5008	,	,		17191	0.1905		0.0179	False		,,,				2504	0.0828				p.P93R		Atlas-SNP	.											AASDH,NS,osteosarcoma,0,1	AASDH	101	1	0			c.C278G						scavenged	.	G	ARG/PRO	58,4348	53.6+/-89.4	0,58,2145	70.0	71.0	71.0		278	5.0	1.0	4	dbSNP_126	71	179,8421	80.9+/-143.5	1,177,4122	yes	missense	AASDH	NM_181806.2	103	1,235,6267	CC,CG,GG		2.0814,1.3164,1.8222	probably-damaging	93/1099	57248716	237,12769	2203	4300	6503	SO:0001583	missense	132949	exon3			GACGGTGGTGAAT	AF516672	CCDS3504.1, CCDS68705.1, CCDS68706.1, CCDS75126.1, CCDS75127.1	4q12	2010-12-14			ENSG00000157426	ENSG00000157426	1.2.1.31	"""Acyl-CoA synthetase family"""	23993	protein-coding gene	gene with protein product	"""acyl-CoA synthetase family member 4"""	614365				15865210, 12712191, 17762044	Standard	XM_005265721		Approved	NRPS998, LYS2, ACSF4	uc003hbn.3	Q4L235	OTTHUMG00000128841	ENST00000205214.6:c.278C>G	4.37:g.57248716G>C	ENSP00000205214:p.Pro93Arg	Somatic	192	1	0.00520833		WXS	Illumina HiSeq	Phase_I	133	68	0.511278	NM_181806	A5D8V3|A5PL22|Q63HK2|Q63HR7|Q6IPP8|Q6TFZ6|Q7Z5Y3|Q96BW4|Q9P064	Missense_Mutation	SNP	ENST00000205214.6	37	CCDS3504.1	158	0.07234432234432235	12	0.024390243902439025	14	0.03867403314917127	120	0.2097902097902098	12	0.0158311345646438	G	13.98	2.399340	0.42512	0.013164	0.020814	ENSG00000157426	ENST00000205214;ENST00000451613;ENST00000502617	T;T;T	0.54675	0.56;0.8;0.56	5.88	5.03	0.67393	AMP-dependent synthetase/ligase (1);	0.149194	0.64402	D	0.000008	T	0.00178	0.0005	M	0.91768	3.24	0.29112	P	0.880773	D;D;D;D	0.65815	0.993;0.995;0.993;0.995	D;D;D;D	0.69142	0.932;0.959;0.962;0.956	T	0.16041	-1.0416	9	0.66056	D	0.02	-0.9919	12.1108	0.53838	0.1413:0.0:0.8587:0.0	rs34228795	93;93;93;93	Q4L235-4;B4E2K0;Q4L235-3;Q4L235	.;.;.;ACSF4_HUMAN	R	93	ENSP00000205214:P93R;ENSP00000409656:P93R;ENSP00000421171:P93R	ENSP00000205214:P93R	P	-	2	0	AASDH	56943473	1.000000	0.71417	0.977000	0.42913	0.198000	0.23893	4.194000	0.58393	1.468000	0.48064	0.655000	0.94253	CCA	G|0.967;C|0.033	0.033	strong		0.318	AASDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250780.1	NM_181806	
CEP192	55125	hgsc.bcm.edu	37	18	13069782	13069782	+	Missense_Mutation	SNP	C	C	T	rs6505780	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:13069782C>T	ENST00000325971.8	+	25	4906	c.3313C>T	c.(3313-3315)Ctc>Ttc	p.L1105F	CEP192_ENST00000430049.2_Missense_Mutation_p.L1226F|CEP192_ENST00000506447.1_Missense_Mutation_p.L1701F			Q8TEP8	CE192_HUMAN	centrosomal protein 192kDa	1105			L -> F (in dbSNP:rs6505780). {ECO:0000269|PubMed:11230166, ECO:0000269|PubMed:12693554, ECO:0000269|PubMed:15498874}.		centrosome duplication (GO:0051298)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|negative regulation of phosphatase activity (GO:0010923)|spindle assembly (GO:0051225)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)	phosphatase binding (GO:0019902)			NS(1)|breast(4)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(36)|ovary(4)|pancreas(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	71						AAAGAATCTACTCCTTAAACC	0.368													T|||	3857	0.770168	0.9486	0.6455	5008	,	,		22039	0.8105		0.6193	False		,,,				2504	0.7311				p.L1701F		Atlas-SNP	.											.	CEP192	340	.	0			c.C5101T						PASS	.	T	PHE/LEU	3886,520	236.8+/-248.8	1713,460,30	102.0	105.0	104.0		5101	5.5	0.6	18	dbSNP_116	104	5329,3271	490.5+/-372.9	1664,2001,635	yes	missense	CEP192	NM_032142.3	22	3377,2461,665	TT,TC,CC		38.0349,11.8021,29.1481	benign	1701/2538	13069782	9215,3791	2203	4300	6503	SO:0001583	missense	55125	exon27			AATCTACTCCTTA	AK074074	CCDS32792.1, CCDS32792.2	18p11.21	2014-02-20				ENSG00000101639		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	25515	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 62"""					11230166, 14654843	Standard	NM_032142		Approved	KIAA1569, FLJ10352, PPP1R62	uc010xac.2	Q8TEP8		ENST00000325971.8:c.3313C>T	18.37:g.13069782C>T	ENSP00000317156:p.Leu1105Phe	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	65	33	0.507692	NM_032142	A0A060A9S4|E9PF99|Q8WYT8|Q9H0F4|Q9NW27	Missense_Mutation	SNP	ENST00000325971.8	37		1635	0.7486263736263736	461	0.9369918699186992	238	0.6574585635359116	464	0.8111888111888111	472	0.6226912928759895	T	2.206	-0.381800	0.04966	0.881979	0.619651	ENSG00000101639	ENST00000506447;ENST00000325971;ENST00000399863;ENST00000430049	T;T;T	0.42900	0.96;0.96;0.96	5.47	5.47	0.80525	.	0.062950	0.64402	N	0.000004	T	0.00012	0.0000	N	0.00263	-1.745	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	0.40646	-0.9552	9	0.02654	T	1	-10.6382	10.4557	0.44548	0.0:0.0773:0.0:0.9227	rs6505780;rs17660946;rs59425635;rs6505780	1226;1701;303	C9JT09;E9PF99;Q9HCK3	.;.;.	F	1701;1105;1105;1226	ENSP00000427550:L1701F;ENSP00000317156:L1105F;ENSP00000389190:L1226F	ENSP00000317156:L1105F	L	+	1	0	CEP192	13059782	0.968000	0.33430	0.621000	0.29145	0.743000	0.42351	2.323000	0.43823	0.927000	0.37143	-0.361000	0.07541	CTC	C|0.258;T|0.742	0.742	strong		0.368	CEP192-201	KNOWN	basic	protein_coding	protein_coding		NM_032142	
FER	2241	hgsc.bcm.edu	37	5	108281909	108281909	+	Missense_Mutation	SNP	C	C	G	rs2229086	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:108281909C>G	ENST00000281092.4	+	11	1699	c.1315C>G	c.(1315-1317)Ctg>Gtg	p.L439V	FER_ENST00000536402.1_3'UTR|FER_ENST00000438717.2_Missense_Mutation_p.L264V	NM_005246.2	NP_005237.2	P16591	FER_HUMAN	fer (fps/fes related) tyrosine kinase	439			L -> V (in dbSNP:rs34499946). {ECO:0000269|PubMed:1651563, ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:2725517}.		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)		AAAATCTGCACTGGGCTCTTC	0.378													C|||	291	0.058107	0.0045	0.0259	5008	,	,		16093	0.0863		0.0537	False		,,,				2504	0.1288				p.L439V	Colon(146;1051 1799 9836 27344 47401)	Atlas-SNP	.											.	FER	100	.	0			c.C1315G						PASS	.	C	VAL/LEU	42,4362	44.6+/-78.6	0,42,2160	111.0	118.0	116.0		1315	0.2	0.0	5	dbSNP_126	116	482,8118	139.8+/-196.4	10,462,3828	yes	missense	FER	NM_005246.2	32	10,504,5988	GG,GC,CC		5.6047,0.9537,4.0295	benign	439/823	108281909	524,12480	2202	4300	6502	SO:0001583	missense	2241	exon11			TCTGCACTGGGCT	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.1315C>G	5.37:g.108281909C>G	ENSP00000281092:p.Leu439Val	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	59	27	0.457627	NM_005246	B2RCR4|B4DSQ2|H2FLB8	Missense_Mutation	SNP	ENST00000281092.4	37	CCDS4098.1	104	0.047619047619047616	4	0.008130081300813009	10	0.027624309392265192	48	0.08391608391608392	42	0.055408970976253295	C	0.358	-0.941189	0.02322	0.009537	0.056047	ENSG00000151422	ENST00000281092;ENST00000438717	T;T	0.76578	-1.03;-0.99	5.45	0.156	0.14910	.	0.305350	0.32028	N	0.006695	T	0.07728	0.0194	L	0.58669	1.825	0.27111	P	0.9623734	B	0.31383	0.321	B	0.20577	0.03	T	0.34428	-0.9829	9	0.10111	T	0.7	0.8458	4.8822	0.13685	0.1422:0.3896:0.0:0.4682	rs41318630	439	P16591	FER_HUMAN	V	439;264	ENSP00000281092:L439V;ENSP00000394297:L264V	ENSP00000281092:L439V	L	+	1	2	FER	108309808	0.694000	0.27738	0.004000	0.12327	0.485000	0.33311	-0.134000	0.10436	0.022000	0.15160	0.491000	0.48974	CTG	C|0.956;G|0.044	0.044	strong		0.378	FER-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250664.1	NM_005246	
EIF2AK3	9451	hgsc.bcm.edu	37	2	88926522	88926522	+	Nonsense_Mutation	SNP	C	C	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:88926522C>A	ENST00000303236.3	-	1	572	c.271G>T	c.(271-273)Gaa>Taa	p.E91*	AC062029.1_ENST00000606164.1_RNA|EIF2AK3_ENST00000419748.1_5'Flank|AC062029.1_ENST00000453008.2_RNA	NM_004836.5	NP_004827.4	Q9NZJ5	E2AK3_HUMAN	eukaryotic translation initiation factor 2-alpha kinase 3	91					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of signaling protein activity involved in unfolded protein response (GO:0006987)|bone mineralization (GO:0030282)|calcium-mediated signaling (GO:0019722)|cellular protein metabolic process (GO:0044267)|chondrocyte development (GO:0002063)|endocrine pancreas development (GO:0031018)|endoplasmic reticulum organization (GO:0007029)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER overload response (GO:0006983)|fat cell differentiation (GO:0045444)|insulin secretion (GO:0030073)|insulin-like growth factor receptor signaling pathway (GO:0048009)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|lactation (GO:0007595)|negative regulation of apoptotic process (GO:0043066)|negative regulation of gene expression (GO:0010629)|negative regulation of myelination (GO:0031642)|negative regulation of translation (GO:0017148)|negative regulation of translational initiation in response to stress (GO:0032057)|ossification (GO:0001503)|positive regulation of protein binding (GO:0032092)|positive regulation of signal transduction (GO:0009967)|protein autophosphorylation (GO:0046777)|protein homooligomerization (GO:0051260)|protein phosphorylation (GO:0006468)|regulation of fatty acid metabolic process (GO:0019217)|response to endoplasmic reticulum stress (GO:0034976)|skeletal system development (GO:0001501)|SREBP signaling pathway (GO:0032933)|translation (GO:0006412)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|eukaryotic translation initiation factor 2alpha kinase activity (GO:0004694)|identical protein binding (GO:0042802)|protein kinase activity (GO:0004672)|protein phosphatase binding (GO:0019903)|protein serine/threonine kinase activity (GO:0004674)			ovary(3)	3						TCGTCTGGTTCCGGACCCCGA	0.731																																					p.E91X	GBM(138;671 1851 16235 39058 45249)	Atlas-SNP	.											.	EIF2AK3	160	.	0			c.G271T						PASS	.						15.0	18.0	17.0					2																	88926522		2023	4091	6114	SO:0001587	stop_gained	9451	exon1			CTGGTTCCGGACC	AF110146	CCDS33241.1	2p12	2008-05-21			ENSG00000172071	ENSG00000172071			3255	protein-coding gene	gene with protein product		604032				10026192, 10575235	Standard	NM_004836		Approved	PEK, PERK	uc002stc.4	Q9NZJ5	OTTHUMG00000155046	ENST00000303236.3:c.271G>T	2.37:g.88926522C>A	ENSP00000307235:p.Glu91*	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	71	24	0.338028	NM_004836	A0AVH1|A0AVH2|B2RCU9|O95846|Q53QY0|Q53SB1	Nonsense_Mutation	SNP	ENST00000303236.3	37	CCDS33241.1	.	.	.	.	.	.	.	.	.	.	C	26.0	4.692593	0.88735	.	.	ENSG00000172071	ENST00000303236	.	.	.	4.2	4.2	0.49525	.	0.382598	0.20874	N	0.084102	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.18276	T	0.48	-8.9866	12.3586	0.55190	0.0:1.0:0.0:0.0	.	.	.	.	X	91	.	ENSP00000307235:E91X	E	-	1	0	EIF2AK3	88707637	0.245000	0.23899	0.013000	0.15412	0.003000	0.03518	3.145000	0.50623	2.032000	0.59987	0.561000	0.74099	GAA	.	.	none		0.731	EIF2AK3-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000338233.2	NM_004836	
CARS2	79587	hgsc.bcm.edu	37	13	111298392	111298392	+	Silent	SNP	A	A	G	rs436462	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:111298392A>G	ENST00000257347.4	-	12	1302	c.1239T>C	c.(1237-1239)gaT>gaC	p.D413D	CARS2_ENST00000535398.1_5'UTR	NM_024537.2	NP_078813.1	Q9HA77	SYCM_HUMAN	cysteinyl-tRNA synthetase 2, mitochondrial (putative)	413					cysteinyl-tRNA aminoacylation (GO:0006423)|gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|cysteine-tRNA ligase activity (GO:0004817)|metal ion binding (GO:0046872)			autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(2)|prostate(4)|skin(1)	13	all_lung(23;3.61e-05)|Lung NSC(43;0.00144)|Lung SC(71;0.0753)|all_neural(89;0.077)|Medulloblastoma(90;0.148)		BRCA - Breast invasive adenocarcinoma(86;0.163)		L-Cysteine(DB00151)	GTGTGTCAAAATCATCTGCCA	0.612													G|||	2375	0.474241	0.6233	0.5346	5008	,	,		17839	0.4246		0.3082	False		,,,				2504	0.4519				p.D413D		Atlas-SNP	.											.	CARS2	37	.	0			c.T1239C						PASS	.	G		2575,1831	532.8+/-373.5	750,1075,378	153.0	134.0	141.0		1239	4.8	1.0	13	dbSNP_80	141	2794,5806	677.7+/-403.4	438,1918,1944	no	coding-synonymous	CARS2	NM_024537.2		1188,2993,2322	GG,GA,AA		32.4884,41.557,41.2809		413/565	111298392	5369,7637	2203	4300	6503	SO:0001819	synonymous_variant	79587	exon12			GTCAAAATCATCT	BC007220	CCDS9514.1	13q34	2011-07-01	2007-02-22		ENSG00000134905	ENSG00000134905	6.1.1.16	"""Aminoacyl tRNA synthetases / Class I"""	25695	protein-coding gene	gene with protein product	"""cysteine tRNA ligase 2, mitochondrial (putative)"""	612800				15779907	Standard	NM_024537		Approved	FLJ12118	uc001vrd.2	Q9HA77	OTTHUMG00000017347	ENST00000257347.4:c.1239T>C	13.37:g.111298392A>G		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	84	45	0.535714	NM_024537	Q8NI84|Q96IV4	Silent	SNP	ENST00000257347.4	37	CCDS9514.1																																																																																			A|0.580;G|0.420	0.420	strong		0.612	CARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045772.3	NM_024537	
FAM35A	54537	hgsc.bcm.edu	37	10	88911841	88911841	+	Missense_Mutation	SNP	A	A	G	rs77879311	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:88911841A>G	ENST00000298784.1	+	3	844	c.730A>G	c.(730-732)Agt>Ggt	p.S244G	RN7SL733P_ENST00000582253.1_RNA|FAM35A_ENST00000298786.4_Missense_Mutation_p.S244G	NM_019054.2	NP_061927.2	Q86V20	FA35A_HUMAN	family with sequence similarity 35, member A	244										endometrium(2)|kidney(2)|large_intestine(5)|lung(1)|ovary(2)|prostate(2)|skin(2)	16						AGAATTTCTCAGTATAATTAC	0.383													A|||	747	0.149161	0.2466	0.1009	5008	,	,		19063	0.0218		0.169	False		,,,				2504	0.1626				p.S244G	Ovarian(175;703 2004 25460 32514 43441)	Atlas-SNP	.											.	FAM35A	48	.	0			c.A730G						PASS	.	A	GLY/SER	910,3496		95,720,1388	30.0	30.0	30.0		730	4.1	0.9	10	dbSNP_131	30	1339,7255		95,1149,3053	no	missense	FAM35A	NM_019054.2	56	190,1869,4441	GG,GA,AA		15.5806,20.6537,17.3	probably-damaging	244/836	88911841	2249,10751	2203	4297	6500	SO:0001583	missense	54537	exon3			TTTCTCAGTATAA	BC051863	CCDS7383.1	10q23.2	2010-06-02			ENSG00000122376	ENSG00000122376			28773	protein-coding gene	gene with protein product						8619474, 9110174	Standard	NM_019054		Approved	MGC5560, bA163M19.1, FAM35A1	uc001kei.4	Q86V20	OTTHUMG00000018669	ENST00000298784.1:c.730A>G	10.37:g.88911841A>G	ENSP00000298784:p.Ser244Gly	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	83	50	0.60241	NM_019054	O95885|Q9H991	Missense_Mutation	SNP	ENST00000298784.1	37	CCDS7383.1	283	0.1295787545787546	99	0.20121951219512196	39	0.10773480662983426	10	0.017482517482517484	135	0.17810026385224276	a	16.76	3.211731	0.58452	0.206537	0.155806	ENSG00000122376	ENST00000298786;ENST00000298784;ENST00000358313	T;T;T	0.30714	1.53;1.52;1.52	4.09	4.09	0.47781	.	0.268115	0.31963	N	0.006794	T	0.00039	0.0001	M	0.71581	2.175	0.29511	P	0.8541799999999999	D	0.60160	0.987	P	0.61533	0.89	T	0.06661	-1.0814	9	0.72032	D	0.01	-3.893	8.8322	0.35091	0.8326:0.0:0.0:0.1674	.	244	Q86V20	FA35A_HUMAN	G	244	ENSP00000298786:S244G;ENSP00000298784:S244G;ENSP00000351064:S244G	ENSP00000298784:S244G	S	+	1	0	FAM35A	88901821	1.000000	0.71417	0.854000	0.33618	0.963000	0.63663	4.382000	0.59594	1.733000	0.51620	0.438000	0.28831	AGT	A|0.850;G|0.150	0.150	strong		0.383	FAM35A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049196.2	NM_019054	
CRTAC1	55118	hgsc.bcm.edu	37	10	99664456	99664456	+	Silent	SNP	T	T	C	rs7068503	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:99664456T>C	ENST00000370597.3	-	7	1321	c.966A>G	c.(964-966)caA>caG	p.Q322Q	CRTAC1_ENST00000370591.2_Silent_p.Q322Q|CRTAC1_ENST00000298819.4_Silent_p.Q322Q	NM_018058.6	NP_060528.3	Q9NQ79	CRAC1_HUMAN	cartilage acidic protein 1	322						extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|breast(1)|endometrium(6)|kidney(3)|large_intestine(7)|lung(6)|ovary(6)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(1)	35		Colorectal(252;0.24)		Epithelial(162;2.18e-10)|all cancers(201;3.27e-09)		GGGTGCTCATTTGCAGATAGA	0.572													C|||	491	0.0980431	0.1422	0.0476	5008	,	,		15318	0.0863		0.0527	False		,,,				2504	0.1329				p.Q322Q		Atlas-SNP	.											.	CRTAC1	86	.	0			c.A966G						PASS	.	C	,	600,3806	770.2+/-413.7	45,510,1648	100.0	101.0	101.0		966,966	3.1	1.0	10	dbSNP_116	101	632,7968	790.4+/-407.6	24,584,3692	no	coding-synonymous,coding-synonymous	CRTAC1	NM_001206528.2,NM_018058.6	,	69,1094,5340	CC,CT,TT		7.3488,13.6178,9.4726	,	322/646,322/662	99664456	1232,11774	2203	4300	6503	SO:0001819	synonymous_variant	55118	exon7			GCTCATTTGCAGA	AJ276171	CCDS31266.1, CCDS55723.1	10q22	2007-12-03			ENSG00000095713	ENSG00000095713			14882	protein-coding gene	gene with protein product		606276				11139377	Standard	NM_018058		Approved	FLJ10320, CEP-68, ASPIC1	uc001kou.2	Q9NQ79	OTTHUMG00000018871	ENST00000370597.3:c.966A>G	10.37:g.99664456T>C		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	62	27	0.435484	NM_001206528	B1ALN4|Q5T4F8|Q8N4H6|Q8TE52|Q9NQ78|Q9NQ80|Q9NW46	Silent	SNP	ENST00000370597.3	37	CCDS31266.1																																																																																			T|0.914;C|0.086	0.086	strong		0.572	CRTAC1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000049754.1	NM_018058	
GDPGP1	390637	hgsc.bcm.edu	37	15	90784250	90784250	+	Missense_Mutation	SNP	T	T	C	rs7171194	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:90784250T>C	ENST00000558017.1	+	4	530	c.110T>C	c.(109-111)aTg>aCg	p.M37T	GDPGP1_ENST00000329600.6_Missense_Mutation_p.M37T	NM_001013657.2	NP_001013679.2	Q6ZNW5	GDPP1_HUMAN	GDP-D-glucose phosphorylase 1	37			M -> T (in dbSNP:rs7171194). {ECO:0000269|PubMed:14702039}.		glucose metabolic process (GO:0006006)	cytoplasm (GO:0005737)	GDP-D-glucose phosphorylase activity (GO:0080048)|guanyl-nucleotide exchange factor activity (GO:0005085)|hydrolase activity (GO:0016787)|nucleotide binding (GO:0000166)|nucleotidyltransferase activity (GO:0016779)										AAGGATCTCATGGCAGAAGGG	0.522													C|||	4109	0.820487	0.9894	0.7968	5008	,	,		16431	0.7996		0.7018	False		,,,				2504	0.7526				p.M37T		Atlas-SNP	.											.	.	.	.	0			c.T110C						PASS	.	C	THR/MET	4134,264	150.3+/-184.3	1945,244,10	173.0	175.0	175.0		110	-1.4	0.0	15	dbSNP_116	175	5573,3023	466.7+/-366.8	1816,1941,541	yes	missense	C15orf58	NM_001013657.2	81	3761,2185,551	CC,CT,TT		35.1675,6.0027,25.2963	benign	37/386	90784250	9707,3287	2199	4298	6497	SO:0001583	missense	390637	exon4			ATCTCATGGCAGA		CCDS32327.1	15q26.1	2012-05-04	2012-05-04	2012-05-04	ENSG00000183208	ENSG00000183208	2.7.7.78		34360	protein-coding gene	gene with protein product			"""chromosome 15 open reading frame 58"""	C15orf58		21507950	Standard	NM_001013657		Approved		uc002bpc.3	Q6ZNW5		ENST00000558017.1:c.110T>C	15.37:g.90784250T>C	ENSP00000452793:p.Met37Thr	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	161	159	0.987578	NM_001013657		Missense_Mutation	SNP	ENST00000558017.1	37	CCDS32327.1	1723	0.7889194139194139	484	0.983739837398374	276	0.7624309392265194	431	0.7534965034965035	532	0.7018469656992085	C	10.43	1.348781	0.24426	0.939973	0.648325	ENSG00000183208	ENST00000329600	T	0.21031	2.03	5.35	-1.38	0.09027	.	1.611180	0.04811	N	0.435239	T	0.00012	0.0000	N	0.04880	-0.145	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.18304	-1.0341	9	0.12766	T	0.61	0.206	5.664	0.17684	0.0:0.2989:0.1336:0.5674	rs7171194;rs52805724;rs57106931;rs7171194	37	Q6ZNW5	VTC2_HUMAN	T	37	ENSP00000368405:M37T	ENSP00000368405:M37T	M	+	2	0	C15orf58	88585254	0.000000	0.05858	0.000000	0.03702	0.394000	0.30568	0.115000	0.15540	-0.078000	0.12730	-1.384000	0.01168	ATG	T|0.225;C|0.775	0.775	strong		0.522	GDPGP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416973.1	NM_001013657	
LRRTM1	347730	hgsc.bcm.edu	37	2	80529956	80529956	+	Missense_Mutation	SNP	T	T	C	rs6733871	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:80529956T>C	ENST00000295057.3	-	2	1645	c.989A>G	c.(988-990)aAc>aGc	p.N330S	CTNNA2_ENST00000541047.1_Intron|CTNNA2_ENST00000402739.4_Intron|CTNNA2_ENST00000540488.1_Intron|CTNNA2_ENST00000466387.1_Intron|CTNNA2_ENST00000361291.4_Intron|CTNNA2_ENST00000496558.1_Intron|LRRTM1_ENST00000409148.1_Missense_Mutation_p.N330S	NM_178839.4	NP_849161.2	Q86UE6	LRRT1_HUMAN	leucine rich repeat transmembrane neuronal 1	330	LRRCT.		N -> S (in dbSNP:rs6733871). {ECO:0000269|PubMed:12975309, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		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						CTGGAAGTTGTTGAGCCACGA	0.642										HNSCC(69;0.2)			C|||	1840	0.367412	0.5076	0.3213	5008	,	,		19987	0.4831		0.1839	False		,,,				2504	0.2802				p.N330S		Atlas-SNP	.											.	LRRTM1	251	.	0			c.A989G						PASS	.	C	,,SER/ASN	1982,2424	604.8+/-390.4	471,1040,692	34.0	32.0	32.0		,,989	3.5	1.0	2	dbSNP_116	32	1535,7065	732.0+/-406.8	137,1261,2902	yes	intron,intron,missense	CTNNA2,LRRTM1	NM_001164883.1,NM_004389.3,NM_178839.4	,,46	608,2301,3594	CC,CT,TT		17.8488,44.9841,27.0414	,,benign	,,330/523	80529956	3517,9489	2203	4300	6503	SO:0001583	missense	347730	exon2			AAGTTGTTGAGCC	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.989A>G	2.37:g.80529956T>C	ENSP00000295057:p.Asn330Ser	Somatic	195	0	0		WXS	Illumina HiSeq	Phase_I	150	81	0.54	NM_178839	A8K397|D6W5K1|Q96DN1	Missense_Mutation	SNP	ENST00000295057.3	37	CCDS1966.1	801	0.36675824175824173	238	0.483739837398374	103	0.2845303867403315	317	0.5541958041958042	143	0.18865435356200527	C	3.194	-0.165220	0.06461	0.449841	0.178488	ENSG00000162951	ENST00000295057;ENST00000409148	T;T	0.39406	1.08;1.08	5.26	3.46	0.39613	.	0.048240	0.85682	N	0.000000	T	0.00012	0.0000	N	0.00237	-1.79	0.58432	P	6.999999999979245E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.45454	-0.9260	8	.	.	.	.	10.5735	0.45214	0.0:0.7891:0.0:0.2109	rs6733871;rs17846373;rs17859410;rs58032559;rs6733871	330	Q86UE6	LRRT1_HUMAN	S	330	ENSP00000295057:N330S;ENSP00000386646:N330S	.	N	-	2	0	LRRTM1	80383467	1.000000	0.71417	0.999000	0.59377	0.948000	0.59901	2.149000	0.42244	0.219000	0.20840	-0.766000	0.03442	AAC	C|0.316;N|0.000	0.316	strong		0.642	LRRTM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313614.1	NM_178839	
FRAS1	80144	hgsc.bcm.edu	37	4	79455733	79455733	+	Silent	SNP	C	C	T	rs4975139	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:79455733C>T	ENST00000264895.6	+	71	11496	c.11056C>T	c.(11056-11058)Cta>Tta	p.L3686L		NM_025074.6	NP_079350.5	Q86XX4	FRAS1_HUMAN	Fraser extracellular matrix complex subunit 1	3682					cell communication (GO:0007154)|embryonic limb morphogenesis (GO:0030326)|metanephros morphogenesis (GO:0003338)|morphogenesis of an epithelium (GO:0002009)|palate development (GO:0060021)|protein transport (GO:0015031)|skin development (GO:0043588)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sublamina densa (GO:0061618)	metal ion binding (GO:0046872)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(5)|lung(54)|prostate(7)|skin(2)|urinary_tract(4)	103						TGATATGTCACTAGCAGAAAT	0.438													C|||	2579	0.514976	0.3086	0.4395	5008	,	,		21167	0.7758		0.4632	False		,,,				2504	0.6319				p.L3686L		Atlas-SNP	.											.	FRAS1	779	.	0			c.C11056T						PASS	.	C		1271,2491		214,843,824	104.0	93.0	97.0		11056	2.4	1.0	4	dbSNP_111	97	3591,4647		790,2011,1318	no	coding-synonymous	FRAS1	NM_025074.6		1004,2854,2142	TT,TC,CC		43.5907,33.7852,40.5167		3686/4013	79455733	4862,7138	1881	4119	6000	SO:0001819	synonymous_variant	80144	exon71			ATGTCACTAGCAG	AB040933	CCDS54772.1	4q21.21	2014-06-25	2014-06-25		ENSG00000138759	ENSG00000138759			19185	protein-coding gene	gene with protein product		607830	"""Fraser syndrome 1"""			12766769, 3118036	Standard	NM_025074		Approved	FLJ22031, FLJ14927, KIAA1500	uc003hlb.2	Q86XX4	OTTHUMG00000160856	ENST00000264895.6:c.11056C>T	4.37:g.79455733C>T		Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	112	58	0.517857	NM_025074	A2RRR8|Q86UZ4|Q8N3U9|Q8NAU7|Q96JW7|Q9H6N9|Q9P228	Silent	SNP	ENST00000264895.6	37	CCDS54771.1	1143	0.5233516483516484	172	0.34959349593495936	163	0.45027624309392267	453	0.791958041958042	355	0.4683377308707124	C	5.004	0.186442	0.09495	0.337852	0.435907	ENSG00000138759	ENST00000512123	.	.	.	5.05	2.41	0.29592	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999856936	.	.	.	.	.	.	T	0.20940	-1.0260	3	.	.	.	.	6.0073	0.19553	0.1323:0.6491:0.0:0.2186	rs4975139;rs58497218;rs4975139	.	.	.	I	1914	.	.	T	+	2	0	FRAS1	79674757	0.602000	0.26916	0.987000	0.45799	0.774000	0.43823	1.126000	0.31344	0.174000	0.19809	-0.216000	0.12614	ACT	C|0.484;T|0.516	0.516	strong		0.438	FRAS1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
ARHGEF19	128272	hgsc.bcm.edu	37	1	16534255	16534255	+	Missense_Mutation	SNP	C	C	G	rs221057	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:16534255C>G	ENST00000270747.3	-	4	848	c.712G>C	c.(712-714)Gag>Cag	p.E238Q	ARHGEF19_ENST00000478117.1_5'Flank	NM_153213.3	NP_694945.2	Q8IW93	ARHGJ_HUMAN	Rho guanine nucleotide exchange factor (GEF) 19	238			E -> Q (in dbSNP:rs221057). {ECO:0000269|PubMed:14702039}.		regulation of actin cytoskeleton organization (GO:0032956)|wound healing (GO:0042060)		GTPase activator activity (GO:0005096)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			cervix(1)|endometrium(1)|lung(3)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	12		Colorectal(325;0.000147)|Renal(390;0.00145)|Breast(348;0.00224)|Lung NSC(340;0.00566)|all_lung(284;0.00831)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.018)|Colorectal(212;3.48e-07)|COAD - Colon adenocarcinoma(227;2.19e-05)|BRCA - Breast invasive adenocarcinoma(304;9.46e-05)|Kidney(64;0.000171)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(313;0.0117)|READ - Rectum adenocarcinoma(331;0.0649)		CTTCGAGCCTCCATTCCAGAT	0.682													C|||	1337	0.266973	0.1664	0.4063	5008	,	,		14901	0.1528		0.2654	False		,,,				2504	0.4233				p.E238Q		Atlas-SNP	.											.	ARHGEF19	49	.	0			c.G712C						PASS	.	C	GLN/GLU	778,3628	305.5+/-289.0	79,620,1504	46.0	49.0	48.0		712	4.9	0.5	1	dbSNP_79	48	2240,6356	367.8+/-334.9	298,1644,2356	yes	missense	ARHGEF19	NM_153213.3	29	377,2264,3860	GG,GC,CC		26.0586,17.6577,23.2118	benign	238/803	16534255	3018,9984	2203	4298	6501	SO:0001583	missense	128272	exon4			GAGCCTCCATTCC	BC012982	CCDS170.1	1p36.13	2011-11-16			ENSG00000142632	ENSG00000142632		"""Rho guanine nucleotide exchange factors"""	26604	protein-coding gene	gene with protein product		612496				12477932	Standard	NM_153213		Approved	FLJ33962, WGEF	uc001ayc.1	Q8IW93	OTTHUMG00000002219	ENST00000270747.3:c.712G>C	1.37:g.16534255C>G	ENSP00000270747:p.Glu238Gln	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	107	49	0.457944	NM_153213	A6NJ04|Q5TEV2|Q6PJQ4|Q8N244	Missense_Mutation	SNP	ENST00000270747.3	37	CCDS170.1	480	0.21978021978021978	73	0.1483739837398374	123	0.3397790055248619	74	0.12937062937062938	210	0.2770448548812665	C	19.69	3.874660	0.72180	0.176577	0.260586	ENSG00000142632	ENST00000270747;ENST00000421561;ENST00000375607	T;T	0.71579	-0.58;1.81	4.94	4.94	0.65067	.	4.578340	0.00702	N	0.000785	T	0.00012	0.0000	L	0.50333	1.59	0.40022	P	0.024572999999999956	B	0.20052	0.041	B	0.17433	0.018	T	0.04153	-1.0973	9	0.17369	T	0.5	.	13.8258	0.63351	0.0:1.0:0.0:0.0	rs221057;rs221057	238	Q8IW93	ARHGJ_HUMAN	Q	238	ENSP00000270747:E238Q;ENSP00000396001:E238Q	ENSP00000270747:E238Q	E	-	1	0	ARHGEF19	16406842	0.961000	0.32948	0.474000	0.27266	0.043000	0.13939	3.812000	0.55628	2.316000	0.78162	0.549000	0.68633	GAG	C|0.778;G|0.222	0.222	strong		0.682	ARHGEF19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006289.1	NM_153213	
C1orf106	55765	hgsc.bcm.edu	37	1	200867492	200867492	+	Silent	SNP	C	C	G	rs2271018	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:200867492C>G	ENST00000367342.4	+	2	419	c.219C>G	c.(217-219)ccC>ccG	p.P73P	C1orf106_ENST00000413687.2_5'UTR	NM_018265.3	NP_060735.3	Q3KP66	CA106_HUMAN	chromosome 1 open reading frame 106	73										endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(6)|ovary(1)|prostate(2)|skin(3)|stomach(1)|urinary_tract(2)	21						GGTGTCCCCCCTCCCTGCTCT	0.522													C|||	993	0.198283	0.115	0.3112	5008	,	,		20525	0.1577		0.2495	False		,,,				2504	0.2198				p.P87P		Atlas-SNP	.											.	C1orf106	59	.	0			c.C261G						PASS	.	C	,	683,3723	286.9+/-279.0	60,563,1580	134.0	127.0	129.0		,219	0.4	0.1	1	dbSNP_100	129	2025,6575	354.2+/-329.4	266,1493,2541	no	utr-5,coding-synonymous	C1orf106	NM_001142569.2,NM_018265.3	,	326,2056,4121	GG,GC,CC		23.5465,15.5016,20.8212	,	,73/664	200867492	2708,10298	2203	4300	6503	SO:0001819	synonymous_variant	55765	exon2			TCCCCCCTCCCTG	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.219C>G	1.37:g.200867492C>G		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	62	33	0.532258	NM_018265	B4E1K9|E9PFY0|Q9NV65|Q9NVI0	Silent	SNP	ENST00000367342.4	37																																																																																				C|0.788;G|0.212	0.212	strong		0.522	C1orf106-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000087057.2	NM_018265	
CD3E	916	hgsc.bcm.edu	37	11	118178007	118178007	+	Silent	SNP	C	C	T	rs1126924	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:118178007C>T	ENST00000361763.4	+	3	345	c.54C>T	c.(52-54)ggC>ggT	p.G18G	CD3E_ENST00000528600.1_Silent_p.G18G	NM_000733.3	NP_000724.1	P07766	CD3E_HUMAN	CD3e molecule, epsilon (CD3-TCR complex)	18					apoptotic signaling pathway (GO:0097190)|cell surface receptor signaling pathway (GO:0007166)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|negative regulation of smoothened signaling pathway (GO:0045879)|negative thymic T cell selection (GO:0045060)|positive regulation of alpha-beta T cell proliferation (GO:0046641)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of interleukin-4 production (GO:0032753)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of T cell anergy (GO:0002669)|positive regulation of T cell proliferation (GO:0042102)|protein complex assembly (GO:0006461)|regulation of apoptotic process (GO:0042981)|regulation of immune response (GO:0050776)|response to nutrient (GO:0007584)|signal complex assembly (GO:0007172)|T cell activation (GO:0042110)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	alpha-beta T cell receptor complex (GO:0042105)|cell-cell junction (GO:0005911)|external side of plasma membrane (GO:0009897)|immunological synapse (GO:0001772)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|T cell receptor complex (GO:0042101)	protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|receptor signaling complex scaffold activity (GO:0030159)|receptor signaling protein activity (GO:0005057)|SH3 domain binding (GO:0017124)|T cell receptor binding (GO:0042608)|transmembrane signaling receptor activity (GO:0004888)	p.G18G(1)		breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|ovary(2)|stomach(1)	8	all_hematologic(175;0.046)	Medulloblastoma(222;0.0425)|Breast(348;0.181)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;3.09e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0251)	Muromonab(DB00075)	TTCTAGTTGGCGTTTGGGGGC	0.373													C|||	1129	0.225439	0.0386	0.4625	5008	,	,		20142	0.1865		0.3052	False		,,,				2504	0.2679				p.G18G		Atlas-SNP	.											CD3E,NS,carcinoma,0,1	CD3E	23	1	1	Substitution - coding silent(1)	stomach(1)	c.C54T						PASS	.	C		382,4018	194.7+/-219.5	20,342,1838	132.0	116.0	121.0		54	-6.5	0.1	11	dbSNP_111	121	2744,5848	437.2+/-358.5	450,1844,2002	no	coding-synonymous	CD3E	NM_000733.3		470,2186,3840	TT,TC,CC		31.9367,8.6818,24.061		18/208	118178007	3126,9866	2200	4296	6496	SO:0001819	synonymous_variant	916	exon3			AGTTGGCGTTTGG	X03884	CCDS31685.1	11q23	2014-09-17	2006-03-28		ENSG00000198851	ENSG00000198851		"""CD molecules"""	1674	protein-coding gene	gene with protein product		186830	"""CD3e antigen, epsilon polypeptide (TiT3 complex)"""				Standard	NM_000733		Approved		uc001psq.4	P07766	OTTHUMG00000166968	ENST00000361763.4:c.54C>T	11.37:g.118178007C>T		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	41	28	0.682927	NM_000733	A8K997	Silent	SNP	ENST00000361763.4	37	CCDS31685.1																																																																																			C|0.768;T|0.232	0.232	strong		0.373	CD3E-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000392120.1	NM_000733	
GJD2	57369	hgsc.bcm.edu	37	15	35044757	35044757	+	Silent	SNP	C	C	T	rs34964522	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:35044757C>T	ENST00000290374.4	-	2	1364	c.888G>A	c.(886-888)gaG>gaA	p.E296E	RP11-814P5.1_ENST00000503496.1_RNA|RP11-814P5.1_ENST00000558707.1_RNA	NM_020660.2	NP_065711.1	Q9UKL4	CXD2_HUMAN	gap junction protein, delta 2, 36kDa	296					action potential (GO:0001508)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|visual perception (GO:0007601)	connexon complex (GO:0005922)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	gap junction channel activity (GO:0005243)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(10)|ovary(1)|pancreas(1)|urinary_tract(1)	19		all_lung(180;9.67e-07)		all cancers(64;2.75e-18)|GBM - Glioblastoma multiforme(113;1.9e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0156)		TGTTACGAATCTCATAGATTG	0.527													C|||	189	0.0377396	0.0038	0.0605	5008	,	,		20993	0.0		0.1093	False		,,,				2504	0.0327				p.E296E		Atlas-SNP	.											GJD2,bladder,carcinoma,-2,1	GJD2	49	1	0			c.G888A						PASS	.	C		120,4282	90.2+/-128.9	2,116,2083	90.0	75.0	80.0		888	3.9	1.0	15	dbSNP_126	80	995,7601	214.8+/-254.3	61,873,3364	no	coding-synonymous	GJD2	NM_020660.1		63,989,5447	TT,TC,CC		11.5752,2.726,8.5782		296/322	35044757	1115,11883	2201	4298	6499	SO:0001819	synonymous_variant	57369	exon2			ACGAATCTCATAG	AB037509	CCDS10040.1	15q13.1	2008-02-04	2007-11-06	2007-11-06	ENSG00000159248	ENSG00000159248		"""Ion channels / Gap junction proteins (connexins)"""	19154	protein-coding gene	gene with protein product	"""connexin 36"""	607058	"""gap junction protein, alpha 9, 36kDa"""	GJA9		10462698	Standard	NM_020660		Approved	CX36	uc001zis.2	Q9UKL4	OTTHUMG00000129674	ENST00000290374.4:c.888G>A	15.37:g.35044757C>T		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	75	41	0.546667	NM_020660	Q2M241|Q9P2R0	Silent	SNP	ENST00000290374.4	37	CCDS10040.1																																																																																			C|0.925;T|0.075	0.075	strong		0.527	GJD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251875.2		
PHLPP2	23035	hgsc.bcm.edu	37	16	71682830	71682830	+	Missense_Mutation	SNP	C	C	T	rs61733124	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:71682830C>T	ENST00000568954.1	-	19	4313	c.3935G>A	c.(3934-3936)cGg>cAg	p.R1312Q	PHLPP2_ENST00000393524.2_Missense_Mutation_p.R1245Q|PHLPP2_ENST00000540628.1_Intron|PHLPP2_ENST00000356272.3_Missense_Mutation_p.R1312Q|PHLPP2_ENST00000567016.1_Missense_Mutation_p.R1347Q|PHLPP2_ENST00000360429.3_Intron			Q6ZVD8	PHLP2_HUMAN	PH domain and leucine rich repeat protein phosphatase 2	1312				R -> Q (in Ref. 5; AAI29928). {ECO:0000305}.	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)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment membrane (GO:0042622)	metal ion binding (GO:0046872)|protein serine/threonine phosphatase activity (GO:0004722)			central_nervous_system(1)|endometrium(5)|kidney(5)|large_intestine(7)|lung(15)|ovary(1)|prostate(1)|skin(1)|stomach(1)	37						GGGCTCGGTCCGATCCTCTTC	0.587													C|||	386	0.0770767	0.1021	0.1009	5008	,	,		16636	0.0129		0.0895	False		,,,				2504	0.0798				p.R1312Q		Atlas-SNP	.											.	PHLPP2	96	.	0			c.G3935A						PASS	.	C	GLN/ARG	449,3947	215.1+/-234.2	30,389,1779	65.0	63.0	64.0		3935	5.2	1.0	16	dbSNP_129	64	701,7899	173.0+/-223.6	23,655,3622	yes	missense	PHLPP2	NM_015020.2	43	53,1044,5401	TT,TC,CC		8.1512,10.2138,8.8489	benign	1312/1324	71682830	1150,11846	2198	4300	6498	SO:0001583	missense	23035	exon18			TCGGTCCGATCCT	BX647823	CCDS32479.1, CCDS73910.1	16q22.2	2013-01-11	2009-05-26	2009-05-26	ENSG00000040199	ENSG00000040199		"""Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent"", ""Pleckstrin homology (PH) domain containing"""	29149	protein-coding gene	gene with protein product		611066	"""PH domain and leucine rich repeat protein phosphatase-like"""	PHLPPL		17386267	Standard	NM_001289003		Approved	KIAA0931	uc002fax.3	Q6ZVD8		ENST00000568954.1:c.3935G>A	16.37:g.71682830C>T	ENSP00000457991:p.Arg1312Gln	Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	191	110	0.575916	NM_015020	A1L374|Q9NV17|Q9Y2E3	Missense_Mutation	SNP	ENST00000568954.1	37	CCDS32479.1	151	0.06913919413919414	49	0.09959349593495935	40	0.11049723756906077	6	0.01048951048951049	56	0.07387862796833773	C	14.41	2.526248	0.44969	0.102138	0.081512	ENSG00000040199	ENST00000356272;ENST00000393524	T;T	0.43294	1.47;0.95	6.17	5.22	0.72569	.	0.195122	0.36444	N	0.002585	T	0.00412	0.0013	N	0.16478	0.41	0.31221	N	0.697468	B;B	0.15719	0.014;0.008	B;B	0.06405	0.002;0.001	T	0.04509	-1.0946	10	0.15066	T	0.55	-18.9831	7.5241	0.27645	0.0:0.7065:0.1489:0.1446	rs61733124	1245;1312	Q6ZVD8-3;Q6ZVD8	.;PHLP2_HUMAN	Q	1312;1245	ENSP00000348611:R1312Q;ENSP00000377159:R1245Q	ENSP00000348611:R1312Q	R	-	2	0	PHLPP2	70240331	0.994000	0.37717	1.000000	0.80357	0.910000	0.53928	1.489000	0.35562	2.941000	0.99782	0.655000	0.94253	CGG	C|0.917;T|0.083	0.083	strong		0.587	PHLPP2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000434139.1	NM_015020	
FSD2	123722	hgsc.bcm.edu	37	15	83428192	83428192	+	Missense_Mutation	SNP	C	C	T	rs1108134	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:83428192C>T	ENST00000334574.8	-	13	2339	c.2158G>A	c.(2158-2160)Gaa>Aaa	p.E720K	RP11-752G15.6_ENST00000559366.1_RNA|FSD2_ENST00000541889.1_Missense_Mutation_p.E675K|RP11-752G15.6_ENST00000561107.1_RNA|RP11-752G15.6_ENST00000558174.1_RNA			A1L4K1	FSD2_HUMAN	fibronectin type III and SPRY domain containing 2	720	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.		E -> K (in dbSNP:rs1108134).							breast(2)|central_nervous_system(1)|large_intestine(5)|lung(10)	18						TGCACAAATTCGTGAAGCTGA	0.348													c|||	481	0.0960463	0.1256	0.1628	5008	,	,		20459	0.001		0.16	False		,,,				2504	0.0409				p.E720K		Atlas-SNP	.											.	FSD2	45	.	0			c.G2158A						PASS	.		LYS/GLU	526,3170		32,462,1354	71.0	69.0	69.0		2158	1.7	0.0	15	dbSNP_86	69	1379,6823		109,1161,2831	yes	missense	FSD2	NM_001007122.2	56	141,1623,4185	TT,TC,CC		16.813,14.2316,16.0111	benign	720/750	83428192	1905,9993	1848	4101	5949	SO:0001583	missense	123722	exon13			CAAATTCGTGAAG	AK122875	CCDS45332.1, CCDS61738.1	15q25.2	2013-02-11	2006-01-11	2006-01-11		ENSG00000186628		"""Fibronectin type III domain containing"""	18024	protein-coding gene	gene with protein product			"""SPRY domain containing 1"""	SPRYD1			Standard	NM_001007122		Approved	RP11-127F21	uc002bjd.2	A1L4K1		ENST00000334574.8:c.2158G>A	15.37:g.83428192C>T	ENSP00000335651:p.Glu720Lys	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	98	44	0.44898	NM_001007122	B3KVG1|B7ZM02	Missense_Mutation	SNP	ENST00000334574.8	37	CCDS45332.1	257	0.11767399267399267	74	0.15040650406504066	64	0.17679558011049723	4	0.006993006993006993	115	0.1517150395778364	c	7.367	0.626101	0.14257	0.142316	0.16813	ENSG00000186628	ENST00000334574;ENST00000541889	T;T	0.15834	2.39;2.39	5.86	1.71	0.24356	Concanavalin A-like lectin/glucanase (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	0.577689	0.18596	N	0.136589	T	0.00039	0.0001	L	0.52573	1.65	0.80722	P	0.0	B;B	0.09022	0.002;0.001	B;B	0.10450	0.005;0.001	T	0.31943	-0.9925	9	0.17832	T	0.49	0.0763	6.7726	0.23602	0.0658:0.2404:0.5729:0.1209	rs1108134;rs4262919;rs61477553;rs1108134	675;720	B7ZM02;A1L4K1	.;FSD2_HUMAN	K	720;675	ENSP00000335651:E720K;ENSP00000444078:E675K	ENSP00000335651:E720K	E	-	1	0	FSD2	81225246	0.878000	0.30173	0.001000	0.08648	0.483000	0.33249	2.146000	0.42216	0.496000	0.27904	-0.836000	0.03065	GAA	C|0.869;T|0.131	0.131	strong		0.348	FSD2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418385.1	NM_001007122	
EPHB3	2049	hgsc.bcm.edu	37	3	184299167	184299167	+	Silent	SNP	T	T	C	rs1138510	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:184299167T>C	ENST00000330394.2	+	15	3311	c.2859T>C	c.(2857-2859)tcT>tcC	p.S953S	EIF2B5_ENST00000444495.1_Intron	NM_004443.3	NP_004434.2	P54753	EPHB3_HUMAN	EPH receptor B3	953	SAM. {ECO:0000255|PROSITE- ProRule:PRU00184}.				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)			GGTTTGCATCTTTTGACCTGG	0.587													C|||	1660	0.33147	0.5499	0.2435	5008	,	,		18837	0.1677		0.3469	False		,,,				2504	0.2515				p.S953S		Atlas-SNP	.											.	EPHB3	114	.	0			c.T2859C						PASS	.	C		2312,2094	571.9+/-383.2	591,1130,482	93.0	75.0	81.0		2859	3.3	1.0	3	dbSNP_86	81	2718,5882	680.6+/-403.7	437,1844,2019	no	coding-synonymous	EPHB3	NM_004443.3		1028,2974,2501	CC,CT,TT		31.6047,47.5261,38.6745		953/999	184299167	5030,7976	2203	4300	6503	SO:0001819	synonymous_variant	2049	exon15			TGCATCTTTTGAC	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.2859T>C	3.37:g.184299167T>C		Somatic	242	1	0.00413223		WXS	Illumina HiSeq	Phase_I	217	110	0.506912	NM_004443	Q7Z740	Silent	SNP	ENST00000330394.2	37	CCDS3268.1																																																																																			T|0.632;C|0.368	0.368	strong		0.587	EPHB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345413.1	NM_004443	
DCHS2	54798	hgsc.bcm.edu	37	4	155295076	155295076	+	Missense_Mutation	SNP	A	A	G	rs11721758	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:155295076A>G	ENST00000357232.4	-	4	457	c.458T>C	c.(457-459)gTg>gCg	p.V153A	DCHS2_ENST00000339452.1_Intron	NM_017639.3	NP_060109.2	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	153	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.		V -> A (in dbSNP:rs11721758).		homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(1)|cervix(3)|endometrium(8)|kidney(5)|large_intestine(54)|lung(63)|ovary(4)|pancreas(1)|prostate(14)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	176	all_hematologic(180;0.208)	Renal(120;0.0854)		LUSC - Lung squamous cell carcinoma(193;0.107)		CCTTACCTTCACCAGGGCTAA	0.368													A|||	1747	0.348842	0.1362	0.3646	5008	,	,		17591	0.3938		0.4851	False		,,,				2504	0.4387				p.V153A		Atlas-SNP	.											.	DCHS2	594	.	0			c.T458C						PASS	.	A	,ALA/VAL	829,3577	328.0+/-300.3	84,661,1458	135.0	121.0	126.0		,458	-2.7	0.0	4	dbSNP_120	126	3884,4716	544.5+/-384.6	896,2092,1312	yes	intron,missense	DCHS2	NM_001142552.1,NM_017639.3	,64	980,2753,2770	GG,GA,AA		45.1628,18.8153,36.2371	,benign	,153/2917	155295076	4713,8293	2203	4300	6503	SO:0001583	missense	54798	exon4			ACCTTCACCAGGG	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.458T>C	4.37:g.155295076A>G	ENSP00000349768:p.Val153Ala	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	96	39	0.40625	NM_017639	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Missense_Mutation	SNP	ENST00000357232.4	37	CCDS3785.1	814	0.3727106227106227	69	0.1402439024390244	153	0.42265193370165743	218	0.3811188811188811	374	0.49340369393139843	A	9.034	0.987982	0.18966	0.188153	0.451628	ENSG00000197410	ENST00000357232	T	0.52526	0.66	2.74	-2.66	0.06077	Cadherin (3);Cadherin-like (1);	1.741890	0.04532	N	0.386442	T	0.00012	0.0000	N	0.12569	0.235	0.80722	P	0.0	B	0.02656	0.0	B	0.06405	0.002	T	0.44967	-0.9293	9	0.59425	D	0.04	.	5.1587	0.15048	0.2586:0.501:0.2404:0.0	rs11721758;rs52830973;rs57135557;rs11721758	153	Q6V1P9	PCD23_HUMAN	A	153	ENSP00000349768:V153A	ENSP00000349768:V153A	V	-	2	0	DCHS2	155514526	0.000000	0.05858	0.000000	0.03702	0.064000	0.16182	0.317000	0.19487	-0.511000	0.06514	0.377000	0.23210	GTG	A|0.641;G|0.359	0.359	strong		0.368	DCHS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365281.2	NM_001142552	
CSF3R	1441	hgsc.bcm.edu	37	1	36938235	36938235	+	Silent	SNP	G	G	A	rs3918017	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:36938235G>A	ENST00000373106.1	-	7	1273	c.726C>T	c.(724-726)gcC>gcT	p.A242A	CSF3R_ENST00000331941.5_Silent_p.A242A|CSF3R_ENST00000361632.4_Silent_p.A242A|CSF3R_ENST00000440588.2_Silent_p.A242A|CSF3R_ENST00000418048.2_Silent_p.A242A|CSF3R_ENST00000373104.1_Silent_p.A242A|CSF3R_ENST00000373103.1_Silent_p.A242A|CSF3R_ENST00000338937.5_Silent_p.A242A|CSF3R_ENST00000487540.2_5'Flank	NM_000760.3	NP_000751.1	Q99062	CSF3R_HUMAN	colony stimulating factor 3 receptor (granulocyte)	242	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				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)	CCTGGGGAGGGGCCGCTTCAG	0.642													G|||	37	0.00738818	0.0	0.0115	5008	,	,		17020	0.0		0.0288	False		,,,				2504	0.0				p.A242A		Atlas-SNP	.											.	CSF3R	157	.	0			c.C726T						PASS	.	G	,,	15,4339		0,15,2162	14.0	16.0	15.0		726,726,726	-2.1	0.0	1	dbSNP_108	15	154,8372		3,148,4112	no	coding-synonymous,coding-synonymous,coding-synonymous	CSF3R	NM_000760.3,NM_156039.3,NM_172313.2	,,	3,163,6274	AA,AG,GG		1.8062,0.3445,1.3121	,,	242/837,242/864,242/784	36938235	169,12711	2177	4263	6440	SO:0001819	synonymous_variant	1441	exon7			GGGAGGGGCCGCT	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.726C>T	1.37:g.36938235G>A		Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	150	85	0.566667	NM_156039		Silent	SNP	ENST00000373106.1	37	CCDS413.1																																																																																			G|0.987;A|0.013	0.013	strong		0.642	CSF3R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021997.2	NM_156039	
NLRP8	126205	hgsc.bcm.edu	37	19	56485077	56485077	+	Missense_Mutation	SNP	A	A	G	rs61740015	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:56485077A>G	ENST00000291971.3	+	7	2665	c.2594A>G	c.(2593-2595)cAg>cGg	p.Q865R	NLRP8_ENST00000590542.1_Missense_Mutation_p.Q846R	NM_176811.2	NP_789781.2	Q86W28	NALP8_HUMAN	NLR family, pyrin domain containing 8	865					neuron death (GO:0070997)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)			breast(4)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(14)|ovary(5)|skin(2)|stomach(3)|upper_aerodigestive_tract(2)	35		Colorectal(82;0.000147)|Ovarian(87;0.17)		GBM - Glioblastoma multiforme(193;0.0695)		TGTCTCAGGCAGAGTAAGATG	0.507													A|||	229	0.0457268	0.0363	0.049	5008	,	,		20931	0.005		0.0765	False		,,,				2504	0.0665				p.Q865R		Atlas-SNP	.											.	NLRP8	225	.	0			c.A2594G						PASS	.	A	ARG/GLN	166,4240	110.4+/-148.6	4,158,2041	181.0	174.0	177.0		2594	-0.8	0.0	19	dbSNP_129	177	643,7957	164.6+/-216.9	25,593,3682	yes	missense	NLRP8	NM_176811.2	43	29,751,5723	GG,GA,AA		7.4767,3.7676,6.2202	benign	865/1049	56485077	809,12197	2203	4300	6503	SO:0001583	missense	126205	exon7			TCAGGCAGAGTAA	AY154463	CCDS12937.1	19q13.43	2008-02-05	2006-12-08	2006-12-08		ENSG00000179709		"""Nucleotide-binding domain and leucine rich repeat containing"""	22940	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 8"""	609659	"""NACHT, leucine rich repeat and PYD containing 8"""	NALP8		12563287	Standard	NM_176811		Approved	NOD16, PAN4, CLR19.2	uc002qmh.3	Q86W28		ENST00000291971.3:c.2594A>G	19.37:g.56485077A>G	ENSP00000291971:p.Gln865Arg	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	77	43	0.558442	NM_176811	Q7RTR4	Missense_Mutation	SNP	ENST00000291971.3	37	CCDS12937.1	89	0.04075091575091575	12	0.024390243902439025	22	0.06077348066298342	1	0.0017482517482517483	54	0.0712401055408971	A	5.852	0.341485	0.11069	0.037676	0.074767	ENSG00000179709	ENST00000291971	T	0.52526	0.66	2.04	-0.828	0.10799	.	.	.	.	.	T	0.01695	0.0054	N	0.12961	0.28	0.09310	N	1	B;B	0.10296	0.003;0.001	B;B	0.08055	0.003;0.002	T	0.12682	-1.0538	9	0.14656	T	0.56	.	4.6732	0.12699	0.4537:0.0:0.5463:0.0	rs61740015	846;865	Q86W28-2;Q86W28	.;NALP8_HUMAN	R	865	ENSP00000291971:Q865R	ENSP00000291971:Q865R	Q	+	2	0	NLRP8	61176889	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.204000	0.09425	-0.149000	0.11215	-0.476000	0.04901	CAG	A|0.941;G|0.059	0.059	strong		0.507	NLRP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457462.1	NM_176811	
ADIRF	10974	hgsc.bcm.edu	37	10	88730312	88730312	+	Silent	SNP	T	T	C	rs4869	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:88730312T>C	ENST00000372013.3	+	3	557	c.204T>C	c.(202-204)atT>atC	p.I68I	ADIRF-AS1_ENST00000440490.1_RNA|ADIRF-AS1_ENST00000609111.1_RNA|RP11-96C23.15_ENST00000609363.1_RNA|ADIRF-AS1_ENST00000418273.2_RNA|RP11-96C23.5_ENST00000433214.2_RNA	NM_006829.2	NP_006820.1	Q15847	ADIRF_HUMAN	adipogenesis regulatory factor	68					cell differentiation (GO:0030154)|cellular response to cisplatin (GO:0072719)|cellular response to radiation (GO:0071478)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of response to drug (GO:2001023)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)		p.I68I(1)									TCTCTGGGATTGGGAAAAAAT	0.587													N|||	2640	0.527157	0.3585	0.4308	5008	,	,		17157	0.8095		0.6014	False		,,,				2504	0.456				p.I68I		Atlas-SNP	.											C10orf116,NS,carcinoma,0,1	.	.	1	1	Substitution - coding silent(1)	stomach(1)	c.T204C						PASS	.	C		1662,2744	652.1+/-399.3	341,980,882	77.0	70.0	72.0	http://omim.org/entry/178500	204	-8.6	0.0	10	dbSNP_52	72	4610,3990	546.5+/-385.0	1229,2152,919	no	coding-synonymous	C10orf116	NM_006829.2		1570,3132,1801	CC,CT,TT		46.3953,37.7213,48.2239		68/77	88730312	6272,6734	2203	4300	6503	SO:0001819	synonymous_variant	10974	exon3			TGGGATTGGGAAA	BC004471	CCDS7381.1	10q23.31	2013-02-20	2013-02-20	2013-02-20	ENSG00000148671	ENSG00000148671			24043	protein-coding gene	gene with protein product	"""adipose specific 2"", ""adipose most abundant gene transcript 2"", ""adipogenesis factor rich in obesity"""		"""chromosome 10 open reading frame 116"""	C10orf116		8619847, 23239344	Standard	NM_006829		Approved	APM2, AFRO	uc001ked.2	Q15847	OTTHUMG00000018668	ENST00000372013.3:c.204T>C	10.37:g.88730312T>C		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	139	65	0.467626	NM_006829		Silent	SNP	ENST00000372013.3	37	CCDS7381.1																																																																																			T|0.489;C|0.511	0.511	strong		0.587	ADIRF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049194.1	NM_006829	
MOCS2	4338	hgsc.bcm.edu	37	5	52397199	52397199	+	Missense_Mutation	SNP	G	G	A	rs2233218	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:52397199G>A	ENST00000396954.3	-	5	1044	c.367C>T	c.(367-369)Cat>Tat	p.H123Y	MOCS2_ENST00000450852.3_3'UTR|MOCS2_ENST00000584946.1_3'UTR|MOCS2_ENST00000508922.1_3'UTR|MOCS2_ENST00000582677.1_Intron|MOCS2_ENST00000510818.2_3'UTR|MOCS2_ENST00000527216.1_3'UTR|MOCS2_ENST00000361377.4_Intron	NM_004531.3	NP_004522.1			molybdenum cofactor synthesis 2											endometrium(1)|lung(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	5		Lung NSC(810;3.08e-05)|Breast(144;0.0848)				CCAAGTCTATGGAACACTGCT	0.348													G|||	13	0.00259585	0.0	0.0029	5008	,	,		15837	0.0		0.0109	False		,,,				2504	0.0				p.H123Y		Atlas-SNP	.											.	MOCS2	28	.	0			c.C367T						PASS	.	G	TYR/HIS,	6,4400	11.4+/-27.6	0,6,2197	201.0	200.0	200.0		367,	5.8	1.0	5	dbSNP_98	200	47,8553	30.1+/-81.4	1,45,4254	yes	missense,utr-3	MOCS2	NM_004531.3,NM_176806.2	83,	1,51,6451	AA,AG,GG		0.5465,0.1362,0.4075	probably-damaging,	123/189,	52397199	53,12953	2203	4300	6503	SO:0001583	missense	4338	exon5			GTCTATGGAACAC	AF117815	CCDS3958.1, CCDS47205.1	5q11	2008-02-05			ENSG00000164172	ENSG00000164172			7193	protein-coding gene	gene with protein product		603708				10053004, 9889283	Standard	NM_004531		Approved	MOCO1	uc003joz.3	O96007	OTTHUMG00000096981	ENST00000396954.3:c.367C>T	5.37:g.52397199G>A	ENSP00000380157:p.His123Tyr	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	148	71	0.47973	NM_004531		Missense_Mutation	SNP	ENST00000396954.3	37	CCDS3958.1	10	0.004578754578754579	0	0.0	2	0.0055248618784530384	0	0.0	8	0.010554089709762533	G	26.2	4.718212	0.89205	0.001362	0.005465	ENSG00000164172	ENST00000396954;ENST00000527216	T	0.63744	-0.06	5.83	5.83	0.93111	.	0.000000	0.85682	D	0.000000	D	0.85496	0.5710	H	0.98701	4.305	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.91373	0.5121	10	0.87932	D	0	-10.3275	20.1184	0.97949	0.0:0.0:1.0:0.0	rs2233218;rs52802686;rs2233218	123	O96007	MOC2B_HUMAN	Y	123	ENSP00000380157:H123Y	ENSP00000380157:H123Y	H	-	1	0	MOCS2	52432956	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.715000	0.84713	2.775000	0.95449	0.650000	0.86243	CAT	G|0.995;A|0.005	0.005	strong		0.348	MOCS2-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000214053.3	NM_183418	
TCOF1	6949	hgsc.bcm.edu	37	5	149776232	149776232	+	Missense_Mutation	SNP	C	C	T	rs15251	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:149776232C>T	ENST00000504761.2	+	24	4169	c.4169C>T	c.(4168-4170)gCa>gTa	p.A1390V	TCOF1_ENST00000445265.2_Missense_Mutation_p.A1314V|TCOF1_ENST00000513346.1_Missense_Mutation_p.A1390V|TCOF1_ENST00000323668.7_Missense_Mutation_p.A1313V|TCOF1_ENST00000451292.1_Missense_Mutation_p.A1427V|TCOF1_ENST00000377797.3_Missense_Mutation_p.A1391V|TCOF1_ENST00000439160.2_Missense_Mutation_p.A1353V			Q13428	TCOF_HUMAN	Treacher Collins-Franceschetti syndrome 1	1390			A -> V (in dbSNP:rs15251). {ECO:0000269|PubMed:9042910}.		skeletal system development (GO:0001501)|transcription of nuclear large rRNA transcript from RNA polymerase I promoter (GO:0042790)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|transporter activity (GO:0005215)			NS(1)|breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(8)|ovary(2)|pancreas(1)|prostate(2)|skin(1)	35		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			AAGGGGAAAGCAAAGAGAGAC	0.567													C|||	1122	0.224042	0.0567	0.2305	5008	,	,		16898	0.2044		0.2972	False		,,,				2504	0.3906				p.A1390V		Atlas-SNP	.											.	TCOF1	154	.	0			c.C4169T						PASS	.	C	VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA	386,4020	178.7+/-207.4	18,350,1835	24.0	21.0	22.0		3938,4169,4058,3941,4055	2.6	0.1	5	dbSNP_52	22	2349,6251	360.0+/-331.8	313,1723,2264	yes	missense,missense,missense,missense,missense	TCOF1	NM_000356.3,NM_001135243.1,NM_001135244.1,NM_001135245.1,NM_001195141.1	64,64,64,64,64	331,2073,4099	TT,TC,CC		27.314,8.7608,21.0288	benign,benign,benign,benign,benign	1313/1412,1390/1489,1353/1452,1314/1413,1352/1451	149776232	2735,10271	2203	4300	6503	SO:0001583	missense	6949	exon24			GGAAAGCAAAGAG		CCDS4306.1, CCDS47305.1, CCDS47306.1, CCDS47307.1, CCDS54936.1	5q32	2014-06-18			ENSG00000070814	ENSG00000070814			11654	protein-coding gene	gene with protein product		606847				1765376	Standard	NM_001008657		Approved	treacle, TCS	uc003lry.3	Q13428	OTTHUMG00000130081	ENST00000504761.2:c.4169C>T	5.37:g.149776232C>T	ENSP00000421655:p.Ala1390Val	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	88	44	0.5	NM_001135243	A0JLU0|B4E111|Q6SC72|Q7Z5W9|Q96A52|Q99408|Q99860	Missense_Mutation	SNP	ENST00000504761.2	37	CCDS54936.1	471	0.21565934065934067	29	0.05894308943089431	87	0.24033149171270718	125	0.21853146853146854	230	0.3034300791556728	C	15.44	2.833743	0.50951	0.087608	0.27314	ENSG00000070814	ENST00000451292;ENST00000377797;ENST00000445265;ENST00000323668;ENST00000439160;ENST00000427724;ENST00000504761;ENST00000513346	T;T;T;T;T;T;T;T	0.74632	-0.86;-0.86;-0.86;-0.86;-0.86;-0.86;-0.86;-0.86	3.51	2.64	0.31445	.	1.294980	0.05705	N	0.594858	T	0.00012	0.0000	L	0.44542	1.39	0.80722	P	0.0	P;P;P;P;P	0.47409	0.557;0.557;0.557;0.895;0.557	B;B;B;P;B	0.44518	0.125;0.125;0.125;0.452;0.125	T	0.02766	-1.1113	9	0.52906	T	0.07	-0.0123	6.7651	0.23562	0.0:0.873:0.0:0.127	rs15251;rs3180828;rs17713229;rs58771965;rs15251	1353;1313;1352;1390;1314	Q13428-7;Q13428-2;Q13428-6;Q13428;Q13428-8	.;.;.;TCOF_HUMAN;.	V	1427;1391;1314;1313;1353;1352;1390;1390	ENSP00000400939:A1427V;ENSP00000367028:A1391V;ENSP00000409944:A1314V;ENSP00000325223:A1313V;ENSP00000406888:A1353V;ENSP00000390717:A1352V;ENSP00000421655:A1390V;ENSP00000427484:A1390V	ENSP00000325223:A1313V	A	+	2	0	TCOF1	149756425	0.973000	0.33851	0.094000	0.20943	0.882000	0.50991	3.327000	0.52045	1.067000	0.40740	0.561000	0.74099	GCA	C|0.790;T|0.210	0.210	strong		0.567	TCOF1-014	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000380552.1	NM_001008656	
HIST1H2BK	85236	hgsc.bcm.edu	37	6	27114289	27114289	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:27114289T>C	ENST00000356950.1	-	1	288	c.289A>G	c.(289-291)Acg>Gcg	p.T97A	HIST1H2BK_ENST00000396891.4_Missense_Mutation_p.T97A|HIST1H2AH_ENST00000377459.1_5'Flank|MIR3143_ENST00000584253.1_RNA			O60814	H2B1K_HUMAN	histone cluster 1, H2bk	97					antibacterial humoral response (GO:0019731)|chromatin organization (GO:0006325)|defense response to Gram-positive bacterium (GO:0050830)|innate immune response in mucosa (GO:0002227)	extracellular space (GO:0005615)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|skin(1)	13						CGCACGGCCGTCTGGATCTCC	0.622																																					p.T97A		Atlas-SNP	.											.	HIST1H2BK	68	.	0			c.A289G						PASS	.						56.0	62.0	60.0					6																	27114289		2203	4294	6497	SO:0001583	missense	85236	exon1			CGGCCGTCTGGAT	AJ223352	CCDS4621.1	6p22.1	2011-01-27	2006-10-11	2003-02-28	ENSG00000197903	ENSG00000197903		"""Histones / Replication-dependent"""	13954	protein-coding gene	gene with protein product		615045	"""H2B histone family, member T"", ""histone 1, H2bk"""	H2BFT		12408966	Standard	NM_080593		Approved	H2BFAiii	uc003nix.2	O60814	OTTHUMG00000014473	ENST00000356950.1:c.289A>G	6.37:g.27114289T>C	ENSP00000349430:p.Thr97Ala	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	105	34	0.32381	NM_080593	A8K7P7|Q2VPI7	Missense_Mutation	SNP	ENST00000356950.1	37	CCDS4621.1	.	.	.	.	.	.	.	.	.	.	.	26.7	4.762466	0.89932	.	.	ENSG00000197903	ENST00000396891;ENST00000356950	T;T	0.41758	0.99;0.99	4.05	4.05	0.47172	Histone-fold (2);Histone core (1);	0.000000	0.38548	U	0.001653	T	0.61413	0.2345	M	0.92691	3.335	0.46396	D	0.999028	D	0.57899	0.981	D	0.64042	0.921	T	0.71745	-0.4500	10	0.87932	D	0	.	11.5972	0.50981	0.0:0.0:0.0:1.0	.	97	O60814	H2B1K_HUMAN	A	97	ENSP00000380100:T97A;ENSP00000349430:T97A	ENSP00000349430:T97A	T	-	1	0	HIST1H2BK	27222268	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.391000	0.66266	1.783000	0.52377	0.528000	0.53228	ACG	.	.	none		0.622	HIST1H2BK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040141.1	NM_080593	
GALNT18	374378	hgsc.bcm.edu	37	11	11292700	11292700	+	Silent	SNP	G	G	C	rs10831567	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:11292700G>C	ENST00000227756.4	-	11	2226	c.1815C>G	c.(1813-1815)ctC>ctG	p.L605L		NM_198516.2	NP_940918.2	Q6P9A2	GLT18_HUMAN	polypeptide N-acetylgalactosaminyltransferase 18	605					protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)	p.L605L(1)									GTCAGGACGCGAGGCTCCTCA	0.612													c|||	2005	0.400359	0.32	0.5058	5008	,	,		14500	0.38		0.4294	False		,,,				2504	0.4254				p.L605L		Atlas-SNP	.											GALNTL4,NS,carcinoma,0,1	.	.	1	1	Substitution - coding silent(1)	stomach(1)	c.C1815G						PASS	.			1557,2845	668.4+/-402.0	272,1013,916	59.0	56.0	57.0		1815	4.8	1.0	11	dbSNP_120	57	3659,4929	622.1+/-397.3	765,2129,1400	no	coding-synonymous	GALNTL4	NM_198516.2		1037,3142,2316	CC,CG,GG		42.606,35.3703,40.154		605/608	11292700	5216,7774	2201	4294	6495	SO:0001819	synonymous_variant	374378	exon11			GGACGCGAGGCTC	AK055111	CCDS7807.1	11p15	2014-03-13	2014-03-13	2013-01-25	ENSG00000110328	ENSG00000110328	2.4.1.41	"""Glycosyltransferase family 2 domain containing"""	30488	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase 18"""	615136	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase-like 4"", ""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 18"""	GALNTL4		22186971	Standard	NM_198516		Approved	MGC71806, GALNT15, GalNAc-T18	uc001mjo.2	Q6P9A2	OTTHUMG00000165707	ENST00000227756.4:c.1815C>G	11.37:g.11292700G>C		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	64	12	0.1875	NM_198516	O95903|Q8NDY9	Silent	SNP	ENST00000227756.4	37	CCDS7807.1																																																																																			G|0.596;C|0.404	0.404	strong		0.612	GALNT18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385848.1	NM_198516	
HSPG2	3339	hgsc.bcm.edu	37	1	22163402	22163402	+	Silent	SNP	G	G	A	rs41310390	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:22163402G>A	ENST00000374695.3	-	75	10327	c.10248C>T	c.(10246-10248)agC>agT	p.S3416S		NM_005529.5	NP_005520.4	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2	3416	Ig-like C2-type 20.				angiogenesis (GO:0001525)|brain development (GO:0007420)|carbohydrate metabolic process (GO:0005975)|cardiac muscle tissue development (GO:0048738)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|chondrocyte differentiation (GO:0002062)|chondroitin sulfate metabolic process (GO:0030204)|embryonic skeletal system morphogenesis (GO:0048704)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|lipoprotein metabolic process (GO:0042157)|phototransduction, visible light (GO:0007603)|protein localization (GO:0008104)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	basal lamina (GO:0005605)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)			breast(6)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(15)|liver(1)|lung(44)|ovary(10)|pancreas(1)|prostate(10)|skin(9)|upper_aerodigestive_tract(3)|urinary_tract(3)	127		Colorectal(325;3.46e-05)|all_lung(284;7.93e-05)|Lung NSC(340;8.71e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0498)|OV - Ovarian serous cystadenocarcinoma(117;1.14e-26)|Colorectal(126;4.18e-07)|COAD - Colon adenocarcinoma(152;1.82e-05)|GBM - Glioblastoma multiforme(114;3.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000756)|STAD - Stomach adenocarcinoma(196;0.00656)|KIRC - Kidney renal clear cell carcinoma(1967;0.00942)|READ - Rectum adenocarcinoma(331;0.0721)|Lung(427;0.223)	Palifermin(DB00039)	GGAACTCAACGCTGGCCCCAA	0.667													G|||	219	0.04373	0.0333	0.0288	5008	,	,		17121	0.0		0.0606	False		,,,				2504	0.0961				p.S3416S		Atlas-SNP	.											.	HSPG2	311	.	0			c.C10248T	GRCh37	CS011537	HSPG2	S	rs41310390	PASS	.	G		165,4213		5,155,2029	57.0	46.0	50.0		10248	-1.0	0.9	1	dbSNP_127	50	526,8046		15,496,3775	no	coding-synonymous	HSPG2	NM_005529.5		20,651,5804	AA,AG,GG		6.1363,3.7688,5.3359		3416/4392	22163402	691,12259	2189	4286	6475	SO:0001819	synonymous_variant	3339	exon75			CTCAACGCTGGCC	M85289	CCDS30625.1	1p36.1-p35	2013-01-29	2007-02-16	2007-02-16	ENSG00000142798	ENSG00000142798		"""Proteoglycans / Extracellular Matrix : Other"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5273	protein-coding gene	gene with protein product	"""perlecan proteoglycan"""	142461	"""Schwartz-Jampel syndrome 1 (chondrodystrophic myotonia)"""	SJS1		1685141, 11941538	Standard	XM_005245863		Approved	perlecan, PRCAN	uc001bfj.3	P98160	OTTHUMG00000002674	ENST00000374695.3:c.10248C>T	1.37:g.22163402G>A		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	43	16	0.372093	NM_005529	Q16287|Q5SZI3|Q9H3V5	Silent	SNP	ENST00000374695.3	37	CCDS30625.1																																																																																			G|0.954;A|0.046	0.046	strong		0.667	HSPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007598.1	NM_005529	
PPP1R26	9858	hgsc.bcm.edu	37	9	138376972	138376972	+	Missense_Mutation	SNP	A	A	G	rs3928777	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:138376972A>G	ENST00000356818.2	+	4	1165	c.616A>G	c.(616-618)Aag>Gag	p.K206E	PPP1R26_ENST00000604351.1_Missense_Mutation_p.K206E|PPP1R26_ENST00000401470.3_Missense_Mutation_p.K206E|PPP1R26_ENST00000602993.1_Intron|PPP1R26_ENST00000605660.1_Missense_Mutation_p.K206E|PPP1R26_ENST00000605286.1_Missense_Mutation_p.K206E	NM_014811.3	NP_055626.3	Q5T8A7	PPR26_HUMAN	protein phosphatase 1, regulatory subunit 26	206			K -> E (in dbSNP:rs3928777). {ECO:0000269|PubMed:15489334}.		negative regulation of phosphatase activity (GO:0010923)	nucleus (GO:0005634)	phosphatase binding (GO:0019902)|protein phosphatase inhibitor activity (GO:0004864)										GGGATCCAGCAAGGACCAGGG	0.607													G|||	2059	0.411142	0.2927	0.4899	5008	,	,		17027	0.6319		0.2107	False		,,,				2504	0.4939				p.K206E		Atlas-SNP	.											.	.	.	.	0			c.A616G						PASS	.	G	GLU/LYS	1123,3281		138,847,1217	48.0	57.0	54.0		616	-5.0	0.0	9	dbSNP_108	54	1779,6809		195,1389,2710	yes	missense	KIAA0649	NM_014811.3	56	333,2236,3927	GG,GA,AA		20.715,25.4995,22.3368	benign	206/1210	138376972	2902,10090	2202	4294	6496	SO:0001583	missense	9858	exon4			TCCAGCAAGGACC	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.616A>G	9.37:g.138376972A>G	ENSP00000349274:p.Lys206Glu	Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	43	22	0.511628	NM_014811	Q86WU0|Q8WVV0|Q9Y4D3	Missense_Mutation	SNP	ENST00000356818.2	37	CCDS6988.1	825	0.37774725274725274	124	0.25203252032520324	158	0.43646408839779005	385	0.6730769230769231	158	0.20844327176781002	G	1.359	-0.589194	0.03799	0.254995	0.20715	ENSG00000196422	ENST00000356818	T	0.08370	3.1	5.4	-4.97	0.03029	.	1.900700	0.02781	N	0.120907	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	0.38134	-0.9675	9	0.02654	T	1	0.0044	4.3603	0.11199	0.2545:0.4099:0.2528:0.0828	rs3928777;rs17846423;rs17859469;rs56846731	206	Q5T8A7	PPR26_HUMAN	E	206	ENSP00000349274:K206E	ENSP00000349274:K206E	K	+	1	0	KIAA0649	137516793	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.040000	0.12104	-2.103000	0.00844	-2.245000	0.00285	AAG	A|0.724;G|0.276	0.276	strong		0.607	PPP1R26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054987.1	NM_014811	
MUC17	140453	hgsc.bcm.edu	37	7	100684650	100684650	+	Missense_Mutation	SNP	C	C	G	rs12673753	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:100684650C>G	ENST00000306151.4	+	3	10017	c.9953C>G	c.(9952-9954)gCc>gGc	p.A3318G		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	3318	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)					TATTCTCAAGCCAGTTCATCT	0.493													C|||	149	0.0297524	0.0726	0.0058	5008	,	,		28515	0.0278		0.0169	False		,,,				2504	0.0041				p.A3318G		Atlas-SNP	.											.	MUC17	804	.	0			c.C9953G						PASS	.	C	GLY/ALA	324,4082	169.8+/-200.3	11,302,1890	279.0	291.0	287.0		9953	0.1	0.0	7	dbSNP_120	287	93,8507	52.3+/-112.8	0,93,4207	yes	missense	MUC17	NM_001040105.1	60	11,395,6097	GG,GC,CC		1.0814,7.3536,3.2062	probably-damaging	3318/4494	100684650	417,12589	2203	4300	6503	SO:0001583	missense	140453	exon3			CTCAAGCCAGTTC	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.9953C>G	7.37:g.100684650C>G	ENSP00000302716:p.Ala3318Gly	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	63	37	0.587302	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	84	0.038461538461538464	47	0.09552845528455285	3	0.008287292817679558	22	0.038461538461538464	12	0.0158311345646438	c	7.539	0.660367	0.14645	0.073536	0.010814	ENSG00000169876	ENST00000306151	T	0.02421	4.3	1.12	0.056	0.14317	.	.	.	.	.	T	0.00144	0.0004	N	0.24115	0.695	0.09310	N	1	P	0.52463	0.953	D	0.65443	0.935	T	0.50303	-0.8844	9	0.23302	T	0.38	.	5.971	0.19353	0.3067:0.6933:0.0:0.0	rs59785679	3318	Q685J3	MUC17_HUMAN	G	3318	ENSP00000302716:A3318G	ENSP00000302716:A3318G	A	+	2	0	MUC17	100471370	0.000000	0.05858	0.001000	0.08648	0.003000	0.03518	-1.468000	0.02350	0.006000	0.14734	0.196000	0.17591	GCC	C|0.967;G|0.033	0.033	strong		0.493	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
CCDC169	728591	hgsc.bcm.edu	37	13	36857639	36857639	+	Silent	SNP	T	T	C	rs1998800	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:36857639T>C	ENST00000239859.7	-	4	313	c.282A>G	c.(280-282)ctA>ctG	p.L94L	CCDC169_ENST00000239860.6_Intron|CCDC169_ENST00000379862.2_5'UTR|CCDC169_ENST00000491049.2_5'UTR|CCDC169_ENST00000477250.1_5'UTR|SOHLH2_ENST00000554962.1_Intron|CCDC169_ENST00000503173.1_Silent_p.L94L|CCDC169_ENST00000379864.2_5'UTR|CCDC169_ENST00000510088.1_5'UTR|CCDC169-SOHLH2_ENST00000511166.1_Intron			A6NNP5	CC169_HUMAN	coiled-coil domain containing 169	94										breast(1)|endometrium(1)	2						GAATAGAAGATAGTCTATCTA	0.289													T|||	1459	0.291334	0.1589	0.3588	5008	,	,		18877	0.4911		0.2495	False		,,,				2504	0.2597				p.L94L		Atlas-SNP	.											.	CCDC169	20	.	0			c.A282G						PASS	.						199.0	177.0	184.0					13																	36857639		692	1589	2281	SO:0001819	synonymous_variant	728591	exon4			AGAAGATAGTCTA		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.282A>G	13.37:g.36857639T>C		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	107	50	0.46729	NM_001144981	A6NC13|A6NCT2|B7ZW45|B7ZW49|B9EJF2|Q9H1T4|Q9H1T5	Silent	SNP	ENST00000239859.7	37	CCDS45028.1																																																																																			T|0.714;C|0.286	0.286	strong		0.289	CCDC169-014	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368255.1	NM_001144981	
ARSD	414	hgsc.bcm.edu	37	X	2836041	2836041	+	Missense_Mutation	SNP	A	A	T	rs67272620		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	101	0	0		WXS	Illumina HiSeq	Phase_I	93	7	0.0752688	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		
FCGBP	8857	hgsc.bcm.edu	37	19	40363926	40363926	+	Missense_Mutation	SNP	C	C	G	rs3746013	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	130	0	0		WXS	Illumina HiSeq	Phase_I	118	68	0.576271	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	
CLN5	1203	hgsc.bcm.edu	37	13	77574983	77574983	+	Missense_Mutation	SNP	A	A	G	rs386833967|rs1800209	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:77574983A>G	ENST00000377453.3	+	4	2395	c.1103A>G	c.(1102-1104)aAa>aGa	p.K368R	FBXL3_ENST00000477982.1_5'Flank	NM_006493.2	NP_006484.1	O75503	CLN5_HUMAN	ceroid-lipofuscinosis, neuronal 5	319					brain development (GO:0007420)|cell death (GO:0008219)|glycosylation (GO:0070085)|lysosomal lumen acidification (GO:0007042)|neurogenesis (GO:0022008)|neuron maturation (GO:0042551)|protein catabolic process (GO:0030163)|signal peptide processing (GO:0006465)|visual perception (GO:0007601)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|perinuclear region of cytoplasm (GO:0048471)|vacuolar lumen (GO:0005775)	mannose binding (GO:0005537)			breast(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|urinary_tract(1)	16		Acute lymphoblastic leukemia(28;0.205)		GBM - Glioblastoma multiforme(99;0.0503)		ATTGTGCACAAACAGTTCTAT	0.289													G|||	1225	0.244609	0.472	0.2003	5008	,	,		18698	0.2798		0.0974	False		,,,				2504	0.0838				p.K368R		Atlas-SNP	.											.	CLN5	32	.	0			c.A1103G	GRCh37	HD070030	CLN5	D	rs1800209	PASS	.	G	ARG/LYS	1771,2635	618.6+/-393.2	355,1061,787	38.0	40.0	39.0		1103	5.0	1.0	13	dbSNP_89	39	676,7916	751.4+/-407.4	29,618,3649	yes	missense	CLN5	NM_006493.2	26	384,1679,4436	GG,GA,AA		7.8678,40.1952,18.826	benign	368/408	77574983	2447,10551	2203	4296	6499	SO:0001583	missense	1203	exon4			TGCACAAACAGTT		CCDS9456.1	13q21.2-q32	2014-09-17			ENSG00000102805	ENSG00000102805			2076	protein-coding gene	gene with protein product		608102				7942847, 8661106	Standard	NM_006493		Approved		uc001vkc.3	O75503	OTTHUMG00000017100	ENST00000377453.3:c.1103A>G	13.37:g.77574983A>G	ENSP00000366673:p.Lys368Arg	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	94	46	0.489362	NM_006493	B3KQK7	Missense_Mutation	SNP	ENST00000377453.3	37	CCDS9456.1	546	0.25	236	0.4796747967479675	63	0.17403314917127072	170	0.2972027972027972	77	0.10158311345646438	G	2.317	-0.356551	0.05138	0.401952	0.078678	ENSG00000102805	ENST00000377453;ENST00000541907;ENST00000535238	D	0.88124	-2.34	5.84	5.0	0.66597	.	0.120503	0.64402	N	0.000002	T	0.00012	0.0000	N	0.00686	-1.255	0.09310	P	0.9999999999999999	B	0.02656	0.0	B	0.04013	0.001	T	0.33214	-0.9877	9	0.02654	T	1	-19.2369	7.2115	0.25937	0.3589:0.0:0.6411:0.0	rs1800209;rs52828957;rs59116209;rs1800209	319	O75503	CLN5_HUMAN	R	368;319;234	ENSP00000366673:K368R	ENSP00000366673:K368R	K	+	2	0	CLN5	76472984	1.000000	0.71417	0.996000	0.52242	0.513000	0.34164	3.797000	0.55514	0.839000	0.34971	-0.128000	0.14901	AAA	A|0.774;G|0.226	0.226	strong		0.289	CLN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045318.1	NM_006493	
AZU1	566	hgsc.bcm.edu	37	19	830820	830820	+	Missense_Mutation	SNP	G	G	A	rs28626600	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:830820G>A	ENST00000233997.2	+	4	494	c.473G>A	c.(472-474)cGc>cAc	p.R158H		NM_001700.3	NP_001691.1	P20160	CAP7_HUMAN	azurocidin 1	158	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				cellular extravasation (GO:0045123)|defense response to Gram-negative bacterium (GO:0050829)|glial cell migration (GO:0008347)|induction of positive chemotaxis (GO:0050930)|inflammatory response (GO:0006954)|macrophage chemotaxis (GO:0048246)|microglial cell activation (GO:0001774)|monocyte activation (GO:0042117)|negative regulation of apoptotic process (GO:0043066)|positive regulation of cell adhesion (GO:0045785)|positive regulation of fractalkine biosynthetic process (GO:0050754)|positive regulation of interleukin-1 beta biosynthetic process (GO:0050725)|positive regulation of MHC class II biosynthetic process (GO:0045348)|positive regulation of phagocytosis (GO:0050766)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of vascular permeability (GO:0043114)	azurophil granule (GO:0042582)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	heparin binding (GO:0008201)|serine-type endopeptidase activity (GO:0004252)|toxic substance binding (GO:0015643)			NS(1)|endometrium(1)|kidney(1)|lung(4)|pancreas(1)|upper_aerodigestive_tract(2)	10		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;6.59e-06)|all_lung(49;9.97e-06)|Breast(49;0.000172)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GGGAGCCAGCGCAGTGGGGGG	0.657													G|||	285	0.0569089	0.0045	0.0576	5008	,	,		15019	0.0079		0.1223	False		,,,				2504	0.1104				p.R158H		Atlas-SNP	.											AZU1,rectum,carcinoma,0,2	AZU1	31	2	0			c.G473A						PASS	.	G	HIS/ARG	73,4331	58.7+/-95.3	1,71,2130	29.0	28.0	29.0		473	-0.8	0.0	19	dbSNP_125	29	869,7731	189.1+/-236.0	48,773,3479	yes	missense	AZU1	NM_001700.3	29	49,844,5609	AA,AG,GG		10.1047,1.6576,7.2439	probably-damaging	158/252	830820	942,12062	2202	4300	6502	SO:0001583	missense	566	exon4			GCCAGCGCAGTGG	X58794	CCDS12044.1	19p13.3	2012-03-30	2008-08-01		ENSG00000172232	ENSG00000172232			913	protein-coding gene	gene with protein product	"""cationic antimicrobial protein 37"", ""heparin-binding protein"", ""neutrophil azurocidin"""	162815				1919011	Standard	NM_001700		Approved	AZU, CAP37, AZAMP, HBP, NAZC, HUMAZUR	uc002lpz.1	P20160		ENST00000233997.2:c.473G>A	19.37:g.830820G>A	ENSP00000233997:p.Arg158His	Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	42	14	0.333333	NM_001700	P80014|Q52LG4|Q9UCM1|Q9UCT5	Missense_Mutation	SNP	ENST00000233997.2	37	CCDS12044.1	124	0.056776556776556776	2	0.0040650406504065045	26	0.0718232044198895	3	0.005244755244755245	93	0.12269129287598944	G	10.53	1.374773	0.24857	0.016576	0.101047	ENSG00000172232	ENST00000334630;ENST00000233997	D	0.88896	-2.44	1.51	-0.763	0.11030	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	.	.	.	.	T	0.04048	0.0113	N	0.16307	0.4	0.09310	N	1	D	0.65815	0.995	B	0.43950	0.437	T	0.40850	-0.9541	9	0.42905	T	0.14	.	3.9576	0.09396	0.4496:0.0:0.5504:0.0	rs28626600	158	P20160	CAP7_HUMAN	H	172;158	ENSP00000233997:R158H	ENSP00000233997:R158H	R	+	2	0	AZU1	781820	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.143000	0.16115	-0.178000	0.10672	-0.258000	0.10820	CGC	G|0.933;A|0.067	0.067	strong		0.657	AZU1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457472.2	NM_001700	
KLK2	3817	hgsc.bcm.edu	37	19	51379893	51379893	+	Silent	SNP	C	C	T	rs198972	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:51379893C>T	ENST00000325321.3	+	3	597	c.372C>T	c.(370-372)ctC>ctT	p.L124L	AC037199.1_ENST00000594218.1_5'Flank|KLK2_ENST00000358049.4_Silent_p.L124L|KLK2_ENST00000391810.2_Silent_p.L22L			P20151	KLK2_HUMAN	kallikrein-related peptidase 2	124	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	serine-type endopeptidase activity (GO:0004252)		KLK2/ETV1(3)|KLK2/ETV4(2)	large_intestine(3)|lung(6)|ovary(1)|skin(1)	11		all_neural(266;0.026)		OV - Ovarian serous cystadenocarcinoma(262;0.00758)|GBM - Glioblastoma multiforme(134;0.00871)		TCATGCTGCTCCGCCTGTCAG	0.587			T	ETV4	prostate								C|||	2214	0.442093	0.6558	0.3545	5008	,	,		19482	0.2877		0.332	False		,,,				2504	0.4877				p.L124L		Atlas-SNP	.		Dom	yes		19	19q13.41	3817	kallikrein-related peptidase 2		E	.	KLK2	66	.	0			c.C372T						PASS	.	C	,	2707,1699	651.8+/-399.3	845,1017,341	62.0	57.0	59.0		372,372	-5.2	0.0	19	dbSNP_79	59	2686,5914	430.0+/-356.4	414,1858,2028	no	coding-synonymous,coding-synonymous	KLK2	NM_001002231.1,NM_005551.3	,	1259,2875,2369	TT,TC,CC		31.2326,38.5611,41.4655	,	124/224,124/262	51379893	5393,7613	2203	4300	6503	SO:0001819	synonymous_variant	3817	exon3			GCTGCTCCGCCTG	M18157	CCDS12808.1, CCDS42597.1, CCDS58675.1	19q13.33	2008-02-05	2006-10-27				3.4.21.35	"""Kallikreins"""	6363	protein-coding gene	gene with protein product		147960	"""kallikrein 2, prostatic"""			2468530, 16800724, 16800723	Standard	NM_005551		Approved		uc002ptv.3	P20151		ENST00000325321.3:c.372C>T	19.37:g.51379893C>T		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	82	37	0.451219	NM_001002231	B4DU93|B4DUB0|F5H8L3|Q15946|Q9UJZ9	Silent	SNP	ENST00000325321.3	37	CCDS12808.1																																																																																			C|0.585;T|0.415	0.415	strong		0.587	KLK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464438.3	NM_005551.3	
C5orf60	285679	hgsc.bcm.edu	37	5	179071958	179071958	+	Missense_Mutation	SNP	C	C	G	rs7731123	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:179071958C>G	ENST00000448248.2	-	1	89	c.64G>C	c.(64-66)Gac>Cac	p.D22H	C5orf60_ENST00000506142.1_5'UTR	NM_001142306.1	NP_001135778.1	A6NFR6	CE060_HUMAN	chromosome 5 open reading frame 60	22						integral component of membrane (GO:0016021)				NS(1)|breast(1)|kidney(5)	7						ATAACACTGTCCAGAGGAAAG	0.522																																					p.D22H		Atlas-SNP	.											C5orf60,NS,carcinoma,0,1	C5orf60	24	1	0			c.G64C						PASS	.						66.0	64.0	65.0					5																	179071958		692	1591	2283	SO:0001583	missense	285679	exon1			CACTGTCCAGAGG	BC043435	CCDS47353.1	5q35.3	2010-08-19			ENSG00000204661	ENSG00000204661			27753	protein-coding gene	gene with protein product						12477932	Standard	NM_001142306		Approved		uc003mki.3	A6NFR6	OTTHUMG00000163221	ENST00000448248.2:c.64G>C	5.37:g.179071958C>G	ENSP00000404583:p.Asp22His	Somatic	316	0	0		WXS	Illumina HiSeq	Phase_I	276	51	0.184783	NM_001142306	A1L488|B7ZM52|B7ZM53	Missense_Mutation	SNP	ENST00000448248.2	37	CCDS47353.1	.	.	.	.	.	.	.	.	.	.	c	3.367	-0.129222	0.06753	.	.	ENSG00000204661	ENST00000448248	T	0.25250	1.81	0.362	-0.723	0.11181	.	.	.	.	.	T	0.15912	0.0383	N	0.08118	0	0.80722	P	0.0	D;D	0.58268	0.982;0.982	P;P	0.50825	0.651;0.651	T	0.23404	-1.0189	7	0.46703	T	0.11	.	.	.	.	rs7731123;rs7731123	22;22	A6NFR6-2;A6NFR6-4	.;.	H	22	ENSP00000404583:D22H	ENSP00000404583:D22H	D	-	1	0	C5orf60	179004564	0.006000	0.16342	0.027000	0.17364	0.069000	0.16628	-0.549000	0.06041	-0.410000	0.07542	0.134000	0.15878	GAC	C|0.147;G|0.853	0.853	strong		0.522	C5orf60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372148.2	NM_001142306	
ADAM32	203102	hgsc.bcm.edu	37	8	39091526	39091526	+	Silent	SNP	T	T	C	rs4515515	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:39091526T>C	ENST00000379907.4	+	16	1870	c.1743T>C	c.(1741-1743)acT>acC	p.T581T	ADAM32_ENST00000437682.2_Silent_p.T482T|ADAM32_ENST00000519315.1_Silent_p.T475T	NM_145004.5	NP_659441	Q8TC27	ADA32_HUMAN	ADAM metallopeptidase domain 32	581						integral component of membrane (GO:0016021)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(14)|ovary(1)|skin(2)	31		all_cancers(7;3e-05)|all_lung(54;0.00187)|Hepatocellular(245;0.00745)|Lung NSC(58;0.00771)|Breast(189;0.0503)	LUSC - Lung squamous cell carcinoma(45;6.2e-07)|Colorectal(1;0.00699)|READ - Rectum adenocarcinoma(1;0.146)			TATGCATAACTGTAGACTACA	0.373													T|||	1081	0.215855	0.1233	0.2133	5008	,	,		13078	0.2937		0.2396	False		,,,				2504	0.2382				p.T581T		Atlas-SNP	.											ADAM32,NS,carcinoma,0,1	ADAM32	70	1	0			c.T1743C						PASS	.	T		552,3160		55,442,1359	71.0	62.0	65.0		1743	1.0	0.0	8	dbSNP_111	65	1959,6219		244,1471,2374	no	coding-synonymous	ADAM32	NM_145004.5		299,1913,3733	CC,CT,TT		23.9545,14.8707,21.1186		581/788	39091526	2511,9379	1856	4089	5945	SO:0001819	synonymous_variant	203102	exon16			CATAACTGTAGAC	BC026085	CCDS47846.1	8p11.22	2005-08-18	2005-08-18		ENSG00000197140	ENSG00000197140		"""ADAM metallopeptidase domain containing"""	15479	protein-coding gene	gene with protein product			"""a disintegrin and metalloproteinase domain 32"""			12568724	Standard	NM_145004		Approved		uc003xmt.4	Q8TC27	OTTHUMG00000164071	ENST00000379907.4:c.1743T>C	8.37:g.39091526T>C		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	101	25	0.247525	NM_145004	Q8TC42	Silent	SNP	ENST00000379907.4	37	CCDS47846.1																																																																																			T|0.781;C|0.219	0.219	strong		0.373	ADAM32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377089.1	NM_145004	
LY75	4065	hgsc.bcm.edu	37	2	160676350	160676350	+	Missense_Mutation	SNP	T	T	C	rs17827158	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:160676350T>C	ENST00000263636.4	-	29	4067	c.4040A>G	c.(4039-4041)aAg>aGg	p.K1347R	LY75_ENST00000554112.1_Missense_Mutation_p.K1347R|LY75_ENST00000553424.1_Missense_Mutation_p.K1347R|LY75-CD302_ENST00000504764.1_Missense_Mutation_p.K1347R|LY75-CD302_ENST00000505052.1_Missense_Mutation_p.K1347R	NM_002349.3	NP_002340.2	O60449	LY75_HUMAN	lymphocyte antigen 75	1347	C-type lectin 8. {ECO:0000255|PROSITE- ProRule:PRU00040}.		K -> R (in dbSNP:rs17827158).		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)		AGCCAAAAACTTCTCATTTTT	0.363													T|||	365	0.0728834	0.0567	0.0807	5008	,	,		17662	0.0079		0.1044	False		,,,				2504	0.1237				p.K1347R		Atlas-SNP	.											.	LY75	151	.	0			c.A4040G						PASS	.	T	ARG/LYS,ARG/LYS,ARG/LYS	309,4097	162.9+/-194.8	17,275,1911	81.0	86.0	84.0		4040,4040,4040	2.0	0.1	2	dbSNP_123	84	901,7699	202.1+/-245.5	52,797,3451	yes	missense,missense,missense	LY75,LY75-CD302	NM_001198759.1,NM_001198760.1,NM_002349.3	26,26,26	69,1072,5362	CC,CT,TT		10.4767,7.0132,9.3034	benign,benign,benign	1347/1874,1347/1818,1347/1723	160676350	1210,11796	2203	4300	6503	SO:0001583	missense	4065	exon29			AAAAACTTCTCAT	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.4040A>G	2.37:g.160676350T>C	ENSP00000263636:p.Lys1347Arg	Somatic	196	0	0		WXS	Illumina HiSeq	Phase_I	145	65	0.448276	NM_002349	O75913|Q53R46|Q53TF5|Q7Z575|Q7Z577	Missense_Mutation	SNP	ENST00000263636.4	37	CCDS2211.1	161	0.07371794871794872	38	0.07723577235772358	45	0.12430939226519337	3	0.005244755244755245	75	0.09894459102902374	T	8.685	0.905974	0.17760	0.070132	0.104767	ENSG00000054219;ENSG00000054219;ENSG00000054219;ENSG00000248672;ENSG00000248672	ENST00000554112;ENST00000553424;ENST00000263636;ENST00000504764;ENST00000505052	T;T;T;T;T	0.07908	3.15;3.15;3.15;3.15;3.15	5.65	1.98	0.26296	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (2);	.	.	.	.	T	0.00073	0.0002	L	0.32530	0.975	0.80722	P	0.0	B;B;B	0.11235	0.003;0.004;0.004	B;B;B	0.14023	0.009;0.01;0.006	T	0.42916	-0.9423	8	0.15952	T	0.53	-4.5352	1.4096	0.02288	0.1352:0.206:0.1403:0.5185	rs17827158;rs52833817;rs17827158	1347;1347;1347	O60449-3;O60449;O60449-2	.;LY75_HUMAN;.	R	1347	ENSP00000451511:K1347R;ENSP00000451446:K1347R;ENSP00000263636:K1347R;ENSP00000423463:K1347R;ENSP00000421035:K1347R	ENSP00000423463:K1347R	K	-	2	0	LY75;LY75-CD302	160384596	0.000000	0.05858	0.114000	0.21550	0.746000	0.42486	0.646000	0.24797	0.403000	0.25479	0.482000	0.46254	AAG	T|0.915;C|0.085	0.085	strong		0.363	LY75-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255035.1		
CYTH3	9265	hgsc.bcm.edu	37	7	6227341	6227341	+	Silent	SNP	A	A	G	rs41282682	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:6227341A>G	ENST00000350796.3	-	3	265	c.129T>C	c.(127-129)taT>taC	p.Y43Y		NM_004227.3	NP_004218.1	O43739	CYH3_HUMAN	cytohesin 3	43					establishment of epithelial cell polarity (GO:0090162)|Golgi vesicle transport (GO:0048193)|positive regulation of cell adhesion (GO:0045785)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)|regulation of cell adhesion (GO:0030155)	cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(7)|urinary_tract(1)	19						CTGCAATTTCATATTTCAGCC	0.408													A|||	48	0.00958466	0.0008	0.0173	5008	,	,		20705	0.0		0.0199	False		,,,				2504	0.0153				p.Y43Y		Atlas-SNP	.											.	CYTH3	44	.	0			c.T129C						PASS	.	A		14,4392	22.3+/-47.3	0,14,2189	157.0	143.0	148.0		129	-4.4	0.8	7	dbSNP_127	148	196,8404	85.8+/-148.2	2,192,4106	no	coding-synonymous	CYTH3	NM_004227.3		2,206,6295	GG,GA,AA		2.2791,0.3177,1.6146		43/400	6227341	210,12796	2203	4300	6503	SO:0001819	synonymous_variant	9265	exon3			AATTTCATATTTC	AJ223957	CCDS5346.1	7p22.1	2014-05-02	2008-08-14	2008-08-14	ENSG00000008256	ENSG00000008256		"""Pleckstrin homology (PH) domain containing"""	9504	protein-coding gene	gene with protein product		605081	"""pleckstrin homology, Sec7 and coiled-coil domains 3"""	PSCD3		9072969	Standard	NM_004227		Approved	GRP1, ARNO3, cytohesin-3	uc003spt.3	O43739	OTTHUMG00000023440	ENST00000350796.3:c.129T>C	7.37:g.6227341A>G		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	80	58	0.725	NM_004227	A4D2N8	Silent	SNP	ENST00000350796.3	37	CCDS5346.1																																																																																			A|0.986;G|0.014	0.014	strong		0.408	CYTH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207396.2	NM_004227	
DOCK4	9732	hgsc.bcm.edu	37	7	111503547	111503547	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:111503547T>C	ENST00000437633.1	-	23	2610	c.2354A>G	c.(2353-2355)aAc>aGc	p.N785S	DOCK4_ENST00000428084.1_Missense_Mutation_p.N785S|DOCK4_ENST00000476846.1_5'UTR	NM_014705.3	NP_055520.3	Q8N1I0	DOCK4_HUMAN	dedicator of cytokinesis 4	785					cell chemotaxis (GO:0060326)|positive regulation of Rac GTPase activity (GO:0032855)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|membrane (GO:0016020)|stereocilium (GO:0032420)|stereocilium bundle (GO:0032421)	guanyl-nucleotide exchange factor activity (GO:0005085)|PDZ domain binding (GO:0030165)|Rac GTPase activator activity (GO:0030675)|Rac GTPase binding (GO:0048365)|receptor tyrosine kinase binding (GO:0030971)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(13)|lung(31)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(4)	72		Acute lymphoblastic leukemia(1;0.0441)				CTGGACCAAGTTGGCTACTTC	0.498																																					p.N785S		Atlas-SNP	.											.	DOCK4	365	.	0			c.A2354G						PASS	.						56.0	55.0	55.0					7																	111503547		1957	4132	6089	SO:0001583	missense	9732	exon23			ACCAAGTTGGCTA		CCDS47688.1	7q31.1	2007-08-07			ENSG00000128512	ENSG00000128512			19192	protein-coding gene	gene with protein product		607679				12432077, 12628187	Standard	XM_006716188		Approved	FLJ34238, KIAA0716	uc003vfx.3	Q8N1I0	OTTHUMG00000155077	ENST00000437633.1:c.2354A>G	7.37:g.111503547T>C	ENSP00000404179:p.Asn785Ser	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	81	27	0.333333	NM_014705	O14584|O94824|Q8NB45	Missense_Mutation	SNP	ENST00000437633.1	37	CCDS47688.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	13.27|13.27	2.186733|2.186733	0.38609|0.38609	.|.	.|.	ENSG00000128512|ENSG00000128512	ENST00000352877;ENST00000428084;ENST00000437633;ENST00000342288;ENST00000544250|ENST00000423057;ENST00000445943	T;T|.	0.02812|.	4.15;4.15|.	5.23|5.23	4.07|4.07	0.47477|0.47477	.|.	0.213000|.	0.49305|.	D|.	0.000152|.	T|T	0.60843|0.60843	0.2300|0.2300	L|L	0.54323|0.54323	1.7|1.7	0.80722|0.80722	D|D	1|1	B;B;B;B|.	0.17465|.	0.013;0.013;0.013;0.022|.	B;B;B;B|.	0.19666|.	0.017;0.017;0.011;0.026|.	T|T	0.57406|0.57406	-0.7817|-0.7817	10|5	0.09843|.	T|.	0.71|.	.|.	11.1557|11.1557	0.48486|0.48486	0.0:0.0722:0.0:0.9278|0.0:0.0722:0.0:0.9278	.|.	785;785;785;785|.	Q149N2;Q149N5;Q8N1I0;Q8N1I0-2|.	.;.;DOCK4_HUMAN;.|.	S|A	773;785;785;773;784|237;773	ENSP00000410746:N785S;ENSP00000404179:N785S|.	ENSP00000345432:N773S|.	N|T	-|-	2|1	0|0	DOCK4|DOCK4	111290783|111290783	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.861000|0.861000	0.49209|0.49209	4.653000|4.653000	0.61462|0.61462	0.991000|0.991000	0.38814|0.38814	0.460000|0.460000	0.39030|0.39030	AAC|ACT	.	.	none		0.498	DOCK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338369.4	NM_014705	
AOX1	316	hgsc.bcm.edu	37	2	201501687	201501687	+	Silent	SNP	A	A	G	rs149839944	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:201501687A>G	ENST00000374700.2	+	22	2641	c.2400A>G	c.(2398-2400)gtA>gtG	p.V800V	AOX1_ENST00000485106.1_3'UTR	NM_001159.3	NP_001150.3	Q06278	AOXA_HUMAN	aldehyde oxidase 1	800					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)	TGTGCCATGTAAGGCGTGTTG	0.458													A|||	2	0.000399361	0.0	0.0	5008	,	,		21086	0.0		0.002	False		,,,				2504	0.0				p.V800V		Atlas-SNP	.											.	AOX1	152	.	0			c.A2400G						PASS	.	A		1,4405	2.1+/-5.4	0,1,2202	167.0	141.0	150.0		2400	-5.1	0.0	2	dbSNP_134	150	26,8574	18.5+/-59.3	0,26,4274	no	coding-synonymous	AOX1	NM_001159.3		0,27,6476	GG,GA,AA		0.3023,0.0227,0.2076		800/1339	201501687	27,12979	2203	4300	6503	SO:0001819	synonymous_variant	316	exon22			CCATGTAAGGCGT	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.2400A>G	2.37:g.201501687A>G		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	156	75	0.480769	NM_001159	O14765|Q53RR8|Q53TV3|Q9BYF0|Q9UPG6	Silent	SNP	ENST00000374700.2	37	CCDS33360.1																																																																																			A|0.999;G|0.001	0.001	strong		0.458	AOX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335844.1	NM_001159	
DOCK1	1793	hgsc.bcm.edu	37	10	129242515	129242515	+	Silent	SNP	G	G	A	rs11371	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:129242515G>A	ENST00000280333.6	+	50	5431	c.5322G>A	c.(5320-5322)agG>agA	p.R1774R		NM_001380.3	NP_001371.1	Q14185	DOCK1_HUMAN	dedicator of cytokinesis 1	1774					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)		TTACACCAAGGGCCAAGCTCA	0.572													G|||	1690	0.33746	0.2133	0.2824	5008	,	,		19267	0.4653		0.3658	False		,,,				2504	0.3834				p.R1774R		Atlas-SNP	.											.	DOCK1	188	.	0			c.G5322A						PASS	.	G		911,3281		108,695,1293	85.0	96.0	92.0		5277	1.9	0.8	10	dbSNP_52	92	3176,5248		615,1946,1651	no	coding-synonymous	DOCK1	NM_001380.3		723,2641,2944	AA,AG,GG		37.7018,21.7319,32.3954		1759/1851	129242515	4087,8529	2096	4212	6308	SO:0001819	synonymous_variant	1793	exon50			ACCAAGGGCCAAG	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.5322G>A	10.37:g.129242515G>A		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	54	54	1	NM_001380	A9Z1Z5	Silent	SNP	ENST00000280333.6	37																																																																																				G|0.667;A|0.333	0.333	strong		0.572	DOCK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050979.2	NM_001380	
SNX30	401548	hgsc.bcm.edu	37	9	115598610	115598610	+	Missense_Mutation	SNP	A	A	G	rs76424583	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:115598610A>G	ENST00000374232.3	+	5	899	c.735A>G	c.(733-735)atA>atG	p.I245M		NM_001012994.1	NP_001013012.1	Q5VWJ9	SNX30_HUMAN	sorting nexin family member 30	245					apoptotic process (GO:0006915)|intracellular protein transport (GO:0006886)	endosome (GO:0005768)	phosphatidylinositol binding (GO:0035091)			large_intestine(1)|lung(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	8						TTGCTGCCATAGGTGACTACT	0.498													A|||	283	0.0565096	0.0023	0.0793	5008	,	,		21203	0.0655		0.1093	False		,,,				2504	0.0501				p.I245M		Atlas-SNP	.											.	SNX30	32	.	0			c.A735G						PASS	.	A	MET/ILE	95,3805		1,93,1856	116.0	114.0	115.0		735	-8.6	0.3	9	dbSNP_131	115	800,7484		41,718,3383	yes	missense	SNX30	NM_001012994.1	10	42,811,5239	GG,GA,AA		9.6572,2.4359,7.3457	benign	245/438	115598610	895,11289	1950	4142	6092	SO:0001583	missense	401548	exon5			TGCCATAGGTGAC	AK126644	CCDS43865.1	9q33.1	2014-02-12			ENSG00000148158	ENSG00000148158		"""Sorting nexins"""	23685	protein-coding gene	gene with protein product							Standard	NM_001012994		Approved	ATG24A	uc004bgj.4	Q5VWJ9	OTTHUMG00000020512	ENST00000374232.3:c.735A>G	9.37:g.115598610A>G	ENSP00000363349:p.Ile245Met	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	59	26	0.440678	NM_001012994		Missense_Mutation	SNP	ENST00000374232.3	37	CCDS43865.1	143	0.06547619047619048	1	0.0020325203252032522	29	0.08011049723756906	30	0.05244755244755245	83	0.10949868073878628	A	3.654	-0.070970	0.07228	0.024359	0.096572	ENSG00000148158	ENST00000374232	T	0.23754	1.89	5.8	-8.61	0.00885	.	0.139939	0.64402	D	0.000007	T	0.00109	0.0003	N	0.02539	-0.55	0.23758	P	0.99692116	B	0.10296	0.003	B	0.09377	0.004	T	0.11494	-1.0585	9	0.31617	T	0.26	.	2.4477	0.04510	0.3115:0.3028:0.0648:0.3209	.	245	Q5VWJ9	SNX30_HUMAN	M	245	ENSP00000363349:I245M	ENSP00000363349:I245M	I	+	3	3	SNX30	114638431	0.037000	0.19845	0.311000	0.25182	0.711000	0.40976	-0.830000	0.04410	-1.388000	0.02092	-0.327000	0.08410	ATA	A|0.922;G|0.078	0.078	strong		0.498	SNX30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053700.1		
GP2	2813	hgsc.bcm.edu	37	16	20335325	20335325	+	Silent	SNP	G	G	A	rs12930599	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:20335325G>A	ENST00000381362.4	-	3	424	c.348C>T	c.(346-348)gaC>gaT	p.D116D	GP2_ENST00000381360.5_Intron|GP2_ENST00000302555.5_Silent_p.D116D|GP2_ENST00000341642.5_Intron|GP2_ENST00000573897.1_5'Flank	NM_001007240.1|NM_001502.2	NP_001007241.2|NP_001493.2	P55259	GP2_HUMAN	glycoprotein 2 (zymogen granule membrane)	116					antigen transcytosis by M cells in mucosal-associated lymphoid tissue (GO:0002412)	anchored component of membrane (GO:0031225)|apical plasma membrane (GO:0016324)|extracellular vesicular exosome (GO:0070062)	antigen binding (GO:0003823)			breast(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(25)|ovary(3)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	48						ACATGGGAGCGTCTGTCTGGC	0.572													G|||	414	0.0826677	0.0068	0.1772	5008	,	,		18878	0.0089		0.2256	False		,,,				2504	0.047				p.D116D		Atlas-SNP	.											.	GP2	122	.	0			c.C348T						PASS	.	G	,,,	205,4201	124.5+/-161.8	3,199,2001	98.0	77.0	84.0		348,,,348	-10.0	0.0	16	dbSNP_121	84	1890,6710	335.5+/-321.5	201,1488,2611	no	coding-synonymous,intron,intron,coding-synonymous	GP2	NM_001007240.1,NM_001007241.1,NM_001007242.1,NM_001502.2	,,,	204,1687,4612	AA,AG,GG		21.9767,4.6527,16.108	,,,	116/538,,,116/535	20335325	2095,10911	2203	4300	6503	SO:0001819	synonymous_variant	2813	exon3			GGGAGCGTCTGTC	U36221	CCDS10582.2, CCDS42128.1, CCDS45432.1, CCDS45433.1	16p12.3	2008-02-05			ENSG00000169347	ENSG00000169347			4441	protein-coding gene	gene with protein product		602977				9605860	Standard	XM_005255259		Approved		uc002dgw.3	P55259	OTTHUMG00000131489	ENST00000381362.4:c.348C>T	16.37:g.20335325G>A		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	136	51	0.375	NM_001007240	A6NFM9|A6NJA8|Q13338|Q9UIF1	Silent	SNP	ENST00000381362.4	37	CCDS42128.1																																																																																			G|0.865;A|0.135	0.135	strong		0.572	GP2-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000436920.1	NM_016295	
CAMK1G	57172	hgsc.bcm.edu	37	1	209782343	209782343	+	Silent	SNP	A	A	G	rs11119314	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:209782343A>G	ENST00000009105.1	+	8	899	c.654A>G	c.(652-654)ccA>ccG	p.P218P	CAMK1G_ENST00000361322.2_Silent_p.P218P|CAMK1G_ENST00000494990.1_3'UTR			Q96NX5	KCC1G_HUMAN	calcium/calmodulin-dependent protein kinase IG	218	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.					calcium- and calmodulin-dependent protein kinase complex (GO:0005954)|Golgi apparatus (GO:0005794)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)	p.P218P(1)		breast(2)|central_nervous_system(1)|large_intestine(8)|lung(8)|stomach(1)	20				OV - Ovarian serous cystadenocarcinoma(81;0.0475)		GATACCCCCCATTCTATGAAG	0.517													A|||	2732	0.545527	0.7073	0.5476	5008	,	,		20101	0.5714		0.3867	False		,,,				2504	0.4622				p.P218P	Ovarian(163;530 1939 9680 28669 48710)	Atlas-SNP	.											CAMK1G,NS,adenoma,0,2	CAMK1G	49	2	1	Substitution - coding silent(1)	stomach(1)	c.A654G						PASS	.	A		2909,1497	675.5+/-403.1	957,995,251	117.0	112.0	114.0		654	-10.2	0.5	1	dbSNP_120	114	3346,5254	497.4+/-374.5	643,2060,1597	no	coding-synonymous	CAMK1G	NM_020439.2		1600,3055,1848	GG,GA,AA		38.907,33.9764,48.0932		218/477	209782343	6255,6751	2203	4300	6503	SO:0001819	synonymous_variant	57172	exon8			CCCCCCATTCTAT		CCDS1486.1	1q32.2	2012-09-20			ENSG00000008118	ENSG00000008118			14585	protein-coding gene	gene with protein product		614994				12637513	Standard	NM_020439		Approved	VWS1, CLICKIII, dJ272L16.1	uc001hhd.3	Q96NX5	OTTHUMG00000036361	ENST00000009105.1:c.654A>G	1.37:g.209782343A>G		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	122	67	0.54918	NM_020439	Q86UH5|Q9Y3J7	Silent	SNP	ENST00000009105.1	37	CCDS1486.1	1134	0.5192307692307693	350	0.7113821138211383	179	0.494475138121547	327	0.5716783216783217	278	0.36675461741424803	A	6.373	0.436872	0.12104	0.660236	0.38907	ENSG00000008118	ENST00000423146	T	0.64085	-0.08	5.48	-10.2	0.00374	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999999	.	.	.	.	.	.	T	0.38308	-0.9667	5	0.87932	D	0	.	0.8075	0.01086	0.336:0.2448:0.2567:0.1625	rs11119314;rs17846018;rs17859002;rs60747756;rs11119314	.	.	.	R	193	ENSP00000392173:H193R	ENSP00000392173:H193R	H	+	2	0	CAMK1G	207848966	0.000000	0.05858	0.481000	0.27354	0.191000	0.23601	-3.434000	0.00472	-1.907000	0.01087	-2.614000	0.00158	CAT	A|0.485;G|0.515	0.515	strong		0.517	CAMK1G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088526.1	NM_020439	
INPP4A	3631	hgsc.bcm.edu	37	2	99172243	99172243	+	Silent	SNP	C	C	T	rs41486345	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:99172243C>T	ENST00000523221.1	+	15	1809	c.1809C>T	c.(1807-1809)tcC>tcT	p.S603S	INPP4A_ENST00000545415.1_Intron|INPP4A_ENST00000409540.3_Intron|INPP4A_ENST00000074304.5_Silent_p.S603S|INPP4A_ENST00000409463.1_Intron|INPP4A_ENST00000409016.4_Intron|INPP4A_ENST00000409851.3_Silent_p.S598S			Q96PE3	INP4A_HUMAN	inositol polyphosphate-4-phosphatase, type I, 107kDa	603					inositol phosphate metabolic process (GO:0043647)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	phosphatidylinositol-3,4-bisphosphate 4-phosphatase activity (GO:0016316)|phosphatidylinositol-4,5-bisphosphate 4-phosphatase activity (GO:0034597)			breast(1)|endometrium(9)|kidney(2)|large_intestine(5)|lung(16)|ovary(2)|prostate(4)|upper_aerodigestive_tract(4)	43						CCATGCCCTCCACTGCATGCC	0.557													C|||	127	0.0253594	0.0008	0.0187	5008	,	,		21584	0.0		0.0845	False		,,,				2504	0.0286				p.S603S		Atlas-SNP	.											.	INPP4A	205	.	0			c.C1809T						PASS	.	C	,,,	12,1372		0,12,680	207.0	211.0	210.0		1809,1794,,	0.2	0.2	2	dbSNP_127	210	244,2938		9,226,1356	no	coding-synonymous,coding-synonymous,intron,intron	INPP4A	NM_001134224.1,NM_001134225.1,NM_001566.2,NM_004027.2	,,,	9,238,2036	TT,TC,CC		7.6681,0.8671,5.6067	,,,	603/978,598/973,,	99172243	256,4310	692	1591	2283	SO:0001819	synonymous_variant	3631	exon17			GCCCTCCACTGCA	U26398	CCDS46369.1, CCDS46370.1, CCDS46371.1, CCDS46372.1	2q11.2	2008-05-27	2002-08-29		ENSG00000040933	ENSG00000040933			6074	protein-coding gene	gene with protein product		600916	"""inositol polyphosphate-4-phosphatase, type I, 107kD"""	INPP4		7608176, 9295334	Standard	NM_004027		Approved		uc002syy.3	Q96PE3	OTTHUMG00000153106	ENST00000523221.1:c.1809C>T	2.37:g.99172243C>T		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	56	56	1	NM_001134224	O15326|Q13187|Q53TD8|Q8TC02	Silent	SNP	ENST00000523221.1	37	CCDS46369.1																																																																																			C|0.954;T|0.046	0.046	strong		0.557	INPP4A-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000376095.1	NM_001566	
TOM1	10043	hgsc.bcm.edu	37	22	35742925	35742925	+	Silent	SNP	T	T	G	rs743810	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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_ENST00000425375.1_Silent_p.G384G|TOM1_ENST00000382034.5_3'UTR|TOM1_ENST00000436462.2_Silent_p.G391G|TOM1_ENST00000411850.1_Silent_p.G429G	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	40	1	0.025		WXS	Illumina HiSeq	Phase_I	52	26	0.5	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	
GPSM2	29899	hgsc.bcm.edu	37	1	109446750	109446750	+	Missense_Mutation	SNP	G	G	A	rs61754640	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:109446750G>A	ENST00000406462.2	+	11	1839	c.1066G>A	c.(1066-1068)Ggg>Agg	p.G356R	GPSM2_ENST00000264126.3_Missense_Mutation_p.G356R|AKNAD1_ENST00000357393.4_Intron			P81274	GPSM2_HUMAN	G-protein signaling modulator 2	356					establishment of mitotic spindle orientation (GO:0000132)|G-protein coupled receptor signaling pathway (GO:0007186)|lung epithelial cell differentiation (GO:0060487)	apical part of cell (GO:0045177)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	GTPase regulator activity (GO:0030695)|identical protein binding (GO:0042802)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|liver(2)|lung(3)	14		all_epithelial(167;7.64e-05)|all_lung(203;0.000321)|Lung NSC(277;0.000626)		Colorectal(144;0.0353)|Lung(183;0.0984)|COAD - Colon adenocarcinoma(174;0.129)|Epithelial(280;0.175)|all cancers(265;0.209)		GTTGTAGGTTGGGGATAAAAG	0.328													G|||	59	0.0117812	0.0015	0.0245	5008	,	,		11747	0.0		0.0358	False		,,,				2504	0.0041				p.G356R		Atlas-SNP	.											.	GPSM2	56	.	0			c.G1066A						PASS	.	G	ARG/GLY	26,4380	33.5+/-64.1	0,26,2177	73.0	70.0	71.0		1066	5.5	1.0	1	dbSNP_129	71	283,8317	104.8+/-165.8	6,271,4023	yes	missense	GPSM2	NM_013296.4	125	6,297,6200	AA,AG,GG		3.2907,0.5901,2.3758	probably-damaging	356/685	109446750	309,12697	2203	4300	6503	SO:0001583	missense	29899	exon10			TAGGTTGGGGATA	AY136740	CCDS792.2	1p13.3	2013-10-11	2010-06-24		ENSG00000121957	ENSG00000121957		"""Tetratricopeptide (TTC) repeat domain containing"""	29501	protein-coding gene	gene with protein product		609245	"""G-protein signalling modulator 2 (AGS3-like, C. elegans)"", ""deafness, autosomal recessive 82"""	DFNB82		11832491, 8973305, 19888295, 20602914, 21348867	Standard	NM_013296		Approved	LGN, Pins	uc010ovc.2	P81274	OTTHUMG00000011730	ENST00000406462.2:c.1066G>A	1.37:g.109446750G>A	ENSP00000385510:p.Gly356Arg	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	156	71	0.455128	NM_013296	Q5T1N8|Q6IBL7|Q8N0Z5	Missense_Mutation	SNP	ENST00000406462.2	37	CCDS792.2	38	0.0173992673992674	1	0.0020325203252032522	12	0.03314917127071823	0	0.0	25	0.032981530343007916	G	19.29	3.799824	0.70567	0.005901	0.032907	ENSG00000121957	ENST00000406462;ENST00000264126	T;T	0.76186	-1.0;-1.0	5.51	5.51	0.81932	Tetratricopeptide-like helical (1);	0.056584	0.64402	D	0.000001	T	0.80105	0.4562	M	0.73217	2.22	0.52099	D	0.999945	D	0.64830	0.994	P	0.56823	0.807	T	0.82096	-0.0626	10	0.66056	D	0.02	-23.5482	17.5977	0.88016	0.0:0.0:1.0:0.0	rs61754640	356	P81274	GPSM2_HUMAN	R	356	ENSP00000385510:G356R;ENSP00000264126:G356R	ENSP00000264126:G356R	G	+	1	0	GPSM2	109248273	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	9.442000	0.97566	2.580000	0.87095	0.655000	0.94253	GGG	G|0.978;A|0.022	0.022	strong		0.328	GPSM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032400.3	NM_013296	
BNIP2	663	hgsc.bcm.edu	37	15	59963488	59963488	+	Silent	SNP	A	A	G	rs1135148	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:59963488A>G	ENST00000607373.1	-	7	803	c.601T>C	c.(601-603)Tta>Cta	p.L201L	BNIP2_ENST00000267859.3_Silent_p.L322L|BNIP2_ENST00000478981.1_5'Flank|AC092755.4_ENST00000441746.1_RNA|BNIP2_ENST00000415213.2_Silent_p.L263L	NM_004330.2	NP_004321.2	Q12982	BNIP2_HUMAN	BCL2/adenovirus E1B 19kDa interacting protein 2	201	CRAL-TRIO. {ECO:0000255|PROSITE- ProRule:PRU00056}.				apoptotic process (GO:0006915)|muscle cell differentiation (GO:0042692)|negative regulation of apoptotic process (GO:0043066)|positive regulation of GTPase activity (GO:0043547)|positive regulation of muscle cell differentiation (GO:0051149)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|nuclear envelope (GO:0005635)	calcium ion binding (GO:0005509)|GTPase activator activity (GO:0005096)|identical protein binding (GO:0042802)			NS(1)|large_intestine(2)|lung(5)|ovary(1)	9						TCTGCTACTAATAGCTCCAAA	0.338													A|||	1663	0.332069	0.1029	0.3847	5008	,	,		16327	0.5615		0.3519	False		,,,				2504	0.3476				p.L322L	Ovarian(174;1936 1978 6671 8240 38212)	Atlas-SNP	.											.	BNIP2	27	.	0			c.T964C						PASS	.	A		669,3709		56,557,1576	60.0	54.0	56.0		964	3.6	1.0	15	dbSNP_86	56	2929,5643		518,1893,1875	no	coding-synonymous	BNIP2	NM_004330.2		574,2450,3451	GG,GA,AA		34.1694,15.281,27.7838		322/436	59963488	3598,9352	2189	4286	6475	SO:0001819	synonymous_variant	663	exon7			CTACTAATAGCTC	U15173	CCDS10174.2	15q21.3	2008-07-18	2002-08-29		ENSG00000140299	ENSG00000140299			1083	protein-coding gene	gene with protein product		603292	"""BCL2/adenovirus E1B 19kD-interacting protein 2"""			7954800	Standard	NM_004330		Approved	Nip2, BNIP-2	uc010uhc.2	Q12982	OTTHUMG00000132727	ENST00000607373.1:c.601T>C	15.37:g.59963488A>G		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	53	30	0.566038	NM_004330	B4DS94	Silent	SNP	ENST00000607373.1	37																																																																																				A|0.703;G|0.297	0.297	strong		0.338	BNIP2-012	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000470740.1	NM_004330	
LRRC16B	90668	hgsc.bcm.edu	37	14	24527220	24527220	+	Silent	SNP	C	C	T	rs4982853	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:24527220C>T	ENST00000342740.5	+	16	1423	c.1269C>T	c.(1267-1269)taC>taT	p.Y423Y	LRRC16B_ENST00000334420.7_5'UTR	NM_138360.3	NP_612369.3	Q8ND23	LR16B_HUMAN	leucine rich repeat containing 16B	423						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)		GCAGCGCCTACACACTGAGCC	0.657											OREG0022615	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	998	0.199281	0.1014	0.2032	5008	,	,		18014	0.4306		0.0616	False		,,,				2504	0.2321				p.Y423Y		Atlas-SNP	.											.	LRRC16B	120	.	0			c.C1269T						PASS	.	C		442,3964	202.8+/-225.5	21,400,1782	64.0	68.0	67.0		1269	4.2	1.0	14	dbSNP_111	67	476,8124	137.6+/-194.5	11,454,3835	no	coding-synonymous	LRRC16B	NM_138360.3		32,854,5617	TT,TC,CC		5.5349,10.0318,7.0583		423/1373	24527220	918,12088	2203	4300	6503	SO:0001819	synonymous_variant	90668	exon16			CGCCTACACACTG	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.1269C>T	14.37:g.24527220C>T		Somatic	86	0	0	772	WXS	Illumina HiSeq	Phase_I	72	71	0.986111	NM_138360	Q8TEF7|Q96HS9	Silent	SNP	ENST00000342740.5	37	CCDS32054.1																																																																																			C|0.898;T|0.102	0.102	strong		0.657	LRRC16B-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416527.1	NM_138360	
LRP2	4036	hgsc.bcm.edu	37	2	170103351	170103351	+	Silent	SNP	G	G	T	rs2075249	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:170103351G>T	ENST00000263816.3	-	21	3339	c.3054C>A	c.(3052-3054)acC>acA	p.T1018T	LRP2_ENST00000443831.1_Silent_p.T881T	NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	1018					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)"""	GTGGTTCATTGGTTGGGTCCC	0.512													G|||	2286	0.45647	0.208	0.5591	5008	,	,		17421	0.4792		0.4632	False		,,,				2504	0.6892				p.T1018T		Atlas-SNP	.											.	LRP2	751	.	0			c.C3054A						PASS	.	G		1288,3118	436.6+/-344.7	185,918,1100	132.0	120.0	124.0		3054	3.3	0.0	2	dbSNP_96	124	3946,4654	550.0+/-385.7	910,2126,1264	no	coding-synonymous	LRP2	NM_004525.2		1095,3044,2364	TT,TG,GG		45.8837,29.2329,40.243		1018/4656	170103351	5234,7772	2203	4300	6503	SO:0001819	synonymous_variant	4036	exon21			TTCATTGGTTGGG		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.3054C>A	2.37:g.170103351G>T		Somatic	194	0	0		WXS	Illumina HiSeq	Phase_I	175	80	0.457143	NM_004525	O00711|Q16215	Silent	SNP	ENST00000263816.3	37	CCDS2232.1																																																																																			G|0.583;T|0.417	0.417	strong		0.512	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525	
PCYT1A	5130	hgsc.bcm.edu	37	3	195965760	195965760	+	Silent	SNP	A	A	G	rs116712058	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195965760A>G	ENST00000292823.2	-	10	1075	c.903T>C	c.(901-903)caT>caC	p.H301H	PCYT1A_ENST00000419333.1_Silent_p.H301H|PCYT1A_ENST00000431016.1_Silent_p.H301H	NM_005017.2	NP_005008.2	P49585	PCY1A_HUMAN	phosphate cytidylyltransferase 1, choline, alpha	301					CDP-choline pathway (GO:0006657)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|glycogen granule (GO:0042587)	choline-phosphate cytidylyltransferase activity (GO:0004105)|lipid binding (GO:0008289)			cervix(1)|endometrium(3)|large_intestine(8)|lung(5)|ovary(1)	18	all_cancers(143;1.19e-08)|Ovarian(172;0.0634)|Breast(254;0.206)		Epithelial(36;1.28e-24)|all cancers(36;1.01e-22)|OV - Ovarian serous cystadenocarcinoma(49;3.88e-19)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00259)	Choline(DB00122)|Lamivudine(DB00709)	CTTTCAGCATATGTTTCTGCA	0.542													A|||	47	0.00938498	0.003	0.0086	5008	,	,		18327	0.002		0.0179	False		,,,				2504	0.0174				p.H301H		Atlas-SNP	.											.	PCYT1A	34	.	0			c.T903C						PASS	.	A		9,4389		0,9,2190	15.0	15.0	15.0		903	-2.9	1.0	3	dbSNP_132	15	161,8431		1,159,4136	no	coding-synonymous	PCYT1A	NM_005017.2		1,168,6326	GG,GA,AA		1.8738,0.2046,1.3087		301/368	195965760	170,12820	2199	4296	6495	SO:0001819	synonymous_variant	5130	exon10			CAGCATATGTTTC	L28957	CCDS3315.1	3q29	2010-07-19	2005-09-05		ENSG00000161217	ENSG00000161217	2.7.7.15		8754	protein-coding gene	gene with protein product	"""phosphate cytidylyltransferase 1, choline, alpha isoform"""	123695	"""phosphate cytidylyltransferase 1, choline, alpha isoform"""	PCYT1		7918629	Standard	NM_005017		Approved	CT, CTPCT	uc003fwg.3	P49585	OTTHUMG00000155670	ENST00000292823.2:c.903T>C	3.37:g.195965760A>G		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	50	25	0.5	NM_005017	A9LYK9|D3DXB1|Q86Y88	Silent	SNP	ENST00000292823.2	37	CCDS3315.1																																																																																			A|0.988;G|0.012	0.012	strong		0.542	PCYT1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341147.1	NM_005017	
KIAA0319	9856	hgsc.bcm.edu	37	6	24576706	24576706	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:24576706G>A	ENST00000378214.3	-	10	2148	c.1624C>T	c.(1624-1626)Ccc>Tcc	p.P542S	KIAA0319_ENST00000535378.1_Missense_Mutation_p.P533S|KIAA0319_ENST00000543707.1_Missense_Mutation_p.P542S|KIAA0319_ENST00000537886.1_Missense_Mutation_p.P542S|KIAA0319_ENST00000430948.2_Missense_Mutation_p.P497S	NM_001168375.1|NM_014809.3	NP_001161847.1|NP_055624.2	Q5VV43	K0319_HUMAN	KIAA0319	542	PKD 3. {ECO:0000255|PROSITE- ProRule:PRU00151}.				negative regulation of dendrite development (GO:2000171)|neuron migration (GO:0001764)	early endosome (GO:0005769)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(3)|endometrium(6)|kidney(3)|large_intestine(11)|lung(19)|ovary(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)	53						GAGTTTTGGGGCAAAGTTATG	0.498																																					p.P542S		Atlas-SNP	.											.	KIAA0319	117	.	0			c.C1624T						PASS	.						514.0	503.0	507.0					6																	24576706		2203	4300	6503	SO:0001583	missense	9856	exon10			TTTGGGGCAAAGT	AB002317	CCDS34348.1, CCDS54969.1, CCDS54970.1, CCDS54971.1, CCDS75409.1	6p22.3	2013-12-13			ENSG00000137261	ENSG00000137261			21580	protein-coding gene	gene with protein product	"""neuronal migration"""	609269				9205841, 15514892	Standard	NM_014809		Approved	NMIG	uc003neh.1	Q5VV43	OTTHUMG00000014358	ENST00000378214.3:c.1624C>T	6.37:g.24576706G>A	ENSP00000367459:p.Pro542Ser	Somatic	490	0	0		WXS	Illumina HiSeq	Phase_I	359	65	0.181058	NM_001168377	A7MD37|B2RTU7|B4DHA7|B4DK75|B7ZML3|F5H123|Q9UJC8|Q9Y4G7	Missense_Mutation	SNP	ENST00000378214.3	37	CCDS34348.1	.	.	.	.	.	.	.	.	.	.	G	22.8	4.333242	0.81801	.	.	ENSG00000137261	ENST00000537886;ENST00000535378;ENST00000430948;ENST00000378214;ENST00000543707	T;T;T;T;T	0.67523	-0.27;-0.27;-0.27;-0.27;-0.27	3.9	3.9	0.45041	PKD/Chitinase domain (1);PKD/REJ-like protein (1);PKD domain (2);	0.000000	0.64402	D	0.000001	T	0.82268	0.5000	M	0.89968	3.075	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.998;0.999	D	0.86674	0.1912	10	0.72032	D	0.01	-15.2462	16.4334	0.83861	0.0:0.0:1.0:0.0	.	542;533;542	F5H123;Q5VV43-2;Q5VV43	.;.;K0319_HUMAN	S	542;533;497;542;542	ENSP00000439700:P542S;ENSP00000442403:P533S;ENSP00000401086:P497S;ENSP00000367459:P542S;ENSP00000437656:P542S	ENSP00000367459:P542S	P	-	1	0	KIAA0319	24684685	1.000000	0.71417	0.999000	0.59377	0.952000	0.60782	6.424000	0.73366	2.153000	0.67306	0.655000	0.94253	CCC	.	.	none		0.498	KIAA0319-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040009.1	NM_014809	
KRTAP4-12	83755	hgsc.bcm.edu	37	17	39279944	39279944	+	Missense_Mutation	SNP	C	C	G	rs536638484		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:39279944C>G	ENST00000394014.1	-	1	475	c.431G>C	c.(430-432)aGc>aCc	p.S144T		NM_031854.2	NP_114060.1	Q9BQ66	KR412_HUMAN	keratin associated protein 4-12	144	31 X 5 AA repeats of C-C-[GRQVIL]-[SPTR]- [VSTQPC].		Missing (in allele KAP4.12-v1). {ECO:0000269|PubMed:15955084}.			keratin filament (GO:0045095)				endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(1)|prostate(1)|upper_aerodigestive_tract(1)	13		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			gatgcagcagctggggcggca	0.672													C|||	1	0.000199681	0.0	0.0	5008	,	,		15496	0.001		0.0	False		,,,				2504	0.0				p.S144T		Atlas-SNP	.											.	KRTAP4-12	32	.	0			c.G431C						PASS	.						18.0	24.0	22.0					17																	39279944		2195	4276	6471	SO:0001583	missense	83755	exon1			CAGCAGCTGGGGC	AJ406943	CCDS32649.1	17q21.2	2013-06-25			ENSG00000213416	ENSG00000213416		"""Keratin associated proteins"""	16776	protein-coding gene	gene with protein product						11279113	Standard	NM_031854		Approved	KAP4.12	uc002hwa.3	Q9BQ66	OTTHUMG00000133632	ENST00000394014.1:c.431G>C	17.37:g.39279944C>G	ENSP00000377582:p.Ser144Thr	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	55	16	0.290909	NM_031854	A3KMC5|Q495I0	Missense_Mutation	SNP	ENST00000394014.1	37	CCDS32649.1	.	.	.	.	.	.	.	.	.	.	.	10.81	1.455027	0.26161	.	.	ENSG00000213416	ENST00000394014	T	0.01484	4.84	5.33	-2.99	0.05497	.	3.044690	0.01738	N	0.029234	T	0.02083	0.0065	L	0.39085	1.19	0.09310	N	1	B	0.14438	0.01	B	0.15052	0.012	T	0.48758	-0.9007	10	0.21540	T	0.41	.	9.6148	0.39685	0.0998:0.2179:0.611:0.0713	.	144	Q9BQ66	KR412_HUMAN	T	144	ENSP00000377582:S144T	ENSP00000377582:S144T	S	-	2	0	KRTAP4-12	36533470	0.009000	0.17119	0.062000	0.19696	0.021000	0.10359	-0.260000	0.08708	-0.227000	0.09884	0.561000	0.74099	AGC	.	.	none		0.672	KRTAP4-12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257777.1		
LPA	4018	hgsc.bcm.edu	37	6	160952838	160952838	+	Missense_Mutation	SNP	G	G	A	rs3124784	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:160952838G>A	ENST00000316300.5	-	39	6090	c.6046C>T	c.(6046-6048)Cgc>Tgc	p.R2016C	LPA_ENST00000447678.1_Missense_Mutation_p.R2016C			P08519	APOA_HUMAN	lipoprotein, Lp(a)	4524	Kringle 18. {ECO:0000255|PROSITE- ProRule:PRU00121}.				blood circulation (GO:0008015)|lipid metabolic process (GO:0006629)|lipid transport (GO:0006869)|lipoprotein metabolic process (GO:0042157)|negative regulation of endopeptidase activity (GO:0010951)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|plasma lipoprotein particle (GO:0034358)	apolipoprotein binding (GO:0034185)|endopeptidase inhibitor activity (GO:0004866)|fibronectin binding (GO:0001968)|heparin binding (GO:0008201)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(16)|lung(54)|ovary(4)|pancreas(1)|prostate(2)|skin(10)|stomach(1)|urinary_tract(1)	107		Breast(66;0.000496)|Ovarian(120;0.0303)|Prostate(117;0.0965)		OV - Ovarian serous cystadenocarcinoma(65;2.5e-17)|BRCA - Breast invasive adenocarcinoma(81;6.48e-06)	Aminocaproic Acid(DB00513)	TTATTGGGGCGTGCACAGCCA	0.473													G|||	1015	0.202676	0.2421	0.1398	5008	,	,		18973	0.1081		0.2942	False		,,,				2504	0.1973				p.R2016C		Atlas-SNP	.											.	LPA	237	.	0			c.C6046T						PASS	.	G	CYS/ARG	1026,3380	378.7+/-323.0	115,796,1292	149.0	138.0	142.0		6046	3.0	0.5	6	dbSNP_103	142	2377,6223	394.2+/-344.6	337,1703,2260	no	missense	LPA	NM_005577.2	180	452,2499,3552	AA,AG,GG		27.6395,23.2864,26.1648	benign	2016/2041	160952838	3403,9603	2203	4300	6503	SO:0001583	missense	4018	exon40			TGGGGCGTGCACA	X06290	CCDS43523.1	6q25-q26	2012-10-02			ENSG00000198670	ENSG00000198670			6667	protein-coding gene	gene with protein product		152200		LP		3670400	Standard	NM_005577		Approved		uc003qtl.3	P08519	OTTHUMG00000015956	ENST00000316300.5:c.6046C>T	6.37:g.160952838G>A	ENSP00000321334:p.Arg2016Cys	Somatic	521	0	0		WXS	Illumina HiSeq	Phase_I	323	322	0.996904	NM_005577	Q5VTD7|Q9UD88	Missense_Mutation	SNP	ENST00000316300.5	37	CCDS43523.1	464	0.21245421245421245	125	0.2540650406504065	59	0.16298342541436464	62	0.10839160839160839	218	0.287598944591029	g	7.285	0.609824	0.14066	0.232864	0.276395	ENSG00000198670	ENST00000316300;ENST00000447678	D;D	0.89343	-2.5;-2.5	3.02	3.02	0.34903	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	.	.	.	.	D	0.89160	0.6636	L	0.42744	1.35	0.36044	P	0.15972299999999995	D	0.89917	1.0	D	0.80764	0.994	D	0.89179	0.3542	8	0.48119	T	0.1	.	13.9627	0.64191	0.0:0.0:1.0:0.0	rs3124784	4524	P08519	APOA_HUMAN	C	2016	ENSP00000321334:R2016C;ENSP00000395608:R2016C	ENSP00000321334:R2016C	R	-	1	0	LPA	160872828	0.236000	0.23804	0.471000	0.27229	0.041000	0.13682	2.791000	0.47829	1.412000	0.46977	0.184000	0.17185	CGC	G|0.770;A|0.230	0.230	strong		0.473	LPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042957.1	NM_005577	
ITGB2	3689	hgsc.bcm.edu	37	21	46320313	46320313	+	Silent	SNP	C	C	T	rs2230528	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:46320313C>T	ENST00000397850.2	-	8	1271	c.819G>A	c.(817-819)ggG>ggA	p.G273G	ITGB2_ENST00000397854.3_Silent_p.G216G|ITGB2_ENST00000397857.1_Silent_p.G273G|ITGB2_ENST00000397852.1_Silent_p.G273G|ITGB2_ENST00000302347.5_Silent_p.G273G|ITGB2_ENST00000355153.4_Silent_p.G273G			P05107	ITB2_HUMAN	integrin, beta 2 (complement component 3 receptor 3 and 4 subunit)	273	VWFA.		G -> R (in LAD1; dbSNP:rs137852618). {ECO:0000269|PubMed:9884339}.		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)	CGCCCAGCTTCCCGTCGCCCG	0.627													C|||	1117	0.223043	0.1815	0.2709	5008	,	,		17207	0.1607		0.2177	False		,,,				2504	0.3149				p.G273G		Atlas-SNP	.											ITGB2,NS,malignant_melanoma,-2,1	ITGB2	107	1	0			c.G819A						PASS	.	C	,	735,3671	303.2+/-287.8	65,605,1533	105.0	88.0	94.0		819,819	3.2	1.0	21	dbSNP_98	94	2077,6523	359.3+/-331.5	239,1599,2462	no	coding-synonymous,coding-synonymous	ITGB2	NM_000211.3,NM_001127491.1	,	304,2204,3995	TT,TC,CC		24.1512,16.6818,21.6208	,	273/770,273/770	46320313	2812,10194	2203	4300	6503	SO:0001819	synonymous_variant	3689	exon7			CAGCTTCCCGTCG	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.819G>A	21.37:g.46320313C>T		Somatic	213	0	0		WXS	Illumina HiSeq	Phase_I	262	145	0.553435	NM_000211	B3KTS8|D3DSM1|Q16418|Q53HS5|Q9UD72	Silent	SNP	ENST00000397850.2	37	CCDS13716.1																																																																																			T|0.201;G|0.000;C|0.798;N|0.001;A|0.000	0.201	strong		0.627	ITGB2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206566.2	NM_000211	
CA14	23632	hgsc.bcm.edu	37	1	150234657	150234657	+	Silent	SNP	G	G	T	rs34714364	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	111	0	0		WXS	Illumina HiSeq	Phase_I	99	45	0.454545	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	
ZNF584	201514	hgsc.bcm.edu	37	19	58928786	58928786	+	Missense_Mutation	SNP	A	A	G	rs7257872	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:58928786A>G	ENST00000306910.4	+	4	1424	c.901A>G	c.(901-903)Aca>Gca	p.T301A	ZNF584_ENST00000593920.1_Missense_Mutation_p.T256A|ZNF584_ENST00000599238.1_3'UTR|CTD-2619J13.16_ENST00000596296.1_lincRNA	NM_173548.1	NP_775819.1	Q8IVC4	ZN584_HUMAN	zinc finger protein 584	301			T -> A (in dbSNP:rs7257872). {ECO:0000269|PubMed:14702039}.		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|kidney(3)|large_intestine(3)|lung(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	14		all_cancers(17;5.3e-17)|all_epithelial(17;3.71e-12)|Lung NSC(17;8.3e-05)|Colorectal(82;0.000147)|all_lung(17;0.000386)|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;0.0271)		CTATGAGTGTACAGAATGTGG	0.443													A|||	1457	0.290935	0.4592	0.1787	5008	,	,		22805	0.2708		0.2465	False		,,,				2504	0.2096				p.T301A		Atlas-SNP	.											.	ZNF584	31	.	0			c.A901G						PASS	.	A	ALA/THR	1985,2421	559.0+/-380.1	450,1085,668	76.0	78.0	77.0		901	0.2	0.8	19	dbSNP_116	77	2339,6261	391.7+/-343.7	309,1721,2270	yes	missense	ZNF584	NM_173548.1	58	759,2806,2938	GG,GA,AA		27.1977,45.0522,33.2462	benign	301/422	58928786	4324,8682	2203	4300	6503	SO:0001583	missense	201514	exon4			GAGTGTACAGAAT	AK097218	CCDS12979.1	19q13.43	2013-01-08			ENSG00000171574	ENSG00000171574		"""Zinc fingers, C2H2-type"", ""-"""	27318	protein-coding gene	gene with protein product							Standard	NM_173548		Approved	FLJ39899	uc002qsp.3	Q8IVC4		ENST00000306910.4:c.901A>G	19.37:g.58928786A>G	ENSP00000306756:p.Thr301Ala	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	102	38	0.372549	NM_173548	A8K203	Missense_Mutation	SNP	ENST00000306910.4	37	CCDS12979.1	644	0.2948717948717949	220	0.44715447154471544	77	0.212707182320442	151	0.263986013986014	196	0.25857519788918204	A	9.916	1.210741	0.22289	0.450522	0.271977	ENSG00000171574	ENST00000306910;ENST00000354635	T	0.07216	3.21	3.78	0.242	0.15498	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	L	0.34521	1.04	0.58432	P	2.9999999999752447E-6	B	0.06786	0.001	B	0.10450	0.005	T	0.44452	-0.9327	8	0.40728	T	0.16	.	1.8084	0.03085	0.3614:0.3782:0.1017:0.1587	rs7257872;rs52798108;rs59404846;rs7257872	301	Q8IVC4	ZN584_HUMAN	A	301;160	ENSP00000306756:T301A	ENSP00000306756:T301A	T	+	1	0	ZNF584	63620598	0.000000	0.05858	0.822000	0.32727	0.947000	0.59692	-4.685000	0.00198	-0.127000	0.11661	0.454000	0.30748	ACA	A|0.686;G|0.314	0.314	strong		0.443	ZNF584-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467022.1	NM_173548	
C6	729	hgsc.bcm.edu	37	5	41181578	41181578	+	Silent	SNP	T	T	A	rs61734263	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:41181578T>A	ENST00000263413.3	-	7	1074	c.810A>T	c.(808-810)tcA>tcT	p.S270S	C6_ENST00000475349.1_5'UTR|C6_ENST00000337836.5_Silent_p.S270S	NM_001115131.1	NP_001108603.2	P13671	CO6_HUMAN	complement component 6	270	MACPF. {ECO:0000255|PROSITE- ProRule:PRU00745}.				complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|cytolysis (GO:0019835)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane attack complex (GO:0005579)				central_nervous_system(2)|cervix(2)|endometrium(2)|kidney(7)|large_intestine(16)|liver(1)|lung(51)|ovary(3)|prostate(1)|skin(9)|upper_aerodigestive_tract(2)	96		Breast(839;1.07e-05)|Ovarian(839;0.0228)|Lung SC(612;0.0548)|Lung NSC(810;0.128)|all_neural(839;0.157)				GACTTGAGAATGAGCCTTGTT	0.378													T|||	23	0.00459265	0.0	0.0014	5008	,	,		15500	0.0		0.0129	False		,,,				2504	0.0092				p.S270S		Atlas-SNP	.											.	C6	197	.	0			c.A810T						PASS	.	T	,	11,4395	16.8+/-37.8	0,11,2192	81.0	80.0	80.0		810,810	-1.8	0.0	5	dbSNP_129	80	158,8442	75.7+/-138.4	2,154,4144	no	coding-synonymous,coding-synonymous	C6	NM_000065.2,NM_001115131.1	,	2,165,6336	AA,AT,TT		1.8372,0.2497,1.2994	,	270/935,270/935	41181578	169,12837	2203	4300	6503	SO:0001819	synonymous_variant	729	exon7			TGAGAATGAGCCT	J05024	CCDS3936.1	5p13.1	2014-09-17			ENSG00000039537	ENSG00000039537		"""Complement system"""	1339	protein-coding gene	gene with protein product		217050					Standard	NM_001115131		Approved		uc003jmk.3	P13671	OTTHUMG00000094781	ENST00000263413.3:c.810A>T	5.37:g.41181578T>A		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	154	94	0.61039	NM_001115131		Silent	SNP	ENST00000263413.3	37	CCDS3936.1																																																																																			T|0.980;A|0.020	0.020	strong		0.378	C6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211592.1		
UGT2A1	10941	hgsc.bcm.edu	37	4	70512787	70512787	+	Nonsense_Mutation	SNP	A	A	T	rs111696697	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:70512787A>T	ENST00000503640.1	-	1	631	c.576T>A	c.(574-576)taT>taA	p.Y192*	UGT2A1_ENST00000286604.4_Nonsense_Mutation_p.Y192*|UGT2A1_ENST00000514019.1_Nonsense_Mutation_p.Y192*|UGT2A1_ENST00000512704.1_Nonsense_Mutation_p.Y192*	NM_006798.3	NP_006789.2	Q9Y4X1	UD2A1_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide A1, complex locus	192					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						CAGCAGGAACATAGGAAGGAG	0.413													A|||	73	0.0145767	0.0015	0.0231	5008	,	,		19106	0.001		0.0437	False		,,,				2504	0.0102				p.Y192X		Atlas-SNP	.											.	UGT2A1	131	.	0			c.T576A						PASS	.	A	stop/TYR	40,4366	43.8+/-77.6	0,40,2163	95.0	82.0	86.0		576	-0.8	1.0	4	dbSNP_132	86	355,8243	120.1+/-179.3	5,345,3949	yes	stop-gained	UGT2A1	NM_006798.2		5,385,6112	TT,TA,AA		4.1289,0.9079,3.0375		192/528	70512787	395,12609	2203	4299	6502	SO:0001587	stop_gained	10941	exon2			AGGAACATAGGAA	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.576T>A	4.37:g.70512787A>T	ENSP00000424478:p.Tyr192*	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	75	45	0.6	NM_001252274	B4E2F4|D3GER1|D3GER2|E9PDM7|J3KNA3	Nonsense_Mutation	SNP	ENST00000503640.1	37	CCDS3529.1	41	0.018772893772893772	2	0.0040650406504065045	8	0.022099447513812154	1	0.0017482517482517483	30	0.0395778364116095	A	20.6	4.011995	0.75046	0.009079	0.041289	ENSG00000173610	ENST00000503640;ENST00000512704;ENST00000514019;ENST00000286604	.	.	.	5.78	-0.796	0.10912	.	0.191859	0.47093	D	0.000246	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	9.4857	0.38928	0.6123:0.0:0.3877:0.0	.	.	.	.	X	192	.	ENSP00000286604:Y192X	Y	-	3	2	UGT2A1	70547376	0.816000	0.29132	0.994000	0.49952	0.459000	0.32528	0.032000	0.13732	-0.096000	0.12329	-0.326000	0.08463	TAT	A|0.971;T|0.029	0.029	strong		0.413	UGT2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251554.3	NM_006798	
KRT23	25984	hgsc.bcm.edu	37	17	39081713	39081713	+	Silent	SNP	A	A	G	rs8037	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:39081713A>G	ENST00000209718.3	-	7	1459	c.1035T>C	c.(1033-1035)caT>caC	p.H345H	KRT23_ENST00000436344.3_Silent_p.H208H|AC004231.2_ENST00000418393.1_RNA	NM_015515.3	NP_056330.3	Q9C075	K1C23_HUMAN	keratin 23 (histone deacetylase inducible)	345	Coil 2.|Rod.					intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	21		Breast(137;0.000301)|Ovarian(249;0.15)				GCTCCAGTTCATGGCGTAGCT	0.532													G|||	2859	0.570887	0.5643	0.6081	5008	,	,		21238	0.7083		0.4056	False		,,,				2504	0.5818				p.H345H		Atlas-SNP	.											.	KRT23	59	.	0			c.T1035C						PASS	.	G		2354,2052	568.7+/-382.4	628,1098,477	209.0	156.0	174.0		1035	-4.4	0.4	17	dbSNP_52	174	3382,5218	641.7+/-399.7	687,2008,1605	no	coding-synonymous	KRT23	NM_015515.3		1315,3106,2082	GG,GA,AA		39.3256,46.5729,44.1027		345/423	39081713	5736,7270	2203	4300	6503	SO:0001819	synonymous_variant	25984	exon7			CAGTTCATGGCGT	AF102848	CCDS11380.1, CCDS62182.1	17q21.2	2013-01-16			ENSG00000108244	ENSG00000108244		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6438	protein-coding gene	gene with protein product		606194				11135429, 16831889	Standard	NM_015515		Approved	K23, DKFZP434G032, HAIK1, CK23, MGC26158	uc002hvm.1	Q9C075	OTTHUMG00000133376	ENST00000209718.3:c.1035T>C	17.37:g.39081713A>G		Somatic	303	1	0.00330033		WXS	Illumina HiSeq	Phase_I	232	127	0.547414	NM_015515	A8K084|B7Z7J2|I3L3Q6|Q9NUR6	Silent	SNP	ENST00000209718.3	37	CCDS11380.1																																																																																			A|0.501;G|0.499	0.499	strong		0.532	KRT23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257223.1		
CDCP2	200008	hgsc.bcm.edu	37	1	54605769	54605769	+	Silent	SNP	C	C	T	rs372034165		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:54605769C>T	ENST00000371330.1	-	4	1621	c.774G>A	c.(772-774)caG>caA	p.Q258Q	CDCP2_ENST00000530059.1_5'Flank|RP11-446E24.4_ENST00000525949.1_5'Flank	NM_201546.2	NP_963840.2	Q5VXM1	CDCP2_HUMAN	CUB domain containing protein 2	258	CUB 3. {ECO:0000255|PROSITE- ProRule:PRU00059}.					extracellular region (GO:0005576)				kidney(1)|large_intestine(6)|lung(13)|ovary(1)|prostate(2)|stomach(1)	24						TGTATACCTCCTGGCATTCTC	0.612																																					p.Q258Q		Atlas-SNP	.											.	CDCP2	52	.	0			c.G774A						PASS	.	C		0,4218		0,0,2109	39.0	31.0	34.0		774	4.0	1.0	1		34	1,8315		0,1,4157	no	coding-synonymous	CDCP2	NM_201546.2		0,1,6266	TT,TC,CC		0.012,0.0,0.0080		258/450	54605769	1,12533	2109	4158	6267	SO:0001819	synonymous_variant	200008	exon4			TACCTCCTGGCAT		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.774G>A	1.37:g.54605769C>T		Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	138	68	0.492754	NM_201546	Q6ZWJ3	Silent	SNP	ENST00000371330.1	37	CCDS588.2																																																																																			.	.	none		0.612	CDCP2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000022209.2	NM_201546	
CACNA1E	777	hgsc.bcm.edu	37	1	181548341	181548341	+	Silent	SNP	A	A	G	rs17443123	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:181548341A>G	ENST00000367573.2	+	5	750	c.750A>G	c.(748-750)gcA>gcG	p.A250A	CACNA1E_ENST00000358338.5_Silent_p.A201A|CACNA1E_ENST00000360108.3_Silent_p.A250A|CACNA1E_ENST00000526775.1_Silent_p.A250A|CACNA1E_ENST00000357570.5_Silent_p.A201A|CACNA1E_ENST00000367570.1_Silent_p.A250A|CACNA1E_ENST00000367567.4_5'UTR	NM_001205293.1	NP_001192222.1	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type, alpha 1E subunit	250					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						TACATCGAGCATGCTTCATGA	0.468													A|||	321	0.0640974	0.0204	0.0937	5008	,	,		22040	0.0079		0.1491	False		,,,				2504	0.0726				p.A250A		Atlas-SNP	.											CACNA1E,NS,carcinoma,+2,1	CACNA1E	778	1	0			c.A750G						PASS	.	A	,,	148,3768		4,140,1814	332.0	306.0	315.0		750,750,750	-6.0	1.0	1	dbSNP_123	315	1191,7147		75,1041,3053	no	coding-synonymous,coding-synonymous,coding-synonymous	CACNA1E	NM_000721.3,NM_001205293.1,NM_001205294.1	,,	79,1181,4867	GG,GA,AA		14.284,3.7794,10.927	,,	250/2271,250/2314,250/2252	181548341	1339,10915	1958	4169	6127	SO:0001819	synonymous_variant	777	exon5			TCGAGCATGCTTC	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.750A>G	1.37:g.181548341A>G		Somatic	237	0	0		WXS	Illumina HiSeq	Phase_I	181	78	0.430939	NM_001205293	B1AM12|B1AM13|B1AM14|Q14580|Q14581	Silent	SNP	ENST00000367573.2	37	CCDS55664.1																																																																																			A|0.910;G|0.090	0.090	strong		0.468	CACNA1E-003	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090793.2	NM_000721	
LENG8	114823	hgsc.bcm.edu	37	19	54967408	54967408	+	Missense_Mutation	SNP	C	C	T	rs75472495	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:54967408C>T	ENST00000326764.5	+	9	1767	c.1288C>T	c.(1288-1290)Cgc>Tgc	p.R430C	LENG8_ENST00000376514.2_Intron	NM_052925.2	NP_443157.1	Q96PV6	LENG8_HUMAN	leukocyte receptor cluster (LRC) member 8	393										breast(1)|central_nervous_system(3)|endometrium(3)|kidney(1)|large_intestine(6)|lung(9)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	30	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.139)		GTCCCCGACGCGCCACTTCCG	0.617													C|||	4	0.000798722	0.0008	0.0	5008	,	,		16004	0.0		0.003	False		,,,				2504	0.0				p.R430C		Atlas-SNP	.											LENG8,colon,carcinoma,-1,1	LENG8	73	1	0			c.C1288T						PASS	.	C	CYS/ARG	2,4404		0,2,2201	96.0	114.0	107.0		1288	3.7	0.6	19	dbSNP_131	107	26,8566		0,26,4270	yes	missense	LENG8	NM_052925.2	180	0,28,6471	TT,TC,CC		0.3026,0.0454,0.2154	probably-damaging	430/801	54967408	28,12970	2203	4296	6499	SO:0001583	missense	114823	exon9			CCGACGCGCCACT	AF211975	CCDS12894.1	19q13.4	2008-02-05			ENSG00000167615	ENSG00000167615			15500	protein-coding gene	gene with protein product						10941842	Standard	XM_005278248		Approved	KIAA1932, MGC40108, pp13842	uc002qfw.2	Q96PV6	OTTHUMG00000065548	ENST00000326764.5:c.1288C>T	19.37:g.54967408C>T	ENSP00000318374:p.Arg430Cys	Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	128	68	0.53125	NM_052925	B0VJY9|Q8IZ27|Q8NCX6	Missense_Mutation	SNP	ENST00000326764.5	37	CCDS12894.1	4	0.0018315018315018315	1	0.0020325203252032522	0	0.0	0	0.0	3	0.00395778364116095	C	17.47	3.397139	0.62177	4.54E-4	0.003026	ENSG00000167615	ENST00000326764;ENST00000301196;ENST00000376526;ENST00000431846	T;T;T	0.37058	1.26;1.25;1.22	4.73	3.68	0.42216	.	0.063133	0.64402	D	0.000016	T	0.41558	0.1164	N	0.24115	0.695	0.80722	D	1	D;D	0.89917	0.999;1.0	P;D	0.72338	0.855;0.977	T	0.18241	-1.0343	10	0.37606	T	0.19	-12.3824	10.6314	0.45538	0.3457:0.6543:0.0:0.0	.	430;393	Q96PV6-2;F8W9Q9	.;.	C	430;393;393;430	ENSP00000318374:R430C;ENSP00000365709:R393C;ENSP00000388053:R430C	ENSP00000301196:R393C	R	+	1	0	LENG8	59659220	0.987000	0.35691	0.550000	0.28217	0.537000	0.34900	2.804000	0.47931	1.111000	0.41721	0.555000	0.69702	CGC	C|0.998;T|0.002	0.002	strong		0.617	LENG8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140523.2	NM_052925	
MUC4	4585	hgsc.bcm.edu	37	3	195508537	195508537	+	Missense_Mutation	SNP	A	A	G	rs568102602	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195508537A>G	ENST00000463781.3	-	2	10373	c.9914T>C	c.(9913-9915)gTa>gCa	p.V3305A	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.V3305A	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.V3305A(1)|p.V3305_S3320delVSTGHATPLLVTDASS(1)|p.V3305_S3336delVSTGHATPLLVTDASSASTGHATPLHVTSPSS(1)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		ACCTGTGGATACTGAGGAAGT	0.562													.|||	1146	0.228834	0.2572	0.1326	5008	,	,		9930	0.4385		0.1471	False		,,,				2504	0.1268				p.V3305A		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,-1,3	MUC4	1505	3	3	Deletion - In frame(2)|Substitution - Missense(1)	stomach(3)	c.T9914C						PASS	.						23.0	20.0	21.0					3																	195508537		670	1552	2222	SO:0001583	missense	4585	exon2			GTGGATACTGAGG	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.9914T>C	3.37:g.195508537A>G	ENSP00000417498:p.Val3305Ala	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	30	24	0.8	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	1092	0.5	249	0.5060975609756098	158	0.43646408839779005	334	0.583916083916084	351	0.4630606860158311	a	2.758	-0.258537	0.05791	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.33216	1.42;1.42	0.743	-1.49	0.08718	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.33494	0.414	B	0.22386	0.039	T	0.43972	-0.9358	7	.	.	.	.	2.1485	0.03794	0.5029:0.0:0.0:0.4971	.	3177	E7ESK3	.	A	3305	ENSP00000417498:V3305A;ENSP00000420243:V3305A	.	V	-	2	0	MUC4	196993316	0.000000	0.05858	0.038000	0.18304	0.038000	0.13279	-1.464000	0.02359	0.077000	0.16863	0.076000	0.15429	GTA	A|0.500;G|0.500	0.500	strong		0.562	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
MUC4	4585	hgsc.bcm.edu	37	3	195509346	195509346	+	Silent	SNP	G	G	T	rs371492604		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195509346G>T	ENST00000463781.3	-	2	9564	c.9105C>A	c.(9103-9105)acC>acA	p.T3035T	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Silent_p.T3035T	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.T3035T(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)		TGGCGTGACCGGTGGATGCTG	0.597																																					p.T3035T		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	1	Substitution - coding silent(1)	endometrium(1)	c.C9105A						scavenged	.						15.0	10.0	12.0					3																	195509346		658	1542	2200	SO:0001819	synonymous_variant	4585	exon2			GTGACCGGTGGAT	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.9105C>A	3.37:g.195509346G>T		Somatic	39	4	0.102564		WXS	Illumina HiSeq	Phase_I	102	12	0.117647	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Silent	SNP	ENST00000463781.3	37	CCDS54700.1																																																																																			.	.	weak		0.597	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
OR10AD1	121275	hgsc.bcm.edu	37	12	48596484	48596484	+	Missense_Mutation	SNP	A	A	T	rs75413005	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:48596484A>T	ENST00000310248.2	-	1	686	c.592T>A	c.(592-594)Tgg>Agg	p.W198R		NM_001004134.1	NP_001004134.1	Q8NGE0	O10AD_HUMAN	olfactory receptor, family 10, subfamily AD, 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)			endometrium(1)|large_intestine(2)|lung(3)|ovary(1)|stomach(1)|urinary_tract(1)	9						AAGATTGCCCACAGACTAAAC	0.537													T|||	213	0.0425319	0.059	0.036	5008	,	,		20275	0.006		0.0924	False		,,,				2504	0.0112				p.W198R		Atlas-SNP	.											.	OR10AD1	24	.	0			c.T592A						PASS	.	T	ARG/TRP	275,4131	801.1+/-415.6	8,259,1936	61.0	50.0	54.0		592	2.3	0.0	12	dbSNP_131	54	764,7836	784.7+/-407.6	30,704,3566	yes	missense	OR10AD1	NM_001004134.1	101	38,963,5502	TT,TA,AA		8.8837,6.2415,7.9886	benign	198/318	48596484	1039,11967	2203	4300	6503	SO:0001583	missense	121275	exon1			TTGCCCACAGACT		CCDS31787.1	12q13.11	2013-09-24	2002-11-13	2002-11-15	ENSG00000172640	ENSG00000172640		"""GPCR / Class A : Olfactory receptors"""	14819	protein-coding gene	gene with protein product			"""olfactory receptor, family 10, subfamily AD, member 1 pseudogene"""	OR10AD1P			Standard	NM_001004134		Approved		uc001rrl.1	Q8NGE0	OTTHUMG00000168027	ENST00000310248.2:c.592T>A	12.37:g.48596484A>T	ENSP00000308689:p.Trp198Arg	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	86	42	0.488372	NM_001004134	B9EGT9|Q6IFA8	Missense_Mutation	SNP	ENST00000310248.2	37	CCDS31787.1	99	0.04532967032967033	21	0.042682926829268296	9	0.024861878453038673	3	0.005244755244755245	66	0.0870712401055409	T	1.186	-0.636810	0.03557	0.062415	0.088837	ENSG00000172640	ENST00000310248	T	0.00058	8.79	4.77	2.31	0.28768	GPCR, rhodopsin-like superfamily (1);	1.397220	0.05124	N	0.491221	T	0.00012	0.0000	N	0.02286	-0.61	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.14531	-1.0469	10	0.41790	T	0.15	1.3149	2.6005	0.04865	0.1486:0.0845:0.1548:0.6121	.	198	Q8NGE0	O10AD_HUMAN	R	198	ENSP00000308689:W198R	ENSP00000308689:W198R	W	-	1	0	OR10AD1	46882751	0.000000	0.05858	0.000000	0.03702	0.183000	0.23260	-0.220000	0.09215	0.070000	0.16634	-0.448000	0.05591	TGG	A|0.934;T|0.066	0.066	strong		0.537	OR10AD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397577.1		
MUC2	4583	hgsc.bcm.edu	37	11	1092843	1092843	+	Silent	SNP	C	C	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:1092843C>G	ENST00000441003.2	+	30	4689	c.4662C>G	c.(4660-4662)ggC>ggG	p.G1554G	MUC2_ENST00000359061.5_Silent_p.G1555G|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)				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)	CACCCACCGGCACACAGACCC	0.632																																					p.G1554G		Atlas-SNP	.											MUC2_ENST00000441003,trunk,malignant_melanoma,+1,2	MUC2	614	2	0			c.C4662G						PASS	.						88.0	119.0	108.0					11																	1092843		1875	3464	5339	SO:0001819	synonymous_variant	4583	exon30			CACCGGCACACAG	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.4662C>G	11.37:g.1092843C>G		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	67	5	0.0746269	NM_002457	Q14878	Silent	SNP	ENST00000441003.2	37																																																																																				.	.	none		0.632	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
OR2T35	403244	hgsc.bcm.edu	37	1	248801592	248801592	+	Missense_Mutation	SNP	C	C	T	rs78622116	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:248801592C>T	ENST00000317450.3	-	1	967	c.968G>A	c.(967-969)gGc>gAc	p.G323D		NM_001001827.1	NP_001001827.1	Q8NGX2	O2T35_HUMAN	olfactory receptor, family 2, subfamily T, member 35	323						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.G323D(1)		endometrium(1)|large_intestine(1)|lung(1)|ovary(1)|prostate(1)|skin(1)	6	all_cancers(71;2.04e-05)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)	all_cancers(173;0.237)	OV - Ovarian serous cystadenocarcinoma(106;0.0265)			TCCCTGCTAGCCCTTCCTGAT	0.542																																					p.G323D		Atlas-SNP	.											OR2T35,caecum,carcinoma,0,1	OR2T35	19	1	1	Substitution - Missense(1)	large_intestine(1)	c.G968A						scavenged	.						21.0	6.0	12.0					1																	248801592		1918	2711	4629	SO:0001583	missense	403244	exon1			TGCTAGCCCTTCC	BK004475	CCDS31123.1	1q44	2012-08-09			ENSG00000177151	ENSG00000177151		"""GPCR / Class A : Olfactory receptors"""	31257	protein-coding gene	gene with protein product							Standard	NM_001001827		Approved		uc001ies.1	Q8NGX2	OTTHUMG00000040380	ENST00000317450.3:c.968G>A	1.37:g.248801592C>T	ENSP00000324369:p.Gly323Asp	Somatic	33	3	0.0909091		WXS	Illumina HiSeq	Phase_I	11	4	0.363636	NM_001001827	Q6IEY7	Missense_Mutation	SNP	ENST00000317450.3	37	CCDS31123.1	1586	0.7261904761904762	244	0.4959349593495935	286	0.7900552486187845	451	0.7884615384615384	605	0.7981530343007915	.	4.951	0.176629	0.09443	.	.	ENSG00000177151	ENST00000317450	T	0.01647	4.71	0.75	0.75	0.18387	.	.	.	.	.	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	0.03259	-1.1055	8	0.56958	D	0.05	.	2.9607	0.05891	0.0:0.3203:0.0:0.6797	.	323	Q8NGX2	O2T35_HUMAN	D	323	ENSP00000324369:G323D	ENSP00000324369:G323D	G	-	2	0	OR2T35	246868215	0.000000	0.05858	0.003000	0.11579	0.007000	0.05969	0.032000	0.13732	-0.215000	0.10063	-1.461000	0.01025	GGC	C|0.245;T|0.755	0.755	strong		0.542	OR2T35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097130.1	NM_001001827	
AMPH	273	hgsc.bcm.edu	37	7	38431511	38431511	+	Silent	SNP	C	C	T	rs2229922	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:38431511C>T	ENST00000356264.2	-	19	1931	c.1716G>A	c.(1714-1716)gcG>gcA	p.A572A	AMPH_ENST00000428293.2_Silent_p.A530A|AMPH_ENST00000471913.1_5'Flank|AMPH_ENST00000325590.5_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	93	0	0		WXS	Illumina HiSeq	Phase_I	102	27	0.264706	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	
MUC4	4585	hgsc.bcm.edu	37	3	195505960	195505960	+	Missense_Mutation	SNP	G	G	C	rs112020305	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195505960G>C	ENST00000463781.3	-	2	12950	c.12491C>G	c.(12490-12492)aCc>aGc	p.T4164S	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.T4164S	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.T4164S(2)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GGAAGCGTCGGTGACAGGAAG	0.587													.|||	17	0.00339457	0.0129	0.0	5008	,	,		10875	0.0		0.0	False		,,,				2504	0.0				p.T4164S		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,3	MUC4	1505	3	2	Substitution - Missense(2)	kidney(1)|endometrium(1)	c.C12491G						scavenged	.						19.0	12.0	14.0					3																	195505960		671	1528	2199	SO:0001583	missense	4585	exon2			GCGTCGGTGACAG	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.12491C>G	3.37:g.195505960G>C	ENSP00000417498:p.Thr4164Ser	Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	72	5	0.0694444	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	g	4.985	0.182849	0.09495	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.35789	1.38;1.29	.	.	.	.	.	.	.	.	T	0.19248	0.0462	N	0.19112	0.55	0.09310	N	0.999997	P	0.37985	0.613	B	0.35899	0.213	T	0.14587	-1.0467	7	.	.	.	.	5.8529	0.18704	9.0E-4:0.0:0.9991:0.0	.	4036	E7ESK3	.	S	4164	ENSP00000417498:T4164S;ENSP00000420243:T4164S	.	T	-	2	0	MUC4	196990739	0.002000	0.14202	0.025000	0.17156	0.022000	0.10575	0.413000	0.21148	0.073000	0.16731	0.074000	0.15403	ACC	.	.	weak		0.587	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
OR8D1	283159	hgsc.bcm.edu	37	11	124179835	124179835	+	Silent	SNP	C	C	T	rs4936918	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:124179835C>T	ENST00000357821.2	-	1	898	c.828G>A	c.(826-828)gtG>gtA	p.V276V		NM_001002917.1	NP_001002917.1	Q8WZ84	OR8D1_HUMAN	olfactory receptor, family 8, subfamily D, member 1	276						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			kidney(1)|large_intestine(1)|lung(7)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	16		Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0528)		TGGTGTAGAACACAGAGGACA	0.453													T|||	1440	0.28754	0.1626	0.3429	5008	,	,		18422	0.4167		0.4066	False		,,,				2504	0.1616				p.V276V		Atlas-SNP	.											.	OR8D1	53	.	0			c.G828A						PASS	.	T		941,3461	736.0+/-410.7	101,739,1361	111.0	107.0	108.0		828	-3.0	0.2	11	dbSNP_111	108	3384,5214	640.3+/-399.6	673,2038,1588	no	coding-synonymous	OR8D1	NM_001002917.1		774,2777,2949	TT,TC,CC		39.358,21.3766,33.2692		276/309	124179835	4325,8675	2201	4299	6500	SO:0001819	synonymous_variant	283159	exon1			GTAGAACACAGAG	AF238489	CCDS31706.1	11q25	2012-08-09			ENSG00000196341	ENSG00000196341		"""GPCR / Class A : Olfactory receptors"""	8481	protein-coding gene	gene with protein product				OR8D3			Standard	NM_001002917		Approved	OST004	uc010sag.2	Q8WZ84	OTTHUMG00000165977	ENST00000357821.2:c.828G>A	11.37:g.124179835C>T		Somatic	208	0	0		WXS	Illumina HiSeq	Phase_I	123	23	0.186992	NM_001002917	B2RNL4|Q6IEW1|Q8NGH0	Silent	SNP	ENST00000357821.2	37	CCDS31706.1																																																																																			C|0.669;T|0.331	0.331	strong		0.453	OR8D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387285.1	NM_001002917	
ATP9B	374868	hgsc.bcm.edu	37	18	77097360	77097360	+	Missense_Mutation	SNP	A	A	T	rs585033	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:77097360A>T	ENST00000426216.2	+	19	2211	c.2194A>T	c.(2194-2196)Atg>Ttg	p.M732L	ATP9B_ENST00000543761.1_Missense_Mutation_p.M53L|RP11-800A18.4_ENST00000592906.1_RNA|ATP9B_ENST00000307671.7_Missense_Mutation_p.M732L	NM_198531.3	NP_940933.3	O43861	ATP9B_HUMAN	ATPase, class II, type 9B	732			M -> L (in dbSNP:rs585033).		establishment of protein localization to Golgi (GO:0072600)|phospholipid translocation (GO:0045332)	integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|trans-Golgi network (GO:0005802)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(15)|ovary(3)|prostate(1)|skin(2)|stomach(1)	38		Esophageal squamous(42;0.018)|Melanoma(33;0.0964)|Prostate(75;0.171)		OV - Ovarian serous cystadenocarcinoma(15;1.44e-07)|BRCA - Breast invasive adenocarcinoma(31;0.0405)		GGAGAGGGAGATGGAACTGCT	0.652													A|||	162	0.0323482	0.003	0.0562	5008	,	,		20784	0.001		0.1024	False		,,,				2504	0.0153				p.M732L		Atlas-SNP	.											.	ATP9B	96	.	0			c.A2194T						PASS	.	A	LEU/MET	99,4307	77.8+/-116.1	2,95,2106	120.0	100.0	107.0		2194	4.2	1.0	18	dbSNP_83	107	777,7823	184.2+/-232.2	44,689,3567	yes	missense	ATP9B	NM_198531.3	15	46,784,5673	TT,TA,AA		9.0349,2.2469,6.7354	benign	732/1148	77097360	876,12130	2203	4300	6503	SO:0001583	missense	374868	exon19			AGGGAGATGGAAC	R51412	CCDS12014.1	18q23	2010-04-20	2007-09-19		ENSG00000166377	ENSG00000166377		"""ATPases / P-type"""	13541	protein-coding gene	gene with protein product		614446	"""ATPase, Class II, type 9B"""			9548971, 11015572	Standard	NM_198531		Approved	ATPIIB	uc002lmx.3	O43861	OTTHUMG00000132898	ENST00000426216.2:c.2194A>T	18.37:g.77097360A>T	ENSP00000398076:p.Met732Leu	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	38	20	0.526316	NM_198531	O60872|Q08AD8|Q08AD9	Missense_Mutation	SNP	ENST00000426216.2	37	CCDS12014.1	97	0.044413919413919416	1	0.0020325203252032522	21	0.058011049723756904	1	0.0017482517482517483	74	0.09762532981530343	A	8.343	0.829243	0.16749	0.022469	0.090349	ENSG00000166377	ENST00000426216;ENST00000307671;ENST00000543761	T;T;D	0.98835	0.15;0.15;-5.17	5.36	4.18	0.49190	ATPase, cation-transporting, domain N (1);HAD-like domain (1);ATPase, P-type, cytoplasmic domain N (1);	0.039059	0.85682	N	0.000000	T	0.37404	0.1002	N	0.03281	-0.365	0.54753	D	0.999984	B;B;B	0.16396	0.002;0.017;0.014	B;B;B	0.23716	0.012;0.048;0.028	T	0.77667	-0.2502	10	0.02654	T	1	.	11.587	0.50925	0.8662:0.0:0.0:0.1338	rs585033;rs585033	53;732;732	F5H8J1;O43861;O43861-2	.;ATP9B_HUMAN;.	L	732;732;53	ENSP00000398076:M732L;ENSP00000304500:M732L;ENSP00000442015:M53L	ENSP00000304500:M732L	M	+	1	0	ATP9B	75198348	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	6.809000	0.75211	0.850000	0.35239	0.533000	0.62120	ATG	A|0.943;T|0.057	0.057	strong		0.652	ATP9B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256402.3	NM_198531	
CCDC60	160777	hgsc.bcm.edu	37	12	119909961	119909961	+	Silent	SNP	C	C	T	rs17482508	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:119909961C>T	ENST00000327554.2	+	3	798	c.333C>T	c.(331-333)acC>acT	p.T111T	RP11-768F21.1_ENST00000509470.2_lincRNA|CCDC60_ENST00000546345.1_3'UTR	NM_178499.3	NP_848594.2	Q8IWA6	CCD60_HUMAN	coiled-coil domain containing 60	111										endometrium(4)|kidney(3)|large_intestine(8)|lung(15)|ovary(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	40	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.207)		ATGGGGACACCTTATTGAGGT	0.453													C|||	57	0.0113818	0.003	0.0216	5008	,	,		21834	0.0		0.0358	False		,,,				2504	0.002				p.T111T		Atlas-SNP	.											.	CCDC60	84	.	0			c.C333T						PASS	.	C		28,4378	35.2+/-66.4	0,28,2175	174.0	179.0	177.0		333	-10.4	0.0	12	dbSNP_123	177	303,8297	108.0+/-168.7	6,291,4003	no	coding-synonymous	CCDC60	NM_178499.3		6,319,6178	TT,TC,CC		3.5233,0.6355,2.545		111/551	119909961	331,12675	2203	4300	6503	SO:0001819	synonymous_variant	160777	exon3			GGACACCTTATTG	BC040553	CCDS9190.1	12q24.23	2006-02-03			ENSG00000183273	ENSG00000183273			28610	protein-coding gene	gene with protein product						12477932	Standard	NM_178499		Approved	MGC39827	uc001txe.3	Q8IWA6	OTTHUMG00000168943	ENST00000327554.2:c.333C>T	12.37:g.119909961C>T		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	58	31	0.534483	NM_178499		Silent	SNP	ENST00000327554.2	37	CCDS9190.1																																																																																			C|0.976;T|0.024	0.024	strong		0.453	CCDC60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401680.1	NM_178499	
CFAP46	54777	hgsc.bcm.edu	37	10	134649709	134649709	+	Missense_Mutation	SNP	C	C	T	rs76581191	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:134649709C>T	ENST00000368586.5	-	46	6650	c.6550G>A	c.(6550-6552)Ggc>Agc	p.G2184S	TTC40_ENST00000263170.5_Missense_Mutation_p.G345S	NM_001200049.2	NP_001186978.2														breast(1)|endometrium(5)|lung(19)|urinary_tract(3)	28						TAGGCAGCGCCGTACAGACGG	0.647													c|||	33	0.00658946	0.0015	0.0043	5008	,	,		11914	0.0		0.0129	False		,,,				2504	0.0153				p.G2184S		Atlas-SNP	.											TTC40,NS,carcinoma,0,2	TTC40	100	2	0			c.G6550A						PASS	.		SER/GLY	11,4391	16.8+/-37.8	0,11,2190	76.0	58.0	64.0		1486	0.1	0.0	10	dbSNP_131	64	145,8453	70.7+/-133.2	0,145,4154	yes	missense	C10orf92	NM_001200049.1	56	0,156,6344	TT,TC,CC		1.6864,0.2499,1.2	benign	496/1028	134649709	156,12844	2201	4299	6500	SO:0001583	missense	54777	exon46			CAGCGCCGTACAG																												ENST00000368586.5:c.6550G>A	10.37:g.134649709C>T	ENSP00000357575:p.Gly2184Ser	Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	42	20	0.47619	NM_001200049		Missense_Mutation	SNP	ENST00000368586.5	37	CCDS58101.1	8	0.003663003663003663	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	6	0.0079155672823219	c	4.026	0.002278	0.07819	0.002499	0.016864	ENSG00000171811	ENST00000368586;ENST00000263170	T;T	0.25912	2.01;1.77	4.17	0.0804	0.14420	.	0.210433	0.27535	N	0.018933	T	0.06005	0.0156	N	0.25647	0.755	0.09310	N	0.999999	B	0.24132	0.098	B	0.15870	0.014	T	0.11966	-1.0566	10	0.40728	T	0.16	.	3.0641	0.06209	0.1917:0.4861:0.0:0.3222	.	345	Q8IYW2	CJ092_HUMAN	S	2184;345	ENSP00000357575:G2184S;ENSP00000263170:G345S	ENSP00000263170:G345S	G	-	1	0	C10orf93	134499699	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	-0.167000	0.09940	0.040000	0.15660	-0.251000	0.11542	GGC	C|0.990;T|0.010	0.010	strong		0.647	TTC40-001	PUTATIVE	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000051095.3		
KCTD16	57528	hgsc.bcm.edu	37	5	143586416	143586416	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:143586416C>T	ENST00000507359.3	+	2	1230	c.139C>T	c.(139-141)Cct>Tct	p.P47S	KCTD16_ENST00000512467.1_Missense_Mutation_p.P47S	NM_020768.3	NP_065819.1	Q68DU8	KCD16_HUMAN	potassium channel tetramerization domain containing 16	47	BTB.				protein homooligomerization (GO:0051260)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	cell junction (GO:0030054)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|receptor complex (GO:0043235)		p.P47S(1)		large_intestine(5)|lung(9)|ovary(2)|prostate(1)|skin(3)|urinary_tract(1)	21		all_hematologic(541;0.118)	KIRC - Kidney renal clear cell carcinoma(527;0.00111)|Kidney(363;0.00176)			GATAAGCATCCCTCATTCCCT	0.473																																					p.P47S		Atlas-SNP	.											KCTD16,scalp,carcinoma,0,1	KCTD16	70	1	1	Substitution - Missense(1)	skin(1)	c.C139T						scavenged	.						77.0	72.0	74.0					5																	143586416		2203	4300	6503	SO:0001583	missense	57528	exon3			AGCATCCCTCATT	AB037738	CCDS34260.1	5q32	2013-06-20	2013-06-20		ENSG00000183775	ENSG00000183775			29244	protein-coding gene	gene with protein product		613423	"""potassium channel tetramerisation domain containing 16"""			10718198	Standard	NM_020768		Approved	KIAA1317	uc003lnm.1	Q68DU8	OTTHUMG00000163172	ENST00000507359.3:c.139C>T	5.37:g.143586416C>T	ENSP00000426548:p.Pro47Ser	Somatic	208	0	0		WXS	Illumina HiSeq	Phase_I	129	3	0.0232558	NM_020768	Q9P2M9	Missense_Mutation	SNP	ENST00000507359.3	37	CCDS34260.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.070114	0.76301	.	.	ENSG00000183775	ENST00000512467;ENST00000507359	T;T	0.54071	0.59;0.59	5.55	5.55	0.83447	BTB/POZ-like (1);BTB/POZ fold (2);Potassium channel, voltage dependent, Kv, tetramerisation (1);	0.000000	0.85682	D	0.000000	T	0.72003	0.3407	L	0.61387	1.9	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.73251	-0.4042	10	0.66056	D	0.02	.	19.5043	0.95108	0.0:1.0:0.0:0.0	.	47	Q68DU8	KCD16_HUMAN	S	47	ENSP00000424151:P47S;ENSP00000426548:P47S	ENSP00000426548:P47S	P	+	1	0	KCTD16	143566609	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	7.770000	0.85390	2.607000	0.88179	0.561000	0.74099	CCT	.	.	none		0.473	KCTD16-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371898.3	XM_098368	
NTAN1	123803	hgsc.bcm.edu	37	16	15133889	15133889	+	Silent	SNP	T	T	G	rs14347	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:15133889T>G	ENST00000287706.3	-	8	668	c.576A>C	c.(574-576)gcA>gcC	p.A192A	PDXDC1_ENST00000535621.2_Intron	NM_001270766.1|NM_173474.3	NP_001257695.1|NP_775745.1	Q96AB6	NTAN1_HUMAN	N-terminal asparagine amidase	192					adult locomotory behavior (GO:0008344)|memory (GO:0007613)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein-N-terminal asparagine amidohydrolase activity (GO:0008418)			endometrium(1)|large_intestine(4)|lung(3)	8						CTTGAAAGGATGCTCTGTAAA	0.458													G|||	1726	0.344649	0.1846	0.5331	5008	,	,		20562	0.372		0.3072	False		,,,				2504	0.4376				p.A192A		Atlas-SNP	.											.	NTAN1	21	.	0			c.A576C						PASS	.	G		1000,3394	729.0+/-410.0	121,758,1318	115.0	121.0	119.0		576	-1.8	0.9	16	dbSNP_52	119	2588,6012	689.3+/-404.4	360,1868,2072	no	coding-synonymous	NTAN1	NM_173474.2		481,2626,3390	GG,GT,TT		30.093,22.7583,27.6127		192/311	15133889	3588,9406	2197	4300	6497	SO:0001819	synonymous_variant	123803	exon8			AAAGGATGCTCTG	AF092440	CCDS10558.1, CCDS73832.1	16p13	2008-02-05			ENSG00000157045	ENSG00000157045			29909	protein-coding gene	gene with protein product		615367				8910481	Standard	NM_173474		Approved		uc002ddd.4	Q96AB6	OTTHUMG00000129849	ENST00000287706.3:c.576A>C	16.37:g.15133889T>G		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	55	42	0.763636	NM_173474	Q7Z4Z0	Silent	SNP	ENST00000287706.3	37	CCDS10558.1																																																																																			T|0.710;G|0.290	0.290	strong		0.458	NTAN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252089.1	NM_173474	
LGALS2	3957	hgsc.bcm.edu	37	22	37966649	37966649	+	Silent	SNP	G	G	A	rs115686288	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:37966649G>A	ENST00000215886.4	-	3	357	c.183C>T	c.(181-183)gaC>gaT	p.D61D		NM_006498.2	NP_006489.1	P05162	LEG2_HUMAN	lectin, galactoside-binding, soluble, 2	61	Galectin. {ECO:0000255|PROSITE- ProRule:PRU00639}.						carbohydrate binding (GO:0030246)|galactoside binding (GO:0016936)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|skin(1)|stomach(1)	11	Melanoma(58;0.0574)					AGTTGCTGCCGTCCAATGAGT	0.547													G|||	58	0.0115815	0.0023	0.0072	5008	,	,		22085	0.001		0.0129	False		,,,				2504	0.0368				p.D61D	GBM(193;1840 2185 13711 20676 24505)	Atlas-SNP	.											.	LGALS2	16	.	0			c.C183T						PASS	.	G		15,4391	22.3+/-47.3	0,15,2188	194.0	170.0	179.0		183	-7.2	0.0	22	dbSNP_132	179	87,8513	49.8+/-109.6	0,87,4213	no	coding-synonymous	LGALS2	NM_006498.2		0,102,6401	AA,AG,GG		1.0116,0.3404,0.7843		61/133	37966649	102,12904	2203	4300	6503	SO:0001819	synonymous_variant	3957	exon3			GCTGCCGTCCAAT		CCDS13950.1	22q13.1	2011-08-04	2007-02-01		ENSG00000100079	ENSG00000100079		"""Lectins, galactoside-binding"""	6562	protein-coding gene	gene with protein product	"""galectin 2"""	150571				1988031, 15356130	Standard	NM_006498		Approved	HL14	uc003ata.3	P05162	OTTHUMG00000150590	ENST00000215886.4:c.183C>T	22.37:g.37966649G>A		Somatic	207	0	0		WXS	Illumina HiSeq	Phase_I	196	89	0.454082	NM_006498	Q6FGY4	Silent	SNP	ENST00000215886.4	37	CCDS13950.1																																																																																			G|0.993;A|0.007	0.007	strong		0.547	LGALS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318991.1	NM_006498	
MUC4	4585	hgsc.bcm.edu	37	3	195515422	195515422	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195515422G>T	ENST00000463781.3	-	2	3488	c.3029C>A	c.(3028-3030)cCt>cAt	p.P1010H	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.P1010H	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	445	Repeat.|Ser-rich.				cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			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	0.577																																					p.P1010H		Atlas-SNP	.											.	MUC4	1505	.	0			c.C3029A						PASS	.						63.0	35.0	44.0					3																	195515422		692	1591	2283	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.3029C>A	3.37:g.195515422G>T	ENSP00000417498:p.Pro1010His	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	74	23	0.310811	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	5.962	0.361410	0.11296	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.55588	0.51;0.53	1.24	-2.49	0.06403	.	.	.	.	.	T	0.29749	0.0743	N	0.19112	0.55	0.09310	N	1	B	0.12630	0.006	B	0.08055	0.003	T	0.12889	-1.0530	8	.	.	.	.	5.6108	0.17404	0.0:0.3425:0.467:0.1905	.	1010	E7ESK3	.	H	1010	ENSP00000417498:P1010H;ENSP00000420243:P1010H	.	P	-	2	0	MUC4	196999817	.	.	0.000000	0.03702	0.077000	0.17291	.	.	-1.667000	0.01473	0.064000	0.15345	CCT	.	.	none		0.577	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
FAT1	2195	hgsc.bcm.edu	37	4	187516880	187516880	+	Silent	SNP	A	A	G	rs1298865	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:187516880A>G	ENST00000441802.2	-	26	13310	c.13101T>C	c.(13099-13101)tcT>tcC	p.S4367S	FAT1_ENST00000512347.1_5'Flank	NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	4367					actin filament organization (GO:0007015)|anatomical structure morphogenesis (GO:0009653)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(38)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(33)|lung(88)|ovary(13)|pancreas(2)|prostate(16)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	228						AGGAGCTCAGAGACTGCACTT	0.512										HNSCC(5;0.00058)			G|||	2463	0.491813	0.7118	0.5317	5008	,	,		18218	0.5724		0.3698	False		,,,				2504	0.2086				p.S4367S	Colon(197;1040 2055 4143 4984 49344)	Atlas-SNP	.											.	FAT1	500	.	0			c.T13101C						PASS	.	G		2631,1427		845,941,243	119.0	122.0	121.0		13101	-2.1	0.8	4	dbSNP_87	121	3026,5374		568,1890,1742	no	coding-synonymous	FAT1	NM_005245.3		1413,2831,1985	GG,GA,AA		36.0238,35.1651,45.4086		4367/4589	187516880	5657,6801	2029	4200	6229	SO:0001819	synonymous_variant	2195	exon26			GCTCAGAGACTGC	X87241	CCDS47177.1	4q35.2	2013-05-31	2013-05-31	2008-10-30	ENSG00000083857	ENSG00000083857		"""Cadherins / Cadherin-related"""	3595	protein-coding gene	gene with protein product	"""cadherin-related family member 8"""	600976	"""FAT tumor suppressor (Drosophila) homolog"", ""FAT tumor suppressor homolog 1 (Drosophila)"""	FAT		8586420	Standard	XM_005262834		Approved	CDHF7, CDHR8	uc003izf.3	Q14517	OTTHUMG00000160320	ENST00000441802.2:c.13101T>C	4.37:g.187516880A>G		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	107	50	0.46729	NM_005245		Silent	SNP	ENST00000441802.2	37	CCDS47177.1	1159	0.5306776556776557	327	0.6646341463414634	192	0.5303867403314917	353	0.6171328671328671	287	0.3786279683377309	G	10.58	1.389809	0.25118	0.648349	0.360238	ENSG00000083857	ENST00000512772;ENST00000507105	.	.	.	5.34	-2.11	0.07187	.	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.43475	-0.9389	5	0.87932	D	0	.	7.9059	0.29761	0.4922:0.1909:0.3169:0.0	rs1298865;rs17635848;rs60312016;rs1298865	.	.	.	P	135	.	ENSP00000423801:S135P	S	-	1	0	FAT1	187753874	0.073000	0.21202	0.754000	0.31244	0.960000	0.62799	-0.504000	0.06375	-0.690000	0.05142	-0.128000	0.14901	TCT	A|0.468;G|0.532	0.532	strong		0.512	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245	
ARVCF	421	hgsc.bcm.edu	37	22	19965563	19965563	+	Missense_Mutation	SNP	C	C	T	rs16982871	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:19965563C>T	ENST00000263207.3	-	8	1907	c.1616G>A	c.(1615-1617)cGa>cAa	p.R539Q	ARVCF_ENST00000344269.3_Missense_Mutation_p.R476Q|ARVCF_ENST00000406259.1_Missense_Mutation_p.R539Q|ARVCF_ENST00000401994.1_Missense_Mutation_p.R476Q|ARVCF_ENST00000406522.1_Missense_Mutation_p.R476Q	NM_001670.2	NP_001661.1	O00192	ARVC_HUMAN	armadillo repeat gene deleted in velocardiofacial syndrome	539			R -> Q (in dbSNP:rs16982871).		calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|multicellular organismal development (GO:0007275)|single organismal cell-cell adhesion (GO:0016337)	cytoplasm (GO:0005737)|intracellular (GO:0005622)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(1)|cervix(1)|endometrium(3)|liver(1)|lung(4)|prostate(1)|urinary_tract(2)	13	Colorectal(54;0.0993)					CTCCCGGAGTCGCCGCCGGGC	0.667													C|||	11	0.00219649	0.0008	0.0014	5008	,	,		18613	0.0		0.003	False		,,,				2504	0.0061				p.R539Q		Atlas-SNP	.											.	ARVCF	54	.	0			c.G1616A						PASS	.	C	GLN/ARG	9,4397	15.5+/-35.6	0,9,2194	49.0	45.0	47.0		1616	4.0	1.0	22	dbSNP_123	47	79,8517	46.7+/-105.8	0,79,4219	yes	missense	ARVCF	NM_001670.2	43	0,88,6413	TT,TC,CC		0.919,0.2043,0.6768	probably-damaging	539/963	19965563	88,12914	2203	4298	6501	SO:0001583	missense	421	exon8			CGGAGTCGCCGCC		CCDS13771.1	22q11.21	2013-02-14	2010-04-28		ENSG00000099889	ENSG00000099889		"""Armadillo repeat containing"""	728	protein-coding gene	gene with protein product		602269				9126485, 15456900	Standard	NM_001670		Approved		uc002zqz.3	O00192	OTTHUMG00000030426	ENST00000263207.3:c.1616G>A	22.37:g.19965563C>T	ENSP00000263207:p.Arg539Gln	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	95	36	0.378947	NM_001670	B7WNV2	Missense_Mutation	SNP	ENST00000263207.3	37	CCDS13771.1	4	0.0018315018315018315	0	0.0	1	0.0027624309392265192	0	0.0	3	0.00395778364116095	C	30	5.053953	0.93793	0.002043	0.00919	ENSG00000099889	ENST00000263207;ENST00000344269;ENST00000401994;ENST00000406522;ENST00000406259	T;T;T;T;T	0.70986	-0.53;-0.53;-0.53;-0.53;-0.53	4.03	4.03	0.46877	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.70842	0.3270	L	0.37507	1.11	0.58432	D	0.999999	D;D	0.89917	0.995;1.0	P;D	0.79108	0.877;0.992	T	0.73282	-0.4032	9	.	.	.	-9.945	17.0615	0.86548	0.0:1.0:0.0:0.0	rs16982871;rs16982871	539;61	O00192;E7EV58	ARVC_HUMAN;.	Q	539;476;476;476;539	ENSP00000263207:R539Q;ENSP00000342042:R476Q;ENSP00000384341:R476Q;ENSP00000384732:R476Q;ENSP00000385444:R539Q	.	R	-	2	0	ARVCF	18345563	0.394000	0.25246	0.973000	0.42090	0.993000	0.82548	1.722000	0.38042	2.541000	0.85698	0.655000	0.94253	CGA	C|0.995;T|0.005	0.005	strong		0.667	ARVCF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000075314.5	NM_001670	
MACF1	23499	hgsc.bcm.edu	37	1	39549983	39549983	+	Silent	SNP	G	G	A	rs3736890	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:39549983G>A	ENST00000372915.3	+	1	180	c.93G>A	c.(91-93)tcG>tcA	p.S31S	MACF1_ENST00000567887.1_Silent_p.S31S|MACF1_ENST00000361689.2_Silent_p.S31S|MACF1_ENST00000484793.1_Silent_p.S31S|MACF1_ENST00000602421.1_Silent_p.S31S|MACF1_ENST00000545844.1_Silent_p.S31S|MACF1_ENST00000539005.1_Silent_p.S31S|MACF1_ENST00000317713.7_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	79	0	0		WXS	Illumina HiSeq	Phase_I	54	20	0.37037	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	
C14orf159	80017	hgsc.bcm.edu	37	14	91633706	91633706	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:91633706G>A	ENST00000523771.1	+	4	844	c.241G>A	c.(241-243)Gct>Act	p.A81T	C14orf159_ENST00000428926.2_Missense_Mutation_p.A81T|C14orf159_ENST00000521077.2_Missense_Mutation_p.A81T|C14orf159_ENST00000517877.1_Missense_Mutation_p.A81T|C14orf159_ENST00000518665.2_Missense_Mutation_p.A81T|C14orf159_ENST00000298858.4_Missense_Mutation_p.A81T|C14orf159_ENST00000522322.1_Missense_Mutation_p.A81T|C14orf159_ENST00000518868.1_Missense_Mutation_p.A81T|C14orf159_ENST00000520328.1_Missense_Mutation_p.A81T|C14orf159_ENST00000519019.1_Missense_Mutation_p.A81T|C14orf159_ENST00000412671.2_Missense_Mutation_p.A81T|C14orf159_ENST00000525393.2_Intron|C14orf159_ENST00000256324.10_Missense_Mutation_p.A81T|C14orf159_ENST00000523816.1_Missense_Mutation_p.A81T			Q7Z3D6	CN159_HUMAN	chromosome 14 open reading frame 159	81						mitochondrion (GO:0005739)				NS(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	21		all_cancers(154;0.0191)|all_epithelial(191;0.241)		Epithelial(152;0.141)|OV - Ovarian serous cystadenocarcinoma(161;0.207)		CCCTCAAGGTGCTATCTCAGA	0.547																																					p.A81T		Atlas-SNP	.											.	C14orf159	57	.	0			c.G241A						PASS	.						103.0	99.0	100.0					14																	91633706		2203	4300	6503	SO:0001583	missense	80017	exon6			CAAGGTGCTATCT	AK097294	CCDS32141.1, CCDS41979.1, CCDS45150.1, CCDS66693.1, CCDS73677.1	14q32.11	2012-09-26			ENSG00000133943	ENSG00000133943			20498	protein-coding gene	gene with protein product							Standard	NM_001102367		Approved	FLJ39975	uc001xze.2	Q7Z3D6	OTTHUMG00000164980	ENST00000523771.1:c.241G>A	14.37:g.91633706G>A	ENSP00000429655:p.Ala81Thr	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	106	20	0.188679	NM_001102366	B3KUI7|Q86SW3|Q86SX8|Q86SX9|Q86T08|Q86TV5|Q96GW5|Q9H7G0|Q9H8Y9|Q9H9W6	Missense_Mutation	SNP	ENST00000523771.1	37	CCDS32141.1	.	.	.	.	.	.	.	.	.	.	G	15.24	2.773383	0.49786	.	.	ENSG00000133943	ENST00000521334;ENST00000522837;ENST00000518871;ENST00000298858;ENST00000520328;ENST00000256324;ENST00000522170;ENST00000519950;ENST00000523879;ENST00000521077;ENST00000518665;ENST00000518868;ENST00000519019;ENST00000523816;ENST00000517518;ENST00000428926;ENST00000523894;ENST00000522322;ENST00000523771;ENST00000521064;ENST00000412671;ENST00000517877	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.58060	1.52;0.43;1.52;0.77;1.52;1.52;1.52;1.52;0.36;1.52;0.77;1.52;1.52;1.52;1.52;1.52;1.52;1.52;1.52;1.52;1.52;0.78	5.09	2.29	0.28610	.	0.539348	0.18409	N	0.142104	T	0.39835	0.1093	L	0.52126	1.63	0.09310	N	1	P;B;B;B;B;B	0.42203	0.773;0.036;0.036;0.06;0.06;0.06	B;B;B;B;B;B	0.38428	0.273;0.012;0.012;0.028;0.028;0.028	T	0.18461	-1.0336	10	0.17832	T	0.49	.	7.2233	0.26002	0.3591:0.0:0.6409:0.0	.	81;81;81;81;81;81	Q7Z3D6-6;Q7Z3D6;B3KVU6;Q7Z3D6-5;Q7Z3D6-2;Q7Z3D6-3	.;CN159_HUMAN;.;.;.;.	T	81	ENSP00000430022:A81T;ENSP00000427971:A81T;ENSP00000429189:A81T;ENSP00000298858:A81T;ENSP00000429453:A81T;ENSP00000256324:A81T;ENSP00000430666:A81T;ENSP00000428296:A81T;ENSP00000428122:A81T;ENSP00000430137:A81T;ENSP00000429098:A81T;ENSP00000428263:A81T;ENSP00000430318:A81T;ENSP00000428974:A81T;ENSP00000428652:A81T;ENSP00000404343:A81T;ENSP00000429459:A81T;ENSP00000427953:A81T;ENSP00000429655:A81T;ENSP00000429392:A81T;ENSP00000404196:A81T;ENSP00000429949:A81T	ENSP00000256324:A81T	A	+	1	0	C14orf159	90703459	0.000000	0.05858	0.001000	0.08648	0.003000	0.03518	-0.029000	0.12329	0.192000	0.20272	0.561000	0.74099	GCT	.	.	none		0.547	C14orf159-014	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381273.1	NM_024952	
TIAM1	7074	hgsc.bcm.edu	37	21	32638549	32638549	+	Missense_Mutation	SNP	C	C	A	rs386817934|rs2070417	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:32638549C>A	ENST00000286827.3	-	5	1211	c.740G>T	c.(739-741)gGg>gTg	p.G247V	TIAM1_ENST00000469412.1_Intron|TIAM1_ENST00000541036.1_Missense_Mutation_p.G247V	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	109	0	0		WXS	Illumina HiSeq	Phase_I	96	59	0.614583	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	
GCSAM	257144	hgsc.bcm.edu	37	3	111844089	111844089	+	Nonsense_Mutation	SNP	G	G	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:111844089G>T	ENST00000308910.4	-	5	387	c.203C>A	c.(202-204)tCa>tAa	p.S68*	GCSAM_ENST00000484193.1_Nonsense_Mutation_p.S70*|C3orf52_ENST00000467942.2_Intron	NM_001190259.1|NM_001190260.1|NM_152785.4	NP_001177188.1|NP_001177189.1|NP_689998.1	Q8N6F7	GCSAM_HUMAN	germinal center-associated, signaling and motility	68					negative regulation of lymphocyte migration (GO:2000402)|regulation of B cell receptor signaling pathway (GO:0050855)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|myosin II binding (GO:0045159)|protein kinase binding (GO:0019901)										GGGAGTAGATGACATTCTTTC	0.388																																					p.S70X		Atlas-SNP	.											.	.	.	.	0			c.C209A						PASS	.						117.0	117.0	117.0					3																	111844089		2203	4300	6503	SO:0001587	stop_gained	257144	exon5			GTAGATGACATTC	BC030506	CCDS2964.1, CCDS54621.1, CCDS54622.1	3q13.13	2012-09-03	2012-08-23	2012-08-23	ENSG00000174500	ENSG00000174500			20253	protein-coding gene	gene with protein product	"""human germinal center-associated lymphoma"""	607792	"""germinal center expressed transcript 2"""	GCET2			Standard	NM_152785		Approved	MGC40441, HGAL	uc021xcl.1	Q8N6F7	OTTHUMG00000159231	ENST00000308910.4:c.203C>A	3.37:g.111844089G>T	ENSP00000309487:p.Ser68*	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	41	8	0.195122	NM_001190259	C9JD17|C9JUG6	Nonsense_Mutation	SNP	ENST00000308910.4	37	CCDS2964.1	.	.	.	.	.	.	.	.	.	.	G	16.18	3.050229	0.55218	.	.	ENSG00000174500	ENST00000308910;ENST00000484193;ENST00000460387;ENST00000488580;ENST00000487901	.	.	.	4.23	4.23	0.50019	.	0.783537	0.10863	N	0.625847	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	0.8044	12.4209	0.55520	0.0:0.0:1.0:0.0	.	.	.	.	X	68;70;53;51;51	.	ENSP00000309487:S68X	S	-	2	0	GCET2	113326779	0.073000	0.21202	0.007000	0.13788	0.040000	0.13550	3.817000	0.55668	2.656000	0.90262	0.561000	0.74099	TCA	.	.	none		0.388	GCSAM-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000353967.2	NM_152785	
LILRB1	10859	hgsc.bcm.edu	37	19	55148088	55148088	+	Silent	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:55148088G>A	ENST00000396331.1	+	15	2148	c.1791G>A	c.(1789-1791)agG>agA	p.R597R	LILRB1_ENST00000448689.1_3'UTR|AC009892.10_ENST00000456337.1_Intron|LILRB1_ENST00000396315.1_Silent_p.R599R|LILRB1_ENST00000396321.2_Silent_p.R597R|LILRB1_ENST00000324602.7_Silent_p.R599R|LILRB1_ENST00000427581.2_Silent_p.R648R|LILRB1_ENST00000396327.3_Silent_p.R598R|LILRB1_ENST00000434867.2_Silent_p.R597R|LILRB1_ENST00000396317.1_Silent_p.R581R|LILRB1_ENST00000418536.2_Silent_p.R581R|LILRB1_ENST00000396332.4_Silent_p.R598R|LILRB1_ENST00000462628.1_3'UTR	NM_006669.3	NP_006660.3	Q8NHL6	LIRB1_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 1	597					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)		AAGAGGACAGGCAGATGGACA	0.607										HNSCC(37;0.09)																											p.R599R		Atlas-SNP	.											LILRB1,NS,carcinoma,0,1	LILRB1	140	1	0			c.G1797A						scavenged	.						97.0	81.0	86.0					19																	55148088		2201	4296	6497	SO:0001819	synonymous_variant	10859	exon14			GGACAGGCAGATG	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.1791G>A	19.37:g.55148088G>A		Somatic	153	10	0.0653595		WXS	Illumina HiSeq	Phase_I	194	10	0.0515464	NM_001081637	A2IXV4|A8MXT0|O75024|O75025|Q8NHJ9|Q8NHK0	Silent	SNP	ENST00000396331.1	37	CCDS42617.1																																																																																			.	.	none		0.607	LILRB1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000140796.4		
TRIM48	79097	hgsc.bcm.edu	37	11	55029787	55029787	+	Splice_Site	SNP	G	G	A	rs12799381	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:55029787G>A	ENST00000417545.2	+	1	130	c.44G>A	c.(43-45)cGa>cAa	p.R15Q		NM_024114.3	NP_077019.2	Q8IWZ4	TRI48_HUMAN	tripartite motif containing 48	0						intracellular (GO:0005622)	zinc ion binding (GO:0008270)	p.R15Q(1)		endometrium(13)|lung(19)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	38						AGAACCCAGCGGTGAGTGAAA	0.333													.|||	496	0.0990415	0.1505	0.049	5008	,	,		17203	0.0853		0.1113	False		,,,				2504	0.0665				p.R15Q		Atlas-SNP	.											TRIM48_ENST00000417545,caecum,carcinoma,+1,2	TRIM48	149	2	1	Substitution - Missense(1)	stomach(1)	c.G44A						PASS	.	G	GLN/ARG	205,1179		16,173,503	41.0	36.0	38.0		44	-0.8	0.0	11	dbSNP_121	38	343,2839		19,305,1267	no	missense-near-splice	TRIM48	NM_024114.3	43	35,478,1770	AA,AG,GG		10.7794,14.8121,12.0018		15/225	55029787	548,4018	692	1591	2283	SO:0001630	splice_region_variant	79097	exon1			CCCAGCGGTGAGT	AF521869	CCDS7947.2	11q12	2013-01-09	2011-01-25		ENSG00000150244	ENSG00000150244		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	19021	protein-coding gene	gene with protein product			"""tripartite motif-containing 48"""				Standard	NM_024114		Approved	RNF101	uc010rid.2	Q8IWZ4	OTTHUMG00000157011	ENST00000417545.2:c.44+1G>A	11.37:g.55029787G>A		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	88	61	0.693182	NM_024114	Q9BUW4	Missense_Mutation	SNP	ENST00000417545.2	37	CCDS7947.2	227	0.10393772893772894	87	0.17682926829268292	22	0.06077348066298342	35	0.06118881118881119	83	0.10949868073878628	.	6.705	0.498677	0.12762	0.148121	0.107794	ENSG00000150244	ENST00000417545	T	0.73047	-0.71	0.41	-0.821	0.10822	.	.	.	.	.	T	0.00241	0.0007	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.11155	-1.0599	4	0.41790	T	0.15	.	.	.	.	rs12799381	.	.	.	Q	15	ENSP00000402414:R15Q	ENSP00000402414:R15Q	R	+	2	0	TRIM48	54786363	0.006000	0.16342	0.028000	0.17463	0.009000	0.06853	0.470000	0.22084	-0.494000	0.06669	-1.202000	0.01658	CGA	G|0.891;A|0.109	0.109	strong		0.333	TRIM48-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347088.1		Missense_Mutation
TJP2	9414	hgsc.bcm.edu	37	9	71862987	71862987	+	Silent	SNP	G	G	A	rs2095876	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:71862987G>A	ENST00000377245.4	+	19	2935	c.2727G>A	c.(2725-2727)gcG>gcA	p.A909A	TJP2_ENST00000453658.2_Silent_p.A886A|TJP2_ENST00000535702.1_Silent_p.A913A|TJP2_ENST00000265384.7_Silent_p.A909A|TJP2_ENST00000348208.4_Silent_p.A909A|TJP2_ENST00000498204.1_3'UTR|TJP2_ENST00000539225.1_Silent_p.A940A	NM_004817.3	NP_004808.2	Q9UDY2	ZO2_HUMAN	tight junction protein 2	909					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						CCATGGGCGCGGACTATCTGA	0.562													G|||	1423	0.284145	0.1664	0.4539	5008	,	,		18637	0.4504		0.2197	False		,,,				2504	0.2178				p.A940A		Atlas-SNP	.											TJP2,colon,carcinoma,+2,1	TJP2	120	1	0			c.G2820A						PASS	.	G	,,,,,	755,3651	306.9+/-289.7	78,599,1526	84.0	76.0	79.0		2658,2739,2820,2727,2727,2727	3.0	1.0	9	dbSNP_96	79	1812,6788	321.1+/-314.9	196,1420,2684	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	,,,,,	274,2019,4210	AA,AG,GG		21.0698,17.1357,19.737	,,,,,	886/1021,913/1158,940/1222,909/994,909/1191,909/1044	71862987	2567,10439	2203	4300	6503	SO:0001819	synonymous_variant	9414	exon19			GGGCGCGGACTAT	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.2727G>A	9.37:g.71862987G>A		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	56	37	0.660714	NM_001170416	A2A3H9|B7Z2R8|B7Z7T6|F5H301|F5H886|Q15883|Q5VXL0|Q5VXL1|Q8N756|Q8NI14|Q99839|Q9UDY0|Q9UDY1	Silent	SNP	ENST00000377245.4	37	CCDS6627.1																																																																																			G|0.763;A|0.237	0.237	strong		0.562	TJP2-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000052572.2	NM_201629	
PCDHA8	56140	hgsc.bcm.edu	37	5	140221098	140221098	+	Missense_Mutation	SNP	C	C	G	rs62624460	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:140221098C>G	ENST00000531613.1	+	1	192	c.192C>G	c.(190-192)ttC>ttG	p.F64L	PCDHA4_ENST00000512229.2_Intron|PCDHA8_ENST00000378123.3_Missense_Mutation_p.F64L|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|PCDHA5_ENST00000529619.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA1_ENST00000504120.2_Intron	NM_018911.2	NP_061734.1	Q9Y5H6	PCDA8_HUMAN	protocadherin alpha 8	64	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(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)			CGCGCCTGTTCCGGGTGGCGT	0.637													.|||	245	0.0489217	0.034	0.0893	5008	,	,		18022	0.0169		0.0765	False		,,,				2504	0.045				p.F64L		Atlas-SNP	.											.	PCDHA8	366	.	0			c.C192G						PASS	.	C	,,,,,,,LEU/PHE,,,LEU/PHE	183,4223		2,179,2022	42.0	58.0	53.0		,,,,,,,192,,,192	4.0	1.0	5	dbSNP_129	53	826,7768		25,776,3496	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	,,,,,,,22,,,22	27,955,5518	GG,GC,CC		9.6114,4.1534,7.7615	,,,,,,,,,,	,,,,,,,64/951,,,64/815	140221098	1009,11991	2203	4297	6500	SO:0001583	missense	56140	exon1			CCTGTTCCGGGTG	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.192C>G	5.37:g.140221098C>G	ENSP00000434655:p.Phe64Leu	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	49	22	0.44898	NM_031856	B9EGT7|O75281	Missense_Mutation	SNP	ENST00000531613.1	37	CCDS54919.1	134	0.06135531135531135	24	0.04878048780487805	30	0.08287292817679558	14	0.024475524475524476	66	0.0870712401055409	C	13.25	2.181984	0.38511	0.041534	0.096114	ENSG00000204962	ENST00000531613;ENST00000378123	T;T	0.38887	1.11;1.11	3.95	3.95	0.45737	Cadherin, N-terminal (1);Cadherin (3);Cadherin-like (1);	0.000000	0.38720	U	0.001585	T	0.00815	0.0027	L	0.31065	0.9	0.45594	P	0.0014680000000000248	P;P	0.45902	0.868;0.84	B;B	0.42386	0.386;0.281	T	0.09122	-1.0689	9	0.56958	D	0.05	.	7.6064	0.28105	0.0:0.6009:0.3081:0.091	rs62624460	64;64	Q9Y5H6;Q9Y5H6-2	PCDA8_HUMAN;.	L	64	ENSP00000434655:F64L;ENSP00000367363:F64L	ENSP00000367363:F64L	F	+	3	2	PCDHA8	140201282	0.056000	0.20664	1.000000	0.80357	0.983000	0.72400	-0.173000	0.09854	1.905000	0.55150	0.557000	0.71058	TTC	C|0.929;G|0.071	0.071	strong		0.637	PCDHA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372830.2	NM_018911	
RHOBTB2	23221	hgsc.bcm.edu	37	8	22863614	22863614	+	Silent	SNP	C	C	T	rs139953909	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:22863614C>T	ENST00000251822.6	+	4	975	c.438C>T	c.(436-438)taC>taT	p.Y146Y	RHOBTB2_ENST00000519685.1_Silent_p.Y168Y|RHOBTB2_ENST00000522948.1_Silent_p.Y153Y|RP11-875O11.1_ENST00000523884.1_RNA|RP11-875O11.1_ENST00000502083.2_RNA|RHOBTB2_ENST00000523918.1_3'UTR	NM_015178.2	NP_055993.2	Q9BYZ6	RHBT2_HUMAN	Rho-related BTB domain containing 2	146	Rho-like.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(6)|lung(11)|ovary(2)|prostate(2)|skin(1)|urinary_tract(1)	31		Prostate(55;0.0513)|Breast(100;0.214)		Colorectal(74;0.0157)|COAD - Colon adenocarcinoma(73;0.064)		ACCTGCGCTACGCTGACCTGG	0.587													C|||	14	0.00279553	0.0015	0.0014	5008	,	,		20101	0.0		0.0099	False		,,,				2504	0.001				p.Y168Y		Atlas-SNP	.											.	RHOBTB2	67	.	0			c.C504T						PASS	.	C	,,	8,4398	14.3+/-33.2	0,8,2195	190.0	179.0	182.0		504,459,438	-3.4	0.8	8	dbSNP_134	182	129,8471	65.3+/-127.6	3,123,4174	no	coding-synonymous,coding-synonymous,coding-synonymous	RHOBTB2	NM_001160036.1,NM_001160037.1,NM_015178.2	,,	3,131,6369	TT,TC,CC		1.5,0.1816,1.0534	,,	168/750,153/735,146/728	22863614	137,12869	2203	4300	6503	SO:0001819	synonymous_variant	23221	exon6			GCGCTACGCTGAC	AF315385	CCDS6034.1, CCDS55210.1, CCDS55211.1	8p21.2	2013-01-08			ENSG00000008853	ENSG00000008853		"""BTB/POZ domain containing"""	18756	protein-coding gene	gene with protein product		607352				11222756	Standard	NM_001160036		Approved	KIAA0717, DBC2	uc011kzp.1	Q9BYZ6	OTTHUMG00000097827	ENST00000251822.6:c.438C>T	8.37:g.22863614C>T		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	75	54	0.72	NM_001160036	A8K9Z8|D3DSR8|E9PBU2|E9PEI7|O94825|Q8N4A8|Q9BZK6	Silent	SNP	ENST00000251822.6	37	CCDS6034.1																																																																																			C|0.990;T|0.010	0.010	strong		0.587	RHOBTB2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000215101.2		
ZNF883	169834	hgsc.bcm.edu	37	9	115760345	115760345	+	lincRNA	SNP	T	T	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:115760345T>C	ENST00000427548.1	-	0	1468							P0CG24	ZN883_HUMAN	zinc finger protein 883						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)										AAGGTTTCTCTCCAGTATGTA	0.353																																					p.G65G		Atlas-SNP	.											.	.	.	.	0			c.A195G						PASS	.						60.0	67.0	64.0					9																	115760345		2192	4295	6487			169834	exon5			TTTCTCTCCAGTA	AK095843		9q32	2010-07-23			ENSG00000228623	ENSG00000228623		"""Zinc fingers, C2H2-type"""	27271	protein-coding gene	gene with protein product							Standard	NM_001101338		Approved		uc011lwy.2	P0CG24	OTTHUMG00000020514		9.37:g.115760345T>C		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	53	9	0.169811	NM_001101338		Silent	SNP	ENST00000427548.1	37																																																																																				.	.	none		0.353	ZNF883-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000053704.1	NM_001101338	
ZNF469	84627	hgsc.bcm.edu	37	16	88501386	88501386	+	Missense_Mutation	SNP	C	C	A	rs141218390	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:88501386C>A	ENST00000437464.1	+	2	7424	c.7424C>A	c.(7423-7425)gCg>gAg	p.A2475E	ZNF469_ENST00000565624.1_Missense_Mutation_p.A2503E	NM_001127464.1	NP_001120936.1	Q96JG9	ZN469_HUMAN	zinc finger protein 469	2475					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						GGAGCCCCCGCGGAGCCGAGC	0.701													C|||	448	0.0894569	0.062	0.0548	5008	,	,		13126	0.0853		0.0895	False		,,,				2504	0.1554				p.A2475E		Atlas-SNP	.											.	ZNF469	121	.	0			c.C7424A						PASS	.	C	GLU/ALA	63,1317		1,61,628	8.0	11.0	10.0		7424	0.8	0.0	16	dbSNP_134	10	193,2971		6,181,1395	yes	missense	ZNF469	NM_001127464.1	107	7,242,2023	AA,AC,CC		6.0999,4.5652,5.6338	probably-damaging	2475/3926	88501386	256,4288	690	1582	2272	SO:0001583	missense	84627	exon2			CCCCCGCGGAGCC	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.7424C>A	16.37:g.88501386C>A	ENSP00000402343:p.Ala2475Glu	Somatic	15	0	0		WXS	Illumina HiSeq	Phase_I	16	11	0.6875	NM_001127464		Missense_Mutation	SNP	ENST00000437464.1	37	CCDS45544.1	167	0.07646520146520147	30	0.06097560975609756	29	0.08011049723756906	43	0.07517482517482517	65	0.08575197889182058	C	8.663	0.900935	0.17760	0.045652	0.060999	ENSG00000225614	ENST00000437464	T	0.47528	0.84	4.02	0.783	0.18572	.	.	.	.	.	T	0.00724	0.0024	N	0.08118	0	0.80722	P	0.0	B	0.34372	0.451	B	0.24848	0.056	T	0.06991	-1.0796	8	0.56958	D	0.05	.	5.065	0.14578	0.0:0.5808:0.1754:0.2438	.	2475	Q96JG9	ZN469_HUMAN	E	2475	ENSP00000402343:A2475E	ENSP00000402343:A2475E	A	+	2	0	ZNF469	87028887	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	-0.225000	0.09151	0.638000	0.30545	0.491000	0.48974	GCG	C|0.923;A|0.077	0.077	strong		0.701	ZNF469-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NG_012236	
ANO7	50636	hgsc.bcm.edu	37	2	242163359	242163359	+	Missense_Mutation	SNP	G	G	A	rs7590653	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:242163359G>A	ENST00000274979.8	+	24	2837	c.2734G>A	c.(2734-2736)Gag>Aag	p.E912K		NM_001001891.3	NP_001001891.2	Q6IWH7	ANO7_HUMAN	anoctamin 7	912			E -> K (in dbSNP:rs7590653). {ECO:0000269|PubMed:14981236}.		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						TGAGCAGCCCGAGGGCTCAGA	0.622													C|||	712	0.142173	0.2231	0.1945	5008	,	,		17088	0.001		0.2336	False		,,,				2504	0.047				p.E912K		Atlas-SNP	.											.	ANO7	136	.	0			c.G2734A						PASS	.	C	LYS/GLU	867,3539		80,707,1416	70.0	72.0	71.0		2734	1.8	0.0	2	dbSNP_116	71	1897,6703		210,1477,2613	yes	missense	ANO7	NM_001001891.3	56	290,2184,4029	AA,AG,GG		22.0581,19.6777,21.2517	benign	912/934	242163359	2764,10242	2203	4300	6503	SO:0001583	missense	50636	exon24			CAGCCCGAGGGCT	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.2734G>A	2.37:g.242163359G>A	ENSP00000274979:p.Glu912Lys	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	87	42	0.482759	NM_001001891	Q6IWH6	Missense_Mutation	SNP	ENST00000274979.8	37	CCDS33423.1	349	0.15979853479853479	93	0.18902439024390244	80	0.22099447513812154	1	0.0017482517482517483	175	0.23087071240105542	C	13.30	2.196289	0.38806	0.196777	0.220581	ENSG00000146205	ENST00000274979	T	0.69175	-0.38	2.7	1.76	0.24704	.	1.458410	0.05785	U	0.609243	T	0.00012	0.0000	N	0.08118	0	0.58432	P	6.999999999979245E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.05435	-1.0885	9	0.06236	T	0.91	.	3.6191	0.08089	0.0:0.5744:0.2592:0.1664	rs7590653;rs52813858;rs56960627;rs7590653	912	Q6IWH7	ANO7_HUMAN	K	912	ENSP00000274979:E912K	ENSP00000274979:E912K	E	+	1	0	ANO7	241812032	0.006000	0.16342	0.000000	0.03702	0.145000	0.21501	0.999000	0.29757	0.035000	0.15519	-0.647000	0.03941	GAG	G|0.808;A|0.192	0.192	strong		0.622	ANO7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323509.1	NM_001001891	
ZSCAN32	54925	hgsc.bcm.edu	37	16	3434699	3434699	+	Missense_Mutation	SNP	A	A	G	rs27230	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:3434699A>G	ENST00000396852.4	-	6	1301	c.994T>C	c.(994-996)Tat>Cat	p.Y332H	ZSCAN32_ENST00000304926.3_Missense_Mutation_p.Y120H|NAA60_ENST00000576906.1_3'UTR|ZSCAN32_ENST00000439568.2_Missense_Mutation_p.Y43H|ZSCAN32_ENST00000422427.2_Missense_Mutation_p.Y120H|ZSCAN32_ENST00000396846.3_Missense_Mutation_p.Y332H|ZSCAN32_ENST00000573830.1_Missense_Mutation_p.Y43H|ZSCAN32_ENST00000574940.1_Missense_Mutation_p.Y332H	NM_001284527.1|NM_001284529.1	NP_001271456.1|NP_001271458.1	Q9NX65	ZSC32_HUMAN	zinc finger and SCAN domain containing 32	332			Y -> H (in dbSNP:rs27230).		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)										ATTTCCTCATAAAAGATACAA	0.512													A|||	329	0.0656949	0.0091	0.1196	5008	,	,		21176	0.0		0.1779	False		,,,				2504	0.0562				p.Y120H		Atlas-SNP	.											.	.	.	.	0			c.T358C						PASS	.	A	HIS/TYR	162,4232	106.9+/-145.3	5,152,2040	131.0	134.0	133.0		358	0.6	0.0	16	dbSNP_76	133	1605,6995	299.7+/-304.6	159,1287,2854	yes	missense	ZNF434	NM_017810.2	83	164,1439,4894	GG,GA,AA		18.6628,3.6868,13.5986	possibly-damaging	120/486	3434699	1767,11227	2197	4300	6497	SO:0001583	missense	54925	exon5			CCTCATAAAAGAT	AK000424	CCDS10503.1, CCDS66920.1, CCDS66921.1	16p13.3	2013-01-09	2013-01-09	2013-01-09	ENSG00000140987	ENSG00000140987		"""-"", ""Zinc fingers, C2H2-type"""	20812	protein-coding gene	gene with protein product			"""zinc finger protein 434"""	ZNF434			Standard	XM_005255402		Approved	FLJ20417	uc002cux.4	Q9NX65	OTTHUMG00000129357	ENST00000396852.4:c.994T>C	16.37:g.3434699A>G	ENSP00000380061:p.Tyr332His	Somatic	182	0	0		WXS	Illumina HiSeq	Phase_I	198	150	0.757576	NM_017810	B4DWL5|C9JB03|Q6WMU8|Q7Z6G2|Q8NFX8|Q9BU74	Missense_Mutation	SNP	ENST00000396852.4	37		189	0.08653846153846154	5	0.01016260162601626	44	0.12154696132596685	0	0.0	140	0.18469656992084432	A	13.81	2.346838	0.41599	0.036868	0.186628	ENSG00000140987	ENST00000304926;ENST00000396852;ENST00000396846;ENST00000439568;ENST00000422427	T;T;T;T;T	0.52295	0.67;0.67;0.67;0.67;0.67	3.02	0.563	0.17296	.	0.630262	0.11876	N	0.521018	T	0.00178	0.0005	M	0.86651	2.83	0.80722	P	0.0	P;B;B	0.44776	0.843;0.001;0.001	P;B;B	0.58391	0.838;0.008;0.008	T	0.06972	-1.0797	9	0.30854	T	0.27	.	3.4475	0.07486	0.6302:0.233:0.1368:0.0	rs27230;rs17691164;rs57730795;rs27230	120;120;332	B4DR24;Q9NX65;Q6WMU8	.;ZN434_HUMAN;.	H	120;332;332;43;120	ENSP00000302502:Y120H;ENSP00000380061:Y332H;ENSP00000380057:Y332H;ENSP00000391787:Y43H;ENSP00000407312:Y120H	ENSP00000302502:Y120H	Y	-	1	0	ZNF434	3374700	0.000000	0.05858	0.000000	0.03702	0.122000	0.20287	-0.419000	0.07071	-0.156000	0.11079	0.533000	0.62120	TAT	A|0.885;G|0.115	0.115	strong		0.512	ZSCAN32-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000251509.2	NM_017810	
NCAN	1463	hgsc.bcm.edu	37	19	19329924	19329924	+	Missense_Mutation	SNP	C	C	T	rs2228603	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:19329924C>T	ENST00000252575.6	+	3	373	c.274C>T	c.(274-276)Ccc>Tcc	p.P92S		NM_004386.2	NP_004377.2	O14594	NCAN_HUMAN	neurocan	92	Ig-like V-type.		P -> S (in dbSNP:rs2228603).		axon guidance (GO:0007411)|carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|regulation of synapse structural plasticity (GO:0051823)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|hyaluronic acid binding (GO:0005540)			breast(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(32)|ovary(5)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	64			Epithelial(12;0.00544)		Hyaluronan(DB08818)	ACAGGACTTGCCCATCCTGGT	0.647													C|||	220	0.0439297	0.0061	0.0231	5008	,	,		16745	0.0556		0.0676	False		,,,				2504	0.0736				p.P92S		Atlas-SNP	.											NCAN_ENST00000539499,NS,carcinoma,0,4	NCAN	277	4	0			c.C274T						PASS	.	C	SER/PRO	61,4345	57.4+/-93.9	0,61,2142	66.0	54.0	58.0		274	4.7	1.0	19	dbSNP_98	58	637,7963	162.2+/-214.9	19,599,3682	yes	missense	NCAN	NM_004386.2	74	19,660,5824	TT,TC,CC		7.407,1.3845,5.3668	possibly-damaging	92/1322	19329924	698,12308	2203	4300	6503	SO:0001583	missense	1463	exon3			GACTTGCCCATCC	AF026547	CCDS12397.1	19p12	2014-01-30	2007-02-15	2007-02-15	ENSG00000130287	ENSG00000130287		"""Immunoglobulin superfamily / V-set domain containing"", ""Proteoglycans / Extracellular Matrix : Hyalectans"", ""Endogenous ligands"""	2465	protein-coding gene	gene with protein product	"""neurocan proteoglycan"""	600826	"""chondroitin sulfate proteoglycan 3"""	CSPG3		1326557, 21353194	Standard	NM_004386		Approved		uc002nlz.3	O14594		ENST00000252575.6:c.274C>T	19.37:g.19329924C>T	ENSP00000252575:p.Pro92Ser	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	108	56	0.518519	NM_004386	Q9UPK6	Missense_Mutation	SNP	ENST00000252575.6	37	CCDS12397.1	102	0.046703296703296704	3	0.006097560975609756	9	0.024861878453038673	36	0.06293706293706294	54	0.0712401055408971	C	13.92	2.382116	0.42207	0.013845	0.07407	ENSG00000130287	ENST00000539499;ENST00000252575	T	0.02345	4.33	4.66	4.66	0.58398	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.37669	N	0.001987	T	0.00328	0.0010	N	0.13235	0.315	0.80722	D	1	D	0.52996	0.957	P	0.54431	0.752	T	0.66106	-0.6006	10	0.09590	T	0.72	-7.8597	15.0416	0.71796	0.0:1.0:0.0:0.0	rs2228603;rs61710588;rs2228603	92	O14594	NCAN_HUMAN	S	106;92	ENSP00000252575:P92S	ENSP00000252575:P92S	P	+	1	0	NCAN	19190924	0.984000	0.35163	0.982000	0.44146	0.929000	0.56500	1.319000	0.33655	2.119000	0.64992	0.491000	0.48974	CCC	C|0.950;T|0.050	0.050	strong		0.647	NCAN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460111.2	NM_004386	
PASK	23178	hgsc.bcm.edu	37	2	242072357	242072357	+	Silent	SNP	G	G	A	rs34401965	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:242072357G>A	ENST00000405260.1	-	9	2093	c.1395C>T	c.(1393-1395)acC>acT	p.T465T	PASK_ENST00000403638.3_Silent_p.T465T|PASK_ENST00000358649.4_Silent_p.T465T|PASK_ENST00000234040.4_Silent_p.T465T|PASK_ENST00000544142.1_Silent_p.T279T|PASK_ENST00000539818.1_Silent_p.T249T	NM_001252120.1	NP_001239049.1	Q96RG2	PASK_HUMAN	PAS domain containing serine/threonine kinase	465					negative regulation of glycogen biosynthetic process (GO:0045719)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of energy homeostasis (GO:2000505)|regulation of glucagon secretion (GO:0070092)|regulation of respiratory gaseous exchange (GO:0043576)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	ATP binding (GO:0005524)|phosphatidylinositol binding (GO:0035091)|protein serine/threonine kinase activity (GO:0004674)|signal transducer activity (GO:0004871)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(6)|lung(20)|ovary(4)|prostate(4)|skin(1)|stomach(1)|urinary_tract(2)	53		all_cancers(19;4.46e-39)|all_epithelial(40;1.34e-17)|Breast(86;1.53e-05)|Renal(207;0.00179)|all_lung(227;0.00481)|Lung NSC(271;0.017)|Ovarian(221;0.0228)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;1.34e-31)|all cancers(36;1e-28)|OV - Ovarian serous cystadenocarcinoma(60;3.53e-14)|Kidney(56;4.31e-09)|KIRC - Kidney renal clear cell carcinoma(57;4.35e-08)|BRCA - Breast invasive adenocarcinoma(100;5.64e-06)|Lung(119;0.000596)|LUSC - Lung squamous cell carcinoma(224;0.00481)|Colorectal(34;0.014)|COAD - Colon adenocarcinoma(134;0.0968)		TCTGAGTCCCGGTGAAGATGT	0.562													G|||	383	0.0764776	0.056	0.0562	5008	,	,		20239	0.0169		0.0825	False		,,,				2504	0.1738				p.T465T		Atlas-SNP	.											.	PASK	230	.	0			c.C1395T						PASS	.	G		273,4133	154.0+/-187.5	13,247,1943	115.0	96.0	102.0		1395	-5.9	0.0	2	dbSNP_126	102	772,7828	184.3+/-232.3	36,700,3564	no	coding-synonymous	PASK	NM_015148.2		49,947,5507	AA,AG,GG		8.9767,6.1961,8.0348		465/1324	242072357	1045,11961	2203	4300	6503	SO:0001819	synonymous_variant	23178	exon9			AGTCCCGGTGAAG	U79240	CCDS2545.1, CCDS58758.1, CCDS58759.1	2q37.3	2008-05-23			ENSG00000115687	ENSG00000115687			17270	protein-coding gene	gene with protein product		607505				11688972, 11459942, 15148392	Standard	NM_001252119		Approved	PASKIN, KIAA0135, STK37	uc010fzl.2	Q96RG2	OTTHUMG00000133392	ENST00000405260.1:c.1395C>T	2.37:g.242072357G>A		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	112	52	0.464286	NM_015148	G5E9F1|Q05BE4|Q68DY3|Q6GSJ5|Q86XH6|Q99763|Q9UFR7	Silent	SNP	ENST00000405260.1	37	CCDS2545.1																																																																																			G|0.925;A|0.075	0.075	strong		0.562	PASK-003	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000323753.1	NM_015148	
MUC4	4585	hgsc.bcm.edu	37	3	195505801	195505801	+	Missense_Mutation	SNP	G	G	A	rs200432267		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195505801G>A	ENST00000463781.3	-	2	13109	c.12650C>T	c.(12649-12651)gCa>gTa	p.A4217V	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.A4217V	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.A4217E(1)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		ACCTGTGGATGCTGAGGAAGT	0.592																																					p.A4217V		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	1	Substitution - Missense(1)	kidney(1)	c.C12650T						scavenged	.						35.0	29.0	31.0					3																	195505801		692	1582	2274	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.12650C>T	3.37:g.195505801G>A	ENSP00000417498:p.Ala4217Val	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	111	24	0.216216	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	N	1.430	-0.570605	0.03910	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.32515	1.45;1.52	0.93	-1.86	0.07760	.	.	.	.	.	T	0.15609	0.0376	N	0.19112	0.55	0.09310	N	1	B	0.14438	0.01	B	0.04013	0.001	T	0.26155	-1.0111	8	.	.	.	.	6.1781	0.20455	0.43:0.0:0.57:0.0	.	4089	E7ESK3	.	V	4217	ENSP00000417498:A4217V;ENSP00000420243:A4217V	.	A	-	2	0	MUC4	196990580	.	.	0.000000	0.03702	0.000000	0.00434	.	.	-1.621000	0.01562	-1.862000	0.00560	GCA	.	.	weak		0.592	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
OR2B2	81697	hgsc.bcm.edu	37	6	27879982	27879982	+	Missense_Mutation	SNP	A	A	G	rs61742093	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:27879982A>G	ENST00000303324.2	-	1	192	c.116T>C	c.(115-117)aTc>aCc	p.I39T		NM_033057.2	NP_149046.2	Q9GZK3	OR2B2_HUMAN	olfactory receptor, family 2, subfamily B, member 2	39						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(4)|large_intestine(5)|lung(10)|prostate(1)|urinary_tract(1)	22						ATTGCCAAAGATTGTCAAGAT	0.403													A|||	109	0.0217652	0.0106	0.0303	5008	,	,		18381	0.0		0.0736	False		,,,				2504	0.0				p.I39T		Atlas-SNP	.											.	OR2B2	54	.	0			c.T116C						PASS	.	A	THR/ILE	159,4247	106.0+/-144.5	4,151,2048	103.0	102.0	102.0		116	4.4	1.0	6	dbSNP_129	102	753,7847	180.3+/-229.3	35,683,3582	yes	missense	OR2B2	NM_033057.2	89	39,834,5630	GG,GA,AA		8.7558,3.6087,7.0121	possibly-damaging	39/358	27879982	912,12094	2203	4300	6503	SO:0001583	missense	81697	exon1			CCAAAGATTGTCA	Z98744	CCDS4641.1	6p22.3-p21.3	2014-02-19	2002-02-28		ENSG00000168131	ENSG00000168131		"""GPCR / Class A : Olfactory receptors"""	13966	protein-coding gene	gene with protein product			"""olfactory receptor, family 2, subfamily B, member 9"""	OR2B9			Standard	NM_033057		Approved	hs6M1-10, OR6-1, OR2B2Q	uc011dkw.2	Q9GZK3	OTTHUMG00000014495	ENST00000303324.2:c.116T>C	6.37:g.27879982A>G	ENSP00000304419:p.Ile39Thr	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	75	39	0.52	NM_033057	B2RNH2|Q9GZL2|Q9Y299	Missense_Mutation	SNP	ENST00000303324.2	37	CCDS4641.1	74	0.03388278388278388	6	0.012195121951219513	10	0.027624309392265192	0	0.0	58	0.07651715039577836	A	10.95	1.496750	0.26861	0.036087	0.087558	ENSG00000168131	ENST00000303324	T	0.00635	6.06	4.37	4.37	0.52481	.	0.000000	0.39909	U	0.001233	T	0.01061	0.0035	M	0.84433	2.695	0.51012	P	9.599999999998499E-5	P	0.48911	0.917	P	0.49301	0.606	T	0.42531	-0.9446	9	0.87932	D	0	.	12.1623	0.54110	1.0:0.0:0.0:0.0	rs61742093	39	Q9GZK3	OR2B2_HUMAN	T	39	ENSP00000304419:I39T	ENSP00000304419:I39T	I	-	2	0	OR2B2	27987961	0.732000	0.28121	0.994000	0.49952	0.124000	0.20399	5.072000	0.64389	1.901000	0.55032	0.460000	0.39030	ATC	A|0.943;G|0.057	0.057	strong		0.403	OR2B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040163.1		
ZNF341	84905	hgsc.bcm.edu	37	20	32379263	32379263	+	Silent	SNP	T	T	C	rs2626551	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:32379263T>C	ENST00000375200.1	+	15	2870	c.2505T>C	c.(2503-2505)gcT>gcC	p.A835A	RP4-553F4.6_ENST00000423074.1_RNA|RP4-553F4.6_ENST00000443171.1_RNA|RP4-553F4.6_ENST00000439444.1_RNA|ZNF341_ENST00000342427.2_Silent_p.A828A	NM_001282933.1	NP_001269862.1	Q9BYN7	ZN341_HUMAN	zinc finger protein 341	835					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						AGCTGCAGGCTGGGGCCGAGG	0.667													C|||	4074	0.813498	0.9743	0.7493	5008	,	,		15185	0.9355		0.6282	False		,,,				2504	0.7065				p.A828A		Atlas-SNP	.											ZNF341,rectum,carcinoma,0,1	ZNF341	73	1	0			c.T2484C						PASS	.	C		3999,403		1818,363,20	27.0	24.0	25.0		2484	-9.5	0.2	20	dbSNP_100	25	5544,3050		1820,1904,573	no	coding-synonymous	ZNF341	NM_032819.3		3638,2267,593	CC,CT,TT		35.4899,9.1549,26.5697		828/848	32379263	9543,3453	2201	4297	6498	SO:0001819	synonymous_variant	84905	exon15			GCAGGCTGGGGCC	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.2505T>C	20.37:g.32379263T>C		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	52	51	0.980769	NM_032819	A2RUF4|B2RXE5|B7ZM09|Q5JXM8|Q96ST5	Silent	SNP	ENST00000375200.1	37																																																																																				T|0.235;C|0.765	0.765	strong		0.667	ZNF341-201	KNOWN	basic	protein_coding	protein_coding			
PDE4DIP	9659	hgsc.bcm.edu	37	1	144952207	144952207	+	Missense_Mutation	SNP	C	C	T	rs3121544	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:144952207C>T	ENST00000369354.3	-	4	701	c.512G>A	c.(511-513)aGg>aAg	p.R171K	PDE4DIP_ENST00000369359.4_Missense_Mutation_p.R308K|PDE4DIP_ENST00000369349.3_Missense_Mutation_p.R171K|PDE4DIP_ENST00000313382.9_Missense_Mutation_p.R237K|PDE4DIP_ENST00000369347.4_Missense_Mutation_p.R171K|PDE4DIP_ENST00000369356.4_Missense_Mutation_p.R171K|PDE4DIP_ENST00000530740.1_Missense_Mutation_p.R308K|PDE4DIP_ENST00000369348.3_Missense_Mutation_p.R308K|PDE4DIP_ENST00000369351.3_Missense_Mutation_p.R171K			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	171			R -> K (in dbSNP:rs3121544).		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)		CTACTTGTCCCTCTGGGCCAG	0.527			T	PDGFRB	MPD																																p.R308K		Atlas-SNP	.		Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	.	PDE4DIP	817	.	0			c.G923A						PASS	.						157.0	166.0	163.0					1																	144952207		2203	4300	6503	SO:0001583	missense	9659	exon7			TTGTCCCTCTGGG	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.512G>A	1.37:g.144952207C>T	ENSP00000358360:p.Arg171Lys	Somatic	808	0	0		WXS	Illumina HiSeq	Phase_I	790	135	0.170886	NM_022359	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	.	.	.	.	.	.	.	.	.	.	C	14.59	2.580316	0.46006	.	.	ENSG00000178104	ENST00000313382;ENST00000369354;ENST00000369356;ENST00000530740;ENST00000369359;ENST00000369351;ENST00000369349;ENST00000530078;ENST00000534536;ENST00000369347;ENST00000369348	T;T;T;T;T;T;T;T;T;T	0.22336	5.06;5.27;5.31;5.15;5.15;4.23;4.24;1.96;3.05;3.06	4.53	0.392	0.16288	.	.	.	.	.	T	0.02649	0.0080	N	0.16656	0.425	0.80722	D	1	B;B;B	0.25441	0.0;0.126;0.004	B;B;B	0.17433	0.001;0.018;0.002	T	0.39099	-0.9630	9	0.05959	T	0.93	.	7.462	0.27300	0.0:0.5128:0.0:0.4872	rs3121544;rs45611337	171;237;171	Q5VU43-7;Q5VU43-3;Q5VU43	.;.;MYOME_HUMAN	K	237;171;171;308;308;171;171;237;174;171;308	ENSP00000327209:R237K;ENSP00000358360:R171K;ENSP00000358363:R171K;ENSP00000435654:R308K;ENSP00000358366:R308K;ENSP00000358357:R171K;ENSP00000358355:R171K;ENSP00000435920:R174K;ENSP00000358353:R171K;ENSP00000358354:R308K	ENSP00000327209:R237K	R	-	2	0	PDE4DIP	143663564	0.959000	0.32827	0.993000	0.49108	0.990000	0.78478	0.461000	0.21940	0.157000	0.19338	0.555000	0.69702	AGG	.	.	weak		0.527	PDE4DIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000038858.2	NM_022359	
COL13A1	1305	hgsc.bcm.edu	37	10	71678058	71678058	+	Silent	SNP	C	C	G	rs2274181	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:71678058C>G	ENST00000398978.3	+	19	1506	c.1014C>G	c.(1012-1014)gcC>gcG	p.A338A	COL13A1_ENST00000398969.3_Silent_p.A281A|COL13A1_ENST00000398974.3_Silent_p.A326A|COL13A1_ENST00000520133.1_Silent_p.A287A|COL13A1_ENST00000398966.3_Silent_p.A316A|COL13A1_ENST00000398972.3_Silent_p.A338A|COL13A1_ENST00000522165.1_Silent_p.A319A|COL13A1_ENST00000354547.3_Silent_p.A316A|COL13A1_ENST00000520267.1_Silent_p.A281A|COL13A1_ENST00000398964.3_Silent_p.A309A|COL13A1_ENST00000357811.3_Silent_p.A316A|COL13A1_ENST00000398971.3_Silent_p.A338A|COL13A1_ENST00000356340.3_Silent_p.A338A|COL13A1_ENST00000398973.3_Silent_p.A338A|COL13A1_ENST00000517713.1_Silent_p.A316A|COL13A1_ENST00000398968.3_Silent_p.A319A	NM_001130103.1	NP_001123575.1			collagen, type XIII, alpha 1											endometrium(5)|large_intestine(3)|lung(15)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	28						CCGGAATTGCCGTGGCTGGGA	0.597													C|||	1072	0.214058	0.0083	0.2752	5008	,	,		16449	0.2946		0.2217	False		,,,				2504	0.3579				p.A338A		Atlas-SNP	.											COL13A1_ENST00000398978,NS,carcinoma,+2,2	COL13A1	133	2	0			c.C1014G						PASS	.	C	,,,,,	169,3591		8,153,1719	47.0	50.0	49.0		1014,843,957,948,948,861	-8.5	0.0	10	dbSNP_100	49	1913,6315		216,1481,2417	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	COL13A1	NM_001130103.1,NM_080798.3,NM_080800.3,NM_080801.3,NM_080802.3,NM_080805.3	,,,,,	224,1634,4136	GG,GC,CC		23.2499,4.4947,17.3674	,,,,,	338/718,281/646,319/687,316/696,316/669,287/611	71678058	2082,9906	1880	4114	5994	SO:0001819	synonymous_variant	1305	exon19			AATTGCCGTGGCT	AJ293624	CCDS44419.1, CCDS44423.1, CCDS44424.1, CCDS44425.1, CCDS44427.1, CCDS44428.1, CCDS44423.2, CCDS44424.2, CCDS44425.2, CCDS44427.2, CCDS44428.2	10q22	2013-01-16			ENSG00000197467	ENSG00000197467		"""Collagens"""	2190	protein-coding gene	gene with protein product		120350					Standard	NM_001130103		Approved		uc001jql.3	Q5TAT6	OTTHUMG00000018394	ENST00000398978.3:c.1014C>G	10.37:g.71678058C>G		Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	35	18	0.514286	NM_001130103		Silent	SNP	ENST00000398978.3	37	CCDS44419.1																																																																																			C|0.804;G|0.196	0.196	strong		0.597	COL13A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048468.1	NM_005203	
CDC42BPG	55561	hgsc.bcm.edu	37	11	64601933	64601933	+	Silent	SNP	T	T	C	rs7933683	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:64601933T>C	ENST00000342711.5	-	19	2291	c.2292A>G	c.(2290-2292)acA>acG	p.T764T	CDC42BPG_ENST00000491280.1_5'Flank	NM_017525.2	NP_059995.2			CDC42 binding protein kinase gamma (DMPK-like)											central_nervous_system(1)|lung(3)	4						CCTGCACCTGTGTCAGCCGCT	0.706													C|||	1376	0.27476	0.0424	0.2147	5008	,	,		15170	0.4921		0.2575	False		,,,				2504	0.4254				p.T764T		Atlas-SNP	.											.	CDC42BPG	101	.	0			c.A2292G						PASS	.	C		284,3850		12,260,1795	6.0	7.0	6.0		2292	-6.1	0.8	11	dbSNP_116	6	1681,6531		171,1339,2596	no	coding-synonymous	CDC42BPG	NM_017525.2		183,1599,4391	CC,CT,TT		20.47,6.8699,15.9161		764/1552	64601933	1965,10381	2067	4106	6173	SO:0001819	synonymous_variant	55561	exon19			CACCTGTGTCAGC	AY648038	CCDS31601.1	11q13	2013-01-10			ENSG00000171219	ENSG00000171219		"""Pleckstrin homology (PH) domain containing"""	29829	protein-coding gene	gene with protein product		613991				9341881, 15194684	Standard	NM_017525		Approved	HSMDPKIN, MRCKgamma, DMPK2, kappa-200	uc001obs.4	Q6DT37	OTTHUMG00000045365	ENST00000342711.5:c.2292A>G	11.37:g.64601933T>C		Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	27	19	0.703704	NM_017525		Silent	SNP	ENST00000342711.5	37	CCDS31601.1																																																																																			T|0.722;C|0.278	0.278	strong		0.706	CDC42BPG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000105352.4	XM_290516	
HS3ST6	64711	hgsc.bcm.edu	37	16	1962132	1962132	+	Missense_Mutation	SNP	G	G	A	rs8055325	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:1962132G>A	ENST00000293937.3	-	2	487	c.488C>T	c.(487-489)gCc>gTc	p.A163V	HS3ST6_ENST00000443547.1_Missense_Mutation_p.A132V|HS3ST6_ENST00000454677.2_Missense_Mutation_p.A180V			Q96QI5	HS3S6_HUMAN	heparan sulfate (glucosamine) 3-O-sulfotransferase 6	163					carbohydrate metabolic process (GO:0005975)|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 1 activity (GO:0008467)			endometrium(2)|lung(2)	4						GCGGCGGGGGGCCTCTCGCGT	0.672													g|||	2379	0.47504	0.4418	0.3501	5008	,	,		12698	0.498		0.3867	False		,,,				2504	0.6759				p.A132V		Atlas-SNP	.											.	HS3ST6	26	.	0			c.C395T						PASS	.	G	VAL/ALA	1700,2684		315,1070,807	15.0	18.0	17.0		395	3.9	0.8	16	dbSNP_116	17	2972,5620		490,1992,1814	yes	missense	HS3ST6	NM_001009606.2	64	805,3062,2621	AA,AG,GG		34.5903,38.7774,36.0049	probably-damaging	132/312	1962132	4672,8304	2192	4296	6488	SO:0001583	missense	64711	exon2			CGGGGGGCCTCTC			16p13.3	2008-10-30	2003-06-11	2003-06-13	ENSG00000162040	ENSG00000162040		"""Sulfotransferases, membrane-bound"""	14178	protein-coding gene	gene with protein product			"""heparan sulfate (glucosamine) 3-O-sulfotransferase 5"""	HS3ST5		11157797	Standard	NM_001009606		Approved		uc002cnf.3	Q96QI5	OTTHUMG00000047860	ENST00000293937.3:c.488C>T	16.37:g.1962132G>A	ENSP00000293937:p.Ala163Val	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	69	43	0.623188	NM_001009606	Q96RX7	Missense_Mutation	SNP	ENST00000293937.3	37		958	0.43864468864468864	230	0.46747967479674796	125	0.3453038674033149	304	0.5314685314685315	299	0.3944591029023747	g	14.32	2.499876	0.44455	0.387774	0.345903	ENSG00000162040	ENST00000293937;ENST00000443547;ENST00000454677	T;T	0.57273	0.41;0.41	4.83	3.87	0.44632	Sulfotransferase domain (1);	0.051606	0.85682	D	0.000000	T	0.00012	0.0000	N	0.21194	0.64	0.09310	P	0.99999828591	P	0.40302	0.712	B	0.44315	0.446	T	0.40156	-0.9578	9	0.13108	T	0.6	.	11.9296	0.52839	0.0851:0.0:0.9149:0.0	rs8055325;rs8055325	163	Q96QI5	HS3S6_HUMAN	V	163;132;202	ENSP00000293937:A163V;ENSP00000390354:A132V	ENSP00000293937:A163V	A	-	2	0	HS3ST6	1902133	1.000000	0.71417	0.837000	0.33122	0.870000	0.49936	4.707000	0.61852	1.035000	0.39972	0.500000	0.49745	GCC	G|0.549;A|0.451	0.451	strong		0.672	HS3ST6-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001009606	
PCSK9	255738	hgsc.bcm.edu	37	1	55505668	55505668	+	Missense_Mutation	SNP	C	C	T	rs11583680	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:55505668C>T	ENST00000302118.5	+	1	448	c.158C>T	c.(157-159)gCc>gTc	p.A53V	PCSK9_ENST00000543384.1_5'Flank|PCSK9_ENST00000452118.2_Missense_Mutation_p.A53V	NM_174936.3	NP_777596.2	Q8NBP7	PCSK9_HUMAN	proprotein convertase subtilisin/kexin type 9	53			A -> V (polymorphism associated with reduced phosphorylation at Ser-47; dbSNP:rs11583680). {ECO:0000269|PubMed:12730697, ECO:0000269|PubMed:16465619, ECO:0000269|PubMed:22095935, ECO:0000269|Ref.4}.		apoptotic process (GO:0006915)|cellular response to insulin stimulus (GO:0032869)|cellular response to starvation (GO:0009267)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|kidney development (GO:0001822)|lipoprotein metabolic process (GO:0042157)|liver development (GO:0001889)|low-density lipoprotein particle receptor catabolic process (GO:0032802)|lysosomal transport (GO:0007041)|negative regulation of low-density lipoprotein particle clearance (GO:0010989)|negative regulation of receptor recycling (GO:0001920)|neurogenesis (GO:0022008)|neuron differentiation (GO:0030182)|phospholipid metabolic process (GO:0006644)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of receptor internalization (GO:0002092)|protein autoprocessing (GO:0016540)|proteolysis (GO:0006508)|regulation of low-density lipoprotein particle receptor catabolic process (GO:0032803)|regulation of neuron apoptotic process (GO:0043523)|regulation of receptor activity (GO:0010469)|triglyceride metabolic process (GO:0006641)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle (GO:0030134)|extracellular space (GO:0005615)|extrinsic component of external side of plasma membrane (GO:0031232)|Golgi apparatus (GO:0005794)|late endosome (GO:0005770)|lysosome (GO:0005764)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|rough endoplasmic reticulum (GO:0005791)	apolipoprotein binding (GO:0034185)|apolipoprotein receptor binding (GO:0034190)|low-density lipoprotein particle binding (GO:0030169)|low-density lipoprotein particle receptor binding (GO:0050750)|poly(A) RNA binding (GO:0044822)|protein self-association (GO:0043621)|serine-type endopeptidase activity (GO:0004252)|sodium channel inhibitor activity (GO:0019871)|very-low-density lipoprotein particle binding (GO:0034189)|very-low-density lipoprotein particle receptor binding (GO:0070326)			NS(2)|breast(2)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(1)|liver(2)|lung(4)|ovary(3)|prostate(3)|skin(1)|urinary_tract(1)	32						GACGGCCTGGCCGAAGCACCC	0.721													C|||	457	0.091254	0.0068	0.0735	5008	,	,		14703	0.1032		0.1342	False		,,,				2504	0.1616				p.A53V	Pancreas(137;1454 1827 5886 22361 42375)	Atlas-SNP	.											PCSK9,NS,carcinoma,0,1	PCSK9	76	1	0			c.C158T						PASS	.	C	VAL/ALA	126,4246		2,122,2062	32.0	26.0	28.0		158	2.2	0.0	1	dbSNP_120	28	1111,7427		57,997,3215	yes	missense	PCSK9	NM_174936.3	64	59,1119,5277	TT,TC,CC		13.0124,2.882,9.5817	benign	53/693	55505668	1237,11673	2186	4269	6455	SO:0001583	missense	255738	exon1			GCCTGGCCGAAGC	AX207686	CCDS603.1	1p34.1-p32	2014-09-17	2003-05-13		ENSG00000169174	ENSG00000169174			20001	protein-coding gene	gene with protein product		607786	"""hypercholesterolemia, autosomal dominant 3"""	HCHOLA3		12552133, 12730697	Standard	NM_174936		Approved	NARC-1, FH3	uc001cyf.2	Q8NBP7	OTTHUMG00000008136	ENST00000302118.5:c.158C>T	1.37:g.55505668C>T	ENSP00000303208:p.Ala53Val	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	102	55	0.539216	NM_174936	A8T640|C0JYY9|Q5PSM5|Q5SZQ2	Missense_Mutation	SNP	ENST00000302118.5	37	CCDS603.1	197	0.0902014652014652	4	0.008130081300813009	32	0.08839779005524862	65	0.11363636363636363	96	0.1266490765171504	C	8.941	0.965854	0.18659	0.02882	0.130124	ENSG00000169174	ENST00000302118;ENST00000452118	T;T	0.72167	-0.57;-0.63	3.18	2.23	0.28157	.	1.052620	0.07640	N	0.930071	T	0.00580	0.0019	N	0.08118	0	0.58432	P	5.999999999950489E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.06058	-1.0848	9	0.23302	T	0.38	0.36	4.0426	0.09758	0.2278:0.6406:0.0:0.1316	rs11583680;rs11583680	53	Q8NBP7	PCSK9_HUMAN	V	53	ENSP00000303208:A53V;ENSP00000401598:A53V	ENSP00000303208:A53V	A	+	2	0	PCSK9	55278256	0.000000	0.05858	0.000000	0.03702	0.709000	0.40893	0.283000	0.18846	0.478000	0.27488	0.313000	0.20887	GCC	C|0.912;T|0.088	0.088	strong		0.721	PCSK9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022280.1	NM_174936	
ZDHHC13	54503	hgsc.bcm.edu	37	11	19184916	19184916	+	Missense_Mutation	SNP	A	A	G	rs12798330	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:19184916A>G	ENST00000446113.2	+	11	1296	c.1175A>G	c.(1174-1176)tAt>tGt	p.Y392C	ZDHHC13_ENST00000399351.3_Missense_Mutation_p.Y262C	NM_019028.2	NP_061901.2	Q8IUH4	ZDH13_HUMAN	zinc finger, DHHC-type containing 13	392			Y -> C (in dbSNP:rs12798330).		metabolic process (GO:0008152)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi-associated vesicle membrane (GO:0030660)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)	magnesium ion transmembrane transporter activity (GO:0015095)|palmitoyltransferase activity (GO:0016409)|protein-cysteine S-palmitoyltransferase activity (GO:0019706)|signal transducer activity (GO:0004871)|zinc ion binding (GO:0008270)			NS(1)|kidney(1)|lung(2)|skin(1)|upper_aerodigestive_tract(1)	6						TACTTTTTCTATAAGACTTGG	0.373													A|||	42	0.00838658	0.0008	0.0115	5008	,	,		16631	0.0		0.0278	False		,,,				2504	0.0051				p.Y392C		Atlas-SNP	.											.	ZDHHC13	40	.	0			c.A1175G						PASS	.	A	CYS/TYR,CYS/TYR	27,3561		0,27,1767	73.0	68.0	70.0		785,1175	5.3	1.0	11	dbSNP_121	70	295,7851		7,281,3785	yes	missense,missense	ZDHHC13	NM_001001483.2,NM_019028.2	194,194	7,308,5552	GG,GA,AA		3.6214,0.7525,2.7442	probably-damaging,probably-damaging	262/493,392/623	19184916	322,11412	1794	4073	5867	SO:0001583	missense	54503	exon11			TTTTCTATAAGAC	AB024495	CCDS44550.1, CCDS44551.1	11p15.1	2013-01-10			ENSG00000177054	ENSG00000177054		"""Zinc fingers, DHHC-type"", ""Ankyrin repeat domain containing"""	18413	protein-coding gene	gene with protein product		612815				18794299	Standard	NM_001001483		Approved	FLJ10852, FLJ10941, HIP14L	uc001mpi.3	Q8IUH4	OTTHUMG00000166099	ENST00000446113.2:c.1175A>G	11.37:g.19184916A>G	ENSP00000400113:p.Tyr392Cys	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	102	21	0.205882	NM_019028	Q7Z2D3|Q86VK2|Q9NV30|Q9NV99	Missense_Mutation	SNP	ENST00000446113.2	37	CCDS44550.1	18	0.008241758241758242	1	0.0020325203252032522	2	0.0055248618784530384	0	0.0	15	0.01978891820580475	A	18.10	3.549170	0.65311	0.007525	0.036214	ENSG00000177054	ENST00000446113;ENST00000399351	T;T	0.25579	1.79;1.79	5.32	5.32	0.75619	.	0.000000	0.52532	D	0.000066	T	0.19485	0.0468	M	0.77103	2.36	0.48762	D	0.999702	D	0.89917	1.0	D	0.72982	0.979	T	0.21075	-1.0256	10	0.45353	T	0.12	-4.1355	13.5321	0.61627	1.0:0.0:0.0:0.0	rs12798330;rs52798981;rs12798330	392	Q8IUH4	ZDH13_HUMAN	C	392;262	ENSP00000400113:Y392C;ENSP00000382288:Y262C	ENSP00000382288:Y262C	Y	+	2	0	ZDHHC13	19141492	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	5.655000	0.67981	2.136000	0.66102	0.533000	0.62120	TAT	A|0.987;G|0.013	0.013	strong		0.373	ZDHHC13-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387821.1	NM_019028	
FAM120B	84498	hgsc.bcm.edu	37	6	170627797	170627797	+	Missense_Mutation	SNP	A	A	G	rs9366138	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:170627797A>G	ENST00000476287.1	+	2	1427	c.1319A>G	c.(1318-1320)tAt>tGt	p.Y440C	FAM120B_ENST00000537664.1_Missense_Mutation_p.Y463C|FAM120B_ENST00000540480.1_Missense_Mutation_p.Y452C|FAM120B_ENST00000252510.9_Intron	NM_032448.1	NP_115824.1	Q96EK7	F120B_HUMAN	family with sequence similarity 120B	440			Y -> C (in dbSNP:rs9366138).		cell differentiation (GO:0030154)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(11)|liver(1)|lung(15)|ovary(1)|prostate(2)|skin(2)	44		Breast(66;0.000338)|Esophageal squamous(34;0.241)		OV - Ovarian serous cystadenocarcinoma(33;3.94e-22)|BRCA - Breast invasive adenocarcinoma(81;6.47e-06)|GBM - Glioblastoma multiforme(31;0.0899)		GTTCCCATGTATACAGACTCT	0.502													A|||	648	0.129393	0.0711	0.1412	5008	,	,		20067	0.1885		0.1252	False		,,,				2504	0.1431				p.Y440C		Atlas-SNP	.											.	FAM120B	108	.	0			c.A1319G						PASS	.	A	CYS/TYR	390,4016	194.0+/-219.0	20,350,1833	180.0	201.0	194.0		1319	-4.0	0.0	6	dbSNP_119	194	1200,7400	244.3+/-273.6	92,1016,3192	no	missense	FAM120B	NM_032448.1	194	112,1366,5025	GG,GA,AA		13.9535,8.8516,12.2251	benign	440/911	170627797	1590,11416	2203	4300	6503	SO:0001583	missense	84498	exon2			CCATGTATACAGA	AB058741	CCDS5314.1, CCDS75555.1	6q27	2011-04-13	2006-07-04	2006-07-04	ENSG00000112584	ENSG00000112584			21109	protein-coding gene	gene with protein product	"""PPARgamma constitutive coactivator 1"", ""constitutive coactivator of PPAR-gamma"""	612266	"""KIAA1838"""	KIAA1838		14585507	Standard	NM_032448		Approved	PGCC1, CCPG	uc003qxp.3	Q96EK7	OTTHUMG00000016080	ENST00000476287.1:c.1319A>G	6.37:g.170627797A>G	ENSP00000417970:p.Tyr440Cys	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	35	11	0.314286	NM_032448	B4DL34|Q86V68|Q96JI9	Missense_Mutation	SNP	ENST00000476287.1	37	CCDS5314.1	313	0.1433150183150183	47	0.09552845528455285	43	0.11878453038674033	125	0.21853146853146854	98	0.12928759894459102	A	1.156	-0.645179	0.03531	0.088516	0.139535	ENSG00000112584	ENST00000540480;ENST00000537664;ENST00000476287	T;T;T	0.07908	3.16;3.15;3.16	3.11	-3.95	0.04118	.	1.401140	0.04088	N	0.310871	T	0.00440	0.0014	N	0.00159	-1.955	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.47509	-0.9112	9	0.52906	T	0.07	.	1.1118	0.01706	0.4401:0.1202:0.1967:0.243	rs9366138	440;440	Q96EK7;F2Z2E1	F120B_HUMAN;.	C	452;463;440	ENSP00000444125:Y452C;ENSP00000440125:Y463C;ENSP00000417970:Y440C	ENSP00000436640:Y440C	Y	+	2	0	FAM120B	170469722	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.621000	0.00412	-1.599000	0.01605	-0.808000	0.03180	TAT	A|0.870;G|0.130	0.130	strong		0.502	FAM120B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000043259.2	NM_032448	
PASK	23178	hgsc.bcm.edu	37	2	242065624	242065624	+	Silent	SNP	A	A	G	rs2240541	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:242065624A>G	ENST00000405260.1	-	10	3404	c.2706T>C	c.(2704-2706)gaT>gaC	p.D902D	PASK_ENST00000403638.3_Silent_p.D902D|PASK_ENST00000358649.4_Silent_p.D902D|PASK_ENST00000234040.4_Silent_p.D902D|PASK_ENST00000544142.1_Silent_p.D716D|PASK_ENST00000539818.1_Silent_p.D686D	NM_001252120.1	NP_001239049.1	Q96RG2	PASK_HUMAN	PAS domain containing serine/threonine kinase	902					negative regulation of glycogen biosynthetic process (GO:0045719)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of energy homeostasis (GO:2000505)|regulation of glucagon secretion (GO:0070092)|regulation of respiratory gaseous exchange (GO:0043576)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	ATP binding (GO:0005524)|phosphatidylinositol binding (GO:0035091)|protein serine/threonine kinase activity (GO:0004674)|signal transducer activity (GO:0004871)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(6)|lung(20)|ovary(4)|prostate(4)|skin(1)|stomach(1)|urinary_tract(2)	53		all_cancers(19;4.46e-39)|all_epithelial(40;1.34e-17)|Breast(86;1.53e-05)|Renal(207;0.00179)|all_lung(227;0.00481)|Lung NSC(271;0.017)|Ovarian(221;0.0228)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;1.34e-31)|all cancers(36;1e-28)|OV - Ovarian serous cystadenocarcinoma(60;3.53e-14)|Kidney(56;4.31e-09)|KIRC - Kidney renal clear cell carcinoma(57;4.35e-08)|BRCA - Breast invasive adenocarcinoma(100;5.64e-06)|Lung(119;0.000596)|LUSC - Lung squamous cell carcinoma(224;0.00481)|Colorectal(34;0.014)|COAD - Colon adenocarcinoma(134;0.0968)		GCCGTAAGCCATCTCGATGGT	0.642													G|||	872	0.174121	0.4244	0.1153	5008	,	,		17498	0.124		0.0696	False		,,,				2504	0.0368				p.D902D		Atlas-SNP	.											.	PASK	230	.	0			c.T2706C						PASS	.	G		1774,2632	637.0+/-396.7	365,1044,794	63.0	49.0	54.0		2706	-3.9	0.0	2	dbSNP_98	54	648,7952	785.7+/-407.6	25,598,3677	no	coding-synonymous	PASK	NM_015148.2		390,1642,4471	GG,GA,AA		7.5349,40.2633,18.6222		902/1324	242065624	2422,10584	2203	4300	6503	SO:0001819	synonymous_variant	23178	exon10			TAAGCCATCTCGA	U79240	CCDS2545.1, CCDS58758.1, CCDS58759.1	2q37.3	2008-05-23			ENSG00000115687	ENSG00000115687			17270	protein-coding gene	gene with protein product		607505				11688972, 11459942, 15148392	Standard	NM_001252119		Approved	PASKIN, KIAA0135, STK37	uc010fzl.2	Q96RG2	OTTHUMG00000133392	ENST00000405260.1:c.2706T>C	2.37:g.242065624A>G		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	88	44	0.5	NM_015148	G5E9F1|Q05BE4|Q68DY3|Q6GSJ5|Q86XH6|Q99763|Q9UFR7	Silent	SNP	ENST00000405260.1	37	CCDS2545.1																																																																																			A|0.812;G|0.188	0.188	strong		0.642	PASK-003	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000323753.1	NM_015148	
VTI1A	143187	hgsc.bcm.edu	37	10	114427978	114427978	+	Splice_Site	SNP	G	G	A	rs17353359	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:114427978G>A	ENST00000393077.2	+	6	545	c.429G>A	c.(427-429)gaG>gaA	p.E143E	VTI1A_ENST00000432306.1_Splice_Site_p.E143E	NM_145206.2	NP_660207.2	Q96AJ9	VTI1A_HUMAN	vesicle transport through interaction with t-SNAREs 1A	143					intracellular protein transport (GO:0006886)|retrograde transport, endosome to Golgi (GO:0042147)	clathrin-coated vesicle (GO:0030136)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|neuron projection terminus (GO:0044306)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|SNARE complex (GO:0031201)|synaptic vesicle (GO:0008021)	SNAP receptor activity (GO:0005484)		VTI1A/TCF7L2(8)	breast(1)|large_intestine(1)|lung(2)|ovary(1)|skin(1)	6		Colorectal(252;0.0314)|Breast(234;0.183)		Epithelial(162;0.0126)|all cancers(201;0.0487)		TTTCCGTAGAGCAAATTGGTC	0.348			T	TCF7L2	colorectal								G|||	49	0.00978435	0.0023	0.0173	5008	,	,		20168	0.0		0.0308	False		,,,				2504	0.0031				p.E143E		Atlas-SNP	.		Dom	yes		10	10q25.2	143187	vesicle transport through interaction with t-SNAREs homolog 1A		E	.	VTI1A	15	.	0			c.G429A						PASS	.	G		20,4386	27.2+/-55.0	0,20,2183	83.0	77.0	79.0		429	0.2	1.0	10	dbSNP_123	79	230,8368	94.2+/-156.2	3,224,4072	yes	coding-synonymous-near-splice	VTI1A	NM_145206.2		3,244,6255	AA,AG,GG		2.675,0.4539,1.9225		143/218	114427978	250,12754	2203	4299	6502	SO:0001630	splice_region_variant	143187	exon6			CGTAGAGCAAATT	BC017052	CCDS7575.2	10q25.2	2012-12-10	2012-12-10		ENSG00000151532	ENSG00000151532			17792	protein-coding gene	gene with protein product		614316	"""vesicle transport through interaction with t-SNAREs homolog 1A (yeast)"""			9446565	Standard	NM_145206		Approved	MVti1, Vti1a, Vti1-rp2	uc001kzz.3	Q96AJ9	OTTHUMG00000019063	ENST00000393077.2:c.428-1G>A	10.37:g.114427978G>A		Somatic	255	0	0		WXS	Illumina HiSeq	Phase_I	193	84	0.435233	NM_145206	A2A307|B4E137|Q5W0D7	Silent	SNP	ENST00000393077.2	37	CCDS7575.2																																																																																			G|0.980;A|0.020	0.020	strong		0.348	VTI1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050397.2		Silent
PTPRN2	5799	hgsc.bcm.edu	37	7	157931119	157931119	+	Silent	SNP	A	A	G	rs1130500	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:157931119A>G	ENST00000389418.4	-	7	1008	c.999T>C	c.(997-999)gcT>gcC	p.A333A	PTPRN2_ENST00000409483.1_Silent_p.A295A|PTPRN2_ENST00000389416.4_Silent_p.A316A|PTPRN2_ENST00000389413.3_Silent_p.A333A|PTPRN2_ENST00000404321.2_Silent_p.A356A	NM_002847.3	NP_002838.2	Q92932	PTPR2_HUMAN	protein tyrosine phosphatase, receptor type, N polypeptide 2	333					negative regulation of GTPase activity (GO:0034260)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	endoplasmic reticulum lumen (GO:0005788)|integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)|secretory granule (GO:0030141)|terminal bouton (GO:0043195)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|liver(1)|lung(42)|ovary(4)|pleura(1)|prostate(2)|skin(10)|upper_aerodigestive_tract(1)	86	all_neural(206;0.181)	all_cancers(7;8.99e-13)|all_epithelial(9;2.4e-06)|all_hematologic(28;0.0155)|Breast(660;0.132)	OV - Ovarian serous cystadenocarcinoma(82;0.00463)	STAD - Stomach adenocarcinoma(7;0.0875)		CCATCAGCTCAGCCATGCCGT	0.657													G|||	1897	0.378794	0.4516	0.4409	5008	,	,		18883	0.4663		0.2903	False		,,,				2504	0.2372				p.A333A		Atlas-SNP	.											.	PTPRN2	243	.	0			c.T999C						PASS	.		,,	1974,2432	617.8+/-393.0	443,1088,672	71.0	73.0	72.0		999,948,999	-7.1	0.0	7	dbSNP_86	72	2540,6060	691.6+/-404.5	361,1818,2121	no	coding-synonymous,coding-synonymous,coding-synonymous	PTPRN2	NM_002847.3,NM_130842.2,NM_130843.2	,,	804,2906,2793	GG,GA,AA		29.5349,44.8025,34.7071	,,	333/1016,316/999,333/987	157931119	4514,8492	2203	4300	6503	SO:0001819	synonymous_variant	5799	exon7			CAGCTCAGCCATG	AB002385	CCDS5947.1, CCDS5948.1, CCDS5949.1	7q36	2011-06-09			ENSG00000155093	ENSG00000155093		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"""	9677	protein-coding gene	gene with protein product	"""IAR PTPRP"""	601698				8954911, 9220540	Standard	NM_130842		Approved	KIAA0387, phogrin, ICAAR, IA-2beta	uc003wno.3	Q92932	OTTHUMG00000152646	ENST00000389418.4:c.999T>C	7.37:g.157931119A>G		Somatic	124	1	0.00806452		WXS	Illumina HiSeq	Phase_I	91	90	0.989011	NM_130843	E9PC57|Q8N4I5|Q92662|Q9Y4F8|Q9Y4I6	Silent	SNP	ENST00000389418.4	37	CCDS5947.1																																																																																			A|0.625;G|0.375	0.375	strong		0.657	PTPRN2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000353214.1		
KRTAP10-10	353333	hgsc.bcm.edu	37	21	46057711	46057711	+	Missense_Mutation	SNP	G	G	C	rs4818948	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:46057711G>C	ENST00000380095.1	+	1	439	c.377G>C	c.(376-378)tGc>tCc	p.C126S	TSPEAR_ENST00000323084.4_Intron	NM_181688.1	NP_859016.1	P60014	KR10A_HUMAN	keratin associated protein 10-10	126	15 X 5 AA repeats of C-C-X(3).		C -> S (in dbSNP:rs4818948).			keratin filament (GO:0045095)		p.C126S(1)		NS(1)|endometrium(2)|kidney(1)|lung(6)|prostate(1)|skin(2)	13						TCCCCTTCATGCTGCCAGCAG	0.612													G|||	1378	0.27516	0.4781	0.2233	5008	,	,		22902	0.0526		0.2406	False		,,,				2504	0.3027				p.C126S		Atlas-SNP	.											KRTAP10-10,NS,carcinoma,0,1	KRTAP10-10	37	1	1	Substitution - Missense(1)	prostate(1)	c.G377C						scavenged	.	G	,SER/CYS	1974,2432	555.8+/-379.4	449,1076,678	260.0	233.0	242.0		,377	2.2	0.7	21	dbSNP_111	242	2165,6435	369.3+/-335.4	281,1603,2416	yes	intron,missense	TSPEAR,KRTAP10-10	NM_144991.2,NM_181688.1	,112	730,2679,3094	CC,CG,GG		25.1744,44.8025,31.8238	,possibly-damaging	,126/252	46057711	4139,8867	2203	4300	6503	SO:0001583	missense	353333	exon1			CTTCATGCTGCCA	AJ566387	CCDS33585.1	21q22.3	2006-03-13			ENSG00000221859	ENSG00000221859		"""Keratin associated proteins"""	22972	protein-coding gene	gene with protein product							Standard	NM_181688		Approved	KAP10.10, KAP18.10, KRTAP18-10	uc002zfq.3	P60014	OTTHUMG00000057631	ENST00000380095.1:c.377G>C	21.37:g.46057711G>C	ENSP00000369438:p.Cys126Ser	Somatic	128	1	0.0078125		WXS	Illumina HiSeq	Phase_I	156	44	0.282051	NM_181688		Missense_Mutation	SNP	ENST00000380095.1	37	CCDS33585.1	539	0.2467948717948718	232	0.4715447154471545	88	0.2430939226519337	31	0.05419580419580419	188	0.24802110817941952	g	9.775	1.173863	0.21704	0.448025	0.251744	ENSG00000221859	ENST00000380095	T	0.01446	4.88	3.08	2.19	0.27852	.	.	.	.	.	T	0.00012	0.0000	M	0.92317	3.295	0.35991	P	0.163292	B	0.26708	0.157	B	0.30316	0.114	T	0.23904	-1.0175	8	0.40728	T	0.16	.	4.9606	0.14065	0.1295:0.2156:0.6549:0.0	rs4818948;rs52837069;rs58818342	126	P60014	KR10A_HUMAN	S	126	ENSP00000369438:C126S	ENSP00000369438:C126S	C	+	2	0	KRTAP10-10	44882139	0.467000	0.25831	0.745000	0.31077	0.268000	0.26511	2.512000	0.45485	0.411000	0.25702	-0.374000	0.07098	TGC	G|0.711;C|0.289	0.289	strong		0.612	KRTAP10-10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128034.1	NM_181688	
MCMBP	79892	hgsc.bcm.edu	37	10	121596498	121596498	+	Silent	SNP	C	C	T	rs34118671	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:121596498C>T	ENST00000360003.3	-	13	1627	c.1458G>A	c.(1456-1458)caG>caA	p.Q486Q	MCMBP_ENST00000369077.3_Silent_p.Q484Q|MCMBP_ENST00000466047.1_5'UTR	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	486					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						AATCCACCTTCTGCCACGTTA	0.438													C|||	474	0.0946486	0.1142	0.098	5008	,	,		19821	0.001		0.1123	False		,,,				2504	0.1442				p.Q486Q		Atlas-SNP	.											.	MCMBP	49	.	0			c.G1458A						PASS	.	C		516,3890	238.0+/-249.6	27,462,1714	157.0	130.0	139.0		1458	4.3	1.0	10	dbSNP_126	139	1032,7568	219.7+/-257.6	69,894,3337	no	coding-synonymous	MCMBP	NM_024834.2		96,1356,5051	TT,TC,CC		12.0,11.7113,11.9022		486/643	121596498	1548,11458	2203	4300	6503	SO:0001819	synonymous_variant	79892	exon13			CACCTTCTGCCAC	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	ENST00000360003.3:c.1458G>A	10.37:g.121596498C>T		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	56	22	0.392857	NM_024834	B3KSP7|Q6IA56|Q9BVT9|Q9H916	Silent	SNP	ENST00000360003.3	37	CCDS7617.1																																																																																			C|0.887;T|0.113	0.113	strong		0.438	MCMBP-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000050684.1	NM_024834	
WDR90	197335	hgsc.bcm.edu	37	16	708308	708308	+	Silent	SNP	G	G	A	rs369151964		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:708308G>A	ENST00000293879.4	+	22	2730	c.2730G>A	c.(2728-2730)gtG>gtA	p.V910V	WDR90_ENST00000549091.1_Silent_p.V910V|LA16c-349E10.1_ENST00000573609.1_RNA			Q96KV7	WDR90_HUMAN	WD repeat domain 90	910										endometrium(4)|kidney(3)|large_intestine(2)|lung(22)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	37		Hepatocellular(780;0.0218)				ACAGAGTCGTGGTGCTGGATG	0.677																																					p.V910V		Atlas-SNP	.											.	WDR90	107	.	0			c.G2730A						PASS	.						57.0	63.0	61.0					16																	708308		2141	4248	6389	SO:0001819	synonymous_variant	197335	exon22			AGTCGTGGTGCTG	AB067511	CCDS42092.1	16p13.3	2013-01-09			ENSG00000161996	ENSG00000161996		"""WD repeat domain containing"""	26960	protein-coding gene	gene with protein product			"""chromosome 16 open reading frame 17"", ""chromosome 16 open reading frame 15"", ""chromosome 16 open reading frame 16"", ""chromosome 16 open reading frame 19"", ""chromosome 16 open reading frame 18"""	C16orf17, C16orf15, C16orf16, C16orf19, C16orf18		11572484, 11157797	Standard	XM_005255160		Approved	FLJ36483, KIAA1924	uc002cii.1	Q96KV7	OTTHUMG00000048040	ENST00000293879.4:c.2730G>A	16.37:g.708308G>A		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	70	27	0.385714	NM_145294	Q0VA87|Q0VA88|Q6P048|Q6ZMS1|Q6ZTH1|Q8N202|Q8N221|Q8NBB8|Q96PW4|Q96S18	Silent	SNP	ENST00000293879.4	37	CCDS42092.1																																																																																			.	.	alt		0.677	WDR90-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000404335.1	NM_145294	
IRG1	730249	hgsc.bcm.edu	37	13	77527764	77527764	+	Silent	SNP	T	T	A	rs17385627	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:77527764T>A	ENST00000377462.1	+	3	266	c.204T>A	c.(202-204)gtT>gtA	p.V68V	IRG1_ENST00000449753.1_Silent_p.V68V	NM_001258406.1	NP_001245335.1	A6NK06	IRG1_HUMAN	immunoresponsive 1 homolog (mouse)	68					cellular response to interferon-beta (GO:0035458)|cellular response to interferon-gamma (GO:0071346)|cellular response to interleukin-1 (GO:0071347)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to molecule of bacterial origin (GO:0071219)|cellular response to progesterone stimulus (GO:0071393)|cellular response to tumor necrosis factor (GO:0071356)|defense response (GO:0006952)|embryo implantation (GO:0007566)|inflammatory response (GO:0006954)|metabolic process (GO:0008152)|negative regulation of inflammatory response (GO:0050728)|negative regulation of innate immune response (GO:0045824)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of toll-like receptor 2 signaling pathway (GO:0034136)|negative regulation of toll-like receptor 4 signaling pathway (GO:0034144)|negative regulation of type I interferon production (GO:0032480)|positive regulation of antimicrobial humoral response (GO:0002760)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|propionate catabolic process (GO:0019543)|tolerance induction to lipopolysaccharide (GO:0072573)	mitochondrion (GO:0005739)	2-methylcitrate dehydratase activity (GO:0047547)|aconitate decarboxylase activity (GO:0047613)										CCAGCACTGTTTGGGGTCAGC	0.428													T|||	654	0.130591	0.0893	0.2089	5008	,	,		20518	0.1776		0.0905	False		,,,				2504	0.1237				p.V64V		Atlas-SNP	.											.	IRG1	1	.	0			c.T192A						PASS	.																																			SO:0001819	synonymous_variant	730249	exon2			CACTGTTTGGGGT		CCDS58299.1	13q22.3	2013-04-29			ENSG00000102794	ENSG00000102794			33904	protein-coding gene	gene with protein product		615275				23610393	Standard	NM_001258406		Approved		uc031qmi.1	A6NK06	OTTHUMG00000017098	ENST00000377462.1:c.204T>A	13.37:g.77527764T>A		Somatic	191	0	0		WXS	Illumina HiSeq	Phase_I	148	64	0.432432	NM_001258406		Silent	SNP	ENST00000377462.1	37	CCDS58299.1																																																																																			T|0.884;A|0.116	0.116	strong		0.428	IRG1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045311.1	XM_001133269	
MKI67	4288	hgsc.bcm.edu	37	10	129899922	129899922	+	Missense_Mutation	SNP	T	T	C	rs34750407	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:129899922T>C	ENST00000368654.3	-	14	9680	c.9305A>G	c.(9304-9306)gAa>gGa	p.E3102G	MKI67_ENST00000368653.3_Missense_Mutation_p.E2742G	NM_002417.4	NP_002408.3	P46013	KI67_HUMAN	marker of proliferation Ki-67	3102			E -> G (in dbSNP:rs34750407).		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)				TATTTGCTGTTCTGCCTCAGT	0.373													T|||	436	0.0870607	0.2042	0.0346	5008	,	,		19634	0.1052		0.0199	False		,,,				2504	0.0164				p.E3102G		Atlas-SNP	.											MKI67,right_upper_lobe,carcinoma,+1,1	MKI67	363	1	0			c.A9305G						PASS	.	T	GLY/GLU,GLY/GLU	798,3606		72,654,1476	69.0	73.0	72.0		8225,9305	1.6	0.0	10	dbSNP_126	72	236,8360		3,230,4065	yes	missense,missense	MKI67	NM_001145966.1,NM_002417.4	98,98	75,884,5541	CC,CT,TT		2.7455,18.1199,7.9538	possibly-damaging,possibly-damaging	2742/2897,3102/3257	129899922	1034,11966	2202	4298	6500	SO:0001583	missense	4288	exon14			TGCTGTTCTGCCT	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.9305A>G	10.37:g.129899922T>C	ENSP00000357643:p.Glu3102Gly	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	99	43	0.434343	NM_002417	Q5VWH2	Missense_Mutation	SNP	ENST00000368654.3	37	CCDS7659.1	165	0.07554945054945054	76	0.15447154471544716	10	0.027624309392265192	62	0.10839160839160839	17	0.022427440633245383	T	10.17	1.276854	0.23307	0.181199	0.027455	ENSG00000148773	ENST00000368654;ENST00000368653;ENST00000537609	T;T	0.01406	4.97;4.93	3.98	1.57	0.23409	.	0.916850	0.09054	N	0.855383	T	0.00012	0.0000	L	0.27053	0.805	0.80722	P	0.0	D;B	0.54964	0.969;0.104	P;B	0.53313	0.723;0.056	T	0.54268	-0.8319	9	0.46703	T	0.11	.	3.2652	0.06863	0.2033:0.1121:0.0:0.6846	rs34750407	2742;3102	P46013-2;P46013	.;KI67_HUMAN	G	3102;2742;3101	ENSP00000357643:E3102G;ENSP00000357642:E2742G	ENSP00000357642:E2742G	E	-	2	0	MKI67	129789912	0.000000	0.05858	0.001000	0.08648	0.005000	0.04900	0.173000	0.16724	0.197000	0.20387	-0.371000	0.07208	GAA	T|0.926;C|0.074	0.074	strong		0.373	MKI67-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050999.1	NM_002417	
COLGALT1	79709	hgsc.bcm.edu	37	19	17670201	17670201	+	Silent	SNP	C	C	T	rs62119894	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:17670201C>T	ENST00000252599.4	+	2	462	c.342C>T	c.(340-342)tcC>tcT	p.S114S		NM_024656.2	NP_078932.2	Q8NBJ5	GT251_HUMAN	collagen beta(1-O)galactosyltransferase 1	114					extracellular matrix organization (GO:0030198)|lipopolysaccharide biosynthetic process (GO:0009103)	endoplasmic reticulum lumen (GO:0005788)|membrane (GO:0016020)	procollagen galactosyltransferase activity (GO:0050211)										TGTACCATTCCGTGGAGTGGC	0.597													c|||	472	0.0942492	0.0053	0.2277	5008	,	,		15298	0.0714		0.0616	False		,,,				2504	0.1769				p.S114S		Atlas-SNP	.											.	.	.	.	0			c.C342T						PASS	.	C		63,4225		0,63,2081	123.0	93.0	103.0		342	-6.4	0.9	19	dbSNP_129	103	453,7929		8,437,3746	no	coding-synonymous	GLT25D1	NM_024656.2		8,500,5827	TT,TC,CC		5.4044,1.4692,4.0726		114/623	17670201	516,12154	2144	4191	6335	SO:0001819	synonymous_variant	79709	exon2			CCATTCCGTGGAG	AK075541	CCDS12363.1	19p13.11	2013-02-27	2013-02-27	2013-02-27	ENSG00000130309	ENSG00000130309			26182	protein-coding gene	gene with protein product			"""glycosyltransferase 25 domain containing 1"""	GLT25D1		19075007	Standard	NM_024656		Approved	FLJ22329	uc002nhc.1	Q8NBJ5		ENST00000252599.4:c.342C>T	19.37:g.17670201C>T		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	103	53	0.514563	NM_024656	Q8NC64	Silent	SNP	ENST00000252599.4	37	CCDS12363.1																																																																																			C|0.942;T|0.058	0.058	strong		0.597	COLGALT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464216.1	NM_024656	
MUC7	4589	hgsc.bcm.edu	37	4	71339723	71339723	+	Splice_Site	SNP	G	G	A	rs2306949	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:71339723G>A	ENST00000304887.5	+	2	175		c.e2-1		MUC7_ENST00000514512.1_Intron|MUC7_ENST00000456088.1_Splice_Site|MUC7_ENST00000413702.1_Splice_Site	NM_152291.2	NP_689504.2	Q8TAX7	MUC7_HUMAN	mucin 7, secreted						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)			GCTTTTCCCAGGAGACATCAG	0.373													G|||	1045	0.208666	0.2844	0.1354	5008	,	,		19158	0.2044		0.1252	False		,,,				2504	0.2485				.		Atlas-SNP	.											.	MUC7	91	.	0			.						PASS	.	G	,,	1209,3197	420.0+/-338.9	165,879,1159	107.0	105.0	106.0		,,	1.9	0.1	4	dbSNP_100	106	1341,7259	259.1+/-282.5	95,1151,3054	yes	splice-3,splice-3,splice-3	MUC7	NM_001145006.1,NM_001145007.1,NM_152291.2	,,	260,2030,4213	AA,AG,GG		15.593,27.4399,19.6063	,,	,,	71339723	2550,10456	2203	4300	6503	SO:0001630	splice_region_variant	4589	.			TTCCCAGGAGACA	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.-15-1G>A	4.37:g.71339723G>A		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	55	33	0.6	.	Q9UCD7|Q9UCD8	Splice_Site	SNP	ENST00000304887.5	37	CCDS3541.1																																																																																			G|0.840;A|0.160	0.160	strong		0.373	MUC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252168.2	NM_152291	Intron
MUC4	4585	hgsc.bcm.edu	37	3	195507379	195507379	+	Missense_Mutation	SNP	G	G	C	rs371423143		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195507379G>C	ENST00000463781.3	-	2	11531	c.11072C>G	c.(11071-11073)aCa>aGa	p.T3691R	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_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	63	0	0		WXS	Illumina HiSeq	Phase_I	43	16	0.372093	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	
LCT	3938	hgsc.bcm.edu	37	2	136547204	136547204	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:136547204C>T	ENST00000264162.2	-	16	5510	c.5500G>A	c.(5500-5502)Gtg>Atg	p.V1834M		NM_002299.2	NP_002290.2	P09848	LPH_HUMAN	lactase	1834	4 X approximate repeats.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	glycosylceramidase activity (GO:0017042)|lactase activity (GO:0000016)			breast(6)|central_nervous_system(3)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(26)|lung(57)|ovary(7)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(4)	124				BRCA - Breast invasive adenocarcinoma(221;0.169)	Vitamin C(DB00126)	CATCGGACCACAGAGGCGTAG	0.552																																					p.V1834M		Atlas-SNP	.											.	LCT	309	.	0			c.G5500A						PASS	.						102.0	96.0	98.0					2																	136547204		2203	4300	6503	SO:0001583	missense	3938	exon16			GGACCACAGAGGC	X07994	CCDS2178.1	2q21	2014-09-17			ENSG00000115850	ENSG00000115850	3.2.1.108, 3.2.1.62		6530	protein-coding gene	gene with protein product		603202					Standard	NM_002299		Approved		uc002tuu.1	P09848	OTTHUMG00000131738	ENST00000264162.2:c.5500G>A	2.37:g.136547204C>T	ENSP00000264162:p.Val1834Met	Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	101	32	0.316832	NM_002299	Q4ZG58	Missense_Mutation	SNP	ENST00000264162.2	37	CCDS2178.1	.	.	.	.	.	.	.	.	.	.	C	14.22	2.469955	0.43839	.	.	ENSG00000115850	ENST00000264162	T	0.37752	1.18	5.74	-4.63	0.03359	Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.267610	0.39687	N	0.001286	T	0.25344	0.0616	L	0.33792	1.035	0.09310	N	1	B	0.24092	0.097	B	0.32624	0.149	T	0.29366	-1.0014	10	0.87932	D	0	-3.5549	10.4645	0.44600	0.0:0.1835:0.0967:0.7198	.	1834	P09848	LPH_HUMAN	M	1834	ENSP00000264162:V1834M	ENSP00000264162:V1834M	V	-	1	0	LCT	136263674	0.000000	0.05858	0.001000	0.08648	0.814000	0.46013	-0.379000	0.07437	-0.868000	0.04058	0.563000	0.77884	GTG	.	.	none		0.552	LCT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254657.1	NM_002299	
GEMIN5	25929	hgsc.bcm.edu	37	5	154287275	154287275	+	Silent	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:154287275C>T	ENST00000285873.7	-	16	2346	c.2271G>A	c.(2269-2271)tcG>tcA	p.S757S		NM_001252156.1|NM_015465.4	NP_001239085.1|NP_056280.2	Q8TEQ6	GEMI5_HUMAN	gem (nuclear organelle) associated protein 5	757					gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|ncRNA metabolic process (GO:0034660)|protein complex assembly (GO:0006461)|RNA metabolic process (GO:0016070)|spliceosomal snRNP assembly (GO:0000387)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMN complex (GO:0032797)|SMN-Sm protein complex (GO:0034719)	poly(A) RNA binding (GO:0044822)|snRNA binding (GO:0017069)			breast(1)|central_nervous_system(2)|endometrium(5)|kidney(3)|large_intestine(10)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	38	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)			TTCCATCAATCGATTCCAGCT	0.448																																					p.S757S		Atlas-SNP	.											GEMIN5,colon,carcinoma,0,4	GEMIN5	120	4	0			c.G2271A						scavenged	.						203.0	196.0	198.0					5																	154287275		2203	4300	6503	SO:0001819	synonymous_variant	25929	exon16			ATCAATCGATTCC	AK022748	CCDS4330.1	5q34	2013-01-10			ENSG00000082516	ENSG00000082516		"""WD repeat domain containing"""	20043	protein-coding gene	gene with protein product		607005				11714716	Standard	NM_015465		Approved		uc003lvx.3	Q8TEQ6	OTTHUMG00000130189	ENST00000285873.7:c.2271G>A	5.37:g.154287275C>T		Somatic	255	1	0.00392157		WXS	Illumina HiSeq	Phase_I	199	2	0.0100503	NM_015465	Q14CV0|Q8WWV4|Q969W4|Q9H9K3|Q9UFI5	Silent	SNP	ENST00000285873.7	37	CCDS4330.1																																																																																			.	.	none		0.448	GEMIN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252507.1		
TTN	7273	hgsc.bcm.edu	37	2	179462494	179462494	+	Silent	SNP	A	A	G	rs35833641	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:179462494A>G	ENST00000591111.1	-	244	52616	c.52392T>C	c.(52390-52392)caT>caC	p.H17464H	TTN_ENST00000359218.5_Silent_p.H10165H|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000589830.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000589487.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000589234.1_RNA|TTN_ENST00000342992.6_Silent_p.H16537H|TTN-AS1_ENST00000586452.1_RNA|TTN_ENST00000460472.2_Silent_p.H10040H|TTN-AS1_ENST00000591332.1_RNA|TTN_ENST00000589042.1_Silent_p.H19105H|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN_ENST00000342175.6_Silent_p.H10232H|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590932.1_RNA			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	185	0	0		WXS	Illumina HiSeq	Phase_I	131	57	0.435115	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	
MUC20	200958	hgsc.bcm.edu	37	3	195452805	195452805	+	Missense_Mutation	SNP	T	T	C	rs138659995	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195452805T>C	ENST00000447234.2	+	2	1457	c.1331T>C	c.(1330-1332)cTc>cCc	p.L444P	MUC20_ENST00000436408.1_Missense_Mutation_p.L444P|MUC20_ENST00000445522.2_Missense_Mutation_p.L409P|MUC20_ENST00000320736.6_Missense_Mutation_p.L273P	NM_001282506.1	NP_001269435.1	Q8N307	MUC20_HUMAN	mucin 20, cell surface associated	444				L -> P (in Ref. 5; AAH29267). {ECO:0000305}.	activation of MAPK activity (GO:0000187)|cellular protein metabolic process (GO:0044267)|hepatocyte growth factor receptor signaling pathway (GO:0048012)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein homooligomerization (GO:0051260)	basal plasma membrane (GO:0009925)|cell projection (GO:0042995)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)				NS(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(4)|skin(4)|stomach(3)|upper_aerodigestive_tract(1)	23	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)	Lung NSC(153;0.191)	Epithelial(36;1e-21)|all cancers(36;9.02e-20)|OV - Ovarian serous cystadenocarcinoma(49;1.6e-18)|Lung(62;0.000104)|LUSC - Lung squamous cell carcinoma(58;0.000128)	GBM - Glioblastoma multiforme(46;1.66e-05)		GACACAGATCTCATCCCCACG	0.532																																					p.L273P		Atlas-SNP	.											MUC20,NS,carcinoma,0,1	MUC20	84	1	0			c.T818C						PASS	.						33.0	29.0	31.0					3																	195452805		2032	4172	6204	SO:0001583	missense	200958	exon3			CAGATCTCATCCC	AB037780	CCDS63877.1	3q29	2008-08-07	2006-03-14		ENSG00000176945	ENSG00000176945		"""Mucins"""	23282	protein-coding gene	gene with protein product		610360				14565953	Standard	NM_001282506		Approved	FLJ14408, KIAA1359	uc010hzo.3	Q8N307	OTTHUMG00000155823	ENST00000447234.2:c.1331T>C	3.37:g.195452805T>C	ENSP00000414350:p.Leu444Pro	Somatic	456	0	0		WXS	Illumina HiSeq	Phase_I	473	123	0.260042	NM_152673	Q6UX97|Q76I83|Q76I85|Q86ST8|Q8NBY6|Q96KA1|Q9P2I8	Missense_Mutation	SNP	ENST00000447234.2	37		304	0.1391941391941392	136	0.2764227642276423	44	0.12154696132596685	1	0.0017482517482517483	123	0.16226912928759896	A	5.982	0.365171	0.11296	.	.	ENSG00000176945	ENST00000447234;ENST00000320736;ENST00000436408;ENST00000445522	T;T;T;T	0.15487	2.84;2.85;3.01;2.42	4.27	-8.54	0.00912	.	1.966210	0.02326	N	0.073463	T	0.00012	0.0000	N	0.24115	0.695	0.80722	P	0.0	B	0.09022	0.002	B	0.06405	0.002	T	0.24512	-1.0158	9	0.35671	T	0.21	11.8641	1.0464	0.01570	0.1498:0.2084:0.2288:0.413	.	273	E9PH32	.	P	444;273;444;409	ENSP00000414350:L444P;ENSP00000325431:L273P;ENSP00000396774:L444P;ENSP00000405629:L409P	ENSP00000325431:L273P	L	+	2	0	MUC20	196938476	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.973000	0.03798	-3.119000	0.00239	-0.454000	0.05498	CTC	T|0.856;C|0.144	0.144	strong		0.532	MUC20-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000341835.1	NM_152673	
NOS1	4842	hgsc.bcm.edu	37	12	117685270	117685270	+	Silent	SNP	G	G	A	rs1047735	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:117685270G>A	ENST00000338101.4	-	18	2812	c.2808C>T	c.(2806-2808)caC>caT	p.H936H	NOS1_ENST00000317775.6_Silent_p.H902H|NOS1_ENST00000344089.3_3'UTR			Q8WY41	NANO1_HUMAN	nitric oxide synthase 1 (neuronal)	0					cell migration (GO:0016477)|epithelial cell migration (GO:0010631)|negative regulation of translation (GO:0017148)	cytoplasm (GO:0005737)|perinuclear region of cytoplasm (GO:0048471)	RNA binding (GO:0003723)|translation repressor activity (GO:0030371)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(17)|large_intestine(21)|lung(43)|ovary(3)|pancreas(1)|prostate(6)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	117	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.0561)		TGTCCACAGCGTGTCCGAAGG	0.562													g|||	1735	0.346446	0.1982	0.5231	5008	,	,		16579	0.502		0.3151	False		,,,				2504	0.2935				p.H936H	Esophageal Squamous(162;1748 2599 51982 52956)	Atlas-SNP	.											.	NOS1	240	.	0			c.C2808T						PASS	.	G	,,,	692,3256		63,566,1345	87.0	87.0	87.0		2706,1698,1698,2808	-9.2	0.2	12	dbSNP_86	87	2511,5805		390,1731,2037	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NOS1	NM_000620.4,NM_001204213.1,NM_001204214.1,NM_001204218.1	,,,	453,2297,3382	AA,AG,GG		30.1948,17.5279,26.1171	,,,	902/1435,566/1099,566/1099,936/1469	117685270	3203,9061	1974	4158	6132	SO:0001819	synonymous_variant	4842	exon19			CACAGCGTGTCCG		CCDS41842.1, CCDS55890.1	12q24.22	2013-09-19			ENSG00000089250	ENSG00000089250	1.14.13.39		7872	protein-coding gene	gene with protein product		163731		NOS		1385308, 7682706	Standard	NM_001204213		Approved	nNOS	uc001twn.2	P29475	OTTHUMG00000137376	ENST00000338101.4:c.2808C>T	12.37:g.117685270G>A		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	108	61	0.564815	NM_001204218		Silent	SNP	ENST00000338101.4	37	CCDS55890.1																																																																																			G|0.652;A|0.348	0.348	strong		0.562	NOS1-002	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000268053.1		
PKHD1	5314	hgsc.bcm.edu	37	6	51483961	51483961	+	Missense_Mutation	SNP	T	T	C	rs9381994	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:51483961T>C	ENST00000371117.3	-	67	12418	c.12143A>G	c.(12142-12144)cAa>cGa	p.Q4048R	RP3-335N17.2_ENST00000587000.1_RNA|RP3-335N17.2_ENST00000454361.1_RNA|RP3-335N17.2_ENST00000589278.2_RNA	NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	4048			Q -> R (in dbSNP:rs9381994). {ECO:0000269|PubMed:11919560, ECO:0000269|PubMed:12846734}.		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)					TTTCTTCTCTTGGGAAAGCCC	0.547													T|||	2833	0.565695	0.4546	0.6023	5008	,	,		17670	0.6131		0.5487	False		,,,				2504	0.6585				p.Q4048R		Atlas-SNP	.											PKHD1,colon,carcinoma,0,2	PKHD1	927	2	0			c.A12143G						PASS	.	T	ARG/GLN	2120,2286	573.9+/-383.6	521,1078,604	42.0	45.0	44.0		12143	4.0	1.0	6	dbSNP_119	44	4719,3881	605.1+/-394.9	1297,2125,878	yes	missense	PKHD1	NM_138694.3	43	1818,3203,1482	CC,CT,TT		45.1279,48.1162,47.4166	benign	4048/4075	51483961	6839,6167	2203	4300	6503	SO:0001583	missense	5314	exon67			TTCTCTTGGGAAA	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.12143A>G	6.37:g.51483961T>C	ENSP00000360158:p.Gln4048Arg	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	87	86	0.988506	NM_138694	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Missense_Mutation	SNP	ENST00000371117.3	37	CCDS4935.1	1216	0.5567765567765568	222	0.45121951219512196	215	0.5939226519337016	357	0.6241258741258742	422	0.5567282321899736	T	10.82	1.457689	0.26161	0.481162	0.548721	ENSG00000170927	ENST00000371117	D	0.86164	-2.08	5.27	3.95	0.45737	.	0.000000	0.45606	D	0.000358	T	0.63141	0.2486	L	0.31664	0.95	0.09310	P	0.999999999928248	B	0.18863	0.031	B	0.19148	0.024	T	0.54227	-0.8325	9	0.25106	T	0.35	.	5.3886	0.16231	0.0:0.155:0.0:0.845	rs9381994;rs56843543;rs9381994	4048	P08F94	PKHD1_HUMAN	R	4048	ENSP00000360158:Q4048R	ENSP00000360158:Q4048R	Q	-	2	0	PKHD1	51591920	0.634000	0.27190	1.000000	0.80357	0.266000	0.26442	0.430000	0.21428	2.128000	0.65567	0.533000	0.62120	CAA	T|0.458;C|0.542	0.542	strong		0.547	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694	
FBXO8	26269	hgsc.bcm.edu	37	4	175180938	175180938	+	Missense_Mutation	SNP	T	T	C	rs61748174	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:175180938T>C	ENST00000393674.2	-	3	1230	c.368A>G	c.(367-369)aAt>aGt	p.N123S	FBXO8_ENST00000503293.1_Missense_Mutation_p.N82S	NM_012180.2	NP_036312.2	Q9NRD0	FBX8_HUMAN	F-box protein 8	123					actin cytoskeleton organization (GO:0030036)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)|ubiquitin-dependent protein catabolic process (GO:0006511)	cell junction (GO:0030054)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			breast(3)|endometrium(1)|kidney(1)|large_intestine(5)|lung(2)|prostate(1)|urinary_tract(1)	14		Prostate(90;0.00201)|Melanoma(52;0.012)|Renal(120;0.0183)|all_neural(102;0.0887)|all_hematologic(60;0.107)		all cancers(43;7.29e-18)|Epithelial(43;1.85e-15)|OV - Ovarian serous cystadenocarcinoma(60;5.62e-09)|GBM - Glioblastoma multiforme(59;0.00115)|STAD - Stomach adenocarcinoma(60;0.00299)|LUSC - Lung squamous cell carcinoma(193;0.1)		TGGGTTCTTATTGTATATGGA	0.353													T|||	20	0.00399361	0.0	0.0043	5008	,	,		16034	0.002		0.005	False		,,,				2504	0.0102				p.N123S		Atlas-SNP	.											.	FBXO8	34	.	0			c.A368G						PASS	.	T	SER/ASN	3,4403	6.2+/-15.9	0,3,2200	88.0	95.0	92.0		368	5.3	1.0	4	dbSNP_129	92	37,8563	24.6+/-71.5	0,37,4263	yes	missense	FBXO8	NM_012180.2	46	0,40,6463	CC,CT,TT		0.4302,0.0681,0.3076	benign	123/320	175180938	40,12966	2203	4300	6503	SO:0001583	missense	26269	exon3			TTCTTATTGTATA	AF174596	CCDS3820.1	4q34.1	2008-02-05	2004-06-15			ENSG00000164117		"""F-boxes /  ""other"""""	13587	protein-coding gene	gene with protein product		605649	"""F-box only protein 8"""			10531035, 10531037	Standard	NM_012180		Approved	FBX8, FBS	uc003itp.3	Q9NRD0		ENST00000393674.2:c.368A>G	4.37:g.175180938T>C	ENSP00000377280:p.Asn123Ser	Somatic	248	0	0		WXS	Illumina HiSeq	Phase_I	212	99	0.466981	NM_012180	B2RB40|D3DP41|G5E9Z0|Q6UWN4|Q8IWE1|Q9NRP5|Q9UKC4	Missense_Mutation	SNP	ENST00000393674.2	37	CCDS3820.1	7	0.003205128205128205	0	0.0	3	0.008287292817679558	0	0.0	4	0.005277044854881266	T	15.31	2.796300	0.50208	6.81E-4	0.004302	ENSG00000164117	ENST00000393674;ENST00000503293;ENST00000296517;ENST00000513696	T;T;T	0.53423	0.62;0.62;0.62	5.3	5.3	0.74995	.	0.000000	0.85682	D	0.000000	T	0.32041	0.0816	L	0.46157	1.445	0.58432	D	0.999998	B;B	0.20368	0.03;0.044	B;B	0.17433	0.018;0.011	T	0.22068	-1.0227	10	0.10377	T	0.69	.	15.5522	0.76161	0.0:0.0:0.0:1.0	rs61748174	82;123	G5E9Z0;Q9NRD0	.;FBX8_HUMAN	S	123;82;36;123	ENSP00000377280:N123S;ENSP00000422905:N82S;ENSP00000427506:N123S	ENSP00000296517:N36S	N	-	2	0	FBXO8	175417513	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.384000	0.66225	2.140000	0.66376	0.528000	0.53228	AAT	T|0.997;C|0.003	0.003	strong		0.353	FBXO8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362085.2	NM_012180	
MCMDC2	157777	hgsc.bcm.edu	37	8	67796120	67796120	+	Missense_Mutation	SNP	C	C	G	rs17332410	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:67796120C>G	ENST00000422365.2	+	9	1135	c.964C>G	c.(964-966)Ctc>Gtc	p.L322V	MCMDC2_ENST00000313616.5_Missense_Mutation_p.L322V|MCMDC2_ENST00000492775.1_Missense_Mutation_p.L322V|MCMDC2_ENST00000396592.3_Missense_Mutation_p.L322V|MCMDC2_ENST00000541540.1_Missense_Mutation_p.L259V	NM_173518.4	NP_775789.3	Q4G0Z9	MCMD2_HUMAN	minichromosome maintenance domain containing 2	322			L -> V (in dbSNP:rs17332410).		DNA replication (GO:0006260)		ATP binding (GO:0005524)|DNA binding (GO:0003677)			endometrium(2)|kidney(2)|lung(5)	9						TTACAATTTGCTCAAGCTCTG	0.403													C|||	111	0.0221645	0.0045	0.0259	5008	,	,		15855	0.001		0.0785	False		,,,				2504	0.0072				p.L322V		Atlas-SNP	.											.	MCMDC2	84	.	0			c.C964G						PASS	.	C	VAL/LEU,VAL/LEU,VAL/LEU	83,4323	71.4+/-109.4	1,81,2121	77.0	72.0	74.0		964,964,964	4.7	1.0	8	dbSNP_123	74	652,7948	166.5+/-218.5	26,600,3674	yes	missense,missense,missense	C8orf45	NM_001136160.1,NM_001136161.1,NM_173518.4	32,32,32	27,681,5795	GG,GC,CC		7.5814,1.8838,5.6512	possibly-damaging,possibly-damaging,possibly-damaging	322/633,322/591,322/682	67796120	735,12271	2203	4300	6503	SO:0001583	missense	157777	exon9			AATTTGCTCAAGC	BC034576	CCDS6197.2, CCDS47868.1, CCDS47869.1	8q13.1	2012-04-13	2012-04-13	2012-04-13	ENSG00000178460	ENSG00000178460			26368	protein-coding gene	gene with protein product			"""chromosome 8 open reading frame 45"""	C8orf45			Standard	NM_173518		Approved	FLJ25692	uc003xwz.4	Q4G0Z9	OTTHUMG00000157068	ENST00000422365.2:c.964C>G	8.37:g.67796120C>G	ENSP00000413632:p.Leu322Val	Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	92	64	0.695652	NM_173518	B4DYZ3|B4DZM4|B4E293|Q6P533|Q7Z3P4	Missense_Mutation	SNP	ENST00000422365.2	37	CCDS6197.2	69	0.03159340659340659	3	0.006097560975609756	11	0.03038674033149171	1	0.0017482517482517483	54	0.0712401055408971	C	18.15	3.560263	0.65538	0.018838	0.075814	ENSG00000178460	ENST00000379356;ENST00000396592;ENST00000422365;ENST00000492775;ENST00000313616;ENST00000541540	T;T;T;T;T	0.38722	1.12;1.12;1.12;1.12;1.12	5.57	4.68	0.58851	.	0.065812	0.56097	D	0.000029	T	0.04048	0.0113	M	0.65498	2.005	0.45852	D	0.998711	P;P;P;P	0.51537	0.946;0.911;0.911;0.946	P;P;P;P	0.52646	0.705;0.51;0.51;0.487	T	0.00904	-1.1520	10	0.15952	T	0.53	-5.4307	11.6204	0.51115	0.0:0.86:0.0:0.14	rs17332410;rs52814888;rs17332410	259;322;322;322	Q4G0Z9-4;Q4G0Z9;B4DXX4;G3XAN3	.;CH045_HUMAN;.;.	V	194;322;322;322;322;259	ENSP00000379837:L322V;ENSP00000413632:L322V;ENSP00000428037:L322V;ENSP00000317234:L322V;ENSP00000445629:L259V	ENSP00000317234:L322V	L	+	1	0	C8orf45	67958674	0.858000	0.29795	1.000000	0.80357	0.998000	0.95712	1.131000	0.31406	2.785000	0.95823	0.655000	0.94253	CTC	C|0.950;G|0.050	0.050	strong		0.403	MCMDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347350.1	NM_173518	
OR10H2	26538	hgsc.bcm.edu	37	19	15839459	15839459	+	Silent	SNP	G	G	A	rs11669315	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:15839459G>A	ENST00000305899.3	+	1	626	c.606G>A	c.(604-606)ttG>ttA	p.L202L		NM_013939.2	NP_039227.1	O60403	O10H2_HUMAN	olfactory receptor, family 10, subfamily H, member 2	202						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(2)|skin(3)|stomach(1)	27	all_hematologic(1;0.0517)|Acute lymphoblastic leukemia(2;0.074)					GCGTGGGCTTGGTATGTATCA	0.517													G|||	764	0.152556	0.1278	0.121	5008	,	,		23239	0.123		0.17	False		,,,				2504	0.2209				p.L202L		Atlas-SNP	.											.	OR10H2	59	.	0			c.G606A						PASS	.	G		612,3794		46,520,1637	223.0	182.0	196.0		606	2.3	0.0	19	dbSNP_120	196	1652,6948		179,1294,2827	no	coding-synonymous	OR10H2	NM_013939.2		225,1814,4464	AA,AG,GG		19.2093,13.8901,17.4074		202/316	15839459	2264,10742	2203	4300	6503	SO:0001819	synonymous_variant	26538	exon1			GGGCTTGGTATGT	AC004597	CCDS12333.1	19p13.1	2012-08-09				ENSG00000171942		"""GPCR / Class A : Olfactory receptors"""	8173	protein-coding gene	gene with protein product							Standard	NM_013939		Approved		uc002nbm.2	O60403		ENST00000305899.3:c.606G>A	19.37:g.15839459G>A		Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	147	69	0.469388	NM_013939	Q6IFQ1|Q96R58	Silent	SNP	ENST00000305899.3	37	CCDS12333.1																																																																																			G|0.839;A|0.161	0.161	strong		0.517	OR10H2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460917.1		
SETX	23064	hgsc.bcm.edu	37	9	135173685	135173685	+	Missense_Mutation	SNP	T	T	C	rs2296871	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:135173685T>C	ENST00000224140.5	-	13	5745	c.5563A>G	c.(5563-5565)Act>Gct	p.T1855A	SETX_ENST00000393220.1_Missense_Mutation_p.T1855A|SETX_ENST00000372169.2_Missense_Mutation_p.T1855A	NM_015046.5	NP_055861.3	Q7Z333	SETX_HUMAN	senataxin	1855			T -> A (in dbSNP:rs2296871). {ECO:0000269|PubMed:15489334}.|T -> P (in dbSNP:rs2296871).		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)		TAACACTCAGTTTTCCCATTA	0.368													C|||	2219	0.443091	0.6929	0.2262	5008	,	,		21142	0.6379		0.1382	False		,,,				2504	0.3722				p.T1855A		Atlas-SNP	.											.	SETX	234	.	0			c.A5563G						PASS	.	C	ALA/THR	2656,1750	515.0+/-368.8	823,1010,370	75.0	72.0	73.0		5563	-8.4	0.0	9	dbSNP_100	73	1334,7266	754.4+/-407.5	97,1140,3063	yes	missense	SETX	NM_015046.5	58	920,2150,3433	CC,CT,TT		15.5116,39.7186,30.6781	benign	1855/2678	135173685	3990,9016	2203	4300	6503	SO:0001583	missense	23064	exon13			ACTCAGTTTTCCC	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.5563A>G	9.37:g.135173685T>C	ENSP00000224140:p.Thr1855Ala	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	94	40	0.425532	NM_015046	A2A396|B2RPB2|B5ME16|C9JQ10|O75120|Q3KQX4|Q5JUJ1|Q68DW5|Q6AZD7|Q7Z3J6|Q8WX33|Q9H9D1|Q9NVP9	Missense_Mutation	SNP	ENST00000224140.5	37	CCDS6947.1	905	0.4143772893772894	333	0.676829268292683	83	0.2292817679558011	384	0.6713286713286714	105	0.13852242744063326	C	0.839	-0.742489	0.03088	0.602814	0.155116	ENSG00000107290	ENST00000224140;ENST00000436441;ENST00000372169;ENST00000393220	D;D;D;D	0.90069	-2.06;-2.61;-2.15;-1.77	5.88	-8.41	0.00961	.	1.218760	0.05711	N	0.595916	T	0.00012	0.0000	N	0.12182	0.205	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	0.24048	-1.0171	9	0.02654	T	1	.	9.7534	0.40490	0.1415:0.6259:0.0601:0.1724	rs2296871;rs58627825;rs2296871	1855;1855;1855	Q7Z333-3;Q7Z333;Q7Z333-4	.;SETX_HUMAN;.	A	1855;97;1855;1855	ENSP00000224140:T1855A;ENSP00000409143:T97A;ENSP00000361242:T1855A;ENSP00000376913:T1855A	ENSP00000224140:T1855A	T	-	1	0	SETX	134163506	0.000000	0.05858	0.001000	0.08648	0.174000	0.22865	-0.963000	0.03837	-1.814000	0.01224	-2.561000	0.00173	ACT	C|0.380;N|0.000;T|0.620	0.380	strong		0.368	SETX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054774.3	NM_015046	
HLA-DPA1	3113	hgsc.bcm.edu	37	6	33037626	33037626	+	Silent	SNP	C	C	G	rs1042174	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:33037626C>G	ENST00000419277.1	-	3	267	c.138G>C	c.(136-138)acG>acC	p.T46T	HLA-DPA1_ENST00000428995.1_Silent_p.T46T|HLA-DPA1_ENST00000463066.1_5'UTR	NM_001242524.1|NM_001242525.1	NP_001229453.1|NP_001229454.1	P20036	DPA1_HUMAN	major histocompatibility complex, class II, DP alpha 1	46	Alpha-1.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cellular response to interferon-gamma (GO:0071346)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell proliferation (GO:0042102)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			kidney(5)|large_intestine(1)|lung(6)|prostate(1)|skin(2)	15						TTGGTCTATGCGTCTGTACAA	0.433													.|||	2309	0.461062	0.7171	0.2882	5008	,	,		20289	0.6518		0.1491	False		,,,				2504	0.362				p.T46T		Atlas-SNP	.											.	HLA-DPA1	20	.	0			c.G138C						PASS	.	G	,,	1588,1432		465,658,387	56.0	80.0	71.0		138,138,138	-6.2	0.0	6	dbSNP_86	71	710,4706		49,612,2047	yes	coding-synonymous,coding-synonymous,coding-synonymous	HLA-DPA1	NM_001242524.1,NM_001242525.1,NM_033554.3	,,	514,1270,2434	GG,GC,CC		13.1093,47.4172,27.2404	,,	46/261,46/261,46/261	33037626	2298,6138	1510	2708	4218	SO:0001819	synonymous_variant	3113	exon2			TCTATGCGTCTGT	X00457	CCDS4764.1	6p21.3	2013-01-11			ENSG00000231389	ENSG00000231389		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4938	protein-coding gene	gene with protein product		142880		HLA-DP1A		6584734	Standard	NM_033554		Approved		uc003ocs.2	P20036	OTTHUMG00000031058	ENST00000419277.1:c.138G>C	6.37:g.33037626C>G		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	81	26	0.320988	NM_033554	A9YWH7|B9UKH4|O19722|O46883|P01905|P79554|Q2Q060|Q2Q061|Q5EY03|Q5STP1|Q6DQK4|Q9BCQ1|Q9TPX3|Q9XS10	Silent	SNP	ENST00000419277.1	37	CCDS4764.1																																																																																			C|0.687;G|0.313	0.313	strong		0.433	HLA-DPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076071.3	NM_033554	
ZNF423	23090	hgsc.bcm.edu	37	16	49671218	49671218	+	Silent	SNP	C	C	T	rs16947741	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:49671218C>T	ENST00000561648.1	-	4	1898	c.1845G>A	c.(1843-1845)ccG>ccA	p.P615P	ZNF423_ENST00000262383.2_Silent_p.P615P|ZNF423_ENST00000535559.1_Silent_p.P498P|ZNF423_ENST00000563137.2_Silent_p.P555P|ZNF423_ENST00000562520.1_Silent_p.P555P|ZNF423_ENST00000562871.1_Silent_p.P555P|ZNF423_ENST00000567169.1_Silent_p.P498P	NM_001271620.1	NP_001258549.1	Q2M1K9	ZN423_HUMAN	zinc finger protein 423	615					cell differentiation (GO:0030154)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|Notch signaling pathway (GO:0007219)|positive regulation of BMP signaling pathway (GO:0030513)|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)			breast(1)|central_nervous_system(1)|endometrium(8)|kidney(6)|large_intestine(16)|lung(47)|ovary(1)|pancreas(2)|prostate(4)|skin(1)|urinary_tract(2)	89		all_cancers(37;0.0155)				GCTGCCGCTTCGGGGAAGACA	0.552													C|||	113	0.0225639	0.0144	0.0144	5008	,	,		22588	0.0149		0.0398	False		,,,				2504	0.0297				p.P615P		Atlas-SNP	.											ZNF423_ENST00000262383,NS,carcinoma,0,2	ZNF423	463	2	0			c.G1845A						PASS	.	C		91,4305	75.7+/-113.9	0,91,2107	88.0	74.0	79.0		1845	-9.6	0.8	16	dbSNP_123	79	274,8326	104.6+/-165.6	4,266,4030	no	coding-synonymous	ZNF423	NM_015069.2		4,357,6137	TT,TC,CC		3.186,2.0701,2.8086		615/1285	49671218	365,12631	2198	4300	6498	SO:0001819	synonymous_variant	23090	exon4			CCGCTTCGGGGAA	AB018303	CCDS32445.1, CCDS61930.1	16q12	2014-01-28				ENSG00000102935		"""Zinc fingers, C2H2-type"""	16762	protein-coding gene	gene with protein product	"""OLF-1/EBF associated zinc finger gene"", "" Smad- and Olf-interacting zinc finger protein"", ""early B-cell factor associated zinc finger protein"""	604557				9872452, 10660046	Standard	NM_001271620		Approved	KIAA0760, OAZ, Roaz, Ebfaz, Zfp104, NPHP14, JBTS19	uc031qwd.1	Q2M1K9		ENST00000561648.1:c.1845G>A	16.37:g.49671218C>T		Somatic	212	0	0		WXS	Illumina HiSeq	Phase_I	241	95	0.394191	NM_015069	O94860|Q76N04|Q9NZ13	Silent	SNP	ENST00000561648.1	37	CCDS32445.1																																																																																			C|0.973;T|0.027	0.027	strong		0.552	ZNF423-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000423258.1	NM_015069	
HOXA11	3207	hgsc.bcm.edu	37	7	27222437	27222437	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:27222437T>C	ENST00000006015.3	-	2	991	c.920A>G	c.(919-921)tAc>tGc	p.Y307C	HOXA10_ENST00000396344.4_5'Flank|HOXA11-AS_ENST00000522863.1_RNA|HOXA11-AS_ENST00000520395.1_RNA|HOXA11-AS_ENST00000520360.1_RNA|RP1-170O19.20_ENST00000470747.4_5'Flank|HOXA11-AS_ENST00000522674.1_RNA	NM_005523.5	NP_005514.1	P31270	HXA11_HUMAN	homeobox A11	307					anatomical structure morphogenesis (GO:0009653)|anterior/posterior pattern specification (GO:0009952)|branching involved in ureteric bud morphogenesis (GO:0001658)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|developmental growth (GO:0048589)|dorsal/ventral pattern formation (GO:0009953)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal joint morphogenesis (GO:0060272)|male gonad development (GO:0008584)|mesodermal cell fate specification (GO:0007501)|metanephros development (GO:0001656)|multicellular organismal development (GO:0007275)|organ induction (GO:0001759)|positive regulation of cell development (GO:0010720)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of transcription, DNA-templated (GO:0045893)|proximal/distal pattern formation (GO:0009954)|single fertilization (GO:0007338)|skeletal system development (GO:0001501)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)|uterus development (GO:0060065)	nucleus (GO:0005634)|protein complex (GO:0043234)|protein-DNA complex (GO:0032993)|transcription factor complex (GO:0005667)	sequence-specific DNA binding (GO:0043565)			NS(1)|breast(1)|endometrium(1)|large_intestine(2)|lung(8)|ovary(1)|skin(2)	16						ATTTGCTGAGTAGTACTGTAA	0.443			T	NUP98	CML																																p.Y307C		Atlas-SNP	.		Dom	yes		7	7p15-p14.2	3207	homeo box A11		L	.	HOXA11	29	.	0			c.A920G						PASS	.						70.0	70.0	70.0					7																	27222437		2203	4300	6503	SO:0001583	missense	3207	exon2			GCTGAGTAGTACT		CCDS5411.1	7p15.2	2014-09-17	2005-12-22		ENSG00000005073	ENSG00000005073		"""Homeoboxes / ANTP class : HOXL subclass"""	5101	protein-coding gene	gene with protein product		142958	"""homeo box A11"""	HOX1I, HOX1		1973146, 1358459	Standard	NM_005523		Approved		uc003syx.3	P31270	OTTHUMG00000023437	ENST00000006015.3:c.920A>G	7.37:g.27222437T>C	ENSP00000006015:p.Tyr307Cys	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	63	27	0.428571	NM_005523	A4D190	Missense_Mutation	SNP	ENST00000006015.3	37	CCDS5411.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	17.23|17.23	3.336101|3.336101	0.60963|0.60963	.|.	.|.	ENSG00000005073|ENSG00000005073	ENST00000517402|ENST00000006015	.|D	.|0.90844	.|-2.74	5.69|5.69	5.69|5.69	0.88448|0.88448	.|.	.|0.000000	.|0.64402	.|D	.|0.000001	D|D	0.92303|0.92303	0.7558|0.7558	L|L	0.29908|0.29908	0.895|0.895	0.80722|0.80722	D|D	1|1	.|D	.|0.76494	.|0.999	.|D	.|0.76071	.|0.987	D|D	0.93496|0.93496	0.6840|0.6840	5|10	.|0.87932	.|D	.|0	.|.	15.9527|15.9527	0.79855|0.79855	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|307	.|P31270	.|HXA11_HUMAN	A|C	277|307	.|ENSP00000006015:Y307C	.|ENSP00000006015:Y307C	T|Y	-|-	1|2	0|0	HOXA11|HOXA11	27188962|27188962	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.993000|0.993000	0.82548|0.82548	5.017000|5.017000	0.64047|0.64047	2.173000|2.173000	0.68751|0.68751	0.533000|0.533000	0.62120|0.62120	ACT|TAC	.	.	none		0.443	HOXA11-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000358754.1		
CACNA1H	8912	hgsc.bcm.edu	37	16	1254064	1254064	+	Missense_Mutation	SNP	C	C	T	rs145376050	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:1254064C>T	ENST00000348261.5	+	10	2305	c.2057C>T	c.(2056-2058)cCc>cTc	p.P686L	RP11-616M22.3_ENST00000564700.1_RNA|CACNA1H_ENST00000565831.1_Missense_Mutation_p.P686L|CACNA1H_ENST00000358590.4_Missense_Mutation_p.P686L	NM_021098.2	NP_066921.2	O95180	CAC1H_HUMAN	calcium channel, voltage-dependent, T type, alpha 1H subunit	686					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)	TGCCCCCTGCCCAGCCCCCCA	0.701													C|||	7	0.00139776	0.0	0.0014	5008	,	,		14466	0.0		0.006	False		,,,				2504	0.0				p.P686L		Atlas-SNP	.											.	CACNA1H	317	.	0			c.C2057T						PASS	.	C	LEU/PRO,LEU/PRO	1,3833		0,1,1916	8.0	10.0	9.0		2057,2057	4.1	1.0	16	dbSNP_134	9	9,8195		0,9,4093	yes	missense,missense	CACNA1H	NM_001005407.1,NM_021098.2	98,98	0,10,6009	TT,TC,CC		0.1097,0.0261,0.0831	probably-damaging,probably-damaging	686/2348,686/2354	1254064	10,12028	1917	4102	6019	SO:0001583	missense	8912	exon10			CCCTGCCCAGCCC	AL031703	CCDS45375.1, CCDS45376.1	16p13.3	2012-03-07	2007-02-16					"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1395	protein-coding gene	gene with protein product		607904				9670923, 16382099	Standard	NM_021098		Approved	Cav3.2	uc002cks.3	O95180		ENST00000348261.5:c.2057C>T	16.37:g.1254064C>T	ENSP00000334198:p.Pro686Leu	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	73	13	0.178082	NM_021098	B5ME00|F8WFD1|O95802|Q8WWI6|Q96QI6|Q96RZ9|Q9NYY4|Q9NYY5	Missense_Mutation	SNP	ENST00000348261.5	37	CCDS45375.1	4	0.0018315018315018315	0	0.0	1	0.0027624309392265192	0	0.0	3	0.00395778364116095	C	15.89	2.965415	0.53507	2.61E-4	0.001097	ENSG00000196557	ENST00000348261;ENST00000358590	D;D	0.96396	-4.0;-3.95	4.05	4.05	0.47172	.	0.785431	0.10696	U	0.644627	D	0.95526	0.8546	L	0.48642	1.525	0.42385	D	0.992503	D;D	0.53462	0.96;0.958	P;P	0.49252	0.574;0.604	D	0.93067	0.6479	10	0.30854	T	0.27	.	15.3789	0.74637	0.0:1.0:0.0:0.0	.	686;686	O95180-2;O95180	.;CAC1H_HUMAN	L	686	ENSP00000334198:P686L;ENSP00000351401:P686L	ENSP00000334198:P686L	P	+	2	0	CACNA1H	1194065	1.000000	0.71417	1.000000	0.80357	0.925000	0.55904	3.108000	0.50337	2.114000	0.64651	0.561000	0.74099	CCC	C|0.998;T|0.002	0.002	strong		0.701	CACNA1H-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000421601.1	NM_001005407	
OR5L2	26338	hgsc.bcm.edu	37	11	55595116	55595116	+	Missense_Mutation	SNP	G	G	C	rs75822385|rs35214936|rs386753701	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:55595116G>C	ENST00000378397.1	+	1	422	c.422G>C	c.(421-423)cGt>cCt	p.R141P		NM_001004739.1	NP_001004739.1	Q8NGL0	OR5L2_HUMAN	olfactory receptor, family 5, subfamily L, member 2	141						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)|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)				CAGAAGCTGCGTGTGGAGCTG	0.517										HNSCC(27;0.073)			N|||	446	0.0890575	0.1293	0.0403	5008	,	,		21243	0.0843		0.0924	False		,,,				2504	0.0706				p.R141P		Atlas-SNP	.											OR5L2,NS,carcinoma,+1,1	OR5L2	135	1	0			c.G422C						PASS	.						211.0	182.0	192.0					11																	55595116		2200	4296	6496	SO:0001583	missense	26338	exon1			AGCTGCGTGTGGA	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.422G>C	11.37:g.55595116G>C	ENSP00000367650:p.Arg141Pro	Somatic	257	0	0		WXS	Illumina HiSeq	Phase_I	208	144	0.692308	NM_001004739	Q6IF66|Q96RB2	Missense_Mutation	SNP	ENST00000378397.1	37	CCDS31511.1	.	.	.	.	.	.	.	.	.	.	.	11.49	1.653845	0.29425	.	.	ENSG00000205030	ENST00000378397	T	0.37058	1.22	5.18	4.26	0.50523	GPCR, rhodopsin-like superfamily (1);	0.359940	0.24334	N	0.039423	T	0.48003	0.1476	M	0.63843	1.955	0.09310	N	1	P	0.38395	0.629	P	0.51055	0.657	T	0.43442	-0.9391	10	0.87932	D	0	-1.0929	9.6016	0.39607	0.1634:0.0:0.8366:0.0	.	141	Q8NGL0	OR5L2_HUMAN	P	141	ENSP00000367650:R141P	ENSP00000367650:R141P	R	+	2	0	OR5L2	55351692	0.036000	0.19791	0.083000	0.20561	0.052000	0.14988	2.184000	0.42575	1.346000	0.45694	0.626000	0.83405	CGT	A|0.002;C|0.069;G|0.929	0.069	strong		0.517	OR5L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391516.1	NM_001004739	
CTBP2	1488	hgsc.bcm.edu	37	10	126714714	126714714	+	Intron	SNP	G	G	C	rs2946994	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:126714714G>C	ENST00000337195.5	-	3	458				CTBP2_ENST00000494626.2_Intron|CTBP2_ENST00000309035.6_Missense_Mutation_p.Q539E|CTBP2_ENST00000531469.1_Intron|CTBP2_ENST00000411419.2_Intron	NM_001329.2	NP_001320.1	P56545	CTBP2_HUMAN	C-terminal binding protein 2						negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)|viral genome replication (GO:0019079)|white fat cell differentiation (GO:0050872)	cell junction (GO:0030054)|nucleus (GO:0005634)|synapse (GO:0045202)|transcriptional repressor complex (GO:0017053)	NAD binding (GO:0051287)|oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor (GO:0016616)|transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	25		all_lung(145;0.0132)|Lung NSC(174;0.0193)|all_neural(114;0.116)|Colorectal(57;0.173)		Colorectal(40;0.00572)|COAD - Colon adenocarcinoma(40;0.0127)|GBM - Glioblastoma multiforme(135;0.147)		GCCACCTTCTGGTACGGTGAG	0.672													G|||	2342	0.467652	0.3744	0.3357	5008	,	,		13550	0.6607		0.4761	False		,,,				2504	0.4796				p.Q539E		Atlas-SNP	.											CTBP2,colon,carcinoma,0,1	CTBP2	100	1	0			c.C1615G						PASS	.	G	,,GLU/GLN	1695,2711	500.0+/-364.6	309,1077,817	83.0	84.0	84.0		,,1615	5.3	1.0	10	dbSNP_101	84	4263,4337	562.6+/-388.0	1050,2163,1087	yes	intron,intron,missense	CTBP2	NM_001083914.1,NM_001329.2,NM_022802.2	,,29	1359,3240,1904	CC,CG,GG		49.5698,38.4703,45.8096	,,benign	,,539/986	126714714	5958,7048	2203	4300	6503	SO:0001627	intron_variant	1488	exon1			CCTTCTGGTACGG	AF016507	CCDS7643.1, CCDS7644.1	10q26.13	2008-08-01			ENSG00000175029	ENSG00000175029			2495	protein-coding gene	gene with protein product		602619				9479502, 11864595	Standard	NM_022802		Approved	ribeye	uc001lie.4	P56545	OTTHUMG00000019224	ENST00000337195.5:c.58+12851C>G	10.37:g.126714714G>C		Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	148	69	0.466216	NM_022802	A8K2X5|D3DRF5|O43449|Q5SQP7|Q69YI3|Q86SV0|Q9H2T8	Missense_Mutation	SNP	ENST00000337195.5	37	CCDS7643.1	1030	0.4716117216117216	192	0.3902439024390244	124	0.3425414364640884	353	0.6171328671328671	361	0.4762532981530343	G	17.74	3.464348	0.63513	0.384703	0.495698	ENSG00000175029	ENST00000309035	D	0.83419	-1.72	5.29	5.29	0.74685	.	0.768853	0.11608	N	0.547098	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	P	0.49559	0.925	P	0.46339	0.513	T	0.48559	-0.9025	8	0.49607	T	0.09	.	19.3229	0.94250	0.0:0.0:1.0:0.0	rs2946994;rs17710501;rs58027090;rs2946994	539	P56545-2	.	E	539	ENSP00000311825:Q539E	ENSP00000311825:Q539E	Q	-	1	0	CTBP2	126704704	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	9.729000	0.98795	2.642000	0.89623	0.591000	0.81541	CAG	G|0.533;C|0.467	0.467	strong		0.672	CTBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050900.3	NM_001083914	
ZNF469	84627	hgsc.bcm.edu	37	16	88494604	88494604	+	Silent	SNP	C	C	T	rs555256402	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:88494604C>T	ENST00000437464.1	+	1	726	c.726C>T	c.(724-726)agC>agT	p.S242S	ZNF469_ENST00000565624.1_Silent_p.S242S	NM_001127464.1	NP_001120936.1	Q96JG9	ZN469_HUMAN	zinc finger protein 469	242	Pro-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(4)|endometrium(6)|kidney(3)|large_intestine(1)|skin(6)	20						CTGAGAATAGCTTCCCAGGTG	0.677													C|||	4	0.000798722	0.0	0.0	5008	,	,		11142	0.0		0.002	False		,,,				2504	0.002				p.S242S		Atlas-SNP	.											.	ZNF469	121	.	0			c.C726T						PASS	.						8.0	11.0	10.0					16																	88494604		688	1589	2277	SO:0001819	synonymous_variant	84627	exon1			GAATAGCTTCCCA	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.726C>T	16.37:g.88494604C>T		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	100	64	0.64	NM_001127464		Silent	SNP	ENST00000437464.1	37	CCDS45544.1																																																																																			.	.	none		0.677	ZNF469-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NG_012236	
MYOF	26509	hgsc.bcm.edu	37	10	95111005	95111005	+	Silent	SNP	T	T	C	rs35669278	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:95111005T>C	ENST00000359263.4	-	35	3869	c.3870A>G	c.(3868-3870)ctA>ctG	p.L1290L	MYOF_ENST00000358334.5_Silent_p.L1277L|MYOF_ENST00000371502.4_Silent_p.L1290L|MYOF_ENST00000371501.4_Silent_p.L1290L	NM_013451.3	NP_038479.1	Q9NZM1	MYOF_HUMAN	myoferlin	1290					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)			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						GGACCATGTATAGATTTGGCG	0.502													T|||	153	0.0305511	0.0008	0.0447	5008	,	,		19702	0.0		0.0954	False		,,,				2504	0.0256				p.L1290L		Atlas-SNP	.											.	MYOF	177	.	0			c.A3870G						PASS	.	T	,	51,3831		0,51,1890	59.0	60.0	60.0		3870,3831	-5.8	0.8	10	dbSNP_126	60	553,7707		22,509,3599	no	coding-synonymous,coding-synonymous	MYOF	NM_013451.3,NM_133337.2	,	22,560,5489	CC,CT,TT		6.6949,1.3138,4.9745	,	1290/2062,1277/2049	95111005	604,11538	1941	4130	6071	SO:0001819	synonymous_variant	26509	exon35			CATGTATAGATTT	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.3870A>G	10.37:g.95111005T>C		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	93	40	0.430108	NM_013451	B3KQN5|Q5VWW2|Q5VWW3|Q5VWW4|Q5VWW5|Q7Z642|Q8IWH0|Q9HBU3|Q9NZM0|Q9ULL3|Q9Y4U4	Silent	SNP	ENST00000359263.4	37	CCDS41551.1																																																																																			T|0.950;C|0.050	0.050	strong		0.502	MYOF-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000049423.2	NM_013451	
PDE1C	5137	hgsc.bcm.edu	37	7	31920395	31920395	+	Silent	SNP	G	G	A	rs61729940	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:31920395G>A	ENST00000396191.1	-	3	662	c.207C>T	c.(205-207)gcC>gcT	p.A69A	PDE1C_ENST00000321453.7_Silent_p.A69A|PDE1C_ENST00000396193.1_Silent_p.A129A|PDE1C_ENST00000396184.3_Silent_p.A69A|PDE1C_ENST00000396182.2_Silent_p.A69A	NM_001191057.1	NP_001177986.1	Q14123	PDE1C_HUMAN	phosphodiesterase 1C, calmodulin-dependent 70kDa	69					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)			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)	CAAGCACTGTGGCTGCATATT	0.318													G|||	613	0.122404	0.028	0.0893	5008	,	,		17872	0.2103		0.1153	False		,,,				2504	0.1902				p.A129A		Atlas-SNP	.											.	PDE1C	465	.	0			c.C387T						PASS	.	G	,,,,	162,4244	109.9+/-148.2	3,156,2044	151.0	144.0	147.0		207,207,387,207,207	3.6	1.0	7	dbSNP_129	147	936,7664	206.9+/-248.8	55,826,3419	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	,,,,	58,982,5463	AA,AG,GG		10.8837,3.6768,8.4423	,,,,	69/635,69/710,129/770,69/710,69/635	31920395	1098,11908	2203	4300	6503	SO:0001819	synonymous_variant	5137	exon4			CACTGTGGCTGCA	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.207C>T	7.37:g.31920395G>A		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	62	9	0.145161	NM_001191058	B3KPC6|E9PE92|Q14124|Q8NB10	Silent	SNP	ENST00000396191.1	37	CCDS55099.1																																																																																			A|0.094;G|0.906;T|0.000	0.094	strong		0.318	PDE1C-006	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000328458.1		
LILRB1	10859	hgsc.bcm.edu	37	19	55143156	55143156	+	Silent	SNP	T	T	C	rs12462774|rs34880987|rs200526666	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:55143156T>C	ENST00000396331.1	+	5	633	c.276T>C	c.(274-276)caT>caC	p.H92H	LILRB1_ENST00000448689.1_Silent_p.H92H|LILRB1_ENST00000396315.1_Silent_p.H92H|LILRB1_ENST00000396321.2_Silent_p.H92H|LILRB1_ENST00000324602.7_Silent_p.H92H|LILRB1_ENST00000427581.2_Silent_p.H128H|LILRB1_ENST00000396327.3_Silent_p.H92H|LILRB1_ENST00000434867.2_Silent_p.H92H|LILRB1_ENST00000396317.1_Silent_p.H92H|LILRB1_ENST00000418536.2_Silent_p.H92H|AC009892.1_ENST00000578908.1_RNA|LILRB1_ENST00000396332.4_Silent_p.H92H	NM_006669.3	NP_006660.3	Q8NHL6	LIRB1_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 1	92	Ig-like C2-type 1.				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)		CCTGGGAACATGCAGGGCGGT	0.552										HNSCC(37;0.09)			N|||	1071	0.213858	0.0575	0.232	5008	,	,		17947	0.505		0.1312	False		,,,				2504	0.1973				p.H92H		Atlas-SNP	.											.	LILRB1	140	.	0			c.T276C						PASS	.	C	,,,	143,4263		8,127,2068	162.0	148.0	153.0		276,276,276,276	-0.2	0.0	19	dbSNP_120	153	608,7992		74,460,3766	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	LILRB1	NM_001081637.1,NM_001081638.1,NM_001081639.1,NM_006669.3	,,,	82,587,5834	CC,CT,TT		7.0698,3.2456,5.7743	,,,	92/653,92/652,92/652,92/651	55143156	751,12255	2203	4300	6503	SO:0001819	synonymous_variant	10859	exon4			GGAACATGCAGGG	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.276T>C	19.37:g.55143156T>C		Somatic	200	0	0		WXS	Illumina HiSeq	Phase_I	149	148	0.993289	NM_001081637	A2IXV4|A8MXT0|O75024|O75025|Q8NHJ9|Q8NHK0	Silent	SNP	ENST00000396331.1	37	CCDS42617.1																																																																																			.	.	alt		0.552	LILRB1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000140796.4		
ANKK1	255239	hgsc.bcm.edu	37	11	113266821	113266821	+	Missense_Mutation	SNP	G	G	A	rs7118900	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:113266821G>A	ENST00000303941.3	+	5	809	c.715G>A	c.(715-717)Gcg>Acg	p.A239T		NM_178510.1	NP_848605.1	Q8NFD2	ANKK1_HUMAN	ankyrin repeat and kinase domain containing 1	239	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		A -> T (in dbSNP:rs7118900). {ECO:0000269|PubMed:17344846}.				ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(2)|lung(14)|ovary(1)|stomach(1)	29		all_cancers(61;1.53e-11)|all_epithelial(67;3e-06)|Melanoma(852;4.04e-05)|all_hematologic(158;0.000315)|Acute lymphoblastic leukemia(157;0.000966)|Breast(348;0.0461)|Medulloblastoma(222;0.0523)|all_neural(223;0.0663)|Prostate(24;0.194)		BRCA - Breast invasive adenocarcinoma(274;4.82e-06)|Epithelial(105;5.41e-05)|all cancers(92;0.000442)|OV - Ovarian serous cystadenocarcinoma(223;0.238)		TATCCGAGTGGCGGCAGGCAT	0.607													G|||	1605	0.320487	0.3744	0.3069	5008	,	,		16275	0.4058		0.1819	False		,,,				2504	0.3119				p.A239T		Atlas-SNP	.											.	ANKK1	83	.	0			c.G715A						PASS	.	G	THR/ALA	1246,2802		199,848,977	61.0	65.0	63.0		715	2.5	0.0	11	dbSNP_116	63	1518,6826		149,1220,2803	yes	missense	ANKK1	NM_178510.1	58	348,2068,3780	AA,AG,GG		18.1927,30.7806,22.3047	possibly-damaging	239/766	113266821	2764,9628	2024	4172	6196	SO:0001583	missense	255239	exon5			CGAGTGGCGGCAG	AJ541797	CCDS44734.1	11q23.2	2013-01-10			ENSG00000170209	ENSG00000170209		"""Ankyrin repeat domain containing"""	21027	protein-coding gene	gene with protein product		608774				15146457	Standard	NM_178510		Approved	X-kinase	uc001pny.3	Q8NFD2	OTTHUMG00000167715	ENST00000303941.3:c.715G>A	11.37:g.113266821G>A	ENSP00000306678:p.Ala239Thr	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	119	24	0.201681	NM_178510		Missense_Mutation	SNP	ENST00000303941.3	37	CCDS44734.1	634	0.2902930402930403	178	0.3617886178861789	98	0.27071823204419887	223	0.38986013986013984	135	0.17810026385224276	G	12.52	1.963618	0.34659	0.307806	0.181927	ENSG00000170209	ENST00000303941	D	0.82619	-1.63	4.44	2.55	0.30701	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.266529	0.24912	U	0.034605	T	0.00012	0.0000	L	0.31578	0.945	0.44006	P	0.0032879999999999576	B	0.26547	0.152	B	0.37304	0.246	T	0.21484	-1.0244	9	0.44086	T	0.13	-1.7695	12.3831	0.55317	0.157:0.0:0.843:0.0	rs7118900;rs59912012;rs7118900	239	Q8NFD2	ANKK1_HUMAN	T	239	ENSP00000306678:A239T	ENSP00000306678:A239T	A	+	1	0	ANKK1	112772031	0.948000	0.32251	0.002000	0.10522	0.001000	0.01503	2.088000	0.41663	0.150000	0.19136	-1.598000	0.00824	GCG	G|0.714;A|0.286	0.286	strong		0.607	ANKK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395830.1	NM_178510	
RYR3	6263	hgsc.bcm.edu	37	15	33905410	33905410	+	Missense_Mutation	SNP	A	A	G	rs2229116	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:33905410A>G	ENST00000389232.4	+	19	2261	c.2191A>G	c.(2191-2193)Atc>Gtc	p.I731V	RYR3_ENST00000415757.3_Missense_Mutation_p.I731V	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	731	B30.2/SPRY 1. {ECO:0000255|PROSITE- ProRule:PRU00548}.		I -> V (in dbSNP:rs2229116). {ECO:0000269|PubMed:9515741}.		calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cellular response to ATP (GO:0071318)|cellular response to caffeine (GO:0071313)|cellular response to calcium ion (GO:0071277)|cellular response to magnesium ion (GO:0071286)|ion transmembrane transport (GO:0034220)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|protein homotetramerization (GO:0051289)|striated muscle contraction (GO:0006941)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|ryanodine-sensitive calcium-release channel activity (GO:0005219)			NS(3)|breast(9)|central_nervous_system(8)|cervix(2)|endometrium(29)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(55)|lung(148)|ovary(7)|pancreas(1)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(3)	311		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)		TGTGGCTTCCATCAACCAGCA	0.602													A|||	1012	0.202077	0.1271	0.3314	5008	,	,		18103	0.1587		0.2247	False		,,,				2504	0.2331				p.I731V		Atlas-SNP	.											RYR3,colon,carcinoma,0,1	RYR3	760	1	0			c.A2191G						scavenged	.	A	VAL/ILE	576,3604		30,516,1544	38.0	41.0	40.0	http://www.ncbi.nlm.nih.gov/pubmed?term	2191	3.1	1.0	15	dbSNP_98	40	1824,6658		203,1418,2620	yes	missense	RYR3	NM_001036.3	29	233,1934,4164	GG,GA,AA	http://www.ncbi.nlm.nih.gov/pubmed?term	21.5044,13.7799,18.9544	benign	731/4871	33905410	2400,10262	2090	4241	6331	SO:0001583	missense	6263	exon19			GCTTCCATCAACC		CCDS45210.1, CCDS58351.1	15q14-q15	2013-01-10				ENSG00000198838		"""Ion channels / Ryanodine receptors"", ""EF-hand domain containing"""	10485	protein-coding gene	gene with protein product		180903				8276408	Standard	NM_001036		Approved		uc001zhi.3	Q15413		ENST00000389232.4:c.2191A>G	15.37:g.33905410A>G	ENSP00000373884:p.Ile731Val	Somatic	138	1	0.00724638		WXS	Illumina HiSeq	Phase_I	115	55	0.478261	NM_001243996	O15175|Q15412	Missense_Mutation	SNP	ENST00000389232.4	37	CCDS45210.1	477	0.2184065934065934	89	0.18089430894308944	114	0.3149171270718232	98	0.17132867132867133	176	0.23218997361477572	A	8.841	0.942258	0.18281	0.137799	0.215044	ENSG00000198838	ENST00000389232;ENST00000415757;ENST00000361728	T;T	0.68331	-0.32;-0.32	5.4	3.06	0.35304	Concanavalin A-like lectin/glucanase (1);SPla/RYanodine receptor subgroup (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	0.296753	0.33457	N	0.004896	T	0.00012	0.0000	N	0.19112	0.55	0.39187	P	0.037104000000000026	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.18147	-1.0346	9	0.15952	T	0.53	.	2.9905	0.05981	0.4962:0.232:0.2718:0.0	rs2229116;rs2277889;rs8042362;rs17817397;rs52825179;rs58186010;rs2229116	731;731	Q15413-2;Q15413	.;RYR3_HUMAN	V	731	ENSP00000373884:I731V;ENSP00000399610:I731V	ENSP00000354735:I731V	I	+	1	0	RYR3	31692702	0.999000	0.42202	1.000000	0.80357	0.997000	0.91878	0.792000	0.26929	1.079000	0.41038	0.529000	0.55759	ATC	A|0.790;G|0.210	0.210	strong		0.602	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1		
MAP1A	4130	hgsc.bcm.edu	37	15	43816917	43816917	+	Silent	SNP	G	G	A	rs1060939	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:43816917G>A	ENST00000300231.5	+	4	3696	c.3246G>A	c.(3244-3246)ggG>ggA	p.G1082G	MAP1A_ENST00000399453.1_Silent_p.G1082G|MAP1A_ENST00000382031.1_Silent_p.G1320G			P78559	MAP1A_HUMAN	microtubule-associated protein 1A	1082					microtubule cytoskeleton organization (GO:0000226)|sensory perception of sound (GO:0007605)	cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)	structural molecule activity (GO:0005198)			breast(5)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(11)|liver(2)|lung(19)|ovary(5)|pancreas(3)|prostate(2)|skin(6)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	66		all_cancers(109;1.03e-14)|all_epithelial(112;2.23e-12)|Lung NSC(122;2.76e-08)|all_lung(180;3.1e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;3.05e-06)	Estramustine(DB01196)	TTGATGAGGGGCTTACAGGCT	0.542													A|||	2648	0.528754	0.972	0.3329	5008	,	,		20623	0.4177		0.2962	False		,,,				2504	0.4223				p.G1082G		Atlas-SNP	.											.	MAP1A	189	.	0			c.G3246A						PASS	.	A		3210,676		1336,538,69	77.0	81.0	80.0		3246	-0.4	0.0	15	dbSNP_86	80	2441,5843		346,1749,2047	yes	coding-synonymous	MAP1A	NM_002373.5		1682,2287,2116	AA,AG,GG		29.4664,17.3958,46.4339		1082/2804	43816917	5651,6519	1943	4142	6085	SO:0001819	synonymous_variant	4130	exon4			TGAGGGGCTTACA	U38292	CCDS42031.1	15q15.3	2006-06-15			ENSG00000166963	ENSG00000166963			6835	protein-coding gene	gene with protein product		600178		MAP1L		7806212, 7629894	Standard	XM_005254385		Approved		uc001zrt.3	P78559	OTTHUMG00000059756	ENST00000300231.5:c.3246G>A	15.37:g.43816917G>A		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	141	43	0.304965	NM_002373	O95643|Q12973|Q15882|Q9UJT4	Silent	SNP	ENST00000300231.5	37	CCDS42031.1																																																																																			G|0.497;A|0.503	0.503	strong		0.542	MAP1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000132894.5	NM_002373	
HGFAC	3083	hgsc.bcm.edu	37	4	3451109	3451109	+	Missense_Mutation	SNP	G	G	A	rs2498323	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	234	0	0		WXS	Illumina HiSeq	Phase_I	217	99	0.456221	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		
ENTPD6	955	hgsc.bcm.edu	37	20	25193949	25193949	+	Silent	SNP	G	G	A	rs2076561	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:25193949G>A	ENST00000376652.4	+	5	667	c.504G>A	c.(502-504)ccG>ccA	p.P168P	Y_RNA_ENST00000365544.1_RNA|ENTPD6_ENST00000433259.2_Silent_p.P168P|ENTPD6_ENST00000360031.2_Silent_p.P167P|ENTPD6_ENST00000354989.5_Silent_p.P151P			O75354	ENTP6_HUMAN	ectonucleoside triphosphate diphosphohydrolase 6 (putative)	168					response to calcium ion (GO:0051592)|response to magnesium ion (GO:0032026)	cell surface (GO:0009986)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	guanosine-5'-triphosphate,3'-diphosphate diphosphatase activity (GO:0008894)|nucleoside-triphosphatase activity (GO:0017111)|uridine-diphosphatase activity (GO:0045134)			breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(16)|prostate(1)|skin(1)	27						AGGACATTCCGTTCGACTTCT	0.547													G|||	1553	0.310104	0.0983	0.2262	5008	,	,		20740	0.5913		0.3459	False		,,,				2504	0.3292				p.P168P		Atlas-SNP	.											ENTPD6,face,carcinoma,+2,1	ENTPD6	57	1	0			c.G504A						PASS	.	G	,	619,3787	269.2+/-268.9	42,535,1626	169.0	127.0	141.0		453,504	-11.6	0.0	20	dbSNP_96	141	2765,5835	439.7+/-359.3	431,1903,1966	no	coding-synonymous,coding-synonymous	ENTPD6	NM_001114089.1,NM_001247.2	,	473,2438,3592	AA,AG,GG		32.1512,14.049,26.0188	,	151/468,168/485	25193949	3384,9622	2203	4300	6503	SO:0001819	synonymous_variant	955	exon5			CATTCCGTTCGAC	AF039916	CCDS13170.1, CCDS46586.1	20p11.21	2010-06-24	2010-06-24		ENSG00000197586	ENSG00000197586			3368	protein-coding gene	gene with protein product		603160	"""interleukin 6 signal transducer-2"""	CD39L2, IL6ST2		9676430	Standard	NM_001247		Approved	NTPDase-6, dJ738P15.3	uc002wuj.2	O75354	OTTHUMG00000032116	ENST00000376652.4:c.504G>A	20.37:g.25193949G>A		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	66	36	0.545455	NM_001247	A6NCX6|D3DW49|Q5QPJ2|Q5QPJ5|Q7Z5B5|Q8N3H3|Q8TAS7|Q9UJD1	Silent	SNP	ENST00000376652.4	37	CCDS13170.1	755	0.3456959706959707	59	0.11991869918699187	92	0.2541436464088398	346	0.6048951048951049	258	0.3403693931398417	G	0.470	-0.885057	0.02511	0.14049	0.321512	ENSG00000197586	ENST00000433417;ENST00000447877	.	.	.	5.79	-11.6	0.00059	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.99999999861442	.	.	.	.	.	.	T	0.26608	-1.0098	3	.	.	.	-1.1705	1.9584	0.03381	0.1245:0.3117:0.2786:0.2853	rs2076561;rs17250460;rs58880188;rs2076561	.	.	.	H	89;61	.	.	R	+	2	0	ENTPD6	25141949	0.000000	0.05858	0.008000	0.14137	0.056000	0.15407	-2.000000	0.01466	-3.712000	0.00117	-2.589000	0.00165	CGT	G|0.708;A|0.292	0.292	strong		0.547	ENTPD6-020	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078414.2		
RTN3	10313	hgsc.bcm.edu	37	11	63486204	63486204	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:63486204C>T	ENST00000377819.5	+	3	384	c.230C>T	c.(229-231)cCa>cTa	p.P77L	RTN3_ENST00000341307.2_Intron|RTN3_ENST00000339997.4_Missense_Mutation_p.P58L|RTN3_ENST00000540798.1_Intron|RTN3_ENST00000356000.3_Intron|RTN3_ENST00000537981.1_Intron|RTN3_ENST00000354497.4_Intron	NM_001265589.1	NP_001252518.1	O95197	RTN3_HUMAN	reticulon 3	77					apoptotic process (GO:0006915)|endoplasmic reticulum tubular network organization (GO:0071786)|response to stress (GO:0006950)|vesicle-mediated transport (GO:0016192)|viral process (GO:0016032)	endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(9)|ovary(1)|skin(1)|urinary_tract(1)	20						TCTGATGAGCCATCTTCAGAA	0.378																																					p.P77L		Atlas-SNP	.											.	RTN3	104	.	0			c.C230T						PASS	.						44.0	42.0	43.0					11																	63486204		2201	4298	6499	SO:0001583	missense	10313	exon3			ATGAGCCATCTTC	AF059524	CCDS8048.1, CCDS8049.1, CCDS8050.1, CCDS41664.1, CCDS58141.1, CCDS58142.1, CCDS58143.1	11q13	2011-01-14			ENSG00000133318	ENSG00000133318			10469	protein-coding gene	gene with protein product	"""neuroendocrine-specific protein-like 2"", ""NSP-like protein II"", ""isoforme III"", ""ASY interacting protein"", ""homolog of ASY protein"""	604249				10331947	Standard	NM_006054		Approved	NSPL2, NSPLII, ASYIP, HAP, RTN3-A1	uc001nxq.3	O95197		ENST00000377819.5:c.230C>T	11.37:g.63486204C>T	ENSP00000367050:p.Pro77Leu	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	42	12	0.285714	NM_001265589	B3KQS2|B7Z308|B7Z4M0|F5H774|Q147U9|Q496K2|Q53GN3|Q59EP0|Q5UEP2|Q6T930|Q7RTM7|Q7RTM8|Q7RTN3	Missense_Mutation	SNP	ENST00000377819.5	37	CCDS58141.1	.	.	.	.	.	.	.	.	.	.	C	13.42	2.231150	0.39399	.	.	ENSG00000133318	ENST00000377819;ENST00000339997	T;T	0.27104	1.82;1.69	5.84	3.81	0.43845	.	1.261160	0.05469	N	0.552739	T	0.22627	0.0546	L	0.27053	0.805	0.80722	D	1	B;P	0.36535	0.421;0.557	B;B	0.36418	0.04;0.224	T	0.03473	-1.1033	10	0.87932	D	0	-9.0E-4	10.0371	0.42135	0.1446:0.6966:0.1589:0.0	.	77;58	O95197;O95197-2	RTN3_HUMAN;.	L	77;58	ENSP00000367050:P77L;ENSP00000344106:P58L	ENSP00000344106:P58L	P	+	2	0	RTN3	63242780	0.997000	0.39634	1.000000	0.80357	0.466000	0.32739	1.436000	0.34980	1.412000	0.46977	0.591000	0.81541	CCA	.	.	none		0.378	RTN3-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000397846.1	NM_006054	
MYOM2	9172	hgsc.bcm.edu	37	8	2037833	2037833	+	Silent	SNP	G	G	C	rs2294061	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:2037833G>C	ENST00000262113.4	+	15	1788	c.1647G>C	c.(1645-1647)tcG>tcC	p.S549S	MYOM2_ENST00000523438.1_5'UTR	NM_003970.2	NP_003961.2	P54296	MYOM2_HUMAN	myomesin 2	549	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				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)		CTTTGTAGTCGGTGGTGGGGA	0.557													C|||	1122	0.224042	0.4244	0.1628	5008	,	,		18049	0.2083		0.162	False		,,,				2504	0.0767				p.S549S		Atlas-SNP	.											.	MYOM2	251	.	0			c.G1647C						PASS	.	C		1674,2732	650.5+/-399.1	321,1032,850	64.0	65.0	65.0		1647	-5.2	0.0	8	dbSNP_100	65	1257,7343	756.6+/-407.5	92,1073,3135	no	coding-synonymous	MYOM2	NM_003970.2		413,2105,3985	CC,CG,GG		14.6163,37.9936,22.5358		549/1466	2037833	2931,10075	2203	4300	6503	SO:0001819	synonymous_variant	9172	exon15			GTAGTCGGTGGTG		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.1647G>C	8.37:g.2037833G>C		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	90	63	0.7	NM_003970	Q7Z3Y2	Silent	SNP	ENST00000262113.4	37	CCDS5957.1																																																																																			G|0.783;C|0.217	0.217	strong		0.557	MYOM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251249.1	NM_003970	
MUC4	4585	hgsc.bcm.edu	37	3	195513397	195513397	+	Missense_Mutation	SNP	C	C	T	rs201019164		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195513397C>T	ENST00000463781.3	-	2	5513	c.5054G>A	c.(5053-5055)gGc>gAc	p.G1685D	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.G1685D	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.G1685D(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)		TGAGGAAAGGCCGGTGACAGG	0.612																																					p.G1685D		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,-1,3	MUC4	1505	3	2	Substitution - Missense(2)	stomach(2)	c.G5054A						PASS	.						33.0	37.0	36.0					3																	195513397		683	1580	2263	SO:0001583	missense	4585	exon2			GAAAGGCCGGTGA	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.5054G>A	3.37:g.195513397C>T	ENSP00000417498:p.Gly1685Asp	Somatic	240	0	0		WXS	Illumina HiSeq	Phase_I	156	14	0.0897436	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	-	3.321	-0.138745	0.06669	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.31247	1.5;1.7	.	.	.	.	.	.	.	.	T	0.13927	0.0337	N	0.19112	0.55	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.23868	-1.0176	7	.	.	.	.	3.9954	0.09556	0.0:0.3367:0.0:0.6633	.	1685	E7ESK3	.	D	1685	ENSP00000417498:G1685D;ENSP00000420243:G1685D	.	G	-	2	0	MUC4	196997792	0.000000	0.05858	0.011000	0.14972	0.005000	0.04900	0.016000	0.13377	-1.791000	0.01261	-1.780000	0.00649	GGC	.	.	weak		0.612	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
SLC7A6OS	84138	hgsc.bcm.edu	37	16	68336360	68336360	+	Silent	SNP	A	A	G	rs35736950	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:68336360A>G	ENST00000263997.6	-	4	741	c.723T>C	c.(721-723)gaT>gaC	p.D241D		NM_032178.2	NP_115554.2	Q96CW6	S7A6O_HUMAN	solute carrier family 7, member 6 opposite strand	241					hematopoietic progenitor cell differentiation (GO:0002244)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|endometrium(1)|large_intestine(2)|lung(5)|ovary(1)	10		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.034)|Epithelial(162;0.106)		TGTTCTCGTCATCTTCATCGT	0.488													A|||	96	0.0191693	0.0045	0.0274	5008	,	,		22567	0.0		0.0626	False		,,,				2504	0.0082				p.D241D		Atlas-SNP	.											.	SLC7A6OS	22	.	0			c.T723C						PASS	.	A		54,4342	52.9+/-88.7	1,52,2145	355.0	273.0	301.0		723	4.6	1.0	16	dbSNP_126	301	437,8163	133.5+/-191.0	9,419,3872	no	coding-synonymous	SLC7A6OS	NM_032178.2		10,471,6017	GG,GA,AA		5.0814,1.2284,3.7781		241/310	68336360	491,12505	2198	4300	6498	SO:0001819	synonymous_variant	84138	exon4			CTCGTCATCTTCA		CCDS10865.1	16q22.1	2010-03-11			ENSG00000103061	ENSG00000103061			25807	protein-coding gene	gene with protein product							Standard	NM_032178		Approved	FLJ13291	uc002evw.2	Q96CW6	OTTHUMG00000137558	ENST00000263997.6:c.723T>C	16.37:g.68336360A>G		Somatic	280	1	0.00357143		WXS	Illumina HiSeq	Phase_I	323	191	0.591331	NM_032178	Q8TCZ3|Q9H8R8	Silent	SNP	ENST00000263997.6	37	CCDS10865.1																																																																																			A|0.965;G|0.035	0.035	strong		0.488	SLC7A6OS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268894.3	NM_032178	
PCDHB11	56125	hgsc.bcm.edu	37	5	140580772	140580772	+	Silent	SNP	T	T	C	rs57636116	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	122	0	0		WXS	Illumina HiSeq	Phase_I	119	63	0.529412	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	
ILDR1	286676	hgsc.bcm.edu	37	3	121712051	121712051	+	Silent	SNP	A	A	C	rs2877561	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:121712051A>C	ENST00000344209.5	-	7	1671	c.1545T>G	c.(1543-1545)ctT>ctG	p.L515L	ILDR1_ENST00000393631.1_Silent_p.L426L|ILDR1_ENST00000460554.1_5'UTR|ILDR1_ENST00000462014.1_Silent_p.L483L|ILDR1_ENST00000273691.3_Silent_p.L471L	NM_001199799.1	NP_001186728.1	Q86SU0	ILDR1_HUMAN	immunoglobulin-like domain containing receptor 1	515					positive regulation of peptide hormone secretion (GO:0090277)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	high-density lipoprotein particle receptor activity (GO:0070506)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(10)|lung(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	25				GBM - Glioblastoma multiforme(114;0.156)		GAGTGATATCAAGTGAGCGGT	0.637													C|||	3931	0.784944	0.8298	0.5965	5008	,	,		18208	0.9196		0.7087	False		,,,				2504	0.7975				p.L515L		Atlas-SNP	.											.	ILDR1	120	.	0			c.T1545G						PASS	.	C	,,	3599,807	303.0+/-287.7	1478,643,82	43.0	37.0	39.0		1545,1278,1413	3.7	1.0	3	dbSNP_101	39	6127,2473	382.4+/-340.4	2198,1731,371	no	coding-synonymous,coding-synonymous,coding-synonymous	ILDR1	NM_001199799.1,NM_001199800.1,NM_175924.3	,,	3676,2374,453	CC,CA,AA		28.7558,18.3159,25.2191	,,	515/547,426/458,471/503	121712051	9726,3280	2203	4300	6503	SO:0001819	synonymous_variant	286676	exon7			GATATCAAGTGAG	BC044240	CCDS3008.1, CCDS56270.1, CCDS56271.1	3q21.1	2013-10-11			ENSG00000145103	ENSG00000145103			28741	protein-coding gene	gene with protein product		609739	"""deafness, autosomal recessive 42"""	DFNB42		15641023, 21255762	Standard	NM_175924		Approved	MGC50831	uc003ees.3	Q86SU0	OTTHUMG00000159481	ENST00000344209.5:c.1545T>G	3.37:g.121712051A>C		Somatic	222	0	0		WXS	Illumina HiSeq	Phase_I	249	246	0.987952	NM_001199799	Q6ZP61|Q7Z578	Silent	SNP	ENST00000344209.5	37	CCDS56271.1																																																																																			A|0.224;C|0.776	0.776	strong		0.637	ILDR1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355666.1	NM_175924	
DEFB110	245913	hgsc.bcm.edu	37	6	49986788	49986788	+	Nonsense_Mutation	SNP	T	T	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:49986788T>A	ENST00000371148.2	-	2	151	c.106A>T	c.(106-108)Aga>Tga	p.R36*	DEFB110_ENST00000393660.2_Intron	NM_001037497.1	NP_001032586.1	Q30KQ9	DB110_HUMAN	defensin, beta 110 locus	36					defense response to bacterium (GO:0042742)	extracellular region (GO:0005576)				endometrium(1)|lung(1)|ovary(1)	3	Lung NSC(77;0.042)					TTACCTATTCTGCACTCTCTC	0.393																																					p.R36X		Atlas-SNP	.											.	DEFB110	5	.	0			c.A106T						PASS	.						176.0	158.0	164.0					6																	49986788		2203	4300	6503	SO:0001587	stop_gained	245913	exon2			CTATTCTGCACTC	DQ012014, BC148541	CCDS43473.1, CCDS34475.1	6p12.3	2010-11-26	2010-11-26		ENSG00000203970	ENSG00000203970		"""Defensins, beta"""	18091	protein-coding gene	gene with protein product			"""defensin, beta 110"""			11854508, 16033865	Standard	NM_001037728		Approved	DEFB-10, DEFB-11, DEFB111	uc003pac.3	Q30KQ9	OTTHUMG00000160208	ENST00000371148.2:c.106A>T	6.37:g.49986788T>A	ENSP00000360190:p.Arg36*	Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	168	40	0.238095	NM_001037497	Q30KR0	Nonsense_Mutation	SNP	ENST00000371148.2	37	CCDS34475.1	.	.	.	.	.	.	.	.	.	.	T	9.497	1.102324	0.20632	.	.	ENSG00000203970	ENST00000371148	.	.	.	5.03	1.22	0.21188	.	1.271720	0.05234	N	0.510955	.	.	.	.	.	.	0.58432	D	0.999999	.	.	.	.	.	.	.	.	.	.	.	.	.	-0.0123	3.4489	0.07491	0.167:0.1849:0.0:0.6482	.	.	.	.	X	36	.	.	R	-	1	2	DEFB110	50094747	0.848000	0.29623	0.483000	0.27378	0.035000	0.12851	1.146000	0.31589	0.390000	0.25115	-0.333000	0.08304	AGA	.	.	none		0.393	DEFB110-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359664.1	NM_001037728	
ZKSCAN2	342357	hgsc.bcm.edu	37	16	25263278	25263278	+	Missense_Mutation	SNP	G	G	A	rs2112811	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:25263278G>A	ENST00000328086.7	-	4	1560	c.757C>T	c.(757-759)Ctc>Ttc	p.L253F		NM_001012981.4	NP_001012999.3	Q63HK3	ZKSC2_HUMAN	zinc finger with KRAB and SCAN domains 2	253	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.		L -> F (in dbSNP:rs2112811).		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)	p.L253F(1)		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)		TCCCGGTAGAGGTCCCTTTGG	0.463													G|||	1676	0.334665	0.475	0.3026	5008	,	,		18379	0.3284		0.2107	False		,,,				2504	0.3016				p.L253F		Atlas-SNP	.											ZKSCAN2,NS,adenoma,0,2	ZKSCAN2	90	2	1	Substitution - Missense(1)	stomach(1)	c.C757T						PASS	.	G	PHE/LEU	1987,2407	558.4+/-380.0	453,1081,663	112.0	107.0	109.0		757	2.5	0.4	16	dbSNP_96	109	1785,6815	321.8+/-315.3	181,1423,2696	yes	missense	ZKSCAN2	NM_001012981.4	22	634,2504,3359	AA,AG,GG		20.7558,45.2208,29.0288	probably-damaging	253/968	25263278	3772,9222	2197	4300	6497	SO:0001583	missense	342357	exon4			GGTAGAGGTCCCT	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.757C>T	16.37:g.25263278G>A	ENSP00000331626:p.Leu253Phe	Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	186	79	0.424731	NM_001012981	A1L3B4|Q6ZN77	Missense_Mutation	SNP	ENST00000328086.7	37	CCDS32410.1	664	0.304029304029304	234	0.47560975609756095	91	0.2513812154696133	178	0.3111888111888112	161	0.21240105540897097	G	6.020	0.372047	0.11409	0.452208	0.207558	ENSG00000155592	ENST00000328086;ENST00000536768	T	0.01252	5.1	5.94	2.52	0.30459	Krueppel-associated box (3);	0.333284	0.26460	N	0.024258	T	0.00012	0.0000	M	0.83118	2.625	0.80722	P	0.0	B;B;B	0.24651	0.01;0.108;0.014	B;B;B	0.33799	0.019;0.17;0.008	T	0.24012	-1.0172	9	0.25106	T	0.35	-8.6474	8.299	0.32004	0.2803:0.0:0.7197:0.0	rs2112811;rs17717427;rs58715832;rs2112811	49;253;253	B4DYF0;Q63HK3-2;Q63HK3	.;.;ZKSC2_HUMAN	F	253	ENSP00000331626:L253F	ENSP00000331626:L253F	L	-	1	0	ZKSCAN2	25170779	0.020000	0.18652	0.390000	0.26220	0.512000	0.34134	0.592000	0.23984	0.866000	0.35629	0.561000	0.74099	CTC	G|0.696;N|0.000	.	strong		0.463	ZKSCAN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435739.1	NM_001012981	
ATXN1	6310	hgsc.bcm.edu	37	6	16327330	16327330	+	Silent	SNP	T	T	C	rs2075974	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:16327330T>C	ENST00000244769.4	-	8	2148	c.1212A>G	c.(1210-1212)gaA>gaG	p.E404E	ATXN1_ENST00000436367.1_Silent_p.E404E	NM_000332.3	NP_000323.2	P54253	ATX1_HUMAN	ataxin 1	404					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)				AAGGGGAGGCTTCACGATGAG	0.617													C|||	1849	0.369209	0.4569	0.2075	5008	,	,		17432	0.4772		0.2147	False		,,,				2504	0.4131				p.E404E		Atlas-SNP	.											.	ATXN1	117	.	0			c.A1212G						PASS	.	C	,	1908,2498	627.3+/-394.9	401,1106,696	163.0	180.0	174.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1212,1212	0.5	0.9	6	dbSNP_96	174	1746,6854	735.8+/-407.0	165,1416,2719	no	coding-synonymous,coding-synonymous	ATXN1	NM_000332.3,NM_001128164.1	,	566,2522,3415	CC,CT,TT		20.3023,43.3046,28.0947	,	404/816,404/816	16327330	3654,9352	2203	4300	6503	SO:0001819	synonymous_variant	6310	exon7			GGAGGCTTCACGA	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.1212A>G	6.37:g.16327330T>C		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	45	20	0.444444	NM_001128164	Q17S02|Q9UJG2|Q9Y4J1	Silent	SNP	ENST00000244769.4	37	CCDS34342.1																																																																																			T|0.695;C|0.305	0.305	strong		0.617	ATXN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039943.3	NM_000332	
KRTAP12-3	386683	hgsc.bcm.edu	37	21	46077946	46077946	+	Missense_Mutation	SNP	A	A	G	rs9306111	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:46077946A>G	ENST00000397907.1	+	1	98	c.50A>G	c.(49-51)cAc>cGc	p.H17R	TSPEAR_ENST00000323084.4_Intron	NM_198697.2	NP_941970.2	P60328	KR123_HUMAN	keratin associated protein 12-3	17	14 X 5 AA approximate repeats.		H -> R (in dbSNP:rs9306111). {ECO:0000269|PubMed:15028290}.			keratin filament (GO:0045095)				central_nervous_system(1)|lung(2)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	7						TGCTGCATACACAGCCCCTGC	0.647													a|||	3954	0.789537	0.9198	0.7507	5008	,	,		18260	0.6637		0.7624	False		,,,				2504	0.7986				p.H17R		Atlas-SNP	.											.	KRTAP12-3	18	.	0			c.A50G						PASS	.	G	,ARG/HIS	3882,478		1732,418,30	73.0	88.0	83.0		,50	3.0	0.0	21	dbSNP_119	83	6083,2455		2194,1695,380	yes	intron,missense	TSPEAR,KRTAP12-3	NM_144991.2,NM_198697.2	,29	3926,2113,410	GG,GA,AA		28.7538,10.9633,22.74	,benign	,17/97	46077946	9965,2933	2180	4269	6449	SO:0001583	missense	386683	exon1			GCATACACAGCCC	AB076361	CCDS42964.1	21q22.3	2006-03-13			ENSG00000205439	ENSG00000205439		"""Keratin associated proteins"""	20531	protein-coding gene	gene with protein product							Standard	NM_198697		Approved	KRTAP12.3	uc002zft.3	P60328	OTTHUMG00000057630	ENST00000397907.1:c.50A>G	21.37:g.46077946A>G	ENSP00000381005:p.His17Arg	Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	146	144	0.986301	NM_198697		Missense_Mutation	SNP	ENST00000397907.1	37	CCDS42964.1	1680	0.7692307692307693	455	0.9247967479674797	279	0.7707182320441989	366	0.6398601398601399	580	0.7651715039577837	N	4.837	0.155633	0.09236	0.890367	0.712462	ENSG00000205439	ENST00000546091;ENST00000397907	T	0.01304	5.03	4.9	3.03	0.35002	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.08764	-1.0706	7	0.54805	T	0.06	.	3.3378	0.07107	0.1737:0.56:0.1678:0.0985	rs9306111;rs57807884	17	P60328	KR123_HUMAN	R	31;17	ENSP00000381005:H17R	ENSP00000381005:H17R	H	+	2	0	KRTAP12-3	44902374	0.000000	0.05858	0.022000	0.16811	0.028000	0.11728	-0.359000	0.07632	0.116000	0.18110	-2.261000	0.00279	CAC	A|0.246;G|0.754	0.754	strong		0.647	KRTAP12-3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128033.1		
FSCB	84075	hgsc.bcm.edu	37	14	44975349	44975349	+	Missense_Mutation	SNP	G	G	A	rs139581441	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:44975349G>A	ENST00000340446.4	-	1	1133	c.842C>T	c.(841-843)gCg>gTg	p.A281V	RP11-163M18.1_ENST00000557465.1_RNA|RP11-163M18.1_ENST00000555433.1_RNA|RP11-163M18.1_ENST00000556228.1_RNA	NM_032135.3	NP_115511.3	Q5H9T9	FSCB_HUMAN	fibrous sheath CABYR binding protein	281						sperm fibrous sheath (GO:0035686)|sperm principal piece (GO:0097228)	calcium ion binding (GO:0005509)			breast(4)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(10)|lung(47)|ovary(2)|pancreas(1)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(1)	89				GBM - Glioblastoma multiforme(112;0.128)		TCTGGGCTCCGCTTTAGCAGT	0.483													G|||	5	0.000998403	0.003	0.0	5008	,	,		16874	0.0		0.001	False		,,,				2504	0.0				p.A281V		Atlas-SNP	.											FSCB,NS,carcinoma,0,1	FSCB	173	1	0			c.C842T						PASS	.	G	VAL/ALA	11,4395	17.9+/-39.9	0,11,2192	55.0	57.0	56.0		842	-7.7	0.0	14	dbSNP_134	56	30,8570	20.4+/-63.3	1,28,4271	yes	missense	FSCB	NM_032135.3	64	1,39,6463	AA,AG,GG		0.3488,0.2497,0.3152	benign	281/826	44975349	41,12965	2203	4300	6503	SO:0001583	missense	84075	exon1			GGCTCCGCTTTAG	AK124110	CCDS9679.1	14q21.3	2007-11-22	2007-11-22	2007-11-22	ENSG00000189139	ENSG00000189139			20494	protein-coding gene	gene with protein product		611779	"""chromosome 14 open reading frame 155"""	C14orf155		17855365	Standard	NM_032135		Approved	DKFZP434F1017	uc001wvn.3	Q5H9T9	OTTHUMG00000140262	ENST00000340446.4:c.842C>T	14.37:g.44975349G>A	ENSP00000344579:p.Ala281Val	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	89	37	0.41573	NM_032135	Q5H9U7|Q86YI2|Q9H0J3	Missense_Mutation	SNP	ENST00000340446.4	37	CCDS9679.1	.	.	.	.	.	.	.	.	.	.	G	0.019	-1.452098	0.01080	0.002497	0.003488	ENSG00000189139	ENST00000340446;ENST00000537803	T	0.25414	1.8	3.86	-7.73	0.01245	.	.	.	.	.	T	0.11623	0.0283	L	0.29908	0.895	0.09310	N	1	B	0.28971	0.229	B	0.15870	0.014	T	0.12066	-1.0562	9	0.18710	T	0.47	1.4119	6.3551	0.21397	0.1309:0.2257:0.5317:0.1117	.	281	Q5H9T9	FSCB_HUMAN	V	281	ENSP00000344579:A281V	ENSP00000344579:A281V	A	-	2	0	FSCB	44045099	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.261000	0.02855	-2.588000	0.00458	-1.224000	0.01588	GCG	G|0.997;A|0.003	0.003	strong		0.483	FSCB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276788.1	NM_032135	
ANO8	57719	hgsc.bcm.edu	37	19	17439450	17439450	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:17439450C>T	ENST00000159087.4	-	13	1905	c.1747G>A	c.(1747-1749)Gag>Aag	p.E583K		NM_020959.2	NP_066010.1	Q9HCE9	ANO8_HUMAN	anoctamin 8	583	Glu-rich.				chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	intracellular calcium activated chloride channel activity (GO:0005229)			autonomic_ganglia(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(7)|ovary(4)|pancreas(1)|prostate(2)|urinary_tract(3)	27						tcctcgtcctcctcctTGCCC	0.741																																					p.E583K		Atlas-SNP	.											.	ANO8	67	.	0			c.G1747A						PASS	.						7.0	6.0	6.0					19																	17439450		2003	3931	5934	SO:0001583	missense	57719	exon13			CGTCCTCCTCCTT	AB046843	CCDS32949.1	19p13.12	2014-04-09	2008-08-28	2008-08-28		ENSG00000074855		"""Ion channels / Chloride channels : Calcium activated : Anoctamins"""	29329	protein-coding gene	gene with protein product		610216	"""KIAA1623"", ""transmembrane protein 16H"""	KIAA1623, TMEM16H		10997877, 24692353	Standard	NM_020959		Approved		uc002ngf.2	Q9HCE9		ENST00000159087.4:c.1747G>A	19.37:g.17439450C>T	ENSP00000159087:p.Glu583Lys	Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	22	4	0.181818	NM_020959	A6NIJ0	Missense_Mutation	SNP	ENST00000159087.4	37	CCDS32949.1	.	.	.	.	.	.	.	.	.	.	C	16.10	3.027094	0.54683	.	.	ENSG00000074855	ENST00000159087	T	0.61859	0.07	5.3	5.3	0.74995	.	0.247398	0.27836	N	0.017658	T	0.46112	0.1376	N	0.08118	0	0.38121	D	0.937857	P	0.37914	0.611	P	0.45998	0.5	T	0.52200	-0.8607	10	0.31617	T	0.26	.	14.4449	0.67342	0.0:1.0:0.0:0.0	.	583	Q9HCE9	ANO8_HUMAN	K	583	ENSP00000159087:E583K	ENSP00000159087:E583K	E	-	1	0	ANO8	17300450	0.150000	0.22732	0.996000	0.52242	0.352000	0.29268	0.878000	0.28126	2.489000	0.83994	0.484000	0.47621	GAG	.	.	none		0.741	ANO8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462943.1	XM_050644	
ZNF14	7561	hgsc.bcm.edu	37	19	19823270	19823270	+	Missense_Mutation	SNP	T	T	A	rs12973901	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:19823270T>A	ENST00000344099.3	-	4	958	c.820A>T	c.(820-822)Act>Tct	p.T274S		NM_021030.2	NP_066358.2	P17017	ZNF14_HUMAN	zinc finger protein 14	274			T -> S (in dbSNP:rs12973901). {ECO:0000269|Ref.1}.		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|cervix(2)|endometrium(1)|large_intestine(9)|lung(8)|ovary(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)	32		Renal(1328;0.0474)				TTTTCTCCAGTGTGAGTTCTT	0.403													T|||	915	0.182708	0.0265	0.1657	5008	,	,		19776	0.2649		0.2376	False		,,,				2504	0.2648				p.T274S		Atlas-SNP	.											.	ZNF14	89	.	0			c.A820T						PASS	.	T	SER/THR	245,4161	137.7+/-173.5	4,237,1962	47.0	46.0	46.0		820	1.8	0.0	19	dbSNP_121	46	2206,6392	362.0+/-332.6	297,1612,2390	yes	missense	ZNF14	NM_021030.2	58	301,1849,4352	AA,AT,TT		25.6571,5.5606,18.848	benign	274/643	19823270	2451,10553	2203	4299	6502	SO:0001583	missense	7561	exon4			CTCCAGTGTGAGT	AA286756	CCDS12409.1	19p13.11	2013-01-08	2006-05-10					"""Zinc fingers, C2H2-type"", ""-"""	12924	protein-coding gene	gene with protein product		194556	"""zinc finger protein 14 (KOX 6)"""				Standard	NM_021030		Approved	KOX6, GIOT-4	uc002nnk.1	P17017		ENST00000344099.3:c.820A>T	19.37:g.19823270T>A	ENSP00000340514:p.Thr274Ser	Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	44	29	0.659091	NM_021030	B9EGA4|Q9ULZ5	Missense_Mutation	SNP	ENST00000344099.3	37	CCDS12409.1	413	0.1891025641025641	6	0.012195121951219513	72	0.19889502762430938	155	0.270979020979021	180	0.23746701846965698	T	17.92	3.505752	0.64410	0.055606	0.256571	ENSG00000105708	ENST00000344099	T	0.24151	1.87	1.8	1.8	0.24995	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	N	0.25380	0.74	0.40981	P	0.015221999999999958	B	0.22909	0.077	B	0.19666	0.026	T	0.34153	-0.9840	8	0.54805	T	0.06	.	7.2278	0.26026	0.0:0.0:0.0:1.0	rs12973901;rs52831253;rs12973901	274	P17017	ZNF14_HUMAN	S	274	ENSP00000340514:T274S	ENSP00000340514:T274S	T	-	1	0	ZNF14	19684270	1.000000	0.71417	0.013000	0.15412	0.442000	0.32017	5.501000	0.66950	0.811000	0.34303	0.383000	0.25322	ACT	T|0.808;A|0.192	0.192	strong		0.403	ZNF14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460775.1	NM_021030	
BAZ2B	29994	hgsc.bcm.edu	37	2	160294842	160294842	+	Missense_Mutation	SNP	A	A	G	rs3213790	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:160294842A>G	ENST00000392783.2	-	8	1760	c.1265T>C	c.(1264-1266)tTa>tCa	p.L422S	BAZ2B_ENST00000355831.2_Missense_Mutation_p.L422S|BAZ2B_ENST00000392782.1_Missense_Mutation_p.L420S|BAZ2B_ENST00000343439.5_Missense_Mutation_p.L420S	NM_013450.2	NP_038478.2	Q9UIF8	BAZ2B_HUMAN	bromodomain adjacent to zinc finger domain, 2B	422			L -> S (in dbSNP:rs3213790). {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)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(7)|liver(2)|lung(41)|ovary(3)|prostate(1)|skin(2)|soft_tissue(1)|urinary_tract(1)	82						ACTGGTCAATAAACTAGATTC	0.313													G|||	725	0.144768	0.1717	0.0735	5008	,	,		17996	0.1121		0.1103	False		,,,				2504	0.228				p.L422S		Atlas-SNP	.											.	BAZ2B	196	.	0			c.T1265C						PASS	.	G	SER/LEU	572,3022		39,494,1264	53.0	49.0	50.0		1265	2.6	0.8	2	dbSNP_106	50	1014,7118		58,898,3110	yes	missense	BAZ2B	NM_013450.2	145	97,1392,4374	GG,GA,AA		12.4693,15.9154,13.5255	benign	422/2169	160294842	1586,10140	1797	4066	5863	SO:0001583	missense	29994	exon8			GTCAATAAACTAG	AB032255	CCDS2209.2, CCDS74594.1	2q24.2	2013-01-28			ENSG00000123636	ENSG00000123636		"""Zinc fingers, PHD-type"""	963	protein-coding gene	gene with protein product		605683				10662543	Standard	XM_005246488		Approved	WALp4	uc002uao.3	Q9UIF8	OTTHUMG00000132027	ENST00000392783.2:c.1265T>C	2.37:g.160294842A>G	ENSP00000376534:p.Leu422Ser	Somatic	264	0	0		WXS	Illumina HiSeq	Phase_I	205	104	0.507317	NM_013450	D3DPA8|Q96EA1|Q96SQ8|Q9P252|Q9Y4N8	Missense_Mutation	SNP	ENST00000392783.2	37	CCDS2209.2	266	0.12179487179487179	89	0.18089430894308944	34	0.09392265193370165	52	0.09090909090909091	91	0.12005277044854881	G	5.109	0.205678	0.09704	0.159154	0.124693	ENSG00000123636	ENST00000392782;ENST00000392783;ENST00000355831;ENST00000343439;ENST00000546335	D;D;D;D	0.86562	-2.14;-2.14;-2.14;-2.14	5.35	2.62	0.31277	.	0.485309	0.15182	N	0.276044	T	0.00271	0.0008	N	0.02011	-0.69	0.80722	P	0.0	B;B;B;B	0.15141	0.012;0.0;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.03394	-1.1041	9	0.14656	T	0.56	7.6494	8.6754	0.34176	0.2945:0.0:0.7054:0.0	rs3213790;rs17845345;rs17858190;rs52827970;rs57244036;rs3213790	422;420;420;422	Q9UIF8-3;Q9UIF8-2;Q9UIF8-5;Q9UIF8	.;.;.;BAZ2B_HUMAN	S	420;422;422;420;359	ENSP00000376533:L420S;ENSP00000376534:L422S;ENSP00000348087:L422S;ENSP00000339670:L420S	ENSP00000339670:L420S	L	-	2	0	BAZ2B	160003088	0.999000	0.42202	0.847000	0.33407	0.451000	0.32288	1.943000	0.40253	0.021000	0.15133	-0.733000	0.03571	TTA	A|0.860;G|0.140	0.140	strong		0.313	BAZ2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255037.2		
HOXD3	3232	hgsc.bcm.edu	37	2	177036754	177036754	+	Silent	SNP	T	T	C	rs1051929	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:177036754T>C	ENST00000468418.3	+	4	3141	c.1051T>C	c.(1051-1053)Ttg>Ctg	p.L351L	HOXD3_ENST00000249440.3_Silent_p.L351L|HOXD-AS1_ENST00000416928.2_RNA|HOXD3_ENST00000410016.1_Silent_p.L351L			P31249	HXD3_HUMAN	homeobox D3	351					anterior/posterior pattern specification (GO:0009952)|cartilage development (GO:0051216)|cell-matrix adhesion (GO:0007160)|embryonic skeletal system morphogenesis (GO:0048704)|Notch signaling pathway (GO:0007219)|positive regulation of gene expression (GO:0010628)|positive regulation of neuron differentiation (GO:0045666)|thyroid gland development (GO:0030878)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.L351L(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(2)|lung(11)|prostate(1)|upper_aerodigestive_tract(2)	23			OV - Ovarian serous cystadenocarcinoma(117;0.00569)|Epithelial(96;0.0864)|all cancers(119;0.226)	Colorectal(32;0.247)		CAGCGCCAACTTGCAGGGCAG	0.692													C|||	4107	0.820088	0.9463	0.7968	5008	,	,		12088	0.7738		0.675	False		,,,				2504	0.863				p.L351L		Atlas-SNP	.											HOXD3,NS,carcinoma,0,3	HOXD3	65	3	1	Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(1)	c.T1051C						PASS	.	C		3851,519		1709,433,43	11.0	14.0	13.0		1051	4.8	1.0	2	dbSNP_86	13	5868,2704		2014,1840,432	no	coding-synonymous	HOXD3	NM_006898.4		3723,2273,475	CC,CT,TT		31.5446,11.8764,24.9034		351/433	177036754	9719,3223	2185	4286	6471	SO:0001819	synonymous_variant	3232	exon3			GCCAACTTGCAGG		CCDS2270.1	2q31.1	2011-06-20	2005-12-22		ENSG00000128652	ENSG00000128652		"""Homeoboxes / ANTP class : HOXL subclass"""	5137	protein-coding gene	gene with protein product		142980	"""homeo box D3"""	HOX4A, HOX4, HOX1D		1973146, 1358459	Standard	NM_006898		Approved		uc002ukt.1	P31249	OTTHUMG00000132517	ENST00000468418.3:c.1051T>C	2.37:g.177036754T>C		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	58	22	0.37931	NM_006898	Q99955|Q9BSC5	Silent	SNP	ENST00000468418.3	37	CCDS2270.1																																																																																			T|0.243;C|0.757	0.757	strong		0.692	HOXD3-005	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334246.4		
GEMIN4	50628	hgsc.bcm.edu	37	17	650518	650518	+	Silent	SNP	G	G	A	rs35696687	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:650518G>A	ENST00000319004.5	-	2	883	c.765C>T	c.(763-765)gaC>gaT	p.D255D	GEMIN4_ENST00000437269.1_Missense_Mutation_p.T168M|GEMIN4_ENST00000576778.1_Silent_p.D244D	NM_015721.2	NP_056536.2	P57678	GEMI4_HUMAN	gem (nuclear organelle) associated protein 4	255					gene expression (GO:0010467)|ncRNA metabolic process (GO:0034660)|RNA metabolic process (GO:0016070)|rRNA processing (GO:0006364)|spliceosomal snRNP assembly (GO:0000387)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|small nuclear ribonucleoprotein complex (GO:0030532)|SMN complex (GO:0032797)|SMN-Sm protein complex (GO:0034719)				breast(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(4)|lung(4)|ovary(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	22		Myeloproliferative disorder(207;0.204)		UCEC - Uterine corpus endometrioid carcinoma (25;0.022)		CCTGGGGGTCGTCCTCTGTCA	0.612													G|||	370	0.0738818	0.0098	0.0865	5008	,	,		19416	0.002		0.1918	False		,,,				2504	0.1043				p.D255D		Atlas-SNP	.											.	GEMIN4	116	.	0			c.C765T						PASS	.	G		145,4211		2,141,2035	93.0	102.0	99.0		765	-10.7	0.6	17	dbSNP_126	99	1441,7091		136,1169,2961	no	coding-synonymous	GEMIN4	NM_015721.2		138,1310,4996	AA,AG,GG		16.8894,3.3287,12.306		255/1059	650518	1586,11302	2178	4266	6444	SO:0001819	synonymous_variant	50628	exon2			GGGGTCGTCCTCT	AF177341	CCDS45559.1	17p13.3	2008-07-18				ENSG00000179409			15717	protein-coding gene	gene with protein product	"""HCC-associated protein 1"", ""component of gems 4"""	606969				10725331	Standard	NM_015721		Approved	HHRF-1, DKFZP434B131, p97, DKFZP434D174, HC56, HCAP1	uc002frs.1	P57678		ENST00000319004.5:c.765C>T	17.37:g.650518G>A		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	122	56	0.459016	NM_015721	Q9NZS7|Q9UG32|Q9Y4Q2	Silent	SNP	ENST00000319004.5	37	CCDS45559.1	175	0.08012820512820513	2	0.0040650406504065045	30	0.08287292817679558	0	0.0	143	0.18865435356200527	G	0.561	-0.845209	0.02671	0.033287	0.168894	ENSG00000179409	ENST00000437269	T	0.10005	2.92	5.37	-10.7	0.00240	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.09022	0.002	B	0.06405	0.002	T	0.35151	-0.9800	7	0.02654	T	1	-5.5261	7.923	0.29857	0.0985:0.3416:0.4825:0.0775	rs35696687;rs61746325	168	E7EN12	.	M	168	ENSP00000392460:T168M	ENSP00000392460:T168M	T	-	2	0	GEMIN4	597268	0.000000	0.05858	0.616000	0.29078	0.664000	0.39144	-4.479000	0.00227	-2.233000	0.00716	0.557000	0.71058	ACG	G|0.897;A|0.103	0.103	strong		0.612	GEMIN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437181.1	NM_015721	
THBS1	7057	hgsc.bcm.edu	37	15	39879717	39879717	+	Silent	SNP	G	G	A	rs2229364	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:39879717G>A	ENST00000260356.5	+	8	1455	c.1290G>A	c.(1288-1290)aaG>aaA	p.K430K		NM_003246.2	NP_003237.2	P07996	TSP1_HUMAN	thrombospondin 1	430					activation of MAPK activity (GO:0000187)|behavioral response to pain (GO:0048266)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular response to growth factor stimulus (GO:0071363)|cellular response to heat (GO:0034605)|cellular response to tumor necrosis factor (GO:0071356)|chronic inflammatory response (GO:0002544)|endocardial cushion development (GO:0003197)|engulfment of apoptotic cell (GO:0043652)|extracellular matrix organization (GO:0030198)|growth plate cartilage development (GO:0003417)|immune response (GO:0006955)|negative regulation of angiogenesis (GO:0016525)|negative regulation of antigen processing and presentation of peptide or polysaccharide antigen via MHC class II (GO:0002581)|negative regulation of apoptotic process (GO:0043066)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of cGMP-mediated signaling (GO:0010754)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of dendritic cell antigen processing and presentation (GO:0002605)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of nitric oxide mediated signal transduction (GO:0010751)|negative regulation of plasma membrane long-chain fatty acid transport (GO:0010748)|negative regulation of plasminogen activation (GO:0010757)|outflow tract morphogenesis (GO:0003151)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood coagulation (GO:0030194)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of chemotaxis (GO:0050921)|positive regulation of endothelial cell apoptotic process (GO:2000353)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of macrophage activation (GO:0043032)|positive regulation of macrophage chemotaxis (GO:0010759)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of transforming growth factor beta1 production (GO:0032914)|positive regulation of translation (GO:0045727)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|response to calcium ion (GO:0051592)|response to drug (GO:0042493)|response to endoplasmic reticulum stress (GO:0034976)|response to glucose (GO:0009749)|response to hypoxia (GO:0001666)|response to magnesium ion (GO:0032026)|response to mechanical stimulus (GO:0009612)|response to progesterone (GO:0032570)|response to testosterone (GO:0033574)|response to unfolded protein (GO:0006986)|sprouting angiogenesis (GO:0002040)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|sarcoplasmic reticulum (GO:0016529)|secretory granule (GO:0030141)	calcium ion binding (GO:0005509)|collagen V binding (GO:0070052)|fibrinogen binding (GO:0070051)|fibroblast growth factor binding (GO:0017134)|fibronectin binding (GO:0001968)|glycoprotein binding (GO:0001948)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|integrin binding (GO:0005178)|laminin binding (GO:0043236)|low-density lipoprotein particle binding (GO:0030169)|phosphatidylserine binding (GO:0001786)|proteoglycan binding (GO:0043394)|transforming growth factor beta binding (GO:0050431)			breast(1)|central_nervous_system(3)|endometrium(8)|kidney(5)|large_intestine(15)|lung(9)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	53		all_cancers(109;1.35e-17)|all_epithelial(112;2.07e-15)|Lung NSC(122;4.44e-11)|all_lung(180;1.11e-09)|Melanoma(134;0.0574)|Colorectal(260;0.117)|Ovarian(310;0.223)		GBM - Glioblastoma multiforme(113;2.77e-06)|BRCA - Breast invasive adenocarcinoma(123;0.105)		AGTGTGACAAGAGATGTAAGC	0.547													G|||	818	0.163339	0.0688	0.1167	5008	,	,		21225	0.2897		0.1312	False		,,,				2504	0.227				p.K430K		Atlas-SNP	.											.	THBS1	106	.	0			c.G1290A						PASS	.	G		359,4041	180.1+/-208.5	15,329,1856	37.0	34.0	35.0		1290	3.2	1.0	15	dbSNP_98	35	1111,7483	223.7+/-260.4	62,987,3248	no	coding-synonymous	THBS1	NM_003246.2		77,1316,5104	AA,AG,GG		12.9276,8.1591,11.3129		430/1171	39879717	1470,11524	2200	4297	6497	SO:0001819	synonymous_variant	7057	exon8			TGACAAGAGATGT		CCDS32194.1	15q15	2009-04-08			ENSG00000137801	ENSG00000137801			11785	protein-coding gene	gene with protein product	"""thrombospondin-1p180"""	188060				2341158, 2335352	Standard	NM_003246		Approved	TSP1, THBS, TSP, THBS-1, TSP-1	uc001zkh.3	P07996	OTTHUMG00000133665	ENST00000260356.5:c.1290G>A	15.37:g.39879717G>A		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	54	29	0.537037	NM_003246	A8K6H4|B4E3J7|B9EGH6|Q15667|Q59E99	Silent	SNP	ENST00000260356.5	37	CCDS32194.1																																																																																			G|0.874;A|0.126	0.126	strong		0.547	THBS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257831.2	NM_003246	
ADCYAP1R1	117	hgsc.bcm.edu	37	7	31142970	31142970	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:31142970G>A	ENST00000304166.4	+	14	1455	c.1166G>A	c.(1165-1167)gGc>gAc	p.G389D	ADCYAP1R1_ENST00000409489.1_Missense_Mutation_p.G445D|ADCYAP1R1_ENST00000409363.1_Missense_Mutation_p.G368D|ADCYAP1R1_ENST00000396211.2_Missense_Mutation_p.G417D	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	389					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						CTGGGGCTGGGCTCCTTCCAG	0.547																																					p.G417D	Ovarian(44;225 1186 2158 11092)	Atlas-SNP	.											ADCYAP1R1,right_lower_lobe,carcinoma,0,1	ADCYAP1R1	78	1	0			c.G1250A						scavenged	.						100.0	92.0	94.0					7																	31142970		2203	4300	6503	SO:0001583	missense	117	exon15			GGCTGGGCTCCTT		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.1166G>A	7.37:g.31142970G>A	ENSP00000306620:p.Gly389Asp	Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	116	3	0.0258621	NM_001199635	A8K1Y1|B7ZLA7|B8ZZK3|Q17S10	Missense_Mutation	SNP	ENST00000304166.4	37	CCDS5433.1	.	.	.	.	.	.	.	.	.	.	G	22.1	4.238419	0.79800	.	.	ENSG00000078549	ENST00000304166;ENST00000409363;ENST00000396211;ENST00000409489	T;T;T;T	0.43688	1.12;0.94;0.94;0.94	5.58	4.7	0.59300	GPCR, family 2-like (1);	0.000000	0.85682	D	0.000000	T	0.65112	0.2660	M	0.81682	2.555	0.80722	D	1	P;D;D;D;D	0.89917	0.877;1.0;0.999;1.0;1.0	P;D;D;D;D	0.87578	0.714;0.998;0.988;0.995;0.995	T	0.70011	-0.4989	10	0.72032	D	0.01	.	12.5611	0.56281	0.0805:0.0:0.9195:0.0	.	416;417;445;368;389	B7ZLA7;Q17S10;E9PFU5;B8ZZK3;P41586	.;.;.;.;PACR_HUMAN	D	389;368;417;445	ENSP00000306620:G389D;ENSP00000387335:G368D;ENSP00000379514:G417D;ENSP00000386395:G445D	ENSP00000306620:G389D	G	+	2	0	ADCYAP1R1	31109495	1.000000	0.71417	1.000000	0.80357	0.945000	0.59286	9.869000	0.99810	1.509000	0.48786	-0.136000	0.14681	GGC	.	.	none		0.547	ADCYAP1R1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000215041.3	NM_001118	
LINC00283	100874057	hgsc.bcm.edu	37	13	103394421	103394421	+	RNA	SNP	T	T	C	rs111294175	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:103394421T>C	ENST00000430111.1	+	0	0									long intergenic non-protein coding RNA 283																		GTCCTGTCTTTTGGCTTGTCT	0.393													T|||	3	0.000599042	0.0	0.0	5008	,	,		21250	0.0		0.002	False		,,,				2504	0.001				p.K2876E		Atlas-SNP	.											.	.	.	.	0			c.A8626G						PASS	.	T	GLU/LYS	1,1383		0,1,691	142.0	101.0	113.0		8626	-4.6	0.0	13	dbSNP_132	113	12,3168		0,12,1578	yes	missense	CCDC168	NM_001146197.1	56	0,13,2269	CC,CT,TT		0.3774,0.0723,0.2848		2876/7082	103394421	13,4551	692	1590	2282			643677	exon4			TGTCTTTTGGCTT			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.103394421T>C		Somatic	202	0	0		WXS	Illumina HiSeq	Phase_I	191	96	0.502618	NM_001146197		Missense_Mutation	SNP	ENST00000430111.1	37																																																																																				T|0.998;C|0.002	0.002	strong		0.393	LINC00283-001	KNOWN	not_organism_supported|basic	antisense	antisense	OTTHUMT00000045714.1		
GUCY2D	3000	hgsc.bcm.edu	37	17	7909890	7909890	+	Silent	SNP	C	C	T	rs61749678	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:7909890C>T	ENST00000254854.4	+	4	1386	c.1236C>T	c.(1234-1236)gaC>gaT	p.D412D		NM_000180.3	NP_000171.1	Q02846	GUC2D_HUMAN	guanylate cyclase 2D, membrane (retina-specific)	412					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)				CGGCGGGAGACCGGCTTTTTG	0.677													C|||	2	0.000399361	0.0	0.0	5008	,	,		13052	0.0		0.002	False		,,,				2504	0.0				p.D412D		Atlas-SNP	.											.	GUCY2D	82	.	0			c.C1236T						PASS	.	C		0,4406		0,0,2203	30.0	29.0	29.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1236	2.0	0.2	17	dbSNP_129	29	9,8591	6.4+/-24.3	0,9,4291	no	coding-synonymous	GUCY2D	NM_000180.3		0,9,6494	TT,TC,CC		0.1047,0.0,0.0692		412/1104	7909890	9,12997	2203	4300	6503	SO:0001819	synonymous_variant	3000	exon4			GGGAGACCGGCTT	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.1236C>T	17.37:g.7909890C>T		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	79	37	0.468354	NM_000180	Q6LEA7	Silent	SNP	ENST00000254854.4	37	CCDS11127.1																																																																																			C|0.999;T|0.001	0.001	strong		0.677	GUCY2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226973.2		
CWC27	10283	hgsc.bcm.edu	37	5	64273018	64273018	+	Silent	SNP	G	G	A	rs1309581	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:64273018G>A	ENST00000381070.3	+	13	1426	c.1209G>A	c.(1207-1209)acG>acA	p.T403T	CWC27_ENST00000545000.1_3'UTR	NM_005869.2	NP_005860.2	Q6UX04	CWC27_HUMAN	CWC27 spliceosome-associated protein homolog (S. cerevisiae)	403					mRNA splicing, via spliceosome (GO:0000398)|protein folding (GO:0006457)	catalytic step 2 spliceosome (GO:0071013)	peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			breast(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(5)|prostate(1)	21						TTGCTGAAACGCCTGAAAATG	0.358													G|||	1761	0.351637	0.2519	0.3876	5008	,	,		18195	0.3026		0.4125	False		,,,				2504	0.4489				p.T403T		Atlas-SNP	.											.	CWC27	47	.	0			c.G1209A						PASS	.	G		1287,3119	432.8+/-343.4	203,881,1119	80.0	74.0	76.0		1209	0.7	1.0	5	dbSNP_87	76	3875,4725	543.3+/-384.4	906,2063,1331	no	coding-synonymous	CWC27	NM_005869.2		1109,2944,2450	AA,AG,GG		45.0581,29.2102,39.6894		403/473	64273018	5162,7844	2203	4300	6503	SO:0001819	synonymous_variant	10283	exon13			TGAAACGCCTGAA	AF039692	CCDS3982.2, CCDS75252.1	5q12.3	2010-01-26	2010-01-26	2010-01-26	ENSG00000153015	ENSG00000153015			10664	protein-coding gene	gene with protein product			"""serologically defined colon cancer antigen 10"""	SDCCAG10		9610721, 19941820	Standard	XM_005248399		Approved	NY-CO-10	uc003jtn.1	Q6UX04	OTTHUMG00000074069	ENST00000381070.3:c.1209G>A	5.37:g.64273018G>A		Somatic	269	0	0		WXS	Illumina HiSeq	Phase_I	262	146	0.557252	NM_005869	O60529|O60530|Q96EM3	Silent	SNP	ENST00000381070.3	37	CCDS3982.2																																																																																			G|0.631;A|0.369	0.369	strong		0.358	CWC27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157247.4	NM_005869	
KLHL32	114792	hgsc.bcm.edu	37	6	97580539	97580539	+	Silent	SNP	A	A	G	rs13208956	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:97580539A>G	ENST00000369261.4	+	10	1980	c.1617A>G	c.(1615-1617)gaA>gaG	p.E539E	KLHL32_ENST00000544166.1_Silent_p.E95E|KLHL32_ENST00000539200.1_Silent_p.E470E|KLHL32_ENST00000536676.1_Silent_p.E503E	NM_052904.3	NP_443136.2	Q96NJ5	KLH32_HUMAN	kelch-like family member 32	539										breast(2)|endometrium(3)|kidney(4)|large_intestine(9)|lung(13)|ovary(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	38		all_cancers(76;1.19e-06)|Acute lymphoblastic leukemia(125;5.83e-10)|all_hematologic(75;3.67e-07)|all_epithelial(107;0.00778)|Colorectal(196;0.122)		BRCA - Breast invasive adenocarcinoma(108;0.0558)		GCCAAAATGAATCTGGAGTTG	0.343													A|||	154	0.0307508	0.0484	0.0202	5008	,	,		17594	0.001		0.0298	False		,,,				2504	0.046				p.E539E		Atlas-SNP	.											KLHL32,neck,malignant_melanoma,+2,1	KLHL32	85	1	0			c.A1617G						PASS	.	A		178,4228	115.0+/-153.0	5,168,2030	108.0	108.0	108.0		1617	5.6	1.0	6	dbSNP_121	108	340,8260	117.2+/-176.8	2,336,3962	no	coding-synonymous	KLHL32	NM_052904.3		7,504,5992	GG,GA,AA		3.9535,4.0399,3.9828		539/621	97580539	518,12488	2203	4300	6503	SO:0001819	synonymous_variant	114792	exon10			AAATGAATCTGGA	AB067487	CCDS5038.1, CCDS69154.1, CCDS69155.1, CCDS75495.1	6q16.3	2013-02-22	2013-02-22	2007-01-09	ENSG00000186231	ENSG00000186231		"""Kelch-like"", ""BTB/POZ domain containing"""	21221	protein-coding gene	gene with protein product			"""BTB and kelch domain containing 5"", ""KIAA1900"", ""kelch-like 32 (Drosophila)"""	BKLHD5, KIAA1900			Standard	NM_052904		Approved		uc010kcm.1	Q96NJ5	OTTHUMG00000015247	ENST00000369261.4:c.1617A>G	6.37:g.97580539A>G		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	47	24	0.510638	NM_052904	B7Z346|B7Z4E2|E1P528|Q5THT0|Q96PY7	Silent	SNP	ENST00000369261.4	37	CCDS5038.1																																																																																			A|0.967;G|0.033	0.033	strong		0.343	KLHL32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041570.1	NM_052904	
PTPRR	5801	hgsc.bcm.edu	37	12	71029733	71029733	+	IGR	SNP	C	C	T	rs2584021	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:71029733C>T	ENST00000283228.2	-	0	3529				PTPRB_ENST00000551525.1_Missense_Mutation_p.D56N|PTPRB_ENST00000538174.2_5'UTR|PTPRB_ENST00000550358.1_Missense_Mutation_p.D57N|PTPRR_ENST00000537619.2_5'Flank|PTPRB_ENST00000334414.6_Missense_Mutation_p.D57N	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	261	0	0		WXS	Illumina HiSeq	Phase_I	260	130	0.5	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	
SDK2	54549	hgsc.bcm.edu	37	17	71426656	71426656	+	Missense_Mutation	SNP	G	G	T	rs1105353	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:71426656G>T	ENST00000392650.3	-	12	1577	c.1577C>A	c.(1576-1578)aCc>aAc	p.T526N	SDK2_ENST00000388726.3_Missense_Mutation_p.T526N	NM_001144952.1	NP_001138424.1	Q58EX2	SDK2_HUMAN	sidekick cell adhesion molecule 2	526	Ig-like C2-type 6.				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						GTACCTGATGGTTACTCGGGG	0.607													G|||	678	0.135383	0.0431	0.1974	5008	,	,		15499	0.0704		0.2922	False		,,,				2504	0.1217				p.T526N		Atlas-SNP	.											.	SDK2	219	.	0			c.C1577A						PASS	.	G	ASN/THR	367,4039	175.9+/-205.1	13,341,1849	44.0	33.0	37.0		1577	3.9	0.8	17	dbSNP_86	37	2312,6288	358.6+/-331.2	318,1676,2306	yes	missense	SDK2	NM_001144952.1	65	331,2017,4155	TT,TG,GG		26.8837,8.3296,20.5982	benign	526/2173	71426656	2679,10327	2203	4300	6503	SO:0001583	missense	54549	exon12			CTGATGGTTACTC	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.1577C>A	17.37:g.71426656G>T	ENSP00000376421:p.Thr526Asn	Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	23	13	0.565217	NM_001144952	A6NMR8|C9JA57|Q86VY3|Q9NTD2|Q9NVB3|Q9P214	Missense_Mutation	SNP	ENST00000392650.3	37	CCDS45769.1	375|375	0.1717032967032967|0.1717032967032967	27|27	0.054878048780487805|0.054878048780487805	74|74	0.20441988950276244|0.20441988950276244	45|45	0.07867132867132867|0.07867132867132867	229|229	0.3021108179419525|0.3021108179419525	G|G	1.954|1.954	-0.440461|-0.440461	0.04636|0.04636	0.083296|0.083296	0.268837|0.268837	ENSG00000069188|ENSG00000069188	ENST00000416616|ENST00000409227;ENST00000392650;ENST00000388726;ENST00000316893	.|T;T	.|0.67698	.|-0.28;-0.28	3.89|3.89	3.89|3.89	0.44902|0.44902	.|Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.|0.511109	.|0.19375	.|N	.|0.115809	T|T	0.00012|0.00012	0.0000|0.0000	L|L	0.58510|0.58510	1.815|1.815	0.58432|0.58432	P|P	1.0000000000287557E-6|1.0000000000287557E-6	.|B;B	.|0.12630	.|0.002;0.006	.|B;B	.|0.13407	.|0.009;0.009	T|T	0.11542|0.11542	-1.0583|-1.0583	4|9	.|0.17369	.|T	.|0.5	.|.	6.8444|6.8444	0.23980|0.23980	0.0977:0.0:0.7258:0.1765|0.0977:0.0:0.7258:0.1765	rs1105353;rs17184965;rs1105353|rs1105353;rs17184965;rs1105353	.|526;526	.|Q58EX2-2;Q58EX2	.|.;SDK2_HUMAN	K|N	430|150;526;526;526	.|ENSP00000376421:T526N;ENSP00000373378:T526N	.|ENSP00000324967:T526N	N|T	-|-	3|2	2|0	SDK2|SDK2	68938251|68938251	0.177000|0.177000	0.23109|0.23109	0.815000|0.815000	0.32552|0.32552	0.028000|0.028000	0.11728|0.11728	2.817000|2.817000	0.48034|0.48034	1.887000|1.887000	0.54652|0.54652	0.462000|0.462000	0.41574|0.41574	AAC|ACC	G|0.817;N|0.000	.	strong		0.607	SDK2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327598.2	NM_019064	
TGM5	9333	hgsc.bcm.edu	37	15	43545728	43545728	+	Silent	SNP	G	G	A	rs555001	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:43545728G>A	ENST00000220420.5	-	5	667	c.660C>T	c.(658-660)taC>taT	p.Y220Y	TGM5_ENST00000349114.4_Silent_p.Y138Y	NM_201631.3	NP_963925.2	O43548	TGM5_HUMAN	transglutaminase 5	220					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)	CTCTGCTGACGTAGACGGGGC	0.612													G|||	2388	0.476837	0.7579	0.3228	5008	,	,		18010	0.4127		0.336	False		,,,				2504	0.4172				p.Y220Y		Atlas-SNP	.											.	TGM5	88	.	0			c.C660T						PASS	.	G	,	2884,1520	673.0+/-402.7	961,962,279	70.0	63.0	65.0		414,660	-2.3	0.8	15	dbSNP_83	65	2798,5800	443.5+/-360.4	466,1866,1967	no	coding-synonymous,coding-synonymous	TGM5	NM_004245.3,NM_201631.3	,	1427,2828,2246	AA,AG,GG		32.5425,34.5141,43.701	,	138/639,220/721	43545728	5682,7320	2202	4299	6501	SO:0001819	synonymous_variant	9333	exon5			GCTGACGTAGACG	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.660C>T	15.37:g.43545728G>A		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	52	21	0.403846	NM_201631	O43549|Q0VF40|Q9UEZ4	Silent	SNP	ENST00000220420.5	37	CCDS32212.1																																																																																			G|0.539;A|0.461	0.461	strong		0.612	TGM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432257.1	NM_004245	
MUC4	4585	hgsc.bcm.edu	37	3	195509974	195509974	+	Missense_Mutation	SNP	A	A	G	rs200426444		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195509974A>G	ENST00000463781.3	-	2	8936	c.8477T>C	c.(8476-8478)tTc>tCc	p.F2826S	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.F2826S	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.F2826S(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)		ATGACCTGTGAACACTGAGGA	0.587																																					p.F2826S		Atlas-SNP	.											MUC4_ENST00000463781,brain,glioma,0,2	MUC4	1505	2	1	Substitution - Missense(1)	stomach(1)	c.T8477C						scavenged	.						73.0	50.0	57.0					3																	195509974		670	1519	2189	SO:0001583	missense	4585	exon2			CCTGTGAACACTG	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.8477T>C	3.37:g.195509974A>G	ENSP00000417498:p.Phe2826Ser	Somatic	110	1	0.00909091		WXS	Illumina HiSeq	Phase_I	141	30	0.212766	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	.	.	.	.	.	.	.	.	.	.	-	5.771	0.326602	0.10900	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.27557	1.66;1.69	.	.	.	.	.	.	.	.	T	0.11067	0.0270	N	0.03608	-0.345	0.53688	P	2.199999999996649E-5	.	.	.	.	.	.	T	0.35968	-0.9767	3	.	.	.	.	.	.	.	.	2698	E7ESK3	.	S	2826	ENSP00000417498:F2826S;ENSP00000420243:F2826S	.	F	-	2	0	MUC4	196994753	.	.	0.000000	0.03702	0.000000	0.00434	.	.	0.000000	0.14550	0.000000	0.15137	TTC	.	.	weak		0.587	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
CDHR5	53841	hgsc.bcm.edu	37	11	617420	617420	+	Silent	SNP	A	A	G	rs61877857	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:617420A>G	ENST00000358353.3	-	16	2791	c.2469T>C	c.(2467-2469)gaT>gaC	p.D823D	IRF7_ENST00000397562.3_5'Flank|IRF7_ENST00000397574.2_5'Flank|CDHR5_ENST00000397542.2_Silent_p.D823D|IRF7_ENST00000348655.6_5'Flank|IRF7_ENST00000397566.1_5'Flank|IRF7_ENST00000525445.1_5'Flank|IRF7_ENST00000397570.1_5'Flank|CDHR5_ENST00000349570.7_Silent_p.D629D|IRF7_ENST00000330243.5_5'Flank			Q9HBB8	CDHR5_HUMAN	cadherin-related family member 5	823					cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(7)|ovary(1)|skin(2)	23						CCTCGCCCTCATCGCCGCTGC	0.687													G|||	1385	0.276558	0.5855	0.3026	5008	,	,		11465	0.0208		0.2684	False		,,,				2504	0.1125				p.D823D		Atlas-SNP	.											CDHR5,rectum,carcinoma,0,2	CDHR5	77	2	0			c.T2469C						scavenged	.	-	,,	2269,2129		587,1095,517	30.0	28.0	29.0		2451,2469,1887	-1.4	0.0	11	dbSNP_129	29	2475,6121		360,1755,2183	no	coding-synonymous,coding-synonymous,coding-synonymous	CDHR5	NM_001171968.1,NM_021924.4,NM_031264.3	,,	947,2850,2700	GG,GA,AA		28.7925,48.4084,36.5092	,,	817/840,823/846,629/652	617420	4744,8250	2199	4298	6497	SO:0001819	synonymous_variant	53841	exon15			GCCCTCATCGCCG	AF258675	CCDS7707.1, CCDS7708.1	11p15.5	2011-07-01	2010-01-25	2010-01-25	ENSG00000099834	ENSG00000099834		"""Cadherins / Cadherin-related"""	7521	protein-coding gene	gene with protein product		606839	"""mucin and cadherin-like"", ""mucin-like protocadherin"""	MUCDHL, MUPCDH		11031102, 10801787	Standard	NM_021924		Approved	FLJ20219, MU-PCDH	uc001lqj.3	Q9HBB8	OTTHUMG00000132018	ENST00000358353.3:c.2469T>C	11.37:g.617420A>G		Somatic	79	1	0.0126582		WXS	Illumina HiSeq	Phase_I	66	48	0.727273	NM_021924	C9J7X1|Q9H746|Q9HAU3|Q9HBB5|Q9HBB6|Q9HBB7|Q9NX86|Q9NXI9	Silent	SNP	ENST00000358353.3	37	CCDS7707.1																																																																																			A|0.675;G|0.325	0.325	strong		0.687	CDHR5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255023.2	NM_021924	
EPHX1	2052	hgsc.bcm.edu	37	1	226019633	226019633	+	Missense_Mutation	SNP	T	T	C	rs1051740	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:226019633T>C	ENST00000366837.4	+	3	533	c.337T>C	c.(337-339)Tac>Cac	p.Y113H	EPHX1_ENST00000467015.1_3'UTR|EPHX1_ENST00000272167.5_Missense_Mutation_p.Y113H	NM_000120.3	NP_000111.1	P07099	HYEP_HUMAN	epoxide hydrolase 1, microsomal (xenobiotic)	113			Y -> H (in allele EPHX1*3; 55% of wild type enzyme activity; dbSNP:rs1051740). {ECO:0000269|PubMed:11058921, ECO:0000269|PubMed:12173035, ECO:0000269|PubMed:7516776, ECO:0000269|Ref.8}.		aromatic compound catabolic process (GO:0019439)|response to toxic substance (GO:0009636)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	cis-stilbene-oxide hydrolase activity (GO:0033961)|epoxide hydrolase activity (GO:0004301)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(6)|lung(7)|ovary(3)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	28	Breast(184;0.197)					TCTCAACAGATACCCTCACTT	0.448													T|||	1569	0.313299	0.1407	0.3199	5008	,	,		22077	0.4821		0.3042	False		,,,				2504	0.3773				p.Y113H		Atlas-SNP	.											.	EPHX1	57	.	0			c.T337C	GRCh37	CM940369	EPHX1	M	rs1051740	PASS	.	T	HIS/TYR,HIS/TYR	776,3630	314.9+/-293.9	59,658,1486	109.0	98.0	101.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	337,337	5.6	0.9	1	dbSNP_86	101	2577,6023	419.2+/-353.0	395,1787,2118	yes	missense,missense	EPHX1	NM_000120.3,NM_001136018.2	83,83	454,2445,3604	CC,CT,TT		29.9651,17.6123,25.7804	probably-damaging,probably-damaging	113/456,113/456	226019633	3353,9653	2203	4300	6503	SO:0001583	missense	2052	exon3			AACAGATACCCTC	J03518	CCDS1547.1	1q42.1	2009-07-10			ENSG00000143819	ENSG00000143819	3.3.2.9		3401	protein-coding gene	gene with protein product		132810		EPHX		9925921	Standard	NM_000120		Approved		uc001hpk.3	P07099	OTTHUMG00000037743	ENST00000366837.4:c.337T>C	1.37:g.226019633T>C	ENSP00000355802:p.Tyr113His	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	70	39	0.557143	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	
PSG8	440533	hgsc.bcm.edu	37	19	43259169	43259169	+	Missense_Mutation	SNP	C	C	T	rs140722778	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:43259169C>T	ENST00000306511.4	-	4	1056	c.959G>A	c.(958-960)cGc>cAc	p.R320H	PSG8_ENST00000401467.2_Missense_Mutation_p.R227H|PSG8_ENST00000404209.4_Missense_Mutation_p.R320H|PSG8_ENST00000600709.1_Intron|PSG8_ENST00000406636.3_Missense_Mutation_p.R198H	NM_182707.2	NP_874366.1	Q9UQ74	PSG8_HUMAN	pregnancy specific beta-1-glycoprotein 8	320	Ig-like C2-type 2.					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)				TGGGTAACTGCGGATGCCACC	0.488													.|||	4	0.000798722	0.0015	0.0029	5008	,	,		21450	0.0		0.0	False		,,,				2504	0.0				p.R320H		Atlas-SNP	.											PSG8_ENST00000404209,NS,carcinoma,0,5	PSG8	101	5	0			c.G959A						PASS	.	C	HIS/ARG,HIS/ARG,HIS/ARG	8,4398		0,8,2195	180.0	181.0	181.0		959,593,959	-2.8	0.0	19	dbSNP_134	181	0,8598		0,0,4299	no	missense,missense,missense	PSG8	NM_001130167.1,NM_001130168.1,NM_182707.2	29,29,29	0,8,6494	TT,TC,CC		0.0,0.1816,0.0615	benign,benign,benign	320/420,198/298,320/427	43259169	8,12996	2203	4299	6502	SO:0001583	missense	440533	exon4			TAACTGCGGATGC	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.959G>A	19.37:g.43259169C>T	ENSP00000305005:p.Arg320His	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	28	15	0.535714	NM_001130167	A5PKV3|B2RPL4|B4DTI6|O60410|Q68CR6	Missense_Mutation	SNP	ENST00000306511.4	37	CCDS33037.1	10	0.004578754578754579	2	0.0040650406504065045	2	0.0055248618784530384	5	0.008741258741258742	1	0.0013192612137203166	N	0.102	-1.150122	0.01700	0.001816	0.0	ENSG00000124467	ENST00000404209;ENST00000406636;ENST00000401467;ENST00000426252;ENST00000407488;ENST00000306511	T;T;T;T	0.12672	2.66;2.66;2.66;2.66	1.38	-2.76	0.05896	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.08626	0.0214	L	0.59967	1.855	0.09310	N	1	B;B;B;B;B;B	0.21606	0.029;0.058;0.004;0.005;0.005;0.006	B;B;B;B;B;B	0.27887	0.021;0.084;0.005;0.042;0.005;0.009	T	0.24154	-1.0168	9	0.40728	T	0.16	.	3.1318	0.06425	0.1899:0.3611:0.0:0.4489	.	198;227;320;227;320;320	Q9UQ74-2;B5MCQ0;Q9UQ74;E7ENH0;Q9UQ74-3;A5PKV3	.;.;PSG8_HUMAN;.;.;.	H	320;198;227;132;227;320	ENSP00000385869:R320H;ENSP00000385081:R198H;ENSP00000386090:R227H;ENSP00000305005:R320H	ENSP00000305005:R320H	R	-	2	0	PSG8	47951009	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.062000	0.00623	-3.472000	0.00157	-3.315000	0.00045	CGC	C|0.998;T|0.002	0.002	strong		0.488	PSG8-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464526.1		
NRCAM	4897	hgsc.bcm.edu	37	7	107834734	107834734	+	Silent	SNP	C	C	T	rs404287	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:107834734C>T	ENST00000425651.2	-	13	1601	c.1602G>A	c.(1600-1602)gcG>gcA	p.A534A	NRCAM_ENST00000351718.4_Silent_p.A528A|NRCAM_ENST00000413765.2_Silent_p.A515A|NRCAM_ENST00000379022.4_Silent_p.A534A|NRCAM_ENST00000379024.4_Silent_p.A515A|NRCAM_ENST00000379028.3_Silent_p.A534A	NM_001037132.2	NP_001032209.1	Q92823	NRCAM_HUMAN	neuronal cell adhesion molecule	534	Ig-like 5.				angiogenesis (GO:0001525)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|axonogenesis (GO:0007409)|central nervous system development (GO:0007417)|clustering of voltage-gated sodium channels (GO:0045162)|heterotypic cell-cell adhesion (GO:0034113)|neuron migration (GO:0001764)|neuronal action potential propagation (GO:0019227)|positive regulation of neuron differentiation (GO:0045666)|protein localization (GO:0008104)|regulation of axon extension (GO:0030516)|retinal ganglion cell axon guidance (GO:0031290)|single organismal cell-cell adhesion (GO:0016337)|synapse assembly (GO:0007416)	axon initial segment (GO:0043194)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|synapse (GO:0045202)	ankyrin binding (GO:0030506)			breast(4)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(8)|liver(1)|lung(36)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(4)	65						CTTCATTCTTCGCCATCCCTA	0.353													T|||	3494	0.697684	0.4402	0.8012	5008	,	,		21399	0.88		0.7992	False		,,,				2504	0.68				p.A534A		Atlas-SNP	.											.	NRCAM	267	.	0			c.G1602A						PASS	.	T	,,,,	2232,2174	583.8+/-385.9	564,1104,535	168.0	154.0	159.0		1602,1602,1545,1545,1584	2.1	1.0	7	dbSNP_80	159	6706,1894	336.9+/-322.1	2611,1484,205	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NRCAM	NM_001037132.2,NM_001193582.1,NM_001193583.1,NM_001193584.1,NM_005010.4	,,,,	3175,2588,740	TT,TC,CC		22.0233,49.3418,31.2779	,,,,	534/1305,534/1212,515/1193,515/1181,528/1184	107834734	8938,4068	2203	4300	6503	SO:0001819	synonymous_variant	4897	exon13			ATTCTTCGCCATC		CCDS5751.1, CCDS47686.1, CCDS55153.1, CCDS75652.1	7q31	2013-02-11			ENSG00000091129	ENSG00000091129		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	7994	protein-coding gene	gene with protein product	"""NgCAM-related cell adhesion molecule"""	601581				8812479	Standard	NM_001037132		Approved	KIAA0343, Bravo	uc022aka.1	Q92823	OTTHUMG00000154973	ENST00000425651.2:c.1602G>A	7.37:g.107834734C>T		Somatic	479	2	0.00417537		WXS	Illumina HiSeq	Phase_I	354	353	0.997175	NM_001037132	A4D0S3|E9PDA4|O15051|O15179|Q14BM2|Q9UHI3|Q9UHI4	Silent	SNP	ENST00000425651.2	37	CCDS47686.1																																																																																			C|0.299;T|0.701	0.701	strong		0.353	NRCAM-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337942.2	NM_001037132	
FCGBP	8857	hgsc.bcm.edu	37	19	40366374	40366374	+	Silent	SNP	G	G	C	rs2053089	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:40366374G>C	ENST00000221347.6	-	30	13867	c.13860C>G	c.(13858-13860)ccC>ccG	p.P4620P		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	4620	VWFD 11. {ECO:0000255|PROSITE- ProRule:PRU00580}.					extracellular vesicular exosome (GO:0070062)				NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(5)|endometrium(13)|kidney(9)|large_intestine(27)|lung(49)|ovary(8)|pancreas(3)|prostate(13)|skin(9)|stomach(9)|upper_aerodigestive_tract(6)|urinary_tract(3)	165	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			GGTCGTCTGCGGGGTCCTGGT	0.687													G|||	632	0.126198	0.0363	0.2277	5008	,	,		12502	0.0466		0.2197	False		,,,				2504	0.1616				p.P4620P		Atlas-SNP	.											FCGBP,NS,carcinoma,-1,1	FCGBP	416	1	0			c.C13860G						PASS	.	G		355,4049		19,317,1866	40.0	47.0	45.0		13860	-8.6	0.0	19	dbSNP_94	45	2068,6530		258,1552,2489	no	coding-synonymous	FCGBP	NM_003890.2		277,1869,4355	CC,CG,GG		24.0521,8.0609,18.6356		4620/5406	40366374	2423,10579	2202	4299	6501	SO:0001819	synonymous_variant	8857	exon30			GTCTGCGGGGTCC	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.13860C>G	19.37:g.40366374G>C		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	163	71	0.435583	NM_003890	O95784	Silent	SNP	ENST00000221347.6	37	CCDS12546.1																																																																																			G|0.828;C|0.172	0.172	strong		0.687	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890	
NR1I2	8856	hgsc.bcm.edu	37	3	119531709	119531709	+	Silent	SNP	C	C	T	rs61755051	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:119531709C>T	ENST00000337940.4	+	5	861	c.813C>T	c.(811-813)ggC>ggT	p.G271G	NR1I2_ENST00000466380.1_Silent_p.G195G|NR1I2_ENST00000393716.2_Silent_p.G232G	NM_022002.2	NP_071285.1	O75469	NR1I2_HUMAN	nuclear receptor subfamily 1, group I, member 2	232	Ligand-binding.				drug export (GO:0046618)|exogenous drug catabolic process (GO:0042738)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|signal transduction (GO:0007165)|steroid metabolic process (GO:0008202)|transcription initiation from RNA polymerase II promoter (GO:0006367)|xenobiotic metabolic process (GO:0006805)|xenobiotic transport (GO:0042908)	nucleoplasm (GO:0005654)	drug binding (GO:0008144)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|steroid hormone receptor activity (GO:0003707)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			breast(2)|endometrium(1)|kidney(3)|large_intestine(2)|lung(8)|ovary(2)|prostate(2)|skin(3)	23				GBM - Glioblastoma multiforme(114;0.175)	Docetaxel(DB01248)|Erlotinib(DB00530)|Estradiol(DB00783)|Ethinyl Estradiol(DB00977)|Paclitaxel(DB01229)|Rifampicin(DB01045)|Rifaximin(DB01220)|Rilpivirine(DB08864)|Vitamin E(DB00163)	CCGACAGTGGCGGGAAAGAGA	0.547													C|||	23	0.00459265	0.0008	0.0086	5008	,	,		20822	0.002		0.0129	False		,,,				2504	0.001				p.G271G		Atlas-SNP	.											.	NR1I2	44	.	0			c.C813T						PASS	.	C	,,	6,4400	11.4+/-27.6	0,6,2197	60.0	62.0	61.0		696,813,585	-8.5	0.0	3	dbSNP_129	61	81,8519	46.3+/-105.2	0,81,4219	no	coding-synonymous,coding-synonymous,coding-synonymous	NR1I2	NM_003889.3,NM_022002.2,NM_033013.2	,,	0,87,6416	TT,TC,CC		0.9419,0.1362,0.6689	,,	232/435,271/474,195/398	119531709	87,12919	2203	4300	6503	SO:0001819	synonymous_variant	8856	exon5			CAGTGGCGGGAAA	AF061056	CCDS2995.1, CCDS43136.1, CCDS54627.1	3q12-q13.3	2013-03-25			ENSG00000144852	ENSG00000144852		"""Nuclear hormone receptors"""	7968	protein-coding gene	gene with protein product	"""pregnane X receptor"", ""orphan nuclear receptor PXR"""	603065				9727070, 9770465	Standard	NM_003889		Approved	ONR1, PXR, BXR, SXR, PAR2	uc003edk.3	O75469	OTTHUMG00000159400	ENST00000337940.4:c.813C>T	3.37:g.119531709C>T		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	72	33	0.458333	NM_022002	Q006P5|Q008C8|Q96AC7|Q9UJ22|Q9UJ23|Q9UJ24|Q9UJ25|Q9UJ26|Q9UJ27|Q9UNW4	Silent	SNP	ENST00000337940.4	37	CCDS2995.1																																																																																			C|0.993;T|0.007	0.007	strong		0.547	NR1I2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355126.1		
ACAD8	27034	hgsc.bcm.edu	37	11	134128923	134128923	+	Missense_Mutation	SNP	C	C	G	rs113488591	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:134128923C>G	ENST00000281182.4	+	5	618	c.512C>G	c.(511-513)tCt>tGt	p.S171C	ACAD8_ENST00000374752.4_Missense_Mutation_p.S44C|ACAD8_ENST00000537423.1_Missense_Mutation_p.S94C|ACAD8_ENST00000524547.1_3'UTR|ACAD8_ENST00000543332.1_Missense_Mutation_p.S73C	NM_014384.2	NP_055199.1	Q9UKU7	ACAD8_HUMAN	acyl-CoA dehydrogenase family, member 8	171					branched-chain amino acid catabolic process (GO:0009083)|cellular nitrogen compound metabolic process (GO:0034641)|lipid metabolic process (GO:0006629)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)|valine catabolic process (GO:0006574)	mitochondrial matrix (GO:0005759)	acyl-CoA dehydrogenase activity (GO:0003995)|flavin adenine dinucleotide binding (GO:0050660)			endometrium(4)|large_intestine(3)|lung(5)|ovary(1)|urinary_tract(1)	14	all_hematologic(175;0.127)	all_cancers(12;8e-23)|all_epithelial(12;2.59e-16)|all_lung(97;1.19e-05)|Lung NSC(97;2.76e-05)|Breast(109;0.000182)|all_neural(223;0.0189)|Medulloblastoma(222;0.0245)|Esophageal squamous(93;0.0559)		Epithelial(10;1.92e-10)|all cancers(11;2.26e-09)|BRCA - Breast invasive adenocarcinoma(10;8.73e-09)|OV - Ovarian serous cystadenocarcinoma(99;0.00154)|Lung(977;0.21)	Flavin adenine dinucleotide(DB03147)	GATGCTGCCTCTCTTCTGACC	0.522													C|||	34	0.00678914	0.0023	0.0144	5008	,	,		19971	0.0		0.0199	False		,,,				2504	0.001				p.S171C	GBM(65;238 1125 33403 41853 48889)	Atlas-SNP	.											.	ACAD8	33	.	0			c.C512G	GRCh37	CM070644	ACAD8	M	rs113488591	PASS	.	C	CYS/SER	38,4364	43.1+/-76.7	0,38,2163	113.0	106.0	109.0		512	4.8	1.0	11	dbSNP_132	109	190,8404	85.6+/-148.0	0,190,4107	yes	missense	ACAD8	NM_014384.2	112	0,228,6270	GG,GC,CC		2.2108,0.8632,1.7544	probably-damaging	171/416	134128923	228,12768	2201	4297	6498	SO:0001583	missense	27034	exon5			CTGCCTCTCTTCT	AF126245	CCDS8498.1	11q25	2014-09-17	2010-04-30		ENSG00000151498	ENSG00000151498			87	protein-coding gene	gene with protein product		604773	"""acyl-Coenzyme A dehydrogenase family, member 8"""			10524212	Standard	NM_014384		Approved		uc001qhk.3	Q9UKU7	OTTHUMG00000167177	ENST00000281182.4:c.512C>G	11.37:g.134128923C>G	ENSP00000281182:p.Ser171Cys	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	138	26	0.188406	NM_014384	B7Z5W4|Q6ZWP6|Q9BUS8	Missense_Mutation	SNP	ENST00000281182.4	37	CCDS8498.1	20	0.009157509157509158	0	0.0	4	0.011049723756906077	0	0.0	16	0.021108179419525065	C	23.8	4.453578	0.84209	0.008632	0.022108	ENSG00000151498	ENST00000281182;ENST00000537423;ENST00000543332;ENST00000374752;ENST00000537915	D;D;D;D	0.99129	-5.46;-5.46;-5.46;-5.46	5.73	4.82	0.62117	Acyl-CoA dehydrogenase/oxidase (1);Acyl-CoA dehydrogenase, conserved site (1);Acyl-CoA oxidase/dehydrogenase, central domain (2);	0.000000	0.85682	D	0.000000	D	0.98776	0.9588	M	0.92317	3.295	0.80722	D	1	D;D;D;D;D;D	0.89917	0.999;1.0;0.999;0.999;1.0;1.0	D;D;D;D;D;D	0.73708	0.964;0.968;0.98;0.974;0.981;0.98	D	0.93512	0.6854	10	0.72032	D	0.01	.	14.7653	0.69634	0.0:0.9304:0.0:0.0696	.	112;94;73;73;44;171	B7Z767;B7Z5W4;B7Z9L5;B7Z7F1;Q6ZWP6;Q9UKU7	.;.;.;.;.;ACAD8_HUMAN	C	171;94;73;44;133	ENSP00000281182:S171C;ENSP00000443763:S94C;ENSP00000438302:S73C;ENSP00000363884:S44C	ENSP00000281182:S171C	S	+	2	0	ACAD8	133634133	1.000000	0.71417	0.987000	0.45799	0.964000	0.63967	7.385000	0.79763	1.421000	0.47157	-0.140000	0.14226	TCT	C|0.985;G|0.015	0.015	strong		0.522	ACAD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393607.1	NM_014384	
AASDH	132949	hgsc.bcm.edu	37	4	57221348	57221348	+	Splice_Site	SNP	T	T	C	rs3796543	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:57221348T>C	ENST00000205214.6	-	6	1283	c.1103A>G	c.(1102-1104)aAa>aGa	p.K368R	AASDH_ENST00000502617.1_Splice_Site_p.K368R|AASDH_ENST00000602986.1_Splice_Site_p.K215R|AASDH_ENST00000451613.1_Splice_Site_p.K368R|AASDH_ENST00000513376.1_Splice_Site_p.K268R|AASDH_ENST00000434343.2_5'UTR|AASDH_ENST00000510762.1_5'Flank	NM_181806.2	NP_861522.2	Q4L235	ACSF4_HUMAN	aminoadipate-semialdehyde dehydrogenase	368			K -> R (in dbSNP:rs3796543).		fatty acid metabolic process (GO:0006631)		acid-thiol ligase activity (GO:0016878)|ATP binding (GO:0005524)			endometrium(2)|kidney(2)|large_intestine(8)|lung(17)|ovary(4)|prostate(3)|skin(2)|stomach(1)|urinary_tract(1)	40	Glioma(25;0.08)|all_neural(26;0.101)	all_hematologic(202;0.0017)				AAACCCTTACTTGAGAGTAGA	0.348													T|||	324	0.0646965	0.0129	0.0216	5008	,	,		18003	0.1915		0.0179	False		,,,				2504	0.0828				p.K368R		Atlas-SNP	.											.	AASDH	101	.	0			c.A1103G						PASS	.	T	ARG/LYS	58,4348	52.9+/-88.7	0,58,2145	57.0	58.0	58.0		1103	1.8	0.8	4	dbSNP_107	58	178,8422	79.2+/-141.9	1,176,4123	yes	missense-near-splice	AASDH	NM_181806.2	26	1,234,6268	CC,CT,TT		2.0698,1.3164,1.8145	benign	368/1099	57221348	236,12770	2203	4300	6503	SO:0001630	splice_region_variant	132949	exon6			CCTTACTTGAGAG	AF516672	CCDS3504.1, CCDS68705.1, CCDS68706.1, CCDS75126.1, CCDS75127.1	4q12	2010-12-14			ENSG00000157426	ENSG00000157426	1.2.1.31	"""Acyl-CoA synthetase family"""	23993	protein-coding gene	gene with protein product	"""acyl-CoA synthetase family member 4"""	614365				15865210, 12712191, 17762044	Standard	XM_005265721		Approved	NRPS998, LYS2, ACSF4	uc003hbn.3	Q4L235	OTTHUMG00000128841	ENST00000205214.6:c.1103+1A>G	4.37:g.57221348T>C		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	63	29	0.460317	NM_181806	A5D8V3|A5PL22|Q63HK2|Q63HR7|Q6IPP8|Q6TFZ6|Q7Z5Y3|Q96BW4|Q9P064	Missense_Mutation	SNP	ENST00000205214.6	37	CCDS3504.1	159	0.07280219780219781	12	0.024390243902439025	14	0.03867403314917127	121	0.21153846153846154	12	0.0158311345646438	T	2.516	-0.311933	0.05422	0.013164	0.020698	ENSG00000157426	ENST00000205214;ENST00000513376;ENST00000451613;ENST00000503808;ENST00000502617	T;T;T;T	0.42513	0.97;0.97;0.97;0.97	5.59	1.78	0.24846	AMP-dependent synthetase/ligase (1);	0.705587	0.15463	N	0.261049	T	0.00012	0.0000	N	0.01742	-0.745	0.49798	P	1.7999999999995797E-4	B;B;B;B	0.11235	0.004;0.001;0.001;0.003	B;B;B;B	0.11329	0.006;0.003;0.003;0.003	T	0.33701	-0.9858	8	.	.	.	-8.5805	7.1459	0.25583	0.0:0.3876:0.0:0.6124	rs3796543;rs52792608;rs58731313;rs3796543	215;368;368;368	E9PH98;Q4L235-4;Q4L235-3;Q4L235	.;.;.;ACSF4_HUMAN	R	368;268;368;215;368	ENSP00000205214:K368R;ENSP00000423760:K268R;ENSP00000409656:K368R;ENSP00000421171:K368R	.	K	-	2	0	AASDH	56916105	0.886000	0.30341	0.807000	0.32361	0.169000	0.22640	1.158000	0.31737	0.378000	0.24764	0.477000	0.44152	AAA	T|0.950;C|0.050	0.050	strong		0.348	AASDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250780.1	NM_181806	Missense_Mutation
MAP2K2	5605	hgsc.bcm.edu	37	19	4101062	4101062	+	Silent	SNP	G	G	T	rs10250	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:4101062G>T	ENST00000262948.5	-	6	913	c.660C>A	c.(658-660)atC>atA	p.I220I	MAP2K2_ENST00000599345.1_5'Flank|MAP2K2_ENST00000394867.4_Silent_p.I123I	NM_030662.3	NP_109587.1	P36507	MP2K2_HUMAN	mitogen-activated protein kinase kinase 2	220	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|epidermal growth factor receptor signaling pathway (GO:0007173)|ERK1 and ERK2 cascade (GO:0070371)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|MAPK cascade (GO:0000165)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine autophosphorylation (GO:0036289)|positive regulation of cell motility (GO:2000147)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|Ras protein signal transduction (GO:0007265)|regulation of early endosome to late endosome transport (GO:2000641)|regulation of Golgi inheritance (GO:0090170)|regulation of stress-activated MAPK cascade (GO:0032872)|small GTPase mediated signal transduction (GO:0007264)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cell cortex (GO:0005938)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|late endosome (GO:0005770)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|peroxisomal membrane (GO:0005778)	ATP binding (GO:0005524)|MAP kinase kinase activity (GO:0004708)|PDZ domain binding (GO:0030165)|protein serine/threonine kinase activator activity (GO:0043539)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)|scaffold protein binding (GO:0097110)						Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0149)|STAD - Stomach adenocarcinoma(1328;0.18)	Bosutinib(DB06616)|Trametinib(DB08911)	CCATGGAGTCGATGAGCTGGC	0.637													.|||	2170	0.433307	0.2443	0.5562	5008	,	,		13338	0.625		0.4761	False		,,,				2504	0.3599				p.I220I		Atlas-SNP	.											MAP2K2_ENST00000262948,NS,carcinoma,0,2	MAP2K2	72	2	0			c.C660A						PASS	.	G		1264,3138		189,886,1126	62.0	46.0	51.0		660	0.8	1.0	19	dbSNP_52	51	4165,4423		1014,2137,1143	no	coding-synonymous	MAP2K2	NM_030662.3		1203,3023,2269	TT,TG,GG		48.4979,28.7142,41.7937		220/401	4101062	5429,7561	2201	4294	6495	SO:0001819	synonymous_variant	5605	exon6			GGAGTCGATGAGC	L11285	CCDS12120.1	19p13.3	2014-09-17			ENSG00000126934	ENSG00000126934	2.7.12.2	"""Mitogen-activated protein kinase cascade / Kinase kinases"""	6842	protein-coding gene	gene with protein product		601263		PRKMK2		8388392	Standard	NM_030662		Approved	MEK2	uc002lzk.3	P36507	OTTHUMG00000134286	ENST00000262948.5:c.660C>A	19.37:g.4101062G>T		Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	145	68	0.468966	NM_030662		Silent	SNP	ENST00000262948.5	37	CCDS12120.1																																																																																			.	.	weak		0.637	MAP2K2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258957.2		
VCAN	1462	hgsc.bcm.edu	37	5	82816190	82816190	+	Missense_Mutation	SNP	A	A	G	rs61754531	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:82816190A>G	ENST00000265077.3	+	7	2630	c.2065A>G	c.(2065-2067)Aca>Gca	p.T689A	VCAN_ENST00000502527.2_Intron|VCAN_ENST00000512590.2_Missense_Mutation_p.T641A|VCAN_ENST00000343200.5_Intron|VCAN_ENST00000342785.4_Missense_Mutation_p.T689A	NM_004385.4	NP_004376.2	P13611	CSPG2_HUMAN	versican	689	GAG-alpha (glucosaminoglycan attachment domain).				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)	AAGAACAGAAACACTAATACC	0.328													A|||	16	0.00319489	0.0008	0.0014	5008	,	,		20334	0.0		0.0139	False		,,,				2504	0.0				p.T689A		Atlas-SNP	.											.	VCAN	498	.	0			c.A2065G						PASS	.	A	,,ALA/THR,ALA/THR	8,4372		0,8,2182	51.0	53.0	52.0		,,2065,2065	1.6	0.2	5	dbSNP_129	52	90,8492		0,90,4201	yes	intron,intron,missense,missense	VCAN	NM_001126336.2,NM_001164097.1,NM_001164098.1,NM_004385.4	,,58,58	0,98,6383	GG,GA,AA		1.0487,0.1826,0.7561	,,possibly-damaging,possibly-damaging	,,689/1643,689/3397	82816190	98,12864	2190	4291	6481	SO:0001583	missense	1462	exon7			ACAGAAACACTAA	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.2065A>G	5.37:g.82816190A>G	ENSP00000265077:p.Thr689Ala	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	64	34	0.53125	NM_004385	P20754|Q13010|Q13189|Q15123|Q9UCL9|Q9UNW5	Missense_Mutation	SNP	ENST00000265077.3	37	CCDS4060.1	13	0.005952380952380952	0	0.0	1	0.0027624309392265192	0	0.0	12	0.0158311345646438	A	0.784	-0.761296	0.02996	0.001826	0.010487	ENSG00000038427	ENST00000265077;ENST00000342785;ENST00000512590	T;T;T	0.25579	1.79;1.79;1.79	4.03	1.58	0.23477	.	0.518499	0.17701	N	0.164934	T	0.10637	0.0260	M	0.65975	2.015	0.09310	N	1	B;B	0.33940	0.433;0.307	B;B	0.27887	0.084;0.038	T	0.10590	-1.0623	10	0.23302	T	0.38	.	7.4005	0.26960	0.7289:0.0:0.2711:0.0	rs61754531	689;689	P13611-3;P13611	.;CSPG2_HUMAN	A	689;689;641	ENSP00000265077:T689A;ENSP00000342768:T689A;ENSP00000425959:T641A	ENSP00000265077:T689A	T	+	1	0	VCAN	82851946	0.018000	0.18449	0.153000	0.22517	0.029000	0.11900	1.202000	0.32271	0.336000	0.23639	0.533000	0.62120	ACA	A|0.993;G|0.007	0.007	strong		0.328	VCAN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254092.3	NM_004385	
PTBP1	5725	hgsc.bcm.edu	37	19	804642	804642	+	Silent	SNP	C	C	T	rs3170451	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:804642C>T	ENST00000349038.4	+	6	619	c.546C>T	c.(544-546)ccC>ccT	p.P182P	MIR4745_ENST00000577608.1_RNA|PTBP1_ENST00000350092.4_Intron|PTBP1_ENST00000356948.6_Silent_p.P182P|PTBP1_ENST00000394601.4_Silent_p.P182P	NM_031991.3	NP_114368.1	P26599	PTBP1_HUMAN	polypyrimidine tract binding protein 1	182					alternative mRNA splicing, via spliceosome (GO:0000380)|gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|negative regulation of muscle cell differentiation (GO:0051148)|negative regulation of RNA splicing (GO:0033119)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing (GO:0008380)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|poly-pyrimidine tract binding (GO:0008187)|pre-mRNA binding (GO:0036002)|RNA binding (GO:0003723)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|skin(2)|upper_aerodigestive_tract(4)	19		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;6.59e-06)|all_lung(49;9.97e-06)|Breast(49;0.000172)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GGCAGAGCCCCGTGCTCAGGA	0.682													C|||	806	0.160942	0.1331	0.2666	5008	,	,		14242	0.0228		0.1451	False		,,,				2504	0.2822				p.P182P		Atlas-SNP	.											PTBP1,NS,carcinoma,0,1	PTBP1	43	1	0			c.C546T						PASS	.	C	,,,	571,3835	245.3+/-254.3	46,479,1678	60.0	58.0	59.0		546,546,546,	-9.6	0.0	19	dbSNP_105	59	1273,7327	247.4+/-275.4	85,1103,3112	no	coding-synonymous,coding-synonymous,coding-synonymous,intron	PTBP1	NM_002819.4,NM_031990.3,NM_031991.3,NM_175847.2	,,,	131,1582,4790	TT,TC,CC		14.8023,12.9596,14.1781	,,,	182/558,182/551,182/532,	804642	1844,11162	2203	4300	6503	SO:0001819	synonymous_variant	5725	exon6			GAGCCCCGTGCTC	X60648	CCDS32859.1, CCDS42456.1, CCDS45892.1	19p13.3	2013-07-16	2002-01-25	2002-01-25	ENSG00000011304	ENSG00000011304		"""RNA binding motif (RRM) containing"""	9583	protein-coding gene	gene with protein product	"""heterogeneous nuclear ribonucleoprotein I"""	600693	"""polypyrimidine tract binding protein (heterogeneous nuclear ribonucleoprotein I)"""	PTB		1906036, 11024286	Standard	NM_002819		Approved	HNRPI, HNRNP-I, PTB2, PTB3, PTB-1, PTB4, pPTB	uc002lpp.2	P26599		ENST00000349038.4:c.546C>T	19.37:g.804642C>T		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	66	66	1	NM_031990	Q9BUQ0	Silent	SNP	ENST00000349038.4	37	CCDS32859.1																																																																																			C|0.860;T|0.140	0.140	strong		0.682	PTBP1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457605.1		
PROM2	150696	hgsc.bcm.edu	37	2	95947085	95947085	+	Missense_Mutation	SNP	A	A	G	rs12992066	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:95947085A>G	ENST00000317620.9	+	12	1656	c.1523A>G	c.(1522-1524)cAg>cGg	p.Q508R	PROM2_ENST00000317668.4_Missense_Mutation_p.Q508R|PROM2_ENST00000403131.2_Missense_Mutation_p.Q508R|PROM2_ENST00000542147.1_Missense_Mutation_p.Q508R	NM_001165978.1	NP_001159450.1	Q8N271	PROM2_HUMAN	prominin 2	508			Q -> R (in dbSNP:rs12992066). {ECO:0000269|PubMed:12514187, ECO:0000269|PubMed:12975309, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.5}.		negative regulation of caveolin-mediated endocytosis (GO:2001287)|negative regulation of pinocytosis (GO:0048550)|positive regulation of cell projection organization (GO:0031346)|positive regulation of protein phosphorylation (GO:0001934)|regulation of Cdc42 GTPase activity (GO:0043088)	cell projection (GO:0042995)|cell surface (GO:0009986)|cilium (GO:0005929)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|microspike (GO:0044393)|microvillus (GO:0005902)|prominosome (GO:0071914)	cholesterol binding (GO:0015485)			breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(8)|lung(12)|ovary(3)|prostate(1)|skin(1)|urinary_tract(1)	32						CTGGTGTGCCAGAGCTGGGAG	0.637													G|||	4005	0.79972	0.9085	0.866	5008	,	,		14828	0.6885		0.7664	False		,,,				2504	0.7546				p.Q508R		Atlas-SNP	.											.	PROM2	78	.	0			c.A1523G						PASS	.	G	ARG/GLN,ARG/GLN,ARG/GLN	3875,531	241.2+/-251.7	1700,475,28	68.0	65.0	66.0		1523,1523,1523	-3.9	0.2	2	dbSNP_121	66	6496,2104	364.1+/-333.4	2445,1606,249	yes	missense,missense,missense	PROM2	NM_001165977.1,NM_001165978.1,NM_144707.2	43,43,43	4145,2081,277	GG,GA,AA		24.4651,12.0517,20.2599	benign,benign,benign	508/835,508/835,508/835	95947085	10371,2635	2203	4300	6503	SO:0001583	missense	150696	exon12			TGTGCCAGAGCTG	AF245303	CCDS2012.1	2q11.1	2008-02-05			ENSG00000155066	ENSG00000155066			20685	protein-coding gene	gene with protein product						12514187	Standard	NM_001165978		Approved		uc002sui.3	Q8N271	OTTHUMG00000130393	ENST00000317620.9:c.1523A>G	2.37:g.95947085A>G	ENSP00000318270:p.Gln508Arg	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	77	76	0.987013	NM_001165977	A8K2V1|Q2HIX6|Q8NB84|Q8TAE2	Missense_Mutation	SNP	ENST00000317620.9	37	CCDS2012.1	1732	0.793040293040293	445	0.9044715447154471	324	0.8950276243093923	395	0.6905594405594405	568	0.7493403693931399	G	0.005	-2.208608	0.00292	0.879483	0.755349	ENSG00000155066	ENST00000403131;ENST00000317668;ENST00000317620;ENST00000542147	T;T;T;T	0.45276	0.9;0.9;0.9;0.9	5.07	-3.94	0.04130	.	1.044690	0.07514	N	0.909370	T	0.00012	0.0000	N	0.03115	-0.41	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.34054	-0.9844	9	0.08837	T	0.75	-6.4089	14.3749	0.66867	0.6052:0.0:0.3948:0.0	rs12992066;rs60872367	508	Q8N271	PROM2_HUMAN	R	508	ENSP00000385716:Q508R;ENSP00000318520:Q508R;ENSP00000318270:Q508R;ENSP00000442542:Q508R	ENSP00000318270:Q508R	Q	+	2	0	PROM2	95310812	0.979000	0.34478	0.158000	0.22627	0.183000	0.23260	0.082000	0.14847	-2.531000	0.00491	-3.265000	0.00048	CAG	A|0.207;C|0.000;G|0.793;T|0.000	0.793	strong		0.637	PROM2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252771.1	NM_144707	
COL6A3	1293	hgsc.bcm.edu	37	2	238243292	238243292	+	Missense_Mutation	SNP	G	G	A	rs1131296	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:238243292G>A	ENST00000295550.4	-	41	9658	c.9206C>T	c.(9205-9207)aCc>aTc	p.T3069I	COL6A3_ENST00000346358.4_Missense_Mutation_p.T2869I|COL6A3_ENST00000347401.3_Missense_Mutation_p.T2868I|COL6A3_ENST00000472056.1_Missense_Mutation_p.T2462I|COL6A3_ENST00000353578.4_Missense_Mutation_p.T2863I|COL6A3_ENST00000409809.1_Missense_Mutation_p.T2863I	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	3069	Fibronectin type-III. {ECO:0000255|PROSITE-ProRule:PRU00316}.|Nonhelical region.		T -> I (in dbSNP:rs1131296). {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)		TCCGTGGTAGGTGGCTCTGAC	0.502													G|||	1734	0.346246	0.2504	0.3256	5008	,	,		18933	0.4802		0.4036	False		,,,				2504	0.2935				p.T3069I		Atlas-SNP	.											.	COL6A3	608	.	0			c.C9206T						PASS	.	G	ILE/THR,ILE/THR,ILE/THR	1256,3150	430.6+/-342.6	191,874,1138	71.0	60.0	63.0		8588,7385,9206	-1.1	0.2	2	dbSNP_86	63	3456,5144	507.7+/-376.9	696,2064,1540	yes	missense,missense,missense	COL6A3	NM_057167.3,NM_057166.4,NM_004369.3	89,89,89	887,2938,2678	AA,AG,GG		40.186,28.5066,36.2294	benign,benign,benign	2863/2972,2462/2571,3069/3178	238243292	4712,8294	2203	4300	6503	SO:0001583	missense	1293	exon41			TGGTAGGTGGCTC	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.9206C>T	2.37:g.238243292G>A	ENSP00000295550:p.Thr3069Ile	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	101	44	0.435644	NM_004369	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Missense_Mutation	SNP	ENST00000295550.4	37	CCDS33412.1	826	0.3782051282051282	127	0.258130081300813	121	0.3342541436464088	284	0.4965034965034965	294	0.38786279683377306	G	11.26	1.586755	0.28268	0.285066	0.40186	ENSG00000163359	ENST00000295550;ENST00000347401;ENST00000353578;ENST00000472056;ENST00000409809;ENST00000346358	T;T;T;T;T;T	0.29142	1.58;1.58;1.58;1.58;1.58;1.58	5.43	-1.13	0.09775	Fibronectin, type III (3);Immunoglobulin-like fold (1);	0.851480	0.10078	N	0.718837	T	0.00012	0.0000	N	0.14661	0.345	0.42095	P	0.008685999999999972	B;B;B	0.10296	0.002;0.003;0.002	B;B;B	0.11329	0.003;0.006;0.003	T	0.48703	-0.9012	9	0.25751	T	0.34	.	9.5989	0.39591	0.4842:0.0:0.5158:0.0	rs1131296;rs2270670;rs3088291;rs3191076;rs11547644;rs17352867;rs59730490;rs1131296	2462;2863;3069	E9PFQ6;P12111-2;P12111	.;.;CO6A3_HUMAN	I	3069;2868;2863;2462;2863;2869	ENSP00000295550:T3069I;ENSP00000315609:T2868I;ENSP00000315873:T2863I;ENSP00000418285:T2462I;ENSP00000386844:T2863I;ENSP00000295546:T2869I	ENSP00000295550:T3069I	T	-	2	0	COL6A3	237908031	0.913000	0.31002	0.164000	0.22755	0.986000	0.74619	0.603000	0.24149	-0.602000	0.05775	0.557000	0.71058	ACC	G|0.635;A|0.365	0.365	strong		0.502	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369	
SLITRK3	22865	hgsc.bcm.edu	37	3	164905688	164905688	+	Silent	SNP	G	G	A	rs17449404	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:164905688G>A	ENST00000475390.1	-	2	3374	c.2931C>T	c.(2929-2931)ttC>ttT	p.F977F	SLITRK3_ENST00000241274.3_Silent_p.F977F			O94933	SLIK3_HUMAN	SLIT and NTRK-like family, member 3	977					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						CTCTCTGTTAGAACCTGTATG	0.378										HNSCC(40;0.11)			G|||	486	0.0970447	0.0862	0.1571	5008	,	,		17821	0.0476		0.0785	False		,,,				2504	0.1391				p.F977F		Atlas-SNP	.											.	SLITRK3	263	.	0			c.C2931T						PASS	.	G		377,4029	184.0+/-211.4	14,349,1840	93.0	95.0	94.0		2931	5.7	1.0	3	dbSNP_123	94	768,7832	178.5+/-227.8	27,714,3559	no	coding-synonymous	SLITRK3	NM_014926.2		41,1063,5399	AA,AG,GG		8.9302,8.5565,8.8036		977/978	164905688	1145,11861	2203	4300	6503	SO:0001819	synonymous_variant	22865	exon2			CTGTTAGAACCTG	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.2931C>T	3.37:g.164905688G>A		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	102	50	0.490196	NM_014926	Q1RMY6	Silent	SNP	ENST00000475390.1	37	CCDS3197.1																																																																																			G|0.914;A|0.086	0.086	strong		0.378	SLITRK3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350126.1	NM_014926	
RALGAPA2	57186	hgsc.bcm.edu	37	20	20493222	20493222	+	Silent	SNP	G	G	A	rs35039408	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:20493222G>A	ENST00000202677.7	-	32	4798	c.4791C>T	c.(4789-4791)ccC>ccT	p.P1597P		NM_020343.3	NP_065076.2	Q2PPJ7	RGPA2_HUMAN	Ral GTPase activating protein, alpha subunit 2 (catalytic)	1597					activation of Ral GTPase activity (GO:0032859)|membrane organization (GO:0061024)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	protein heterodimerization activity (GO:0046982)|Ral GTPase activator activity (GO:0017123)	p.P1597P(3)		endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|liver(1)|lung(25)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	54						AGGGTCCTCGGGGCTCCACTG	0.458													G|||	1355	0.270567	0.0295	0.4395	5008	,	,		18071	0.2163		0.4195	False		,,,				2504	0.3793				p.P1597P		Atlas-SNP	.											RALGAPA2_ENST00000202677,NS,carcinoma,0,3	RALGAPA2	274	3	3	Substitution - coding silent(3)	prostate(2)|stomach(1)	c.C4791T						PASS	.	G		345,3435		16,313,1561	55.0	55.0	55.0		4791	-1.7	0.9	20	dbSNP_126	55	3405,4817		696,2013,1402	no	coding-synonymous	RALGAPA2	NM_020343.3		712,2326,2963	AA,AG,GG		41.4133,9.127,31.2448		1597/1874	20493222	3750,8252	1890	4111	6001	SO:0001819	synonymous_variant	57186	exon32			TCCTCGGGGCTCC	AL078634, DQ310704	CCDS46584.1	20p11.23	2009-09-09	2009-09-09	2009-09-09	ENSG00000188559	ENSG00000188559			16207	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 74"""	C20orf74		16490346, 19520869	Standard	NM_020343		Approved	dJ1049G11.4, AS250, KIAA1272, RapGAPalpha2	uc002wrz.3	Q2PPJ7	OTTHUMG00000032010	ENST00000202677.7:c.4791C>T	20.37:g.20493222G>A		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	96	96	1	NM_020343	Q4VXU6|Q5JUA3|Q5JUA4|Q5T9K3|Q96CX9|Q9BQT7|Q9H9D9|Q9ULE8	Silent	SNP	ENST00000202677.7	37	CCDS46584.1	609	0.27884615384615385	22	0.044715447154471545	151	0.4171270718232044	122	0.21328671328671328	314	0.41424802110817943	G	8.371	0.835272	0.16820	0.09127	0.414133	ENSG00000188559	ENST00000430436;ENST00000427175	D;D	0.94184	-3.37;-3.37	5.97	-1.68	0.08212	.	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999810333	.	.	.	.	.	.	T	0.02238	-1.1190	6	0.62326	D	0.03	.	5.9471	0.19225	0.1225:0.0744:0.498:0.305	rs35039408;rs61739707	.	.	.	L	1414;8	ENSP00000400085:P1414L;ENSP00000388695:P8L	ENSP00000388695:P8L	P	-	2	0	RALGAPA2	20441222	0.002000	0.14202	0.914000	0.36105	0.978000	0.69477	-1.513000	0.02256	-0.136000	0.11475	0.561000	0.74099	CCC	G|0.683;A|0.317	0.317	strong		0.458	RALGAPA2-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000471941.1	NM_020343	
LY75	4065	hgsc.bcm.edu	37	2	160711045	160711045	+	Splice_Site	SNP	G	G	C	rs3951216	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:160711045G>C	ENST00000263636.4	-	18	2448	c.2421C>G	c.(2419-2421)gaC>gaG	p.D807E	LY75_ENST00000554112.1_Splice_Site_p.D807E|LY75_ENST00000553424.1_Splice_Site_p.D807E|LY75-CD302_ENST00000504764.1_Splice_Site_p.D807E|LY75-CD302_ENST00000505052.1_Splice_Site_p.D807E	NM_002349.3	NP_002340.2	O60449	LY75_HUMAN	lymphocyte antigen 75	807			D -> E (in dbSNP:rs3951216). {ECO:0000269|PubMed:9862343}.		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)		TTCCAGCACGGTCTAAAGAAG	0.358													C|||	2834	0.565895	0.3896	0.5778	5008	,	,		15355	0.7093		0.4304	False		,,,				2504	0.7873				p.D807E		Atlas-SNP	.											.	LY75	151	.	0			c.C2421G						PASS	.	C	GLU/ASP,GLU/ASP,GLU/ASP	1718,2688	648.1+/-398.7	316,1086,801	61.0	61.0	61.0		2421,2421,2421	3.7	1.0	2	dbSNP_108	61	3765,4835	614.7+/-396.3	810,2145,1345	yes	missense-near-splice,missense-near-splice,missense-near-splice	LY75,LY75-CD302	NM_001198759.1,NM_001198760.1,NM_002349.3	45,45,45	1126,3231,2146	CC,CG,GG		43.7791,38.9923,42.1575	benign,benign,benign	807/1874,807/1818,807/1723	160711045	5483,7523	2203	4300	6503	SO:0001630	splice_region_variant	4065	exon18			AGCACGGTCTAAA	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.2420-1C>G	2.37:g.160711045G>C		Somatic	182	0	0		WXS	Illumina HiSeq	Phase_I	170	75	0.441176	NM_002349	O75913|Q53R46|Q53TF5|Q7Z575|Q7Z577	Missense_Mutation	SNP	ENST00000263636.4	37	CCDS2211.1	1136	0.5201465201465202	193	0.39227642276422764	201	0.5552486187845304	413	0.722027972027972	329	0.4340369393139842	C	1.959	-0.439447	0.04636	0.389923	0.437791	ENSG00000054219;ENSG00000054219;ENSG00000054219;ENSG00000248672;ENSG00000248672	ENST00000554112;ENST00000553424;ENST00000263636;ENST00000504764;ENST00000505052	T;T;T;T;T	0.09073	3.05;3.05;3.02;3.05;3.05	5.69	3.67	0.42095	.	0.242674	0.21217	N	0.078215	T	0.00012	0.0000	N	0.01482	-0.84	0.47009	P	7.190000000000252E-4	B;B;B	0.09022	0.0;0.002;0.0	B;B;B	0.09377	0.001;0.004;0.001	T	0.32322	-0.9911	9	0.02654	T	1	.	7.5174	0.27608	0.4063:0.4503:0.1434:0.0	rs3951216;rs52796448	807;807;807	O60449-3;O60449;O60449-2	.;LY75_HUMAN;.	E	807	ENSP00000451511:D807E;ENSP00000451446:D807E;ENSP00000263636:D807E;ENSP00000423463:D807E;ENSP00000421035:D807E	ENSP00000423463:D807E	D	-	3	2	LY75;LY75-CD302	160419291	1.000000	0.71417	1.000000	0.80357	0.773000	0.43773	1.124000	0.31320	0.715000	0.32103	-0.120000	0.15030	GAC	G|0.536;C|0.464	0.464	strong		0.358	LY75-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255035.1		Missense_Mutation
ARSD	414	hgsc.bcm.edu	37	X	2835964	2835964	+	Silent	SNP	G	G	A	rs73632972	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	166	0	0		WXS	Illumina HiSeq	Phase_I	148	16	0.108108	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		
RP1L1	94137	hgsc.bcm.edu	37	8	10467571	10467571	+	Missense_Mutation	SNP	C	C	T	rs200175359		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	138	1	0.00724638		WXS	Illumina HiSeq	Phase_I	107	8	0.0747664	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		
SORCS1	114815	hgsc.bcm.edu	37	10	108389111	108389111	+	Silent	SNP	A	A	G	rs3802553	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:108389111A>G	ENST00000263054.6	-	19	2518	c.2511T>C	c.(2509-2511)ttT>ttC	p.F837F	SORCS1_ENST00000344440.6_Silent_p.F837F|SORCS1_ENST00000369698.1_Silent_p.F372F	NM_001206570.1|NM_052918.4	NP_001193499.1|NP_443150.3	Q8WY21	SORC1_HUMAN	sortilin-related VPS10 domain containing receptor 1	837	PKD. {ECO:0000255|PROSITE- ProRule:PRU00151}.				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)		TACCATCGCCAAAGTCCACTT	0.512													A|||	1162	0.232029	0.2829	0.1052	5008	,	,		21478	0.3383		0.0815	False		,,,				2504	0.2986				p.F837F		Atlas-SNP	.											.	SORCS1	534	.	0			c.T2511C						PASS	.	A	,,,,,	1141,3265	404.6+/-333.2	146,849,1208	141.0	102.0	115.0		2511,2511,2511,2511,2511,2511	-9.0	0.1	10	dbSNP_107	115	637,7963	163.8+/-216.2	27,583,3690	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	,,,,,	173,1432,4898	GG,GA,AA		7.407,25.8965,13.6706	,,,,,	837/1199,837/1180,837/1131,837/1160,837/1180,837/1169	108389111	1778,11228	2203	4300	6503	SO:0001819	synonymous_variant	114815	exon19			ATCGCCAAAGTCC	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.2511T>C	10.37:g.108389111A>G		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	82	39	0.47561	NM_001206572	A2RRF4|Q59GG7|Q5JVT7|Q5JVT8|Q5VY14|Q86WQ1|Q86WQ2|Q9H1Y1|Q9H1Y2	Silent	SNP	ENST00000263054.6	37	CCDS7559.1																																																																																			A|0.841;G|0.159	0.159	strong		0.512	SORCS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050232.4	NM_052918	
KCNJ12	3768	hgsc.bcm.edu	37	17	21319399	21319399	+	Missense_Mutation	SNP	A	A	G	rs4985866	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:21319399A>G	ENST00000583088.1	+	3	1640	c.745A>G	c.(745-747)Atc>Gtc	p.I249V	KCNJ12_ENST00000331718.5_Missense_Mutation_p.I249V	NM_021012.4	NP_066292.2	Q14500	KCJ12_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 12	249			I -> V (in dbSNP:rs4985866).		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)	GCTGGACCAGATCGACATCGA	0.622										Prostate(3;0.18)																											p.I249V		Atlas-SNP	.											KCNJ12,NS,neuroblastoma,0,1	.	.	1	0			c.A745G						PASS	.	A	VAL/ILE	964,3442		0,964,1239	127.0	92.0	104.0		745	4.3	1.0	17	dbSNP_111	104	2315,6285		0,2315,1985	yes	missense	KCNJ12	NM_021012.4	29	0,3279,3224	GG,GA,AA		26.9186,21.8793,25.2114	benign	249/434	21319399	3279,9727	2203	4300	6503	SO:0001583	missense	100134444	exon3			GACCAGATCGACA	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.745A>G	17.37:g.21319399A>G	ENSP00000463778:p.Ile249Val	Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	148	29	0.195946	NM_001194958	O43401|Q15756|Q8NG63	Missense_Mutation	SNP	ENST00000583088.1	37	CCDS11219.1	816	0.37362637362637363	160	0.3252032520325203	129	0.356353591160221	276	0.4825174825174825	251	0.3311345646437995	A	6.561	0.471839	0.12461	0.218793	0.269186	ENSG00000184185	ENST00000331718	D	0.91180	-2.8	5.43	4.33	0.51752	Immunoglobulin E-set (1);Potassium channel, inwardly rectifying, Kir, conserved region 2 (1);Potassium channel, inwardly rectifying, Kir, cytoplasmic (1);	0.052254	0.85682	D	0.000000	T	0.00012	0.0000	N	0.05124	-0.11	0.23735	P	0.99698559	B	0.06786	0.001	B	0.04013	0.001	T	0.24548	-1.0157	9	0.14656	T	0.56	.	12.5199	0.56054	0.8604:0.1396:0.0:0.0	rs4985866;rs4985866	249	Q14500	IRK12_HUMAN	V	249	ENSP00000328150:I249V	ENSP00000328150:I249V	I	+	1	0	KCNJ12	21259992	1.000000	0.71417	0.998000	0.56505	0.988000	0.76386	5.809000	0.69172	0.873000	0.35799	0.533000	0.62120	ATC	A|0.625;G|0.375	0.375	strong		0.622	KCNJ12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255060.2	NM_021012	
CD207	50489	hgsc.bcm.edu	37	2	71058184	71058184	+	Silent	SNP	C	C	T	rs13421115	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:71058184C>T	ENST00000410009.3	-	6	1029	c.984G>A	c.(982-984)ccG>ccA	p.P328P		NM_015717.3	NP_056532	Q9UJ71	CLC4K_HUMAN	CD207 molecule, langerin	328					antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|defense response to virus (GO:0051607)	clathrin-coated endocytic vesicle membrane (GO:0030669)|early endosome membrane (GO:0031901)|endocytic vesicle (GO:0030139)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|mannose binding (GO:0005537)			endometrium(1)|kidney(2)|large_intestine(2)|lung(13)|ovary(1)|stomach(1)	20						TGTCCTGTCACGGTTCTGATG	0.488													T|||	812	0.162141	0.1959	0.1744	5008	,	,		19961	0.004		0.2734	False		,,,				2504	0.1564				p.P328P		Atlas-SNP	.											.	CD207	47	.	0			c.G984A						PASS	.	T		844,3040		89,666,1187	75.0	71.0	72.0		984	-2.8	0.0	2	dbSNP_121	72	2258,6028		309,1640,2194	no	coding-synonymous	CD207	NM_015717.3		398,2306,3381	TT,TC,CC		27.2508,21.7302,25.4889		328/329	71058184	3102,9068	1942	4143	6085	SO:0001819	synonymous_variant	50489	exon6			CTGTCACGGTTCT	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.984G>A	2.37:g.71058184C>T		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	93	93	1	NM_015717		Silent	SNP	ENST00000410009.3	37																																																																																				C|0.806;T|0.194	0.194	strong		0.488	CD207-001	KNOWN	non_canonical_conserved|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000329959.4	NM_015717	
UBXN11	91544	hgsc.bcm.edu	37	1	26608877	26608877	+	Silent	SNP	G	G	A	rs1134582|rs140364749	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:26608877G>A	ENST00000374222.1	-	16	1940	c.1476C>T	c.(1474-1476)ggC>ggT	p.G492G	UBXN11_ENST00000314675.7_Silent_p.G372G|UBXN11_ENST00000374221.3_Silent_p.G492G|UBXN11_ENST00000374217.2_Silent_p.G459G|UBXN11_ENST00000357089.4_Silent_p.G459G|UBXN11_ENST00000374223.1_Silent_p.G249G			Q5T124	UBX11_HUMAN	UBX domain protein 11	492	3 X 8 AA tandem repeats of P-G-P-G-P-G-P- S.|Pro-rich.		Missing.|Missing. {ECO:0000269|PubMed:14702039, ECO:0000269|Ref.2}.			cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)		p.G490_P515delGPGPSPGPGPGPSPGPGPGPSPCPGP(1)		endometrium(3)|kidney(2)|large_intestine(4)|lung(6)|ovary(2)|prostate(3)|upper_aerodigestive_tract(3)	23						cgggactggggccgggaccgg	0.721																																					p.G492G		Atlas-SNP	.											UBXN11,NS,carcinoma,0,2	UBXN11	54	2	1	Deletion - In frame(1)	ovary(1)	c.C1476T						scavenged	.						33.0	40.0	38.0					1																	26608877		1787	4040	5827	SO:0001819	synonymous_variant	91544	exon16			ACTGGGGCCGGGA	AF521017	CCDS41286.1, CCDS41287.1, CCDS41288.1	1p36.11	2008-07-25	2008-07-25	2008-07-25	ENSG00000158062	ENSG00000158062		"""UBX domain containing"""	30600	protein-coding gene	gene with protein product	"""socius"""	609151	"""UBX domain containing 5"""	UBXD5		11940653	Standard	NM_183008		Approved	SOC, SOCI	uc001blw.3	Q5T124	OTTHUMG00000003382	ENST00000374222.1:c.1476C>T	1.37:g.26608877G>A		Somatic	25	1	0.04		WXS	Illumina HiSeq	Phase_I	29	12	0.413793	NM_183008	D3DPK6|Q5T117|Q5T120|Q5T125|Q5T126|Q5T129|Q5T131|Q5T133|Q63HM6|Q71RB3|Q8IY27|Q8N1L6|Q8N9M4|Q8NA18|Q8NFE3|Q8NFE4|Q8NFE6	Silent	SNP	ENST00000374222.1	37	CCDS41288.1																																																																																			G|0.870;A|0.130	0.130	strong		0.721	UBXN11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000009500.1	NM_145345	
PLCB2	5330	hgsc.bcm.edu	37	15	40590134	40590134	+	Silent	SNP	G	G	A	rs2229690	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:40590134G>A	ENST00000260402.3	-	12	1431	c.1182C>T	c.(1180-1182)agC>agT	p.S394S	PLCB2_ENST00000456256.2_Silent_p.S394S|PLCB2_ENST00000557821.1_Silent_p.S394S|PLCB2-AS1_ENST00000559520.1_RNA	NM_001284297.1|NM_004573.2	NP_001271226.1|NP_004564.2	Q00722	PLCB2_HUMAN	phospholipase C, beta 2	394	PI-PLC X-box. {ECO:0000255|PROSITE- ProRule:PRU00270}.				activation of phospholipase C activity (GO:0007202)|inositol phosphate metabolic process (GO:0043647)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|phospholipid metabolic process (GO:0006644)|sensory perception of bitter taste (GO:0050913)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)	calcium ion binding (GO:0005509)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|signal transducer activity (GO:0004871)	p.S394R(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(13)|ovary(4)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(3)	39		all_cancers(109;9.35e-19)|all_epithelial(112;1.18e-15)|Lung NSC(122;2.45e-11)|all_lung(180;6.47e-10)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;9.38e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0508)		TCTTAAAGGCGCTTTCTGCAA	0.542													A|||	3458	0.690495	0.8298	0.6744	5008	,	,		20222	0.7887		0.4742	False		,,,				2504	0.635				p.S394S		Atlas-SNP	.											PLCB2_ENST00000260402,NS,carcinoma,0,2	PLCB2	177	2	1	Substitution - Missense(1)	pancreas(1)	c.C1182T						PASS	.	A		3353,941		1314,725,108	91.0	111.0	105.0		1182	-0.4	1.0	15	dbSNP_98	105	4142,4372		1011,2120,1126	no	coding-synonymous	PLCB2	NM_004573.2		2325,2845,1234	AA,AG,GG		48.6493,21.9143,41.4819		394/1186	40590134	7495,5313	2147	4257	6404	SO:0001819	synonymous_variant	5330	exon12			AAAGGCGCTTTCT		CCDS42020.1, CCDS61591.1, CCDS61592.1, CCDS73704.1	15q15.1	2012-01-23			ENSG00000137841	ENSG00000137841	3.1.4.11		9055	protein-coding gene	gene with protein product		604114				1644792, 9925923	Standard	XM_005254448		Approved	FLJ38135	uc001zld.3	Q00722	OTTHUMG00000172412	ENST00000260402.3:c.1182C>T	15.37:g.40590134G>A		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	90	43	0.477778	NM_004573	A8K6J2|B9EGH5	Silent	SNP	ENST00000260402.3	37	CCDS42020.1																																																																																			G|0.349;A|0.651	0.651	strong		0.542	PLCB2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000418430.1		
ALMS1	7840	hgsc.bcm.edu	37	2	73717656	73717656	+	Missense_Mutation	SNP	A	A	G	rs10193972	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:73717656A>G	ENST00000264448.6	+	10	8678	c.8567A>G	c.(8566-8568)aAc>aGc	p.N2856S	AC096546.1_ENST00000408160.1_RNA|ALMS1_ENST00000409009.1_Missense_Mutation_p.N2814S	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	2856			N -> S (in dbSNP:rs10193972).		endosomal transport (GO:0016197)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of stress fiber assembly (GO:0051492)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)				breast(4)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(31)|lung(68)|ovary(4)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	147						CTAGGAGTAAACAGATCGAGT	0.403													G|||	1794	0.358227	0.8578	0.3905	5008	,	,		20831	0.0089		0.2266	False		,,,				2504	0.1554				p.N2856S		Atlas-SNP	.											.	ALMS1	384	.	0			c.A8567G						PASS	.	G	SER/ASN	2743,1043		1007,729,157	78.0	74.0	75.0		8567	0.2	0.2	2	dbSNP_119	75	1947,6251		221,1505,2373	yes	missense	ALMS1	NM_015120.4	46	1228,2234,2530	GG,GA,AA		23.7497,27.5489,39.1355	benign	2856/4168	73717656	4690,7294	1893	4099	5992	SO:0001583	missense	7840	exon10			GAGTAAACAGATC	AB002326	CCDS42697.1	2p13.1	2014-09-17			ENSG00000116127	ENSG00000116127			428	protein-coding gene	gene with protein product		606844				9063741	Standard	NM_015120		Approved	KIAA0328	uc002sje.1	Q8TCU4	OTTHUMG00000152812	ENST00000264448.6:c.8567A>G	2.37:g.73717656A>G	ENSP00000264448:p.Asn2856Ser	Somatic	137	1	0.00729927		WXS	Illumina HiSeq	Phase_I	136	136	1	NM_015120	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Missense_Mutation	SNP	ENST00000264448.6	37	CCDS42697.1	730	0.3342490842490842	418	0.8495934959349594	126	0.34806629834254144	8	0.013986013986013986	178	0.23482849604221637	G	1.761	-0.486860	0.04352	0.724511	0.237497	ENSG00000116127	ENST00000409009;ENST00000264448	T;T	0.06528	3.29;3.29	0.225	0.225	0.15325	.	.	.	.	.	T	0.00012	0.0000	N	0.02011	-0.69	0.58432	P	4.000000000004E-6	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.04900	-1.0919	7	0.16896	T	0.51	.	.	.	.	rs10193972;rs17434201;rs17848864;rs52794198;rs60480147;rs10193972	2856;2814;2856	Q8TCU4-3;B8ZZJ3;Q8TCU4	.;.;ALMS1_HUMAN	S	2814;2856	ENSP00000386627:N2814S;ENSP00000264448:N2856S	ENSP00000264448:N2856S	N	+	2	0	ALMS1	73571164	0.532000	0.26346	0.192000	0.23308	0.725000	0.41563	-0.691000	0.05133	-0.690000	0.05142	-0.684000	0.03749	AAC	A|0.675;G|0.325	0.325	strong		0.403	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120	
SHANK3	85358	hgsc.bcm.edu	37	22	51153371	51153371	+	Missense_Mutation	SNP	G	G	A	rs61729471	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:51153371G>A	ENST00000414786.2	+	19	2346	c.2119G>A	c.(2119-2121)Gcc>Acc	p.A707T	SHANK3_ENST00000262795.3_Missense_Mutation_p.A737T|SHANK3_ENST00000445220.2_Missense_Mutation_p.A723T			Q9BYB0	SHAN3_HUMAN	SH3 and multiple ankyrin repeat domains 3	721					adult behavior (GO:0030534)|alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor clustering (GO:0097113)|brain morphogenesis (GO:0048854)|dendritic spine morphogenesis (GO:0060997)|guanylate kinase-associated protein clustering (GO:0097117)|learning (GO:0007612)|MAPK cascade (GO:0000165)|memory (GO:0007613)|N-methyl-D-aspartate receptor clustering (GO:0097114)|negative regulation of actin filament bundle assembly (GO:0032232)|negative regulation of cell volume (GO:0045794)|positive regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000969)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of glutamate receptor signaling pathway (GO:1900451)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of synapse structural plasticity (GO:0051835)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|postsynaptic density assembly (GO:0097107)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of long term synaptic depression (GO:1900452)|regulation of long-term synaptic potentiation (GO:1900271)|social behavior (GO:0035176)|striatal medium spiny neuron differentiation (GO:0021773)|synapse assembly (GO:0007416)|vocal learning (GO:0042297)|vocalization behavior (GO:0071625)	cell junction (GO:0030054)|ciliary membrane (GO:0060170)|cytoplasm (GO:0005737)|neuron projection (GO:0043005)|neuron spine (GO:0044309)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	GKAP/Homer scaffold activity (GO:0030160)|identical protein binding (GO:0042802)|ionotropic glutamate receptor binding (GO:0035255)|protein C-terminus binding (GO:0008022)|scaffold protein binding (GO:0097110)|SH3 domain binding (GO:0017124)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(1)|lung(5)	8		all_cancers(38;3.75e-11)|all_epithelial(38;1.82e-09)|Breast(42;0.000448)|all_lung(38;0.000665)|Lung NSC(38;0.0104)|Ovarian(80;0.104)|Lung SC(80;0.162)|Hepatocellular(38;0.178)		BRCA - Breast invasive adenocarcinoma(115;0.22)		GCTGGCAGCCGCCGCAGAGCC	0.662													G|||	127	0.0253594	0.0	0.0274	5008	,	,		14931	0.003		0.0268	False		,,,				2504	0.0798				p.A707T		Atlas-SNP	.											.	SHANK3	96	.	0			c.G2119A						PASS	.	G	THR/ALA	31,4295		0,31,2132	11.0	14.0	13.0		2209	4.1	0.2	22	dbSNP_129	13	274,8220		7,260,3980	yes	missense	SHANK3	NM_001080420.1	58	7,291,6112	AA,AG,GG		3.2258,0.7166,2.3791	possibly-damaging	737/1748	51153371	305,12515	2163	4247	6410	SO:0001583	missense	85358	exon19			GCAGCCGCCGCAG	AB051437		22q13.3	2013-11-14			ENSG00000251322	ENSG00000251322		"""Sterile alpha motif (SAM) domain containing"", ""Ankyrin repeat domain containing"""	14294	protein-coding gene	gene with protein product	"""proline rich synapse associated protein 2"", ""shank postsynaptic density protein"""	606230				11258795, 11431708, 10806096, 17173049	Standard	NM_033517		Approved	SPANK-2, prosap2, KIAA1650, PSAP2	uc031ryd.1	Q9BYB0	OTTHUMG00000150169	ENST00000414786.2:c.2119G>A	22.37:g.51153371G>A	ENSP00000464552:p.Ala707Thr	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	58	32	0.551724	NM_033517	D7UT47|Q8TET3	Missense_Mutation	SNP	ENST00000414786.2	37		26	0.011904761904761904	1	0.0020325203252032522	7	0.019337016574585635	0	0.0	18	0.023746701846965697	G	14.08	2.427407	0.43122	0.007166	0.032258	ENSG00000251322	ENST00000262795;ENST00000445220	T;T	0.39229	1.09;1.12	4.06	4.06	0.47325	.	.	.	.	.	T	0.10809	0.0264	L	0.47190	1.495	0.09310	N	0.999996	P;P	0.50710	0.739;0.938	B;B	0.29353	0.041;0.101	T	0.18840	-1.0324	9	0.62326	D	0.03	.	9.0818	0.36556	0.0:0.0:0.7811:0.2189	rs61729471	722;737	Q9BYB0;F2Z3L0	SHAN3_HUMAN;.	T	737;723	ENSP00000442518:A737T;ENSP00000446078:A723T	ENSP00000442518:A737T	A	+	1	0	SHANK3	49500237	1.000000	0.71417	0.169000	0.22859	0.821000	0.46438	3.411000	0.52672	2.102000	0.63906	0.511000	0.50034	GCC	G|0.988;A|0.012	0.012	strong		0.662	SHANK3-001	KNOWN	non_canonical_polymorphism|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000316674.2	NM_001080420	
ZNF217	7764	hgsc.bcm.edu	37	20	52193542	52193542	+	Silent	SNP	C	C	T	rs61748380	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:52193542C>T	ENST00000371471.2	-	4	2186	c.1761G>A	c.(1759-1761)ctG>ctA	p.L587L	ZNF217_ENST00000302342.3_Silent_p.L587L|RP4-724E16.2_ENST00000424252.1_RNA			O75362	ZN217_HUMAN	zinc finger protein 217	587					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)			CAGCGCTGCCCAGAACATTCT	0.428													C|||	9	0.00179712	0.0	0.0	5008	,	,		20409	0.0		0.0089	False		,,,				2504	0.0				p.L587L		Atlas-SNP	.											.	ZNF217	227	.	0			c.G1761A						PASS	.	C		3,4403	6.2+/-15.9	0,3,2200	121.0	113.0	116.0		1761	1.9	1.0	20	dbSNP_129	116	24,8576	17.3+/-56.4	0,24,4276	no	coding-synonymous	ZNF217	NM_006526.2		0,27,6476	TT,TC,CC		0.2791,0.0681,0.2076		587/1049	52193542	27,12979	2203	4300	6503	SO:0001819	synonymous_variant	7764	exon3			GCTGCCCAGAACA	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.1761G>A	20.37:g.52193542C>T		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	122	68	0.557377	NM_006526	E1P5Y6|Q14DB8	Silent	SNP	ENST00000371471.2	37	CCDS13443.1																																																																																			C|0.998;T|0.002	0.002	strong		0.428	ZNF217-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079757.2	NM_006526	
HTRA1	5654	hgsc.bcm.edu	37	10	124249118	124249118	+	Silent	SNP	C	C	T	rs17624021	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	139	0	0		WXS	Illumina HiSeq	Phase_I	98	46	0.469388	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	
MS4A6E	245802	hgsc.bcm.edu	37	11	60102507	60102507	+	Missense_Mutation	SNP	G	G	T	rs2304933	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	175	0	0		WXS	Illumina HiSeq	Phase_I	129	90	0.697674	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		
APOA5	116519	hgsc.bcm.edu	37	11	116662407	116662407	+	Missense_Mutation	SNP	G	G	C	rs3135506	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:116662407G>C	ENST00000227665.4	-	2	90	c.56C>G	c.(55-57)tCg>tGg	p.S19W	APOA5_ENST00000542499.1_Missense_Mutation_p.S19W			Q6Q788	APOA5_HUMAN	apolipoprotein A-V	19			S -> W (in allele APOA5*3; associated with high plasma triglyceride levels; dbSNP:rs3135506). {ECO:0000269|PubMed:12417524, ECO:0000269|PubMed:12920097, ECO:0000269|PubMed:15108119}.		acylglycerol homeostasis (GO:0055090)|cellular lipid metabolic process (GO:0044255)|cholesterol homeostasis (GO:0042632)|lipid transport (GO:0006869)|lipoprotein metabolic process (GO:0042157)|organ regeneration (GO:0031100)|positive regulation of fatty acid biosynthetic process (GO:0045723)|positive regulation of lipid catabolic process (GO:0050996)|positive regulation of lipoprotein lipase activity (GO:0051006)|positive regulation of receptor-mediated endocytosis (GO:0048260)|positive regulation of triglyceride catabolic process (GO:0010898)|positive regulation of very-low-density lipoprotein particle remodeling (GO:0010902)|response to hormone (GO:0009725)|small molecule metabolic process (GO:0044281)|tissue regeneration (GO:0042246)|triglyceride catabolic process (GO:0019433)|triglyceride homeostasis (GO:0070328)|triglyceride metabolic process (GO:0006641)|triglyceride-rich lipoprotein particle remodeling (GO:0034370)	chylomicron (GO:0042627)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|high-density lipoprotein particle (GO:0034364)|very-low-density lipoprotein particle (GO:0034361)	enzyme activator activity (GO:0008047)|enzyme binding (GO:0019899)|heparin binding (GO:0008201)|lipase activator activity (GO:0060229)|lipase binding (GO:0035473)|lipid binding (GO:0008289)|lipoprotein lipase activator activity (GO:0060230)|lipoprotein particle receptor binding (GO:0070325)|low-density lipoprotein particle receptor binding (GO:0050750)|phosphatidylcholine binding (GO:0031210)|phospholipid binding (GO:0005543)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(8)|urinary_tract(1)	14	all_hematologic(175;0.0487)	all_cancers(61;3.31e-09)|all_epithelial(67;8.03e-06)|Breast(348;0.0126)|Melanoma(852;0.0153)|Acute lymphoblastic leukemia(157;0.0257)|Medulloblastoma(222;0.0425)|all_hematologic(158;0.0433)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|Epithelial(105;4.93e-06)|all cancers(92;0.000123)|OV - Ovarian serous cystadenocarcinoma(223;0.149)		CTGGGTGGCCGAAAACGCTGT	0.637											OREG0021366	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	279	0.0557109	0.0673	0.1167	5008	,	,		19485	0.0		0.0676	False		,,,				2504	0.0419				p.S19W		Atlas-SNP	.											APOA5,colon,carcinoma,0,1	APOA5	34	1	0			c.C56G	GRCh37	CM023881	APOA5	M	rs3135506	PASS	.	G	TRP/SER,TRP/SER	269,4133	143.1+/-178.2	9,251,1941	65.0	57.0	60.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	56,56	5.4	0.0	11	dbSNP_103	60	558,8034	143.7+/-199.7	19,520,3757	yes	missense,missense	APOA5	NM_001166598.1,NM_052968.4	177,177	28,771,5698	CC,CG,GG		6.4944,6.1109,6.3645	probably-damaging,probably-damaging	19/367,19/367	116662407	827,12167	2201	4296	6497	SO:0001583	missense	116519	exon3			GTGGCCGAAAACG	AF202889	CCDS8376.2	11q23	2013-01-24			ENSG00000110243	ENSG00000110243		"""Apolipoproteins"""	17288	protein-coding gene	gene with protein product		606368				11588264, 11577099	Standard	NM_001166598		Approved	RAP3, APOA-V	uc009yzf.3	Q6Q788	OTTHUMG00000046116	ENST00000227665.4:c.56C>G	11.37:g.116662407G>C	ENSP00000227665:p.Ser19Trp	Somatic	122	0	0	1475	WXS	Illumina HiSeq	Phase_I	133	32	0.240602	NM_001166598	B0YIV9|Q3MIK6|Q6UWK9|Q9UBJ3	Missense_Mutation	SNP	ENST00000227665.4	37	CCDS8376.2	100	0.045787545787545784	24	0.04878048780487805	33	0.09116022099447514	0	0.0	43	0.05672823218997362	G	20.5	4.006633	0.74932	0.061109	0.064944	ENSG00000110243	ENST00000227665;ENST00000542499;ENST00000433069	T;T;T	0.74737	-0.46;-0.46;-0.87	5.41	5.41	0.78517	.	0.910838	0.09256	N	0.827241	T	0.19846	0.0477	M	0.67953	2.075	0.09310	N	1	D	0.63880	0.993	P	0.57548	0.823	T	0.53753	-0.8394	10	0.87932	D	0	0.0	14.5768	0.68255	0.0:0.0:1.0:0.0	rs3135506;rs28939090	19	Q6Q788	APOA5_HUMAN	W	19	ENSP00000227665:S19W;ENSP00000445002:S19W;ENSP00000399701:S19W	ENSP00000227665:S19W	S	-	2	0	APOA5	116167617	0.412000	0.25392	0.008000	0.14137	0.215000	0.24574	2.796000	0.47869	2.826000	0.97356	0.561000	0.74099	TCG	G|0.891;C|0.109	0.109	strong		0.637	APOA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106285.2		
SLC15A2	6565	hgsc.bcm.edu	37	3	121641693	121641693	+	Silent	SNP	G	G	A	rs2293616	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:121641693G>A	ENST00000489711.1	+	9	1240	c.852G>A	c.(850-852)gcG>gcA	p.A284A	SLC15A2_ENST00000295605.2_Silent_p.A253A|AC072031.1_ENST00000581491.1_RNA	NM_021082.3	NP_066568.3	Q16348	S15A2_HUMAN	solute carrier family 15 (oligopeptide transporter), member 2	284					drug transport (GO:0015893)|ion transport (GO:0006811)|protein transport (GO:0015031)|proton transport (GO:0015992)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	antibiotic transporter activity (GO:0042895)|dipeptide transporter activity (GO:0042936)|high-affinity oligopeptide transporter activity (GO:0015334)|peptide:proton symporter activity (GO:0015333)			NS(1)|endometrium(1)|kidney(4)|large_intestine(5)|lung(17)|skin(6)|upper_aerodigestive_tract(2)	36				GBM - Glioblastoma multiforme(114;0.0967)	Aminolevulinic acid(DB00855)|Amoxicillin(DB01060)|Ampicillin(DB00415)|Azidocillin(DB08795)|Benazepril(DB00542)|Benzylpenicillin(DB01053)|Cefaclor(DB00833)|Cefadroxil(DB01140)|Cefalotin(DB00456)|Cefdinir(DB00535)|Cefepime(DB01413)|Cefixime(DB00671)|Cefmetazole(DB00274)|Cefotaxime(DB00493)|Cefradine(DB01333)|Ceftazidime(DB00438)|Ceftibuten(DB01415)|Ceftriaxone(DB01212)|Cefuroxime(DB01112)|Cephalexin(DB00567)|Chlorpropamide(DB00672)|Cilazapril(DB01340)|Cloxacillin(DB01147)|Cyclacillin(DB01000)|Dicloxacillin(DB00485)|Fosinopril(DB00492)|Glyburide(DB01016)|Moexipril(DB00691)|Nateglinide(DB00731)|Oxacillin(DB00713)|Perindopril(DB00790)|Quinapril(DB00881)|Ramipril(DB00178)|Spirapril(DB01348)|Tolbutamide(DB01124)|Trandolapril(DB00519)|Tranexamic Acid(DB00302)|Valaciclovir(DB00577)|Valganciclovir(DB01610)	TAGACTGGGCGGCTGAGAAAT	0.428													A|||	2265	0.452276	0.4849	0.2939	5008	,	,		18743	0.6984		0.4235	False		,,,				2504	0.2965				p.A284A		Atlas-SNP	.											.	SLC15A2	92	.	0			c.G852A						PASS	.	A	,	2156,2250	593.1+/-387.9	534,1088,581	52.0	51.0	51.0		759,852	4.6	1.0	3	dbSNP_100	51	3904,4696	604.6+/-394.8	879,2146,1275	no	coding-synonymous,coding-synonymous	SLC15A2	NM_001145998.1,NM_021082.3	,	1413,3234,1856	AA,AG,GG		45.3953,48.9333,46.5939	,	253/699,284/730	121641693	6060,6946	2203	4300	6503	SO:0001819	synonymous_variant	6565	exon9			CTGGGCGGCTGAG	BC044572	CCDS3007.1, CCDS54631.1	3q21.1	2013-07-18	2013-07-18		ENSG00000163406	ENSG00000163406		"""Solute carriers"""	10921	protein-coding gene	gene with protein product		602339	"""solute carrier family 15 (H+/peptide transporter), member 2"""			7756356	Standard	NM_021082		Approved	PEPT2	uc003eep.2	Q16348	OTTHUMG00000159423	ENST00000489711.1:c.852G>A	3.37:g.121641693G>A		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	71	29	0.408451	NM_021082	A8K1A5|B4E2A7	Silent	SNP	ENST00000489711.1	37	CCDS3007.1																																																																																			G|0.524;A|0.476	0.476	strong		0.428	SLC15A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355239.1	NM_021082	
MRPL43	84545	hgsc.bcm.edu	37	10	102746503	102746503	+	Intron	SNP	C	C	T	rs2863095	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:102746503C>T	ENST00000318325.2	-	3	519				C10orf2_ENST00000311916.2_5'Flank|MRPL43_ENST00000493646.1_5'UTR|MRPL43_ENST00000370234.4_Intron|C10orf2_ENST00000370228.1_5'Flank|MRPL43_ENST00000477279.1_3'UTR|RP11-108L7.4_ENST00000447344.1_RNA|MRPL43_ENST00000318364.8_Silent_p.V156V|MRPL43_ENST00000342071.1_Intron|MRPL43_ENST00000299179.5_Intron|MRPL43_ENST00000370236.1_Silent_p.V156V|MRPL43_ENST00000370241.3_Intron|MRPL43_ENST00000370242.4_Intron	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	68	0	0		WXS	Illumina HiSeq	Phase_I	46	17	0.369565	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		
WDR35	57539	hgsc.bcm.edu	37	2	20131079	20131079	+	Missense_Mutation	SNP	T	T	C	rs1191778	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:20131079T>C	ENST00000345530.3	-	25	3063	c.2948A>G	c.(2947-2949)gAa>gGa	p.E983G	WDR35_ENST00000416055.2_Missense_Mutation_p.E456G|WDR35_ENST00000281405.4_Missense_Mutation_p.E972G	NM_001006657.1	NP_001006658.1	Q9P2L0	WDR35_HUMAN	WD repeat domain 35	983			E -> G (in dbSNP:rs1191778). {ECO:0000269|PubMed:14702039}.		cilium assembly (GO:0042384)|intraciliary retrograde transport (GO:0035721)	axoneme (GO:0005930)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|intraciliary transport particle A (GO:0030991)				breast(1)|endometrium(5)|kidney(8)|large_intestine(8)|lung(16)|ovary(2)|prostate(1)|skin(1)|stomach(1)	43	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CTTCATCTGTTCATGGTATTG	0.358													T|||	1164	0.232428	0.1097	0.3588	5008	,	,		16337	0.1171		0.4443	False		,,,				2504	0.2096				p.E983G		Atlas-SNP	.											WDR35,NS,carcinoma,-1,1	WDR35	92	1	0			c.A2948G						PASS	.	T	GLY/GLU,GLY/GLU	709,3697	293.8+/-282.8	52,605,1546	166.0	159.0	161.0		2948,2915	4.8	0.0	2	dbSNP_87	161	3463,5137	508.0+/-377.0	689,2085,1526	yes	missense,missense	WDR35	NM_001006657.1,NM_020779.3	98,98	741,2690,3072	CC,CT,TT		40.2674,16.0917,32.0775	benign,benign	983/1182,972/1171	20131079	4172,8834	2203	4300	6503	SO:0001583	missense	57539	exon25			ATCTGTTCATGGT	AB037757	CCDS1695.1, CCDS33152.1	2p24.3	2014-02-21			ENSG00000118965	ENSG00000118965		"""WD repeat domain containing"", ""Intraflagellar transport homologs"""	29250	protein-coding gene	gene with protein product		613602				10718198	Standard	NM_001006657		Approved	MGC33196, KIAA1336, IFT121, IFTA1	uc002rdi.3	Q9P2L0	OTTHUMG00000090737	ENST00000345530.3:c.2948A>G	2.37:g.20131079T>C	ENSP00000314444:p.Glu983Gly	Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	168	96	0.571429	NM_001006657	B3KVI5|Q4ZG01|Q8NE11	Missense_Mutation	SNP	ENST00000345530.3	37	CCDS33152.1	611	0.27976190476190477	53	0.10772357723577236	139	0.3839779005524862	87	0.1520979020979021	332	0.43799472295514513	T	12.10	1.837657	0.32513	0.160917	0.402674	ENSG00000118965	ENST00000345530;ENST00000281405;ENST00000416055	T;T;T	0.74526	-0.23;-0.23;-0.85	4.82	4.82	0.62117	.	0.210756	0.48767	D	0.000173	T	0.00012	0.0000	M	0.76002	2.32	0.40456	P	0.01980599999999999	B;B;P	0.42692	0.348;0.073;0.787	B;B;P	0.46758	0.156;0.066;0.526	T	0.17806	-1.0357	9	0.54805	T	0.06	-18.7985	13.8697	0.63610	0.0:0.0:0.0:1.0	rs1191778;rs1658525;rs52827575;rs61210615;rs1191778	972;983;456	Q9P2L0-2;Q9P2L0;B3KR94	.;WDR35_HUMAN;.	G	983;972;456	ENSP00000314444:E983G;ENSP00000281405:E972G;ENSP00000399159:E456G	ENSP00000281405:E972G	E	-	2	0	WDR35	19994560	0.992000	0.36948	0.019000	0.16419	0.680000	0.39746	3.878000	0.56130	1.933000	0.56026	0.482000	0.46254	GAA	T|0.710;C|0.290	0.290	strong		0.358	WDR35-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000207472.2	NM_020779	
TNFRSF6B	8771	hgsc.bcm.edu	37	20	62328829	62328829	+	Silent	SNP	C	C	G	rs1291205	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:62328829C>G	ENST00000369996.1	+	2	673	c.573C>G	c.(571-573)acC>acG	p.T191T	ARFRP1_ENST00000485858.1_5'Flank|RTEL1-TNFRSF6B_ENST00000482936.1_3'UTR	NM_003823.3	NP_003814.1	O95407	TNF6B_HUMAN	tumor necrosis factor receptor superfamily, member 6b, decoy	191					apoptotic process (GO:0006915)|negative regulation of apoptotic process (GO:0043066)	extracellular space (GO:0005615)	receptor activity (GO:0004872)			central_nervous_system(1)|lung(2)|skin(1)	4	all_cancers(38;4.66e-12)|all_epithelial(29;2.56e-13)|Lung NSC(23;1.06e-08)|all_lung(23;3.34e-08)		Epithelial(9;1.78e-08)|all cancers(9;7.89e-08)|OV - Ovarian serous cystadenocarcinoma(5;0.00504)			CCCATGACACCCTGTGCACCA	0.672													C|||	1320	0.263578	0.0242	0.2637	5008	,	,		19651	0.6468		0.2038	False		,,,				2504	0.2536				p.T191T		Atlas-SNP	.											TNFRSF6B,caecum,carcinoma,0,1	TNFRSF6B	22	1	0			c.C573G						PASS	.	C		297,4031		14,269,1881	29.0	21.0	24.0		573	2.5	0.6	20	dbSNP_87	24	1884,6654		220,1444,2605	no	coding-synonymous	TNFRSF6B	NM_003823.3		234,1713,4486	GG,GC,CC		22.0661,6.8623,16.9517		191/301	62328829	2181,10685	2164	4269	6433	SO:0001819	synonymous_variant	8771	exon2			TGACACCCTGTGC	AF104419	CCDS13532.1	20q13.33	2012-06-27						"""Tumor necrosis factor receptor superfamily"""	11921	protein-coding gene	gene with protein product		603361				9872321, 10318773	Standard	NM_003823		Approved	DcR3, DCR3, TR6, M68	uc002yfz.3	O95407	OTTHUMG00000143724	ENST00000369996.1:c.573C>G	20.37:g.62328829C>G		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	109	65	0.59633	NM_003823		Silent	SNP	ENST00000369996.1	37	CCDS13532.1																																																																																			C|0.792;G|0.208	0.208	strong		0.672	TNFRSF6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080182.1		
SBNO1	55206	hgsc.bcm.edu	37	12	123794104	123794104	+	Silent	SNP	G	G	T	rs3825141	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:123794104G>T	ENST00000602398.1	-	27	3596	c.3469C>A	c.(3469-3471)Cgg>Agg	p.R1157R	SBNO1_ENST00000420886.2_Silent_p.R1157R|SBNO1_ENST00000267176.4_Silent_p.R1156R|SBNO1_ENST00000602750.1_Silent_p.R1156R			A3KN83	SBNO1_HUMAN	strawberry notch homolog 1 (Drosophila)	1157					regulation of transcription, DNA-templated (GO:0006355)			p.R1156R(1)		NS(2)|breast(6)|cervix(2)|endometrium(8)|kidney(3)|large_intestine(11)|lung(18)|ovary(2)|pancreas(1)|prostate(3)|skin(4)|stomach(2)	62	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000701)|Epithelial(86;0.00197)		TCACTTTTCCGCACTTTTTCA	0.333													T|||	445	0.0888578	0.0356	0.062	5008	,	,		20085	0.255		0.0507	False		,,,				2504	0.0481				p.R1157R		Atlas-SNP	.											SBNO1,NS,carcinoma,+1,2	SBNO1	138	2	1	Substitution - coding silent(1)	stomach(1)	c.C3469A						scavenged	.	T	,	188,4218	799.0+/-415.5	2,184,2017	132.0	146.0	141.0		3469,3466	4.9	1.0	12	dbSNP_107	141	330,8270	803.1+/-407.3	10,310,3980	no	coding-synonymous,coding-synonymous	SBNO1	NM_001167856.1,NM_018183.3	,	12,494,5997	TT,TG,GG		3.8372,4.2669,3.9828	,	1157/1394,1156/1393	123794104	518,12488	2203	4300	6503	SO:0001819	synonymous_variant	55206	exon26			TTTTCCGCACTTT	AK001563	CCDS9246.1, CCDS53844.1	12q24.31	2006-10-06	2006-10-06			ENSG00000139697			22973	protein-coding gene	gene with protein product		614274	"""sno, strawberry notch homolog 1 (Drosophila)"""				Standard	NM_018183		Approved	MOP3, FLJ10701, FLJ10833, Sno	uc010tap.2	A3KN83		ENST00000602398.1:c.3469C>A	12.37:g.123794104G>T		Somatic	128	1	0.0078125		WXS	Illumina HiSeq	Phase_I	92	44	0.478261	NM_001167856	Q05C06|Q3ZTS3|Q9H3T8|Q9NVB2	Silent	SNP	ENST00000602398.1	37	CCDS53844.1																																																																																			G|0.932;T|0.068	0.068	strong		0.333	SBNO1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000467684.1	NM_018183	
PRKAA2	5563	hgsc.bcm.edu	37	1	57158051	57158051	+	Silent	SNP	G	G	A	rs17848595	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:57158051G>A	ENST00000371244.4	+	4	417	c.351G>A	c.(349-351)agG>agA	p.R117R		NM_006252.3	NP_006243.2	P54646	AAPK2_HUMAN	protein kinase, AMP-activated, alpha 2 catalytic subunit	117	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				autophagy (GO:0006914)|carnitine shuttle (GO:0006853)|cell cycle arrest (GO:0007050)|cellular lipid metabolic process (GO:0044255)|cellular response to glucose starvation (GO:0042149)|cellular response to nutrient levels (GO:0031669)|cholesterol biosynthetic process (GO:0006695)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|fatty acid homeostasis (GO:0055089)|glucose homeostasis (GO:0042593)|insulin receptor signaling pathway (GO:0008286)|lipid biosynthetic process (GO:0008610)|membrane organization (GO:0061024)|negative regulation of apoptotic process (GO:0043066)|negative regulation of TOR signaling (GO:0032007)|positive regulation of autophagy (GO:0010508)|positive regulation of glycolytic process (GO:0045821)|protein phosphorylation (GO:0006468)|regulation of circadian rhythm (GO:0042752)|regulation of energy homeostasis (GO:2000505)|regulation of fatty acid biosynthetic process (GO:0042304)|regulation of transcription, DNA-templated (GO:0006355)|response to stress (GO:0006950)|rhythmic process (GO:0048511)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	[acetyl-CoA carboxylase] kinase activity (GO:0050405)|[hydroxymethylglutaryl-CoA reductase (NADPH)] kinase activity (GO:0047322)|AMP-activated protein kinase activity (GO:0004679)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|histone serine kinase activity (GO:0035174)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)			breast(6)|endometrium(1)|large_intestine(6)|lung(7)|ovary(1)|prostate(1)|stomach(1)	23					Acetylsalicylic acid(DB00945)	TGGAAGCCAGGCGGCTCTTTC	0.483													G|||	870	0.173722	0.2231	0.0677	5008	,	,		17103	0.2252		0.0437	False		,,,				2504	0.2628				p.R117R		Atlas-SNP	.											.	PRKAA2	177	.	0			c.G351A						PASS	.	G		801,3605	321.5+/-297.2	76,649,1478	173.0	167.0	169.0		351	-0.7	0.5	1	dbSNP_123	169	423,8177	131.5+/-189.3	12,399,3889	no	coding-synonymous	PRKAA2	NM_006252.3		88,1048,5367	AA,AG,GG		4.9186,18.1798,9.411		117/553	57158051	1224,11782	2203	4300	6503	SO:0001819	synonymous_variant	5563	exon4			AGCCAGGCGGCTC	BC069823	CCDS605.1	1p31	2011-08-25			ENSG00000162409	ENSG00000162409			9377	protein-coding gene	gene with protein product		600497		PRKAA		7959015	Standard	NM_006252		Approved	AMPK, AMPKa2	uc001cyk.4	P54646	OTTHUMG00000008282	ENST00000371244.4:c.351G>A	1.37:g.57158051G>A		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	190	108	0.568421	NM_006252	Q9H1E8|Q9UD43	Silent	SNP	ENST00000371244.4	37	CCDS605.1																																																																																			G|0.891;A|0.109	0.109	strong		0.483	PRKAA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022753.2	NM_006252	
USHBP1	83878	hgsc.bcm.edu	37	19	17366278	17366278	+	Silent	SNP	T	T	C	rs4430871	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:17366278T>C	ENST00000252597.3	-	10	1781	c.1608A>G	c.(1606-1608)gcA>gcG	p.A536A	AC010646.3_ENST00000594059.1_5'Flank|USHBP1_ENST00000431146.2_Silent_p.A472A	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						CCTGGAGCTCTGCCCGTTCCC	0.682													C|||	3903	0.779353	0.9766	0.7709	5008	,	,		15195	0.7996		0.5805	False		,,,				2504	0.7025				p.A536A		Atlas-SNP	.											.	USHBP1	85	.	0			c.A1608G						PASS	.	C		4049,357	180.1+/-208.5	1861,327,15	53.0	57.0	56.0		1608	-9.9	0.0	19	dbSNP_111	56	5186,3414	495.0+/-374.0	1575,2036,689	no	coding-synonymous	USHBP1	NM_031941.3		3436,2363,704	CC,CT,TT		39.6977,8.1026,28.9943		536/704	17366278	9235,3771	2203	4300	6503	SO:0001819	synonymous_variant	83878	exon10			GAGCTCTGCCCGT	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.1608A>G	19.37:g.17366278T>C		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	56	56	1	NM_031941		Silent	SNP	ENST00000252597.3	37	CCDS12353.1																																																																																			T|0.284;C|0.716	0.716	strong		0.682	USHBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463328.1	NM_031941	
ZNF446	55663	hgsc.bcm.edu	37	19	58991900	58991900	+	Missense_Mutation	SNP	G	G	A	rs882610	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:58991900G>A	ENST00000594369.1	+	7	1541	c.1160G>A	c.(1159-1161)cGc>cAc	p.R387H	ZNF446_ENST00000596341.1_Missense_Mutation_p.R336H|ZNF446_ENST00000335841.4_3'UTR	NM_017908.2	NP_060378.1	Q9NWS9	ZN446_HUMAN	zinc finger protein 446	387			R -> H (in dbSNP:rs882610).		regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	extracellular space (GO:0005615)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			endometrium(2)|large_intestine(1)|lung(3)|ovary(1)|skin(1)	8		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;0.0164)|Lung(386;0.179)		CACCCCCGACGCTCACTCACA	0.662													G|||	1423	0.284145	0.4349	0.1772	5008	,	,		15898	0.2619		0.2535	False		,,,				2504	0.2106				p.R387H		Atlas-SNP	.											ZNF446,NS,carcinoma,+1,1	ZNF446	22	1	0			c.G1160A						scavenged	.	G	HIS/ARG	1827,2579		381,1065,757	23.0	27.0	25.0		1160	2.0	0.0	19	dbSNP_86	25	2383,6213		332,1719,2247	yes	missense	ZNF446	NM_017908.2	29	713,2784,3004	AA,AG,GG		27.7222,41.4662,32.3796	benign	387/451	58991900	4210,8792	2203	4298	6501	SO:0001583	missense	55663	exon7			CCCGACGCTCACT		CCDS12982.1	19q13.43	2013-01-09				ENSG00000083838		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	21036	protein-coding gene	gene with protein product							Standard	NM_017908		Approved	ZKSCAN20, FLJ20626, ZSCAN52	uc002qsz.3	Q9NWS9		ENST00000594369.1:c.1160G>A	19.37:g.58991900G>A	ENSP00000472802:p.Arg387His	Somatic	78	1	0.0128205		WXS	Illumina HiSeq	Phase_I	91	27	0.296703	NM_017908		Missense_Mutation	SNP	ENST00000594369.1	37	CCDS12982.1	634	0.2902930402930403	217	0.4410569105691057	73	0.20165745856353592	142	0.24825174825174826	202	0.26649076517150394	G	5.166	0.216171	0.09810	0.414662	0.277222	ENSG00000083838	ENST00000335841;ENST00000540481;ENST00000391694	.	.	.	3.05	2.0	0.26442	.	0.739778	0.11129	N	0.596567	T	0.00012	0.0000	L	0.61036	1.89	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.33420	-0.9869	8	0.66056	D	0.02	-9.4638	6.2625	0.20907	0.1125:0.0:0.7073:0.1802	rs882610;rs57562390;rs882610	387	Q9NWS9	ZN446_HUMAN	H	387;387;284	.	ENSP00000336565:R387H	R	+	2	0	ZNF446	63683712	0.018000	0.18449	0.000000	0.03702	0.000000	0.00434	1.172000	0.31908	0.327000	0.23409	-1.164000	0.01763	CGC	G|0.697;A|0.303	0.303	strong		0.662	ZNF446-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000467052.1	NM_017908	
KIAA1217	56243	hgsc.bcm.edu	37	10	24813585	24813585	+	Silent	SNP	G	G	A	rs145162894	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:24813585G>A	ENST00000376454.3	+	13	2820	c.2790G>A	c.(2788-2790)tcG>tcA	p.S930S	KIAA1217_ENST00000396446.1_Silent_p.S613S|KIAA1217_ENST00000430453.2_Intron|KIAA1217_ENST00000376452.3_Silent_p.S895S|KIAA1217_ENST00000396445.1_Silent_p.S613S|KIAA1217_ENST00000376451.2_Silent_p.S613S|KIAA1217_ENST00000307544.6_Silent_p.S613S|KIAA1217_ENST00000458595.1_Silent_p.S895S|KIAA1217_ENST00000376462.1_Silent_p.S850S	NM_019590.3	NP_062536.2	Q5T5P2	SKT_HUMAN	KIAA1217	930					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						TGCAGATGTCGCAGGCTCCGC	0.592													G|||	8	0.00159744	0.0	0.0	5008	,	,		18873	0.001		0.007	False		,,,				2504	0.0				p.S930S		Atlas-SNP	.											.	KIAA1217	235	.	0			c.G2790A						PASS	.	G	,,	4,4402	8.1+/-20.4	0,4,2199	49.0	46.0	47.0		2550,2685,2790	-8.3	0.0	10	dbSNP_134	47	49,8551	31.7+/-84.0	0,49,4251	no	coding-synonymous,coding-synonymous,coding-synonymous	KIAA1217	NM_001098500.1,NM_001098501.1,NM_019590.3	,,	0,53,6450	AA,AG,GG		0.5698,0.0908,0.4075	,,	850/1265,895/1310,930/1944	24813585	53,12953	2203	4300	6503	SO:0001819	synonymous_variant	56243	exon13			GATGTCGCAGGCT	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.2790G>A	10.37:g.24813585G>A		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	61	32	0.52459	NM_019590	A5LHW9|A6NLF3|A6PVQ5|A6PVQ6|A6PVQ7|B9EGK4|Q4KMG4|Q5T5P3|Q5T7H3|Q6MZZ6|Q6ZUI4|Q8WV45|Q9NSR2|Q9ULK3	Silent	SNP	ENST00000376454.3	37	CCDS31165.1																																																																																			G|0.996;A|0.004	0.004	strong		0.592	KIAA1217-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047223.2	NM_019590	
IMMT	10989	hgsc.bcm.edu	37	2	86385728	86385728	+	Silent	SNP	C	C	T	rs1131071	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:86385728C>T	ENST00000410111.3	-	10	1536	c.1149G>A	c.(1147-1149)ggG>ggA	p.G383G	Y_RNA_ENST00000363371.1_RNA|IMMT_ENST00000254636.5_Silent_p.G284G|IMMT_ENST00000409051.2_Silent_p.G336G|IMMT_ENST00000449247.2_Silent_p.G372G|IMMT_ENST00000490238.1_5'UTR|IMMT_ENST00000442664.2_Silent_p.G382G	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	104	0	0		WXS	Illumina HiSeq	Phase_I	110	109	0.990909	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	
TMTC4	84899	hgsc.bcm.edu	37	13	101287365	101287365	+	Silent	SNP	T	T	C	rs946838	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:101287365T>C	ENST00000376234.3	-	10	1419	c.1230A>G	c.(1228-1230)gcA>gcG	p.A410A	TMTC4_ENST00000462211.1_5'UTR|TMTC4_ENST00000328767.5_Silent_p.A299A|TMTC4_ENST00000342624.5_Silent_p.A429A	NM_001079669.1	NP_001073137.1	Q5T4D3	TMTC4_HUMAN	transmembrane and tetratricopeptide repeat containing 4	410						integral component of membrane (GO:0016021)				breast(3)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(14)|ovary(2)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	34	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)					GGACACGCTCTGCGACCACGA	0.517													.|||	4195	0.83766	0.6437	0.889	5008	,	,		19029	0.9901		0.8708	False		,,,				2504	0.8722				p.A429A		Atlas-SNP	.											.	TMTC4	103	.	0			c.A1287G						PASS	.	C	,	3025,1381	456.5+/-351.3	1039,947,217	70.0	62.0	65.0		1230,1287	-11.0	0.0	13	dbSNP_86	65	7465,1135	233.2+/-266.6	3230,1005,65	no	coding-synonymous,coding-synonymous	TMTC4	NM_001079669.1,NM_032813.2	,	4269,1952,282	CC,CT,TT		13.1977,31.3436,19.3449	,	410/742,429/761	101287365	10490,2516	2203	4300	6503	SO:0001819	synonymous_variant	84899	exon11			ACGCTCTGCGACC		CCDS9497.2, CCDS41904.1, CCDS66575.1	13q32.3	2013-01-10	2006-01-06		ENSG00000125247	ENSG00000125247		"""Tetratricopeptide (TTC) repeat domain containing"""	25904	protein-coding gene	gene with protein product							Standard	XM_005254082		Approved	FLJ14624, FLJ22153	uc001vot.3	Q5T4D3	OTTHUMG00000017289	ENST00000376234.3:c.1230A>G	13.37:g.101287365T>C		Somatic	121	1	0.00826446		WXS	Illumina HiSeq	Phase_I	122	122	1	NM_032813	A6NLI7|B7Z666|Q5T4D4|Q5T4D5|Q5T4D6|Q8WV63|Q96SU8	Silent	SNP	ENST00000376234.3	37	CCDS41904.1																																																																																			T|0.170;C|0.830	0.830	strong		0.517	TMTC4-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045649.2	NM_032813	
FFAR4	338557	hgsc.bcm.edu	37	10	95347041	95347041	+	Missense_Mutation	SNP	G	G	A	rs116454156	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:95347041G>A	ENST00000371483.4	+	4	865	c.809G>A	c.(808-810)cGc>cAc	p.R270H	FFAR4_ENST00000604414.1_Intron|FFAR4_ENST00000371481.4_Missense_Mutation_p.R254H	NM_181745.3	NP_859529.2	Q5NUL3	FFAR4_HUMAN	free fatty acid receptor 4	270			R -> H (polymorphism associated with increased risk of obesity; dbSNP:rs116454156). {ECO:0000269|PubMed:22343897}.		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)										CACCAGATCCGCGTGTCCCAG	0.562													G|||	75	0.014976	0.0008	0.0072	5008	,	,		18560	0.001		0.0149	False		,,,				2504	0.0542				p.R270H		Atlas-SNP	.											.	.	.	.	0			c.G809A						PASS	.	G	HIS/ARG,HIS/ARG	21,4385	27.2+/-55.0	0,21,2182	110.0	103.0	105.0		761,809	5.0	1.0	10	dbSNP_132	105	150,8450	72.9+/-135.5	1,148,4151	yes	missense,missense	O3FAR1	NM_001195755.1,NM_181745.3	29,29	1,169,6333	AA,AG,GG		1.7442,0.4766,1.3148	benign,benign	254/362,270/378	95347041	171,12835	2203	4300	6503	SO:0001583	missense	338557	exon4			AGATCCGCGTGTC		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.809G>A	10.37:g.95347041G>A	ENSP00000360538:p.Arg270His	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	97	59	0.608247	NM_181745	Q495H1|Q5VY25|Q5VY26|Q7Z605|Q86SM7	Missense_Mutation	SNP	ENST00000371483.4	37	CCDS31248.1	16	0.007326007326007326	1	0.0020325203252032522	4	0.011049723756906077	0	0.0	11	0.014511873350923483	G	15.28	2.785286	0.49997	0.004766	0.017442	ENSG00000186188	ENST00000371481;ENST00000371483	T;T	0.72725	-0.68;-0.68	4.99	4.99	0.66335	GPCR, rhodopsin-like superfamily (1);	0.096786	0.44097	D	0.000500	T	0.48390	0.1497	L	0.57536	1.79	0.29401	N	0.861934	B;B	0.26195	0.07;0.144	B;B	0.18561	0.019;0.022	T	0.60146	-0.7320	10	0.59425	D	0.04	-20.7853	10.4759	0.44665	0.1505:0.0:0.8495:0.0	.	254;270	Q5NUL3-2;Q5NUL3	.;O3FA1_HUMAN	H	254;270	ENSP00000360536:R254H;ENSP00000360538:R270H	ENSP00000360536:R254H	R	+	2	0	O3FAR1	95337031	0.617000	0.27043	0.998000	0.56505	0.924000	0.55760	1.721000	0.38032	2.741000	0.93983	0.555000	0.69702	CGC	G|0.987;A|0.013	0.013	strong		0.562	FFAR4-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000083179.1	NM_181745	
CA5B	11238	hgsc.bcm.edu	37	X	15800751	15800751	+	Silent	SNP	G	G	A	rs1808	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:15800751G>A	ENST00000318636.3	+	8	1054	c.918G>A	c.(916-918)gcG>gcA	p.A306A	CA5B_ENST00000454127.2_Silent_p.A306A	NM_007220.3	NP_009151.1	Q8WTZ4	CA5BL_HUMAN	carbonic anhydrase VB, mitochondrial	0						mitochondrion (GO:0005739)	carbonate dehydratase activity (GO:0004089)|zinc ion binding (GO:0008270)	p.A306A(1)		endometrium(1)|kidney(2)|lung(3)|prostate(1)|stomach(2)	9	Hepatocellular(33;0.183)					ATGTACAAGCGAAACCCAAGC	0.433													G|||	1313	0.347815	0.2383	0.3415	3775	,	,		13207	0.2996		0.2505	False		,,,				2504	0.2117				p.A306A		Atlas-SNP	.											.	CA5B	23	.	1	Substitution - coding silent(1)	stomach(1)	c.G918A						PASS	.	G		1072,2763		117,670,168,845,403	95.0	79.0	85.0		918	-8.9	0.0	X	dbSNP_36	85	2276,4452		266,1088,656,1074,1216	no	coding-synonymous	CA5B	NM_007220.3		383,1758,824,1919,1619	AA,AG,A,GG,G		33.8288,27.9531,31.6955		306/318	15800751	3348,7215	2203	4300	6503	SO:0001819	synonymous_variant	11238	exon8			ACAAGCGAAACCC	AB021660	CCDS14171.1	Xp22.1	2008-08-13			ENSG00000169239	ENSG00000169239		"""Carbonic anhydrases"""	1378	protein-coding gene	gene with protein product		300230				10409679	Standard	XM_005274442		Approved		uc004cxe.3	Q9Y2D0	OTTHUMG00000021183	ENST00000318636.3:c.918G>A	X.37:g.15800751G>A		Somatic	155	1	0.00645161		WXS	Illumina HiSeq	Phase_I	95	95	1	NM_007220	A6NEZ4	Silent	SNP	ENST00000318636.3	37	CCDS14171.1																																																																																			G|0.655;0|0.003	.	strong		0.433	CA5B-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354933.1	NM_007220	
FAT4	79633	hgsc.bcm.edu	37	4	126336201	126336201	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:126336201C>T	ENST00000394329.3	+	5	6096	c.6083C>T	c.(6082-6084)gCc>gTc	p.A2028V	FAT4_ENST00000335110.5_Missense_Mutation_p.A326V	NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	2028	Cadherin 19. {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						CAGATTCCAGCCTCCAGATTC	0.423																																					p.A2028V		Atlas-SNP	.											.	FAT4	1752	.	0			c.C6083T						PASS	.						162.0	167.0	165.0					4																	126336201		2203	4300	6503	SO:0001583	missense	79633	exon5			TTCCAGCCTCCAG	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.6083C>T	4.37:g.126336201C>T	ENSP00000377862:p.Ala2028Val	Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	156	15	0.0961538	NM_024582	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Missense_Mutation	SNP	ENST00000394329.3	37	CCDS3732.3	.	.	.	.	.	.	.	.	.	.	C	12.10	1.837537	0.32513	.	.	ENSG00000196159	ENST00000394329;ENST00000335110	T;T	0.53206	0.63;0.63	5.1	4.24	0.50183	Cadherin (4);Cadherin-like (1);	0.239720	0.20285	U	0.095376	T	0.43523	0.1251	L	0.43923	1.385	0.30709	N	0.749492	B;B	0.24675	0.053;0.109	B;B	0.28916	0.096;0.047	T	0.43589	-0.9382	10	0.30854	T	0.27	.	15.7102	0.77620	0.0:0.8632:0.1368:0.0	.	326;2028	Q6V0I7-2;Q6V0I7	.;FAT4_HUMAN	V	2028;326	ENSP00000377862:A2028V;ENSP00000335169:A326V	ENSP00000335169:A326V	A	+	2	0	FAT4	126555651	0.140000	0.22579	0.932000	0.37286	0.927000	0.56198	2.732000	0.47352	1.111000	0.41721	0.557000	0.71058	GCC	.	.	none		0.423	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582	
ECHDC3	79746	hgsc.bcm.edu	37	10	11805339	11805339	+	Silent	SNP	C	C	T	rs17850531	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:11805339C>T	ENST00000379215.4	+	5	919	c.708C>T	c.(706-708)atC>atT	p.I236I	ECHDC3_ENST00000496136.1_3'UTR	NM_024693.4	NP_078969	Q96DC8	ECHD3_HUMAN	enoyl CoA hydratase domain containing 3	236						mitochondrion (GO:0005739)	catalytic activity (GO:0003824)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)	4						CCATGCGGATCGCTAGGAAGA	0.622													C|||	987	0.197085	0.0197	0.2435	5008	,	,		19195	0.3075		0.2107	False		,,,				2504	0.2761				p.I236I		Atlas-SNP	.											.	ECHDC3	12	.	0			c.C708T						PASS	.	C		239,4167	140.0+/-175.5	9,221,1973	90.0	74.0	79.0		708	-11.5	0.0	10	dbSNP_123	79	1777,6823	318.6+/-313.7	173,1431,2696	no	coding-synonymous	ECHDC3	NM_024693.4		182,1652,4669	TT,TC,CC		20.6628,5.4244,15.5005		236/304	11805339	2016,10990	2203	4300	6503	SO:0001819	synonymous_variant	79746	exon5			GCGGATCGCTAGG	AF275677	CCDS7084.1	10p14	2010-04-30	2010-04-30		ENSG00000134463	ENSG00000134463			23489	protein-coding gene	gene with protein product			"""enoyl Coenzyme A hydratase domain containing 3"""			12477932	Standard	NM_024693		Approved	FLJ20909	uc001ikw.4	Q96DC8	OTTHUMG00000017675	ENST00000379215.4:c.708C>T	10.37:g.11805339C>T		Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	35	19	0.542857	NM_024693	Q53HR9|Q5W0J7|Q8WYY8|Q9BVL8|Q9H7G4	Silent	SNP	ENST00000379215.4	37	CCDS7084.1																																																																																			C|0.831;T|0.169	0.169	strong		0.622	ECHDC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046771.1	NM_024693	
ZNF142	7701	hgsc.bcm.edu	37	2	219508372	219508372	+	Missense_Mutation	SNP	A	A	T	rs3770213	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	87	0	0		WXS	Illumina HiSeq	Phase_I	84	48	0.571429	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	
COBL	23242	hgsc.bcm.edu	37	7	51094269	51094269	+	Missense_Mutation	SNP	G	G	A	rs61737954	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:51094269G>A	ENST00000265136.7	-	11	3643	c.3478C>T	c.(3478-3480)Cac>Tac	p.H1160Y	COBL_ENST00000395542.2_Missense_Mutation_p.H1242Y	NM_015198.3	NP_056013.2	O75128	COBL_HUMAN	cordon-bleu WH2 repeat protein	1160	WH2 2. {ECO:0000255|PROSITE- ProRule:PRU00406}.				actin filament network formation (GO:0051639)|actin filament polymerization (GO:0030041)|collateral sprouting in absence of injury (GO:0048669)|digestive tract development (GO:0048565)|embryonic axis specification (GO:0000578)|floor plate development (GO:0033504)|liver development (GO:0001889)|neural tube closure (GO:0001843)|notochord development (GO:0030903)|positive regulation of dendrite development (GO:1900006)|somite specification (GO:0001757)	actin filament (GO:0005884)|axon (GO:0030424)|axonal growth cone (GO:0044295)|cell cortex (GO:0005938)|dendrite (GO:0030425)|dendritic growth cone (GO:0044294)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	actin monomer binding (GO:0003785)			NS(2)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(26)|ovary(3)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	65	Glioma(55;0.08)					GTGCCGCTGTGCCCGCGGATA	0.632													G|||	157	0.0313498	0.003	0.0245	5008	,	,		19629	0.001		0.0606	False		,,,				2504	0.0757				p.H1160Y	NSCLC(189;2119 2138 12223 30818 34679)	Atlas-SNP	.											.	COBL	167	.	0			c.C3478T						PASS	.	G	TYR/HIS	67,4339	62.3+/-99.4	0,67,2136	91.0	79.0	83.0		3478	5.0	0.9	7	dbSNP_129	83	681,7919	168.7+/-220.2	28,625,3647	yes	missense	COBL	NM_015198.3	83	28,692,5783	AA,AG,GG		7.9186,1.5207,5.7512	probably-damaging	1160/1262	51094269	748,12258	2203	4300	6503	SO:0001583	missense	23242	exon11			CGCTGTGCCCGCG	AB014533	CCDS34637.1, CCDS75601.1, CCDS75602.1	7p12.2-p12.1	2012-12-07	2012-12-07		ENSG00000106078	ENSG00000106078			22199	protein-coding gene	gene with protein product		610317	"""cordon-bleu homolog (mouse)"""				Standard	NM_015198		Approved	KIAA0633	uc003tpr.4	O75128	OTTHUMG00000155999	ENST00000265136.7:c.3478C>T	7.37:g.51094269G>A	ENSP00000265136:p.His1160Tyr	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	56	27	0.482143	NM_015198	A4D257|A7E2B0|B7ZLW9|B9EGF8|Q2T9J3|Q504Y4|Q86XA7|Q8N304|Q8TCM1	Missense_Mutation	SNP	ENST00000265136.7	37	CCDS34637.1	69	0.03159340659340659	3	0.006097560975609756	10	0.027624309392265192	1	0.0017482517482517483	55	0.07255936675461741	G	15.29	2.788493	0.49997	0.015207	0.079186	ENSG00000106078	ENST00000265136;ENST00000445054;ENST00000431948;ENST00000395542	T;T;T;T	0.42900	0.96;0.96;0.96;0.96	5.0	5.0	0.66597	Actin-binding WH2 (3);	0.000000	0.43747	D	0.000526	T	0.05135	0.0137	L	0.34521	1.04	0.38943	D	0.958182	D;D;D;D;D	0.89917	0.998;0.998;0.999;0.998;1.0	D;D;D;D;D	0.91635	0.994;0.994;0.984;0.994;0.999	T	0.08597	-1.0714	10	0.45353	T	0.12	.	15.0181	0.71605	0.0:0.0:1.0:0.0	.	1160;1217;1160;1242;702	O75128-3;O75128-7;O75128;O75128-2;O75128-6	.;.;COBL_HUMAN;.;.	Y	1160;1052;1045;1242	ENSP00000265136:H1160Y;ENSP00000401204:H1052Y;ENSP00000413498:H1045Y;ENSP00000378912:H1242Y	ENSP00000265136:H1160Y	H	-	1	0	COBL	51061763	1.000000	0.71417	0.891000	0.34965	0.033000	0.12548	7.524000	0.81866	2.294000	0.77228	0.563000	0.77884	CAC	G|0.947;A|0.053	0.053	strong		0.632	COBL-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000342682.1	NM_015198	
SIN3B	23309	hgsc.bcm.edu	37	19	16976289	16976289	+	Silent	SNP	T	T	C	rs2303091	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:16976289T>C	ENST00000248054.5	+	11	1473	c.1452T>C	c.(1450-1452)tcT>tcC	p.S484S	SIN3B_ENST00000379803.1_Silent_p.S516S|SIN3B_ENST00000595541.1_Silent_p.S74S					SIN3 transcription regulator family member B											endometrium(4)|kidney(2)|large_intestine(8)|lung(8)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	26						AGAAGCTATCTCGGATGGCGC	0.582													T|||	792	0.158147	0.0204	0.2104	5008	,	,		12089	0.2778		0.162	False		,,,				2504	0.18				p.S516S		Atlas-SNP	.											.	SIN3B	90	.	0			c.T1548C						PASS	.	T		182,4224	118.0+/-155.7	4,174,2025	90.0	80.0	83.0		1548	-9.6	0.0	19	dbSNP_100	83	1355,7245	263.7+/-285.1	117,1121,3062	no	coding-synonymous	SIN3B	NM_015260.2		121,1295,5087	CC,CT,TT		15.7558,4.1307,11.8176		516/1163	16976289	1537,11469	2203	4300	6503	SO:0001819	synonymous_variant	23309	exon12			GCTATCTCGGATG	AB014600	CCDS32946.1, CCDS74308.1	19p13.12	2013-08-21	2013-08-21						19354	protein-coding gene	gene with protein product		607777	"""SIN3 homolog B, transcription regulator (yeast)"", ""SIN3 transcription regulator homolog B (yeast)"""			9734811	Standard	XM_005259832		Approved	KIAA0700	uc002ney.2	O75182		ENST00000248054.5:c.1452T>C	19.37:g.16976289T>C		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	121	121	1	NM_015260		Silent	SNP	ENST00000248054.5	37																																																																																				T|0.859;C|0.141	0.141	strong		0.582	SIN3B-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000462846.1	NM_015260	
NOP58	51602	hgsc.bcm.edu	37	2	203139844	203139844	+	Silent	SNP	T	T	C	rs80282360	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:203139844T>C	ENST00000264279.5	+	2	280	c.54T>C	c.(52-54)aaT>aaC	p.N18N	SNORD70_ENST00000391232.1_RNA|NOP58_ENST00000467734.1_Intron|SNORD70_ENST00000391007.1_RNA	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	277	0	0		WXS	Illumina HiSeq	Phase_I	198	102	0.515152	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	
SLC35G6	643664	hgsc.bcm.edu	37	17	7386272	7386272	+	Silent	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	115	1	0.00869565		WXS	Illumina HiSeq	Phase_I	96	8	0.0833333	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	
DCLK1	9201	hgsc.bcm.edu	37	13	36385031	36385031	+	Silent	SNP	G	G	T	rs2322807	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:36385031G>T	ENST00000360631.3	-	12	1840	c.1629C>A	c.(1627-1629)ccC>ccA	p.P543P	DCLK1_ENST00000379893.1_Silent_p.P236P|DCLK1_ENST00000255448.4_Silent_p.P543P			O15075	DCLK1_HUMAN	doublecortin-like kinase 1	543	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axon extension (GO:0048675)|central nervous system development (GO:0007417)|central nervous system projection neuron axonogenesis (GO:0021952)|dendrite morphogenesis (GO:0048813)|endosomal transport (GO:0016197)|forebrain development (GO:0030900)|nervous system development (GO:0007399)|neuron migration (GO:0001764)|protein phosphorylation (GO:0006468)|response to virus (GO:0009615)	integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein activity (GO:0005057)			breast(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(18)|lung(17)|ovary(2)|prostate(3)|skin(4)|stomach(6)|urinary_tract(1)	64		Breast(139;0.0147)|Lung SC(185;0.0685)|Prostate(109;0.122)	KIRC - Kidney renal clear cell carcinoma(5;0.119)|Kidney(79;0.169)	all cancers(112;1.72e-06)|Epithelial(112;4.24e-05)|BRCA - Breast invasive adenocarcinoma(63;0.00159)|OV - Ovarian serous cystadenocarcinoma(117;0.0158)|GBM - Glioblastoma multiforme(144;0.0638)		CTGTGTACAGGGGGCCGTCTA	0.458													G|||	1492	0.297923	0.4289	0.2421	5008	,	,		16326	0.2778		0.2296	False		,,,				2504	0.2515				p.P543P		Atlas-SNP	.											.	DCLK1	350	.	0			c.C1629A						PASS	.	G	,,	1867,2539	539.6+/-375.3	401,1065,737	170.0	164.0	166.0		708,708,1629	1.0	1.0	13	dbSNP_100	166	1842,6758	329.8+/-318.9	187,1468,2645	no	coding-synonymous,coding-synonymous,coding-synonymous	DCLK1	NM_001195415.1,NM_001195416.1,NM_004734.4	,,	588,2533,3382	TT,TG,GG		21.4186,42.374,28.5176	,,	236/423,236/434,543/730	36385031	3709,9297	2203	4300	6503	SO:0001819	synonymous_variant	9201	exon12			GTACAGGGGGCCG	AB002367	CCDS9354.1, CCDS55895.1, CCDS73561.1	13q13.3	2008-02-05	2007-04-02	2007-04-02	ENSG00000133083	ENSG00000133083			2700	protein-coding gene	gene with protein product		604742	"""doublecortin and CaM kinase-like 1"""	DCAMKL1		9747029, 10036192	Standard	NM_004734		Approved	KIAA0369, DCLK, DCDC3A	uc001uvf.3	O15075	OTTHUMG00000016729	ENST00000360631.3:c.1629C>A	13.37:g.36385031G>T		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	102	35	0.343137	NM_004734	B7Z3E9|Q5VZY8|Q5VZZ0|Q5VZZ1	Silent	SNP	ENST00000360631.3	37																																																																																				G|0.713;T|0.287	0.287	strong		0.458	DCLK1-010	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000044487.1	NM_004734	
CASQ2	845	hgsc.bcm.edu	37	1	116310967	116310967	+	Missense_Mutation	SNP	T	T	C	rs4074536	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:116310967T>C	ENST00000261448.5	-	1	435	c.196A>G	c.(196-198)Acg>Gcg	p.T66A	CASQ2_ENST00000456138.2_Missense_Mutation_p.T66A	NM_001232.3	NP_001223.2	O14958	CASQ2_HUMAN	calsequestrin 2 (cardiac muscle)	66			T -> A (no effect on calcium-binding and calcium-dependent dimerization; dbSNP:rs4074536). {ECO:0000269|PubMed:14571276, ECO:0000269|PubMed:17881003}.		cardiac muscle contraction (GO:0060048)|cellular response to caffeine (GO:0071313)|detection of calcium ion (GO:0005513)|ion transmembrane transport (GO:0034220)|negative regulation of potassium ion transmembrane transporter activity (GO:1901017)|negative regulation of potassium ion transport (GO:0043267)|negative regulation of ryanodine-sensitive calcium-release channel activity (GO:0060315)|protein polymerization (GO:0051258)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cell communication by electrical coupling (GO:0010649)|regulation of heart rate (GO:0002027)|regulation of membrane repolarization (GO:0060306)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|sequestering of calcium ion (GO:0051208)|striated muscle contraction (GO:0006941)|transmembrane transport (GO:0055085)	calcium channel complex (GO:0034704)|cytoplasm (GO:0005737)|intracellular (GO:0005622)|junctional sarcoplasmic reticulum membrane (GO:0014701)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum lumen (GO:0033018)|sarcoplasmic reticulum membrane (GO:0033017)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|calcium-dependent protein binding (GO:0048306)|protein homodimerization activity (GO:0042803)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(9)|skin(1)	18	Lung SC(450;0.211)	all_cancers(81;1.25e-06)|all_epithelial(167;1.02e-06)|all_lung(203;8.03e-06)|Lung NSC(69;5.01e-05)		Lung(183;0.0171)|Colorectal(144;0.0686)|LUSC - Lung squamous cell carcinoma(189;0.0903)|all cancers(265;0.108)|COAD - Colon adenocarcinoma(174;0.111)|Epithelial(280;0.12)		TGTTTTTGCGTGACCTTATCT	0.473													C|||	2009	0.401158	0.4856	0.3674	5008	,	,		19899	0.5159		0.2922	False		,,,				2504	0.3047				p.T66A		Atlas-SNP	.											CASQ2,colon,carcinoma,0,1	CASQ2	54	1	0			c.A196G						PASS	.	C	ALA/THR	1928,2478	622.1+/-393.9	416,1096,691	175.0	166.0	169.0	http://www.ncbi.nlm.nih.gov/pubmed?term	196	3.4	0.0	1	dbSNP_108	169	2486,6114	695.2+/-404.8	347,1792,2161	yes	missense	CASQ2	NM_001232.3	58	763,2888,2852	CC,CT,TT	http://www.ncbi.nlm.nih.gov/pubmed?term	28.907,43.7585,33.9382	benign	66/400	116310967	4414,8592	2203	4300	6503	SO:0001583	missense	845	exon1			TTTGCGTGACCTT	BC022288	CCDS884.1	1p13.1	2014-09-17			ENSG00000118729	ENSG00000118729		"""Protein disulfide isomerases"""	1513	protein-coding gene	gene with protein product		114251				8406504	Standard	NM_001232		Approved	PDIB2	uc001efx.4	O14958	OTTHUMG00000011970	ENST00000261448.5:c.196A>G	1.37:g.116310967T>C	ENSP00000261448:p.Thr66Ala	Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	155	76	0.490323	NM_001232	B2R7M6|B4DIB0|Q5T1D2|Q8TBW8	Missense_Mutation	SNP	ENST00000261448.5	37	CCDS884.1	902	0.413003663003663	253	0.5142276422764228	133	0.3674033149171271	285	0.4982517482517482	231	0.30474934036939316	C	0.005	-2.171649	0.00315	0.437585	0.28907	ENSG00000118729	ENST00000261448;ENST00000456138;ENST00000446755	T;T	0.37752	1.18;1.18	5.49	3.44	0.39384	Thioredoxin-like fold (2);	0.442334	0.26300	N	0.025162	T	0.02047	0.0064	N	0.00289	-1.7	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.43410	-0.9393	9	0.05959	T	0.93	-3.1292	8.6205	0.33857	0.3705:0.5482:0.0:0.0813	rs4074536;rs52800545;rs59883665;rs4074536	66;66	B4DIB0;O14958	.;CASQ2_HUMAN	A	66	ENSP00000261448:T66A;ENSP00000403858:T66A	ENSP00000261448:T66A	T	-	1	0	CASQ2	116112490	0.257000	0.24022	0.001000	0.08648	0.019000	0.09904	1.594000	0.36697	0.685000	0.31468	-0.186000	0.12905	ACG	T|0.631;C|0.369	0.369	strong		0.473	CASQ2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033091.1	NM_001232	
GPS2	2874	hgsc.bcm.edu	37	17	7217463	7217463	+	Silent	SNP	T	T	C	rs2292064	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:7217463T>C	ENST00000380728.2	-	5	633	c.333A>G	c.(331-333)ctA>ctG	p.L111L	GPS2_ENST00000389167.5_Silent_p.L111L|GPS2_ENST00000391950.3_Silent_p.L111L|RP11-542C16.2_ENST00000575474.1_3'UTR			Q13227	GPS2_HUMAN	G protein pathway suppressor 2	111					cell cycle (GO:0007049)|inactivation of MAPK activity (GO:0000188)|JNK cascade (GO:0007254)|negative regulation of JNK cascade (GO:0046329)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	GTPase inhibitor activity (GO:0005095)|transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(1)|ovary(2)|pancreas(1)|prostate(1)|stomach(1)|urinary_tract(4)	24		Prostate(122;0.157)				CAGCTGATGTTAGGGTGGTCA	0.493													C|||	2879	0.57488	0.4592	0.6484	5008	,	,		23632	0.6796		0.5179	False		,,,				2504	0.6299				p.L111L		Atlas-SNP	.											GPS2,NS,carcinoma,0,2	GPS2	44	2	0			c.A333G						PASS	.	C		2073,2333	606.4+/-390.7	487,1099,617	175.0	162.0	166.0		333	1.3	1.0	17	dbSNP_100	166	4552,4048	558.3+/-387.2	1227,2098,975	yes	coding-synonymous	GPS2	NM_004489.4		1714,3197,1592	CC,CT,TT		47.0698,47.0495,49.062		111/328	7217463	6625,6381	2203	4300	6503	SO:0001819	synonymous_variant	2874	exon5			TGATGTTAGGGTG	U28963	CCDS11100.1	17p13.1	2006-04-29			ENSG00000132522	ENSG00000132522			4550	protein-coding gene	gene with protein product		601935				8943324	Standard	NM_004489		Approved		uc002gfx.1	Q13227	OTTHUMG00000102198	ENST00000380728.2:c.333A>G	17.37:g.7217463T>C		Somatic	231	0	0		WXS	Illumina HiSeq	Phase_I	208	101	0.485577	NM_004489	B4DXA1|Q6FHM8	Silent	SNP	ENST00000380728.2	37	CCDS11100.1																																																																																			T|0.494;C|0.506	0.506	strong		0.493	GPS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000220048.4	NM_004489	
ZNF578	147660	hgsc.bcm.edu	37	19	53015384	53015384	+	Missense_Mutation	SNP	A	A	G	rs4802965	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:53015384A>G	ENST00000421239.2	+	6	1994	c.1750A>G	c.(1750-1752)Atc>Gtc	p.I584V	CTD-3099C6.5_ENST00000599143.1_RNA	NM_001099694.1	NP_001093164.1	Q96N58	ZN578_HUMAN	zinc finger protein 578	584					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)								GBM - Glioblastoma multiforme(134;0.00819)|OV - Ovarian serous cystadenocarcinoma(262;0.01)		TGATTCATCAATCAAGCCTTG	0.393													A|||	1698	0.339058	0.2564	0.3991	5008	,	,		23888	0.5198		0.2425	False		,,,				2504	0.3211				p.I584V		Atlas-SNP	.											.	.	.	.	0			c.A1750G						PASS	.	A	VAL/ILE	1064,3334		147,770,1282	52.0	55.0	54.0		1750	-3.0	0.0	19	dbSNP_111	54	2015,6583		247,1521,2531	yes	missense	ZNF578	NM_001099694.1	29	394,2291,3813	GG,GA,AA		23.4357,24.1928,23.6919	benign	584/591	53015384	3079,9917	2199	4299	6498	SO:0001583	missense	147660	exon6			TCATCAATCAAGC	AK095562	CCDS54310.1	19q13.41	2013-09-20			ENSG00000258405	ENSG00000258405		"""Zinc fingers, C2H2-type"", ""-"""	26449	protein-coding gene	gene with protein product							Standard	NM_001099694		Approved	FLJ31384	uc002pzp.4	Q96N58	OTTHUMG00000156468	ENST00000421239.2:c.1750A>G	19.37:g.53015384A>G	ENSP00000459216:p.Ile584Val	Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	30	15	0.5	NM_001099694	B4DR51|I3L1Y6	Missense_Mutation	SNP	ENST00000421239.2	37	CCDS54310.1	698	0.31959706959706957	112	0.22764227642276422	120	0.3314917127071823	288	0.5034965034965035	178	0.23482849604221637	-	0.003	-2.427475	0.00184	0.241928	0.234357	ENSG00000258405	ENST00000553364	.	.	.	1.48	-2.97	0.05530	.	.	.	.	.	T	0.00012	0.0000	N	0.12961	0.28	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.48570	-0.9024	6	.	.	.	.	1.6868	0.02843	0.1813:0.1558:0.4532:0.2096	rs4802965;rs4802965	584	G3V4F6	.	V	584	.	.	I	+	1	0	ZNF578	57707196	0.009000	0.17119	0.000000	0.03702	0.001000	0.01503	0.000000	0.12993	-0.878000	0.04007	-1.134000	0.01955	ATC	A|0.687;G|0.313	0.313	strong		0.393	ZNF578-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344298.3	NM_152472	
MYH7B	57644	hgsc.bcm.edu	37	20	33584289	33584289	+	Silent	SNP	C	C	T	rs3746438	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:33584289C>T	ENST00000262873.7	+	27	3302	c.3210C>T	c.(3208-3210)acC>acT	p.T1070T		NM_020884.3	NP_065935.2	A7E2Y1	MYH7B_HUMAN	myosin, heavy chain 7B, cardiac muscle, beta	1028						membrane (GO:0016020)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(2)|breast(5)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(19)|ovary(5)|prostate(3)|upper_aerodigestive_tract(2)|urinary_tract(3)	54			BRCA - Breast invasive adenocarcinoma(18;0.00691)			GCGCGCTGACCAAGGCCAAGC	0.701													C|||	2201	0.439497	0.2738	0.6326	5008	,	,		17071	0.5893		0.495	False		,,,				2504	0.3149				p.T1070T		Atlas-SNP	.											.	MYH7B	145	.	0			c.C3210T						PASS	.	C		1395,3007	418.0+/-338.2	225,945,1031	27.0	33.0	31.0		3210	0.6	1.0	20	dbSNP_107	31	3800,4790	512.2+/-377.9	823,2154,1318	no	coding-synonymous	MYH7B	NM_020884.3		1048,3099,2349	TT,TC,CC		44.2375,31.6901,39.9861		1070/1984	33584289	5195,7797	2201	4295	6496	SO:0001819	synonymous_variant	57644	exon29			GCTGACCAAGGCC	AB040945	CCDS42869.1	20q11	2011-09-27	2006-09-29		ENSG00000078814	ENSG00000078814		"""Myosins / Myosin superfamily : Class II"""	15906	protein-coding gene	gene with protein product		609928	"""myosin, heavy polypeptide 7B, cardiac muscle, beta"""			11919279, 15014174	Standard	XM_006723839		Approved	KIAA1512, dJ756N5.1, MYH14, MHC14	uc002xbi.2	A7E2Y1	OTTHUMG00000032320	ENST00000262873.7:c.3210C>T	20.37:g.33584289C>T		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	89	42	0.47191	NM_020884	Q5JVW7|Q6NT44|Q6NT57|Q6WG75|Q96I57|Q9NWE2|Q9P216	Silent	SNP	ENST00000262873.7	37	CCDS42869.1																																																																																			C|0.542;T|0.458	0.458	strong		0.701	MYH7B-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000078833.2	NM_020884	
LAMC2	3918	hgsc.bcm.edu	37	1	183201970	183201970	+	Missense_Mutation	SNP	G	G	C	rs2296303	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:183201970G>C	ENST00000264144.4	+	14	2263	c.2198G>C	c.(2197-2199)aGt>aCt	p.S733T	LAMC2_ENST00000493293.1_Missense_Mutation_p.S733T	NM_005562.2	NP_005553.2	Q13753	LAMC2_HUMAN	laminin, gamma 2	733	Domain II and I.		S -> T (in dbSNP:rs2296303).		cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	cell cortex (GO:0005938)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|laminin-2 complex (GO:0005607)|laminin-5 complex (GO:0005610)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)	heparin binding (GO:0008201)			breast(2)|endometrium(6)|kidney(8)|large_intestine(11)|lung(18)|ovary(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	55						CTGGCAGAAAGTGAAGCTTCC	0.483													G|||	726	0.144968	0.2186	0.1556	5008	,	,		21932	0.1468		0.1024	False		,,,				2504	0.0798				p.S733T		Atlas-SNP	.											.	LAMC2	113	.	0			c.G2198C						PASS	.	G	THR/SER,THR/SER	997,3409	368.3+/-318.6	131,735,1337	71.0	72.0	72.0		2198,2198	1.7	0.0	1	dbSNP_100	72	1107,7493	228.9+/-263.8	66,975,3259	yes	missense,missense	LAMC2	NM_005562.2,NM_018891.2	58,58	197,1710,4596	CC,CG,GG		12.8721,22.6282,16.1771	benign,benign	733/1194,733/1112	183201970	2104,10902	2203	4300	6503	SO:0001583	missense	3918	exon14			CAGAAAGTGAAGC	Z15008	CCDS1352.1, CCDS44285.1	1q25-q31	2013-03-01	2002-08-29		ENSG00000058085	ENSG00000058085		"""Laminins"""	6493	protein-coding gene	gene with protein product		150292	"""laminin, gamma 2 (nicein (100kD), kalinin (105kD), BM600 (100kD), Herlitz junctional epidermolysis bullosa))"""	EBR2, LAMB2T, LAMNB2, EBR2A		1383240	Standard	NM_005562		Approved	nicein-100kDa, kalinin-105kDa, BM600-100kDa	uc001gqa.2	Q13753	OTTHUMG00000035520	ENST00000264144.4:c.2198G>C	1.37:g.183201970G>C	ENSP00000264144:p.Ser733Thr	Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	37	24	0.648649	NM_005562	Q02536|Q02537|Q13752|Q14941|Q14DF7|Q2M1N2|Q5VYE8	Missense_Mutation	SNP	ENST00000264144.4	37	CCDS1352.1	335	0.1533882783882784	110	0.22357723577235772	54	0.14917127071823205	90	0.15734265734265734	81	0.10686015831134564	G	6.469	0.454627	0.12283	0.226282	0.128721	ENSG00000058085	ENST00000493293;ENST00000537180;ENST00000264144	T;T	0.16743	2.47;2.32	5.67	1.73	0.24493	.	0.170371	0.53938	D	0.000055	T	0.00012	0.0000	M	0.67953	2.075	0.38090	P	0.06306900000000004	B;B;B	0.29432	0.104;0.244;0.167	B;B;B	0.33750	0.081;0.125;0.169	T	0.34054	-0.9844	9	0.22109	T	0.4	.	6.3536	0.21389	0.2164:0.1312:0.6524:0.0	rs2296303;rs60229317	733;733;733	Q2M1N2;Q13753;Q13753-2	.;LAMC2_HUMAN;.	T	733	ENSP00000432063:S733T;ENSP00000264144:S733T	ENSP00000264144:S733T	S	+	2	0	LAMC2	181468593	0.348000	0.24861	0.002000	0.10522	0.005000	0.04900	1.207000	0.32333	0.063000	0.16370	-0.143000	0.13931	AGT	G|0.841;C|0.159	0.159	strong		0.483	LAMC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086258.1	NM_005562	
XPC	7508	hgsc.bcm.edu	37	3	14187449	14187449	+	Missense_Mutation	SNP	G	G	T	rs2228001	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:14187449G>T	ENST00000285021.7	-	16	3029	c.2815C>A	c.(2815-2817)Cag>Aag	p.Q939K	XPC_ENST00000449060.2_Missense_Mutation_p.Q902K|RP11-434D12.1_ENST00000601399.1_Intron|AC093495.4_ENST00000428681.3_RNA|AC093495.4_ENST00000420253.1_RNA|RP11-434D12.1_ENST00000608606.1_Intron	NM_001145769.1|NM_004628.4	NP_001139241.1|NP_004619.3	Q01831	XPC_HUMAN	xeroderma pigmentosum, complementation group C	939	Interaction with ERCC2 and GTF2H1.		Q -> K (in dbSNP:rs2228001). {ECO:0000269|PubMed:12177305, ECO:0000269|PubMed:8168482, ECO:0000269|Ref.4}.		DNA repair (GO:0006281)|intra-S DNA damage checkpoint (GO:0031573)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage recognition (GO:0000715)|nucleotide-excision repair, DNA damage removal (GO:0000718)|regulation of mitotic cell cycle phase transition (GO:1901990)|response to drug (GO:0042493)|response to UV-B (GO:0010224)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|XPC complex (GO:0071942)	bubble DNA binding (GO:0000405)|damaged DNA binding (GO:0003684)|heteroduplex DNA loop binding (GO:0000404)|single-stranded DNA binding (GO:0003697)			NS(1)|breast(2)|endometrium(1)|kidney(3)|large_intestine(4)|lung(5)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						GCTCACAGCTGCTCAAATGGG	0.587			"""Mis, N, F, S"""			"""skin basal cell, skin squamous cell, melanoma"""		Nucleotide excision repair (NER)	Xeroderma Pigmentosum				T|||	3429	0.684704	0.7511	0.7176	5008	,	,		18472	0.6667		0.5954	False		,,,				2504	0.682				p.Q939K		Atlas-SNP	.	yes	Rec		Xeroderma pigmentosum (C)	3	3p25	7508	"""xeroderma pigmentosum, complementation group C"""		E	.	XPC	60	.	0			c.C2815A	GRCh37	CM070359	XPC	M	rs2228001	PASS	.	T	LYS/GLN,LYS/GLN	2775,1027		1008,759,134	68.0	75.0	73.0		2704,2815	4.2	1.0	3	dbSNP_98	73	4949,3279		1507,1935,672	yes	missense,missense	XPC	NM_001145769.1,NM_004628.4	53,53	2515,2694,806	TT,TG,GG		39.8517,27.0121,35.7938	benign,benign	902/904,939/941	14187449	7724,4306	1901	4114	6015	SO:0001583	missense	7508	exon16	Familial Cancer Database	incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV	ACAGCTGCTCAAA		CCDS46763.1	3p25.1	2014-09-17			ENSG00000154767	ENSG00000154767			12816	protein-coding gene	gene with protein product	"""xeroderma pigmentosum group C protein"""	613208				1522891	Standard	NM_004628		Approved	XPCC, RAD4	uc011ave.2	Q01831	OTTHUMG00000155526	ENST00000285021.7:c.2815C>A	3.37:g.14187449G>T	ENSP00000285021:p.Gln939Lys	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	74	42	0.567568	NM_004628	B4DIP3|E9PB96|E9PH69|Q53GT7|Q96AX0	Missense_Mutation	SNP	ENST00000285021.7	37	CCDS46763.1	1433	0.6561355311355311	350	0.7113821138211383	264	0.7292817679558011	371	0.6486013986013986	448	0.5910290237467019	T	4.792	0.147259	0.09134	0.729879	0.601483	ENSG00000154767	ENST00000285021;ENST00000449060	T;T	0.25085	1.93;1.82	5.39	4.24	0.50183	.	0.104089	0.64402	N	0.000004	T	0.00012	0.0000	N	0.00104	-2.125	0.58432	P	2.9999999999752447E-6	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.40608	-0.9554	9	0.02654	T	1	-18.7298	7.9245	0.29865	0.0:0.071:0.1388:0.7902	rs2228001;rs3729583;rs17620623;rs17856505;rs60736379;rs2228001	902;939	E9PH69;Q01831	.;XPC_HUMAN	K	939;902	ENSP00000285021:Q939K;ENSP00000404002:Q902K	ENSP00000285021:Q939K	Q	-	1	0	XPC	14162450	1.000000	0.71417	1.000000	0.80357	0.804000	0.45430	2.905000	0.48727	0.882000	0.36016	-0.539000	0.04255	CAG	G|0.341;T|0.659	0.659	strong		0.587	XPC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000340517.3	NM_004628	
CCDC60	160777	hgsc.bcm.edu	37	12	119866533	119866533	+	Missense_Mutation	SNP	A	A	G	rs1064319	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:119866533A>G	ENST00000327554.2	+	2	601	c.136A>G	c.(136-138)Ata>Gta	p.I46V	CCDC60_ENST00000539847.1_Missense_Mutation_p.I46V|CCDC60_ENST00000536742.1_Missense_Mutation_p.I46V|RP11-768F21.1_ENST00000509470.2_lincRNA|CCDC60_ENST00000546345.1_3'UTR	NM_178499.3	NP_848594.2	Q8IWA6	CCD60_HUMAN	coiled-coil domain containing 60	46			I -> V (in dbSNP:rs1064319).							endometrium(4)|kidney(3)|large_intestine(8)|lung(15)|ovary(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	40	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.207)		GGACAAGGAAATAATAAACCT	0.438													A|||	1268	0.253195	0.2194	0.245	5008	,	,		22575	0.2788		0.326	False		,,,				2504	0.2035				p.I46V		Atlas-SNP	.											CCDC60,NS,carcinoma,0,1	CCDC60	84	1	0			c.A136G						PASS	.	A	VAL/ILE	971,3435	357.9+/-314.1	124,723,1356	79.0	69.0	72.0		136	0.9	0.0	12	dbSNP_86	72	2863,5737	435.0+/-357.9	479,1905,1916	yes	missense	CCDC60	NM_178499.3	29	603,2628,3272	GG,GA,AA		33.2907,22.0381,29.4787	probably-damaging	46/551	119866533	3834,9172	2203	4300	6503	SO:0001583	missense	160777	exon2			AAGGAAATAATAA	BC040553	CCDS9190.1	12q24.23	2006-02-03			ENSG00000183273	ENSG00000183273			28610	protein-coding gene	gene with protein product						12477932	Standard	NM_178499		Approved	MGC39827	uc001txe.3	Q8IWA6	OTTHUMG00000168943	ENST00000327554.2:c.136A>G	12.37:g.119866533A>G	ENSP00000333374:p.Ile46Val	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	82	36	0.439024	NM_178499		Missense_Mutation	SNP	ENST00000327554.2	37	CCDS9190.1	600	0.27472527472527475	105	0.21341463414634146	99	0.27348066298342544	150	0.26223776223776224	246	0.3245382585751979	A	11.70	1.717191	0.30413	0.220381	0.332907	ENSG00000183273	ENST00000536742;ENST00000327554;ENST00000539847	T;T;T	0.58797	0.51;1.85;0.31	4.54	0.905	0.19307	.	0.502010	0.18504	N	0.139250	T	0.00012	0.0000	L	0.44542	1.39	0.80722	P	0.0	B	0.12630	0.006	B	0.14578	0.011	T	0.29458	-1.0011	8	.	.	.	-11.3508	6.5238	0.22289	0.7105:0.0:0.2895:0.0	rs1064319;rs3742048;rs17627026;rs60254996;rs1064319	46	Q8IWA6	CCD60_HUMAN	V	46	ENSP00000445505:I46V;ENSP00000333374:I46V;ENSP00000443403:I46V	.	I	+	1	0	CCDC60	118350916	0.623000	0.27094	0.044000	0.18714	0.858000	0.48976	0.868000	0.27982	0.151000	0.19162	-0.256000	0.11100	ATA	A|0.720;G|0.280	0.280	strong		0.438	CCDC60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401680.1	NM_178499	
SLC35C1	55343	hgsc.bcm.edu	37	11	45832509	45832509	+	Missense_Mutation	SNP	A	A	G	rs7130656	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:45832509A>G	ENST00000314134.3	+	2	2114	c.718A>G	c.(718-720)Atc>Gtc	p.I240V	CTD-2210P24.6_ENST00000534128.1_lincRNA|SLC35C1_ENST00000442528.2_Missense_Mutation_p.I227V|SLC35C1_ENST00000456334.1_Missense_Mutation_p.I227V	NM_018389.4	NP_060859.4	Q96A29	FUCT1_HUMAN	solute carrier family 35 (GDP-fucose transporter), member C1	240			I -> V (in dbSNP:rs7130656).		carbohydrate transport (GO:0008643)|lipid glycosylation (GO:0030259)|negative regulation of Notch signaling pathway (GO:0045746)|transmembrane transport (GO:0055085)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)				endometrium(3)|kidney(1)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	10				GBM - Glioblastoma multiforme(35;0.227)		CAACGCCTGCATCCTCTTCCT	0.632													G|||	515	0.102835	0.2337	0.0677	5008	,	,		19582	0.001		0.1382	False		,,,				2504	0.0194				p.I240V		Atlas-SNP	.											SLC35C1,NS,carcinoma,0,2	SLC35C1	23	2	0			c.A718G						PASS	.	G	VAL/ILE,VAL/ILE,VAL/ILE	906,3500	738.9+/-411.0	86,734,1383	57.0	54.0	55.0		679,679,718	1.1	1.0	11	dbSNP_116	55	959,7639	774.1+/-407.7	68,823,3408	yes	missense,missense,missense	SLC35C1	NM_001145265.1,NM_001145266.1,NM_018389.4	29,29,29	154,1557,4791	GG,GA,AA		11.1538,20.5629,14.3417	benign,benign,benign	227/352,227/352,240/365	45832509	1865,11139	2203	4299	6502	SO:0001583	missense	55343	exon2			GCCTGCATCCTCT		CCDS7914.1, CCDS44575.1	11p11.2	2014-09-17	2013-07-17			ENSG00000181830		"""Solute carriers"""	20197	protein-coding gene	gene with protein product		605881	"""solute carrier family 35, member C1"""			11326279, 11326280	Standard	NM_018389		Approved	FUCT1, FLJ11320	uc010rgm.2	Q96A29		ENST00000314134.3:c.718A>G	11.37:g.45832509A>G	ENSP00000313318:p.Ile240Val	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	45	45	1	NM_018389	B2RDB2|Q9BV76|Q9NUJ8	Missense_Mutation	SNP	ENST00000314134.3	37	CCDS7914.1	259	0.11858974358974358	119	0.241869918699187	34	0.09392265193370165	0	0.0	106	0.13984168865435356	G	2.482	-0.319429	0.05386	0.205629	0.111538	ENSG00000181830	ENST00000442528;ENST00000456334;ENST00000530670;ENST00000314134;ENST00000540685	T;T;T	0.65916	-0.18;-0.18;-0.18	6.17	1.14	0.20703	Domain of unknown function DUF250 (1);	0.522394	0.21103	N	0.080121	T	0.00012	0.0000	N	0.02539	-0.55	0.80722	P	0.0	B	0.02656	0.0	B	0.08055	0.003	T	0.13415	-1.0510	9	0.07175	T	0.84	-22.5421	5.0846	0.14675	0.2866:0.0:0.5:0.2134	rs7130656;rs17725077;rs57668458;rs7130656	240	Q96A29	FUCT1_HUMAN	V	227;227;161;240;240	ENSP00000412408:I227V;ENSP00000399779:I227V;ENSP00000313318:I240V	ENSP00000313318:I240V	I	+	1	0	SLC35C1	45789085	0.391000	0.25221	0.969000	0.41365	0.663000	0.39108	0.551000	0.23361	0.186000	0.20125	-1.617000	0.00794	ATC	A|0.866;G|0.134	0.134	strong		0.632	SLC35C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390139.1	NM_018389	
DOC2A	8448	hgsc.bcm.edu	37	16	30021402	30021402	+	Missense_Mutation	SNP	C	C	T	rs1140239	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:30021402C>T	ENST00000350119.4	-	2	332	c.142G>A	c.(142-144)Ggc>Agc	p.G48S	DOC2A_ENST00000564944.1_Missense_Mutation_p.G48S|DOC2A_ENST00000564979.1_Missense_Mutation_p.G48S|DOC2A_ENST00000567824.1_5'Flank	NM_001282062.1|NM_001282063.1|NM_001282068.1|NM_003586.2	NP_001268991.1|NP_001268992.1|NP_001268997.1|NP_003577.2	Q14183	DOC2A_HUMAN	double C2-like domains, alpha	48	Interaction with UNC13D and DYNLT1.		G -> S (in dbSNP:rs1140239). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:7826360}.		nervous system development (GO:0007399)|regulation of calcium ion-dependent exocytosis (GO:0017158)|synaptic transmission (GO:0007268)|synaptic vesicle exocytosis (GO:0016079)	cell junction (GO:0030054)|lysosome (GO:0005764)|membrane (GO:0016020)|neuron projection (GO:0043005)|synaptic vesicle (GO:0008021)	calcium-dependent phospholipid binding (GO:0005544)|transporter activity (GO:0005215)			central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(2)|ovary(2)	9						tccccgccgcccccgccgccc	0.731													C|||	1633	0.326078	0.1604	0.2954	5008	,	,		12182	0.376		0.3847	False		,,,				2504	0.4601				p.G48S		Atlas-SNP	.											.	DOC2A	40	.	0			c.G142A						PASS	.	C	SER/GLY	684,3516		73,538,1489	13.0	16.0	15.0		142	1.8	0.0	16	dbSNP_86	15	3170,5200		638,1894,1653	yes	missense	DOC2A	NM_003586.2	56	711,2432,3142	TT,TC,CC		37.8734,16.2857,30.6603	benign	48/401	30021402	3854,8716	2100	4185	6285	SO:0001583	missense	8448	exon2			CGCCGCCCCCGCC	D31897	CCDS10666.1	16p11.2	2014-07-02			ENSG00000149927	ENSG00000149927		"""Synaptotagmins"""	2985	protein-coding gene	gene with protein product		604567				7826360, 9736751	Standard	NM_003586		Approved		uc002dvn.3	Q14183	OTTHUMG00000132109	ENST00000350119.4:c.142G>A	16.37:g.30021402C>T	ENSP00000340017:p.Gly48Ser	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	161	159	0.987578	NM_003586	B4DEJ2|H3BNH6|Q6P4G4|Q7Z5G0|Q8IVX0	Missense_Mutation	SNP	ENST00000350119.4	37	CCDS10666.1	692	0.31684981684981683	80	0.16260162601626016	117	0.32320441988950277	206	0.36013986013986016	289	0.3812664907651715	C	4.206	0.036904	0.08148	0.162857	0.378734	ENSG00000149927	ENST00000350119	T	0.61040	0.14	3.79	1.81	0.25067	.	0.654184	0.12703	N	0.446200	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B	0.09022	0.002	B	0.04013	0.001	T	0.35201	-0.9798	9	0.05721	T	0.95	.	5.7904	0.18357	0.0:0.7533:0.0:0.2467	rs1140239;rs3814879;rs17846636;rs17859727;rs1140239	48	Q14183	DOC2A_HUMAN	S	48	ENSP00000340017:G48S	ENSP00000340017:G48S	G	-	1	0	DOC2A	29928903	0.000000	0.05858	0.003000	0.11579	0.081000	0.17604	0.322000	0.19576	0.401000	0.25424	0.561000	0.74099	GGC	C|0.733;T|0.267	0.267	strong		0.731	DOC2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255148.2	NM_003586	
KREMEN1	83999	hgsc.bcm.edu	37	22	29533572	29533572	+	Missense_Mutation	SNP	C	C	G	rs34920087	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:29533572C>G	ENST00000407188.1	+	6	868	c.868C>G	c.(868-870)Ctg>Gtg	p.L290V	KREMEN1_ENST00000400335.4_Missense_Mutation_p.L292V|KREMEN1_ENST00000327813.5_Missense_Mutation_p.L292V|KREMEN1_ENST00000400338.2_Missense_Mutation_p.L292V			Q96MU8	KREM1_HUMAN	kringle containing transmembrane protein 1	290	CUB. {ECO:0000255|PROSITE- ProRule:PRU00059}.				cell communication (GO:0007154)|regulation of canonical Wnt signaling pathway (GO:0060828)|Wnt signaling pathway (GO:0016055)	integral component of membrane (GO:0016021)|membrane (GO:0016020)				breast(1)|endometrium(3)|large_intestine(2)|lung(8)|ovary(3)|prostate(1)|upper_aerodigestive_tract(2)	20						CCGCCCACCTCTGTCCTTCAA	0.542													C|||	543	0.108427	0.0726	0.111	5008	,	,		18222	0.0427		0.1958	False		,,,				2504	0.1329				p.L292V		Atlas-SNP	.											.	KREMEN1	46	.	0			c.C874G						PASS	.	C	VAL/LEU,VAL/LEU	314,3586		11,292,1647	68.0	69.0	69.0		874,874	-8.7	0.0	22	dbSNP_126	69	1438,6846		130,1178,2834	yes	missense,missense	KREMEN1	NM_001039570.2,NM_032045.4	32,32	141,1470,4481	GG,GC,CC		17.3588,8.0513,14.3795	benign,benign	292/459,292/493	29533572	1752,10432	1950	4142	6092	SO:0001583	missense	83999	exon6			CCACCTCTGTCCT	AB059618	CCDS43000.1, CCDS13849.1, CCDS43000.2	22q12.1	2008-03-27	2002-11-13	2002-11-15	ENSG00000183762	ENSG00000183762			17550	protein-coding gene	gene with protein product		609898	"""kringle containing transmembrane protein"""	KREMEN		11267660	Standard	NM_001039570		Approved	KRM1	uc011akm.1	Q96MU8	OTTHUMG00000030987	ENST00000407188.1:c.868C>G	22.37:g.29533572C>G	ENSP00000385431:p.Leu290Val	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	55	33	0.6	NM_001039570	B0QY46|B0QY47|B1AJR5|Q5TIB9|Q6P3X6|Q9BY70|Q9UGS5|Q9UGU1	Missense_Mutation	SNP	ENST00000407188.1	37	CCDS43000.2	250	0.11446886446886446	44	0.08943089430894309	41	0.1132596685082873	12	0.02097902097902098	153	0.20184696569920843	C	12.47	1.946617	0.34377	0.080513	0.173588	ENSG00000183762	ENST00000400335;ENST00000400338;ENST00000327813;ENST00000407188	T;T;T;T	0.18016	2.24;2.24;2.24;2.24	4.99	-8.68	0.00859	CUB (5);	0.511667	0.15093	N	0.280963	T	0.00012	0.0000	L	0.45137	1.4	0.80722	P	0.0	B;B;B	0.27625	0.183;0.152;0.065	B;B;B	0.30943	0.122;0.08;0.035	T	0.01500	-1.1339	9	0.25106	T	0.35	.	20.4747	0.99174	0.0:0.9009:0.0:0.0991	rs34920087;rs58049194;rs61741867	290;292;292	Q96MU8;Q96MU8-2;Q96MU8-3	KREM1_HUMAN;.;.	V	292;292;292;290	ENSP00000383189:L292V;ENSP00000383192:L292V;ENSP00000331242:L292V;ENSP00000385431:L290V	ENSP00000331242:L292V	L	+	1	2	KREMEN1	27863572	0.000000	0.05858	0.010000	0.14722	0.982000	0.71751	-0.438000	0.06905	-1.629000	0.01546	0.467000	0.42956	CTG	C|0.862;G|0.138	0.138	strong		0.542	KREMEN1-004	KNOWN	non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320947.1		
KIF2B	84643	hgsc.bcm.edu	37	17	51901385	51901385	+	Silent	SNP	C	C	T	rs3803826	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:51901385C>T	ENST00000268919.4	+	1	1147	c.991C>T	c.(991-993)Ctg>Ttg	p.L331L		NM_032559.4	NP_115948.4	Q8N4N8	KIF2B_HUMAN	kinesin family member 2B	331	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|metabolic process (GO:0008152)|microtubule depolymerization (GO:0007019)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|regulation of chromosome segregation (GO:0051983)	cytosol (GO:0005829)|kinesin complex (GO:0005871)|kinetochore (GO:0000776)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(1)|breast(2)|endometrium(7)|kidney(2)|large_intestine(15)|lung(58)|ovary(5)|prostate(4)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	104						CATTTATGCTCTGGTGGCACA	0.493													C|||	1675	0.334465	0.1074	0.4107	5008	,	,		22113	0.5863		0.3658	False		,,,				2504	0.2955				p.L331L		Atlas-SNP	.											.	KIF2B	254	.	0			c.C991T						PASS	.	C		656,3750	279.6+/-274.9	41,574,1588	107.0	108.0	107.0		991	-5.5	0.0	17	dbSNP_107	107	3075,5525	471.6+/-368.1	562,1951,1787	no	coding-synonymous	KIF2B	NM_032559.4		603,2525,3375	TT,TC,CC		35.7558,14.8888,28.6868		331/674	51901385	3731,9275	2203	4300	6503	SO:0001819	synonymous_variant	84643	exon1			TATGCTCTGGTGG	AF333335	CCDS32685.1	17q22	2014-08-12			ENSG00000141200	ENSG00000141200		"""Kinesins"""	29443	protein-coding gene	gene with protein product		615142				11416179	Standard	NM_032559		Approved		uc002iua.2	Q8N4N8	OTTHUMG00000177756	ENST00000268919.4:c.991C>T	17.37:g.51901385C>T		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	59	26	0.440678	NM_032559	Q96MA2|Q9BXG6	Silent	SNP	ENST00000268919.4	37	CCDS32685.1																																																																																			C|0.677;T|0.323	0.323	strong		0.493	KIF2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438854.1	NM_032559	
MUC4	4585	hgsc.bcm.edu	37	3	195506982	195506982	+	Silent	SNP	G	G	C	rs562381906	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195506982G>C	ENST00000463781.3	-	2	11928	c.11469C>G	c.(11467-11469)acC>acG	p.T3823T	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_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	73	1	0.0136986		WXS	Illumina HiSeq	Phase_I	52	12	0.230769	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	
ZNF701	55762	hgsc.bcm.edu	37	19	53085813	53085813	+	Silent	SNP	T	T	C	rs3745101	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:53085813T>C	ENST00000540331.1	+	5	924	c.699T>C	c.(697-699)gcT>gcC	p.A233A	ZNF701_ENST00000391785.3_Silent_p.A167A|CTD-3099C6.7_ENST00000599222.1_RNA|ZNF701_ENST00000301093.2_Silent_p.A233A	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	131	0	0		WXS	Illumina HiSeq	Phase_I	86	85	0.988372	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	
IPO4	79711	hgsc.bcm.edu	37	14	24653523	24653523	+	Missense_Mutation	SNP	G	G	C	rs11550452	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:24653523G>C	ENST00000354464.6	-	17	1914	c.1738C>G	c.(1738-1740)Cct>Gct	p.P580A	RP11-468E2.2_ENST00000561419.1_3'UTR	NM_024658.3	NP_078934.3	Q8TEX9	IPO4_HUMAN	importin 4	580			P -> A (in dbSNP:rs11550452). {ECO:0000269|PubMed:11823430, ECO:0000269|PubMed:14702039}.		DNA replication-dependent nucleosome assembly (GO:0006335)|DNA replication-independent nucleosome assembly (GO:0006336)|intracellular protein transport (GO:0006886)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|protein complex (GO:0043234)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|lung(10)|ovary(1)|stomach(2)|urinary_tract(1)	33				GBM - Glioblastoma multiforme(265;0.0087)		CGCAAGTCAGGGTCGTCTACC	0.672													G|||	1580	0.315495	0.1831	0.2493	5008	,	,		15854	0.4196		0.2922	False		,,,				2504	0.4581				p.P580A		Atlas-SNP	.											.	IPO4	74	.	0			c.C1738G						PASS	.	G	ALA/PRO	1023,3323		149,725,1299	15.0	21.0	19.0		1738	5.4	1.0	14	dbSNP_120	19	2806,5736		475,1856,1940	yes	missense	IPO4	NM_024658.3	27	624,2581,3239	CC,CG,GG		32.8494,23.5389,29.7098	probably-damaging	580/1082	24653523	3829,9059	2173	4271	6444	SO:0001583	missense	79711	exon17			AGTCAGGGTCGTC	AF411122	CCDS9616.1	14q11.2	2003-03-10			ENSG00000196497	ENSG00000196497		"""Importins"""	19426	protein-coding gene	gene with protein product						11823430	Standard	NR_051979		Approved	Imp4, FLJ23338	uc001wmv.1	Q8TEX9	OTTHUMG00000028801	ENST00000354464.6:c.1738C>G	14.37:g.24653523G>C	ENSP00000346453:p.Pro580Ala	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	109	49	0.449541	NM_024658	B2RN95|Q2NL96|Q86TZ9|Q8NCG8|Q96SJ3|Q9BTI4|Q9H5L0	Missense_Mutation	SNP	ENST00000354464.6	37	CCDS9616.1	660	0.3021978021978022	96	0.1951219512195122	96	0.26519337016574585	250	0.4370629370629371	218	0.287598944591029	G	24.1	4.495905	0.85069	0.235389	0.328494	ENSG00000196497	ENST00000354464;ENST00000399536	T	0.50277	0.75	5.4	5.4	0.78164	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	M	0.66297	2.02	0.09310	P	0.999999999258	D;P	0.76494	0.999;0.953	D;P	0.71414	0.973;0.867	T	0.37776	-0.9691	9	0.40728	T	0.16	-14.7544	18.116	0.89555	0.0:0.0:1.0:0.0	rs11550452;rs12586264;rs17184519;rs11550452	580;580	Q8TEX9;Q8TEX9-2	IPO4_HUMAN;.	A	580;256	ENSP00000346453:P580A	ENSP00000346453:P580A	P	-	1	0	IPO4	23723363	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.795000	0.85887	2.814000	0.96858	0.655000	0.94253	CCT	G|0.693;C|0.307	0.307	strong		0.672	IPO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071931.4	NM_024658	
DHX38	9785	hgsc.bcm.edu	37	16	72130203	72130203	+	Silent	SNP	C	C	G	rs1050361	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:72130203C>G	ENST00000268482.3	+	2	656	c.147C>G	c.(145-147)ctC>ctG	p.L49L	TXNL4B_ENST00000426362.2_5'Flank|TXNL4B_ENST00000268483.3_5'Flank|TXNL4B_ENST00000423037.1_5'Flank|DHX38_ENST00000536867.1_Silent_p.L49L	NM_014003.3	NP_054722.2	Q92620	PRP16_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 38	49					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.L49L(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)				CTTCATTACTCGGACTGGACT	0.552													G|||	2570	0.513179	0.8094	0.3588	5008	,	,		19448	0.3542		0.3986	False		,,,				2504	0.5041				p.L49L	Melanoma(97;711 1442 7855 13832 28836)	Atlas-SNP	.											DHX38,NS,carcinoma,0,1	DHX38	91	1	1	Substitution - coding silent(1)	stomach(1)	c.C147G						PASS	.	G		3193,1203	418.7+/-338.4	1177,839,182	60.0	55.0	57.0		147	2.6	1.0	16	dbSNP_86	57	3668,4932	622.1+/-397.3	776,2116,1408	no	coding-synonymous	DHX38	NM_014003.3		1953,2955,1590	GG,GC,CC		42.6512,27.3658,47.2068		49/1228	72130203	6861,6135	2198	4300	6498	SO:0001819	synonymous_variant	9785	exon2			ATTACTCGGACTG	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.147C>G	16.37:g.72130203C>G		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	170	64	0.376471	NM_014003	B4DVG8|D3DWS7|O75212|Q96HN7	Silent	SNP	ENST00000268482.3	37	CCDS10907.1																																																																																			C|0.490;G|0.510	0.510	strong		0.552	DHX38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269004.3	NM_014003	
LAMC2	3918	hgsc.bcm.edu	37	1	183192304	183192304	+	Silent	SNP	T	T	G	rs1047980	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:183192304T>G	ENST00000264144.4	+	7	863	c.798T>G	c.(796-798)ggT>ggG	p.G266G	LAMC2_ENST00000493293.1_Silent_p.G266G	NM_005562.2	NP_005553.2	Q13753	LAMC2_HUMAN	laminin, gamma 2	266	Laminin IV type A. {ECO:0000255|PROSITE- ProRule:PRU00458}.				cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	cell cortex (GO:0005938)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|laminin-2 complex (GO:0005607)|laminin-5 complex (GO:0005610)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)	heparin binding (GO:0008201)	p.G266G(1)		breast(2)|endometrium(6)|kidney(8)|large_intestine(11)|lung(18)|ovary(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	55						TGAGCTATGGTCAAAGCCTGT	0.473													G|||	1778	0.355032	0.5477	0.3314	5008	,	,		22321	0.3363		0.159	False		,,,				2504	0.3323				p.G266G		Atlas-SNP	.											LAMC2,NS,carcinoma,0,1	LAMC2	113	1	1	Substitution - coding silent(1)	stomach(1)	c.T798G						PASS	.	G	,	2208,2198	587.3+/-386.7	578,1052,573	90.0	87.0	88.0		798,798	3.2	1.0	1	dbSNP_86	88	1526,7074	747.2+/-407.3	132,1262,2906	no	coding-synonymous,coding-synonymous	LAMC2	NM_005562.2,NM_018891.2	,	710,2314,3479	GG,GT,TT		17.7442,49.8865,28.7098	,	266/1194,266/1112	183192304	3734,9272	2203	4300	6503	SO:0001819	synonymous_variant	3918	exon7			CTATGGTCAAAGC	Z15008	CCDS1352.1, CCDS44285.1	1q25-q31	2013-03-01	2002-08-29		ENSG00000058085	ENSG00000058085		"""Laminins"""	6493	protein-coding gene	gene with protein product		150292	"""laminin, gamma 2 (nicein (100kD), kalinin (105kD), BM600 (100kD), Herlitz junctional epidermolysis bullosa))"""	EBR2, LAMB2T, LAMNB2, EBR2A		1383240	Standard	NM_005562		Approved	nicein-100kDa, kalinin-105kDa, BM600-100kDa	uc001gqa.2	Q13753	OTTHUMG00000035520	ENST00000264144.4:c.798T>G	1.37:g.183192304T>G		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	139	73	0.52518	NM_005562	Q02536|Q02537|Q13752|Q14941|Q14DF7|Q2M1N2|Q5VYE8	Silent	SNP	ENST00000264144.4	37	CCDS1352.1																																																																																			T|0.692;G|0.308	0.308	strong		0.473	LAMC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086258.1	NM_005562	
CCDC13	152206	hgsc.bcm.edu	37	3	42787469	42787469	+	Silent	SNP	A	A	G	rs2240859	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:42787469A>G	ENST00000310232.6	-	7	854	c.771T>C	c.(769-771)tcT>tcC	p.S257S	CCDC13-AS1_ENST00000446950.1_RNA|CCDC13-AS1_ENST00000418161.1_RNA	NM_144719.3	NP_653320.3	Q8IYE1	CCD13_HUMAN	coiled-coil domain containing 13	257										endometrium(1)|kidney(1)|large_intestine(5)|liver(1)|lung(11)|ovary(1)|prostate(3)|skin(1)|urinary_tract(1)	25						TCCCTGGCGAAGATAGGAGCT	0.512													G|||	2511	0.501398	0.5439	0.402	5008	,	,		18576	0.4534		0.4592	False		,,,				2504	0.6074				p.S257S		Atlas-SNP	.											.	CCDC13	71	.	0			c.T771C						PASS	.	G		2397,2009	561.2+/-380.7	650,1097,456	93.0	90.0	91.0		771	2.1	0.9	3	dbSNP_98	91	3943,4657	602.8+/-394.6	898,2147,1255	yes	coding-synonymous	CCDC13	NM_144719.3		1548,3244,1711	GG,GA,AA		45.8488,45.5969,48.7467		257/716	42787469	6340,6666	2203	4300	6503	SO:0001819	synonymous_variant	152206	exon7			TGGCGAAGATAGG	AK058196	CCDS2705.1	3p22.1	2005-01-25			ENSG00000244607	ENSG00000244607			26358	protein-coding gene	gene with protein product						12477932	Standard	NM_144719		Approved	FLJ25467	uc003cly.4	Q8IYE1	OTTHUMG00000133046	ENST00000310232.6:c.771T>C	3.37:g.42787469A>G		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	69	38	0.550725	NM_144719		Silent	SNP	ENST00000310232.6	37	CCDS2705.1																																																																																			A|0.512;G|0.488	0.488	strong		0.512	CCDC13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256652.1	NM_144719	
ROBO2	6092	hgsc.bcm.edu	37	3	77607099	77607099	+	Missense_Mutation	SNP	G	G	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:77607099G>C	ENST00000461745.1	+	9	2136	c.1236G>C	c.(1234-1236)ttG>ttC	p.L412F	ROBO2_ENST00000487694.3_Missense_Mutation_p.L428F|ROBO2_ENST00000332191.8_Missense_Mutation_p.L412F	NM_002942.4	NP_002933.1	Q9HCK4	ROBO2_HUMAN	roundabout, axon guidance receptor, homolog 2 (Drosophila)	412					apoptotic process involved in luteolysis (GO:0061364)|axon guidance (GO:0007411)|axon midline choice point recognition (GO:0016199)|brain development (GO:0007420)|cellular response to hormone stimulus (GO:0032870)|central nervous system development (GO:0007417)|homophilic cell adhesion (GO:0007156)|metanephros development (GO:0001656)|negative regulation of negative chemotaxis (GO:0050925)|negative regulation of synapse assembly (GO:0051964)|olfactory bulb interneuron development (GO:0021891)|positive regulation of axonogenesis (GO:0050772)|retinal ganglion cell axon guidance (GO:0031290)|ureteric bud development (GO:0001657)	axolemma (GO:0030673)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	axon guidance receptor activity (GO:0008046)|identical protein binding (GO:0042802)			NS(1)|biliary_tract(5)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(23)|liver(1)|lung(52)|ovary(2)|pancreas(2)|prostate(5)|skin(8)|upper_aerodigestive_tract(1)	117				Epithelial(33;0.00199)|LUSC - Lung squamous cell carcinoma(21;0.008)|BRCA - Breast invasive adenocarcinoma(55;0.00884)|Lung(72;0.0183)|KIRC - Kidney renal clear cell carcinoma(39;0.0832)|Kidney(39;0.103)		CTTCAGTTTTGACAGATAGAC	0.413																																					p.L412F		Atlas-SNP	.											.	ROBO2	527	.	0			c.G1236C						PASS	.						67.0	70.0	69.0					3																	77607099		1853	4083	5936	SO:0001583	missense	6092	exon9			AGTTTTGACAGAT	AF040991	CCDS43109.1, CCDS54609.1	3p12.3	2013-02-11	2001-11-28		ENSG00000185008	ENSG00000185008		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	10250	protein-coding gene	gene with protein product		602431	"""roundabout (axon guidance receptor, Drosophila) homolog 2"""			9458045	Standard	NM_002942		Approved	KIAA1568	uc003dpy.4	Q9HCK4	OTTHUMG00000158935	ENST00000461745.1:c.1236G>C	3.37:g.77607099G>C	ENSP00000417164:p.Leu412Phe	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	103	32	0.31068	NM_002942	O43608|Q19AB4|Q19AB5	Missense_Mutation	SNP	ENST00000461745.1	37	CCDS43109.1	.	.	.	.	.	.	.	.	.	.	G	2.000	-0.429551	0.04701	.	.	ENSG00000185008	ENST00000487694;ENST00000403211;ENST00000343019;ENST00000461745;ENST00000332191;ENST00000398467	T;T;T	0.65364	-0.15;-0.13;-0.13	5.53	0.656	0.17844	.	0.203361	0.24178	N	0.040830	T	0.61813	0.2377	L	0.31526	0.94	0.43234	D	0.995137	D;D;D	0.69078	0.994;0.997;0.994	D;D;D	0.72075	0.947;0.976;0.921	T	0.63637	-0.6592	9	0.19147	T	0.46	.	9.9156	0.41432	0.4075:0.0:0.5925:0.0	.	428;412;412	Q19AB5;F8W703;Q9HCK4	.;.;ROBO2_HUMAN	F	428;428;432;412;412;133	ENSP00000417335:L428F;ENSP00000417164:L412F;ENSP00000327536:L412F	ENSP00000327536:L412F	L	+	3	2	ROBO2	77689789	1.000000	0.71417	0.998000	0.56505	0.232000	0.25224	1.789000	0.38724	0.111000	0.17947	0.585000	0.79938	TTG	.	.	none		0.413	ROBO2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000352600.2	XM_031246	
RET	5979	hgsc.bcm.edu	37	10	43615633	43615633	+	Silent	SNP	C	C	G	rs1800863	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:43615633C>G	ENST00000355710.3	+	15	2944	c.2712C>G	c.(2710-2712)tcC>tcG	p.S904S	RET_ENST00000340058.5_Silent_p.S904S	NM_020975.4	NP_066124.1	P07949	RET_HUMAN	ret proto-oncogene	904	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.			S -> P (in Ref. 6; AAA36786). {ECO:0000305}.	activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|cellular response to retinoic acid (GO:0071300)|embryonic epithelial tube formation (GO:0001838)|enteric nervous system development (GO:0048484)|homophilic cell adhesion (GO:0007156)|innervation (GO:0060384)|lymphocyte migration into lymphoid organs (GO:0097021)|MAPK cascade (GO:0000165)|membrane protein proteolysis (GO:0033619)|neural crest cell migration (GO:0001755)|neuron cell-cell adhesion (GO:0007158)|neuron maturation (GO:0042551)|peptidyl-tyrosine phosphorylation (GO:0018108)|Peyer's patch morphogenesis (GO:0061146)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of cell migration (GO:0030335)|positive regulation of cell size (GO:0045793)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of metanephric glomerulus development (GO:0072300)|positive regulation of neuron maturation (GO:0014042)|positive regulation of neuron projection development (GO:0010976)|positive regulation of transcription, DNA-templated (GO:0045893)|posterior midgut development (GO:0007497)|protein phosphorylation (GO:0006468)|regulation of axonogenesis (GO:0050770)|regulation of cell adhesion (GO:0030155)|response to drug (GO:0042493)|response to pain (GO:0048265)|retina development in camera-type eye (GO:0060041)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|ureter maturation (GO:0035799)|ureteric bud development (GO:0001657)	endosome membrane (GO:0010008)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|protein tyrosine kinase activity (GO:0004713)|receptor activity (GO:0004872)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)		CCDC6/RET(4)|KIF5B/RET(79)	NS(2)|adrenal_gland(26)|breast(5)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(7)|kidney(2)|large_intestine(14)|lung(27)|ovary(5)|prostate(3)|skin(1)|thyroid(504)|upper_aerodigestive_tract(1)|urinary_tract(1)	607		Ovarian(717;0.0423)			Cabozantinib(DB08875)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)	AAGAGGATTCCTACGTGAAGA	0.592		1	"""T, Mis, N, F"""	"""H4, PRKAR1A, NCOA4, PCM1, GOLGA5, TRIM33, KTN1, TRIM27, HOOK3, KIF5B, CCDC6"""	"""medullary thyroid,  papillary thyroid, pheochromocytoma, NSCLC"""	"""medullary thyroid,  papillary thyroid, pheochromocytoma"""	Hirschsprung disease		Multiple Endocrine Neoplasia, type 2B;Multiple Endocrine Neoplasia, type 2A;Familial Medullary Thyroid Carcinoma				C|||	864	0.172524	0.1051	0.2536	5008	,	,		15815	0.121		0.1928	False		,,,				2504	0.2382				p.S904S	Melanoma(102;360 522 3376 9752 9881 14372 17251 18341 20876 24662 34807 43144 48149)	Atlas-SNP	.	yes	Dom	yes	Multiple endocrine neoplasia 2A/2B	10	10q11.2	5979	ret proto-oncogene	yes	"""E, O"""	.	RET	916	.	0			c.C2712G	GRCh37	CM023822	RET	M	rs1800863	PASS	.	C	,	489,3917	225.2+/-241.2	24,441,1738	64.0	57.0	59.0		2712,2712	3.7	1.0	10	dbSNP_89	59	1604,6994	293.1+/-301.2	159,1286,2854	no	coding-synonymous,coding-synonymous	RET	NM_020630.4,NM_020975.4	,	183,1727,4592	GG,GC,CC		18.6555,11.0985,16.095	,	904/1073,904/1115	43615633	2093,10911	2203	4299	6502	SO:0001819	synonymous_variant	5979	exon15	Familial Cancer Database	MEN2B, Wagenmann-Froboese s.;MEN2A, Sipple disease, incl MEN2C;FMTC	GGATTCCTACGTG	BC004257	CCDS7200.1, CCDS53525.1	10q11.2	2014-09-17	2007-02-16		ENSG00000165731	ENSG00000165731		"""Cadherins / Cadherin-related"""	9967	protein-coding gene	gene with protein product	"""cadherin-related family member 16"""	164761	"""multiple endocrine neoplasia and medullary thyroid carcinoma 1"", ""Hirschsprung disease 1"""	HSCR1, MEN2A, MTC1, MEN2B		2687772, 1611909	Standard	NM_020975		Approved	PTC, CDHF12, RET51, CDHR16	uc001jal.3	P07949	OTTHUMG00000018024	ENST00000355710.3:c.2712C>G	10.37:g.43615633C>G		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	90	40	0.444444	NM_020630	A8K6Z2|Q15250|Q9BTB0|Q9H4A2	Silent	SNP	ENST00000355710.3	37	CCDS7200.1																																																																																			C|0.844;G|0.156	0.156	strong		0.592	RET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047694.2	NM_020975	
OR52R1	119695	hgsc.bcm.edu	37	11	4825349	4825349	+	Missense_Mutation	SNP	A	A	G	rs17327254	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:4825349A>G	ENST00000356069.2	-	1	261	c.262T>C	c.(262-264)Ttc>Ctc	p.F88L	OR52R1_ENST00000380382.1_Missense_Mutation_p.F167L|MMP26_ENST00000477339.1_Intron|MMP26_ENST00000380390.1_Intron	NM_001005177.3	NP_001005177.3	Q8NGF1	O52R1_HUMAN	olfactory receptor, family 52, subfamily R, member 1	88			F -> L (in dbSNP:rs17327254).			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)		TGAAACCAGAATATGGCCAAC	0.517													A|||	157	0.0313498	0.0053	0.0548	5008	,	,		23740	0.0		0.0964	False		,,,				2504	0.0153				p.F88L		Atlas-SNP	.											.	OR52R1	81	.	0			c.T262C						PASS	.	A	LEU/PHE	107,4295	82.4+/-120.9	1,105,2095	143.0	127.0	133.0		262	-2.7	0.5	11	dbSNP_123	133	845,7751	194.8+/-240.1	47,751,3500	yes	missense	OR52R1	NM_001005177.3	22	48,856,5595	GG,GA,AA		9.8302,2.4307,7.3242	benign	88/316	4825349	952,12046	2201	4298	6499	SO:0001583	missense	119695	exon1			ACCAGAATATGGC	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.262T>C	11.37:g.4825349A>G	ENSP00000348368:p.Phe88Leu	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	117	27	0.230769	NM_001005177	Q6IFI0	Missense_Mutation	SNP	ENST00000356069.2	37	CCDS31360.2	101	0.04624542124542125	2	0.0040650406504065045	25	0.06906077348066299	0	0.0	74	0.09762532981530343	A	12.39	1.922678	0.33908	0.024307	0.098302	ENSG00000176937	ENST00000356069;ENST00000380382	T;T	0.00912	5.55;5.55	5.57	-2.66	0.06077	GPCR, rhodopsin-like superfamily (1);	0.443885	0.19125	N	0.122063	T	0.00039	0.0001	L	0.31845	0.965	0.53688	P	2.6999999999999247E-5	B	0.02656	0.0	B	0.06405	0.002	T	0.38714	-0.9648	9	0.46703	T	0.11	.	13.3316	0.60490	0.8457:0.0:0.1543:0.0	rs17327254;rs52793345;rs17327254	88	Q8NGF1	O52R1_HUMAN	L	88;167	ENSP00000348368:F88L;ENSP00000369742:F167L	ENSP00000348368:F88L	F	-	1	0	OR52R1	4781925	0.013000	0.17824	0.458000	0.27068	0.944000	0.59088	0.193000	0.17116	-0.316000	0.08690	0.528000	0.53228	TTC	A|0.937;G|0.063	0.063	strong		0.517	OR52R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142183.1	NM_001005177	
PTGER1	5731	hgsc.bcm.edu	37	19	14583582	14583582	+	Silent	SNP	C	C	T	rs11668633	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:14583582C>T	ENST00000292513.3	-	3	1116	c.999G>A	c.(997-999)ctG>ctA	p.L333L		NM_000955.2	NP_000946.2	P34995	PE2R1_HUMAN	prostaglandin E receptor 1 (subtype EP1), 42kDa	333					G-protein coupled receptor signaling pathway (GO:0007186)|response to lipopolysaccharide (GO:0032496)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	prostaglandin E receptor activity (GO:0004957)									Alprostadil(DB00770)|Bimatoprost(DB00905)|Bupivacaine(DB00297)|Carboprost Tromethamine(DB00429)|Dinoprostone(DB00917)|Iloprost(DB01088)	CGGCCAGGAACAGTGGCCGCT	0.677													C|||	557	0.111222	0.0401	0.1527	5008	,	,		11945	0.0089		0.2495	False		,,,				2504	0.1411				p.L333L		Atlas-SNP	.											PTGER1,NS,carcinoma,0,1	PTGER1	5	1	0			c.G999A						scavenged	.	C		324,4038		17,290,1874	20.0	18.0	19.0		999	-2.9	0.3	19	dbSNP_120	19	2357,6209		353,1651,2279	no	coding-synonymous	PTGER1	NM_000955.2		370,1941,4153	TT,TC,CC		27.5158,7.4278,20.7379		333/403	14583582	2681,10247	2181	4283	6464	SO:0001819	synonymous_variant	5731	exon3			CAGGAACAGTGGC		CCDS12309.1	19p13.1	2012-08-08	2002-08-29		ENSG00000160951	ENSG00000160951		"""GPCR / Class A : Prostanoid receptors"""	9593	protein-coding gene	gene with protein product		176802	"""prostaglandin E receptor 1 (subtype EP1), 42kD"""			8253813	Standard	NM_000955		Approved	EP1	uc002mys.3	P34995	OTTHUMG00000039610	ENST00000292513.3:c.999G>A	19.37:g.14583582C>T		Somatic	36	1	0.0277778		WXS	Illumina HiSeq	Phase_I	37	20	0.540541	NM_000955	Q5U5U4|Q86UH3|Q86VB5|Q8NHB2	Silent	SNP	ENST00000292513.3	37	CCDS12309.1																																																																																			C|0.862;T|0.138	0.138	strong		0.677	PTGER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095509.1		
HHIPL2	79802	hgsc.bcm.edu	37	1	222713631	222713631	+	Missense_Mutation	SNP	G	G	C	rs3748666	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:222713631G>C	ENST00000343410.6	-	4	1229	c.1171C>G	c.(1171-1173)Cat>Gat	p.H391D		NM_024746.3	NP_079022.2	Q6UWX4	HIPL2_HUMAN	HHIP-like 2	391			H -> D (in dbSNP:rs3748666).		carbohydrate metabolic process (GO:0005975)	extracellular region (GO:0005576)	oxidoreductase activity, acting on the CH-OH group of donors, quinone or similar compound as acceptor (GO:0016901)|quinone binding (GO:0048038)			NS(2)|endometrium(8)|kidney(4)|large_intestine(7)|lung(28)|ovary(1)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	59				GBM - Glioblastoma multiforme(131;0.0185)		CGCTTGCCATGTGAGCCTGCC	0.527													C|||	1881	0.375599	0.3434	0.5058	5008	,	,		17707	0.5089		0.2604	False		,,,				2504	0.3078				p.H391D		Atlas-SNP	.											.	HHIPL2	122	.	0			c.C1171G						PASS	.	C	ASP/HIS	1448,2958	681.8+/-404.0	222,1004,977	70.0	66.0	68.0		1171	1.0	0.0	1	dbSNP_107	68	2505,6095	694.4+/-404.7	365,1775,2160	yes	missense	HHIPL2	NM_024746.3	81	587,2779,3137	CC,CG,GG		29.1279,32.8643,30.3937	benign	391/725	222713631	3953,9053	2203	4300	6503	SO:0001583	missense	79802	exon4			TGCCATGTGAGCC	BC007638	CCDS1530.2	1q41	2008-02-05	2008-01-16	2008-01-16	ENSG00000143512	ENSG00000143512			25842	protein-coding gene	gene with protein product			"""KIAA1822-like"""	KIAA1822L		12975309	Standard	NM_024746		Approved	FLJ13840	uc001hnh.1	Q6UWX4	OTTHUMG00000037545	ENST00000343410.6:c.1171C>G	1.37:g.222713631G>C	ENSP00000342118:p.His391Asp	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	88	30	0.340909	NM_024746	Q6GU65|Q96BT4|Q96BU5|Q9H8A0	Missense_Mutation	SNP	ENST00000343410.6	37	CCDS1530.2	822	0.37637362637362637	177	0.3597560975609756	151	0.4171270718232044	296	0.5174825174825175	198	0.2612137203166227	C	0	-2.657277	0.00108	0.328643	0.291279	ENSG00000143512	ENST00000343410	T	0.11169	2.8	4.43	1.02	0.19986	Soluble quinoprotein glucose/sorbosone dehydrogenase (1);Six-bladed beta-propeller, TolB-like (1);	1.441690	0.04055	N	0.305409	T	0.00012	0.0000	N	0.00116	-2.08	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.47471	-0.9115	9	0.05620	T	0.96	0.189	3.6679	0.08262	0.2757:0.379:0.2683:0.077	rs3748666	391	Q6UWX4	HIPL2_HUMAN	D	391	ENSP00000342118:H391D	ENSP00000342118:H391D	H	-	1	0	HHIPL2	220780254	0.000000	0.05858	0.000000	0.03702	0.194000	0.23727	0.545000	0.23268	0.046000	0.15833	-0.647000	0.03941	CAT	G|0.678;C|0.322	0.322	strong		0.527	HHIPL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091499.2	NM_024746	
CNBD2	140894	hgsc.bcm.edu	37	20	34560609	34560609	+	Missense_Mutation	SNP	G	G	A	rs17347958	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:34560609G>A	ENST00000373973.3	+	2	283	c.110G>A	c.(109-111)cGc>cAc	p.R37H	CNBD2_ENST00000349339.1_Missense_Mutation_p.R37H|CNBD2_ENST00000538900.1_Missense_Mutation_p.R37H			Q96M20	CNBD2_HUMAN	cyclic nucleotide binding domain containing 2	37			R -> H (in dbSNP:rs17347958).														AAAATGTTCCGCCAAGGCCTC	0.463													G|||	253	0.0505192	0.0015	0.0231	5008	,	,		22174	0.002		0.0467	False		,,,				2504	0.1902				p.R37H		Atlas-SNP	.											.	.	.	.	0			c.G110A						PASS	.	G	HIS/ARG,HIS/ARG	40,4366	43.8+/-77.6	0,40,2163	170.0	156.0	161.0		110,110	5.9	1.0	20	dbSNP_123	161	420,8180	130.5+/-188.4	12,396,3892	yes	missense,missense	C20orf152	NM_001207076.1,NM_080834.2	29,29	12,436,6055	AA,AG,GG		4.8837,0.9079,3.5368	probably-damaging,probably-damaging	37/424,37/573	34560609	460,12546	2203	4300	6503	SO:0001583	missense	140894	exon2			TGTTCCGCCAAGG	AL359828	CCDS13270.1, CCDS56189.1	20q11.23	2012-11-15	2012-11-15	2012-11-15	ENSG00000149646	ENSG00000149646			16145	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 152"", ""cyclic nucleotide (cNMP) binding domain containing 1"""	C20orf152, CNMPD1		11780052	Standard	NM_080834		Approved	dJ954P9.1	uc002xer.1	Q96M20	OTTHUMG00000032371	ENST00000373973.3:c.110G>A	20.37:g.34560609G>A	ENSP00000363084:p.Arg37His	Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	140	73	0.521429	NM_080834	Q14C79|Q5JWY7|Q5T3S1|Q9BR36|Q9BWY5	Missense_Mutation	SNP	ENST00000373973.3	37		50	0.022893772893772892	0	0.0	10	0.027624309392265192	1	0.0017482517482517483	39	0.051451187335092345	G	28.4	4.914985	0.92178	0.009079	0.048837	ENSG00000149646	ENST00000373973;ENST00000349339;ENST00000538900	T;T;T	0.14391	2.51;2.51;2.53	5.9	5.9	0.94986	.	0.000000	0.64402	D	0.000009	T	0.07593	0.0191	M	0.66939	2.045	0.39928	D	0.97424	D;D	0.89917	1.0;1.0	D;D	0.76071	0.971;0.987	T	0.00142	-1.1997	10	0.87932	D	0	-18.62	15.779	0.78246	0.0:0.0:1.0:0.0	rs17347958;rs52836568;rs17347958	37;37	Q96M20;Q96M20-2	CT152_HUMAN;.	H	37	ENSP00000363084:R37H;ENSP00000340954:R37H;ENSP00000442729:R37H	ENSP00000340954:R37H	R	+	2	0	C20orf152	34024023	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	4.788000	0.62439	2.788000	0.95919	0.650000	0.86243	CGC	G|0.966;A|0.034	0.034	strong		0.463	CNBD2-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000078960.2	NM_080834	
TPTE	7179	hgsc.bcm.edu	37	21	10942927	10942927	+	Silent	SNP	T	T	C	rs113444703|rs386816290|rs3047743|rs558478158		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:10942927T>C	ENST00000361285.4	-	12	989	c.660A>G	c.(658-660)agA>agG	p.R220R	TPTE_ENST00000415664.2_5'UTR|TPTE_ENST00000298232.7_Silent_p.R202R|TPTE_ENST00000342420.5_Silent_p.R182R	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)		TTACCCGCCTTCTTATCAGCT	0.323																																					p.R220R		Atlas-SNP	.											TPTE_ENST00000361285,NS,carcinoma,-2,2	TPTE	513	2	0			c.A660G						scavenged	.						91.0	82.0	85.0					21																	10942927		2203	4299	6502	SO:0001819	synonymous_variant	7179	exon12			CCGCCTTCTTATC	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.660A>G	21.37:g.10942927T>C		Somatic	340	0	0		WXS	Illumina HiSeq	Phase_I	250	5	0.02	NM_199261	B2RAP7|C9J6D6|C9JKK8|Q6XPS4|Q6XPS5|Q71JA8|Q8NCS8	Silent	SNP	ENST00000361285.4	37	CCDS13560.2																																																																																			.	.	none		0.323	TPTE-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000157413.1		
ZNF426	79088	hgsc.bcm.edu	37	19	9646898	9646898	+	Missense_Mutation	SNP	G	G	A	rs2042200	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:9646898G>A	ENST00000535489.1	-	1	347	c.11C>T	c.(10-12)gCt>gTt	p.A4V	ZNF426_ENST00000253115.2_Missense_Mutation_p.A4V|ZNF426_ENST00000593003.1_5'UTR|ZNF426_ENST00000589289.1_Missense_Mutation_p.A4V			Q9BUY5	ZN426_HUMAN	zinc finger protein 426	4			A -> V (in dbSNP:rs2042200).		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(7)|lung(3)|ovary(1)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	20						GGACAAATCAGCAGCTGCCAT	0.468													A|||	1038	0.207268	0.4478	0.1571	5008	,	,		21447	0.0466		0.0815	False		,,,				2504	0.2127				p.A4V		Atlas-SNP	.											.	ZNF426	56	.	0			c.C11T						PASS	.	A	VAL/ALA	1579,2827	667.0+/-401.8	285,1009,909	150.0	119.0	129.0		11	-0.1	0.0	19	dbSNP_94	129	742,7858	785.5+/-407.6	30,682,3588	yes	missense	ZNF426	NM_024106.1	64	315,1691,4497	AA,AG,GG		8.6279,35.8375,17.8456	benign	4/555	9646898	2321,10685	2203	4300	6503	SO:0001583	missense	79088	exon3			AAATCAGCAGCTG	AK095759	CCDS12215.1, CCDS74279.1	19p13.2	2013-01-08				ENSG00000130818		"""Zinc fingers, C2H2-type"", ""-"""	20725	protein-coding gene	gene with protein product							Standard	NM_024106		Approved	MGC2663	uc002mlq.3	Q9BUY5		ENST00000535489.1:c.11C>T	19.37:g.9646898G>A	ENSP00000439017:p.Ala4Val	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	59	26	0.440678	NM_024106	B3KTL2	Missense_Mutation	SNP	ENST00000535489.1	37	CCDS12215.1	348	0.15934065934065933	218	0.44308943089430897	54	0.14917127071823205	18	0.03146853146853147	58	0.07651715039577836	A	0.007	-1.992040	0.00439	0.358375	0.086279	ENSG00000130818	ENST00000253115;ENST00000535489	T;T	0.04917	3.53;3.53	1.14	-0.0831	0.13695	.	.	.	.	.	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	0.42982	-0.9419	8	0.05620	T	0.96	.	1.4751	0.02424	0.4546:0.0:0.233:0.3124	rs2042200;rs57811283;rs2042200	4	Q9BUY5	ZN426_HUMAN	V	4	ENSP00000253115:A4V;ENSP00000439017:A4V	ENSP00000253115:A4V	A	-	2	0	ZNF426	9507898	0.000000	0.05858	0.000000	0.03702	0.118000	0.20060	0.021000	0.13489	-0.654000	0.05394	-0.817000	0.03123	GCT	G|0.820;A|0.180	0.180	strong		0.468	ZNF426-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449905.1	NM_024106	
SEMA3A	10371	hgsc.bcm.edu	37	7	83634713	83634713	+	Silent	SNP	A	A	G	rs7804122	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:83634713A>G	ENST00000265362.4	-	11	1616	c.1302T>C	c.(1300-1302)atT>atC	p.I434I	SEMA3A_ENST00000436949.1_Silent_p.I434I	NM_006080.2	NP_006071.1	Q14563	SEM3A_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3A	434	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				apoptotic process (GO:0006915)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|axonogenesis involved in innervation (GO:0060385)|branchiomotor neuron axon guidance (GO:0021785)|dendrite morphogenesis (GO:0048813)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|facial nerve structural organization (GO:0021612)|gonadotrophin-releasing hormone neuronal migration to the hypothalamus (GO:0021828)|negative regulation of axon extension involved in axon guidance (GO:0048843)|negative regulation of epithelial cell migration (GO:0010633)|nerve development (GO:0021675)|neural crest cell migration involved in autonomic nervous system development (GO:1901166)|neural crest cell migration involved in sympathetic nervous system development (GO:1903045)|neuron migration (GO:0001764)|olfactory bulb development (GO:0021772)|positive regulation of male gonad development (GO:2000020)|positive regulation of neuron migration (GO:2001224)|regulation of axon extension involved in axon guidance (GO:0048841)|regulation of heart rate (GO:0002027)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|semaphorin-plexin signaling pathway involved in neuron projection guidance (GO:1902285)|sensory system development (GO:0048880)|sympathetic ganglion development (GO:0061549)|sympathetic nervous system development (GO:0048485)|sympathetic neuron projection extension (GO:0097490)|sympathetic neuron projection guidance (GO:0097491)|trigeminal nerve structural organization (GO:0021637)	axon (GO:0030424)|dendrite (GO:0030425)|extracellular region (GO:0005576)|membrane (GO:0016020)	chemorepellent activity (GO:0045499)|neuropilin binding (GO:0038191)|receptor activity (GO:0004872)			breast(3)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|liver(1)|lung(22)|ovary(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	53						GGTCTACGACAATTTGTGTAA	0.368													A|||	1128	0.22524	0.2678	0.1729	5008	,	,		15936	0.1548		0.2058	False		,,,				2504	0.2975				p.I434I		Atlas-SNP	.											SEMA3A,colon,carcinoma,0,1	SEMA3A	121	1	0			c.T1302C						PASS	.	A		1158,3248	408.4+/-334.6	161,836,1206	195.0	175.0	182.0		1302	-0.1	1.0	7	dbSNP_116	182	1894,6706	332.4+/-320.1	221,1452,2627	no	coding-synonymous	SEMA3A	NM_006080.2		382,2288,3833	GG,GA,AA		22.0233,26.2823,23.4661		434/772	83634713	3052,9954	2203	4300	6503	SO:0001819	synonymous_variant	10371	exon11			TACGACAATTTGT	L26081	CCDS5599.1	7p12.1	2013-01-11			ENSG00000075213	ENSG00000075213		"""Semaphorins"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	10723	protein-coding gene	gene with protein product	"""sema III"""	603961		SEMAD		8269517, 7748561	Standard	NM_006080		Approved	SEMA1, SemD, coll-1, Hsema-I	uc003uhz.3	Q14563	OTTHUMG00000023443	ENST00000265362.4:c.1302T>C	7.37:g.83634713A>G		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	133	56	0.421053	NM_006080		Silent	SNP	ENST00000265362.4	37	CCDS5599.1																																																																																			A|0.771;G|0.229	0.229	strong		0.368	SEMA3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253355.2	NM_006080	
PLEKHG4B	153478	hgsc.bcm.edu	37	5	163300	163300	+	Missense_Mutation	SNP	C	C	T	rs138837556	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:163300C>T	ENST00000283426.6	+	11	2095	c.2045C>T	c.(2044-2046)tCc>tTc	p.S682F		NM_052909.3	NP_443141.3	Q96PX9	PKH4B_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 4B	682							Rho guanyl-nucleotide exchange factor activity (GO:0005089)			endometrium(1)|large_intestine(2)|lung(2)|prostate(3)|skin(3)	11			all cancers(22;0.0253)|Lung(60;0.113)	Kidney(1;0.119)		GACCCACTGTCCCTCCTCAGG	0.706													C|||	2	0.000399361	0.0	0.0	5008	,	,		14300	0.0		0.0	False		,,,				2504	0.002				p.S682F		Atlas-SNP	.											.	PLEKHG4B	167	.	0			c.C2045T						PASS	.	C	PHE/SER	2,4392		0,2,2195	14.0	18.0	17.0		2045	2.4	0.0	5	dbSNP_134	17	10,8576		0,10,4283	no	missense	PLEKHG4B	NM_052909.3	155	0,12,6478	TT,TC,CC		0.1165,0.0455,0.0924	possibly-damaging	682/1272	163300	12,12968	2197	4293	6490	SO:0001583	missense	153478	exon11			CACTGTCCCTCCT	BC008352	CCDS34124.1	5p15.33	2013-01-11			ENSG00000153404	ENSG00000153404		"""Pleckstrin homology (PH) domain containing"""	29399	protein-coding gene	gene with protein product						11572484	Standard	NM_052909		Approved	KIAA1909	uc003jak.2	Q96PX9	OTTHUMG00000161570	ENST00000283426.6:c.2045C>T	5.37:g.163300C>T	ENSP00000283426:p.Ser682Phe	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	96	53	0.552083	NM_052909		Missense_Mutation	SNP	ENST00000283426.6	37	CCDS34124.1	.	.	.	.	.	.	.	.	.	.	C	11.06	1.529140	0.27387	4.55E-4	0.001165	ENSG00000153404	ENST00000283426	T	0.34275	1.37	2.43	2.43	0.29744	.	.	.	.	.	T	0.33089	0.0851	N	0.19112	0.55	0.09310	N	1	D	0.61080	0.989	P	0.53912	0.737	T	0.09314	-1.0680	9	0.54805	T	0.06	.	8.1621	0.31204	0.0:1.0:0.0:0.0	.	682	Q96PX9	PKH4B_HUMAN	F	682	ENSP00000283426:S682F	ENSP00000283426:S682F	S	+	2	0	PLEKHG4B	216300	0.002000	0.14202	0.001000	0.08648	0.006000	0.05464	1.008000	0.29872	0.849000	0.35215	0.460000	0.39030	TCC	C|0.999;T|0.001	0.001	strong		0.706	PLEKHG4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365359.1	NM_052909	
DHX34	9704	hgsc.bcm.edu	37	19	47878858	47878858	+	Missense_Mutation	SNP	C	C	T	rs61751860	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:47878858C>T	ENST00000328771.4	+	10	2549	c.2200C>T	c.(2200-2202)Cgc>Tgc	p.R734C		NM_014681.5	NP_055496.2	Q14147	DHX34_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 34	734					negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:2000623)|nuclear-transcribed mRNA catabolic process (GO:0000956)	membrane (GO:0016020)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)	p.R734C(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(8)|ovary(5)|prostate(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	36		all_cancers(25;1.65e-09)|all_epithelial(76;9.95e-08)|all_lung(116;7.27e-07)|Lung NSC(112;1.6e-06)|Ovarian(192;0.0139)|all_neural(266;0.026)|Breast(70;0.0503)		all cancers(93;7.16e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.000489)|GBM - Glioblastoma multiforme(486;0.00413)|Epithelial(262;0.0132)		GGGCGCGGGGCGCAGGCGCAA	0.736													C|||	437	0.0872604	0.0703	0.1037	5008	,	,		14605	0.0069		0.1451	False		,,,				2504	0.1217				p.R734C		Atlas-SNP	.											DHX34,NS,carcinoma,0,1	DHX34	98	1	1	Substitution - Missense(1)	prostate(1)	c.C2200T						PASS	.	C	CYS/ARG	305,3761		17,271,1745	5.0	6.0	5.0		2200	3.8	0.8	19	dbSNP_129	5	1045,6847		59,927,2960	no	missense	DHX34	NM_014681.5	180	76,1198,4705	TT,TC,CC		13.2413,7.5012,11.2895	probably-damaging	734/1144	47878858	1350,10608	2033	3946	5979	SO:0001583	missense	9704	exon10			GCGGGGCGCAGGC	D50924	CCDS12700.1	19q13.3	2003-06-13	2003-06-13	2003-06-13	ENSG00000134815	ENSG00000134815		"""DEAH-boxes"""	16719	protein-coding gene	gene with protein product		615475	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 34"""	DDX34		10708517, 8590280	Standard	NM_014681		Approved	KIAA0134	uc010xyn.2	Q14147	OTTHUMG00000149959	ENST00000328771.4:c.2200C>T	19.37:g.47878858C>T	ENSP00000331907:p.Arg734Cys	Somatic	3	0	0		WXS	Illumina HiSeq	Phase_I	10	9	0.9	NM_014681	B4DMY8	Missense_Mutation	SNP	ENST00000328771.4	37	CCDS12700.1	207	0.09478021978021978	49	0.09959349593495935	43	0.11878453038674033	6	0.01048951048951049	109	0.1437994722955145	C	17.50	3.405316	0.62288	0.075012	0.132413	ENSG00000134815	ENST00000328771	T	0.03358	3.96	4.84	3.78	0.43462	Domain of unknown function DUF1605 (1);	0.220976	0.31772	N	0.007088	T	0.00109	0.0003	L	0.49571	1.57	0.20307	P	0.9999100385	D	0.89917	1.0	D	0.71414	0.973	T	0.15150	-1.0447	9	0.87932	D	0	-25.7329	13.9845	0.64326	0.0:0.8468:0.1532:0.0	rs61751860	734	Q14147	DHX34_HUMAN	C	734	ENSP00000331907:R734C	ENSP00000331907:R734C	R	+	1	0	DHX34	52570657	0.811000	0.29063	0.779000	0.31741	0.581000	0.36288	2.044000	0.41241	1.240000	0.43803	0.655000	0.94253	CGC	C|0.904;T|0.096	0.096	strong		0.736	DHX34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314313.3	NM_014681	
NR4A3	8013	hgsc.bcm.edu	37	9	102595069	102595069	+	Silent	SNP	G	G	A	rs41274654	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:102595069G>A	ENST00000395097.2	+	4	1779	c.1050G>A	c.(1048-1050)caG>caA	p.Q350Q	NR4A3_ENST00000338488.4_Silent_p.Q350Q|NR4A3_ENST00000330847.1_Silent_p.Q361Q	NM_006981.3|NM_173200.2	NP_008912.2|NP_775292.1	Q92570	NR4A3_HUMAN	nuclear receptor subfamily 4, group A, member 3	350					gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|steroid hormone receptor activity (GO:0003707)|thyroid hormone receptor activity (GO:0004887)|zinc ion binding (GO:0008270)		TCF12/NR4A3(2)|TAF15/NR4A3(33)|EWSR1/NR4A3(146)|TFG/NR4A3(2)				Acute lymphoblastic leukemia(62;0.0559)|all_hematologic(171;0.189)				GTCGATTTCAGAAGTGTCTCA	0.363			T	EWSR1	extraskeletal myxoid chondrosarcoma								G|||	399	0.0796725	0.0189	0.1239	5008	,	,		17709	0.0625		0.1441	False		,,,				2504	0.0818				p.Q361Q		Atlas-SNP	.		Dom	yes		9	9q22	8013	"""nuclear receptor subfamily 4, group A, member 3 (NOR1)"""		M	.	NR4A3	80	.	0			c.G1083A						PASS	.	G	,,	182,4224	116.3+/-154.2	3,176,2024	138.0	133.0	135.0		1050,1050,1083	2.8	1.0	9	dbSNP_127	135	1217,7383	246.5+/-274.9	66,1085,3149	no	coding-synonymous,coding-synonymous,coding-synonymous	NR4A3	NM_006981.3,NM_173199.2,NM_173200.2	,,	69,1261,5173	AA,AG,GG		14.1512,4.1307,10.7566	,,	350/627,350/444,361/638	102595069	1399,11607	2203	4300	6503	SO:0001819	synonymous_variant	8013	exon5			ATTTCAGAAGTGT	U12767	CCDS6742.1, CCDS6743.1, CCDS6744.1	9q22	2013-01-16			ENSG00000119508	ENSG00000119508		"""Nuclear hormone receptors"""	7982	protein-coding gene	gene with protein product		600542				8614405	Standard	NM_006981		Approved	CSMF, CHN, NOR1, MINOR	uc004baf.1	Q92570	OTTHUMG00000021030	ENST00000395097.2:c.1050G>A	9.37:g.102595069G>A		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	99	43	0.434343	NM_173200	A2A3I7|Q12935|Q14979|Q16420|Q4VXA8|Q4VXA9|Q9UEK2|Q9UEK3	Silent	SNP	ENST00000395097.2	37	CCDS6743.1																																																																																			G|0.892;A|0.108	0.108	strong		0.363	NR4A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055482.1		
OR5H2	79310	hgsc.bcm.edu	37	3	98001777	98001777	+	Missense_Mutation	SNP	G	G	C	rs72487753	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:98001777G>C	ENST00000355273.2	+	1	46	c.46G>C	c.(46-48)Gag>Cag	p.E16Q	RP11-325B23.2_ENST00000508616.1_lincRNA	NM_001005482.1	NP_001005482.1	Q8NGV7	OR5H2_HUMAN	olfactory receptor, family 5, subfamily H, member 2	16						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						ATTGCTGACAGAGTTTGTTCT	0.408													g|||	820	0.163738	0.1641	0.1715	5008	,	,		19493	0.2619		0.1004	False		,,,				2504	0.1217				p.E16Q		Atlas-SNP	.											.	OR5H2	63	.	0			c.G46C						PASS	.	T	GLN/GLU	664,3742	282.2+/-276.4	50,564,1589	231.0	218.0	222.0		46	2.3	0.8	3	dbSNP_130	222	1036,7564	219.5+/-257.5	67,902,3331	yes	missense	OR5H2	NM_001005482.1	29	117,1466,4920	CC,CG,GG		12.0465,15.0704,13.0709	benign	16/315	98001777	1700,11306	2203	4300	6503	SO:0001583	missense	79310	exon1			CTGACAGAGTTTG		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.46G>C	3.37:g.98001777G>C	ENSP00000347418:p.Glu16Gln	Somatic	211	0	0		WXS	Illumina HiSeq	Phase_I	156	84	0.538462	NM_001005482	Q6IF87	Missense_Mutation	SNP	ENST00000355273.2	37	CCDS33801.1	346	0.15842490842490842	75	0.1524390243902439	71	0.19613259668508287	126	0.2202797202797203	74	0.09762532981530343	g	8.565	0.878592	0.17395	0.150704	0.120465	ENSG00000197938	ENST00000355273	T	0.01126	5.3	3.2	2.32	0.28847	.	0.571542	0.14429	U	0.320122	T	0.00012	0.0000	M	0.80982	2.52	0.52501	P	4.499999999996174E-5	B	0.24043	0.096	B	0.20767	0.031	T	0.22661	-1.0210	9	0.59425	D	0.04	.	9.63	0.39774	0.0:0.0:0.789:0.211	.	16	Q8NGV7	OR5H2_HUMAN	Q	16	ENSP00000347418:E16Q	ENSP00000347418:E16Q	E	+	1	0	OR5H2	99484467	0.005000	0.15991	0.815000	0.32552	0.699000	0.40488	0.774000	0.26675	0.686000	0.31488	-0.249000	0.11873	GAG	G|0.858;C|0.142	0.142	strong		0.408	OR5H2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359113.2		
FN1	2335	hgsc.bcm.edu	37	2	216242917	216242917	+	Silent	SNP	T	T	A	rs1132741	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:216242917T>A	ENST00000359671.1	-	34	5683	c.5418A>T	c.(5416-5418)ggA>ggT	p.G1806G	FN1_ENST00000357867.4_Silent_p.G1716G|FN1_ENST00000446046.1_Silent_p.G1806G|FN1_ENST00000354785.4_Silent_p.G1897G|FN1_ENST00000490833.1_5'Flank|FN1_ENST00000323926.6_Silent_p.G1897G|FN1_ENST00000432072.2_Silent_p.G1807G|FN1_ENST00000336916.4_Silent_p.G1806G|FN1_ENST00000345488.5_Silent_p.G1806G|FN1_ENST00000357009.2_Silent_p.G1806G|FN1_ENST00000421182.1_Silent_p.G1716G|FN1_ENST00000356005.4_Silent_p.G1716G|FN1_ENST00000346544.3_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	46	0	0		WXS	Illumina HiSeq	Phase_I	41	14	0.341463	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	
HTT	3064	hgsc.bcm.edu	37	4	3215835	3215835	+	Missense_Mutation	SNP	T	T	C	rs362331	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:3215835T>C	ENST00000355072.5	+	50	7070	c.6925T>C	c.(6925-6927)Tac>Cac	p.Y2309H		NM_002111.6	NP_002102	P42858	HD_HUMAN	huntingtin	2309			Y -> H (in dbSNP:rs362331).		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)		CTCCCTCATCTACTGTGTGCA	0.582													C|||	2210	0.441294	0.5862	0.4294	5008	,	,		19331	0.3859		0.4334	False		,,,				2504	0.319				p.Y2309H		Atlas-SNP	.											HTT,NS,carcinoma,0,1	HTT	221	1	0			c.T6925C						PASS	.	C	HIS/TYR	2355,1813		681,993,410	34.0	38.0	36.0		6925	5.7	1.0	4	dbSNP_79	36	3533,4873		764,2005,1434	yes	missense	HTT	NM_002111.6	83	1445,2998,1844	CC,CT,TT		42.0295,43.4981,46.8268	benign	2309/3143	3215835	5888,6686	2084	4203	6287	SO:0001583	missense	3064	exon50			CTCATCTACTGTG	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.6925T>C	4.37:g.3215835T>C	ENSP00000347184:p.Tyr2309His	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	98	98	1	NM_002111	Q9UQB7	Missense_Mutation	SNP	ENST00000355072.5	37	CCDS43206.1	995	0.4555860805860806	281	0.5711382113821138	161	0.4447513812154696	220	0.38461538461538464	333	0.4393139841688654	C	9.562	1.118641	0.20877	0.565019	0.420295	ENSG00000197386	ENST00000355072	T	0.04603	3.59	5.7	5.7	0.88788	.	0.117131	0.64402	N	0.000015	T	0.00012	0.0000	N	0.00583	-1.355	0.47065	P	6.969999999999477E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.21518	-1.0243	9	0.13853	T	0.58	.	8.2136	0.31499	0.2523:0.6699:0.0:0.0778	rs362331;rs878244;rs2229983;rs3821970;rs17793687;rs52791365;rs58994081;rs362331	2309	P42858	HD_HUMAN	H	2309	ENSP00000347184:Y2309H	ENSP00000347184:Y2309H	Y	+	1	0	HTT	3185633	1.000000	0.71417	1.000000	0.80357	0.916000	0.54674	3.175000	0.50855	1.427000	0.47276	-0.119000	0.15052	TAC	C|0.453;N|0.000	0.453	strong		0.582	HTT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358234.2	NM_002111	
HOXC11	3227	hgsc.bcm.edu	37	12	54367690	54367690	+	Missense_Mutation	SNP	C	C	T	rs12427129	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:54367690C>T	ENST00000546378.1	+	1	781	c.665C>T	c.(664-666)gCc>gTc	p.A222V	HOXC11_ENST00000243082.4_Missense_Mutation_p.A222V|HOTAIR_ENST00000455246.1_RNA|HOTAIR_ENST00000424518.1_RNA			O43248	HXC11_HUMAN	homeobox C11	222			A -> V (in dbSNP:rs12427129).		anterior/posterior pattern specification (GO:0009952)|embryonic digit morphogenesis (GO:0042733)|embryonic skeletal joint morphogenesis (GO:0060272)|endoderm development (GO:0007492)|metanephros development (GO:0001656)|organ induction (GO:0001759)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|proximal/distal pattern formation (GO:0009954)	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)			large_intestine(1)|ovary(1)	2						AAGGAGCCGGCCAAAGGAGCC	0.716			T	NUP98	AML								C|||	328	0.0654952	0.0061	0.1153	5008	,	,		9813	0.0833		0.0696	False		,,,				2504	0.0879				p.A222V		Atlas-SNP	.		Dom	yes		12	12q13.3	3227	homeo box C11		L	.	HOXC11	32	.	0			c.C665T						PASS	.	C	VAL/ALA	39,3043		0,39,1502	2.0	3.0	3.0		665	2.2	1.0	12	dbSNP_120	3	363,5283		3,357,2463	yes	missense	HOXC11	NM_014212.3	64	3,396,3965	TT,TC,CC		6.4293,1.2654,4.6059	benign	222/305	54367690	402,8326	1541	2823	4364	SO:0001583	missense	3227	exon1			AGCCGGCCAAAGG		CCDS8867.1	12q13.13	2011-06-20	2005-12-22		ENSG00000123388	ENSG00000123388		"""Homeoboxes / ANTP class : HOXL subclass"""	5123	protein-coding gene	gene with protein product		605559	"""homeo box C11"""	HOX3H		1973146, 1358459	Standard	NM_014212		Approved		uc001sem.3	O43248	OTTHUMG00000160011	ENST00000546378.1:c.665C>T	12.37:g.54367690C>T	ENSP00000446680:p.Ala222Val	Somatic	16	0	0		WXS	Illumina HiSeq	Phase_I	17	10	0.588235	NM_014212	A8K7D1|Q96DH2	Missense_Mutation	SNP	ENST00000546378.1	37	CCDS8867.1	152	0.0695970695970696	5	0.01016260162601626	46	0.1270718232044199	47	0.08216783216783216	54	0.0712401055408971	C	11.96	1.794544	0.31777	0.012654	0.064293	ENSG00000123388	ENST00000546378;ENST00000243082	D;T	0.95588	-3.75;1.83	4.22	2.24	0.28232	Homeodomain-related (1);Homeodomain-like (1);	0.306670	0.38111	N	0.001816	T	0.07143	0.0181	N	0.08118	0	0.37475	P	0.08421400000000001	B	0.17465	0.022	B	0.20184	0.028	T	0.64820	-0.6317	9	0.54805	T	0.06	.	7.8855	0.29648	0.0:0.6473:0.2562:0.0965	rs12427129	222	O43248	HXC11_HUMAN	V	222	ENSP00000446680:A222V;ENSP00000243082:A222V	ENSP00000243082:A222V	A	+	2	0	HOXC11	52653957	1.000000	0.71417	0.999000	0.59377	0.992000	0.81027	2.208000	0.42797	1.127000	0.42034	0.561000	0.74099	GCC	C|0.931;T|0.069	0.069	strong		0.716	HOXC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358869.2		
NTRK1	4914	hgsc.bcm.edu	37	1	156848946	156848946	+	Missense_Mutation	SNP	G	G	T	rs6339	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:156848946G>T	ENST00000524377.1	+	15	1879	c.1838G>T	c.(1837-1839)gGt>gTt	p.G613V	NTRK1_ENST00000392302.2_Missense_Mutation_p.G577V|NTRK1_ENST00000368196.3_Missense_Mutation_p.G607V|NTRK1_ENST00000358660.3_Missense_Mutation_p.G610V	NM_002529.3	NP_002520.2	P04629	NTRK1_HUMAN	neurotrophic tyrosine kinase, receptor, type 1	613	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		G -> V (in dbSNP:rs6339). {ECO:0000269|PubMed:10330344, ECO:0000269|PubMed:10391209, ECO:0000269|PubMed:10443680, ECO:0000269|PubMed:10861667, ECO:0000269|PubMed:11310631, ECO:0000269|PubMed:17344846}.		activation of adenylate cyclase activity (GO:0007190)|activation of MAPKK activity (GO:0000186)|activation of phospholipase C activity (GO:0007202)|aging (GO:0007568)|axon guidance (GO:0007411)|axonogenesis involved in innervation (GO:0060385)|B cell differentiation (GO:0030183)|cellular response to nerve growth factor stimulus (GO:1990090)|cellular response to nicotine (GO:0071316)|circadian rhythm (GO:0007623)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|detection of temperature stimulus involved in sensory perception of pain (GO:0050965)|developmental programmed cell death (GO:0010623)|learning or memory (GO:0007611)|mechanoreceptor differentiation (GO:0042490)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|olfactory nerve development (GO:0021553)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of angiogenesis (GO:0045766)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of neuron projection development (GO:0010976)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of programmed cell death (GO:0043068)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of Ras protein signal transduction (GO:0046579)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|Ras protein signal transduction (GO:0007265)|response to activity (GO:0014823)|response to axon injury (GO:0048678)|response to drug (GO:0042493)|response to electrical stimulus (GO:0051602)|response to ethanol (GO:0045471)|response to hydrostatic pressure (GO:0051599)|response to nutrient levels (GO:0031667)|response to radiation (GO:0009314)|Sertoli cell development (GO:0060009)|small GTPase mediated signal transduction (GO:0007264)|sympathetic nervous system development (GO:0048485)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	axon (GO:0030424)|cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|dendrite (GO:0030425)|early endosome (GO:0005769)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|nerve growth factor binding (GO:0048406)|nerve growth factor receptor activity (GO:0010465)|neurotrophin binding (GO:0043121)|protein homodimerization activity (GO:0042803)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(3)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(7)|lung(35)|ovary(8)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	74	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)				Amitriptyline(DB00321)|Imatinib(DB00619)|Regorafenib(DB08896)	CTGCTGGCTGGTGGGGAGGAT	0.622			T	"""TPM3, TPR, TFG"""	papillary thyroid					TSP Lung(10;0.080)			G|||	115	0.0229633	0.0015	0.0288	5008	,	,		19599	0.0		0.0378	False		,,,				2504	0.0562				p.G613V		Atlas-SNP	.		Dom	yes		1	1q21-q22	4914	"""neurotrophic tyrosine kinase, receptor, type 1"""		E	.	NTRK1	287	.	0			c.G1838T	GRCh37	CM990978	NTRK1	M	rs6339	PASS	.	G	VAL/GLY,VAL/GLY,VAL/GLY	51,4355	48.9+/-83.8	0,51,2152	27.0	29.0	29.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1730,1820,1838	3.4	1.0	1	dbSNP_52	29	519,8081	141.9+/-198.1	21,477,3802	yes	missense,missense,missense	NTRK1	NM_001007792.1,NM_001012331.1,NM_002529.3	109,109,109	21,528,5954	TT,TG,GG		6.0349,1.1575,4.3826	benign,benign,benign	577/761,607/791,613/797	156848946	570,12436	2203	4300	6503	SO:0001583	missense	4914	exon15			TGGCTGGTGGGGA	Y09028	CCDS1161.1, CCDS30890.1, CCDS30891.1	1q21-q22	2014-09-17			ENSG00000198400	ENSG00000198400	2.7.10.1	"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	8031	protein-coding gene	gene with protein product	"""high affinity nerve growth factor receptor"""	191315				2869410	Standard	NM_001007792		Approved	TRK, TRKA, MTC	uc001fqh.1	P04629	OTTHUMG00000041304	ENST00000524377.1:c.1838G>T	1.37:g.156848946G>T	ENSP00000431418:p.Gly613Val	Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	157	70	0.44586	NM_002529	B2R6T5|B7ZM34|P08119|Q15655|Q15656|Q5D056|Q5VZS2|Q7Z5C3|Q9UIU7	Missense_Mutation	SNP	ENST00000524377.1	37	CCDS1161.1	41	0.018772893772893772	0	0.0	10	0.027624309392265192	0	0.0	31	0.040897097625329816	G	15.68	2.904594	0.52333	0.011575	0.060349	ENSG00000198400	ENST00000392302;ENST00000368196;ENST00000524377;ENST00000358660	D;D;D;D	0.88586	-2.4;-2.4;-2.4;-2.4	4.37	3.44	0.39384	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.663421	0.13970	N	0.350264	T	0.71367	0.3331	L	0.38692	1.165	0.54753	A	0.999986	B;B;B;P	0.36909	0.009;0.127;0.379;0.573	B;B;B;B	0.34590	0.027;0.047;0.129;0.186	T	0.66752	-0.5844	9	0.44086	T	0.13	.	4.9855	0.14187	0.2655:0.0:0.7345:0.0	rs6339;rs17838191;rs6339	610;607;613;577	A8K3Z4;P04629-2;P04629;A6NF12	.;.;NTRK1_HUMAN;.	V	577;607;613;610	ENSP00000376120:G577V;ENSP00000357179:G607V;ENSP00000431418:G613V;ENSP00000351486:G610V	ENSP00000351486:G610V	G	+	2	0	NTRK1	155115570	0.904000	0.30761	0.988000	0.46212	0.919000	0.55068	3.522000	0.53480	2.432000	0.82394	0.561000	0.74099	GGT	G|0.965;T|0.035	0.035	strong		0.622	NTRK1-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000392279.1	NM_002529	
NRAP	4892	hgsc.bcm.edu	37	10	115389366	115389366	+	Missense_Mutation	SNP	G	G	A	rs2286735	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:115389366G>A	ENST00000359988.3	-	19	2265	c.2021C>T	c.(2020-2022)gCc>gTc	p.A674V	NRAP_ENST00000360478.3_Missense_Mutation_p.A639V|NRAP_ENST00000369358.4_Missense_Mutation_p.A682V|NRAP_ENST00000369360.3_Missense_Mutation_p.A647V	NM_001261463.1|NM_198060.3	NP_001248392.1|NP_932326.2			nebulin-related anchoring protein											autonomic_ganglia(1)|breast(2)|central_nervous_system(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(18)|lung(39)|ovary(6)|prostate(3)|skin(1)|stomach(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	95		Colorectal(252;0.0233)|Breast(234;0.188)		Epithelial(162;0.00392)|all cancers(201;0.00569)		GAGCCCATAGGCCTTCTTGGC	0.498													G|||	1376	0.27476	0.1823	0.3948	5008	,	,		20479	0.2817		0.2962	False		,,,				2504	0.2853				p.A674V		Atlas-SNP	.											.	NRAP	208	.	0			c.C2021T						PASS	.	G	VAL/ALA,VAL/ALA	940,3466	354.9+/-312.8	96,748,1359	118.0	100.0	106.0		1916,2021	3.3	1.0	10	dbSNP_100	106	2620,5980	424.4+/-354.6	371,1878,2051	yes	missense,missense	NRAP	NM_006175.3,NM_198060.2	64,64	467,2626,3410	AA,AG,GG		30.4651,21.3345,27.372	benign,benign	639/1696,674/1731	115389366	3560,9446	2203	4300	6503	SO:0001583	missense	4892	exon19			CCATAGGCCTTCT		CCDS7578.1, CCDS7579.1, CCDS73199.1	10q24-q26	2008-08-01			ENSG00000197893	ENSG00000197893			7988	protein-coding gene	gene with protein product		602873				12789664, 10320340	Standard	NM_006175		Approved		uc001lal.4	Q86VF7	OTTHUMG00000019072	ENST00000359988.3:c.2021C>T	10.37:g.115389366G>A	ENSP00000353078:p.Ala674Val	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	93	46	0.494624	NM_001261463		Missense_Mutation	SNP	ENST00000359988.3	37	CCDS7579.1	626	0.2866300366300366	111	0.22560975609756098	132	0.36464088397790057	153	0.2674825174825175	230	0.3034300791556728	G	14.72	2.619352	0.46736	0.213345	0.304651	ENSG00000197893	ENST00000369358;ENST00000369360;ENST00000359988;ENST00000360478	T;T;T;T	0.41758	0.99;0.99;0.99;0.99	5.19	3.31	0.37934	.	0.101608	0.64402	N	0.000002	T	0.00012	0.0000	L	0.53617	1.68	0.25327	P	0.9890645	B;B;B	0.09022	0.002;0.002;0.001	B;B;B	0.18263	0.021;0.015;0.008	T	0.32534	-0.9903	9	0.40728	T	0.16	.	8.5936	0.33701	0.2316:0.0:0.7684:0.0	rs2286735;rs17772920;rs58094688;rs2286735	674;639;674	A0AVL2;Q86VF7-4;Q86VF7	.;.;NRAP_HUMAN	V	682;647;674;639	ENSP00000358365:A682V;ENSP00000358367:A647V;ENSP00000353078:A674V;ENSP00000353666:A639V	ENSP00000353078:A674V	A	-	2	0	NRAP	115379356	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	5.737000	0.68606	1.319000	0.45190	0.561000	0.74099	GCC	G|0.726;N|0.001	.	strong		0.498	NRAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050425.2	NM_006175	
TGM4	7047	hgsc.bcm.edu	37	3	44948479	44948479	+	Missense_Mutation	SNP	C	C	T	rs3749195	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:44948479C>T	ENST00000296125.4	+	10	1182	c.1114C>T	c.(1114-1116)Cgc>Tgc	p.R372C		NM_003241.3	NP_003232.2	P49221	TGM4_HUMAN	transglutaminase 4	372			R -> C (in dbSNP:rs3749195).|R -> H (in dbSNP:rs13326552).		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)	GACCGCCATCCGCAAAGGTGA	0.562													C|||	3378	0.674521	0.671	0.5807	5008	,	,		18727	0.8869		0.4463	False		,,,				2504	0.7618				p.R372C		Atlas-SNP	.											.	TGM4	82	.	0			c.C1114T						PASS	.	C	CYS/ARG	2848,1558	670.1+/-402.3	915,1018,270	109.0	99.0	102.0		1114	2.0	0.0	3	dbSNP_107	102	4076,4524	559.7+/-387.5	947,2182,1171	yes	missense	TGM4	NM_003241.3	180	1862,3200,1441	TT,TC,CC		47.3953,35.3609,46.763	possibly-damaging	372/685	44948479	6924,6082	2203	4300	6503	SO:0001583	missense	7047	exon10			GCCATCCGCAAAG	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.1114C>T	3.37:g.44948479C>T	ENSP00000296125:p.Arg372Cys	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	95	42	0.442105	NM_003241	Q16707|Q96QN4	Missense_Mutation	SNP	ENST00000296125.4	37	CCDS2723.1	1378	0.6309523809523809	320	0.6504065040650406	198	0.5469613259668509	510	0.8916083916083916	350	0.46174142480211083	C	12.00	1.805339	0.31961	0.646391	0.473953	ENSG00000163810	ENST00000296125	T	0.22743	1.94	2.03	2.03	0.26663	.	0.367618	0.14845	U	0.295032	T	0.00012	0.0000	M	0.83312	2.635	0.33547	P	0.404331	D	0.57571	0.98	B	0.43680	0.427	T	0.07009	-1.0795	9	0.87932	D	0	.	9.0882	0.36594	0.4175:0.5825:0.0:0.0	rs3749195;rs17631979;rs59778563;rs3749195	372	P49221	TGM4_HUMAN	C	372	ENSP00000296125:R372C	ENSP00000296125:R372C	R	+	1	0	TGM4	44923483	0.000000	0.05858	0.020000	0.16555	0.517000	0.34286	-0.551000	0.06027	1.039000	0.40074	0.460000	0.39030	CGC	C|0.414;T|0.586	0.586	strong		0.562	TGM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256755.2	NM_003241	
HLA-DPA1	3113	hgsc.bcm.edu	37	6	33036548	33036548	+	Missense_Mutation	SNP	G	G	A	rs56046206	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:33036548G>A	ENST00000419277.1	-	5	791	c.662C>T	c.(661-663)aCg>aTg	p.T221M	HLA-DPA1_ENST00000428995.1_Missense_Mutation_p.T221M|HLA-DPA1_ENST00000463066.1_5'Flank	NM_001242524.1|NM_001242525.1	NP_001229453.1|NP_001229454.1	P20036	DPA1_HUMAN	major histocompatibility complex, class II, DP alpha 1	221	Connecting peptide.		T -> A (in allele DPA1*04:01).		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cellular response to interferon-gamma (GO:0071346)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell proliferation (GO:0042102)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			kidney(5)|large_intestine(1)|lung(6)|prostate(1)|skin(2)	15						CACAGTCTCCGTTGTCTCAGG	0.592													g|||	11	0.00219649	0.0	0.0014	5008	,	,		18464	0.0		0.0099	False		,,,				2504	0.0				p.T221M		Atlas-SNP	.											.	HLA-DPA1	20	.	0			c.C662T						PASS	.	C	MET/THR,MET/THR,MET/THR	6,3012		0,6,1503	93.0	110.0	104.0		662,662,662	-2.6	0.0	6	dbSNP_129	104	45,5373		0,45,2664	yes	missense,missense,missense	HLA-DPA1	NM_001242524.1,NM_001242525.1,NM_033554.3	81,81,81	0,51,4167	AA,AG,GG		0.8306,0.1988,0.6046	benign,benign,benign	221/261,221/261,221/261	33036548	51,8385	1509	2709	4218	SO:0001583	missense	3113	exon4			GTCTCCGTTGTCT	X00457	CCDS4764.1	6p21.3	2013-01-11			ENSG00000231389	ENSG00000231389		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4938	protein-coding gene	gene with protein product		142880		HLA-DP1A		6584734	Standard	NM_033554		Approved		uc003ocs.2	P20036	OTTHUMG00000031058	ENST00000419277.1:c.662C>T	6.37:g.33036548G>A	ENSP00000393566:p.Thr221Met	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	119	42	0.352941	NM_033554	A9YWH7|B9UKH4|O19722|O46883|P01905|P79554|Q2Q060|Q2Q061|Q5EY03|Q5STP1|Q6DQK4|Q9BCQ1|Q9TPX3|Q9XS10	Missense_Mutation	SNP	ENST00000419277.1	37	CCDS4764.1	7	0.003205128205128205	0	0.0	0	0.0	0	0.0	7	0.009234828496042216	g	2.008	-0.427682	0.04701	0.001988	0.008306	ENSG00000231389	ENST00000419277;ENST00000428995;ENST00000448544	T;T	0.01854	4.6;4.6	3.4	-2.64	0.06114	Immunoglobulin-like fold (1);	0.385106	0.23966	U	0.042812	T	0.00637	0.0021	L	0.46947	1.48	0.09310	N	1	B	0.17667	0.023	B	0.21151	0.033	T	0.46386	-0.9195	10	0.56958	D	0.05	.	0.9278	0.01328	0.2378:0.3387:0.2518:0.1716	rs56046206	221	P20036	DPA1_HUMAN	M	221;221;188	ENSP00000393566:T221M;ENSP00000402872:T221M	ENSP00000393566:T221M	T	-	2	0	HLA-DPA1	33144526	0.000000	0.05858	0.021000	0.16686	0.116000	0.19942	-0.064000	0.11636	-0.375000	0.07955	-0.756000	0.03474	ACG	G|0.995;A|0.005	0.005	strong		0.592	HLA-DPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076071.3	NM_033554	
CUL9	23113	hgsc.bcm.edu	37	6	43193877	43193877	+	IGR	SNP	G	G	A	rs7832	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:43193877G>A	ENST00000252050.4	+	0	7780				DNPH1_ENST00000393987.2_Silent_p.V90V|RP3-330M21.5_ENST00000500590.1_RNA|DNPH1_ENST00000230431.6_Silent_p.V90V	NM_015089.2	NP_055904.1	Q8IWT3	CUL9_HUMAN	cullin 9						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						CTTCTGCCACGACCACTGGGA	0.592													G|||	208	0.0415335	0.0023	0.0908	5008	,	,		21379	0.003		0.0706	False		,,,				2504	0.0695				p.V90V		Atlas-SNP	.											C6orf108_ENST00000393987,NS,carcinoma,0,2	.	.	2	0			c.C270T						PASS	.	G	,	85,4303		1,83,2110	30.0	24.0	26.0		270,270	-9.2	0.0	6	dbSNP_52	26	882,7688		43,796,3446	no	coding-synonymous,coding-synonymous	C6orf108	NM_006443.2,NM_199184.1	,	44,879,5556	AA,AG,GG		10.2917,1.9371,7.4626	,	90/175,90/149	43193877	967,11991	2194	4285	6479	SO:0001628	intergenic_variant	10591	exon3			TGCCACGACCACT	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		6.37:g.43193877G>A		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	27	6	0.222222	NM_006443	O75188|Q5TCY3|Q68CP2|Q68D92|Q8N3W9|Q9BU56	Silent	SNP	ENST00000252050.4	37	CCDS4890.1																																																																																			G|0.942;A|0.058	0.058	strong		0.592	CUL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040582.2	NM_015089	
ABCA7	10347	hgsc.bcm.edu	37	19	1042809	1042809	+	Missense_Mutation	SNP	A	A	G	rs3764645	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:1042809A>G	ENST00000263094.6	+	7	794	c.563A>G	c.(562-564)gAg>gGg	p.E188G	ABCA7_ENST00000435683.2_Missense_Mutation_p.E50G|ABCA7_ENST00000433129.1_Missense_Mutation_p.E188G	NM_019112.3	NP_061985.2	Q8IZY2	ABCA7_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 7	188			E -> G (in dbSNP:rs3764645). {ECO:0000269|PubMed:11435699, ECO:0000269|PubMed:12111378}.		apolipoprotein A-I-mediated signaling pathway (GO:0038027)|ATP catabolic process (GO:0006200)|cholesterol efflux (GO:0033344)|high-density lipoprotein particle assembly (GO:0034380)|memory (GO:0007613)|negative regulation of amyloid precursor protein biosynthetic process (GO:0042985)|negative regulation of ATPase activity (GO:0032780)|negative regulation of beta-amyloid formation (GO:1902430)|peptide cross-linking (GO:0018149)|phagocytosis (GO:0006909)|phospholipid efflux (GO:0033700)|phospholipid scrambling (GO:0017121)|positive regulation of ATPase activity (GO:0032781)|positive regulation of beta-amyloid clearance (GO:1900223)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of engulfment of apoptotic cell (GO:1901076)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of phagocytosis (GO:0050766)|positive regulation of phospholipid efflux (GO:1902995)|protein localization to nucleus (GO:0034504)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|ATP-binding cassette (ABC) transporter complex (GO:0043190)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|phagocytic cup (GO:0001891)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	apolipoprotein A-I receptor activity (GO:0034188)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|phospholipid transporter activity (GO:0005548)|transporter activity (GO:0005215)			NS(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(7)|lung(22)|ovary(1)|pancreas(7)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	65		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GAGGCCGCTGAGGACCTGGCC	0.657													A|||	2001	0.399561	0.1657	0.6268	5008	,	,		17314	0.4355		0.4463	False		,,,				2504	0.4693				p.E188G		Atlas-SNP	.											.	ABCA7	174	.	0			c.A563G						PASS	.	A	GLY/GLU	979,3427	364.9+/-317.2	113,753,1337	58.0	57.0	58.0		563	-0.6	0.0	19	dbSNP_107	58	4076,4524	556.1+/-386.8	998,2080,1222	yes	missense	ABCA7	NM_019112.3	98	1111,2833,2559	GG,GA,AA		47.3953,22.2197,38.8667	benign	188/2147	1042809	5055,7951	2203	4300	6503	SO:0001583	missense	10347	exon7			CCGCTGAGGACCT	AF328787	CCDS12055.1	19p13.3	2012-03-14			ENSG00000064687	ENSG00000064687		"""ATP binding cassette transporters / subfamily A"""	37	protein-coding gene	gene with protein product		605414					Standard	NM_019112		Approved	ABCX	uc002lqw.4	Q8IZY2	OTTHUMG00000167547	ENST00000263094.6:c.563A>G	19.37:g.1042809A>G	ENSP00000263094:p.Glu188Gly	Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	51	30	0.588235	NM_019112	Q96S58|Q9BZC4|Q9NR73|Q9UKP8	Missense_Mutation	SNP	ENST00000263094.6	37	CCDS12055.1	901	0.4125457875457875	71	0.1443089430894309	219	0.6049723756906077	269	0.47027972027972026	342	0.45118733509234826	A	7.460	0.644520	0.14451	0.222197	0.473953	ENSG00000064687	ENST00000263094;ENST00000433129	D;D	0.86497	-2.13;-2.13	4.3	-0.62	0.11567	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B	0.32160	0.358;0.244	B;B	0.25140	0.058;0.037	T	0.41106	-0.9527	8	0.17832	T	0.49	.	4.1058	0.10037	0.4862:0.1825:0.3312:0.0	rs3764645	50;188	Q8IZY2-2;Q8IZY2	.;ABCA7_HUMAN	G	188	ENSP00000263094:E188G;ENSP00000414062:E188G	ENSP00000263094:E188G	E	+	2	0	ABCA7	993809	0.000000	0.05858	0.000000	0.03702	0.396000	0.30629	-1.730000	0.01855	-0.436000	0.07254	0.379000	0.24179	GAG	A|0.609;G|0.391	0.391	strong		0.657	ABCA7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000394993.1	NM_019112	
RTP2	344892	hgsc.bcm.edu	37	3	187416666	187416666	+	Missense_Mutation	SNP	C	C	T	rs11927120	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:187416666C>T	ENST00000358241.1	-	2	726	c.298G>A	c.(298-300)Ggc>Agc	p.G100S		NM_001004312.2	NP_001004312.2	Q5QGT7	RTP2_HUMAN	receptor (chemosensory) transporter protein 2	100					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)		CGCGCCGTGCCGCACTCATAG	0.647													C|||	912	0.182109	0.1725	0.1081	5008	,	,		16063	0.1339		0.1958	False		,,,				2504	0.2832				p.G100S		Atlas-SNP	.											RTP2,NS,carcinoma,0,1	RTP2	38	1	0			c.G298A						scavenged	.	C	SER/GLY	708,3694		54,600,1547	25.0	23.0	24.0		298	4.2	1.0	3	dbSNP_120	24	1668,6876		142,1384,2746	no	missense	RTP2	NM_001004312.2	56	196,1984,4293	TT,TC,CC		19.5225,16.0836,18.3532	probably-damaging	100/226	187416666	2376,10570	2201	4272	6473	SO:0001583	missense	344892	exon2			CCGTGCCGCACTC	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.298G>A	3.37:g.187416666C>T	ENSP00000350976:p.Gly100Ser	Somatic	203	1	0.00492611		WXS	Illumina HiSeq	Phase_I	216	100	0.462963	NM_001004312	Q6NVH4	Missense_Mutation	SNP	ENST00000358241.1	37	CCDS33911.1	329	0.15064102564102563	81	0.16463414634146342	37	0.10220994475138122	57	0.09965034965034965	154	0.20316622691292877	C	12.86	2.063669	0.36373	0.160836	0.195225	ENSG00000198471	ENST00000358241	T	0.13196	2.61	4.17	4.17	0.49024	.	0.485095	0.23842	N	0.044031	T	0.00012	0.0000	N	0.11154	0.105	0.29340	P	0.866106	D	0.55172	0.97	P	0.48425	0.577	T	0.25187	-1.0139	9	0.07325	T	0.83	-51.3596	12.2956	0.54844	0.0:1.0:0.0:0.0	rs11927120	100	Q5QGT7	RTP2_HUMAN	S	100	ENSP00000350976:G100S	ENSP00000350976:G100S	G	-	1	0	RTP2	188899360	0.966000	0.33281	1.000000	0.80357	0.466000	0.32739	2.796000	0.47869	2.621000	0.88768	0.563000	0.77884	GGC	C|0.839;T|0.161	0.161	strong		0.647	RTP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344259.1	NM_001004312	
SUPT20HL2	170067	hgsc.bcm.edu	37	X	24330386	24330386	+	IGR	SNP	G	G	A	rs73205129		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:24330386G>A								AC096509.1 (25592 upstream) : AC004552.1 (36539 downstream)																							TTGGCTTGGTGTCCCAGGCCT	0.552													G|||	297	0.0786755	0.0023	0.0403	3775	,	,		15768	0.0942		0.0805	False		,,,				2504	0.092				p.D349D		Atlas-SNP	.											.	.	.	.	0			c.C1047T						PASS	.	G		32,2595		0,28,4,1031,505	121.0	102.0	108.0		1047	-2.4	0.0	X	dbSNP_130	108	503,4995		12,338,141,1566,1525	no	coding-synonymous	FAM48B2	NM_001136233.1		12,366,145,2597,2030	AA,AG,A,GG,G		9.1488,1.2181,6.5846		349/818	24330386	535,7590	1568	3582	5150	SO:0001628	intergenic_variant	170067	exon1			CTTGGTGTCCCAG																													X.37:g.24330386G>A		Somatic	707	1	0.00141443		WXS	Illumina HiSeq	Phase_I	519	517	0.996146	NM_001136233		Silent	SNP		37																																																																																				G|0.929;A|0.071	0.071	strong	0	0.552								
FAM179A	165186	hgsc.bcm.edu	37	2	29240783	29240783	+	Missense_Mutation	SNP	A	A	G	rs1109758	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:29240783A>G	ENST00000379558.4	+	10	1672	c.1321A>G	c.(1321-1323)Atc>Gtc	p.I441V	FAM179A_ENST00000403861.2_Intron|FAM179A_ENST00000465300.1_Intron	NM_199280.2	NP_954974.2	Q6ZUX3	F179A_HUMAN	family with sequence similarity 179, member A	441			I -> V (in dbSNP:rs1109758).							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						CAGCATCCCCATCAGCCGGCA	0.677													G|||	2010	0.401358	0.6679	0.304	5008	,	,		15556	0.3224		0.341	False		,,,				2504	0.2536				p.I441V		Atlas-SNP	.											.	FAM179A	106	.	0			c.A1321G						PASS	.	G	VAL/ILE	2212,1698		640,932,383	13.0	18.0	16.0		1321	1.1	0.1	2	dbSNP_86	16	2639,5645		431,1777,1934	yes	missense	FAM179A	NM_199280.2	29	1071,2709,2317	GG,GA,AA		31.8566,43.4271,39.7819	benign	441/1020	29240783	4851,7343	1955	4142	6097	SO:0001583	missense	165186	exon10			ATCCCCATCAGCC	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.1321A>G	2.37:g.29240783A>G	ENSP00000368876:p.Ile441Val	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	134	63	0.470149	NM_199280	Q6ZUF5	Missense_Mutation	SNP	ENST00000379558.4	37	CCDS1769.2	888	0.4065934065934066	337	0.6849593495934959	113	0.31215469613259667	181	0.31643356643356646	257	0.3390501319261214	G	0	-2.582335	0.00129	0.565729	0.318566	ENSG00000189350	ENST00000379558	T	0.04502	3.61	4.26	1.07	0.20283	.	.	.	.	.	T	0.00012	0.0000	N	0.04508	-0.205	0.38475	P	0.052425000000000055	B	0.02656	0.0	B	0.01281	0.0	T	0.10847	-1.0612	8	0.08599	T	0.76	.	8.8404	0.35137	0.4176:0.0:0.5824:0.0	rs1109758;rs4420672;rs17007448;rs58321497;rs1109758	441	Q6ZUX3	F179A_HUMAN	V	441	ENSP00000368876:I441V	ENSP00000368876:I441V	I	+	1	0	FAM179A	29094287	0.064000	0.20934	0.083000	0.20561	0.007000	0.05969	0.232000	0.17891	-0.122000	0.11766	-0.914000	0.02751	ATC	A|0.599;G|0.401	0.401	strong		0.677	FAM179A-003	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317848.4	NM_199280	
CNTRL	11064	hgsc.bcm.edu	37	9	123903840	123903840	+	Missense_Mutation	SNP	G	G	A	rs17292952	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:123903840G>A	ENST00000373855.1	+	18	2925	c.2665G>A	c.(2665-2667)Gcc>Acc	p.A889T	CNTRL_ENST00000373847.1_Missense_Mutation_p.A337T|CNTRL_ENST00000238341.5_Missense_Mutation_p.A889T|CNTRL_ENST00000373850.1_Missense_Mutation_p.A337T			Q7Z7A1	CNTRL_HUMAN	centriolin	889			A -> T (in dbSNP:rs17292952).		cell division (GO:0051301)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)				haematopoietic_and_lymphoid_tissue(2)|large_intestine(9)|lung(2)|ovary(4)|skin(3)	20						GTTCAGGCAGGCCTGTGAGAG	0.458													G|||	72	0.014377	0.0008	0.0173	5008	,	,		19797	0.0		0.0318	False		,,,				2504	0.0276				p.A889T		Atlas-SNP	.											.	CNTRL	161	.	0			c.G2665A						PASS	.	G	THR/ALA	35,4371	39.2+/-71.8	0,35,2168	48.0	47.0	47.0		2665	5.8	1.0	9	dbSNP_123	47	348,8252	117.9+/-177.5	14,320,3966	yes	missense	CNTRL	NM_007018.4	58	14,355,6134	AA,AG,GG		4.0465,0.7944,2.9448	probably-damaging	889/2326	123903840	383,12623	2203	4300	6503	SO:0001583	missense	11064	exon16			AGGCAGGCCTGTG	AF513978	CCDS35118.1	9q33.2	2014-02-20	2011-05-23	2011-05-23	ENSG00000119397	ENSG00000119397			1858	protein-coding gene	gene with protein product		605496	"""centrosomal protein 1"", ""centrosomal protein 110kDa"""	CEP1, CEP110		10688839	Standard	XM_005251679		Approved		uc004bkx.1	Q7Z7A1	OTTHUMG00000020581	ENST00000373855.1:c.2665G>A	9.37:g.123903840G>A	ENSP00000362962:p.Ala889Thr	Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	33	22	0.666667	NM_007018	A2A2Y1|B2RP67|Q3MN79|Q5FWF8|Q5JVD0|Q6MZR3|Q6PKC1|Q8TEP3|Q9Y489	Missense_Mutation	SNP	ENST00000373855.1	37	CCDS35118.1	31	0.014194139194139194	0	0.0	7	0.019337016574585635	0	0.0	24	0.0316622691292876	G	24.3	4.519961	0.85495	0.007944	0.040465	ENSG00000119397	ENST00000373855;ENST00000238341;ENST00000454238;ENST00000373851;ENST00000373850;ENST00000373847	T;T;T;T	0.54866	0.55;0.55;0.55;0.55	5.76	5.76	0.90799	.	.	.	.	.	T	0.22244	0.0536	L	0.29908	0.895	0.41023	D	0.985093	P;P;P	0.51537	0.506;0.946;0.91	B;P;P	0.51453	0.102;0.67;0.469	T	0.17992	-1.0351	9	0.34782	T	0.22	.	18.9576	0.92665	0.0:0.0:1.0:0.0	rs17292952;rs52800952;rs17292952	889;889;889	B2RP65;F5GZN0;Q7Z7A1	.;.;CNTRL_HUMAN	T	889;889;889;371;337;337	ENSP00000362962:A889T;ENSP00000238341:A889T;ENSP00000362956:A337T;ENSP00000362953:A337T	ENSP00000238341:A889T	A	+	1	0	CNTRL	122943661	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	3.754000	0.55189	2.719000	0.93026	0.655000	0.94253	GCC	G|0.976;A|0.024	0.024	strong		0.458	CNTRL-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250216.1	NM_007018	
LTN1	26046	hgsc.bcm.edu	37	21	30341891	30341891	+	Missense_Mutation	SNP	A	A	G	rs2254796	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:30341891A>G	ENST00000361371.5	-	9	1287	c.1208T>C	c.(1207-1209)tTa>tCa	p.L403S	LTN1_ENST00000389195.2_Missense_Mutation_p.L449S|LTN1_ENST00000389194.2_Missense_Mutation_p.L449S			O94822	LTN1_HUMAN	listerin E3 ubiquitin protein ligase 1	403			L -> S (in dbSNP:rs2254796). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9872452, ECO:0000269|Ref.6}.		protein ubiquitination (GO:0016567)		ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(1)|endometrium(4)|kidney(5)|large_intestine(12)|lung(19)|ovary(5)|pancreas(1)|prostate(2)|skin(6)|stomach(2)|upper_aerodigestive_tract(2)	60						CGAGGACTCTAAAGAGCTGGT	0.343													G|||	3599	0.71865	0.8631	0.6614	5008	,	,		15657	0.8333		0.6024	False		,,,				2504	0.5654				p.L449S		Atlas-SNP	.											.	LTN1	141	.	0			c.T1346C						PASS	.	G	SER/LEU	3576,828	326.7+/-299.7	1459,658,85	70.0	72.0	71.0		1346	4.9	1.0	21	dbSNP_100	71	4751,3849	540.6+/-383.8	1318,2115,867	yes	missense	LTN1	NM_015565.2	145	2777,2773,952	GG,GA,AA		44.7558,18.8011,35.9659	benign	449/1813	30341891	8327,4677	2202	4300	6502	SO:0001583	missense	26046	exon9			GACTCTAAAGAGC	AK001915	CCDS33527.1, CCDS33527.2	21q21.3	2013-01-09	2010-09-17	2010-09-17	ENSG00000198862	ENSG00000198862		"""RING-type (C3HC4) zinc fingers"""	13082	protein-coding gene	gene with protein product	"""listerin"""	613083	"""chromosome 21 open reading frame 98"", ""zinc finger protein 294"", ""ring finger protein 160"""	C21orf98, C21orf10, ZNF294, RNF160		20835226, 19196968	Standard	NM_015565		Approved	KIAA0714, FLJ11053, LISTERIN	uc002ymr.2	O94822	OTTHUMG00000078803	ENST00000361371.5:c.1208T>C	21.37:g.30341891A>G	ENSP00000354977:p.Leu403Ser	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	78	38	0.487179	NM_015565	A6NL41|A7E2D0|B2RTS0|C9J7U3|J3KPL4|Q05C47|Q9H8M4|Q9NUY5|Q9P0E9	Missense_Mutation	SNP	ENST00000361371.5	37		1594	0.7298534798534798	419	0.8516260162601627	251	0.6933701657458563	477	0.833916083916084	447	0.5897097625329816	G	1.147	-0.647937	0.03506	0.811989	0.552442	ENSG00000198862	ENST00000389194;ENST00000361371;ENST00000446611;ENST00000389195	T;T;T	0.64438	3.73;3.73;-0.1	4.91	4.91	0.64330	Armadillo-type fold (1);	0.077470	0.53938	N	0.000041	T	0.00012	0.0000	N	0.00621	-1.32	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.39272	-0.9622	9	0.02654	T	1	.	11.0688	0.47991	0.0873:0.0:0.9127:0.0	rs2254796;rs52795528;rs61451660;rs2254796	403	O94822	LTN1_HUMAN	S	449;403;405;449	ENSP00000373846:L449S;ENSP00000354977:L403S;ENSP00000373847:L449S	ENSP00000354977:L403S	L	-	2	0	LTN1	29263762	1.000000	0.71417	0.993000	0.49108	0.345000	0.29048	4.344000	0.59354	1.456000	0.47831	-0.119000	0.15052	TTA	A|0.317;G|0.683	0.683	strong		0.343	LTN1-008	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000472108.1	NM_015565	
COL28A1	340267	hgsc.bcm.edu	37	7	7398423	7398423	+	Silent	SNP	C	C	T	rs373840985	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:7398423C>T	ENST00000399429.3	-	35	3359	c.3219G>A	c.(3217-3219)ttG>ttA	p.L1073L		NM_001037763.2	NP_001032852.2	Q2UY09	COSA1_HUMAN	collagen, type XXVIII, alpha 1	1073	BPTI/Kunitz inhibitor. {ECO:0000255|PROSITE-ProRule:PRU00031}.				cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(23)|prostate(1)|skin(4)|stomach(1)|urinary_tract(1)	42		Ovarian(82;0.0789)		UCEC - Uterine corpus endometrioid carcinoma (126;0.228)		TCAAGGCTTCCAAACATCTAG	0.358													C|||	2	0.000399361	0.0015	0.0	5008	,	,		18071	0.0		0.0	False		,,,				2504	0.0				p.L1073L		Atlas-SNP	.											.	COL28A1	113	.	0			c.G3219A						PASS	.	C		2,3712		0,2,1855	132.0	116.0	121.0		3219	-3.5	0.0	7		121	0,8186		0,0,4093	no	coding-synonymous	COL28A1	NM_001037763.2		0,2,5948	TT,TC,CC		0.0,0.0539,0.0168		1073/1126	7398423	2,11898	1857	4093	5950	SO:0001819	synonymous_variant	340267	exon35			GGCTTCCAAACAT	AJ890451	CCDS43553.1	7p21.3	2013-01-16			ENSG00000215018	ENSG00000215018		"""Collagens"""	22442	protein-coding gene	gene with protein product		609996				16330543	Standard	NM_001037763		Approved		uc003src.1	Q2UY09	OTTHUMG00000150034	ENST00000399429.3:c.3219G>A	7.37:g.7398423C>T		Somatic	201	0	0		WXS	Illumina HiSeq	Phase_I	166	40	0.240964	NM_001037763	A4D101|A4D106|A4D107|A8MVR2|B9EGX9|Q2UY07|Q2UY08	Silent	SNP	ENST00000399429.3	37	CCDS43553.1																																																																																			.	.	weak		0.358	COL28A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315899.1	NM_001037763	
PHRF1	57661	hgsc.bcm.edu	37	11	609353	609353	+	Silent	SNP	G	G	A	rs11539530	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:609353G>A	ENST00000264555.5	+	14	4025	c.3897G>A	c.(3895-3897)ccG>ccA	p.P1299P	PHRF1_ENST00000533464.1_Silent_p.P1295P|PHRF1_ENST00000413872.2_Silent_p.P1297P|PHRF1_ENST00000416188.2_Silent_p.P1298P	NM_020901.2	NP_065952.2	Q9P1Y6	PHRF1_HUMAN	PHD and ring finger domains 1	1299					mRNA processing (GO:0006397)|transcription from RNA polymerase II promoter (GO:0006366)	membrane (GO:0016020)	RNA polymerase binding (GO:0070063)|zinc ion binding (GO:0008270)			breast(1)|cervix(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(13)|urinary_tract(2)	28						ACTCTTCCCCGGAGCGAGACT	0.597													G|||	936	0.186901	0.3359	0.2507	5008	,	,		15166	0.0198		0.2147	False		,,,				2504	0.0838				p.P1298P		Atlas-SNP	.											.	PHRF1	188	.	0			c.G3894A						PASS	.	G		1354,2928		218,918,1005	32.0	38.0	36.0		3894	-7.1	1.0	11	dbSNP_120	36	2031,6479		227,1577,2451	no	coding-synonymous	PHRF1	NM_020901.2		445,2495,3456	AA,AG,GG		23.866,31.6207,26.4619		1298/1649	609353	3385,9407	2141	4255	6396	SO:0001819	synonymous_variant	57661	exon14			TTCCCCGGAGCGA	BC004950	CCDS44507.1, CCDS65987.1, CCDS65988.1, CCDS65989.1	11p15.5	2014-06-13			ENSG00000070047	ENSG00000070047		"""RING-type (C3HC4) zinc fingers"", ""Zinc fingers, PHD-type"""	24351	protein-coding gene	gene with protein product	"""CTD binding SR like protein rA9"", ""protein phosphatase 1, regulatory subunit 125"""	611780		RNF221			Standard	XM_005253027		Approved	KIAA1542, PPP1R125	uc010qwc.2	Q9P1Y6	OTTHUMG00000165141	ENST00000264555.5:c.3897G>A	11.37:g.609353G>A		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	83	57	0.686747	NM_020901	A6H8W1|B7ZM64|B9EGP0|C9JS82|Q6PJP2|Q8IVY2|Q8N2Y7|Q9BSM2	Silent	SNP	ENST00000264555.5	37																																																																																				G|0.798;A|0.202	0.202	strong		0.597	PHRF1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000382133.1	NM_020901	
MYH11	4629	hgsc.bcm.edu	37	16	15850204	15850204	+	Silent	SNP	A	A	G	rs2272554	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:15850204A>G	ENST00000300036.5	-	14	1852	c.1743T>C	c.(1741-1743)gcT>gcC	p.A581A	MYH11_ENST00000576790.2_Silent_p.A581A|MYH11_ENST00000452625.2_Silent_p.A588A|MYH11_ENST00000396324.3_Silent_p.A588A	NM_002474.2	NP_002465.1	P35749	MYH11_HUMAN	myosin, heavy chain 11, smooth muscle	581	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						GTACCTTCCCAGCATAATGGA	0.597			T	CBFB	AML						OREG0023636	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	2745	0.548123	0.7481	0.3905	5008	,	,		18888	0.6647		0.4245	False		,,,				2504	0.3967				p.A588A		Atlas-SNP	.		Dom	yes		16	16p13.13-p13.12	4629	"""myosin, heavy polypeptide 11, smooth muscle"""		L	.	MYH11	520	.	0			c.T1764C						PASS	.	G	,,,	2995,1399	459.2+/-352.2	1023,949,225	88.0	72.0	77.0		1764,1764,1743,1743	-10.8	0.1	16	dbSNP_100	77	3489,5111	632.5+/-398.6	727,2035,1538	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	MYH11	NM_001040113.1,NM_001040114.1,NM_002474.2,NM_022844.2	,,,	1750,2984,1763	GG,GA,AA		40.5698,31.8389,49.9	,,,	588/1946,588/1980,581/1973,581/1939	15850204	6484,6510	2197	4300	6497	SO:0001819	synonymous_variant	4629	exon15			CTTCCCAGCATAA	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.1743T>C	16.37:g.15850204A>G		Somatic	140	0	0	705	WXS	Illumina HiSeq	Phase_I	113	24	0.212389	NM_001040114	D2JYH7|O00396|O94944|P78422|Q3MIV8|Q3MNF0|Q3MNF1	Silent	SNP	ENST00000300036.5	37	CCDS10565.1																																																																																			A|0.465;G|0.535	0.535	strong		0.597	MYH11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252192.2	NM_001040113	
OR5L1	219437	hgsc.bcm.edu	37	11	55578991	55578991	+	Silent	SNP	C	C	T	rs61732387|rs386753698	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:55578991C>T	ENST00000333973.2	+	1	138	c.49C>T	c.(49-51)Cta>Tta	p.L17L		NM_001004738.1	NP_001004738.1	Q8NGL2	OR5L1_HUMAN	olfactory receptor, family 5, subfamily L, member 1	17						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L17L(1)		NS(1)|breast(2)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(4)|liver(4)|lung(36)|ovary(2)|pancreas(1)|prostate(5)|skin(9)|stomach(4)|upper_aerodigestive_tract(3)	78		all_epithelial(135;0.208)				TCTCCTTGGACTATCAGATGT	0.438													N|||	525	0.104832	0.1884	0.0461	5008	,	,		18141	0.0813		0.0924	False		,,,				2504	0.0706				p.L17L		Atlas-SNP	.											OR5L1,NS,carcinoma,0,1	OR5L1	145	1	1	Substitution - coding silent(1)	stomach(1)	c.C49T						PASS	.	T		670,3730	763.4+/-413.2	63,544,1593	208.0	196.0	200.0		49	-2.0	0.0	11	dbSNP_130	200	724,7862	785.1+/-407.6	32,660,3601	no	coding-synonymous	OR5L1	NM_001004738.1		95,1204,5194	TT,TC,CC		8.4323,15.2273,10.7346		17/312	55578991	1394,11592	2200	4293	6493	SO:0001819	synonymous_variant	219437	exon1			CTTGGACTATCAG	AB065780	CCDS31509.1	11q11	2012-08-09			ENSG00000186117	ENSG00000186117		"""GPCR / Class A : Olfactory receptors"""	8350	protein-coding gene	gene with protein product							Standard	NM_001004738		Approved	OST262	uc001nhw.1	Q8NGL2	OTTHUMG00000166810	ENST00000333973.2:c.49C>T	11.37:g.55578991C>T		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	64	46	0.71875	NM_001004738	B2RNK6|Q6IFD0	Silent	SNP	ENST00000333973.2	37	CCDS31509.1																																																																																			C|0.899;T|0.101	0.101	strong		0.438	OR5L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391514.1	NM_001004738	
ATP2C1	27032	hgsc.bcm.edu	37	3	130718472	130718472	+	Silent	SNP	G	G	A	rs16835513	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:130718472G>A	ENST00000510168.1	+	27	3148	c.2598G>A	c.(2596-2598)aaG>aaA	p.K866K	ATP2C1_ENST00000328560.8_Silent_p.K866K|ATP2C1_ENST00000504381.1_Silent_p.K811K|ATP2C1_ENST00000428331.2_Silent_p.K866K|ATP2C1_ENST00000359644.3_Silent_p.K866K|ATP2C1_ENST00000504948.1_Silent_p.K850K|ATP2C1_ENST00000508532.1_Silent_p.K866K|ATP2C1_ENST00000507488.2_Silent_p.K850K|ATP2C1_ENST00000533801.2_Silent_p.K861K|ATP2C1_ENST00000422190.2_Silent_p.K866K|ATP2C1_ENST00000505330.1_Silent_p.K850K|ATP2C1_ENST00000513801.1_Silent_p.K850K|ATP2C1_ENST00000393221.4_Silent_p.K900K			P98194	AT2C1_HUMAN	ATPase, Ca++ transporting, type 2C, member 1	866					actin cytoskeleton reorganization (GO:0031532)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|calcium-dependent cell-cell adhesion (GO:0016339)|cellular calcium ion homeostasis (GO:0006874)|cellular manganese ion homeostasis (GO:0030026)|epidermis development (GO:0008544)|Golgi calcium ion homeostasis (GO:0032468)|Golgi calcium ion transport (GO:0032472)|ion transmembrane transport (GO:0034220)|manganese ion transmembrane transport (GO:0071421)|manganese ion transport (GO:0006828)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)|transmembrane transport (GO:0055085)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|trans-Golgi network (GO:0005802)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calcium-transporting ATPase activity (GO:0005388)|manganese ion binding (GO:0030145)|manganese-transporting ATPase activity (GO:0015410)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)			breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|lung(15)|prostate(2)|skin(2)|urinary_tract(1)	39					Desflurane(DB01189)|Enflurane(DB00228)|Halothane(DB01159)|Isoflurane(DB00753)|Methoxyflurane(DB01028)|Sevoflurane(DB01236)	CGCTTCAGAAGGTTTTTCAGA	0.328									Hailey-Hailey disease				G|||	574	0.114617	0.0045	0.1527	5008	,	,		16391	0.1597		0.1461	False		,,,				2504	0.1575				p.K900K	Esophageal Squamous(99;456 1443 27647 34099 42636)	Atlas-SNP	.											.	ATP2C1	94	.	0			c.G2700A						PASS	.	G	,,,,,,,,,,	134,4272	93.0+/-131.7	0,134,2069	106.0	99.0	101.0		2598,2598,2598,2598,2700,2700,2583,2550,2550,2598,2598	3.8	1.0	3	dbSNP_123	101	1357,7243	258.6+/-282.2	105,1147,3048	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ATP2C1	NM_001001485.2,NM_001001486.1,NM_001001487.1,NM_001199179.1,NM_001199180.1,NM_001199181.1,NM_001199182.1,NM_001199183.1,NM_001199184.1,NM_001199185.1,NM_014382.3	,,,,,,,,,,	105,1281,5117	AA,AG,GG		15.7791,3.0413,11.4639	,,,,,,,,,,	866/889,866/950,866/940,866/920,900/974,900/954,861/945,850/924,850/904,866/889,866/920	130718472	1491,11515	2203	4300	6503	SO:0001819	synonymous_variant	27032	exon26	Familial Cancer Database	HHD, Familial Benign Chronic Pemphigus, Benign Familial Pemphigus	TCAGAAGGTTTTT	AF181120	CCDS33856.1, CCDS46912.1, CCDS46913.1, CCDS46914.1, CCDS56278.1, CCDS56279.1, CCDS56280.1, CCDS56281.1, CCDS75006.1	3q21.3	2012-10-22			ENSG00000017260	ENSG00000017260	3.6.3.8	"""ATPases / P-type"""	13211	protein-coding gene	gene with protein product	"""secretory pathway Ca2+/Mn2+ ATPase 1"", ""calcium-transporting ATPase type 2C member 1"""	604384	"""benign chronic pemphigus (Hailey-Hailey disease)"""	BCPM		10615129, 10767338	Standard	NM_001001485		Approved	KIAA1347, ATP2C1A, PMR1, SPCA1	uc011bli.2	P98194	OTTHUMG00000136802	ENST00000510168.1:c.2598G>A	3.37:g.130718472G>A		Somatic	149	1	0.00671141		WXS	Illumina HiSeq	Phase_I	88	88	1	NM_001199181	B2RAT7|B4DSW3|B7Z3X9|G3XAH8|G8JLN9|O76005|Q86V72|Q86V73|Q8N6V1|Q8NCJ7	Silent	SNP	ENST00000510168.1	37	CCDS46914.1	265	0.12133699633699634	3	0.006097560975609756	52	0.143646408839779	84	0.14685314685314685	126	0.1662269129287599	G	8.516	0.867692	0.17250	0.030413	0.157791	ENSG00000017260	ENST00000504612	.	.	.	5.91	3.84	0.44239	.	.	.	.	.	T	0.00144	0.0004	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.10382	-1.0632	3	.	.	.	.	7.2415	0.26100	0.4737:0.0:0.5263:0.0	rs16835513	.	.	.	K	820	.	.	R	+	2	0	ATP2C1	132201162	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	1.041000	0.30291	1.287000	0.44583	0.655000	0.94253	AGG	G|0.886;A|0.114	0.114	strong		0.328	ATP2C1-008	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356648.2	NM_001001486	
SYNE1	23345	hgsc.bcm.edu	37	6	152771849	152771849	+	Silent	SNP	G	G	A	rs17082701	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:152771849G>A	ENST00000367255.5	-	27	3907	c.3306C>T	c.(3304-3306)caC>caT	p.H1102H	SYNE1_ENST00000367253.4_Silent_p.H1102H|SYNE1_ENST00000367248.3_Silent_p.H1092H|SYNE1_ENST00000265368.4_Silent_p.H1102H|SYNE1_ENST00000413186.2_Silent_p.H1102H|SYNE1_ENST00000448038.1_Silent_p.H1109H|SYNE1_ENST00000423061.1_Silent_p.H1109H|SYNE1_ENST00000341594.5_Silent_p.H1168H	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	1102					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)		TGAGAGTCACGTGACAGGTTC	0.522										HNSCC(10;0.0054)			G|||	244	0.048722	0.0688	0.0389	5008	,	,		16107	0.003		0.0746	False		,,,				2504	0.0491				p.H1109H		Atlas-SNP	.											.	SYNE1	3227	.	0			c.C3327T						PASS	.	G	,	345,4061	181.2+/-209.3	17,311,1875	173.0	165.0	168.0		3327,3306	-3.5	0.0	6	dbSNP_123	168	585,8015	155.7+/-209.7	30,525,3745	no	coding-synonymous,coding-synonymous	SYNE1	NM_033071.3,NM_182961.3	,	47,836,5620	AA,AG,GG		6.8023,7.8302,7.1505	,	1109/8750,1102/8798	152771849	930,12076	2203	4300	6503	SO:0001819	synonymous_variant	23345	exon27			AGTCACGTGACAG	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.3306C>T	6.37:g.152771849G>A		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	77	53	0.688312	NM_033071	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Silent	SNP	ENST00000367255.5	37	CCDS5236.2																																																																																			G|0.931;A|0.069	0.069	strong		0.522	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961	
CLPTM1	1209	hgsc.bcm.edu	37	19	45490570	45490570	+	Silent	SNP	A	A	G	rs3786505	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:45490570A>G	ENST00000337392.5	+	8	1077	c.927A>G	c.(925-927)ccA>ccG	p.P309P	CLPTM1_ENST00000541297.2_Silent_p.P295P|CLPTM1_ENST00000546079.1_Silent_p.P207P|CLPTM1_ENST00000589158.1_3'UTR	NM_001282175.1|NM_001282176.1|NM_001294.2	NP_001269104.1|NP_001269105.1|NP_001285.1	O96005	CLPT1_HUMAN	cleft lip and palate associated transmembrane protein 1	309					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|regulation of T cell differentiation in thymus (GO:0033081)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)				endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(11)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	23		all_neural(266;0.224)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.00354)|Epithelial(262;0.187)		CCTTCTGCCCACTCTCGCTTT	0.577													G|||	2137	0.426717	0.4788	0.4222	5008	,	,		19997	0.5288		0.341	False		,,,				2504	0.3425				p.P309P		Atlas-SNP	.											.	CLPTM1	109	.	0			c.A927G						PASS	.	G		2131,2275	598.7+/-389.1	502,1127,574	100.0	103.0	102.0		927	-9.3	0.7	19	dbSNP_107	102	2764,5836	678.7+/-403.5	456,1852,1992	no	coding-synonymous	CLPTM1	NM_001294.2		958,2979,2566	GG,GA,AA		32.1395,48.3659,37.6365		309/670	45490570	4895,8111	2203	4300	6503	SO:0001819	synonymous_variant	1209	exon8			CTGCCCACTCTCG	AF037339	CCDS12651.1, CCDS74394.1, CCDS74395.1	19q13.3	2008-02-05				ENSG00000104853			2087	protein-coding gene	gene with protein product		604783				9828125	Standard	NM_001294		Approved		uc002pai.3	O96005		ENST00000337392.5:c.927A>G	19.37:g.45490570A>G		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	79	41	0.518987	NM_001294	B3KQH2|B4DDS3|B4E2X9|B7Z9X9|F5H8J3|Q53ET6|Q9BSS5	Silent	SNP	ENST00000337392.5	37	CCDS12651.1																																																																																			A|0.596;G|0.404	0.404	strong		0.577	CLPTM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453267.1	NM_001294	
PLXNC1	10154	hgsc.bcm.edu	37	12	94575307	94575307	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:94575307T>C	ENST00000258526.4	+	3	1538	c.1289T>C	c.(1288-1290)gTt>gCt	p.V430A	RP11-74K11.2_ENST00000550759.1_RNA	NM_005761.2	NP_005752.1	O60486	PLXC1_HUMAN	plexin C1	430	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|membrane (GO:0016020)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)|receptor binding (GO:0005102)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(4)|kidney(4)|large_intestine(12)|lung(30)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	64						TACAAACTCGTTCCTGATCCT	0.313																																					p.V430A		Atlas-SNP	.											PLXNC1,caecum,carcinoma,0,2	PLXNC1	135	2	0			c.T1289C						scavenged	.						97.0	108.0	104.0					12																	94575307		2203	4300	6503	SO:0001583	missense	10154	exon3			AACTCGTTCCTGA	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.1289T>C	12.37:g.94575307T>C	ENSP00000258526:p.Val430Ala	Somatic	249	0	0		WXS	Illumina HiSeq	Phase_I	214	7	0.0327103	NM_005761	Q59H25	Missense_Mutation	SNP	ENST00000258526.4	37	CCDS9049.1	.	.	.	.	.	.	.	.	.	.	T	1.036	-0.680247	0.03353	.	.	ENSG00000136040	ENST00000258526;ENST00000551850	T;T	0.04502	3.61;3.61	6.08	4.95	0.65309	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (2);	0.698869	0.15271	N	0.271252	T	0.03095	0.0091	N	0.22421	0.69	0.80722	D	1	B	0.17852	0.024	B	0.12156	0.007	T	0.42716	-0.9435	10	0.10902	T	0.67	.	5.0487	0.14497	0.1608:0.0823:0.0:0.7569	.	430	O60486	PLXC1_HUMAN	A	430;46	ENSP00000258526:V430A;ENSP00000447843:V46A	ENSP00000258526:V430A	V	+	2	0	PLXNC1	93099438	0.993000	0.37304	0.954000	0.39281	0.360000	0.29518	0.949000	0.29109	2.333000	0.79357	0.482000	0.46254	GTT	.	.	none		0.313	PLXNC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408126.2		
MUC4	4585	hgsc.bcm.edu	37	3	195515194	195515194	+	Missense_Mutation	SNP	G	G	C	rs201370057	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195515194G>C	ENST00000463781.3	-	2	3716	c.3257C>G	c.(3256-3258)aCc>aGc	p.T1086S	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.T1086S	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	518					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.T1086S(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)		AAGAGGGGTGGTGTCACCTGT	0.572													.|||	109	0.0217652	0.0582	0.0072	5008	,	,		18106	0.0159		0.0099	False		,,,				2504	0.001				p.T1086S		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	1	Substitution - Missense(1)	endometrium(1)	c.C3257G						scavenged	.						18.0	14.0	15.0					3																	195515194		685	1579	2264	SO:0001583	missense	4585	exon2			GGGGTGGTGTCAC	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.3257C>G	3.37:g.195515194G>C	ENSP00000417498:p.Thr1086Ser	Somatic	43	1	0.0232558		WXS	Illumina HiSeq	Phase_I	60	12	0.2	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	-	3.733	-0.055087	0.07362	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.34859	1.34;1.34	0.814	0.814	0.18756	.	.	.	.	.	T	0.34279	0.0892	N	0.19112	0.55	0.09310	N	1	D	0.60160	0.987	D	0.65684	0.937	T	0.14309	-1.0477	8	.	.	.	.	3.1761	0.06569	0.3046:0.0:0.6954:0.0	.	1086	E7ESK3	.	S	1086	ENSP00000417498:T1086S;ENSP00000420243:T1086S	.	T	-	2	0	MUC4	196999589	0.000000	0.05858	0.011000	0.14972	0.090000	0.18270	0.417000	0.21214	0.776000	0.33473	0.064000	0.15345	ACC	G|0.939;C|0.061	0.061	strong		0.572	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
ZNF169	169841	hgsc.bcm.edu	37	9	97062981	97062981	+	Missense_Mutation	SNP	C	C	T	rs12236219	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:97062981C>T	ENST00000395395.2	+	5	1231	c.1141C>T	c.(1141-1143)Cgt>Tgt	p.R381C	ZNF169_ENST00000340911.4_3'UTR	NM_194320.2	NP_919301.2	Q14929	ZN169_HUMAN	zinc finger protein 169	381			R -> C (in dbSNP:rs12236219).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|kidney(2)|large_intestine(3)|lung(8)|ovary(2)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	24		Acute lymphoblastic leukemia(62;0.136)				TGAGTGTGGGCGTAGCTTCAG	0.567													C|||	873	0.174321	0.0938	0.2565	5008	,	,		21660	0.3542		0.0517	False		,,,				2504	0.1656				p.R381C		Atlas-SNP	.											ZNF169,NS,carcinoma,-1,1	ZNF169	60	1	0			c.C1141T						scavenged	.	C	CYS/ARG	347,4059	179.0+/-207.6	14,319,1870	64.0	56.0	59.0		1141	0.9	0.9	9	dbSNP_120	59	380,8220	123.4+/-182.3	10,360,3930	yes	missense	ZNF169	NM_194320.2	180	24,679,5800	TT,TC,CC		4.4186,7.8756,5.5897	probably-damaging	381/604	97062981	727,12279	2203	4300	6503	SO:0001583	missense	169841	exon5			TGTGGGCGTAGCT	U28322	CCDS6709.2	9q22.32	2014-07-30			ENSG00000175787	ENSG00000175787		"""Zinc fingers, C2H2-type"", ""-"""	12957	protein-coding gene	gene with protein product		603404				9186526, 9071574	Standard	NM_001301275		Approved	MGC51961	uc004aum.1	Q14929	OTTHUMG00000020264	ENST00000395395.2:c.1141C>T	9.37:g.97062981C>T	ENSP00000378792:p.Arg381Cys	Somatic	66	1	0.0151515		WXS	Illumina HiSeq	Phase_I	46	16	0.347826	NM_194320	A2AGP5|A8K127|Q6PI28	Missense_Mutation	SNP	ENST00000395395.2	37	CCDS6709.2	362	0.16575091575091574	43	0.08739837398373984	81	0.22375690607734808	192	0.3356643356643357	46	0.06068601583113457	C	9.160	1.018407	0.19355	0.078756	0.044186	ENSG00000175787	ENST00000395395;ENST00000340911	T	0.19806	2.12	2.71	0.852	0.18995	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	M	0.65677	2.01	0.43703	P	0.003834000000000004	D	0.89917	1.0	D	0.79784	0.993	T	0.31861	-0.9928	8	0.87932	D	0	.	2.4738	0.04571	0.2347:0.4919:0.0:0.2734	rs12236219;rs52793080;rs59355579;rs12236219	381	Q14929	ZN169_HUMAN	C	381;190	ENSP00000378792:R381C	ENSP00000340711:R190C	R	+	1	0	ZNF169	96102802	0.417000	0.25432	0.911000	0.35937	0.002000	0.02628	0.802000	0.27069	0.230000	0.21059	-0.199000	0.12753	CGT	C|0.894;T|0.106	0.106	strong		0.567	ZNF169-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253714.1	NM_194320	
ESRRA	2101	hgsc.bcm.edu	37	11	64081445	64081445	+	Silent	SNP	G	G	A	rs2276014	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:64081445G>A	ENST00000405666.1	+	3	582	c.348G>A	c.(346-348)ccG>ccA	p.P116P	ESRRA_ENST00000406310.1_Silent_p.P116P|ESRRA_ENST00000000442.6_Silent_p.P116P	NM_001282450.1	NP_001269379.1	P11474	ERR1_HUMAN	estrogen-related receptor alpha	116					cartilage development (GO:0051216)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell proliferation (GO:0042127)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	intercellular bridge (GO:0045171)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein domain specific binding (GO:0019904)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|steroid binding (GO:0005496)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(4)|lung(8)	14						ACAGCTGTCCGGCCTCCAACG	0.672													G|||	447	0.0892572	0.0242	0.1254	5008	,	,		14349	0.1052		0.161	False		,,,				2504	0.0613				p.P116P		Atlas-SNP	.											.	ESRRA	56	.	0			c.G348A						PASS	.	G		202,4146		5,192,1977	12.0	14.0	13.0		348	0.3	1.0	11	dbSNP_100	13	1308,7264		113,1082,3091	no	coding-synonymous	ESRRA	NM_004451.3		118,1274,5068	AA,AG,GG		15.259,4.6458,11.6873		116/424	64081445	1510,11410	2174	4286	6460	SO:0001819	synonymous_variant	2101	exon3			CTGTCCGGCCTCC	X51416, L38487	CCDS41667.1, CCDS60830.1	11q12	2013-01-16			ENSG00000173153	ENSG00000173153		"""Nuclear hormone receptors"""	3471	protein-coding gene	gene with protein product		601998		ESRL1		3267207	Standard	NM_004451		Approved	ERR1, ERRalpha, NR3B1, ERRa	uc001nzq.1	P11474	OTTHUMG00000150641	ENST00000405666.1:c.348G>A	11.37:g.64081445G>A		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	137	107	0.781022	NM_004451	Q14514	Silent	SNP	ENST00000405666.1	37	CCDS41667.1																																																																																			G|0.895;A|0.105	0.105	strong		0.672	ESRRA-003	KNOWN	alternative_5_UTR|NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319304.1	NM_004451	
PDE4DIP	9659	hgsc.bcm.edu	37	1	144859792	144859792	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:144859792T>C	ENST00000369354.3	-	38	6481	c.6292A>G	c.(6292-6294)Act>Gct	p.T2098A	PDE4DIP_ENST00000369359.4_Missense_Mutation_p.T2234A|PDE4DIP_ENST00000313382.9_Missense_Mutation_p.T1992A|PDE4DIP_ENST00000369356.4_Missense_Mutation_p.T2098A|RP4-791M13.4_ENST00000532137.1_RNA|PDE4DIP_ENST00000530740.1_Missense_Mutation_p.T2183A|PDE4DIP_ENST00000524974.1_5'UTR			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	2098					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)		CCAGGGTCAGTGCTGGCTGGG	0.572			T	PDGFRB	MPD																																p.T2098A		Atlas-SNP	.		Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	.	PDE4DIP	817	.	0			c.A6292G						PASS	.						66.0	64.0	65.0					1																	144859792		2203	4300	6503	SO:0001583	missense	9659	exon38			GGTCAGTGCTGGC	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.6292A>G	1.37:g.144859792T>C	ENSP00000358360:p.Thr2098Ala	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	151	10	0.0662252	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	.	.	.	.	.	.	.	.	.	.	C	6.344	0.431590	0.12045	.	.	ENSG00000178104	ENST00000313382;ENST00000369354;ENST00000369356;ENST00000530740;ENST00000369359	T;T;T;T;T	0.01647	4.71;4.8;4.8;4.8;4.8	4.91	-3.04	0.05412	.	.	.	.	.	T	0.00271	0.0008	N	0.16166	0.38	0.09310	N	0.999999	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.43893	-0.9363	9	0.02654	T	1	.	7.2849	0.26333	0.0:0.2735:0.1194:0.6071	.	1992;2098	Q5VU43-3;Q5VU43	.;MYOME_HUMAN	A	1992;2098;2098;2183;2234	ENSP00000327209:T1992A;ENSP00000358360:T2098A;ENSP00000358363:T2098A;ENSP00000435654:T2183A;ENSP00000358366:T2234A	ENSP00000327209:T1992A	T	-	1	0	PDE4DIP	143571149	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.278000	0.02809	-1.197000	0.02673	-1.569000	0.00873	ACT	.	.	none		0.572	PDE4DIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000038858.2	NM_022359	
CTXN3	613212	hgsc.bcm.edu	37	5	126993282	126993282	+	Missense_Mutation	SNP	G	G	A	rs2280170	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:126993282G>A	ENST00000379445.3	+	3	620	c.69G>A	c.(67-69)atG>atA	p.M23I	CTC-548H10.2_ENST00000512352.1_RNA|CTXN3_ENST00000395322.3_Missense_Mutation_p.M23I	NM_001048252.2	NP_001041717.1	Q4LDR2	CTXN3_HUMAN	cortexin 3	23			M -> I (in dbSNP:rs2280170).			integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(2)|lung(1)	4		Prostate(80;0.165)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	Epithelial(69;0.0128)|COAD - Colon adenocarcinoma(49;0.0234)|OV - Ovarian serous cystadenocarcinoma(64;0.038)		ATTCTAGCATGTCCCTGGAGC	0.483													G|||	661	0.131989	0.1467	0.1556	5008	,	,		21182	0.2569		0.0119	False		,,,				2504	0.09				p.M23I		Atlas-SNP	.											.	CTXN3	19	.	0			c.G69A						PASS	.	G	ILE/MET,ILE/MET	514,3892	237.7+/-249.4	26,462,1715	147.0	126.0	133.0		69,69	4.5	1.0	5	dbSNP_100	133	147,8453	71.3+/-133.9	1,145,4154	yes	missense,missense	CTXN3	NM_001048252.2,NM_001127385.1	10,10	27,607,5869	AA,AG,GG		1.7093,11.6659,5.0823	benign,benign	23/82,23/82	126993282	661,12345	2203	4300	6503	SO:0001583	missense	613212	exon3			TAGCATGTCCCTG	AB219764	CCDS34221.1	5q23.2	2006-09-21				ENSG00000205279			31110	protein-coding gene	gene with protein product							Standard	NM_001048252		Approved		uc003kum.4	Q4LDR2		ENST00000379445.3:c.69G>A	5.37:g.126993282G>A	ENSP00000368758:p.Met23Ile	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	82	42	0.512195	NM_001048252	B2RV32|D3DQ82	Missense_Mutation	SNP	ENST00000379445.3	37	CCDS34221.1	256	0.11721611721611722	68	0.13821138211382114	49	0.13535911602209943	133	0.23251748251748253	6	0.0079155672823219	G	15.72	2.915812	0.52546	0.116659	0.017093	ENSG00000205279	ENST00000379445;ENST00000395322	T;T	0.27557	1.66;1.66	4.52	4.52	0.55395	.	0.141535	0.64402	D	0.000008	T	0.00012	0.0000	.	.	.	0.09310	P	0.99999553293	B	0.14012	0.009	B	0.15052	0.012	T	0.11372	-1.0590	8	0.38643	T	0.18	-0.7381	13.9817	0.64308	0.0:0.0:0.8476:0.1523	rs2280170;rs2280170	23	Q4LDR2	CTXN3_HUMAN	I	23	ENSP00000368758:M23I;ENSP00000378732:M23I	ENSP00000368758:M23I	M	+	3	0	CTXN3	127021181	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.994000	0.56994	2.793000	0.96121	0.655000	0.94253	ATG	G|0.917;A|0.083	0.083	strong		0.483	CTXN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372467.1	XM_932841	
COL6A5	256076	hgsc.bcm.edu	37	3	130129322	130129322	+	Missense_Mutation	SNP	G	G	C	rs35886424	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	129	0	0		WXS	Illumina HiSeq	Phase_I	92	45	0.48913	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	
MUC4	4585	hgsc.bcm.edu	37	3	195515411	195515411	+	Missense_Mutation	SNP	G	G	C	rs55803325	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195515411G>C	ENST00000463781.3	-	2	3499	c.3040C>G	c.(3040-3042)Cct>Gct	p.P1014A	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.P1014A	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	449	Repeat.				cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.S1013_T1028delSPSSVSTGHTTPLPVT(4)		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)		ACTGAGGAAGGGCTGGTGACA	0.572																																					p.P1014A		Atlas-SNP	.											.	MUC4	1505	.	4	Deletion - In frame(4)	stomach(4)	c.C3040G						PASS	.						51.0	28.0	35.0					3																	195515411		686	1591	2277	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.3040C>G	3.37:g.195515411G>C	ENSP00000417498:p.Pro1014Ala	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	72	26	0.361111	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	.	.	.	.	.	.	.	.	.	.	-	4.439	0.081317	0.08533	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.30448	1.53;1.53	0.814	-1.63	0.08345	.	.	.	.	.	T	0.13372	0.0324	N	0.14661	0.345	0.09310	N	1	B	0.11235	0.004	B	0.01281	0.0	T	0.21109	-1.0255	8	.	.	.	.	3.0122	0.06048	0.0:0.2389:0.4536:0.3075	.	1014	E7ESK3	.	A	1014	ENSP00000417498:P1014A;ENSP00000420243:P1014A	.	P	-	1	0	MUC4	196999806	.	.	0.000000	0.03702	0.011000	0.07611	.	.	-2.334000	0.00630	-2.366000	0.00237	CCT	G|0.993;T|0.007	.	alt		0.572	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
CPA4	51200	hgsc.bcm.edu	37	7	129962414	129962414	+	Silent	SNP	C	C	T	rs2306848	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:129962414C>T	ENST00000222482.4	+	11	1192	c.1164C>T	c.(1162-1164)acC>acT	p.T388T	CPA4_ENST00000445470.2_Silent_p.T355T|CPA4_ENST00000493259.1_Silent_p.T284T	NM_016352.3	NP_057436.2	Q9UI42	CBPA4_HUMAN	carboxypeptidase A4	388					histone acetylation (GO:0016573)	extracellular region (GO:0005576)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	21	Melanoma(18;0.0435)					ATACCGGGACCTATGGCTTCC	0.537													C|||	222	0.0443291	0.0613	0.0591	5008	,	,		21653	0.0139		0.0636	False		,,,				2504	0.0225				p.T388T		Atlas-SNP	.											.	CPA4	47	.	0			c.C1164T						PASS	.	C	,	269,4137	151.8+/-185.6	10,249,1944	179.0	160.0	166.0		1065,1164	2.9	0.1	7	dbSNP_100	166	658,7942	167.7+/-219.4	23,612,3665	no	coding-synonymous,coding-synonymous	CPA4	NM_001163446.1,NM_016352.3	,	33,861,5609	TT,TC,CC		7.6512,6.1053,7.1275	,	355/389,388/422	129962414	927,12079	2203	4300	6503	SO:0001819	synonymous_variant	51200	exon11			CGGGACCTATGGC	AF095719	CCDS5818.1, CCDS55163.1	7q32	2008-07-18			ENSG00000128510	ENSG00000128510			15740	protein-coding gene	gene with protein product	"""carboxypeptidase A3"""	607635				10383164, 10860668	Standard	NM_016352		Approved	CPA3	uc003vpr.3	Q9UI42	OTTHUMG00000157825	ENST00000222482.4:c.1164C>T	7.37:g.129962414C>T		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	118	62	0.525424	NM_016352	B7Z576|Q86UY9	Silent	SNP	ENST00000222482.4	37	CCDS5818.1																																																																																			C|0.941;T|0.059	0.059	strong		0.537	CPA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349725.1	NM_016352	
PRODH	5625	hgsc.bcm.edu	37	22	18910355	18910355	+	Missense_Mutation	SNP	G	G	T	rs5747933	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:18910355G>T	ENST00000357068.6	-	6	1089	c.824C>A	c.(823-825)aCc>aAc	p.T275N	PRODH_ENST00000334029.2_Missense_Mutation_p.T167N|PRODH_ENST00000420436.1_Missense_Mutation_p.T167N	NM_016335.4	NP_057419	O43272	PROD_HUMAN	proline dehydrogenase (oxidase) 1	275			T -> N. {ECO:0000269|PubMed:17135275}.		4-hydroxyproline catabolic process (GO:0019470)|cellular nitrogen compound metabolic process (GO:0034641)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|proline catabolic process (GO:0006562)|proline catabolic process to glutamate (GO:0010133)|proline metabolic process (GO:0006560)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)	FAD binding (GO:0071949)|proline dehydrogenase activity (GO:0004657)			breast(1)|endometrium(3)|lung(4)|upper_aerodigestive_tract(1)	9					L-Proline(DB00172)	CTCCAGCTTGGTGTCCATGGC	0.647													.|||	361	0.0720847	0.003	0.1556	5008	,	,		14777	0.1706		0.0467	False		,,,				2504	0.0307				p.T275N		Atlas-SNP	.											.	PRODH	42	.	0			c.C824A						PASS	.	G	ASN/THR,ASN/THR	66,4340		1,64,2138	78.0	76.0	77.0		500,824	0.8	0.6	22	dbSNP_114	77	367,8233		7,353,3940	yes	missense,missense	PRODH	NM_001195226.1,NM_016335.4	65,65	8,417,6078	TT,TG,GG		4.2674,1.498,3.3292	possibly-damaging,possibly-damaging	167/493,275/601	18910355	433,12573	2203	4300	6503	SO:0001583	missense	5625	exon7			AGCTTGGTGTCCA	AF010310	CCDS13754.1, CCDS56223.1	22q11.2	2014-07-10	2001-12-05		ENSG00000100033	ENSG00000100033	1.5.5.2		9453	protein-coding gene	gene with protein product		606810	"""proline dehydrogenase (proline oxidase )"""			9385373, 10192398	Standard	NM_001195226		Approved	HSPOX2, PRODH1, PIG6, PRODH2, TP53I6	uc002zok.4	O43272	OTTHUMG00000150163	ENST00000357068.6:c.824C>A	22.37:g.18910355G>T	ENSP00000349577:p.Thr275Asn	Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	123	58	0.471545	NM_016335	A6NF53|O14680|Q0P507|Q147W8|Q504W1|Q59FI8|Q6NV86|Q9UF13	Missense_Mutation	SNP	ENST00000357068.6	37	CCDS13754.1	189|189	0.08653846153846154|0.08653846153846154	1|1	0.0020325203252032522|0.0020325203252032522	46|46	0.1270718232044199|0.1270718232044199	104|104	0.18181818181818182|0.18181818181818182	38|38	0.05013192612137203|0.05013192612137203	.|.	7.274|7.274	0.607759|0.607759	0.14002|0.14002	0.01498|0.01498	0.042674|0.042674	ENSG00000100033|ENSG00000100033	ENST00000438924|ENST00000357068;ENST00000399694;ENST00000450579	.|T;T	.|0.32988	.|1.43;1.49	4.18|4.18	0.756|0.756	0.18421|0.18421	.|Proline dehydrogenase (1);	.|0.496209	.|0.22070	.|N	.|0.065048	T|T	0.00039|0.00039	0.0001|0.0001	L|L	0.41236|0.41236	1.265|1.265	0.80722|0.80722	P|P	0.0|0.0	.|B;B;B	.|0.33318	.|0.355;0.408;0.372	.|B;B;B	.|0.35240	.|0.08;0.198;0.175	T|T	0.24977|0.24977	-1.0145|-1.0145	4|9	.|0.17369	.|T	.|0.5	-4.6861|-4.6861	6.2685|6.2685	0.20941|0.20941	0.3838:0.0:0.6162:0.0|0.3838:0.0:0.6162:0.0	rs5747933|rs5747933	.|191;275;167	.|O43272-1;O43272;E7EQL6	.|.;PROD_HUMAN;.	Q|N	135|275;68;116	.|ENSP00000349577:T275N;ENSP00000396806:T116N	.|ENSP00000334726:T167N	H|T	-|-	3|2	2|0	PRODH|PRODH	17290355|17290355	0.000000|0.000000	0.05858|0.05858	0.594000|0.594000	0.28785|0.28785	0.889000|0.889000	0.51656|0.51656	-0.022000|-0.022000	0.12480|0.12480	0.320000|0.320000	0.23234|0.23234	-0.158000|-0.158000	0.13435|0.13435	CAC|ACC	G|0.951;T|0.049	0.049	strong		0.647	PRODH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316637.2	NM_016335	
AKAP10	11216	hgsc.bcm.edu	37	17	19812541	19812541	+	Missense_Mutation	SNP	T	T	C	rs203462	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:19812541T>C	ENST00000225737.6	-	14	2093	c.1936A>G	c.(1936-1938)Att>Gtt	p.I646V	AKAP10_ENST00000395536.3_Missense_Mutation_p.I588V	NM_007202.3	NP_009133.2	O43572	AKA10_HUMAN	A kinase (PRKA) anchor protein 10	646	PKA-RII subunit binding.		I -> V (associated with increased basal heart rate and decreased heart rate variability; dbSNP:rs203462). {ECO:0000269|PubMed:17485678}.		blood coagulation (GO:0007596)|protein localization (GO:0008104)|signal transduction (GO:0007165)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)				NS(1)|endometrium(3)|kidney(1)|large_intestine(4)|liver(1)|lung(3)|ovary(1)|prostate(1)|skin(3)|stomach(1)|urinary_tract(2)	21	all_cancers(12;2.08e-05)|all_epithelial(12;0.00158)|Breast(13;0.165)					TGCTGCATAATGTCACTGACT	0.353													C|||	1973	0.39397	0.6248	0.4179	5008	,	,		19441	0.1895		0.3946	False		,,,				2504	0.2751				p.I646V		Atlas-SNP	.											.	AKAP10	47	.	0			c.A1936G	GRCh37	CM030773	AKAP10	M	rs203462	PASS	.	C	VAL/ILE	2560,1846	536.2+/-374.4	750,1060,393	127.0	120.0	122.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1936	5.9	1.0	17	dbSNP_79	122	3298,5302	647.1+/-400.3	633,2032,1635	yes	missense	AKAP10	NM_007202.2	29	1383,3092,2028	CC,CT,TT		38.3488,41.8974,45.0408	benign	646/663	19812541	5858,7148	2203	4300	6503	SO:0001583	missense	11216	exon14			GCATAATGTCACT	AF037439	CCDS11214.1	17p11.1	2008-07-18			ENSG00000108599	ENSG00000108599		"""A-kinase anchor proteins"""	368	protein-coding gene	gene with protein product	"""dual-specificity A-kinase anchoring protein 2"", ""protein kinase A anchoring protein 10"", ""mitochondrial A kinase PPKA anchor protein 10"""	604694				9326583	Standard	NM_007202		Approved	D-AKAP2, PRKA10, MGC9414	uc002gwo.4	O43572	OTTHUMG00000059515	ENST00000225737.6:c.1936A>G	17.37:g.19812541T>C	ENSP00000225737:p.Ile646Val	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	89	48	0.539326	NM_007202	B2R650|Q96AJ7	Missense_Mutation	SNP	ENST00000225737.6	37	CCDS11214.1	862	0.3946886446886447	314	0.6382113821138211	150	0.4143646408839779	101	0.17657342657342656	297	0.391820580474934	C	6.323	0.427698	0.11987	0.581026	0.383488	ENSG00000108599	ENST00000225737;ENST00000395536	T	0.21361	2.01	5.88	5.88	0.94601	.	0.000000	0.85682	N	0.000000	T	0.00012	0.0000	N	0.00972	-1.085	0.49483	P	2.0299999999995322E-4	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.37865	-0.9687	9	0.02654	T	1	-8.2079	12.6849	0.56942	0.0:0.9244:0.0:0.0756	rs203462;rs1182243;rs16960528;rs17685331;rs52835669;rs57728914;rs203462	588;588;646	E7EMD6;Q2XPN4;O43572	.;.;AKA10_HUMAN	V	646;588	ENSP00000225737:I646V	ENSP00000225737:I646V	I	-	1	0	AKAP10	19753133	0.997000	0.39634	0.965000	0.40720	0.790000	0.44656	4.154000	0.58125	1.505000	0.48720	-0.119000	0.15052	ATT	T|0.572;G|0.003	.	strong		0.353	AKAP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132380.2	NM_007202	
KRTAP4-8	728224	hgsc.bcm.edu	37	17	39254142	39254142	+	Silent	SNP	A	A	G	rs375280428	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:39254142A>G	ENST00000333822.4	-	1	251	c.195T>C	c.(193-195)tgT>tgC	p.C65C		NM_031960.2	NP_114166.1	Q9BYQ9	KRA48_HUMAN	keratin associated protein 4-8	65	25 X 5 AA repeats of C-C-[IKRQVHEC]- [SPRT]-[STCVQPR].				aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)				endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(1)|prostate(1)	11						AGCTGGGGCGACAGCAGGTGG	0.657													G|||	2063	0.411941	0.469	0.4352	5008	,	,		13020	0.3234		0.4453	False		,,,				2504	0.3753				p.C65C		Atlas-SNP	.											KRTAP4-8,rectum,carcinoma,0,2	KRTAP4-8	57	2	0			c.T195C						scavenged	.						6.0	9.0	8.0					17																	39254142		633	1475	2108	SO:0001819	synonymous_variant	728224	exon1			GGGGCGACAGCAG	AJ406940	CCDS45674.1	17q21.2	2013-06-25			ENSG00000204880	ENSG00000204880		"""Keratin associated proteins"""	17230	protein-coding gene	gene with protein product						11279113	Standard	NM_031960		Approved	KAP4.8	uc010wfo.2	Q9BYQ9	OTTHUMG00000133580	ENST00000333822.4:c.195T>C	17.37:g.39254142A>G		Somatic	50	1	0.02		WXS	Illumina HiSeq	Phase_I	36	5	0.138889	NM_031960	A8MSH3	Silent	SNP	ENST00000333822.4	37	CCDS45674.1																																																																																			.	.	weak		0.657	KRTAP4-8-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257684.1	NM_031960	
CRACR2A	84766	hgsc.bcm.edu	37	12	3788188	3788188	+	Silent	SNP	C	C	T	rs3803135	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	109	0	0		WXS	Illumina HiSeq	Phase_I	108	48	0.444444	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		
BCL11A	53335	hgsc.bcm.edu	37	2	60687959	60687959	+	Silent	SNP	A	A	G	rs7569946	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:60687959A>G	ENST00000335712.6	-	4	2315	c.2088T>C	c.(2086-2088)agT>agC	p.S696S	BCL11A_ENST00000359629.5_Intron|BCL11A_ENST00000477659.1_5'UTR|BCL11A_ENST00000358510.4_Silent_p.S662S|BCL11A_ENST00000538214.1_Silent_p.S662S|BCL11A_ENST00000537768.1_Silent_p.S365S|BCL11A_ENST00000356842.4_Silent_p.S696S	NM_022893.3	NP_075044.2	Q9H165	BC11A_HUMAN	B-cell CLL/lymphoma 11A (zinc finger protein)	696					B cell differentiation (GO:0030183)|negative regulation of axon extension (GO:0030517)|negative regulation of collateral sprouting (GO:0048671)|negative regulation of dendrite development (GO:2000171)|negative regulation of neuron projection development (GO:0010977)|negative regulation of protein homooligomerization (GO:0032463)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of collateral sprouting (GO:0048672)|positive regulation of neuron projection development (GO:0010976)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein sumoylation (GO:0016925)|regulation of dendrite development (GO:0050773)|T cell differentiation (GO:0030217)	cytoplasm (GO:0005737)|nuclear body (GO:0016604)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|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 negative regulation of transcription (GO:0001078)|transcription corepressor activity (GO:0003714)			NS(1)|breast(6)|central_nervous_system(6)|endometrium(4)|kidney(1)|large_intestine(8)|lung(25)|ovary(2)|pancreas(1)|prostate(2)|skin(3)	59			LUSC - Lung squamous cell carcinoma(5;9.29e-08)|Lung(5;1.34e-06)|Epithelial(17;0.0562)|all cancers(80;0.199)			AGAAGCGCAAACTCCCGTTCT	0.647			T	IGH@	B-CLL								G|||	4157	0.830072	0.9486	0.7738	5008	,	,		17011	0.998		0.5984	False		,,,				2504	0.7751				p.S696S		Atlas-SNP	.		Dom	yes		2	2p13	53335	B-cell CLL/lymphoma 11A		L	.	BCL11A	298	.	0			c.T2088C						PASS	.	G	,,	3996,406	176.9+/-206.0	1819,358,24	35.0	43.0	41.0		2088,2088,	5.9	1.0	2	dbSNP_116	41	5265,3331	477.7+/-369.7	1598,2069,631	yes	coding-synonymous,coding-synonymous,intron	BCL11A	NM_018014.3,NM_022893.3,NM_138559.1	,,	3417,2427,655	GG,GA,AA		38.7506,9.2231,28.7506	,,	696/774,696/836,	60687959	9261,3737	2201	4298	6499	SO:0001819	synonymous_variant	53335	exon4			GCGCAAACTCCCG	AJ404611	CCDS1861.1, CCDS1862.1, CCDS46295.1	2p16.1	2013-01-08	2002-05-08		ENSG00000119866	ENSG00000119866		"""Zinc fingers, C2H2-type"""	13221	protein-coding gene	gene with protein product		606557	"""ecotropic viral integration site 9"""	EVI9		11719382, 18245381	Standard	NM_018014		Approved	BCL11A-XL, BCL11A-L, BCL11A-S, CTIP1, HBFQTL5, ZNF856	uc002sae.1	Q9H165	OTTHUMG00000129420	ENST00000335712.6:c.2088T>C	2.37:g.60687959A>G		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	115	115	1	NM_018014	D6W5D7|Q86W14|Q8WU92|Q96JL6|Q9H163|Q9H164|Q9H3G9|Q9NWA7	Silent	SNP	ENST00000335712.6	37	CCDS1862.1																																																																																			A|0.278;G|0.722	0.722	strong		0.647	BCL11A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251579.2	NM_022893	
PPL	5493	hgsc.bcm.edu	37	16	4935985	4935985	+	Missense_Mutation	SNP	C	C	G	rs35869286	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	72	0	0		WXS	Illumina HiSeq	Phase_I	59	49	0.830508	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	
STYXL1	51657	hgsc.bcm.edu	37	7	75630274	75630274	+	Silent	SNP	T	T	C	rs8565	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:75630274T>C	ENST00000248600.1	-	8	1086	c.744A>G	c.(742-744)caA>caG	p.Q248Q	STYXL1_ENST00000359697.3_Silent_p.Q248Q|STYXL1_ENST00000431581.1_Silent_p.Q248Q|STYXL1_ENST00000451157.1_Silent_p.Q248Q|STYXL1_ENST00000340062.5_Silent_p.Q152Q|STYXL1_ENST00000360591.3_3'UTR	NM_016086.2	NP_057170.1	Q9Y6J8	STYL1_HUMAN	serine/threonine/tyrosine interacting-like 1	248	Tyrosine-protein phosphatase.				intracellular signal transduction (GO:0035556)|protein dephosphorylation (GO:0006470)		protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			endometrium(1)|large_intestine(2)|lung(4)|ovary(1)|prostate(1)|skin(1)	10						GGCTGATACCTTGGGTGGAAA	0.572													T|||	3124	0.623802	0.5953	0.6671	5008	,	,		21036	0.5585		0.7127	False		,,,				2504	0.6074				p.Q248Q		Atlas-SNP	.											STYXL1,NS,carcinoma,-2,1	STYXL1	35	1	0			c.A744G						scavenged	.	T		2759,1647	659.5+/-400.6	862,1035,306	144.0	120.0	129.0		744	2.8	0.7	7	dbSNP_52	129	6275,2325	705.6+/-405.5	2272,1731,297	no	coding-synonymous	STYXL1	NM_016086.2		3134,2766,603	CC,CT,TT		27.0349,37.3808,30.5398		248/314	75630274	9034,3972	2203	4300	6503	SO:0001819	synonymous_variant	51657	exon8			GATACCTTGGGTG	AF069762	CCDS5580.1	7q11.23	2011-06-09	2005-09-22	2005-09-22	ENSG00000127952	ENSG00000127952		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : MAP kinase phosphatases"""	18165	protein-coding gene	gene with protein product			"""dual specificity phosphatase 24 (putative)"""	DUSP24		9757831	Standard	NM_016086		Approved	MK-STYX	uc003uel.3	Q9Y6J8	OTTHUMG00000130459	ENST00000248600.1:c.744A>G	7.37:g.75630274T>C		Somatic	128	1	0.0078125		WXS	Illumina HiSeq	Phase_I	117	66	0.564103	NM_016086	Q9UBP1|Q9UK06|Q9UK07|Q9UKG2|Q9UKG3	Silent	SNP	ENST00000248600.1	37	CCDS5580.1																																																																																			T|0.318;C|0.682	0.682	strong		0.572	STYXL1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344825.1	NM_016086	
GIT2	9815	hgsc.bcm.edu	37	12	110383141	110383141	+	Missense_Mutation	SNP	G	G	A	rs11068997	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:110383141G>A	ENST00000355312.3	-	16	1654	c.1655C>T	c.(1654-1656)gCa>gTa	p.A552V	GIT2_ENST00000343646.5_Intron|GIT2_ENST00000338373.5_Missense_Mutation_p.A454V|GIT2_ENST00000361006.5_Intron|GIT2_ENST00000551209.1_Missense_Mutation_p.A501V|TCHP_ENST00000550780.1_Intron|GIT2_ENST00000553118.1_Intron|GIT2_ENST00000356259.4_Intron|GIT2_ENST00000360185.4_Missense_Mutation_p.A502V|GIT2_ENST00000354574.4_Intron|GIT2_ENST00000457474.2_Intron	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	52	0	0		WXS	Illumina HiSeq	Phase_I	47	22	0.468085	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	
MFHAS1	9258	hgsc.bcm.edu	37	8	8748013	8748013	+	Missense_Mutation	SNP	G	G	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:8748013G>C	ENST00000276282.6	-	1	3142	c.2556C>G	c.(2554-2556)tgC>tgG	p.C852W		NM_004225.2	NP_004216.2	Q9Y4C4	MFHA1_HUMAN	malignant fibrous histiocytoma amplified sequence 1	852										endometrium(1)|kidney(3)|large_intestine(7)|lung(6)|ovary(1)|prostate(2)|stomach(1)	21		Hepatocellular(245;0.217)		COAD - Colon adenocarcinoma(149;0.124)		TCTGCACATAGCATGGGAACT	0.507																																					p.C852W	Melanoma(103;1201 2045 17515 28966)	Atlas-SNP	.											.	MFHAS1	58	.	0			c.C2556G						PASS	.						80.0	76.0	77.0					8																	8748013		2203	4300	6503	SO:0001583	missense	9258	exon1			CACATAGCATGGG	AB016816	CCDS34844.1	8p23.1	2014-03-07			ENSG00000147324	ENSG00000147324			16982	protein-coding gene	gene with protein product	"""leucine rich repeat containing 65"", ""malignant fibrous histiocytoma-amplified sequences with leucine-rich tandem repeats 1"""	605352				9973190	Standard	NM_004225		Approved	MASL1, LRRC65	uc003wsj.1	Q9Y4C4	OTTHUMG00000163676	ENST00000276282.6:c.2556C>G	8.37:g.8748013G>C	ENSP00000276282:p.Cys852Trp	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	53	30	0.566038	NM_004225	Q96CI0	Missense_Mutation	SNP	ENST00000276282.6	37	CCDS34844.1	.	.	.	.	.	.	.	.	.	.	G	11.37	1.617809	0.28801	.	.	ENSG00000147324	ENST00000276282	T	0.30448	1.53	5.04	4.17	0.49024	.	0.117044	0.64402	D	0.000016	T	0.20210	0.0486	N	0.08118	0	0.58432	D	0.999999	D	0.57571	0.98	P	0.46975	0.533	T	0.04440	-1.0951	10	0.36615	T	0.2	.	12.5332	0.56128	0.0798:0.0:0.9202:0.0	.	852	Q9Y4C4	MFHA1_HUMAN	W	852	ENSP00000276282:C852W	ENSP00000276282:C852W	C	-	3	2	MFHAS1	8785423	1.000000	0.71417	0.973000	0.42090	0.980000	0.70556	5.899000	0.69846	1.359000	0.45940	0.655000	0.94253	TGC	.	.	none		0.507	MFHAS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374724.2	NM_004225	
KCNG4	93107	hgsc.bcm.edu	37	16	84270476	84270476	+	Missense_Mutation	SNP	G	G	A	rs11646443	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:84270476G>A	ENST00000308251.4	-	2	684	c.616C>T	c.(616-618)Cgg>Tgg	p.R206W	KCNG4_ENST00000568181.1_Missense_Mutation_p.R206W	NM_172347.2	NP_758857.1	Q8TDN1	KCNG4_HUMAN	potassium voltage-gated channel, subfamily G, member 4	206			R -> W (in dbSNP:rs11646443).		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						TCGCGCAGCCGGTTCATGCAC	0.682													G|||	1371	0.273762	0.2262	0.2507	5008	,	,		15093	0.1161		0.3628	False		,,,				2504	0.4254				p.R206W		Atlas-SNP	.											.	KCNG4	71	.	0			c.C616T						PASS	.	G	TRP/ARG	1081,3315		131,819,1248	26.0	28.0	27.0		616	3.0	0.4	16	dbSNP_120	27	2877,5719		495,1887,1916	yes	missense	KCNG4	NM_172347.2	101	626,2706,3164	AA,AG,GG		33.4691,24.5905,30.4649	benign	206/520	84270476	3958,9034	2198	4298	6496	SO:0001583	missense	93107	exon2			GCAGCCGGTTCAT	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.616C>T	16.37:g.84270476G>A	ENSP00000312129:p.Arg206Trp	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	130	71	0.546154	NM_172347	Q96H24	Missense_Mutation	SNP	ENST00000308251.4	37	CCDS10945.1	519	0.23763736263736263	94	0.1910569105691057	91	0.2513812154696133	62	0.10839160839160839	272	0.35883905013192613	G	11.56	1.675051	0.29783	0.245905	0.334691	ENSG00000168418	ENST00000308251	D	0.97016	-4.21	5.11	3.0	0.34707	.	0.882556	0.09392	U	0.808448	T	0.00012	0.0000	L	0.27053	0.805	0.80722	P	0.0	B;B	0.21381	0.028;0.055	B;B	0.14578	0.009;0.011	T	0.04386	-1.0955	9	0.39692	T	0.17	.	5.8407	0.18633	0.0983:0.0:0.4371:0.4646	rs11646443;rs17736772;rs11646443	206;206	Q8TDN1;Q8TDN1-2	KCNG4_HUMAN;.	W	206	ENSP00000312129:R206W	ENSP00000312129:R206W	R	-	1	2	KCNG4	82827977	0.249000	0.23941	0.367000	0.25926	0.856000	0.48823	1.442000	0.35046	0.386000	0.24997	0.549000	0.68633	CGG	G|0.721;A|0.279	0.279	strong		0.682	KCNG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269079.2	NM_172347	
OR56A4	120793	hgsc.bcm.edu	37	11	6024031	6024031	+	Silent	SNP	G	G	A	rs143488149	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:6024031G>A	ENST00000330728.4	-	1	393	c.348C>T	c.(346-348)taC>taT	p.Y116Y		NM_001005179.2	NP_001005179.2	Q8NGH8	O56A4_HUMAN	olfactory receptor, family 56, subfamily A, member 4	64						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)		GGCTGAGCAGGTAGTACAGGG	0.607													.|||	3	0.000599042	0.0	0.0	5008	,	,		20915	0.0		0.003	False		,,,				2504	0.0				p.Y116Y		Atlas-SNP	.											.	OR56A4	66	.	0			c.C348T						PASS	.	G		0,4400		0,0,2200	69.0	69.0	69.0		348	1.7	1.0	11	dbSNP_134	69	14,8534	10.5+/-38.8	0,14,4260	no	coding-synonymous	OR56A4	NM_001005179.2		0,14,6460	AA,AG,GG		0.1638,0.0,0.1081		116/366	6024031	14,12934	2200	4274	6474	SO:0001819	synonymous_variant	120793	exon1			GAGCAGGTAGTAC	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.348C>T	11.37:g.6024031G>A		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	160	110	0.6875	NM_001005179	B9EH17	Silent	SNP	ENST00000330728.4	37	CCDS31404.1																																																																																			G|0.999;A|0.001	0.001	strong		0.607	OR56A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383756.2	NM_001005179	
LCMT2	9836	hgsc.bcm.edu	37	15	43621947	43621947	+	Silent	SNP	A	A	G	rs3742969	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:43621947A>G	ENST00000305641.5	-	1	856	c.741T>C	c.(739-741)cgT>cgC	p.R247R	ADAL_ENST00000422466.2_5'Flank|LCMT2_ENST00000567039.1_Intron|LCMT2_ENST00000544735.1_Intron|ADAL_ENST00000389651.4_5'Flank|ADAL_ENST00000428046.3_5'Flank	NM_014793.4	NP_055608.2	O60294	TYW4_HUMAN	leucine carboxyl methyltransferase 2	247					tRNA processing (GO:0008033)		methyltransferase activity (GO:0008168)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(2)|liver(1)|lung(9)|skin(1)|urinary_tract(1)	20		all_cancers(109;2.12e-14)|all_epithelial(112;1.99e-12)|Lung NSC(122;2.46e-08)|all_lung(180;2.75e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;8.1e-07)	L-Leucine(DB00149)	CGTCAGGAAAACGCTCCAGGC	0.572													G|||	1983	0.395966	0.7322	0.2291	5008	,	,		17524	0.4683		0.1262	False		,,,				2504	0.2628				p.R247R		Atlas-SNP	.											.	LCMT2	48	.	0			c.T741C						PASS	.	G		2646,1756	502.0+/-365.1	803,1040,358	38.0	41.0	40.0		741	2.5	0.6	15	dbSNP_107	40	1093,7505	748.1+/-407.3	78,937,3284	no	coding-synonymous	LCMT2	NM_014793.4		881,1977,3642	GG,GA,AA		12.7123,39.891,28.7615		247/687	43621947	3739,9261	2201	4299	6500	SO:0001819	synonymous_variant	9836	exon1			AGGAAAACGCTCC	AF265443	CCDS10094.1	15q15.3	2007-01-26			ENSG00000168806	ENSG00000168806			17558	protein-coding gene	gene with protein product	"""tRNA-yW synthesizing protein 4"""	611246				9628581, 17150819	Standard	NM_014793		Approved	KIAA0547, MGC9534, TYW4, PPM2	uc001zrg.3	O60294	OTTHUMG00000130705	ENST00000305641.5:c.741T>C	15.37:g.43621947A>G		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	53	26	0.490566	NM_014793	Q4JFT6|Q96B55|Q9NR10	Silent	SNP	ENST00000305641.5	37	CCDS10094.1																																																																																			A|0.668;G|0.332	0.332	strong		0.572	LCMT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253205.1	NM_014793	
NTRK1	4914	hgsc.bcm.edu	37	1	156846233	156846233	+	Silent	SNP	G	G	A	rs6334	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:156846233G>A	ENST00000524377.1	+	14	1715	c.1674G>A	c.(1672-1674)caG>caA	p.Q558Q	NTRK1_ENST00000392302.2_Silent_p.Q522Q|NTRK1_ENST00000368196.3_Silent_p.Q552Q|NTRK1_ENST00000358660.3_Silent_p.Q555Q	NM_002529.3	NP_002520.2	P04629	NTRK1_HUMAN	neurotrophic tyrosine kinase, receptor, type 1	558	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of adenylate cyclase activity (GO:0007190)|activation of MAPKK activity (GO:0000186)|activation of phospholipase C activity (GO:0007202)|aging (GO:0007568)|axon guidance (GO:0007411)|axonogenesis involved in innervation (GO:0060385)|B cell differentiation (GO:0030183)|cellular response to nerve growth factor stimulus (GO:1990090)|cellular response to nicotine (GO:0071316)|circadian rhythm (GO:0007623)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|detection of temperature stimulus involved in sensory perception of pain (GO:0050965)|developmental programmed cell death (GO:0010623)|learning or memory (GO:0007611)|mechanoreceptor differentiation (GO:0042490)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|olfactory nerve development (GO:0021553)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of angiogenesis (GO:0045766)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of neuron projection development (GO:0010976)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of programmed cell death (GO:0043068)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of Ras protein signal transduction (GO:0046579)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|Ras protein signal transduction (GO:0007265)|response to activity (GO:0014823)|response to axon injury (GO:0048678)|response to drug (GO:0042493)|response to electrical stimulus (GO:0051602)|response to ethanol (GO:0045471)|response to hydrostatic pressure (GO:0051599)|response to nutrient levels (GO:0031667)|response to radiation (GO:0009314)|Sertoli cell development (GO:0060009)|small GTPase mediated signal transduction (GO:0007264)|sympathetic nervous system development (GO:0048485)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	axon (GO:0030424)|cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|dendrite (GO:0030425)|early endosome (GO:0005769)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|nerve growth factor binding (GO:0048406)|nerve growth factor receptor activity (GO:0010465)|neurotrophin binding (GO:0043121)|protein homodimerization activity (GO:0042803)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(3)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(7)|lung(35)|ovary(8)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	74	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)				Amitriptyline(DB00321)|Imatinib(DB00619)|Regorafenib(DB08896)	AGGACTTCCAGCGTGAGGCTG	0.632			T	"""TPM3, TPR, TFG"""	papillary thyroid					TSP Lung(10;0.080)			G|||	1066	0.212859	0.1142	0.2205	5008	,	,		16483	0.3204		0.1968	False		,,,				2504	0.2464				p.Q558Q		Atlas-SNP	.		Dom	yes		1	1q21-q22	4914	"""neurotrophic tyrosine kinase, receptor, type 1"""		E	.	NTRK1	287	.	0			c.G1674A						PASS	.	G	,,	631,3775	268.9+/-268.7	53,525,1625	52.0	48.0	49.0		1566,1656,1674	3.4	1.0	1	dbSNP_52	49	1887,6713	333.1+/-320.4	209,1469,2622	no	coding-synonymous,coding-synonymous,coding-synonymous	NTRK1	NM_001007792.1,NM_001012331.1,NM_002529.3	,,	262,1994,4247	AA,AG,GG		21.9419,14.3214,19.3603	,,	522/761,552/791,558/797	156846233	2518,10488	2203	4300	6503	SO:0001819	synonymous_variant	4914	exon14			CTTCCAGCGTGAG	Y09028	CCDS1161.1, CCDS30890.1, CCDS30891.1	1q21-q22	2014-09-17			ENSG00000198400	ENSG00000198400	2.7.10.1	"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	8031	protein-coding gene	gene with protein product	"""high affinity nerve growth factor receptor"""	191315				2869410	Standard	NM_001007792		Approved	TRK, TRKA, MTC	uc001fqh.1	P04629	OTTHUMG00000041304	ENST00000524377.1:c.1674G>A	1.37:g.156846233G>A		Somatic	188	0	0		WXS	Illumina HiSeq	Phase_I	176	86	0.488636	NM_002529	B2R6T5|B7ZM34|P08119|Q15655|Q15656|Q5D056|Q5VZS2|Q7Z5C3|Q9UIU7	Silent	SNP	ENST00000524377.1	37	CCDS1161.1																																																																																			G|0.804;A|0.196	0.196	strong		0.632	NTRK1-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000392279.1	NM_002529	
GLP2R	9340	hgsc.bcm.edu	37	17	9792768	9792768	+	Missense_Mutation	SNP	G	G	A	rs17681684	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:9792768G>A	ENST00000262441.5	+	13	1921	c.1408G>A	c.(1408-1410)Gac>Aac	p.D470N	GLP2R_ENST00000574745.1_Missense_Mutation_p.D290N	NM_004246.1	NP_004237.1	O95838	GLP2R_HUMAN	glucagon-like peptide 2 receptor	470			D -> N (in dbSNP:rs17681684). {ECO:0000269|PubMed:15489334}.		adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|positive regulation of cell proliferation (GO:0008284)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|glucagon receptor activity (GO:0004967)			endometrium(4)|large_intestine(7)|lung(22)|ovary(2)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)	44					Glucagon recombinant(DB00040)|Teduglutide(DB08900)	CCTGGGGAAGGACTTCCGGTT	0.592													A|||	504	0.100639	0.0212	0.1571	5008	,	,		19847	0.002		0.2773	False		,,,				2504	0.0879				p.D470N		Atlas-SNP	.											.	GLP2R	90	.	0			c.G1408A						PASS	.	A	ASN/ASP	323,4083	784.0+/-414.7	11,301,1891	50.0	52.0	51.0		1408	1.8	1.0	17	dbSNP_123	51	2708,5892	669.9+/-402.7	428,1852,2020	yes	missense	GLP2R	NM_004246.1	23	439,2153,3911	AA,AG,GG		31.4884,7.3309,23.3046	benign	470/554	9792768	3031,9975	2203	4300	6503	SO:0001583	missense	9340	exon13			GGGAAGGACTTCC	AF105367	CCDS11150.1	17p13.3	2012-08-10			ENSG00000065325	ENSG00000065325		"""GPCR / Class B : Glucagon receptors"""	4325	protein-coding gene	gene with protein product		603659				9990065	Standard	NM_004246		Approved		uc002gmd.1	O95838	OTTHUMG00000130269	ENST00000262441.5:c.1408G>A	17.37:g.9792768G>A	ENSP00000262441:p.Asp470Asn	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	78	37	0.474359	NM_004246	Q4VAT3	Missense_Mutation	SNP	ENST00000262441.5	37	CCDS11150.1	306	0.1401098901098901	15	0.03048780487804878	69	0.19060773480662985	1	0.0017482517482517483	221	0.29155672823219	A	8.451	0.853055	0.17106	0.073309	0.314884	ENSG00000065325	ENST00000396206;ENST00000262441	T	0.53640	0.61	5.43	1.83	0.25207	.	0.340133	0.21431	N	0.074649	T	0.00012	0.0000	N	0.03029	-0.43	0.54753	P	1.3000000000040757E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.40098	-0.9581	9	0.11485	T	0.65	.	5.4283	0.16438	0.5741:0.2756:0.1503:0.0	rs17681684;rs17681684	470	O95838	GLP2R_HUMAN	N	470	ENSP00000262441:D470N	ENSP00000262441:D470N	D	+	1	0	GLP2R	9733493	1.000000	0.71417	0.969000	0.41365	0.051000	0.14879	0.930000	0.28858	-0.146000	0.11274	-0.269000	0.10298	GAC	G|0.822;A|0.178	0.178	strong		0.592	GLP2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252601.4		
SSH2	85464	hgsc.bcm.edu	37	17	27959903	27959903	+	Missense_Mutation	SNP	G	G	A	rs2289629	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:27959903G>A	ENST00000269033.3	-	15	2379	c.2228C>T	c.(2227-2229)tCg>tTg	p.S743L	SSH2_ENST00000540801.1_Missense_Mutation_p.S770L|RP11-68I3.2_ENST00000581474.1_RNA	NM_001282129.1|NM_033389.2	NP_001269058.1|NP_203747.2	Q76I76	SSH2_HUMAN	slingshot protein phosphatase 2	743			S -> L (in dbSNP:rs2289629).		actin cytoskeleton organization (GO:0030036)|protein dephosphorylation (GO:0006470)|regulation of actin polymerization or depolymerization (GO:0008064)|regulation of axonogenesis (GO:0050770)|regulation of lamellipodium assembly (GO:0010591)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular space (GO:0005615)	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)		SSH2/SUZ12(2)	breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(16)|ovary(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						TGCATTTTCCGAGTGAGACTG	0.403													G|||	925	0.184704	0.1044	0.2983	5008	,	,		22841	0.0764		0.335	False		,,,				2504	0.1697				p.S743L		Atlas-SNP	.											.	SSH2	107	.	0			c.C2228T						PASS	.	G	LEU/SER	680,3726	284.9+/-277.9	48,584,1571	71.0	65.0	67.0		2228	4.1	1.0	17	dbSNP_100	67	2861,5739	448.8+/-361.9	484,1893,1923	yes	missense	SSH2	NM_033389.2	145	532,2477,3494	AA,AG,GG		33.2674,15.4335,27.2259	benign	743/1424	27959903	3541,9465	2203	4300	6503	SO:0001583	missense	85464	exon15			TTTTCCGAGTGAG	AB072359	CCDS11253.1, CCDS74024.1	17q11.2	2013-03-05	2013-03-05		ENSG00000141298	ENSG00000141298		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Slingshots"""	30580	protein-coding gene	gene with protein product		606779	"""slingshot homolog 2 (Drosophila)"""			11832213, 11214970	Standard	XM_005258059		Approved	KIAA1725	uc002heo.1	Q76I76	OTTHUMG00000132752	ENST00000269033.3:c.2228C>T	17.37:g.27959903G>A	ENSP00000269033:p.Ser743Leu	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	74	34	0.459459	NM_033389	Q8TDB5|Q8WYL1|Q8WYL2|Q96F40|Q96H36|Q9C0D8	Missense_Mutation	SNP	ENST00000269033.3	37	CCDS11253.1	432	0.1978021978021978	50	0.1016260162601626	108	0.2983425414364641	35	0.06118881118881119	239	0.3153034300791557	G	14.83	2.653224	0.47362	0.154335	0.332674	ENSG00000141298	ENST00000269033;ENST00000540801	T;T	0.54675	0.56;0.56	6.08	4.1	0.47936	.	0.456816	0.22979	N	0.053336	T	0.00012	0.0000	M	0.66939	2.045	0.09310	P	0.9999999999999972	B;B	0.26081	0.141;0.087	B;B	0.20184	0.028;0.013	T	0.09530	-1.0670	9	0.48119	T	0.1	-1.9919	17.9574	0.89073	0.0645:0.0:0.9355:0.0	rs2289629;rs17766954;rs52836060;rs59862381;rs2289629	770;743	F5H527;Q76I76	.;SSH2_HUMAN	L	743;770	ENSP00000269033:S743L;ENSP00000444743:S770L	ENSP00000269033:S743L	S	-	2	0	SSH2	24984029	1.000000	0.71417	1.000000	0.80357	0.923000	0.55619	3.615000	0.54167	0.907000	0.36646	-0.940000	0.02684	TCG	G|0.775;A|0.225	0.225	strong		0.403	SSH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256116.1	NM_033389	
ZNF319	57567	hgsc.bcm.edu	37	16	58032026	58032026	+	Silent	SNP	G	G	A	rs56347618	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:58032026G>A	ENST00000299237.2	-	2	766	c.144C>T	c.(142-144)gcC>gcT	p.A48A	USB1_ENST00000561743.1_5'Flank	NM_020807.1	NP_065858.1	Q9P2F9	ZN319_HUMAN	zinc finger protein 319	48	Pro-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			large_intestine(2)|lung(4)|ovary(1)|urinary_tract(1)	8						TGCCATAGACGGCACAGCCCA	0.697													G|||	101	0.0201677	0.003	0.0418	5008	,	,		15425	0.0		0.0567	False		,,,				2504	0.0112				p.A48A		Atlas-SNP	.											.	ZNF319	42	.	0			c.C144T						PASS	.	G		34,4362	42.3+/-75.8	0,34,2164	40.0	41.0	41.0		144	-10.4	0.1	16	dbSNP_129	41	421,8177	130.2+/-188.1	5,411,3883	no	coding-synonymous	ZNF319	NM_020807.1		5,445,6047	AA,AG,GG		4.8965,0.7734,3.5016		48/583	58032026	455,12539	2198	4299	6497	SO:0001819	synonymous_variant	57567	exon2			ATAGACGGCACAG	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		ENST00000299237.2:c.144C>T	16.37:g.58032026G>A		Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	71	30	0.422535	NM_020807	Q52LH8	Silent	SNP	ENST00000299237.2	37	CCDS32462.1																																																																																			G|0.970;A|0.030	0.030	strong		0.697	ZNF319-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430317.1		
CERS2	29956	hgsc.bcm.edu	37	1	150940625	150940625	+	Missense_Mutation	SNP	T	T	G	rs267738	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:150940625T>G	ENST00000271688.6	-	4	730	c.344A>C	c.(343-345)gAg>gCg	p.E115A	CERS2_ENST00000368954.5_Missense_Mutation_p.E115A|CERS2_ENST00000345896.4_5'UTR|RP11-316M1.12_ENST00000561111.1_RNA|RP11-316M1.12_ENST00000560481.1_RNA|CERS2_ENST00000561294.1_Missense_Mutation_p.E106A	NM_181746.3	NP_859530.1	Q96G23	CERS2_HUMAN	ceramide synthase 2	115			E -> A (in dbSNP:rs267738).		ceramide biosynthetic process (GO:0046513)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear membrane (GO:0031965)	DNA binding (GO:0003677)|sphingosine N-acyltransferase activity (GO:0050291)										GAACCAACGCTCTACCTGGCG	0.607													T|||	341	0.0680911	0.0061	0.0951	5008	,	,		16202	0.0258		0.1909	False		,,,				2504	0.0501				p.E115A		Atlas-SNP	.											LASS2,colon,carcinoma,0,1	.	.	1	0			c.A344C						PASS	.	T	ALA/GLU,ALA/GLU	176,4230	115.4+/-153.4	1,174,2028	67.0	73.0	71.0		344,344	4.9	1.0	1	dbSNP_79	71	1821,6779	325.8+/-317.1	200,1421,2679	yes	missense,missense	CERS2	NM_022075.4,NM_181746.3	107,107	201,1595,4707	GG,GT,TT		21.1744,3.9946,15.3545	probably-damaging,probably-damaging	115/381,115/381	150940625	1997,11009	2203	4300	6503	SO:0001583	missense	29956	exon4			CAACGCTCTACCT	AF189062	CCDS973.1	1q21.3	2012-09-20	2011-07-08	2011-07-08	ENSG00000143418	ENSG00000143418		"""Homeoboxes / CERS class"""	14076	protein-coding gene	gene with protein product		606920	"""longevity assurance (LAG1, S. cerevisiae) homolog 2"", ""LAG1 longevity assurance homolog 2 (S. cerevisiae)"", ""LAG1 homolog, ceramide synthase 2"""	LASS2		11543633	Standard	NM_181746		Approved	SP260, FLJ10243	uc001evz.3	Q96G23	OTTHUMG00000035064	ENST00000271688.6:c.344A>C	1.37:g.150940625T>G	ENSP00000271688:p.Glu115Ala	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	54	53	0.981481	NM_022075	D3DV06|Q5SZE5|Q9HD96|Q9NW79	Missense_Mutation	SNP	ENST00000271688.6	37	CCDS973.1	217	0.09935897435897435	4	0.008130081300813009	40	0.11049723756906077	19	0.033216783216783216	154	0.20316622691292877	T	32	5.158232	0.94686	0.039946	0.211744	ENSG00000143418	ENST00000368954;ENST00000271688;ENST00000368949;ENST00000361419;ENST00000421609;ENST00000457392	D;D;D;D;D;D	0.96041	-3.89;-3.89;-3.89;-3.89;-3.89;-3.89	4.9	4.9	0.64082	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);	0.115318	0.64402	D	0.000015	D	0.95915	0.8670	M	0.81942	2.565	0.09310	P	0.999999635895	P	0.45634	0.863	P	0.54590	0.756	D	0.95090	0.8221	9	0.30078	T	0.28	-19.5384	14.3739	0.66860	0.0:0.0:0.0:1.0	rs267738;rs556626;rs56588434;rs60175401;rs267738	115	Q96G23	CERS2_HUMAN	A	115;115;135;115;115;115	ENSP00000357950:E115A;ENSP00000271688:E115A;ENSP00000357945:E135A;ENSP00000355020:E115A;ENSP00000393239:E115A;ENSP00000394012:E115A	ENSP00000271688:E115A	E	-	2	0	CERS2	149207249	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	7.460000	0.80816	2.058000	0.61347	0.533000	0.62120	GAG	T|0.878;G|0.122	0.122	strong		0.607	CERS2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084897.2	NM_022075	
ZCCHC2	54877	hgsc.bcm.edu	37	18	60231851	60231851	+	Silent	SNP	A	A	G	rs12956093	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	216	0	0		WXS	Illumina HiSeq	Phase_I	167	81	0.48503	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	
THRB	7068	hgsc.bcm.edu	37	3	24184995	24184995	+	Silent	SNP	G	G	A	rs3752874	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:24184995G>A	ENST00000356447.4	-	7	1019	c.735C>T	c.(733-735)ttC>ttT	p.F245F	THRB_ENST00000396671.2_Silent_p.F245F|THRB_ENST00000416420.1_Silent_p.F245F|THRB_ENST00000280696.5_Silent_p.F260F	NM_000461.4|NM_001128177.1	NP_000452.2|NP_001121649.1	P10828	THB_HUMAN	thyroid hormone receptor, beta	245	Interaction with NR2F6.|Ligand-binding.				female courtship behavior (GO:0008050)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of female receptivity (GO:0007621)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|organ morphogenesis (GO:0009887)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of heart contraction (GO:0008016)|sensory perception of sound (GO:0007605)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|Type I pneumocyte differentiation (GO:0060509)	extracellular vesicular exosome (GO:0070062)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|thyroid hormone binding (GO:0070324)|thyroid hormone receptor activity (GO:0004887)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(6)|pancreas(2)|prostate(1)|skin(3)	19					Dextrothyroxine(DB00509)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Liotrix(DB01583)	GCCTTACCAGGAATTTCCGTT	0.488													G|||	789	0.157548	0.1536	0.1873	5008	,	,		21207	0.0605		0.1531	False		,,,				2504	0.2464				p.F245F	Melanoma(21;896 1043 15021 37958)	Atlas-SNP	.											.	THRB	52	.	0			c.C735T						PASS	.	G	,,	660,3746	280.5+/-275.4	56,548,1599	128.0	133.0	131.0		735,735,735	-1.0	1.0	3	dbSNP_107	131	1338,7262	261.3+/-283.8	117,1104,3079	no	coding-synonymous,coding-synonymous,coding-synonymous	THRB	NM_000461.4,NM_001128176.1,NM_001128177.1	,,	173,1652,4678	AA,AG,GG		15.5581,14.9796,15.3621	,,	245/462,245/462,245/462	24184995	1998,11008	2203	4300	6503	SO:0001819	synonymous_variant	7068	exon7			TACCAGGAATTTC		CCDS2641.1	3p24.2	2013-01-16	2011-05-19		ENSG00000151090	ENSG00000151090		"""Nuclear hormone receptors"""	11799	protein-coding gene	gene with protein product	"""avian erythroblastic leukemia viral (v-erb-a) oncogene homolog 2"", ""oncogene ERBA2"", ""generalized resistance to thyroid hormone"", ""thyroid hormone receptor beta 1"""	190160	"""thyroid hormone receptor, beta (avian erythroblastic leukemia viral (v-erb-a) oncogene homolog 2)"", ""pituitary resistance to thyroid hormone"", ""thyroid hormone receptor, beta (erythroblastic leukemia viral (v-erb-a) oncogene homolog 2, avian)"""	ERBA2, PRTH		1973914, 8040303	Standard	NM_000461		Approved	THRB1, THRB2, NR1A2, THR1, ERBA-BETA, GRTH	uc003ccy.4	P10828	OTTHUMG00000130478	ENST00000356447.4:c.735C>T	3.37:g.24184995G>A		Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	132	73	0.55303	NM_000461	B3KU79|P37243|Q13986|Q3KP35|Q6WGL2|Q9UD41	Silent	SNP	ENST00000356447.4	37	CCDS2641.1																																																																																			G|0.858;A|0.142	0.142	strong		0.488	THRB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252877.3	NM_000461	
CLHC1	130162	hgsc.bcm.edu	37	2	55449464	55449464	+	Silent	SNP	T	T	C	rs17852670	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:55449464T>C	ENST00000401408.1	-	3	429	c.84A>G	c.(82-84)caA>caG	p.Q28Q	CLHC1_ENST00000407122.1_Silent_p.Q28Q|CLHC1_ENST00000406437.2_5'UTR|CLHC1_ENST00000406076.1_Intron|CLHC1_ENST00000494539.1_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	209	0	0		WXS	Illumina HiSeq	Phase_I	394	80	0.203046	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	
SMC1B	27127	hgsc.bcm.edu	37	22	45767369	45767369	+	Silent	SNP	A	A	G	rs470062	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:45767369A>G	ENST00000357450.4	-	14	2294	c.2295T>C	c.(2293-2295)ttT>ttC	p.F765F	SMC1B_ENST00000404354.3_Silent_p.F765F	NM_148674.3	NP_683515.3	Q8NDV3	SMC1B_HUMAN	structural maintenance of chromosomes 1B	765					meiotic nuclear division (GO:0007126)|sister chromatid cohesion (GO:0007062)	chromosome, centromeric region (GO:0000775)|lateral element (GO:0000800)|meiotic cohesin complex (GO:0030893)|nuclear meiotic cohesin complex (GO:0034991)	ATP binding (GO:0005524)|DNA binding (GO:0003677)			breast(2)|endometrium(4)|kidney(3)|large_intestine(6)|lung(15)|ovary(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	37		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0182)		TCTTTTCTTGAAATTCTTTAA	0.303													A|||	836	0.166933	0.1309	0.1427	5008	,	,		18405	0.1746		0.1332	False		,,,				2504	0.2597				p.F765F		Atlas-SNP	.											.	SMC1B	215	.	0			c.T2295C						PASS	.	A		475,3149		23,429,1360	100.0	91.0	94.0		2295	2.4	1.0	22	dbSNP_80	94	1026,7122		64,898,3112	no	coding-synonymous	SMC1B	NM_148674.3		87,1327,4472	GG,GA,AA		12.592,13.1071,12.7506		765/1236	45767369	1501,10271	1812	4074	5886	SO:0001819	synonymous_variant	27127	exon14			TTCTTGAAATTCT	AJ504806	CCDS43027.1, CCDS74876.1	22q13	2006-07-06	2006-07-06	2006-07-06	ENSG00000077935	ENSG00000077935		"""Structural maintenance of chromosomes proteins"""	11112	protein-coding gene	gene with protein product		608685	"""SMC1 (structural maintenance of chromosomes 1, yeast)-like 1"", ""SMC1 structural maintenance of chromosomes 1-like 2 (yeast)"""	SMC1L2		10591208, 11564881	Standard	XM_005261566		Approved	bK268H5	uc003bgc.3	Q8NDV3	OTTHUMG00000151334	ENST00000357450.4:c.2295T>C	22.37:g.45767369A>G		Somatic	240	0	0		WXS	Illumina HiSeq	Phase_I	193	94	0.487047	NM_148674	A0AV46|B0QY23|B0QY24|Q5TIC3|Q6ZUF9|Q9Y3G5	Silent	SNP	ENST00000357450.4	37	CCDS43027.1																																																																																			A|0.862;G|0.138	0.138	strong		0.303	SMC1B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322256.2	NM_148674	
MUC4	4585	hgsc.bcm.edu	37	3	195509429	195509429	+	Missense_Mutation	SNP	A	A	G	rs28542401	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195509429A>G	ENST00000463781.3	-	2	9481	c.9022T>C	c.(9022-9024)Tct>Cct	p.S3008P	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.S3008P	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)		ACAGGAAGAGAGGTGGCGTGA	0.592																																					p.S3008P		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	0			c.T9022C						scavenged	.						16.0	13.0	14.0					3																	195509429		653	1561	2214	SO:0001583	missense	4585	exon2			GAAGAGAGGTGGC	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.9022T>C	3.37:g.195509429A>G	ENSP00000417498:p.Ser3008Pro	Somatic	30	2	0.0666667		WXS	Illumina HiSeq	Phase_I	60	58	0.966667	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	1217	0.5572344322344323	303	0.6158536585365854	180	0.4972375690607735	360	0.6293706293706294	374	0.49340369393139843	N	1.745	-0.490680	0.04322	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.34275	1.37;1.43	.	.	.	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.46028	P	0.0011740000000000084	B	0.14438	0.01	B	0.15870	0.014	T	0.41466	-0.9507	6	.	.	.	.	3.1064	0.06344	0.6149:0.0:0.0:0.385	rs28542401;rs57320341	2880	E7ESK3	.	P	3008	ENSP00000417498:S3008P;ENSP00000420243:S3008P	.	S	-	1	0	MUC4	196994208	0.018000	0.18449	0.195000	0.23364	0.000000	0.00434	-2.448000	0.01009	0.402000	0.25451	0.000000	0.15137	TCT	A|0.389;C|0.096;G|0.515	0.515	strong		0.592	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
OR5I1	10798	hgsc.bcm.edu	37	11	55703728	55703728	+	Missense_Mutation	SNP	A	A	G	rs4367963	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:55703728A>G	ENST00000301532.3	-	1	148	c.149T>C	c.(148-150)tTg>tCg	p.L50S		NM_006637.1	NP_006628.1	Q13606	OR5I1_HUMAN	olfactory receptor, family 5, subfamily I, member 1	50			L -> S (in dbSNP:rs4367963).		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)	p.L50S(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(34)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	52						AATCCTGATCAACAGCATCAA	0.398													A|||	457	0.091254	0.1286	0.0418	5008	,	,		16386	0.0903		0.0954	False		,,,				2504	0.0726				p.L50S		Atlas-SNP	.											OR5I1,caecum,carcinoma,+1,2	OR5I1	110	2	1	Substitution - Missense(1)	stomach(1)	c.T149C						PASS	.	A	SER/LEU	502,3900	229.1+/-243.8	32,438,1731	70.0	69.0	69.0		149	5.1	0.2	11	dbSNP_111	69	720,7872	174.2+/-224.5	31,658,3607	yes	missense	OR5I1	NM_006637.1	145	63,1096,5338	GG,GA,AA		8.3799,11.4039,9.4043	probably-damaging	50/315	55703728	1222,11772	2201	4296	6497	SO:0001583	missense	10798	exon1			CTGATCAACAGCA	BC069093	CCDS7949.1	11q11	2012-08-09			ENSG00000167825	ENSG00000167825		"""GPCR / Class A : Olfactory receptors"""	8347	protein-coding gene	gene with protein product		608496				9017400, 9787077	Standard	NM_006637		Approved	HSOlf1, OLF1	uc010ris.2	Q13606	OTTHUMG00000166821	ENST00000301532.3:c.149T>C	11.37:g.55703728A>G	ENSP00000301532:p.Leu50Ser	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	80	55	0.6875	NM_006637	Q6IEU4	Missense_Mutation	SNP	ENST00000301532.3	37	CCDS7949.1	202	0.0924908424908425	73	0.1483739837398374	18	0.049723756906077346	44	0.07692307692307693	67	0.08839050131926121	A	18.62	3.663270	0.67700	0.114039	0.083799	ENSG00000167825	ENST00000301532	T	0.02837	4.14	5.05	5.05	0.67936	GPCR, rhodopsin-like superfamily (1);	0.000000	0.36703	N	0.002444	T	0.00073	0.0002	M	0.65498	2.005	0.52501	P	4.4000000000044004E-5	D	0.76494	0.999	D	0.80764	0.994	T	0.08186	-1.0734	9	0.87932	D	0	.	13.0502	0.58950	1.0:0.0:0.0:0.0	rs4367963;rs52814279;rs57530320;rs4367963	50	Q13606	OR5I1_HUMAN	S	50	ENSP00000301532:L50S	ENSP00000301532:L50S	L	-	2	0	OR5I1	55460304	0.186000	0.23225	0.247000	0.24249	0.903000	0.53119	4.378000	0.59568	2.020000	0.59435	0.519000	0.50382	TTG	A|0.901;G|0.099	0.099	strong		0.398	OR5I1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391528.1	NM_006637	
RASGRP4	115727	hgsc.bcm.edu	37	19	38912764	38912764	+	Missense_Mutation	SNP	A	A	G	rs892055	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:38912764A>G	ENST00000587738.1	-	2	123	c.53T>C	c.(52-54)aTa>aCa	p.I18T	RASGRP4_ENST00000587753.1_Missense_Mutation_p.I18T|RASGRP4_ENST00000293062.9_Missense_Mutation_p.I18T|RASGRP4_ENST00000586305.1_Missense_Mutation_p.I18T|RASGRP4_ENST00000454404.2_Missense_Mutation_p.I18T|RASGRP4_ENST00000433821.2_Missense_Mutation_p.I18T|RASGRP4_ENST00000426920.2_Missense_Mutation_p.I18T			Q8TDF6	GRP4_HUMAN	RAS guanyl releasing protein 4	18			I -> T (in dbSNP:rs892055). {ECO:0000269|PubMed:11880369, ECO:0000269|PubMed:11956218, ECO:0000269|PubMed:15489334}.		activation of phospholipase C activity (GO:0007202)|cell growth (GO:0016049)|cell proliferation (GO:0008283)|myeloid cell differentiation (GO:0030099)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of Ras protein signal transduction (GO:0046579)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|response to extracellular stimulus (GO:0009991)|small GTPase mediated signal transduction (GO:0007264)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytoplasm (GO:0005737)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|diacylglycerol binding (GO:0019992)|GTP-dependent protein binding (GO:0030742)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)			cervix(1)|kidney(1)|large_intestine(4)|lung(12)|pancreas(1)|prostate(3)|skin(1)	23	all_cancers(60;4.21e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)			TCGCCCTCCTATTTTTCCGGT	0.602													G|||	2696	0.538339	0.6604	0.4539	5008	,	,		12805	0.5536		0.3549	False		,,,				2504	0.6063				p.I18T		Atlas-SNP	.											.	RASGRP4	54	.	0			c.T53C						PASS	.	G	THR/ILE,THR/ILE,THR/ILE,THR/ILE,THR/ILE,THR/ILE,THR/ILE	2221,1617		637,947,335	35.0	41.0	39.0	http://www.ncbi.nlm.nih.gov/pubmed?term	53,53,53,53,53,53,53	4.1	0.1	19	dbSNP_86	39	2908,5338		539,1830,1754	yes	missense,missense,missense,missense,missense,missense,missense	RASGRP4	NM_001146202.1,NM_001146203.1,NM_001146204.1,NM_001146205.1,NM_001146206.1,NM_001146207.1,NM_170604.2	89,89,89,89,89,89,89	1176,2777,2089	GG,GA,AA	http://www.ncbi.nlm.nih.gov/pubmed?term	35.2656,42.1313,42.4446	benign,benign,benign,benign,benign,benign,benign	18/660,18/582,18/605,18/640,18/485,18/577,18/674	38912764	5129,6955	1919	4123	6042	SO:0001583	missense	115727	exon2			CCTCCTATTTTTC	AY048119	CCDS46068.1, CCDS54262.1, CCDS54263.1, CCDS54264.1	19q13.1	2013-01-10						"""EF-hand domain containing"""	18958	protein-coding gene	gene with protein product		607320				11956218	Standard	NM_170604		Approved		uc021uub.1	Q8TDF6		ENST00000587738.1:c.53T>C	19.37:g.38912764A>G	ENSP00000465772:p.Ile18Thr	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	88	87	0.988636	NM_001146206	A6H8M4|C0LTP2|C0LTP3|C0LTP4|C0LTP5|C0LTP7|C9J416|C9JHZ1|Q8N858|Q96QN5|Q96QN6|Q96QN7	Missense_Mutation	SNP	ENST00000587738.1	37	CCDS46068.1	1068	0.489010989010989	317	0.6443089430894309	152	0.4198895027624309	322	0.5629370629370629	277	0.3654353562005277	G	0.005	-2.119697	0.00346	0.578687	0.352656	ENSG00000171777	ENST00000433821;ENST00000293062;ENST00000426920;ENST00000405332;ENST00000454404	T;T;T;T	0.26957	1.7;1.7;1.7;1.7	4.07	4.07	0.47477	.	0.919137	0.09218	N	0.832255	T	0.00012	0.0000	N	0.00538	-1.39	0.80722	P	0.0	B;B;B;B;B;B;B	0.16802	0.0;0.0;0.019;0.0;0.0;0.0;0.0	B;B;B;B;B;B;B	0.14578	0.0;0.0;0.011;0.0;0.0;0.0;0.0	T	0.44112	-0.9349	9	0.02654	T	1	0.0828	10.0232	0.42055	0.1009:0.0:0.8991:0.0	rs892055;rs17778342;rs57508829;rs892055	18;18;18;18;18;18;18	C0LTP5;C0LTP7;C0LTP2;C0LTP4;C0LTP3;Q8TDF6-2;Q8TDF6	.;.;.;.;.;.;GRP4_HUMAN	T	18	ENSP00000411878:I18T;ENSP00000293062:I18T;ENSP00000445966:I18T;ENSP00000416463:I18T	ENSP00000293062:I18T	I	-	2	0	RASGRP4	43604604	0.427000	0.25514	0.059000	0.19551	0.101000	0.19017	2.730000	0.47335	1.089000	0.41292	-0.355000	0.07637	ATA	A|0.489;G|0.510	0.510	strong		0.602	RASGRP4-013	KNOWN	non_canonical_other|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460540.1	NM_170604	
FGFR2	2263	hgsc.bcm.edu	37	10	123239112	123239112	+	3'UTR	SNP	G	G	A	rs1047057	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:123239112G>A	ENST00000358487.5	-	0	2997				FGFR2_ENST00000369061.4_3'UTR|FGFR2_ENST00000369060.4_3'UTR|FGFR2_ENST00000478859.1_3'UTR|FGFR2_ENST00000356226.4_3'UTR|FGFR2_ENST00000357555.5_Silent_p.L703L	NM_000141.4	NP_000132.3	P21802	FGFR2_HUMAN	fibroblast growth factor receptor 2						angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|axonogenesis (GO:0007409)|bone development (GO:0060348)|bone mineralization (GO:0030282)|bone morphogenesis (GO:0060349)|branch elongation involved in salivary gland morphogenesis (GO:0060667)|branching involved in labyrinthine layer morphogenesis (GO:0060670)|branching involved in prostate gland morphogenesis (GO:0060442)|branching involved in salivary gland morphogenesis (GO:0060445)|branching morphogenesis of a nerve (GO:0048755)|bud elongation involved in lung branching (GO:0060449)|cell fate commitment (GO:0045165)|cell-cell signaling (GO:0007267)|coronal suture morphogenesis (GO:0060365)|digestive tract development (GO:0048565)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic organ development (GO:0048568)|embryonic organ morphogenesis (GO:0048562)|embryonic pattern specification (GO:0009880)|endodermal digestive tract morphogenesis (GO:0061031)|epidermal growth factor receptor signaling pathway (GO:0007173)|epidermis morphogenesis (GO:0048730)|epithelial cell differentiation (GO:0030855)|epithelial cell proliferation involved in salivary gland morphogenesis (GO:0060664)|epithelial to mesenchymal transition (GO:0001837)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|fibroblast growth factor receptor signaling pathway involved in hemopoiesis (GO:0035603)|fibroblast growth factor receptor signaling pathway involved in mammary gland specification (GO:0060595)|fibroblast growth factor receptor signaling pathway involved in negative regulation of apoptotic process in bone marrow (GO:0035602)|fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development (GO:0035607)|fibroblast growth factor receptor signaling pathway involved in positive regulation of cell proliferation in bone marrow (GO:0035604)|gland morphogenesis (GO:0022612)|hair follicle morphogenesis (GO:0031069)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|inner ear morphogenesis (GO:0042472)|insulin receptor signaling pathway (GO:0008286)|lacrimal gland development (GO:0032808)|lateral sprouting from an epithelium (GO:0060601)|lens fiber cell development (GO:0070307)|limb bud formation (GO:0060174)|lung alveolus development (GO:0048286)|lung development (GO:0030324)|lung lobe morphogenesis (GO:0060463)|lung-associated mesenchyme development (GO:0060484)|mammary gland bud formation (GO:0060615)|membranous septum morphogenesis (GO:0003149)|mesenchymal cell differentiation (GO:0048762)|mesenchymal cell differentiation involved in lung development (GO:0060915)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesodermal cell differentiation (GO:0048333)|midbrain development (GO:0030901)|morphogenesis of embryonic epithelium (GO:0016331)|multicellular organism growth (GO:0035264)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of mitosis (GO:0045839)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuromuscular junction development (GO:0007528)|neurotrophin TRK receptor signaling pathway (GO:0048011)|odontogenesis (GO:0042476)|orbitofrontal cortex development (GO:0021769)|organ growth (GO:0035265)|organ morphogenesis (GO:0009887)|otic vesicle formation (GO:0030916)|outflow tract septum morphogenesis (GO:0003148)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of epithelial cell proliferation involved in lung morphogenesis (GO:0060501)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of Wnt signaling pathway (GO:0030177)|post-embryonic development (GO:0009791)|prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis (GO:0060527)|prostate epithelial cord elongation (GO:0060523)|prostate gland morphogenesis (GO:0060512)|protein autophosphorylation (GO:0046777)|pyramidal neuron development (GO:0021860)|regulation of branching involved in prostate gland morphogenesis (GO:0060687)|regulation of cell fate commitment (GO:0010453)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)|regulation of morphogenesis of a branching structure (GO:0060688)|regulation of multicellular organism growth (GO:0040014)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoblast proliferation (GO:0033688)|regulation of smooth muscle cell differentiation (GO:0051150)|regulation of smoothened signaling pathway (GO:0008589)|reproductive structure development (GO:0048608)|skeletal system morphogenesis (GO:0048705)|squamous basal epithelial stem cell differentiation involved in prostate gland acinus development (GO:0060529)|synaptic vesicle transport (GO:0048489)|ureteric bud development (GO:0001657)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|ventricular zone neuroblast division (GO:0021847)	cell cortex (GO:0005938)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|excitatory synapse (GO:0060076)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|fibroblast growth factor binding (GO:0017134)|fibroblast growth factor-activated receptor activity (GO:0005007)|heparin binding (GO:0008201)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)	p.L703L(1)		breast(3)|central_nervous_system(3)|cervix(2)|endometrium(98)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(7)|lung(21)|ovary(4)|skin(30)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(2)	181		Lung NSC(174;0.0841)|all_lung(145;0.106)|all_neural(114;0.107)	STAD - Stomach adenocarcinoma(1;7.52e-05)|all cancers(1;0.0722)	all cancers(201;9.73e-05)|GBM - Glioblastoma multiforme(135;0.0845)	Palifermin(DB00039)|Ponatinib(DB08901)|Regorafenib(DB08896)|Thalidomide(DB01041)	TCCACAGCCAGTACGCACGGC	0.483		5	Mis		"""gastric. NSCLC, endometrial"""		"""Crouzon, Pfeiffer, and Apert syndromes"""		Saethre-Chotzen syndrome;Apert syndrome				G|||	2075	0.414337	0.0938	0.6873	5008	,	,		15689	0.3512		0.5099	False		,,,				2504	0.6207				p.L703L		Atlas-SNP	.		Dom	yes		10	10q26	2263	fibroblast growth factor receptor 2	yes	E	FGFR2_ENST00000357555,NS,carcinoma,0,1	FGFR2	758	1	1	Substitution - coding silent(1)	stomach(1)	c.C2107T						PASS	.	G	,,,,,,	237,1147		19,199,474	86.0	84.0	85.0		,,2107,,,,	4.5	0.9	10	dbSNP_86	85	1747,1435		500,747,344	no	utr-3,utr-3,coding-synonymous,utr-3,utr-3,utr-3,utr-3	FGFR2	NM_000141.4,NM_001144914.1,NM_001144915.1,NM_001144916.1,NM_001144917.1,NM_001144918.1,NM_022970.3	,,,,,,	519,946,818	AA,AG,GG		45.0974,17.1243,43.4516	,,,,,,	,,703/708,,,,	123239112	1984,2582	692	1591	2283	SO:0001624	3_prime_UTR_variant	2263	exon17	Familial Cancer Database	Acrocephalosyndactyly type III;Acrocephalosyndactyly type I and II, ACS1. ACS2, incl Apert-Crouzon s.	CAGCCAGTACGCA	AK026508	CCDS7620.2, CCDS31298.1, CCDS44485.1, CCDS44486.1, CCDS44487.1, CCDS44488.1, CCDS44489.1, CCDS53584.1, CCDS73210.1	10q25.3-q26	2013-01-11	2008-08-01		ENSG00000066468	ENSG00000066468		"""CD molecules"", ""Immunoglobulin superfamily / I-set domain containing"""	3689	protein-coding gene	gene with protein product	"""Crouzon syndrome"", ""Pfeiffer syndrome"""	176943	"""bacteria-expressed kinase"", ""keratinocyte growth factor receptor"", ""craniofacial dysostosis 1"", ""Jackson-Weiss syndrome"""	KGFR, BEK, CFD1, JWS			Standard	NM_022970		Approved	CEK3, TK14, TK25, ECT1, K-SAM, CD332	uc021pzy.1	P21802	OTTHUMG00000019175	ENST00000358487.5:c.*259C>T	10.37:g.123239112G>A		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	76	35	0.460526	NM_001144915	B4DFC2|E7EVR6|E9PCR0|P18443|Q01742|Q12922|Q14300|Q14301|Q14302|Q14303|Q14304|Q14305|Q14672|Q14718|Q14719|Q1KHY5|Q86YI4|Q8IXC7|Q96KL9|Q96KM0|Q96KM1|Q96KM2|Q9NZU2|Q9NZU3|Q9UD01|Q9UD02|Q9UIH3|Q9UIH4|Q9UIH5|Q9UIH6|Q9UIH7|Q9UIH8|Q9UM87|Q9UMC6|Q9UNS7|Q9UQH7|Q9UQH8|Q9UQH9|Q9UQI0	Silent	SNP	ENST00000358487.5	37	CCDS31298.1																																																																																			G|0.609;A|0.391	0.391	strong		0.483	FGFR2-001	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000050715.1	NM_022976, NM_000141	
AKAP10	11216	hgsc.bcm.edu	37	17	19861458	19861458	+	Missense_Mutation	SNP	C	C	T	rs2108978	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:19861458C>T	ENST00000225737.6	-	4	903	c.746G>A	c.(745-747)cGt>cAt	p.R249H	AKAP10_ENST00000395536.3_Missense_Mutation_p.R249H|AKAP10_ENST00000572155.1_5'Flank	NM_007202.3	NP_009133.2	O43572	AKA10_HUMAN	A kinase (PRKA) anchor protein 10	249	RGS 1. {ECO:0000255|PROSITE- ProRule:PRU00171}.		R -> H (in dbSNP:rs2108978).		blood coagulation (GO:0007596)|protein localization (GO:0008104)|signal transduction (GO:0007165)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)				NS(1)|endometrium(3)|kidney(1)|large_intestine(4)|liver(1)|lung(3)|ovary(1)|prostate(1)|skin(3)|stomach(1)|urinary_tract(2)	21	all_cancers(12;2.08e-05)|all_epithelial(12;0.00158)|Breast(13;0.165)					CATTTCAAGACGGAGAGAATG	0.443													T|||	1951	0.389577	0.6104	0.4135	5008	,	,		18641	0.1895		0.3946	False		,,,				2504	0.2751				p.R249H		Atlas-SNP	.											.	AKAP10	47	.	0			c.G746A	GRCh37	CM067336	AKAP10	M	rs2108978	PASS	.	T	HIS/ARG	2491,1915	546.9+/-377.1	716,1059,428	139.0	132.0	134.0		746	2.4	1.0	17	dbSNP_96	134	3296,5304	647.3+/-400.4	633,2030,1637	yes	missense	AKAP10	NM_007202.2	29	1349,3089,2065	TT,TC,CC		38.3256,43.4635,44.4948	benign	249/663	19861458	5787,7219	2203	4300	6503	SO:0001583	missense	11216	exon4			TCAAGACGGAGAG	AF037439	CCDS11214.1	17p11.1	2008-07-18			ENSG00000108599	ENSG00000108599		"""A-kinase anchor proteins"""	368	protein-coding gene	gene with protein product	"""dual-specificity A-kinase anchoring protein 2"", ""protein kinase A anchoring protein 10"", ""mitochondrial A kinase PPKA anchor protein 10"""	604694				9326583	Standard	NM_007202		Approved	D-AKAP2, PRKA10, MGC9414	uc002gwo.4	O43572	OTTHUMG00000059515	ENST00000225737.6:c.746G>A	17.37:g.19861458C>T	ENSP00000225737:p.Arg249His	Somatic	260	1	0.00384615		WXS	Illumina HiSeq	Phase_I	208	100	0.480769	NM_007202	B2R650|Q96AJ7	Missense_Mutation	SNP	ENST00000225737.6	37	CCDS11214.1	851	0.38965201465201466	303	0.6158536585365854	150	0.4143646408839779	101	0.17657342657342656	297	0.391820580474934	T	0.011	-1.725654	0.00694	0.565365	0.383256	ENSG00000108599	ENST00000225737;ENST00000395536	T	0.19105	2.17	5.87	2.36	0.29203	Regulator of G protein signalling (2);Regulator of G protein signalling superfamily (1);	0.366125	0.33938	N	0.004410	T	0.00012	0.0000	N	0.00347	-1.61	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	0.36792	-0.9733	9	0.08179	T	0.78	-3.256	6.0625	0.19846	0.0:0.2526:0.2253:0.5221	rs2108978;rs17668228;rs59137256;rs2108978	249;249;249	E7EMD6;Q2XPN4;O43572	.;.;AKA10_HUMAN	H	249	ENSP00000225737:R249H	ENSP00000225737:R249H	R	-	2	0	AKAP10	19802050	0.989000	0.36119	0.995000	0.50966	0.206000	0.24218	0.073000	0.14640	0.128000	0.18479	-0.332000	0.08345	CGT	C|0.582;T|0.418	0.418	strong		0.443	AKAP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132380.2	NM_007202	
FAAH	2166	hgsc.bcm.edu	37	1	46870761	46870761	+	Missense_Mutation	SNP	C	C	A	rs324420	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:46870761C>A	ENST00000243167.8	+	3	469	c.385C>A	c.(385-387)Cca>Aca	p.P129T	FAAH_ENST00000493735.1_3'UTR	NM_001441.2	NP_001432.2	O00519	FAAH1_HUMAN	fatty acid amide hydrolase	129			P -> T (polymorphism associated with susceptibility to drug abuse; the mutant enzyme is more sensitive to proteolytic degradation; displays reduced cellular expression probably due to a post- translational mechanism preceding productive folding; dbSNP:rs324420). {ECO:0000269|Ref.3, ECO:0000269|Ref.5}.		fatty acid catabolic process (GO:0009062)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|organelle membrane (GO:0031090)	acylglycerol lipase activity (GO:0047372)|carbon-nitrogen ligase activity, with glutamine as amido-N-donor (GO:0016884)|fatty acid amide hydrolase activity (GO:0017064)			breast(3)|endometrium(4)|kidney(2)|large_intestine(3)|lung(7)|ovary(2)|skin(1)	22	Acute lymphoblastic leukemia(166;0.155)				Propofol(DB00818)|Thiopental(DB00599)	GTCTCAGGCCCCAAGGCAGGG	0.582													C|||	1310	0.261581	0.3676	0.3516	5008	,	,		20101	0.1756		0.2107	False		,,,				2504	0.1953				p.P129T		Atlas-SNP	.											.	FAAH	36	.	0			c.C385A	GRCh37	CM023913	FAAH	M	rs324420	PASS	.	C	THR/PRO	1533,2873	485.7+/-360.4	274,985,944	79.0	72.0	74.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	385	3.1	0.4	1	dbSNP_79	74	1722,6878	313.8+/-311.5	172,1378,2750	yes	missense	FAAH	NM_001441.2	38	446,2363,3694	AA,AC,CC		20.0233,34.7935,25.0269	benign	129/580	46870761	3255,9751	2203	4300	6503	SO:0001583	missense	2166	exon3			CAGGCCCCAAGGC	U82535	CCDS535.1	1p35-p34	2008-02-05			ENSG00000117480	ENSG00000117480			3553	protein-coding gene	gene with protein product		602935				9122178	Standard	NM_001441		Approved	FAAH-1	uc001cpu.2	O00519	OTTHUMG00000007811	ENST00000243167.8:c.385C>A	1.37:g.46870761C>A	ENSP00000243167:p.Pro129Thr	Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	156	82	0.525641	NM_001441	D3DQ19|Q52M86|Q5TDF8	Missense_Mutation	SNP	ENST00000243167.8	37	CCDS535.1	542	0.24816849816849818	180	0.36585365853658536	101	0.27900552486187846	100	0.17482517482517482	161	0.21240105540897097	C	3.886	-0.024929	0.07589	0.347935	0.200233	ENSG00000117480	ENST00000243167	T	0.53640	0.61	5.17	3.08	0.35506	Amidase signature domain (2);	0.475915	0.21894	N	0.067550	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B	0.15719	0.014	B	0.17433	0.018	T	0.38929	-0.9638	9	0.18276	T	0.48	-12.2653	7.2179	0.25969	0.2941:0.6151:0.0:0.0908	rs324420;rs57947754;rs324420	129	O00519	FAAH1_HUMAN	T	129	ENSP00000243167:P129T	ENSP00000243167:P129T	P	+	1	0	FAAH	46643348	0.001000	0.12720	0.395000	0.26283	0.407000	0.30961	0.726000	0.25984	2.417000	0.82017	0.313000	0.20887	CCA	C|0.749;A|0.251	0.251	strong		0.582	FAAH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021443.1	NM_001441	
TGM4	7047	hgsc.bcm.edu	37	3	44948590	44948590	+	Missense_Mutation	SNP	G	G	A	rs9876921	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:44948590G>A	ENST00000296125.4	+	10	1293	c.1225G>A	c.(1225-1227)Gta>Ata	p.V409I		NM_003241.3	NP_003232.2	P49221	TGM4_HUMAN	transglutaminase 4	409			V -> I (in dbSNP:rs9876921).		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)	GGAGTTACACGTAATTTCAAT	0.468													G|||	3102	0.619409	0.4743	0.5677	5008	,	,		19381	0.8849		0.4463	False		,,,				2504	0.7566				p.V409I		Atlas-SNP	.											.	TGM4	82	.	0			c.G1225A						PASS	.	G	ILE/VAL	2047,2359	567.7+/-382.2	489,1069,645	158.0	148.0	152.0		1225	-4.1	0.0	3	dbSNP_119	152	4066,4534	558.9+/-387.3	943,2180,1177	yes	missense	TGM4	NM_003241.3	29	1432,3249,1822	AA,AG,GG		47.2791,46.4594,47.0014	benign	409/685	44948590	6113,6893	2203	4300	6503	SO:0001583	missense	7047	exon10			TTACACGTAATTT	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.1225G>A	3.37:g.44948590G>A	ENSP00000296125:p.Val409Ile	Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	145	74	0.510345	NM_003241	Q16707|Q96QN4	Missense_Mutation	SNP	ENST00000296125.4	37	CCDS2723.1	1284	0.5879120879120879	231	0.4695121951219512	193	0.5331491712707183	510	0.8916083916083916	350	0.46174142480211083	G	0.007	-2.000963	0.00431	0.464594	0.472791	ENSG00000163810	ENST00000296125	T	0.79352	-1.26	2.03	-4.07	0.03975	.	6.005810	0.02973	N	0.144636	T	0.00012	0.0000	N	0.03983	-0.305	0.80722	P	0.0	B	0.09022	0.002	B	0.06405	0.002	T	0.39440	-0.9614	9	0.40728	T	0.16	.	2.4576	0.04533	0.3167:0.3687:0.2126:0.102	rs9876921;rs17556393;rs9876921	409	P49221	TGM4_HUMAN	I	409	ENSP00000296125:V409I	ENSP00000296125:V409I	V	+	1	0	TGM4	44923594	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.059000	0.14322	-2.460000	0.00537	-3.119000	0.00061	GTA	G|0.470;A|0.530	0.530	strong		0.468	TGM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256755.2	NM_003241	
AMZ1	155185	hgsc.bcm.edu	37	7	2752152	2752152	+	Silent	SNP	G	G	A	rs798565	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:2752152G>A	ENST00000312371.4	+	7	1505	c.1137G>A	c.(1135-1137)tcG>tcA	p.S379S	AMZ1_ENST00000489665.1_Intron|AMZ1_ENST00000407112.1_3'UTR	NM_133463.1	NP_597720.1	Q400G9	AMZ1_HUMAN	archaelysin family metallopeptidase 1	379							metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(2)|kidney(1)|large_intestine(4)|lung(8)|skin(1)	16		Ovarian(82;0.0779)		OV - Ovarian serous cystadenocarcinoma(56;5.03e-14)		CCTTCGCCTCGGGGCCAGAGG	0.687													G|||	900	0.179712	0.0794	0.2464	5008	,	,		16592	0.2004		0.2793	False		,,,				2504	0.1442				p.S379S		Atlas-SNP	.											AMZ1,colon,carcinoma,0,3	AMZ1	41	3	0			c.G1137A						PASS	.	G		440,3958		30,380,1789	20.0	23.0	22.0		1137	-6.0	0.0	7	dbSNP_86	22	2435,6163		364,1707,2228	no	coding-synonymous	AMZ1	NM_133463.1		394,2087,4017	AA,AG,GG		28.3205,10.0045,22.1222		379/499	2752152	2875,10121	2199	4299	6498	SO:0001819	synonymous_variant	155185	exon7			CGCCTCGGGGCCA	AB075830	CCDS34589.1, CCDS64582.1	7p22.3	2008-01-17			ENSG00000174945	ENSG00000174945			22231	protein-coding gene	gene with protein product	"""archaemetzincin-1"""	615168				15972818	Standard	NM_133463		Approved	KIAA1950	uc003smr.1	Q400G9	OTTHUMG00000152111	ENST00000312371.4:c.1137G>A	7.37:g.2752152G>A		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	63	14	0.222222	NM_133463	B3KRS0|Q8TF51	Silent	SNP	ENST00000312371.4	37	CCDS34589.1																																																																																			G|0.793;A|0.207	0.207	strong		0.687	AMZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325244.1	NM_133463	
PHKG2	5261	hgsc.bcm.edu	37	16	30762886	30762886	+	Silent	SNP	C	C	T	rs56029513		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:30762886C>T	ENST00000563588.1	+	4	527	c.288C>T	c.(286-288)tcC>tcT	p.S96S	PHKG2_ENST00000328273.7_Silent_p.S96S|RP11-2C24.4_ENST00000483578.1_lincRNA|PHKG2_ENST00000424889.3_Silent_p.S96S	NM_000294.2	NP_000285.1	P15735	PHKG2_HUMAN	phosphorylase kinase, gamma 2 (testis)	96	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				carbohydrate metabolic process (GO:0005975)|generation of precursor metabolites and energy (GO:0006091)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|glycogen catabolic process (GO:0005980)|glycogen metabolic process (GO:0005977)|positive regulation of glycogen catabolic process (GO:0045819)|protein phosphorylation (GO:0006468)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|phosphorylase kinase complex (GO:0005964)	ATP binding (GO:0005524)|phosphorylase kinase activity (GO:0004689)|protein serine/threonine kinase activity (GO:0004674)|tau-protein kinase activity (GO:0050321)			ovary(1)|skin(1)	2			Colorectal(24;0.198)			TCATCGATTCCTACGAGTCTT	0.547													c|||	1	0.000199681	0.0008	0.0	5008	,	,		22627	0.0		0.0	False		,,,				2504	0.0				p.S96S		Atlas-SNP	.											.	PHKG2	29	.	0			c.C288T						PASS	.	G	,	3,4391	6.2+/-15.9	0,3,2194	522.0	465.0	484.0		288,288	3.2	1.0	16	dbSNP_129	484	21,8579	15.3+/-51.7	0,21,4279	no	coding-synonymous,coding-synonymous	PHKG2	NM_000294.2,NM_001172432.1	,	0,24,6473	TT,TC,CC		0.2442,0.0683,0.1847	,	96/407,96/375	30762886	24,12970	2197	4300	6497	SO:0001819	synonymous_variant	5261	exon4			CGATTCCTACGAG	S73483, M31606	CCDS10690.1, CCDS54002.1	16p11.2	2008-02-05			ENSG00000156873	ENSG00000156873			8931	protein-coding gene	gene with protein product		172471				2915644, 8020963	Standard	NM_000294		Approved		uc021tgo.1	P15735	OTTHUMG00000132400	ENST00000563588.1:c.288C>T	16.37:g.30762886C>T		Somatic	533	1	0.00187617		WXS	Illumina HiSeq	Phase_I	672	239	0.355655	NM_001172432	A8K0C7|B4DEB7|E9PEU3|P11800	Silent	SNP	ENST00000563588.1	37	CCDS10690.1																																																																																			C|0.997;T|0.003	0.003	strong		0.547	PHKG2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255531.2	NM_000294	
CSRP3	8048	hgsc.bcm.edu	37	11	19207841	19207841	+	Silent	SNP	C	C	T	rs13451	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:19207841C>T	ENST00000533783.1	-	5	576	c.336G>A	c.(334-336)gcG>gcA	p.A112A	CSRP3_ENST00000265968.3_Silent_p.A112A	NM_003476.4	NP_003467.1	P50461	CSRP3_HUMAN	cysteine and glycine-rich protein 3 (cardiac LIM protein)	112					cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue development (GO:0048738)|cardiac myofibril assembly (GO:0055003)|cellular calcium ion homeostasis (GO:0006874)|detection of muscle stretch (GO:0035995)|protein localization to organelle (GO:0033365)|regulation of the force of heart contraction (GO:0002026)|skeletal muscle tissue development (GO:0007519)	cytoskeleton (GO:0005856)|nucleus (GO:0005634)|Z disc (GO:0030018)	actinin binding (GO:0042805)|structural constituent of muscle (GO:0008307)|telethonin binding (GO:0031433)|zinc ion binding (GO:0008270)			kidney(2)|large_intestine(2)|lung(4)|upper_aerodigestive_tract(2)	10						CTCCAAACTTCGCAGTGAATT	0.502													C|||	214	0.0427316	0.0038	0.0519	5008	,	,		22172	0.0069		0.1103	False		,,,				2504	0.0562				p.A112A		Atlas-SNP	.											CSRP3,NS,adenocarcinoma,-1,1	CSRP3	24	1	0			c.G336A						PASS	.	C	,	85,4313	73.1+/-111.1	0,85,2114	145.0	124.0	131.0		336,336	-11.7	0.0	11	dbSNP_52	131	921,7665	204.0+/-246.8	56,809,3428	no	coding-synonymous,coding-synonymous	CSRP3	NM_001127656.1,NM_003476.3	,	56,894,5542	TT,TC,CC		10.7268,1.9327,7.748	,	112/195,112/195	19207841	1006,11978	2199	4293	6492	SO:0001819	synonymous_variant	8048	exon5			AAACTTCGCAGTG	U20324	CCDS7848.1	11p15.1	2014-09-17				ENSG00000129170			2472	protein-coding gene	gene with protein product		600824				7490106	Standard	NM_003476		Approved	CLP, MLP, CMD1M	uc001mpk.3	P50461		ENST00000533783.1:c.336G>A	11.37:g.19207841C>T		Somatic	162	1	0.00617284		WXS	Illumina HiSeq	Phase_I	148	104	0.702703	NM_003476	Q9P131	Silent	SNP	ENST00000533783.1	37	CCDS7848.1																																																																																			T|0.065;G|0.005	0.065	strong		0.502	CSRP3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394484.1	NM_003476	
ZSCAN12	9753	hgsc.bcm.edu	37	6	28366151	28366151	+	Missense_Mutation	SNP	A	A	G	rs2232423	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:28366151A>G	ENST00000361028.1	-	2	177	c.32T>C	c.(31-33)aTg>aCg	p.M11T	ZSCAN12_ENST00000396827.3_Missense_Mutation_p.M11T			O43309	ZSC12_HUMAN	zinc finger and SCAN domain containing 12	11					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|endometrium(3)|urinary_tract(1)	6						ATCCTGGTCCATGTGGGCCTG	0.468													A|||	116	0.0231629	0.0242	0.0216	5008	,	,		18098	0.0		0.0686	False		,,,				2504	0.0				p.M11T		Atlas-SNP	.											.	ZSCAN12	35	.	0			c.T32C						PASS	.	A	THR/MET	58,1326		2,54,636	184.0	161.0	168.0		32	-0.9	0.0	6	dbSNP_98	168	306,2876		11,284,1296	yes	missense	ZSCAN12	NM_001163391.1	81	13,338,1932	GG,GA,AA		9.6166,4.1908,7.972	benign	11/612	28366151	364,4202	692	1591	2283	SO:0001583	missense	9753	exon2			TGGTCCATGTGGG	AB007886		6p21	2013-01-08	2007-02-20	2007-02-20	ENSG00000158691	ENSG00000158691		"""-"", ""Zinc fingers, C2H2-type"""	13172	protein-coding gene	gene with protein product		603978	"""zinc finger protein 305"", ""zinc finger protein 96"""	ZNF305, ZNF96		9244436	Standard	NM_001163391		Approved	KIAA0426, ZNF29K1, ZFP96, dJ29K1.2	uc011dlh.2	O43309	OTTHUMG00000014522	ENST00000361028.1:c.32T>C	6.37:g.28366151A>G	ENSP00000354305:p.Met11Thr	Somatic	259	0	0		WXS	Illumina HiSeq	Phase_I	239	124	0.518828	NM_001163391	O43724	Missense_Mutation	SNP	ENST00000361028.1	37		76	0.0347985347985348	11	0.022357723577235773	8	0.022099447513812154	0	0.0	57	0.07519788918205805	A	3.426	-0.117064	0.06838	0.041908	0.096166	ENSG00000158691	ENST00000361028;ENST00000396827	T;T	0.06068	3.35;3.35	3.26	-0.902	0.10537	.	0.992491	0.08160	N	0.988573	T	0.00754	0.0025	N	0.08118	0	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.48896	-0.8994	10	0.27785	T	0.31	.	0.7463	0.00982	0.2025:0.1214:0.1994:0.4767	rs2232423;rs52816048;rs2232423	11;11	A8K187;O43309	.;ZSC12_HUMAN	T	11	ENSP00000354305:M11T;ENSP00000380039:M11T	ENSP00000354305:M11T	M	-	2	0	ZSCAN12	28474130	0.000000	0.05858	0.000000	0.03702	0.042000	0.13812	-1.260000	0.02858	-0.281000	0.09141	-0.418000	0.06021	ATG	A|0.959;G|0.041	0.041	strong		0.468	ZSCAN12-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000040190.1	NM_014724	
SGK1	6446	hgsc.bcm.edu	37	6	134494619	134494619	+	Missense_Mutation	SNP	C	C	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:134494619C>G	ENST00000237305.7	-	4	402	c.314G>C	c.(313-315)gGa>gCa	p.G105A	SGK1_ENST00000475719.2_Missense_Mutation_p.G105A|SGK1_ENST00000489458.2_5'UTR|SGK1_ENST00000528577.1_Missense_Mutation_p.G133A|SGK1_ENST00000367858.5_Missense_Mutation_p.G200A|SGK1_ENST00000367857.5_Missense_Mutation_p.G95A|SGK1_ENST00000413996.3_Missense_Mutation_p.G119A	NM_005627.3	NP_005618.2	O00141	SGK1_HUMAN	serum/glucocorticoid regulated kinase 1	105	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|cellular response to DNA damage stimulus (GO:0006974)|ion transmembrane transport (GO:0034220)|long-term memory (GO:0007616)|positive regulation of transporter activity (GO:0032411)|protein phosphorylation (GO:0006468)|regulation of apoptotic process (GO:0042981)|regulation of blood pressure (GO:0008217)|regulation of catalytic activity (GO:0050790)|regulation of cell growth (GO:0001558)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of gastric acid secretion (GO:0060453)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|renal sodium ion absorption (GO:0070294)|response to stress (GO:0006950)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium channel regulator activity (GO:0005246)|chloride channel regulator activity (GO:0017081)|potassium channel regulator activity (GO:0015459)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|sodium channel regulator activity (GO:0017080)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(21)|kidney(3)|large_intestine(3)|lung(10)|ovary(1)|skin(4)|stomach(1)	46	Colorectal(23;0.221)			OV - Ovarian serous cystadenocarcinoma(155;0.00317)|GBM - Glioblastoma multiforme(68;0.00847)		ACTGCCCTTTCCGATCACTTT	0.398																																					p.G200A		Atlas-SNP	.											.	SGK1	387	.	0			c.G599C						PASS	.						63.0	68.0	66.0					6																	134494619		2203	4300	6503	SO:0001583	missense	6446	exon6			CCCTTTCCGATCA	AJ000512	CCDS5170.1, CCDS47476.1, CCDS47477.1, CCDS47478.1	6q23	2008-02-05	2007-12-05	2007-12-05	ENSG00000118515	ENSG00000118515			10810	protein-coding gene	gene with protein product		602958	"""serum/glucocorticoid regulated kinase"""	SGK		9114008, 9722955	Standard	NM_005627		Approved		uc003qeo.4	O00141	OTTHUMG00000015613	ENST00000237305.7:c.314G>C	6.37:g.134494619C>G	ENSP00000237305:p.Gly105Ala	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	89	19	0.213483	NM_001143676	B7UUP7|B7UUP8|B7UUP9|B7Z5B2|E1P583|Q5TCN2|Q5TCN3|Q5TCN4|Q5VY65|Q9UN56	Missense_Mutation	SNP	ENST00000237305.7	37	CCDS5170.1	.	.	.	.	.	.	.	.	.	.	C	29.4	5.000125	0.93227	.	.	ENSG00000118515	ENST00000367858;ENST00000413996;ENST00000237305;ENST00000367857;ENST00000528577;ENST00000475719	D;D;D;D;D;T	0.82081	-1.57;-1.57;-1.57;-1.57;-1.57;0.61	6.02	6.02	0.97574	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.91965	0.7455	M	0.85041	2.73	0.80722	D	1	D;D;D;D;D;D	0.89917	0.999;1.0;1.0;0.999;0.999;1.0	D;D;D;D;D;D	0.97110	0.999;0.998;1.0;0.999;0.998;0.999	D	0.91872	0.5508	10	0.87932	D	0	.	20.5407	0.99260	0.0:1.0:0.0:0.0	.	133;119;105;95;200;105	O00141-5;O00141-3;E9PR89;O00141-4;O00141-2;O00141	.;.;.;.;.;SGK1_HUMAN	A	200;119;105;95;133;105	ENSP00000356832:G200A;ENSP00000396242:G119A;ENSP00000237305:G105A;ENSP00000356831:G95A;ENSP00000434450:G133A;ENSP00000434302:G105A	ENSP00000237305:G105A	G	-	2	0	SGK1	134536312	1.000000	0.71417	0.989000	0.46669	0.951000	0.60555	7.818000	0.86416	2.865000	0.98341	0.655000	0.94253	GGA	.	.	none		0.398	SGK1-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042312.2		
KRTAP10-10	353333	hgsc.bcm.edu	37	21	46058060	46058060	+	Silent	SNP	C	C	T	rs13051517	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:46058060C>T	ENST00000380095.1	+	1	788	c.726C>T	c.(724-726)agC>agT	p.S242S	TSPEAR_ENST00000323084.4_Intron	NM_181688.1	NP_859016.1	P60014	KR10A_HUMAN	keratin associated protein 10-10	242						keratin filament (GO:0045095)				NS(1)|endometrium(2)|kidney(1)|lung(6)|prostate(1)|skin(2)	13						CCTGCTACAGCCTCTGCTCTG	0.687													C|||	1782	0.355831	0.2799	0.4813	5008	,	,		18886	0.3333		0.4364	False		,,,				2504	0.3098				p.S242S		Atlas-SNP	.											.	KRTAP10-10	37	.	0			c.C726T						PASS	.	C	,	1303,3099	389.3+/-327.3	187,929,1085	37.0	41.0	40.0		,726	2.0	0.0	21	dbSNP_121	40	3267,5325	463.0+/-365.8	638,1991,1667	no	intron,coding-synonymous	TSPEAR,KRTAP10-10	NM_144991.2,NM_181688.1	,	825,2920,2752	TT,TC,CC		38.0237,29.6002,35.1701	,	,242/252	46058060	4570,8424	2201	4296	6497	SO:0001819	synonymous_variant	353333	exon1			CTACAGCCTCTGC	AJ566387	CCDS33585.1	21q22.3	2006-03-13			ENSG00000221859	ENSG00000221859		"""Keratin associated proteins"""	22972	protein-coding gene	gene with protein product							Standard	NM_181688		Approved	KAP10.10, KAP18.10, KRTAP18-10	uc002zfq.3	P60014	OTTHUMG00000057631	ENST00000380095.1:c.726C>T	21.37:g.46058060C>T		Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	195	113	0.579487	NM_181688		Silent	SNP	ENST00000380095.1	37	CCDS33585.1																																																																																			T|1.000;|0.000	1.000	weak		0.687	KRTAP10-10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128034.1	NM_181688	
DFNB59	494513	hgsc.bcm.edu	37	2	179325714	179325714	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:179325714A>G	ENST00000409117.3	+	7	1128	c.772A>G	c.(772-774)Aga>Gga	p.R258G	DFNB59_ENST00000375129.4_Missense_Mutation_p.R258G	NM_001042702.3	NP_001036167.1	Q0ZLH3	PJVK_HUMAN	deafness, autosomal recessive 59	258					sensory perception of sound (GO:0007605)	neuronal cell body (GO:0043025)				breast(2)|endometrium(3)|kidney(2)|large_intestine(2)|lung(8)|upper_aerodigestive_tract(1)	18			OV - Ovarian serous cystadenocarcinoma(117;0.00406)|Epithelial(96;0.0159)|all cancers(119;0.0564)			TTTAGATAGAAGAGTGATGGA	0.323																																					p.R258G		Atlas-SNP	.											.	DFNB59	37	.	0			c.A772G						PASS	.						186.0	164.0	171.0					2																	179325714		1845	4095	5940	SO:0001583	missense	494513	exon7			GATAGAAGAGTGA	BC020859, BQ887979	CCDS42787.1	2q31.2	2011-07-01			ENSG00000204311	ENSG00000204311			29502	protein-coding gene	gene with protein product		610219				16804542	Standard	NM_001042702		Approved	pejvakin	uc002umi.4	Q0ZLH3	OTTHUMG00000154425	ENST00000409117.3:c.772A>G	2.37:g.179325714A>G	ENSP00000386647:p.Arg258Gly	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	71	4	0.056338	NM_001042702	A0PK14|B9EJE2	Missense_Mutation	SNP	ENST00000409117.3	37	CCDS42787.1	.	.	.	.	.	.	.	.	.	.	A	14.69	2.610445	0.46527	.	.	ENSG00000204311	ENST00000409117;ENST00000375129	T;T	0.62788	0.0;0.0	6.04	6.04	0.98038	.	0.105144	0.33959	U	0.004397	T	0.54062	0.1835	L	0.47716	1.5	0.51012	D	0.999909	B	0.09022	0.002	B	0.12156	0.007	T	0.49283	-0.8956	10	0.22706	T	0.39	-25.5225	12.3569	0.55180	0.9331:0.0:0.0669:0.0	.	258	Q0ZLH3	PJVK_HUMAN	G	258	ENSP00000386647:R258G;ENSP00000364271:R258G	ENSP00000364271:R258G	R	+	1	2	DFNB59	179033960	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	2.839000	0.48207	2.317000	0.78254	0.460000	0.39030	AGA	.	.	none		0.323	DFNB59-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335160.1		
DUOX2	50506	hgsc.bcm.edu	37	15	45402883	45402883	+	Missense_Mutation	SNP	G	G	C	rs151261408	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:45402883G>C	ENST00000603300.1	-	8	1110	c.908C>G	c.(907-909)cCc>cGc	p.P303R	DUOX2_ENST00000389039.6_Missense_Mutation_p.P303R	NM_014080.4	NP_054799.4	Q9NRD8	DUOX2_HUMAN	dual oxidase 2	303	Peroxidase-like; mediates peroxidase activity. {ECO:0000250}.				adenohypophysis morphogenesis (GO:0048855)|bone mineralization (GO:0030282)|cuticle development (GO:0042335)|cytokine-mediated signaling pathway (GO:0019221)|fertilization (GO:0009566)|hormone biosynthetic process (GO:0042446)|hydrogen peroxide catabolic process (GO:0042744)|inner ear development (GO:0048839)|multicellular organism growth (GO:0035264)|oxidation-reduction process (GO:0055114)|response to cAMP (GO:0051591)|response to virus (GO:0009615)|thyroid gland development (GO:0030878)|thyroid hormone generation (GO:0006590)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|heme binding (GO:0020037)|NAD(P)H oxidase activity (GO:0016174)|peroxidase activity (GO:0004601)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(28)|ovary(3)|pancreas(1)|prostate(4)|skin(7)|urinary_tract(1)	63		all_cancers(109;3.79e-11)|all_epithelial(112;2.92e-09)|Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;1.05e-18)|GBM - Glioblastoma multiforme(94;4.23e-07)|COAD - Colon adenocarcinoma(120;0.0668)|Colorectal(133;0.068)		CAGGAAGCTGGGCAGCCACTC	0.612													G|||	18	0.00359425	0.0008	0.0072	5008	,	,		16381	0.0		0.0089	False		,,,				2504	0.0031				p.P303R		Atlas-SNP	.											DUOX2,NS,carcinoma,0,2	DUOX2	137	2	0			c.C908G						PASS	.	G	ARG/PRO	11,4385		0,11,2187	52.0	48.0	49.0		908	5.6	1.0	15	dbSNP_134	49	152,8436		4,144,4146	no	missense	DUOX2	NM_014080.4	103	4,155,6333	CC,CG,GG		1.7699,0.2502,1.2554	probably-damaging	303/1549	45402883	163,12821	2198	4294	6492	SO:0001583	missense	50506	exon8			AAGCTGGGCAGCC	AF181972	CCDS10117.1	15q15.3-q21	2013-01-10			ENSG00000140279	ENSG00000140279		"""EF-hand domain containing"""	13273	protein-coding gene	gene with protein product	"""dual oxidase-like domains 2"", ""nicotinamide adenine dinucleotide phosphate oxidase"", ""flavoprotein NADPH oxidase"", ""NADPH thyroid oxidase 2"", ""NADH/NADPH thyroid oxidase p138-tox"", ""NADPH oxidase/peroxidase DUOX2"""	606759				10601291, 10806195	Standard	NM_014080		Approved	P138-TOX, P138(TOX), THOX2, LNOX2	uc010bea.3	Q9NRD8	OTTHUMG00000131355	ENST00000603300.1:c.908C>G	15.37:g.45402883G>C	ENSP00000475084:p.Pro303Arg	Somatic	216	0	0		WXS	Illumina HiSeq	Phase_I	249	145	0.582329	NM_014080	A8MQ13|D2XI64|Q9NR02|Q9UHF9	Missense_Mutation	SNP	ENST00000603300.1	37	CCDS10117.1	11	0.005036630036630037	2	0.0040650406504065045	5	0.013812154696132596	0	0.0	4	0.005277044854881266	.	29.5	5.009931	0.93346	0.002502	0.017699	ENSG00000140279	ENST00000389039	.	.	.	5.58	5.58	0.84498	.	0.000000	0.85682	D	0.000000	T	0.80193	0.4578	H	0.95816	3.725	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.87923	0.2705	9	0.87932	D	0	-26.2273	18.551	0.91065	0.0:0.0:1.0:0.0	.	303	Q9NRD8	DUOX2_HUMAN	R	303	.	ENSP00000373691:P303R	P	-	2	0	DUOX2	43190175	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	7.081000	0.76844	2.636000	0.89361	0.313000	0.20887	CCC	G|0.990;C|0.010	0.010	strong		0.612	DUOX2-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_014080	
PIM1	5292	hgsc.bcm.edu	37	6	37138345	37138345	+	5'UTR	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:37138345G>A	ENST00000373509.5	+	0	367					NM_001243186.1|NM_002648.3	NP_001230115.1|NP_002639.1	P11309	PIM1_HUMAN	Pim-1 proto-oncogene, serine/threonine kinase						apoptotic process (GO:0006915)|cell cycle (GO:0007049)|cell proliferation (GO:0008283)|hyaluronan metabolic process (GO:0030212)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|manganese ion binding (GO:0030145)|protein serine/threonine kinase activity (GO:0004674)|ribosomal small subunit binding (GO:0043024)|transcription factor binding (GO:0008134)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(17)|large_intestine(4)|lung(3)|prostate(2)|skin(2)	30			OV - Ovarian serous cystadenocarcinoma(102;0.241)		Adenosine monophosphate(DB00131)	ACATCCTGGAGGTTGGGATGC	0.687			T	BCL6	NHL																																p.E89E		Atlas-SNP	.		Dom	yes		6	6p21.2	5292	pim-1 oncogene		L	.	PIM1	71	.	0			c.G267A						PASS	.						28.0	27.0	27.0					6																	37138345		2200	4298	6498	SO:0001623	5_prime_UTR_variant	5292	exon1			CCTGGAGGTTGGG		CCDS4830.1	6p21	2014-06-25	2014-06-25		ENSG00000137193	ENSG00000137193			8986	protein-coding gene	gene with protein product		164960	"""pim-1 oncogene"""	PIM			Standard	NM_002648		Approved		uc003onk.3	P11309	OTTHUMG00000016426	ENST00000373509.5:c.-7G>A	6.37:g.37138345G>A		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	63	15	0.238095	NM_001243186	Q38RT9|Q5T7H7|Q96RG3	Silent	SNP	ENST00000373509.5	37	CCDS4830.1																																																																																			.	.	none		0.687	PIM1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043903.1		
KIAA1671	85379	hgsc.bcm.edu	37	22	25577688	25577688	+	Silent	SNP	G	G	A	rs763279	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:25577688G>A	ENST00000406486.4	+	11	5484	c.5097G>A	c.(5095-5097)gaG>gaA	p.E1699E	KIAA1671_ENST00000401395.1_Silent_p.E206E|KIAA1671_ENST00000358431.3_Silent_p.E1699E			Q9BY89	K1671_HUMAN	KIAA1671	1699								p.E1699E(1)		autonomic_ganglia(1)|breast(1)|endometrium(2)|lung(2)|prostate(1)|stomach(2)	9						CCAGGAAGGAGGAGTCGGATG	0.527													A|||	1802	0.359824	0.2269	0.4769	5008	,	,		19327	0.496		0.3658	False		,,,				2504	0.3098				p.E1699E		Atlas-SNP	.											KIAA1671,NS,carcinoma,0,1	KIAA1671	28	1	1	Substitution - coding silent(1)	stomach(1)	c.G5097A						PASS	.	A		349,1035		46,257,389	65.0	68.0	67.0		5097	-3.1	0.3	22	dbSNP_86	67	1081,2101		189,703,699	no	coding-synonymous	KIAA1671	NM_001145206.1		235,960,1088	AA,AG,GG		33.9723,25.2168,31.3184		1699/1807	25577688	1430,3136	692	1591	2283	SO:0001819	synonymous_variant	85379	exon8			GAAGGAGGAGTCG		CCDS46676.1	22q11.23	2009-07-09			ENSG00000197077	ENSG00000197077			29345	protein-coding gene	gene with protein product						15289310	Standard	NM_001145206		Approved		uc003abn.3	Q9BY89	OTTHUMG00000150841	ENST00000406486.4:c.5097G>A	22.37:g.25577688G>A		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	121	55	0.454545	NM_001145206	B0QYF2|B7ZW08|Q5THZ5	Silent	SNP	ENST00000406486.4	37	CCDS46676.1																																																																																			G|0.654;A|0.346	0.346	strong		0.527	KIAA1671-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320306.6	NM_001145206	
FREM1	158326	hgsc.bcm.edu	37	9	14747412	14747412	+	Silent	SNP	A	A	G	rs4741426	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:14747412A>G	ENST00000380880.3	-	33	6642	c.5859T>C	c.(5857-5859)gtT>gtC	p.V1953V	FREM1_ENST00000380894.1_Silent_p.V489V|FREM1_ENST00000380881.4_Silent_p.V1954V|FREM1_ENST00000422223.2_Silent_p.V1953V			Q5H8C1	FREM1_HUMAN	FRAS1 related extracellular matrix 1	1953					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)		GTTTCAAGGAAACTATCCCAT	0.368													A|||	688	0.13738	0.0076	0.2161	5008	,	,		17179	0.1806		0.1839	False		,,,				2504	0.1646				p.V1953V		Atlas-SNP	.											.	FREM1	261	.	0			c.T5859C						PASS	.	A	,	158,3628		3,152,1738	114.0	99.0	103.0		1467,5859	-0.1	0.1	9	dbSNP_111	103	1590,6650		151,1288,2681	no	coding-synonymous,coding-synonymous	FREM1	NM_001177704.1,NM_144966.5	,	154,1440,4419	GG,GA,AA		19.2961,4.1733,14.5352	,	489/716,1953/2180	14747412	1748,10278	1893	4120	6013	SO:0001819	synonymous_variant	158326	exon34			CAAGGAAACTATC	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.5859T>C	9.37:g.14747412A>G		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	131	63	0.480916	NM_144966	B7ZBX4|Q5VV00|Q5VV01|Q6MZI4|Q8NEG9|Q96LI3	Silent	SNP	ENST00000380880.3	37	CCDS47952.1																																																																																			A|0.848;G|0.152	0.152	strong		0.368	FREM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339474.2	NM_144966	
CLIC5	53405	hgsc.bcm.edu	37	6	46047458	46047458	+	Silent	SNP	C	C	T	rs3734207	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:46047458C>T	ENST00000185206.6	-	1	674	c.522G>A	c.(520-522)gaG>gaA	p.E174E		NM_001114086.1	NP_001107558.1	Q9NZA1	CLIC5_HUMAN	chloride intracellular channel 5	174					auditory receptor cell stereocilium organization (GO:0060088)|chloride transport (GO:0006821)|diet induced thermogenesis (GO:0002024)|female pregnancy (GO:0007565)|neuromuscular process controlling balance (GO:0050885)|protein localization (GO:0008104)|sensory perception of sound (GO:0007605)|transport (GO:0006810)	actin cytoskeleton (GO:0015629)|chloride channel complex (GO:0034707)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|stereocilium (GO:0032420)	voltage-gated chloride channel activity (GO:0005247)			endometrium(1)|kidney(2)|large_intestine(2)|lung(2)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)	13						AGAGGTAAATCTCAGGGTTCA	0.453													C|||	983	0.196286	0.0303	0.1196	5008	,	,		23723	0.3343		0.174	False		,,,				2504	0.3558				p.E174E		Atlas-SNP	.											.	CLIC5	48	.	0			c.G522A						PASS	.						75.0	70.0	71.0					6																	46047458		692	1591	2283	SO:0001819	synonymous_variant	53405	exon1			GTAAATCTCAGGG	AF216941	CCDS4914.1, CCDS47438.1, CCDS59022.1	6p12.3	2014-03-14			ENSG00000112782	ENSG00000112782		"""Ion channels / Chloride channels : Intracellular"""	13517	protein-coding gene	gene with protein product		607293				10793131	Standard	NM_001114086		Approved		uc003oxv.3	Q9NZA1	OTTHUMG00000014775	ENST00000185206.6:c.522G>A	6.37:g.46047458C>T		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	101	34	0.336634	NM_001114086	B3KUF1|Q5T4Z0|Q8NBY3|Q96JT5|Q9BWZ0	Silent	SNP	ENST00000185206.6	37	CCDS47438.1																																																																																			C|0.815;T|0.185	0.185	strong		0.453	CLIC5-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000040761.1		
SGK1	6446	hgsc.bcm.edu	37	6	134494661	134494661	+	Missense_Mutation	SNP	G	G	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:134494661G>C	ENST00000237305.7	-	4	360	c.272C>G	c.(271-273)cCt>cGt	p.P91R	SGK1_ENST00000475719.2_Missense_Mutation_p.P91R|SGK1_ENST00000489458.2_5'UTR|SGK1_ENST00000528577.1_Missense_Mutation_p.P119R|SGK1_ENST00000367858.5_Missense_Mutation_p.P186R|SGK1_ENST00000367857.5_Missense_Mutation_p.P81R|SGK1_ENST00000413996.3_Missense_Mutation_p.P105R	NM_005627.3	NP_005618.2	O00141	SGK1_HUMAN	serum/glucocorticoid regulated kinase 1	91					apoptotic process (GO:0006915)|cellular response to DNA damage stimulus (GO:0006974)|ion transmembrane transport (GO:0034220)|long-term memory (GO:0007616)|positive regulation of transporter activity (GO:0032411)|protein phosphorylation (GO:0006468)|regulation of apoptotic process (GO:0042981)|regulation of blood pressure (GO:0008217)|regulation of catalytic activity (GO:0050790)|regulation of cell growth (GO:0001558)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of gastric acid secretion (GO:0060453)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|renal sodium ion absorption (GO:0070294)|response to stress (GO:0006950)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium channel regulator activity (GO:0005246)|chloride channel regulator activity (GO:0017081)|potassium channel regulator activity (GO:0015459)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|sodium channel regulator activity (GO:0017080)	p.P186L(1)|p.P81L(1)|p.P91L(1)		central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(21)|kidney(3)|large_intestine(3)|lung(10)|ovary(1)|skin(4)|stomach(1)	46	Colorectal(23;0.221)			OV - Ovarian serous cystadenocarcinoma(155;0.00317)|GBM - Glioblastoma multiforme(68;0.00847)		TTTAGCATGAGGATTGGACGA	0.378																																					p.P186R		Atlas-SNP	.											SGK1_ENST00000367858,lymph_node,lymphoid_neoplasm,0,3	SGK1	387	3	3	Substitution - Missense(3)	haematopoietic_and_lymphoid_tissue(3)	c.C557G						PASS	.						73.0	77.0	76.0					6																	134494661		2203	4300	6503	SO:0001583	missense	6446	exon6			GCATGAGGATTGG	AJ000512	CCDS5170.1, CCDS47476.1, CCDS47477.1, CCDS47478.1	6q23	2008-02-05	2007-12-05	2007-12-05	ENSG00000118515	ENSG00000118515			10810	protein-coding gene	gene with protein product		602958	"""serum/glucocorticoid regulated kinase"""	SGK		9114008, 9722955	Standard	NM_005627		Approved		uc003qeo.4	O00141	OTTHUMG00000015613	ENST00000237305.7:c.272C>G	6.37:g.134494661G>C	ENSP00000237305:p.Pro91Arg	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	70	14	0.2	NM_001143676	B7UUP7|B7UUP8|B7UUP9|B7Z5B2|E1P583|Q5TCN2|Q5TCN3|Q5TCN4|Q5VY65|Q9UN56	Missense_Mutation	SNP	ENST00000237305.7	37	CCDS5170.1	.	.	.	.	.	.	.	.	.	.	G	17.43	3.388841	0.61956	.	.	ENSG00000118515	ENST00000367858;ENST00000413996;ENST00000237305;ENST00000367857;ENST00000528577;ENST00000475719	T;T;T;T;T;T	0.73152	3.18;3.18;3.18;3.18;3.18;-0.72	6.02	6.02	0.97574	Protein kinase-like domain (1);	0.000000	0.85682	D	0.000000	T	0.79100	0.4389	M	0.62723	1.935	0.80722	D	1	B;D;B;B;P;B	0.67145	0.105;0.996;0.023;0.086;0.503;0.102	B;D;B;B;B;B	0.63703	0.093;0.917;0.046;0.082;0.248;0.059	T	0.75371	-0.3341	10	0.41790	T	0.15	.	20.5407	0.99260	0.0:0.0:1.0:0.0	.	119;105;91;81;186;91	O00141-5;O00141-3;E9PR89;O00141-4;O00141-2;O00141	.;.;.;.;.;SGK1_HUMAN	R	186;105;91;81;119;91	ENSP00000356832:P186R;ENSP00000396242:P105R;ENSP00000237305:P91R;ENSP00000356831:P81R;ENSP00000434450:P119R;ENSP00000434302:P91R	ENSP00000237305:P91R	P	-	2	0	SGK1	134536354	1.000000	0.71417	1.000000	0.80357	0.870000	0.49936	9.790000	0.99075	2.865000	0.98341	0.655000	0.94253	CCT	.	.	none		0.378	SGK1-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042312.2		
FAM136A	84908	hgsc.bcm.edu	37	2	70524577	70524577	+	Silent	SNP	G	G	A	rs2618235	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:70524577G>A	ENST00000037869.3	-	3	339	c.261C>T	c.(259-261)aaC>aaT	p.N87N	FAM136A_ENST00000430566.1_Silent_p.N194N|FAM136A_ENST00000450256.1_3'UTR	NM_032822.2	NP_116211.2	Q96C01	F136A_HUMAN	family with sequence similarity 136, member A	87						cytoplasm (GO:0005737)|mitochondrion (GO:0005739)				breast(1)|kidney(1)|large_intestine(1)|lung(2)|prostate(1)	6						TGGCTTTGTCGTTGCAATGCA	0.512													G|||	1321	0.263778	0.1339	0.2075	5008	,	,		18619	0.3829		0.3141	False		,,,				2504	0.3047				p.N87N		Atlas-SNP	.											FAM136A,right_upper_lobe,carcinoma,-2,1	FAM136A	14	1	0			c.C261T						scavenged	.	G		732,3674	301.5+/-286.9	64,604,1535	98.0	91.0	94.0		261	-10.0	0.3	2	dbSNP_100	94	2716,5884	424.1+/-354.6	408,1900,1992	no	coding-synonymous	FAM136A	NM_032822.2		472,2504,3527	AA,AG,GG		31.5814,16.6137,26.5108		87/139	70524577	3448,9558	2203	4300	6503	SO:0001819	synonymous_variant	84908	exon3			TTTGTCGTTGCAA	BC014975	CCDS1904.1	2p14	2014-02-12	2007-07-10		ENSG00000035141	ENSG00000035141			25911	protein-coding gene	gene with protein product	"""hypothetical protein FLJ14668"""					12477932	Standard	NM_032822		Approved	FLJ14668	uc002sgq.4	Q96C01	OTTHUMG00000129668	ENST00000037869.3:c.261C>T	2.37:g.70524577G>A		Somatic	51	1	0.0196078		WXS	Illumina HiSeq	Phase_I	58	34	0.586207	NM_032822	Q96SS3	Silent	SNP	ENST00000037869.3	37	CCDS1904.1																																																																																			G|0.748;A|0.252	0.252	strong		0.512	FAM136A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251869.2	NM_032822	
MUC20	200958	hgsc.bcm.edu	37	3	195453288	195453288	+	Missense_Mutation	SNP	A	A	C	rs3828405	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195453288A>C	ENST00000447234.2	+	2	1940	c.1814A>C	c.(1813-1815)gAc>gCc	p.D605A	MUC20_ENST00000436408.1_Missense_Mutation_p.D605A|MUC20_ENST00000445522.2_Missense_Mutation_p.D570A|MUC20_ENST00000320736.6_Missense_Mutation_p.D434A	NM_001282506.1	NP_001269435.1	Q8N307	MUC20_HUMAN	mucin 20, cell surface associated	605	Involved in oligomerization.|Thr-rich.				activation of MAPK activity (GO:0000187)|cellular protein metabolic process (GO:0044267)|hepatocyte growth factor receptor signaling pathway (GO:0048012)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein homooligomerization (GO:0051260)	basal plasma membrane (GO:0009925)|cell projection (GO:0042995)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)		p.D605A(1)		NS(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(4)|skin(4)|stomach(3)|upper_aerodigestive_tract(1)	23	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)	Lung NSC(153;0.191)	Epithelial(36;1e-21)|all cancers(36;9.02e-20)|OV - Ovarian serous cystadenocarcinoma(49;1.6e-18)|Lung(62;0.000104)|LUSC - Lung squamous cell carcinoma(58;0.000128)	GBM - Glioblastoma multiforme(46;1.66e-05)		ACCAGCAGGGACCCTCTTCCT	0.597																																					p.D434A		Atlas-SNP	.											MUC20,NS,carcinoma,0,1	MUC20	84	1	1	Substitution - Missense(1)	stomach(1)	c.A1301C						scavenged	.						62.0	67.0	65.0					3																	195453288		2096	4204	6300	SO:0001583	missense	200958	exon3			GCAGGGACCCTCT	AB037780	CCDS63877.1	3q29	2008-08-07	2006-03-14		ENSG00000176945	ENSG00000176945		"""Mucins"""	23282	protein-coding gene	gene with protein product		610360				14565953	Standard	NM_001282506		Approved	FLJ14408, KIAA1359	uc010hzo.3	Q8N307	OTTHUMG00000155823	ENST00000447234.2:c.1814A>C	3.37:g.195453288A>C	ENSP00000414350:p.Asp605Ala	Somatic	139	4	0.028777		WXS	Illumina HiSeq	Phase_I	111	40	0.36036	NM_152673	Q6UX97|Q76I83|Q76I85|Q86ST8|Q8NBY6|Q96KA1|Q9P2I8	Missense_Mutation	SNP	ENST00000447234.2	37		165	0.07554945054945054	35	0.07113821138211382	19	0.052486187845303865	66	0.11538461538461539	45	0.059366754617414245	A	9.201	1.028502	0.19512	.	.	ENSG00000176945	ENST00000381954;ENST00000447234;ENST00000320736;ENST00000436408;ENST00000445522	T;T;T;T	0.13657	2.99;2.99;3.16;2.57	4.81	-2.05	0.07321	.	1.913230	0.02235	N	0.065225	T	0.00144	0.0004	N	0.24115	0.695	0.09310	N	1	B	0.19331	0.035	B	0.19946	0.027	T	0.31779	-0.9931	10	0.24483	T	0.36	4.6485	5.3684	0.16127	0.4954:0.1476:0.357:0.0	rs3828405;rs60077383	434	E9PH32	.	A	416;605;434;605;570	ENSP00000414350:D605A;ENSP00000325431:D434A;ENSP00000396774:D605A;ENSP00000405629:D570A	ENSP00000325431:D434A	D	+	2	0	MUC20	196938959	0.000000	0.05858	0.000000	0.03702	0.150000	0.21749	-0.537000	0.06128	-0.538000	0.06281	-0.468000	0.05107	GAC	A|0.928;C|0.072	0.072	strong		0.597	MUC20-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000341835.1	NM_152673	
KDR	3791	hgsc.bcm.edu	37	4	55972946	55972946	+	Missense_Mutation	SNP	A	A	G	rs34231037	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:55972946A>G	ENST00000263923.4	-	11	1739	c.1444T>C	c.(1444-1446)Tgt>Cgt	p.C482R		NM_002253.2	NP_002244.1	P35968	VGFR2_HUMAN	kinase insert domain receptor (a type III receptor tyrosine kinase)	482	Ig-like C2-type 5.		C -> R (in HCI susceptibility; expression of FLT1 in hemangioma endothelial cells is markedly reduced and KDR activity is increased compared to controls; low FLT1 expression in hemangioma cells is caused by reduced activity of a pathway involving ITGB1, ANTXR1, KDR and NFATC2IP; the mutation predicts to result in loss-of-function and disruption of the normal association of these molecules; dbSNP:rs34231037). {ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:18931684}.		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)	CATTCTTCACAAGGGTATGGG	0.333			Mis		"""NSCLC, angiosarcoma"""					TSP Lung(20;0.16)			A|||	45	0.00898562	0.0015	0.0144	5008	,	,		18156	0.0		0.0308	False		,,,				2504	0.002				p.C482R		Atlas-SNP	.		Dom	yes		4	4q11-q12	3791	vascular endothelial growth factor receptor 2		E	KDR,middle_lobe,carcinoma,+2,1	KDR	307	1	0			c.T1444C						PASS	.	A	ARG/CYS	23,4383	31.7+/-61.6	0,23,2180	81.0	85.0	83.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1444	5.7	0.9	4	dbSNP_126	83	242,8358	97.2+/-158.9	4,234,4062	yes	missense	KDR	NM_002253.2	180	4,257,6242	GG,GA,AA		2.814,0.522,2.0375	probably-damaging	482/1357	55972946	265,12741	2203	4300	6503	SO:0001583	missense	3791	exon11			CTTCACAAGGGTA	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.1444T>C	4.37:g.55972946A>G	ENSP00000263923:p.Cys482Arg	Somatic	187	0	0		WXS	Illumina HiSeq	Phase_I	176	89	0.505682	NM_002253	A2RRS0|B5A925|C5IFA0|O60723|Q14178	Missense_Mutation	SNP	ENST00000263923.4	37	CCDS3497.1	30	0.013736263736263736	0	0.0	6	0.016574585635359115	0	0.0	24	0.0316622691292876	A	13.84	2.356951	0.41801	0.00522	0.02814	ENSG00000128052	ENST00000263923	T	0.76839	-1.05	5.67	5.67	0.87782	Immunoglobulin subtype (1);Immunoglobulin-like (1);	0.000000	0.85682	D	0.000000	T	0.75436	0.3849	M	0.81497	2.545	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.82382	-0.0485	10	0.40728	T	0.16	.	15.905	0.79419	1.0:0.0:0.0:0.0	rs34231037	482;482	P35968-2;P35968	.;VGFR2_HUMAN	R	482	ENSP00000263923:C482R	ENSP00000263923:C482R	C	-	1	0	KDR	55667703	1.000000	0.71417	0.927000	0.36925	0.088000	0.18126	6.349000	0.73013	2.150000	0.67090	0.533000	0.62120	TGT	A|0.980;G|0.020	0.020	strong		0.333	KDR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250645.1		
GC	2638	hgsc.bcm.edu	37	4	72618323	72618323	+	Missense_Mutation	SNP	G	G	T	rs4588	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:72618323G>T	ENST00000273951.8	-	11	1650	c.1307C>A	c.(1306-1308)aCg>aAg	p.T436K	GC_ENST00000513476.1_Missense_Mutation_p.T436K|GC_ENST00000504199.1_Missense_Mutation_p.T455K|GC_ENST00000503472.1_5'UTR	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	159	0	0		WXS	Illumina HiSeq	Phase_I	135	135	1	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		
SLC8A3	6547	hgsc.bcm.edu	37	14	70633998	70633998	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:70633998G>A	ENST00000381269.2	-	2	1895	c.1142C>T	c.(1141-1143)tCc>tTc	p.S381F	SLC8A3_ENST00000534137.1_Missense_Mutation_p.S381F|SLC8A3_ENST00000357887.3_Missense_Mutation_p.S381F|SLC8A3_ENST00000356921.2_Missense_Mutation_p.S381F|SLC8A3_ENST00000528359.1_Missense_Mutation_p.S381F	NM_058240.2|NM_183002.1	NP_489479.1|NP_892114.1	P57103	NAC3_HUMAN	solute carrier family 8 (sodium/calcium exchanger), member 3	381					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)		GCTCATGCTGGAGGCCTTCTT	0.517																																					p.S381F		Atlas-SNP	.											.	SLC8A3	234	.	0			c.C1142T						PASS	.						126.0	115.0	119.0					14																	70633998		2203	4300	6503	SO:0001583	missense	6547	exon2			ATGCTGGAGGCCT	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.1142C>T	14.37:g.70633998G>A	ENSP00000370669:p.Ser381Phe	Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	148	40	0.27027	NM_183002	Q5K3P6|Q5K3P7|Q8IUE9|Q8IUF0|Q8NFI7|Q96QG1|Q96QG2	Missense_Mutation	SNP	ENST00000381269.2	37	CCDS35498.1	.	.	.	.	.	.	.	.	.	.	G	9.140	1.013566	0.19277	.	.	ENSG00000100678	ENST00000356921;ENST00000381269;ENST00000357887;ENST00000534137;ENST00000528359	T;T;T;T;T	0.36699	1.32;1.24;1.38;1.32;1.38	5.83	5.83	0.93111	.	0.446831	0.24891	N	0.034769	T	0.43077	0.1231	L	0.50333	1.59	0.46396	D	0.999023	B;B;B;B	0.32543	0.135;0.083;0.375;0.242	B;B;B;B	0.39590	0.213;0.066;0.304;0.136	T	0.14671	-1.0464	10	0.35671	T	0.21	.	20.1242	0.97973	0.0:0.0:1.0:0.0	.	381;381;381;381	P57103-2;P57103;Q96QG2;Q96QG1	.;NAC3_HUMAN;.;.	F	381	ENSP00000349392:S381F;ENSP00000370669:S381F;ENSP00000350560:S381F;ENSP00000436688:S381F;ENSP00000433531:S381F	ENSP00000349392:S381F	S	-	2	0	SLC8A3	69703751	1.000000	0.71417	0.991000	0.47740	0.909000	0.53808	4.043000	0.57354	2.744000	0.94065	0.643000	0.83706	TCC	.	.	none		0.517	SLC8A3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390736.1		
CYP4F12	66002	hgsc.bcm.edu	37	19	15807305	15807305	+	Silent	SNP	T	T	C	rs688755	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:15807305T>C	ENST00000550308.1	+	12	1760	c.1380T>C	c.(1378-1380)ccT>ccC	p.P460P	CYP4F12_ENST00000324632.10_Silent_p.P460P	NM_023944.3	NP_076433	Q9HCS2	CP4FC_HUMAN	cytochrome P450, family 4, subfamily F, polypeptide 12	460					arachidonic acid metabolic process (GO:0019369)|drug metabolic process (GO:0017144)|epoxygenase P450 pathway (GO:0019373)|leukotriene B4 catabolic process (GO:0036101)|long-chain fatty acid metabolic process (GO:0001676)|negative regulation of blood coagulation (GO:0030195)|oxidation-reduction process (GO:0055114)|pressure natriuresis (GO:0003095)|renal water homeostasis (GO:0003091)|small molecule metabolic process (GO:0044281)|sodium ion homeostasis (GO:0055078)|very long-chain fatty acid metabolic process (GO:0000038)|vitamin E metabolic process (GO:0042360)|vitamin K biosynthetic process (GO:0042371)|xenobiotic metabolic process (GO:0006805)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)	alkane 1-monooxygenase activity (GO:0018685)|arachidonic acid epoxygenase activity (GO:0008392)|aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|leukotriene-B4 20-monooxygenase activity (GO:0050051)|vitamin-K-epoxide reductase (warfarin-sensitive) activity (GO:0047057)			NS(1)|central_nervous_system(3)|endometrium(4)|kidney(2)|large_intestine(7)|lung(12)|ovary(3)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	41	Acute lymphoblastic leukemia(2;0.0367)				Fingolimod(DB08868)	CTTTTATTCCTTTCTCCGCAG	0.562													t|||	1209	0.241414	0.4024	0.2421	5008	,	,		18267	0.0139		0.2763	False		,,,				2504	0.2219				p.P460P		Atlas-SNP	.											.	CYP4F12	89	.	0			c.T1380C						PASS	.	G		1685,2719		320,1045,837	122.0	115.0	117.0		1380	-2.6	0.9	19	dbSNP_83	117	2117,6483		294,1529,2477	no	coding-synonymous	CYP4F12	NM_023944.3		614,2574,3314	CC,CT,TT		24.6163,38.2607,29.2372		460/525	15807305	3802,9202	2202	4300	6502	SO:0001819	synonymous_variant	66002	exon12			TATTCCTTTCTCC	AB035130	CCDS42517.1	19p13.1	2008-02-05	2003-01-14		ENSG00000186204	ENSG00000186204		"""Cytochrome P450s"""	18857	protein-coding gene	gene with protein product		611485	"""cytochrome P450, subfamily IVF, polypeptide 12"""			11162607	Standard	NM_023944		Approved		uc002nbl.3	Q9HCS2	OTTHUMG00000164477	ENST00000550308.1:c.1380T>C	19.37:g.15807305T>C		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	130	83	0.638462	NM_023944	E7ET51|O60389|Q5JPJ7|Q9HCS1	Silent	SNP	ENST00000550308.1	37	CCDS42517.1																																																																																			T|0.764;C|0.236	0.236	strong		0.562	CYP4F12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378938.9		
FAM111A	63901	hgsc.bcm.edu	37	11	58919813	58919813	+	Silent	SNP	A	A	G	rs10896928	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:58919813A>G	ENST00000528737.1	+	5	3490	c.672A>G	c.(670-672)gcA>gcG	p.A224A	FAM111A_ENST00000533703.1_Silent_p.A224A|FAM111A_ENST00000420244.1_Silent_p.A224A|FAM111A_ENST00000361723.3_Silent_p.A224A|FAM111A_ENST00000531147.1_Silent_p.A224A			Q96PZ2	F111A_HUMAN	family with sequence similarity 111, member A	224					defense response to virus (GO:0051607)|DNA replication (GO:0006260)|negative regulation of viral genome replication (GO:0045071)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	catalytic activity (GO:0003824)			breast(2)|endometrium(2)|kidney(1)|large_intestine(5)|lung(5)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	22		all_epithelial(135;0.139)				TCAAGGATGCACTGTGCAAGG	0.408													G|||	1408	0.28115	0.3971	0.2507	5008	,	,		20950	0.2917		0.2028	False		,,,				2504	0.2157				p.A224A		Atlas-SNP	.											.	FAM111A	57	.	0			c.A672G						PASS	.	G	,,,,	1481,2921	677.6+/-403.4	255,971,975	122.0	122.0	122.0		672,672,672,672,672	-4.8	0.0	11	dbSNP_120	122	1826,6764	731.4+/-406.8	201,1424,2670	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	FAM111A	NM_001142519.1,NM_001142520.1,NM_001142521.1,NM_022074.3,NM_198847.2	,,,,	456,2395,3645	GG,GA,AA		21.2573,33.6438,25.4541	,,,,	224/612,224/612,224/612,224/612,224/612	58919813	3307,9685	2201	4295	6496	SO:0001819	synonymous_variant	63901	exon5			GGATGCACTGTGC	AK092953	CCDS7973.1	11q12.1	2014-03-13				ENSG00000166801			24725	protein-coding gene	gene with protein product		615292				11572484, 23996431, 23684011	Standard	NM_022074		Approved	FLJ22794, KIAA1895	uc001nnq.3	Q96PZ2		ENST00000528737.1:c.672A>G	11.37:g.58919813A>G		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	54	12	0.222222	NM_001142520	A8K5Y8|Q5RKS9|Q5XKM2|Q68DK9|Q6IPR7|Q9H5Y1	Silent	SNP	ENST00000528737.1	37	CCDS7973.1																																																																																			A|0.739;G|0.261	0.261	strong		0.408	FAM111A-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393975.1	NM_022074	
UMODL1	89766	hgsc.bcm.edu	37	21	43510427	43510427	+	Silent	SNP	T	T	C	rs67055914	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:43510427T>C	ENST00000408910.2	+	6	810	c.810T>C	c.(808-810)taT>taC	p.Y270Y	UMODL1_ENST00000400427.1_Silent_p.Y198Y|UMODL1_ENST00000400424.2_Silent_p.Y198Y|UMODL1_ENST00000408989.2_Silent_p.Y270Y	NM_001004416.2	NP_001004416	Q5DID0	UROL1_HUMAN	uromodulin-like 1	270	EGF-like 1; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				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						AGTGTTTCTATGAGGAGCTCA	0.567													C|||	1506	0.300719	0.2965	0.2997	5008	,	,		20986	0.374		0.2018	False		,,,				2504	0.3333				p.Y270Y	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.T810C						PASS	.	C	,,,	1047,3241		136,775,1233	124.0	127.0	126.0		810,594,594,810	-3.2	0.0	21	dbSNP_130	126	1778,6702		189,1400,2651	yes	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	UMODL1	NM_001004416.2,NM_001199527.1,NM_001199528.2,NM_173568.3	,,,	325,2175,3884	CC,CT,TT		20.967,24.417,22.1256	,,,	270/1319,198/1375,198/1247,270/1447	43510427	2825,9943	2144	4240	6384	SO:0001819	synonymous_variant	89766	exon6			TTTCTATGAGGAG		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.810T>C	21.37:g.43510427T>C		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	132	52	0.393939	NM_173568	C9JCE6|Q5DIC9|Q6LA40|Q6LA41|Q8N216	Silent	SNP	ENST00000408910.2	37	CCDS42936.1	601	0.2751831501831502	134	0.27235772357723576	110	0.30386740331491713	209	0.36538461538461536	148	0.19525065963060687	C	0.005	-2.138538	0.00335	0.24417	0.20967	ENSG00000177398	ENST00000423139	.	.	.	3.89	-3.21	0.05140	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.27640	-1.0068	3	.	.	.	-3.4913	11.1076	0.48212	0.0:0.3109:0.0:0.6891	.	.	.	.	T	43	.	.	M	+	2	0	UMODL1	42383496	0.000000	0.05858	0.000000	0.03702	0.050000	0.14768	-2.077000	0.01371	-1.396000	0.02071	-1.741000	0.00685	ATG	T|0.748;C|0.252	0.252	strong		0.567	UMODL1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195292.2		
CCDC86	79080	hgsc.bcm.edu	37	11	60610056	60610056	+	Missense_Mutation	SNP	G	G	C	rs2074421	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:60610056G>C	ENST00000227520.5	+	1	513	c.459G>C	c.(457-459)caG>caC	p.Q153H	RP11-804A23.2_ENST00000539897.1_RNA|RP11-804A23.4_ENST00000538705.1_RNA	NM_024098.3	NP_077003.1	Q9H6F5	CCD86_HUMAN	coiled-coil domain containing 86	153	Pro-rich.		Q -> H (in dbSNP:rs2074421).		viral process (GO:0016032)	nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(1)|large_intestine(2)|liver(2)|lung(2)|urinary_tract(3)	10						CCCAGCATCAGCTACCGCCGG	0.647													G|||	403	0.0804712	0.0461	0.196	5008	,	,		13962	0.0496		0.1024	False		,,,				2504	0.0542				p.Q153H		Atlas-SNP	.											.	CCDC86	24	.	0			c.G459C						PASS	.	G	HIS/GLN	244,4148		7,230,1959	24.0	30.0	28.0		459	2.5	0.1	11	dbSNP_96	28	882,7686		54,774,3456	yes	missense	CCDC86	NM_024098.3	24	61,1004,5415	CC,CG,GG		10.2941,5.5556,8.6883	probably-damaging	153/361	60610056	1126,11834	2196	4284	6480	SO:0001583	missense	79080	exon1			GCATCAGCTACCG	AK025974	CCDS7993.1	11q12.2	2006-03-16			ENSG00000110104	ENSG00000110104			28359	protein-coding gene	gene with protein product		611293					Standard	NM_024098		Approved	MGC2574	uc001nqa.2	Q9H6F5	OTTHUMG00000167706	ENST00000227520.5:c.459G>C	11.37:g.60610056G>C	ENSP00000227520:p.Gln153His	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	72	72	1	NM_024098	B4DY99	Missense_Mutation	SNP	ENST00000227520.5	37	CCDS7993.1	198	0.09065934065934066	24	0.04878048780487805	59	0.16298342541436464	33	0.057692307692307696	82	0.10817941952506596	G	11.56	1.673993	0.29693	0.055556	0.102941	ENSG00000110104	ENST00000227520;ENST00000339492	T	0.47528	0.84	2.46	2.46	0.29980	.	0.303860	0.26635	N	0.023285	T	0.00384	0.0012	L	0.60455	1.87	0.09310	P	0.999999999980983	D	0.69078	0.997	D	0.68353	0.957	T	0.13818	-1.0495	9	0.52906	T	0.07	.	11.0471	0.47865	0.0:0.0:1.0:0.0	rs2074421	153	Q9H6F5	CCD86_HUMAN	H	153;117	ENSP00000227520:Q153H	ENSP00000227520:Q153H	Q	+	3	2	CCDC86	60366632	0.001000	0.12720	0.113000	0.21522	0.081000	0.17604	-0.240000	0.08952	1.686000	0.51046	0.561000	0.74099	CAG	G|0.909;C|0.091	0.091	strong		0.647	CCDC86-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395743.1	NM_024098	
ARSA	410	hgsc.bcm.edu	37	22	51064039	51064039	+	Missense_Mutation	SNP	G	G	C	rs743616	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:51064039G>C	ENST00000547307.1	-	7	1577	c.1172C>G	c.(1171-1173)aCt>aGt	p.T391S	ARSA_ENST00000216124.5_Missense_Mutation_p.T393S|ARSA_ENST00000356098.5_Missense_Mutation_p.T393S|ARSA_ENST00000547805.1_Missense_Mutation_p.T391S|ARSA_ENST00000395621.3_Missense_Mutation_p.T393S|ARSA_ENST00000453344.2_Missense_Mutation_p.T307S|ARSA_ENST00000395619.3_Missense_Mutation_p.T393S|ARSA_ENST00000610191.1_5'Flank			P15289	ARSA_HUMAN	arylsulfatase A	391			T -> S (in dbSNP:rs743616). {ECO:0000269|PubMed:10477432, ECO:0000269|PubMed:11061266, ECO:0000269|PubMed:11456299, ECO:0000269|PubMed:11941485, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15326627, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:1670590, ECO:0000269|PubMed:9888390, ECO:0000269|Ref.6}.		autophagy (GO:0006914)|binding of sperm to zona pellucida (GO:0007339)|cellular protein metabolic process (GO:0044267)|central nervous system development (GO:0007417)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|response to estrogen (GO:0043627)|response to ethanol (GO:0045471)|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)	acrosomal vesicle (GO:0001669)|endoplasmic reticulum lumen (GO:0005788)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|integral component of membrane (GO:0016021)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)	arylsulfatase activity (GO:0004065)|calcium ion binding (GO:0005509)|cerebroside-sulfatase activity (GO:0004098)|sulfuric ester hydrolase activity (GO:0008484)			endometrium(1)|large_intestine(1)|lung(5)|pancreas(1)|skin(1)	9		all_cancers(38;8.8e-15)|all_epithelial(38;1.12e-12)|all_lung(38;3.07e-05)|Breast(42;6.27e-05)|Lung NSC(38;0.000813)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)	Micafungin(DB01141)|Suramin(DB04786)	GTACTTTCCAGTCCGCACAGC	0.652													C|||	2031	0.405551	0.3578	0.4697	5008	,	,		14864	0.3214		0.5288	False		,,,				2504	0.3845				p.T393S		Atlas-SNP	.											.	ARSA	19	.	0			c.C1178G	GRCh37	CM910052	ARSA	M	rs743616	PASS	.	C	SER/THR,SER/THR,SER/THR,SER/THR,SER/THR	1736,2670	646.8+/-398.4	352,1032,819	69.0	82.0	78.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1178,1178,1178,1178,920	-0.0	0.9	22	dbSNP_86	78	4560,4040	555.3+/-386.7	1220,2120,960	yes	missense,missense,missense,missense,missense	ARSA	NM_000487.5,NM_001085425.2,NM_001085426.2,NM_001085427.2,NM_001085428.2	58,58,58,58,58	1572,3152,1779	CC,CG,GG		46.9767,39.4008,48.4084	benign,benign,benign,benign,benign	393/510,393/510,393/510,393/510,307/424	51064039	6296,6710	2203	4300	6503	SO:0001583	missense	410	exon8			TTTCCAGTCCGCA	X52150	CCDS14100.1, CCDS46736.1, CCDS14100.2	22q13.33	2013-09-19			ENSG00000100299	ENSG00000100299	3.1.6.8	"""Arylsulfatase family"""	713	protein-coding gene	gene with protein product	"""metachromatic leucodystrophy"""	607574				15772092	Standard	NM_000487		Approved		uc003bmz.5	P15289	OTTHUMG00000150180	ENST00000547307.1:c.1172C>G	22.37:g.51064039G>C	ENSP00000448440:p.Thr391Ser	Somatic	195	1	0.00512821		WXS	Illumina HiSeq	Phase_I	177	95	0.536723	NM_001085426	B2RCA6|B7XD04|F8WCC8|Q6ICI5|Q96CJ0	Missense_Mutation	SNP	ENST00000547307.1	37		930	0.4258241758241758	181	0.3678861788617886	176	0.4861878453038674	185	0.32342657342657344	388	0.5118733509234829	C	8.274	0.813939	0.16537	0.394008	0.530233	ENSG00000100299	ENST00000356098;ENST00000216124;ENST00000547307;ENST00000547805;ENST00000395621;ENST00000453344;ENST00000395619	D;D;D;D;D;D;D	0.89485	-2.52;-2.52;-2.52;-2.52;-2.52;-2.52;-2.52	5.59	-0.0288	0.13920	Sulfatase (1);Alkaline-phosphatase-like, core domain (1);	1.175200	0.06015	N	0.650226	T	0.00012	0.0000	N	0.03071	-0.42	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.24012	-1.0172	9	0.21014	T	0.42	.	1.5892	0.02650	0.1364:0.3411:0.1333:0.3891	rs743616;rs1051552;rs3171785;rs17184315;rs17856452;rs60738949;rs743616	391	P15289	ARSA_HUMAN	S	393;393;391;391;393;307;393	ENSP00000348406:T393S;ENSP00000216124:T393S;ENSP00000448440:T391S;ENSP00000448932:T391S;ENSP00000378983:T393S;ENSP00000412542:T307S;ENSP00000378981:T393S	ENSP00000216124:T393S	T	-	2	0	ARSA	49410905	0.000000	0.05858	0.862000	0.33874	0.935000	0.57460	0.103000	0.15292	0.053000	0.16036	-0.934000	0.02701	ACT	G|0.545;C|0.455	0.455	strong		0.652	ARSA-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_000487	
MUC6	4588	hgsc.bcm.edu	37	11	1018436	1018436	+	Silent	SNP	C	C	T	rs12802800	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:1018436C>T	ENST00000421673.2	-	31	4415	c.4365G>A	c.(4363-4365)gtG>gtA	p.V1455V		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming	1455	Pro-rich.|Thr-rich.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)	extracellular matrix structural constituent (GO:0005201)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(8)|kidney(10)|large_intestine(6)|lung(43)|ovary(4)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	80		all_cancers(49;3.3e-08)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		all cancers(45;1.24e-24)|BRCA - Breast invasive adenocarcinoma(625;0.00031)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		TACTTGGAGTCACCAAGGAGG	0.542													c|||	579	0.115615	0.3124	0.0836	5008	,	,		20997	0.001		0.0875	False		,,,				2504	0.0194				p.V1455V		Atlas-SNP	.											.	MUC6	408	.	0			c.G4365A						PASS	.	C		922,3468		0,922,1273	344.0	334.0	337.0		4365	-1.0	0.0	11	dbSNP_121	337	585,7991		0,585,3703	no	coding-synonymous	MUC6	NM_005961.2		0,1507,4976	TT,TC,CC		6.8214,21.0023,11.6227		1455/2440	1018436	1507,11459	2195	4288	6483	SO:0001819	synonymous_variant	4588	exon31			TGGAGTCACCAAG	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.4365G>A	11.37:g.1018436C>T		Somatic	331	1	0.00302115		WXS	Illumina HiSeq	Phase_I	355	152	0.428169	NM_005961	O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	Silent	SNP	ENST00000421673.2	37	CCDS44513.1																																																																																			C|0.911;T|0.089	0.089	strong		0.542	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382120.2	XM_290540	
ABCA13	154664	hgsc.bcm.edu	37	7	48314279	48314279	+	Silent	SNP	G	G	A	rs6955212	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:48314279G>A	ENST00000435803.1	+	17	5040	c.5016G>A	c.(5014-5016)aaG>aaA	p.K1672K		NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	1672					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						CCCTTAAGAAGGCAGACATAG	0.393													G|||	968	0.193291	0.1498	0.2709	5008	,	,		22975	0.2153		0.1322	False		,,,				2504	0.2372				p.K1672K		Atlas-SNP	.											ABCA13_ENST00000435803,NS,carcinoma,+1,2	ABCA13	1192	2	0			c.G5016A						PASS	.	G		585,3223		48,489,1367	153.0	145.0	148.0		5016	2.3	0.3	7	dbSNP_116	148	1164,7050		92,980,3035	no	coding-synonymous	ABCA13	NM_152701.3		140,1469,4402	AA,AG,GG		14.1709,15.3624,14.5483		1672/5059	48314279	1749,10273	1904	4107	6011	SO:0001819	synonymous_variant	154664	exon17			TAAGAAGGCAGAC	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.5016G>A	7.37:g.48314279G>A		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	82	24	0.292683	NM_152701	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Silent	SNP	ENST00000435803.1	37	CCDS47584.1																																																																																			G|0.816;A|0.184	0.184	strong		0.393	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701	
PALLD	23022	hgsc.bcm.edu	37	4	169432673	169432673	+	Silent	SNP	C	C	T	rs61051061	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:169432673C>T	ENST00000505667.1	+	2	191	c.18C>T	c.(16-18)tcC>tcT	p.S6S	PALLD_ENST00000261509.6_Silent_p.S6S|PALLD_ENST00000335742.7_5'UTR|PALLD_ENST00000333488.4_5'Flank			Q8WX93	PALLD_HUMAN	palladin, cytoskeletal associated protein	6					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)		GGACCTCCTCCCATGAGTCCT	0.483									Pancreatic Cancer, Familial Clustering of				C|||	926	0.184904	0.2292	0.1441	5008	,	,		17777	0.1925		0.1958	False		,,,				2504	0.135				p.S6S	Esophageal Squamous(109;1482 1532 18347 40239 51172)	Atlas-SNP	.											.	PALLD	179	.	0			c.C18T						PASS	.	C	,	1033,3373	373.0+/-320.6	129,775,1299	67.0	67.0	67.0		18,18	2.9	0.9	4	dbSNP_129	67	1775,6825	309.3+/-309.3	184,1407,2709	yes	coding-synonymous,coding-synonymous	PALLD	NM_001166108.1,NM_016081.3	,	313,2182,4008	TT,TC,CC		20.6395,23.4453,21.59	,	6/1124,6/1107	169432673	2808,10198	2203	4300	6503	SO:0001819	synonymous_variant	23022	exon2	Familial Cancer Database	incl.: Hereditary Pancreatic Adenocarcinoma, Insulin-Dependent Diabetes Mellitus - Exocrine Insufficiency - Familial Pancreatic Cancer, PNCA1	CTCCTCCCATGAG	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.18C>T	4.37:g.169432673C>T		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	40	21	0.525	NM_001166108	B3KTG2|B5MD56|B7ZMM5|Q7L3E0|Q7Z3W0|Q86WE8|Q8N1M2|Q9UGA0|Q9UQF5|Q9Y2J6|Q9Y3E9	Silent	SNP	ENST00000505667.1	37	CCDS54818.1																																																																																			C|0.791;T|0.209	0.209	strong		0.483	PALLD-002	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000363762.1	NM_016081	
MGAT3	4248	hgsc.bcm.edu	37	22	39883736	39883736	+	Silent	SNP	G	G	C	rs9623008	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:39883736G>C	ENST00000341184.6	+	2	599	c.384G>C	c.(382-384)ccG>ccC	p.P128P		NM_001098270.1|NM_002409.4	NP_001091740.1|NP_002400.3	Q09327	MGAT3_HUMAN	mannosyl (beta-1,4-)-glycoprotein beta-1,4-N-acetylglucosaminyltransferase	128					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)	beta-1,4-mannosylglycoprotein 4-beta-N-acetylglucosaminyltransferase activity (GO:0003830)			endometrium(4)|kidney(1)|large_intestine(5)|lung(12)|prostate(1)|skin(1)	24	Melanoma(58;0.04)					TGGAGAGGCCGCCCCCGGGAC	0.731													G|||	584	0.116613	0.2156	0.036	5008	,	,		11864	0.1528		0.0527	False		,,,				2504	0.0685				p.P128P		Atlas-SNP	.											MGAT3,NS,carcinoma,+1,1	MGAT3	65	1	0			c.G384C						PASS	.	G	,	503,3591		25,453,1569	4.0	6.0	5.0		384,384	-1.2	0.0	22	dbSNP_119	5	254,7810		7,240,3785	no	coding-synonymous,coding-synonymous	MGAT3	NM_001098270.1,NM_002409.4	,	32,693,5354	CC,CG,GG		3.1498,12.2863,6.2264	,	128/534,128/534	39883736	757,11401	2047	4032	6079	SO:0001819	synonymous_variant	4248	exon2			GAGGCCGCCCCCG	D13789	CCDS13994.2	22q13.1	2013-02-25			ENSG00000128268	ENSG00000128268	2.4.1.144	"""Mannosyl-glycoprotein beta N-acetylglucosaminyltransferases"""	7046	protein-coding gene	gene with protein product		604621				8370666	Standard	NM_002409		Approved	GNT-III	uc010gxy.3	Q09327	OTTHUMG00000030185	ENST00000341184.6:c.384G>C	22.37:g.39883736G>C		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	47	31	0.659574	NM_002409	A6NGD0|Q14CK5|Q6IC49|Q9UH32	Silent	SNP	ENST00000341184.6	37	CCDS13994.2																																																																																			G|0.887;C|0.113	0.113	strong		0.731	MGAT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075039.2	NM_002409	
LAMA5	3911	hgsc.bcm.edu	37	20	60889385	60889385	+	Missense_Mutation	SNP	G	G	T	rs117480847	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:60889385G>T	ENST00000252999.3	-	62	8545	c.8479C>A	c.(8479-8481)Cag>Aag	p.Q2827K		NM_005560.3	NP_005551.3	O15230	LAMA5_HUMAN	laminin, alpha 5	2827	Laminin G-like 1. {ECO:0000255|PROSITE- ProRule:PRU00122}.				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)			GCTGCGAACTGCTCCCCAATG	0.627													.|||	61	0.0121805	0.0	0.0115	5008	,	,		16760	0.0		0.0189	False		,,,				2504	0.0348				p.Q2827K		Atlas-SNP	.											LAMA5,NS,haematopoietic_neoplasm,0,1	LAMA5	268	1	0			c.C8479A						scavenged	.	G	LYS/GLN	21,4383	28.1+/-56.4	0,21,2181	113.0	97.0	103.0		8479	2.6	1.0	20	dbSNP_132	103	174,8422	79.8+/-142.4	0,174,4124	yes	missense	LAMA5	NM_005560.3	53	0,195,6305	TT,TG,GG		2.0242,0.4768,1.5	benign	2827/3696	60889385	195,12805	2202	4298	6500	SO:0001583	missense	3911	exon62			CGAACTGCTCCCC	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.8479C>A	20.37:g.60889385G>T	ENSP00000252999:p.Gln2827Lys	Somatic	94	1	0.0106383		WXS	Illumina HiSeq	Phase_I	75	36	0.48	NM_005560	Q8TDF8|Q8WZA7|Q9H1P1	Missense_Mutation	SNP	ENST00000252999.3	37	CCDS33502.1	20	0.009157509157509158	0	0.0	5	0.013812154696132596	0	0.0	15	0.01978891820580475	g	8.022	0.759813	0.15846	0.004768	0.020242	ENSG00000130702	ENST00000252999	T	0.78126	-1.15	3.61	2.62	0.31277	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	0.621906	0.16406	U	0.215834	T	0.51517	0.1679	L	0.40543	1.245	0.80722	D	1	B	0.33345	0.409	B	0.34489	0.184	T	0.49808	-0.8900	10	0.15952	T	0.53	.	11.3438	0.49548	0.0:0.3552:0.6448:0.0	.	2827	O15230	LAMA5_HUMAN	K	2827	ENSP00000252999:Q2827K	ENSP00000252999:Q2827K	Q	-	1	0	LAMA5	60322780	1.000000	0.71417	1.000000	0.80357	0.099000	0.18886	1.300000	0.33436	0.469000	0.27268	0.457000	0.33378	CAG	G|0.986;T|0.014	0.014	strong		0.627	LAMA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080014.2	NM_005560	
SCN4A	6329	hgsc.bcm.edu	37	17	62019103	62019103	+	Silent	SNP	G	G	T	rs56342400	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:62019103G>T	ENST00000435607.1	-	24	4615	c.4539C>A	c.(4537-4539)atC>atA	p.I1513I	SCN4A_ENST00000578147.1_Silent_p.I1513I	NM_000334.4	NP_000325.4	P35499	SCN4A_HUMAN	sodium channel, voltage-gated, type IV, alpha subunit	1513					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.I1513I(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)	ACATATCATCGATGCCCGACT	0.552													g|||	702	0.140176	0.1452	0.1254	5008	,	,		18534	0.1062		0.1968	False		,,,				2504	0.1207				p.I1513I		Atlas-SNP	.											SCN4A,NS,carcinoma,0,1	SCN4A	205	1	1	Substitution - coding silent(1)	stomach(1)	c.C4539A						PASS	.	A		587,3819	246.8+/-255.3	38,511,1654	127.0	122.0	123.0		4539	-0.3	1.0	17	dbSNP_129	123	1683,6917	304.6+/-307.0	154,1375,2771	no	coding-synonymous	SCN4A	NM_000334.4		192,1886,4425	TT,TG,GG		19.5698,13.3227,17.4535		1513/1837	62019103	2270,10736	2203	4300	6503	SO:0001819	synonymous_variant	6329	exon24			ATCATCGATGCCC	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.4539C>A	17.37:g.62019103G>T		Somatic	191	0	0		WXS	Illumina HiSeq	Phase_I	165	89	0.539394	NM_000334	Q15478|Q16447|Q7Z6B1	Silent	SNP	ENST00000435607.1	37	CCDS45761.1																																																																																			A|0.000;C|0.000;G|0.831;T|0.168	0.168	strong		0.552	SCN4A-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_000334	
ZNF263	10127	hgsc.bcm.edu	37	16	3339435	3339435	+	Missense_Mutation	SNP	G	G	C	rs220379	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:3339435G>C	ENST00000219069.5	+	6	1805	c.929G>C	c.(928-930)tGc>tCc	p.C310S	ZNF263_ENST00000538765.1_5'UTR|ZNF263_ENST00000574253.1_Missense_Mutation_p.A144P	NM_005741.4	NP_005732.2	O14978	ZN263_HUMAN	zinc finger protein 263	310			C -> S (in dbSNP:rs220379).		negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|endometrium(2)|large_intestine(4)|lung(5)|ovary(1)|skin(4)|urinary_tract(3)	20						CCGTCTGTATGCTCTGAGAAC	0.522													C|||	1363	0.272165	0.5378	0.3545	5008	,	,		18726	0.0357		0.2634	False		,,,				2504	0.1074				p.C310S		Atlas-SNP	.											.	ZNF263	58	.	0			c.G929C						PASS	.	C	SER/CYS	2258,2136	573.1+/-383.5	601,1056,540	85.0	95.0	92.0		929	-0.9	0.0	16	dbSNP_79	92	2111,6489	709.8+/-405.7	253,1605,2442	yes	missense	ZNF263	NM_005741.4	112	854,2661,2982	CC,CG,GG		24.5465,48.6117,33.6232	benign	310/684	3339435	4369,8625	2197	4300	6497	SO:0001583	missense	10127	exon6			CTGTATGCTCTGA	AC004232	CCDS10499.1	16p13.3	2013-01-09			ENSG00000006194	ENSG00000006194		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	13056	protein-coding gene	gene with protein product		604191				9256059	Standard	NM_005741		Approved	FPM315, ZKSCAN12, ZSCAN44	uc002cuq.3	O14978	OTTHUMG00000129323	ENST00000219069.5:c.929G>C	16.37:g.3339435G>C	ENSP00000219069:p.Cys310Ser	Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	107	21	0.196262	NM_005741	B2R634|O43387|Q96H95	Missense_Mutation	SNP	ENST00000219069.5	37	CCDS10499.1	588	0.2692307692307692	244	0.4959349593495935	131	0.36187845303867405	21	0.03671328671328671	192	0.2532981530343008	C	2.814	-0.246389	0.05867	0.513883	0.245465	ENSG00000006194	ENST00000219069	T	0.04654	3.58	5.49	-0.916	0.10489	.	0.709753	0.12876	N	0.431863	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	0.38757	-0.9646	9	0.05525	T	0.97	.	2.0718	0.03615	0.1501:0.2518:0.3966:0.2015	rs220379;rs220379	310	O14978	ZN263_HUMAN	S	310	ENSP00000219069:C310S	ENSP00000219069:C310S	C	+	2	0	ZNF263	3279436	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.858000	0.04281	-0.156000	0.11079	-0.120000	0.15030	TGC	G|0.701;C|0.299	0.299	strong		0.522	ZNF263-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251463.2		
SBNO1	55206	hgsc.bcm.edu	37	12	123799938	123799938	+	Silent	SNP	C	C	T	rs61751327	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:123799938C>T	ENST00000602398.1	-	23	3229	c.3102G>A	c.(3100-3102)agG>agA	p.R1034R	SBNO1_ENST00000420886.2_Silent_p.R1034R|SBNO1_ENST00000267176.4_Silent_p.R1033R|SBNO1_ENST00000602750.1_Silent_p.R1033R			A3KN83	SBNO1_HUMAN	strawberry notch homolog 1 (Drosophila)	1034					regulation of transcription, DNA-templated (GO:0006355)			p.R1033R(1)		NS(2)|breast(6)|cervix(2)|endometrium(8)|kidney(3)|large_intestine(11)|lung(18)|ovary(2)|pancreas(1)|prostate(3)|skin(4)|stomach(2)	62	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000701)|Epithelial(86;0.00197)		CAAAGTTGAACCTGCTCAGAT	0.373													C|||	445	0.0888578	0.0356	0.062	5008	,	,		20260	0.254		0.0507	False		,,,				2504	0.0491				p.R1034R		Atlas-SNP	.											SBNO1,NS,carcinoma,0,1	SBNO1	138	1	1	Substitution - coding silent(1)	stomach(1)	c.G3102A						PASS	.	C	,	188,4218	121.7+/-159.2	2,184,2017	137.0	128.0	131.0		3102,3099	2.0	1.0	12	dbSNP_129	131	330,8270	115.0+/-174.9	10,310,3980	no	coding-synonymous,coding-synonymous	SBNO1	NM_001167856.1,NM_018183.3	,	12,494,5997	TT,TC,CC		3.8372,4.2669,3.9828	,	1034/1394,1033/1393	123799938	518,12488	2203	4300	6503	SO:0001819	synonymous_variant	55206	exon22			GTTGAACCTGCTC	AK001563	CCDS9246.1, CCDS53844.1	12q24.31	2006-10-06	2006-10-06			ENSG00000139697			22973	protein-coding gene	gene with protein product		614274	"""sno, strawberry notch homolog 1 (Drosophila)"""				Standard	NM_018183		Approved	MOP3, FLJ10701, FLJ10833, Sno	uc010tap.2	A3KN83		ENST00000602398.1:c.3102G>A	12.37:g.123799938C>T		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	69	15	0.217391	NM_001167856	Q05C06|Q3ZTS3|Q9H3T8|Q9NVB2	Silent	SNP	ENST00000602398.1	37	CCDS53844.1																																																																																			C|0.943;T|0.057	0.057	strong		0.373	SBNO1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000467684.1	NM_018183	
HIST1H2AI	8329	hgsc.bcm.edu	37	6	27776002	27776002	+	Silent	SNP	C	C	T	rs493283	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:27776002C>T	ENST00000358739.3	+	1	104	c.15C>T	c.(13-15)ggC>ggT	p.G5G	HIST1H3H_ENST00000369163.2_5'Flank|HIST1H2BL_ENST00000377401.2_5'Flank	NM_003509.2	NP_003500.1	P0C0S8	H2A1_HUMAN	histone cluster 1, H2ai	5						extracellular vesicular exosome (GO:0070062)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)			lung(3)	3						CTGGGCGTGGCAAGCAGGGAG	0.547																																					p.G5G		Atlas-SNP	.											.	HIST1H2AI	9	.	0			c.C15T						PASS	.						66.0	77.0	73.0					6																	27776002		2203	4300	6503	SO:0001819	synonymous_variant	8329	exon1			GCGTGGCAAGCAG	Z83742	CCDS4626.1	6p22.1	2011-01-27	2006-10-11	2003-02-28	ENSG00000196747	ENSG00000196747		"""Histones / Replication-dependent"""	4725	protein-coding gene	gene with protein product		602787	"""H2A histone family, member C"", ""histone 1, H2ai"""	H2AFC		9439656, 12408966	Standard	NM_003509		Approved	H2A/c		P0C0S8	OTTHUMG00000014484	ENST00000358739.3:c.15C>T	6.37:g.27776002C>T		Somatic	223	0	0		WXS	Illumina HiSeq	Phase_I	225	25	0.111111	NM_003509	P02261|Q2M1R2|Q76PA6	Silent	SNP	ENST00000358739.3	37	CCDS4626.1																																																																																			C|0.988;T|0.012	0.012	strong		0.547	HIST1H2AI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040152.1	NM_003509	
PCNT	5116	hgsc.bcm.edu	37	21	47850484	47850484	+	Missense_Mutation	SNP	G	G	C	rs2070426	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:47850484G>C	ENST00000359568.5	+	37	8084	c.7977G>C	c.(7975-7977)caG>caC	p.Q2659H	PCNT_ENST00000480896.1_3'UTR	NM_006031.5	NP_006022.3	O95613	PCNT_HUMAN	pericentrin	2659			Q -> H (in dbSNP:rs2070426).		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)					AGAGTGAGCAGGGGAAGGGGC	0.627													G|||	2445	0.488219	0.3321	0.451	5008	,	,		20208	0.6141		0.5586	False		,,,				2504	0.5235				p.Q2659H		Atlas-SNP	.											.	PCNT	283	.	0			c.G7977C						PASS	.	G	HIS/GLN	1499,2885		286,927,979	32.0	28.0	29.0		7977	-9.5	0.0	21	dbSNP_96	29	4764,3790		1354,2056,867	yes	missense	PCNT	NM_006031.5	24	1640,2983,1846	CC,CG,GG		44.3068,34.1925,48.4078	benign	2659/3337	47850484	6263,6675	2192	4277	6469	SO:0001583	missense	5116	exon37			TGAGCAGGGGAAG	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.7977G>C	21.37:g.47850484G>C	ENSP00000352572:p.Gln2659His	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	159	69	0.433962	NM_006031	O43152|Q7Z7C9	Missense_Mutation	SNP	ENST00000359568.5	37	CCDS33592.1	1126	0.5155677655677655	161	0.32723577235772355	166	0.4585635359116022	372	0.6503496503496503	427	0.5633245382585752	G	12.67	2.006586	0.35415	0.341925	0.556932	ENSG00000160299	ENST00000359568	T	0.02158	4.42	4.76	-9.46	0.00597	.	0.556644	0.13677	N	0.370482	T	0.00012	0.0000	L	0.43923	1.385	0.80722	P	0.0	B;B	0.18863	0.001;0.031	B;B	0.08055	0.003;0.003	T	0.46400	-0.9194	9	0.66056	D	0.02	.	4.3016	0.10927	0.0772:0.2126:0.3976:0.3127	rs2070426;rs58578374;rs2070426	2541;2659	O95613-2;O95613	.;PCNT_HUMAN	H	2659	ENSP00000352572:Q2659H	ENSP00000352572:Q2659H	Q	+	3	2	PCNT	46674912	0.000000	0.05858	0.000000	0.03702	0.187000	0.23431	-3.277000	0.00529	-1.418000	0.02014	-0.302000	0.09304	CAG	G|0.520;C|0.480	0.480	strong		0.627	PCNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207336.1	NM_006031	
FAM184B	27146	hgsc.bcm.edu	37	4	17635336	17635336	+	Missense_Mutation	SNP	G	G	A	rs61741403	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:17635336G>A	ENST00000265018.3	-	17	3277	c.3065C>T	c.(3064-3066)tCt>tTt	p.S1022F	MED28_ENST00000237380.7_3'UTR	NM_015688.1	NP_056503.1	Q9ULE4	F184B_HUMAN	family with sequence similarity 184, member B	1022										NS(1)|central_nervous_system(1)|endometrium(1)|prostate(1)	4						TGCATCTGTAGACTGGTTGGG	0.512													G|||	50	0.00998403	0.003	0.0173	5008	,	,		16527	0.0		0.0288	False		,,,				2504	0.0051				p.S1022F		Atlas-SNP	.											.	FAM184B	38	.	0			c.C3065T						PASS	.	G	PHE/SER	3,1381		0,3,689	88.0	83.0	84.0		3065	3.7	0.0	4	dbSNP_129	84	128,3054		0,128,1463	yes	missense	FAM184B	NM_015688.1	155	0,131,2152	AA,AG,GG		4.0226,0.2168,2.869	probably-damaging	1022/1061	17635336	131,4435	692	1591	2283	SO:0001583	missense	27146	exon17			TCTGTAGACTGGT		CCDS47033.1	4p16	2009-04-22			ENSG00000047662	ENSG00000047662			29235	protein-coding gene	gene with protein product						10574462	Standard	NM_015688		Approved	KIAA1276	uc003gpm.4	Q9ULE4	OTTHUMG00000160287	ENST00000265018.3:c.3065C>T	4.37:g.17635336G>A	ENSP00000265018:p.Ser1022Phe	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	128	47	0.367188	NM_015688		Missense_Mutation	SNP	ENST00000265018.3	37	CCDS47033.1	34	0.015567765567765568	2	0.0040650406504065045	7	0.019337016574585635	0	0.0	25	0.032981530343007916	G	11.82	1.752653	0.31046	0.002168	0.040226	ENSG00000047662	ENST00000265018	T	0.34072	1.38	5.43	3.68	0.42216	.	0.700610	0.13870	N	0.357090	T	0.07007	0.0178	L	0.44542	1.39	0.09310	N	1	P	0.44380	0.834	B	0.34242	0.178	T	0.02581	-1.1138	10	0.59425	D	0.04	2.9877	9.7468	0.40451	0.153:0.0:0.847:0.0	rs61741403	1022	Q9ULE4	F184B_HUMAN	F	1022	ENSP00000265018:S1022F	ENSP00000265018:S1022F	S	-	2	0	FAM184B	17244434	0.032000	0.19561	0.002000	0.10522	0.385000	0.30292	2.170000	0.42443	0.756000	0.33013	0.655000	0.94253	TCT	G|0.979;A|0.021	0.021	strong		0.512	FAM184B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360137.1	NM_015688	
GSG2	83903	hgsc.bcm.edu	37	17	3627840	3627840	+	Missense_Mutation	SNP	G	G	A	rs220462	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:3627840G>A	ENST00000325418.4	+	1	630	c.611G>A	c.(610-612)gGc>gAc	p.G204D	ITGAE_ENST00000263087.4_Intron|CTD-3195I5.3_ENST00000571741.1_RNA|ITGAE_ENST00000571185.1_5'UTR	NM_031965.2	NP_114171.2	Q8TF76	HASP_HUMAN	germ cell associated 2 (haspin)	204			G -> D (in dbSNP:rs220462). {ECO:0000269|PubMed:11311556, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17344846}.		histone H3-T3 phosphorylation involved in chromosome passenger complex localization to kinetochore (GO:2000751)|intracellular signal transduction (GO:0035556)|mitotic sister chromatid cohesion (GO:0007064)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|protein localization to chromosome, centromeric region (GO:0071459)|protein phosphorylation (GO:0006468)|regulation of spindle checkpoint (GO:0090231)	centrosome (GO:0005813)|chromosome (GO:0005694)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|spindle (GO:0005819)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|histone kinase activity (H3-T3 specific) (GO:0072354)|protein kinase activity (GO:0004672)										GTCCCGAGCGGCCTCCACCTC	0.662													G|||	1291	0.257788	0.0356	0.1556	5008	,	,		16159	0.3006		0.3101	False		,,,				2504	0.5327				p.G204D		Atlas-SNP	.											.	GSG2	48	.	0			c.G611A						PASS	.	G	,ASP/GLY	346,4060	179.7+/-208.2	21,304,1878	60.0	65.0	63.0		,611	-1.8	0.0	17	dbSNP_79	63	2761,5839	435.2+/-358.0	439,1883,1978	yes	intron,missense	ITGAE,GSG2	NM_002208.4,NM_031965.2	,94	460,2187,3856	AA,AG,GG		32.1047,7.8529,23.889	,benign	,204/799	3627840	3107,9899	2203	4300	6503	SO:0001583	missense	83903	exon1			CGAGCGGCCTCCA	AB039834	CCDS11036.1	17p13	2005-01-19			ENSG00000177602	ENSG00000177602			19682	protein-coding gene	gene with protein product		609240					Standard	NM_031965		Approved	haspin	uc002fwp.3	Q8TF76	OTTHUMG00000090703	ENST00000325418.4:c.611G>A	17.37:g.3627840G>A	ENSP00000325290:p.Gly204Asp	Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	103	34	0.330097	NM_031965	Q5U5K3|Q96MN1|Q9BXS7	Missense_Mutation	SNP	ENST00000325418.4	37	CCDS11036.1	500	0.22893772893772893	20	0.04065040650406504	65	0.17955801104972377	177	0.3094405594405594	238	0.31398416886543534	G	13.17	2.158020	0.38119	0.078529	0.321047	ENSG00000177602	ENST00000325418	T	0.08458	3.09	4.02	-1.77	0.07982	.	1.355760	0.05475	N	0.553742	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B	0.06786	0.001	B	0.08055	0.003	T	0.48433	-0.9036	9	0.87932	D	0	-26.5025	9.7666	0.40565	0.5364:0.0:0.4636:0.0	rs220462;rs220462	204	Q8TF76	HASP_HUMAN	D	204	ENSP00000325290:G204D	ENSP00000325290:G204D	G	+	2	0	GSG2	3574589	0.000000	0.05858	0.000000	0.03702	0.019000	0.09904	-0.148000	0.10219	-0.416000	0.07473	-0.136000	0.14681	GGC	G|0.759;A|0.241	0.241	strong		0.662	GSG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207391.1	NM_031965	
MYEOV	26579	hgsc.bcm.edu	37	11	69063572	69063572	+	Missense_Mutation	SNP	A	A	G	rs17856376	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:69063572A>G	ENST00000308946.3	+	3	1105	c.655A>G	c.(655-657)Atg>Gtg	p.M219V	MYEOV_ENST00000441339.2_Missense_Mutation_p.M219V|MYEOV_ENST00000535407.1_Missense_Mutation_p.M161V	NM_138768.2	NP_620123.2	Q96EZ4	MYEOV_HUMAN	myeloma overexpressed	219				M -> V (in Ref. 3; AAH11815). {ECO:0000305}.						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)		GGCACTCTGCATGACCCTGGC	0.637													A|||	1163	0.232228	0.5461	0.0865	5008	,	,		17519	0.2183		0.0596	False		,,,				2504	0.1033				p.M219V		Atlas-SNP	.											.	MYEOV	42	.	0			c.A655G						PASS	.	A	VAL/MET	2052,2348	567.8+/-382.2	475,1102,623	92.0	91.0	91.0		655	-2.9	0.0	11	dbSNP_123	91	560,8028	151.3+/-206.1	22,516,3756	yes	missense	MYEOV	NM_138768.2	21	497,1618,4379	GG,GA,AA		6.5207,46.6364,20.1109	benign	219/314	69063572	2612,10376	2200	4294	6494	SO:0001583	missense	26579	exon3			CTCTGCATGACCC	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.655A>G	11.37:g.69063572A>G	ENSP00000308330:p.Met219Val	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	70	17	0.242857	NM_138768	Q9UGN6|Q9UGN7	Missense_Mutation	SNP	ENST00000308946.3	37	CCDS8190.1	465	0.2129120879120879	240	0.4878048780487805	29	0.08011049723756906	152	0.26573426573426573	44	0.05804749340369393	A	1.216	-0.628404	0.03610	0.466364	0.065207	ENSG00000172927	ENST00000441339;ENST00000308946;ENST00000535407	T;T;T	0.19669	2.13;2.13;2.13	1.44	-2.88	0.05682	.	.	.	.	.	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	0.46693	-0.9173	8	0.87932	D	0	.	6.1583	0.20350	0.4925:0.0:0.5075:0.0	rs17856376	219	Q96EZ4	MYEOV_HUMAN	V	219;219;161	ENSP00000412482:M219V;ENSP00000308330:M219V;ENSP00000438100:M161V	ENSP00000308330:M219V	M	+	1	0	MYEOV	68820148	0.000000	0.05858	0.000000	0.03702	0.025000	0.11179	-0.125000	0.10579	-1.138000	0.02884	-0.589000	0.04120	ATG	A|0.808;C|0.000;G|0.192	0.192	strong		0.637	MYEOV-004	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396548.1		
PCDHB15	56121	hgsc.bcm.edu	37	5	140626724	140626724	+	Silent	SNP	T	T	G	rs3776091	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	232	0	0		WXS	Illumina HiSeq	Phase_I	231	103	0.445887	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	
WISP3	8838	hgsc.bcm.edu	37	6	112390565	112390565	+	Silent	SNP	A	A	G	rs17219737	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:112390565A>G	ENST00000368666.2	+	5	1093	c.807A>G	c.(805-807)caA>caG	p.Q269Q	WISP3_ENST00000230529.5_Silent_p.Q269Q|WISP3_ENST00000361714.1_Silent_p.Q287Q|TUBE1_ENST00000604814.1_5'Flank|WISP3_ENST00000604763.1_Silent_p.Q269Q|WISP3_ENST00000409166.1_Silent_p.Q45Q|WISP3_ENST00000368663.3_Silent_p.Q246Q	NM_198239.1	NP_937882.1	O95389	WISP3_HUMAN	WNT1 inducible signaling pathway protein 3	269	CTCK. {ECO:0000255|PROSITE- ProRule:PRU00039}.				cell-cell signaling (GO:0007267)|regulation of cell growth (GO:0001558)|signal transduction (GO:0007165)	extracellular space (GO:0005615)				breast(1)|central_nervous_system(1)|large_intestine(3)|lung(7)|prostate(1)	13		all_cancers(87;0.000196)|Acute lymphoblastic leukemia(125;1.18e-05)|all_hematologic(75;0.000114)|all_epithelial(87;0.00542)|Colorectal(196;0.0209)		all cancers(137;0.0283)|OV - Ovarian serous cystadenocarcinoma(136;0.0613)|Epithelial(106;0.0827)|GBM - Glioblastoma multiforme(226;0.0972)|BRCA - Breast invasive adenocarcinoma(108;0.246)		AAACATGCCAACCTACTTTCC	0.313													A|||	123	0.0245607	0.0045	0.0533	5008	,	,		17739	0.0		0.0736	False		,,,				2504	0.0061				p.Q287Q		Atlas-SNP	.											.	WISP3	33	.	0			c.A861G						PASS	.	A	,	57,4347	48.9+/-83.8	0,57,2145	61.0	63.0	63.0		807,861	1.5	1.0	6	dbSNP_123	63	546,8054	148.9+/-204.1	25,496,3779	no	coding-synonymous,coding-synonymous	WISP3	NM_003880.3,NM_198239.1	,	25,553,5924	GG,GA,AA		6.3488,1.2943,4.637	,	269/355,287/373	112390565	603,12401	2202	4300	6502	SO:0001819	synonymous_variant	8838	exon5			ATGCCAACCTACT	AF100781	CCDS5097.1, CCDS5098.1	6q21	2014-05-06			ENSG00000112761	ENSG00000112761			12771	protein-coding gene	gene with protein product		603400				9843955	Standard	NM_003880		Approved	CCN6	uc003pvo.3	O95389	OTTHUMG00000185101	ENST00000368666.2:c.807A>G	6.37:g.112390565A>G		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	59	29	0.491525	NM_198239	Q3KR29|Q5H8W4|Q6UXH6	Silent	SNP	ENST00000368666.2	37	CCDS5098.1																																																																																			A|0.956;G|0.044	0.044	strong		0.313	WISP3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041873.2	NM_003880	
CA6	765	hgsc.bcm.edu	37	1	9009406	9009406	+	Missense_Mutation	SNP	C	C	T	rs2274327	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:9009406C>T	ENST00000377443.2	+	2	168	c.164C>T	c.(163-165)aCg>aTg	p.T55M	CA6_ENST00000476083.1_Intron|CA6_ENST00000377436.3_Missense_Mutation_p.T55M|CA6_ENST00000377442.2_Intron|CA6_ENST00000480186.3_Missense_Mutation_p.T55M	NM_001215.3	NP_001206.2	P23280	CAH6_HUMAN	carbonic anhydrase VI	55			T -> M (in dbSNP:rs2274327).		bicarbonate transport (GO:0015701)|detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|one-carbon metabolic process (GO:0006730)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	carbonate dehydratase activity (GO:0004089)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(2)|prostate(1)|skin(5)	16	Ovarian(185;0.112)|all_lung(157;0.143)	all_epithelial(116;1.02e-19)|all_lung(118;3.6e-06)|Lung NSC(185;7.94e-06)|Renal(390;0.000147)|Breast(348;0.00123)|Colorectal(325;0.00205)|Hepatocellular(190;0.00825)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.9e-07)|COAD - Colon adenocarcinoma(227;8.28e-05)|Kidney(185;0.000268)|KIRC - Kidney renal clear cell carcinoma(229;0.000971)|STAD - Stomach adenocarcinoma(132;0.00184)|BRCA - Breast invasive adenocarcinoma(304;0.00192)|READ - Rectum adenocarcinoma(331;0.0649)	Mafenide(DB06795)|Zonisamide(DB00909)	CTACAGAGGACGAAGGTGCGG	0.582													C|||	1353	0.270168	0.0809	0.3775	5008	,	,		19246	0.2431		0.4155	False		,,,				2504	0.3282				p.T55M		Atlas-SNP	.											.	CA6	47	.	0			c.C164T						PASS	.	C	MET/THR	635,3771	274.0+/-271.7	53,529,1621	56.0	49.0	51.0		164	-7.7	0.0	1	dbSNP_100	51	3559,5041	516.5+/-378.8	732,2095,1473	yes	missense	CA6	NM_001215.2	81	785,2624,3094	TT,TC,CC		41.3837,14.4122,32.2467	probably-damaging	55/309	9009406	4194,8812	2203	4300	6503	SO:0001583	missense	765	exon2			AGAGGACGAAGGT	M57892	CCDS30578.1, CCDS57970.1, CCDS57971.1	1p36.2	2008-02-05			ENSG00000131686	ENSG00000131686	4.2.1.1	"""Carbonic anhydrases"""	1380	protein-coding gene	gene with protein product		114780				9691177	Standard	NM_001215		Approved		uc031plc.1	P23280	OTTHUMG00000001763	ENST00000377443.2:c.164C>T	1.37:g.9009406C>T	ENSP00000366662:p.Thr55Met	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	102	47	0.460784	NM_001270500	E7EMQ1|Q5FBW3|Q5FC00|Q96QX8|Q9UF03	Missense_Mutation	SNP	ENST00000377443.2	37	CCDS30578.1	639	0.2925824175824176	48	0.0975609756097561	145	0.4005524861878453	147	0.256993006993007	299	0.3944591029023747	C	16.20	3.056074	0.55325	0.144122	0.413837	ENSG00000131686	ENST00000319474;ENST00000549778;ENST00000377443;ENST00000377436	T;T;T;T	0.68331	-0.32;-0.32;-0.32;-0.32	5.55	-7.73	0.01245	Carbonic anhydrase, alpha-class, catalytic domain (4);	0.896444	0.09959	N	0.733659	T	0.00012	0.0000	L	0.31420	0.93	0.80722	P	0.0	D	0.60160	0.987	P	0.53006	0.715	T	0.20140	-1.0284	9	0.56958	D	0.05	.	12.5466	0.56203	0.2599:0.1215:0.6186:0.0	rs2274327;rs17389244;rs60942560;rs2274327	55	P23280	CAH6_HUMAN	M	55	ENSP00000325786:T55M;ENSP00000447108:T55M;ENSP00000366662:T55M;ENSP00000366654:T55M	ENSP00000325786:T55M	T	+	2	0	CA6	8931993	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.262000	0.08682	-1.540000	0.01730	-1.053000	0.02334	ACG	C|0.706;N|0.000	.	strong		0.582	CA6-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000004911.1		
TYR	7299	hgsc.bcm.edu	37	11	88911696	88911696	+	Missense_Mutation	SNP	C	C	A	rs1042602	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	101	0	0		WXS	Illumina HiSeq	Phase_I	87	15	0.172414	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	
CEP350	9857	hgsc.bcm.edu	37	1	179989742	179989742	+	Missense_Mutation	SNP	G	G	C	rs2477120	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:179989742G>C	ENST00000367607.3	+	12	3251	c.2833G>C	c.(2833-2835)Gaa>Caa	p.E945Q		NM_014810.4	NP_055625.4	Q5VT06	CE350_HUMAN	centrosomal protein 350kDa	945			E -> Q (in dbSNP:rs2477120). {ECO:0000269|Ref.1}.		microtubule anchoring (GO:0034453)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(7)|lung(35)|ovary(4)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	66						TCCCAAACCAGAAGGGCTACT	0.438													G|||	2826	0.564297	0.2436	0.7349	5008	,	,		20768	0.7044		0.6461	False		,,,				2504	0.6483				p.E945Q		Atlas-SNP	.											.	CEP350	418	.	0			c.G2833C						PASS	.	G	GLN/GLU	1467,2939	472.6+/-356.4	240,987,976	86.0	86.0	86.0		2833	6.0	1.0	1	dbSNP_100	86	5532,3068	660.8+/-401.8	1795,1942,563	yes	missense	CEP350	NM_014810.4	29	2035,2929,1539	CC,CG,GG		35.6744,33.2955,46.1864	benign	945/3118	179989742	6999,6007	2203	4300	6503	SO:0001583	missense	9857	exon12			AAACCAGAAGGGC	AF287356	CCDS1336.1	1q25.2	2014-02-20			ENSG00000135837	ENSG00000135837			24238	protein-coding gene	gene with protein product	"""centrosome associated protein 350"""					16314388, 15615782	Standard	NM_014810		Approved	KIAA0480, CAP350	uc001gnt.3	Q5VT06	OTTHUMG00000035269	ENST00000367607.3:c.2833G>C	1.37:g.179989742G>C	ENSP00000356579:p.Glu945Gln	Somatic	166	1	0.0060241		WXS	Illumina HiSeq	Phase_I	144	143	0.993056	NM_014810	O75068|Q8TDK3|Q8WY20	Missense_Mutation	SNP	ENST00000367607.3	37	CCDS1336.1	1286	0.5888278388278388	128	0.2601626016260163	255	0.7044198895027625	414	0.7237762237762237	489	0.6451187335092349	G	9.910	1.209166	0.22205	0.332955	0.643256	ENSG00000135837	ENST00000367607	T	0.08546	3.08	6.02	6.02	0.97574	.	0.136062	0.33235	N	0.005124	T	0.00012	0.0000	L	0.29908	0.895	0.34091	P	0.33927300000000005	D;B	0.53885	0.963;0.038	P;B	0.47299	0.543;0.029	T	0.09335	-1.0679	8	.	.	.	.	20.1358	0.98028	0.0:0.0:1.0:0.0	rs2477120;rs12737315;rs17371220;rs52804523;rs56997988;rs2477120	945;945	E7EU22;Q5VT06	.;CE350_HUMAN	Q	945	ENSP00000356579:E945Q	.	E	+	1	0	CEP350	178256365	1.000000	0.71417	1.000000	0.80357	0.701000	0.40568	4.603000	0.61105	2.865000	0.98341	0.655000	0.94253	GAA	G|0.450;C|0.550	0.550	strong		0.438	CEP350-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085315.2	NM_014810	
LRIT2	340745	hgsc.bcm.edu	37	10	85981801	85981801	+	Missense_Mutation	SNP	T	T	G	rs6585847	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:85981801T>G	ENST00000372113.4	-	3	1533	c.1528A>C	c.(1528-1530)Acc>Ccc	p.T510P	LRIT2_ENST00000538192.1_Missense_Mutation_p.T520P	NM_001017924.2	NP_001017924.1	A6NDA9	LRIT2_HUMAN	leucine-rich repeat, immunoglobulin-like and transmembrane domains 2	510			T -> P (in dbSNP:rs6585847).			integral component of membrane (GO:0016021)				central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(13)|ovary(3)|prostate(6)|urinary_tract(1)	32						GCTGCAGGGGTGCAGCTGGGG	0.627													G|||	2780	0.555112	0.8192	0.5346	5008	,	,		18652	0.4107		0.4662	False		,,,				2504	0.453				p.T510P		Atlas-SNP	.											LRIT2,colon,carcinoma,0,3	LRIT2	81	3	0			c.A1528C						PASS	.	G	PRO/THR	3294,1108		1273,748,180	55.0	62.0	60.0		1528	5.1	0.1	10	dbSNP_116	60	3909,4689		934,2041,1324	yes	missense	LRIT2	NM_001017924.2	38	2207,2789,1504	GG,GT,TT		45.4641,25.1704,44.5923	benign	510/551	85981801	7203,5797	2201	4299	6500	SO:0001583	missense	340745	exon3			CAGGGGTGCAGCT		CCDS31234.1, CCDS60581.1	10q23.2	2013-01-11	2007-06-19	2007-06-19	ENSG00000204033	ENSG00000204033		"""Immunoglobulin superfamily / I-set domain containing"""	23443	protein-coding gene	gene with protein product			"""leucine rich repeat containing 22"""	LRRC22			Standard	NM_001017924		Approved	AC022389.4	uc001kcy.3	A6NDA9	OTTHUMG00000018633	ENST00000372113.4:c.1528A>C	10.37:g.85981801T>G	ENSP00000361185:p.Thr510Pro	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	64	28	0.4375	NM_001017924	B7ZME6	Missense_Mutation	SNP	ENST00000372113.4	37	CCDS31234.1	1173	0.5370879120879121	410	0.8333333333333334	189	0.5220994475138122	219	0.38286713286713286	355	0.4683377308707124	G	2.589	-0.295668	0.05532	0.748296	0.454641	ENSG00000204033	ENST00000372113;ENST00000538192	T;T	0.10099	2.91;2.91	5.06	5.06	0.68205	.	0.677483	0.14615	N	0.308798	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	0.28235	-1.0050	9	0.02654	T	1	.	11.3765	0.49730	0.0:0.0:0.8184:0.1816	rs6585847;rs57540747	520;510	B7ZME6;A6NDA9	.;LRIT2_HUMAN	P	510;520	ENSP00000361185:T510P;ENSP00000438264:T520P	ENSP00000361185:T510P	T	-	1	0	LRIT2	85971781	0.039000	0.19947	0.109000	0.21407	0.030000	0.12068	1.715000	0.37971	1.288000	0.44600	-0.121000	0.15023	ACC	T|0.443;G|0.557	0.557	strong		0.627	LRIT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049110.4	XM_291697	
SEMA6B	10501	hgsc.bcm.edu	37	19	4555084	4555084	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:4555084C>A	ENST00000586582.1	-	8	896	c.586G>T	c.(586-588)Gtt>Ttt	p.V196F	SEMA6B_ENST00000301293.3_Missense_Mutation_p.V196F|SEMA6B_ENST00000586965.1_Missense_Mutation_p.V196F	NM_032108.3	NP_115484.2	Q9H3T3	SEM6B_HUMAN	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6B	196	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				cell differentiation (GO:0030154)|nervous system development (GO:0007399)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			breast(1)|central_nervous_system(2)|large_intestine(4)|lung(11)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0149)|STAD - Stomach adenocarcinoma(1328;0.18)		AAGTCGGTAACAGTAGCTGTG	0.587																																					p.V196F		Atlas-SNP	.											.	SEMA6B	51	.	0			c.G586T						PASS	.						109.0	87.0	95.0					19																	4555084		2203	4300	6503	SO:0001583	missense	10501	exon8			CGGTAACAGTAGC	AB022433	CCDS12131.1	19p13.3	2008-07-22				ENSG00000167680		"""Semaphorins"""	10739	protein-coding gene	gene with protein product	"""Sema VIb"", ""semaphorin Z"", ""semaphorin VIB"""	608873		SEMAN		9361278	Standard	NM_032108		Approved	semaZ, SEMA-VIB, SEM-SEMA-Y	uc010dud.2	Q9H3T3		ENST00000586582.1:c.586G>T	19.37:g.4555084C>A	ENSP00000467290:p.Val196Phe	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	46	17	0.369565	NM_032108	A5PKU4|F6IB19|Q9NRK9	Missense_Mutation	SNP	ENST00000586582.1	37	CCDS12131.1	.	.	.	.	.	.	.	.	.	.	C	18.29	3.592476	0.66219	.	.	ENSG00000167680	ENST00000301293;ENST00000301292	T	0.12147	2.71	2.8	2.8	0.32819	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.141549	0.46145	D	0.000304	T	0.39600	0.1084	M	0.85197	2.74	0.51012	D	0.999904	D;D	0.89917	1.0;1.0	D;D	0.97110	0.995;1.0	T	0.50285	-0.8846	10	0.87932	D	0	.	13.2603	0.60101	0.0:1.0:0.0:0.0	.	196;196	B4DT36;Q9H3T3	.;SEM6B_HUMAN	F	196	ENSP00000301293:V196F	ENSP00000301292:V196F	V	-	1	0	SEMA6B	4506084	1.000000	0.71417	0.087000	0.20705	0.468000	0.32798	5.648000	0.67930	1.882000	0.54519	0.455000	0.32223	GTT	.	.	none		0.587	SEMA6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458656.2	NM_032108	
LILRB1	10859	hgsc.bcm.edu	37	19	55143157	55143157	+	Missense_Mutation	SNP	G	G	A	rs12460501|rs34880987|rs200526666	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:55143157G>A	ENST00000396331.1	+	5	634	c.277G>A	c.(277-279)Gca>Aca	p.A93T	LILRB1_ENST00000448689.1_Missense_Mutation_p.A93T|LILRB1_ENST00000396315.1_Missense_Mutation_p.A93T|LILRB1_ENST00000396321.2_Missense_Mutation_p.A93T|LILRB1_ENST00000324602.7_Missense_Mutation_p.A93T|LILRB1_ENST00000427581.2_Missense_Mutation_p.A129T|LILRB1_ENST00000396327.3_Missense_Mutation_p.A93T|LILRB1_ENST00000434867.2_Missense_Mutation_p.A93T|LILRB1_ENST00000396317.1_Missense_Mutation_p.A93T|LILRB1_ENST00000418536.2_Missense_Mutation_p.A93T|AC009892.1_ENST00000578908.1_RNA|LILRB1_ENST00000396332.4_Missense_Mutation_p.A93T	NM_006669.3	NP_006660.3	Q8NHL6	LIRB1_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 1	93	Ig-like C2-type 1.		A -> T (in dbSNP:rs12460501). {ECO:0000269|PubMed:20600445}.		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)		CTGGGAACATGCAGGGCGGTA	0.552										HNSCC(37;0.09)			g|||	1071	0.213858	0.0575	0.232	5008	,	,		17924	0.505		0.1312	False		,,,				2504	0.1973				p.A93T		Atlas-SNP	.											.	LILRB1	140	.	0			c.G277A						PASS	.	G	THR/ALA,THR/ALA,THR/ALA,THR/ALA	156,4250		8,140,2055	160.0	146.0	151.0		277,277,277,277	-0.3	0.0	19	dbSNP_120	151	644,7956		78,488,3734	no	missense,missense,missense,missense	LILRB1	NM_001081637.1,NM_001081638.1,NM_001081639.1,NM_006669.3	58,58,58,58	86,628,5789	AA,AG,GG		7.4884,3.5406,6.151	benign,benign,benign,benign	93/653,93/652,93/652,93/651	55143157	800,12206	2203	4300	6503	SO:0001583	missense	10859	exon4			GAACATGCAGGGC	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.277G>A	19.37:g.55143157G>A	ENSP00000379622:p.Ala93Thr	Somatic	197	0	0		WXS	Illumina HiSeq	Phase_I	148	146	0.986486	NM_001081637	A2IXV4|A8MXT0|O75024|O75025|Q8NHJ9|Q8NHK0	Missense_Mutation	SNP	ENST00000396331.1	37	CCDS42617.1	376	0.17216117216117216	19	0.03861788617886179	57	0.1574585635359116	231	0.40384615384615385	69	0.09102902374670185	G	10.20	1.283574	0.23392	0.035406	0.074884	ENSG00000104972	ENST00000396321;ENST00000418536;ENST00000448689;ENST00000396331;ENST00000396327;ENST00000324602;ENST00000434867;ENST00000396332;ENST00000427581;ENST00000396317;ENST00000396315	T;T;T;T;T;T;T;T;T;T;T	0.14766	2.48;2.48;2.48;2.48;2.48;2.48;2.48;2.48;2.48;2.48;2.48	2.11	-0.338	0.12651	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.246452	0.28544	N	0.014975	T	0.00012	0.0000	L	0.47190	1.495	0.80722	P	0.0	D;B;P;P;B	0.54601	0.967;0.136;0.914;0.631;0.313	P;B;P;B;B	0.56127	0.792;0.103;0.657;0.393;0.314	T	0.47005	-0.9150	9	0.45353	T	0.12	.	5.5388	0.17026	0.3128:0.0:0.6872:0.0	rs12460501;rs57567657;rs12460501	93;93;93;93;93	A8MVE2;Q8NHL6-3;A2IXV4;Q8NHL6-2;Q8NHL6	.;.;.;.;LIRB1_HUMAN	T	93;93;93;93;93;93;93;93;129;93;93	ENSP00000379614:A93T;ENSP00000391514:A93T;ENSP00000409968:A93T;ENSP00000379622:A93T;ENSP00000379618:A93T;ENSP00000315997:A93T;ENSP00000405243:A93T;ENSP00000379623:A93T;ENSP00000395004:A129T;ENSP00000379610:A93T;ENSP00000379608:A93T	ENSP00000315997:A93T	A	+	1	0	LILRB1	59834969	0.000000	0.05858	0.005000	0.12908	0.009000	0.06853	-0.346000	0.07760	-0.222000	0.09958	-1.050000	0.02344	GCA	G|0.855;A|0.145	0.145	strong		0.552	LILRB1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000140796.4		
ZNF256	10172	hgsc.bcm.edu	37	19	58453342	58453342	+	Silent	SNP	T	T	C	rs959231	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:58453342T>C	ENST00000282308.3	-	3	1030	c.834A>G	c.(832-834)caA>caG	p.Q278Q	ZNF256_ENST00000598928.1_3'UTR	NM_005773.2	NP_005764.2	Q9Y2P7	ZN256_HUMAN	zinc finger protein 256	278					multicellular organismal development (GO:0007275)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|kidney(3)|large_intestine(6)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	19		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0155)		GGCTAGAGCTTTGCCTATAGG	0.393													T|||	1336	0.266773	0.1596	0.3112	5008	,	,		24363	0.3145		0.3002	False		,,,				2504	0.2965				p.Q278Q	NSCLC(55;1313 1552 8040 11996)	Atlas-SNP	.											.	ZNF256	117	.	0			c.A834G						PASS	.	T		767,3639		72,623,1508	114.0	108.0	110.0		834	0.9	0.0	19	dbSNP_86	110	2549,6051		369,1811,2120	no	coding-synonymous	ZNF256	NM_005773.2		441,2434,3628	CC,CT,TT		29.6395,17.4081,25.4959		278/628	58453342	3316,9690	2203	4300	6503	SO:0001819	synonymous_variant	10172	exon3			AGAGCTTTGCCTA	AF067165	CCDS12966.1	19q13	2013-01-08				ENSG00000152454		"""Zinc fingers, C2H2-type"", ""-"""	13049	protein-coding gene	gene with protein product		606956					Standard	NM_005773		Approved	BMZF-3	uc002qqu.3	Q9Y2P7		ENST00000282308.3:c.834A>G	19.37:g.58453342T>C		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	116	77	0.663793	NM_005773	B2RA92|Q53Y85|Q9BV71	Silent	SNP	ENST00000282308.3	37	CCDS12966.1																																																																																			T|0.741;C|0.259	0.259	strong		0.393	ZNF256-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466702.1		
BMP5	653	hgsc.bcm.edu	37	6	55639028	55639028	+	Silent	SNP	G	G	A	rs41271330	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:55639028G>A	ENST00000370830.3	-	4	1544	c.846C>T	c.(844-846)aaC>aaT	p.N282N	BMP5_ENST00000446683.2_Silent_p.N282N	NM_021073.2	NP_066551.1	P22003	BMP5_HUMAN	bone morphogenetic protein 5	282					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)	p.N282K(1)		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)			CAGATTTTACGTTGATACTGC	0.423													G|||	458	0.0914537	0.0061	0.0965	5008	,	,		19513	0.2054		0.1193	False		,,,				2504	0.0573				p.N282N		Atlas-SNP	.											BMP5,NS,carcinoma,0,1	BMP5	94	1	1	Substitution - Missense(1)	lung(1)	c.C846T						PASS	.	G		150,4256	102.5+/-141.1	3,144,2056	165.0	146.0	153.0		846	-3.8	0.7	6	dbSNP_127	153	1087,7513	227.8+/-263.0	65,957,3278	no	coding-synonymous	BMP5	NM_021073.2		68,1101,5334	AA,AG,GG		12.6395,3.4044,9.511		282/455	55639028	1237,11769	2203	4300	6503	SO:0001819	synonymous_variant	653	exon4			TTTTACGTTGATA		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.846C>T	6.37:g.55639028G>A		Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	142	59	0.415493	NM_021073	B4E0Y4|Q9H547|Q9NTM5	Silent	SNP	ENST00000370830.3	37	CCDS4958.1																																																																																			G|0.903;A|0.097	0.097	strong		0.423	BMP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041000.1		
ILVBL	10994	hgsc.bcm.edu	37	19	15226970	15226970	+	Silent	SNP	G	G	A	rs2074262	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:15226970G>A	ENST00000263383.3	-	12	1603	c.1464C>T	c.(1462-1464)ctC>ctT	p.L488L	ILVBL_ENST00000534378.1_Silent_p.L381L	NM_006844.3	NP_006835.2	A1L0T0	ILVBL_HUMAN	ilvB (bacterial acetolactate synthase)-like	488	Thiamine pyrophosphate binding. {ECO:0000250}.					integral component of membrane (GO:0016021)|membrane (GO:0016020)	magnesium ion binding (GO:0000287)|thiamine pyrophosphate binding (GO:0030976)|transferase activity (GO:0016740)			NS(3)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(5)|ovary(2)|skin(1)	26						TACCAGGATCGAGCCAGCGCA	0.642													G|||	2062	0.411741	0.2458	0.4741	5008	,	,		15867	0.4782		0.507	False		,,,				2504	0.4254				p.L488L		Atlas-SNP	.											.	ILVBL	54	.	0			c.C1464T						PASS	.	G		1253,3153	422.3+/-339.7	169,915,1119	42.0	42.0	42.0		1464	-10.4	0.0	19	dbSNP_96	42	4252,4348	564.0+/-388.2	1053,2146,1101	no	coding-synonymous	ILVBL	NM_006844.3		1222,3061,2220	AA,AG,GG		49.4419,28.4385,42.3266		488/633	15226970	5505,7501	2203	4300	6503	SO:0001819	synonymous_variant	10994	exon12			AGGATCGAGCCAG	U61263	CCDS12325.1	19p13.1	2008-07-16			ENSG00000105135	ENSG00000105135			6041	protein-coding gene	gene with protein product	"""acetolactate synthase homolog"""	605770				8954801	Standard	NM_006844		Approved	209L8, AHAS, ILV2H, MGC1269, FLJ39061, MGC19535	uc002nam.3	A1L0T0	OTTHUMG00000165630	ENST00000263383.3:c.1464C>T	19.37:g.15226970G>A		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	42	17	0.404762	NM_006844	O43341|Q96F08|Q99651|Q9BWN5|Q9UEB2	Silent	SNP	ENST00000263383.3	37	CCDS12325.1																																																																																			G|0.577;A|0.423	0.423	strong		0.642	ILVBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385439.1	NM_006844	
OR52E2	119678	hgsc.bcm.edu	37	11	5080068	5080068	+	Missense_Mutation	SNP	G	G	A	rs2500052	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:5080068G>A	ENST00000321522.2	-	1	789	c.790C>T	c.(790-792)Cgc>Tgc	p.R264C		NM_001005164.2	NP_001005164.2	Q8NGJ4	O52E2_HUMAN	olfactory receptor, family 52, subfamily E, member 2	264			R -> C (in dbSNP:rs2500052). {ECO:0000269|Ref.1}.			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(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)		CGGCCAAAGCGATGAGTCATA	0.468													G|||	2557	0.510583	0.6717	0.5086	5008	,	,		18255	0.2619		0.5089	False		,,,				2504	0.5521				p.R264C		Atlas-SNP	.											OR52E2,colon,carcinoma,0,1	OR52E2	63	1	0			c.C790T						PASS	.	G	CYS/ARG	2734,1668	656.7+/-400.1	869,996,336	92.0	92.0	92.0		790	3.8	0.9	11	dbSNP_100	92	4308,4288	577.8+/-390.6	1068,2172,1058	no	missense	OR52E2	NM_001005164.2	180	1937,3168,1394	AA,AG,GG		49.8837,37.8919,45.8224	probably-damaging	264/326	5080068	7042,5956	2201	4298	6499	SO:0001583	missense	119678	exon1			CAAAGCGATGAGT	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.790C>T	11.37:g.5080068G>A	ENSP00000322088:p.Arg264Cys	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	92	92	1	NM_001005164		Missense_Mutation	SNP	ENST00000321522.2	37	CCDS31371.1	1036	0.47435897435897434	330	0.6707317073170732	172	0.47513812154696133	149	0.26048951048951047	385	0.5079155672823219	G	14.78	2.636499	0.47049	0.621081	0.501163	ENSG00000176787	ENST00000321522	T	0.37411	1.2	3.76	3.76	0.43208	GPCR, rhodopsin-like superfamily (1);	0.123911	0.34200	N	0.004162	T	0.00012	0.0000	M	0.89353	3.025	0.29331	P	0.866687	D	0.54397	0.966	P	0.51385	0.668	T	0.47935	-0.9078	9	0.87932	D	0	.	10.7329	0.46107	0.0:0.0:0.8091:0.1909	rs2500052;rs12794355;rs17260181;rs2500052	264	Q8NGJ4	O52E2_HUMAN	C	264	ENSP00000322088:R264C	ENSP00000322088:R264C	R	-	1	0	OR52E2	5036644	0.000000	0.05858	0.937000	0.37676	0.695000	0.40330	0.184000	0.16939	2.425000	0.82216	0.644000	0.83932	CGC	G|0.476;A|0.524	0.524	strong		0.468	OR52E2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142815.1	NM_001005164	
SIGLEC5	8778	hgsc.bcm.edu	37	19	52133292	52133292	+	Missense_Mutation	SNP	A	A	G	rs1973019	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:52133292A>G	ENST00000534261.2	-	3	614	c.215T>C	c.(214-216)gTt>gCt	p.V72A	SIGLEC5_ENST00000222107.4_Intron|SIGLEC5_ENST00000429354.3_Missense_Mutation_p.V72A|SIGLEC5_ENST00000599649.1_Intron|SIGLEC5_ENST00000570106.2_Missense_Mutation_p.V72A			O15389	SIGL5_HUMAN	sialic acid binding Ig-like lectin 5	72	Ig-like V-type.		V -> A (in dbSNP:rs1973019).		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)		TGTGGCCACAACCTCAGCGTA	0.577													G|||	482	0.096246	0.0121	0.1974	5008	,	,		15121	0.002		0.1988	False		,,,				2504	0.1299				p.V72A		Atlas-SNP	.											SIGLEC5,NS,carcinoid-endocrine_tumour,0,1	SIGLEC5	67	1	0			c.T215C						scavenged	.						6.0	6.0	6.0					19																	52133292		1790	3344	5134	SO:0001583	missense	8778	exon2			GCCACAACCTCAG	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.215T>C	19.37:g.52133292A>G	ENSP00000473238:p.Val72Ala	Somatic	1154	5	0.00433276		WXS	Illumina HiSeq	Phase_I	964	510	0.529046	NM_003830		Missense_Mutation	SNP	ENST00000534261.2	37	CCDS33088.1	.	.	.	.	.	.	.	.	.	.	a	5.405	0.259892	0.10239	.	.	ENSG00000105501	ENST00000429354	T	0.68025	-0.3	4.24	-4.0	0.04057	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.544624	0.15369	N	0.265939	T	0.46870	0.1415	N	0.25485	0.75	0.80722	P	0.0	B	0.06786	0.001	B	0.12156	0.007	T	0.27640	-1.0068	9	0.30854	T	0.27	.	10.8806	0.46935	0.6567:0.0:0.3433:0.0	.	72	O15389	SIGL5_HUMAN	A	72	ENSP00000415200:V72A	ENSP00000415200:V72A	V	-	2	0	SIGLEC5	56825104	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.459000	0.06728	-0.793000	0.04475	-0.880000	0.02959	GTT	A|0.500;G|0.500	0.500	strong		0.577	SIGLEC5-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466897.2	NM_003830	
NOTCH1	4851	hgsc.bcm.edu	37	9	139397707	139397707	+	Silent	SNP	G	G	A	rs10521	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:139397707G>A	ENST00000277541.6	-	27	5169	c.5094C>T	c.(5092-5094)gaC>gaT	p.D1698D		NM_017617.3	NP_060087.3	P46531	NOTC1_HUMAN	notch 1	1698					anagen (GO:0042640)|aortic valve morphogenesis (GO:0003180)|apoptotic process involved in embryonic digit morphogenesis (GO:1902263)|arterial endothelial cell differentiation (GO:0060842)|atrioventricular node development (GO:0003162)|atrioventricular valve morphogenesis (GO:0003181)|auditory receptor cell fate commitment (GO:0009912)|axonogenesis (GO:0007409)|branching morphogenesis of an epithelial tube (GO:0048754)|cardiac atrium morphogenesis (GO:0003209)|cardiac chamber formation (GO:0003207)|cardiac epithelial to mesenchymal transition (GO:0060317)|cardiac left ventricle morphogenesis (GO:0003214)|cardiac muscle cell proliferation (GO:0060038)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac right atrium morphogenesis (GO:0003213)|cardiac right ventricle formation (GO:0003219)|cardiac septum morphogenesis (GO:0060411)|cardiac vascular smooth muscle cell development (GO:0060948)|cardiac ventricle morphogenesis (GO:0003208)|cell fate specification (GO:0001708)|cell migration involved in endocardial cushion formation (GO:0003273)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|cilium morphogenesis (GO:0060271)|collecting duct development (GO:0072044)|compartment pattern specification (GO:0007386)|coronary artery morphogenesis (GO:0060982)|coronary vein morphogenesis (GO:0003169)|determination of left/right symmetry (GO:0007368)|distal tubule development (GO:0072017)|embryonic hindlimb morphogenesis (GO:0035116)|endocardial cell differentiation (GO:0060956)|endocardial cushion morphogenesis (GO:0003203)|endocardium development (GO:0003157)|endocardium morphogenesis (GO:0003160)|endoderm development (GO:0007492)|epithelial to mesenchymal transition (GO:0001837)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|forebrain development (GO:0030900)|foregut morphogenesis (GO:0007440)|gene expression (GO:0010467)|glial cell differentiation (GO:0010001)|glomerular mesangial cell development (GO:0072144)|growth involved in heart morphogenesis (GO:0003241)|hair follicle morphogenesis (GO:0031069)|heart development (GO:0007507)|heart looping (GO:0001947)|heart trabecula morphogenesis (GO:0061384)|humoral immune response (GO:0006959)|immune response (GO:0006955)|in utero embryonic development (GO:0001701)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-4 secretion (GO:0072602)|keratinocyte differentiation (GO:0030216)|left/right axis specification (GO:0070986)|liver development (GO:0001889)|lung development (GO:0030324)|mesenchymal cell development (GO:0014031)|mitral valve formation (GO:0003192)|negative regulation of anoikis (GO:2000811)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of calcium ion-dependent exocytosis (GO:0045955)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cell migration involved in sprouting angiogenesis (GO:0090051)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of endothelial cell chemotaxis (GO:2001027)|negative regulation of glial cell proliferation (GO:0060253)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of neurogenesis (GO:0050768)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of ossification (GO:0030279)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of photoreceptor cell differentiation (GO:0046533)|negative regulation of pro-B cell differentiation (GO:2000974)|negative regulation of stem cell differentiation (GO:2000737)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube development (GO:0021915)|neuronal stem cell maintenance (GO:0097150)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|Notch signaling pathway involved in regulation of secondary heart field cardioblast proliferation (GO:0003270)|pericardium morphogenesis (GO:0003344)|positive regulation of apoptotic process (GO:0043065)|positive regulation of astrocyte differentiation (GO:0048711)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061419)|positive regulation of transcription of Notch receptor target (GO:0007221)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland epithelium morphogenesis (GO:0060740)|pulmonary valve morphogenesis (GO:0003184)|regulation of epithelial cell proliferation involved in prostate gland development (GO:0060768)|regulation of extracellular matrix assembly (GO:1901201)|regulation of somitogenesis (GO:0014807)|regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation (GO:0003256)|regulation of transcription, DNA-templated (GO:0006355)|response to muramyl dipeptide (GO:0032495)|secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development (GO:0060528)|skeletal muscle cell differentiation (GO:0035914)|somatic stem cell division (GO:0048103)|sprouting angiogenesis (GO:0002040)|transcription initiation from RNA polymerase II promoter (GO:0006367)|tube formation (GO:0035148)|vasculogenesis involved in coronary vascular morphogenesis (GO:0060979)|venous endothelial cell differentiation (GO:0060843)|ventricular septum morphogenesis (GO:0060412)|ventricular trabecula myocardium morphogenesis (GO:0003222)	cell surface (GO:0009986)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|MAML1-RBP-Jkappa- ICN1 complex (GO:0002193)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)|receptor activity (GO:0004872)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.D1699D(11)		breast(16)|central_nervous_system(17)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1183)|kidney(4)|large_intestine(1)|lung(57)|oesophagus(2)|ovary(3)|pancreas(1)|prostate(3)|skin(21)|upper_aerodigestive_tract(39)|urinary_tract(3)	1359	all_cancers(76;0.223)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;5.34e-06)|Epithelial(140;7.77e-06)		ATGCGGCCACGTCGGTGGCAC	0.632			"""T, Mis, O"""	TRB@	T-ALL					HNSCC(8;0.001)			G|||	2772	0.553514	0.5552	0.5115	5008	,	,		17626	0.9018		0.4046	False		,,,				2504	0.3753				p.D1698D		Atlas-SNP	.		Dom	yes		9	9q34.3	4851	"""Notch homolog 1, translocation-associated (Drosophila) (TAN1)"""		L	NOTCH1_ENST00000277541,colon,carcinoma,0,19	NOTCH1	1980	19	11	Substitution - coding silent(11)	haematopoietic_and_lymphoid_tissue(11)	c.C5094T						PASS	.	G		2208,2062		587,1034,514	57.0	67.0	64.0		5094	-4.9	0.8	9	dbSNP_52	64	3010,5508		545,1920,1794	no	coding-synonymous	NOTCH1	NM_017617.3		1132,2954,2308	AA,AG,GG		35.3369,48.2904,40.8039		1698/2556	139397707	5218,7570	2135	4259	6394	SO:0001819	synonymous_variant	4851	exon27			GGCCACGTCGGTG	AF308602	CCDS43905.1	9q34.3	2013-01-10	2010-06-24		ENSG00000148400	ENSG00000148400		"""Ankyrin repeat domain containing"""	7881	protein-coding gene	gene with protein product		190198	"""Notch (Drosophila) homolog 1 (translocation-associated)"", ""Notch homolog 1, translocation-associated (Drosophila)"""	TAN1		1831692	Standard	NM_017617		Approved		uc004chz.3	P46531	OTTHUMG00000020935	ENST00000277541.6:c.5094C>T	9.37:g.139397707G>A		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	73	37	0.506849	NM_017617	Q59ED8|Q5SXM3	Silent	SNP	ENST00000277541.6	37	CCDS43905.1																																																																																			G|0.466;A|0.534	0.534	strong		0.632	NOTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055087.1	NM_017617	
KRTAP10-6	386674	hgsc.bcm.edu	37	21	46011719	46011719	+	Missense_Mutation	SNP	G	G	A	rs202022037	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	232	0	0		WXS	Illumina HiSeq	Phase_I	245	18	0.0734694	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	
C14orf159	80017	hgsc.bcm.edu	37	14	91671124	91671124	+	Missense_Mutation	SNP	G	G	A	rs2295524	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:91671124G>A	ENST00000523771.1	+	12	2107	c.1504G>A	c.(1504-1506)Gat>Aat	p.D502N	C14orf159_ENST00000428926.2_Missense_Mutation_p.D502N|C14orf159_ENST00000521077.2_Intron|C14orf159_ENST00000522322.1_Missense_Mutation_p.D502N|C14orf159_ENST00000518868.1_Missense_Mutation_p.D507N|C14orf159_ENST00000520328.1_Intron|C14orf159_ENST00000412671.2_Missense_Mutation_p.D507N|C14orf159_ENST00000525393.2_Missense_Mutation_p.D378N|C14orf159_ENST00000256324.10_Missense_Mutation_p.D507N|C14orf159_ENST00000523816.1_Missense_Mutation_p.D502N			Q7Z3D6	CN159_HUMAN	chromosome 14 open reading frame 159	502			D -> N (in dbSNP:rs2295524).			mitochondrion (GO:0005739)				NS(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	21		all_cancers(154;0.0191)|all_epithelial(191;0.241)		Epithelial(152;0.141)|OV - Ovarian serous cystadenocarcinoma(161;0.207)		ACGGCACGGGGATGTCATCGC	0.627													G|||	924	0.184505	0.289	0.0908	5008	,	,		19941	0.2123		0.0915	False		,,,				2504	0.1769				p.D507N		Atlas-SNP	.											.	C14orf159	57	.	0			c.G1519A						PASS	.	G	ASN/ASP,ASN/ASP,ASN/ASP,,ASN/ASP	1127,3279	404.4+/-333.1	134,859,1210	162.0	107.0	126.0		1504,1504,1519,,1504	5.0	0.9	14	dbSNP_100	126	697,7903	171.6+/-222.5	33,631,3636	yes	missense,missense,missense,intron,missense	C14orf159	NM_001102366.1,NM_001102367.1,NM_001102368.1,NM_001102369.1,NM_024952.6	23,23,23,,23	167,1490,4846	AA,AG,GG		8.1047,25.5788,14.0243	possibly-damaging,possibly-damaging,possibly-damaging,,possibly-damaging	502/617,502/617,507/622,,502/617	91671124	1824,11182	2203	4300	6503	SO:0001583	missense	80017	exon12			CACGGGGATGTCA	AK097294	CCDS32141.1, CCDS41979.1, CCDS45150.1, CCDS66693.1, CCDS73677.1	14q32.11	2012-09-26			ENSG00000133943	ENSG00000133943			20498	protein-coding gene	gene with protein product							Standard	NM_001102367		Approved	FLJ39975	uc001xze.2	Q7Z3D6	OTTHUMG00000164980	ENST00000523771.1:c.1504G>A	14.37:g.91671124G>A	ENSP00000429655:p.Asp502Asn	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	85	83	0.976471	NM_001102368	B3KUI7|Q86SW3|Q86SX8|Q86SX9|Q86T08|Q86TV5|Q96GW5|Q9H7G0|Q9H8Y9|Q9H9W6	Missense_Mutation	SNP	ENST00000523771.1	37	CCDS32141.1	335	0.1533882783882784	125	0.2540650406504065	41	0.1132596685082873	100	0.17482517482517482	69	0.09102902374670185	G	17.51	3.407587	0.62399	0.255788	0.081047	ENSG00000133943	ENST00000256324;ENST00000518868;ENST00000523816;ENST00000525393;ENST00000428926;ENST00000522322;ENST00000523771;ENST00000412671	T;T;T;T;T;T;T;T	0.18810	2.19;2.19;2.19;2.19;2.19;2.19;2.19;2.19	4.96	4.96	0.65561	.	0.660719	0.15819	N	0.243086	T	0.00012	0.0000	M	0.69523	2.12	0.27463	P	0.9531044	P;D	0.57571	0.891;0.98	P;P	0.53649	0.673;0.731	T	0.05954	-1.0854	9	0.56958	D	0.05	.	17.8327	0.88687	0.0:0.0:1.0:0.0	rs2295524;rs17188983;rs57590208;rs2295524	502;507	Q7Z3D6;Q7Z3D6-2	CN159_HUMAN;.	N	507;507;502;378;502;502;502;507	ENSP00000256324:D507N;ENSP00000428263:D507N;ENSP00000428974:D502N;ENSP00000435459:D378N;ENSP00000404343:D502N;ENSP00000427953:D502N;ENSP00000429655:D502N;ENSP00000404196:D507N	ENSP00000256324:D507N	D	+	1	0	C14orf159	90740877	1.000000	0.71417	0.916000	0.36221	0.146000	0.21551	3.311000	0.51919	2.296000	0.77279	0.591000	0.81541	GAT	G|0.835;A|0.165	0.165	strong		0.627	C14orf159-014	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381273.1	NM_024952	
MUC4	4585	hgsc.bcm.edu	37	3	195512287	195512287	+	Missense_Mutation	SNP	G	G	A	rs113602668	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195512287G>A	ENST00000463781.3	-	2	6623	c.6164C>T	c.(6163-6165)tCc>tTc	p.S2055F	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.S2055F	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GGATACTGAGGAAAGGCTGGT	0.572																																					p.S2055F		Atlas-SNP	.											.	MUC4	1505	.	0			c.C6164T						PASS	.						18.0	18.0	18.0					3																	195512287		686	1573	2259	SO:0001583	missense	4585	exon2			ACTGAGGAAAGGC	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.6164C>T	3.37:g.195512287G>A	ENSP00000417498:p.Ser2055Phe	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	85	20	0.235294	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	G	5.081	0.200645	0.09652	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.32988	1.43;1.43	.	.	.	.	.	.	.	.	T	0.14056	0.0340	N	0.19112	0.55	0.09310	N	1	P	0.35139	0.486	B	0.22601	0.04	T	0.15752	-1.0426	6	.	.	.	.	.	.	.	.	2055	E7ESK3	.	F	2055	ENSP00000417498:S2055F;ENSP00000420243:S2055F	.	S	-	2	0	MUC4	196996682	.	.	0.002000	0.10522	0.014000	0.08584	.	.	0.488000	0.27723	0.064000	0.15345	TCC	G|0.843;A|0.157	0.157	strong		0.572	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
NDUFA6	4700	hgsc.bcm.edu	37	22	42486723	42486723	+	Missense_Mutation	SNP	G	G	A	rs1801311	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:42486723G>A	ENST00000498737.2	-	1	236	c.104C>T	c.(103-105)gCt>gTt	p.A35V	NDUFA6-AS1_ENST00000416037.2_RNA|NDUFA6_ENST00000602404.1_Missense_Mutation_p.A9V|NDUFA6-AS1_ENST00000595777.1_RNA|NDUFA6-AS1_ENST00000417327.1_RNA|NDUFA6-AS1_ENST00000600968.1_RNA|RP1-257I20.14_ENST00000602718.1_RNA|NDUFA6-AS1_ENST00000434834.1_RNA|NDUFA6-AS1_ENST00000439129.1_RNA|NDUFA6-AS1_ENST00000608974.1_RNA|NDUFA6-AS1_ENST00000536447.2_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	119	0	0		WXS	Illumina HiSeq	Phase_I	100	97	0.97	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	
NAV2	89797	hgsc.bcm.edu	37	11	20124807	20124807	+	Missense_Mutation	SNP	C	C	T	rs34329467	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:20124807C>T	ENST00000396087.3	+	36	6700	c.6601C>T	c.(6601-6603)Cgc>Tgc	p.R2201C	NAV2_ENST00000527559.2_Missense_Mutation_p.R2130C|NAV2_ENST00000540292.1_Missense_Mutation_p.R2132C|NAV2_ENST00000360655.4_Missense_Mutation_p.R2078C|NAV2_ENST00000533917.1_Missense_Mutation_p.R1206C|NAV2_ENST00000349880.4_Missense_Mutation_p.R2142C|NAV2_ENST00000311043.8_Missense_Mutation_p.R1206C|NAV2_ENST00000396085.1_Missense_Mutation_p.R2145C	NM_001244963.1	NP_001231892.1	Q8IVL1	NAV2_HUMAN	neuron navigator 2	2201					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						ATAGGAATTGCGCCAGTACCT	0.567													C|||	3	0.000599042	0.0008	0.0	5008	,	,		23293	0.0		0.002	False		,,,				2504	0.0				p.R2201C		Atlas-SNP	.											.	NAV2	255	.	0			c.C6601T						PASS	.	C	CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG	4,4402	8.1+/-20.4	0,4,2199	167.0	130.0	143.0		6232,3616,6424,6433	5.6	1.0	11	dbSNP_126	143	29,8571	19.8+/-62.0	0,29,4271	yes	missense,missense,missense,missense	NAV2	NM_001111018.1,NM_001111019.1,NM_145117.4,NM_182964.5	180,180,180,180	0,33,6470	TT,TC,CC		0.3372,0.0908,0.2537	probably-damaging,probably-damaging,probably-damaging,probably-damaging	2078/2366,1206/1494,2142/2430,2145/2433	20124807	33,12973	2203	4300	6503	SO:0001583	missense	89797	exon35			GAATTGCGCCAGT	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.6601C>T	11.37:g.20124807C>T	ENSP00000379396:p.Arg2201Cys	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	75	20	0.266667	NM_001244963	A6NEC1|Q8IVK3|Q8IVK4|Q8IVK5|Q8IVK6|Q8IVK7|Q8IVK8|Q8NHC9|Q8NHD0|Q8TDE9|Q8TDF0|Q8TEB3|Q96B30|Q9NUZ6|Q9NVM7|Q9P2C8	Missense_Mutation	SNP	ENST00000396087.3	37	CCDS58126.1	2	9.157509157509158E-4	1	0.0020325203252032522	0	0.0	0	0.0	1	0.0013192612137203166	C	23.6	4.432361	0.83776	9.08E-4	0.003372	ENSG00000166833	ENST00000360655;ENST00000396085;ENST00000349880;ENST00000396087;ENST00000527559;ENST00000540292;ENST00000533917;ENST00000311043	D;D;D;D;D;D;D;D	0.89123	-2.47;-2.47;-2.47;-2.47;-2.47;-2.47;-2.47;-2.47	5.6	5.6	0.85130	.	0.000000	0.64402	D	0.000003	D	0.94988	0.8378	M	0.83384	2.64	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.978;0.984;0.993;0.999	D	0.94611	0.7804	9	.	.	.	.	19.2099	0.93749	0.0:1.0:0.0:0.0	rs34329467	2145;1206;2142;2078	A7E2D6;Q8IVL1-5;Q8IVL1-3;Q8IVL1-4	.;.;.;.	C	2078;2145;2142;2201;2130;2132;1206;1206	ENSP00000353871:R2078C;ENSP00000379394:R2145C;ENSP00000309577:R2142C;ENSP00000379396:R2201C;ENSP00000435395:R2130C;ENSP00000443489:R2132C;ENSP00000437316:R1206C;ENSP00000312169:R1206C	.	R	+	1	0	NAV2	20081383	1.000000	0.71417	1.000000	0.80357	0.886000	0.51366	5.954000	0.70298	2.631000	0.89168	0.655000	0.94253	CGC	C|0.997;T|0.003	0.003	strong		0.567	NAV2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324112.1	NM_145117	
TMX4	56255	hgsc.bcm.edu	37	20	7963041	7963041	+	Missense_Mutation	SNP	C	C	T	rs2076015	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:7963041C>T	ENST00000246024.2	-	8	1122	c.907G>A	c.(907-909)Gga>Aga	p.G303R		NM_021156.2	NP_066979.2	Q9H1E5	TMX4_HUMAN	thioredoxin-related transmembrane protein 4	303	Glu-rich.		G -> R (in dbSNP:rs2076015). {ECO:0000269|PubMed:15489334}.		cell redox homeostasis (GO:0045454)|oxidation-reduction process (GO:0055114)|protein folding (GO:0006457)|response to endoplasmic reticulum stress (GO:0034976)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	protein disulfide isomerase activity (GO:0003756)			endometrium(3)|large_intestine(2)|lung(11)|skin(1)	17						CCGTCCTCTCCTGGGGGCCCC	0.582													C|||	1773	0.354034	0.6483	0.2334	5008	,	,		16298	0.5883		0.0726	False		,,,				2504	0.09				p.G303R		Atlas-SNP	.											.	TMX4	39	.	0			c.G907A						PASS	.	C	ARG/GLY	2456,1950	623.1+/-394.1	683,1090,430	140.0	123.0	129.0		907	-0.6	0.0	20	dbSNP_96	129	581,8019	156.0+/-209.9	22,537,3741	yes	missense	TMX4	NM_021156.2	125	705,1627,4171	TT,TC,CC		6.7558,44.2578,23.3508	benign	303/350	7963041	3037,9969	2203	4300	6503	SO:0001583	missense	56255	exon8			CCTCTCCTGGGGG		CCDS13101.1	20p12	2011-10-19	2009-02-23	2009-02-23	ENSG00000125827	ENSG00000125827		"""Protein disulfide isomerases"""	25237	protein-coding gene	gene with protein product	"""protein disulfide isomerase family A, member 14"""		"""thioredoxin domain containing 13"""	TXNDC13			Standard	NM_021156		Approved	DJ971N18.2, KIAA1162, PDIA14	uc002wmx.1	Q9H1E5	OTTHUMG00000031843	ENST00000246024.2:c.907G>A	20.37:g.7963041C>T	ENSP00000246024:p.Gly303Arg	Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	97	41	0.42268	NM_021156	Q8N4P7|Q8NCC1|Q9UJA1|Q9ULQ8	Missense_Mutation	SNP	ENST00000246024.2	37	CCDS13101.1	764	0.3498168498168498	308	0.6260162601626016	73	0.20165745856353592	325	0.5681818181818182	58	0.07651715039577836	C	2.423	-0.332568	0.05314	0.557422	0.067558	ENSG00000125827	ENST00000246024	T	0.09255	3.0	5.72	-0.564	0.11774	.	0.974158	0.08471	N	0.940949	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	0.33033	-0.9884	9	0.10111	T	0.7	0.0112	5.9282	0.19124	0.0:0.2476:0.1306:0.6218	rs2076015;rs17846062;rs17859056;rs52797785;rs60332072;rs2076015	303	Q9H1E5	TMX4_HUMAN	R	303	ENSP00000246024:G303R	ENSP00000246024:G303R	G	-	1	0	TMX4	7911041	0.000000	0.05858	0.000000	0.03702	0.019000	0.09904	-1.068000	0.03447	-0.104000	0.12154	-1.353000	0.01230	GGA	C|0.693;T|0.307	0.307	strong		0.582	TMX4-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000077928.2	NM_021156	
KRT84	3890	hgsc.bcm.edu	37	12	52777580	52777580	+	Silent	SNP	A	A	C	rs386763043|rs1613929	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	110	0	0		WXS	Illumina HiSeq	Phase_I	90	44	0.488889	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	
FCHO2	115548	hgsc.bcm.edu	37	5	72347223	72347223	+	Silent	SNP	A	A	G	rs7712838	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:72347223A>G	ENST00000430046.2	+	12	1103	c.987A>G	c.(985-987)acA>acG	p.T329T	FCHO2_ENST00000512348.1_Silent_p.T296T|FCHO2_ENST00000341845.6_Silent_p.T329T	NM_001146032.1|NM_138782.2	NP_001139504.1|NP_620137.2	Q0JRZ9	FCHO2_HUMAN	FCH domain only 2	329					clathrin coat assembly (GO:0048268)|clathrin-mediated endocytosis (GO:0072583)|membrane invagination (GO:0010324)|protein localization to plasma membrane (GO:0072659)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|plasma membrane (GO:0005886)	phosphatidylinositol binding (GO:0035091)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylserine binding (GO:0001786)			cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(4)|ovary(1)|prostate(1)	17		Lung NSC(167;0.0465)|Ovarian(174;0.0908)|Prostate(461;0.165)		OV - Ovarian serous cystadenocarcinoma(47;4.6e-53)		AACCAGAAACAAATCAGAATG	0.294													A|||	1513	0.302117	0.2897	0.1859	5008	,	,		16811	0.4782		0.3181	False		,,,				2504	0.2035				p.T329T		Atlas-SNP	.											.	FCHO2	96	.	0			c.A987G						PASS	.	A	,	914,2522		132,650,936	75.0	72.0	73.0		888,987	3.9	1.0	5	dbSNP_116	73	2096,5608		294,1508,2050	no	coding-synonymous,coding-synonymous	FCHO2	NM_001146032.1,NM_138782.2	,	426,2158,2986	GG,GA,AA		27.2066,26.6007,27.0197	,	296/778,329/811	72347223	3010,8130	1718	3852	5570	SO:0001819	synonymous_variant	115548	exon12			AGAAACAAATCAG	AL831971	CCDS47230.1, CCDS54868.1	5q13.2	2005-08-15			ENSG00000157107	ENSG00000157107			25180	protein-coding gene	gene with protein product		613438				15254787	Standard	NM_138782		Approved		uc003kcl.3	Q0JRZ9	OTTHUMG00000162413	ENST00000430046.2:c.987A>G	5.37:g.72347223A>G		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	124	69	0.556452	NM_138782	A8K6W7|B2RNQ9|B4DHK0|E9PG79|Q0JTJ3|Q96CF5	Silent	SNP	ENST00000430046.2	37	CCDS47230.1																																																																																			A|0.673;G|0.327	0.327	strong		0.294	FCHO2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000368795.3	XM_291142	
TEDDM1	127670	hgsc.bcm.edu	37	1	182369078	182369078	+	Silent	SNP	G	G	A	rs6698722	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	191	0	0		WXS	Illumina HiSeq	Phase_I	190	95	0.5	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	
SERPINF1	5176	hgsc.bcm.edu	37	17	1674429	1674429	+	Silent	SNP	T	T	C	rs8074840	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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						PASS	.	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	92	0	0		WXS	Illumina HiSeq	Phase_I	85	85	1	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	
KLHL33	123103	hgsc.bcm.edu	37	14	20897676	20897676	+	Missense_Mutation	SNP	T	T	C	rs1953225	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	66	0	0		WXS	Illumina HiSeq	Phase_I	59	42	0.711864	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	
CCDC67	159989	hgsc.bcm.edu	37	11	93103330	93103330	+	Missense_Mutation	SNP	C	C	T	rs34205920	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:93103330C>T	ENST00000298050.3	+	6	624	c.524C>T	c.(523-525)tCt>tTt	p.S175F		NM_181645.3	NP_857596.2	Q05D60	DEUP1_HUMAN	coiled-coil domain containing 67	175			S -> F (in dbSNP:rs34205920).		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)				AAATTATTATCTGAGAAGTGT	0.294													C|||	17	0.00339457	0.0008	0.0058	5008	,	,		16637	0.0		0.004	False		,,,				2504	0.0082				p.S175F		Atlas-SNP	.											.	CCDC67	57	.	0			c.C524T						PASS	.	C	PHE/SER	9,3589		0,9,1790	52.0	51.0	51.0		524	5.5	1.0	11	dbSNP_126	51	75,8049		0,75,3987	yes	missense	CCDC67	NM_181645.3	155	0,84,5777	TT,TC,CC		0.9232,0.2501,0.7166	probably-damaging	175/605	93103330	84,11638	1799	4062	5861	SO:0001583	missense	159989	exon6			TATTATCTGAGAA	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.524C>T	11.37:g.93103330C>T	ENSP00000298050:p.Ser175Phe	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	115	19	0.165217	NM_181645	Q8NEF1|Q96LL7	Missense_Mutation	SNP	ENST00000298050.3	37	CCDS44707.1	6	0.0027472527472527475	1	0.0020325203252032522	2	0.0055248618784530384	0	0.0	3	0.00395778364116095	C	21.3	4.121920	0.77436	0.002501	0.009232	ENSG00000165325	ENST00000534747;ENST00000298050;ENST00000532819	T;T;T	0.22743	1.94;1.94;1.94	5.5	5.5	0.81552	.	0.081678	0.53938	D	0.000059	T	0.36608	0.0973	L	0.59436	1.845	0.41448	D	0.987964	D;D;D	0.76494	0.999;0.998;0.998	D;D;D	0.73708	0.972;0.972;0.981	T	0.24584	-1.0156	10	0.72032	D	0.01	.	18.4132	0.90559	0.0:1.0:0.0:0.0	rs34205920	175;175;167	Q05D60;E9PJR5;Q6ZRU6	CCD67_HUMAN;.;.	F	175	ENSP00000432111:S175F;ENSP00000298050:S175F;ENSP00000434635:S175F	ENSP00000298050:S175F	S	+	2	0	CCDC67	92742978	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	3.401000	0.52601	2.584000	0.87258	0.563000	0.77884	TCT	C|0.989;T|0.011	0.011	strong		0.294	CCDC67-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_181645	
HRG	3273	hgsc.bcm.edu	37	3	186395572	186395572	+	Missense_Mutation	SNP	A	A	T	rs1042464	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:186395572A>T	ENST00000232003.4	+	7	1558	c.1478A>T	c.(1477-1479)aAt>aTt	p.N493I		NM_000412.2	NP_000403.1	P04196	HRG_HUMAN	histidine-rich glycoprotein	493	His/Pro-rich (HRR).		N -> I (in dbSNP:rs1042464).		angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|chemotaxis (GO:0006935)|defense response to fungus (GO:0050832)|fibrinolysis (GO:0042730)|heme export (GO:0097037)|negative regulation of angiogenesis (GO:0016525)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell adhesion mediated by integrin (GO:0033629)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of endothelial cell chemotaxis (GO:2001027)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of lamellipodium assembly (GO:0010593)|negative regulation of vascular endothelial growth factor signaling pathway (GO:1900747)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of apoptotic process (GO:0043065)|positive regulation of blood vessel remodeling (GO:2000504)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of immune response to tumor cell (GO:0002839)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|regulation of platelet activation (GO:0010543)|regulation of protein complex assembly (GO:0043254)|regulation of transcription from RNA polymerase II promoter in response to iron (GO:0034395)|response to organic cyclic compound (GO:0014070)	blood microparticle (GO:0072562)|endolysosome (GO:0036019)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|phagolysosome membrane (GO:0061474)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	cysteine-type endopeptidase inhibitor activity (GO:0004869)|heme binding (GO:0020037)|heparan sulfate proteoglycan binding (GO:0043395)|heparin binding (GO:0008201)|immunoglobulin binding (GO:0019865)|metal ion binding (GO:0046872)|receptor binding (GO:0005102)|serine-type endopeptidase inhibitor activity (GO:0004867)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(12)|lung(13)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	37	all_cancers(143;6.64e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;5.73e-20)	GBM - Glioblastoma multiforme(93;0.0683)		AAGCCAGACAATCAGCCCTTT	0.458													T|||	3258	0.650559	0.711	0.5879	5008	,	,		20248	0.8145		0.4831	False		,,,				2504	0.6166				p.N493I		Atlas-SNP	.											.	HRG	81	.	0			c.A1478T						PASS	.	T	ILE/ASN	3006,1400	460.5+/-352.6	1027,952,224	132.0	123.0	126.0		1478	4.6	0.9	3	dbSNP_86	126	4171,4429	587.5+/-392.2	1009,2153,1138	yes	missense	HRG	NM_000412.2	149	2036,3105,1362	TT,TA,AA		48.5,31.7749,44.8178	benign	493/526	186395572	7177,5829	2203	4300	6503	SO:0001583	missense	3273	exon7			CAGACAATCAGCC		CCDS3280.1	3q27	2008-07-18			ENSG00000113905	ENSG00000113905			5181	protein-coding gene	gene with protein product	"""histidine-proline rich glycoprotein"", ""thrombophilia due to elevated HRG"""	142640				1678514	Standard	NM_000412		Approved	HRGP, HPRG	uc003fqq.3	P04196	OTTHUMG00000156578	ENST00000232003.4:c.1478A>T	3.37:g.186395572A>T	ENSP00000232003:p.Asn493Ile	Somatic	258	0	0		WXS	Illumina HiSeq	Phase_I	213	213	1	NM_000412	B9EK35|D3DNU7	Missense_Mutation	SNP	ENST00000232003.4	37	CCDS3280.1	1390	0.6364468864468864	353	0.717479674796748	223	0.6160220994475138	447	0.7814685314685315	367	0.4841688654353562	T	0.028	-1.358397	0.01245	0.682251	0.485	ENSG00000113905	ENST00000232003	T	0.05319	3.46	4.57	4.57	0.56435	.	0.140337	0.32655	N	0.005807	T	0.00012	0.0000	N	0.00066	-2.3	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.29243	-1.0018	9	0.02654	T	1	-1.7832	7.778	0.29048	0.1861:0.0:0.0:0.8139	rs1042464;rs3181948;rs17297999;rs1042464	493	P04196	HRG_HUMAN	I	493	ENSP00000232003:N493I	ENSP00000232003:N493I	N	+	2	0	HRG	187878266	0.913000	0.31002	0.877000	0.34402	0.250000	0.25880	1.915000	0.39976	0.724000	0.32296	-0.868000	0.02995	AAT	A|0.351;T|0.649	0.649	strong		0.458	HRG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344655.1	NM_000412	
TRIM50	135892	hgsc.bcm.edu	37	7	72732848	72732848	+	Silent	SNP	G	G	T	rs201525569	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:72732848G>T	ENST00000333149.2	-	4	899	c.699C>A	c.(697-699)ggC>ggA	p.G233G	TRIM50_ENST00000453152.1_Silent_p.G233G	NM_178125.2	NP_835226.2	Q86XT4	TRI50_HUMAN	tripartite motif containing 50	233						cytoplasm (GO:0005737)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			endometrium(3)|kidney(1)|large_intestine(2)|lung(11)|ovary(1)|skin(2)	20						GGTCCTCATTGCCGAACTGTT	0.657													G|||	5	0.000998403	0.0008	0.0043	5008	,	,		17310	0.0		0.001	False		,,,				2504	0.0				p.G233G		Atlas-SNP	.											.	TRIM50	78	.	0			c.C699A						PASS	.						153.0	138.0	143.0					7																	72732848		2203	4300	6503	SO:0001819	synonymous_variant	135892	exon4			CTCATTGCCGAAC	AY081948	CCDS34654.1	7q11.23	2013-01-09	2011-01-25	2006-03-31	ENSG00000146755	ENSG00000146755		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	19017	protein-coding gene	gene with protein product		612548	"""tripartite motif-containing 50A"", ""tripartite motif-containing 50"""	TRIM50A			Standard	NM_001281450		Approved	FLJ32804	uc003txy.1	Q86XT4	OTTHUMG00000156805	ENST00000333149.2:c.699C>A	7.37:g.72732848G>T		Somatic	463	0	0		WXS	Illumina HiSeq	Phase_I	457	32	0.0700219	NM_178125	Q86XT3	Silent	SNP	ENST00000333149.2	37	CCDS34654.1																																																																																			G|0.999;T|0.001	0.001	weak		0.657	TRIM50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345925.1	NM_178125	
MMRN2	79812	hgsc.bcm.edu	37	10	88703122	88703122	+	Silent	SNP	G	G	C	rs146872793	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:88703122G>C	ENST00000372027.5	-	6	1740	c.1419C>G	c.(1417-1419)ctC>ctG	p.L473L	MMRN2_ENST00000488950.1_5'Flank	NM_024756.2	NP_079032.2	Q9H8L6	MMRN2_HUMAN	multimerin 2	473					angiogenesis (GO:0001525)|negative regulation of cell migration involved in sprouting angiogenesis (GO:0090051)|negative regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030948)	basement membrane (GO:0005604)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				breast(1)|kidney(1)|large_intestine(6)|lung(7)|prostate(2)|skin(1)|stomach(1)	19						GCTGCAGCGTGAGGTTGAGCT	0.587													G|||	8	0.00159744	0.0	0.0	5008	,	,		16469	0.0		0.003	False		,,,				2504	0.0051				p.L473L		Atlas-SNP	.											.	MMRN2	49	.	0			c.C1419G						PASS	.	G		0,4406		0,0,2203	50.0	44.0	46.0		1419	3.4	1.0	10	dbSNP_134	46	24,8576	17.3+/-56.4	0,24,4276	no	coding-synonymous	MMRN2	NM_024756.2		0,24,6479	CC,CG,GG		0.2791,0.0,0.1845		473/950	88703122	24,12982	2203	4300	6503	SO:0001819	synonymous_variant	79812	exon6			CAGCGTGAGGTTG	AK023527	CCDS7379.1	10q23.31	2004-03-10	2004-03-02	2004-03-02	ENSG00000173269	ENSG00000173269		"""EMI domain containing"""	19888	protein-coding gene	gene with protein product		608925	"""elastin microfibril interfacer 3"""	EMILIN3		11559704	Standard	NM_024756		Approved	EndoGlyx-1, FLJ13465	uc001kea.3	Q9H8L6	OTTHUMG00000018663	ENST00000372027.5:c.1419C>G	10.37:g.88703122G>C		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	117	67	0.57265	NM_024756	Q504V7|Q6P2N2	Silent	SNP	ENST00000372027.5	37	CCDS7379.1																																																																																			G|0.998;C|0.002	0.002	strong		0.587	MMRN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049179.2	NM_024756	
MFAP1	4236	hgsc.bcm.edu	37	15	44102010	44102010	+	Silent	SNP	A	A	C	rs2228368	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:44102010A>C	ENST00000267812.3	-	7	1222	c.990T>G	c.(988-990)gcT>gcG	p.A330A		NM_005926.2	NP_005917.2	P55081	MFAP1_HUMAN	microfibrillar-associated protein 1	330					extracellular matrix organization (GO:0030198)	extracellular region (GO:0005576)|microfibril (GO:0001527)	poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(1)|kidney(1)|lung(6)|skin(2)|upper_aerodigestive_tract(3)	15		all_cancers(109;7.57e-15)|all_epithelial(112;3.51e-12)|Lung NSC(122;4.72e-08)|all_lung(180;4.9e-07)|Melanoma(134;0.027)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;4.33e-07)		TGCCCTTAACAGCTTTGTTGG	0.433													A|||	1015	0.202676	0.2935	0.1801	5008	,	,		19004	0.2599		0.0954	False		,,,				2504	0.1472				p.A330A		Atlas-SNP	.											.	MFAP1	36	.	0			c.T990G						PASS	.	A		1052,3344	383.5+/-324.9	117,818,1263	252.0	231.0	238.0		990	3.3	1.0	15	dbSNP_98	238	824,7772	190.8+/-237.2	39,746,3513	no	coding-synonymous	MFAP1	NM_005926.2		156,1564,4776	CC,CA,AA		9.5859,23.9308,14.4397		330/440	44102010	1876,11116	2198	4298	6496	SO:0001819	synonymous_variant	4236	exon7			CTTAACAGCTTTG		CCDS10105.1	15q15-q21	2014-05-20			ENSG00000140259	ENSG00000140259			7032	protein-coding gene	gene with protein product		600215				7835894	Standard	NM_005926		Approved		uc001zth.1	P55081	OTTHUMG00000060145	ENST00000267812.3:c.990T>G	15.37:g.44102010A>C		Somatic	242	0	0		WXS	Illumina HiSeq	Phase_I	210	67	0.319048	NM_005926	Q86TG6	Silent	SNP	ENST00000267812.3	37	CCDS10105.1																																																																																			T|0.141;G|0.046	.	strong		0.433	MFAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133491.2	NM_005926	
HTR3D	200909	hgsc.bcm.edu	37	3	183756742	183756742	+	Silent	SNP	C	C	T	rs55674402	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:183756742C>T	ENST00000382489.3	+	8	1344	c.1344C>T	c.(1342-1344)gtC>gtT	p.V448V	HTR3D_ENST00000334128.2_Silent_p.V273V|HTR3D_ENST00000453435.1_Silent_p.V227V|HTR3D_ENST00000428798.2_Silent_p.V398V	NM_001163646.1	NP_001157118.1	Q70Z44	5HT3D_HUMAN	5-hydroxytryptamine (serotonin) receptor 3D, ionotropic	448					ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	extracellular ligand-gated ion channel activity (GO:0005230)	p.V273V(1)		large_intestine(3)|lung(3)|prostate(1)|skin(1)|stomach(2)	10	all_cancers(143;2.33e-10)|Ovarian(172;0.0303)		Epithelial(37;6.23e-36)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)		Ergoloid mesylate(DB01049)	TCATCACCGTCATATGCCTCT	0.567													C|||	1558	0.311102	0.1906	0.3487	5008	,	,		19416	0.3194		0.4066	False		,,,				2504	0.3405				p.V448V		Atlas-SNP	.											HTR3D,NS,carcinoma,0,1	HTR3D	65	1	1	Substitution - coding silent(1)	stomach(1)	c.C1344T						PASS	.	C	,,	941,3465		102,737,1364	154.0	140.0	145.0		1194,1344,819	3.2	0.0	3	dbSNP_129	145	3469,5131		720,2029,1551	no	coding-synonymous,coding-synonymous,coding-synonymous	HTR3D	NM_001145143.1,NM_001163646.1,NM_182537.2	,,	822,2766,2915	TT,TC,CC		40.3372,21.3572,33.9074	,,	398/405,448/455,273/280	183756742	4410,8596	2203	4300	6503	SO:0001819	synonymous_variant	200909	exon8			CACCGTCATATGC	AY159812	CCDS3249.1, CCDS46966.1, CCDS54685.1	3q27	2012-05-22	2012-02-03		ENSG00000186090	ENSG00000186090		"""5-HT (serotonin) receptors"", ""Ligand-gated ion channels / 5-HT (serotonin) receptors, ionotropic"""	24004	protein-coding gene	gene with protein product		610122	"""5-hydroxytryptamine (serotonin) receptor 3 family member D"""			12801637	Standard	NM_001145143		Approved		uc011bqv.2	Q70Z44	OTTHUMG00000156858	ENST00000382489.3:c.1344C>T	3.37:g.183756742C>T		Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	135	64	0.474074	NM_001163646	C9J2I6|J3QT78|Q495N5|Q495N6|Q7Z6B3	Silent	SNP	ENST00000382489.3	37	CCDS54685.1																																																																																			C|0.658;T|0.342	0.342	strong		0.567	HTR3D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000346289.1	NM_182537	
MRPL52	122704	hgsc.bcm.edu	37	14	23299135	23299135	+	Missense_Mutation	SNP	G	G	T	rs1135641	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:23299135G>T	ENST00000355151.5	+	1	44	c.14G>T	c.(13-15)gGg>gTg	p.G5V	MRPL52_ENST00000397505.2_Missense_Mutation_p.G5V|MRPL52_ENST00000311892.6_5'UTR|MRPL52_ENST00000556840.1_5'UTR|MRPL52_ENST00000555345.1_5'UTR|MRPL52_ENST00000557221.1_5'UTR|MRPL52_ENST00000432849.3_Missense_Mutation_p.G5V|MRPL52_ENST00000553711.1_5'UTR|MRPL52_ENST00000555536.1_5'Flank|MRPL52_ENST00000397496.3_Missense_Mutation_p.G5V	NM_178336.2|NM_180982.2|NM_181306.2	NP_848026.1|NP_851313.1|NP_851823.1	Q86TS9	RM52_HUMAN	mitochondrial ribosomal protein L52	5			G -> V (in dbSNP:rs1135641).		translation (GO:0006412)	mitochondrial large ribosomal subunit (GO:0005762)	structural constituent of ribosome (GO:0003735)					all_cancers(95;9.47e-05)			GBM - Glioblastoma multiforme(265;0.00551)		GCTGCTTTAGGGACTGTTCTC	0.652													G|||	2575	0.514177	0.559	0.3862	5008	,	,		15800	0.5516		0.5129	False		,,,				2504	0.5072				p.G5V		Atlas-SNP	.											.	MRPL52	7	.	0			c.G14T						PASS	.	G	VAL/GLY,VAL/GLY,,,,VAL/GLY	2318,2088		617,1084,502	17.0	20.0	19.0		14,14,,,,14	-1.7	0.0	14	dbSNP_86	19	4392,4206		1117,2158,1024	yes	missense,missense,utr-5,utr-5,utr-5,missense	MRPL52	NM_178336.2,NM_180982.2,NM_181304.2,NM_181305.2,NM_181306.2,NM_181307.2	109,109,,,,109	1734,3242,1526	TT,TG,GG		48.9184,47.3899,48.4005	benign,benign,,,,benign	5/124,5/123,,,,5/88	23299135	6710,6294	2203	4299	6502	SO:0001583	missense	122704	exon1			CTTTAGGGACTGT	AK000450	CCDS9575.1, CCDS9576.1, CCDS41917.1, CCDS41918.1	14q11.2	2012-09-13			ENSG00000172590	ENSG00000172590		"""Mitochondrial ribosomal proteins / large subunits"""	16655	protein-coding gene	gene with protein product		611856				11551941, 11943462	Standard	NM_178336		Approved		uc001wgw.4	Q86TS9	OTTHUMG00000028703	ENST00000355151.5:c.14G>T	14.37:g.23299135G>T	ENSP00000347277:p.Gly5Val	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	59	32	0.542373	NM_180982	A6NMQ8|A8MXK5|A8MYI6|G3XCN9|Q6NVH8	Missense_Mutation	SNP	ENST00000355151.5	37	CCDS41917.1	1151	0.527014652014652	280	0.5691056910569106	173	0.47790055248618785	309	0.5402097902097902	389	0.5131926121372031	G	14.78	2.637096	0.47049	0.526101	0.510816	ENSG00000172590	ENST00000355151;ENST00000397496;ENST00000432849;ENST00000556465;ENST00000397505	T;T;T;T;T	0.23147	1.92;1.92;1.92;1.92;1.92	5.27	-1.72	0.08107	.	0.718559	0.13377	N	0.392413	T	0.00012	0.0000	L	0.44542	1.39	0.58432	P	4.000000000004E-6	B;B;B	0.25743	0.069;0.042;0.133	B;B;B	0.32342	0.05;0.093;0.144	T	0.43734	-0.9373	9	0.46703	T	0.11	-0.8	6.902	0.24288	0.0767:0.3534:0.4665:0.1034	rs1135641;rs3811188;rs17211957;rs17356225;rs52823058;rs58454590;rs3811188	5;5;5	A8MXK5;G3XCN9;Q86TS9	.;.;RM52_HUMAN	V	5	ENSP00000347277:G5V;ENSP00000380633:G5V;ENSP00000406655:G5V;ENSP00000451832:G5V;ENSP00000380642:G5V	ENSP00000310762:G5V	G	+	2	0	MRPL52	22368975	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.056000	0.11787	-0.184000	0.10567	-2.119000	0.00349	GGG	T|0.503;G|0.497;N|0.000;A|0.000	0.503	strong		0.652	MRPL52-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000071657.4	NM_180982	
SLC30A3	7781	hgsc.bcm.edu	37	2	27481661	27481661	+	Silent	SNP	G	G	A	rs41288821	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:27481661G>A	ENST00000233535.4	-	2	589	c.237C>T	c.(235-237)gcC>gcT	p.A79A	SLC30A3_ENST00000447008.2_Silent_p.A74A	NM_003459.4	NP_003450.2	Q99726	ZNT3_HUMAN	solute carrier family 30 (zinc transporter), member 3	79					positive regulation of transport (GO:0051050)|regulation of sequestering of zinc ion (GO:0061088)|transmembrane transport (GO:0055085)|transport (GO:0006810)|zinc ion transmembrane transport (GO:0071577)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|membrane (GO:0016020)|neuron projection (GO:0043005)|synaptic vesicle (GO:0008021)|synaptic vesicle membrane (GO:0030672)	zinc transporting ATPase activity (GO:0015633)			NS(1)|breast(1)|cervix(1)|endometrium(2)|large_intestine(3)|lung(11)|pancreas(1)	20	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					AAACGGCACAGGCAGCATATA	0.602													G|||	13	0.00259585	0.0008	0.0072	5008	,	,		18488	0.0		0.006	False		,,,				2504	0.001				p.A79A		Atlas-SNP	.											.	SLC30A3	39	.	0			c.C237T						PASS	.	G		10,4396	11.4+/-27.6	0,10,2193	58.0	62.0	61.0		237	4.4	1.0	2	dbSNP_127	61	84,8516	47.2+/-106.3	0,84,4216	no	coding-synonymous	SLC30A3	NM_003459.4		0,94,6409	AA,AG,GG		0.9767,0.227,0.7227		79/389	27481661	94,12912	2203	4300	6503	SO:0001819	synonymous_variant	7781	exon2			GGCACAGGCAGCA	U76010	CCDS1743.1	2p23.3	2013-05-22			ENSG00000115194	ENSG00000115194		"""Solute carriers"""	11014	protein-coding gene	gene with protein product		602878		ZNT3		8962159	Standard	NM_003459		Approved		uc002rjj.3	Q99726	OTTHUMG00000128409	ENST00000233535.4:c.237C>T	2.37:g.27481661G>A		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	91	62	0.681319	NM_003459	Q8TC03	Silent	SNP	ENST00000233535.4	37	CCDS1743.1																																																																																			G|0.993;A|0.007	0.007	strong		0.602	SLC30A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250189.2		
GABRG2	2566	hgsc.bcm.edu	37	5	161528280	161528280	+	Silent	SNP	C	C	T	rs211037	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:161528280C>T	ENST00000361925.4	+	5	808	c.588C>T	c.(586-588)aaC>aaT	p.N196N	GABRG2_ENST00000414552.2_Silent_p.N196N|GABRG2_ENST00000356592.3_Silent_p.N196N|GABRG2_ENST00000393933.4_Silent_p.N101N			P18507	GBRG2_HUMAN	gamma-aminobutyric acid (GABA) A receptor, gamma 2	196					adult behavior (GO:0030534)|cellular response to histamine (GO:0071420)|chloride transmembrane transport (GO:1902476)|gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|post-embryonic development (GO:0009791)|synaptic transmission (GO:0007268)|synaptic transmission, GABAergic (GO:0051932)|transmembrane transport (GO:0055085)|transport (GO:0006810)	axon (GO:0030424)|cell junction (GO:0030054)|chloride channel complex (GO:0034707)|cytoplasm (GO:0005737)|dendrite membrane (GO:0032590)|GABA-A receptor complex (GO:1902711)|inhibitory synapse (GO:0060077)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	benzodiazepine receptor activity (GO:0008503)|chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)	p.N196N(1)		NS(1)|breast(1)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(15)|lung(24)|ovary(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	62	Renal(175;0.000319)	Medulloblastoma(196;0.0208)|all_neural(177;0.0672)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0734)|OV - Ovarian serous cystadenocarcinoma(192;0.135)|Epithelial(171;0.136)	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)|Ginkgo biloba(DB01381)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|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)	AATTGCACAACTTTCCAATGG	0.358													C|||	1861	0.371605	0.4682	0.2507	5008	,	,		17256	0.6012		0.2435	False		,,,				2504	0.2219				p.N196N		Atlas-SNP	.											GABRG2,NS,carcinoma,0,1	GABRG2	142	1	1	Substitution - coding silent(1)	stomach(1)	c.C588T						PASS	.	C	,,	1906,2500	545.1+/-376.7	413,1080,710	112.0	104.0	106.0		588,588,588	3.5	1.0	5	dbSNP_79	106	2088,6512	358.8+/-331.3	269,1550,2481	no	coding-synonymous,coding-synonymous,coding-synonymous	GABRG2	NM_000816.3,NM_198903.2,NM_198904.2	,,	682,2630,3191	TT,TC,CC		24.2791,43.2592,30.7089	,,	196/468,196/516,196/476	161528280	3994,9012	2203	4300	6503	SO:0001819	synonymous_variant	2566	exon5			GCACAACTTTCCA		CCDS4358.1, CCDS4359.1, CCDS47333.1	5q34	2012-06-22			ENSG00000113327	ENSG00000113327		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	4087	protein-coding gene	gene with protein product	"""GABA(A) receptor, gamma 2"""	137164					Standard	NM_198904		Approved		uc010jjc.3	P18507	OTTHUMG00000130350	ENST00000361925.4:c.588C>T	5.37:g.161528280C>T		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	106	48	0.45283	NM_198904	F5HB82|Q6GRL6|Q6PCC3|Q9UDB3|Q9UN15	Silent	SNP	ENST00000361925.4	37	CCDS4358.1																																																																																			C|0.648;T|0.352	0.352	strong		0.358	GABRG2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252706.1		
METTL21C	196541	hgsc.bcm.edu	37	13	103339365	103339365	+	Silent	SNP	A	A	G	rs660207	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:103339365A>G	ENST00000267273.6	-	3	330	c.325T>C	c.(325-327)Ttg>Ctg	p.L109L		NM_001010977.1	NP_001010977.1	Q5VZV1	MT21C_HUMAN	methyltransferase like 21C	109					peptidyl-lysine methylation (GO:0018022)|protein methylation (GO:0006479)	nucleus (GO:0005634)	protein-lysine N-methyltransferase activity (GO:0016279)			breast(1)|large_intestine(3)|lung(2)|skin(1)	7						TGGAAATTCAATTCCTCGGCA	0.393													G|||	2396	0.478435	0.6286	0.3847	5008	,	,		19452	0.4544		0.4712	False		,,,				2504	0.3742				p.L109L		Atlas-SNP	.											METTL21C,NS,carcinoma,+2,1	METTL21C	23	1	0			c.T325C						PASS	.	G		2717,1689	512.9+/-368.2	821,1075,307	83.0	77.0	79.0		325	-0.1	0.9	13	dbSNP_83	79	4128,4472	590.2+/-392.6	955,2218,1127	no	coding-synonymous	METTL21C	NM_001010977.1		1776,3293,1434	GG,GA,AA		48.0,38.3341,47.3704		109/265	103339365	6845,6161	2203	4300	6503	SO:0001819	synonymous_variant	196541	exon3			AATTCAATTCCTC		CCDS32003.1	13q33.1	2011-03-03	2011-03-03	2011-03-03	ENSG00000139780	ENSG00000139780			33717	protein-coding gene	gene with protein product		615259	"""chromosome 13 open reading frame 39"""	C13orf39			Standard	NM_001010977		Approved	LOC196541	uc001vpj.4	Q5VZV1	OTTHUMG00000017304	ENST00000267273.6:c.325T>C	13.37:g.103339365A>G		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	71	32	0.450704	NM_001010977		Silent	SNP	ENST00000267273.6	37	CCDS32003.1																																																																																			A|0.483;G|0.517	0.517	strong		0.393	METTL21C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045682.2	NM_001010977	
IWS1	55677	hgsc.bcm.edu	37	2	128244216	128244216	+	Silent	SNP	T	T	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:128244216T>C	ENST00000295321.4	-	13	2500	c.2241A>G	c.(2239-2241)ggA>ggG	p.G747G	AC010976.2_ENST00000598065.1_RNA|AC010976.2_ENST00000596439.1_RNA|AC010976.2_ENST00000595561.1_RNA|AC010976.2_ENST00000599001.1_RNA|AC010976.2_ENST00000454503.2_RNA	NM_017969.2	NP_060439.2	Q96ST2	IWS1_HUMAN	IWS1 homolog (S. cerevisiae)	747	Interaction with SUPT6H and ALYREF.				mRNA processing (GO:0006397)|mRNA transport (GO:0051028)|regulation of histone H3-K36 trimethylation (GO:2001253)|regulation of histone H4 acetylation (GO:0090239)|regulation of mRNA export from nucleus (GO:0010793)|regulation of mRNA processing (GO:0050684)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)			cervix(1)|endometrium(2)|kidney(6)|large_intestine(2)|lung(12)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	28	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0735)		GGGCACAGAATCCAGGATCTC	0.517																																					p.G747G		Atlas-SNP	.											.	IWS1	61	.	0			c.A2241G						PASS	.						96.0	89.0	91.0					2																	128244216		2203	4300	6503	SO:0001819	synonymous_variant	55677	exon13			ACAGAATCCAGGA	AK000868	CCDS2146.1	2q14.3	2006-03-17			ENSG00000163166	ENSG00000163166			25467	protein-coding gene	gene with protein product							Standard	NM_017969		Approved	DKFZp761G0123, FLJ10006, FLJ14655, FLJ32319	uc002ton.2	Q96ST2	OTTHUMG00000131527	ENST00000295321.4:c.2241A>G	2.37:g.128244216T>C		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	142	29	0.204225	NM_017969	Q2TB65|Q6P157|Q8N3E8|Q96MI7|Q9NV97|Q9NWH8	Silent	SNP	ENST00000295321.4	37	CCDS2146.1																																																																																			.	.	none		0.517	IWS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254384.2	NM_017969	
FAT2	2196	hgsc.bcm.edu	37	5	150901630	150901630	+	Silent	SNP	G	G	T	rs3734049	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:150901630G>T	ENST00000261800.5	-	18	10536	c.10524C>A	c.(10522-10524)atC>atA	p.I3508I		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	3508	Cadherin 31. {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)			AGAGGGGAGGGATGCCACTGT	0.572													G|||	488	0.0974441	0.0083	0.1585	5008	,	,		20709	0.126		0.1948	False		,,,				2504	0.045				p.I3508I		Atlas-SNP	.											.	FAT2	465	.	0			c.C10524A						PASS	.	G		161,4245	104.3+/-142.8	5,151,2047	39.0	34.0	35.0		10524	2.3	0.5	5	dbSNP_107	35	1819,6781	314.2+/-311.7	203,1413,2684	no	coding-synonymous	FAT2	NM_001447.2		208,1564,4731	TT,TG,GG		21.1512,3.6541,15.2237		3508/4350	150901630	1980,11026	2203	4300	6503	SO:0001819	synonymous_variant	2196	exon18			GGGAGGGATGCCA	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.10524C>A	5.37:g.150901630G>T		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	38	10	0.263158	NM_001447	O75091|Q9NSR7	Silent	SNP	ENST00000261800.5	37	CCDS4317.1	290	0.13278388278388278	6	0.012195121951219513	65	0.17955801104972377	82	0.14335664335664336	137	0.18073878627968337	G	6.259	0.415816	0.11870	0.036541	0.211512	ENSG00000086570	ENST00000520200	.	.	.	5.14	2.28	0.28536	.	.	.	.	.	T	0.00039	0.0001	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.18053	-1.0349	3	.	.	.	.	4.0795	0.09919	0.1445:0.1277:0.5961:0.1316	rs3734049;rs59902096;rs3734049	.	.	.	T	367	.	.	P	-	1	0	FAT2	150881823	0.930000	0.31532	0.496000	0.27539	0.869000	0.49853	1.367000	0.34204	0.652000	0.30806	0.563000	0.77884	CCC	G|0.872;T|0.128	0.128	strong		0.572	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447	
FREM1	158326	hgsc.bcm.edu	37	9	14801687	14801687	+	Silent	SNP	T	T	C	rs10738380	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:14801687T>C	ENST00000380880.3	-	20	4440	c.3657A>G	c.(3655-3657)gcA>gcG	p.A1219A	FREM1_ENST00000380881.4_Silent_p.A1220A|FREM1_ENST00000422223.2_Silent_p.A1219A			Q5H8C1	FREM1_HUMAN	FRAS1 related extracellular matrix 1	1219					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)		TGTGAACAGGTGCATGTTTCT	0.443													T|||	886	0.176917	0.0325	0.1945	5008	,	,		19888	0.2312		0.2336	False		,,,				2504	0.2454				p.A1219A		Atlas-SNP	.											.	FREM1	261	.	0			c.A3657G						PASS	.	T		241,3679		4,233,1723	130.0	129.0	129.0		3657	0.3	0.0	9	dbSNP_120	129	1933,6383		235,1463,2460	no	coding-synonymous	FREM1	NM_144966.5		239,1696,4183	CC,CT,TT		23.2443,6.148,17.7672		1219/2180	14801687	2174,10062	1960	4158	6118	SO:0001819	synonymous_variant	158326	exon21			AACAGGTGCATGT	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.3657A>G	9.37:g.14801687T>C		Somatic	233	1	0.00429185		WXS	Illumina HiSeq	Phase_I	224	101	0.450893	NM_144966	B7ZBX4|Q5VV00|Q5VV01|Q6MZI4|Q8NEG9|Q96LI3	Silent	SNP	ENST00000380880.3	37	CCDS47952.1																																																																																			T|0.834;C|0.166	0.166	strong		0.443	FREM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339474.2	NM_144966	
AHNAK2	113146	hgsc.bcm.edu	37	14	105415265	105415265	+	Missense_Mutation	SNP	A	A	T	rs201824674	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:105415265A>T	ENST00000333244.5	-	7	6642	c.6523T>A	c.(6523-6525)Tcg>Acg	p.S2175T	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	2175						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)			ACATCCACCGAGGCCTCGATG	0.582													.|||	476	0.0950479	0.1543	0.0418	5008	,	,		17262	0.0734		0.0258	False		,,,				2504	0.1462				p.S2175T		Atlas-SNP	.											AHNAK2_ENST00000333244,NS,carcinoma,+1,1	AHNAK2	719	1	0			c.T6523A						scavenged	.						174.0	120.0	137.0					14																	105415265		1941	4093	6034	SO:0001583	missense	113146	exon7			CCACCGAGGCCTC	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.6523T>A	14.37:g.105415265A>T	ENSP00000353114:p.Ser2175Thr	Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	114	19	0.166667	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	.	.	.	.	.	.	.	.	.	.	N	11.85	1.762488	0.31228	.	.	ENSG00000185567	ENST00000333244	T	0.00932	5.53	3.99	-3.83	0.04269	.	.	.	.	.	T	0.01454	0.0047	M	0.87456	2.885	0.09310	N	1	B	0.22211	0.066	B	0.25405	0.06	T	0.44251	-0.9340	9	0.27082	T	0.32	.	0.8437	0.01156	0.2858:0.3253:0.1542:0.2347	.	2175	Q8IVF2	AHNK2_HUMAN	T	2175	ENSP00000353114:S2175T	ENSP00000353114:S2175T	S	-	1	0	AHNAK2	104486310	0.000000	0.05858	0.000000	0.03702	0.051000	0.14879	-6.243000	0.00074	-0.976000	0.03542	0.397000	0.26171	TCG	A|0.980;T|0.019	0.019	strong		0.582	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
TSPAN6	7105	hgsc.bcm.edu	37	X	99890204	99890204	+	Missense_Mutation	SNP	C	C	T	rs1802288	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	195	0	0		WXS	Illumina HiSeq	Phase_I	134	134	1	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		
KRTAP10-2	386679	hgsc.bcm.edu	37	21	45971023	45971023	+	Missense_Mutation	SNP	G	G	T	rs478967	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:45971023G>T	ENST00000391621.1	-	1	365	c.319C>A	c.(319-321)Cct>Act	p.P107T	TSPEAR_ENST00000397916.1_Intron|TSPEAR_ENST00000323084.4_Intron|KRTAP10-2_ENST00000498210.1_Intron	NM_198693.2	NP_941966.1	P60368	KR102_HUMAN	keratin associated protein 10-2	107	22 X 5 AA repeats of C-C-X(3).		P -> T (in dbSNP:rs478967). {ECO:0000269|PubMed:15028290}.			keratin filament (GO:0045095)				large_intestine(1)|lung(4)|skin(1)	6						CAGCACACAGGCTTGCAGCAG	0.662													g|||	1139	0.227436	0.2171	0.1585	5008	,	,		20659	0.369		0.2048	False		,,,				2504	0.1677				p.P107T		Atlas-SNP	.											.	KRTAP10-2	21	.	0			c.C319A						PASS	.	T	,THR/PRO	996,3408	350.8+/-311.0	91,814,1297	104.0	107.0	106.0		,319	0.7	0.0	21	dbSNP_83	106	1678,6922	302.0+/-305.7	148,1382,2770	no	intron,missense	TSPEAR,KRTAP10-2	NM_144991.2,NM_198693.2	,38	239,2196,4067	TT,TG,GG		19.5116,22.6158,20.5629	,benign	,107/256	45971023	2674,10330	2202	4300	6502	SO:0001583	missense	386679	exon1			ACACAGGCTTGCA	AJ566381	CCDS42955.1	21q22.3	2007-10-05			ENSG00000205445	ENSG00000205445		"""Keratin associated proteins"""	22967	protein-coding gene	gene with protein product				KRTAP18-2			Standard	NM_198693		Approved	KAP10.2, KAP18.2	uc002zfi.1	P60368	OTTHUMG00000057625	ENST00000391621.1:c.319C>A	21.37:g.45971023G>T	ENSP00000375479:p.Pro107Thr	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	158	61	0.386076	NM_198693	Q70LJ5	Missense_Mutation	SNP	ENST00000391621.1	37	CCDS42955.1	522	0.23901098901098902	101	0.20528455284552846	61	0.1685082872928177	200	0.34965034965034963	160	0.21108179419525067	g	2.743	-0.261873	0.05791	0.226158	0.195116	ENSG00000205445	ENST00000391621	T	0.04360	3.64	3.77	0.683	0.17998	.	.	.	.	.	T	0.00012	0.0000	M	0.78285	2.405	0.80722	P	0.0	B	0.25351	0.124	B	0.27887	0.084	T	0.41413	-0.9510	8	0.39692	T	0.17	.	1.2578	0.01995	0.2057:0.1724:0.4448:0.177	rs56265636	107	P60368	KR102_HUMAN	T	107	ENSP00000375479:P107T	ENSP00000375479:P107T	P	-	1	0	KRTAP10-2	44795451	0.669000	0.27502	0.004000	0.12327	0.026000	0.11368	1.776000	0.38594	0.131000	0.18576	-0.369000	0.07265	CCT	G|0.811;T|0.189	0.189	strong		0.662	KRTAP10-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128027.1		
SIRPG	55423	hgsc.bcm.edu	37	20	1610894	1610894	+	Silent	SNP	G	G	A	rs3746721	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:1610894G>A	ENST00000303415.3	-	5	1204	c.1140C>T	c.(1138-1140)taC>taT	p.Y380Y	SIRPG_ENST00000344103.4_Silent_p.Y163Y|SIRPG_ENST00000381583.2_Silent_p.Y269Y|SIRPG_ENST00000478145.2_5'UTR|SIRPG_ENST00000381580.1_Silent_p.Y347Y|SIRPG_ENST00000216927.4_Silent_p.Y269Y	NM_018556.3	NP_061026.2	Q9P1W8	SIRPG_HUMAN	signal-regulatory protein gamma	380					blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|intracellular signal transduction (GO:0035556)|leukocyte migration (GO:0050900)|negative regulation of cell proliferation (GO:0008285)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of T cell activation (GO:0050870)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(14)|ovary(1)|prostate(2)|stomach(1)	27						TCCAGGGGACGTAGATGGGGC	0.582													g|||	1724	0.344249	0.1014	0.268	5008	,	,		18842	0.625		0.2594	False		,,,				2504	0.5245				p.Y380Y		Atlas-SNP	.											SIRPG,NS,carcinoma,0,1	SIRPG	61	1	0			c.C1140T						PASS	.	G	,,	502,3902		26,450,1726	63.0	50.0	54.0		807,1140,489	-4.2	0.0	20	dbSNP_107	54	2159,6433		279,1601,2416	no	coding-synonymous,coding-synonymous,coding-synonymous	SIRPG	NM_001039508.1,NM_018556.3,NM_080816.2	,,	305,2051,4142	AA,AG,GG		25.128,11.3987,20.4755	,,	269/277,380/388,163/171	1610894	2661,10335	2202	4296	6498	SO:0001819	synonymous_variant	55423	exon5			GGGGACGTAGATG	AB042624	CCDS13020.2, CCDS13021.2, CCDS33434.1	20p13	2013-01-11	2006-02-03	2006-02-03	ENSG00000089012	ENSG00000089012		"""Signal-regulatory proteins"", ""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C1-set domain containing"""	15757	protein-coding gene	gene with protein product		605466	"""signal-regulatory protein beta 2"""	SIRPB2		11185750, 16339511	Standard	XM_005260749		Approved	bA77C3.1, SIRP-B2, SIRPgamma, CD172g	uc002wfm.1	Q9P1W8	OTTHUMG00000031680	ENST00000303415.3:c.1140C>T	20.37:g.1610894G>A		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	45	26	0.577778	NM_018556	B1AKP6|Q5D051|Q5JV25|Q5MKL4|Q8WWA5|Q9NQK8	Silent	SNP	ENST00000303415.3	37	CCDS13020.2																																																																																			G|0.742;A|0.258	0.258	strong		0.582	SIRPG-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077566.2	NM_018556	
FAIM3	9214	hgsc.bcm.edu	37	1	207087435	207087435	+	Silent	SNP	C	C	T	rs167082	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:207087435C>T	ENST00000367091.3	-	2	185	c.42G>A	c.(40-42)tcG>tcA	p.S14S	FAIM3_ENST00000528654.1_Intron|FAIM3_ENST00000442471.2_Intron|FAIM3_ENST00000420007.2_Silent_p.S14S	NM_005449.4	NP_005440.1	O60667	FAIM3_HUMAN	Fas apoptotic inhibitory molecule 3	14					cellular defense response (GO:0006968)|immune system process (GO:0002376)|negative regulation of apoptotic process (GO:0043066)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(5)|skin(1)|upper_aerodigestive_tract(1)	15	Breast(84;0.201)					TCAGGGCCCCCGATACTGCAG	0.547													C|||	1223	0.244209	0.1717	0.3069	5008	,	,		17435	0.1339		0.4543	False		,,,				2504	0.1953				p.S14S		Atlas-SNP	.											.	FAIM3	36	.	0			c.G42A						PASS	.	C	,,	889,3517	338.9+/-305.5	89,711,1403	57.0	53.0	54.0		,42,42	-8.0	0.0	1	dbSNP_79	54	4007,4593	541.3+/-384.0	953,2101,1246	no	intron,coding-synonymous,coding-synonymous	FAIM3	NM_001142473.1,NM_001193338.1,NM_005449.4	,,	1042,2812,2649	TT,TC,CC		46.593,20.177,37.6442	,,	,14/307,14/391	207087435	4896,8110	2203	4300	6503	SO:0001819	synonymous_variant	9214	exon2			GGCCCCCGATACT	AF057557	CCDS1473.1, CCDS44304.1	1q32.1	2013-01-11			ENSG00000162894	ENSG00000162894		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	14315	protein-coding gene	gene with protein product		606015				9586636, 1563211	Standard	NM_005449		Approved	TOSO	uc001hey.3	O60667	OTTHUMG00000036457	ENST00000367091.3:c.42G>A	1.37:g.207087435C>T		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	55	31	0.563636	NM_005449	A8K7J2|B7Z6Z0|D9MWM3	Silent	SNP	ENST00000367091.3	37	CCDS1473.1																																																																																			C|0.648;T|0.352	0.352	strong		0.547	FAIM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088677.1	NM_005449	
CCDC176	80127	hgsc.bcm.edu	37	14	74523869	74523869	+	Missense_Mutation	SNP	A	A	G	rs3742809	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:74523869A>G	ENST00000394009.3	+	11	1609	c.1486A>G	c.(1486-1488)Aaa>Gaa	p.K496E	ALDH6A1_ENST00000553458.1_3'UTR|AC005484.5_ENST00000492026.1_RNA|CCDC176_ENST00000553773.1_Missense_Mutation_p.K221E|CCDC176_ENST00000492247.2_Missense_Mutation_p.K40E	NM_025057.2	NP_079333.2	Q8ND07	BBOF1_HUMAN	coiled-coil domain containing 176	496			K -> E (in dbSNP:rs3742809).		motile cilium assembly (GO:0044458)	ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)											GCTTCAAGATAAAATCTTCAT	0.398													A|||	1210	0.241613	0.1566	0.1671	5008	,	,		19313	0.2371		0.1849	False		,,,				2504	0.4724				p.K496E		Atlas-SNP	.											.	.	.	.	0			c.A1486G						PASS	.	A	GLU/LYS	733,3673	301.0+/-286.6	66,601,1536	76.0	76.0	76.0		1486	2.7	0.8	14	dbSNP_107	76	1566,7034	292.6+/-300.9	136,1294,2870	yes	missense	C14orf45	NM_025057.2	56	202,1895,4406	GG,GA,AA		18.2093,16.6364,17.6765	benign	496/530	74523869	2299,10707	2203	4300	6503	SO:0001583	missense	80127	exon11			CAAGATAAAATCT	BI457605	CCDS32119.2	14q24.3	2013-01-04	2012-09-25	2012-09-25	ENSG00000119636	ENSG00000119636			19855	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 45"""	C14orf45			Standard	NM_025057		Approved		uc010tup.2	Q8ND07	OTTHUMG00000152786	ENST00000394009.3:c.1486A>G	14.37:g.74523869A>G	ENSP00000377577:p.Lys496Glu	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	77	41	0.532468	NM_025057	Q0P604|Q9H5P8	Missense_Mutation	SNP	ENST00000394009.3	37	CCDS32119.2	408	0.18681318681318682	70	0.14227642276422764	64	0.17679558011049723	137	0.2395104895104895	137	0.18073878627968337	A	9.915	1.210595	0.22289	0.166364	0.182093	ENSG00000119636	ENST00000394009;ENST00000553773;ENST00000492247	T;T;T	0.49720	2.29;0.94;0.77	4.59	2.71	0.32032	.	0.659026	0.12998	N	0.421864	T	0.00012	0.0000	N	0.22421	0.69	0.29472	P	0.8569869999999999	B	0.02656	0.0	B	0.04013	0.001	T	0.22521	-1.0214	9	0.22109	T	0.4	1.0849	8.9085	0.35539	0.1716:0.6698:0.1585:0.0	rs3742809;rs52797532;rs59742664;rs3742809	496	Q8ND07	CN045_HUMAN	E	496;221;40	ENSP00000377577:K496E;ENSP00000451097:K221E;ENSP00000451020:K40E	ENSP00000377577:K496E	K	+	1	0	C14orf45	73593622	0.912000	0.30974	0.783000	0.31826	0.680000	0.39746	0.991000	0.29654	0.640000	0.30582	-1.290000	0.01357	AAA	G|0.185;N|0.001	0.185	strong		0.398	CCDC176-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327863.1	NM_025057	
CYP4F12	66002	hgsc.bcm.edu	37	19	15789140	15789140	+	Missense_Mutation	SNP	A	A	G	rs609290	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:15789140A>G	ENST00000550308.1	+	3	648	c.268A>G	c.(268-270)Ata>Gta	p.I90V	CYP4F12_ENST00000324632.10_Missense_Mutation_p.I90V	NM_023944.3	NP_076433	Q9HCS2	CP4FC_HUMAN	cytochrome P450, family 4, subfamily F, polypeptide 12	90			I -> V (in dbSNP:rs609290). {ECO:0000269|PubMed:11162607, ECO:0000269|PubMed:11162645, ECO:0000269|PubMed:12975309, ECO:0000269|Ref.7}.		arachidonic acid metabolic process (GO:0019369)|drug metabolic process (GO:0017144)|epoxygenase P450 pathway (GO:0019373)|leukotriene B4 catabolic process (GO:0036101)|long-chain fatty acid metabolic process (GO:0001676)|negative regulation of blood coagulation (GO:0030195)|oxidation-reduction process (GO:0055114)|pressure natriuresis (GO:0003095)|renal water homeostasis (GO:0003091)|small molecule metabolic process (GO:0044281)|sodium ion homeostasis (GO:0055078)|very long-chain fatty acid metabolic process (GO:0000038)|vitamin E metabolic process (GO:0042360)|vitamin K biosynthetic process (GO:0042371)|xenobiotic metabolic process (GO:0006805)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)	alkane 1-monooxygenase activity (GO:0018685)|arachidonic acid epoxygenase activity (GO:0008392)|aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|leukotriene-B4 20-monooxygenase activity (GO:0050051)|vitamin-K-epoxide reductase (warfarin-sensitive) activity (GO:0047057)			NS(1)|central_nervous_system(3)|endometrium(4)|kidney(2)|large_intestine(7)|lung(12)|ovary(3)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	41	Acute lymphoblastic leukemia(2;0.0367)				Fingolimod(DB08868)	GGGCTTTACGATATGGCTGGG	0.537													.|||	4100	0.81869	0.7163	0.8934	5008	,	,		1889	0.9712		0.8151	False		,,,				2504	0.7505				p.I90V		Atlas-SNP	.											CYP4F12,tonsil,carcinoma,0,1	CYP4F12	89	1	0			c.A268G	GRCh37	CM043943	CYP4F12	M	rs609290	PASS	.	A	VAL/ILE	3930,426		1775,380,23	138.0	139.0	138.0		268	-2.6	0.0	19	dbSNP_83	138	7980,596		3710,560,18	yes	missense	CYP4F12	NM_023944.3	29	5485,940,41	GG,GA,AA		6.9496,9.7796,7.9029	benign	90/525	15789140	11910,1022	2178	4288	6466	SO:0001583	missense	66002	exon3			TTTACGATATGGC	AB035130	CCDS42517.1	19p13.1	2008-02-05	2003-01-14		ENSG00000186204	ENSG00000186204		"""Cytochrome P450s"""	18857	protein-coding gene	gene with protein product		611485	"""cytochrome P450, subfamily IVF, polypeptide 12"""			11162607	Standard	NM_023944		Approved		uc002nbl.3	Q9HCS2	OTTHUMG00000164477	ENST00000550308.1:c.268A>G	19.37:g.15789140A>G	ENSP00000448998:p.Ile90Val	Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	129	129	1	NM_023944	E7ET51|O60389|Q5JPJ7|Q9HCS1	Missense_Mutation	SNP	ENST00000550308.1	37	CCDS42517.1	2050	0.9386446886446886	430	0.8739837398373984	350	0.9668508287292817	572	1.0	698	0.920844327176781	.	3.189	-0.166277	0.06461	0.902204	0.930504	ENSG00000186204	ENST00000550308;ENST00000551607;ENST00000324632	D;D;D	0.87966	-2.32;-2.32;-2.32	2.92	-2.63	0.06133	.	0.412733	0.22104	U	0.064575	T	0.00012	0.0000	N	0.11560	0.145	0.80722	P	0.0	B;B	0.09022	0.002;0.0	B;B	0.11329	0.006;0.004	T	0.35151	-0.9800	9	0.10111	T	0.7	.	2.3299	0.04233	0.3539:0.0:0.2583:0.3877	rs609290;rs17853420;rs52795990;rs57087881;rs609290	90;90	B4E2R2;Q9HCS2	.;CP4FC_HUMAN	V	90;43;90	ENSP00000448998:I90V;ENSP00000447922:I43V;ENSP00000321821:I90V	ENSP00000321821:I90V	I	+	1	0	CYP4F12	15650140	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.577000	0.05847	-0.918000	0.03808	0.402000	0.26972	ATA	A|0.061;G|0.939	0.939	strong		0.537	CYP4F12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378938.9		
TTC21A	199223	hgsc.bcm.edu	37	3	39161456	39161456	+	Missense_Mutation	SNP	G	G	A	rs1274972	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:39161456G>A	ENST00000431162.2	+	8	1003	c.869G>A	c.(868-870)aGg>aAg	p.R290K	TTC21A_ENST00000301819.6_Missense_Mutation_p.R290K|TTC21A_ENST00000440121.1_Missense_Mutation_p.R241K			Q8NDW8	TT21A_HUMAN	tetratricopeptide repeat domain 21A	290			R -> K (in dbSNP:rs1274972).							NS(1)|breast(2)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(9)|lung(23)|ovary(1)|prostate(1)|skin(3)	50				KIRC - Kidney renal clear cell carcinoma(284;0.0588)|Kidney(284;0.0738)		CTAGAGACAAGGGAACCCGAA	0.458													G|||	2282	0.455671	0.8495	0.3429	5008	,	,		18365	0.2738		0.334	False		,,,				2504	0.316				p.R290K		Atlas-SNP	.											.	TTC21A	96	.	0			c.G869A						PASS	.	G	LYS/ARG,LYS/ARG	2803,953		1044,715,119	114.0	123.0	120.0		722,869	1.8	0.4	3	dbSNP_87	120	2777,5435		486,1805,1815	yes	missense,missense	TTC21A	NM_001105513.2,NM_145755.2	26,26	1530,2520,1934	AA,AG,GG		33.8164,25.3727,46.6243	benign,benign	241/1273,290/1321	39161456	5580,6388	1878	4106	5984	SO:0001583	missense	199223	exon8			AGACAAGGGAACC	AJ487015	CCDS43068.1, CCDS46800.1, CCDS43068.2	3p22.2	2014-09-04			ENSG00000168026	ENSG00000168026		"""Tetratricopeptide (TTC) repeat domain containing"""	30761	protein-coding gene	gene with protein product		611430					Standard	NM_145755		Approved	STI2	uc003cjc.2	Q8NDW8	OTTHUMG00000155973	ENST00000431162.2:c.869G>A	3.37:g.39161456G>A	ENSP00000398211:p.Arg290Lys	Somatic	225	0	0		WXS	Illumina HiSeq	Phase_I	164	70	0.426829	NM_145755	A1L388|B4DYF6|B4DYJ3|D3YTE7|D4PHA5|Q6P5W8|Q8N7G5|Q8NA02	Missense_Mutation	SNP	ENST00000431162.2	37	CCDS46800.1	959	0.4391025641025641	410	0.8333333333333334	133	0.3674033149171271	166	0.2902097902097902	250	0.32981530343007914	G	3.931	-0.016256	0.07681	0.746273	0.338164	ENSG00000168026	ENST00000301819;ENST00000424305;ENST00000431162;ENST00000440121	T;T;T	0.34472	1.36;1.36;2.31	5.67	1.76	0.24704	.	0.359920	0.28989	N	0.013481	T	0.00012	0.0000	L	0.33485	1.01	0.80722	P	0.0	B;B;B	0.11235	0.001;0.004;0.002	B;B;B	0.14578	0.006;0.011;0.005	T	0.13872	-1.0493	9	0.27785	T	0.31	-0.8765	6.5884	0.22634	0.2034:0.2446:0.552:0.0	rs1274972;rs61530584;rs1274972	241;290;290	Q8NDW8-6;Q8NDW8-7;Q8NDW8	.;.;TT21A_HUMAN	K	290;282;290;241	ENSP00000301819:R290K;ENSP00000398211:R290K;ENSP00000410882:R241K	ENSP00000301819:R290K	R	+	2	0	TTC21A	39136460	0.007000	0.16637	0.354000	0.25760	0.288000	0.27193	0.778000	0.26732	0.315000	0.23110	-0.175000	0.13238	AGG	G|0.555;A|0.445	0.445	strong		0.458	TTC21A-021	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000377829.1	NM_145755	
USH1C	10083	hgsc.bcm.edu	37	11	17531146	17531146	+	Intron	SNP	G	G	A	rs17776775	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:17531146G>A	ENST00000318024.4	-	16	1393				USH1C_ENST00000005226.7_Silent_p.A590A|USH1C_ENST00000527720.1_Intron|USH1C_ENST00000529563.1_Intron|USH1C_ENST00000527020.1_Intron	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	29	0	0		WXS	Illumina HiSeq	Phase_I	29	23	0.793103	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	
GLRB	2743	hgsc.bcm.edu	37	4	158060077	158060077	+	Missense_Mutation	SNP	T	T	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:158060077T>A	ENST00000264428.4	+	7	997	c.727T>A	c.(727-729)Tgt>Agt	p.C243S	GLRB_ENST00000541722.1_Missense_Mutation_p.C243S|GLRB_ENST00000509282.1_Missense_Mutation_p.C243S|GLRB_ENST00000512619.1_Intron	NM_000824.4	NP_000815.1	P48167	GLRB_HUMAN	glycine receptor, beta	243					acrosome reaction (GO:0007340)|adult walking behavior (GO:0007628)|chloride transmembrane transport (GO:1902476)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|nervous system development (GO:0007399)|neuropeptide signaling pathway (GO:0007218)|protein heterooligomerization (GO:0051291)|regulation of membrane potential (GO:0042391)|righting reflex (GO:0060013)|startle response (GO:0001964)|synaptic transmission (GO:0007268)|synaptic transmission, glycinergic (GO:0060012)|transmembrane transport (GO:0055085)|visual perception (GO:0007601)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	extracellular-glycine-gated chloride channel activity (GO:0016934)|extracellular-glycine-gated ion channel activity (GO:0016933)|glycine binding (GO:0016594)			central_nervous_system(1)|endometrium(3)|large_intestine(11)|lung(6)|skin(5)|upper_aerodigestive_tract(1)	27	all_hematologic(180;0.24)	Renal(120;0.0458)		KIRC - Kidney renal clear cell carcinoma(143;0.0564)|COAD - Colon adenocarcinoma(41;0.0642)|Kidney(143;0.0707)	Enflurane(DB00228)|Glycine(DB00145)|Lindane(DB00431)	ATATGGTAACTGTACAAAATA	0.313																																					p.C243S		Atlas-SNP	.											GLRB,caecum,carcinoma,-2,1	GLRB	74	1	0			c.T727A						PASS	.						57.0	62.0	60.0					4																	158060077		2203	4295	6498	SO:0001583	missense	2743	exon7			GGTAACTGTACAA	U33267	CCDS3796.1, CCDS54813.1	4q31.3	2008-02-05			ENSG00000109738	ENSG00000109738			4329	protein-coding gene	gene with protein product		138492				9676428, 8717357	Standard	NM_000824		Approved		uc003ipj.2	P48167	OTTHUMG00000161954	ENST00000264428.4:c.727T>A	4.37:g.158060077T>A	ENSP00000264428:p.Cys243Ser	Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	124	20	0.16129	NM_000824	A8K3K2|D3DP23|F5GWE1	Missense_Mutation	SNP	ENST00000264428.4	37	CCDS3796.1	.	.	.	.	.	.	.	.	.	.	T	27.4	4.825550	0.90955	.	.	ENSG00000109738	ENST00000264428;ENST00000541722;ENST00000509282	T;T;T	0.77620	-1.11;-1.11;-1.11	5.5	5.5	0.81552	Neurotransmitter-gated ion-channel ligand-binding (3);	0.093422	0.85682	D	0.000000	D	0.84392	0.5462	L	0.49455	1.56	0.80722	D	1	D	0.54772	0.968	D	0.69824	0.966	D	0.83745	0.0206	10	0.39692	T	0.17	.	15.5984	0.76606	0.0:0.0:0.0:1.0	.	243	P48167	GLRB_HUMAN	S	243	ENSP00000264428:C243S;ENSP00000441873:C243S;ENSP00000427186:C243S	ENSP00000264428:C243S	C	+	1	0	GLRB	158279527	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	7.961000	0.87903	2.090000	0.63153	0.528000	0.53228	TGT	.	.	none		0.313	GLRB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366507.1	NM_000824	
LRRC71	149499	hgsc.bcm.edu	37	1	156902259	156902259	+	Silent	SNP	G	G	A	rs822430	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:156902259G>A	ENST00000337428.7	+	14	1639	c.1485G>A	c.(1483-1485)acG>acA	p.T495T	ARHGEF11_ENST00000487682.1_5'Flank|LRRC71_ENST00000490146.1_3'UTR	NM_144702.2	NP_653303.2	Q8N4P6	LRC71_HUMAN	leucine rich repeat containing 71	495										endometrium(2)|large_intestine(3)|lung(5)|ovary(1)|stomach(1)	12						TCCTCGCCACGGTGCAGTATC	0.597													A|||	3780	0.754792	0.888	0.7061	5008	,	,		18256	0.8492		0.5318	False		,,,				2504	0.7413				p.T495T		Atlas-SNP	.											.	LRRC71	33	.	0			c.G1485A						PASS	.	A		3613,699		1530,553,73	56.0	65.0	62.0		1485	-10.0	0.0	1	dbSNP_86	62	4604,3916		1255,2094,911	no	coding-synonymous	LRRC71	NM_144702.2		2785,2647,984	AA,AG,GG		45.9624,16.2106,35.9648		495/560	156902259	8217,4615	2156	4260	6416	SO:0001819	synonymous_variant	149499	exon14			CGCCACGGTGCAG	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.1485G>A	1.37:g.156902259G>A		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	102	101	0.990196	NM_144702	Q96M24	Silent	SNP	ENST00000337428.7	37	CCDS44249.1																																																																																			G|0.286;A|0.714	0.714	strong		0.597	LRRC71-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098961.1	NM_144702	
POTEF	728378	hgsc.bcm.edu	37	2	130872791	130872791	+	Missense_Mutation	SNP	A	A	G	rs200596208	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:130872791A>G	ENST00000409914.2	-	4	1031	c.632T>C	c.(631-633)aTa>aCa	p.I211T	POTEF_ENST00000357462.5_Missense_Mutation_p.I211T|POTEF_ENST00000361163.4_Missense_Mutation_p.I211T|POTEF_ENST00000360967.5_Missense_Mutation_p.I211T	NM_001099771.2	NP_001093241.1	A5A3E0	POTEF_HUMAN	POTE ankyrin domain family, member F	211					retina homeostasis (GO:0001895)	blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				breast(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(4)|lung(28)|ovary(3)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	53						GCATACCTTTATCAGAGCTGT	0.393																																					p.I211T		Atlas-SNP	.											POTEF,brain,glioma,0,2	POTEF	140	2	0			c.T632C						scavenged	.						17.0	19.0	18.0					2																	130872791		2062	4036	6098	SO:0001583	missense	728378	exon4			ACCTTTATCAGAG	EF523384	CCDS46409.1	2q21.1	2013-01-10	2008-11-26	2008-11-26	ENSG00000196604	ENSG00000196604		"""POTE ankyrin domain containing"", ""Ankyrin repeat domain containing"""	33905	protein-coding gene	gene with protein product			"""ANKRD26-like family C, member 1B"""	A26C1B		17101985	Standard	NM_001099771		Approved	POTEACTIN, POTE2alpha	uc010fmh.2	A5A3E0	OTTHUMG00000153628	ENST00000409914.2:c.632T>C	2.37:g.130872791A>G	ENSP00000386786:p.Ile211Thr	Somatic	199	0	0		WXS	Illumina HiSeq	Phase_I	188	9	0.0478723	NM_001099771	A6NC34	Missense_Mutation	SNP	ENST00000409914.2	37	CCDS46409.1	.	.	.	.	.	.	.	.	.	.	.	2.324	-0.354989	0.05138	.	.	ENSG00000196604	ENST00000357462;ENST00000409914;ENST00000360967;ENST00000361163	T;T;T;T	0.64991	-0.13;-0.13;-0.13;1.69	1.13	-0.185	0.13276	Ankyrin repeat-containing domain (4);	1.226600	0.05905	N	0.630695	T	0.44993	0.1320	L	0.33668	1.02	0.20926	N	0.999828	B	0.17465	0.022	B	0.14023	0.01	T	0.15752	-1.0426	10	0.13470	T	0.59	.	4.0452	0.09770	0.7642:0.0:0.2358:0.0	.	211	A5A3E0	POTEF_HUMAN	T	211	ENSP00000350052:I211T;ENSP00000386786:I211T;ENSP00000354232:I211T;ENSP00000355012:I211T	ENSP00000350052:I211T	I	-	2	0	POTEF	130589261	0.920000	0.31207	0.006000	0.13384	0.033000	0.12548	1.415000	0.34748	-0.249000	0.09569	-1.353000	0.01230	ATA	A|0.951;G|0.049	0.049	strong		0.393	POTEF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331889.2	NM_001099771	
TENM3	55714	hgsc.bcm.edu	37	4	183674697	183674697	+	Silent	SNP	C	C	T	rs17263582	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:183674697C>T	ENST00000511685.1	+	21	4080	c.3957C>T	c.(3955-3957)ggC>ggT	p.G1319G	TENM3_ENST00000406950.2_Silent_p.G1319G|TENM3_ENST00000502950.1_3'UTR			Q9P273	TEN3_HUMAN	teneurin transmembrane protein 3	1319					camera-type eye morphogenesis (GO:0048593)|homophilic cell adhesion (GO:0007156)|positive regulation of neuron projection development (GO:0010976)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cell projection (GO:0042995)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)	p.G1319G(1)									CTCTTCTGGGCTCTAACGATT	0.393													C|||	825	0.164736	0.0628	0.1931	5008	,	,		17204	0.1587		0.2505	False		,,,				2504	0.2004				p.G1319G		Atlas-SNP	.											ODZ3,NS,carcinoma,0,1	.	.	1	1	Substitution - coding silent(1)	prostate(1)	c.C3957T						PASS	.	C		304,3592		7,290,1651	101.0	101.0	101.0		3957	3.0	1.0	4	dbSNP_123	101	1792,6530		194,1404,2563	no	coding-synonymous	ODZ3	NM_001080477.1		201,1694,4214	TT,TC,CC		21.5333,7.8029,17.155		1319/2700	183674697	2096,10122	1948	4161	6109	SO:0001819	synonymous_variant	55714	exon20			TCTGGGCTCTAAC	AF195420	CCDS47165.1	4q35	2012-10-02	2012-10-02	2012-10-02	ENSG00000218336	ENSG00000218336			29944	protein-coding gene	gene with protein product		610083	"""odz, odd Oz/ten-m homolog 3 (Drosophila)"""	ODZ3		10331952, 10625539	Standard	NM_001080477		Approved	Ten-M3, KIAA1455	uc003ivd.1	Q9P273	OTTHUMG00000160682	ENST00000511685.1:c.3957C>T	4.37:g.183674697C>T		Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	157	77	0.490446	NM_001080477	Q5XUL9|Q96SY2|Q9NV77|Q9NVW1|Q9NZJ2	Silent	SNP	ENST00000511685.1	37	CCDS47165.1																																																																																			C|0.827;T|0.173	0.173	strong		0.393	TENM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361734.1		
DHX33	56919	hgsc.bcm.edu	37	17	5347788	5347788	+	Missense_Mutation	SNP	G	G	A	rs75426953	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:5347788G>A	ENST00000225296.3	-	12	2061	c.1861C>T	c.(1861-1863)Cgc>Tgc	p.R621C	DHX33_ENST00000433302.3_Missense_Mutation_p.R397C	NM_001199699.1|NM_020162.3	NP_001186628.1|NP_064547.2	Q9H6R0	DHX33_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 33	621					positive regulation of transcription from RNA polymerase I promoter (GO:0045943)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)|rDNA binding (GO:0000182)			breast(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(2)|lung(2)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17						AGGCAGCGGCGGACACTCTCC	0.607													G|||	35	0.00698882	0.0008	0.0086	5008	,	,		19061	0.001		0.0239	False		,,,				2504	0.0031				p.R621C		Atlas-SNP	.											DHX33,NS,carcinoma,0,1	DHX33	41	1	0			c.C1861T						scavenged	.	G	CYS/ARG,CYS/ARG	24,4382	30.8+/-60.4	1,22,2180	74.0	69.0	70.0		1342,1861	4.6	1.0	17	dbSNP_131	70	203,8397	88.4+/-150.7	2,199,4099	yes	missense,missense	DHX33	NM_001199699.1,NM_020162.3	180,180	3,221,6279	AA,AG,GG		2.3605,0.5447,1.7453	probably-damaging,probably-damaging	448/535,621/708	5347788	227,12779	2203	4300	6503	SO:0001583	missense	56919	exon12			AGCGGCGGACACT	AL359945	CCDS11072.1	17p13	2003-06-13	2003-06-13	2003-06-13	ENSG00000005100	ENSG00000005100		"""DEAH-boxes"""	16718	protein-coding gene	gene with protein product		614405	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 33"""	DDX33			Standard	NM_020162		Approved	FLJ21972, DKFZp762F2011	uc002gca.3	Q9H6R0	OTTHUMG00000102041	ENST00000225296.3:c.1861C>T	17.37:g.5347788G>A	ENSP00000225296:p.Arg621Cys	Somatic	119	1	0.00840336		WXS	Illumina HiSeq	Phase_I	96	54	0.5625	NM_020162	B4DHF9|Q4G149|Q5CZ73|Q9H5M9	Missense_Mutation	SNP	ENST00000225296.3	37	CCDS11072.1	24	0.01098901098901099	1	0.0020325203252032522	5	0.013812154696132596	1	0.0017482517482517483	17	0.022427440633245383	G	25.8	4.678553	0.88542	0.005447	0.023605	ENSG00000005100	ENST00000225296;ENST00000433302	T;T	0.02890	4.12;4.12	4.59	4.59	0.56863	Domain of unknown function DUF1605 (1);	0.000000	0.85682	D	0.000000	T	0.08846	0.0219	M	0.85373	2.75	0.80722	D	1	D;P	0.89917	1.0;0.626	D;B	0.81914	0.995;0.287	T	0.00235	-1.1892	10	0.66056	D	0.02	.	16.9197	0.86161	0.0:0.0:1.0:0.0	.	397;621	Q05BE5;Q9H6R0	.;DHX33_HUMAN	C	621;397	ENSP00000225296:R621C;ENSP00000413779:R397C	ENSP00000225296:R621C	R	-	1	0	DHX33	5288512	1.000000	0.71417	1.000000	0.80357	0.931000	0.56810	9.073000	0.93992	2.548000	0.85928	0.561000	0.74099	CGC	A|0.014;C|0.000;G|0.986	0.014	strong		0.607	DHX33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219826.2	NM_020162	
FCHSD1	89848	hgsc.bcm.edu	37	5	141026182	141026182	+	Missense_Mutation	SNP	G	G	T	rs3749760	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:141026182G>T	ENST00000435817.2	-	11	1082	c.1032C>A	c.(1030-1032)aaC>aaA	p.N344K	FCHSD1_ENST00000523856.1_5'UTR|FCHSD1_ENST00000522126.1_Missense_Mutation_p.N268K|FCHSD1_ENST00000522783.1_Missense_Mutation_p.N342K	NM_033449.2	NP_258260.1	Q86WN1	FCSD1_HUMAN	FCH and double SH3 domains 1	344			N -> K (in dbSNP:rs3749760).						FCHSD1/BRAF(2)	central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(8)|lung(5)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	24			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GATGCCCATGGTTCTGGATCT	0.592													G|||	65	0.0129792	0.0015	0.0259	5008	,	,		19308	0.0258		0.0119	False		,,,				2504	0.0072				p.N344K		Atlas-SNP	.											.	FCHSD1	51	.	0			c.C1032A						PASS	.	G	LYS/ASN	8,3962		0,8,1977	33.0	37.0	36.0		1032	2.2	1.0	5	dbSNP_107	36	131,8141		2,127,4007	yes	missense	FCHSD1	NM_033449.2	94	2,135,5984	TT,TG,GG		1.5837,0.2015,1.1354	benign	344/691	141026182	139,12103	1985	4136	6121	SO:0001583	missense	89848	exon11			CCCATGGTTCTGG	AK027281	CCDS47295.1	5q31.3	2008-02-05			ENSG00000197948	ENSG00000197948			25463	protein-coding gene	gene with protein product						11214971, 15067381	Standard	NM_033449		Approved	FLJ00007	uc003llk.3	Q86WN1	OTTHUMG00000163762	ENST00000435817.2:c.1032C>A	5.37:g.141026182G>T	ENSP00000399259:p.Asn344Lys	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	63	32	0.507937	NM_033449	Q6UX75|Q86Y77|Q9NXX8	Missense_Mutation	SNP	ENST00000435817.2	37	CCDS47295.1	39	0.017857142857142856	3	0.006097560975609756	8	0.022099447513812154	18	0.03146853146853147	10	0.013192612137203167	G	15.12	2.738413	0.49045	0.002015	0.015837	ENSG00000197948	ENST00000435817;ENST00000522126;ENST00000522783	T;T;T	0.39997	1.84;1.05;1.44	5.47	2.22	0.28083	.	0.849984	0.10666	N	0.648098	T	0.09069	0.0224	N	0.22421	0.69	0.80722	D	1	B	0.16396	0.017	B	0.20184	0.028	T	0.08146	-1.0736	10	0.02654	T	1	-17.3402	9.4986	0.39004	0.2876:0.0:0.7124:0.0	rs3749760;rs52802373;rs3749760	344	Q86WN1	FCSD1_HUMAN	K	344;268;342	ENSP00000399259:N344K;ENSP00000427796:N268K;ENSP00000428677:N342K	ENSP00000399259:N344K	N	-	3	2	FCHSD1	141006366	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	0.933000	0.28897	0.673000	0.31224	0.462000	0.41574	AAC	G|0.981;T|0.019	0.019	strong		0.592	FCHSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375282.2	NM_033449	
SCN2A	6326	hgsc.bcm.edu	37	2	166152389	166152389	+	Missense_Mutation	SNP	G	G	A	rs17183814	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:166152389G>A	ENST00000375437.2	+	2	346	c.56G>A	c.(55-57)aGg>aAg	p.R19K	SCN2A_ENST00000283256.6_Missense_Mutation_p.R19K|SCN2A_ENST00000357398.3_Missense_Mutation_p.R19K|SCN2A_ENST00000375427.2_Missense_Mutation_p.R19K	NM_001040142.1	NP_001035232.1	Q99250	SCN2A_HUMAN	sodium channel, voltage-gated, type II, alpha subunit	19			R -> K (in dbSNP:rs17183814). {ECO:0000269|PubMed:11371648, ECO:0000269|PubMed:12610651, ECO:0000269|PubMed:19786696}.		intrinsic apoptotic signaling pathway in response to osmotic stress (GO:0008627)|membrane depolarization during action potential (GO:0086010)|myelination (GO:0042552)|neuron apoptotic process (GO:0051402)|neuronal action potential (GO:0019228)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	axon (GO:0030424)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|intrinsic component of plasma membrane (GO:0031226)|node of Ranvier (GO:0033268)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|sodium channel complex (GO:0034706)|T-tubule (GO:0030315)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			NS(1)|breast(7)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(27)|liver(2)|lung(49)|ovary(6)|pancreas(1)|prostate(2)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	118					Lamotrigine(DB00555)|Propofol(DB00818)|Valproic Acid(DB00313)|Zonisamide(DB00909)	TTCTTTACCAGGGAATCCCTT	0.483													G|||	420	0.0838658	0.0212	0.0821	5008	,	,		20245	0.1379		0.0567	False		,,,				2504	0.1421				p.R19K		Atlas-SNP	.											.	SCN2A	589	.	0			c.G56A						PASS	.	G	LYS/ARG,LYS/ARG,LYS/ARG	148,4258	103.4+/-141.9	2,144,2057	84.0	75.0	78.0		56,56,56	5.6	1.0	2	dbSNP_123	78	616,7984	160.4+/-213.5	21,574,3705	yes	missense,missense,missense	SCN2A	NM_001040142.1,NM_001040143.1,NM_021007.2	26,26,26	23,718,5762	AA,AG,GG		7.1628,3.3591,5.8742	probably-damaging,probably-damaging,probably-damaging	19/2006,19/2006,19/2006	166152389	764,12242	2203	4300	6503	SO:0001583	missense	6326	exon1			TTACCAGGGAATC	AB208888	CCDS33313.1, CCDS33314.1	2q24.3	2012-02-26	2007-01-23	2007-01-23	ENSG00000136531	ENSG00000136531		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10588	protein-coding gene	gene with protein product		182390	"""sodium channel, voltage-gated, type II, alpha 2 polypeptide"", ""sodium channel, voltage-gated, type II, alpha 1 polypeptide"""	SCN2A1, SCN2A2		1317301, 16382098	Standard	XM_005246753		Approved	Nav1.2, HBSCII, HBSCI	uc002ude.3	Q99250	OTTHUMG00000044172	ENST00000375437.2:c.56G>A	2.37:g.166152389G>A	ENSP00000364586:p.Arg19Lys	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	104	66	0.634615	NM_001040143	A6NC14|A6NIQ5|Q14472|Q53T77|Q9BZC9|Q9BZD0	Missense_Mutation	SNP	ENST00000375437.2	37	CCDS33314.1	159	0.07280219780219781	9	0.018292682926829267	30	0.08287292817679558	74	0.12937062937062938	46	0.06068601583113457	G	11.85	1.760255	0.31137	0.033591	0.071628	ENSG00000136531	ENST00000424833;ENST00000375437;ENST00000357398;ENST00000283256;ENST00000375427	D;D;D;D;D	0.96459	-4.02;-4.0;-4.0;-4.0;-4.0	5.55	5.55	0.83447	.	0.000000	0.85682	D	0.000000	T	0.22820	0.0551	M	0.65975	2.015	0.36123	P	0.15438799999999997	B;B	0.09022	0.002;0.001	B;B	0.16289	0.015;0.007	T	0.71477	-0.4581	9	0.44086	T	0.13	.	13.7552	0.62933	0.0732:0.0:0.9268:0.0	rs17183814;rs52803852;rs17183814	19;19	Q99250-2;Q99250	.;SCN2A_HUMAN	K	19	ENSP00000406454:R19K;ENSP00000364586:R19K;ENSP00000349973:R19K;ENSP00000283256:R19K;ENSP00000364576:R19K	ENSP00000283256:R19K	R	+	2	0	SCN2A	165860635	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.409000	0.44583	2.619000	0.88677	0.655000	0.94253	AGG	G|0.933;A|0.067	0.067	strong		0.483	SCN2A-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000102659.2	NM_021007	
SENP7	57337	hgsc.bcm.edu	37	3	101085413	101085413	+	Silent	SNP	G	G	A	rs939443	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:101085413G>A	ENST00000394095.2	-	9	1232	c.1179C>T	c.(1177-1179)acC>acT	p.T393T	SENP7_ENST00000314261.7_Silent_p.T327T|SENP7_ENST00000394094.2_Silent_p.T328T|SENP7_ENST00000358203.3_Silent_p.T229T|SENP7_ENST00000394091.1_Silent_p.T229T|SENP7_ENST00000348610.3_Silent_p.T360T	NM_001282802.1|NM_020654.3	NP_001269731.1|NP_065705.3	Q9BQF6	SENP7_HUMAN	SUMO1/sentrin specific peptidase 7	393						intracellular (GO:0005622)|nucleus (GO:0005634)	cysteine-type peptidase activity (GO:0008234)			breast(2)|endometrium(1)|kidney(1)|large_intestine(16)|lung(15)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44						AGTTCTCAACGGTTTCAGTGG	0.403													A|||	2139	0.427117	0.3502	0.5533	5008	,	,		18015	0.4831		0.4125	False		,,,				2504	0.3988				p.T393T		Atlas-SNP	.											.	SENP7	170	.	0			c.C1179T						PASS	.	A	,	1414,2992	685.4+/-404.6	236,942,1025	101.0	101.0	101.0		984,1179	-4.7	0.0	3	dbSNP_86	101	3472,5128	634.7+/-398.9	705,2062,1533	no	coding-synonymous,coding-synonymous	SENP7	NM_001077203.1,NM_020654.3	,	941,3004,2558	AA,AG,GG		40.3721,32.0926,37.5673	,	328/986,393/1051	101085413	4886,8120	2203	4300	6503	SO:0001819	synonymous_variant	57337	exon9			CTCAACGGTTTCA		CCDS2941.2, CCDS43121.1, CCDS63704.1, CCDS63705.1, CCDS63706.1	3q12	2008-02-05	2005-08-17		ENSG00000138468	ENSG00000138468			30402	protein-coding gene	gene with protein product		612846	"""SUMO1/sentrin specific protease 7"""			11214970, 11230166	Standard	NM_001282802		Approved		uc003dut.3	Q9BQF6	OTTHUMG00000149927	ENST00000394095.2:c.1179C>T	3.37:g.101085413G>A		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	131	130	0.992366	NM_020654	A1L3A5|A8MW39|B7WNW8|Q7Z3F4|Q96PS5|Q9C0F6|Q9HBT5	Silent	SNP	ENST00000394095.2	37	CCDS2941.2																																																																																			G|0.603;A|0.397	0.397	strong		0.403	SENP7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313957.2	NM_020654	
HLA-B	3106	hgsc.bcm.edu	37	6	31324089	31324089	+	Silent	SNP	G	G	A	rs1050370|rs281864628	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:31324089G>A	ENST00000412585.2	-	3	502	c.474C>T	c.(472-474)acC>acT	p.T158T		NM_005514.6	NP_005505.2	P30486	1B48_HUMAN	major histocompatibility complex, class I, B	158	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						TGTCCGCGGCGGTCCAGGAGC	0.711									Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of				G|||	71	0.0141773	0.0068	0.0072	5008	,	,		12015	0.0089		0.0239	False		,,,				2504	0.0245				p.T158T		Atlas-SNP	.											.	HLA-B	54	.	0			c.C474T	GRCh37	CD004225	HLA-B	D	rs1050370	PASS	.	G		39,4175		0,39,2068	29.0	21.0	24.0		474	-0.1	0.4	6	dbSNP_134	24	165,8233		0,165,4034	no	coding-synonymous	HLA-B	NM_005514.6		0,204,6102	AA,AG,GG		1.9648,0.9255,1.6175		158/363	31324089	204,12408	2107	4199	6306	SO:0001819	synonymous_variant	3106	exon3	Familial Cancer Database	;Lichen Sclerosis, Familial	CGCGGCGGTCCAG	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.474C>T	6.37:g.31324089G>A		Somatic	231	0	0		WXS	Illumina HiSeq	Phase_I	100	57	0.57	NM_005514	Q29764	Silent	SNP	ENST00000412585.2	37	CCDS34394.1																																																																																			G|0.971;A|0.029	0.029	strong		0.711	HLA-B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076280.4	NM_005514	
OR12D3	81797	hgsc.bcm.edu	37	6	29342775	29342775	+	Missense_Mutation	SNP	G	G	A	rs3749971	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:29342775G>A	ENST00000396806.3	-	1	293	c.290C>T	c.(289-291)aCc>aTc	p.T97I	OR5V1_ENST00000377154.1_Intron	NM_030959.2	NP_112221.1	Q9UGF7	O12D3_HUMAN	olfactory receptor, family 12, subfamily D, member 3	97			T -> I (in dbSNP:rs3749971). {ECO:0000269|PubMed:14574404}.			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(6)|ovary(2)|skin(1)|upper_aerodigestive_tract(3)	23						GTGTAGCTGGGTGATACAGCC	0.468													G|||	155	0.0309505	0.0106	0.0288	5008	,	,		20049	0.0327		0.0746	False		,,,				2504	0.0133				p.T97I		Atlas-SNP	.											OR12D3,NS,carcinoma,0,3	OR12D3	55	3	0			c.C290T						PASS	.	G	ILE/THR	71,2949		1,69,1440	57.0	60.0	59.0		290	2.3	0.8	6	dbSNP_107	59	515,4901		28,459,2221	yes	missense	OR12D3	NM_030959.2	89	29,528,3661	AA,AG,GG		9.5089,2.351,6.9464	benign	97/317	29342775	586,7850	1510	2708	4218	SO:0001583	missense	81797	exon1			AGCTGGGTGATAC		CCDS4658.1	6p22.1	2013-09-24			ENSG00000112462	ENSG00000112462		"""GPCR / Class A : Olfactory receptors"""	13963	protein-coding gene	gene with protein product							Standard	NM_030959		Approved	hs6M1-27	uc003nme.3	Q9UGF7	OTTHUMG00000031051	ENST00000396806.3:c.290C>T	6.37:g.29342775G>A	ENSP00000380023:p.Thr97Ile	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	110	51	0.463636	NM_030959	A2BDZ1|Q5SQI8|Q6IF23	Missense_Mutation	SNP	ENST00000396806.3	37	CCDS4658.1	96	0.04395604395604396	8	0.016260162601626018	9	0.024861878453038673	18	0.03146853146853147	61	0.08047493403693931	G	2.381	-0.342065	0.05243	0.02351	0.095089	ENSG00000112462	ENST00000377143;ENST00000396806	T	0.01240	5.12	4.18	2.32	0.28847	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00608	0.0020	L	0.35723	1.085	0.80722	P	0.0	B	0.17465	0.022	B	0.18561	0.022	T	0.41752	-0.9491	8	0.38643	T	0.18	-4.3866	9.8495	0.41048	0.1766:0.0:0.8234:0.0	rs3749971;rs17346008;rs58992854;rs3749971	97	Q9UGF7	O12D3_HUMAN	I	97	ENSP00000380023:T97I	ENSP00000366348:T97I	T	-	2	0	OR12D3	29450754	0.000000	0.05858	0.829000	0.32907	0.092000	0.18411	0.870000	0.28010	0.946000	0.37632	0.195000	0.17529	ACC	G|0.942;A|0.058	0.058	strong		0.468	OR12D3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076056.3		
ELOVL5	60481	hgsc.bcm.edu	37	6	53159090	53159090	+	Intron	SNP	G	G	T	rs2294857	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:53159090G>T	ENST00000542638.1	-	2	506				ELOVL5_ENST00000541407.1_Intron|ELOVL5_ENST00000304434.6_Intron|ELOVL5_ENST00000370918.4_Intron|ELOVL5_ENST00000486973.1_Intron|ELOVL5_ENST00000370913.5_Silent_p.A86A			Q9NYP7	ELOV5_HUMAN	ELOVL fatty acid elongase 5						alpha-linolenic acid metabolic process (GO:0036109)|cellular lipid metabolic process (GO:0044255)|fatty acid elongation, monounsaturated fatty acid (GO:0034625)|fatty acid elongation, polyunsaturated fatty acid (GO:0034626)|linoleic acid metabolic process (GO:0043651)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|unsaturated fatty acid biosynthetic process (GO:0006636)|unsaturated fatty acid metabolic process (GO:0033559)|very long-chain fatty acid biosynthetic process (GO:0042761)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	fatty acid elongase activity (GO:0009922)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)	7	Lung NSC(77;0.116)					ttcaggcaggggcatgtgaag	0.517													G|||	331	0.0660942	0.0061	0.2579	5008	,	,		17072	0.0407		0.0765	False		,,,				2504	0.0266				p.A86A		Atlas-SNP	.											.	ELOVL5	25	.	0			c.C258A						PASS	.	G	,,,	24,1720		0,24,848	10.0	9.0	9.0		,,258,	-2.7	0.0	6	dbSNP_100	9	213,3759		4,205,1777	no	intron,intron,coding-synonymous,intron	ELOVL5	NM_001242828.1,NM_001242830.1,NM_001242831.1,NM_021814.4	,,,	4,229,2625	TT,TG,GG		5.3625,1.3761,4.1463	,,,	,,86/89,	53159090	237,5479	872	1986	2858	SO:0001627	intron_variant	60481	exon3			GGCAGGGGCATGT	AF052129	CCDS4951.1, CCDS56433.1, CCDS56434.1, CCDS75470.1	6p21.1-p12.1	2014-07-30	2011-05-25		ENSG00000012660	ENSG00000012660			21308	protein-coding gene	gene with protein product		611805	"""ELOVL family member 5, elongation of long chain fatty acids (FEN1/Elo2, SUR4/Elo3-like, yeast)"", ""spinocerebellar ataxia 38"""	SCA38		10970790, 25065913	Standard	NM_021814		Approved	HELO1, dJ483K16.1	uc011dwx.2	Q9NYP7	OTTHUMG00000016249	ENST00000542638.1:c.58+1349C>A	6.37:g.53159090G>T		Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	124	53	0.427419	NM_001242831	B4DZJ2|F6SH78|Q59EL3|Q5TGH5|Q6NXE7|Q7L2S5|Q8NCG4|Q9UI22	Silent	SNP	ENST00000542638.1	37	CCDS4951.1																																																																																			G|0.922;T|0.078	0.078	strong		0.517	ELOVL5-203	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043566.1	NM_021814	
NGFR	4804	hgsc.bcm.edu	37	17	47588000	47588000	+	Silent	SNP	C	C	T	rs11466155	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:47588000C>T	ENST00000172229.3	+	4	920	c.795C>T	c.(793-795)ggC>ggT	p.G265G	RP5-1029K10.2_ENST00000514506.1_RNA|NGFR_ENST00000504201.1_Silent_p.G171G	NM_002507.3	NP_002498.1	P08138	TNR16_HUMAN	nerve growth factor receptor	265					apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|central nervous system development (GO:0007417)|circadian regulation of gene expression (GO:0032922)|detection of temperature stimulus (GO:0016048)|glucose homeostasis (GO:0042593)|hair follicle morphogenesis (GO:0031069)|intracellular protein transport (GO:0006886)|membrane protein intracellular domain proteolysis (GO:0031293)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell cycle (GO:0045786)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of hair follicle development (GO:0051799)|nerve development (GO:0021675)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of axonogenesis (GO:0050772)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of odontogenesis of dentin-containing tooth (GO:0042488)|regulation of axonogenesis (GO:0050770)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of glucose import in response to insulin stimulus (GO:2001273)	cell surface (GO:0009986)|cytosol (GO:0005829)|endosome (GO:0005768)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|neuronal postsynaptic density (GO:0097481)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)	death receptor activity (GO:0005035)|Rab GTPase binding (GO:0017137)|receptor activity (GO:0004872)|signal transducer activity (GO:0004871)|transmembrane signaling receptor activity (GO:0004888)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(1)|lung(7)|ovary(1)	17	all_cancers(4;1.45e-13)|Breast(4;6.34e-28)|all_epithelial(4;4.95e-17)					TGGTTGTGGGCCTTGTGGCCT	0.582													C|||	1151	0.229832	0.0477	0.3141	5008	,	,		20799	0.0823		0.3231	False		,,,				2504	0.4724				p.G265G		Atlas-SNP	.											NGFR,colon,carcinoma,0,2	NGFR	46	2	0			c.C795T						PASS	.	C		398,4008	197.7+/-221.8	15,368,1820	117.0	104.0	108.0		795	-0.8	1.0	17	dbSNP_120	108	2848,5752	448.3+/-361.8	484,1880,1936	no	coding-synonymous	NGFR	NM_002507.3		499,2248,3756	TT,TC,CC		33.1163,9.0331,24.9577		265/428	47588000	3246,9760	2203	4300	6503	SO:0001819	synonymous_variant	4804	exon4			TGTGGGCCTTGTG	M14764	CCDS11549.1	17q21-q22	2013-05-22	2010-04-28		ENSG00000064300	ENSG00000064300		"""Tumor necrosis factor receptor superfamily"", ""CD molecules"""	7809	protein-coding gene	gene with protein product	"""low affinity nerve growth factor receptor"", ""TNFR superfamily, member 16"""	162010	"""nerve growth factor receptor (TNFR superfamily, member 16)"""			3022937, 3006050	Standard	NM_002507		Approved	TNFRSF16, CD271, p75NTR	uc002ioz.4	P08138	OTTHUMG00000161495	ENST00000172229.3:c.795C>T	17.37:g.47588000C>T		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	159	155	0.974843	NM_002507	B2R961|B4E096	Silent	SNP	ENST00000172229.3	37	CCDS11549.1																																																																																			C|0.763;T|0.237	0.237	strong		0.582	NGFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365150.1		
RHOT2	89941	hgsc.bcm.edu	37	16	718514	718514	+	Silent	SNP	C	C	G	rs7204542	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:718514C>G	ENST00000315082.4	+	3	237	c.123C>G	c.(121-123)acC>acG	p.T41T	RHOT2_ENST00000569943.2_3'UTR	NM_138769.2	NP_620124.1	Q8IXI1	MIRO2_HUMAN	ras homolog family member T2	41	Miro 1.				cellular homeostasis (GO:0019725)|mitochondrial outer membrane permeabilization (GO:0097345)|mitochondrion transport along microtubule (GO:0047497)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of mitochondrial outer membrane (GO:0031307)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)			endometrium(2)|kidney(3)|lung(4)|ovary(1)|pancreas(2)|prostate(1)	13		Hepatocellular(780;0.0218)				AGGAGATCACCATCCCCGCGG	0.766													G|||	2738	0.546725	0.612	0.5461	5008	,	,		11130	0.3175		0.662	False		,,,				2504	0.5767				p.T41T		Atlas-SNP	.											RHOT2,colon,carcinoma,0,3	RHOT2	35	3	0			c.C123G						PASS	.	G		2826,1408		946,934,237	16.0	21.0	19.0		123	0.0	1.0	16	dbSNP_116	19	5819,2627		2024,1771,428	no	coding-synonymous	RHOT2	NM_138769.1		2970,2705,665	GG,GC,CC		31.1035,33.2546,31.8218		41/619	718514	8645,4035	2117	4223	6340	SO:0001819	synonymous_variant	89941	exon3			GATCACCATCCCC	BC014942	CCDS10417.1	16p13.3	2013-01-10	2012-02-27	2004-03-24	ENSG00000140983	ENSG00000140983		"""EF-hand domain containing"""	21169	protein-coding gene	gene with protein product	"""mitochondrial Rho (MIRO) GTPase 2"""	613889	"""chromosome 16 open reading frame 39"", ""ras homolog gene family, member T2"""	C16orf39, ARHT2		12482879	Standard	NM_138769		Approved	MIRO-2	uc002cip.3	Q8IXI1	OTTHUMG00000121139	ENST00000315082.4:c.123C>G	16.37:g.718514C>G		Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	29	29	1	NM_138769	A2IDC2|Q8NF53|Q96C13|Q96S17|Q9BT60|Q9H7M8	Silent	SNP	ENST00000315082.4	37	CCDS10417.1																																																																																			C|0.369;G|0.631	0.631	strong		0.766	RHOT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241617.1	NM_138769	
PXDNL	137902	hgsc.bcm.edu	37	8	52232487	52232487	+	Missense_Mutation	SNP	G	G	T	rs1052704	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:52232487G>T	ENST00000356297.4	-	23	4456	c.4356C>A	c.(4354-4356)gaC>gaA	p.D1452E	PXDNL_ENST00000543296.1_3'UTR|RP11-401H2.1_ENST00000521294.1_RNA	NM_144651.4	NP_653252	A1KZ92	PXDNL_HUMAN	peroxidasin homolog (Drosophila)-like	1452			D -> E (in dbSNP:rs1052704). {ECO:0000269|Ref.2}.		hydrogen peroxide catabolic process (GO:0042744)|oxidation-reduction process (GO:0055114)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	endonuclease activity (GO:0004519)|heme binding (GO:0020037)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)			NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(6)|lung(25)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	48		all_cancers(86;0.107)|Lung NSC(129;0.00641)|all_epithelial(80;0.00716)|all_lung(136;0.015)				GCATTCCTCGGTCTCTGCAAA	0.502													G|||	1565	0.3125	0.6377	0.2118	5008	,	,		15484	0.1111		0.2396	False		,,,				2504	0.227				p.D1452E		Atlas-SNP	.											.	PXDNL	414	.	0			c.C4356A						PASS	.	G	GLU/ASP	2093,1689		584,925,382	56.0	56.0	56.0		4356	-0.1	0.1	8	dbSNP_86	56	2148,6056		297,1554,2251	yes	missense	PXDNL	NM_144651.4	45	881,2479,2633	TT,TG,GG		26.1824,44.6589,35.3829	benign	1452/1464	52232487	4241,7745	1891	4102	5993	SO:0001583	missense	137902	exon23			TCCTCGGTCTCTG		CCDS47855.1	8q11.21-q11.22	2013-02-18	2007-01-12		ENSG00000147485	ENSG00000147485		"""Immunoglobulin superfamily / I-set domain containing"""	26359	protein-coding gene	gene with protein product	"""polysomal ribonuclease 1 homolog (Xenopus)"""	615904	"""peroxidasin homolog-like (Drosophila)"""			22543864	Standard	NM_144651		Approved	FLJ25471, PMR1	uc003xqu.4	A1KZ92	OTTHUMG00000164244	ENST00000356297.4:c.4356C>A	8.37:g.52232487G>T	ENSP00000348645:p.Asp1452Glu	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	88	21	0.238636	NM_144651	B5ME43|B6CGZ3|H0YBM9|Q6ZMR2|Q96LH9	Missense_Mutation	SNP	ENST00000356297.4	37	CCDS47855.1	651|651	0.2980769230769231|0.2980769230769231	311|311	0.6321138211382114|0.6321138211382114	88|88	0.2430939226519337|0.2430939226519337	69|69	0.12062937062937062|0.12062937062937062	183|183	0.24142480211081793|0.24142480211081793	G|G	4.215|4.215	0.038775|0.038775	0.08148|0.08148	0.553411|0.553411	0.261824|0.261824	ENSG00000147485|ENSG00000147485	ENST00000356297|ENST00000522933	T|.	0.64803|.	-0.12|.	4.37|4.37	-0.13|-0.13	0.13498|0.13498	.|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.11313|0.11313	0.125|0.125	0.80722|0.80722	P|P	0.0|0.0	B|.	0.13594|.	0.008|.	B|.	0.09377|.	0.004|.	T|T	0.39375|0.39375	-0.9617|-0.9617	8|4	0.07482|.	T|.	0.82|.	.|.	3.7549|3.7549	0.08581|0.08581	0.4103:0.2151:0.3746:0.0|0.4103:0.2151:0.3746:0.0	rs1052704;rs1052704|rs1052704;rs1052704	1452|.	A1KZ92|.	PXDNL_HUMAN|.	E|N	1452|526	ENSP00000348645:D1452E|.	ENSP00000348645:D1452E|.	D|T	-|-	3|2	2|0	PXDNL|PXDNL	52395040|52395040	0.005000|0.005000	0.15991|0.15991	0.050000|0.050000	0.19076|0.19076	0.002000|0.002000	0.02628|0.02628	-0.186000|-0.186000	0.09670|0.09670	-0.131000|-0.131000	0.11578|0.11578	-0.136000|-0.136000	0.14681|0.14681	GAC|ACC	G|0.688;T|0.312	0.312	strong		0.502	PXDNL-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377905.1	NM_144651	
MUC4	4585	hgsc.bcm.edu	37	3	195510762	195510762	+	Silent	SNP	G	G	A	rs2911273	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195510762G>A	ENST00000463781.3	-	2	8148	c.7689C>T	c.(7687-7689)gtC>gtT	p.V2563V	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Silent_p.V2563V	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.V2563V(2)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		AAGTGTCGGTGACAGGAAGAG	0.582													.|||	2626	0.524361	0.4455	0.4481	5008	,	,		10641	0.7252		0.5129	False		,,,				2504	0.4898				p.V2563V		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,3	MUC4	1505	3	2	Substitution - coding silent(2)	stomach(2)	c.C7689T						PASS	.						48.0	42.0	44.0					3																	195510762		666	1588	2254	SO:0001819	synonymous_variant	4585	exon2			GTCGGTGACAGGA	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.7689C>T	3.37:g.195510762G>A		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	152	41	0.269737	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|0.625;A|0.375	0.375	strong		0.582	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
MUC4	4585	hgsc.bcm.edu	37	3	195515414	195515414	+	Missense_Mutation	SNP	T	T	C	rs200193644|rs71180964	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195515414T>C	ENST00000463781.3	-	2	3496	c.3037A>G	c.(3037-3039)Agc>Ggc	p.S1013G	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.S1013G	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	448	Repeat.|Ser-rich.				cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.S1013_T1028delSPSSVSTGHTTPLPVT(4)|p.S1013G(2)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GAGGAAGGGCTGGTGACAGGA	0.577													.|||	808	0.161342	0.152	0.1124	5008	,	,		17653	0.2321		0.1352	False		,,,				2504	0.1626				p.S1013G		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	6	Deletion - In frame(4)|Substitution - Missense(2)	stomach(6)	c.A3037G						PASS	.						54.0	29.0	36.0					3																	195515414		687	1591	2278	SO:0001583	missense	4585	exon2			AAGGGCTGGTGAC	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.3037A>G	3.37:g.195515414T>C	ENSP00000417498:p.Ser1013Gly	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	72	41	0.569444	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	-	0.269	-0.994094	0.02145	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.33438	1.42;1.41	0.814	-1.63	0.08345	.	.	.	.	.	T	0.11623	0.0283	N	0.19112	0.55	0.09310	N	1	P	0.42584	0.784	B	0.28638	0.092	T	0.12041	-1.0563	8	.	.	.	.	2.4902	0.04608	0.3389:0.3247:0.0:0.3364	.	1013	E7ESK3	.	G	1013	ENSP00000417498:S1013G;ENSP00000420243:S1013G	.	S	-	1	0	MUC4	196999809	.	.	0.000000	0.03702	0.012000	0.07955	.	.	-3.949000	0.00088	-2.075000	0.00382	AGC	T|0.963;C|0.037	0.037	strong		0.577	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
DIRAS1	148252	hgsc.bcm.edu	37	19	2717513	2717513	+	Missense_Mutation	SNP	C	C	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:2717513C>G	ENST00000323469.4	-	2	475	c.292G>C	c.(292-294)Ggg>Cgg	p.G98R	DIRAS1_ENST00000585334.1_Missense_Mutation_p.G98R	NM_145173.3	NP_660156.1	O95057	DIRA1_HUMAN	DIRAS family, GTP-binding RAS-like 1	98					GTP catabolic process (GO:0006184)|small GTPase mediated signal transduction (GO:0007264)	plasma membrane (GO:0005886)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			kidney(1)|lung(2)|ovary(2)|prostate(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)		TAGATGGGCCCCAGCTCCTCC	0.627																																					p.G98R		Atlas-SNP	.											.	DIRAS1	26	.	0			c.G292C						PASS	.						45.0	40.0	41.0					19																	2717513		2203	4297	6500	SO:0001583	missense	148252	exon2			TGGGCCCCAGCTC	BC030660	CCDS12092.1	19p13.3	2014-05-09				ENSG00000176490			19127	protein-coding gene	gene with protein product		607862				12107278	Standard	NM_145173		Approved	Di-Ras1, GBTS1, RIG	uc002lwf.3	O95057		ENST00000323469.4:c.292G>C	19.37:g.2717513C>G	ENSP00000325836:p.Gly98Arg	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	71	21	0.295775	NM_145173		Missense_Mutation	SNP	ENST00000323469.4	37	CCDS12092.1	.	.	.	.	.	.	.	.	.	.	C	9.401	1.078074	0.20227	.	.	ENSG00000176490	ENST00000323469	T	0.75477	-0.94	4.07	-0.695	0.11291	Small GTP-binding protein domain (1);	0.169303	0.49305	D	0.000145	T	0.42017	0.1184	N	0.04245	-0.25	0.26980	N	0.965374	B	0.02656	0.0	B	0.06405	0.002	T	0.17745	-1.0359	10	0.20519	T	0.43	.	3.7079	0.08408	0.0:0.3451:0.3048:0.35	.	98	O95057	DIRA1_HUMAN	R	98	ENSP00000325836:G98R	ENSP00000325836:G98R	G	-	1	0	DIRAS1	2668513	1.000000	0.71417	1.000000	0.80357	0.743000	0.42351	1.026000	0.30103	0.692000	0.31613	0.549000	0.68633	GGG	.	.	none		0.627	DIRAS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451350.1		
GRM6	2916	hgsc.bcm.edu	37	5	178413947	178413947	+	Silent	SNP	T	T	C	rs11746675	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:178413947T>C	ENST00000517717.1	-	8	1430	c.1392A>G	c.(1390-1392)ggA>ggG	p.G464G	RP11-281O15.4_ENST00000519491.1_RNA|GRM6_ENST00000231188.5_Silent_p.G464G			O15303	GRM6_HUMAN	glutamate receptor, metabotropic 6	464					adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|detection of light stimulus involved in visual perception (GO:0050908)|detection of visible light (GO:0009584)|G-protein coupled glutamate receptor signaling pathway (GO:0007216)|locomotory behavior (GO:0007626)|positive regulation of calcium ion import (GO:0090280)|regulation of synaptic transmission, glutamatergic (GO:0051966)|retina development in camera-type eye (GO:0060041)|synaptic transmission (GO:0007268)	cell projection (GO:0042995)|endoplasmic reticulum membrane (GO:0005789)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|new growing cell tip (GO:0035841)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)|group III metabotropic glutamate receptor activity (GO:0001642)|protein homodimerization activity (GO:0042803)			NS(2)|breast(4)|endometrium(9)|large_intestine(12)|lung(21)|ovary(2)|pancreas(1)|prostate(3)|urinary_tract(1)	55	all_cancers(89;0.000828)|Renal(175;0.000159)|all_epithelial(37;0.000167)|Lung NSC(126;0.00199)|all_lung(126;0.00351)	all_cancers(40;0.0156)|all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.245)		CGGGCGCATCTCCGTTCTCGT	0.647													T|||	2682	0.535543	0.3971	0.6066	5008	,	,		17555	0.5863		0.6382	False		,,,				2504	0.5143				p.G464G		Atlas-SNP	.											.	GRM6	149	.	0			c.A1392G						PASS	.	T		1911,2495	546.7+/-377.1	419,1073,711	72.0	60.0	64.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1392	-2.8	0.8	5	dbSNP_120	64	5482,3118	653.9+/-401.1	1739,2004,557	yes	coding-synonymous	GRM6	NM_000843.3		2158,3077,1268	CC,CT,TT		36.2558,43.3727,43.157		464/878	178413947	7393,5613	2203	4300	6503	SO:0001819	synonymous_variant	2916	exon7			CGCATCTCCGTTC	U82083	CCDS4442.1	5q35	2014-01-28						"""GPCR / Class C : Glutamate receptors, metabotropic"", ""Glutamate receptors"""	4598	protein-coding gene	gene with protein product		604096				9215706	Standard	NM_000843		Approved	GPRC1F, mGlu6, MGLUR6, CSNB1B	uc003mjr.3	O15303	OTTHUMG00000130889	ENST00000517717.1:c.1392A>G	5.37:g.178413947T>C		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	97	97	1	NM_000843		Silent	SNP	ENST00000517717.1	37	CCDS4442.1																																																																																			T|0.434;C|0.566	0.566	strong		0.647	GRM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253474.2		
KLF17	128209	hgsc.bcm.edu	37	1	44595047	44595047	+	Missense_Mutation	SNP	T	T	A	rs11210969	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:44595047T>A	ENST00000372299.3	+	2	162	c.104T>A	c.(103-105)aTc>aAc	p.I35N	KLF17_ENST00000476802.1_3'UTR	NM_173484.3	NP_775755.3	Q5JT82	KLF17_HUMAN	Kruppel-like factor 17	35			I -> N (in dbSNP:rs11210969). {ECO:0000269|PubMed:14702039}.		gamete generation (GO:0007276)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)	p.I35N(1)		NS(1)|breast(2)|central_nervous_system(1)|large_intestine(1)|lung(6)|ovary(3)|prostate(1)|skin(2)|stomach(1)	18	Acute lymphoblastic leukemia(166;0.155)					TCAGCGCCCATCTTGAACATG	0.498													T|||	1089	0.217452	0.121	0.255	5008	,	,		18875	0.2044		0.2962	False		,,,				2504	0.2536				p.I35N		Atlas-SNP	.											KLF17,NS,carcinoma,0,1	KLF17	92	1	1	Substitution - Missense(1)	stomach(1)	c.T104A						PASS	.	T	ASN/ILE	645,3761	276.0+/-272.9	56,533,1614	126.0	118.0	120.0		104	1.2	0.0	1	dbSNP_120	120	2509,6091	411.2+/-350.4	361,1787,2152	yes	missense	KLF17	NM_173484.3	149	417,2320,3766	AA,AT,TT		29.1744,14.6391,24.2503	benign	35/390	44595047	3154,9852	2203	4300	6503	SO:0001583	missense	128209	exon2			CGCCCATCTTGAA	BC049844	CCDS508.1	1p34.1	2011-11-15	2006-02-17	2006-02-17	ENSG00000171872	ENSG00000171872		"""Zinc fingers, C2H2-type"", ""Kruppel-like transcription factors"""	18830	protein-coding gene	gene with protein product		609602	"""zinc finger protein 393"""	ZNF393		16460907	Standard	NM_173484		Approved	Zfp393, FLJ40160	uc001clp.3	Q5JT82	OTTHUMG00000009664	ENST00000372299.3:c.104T>A	1.37:g.44595047T>A	ENSP00000361373:p.Ile35Asn	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	112	51	0.455357	NM_173484	Q86VQ7|Q8N805	Missense_Mutation	SNP	ENST00000372299.3	37	CCDS508.1	502	0.22985347985347984	60	0.12195121951219512	91	0.2513812154696133	125	0.21853146853146854	226	0.29815303430079154	T	8.842	0.942534	0.18281	0.146391	0.291744	ENSG00000171872	ENST00000372299	T	0.13420	2.59	4.78	1.18	0.20946	.	1.018550	0.07854	N	0.965188	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	P	0.45902	0.868	B	0.42851	0.4	T	0.45600	-0.9250	9	0.54805	T	0.06	.	3.9088	0.09194	0.0:0.1891:0.1838:0.6271	rs11210969;rs17381026;rs52807679;rs56504303;rs11210969	35	Q5JT82	KLF17_HUMAN	N	35	ENSP00000361373:I35N	ENSP00000361373:I35N	I	+	2	0	KLF17	44367634	0.001000	0.12720	0.000000	0.03702	0.014000	0.08584	0.624000	0.24462	0.189000	0.20188	-0.263000	0.10527	ATC	T|0.767;A|0.233	0.233	strong		0.498	KLF17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026646.1	NM_173484	
USP40	55230	hgsc.bcm.edu	37	2	234442134	234442134	+	Missense_Mutation	SNP	G	G	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:234442134G>C	ENST00000427112.2	-	10	1494	c.1459C>G	c.(1459-1461)Ccc>Gcc	p.P487A	USP40_ENST00000450966.1_Missense_Mutation_p.P499A|USP40_ENST00000251722.6_Missense_Mutation_p.P487A			Q9NVE5	UBP40_HUMAN	ubiquitin specific peptidase 40	487					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)		CCTTCAGGGGGTCTCTGCAAC	0.348																																					p.P499A		Atlas-SNP	.											.	USP40	174	.	0			c.C1495G						PASS	.						101.0	97.0	98.0					2																	234442134		1836	4076	5912	SO:0001583	missense	55230	exon10			CAGGGGGTCTCTG	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.1459C>G	2.37:g.234442134G>C	ENSP00000387898:p.Pro487Ala	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	125	32	0.256	NM_018218	Q6NX38|Q70EL0	Missense_Mutation	SNP	ENST00000427112.2	37	CCDS46547.1	.	.	.	.	.	.	.	.	.	.	G	21.8	4.207921	0.79240	.	.	ENSG00000085982	ENST00000450966;ENST00000251722;ENST00000427112	T;T;T	0.05513	3.43;3.43;3.43	5.23	5.23	0.72850	.	0.763029	0.12385	N	0.473527	T	0.26955	0.0660	M	0.74258	2.255	0.80722	D	1	D;D	0.71674	0.997;0.998	P;D	0.68039	0.904;0.955	T	0.00567	-1.1667	10	0.40728	T	0.16	.	18.8586	0.92264	0.0:0.0:1.0:0.0	.	487;499	Q9NVE5;Q9NVE5-3	UBP40_HUMAN;.	A	499;487;487	ENSP00000415434:P499A;ENSP00000251722:P487A;ENSP00000387898:P487A	ENSP00000251722:P487A	P	-	1	0	USP40	234106873	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	9.406000	0.97321	2.458000	0.83093	0.586000	0.80456	CCC	.	.	none		0.348	USP40-017	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000397235.1	XM_114294	
KCNH6	81033	hgsc.bcm.edu	37	17	61623052	61623052	+	Missense_Mutation	SNP	C	C	T	rs35819807	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:61623052C>T	ENST00000583023.1	+	14	2785	c.2774C>T	c.(2773-2775)aCg>aTg	p.T925M	KCNH6_ENST00000456941.2_Missense_Mutation_p.T836M|KCNH6_ENST00000581784.1_Missense_Mutation_p.T836M|KCNH6_ENST00000314672.5_Missense_Mutation_p.T889M	NM_030779.2	NP_110406.1	Q9H252	KCNH6_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 6	925			T -> M (in dbSNP:rs35819807). {ECO:0000269|PubMed:14702039}.		potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	signal transducer activity (GO:0004871)|voltage-gated potassium channel activity (GO:0005249)			breast(2)|central_nervous_system(2)|endometrium(9)|kidney(4)|large_intestine(6)|lung(20)|ovary(2)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	54					Doxazosin(DB00590)|Ibutilide(DB00308)|Miconazole(DB01110)|Prazosin(DB00457)|Terazosin(DB01162)	GCTGTGGCAACGGACAAAACT	0.567													C|||	701	0.139976	0.1626	0.1052	5008	,	,		18935	0.0367		0.2485	False		,,,				2504	0.1288				p.T925M		Atlas-SNP	.											.	KCNH6	122	.	0			c.C2774T						PASS	.	C	MET/THR,MET/THR	723,3683	298.4+/-285.3	64,595,1544	102.0	91.0	95.0		2774,2507	-7.6	0.0	17	dbSNP_126	95	2122,6478	366.0+/-334.1	277,1568,2455	yes	missense,missense	KCNH6	NM_030779.2,NM_173092.1	81,81	341,2163,3999	TT,TC,CC		24.6744,16.4094,21.8745	benign,benign	925/995,836/906	61623052	2845,10161	2203	4300	6503	SO:0001583	missense	81033	exon14			TGGCAACGGACAA	AF311913	CCDS11638.1, CCDS11639.1, CCDS62290.1	17q23.3	2012-07-05				ENSG00000173826		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	18862	protein-coding gene	gene with protein product		608168				16382104	Standard	NM_030779		Approved	Kv11.2, erg2, HERG2	uc002jay.3	Q9H252		ENST00000583023.1:c.2774C>T	17.37:g.61623052C>T	ENSP00000463533:p.Thr925Met	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	48	26	0.541667	NM_030779	Q9BRD7	Missense_Mutation	SNP	ENST00000583023.1	37	CCDS11638.1	343	0.15705128205128205	86	0.17479674796747968	45	0.12430939226519337	22	0.038461538461538464	190	0.25065963060686014	C	9.316	1.056938	0.19907	0.164094	0.246744	ENSG00000173826	ENST00000314672;ENST00000456941	D	0.99220	-5.58	5.02	-7.62	0.01294	.	1.666530	0.04760	N	0.426110	T	0.00356	0.0011	N	0.16478	0.41	0.80722	P	0.0	B;B;B	0.14012	0.007;0.003;0.009	B;B;B	0.09377	0.003;0.004;0.002	T	0.73575	-0.3939	9	0.30078	T	0.28	.	6.9583	0.24583	0.0995:0.493:0.2976:0.1098	rs35819807	889;836;925	B4DKC0;Q9H252-2;Q9H252	.;.;KCNH6_HUMAN	M	925;836	ENSP00000396900:T836M	ENSP00000318212:T925M	T	+	2	0	KCNH6	58976784	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.188000	0.17018	-1.025000	0.03334	-1.092000	0.02172	ACG	C|0.804;T|0.196	0.196	strong		0.567	KCNH6-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443853.1	NM_030779	
BPIFB2	80341	hgsc.bcm.edu	37	20	31596472	31596472	+	Missense_Mutation	SNP	A	A	T	rs6088066	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:31596472A>T	ENST00000170150.3	+	2	287	c.92A>T	c.(91-93)aAg>aTg	p.K31M		NM_025227.1	NP_079503.1	Q8N4F0	BPIB2_HUMAN	BPI fold containing family B, member 2	31			K -> M (in dbSNP:rs6088066).			extracellular vesicular exosome (GO:0070062)	lipid binding (GO:0008289)										CGACTCAACAAGGCAGCATTG	0.602													A|||	685	0.136781	0.1641	0.1527	5008	,	,		20203	0.0089		0.2406	False		,,,				2504	0.1135				p.K31M		Atlas-SNP	.											.	.	.	.	0			c.A92T						PASS	.	A	MET/LYS	801,3605	297.3+/-284.7	74,653,1476	67.0	54.0	58.0		92	-0.2	0.2	20	dbSNP_114	58	1920,6678	305.7+/-307.6	206,1508,2585	yes	missense	BPIFB2	NM_025227.1	95	280,2161,4061	TT,TA,AA		22.3308,18.1798,20.9243	possibly-damaging	31/459	31596472	2721,10283	2203	4299	6502	SO:0001583	missense	80341	exon2			TCAACAAGGCAGC	AF465765	CCDS13210.1	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000078898	ENSG00000078898		"""BPI fold containing"""	16177	protein-coding gene	gene with protein product		614108	"""bactericidal/permeability-increasing protein-like 1"""	C20orf184, BPIL1		12185532, 21787333	Standard	NM_025227		Approved	dJ726C3.2, LPLUNC2	uc002wyj.4	Q8N4F0	OTTHUMG00000032232	ENST00000170150.3:c.92A>T	20.37:g.31596472A>T	ENSP00000170150:p.Lys31Met	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	134	68	0.507463	NM_025227	Q6UWN3|Q6ZME0|Q8NFQ7	Missense_Mutation	SNP	ENST00000170150.3	37	CCDS13210.1	336	0.15384615384615385	87	0.17682926829268292	66	0.18232044198895028	3	0.005244755244755245	180	0.23746701846965698	A	17.05	3.290903	0.59976	0.181798	0.223308	ENSG00000078898	ENST00000170150	T	0.05447	3.44	5.17	-0.229	0.13094	.	1.213840	0.05841	N	0.619432	T	0.00012	0.0000	L	0.27053	0.805	0.80722	P	0.0	B	0.26002	0.139	B	0.19946	0.027	T	0.48445	-0.9035	9	0.31617	T	0.26	-0.6592	3.7776	0.08667	0.5174:0.0:0.3235:0.1591	rs6088066;rs17372659;rs52836575;rs6088066	31	Q8N4F0	BPIB2_HUMAN	M	31	ENSP00000170150:K31M	ENSP00000170150:K31M	K	+	2	0	BPIFB2	31060133	0.259000	0.24043	0.152000	0.22495	0.471000	0.32888	0.371000	0.20450	-0.154000	0.11118	0.528000	0.53228	AAG	A|0.820;T|0.180	0.180	strong		0.602	BPIFB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078652.2	NM_025227	
GJD2	57369	hgsc.bcm.edu	37	15	35045057	35045057	+	Silent	SNP	G	G	A	rs3743123	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:35045057G>A	ENST00000290374.4	-	2	1064	c.588C>T	c.(586-588)tcC>tcT	p.S196S	RP11-814P5.1_ENST00000503496.1_RNA|RP11-814P5.1_ENST00000558707.1_RNA	NM_020660.2	NP_065711.1	Q9UKL4	CXD2_HUMAN	gap junction protein, delta 2, 36kDa	196					action potential (GO:0001508)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|visual perception (GO:0007601)	connexon complex (GO:0005922)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	gap junction channel activity (GO:0005243)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(10)|ovary(1)|pancreas(1)|urinary_tract(1)	19		all_lung(180;9.67e-07)		all cancers(64;2.75e-18)|GBM - Glioblastoma multiforme(113;1.9e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0156)		TGTAGAAGCGGGAGATGCCTT	0.483													G|||	1547	0.308906	0.2897	0.3184	5008	,	,		19922	0.255		0.2922	False		,,,				2504	0.4008				p.S196S		Atlas-SNP	.											.	GJD2	49	.	0			c.C588T	GRCh37	CM041873	GJD2	M	rs3743123	PASS	.	G		1356,3046	449.4+/-349.0	204,948,1049	119.0	125.0	123.0		588	2.1	1.0	15	dbSNP_107	123	2653,5943	426.5+/-355.3	397,1859,2042	no	coding-synonymous	GJD2	NM_020660.1		601,2807,3091	AA,AG,GG		30.8632,30.8042,30.8432		196/322	35045057	4009,8989	2201	4298	6499	SO:0001819	synonymous_variant	57369	exon2			GAAGCGGGAGATG	AB037509	CCDS10040.1	15q13.1	2008-02-04	2007-11-06	2007-11-06	ENSG00000159248	ENSG00000159248		"""Ion channels / Gap junction proteins (connexins)"""	19154	protein-coding gene	gene with protein product	"""connexin 36"""	607058	"""gap junction protein, alpha 9, 36kDa"""	GJA9		10462698	Standard	NM_020660		Approved	CX36	uc001zis.2	Q9UKL4	OTTHUMG00000129674	ENST00000290374.4:c.588C>T	15.37:g.35045057G>A		Somatic	247	1	0.00404858		WXS	Illumina HiSeq	Phase_I	161	73	0.453416	NM_020660	Q2M241|Q9P2R0	Silent	SNP	ENST00000290374.4	37	CCDS10040.1																																																																																			G|0.695;A|0.305	0.305	strong		0.483	GJD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251875.2		
CPAMD8	27151	hgsc.bcm.edu	37	19	17091368	17091368	+	Silent	SNP	T	T	G	rs8103646	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	99	0	0		WXS	Illumina HiSeq	Phase_I	80	80	1	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	
IGSF3	3321	hgsc.bcm.edu	37	1	117158745	117158745	+	Missense_Mutation	SNP	A	A	C	rs373093989		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:117158745A>C	ENST00000369486.3	-	3	1143	c.378T>G	c.(376-378)gaT>gaG	p.D126E	IGSF3_ENST00000369483.1_Missense_Mutation_p.D126E|IGSF3_ENST00000318837.6_Missense_Mutation_p.D126E	NM_001007237.1	NP_001007238.1	O75054	IGSF3_HUMAN	immunoglobulin superfamily, member 3	126	Ig-like C2-type 1.				lacrimal gland development (GO:0032808)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)		p.D126E(1)		NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(31)|ovary(4)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	62	Lung SC(450;0.225)	all_cancers(81;1.24e-06)|all_epithelial(167;4.85e-07)|all_lung(203;1.66e-06)|Lung NSC(69;1.11e-05)		Lung(183;0.0142)|Colorectal(144;0.0929)|LUSC - Lung squamous cell carcinoma(189;0.108)|COAD - Colon adenocarcinoma(174;0.139)|all cancers(265;0.159)|Epithelial(280;0.166)		AGTATTGCTTATCAGTGCTGG	0.498																																					p.D126E		Atlas-SNP	.											IGSF3,extremity,malignant_melanoma,0,1	IGSF3	294	1	1	Substitution - Missense(1)	skin(1)	c.T378G						scavenged	.						61.0	55.0	57.0					1																	117158745		2203	4300	6503	SO:0001583	missense	3321	exon3			TTGCTTATCAGTG	AF031174	CCDS30813.1, CCDS30814.1	1p13	2013-01-29			ENSG00000143061	ENSG00000143061		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5950	protein-coding gene	gene with protein product		603491				9790749	Standard	NM_001007237		Approved	V8, EWI-3, MGC117164	uc031pnr.1	O75054	OTTHUMG00000022751	ENST00000369486.3:c.378T>G	1.37:g.117158745A>C	ENSP00000358498:p.Asp126Glu	Somatic	292	14	0.0479452		WXS	Illumina HiSeq	Phase_I	216	8	0.037037	NM_001542	A6NJZ6|A6NMC7	Missense_Mutation	SNP	ENST00000369486.3	37	CCDS30813.1	.	.	.	.	.	.	.	.	.	.	A	8.319	0.823848	0.16678	.	.	ENSG00000143061	ENST00000369486;ENST00000369483;ENST00000318837	T;T;T	0.65364	-0.15;-0.15;-0.15	4.63	-8.69	0.00855	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.109427	0.64402	N	0.000011	T	0.34250	0.0891	M	0.69523	2.12	0.30895	N	0.729963	B;B	0.10296	0.003;0.002	B;B	0.20384	0.015;0.029	T	0.06481	-1.0824	10	0.66056	D	0.02	-9.8434	10.4193	0.44341	0.1981:0.2275:0.5744:0.0	.	126;126	O75054;A6NJZ6	IGSF3_HUMAN;.	E	126	ENSP00000358498:D126E;ENSP00000358495:D126E;ENSP00000321184:D126E	ENSP00000321184:D126E	D	-	3	2	IGSF3	116960268	0.000000	0.05858	0.000000	0.03702	0.048000	0.14542	-2.110000	0.01334	-1.801000	0.01245	0.454000	0.30748	GAT	.	.	none		0.498	IGSF3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000059040.1	NM_001542	
MYH8	4626	hgsc.bcm.edu	37	17	10310246	10310246	+	Silent	SNP	G	G	A	rs12936716	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:10310246G>A	ENST00000403437.2	-	18	2110	c.2016C>T	c.(2014-2016)ttC>ttT	p.F672F	CTC-297N7.11_ENST00000587182.2_RNA|RP11-799N11.1_ENST00000399342.2_RNA|RP11-799N11.1_ENST00000581304.1_RNA	NM_002472.2	NP_002463.2	P13535	MYH8_HUMAN	myosin, heavy chain 8, skeletal muscle, perinatal	672	Actin-binding.|Myosin motor.				ATP catabolic process (GO:0006200)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|skeletal muscle contraction (GO:0003009)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|sarcomere (GO:0030017)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)|myosin light chain binding (GO:0032027)|structural constituent of muscle (GO:0008307)			NS(3)|breast(8)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(61)|ovary(3)|prostate(3)|skin(10)|upper_aerodigestive_tract(2)|urinary_tract(2)	134						TACACCGTACGAAGTGAGGGT	0.383									Trismus-Pseudocamptodactyly Syndrome with Cardiac Myxoma and Freckling				G|||	280	0.0559105	0.0393	0.0346	5008	,	,		19874	0.0308		0.0517	False		,,,				2504	0.1237				p.F672F		Atlas-SNP	.											.	MYH8	346	.	0			c.C2016T						PASS	.	G		194,4212	121.7+/-159.2	4,186,2013	96.0	88.0	91.0		2016	-7.3	0.9	17	dbSNP_121	91	524,8076	146.6+/-202.2	16,492,3792	no	coding-synonymous	MYH8	NM_002472.2		20,678,5805	AA,AG,GG		6.093,4.4031,5.5205		672/1938	10310246	718,12288	2203	4300	6503	SO:0001819	synonymous_variant	4626	exon18	Familial Cancer Database	Carney Complex Variant	CCGTACGAAGTGA		CCDS11153.1	17p13.1	2013-09-19	2006-09-29		ENSG00000133020	ENSG00000133020		"""Myosins / Myosin superfamily : Class II"""	7578	protein-coding gene	gene with protein product		160741	"""myosin, heavy polypeptide 8, skeletal muscle, perinatal"""			2373371	Standard	NM_002472		Approved	MyHC-peri, MyHC-pn	uc002gmm.2	P13535	OTTHUMG00000130361	ENST00000403437.2:c.2016C>T	17.37:g.10310246G>A		Somatic	249	0	0		WXS	Illumina HiSeq	Phase_I	195	95	0.487179	NM_002472	Q14910	Silent	SNP	ENST00000403437.2	37	CCDS11153.1																																																																																			G|0.945;A|0.055	0.055	strong		0.383	MYH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252724.2	NM_002472	
NTAN1	123803	hgsc.bcm.edu	37	16	15131974	15131974	+	Missense_Mutation	SNP	G	G	T	rs1136001	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:15131974G>T	ENST00000287706.3	-	10	939	c.847C>A	c.(847-849)Cac>Aac	p.H283N	PDXDC1_ENST00000535621.2_Intron	NM_001270766.1|NM_173474.3	NP_001257695.1|NP_775745.1	Q96AB6	NTAN1_HUMAN	N-terminal asparagine amidase	283			H -> N (in dbSNP:rs1136001).		adult locomotory behavior (GO:0008344)|memory (GO:0007613)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein-N-terminal asparagine amidohydrolase activity (GO:0008418)			endometrium(1)|large_intestine(4)|lung(3)	8						AACAGTGTGTGAGCTGGAGAT	0.383													T|||	1719	0.343251	0.1838	0.5331	5008	,	,		17380	0.3661		0.3072	False		,,,				2504	0.4376				p.H283N		Atlas-SNP	.											.	NTAN1	21	.	0			c.C847A						PASS	.	T	ASN/HIS	992,3402	725.7+/-409.6	118,756,1323	79.0	80.0	80.0	http://www.ncbi.nlm.nih.gov/pubmed?term	847	1.8	0.0	16	dbSNP_86	80	2583,6017	688.7+/-404.3	358,1867,2075	yes	missense	NTAN1	NM_173474.2	68	476,2623,3398	TT,TG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	30.0349,22.5762,27.5127	benign	283/311	15131974	3575,9419	2197	4300	6497	SO:0001583	missense	123803	exon10			GTGTGTGAGCTGG	AF092440	CCDS10558.1, CCDS73832.1	16p13	2008-02-05			ENSG00000157045	ENSG00000157045			29909	protein-coding gene	gene with protein product		615367				8910481	Standard	NM_173474		Approved		uc002ddd.4	Q96AB6	OTTHUMG00000129849	ENST00000287706.3:c.847C>A	16.37:g.15131974G>T	ENSP00000287706:p.His283Asn	Somatic	178	1	0.00561798		WXS	Illumina HiSeq	Phase_I	112	80	0.714286	NM_173474	Q7Z4Z0	Missense_Mutation	SNP	ENST00000287706.3	37	CCDS10558.1	727	0.33287545787545786	94	0.1910569105691057	174	0.48066298342541436	216	0.3776223776223776	243	0.32058047493403696	T	1.619	-0.522108	0.04171	0.225762	0.300349	ENSG00000157045	ENST00000287706	T	0.27720	1.65	5.35	1.84	0.25277	.	0.385250	0.30565	N	0.009345	T	0.00012	0.0000	N	0.01576	-0.805	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.47355	-0.9124	9	0.17369	T	0.5	-18.7544	6.9113	0.24336	0.0:0.1394:0.3861:0.4745	rs1136001;rs3199049;rs16966957;rs52834819;rs58508909;rs1136001	283	Q96AB6	NTAN1_HUMAN	N	283	ENSP00000287706:H283N	ENSP00000287706:H283N	H	-	1	0	NTAN1	15039475	0.000000	0.05858	0.000000	0.03702	0.756000	0.42949	0.598000	0.24074	-0.026000	0.13895	-1.131000	0.01979	CAC	G|0.706;T|0.294	0.294	strong		0.383	NTAN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252089.1	NM_173474	
STAG2	10735	hgsc.bcm.edu	37	X	123176493	123176493	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:123176493G>A	ENST00000371160.1	+	7	750	c.460G>A	c.(460-462)Gag>Aag	p.E154K	STAG2_ENST00000354548.5_Missense_Mutation_p.E85K|STAG2_ENST00000469481.1_Intron|STAG2_ENST00000371157.3_Missense_Mutation_p.E154K|STAG2_ENST00000371144.3_Missense_Mutation_p.E154K|STAG2_ENST00000218089.9_Missense_Mutation_p.E154K|STAG2_ENST00000371145.3_Missense_Mutation_p.E154K	NM_001282418.1	NP_001269347.1	Q8N3U4	STAG2_HUMAN	stromal antigen 2	154					meiotic nuclear division (GO:0007126)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of DNA endoreduplication (GO:0032876)|sister chromatid cohesion (GO:0007062)|stem cell maintenance (GO:0019827)	actin cytoskeleton (GO:0015629)|chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	chromatin binding (GO:0003682)			breast(5)|central_nervous_system(4)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(9)|lung(21)|ovary(5)|prostate(2)|skin(5)|urinary_tract(4)	78						AGAATTCGATGAGGTAACTTA	0.323																																					p.E154K		Atlas-SNP	.											.	STAG2	309	.	0			c.G460A						PASS	.						78.0	73.0	74.0					X																	123176493		2203	4300	6503	SO:0001583	missense	10735	exon7			TTCGATGAGGTAA	Z75331	CCDS14607.1, CCDS43990.1	Xq25	2014-09-17			ENSG00000101972	ENSG00000101972			11355	protein-coding gene	gene with protein product		300826				9305759	Standard	NM_001042750		Approved	SA-2, SCC3B	uc004eua.3	Q8N3U4	OTTHUMG00000022725	ENST00000371160.1:c.460G>A	X.37:g.123176493G>A	ENSP00000360202:p.Glu154Lys	Somatic	446	1	0.00224215		WXS	Illumina HiSeq	Phase_I	257	68	0.264591	NM_001042749	B1AMT5|D3DTF5|O00540|Q5JTI6|Q68DE9|Q9H1N8	Missense_Mutation	SNP	ENST00000371160.1	37	CCDS14607.1	.	.	.	.	.	.	.	.	.	.	G	35	5.463084	0.96257	.	.	ENSG00000101972	ENST00000218089;ENST00000455404;ENST00000354548;ENST00000371160;ENST00000435103;ENST00000371157;ENST00000371145;ENST00000371144;ENST00000428941;ENST00000435215	T;T;T;T;T;T;T;T	0.48522	0.81;0.81;0.81;0.81;0.81;0.81;0.81;0.81	5.74	5.74	0.90152	STAG (1);	0.000000	0.85682	D	0.000000	T	0.75087	0.3802	M	0.92077	3.27	0.80722	D	1	D;D	0.55605	0.966;0.972	P;P	0.61940	0.747;0.896	T	0.79264	-0.1875	10	0.44086	T	0.13	-12.9428	18.9534	0.92649	0.0:0.0:1.0:0.0	.	154;154	Q8N3U4-2;Q8N3U4	.;STAG2_HUMAN	K	154;154;85;154;154;154;154;154;154;154	ENSP00000218089:E154K;ENSP00000397265:E154K;ENSP00000346555:E85K;ENSP00000360202:E154K;ENSP00000360199:E154K;ENSP00000360187:E154K;ENSP00000360186:E154K;ENSP00000392118:E154K	ENSP00000218089:E154K	E	+	1	0	STAG2	123004174	1.000000	0.71417	1.000000	0.80357	0.878000	0.50629	9.740000	0.98839	2.425000	0.82216	0.522000	0.50473	GAG	.	.	none		0.323	STAG2-018	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000156159.2	NM_006603	
LRIT1	26103	hgsc.bcm.edu	37	10	85993910	85993910	+	Silent	SNP	G	G	A	rs3814206	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:85993910G>A	ENST00000372105.3	-	3	835	c.814C>T	c.(814-816)Ctg>Ttg	p.L272L		NM_015613.2	NP_056428.1	Q9P2V4	LRIT1_HUMAN	leucine-rich repeat, immunoglobulin-like and transmembrane domains 1	272	Ig-like C2-type.					integral component of endoplasmic reticulum membrane (GO:0030176)				breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(13)|skin(1)	23						CAGCGTAGCAGTGCTGTGCCA	0.612													A|||	2867	0.572484	0.8941	0.5418	5008	,	,		18907	0.4058		0.4722	False		,,,				2504	0.4346				p.L272L		Atlas-SNP	.											.	LRIT1	73	.	0			c.C814T						PASS	.	A		3585,821	327.5+/-300.1	1468,649,86	71.0	69.0	70.0		814	-5.1	0.0	10	dbSNP_107	70	3877,4723	607.6+/-395.3	903,2071,1326	no	coding-synonymous	LRIT1	NM_015613.2		2371,2720,1412	AA,AG,GG		45.0814,18.6337,42.6265		272/624	85993910	7462,5544	2203	4300	6503	SO:0001819	synonymous_variant	26103	exon3			GTAGCAGTGCTGT	AB031547	CCDS7373.1	10q23	2013-02-11	2007-06-19	2007-06-19	ENSG00000148602	ENSG00000148602		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	23404	protein-coding gene	gene with protein product	"""fibronectin type III, immunoglobulin and leucine rich repeat domains 9"""		"""leucine rich repeat containing 21"""	LRRC21		10777785	Standard	NM_015613		Approved	PAL, DKFZP434K091, FIGLER9	uc001kcz.1	Q9P2V4	OTTHUMG00000018632	ENST00000372105.3:c.814C>T	10.37:g.85993910G>A		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	62	62	1	NM_015613	Q0QD41|Q9Y4N7	Silent	SNP	ENST00000372105.3	37	CCDS7373.1																																																																																			G|0.431;A|0.569	0.569	strong		0.612	LRIT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049109.1	NM_015613	
POTEC	388468	hgsc.bcm.edu	37	18	14542693	14542693	+	Silent	SNP	C	C	T	rs371316587		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:14542693C>T	ENST00000358970.5	-	1	452	c.453G>A	c.(451-453)aaG>aaA	p.K151K	POTEC_ENST00000389891.4_5'UTR	NM_001137671.1	NP_001131143.1	B2RU33	POTEC_HUMAN	POTE ankyrin domain family, member C	151								p.K151K(2)		NS(2)|breast(1)|endometrium(9)|kidney(13)|lung(14)|prostate(3)|skin(6)|soft_tissue(1)|urinary_tract(3)	52						TTCTGGGGACCTTACCCCACC	0.592																																					p.K151K		Atlas-SNP	.											POTEC,NS,carcinoma,0,4	POTEC	129	4	2	Substitution - coding silent(2)	lung(1)|endometrium(1)	c.G453A						scavenged	.						172.0	158.0	163.0					18																	14542693		692	1591	2283	SO:0001819	synonymous_variant	388468	exon1			GGGGACCTTACCC	BX649118	CCDS45835.1	18p11.21	2013-01-10	2008-11-26	2008-11-26	ENSG00000183206	ENSG00000183206		"""POTE ankyrin domain containing"", ""Ankyrin repeat domain containing"""	33894	protein-coding gene	gene with protein product	"""cancer/testis antigen family 104, member 6"""		"""ANKRD26-like family B, member 2"""	A26B2			Standard	NM_001137671		Approved	POTE18, POTE-18, DKFZp686J0529, CT104.6	uc010dln.3	B2RU33	OTTHUMG00000162963	ENST00000358970.5:c.453G>A	18.37:g.14542693C>T		Somatic	393	0	0		WXS	Illumina HiSeq	Phase_I	370	5	0.0135135	NM_001137671		Silent	SNP	ENST00000358970.5	37	CCDS45835.1																																																																																			.	.	weak		0.592	POTEC-002	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371179.1	XM_496269	
PLA2G3	50487	hgsc.bcm.edu	37	22	31533967	31533967	+	Silent	SNP	G	G	A	rs2074739	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:31533967G>A	ENST00000215885.3	-	4	1047	c.795C>T	c.(793-795)taC>taT	p.Y265Y		NM_015715.3	NP_056530.2	Q9NZ20	PA2G3_HUMAN	phospholipase A2, group III	265	Phospholipase A2-like.				acrosome assembly (GO:0001675)|cilium morphogenesis (GO:0060271)|glycerophospholipid biosynthetic process (GO:0046474)|lipid catabolic process (GO:0016042)|lipoxygenase pathway (GO:0019372)|mast cell degranulation (GO:0043303)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|sperm axoneme assembly (GO:0007288)	centriole (GO:0005814)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|mast cell granule (GO:0042629)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|calcium-dependent phospholipase A2 activity (GO:0047498)			large_intestine(1)|lung(10)|ovary(1)|prostate(2)|skin(3)|urinary_tract(1)	18						GCACTGTGCCGTACATCCTAC	0.637													A|||	2686	0.536342	0.472	0.4395	5008	,	,		16981	0.3948		0.5736	False		,,,				2504	0.7996				p.Y265Y		Atlas-SNP	.											.	PLA2G3	85	.	0			c.C795T						PASS	.	A		2050,2356	599.3+/-389.2	476,1098,629	37.0	43.0	41.0		795	1.6	1.0	22	dbSNP_96	41	5022,3578	506.9+/-376.7	1475,2072,753	yes	coding-synonymous	PLA2G3	NM_015715.3		1951,3170,1382	AA,AG,GG		41.6047,46.5275,45.6251		265/510	31533967	7072,5934	2203	4300	6503	SO:0001819	synonymous_variant	50487	exon4			TGTGCCGTACATC	AF220490	CCDS13889.1	22q12.2	2008-09-19			ENSG00000100078	ENSG00000100078	3.1.1.4		17934	protein-coding gene	gene with protein product		611651				10713052	Standard	NM_015715		Approved	GIII-SPLA2	uc003aka.3	Q9NZ20	OTTHUMG00000151255	ENST00000215885.3:c.795C>T	22.37:g.31533967G>A		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	50	27	0.54	NM_015715	O95768	Silent	SNP	ENST00000215885.3	37	CCDS13889.1																																																																																			G|0.488;N|0.000	.	strong		0.637	PLA2G3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321938.1	NM_015715	
ZNF469	84627	hgsc.bcm.edu	37	16	88500430	88500430	+	Silent	SNP	G	G	T	rs12919507	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:88500430G>T	ENST00000437464.1	+	2	6468	c.6468G>T	c.(6466-6468)acG>acT	p.T2156T	ZNF469_ENST00000565624.1_Silent_p.T2184T	NM_001127464.1	NP_001120936.1	Q96JG9	ZN469_HUMAN	zinc finger protein 469	2156					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						TCCAAGCCACGACAGATACTG	0.657													G|||	472	0.0942492	0.0651	0.062	5008	,	,		16209	0.0933		0.1064	False		,,,				2504	0.1452				p.T2156T		Atlas-SNP	.											.	ZNF469	121	.	0			c.G6468T						PASS	.						19.0	21.0	20.0					16																	88500430		692	1586	2278	SO:0001819	synonymous_variant	84627	exon2			AGCCACGACAGAT	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.6468G>T	16.37:g.88500430G>T		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	74	42	0.567568	NM_001127464		Silent	SNP	ENST00000437464.1	37	CCDS45544.1																																																																																			G|0.916;T|0.084	0.084	strong		0.657	ZNF469-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NG_012236	
FAT4	79633	hgsc.bcm.edu	37	4	126336347	126336347	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:126336347C>A	ENST00000394329.3	+	5	6242	c.6229C>A	c.(6229-6231)Cca>Aca	p.P2077T	FAT4_ENST00000335110.5_Missense_Mutation_p.P375T	NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	2077	Cadherin 20. {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.P2077>?(2)		NS(6)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(93)|liver(3)|lung(120)|ovary(9)|pancreas(2)|prostate(21)|skin(31)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(6)	355						AGCAACTGACCCAGATAGTGG	0.418																																					p.P2077T		Atlas-SNP	.											.	FAT4	1752	.	2	Complex(2)	large_intestine(2)	c.C6229A						PASS	.						138.0	141.0	140.0					4																	126336347		2203	4300	6503	SO:0001583	missense	79633	exon5			ACTGACCCAGATA	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.6229C>A	4.37:g.126336347C>A	ENSP00000377862:p.Pro2077Thr	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	108	8	0.0740741	NM_024582	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Missense_Mutation	SNP	ENST00000394329.3	37	CCDS3732.3	.	.	.	.	.	.	.	.	.	.	C	11.14	1.550366	0.27739	.	.	ENSG00000196159	ENST00000394329;ENST00000335110	T;T	0.52983	0.64;0.64	5.0	4.1	0.47936	Cadherin (4);Cadherin-like (1);	0.000000	0.34314	U	0.004066	T	0.49047	0.1534	L	0.53729	1.69	0.39232	D	0.96369	B;B	0.28783	0.222;0.087	B;B	0.37550	0.253;0.155	T	0.54721	-0.8251	10	0.42905	T	0.14	.	14.821	0.70074	0.0:0.8556:0.1444:0.0	.	375;2077	Q6V0I7-2;Q6V0I7	.;FAT4_HUMAN	T	2077;375	ENSP00000377862:P2077T;ENSP00000335169:P375T	ENSP00000335169:P375T	P	+	1	0	FAT4	126555797	1.000000	0.71417	1.000000	0.80357	0.900000	0.52787	2.603000	0.46266	2.308000	0.77769	0.557000	0.71058	CCA	.	.	none		0.418	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582	
FCGBP	8857	hgsc.bcm.edu	37	19	40392802	40392802	+	Missense_Mutation	SNP	C	C	T	rs149844303		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:40392802C>T	ENST00000221347.6	-	16	7709	c.7702G>A	c.(7702-7704)Gcc>Acc	p.A2568T		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	2568	VWFD 6. {ECO:0000255|PROSITE- ProRule:PRU00580}.					extracellular vesicular exosome (GO:0070062)				NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(5)|endometrium(13)|kidney(9)|large_intestine(27)|lung(49)|ovary(8)|pancreas(3)|prostate(13)|skin(9)|stomach(9)|upper_aerodigestive_tract(6)|urinary_tract(3)	165	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			AGGTCGTAGGCCACACGCAGG	0.582																																					p.A2568T		Atlas-SNP	.											FCGBP,NS,carcinoma,0,1	FCGBP	416	1	0			c.G7702A						scavenged	.						4.0	4.0	4.0					19																	40392802		1744	3652	5396	SO:0001583	missense	8857	exon16			CGTAGGCCACACG	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.7702G>A	19.37:g.40392802C>T	ENSP00000221347:p.Ala2568Thr	Somatic	351	0	0		WXS	Illumina HiSeq	Phase_I	465	75	0.16129	NM_003890	O95784	Missense_Mutation	SNP	ENST00000221347.6	37	CCDS12546.1	.	.	.	.	.	.	.	.	.	.	C	4.458	0.084878	0.08583	.	.	ENSG00000090920	ENST00000221347	T	0.59224	0.28	2.66	1.61	0.23674	von Willebrand factor, type D domain (3);	.	.	.	.	T	0.32255	0.0823	N	0.01197	-0.965	0.21762	N	0.999551	B	0.28880	0.226	P	0.44447	0.45	T	0.50268	-0.8848	9	0.09843	T	0.71	.	5.9813	0.19409	0.0:0.7321:0.0:0.2679	.	2568	Q9Y6R7	FCGBP_HUMAN	T	2568	ENSP00000221347:A2568T	ENSP00000221347:A2568T	A	-	1	0	FCGBP	45084642	0.000000	0.05858	0.998000	0.56505	0.350000	0.29205	-2.239000	0.01198	1.495000	0.48549	0.298000	0.19748	GCC	.	.	weak		0.582	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890	
PIEZO1	9780	hgsc.bcm.edu	37	16	88781040	88781040	+	IGR	SNP	A	A	G	rs8059048	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:88781040A>G	ENST00000301015.9	-	0	8072				MIR4722_ENST00000578292.1_RNA|CTU2_ENST00000312060.5_Missense_Mutation_p.Q416R|CTU2_ENST00000453996.2_Missense_Mutation_p.Q416R|CTU2_ENST00000378384.3_Missense_Mutation_p.Q329R|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	192	0	0		WXS	Illumina HiSeq	Phase_I	209	207	0.990431	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	
RAPGEF5	9771	hgsc.bcm.edu	37	7	22233635	22233635	+	5'Flank	SNP	G	G	A	rs375862364		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:22233635G>A	ENST00000401957.2	-	0	0				RAPGEF5_ENST00000475788.1_5'UTR|RAPGEF5_ENST00000405243.1_Missense_Mutation_p.T338M|RAPGEF5_ENST00000344041.6_Missense_Mutation_p.T185M			Q92565	RPGF5_HUMAN	Rap guanine nucleotide exchange factor (GEF) 5						nervous system development (GO:0007399)|positive regulation of Rap GTPase activity (GO:0032854)|positive regulation of Ras GTPase activity (GO:0032320)|small GTPase mediated signal transduction (GO:0007264)	nucleus (GO:0005634)	GTP-dependent protein binding (GO:0030742)|Rap guanyl-nucleotide exchange factor activity (GO:0017034)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)			central_nervous_system(1)|endometrium(1)|kidney(1)|lung(2)|ovary(1)	6						CTGAACAGTCGTCACTTCATC	0.493																																					p.T185M		Atlas-SNP	.											.	RAPGEF5	96	.	0			c.C554T						PASS	.	G	MET/THR	0,4052		0,0,2026	192.0	196.0	195.0		554	2.4	0.1	7		195	2,8352		0,2,4175	no	missense	RAPGEF5	NM_012294.3	81	0,2,6201	AA,AG,GG		0.0239,0.0,0.0161	possibly-damaging	185/731	22233635	2,12404	2026	4177	6203	SO:0001631	upstream_gene_variant	9771	exon10			ACAGTCGTCACTT	D87467	CCDS55093.1	7p15.3	2004-03-01			ENSG00000136237	ENSG00000136237			16862	protein-coding gene	gene with protein product	"""M-Ras-regulated GEF"""	609527				9039502, 10486569	Standard	NM_012294		Approved	KIAA0277, GFR, MR-GEF	uc003svg.3	Q92565	OTTHUMG00000152525		7.37:g.22233635G>A	Exception_encountered	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	77	12	0.155844	NM_012294	A4D140|Q8IXU5	Missense_Mutation	SNP	ENST00000401957.2	37		.	.	.	.	.	.	.	.	.	.	G	11.73	1.724513	0.30593	0.0	2.39E-4	ENSG00000136237	ENST00000344041;ENST00000420196;ENST00000405243	D;D;D	0.85339	-1.97;-1.97;-1.97	5.31	2.44	0.29823	.	4.131740	0.00935	N	0.002779	T	0.82204	0.4986	L	0.40543	1.245	0.09310	N	1	D	0.55385	0.971	B	0.42062	0.374	T	0.69146	-0.5222	10	0.72032	D	0.01	.	9.6692	0.40002	0.0745:0.2663:0.6593:0.0	.	185	A8MQ07	.	M	185;66;338	ENSP00000343656:T185M;ENSP00000395729:T66M;ENSP00000384870:T338M	ENSP00000343656:T185M	T	-	2	0	RAPGEF5	22200160	0.005000	0.15991	0.061000	0.19648	0.976000	0.68499	0.648000	0.24828	0.213000	0.20722	0.563000	0.77884	ACG	.	.	weak		0.493	RAPGEF5-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000326590.2	NM_012294	
DOCK5	80005	hgsc.bcm.edu	37	8	25220581	25220581	+	Missense_Mutation	SNP	T	T	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:25220581T>A	ENST00000276440.7	+	29	3012	c.2968T>A	c.(2968-2970)Ttt>Att	p.F990I		NM_024940.6	NP_079216.4	Q9H7D0	DOCK5_HUMAN	dedicator of cytokinesis 5	990					positive regulation of GTPase activity (GO:0043547)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	guanyl-nucleotide exchange factor activity (GO:0005085)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(12)|kidney(9)|large_intestine(13)|lung(20)|ovary(3)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	72		all_cancers(63;0.0361)|Ovarian(32;0.000711)|all_epithelial(46;0.0153)|Hepatocellular(4;0.115)|Prostate(55;0.13)|Breast(100;0.143)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0267)|Epithelial(17;1.07e-11)|Colorectal(74;0.0276)|COAD - Colon adenocarcinoma(73;0.0828)		CATGGAAACTTTTATCATGTT	0.458																																					p.F990I	Pancreas(145;34 1887 3271 10937 30165)	Atlas-SNP	.											.	DOCK5	167	.	0			c.T2968A						PASS	.						136.0	134.0	135.0					8																	25220581		2203	4300	6503	SO:0001583	missense	80005	exon29			GAAACTTTTATCA		CCDS6047.1	8p21.2	2009-04-17			ENSG00000147459	ENSG00000147459			23476	protein-coding gene	gene with protein product						12432077	Standard	NM_024940		Approved	FLJ21034	uc003xeg.3	Q9H7D0	OTTHUMG00000131991	ENST00000276440.7:c.2968T>A	8.37:g.25220581T>A	ENSP00000276440:p.Phe990Ile	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	84	47	0.559524	NM_024940	B2RNY0|Q5XKD5|Q6AI11|Q6PJS6|Q6ZTS6	Missense_Mutation	SNP	ENST00000276440.7	37	CCDS6047.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	34|34	5.392449|5.392449	0.96009|0.96009	.|.	.|.	ENSG00000147459|ENSG00000147459	ENST00000276440|ENST00000444569	T|.	0.26223|.	1.75|.	5.68|5.68	5.68|5.68	0.88126|0.88126	.|.	0.000000|0.000000	0.85682|0.85682	D|D	0.000000|0.000000	T|T	0.79281|0.79281	0.4419|0.4419	M|M	0.85542|0.85542	2.76|2.76	0.80722|0.80722	D|D	1|1	P;P;D|.	0.56968|.	0.94;0.898;0.978|.	P;P;P|.	0.57620|.	0.824;0.642;0.824|.	T|T	0.81795|0.81795	-0.0769|-0.0769	10|6	0.72032|.	D|.	0.01|.	.|.	15.9289|15.9289	0.79644|0.79644	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	980;765;990|.	D3DSS6;Q68DL4;Q9H7D0|.	.;.;DOCK5_HUMAN|.	I|Y	990|761	ENSP00000276440:F990I|.	ENSP00000276440:F990I|.	F|F	+|+	1|2	0|0	DOCK5|DOCK5	25276498|25276498	1.000000|1.000000	0.71417|0.71417	0.997000|0.997000	0.53966|0.53966	0.977000|0.977000	0.68977|0.68977	7.991000|7.991000	0.88244|0.88244	2.173000|2.173000	0.68751|0.68751	0.528000|0.528000	0.53228|0.53228	TTT|TTT	.	.	none		0.458	DOCK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254955.2	NM_024940	
FOXQ1	94234	hgsc.bcm.edu	37	6	1313470	1313470	+	Silent	SNP	C	C	T	rs4435985	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:1313470C>T	ENST00000296839.2	+	1	796	c.531C>T	c.(529-531)ttC>ttT	p.F177F		NM_033260.3	NP_150285.3	Q9C009	FOXQ1_HUMAN	forkhead box Q1	177					hair follicle morphogenesis (GO:0031069)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			lung(1)|urinary_tract(1)	2	Ovarian(93;0.0733)	Breast(5;0.052)|all_lung(73;0.0713)|all_hematologic(90;0.0895)		OV - Ovarian serous cystadenocarcinoma(45;0.0954)|BRCA - Breast invasive adenocarcinoma(62;0.18)		ACGACTGCTTCGTCAAGGTGC	0.622													C|||	956	0.190895	0.1241	0.1167	5008	,	,		7348	0.2986		0.2048	False		,,,				2504	0.2086				p.F177F		Atlas-SNP	.											FOXQ1,NS,carcinoma,0,1	FOXQ1	8	1	0			c.C531T						scavenged	.	C		619,3785		37,545,1620	43.0	45.0	44.0		531	3.8	1.0	6	dbSNP_111	44	1699,6897		159,1381,2758	no	coding-synonymous	FOXQ1	NM_033260.3		196,1926,4378	TT,TC,CC		19.765,14.0554,17.8308		177/404	1313470	2318,10682	2202	4298	6500	SO:0001819	synonymous_variant	94234	exon1			CTGCTTCGTCAAG	AF153341	CCDS4471.1	6p25	2008-02-05			ENSG00000164379	ENSG00000164379		"""Forkhead boxes"""	20951	protein-coding gene	gene with protein product		612788				11747606, 12011061	Standard	NM_033260		Approved	HFH1	uc003mtl.4	Q9C009	OTTHUMG00000016160	ENST00000296839.2:c.531C>T	6.37:g.1313470C>T		Somatic	173	1	0.00578035		WXS	Illumina HiSeq	Phase_I	201	80	0.39801	NM_033260	Q9NS06	Silent	SNP	ENST00000296839.2	37	CCDS4471.1																																																																																			C|0.811;T|0.189	0.189	strong		0.622	FOXQ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043410.1	NM_033260	
SLC16A6	9120	hgsc.bcm.edu	37	17	66267691	66267691	+	Missense_Mutation	SNP	A	A	T	rs7222013	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:66267691A>T	ENST00000327268.4	-	6	774	c.610T>A	c.(610-612)Ttt>Att	p.F204I	SLC16A6_ENST00000580666.1_Missense_Mutation_p.F204I|ARSG_ENST00000448504.2_Intron	NM_001174166.1	NP_001167637.1	O15403	MOT7_HUMAN	solute carrier family 16, member 6	204			F -> I (in dbSNP:rs7222013). {ECO:0000269|PubMed:9425115}.		monocarboxylic acid transport (GO:0015718)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	monocarboxylic acid transmembrane transporter activity (GO:0008028)|symporter activity (GO:0015293)			large_intestine(3)|lung(8)|prostate(1)|skin(1)|urinary_tract(2)	15	all_cancers(12;1.24e-09)		BRCA - Breast invasive adenocarcinoma(8;3.17e-08)|LUSC - Lung squamous cell carcinoma(166;0.24)		Pyruvic acid(DB00119)	CCTCTGATAAAGATGGGTCTG	0.473													T|||	1901	0.379593	0.6853	0.3746	5008	,	,		18980	0.247		0.1928	False		,,,				2504	0.2986				p.F204I		Atlas-SNP	.											.	SLC16A6	56	.	0			c.T610A						PASS	.	T	ILE/PHE,ILE/PHE,	2758,1648	505.9+/-366.3	868,1022,313	116.0	112.0	113.0		610,610,	-0.5	0.0	17	dbSNP_116	113	2012,6588	722.1+/-406.4	239,1534,2527	yes	missense,missense,intron	SLC16A6,ARSG	NM_001174166.1,NM_004694.4,NM_014960.3	21,21,	1107,2556,2840	TT,TA,AA		23.3953,37.4035,36.6754	benign,benign,	204/524,204/524,	66267691	4770,8236	2203	4300	6503	SO:0001583	missense	9120	exon6			TGATAAAGATGGG	U79745	CCDS11675.1	17q24.2	2013-07-18	2013-07-18		ENSG00000108932	ENSG00000108932		"""Solute carriers"""	10927	protein-coding gene	gene with protein product		603880	"""solute carrier family 16 (monocarboxylic acid transporters), member 6"", ""solute carrier family 16, member 6 (monocarboxylic acid transporter 7)"""			9425115	Standard	NM_004694		Approved	MCT6, MCT7	uc002jgz.2	O15403	OTTHUMG00000179812	ENST00000327268.4:c.610T>A	17.37:g.66267691A>T	ENSP00000319991:p.Phe204Ile	Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	144	82	0.569444	NM_001174166	Q6P1X3	Missense_Mutation	SNP	ENST00000327268.4	37	CCDS11675.1	725	0.33195970695970695	326	0.6626016260162602	133	0.3674033149171271	137	0.2395104895104895	129	0.17018469656992086	T	0.008	-1.881272	0.00532	0.625965	0.233953	ENSG00000108932	ENST00000327268	T	0.03889	3.77	4.33	-0.528	0.11905	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.619301	0.16867	N	0.196264	T	0.00012	0.0000	N	0.00138	-2.015	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.08493	-1.0719	9	0.33141	T	0.24	.	6.1866	0.20500	0.1265:0.4151:0.0:0.4584	rs7222013;rs7222013	204	O15403	MOT7_HUMAN	I	204	ENSP00000319991:F204I	ENSP00000319991:F204I	F	-	1	0	SLC16A6	63779286	0.000000	0.05858	0.000000	0.03702	0.133000	0.20885	-2.006000	0.01459	-0.690000	0.05142	-0.514000	0.04452	TTT	A|0.636;T|0.364	0.364	strong		0.473	SLC16A6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448323.1	NM_004694	
HSD3B1	3283	hgsc.bcm.edu	37	1	120057158	120057158	+	Silent	SNP	C	C	T	rs6203	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:120057158C>T	ENST00000369413.3	+	4	1157	c.1012C>T	c.(1012-1014)Ctg>Ttg	p.L338L	HSD3B1_ENST00000528909.1_Silent_p.L338L|HSD3B1_ENST00000235547.6_Silent_p.L340L			P14060	3BHS1_HUMAN	hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 1	338					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)	TCAGCGAGATCTGGCGTATAA	0.512													C|||	1837	0.366813	0.0333	0.4813	5008	,	,		21293	0.6528		0.4254	False		,,,				2504	0.3814				p.L338L		Atlas-SNP	.											.	HSD3B1	53	.	0			c.C1012T	GRCh37	CM021275	HSD3B1	M	rs6203	PASS	.	C		457,3949	217.4+/-235.8	28,401,1774	88.0	77.0	81.0		1012	1.3	0.9	1	dbSNP_52	81	3730,4870	530.5+/-381.8	818,2094,1388	no	coding-synonymous	HSD3B1	NM_000862.2		846,2495,3162	TT,TC,CC		43.3721,10.3722,32.1928		338/374	120057158	4187,8819	2203	4300	6503	SO:0001819	synonymous_variant	3283	exon4			CGAGATCTGGCGT	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.1012C>T	1.37:g.120057158C>T		Somatic	190	0	0		WXS	Illumina HiSeq	Phase_I	179	72	0.402235	NM_000862	A8K691|Q14545|Q8IV65	Silent	SNP	ENST00000369413.3	37	CCDS903.1																																																																																			C|0.647;T|0.353	0.353	strong		0.512	HSD3B1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000034993.3	NM_000862	
KRT77	374454	hgsc.bcm.edu	37	12	53091566	53091566	+	Missense_Mutation	SNP	C	C	A	rs1567759	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:53091566C>A	ENST00000341809.3	-	2	686	c.658G>T	c.(658-660)Ggt>Tgt	p.G220C	RP11-641A6.3_ENST00000547533.1_RNA|KRT77_ENST00000537195.1_5'UTR	NM_175078.2	NP_778253.2	Q7Z794	K2C1B_HUMAN	keratin 77	220	Coil 1B.|Rod.					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						CGCAGGTCACCGATGTAGTTC	0.562													C|||	2036	0.40655	0.4811	0.4121	5008	,	,		20180	0.246		0.4026	False		,,,				2504	0.4714				p.G220C		Atlas-SNP	.											KRT77,colon,carcinoma,0,1	KRT77	58	1	0			c.G658T						PASS	.	C	CYS/GLY	1988,2418	557.0+/-379.6	437,1114,652	222.0	215.0	217.0		658	-2.0	0.0	12	dbSNP_88	217	3625,4975	522.6+/-380.1	764,2097,1439	yes	missense	KRT77	NM_175078.2	159	1201,3211,2091	AA,AC,CC		42.1512,45.1203,43.157	probably-damaging	220/579	53091566	5613,7393	2203	4300	6503	SO:0001583	missense	374454	exon2			GGTCACCGATGTA	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.658G>T	12.37:g.53091566C>A	ENSP00000342710:p.Gly220Cys	Somatic	190	0	0		WXS	Illumina HiSeq	Phase_I	142	84	0.591549	NM_175078	Q7RTS8	Missense_Mutation	SNP	ENST00000341809.3	37	CCDS8837.1	800	0.3663003663003663	226	0.45934959349593496	137	0.3784530386740331	127	0.22202797202797203	310	0.40897097625329815	C	13.82	2.350744	0.41599	0.451203	0.421512	ENSG00000189182	ENST00000341809	D	0.88818	-2.43	4.4	-2.05	0.07321	Filament (1);	.	.	.	.	T	0.00012	0.0000	L	0.44542	1.39	0.39443	P	0.03272200000000003	D	0.76494	0.999	D	0.72075	0.976	T	0.14144	-1.0483	8	0.56958	D	0.05	.	7.0738	0.25193	0.0:0.4467:0.1351:0.4182	rs1567759;rs52816334;rs58131065;rs1567759	220	Q7Z794	K2C1B_HUMAN	C	220	ENSP00000342710:G220C	ENSP00000342710:G220C	G	-	1	0	KRT77	51377833	0.000000	0.05858	0.010000	0.14722	0.000000	0.00434	-1.970000	0.01504	-0.220000	0.09988	-1.240000	0.01540	GGT	C|0.593;A|0.407	0.407	strong		0.562	KRT77-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404111.1	NM_175078	
STRC	161497	hgsc.bcm.edu	37	15	43893072	43893072	+	Silent	SNP	G	G	A	rs3097773	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:43893072G>A	ENST00000450892.2	-	25	4919	c.4842C>T	c.(4840-4842)ttC>ttT	p.F1614F	RNU6-554P_ENST00000410466.1_RNA|STRC_ENST00000541030.1_Silent_p.F841F	NM_153700.2	NP_714544.1	Q7RTU9	STRC_HUMAN	stereocilin	1614					auditory receptor cell stereocilium organization (GO:0060088)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)	kinocilium (GO:0060091)|stereocilium bundle tip (GO:0032426)				skin(4)	4		all_cancers(109;3.26e-15)|all_epithelial(112;1.48e-12)|Lung NSC(122;2.76e-08)|all_lung(180;3.1e-07)|Melanoma(134;0.027)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;3.56e-07)		CAAATGACCTGAACTCCCAAC	0.552													A|||	1982	0.395767	0.7943	0.2291	5008	,	,		18022	0.4216		0.1064	False		,,,				2504	0.2464				p.F1614F		Atlas-SNP	.											.	STRC	58	.	0			c.C4842T						PASS	.	A		2942,1458	442.0+/-346.6	1020,902,278	75.0	97.0	89.0		4842	2.1	1.0	15	dbSNP_103	89	865,7729	769.3+/-407.6	55,755,3487	no	coding-synonymous	STRC	NM_153700.2		1075,1657,3765	AA,AG,GG		10.0652,33.1364,29.2981		1614/1776	43893072	3807,9187	2200	4297	6497	SO:0001819	synonymous_variant	161497	exon25			TGACCTGAACTCC	BK000138	CCDS10098.1	15q15.3	2010-02-26			ENSG00000242866	ENSG00000242866			16035	protein-coding gene	gene with protein product		606440		DFNB16		11687802, 9429146	Standard	NM_153700		Approved		uc001zsf.3	Q7RTU9	OTTHUMG00000059899	ENST00000450892.2:c.4842C>T	15.37:g.43893072G>A		Somatic	221	0	0		WXS	Illumina HiSeq	Phase_I	197	63	0.319797	NM_153700		Silent	SNP	ENST00000450892.2	37	CCDS10098.1																																																																																			.	.	weak		0.552	STRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133140.1	NM_153700	
TEX40	25858	hgsc.bcm.edu	37	11	64068310	64068310	+	Missense_Mutation	SNP	C	C	T	rs2286614	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:64068310C>T	ENST00000328404.6	+	2	223	c.203C>T	c.(202-204)cCg>cTg	p.P68L	TEX40_ENST00000539943.1_Missense_Mutation_p.P26L|RP11-783K16.10_ENST00000539086.1_RNA	NM_001039496.1	NP_001034585.1	Q9NTU4	TEX40_HUMAN	testis expressed 40	68			P -> L (in dbSNP:rs2286614).		cell differentiation (GO:0030154)|male meiosis (GO:0007140)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)											TGGCACAGCCCGGGGCGGGGC	0.682											OREG0021050	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	442	0.0882588	0.025	0.1182	5008	,	,		13923	0.1071		0.16	False		,,,				2504	0.0593				p.P68L		Atlas-SNP	.											.	.	.	.	0			c.C203T						PASS	.	C	LEU/PRO	167,3713		6,155,1779	7.0	9.0	8.0		203	-6.6	0.0	11	dbSNP_100	8	1167,6977		94,979,2999	yes	missense	C11orf20	NM_001039496.1	98	100,1134,4778	TT,TC,CC		14.3296,4.3041,11.0945	possibly-damaging	68/201	64068310	1334,10690	1940	4072	6012	SO:0001583	missense	25858	exon2			ACAGCCCGGGGCG			11q13.1	2013-01-11	2013-01-11	2013-01-11	ENSG00000219435	ENSG00000219435			19231	protein-coding gene	gene with protein product			"""chromosome 11 open reading frame 20"""	C11orf20			Standard	NM_001039496		Approved	DKFZP566E164	uc009ypm.3	Q9NTU4	OTTHUMG00000167820	ENST00000328404.6:c.203C>T	11.37:g.64068310C>T	ENSP00000330877:p.Pro68Leu	Somatic	118	0	0	1073	WXS	Illumina HiSeq	Phase_I	109	79	0.724771	NM_001039496		Missense_Mutation	SNP	ENST00000328404.6	37		237	0.10851648351648352	11	0.022357723577235773	44	0.12154696132596685	61	0.10664335664335664	121	0.15963060686015831	C	11.23	1.578537	0.28180	0.043041	0.143296	ENSG00000219435	ENST00000328404;ENST00000539943	T;T	0.44083	0.93;0.94	3.28	-6.56	0.01848	.	.	.	.	.	T	0.00073	0.0002	N	0.08118	0	0.80722	P	0.0	B	0.09022	0.002	B	0.06405	0.002	T	0.16928	-1.0386	8	0.45353	T	0.12	-0.0108	2.1128	0.03707	0.26:0.2503:0.3698:0.1199	rs2286614;rs60336112;rs2286614	68	Q9NTU4	CK020_HUMAN	L	68;26	ENSP00000330877:P68L;ENSP00000443917:P26L	ENSP00000330877:P68L	P	+	2	0	C11orf20	63824886	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.403000	0.01046	-1.516000	0.01782	-0.410000	0.06199	CCG	C|0.899;T|0.101	0.101	strong		0.682	TEX40-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001039496	
SIRT5	23408	hgsc.bcm.edu	37	6	13604710	13604710	+	Missense_Mutation	SNP	A	A	T	rs41273886	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:13604710A>T	ENST00000379262.4	+	10	1078	c.860A>T	c.(859-861)cAt>cTt	p.H287L	SIRT5_ENST00000359782.3_Intron|SIRT5_ENST00000397350.2_Intron|SIRT5_ENST00000606117.1_Intron	NM_031244.3	NP_112534.1			sirtuin 5											breast(1)|endometrium(1)|large_intestine(3)|lung(1)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	11	Breast(50;0.00669)|Ovarian(93;0.0634)	all_hematologic(90;0.117)	Epithelial(50;0.176)			CTTTTCAGTCATTTGATCTCC	0.343													A|||	28	0.00559105	0.0015	0.013	5008	,	,		18582	0.0		0.0159	False		,,,				2504	0.001				p.H287L		Atlas-SNP	.											.	SIRT5	45	.	0			c.A860T						PASS	.	A	,,,LEU/HIS	9,4397	15.5+/-35.6	0,9,2194	122.0	124.0	123.0		,,,860	-3.9	0.0	6	dbSNP_127	123	161,8439	75.7+/-138.4	1,159,4140	yes	intron,intron,intron,missense	SIRT5	NM_001193267.2,NM_001242827.1,NM_012241.4,NM_031244.3	,,,99	1,168,6334	TT,TA,AA		1.8721,0.2043,1.3071	,,,	,,,287/300	13604710	170,12836	2203	4300	6503	SO:0001583	missense	23408	exon10			TCAGTCATTTGAT	AF083110	CCDS4526.1, CCDS4527.1, CCDS54966.1, CCDS56398.1	6p23	2010-08-05	2010-06-25		ENSG00000124523	ENSG00000124523			14933	protein-coding gene	gene with protein product		604483	"""sirtuin (silent mating type information regulation 2, S.cerevisiae, homolog) 5"", ""sirtuin (silent mating type information regulation 2 homolog) 5 (S. cerevisiae)"""			10381378	Standard	NM_012241		Approved		uc003nay.3	Q9NXA8	OTTHUMG00000014278	ENST00000379262.4:c.860A>T	6.37:g.13604710A>T	ENSP00000368564:p.His287Leu	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	91	43	0.472527	NM_031244		Missense_Mutation	SNP	ENST00000379262.4	37	CCDS4527.1	20	0.009157509157509158	0	0.0	7	0.019337016574585635	0	0.0	13	0.017150395778364115	A	1.015	-0.686773	0.03328	0.002043	0.018721	ENSG00000124523	ENST00000379262	T	0.36520	1.25	1.95	-3.91	0.04168	.	.	.	.	.	T	0.03520	0.0101	.	.	.	0.09310	N	1	B	0.19200	0.034	B	0.19946	0.027	T	0.36986	-0.9725	8	0.10902	T	0.67	.	0.4034	0.00429	0.2905:0.2073:0.2982:0.2041	rs41273886	287	Q9NXA8-2	.	L	287	ENSP00000368564:H287L	ENSP00000368564:H287L	H	+	2	0	SIRT5	13712689	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-1.478000	0.02329	-1.158000	0.02811	-0.691000	0.03719	CAT	A|0.989;T|0.011	0.011	strong		0.343	SIRT5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000039907.1		
KRTAP12-2	353323	hgsc.bcm.edu	37	21	46086457	46086457	+	Missense_Mutation	SNP	G	G	A	rs12483730	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:46086457G>A	ENST00000360770.3	-	1	387	c.347C>T	c.(346-348)gCg>gTg	p.A116V	TSPEAR_ENST00000323084.4_Intron	NM_181684.2	NP_859012.1	P59991	KR122_HUMAN	keratin associated protein 12-2	116	23 X 5 AA approximate repeats.		A -> V (in dbSNP:rs12483730).			keratin filament (GO:0045095)				central_nervous_system(1)|endometrium(1)|lung(3)	5						GGACGGAGCCGCATACACGAC	0.627													G|||	723	0.144369	0.0877	0.1657	5008	,	,		18686	0.0923		0.2078	False		,,,				2504	0.1943				p.A116V		Atlas-SNP	.											.	KRTAP12-2	10	.	0			c.C347T						PASS	.	G	,VAL/ALA	387,3947		21,345,1801	55.0	64.0	61.0		,347	0.4	0.0	21	dbSNP_120	61	1745,6771		173,1399,2686	yes	intron,missense	TSPEAR,KRTAP12-2	NM_144991.2,NM_181684.2	,64	194,1744,4487	AA,AG,GG		20.4908,8.9294,16.5914	,possibly-damaging	,116/147	46086457	2132,10718	2167	4258	6425	SO:0001583	missense	353323	exon1			GGAGCCGCATACA	AJ566389	CCDS42965.1	21q22.3	2006-03-13			ENSG00000221864	ENSG00000221864		"""Keratin associated proteins"""	20530	protein-coding gene	gene with protein product							Standard	NM_181684		Approved	KRTAP12.2, KAP12.2	uc002zfu.3	P59991	OTTHUMG00000057636	ENST00000360770.3:c.347C>T	21.37:g.46086457G>A	ENSP00000354001:p.Ala116Val	Somatic	206	0	0		WXS	Illumina HiSeq	Phase_I	263	110	0.418251	NM_181684	A6NIS1|A6NMS9|Q0VAS4	Missense_Mutation	SNP	ENST00000360770.3	37	CCDS42965.1	320	0.14652014652014653	44	0.08943089430894309	61	0.1685082872928177	56	0.0979020979020979	159	0.20976253298153033	g	0.632	-0.816857	0.02776	0.089294	0.204908	ENSG00000221864	ENST00000360770;ENST00000539483	T	0.02944	4.1	2.9	0.394	0.16299	.	.	.	.	.	T	0.00012	0.0000	N	0.00507	-1.42	0.58432	P	1.0000000000287557E-6	B	0.12630	0.006	B	0.04013	0.001	T	0.44267	-0.9339	8	0.27082	T	0.32	.	4.4209	0.11479	0.6485:0.0:0.3515:0.0	rs12483730	116	P59991	KR122_HUMAN	V	116;66	ENSP00000354001:A116V	ENSP00000354001:A116V	A	-	2	0	KRTAP12-2	44910885	0.002000	0.14202	0.006000	0.13384	0.001000	0.01503	0.492000	0.22435	0.175000	0.19841	-0.481000	0.04817	GCG	G|0.846;A|0.154	0.154	strong		0.627	KRTAP12-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128039.1	NM_181684	
USP48	84196	hgsc.bcm.edu	37	1	22109370	22109370	+	Silent	SNP	G	G	A	rs10917042	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:22109370G>A	ENST00000308271.9	-	1	729	c.81C>T	c.(79-81)caC>caT	p.H27H	USP48_ENST00000400301.1_Silent_p.H27H|USP48_ENST00000421625.2_Silent_p.H27H|USP48_ENST00000529637.1_Silent_p.H27H	NM_032236.5	NP_115612.4	Q86UV5	UBP48_HUMAN	ubiquitin specific peptidase 48	27					ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ubiquitin-specific protease activity (GO:0004843)			NS(1)|endometrium(6)|kidney(2)|large_intestine(11)|lung(14)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	42		Colorectal(325;3.46e-05)|all_lung(284;4.29e-05)|Lung NSC(340;4.66e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|OV - Ovarian serous cystadenocarcinoma(117;4.74e-26)|COAD - Colon adenocarcinoma(152;1.3e-05)|GBM - Glioblastoma multiforme(114;1.86e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000614)|STAD - Stomach adenocarcinoma(196;0.00644)|KIRC - Kidney renal clear cell carcinoma(1967;0.00711)|Lung(427;0.0327)|READ - Rectum adenocarcinoma(331;0.0657)|LUSC - Lung squamous cell carcinoma(448;0.0753)		CGGTCTCGATGTGCTCCTGCG	0.736													G|||	1411	0.281749	0.028	0.5274	5008	,	,		12624	0.5893		0.2197	False		,,,				2504	0.1973				p.H27H		Atlas-SNP	.											.	USP48	91	.	0			c.C81T						PASS	.	G	,	275,4053		11,253,1900	18.0	16.0	17.0		81,81	0.8	1.0	1	dbSNP_120	17	1858,6642		203,1452,2595	no	coding-synonymous,coding-synonymous	USP48	NM_001032730.1,NM_032236.5	,	214,1705,4495	AA,AG,GG		21.8588,6.354,16.6277	,	27/486,27/1036	22109370	2133,10695	2164	4250	6414	SO:0001819	synonymous_variant	84196	exon1			CTCGATGTGCTCC	AF502942	CCDS30623.1, CCDS44084.1	1p36.12	2008-02-05	2005-08-08	2004-04-07	ENSG00000090686	ENSG00000090686		"""Ubiquitin-specific peptidases"""	18533	protein-coding gene	gene with protein product			"""ubiquitin specific protease 31"", ""ubiquitin specific protease 48"""	USP31		12838346	Standard	XM_005246009		Approved	FLJ23277, FLJ11328, FLJ20103, FLJ23054, MGC14879	uc001bfb.3	Q86UV5	OTTHUMG00000007798	ENST00000308271.9:c.81C>T	1.37:g.22109370G>A		Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	79	38	0.481013	NM_001032730	B7ZKS7|Q2M3I4|Q5SZI4|Q5T3T5|Q6NX53|Q8N3F6|Q96F64|Q96IQ3|Q9H5N3|Q9H5T7|Q9NUJ6|Q9NXR0	Silent	SNP	ENST00000308271.9	37	CCDS30623.1																																																																																			G|0.772;A|0.228	0.228	strong		0.736	USP48-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021372.1	NM_032236	
RHBDL2	54933	hgsc.bcm.edu	37	1	39352271	39352271	+	Missense_Mutation	SNP	G	G	T	rs2147914	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:39352271G>T	ENST00000289248.2	-	8	1825	c.817C>A	c.(817-819)Ctg>Atg	p.L273M	RHBDL2_ENST00000372985.3_Missense_Mutation_p.L353M|RP5-864K19.4_ENST00000433671.2_RNA|RHBDL2_ENST00000538156.1_Missense_Mutation_p.L340M|RHBDL2_ENST00000372990.1_Missense_Mutation_p.L273M			Q9NX52	RHBL2_HUMAN	rhomboid, veinlet-like 2 (Drosophila)	273			L -> M (in dbSNP:rs2147914).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(3)	8	Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;8.23e-17)			GGATCTTTCAGCAGTGCTTTA	0.428													G|||	1555	0.310503	0.1452	0.4798	5008	,	,		19848	0.2718		0.4513	False		,,,				2504	0.3088				p.L273M		Atlas-SNP	.											RHBDL2,bladder,carcinoma,+2,1	RHBDL2	28	1	0			c.C817A						PASS	.	G	MET/LEU	827,3579	328.0+/-300.3	81,665,1457	126.0	118.0	121.0		817	6.0	1.0	1	dbSNP_96	121	3915,4685	546.8+/-385.0	881,2153,1266	yes	missense	RHBDL2	NM_017821.3	15	962,2818,2723	TT,TG,GG		45.5233,18.7699,36.4601	probably-damaging	273/304	39352271	4742,8264	2203	4300	6503	SO:0001583	missense	54933	exon8			CTTTCAGCAGTGC	AK000442	CCDS30680.1	1p35.1	2014-01-28	2001-11-28		ENSG00000158315	ENSG00000158315			16083	protein-coding gene	gene with protein product		608962	"""rhomboid (veinlet, Drosophila)-like 2"""				Standard	NM_017821		Approved	FLJ20435	uc001ccu.1	Q9NX52	OTTHUMG00000000487	ENST00000289248.2:c.817C>A	1.37:g.39352271G>T	ENSP00000289248:p.Leu273Met	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	81	42	0.518519	NM_017821	B2RNT3|B9EH75|Q6P175|Q8NER8|Q96E02	Missense_Mutation	SNP	ENST00000289248.2	37	CCDS30680.1	754	0.34523809523809523	74	0.15040650406504066	170	0.4696132596685083	168	0.2937062937062937	342	0.45118733509234826	G	19.75	3.885071	0.72410	0.187699	0.455233	ENSG00000158315	ENST00000372990;ENST00000289248;ENST00000538156;ENST00000372985	T;T;T;T	0.34667	1.41;1.41;1.36;1.35	6.03	6.03	0.97812	.	0.071091	0.64402	D	0.000020	T	0.00012	0.0000	L	0.47716	1.5	0.23361	P	0.99783142	D;D	0.64830	0.994;0.988	P;P	0.59221	0.854;0.74	T	0.53201	-0.8472	9	0.33141	T	0.24	-13.991	10.462	0.44585	0.0:0.1432:0.7085:0.1483	rs2147914;rs3790440;rs17559036;rs61115096;rs2147914	353;273	B7Z1Y9;Q9NX52	.;RHBL2_HUMAN	M	273;273;340;353	ENSP00000362081:L273M;ENSP00000289248:L273M;ENSP00000439227:L340M;ENSP00000362076:L353M	ENSP00000289248:L273M	L	-	1	2	RHBDL2	39124858	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	2.757000	0.47557	2.861000	0.98227	0.655000	0.94253	CTG	G|0.652;T|0.348	0.348	strong		0.428	RHBDL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001216.1	NM_017821	
TLR6	10333	hgsc.bcm.edu	37	4	38829163	38829163	+	Silent	SNP	A	A	C	rs5743818	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:38829163A>C	ENST00000381950.1	-	1	1997	c.1932T>G	c.(1930-1932)gcT>gcG	p.A644A	TLR6_ENST00000436693.2_Silent_p.A644A			Q9Y2C9	TLR6_HUMAN	toll-like receptor 6	644	TIR. {ECO:0000255|PROSITE- ProRule:PRU00204}.				activation of NF-kappaB-inducing kinase activity (GO:0007250)|cellular response to diacyl bacterial lipopeptide (GO:0071726)|defense response to bacterium (GO:0042742)|detection of diacyl bacterial lipopeptide (GO:0042496)|immune response (GO:0006955)|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)|nitric oxide metabolic process (GO:0046209)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-6 biosynthetic process (GO:0045410)|positive regulation of JUN kinase activity (GO:0043507)|regulation of cytokine secretion (GO:0050707)|signal transduction (GO:0007165)|T-helper 1 type immune response (GO:0042088)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 6 signaling pathway (GO:0034150)|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)	cytoplasmic vesicle (GO:0031410)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|Toll-like receptor 2-Toll-like receptor 6 protein complex (GO:0035355)	diacyl lipopeptide binding (GO:0042498)|lipopeptide binding (GO:0071723)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(7)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						ATGAAATAAAAGCATGAAACT	0.438													A|||	449	0.0896565	0.0416	0.0879	5008	,	,		20982	0.0089		0.2445	False		,,,				2504	0.0798				p.A644A		Atlas-SNP	.											.	TLR6	67	.	0			c.T1932G						PASS	.	A		357,4049	185.7+/-212.7	14,329,1860	88.0	92.0	91.0		1932	-2.6	1.0	4	dbSNP_114	91	2312,6288	389.5+/-342.9	331,1650,2319	no	coding-synonymous	TLR6	NM_006068.4		345,1979,4179	CC,CA,AA		26.8837,8.1026,20.5213		644/797	38829163	2669,10337	2203	4300	6503	SO:0001819	synonymous_variant	10333	exon2			AATAAAAGCATGA		CCDS3446.1	4p16.1	2009-11-23			ENSG00000174130	ENSG00000174130		"""CD molecules"""	16711	protein-coding gene	gene with protein product		605403				10231569	Standard	NM_006068		Approved	CD286	uc010ifg.2	Q9Y2C9	OTTHUMG00000128579	ENST00000381950.1:c.1932T>G	4.37:g.38829163A>C		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	88	56	0.636364	NM_006068	B3Y640|B6CH35|B6RFS4|B6RFS5|Q2NKL3	Silent	SNP	ENST00000381950.1	37	CCDS3446.1																																																																																			A|0.842;C|0.158	0.158	strong		0.438	TLR6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250431.1		
AIRE	326	hgsc.bcm.edu	37	21	45712983	45712983	+	Silent	SNP	T	T	C	rs61737072	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:45712983T>C	ENST00000291582.5	+	10	1330	c.1203T>C	c.(1201-1203)ccT>ccC	p.P401P	AIRE_ENST00000329347.4_Intron|AIRE_ENST00000355347.4_Silent_p.P194P	NM_000383.3	NP_000374.1	O43918	AIRE_HUMAN	autoimmune regulator	401					humoral immune response (GO:0006959)|immune response (GO:0006955)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|histone binding (GO:0042393)|transcription regulatory region DNA binding (GO:0044212)|translation regulator activity (GO:0045182)|zinc ion binding (GO:0008270)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(7)|skin(2)|urinary_tract(1)	14				Colorectal(79;0.0806)		CGGCTCCGCCTTCTGCAGCCC	0.677									Autoimmune PolyEndocrinopathy Candidiasis Ectodermal Dystrophy				T|||	232	0.0463259	0.1649	0.0202	5008	,	,		10975	0.0		0.0	False		,,,				2504	0.0				p.P401P		Atlas-SNP	.											.	AIRE	61	.	0			c.T1203C						PASS	.	T	,	665,3717		60,545,1586	22.0	26.0	24.0		1203,612	-2.4	0.0	21	dbSNP_129	24	2,8586		0,2,4292	no	coding-synonymous,coding-synonymous	AIRE	NM_000383.2,NM_000658.2	,	60,547,5878	CC,CT,TT		0.0233,15.1757,5.1426	,	401/546,204/349	45712983	667,12303	2191	4294	6485	SO:0001819	synonymous_variant	326	exon10	Familial Cancer Database	APECED	TCCGCCTTCTGCA	AB006684	CCDS13706.1	21q22.3	2014-09-17	2007-06-20		ENSG00000160224	ENSG00000160224		"""Zinc fingers, PHD-type"""	360	protein-coding gene	gene with protein product	"""autoimmune polyendocrinopathy candidiasis ectodermal dystrophy"""	607358	"""autoimmune regulator (autoimmune polyendocrinopathy candidiasis ectodermal dystrophy)"""	APECED		9398840	Standard	NM_000383		Approved	PGA1, APS1	uc002zei.3	O43918	OTTHUMG00000086921	ENST00000291582.5:c.1203T>C	21.37:g.45712983T>C		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	63	24	0.380952	NM_000383	B2RP50|O43922|O43932|O75745	Silent	SNP	ENST00000291582.5	37	CCDS13706.1																																																																																			T|0.951;C|0.049	0.049	strong		0.677	AIRE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195842.2		
CDH11	1009	hgsc.bcm.edu	37	16	65025718	65025718	+	Missense_Mutation	SNP	G	G	A	rs35195	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:65025718G>A	ENST00000268603.4	-	6	1379	c.764C>T	c.(763-765)aCg>aTg	p.T255M	CDH11_ENST00000394156.3_Missense_Mutation_p.T255M|CDH11_ENST00000566827.1_Missense_Mutation_p.T129M	NM_001797.2	NP_001788.2	P55287	CAD11_HUMAN	cadherin 11, type 2, OB-cadherin (osteoblast)	255	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.		T -> M (in dbSNP:rs35195).		adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|corticospinal tract morphogenesis (GO:0021957)|homophilic cell adhesion (GO:0007156)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(19)|lung(40)|ovary(3)|prostate(3)|skin(2)|urinary_tract(2)	88		Ovarian(137;0.0973)		OV - Ovarian serous cystadenocarcinoma(108;0.205)		CAGTGTGATCGTCACTTTGGT	0.537			T	USP6	aneurysmal bone cysts					TSP Lung(24;0.17)			G|||	909	0.18151	0.0234	0.2075	5008	,	,		18677	0.2044		0.331	False		,,,				2504	0.1994				p.T255M		Atlas-SNP	.		Dom	yes		16	16q22.1	1009	"""cadherin 11, type 2, OB-cadherin (osteoblast)"""		M	CDH11,NS,carcinoma,+1,1	CDH11	260	1	0			c.C764T						PASS	.	G	MET/THR	321,4085	170.9+/-201.2	12,297,1894	344.0	230.0	269.0		764	4.6	1.0	16	dbSNP_76	269	3062,5538	471.8+/-368.2	536,1990,1774	yes	missense	CDH11	NM_001797.2	81	548,2287,3668	AA,AG,GG		35.6047,7.2855,26.0111	probably-damaging	255/797	65025718	3383,9623	2203	4300	6503	SO:0001583	missense	1009	exon6			GTGATCGTCACTT	D21255	CCDS10803.1	16q21	2010-01-26			ENSG00000140937	ENSG00000140937		"""Cadherins / Major cadherins"""	1750	protein-coding gene	gene with protein product	"""OB-Cadherin"""	600023				9615235	Standard	NM_001797		Approved	OB, CAD11	uc002eoi.3	P55287	OTTHUMG00000137494	ENST00000268603.4:c.764C>T	16.37:g.65025718G>A	ENSP00000268603:p.Thr255Met	Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	163	163	1	NM_001797	A8K5D6|A8MZC8|B7WP28|Q15065|Q15066|Q9UQ93|Q9UQ94	Missense_Mutation	SNP	ENST00000268603.4	37	CCDS10803.1	484	0.2216117216117216	14	0.028455284552845527	92	0.2541436464088398	133	0.23251748251748253	245	0.3232189973614776	G	19.20	3.782474	0.70222	0.072855	0.356047	ENSG00000140937	ENST00000268603;ENST00000394156;ENST00000538390	T;T	0.03468	3.92;3.92	5.54	4.59	0.56863	Cadherin (5);Cadherin-like (1);	0.145674	0.64402	N	0.000008	T	0.00012	0.0000	M	0.72576	2.205	0.21675	P	0.999594887	D;D	0.67145	0.986;0.996	B;P	0.60886	0.219;0.88	T	0.48885	-0.8995	9	0.72032	D	0.01	.	13.2834	0.60228	0.076:0.0:0.924:0.0	rs35195;rs966262;rs1200180;rs2229572;rs17851050;rs52827080;rs57188221;rs35195	255;255	P55287-2;P55287	.;CAD11_HUMAN	M	255;255;238	ENSP00000268603:T255M;ENSP00000377711:T255M	ENSP00000268603:T255M	T	-	2	0	CDH11	63583219	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	3.388000	0.52509	1.344000	0.45657	0.650000	0.86243	ACG	G|0.763;A|0.237	0.237	strong		0.537	CDH11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268755.1	NM_033664	
PLIN4	729359	hgsc.bcm.edu	37	19	4511890	4511890	+	Silent	SNP	G	G	A	rs200897749	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:4511890G>A	ENST00000301286.3	-	3	2039	c.2040C>T	c.(2038-2040)acC>acT	p.T680T		NM_001080400.1	NP_001073869.1	Q96Q06	PLIN4_HUMAN	perilipin 4	680	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						CCTTGGTGCCGGTCAGCACGG	0.577																																					p.T680T		Atlas-SNP	.											.	PLIN4	191	.	0			c.C2040T						PASS	.	G		109,4179		0,109,2035	193.0	206.0	201.0		2040	-10.6	0.0	19	dbSNP_132	201	121,8343		0,121,4111	no	coding-synonymous	PLIN4	NM_001080400.1		0,230,6146	AA,AG,GG		1.4296,2.542,1.8036		680/1358	4511890	230,12522	2144	4232	6376	SO:0001819	synonymous_variant	729359	exon3			GGTGCCGGTCAGC	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.2040C>T	19.37:g.4511890G>A		Somatic	230	0	0		WXS	Illumina HiSeq	Phase_I	236	38	0.161017	NM_001080400	A6NEI2	Silent	SNP	ENST00000301286.3	37	CCDS45927.1																																																																																			G|0.982;A|0.018	0.018	strong		0.577	PLIN4-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395095.1	XM_170901	
APCDD1	147495	hgsc.bcm.edu	37	18	10471732	10471732	+	Missense_Mutation	SNP	G	G	A	rs3748415	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:10471732G>A	ENST00000355285.5	+	3	802	c.448G>A	c.(448-450)Gtc>Atc	p.V150I	APCDD1_ENST00000578882.1_Missense_Mutation_p.V150I	NM_153000.4	NP_694545.1			adenomatosis polyposis coli down-regulated 1											NS(1)|breast(1)|endometrium(3)|large_intestine(5)|lung(7)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22				READ - Rectum adenocarcinoma(15;0.08)		GCTGCACAACGTCCAGGTGAT	0.642													G|||	484	0.0966454	0.0068	0.0778	5008	,	,		16584	0.1518		0.1123	False		,,,				2504	0.1585				p.V150I		Atlas-SNP	.											.	APCDD1	57	.	0			c.G448A						PASS	.	G	ILE/VAL	108,4298	82.9+/-121.4	1,106,2096	51.0	56.0	55.0		448	4.4	0.2	18	dbSNP_107	55	1034,7566	219.0+/-257.2	60,914,3326	yes	missense	APCDD1	NM_153000.4	29	61,1020,5422	AA,AG,GG		12.0233,2.4512,8.7806	benign	150/515	10471732	1142,11864	2203	4300	6503	SO:0001583	missense	147495	exon3			CACAACGTCCAGG	AB056722	CCDS11849.1	18p11.21	2006-07-07			ENSG00000154856	ENSG00000154856			15718	protein-coding gene	gene with protein product		607479				12384519	Standard	NM_153000		Approved	B7323	uc002kom.4	Q8J025	OTTHUMG00000131635	ENST00000355285.5:c.448G>A	18.37:g.10471732G>A	ENSP00000347433:p.Val150Ile	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	49	30	0.612245	NM_153000		Missense_Mutation	SNP	ENST00000355285.5	37	CCDS11849.1	209	0.09569597069597069	6	0.012195121951219513	26	0.0718232044198895	80	0.13986013986013987	97	0.1279683377308707	G	9.715	1.157999	0.21454	0.024512	0.120233	ENSG00000154856	ENST00000355285;ENST00000423585	T	0.25749	1.78	5.3	4.42	0.53409	.	0.237199	0.43260	D	0.000594	T	0.00144	0.0004	L	0.50333	1.59	0.29071	P	0.883319	B	0.32893	0.389	B	0.30782	0.12	T	0.07347	-1.0777	9	0.42905	T	0.14	-52.7739	8.1421	0.31089	0.1852:0.0:0.8148:0.0	rs3748415;rs52837795;rs61043980;rs3748415	150	Q8J025	APCD1_HUMAN	I	150;201	ENSP00000347433:V150I	ENSP00000347433:V150I	V	+	1	0	APCDD1	10461732	0.969000	0.33509	0.151000	0.22473	0.531000	0.34715	1.918000	0.40006	2.477000	0.83638	0.655000	0.94253	GTC	G|0.906;A|0.094	0.094	strong		0.642	APCDD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254529.2	NM_153000	
KDM2B	84678	hgsc.bcm.edu	37	12	121880520	121880520	+	Silent	SNP	G	G	A	rs3751131	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:121880520G>A	ENST00000377071.4	-	19	2796	c.2724C>T	c.(2722-2724)gaC>gaT	p.D908D	KDM2B_ENST00000542973.1_Silent_p.D276D|KDM2B_ENST00000377069.4_Silent_p.D839D|KDM2B_ENST00000536437.1_Intron	NM_032590.4	NP_115979.3	Q8NHM5	KDM2B_HUMAN	lysine (K)-specific demethylase 2B	908					embryonic camera-type eye morphogenesis (GO:0048596)|forebrain development (GO:0030900)|fourth ventricle development (GO:0021592)|hindbrain development (GO:0030902)|histone demethylation (GO:0016577)|histone H2A monoubiquitination (GO:0035518)|initiation of neural tube closure (GO:0021993)|lateral ventricle development (GO:0021670)|midbrain development (GO:0030901)|midbrain-hindbrain boundary morphogenesis (GO:0021555)|negative regulation of neural precursor cell proliferation (GO:2000178)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|spermatogenesis (GO:0007283)|third ventricle development (GO:0021678)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone demethylase activity (GO:0032452)|histone demethylase activity (H3-K36 specific) (GO:0051864)|rRNA binding (GO:0019843)|zinc ion binding (GO:0008270)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	19						AGCGGGAGTGGTCGCTCTCCC	0.706													G|||	1675	0.334465	0.1566	0.4006	5008	,	,		12186	0.4534		0.4046	False		,,,				2504	0.3333				p.D908D		Atlas-SNP	.											KDM2B_ENST00000377071,colon,carcinoma,-2,2	KDM2B	218	2	0			c.C2724T						PASS	.	G	,	708,3046		79,550,1248	12.0	13.0	13.0		2517,2724	2.2	1.0	12	dbSNP_107	13	3078,5096		591,1896,1600	no	coding-synonymous,coding-synonymous	KDM2B	NM_001005366.1,NM_032590.4	,	670,2446,2848	AA,AG,GG		37.656,18.8599,31.7404	,	839/1266,908/1337	121880520	3786,8142	1877	4087	5964	SO:0001819	synonymous_variant	84678	exon19			GGAGTGGTCGCTC	AJ459424	CCDS41849.1, CCDS41850.1	12q24.31	2014-02-18	2009-04-06	2009-04-06	ENSG00000089094	ENSG00000089094		"""F-boxes / Leucine-rich repeats"", ""Chromatin-modifying enzymes / K-demethylases"""	13610	protein-coding gene	gene with protein product	"""jumonji C domain-containing histone demethylase 1B"""	609078	"""F-box and leucine-rich repeat protein 10"""	FBXL10		10799292	Standard	NM_032590		Approved	PCCX2, CXXC2, Fbl10, JHDM1B	uc001uat.3	Q8NHM5	OTTHUMG00000169071	ENST00000377071.4:c.2724C>T	12.37:g.121880520G>A		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	85	33	0.388235	NM_032590	A8MRS1|Q8NCI2|Q96HC7|Q96SL0|Q96T03|Q9NS96|Q9UF75	Silent	SNP	ENST00000377071.4	37	CCDS41850.1																																																																																			G|0.651;A|0.349	0.349	strong		0.706	KDM2B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000402132.2	NM_032590	
ENDOG	2021	hgsc.bcm.edu	37	9	131584729	131584729	+	Missense_Mutation	SNP	G	G	T	rs61737988	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:131584729G>T	ENST00000372642.4	+	3	945	c.734G>T	c.(733-735)cGc>cTc	p.R245L	C9orf114_ENST00000361256.5_3'UTR	NM_004435.2	NP_004426.2	Q14249	NUCG_HUMAN	endonuclease G	245					apoptotic DNA fragmentation (GO:0006309)|DNA recombination (GO:0006310)|in utero embryonic development (GO:0001701)|positive regulation of apoptotic process (GO:0043065)|response to antibiotic (GO:0046677)|response to tumor necrosis factor (GO:0034612)	mitochondrion (GO:0005739)	endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)|nuclease activity (GO:0004518)|nucleic acid binding (GO:0003676)										ATTGAGCTCCGCACCTACGTG	0.587													G|||	5	0.000998403	0.0	0.0014	5008	,	,		21105	0.0		0.001	False		,,,				2504	0.0031				p.R245L		Atlas-SNP	.											.	ENDOG	8	.	0			c.G734T						PASS	.	G	LEU/ARG,	3,4401		0,3,2199	70.0	61.0	64.0		734,	4.7	1.0	9	dbSNP_129	64	19,8581		0,19,4281	yes	missense,utr-3	ENDOG,C9orf114	NM_004435.2,NM_016390.2	102,	0,22,6480	TT,TG,GG		0.2209,0.0681,0.1692	possibly-damaging,	245/298,	131584729	22,12982	2202	4300	6502	SO:0001583	missense	2021	exon3			AGCTCCGCACCTA	X79444	CCDS6912.1	9q34.1	2008-06-04			ENSG00000167136	ENSG00000167136			3346	protein-coding gene	gene with protein product		600440				7789991	Standard	NM_004435		Approved		uc004bwc.3	Q14249	OTTHUMG00000020763	ENST00000372642.4:c.734G>T	9.37:g.131584729G>T	ENSP00000361725:p.Arg245Leu	Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	143	74	0.517483	NM_004435	Q5T281|Q9BSP2	Missense_Mutation	SNP	ENST00000372642.4	37	CCDS6912.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	G	18.18	3.566808	0.65651	6.81E-4	0.002209	ENSG00000167136	ENST00000372642	T	0.66995	-0.24	5.63	4.74	0.60224	DNA/RNA non-specific endonuclease (2);Extracellular Endonuclease, subunit A (2);	0.063724	0.64402	D	0.000004	T	0.66157	0.2761	L	0.39633	1.23	0.80722	D	1	P	0.51537	0.946	P	0.49953	0.627	T	0.68232	-0.5463	10	0.52906	T	0.07	-1.808	13.8836	0.63696	0.0731:0.0:0.9269:0.0	rs61737988	245	Q14249	NUCG_HUMAN	L	245	ENSP00000361725:R245L	ENSP00000361725:R245L	R	+	2	0	ENDOG	130624550	1.000000	0.71417	0.977000	0.42913	0.284000	0.27059	6.040000	0.70980	1.384000	0.46424	-0.463000	0.05309	CGC	G|0.998;T|0.002	0.002	strong		0.587	ENDOG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054505.1	NM_004435	
GPS2	2874	hgsc.bcm.edu	37	17	7216540	7216540	+	Silent	SNP	G	G	A	rs2270981	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:7216540G>A	ENST00000380728.2	-	9	1095	c.795C>T	c.(793-795)ttC>ttT	p.F265F	GPS2_ENST00000389167.5_Silent_p.F265F|GPS2_ENST00000391950.3_Silent_p.F265F|RP11-542C16.2_ENST00000575474.1_3'UTR			Q13227	GPS2_HUMAN	G protein pathway suppressor 2	265					cell cycle (GO:0007049)|inactivation of MAPK activity (GO:0000188)|JNK cascade (GO:0007254)|negative regulation of JNK cascade (GO:0046329)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	GTPase inhibitor activity (GO:0005095)|transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(1)|ovary(2)|pancreas(1)|prostate(1)|stomach(1)|urinary_tract(4)	24		Prostate(122;0.157)				CTGAGTCGGAGAAGCCAGTCT	0.547											OREG0024133	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	507	0.101238	0.0386	0.0922	5008	,	,		20827	0.252		0.0457	False		,,,				2504	0.0941				p.F265F		Atlas-SNP	.											.	GPS2	44	.	0			c.C795T						PASS	.						131.0	128.0	129.0					17																	7216540		2203	4300	6503	SO:0001819	synonymous_variant	2874	exon9			GTCGGAGAAGCCA	U28963	CCDS11100.1	17p13.1	2006-04-29			ENSG00000132522	ENSG00000132522			4550	protein-coding gene	gene with protein product		601935				8943324	Standard	NM_004489		Approved		uc002gfx.1	Q13227	OTTHUMG00000102198	ENST00000380728.2:c.795C>T	17.37:g.7216540G>A		Somatic	93	0	0	640	WXS	Illumina HiSeq	Phase_I	110	49	0.445455	NM_004489	B4DXA1|Q6FHM8	Silent	SNP	ENST00000380728.2	37	CCDS11100.1																																																																																			G|0.879;A|0.121	0.121	strong		0.547	GPS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000220048.4	NM_004489	
NPVF	64111	hgsc.bcm.edu	37	7	25267934	25267934	+	Missense_Mutation	SNP	T	T	C	rs877834	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:25267934T>C	ENST00000222674.2	-	1	171	c.125A>G	c.(124-126)gAc>gGc	p.D42G		NM_022150.3	NP_071433	Q9HCQ7	NPVF_HUMAN	neuropeptide VF precursor	42			D -> G (in dbSNP:rs877834). {ECO:0000269|PubMed:11951088}.		negative regulation of gonadotropin secretion (GO:0032277)|neuropeptide signaling pathway (GO:0007218)	extracellular region (GO:0005576)				cervix(1)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|urinary_tract(1)	15						AGAATATTTGTCATAATTTTC	0.279													T|||	1238	0.247204	0.0908	0.2594	5008	,	,		18226	0.5129		0.1849	False		,,,				2504	0.2403				p.D42G		Atlas-SNP	.											.	NPVF	36	.	0			c.A125G						PASS	.	T	GLY/ASP	482,3916	217.8+/-236.0	32,418,1749	54.0	60.0	58.0		125	0.3	0.0	7	dbSNP_86	58	1574,7004	291.3+/-300.3	141,1292,2856	yes	missense	NPVF	NM_022150.3	94	173,1710,4605	CC,CT,TT		18.3493,10.9595,15.8446	benign	42/197	25267934	2056,10920	2199	4289	6488	SO:0001583	missense	64111	exon1			TATTTGTCATAAT	AB040290	CCDS5395.1	7p21-p15	2013-02-28	2006-10-06	2006-10-06	ENSG00000105954	ENSG00000105954		"""Endogenous ligands"""	13782	protein-coding gene	gene with protein product	"""RFamide-related peptide precursor"", ""FMRFamide-related peptide precursor"""		"""chromosome 7 open reading frame 9"""	C7orf9		11951088, 11173868	Standard	NM_022150		Approved	RFRP	uc003sxo.3	Q9HCQ7	OTTHUMG00000128509	ENST00000222674.2:c.125A>G	7.37:g.25267934T>C	ENSP00000222674:p.Asp42Gly	Somatic	158	1	0.00632911		WXS	Illumina HiSeq	Phase_I	103	80	0.776699	NM_022150	A4D164|Q7LE27|Q96PI9	Missense_Mutation	SNP	ENST00000222674.2	37	CCDS5395.1	572	0.2619047619047619	44	0.08943089430894309	92	0.2541436464088398	293	0.5122377622377622	143	0.18865435356200527	T	8.124	0.781553	0.16120	0.109595	0.183493	ENSG00000105954	ENST00000222674	T	0.30981	1.51	5.57	0.266	0.15617	.	0.473353	0.19711	N	0.107806	T	0.00012	0.0000	L	0.54908	1.71	0.58432	P	1.0000000000287557E-6	B	0.11235	0.004	B	0.11329	0.006	T	0.43310	-0.9399	9	0.35671	T	0.21	-12.9291	4.4368	0.11554	0.0:0.281:0.1623:0.5567	rs877834;rs1130038;rs3177707;rs3188502;rs16873801;rs17412537;rs57473358;rs877834	42	Q9HCQ7	RFRP_HUMAN	G	42	ENSP00000222674:D42G	ENSP00000222674:D42G	D	-	2	0	NPVF	25234459	0.091000	0.21658	0.004000	0.12327	0.871000	0.50021	0.069000	0.14552	0.085000	0.17107	0.528000	0.53228	GAC	C|0.206;N|0.000	0.206	strong		0.279	NPVF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250315.1	NM_022150	
SMIM11	54065	hgsc.bcm.edu	37	21	35757787	35757787	+	Silent	SNP	C	C	T	rs61747964	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:35757787C>T	ENST00000399295.2	+	3	394	c.24C>T	c.(22-24)caC>caT	p.H8H	SMIM11_ENST00000399292.3_Silent_p.H8H|SMIM11_ENST00000481710.1_3'UTR|SMIM11_ENST00000399299.1_Intron			P58511	SIM11_HUMAN	small integral membrane protein 11	8						integral component of membrane (GO:0016021)											TTCTTGAGCACGTGCCCCTGC	0.403													C|||	121	0.0241613	0.0408	0.0245	5008	,	,		20251	0.002		0.0129	False		,,,				2504	0.0358				p.H8H		Atlas-SNP	.											.	.	.	.	0			c.C24T						PASS	.	C		200,4206	126.1+/-163.2	2,196,2005	106.0	89.0	95.0		24	0.4	0.8	21	dbSNP_129	95	269,8331	103.8+/-164.8	4,261,4035	no	coding-synonymous	FAM165B	NM_058182.4		6,457,6040	TT,TC,CC		3.1279,4.5393,3.606		8/59	35757787	469,12537	2203	4300	6503	SO:0001819	synonymous_variant	54065	exon3			TGAGCACGTGCCC	BC015596	CCDS33550.1	21q22.12	2012-12-03	2012-12-03	2012-12-03	ENSG00000205670	ENSG00000205670			1293	protein-coding gene	gene with protein product			"""chromosome 21 open reading frame 51"", ""family with sequence similarity 165, member B"""	C21orf51, FAM165B			Standard	NM_058182		Approved		uc002ytu.4	P58511	OTTHUMG00000086193	ENST00000399295.2:c.24C>T	21.37:g.35757787C>T		Somatic	307	0	0		WXS	Illumina HiSeq	Phase_I	290	107	0.368966	NM_058182		Silent	SNP	ENST00000399295.2	37	CCDS33550.1																																																																																			C|0.971;T|0.029	0.029	strong		0.403	SMIM11-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194078.1	NM_058182	
ZNF71	58491	hgsc.bcm.edu	37	19	57132968	57132968	+	Missense_Mutation	SNP	G	G	A	rs2072501	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:57132968G>A	ENST00000328070.6	+	3	547	c.313G>A	c.(313-315)Gta>Ata	p.V105I		NM_021216.4	NP_067039.1	Q9NQZ8	ZNF71_HUMAN	zinc finger protein 71	105			V -> I (in dbSNP:rs2072501).		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)|large_intestine(5)|lung(13)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	26				GBM - Glioblastoma multiforme(193;0.062)|Lung(386;0.0681)|LUSC - Lung squamous cell carcinoma(496;0.18)		CTGTCCACCCGTAAGGCGTGG	0.587													A|||	1267	0.252995	0.3192	0.2522	5008	,	,		18396	0.2718		0.1899	False		,,,				2504	0.2096				p.V105I		Atlas-SNP	.											.	ZNF71	69	.	0			c.G313A						PASS	.	A	ILE/VAL	1368,3038	690.4+/-405.3	208,952,1043	53.0	50.0	51.0		313	-0.3	0.0	19	dbSNP_96	51	1575,7025	744.3+/-407.2	137,1301,2862	yes	missense	ZNF71	NM_021216.4	29	345,2253,3905	AA,AG,GG		18.314,31.0486,22.628	benign	105/490	57132968	2943,10063	2203	4300	6503	SO:0001583	missense	58491	exon3			CCACCCGTAAGGC	X60074	CCDS12947.1	19q13.4	2013-01-08	2006-05-12			ENSG00000197951		"""Zinc fingers, C2H2-type"""	13141	protein-coding gene	gene with protein product		194545	"""zinc finger protein 71 (Cos26)"""			1639391	Standard	NM_021216		Approved	Cos26, EZFIT	uc002qnm.4	Q9NQZ8		ENST00000328070.6:c.313G>A	19.37:g.57132968G>A	ENSP00000328245:p.Val105Ile	Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	37	37	1	NM_021216	Q15919|Q9UC09|Q9UQD3	Missense_Mutation	SNP	ENST00000328070.6	37	CCDS12947.1	507	0.23214285714285715	135	0.27439024390243905	81	0.22375690607734808	152	0.26573426573426573	139	0.18337730870712401	A	2.889	-0.230028	0.06022	0.310486	0.18314	ENSG00000197951	ENST00000328070	T	0.06933	3.24	3.22	-0.309	0.12769	.	.	.	.	.	T	0.00012	0.0000	N	0.05510	-0.035	0.80722	P	0.0	B	0.06786	0.001	B	0.01281	0.0	T	0.45948	-0.9226	8	0.66056	D	0.02	.	10.2829	0.43550	0.095:0.0:0.7712:0.1338	rs2072501;rs61244850;rs2072501	105	Q9NQZ8	ZNF71_HUMAN	I	105	ENSP00000328245:V105I	ENSP00000328245:V105I	V	+	1	0	ZNF71	61824780	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.271000	0.08572	-0.371000	0.08004	-2.461000	0.00205	GTA	G|0.766;A|0.234	0.234	strong		0.587	ZNF71-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459798.2	NM_021216	
LARP6	55323	hgsc.bcm.edu	37	15	71125339	71125339	+	Silent	SNP	G	G	A	rs28676469	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:71125339G>A	ENST00000299213.8	-	3	598	c.528C>T	c.(526-528)ttC>ttT	p.F176F	RP11-138H8.7_ENST00000592096.1_lincRNA	NM_018357.2	NP_060827.2	Q9BRS8	LARP6_HUMAN	La ribonucleoprotein domain family, member 6	176	HTH La-type RNA-binding. {ECO:0000255|PROSITE-ProRule:PRU00332}.				regulation of translation (GO:0006417)|RNA processing (GO:0006396)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			breast(1)|cervix(1)|endometrium(1)|large_intestine(5)|lung(9)|skin(1)|upper_aerodigestive_tract(1)	19						TCTCGTTGGGGAACAGTGGGA	0.562													G|||	283	0.0565096	0.1293	0.036	5008	,	,		18525	0.0		0.0477	False		,,,				2504	0.0399				p.F176F		Atlas-SNP	.											.	LARP6	43	.	0			c.C528T						PASS	.	G		499,3899	227.5+/-242.7	23,453,1723	70.0	71.0	71.0		528	4.2	1.0	15	dbSNP_125	71	448,8146	133.3+/-190.8	15,418,3864	no	coding-synonymous	LARP6	NM_018357.2		38,871,5587	AA,AG,GG		5.2129,11.3461,7.2891		176/492	71125339	947,12045	2199	4297	6496	SO:0001819	synonymous_variant	55323	exon3			GTTGGGGAACAGT	BC009446	CCDS10236.1, CCDS32281.1	15q23	2012-11-19			ENSG00000166173	ENSG00000166173		"""La ribonucleoprotein domain containing"""	24012	protein-coding gene	gene with protein product		611300				12477932	Standard	NM_018357		Approved	acheron, FLJ11196	uc002ass.3	Q9BRS8	OTTHUMG00000172179	ENST00000299213.8:c.528C>T	15.37:g.71125339G>A		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	104	39	0.375	NM_018357	Q5XKE4|Q8N3N2|Q9NUR0	Silent	SNP	ENST00000299213.8	37	CCDS32281.1																																																																																			G|0.929;A|0.071	0.071	strong		0.562	LARP6-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417197.2	NM_018357	
ULK3	25989	hgsc.bcm.edu	37	15	75131959	75131959	+	Silent	SNP	A	A	G	rs936227	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:75131959A>G	ENST00000440863.2	-	7	883	c.792T>C	c.(790-792)ttT>ttC	p.F264F	ULK3_ENST00000568667.1_Silent_p.F275F|ULK3_ENST00000569437.1_Silent_p.F264F	NM_001099436.1	NP_001092906	Q6PHR2	ULK3_HUMAN	unc-51 like kinase 3	264	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				autophagic vacuole assembly (GO:0000045)|autophagy (GO:0006914)|cellular senescence (GO:0090398)|negative regulation of smoothened signaling pathway (GO:0045879)|positive regulation of smoothened signaling pathway (GO:0045880)|protein autophosphorylation (GO:0046777)|regulation of autophagy (GO:0010506)	ATG1/UKL1 signaling complex (GO:0034273)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|pre-autophagosomal structure (GO:0000407)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)	2						GGTGCGCAAAAAAGTCCTGGA	0.692													G|||	2301	0.459465	0.3533	0.5519	5008	,	,		15912	0.3383		0.5825	False		,,,				2504	0.5358				p.F264F		Atlas-SNP	.											.	ULK3	30	.	0			c.T792C						PASS	.	G		1577,2287		351,875,706	15.0	19.0	18.0		792	4.4	1.0	15	dbSNP_86	18	4971,3217		1575,1821,698	no	coding-synonymous	ULK3	NM_001099436.1		1926,2696,1404	GG,GA,AA		39.2892,40.8126,45.6688		264/473	75131959	6548,5504	1932	4094	6026	SO:0001819	synonymous_variant	25989	exon7			CGCAAAAAAGTCC	BC048289		15q24.1	2013-07-02	2013-07-02			ENSG00000140474			19703	protein-coding gene	gene with protein product		613472	"""unc-51-like kinase 3 (C. elegans)"""				Standard	XM_005254289		Approved	DKFZP434C131, FLJ90566	uc010bkf.1	Q6PHR2		ENST00000440863.2:c.792T>C	15.37:g.75131959A>G		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	76	76	1	NM_001099436	B2RXK3|B4DRQ7|D3DW68|Q9NPN5|Q9UFS4	Silent	SNP	ENST00000440863.2	37	CCDS45305.1																																																																																			A|0.563;G|0.437	0.437	strong		0.692	ULK3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000421734.4	NM_015518	
CFAP74	85452	hgsc.bcm.edu	37	1	1896440	1896440	+	IGR	SNP	G	G	A	rs16824585	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:1896440G>A								TMEM52 (45728 upstream) : C1orf222 (23122 downstream)																							GTGCGCTCCAGGATGTCCTTG	0.647													g|||	1085	0.216653	0.2489	0.2032	5008	,	,		16690	0.2718		0.2276	False		,,,				2504	0.1145				p.L488L		Atlas-SNP	.											.	KIAA1751	92	.	0			c.C1462T						PASS	.			949,3145		126,697,1224	40.0	44.0	43.0		1462	2.2	1.0	1	dbSNP_123	43	2052,6326		258,1536,2395	no	coding-synonymous	KIAA1751	NM_001080484.1		384,2233,3619	AA,AG,GG		24.4927,23.1803,24.0619		488/763	1896440	3001,9471	2047	4189	6236	SO:0001628	intergenic_variant	85452	exon13			GCTCCAGGATGTC																													1.37:g.1896440G>A		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	56	17	0.303571	NM_001080484		Silent	SNP		37																																																																																				G|0.764;A|0.236	0.236	strong	0	0.647								
ABCA13	154664	hgsc.bcm.edu	37	7	48287840	48287840	+	Missense_Mutation	SNP	G	G	A	rs2361519	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:48287840G>A	ENST00000435803.1	+	14	1688	c.1664G>A	c.(1663-1665)cGt>cAt	p.R555H		NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	555			R -> H (in dbSNP:rs2361519).		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						GTTAAGGATCGTATTTTGCAA	0.378													G|||	992	0.198083	0.3003	0.1873	5008	,	,		19918	0.1508		0.1123	False		,,,				2504	0.2045				p.R555H		Atlas-SNP	.											.	ABCA13	1192	.	0			c.G1664A						PASS	.	G	HIS/ARG	990,2674		139,712,981	57.0	55.0	56.0		1664	-8.6	0.0	7	dbSNP_100	56	924,7248		55,814,3217	yes	missense	ABCA13	NM_152701.3	29	194,1526,4198	AA,AG,GG		11.3069,27.0197,16.171	benign	555/5059	48287840	1914,9922	1832	4086	5918	SO:0001583	missense	154664	exon14			AGGATCGTATTTT	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.1664G>A	7.37:g.48287840G>A	ENSP00000411096:p.Arg555His	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	32	10	0.3125	NM_152701	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Missense_Mutation	SNP	ENST00000435803.1	37	CCDS47584.1	409	0.18727106227106227	155	0.3150406504065041	65	0.17955801104972377	102	0.17832167832167833	87	0.11477572559366754	G	0.438	-0.899834	0.02472	0.270197	0.113069	ENSG00000179869	ENST00000435803	D	0.88201	-2.35	4.29	-8.57	0.00900	.	1.686530	0.03124	N	0.164131	T	0.00012	0.0000	N	0.04880	-0.145	0.80722	P	0.0	B	0.09022	0.002	B	0.04013	0.001	T	0.46898	-0.9158	9	0.02654	T	1	.	15.1309	0.72523	0.3917:0.0:0.6083:0.0	rs2361519;rs4283998;rs2361519	555	Q86UQ4	ABCAD_HUMAN	H	555	ENSP00000411096:R555H	ENSP00000411096:R555H	R	+	2	0	ABCA13	48258386	0.000000	0.05858	0.002000	0.10522	0.607000	0.37147	-1.368000	0.02580	-1.979000	0.00992	-1.099000	0.02127	CGT	G|0.802;A|0.197	0.197	strong		0.378	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701	
MUC17	140453	hgsc.bcm.edu	37	7	100676968	100676968	+	Silent	SNP	G	G	A	rs138994021|rs71525818	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:100676968G>A	ENST00000306151.4	+	3	2335	c.2271G>A	c.(2269-2271)acG>acA	p.T757T		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	757	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)					TCAGCAAAACGCTGTTGACCA	0.483													A|||	20	0.00399361	0.0045	0.0	5008	,	,		28523	0.0		0.0139	False		,,,				2504	0.0				p.T757T		Atlas-SNP	.											.	MUC17	804	.	0			c.G2271A						PASS	.	G		23,4383	29.0+/-57.7	0,23,2180	300.0	301.0	300.0		2271	-1.3	0.0	7	dbSNP_134	300	94,8506	52.7+/-113.3	0,94,4206	no	coding-synonymous	MUC17	NM_001040105.1		0,117,6386	AA,AG,GG		1.093,0.522,0.8996		757/4494	100676968	117,12889	2203	4300	6503	SO:0001819	synonymous_variant	140453	exon3			CAAAACGCTGTTG	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.2271G>A	7.37:g.100676968G>A		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	58	29	0.5	NM_001040105	O14761|Q685J2|Q8TDH7	Silent	SNP	ENST00000306151.4	37	CCDS34711.1																																																																																			G|0.991;A|0.009	0.009	strong		0.483	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
CBY1	25776	hgsc.bcm.edu	37	22	39069181	39069181	+	Silent	SNP	T	T	C	rs3747174	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:39069181T>C	ENST00000216029.3	+	5	455	c.321T>C	c.(319-321)gcT>gcC	p.A107A	RP3-508I15.9_ENST00000422408.2_RNA|RP3-508I15.9_ENST00000412067.1_RNA|RP3-508I15.9_ENST00000431924.2_RNA|RP3-508I15.9_ENST00000444381.1_RNA	NM_015373.3	NP_056188.1	Q9Y3M2	CBY1_HUMAN	chibby homolog 1 (Drosophila)	107	Minimal region for the interaction with PKD2.				cardiac muscle cell differentiation (GO:0055007)|cilium assembly (GO:0042384)|fat cell differentiation (GO:0045444)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of Wnt signaling pathway (GO:0030178)|protein localization (GO:0008104)	ciliary basal body (GO:0036064)|nucleus (GO:0005634)|trans-Golgi network (GO:0005802)	beta-catenin binding (GO:0008013)|identical protein binding (GO:0042802)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|ovary(1)	4	Melanoma(58;0.04)					AGTCCACTGCTGAATCCCACT	0.498													C|||	1431	0.285743	0.2897	0.2032	5008	,	,		20300	0.3502		0.2932	False		,,,				2504	0.2648				p.A150A		Atlas-SNP	.											.	CBY1	10	.	0			c.T450C						PASS	.	C	,	1279,3127	700.4+/-406.6	186,907,1110	71.0	65.0	67.0		321,321	-10.1	0.1	22	dbSNP_107	67	2514,6086	693.3+/-404.6	362,1790,2148	no	coding-synonymous,coding-synonymous	CBY1	NM_001002880.1,NM_015373.3	,	548,2697,3258	CC,CT,TT		29.2326,29.0286,29.1635	,	107/127,107/127	39069181	3793,9213	2203	4300	6503	SO:0001819	synonymous_variant	25776	exon6			CACTGCTGAATCC	BK005534	CCDS13974.1, CCDS74861.1	22q12	2014-02-06	2007-01-26	2007-01-26	ENSG00000100211	ENSG00000100211			1307	protein-coding gene	gene with protein product	"""chibby CTNNB1-mediated transcription inhibitor"""	607757	"""chromosome 22 open reading frame 2"", ""PKD2 interactor, golgi and endoplasmic reticulum associated 1"""	C22orf2, PGEA1		10591208, 15194699	Standard	NM_015373		Approved	PIGEA14, PIGEA-14, Chibby, Cby	uc003awb.4	Q9Y3M2	OTTHUMG00000150990	ENST00000216029.3:c.321T>C	22.37:g.39069181T>C		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	68	32	0.470588	NM_001002880	B2R4S2|Q66GT6|Q9UIK9	Silent	SNP	ENST00000216029.3	37	CCDS13974.1																																																																																			T|0.702;C|0.298	0.298	strong		0.498	CBY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320832.1	NM_015373	
THSD7A	221981	hgsc.bcm.edu	37	7	11581134	11581134	+	Silent	SNP	T	T	C	rs2074603	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:11581134T>C	ENST00000423059.4	-	6	1985	c.1734A>G	c.(1732-1734)gcA>gcG	p.A578A		NM_015204.2	NP_056019.1	Q9UPZ6	THS7A_HUMAN	thrombospondin, type I, domain containing 7A	578					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)		CCAGTCTCACTGCTTTCCAGT	0.527										HNSCC(18;0.044)			T|||	2362	0.471645	0.4902	0.3775	5008	,	,		17905	0.5387		0.4245	False		,,,				2504	0.4928				p.A578A		Atlas-SNP	.											.	THSD7A	219	.	0			c.A1734G						PASS	.	T		1846,2132		446,954,589	92.0	94.0	93.0		1734	-3.8	1.0	7	dbSNP_96	93	3470,4848		713,2044,1402	no	coding-synonymous	THSD7A	NM_015204.2		1159,2998,1991	CC,CT,TT		41.7168,46.4052,43.2336		578/1658	11581134	5316,6980	1989	4159	6148	SO:0001819	synonymous_variant	221981	exon6			TCTCACTGCTTTC		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.1734A>G	7.37:g.11581134T>C		Somatic	215	0	0		WXS	Illumina HiSeq	Phase_I	205	150	0.731707	NM_015204		Silent	SNP	ENST00000423059.4	37	CCDS47543.1																																																																																			T|0.532;C|0.468	0.468	strong		0.527	THSD7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325944.4	XM_928187.2	
ITGAM	3684	hgsc.bcm.edu	37	16	31336888	31336888	+	Missense_Mutation	SNP	C	C	T	rs1143683	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:31336888C>T	ENST00000287497.8	+	21	2648	c.2573C>T	c.(2572-2574)gCc>gTc	p.A858V	ITGAM_ENST00000544665.3_Missense_Mutation_p.A859V			P11215	ITAM_HUMAN	integrin, alpha M (complement component 3 receptor 3 subunit)	858			A -> V (in dbSNP:rs1143683). {ECO:0000269|PubMed:15489334}.		activated T cell proliferation (GO:0050798)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cellular extravasation (GO:0045123)|ectodermal cell differentiation (GO:0010668)|extracellular matrix organization (GO:0030198)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|leukocyte migration involved in inflammatory response (GO:0002523)|microglia development (GO:0014005)|neutrophil chemotaxis (GO:0030593)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integrin complex (GO:0008305)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	glycoprotein binding (GO:0001948)|heparin binding (GO:0008201)|metal ion binding (GO:0046872)			endometrium(7)|kidney(1)|large_intestine(10)|lung(32)|ovary(1)|prostate(4)|skin(1)	56						GTGTCTGGGGCCTTGAAGAGC	0.572													C|||	814	0.16254	0.1906	0.1311	5008	,	,		15814	0.0278		0.1809	False		,,,				2504	0.2669				p.A859V		Atlas-SNP	.											.	ITGAM	137	.	0			c.C2576T						PASS	.	C	VAL/ALA,VAL/ALA	716,3326		64,588,1369	61.0	65.0	64.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	2576,2573	-1.5	0.0	16	dbSNP_86	64	1324,7012		123,1078,2967	yes	missense,missense	ITGAM	NM_001145808.1,NM_000632.3	64,64	187,1666,4336	TT,TC,CC		15.8829,17.714,16.4809	benign,benign	859/1154,858/1153	31336888	2040,10338	2021	4168	6189	SO:0001583	missense	3684	exon21			CTGGGGCCTTGAA	J03925	CCDS45470.1, CCDS54004.1	16p11.2	2010-03-23	2006-02-10			ENSG00000169896		"""CD molecules"", ""Complement system"", ""Integrins"""	6149	protein-coding gene	gene with protein product		120980	"""integrin, alpha M (complement component receptor 3, alpha; also known as CD11b (p170), macrophage antigen alpha polypeptide)"""	CR3A, CD11B			Standard	NM_001145808		Approved	MAC-1, CD11b	uc002ebr.3	P11215		ENST00000287497.8:c.2573C>T	16.37:g.31336888C>T	ENSP00000287497:p.Ala858Val	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	76	41	0.539474	NM_001145808	Q4VAK0|Q4VAK1|Q4VAK2	Missense_Mutation	SNP	ENST00000287497.8	37	CCDS45470.1	264	0.12087912087912088	78	0.15853658536585366	48	0.13259668508287292	1	0.0017482517482517483	137	0.18073878627968337	C	8.716	0.913114	0.17907	0.17714	0.158829	ENSG00000169896	ENST00000544665;ENST00000287497	T;T	0.53423	0.62;0.62	4.7	-1.51	0.08664	Integrin alpha-2 (1);	.	.	.	.	T	0.00073	0.0002	N	0.20401	0.57	0.80722	P	0.0	B;B	0.12630	0.006;0.001	B;B	0.16289	0.015;0.009	T	0.20840	-1.0263	8	0.25106	T	0.35	.	10.8691	0.46872	0.0:0.4306:0.4915:0.0779	rs1143683;rs7201448;rs17839488;rs52803561;rs60433541;rs1143683	264;858	B3KXM6;P11215	.;ITAM_HUMAN	V	859;858	ENSP00000441691:A859V;ENSP00000287497:A858V	ENSP00000287497:A858V	A	+	2	0	ITGAM	31244389	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.193000	0.09573	0.007000	0.14760	0.650000	0.86243	GCC	C|0.870;T|0.130	0.130	strong		0.572	ITGAM-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000432816.1	NM_000632	
CRIPAK	285464	hgsc.bcm.edu	37	4	1389007	1389007	+	Silent	SNP	C	C	T	rs78871723	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:1389007C>T	ENST00000324803.4	+	1	3668	c.708C>T	c.(706-708)tgC>tgT	p.C236C		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)			CGTGCCGATGCGGAGTGCCCG	0.677													t|||	434	0.0866613	0.1702	0.0605	5008	,	,		14541	0.002		0.0805	False		,,,				2504	0.0859				p.C236C		Atlas-SNP	.											CRIPAK,rectum,NS,+2,1	CRIPAK	185	1	0			c.C708T						scavenged	.						160.0	133.0	142.0					4																	1389007		2188	4293	6481	SO:0001819	synonymous_variant	285464	exon1			CCGATGCGGAGTG	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.708C>T	4.37:g.1389007C>T		Somatic	81	5	0.0617284		WXS	Illumina HiSeq	Phase_I	19	10	0.526316	NM_175918	Q8NB03	Silent	SNP	ENST00000324803.4	37	CCDS3349.1																																																																																			C|0.918;T|0.082	0.082	strong		0.677	CRIPAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241607.2	NM_175918	
DYSF	8291	hgsc.bcm.edu	37	2	71906278	71906278	+	Silent	SNP	A	A	C	rs17718530	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:71906278A>C	ENST00000258104.3	+	52	6136	c.5859A>C	c.(5857-5859)ccA>ccC	p.P1953P	DYSF_ENST00000413539.2_Silent_p.P1984P|DYSF_ENST00000479049.2_3'UTR|DYSF_ENST00000394120.2_Silent_p.P1954P|DYSF_ENST00000409651.1_Silent_p.P1985P|DYSF_ENST00000409366.1_Silent_p.P1975P|DYSF_ENST00000409762.1_Silent_p.P1970P|DYSF_ENST00000429174.2_Silent_p.P1974P|DYSF_ENST00000409582.3_Silent_p.P1991P|DYSF_ENST00000410020.3_Silent_p.P1992P|DYSF_ENST00000410041.1_Silent_p.P1971P|DYSF_ENST00000409744.1_Silent_p.P1961P	NM_001130976.1|NM_003494.3	NP_001124448.1|NP_003485.1	O75923	DYSF_HUMAN	dysferlin	1953					plasma membrane repair (GO:0001778)|vesicle fusion (GO:0006906)	cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|phospholipid binding (GO:0005543)			autonomic_ganglia(2)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|lung(57)|ovary(3)|pancreas(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(2)	111						CTTTCCACCCAGAATGGTTTG	0.532													A|||	846	0.16893	0.1513	0.1225	5008	,	,		19686	0.0655		0.2584	False		,,,				2504	0.2403				p.P1992P		Atlas-SNP	.											.	DYSF	536	.	0			c.A5976C						PASS	.	A	,,,,,,,,,,,,,	758,3648	310.0+/-291.3	63,632,1508	136.0	122.0	126.0		5862,5817,5880,5922,5952,5910,5973,5955,5925,5883,5913,5820,5976,5859	-10.6	0.4	2	dbSNP_123	126	2153,6447	369.4+/-335.5	282,1589,2429	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	DYSF	NM_001130455.1,NM_001130976.1,NM_001130977.1,NM_001130978.1,NM_001130979.1,NM_001130980.1,NM_001130981.1,NM_001130982.1,NM_001130983.1,NM_001130984.1,NM_001130985.1,NM_001130986.1,NM_001130987.1,NM_003494.3	,,,,,,,,,,,,,	345,2221,3937	CC,CA,AA		25.0349,17.2038,22.382	,,,,,,,,,,,,,	1954/2082,1939/2067,1960/2088,1974/2102,1984/2112,1970/2098,1991/2119,1985/2113,1975/2103,1961/2089,1971/2099,1940/2068,1992/2120,1953/2081	71906278	2911,10095	2203	4300	6503	SO:0001819	synonymous_variant	8291	exon53			CCACCCAGAATGG	AF075575	CCDS1918.1, CCDS46323.1, CCDS46324.1, CCDS46325.1, CCDS46326.1, CCDS46327.1, CCDS46328.1, CCDS46329.1, CCDS46330.1, CCDS46331.1, CCDS46332.1	2p13.3	2014-09-17	2013-09-12		ENSG00000135636	ENSG00000135636			3097	protein-coding gene	gene with protein product	"""fer-1-like family member 1"""	603009	"""limb girdle muscular dystrophy 2B (autosomal recessive)"""	LGMD2B		8320700	Standard	NM_003494		Approved	FER1L1	uc010fen.3	O75923	OTTHUMG00000129757	ENST00000258104.3:c.5859A>C	2.37:g.71906278A>C		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	89	31	0.348315	NM_001130987	A0FK00|B1PZ70|B1PZ71|B1PZ72|B1PZ73|B1PZ74|B1PZ75|B1PZ76|B1PZ77|B1PZ78|B1PZ79|B1PZ80|B1PZ81|B3KQB9|O75696|Q09EX5|Q0H395|Q53QY3|Q53TD2|Q8TEL8|Q9UEN7	Silent	SNP	ENST00000258104.3	37	CCDS1918.1																																																																																			A|0.799;C|0.201;T|0.000	0.201	strong		0.532	DYSF-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251970.3	NM_003494	
CAB39L	81617	hgsc.bcm.edu	37	13	49956980	49956980	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:49956980C>A	ENST00000355854.4	-	2	564	c.67G>T	c.(67-69)Gac>Tac	p.D23Y	CAB39L_ENST00000409308.1_Missense_Mutation_p.D23Y|CAB39L_ENST00000410043.1_Missense_Mutation_p.D23Y|CAB39L_ENST00000347776.5_Missense_Mutation_p.D23Y|CAB39L_ENST00000476943.1_5'UTR	NM_030925.2	NP_112187.2	Q9H9S4	CB39L_HUMAN	calcium binding protein 39-like	23					cell cycle arrest (GO:0007050)|insulin receptor signaling pathway (GO:0008286)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(2)|large_intestine(4)|lung(3)|pancreas(1)|stomach(1)	12		Lung NSC(96;2.11e-05)|Breast(56;0.00017)|Prostate(109;0.00314)|Hepatocellular(98;0.0207)|Myeloproliferative disorder(33;0.163)|Lung SC(185;0.187)|all_neural(104;0.19)	KIRC - Kidney renal clear cell carcinoma(9;0.206)	GBM - Glioblastoma multiforme(99;3.66e-09)|COAD - Colon adenocarcinoma(199;0.226)		GCCAAATTGTCTTTCAGGATT	0.328																																					p.D23Y		Atlas-SNP	.											.	CAB39L	35	.	0			c.G67T						PASS	.						177.0	159.0	165.0					13																	49956980		1834	4084	5918	SO:0001583	missense	81617	exon2			AATTGTCTTTCAG	AK022639	CCDS9416.2	13q14.11	2008-02-05			ENSG00000102547	ENSG00000102547			20290	protein-coding gene	gene with protein product		612175					Standard	NM_030925		Approved	bA103J18.3, FLJ12577, MO2L	uc001vcw.3	Q9H9S4	OTTHUMG00000016914	ENST00000355854.4:c.67G>T	13.37:g.49956980C>A	ENSP00000348113:p.Asp23Tyr	Somatic	225	0	0		WXS	Illumina HiSeq	Phase_I	254	63	0.248031	NM_030925	Q5TAW6|Q6WG71|Q96FG1|Q9BZ33	Missense_Mutation	SNP	ENST00000355854.4	37	CCDS9416.2	.	.	.	.	.	.	.	.	.	.	C	29.1	4.976567	0.92982	.	.	ENSG00000102547	ENST00000355854;ENST00000347776;ENST00000378341;ENST00000409308;ENST00000410043;ENST00000457041;ENST00000413278;ENST00000409082	T;T;T;T;T;T;T	0.37584	1.19;1.19;1.19;1.19;1.19;1.19;1.19	5.88	5.88	0.94601	Armadillo-type fold (1);	0.189850	0.56097	D	0.000036	T	0.64294	0.2585	M	0.88979	2.995	0.80722	D	1	P	0.43909	0.821	P	0.55455	0.776	T	0.66236	-0.5974	9	.	.	.	-13.9564	19.2196	0.93791	0.0:1.0:0.0:0.0	.	23	Q9H9S4	CB39L_HUMAN	Y	23;23;20;23;23;23;23;23	ENSP00000348113:D23Y;ENSP00000261669:D23Y;ENSP00000386375:D23Y;ENSP00000386328:D23Y;ENSP00000409253:D23Y;ENSP00000404028:D23Y;ENSP00000386979:D23Y	.	D	-	1	0	CAB39L	48854981	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.327000	0.79147	2.789000	0.95967	0.591000	0.81541	GAC	.	.	none		0.328	CAB39L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044908.3	NM_030925	
DDB1	1642	hgsc.bcm.edu	37	11	61099072	61099072	+	Silent	SNP	G	G	A	rs2230356	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:61099072G>A	ENST00000301764.7	-	2	550	c.153C>T	c.(151-153)ccC>ccT	p.P51P	DDB1_ENST00000450997.2_Silent_p.P51P|DAK_ENST00000394900.3_5'Flank	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	145	0	0		WXS	Illumina HiSeq	Phase_I	129	41	0.317829	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	
MECOM	2122	hgsc.bcm.edu	37	3	168810874	168810874	+	Silent	SNP	C	C	T	rs17466625	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:168810874C>T	ENST00000464456.1	-	12	3645	c.2445G>A	c.(2443-2445)tcG>tcA	p.S815S	MECOM_ENST00000460814.1_Silent_p.S815S|MECOM_ENST00000468789.1_Silent_p.S824S|MECOM_ENST00000392736.3_Silent_p.S824S|MECOM_ENST00000494292.1_Silent_p.S1003S|MECOM_ENST00000433243.2_Silent_p.S825S|MECOM_ENST00000264674.3_Silent_p.S889S|MECOM_ENST00000472280.1_Silent_p.S825S	NM_001164000.1	NP_001157472.1	Q13465	MDS1_HUMAN	MDS1 and EVI1 complex locus	0					regulation of transcription, DNA-templated (GO:0006355)		sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(13)|liver(1)|lung(28)|ovary(2)|pancreas(1)|prostate(2)|skin(12)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(4)	85						CAGAATGAGGCGACGATGTTG	0.393													C|||	455	0.0908546	0.0159	0.1037	5008	,	,		18533	0.0694		0.2008	False		,,,				2504	0.092				p.S1012S		Atlas-SNP	.											.	MECOM	216	.	0			c.G3036A						PASS	.	C	,,,,,,	206,4200	127.8+/-164.7	5,196,2002	111.0	100.0	104.0		2667,2472,2448,2445,2472,3036,2472	-1.1	1.0	3	dbSNP_123	104	1750,6850	317.2+/-313.1	180,1390,2730	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	MECOM	NM_001105077.3,NM_001105078.3,NM_001163999.1,NM_001164000.1,NM_001205194.1,NM_004991.3,NM_005241.3	,,,,,,	185,1586,4732	TT,TC,CC		20.3488,4.6754,15.0392	,,,,,,	889/1117,824/1052,816/1044,815/1043,824/1052,1012/1240,824/1052	168810874	1956,11050	2203	4300	6503	SO:0001819	synonymous_variant	2122	exon14			ATGAGGCGACGAT	S82592, AF164154	CCDS3205.1, CCDS54669.1, CCDS54670.1	3q26.2	2013-01-08	2009-08-07	2009-08-07	ENSG00000085276	ENSG00000085276		"""Zinc fingers, C2H2-type"""	3498	protein-coding gene	gene with protein product		165215	"""myelodysplasia syndrome 1"", ""ecotropic viral integration site 1"""	MDS1, EVI1		2115646, 8171026, 8643684	Standard	NM_001105077		Approved	MDS1-EVI1, PRDM3	uc011bpj.1	Q03112	OTTHUMG00000158596	ENST00000464456.1:c.2445G>A	3.37:g.168810874C>T		Somatic	137	1	0.00729927		WXS	Illumina HiSeq	Phase_I	97	97	1	NM_004991	Q13466|Q6FH90	Silent	SNP	ENST00000464456.1	37	CCDS54669.1																																																																																			C|0.871;T|0.129	0.129	strong		0.393	MECOM-020	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000351519.1	NM_005241, NM_004991	
CIITA	4261	hgsc.bcm.edu	37	16	11001770	11001770	+	Silent	SNP	G	G	T	rs34654419	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:11001770G>T	ENST00000324288.8	+	11	2554	c.2421G>T	c.(2419-2421)ctG>ctT	p.L807L	CIITA_ENST00000537380.1_Intron|CIITA_ENST00000381835.5_Intron	NM_000246.3	NP_000237	P33076	C2TA_HUMAN	class II, major histocompatibility complex, transactivator	807					aging (GO:0007568)|cellular response to electrical stimulus (GO:0071257)|cellular response to exogenous dsRNA (GO:0071360)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|inflammatory response (GO:0006954)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of collagen biosynthetic process (GO:0032966)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of MHC class I biosynthetic process (GO:0045345)|positive regulation of MHC class II biosynthetic process (GO:0045348)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|response to antibiotic (GO:0046677)|response to interferon-gamma (GO:0034341)|transcription, DNA-templated (GO:0006351)	cell surface (GO:0009986)|nucleoplasm (GO:0005654)|PML body (GO:0016605)	activating transcription factor binding (GO:0033613)|ATP binding (GO:0005524)|GTP binding (GO:0005525)|kinase activity (GO:0016301)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)|transferase activity, transferring acyl groups (GO:0016746)	p.L807L(1)		central_nervous_system(1)|large_intestine(7)|ovary(1)|skin(1)|stomach(2)	12						GGCAGCTGCTGGAGCTGCTGC	0.687			T	"""FLJ27352, CD274, CD273, RALGDS, RUNDC2A, C16orf75, BCL6"""	"""PMBL, Hodgkin Lymphona, """								G|||	1081	0.215855	0.2057	0.3876	5008	,	,		12685	0.1329		0.1869	False		,,,				2504	0.2229				p.L807L		Atlas-SNP	.		Dom	yes		16	16p13	4261	"""class II, major histocompatibility complex, transactivator"""		L	CIITA_ENST00000324288,NS,lymphoid_neoplasm,0,1	CIITA	92	1	1	Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(1)	c.G2421T						PASS	.	G		828,3494		88,652,1421	19.0	27.0	24.0		2421	2.8	1.0	16	dbSNP_126	24	1706,6752		189,1328,2712	no	coding-synonymous	CIITA	NM_000246.3		277,1980,4133	TT,TG,GG		20.1703,19.1578,19.8279		807/1131	11001770	2534,10246	2161	4229	6390	SO:0001819	synonymous_variant	4261	exon11			GCTGCTGGAGCTG	U18259	CCDS10544.1, CCDS66943.1, CCDS73826.1	16p13	2014-09-17	2005-08-12	2005-08-12	ENSG00000179583	ENSG00000179583		"""Nucleotide-binding domain and leucine rich repeat containing"""	7067	protein-coding gene	gene with protein product	"""NLR family, acid domain containing"", ""nucleotide-binding oligomerization domain, leucine rich repeat and acid domain containing"""	600005	"""MHC class II transactivator"""	MHC2TA		8402893	Standard	NM_000246		Approved	C2TA, NLRA	uc002dai.4	P33076	OTTHUMG00000129753	ENST00000324288.8:c.2421G>T	16.37:g.11001770G>T		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	48	43	0.895833	NM_000246	A0N0N9|D3DUG0|E9PFE0|Q29675|Q8SNB8|Q96KL4	Silent	SNP	ENST00000324288.8	37	CCDS10544.1																																																																																			T|0.193;G|0.806;C|0.000	0.193	strong		0.687	CIITA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251966.2	NM_000246	
A2ML1	144568	hgsc.bcm.edu	37	12	9010671	9010671	+	Silent	SNP	G	G	A	rs11612600	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:9010671G>A	ENST00000299698.7	+	26	3417	c.3237G>A	c.(3235-3237)gtG>gtA	p.V1079V	A2ML1_ENST00000539547.1_Silent_p.V588V	NM_001282424.1|NM_144670.4	NP_001269353.1|NP_653271			alpha-2-macroglobulin-like 1									p.V1079V(1)		NS(2)|breast(5)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|liver(2)|lung(36)|ovary(2)|skin(4)|stomach(1)|urinary_tract(1)	80						ATGCCAACGTGGGAAATCTCC	0.537													G|||	1274	0.254393	0.1944	0.2305	5008	,	,		-128	0.1696		0.3648	False		,,,				2504	0.3262				p.V1079V		Atlas-SNP	.											A2ML1,NS,carcinoma,0,1	A2ML1	199	1	1	Substitution - coding silent(1)	stomach(1)	c.G3237A						PASS	.	G		827,3139		96,635,1252	52.0	53.0	53.0		3237	2.2	0.9	12	dbSNP_120	53	2942,5388		526,1890,1749	yes	coding-synonymous	A2ML1	NM_144670.3		622,2525,3001	AA,AG,GG		35.3181,20.8522,30.6522		1079/1455	9010671	3769,8527	1983	4165	6148	SO:0001819	synonymous_variant	144568	exon26			CAACGTGGGAAAT	AK057908	CCDS8596.2, CCDS73439.1	12p13	2010-12-14	2005-09-01	2005-09-01	ENSG00000166535	ENSG00000166535			23336	protein-coding gene	gene with protein product		610627	"""C3 and PZP-like, alpha-2-macroglobulin domain containing 9"""	CPAMD9		16298998	Standard	NM_144670		Approved	FLJ25179	uc001quz.5	A8K2U0	OTTHUMG00000128499	ENST00000299698.7:c.3237G>A	12.37:g.9010671G>A		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	69	68	0.985507	NM_144670		Silent	SNP	ENST00000299698.7	37	CCDS8596.2																																																																																			G|0.729;A|0.271	0.271	strong		0.537	A2ML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250304.3	NM_144670	
OR1A2	26189	hgsc.bcm.edu	37	17	3100827	3100827	+	Silent	SNP	T	T	C	rs2241093	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	90	0	0		WXS	Illumina HiSeq	Phase_I	81	80	0.987654	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	
KNG1	3827	hgsc.bcm.edu	37	3	186435370	186435370	+	Silent	SNP	G	G	A	rs1050274	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:186435370G>A	ENST00000265023.4	+	1	251	c.39G>A	c.(37-39)ctG>ctA	p.L13L	KNG1_ENST00000287611.2_Silent_p.L13L|RP11-573D15.8_ENST00000599314.1_RNA|KNG1_ENST00000447445.1_Silent_p.L13L	NM_001102416.2	NP_001095886.1	P01042	KNG1_HUMAN	kininogen 1	13					blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|inflammatory response (GO:0006954)|negative regulation of blood coagulation (GO:0030195)|negative regulation of cell adhesion (GO:0007162)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of proteolysis (GO:0045861)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of urine volume (GO:0035810)|smooth muscle contraction (GO:0006939)|vasodilation (GO:0042311)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	cysteine-type endopeptidase inhibitor activity (GO:0004869)|heparin binding (GO:0008201)|receptor binding (GO:0005102)|zinc ion binding (GO:0008270)			endometrium(1)|lung(15)|prostate(1)|skin(2)|stomach(2)	21	all_cancers(143;8.96e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;4.12e-20)	GBM - Glioblastoma multiforme(93;0.0798)		GCTCCAGGCTGCTACTAAGTT	0.428													G|||	1953	0.389976	0.4728	0.3098	5008	,	,		15579	0.3393		0.3241	False		,,,				2504	0.455				p.L13L		Atlas-SNP	.											KNG1_ENST00000265023,NS,adenoma,0,2	KNG1	129	2	0			c.G39A						PASS	.	G	,,	2047,2359	565.1+/-381.6	473,1101,629	112.0	115.0	114.0		39,39,39	3.3	1.0	3	dbSNP_86	114	2755,5845	437.2+/-358.5	444,1867,1989	no	coding-synonymous,coding-synonymous,coding-synonymous	KNG1	NM_000893.3,NM_001102416.2,NM_001166451.1	,,	917,2968,2618	AA,AG,GG		32.0349,46.4594,36.9214	,,	13/428,13/645,13/392	186435370	4802,8204	2203	4300	6503	SO:0001819	synonymous_variant	3827	exon1			CAGGCTGCTACTA		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.39G>A	3.37:g.186435370G>A		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	69	31	0.449275	NM_000893	A8K474|B2RCR2|C9JEX1|P01043|Q53EQ0|Q6PAU9|Q7M4P1	Silent	SNP	ENST00000265023.4	37	CCDS43183.1																																																																																			G|0.637;A|0.363	0.363	strong		0.428	KNG1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317738.1	NM_001102416	
PPP1R18	170954	hgsc.bcm.edu	37	6	30652872	30652872	+	Silent	SNP	G	G	A	rs2269706	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:30652872G>A	ENST00000274853.3	-	1	2800	c.924C>T	c.(922-924)tcC>tcT	p.S308S	PPP1R18_ENST00000399199.3_Silent_p.S308S|NRM_ENST00000470733.1_5'Flank|PPP1R18_ENST00000488324.1_Intron	NM_133471.3	NP_597728.1	Q6NYC8	PPR18_HUMAN	protein phosphatase 1, regulatory subunit 18	308						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)											CCACTCCTGCGGAACTGTTGC	0.582													G|||	768	0.153355	0.0658	0.0778	5008	,	,		15807	0.256		0.0765	False		,,,				2504	0.2986				p.S308S		Atlas-SNP	.											.	.	.	.	0			c.C924T						PASS	.	G	,	133,2749		5,123,1313	84.0	102.0	95.0		924,924	-9.9	0.0	6	dbSNP_100	95	420,4918		17,386,2266	yes	coding-synonymous,coding-synonymous	KIAA1949	NM_001134870.1,NM_133471.3	,	22,509,3579	AA,AG,GG		7.8681,4.6149,6.7275	,	308/614,308/614	30652872	553,7667	1441	2669	4110	SO:0001819	synonymous_variant	170954	exon2			TCCTGCGGAACTG	AK097089	CCDS43444.1	6p21.3	2012-04-17	2011-10-11	2011-10-11	ENSG00000146112	ENSG00000146112		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	29413	protein-coding gene	gene with protein product	"""protein phosphatase 1 F-actin cytoskeleton targeting subunit"""	610990	"""KIAA1949"""	KIAA1949		11853319	Standard	NM_001134870		Approved	phostensin	uc003nra.3	Q6NYC8	OTTHUMG00000031237	ENST00000274853.3:c.924C>T	6.37:g.30652872G>A		Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	140	68	0.485714	NM_001134870	A2AB01|A2AIB8|A4UBI6|A6NCB7|A8MSS7|B7ZCV7|Q68CK8|Q6ZTV1|Q6ZUJ6|Q8NDQ4|Q8TF52|Q9BRL9	Silent	SNP	ENST00000274853.3	37	CCDS43444.1																																																																																			G|0.875;A|0.125	0.125	strong		0.582	PPP1R18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076498.2	NM_133471	
TUB	7275	hgsc.bcm.edu	37	11	8122143	8122143	+	Missense_Mutation	SNP	C	C	T	rs139170512	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:8122143C>T	ENST00000299506.2	+	10	1359	c.1210C>T	c.(1210-1212)Cgc>Tgc	p.R404C	TUB_ENST00000305253.4_Missense_Mutation_p.R459C|TUB_ENST00000534099.1_Missense_Mutation_p.R410C	NM_177972.2	NP_813977.1	P50607	TUB_HUMAN	tubby bipartite transcription factor	404					multicellular organismal macromolecule metabolic process (GO:0044259)|phagocytosis (GO:0006909)|phototransduction (GO:0007602)|positive regulation of phagocytosis (GO:0050766)|response to hormone (GO:0009725)|retina development in camera-type eye (GO:0060041)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	G-protein coupled photoreceptor activity (GO:0008020)|protein complex binding (GO:0032403)			breast(1)|cervix(1)|endometrium(9)|large_intestine(7)|lung(5)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	26		all_lung(207;6.91e-20)|Lung NSC(207;3.36e-17)		Epithelial(150;1.69e-62)|BRCA - Breast invasive adenocarcinoma(625;8.54e-06)|LUSC - Lung squamous cell carcinoma(625;0.000184)		TATCCGCCCCCGCAACGTGAG	0.537													C|||	2	0.000399361	0.0008	0.0	5008	,	,		19350	0.0		0.0	False		,,,				2504	0.001				p.R459C		Atlas-SNP	.											TUB,NS,carcinoma,-1,1	TUB	71	1	0			c.C1375T						PASS	.	C	CYS/ARG,CYS/ARG	0,4402		0,0,2201	142.0	112.0	122.0		1375,1210	4.6	1.0	11	dbSNP_134	122	1,8591	1.2+/-3.3	0,1,4295	no	missense,missense	TUB	NM_003320.4,NM_177972.2	180,180	0,1,6496	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging	459/562,404/507	8122143	1,12993	2201	4296	6497	SO:0001583	missense	7275	exon11			CGCCCCCGCAACG	U54644	CCDS7786.1, CCDS7787.1	11p15.5	2013-08-06	2013-08-06		ENSG00000166402	ENSG00000166402			12406	protein-coding gene	gene with protein product		601197	"""tubby (mouse) homolog"", ""tubby homolog (mouse)"""			8612280	Standard	NM_003320		Approved	rd5	uc001mfy.3	P50607	OTTHUMG00000165690	ENST00000299506.2:c.1210C>T	11.37:g.8122143C>T	ENSP00000299506:p.Arg404Cys	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	79	55	0.696203	NM_003320	D3DQU4|O00293|Q6B007	Missense_Mutation	SNP	ENST00000299506.2	37	CCDS7787.1	.	.	.	.	.	.	.	.	.	.	C	19.20	3.780775	0.70222	0.0	1.16E-4	ENSG00000166402	ENST00000534099;ENST00000305253;ENST00000299506	D;D;D	0.85484	-1.99;-1.99;-1.99	4.59	4.59	0.56863	Tubby, C-terminal (3);	0.055535	0.64402	D	0.000001	D	0.92564	0.7638	M	0.88570	2.965	0.80722	D	1	D;D;D	0.76494	0.998;0.999;0.999	D;D;D	0.65874	0.939;0.931;0.935	D	0.93741	0.7050	10	0.66056	D	0.02	-18.1139	14.2881	0.66258	0.1492:0.8507:0.0:0.0	.	410;404;459	E9PQR4;P50607;P50607-2	.;TUB_HUMAN;.	C	410;459;404	ENSP00000434400:R410C;ENSP00000305426:R459C;ENSP00000299506:R404C	ENSP00000299506:R404C	R	+	1	0	TUB	8078719	1.000000	0.71417	1.000000	0.80357	0.809000	0.45718	4.811000	0.62606	2.277000	0.76020	0.563000	0.77884	CGC	C|1.000;T|0.000	0.000	weak		0.537	TUB-003	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385823.1	NM_003320	
ZNF285	26974	hgsc.bcm.edu	37	19	44890651	44890651	+	Nonsense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:44890651G>A	ENST00000330997.4	-	4	1820	c.1756C>T	c.(1756-1758)Cag>Tag	p.Q586*	ZNF285_ENST00000591679.1_Nonsense_Mutation_p.Q593*|ZNF285_ENST00000544719.2_Nonsense_Mutation_p.Q586*|CTC-512J12.6_ENST00000588212.1_Intron	NM_152354.3	NP_689567.3	Q96NJ3	ZN285_HUMAN	zinc finger protein 285	586					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						GTTTCTCTCTGCTCATGTAGT	0.433																																					p.Q586X		Atlas-SNP	.											.	ZNF285	86	.	0			c.C1756T						PASS	.						123.0	103.0	110.0					19																	44890651		2203	4300	6503	SO:0001587	stop_gained	26974	exon4			CTCTCTGCTCATG	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.1756C>T	19.37:g.44890651G>A	ENSP00000333595:p.Gln586*	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	87	18	0.206897	NM_152354	Q17RJ3|Q6B0A8|Q6ISR5	Nonsense_Mutation	SNP	ENST00000330997.4	37	CCDS12638.1	.	.	.	.	.	.	.	.	.	.	G	20.2	3.955111	0.73902	.	.	ENSG00000062370	ENST00000544719;ENST00000330997	.	.	.	3.28	-2.27	0.06846	.	.	.	.	.	.	.	.	.	.	.	0.19775	N	0.999953	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	.	2.2056	0.03934	0.1362:0.097:0.2974:0.4695	.	.	.	.	X	609;586	.	ENSP00000333595:Q586X	Q	-	1	0	ZNF285	49582491	0.891000	0.30450	0.000000	0.03702	0.024000	0.10985	1.365000	0.34182	-0.266000	0.09339	-0.552000	0.04208	CAG	.	.	none		0.433	ZNF285-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443600.1	NM_152354	
LAIR2	3904	hgsc.bcm.edu	37	19	55021777	55021777	+	Nonstop_Mutation	SNP	T	T	A	rs62131570	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:55021777T>A	ENST00000301202.2	+	5	579	c.457T>A	c.(457-459)Tga>Aga	p.*153R	LAIR2_ENST00000351841.2_Nonstop_Mutation_p.*136R	NM_002288.4	NP_002279.2	Q6ISS4	LAIR2_HUMAN	leukocyte-associated immunoglobulin-like receptor 2	0						extracellular region (GO:0005576)				central_nervous_system(1)|kidney(3)|large_intestine(3)|lung(8)|ovary(1)|prostate(1)|skin(1)	18	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.0967)		TGATGCACCATGAATGAGGAG	0.433																																					p.X153R		Atlas-SNP	.											.	LAIR2	30	.	0			c.T457A						PASS	.						106.0	96.0	100.0					19																	55021777		2203	4299	6502	SO:0001578	stop_lost	3904	exon5			GCACCATGAATGA	AF013250	CCDS12897.1, CCDS12898.1	19q13.4	2013-01-29	2006-03-23		ENSG00000167618	ENSG00000167618		"""Leukocyte-associated Ig like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6478	protein-coding gene	gene with protein product		602993	"""leukocyte-associated Ig-like receptor 2"""			9285412	Standard	XM_005277264		Approved	CD306	uc002qgc.3	Q6ISS4	OTTHUMG00000065697	ENST00000301202.2:c.457T>A	19.37:g.55021777T>A	ENSP00000301202:p.*153Argext*?	Somatic	322	0	0		WXS	Illumina HiSeq	Phase_I	200	61	0.305	NM_002288	Q6PEZ4	Missense_Mutation	SNP	ENST00000301202.2	37	CCDS12897.1	62	0.028388278388278388	4	0.008130081300813009	12	0.03314917127071823	1	0.0017482517482517483	45	0.059366754617414245	T	0.258	-1.001502	0.02128	.	.	ENSG00000167618	ENST00000301202;ENST00000351841	.	.	.	0.829	-0.424	0.12321	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	2.7709	0.05334	0.4189:0.0:0.0:0.5811	rs62131570	.	.	.	R	153;136	.	.	X	+	1	0	LAIR2	59713589	0.000000	0.05858	0.001000	0.08648	0.026000	0.11368	-0.191000	0.09601	-0.225000	0.09913	0.260000	0.18958	TGA	T|0.976;A|0.024	0.024	strong		0.433	LAIR2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000140801.1		
CDHR1	92211	hgsc.bcm.edu	37	10	85978939	85978939	+	IGR	SNP	G	G	A	rs4244947	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:85978939G>A	ENST00000372117.3	+	0	5428				CDHR1_ENST00000332904.3_Silent_p.L715L	NM_033100.2	NP_149091.1	Q96JP9	CDHR1_HUMAN	cadherin-related family member 1						cellular process (GO:0009987)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)	integral component of plasma membrane (GO:0005887)|photoreceptor outer segment membrane (GO:0042622)	calcium ion binding (GO:0005509)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(21)|ovary(1)|prostate(1)|skin(1)	36						gCCAGGGTCTGTTCTTGCATC	0.398													A|||	2775	0.554113	0.8185	0.5331	5008	,	,		18287	0.4107		0.4632	False		,,,				2504	0.453				p.L715L		Atlas-SNP	.											.	CDHR1	122	.	0			c.G2145A						PASS	.																																			SO:0001628	intergenic_variant	92211	exon17			GGGTCTGTTCTTG	AB053448	CCDS7372.1, CCDS53548.1	10q23.1	2014-01-28	2010-01-25	2010-01-25	ENSG00000148600	ENSG00000148600		"""Cadherins / Cadherin-related"""	14550	protein-coding gene	gene with protein product		609502	"""protocadherin 21"""	PCDH21		11597768	Standard	NM_001171971		Approved	KIAA1775, CORD15, RP65	uc001kcv.3	Q96JP9	OTTHUMG00000018634		10.37:g.85978939G>A		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	98	52	0.530612	NM_001171971	Q69YZ8|Q8IXY5	Silent	SNP	ENST00000372117.3	37	CCDS7372.1																																																																																			G|0.460;A|0.540	0.540	strong		0.398	CDHR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049111.1	NM_033100	
DES	1674	hgsc.bcm.edu	37	2	220283592	220283592	+	Silent	SNP	C	C	T	rs111828114	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:220283592C>T	ENST00000373960.3	+	1	494	c.408C>T	c.(406-408)ctC>ctT	p.L136L		NM_001927.3	NP_001918.3	P17661	DESM_HUMAN	desmin	136	Coil 1A.|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)		ACGCGGCGCTCGCCGCCGAAG	0.672													C|||	62	0.0123802	0.0015	0.0159	5008	,	,		11251	0.0		0.0457	False		,,,				2504	0.0031				p.L136L		Atlas-SNP	.											DES,brain,glioma,0,2	DES	53	2	0			c.C408T						scavenged	.	C		29,4337		1,27,2155	16.0	15.0	15.0		408	1.4	1.0	2	dbSNP_132	15	301,8259		3,295,3982	no	coding-synonymous	DES	NM_001927.3		4,322,6137	TT,TC,CC		3.5164,0.6642,2.553		136/471	220283592	330,12596	2183	4280	6463	SO:0001819	synonymous_variant	1674	exon1			GGCGCTCGCCGCC	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.408C>T	2.37:g.220283592C>T		Somatic	103	1	0.00970874		WXS	Illumina HiSeq	Phase_I	111	61	0.54955	NM_001927	Q15787|Q549R7|Q549R8|Q549R9|Q8IZR1|Q8IZR6|Q8NES2|Q8NEU6|Q8TAC4|Q8TCX2|Q8TD99|Q9UHN5|Q9UJ80	Silent	SNP	ENST00000373960.3	37	CCDS33383.1																																																																																			C|0.979;T|0.021	0.021	strong		0.672	DES-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130240.1	NM_001927	
SLC9C1	285335	hgsc.bcm.edu	37	3	111996554	111996554	+	Missense_Mutation	SNP	T	T	C	rs9828502	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:111996554T>C	ENST00000305815.5	-	5	724	c.472A>G	c.(472-474)Ata>Gta	p.I158V	SLC9C1_ENST00000487372.1_Missense_Mutation_p.I158V|SLC9C1_ENST00000467397.1_5'Flank	NM_183061.1	NP_898884.1	Q4G0N8	SL9C1_HUMAN	solute carrier family 9, subfamily C (Na+-transporting carboxylic acid decarboxylase), member 1	158			I -> V (in dbSNP:rs9828502). {ECO:0000269|PubMed:14702039}.		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)										AGGTCTCTTATAGCAGCTGCG	0.333													T|||	1557	0.310903	0.3116	0.4006	5008	,	,		17507	0.2976		0.2346	False		,,,				2504	0.3384				p.I158V		Atlas-SNP	.											.	.	.	.	0			c.A472G						PASS	.	T	VAL/ILE	1392,3014	448.5+/-348.7	219,954,1030	72.0	77.0	75.0		472	-1.3	0.3	3	dbSNP_119	75	2333,6267	386.0+/-341.7	321,1691,2288	yes	missense	SLC9A10	NM_183061.1	29	540,2645,3318	CC,CT,TT		27.1279,31.5933,28.6406	possibly-damaging	158/1178	111996554	3725,9281	2203	4300	6503	SO:0001583	missense	285335	exon5			CTCTTATAGCAGC	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.472A>G	3.37:g.111996554T>C	ENSP00000306627:p.Ile158Val	Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	135	135	1	NM_183061	Q6ZRP4|Q7RTP2	Missense_Mutation	SNP	ENST00000305815.5	37	CCDS33817.1	649	0.29716117216117216	157	0.31910569105691056	137	0.3784530386740331	173	0.30244755244755245	182	0.24010554089709762	T	0.080	-1.185856	0.01620	0.315933	0.271279	ENSG00000172139	ENST00000305815;ENST00000487372;ENST00000486574	T;T;T	0.13420	2.59;2.59;3.95	5.45	-1.34	0.09143	Cation/H+ exchanger (1);	0.188565	0.36854	N	0.002361	T	0.00012	0.0000	L	0.53249	1.67	0.58432	P	6.999999999979245E-6	B;B	0.10296	0.002;0.003	B;B	0.14578	0.005;0.011	T	0.44174	-0.9345	9	0.56958	D	0.05	.	5.697	0.17861	0.1198:0.302:0.0:0.5782	rs9828502;rs9828502	158;158	Q4G0N8-2;Q4G0N8	.;S9A10_HUMAN	V	158;158;85	ENSP00000306627:I158V;ENSP00000420688:I158V;ENSP00000417274:I85V	ENSP00000306627:I158V	I	-	1	0	SLC9A10	113479244	0.992000	0.36948	0.281000	0.24762	0.037000	0.13140	0.134000	0.15932	-0.872000	0.04037	-2.485000	0.00197	ATA	T|0.713;C|0.287	0.287	strong		0.333	SLC9C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354066.1	NM_183061	
RNASE8	122665	hgsc.bcm.edu	37	14	21526079	21526079	+	Missense_Mutation	SNP	C	C	T	rs12437266	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:21526079C>T	ENST00000308227.2	+	1	99	c.28C>T	c.(28-30)Ccc>Tcc	p.P10S	NDRG2_ENST00000403829.3_Intron	NM_138331.1	NP_612204.1	Q8TDE3	RNAS8_HUMAN	ribonuclease, RNase A family, 8	10			P -> S (in dbSNP:rs12437266). {ECO:0000269|PubMed:15489334}.		RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)	extracellular region (GO:0005576)	nucleic acid binding (GO:0003676)|pancreatic ribonuclease activity (GO:0004522)			endometrium(1)|kidney(1)|large_intestine(1)|lung(1)	4	all_cancers(95;0.000759)		OV - Ovarian serous cystadenocarcinoma(11;3.42e-11)|Epithelial(56;5.57e-09)|all cancers(55;2.36e-08)	GBM - Glioblastoma multiforme(265;0.0188)		AGGATGCTGCCCCCTGCTGCT	0.547													C|||	2736	0.546326	0.4024	0.5922	5008	,	,		15156	0.6151		0.6412	False		,,,				2504	0.5399				p.P10S		Atlas-SNP	.											.	RNASE8	11	.	0			c.C28T						PASS	.	C	SER/PRO	1842,2564	534.7+/-374.0	369,1104,730	64.0	55.0	58.0		28	-4.9	0.0	14	dbSNP_120	58	5287,3313	644.1+/-400.0	1626,2035,639	yes	missense	RNASE8	NM_138331.1	74	1995,3139,1369	TT,TC,CC		38.5233,41.8066,45.1868	possibly-damaging	10/155	21526079	7129,5877	2203	4300	6503	SO:0001583	missense	122665	exon1			TGCTGCCCCCTGC	AF473854	CCDS9567.1	14q11.1	2003-03-13			ENSG00000173431	ENSG00000173431		"""Ribonucleases, RNase A"""	19277	protein-coding gene	gene with protein product		612485				11861908	Standard	NM_138331		Approved		uc010tlm.2	Q8TDE3	OTTHUMG00000029645	ENST00000308227.2:c.28C>T	14.37:g.21526079C>T	ENSP00000311398:p.Pro10Ser	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	54	15	0.277778	NM_138331	B2RPP6|B2RPP7	Missense_Mutation	SNP	ENST00000308227.2	37	CCDS9567.1	1229	0.5627289377289377	193	0.39227642276422764	206	0.569060773480663	350	0.6118881118881119	480	0.633245382585752	C	11.77	1.737464	0.30774	0.418066	0.614767	ENSG00000173431	ENST00000308227	T	0.78003	-1.14	4.32	-4.89	0.03103	.	1.069470	0.07227	N	0.861806	T	0.00012	0.0000	L	0.58810	1.83	0.80722	P	0.0	B	0.16603	0.018	B	0.17098	0.017	T	0.42699	-0.9436	9	0.49607	T	0.09	-7.0205	7.2534	0.26162	0.0:0.2374:0.1351:0.6275	rs12437266;rs59321589	10	Q8TDE3	RNAS8_HUMAN	S	10	ENSP00000311398:P10S	ENSP00000311398:P10S	P	+	1	0	RNASE8	20595919	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.080000	0.03407	-1.275000	0.02417	-1.109000	0.02080	CCC	C|0.481;T|0.519	0.519	strong		0.547	RNASE8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073925.3	NM_138331	
OSBPL7	114881	hgsc.bcm.edu	37	17	45885756	45885756	+	Silent	SNP	C	C	T	rs9911983	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:45885756C>T	ENST00000007414.3	-	23	2621	c.2430G>A	c.(2428-2430)acG>acA	p.T810T	OSBPL7_ENST00000392507.3_Silent_p.T810T	NM_145798.2	NP_665741.1	Q9BZF2	OSBL7_HUMAN	oxysterol binding protein-like 7	810					cellular response to cholesterol (GO:0071397)|lipid transport (GO:0006869)|positive regulation of proteasomal protein catabolic process (GO:1901800)	autophagic vacuole (GO:0005776)|cytosol (GO:0005829)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)	cholesterol binding (GO:0015485)			autonomic_ganglia(1)|endometrium(6)|kidney(2)|large_intestine(5)|liver(2)|lung(13)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	32						CGCTGCTATCCGTCTGCCGCC	0.627													T|||	2374	0.474042	0.7005	0.4352	5008	,	,		19535	0.1528		0.5298	False		,,,				2504	0.4693				p.T810T		Atlas-SNP	.											OSBPL7,colon,carcinoma,-1,1	OSBPL7	65	1	0			c.G2430A						PASS	.	T		3093,1313	444.5+/-347.4	1094,905,204	61.0	56.0	58.0		2430	-8.4	0.8	17	dbSNP_119	58	4785,3815	538.2+/-383.4	1362,2061,877	no	coding-synonymous	OSBPL7	NM_145798.2		2456,2966,1081	TT,TC,CC		44.3605,29.8003,39.428		810/843	45885756	7878,5128	2203	4300	6503	SO:0001819	synonymous_variant	114881	exon23			GCTATCCGTCTGC	AF392446	CCDS11515.1	17q21	2013-01-10				ENSG00000006025		"""Oxysterol binding proteins"", ""Pleckstrin homology (PH) domain containing"""	16387	protein-coding gene	gene with protein product		606735				14593528, 11735225	Standard	NM_145798		Approved	ORP7, MGC71150	uc002ilx.1	Q9BZF2		ENST00000007414.3:c.2430G>A	17.37:g.45885756C>T		Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	125	59	0.472	NM_145798	D3DTT6|Q6PIV6	Silent	SNP	ENST00000007414.3	37	CCDS11515.1																																																																																			C|0.449;T|0.551	0.551	strong		0.627	OSBPL7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441367.1	NM_017731	
KRT77	374454	hgsc.bcm.edu	37	12	53090190	53090190	+	Silent	SNP	C	C	T	rs7138818	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:53090190C>T	ENST00000341809.3	-	3	811	c.783G>A	c.(781-783)agG>agA	p.R261R	RP11-641A6.3_ENST00000547533.1_RNA|KRT77_ENST00000537195.1_Silent_p.R28R	NM_175078.2	NP_778253.2	Q7Z794	K2C1B_HUMAN	keratin 77	261	Coil 1B.|Rod.					cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)	p.R261R(1)		NS(2)|endometrium(2)|large_intestine(3)|lung(11)|ovary(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	25						CGCTGCCAGTCCTCTTGTTGA	0.567													C|||	2038	0.406949	0.4826	0.4092	5008	,	,		21399	0.25		0.4026	False		,,,				2504	0.4693				p.R261R		Atlas-SNP	.											KRT77,NS,carcinoma,0,1	KRT77	58	1	1	Substitution - coding silent(1)	stomach(1)	c.G783A						scavenged	.	C		1987,2419	557.0+/-379.6	439,1109,655	164.0	118.0	134.0		783	3.6	0.8	12	dbSNP_116	134	3625,4975	522.2+/-380.1	763,2099,1438	no	coding-synonymous	KRT77	NM_175078.2		1202,3208,2093	TT,TC,CC		42.1512,45.0976,43.1493		261/579	53090190	5612,7394	2203	4300	6503	SO:0001819	synonymous_variant	374454	exon3			GCCAGTCCTCTTG	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.783G>A	12.37:g.53090190C>T		Somatic	44	1	0.0227273		WXS	Illumina HiSeq	Phase_I	29	16	0.551724	NM_175078	Q7RTS8	Silent	SNP	ENST00000341809.3	37	CCDS8837.1																																																																																			C|0.590;T|0.410	0.410	strong		0.567	KRT77-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404111.1	NM_175078	
HLA-G	3135	hgsc.bcm.edu	37	6	29796327	29796327	+	Silent	SNP	C	C	T	rs1130356	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:29796327C>T	ENST00000360323.6	+	3	375	c.351C>T	c.(349-351)caC>caT	p.H117H	HLA-G_ENST00000376818.3_Intron|HLA-G_ENST00000376815.3_Intron|HLA-G_ENST00000428701.1_Silent_p.H117H|HLA-G_ENST00000376828.2_Silent_p.H122H			P17693	HLAG_HUMAN	major histocompatibility complex, class I, G	117	Alpha-2.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular defense response (GO:0006968)|cytokine-mediated signaling pathway (GO:0019221)|immune response-inhibiting cell surface receptor signaling pathway (GO:0002767)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of dendritic cell differentiation (GO:2001199)|negative regulation of T cell proliferation (GO:0042130)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of regulatory T cell differentiation (GO:0045591)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|positive regulation of T cell tolerance induction (GO:0002666)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)	early endosome membrane (GO:0031901)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|membrane (GO:0016020)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	peptide antigen binding (GO:0042605)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)			central_nervous_system(1)|endometrium(1)|large_intestine(5)|lung(4)|ovary(3)|pancreas(1)|prostate(5)|skin(1)	21						CAGGTTCTCACACCCTCCAGT	0.662													c|||	1253	0.2502	0.2625	0.2565	5008	,	,		13097	0.1141		0.2763	False		,,,				2504	0.3425				p.H117H		Atlas-SNP	.											.	HLA-G	90	.	0			c.C351T						PASS	.	C		823,2195		112,599,798	68.0	72.0	71.0		351	0.8	0.2	6	dbSNP_86	71	1692,3724		272,1148,1288	no	coding-synonymous	HLA-G	NM_002127.5		384,1747,2086	TT,TC,CC		31.2408,27.2697,29.8198		117/339	29796327	2515,5919	1509	2708	4217	SO:0001819	synonymous_variant	3135	exon4			TTCTCACACCCTC		CCDS4668.1	6p21.3	2013-01-11	2007-12-12		ENSG00000204632	ENSG00000204632		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4964	protein-coding gene	gene with protein product	"""b2 microglobulin"""	142871	"""HLA-G histocompatibility antigen, class I, G"""				Standard	NM_002127		Approved		uc003nnw.2	P17693	OTTHUMG00000031157	ENST00000360323.6:c.351C>T	6.37:g.29796327C>T		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	85	83	0.976471	NM_002127		Silent	SNP	ENST00000360323.6	37	CCDS4668.1																																																																																			C|0.734;T|0.266	0.266	strong		0.662	HLA-G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076286.2	NM_002127	
C2orf16	84226	hgsc.bcm.edu	37	2	27801493	27801493	+	Missense_Mutation	SNP	T	T	C	rs1919127	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:27801493T>C	ENST00000408964.2	+	1	2105	c.2054T>C	c.(2053-2055)gTg>gCg	p.V685A		NM_032266.3	NP_115642.3	Q68DN1	CB016_HUMAN	chromosome 2 open reading frame 16	685			V -> A (in dbSNP:rs1919127).			extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(33)|urinary_tract(1)	47	Acute lymphoblastic leukemia(172;0.155)					CTTCAGGCTGTGAAATCTACA	0.403													T|||	1539	0.307308	0.1732	0.5231	5008	,	,		21205	0.5079		0.2644	False		,,,				2504	0.1728				p.V685A		Atlas-SNP	.											.	C2orf16	357	.	0			c.T2054C						PASS	.	T	ALA/VAL	687,3047		60,567,1240	82.0	78.0	79.0		2054	1.8	0.0	2	dbSNP_92	79	2218,6008		299,1620,2194	yes	missense	C2orf16	NM_032266.3	64	359,2187,3434	CC,CT,TT		26.9633,18.3985,24.2893	possibly-damaging	685/1985	27801493	2905,9055	1867	4113	5980	SO:0001583	missense	84226	exon1			AGGCTGTGAAATC	AL136898	CCDS42666.1	2p23.3	2013-09-20			ENSG00000221843	ENSG00000221843			25275	protein-coding gene	gene with protein product	"""P-S-E-R-S-H-H-S repeats containing"""						Standard	NM_032266		Approved	DKFZp434G118	uc002rkz.4	Q68DN1	OTTHUMG00000159099	ENST00000408964.2:c.2054T>C	2.37:g.27801493T>C	ENSP00000386190:p.Val685Ala	Somatic	196	1	0.00510204		WXS	Illumina HiSeq	Phase_I	163	100	0.613497	NM_032266	B9EIQ4|Q53S01|Q8ND64|Q9H088	Missense_Mutation	SNP	ENST00000408964.2	37	CCDS42666.1	772	0.3534798534798535	72	0.14634146341463414	171	0.4723756906077348	322	0.5629370629370629	207	0.27308707124010556	T	12.13	1.845535	0.32606	0.183985	0.269633	ENSG00000221843	ENST00000408964	T	0.07021	3.23	4.27	1.81	0.25067	.	.	.	.	.	T	0.00012	0.0000	N	0.24115	0.695	0.80722	P	0.0	B	0.33318	0.408	B	0.28553	0.091	T	0.27706	-1.0066	8	0.30078	T	0.28	.	3.4217	0.07396	0.2069:0.1085:0.0:0.6846	rs1919127;rs17006144;rs57887820;rs1919127	685	Q68DN1	CB016_HUMAN	A	685	ENSP00000386190:V685A	ENSP00000386190:V685A	V	+	2	0	C2orf16	27654997	0.001000	0.12720	0.003000	0.11579	0.752000	0.42762	0.405000	0.21015	0.391000	0.25143	0.459000	0.35465	GTG	T|0.680;C|0.320	0.320	strong		0.403	C2orf16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353292.1	NM_032266	
CCDC121	79635	hgsc.bcm.edu	37	2	27851918	27851918	+	5'Flank	SNP	G	G	A	rs3749147	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:27851918G>A	ENST00000324364.3	-	0	0				GPN1_ENST00000424214.1_Intron|GPN1_ENST00000610189.1_5'Flank|GPN1_ENST00000458167.2_Intron|RP11-158I13.2_ENST00000505973.1_RNA|GPN1_ENST00000407583.3_Intron|GPN1_ENST00000264718.3_Missense_Mutation_p.R12K|ZNF512_ENST00000556601.1_Intron|GPN1_ENST00000503738.1_Intron|GPN1_ENST00000515877.1_Intron|CCDC121_ENST00000394775.3_5'Flank	NM_024584.4	NP_078860.2	Q6ZUS5	CC121_HUMAN	coiled-coil domain containing 121											breast(1)|endometrium(3)|large_intestine(2)|lung(6)|prostate(2)	14	Acute lymphoblastic leukemia(172;0.155)					GGTGGGGCCAGGAGGAAGATG	0.632													G|||	919	0.183506	0.0287	0.2089	5008	,	,		15900	0.3185		0.2535	False		,,,				2504	0.1636				p.R12K		Atlas-SNP	.											.	GPN1	28	.	0			c.G35A						PASS	.	G	,,,LYS/ARG	292,4114	158.1+/-190.9	5,282,1916	51.0	54.0	53.0	http://www.ncbi.nlm.nih.gov/pubmed?term	,,,35	1.9	0.0	2	dbSNP_107	53	2283,6317	382.8+/-340.5	306,1671,2323	yes	intron,intron,intron,missense	GPN1	NM_001145047.1,NM_001145048.1,NM_001145049.1,NM_007266.3	,,,26	311,1953,4239	AA,AG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	26.5465,6.6273,19.7986	,,,benign	,,,12/389	27851918	2575,10431	2203	4300	6503	SO:0001631	upstream_gene_variant	11321	exon1			GGGCCAGGAGGAA	AK125354	CCDS1759.1, CCDS46247.1	2p23.2	2008-02-05			ENSG00000176714	ENSG00000176714			25833	protein-coding gene	gene with protein product							Standard	NM_024584		Approved	FLJ43364, FLJ13646	uc002rld.3	Q6ZUS5	OTTHUMG00000128427		2.37:g.27851918G>A	Exception_encountered	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	115	65	0.565217	NM_007266	B3KW66|J3KQZ8|Q9H8G6	Missense_Mutation	SNP	ENST00000324364.3	37	CCDS1759.1	501	0.22939560439560439	15	0.03048780487804878	89	0.24585635359116023	200	0.34965034965034963	197	0.2598944591029024	G	14.10	2.434824	0.43224	0.066273	0.265465	ENSG00000198522	ENST00000264718	T	0.48201	0.82	4.74	1.89	0.25635	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.53005	P	3.2999999999949736E-5	B	0.10296	0.003	B	0.08055	0.003	T	0.40136	-0.9579	8	0.07030	T	0.85	.	5.3503	0.16032	0.1889:0.1672:0.6438:0.0	rs3749147;rs3749147	12	B4DQM4	.	K	12	ENSP00000264718:R12K	ENSP00000264718:R12K	R	+	2	0	GPN1	27705422	0.000000	0.05858	0.000000	0.03702	0.518000	0.34316	0.149000	0.16243	0.285000	0.22329	0.591000	0.81541	AGG	G|0.772;A|0.228	0.228	strong		0.632	CCDC121-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000250215.1	NM_024584	
ABCA3	21	hgsc.bcm.edu	37	16	2348528	2348528	+	Silent	SNP	G	G	C	rs323043	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:2348528G>C	ENST00000301732.5	-	15	2455	c.1755C>G	c.(1753-1755)ccC>ccG	p.P585P	ABCA3_ENST00000382381.3_Silent_p.P527P	NM_001089.2	NP_001080.2	Q99758	ABCA3_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 3	585	ABC transporter 1. {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)	GTCCACTGGTGGGGGGAAAGA	0.602													G|||	409	0.0816693	0.0507	0.1124	5008	,	,		16245	0.0198		0.1819	False		,,,				2504	0.0624				p.P585P		Atlas-SNP	.											.	ABCA3	176	.	0			c.C1755G						PASS	.	G		329,4067	173.4+/-203.2	10,309,1879	60.0	59.0	60.0		1755	-12.3	0.0	16	dbSNP_79	60	1702,6898	309.0+/-309.2	173,1356,2771	no	coding-synonymous	ABCA3	NM_001089.2		183,1665,4650	CC,CG,GG		19.7907,7.4841,15.6279		585/1705	2348528	2031,10965	2198	4300	6498	SO:0001819	synonymous_variant	21	exon15			ACTGGTGGGGGGA	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.1755C>G	16.37:g.2348528G>C		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	121	23	0.190083	NM_001089	B2RU09|Q54A95|Q6P5P9|Q92473	Silent	SNP	ENST00000301732.5	37	CCDS10466.1																																																																																			G|0.858;C|0.142	0.142	strong		0.602	ABCA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250784.2	NM_001089	
ZNF415	55786	hgsc.bcm.edu	37	19	53612311	53612311	+	Silent	SNP	T	T	C	rs4803051	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:53612311T>C	ENST00000500065.4	-	4	1320	c.987A>G	c.(985-987)acA>acG	p.T329T	ZNF415_ENST00000440291.1_Silent_p.T316T|ZNF415_ENST00000601493.1_Silent_p.T99T|ZNF415_ENST00000455735.2_Silent_p.T377T|ZNF415_ENST00000448501.1_Silent_p.T377T|ZNF415_ENST00000243643.4_Silent_p.T329T|ZNF415_ENST00000597748.1_3'UTR|ZNF415_ENST00000421033.1_Silent_p.T341T|ZNF415_ENST00000594011.1_3'UTR|ZNF415_ENST00000597503.1_3'UTR|ZNF415_ENST00000595193.1_3'UTR	NM_001136038.2	NP_001129510.2	Q09FC8	ZN415_HUMAN	zinc finger protein 415	377					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|kidney(3)|large_intestine(8)|lung(11)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31				GBM - Glioblastoma multiforme(134;0.0191)		ACTCTTTACATGTGTAAGGTT	0.398													C|||	2391	0.477436	0.2405	0.6254	5008	,	,		23834	0.6151		0.496	False		,,,				2504	0.5317				p.T329T		Atlas-SNP	.											.	ZNF415	68	.	0			c.A987G						PASS	.	C	,,	1235,3171	705.9+/-407.3	185,865,1153	83.0	76.0	79.0		987,987,987	-5.1	0.0	19	dbSNP_111	79	4193,4407	585.6+/-391.9	1029,2135,1136	no	coding-synonymous,coding-synonymous,coding-synonymous	ZNF415	NM_001136038.2,NM_001164309.1,NM_018355.2	,,	1214,3000,2289	CC,CT,TT		48.7558,28.03,41.7346	,,	329/556,329/556,329/556	53612311	5428,7578	2203	4300	6503	SO:0001819	synonymous_variant	55786	exon4			TTTACATGTGTAA	AK002053	CCDS12860.1, CCDS54313.1	19q13.42	2014-03-18			ENSG00000170954	ENSG00000170954		"""Zinc fingers, C2H2-type"", ""-"""	20636	protein-coding gene	gene with protein product						14702039	Standard	NM_001136038		Approved		uc002qaw.3	Q09FC8	OTTHUMG00000182865	ENST00000500065.4:c.987A>G	19.37:g.53612311T>C		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	36	21	0.583333	NM_018355	F5H287|Q09FC7|Q09FC9|Q09FD0|Q6NSZ2|Q6P3S0|Q9NUR2	Silent	SNP	ENST00000500065.4	37	CCDS54313.1																																																																																			T|0.561;C|0.439	0.439	strong		0.398	ZNF415-025	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464043.1	NM_018355	
BRF1	2972	hgsc.bcm.edu	37	14	105722726	105722726	+	Intron	SNP	T	T	C	rs1008628	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:105722726T>C	ENST00000546474.1	-	4	15431				BRF1_ENST00000440513.3_Intron|BRF1_ENST00000379937.2_Intron|BRF1_ENST00000327359.3_Intron|BRF1_ENST00000548421.1_Silent_p.P200P	NM_001242787.1|NM_001519.3	NP_001229716.1|NP_001510.2	Q92994	TF3B_HUMAN	BRF1, RNA polymerase III transcription initiation factor 90 kDa subunit						gene expression (GO:0010467)|regulation of mRNA stability (GO:0043488)|regulation of transcription, DNA-templated (GO:0006355)|rRNA transcription (GO:0009303)|transcription from RNA polymerase III promoter (GO:0006383)|transcription initiation from RNA polymerase III promoter (GO:0006384)|tRNA transcription (GO:0009304)	nucleoplasm (GO:0005654)|transcription factor TFIIIB complex (GO:0000126)	zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(1)|endometrium(5)|large_intestine(4)|lung(5)|ovary(3)|prostate(1)|skin(2)|urinary_tract(2)	24		all_cancers(154;0.0231)|all_epithelial(191;0.0694)|Melanoma(154;0.155)	OV - Ovarian serous cystadenocarcinoma(23;0.00753)|all cancers(16;0.00925)|Epithelial(46;0.0221)	Epithelial(152;0.14)		ACTTCCTGACTGGGCAGGCAG	0.622													C|||	1115	0.222644	0.1989	0.1916	5008	,	,		15484	0.123		0.2903	False		,,,				2504	0.3098				p.P200P		Atlas-SNP	.											.	BRF1	102	.	0			c.A600G						PASS	.																																			SO:0001627	intron_variant	2972	exon4			CCTGACTGGGCAG	U28838	CCDS10001.1, CCDS42001.1, CCDS55949.1, CCDS55950.1, CCDS55951.1, CCDS55952.1, CCDS55953.1	14q32.33	2014-04-02	2013-05-29	2001-12-07	ENSG00000185024	ENSG00000185024		"""General transcription factors"""	11551	protein-coding gene	gene with protein product		604902	"""TATA box binding protein (TBP)-associated factor, RNA polymerase III, GTF3B subunit 2"", ""BRF1 homolog, subunit of RNA polymerase III transcription initiation factor IIIB (S. cerevisiae)"""	TAF3B2, TAF3C, GTF3B		7624363, 8943358	Standard	NM_145685		Approved	TFIIIB90, BRF, hBRF	uc001yqp.2	Q92994	OTTHUMG00000029884	ENST00000546474.1:c.471+128A>G	14.37:g.105722726T>C		Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	22	9	0.409091	NM_001242790	B3KU36|B4DIG5|B7Z2N3|F5H5Z7|F8WA46|Q13223|Q3SYD9|Q5PR24|Q6IQ02|Q96KX3|Q9HCW6|Q9HCW7|Q9HCW8	Silent	SNP	ENST00000546474.1	37	CCDS10001.1	492	0.22527472527472528	100	0.2032520325203252	80	0.22099447513812154	87	0.1520979020979021	225	0.29683377308707126	C	2.261	-0.369157	0.05069	.	.	ENSG00000185024	ENST00000345053	.	.	.	1.08	-2.16	0.07080	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.36915	-0.9728	4	0.30854	T	0.27	.	0.1578	0.00100	0.336:0.246:0.2015:0.2165	rs1008628;rs17845500;rs17858387;rs52792575;rs57994825;rs1008628	.	.	.	G	200	.	ENSP00000339442:S200G	S	-	1	0	BRF1	104793771	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.214000	0.01223	-1.634000	0.01537	-1.464000	0.01018	AGT	T|0.783;C|0.217	0.217	strong		0.622	BRF1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000074548.4	NM_001519	
OSCP1	127700	hgsc.bcm.edu	37	1	36886117	36886117	+	Missense_Mutation	SNP	C	C	T	rs2275477	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:36886117C>T	ENST00000356637.5	-	9	1012	c.949G>A	c.(949-951)Gga>Aga	p.G317R	OSCP1_ENST00000315643.9_Missense_Mutation_p.G317R|OSCP1_ENST00000235532.5_Missense_Mutation_p.G307R|SNORA63_ENST00000364578.1_RNA|OSCP1_ENST00000495222.1_Intron|OSCP1_ENST00000433045.2_Missense_Mutation_p.G262R			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	128	1	0.0078125	866	WXS	Illumina HiSeq	Phase_I	136	75	0.551471	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	
CSPG4	1464	hgsc.bcm.edu	37	15	75982058	75982058	+	Missense_Mutation	SNP	T	T	A	rs147116973	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:75982058T>A	ENST00000308508.5	-	3	1440	c.1348A>T	c.(1348-1350)Agg>Tgg	p.R450W		NM_001897.4	NP_001888.2	Q6UVK1	CSPG4_HUMAN	chondroitin sulfate proteoglycan 4	450	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						TGCACATGCCTCCACTCAAGC	0.647																																					p.R450W		Atlas-SNP	.											CSPG4,NS,haematopoietic_neoplasm,0,1	CSPG4	175	1	0			c.A1348T						PASS	.						53.0	52.0	53.0					15																	75982058		2197	4293	6490	SO:0001583	missense	1464	exon3			CATGCCTCCACTC	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.1348A>T	15.37:g.75982058T>A	ENSP00000312506:p.Arg450Trp	Somatic	229	0	0		WXS	Illumina HiSeq	Phase_I	224	20	0.0892857	NM_001897	D3DW77|Q92675	Missense_Mutation	SNP	ENST00000308508.5	37	CCDS10284.1	.	.	.	.	.	.	.	.	.	.	.	10.03	1.238374	0.22711	.	.	ENSG00000173546	ENST00000308508	T	0.20332	2.08	5.26	3.18	0.36537	.	0.318723	0.26328	N	0.025018	T	0.24044	0.0582	M	0.65498	2.005	0.22330	N	0.999195	D	0.55800	0.973	B	0.43754	0.43	T	0.16541	-1.0399	10	0.87932	D	0	.	9.1439	0.36921	0.0:0.1134:0.5474:0.3393	.	450	Q6UVK1	CSPG4_HUMAN	W	450	ENSP00000312506:R450W	ENSP00000312506:R450W	R	-	1	2	CSPG4	73769113	0.968000	0.33430	0.998000	0.56505	0.385000	0.30292	1.547000	0.36190	1.229000	0.43630	-0.238000	0.12139	AGG	T|0.988;A|0.013	0.013	strong		0.647	CSPG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286472.1	NM_001897	
SPATA22	84690	hgsc.bcm.edu	37	17	3343519	3343519	+	Silent	SNP	T	T	C	rs17822627	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	402	0	0		WXS	Illumina HiSeq	Phase_I	353	171	0.484419	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	
TTN	7273	hgsc.bcm.edu	37	2	179482633	179482633	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:179482633G>T	ENST00000591111.1	-	203	42746	c.42522C>A	c.(42520-42522)gaC>gaA	p.D14174E	TTN_ENST00000359218.5_Missense_Mutation_p.D6875E|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000589830.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000589487.1_RNA|TTN-AS1_ENST00000592750.1_RNA|RP11-171I2.4_ENST00000605334.1_lincRNA|TTN_ENST00000342992.6_Missense_Mutation_p.D13247E|TTN_ENST00000460472.2_Missense_Mutation_p.D6750E|TTN-AS1_ENST00000604956.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.D15815E|TTN_ENST00000342175.6_Missense_Mutation_p.D6942E|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000592630.1_RNA			Q8WZ42	TITIN_HUMAN	titin	14174	Fibronectin type-III 2. {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)			TTGCAGACAGGTCTTCAGCTC	0.463																																					p.D15815E		Atlas-SNP	.											.	TTN	18412	.	0			c.C47445A						PASS	.						184.0	178.0	180.0					2																	179482633		1997	4162	6159	SO:0001583	missense	7273	exon253			AGACAGGTCTTCA	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.42522C>A	2.37:g.179482633G>T	ENSP00000465570:p.Asp14174Glu	Somatic	323	0	0		WXS	Illumina HiSeq	Phase_I	276	76	0.275362	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		.	.	.	.	.	.	.	.	.	.	G	10.34	1.324434	0.24080	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.56611	0.45;0.45;0.45;0.45	5.63	-0.558	0.11796	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.25865	0.0630	N	0.03999	-0.3	0.33357	D	0.571856	B;B;B;B	0.12630	0.006;0.006;0.006;0.006	B;B;B;B	0.15484	0.013;0.013;0.013;0.013	T	0.13415	-1.0510	9	0.87932	D	0	.	5.0288	0.14398	0.3413:0.0:0.3539:0.3048	.	6750;6875;6942;14174	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	E	13247;6750;6942;6875;6750	ENSP00000343764:D13247E;ENSP00000434586:D6750E;ENSP00000340554:D6942E;ENSP00000352154:D6875E	ENSP00000340554:D6942E	D	-	3	2	TTN	179190878	0.751000	0.28327	0.993000	0.49108	0.985000	0.73830	-0.159000	0.10056	-0.079000	0.12707	0.655000	0.94253	GAC	.	.	none		0.463	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
ADAM32	203102	hgsc.bcm.edu	37	8	39044565	39044565	+	Splice_Site	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:39044565G>A	ENST00000379907.4	+	11	1179		c.e11+1		ADAM32_ENST00000437682.2_Intron|ADAM32_ENST00000519315.1_Intron	NM_145004.5	NP_659441	Q8TC27	ADA32_HUMAN	ADAM metallopeptidase domain 32							integral component of membrane (GO:0016021)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(14)|ovary(1)|skin(2)	31		all_cancers(7;3e-05)|all_lung(54;0.00187)|Hepatocellular(245;0.00745)|Lung NSC(58;0.00771)|Breast(189;0.0503)	LUSC - Lung squamous cell carcinoma(45;6.2e-07)|Colorectal(1;0.00699)|READ - Rectum adenocarcinoma(1;0.146)			CAGAAGTTGTGTAAGTTTTAA	0.313																																					.		Atlas-SNP	.											.	ADAM32	70	.	0			c.1052+1G>A						PASS	.						72.0	70.0	71.0					8																	39044565		1807	4076	5883	SO:0001630	splice_region_variant	203102	exon11			AGTTGTGTAAGTT	BC026085	CCDS47846.1	8p11.22	2005-08-18	2005-08-18		ENSG00000197140	ENSG00000197140		"""ADAM metallopeptidase domain containing"""	15479	protein-coding gene	gene with protein product			"""a disintegrin and metalloproteinase domain 32"""			12568724	Standard	NM_145004		Approved		uc003xmt.4	Q8TC27	OTTHUMG00000164071	ENST00000379907.4:c.1052+1G>A	8.37:g.39044565G>A		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	38	18	0.473684	NM_145004	Q8TC42	Splice_Site	SNP	ENST00000379907.4	37	CCDS47846.1	.	.	.	.	.	.	.	.	.	.	G	13.48	2.249507	0.39797	.	.	ENSG00000197140	ENST00000379907	.	.	.	5.47	5.47	0.80525	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.1764	0.72916	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	ADAM32	39163722	1.000000	0.71417	0.992000	0.48379	0.318000	0.28184	4.950000	0.63603	2.734000	0.93682	0.650000	0.86243	.	.	.	none		0.313	ADAM32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377089.1	NM_145004	Intron
AQP8	343	hgsc.bcm.edu	37	16	25239805	25239805	+	Missense_Mutation	SNP	G	G	C	rs2287798	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:25239805G>C	ENST00000219660.5	+	6	903	c.778G>C	c.(778-780)Gct>Cct	p.A260P	AQP8_ENST00000566125.1_Missense_Mutation_p.A254P	NM_001169.2	NP_001160.2	O94778	AQP8_HUMAN	aquaporin 8	260			A -> P (in dbSNP:rs2287798).		canalicular bile acid transport (GO:0015722)|cellular response to cAMP (GO:0071320)|transmembrane transport (GO:0055085)|transport (GO:0006810)|water transport (GO:0006833)	apical part of cell (GO:0045177)|integral component of plasma membrane (GO:0005887)|intracellular canaliculus (GO:0046691)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)	water channel activity (GO:0015250)	p.A260P(2)		NS(1)|breast(1)|large_intestine(3)|lung(8)|pancreas(1)|stomach(1)|upper_aerodigestive_tract(1)	16				GBM - Glioblastoma multiforme(48;0.044)		CATCCTGAAGGCTCGGTGAAG	0.592													G|||	2074	0.414137	0.4077	0.4308	5008	,	,		19369	0.5298		0.3459	False		,,,				2504	0.362				p.A260P		Atlas-SNP	.											AQP8_ENST00000219660,NS,carcinoma,0,2	AQP8	75	2	2	Substitution - Missense(2)	stomach(2)	c.G778C						scavenged	.	G	PRO/ALA	1822,2572	533.3+/-373.7	378,1066,753	97.0	84.0	88.0		778	-1.5	0.0	16	dbSNP_100	88	3191,5409	482.4+/-370.9	578,2035,1687	yes	missense	AQP8	NM_001169.2	27	956,3101,2440	CC,CG,GG		37.1047,41.4656,38.5793	benign	260/262	25239805	5013,7981	2197	4300	6497	SO:0001583	missense	343	exon6			CTGAAGGCTCGGT	BC040630	CCDS10626.1	16p12	2008-02-05			ENSG00000103375	ENSG00000103375		"""Ion channels / Aquaporins"""	642	protein-coding gene	gene with protein product		603750				9806845, 10393433	Standard	NM_001169		Approved		uc002doc.3	O94778	OTTHUMG00000097013	ENST00000219660.5:c.778G>C	16.37:g.25239805G>C	ENSP00000219660:p.Ala260Pro	Somatic	92	1	0.0108696		WXS	Illumina HiSeq	Phase_I	112	42	0.375	NM_001169	Q8IUU3|Q9UIA4	Missense_Mutation	SNP	ENST00000219660.5	37	CCDS10626.1	903	0.41346153846153844	203	0.41260162601626016	146	0.40331491712707185	291	0.5087412587412588	263	0.3469656992084433	G	9.751	1.167366	0.21621	0.414656	0.371047	ENSG00000103375	ENST00000219660	D	0.90844	-2.74	4.71	-1.46	0.08800	Aquaporin-like (1);	2.407790	0.01641	N	0.024060	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.26975	0.165	B	0.23018	0.043	T	0.21449	-1.0245	9	0.40728	T	0.16	1.6603	8.6705	0.34147	0.0:0.1258:0.4556:0.4186	rs2287798;rs56573772;rs2287798	260	O94778	AQP8_HUMAN	P	260	ENSP00000219660:A260P	ENSP00000219660:A260P	A	+	1	0	AQP8	25147306	0.174000	0.23070	0.003000	0.11579	0.003000	0.03518	0.297000	0.19101	-0.007000	0.14345	-0.831000	0.03077	GCT	G|0.599;C|0.401	0.401	strong		0.592	AQP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214102.2	NM_001169	
TTLL5	23093	hgsc.bcm.edu	37	14	76156609	76156609	+	Missense_Mutation	SNP	C	C	T	rs2303345	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:76156609C>T	ENST00000298832.9	+	6	651	c.446C>T	c.(445-447)gCt>gTt	p.A149V	TTLL5_ENST00000557636.1_Missense_Mutation_p.A149V|TTLL5_ENST00000286650.5_Missense_Mutation_p.A149V	NM_015072.4	NP_055887.3	Q6EMB2	TTLL5_HUMAN	tubulin tyrosine ligase-like family, member 5	149	TTL. {ECO:0000255|PROSITE- ProRule:PRU00568}.		A -> V (in dbSNP:rs2303345). {ECO:0000269|PubMed:10231032, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17116691, ECO:0000269|Ref.3}.		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)		GGATTCAAGGCTTTTCACATC	0.453													C|||	1975	0.394369	0.0242	0.5778	5008	,	,		18647	0.3552		0.661	False		,,,				2504	0.5307				p.A149V		Atlas-SNP	.											.	TTLL5	102	.	0			c.C446T						PASS	.	C	VAL/ALA	600,3806	261.9+/-264.6	46,508,1649	160.0	128.0	139.0		446	5.3	1.0	14	dbSNP_100	139	5601,2999	665.1+/-402.2	1832,1937,531	yes	missense	TTLL5	NM_015072.4	64	1878,2445,2180	TT,TC,CC		34.8721,13.6178,47.678	benign	149/1282	76156609	6201,6805	2203	4300	6503	SO:0001583	missense	23093	exon6			TCAAGGCTTTTCA	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.446C>T	14.37:g.76156609C>T	ENSP00000298832:p.Ala149Val	Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	112	111	0.991071	NM_015072	B9EGH8|B9EGH9|Q9BUB0|Q9H0G4|Q9H7W2|Q9P1V5|Q9UPZ4	Missense_Mutation	SNP	ENST00000298832.9	37	CCDS32124.1	956	0.43772893772893773	20	0.04065040650406504	216	0.5966850828729282	212	0.3706293706293706	508	0.6701846965699209	C	14.43	2.533249	0.45073	0.136178	0.651279	ENSG00000119685	ENST00000557003;ENST00000557636;ENST00000286650;ENST00000298832	T;T;T	0.07327	3.93;3.2;4.01	5.26	5.26	0.73747	.	0.307175	0.34178	N	0.004189	T	0.00012	0.0000	L	0.33710	1.025	0.09310	P	0.9999999999999999	P;P;B	0.39216	0.613;0.664;0.38	B;B;B	0.40329	0.219;0.326;0.108	T	0.04005	-1.0985	9	0.30078	T	0.28	.	9.1787	0.37127	0.1625:0.6802:0.1573:0.0	rs2303345;rs57094674;rs2303345	149;149;149	G3V2J9;Q6EMB2;Q6EMB2-3	.;TTLL5_HUMAN;.	V	149	ENSP00000450713:A149V;ENSP00000286650:A149V;ENSP00000298832:A149V	ENSP00000286650:A149V	A	+	2	0	TTLL5	75226362	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.849000	0.62882	2.442000	0.82660	0.655000	0.94253	GCT	C|0.562;T|0.438	0.438	strong		0.453	TTLL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414453.1	NM_015072	
CD27	939	hgsc.bcm.edu	37	12	6554628	6554628	+	Missense_Mutation	SNP	G	G	A	rs25680	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:6554628G>A	ENST00000266557.3	+	2	404	c.175G>A	c.(175-177)Gct>Act	p.A59T	CD27-AS1_ENST00000399492.2_RNA|CD27-AS1_ENST00000545339.1_RNA|CD27_ENST00000541233.1_3'UTR	NM_001242.4	NP_001233	P26842	CD27_HUMAN	CD27 molecule	59			A -> T (in dbSNP:rs25680). {ECO:0000269|PubMed:1334106, ECO:0000269|PubMed:14702039, ECO:0000269|Ref.4}.		cell surface receptor signaling pathway (GO:0007166)|extrinsic apoptotic signaling pathway (GO:0097191)|immunoglobulin mediated immune response (GO:0016064)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of T cell apoptotic process (GO:0070233)|positive regulation of B cell differentiation (GO:0045579)|positive regulation of JNK cascade (GO:0046330)|release of cytoplasmic sequestered NF-kappaB (GO:0008588)|response to ethanol (GO:0045471)	external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|transmembrane signaling receptor activity (GO:0004888)			kidney(1)|large_intestine(5)|lung(1)|urinary_tract(3)	10						GCATAGAAAGGCTGCTCAGTG	0.572													G|||	839	0.167532	0.1505	0.1239	5008	,	,		19642	0.0536		0.1968	False		,,,				2504	0.3088				p.A59T		Atlas-SNP	.											.	CD27	17	.	0			c.G175A						PASS	.	G	THR/ALA	777,3629	314.4+/-293.6	77,623,1503	150.0	123.0	133.0		175	2.7	0.0	12	dbSNP_72	133	1977,6623	349.1+/-327.3	244,1489,2567	yes	missense	CD27	NM_001242.4	58	321,2112,4070	AA,AG,GG		22.9884,17.635,21.1748	benign	59/261	6554628	2754,10252	2203	4300	6503	SO:0001583	missense	939	exon2			AGAAAGGCTGCTC	M63928	CCDS8545.1	12p13	2014-09-17	2006-10-27	2006-10-27	ENSG00000139193	ENSG00000139193		"""Tumor necrosis factor receptor superfamily"", ""CD molecules"""	11922	protein-coding gene	gene with protein product		186711	"""tumor necrosis factor receptor superfamily, member 7"""	TNFRSF7		2442250, 8530100	Standard	NM_001242		Approved	S152, Tp55	uc001qod.3	P26842	OTTHUMG00000168316	ENST00000266557.3:c.175G>A	12.37:g.6554628G>A	ENSP00000266557:p.Ala59Thr	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	62	26	0.419355	NM_001242	B2RDZ0	Missense_Mutation	SNP	ENST00000266557.3	37	CCDS8545.1	267	0.12225274725274725	58	0.11788617886178862	59	0.16298342541436464	13	0.022727272727272728	137	0.18073878627968337	G	13.38	2.219840	0.39201	0.17635	0.229884	ENSG00000139193	ENST00000266557	D	0.83591	-1.74	4.54	2.66	0.31614	TNFR/CD27/30/40/95 cysteine-rich region (2);	0.547236	0.15247	N	0.272531	T	0.00073	0.0002	L	0.29908	0.895	0.80722	P	0.0	P	0.34864	0.473	B	0.38106	0.265	T	0.03555	-1.1025	9	0.13470	T	0.59	-2.4359	6.0197	0.19623	0.104:0.1919:0.704:0.0	rs25680;rs758738;rs17787459;rs52809900;rs58117019;rs25680	59	P26842	CD27_HUMAN	T	59	ENSP00000266557:A59T	ENSP00000266557:A59T	A	+	1	0	CD27	6424889	0.001000	0.12720	0.002000	0.10522	0.812000	0.45895	0.839000	0.27586	0.513000	0.28278	0.563000	0.77884	GCT	G|0.844;A|0.156	0.156	strong		0.572	CD27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399258.1		
MAP1B	4131	hgsc.bcm.edu	37	5	71495041	71495041	+	Silent	SNP	T	T	C	rs3805452	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	57	0	0		WXS	Illumina HiSeq	Phase_I	58	21	0.362069	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	
KY	339855	hgsc.bcm.edu	37	3	134322742	134322742	+	Silent	SNP	A	A	G	rs2293293	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:134322742A>G	ENST00000423778.2	-	11	1726	c.1665T>C	c.(1663-1665)ctT>ctC	p.L555L	KY_ENST00000508956.1_Silent_p.L534L|KY_ENST00000503669.1_3'UTR	NM_178554.4	NP_848649.3	Q8NBH2	KY_HUMAN	kyphoscoliosis peptidase	557					muscle organ development (GO:0007517)|neuromuscular junction development (GO:0007528)	cytoskeleton (GO:0005856)|Z disc (GO:0030018)	peptidase activity (GO:0008233)			central_nervous_system(1)|endometrium(3)|kidney(1)|lung(12)|ovary(2)|upper_aerodigestive_tract(2)	21						CACAGCATACAAGGTAATTAA	0.512													G|||	3426	0.684105	0.5333	0.7507	5008	,	,		19437	0.8829		0.668	False		,,,				2504	0.6524				p.L555L		Atlas-SNP	.											.	KY	92	.	0			c.T1665C						PASS	.	G		2192,1732		632,928,402	81.0	81.0	81.0		1665	-0.7	0.2	3	dbSNP_100	81	5313,2995		1727,1859,568	no	coding-synonymous	KY	NM_178554.4		2359,2787,970	GG,GA,AA		36.0496,44.1386,38.6445		555/662	134322742	7505,4727	1962	4154	6116	SO:0001819	synonymous_variant	339855	exon11			GCATACAAGGTAA	AK090526	CCDS46920.1	3q22.1	2010-11-23			ENSG00000174611	ENSG00000174611			26576	protein-coding gene	gene with protein product		605739					Standard	NM_178554		Approved	FLJ33207	uc010hty.3	Q8NBH2	OTTHUMG00000159788	ENST00000423778.2:c.1665T>C	3.37:g.134322742A>G		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	69	39	0.565217	NM_178554	B7Z1S4|Q6ZT15	Silent	SNP	ENST00000423778.2	37	CCDS46920.1																																																																																			A|0.316;G|0.684	0.684	strong		0.512	KY-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357320.1	NM_178554	
SNX15	29907	hgsc.bcm.edu	37	11	64799998	64799998	+	Silent	SNP	T	T	C	rs534236	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:64799998T>C	ENST00000377244.3	+	3	361	c.231T>C	c.(229-231)ccT>ccC	p.P77P	RP11-399J13.3_ENST00000301886.3_3'UTR|SNX15_ENST00000352068.5_Silent_p.P77P	NM_013306.4|NM_147777.3	NP_037438.2|NP_680086.2	Q9NRS6	SNX15_HUMAN	sorting nexin 15	77	PX. {ECO:0000255|PROSITE- ProRule:PRU00147}.				intracellular protein transport (GO:0006886)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleolus (GO:0005730)	phosphatidylinositol binding (GO:0035091)			endometrium(1)|large_intestine(1)|lung(6)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	14						AGGAGTTCCCTGCTTTCCCCC	0.627													T|||	1876	0.374601	0.2148	0.6052	5008	,	,		17784	0.1825		0.6213	False		,,,				2504	0.3712				p.P77P	Esophageal Squamous(56;269 1304 3324 8253)	Atlas-SNP	.											.	SNX15	35	.	0			c.T231C						PASS	.	T	,	1272,3130	432.0+/-343.1	181,910,1110	65.0	55.0	59.0		231,231	-7.7	0.1	11	dbSNP_83	59	5552,3042	661.1+/-401.8	1775,2002,520	no	coding-synonymous,coding-synonymous	SNX15	NM_013306.4,NM_147777.3	,	1956,2912,1630	CC,CT,TT		35.3968,28.896,47.4915	,	77/343,77/257	64799998	6824,6172	2201	4297	6498	SO:0001819	synonymous_variant	29907	exon3			GTTCCCTGCTTTC	AF175267	CCDS8089.1, CCDS8090.1	11q12	2008-05-22			ENSG00000110025	ENSG00000110025		"""Sorting nexins"""	14978	protein-coding gene	gene with protein product		605964				11208079	Standard	NM_013306		Approved			Q9NRS6	OTTHUMG00000037387	ENST00000377244.3:c.231T>C	11.37:g.64799998T>C		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	53	18	0.339623	NM_147777	E5KQS6|Q9NRS5	Silent	SNP	ENST00000377244.3	37	CCDS8089.1	937	0.429029304029304	135	0.27439024390243905	223	0.6160220994475138	102	0.17832167832167833	477	0.6292875989445911	T	8.195	0.796932	0.16327	0.28896	0.646032	ENSG00000110025	ENST00000525648	.	.	.	4.89	-7.72	0.01250	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.22745	P	0.99878566	.	.	.	.	.	.	T	0.45116	-0.9283	3	.	.	.	-21.2781	0.5102	0.00594	0.2697:0.1373:0.207:0.386	rs534236;rs17850569;rs534236	.	.	.	P	36	.	.	L	+	2	0	SNX15	64556574	0.000000	0.05858	0.061000	0.19648	0.029000	0.11900	-4.252000	0.00266	-1.237000	0.02539	-0.242000	0.12053	CTG	T|0.524;C|0.476	0.476	strong		0.627	SNX15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091004.3		
SPATA18	132671	hgsc.bcm.edu	37	4	52946016	52946016	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:52946016C>A	ENST00000295213.4	+	9	1660	c.1286C>A	c.(1285-1287)gCa>gAa	p.A429E	SPATA18_ENST00000419395.2_Missense_Mutation_p.A397E	NM_145263.2	NP_660306.1	Q8TC71	MIEAP_HUMAN	spermatogenesis associated 18	429					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)			ATTGCCTTTGCAATGCAGGCC	0.443																																					p.A429E		Atlas-SNP	.											.	SPATA18	222	.	0			c.C1286A						PASS	.						250.0	234.0	240.0					4																	52946016		2203	4300	6503	SO:0001583	missense	132671	exon9			CCTTTGCAATGCA	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.1286C>A	4.37:g.52946016C>A	ENSP00000295213:p.Ala429Glu	Somatic	227	0	0		WXS	Illumina HiSeq	Phase_I	191	45	0.235602	NM_145263	B4E2R0|E5RLK1|Q8IY48|Q8N7D7	Missense_Mutation	SNP	ENST00000295213.4	37	CCDS3489.1	.	.	.	.	.	.	.	.	.	.	C	16.34	3.096593	0.56075	.	.	ENSG00000163071	ENST00000295213;ENST00000419395	T;T	0.32023	1.47;1.48	5.35	5.35	0.76521	.	0.051108	0.85682	D	0.000000	T	0.46367	0.1389	L	0.39633	1.23	0.80722	D	1	D;D;D	0.89917	0.999;0.999;1.0	D;D;D	0.87578	0.964;0.964;0.998	T	0.09618	-1.0666	10	0.27785	T	0.31	-16.3661	16.606	0.84830	0.0:1.0:0.0:0.0	.	397;429;429	Q8TC71-2;Q8TC71;Q96M13	.;MIEAP_HUMAN;.	E	429;397	ENSP00000295213:A429E;ENSP00000415309:A397E	ENSP00000295213:A429E	A	+	2	0	SPATA18	52640773	1.000000	0.71417	0.974000	0.42286	0.600000	0.36913	5.025000	0.64097	2.789000	0.95967	0.655000	0.94253	GCA	.	.	none		0.443	SPATA18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250597.2	NM_145263	
EPS8L2	64787	hgsc.bcm.edu	37	11	722709	722709	+	Silent	SNP	C	C	T	rs10902205	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:722709C>T	ENST00000533256.1	+	15	1620	c.1245C>T	c.(1243-1245)taC>taT	p.Y415Y	EPS8L2_ENST00000530636.1_Silent_p.Y415Y|EPS8L2_ENST00000526198.1_Silent_p.Y431Y|EPS8L2_ENST00000318562.8_Silent_p.Y415Y|AP006621.9_ENST00000527021.2_RNA			Q9H6S3	ES8L2_HUMAN	EPS8-like 2	415					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)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|ruffle membrane (GO:0032587)|vesicle (GO:0031982)	actin binding (GO:0003779)			NS(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(2)|pancreas(1)|prostate(2)|soft_tissue(1)|urinary_tract(1)	13		all_cancers(49;1.24e-08)|all_epithelial(84;1.87e-05)|Breast(177;0.000286)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.106)|all_lung(207;0.136)		all cancers(45;4.37e-27)|Epithelial(43;2.81e-26)|OV - Ovarian serous cystadenocarcinoma(40;1.33e-20)|BRCA - Breast invasive adenocarcinoma(625;4.29e-05)|Lung(200;0.0582)|LUSC - Lung squamous cell carcinoma(625;0.0703)		TGCCCCTCTACGTGCCCAAGT	0.682													c|||	538	0.107428	0.2474	0.0692	5008	,	,		9206	0.0357		0.0805	False		,,,				2504	0.047				p.Y415Y		Atlas-SNP	.											.	EPS8L2	42	.	0			c.C1245T						PASS	.			951,3443		95,761,1341	18.0	23.0	21.0		1245	-2.8	0.3	11	dbSNP_120	21	785,7807		44,697,3555	no	coding-synonymous	EPS8L2	NM_022772.3		139,1458,4896	TT,TC,CC		9.1364,21.6431,13.3682		415/716	722709	1736,11250	2197	4296	6493	SO:0001819	synonymous_variant	64787	exon14			CCTCTACGTGCCC	AF318331	CCDS31328.1	11p15.5	2008-02-05				ENSG00000177106			21296	protein-coding gene	gene with protein product		614988				12620401	Standard	NM_022772		Approved	FLJ21935, FLJ22171, MGC3088	uc001lqt.3	Q9H6S3		ENST00000533256.1:c.1245C>T	11.37:g.722709C>T		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	134	115	0.858209	NM_022772	B3KSX1|B7ZKL3|Q53GM8|Q8WYW7|Q96K06|Q9H6K9	Silent	SNP	ENST00000533256.1	37	CCDS31328.1																																																																																			A|0.000;C|0.882;G|0.000;T|0.118	0.118	strong		0.682	EPS8L2-003	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382344.1	NM_022772	
DHX34	9704	hgsc.bcm.edu	37	19	47883086	47883086	+	Silent	SNP	T	T	G	rs28522883	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:47883086T>G	ENST00000328771.4	+	14	3175	c.2826T>G	c.(2824-2826)gcT>gcG	p.A942A		NM_014681.5	NP_055496.2	Q14147	DHX34_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 34	942					negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:2000623)|nuclear-transcribed mRNA catabolic process (GO:0000956)	membrane (GO:0016020)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(8)|ovary(5)|prostate(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	36		all_cancers(25;1.65e-09)|all_epithelial(76;9.95e-08)|all_lung(116;7.27e-07)|Lung NSC(112;1.6e-06)|Ovarian(192;0.0139)|all_neural(266;0.026)|Breast(70;0.0503)		all cancers(93;7.16e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.000489)|GBM - Glioblastoma multiforme(486;0.00413)|Epithelial(262;0.0132)		TCCTGGCGGCTTCCCTGCGGC	0.662													T|||	438	0.0874601	0.0734	0.1009	5008	,	,		17228	0.0069		0.1441	False		,,,				2504	0.1217				p.A942A		Atlas-SNP	.											.	DHX34	98	.	0			c.T2826G						PASS	.	T		380,4026	191.2+/-216.9	17,346,1840	46.0	48.0	47.0		2826	-7.4	0.0	19	dbSNP_125	47	1323,7277	257.3+/-281.4	80,1163,3057	no	coding-synonymous	DHX34	NM_014681.5		97,1509,4897	GG,GT,TT		15.3837,8.6246,13.094		942/1144	47883086	1703,11303	2203	4300	6503	SO:0001819	synonymous_variant	9704	exon14			GGCGGCTTCCCTG	D50924	CCDS12700.1	19q13.3	2003-06-13	2003-06-13	2003-06-13	ENSG00000134815	ENSG00000134815		"""DEAH-boxes"""	16719	protein-coding gene	gene with protein product		615475	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 34"""	DDX34		10708517, 8590280	Standard	NM_014681		Approved	KIAA0134	uc010xyn.2	Q14147	OTTHUMG00000149959	ENST00000328771.4:c.2826T>G	19.37:g.47883086T>G		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	50	48	0.96	NM_014681	B4DMY8	Silent	SNP	ENST00000328771.4	37	CCDS12700.1																																																																																			T|0.878;G|0.122	0.122	strong		0.662	DHX34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314313.3	NM_014681	
KRT84	3890	hgsc.bcm.edu	37	12	52778947	52778947	+	Silent	SNP	A	A	G	rs1791631	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	101	0	0		WXS	Illumina HiSeq	Phase_I	79	41	0.518987	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	
OR5B3	441608	hgsc.bcm.edu	37	11	58170738	58170738	+	Missense_Mutation	SNP	A	A	G	rs11229413	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:58170738A>G	ENST00000309403.2	-	1	144	c.145T>C	c.(145-147)Tgg>Cgg	p.W49R		NM_001005469.1	NP_001005469.1	Q8NH48	OR5B3_HUMAN	olfactory receptor, family 5, subfamily B, member 3	49			W -> R (in dbSNP:rs11229413).			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(4)|lung(17)|ovary(1)|prostate(1)|skin(2)|stomach(6)|upper_aerodigestive_tract(1)	34	Esophageal squamous(5;0.0027)	Breast(21;0.0778)				CAGGAATCCCAGAATATCAAT	0.428													A|||	1453	0.290136	0.3533	0.2695	5008	,	,		19289	0.1448		0.3628	False		,,,				2504	0.2945				p.W49R		Atlas-SNP	.											.	OR5B3	65	.	0			c.T145C						PASS	.	A	ARG/TRP	1443,2959	465.3+/-354.1	229,985,987	86.0	86.0	86.0		145	-8.4	0.0	11	dbSNP_120	86	3094,5496	473.0+/-368.5	550,1994,1751	yes	missense	OR5B3	NM_001005469.1	101	779,2979,2738	GG,GA,AA		36.0186,32.7806,34.9215	benign	49/315	58170738	4537,8455	2201	4295	6496	SO:0001583	missense	441608	exon1			AATCCCAGAATAT	AB065545	CCDS31549.1	11q12.1	2012-08-09			ENSG00000172769	ENSG00000172769		"""GPCR / Class A : Olfactory receptors"""	8324	protein-coding gene	gene with protein product				OR5B13			Standard	NM_001005469		Approved	OST129	uc010rkf.2	Q8NH48	OTTHUMG00000167516	ENST00000309403.2:c.145T>C	11.37:g.58170738A>G	ENSP00000308270:p.Trp49Arg	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	86	60	0.697674	NM_001005469	Q6IEV6	Missense_Mutation	SNP	ENST00000309403.2	37	CCDS31549.1	655	0.2999084249084249	195	0.39634146341463417	89	0.24585635359116023	95	0.1660839160839161	276	0.3641160949868074	a	1.754	-0.488586	0.04352	0.327806	0.360186	ENSG00000172769	ENST00000309403	T	0.02890	4.12	4.19	-8.38	0.00973	GPCR, rhodopsin-like superfamily (1);	1.091390	0.07307	N	0.875172	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B	0.22683	0.073	B	0.27887	0.084	T	0.40534	-0.9558	9	0.54805	T	0.06	-5.7297	14.7401	0.69448	0.417:0.0:0.583:0.0	rs11229413;rs52835299;rs58298363;rs11229413	49	Q8NH48	OR5B3_HUMAN	R	49	ENSP00000308270:W49R	ENSP00000308270:W49R	W	-	1	0	OR5B3	57927314	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-3.698000	0.00390	-2.118000	0.00828	-0.361000	0.07541	TGG	A|0.675;G|0.325	0.325	strong		0.428	OR5B3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394886.1	NM_001005469	
OR10G4	390264	hgsc.bcm.edu	37	11	123887175	123887175	+	Silent	SNP	G	G	A	rs61908597	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:123887175G>A	ENST00000320891.4	+	1	894	c.894G>A	c.(892-894)gtG>gtA	p.V298V		NM_001004462.1	NP_001004462.1	Q8NGN3	O10G4_HUMAN	olfactory receptor, family 10, subfamily G, member 4	298						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(8)|lung(19)|ovary(1)|prostate(1)|skin(4)|stomach(6)|upper_aerodigestive_tract(1)	48		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0401)		AGAAAGCTGTGTTGAAACTTA	0.388													g|||	203	0.0405351	0.0159	0.0461	5008	,	,		21200	0.0079		0.1064	False		,,,				2504	0.0358				p.V298V		Atlas-SNP	.											OR10G4,NS,carcinoma,+2,1	OR10G4	77	1	0			c.G894A						PASS	.	G		99,4303	79.3+/-117.8	1,97,2103	73.0	68.0	70.0		894	0.2	0.0	11	dbSNP_129	70	744,7854	178.0+/-227.5	37,670,3592	no	coding-synonymous	OR10G4	NM_001004462.1		38,767,5695	AA,AG,GG		8.6532,2.249,6.4846		298/312	123887175	843,12157	2201	4299	6500	SO:0001819	synonymous_variant	390264	exon1			AGCTGTGTTGAAA	AB065757	CCDS31702.1	11q24.1	2012-08-09			ENSG00000254737	ENSG00000254737		"""GPCR / Class A : Olfactory receptors"""	14809	protein-coding gene	gene with protein product							Standard	NM_001004462		Approved		uc010sac.2	Q8NGN3	OTTHUMG00000165966	ENST00000320891.4:c.894G>A	11.37:g.123887175G>A		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	89	69	0.775281	NM_001004462	Q6IEW0	Silent	SNP	ENST00000320891.4	37	CCDS31702.1																																																																																			G|0.940;A|0.060	0.060	strong		0.388	OR10G4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387268.1	NM_001004462	
PIEZO1	9780	hgsc.bcm.edu	37	16	88783449	88783449	+	Silent	SNP	C	C	G	rs8057031	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:88783449C>G	ENST00000301015.9	-	45	6888	c.6642G>C	c.(6640-6642)ctG>ctC	p.L2214L	MIR4722_ENST00000578292.1_RNA|PIEZO1_ENST00000327397.7_Silent_p.L82L|RP5-1142A6.9_ENST00000564984.1_RNA	NM_001142864.2	NP_001136336.2	Q92508	PIEZ1_HUMAN	piezo-type mechanosensitive ion channel component 1	2214					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						CGCCCAGCTTCAGGGTGACGG	0.622													G|||	3434	0.685703	0.7716	0.7176	5008	,	,		18796	0.8313		0.5596	False		,,,				2504	0.5266				p.L2214L		Atlas-SNP	.											.	PIEZO1	79	.	0			c.G6642C						PASS	.	G		1035,349		392,251,49	169.0	168.0	168.0		6642	1.0	1.0	16	dbSNP_116	168	1848,1334		524,800,267	no	coding-synonymous	PIEZO1	NM_001142864.2		916,1051,316	GG,GC,CC		41.9233,25.2168,36.8594		2214/2522	88783449	2883,1683	692	1591	2283	SO:0001819	synonymous_variant	9780	exon45			CAGCTTCAGGGTG	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.6642G>C	16.37:g.88783449C>G		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	108	108	1	NM_001142864	A6NHT9|A7E2B7|Q0KKZ9	Silent	SNP	ENST00000301015.9	37	CCDS54058.1	1539	0.7046703296703297	371	0.7540650406504065	244	0.6740331491712708	486	0.8496503496503497	438	0.5778364116094987	G	0.207	-1.040115	0.02013	0.747832	0.580767	ENSG00000103335	ENST00000451779	.	.	.	4.54	1.05	0.20165	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999999	.	.	.	.	.	.	T	0.17531	-1.0366	3	.	.	.	-28.0485	5.2143	0.15334	0.3531:0.1385:0.5084:0.0	rs8057031;rs11547380;rs60291860	.	.	.	Q	2160	.	.	E	-	1	0	FAM38A	87310950	1.000000	0.71417	0.992000	0.48379	0.103000	0.19146	0.982000	0.29539	-0.209000	0.10156	-0.216000	0.12614	GAA	C|0.318;G|0.682	0.682	strong		0.622	PIEZO1-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000345699.4	NM_014745	
CD101	9398	hgsc.bcm.edu	37	1	117554421	117554421	+	Missense_Mutation	SNP	A	A	G	rs3754112	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:117554421A>G	ENST00000256652.4	+	3	732	c.674A>G	c.(673-675)aAc>aGc	p.N225S	CD101_ENST00000369470.1_Missense_Mutation_p.N225S	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	225	Ig-like C2-type 2.		N -> S (in dbSNP:rs3754112).		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						GTACAGCTCAACAAACTGGGA	0.502													A|||	753	0.150359	0.0348	0.2017	5008	,	,		19749	0.0635		0.337	False		,,,				2504	0.1677				p.N225S		Atlas-SNP	.											CD101,NS,adenoma,0,1	CD101	95	1	0			c.A674G						PASS	.	A	SER/ASN	392,4014	197.4+/-221.5	19,354,1830	83.0	73.0	76.0		674	-2.3	0.1	1	dbSNP_107	76	2794,5806	442.4+/-360.1	457,1880,1963	yes	missense	CD101	NM_004258.3	46	476,2234,3793	GG,GA,AA		32.4884,8.897,24.4964	benign	225/1022	117554421	3186,9820	2203	4300	6503	SO:0001583	missense	9398	exon3			AGCTCAACAAACT	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.674A>G	1.37:g.117554421A>G	ENSP00000256652:p.Asn225Ser	Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	150	83	0.553333	NM_001256109	Q15856	Missense_Mutation	SNP	ENST00000256652.4	37	CCDS891.1	371	0.16987179487179488	13	0.026422764227642278	92	0.2541436464088398	34	0.05944055944055944	232	0.30606860158311344	A	8.266	0.812367	0.16537	0.08897	0.324884	ENSG00000134256	ENST00000256652;ENST00000369470	T;T	0.63913	-0.07;-0.07	5.57	-2.28	0.06826	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.652897	0.14980	N	0.287292	T	0.15869	0.0382	N	0.08118	0	0.42336	P	0.007686999999999999	B	0.02656	0.0	B	0.04013	0.001	T	0.06516	-1.0822	9	0.42905	T	0.14	-6.1484	6.0936	0.20008	0.5508:0.1307:0.3185:0.0	rs3754112;rs17229361;rs17581002;rs52790018;rs57787687;rs3754112	225	Q93033	IGSF2_HUMAN	S	225	ENSP00000256652:N225S;ENSP00000358482:N225S	ENSP00000256652:N225S	N	+	2	0	CD101	117355944	0.989000	0.36119	0.077000	0.20336	0.004000	0.04260	0.914000	0.28624	-0.239000	0.09710	-0.285000	0.09966	AAC	G|0.210;N|0.000	0.210	strong		0.502	CD101-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033274.1	NM_004258	
NOD1	10392	hgsc.bcm.edu	37	7	30496382	30496382	+	Silent	SNP	G	G	C	rs2075818	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:30496382G>C	ENST00000222823.4	-	4	681	c.156C>G	c.(154-156)gcC>gcG	p.A52A	NOD1_ENST00000423334.2_Silent_p.A52A	NM_006092.2	NP_006083.1	Q9Y239	NOD1_HUMAN	nucleotide-binding oligomerization domain containing 1	52	CARD. {ECO:0000255|PROSITE- ProRule:PRU00046}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of MAPK activity (GO:0000187)|apoptotic process (GO:0006915)|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)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interleukin-8 biosynthetic process (GO:0042228)|intracellular signal transduction (GO:0035556)|JNK cascade (GO:0007254)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of dendritic cell antigen processing and presentation (GO:0002606)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of JNK cascade (GO:0046330)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of tumor necrosis factor production (GO:0032760)|protein oligomerization (GO:0051259)|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)	basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|cytosol (GO:0005829)	ATP binding (GO:0005524)|CARD domain binding (GO:0050700)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|identical protein binding (GO:0042802)|peptidoglycan binding (GO:0042834)|protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(17)|ovary(2)|prostate(1)|skin(2)	39						CCGCATCTTCGGCCGAGAAGT	0.547													G|||	1849	0.369209	0.5166	0.1902	5008	,	,		18461	0.3859		0.2326	False		,,,				2504	0.4202				p.A52A		Atlas-SNP	.											.	NOD1	79	.	0			c.C156G						PASS	.	G		2093,2313	573.3+/-383.5	502,1089,612	126.0	112.0	116.0		156	-11.6	0.0	7	dbSNP_96	116	2137,6463	367.3+/-334.7	284,1569,2447	no	coding-synonymous	NOD1	NM_006092.2		786,2658,3059	CC,CG,GG		24.8488,47.5034,32.5235		52/954	30496382	4230,8776	2203	4300	6503	SO:0001819	synonymous_variant	10392	exon4			ATCTTCGGCCGAG	AF126484	CCDS5427.1	7p15-p14	2006-12-08	2006-12-08	2006-12-08	ENSG00000106100	ENSG00000106100		"""Nucleotide-binding domain and leucine rich repeat containing"""	16390	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 1"", ""NLR family, CARD domain containing 1"""	605980	"""caspase recruitment domain family, member 4"""	CARD4		10224040, 10329646	Standard	NM_006092		Approved	NLRC1, CLR7.1	uc003tav.3	Q9Y239	OTTHUMG00000023923	ENST00000222823.4:c.156C>G	7.37:g.30496382G>C		Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	136	38	0.279412	NM_006092	B4DTU3|Q549U4|Q8IWF5	Silent	SNP	ENST00000222823.4	37	CCDS5427.1																																																																																			G|0.683;C|0.317	0.317	strong		0.547	NOD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250443.2		
FYCO1	79443	hgsc.bcm.edu	37	3	46009864	46009864	+	Missense_Mutation	SNP	C	C	G	rs3733100|rs200041037	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:46009864C>G	ENST00000296137.2	-	8	1167	c.962G>C	c.(961-963)gGc>gCc	p.G321A	FYCO1_ENST00000535325.1_Missense_Mutation_p.G321A	NM_024513.3	NP_078789.2	Q9BQS8	FYCO1_HUMAN	FYVE and coiled-coil domain containing 1	321			G -> A (in dbSNP:rs3733100). {ECO:0000269|PubMed:11896456, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005}.		plus-end-directed vesicle transport along microtubule (GO:0072383)	autophagic vacuole (GO:0005776)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)	metal ion binding (GO:0046872)			NS(4)|breast(3)|central_nervous_system(1)|endometrium(11)|kidney(2)|large_intestine(9)|lung(17)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	54				BRCA - Breast invasive adenocarcinoma(193;0.00147)|KIRC - Kidney renal clear cell carcinoma(197;0.0272)|Kidney(197;0.0323)		TAGCTCCAGGCCCTGCAGGCA	0.617													G|||	2669	0.532947	0.2095	0.6427	5008	,	,		19103	0.6667		0.5557	False		,,,				2504	0.7311				p.G321A		Atlas-SNP	.											.	FYCO1	115	.	0			c.G962C						PASS	.	G	ALA/GLY	1086,3320	720.4+/-409.1	143,800,1260	70.0	62.0	65.0		962	3.8	1.0	3	dbSNP_107	65	4678,3922	545.1+/-384.7	1275,2128,897	yes	missense	FYCO1	NM_024513.2	60	1418,2928,2157	GG,GC,CC		45.6047,24.6482,44.318	benign	321/1479	46009864	5764,7242	2203	4300	6503	SO:0001583	missense	79443	exon8			TCCAGGCCCTGCA	AJ292348	CCDS2734.1	3p21.3	2008-02-05			ENSG00000163820	ENSG00000163820		"""Zinc fingers, FYVE domain containing"""	14673	protein-coding gene	gene with protein product		607182				11896456	Standard	NM_024513		Approved	FLJ13335, ZFYVE7	uc003cpb.5	Q9BQS8	OTTHUMG00000133447	ENST00000296137.2:c.962G>C	3.37:g.46009864C>G	ENSP00000296137:p.Gly321Ala	Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	36	19	0.527778	NM_024513	B7ZKT7|Q3MJE6|Q86T41|Q86TB1|Q8TEF9|Q96IV5|Q9H8P9	Missense_Mutation	SNP	ENST00000296137.2	37	CCDS2734.1	1137	0.5206043956043956	111	0.22560975609756098	224	0.6187845303867403	366	0.6398601398601399	436	0.575197889182058	G	0.101	-1.151688	0.01700	0.246482	0.543953	ENSG00000163820	ENST00000296137;ENST00000535325	T;T	0.18338	2.22;2.22	5.66	3.84	0.44239	.	0.179817	0.48767	N	0.000179	T	0.00012	0.0000	N	0.00138	-2.015	0.58432	P	1.0000000000287557E-6	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.42327	-0.9458	9	0.02654	T	1	-9.0624	7.6507	0.28346	0.1322:0.2524:0.6154:0.0	rs3733100;rs17845108;rs17857899;rs59462026;rs3733100	321;321	B7ZKT7;Q9BQS8	.;FYCO1_HUMAN	A	321	ENSP00000296137:G321A;ENSP00000441178:G321A	ENSP00000296137:G321A	G	-	2	0	FYCO1	45984868	0.204000	0.23447	1.000000	0.80357	0.335000	0.28730	1.625000	0.37029	0.750000	0.32877	-0.815000	0.03128	GGC	C|0.537;G|0.463	0.463	strong		0.617	FYCO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257320.2	NM_024513	
ULK2	9706	hgsc.bcm.edu	37	17	19720109	19720109	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:19720109G>A	ENST00000395544.4	-	13	1548	c.1049C>T	c.(1048-1050)aCg>aTg	p.T350M	ULK2_ENST00000361658.2_Missense_Mutation_p.T350M|ULK2_ENST00000580130.1_Intron	NM_014683.3	NP_055498.3	Q8IYT8	ULK2_HUMAN	unc-51 like autophagy activating kinase 2	350					autophagic vacuole assembly (GO:0000045)|axon extension (GO:0048675)|negative regulation of collateral sprouting (GO:0048671)|protein autophosphorylation (GO:0046777)|regulation of autophagy (GO:0010506)|response to starvation (GO:0042594)|signal transduction (GO:0007165)	ATG1/UKL1 signaling complex (GO:0034273)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|pre-autophagosomal structure membrane (GO:0034045)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			large_intestine(1)|skin(4)|stomach(1)	6	all_cancers(12;4.97e-05)|all_epithelial(12;0.00362)|Breast(13;0.186)					AAAGTCATCCGTGTCACAAGA	0.408																																					p.T350M		Atlas-SNP	.											.	ULK2	142	.	0			c.C1049T						PASS	.						127.0	116.0	120.0					17																	19720109		2203	4300	6503	SO:0001583	missense	9706	exon13			TCATCCGTGTCAC	AB014523	CCDS11213.1	17p11.2	2014-02-12	2013-07-02		ENSG00000083290	ENSG00000083290	2.7.11.1		13480	protein-coding gene	gene with protein product		608650	"""unc-51 (C. elegans)-like kinase 2"", ""unc-51-like kinase 2 (C. elegans)"""			10557072	Standard	NM_014683		Approved	KIAA0623, Unc51.2, ATG1B	uc002gwn.3	Q8IYT8	OTTHUMG00000059511	ENST00000395544.4:c.1049C>T	17.37:g.19720109G>A	ENSP00000378914:p.Thr350Met	Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	113	17	0.150442	NM_001142610	A8MY69|O75119	Missense_Mutation	SNP	ENST00000395544.4	37	CCDS11213.1	.	.	.	.	.	.	.	.	.	.	G	22.8	4.333603	0.81801	.	.	ENSG00000083290	ENST00000361658;ENST00000395544	T;T	0.76709	-1.04;-1.04	5.47	4.5	0.54988	.	0.000000	0.85682	D	0.000000	D	0.86859	0.6034	M	0.73962	2.25	0.48762	D	0.999707	D	0.89917	1.0	D	0.83275	0.996	D	0.88117	0.2829	10	0.87932	D	0	-8.4158	13.0776	0.59095	0.0771:0.0:0.9229:0.0	.	350	Q8IYT8	ULK2_HUMAN	M	350	ENSP00000354877:T350M;ENSP00000378914:T350M	ENSP00000354877:T350M	T	-	2	0	ULK2	19660701	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.097000	0.76967	1.281000	0.44480	0.557000	0.71058	ACG	.	.	none		0.408	ULK2-001	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132375.2	NM_014683	
SELPLG	6404	hgsc.bcm.edu	37	12	109017680	109017680	+	Missense_Mutation	SNP	T	T	G	rs63748999|rs200527674|rs372173288	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:109017680T>G	ENST00000550948.1	-	2	628	c.404A>C	c.(403-405)cAa>cCa	p.Q135P	SELPLG_ENST00000228463.6_Missense_Mutation_p.Q151P|SELPLG_ENST00000388962.3_Intron			Q14242	SELPL_HUMAN	selectin P ligand	135	12 X 10 AA tandem repeats.		Missing (in short form; not an alternative splicing; dbSNP:rs63748999). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:7505206}.		blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cellular response to interleukin-6 (GO:0071354)|leukocyte adhesive activation (GO:0050902)|leukocyte migration (GO:0050900)|leukocyte tethering or rolling (GO:0050901)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)	p.Q135P(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(3)|prostate(3)|skin(1)	12						GGGCACTGGTTGAGTGGTCTG	0.617																																					p.Q151P		Atlas-SNP	.											SELPLG_ENST00000550948,NS,haematopoietic_neoplasm,0,1	SELPLG	138	1	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.A452C						PASS	.						165.0	129.0	141.0					12																	109017680		2201	4282	6483	SO:0001583	missense	6404	exon2			ACTGGTTGAGTGG		CCDS31895.1, CCDS31895.2, CCDS55881.1	12q24	2014-01-30						"""CD molecules"", ""Endogenous ligands"""	10722	protein-coding gene	gene with protein product		600738				7505206	Standard	NM_003006		Approved	PSGL-1, CD162	uc010sxe.2	Q14242		ENST00000550948.1:c.404A>C	12.37:g.109017680T>G	ENSP00000447752:p.Gln135Pro	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	101	22	0.217822	NM_001206609	A8K2Y0|B4DQC3|B7Z5C7|J3KMX6|Q12775|Q6GTW7|Q8N7J7	Missense_Mutation	SNP	ENST00000550948.1	37	CCDS31895.2	.	.	.	.	.	.	.	.	.	.	N	7.318	0.616396	0.14129	.	.	ENSG00000110876	ENST00000550948;ENST00000228463	T;T	0.28666	1.6;1.6	3.51	-7.02	0.01589	.	3.684700	0.01036	N	0.004222	T	0.23727	0.0574	L	0.54323	1.7	0.09310	N	1	P;P	0.47604	0.898;0.898	B;B	0.40165	0.321;0.321	T	0.41088	-0.9528	10	0.29301	T	0.29	1.368	4.4646	0.11682	0.2642:0.4833:0.0955:0.157	.	151;135	B7Z5C7;Q14242	.;SELPL_HUMAN	P	135;151	ENSP00000447752:Q135P;ENSP00000228463:Q151P	ENSP00000228463:Q151P	Q	-	2	0	SELPLG	107541809	0.000000	0.05858	0.000000	0.03702	0.013000	0.08279	-0.658000	0.05329	-1.703000	0.01409	-0.441000	0.05720	CAA	T|0.986;G|0.014	0.014	strong		0.617	SELPLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403904.1		
C8orf31	286122	hgsc.bcm.edu	37	8	144124609	144124609	+	Missense_Mutation	SNP	T	T	C	rs11136300	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	109	0	0		WXS	Illumina HiSeq	Phase_I	86	24	0.27907	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	
OR51L1	119682	hgsc.bcm.edu	37	11	5020799	5020799	+	Missense_Mutation	SNP	C	C	T	rs10768448	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:5020799C>T	ENST00000321543.1	+	1	587	c.587C>T	c.(586-588)aCc>aTc	p.T196I		NM_001004755.1	NP_001004755.1	Q8NGJ5	O51L1_HUMAN	olfactory receptor, family 51, subfamily L, member 1	196			T -> I (in dbSNP:rs10768448).			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)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(3)|lung(19)|skin(2)|stomach(1)	31		Medulloblastoma(188;0.0061)|all_neural(188;0.0479)|Breast(177;0.086)		Epithelial(150;1.75e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0285)|LUSC - Lung squamous cell carcinoma(625;0.19)		GATGCCAGGACCAACAGTATT	0.428													T|||	1223	0.244209	0.3502	0.1643	5008	,	,		25413	0.0694		0.3131	False		,,,				2504	0.2669				p.T196I		Atlas-SNP	.											.	OR51L1	60	.	0			c.C587T						PASS	.	T	ILE/THR	1520,2882	672.9+/-402.7	237,1046,918	225.0	192.0	203.0		587	4.0	0.0	11	dbSNP_120	203	2567,6029	690.3+/-404.4	383,1801,2114	yes	missense	OR51L1	NM_001004755.1	89	620,2847,3032	TT,TC,CC		29.8627,34.5298,31.4433	benign	196/316	5020799	4087,8911	2201	4298	6499	SO:0001583	missense	119682	exon1			CCAGGACCAACAG	AB065799	CCDS31369.1	11p15.4	2012-08-09			ENSG00000176798	ENSG00000176798		"""GPCR / Class A : Olfactory receptors"""	14759	protein-coding gene	gene with protein product							Standard	NM_001004755		Approved		uc010qyu.2	Q8NGJ5	OTTHUMG00000066605	ENST00000321543.1:c.587C>T	11.37:g.5020799C>T	ENSP00000322156:p.Thr196Ile	Somatic	399	1	0.00250627		WXS	Illumina HiSeq	Phase_I	374	373	0.997326	NM_001004755	Q6IFE5	Missense_Mutation	SNP	ENST00000321543.1	37	CCDS31369.1	519	0.23763736263736263	169	0.3434959349593496	68	0.1878453038674033	41	0.07167832167832168	241	0.3179419525065963	T	0.001	-3.309023	0.00018	0.345298	0.298627	ENSG00000176798	ENST00000321543	T	0.00030	8.9	5.18	4.02	0.46733	GPCR, rhodopsin-like superfamily (1);	0.550755	0.15346	N	0.267206	T	0.00012	0.0000	N	0.00074	-2.255	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.27706	-1.0066	9	0.02654	T	1	.	5.3792	0.16181	0.0:0.1584:0.1506:0.6911	rs10768448;rs52829062;rs57450622;rs10768448	196	Q8NGJ5	O51L1_HUMAN	I	196	ENSP00000322156:T196I	ENSP00000322156:T196I	T	+	2	0	OR51L1	4977375	0.000000	0.05858	0.002000	0.10522	0.015000	0.08874	0.673000	0.25203	0.411000	0.25702	-0.381000	0.06696	ACC	C|0.707;T|0.293	0.293	strong		0.428	OR51L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142812.1	NM_001004755	
STPG2	285555	hgsc.bcm.edu	37	4	98893437	98893437	+	Silent	SNP	A	A	G	rs783960	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:98893437A>G	ENST00000295268.3	-	7	1016	c.927T>C	c.(925-927)gaT>gaC	p.D309D		NM_174952.2	NP_777612.1	Q8N412	STPG2_HUMAN	sperm-tail PG-rich repeat containing 2	309								p.D309D(1)									TTACCTGATAATCAGCAGGTC	0.348													A|||	2048	0.408946	0.3707	0.5403	5008	,	,		15222	0.2431		0.4742	False		,,,				2504	0.4714				p.D309D		Atlas-SNP	.											C4orf37,NS,carcinoma,0,2	.	.	2	1	Substitution - coding silent(1)	prostate(1)	c.T927C						PASS	.	A		1578,2828	489.9+/-361.6	297,984,922	73.0	74.0	74.0		927	-1.8	0.8	4	dbSNP_86	74	3999,4601	551.5+/-385.9	936,2127,1237	no	coding-synonymous	C4orf37	NM_174952.2		1233,3111,2159	GG,GA,AA		46.5,35.8148,42.8802		309/460	98893437	5577,7429	2203	4300	6503	SO:0001819	synonymous_variant	285555	exon7			CTGATAATCAGCA	BC036870	CCDS3645.1	4q22.3-q23	2013-10-11	2012-07-30	2012-07-30	ENSG00000163116	ENSG00000163116			28712	protein-coding gene	gene with protein product			"""chromosome 4 open reading frame 37"""	C4orf37		23031811	Standard	NM_174952		Approved	MGC46496	uc003htt.2	Q8N412	OTTHUMG00000131009	ENST00000295268.3:c.927T>C	4.37:g.98893437A>G		Somatic	205	0	0		WXS	Illumina HiSeq	Phase_I	156	153	0.980769	NM_174952		Silent	SNP	ENST00000295268.3	37	CCDS3645.1																																																																																			A|0.578;G|0.422	0.422	strong		0.348	STPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253642.1	NM_174952	
LRRFIP1	9208	hgsc.bcm.edu	37	2	238672703	238672703	+	Missense_Mutation	SNP	C	C	G	rs3739038	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:238672703C>G	ENST00000392000.4	+	11	2464	c.2347C>G	c.(2347-2349)Cac>Gac	p.H783D	LRRFIP1_ENST00000308482.9_Intron|LRRFIP1_ENST00000244815.5_Missense_Mutation_p.H759D|LRRFIP1_ENST00000289175.6_Missense_Mutation_p.H727D	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	86	0	0		WXS	Illumina HiSeq	Phase_I	101	49	0.485149	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	
GABRA6	2559	hgsc.bcm.edu	37	5	161119125	161119125	+	Silent	SNP	C	C	G	rs13184586	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:161119125C>G	ENST00000274545.5	+	8	1438	c.1005C>G	c.(1003-1005)gcC>gcG	p.A335A	GABRA6_ENST00000523217.1_Silent_p.A325A|RP11-348M17.2_ENST00000521984.1_RNA			Q16445	GBRA6_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha 6	335					gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	benzodiazepine receptor activity (GO:0008503)|chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			breast(1)|central_nervous_system(2)|endometrium(6)|large_intestine(9)|liver(2)|lung(22)|ovary(7)|skin(6)|urinary_tract(2)	57	Renal(175;0.00259)	Medulloblastoma(196;0.0208)|all_neural(177;0.0672)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)		Acamprosate(DB00659)|Alprazolam(DB00404)|Amobarbital(DB01351)|Amoxapine(DB00543)|Aprobarbital(DB01352)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Chlordiazepoxide(DB00475)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Flumazenil(DB01205)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Secobarbital(DB00418)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Thiopental(DB00599)|Topiramate(DB00273)|Triazolam(DB00897)	CACAGAAGGCCAAAAGGAAGG	0.433										TCGA Ovarian(5;0.080)			C|||	2009	0.401158	0.3351	0.3732	5008	,	,		19042	0.3185		0.5736	False		,,,				2504	0.4182				p.A335A		Atlas-SNP	.											.	GABRA6	139	.	0			c.C1005G						PASS	.	C		1564,2842	491.3+/-362.1	273,1018,912	161.0	139.0	146.0		1005	-1.1	1.0	5	dbSNP_121	146	4784,3816	613.0+/-396.0	1320,2144,836	no	coding-synonymous	GABRA6	NM_000811.2		1593,3162,1748	GG,GC,CC		44.3721,35.497,48.8082		335/454	161119125	6348,6658	2203	4300	6503	SO:0001819	synonymous_variant	2559	exon8			GAAGGCCAAAAGG		CCDS4356.1	5q34	2012-06-22			ENSG00000145863	ENSG00000145863		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	4080	protein-coding gene	gene with protein product	"""GABA(A) receptor, alpha 6"""	137143				8020978	Standard	NM_000811		Approved		uc003lyu.2	Q16445	OTTHUMG00000130351	ENST00000274545.5:c.1005C>G	5.37:g.161119125C>G		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	129	127	0.984496	NM_000811	A8K096|Q4VAV2	Silent	SNP	ENST00000274545.5	37	CCDS4356.1																																																																																			C|0.535;G|0.465	0.465	strong		0.433	GABRA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252707.2		
MYH14	79784	hgsc.bcm.edu	37	19	50812315	50812315	+	Silent	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:50812315C>T	ENST00000596571.1	+	39	5718	c.5718C>T	c.(5716-5718)gcC>gcT	p.A1906A	CTB-191K22.5_ENST00000595563.1_RNA|MYH14_ENST00000440075.2_Silent_p.A1947A|MYH14_ENST00000262269.8_Silent_p.A1947A|MYH14_ENST00000425460.1_Silent_p.A1914A|MYH14_ENST00000376970.2_Silent_p.A1939A|MYH14_ENST00000601313.1_Silent_p.A1947A|MYH14_ENST00000598205.1_Silent_p.A1914A			Q7Z406	MYH14_HUMAN	myosin, heavy chain 14, non-muscle	1906					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)		TGGAGGAGGCCGAGGAGGAGG	0.612																																					p.A1947A		Atlas-SNP	.											.	MYH14	261	.	0			c.C5841T						PASS	.						32.0	38.0	36.0					19																	50812315		2059	4204	6263	SO:0001819	synonymous_variant	79784	exon42			GGAGGCCGAGGAG	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.5718C>T	19.37:g.50812315C>T		Somatic	187	0	0		WXS	Illumina HiSeq	Phase_I	196	98	0.5	NM_001145809	B0I1S2|C3TTN4|Q5CZ75|Q6XYE4|Q76B62|Q8WV23|Q96I22|Q9BT27|Q9BW35|Q9H882	Silent	SNP	ENST00000596571.1	37	CCDS59411.1																																																																																			.	.	none		0.612	MYH14-008	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464710.2	NM_024729	
XDH	7498	hgsc.bcm.edu	37	2	31588395	31588395	+	Silent	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:31588395C>T	ENST00000379416.3	-	23	2520	c.2472G>A	c.(2470-2472)gtG>gtA	p.V824V		NM_000379.3	NP_000370.2	P47989	XDH_HUMAN	xanthine dehydrogenase	824					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)	GCATGCATCGCACAGGGCGGC	0.567																																					p.V824V	Colon(66;682 1445 30109 40147)	Atlas-SNP	.											.	XDH	191	.	0			c.G2472A						PASS	.						115.0	100.0	105.0					2																	31588395		2203	4300	6503	SO:0001819	synonymous_variant	7498	exon23			GCATCGCACAGGG	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.2472G>A	2.37:g.31588395C>T		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	135	45	0.333333	NM_000379	Q16681|Q16712|Q4PJ16	Silent	SNP	ENST00000379416.3	37	CCDS1775.1																																																																																			.	.	none		0.567	XDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216840.1	NM_000379	
TRPA1	8989	hgsc.bcm.edu	37	8	72975801	72975801	+	Missense_Mutation	SNP	T	T	G	rs7819749	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:72975801T>G	ENST00000262209.4	-	5	765	c.558A>C	c.(556-558)aaA>aaC	p.K186N		NM_007332.2	NP_015628.2	O75762	TRPA1_HUMAN	transient receptor potential cation channel, subfamily A, member 1	186			K -> N (in dbSNP:rs7819749). {ECO:0000269|PubMed:10066796}.		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)	TAGCTCCTTTTTTAAGCTGGA	0.368													G|||	4145	0.827676	0.9705	0.7695	5008	,	,		17843	0.9752		0.6074	False		,,,				2504	0.7505				p.K186N		Atlas-SNP	.											TRPA1,NS,carcinoma,-2,1	TRPA1	256	1	0			c.A558C						PASS	.	G	ASN/LYS	4042,364	186.4+/-213.3	1848,346,9	82.0	78.0	79.0		558	-11.2	0.0	8	dbSNP_116	79	5176,3424	502.1+/-375.6	1565,2046,689	yes	missense	TRPA1	NM_007332.2	94	3413,2392,698	GG,GT,TT		39.814,8.2615,29.125	benign	186/1120	72975801	9218,3788	2203	4300	6503	SO:0001583	missense	8989	exon5			TCCTTTTTTAAGC	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.558A>C	8.37:g.72975801T>G	ENSP00000262209:p.Lys186Asn	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	56	51	0.910714	NM_007332	A6NIN6	Missense_Mutation	SNP	ENST00000262209.4	37	CCDS34908.1	1780	0.815018315018315	474	0.9634146341463414	270	0.7458563535911602	564	0.986013986013986	472	0.6226912928759895	G	13.30	2.195311	0.38806	0.917385	0.60186	ENSG00000104321	ENST00000523582;ENST00000262209	T;T	0.65178	-0.14;-0.14	5.62	-11.2	0.00127	Ankyrin repeat-containing domain (3);	0.613786	0.18960	N	0.126429	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	0.36359	-0.9751	9	0.21014	T	0.42	-3.1234	5.4121	0.16354	0.1633:0.0702:0.1695:0.5971	rs7819749;rs17740534;rs57998894;rs7819749	186	O75762	TRPA1_HUMAN	N	38;186	ENSP00000428151:K38N;ENSP00000262209:K186N	ENSP00000262209:K186N	K	-	3	2	TRPA1	73138355	0.150000	0.22732	0.019000	0.16419	0.830000	0.47004	-0.526000	0.06207	-2.413000	0.00569	-1.104000	0.02111	AAA	T|0.245;G|0.755	0.755	strong		0.368	TRPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379079.2	NM_007332	
ARL5B	221079	hgsc.bcm.edu	37	10	18964097	18964097	+	Splice_Site	SNP	G	G	A	rs12359433	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:18964097G>A	ENST00000377275.3	+	6	725	c.492G>A	c.(490-492)ggG>ggA	p.G164G		NM_178815.3	NP_848930.1	Q96KC2	ARL5B_HUMAN	ADP-ribosylation factor-like 5B	164					small GTPase mediated signal transduction (GO:0007264)	intracellular (GO:0005622)	GTP binding (GO:0005525)			lung(1)|ovary(1)	2						TTTTGTTTAGGTTATGCCAAG	0.333													G|||	139	0.0277556	0.0015	0.0476	5008	,	,		17001	0.0		0.0905	False		,,,				2504	0.0133				p.G164G		Atlas-SNP	.											.	ARL5B	12	.	0			c.G492A						PASS	.	G		60,4346	56.8+/-93.2	0,60,2143	133.0	129.0	130.0		492	3.1	1.0	10	dbSNP_120	130	670,7930	167.7+/-219.4	30,610,3660	yes	coding-synonymous-near-splice	ARL5B	NM_178815.3		30,670,5803	AA,AG,GG		7.7907,1.3618,5.6128		164/180	18964097	730,12276	2203	4300	6503	SO:0001630	splice_region_variant	221079	exon6			GTTTAGGTTATGC	AF494061	CCDS7131.1	10p13	2014-05-09	2005-11-03	2005-11-03	ENSG00000165997	ENSG00000165997		"""ADP-ribosylation factors-like"", ""ADP-ribosylation factors"""	23052	protein-coding gene	gene with protein product		608909	"""ADP-ribosylation factor-like 8"""	ARL8		12853149	Standard	XM_005252400		Approved		uc001iqd.1	Q96KC2	OTTHUMG00000017765	ENST00000377275.3:c.492-1G>A	10.37:g.18964097G>A		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	129	62	0.48062	NM_178815		Silent	SNP	ENST00000377275.3	37	CCDS7131.1																																																																																			G|0.945;A|0.055	0.055	strong		0.333	ARL5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047078.1	NM_178815	Silent
HLA-A	3105	hgsc.bcm.edu	37	6	29910719	29910719	+	Missense_Mutation	SNP	G	G	A	rs386698552|rs201574821|rs2230991	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:29910719G>A	ENST00000396634.1	+	4	600	c.259G>A	c.(259-261)Gag>Aag	p.E87K	HLA-A_ENST00000376802.2_Missense_Mutation_p.E87K|HLA-A_ENST00000376809.5_Missense_Mutation_p.E87K|HLA-A_ENST00000376806.5_Missense_Mutation_p.E87K			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	87	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						TTGGGACCAGGAGACACGGAA	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)			g|||	895	0.178714	0.2746	0.1268	5008	,	,		11579	0.131		0.1004	False		,,,				2504	0.2157				p.E87K		Atlas-SNP	.											.	HLA-A	89	.	0			c.G259A						PASS	.						74.0	79.0	77.0					6																	29910719		2202	4294	6496	SO:0001583	missense	3105	exon2	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	GACCAGGAGACAC	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.259G>A	6.37:g.29910719G>A	ENSP00000379873:p.Glu87Lys	Somatic	264	0	0		WXS	Illumina HiSeq	Phase_I	188	69	0.367021	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Missense_Mutation	SNP	ENST00000396634.1	37	CCDS34373.1	.	.	.	.	.	.	.	.	.	.	.	9.501	1.103302	0.20632	.	.	ENSG00000206503	ENST00000396634;ENST00000376806;ENST00000376809;ENST00000355767;ENST00000376802	T;T;T;T	0.00882	5.58;5.58;5.58;5.58	3.57	-7.15	0.01521	MHC class I, alpha chain, alpha1/alpha2 (6);MHC classes I/II-like antigen recognition protein (3);MHC class I-like antigen recognition (3);	0.306974	0.16761	U	0.200603	T	0.02119	0.0066	M	0.90922	3.16	0.80722	P	0.0	B;D;B;D;B	0.67145	0.084;0.996;0.054;0.996;0.054	B;D;B;D;B	0.85130	0.123;0.997;0.213;0.997;0.123	T	0.00000	-1.3060	9	0.87932	D	0	.	11.2996	0.49298	0.2395:0.635:0.1255:0.0	rs2230991;rs3167671;rs9260132;rs16896278;rs41539920	87;87;87;87;87	P13746;Q5SRN7;P16188;Q5SRN5;P04439	1A11_HUMAN;.;1A30_HUMAN;.;1A03_HUMAN	K	87	ENSP00000379873:E87K;ENSP00000366002:E87K;ENSP00000366005:E87K;ENSP00000365998:E87K	ENSP00000348012:E87K	E	+	1	0	HLA-A	30018698	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-5.288000	0.00134	-2.576000	0.00465	-0.350000	0.07774	GAG	A|0.110;C|0.022;G|0.868	0.110	strong		0.672	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
LTB	4050	hgsc.bcm.edu	37	6	31549364	31549364	+	Silent	SNP	G	G	A	rs4647186		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:31549364G>A	ENST00000429299.2	-	3	259	c.252C>T	c.(250-252)agC>agT	p.S84S	LTB_ENST00000446745.2_Missense_Mutation_p.A69V|LTB_ENST00000483972.1_5'UTR	NM_002341.1	NP_002332.1	Q06643	TNFC_HUMAN	lymphotoxin beta (TNF superfamily, member 3)	84			S -> R (in dbSNP:rs4647186). {ECO:0000269|Ref.7}.		cell-cell signaling (GO:0007267)|gene expression (GO:0010467)|immune response (GO:0006955)|lymph node development (GO:0048535)|positive regulation of interleukin-12 biosynthetic process (GO:0045084)|signal transduction (GO:0007165)|skin development (GO:0043588)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	receptor binding (GO:0005102)	p.S84S(1)		haematopoietic_and_lymphoid_tissue(3)|large_intestine(2)|lung(2)|prostate(1)|upper_aerodigestive_tract(1)	9						GGAGCCCGGGGCTGAGATCTG	0.572													G|||	1	0.000199681	0.0	0.0	5008	,	,		16763	0.0		0.001	False		,,,				2504	0.0				p.A69V		Atlas-SNP	.											LTB,NS,lymphoid_neoplasm,0,1	LTB	19	1	1	Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(1)	c.C206T						PASS	.						92.0	108.0	103.0					6																	31549364		1510	2709	4219	SO:0001819	synonymous_variant	4050	exon2			CCCGGGGCTGAGA	L11015	CCDS4703.1, CCDS4704.1	6p21.3	2013-05-22			ENSG00000227507	ENSG00000227507		"""Tumor necrosis factor (ligand) superfamily"""	6711	protein-coding gene	gene with protein product		600978		TNFC		7916655, 1714477	Standard	NM_002341		Approved	p33, TNFSF3	uc003nuk.3	Q06643	OTTHUMG00000031136	ENST00000429299.2:c.252C>T	6.37:g.31549364G>A		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	92	31	0.336957	NM_009588	P78370|Q52LU8|Q99761	Missense_Mutation	SNP	ENST00000429299.2	37	CCDS4703.1	.	.	.	.	.	.	.	.	.	.	G	15.63	2.889480	0.52014	.	.	ENSG00000227507	ENST00000446745	.	.	.	5.26	-2.05	0.07321	.	.	.	.	.	T	0.10078	0.0247	.	.	.	0.09310	N	1	B	0.10296	0.003	B	0.09377	0.004	T	0.34650	-0.9820	7	0.38643	T	0.18	-10.8294	6.3303	0.21266	0.4617:0.1263:0.412:0.0	.	69	Q52LU8	.	V	69	.	ENSP00000416113:A69V	A	-	2	0	LTB	31657343	0.000000	0.05858	0.002000	0.10522	0.609000	0.37215	0.051000	0.14141	-0.159000	0.11021	-0.783000	0.03347	GCC	G|0.994;C|0.006	.	alt		0.572	LTB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076239.3		
PLEKHG1	57480	hgsc.bcm.edu	37	6	151121915	151121915	+	Silent	SNP	G	G	A	rs2073061	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	118	0	0		WXS	Illumina HiSeq	Phase_I	92	59	0.641304	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		
ZNF404	342908	hgsc.bcm.edu	37	19	44376937	44376937	+	Missense_Mutation	SNP	G	G	A	rs76311065	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:44376937G>A	ENST00000587539.1	-	3	1428	c.1429C>T	c.(1429-1431)Cgt>Tgt	p.R477C	ZNF404_ENST00000324394.6_Missense_Mutation_p.R475C	NM_001033719.2	NP_001028891.2	Q494X3	ZN404_HUMAN	zinc finger protein 404	477					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)				GAGATAGAACGAAAGGCCTTC	0.343													G|||	112	0.0223642	0.0045	0.0259	5008	,	,		20926	0.001		0.0805	False		,,,				2504	0.0061				p.R474C		Atlas-SNP	.											.	ZNF404	46	.	0			c.C1420T						PASS	.	G	CYS/ARG	41,4251		1,39,2106	43.0	45.0	44.0		1429	-4.0	0.0	19	dbSNP_131	44	556,7934		11,534,3700	yes	missense	ZNF404	NM_001033719.2	180	12,573,5806	AA,AG,GG		6.5489,0.9553,4.6706	probably-damaging	477/553	44376937	597,12185	2146	4245	6391	SO:0001583	missense	342908	exon2			TAGAACGAAAGGC	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.1429C>T	19.37:g.44376937G>A	ENSP00000466051:p.Arg477Cys	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	58	36	0.62069	NM_001033719	A4FU30|K7ELF2	Missense_Mutation	SNP	ENST00000587539.1	37	CCDS59394.1	73	0.033424908424908424	2	0.0040650406504065045	9	0.024861878453038673	1	0.0017482517482517483	61	0.08047493403693931	G	4.133	0.023005	0.08006	0.009553	0.065489	ENSG00000176222	ENST00000324394	T	0.07444	3.19	2.33	-3.98	0.04082	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00666	0.0022	L	0.43554	1.36	0.09310	N	0.999998	D	0.76494	0.999	D	0.63793	0.918	T	0.08659	-1.0711	9	0.56958	D	0.05	.	5.3718	0.16144	0.1228:0.0:0.3766:0.5006	.	477	Q494X3	ZN404_HUMAN	C	475	ENSP00000319479:R475C	ENSP00000319479:R475C	R	-	1	0	ZNF404	49068777	0.000000	0.05858	0.004000	0.12327	0.101000	0.19017	-2.781000	0.00773	-0.530000	0.06349	-0.310000	0.09108	CGT	G|0.962;A|0.038	0.038	strong		0.343	ZNF404-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460019.1	NM_001033719	
DDX26B	203522	hgsc.bcm.edu	37	X	134713855	134713855	+	Silent	SNP	G	G	A	rs2298301	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:134713855G>A	ENST00000370752.4	+	15	2485	c.2151G>A	c.(2149-2151)ctG>ctA	p.L717L	DDX26B_ENST00000481908.1_3'UTR	NM_182540.4	NP_872346.3	Q5JSJ4	DX26B_HUMAN	DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 26B	717										large_intestine(1)|lung(8)	9	Acute lymphoblastic leukemia(192;6.56e-05)					TGGATTCTCTGTCTGACGACT	0.453													G|||	423	0.112053	0.0582	0.0908	3775	,	,		15304	0.0903		0.1362	False		,,,				2504	0.0562				p.L717L		Atlas-SNP	.											.	DDX26B	130	.	0			c.G2151A						PASS	.	G		304,3531		6,236,56,1390,515	80.0	72.0	75.0		2151	-6.8	0.0	X	dbSNP_100	75	1049,5679		59,632,299,1737,1573	no	coding-synonymous	DDX26B	NM_182540.4		65,868,355,3127,2088	AA,AG,A,GG,G		15.5916,7.927,12.8089		717/862	134713855	1353,9210	2203	4300	6503	SO:0001819	synonymous_variant	203522	exon15			TTCTCTGTCTGAC	AK096544	CCDS35401.1	Xq26	2008-02-05			ENSG00000165359	ENSG00000165359		"""DEAD-boxes"""	27334	protein-coding gene	gene with protein product							Standard	NM_182540		Approved	FLJ41215	uc004eyw.4	Q5JSJ4	OTTHUMG00000022484	ENST00000370752.4:c.2151G>A	X.37:g.134713855G>A		Somatic	520	1	0.00192308		WXS	Illumina HiSeq	Phase_I	318	316	0.993711	NM_182540	Q5CZA2|Q6IPS3|Q6ZTU5|Q6ZWE4	Silent	SNP	ENST00000370752.4	37	CCDS35401.1																																																																																			G|0.877;A|0.123	0.123	strong		0.453	DDX26B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058420.1	NM_182540	
SNAPC4	6621	hgsc.bcm.edu	37	9	139276430	139276430	+	Silent	SNP	G	G	A	rs34850728	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:139276430G>A	ENST00000298532.2	-	17	2531	c.2163C>T	c.(2161-2163)caC>caT	p.H721H		NM_003086.2	NP_003077.2			small nuclear RNA activating complex, polypeptide 4, 190kDa											biliary_tract(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(13)|ovary(1)|prostate(3)|skin(2)|urinary_tract(1)	33		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;5.31e-06)|Epithelial(140;7.13e-06)		GGGTGGCTCTGTGCCGTAGCC	0.667													G|||	527	0.105232	0.0068	0.1081	5008	,	,		16781	0.002		0.1799	False		,,,				2504	0.2658				p.H721H		Atlas-SNP	.											.	SNAPC4	82	.	0			c.C2163T						PASS	.	G		175,4219		3,169,2025	20.0	21.0	20.0		2163	-1.1	0.0	9	dbSNP_126	20	1685,6903		166,1353,2775	no	coding-synonymous	SNAPC4	NM_003086.2		169,1522,4800	AA,AG,GG		19.6204,3.9827,14.3275		721/1470	139276430	1860,11122	2197	4294	6491	SO:0001819	synonymous_variant	6621	exon17			GGCTCTGTGCCGT	AF032387	CCDS6998.1	9q34.3	2008-07-21	2002-08-29		ENSG00000165684	ENSG00000165684			11137	protein-coding gene	gene with protein product		602777	"""small nuclear RNA activating complex, polypeptide 4, 190kD"""			9418884	Standard	XM_005266096		Approved	SNAP190, PTFalpha, FLJ13451	uc004chh.3	Q5SXM2	OTTHUMG00000020929	ENST00000298532.2:c.2163C>T	9.37:g.139276430G>A		Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	122	52	0.42623	NM_003086		Silent	SNP	ENST00000298532.2	37	CCDS6998.1																																																																																			G|0.876;A|0.124	0.124	strong		0.667	SNAPC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055071.1	NM_003086	
BARD1	580	hgsc.bcm.edu	37	2	215632255	215632255	+	Missense_Mutation	SNP	C	C	T	rs2070094|rs386654966	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:215632255C>T	ENST00000260947.4	-	6	1653	c.1519G>A	c.(1519-1521)Gtg>Atg	p.V507M	BARD1_ENST00000449967.2_Missense_Mutation_p.V363M	NM_000465.2|NM_001282543.1|NM_001282545.1|NM_001282548.1	NP_000456.2|NP_001269472.1|NP_001269474.1|NP_001269477.1	Q99728	BARD1_HUMAN	BRCA1 associated RING domain 1	507			V -> M (in dbSNP:rs2070094). {ECO:0000269|PubMed:9425226}.		cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|negative regulation of apoptotic process (GO:0043066)|negative regulation of mRNA 3'-end processing (GO:0031441)|negative regulation of protein export from nucleus (GO:0046826)|positive regulation of apoptotic process (GO:0043065)|positive regulation of protein catabolic process (GO:0045732)|protein K6-linked ubiquitination (GO:0085020)|protein ubiquitination (GO:0016567)|regulation of phosphorylation (GO:0042325)|tissue homeostasis (GO:0001894)	BRCA1-A complex (GO:0070531)|BRCA1-BARD1 complex (GO:0031436)|cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	kinase binding (GO:0019900)|ligase activity (GO:0016874)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|RNA binding (GO:0003723)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(2)|breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(1)|lung(14)|prostate(4)|upper_aerodigestive_tract(1)	35		Renal(323;0.0243)		Epithelial(149;3.2e-06)|all cancers(144;0.000461)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.011)		ACTATATCCACATGCCCATTC	0.408									Neuroblastoma, Familial Clustering of;Congenital Central Hypoventilation Syndrome				C|||	1834	0.366214	0.3608	0.3069	5008	,	,		18664	0.3433		0.3976	False		,,,				2504	0.407				p.V507M		Atlas-SNP	.											.	BARD1	138	.	0			c.G1519A	GRCh37	CM034384	BARD1	M	rs2070094	PASS	.	C	MET/VAL	1278,3128		281,716,1206	127.0	116.0	119.0		1519	-11.3	0.0	2	dbSNP_96	119	2372,6228		550,1272,2478	yes	missense	BARD1	NM_000465.2	21	831,1988,3684	TT,TC,CC		27.5814,29.0059,28.064	benign	507/778	215632255	3650,9356	2203	4300	6503	SO:0001583	missense	580	exon6	Familial Cancer Database	Familial Neuroblastoma;CCHS, Ondine Curse, incl. Ondine-Hirschsprung Disease	TATCCACATGCCC		CCDS2397.1, CCDS74645.1, CCDS74646.1, CCDS74647.1, CCDS74648.1	2q34-q35	2013-01-10			ENSG00000138376	ENSG00000138376		"""Ankyrin repeat domain containing"""	952	protein-coding gene	gene with protein product		601593				8944023, 9425226, 15159397	Standard	NM_001282548		Approved		uc002veu.2	Q99728	OTTHUMG00000133016	ENST00000260947.4:c.1519G>A	2.37:g.215632255C>T	ENSP00000260947:p.Val507Met	Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	198	91	0.459596	NM_000465	F6MDH7|F6MDH8|F6MDH9|O43574|Q53SS5	Missense_Mutation	SNP	ENST00000260947.4	37	CCDS2397.1	622	0.2847985347985348	113	0.22967479674796748	110	0.30386740331491713	169	0.29545454545454547	230	0.3034300791556728	C	9.530	1.110597	0.20714	0.290059	0.275814	ENSG00000138376	ENST00000260947;ENST00000449967	T;T	0.65732	-0.17;-0.17	5.64	-11.3	0.00108	Ankyrin repeat-containing domain (3);	1.450850	0.03685	N	0.246137	T	0.00012	0.0000	L	0.60957	1.885	0.80722	P	0.0	B;B	0.21606	0.001;0.058	B;B	0.17722	0.005;0.019	T	0.04178	-1.0971	9	0.39692	T	0.17	0.2604	2.0607	0.03592	0.1372:0.2469:0.238:0.3779	rs2070094;rs4151064;rs17838599;rs59469134;rs2070094	363;507	E7EUI3;Q99728	.;BARD1_HUMAN	M	507;363	ENSP00000260947:V507M;ENSP00000406752:V363M	ENSP00000260947:V507M	V	-	1	0	BARD1	215340500	0.000000	0.05858	0.001000	0.08648	0.907000	0.53573	-5.264000	0.00136	-3.328000	0.00186	-1.452000	0.01034	GTG	C|0.656;T|0.344	0.344	strong		0.408	BARD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256602.1	NM_000465	
KRT84	3890	hgsc.bcm.edu	37	12	52777502	52777502	+	Silent	SNP	A	A	G	rs1945297	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	172	0	0		WXS	Illumina HiSeq	Phase_I	145	70	0.482759	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	
RGS3	5998	hgsc.bcm.edu	37	9	116279880	116279880	+	Silent	SNP	T	T	C	rs35270441	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:116279880T>C	ENST00000374140.2	+	17	1943	c.1734T>C	c.(1732-1734)taT>taC	p.Y578Y	RGS3_ENST00000350696.5_Silent_p.Y578Y|RGS3_ENST00000394646.3_Silent_p.Y297Y|RGS3_ENST00000343817.5_Silent_p.Y297Y|RGS3_ENST00000317613.6_Silent_p.Y466Y|RGS3_ENST00000374136.1_Silent_p.Y204Y	NM_001282923.1|NM_144488.4	NP_001269852.1|NP_652759.3	P49796	RGS3_HUMAN	regulator of G-protein signaling 3	578					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						TGCTGCTGTATGAAGGGAGGA	0.537													C|||	417	0.0832668	0.1785	0.0663	5008	,	,		15392	0.0		0.0964	False		,,,				2504	0.0389				p.Y578Y		Atlas-SNP	.											.	RGS3	251	.	0			c.T1734C						PASS	.	C	,,	803,3603	750.3+/-412.1	87,629,1487	99.0	100.0	99.0		1398,891,1734	-4.2	0.8	9	dbSNP_126	99	861,7739	780.3+/-407.7	39,783,3478	no	coding-synonymous,coding-synonymous,coding-synonymous	RGS3	NM_017790.3,NM_130795.2,NM_144488.4	,,	126,1412,4965	CC,CT,TT		10.0116,18.2251,12.7941	,,	466/603,297/918,578/1199	116279880	1664,11342	2203	4300	6503	SO:0001819	synonymous_variant	5998	exon17			GCTGTATGAAGGG	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.1734T>C	9.37:g.116279880T>C		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	69	33	0.478261	NM_144488	A6NHA0|A8K0V1|B3KUB2|Q5VXB8|Q5VXC1|Q5VZ05|Q5VZ06|Q6ZRM5|Q8IUQ1|Q8NC47|Q8NFN4|Q8NFN5|Q8NFN6|Q8TD59|Q8TD68|Q8WV02|Q8WXA0	Silent	SNP	ENST00000374140.2	37	CCDS43869.1	184	0.08424908424908426	81	0.16463414634146342	27	0.07458563535911603	0	0.0	76	0.10026385224274406	C	8.330	0.826272	0.16749	0.182251	0.100116	ENSG00000138835	ENST00000496113	.	.	.	4.88	-4.22	0.03800	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	0.9999999999665589	.	.	.	.	.	.	.	.	.	.	.	.	.	.	8.128	0.31010	0.1119:0.2787:0.0:0.6094	rs35270441;rs61749205	.	.	.	R	33	.	.	X	+	1	0	RGS3	115319701	0.008000	0.16893	0.781000	0.31783	0.895000	0.52256	-1.812000	0.01726	-1.163000	0.02793	-1.476000	0.00998	TGA	T|0.889;C|0.111	0.111	strong		0.537	RGS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055561.3	NM_017790	
HAP1	9001	hgsc.bcm.edu	37	17	39888636	39888636	+	Missense_Mutation	SNP	G	G	T	rs142535684	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:39888636G>T	ENST00000310778.5	-	3	569	c.560C>A	c.(559-561)cCt>cAt	p.P187H	HAP1_ENST00000347901.4_Missense_Mutation_p.P187H|HAP1_ENST00000393939.2_Missense_Mutation_p.P187H|RN7SL399P_ENST00000471648.2_RNA|HAP1_ENST00000341193.5_Missense_Mutation_p.P195H|JUP_ENST00000540235.1_Intron			P54257	HAP1_HUMAN	huntingtin-associated protein 1	187	HAP1 N-terminal.			Missing (in Ref. 6; CAB82785). {ECO:0000305}.	anterograde axon cargo transport (GO:0008089)|autophagy (GO:0006914)|brain development (GO:0007420)|cell projection organization (GO:0030030)|exocytosis (GO:0006887)|negative regulation of beta-amyloid formation (GO:1902430)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of epidermal growth factor receptor signaling pathway (GO:0045742)|positive regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0031587)|positive regulation of neurotrophin production (GO:0032901)|positive regulation of nonmotile primary cilium assembly (GO:1902857)|positive regulation of synaptic transmission, GABAergic (GO:0032230)|protein localization (GO:0008104)|protein transport (GO:0015031)|regulation of exocytosis (GO:0017157)|regulation of organelle transport along microtubule (GO:1902513)|retrograde axon cargo transport (GO:0008090)|synaptic transmission (GO:0007268)|vesicle transport along microtubule (GO:0047496)	actin cytoskeleton (GO:0015629)|cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|inclusion body (GO:0016234)|lysosome (GO:0005764)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|synapse (GO:0045202)	brain-derived neurotrophic factor binding (GO:0048403)|ion channel binding (GO:0044325)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(4)|lung(5)|ovary(4)|skin(1)	21		Breast(137;0.000162)	BRCA - Breast invasive adenocarcinoma(4;0.0677)			CTCCCAGACAGGTGGGAGAAG	0.582													G|||	6	0.00119808	0.0	0.0029	5008	,	,		19039	0.0		0.004	False		,,,				2504	0.0				p.P195H		Atlas-SNP	.											.	HAP1	48	.	0			c.C584A						PASS	.	G	HIS/PRO,HIS/PRO,HIS/PRO	4,4402	4.2+/-10.8	0,4,2199	33.0	33.0	33.0		584,560,560	0.2	0.4	17	dbSNP_134	33	10,8590	7.1+/-27.0	0,10,4290	yes	missense,missense,missense	HAP1	NM_001079870.1,NM_001079871.1,NM_177977.2	77,77,77	0,14,6489	TT,TG,GG		0.1163,0.0908,0.1076	probably-damaging,probably-damaging,probably-damaging	195/603,187/595,187/620	39888636	14,12992	2203	4300	6503	SO:0001583	missense	9001	exon3			CAGACAGGTGGGA	AF040723	CCDS11406.1, CCDS42338.1, CCDS42339.1	17q21.2-q21.3	2008-04-23	2008-04-23		ENSG00000173805	ENSG00000173805			4812	protein-coding gene	gene with protein product	"""neuroan 1"""	600947		HAP2		7477378, 9668110	Standard	NM_177977		Approved	HLP, hHLP1, HIP5	uc002hxn.1	P54257	OTTHUMG00000133498	ENST00000310778.5:c.560C>A	17.37:g.39888636G>T	ENSP00000309392:p.Pro187His	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	93	43	0.462366	NM_001079870	A8MQB5|O75358|Q59GK4|Q9H4G3|Q9HA98|Q9NY90	Missense_Mutation	SNP	ENST00000310778.5	37		6	0.0027472527472527475	0	0.0	2	0.0055248618784530384	0	0.0	4	0.005277044854881266	G	12.60	1.985337	0.35036	9.08E-4	0.001163	ENSG00000173805	ENST00000393939;ENST00000310778;ENST00000347901;ENST00000341193	T;T;T;T	0.67171	3.0;3.19;3.14;-0.25	3.42	0.204	0.15199	.	.	.	.	.	T	0.49779	0.1577	N	0.22421	0.69	0.09310	N	1	D;D;D;D	0.61697	0.99;0.99;0.971;0.977	P;P;P;P	0.54590	0.642;0.642;0.642;0.756	T	0.45775	-0.9238	9	0.87932	D	0	0.0581	3.2202	0.06712	0.2633:0.2282:0.5085:0.0	.	187;195;187;187	P54257-3;P54257-4;P54257-2;P54257	.;.;.;HAP1_HUMAN	H	187;187;187;195	ENSP00000377513:P187H;ENSP00000309392:P187H;ENSP00000334002:P187H;ENSP00000343170:P195H	ENSP00000309392:P187H	P	-	2	0	HAP1	37142162	0.031000	0.19500	0.391000	0.26233	0.448000	0.32197	0.694000	0.25512	0.254000	0.21573	0.462000	0.41574	CCT	G|0.998;T|0.002	0.002	strong		0.582	HAP1-006	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000389619.1	NM_003949	
MPP6	51678	hgsc.bcm.edu	37	7	24703298	24703298	+	Silent	SNP	G	G	A	rs1053962	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:24703298G>A	ENST00000222644.5	+	6	991	c.741G>A	c.(739-741)gaG>gaA	p.E247E	MPP6_ENST00000396475.2_Silent_p.E247E|MPP6_ENST00000409761.1_Silent_p.E135E			Q99547	MPH6_HUMAN	membrane protein, palmitoylated 6 (MAGUK p55 subfamily member 6)	0					maturation of 5.8S rRNA (GO:0000460)	cytoplasm (GO:0005737)|exosome (RNase complex) (GO:0000178)|nucleolus (GO:0005730)|nucleus (GO:0005634)	RNA binding (GO:0003723)			breast(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(7)|pancreas(1)|skin(2)	20						CCAAAGGAGAGATTCTTCAGA	0.338													A|||	3233	0.645567	0.9153	0.4409	5008	,	,		18088	0.7996		0.3499	False		,,,				2504	0.5716				p.E247E		Atlas-SNP	.											.	MPP6	62	.	0			c.G741A						PASS	.	A		3577,829	327.5+/-300.1	1452,673,78	99.0	110.0	106.0		741	4.9	1.0	7	dbSNP_86	106	2851,5749	672.5+/-402.9	465,1921,1914	no	coding-synonymous	MPP6	NM_016447.2		1917,2594,1992	AA,AG,GG		33.1512,18.8153,49.4233		247/541	24703298	6428,6578	2203	4300	6503	SO:0001819	synonymous_variant	51678	exon7			AGGAGAGATTCTT	AF162130	CCDS5388.1	7p15	2007-08-01			ENSG00000105926	ENSG00000105926			18167	protein-coding gene	gene with protein product		606959				10753959, 11311936	Standard	NM_016447		Approved	PALS2, VAM-1, p55T	uc003swx.3	Q9NZW5	OTTHUMG00000023507	ENST00000222644.5:c.741G>A	7.37:g.24703298G>A		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	76	18	0.236842	NM_016447	B2RAF0	Silent	SNP	ENST00000222644.5	37	CCDS5388.1																																																																																			A|0.556;C|0.001	0.556	strong		0.338	MPP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250272.4		
COL15A1	1306	hgsc.bcm.edu	37	9	101822220	101822220	+	Silent	SNP	C	C	T	rs4480177	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:101822220C>T	ENST00000375001.3	+	36	3810	c.3387C>T	c.(3385-3387)ccC>ccT	p.P1129P		NM_001855.3	NP_001846.3	P39059	COFA1_HUMAN	collagen, type XV, alpha 1	1129	Triple-helical region 9 (COL9).				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)				CAGGGCTTCCCGGATCCAGAA	0.463													C|||	1930	0.385383	0.4024	0.3473	5008	,	,		15742	0.5268		0.2038	False		,,,				2504	0.4305				p.P1129P		Atlas-SNP	.											.	COL15A1	211	.	0			c.C3387T						PASS	.	C		1684,2722	512.4+/-368.1	327,1030,846	138.0	135.0	136.0		3387	-11.1	0.1	9	dbSNP_111	136	1741,6859	317.0+/-313.0	183,1375,2742	no	coding-synonymous	COL15A1	NM_001855.3		510,2405,3588	TT,TC,CC		20.2442,38.2206,26.334		1129/1389	101822220	3425,9581	2203	4300	6503	SO:0001819	synonymous_variant	1306	exon36			GCTTCCCGGATCC	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.3387C>T	9.37:g.101822220C>T		Somatic	211	0	0		WXS	Illumina HiSeq	Phase_I	176	88	0.5	NM_001855	Q5T6J4|Q9UDC5|Q9Y4W4	Silent	SNP	ENST00000375001.3	37	CCDS35081.1																																																																																			C|0.706;T|0.294	0.294	strong		0.463	COL15A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053386.3	NM_001855	
MYO1H	283446	hgsc.bcm.edu	37	12	109848567	109848567	+	Silent	SNP	T	T	C	rs7315991	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	57	0	0		WXS	Illumina HiSeq	Phase_I	57	29	0.508772	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	
KRTAP4-7	100132476	hgsc.bcm.edu	37	17	39240511	39240511	+	Missense_Mutation	SNP	A	A	T	rs383835	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:39240511A>T	ENST00000391417.4	+	1	53	c.53A>T	c.(52-54)gAc>gTc	p.D18V		NM_033061.3	NP_149050.3	Q9BYR0	KRA47_HUMAN	keratin associated protein 4-7	18	31 X 5 AA repeats of C-C-[GIKRQVHEML]- [SPTRV]-[STVQRCP].		D -> V. {ECO:0000269|PubMed:11279113, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:15955084}.		aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)				NS(1)|endometrium(3)|kidney(1)|lung(1)|prostate(2)|urinary_tract(1)	9						TGCAGCCAAGACCTCTGTCAG	0.612													a|||	2763	0.551717	0.6445	0.6081	5008	,	,		14149	0.3879		0.6024	False		,,,				2504	0.5031				p.D18V		Atlas-SNP	.											.	KRTAP4-7	49	.	0			c.A53T						PASS	.						9.0	17.0	15.0					17																	39240511		677	1582	2259	SO:0001583	missense	100132476	exon1			GCCAAGACCTCTG	AJ406939	CCDS45673.1	17q21.2	2013-06-25			ENSG00000240871	ENSG00000240871		"""Keratin associated proteins"""	18898	protein-coding gene	gene with protein product						11279113	Standard	NM_033061		Approved	KAP4.7	uc010wfn.2	Q9BYR0	OTTHUMG00000133582	ENST00000391417.4:c.53A>T	17.37:g.39240511A>T	ENSP00000375236:p.Asp18Val	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	49	17	0.346939	NM_033061	A0AVM6|A8MQ08|A8MTL4	Missense_Mutation	SNP	ENST00000391417.4	37	CCDS45673.1	1033	0.47298534798534797	274	0.556910569105691	200	0.5524861878453039	184	0.32167832167832167	375	0.4947229551451187	.	0.459	-0.889937	0.02511	.	.	ENSG00000240871;ENSG00000212722	ENST00000391417;ENST00000377734	T	0.00608	6.25	1.02	-1.55	0.08558	.	0.471385	0.15244	U	0.272684	T	0.00012	0.0000	.	.	.	0.53688	P	2.2999999999995246E-5	B	0.20261	0.043	B	0.12156	0.007	T	0.14924	-1.0455	8	0.45353	T	0.12	.	2.8192	0.05467	0.404:0.251:0.345:0.0	rs62068121	18	Q9BYR0	KRA47_HUMAN	V	18	ENSP00000375236:D18V	ENSP00000375236:D18V	D	+	2	0	KRTAP4-9;KRTAP4-7	36494037	0.086000	0.21541	0.114000	0.21550	0.074000	0.17049	0.065000	0.14466	-0.591000	0.05859	0.260000	0.18958	GAC	A|0.527;T|0.473	0.473	strong		0.612	KRTAP4-7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257686.1		
SUN1	23353	hgsc.bcm.edu	37	7	897492	897492	+	Silent	SNP	A	A	G	rs10950789	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:897492A>G	ENST00000405266.1	+	14	1557	c.1533A>G	c.(1531-1533)acA>acG	p.T511T	SUN1_ENST00000389574.3_Silent_p.T391T|SUN1_ENST00000413514.2_Silent_p.T272T|SUN1_ENST00000456758.2_Silent_p.T663T|SUN1_ENST00000452783.2_Silent_p.T371T|SUN1_ENST00000401592.1_Silent_p.T474T|SUN1_ENST00000425407.2_Silent_p.T391T			O94901	SUN1_HUMAN	Sad1 and UNC84 domain containing 1	501					cytoskeletal anchoring at nuclear membrane (GO:0090286)|nuclear envelope organization (GO:0006998)|nuclear matrix anchoring at nuclear membrane (GO:0090292)	acrosomal membrane (GO:0002080)|integral component of nuclear inner membrane (GO:0005639)|nuclear envelope (GO:0005635)|SUN-KASH complex (GO:0034993)				NS(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(17)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						TCCTGCCCACAGTCGAGCACC	0.567													G|||	2188	0.436901	0.5144	0.4669	5008	,	,		15932	0.4821		0.3479	False		,,,				2504	0.3558				p.T474T		Atlas-SNP	.											.	SUN1	157	.	0			c.A1422G						PASS	.	G	,,	2013,2181		509,995,593	168.0	182.0	178.0		1422,1113,1173	-6.4	0.0	7	dbSNP_120	178	2755,5677		454,1847,1915	no	coding-synonymous,coding-synonymous,coding-synonymous	SUN1	NM_001130965.2,NM_001171944.1,NM_025154.5	,,	963,2842,2508	GG,GA,AA		32.6731,47.9971,37.7633	,,	474/786,371/683,391/703	897492	4768,7858	2097	4216	6313	SO:0001819	synonymous_variant	23353	exon13			GCCCACAGTCGAG	AF202724	CCDS43533.1, CCDS47525.1, CCDS55078.1, CCDS55079.1, CCDS55080.1	7p22.3	2010-01-27	2010-01-27	2010-01-27	ENSG00000164828	ENSG00000164828			18587	protein-coding gene	gene with protein product	"""Sad1 unc-84 domain protein 1"""	607723	"""unc-84 homolog A (C. elegans)"""	UNC84A		11593002	Standard	NM_001130965		Approved	KIAA0810, FLJ12407	uc021zym.1	O94901	OTTHUMG00000151426	ENST00000405266.1:c.1533A>G	7.37:g.897492A>G		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	86	16	0.186047	NM_001130965	A5PL20|B3KMV7|B4DZF7|B7WNY4|B7WP53|E9PDU4|E9PF23|F8WD13|Q96CZ7|Q9HA14|Q9UH98	Silent	SNP	ENST00000405266.1	37		968	0.4432234432234432	235	0.47764227642276424	175	0.48342541436464087	290	0.506993006993007	268	0.35356200527704484	G	5.560	0.288222	0.10513	0.479971	0.326731	ENSG00000164828	ENST00000433212	.	.	.	5.08	-6.38	0.01957	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.47983	-0.9074	3	.	.	.	0.04	0.2186	0.00165	0.314:0.1549:0.2327:0.2983	rs10950789;rs11555975;rs60471374	.	.	.	G	323	.	.	S	+	1	0	SUN1	864018	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.960000	0.03849	-1.729000	0.01364	-2.212000	0.00299	AGT	A|0.604;G|0.396	0.396	strong		0.567	SUN1-001	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000322566.1	NM_025154	
ZNF609	23060	hgsc.bcm.edu	37	15	64962630	64962630	+	Silent	SNP	A	A	C	rs11633399	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:64962630A>C	ENST00000326648.3	+	3	1187	c.1059A>C	c.(1057-1059)ccA>ccC	p.P353P	RNU6-549P_ENST00000384433.1_RNA|ZNF609_ENST00000559364.1_3'UTR	NM_015042.1	NP_055857.1	O15014	ZN609_HUMAN	zinc finger protein 609	353						nucleus (GO:0005634)	metal ion binding (GO:0046872)			breast(3)|central_nervous_system(2)|endometrium(5)|kidney(1)|large_intestine(9)|lung(11)|ovary(1)|pancreas(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						GGGCACCCCCAAGGTAAGCAC	0.408													A|||	1472	0.29393	0.3215	0.3141	5008	,	,		14822	0.0565		0.5417	False		,,,				2504	0.2321				p.P353P		Atlas-SNP	.											.	ZNF609	106	.	0			c.A1059C						PASS	.	A		1535,2871	473.0+/-356.5	262,1011,930	189.0	160.0	170.0		1059	0.5	1.0	15	dbSNP_120	170	4248,4350	560.6+/-387.6	1050,2148,1101	yes	coding-synonymous	ZNF609	NM_015042.1		1312,3159,2031	CC,CA,AA		49.4068,34.8389,44.4709		353/1412	64962630	5783,7221	2203	4299	6502	SO:0001819	synonymous_variant	23060	exon3			ACCCCCAAGGTAA	BC014251	CCDS32270.1	15q22.1	2008-05-02				ENSG00000180357		"""Zinc fingers, C2H2-type"""	29003	protein-coding gene	gene with protein product						9205841	Standard	NM_015042		Approved	KIAA0295	uc002ann.3	O15014		ENST00000326648.3:c.1059A>C	15.37:g.64962630A>C		Somatic	214	1	0.0046729		WXS	Illumina HiSeq	Phase_I	208	104	0.5	NM_015042	Q0D2I2	Silent	SNP	ENST00000326648.3	37	CCDS32270.1																																																																																			A|0.631;C|0.369	0.369	strong		0.408	ZNF609-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418130.1	XM_042833	
HLA-DQA1	3117	hgsc.bcm.edu	37	6	32609874	32609874	+	Missense_Mutation	SNP	T	T	G	rs386699556|rs41547417	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:32609874T>G	ENST00000343139.5	+	3	559	c.457T>G	c.(457-459)Tca>Gca	p.S153A	HLA-DQA1_ENST00000395363.1_Missense_Mutation_p.S153A|HLA-DQA1_ENST00000374949.2_Missense_Mutation_p.S153A	NM_002122.3	NP_002113.2	P01909	DQA1_HUMAN	major histocompatibility complex, class II, DQ alpha 1	152	Alpha-2.|Ig-like C1-type.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			NS(1)|lung(3)|skin(1)|upper_aerodigestive_tract(1)	6						CAATGGGCAGTCAGTCACAGA	0.498													.|||	543	0.108427	0.0484	0.0663	5008	,	,		13755	0.1171		0.0666	False		,,,				2504	0.2536				p.S153A		Atlas-SNP	.											.	HLA-DQA1	52	.	0			c.T457G						PASS	.						136.0	93.0	109.0					6																	32609874		1509	2704	4213	SO:0001583	missense	3117	exon3			GGGCAGTCAGTCA		CCDS4752.1	6p21.3	2013-01-11			ENSG00000196735	ENSG00000196735		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4942	protein-coding gene	gene with protein product		146880		HLA-DQA			Standard	NM_002122		Approved	CELIAC1	uc003obr.3	P01909	OTTHUMG00000031106	ENST00000343139.5:c.457T>G	6.37:g.32609874T>G	ENSP00000339398:p.Ser153Ala	Somatic	220	0	0		WXS	Illumina HiSeq	Phase_I	171	104	0.608187	NM_002122	O19630|O19706|P01907|P01908|P04225|P04226|P05536|P79553|Q06751|Q29876|Q29994|Q2Q6Y6|Q2Q6Y7|Q2Q6Y8|Q2WCM3|Q30064|Q30067|Q30068|Q30070|Q30071|Q30072|Q30073|Q30086|Q30101|Q5Y7D5|Q5Y7F5|Q6ICU6|Q6PR46|Q6QDB1|Q860W2|Q860W4|Q9BD37|Q9TPM3|Q9UM31	Missense_Mutation	SNP	ENST00000343139.5	37	CCDS4752.1	164|164	0.07509157509157509|0.07509157509157509	24|24	0.04878048780487805|0.04878048780487805	18|18	0.049723756906077346|0.049723756906077346	79|79	0.1381118881118881|0.1381118881118881	43|43	0.05672823218997362|0.05672823218997362	.|.	6.438|6.438	0.448876|0.448876	0.12223|0.12223	.|.	.|.	ENSG00000196735|ENSG00000196735	ENST00000343139;ENST00000395364;ENST00000395363;ENST00000496318;ENST00000374949|ENST00000486548	T;T;T;T|.	0.02812|.	4.15;4.15;4.15;4.15|.	4.1|4.1	-6.01|-6.01	0.02199|0.02199	.|.	1.836940|1.836940	0.02875|0.02875	N|U	0.132111|0.132111	T|T	0.05547|0.05547	0.0146|0.0146	.|.	.|.	.|.	0.80722|0.80722	P|P	0.0|0.0	B;B|.	0.12013|.	0.005;0.0|.	B;B|.	0.24848|.	0.056;0.001|.	T|T	0.11717|0.11717	-1.0576|-1.0576	8|4	0.42905|.	T|.	0.14|.	.|.	4.1694|4.1694	0.10322|0.10322	0.4723:0.2618:0.0:0.2659|0.4723:0.2618:0.0:0.2659	rs41547417;rs62404090|rs41547417;rs62404090	159;153|.	Q59F33;G4XQK2|.	.;.|.	A|R	153|125	ENSP00000339398:S153A;ENSP00000378767:S153A;ENSP00000437302:S153A;ENSP00000364087:S153A|.	ENSP00000339398:S153A|.	S|S	+|+	1|3	0|2	HLA-DQA1|HLA-DQA1	32717852|32717852	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.555000|0.555000	0.35460|0.35460	-1.111000|-1.111000	0.03303|0.03303	-0.795000|-0.795000	0.04462|0.04462	-0.290000|-0.290000	0.09829|0.09829	TCA|AGT	T|0.928;G|0.072	0.072	strong		0.498	HLA-DQA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076176.3	NM_002122	
RNH1	6050	hgsc.bcm.edu	37	11	494942	494942	+	Silent	SNP	G	G	C	rs7983	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:494942G>C	ENST00000534797.1	-	8	2646	c.1239C>G	c.(1237-1239)gcC>gcG	p.A413A	RNH1_ENST00000354420.2_Silent_p.A413A|RNH1_ENST00000438658.2_Silent_p.A413A|RNH1_ENST00000397615.2_Silent_p.A413A|RNH1_ENST00000533410.1_Silent_p.A413A|RNH1_ENST00000397614.1_Silent_p.A413A|RNH1_ENST00000356187.5_Silent_p.A413A|RNH1_ENST00000397604.3_Silent_p.A413A			O60930	RNH1_HUMAN	ribonuclease/angiogenin inhibitor 1	0					mitochondrial DNA replication (GO:0006264)|RNA catabolic process (GO:0006401)|RNA phosphodiester bond hydrolysis (GO:0090501)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	magnesium ion binding (GO:0000287)|nucleic acid binding (GO:0003676)|ribonuclease activity (GO:0004540)|RNA binding (GO:0003723)|RNA-DNA hybrid ribonuclease activity (GO:0004523)			endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)	10		all_cancers(49;3.02e-09)|all_epithelial(84;2.09e-06)|Breast(177;0.000162)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.0538)|all_lung(207;0.0713)		all cancers(45;1.26e-26)|Epithelial(43;1.34e-25)|OV - Ovarian serous cystadenocarcinoma(40;5.31e-20)|BRCA - Breast invasive adenocarcinoma(625;8.01e-05)|Lung(200;0.0378)|LUSC - Lung squamous cell carcinoma(625;0.0703)		GCAGGATGCCGGCGTCCCCCA	0.692													C|||	1667	0.332867	0.5272	0.366	5008	,	,		15352	0.1865		0.3101	False		,,,				2504	0.2209				p.A413A		Atlas-SNP	.											.	RNH1	24	.	0			c.C1239G						PASS	.	C	,,,,,,,	2181,2223		564,1053,585	26.0	28.0	27.0		1239,1239,1239,1239,1239,1239,1239,1239	-6.5	0.0	11	dbSNP_52	27	2704,5896		430,1844,2026	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	RNH1	NM_002939.3,NM_203383.1,NM_203384.1,NM_203385.1,NM_203386.1,NM_203387.1,NM_203388.1,NM_203389.1	,,,,,,,	994,2897,2611	CC,CG,GG		31.4419,49.5232,37.5654	,,,,,,,	413/462,413/462,413/462,413/462,413/462,413/462,413/462,413/462	494942	4885,8119	2202	4300	6502	SO:0001819	synonymous_variant	6050	exon9			GATGCCGGCGTCC		CCDS7697.1	11p15.5	2008-02-05	2005-06-01	2005-06-01	ENSG00000023191	ENSG00000023191			10074	protein-coding gene	gene with protein product		173320	"""ribonuclease/angiogenin inhibitor"""	RNH			Standard	NM_203386		Approved	RAI	uc001lpo.1	P13489	OTTHUMG00000119086	ENST00000534797.1:c.1239C>G	11.37:g.494942G>C		Somatic	263	1	0.00380228		WXS	Illumina HiSeq	Phase_I	295	242	0.820339	NM_203384	B3KQU4|O60523|O60857|Q57Z93|Q5U0C1|Q6FHD4	Silent	SNP	ENST00000534797.1	37	CCDS7697.1																																																																																			G|0.627;C|0.373	0.373	strong		0.692	RNH1-009	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384301.1	NM_203389	
MUC4	4585	hgsc.bcm.edu	37	3	195489067	195489067	+	Silent	SNP	C	C	G	rs2246980	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195489067C>G	ENST00000346145.4	-	13	1734	c.1695G>C	c.(1693-1695)tcG>tcC	p.S565S	MUC4_ENST00000349607.4_Silent_p.S514S|MUC4_ENST00000463781.3_Silent_p.S4801S|MUC4_ENST00000475231.1_Silent_p.S4749S	NM_004532.5	NP_004523.3	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	1558					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		CGAAGCTGGCCGAGACCTCAG	0.687													.|||	2125	0.424321	0.1513	0.415	5008	,	,		11346	0.7599		0.4533	False		,,,				2504	0.4243				p.S4801S		Atlas-SNP	.											MUC4_ENST00000463781,colon,carcinoma,0,3	MUC4	1505	3	0			c.G14403C						PASS	.	C	,,	923,3469		101,721,1374	27.0	24.0	25.0		1695,14403,1542	-4.3	0.9	3	dbSNP_100	25	3919,4669		941,2037,1316	no	coding-synonymous,coding-synonymous,coding-synonymous	MUC4	NM_004532.5,NM_018406.6,NM_138297.4	,,	1042,2758,2690	GG,GC,CC		45.6334,21.0155,37.3035	,,	565/1177,4801/5413,514/1126	195489067	4842,8138	2196	4294	6490	SO:0001819	synonymous_variant	4585	exon14			GCTGGCCGAGACC	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000346145.4:c.1695G>C	3.37:g.195489067C>G		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	155	73	0.470968	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Silent	SNP	ENST00000346145.4	37	CCDS3310.1																																																																																			C|0.619;G|0.381	0.381	strong		0.687	MUC4-015	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341862.1	NM_018406	
ZNF169	169841	hgsc.bcm.edu	37	9	97062852	97062852	+	Missense_Mutation	SNP	A	A	T	rs61154129	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:97062852A>T	ENST00000395395.2	+	5	1102	c.1012A>T	c.(1012-1014)Agg>Tgg	p.R338W	ZNF169_ENST00000340911.4_3'UTR	NM_194320.2	NP_919301.2	Q14929	ZN169_HUMAN	zinc finger protein 169	338					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|kidney(2)|large_intestine(3)|lung(8)|ovary(2)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	24		Acute lymphoblastic leukemia(62;0.136)				TCTACACCAGAGGACGCACTT	0.562													A|||	187	0.0373403	0.0091	0.0706	5008	,	,		20580	0.0833		0.006	False		,,,				2504	0.0368				p.R338W		Atlas-SNP	.											.	ZNF169	60	.	0			c.A1012T						PASS	.	A	TRP/ARG	48,4358	48.9+/-83.8	1,46,2156	99.0	89.0	93.0		1012	1.3	1.0	9	dbSNP_129	93	92,8508	51.1+/-111.2	1,90,4209	yes	missense	ZNF169	NM_194320.2	101	2,136,6365	TT,TA,AA		1.0698,1.0894,1.0764	probably-damaging	338/604	97062852	140,12866	2203	4300	6503	SO:0001583	missense	169841	exon5			CACCAGAGGACGC	U28322	CCDS6709.2	9q22.32	2014-07-30			ENSG00000175787	ENSG00000175787		"""Zinc fingers, C2H2-type"", ""-"""	12957	protein-coding gene	gene with protein product		603404				9186526, 9071574	Standard	NM_001301275		Approved	MGC51961	uc004aum.1	Q14929	OTTHUMG00000020264	ENST00000395395.2:c.1012A>T	9.37:g.97062852A>T	ENSP00000378792:p.Arg338Trp	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	37	24	0.648649	NM_194320	A2AGP5|A8K127|Q6PI28	Missense_Mutation	SNP	ENST00000395395.2	37	CCDS6709.2	66	0.03021978021978022	5	0.01016260162601626	17	0.04696132596685083	38	0.06643356643356643	6	0.0079155672823219	A	13.18	2.159857	0.38119	0.010894	0.010698	ENSG00000175787	ENST00000395395;ENST00000340911	T	0.25579	1.79	2.53	1.32	0.21799	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.07369	0.0186	M	0.93978	3.48	0.09310	P	0.9999999999972624	D	0.71674	0.998	P	0.62813	0.907	T	0.48055	-0.9068	8	0.87932	D	0	.	6.7697	0.23587	0.7458:0.2542:0.0:0.0	rs61154129	338	Q14929	ZN169_HUMAN	W	338;147	ENSP00000378792:R338W	ENSP00000340711:R147W	R	+	1	2	ZNF169	96102673	0.000000	0.05858	0.998000	0.56505	0.364000	0.29643	-0.100000	0.10990	0.372000	0.24591	0.491000	0.48974	AGG	A|0.985;T|0.015	0.015	strong		0.562	ZNF169-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253714.1	NM_194320	
TXLNB	167838	hgsc.bcm.edu	37	6	139609755	139609755	+	Silent	SNP	T	T	C	rs6933125	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:139609755T>C	ENST00000358430.3	-	2	514	c.282A>G	c.(280-282)tcA>tcG	p.S94S	RP11-445F6.2_ENST00000441249.1_RNA|RP11-445F6.2_ENST00000440518.1_RNA	NM_153235.3	NP_694967.3	Q8N3L3	TXLNB_HUMAN	taxilin beta	94						cytoplasm (GO:0005737)				breast(2)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(5)|lung(14)|ovary(2)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)	37				OV - Ovarian serous cystadenocarcinoma(155;0.000185)|GBM - Glioblastoma multiforme(68;0.000235)		CGTTGTCAGGTGATTCTGCAT	0.552													T|||	401	0.0800719	0.1626	0.072	5008	,	,		19227	0.1161		0.001	False		,,,				2504	0.0184				p.S94S		Atlas-SNP	.											.	TXLNB	96	.	0			c.A282G						PASS	.	T		593,3813	261.3+/-264.2	38,517,1648	113.0	110.0	111.0		282	-2.8	0.0	6	dbSNP_116	111	25,8575	16.6+/-54.9	0,25,4275	no	coding-synonymous	TXLNB	NM_153235.3		38,542,5923	CC,CT,TT		0.2907,13.4589,4.7517		94/685	139609755	618,12388	2203	4300	6503	SO:0001819	synonymous_variant	167838	exon2			GTCAGGTGATTCT		CCDS34545.1	6q23.3	2008-02-05	2005-07-29	2005-07-29	ENSG00000164440	ENSG00000164440			21617	protein-coding gene	gene with protein product		611438	"""chromosome 6 open reading frame 198"""	C6orf198		15184072	Standard	NM_153235		Approved	DKFZp451A175, MDP77, dJ522B19.2	uc021zfy.1	Q8N3L3	OTTHUMG00000015688	ENST00000358430.3:c.282A>G	6.37:g.139609755T>C		Somatic	327	0	0		WXS	Illumina HiSeq	Phase_I	192	68	0.354167	NM_153235	Q5VTF3|Q76L25|Q86T52|Q8N3S2	Silent	SNP	ENST00000358430.3	37	CCDS34545.1																																																																																			T|0.935;C|0.065	0.065	strong		0.552	TXLNB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042458.1	NM_153235	
EPS15	2060	hgsc.bcm.edu	37	1	51869184	51869184	+	Silent	SNP	T	T	G	rs144030750	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:51869184T>G	ENST00000371733.3	-	17	1794	c.1698A>C	c.(1696-1698)ctA>ctC	p.L566L	EPS15_ENST00000493793.1_5'UTR|EPS15_ENST00000371730.2_Silent_p.L432L|EPS15_ENST00000396122.4_Silent_p.L243L	NM_001981.2	NP_001972.1	P42566	EPS15_HUMAN	epidermal growth factor receptor pathway substrate 15	566					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						CAGAAGGCAGTAGTTCAGGAC	0.338			T	MLL	ALL																																p.L566L		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.A1698C						PASS	.	T	,	2,4404	6.2+/-15.9	0,2,2201	95.0	92.0	93.0		756,1698	2.2	0.8	1	dbSNP_134	93	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	EPS15	NM_001159969.1,NM_001981.2	,	0,3,6500	GG,GT,TT		0.0116,0.0454,0.0231	,	252/583,566/897	51869184	3,13003	2203	4300	6503	SO:0001819	synonymous_variant	2060	exon17			AGGCAGTAGTTCA	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.1698A>C	1.37:g.51869184T>G		Somatic	242	0	0		WXS	Illumina HiSeq	Phase_I	203	104	0.512315	NM_001981	B2R8J7|D3DPJ2|Q5SRH4	Silent	SNP	ENST00000371733.3	37	CCDS557.1																																																																																			T|0.999;G|0.001	0.001	strong		0.338	EPS15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022422.1	NM_001981	
MUC2	4583	hgsc.bcm.edu	37	11	1092928	1092928	+	Missense_Mutation	SNP	T	T	A	rs12791677		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:1092928T>A	ENST00000441003.2	+	30	4774	c.4747T>A	c.(4747-4749)Tcg>Acg	p.S1583T	MUC2_ENST00000359061.5_Missense_Mutation_p.S1584T|MUC2_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)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	gaccccaacatcgacacccat	0.632																																					p.S1583T		Atlas-SNP	.											MUC2_ENST00000441003,rectum,carcinoma,0,4	MUC2	614	4	0			c.T4747A						scavenged	.																																			SO:0001583	missense	4583	exon30			CCAACATCGACAC	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"""Mucins"""	7512	protein-coding gene	gene with protein product		158370	"""mucin 2, intestinal/tracheal"""			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.4747T>A	11.37:g.1092928T>A	ENSP00000415183:p.Ser1583Thr	Somatic	41	8	0.195122		WXS	Illumina HiSeq	Phase_I	68	12	0.176471	NM_002457	Q14878	Missense_Mutation	SNP	ENST00000441003.2	37		.	.	.	.	.	.	.	.	.	.	T	0.629	-0.817927	0.02776	.	.	ENSG00000198788	ENST00000441003;ENST00000359061	T;T	0.12255	2.7;3.41	1.75	-3.51	0.04696	.	3.022220	0.02729	N	0.114829	T	0.06005	0.0156	.	.	.	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.29119	-1.0022	9	0.12766	T	0.61	.	0.5592	0.00676	0.2873:0.3401:0.1565:0.2162	.	1583	E7EUV1	.	T	1583;1584	ENSP00000415183:S1583T;ENSP00000351956:S1584T	ENSP00000351956:S1584T	S	+	1	0	MUC2	1082928	0.000000	0.05858	0.000000	0.03702	0.029000	0.11900	-3.679000	0.00395	-2.640000	0.00429	-1.550000	0.00899	TCG	.	.	weak		0.632	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
OR5B3	441608	hgsc.bcm.edu	37	11	58170143	58170143	+	Missense_Mutation	SNP	C	C	G	rs11229409	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:58170143C>G	ENST00000309403.2	-	1	739	c.740G>C	c.(739-741)gGc>gCc	p.G247A		NM_001005469.1	NP_001005469.1	Q8NH48	OR5B3_HUMAN	olfactory receptor, family 5, subfamily B, member 3	247			G -> A (in dbSNP:rs11229409).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.G247A(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(17)|ovary(1)|prostate(1)|skin(2)|stomach(6)|upper_aerodigestive_tract(1)	34	Esophageal squamous(5;0.0027)	Breast(21;0.0778)				ATAGAAGATGCCGACTGCAAT	0.428													G|||	1453	0.290136	0.3533	0.2695	5008	,	,		22285	0.1448		0.3628	False		,,,				2504	0.2945				p.G247A		Atlas-SNP	.											OR5B3,colon,carcinoma,-1,2	OR5B3	65	2	1	Substitution - Missense(1)	stomach(1)	c.G740C						PASS	.	G	ALA/GLY	1442,2960	681.5+/-404.0	229,984,988	88.0	88.0	88.0		740	4.1	0.8	11	dbSNP_120	88	3093,5497	658.3+/-401.6	549,1995,1751	yes	missense	OR5B3	NM_001005469.1	60	778,2979,2739	GG,GC,CC		36.007,32.7578,34.9061	benign	247/315	58170143	4535,8457	2201	4295	6496	SO:0001583	missense	441608	exon1			AAGATGCCGACTG	AB065545	CCDS31549.1	11q12.1	2012-08-09			ENSG00000172769	ENSG00000172769		"""GPCR / Class A : Olfactory receptors"""	8324	protein-coding gene	gene with protein product				OR5B13			Standard	NM_001005469		Approved	OST129	uc010rkf.2	Q8NH48	OTTHUMG00000167516	ENST00000309403.2:c.740G>C	11.37:g.58170143C>G	ENSP00000308270:p.Gly247Ala	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	61	47	0.770492	NM_001005469	Q6IEV6	Missense_Mutation	SNP	ENST00000309403.2	37	CCDS31549.1	655	0.2999084249084249	195	0.39634146341463417	89	0.24585635359116023	95	0.1660839160839161	276	0.3641160949868074	g	4.175	0.031006	0.08101	0.327578	0.36007	ENSG00000172769	ENST00000309403	T	0.35789	1.29	4.05	4.05	0.47172	GPCR, rhodopsin-like superfamily (1);	0.290390	0.25050	N	0.033521	T	0.00012	0.0000	N	0.05230	-0.09	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.44892	-0.9298	9	0.33141	T	0.24	-22.6339	6.9802	0.24698	0.096:0.1787:0.7253:0.0	rs11229409;rs52829287;rs60600384;rs11229409	247	Q8NH48	OR5B3_HUMAN	A	247	ENSP00000308270:G247A	ENSP00000308270:G247A	G	-	2	0	OR5B3	57926719	0.000000	0.05858	0.764000	0.31436	0.106000	0.19336	0.063000	0.14410	1.070000	0.40811	-0.127000	0.14921	GGC	C|0.674;G|0.326	0.326	strong		0.428	OR5B3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394886.1	NM_001005469	
ZP1	22917	hgsc.bcm.edu	37	11	60637164	60637164	+	Missense_Mutation	SNP	C	C	T	rs489172	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:60637164C>T	ENST00000278853.5	+	3	473	c.473C>T	c.(472-474)aCc>aTc	p.T158I		NM_207341.2	NP_997224.2	P60852	ZP1_HUMAN	zona pellucida glycoprotein 1 (sperm receptor)	158			T -> I (in dbSNP:rs489172).		binding of sperm to zona pellucida (GO:0007339)|multicellular organism reproduction (GO:0032504)|single fertilization (GO:0007338)	extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)|secretory granule (GO:0030141)				breast(3)|endometrium(2)|large_intestine(8)|lung(8)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	26						TCTGTCTCAACCCCACAAACC	0.612													C|||	3472	0.693291	0.8359	0.8213	5008	,	,		18680	0.4038		0.8161	False		,,,				2504	0.5818				p.T158I		Atlas-SNP	.											.	ZP1	69	.	0			c.C473T						PASS	.	C	ILE/THR	3714,692	761.0+/-413.0	1565,584,54	121.0	128.0	126.0		473	1.2	0.0	11	dbSNP_83	126	7055,1543	746.7+/-407.3	2904,1247,148	yes	missense	ZP1	NM_207341.2	89	4469,1831,202	TT,TC,CC		17.946,15.7059,17.187	benign	158/639	60637164	10769,2235	2203	4299	6502	SO:0001583	missense	22917	exon3			TCTCAACCCCACA	BC067899	CCDS31572.1	11q12.2	2013-01-17			ENSG00000149506	ENSG00000149506		"""Zona pellucida glycoproteins"""	13187	protein-coding gene	gene with protein product		195000				10542331	Standard	NM_207341		Approved		uc001nqd.3	P60852	OTTHUMG00000167797	ENST00000278853.5:c.473C>T	11.37:g.60637164C>T	ENSP00000278853:p.Thr158Ile	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	122	122	1	NM_207341		Missense_Mutation	SNP	ENST00000278853.5	37	CCDS31572.1	1545	0.7074175824175825	402	0.8170731707317073	308	0.850828729281768	222	0.3881118881118881	613	0.8087071240105541	C	8.909	0.958155	0.18507	0.842941	0.82054	ENSG00000149506	ENST00000278853	T	0.23552	1.9	4.44	1.19	0.21007	.	1.737840	0.03416	N	0.205604	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	B	0.21821	0.061	B	0.11329	0.006	T	0.31280	-0.9949	9	0.15952	T	0.53	-5.3892	4.4002	0.11383	0.0:0.5988:0.1863:0.2149	rs489172;rs52811766;rs489172	158	P60852	ZP1_HUMAN	I	158	ENSP00000278853:T158I	ENSP00000278853:T158I	T	+	2	0	ZP1	60393740	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.258000	0.08733	0.406000	0.25560	0.460000	0.39030	ACC	C|0.222;T|0.778	0.778	strong		0.612	ZP1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396329.1	NM_207341	
GBP5	115362	hgsc.bcm.edu	37	1	89732237	89732237	+	Silent	SNP	G	G	A	rs61729628	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:89732237G>A	ENST00000370459.3	-	6	787	c.660C>T	c.(658-660)ccC>ccT	p.P220P	RP4-620F22.2_ENST00000437128.1_RNA|GBP5_ENST00000343435.5_Silent_p.P220P			Q96PP8	GBP5_HUMAN	guanylate binding protein 5	220	GB1/RHD3-type G.|GTPase domain (Globular). {ECO:0000250}.					cytoplasm (GO:0005737)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)			breast(1)|endometrium(1)|large_intestine(6)|lung(14)|ovary(1)|prostate(1)	24				all cancers(265;0.00784)|Epithelial(280;0.0286)		TACACAGACGGGGCAAATTGA	0.343													G|||	719	0.14357	0.0371	0.1441	5008	,	,		16167	0.245		0.1581	False		,,,				2504	0.1677				p.P220P		Atlas-SNP	.											.	GBP5	65	.	0			c.C660T						PASS	.	G	,	244,4162	143.1+/-178.2	7,230,1966	97.0	101.0	99.0		660,660	-1.9	0.5	1	dbSNP_129	99	1507,7093	284.6+/-296.7	114,1279,2907	no	coding-synonymous,coding-synonymous	GBP5	NM_001134486.2,NM_052942.3	,	121,1509,4873	AA,AG,GG		17.5233,5.5379,13.463	,	220/587,220/587	89732237	1751,11255	2203	4300	6503	SO:0001819	synonymous_variant	115362	exon7			CAGACGGGGCAAA	AF430642	CCDS722.1	1p22.2	2008-02-05			ENSG00000154451	ENSG00000154451			19895	protein-coding gene	gene with protein product		611467					Standard	NM_052942		Approved		uc001dnd.3	Q96PP8	OTTHUMG00000010006	ENST00000370459.3:c.660C>T	1.37:g.89732237G>A		Somatic	203	0	0		WXS	Illumina HiSeq	Phase_I	109	52	0.477064	NM_052942	B2RCE1|Q86TM5	Silent	SNP	ENST00000370459.3	37	CCDS722.1																																																																																			G|0.859;A|0.141	0.141	strong		0.343	GBP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027700.1	NM_052942	
MUC4	4585	hgsc.bcm.edu	37	3	195515412	195515412	+	Silent	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195515412G>A	ENST00000463781.3	-	2	3498	c.3039C>T	c.(3037-3039)agC>agT	p.S1013S	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Silent_p.S1013S	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	448	Repeat.|Ser-rich.				cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.S1013_T1028delSPSSVSTGHTTPLPVT(4)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		CTGAGGAAGGGCTGGTGACAG	0.572																																					p.S1013S		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,-2,2	MUC4	1505	2	4	Deletion - In frame(4)	stomach(4)	c.C3039T						PASS	.						52.0	28.0	36.0					3																	195515412		687	1591	2278	SO:0001819	synonymous_variant	4585	exon2			GGAAGGGCTGGTG	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.3039C>T	3.37:g.195515412G>A		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	72	26	0.361111	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		0.572	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
TIPIN	54962	hgsc.bcm.edu	37	15	66629403	66629403	+	Missense_Mutation	SNP	C	C	A	rs3759786	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:66629403C>A	ENST00000261881.4	-	8	884	c.799G>T	c.(799-801)Gct>Tct	p.A267S	TIPIN_ENST00000367709.4_Missense_Mutation_p.A166S	NM_017858.2	NP_060328	Q9BVW5	TIPIN_HUMAN	TIMELESS interacting protein	267			A -> S (in dbSNP:rs3759786). {ECO:0000269|Ref.2}.		cell cycle phase transition (GO:0044770)|DNA replication checkpoint (GO:0000076)|intra-S DNA damage checkpoint (GO:0031573)|mitotic nuclear division (GO:0007067)|positive regulation of cell proliferation (GO:0008284)|regulation of nuclear cell cycle DNA replication (GO:0033262)|replication fork protection (GO:0048478)|response to UV (GO:0009411)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)				autonomic_ganglia(1)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|ovary(1)|skin(1)|stomach(1)	7						TTGGCAATAGCATCATTACAT	0.398													C|||	352	0.0702875	0.0091	0.1153	5008	,	,		16411	0.0645		0.1252	False		,,,				2504	0.0706				p.A267S		Atlas-SNP	.											.	TIPIN	23	.	0			c.G799T						PASS	.	C	SER/ALA	133,4267	95.7+/-134.4	3,127,2070	194.0	171.0	179.0		799	2.6	0.0	15	dbSNP_107	179	1337,7261	261.2+/-283.7	104,1129,3066	yes	missense	TIPIN	NM_017858.2	99	107,1256,5136	AA,AC,CC		15.5501,3.0227,11.3094	benign	267/302	66629403	1470,11528	2200	4299	6499	SO:0001583	missense	54962	exon8			CAATAGCATCATT	BK001386	CCDS10215.1	15q22.31	2012-03-02	2006-08-08		ENSG00000075131	ENSG00000075131			30750	protein-coding gene	gene with protein product	"""CSM3 homolog (S. cerevisiae)"""	610716				12875843, 17102137	Standard	NM_017858		Approved	FLJ20516	uc002apr.2	Q9BVW5	OTTHUMG00000133188	ENST00000261881.4:c.799G>T	15.37:g.66629403C>A	ENSP00000261881:p.Ala267Ser	Somatic	197	0	0		WXS	Illumina HiSeq	Phase_I	254	94	0.370079	NM_017858	B2CW64|Q9NWZ6	Missense_Mutation	SNP	ENST00000261881.4	37	CCDS10215.1	200	0.09157509157509157	7	0.014227642276422764	47	0.1298342541436464	41	0.07167832167832168	105	0.13852242744063326	C	10.10	1.258058	0.22965	0.030227	0.155501	ENSG00000075131	ENST00000367709;ENST00000261881	T;T	0.16743	2.32;2.52	4.56	2.61	0.31194	.	0.583198	0.18045	N	0.153471	T	0.00039	0.0001	L	0.52573	1.65	0.80722	P	0.0	B	0.24186	0.099	B	0.19946	0.027	T	0.29912	-0.9996	9	0.17832	T	0.49	-0.9187	7.2861	0.26340	0.0:0.7271:0.177:0.096	rs3759786;rs17258633;rs58300243;rs3759786	267	Q9BVW5	TIPIN_HUMAN	S	166;267	ENSP00000356682:A166S;ENSP00000261881:A267S	ENSP00000261881:A267S	A	-	1	0	TIPIN	64416457	0.014000	0.17966	0.009000	0.14445	0.007000	0.05969	0.374000	0.20501	0.437000	0.26423	-0.137000	0.14449	GCT	C|0.895;A|0.105	0.105	strong		0.398	TIPIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256897.2	NM_017858	
PLIN4	729359	hgsc.bcm.edu	37	19	4510530	4510530	+	Missense_Mutation	SNP	G	G	A	rs7250947	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:4510530G>A	ENST00000301286.3	-	3	3399	c.3400C>T	c.(3400-3402)Cgc>Tgc	p.R1134C		NM_001080400.1	NP_001073869.1	Q96Q06	PLIN4_HUMAN	perilipin 4	1134			R -> C (in dbSNP:rs7250947).			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						ATTGCCAAGCGTGGGGCTTCT	0.657													G|||	332	0.0662939	0.1339	0.0821	5008	,	,		16074	0.001		0.0835	False		,,,				2504	0.0133				p.R1134C		Atlas-SNP	.											.	PLIN4	191	.	0			c.C3400T						PASS	.	G	CYS/ARG	485,3683		21,443,1620	46.0	51.0	50.0		3400	-7.8	0.0	19	dbSNP_116	50	692,7724		26,640,3542	yes	missense	PLIN4	NM_001080400.1	180	47,1083,5162	AA,AG,GG		8.2224,11.6363,9.3531	possibly-damaging	1134/1358	4510530	1177,11407	2084	4208	6292	SO:0001583	missense	729359	exon3			CCAAGCGTGGGGC	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.3400C>T	19.37:g.4510530G>A	ENSP00000301286:p.Arg1134Cys	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	117	57	0.487179	NM_001080400	A6NEI2	Missense_Mutation	SNP	ENST00000301286.3	37	CCDS45927.1	183	0.08379120879120878	77	0.1565040650406504	35	0.09668508287292818	1	0.0017482517482517483	70	0.09234828496042216	G	11.86	1.764994	0.31228	0.116363	0.082224	ENSG00000167676	ENST00000301286	T	0.03496	3.91	3.93	-7.85	0.01192	.	1.273050	0.05905	N	0.630730	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	D	0.53151	0.958	B	0.38296	0.27	T	0.43782	-0.9370	9	0.49607	T	0.09	.	1.3532	0.02177	0.1302:0.2043:0.2664:0.399	rs7250947;rs60853748;rs7250947	1134	Q96Q06	PLIN4_HUMAN	C	1134	ENSP00000301286:R1134C	ENSP00000301286:R1134C	R	-	1	0	PLIN4	4461530	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.071000	0.03437	-0.976000	0.03542	-0.416000	0.06073	CGC	G|0.909;A|0.091	0.091	strong		0.657	PLIN4-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395095.1	XM_170901	
MDGA1	266727	hgsc.bcm.edu	37	6	37626142	37626142	+	Silent	SNP	C	C	T	rs2273110	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:37626142C>T	ENST00000434837.3	-	3	1439	c.261G>A	c.(259-261)tcG>tcA	p.S87S	MDGA1_ENST00000505425.1_Silent_p.S87S|MDGA1_ENST00000297153.7_Silent_p.S87S	NM_153487.3	NP_705691.1	Q8NFP4	MDGA1_HUMAN	MAM domain containing glycosylphosphatidylinositol anchor 1	87	Ig-like 1.				brain development (GO:0007420)|cerebral cortex radially oriented cell migration (GO:0021799)|neuron migration (GO:0001764)|spinal cord association neuron differentiation (GO:0021527)	anchored component of plasma membrane (GO:0046658)|extracellular space (GO:0005615)				central_nervous_system(2)|endometrium(6)|kidney(3)|large_intestine(12)|lung(11)|prostate(1)|skin(2)|urinary_tract(1)	38						CGTTGAACACCGATGTCTCCT	0.647													C|||	681	0.135982	0.0454	0.1499	5008	,	,		17612	0.1627		0.1988	False		,,,				2504	0.1564				p.S87S		Atlas-SNP	.											.	MDGA1	104	.	0			c.G261A						PASS	.	C		294,3960		12,270,1845	86.0	95.0	92.0		261	-4.2	0.8	6	dbSNP_100	92	1645,6795		162,1321,2737	no	coding-synonymous	MDGA1	NM_153487.3		174,1591,4582	TT,TC,CC		19.4905,6.9111,15.2749		87/956	37626142	1939,10755	2127	4220	6347	SO:0001819	synonymous_variant	266727	exon3			GAACACCGATGTC	AF478693	CCDS47417.1	6p21	2013-01-29			ENSG00000112139	ENSG00000112139		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	19267	protein-coding gene	gene with protein product		609626				15922729, 15019943	Standard	NM_153487		Approved	GPIM, MAMDC3	uc003onu.1	Q8NFP4	OTTHUMG00000014626	ENST00000434837.3:c.261G>A	6.37:g.37626142C>T		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	53	28	0.528302	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		
PCSK5	5125	hgsc.bcm.edu	37	9	78938043	78938043	+	Missense_Mutation	SNP	G	G	A	rs2495207	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:78938043G>A	ENST00000545128.1	+	31	4635	c.4097G>A	c.(4096-4098)cGc>cAc	p.R1366H		NM_001190482.1	NP_001177411.1	Q92824	PCSK5_HUMAN	proprotein convertase subtilisin/kexin type 5	1366	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						GCAGACTCGCGCCACTGTGTC	0.567													G|||	1605	0.320487	0.4667	0.2349	5008	,	,		14582	0.1369		0.3529	False		,,,				2504	0.3395				p.R1366H		Atlas-SNP	.											.	PCSK5	329	.	0			c.G4097A						PASS	.	G	HIS/ARG	793,959		189,415,272	30.0	28.0	28.0		4097	-1.5	0.0	9	dbSNP_100	28	1346,2636		236,874,881	yes	missense	PCSK5	NM_001190482.1	29	425,1289,1153	AA,AG,GG		33.8021,45.2626,37.3038	possibly-damaging	1366/1861	78938043	2139,3595	876	1991	2867	SO:0001583	missense	5125	exon31			ACTCGCGCCACTG		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.4097G>A	9.37:g.78938043G>A	ENSP00000446280:p.Arg1366His	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	107	48	0.448598	NM_001190482	F5H2G7|Q13527|Q96EP4	Missense_Mutation	SNP	ENST00000545128.1	37	CCDS55320.1	685	0.31364468864468864	239	0.48577235772357724	98	0.27071823204419887	76	0.13286713286713286	272	0.35883905013192613	G	12.57	1.976900	0.34848	0.452626	0.338021	ENSG00000099139	ENST00000545128;ENST00000376754;ENST00000424854	T;T	0.29397	1.57;1.6	5.65	-1.45	0.08828	.	0.871179	0.10360	N	0.684122	T	0.00012	0.0000	M	0.62016	1.91	0.80722	P	0.0	.	.	.	.	.	.	T	0.47923	-0.9079	7	0.42905	T	0.14	-12.1217	7.6077	0.28112	0.4202:0.1113:0.4685:0.0	rs2495207;rs17721339;rs56436828;rs61557544;rs2495207	.	.	.	H	1366;1096;1066	ENSP00000446280:R1366H;ENSP00000411654:R1066H	ENSP00000365945:R1096H	R	+	2	0	PCSK5	78127863	0.000000	0.05858	0.013000	0.15412	0.082000	0.17680	-0.184000	0.09698	0.077000	0.16863	0.650000	0.86243	CGC	G|0.668;A|0.332	0.332	strong		0.567	PCSK5-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
DLG1	1739	hgsc.bcm.edu	37	3	196771513	196771513	+	Missense_Mutation	SNP	G	G	A	rs34492126	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:196771513G>A	ENST00000419354.1	-	26	2982	c.2696C>T	c.(2695-2697)cCg>cTg	p.P899L	DLG1_ENST00000448528.2_Missense_Mutation_p.P899L|DLG1_ENST00000443183.1_Missense_Mutation_p.P795L|DLG1_ENST00000314062.3_Missense_Mutation_p.P848L|DLG1_ENST00000357674.4_Missense_Mutation_p.P888L|DLG1_ENST00000450955.1_Missense_Mutation_p.P888L|DLG1_ENST00000452595.1_Missense_Mutation_p.P783L|DLG1_ENST00000392382.2_Missense_Mutation_p.P866L|DLG1_ENST00000422288.1_Missense_Mutation_p.P848L|DLG1_ENST00000346964.2_Missense_Mutation_p.P921L			Q12959	DLG1_HUMAN	discs, large homolog 1 (Drosophila)	899			P -> L (in dbSNP:rs34492126).		actin filament organization (GO:0007015)|activation of protein kinase activity (GO:0032147)|amyloid precursor protein metabolic process (GO:0042982)|axon guidance (GO:0007411)|branching involved in ureteric bud morphogenesis (GO:0001658)|cortical actin cytoskeleton organization (GO:0030866)|dephosphorylation (GO:0016311)|embryonic skeletal system morphogenesis (GO:0048704)|endothelial cell proliferation (GO:0001935)|establishment or maintenance of cell polarity (GO:0007163)|hard palate development (GO:0060022)|immunological synapse formation (GO:0001771)|lens development in camera-type eye (GO:0002088)|membrane raft organization (GO:0031579)|mitotic cell cycle checkpoint (GO:0007093)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of T cell proliferation (GO:0042130)|nucleotide phosphorylation (GO:0046939)|peristalsis (GO:0030432)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cell proliferation (GO:0008284)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of potassium ion transport (GO:0043268)|protein localization to plasma membrane (GO:0072659)|regulation of membrane potential (GO:0042391)|regulation of myelination (GO:0031641)|regulation of sodium ion transmembrane transport (GO:1902305)|reproductive structure development (GO:0048608)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle tissue development (GO:0048745)|synaptic transmission (GO:0007268)|T cell activation (GO:0042110)|T cell cytokine production (GO:0002369)|tight junction assembly (GO:0070830)|viral process (GO:0016032)	basal lamina (GO:0005605)|basolateral plasma membrane (GO:0016323)|cell junction (GO:0030054)|cell projection membrane (GO:0031253)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|immunological synapse (GO:0001772)|intercalated disc (GO:0014704)|lateral loop (GO:0043219)|lateral plasma membrane (GO:0016328)|membrane raft (GO:0045121)|microtubule (GO:0005874)|MPP7-DLG1-LIN7 complex (GO:0097025)|myelin sheath abaxonal region (GO:0035748)|neuromuscular junction (GO:0031594)|node of Ranvier (GO:0033268)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|tight junction (GO:0005923)	cytoskeletal protein binding (GO:0008092)|guanylate kinase activity (GO:0004385)|ion channel binding (GO:0044325)|L27 domain binding (GO:0097016)|mitogen-activated protein kinase kinase binding (GO:0031434)|phosphatase binding (GO:0019902)|phosphoprotein phosphatase activity (GO:0004721)|potassium channel regulator activity (GO:0015459)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)			breast(2)|endometrium(1)|kidney(3)|large_intestine(4)|liver(1)|lung(9)|ovary(3)|prostate(1)|skin(1)|urinary_tract(1)	26	all_cancers(143;6.22e-10)|Ovarian(172;0.0418)|Breast(254;0.0589)	Lung NSC(153;0.133)	Epithelial(36;3.23e-24)|all cancers(36;2.15e-22)|OV - Ovarian serous cystadenocarcinoma(49;3.88e-19)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.0148)		TTCTTTTGCCGGAACCCAGAT	0.393													G|||	126	0.0251597	0.003	0.0303	5008	,	,		17679	0.0		0.0577	False		,,,				2504	0.044				p.P921L		Atlas-SNP	.											DLG1_ENST00000419354,NS,adenoma,0,3	DLG1	120	3	0			c.C2762T						PASS	.	G	LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO	57,4349	56.2+/-92.4	0,57,2146	149.0	143.0	145.0		2696,2660,2384,2348,2762	5.5	1.0	3	dbSNP_126	145	405,8195	129.0+/-187.1	9,387,3904	yes	missense,missense,missense,missense,missense	DLG1	NM_001098424.1,NM_001204386.1,NM_001204387.1,NM_001204388.1,NM_004087.2	98,98,98,98,98	9,444,6050	AA,AG,GG		4.7093,1.2937,3.5522	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	899/905,887/893,795/801,783/789,921/927	196771513	462,12544	2203	4300	6503	SO:0001583	missense	1739	exon26			TTTGCCGGAACCC	U13897	CCDS3327.1, CCDS43194.1, CCDS56300.1, CCDS56301.1, CCDS75072.1	3q29	2008-12-15	2001-11-28		ENSG00000075711	ENSG00000075711			2900	protein-coding gene	gene with protein product	"""discs large homolog 1"", ""presynaptic protein SAP97"", ""synapse-associated protein 97"""	601014	"""discs, large (Drosophila) homolog 1"""			7937897, 8825652	Standard	NM_004087		Approved	SAP97, SAP-97, hdlg, DLGH1, dJ1061C18.1.1	uc003fxn.4	Q12959	OTTHUMG00000047972	ENST00000419354.1:c.2696C>T	3.37:g.196771513G>A	ENSP00000407531:p.Pro899Leu	Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	120	61	0.508333	NM_004087	A5YKK7|B4DGU1|B4DGZ8|B7ZMM0|B9EIQ5|D3DXB8|D3DXB9|E7EWL7|E9PG21|Q12958	Missense_Mutation	SNP	ENST00000419354.1	37	CCDS43194.1	58	0.026556776556776556	2	0.0040650406504065045	13	0.03591160220994475	0	0.0	43	0.05672823218997362	G	20.6	4.022579	0.75275	0.012937	0.047093	ENSG00000075711	ENST00000346964;ENST00000359922;ENST00000357674;ENST00000381807;ENST00000314062;ENST00000419354;ENST00000452595;ENST00000422288;ENST00000448528;ENST00000443183;ENST00000392382;ENST00000450955	T;T;T;T;T;T;T;T;T;T	0.39229	1.09;1.09;1.09;1.09;1.09;1.09;1.09;1.09;1.09;1.09	5.48	5.48	0.80851	.	0.064498	0.64402	D	0.000007	T	0.22126	0.0533	M	0.87682	2.9	0.80722	D	1	D;D;D;D;D	0.76494	0.999;0.998;0.992;0.997;0.999	D;P;P;P;P	0.65010	0.931;0.854;0.684;0.806;0.899	T	0.60311	-0.7288	10	0.87932	D	0	.	18.3398	0.90302	0.0:0.0:1.0:0.0	rs34492126	888;783;795;899;921	Q12959-4;E9PG21;E7EWL7;Q12959;Q12959-2	.;.;.;DLG1_HUMAN;.	L	921;912;888;886;848;899;783;848;899;795;866;888	ENSP00000345731:P921L;ENSP00000350303:P888L;ENSP00000321087:P848L;ENSP00000407531:P899L;ENSP00000398939:P783L;ENSP00000413238:P848L;ENSP00000391732:P899L;ENSP00000396658:P795L;ENSP00000376187:P866L;ENSP00000411278:P888L	ENSP00000321087:P848L	P	-	2	0	DLG1	198255910	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	4.461000	0.60115	2.587000	0.87381	0.655000	0.94253	CCG	G|0.966;A|0.034	0.034	strong		0.393	DLG1-008	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000258170.2	NM_004087	
VWA3B	200403	hgsc.bcm.edu	37	2	98928323	98928323	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:98928323C>T	ENST00000477737.1	+	27	3767	c.3563C>T	c.(3562-3564)cCa>cTa	p.P1188L	VWA3B_ENST00000490947.2_3'UTR	NM_144992.4	NP_659429.4	Q502W6	VWA3B_HUMAN	von Willebrand factor A domain containing 3B	1188										NS(3)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(10)|lung(33)|ovary(3)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	70						CTCTTCTGGCCACTGAAAGAA	0.587																																					p.P1188L		Atlas-SNP	.											.	VWA3B	138	.	0			c.C3563T						PASS	.						24.0	30.0	28.0					2																	98928323		1936	4132	6068	SO:0001583	missense	200403	exon27			TCTGGCCACTGAA	AL832761	CCDS42718.1	2q11.2	2008-02-05			ENSG00000168658	ENSG00000168658			28385	protein-coding gene	gene with protein product						12477932	Standard	NM_144992		Approved	DKFZp686F2227, MGC26733	uc002syo.3	Q502W6	OTTHUMG00000153104	ENST00000477737.1:c.3563C>T	2.37:g.98928323C>T	ENSP00000417955:p.Pro1188Leu	Somatic	219	0	0		WXS	Illumina HiSeq	Phase_I	202	53	0.262376	NM_144992	B9EK71|Q86T73|Q8N2D0|Q8N770|Q8NA79|Q8ND63|Q8ND65|Q8WW02	Missense_Mutation	SNP	ENST00000477737.1	37	CCDS42718.1	.	.	.	.	.	.	.	.	.	.	C	11.57	1.676780	0.29783	.	.	ENSG00000168658	ENST00000477737;ENST00000358269	T	0.08458	3.09	3.79	2.9	0.33743	.	.	.	.	.	T	0.06096	0.0158	N	0.22421	0.69	0.09310	N	0.99999	B;B	0.32829	0.386;0.164	B;B	0.30716	0.119;0.056	T	0.33979	-0.9847	9	0.46703	T	0.11	.	8.715	0.34405	0.2264:0.7736:0.0:0.0	.	580;1188	Q502W6-5;Q502W6	.;VWA3B_HUMAN	L	1188;310	ENSP00000417955:P1188L	ENSP00000351009:P310L	P	+	2	0	VWA3B	98294755	0.053000	0.20554	0.002000	0.10522	0.008000	0.06430	1.626000	0.37039	1.155000	0.42497	0.491000	0.48974	CCA	.	.	none		0.587	VWA3B-020	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353469.2	NM_144992	
LSP1	4046	hgsc.bcm.edu	37	11	1902793	1902793	+	Missense_Mutation	SNP	A	A	T	rs11545725	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:1902793A>T	ENST00000311604.3	+	3	498	c.323A>T	c.(322-324)cAg>cTg	p.Q108L	LSP1_ENST00000405957.2_Missense_Mutation_p.Q46L|LSP1_ENST00000485341.1_3'UTR|LSP1_ENST00000381775.1_Missense_Mutation_p.Q236L|LSP1_ENST00000406638.2_Missense_Mutation_p.Q46L	NM_002339.2	NP_002330.1	P33241	LSP1_HUMAN	lymphocyte-specific protein 1	108			Q -> L (in dbSNP:rs11545725).		cellular component movement (GO:0006928)|cellular defense response (GO:0006968)|chemotaxis (GO:0006935)	actin cytoskeleton (GO:0015629)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|signal transducer activity (GO:0004871)			haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(9)|prostate(1)|skin(1)	16		all_epithelial(84;0.000138)|Breast(177;0.000962)|Ovarian(85;0.0014)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00147)|Lung(200;0.0729)|LUSC - Lung squamous cell carcinoma(625;0.0856)		GAGCCCCCCCAGTGCAGGAGT	0.716													a|||	728	0.145367	0.3313	0.098	5008	,	,		13935	0.0992		0.0686	False		,,,				2504	0.0542				p.Q236L		Atlas-SNP	.											.	LSP1	59	.	0			c.A707T						PASS	.	G	LEU/GLN,LEU/GLN,LEU/GLN,LEU/GLN	1117,3107		140,837,1135	11.0	12.0	12.0		137,137,137,323	-7.0	0.0	11	dbSNP_120	12	746,7534		40,666,3434	yes	missense,missense,missense,missense	LSP1	NM_001013253.1,NM_001013254.1,NM_001013255.1,NM_002339.2	113,113,113,113	180,1503,4569	TT,TA,AA		9.0097,26.4441,14.8992	benign,benign,benign,benign	46/278,46/278,46/278,108/340	1902793	1863,10641	2112	4140	6252	SO:0001583	missense	4046	exon4			CCCCCCAGTGCAG	M33552	CCDS31334.1, CCDS31335.1, CCDS58110.1	11p15.5	2008-02-05			ENSG00000130592	ENSG00000130592			6707	protein-coding gene	gene with protein product		153432				2174784	Standard	NM_001242932		Approved	WP34	uc001luj.3	P33241	OTTHUMG00000012252	ENST00000311604.3:c.323A>T	11.37:g.1902793A>T	ENSP00000308383:p.Gln108Leu	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	196	157	0.80102	NM_001242932	B3KPP1|B3KRR6|E9PBV6|E9PFP3|Q16096|Q53H48|Q6FHM3|Q9BUY8	Missense_Mutation	SNP	ENST00000311604.3	37	CCDS31334.1	294	0.1346153846153846	149	0.30284552845528456	49	0.13535911602209943	49	0.08566433566433566	47	0.06200527704485488	.	7.382	0.629076	0.14257	0.264441	0.090097	ENSG00000130592	ENST00000311604;ENST00000421485;ENST00000446808;ENST00000381775;ENST00000405957;ENST00000451814;ENST00000457279;ENST00000429923;ENST00000406638;ENST00000417766;ENST00000432093	T;T;T;T;T;T;T;T;T;T;T	0.33654	1.94;1.4;1.47;1.88;1.94;1.41;1.93;1.5;1.94;1.93;1.93	3.51	-7.01	0.01594	.	3.014530	0.01520	N	0.018318	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	B;B	0.06786	0.001;0.0	B;B	0.06405	0.002;0.0	T	0.13495	-1.0507	9	0.33940	T	0.23	-1.4335	2.1371	0.03765	0.5109:0.1126:0.1496:0.2269	rs11545725	236;108	E9PFP3;P33241	.;LSP1_HUMAN	L	108;46;46;236;46;46;99;91;46;46;46	ENSP00000308383:Q108L;ENSP00000411191:Q46L;ENSP00000402543:Q46L;ENSP00000371194:Q236L;ENSP00000383932:Q46L;ENSP00000414106:Q46L;ENSP00000400346:Q99L;ENSP00000400999:Q91L;ENSP00000384022:Q46L;ENSP00000416363:Q46L;ENSP00000412405:Q46L	ENSP00000308383:Q108L	Q	+	2	0	LSP1	1859369	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.430000	0.01024	-2.310000	0.00650	-1.372000	0.01188	CAG	A|0.864;T|0.136	0.136	strong		0.716	LSP1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000034045.3	NM_002339	
HCAR3	8843	hgsc.bcm.edu	37	12	123200693	123200693	+	Missense_Mutation	SNP	A	A	G	rs17884481	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:123200693A>G	ENST00000528880.2	-	1	746	c.592T>C	c.(592-594)Ttc>Ctc	p.F198L	RP11-324E6.6_ENST00000543611.1_lincRNA|HCAR1_ENST00000356987.2_Intron	NM_006018.2	NP_006009.2	P49019	HCAR3_HUMAN	hydroxycarboxylic acid receptor 3	198			F -> L (in dbSNP:rs17884481). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:7505609, ECO:0000269|Ref.2}.		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)	AGGGGCAGGAAGAACTCCAGG	0.532													a|||	2323	0.463858	0.5008	0.4409	5008	,	,		21080	0.495		0.5716	False		,,,				2504	0.2873				p.F198L		Atlas-SNP	.											HCAR3_ENST00000528880,colon,carcinoma,0,3	HCAR3	49	3	0			c.T592C						PASS	.						81.0	83.0	82.0					12																	123200693		2203	4300	6503	SO:0001583	missense	8843	exon1			GCAGGAAGAACTC	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.592T>C	12.37:g.123200693A>G	ENSP00000436714:p.Phe198Leu	Somatic	216	0	0		WXS	Illumina HiSeq	Phase_I	168	156	0.928571	NM_006018	A8K4G5|B2R830|E9PI97|Q8NGE4	Missense_Mutation	SNP	ENST00000528880.2	37	CCDS53842.1	1139	0.5215201465201466	251	0.5101626016260162	169	0.46685082872928174	304	0.5314685314685315	415	0.5474934036939314	A	12.20	1.867061	0.32977	.	.	ENSG00000255398	ENST00000528880	T	0.70164	-0.46	3.41	2.2	0.27929	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.37167	P	0.09715600000000002	P	0.39782	0.688	B	0.39617	0.305	T	0.40194	-0.9576	7	0.07325	T	0.83	.	7.2126	0.25941	0.8006:0.0:0.0:0.1994	rs17884481	198	E9PI97	.	L	198	ENSP00000436714:F198L	ENSP00000436714:F198L	F	-	1	0	HCAR3	121766646	0.368000	0.25031	0.996000	0.52242	0.626000	0.37791	0.279000	0.18771	0.289000	0.22422	0.155000	0.16302	TTC	A|0.479;G|0.521	0.521	strong		0.532	HCAR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387549.2	NM_006018	
APOL6	80830	hgsc.bcm.edu	37	22	36055406	36055406	+	Silent	SNP	A	A	C	rs34014315	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:36055406A>C	ENST00000409652.4	+	3	1071	c.795A>C	c.(793-795)acA>acC	p.T265T		NM_030641.3	NP_085144.1	Q9BWW8	APOL6_HUMAN	apolipoprotein L, 6	265					lipid transport (GO:0006869)|lipoprotein metabolic process (GO:0042157)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)	lipid binding (GO:0008289)			haematopoietic_and_lymphoid_tissue(1)|lung(4)	5						GAGCAAGGACAAAGTTTGCGG	0.532													A|||	110	0.0219649	0.0038	0.0375	5008	,	,		21399	0.0		0.0398	False		,,,				2504	0.0399				p.T265T		Atlas-SNP	.											.	APOL6	26	.	0			c.A795C						PASS	.	A		36,4370	41.6+/-74.8	0,36,2167	79.0	77.0	77.0		795	-8.8	0.0	22	dbSNP_126	77	404,8196	127.0+/-185.4	14,376,3910	no	coding-synonymous	APOL6	NM_030641.3		14,412,6077	CC,CA,AA		4.6977,0.8171,3.3831		265/344	36055406	440,12566	2203	4300	6503	SO:0001819	synonymous_variant	80830	exon3			AAGGACAAAGTTT	AY014879	CCDS13919.1	22q12.3	2013-01-24			ENSG00000221963	ENSG00000221963		"""Apolipoproteins"""	14870	protein-coding gene	gene with protein product		607256				11374903, 15671246	Standard	NM_030641		Approved	APOL-VI, APOLVI	uc003aoe.3	Q9BWW8	OTTHUMG00000150615	ENST00000409652.4:c.795A>C	22.37:g.36055406A>C		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	70	31	0.442857	NM_030641	Q5R3S1|Q658J1|Q8IXX6|Q9UGG1	Silent	SNP	ENST00000409652.4	37	CCDS13919.1																																																																																			A|0.965;C|0.035	0.035	strong		0.532	APOL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319081.2	NM_030641	
DIDO1	11083	hgsc.bcm.edu	37	20	61513649	61513649	+	Missense_Mutation	SNP	G	G	T	rs6011441	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:61513649G>T	ENST00000266070.4	-	16	3984	c.3659C>A	c.(3658-3660)cCg>cAg	p.P1220Q	DIDO1_ENST00000395343.1_Missense_Mutation_p.P1220Q	NM_033081.2	NP_149072.2	Q9BTC0	DIDO1_HUMAN	death inducer-obliterator 1	1220			P -> Q (in dbSNP:rs6011441).		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)					CGCTTCTTCCGGTTGAAGTCG	0.512													g|||	915	0.182708	0.5295	0.0692	5008	,	,		14709	0.0238		0.0755	False		,,,				2504	0.0685				p.P1220Q	Melanoma(25;381 482 3385 5362 7955 17159 17174 40604 47095)	Atlas-SNP	.											DIDO1,NS,carcinoma,+1,1	DIDO1	321	1	0			c.C3659A						PASS	.	G	GLN/PRO,GLN/PRO	2121,2285	573.1+/-383.5	507,1107,589	95.0	103.0	100.0		3659,3659	-0.3	0.0	20	dbSNP_114	100	815,7785	188.1+/-235.2	49,717,3534	yes	missense,missense	DIDO1	NM_001193369.1,NM_033081.2	76,76	556,1824,4123	TT,TG,GG		9.4767,48.1389,22.5742	benign,benign	1220/2241,1220/2241	61513649	2936,10070	2203	4300	6503	SO:0001583	missense	11083	exon16			TCTTCCGGTTGAA	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.3659C>A	20.37:g.61513649G>T	ENSP00000266070:p.Pro1220Gln	Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	133	79	0.593985	NM_001193369	A8MY65|B9EH82|E1P5I1|O15043|Q3ZTL7|Q3ZTL8|Q4VXS1|Q4VXS2|Q4VXV8|Q4VXV9|Q96D72|Q9BQW0|Q9BW03|Q9H4G6|Q9H4G7|Q9NTU8|Q9NUM8|Q9UFB6	Missense_Mutation	SNP	ENST00000266070.4	37	CCDS33506.1	356	0.163003663003663	250	0.508130081300813	29	0.08011049723756906	13	0.022727272727272728	64	0.08443271767810026	g	5.265	0.234363	0.09969	0.481389	0.094767	ENSG00000101191	ENST00000266070;ENST00000395343	T;T	0.07908	3.15;3.15	5.2	-0.263	0.12954	.	0.614591	0.13264	N	0.401065	T	0.00012	0.0000	N	0.00926	-1.1	0.50171	P	1.44000000000033E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.44034	-0.9354	9	0.06494	T	0.89	-5.6941	15.0221	0.71637	0.0:0.0:0.5494:0.4506	rs6011441;rs60572892;rs6011441	1220	Q9BTC0	DIDO1_HUMAN	Q	1220	ENSP00000266070:P1220Q;ENSP00000378752:P1220Q	ENSP00000266070:P1220Q	P	-	2	0	DIDO1	60984094	0.094000	0.21725	0.000000	0.03702	0.003000	0.03518	0.750000	0.26334	-0.261000	0.09405	-0.527000	0.04329	CCG	A|0.000;G|0.803;T|0.197	0.197	strong		0.512	DIDO1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080091.2	NM_080796	
TAMM41	132001	hgsc.bcm.edu	37	3	11871215	11871215	+	Missense_Mutation	SNP	T	T	C	rs11551661	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:11871215T>C	ENST00000444133.2	-	4	677	c.535A>G	c.(535-537)Ata>Gta	p.I179V	TAMM41_ENST00000455809.1_Missense_Mutation_p.I179V|TAMM41_ENST00000273037.5_Missense_Mutation_p.I179V			Q96BW9	TAM41_HUMAN	TAM41, mitochondrial translocator assembly and maintenance protein, homolog (S. cerevisiae)	179			I -> V (in dbSNP:rs11551661).		cardiolipin biosynthetic process (GO:0032049)|CDP-diacylglycerol biosynthetic process (GO:0016024)	extrinsic component of mitochondrial inner membrane (GO:0031314)	phosphatidate cytidylyltransferase activity (GO:0004605)										GCAATCTCTATGAAGAGGTCT	0.463													T|||	260	0.0519169	0.003	0.0677	5008	,	,		18490	0.005		0.1352	False		,,,				2504	0.0695				p.I179V		Atlas-SNP	.											.	.	.	.	0			c.A535G						PASS	.	T	VAL/ILE	135,4271	95.7+/-134.4	1,133,2069	114.0	120.0	118.0		535	-8.1	0.0	3	dbSNP_120	118	1185,7415	241.3+/-271.7	93,999,3208	yes	missense	TAMM41	NM_138807.2	29	94,1132,5277	CC,CT,TT		13.7791,3.064,10.1492	benign	179/317	11871215	1320,11686	2203	4300	6503	SO:0001583	missense	132001	exon4			TCTCTATGAAGAG		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.535A>G	3.37:g.11871215T>C	ENSP00000388598:p.Ile179Val	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	73	29	0.39726	NM_138807	B4DIY7|C9J2U4	Missense_Mutation	SNP	ENST00000444133.2	37		133	0.060897435897435896	1	0.0020325203252032522	27	0.07458563535911603	2	0.0034965034965034965	103	0.1358839050131926	T	9.840	1.190737	0.21954	0.03064	0.137791	ENSG00000144559	ENST00000455809;ENST00000273037;ENST00000444133	T;T;T	0.28895	1.59;1.59;1.59	5.41	-8.09	0.01090	.	0.885835	0.10174	N	0.706685	T	0.00073	0.0002	N	0.12182	0.205	0.80722	P	0.0	B;B;B	0.20261	0.043;0.0;0.0	B;B;B	0.15484	0.013;0.001;0.003	T	0.26573	-1.0099	9	0.11182	T	0.66	-21.6492	5.1122	0.14815	0.0848:0.2732:0.427:0.215	rs11551661;rs52814154;rs58905270;rs11551661	179;179;179	B4DIY7;C9J2U4;Q96BW9	.;.;TAM41_HUMAN	V	179	ENSP00000398596:I179V;ENSP00000273037:I179V;ENSP00000388598:I179V	ENSP00000273037:I179V	I	-	1	0	TAMM41	11846215	0.136000	0.22515	0.000000	0.03702	0.969000	0.65631	-0.515000	0.06290	-1.279000	0.02405	0.460000	0.39030	ATA	T|0.916;C|0.084	0.084	strong		0.463	TAMM41-008	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000339258.2	NM_138807	
NANOS2	339345	hgsc.bcm.edu	37	19	46417625	46417625	+	Silent	SNP	A	A	G	rs142962668	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:46417625A>G	ENST00000341294.2	-	1	411	c.327T>C	c.(325-327)caT>caC	p.H109H		NM_001029861.2	NP_001025032.1	P60321	NANO2_HUMAN	nanos homolog 2 (Drosophila)	109					germ-line stem cell maintenance (GO:0030718)|mRNA catabolic process (GO:0006402)|multicellular organismal development (GO:0007275)|negative regulation of meiosis (GO:0045835)|regulation of translation (GO:0006417)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	mRNA binding (GO:0003729)|zinc ion binding (GO:0008270)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(2)	6		Ovarian(192;0.0308)|all_neural(266;0.0476)		OV - Ovarian serous cystadenocarcinoma(262;0.00442)|GBM - Glioblastoma multiforme(486;0.0668)|Epithelial(262;0.231)		ACTTGAGCGTATGGGCCTGGT	0.657													A|||	26	0.00519169	0.0008	0.0115	5008	,	,		14495	0.0		0.0149	False		,,,				2504	0.002				p.H109H		Atlas-SNP	.											.	NANOS2	10	.	0			c.T327C						PASS	.	A		8,4398	14.3+/-33.2	0,8,2195	61.0	56.0	58.0		327	2.5	1.0	19	dbSNP_134	58	92,8508	49.8+/-109.6	1,90,4209	no	coding-synonymous	NANOS2	NM_001029861.2		1,98,6404	GG,GA,AA		1.0698,0.1816,0.7689		109/139	46417625	100,12906	2203	4300	6503	SO:0001819	synonymous_variant	339345	exon1			GAGCGTATGGGCC	BC042883	CCDS33056.1	19q13.32	2003-12-01				ENSG00000188425			23292	protein-coding gene	gene with protein product		608228				12947200, 12690449	Standard	NM_001029861		Approved	NOS2	uc002pdu.3	P60321		ENST00000341294.2:c.327T>C	19.37:g.46417625A>G		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	78	40	0.512821	NM_001029861	Q17R30|Q4G0P8	Silent	SNP	ENST00000341294.2	37	CCDS33056.1																																																																																			A|0.993;G|0.007	0.007	strong		0.657	NANOS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461685.1		
CCDC15	80071	hgsc.bcm.edu	37	11	124857198	124857198	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:124857198A>G	ENST00000344762.5	+	8	1335	c.1076A>G	c.(1075-1077)gAt>gGt	p.D359G	CCDC15_ENST00000529051.1_Missense_Mutation_p.D359G	NM_025004.2	NP_079280.2	Q0P6D6	CCD15_HUMAN	coiled-coil domain containing 15	359						centrosome (GO:0005813)				central_nervous_system(1)|cervix(1)|large_intestine(6)|lung(10)|ovary(1)|prostate(3)|skin(1)	23	all_hematologic(175;0.215)	Breast(109;0.00222)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.68e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0413)		GTTAAGCCAGATACCCAGGCT	0.478																																					p.D359G		Atlas-SNP	.											CCDC15_ENST00000344762,NS,carcinoma,+1,2	CCDC15	134	2	0			c.A1076G						scavenged	.						124.0	119.0	121.0					11																	124857198		1844	4096	5940	SO:0001583	missense	80071	exon8			AGCCAGATACCCA	BC018540	CCDS44756.1	11q24.2	2008-02-05			ENSG00000149548	ENSG00000149548			25798	protein-coding gene	gene with protein product							Standard	NM_025004		Approved	FLJ13215	uc001qbm.4	Q0P6D6	OTTHUMG00000165940	ENST00000344762.5:c.1076A>G	11.37:g.124857198A>G	ENSP00000341684:p.Asp359Gly	Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	147	3	0.0204082	NM_025004	Q9H8U7	Missense_Mutation	SNP	ENST00000344762.5	37	CCDS44756.1	.	.	.	.	.	.	.	.	.	.	A	13.33	2.204691	0.38905	.	.	ENSG00000149548	ENST00000529051;ENST00000344762	T;T	0.33216	1.42;1.43	4.09	2.93	0.34026	.	0.908386	0.09262	N	0.826439	T	0.19446	0.0467	N	0.26042	0.785	0.09310	N	1	P	0.37500	0.597	B	0.35278	0.199	T	0.20874	-1.0262	10	0.62326	D	0.03	-0.4323	3.3894	0.07283	0.6941:0.0:0.1053:0.2006	.	359	Q0P6D6	CCD15_HUMAN	G	359	ENSP00000435403:D359G;ENSP00000341684:D359G	ENSP00000341684:D359G	D	+	2	0	CCDC15	124362408	0.000000	0.05858	0.003000	0.11579	0.007000	0.05969	0.145000	0.16157	0.888000	0.36160	0.379000	0.24179	GAT	.	.	none		0.478	CCDC15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387131.1	NM_025004	
MUC4	4585	hgsc.bcm.edu	37	3	195513398	195513398	+	Missense_Mutation	SNP	C	C	T	rs376864964	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195513398C>T	ENST00000463781.3	-	2	5512	c.5053G>A	c.(5053-5055)Ggc>Agc	p.G1685S	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.G1685S	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)		GAGGAAAGGCCGGTGACAGGA	0.617													.|||	29	0.00579073	0.0038	0.0	5008	,	,		21303	0.0129		0.006	False		,,,				2504	0.0051				p.G1685S		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,3	MUC4	1505	3	0			c.G5053A						scavenged	.						32.0	36.0	35.0					3																	195513398		683	1581	2264	SO:0001583	missense	4585	exon2			AAAGGCCGGTGAC	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.5053G>A	3.37:g.195513398C>T	ENSP00000417498:p.Gly1685Ser	Somatic	243	0	0		WXS	Illumina HiSeq	Phase_I	160	5	0.03125	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	.	.	.	.	.	.	.	.	.	.	-	4.347	0.063909	0.08388	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.31247	1.5;1.53	.	.	.	.	.	.	.	.	T	0.13243	0.0321	N	0.19112	0.55	0.09310	N	1	B	0.17268	0.021	B	0.01281	0.0	T	0.22487	-1.0215	7	.	.	.	.	2.2023	0.03927	0.0:0.3379:0.3332:0.3289	.	1685	E7ESK3	.	S	1685	ENSP00000417498:G1685S;ENSP00000420243:G1685S	.	G	-	1	0	MUC4	196997793	0.000000	0.05858	0.014000	0.15608	0.007000	0.05969	-0.458000	0.06737	-1.862000	0.01151	-1.862000	0.00560	GGC	.	.	weak		0.617	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
APOBEC3F	200316	hgsc.bcm.edu	37	22	39445554	39445554	+	Missense_Mutation	SNP	G	G	A	rs2076101	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:39445554G>A	ENST00000308521.5	+	5	1048	c.691G>A	c.(691-693)Gtc>Atc	p.V231I	APOBEC3G_ENST00000452957.2_Intron	NM_145298.5	NP_660341.2	Q8IUX4	ABC3F_HUMAN	apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3F	231			V -> I (in dbSNP:rs2076101). {ECO:0000269|Ref.2}.		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)					CCACTCACCTGTCTCCTGGAA	0.463													G|||	2481	0.495407	0.1868	0.6182	5008	,	,		18426	0.7113		0.4901	False		,,,				2504	0.6084				p.V231I		Atlas-SNP	.											APOBEC3F,NS,carcinoma,-2,1	APOBEC3F	37	1	0			c.G691A						scavenged	.	G	ILE/VAL	1093,3313		144,805,1254	135.0	121.0	125.0		691	0.5	0.0	22	dbSNP_96	125	4555,4045		1204,2147,949	yes	missense	APOBEC3F	NM_145298.5	29	1348,2952,2203	AA,AG,GG		47.0349,24.8071,43.4261	possibly-damaging	231/374	39445554	5648,7358	2203	4300	6503	SO:0001583	missense	200316	exon5			TCACCTGTCTCCT	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.691G>A	22.37:g.39445554G>A	ENSP00000309749:p.Val231Ile	Somatic	93	1	0.0107527		WXS	Illumina HiSeq	Phase_I	87	40	0.45977	NM_145298	B0QYD4|Q45F03|Q6ICH3|Q7Z2N2|Q7Z2N5	Missense_Mutation	SNP	ENST00000308521.5	37	CCDS33648.1	1095	0.5013736263736264	99	0.20121951219512196	234	0.6464088397790055	405	0.708041958041958	357	0.470976253298153	.	11.41	1.630907	0.28978	0.248071	0.529651	ENSG00000128394	ENST00000308521	T	0.66099	-0.19	1.53	0.462	0.16695	APOBEC-like, N-terminal (1);Cytidine deaminase-like (1);	.	.	.	.	T	0.00012	0.0000	L	0.56280	1.765	0.80722	P	0.0	D	0.57257	0.979	P	0.56960	0.81	T	0.43956	-0.9359	8	0.38643	T	0.18	.	3.9175	0.09230	0.2397:0.0:0.7603:0.0	rs2076101;rs17372110;rs17853859;rs56827480;rs2076101	231	Q8IUX4	ABC3F_HUMAN	I	231	ENSP00000309749:V231I	ENSP00000309749:V231I	V	+	1	0	APOBEC3F	37775500	0.002000	0.14202	0.002000	0.10522	0.012000	0.07955	0.354000	0.20146	0.212000	0.20703	0.505000	0.49811	GTC	G|0.532;A|0.468	0.468	strong		0.463	APOBEC3F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321216.1	NM_145298	
TBC1D19	55296	hgsc.bcm.edu	37	4	26585881	26585881	+	Silent	SNP	C	C	T	rs4692549	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:26585881C>T	ENST00000264866.4	+	1	344	c.66C>T	c.(64-66)tcC>tcT	p.S22S	TBC1D19_ENST00000511789.1_Silent_p.S22S	NM_018317.2	NP_060787.2	Q8N5T2	TBC19_HUMAN	TBC1 domain family, member 19	22							Rab GTPase activator activity (GO:0005097)			breast(4)|endometrium(1)|kidney(1)|large_intestine(1)|lung(8)|skin(1)|upper_aerodigestive_tract(1)	17		Breast(46;0.0503)				TCAAGGGCTCCAATTTGTACT	0.607													C|||	1568	0.313099	0.1672	0.2795	5008	,	,		15170	0.3601		0.3946	False		,,,				2504	0.4018				p.S22S		Atlas-SNP	.											.	TBC1D19	53	.	0			c.C66T						PASS	.	C		951,3455	349.5+/-310.4	118,715,1370	50.0	49.0	49.0		66	2.2	0.9	4	dbSNP_111	49	3513,5087	501.4+/-375.5	720,2073,1507	no	coding-synonymous	TBC1D19	NM_018317.2		838,2788,2877	TT,TC,CC		40.8488,21.5842,34.3226		22/527	26585881	4464,8542	2203	4300	6503	SO:0001819	synonymous_variant	55296	exon1			GGGCTCCAATTTG	AK001944	CCDS3439.1, CCDS75115.1	4p15.2	2008-02-05			ENSG00000109680	ENSG00000109680			25624	protein-coding gene	gene with protein product							Standard	XM_006713967		Approved	FLJ11082	uc003gsf.4	Q8N5T2	OTTHUMG00000097797	ENST00000264866.4:c.66C>T	4.37:g.26585881C>T		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	82	40	0.487805	NM_018317	B9A6M0|Q9NUX1	Silent	SNP	ENST00000264866.4	37	CCDS3439.1																																																																																			C|0.679;T|0.321	0.321	strong		0.607	TBC1D19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215052.2	NM_018317	
PSD3	23362	hgsc.bcm.edu	37	8	18729496	18729496	+	Missense_Mutation	SNP	G	G	A	rs13263453	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:18729496G>A	ENST00000327040.8	-	3	980	c.878C>T	c.(877-879)cCa>cTa	p.P293L	PSD3_ENST00000523619.1_Missense_Mutation_p.P228L|PSD3_ENST00000440756.2_Missense_Mutation_p.P293L	NM_015310.3	NP_056125.3	Q9NYI0	PSD3_HUMAN	pleckstrin and Sec7 domain containing 3	293			P -> L (in dbSNP:rs13263453).		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)		GACCCGGCCTGGGCGTCCCAT	0.527													G|||	1056	0.210863	0.239	0.1326	5008	,	,		18150	0.3065		0.1143	False		,,,				2504	0.229				p.P293L		Atlas-SNP	.											.	PSD3	142	.	0			c.C878T						PASS	.	G	LEU/PRO	837,3101		97,643,1229	77.0	79.0	78.0		878	2.0	0.0	8	dbSNP_121	78	853,7449		47,759,3345	yes	missense	PSD3	NM_015310.3	98	144,1402,4574	AA,AG,GG		10.2746,21.2544,13.8072	benign	293/1048	18729496	1690,10550	1969	4151	6120	SO:0001583	missense	23362	exon3			CGGCCTGGGCGTC	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.878C>T	8.37:g.18729496G>A	ENSP00000324127:p.Pro293Leu	Somatic	199	0	0		WXS	Illumina HiSeq	Phase_I	197	141	0.715736	NM_015310	A6NFQ4|E9KL50|Q6B003|Q9Y2F1	Missense_Mutation	SNP	ENST00000327040.8	37	CCDS43720.1	458	0.2097069597069597	135	0.27439024390243905	48	0.13259668508287292	183	0.31993006993006995	92	0.12137203166226913	G	3.355	-0.131800	0.06753	0.212544	0.102746	ENSG00000156011	ENST00000327040;ENST00000440756;ENST00000523619	T;T;T	0.10005	2.92;2.92;2.92	5.86	1.96	0.26148	.	0.823455	0.10741	N	0.639470	T	0.00012	0.0000	N	0.24115	0.695	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.47636	-0.9102	9	0.35671	T	0.21	.	3.943	0.09336	0.0787:0.1377:0.4812:0.3024	rs13263453;rs52798678;rs58976907;rs13263453	293	E9KL50	.	L	293;293;228	ENSP00000324127:P293L;ENSP00000401704:P293L;ENSP00000430640:P228L	ENSP00000324127:P293L	P	-	2	0	PSD3	18773776	0.992000	0.36948	0.001000	0.08648	0.060000	0.15804	0.642000	0.24735	0.075000	0.16796	-0.972000	0.02603	CCA	G|0.801;A|0.199	0.199	strong		0.527	PSD3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000374867.1	NM_015310	
WNT5A	7474	hgsc.bcm.edu	37	3	55513589	55513589	+	Silent	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:55513589C>T	ENST00000474267.1	-	4	665	c.144G>A	c.(142-144)tcG>tcA	p.S48S	WNT5A_ENST00000264634.4_Silent_p.S48S|WNT5A_ENST00000497027.1_Silent_p.S33S			P41221	WNT5A_HUMAN	wingless-type MMTV integration site family, member 5A	48					activation of JUN kinase activity (GO:0007257)|activation of MAPK activity (GO:0000187)|activation of protein kinase B activity (GO:0032148)|ameboidal cell migration (GO:0001667)|anterior/posterior axis specification, embryo (GO:0008595)|axon guidance (GO:0007411)|canonical Wnt signaling pathway (GO:0060070)|cartilage development (GO:0051216)|cell fate commitment (GO:0045165)|cellular protein localization (GO:0034613)|cellular response to calcium ion (GO:0071277)|cellular response to interferon-gamma (GO:0071346)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to retinoic acid (GO:0071300)|cellular response to transforming growth factor beta stimulus (GO:0071560)|cervix development (GO:0060067)|cochlea morphogenesis (GO:0090103)|convergent extension involved in organogenesis (GO:0060029)|dopaminergic neuron differentiation (GO:0071542)|embryonic digit morphogenesis (GO:0042733)|embryonic skeletal system development (GO:0048706)|epithelial cell proliferation involved in mammary gland duct elongation (GO:0060750)|epithelial to mesenchymal transition (GO:0001837)|establishment of planar polarity (GO:0001736)|face development (GO:0060324)|genitalia development (GO:0048806)|heart looping (GO:0001947)|hematopoietic stem cell proliferation (GO:0071425)|hindgut morphogenesis (GO:0007442)|hypophysis morphogenesis (GO:0048850)|keratinocyte differentiation (GO:0030216)|lateral sprouting involved in mammary gland duct morphogenesis (GO:0060599)|lens development in camera-type eye (GO:0002088)|lung development (GO:0030324)|male gonad development (GO:0008584)|mammary gland branching involved in thelarche (GO:0060744)|mesenchymal-epithelial cell signaling (GO:0060638)|midgut development (GO:0007494)|negative chemotaxis (GO:0050919)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axon extension involved in axon guidance (GO:0048843)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of mesenchymal cell proliferation (GO:0072201)|negative regulation of prostatic bud formation (GO:0060686)|negative regulation of synapse assembly (GO:0051964)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube closure (GO:0001843)|neuron differentiation (GO:0030182)|non-canonical Wnt signaling pathway via JNK cascade (GO:0038031)|olfactory bulb interneuron development (GO:0021891)|optic cup formation involved in camera-type eye development (GO:0003408)|palate development (GO:0060021)|planar cell polarity pathway involved in cardiac muscle tissue morphogenesis (GO:0061350)|planar cell polarity pathway involved in cardiac right atrium morphogenesis (GO:0061349)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|planar cell polarity pathway involved in outflow tract morphogenesis (GO:0061347)|planar cell polarity pathway involved in pericardium morphogenesis (GO:0061354)|planar cell polarity pathway involved in ventricular septum morphogenesis (GO:0061348)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cartilage development (GO:0061036)|positive regulation of cell-cell adhesion mediated by cadherin (GO:2000049)|positive regulation of cGMP metabolic process (GO:0030825)|positive regulation of chemokine biosynthetic process (GO:0045080)|positive regulation of cytokine secretion involved in immune response (GO:0002741)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-1 beta secretion (GO:0050718)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of interleukin-8 secretion (GO:2000484)|positive regulation of JNK cascade (GO:0046330)|positive regulation of macrophage activation (GO:0043032)|positive regulation of macrophage cytokine production (GO:0060907)|positive regulation of meiosis (GO:0045836)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of neuron projection development (GO:0010976)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of ossification (GO:0045778)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein kinase C signaling (GO:0090037)|positive regulation of response to cytokine stimulus (GO:0060760)|positive regulation of T cell chemotaxis (GO:0010820)|positive regulation of thymocyte apoptotic process (GO:0070245)|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-mediated signaling pathway (GO:0060340)|post-anal tail morphogenesis (GO:0036342)|primitive streak formation (GO:0090009)|protein phosphorylation (GO:0006468)|regulation of branching involved in mammary gland duct morphogenesis (GO:0060762)|response to organic substance (GO:0010033)|somitogenesis (GO:0001756)|type B pancreatic cell development (GO:0003323)|urinary bladder development (GO:0060157)|uterus development (GO:0060065)|vagina development (GO:0060068)|Wnt signaling pathway (GO:0016055)|Wnt signaling pathway, calcium modulating pathway (GO:0007223)|wound healing (GO:0042060)	cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	frizzled binding (GO:0005109)|receptor agonist activity (GO:0048018)|receptor tyrosine kinase-like orphan receptor binding (GO:0005115)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|endometrium(1)|large_intestine(4)|lung(3)|prostate(2)|urinary_tract(1)	13				KIRC - Kidney renal clear cell carcinoma(284;0.00377)|Kidney(284;0.00408)|OV - Ovarian serous cystadenocarcinoma(275;0.204)		TCATACCTAGCGACCTGCAAG	0.463																																					p.S48S		Atlas-SNP	.											WNT5A,colon,carcinoma,0,2	WNT5A	43	2	0			c.G144A						scavenged	.						133.0	129.0	130.0					3																	55513589		1880	4104	5984	SO:0001819	synonymous_variant	7474	exon3			ACCTAGCGACCTG	L20861	CCDS46850.1, CCDS58835.1	3p21-p14	2013-02-28			ENSG00000114251	ENSG00000114251		"""Wingless-type MMTV integration sites"", ""Endogenous ligands"""	12784	protein-coding gene	gene with protein product	"""WNT-5A protein"""	164975				8288227	Standard	NM_001256105		Approved	hWNT5A	uc010hmw.4	P41221	OTTHUMG00000158361	ENST00000474267.1:c.144G>A	3.37:g.55513589C>T		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	105	2	0.0190476	NM_003392	A8K4A4|Q6P278	Silent	SNP	ENST00000474267.1	37	CCDS46850.1																																																																																			.	.	none		0.463	WNT5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350793.3	NM_003392	
DDHD2	23259	hgsc.bcm.edu	37	8	38095662	38095662	+	Missense_Mutation	SNP	C	C	T	rs2306899	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:38095662C>T	ENST00000397166.2	+	5	1082	c.557C>T	c.(556-558)aCg>aTg	p.T186M	DDHD2_ENST00000520272.2_Missense_Mutation_p.T186M	NM_015214.2	NP_056029.2	O94830	DDHD2_HUMAN	DDHD domain containing 2	186			T -> M (in dbSNP:rs2306899). {ECO:0000269|PubMed:9872452}.		cell death (GO:0008219)|lipid catabolic process (GO:0016042)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|microtubule organizing center (GO:0005815)	hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			endometrium(4)|kidney(1)|large_intestine(5)|lung(14)|ovary(1)|skin(1)|urinary_tract(2)	28	Colorectal(12;0.000442)	all_lung(54;0.0657)|Lung NSC(58;0.175)	BRCA - Breast invasive adenocarcinoma(5;3.76e-25)|COAD - Colon adenocarcinoma(9;0.0977)			TCAACACCCACGGAGCAGGGT	0.408													C|||	860	0.171725	0.0227	0.2392	5008	,	,		20303	0.3194		0.2545	False		,,,				2504	0.0879				p.T186M		Atlas-SNP	.											DDHD2,NS,carcinoma,-1,1	DDHD2	60	1	0			c.C557T						PASS	.	C	MET/THR,MET/THR,MET/THR	297,4109	161.8+/-193.9	14,269,1920	209.0	190.0	196.0		557,557,557	5.0	0.2	8	dbSNP_100	196	1977,6623	347.8+/-326.7	225,1527,2548	yes	missense,missense,missense	DDHD2	NM_001164232.1,NM_001164234.1,NM_015214.2	81,81,81	239,1796,4468	TT,TC,CC		22.9884,6.7408,17.4842	probably-damaging,probably-damaging,probably-damaging	186/712,186/228,186/712	38095662	2274,10732	2203	4300	6503	SO:0001583	missense	23259	exon5			CACCCACGGAGCA	AK056525	CCDS34883.1	8p11.23	2014-03-03	2004-04-05	2004-04-07				"""Sterile alpha motif (SAM) domain containing"""	29106	protein-coding gene	gene with protein product		615003	"""SAM, WWE and DDHD domain containing 1"""	SAMWD1		9872452, 11788596, 19632984, 20932832	Standard	NM_015214		Approved	KIAA0725, SPG54	uc003xlc.3	O94830		ENST00000397166.2:c.557C>T	8.37:g.38095662C>T	ENSP00000380352:p.Thr186Met	Somatic	301	0	0		WXS	Illumina HiSeq	Phase_I	248	48	0.193548	NM_001164232	B3KWV2|B3KXB5|Q9H8X7	Missense_Mutation	SNP	ENST00000397166.2	37	CCDS34883.1	481	0.22023809523809523	13	0.026422764227642278	91	0.2513812154696133	189	0.3304195804195804	188	0.24802110817941952	C	11.77	1.738693	0.30774	0.067408	0.229884	ENSG00000085788	ENST00000397166;ENST00000532222;ENST00000520272	T;T;T	0.49139	0.79;1.43;0.79	5.91	5.03	0.67393	.	0.398117	0.28114	N	0.016542	T	0.00012	0.0000	L	0.50333	1.59	0.52501	P	4.4000000000044004E-5	P;B	0.45634	0.863;0.017	B;B	0.39531	0.302;0.009	T	0.35748	-0.9776	9	0.51188	T	0.08	-7.3516	9.7953	0.40731	0.0:0.7869:0.1398:0.0732	rs2306899;rs52819565;rs58300296;rs2306899	186;186	O94830;E9PKE6	DDHD2_HUMAN;.	M	186	ENSP00000380352:T186M;ENSP00000433578:T186M;ENSP00000429932:T186M	ENSP00000380352:T186M	T	+	2	0	DDHD2	38214819	0.001000	0.12720	0.236000	0.24074	0.069000	0.16628	1.292000	0.33342	1.510000	0.48803	0.558000	0.71614	ACG	C|0.805;T|0.195	0.195	strong		0.408	DDHD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377251.2	XM_291291	
PDIA6	10130	hgsc.bcm.edu	37	2	10930903	10930903	+	Missense_Mutation	SNP	T	T	C	rs4807	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:10930903T>C	ENST00000272227.3	-	7	788	c.641A>G	c.(640-642)aAa>aGa	p.K214R	PDIA6_ENST00000404371.2_Missense_Mutation_p.K266R|PDIA6_ENST00000381611.4_Missense_Mutation_p.K219R|PDIA6_ENST00000540494.1_Missense_Mutation_p.K211R|PDIA6_ENST00000404824.2_Missense_Mutation_p.K262R	NM_001282707.1|NM_005742.2	NP_001269636.1|NP_005733.1	Q15084	PDIA6_HUMAN	protein disulfide isomerase family A, member 6	214	Thioredoxin 2. {ECO:0000255|PROSITE- ProRule:PRU00691}.		K -> R (in dbSNP:rs4807). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:9110174}.		activation of signaling protein activity involved in unfolded protein response (GO:0006987)|apoptotic cell clearance (GO:0043277)|cell redox homeostasis (GO:0045454)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|protein folding (GO:0006457)|response to endoplasmic reticulum stress (GO:0034976)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	protein disulfide isomerase activity (GO:0003756)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(8)|prostate(2)	18	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.191)			Epithelial(75;0.149)|OV - Ovarian serous cystadenocarcinoma(76;0.15)		CAGTTTCACTTTTCCTTTCGT	0.438													T|||	1409	0.28135	0.1059	0.3372	5008	,	,		22101	0.3948		0.2654	False		,,,				2504	0.3783				p.K214R	GBM(73;509 1219 34219 41343 41551)	Atlas-SNP	.											PDIA6,colon,carcinoma,0,1	PDIA6	31	1	0			c.A641G						PASS	.	T	ARG/LYS	547,3859	246.2+/-254.9	35,477,1691	153.0	148.0	150.0		641	4.6	0.9	2	dbSNP_52	150	2453,6147	404.7+/-348.2	368,1717,2215	yes	missense	PDIA6	NM_005742.2	26	403,2194,3906	CC,CT,TT		28.5233,12.4149,23.0663	possibly-damaging	214/441	10930903	3000,10006	2203	4300	6503	SO:0001583	missense	10130	exon7			TTCACTTTTCCTT	BC001312	CCDS1675.1, CCDS62852.1, CCDS62853.1, CCDS62854.1, CCDS62855.1	2p25.1	2009-11-20	2005-06-29	2005-03-03	ENSG00000143870	ENSG00000143870	5.3.4.1	"""Protein disulfide isomerases"""	30168	protein-coding gene	gene with protein product	"""protein disulfide isomerase-related protein"""	611099	"""thioredoxin domain containing 7 (protein disulfide isomerase)"", ""protein disulfide isomerase-associated 6"""	TXNDC7		7590364, 12204115	Standard	XM_005246145		Approved	P5, ERp5	uc002rau.3	Q15084	OTTHUMG00000090479	ENST00000272227.3:c.641A>G	2.37:g.10930903T>C	ENSP00000272227:p.Lys214Arg	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	156	63	0.403846	NM_005742	B3KY95|B5MCQ5|B7Z254|B7Z4M8|F8WA83|Q53RC7|Q6ZSH5|Q99778	Missense_Mutation	SNP	ENST00000272227.3	37	CCDS1675.1	592	0.27106227106227104	57	0.11585365853658537	130	0.35911602209944754	202	0.3531468531468531	203	0.2678100263852243	T	17.41	3.381466	0.61845	0.124149	0.285233	ENSG00000143870	ENST00000272227;ENST00000404371;ENST00000404824;ENST00000540494;ENST00000381611	T;T;T;T;T	0.03524	3.9;3.9;3.9;3.9;3.9	5.71	4.56	0.56223	Thioredoxin domain (1);Thioredoxin-like fold (3);Disulphide isomerase (1);	0.044045	0.85682	N	0.000000	T	0.00012	0.0000	L	0.39467	1.215	0.09310	P	0.99999999214648	B;B;B;B	0.20887	0.049;0.014;0.007;0.003	P;B;B;B	0.45099	0.469;0.084;0.033;0.027	T	0.51733	-0.8668	9	0.54805	T	0.06	.	11.426	0.50012	0.0:0.07:0.0:0.93	rs4807;rs1059775;rs3200587;rs3732109;rs52800710;rs60679704;rs4807	211;262;266;214	B7Z254;B5MCQ5;Q15084-2;Q15084	.;.;.;PDIA6_HUMAN	R	214;266;262;211;219	ENSP00000272227:K214R;ENSP00000385385:K266R;ENSP00000384459:K262R;ENSP00000438778:K211R;ENSP00000371024:K219R	ENSP00000272227:K214R	K	-	2	0	PDIA6	10848354	1.000000	0.71417	0.930000	0.37139	0.986000	0.74619	5.144000	0.64832	1.016000	0.39470	0.533000	0.62120	AAA	T|0.748;C|0.252	0.252	strong		0.438	PDIA6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000206933.1	NM_005742	
COL5A3	50509	hgsc.bcm.edu	37	19	10071347	10071347	+	Missense_Mutation	SNP	C	C	T	rs2277969	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:10071347C>T	ENST00000264828.3	-	66	5156	c.5071G>A	c.(5071-5073)Gtc>Atc	p.V1691I		NM_015719.3	NP_056534.2	P25940	CO5A3_HUMAN	collagen, type V, alpha 3	1691	Fibrillar collagen NC1. {ECO:0000255|PROSITE-ProRule:PRU00793}.		V -> I (in dbSNP:rs2277969).		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)			TCCTGGGGGACGCTGACAGTG	0.627													C|||	1267	0.252995	0.385	0.2853	5008	,	,		17190	0.1091		0.1889	False		,,,				2504	0.2658				p.V1691I		Atlas-SNP	.											.	COL5A3	243	.	0			c.G5071A						PASS	.	C	ILE/VAL	1505,2901	476.6+/-357.7	230,1045,928	64.0	65.0	65.0		5071	1.8	0.4	19	dbSNP_100	65	1632,6968	300.4+/-304.9	139,1354,2807	yes	missense	COL5A3	NM_015719.3	29	369,2399,3735	TT,TC,CC		18.9767,34.158,24.1196	benign	1691/1746	10071347	3137,9869	2203	4300	6503	SO:0001583	missense	50509	exon66			GGGGGACGCTGAC	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.5071G>A	19.37:g.10071347C>T	ENSP00000264828:p.Val1691Ile	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	23	14	0.608696	NM_015719	Q9NZQ6	Missense_Mutation	SNP	ENST00000264828.3	37	CCDS12222.1	469	0.21474358974358973	176	0.35772357723577236	89	0.24585635359116023	59	0.10314685314685315	145	0.19129287598944592	C	10.12	1.262374	0.23051	0.34158	0.189767	ENSG00000080573	ENST00000264828	T	0.75704	-0.96	4.03	1.81	0.25067	Fibrillar collagen, C-terminal (4);	0.297436	0.26213	U	0.025666	T	0.00012	0.0000	L	0.46157	1.445	0.52501	P	4.300000000001525E-5	B	0.15930	0.015	B	0.10450	0.005	T	0.17684	-1.0361	9	0.41790	T	0.15	.	8.4159	0.32670	0.0:0.7959:0.0:0.2041	rs2277969;rs3207622;rs59814308;rs2277969	1691	P25940	CO5A3_HUMAN	I	1691	ENSP00000264828:V1691I	ENSP00000264828:V1691I	V	-	1	0	COL5A3	9932347	0.747000	0.28283	0.354000	0.25760	0.078000	0.17371	1.637000	0.37155	0.917000	0.36895	0.462000	0.41574	GTC	C|0.770;T|0.230	0.230	strong		0.627	COL5A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315788.1	NM_015719	
SEC24D	9871	hgsc.bcm.edu	37	4	119736796	119736796	+	Silent	SNP	A	A	C	rs2389688	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:119736796A>C	ENST00000280551.6	-	5	721	c.483T>G	c.(481-483)ccT>ccG	p.P161P	SEC24D_ENST00000419654.2_5'UTR|SEC24D_ENST00000379735.5_Silent_p.P161P			O94855	SC24D_HUMAN	SEC24 family member D	161	Pro-rich.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular protein metabolic process (GO:0044267)|COPII vesicle coating (GO:0048208)|ER to Golgi vesicle-mediated transport (GO:0006888)|in utero embryonic development (GO:0001701)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|small molecule metabolic process (GO:0044281)	COPII vesicle coat (GO:0030127)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)	zinc ion binding (GO:0008270)	p.P161P(1)		breast(3)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(13)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	37						GCAAAATGGAAGGCTGTGGAG	0.562													c|||	2188	0.436901	0.2436	0.5807	5008	,	,		18170	0.5506		0.4354	False		,,,				2504	0.4806				p.P161P		Atlas-SNP	.											SEC24D,NS,carcinoma,0,1	SEC24D	96	1	1	Substitution - coding silent(1)	prostate(1)	c.T483G						PASS	.	T		1283,3123	700.8+/-406.7	192,899,1112	238.0	212.0	221.0		483	-11.4	0.0	4	dbSNP_100	221	3875,4725	608.7+/-395.4	892,2091,1317	no	coding-synonymous	SEC24D	NM_014822.2		1084,2990,2429	CC,CA,AA		45.0581,29.1194,39.6586		161/1033	119736796	5158,7848	2203	4300	6503	SO:0001819	synonymous_variant	9871	exon5			AATGGAAGGCTGT	AB018298	CCDS3710.1	4q26	2013-10-21	2013-10-21		ENSG00000150961	ENSG00000150961			10706	protein-coding gene	gene with protein product		607186	"""SEC24 (S. cerevisiae) related gene family, member D"", ""SEC24 family, member D (S. cerevisiae)"""			9872452, 10075675	Standard	NM_014822		Approved	KIAA0755	uc003ici.4	O94855	OTTHUMG00000132957	ENST00000280551.6:c.483T>G	4.37:g.119736796A>C		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	130	58	0.446154	NM_014822	Q8IYI7	Silent	SNP	ENST00000280551.6	37	CCDS3710.1																																																																																			T|0.108;G|0.070	.	strong		0.562	SEC24D-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000256514.4		
AGO2	27161	hgsc.bcm.edu	37	8	141559358	141559358	+	Silent	SNP	G	G	A	rs2292781	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:141559358G>A	ENST00000220592.5	-	12	1555	c.1443C>T	c.(1441-1443)gcC>gcT	p.A481A	AGO2_ENST00000519980.1_Silent_p.A481A	NM_012154.3	NP_036286.2	Q9UKV8	AGO2_HUMAN	argonaute RISC catalytic component 2	481					epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|innate immune response (GO:0045087)|mRNA cleavage involved in gene silencing by miRNA (GO:0035279)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|negative regulation of translational initiation (GO:0045947)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|post-embryonic development (GO:0009791)|pre-miRNA processing (GO:0031054)|regulation of transcription, DNA-templated (GO:0006355)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|transcription, DNA-templated (GO:0006351)|translation (GO:0006412)|translational initiation (GO:0006413)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|membrane (GO:0016020)|micro-ribonucleoprotein complex (GO:0035068)|mRNA cap binding complex (GO:0005845)|nucleus (GO:0005634)|polysome (GO:0005844)|ribonucleoprotein complex (GO:0030529)|RISC complex (GO:0016442)	endoribonuclease activity (GO:0004521)|endoribonuclease activity, cleaving siRNA-paired mRNA (GO:0070551)|metal ion binding (GO:0046872)|miRNA binding (GO:0035198)|mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|RNA 7-methylguanosine cap binding (GO:0000340)|siRNA binding (GO:0035197)|translation initiation factor activity (GO:0003743)										TGGGCATGCCGGCGTCTCTCG	0.627													G|||	2366	0.472444	0.4546	0.4856	5008	,	,		17806	0.5942		0.3429	False		,,,				2504	0.4949				p.A481A		Atlas-SNP	.											.	.	.	.	0			c.C1443T						PASS	.	G	,	1891,2513	540.1+/-375.4	403,1085,714	45.0	42.0	43.0		1443,1443	-10.6	0.0	8	dbSNP_100	43	3276,5324	488.1+/-372.3	627,2022,1651	no	coding-synonymous,coding-synonymous	EIF2C2	NM_001164623.1,NM_012154.3	,	1030,3107,2365	AA,AG,GG		38.093,42.9382,39.7339	,	481/826,481/860	141559358	5167,7837	2202	4300	6502	SO:0001819	synonymous_variant	27161	exon12			CATGCCGGCGTCT	AF121255	CCDS6380.1, CCDS55279.1	8q24.3	2013-02-15	2013-02-15	2013-02-15	ENSG00000123908	ENSG00000123908		"""Argonaute/PIWI family"""	3263	protein-coding gene	gene with protein product	"""argonaute 2"""	606229	"""eukaryotic translation initiation factor 2C, 2"""	EIF2C2		10534406, 12906857	Standard	NM_012154		Approved	hAGO2, Q10	uc003yvn.3	Q9UKV8	OTTHUMG00000164232	ENST00000220592.5:c.1443C>T	8.37:g.141559358G>A		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	133	98	0.736842	NM_012154	Q8TCZ5|Q8WV58|Q96ID1	Silent	SNP	ENST00000220592.5	37	CCDS6380.1																																																																																			G|0.586;N|0.000	.	strong		0.627	AGO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377866.4		
HIVEP2	3097	hgsc.bcm.edu	37	6	143090734	143090734	+	Silent	SNP	T	T	C	rs34530989	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:143090734T>C	ENST00000367604.1	-	4	5781	c.5142A>G	c.(5140-5142)ggA>ggG	p.G1714G	HIVEP2_ENST00000012134.2_Silent_p.G1714G|HIVEP2_ENST00000367603.2_Silent_p.G1714G			P31629	ZEP2_HUMAN	human immunodeficiency virus type I enhancer binding protein 2	1714					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|breast(4)|central_nervous_system(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(19)|lung(35)|ovary(4)|prostate(6)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	100				OV - Ovarian serous cystadenocarcinoma(155;1.61e-05)|GBM - Glioblastoma multiforme(68;0.0102)		GCTTGCCGGTTCCAGGCCTAT	0.438													T|||	704	0.140575	0.0968	0.1124	5008	,	,		18652	0.0804		0.1968	False		,,,				2504	0.2239				p.G1714G	Esophageal Squamous(107;843 1510 13293 16805 42198)	Atlas-SNP	.											.	HIVEP2	225	.	0			c.A5142G						PASS	.	T		375,3357		24,327,1515	117.0	107.0	110.0		5142	-1.1	0.2	6	dbSNP_126	110	1552,6686		140,1272,2707	no	coding-synonymous	HIVEP2	NM_006734.3		164,1599,4222	CC,CT,TT		18.8395,10.0482,16.0986		1714/2447	143090734	1927,10043	1866	4119	5985	SO:0001819	synonymous_variant	3097	exon5			GCCGGTTCCAGGC	M60119	CCDS43510.1	6q23-q24	2013-01-08	2001-11-28		ENSG00000010818	ENSG00000010818		"""Zinc fingers, C2H2-type"""	4921	protein-coding gene	gene with protein product	"""c-myc intron binding protein 1"""	143054	"""human immunodeficiency virus type I enhancer-binding protein 2"""			1733857, 2022670	Standard	NM_006734		Approved	MBP-2, HIV-EP2, MIBP1, ZAS2, Schnurri-2, ZNF40B	uc003qjd.3	P31629	OTTHUMG00000015713	ENST00000367604.1:c.5142A>G	6.37:g.143090734T>C		Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	88	65	0.738636	NM_006734	Q02646|Q5THT5|Q9NS05	Silent	SNP	ENST00000367604.1	37	CCDS43510.1																																																																																			T|0.858;C|0.142	0.142	strong		0.438	HIVEP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042495.1		
MB	4151	hgsc.bcm.edu	37	22	36007045	36007045	+	Silent	SNP	G	G	A	rs7292	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:36007045G>A	ENST00000397326.2	-	2	402	c.204C>T	c.(202-204)acC>acT	p.T68T	MB_ENST00000401702.1_Silent_p.T13T|MB_ENST00000406324.1_Silent_p.T68T|MB_ENST00000359787.1_Silent_p.T68T|MB_ENST00000397328.1_Silent_p.T68T	NM_005368.2	NP_005359.1	P02144	MYG_HUMAN	myoglobin	68					brown fat cell differentiation (GO:0050873)|enucleate erythrocyte differentiation (GO:0043353)|heart development (GO:0007507)|response to hormone (GO:0009725)|response to hydrogen peroxide (GO:0042542)|response to hypoxia (GO:0001666)|slow-twitch skeletal muscle fiber contraction (GO:0031444)	extracellular vesicular exosome (GO:0070062)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxygen binding (GO:0019825)|oxygen transporter activity (GO:0005344)			lung(1)	1						CGGTGAGCACGGTGGCACCAT	0.552													G|||	2826	0.564297	0.5703	0.4798	5008	,	,		21661	0.747		0.4493	False		,,,				2504	0.546				p.T68T	GBM(49;694 1113 16998 18419)|Esophageal Squamous(101;120 1973 10459 37086)	Atlas-SNP	.											.	MB	7	.	0			c.C204T						PASS	.	G	,,	2425,1981	618.2+/-393.1	678,1069,456	130.0	100.0	110.0		204,204,204	-10.6	0.0	22	dbSNP_52	110	4022,4578	556.1+/-386.8	958,2106,1236	no	coding-synonymous,coding-synonymous,coding-synonymous	MB	NM_005368.2,NM_203377.1,NM_203378.1	,,	1636,3175,1692	AA,AG,GG		46.7674,44.9614,49.5694	,,	68/155,68/155,68/155	36007045	6447,6559	2203	4300	6503	SO:0001819	synonymous_variant	4151	exon3			GAGCACGGTGGCA		CCDS13917.1	22q13.1	2012-10-02			ENSG00000198125	ENSG00000198125			6915	protein-coding gene	gene with protein product		160000				10591208, 2989088	Standard	NM_005368		Approved	PVALB	uc003anz.3	P02144	OTTHUMG00000150606	ENST00000397326.2:c.204C>T	22.37:g.36007045G>A		Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	158	85	0.537975	NM_203377	Q52H51|Q5THY7	Silent	SNP	ENST00000397326.2	37	CCDS13917.1																																																																																			G|0.474;A|0.526	0.526	strong		0.552	MB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319057.2	NM_203377	
TAMM41	132001	hgsc.bcm.edu	37	3	11887991	11887991	+	Silent	SNP	C	C	G	rs408600	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:11887991C>G	ENST00000444133.2	-	1	262	c.120G>C	c.(118-120)ccG>ccC	p.P40P	TAMM41_ENST00000455809.1_Silent_p.P40P|TAMM41_ENST00000273037.5_Silent_p.P40P			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)										GGTCTGAACTCGGCCCTGCCT	0.622													G|||	2175	0.434305	0.5303	0.4135	5008	,	,		17449	0.2589		0.4702	False		,,,				2504	0.4632				p.P40P		Atlas-SNP	.											.	.	.	.	0			c.G120C						PASS	.	G		2252,2154	578.4+/-384.7	584,1084,535	63.0	63.0	63.0		120	4.7	0.9	3	dbSNP_80	63	3952,4648	596.2+/-393.6	936,2080,1284	no	coding-synonymous	TAMM41	NM_138807.2		1520,3164,1819	GG,GC,CC		45.9535,48.8879,47.7011		40/317	11887991	6204,6802	2203	4300	6503	SO:0001819	synonymous_variant	132001	exon1			TGAACTCGGCCCT		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.120G>C	3.37:g.11887991C>G		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	116	114	0.982759	NM_138807	B4DIY7|C9J2U4	Silent	SNP	ENST00000444133.2	37																																																																																				C|0.543;G|0.457	0.457	strong		0.622	TAMM41-008	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000339258.2	NM_138807	
TSC22D1	8848	hgsc.bcm.edu	37	13	45147305	45147305	+	Missense_Mutation	SNP	T	T	A	rs144252895	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:45147305T>A	ENST00000458659.2	-	1	3396	c.2906A>T	c.(2905-2907)gAt>gTt	p.D969V	TSC22D1_ENST00000501704.2_Intron|TSC22D1_ENST00000460842.1_5'UTR	NM_183422.3	NP_904358.2	Q15714	T22D1_HUMAN	TSC22 domain family, member 1	969					negative regulation of apoptotic process (GO:0043066)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell proliferation (GO:0008284)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(4)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	27		all_hematologic(4;8.74e-08)|Acute lymphoblastic leukemia(4;1.78e-07)|Lung NSC(96;2.21e-05)|Breast(139;0.000625)|Prostate(109;0.000947)|Hepatocellular(98;0.0202)|Lung SC(185;0.0262)		GBM - Glioblastoma multiforme(144;0.000522)|BRCA - Breast invasive adenocarcinoma(63;0.118)		TTACCTCTCATCCTCGCCATC	0.443													T|||	2	0.000399361	0.0	0.0	5008	,	,		19730	0.0		0.002	False		,,,				2504	0.0				p.D969V		Atlas-SNP	.											.	TSC22D1	88	.	0			c.A2906T						PASS	.	T	VAL/ASP	4,4402	8.1+/-20.4	0,4,2199	48.0	47.0	47.0		2906	5.2	1.0	13	dbSNP_134	47	15,8585	9.8+/-36.6	0,15,4285	yes	missense	TSC22D1	NM_183422.3	152	0,19,6484	AA,AT,TT		0.1744,0.0908,0.1461	benign	969/1074	45147305	19,12987	2203	4300	6503	SO:0001583	missense	8848	exon1			CTCTCATCCTCGC	AJ222700	CCDS9392.1, CCDS31966.1, CCDS58291.1, CCDS73565.1	13q14	2008-02-05	2005-03-01	2005-03-03	ENSG00000102804	ENSG00000102804			16826	protein-coding gene	gene with protein product		607715	"""transforming growth factor beta 1 induced transcript 4"""	TGFB1I4		8651929, 9022669	Standard	NM_183422		Approved	TSC22, MGC17597	uc001uzn.4	Q15714	OTTHUMG00000016838	ENST00000458659.2:c.2906A>T	13.37:g.45147305T>A	ENSP00000397435:p.Asp969Val	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	90	47	0.522222	NM_183422	B3KRL7|B9EGI0|O00666|Q6AHX5|Q6IBU1|Q8NCN1|Q96JS5	Missense_Mutation	SNP	ENST00000458659.2	37	CCDS31966.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	T	17.27	3.348233	0.61183	9.08E-4	0.001744	ENSG00000102804	ENST00000458659	T	0.35421	1.31	5.16	5.16	0.70880	.	0.000000	0.64402	D	0.000012	T	0.49098	0.1537	L	0.32530	0.975	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.50499	-0.8821	10	0.62326	D	0.03	.	14.3252	0.66515	0.0:0.0:0.0:1.0	.	969	Q15714	T22D1_HUMAN	V	969	ENSP00000397435:D969V	ENSP00000397435:D969V	D	-	2	0	TSC22D1	44045305	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.659000	0.68010	2.163000	0.67991	0.459000	0.35465	GAT	T|0.998;A|0.002	0.002	strong		0.443	TSC22D1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000044743.2	NM_006022	
PVRL2	5819	hgsc.bcm.edu	37	19	45391553	45391553	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:45391553A>G	ENST00000252483.5	+	9	1534	c.1534A>G	c.(1534-1536)Atc>Gtc	p.I512V	TOMM40_ENST00000592434.1_5'Flank|CTB-129P6.4_ENST00000585408.1_RNA|TOMM40_ENST00000426677.2_5'Flank|TOMM40_ENST00000405636.2_5'Flank|TOMM40_ENST00000252487.5_5'Flank	NM_001042724.1	NP_001036189.1	Q92692	PVRL2_HUMAN	poliovirus receptor-related 2 (herpesvirus entry mediator B)	512					acrosome assembly (GO:0001675)|adherens junction organization (GO:0034332)|adhesion of symbiont to host (GO:0044406)|cell junction assembly (GO:0034329)|cell part morphogenesis (GO:0032990)|cell-cell junction organization (GO:0045216)|cilium organization (GO:0044782)|coreceptor-mediated virion attachment to host cell (GO:0046814)|cytoskeleton organization (GO:0007010)|establishment of mitochondrion localization (GO:0051654)|fertilization (GO:0009566)|fusion of virus membrane with host plasma membrane (GO:0019064)|homophilic cell adhesion (GO:0007156)|positive regulation of immunoglobulin mediated immune response (GO:0002891)|positive regulation of mast cell activation (GO:0033005)|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)|signal transduction (GO:0007165)|sperm mitochondrion organization (GO:0030382)|spermatid development (GO:0007286)|spermatid nucleus differentiation (GO:0007289)|susceptibility to natural killer cell mediated cytotoxicity (GO:0042271)|susceptibility to T cell mediated cytotoxicity (GO:0060370)	cell surface (GO:0009986)|cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|zonula adherens (GO:0005915)	cell adhesion molecule binding (GO:0050839)|coreceptor activity (GO:0015026)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|virus receptor activity (GO:0001618)			breast(1)|endometrium(1)|large_intestine(6)|lung(5)	13	Lung NSC(12;0.00195)|all_lung(12;0.00522)	Ovarian(192;0.0728)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.0143)		GATCAACCCCATCTATGATGC	0.577																																					p.I512V		Atlas-SNP	.											.	PVRL2	58	.	0			c.A1534G						PASS	.						100.0	95.0	97.0					19																	45391553		1973	4146	6119	SO:0001583	missense	5819	exon9			AACCCCATCTATG	X80038	CCDS12645.1, CCDS42576.1	19q13.32	2013-01-29			ENSG00000130202	ENSG00000130202		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9707	protein-coding gene	gene with protein product		600798		HVEB		7622062, 10196354	Standard	NM_001042724		Approved	PVRR2, PRR2, CD112	uc002ozw.1	Q92692	OTTHUMG00000180839	ENST00000252483.5:c.1534A>G	19.37:g.45391553A>G	ENSP00000252483:p.Ile512Val	Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	198	114	0.575758	NM_001042724	A8K5L5|O75455|Q6IBI6|Q96J29	Missense_Mutation	SNP	ENST00000252483.5	37	CCDS42576.1	.	.	.	.	.	.	.	.	.	.	A	6.458	0.452676	0.12283	.	.	ENSG00000130202	ENST00000252483	D	0.89415	-2.51	4.67	2.59	0.31030	.	0.128913	0.36002	N	0.002850	T	0.79782	0.4505	L	0.29908	0.895	0.33232	D	0.556026	B	0.02656	0.0	B	0.08055	0.003	T	0.73248	-0.4043	10	0.31617	T	0.26	.	7.5527	0.27806	0.8183:0.0:0.1817:0.0	.	512	Q92692	PVRL2_HUMAN	V	512	ENSP00000252483:I512V	ENSP00000252483:I512V	I	+	1	0	PVRL2	50083393	1.000000	0.71417	1.000000	0.80357	0.116000	0.19942	1.310000	0.33551	0.392000	0.25172	-0.609000	0.04063	ATC	.	.	none		0.577	PVRL2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000453231.1	NM_002856	
IGLL1	3543	hgsc.bcm.edu	37	22	23915652	23915652	+	Missense_Mutation	SNP	G	G	A	rs73157031	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:23915652G>A	ENST00000330377.2	-	3	560	c.443C>T	c.(442-444)aCc>aTc	p.T148I	AP000345.2_ENST00000458318.1_RNA|IGLL1_ENST00000249053.3_3'UTR|AP000345.2_ENST00000454863.1_RNA	NM_020070.3	NP_064455.1	P15814	IGLL1_HUMAN	immunoglobulin lambda-like polypeptide 1	148	C region (By similarity to lambda light- chain).|Ig-like C1-type.				immune response (GO:0006955)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)		p.T148I(1)		kidney(1)|large_intestine(1)|lung(5)|skin(4)|stomach(1)	12						TGCCTTCCAGGTCACCGTCAA	0.572													g|||	695	0.138778	0.0106	0.2378	5008	,	,		19637	0.2014		0.1203	False		,,,				2504	0.1963				p.T148I		Atlas-SNP	.											IGLL1,NS,carcinoma,0,1	IGLL1	27	1	1	Substitution - Missense(1)	stomach(1)	c.C443T						PASS	.	G	ILE/THR,	130,4276		1,128,2074	125.0	111.0	116.0		443,	1.3	0.1	22	dbSNP_131	116	1146,7454		78,990,3232	no	missense,utr-3	IGLL1	NM_020070.2,NM_152855.1	89,	79,1118,5306	AA,AG,GG		13.3256,2.9505,9.8109	benign,	148/214,	23915652	1276,11730	2203	4300	6503	SO:0001583	missense	3543	exon3			TTCCAGGTCACCG	X52204	CCDS13809.1, CCDS13810.1	22q11.23	2014-09-17			ENSG00000128322	ENSG00000128322		"""CD molecules"", ""Immunoglobulin superfamily / C1-set domain containing"""	5870	protein-coding gene	gene with protein product		146770		IGLL		3139558, 2511029	Standard	NM_020070		Approved	IGVPB, IGL5, 14.1, CD179B	uc002zxd.3	P15814	OTTHUMG00000150673	ENST00000330377.2:c.443C>T	22.37:g.23915652G>A	ENSP00000329312:p.Thr148Ile	Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	182	92	0.505495	NM_020070	Q0P681	Missense_Mutation	SNP	ENST00000330377.2	37	CCDS13809.1	294	0.1346153846153846	10	0.02032520325203252	72	0.19889502762430938	116	0.20279720279720279	96	0.1266490765171504	-	1.226	-0.625430	0.03610	0.029505	0.133256	ENSG00000128322	ENST00000330377;ENST00000438703	T;T	0.03358	3.96;3.96	2.45	1.32	0.21799	Immunoglobulin-like (1);Immunoglobulin C1-set (2);Immunoglobulin-like fold (1);	1.436920	0.04201	N	0.329970	T	0.00012	0.0000	L	0.52905	1.665	0.53688	P	2.599999999997049E-5	B	0.02656	0.0	B	0.12156	0.007	T	0.43572	-0.9383	9	0.56958	D	0.05	.	7.243	0.26107	0.0:0.0:0.5367:0.4632	.	148	P15814	IGLL1_HUMAN	I	148;149	ENSP00000329312:T148I;ENSP00000403391:T149I	ENSP00000329312:T148I	T	-	2	0	IGLL1	22245652	0.086000	0.21541	0.126000	0.21872	0.013000	0.08279	0.282000	0.18829	0.318000	0.23185	0.165000	0.16767	ACC	G|0.891;A|0.109	0.109	strong		0.572	IGLL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319569.1	NM_020070	
APOL5	80831	hgsc.bcm.edu	37	22	36124860	36124860	+	Missense_Mutation	SNP	C	C	G	rs2076673	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:36124860C>G	ENST00000249044.2	+	4	1217	c.1217C>G	c.(1216-1218)tCt>tGt	p.S406C		NM_030642.1	NP_085145.1	Q9BWW9	APOL5_HUMAN	apolipoprotein L, 5	406			S -> C (in dbSNP:rs2076673).		lipid metabolic process (GO:0006629)|lipid transport (GO:0006869)|lipoprotein metabolic process (GO:0042157)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)	high-density lipoprotein particle binding (GO:0008035)|lipid binding (GO:0008289)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(6)|skin(2)|urinary_tract(1)	19						AGGACAGTCTCTGCCCCAAGG	0.627													C|||	1813	0.362021	0.2292	0.2291	5008	,	,		14719	0.5942		0.2942	False		,,,				2504	0.4663				p.S406C		Atlas-SNP	.											.	APOL5	45	.	0			c.C1217G						PASS	.	C	CYS/SER	951,3455	361.9+/-315.9	108,735,1360	84.0	75.0	78.0		1217	0.9	0.0	22	dbSNP_96	78	2703,5897	434.0+/-357.6	445,1813,2042	yes	missense	APOL5	NM_030642.1	112	553,2548,3402	GG,GC,CC		31.4302,21.5842,28.0947	probably-damaging	406/434	36124860	3654,9352	2203	4300	6503	SO:0001583	missense	80831	exon4			CAGTCTCTGCCCC	AY014878	CCDS13920.1	22q12.3	2013-01-24			ENSG00000128313	ENSG00000128313		"""Apolipoproteins"""	14869	protein-coding gene	gene with protein product		607255				11374903	Standard	NM_030642		Approved	APOLV	uc003aof.3	Q9BWW9	OTTHUMG00000150588	ENST00000249044.2:c.1217C>G	22.37:g.36124860C>G	ENSP00000249044:p.Ser406Cys	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	76	40	0.526316	NM_030642	Q5TFL9|Q9UGW5	Missense_Mutation	SNP	ENST00000249044.2	37	CCDS13920.1	760	0.34798534798534797	119	0.241869918699187	88	0.2430939226519337	336	0.5874125874125874	217	0.2862796833773087	C	11.68	1.710932	0.30322	0.215842	0.314302	ENSG00000128313	ENST00000249044	T	0.05199	3.48	1.95	0.921	0.19403	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	D	0.71674	0.998	D	0.67725	0.953	T	0.40720	-0.9548	8	0.87932	D	0	.	4.2875	0.10862	0.0:0.7956:0.0:0.2044	rs2076673;rs2076673	406	Q9BWW9	APOL5_HUMAN	C	406	ENSP00000249044:S406C	ENSP00000249044:S406C	S	+	2	0	APOL5	34454806	0.011000	0.17503	0.008000	0.14137	0.089000	0.18198	-0.128000	0.10531	0.387000	0.25024	0.195000	0.17529	TCT	C|0.692;G|0.308	0.308	strong		0.627	APOL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318979.1	NM_030642	
KIAA0368	23392	hgsc.bcm.edu	37	9	114172438	114172438	+	Silent	SNP	C	C	T	rs61744546	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:114172438C>T	ENST00000338205.5	-	22	2652	c.2433G>A	c.(2431-2433)ctG>ctA	p.L811L	RNA5SP294_ENST00000411306.1_RNA|KIAA0368_ENST00000374378.3_5'Flank|KIAA0368_ENST00000259335.4_Silent_p.L989L			Q5VYK3	ECM29_HUMAN	KIAA0368	817					ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)	centrosome (GO:0005813)|cytoplasmic membrane-bounded vesicle (GO:0016023)|early endosome (GO:0005769)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle (GO:0030134)|late endosome (GO:0005770)|membrane (GO:0016020)|multivesicular body (GO:0005771)|nucleus (GO:0005634)|proteasome complex (GO:0000502)				NS(2)|breast(3)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(23)|prostate(3)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	65						CAATTTCACCCAGGGCTGTGC	0.443													C|||	16	0.00319489	0.0	0.0043	5008	,	,		18148	0.0		0.0089	False		,,,				2504	0.0041				p.L989L		Atlas-SNP	.											.	KIAA0368	144	.	0			c.G2967A						PASS	.	C		1,3801		0,1,1900	53.0	53.0	53.0		2967	5.0	1.0	9	dbSNP_129	53	101,8165		0,101,4032	no	coding-synonymous	KIAA0368	NM_001080398.1		0,102,5932	TT,TC,CC		1.2219,0.0263,0.8452		989/2018	114172438	102,11966	1901	4133	6034	SO:0001819	synonymous_variant	23392	exon24			TTCACCCAGGGCT	AK025689	CCDS48006.1	9q32	2012-11-29	2006-11-23	2006-11-23	ENSG00000136813	ENSG00000136813			29020	protein-coding gene	gene with protein product	"""ECM29 homolog (S. cerevisiae)"""					9205841, 15496406, 20682791	Standard	NM_001080398		Approved	FLJ22036, ECM29	uc004bfe.1	Q5VYK3	OTTHUMG00000020489	ENST00000338205.5:c.2433G>A	9.37:g.114172438C>T		Somatic	212	0	0		WXS	Illumina HiSeq	Phase_I	159	63	0.396226	NM_001080398	O15074|Q8WU82	Silent	SNP	ENST00000338205.5	37																																																																																				C|0.993;T|0.007	0.007	strong		0.443	KIAA0368-001	NOVEL	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000053637.2	NM_014686	
FOXO1	2308	hgsc.bcm.edu	37	13	41134629	41134629	+	Silent	SNP	G	G	A	rs139436481	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:41134629G>A	ENST00000379561.5	-	2	1383	c.999C>T	c.(997-999)acC>acT	p.T333T	FOXO1_ENST00000473775.1_5'Flank	NM_002015.3	NP_002006.2	Q12778	FOXO1_HUMAN	forkhead box O1	333	Sufficient for interaction with NLK. {ECO:0000250}.				apoptotic process (GO:0006915)|autophagy (GO:0006914)|blood vessel development (GO:0001568)|cellular glucose homeostasis (GO:0001678)|cellular response to cold (GO:0070417)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to hyperoxia (GO:0071455)|cellular response to insulin stimulus (GO:0032869)|cellular response to nitric oxide (GO:0071732)|cellular response to oxidative stress (GO:0034599)|cellular response to starvation (GO:0009267)|endocrine pancreas development (GO:0031018)|epidermal growth factor receptor signaling pathway (GO:0007173)|fat cell differentiation (GO:0045444)|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 apoptotic process (GO:0043066)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of stress-activated MAPK cascade (GO:0032873)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of apoptotic process (GO:0043065)|positive regulation of autophagy (GO:0010508)|positive regulation of gluconeogenesis (GO:0045722)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein acetylation (GO:0006473)|regulation of cell proliferation (GO:0042127)|regulation of energy homeostasis (GO:2000505)|regulation of gluconeogenesis by regulation of transcription from RNA polymerase II promoter (GO:0035947)|temperature homeostasis (GO:0001659)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|protein phosphatase 2A binding (GO:0051721)|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 (GO:0043565)|transcription factor binding transcription factor activity (GO:0000989)|ubiquitin protein ligase binding (GO:0031625)		PAX7/FOXO1(197)|PAX3/FOXO1(749)	central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(7)|kidney(1)|large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)	20		Lung NSC(96;1.18e-05)|Breast(139;0.00394)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(188;0.194)		all cancers(112;7.32e-09)|Epithelial(112;2.87e-06)|OV - Ovarian serous cystadenocarcinoma(117;6.98e-05)|GBM - Glioblastoma multiforme(144;0.00394)|BRCA - Breast invasive adenocarcinoma(63;0.0815)		CATCCTGTTCGGTCATAATGG	0.473													G|||	8	0.00159744	0.0008	0.0029	5008	,	,		21916	0.0		0.004	False		,,,				2504	0.001				p.T333T		Atlas-SNP	.											.	FOXO1	110	.	0			c.C999T						PASS	.	G		12,4394	19.1+/-41.9	0,12,2191	153.0	135.0	141.0		999	-3.3	0.7	13	dbSNP_134	141	62,8538	38.3+/-94.2	0,62,4238	no	coding-synonymous	FOXO1	NM_002015.3		0,74,6429	AA,AG,GG		0.7209,0.2724,0.569		333/656	41134629	74,12932	2203	4300	6503	SO:0001819	synonymous_variant	2308	exon2			CTGTTCGGTCATA		CCDS9371.1	13q14.1	2011-08-01	2007-05-02	2007-05-02	ENSG00000150907	ENSG00000150907		"""Forkhead boxes"""	3819	protein-coding gene	gene with protein product		136533	"""forkhead homolog in rhabdomyosarcoma"""	FKHR, FOXO1A		8275086, 15057823	Standard	NM_002015		Approved	FKH1	uc001uxl.4	Q12778	OTTHUMG00000016775	ENST00000379561.5:c.999C>T	13.37:g.41134629G>A		Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	157	81	0.515924	NM_002015	O43523|Q5VYC7|Q6NSK6	Silent	SNP	ENST00000379561.5	37	CCDS9371.1																																																																																			G|0.996;A|0.004	0.004	strong		0.473	FOXO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044634.3	NM_002015	
MROH2B	133558	hgsc.bcm.edu	37	5	41061715	41061715	+	Nonsense_Mutation	SNP	C	C	T	rs1023840|rs386687544	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:41061715C>T	ENST00000399564.4	-	6	1022	c.572G>A	c.(571-573)tGg>tAg	p.W191*		NM_173489.4	NP_775760.3	Q7Z745	MRO2B_HUMAN	maestro heat-like repeat family member 2B	191			W -> R (in dbSNP:rs865093). {ECO:0000269|PubMed:15489334}.														CATTATATACCAGAACAGCAT	0.488													C|||	1043	0.208267	0.025	0.3329	5008	,	,		17005	0.2996		0.1819	False		,,,				2504	0.3006				p.W191X		Atlas-SNP	.											.	.	.	.	0			c.G572A						PASS	.	C	stop/TRP	210,3656		2,206,1725	175.0	168.0	170.0		572	2.9	1.0	5	dbSNP_86	170	1643,6603		176,1291,2656	yes	stop-gained	HEATR7B2	NM_173489.4		178,1497,4381	TT,TC,CC		19.9248,5.432,15.2989		191/1586	41061715	1853,10259	1933	4123	6056	SO:0001587	stop_gained	133558	exon6			ATATACCAGAACA		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.572G>A	5.37:g.41061715C>T	ENSP00000382476:p.Trp191*	Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	160	160	1	NM_173489	Q68DM1|Q7Z4U4|Q8N7X3	Nonsense_Mutation	SNP	ENST00000399564.4	37	CCDS47202.1	337	0.1543040293040293	10	0.02032520325203252	97	0.26795580110497236	142	0.24825174825174826	88	0.11609498680738786	C	40	8.282932	0.98742	0.05432	0.199248	ENSG00000171495	ENST00000399564	.	.	.	5.81	2.91	0.33838	.	0.249672	0.28257	N	0.016016	.	.	.	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	.	6.9332	0.24453	0.0:0.6857:0.0:0.3143	rs1023840;rs60925153;rs1023840	.	.	.	X	191	.	ENSP00000382476:W191X	W	-	2	0	HEATR7B2	41097472	0.586000	0.26782	0.992000	0.48379	0.991000	0.79684	-0.147000	0.10234	0.299000	0.22661	0.655000	0.94253	TGG	C|0.821;T|0.179	0.179	strong		0.488	MROH2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367558.2	NM_173489	
CAPN13	92291	hgsc.bcm.edu	37	2	30957326	30957326	+	Missense_Mutation	SNP	A	A	G	rs2276568	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:30957326A>G	ENST00000295055.8	-	19	1963	c.1787T>C	c.(1786-1788)aTa>aCa	p.I596T	CAPN13_ENST00000534090.2_Missense_Mutation_p.I596T	NM_144575.2	NP_653176.2	Q6MZZ7	CAN13_HUMAN	calpain 13	596			I -> T (in dbSNP:rs2276568).		proteolysis (GO:0006508)	cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(5)|large_intestine(5)|lung(11)|ovary(1)|prostate(1)|stomach(2)|urinary_tract(1)	30	all_hematologic(175;0.0487)|Acute lymphoblastic leukemia(172;0.155)					TGTATTCTCTATGGCCTTCCA	0.547													A|||	407	0.08127	0.0076	0.0418	5008	,	,		19964	0.1726		0.0676	False		,,,				2504	0.1288				p.I596T		Atlas-SNP	.											.	CAPN13	70	.	0			c.T1787C						PASS	.	A	THR/ILE	59,3735		1,57,1839	84.0	92.0	89.0		1787	4.8	0.8	2	dbSNP_100	89	547,7695		13,521,3587	yes	missense	CAPN13	NM_144575.2	89	14,578,5426	GG,GA,AA		6.6367,1.5551,5.0349	probably-damaging	596/670	30957326	606,11430	1897	4121	6018	SO:0001583	missense	92291	exon19			TTCTCTATGGCCT		CCDS46252.1	2p22-p21	2008-02-05			ENSG00000162949	ENSG00000162949			16663	protein-coding gene	gene with protein product		610228				11675017	Standard	NM_144575		Approved	FLJ23523	uc021vfm.1	Q6MZZ7	OTTHUMG00000152053	ENST00000295055.8:c.1787T>C	2.37:g.30957326A>G	ENSP00000295055:p.Ile596Thr	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	101	99	0.980198	NM_144575	Q17RF0|Q580X1|Q8TE80	Missense_Mutation	SNP	ENST00000295055.8	37	CCDS46252.1	176	0.08058608058608059	6	0.012195121951219513	19	0.052486187845303865	100	0.17482517482517482	51	0.06728232189973615	A	12.47	1.946949	0.34377	0.015551	0.066367	ENSG00000162949	ENST00000295055;ENST00000534090	T;T	0.30714	1.52;1.52	4.84	4.84	0.62591	EF-hand-like domain (1);	0.327577	0.35870	N	0.002940	T	0.00178	0.0005	M	0.75264	2.295	0.27103	P	0.9625789	D	0.71674	0.998	P	0.59357	0.856	T	0.08432	-1.0722	9	0.72032	D	0.01	.	11.1009	0.48174	1.0:0.0:0.0:0.0	rs2276568;rs60007648;rs2276568	596	Q6MZZ7	CAN13_HUMAN	T	596	ENSP00000295055:I596T;ENSP00000431298:I596T	ENSP00000295055:I596T	I	-	2	0	CAPN13	30810830	0.974000	0.33945	0.849000	0.33467	0.062000	0.15995	4.160000	0.58164	1.952000	0.56665	0.374000	0.22700	ATA	A|0.920;G|0.080	0.080	strong		0.547	CAPN13-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000325101.2	NM_144575	
CRIPAK	285464	hgsc.bcm.edu	37	4	1388944	1388944	+	Missense_Mutation	SNP	G	G	A	rs200759023	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:1388944G>A	ENST00000324803.4	+	1	3605	c.645G>A	c.(643-645)atG>atA	p.M215I		NM_175918.3	NP_787114.2	Q8N1N5	CRPAK_HUMAN	cysteine-rich PAK1 inhibitor	215					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)			ACGTGCCCATGTGGAGTGTTC	0.657													N|||	445	0.0888578	0.1619	0.0677	5008	,	,		12756	0.001		0.0934	False		,,,				2504	0.091				p.M215I		Atlas-SNP	.											.	CRIPAK	185	.	0			c.G645A						PASS	.	G	ILE/MET	423,3903		140,143,1880	215.0	149.0	173.0		645	0.5	0.0	4		173	744,6886		259,226,3330	no	missense	CRIPAK	NM_175918.3	10	399,369,5210	AA,AG,GG		9.751,9.7781,9.7608	benign	215/447	1388944	1167,10789	2163	3815	5978	SO:0001583	missense	285464	exon1			GCCCATGTGGAGT	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.645G>A	4.37:g.1388944G>A	ENSP00000323978:p.Met215Ile	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	12	12	1	NM_175918	Q8NB03	Missense_Mutation	SNP	ENST00000324803.4	37	CCDS3349.1	.	.	.	.	.	.	.	.	.	.	g	4.551	0.102411	0.08731	0.097781	0.09751	ENSG00000179979	ENST00000324803	T	0.17528	2.27	1.41	0.509	0.16977	Post-SET domain (1);	.	.	.	.	T	0.00210	0.0006	N	0.08118	0	0.09310	N	1	B	0.17852	0.024	B	0.12156	0.007	T	0.42865	-0.9426	9	0.18710	T	0.47	.	4.0015	0.09582	0.431:0.0:0.569:0.0	.	215	Q8N1N5	CRPAK_HUMAN	I	215	ENSP00000323978:M215I	ENSP00000323978:M215I	M	+	3	0	CRIPAK	1378944	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.348000	0.02629	0.169000	0.19679	-0.506000	0.04501	ATG	.	.	weak		0.657	CRIPAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241607.2	NM_175918	
SYMPK	8189	hgsc.bcm.edu	37	19	46329624	46329624	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:46329624G>A	ENST00000245934.7	-	17	2433	c.2189C>T	c.(2188-2190)tCc>tTc	p.S730F	SYMPK_ENST00000598155.1_5'Flank	NM_004819.2	NP_004810.2	Q92797	SYMPK_HUMAN	symplekin	730					cell adhesion (GO:0007155)|mRNA polyadenylation (GO:0006378)|positive regulation of protein dephosphorylation (GO:0035307)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|tight junction (GO:0005923)				breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(7)|liver(1)|lung(25)|ovary(1)|urinary_tract(1)	45		all_neural(266;0.0299)|Ovarian(192;0.0308)		OV - Ovarian serous cystadenocarcinoma(262;0.00509)|GBM - Glioblastoma multiforme(486;0.0593)		CAGGGCCTGGGAGCGCACCTG	0.547																																					p.S730F		Atlas-SNP	.											.	SYMPK	104	.	0			c.C2189T						PASS	.						89.0	73.0	78.0					19																	46329624		2203	4300	6503	SO:0001583	missense	8189	exon17			GCCTGGGAGCGCA	U49240	CCDS12676.2	19q13.3	2008-02-05			ENSG00000125755	ENSG00000125755			22935	protein-coding gene	gene with protein product		602388				9330635	Standard	NM_004819		Approved	SYM, SPK	uc002pdn.3	Q92797	OTTHUMG00000150151	ENST00000245934.7:c.2189C>T	19.37:g.46329624G>A	ENSP00000245934:p.Ser730Phe	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	53	31	0.584906	NM_004819	O00521|O00689|O00733|Q59GT5|Q8N2U5	Missense_Mutation	SNP	ENST00000245934.7	37	CCDS12676.2	.	.	.	.	.	.	.	.	.	.	G	15.97	2.990202	0.54041	.	.	ENSG00000125755	ENST00000245934	T	0.34275	1.37	4.17	4.17	0.49024	Armadillo-like helical (1);Armadillo-type fold (1);	0.287715	0.34750	N	0.003702	T	0.35799	0.0944	L	0.55481	1.735	0.50039	D	0.999846	P;B	0.47604	0.898;0.396	P;B	0.44447	0.45;0.212	T	0.25257	-1.0137	10	0.72032	D	0.01	.	9.6197	0.39714	0.0:0.0:0.7915:0.2085	.	745;730	Q4LE61;Q92797	.;SYMPK_HUMAN	F	730	ENSP00000245934:S730F	ENSP00000245934:S730F	S	-	2	0	SYMPK	51021464	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	2.873000	0.48475	2.339000	0.79563	0.555000	0.69702	TCC	.	.	none		0.547	SYMPK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316581.1	NM_004819	
AMACR	23600	hgsc.bcm.edu	37	5	33998768	33998768	+	Missense_Mutation	SNP	C	C	A	rs34677	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:33998768C>A	ENST00000335606.6	-	4	805	c.717G>T	c.(715-717)caG>caT	p.Q239H	AMACR_ENST00000502637.1_Missense_Mutation_p.Q224H|RP11-1084J3.4_ENST00000382079.3_3'UTR|AMACR_ENST00000512079.1_Missense_Mutation_p.Q239H|AMACR_ENST00000426255.2_Missense_Mutation_p.Q239H|AMACR_ENST00000382072.2_Missense_Mutation_p.V186F|AMACR_ENST00000382085.3_Missense_Mutation_p.Q239H|AMACR_ENST00000514195.1_5'UTR|AMACR_ENST00000382068.3_Missense_Mutation_p.V186F|AMACR_ENST00000441713.2_Missense_Mutation_p.V186F	NM_001167595.1|NM_014324.5	NP_001161067.1|NP_055139.4	Q9UHK6	AMACR_HUMAN	alpha-methylacyl-CoA racemase	239			Q -> H (in dbSNP:rs34677).		bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	alpha-methylacyl-CoA racemase activity (GO:0008111)|receptor binding (GO:0005102)	p.Q239H(1)		endometrium(3)|kidney(1)|large_intestine(4)|lung(9)|stomach(1)|urinary_tract(1)	19						GCTCGTAGAACTGGGGTTCTA	0.478													C|||	573	0.114417	0.0582	0.0749	5008	,	,		16572	0.1706		0.1382	False		,,,				2504	0.136				p.Q239H		Atlas-SNP	.											AMACR,NS,carcinoma,0,1	AMACR	38	1	1	Substitution - Missense(1)	stomach(1)	c.G717T						PASS	.	C	HIS/GLN,HIS/GLN,PHE/VAL	310,4096	166.5+/-197.7	8,294,1901	119.0	109.0	113.0		717,717,556	3.3	1.0	5	dbSNP_76	113	1250,7350	250.8+/-277.5	84,1082,3134	yes	missense,missense,missense	AMACR	NM_001167595.1,NM_014324.5,NM_203382.2	24,24,50	92,1376,5035	AA,AC,CC		14.5349,7.0359,11.9945	probably-damaging,probably-damaging,probably-damaging	239/395,239/383,186/199	33998768	1560,11446	2203	4300	6503	SO:0001583	missense	23600	exon4			GTAGAACTGGGGT	AF047020	CCDS3902.1, CCDS3903.1, CCDS54836.1	5p13.2	2012-05-16			ENSG00000242110	ENSG00000242110	5.1.99.4		451	protein-coding gene	gene with protein product		604489				9307041	Standard	NM_014324		Approved	RACE	uc003jij.3	Q9UHK6	OTTHUMG00000090734	ENST00000335606.6:c.717G>T	5.37:g.33998768C>A	ENSP00000334424:p.Gln239His	Somatic	198	0	0		WXS	Illumina HiSeq	Phase_I	247	115	0.465587	NM_014324	A5YM47|B8Y916|B8Y918|F8W9N1|O43673|Q3KT79|Q96GH1|Q9Y3Q1	Missense_Mutation	SNP	ENST00000335606.6	37	CCDS3902.1	254|254	0.1163003663003663|0.1163003663003663	28|28	0.056910569105691054|0.056910569105691054	34|34	0.09392265193370165|0.09392265193370165	85|85	0.1486013986013986|0.1486013986013986	107|107	0.14116094986807387|0.14116094986807387	C|C	10.02|10.02	1.237003|1.237003	0.22711|0.22711	0.070359|0.070359	0.145349|0.145349	ENSG00000242110|ENSG00000242110	ENST00000335606;ENST00000382085;ENST00000502637|ENST00000382072;ENST00000441713	T;T;T|T;T	0.50813|0.69561	0.73;0.73;0.73|-0.33;-0.41	5.34|5.34	3.26|3.26	0.37387|0.37387	CoA-transferase family III domain (2);|.	0.052954|.	0.85682|.	D|.	0.000000|.	T|T	0.01029|0.01029	0.0034|0.0034	L|L	0.58101|0.58101	1.795|1.795	0.09310|0.09310	P|P	1.0|1.0	P;P;P;P|D;D	0.41710|0.71674	0.76;0.654;0.703;0.703|0.998;0.992	B;B;B;B|D;P	0.40134|0.70487	0.275;0.287;0.32;0.32|0.969;0.9	T|T	0.37244|0.37244	-0.9714|-0.9714	9|8	0.66056|0.38643	D|T	0.02|0.18	-18.029|-18.029	8.5827|8.5827	0.33640|0.33640	0.0:0.6599:0.0:0.3401|0.0:0.6599:0.0:0.3401	rs34677;rs52819324;rs60234651;rs34677|rs34677;rs52819324;rs60234651;rs34677	239;239;224;239|186;186	B3KMU8;F8W9N1;D6RB81;Q9UHK6|Q6VRU4;Q9UHK6-4	.;.;.;AMACR_HUMAN|.;.	H|F	239;239;224|186	ENSP00000334424:Q239H;ENSP00000371517:Q239H;ENSP00000424351:Q224H|ENSP00000371504:V186F;ENSP00000403800:V186F	ENSP00000334424:Q239H|ENSP00000371504:V186F	Q|V	-|-	3|1	2|0	AMACR|AMACR	34034525|34034525	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.391000|0.391000	0.30476|0.30476	1.867000|1.867000	0.39499|0.39499	1.000000|1.000000	0.39049|0.39049	0.563000|0.563000	0.77884|0.77884	CAG|GTT	T|0.007;G|0.005	.	strong		0.478	AMACR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207467.1	NM_014324	
TLN2	83660	hgsc.bcm.edu	37	15	62939591	62939591	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:62939591T>C	ENST00000561311.1	+	3	312	c.82T>C	c.(82-84)Tac>Cac	p.Y28H	RP11-625H11.1_ENST00000558940.1_5'Flank|RP11-625H11.1_ENST00000560347.1_5'Flank|TLN2_ENST00000306829.6_Missense_Mutation_p.Y28H			Q9Y4G6	TLN2_HUMAN	talin 2	28					cell adhesion (GO:0007155)|cell-cell junction assembly (GO:0007043)|cytoskeletal anchoring at plasma membrane (GO:0007016)	actin cytoskeleton (GO:0015629)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|synapse (GO:0045202)	actin binding (GO:0003779)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			NS(3)|breast(6)|central_nervous_system(3)|endometrium(8)|kidney(8)|large_intestine(20)|lung(34)|ovary(6)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)	99						TACAGCTGTGTACGATGCGTG	0.493																																					p.Y28H		Atlas-SNP	.											.	TLN2	253	.	0			c.T82C						PASS	.						217.0	191.0	200.0					15																	62939591		2203	4300	6503	SO:0001583	missense	83660	exon1			GCTGTGTACGATG	AB002318	CCDS32261.1	15q15-q21	2008-07-03			ENSG00000171914	ENSG00000171914			15447	protein-coding gene	gene with protein product		607349				9205841, 11527381	Standard	NM_015059		Approved	KIAA0320, ILWEQ	uc002alb.4	Q9Y4G6	OTTHUMG00000133679	ENST00000561311.1:c.82T>C	15.37:g.62939591T>C	ENSP00000453508:p.Tyr28His	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	110	7	0.0636364	NM_015059	A6NLB8	Missense_Mutation	SNP	ENST00000561311.1	37	CCDS32261.1	.	.	.	.	.	.	.	.	.	.	T	14.05	2.420151	0.42918	.	.	ENSG00000171914	ENST00000306829	T	0.69561	-0.41	5.5	5.5	0.81552	.	0.000000	0.85682	D	0.000000	T	0.77239	0.4101	L	0.51914	1.62	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.76724	-0.2854	10	0.42905	T	0.14	-10.8689	15.0808	0.72113	0.0:0.0:0.0:1.0	.	28	Q9Y4G6	TLN2_HUMAN	H	28	ENSP00000303476:Y28H	ENSP00000303476:Y28H	Y	+	1	0	TLN2	60726883	1.000000	0.71417	0.970000	0.41538	0.108000	0.19459	7.988000	0.88194	2.219000	0.72066	0.533000	0.62120	TAC	.	.	none		0.493	TLN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257878.2		
PHIP	55023	hgsc.bcm.edu	37	6	79656570	79656570	+	Silent	SNP	G	G	A	rs2275290	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:79656570G>A	ENST00000275034.4	-	37	4395	c.4228C>T	c.(4228-4230)Ctg>Ttg	p.L1410L	PHIP_ENST00000479165.1_5'UTR	NM_017934.5	NP_060404	Q8WWQ0	PHIP_HUMAN	pleckstrin homology domain interacting protein	1410					cytoskeleton organization (GO:0007010)|insulin receptor signaling pathway (GO:0008286)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of mitosis (GO:0045840)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein import into nucleus (GO:0006606)|regulation of cell morphogenesis (GO:0022604)|regulation of growth (GO:0040008)|regulation of protein phosphorylation (GO:0001932)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	insulin receptor binding (GO:0005158)|lysine-acetylated histone binding (GO:0070577)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(10)|kidney(4)|large_intestine(20)|lung(20)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	68		all_cancers(76;0.00125)|Acute lymphoblastic leukemia(125;1.1e-05)|all_hematologic(105;0.00117)|all_epithelial(107;0.219)		BRCA - Breast invasive adenocarcinoma(397;0.231)		AAAGCAGACAGGCGCAAACTC	0.328													G|||	1393	0.278155	0.3359	0.317	5008	,	,		15389	0.1855		0.3688	False		,,,				2504	0.1748				p.L1410L		Atlas-SNP	.											.	PHIP	177	.	0			c.C4228T						PASS	.	G		1502,2904	450.8+/-349.5	255,992,956	61.0	62.0	62.0		4228	2.9	0.6	6	dbSNP_100	62	2994,5606	455.9+/-363.9	524,1946,1830	no	coding-synonymous	PHIP	NM_017934.5		779,2938,2786	AA,AG,GG		34.814,34.0899,34.5687		1410/1822	79656570	4496,8510	2203	4300	6503	SO:0001819	synonymous_variant	55023	exon37			CAGACAGGCGCAA	AF310250	CCDS4987.1	6q14	2013-01-09			ENSG00000146247	ENSG00000146247		"""WD repeat domain containing"", ""DDB1 and CUL4 associated factors"""	15673	protein-coding gene	gene with protein product	"""DDB1 and CUL4 associated factor 14"""	612870		WDR11		11018022	Standard	NM_017934		Approved	ndrp, FLJ20705, DCAF14, BRWD2	uc003pir.3	Q8WWQ0	OTTHUMG00000015071	ENST00000275034.4:c.4228C>T	6.37:g.79656570G>A		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	60	60	1	NM_017934	A7J992|B2RPK4|Q05CQ9|Q5VVH4|Q66I29|Q69YV1|Q8NBZ5|Q96H52|Q96ME2|Q9H261	Silent	SNP	ENST00000275034.4	37	CCDS4987.1																																																																																			G|0.674;A|0.326	0.326	strong		0.328	PHIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041297.2		
CCDC168	643677	hgsc.bcm.edu	37	13	103384712	103384712	+	Missense_Mutation	SNP	G	G	A	rs17507827	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:103384712G>A	ENST00000322527.2	-	1	4447	c.4448C>T	c.(4447-4449)aCg>aTg	p.T1483M		NM_001146197.1	NP_001139669.1	Q8NDH2	CC168_HUMAN	coiled-coil domain containing 168	1483			T -> M (in dbSNP:rs17507827).														ACCACGCCCCGTGATATTAAG	0.348													G|||	87	0.0173722	0.0023	0.0173	5008	,	,		19185	0.001		0.0249	False		,,,				2504	0.047				p.T6112M		Atlas-SNP	.											.	.	.	.	0			c.C18335T						PASS	.	G	MET/THR	2,1382		0,2,690	187.0	149.0	160.0		18335	-0.7	0.0	13	dbSNP_123	160	61,3119		2,57,1531	yes	missense	CCDC168	NM_001146197.1	81	2,59,2221	AA,AG,GG		1.9182,0.1445,1.3804	possibly-damaging	6112/7082	103384712	63,4501	692	1590	2282	SO:0001583	missense	643677	exon4			CGCCCCGTGATAT		CCDS73596.1	13q33.1	2014-06-17	2011-08-09	2011-08-09	ENSG00000175820	ENSG00000175820			26851	protein-coding gene	gene with protein product			"""chromosome 13 open reading frame 40"""	C13orf40			Standard	NM_001146197		Approved	FLJ40176	uc001vpm.3	Q8NDH2	OTTHUMG00000187287	ENST00000322527.2:c.4448C>T	13.37:g.103384712G>A	ENSP00000320232:p.Thr1483Met	Somatic	207	1	0.00483092		WXS	Illumina HiSeq	Phase_I	190	95	0.5	NM_001146197	Q8N800	Missense_Mutation	SNP	ENST00000322527.2	37		30	0.013736263736263736	3	0.006097560975609756	6	0.016574585635359115	0	0.0	21	0.027704485488126648	G	12.04	1.819103	0.32145	0.001445	0.019182	ENSG00000175820	ENST00000322527	T	0.03745	3.82	3.31	-0.667	0.11395	.	.	.	.	.	T	0.00580	0.0019	N	0.14661	0.345	0.09310	N	1	P	0.47350	0.894	B	0.34180	0.177	T	0.44452	-0.9327	9	0.72032	D	0.01	.	0.6482	0.00822	0.2357:0.1909:0.378:0.1953	rs17507827;rs52826516;rs17507827	1483	Q8NDH2	CC168_HUMAN	M	1483	ENSP00000320232:T1483M	ENSP00000320232:T1483M	T	-	2	0	CCDC168	102182713	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.416000	0.07097	-0.190000	0.10465	-1.136000	0.01936	ACG	G|0.983;A|0.017	0.017	strong		0.348	CCDC168-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001146197	
NUP214	8021	hgsc.bcm.edu	37	9	134073622	134073622	+	Missense_Mutation	SNP	G	G	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:134073622G>C	ENST00000359428.5	+	29	4885	c.4741G>C	c.(4741-4743)Gca>Cca	p.A1581P	NUP214_ENST00000451030.1_Missense_Mutation_p.A1582P|NUP214_ENST00000483497.2_Missense_Mutation_p.A407P|NUP214_ENST00000411637.2_Missense_Mutation_p.A1571P			P35658	NU214_HUMAN	nucleoporin 214kDa	1581	11 X 3 AA approximate repeats.|11 X 5 AA approximate repeats.|18 X 4 AA approximate repeats.|Pro/Ser/Thr-rich.				carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|gene expression (GO:0010467)|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)|mRNA metabolic process (GO:0016071)|protein export from nucleus (GO:0006611)|protein import into nucleus (GO:0006606)|regulation of cell cycle (GO:0051726)|regulation of glucose transport (GO:0010827)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|focal adhesion (GO:0005925)|intracellular membrane-bounded organelle (GO:0043231)|nuclear pore (GO:0005643)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleocytoplasmic transporter activity (GO:0005487)|transporter activity (GO:0005215)			NS(1)|breast(9)|central_nervous_system(3)|endometrium(13)|kidney(2)|large_intestine(9)|liver(2)|lung(29)|ovary(2)|prostate(3)|skin(7)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	86	all_hematologic(7;0.0028)	Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;3.42e-05)|Epithelial(140;0.000256)		CAGGACGGAGGCAGTACCACC	0.572			T	"""DEK, SET, ABL1"""	"""AML, T-ALL"""																																p.A1581P	Pancreas(4;24 48 25510 30394 32571)	Atlas-SNP	.		Dom	yes		9	9q34.1	8021	nucleoporin 214kDa (CAN)		L	.	NUP214	166	.	0			c.G4741C						PASS	.						75.0	78.0	77.0					9																	134073622		2203	4300	6503	SO:0001583	missense	8021	exon29			ACGGAGGCAGTAC	X64228	CCDS6940.1	9q34	2008-07-21	2002-08-29		ENSG00000126883	ENSG00000126883			8064	protein-coding gene	gene with protein product	"""nuclear pore complex protein Nup214"", ""CAN protein, putative oncogene"""	114350	"""nucleoporin 214kD (CAIN)"""			8108440, 2370860	Standard	NM_005085		Approved	CAIN, CAN, D9S46E, N214	uc004cag.3	P35658	OTTHUMG00000020816	ENST00000359428.5:c.4741G>C	9.37:g.134073622G>C	ENSP00000352400:p.Ala1581Pro	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	106	30	0.283019	NM_005085	A6NFQ0|Q15010|Q3KQZ0|Q5JUP7|Q75R47|Q86XD3	Missense_Mutation	SNP	ENST00000359428.5	37	CCDS6940.1	.	.	.	.	.	.	.	.	.	.	G	12.61	1.989651	0.35131	.	.	ENSG00000126883	ENST00000359428;ENST00000411637;ENST00000451030;ENST00000541375;ENST00000540899;ENST00000438605;ENST00000483497;ENST00000531600;ENST00000541688	T;T;T;T;T	0.50277	0.96;0.79;0.79;0.79;0.75	5.44	2.63	0.31362	.	0.924894	0.08948	N	0.870525	T	0.26593	0.0650	N	0.08118	0	0.09310	N	1	B;B;B;B;B	0.10296	0.001;0.001;0.001;0.001;0.003	B;B;B;B;B	0.11329	0.006;0.003;0.003;0.003;0.004	T	0.26503	-1.0101	10	0.22109	T	0.4	-0.1467	7.7656	0.28978	0.0:0.1889:0.4379:0.3732	.	407;1010;1175;1571;1581	B7ZAV2;F5H131;Q5JUP9;P35658-4;P35658	.;.;.;.;NU214_HUMAN	P	1581;1571;1582;1560;1175;1010;407;358;358	ENSP00000352400:A1581P;ENSP00000396576:A1571P;ENSP00000405014:A1582P;ENSP00000436793:A407P;ENSP00000435364:A358P	ENSP00000352400:A1581P	A	+	1	0	NUP214	133063443	0.000000	0.05858	0.033000	0.17914	0.128000	0.20619	-0.086000	0.11233	0.285000	0.22329	-0.475000	0.04921	GCA	.	.	none		0.572	NUP214-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000054694.2	NM_005085	
MKLN1	4289	hgsc.bcm.edu	37	7	131082040	131082040	+	Missense_Mutation	SNP	T	T	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:131082040T>A	ENST00000352689.6	+	5	455	c.415T>A	c.(415-417)Tgg>Agg	p.W139R	MKLN1_ENST00000421797.2_Missense_Mutation_p.W47R|MKLN1_ENST00000429546.1_Missense_Mutation_p.W47R	NM_013255.4	NP_037387.2	Q9UL63	MKLN1_HUMAN	muskelin 1, intracellular mediator containing kelch motifs	139					signal transduction (GO:0007165)	cytoplasm (GO:0005737)				breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(10)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	28	Melanoma(18;0.162)					ACTCTTGTCCTGGGGACCCAG	0.358																																					p.W139R		Atlas-SNP	.											MKLN1,NS,carcinoma,-1,1	MKLN1	67	1	0			c.T415A						scavenged	.						131.0	119.0	123.0					7																	131082040		2203	4300	6503	SO:0001583	missense	4289	exon5			TTGTCCTGGGGAC	AF047489	CCDS34754.1	7q32	2008-07-18			ENSG00000128585	ENSG00000128585			7109	protein-coding gene	gene with protein product		605623				10640805	Standard	NM_001145354		Approved	TWA2	uc011kpm.2	Q9UL63	OTTHUMG00000154880	ENST00000352689.6:c.415T>A	7.37:g.131082040T>A	ENSP00000323527:p.Trp139Arg	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	114	3	0.0263158	NM_013255	A4D1M8|A6NG43|Q9NSK4|Q9NUS8	Missense_Mutation	SNP	ENST00000352689.6	37	CCDS34754.1	.	.	.	.	.	.	.	.	.	.	T	17.17	3.320313	0.60634	.	.	ENSG00000128585	ENST00000421797;ENST00000416992;ENST00000429546;ENST00000446815;ENST00000352689	T;D;D;D	0.97575	1.81;-4.44;-4.44;-4.44	6.16	6.16	0.99307	Muskelin, N-terminal (1);Galactose-binding domain-like (1);	0.000000	0.85682	D	0.000000	D	0.97911	0.9313	L	0.60845	1.875	0.80722	D	1	P;D;D	0.89917	0.929;1.0;1.0	P;D;D	0.97110	0.763;1.0;1.0	D	0.98427	1.0580	10	0.54805	T	0.06	-7.3526	15.9872	0.80168	0.0:0.0:0.0:1.0	.	139;116;47	Q9UL63;B4DG30;C9J7E8	MKLN1_HUMAN;.;.	R	47;47;47;47;139	ENSP00000398094:W47R;ENSP00000399954:W47R;ENSP00000412815:W47R;ENSP00000323527:W139R	ENSP00000323527:W139R	W	+	1	0	MKLN1	130732580	1.000000	0.71417	0.997000	0.53966	0.337000	0.28794	8.040000	0.89188	2.367000	0.80283	0.528000	0.53228	TGG	.	.	none		0.358	MKLN1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000337473.4	NM_013255	
REST	5978	hgsc.bcm.edu	37	4	57796900	57796900	+	Missense_Mutation	SNP	G	G	A	rs2228991	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:57796900G>A	ENST00000309042.7	+	4	2190	c.1876G>A	c.(1876-1878)Gtt>Att	p.V626I		NM_001193508.1|NM_005612.4	NP_001180437.1|NP_005603.3	Q13127	REST_HUMAN	RE1-silencing transcription factor	626	Pro-rich.		V -> I (in dbSNP:rs2228991). {ECO:0000269|PubMed:15489334}.		cardiac muscle cell myoblast differentiation (GO:0060379)|cellular response to drug (GO:0035690)|cellular response to electrical stimulus (GO:0071257)|cellular response to glucocorticoid stimulus (GO:0071385)|hematopoietic progenitor cell differentiation (GO:0002244)|histone H4 deacetylation (GO:0070933)|negative regulation by host of viral transcription (GO:0043922)|negative regulation of aldosterone biosynthetic process (GO:0032348)|negative regulation of amniotic stem cell differentiation (GO:2000798)|negative regulation of calcium ion-dependent exocytosis (GO:0045955)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cortisol biosynthetic process (GO:2000065)|negative regulation of dense core granule biogenesis (GO:2000706)|negative regulation of gene expression (GO:0010629)|negative regulation of insulin secretion (GO:0046676)|negative regulation of mesenchymal stem cell differentiation (GO:2000740)|negative regulation of neurogenesis (GO:0050768)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of transcription, DNA-templated (GO:0045893)|potassium ion transmembrane transport (GO:0071805)|regulation of transcription, DNA-templated (GO:0006355)	cytosol (GO:0005829)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|core promoter binding (GO:0001047)|core promoter sequence-specific DNA binding (GO:0001046)|metal ion binding (GO:0046872)|outward rectifier potassium channel activity (GO:0015271)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(2)|lung(22)|ovary(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	50	Glioma(25;0.08)|all_neural(26;0.181)					GAAGGGGCCCGTTCAGGTGGA	0.607													G|||	597	0.119209	0.1263	0.2522	5008	,	,		15051	0.2024		0.0328	False		,,,				2504	0.0184				p.V626I		Atlas-SNP	.											.	REST	104	.	0			c.G1876A						PASS	.	G	ILE/VAL,ILE/VAL	527,3873		28,471,1701	22.0	25.0	24.0		1876,1876	-5.2	0.0	4	dbSNP_98	24	348,8236		10,328,3954	yes	missense,missense	REST	NM_001193508.1,NM_005612.4	29,29	38,799,5655	AA,AG,GG		4.0541,11.9773,6.7391	benign,benign	626/1098,626/1098	57796900	875,12109	2200	4292	6492	SO:0001583	missense	5978	exon4			GGGCCCGTTCAGG	U13879	CCDS3509.1	4q12	2008-02-05			ENSG00000084093	ENSG00000084093			9966	protein-coding gene	gene with protein product		600571				7871435, 7697725	Standard	NM_005612		Approved	NRSF, XBR	uc003hci.3	Q13127	OTTHUMG00000128770	ENST00000309042.7:c.1876G>A	4.37:g.57796900G>A	ENSP00000311816:p.Val626Ile	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	100	46	0.46	NM_001193508	A2RUE0|B9EGJ0|Q12956|Q12957|Q13134|Q59ER1|Q8IWI3	Missense_Mutation	SNP	ENST00000309042.7	37	CCDS3509.1	291	0.13324175824175824	53	0.10772357723577236	84	0.23204419889502761	133	0.23251748251748253	21	0.027704485488126648	G	9.343	1.063647	0.20067	0.119773	0.040541	ENSG00000084093	ENST00000309042;ENST00000358605	T	0.07327	3.2	4.0	-5.2	0.02823	.	1.058360	0.07544	N	0.914444	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B;B	0.24675	0.109;0.017	B;B	0.12156	0.007;0.003	T	0.48768	-0.9006	9	0.25751	T	0.34	.	2.1845	0.03883	0.2238:0.3785:0.2704:0.1273	rs2228991;rs3733302;rs58607248;rs2228991	603;626	F8WAN5;Q13127	.;REST_HUMAN	I	626;603	ENSP00000311816:V626I	ENSP00000311816:V626I	V	+	1	0	REST	57491657	0.000000	0.05858	0.000000	0.03702	0.013000	0.08279	-0.254000	0.08781	-0.804000	0.04410	-0.315000	0.08773	GTT	G|0.906;A|0.094	0.094	strong		0.607	REST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250691.2	NM_005612	
CCDC110	256309	hgsc.bcm.edu	37	4	186380846	186380846	+	Missense_Mutation	SNP	A	A	T	rs7698680	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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_ENST00000393540.3_Missense_Mutation_p.L262M|CCDC110_ENST00000507501.1_5'Flank	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	82	0	0		WXS	Illumina HiSeq	Phase_I	79	32	0.405063	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	
GATA5	140628	hgsc.bcm.edu	37	20	61040453	61040453	+	Silent	SNP	C	C	G	rs6061243	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:61040453C>G	ENST00000252997.2	-	6	1042	c.981G>C	c.(979-981)tcG>tcC	p.S327S		NM_080473.4	NP_536721.1	Q9BWX5	GATA5_HUMAN	GATA binding protein 5	327					blood coagulation (GO:0007596)|cellular response to BMP stimulus (GO:0071773)|intestinal epithelial cell differentiation (GO:0060575)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	enhancer sequence-specific DNA binding (GO:0001158)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			kidney(1)|lung(3)|ovary(1)|stomach(1)	6	Breast(26;2.05e-08)		BRCA - Breast invasive adenocarcinoma(19;3.08e-06)			GCTTGGCTTTCGAAGTGGCTG	0.672													C|||	2677	0.534545	0.7171	0.4755	5008	,	,		12861	0.4613		0.4642	False		,,,				2504	0.4775				p.S327S		Atlas-SNP	.											GATA5,NS,carcinoma,-1,1	GATA5	22	1	0			c.G981C						PASS	.	C		2852,1552		949,954,299	29.0	30.0	30.0		981	2.8	0.0	20	dbSNP_114	30	4161,4435		1004,2153,1141	no	coding-synonymous	GATA5	NM_080473.4		1953,3107,1440	GG,GC,CC		48.4062,35.2407,46.0538		327/398	61040453	7013,5987	2202	4298	6500	SO:0001819	synonymous_variant	140628	exon6			GGCTTTCGAAGTG	BC047790, BC117356	CCDS13499.1	20q13.33	2013-07-17	2001-11-28		ENSG00000130700	ENSG00000130700		"""GATA zinc finger domain containing"""	15802	protein-coding gene	gene with protein product		611496	"""GATA-binding protein 5"""			9566909	Standard	NM_080473		Approved	bB379O24.1, GATAS	uc002ycx.1	Q9BWX5	OTTHUMG00000032919	ENST00000252997.2:c.981G>C	20.37:g.61040453C>G		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	45	31	0.688889	NM_080473	D9ZGF7|Q17RE2|Q86VU4	Silent	SNP	ENST00000252997.2	37	CCDS13499.1																																																																																			C|0.467;G|0.533	0.533	strong		0.672	GATA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080038.2	NM_080473	
GRAMD1A	57655	hgsc.bcm.edu	37	19	35504539	35504539	+	Missense_Mutation	SNP	C	C	T	rs201394899		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:35504539C>T	ENST00000317991.5	+	9	1006	c.814C>T	c.(814-816)Cgc>Tgc	p.R272C	CTD-2527I21.14_ENST00000605640.1_RNA|GRAMD1A_ENST00000599564.1_Missense_Mutation_p.R359C|GRAMD1A_ENST00000504615.2_Missense_Mutation_p.R38C|GRAMD1A_ENST00000411896.2_Missense_Mutation_p.R265C	NM_020895.3	NP_065946.2	Q96CP6	GRM1A_HUMAN	GRAM domain containing 1A	272						integral component of membrane (GO:0016021)				NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(10)|prostate(1)|upper_aerodigestive_tract(1)	19	all_lung(56;2.66e-08)|Lung NSC(56;4.13e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0849)			AGTGGGTTCGCGCCGTGGCCA	0.647																																					p.R272C		Atlas-SNP	.											.	GRAMD1A	39	.	0			c.C814T						PASS	.	C	CYS/ARG,CYS/ARG	2,4180		0,2,2089	26.0	31.0	29.0		793,814	2.5	0.2	19		29	9,8429		0,9,4210	yes	missense,missense	GRAMD1A	NM_001136199.1,NM_020895.3	180,180	0,11,6299	TT,TC,CC		0.1067,0.0478,0.0872	probably-damaging,probably-damaging	265/714,272/725	35504539	11,12609	2091	4219	6310	SO:0001583	missense	57655	exon9			GGTTCGCGCCGTG	AK074864	CCDS42546.1, CCDS46046.1	19q13.13	2008-02-05	2005-11-02	2005-11-02		ENSG00000089351			29305	protein-coding gene	gene with protein product			"""KIAA1533"""	KIAA1533		10819331	Standard	NM_020895		Approved	FLJ90346	uc010xse.1	Q96CP6		ENST00000317991.5:c.814C>T	19.37:g.35504539C>T	ENSP00000441032:p.Arg272Cys	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	101	57	0.564356	NM_020895	A6NKY7|Q8NC77|Q9P1Z5	Missense_Mutation	SNP	ENST00000317991.5	37	CCDS42546.1	.	.	.	.	.	.	.	.	.	.	C	11.00	1.509632	0.27036	4.78E-4	0.001067	ENSG00000089351	ENST00000453966;ENST00000504615;ENST00000317991;ENST00000411896	T;T;T	0.52754	0.65;1.91;1.9	4.71	2.5	0.30297	.	0.934879	0.09007	N	0.862100	T	0.52289	0.1725	L	0.29908	0.895	0.09310	N	0.999997	P;D;D;D;P	0.76494	0.675;0.975;0.993;0.999;0.575	B;B;P;D;B	0.65987	0.039;0.249;0.616;0.94;0.068	T	0.37267	-0.9713	10	0.59425	D	0.04	.	6.9609	0.24597	0.1794:0.726:0.0:0.0946	.	272;272;38;265;359	Q96CP6-3;Q96CP6;B3KQF7;Q96CP6-2;F5GZ02	.;GRM1A_HUMAN;.;.;.	C	359;38;272;265	ENSP00000423728:R38C;ENSP00000441032:R272C;ENSP00000439267:R265C	ENSP00000441032:R272C	R	+	1	0	GRAMD1A	40196379	0.680000	0.27605	0.169000	0.22859	0.103000	0.19146	1.547000	0.36190	0.542000	0.28846	0.485000	0.47835	CGC	.	.	weak		0.647	GRAMD1A-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000461557.1	NM_020895	
VSIG10	54621	hgsc.bcm.edu	37	12	118506186	118506186	+	Silent	SNP	A	A	T	rs67405503	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:118506186A>T	ENST00000359236.5	-	8	1839	c.1563T>A	c.(1561-1563)ctT>ctA	p.L521L		NM_019086.5	NP_061959.2	Q8N0Z9	VSI10_HUMAN	V-set and immunoglobulin domain containing 10	521						integral component of membrane (GO:0016021)				endometrium(5)|large_intestine(3)|lung(6)|skin(1)|stomach(1)|urinary_tract(1)	17						GCTTACCTTGAAGATCCTGGA	0.448													T|||	2110	0.421326	0.4516	0.4582	5008	,	,		18101	0.372		0.4036	False		,,,				2504	0.4233				p.L521L		Atlas-SNP	.											.	VSIG10	41	.	0			c.T1563A						PASS	.	T		1649,2181		344,961,610	187.0	183.0	184.0		1563	-8.2	0.3	12	dbSNP_130	184	3170,5072		618,1934,1569	no	coding-synonymous	VSIG10	NM_019086.5		962,2895,2179	TT,TA,AA		38.4615,43.0548,39.9188		521/541	118506186	4819,7253	1915	4121	6036	SO:0001819	synonymous_variant	54621	exon8			ACCTTGAAGATCC		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.1563T>A	12.37:g.118506186A>T		Somatic	243	0	0		WXS	Illumina HiSeq	Phase_I	219	102	0.465753	NM_019086	Q9NWQ7	Silent	SNP	ENST00000359236.5	37	CCDS44992.1																																																																																			A|0.602;T|0.398	0.398	strong		0.448	VSIG10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401273.2	NM_019086	
MUC7	4589	hgsc.bcm.edu	37	4	71346701	71346701	+	Missense_Mutation	SNP	C	C	G	rs6826961	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:71346701C>G	ENST00000304887.5	+	3	430	c.240C>G	c.(238-240)aaC>aaG	p.N80K	MUC7_ENST00000514512.1_3'UTR|MUC7_ENST00000456088.1_Missense_Mutation_p.N80K|MUC7_ENST00000413702.1_Missense_Mutation_p.N80K	NM_152291.2	NP_689504.2	Q8TAX7	MUC7_HUMAN	mucin 7, secreted	80			N -> K (in dbSNP:rs6826961).		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)			CACCTAATAACCCCCCCAAAT	0.458													C|||	1554	0.310304	0.2973	0.196	5008	,	,		20095	0.4077		0.2207	False		,,,				2504	0.4008				p.N80K		Atlas-SNP	.											.	MUC7	91	.	0			c.C240G						PASS	.	C	LYS/ASN,LYS/ASN,LYS/ASN	1322,3084	445.9+/-347.8	195,932,1076	122.0	120.0	121.0		240,240,240	-3.1	0.0	4	dbSNP_116	121	2029,6571	353.4+/-329.1	227,1575,2498	yes	missense,missense,missense	MUC7	NM_152291.2,NM_001145007.1,NM_001145006.1	94,94,94	422,2507,3574	GG,GC,CC		23.593,30.0045,25.765	benign,benign,benign	80/378,80/378,80/378	71346701	3351,9655	2203	4300	6503	SO:0001583	missense	4589	exon4			TAATAACCCCCCC	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.240C>G	4.37:g.71346701C>G	ENSP00000302021:p.Asn80Lys	Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	124	66	0.532258	NM_001145007	Q9UCD7|Q9UCD8	Missense_Mutation	SNP	ENST00000304887.5	37	CCDS3541.1	603	0.2760989010989011	144	0.2926829268292683	67	0.1850828729281768	216	0.3776223776223776	176	0.23218997361477572	C	0.004	-2.263479	0.00262	0.300045	0.23593	ENSG00000171195	ENST00000413702;ENST00000505411;ENST00000456088;ENST00000304887	T;T;T;T	0.52526	0.67;0.66;0.67;0.67	1.55	-3.1	0.05315	.	.	.	.	.	T	0.00012	0.0000	N	0.12182	0.205	0.80722	P	0.0	B	0.12630	0.006	B	0.10450	0.005	T	0.41787	-0.9489	8	0.11794	T	0.64	.	0.0984	0.00046	0.2439:0.1942:0.2126:0.3492	rs6826961;rs52803154;rs6826961	80	Q8TAX7	MUC7_HUMAN	K	80	ENSP00000407422:N80K;ENSP00000427594:N80K;ENSP00000400585:N80K;ENSP00000302021:N80K	ENSP00000302021:N80K	N	+	3	2	MUC7	71381290	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-3.185000	0.00567	-1.398000	0.02066	-0.344000	0.07964	AAC	C|0.738;G|0.262	0.262	strong		0.458	MUC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252168.2	NM_152291	
NOS1	4842	hgsc.bcm.edu	37	12	117669914	117669914	+	Silent	SNP	G	G	A	rs3741475	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:117669914G>A	ENST00000338101.4	-	22	3364	c.3360C>T	c.(3358-3360)gaC>gaT	p.D1120D	NOS1_ENST00000317775.6_Silent_p.D1086D|NOS1_ENST00000344089.3_3'UTR			Q8WY41	NANO1_HUMAN	nitric oxide synthase 1 (neuronal)	0					cell migration (GO:0016477)|epithelial cell migration (GO:0010631)|negative regulation of translation (GO:0017148)	cytoplasm (GO:0005737)|perinuclear region of cytoplasm (GO:0048471)	RNA binding (GO:0003723)|translation repressor activity (GO:0030371)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(17)|large_intestine(21)|lung(43)|ovary(3)|pancreas(1)|prostate(6)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	117	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.0561)		GGCGGAGCTCGTCTGTCCAGT	0.607													G|||	1294	0.258387	0.2821	0.2118	5008	,	,		6092	0.3304		0.2137	False		,,,				2504	0.2311				p.D1120D	Esophageal Squamous(162;1748 2599 51982 52956)	Atlas-SNP	.											NOS1,colon,carcinoma,0,1	NOS1	240	1	0			c.C3360T						PASS	.	G	,,,	1041,3247		136,769,1239	62.0	69.0	67.0		3258,2250,2250,3360	-5.2	0.7	12	dbSNP_107	67	1712,6796		187,1338,2729	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NOS1	NM_000620.4,NM_001204213.1,NM_001204214.1,NM_001204218.1	,,,	323,2107,3968	AA,AG,GG		20.1222,24.2771,21.5145	,,,	1086/1435,750/1099,750/1099,1120/1469	117669914	2753,10043	2144	4254	6398	SO:0001819	synonymous_variant	4842	exon23			GAGCTCGTCTGTC		CCDS41842.1, CCDS55890.1	12q24.22	2013-09-19			ENSG00000089250	ENSG00000089250	1.14.13.39		7872	protein-coding gene	gene with protein product		163731		NOS		1385308, 7682706	Standard	NM_001204213		Approved	nNOS	uc001twn.2	P29475	OTTHUMG00000137376	ENST00000338101.4:c.3360C>T	12.37:g.117669914G>A		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	109	56	0.513761	NM_001204218		Silent	SNP	ENST00000338101.4	37	CCDS55890.1																																																																																			G|0.747;A|0.253	0.253	strong		0.607	NOS1-002	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000268053.1		
RBP3	5949	hgsc.bcm.edu	37	10	48388508	48388508	+	Silent	SNP	G	G	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:48388508G>C	ENST00000224600.4	-	1	2483	c.2370C>G	c.(2368-2370)tcC>tcG	p.S790S	AL731561.2_ENST00000581861.1_RNA	NM_002900.2	NP_002891.1	P10745	RET3_HUMAN	retinol binding protein 3, interstitial	790	4 X approximate tandem repeats.				lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|transport (GO:0006810)|visual perception (GO:0007601)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|interphotoreceptor matrix (GO:0033165)|vesicle (GO:0031982)	retinal binding (GO:0016918)|retinoid binding (GO:0005501)|retinol binding (GO:0019841)|serine-type peptidase activity (GO:0008236)			central_nervous_system(3)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(30)|ovary(1)|prostate(7)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	59					Vitamin A(DB00162)	GGATGGCCGTGGAGTAGCTGC	0.617																																					p.S790S		Atlas-SNP	.											.	RBP3	152	.	0			c.C2370G						PASS	.						28.0	26.0	27.0					10																	48388508		2201	4298	6499	SO:0001819	synonymous_variant	5949	exon1			GGCCGTGGAGTAG	M22453	CCDS73119.1	10q11.2	2014-05-06	2001-11-28		ENSG00000107618	ENSG00000265203			9921	protein-coding gene	gene with protein product		180290	"""retinol-binding protein 3, interstitial"""				Standard	NM_002900		Approved	D10S64, D10S65, D10S66, RP66	uc001jez.3	P10745	OTTHUMG00000188321	ENST00000224600.4:c.2370C>G	10.37:g.48388508G>C		Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	144	60	0.416667	NM_002900	Q0QD34|Q5VSR0|Q8IXN0	Silent	SNP	ENST00000224600.4	37	CCDS7218.1																																																																																			.	.	none		0.617	RBP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047888.1	NM_002900	
NOTCH1	4851	hgsc.bcm.edu	37	9	139413908	139413908	+	Silent	SNP	C	C	T	rs2229975	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:139413908C>T	ENST00000277541.6	-	5	927	c.852G>A	c.(850-852)ccG>ccA	p.P284P	MIR4673_ENST00000584777.1_RNA	NM_017617.3	NP_060087.3	P46531	NOTC1_HUMAN	notch 1	284	EGF-like 7; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				anagen (GO:0042640)|aortic valve morphogenesis (GO:0003180)|apoptotic process involved in embryonic digit morphogenesis (GO:1902263)|arterial endothelial cell differentiation (GO:0060842)|atrioventricular node development (GO:0003162)|atrioventricular valve morphogenesis (GO:0003181)|auditory receptor cell fate commitment (GO:0009912)|axonogenesis (GO:0007409)|branching morphogenesis of an epithelial tube (GO:0048754)|cardiac atrium morphogenesis (GO:0003209)|cardiac chamber formation (GO:0003207)|cardiac epithelial to mesenchymal transition (GO:0060317)|cardiac left ventricle morphogenesis (GO:0003214)|cardiac muscle cell proliferation (GO:0060038)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac right atrium morphogenesis (GO:0003213)|cardiac right ventricle formation (GO:0003219)|cardiac septum morphogenesis (GO:0060411)|cardiac vascular smooth muscle cell development (GO:0060948)|cardiac ventricle morphogenesis (GO:0003208)|cell fate specification (GO:0001708)|cell migration involved in endocardial cushion formation (GO:0003273)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|cilium morphogenesis (GO:0060271)|collecting duct development (GO:0072044)|compartment pattern specification (GO:0007386)|coronary artery morphogenesis (GO:0060982)|coronary vein morphogenesis (GO:0003169)|determination of left/right symmetry (GO:0007368)|distal tubule development (GO:0072017)|embryonic hindlimb morphogenesis (GO:0035116)|endocardial cell differentiation (GO:0060956)|endocardial cushion morphogenesis (GO:0003203)|endocardium development (GO:0003157)|endocardium morphogenesis (GO:0003160)|endoderm development (GO:0007492)|epithelial to mesenchymal transition (GO:0001837)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|forebrain development (GO:0030900)|foregut morphogenesis (GO:0007440)|gene expression (GO:0010467)|glial cell differentiation (GO:0010001)|glomerular mesangial cell development (GO:0072144)|growth involved in heart morphogenesis (GO:0003241)|hair follicle morphogenesis (GO:0031069)|heart development (GO:0007507)|heart looping (GO:0001947)|heart trabecula morphogenesis (GO:0061384)|humoral immune response (GO:0006959)|immune response (GO:0006955)|in utero embryonic development (GO:0001701)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-4 secretion (GO:0072602)|keratinocyte differentiation (GO:0030216)|left/right axis specification (GO:0070986)|liver development (GO:0001889)|lung development (GO:0030324)|mesenchymal cell development (GO:0014031)|mitral valve formation (GO:0003192)|negative regulation of anoikis (GO:2000811)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of calcium ion-dependent exocytosis (GO:0045955)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cell migration involved in sprouting angiogenesis (GO:0090051)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of endothelial cell chemotaxis (GO:2001027)|negative regulation of glial cell proliferation (GO:0060253)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of neurogenesis (GO:0050768)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of ossification (GO:0030279)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of photoreceptor cell differentiation (GO:0046533)|negative regulation of pro-B cell differentiation (GO:2000974)|negative regulation of stem cell differentiation (GO:2000737)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube development (GO:0021915)|neuronal stem cell maintenance (GO:0097150)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|Notch signaling pathway involved in regulation of secondary heart field cardioblast proliferation (GO:0003270)|pericardium morphogenesis (GO:0003344)|positive regulation of apoptotic process (GO:0043065)|positive regulation of astrocyte differentiation (GO:0048711)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061419)|positive regulation of transcription of Notch receptor target (GO:0007221)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland epithelium morphogenesis (GO:0060740)|pulmonary valve morphogenesis (GO:0003184)|regulation of epithelial cell proliferation involved in prostate gland development (GO:0060768)|regulation of extracellular matrix assembly (GO:1901201)|regulation of somitogenesis (GO:0014807)|regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation (GO:0003256)|regulation of transcription, DNA-templated (GO:0006355)|response to muramyl dipeptide (GO:0032495)|secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development (GO:0060528)|skeletal muscle cell differentiation (GO:0035914)|somatic stem cell division (GO:0048103)|sprouting angiogenesis (GO:0002040)|transcription initiation from RNA polymerase II promoter (GO:0006367)|tube formation (GO:0035148)|vasculogenesis involved in coronary vascular morphogenesis (GO:0060979)|venous endothelial cell differentiation (GO:0060843)|ventricular septum morphogenesis (GO:0060412)|ventricular trabecula myocardium morphogenesis (GO:0003222)	cell surface (GO:0009986)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|MAML1-RBP-Jkappa- ICN1 complex (GO:0002193)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)|receptor activity (GO:0004872)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(16)|central_nervous_system(17)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1183)|kidney(4)|large_intestine(1)|lung(57)|oesophagus(2)|ovary(3)|pancreas(1)|prostate(3)|skin(21)|upper_aerodigestive_tract(39)|urinary_tract(3)	1359	all_cancers(76;0.223)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;5.34e-06)|Epithelial(140;7.77e-06)		TCCACTCTGGCGGGCAGCGGC	0.617			"""T, Mis, O"""	TRB@	T-ALL					HNSCC(8;0.001)			C|||	612	0.122204	0.087	0.0793	5008	,	,		16798	0.0962		0.1163	False		,,,				2504	0.2331				p.P284P		Atlas-SNP	.		Dom	yes		9	9q34.3	4851	"""Notch homolog 1, translocation-associated (Drosophila) (TAN1)"""		L	.	NOTCH1	1980	.	0			c.G852A						PASS	.	C		400,3480		29,342,1569	54.0	68.0	64.0		852	-10.4	0.0	9	dbSNP_98	64	1122,7160		75,972,3094	no	coding-synonymous	NOTCH1	NM_017617.3		104,1314,4663	TT,TC,CC		13.5475,10.3093,12.5144		284/2556	139413908	1522,10640	1940	4141	6081	SO:0001819	synonymous_variant	4851	exon5			CTCTGGCGGGCAG	AF308602	CCDS43905.1	9q34.3	2013-01-10	2010-06-24		ENSG00000148400	ENSG00000148400		"""Ankyrin repeat domain containing"""	7881	protein-coding gene	gene with protein product		190198	"""Notch (Drosophila) homolog 1 (translocation-associated)"", ""Notch homolog 1, translocation-associated (Drosophila)"""	TAN1		1831692	Standard	NM_017617		Approved		uc004chz.3	P46531	OTTHUMG00000020935	ENST00000277541.6:c.852G>A	9.37:g.139413908C>T		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	85	38	0.447059	NM_017617	Q59ED8|Q5SXM3	Silent	SNP	ENST00000277541.6	37	CCDS43905.1																																																																																			T|0.113;G|0.000;C|0.886	0.113	strong		0.617	NOTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055087.1	NM_017617	
OR10H1	26539	hgsc.bcm.edu	37	19	15918647	15918647	+	Silent	SNP	G	G	T	rs4081570	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:15918647G>T	ENST00000334920.2	-	1	289	c.201C>A	c.(199-201)tcC>tcA	p.S67S		NM_013940.2	NP_039228.1	Q9Y4A9	O10H1_HUMAN	olfactory receptor, family 10, subfamily H, member 1	67						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(3)|kidney(4)|large_intestine(6)|lung(8)|ovary(4)|skin(2)|urinary_tract(1)	29						TCTCGGAGACGGAGAGGGCGC	0.642													.|||	1522	0.303914	0.4622	0.3184	5008	,	,		20278	0.0417		0.4145	False		,,,				2504	0.2362				p.S67S		Atlas-SNP	.											OR10H1,NS,malignant_melanoma,-1,1	OR10H1	59	1	0			c.C201A						scavenged	.						103.0	93.0	96.0					19																	15918647		2194	4278	6472	SO:0001819	synonymous_variant	26539	exon1			GGAGACGGAGAGG	AC004510	CCDS12335.1	19p13.1	2012-08-09				ENSG00000186723		"""GPCR / Class A : Olfactory receptors"""	8172	protein-coding gene	gene with protein product							Standard	NM_013940		Approved		uc002nbq.2	Q9Y4A9		ENST00000334920.2:c.201C>A	19.37:g.15918647G>T		Somatic	212	1	0.00471698		WXS	Illumina HiSeq	Phase_I	75	73	0.973333	NM_013940	Q6IFQ2|Q96R59	Silent	SNP	ENST00000334920.2	37	CCDS12335.1																																																																																			T|1.000;|0.000	1.000	weak		0.642	OR10H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460364.1		
SPP1	6696	hgsc.bcm.edu	37	4	88903853	88903853	+	Silent	SNP	C	C	T	rs397897575|rs1126616	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:88903853C>T	ENST00000395080.3	+	7	877	c.750C>T	c.(748-750)gcC>gcT	p.A250A	SPP1_ENST00000237623.7_Silent_p.A236A|SPP1_ENST00000360804.4_Silent_p.A223A|SPP1_ENST00000509659.1_3'UTR	NM_001040058.1|NM_001251830.1	NP_001035147.1|NP_001238759.1	P10451	OSTP_HUMAN	secreted phosphoprotein 1	250					biomineral tissue development (GO:0031214)|cell adhesion (GO:0007155)|decidualization (GO:0046697)|embryo implantation (GO:0007566)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|inflammatory response (GO:0006954)|negative regulation of collateral sprouting of intact axon in response to injury (GO:0048685)|neutrophil chemotaxis (GO:0030593)|osteoblast differentiation (GO:0001649)|positive regulation of bone resorption (GO:0045780)|positive regulation of cell-substrate adhesion (GO:0010811)|response to steroid hormone (GO:0048545)|response to vitamin D (GO:0033280)	apical part of cell (GO:0045177)|cell projection (GO:0042995)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|perinuclear region of cytoplasm (GO:0048471)	extracellular matrix binding (GO:0050840)	p.A250A(1)		NS(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|prostate(3)|skin(1)	13		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;9.87e-05)		AGCGGAAAGCCAATGATGAGA	0.473													C|||	1810	0.361422	0.1543	0.3775	5008	,	,		19862	0.7063		0.2813	False		,,,				2504	0.3569				p.A263A		Atlas-SNP	.											SPP1,NS,carcinoma,0,1	SPP1	35	1	1	Substitution - coding silent(1)	prostate(1)	c.C789T						PASS	.	C	,,	784,3622	315.5+/-294.2	59,666,1478	145.0	137.0	140.0		708,750,669	-1.2	0.0	4	dbSNP_86	140	2340,6260	391.7+/-343.7	348,1644,2308	no	coding-synonymous,coding-synonymous,coding-synonymous	SPP1	NM_000582.2,NM_001040058.1,NM_001040060.1	,,	407,2310,3786	TT,TC,CC		27.2093,17.7939,24.0197	,,	236/301,250/315,223/288	88903853	3124,9882	2203	4300	6503	SO:0001819	synonymous_variant	6696	exon8			GAAAGCCAATGAT		CCDS3626.1, CCDS34027.1, CCDS43250.1	4q22.1	2014-01-30	2008-07-31		ENSG00000118785	ENSG00000118785		"""Endogenous ligands"""	11255	protein-coding gene	gene with protein product	"""early T-lymphocyte activation 1"""	166490	"""osteopontin"", ""bone sialoprotein I"""	BNSP, OPN		1575754	Standard	NM_001251829		Approved	BSPI, ETA-1	uc003hra.3	P10451	OTTHUMG00000130599	ENST00000395080.3:c.750C>T	4.37:g.88903853C>T		Somatic	208	1	0.00480769		WXS	Illumina HiSeq	Phase_I	143	143	1	NM_001251830	B2RDA1|Q15681|Q15682|Q15683|Q4W597|Q567T5|Q8NBK2|Q96IZ1	Silent	SNP	ENST00000395080.3	37	CCDS43250.1																																																																																			C|0.733;G|0.000;T|0.267	0.267	strong		0.473	SPP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253048.3		
ADORA3	140	hgsc.bcm.edu	37	1	112042787	112042787	+	Missense_Mutation	SNP	T	T	G	rs35511654	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:112042787T>G	ENST00000241356.4	-	2	1147	c.742A>C	c.(742-744)Atc>Ctc	p.I248L	ADORA3_ENST00000369717.4_Intron|ADORA3_ENST00000486342.1_5'Flank|ADORA3_ENST00000369716.4_Intron	NM_000677.3	NP_000668.1	P33765	AA3R_HUMAN	adenosine A3 receptor	248			I -> L (in dbSNP:rs35511654). {ECO:0000269|Ref.3}.		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)	CAGTTGATGATAGATAAAGGC	0.463													T|||	298	0.0595048	0.0628	0.0836	5008	,	,		21916	0.001		0.1402	False		,,,				2504	0.0153				p.I248L		Atlas-SNP	.											ADORA3,caecum,carcinoma,0,1	ADORA3	104	1	0			c.A742C	GRCh37	CM077860	ADORA3	M	rs35511654	PASS	.	T	LEU/ILE,,	256,4150	147.6+/-182.1	13,230,1960	106.0	102.0	104.0		742,,	3.9	1.0	1	dbSNP_126	104	1175,7425	240.0+/-270.9	87,1001,3212	yes	missense,intron,intron	ADORA3	NM_000677.3,NM_001081976.1,NM_020683.6	5,,	100,1231,5172	GG,GT,TT		13.6628,5.8103,11.0026	possibly-damaging,,	248/319,,	112042787	1431,11575	2203	4300	6503	SO:0001583	missense	140	exon2			TGATGATAGATAA	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.742A>C	1.37:g.112042787T>G	ENSP00000241356:p.Ile248Leu	Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	171	71	0.415205	NM_000677	A2A3P4|Q6UWU0|Q9BYZ1	Missense_Mutation	SNP	ENST00000241356.4	37	CCDS839.1	169	0.07738095238095238	26	0.052845528455284556	31	0.0856353591160221	1	0.0017482517482517483	111	0.14643799472295516	T	18.52	3.642415	0.67244	0.058103	0.136628	ENSG00000121933	ENST00000241356	T	0.74421	-0.84	5.01	3.86	0.44501	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.68531	0.3011	L	0.37850	1.14	0.30315	P	0.788123	D	0.63880	0.993	D	0.64687	0.928	T	0.70178	-0.4943	8	0.42905	T	0.14	.	10.9921	0.47555	0.1402:0.0:0.0:0.8598	rs35511654;rs62617132	248	P33765	AA3R_HUMAN	L	248	ENSP00000241356:I248L	ENSP00000241356:I248L	I	-	1	0	ADORA3	111844310	1.000000	0.71417	0.998000	0.56505	0.508000	0.34012	3.192000	0.50989	0.834000	0.34852	0.528000	0.53228	ATC	T|0.898;G|0.102	0.102	strong		0.463	ADORA3-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033065.1	NM_000677, NM_020683	
SF3B2	10992	hgsc.bcm.edu	37	11	65826704	65826704	+	Silent	SNP	G	G	A	rs1049872	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:65826704G>A	ENST00000322535.6	+	11	1264	c.1215G>A	c.(1213-1215)aaG>aaA	p.K405K	SF3B2_ENST00000528302.1_Silent_p.K388K	NM_006842.2	NP_006833.2	Q13435	SF3B2_HUMAN	splicing factor 3b, subunit 2, 145kDa	405					gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|viral process (GO:0016032)	catalytic step 2 spliceosome (GO:0071013)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U12-type spliceosomal complex (GO:0005689)	poly(A) RNA binding (GO:0044822)			breast(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|liver(2)|lung(14)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	41						AGAAAGAGAAGGAGCCAGAGA	0.512													G|||	979	0.195487	0.1165	0.3991	5008	,	,		18649	0.2292		0.2445	False		,,,				2504	0.0726				p.K405K		Atlas-SNP	.											.	SF3B2	85	.	0			c.G1215A						PASS	.	G		638,3764	273.7+/-271.5	45,548,1608	60.0	58.0	59.0		1215	4.2	1.0	11	dbSNP_86	59	2077,6513	356.0+/-330.1	240,1597,2458	no	coding-synonymous	SF3B2	NM_006842.2		285,2145,4066	AA,AG,GG		24.1793,14.4934,20.8975		405/896	65826704	2715,10277	2201	4295	6496	SO:0001819	synonymous_variant	10992	exon11			AGAGAAGGAGCCA	U41371	CCDS31612.1	11q13	2010-07-21	2002-08-29		ENSG00000087365	ENSG00000087365			10769	protein-coding gene	gene with protein product		605591	"""splicing factor 3b, subunit 2, 145kD"""			8566756	Standard	XM_005273726		Approved	SAP145, SF3b1, Cus1, SF3b145	uc001ogy.1	Q13435	OTTHUMG00000166751	ENST00000322535.6:c.1215G>A	11.37:g.65826704G>A		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	81	65	0.802469	NM_006842	A8K485|B4DT19|Q7L4T5|Q7Z627|Q969K1|Q96CM6|Q9BWD2	Silent	SNP	ENST00000322535.6	37	CCDS31612.1																																																																																			G|0.791;A|0.209	0.209	strong		0.512	SF3B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391352.2		
GPR112	139378	hgsc.bcm.edu	37	X	135474420	135474420	+	Silent	SNP	C	C	A	rs1329546	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:135474420C>A	ENST00000394143.1	+	17	8232	c.7941C>A	c.(7939-7941)acC>acA	p.T2647T	GPR112_ENST00000412101.1_Silent_p.T2442T|GPR112_ENST00000370652.1_Silent_p.T2647T|GPR112_ENST00000287534.4_Silent_p.T2400T|GPR112_ENST00000394141.1_Silent_p.T2442T	NM_153834.3	NP_722576.3	Q8IZF6	GP112_HUMAN	G protein-coupled receptor 112	2647					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(13)|central_nervous_system(2)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(33)|lung(97)|ovary(5)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(2)	199	Acute lymphoblastic leukemia(192;0.000127)					CATTAACCACCTATGTTGTGA	0.363													A|||	2783	0.737219	0.5242	0.5879	3775	,	,		15234	0.7014		0.4801	False		,,,				2504	0.5031				p.T2647T		Atlas-SNP	.											.	GPR112	459	.	0			c.C7941A						PASS	.	A		2635,1200		770,695,400,167,171	107.0	99.0	102.0		7941	-9.6	0.4	X	dbSNP_88	102	4075,2653		890,1161,1134,377,738	no	coding-synonymous	GPR112	NM_153834.3		1660,1856,1534,544,909	AA,AC,A,CC,C		39.4322,31.2907,36.4764		2647/3081	135474420	6710,3853	2203	4300	6503	SO:0001819	synonymous_variant	139378	exon17			AACCACCTATGTT	AY140954	CCDS35409.1	Xq26.3	2014-08-08			ENSG00000156920	ENSG00000156920		"""-"", ""GPCR / Class B : Orphans"""	18992	protein-coding gene	gene with protein product						12435584	Standard	XM_005262367		Approved	RP1-299I16, PGR17	uc004ezu.1	Q8IZF6	OTTHUMG00000022508	ENST00000394143.1:c.7941C>A	X.37:g.135474420C>A		Somatic	388	0	0		WXS	Illumina HiSeq	Phase_I	210	208	0.990476	NM_153834	A2A2J1|A2A2J2|Q5EGP2|Q86SM6	Silent	SNP	ENST00000394143.1	37	CCDS35409.1																																																																																			C|0.328;A|0.672	0.672	strong		0.363	GPR112-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000286639.1		
COL2A1	1280	hgsc.bcm.edu	37	12	48378380	48378380	+	Silent	SNP	A	A	G	rs41317939	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:48378380A>G	ENST00000380518.3	-	28	2000	c.1836T>C	c.(1834-1836)ggT>ggC	p.G612G	COL2A1_ENST00000493991.1_5'UTR|COL2A1_ENST00000337299.6_Silent_p.G543G	NM_001844.4|NM_033150.2	NP_001835.3|NP_149162.2	P02458	CO2A1_HUMAN	collagen, type II, alpha 1	612	Triple-helical region.				axon guidance (GO:0007411)|cartilage condensation (GO:0001502)|cartilage development (GO:0051216)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|cellular response to BMP stimulus (GO:0071773)|central nervous system development (GO:0007417)|chondrocyte differentiation (GO:0002062)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|embryonic skeletal joint morphogenesis (GO:0060272)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart morphogenesis (GO:0003007)|inner ear morphogenesis (GO:0042472)|limb bud formation (GO:0060174)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|notochord development (GO:0030903)|otic vesicle development (GO:0071599)|palate development (GO:0060021)|proteoglycan metabolic process (GO:0006029)|regulation of gene expression (GO:0010468)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|tissue homeostasis (GO:0001894)|visual perception (GO:0007601)	basement membrane (GO:0005604)|collagen type II trimer (GO:0005585)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(9)|lung(25)|ovary(1)|prostate(1)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(3)	64		Acute lymphoblastic leukemia(13;0.108)|all_hematologic(14;0.214)			Collagenase(DB00048)	TGCCAGGCTCACCCTGAAGGA	0.632													G|||	104	0.0207668	0.0106	0.0173	5008	,	,		17516	0.0		0.0696	False		,,,				2504	0.0082				p.G612G		Atlas-SNP	.											.	COL2A1	368	.	0			c.T1836C						PASS	.	G	,	86,4320	816.9+/-416.3	1,84,2118	88.0	63.0	71.0		1836,1629	-8.8	0.9	12	dbSNP_127	71	551,8049	793.7+/-407.5	21,509,3770	no	coding-synonymous,coding-synonymous	COL2A1	NM_001844.4,NM_033150.2	,	22,593,5888	GG,GA,AA		6.407,1.9519,4.8977	,	612/1488,543/1419	48378380	637,12369	2203	4300	6503	SO:0001819	synonymous_variant	1280	exon28			AGGCTCACCCTGA	X16468	CCDS8759.1, CCDS41778.1	12q12-q13.2	2013-11-14	2008-02-04		ENSG00000139219	ENSG00000139219		"""Collagens"""	2200	protein-coding gene	gene with protein product		120140	"""collagen, type II, alpha 1 (primary osteoarthritis, spondyloepiphyseal dysplasia, congenital)"", ""arthroophthalmopathy, progressive (Stickler syndrome)"""	SEDC, AOM		1677770	Standard	NM_033150		Approved	STL1	uc001rqu.3	P02458	OTTHUMG00000149896	ENST00000380518.3:c.1836T>C	12.37:g.48378380A>G		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	38	15	0.394737	NM_001844	A6NGA0|Q12985|Q14009|Q14044|Q14045|Q14046|Q14047|Q14056|Q14058|Q16672|Q1JQ82|Q2V4X7|Q6LBY1|Q6LBY2|Q6LBY3|Q96IT5|Q99227|Q9UE38|Q9UE39|Q9UE40|Q9UE41|Q9UE42|Q9UE43	Silent	SNP	ENST00000380518.3	37	CCDS41778.1																																																																																			A|0.958;G|0.042	0.042	strong		0.632	COL2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313810.2	NM_001844	
OBSCN	84033	hgsc.bcm.edu	37	1	228524961	228524961	+	Silent	SNP	C	C	A	rs3795808	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:228524961C>A	ENST00000422127.1	+	66	16721	c.16677C>A	c.(16675-16677)ccC>ccA	p.P5559P	OBSCN_ENST00000284548.11_Silent_p.P5559P|OBSCN_ENST00000570156.2_Silent_p.P6516P|OBSCN_ENST00000366709.4_Silent_p.P2678P|OBSCN_ENST00000366707.4_Silent_p.P3193P	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	5559					apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				TGCAGGTGCCCGGAGGTGACA	0.632													T|||	1201	0.239816	0.0575	0.3458	5008	,	,		18520	0.25		0.4185	False		,,,				2504	0.2168				p.P6516P		Atlas-SNP	.											.	OBSCN	2142	.	0			c.C19548A						PASS	.	T	,	412,3738		29,354,1692	30.0	39.0	36.0		16677,16677	-4.5	0.8	1	dbSNP_107	36	3541,4839		761,2019,1410	no	coding-synonymous,coding-synonymous	OBSCN	NM_001098623.1,NM_052843.2	,	790,2373,3102	AA,AC,CC		42.2554,9.9277,31.5483	,	5559/7969,5559/6621	228524961	3953,8577	2075	4190	6265	SO:0001819	synonymous_variant	84033	exon77			GGTGCCCGGAGGT	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"""Rho guanine nucleotide exchange factors"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.16677C>A	1.37:g.228524961C>A		Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	123	57	0.463415	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Silent	SNP	ENST00000422127.1	37	CCDS58065.1																																																																																			A|0.286;C|0.714;G|0.000	0.286	strong		0.632	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
FDXR	2232	hgsc.bcm.edu	37	17	72862593	72862593	+	Missense_Mutation	SNP	C	C	T	rs690514	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:72862593C>T	ENST00000293195.5	-	4	446	c.368G>A	c.(367-369)cGg>cAg	p.R123Q	FDXR_ENST00000413947.2_Missense_Mutation_p.R154Q|FDXR_ENST00000581969.1_5'UTR|FDXR_ENST00000583917.1_Missense_Mutation_p.R124Q|FDXR_ENST00000442102.2_Missense_Mutation_p.R166Q|FDXR_ENST00000544854.1_Missense_Mutation_p.R71Q|FDXR_ENST00000420580.2_Intron|FDXR_ENST00000582944.1_Missense_Mutation_p.R115Q|FDXR_ENST00000455107.2_Missense_Mutation_p.R79Q|FDXR_ENST00000581530.1_Missense_Mutation_p.R123Q	NM_001258014.1|NM_004110.3|NM_024417.2	NP_001244943.1|NP_004101.2|NP_077728.2	P22570	ADRO_HUMAN	ferredoxin reductase	123			R -> Q (in dbSNP:rs690514). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:2845396, ECO:0000269|Ref.3}.		cholesterol metabolic process (GO:0008203)|generation of precursor metabolites and energy (GO:0006091)|NADPH oxidation (GO:0070995)|oxidation-reduction process (GO:0055114)|small molecule metabolic process (GO:0044281)|steroid biosynthetic process (GO:0006694)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ferredoxin-NADP+ reductase activity (GO:0004324)|NADPH binding (GO:0070402)|NADPH-adrenodoxin reductase activity (GO:0015039)			central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(9)|prostate(1)|skin(1)	16	all_lung(278;0.172)|Lung NSC(278;0.207)				Flavin adenine dinucleotide(DB03147)	GTAGGCCTCCCGCAGCTCCGG	0.662													C|||	927	0.185104	0.0333	0.1571	5008	,	,		17901	0.378		0.2147	False		,,,				2504	0.181				p.R166Q		Atlas-SNP	.											FDXR_ENST00000581530,NS,carcinoma,0,4	FDXR	68	4	0			c.G497A						PASS	.	C	GLN/ARG,GLN/ARG	287,4119	150.7+/-184.7	7,273,1923	34.0	29.0	31.0		368,368	-2.0	1.0	17	dbSNP_83	31	1895,6703	315.5+/-312.3	198,1499,2602	yes	missense,missense	FDXR	NM_004110.3,NM_024417.2	43,43	205,1772,4525	TT,TC,CC		22.04,6.5138,16.7795	benign,benign	123/498,123/492	72862593	2182,10822	2203	4299	6502	SO:0001583	missense	2232	exon4			GCCTCCCGCAGCT	J03826	CCDS11707.1, CCDS58591.1, CCDS58592.1, CCDS58593.1, CCDS58594.1, CCDS58595.1, CCDS58596.1	17q25.1	2013-06-18			ENSG00000161513	ENSG00000161513	1.18.1.6		3642	protein-coding gene	gene with protein product	"""adrenodoxin-NADP(+) reductase"", ""adrenodoxin reductase"""	103270		ADXR		2969697	Standard	NM_001258014		Approved		uc010wrl.2	P22570	OTTHUMG00000179026	ENST00000293195.5:c.368G>A	17.37:g.72862593C>T	ENSP00000293195:p.Arg123Gln	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	158	72	0.455696	NM_001258012	B4DDI7|B4DHX5|B4DQQ4|B4DX24|B7Z7G2|E7EQC1|Q13716|Q4PJI0|Q9BU12	Missense_Mutation	SNP	ENST00000293195.5	37	CCDS58593.1	465	0.2129120879120879	16	0.032520325203252036	59	0.16298342541436464	224	0.3916083916083916	166	0.21899736147757257	C	11.28	1.591102	0.28357	0.065138	0.2204	ENSG00000161513	ENST00000544854;ENST00000293195;ENST00000455107;ENST00000442102;ENST00000413947	T;T;T;T;T	0.69175	-0.38;-0.38;-0.38;-0.38;-0.38	5.05	-1.99	0.07457	.	0.565182	0.18746	N	0.132305	T	0.00012	0.0000	N	0.25825	0.765	0.22629	P	0.99891839	B;B;B;B;B;B;B;B	0.21905	0.005;0.028;0.062;0.005;0.003;0.006;0.003;0.011	B;B;B;B;B;B;B;B	0.17979	0.02;0.01;0.015;0.013;0.004;0.009;0.004;0.02	T	0.38457	-0.9660	9	0.27785	T	0.31	2.9856	11.0447	0.47852	0.0:0.2718:0.0:0.7282	rs690514;rs1130204;rs2228624;rs690514	166;154;121;71;123;115;123;123	B4DHX5;E7EQC1;B4DDI9;B7Z7G2;Q6GSK2;B4DX24;P22570;P22570-2	.;.;.;.;.;.;ADRO_HUMAN;.	Q	71;123;79;166;154	ENSP00000445432:R71Q;ENSP00000293195:R123Q;ENSP00000390875:R79Q;ENSP00000416515:R166Q;ENSP00000408595:R154Q	ENSP00000293195:R123Q	R	-	2	0	FDXR	70374188	0.000000	0.05858	0.953000	0.39169	0.431000	0.31685	-1.415000	0.02469	-0.351000	0.08249	-0.367000	0.07326	CGG	C|0.813;T|0.187	0.187	strong		0.662	FDXR-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000444449.1	NM_004110	
KLHL29	114818	hgsc.bcm.edu	37	2	23926233	23926233	+	Silent	SNP	C	C	T	rs72796138	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:23926233C>T	ENST00000486442.1	+	12	3000	c.2283C>T	c.(2281-2283)atC>atT	p.I761I		NM_052920.1	NP_443152.1	Q96CT2	KLH29_HUMAN	kelch-like family member 29	761										breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|lung(1)|ovary(3)	10						GGAGCTTCATCGAGTCCCCAA	0.592													C|||	446	0.0890575	0.0499	0.085	5008	,	,		21030	0.0526		0.1372	False		,,,				2504	0.1329				p.I761I		Atlas-SNP	.											.	KLHL29	47	.	0			c.C2283T						PASS	.	C		100,1284		2,96,594	74.0	76.0	76.0		2283	-0.4	1.0	2	dbSNP_130	76	380,2802		27,326,1238	no	coding-synonymous	KLHL29	NM_052920.1		29,422,1832	TT,TC,CC		11.9422,7.2254,10.5125		761/876	23926233	480,4086	692	1591	2283	SO:0001819	synonymous_variant	114818	exon12			CTTCATCGAGTCC		CCDS54335.1	2p23.3	2013-09-27	2013-02-22	2007-01-09	ENSG00000119771	ENSG00000119771		"""Kelch-like"", ""BTB/POZ domain containing"""	29404	protein-coding gene	gene with protein product			"""kelch repeat and BTB (POZ) domain containing 9"", ""kelch-like 29 (Drosophila)"""	KBTBD9		11572484	Standard	NM_052920		Approved	KIAA1921	uc010ykg.2	Q96CT2	OTTHUMG00000151899	ENST00000486442.1:c.2283C>T	2.37:g.23926233C>T		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	45	22	0.488889	NM_052920	Q8N388|Q96BF0|Q96PW7	Silent	SNP	ENST00000486442.1	37	CCDS54335.1																																																																																			C|0.912;T|0.088	0.088	strong		0.592	KLHL29-001	KNOWN	mRNA_start_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324315.3	NM_052920	
MANEA	79694	hgsc.bcm.edu	37	6	96034612	96034612	+	Silent	SNP	G	G	A	rs62417813	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:96034612G>A	ENST00000358812.4	+	2	431	c.297G>A	c.(295-297)ctG>ctA	p.L99L	MANEA_ENST00000369293.1_Silent_p.L99L	NM_024641.3	NP_078917.2	Q5SRI9	MANEA_HUMAN	mannosidase, endo-alpha	99	Catalytic. {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)		TACCACCTCTGAACAATTATC	0.338													G|||	174	0.0347444	0.0053	0.0317	5008	,	,		17517	0.003		0.1083	False		,,,				2504	0.0337				p.L99L		Atlas-SNP	.											.	MANEA	58	.	0			c.G297A						PASS	.	G		102,4304	75.7+/-113.9	5,92,2106	102.0	106.0	105.0		297	2.8	1.0	6	dbSNP_129	105	979,7621	210.7+/-251.5	66,847,3387	no	coding-synonymous	MANEA	NM_024641.3		71,939,5493	AA,AG,GG		11.3837,2.315,8.3115		99/463	96034612	1081,11925	2203	4300	6503	SO:0001819	synonymous_variant	79694	exon2			ACCTCTGAACAAT	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.297G>A	6.37:g.96034612G>A		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	44	19	0.431818	NM_024641	A6H8M6|Q5SRJ0|Q6MZV0|Q70JE9|Q7Z3V7|Q8WWX5|Q9H9D2	Silent	SNP	ENST00000358812.4	37	CCDS5032.1																																																																																			G|0.929;A|0.070	0.070	strong		0.338	MANEA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043644.1	NM_024641	
XRCC6BP1	91419	hgsc.bcm.edu	37	12	58350631	58350631	+	Silent	SNP	C	C	T	rs10122	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	116	0	0		WXS	Illumina HiSeq	Phase_I	105	62	0.590476	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	
HIST1H2AM	8336	hgsc.bcm.edu	37	6	27860579	27860579	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:27860579G>A	ENST00000359611.2	-	1	384	c.349C>T	c.(349-351)Ctc>Ttc	p.L117F	HIST1H3J_ENST00000359303.2_5'Flank|HIST1H2BO_ENST00000303806.4_5'Flank|HIST1H3J_ENST00000479986.1_5'UTR	NM_003514.2	NP_003505.1	P0C0S8	H2A1_HUMAN	histone cluster 1, H2am	117						extracellular vesicular exosome (GO:0070062)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)			endometrium(3)|kidney(2)|large_intestine(1)|lung(6)|ovary(2)	14						TTCTTGGGGAGCAGTACGGCC	0.507																																					p.L117F		Atlas-SNP	.											.	HIST1H2AM	27	.	0			c.C349T						PASS	.						131.0	126.0	128.0					6																	27860579		2203	4300	6503	SO:0001583	missense	8336	exon1			TGGGGAGCAGTAC	X57138	CCDS4639.1	6p22.1	2011-01-27	2006-10-11	2003-02-14	ENSG00000233224	ENSG00000278677		"""Histones / Replication-dependent"""	4735	protein-coding gene	gene with protein product		602796	"""H2A histone family, member N"", ""histone 1, H2am"""	H2AFN		1768865, 9439656, 12408966	Standard	NM_003514		Approved	H2A/n, H2A.1	uc003nkb.1	P0C0S8	OTTHUMG00000014494	ENST00000359611.2:c.349C>T	6.37:g.27860579G>A	ENSP00000352627:p.Leu117Phe	Somatic	214	0	0		WXS	Illumina HiSeq	Phase_I	181	41	0.226519	NM_003514	P02261|Q2M1R2|Q76PA6	Missense_Mutation	SNP	ENST00000359611.2	37	CCDS4639.1	.	.	.	.	.	.	.	.	.	.	G	11.88	1.770382	0.31320	.	.	ENSG00000233224	ENST00000359611	T	0.52057	0.68	4.06	3.19	0.36642	.	0.000000	0.26130	U	0.026178	T	0.48840	0.1522	M	0.79475	2.455	0.32139	N	0.585724	.	.	.	.	.	.	T	0.54351	-0.8307	8	0.87932	D	0	.	11.3928	0.49824	0.0916:0.0:0.9084:0.0	.	.	.	.	F	117	ENSP00000352627:L117F	ENSP00000352627:L117F	L	-	1	0	HIST1H2AM	27968558	1.000000	0.71417	1.000000	0.80357	0.154000	0.21943	3.207000	0.51106	1.298000	0.44778	-0.136000	0.14681	CTC	.	.	none		0.507	HIST1H2AM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040162.1	NM_003514	
MUC15	143662	hgsc.bcm.edu	37	11	26587133	26587133	+	Silent	SNP	T	T	C	rs293980	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:26587133T>C	ENST00000455601.2	-	2	391	c.273A>G	c.(271-273)tcA>tcG	p.S91S	MUC15_ENST00000281268.8_Silent_p.S118S|MUC15_ENST00000529533.1_Silent_p.S118S|MUC15_ENST00000527569.1_Silent_p.S118S|ANO3_ENST00000525139.1_Intron|MUC15_ENST00000436318.2_Silent_p.S118S|ANO3_ENST00000537978.1_Intron|ANO3_ENST00000256737.3_Intron|ANO3_ENST00000531568.1_Intron	NM_145650.3	NP_663625.2	Q8N387	MUC15_HUMAN	mucin 15, cell surface associated	91					cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(7)|ovary(1)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	25						GCTCTGCTGATGAGTTACTGG	0.433													C|||	3344	0.667732	0.7073	0.7954	5008	,	,		19048	0.4772		0.7256	False		,,,				2504	0.6605				p.S118S		Atlas-SNP	.											MUC15,NS,carcinoma,-1,1	MUC15	88	1	0			c.A354G						PASS	.	C	,,,	3210,1196	418.3+/-338.2	1167,876,160	159.0	143.0	149.0		354,354,,273	-1.7	0.0	11	dbSNP_79	149	6367,2233	379.5+/-339.3	2333,1701,266	no	coding-synonymous,coding-synonymous,intron,coding-synonymous	ANO3,MUC15	NM_001135091.1,NM_001135092.1,NM_031418.2,NM_145650.3	,,,	3500,2577,426	CC,CT,TT		25.9651,27.1448,26.3648	,,,	118/362,118/312,,91/335	26587133	9577,3429	2203	4300	6503	SO:0001819	synonymous_variant	143662	exon3			TGCTGATGAGTTA	AJ417818	CCDS7859.1, CCDS44556.1, CCDS44557.1	11p14.3	2007-01-17	2006-03-14					"""Mucins"""	14956	protein-coding gene	gene with protein product		608566				12047385	Standard	NM_145650		Approved		uc001mqw.3	Q8N387		ENST00000455601.2:c.273A>G	11.37:g.26587133T>C		Somatic	315	0	0		WXS	Illumina HiSeq	Phase_I	259	187	0.722008	NM_001135092	B3KY00|E9PII6|F8W945|Q6UWS3|Q8IXI8|Q8WW41	Silent	SNP	ENST00000455601.2	37	CCDS7859.1																																																																																			T|0.311;C|0.689	0.689	strong		0.433	MUC15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387866.1	NM_145650	
RAB20	55647	hgsc.bcm.edu	37	13	111176519	111176519	+	Silent	SNP	G	G	T	rs375814	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:111176519G>T	ENST00000267328.3	-	2	411	c.198C>A	c.(196-198)ggC>ggA	p.G66G		NM_017817.1	NP_060287.1	Q9NX57	RAB20_HUMAN	RAB20, member RAS oncogene family	66					phagosome acidification (GO:0090383)|phagosome-lysosome fusion (GO:0090385)|protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)	Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|phagocytic vesicle (GO:0045335)	GTP binding (GO:0005525)			endometrium(2)|large_intestine(2)|lung(3)	7	all_cancers(4;1.54e-11)|all_epithelial(4;1.22e-06)|all_lung(23;1e-05)|Lung NSC(43;0.000453)|Colorectal(4;0.00323)|Lung SC(71;0.0753)|all_neural(89;0.077)|Medulloblastoma(90;0.148)		BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.197)			AGTACATGGAGCCCAGGCCGT	0.612													G|||	1904	0.380192	0.4675	0.4539	5008	,	,		18442	0.2808		0.3827	False		,,,				2504	0.3098				p.G66G		Atlas-SNP	.											RAB20_ENST00000267328,NS,carcinoma,0,2	RAB20	34	2	0			c.C198A						PASS	.	G		2009,2397		468,1073,662	30.0	33.0	32.0		198	2.1	1.0	13	dbSNP_80	32	3125,5471		594,1937,1767	no	coding-synonymous	RAB20	NM_017817.1		1062,3010,2429	TT,TG,GG		36.3541,45.5969,39.4862		66/235	111176519	5134,7868	2203	4298	6501	SO:0001819	synonymous_variant	55647	exon2			CATGGAGCCCAGG	AK000436	CCDS9512.1	13q34	2008-07-18			ENSG00000139832	ENSG00000139832		"""RAB, member RAS oncogene"""	18260	protein-coding gene	gene with protein product						11697911	Standard	NM_017817		Approved	FLJ20429	uc001vqy.3	Q9NX57	OTTHUMG00000017343	ENST00000267328.3:c.198C>A	13.37:g.111176519G>T		Somatic	12	0	0		WXS	Illumina HiSeq	Phase_I	13	13	1	NM_017817	Q5T9X5|Q9NX49	Silent	SNP	ENST00000267328.3	37	CCDS9512.1																																																																																			G|0.614;T|0.386	0.386	strong		0.612	RAB20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045760.2	NM_017817	
OR10H1	26539	hgsc.bcm.edu	37	19	15918802	15918802	+	Missense_Mutation	SNP	C	C	G	rs4808383	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:15918802C>G	ENST00000334920.2	-	1	134	c.46G>C	c.(46-48)Ggc>Cgc	p.G16R		NM_013940.2	NP_039228.1	Q9Y4A9	O10H1_HUMAN	olfactory receptor, family 10, subfamily H, member 1	16			G -> R (in dbSNP:rs4808383).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(3)|kidney(4)|large_intestine(6)|lung(8)|ovary(4)|skin(2)|urinary_tract(1)	29						ACAGAGAAGCCGACGAGGATG	0.557													.|||	766	0.152955	0.1331	0.1124	5008	,	,		20065	0.12		0.1779	False		,,,				2504	0.2168				p.G16R		Atlas-SNP	.											.	OR10H1	59	.	0			c.G46C						PASS	.	C	ARG/GLY	612,3794	266.2+/-267.1	52,508,1643	153.0	145.0	148.0		46	2.3	0.3	19	dbSNP_111	148	1695,6905	311.7+/-310.5	175,1345,2780	yes	missense	OR10H1	NM_013940.2	125	227,1853,4423	GG,GC,CC		19.7093,13.8901,17.738	probably-damaging	16/319	15918802	2307,10699	2203	4300	6503	SO:0001583	missense	26539	exon1			AGAAGCCGACGAG	AC004510	CCDS12335.1	19p13.1	2012-08-09				ENSG00000186723		"""GPCR / Class A : Olfactory receptors"""	8172	protein-coding gene	gene with protein product							Standard	NM_013940		Approved		uc002nbq.2	Q9Y4A9		ENST00000334920.2:c.46G>C	19.37:g.15918802C>G	ENSP00000335596:p.Gly16Arg	Somatic	187	0	0		WXS	Illumina HiSeq	Phase_I	147	65	0.442177	NM_013940	Q6IFQ2|Q96R59	Missense_Mutation	SNP	ENST00000334920.2	37	CCDS12335.1	318	0.14560439560439561	66	0.13414634146341464	36	0.09944751381215469	77	0.1346153846153846	139	0.18337730870712401	c	13.00	2.105991	0.37145	0.138901	0.197093	ENSG00000186723	ENST00000334920	T	0.00659	5.94	4.47	2.28	0.28536	.	0.000000	0.50627	D	0.000103	T	0.00012	0.0000	M	0.93939	3.475	0.30892	P	0.730259	D	0.89917	1.0	D	0.70716	0.97	T	0.15150	-1.0447	9	0.72032	D	0.01	.	6.9577	0.24580	0.1726:0.7323:0.0:0.0952	rs4808383;rs52830115;rs4808383	16	Q9Y4A9	O10H1_HUMAN	R	16	ENSP00000335596:G16R	ENSP00000335596:G16R	G	-	1	0	OR10H1	15779802	0.285000	0.24296	0.320000	0.25306	0.003000	0.03518	1.939000	0.40213	0.323000	0.23307	0.643000	0.83706	GGC	C|0.832;G|0.168	0.168	strong		0.557	OR10H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460364.1		
ETS2	2114	hgsc.bcm.edu	37	21	40191638	40191638	+	Silent	SNP	A	A	G	rs461155	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:40191638A>G	ENST00000360214.3	+	9	1483	c.1023A>G	c.(1021-1023)ccA>ccG	p.P341P	ETS2_ENST00000360938.3_Silent_p.P341P	NM_001256295.1	NP_001243224.1	P15036	ETS2_HUMAN	v-ets avian erythroblastosis virus E26 oncogene homolog 2	341					cell differentiation (GO:0030154)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|skeletal system development (GO:0001501)|transcription from RNA polymerase II promoter (GO:0006366)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(2)|endometrium(1)|large_intestine(3)|lung(5)|ovary(1)|pancreas(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	18		Prostate(19;6.33e-08)|all_epithelial(19;0.123)				GGAGTGACCCAGTGGAGCAAG	0.552													G|||	2908	0.580671	0.5613	0.5778	5008	,	,		18494	0.4563		0.838	False		,,,				2504	0.4724				p.P481P		Atlas-SNP	.											.	ETS2	87	.	0			c.A1443G						PASS	.	G		2730,1676	509.8+/-367.3	870,990,343	63.0	50.0	54.0		1023	-5.8	0.0	21	dbSNP_80	54	7292,1308	257.3+/-281.4	3085,1122,93	no	coding-synonymous	ETS2	NM_005239.4		3955,2112,436	GG,GA,AA		15.2093,38.039,22.9433		341/470	40191638	10022,2984	2203	4300	6503	SO:0001819	synonymous_variant	2114	exon9			TGACCCAGTGGAG		CCDS13659.1	21q22.3	2013-07-09	2013-07-09		ENSG00000157557	ENSG00000157557			3489	protein-coding gene	gene with protein product		164740	"""v-ets erythroblastosis virus E26 oncogene homolog 2 (avian)"""			17986575	Standard	NM_001256295		Approved		uc002yxf.3	P15036	OTTHUMG00000090769	ENST00000360214.3:c.1023A>G	21.37:g.40191638A>G		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	57	57	1	NM_001256295	A6NM68|D3DSH6|Q53Y89	Silent	SNP	ENST00000360214.3	37	CCDS13659.1																																																																																			A|0.297;G|0.703	0.703	strong		0.552	ETS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207544.1		
C4BPB	725	hgsc.bcm.edu	37	1	207269919	207269919	+	Silent	SNP	C	C	T	rs8942	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:207269919C>T	ENST00000243611.5	+	4	756	c.462C>T	c.(460-462)aaC>aaT	p.N154N	C4BPB_ENST00000367076.3_Silent_p.N153N|C4BPB_ENST00000391923.1_Silent_p.N154N|C4BPB_ENST00000367078.3_Silent_p.N154N	NM_000716.3	NP_000707.1	P20851	C4BPB_HUMAN	complement component 4 binding protein, beta	154	Sushi 3. {ECO:0000255|PROSITE- ProRule:PRU00302}.				blood coagulation (GO:0007596)|complement activation, classical pathway (GO:0006958)|innate immune response (GO:0045087)|negative regulation of complement activation, classical pathway (GO:0045959)|positive regulation of protein catabolic process (GO:0045732)|regulation of complement activation (GO:0030449)|regulation of opsonization (GO:1903027)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|other organism cell (GO:0044216)|plasma membrane (GO:0005886)				breast(2)|lung(1)|ovary(1)	4						AAGGAAATAACTTCACCTTAG	0.468													T|||	1952	0.389776	0.885	0.2867	5008	,	,		20355	0.1617		0.1769	False		,,,				2504	0.2474				p.N154N		Atlas-SNP	.											.	C4BPB	19	.	0			c.C462T						PASS	.	T	,,,,	3366,1040	381.8+/-324.2	1304,758,141	101.0	101.0	101.0		462,459,462,459,462	-2.0	0.0	1	dbSNP_52	101	1614,6986	742.6+/-407.2	155,1304,2841	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	C4BPB	NM_000716.3,NM_001017364.1,NM_001017365.1,NM_001017366.1,NM_001017367.1	,,,,	1459,2062,2982	TT,TC,CC		18.7674,23.6042,38.29	,,,,	154/253,153/252,154/253,153/252,154/253	207269919	4980,8026	2203	4300	6503	SO:0001819	synonymous_variant	725	exon5			AAATAACTTCACC	L11245	CCDS1476.1, CCDS31005.1	1q32	2008-07-18	2001-11-28		ENSG00000123843	ENSG00000123843			1328	protein-coding gene	gene with protein product	"""complement component 4 binding protein, beta chain"", ""C4b binding protein, beta chain"""	120831	"""complement component 4-binding protein, beta"""	C4BP		2300577, 8325877	Standard	XM_005273255		Approved		uc001hfj.3	P20851	OTTHUMG00000036035	ENST00000243611.5:c.462C>T	1.37:g.207269919C>T		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	86	31	0.360465	NM_001017365	A5JYP8|D3DT81|Q5VVR0|Q9BS25	Silent	SNP	ENST00000243611.5	37	CCDS1476.1																																																																																			C|0.623;T|0.377	0.377	strong		0.468	C4BPB-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000087847.2	NM_000716	
VAPA	9218	hgsc.bcm.edu	37	18	9944960	9944960	+	Intron	SNP	A	A	G	rs29132	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:9944960A>G	ENST00000400000.2	+	5	672				VAPA_ENST00000340541.4_Missense_Mutation_p.M153V|VAPA_ENST00000584796.1_Intron	NM_003574.5|NM_194434.2	NP_003565.4|NP_919415.2	Q9P0L0	VAPA_HUMAN	VAMP (vesicle-associated membrane protein)-associated protein A, 33kDa						cell death (GO:0008219)|membrane fusion (GO:0061025)|neuron projection development (GO:0031175)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|protein localization to endoplasmic reticulum (GO:0070972)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|microtubule cytoskeleton (GO:0015630)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	protein heterodimerization activity (GO:0046982)|signal transducer activity (GO:0004871)|structural molecule activity (GO:0005198)			breast(1)|lung(2)|prostate(1)	4						TGTCACTTCAATGAGCAGCAT	0.473													A|||	421	0.0840655	0.1263	0.1052	5008	,	,		19233	0.0774		0.0527	False		,,,				2504	0.0511				p.M153V		Atlas-SNP	.											.	VAPA	28	.	0			c.A457G						PASS	.	A	VAL/MET,	513,3489		29,455,1517	115.0	106.0	109.0		457,	-11.3	0.0	18	dbSNP_76	109	452,7896		16,420,3738	yes	missense,intron	VAPA	NM_003574.5,NM_194434.2	21,	45,875,5255	GG,GA,AA		5.4145,12.8186,7.8138	benign,	153/295,	9944960	965,11385	2001	4174	6175	SO:0001627	intron_variant	9218	exon5			ACTTCAATGAGCA		CCDS11847.2, CCDS11848.2	18p11.2	2008-07-28	2002-08-29		ENSG00000101558	ENSG00000101558			12648	protein-coding gene	gene with protein product		605703	"""VAMP (vesicle-associated membrane protein)-associated protein A (33kD)"""			9920726, 9657962	Standard	NM_003574		Approved	hVAP-33, VAP-A	uc002koj.3	Q9P0L0	OTTHUMG00000131603	ENST00000400000.2:c.418-5432A>G	18.37:g.9944960A>G		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	92	47	0.51087	NM_003574	A6NDZ0|D3DUI3|O75453|Q5U0E7|Q9UBZ2	Missense_Mutation	SNP	ENST00000400000.2	37	CCDS11848.2	176	0.08058608058608059	72	0.14634146341463414	24	0.06629834254143646	38	0.06643356643356643	42	0.055408970976253295	A	0.572	-0.840846	0.02692	0.128186	0.054145	ENSG00000101558	ENST00000340541	T	0.28895	1.59	5.64	-11.3	0.00108	.	1.738670	0.02923	N	0.138171	T	0.00073	0.0002	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.04678	-1.0934	7	.	.	.	6.1745	5.3834	0.16204	0.1589:0.2096:0.4605:0.171	rs29132	153	Q9P0L0-2	.	V	153	ENSP00000345656:M153V	.	M	+	1	0	VAPA	9934960	0.000000	0.05858	0.000000	0.03702	0.963000	0.63663	-2.575000	0.00910	-4.044000	0.00079	-0.359000	0.07587	ATG	A|0.931;G|0.069	0.069	strong		0.473	VAPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254490.1		
EFCAB2	84288	hgsc.bcm.edu	37	1	245245402	245245402	+	Silent	SNP	C	C	T	rs10927387	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:245245402C>T	ENST00000366522.2	+	5	750	c.609C>T	c.(607-609)ccC>ccT	p.P203P	EFCAB2_ENST00000366523.1_Silent_p.P67P|EFCAB2_ENST00000447569.2_Silent_p.P67P|EFCAB2_ENST00000487845.1_3'UTR			Q5VUJ9	EFCB2_HUMAN	EF-hand calcium binding domain 2	203							calcium ion binding (GO:0005509)	p.P67P(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|prostate(1)|stomach(2)	13	all_cancers(71;2.93e-06)|all_epithelial(71;2.13e-05)|all_lung(81;0.0337)|Lung NSC(105;0.0472)|Ovarian(71;0.0584)|Breast(184;0.0716)|all_neural(11;0.0982)		OV - Ovarian serous cystadenocarcinoma(106;0.015)			AAGAAGAACCCACTGGATACA	0.353													C|||	1449	0.289337	0.2489	0.2853	5008	,	,		22027	0.1935		0.4453	False		,,,				2504	0.2853				p.P67P		Atlas-SNP	.											EFCAB2,NS,carcinoma,0,1	EFCAB2	19	1	1	Substitution - coding silent(1)	stomach(1)	c.C201T						PASS	.	C	,	1111,3295	394.9+/-329.4	145,821,1237	101.0	96.0	97.0		201,201	2.6	1.0	1	dbSNP_120	97	3394,5206	502.2+/-375.6	647,2100,1553	no	coding-synonymous,coding-synonymous	EFCAB2	NM_001143943.1,NM_032328.3	,	792,2921,2790	TT,TC,CC		39.4651,25.2156,34.6379	,	67/134,67/163	245245402	4505,8501	2203	4300	6503	SO:0001819	synonymous_variant	84288	exon4			AGAACCCACTGGA	AB209286	CCDS31082.1, CCDS44341.1	1q44	2014-07-18			ENSG00000203666	ENSG00000203666		"""EF-hand domain containing"""	28166	protein-coding gene	gene with protein product	"""dynein regulatory complex subunit 8"""					23427265	Standard	NM_032328		Approved	MGC12458, DRC8, CFAP200	uc001ibc.2	Q5VUJ9	OTTHUMG00000040474	ENST00000366522.2:c.609C>T	1.37:g.245245402C>T		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	52	28	0.538462	NM_001143943	B4DZE9|Q59G23|Q9BS36	Silent	SNP	ENST00000366522.2	37		694|694	0.31776556776556775|0.31776556776556775	135|135	0.27439024390243905|0.27439024390243905	113|113	0.31215469613259667|0.31215469613259667	123|123	0.21503496503496503|0.21503496503496503	323|323	0.4261213720316623|0.4261213720316623	C|C	9.619|9.619	1.133382|1.133382	0.21041|0.21041	0.252156|0.252156	0.394651|0.394651	ENSG00000203666|ENSG00000203666	ENST00000366521|ENST00000551317;ENST00000425550	.|T;T	.|0.80393	.|-1.24;-1.37	5.61|5.61	2.57|2.57	0.30868|0.30868	.|.	.|0.390107	.|0.23325	.|N	.|0.049410	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.09310|0.09310	P|P	0.9999999999999979|0.9999999999999979	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.25984|0.25984	-1.0116|-1.0116	3|6	.|0.87932	.|D	.|0	.|.	3.9513|3.9513	0.09371|0.09371	0.1661:0.5755:0.0:0.2584|0.1661:0.5755:0.0:0.2584	rs10927387;rs60076946;rs10927387|rs10927387;rs60076946;rs10927387	.|.	.|.	.|.	Y|L	126|59	.|ENSP00000447807:P59L;ENSP00000405269:P59L	.|ENSP00000405269:P59L	H|P	+|+	1|2	0|0	EFCAB2|EFCAB2	243312025|243312025	0.842000|0.842000	0.29525|0.29525	1.000000|1.000000	0.80357|0.80357	0.978000|0.978000	0.69477|0.69477	-0.343000|-0.343000	0.07791|0.07791	0.722000|0.722000	0.32252|0.32252	0.557000|0.557000	0.71058|0.71058	CAC|CCA	C|0.661;T|0.339	0.339	strong		0.353	EFCAB2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000097407.2		
RTL1	388015	hgsc.bcm.edu	37	14	101350274	101350274	+	Silent	SNP	C	C	T	rs61993320	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:101350274C>T	ENST00000534062.1	-	1	910	c.852G>A	c.(850-852)ctG>ctA	p.L284L	MIR136_ENST00000385207.1_RNA|MIR431_ENST00000385266.1_RNA|MIR433_ENST00000384837.1_RNA|MIR127_ENST00000384876.1_RNA|MIR432_ENST00000606207.1_RNA	NM_001134888.2	NP_001128360.1	A6NKG5	RTL1_HUMAN	retrotransposon-like 1	284					multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)				breast(1)|endometrium(5)|kidney(4)|large_intestine(1)|lung(5)|pancreas(1)|prostate(2)|skin(2)	21						CTGCCACACGCAGTGCCTGGC	0.592													C|||	60	0.0119808	0.0008	0.0245	5008	,	,		18928	0.0		0.0328	False		,,,				2504	0.0092				p.L284L		Atlas-SNP	.											.	RTL1	120	.	0			c.G852A						PASS	.	C		6,1378		0,6,686	57.0	53.0	54.0		852	0.5	0.1	14	dbSNP_129	54	104,3078		0,104,1487	no	coding-synonymous	RTL1	NM_001134888.2		0,110,2173	TT,TC,CC		3.2684,0.4335,2.4091		284/1359	101350274	110,4456	692	1591	2283	SO:0001819	synonymous_variant	388015	exon1			CACACGCAGTGCC		CCDS53910.1	14q32.2	2012-04-18			ENSG00000254656	ENSG00000254656			14665	protein-coding gene	gene with protein product		611896				16155747, 15854907, 12796779	Standard	NM_001134888		Approved	PEG11, MART1, Mar1	uc010txj.1	A6NKG5	OTTHUMG00000167573	ENST00000534062.1:c.852G>A	14.37:g.101350274C>T		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	49	22	0.44898	NM_001134888	E9PKS8	Silent	SNP	ENST00000534062.1	37	CCDS53910.1																																																																																			C|0.983;T|0.017	0.017	strong		0.592	RTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395127.1	NM_001134888	
KRT40	125115	hgsc.bcm.edu	37	17	39135207	39135207	+	Missense_Mutation	SNP	A	A	G	rs386797018|rs150812789	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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						PASS	.	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	124	0	0		WXS	Illumina HiSeq	Phase_I	126	52	0.412698	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	
TATDN1	83940	hgsc.bcm.edu	37	8	125528135	125528135	+	Silent	SNP	G	G	A	rs11542673	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:125528135G>A	ENST00000276692.6	-	5	376	c.339C>T	c.(337-339)tgC>tgT	p.C113C	TATDN1_ENST00000517678.1_Silent_p.C59C|TATDN1_ENST00000519548.1_Silent_p.C66C|TATDN1_ENST00000605953.1_Silent_p.C113C|TATDN1_ENST00000521546.1_5'UTR	NM_032026.3	NP_114415.1	Q6P1N9	TATD1_HUMAN	TatD DNase domain containing 1	113					DNA catabolic process (GO:0006308)	intracellular organelle (GO:0043229)|nucleus (GO:0005634)	deoxyribonuclease activity (GO:0004536)|endodeoxyribonuclease activity, producing 5'-phosphomonoesters (GO:0016888)|metal ion binding (GO:0046872)			endometrium(1)|kidney(2)|large_intestine(3)|lung(6)|prostate(2)|upper_aerodigestive_tract(1)	15	Ovarian(258;0.00438)|all_neural(195;0.0779)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.00288)			CACCAAGTCCGCATTCTCCTA	0.353													A|||	774	0.154553	0.1248	0.0504	5008	,	,		16843	0.1915		0.0338	False		,,,				2504	0.3548				p.C113C		Atlas-SNP	.											.	TATDN1	29	.	0			c.C339T						PASS	.	A	,	482,3924	781.9+/-414.5	26,430,1747	116.0	110.0	112.0		198,339	5.6	1.0	8	dbSNP_120	112	437,8163	799.7+/-407.4	12,413,3875	no	coding-synonymous,coding-synonymous	TATDN1	NM_001146160.1,NM_032026.3	,	38,843,5622	AA,AG,GG		5.0814,10.9396,7.066	,	66/251,113/298	125528135	919,12087	2203	4300	6503	SO:0001819	synonymous_variant	83940	exon5			AAGTCCGCATTCT	AF212250	CCDS6351.1, CCDS55273.1	8q24.13	2004-06-07			ENSG00000147687	ENSG00000147687			24220	protein-coding gene	gene with protein product						12477932	Standard	NM_032026		Approved	CDA11	uc003yrd.2	Q6P1N9	OTTHUMG00000165068	ENST00000276692.6:c.339C>T	8.37:g.125528135G>A		Somatic	236	0	0		WXS	Illumina HiSeq	Phase_I	202	40	0.19802	NM_032026	B2R5J0|Q8TD02|Q9BY40	Silent	SNP	ENST00000276692.6	37	CCDS6351.1	207	0.09478021978021978	58	0.11788617886178862	17	0.04696132596685083	106	0.1853146853146853	26	0.03430079155672823	A	2.848	-0.238970	0.05944	0.109396	0.050814	ENSG00000147687	ENST00000519232	.	.	.	5.57	5.57	0.84162	.	.	.	.	.	T	0.00109	0.0003	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.14615	-1.0466	3	.	.	.	-8.7102	8.8495	0.35190	0.8556:0.0:0.1444:0.0	rs11542673	.	.	.	W	143	.	.	R	-	1	2	TATDN1	125597316	1.000000	0.71417	1.000000	0.80357	0.348000	0.29142	4.268000	0.58883	0.950000	0.37743	-0.360000	0.07572	CGG	G|0.918;A|0.082	0.082	strong		0.353	TATDN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381655.1	NM_032026	
DND1	373863	hgsc.bcm.edu	37	5	140051086	140051086	+	Nonsense_Mutation	SNP	C	C	T	rs560601583	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:140051086C>T	ENST00000542735.1	-	4	897	c.854G>A	c.(853-855)tGg>tAg	p.W285*	WDR55_ENST00000520764.1_3'UTR|WDR55_ENST00000358337.5_3'UTR	NM_194249.2	NP_919225.1	Q8IYX4	DND1_HUMAN	DND microRNA-mediated repression inhibitor 1	285					germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|negative regulation of gene silencing by miRNA (GO:0060965)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	AU-rich element binding (GO:0017091)|nucleotide binding (GO:0000166)			central_nervous_system(1)|prostate(4)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GAAGCGGTGCCAGCCAGCAGG	0.612													C|||	80	0.0159744	0.0015	0.0159	5008	,	,		21508	0.001		0.0497	False		,,,				2504	0.0164				p.W285X		Atlas-SNP	.											DND1,NS,haematopoietic_neoplasm,0,1	DND1	15	1	0			c.G854A						scavenged	.						9.0	9.0	9.0					5																	140051086		2169	4220	6389	SO:0001587	stop_gained	373863	exon4			CGGTGCCAGCCAG	AY321065	CCDS4236.1	5q31.3	2013-07-31	2013-07-31		ENSG00000256453	ENSG00000256453		"""RNA binding motif (RRM) containing"""	23799	protein-coding gene	gene with protein product		609385	"""dead end homolog 1 (zebrafish)"""			12932328	Standard	NM_194249		Approved	MGC34750, RBMS4	uc003lgt.3	Q8IYX4	OTTHUMG00000129499	ENST00000542735.1:c.854G>A	5.37:g.140051086C>T	ENSP00000445366:p.Trp285*	Somatic	446	1	0.00224215		WXS	Illumina HiSeq	Phase_I	256	43	0.167969	NM_194249		Nonsense_Mutation	SNP	ENST00000542735.1	37	CCDS4236.1	.	.	.	.	.	.	.	.	.	.	C	20.6	4.014746	0.75161	.	.	ENSG00000256453	ENST00000542735	.	.	.	5.37	4.5	0.54988	.	0.187603	0.38605	N	0.001639	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-4.1421	13.1357	0.59407	0.0:0.9222:0.0:0.0778	.	.	.	.	X	285	.	ENSP00000445366:W285X	W	-	2	0	DND1	140031270	1.000000	0.71417	1.000000	0.80357	0.887000	0.51463	3.792000	0.55476	1.520000	0.48965	-0.268000	0.10319	TGG	.	.	none		0.612	DND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251669.2	NM_194249	
GPR180	160897	hgsc.bcm.edu	37	13	95273447	95273447	+	Silent	SNP	G	G	A	rs12429818	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	138	0	0		WXS	Illumina HiSeq	Phase_I	122	117	0.959016	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	
RBL2	5934	hgsc.bcm.edu	37	16	53499374	53499374	+	Missense_Mutation	SNP	G	G	C	rs76818213	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:53499374G>C	ENST00000262133.6	+	13	1860	c.1723G>C	c.(1723-1725)Gaa>Caa	p.E575Q	RBL2_ENST00000544545.1_Missense_Mutation_p.E359Q|RBL2_ENST00000379935.4_3'UTR	NM_005611.3	NP_005602.3	Q08999	RBL2_HUMAN	retinoblastoma-like 2	575	Domain A.|Pocket; binds E1A.				chromatin modification (GO:0016568)|mitotic cell cycle (GO:0000278)|regulation of cell cycle (GO:0051726)|regulation of lipid kinase activity (GO:0043550)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)			breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(17)|ovary(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	45						CATTAGAGCAGAAGATGGCCT	0.318													G|||	51	0.0101837	0.0	0.0115	5008	,	,		13423	0.0		0.0258	False		,,,				2504	0.0174				p.E575Q		Atlas-SNP	.											.	RBL2	115	.	0			c.G1723C						PASS	.	G	GLN/GLU	21,4371	25.3+/-52.1	0,21,2175	70.0	73.0	72.0		1723	5.1	1.0	16	dbSNP_131	72	182,8418	80.6+/-143.3	0,182,4118	yes	missense	RBL2	NM_005611.3	29	0,203,6293	CC,CG,GG		2.1163,0.4781,1.5625	probably-damaging	575/1140	53499374	203,12789	2196	4300	6496	SO:0001583	missense	5934	exon13			AGAGCAGAAGATG	X74594	CCDS10748.1	16q12.2	2014-03-11	2014-03-11		ENSG00000103479	ENSG00000103479			9894	protein-coding gene	gene with protein product		180203				8361765, 8643454	Standard	NM_005611		Approved	Rb2, p130	uc002ehi.4	Q08999	OTTHUMG00000133198	ENST00000262133.6:c.1723G>C	16.37:g.53499374G>C	ENSP00000262133:p.Glu575Gln	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	133	73	0.548872	NM_005611	B7Z913|Q15073|Q16084|Q8NE70|Q92812	Missense_Mutation	SNP	ENST00000262133.6	37	CCDS10748.1	22	0.010073260073260074	1	0.0020325203252032522	2	0.0055248618784530384	0	0.0	19	0.025065963060686015	G	15.82	2.945997	0.53079	0.004781	0.021163	ENSG00000103479	ENST00000262133;ENST00000544405;ENST00000379935;ENST00000544545	D;D;D	0.93307	-3.2;-3.2;-3.2	5.09	5.09	0.68999	Retinoblastoma-associated protein, A-box (1);Cyclin-like (2);	0.051101	0.85682	D	0.000000	D	0.93504	0.7927	M	0.90483	3.12	0.58432	D	0.999998	D;D;D;D	0.89917	0.992;1.0;1.0;1.0	P;D;D;D	0.97110	0.856;1.0;0.998;0.998	D	0.92164	0.5738	10	0.87932	D	0	-18.467	18.8565	0.92254	0.0:0.0:1.0:0.0	.	359;575;285;575	B7Z913;Q8NE70;E9PG04;Q08999	.;.;.;RBL2_HUMAN	Q	575;501;285;359	ENSP00000262133:E575Q;ENSP00000443744:E501Q;ENSP00000444685:E359Q	ENSP00000262133:E575Q	E	+	1	0	RBL2	52056875	1.000000	0.71417	1.000000	0.80357	0.313000	0.28021	9.564000	0.98151	2.520000	0.84964	0.655000	0.94253	GAA	G|0.984;C|0.016	0.016	strong		0.318	RBL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256908.3	NM_005611	
RANBP2	5903	hgsc.bcm.edu	37	2	109371659	109371659	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:109371659G>A	ENST00000283195.6	+	17	2536	c.2410G>A	c.(2410-2412)Gca>Aca	p.A804T		NM_006267.4	NP_006258.3	P49792	RBP2_HUMAN	RAN binding protein 2	804					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						ACCTCGATGGGCAGAAGATCA	0.308																																					p.A804T		Atlas-SNP	.											RANBP2_ENST00000283195,NS,carcinoma,0,2	RANBP2	488	2	0			c.G2410A						scavenged	.						140.0	163.0	155.0					2																	109371659		2199	4297	6496	SO:0001583	missense	5903	exon17			CGATGGGCAGAAG	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.2410G>A	2.37:g.109371659G>A	ENSP00000283195:p.Ala804Thr	Somatic	614	5	0.00814332		WXS	Illumina HiSeq	Phase_I	532	6	0.0112782	NM_006267	Q13074|Q15280|Q53TE2|Q59FH7	Missense_Mutation	SNP	ENST00000283195.6	37	CCDS2079.1	.	.	.	.	.	.	.	.	.	.	g	28.4	4.919938	0.92249	.	.	ENSG00000153201	ENST00000409491;ENST00000283195	T	0.19105	2.17	5.8	5.8	0.92144	.	.	.	.	.	T	0.34337	0.0894	L	0.34521	1.04	0.49130	D	0.999754	D	0.67145	0.996	P	0.58331	0.837	T	0.01532	-1.1331	9	0.54805	T	0.06	-13.8517	20.0609	0.97674	0.0:0.0:1.0:0.0	.	804	P49792	RBP2_HUMAN	T	804	ENSP00000283195:A804T	ENSP00000283195:A804T	A	+	1	0	RANBP2	108738091	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.714000	0.74692	2.737000	0.93849	0.542000	0.68232	GCA	.	.	none		0.308	RANBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253594.1	NM_006267	
AIFM3	150209	hgsc.bcm.edu	37	22	21330787	21330787	+	Silent	SNP	C	C	T	rs7285694	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:21330787C>T	ENST00000399167.2	+	11	1230	c.990C>T	c.(988-990)gcC>gcT	p.A330A	AIFM3_ENST00000440238.2_Silent_p.A330A|AIFM3_ENST00000335375.5_Silent_p.A318A|AIFM3_ENST00000333607.6_Silent_p.A330A|AIFM3_ENST00000465606.1_3'UTR|AIFM3_ENST00000405089.1_Silent_p.A336A|AIFM3_ENST00000399163.2_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	47	0	0		WXS	Illumina HiSeq	Phase_I	36	9	0.25	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	
MGAT5B	146664	hgsc.bcm.edu	37	17	74936576	74936576	+	Silent	SNP	G	G	A	rs8081793	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:74936576G>A	ENST00000569840.2	+	14	2251	c.1677G>A	c.(1675-1677)ccG>ccA	p.P559P	MGAT5B_ENST00000301618.4_Silent_p.P557P|MGAT5B_ENST00000428789.2_Silent_p.P568P	NM_001199172.1	NP_001186101.1	Q3V5L5	MGT5B_HUMAN	mannosyl (alpha-1,6-)-glycoprotein beta-1,6-N-acetyl-glucosaminyltransferase, isozyme B	559					protein N-linked glycosylation (GO:0006487)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase activity (GO:0030144)|metal ion binding (GO:0046872)			breast(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(15)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						GCTTCAGCCCGCCCCACAGCT	0.647													G|||	1327	0.264976	0.2451	0.1744	5008	,	,		16308	0.371		0.2674	False		,,,				2504	0.2444				p.P568P		Atlas-SNP	.											.	MGAT5B	98	.	0			c.G1704A						PASS	.	G	,,	1125,3281	401.3+/-331.9	145,835,1223	76.0	69.0	71.0		1677,1671,1704	-8.8	0.6	17	dbSNP_116	71	2155,6445	370.6+/-335.9	294,1567,2439	no	coding-synonymous,coding-synonymous,coding-synonymous	MGAT5B	NM_001199172.1,NM_144677.2,NM_198955.1	,,	439,2402,3662	AA,AG,GG		25.0581,25.5334,25.2191	,,	559/793,557/791,568/802	74936576	3280,9726	2203	4300	6503	SO:0001819	synonymous_variant	146664	exon12			CAGCCCGCCCCAC	AB109185	CCDS11751.1, CCDS45788.1, CCDS59299.1	17q25.3	2013-02-25	2005-11-16		ENSG00000167889	ENSG00000167889		"""Mannosyl-glycoprotein beta N-acetylglucosaminyltransferases"""	24140	protein-coding gene	gene with protein product		612441	"""mannosyl (alpha-1,6-)-glycoprotein beta-1,6-N-acetyl-glucosaminyltransferase, isoenzyme B"""			14617637, 14623122	Standard	NM_001199172		Approved	GnT-IX, FLJ25132, GnT-VB	uc002jth.3	Q3V5L5	OTTHUMG00000177278	ENST00000569840.2:c.1677G>A	17.37:g.74936576G>A		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	76	34	0.447368	NM_198955	Q6P3S8|Q6P6B3|Q766X5|Q76D04|Q96LS2	Silent	SNP	ENST00000569840.2	37	CCDS59299.1																																																																																			G|0.734;A|0.266	0.266	strong		0.647	MGAT5B-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460624.2	NM_144677	
PELI1	57162	hgsc.bcm.edu	37	2	64327592	64327592	+	Silent	SNP	T	T	C	rs329497	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:64327592T>C	ENST00000358912.4	-	4	685	c.243A>G	c.(241-243)ttA>ttG	p.L81L	PELI1_ENST00000466177.2_5'UTR	NM_020651.3	NP_065702.2	Q96FA3	PELI1_HUMAN	pellino E3 ubiquitin protein ligase 1	81					innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of T cell proliferation (GO:0042130)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cytokine production (GO:0001819)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of toll-like receptor 3 signaling pathway (GO:0034141)|positive regulation of toll-like receptor 4 signaling pathway (GO:0034145)|protein K48-linked ubiquitination (GO:0070936)|response to dsRNA (GO:0043331)|response to lipopolysaccharide (GO:0032496)|Toll signaling pathway (GO:0008063)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)	cytosol (GO:0005829)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(9)|ovary(1)|urinary_tract(1)	19						GGGCCCGAGATAAAGTATATG	0.343													T|||	1754	0.35024	0.0688	0.3112	5008	,	,		15865	0.752		0.2992	False		,,,				2504	0.3967				p.L81L		Atlas-SNP	.											.	PELI1	34	.	0			c.A243G						PASS	.	T		535,3871	241.5+/-251.9	33,469,1701	168.0	148.0	155.0		243	0.1	1.0	2	dbSNP_79	155	2617,5983	424.1+/-354.6	403,1811,2086	no	coding-synonymous	PELI1	NM_020651.3		436,2280,3787	CC,CT,TT		30.4302,12.1425,24.235		81/419	64327592	3152,9854	2203	4300	6503	SO:0001819	synonymous_variant	57162	exon4			CCGAGATAAAGTA		CCDS1876.1	2p13.3	2012-02-23	2012-02-23		ENSG00000197329	ENSG00000197329		"""Pellino homologs"""	8827	protein-coding gene	gene with protein product		614797	"""pellino (Drosophila) homolog 1"", ""pellino homolog 1 (Drosophila)"""			11306823, 16951688	Standard	NM_020651		Approved		uc002sct.4	Q96FA3	OTTHUMG00000129511	ENST00000358912.4:c.243A>G	2.37:g.64327592T>C		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	304	66	0.217105	NM_020651	Q96SM0|Q9GZY5|Q9HCX0	Silent	SNP	ENST00000358912.4	37	CCDS1876.1																																																																																			T|0.705;C|0.295	0.295	strong		0.343	PELI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251686.1	NM_020651	
ZNF106	64397	hgsc.bcm.edu	37	15	42743209	42743209	+	Missense_Mutation	SNP	G	G	A	rs201738274		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:42743209G>A	ENST00000263805.4	-	2	1518	c.1192C>T	c.(1192-1194)Cgt>Tgt	p.R398C	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	398					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)										GGGGAATTACGTGTTTCATCA	0.408																																					p.R398C		Atlas-SNP	.											.	ZFP106	117	.	0			c.C1192T						PASS	.	G	CYS/ARG	0,4406		0,0,2203	310.0	293.0	299.0		1192	0.3	0.0	15		299	2,8596	2.2+/-6.3	0,2,4297	no	missense	ZFP106	NM_022473.1	180	0,2,6500	AA,AG,GG		0.0233,0.0,0.0154	benign	398/1884	42743209	2,13002	2203	4299	6502	SO:0001583	missense	64397	exon2			AATTACGTGTTTC	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.1192C>T	15.37:g.42743209G>A	ENSP00000263805:p.Arg398Cys	Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	187	37	0.197861	NM_022473	B4DZ40|E9PE29|Q6NSD9|Q6PEK1|Q86T43|Q86T45|Q86T50|Q86T58|Q86TA9|Q96M37|Q9H7B8	Missense_Mutation	SNP	ENST00000263805.4	37	CCDS32208.1	.	.	.	.	.	.	.	.	.	.	G	3.212	-0.161477	0.06502	0.0	2.33E-4	ENSG00000103994	ENST00000263805	T	0.55760	0.5	5.24	0.285	0.15705	.	1.426730	0.03878	N	0.276673	T	0.29556	0.0737	N	0.08118	0	0.09310	N	1	P;P	0.45078	0.85;0.476	B;B	0.36885	0.235;0.118	T	0.25710	-1.0124	10	0.66056	D	0.02	-0.4934	4.7175	0.12903	0.0:0.4549:0.2139:0.3312	.	181;398	B4DGC7;Q9H2Y7	.;ZF106_HUMAN	C	398	ENSP00000263805:R398C	ENSP00000263805:R398C	R	-	1	0	ZFP106	40530501	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.176000	0.16782	0.120000	0.18254	-0.269000	0.10298	CGT	G|0.999;A|0.001	0.001	weak		0.408	ZNF106-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422587.1	NM_022473	
KIRREL2	84063	hgsc.bcm.edu	37	19	36351935	36351935	+	Silent	SNP	G	G	T	rs35854130	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:36351935G>T	ENST00000360202.5	+	8	1251	c.1053G>T	c.(1051-1053)gcG>gcT	p.A351A	KIRREL2_ENST00000347900.6_Silent_p.A301A|KIRREL2_ENST00000262625.7_Silent_p.A351A|NPHS1_ENST00000591817.1_Intron|KIRREL2_ENST00000592409.1_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	38	0	0		WXS	Illumina HiSeq	Phase_I	25	14	0.56	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	
TCP10L	140290	hgsc.bcm.edu	37	21	33956579	33956579	+	Silent	SNP	T	T	C	rs2017816	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:33956579T>C	ENST00000300258.3	-	2	149	c.36A>G	c.(34-36)aaA>aaG	p.K12K	TCP10L_ENST00000472557.1_Intron|AP000275.65_ENST00000553001.1_Intron	NM_144659.5	NP_653260.1	Q8TDR4	TCP1L_HUMAN	t-complex 10-like	12					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	nucleus (GO:0005634)	protein self-association (GO:0043621)|repressing transcription factor binding (GO:0070491)|RNA polymerase II transcription corepressor activity (GO:0001106)			breast(1)|central_nervous_system(1)|liver(1)|skin(1)	4						GGGTGCCCTCTTTGGGGTCCC	0.637													C|||	2175	0.434305	0.553	0.3703	5008	,	,		17914	0.3492		0.3767	False		,,,				2504	0.4663				p.K12K		Atlas-SNP	.											TCP10L,rectum,carcinoma,0,1	TCP10L	24	1	0			c.A36G						PASS	.	C		2319,2087		596,1127,480	48.0	44.0	46.0		36	-0.9	0.0	21	dbSNP_92	46	3178,5422		607,1964,1729	no	coding-synonymous	TCP10L	NM_144659.5		1203,3091,2209	CC,CT,TT		36.9535,47.3672,42.2651		12/216	33956579	5497,7509	2203	4300	6503	SO:0001819	synonymous_variant	140290	exon2			GCCCTCTTTGGGG	AF115967	CCDS13616.1	21p22.11	2012-09-20	2012-09-20		ENSG00000242220	ENSG00000242220			11657	protein-coding gene	gene with protein product		608365	"""t-complex 10 (a murine tcp homolog)-like"", ""t-complex 10 (mouse)-like"""			10830953	Standard	NM_144659		Approved	PRED77		Q8TDR4	OTTHUMG00000064901	ENST00000300258.3:c.36A>G	21.37:g.33956579T>C		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	172	67	0.389535	NM_144659	Q53EW0|Q96LN5	Silent	SNP	ENST00000300258.3	37	CCDS13616.1																																																																																			T|0.582;C|0.418	0.418	strong		0.637	TCP10L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139350.1	NM_144659	
WDR27	253769	hgsc.bcm.edu	37	6	170068086	170068086	+	Missense_Mutation	SNP	C	C	T	rs41265385	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:170068086C>T	ENST00000448612.1	-	5	761	c.652G>A	c.(652-654)Ggc>Agc	p.G218S	WDR27_ENST00000423258.1_Intron|WDR27_ENST00000546525.1_5'Flank|WDR27_ENST00000420344.2_Intron|WDR27_ENST00000333572.6_Missense_Mutation_p.G218S	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	66	0	0		WXS	Illumina HiSeq	Phase_I	29	11	0.37931	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	
EXOC3L1	283849	hgsc.bcm.edu	37	16	67221737	67221737	+	Missense_Mutation	SNP	G	G	A	rs149684674		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:67221737G>A	ENST00000314586.6	-	5	671	c.431C>T	c.(430-432)cCg>cTg	p.P144L	EXOC3L1_ENST00000562887.1_Intron	NM_178516.3	NP_848611.2	Q86VI1	EX3L1_HUMAN	exocyst complex component 3-like 1	144	Mediates interaction with EXOC2, EXOC4 and EXOC5. {ECO:0000250}.				exocytosis (GO:0006887)|peptide hormone secretion (GO:0030072)	exocyst (GO:0000145)|secretory granule (GO:0030141)				breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(6)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	21						CACTGCAGCCGGCACTAATGA	0.592													G|||	1	0.000199681	0.0	0.0014	5008	,	,		19157	0.0		0.0	False		,,,				2504	0.0				p.P144L		Atlas-SNP	.											LOC283849,caecum,carcinoma,0,2	EXOC3L1	52	2	0			c.C431T						PASS	.	G	LEU/PRO	1,4393		0,1,2196	60.0	70.0	67.0		431	5.7	1.0	16	dbSNP_134	67	12,8588		0,12,4288	yes	missense	EXOC3L1	NM_178516.3	98	0,13,6484	AA,AG,GG		0.1395,0.0228,0.1	probably-damaging	144/747	67221737	13,12981	2197	4300	6497	SO:0001583	missense	283849	exon5			GCAGCCGGCACTA	AK092858	CCDS10832.1	16q22.1	2011-01-31	2011-01-31	2011-01-31	ENSG00000179044	ENSG00000179044			27540	protein-coding gene	gene with protein product		614117	"""exocyst complex component 3-like"""	EXOC3L		12477932	Standard	NM_178516		Approved	FLJ35539, FLJ35587	uc002erx.1	Q86VI1	OTTHUMG00000137508	ENST00000314586.6:c.431C>T	16.37:g.67221737G>A	ENSP00000325674:p.Pro144Leu	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	83	45	0.542169	NM_178516	A8K7I9|Q8NAD2|Q8TEN2	Missense_Mutation	SNP	ENST00000314586.6	37	CCDS10832.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	G	16.54	3.151062	0.57151	2.28E-4	0.001395	ENSG00000179044	ENST00000314586;ENST00000545725;ENST00000314553	T;T	0.22134	2.77;1.97	5.74	5.74	0.90152	.	0.179126	0.49916	D	0.000134	T	0.46288	0.1385	M	0.77103	2.36	0.58432	D	0.999998	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.69307	0.963;0.92;0.95	T	0.34329	-0.9833	10	0.46703	T	0.11	-20.7533	14.2617	0.66090	0.0:0.0:0.8505:0.1495	.	83;83;144	F5H4W1;B7Z6U0;Q86VI1	.;.;EX3L1_HUMAN	L	144;83;88	ENSP00000325674:P144L;ENSP00000439910:P83L	ENSP00000325008:P88L	P	-	2	0	EXOC3L1	65779238	0.976000	0.34144	0.962000	0.40283	0.656000	0.38851	1.800000	0.38833	2.716000	0.92895	0.650000	0.86243	CCG	G|0.999;A|0.001	0.001	strong		0.592	EXOC3L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268827.2	NM_178516	
CTBP2	1488	hgsc.bcm.edu	37	10	126714966	126714966	+	Intron	SNP	A	A	G	rs3012075	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:126714966A>G	ENST00000337195.5	-	3	458				CTBP2_ENST00000494626.2_Intron|CTBP2_ENST00000309035.6_Missense_Mutation_p.Y455H|CTBP2_ENST00000531469.1_Intron|CTBP2_ENST00000411419.2_Intron	NM_001329.2	NP_001320.1	P56545	CTBP2_HUMAN	C-terminal binding protein 2						negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)|viral genome replication (GO:0019079)|white fat cell differentiation (GO:0050872)	cell junction (GO:0030054)|nucleus (GO:0005634)|synapse (GO:0045202)|transcriptional repressor complex (GO:0017053)	NAD binding (GO:0051287)|oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor (GO:0016616)|transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	25		all_lung(145;0.0132)|Lung NSC(174;0.0193)|all_neural(114;0.116)|Colorectal(57;0.173)		Colorectal(40;0.00572)|COAD - Colon adenocarcinoma(40;0.0127)|GBM - Glioblastoma multiforme(135;0.147)		TGCAGGGGGTACGTGGGGCTC	0.672													A|||	2243	0.447883	0.298	0.3343	5008	,	,		14085	0.6597		0.4811	False		,,,				2504	0.4785				p.Y455H		Atlas-SNP	.											.	CTBP2	100	.	0			c.T1363C						PASS	.	A	,,HIS/TYR	1449,2953		226,997,978	35.0	40.0	38.0		,,1363	4.0	0.0	10	dbSNP_101	38	4276,4324		1059,2158,1083	yes	intron,intron,missense	CTBP2	NM_001083914.1,NM_001329.2,NM_022802.2	,,83	1285,3155,2061	GG,GA,AA		49.7209,32.9169,44.0317	,,possibly-damaging	,,455/986	126714966	5725,7277	2201	4300	6501	SO:0001627	intron_variant	1488	exon1			GGGGGTACGTGGG	AF016507	CCDS7643.1, CCDS7644.1	10q26.13	2008-08-01			ENSG00000175029	ENSG00000175029			2495	protein-coding gene	gene with protein product		602619				9479502, 11864595	Standard	NM_022802		Approved	ribeye	uc001lie.4	P56545	OTTHUMG00000019224	ENST00000337195.5:c.58+12599T>C	10.37:g.126714966A>G		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	72	34	0.472222	NM_022802	A8K2X5|D3DRF5|O43449|Q5SQP7|Q69YI3|Q86SV0|Q9H2T8	Missense_Mutation	SNP	ENST00000337195.5	37	CCDS7643.1	1004	0.4597069597069597	160	0.3252032520325203	124	0.3425414364640884	353	0.6171328671328671	367	0.4841688654353562	A	14.35	2.507941	0.44558	0.329169	0.497209	ENSG00000175029	ENST00000309035	D	0.83250	-1.7	4.04	4.04	0.47022	.	1.938270	0.02364	N	0.077162	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999341817	B	0.06786	0.001	B	0.08055	0.003	T	0.42582	-0.9443	8	0.62326	D	0.03	.	12.024	0.53360	1.0:0.0:0.0:0.0	rs3012075;rs3781414;rs17710513;rs60363956;rs3012075	455	P56545-2	.	H	455	ENSP00000311825:Y455H	ENSP00000311825:Y455H	Y	-	1	0	CTBP2	126704956	0.534000	0.26362	0.003000	0.11579	0.562000	0.35680	4.895000	0.63214	1.829000	0.53265	0.383000	0.25322	TAC	A|0.547;G|0.453	0.453	strong		0.672	CTBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050900.3	NM_001083914	
ZNF567	163081	hgsc.bcm.edu	37	19	37210529	37210529	+	Silent	SNP	A	A	G	rs3108200	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:37210529A>G	ENST00000536254.2	+	6	1125	c.903A>G	c.(901-903)agA>agG	p.R301R	ZNF567_ENST00000360729.4_Silent_p.R270R|ZNF850_ENST00000589390.1_Intron|ZNF567_ENST00000392163.2_Silent_p.R270R|ZNF567_ENST00000585696.1_Silent_p.R270R|ZNF567_ENST00000588311.1_Silent_p.R270R			Q8N184	ZN567_HUMAN	zinc finger protein 567	301					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(6)|lung(8)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	24	Esophageal squamous(110;0.198)		COAD - Colon adenocarcinoma(19;0.0454)|Colorectal(19;0.065)			ATCATCAGAGAACTCACACAG	0.423													A|||	1345	0.26857	0.3654	0.2032	5008	,	,		20404	0.2113		0.2942	False		,,,				2504	0.2168				p.R270R		Atlas-SNP	.											.	ZNF567	61	.	0			c.A810G						PASS	.	A		1515,2891	478.1+/-358.1	242,1031,930	50.0	52.0	52.0		810	1.5	1.0	19	dbSNP_103	52	2553,6047	414.9+/-351.6	383,1787,2130	no	coding-synonymous	ZNF567	NM_152603.2		625,2818,3060	GG,GA,AA		29.686,34.3849,31.2779		270/617	37210529	4068,8938	2203	4300	6503	SO:0001819	synonymous_variant	163081	exon4			TCAGAGAACTCAC	AK093034	CCDS12495.1, CCDS74349.1	19q13.12	2013-10-08				ENSG00000189042		"""Zinc fingers, C2H2-type"", ""-"""	28696	protein-coding gene	gene with protein product						12477932	Standard	XM_006723064		Approved	MGC45586	uc002oep.4	Q8N184		ENST00000536254.2:c.903A>G	19.37:g.37210529A>G		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	94	41	0.43617	NM_152603	B3KX49|Q6N044	Silent	SNP	ENST00000536254.2	37																																																																																				A|0.701;G|0.299	0.299	strong		0.423	ZNF567-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000453549.1	NM_152603	
PABPC4L	132430	hgsc.bcm.edu	37	4	135121368	135121368	+	Silent	SNP	G	G	T	rs2044116	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:135121368G>T	ENST00000421491.3	-	2	1063	c.807C>A	c.(805-807)gtC>gtA	p.V269V	PABPC4L_ENST00000529122.2_Silent_p.V327V			P0CB38	PAB4L_HUMAN	poly(A) binding protein, cytoplasmic 4-like	269							nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			breast(1)|endometrium(2)	3						CCTGTCGCTCGACTTTCTTTT	0.448													T|||	3190	0.636981	0.7186	0.5403	5008	,	,		17612	0.9841		0.329	False		,,,				2504	0.5542				p.V327V		Atlas-SNP	.											.	PABPC4L	60	.	0			c.C981A						PASS	.	T		925,459		310,305,77	75.0	61.0	65.0		981	-3.3	0.1	4	dbSNP_94	65	980,2202		142,696,753	no	coding-synonymous	PABPC4L	NM_001114734.1		452,1001,830	TT,TG,GG		30.7982,33.1647,41.7214		327/429	135121368	1905,2661	692	1591	2283	SO:0001819	synonymous_variant	132430	exon2			TCGCTCGACTTTC	AY672099		4q28.3	2013-02-12				ENSG00000254535		"""RNA binding motif (RRM) containing"""	31955	protein-coding gene	gene with protein product							Standard	NM_001114734		Approved		uc010ioe.3	P0CB38		ENST00000421491.3:c.807C>A	4.37:g.135121368G>T		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	70	70	1	NM_001114734		Silent	SNP	ENST00000421491.3	37																																																																																				G|0.347;T|0.653	0.653	strong		0.448	PABPC4L-001	KNOWN	upstream_ATG|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000364399.2	NM_001114734	
USP8	9101	hgsc.bcm.edu	37	15	50782703	50782703	+	Missense_Mutation	SNP	A	A	G	rs11638390	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:50782703A>G	ENST00000396444.3	+	14	2553	c.2215A>G	c.(2215-2217)Aca>Gca	p.T739A	USP8_ENST00000433963.1_Missense_Mutation_p.T739A|USP8_ENST00000307179.4_Missense_Mutation_p.T739A|USP8_ENST00000425032.3_Missense_Mutation_p.T633A	NM_001128610.1|NM_005154.3	NP_001122082.1|NP_005145.3	P40818	UBP8_HUMAN	ubiquitin specific peptidase 8	739			T -> A (in dbSNP:rs11638390).		cell proliferation (GO:0008283)|endosome organization (GO:0007032)|mitotic cytokinesis (GO:0000281)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)|Ras protein signal transduction (GO:0007265)|ubiquitin-dependent protein catabolic process (GO:0006511)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|extrinsic component of plasma membrane (GO:0019897)|midbody (GO:0030496)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|ubiquitin-specific protease activity (GO:0004843)			central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(5)|lung(16)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	35				all cancers(107;0.000225)|GBM - Glioblastoma multiforme(94;0.000771)		AGTAACTCCAACAGTTAATCG	0.413													a|||	578	0.115415	0.0265	0.2406	5008	,	,		19297	0.002		0.1789	False		,,,				2504	0.1984				p.T739A		Atlas-SNP	.											.	USP8	90	.	0			c.A2215G						PASS	.	G	ALA/THR,ALA/THR,ALA/THR	221,4171	129.8+/-166.5	6,209,1981	107.0	108.0	107.0		2215,2215,2215	-6.6	0.0	15	dbSNP_120	107	1571,7017	292.4+/-300.8	157,1257,2880	yes	missense,missense,missense	USP8	NM_001128610.1,NM_001128611.1,NM_005154.3	58,58,58	163,1466,4861	GG,GA,AA		18.293,5.0319,13.8059	benign,benign,benign	739/1119,739/1119,739/1119	50782703	1792,11188	2196	4294	6490	SO:0001583	missense	9101	exon14			ACTCCAACAGTTA	D29956	CCDS10137.1, CCDS61632.1	15q21.1	2014-03-03	2005-08-08		ENSG00000138592	ENSG00000138592		"""Ubiquitin-specific peptidases"""	12631	protein-coding gene	gene with protein product		603158	"""ubiquitin specific protease 8"""			12838346, 9582025, 24482476	Standard	NM_005154		Approved	HumORF8, KIAA0055, UBPY, SPG59	uc001zyl.4	P40818	OTTHUMG00000131645	ENST00000396444.3:c.2215A>G	15.37:g.50782703A>G	ENSP00000379721:p.Thr739Ala	Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	38	21	0.552632	NM_001128610	B4DKA8|Q2TB31|Q7Z3U2|Q86VA0|Q8IWI7	Missense_Mutation	SNP	ENST00000396444.3	37	CCDS10137.1	236	0.10805860805860806	18	0.036585365853658534	88	0.2430939226519337	0	0.0	130	0.17150395778364116	a	0.126	-1.118975	0.01785	0.050319	0.18293	ENSG00000138592	ENST00000396444;ENST00000433963;ENST00000307179;ENST00000425032	T;T;T;T	0.17213	2.29;2.29;2.29;4.38	5.6	-6.61	0.01818	.	0.928719	0.09316	N	0.818875	T	0.00012	0.0000	N	0.04508	-0.205	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.47471	-0.9115	9	0.16896	T	0.51	-0.0226	8.1026	0.30865	0.2895:0.0902:0.5314:0.0889	rs11638390;rs17519682;rs52795257;rs11638390	633;739	B4DKA8;P40818	.;UBP8_HUMAN	A	739;739;739;633	ENSP00000379721:T739A;ENSP00000405537:T739A;ENSP00000302239:T739A;ENSP00000412682:T633A	ENSP00000302239:T739A	T	+	1	0	USP8	48569995	0.000000	0.05858	0.003000	0.11579	0.003000	0.03518	-1.084000	0.03393	-1.515000	0.01784	-1.926000	0.00513	ACA	A|0.874;G|0.126	0.126	strong		0.413	USP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254541.1	NM_005154	
IFIT1	3434	hgsc.bcm.edu	37	10	91162182	91162182	+	Silent	SNP	C	C	T	rs41284944	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:91162182C>T	ENST00000371804.3	+	2	317	c.150C>T	c.(148-150)taC>taT	p.Y50Y	IFIT1_ENST00000546318.1_Silent_p.Y19Y|LIPA_ENST00000371837.1_Intron	NM_001270927.1|NM_001548.4	NP_001257856.1|NP_001539.3	P09914	IFIT1_HUMAN	interferon-induced protein with tetratricopeptide repeats 1	50					cellular response to exogenous dsRNA (GO:0071360)|cellular response to type I interferon (GO:0071357)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|intracellular transport of viral protein in host cell (GO:0019060)|negative regulation of defense response to virus by host (GO:0050689)|negative regulation of helicase activity (GO:0051097)|negative regulation of protein binding (GO:0032091)|negative regulation of viral genome replication (GO:0045071)|positive regulation of viral genome replication (GO:0045070)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	RNA binding (GO:0003723)			breast(1)|central_nervous_system(1)|kidney(2)|large_intestine(6)|lung(2)|prostate(2)|upper_aerodigestive_tract(1)	15						ACACCAAATACAGTGTGGGAA	0.408													.|||	396	0.0790735	0.1672	0.0346	5008	,	,		21574	0.1052		0.0388	False		,,,				2504	0.0061				p.Y50Y		Atlas-SNP	.											.	IFIT1	30	.	0			c.C150T						PASS	.	C		582,3824	256.1+/-261.0	42,498,1663	102.0	94.0	96.0		150	4.2	0.1	10	dbSNP_127	96	256,8344	99.5+/-161.0	7,242,4051	no	coding-synonymous	IFIT1	NM_001548.3		49,740,5714	TT,TC,CC		2.9767,13.2093,6.4432		50/479	91162182	838,12168	2203	4300	6503	SO:0001819	synonymous_variant	3434	exon3			CAAATACAGTGTG	M24594	CCDS31243.1, CCDS59220.1	10q23.31	2014-05-22			ENSG00000185745	ENSG00000185745		"""Tetratricopeptide (TTC) repeat domain containing"""	5407	protein-coding gene	gene with protein product		147690		G10P1, IFI56, IFNAI1		1377167, 3360121	Standard	NM_001548		Approved	GARG-16	uc001kgi.4	P09914	OTTHUMG00000018712	ENST00000371804.3:c.150C>T	10.37:g.91162182C>T		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	128	65	0.507812	NM_001270927	B3KS50|D3DR31|Q5T7J1|Q96QM5	Silent	SNP	ENST00000371804.3	37	CCDS31243.1																																																																																			C|0.933;T|0.067	0.067	strong		0.408	IFIT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049302.1	NM_001548	
DPP4	1803	hgsc.bcm.edu	37	2	162876789	162876789	+	Silent	SNP	T	T	C	rs200990780		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:162876789T>C	ENST00000360534.3	-	14	1754	c.1194A>G	c.(1192-1194)acA>acG	p.T398T	DPP4_ENST00000491591.1_5'Flank	NM_001935.3	NP_001926.2	P27487	DPP4_HUMAN	dipeptidyl-peptidase 4	398					cell adhesion (GO:0007155)|endothelial cell migration (GO:0043542)|negative regulation of extracellular matrix disassembly (GO:0010716)|positive regulation of cell proliferation (GO:0008284)|regulation of cell-cell adhesion mediated by integrin (GO:0033632)|response to hypoxia (GO:0001666)|T cell activation (GO:0042110)|T cell costimulation (GO:0031295)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|endocytic vesicle (GO:0030139)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intercellular canaliculus (GO:0046581)|invadopodium membrane (GO:0071438)|lamellipodium (GO:0030027)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|plasma membrane (GO:0005886)	dipeptidyl-peptidase activity (GO:0008239)|identical protein binding (GO:0042802)|protease binding (GO:0002020)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(1)|lung(21)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	48					Alogliptin(DB06203)|Atorvastatin(DB01076)|Linagliptin(DB08882)|Liraglutide(DB06655)|Saxagliptin(DB06335)|Sitagliptin(DB01261)|Vildagliptin(DB04876)	AGGTGCCTTTTGTAATAAATG	0.323																																					p.T398T		Atlas-SNP	.											.	DPP4	90	.	0			c.A1194G						PASS	.						95.0	90.0	92.0					2																	162876789		2203	4300	6503	SO:0001819	synonymous_variant	1803	exon14			GCCTTTTGTAATA	M74777	CCDS2216.1	2q24.2	2013-09-19	2008-08-01		ENSG00000197635	ENSG00000197635	3.4.14.5	"""CD molecules"""	3009	protein-coding gene	gene with protein product		102720	"""dipeptidylpeptidase IV (CD26, adenosine deaminase complexing protein 2)"", ""adenosine deaminase complexing protein 2"""	CD26, ADCP2		8101391	Standard	NM_001935		Approved	DPPIV	uc002ubz.3	P27487	OTTHUMG00000132056	ENST00000360534.3:c.1194A>G	2.37:g.162876789T>C		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	73	35	0.479452	NM_001935	Q53TN1	Silent	SNP	ENST00000360534.3	37	CCDS2216.1																																																																																			.	.	weak		0.323	DPP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255079.2		
MUC4	4585	hgsc.bcm.edu	37	3	195506661	195506661	+	Silent	SNP	G	G	C	rs143659849	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195506661G>C	ENST00000463781.3	-	2	12249	c.11790C>G	c.(11788-11790)tcC>tcG	p.S3930S	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Silent_p.S3930S	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)		CATGTCCTGTGGATGCCGAGG	0.582													.|||	177	0.0353435	0.0129	0.0807	5008	,	,		11453	0.0149		0.0845	False		,,,				2504	0.0041				p.S3930S		Atlas-SNP	.											.	MUC4	1505	.	0			c.C11790G						PASS	.						23.0	21.0	22.0					3																	195506661		487	1106	1593	SO:0001819	synonymous_variant	4585	exon2			TCCTGTGGATGCC	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.11790C>G	3.37:g.195506661G>C		Somatic	203	0	0		WXS	Illumina HiSeq	Phase_I	95	89	0.936842	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|0.964;C|0.036	0.036	strong		0.582	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
TTLL1	25809	hgsc.bcm.edu	37	22	43455432	43455432	+	Silent	SNP	G	G	A	rs5759125	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:43455432G>A	ENST00000266254.7	-	8	1089	c.849C>T	c.(847-849)gaC>gaT	p.D283D	TTLL1_ENST00000331018.7_Silent_p.D283D	NM_012263.4	NP_036395.1	O95922	TTLL1_HUMAN	tubulin tyrosine ligase-like family, member 1	283	TTL. {ECO:0000255|PROSITE- ProRule:PRU00568}.				axoneme assembly (GO:0035082)|epithelial cilium movement (GO:0003351)|protein polyglutamylation (GO:0018095)	cytoplasm (GO:0005737)|microtubule (GO:0005874)	tubulin-glutamic acid ligase activity (GO:0070740)			breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(7)|ovary(1)|skin(2)|stomach(1)	23		Ovarian(80;0.0694)		BRCA - Breast invasive adenocarcinoma(115;0.00461)		AGTGGATCTCGTCGAACAGCT	0.642													G|||	1998	0.398962	0.4977	0.3141	5008	,	,		16415	0.7173		0.1064	False		,,,				2504	0.2986				p.D283D		Atlas-SNP	.											TTLL1,NS,carcinoma,0,1	TTLL1	41	1	0			c.C849T						PASS	.	G		1891,2515	541.3+/-375.7	411,1069,723	99.0	80.0	86.0		849	-2.6	1.0	22	dbSNP_114	86	921,7679	205.1+/-247.6	50,821,3429	no	coding-synonymous	TTLL1	NM_012263.4		461,1890,4152	AA,AG,GG		10.7093,42.9187,21.6208		283/424	43455432	2812,10194	2203	4300	6503	SO:0001819	synonymous_variant	25809	exon8			GATCTCGTCGAAC	AL096886	CCDS14043.1	22q13.1	2013-02-14			ENSG00000100271	ENSG00000100271		"""Tubulin tyrosine ligase-like family"""	1312	protein-coding gene	gene with protein product		608955	"""tubulin tyrosine ligase-like 1"""	C22orf7		10591208, 11054573	Standard	NM_012263		Approved		uc003bdi.3	O95922	OTTHUMG00000150699	ENST00000266254.7:c.849C>T	22.37:g.43455432G>A		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	99	45	0.454545	NM_012263	B2RDS7|Q9BR27|Q9NRS9|Q9UMU0	Silent	SNP	ENST00000266254.7	37	CCDS14043.1	782	0.35805860805860806	218	0.44308943089430897	104	0.287292817679558	391	0.6835664335664335	69	0.09102902374670185	G	10.57	1.387949	0.25118	0.429187	0.107093	ENSG00000100271	ENST00000495814	.	.	.	5.48	-2.61	0.06171	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999984994	.	.	.	.	.	.	T	0.40194	-0.9576	3	.	.	.	.	5.4795	0.16715	0.5278:0.2927:0.1795:0.0	rs5759125;rs61106588;rs5759125	.	.	.	M	209	.	.	T	-	2	0	TTLL1	41785376	1.000000	0.71417	0.959000	0.39883	0.991000	0.79684	1.739000	0.38217	-0.226000	0.09899	0.561000	0.74099	ACG	G|0.704;A|0.296	0.296	strong		0.642	TTLL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319659.1	NM_012263	
RANBP6	26953	hgsc.bcm.edu	37	9	6012734	6012734	+	Silent	SNP	A	A	C	rs106033	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:6012734A>C	ENST00000259569.5	-	1	2884	c.2874T>G	c.(2872-2874)ctT>ctG	p.L958L	RANBP6_ENST00000485372.1_5'Flank	NM_001243202.1|NM_001243203.1|NM_012416.3	NP_001230131.1|NP_001230132.1|NP_036548.1	O60518	RNBP6_HUMAN	RAN binding protein 6	958					protein transport (GO:0015031)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				NS(1)|breast(4)|central_nervous_system(1)|endometrium(8)|kidney(5)|large_intestine(8)|lung(9)|ovary(7)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	51		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.00522)|Lung(218;0.101)		CTTTTACCAGAAGTGGAACAG	0.403													C|||	2134	0.426118	0.5734	0.3112	5008	,	,		20773	0.4266		0.2435	False		,,,				2504	0.4959				p.L958L		Atlas-SNP	.											.	RANBP6	127	.	0			c.T2874G						PASS	.	C		2286,2120	576.0+/-384.1	575,1136,492	85.0	80.0	82.0		2874	2.6	1.0	9	dbSNP_79	82	1997,6603	721.1+/-406.3	220,1557,2523	no	coding-synonymous	RANBP6	NM_012416.3		795,2693,3015	CC,CA,AA		23.2209,48.1162,32.931		958/1106	6012734	4283,8723	2203	4300	6503	SO:0001819	synonymous_variant	26953	exon1			TACCAGAAGTGGA	AF039023	CCDS6467.1	9p24.1	2008-03-26			ENSG00000137040	ENSG00000137040			9851	protein-coding gene	gene with protein product							Standard	NM_001243202		Approved		uc003zjr.3	O60518	OTTHUMG00000019512	ENST00000259569.5:c.2874T>G	9.37:g.6012734A>C		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	92	55	0.597826	NM_012416	Q5T7X4|Q7Z3V2|Q96E78	Silent	SNP	ENST00000259569.5	37	CCDS6467.1																																																																																			A|0.647;C|0.353	0.353	strong		0.403	RANBP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051650.1	NM_012416	
MRPS2	51116	hgsc.bcm.edu	37	9	138395624	138395624	+	Missense_Mutation	SNP	C	C	T	rs34149047	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:138395624C>T	ENST00000371785.1	+	5	745	c.536C>T	c.(535-537)gCg>gTg	p.A179V	C9orf116_ENST00000371791.1_5'Flank|RP11-426A6.5_ENST00000415062.1_RNA|MRPS2_ENST00000488610.1_3'UTR|MRPS2_ENST00000241600.5_Missense_Mutation_p.A179V			Q9Y399	RT02_HUMAN	mitochondrial ribosomal protein S2	179					translation (GO:0006412)	mitochondrion (GO:0005739)|small ribosomal subunit (GO:0015935)	structural constituent of ribosome (GO:0003735)			large_intestine(2)|lung(1)|prostate(2)|urinary_tract(1)	6				OV - Ovarian serous cystadenocarcinoma(145;1.46e-53)|Epithelial(140;2.04e-47)|all cancers(34;1.23e-42)		CTGACCAACGCGCGCCTCCTC	0.617													C|||	78	0.0155751	0.0	0.062	5008	,	,		17660	0.0		0.0149	False		,,,				2504	0.0204				p.A179V		Atlas-SNP	.											.	MRPS2	17	.	0			c.C536T						PASS	.	C	VAL/ALA	10,4396	16.8+/-37.8	0,10,2193	55.0	53.0	54.0		536	2.7	0.1	9	dbSNP_126	54	103,8497	56.4+/-117.6	1,101,4198	yes	missense	MRPS2	NM_016034.3	64	1,111,6391	TT,TC,CC		1.1977,0.227,0.8688	possibly-damaging	179/297	138395624	113,12893	2203	4300	6503	SO:0001583	missense	51116	exon4			CCAACGCGCGCCT	AB051627	CCDS6990.1	9q34	2012-09-13			ENSG00000122140	ENSG00000122140		"""Mitochondrial ribosomal proteins / small subunits"""	14495	protein-coding gene	gene with protein product		611971					Standard	NM_016034		Approved	CGI-91	uc004cfv.5	Q9Y399	OTTHUMG00000020910	ENST00000371785.1:c.536C>T	9.37:g.138395624C>T	ENSP00000360850:p.Ala179Val	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	44	21	0.477273	NM_016034	Q5T899|Q9BSQ4	Missense_Mutation	SNP	ENST00000371785.1	37	CCDS6990.1	34	0.015567765567765568	0	0.0	21	0.058011049723756904	0	0.0	13	0.017150395778364115	C	12.60	1.987015	0.35036	0.00227	0.011977	ENSG00000122140	ENST00000371785;ENST00000241600;ENST00000453385	T;T;T	0.22134	1.97;1.97;1.97	4.56	2.7	0.31948	Ribosomal protein S2, flavodoxin-like domain (1);	0.311321	0.33419	N	0.004940	T	0.05868	0.0153	M	0.76328	2.33	0.50313	D	0.999862	D;D	0.76494	0.997;0.999	D;D	0.66497	0.91;0.944	T	0.00166	-1.1965	10	0.48119	T	0.1	-17.8138	8.6428	0.33987	0.0:0.7607:0.1536:0.0857	rs34149047	193;179	Q5T8A0;Q9Y399	.;RT02_HUMAN	V	179;179;193	ENSP00000360850:A179V;ENSP00000241600:A179V;ENSP00000400082:A193V	ENSP00000241600:A179V	A	+	2	0	MRPS2	137535445	0.997000	0.39634	0.114000	0.21550	0.205000	0.24178	5.095000	0.64529	0.535000	0.28714	0.585000	0.79938	GCG	C|0.990;T|0.010	0.010	strong		0.617	MRPS2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054998.1		
HTR3D	200909	hgsc.bcm.edu	37	3	183754294	183754294	+	Splice_Site	SNP	G	G	C	rs6443930	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:183754294G>C	ENST00000382489.3	+	4	511		c.e4+1		HTR3D_ENST00000334128.2_Missense_Mutation_p.G36A|HTR3D_ENST00000453435.1_Intron|HTR3D_ENST00000428798.2_Missense_Mutation_p.G110A	NM_001163646.1	NP_001157118.1	Q70Z44	5HT3D_HUMAN	5-hydroxytryptamine (serotonin) receptor 3D, ionotropic						ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	extracellular ligand-gated ion channel activity (GO:0005230)	p.G36A(1)		large_intestine(3)|lung(3)|prostate(1)|skin(1)|stomach(2)	10	all_cancers(143;2.33e-10)|Ovarian(172;0.0303)		Epithelial(37;6.23e-36)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)		Ergoloid mesylate(DB01049)	ATGGACAGAGGTGAACGCTCT	0.483													c|||	2673	0.533746	0.708	0.4582	5008	,	,		22552	0.4841		0.4712	False		,,,				2504	0.4673				p.G110A		Atlas-SNP	.											HTR3D,NS,carcinoma,0,1	HTR3D	65	1	1	Substitution - Missense(1)	stomach(1)	c.G329C						scavenged	.		ALA/GLY,,ALA/GLY	2848,1558	488.8+/-361.3	929,990,284	133.0	107.0	116.0		329,,107	4.1	0.2	3	dbSNP_116	116	3862,4738	609.3+/-395.5	879,2104,1317	yes	missense,splice-5,missense	HTR3D	NM_001145143.1,NM_001163646.1,NM_182537.2	60,,60	1808,3094,1601	CC,CG,GG		44.907,35.3609,48.4084	,,	110/405,,36/280	183754294	6710,6296	2203	4300	6503	SO:0001630	splice_region_variant	200909	exon4			ACAGAGGTGAACG	AY159812	CCDS3249.1, CCDS46966.1, CCDS54685.1	3q27	2012-05-22	2012-02-03		ENSG00000186090	ENSG00000186090		"""5-HT (serotonin) receptors"", ""Ligand-gated ion channels / 5-HT (serotonin) receptors, ionotropic"""	24004	protein-coding gene	gene with protein product		610122	"""5-hydroxytryptamine (serotonin) receptor 3 family member D"""			12801637	Standard	NM_001145143		Approved		uc011bqv.2	Q70Z44	OTTHUMG00000156858	ENST00000382489.3:c.511+1G>C	3.37:g.183754294G>C		Somatic	174	1	0.00574713		WXS	Illumina HiSeq	Phase_I	137	63	0.459854	NM_001145143	C9J2I6|J3QT78|Q495N5|Q495N6|Q7Z6B3	Missense_Mutation	SNP	ENST00000382489.3	37	CCDS54685.1	1164|1164	0.532967032967033|0.532967032967033	345|345	0.7012195121951219|0.7012195121951219	181|181	0.5|0.5	301|301	0.5262237762237763|0.5262237762237763	337|337	0.4445910290237467|0.4445910290237467	c|c	7.379|7.379	0.628449|0.628449	0.14257|0.14257	0.646391|0.646391	0.44907|0.44907	ENSG00000186090|ENSG00000186090	ENST00000382489|ENST00000334128;ENST00000428798	.|T;T	.|0.74947	.|-0.69;-0.89	4.98|4.98	4.1|4.1	0.47936|0.47936	.|.	.|.	.|.	.|.	.|.	.|T	.|0.00012	.|0.0000	.|.	.|.	.|.	0.09310|0.09310	P|P	0.9999999999993161|0.9999999999993161	.|B	.|0.02656	.|0.0	.|B	.|0.01281	.|0.0	.|T	.|0.39901	.|-0.9591	.|7	.|0.06236	.|T	.|0.91	.|-5.2856	8.6753|8.6753	0.34176|0.34176	0.0:0.7564:0.1574:0.0861|0.0:0.7564:0.1574:0.0861	rs6443930;rs6443930|rs6443930;rs6443930	.|36	.|F6WC43	.|.	.|A	-1|36;110	.|ENSP00000334315:G36A;ENSP00000405409:G110A	.|ENSP00000334315:G36A	.|G	+|+	.|2	.|0	HTR3D|HTR3D	185236988|185236988	0.947000|0.947000	0.32204|0.32204	0.202000|0.202000	0.23494|0.23494	0.107000|0.107000	0.19398|0.19398	0.515000|0.515000	0.22801|0.22801	1.468000|1.468000	0.48064|0.48064	-0.126000|-0.126000	0.14955|0.14955	.|GGT	G|0.481;C|0.519	0.519	strong		0.483	HTR3D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000346289.1	NM_182537	Intron
HES7	84667	hgsc.bcm.edu	37	17	8025712	8025712	+	Silent	SNP	A	A	G	rs1348325	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:8025712A>G	ENST00000317814.4	-	3	174	c.175T>C	c.(175-177)Ttg>Ctg	p.L59L	HES7_ENST00000541682.2_Silent_p.L59L			Q9BYE0	HES7_HUMAN	hes family bHLH transcription factor 7	59	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)										GCGAACTCCAATATCTCCGCT	0.672													G|||	966	0.192891	0.3812	0.1182	5008	,	,		10100	0.1002		0.0974	False		,,,				2504	0.1851				p.L59L		Atlas-SNP	.											.	.	.	.	0			c.T175C						PASS	.	G	,	1188,2462		184,820,821	12.0	13.0	13.0		175,175	3.2	1.0	17	dbSNP_88	13	751,7371		43,665,3353	no	coding-synonymous,coding-synonymous	HES7	NM_001165967.1,NM_032580.3	,	227,1485,4174	GG,GA,AA		9.2465,32.5479,16.4713	,	59/231,59/226	8025712	1939,9833	1825	4061	5886	SO:0001819	synonymous_variant	84667	exon3			ACTCCAATATCTC	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.175T>C	17.37:g.8025712A>G		Somatic	266	0	0		WXS	Illumina HiSeq	Phase_I	283	117	0.413428	NM_001165967	F8VPC9	Silent	SNP	ENST00000317814.4	37	CCDS42258.1																																																																																			A|0.823;G|0.177	0.177	strong		0.672	HES7-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000441479.1	NM_032580	
KLHDC7A	127707	hgsc.bcm.edu	37	1	18807938	18807938	+	Missense_Mutation	SNP	C	C	A	rs2992754	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:18807938C>A	ENST00000400664.1	+	1	515	c.463C>A	c.(463-465)Cct>Act	p.P155T		NM_152375.2	NP_689588.2	Q5VTJ3	KLD7A_HUMAN	kelch domain containing 7A	155						integral component of membrane (GO:0016021)				endometrium(1)|kidney(1)|large_intestine(4)|lung(11)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)	22		Colorectal(325;3.46e-05)|all_lung(284;0.000152)|Lung NSC(340;0.000185)|Breast(348;0.00046)|Renal(390;0.000518)|Ovarian(437;0.0014)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00462)|BRCA - Breast invasive adenocarcinoma(304;1.41e-05)|Kidney(64;0.00017)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)		TAACCCTGACCCTCCCCATTT	0.652													C|||	1336	0.266773	0.174	0.2464	5008	,	,		17697	0.623		0.1252	False		,,,				2504	0.1851				p.P155T		Atlas-SNP	.											.	KLHDC7A	60	.	0			c.C463A						PASS	.	C	THR/PRO	797,3361		75,647,1357	32.0	38.0	36.0		463	5.4	0.0	1	dbSNP_101	36	1208,7214		80,1048,3083	yes	missense	KLHDC7A	NM_152375.2	38	155,1695,4440	AA,AC,CC		14.3434,19.1679,15.938	benign	155/778	18807938	2005,10575	2079	4211	6290	SO:0001583	missense	127707	exon1			CCTGACCCTCCCC	AK096072	CCDS185.2	1p36.13	2008-02-05			ENSG00000179023	ENSG00000179023			26791	protein-coding gene	gene with protein product							Standard	NM_152375		Approved	FLJ38753	uc001bax.3	Q5VTJ3	OTTHUMG00000002431	ENST00000400664.1:c.463C>A	1.37:g.18807938C>A	ENSP00000383505:p.Pro155Thr	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	75	35	0.466667	NM_152375	Q8N8W6	Missense_Mutation	SNP	ENST00000400664.1	37	CCDS185.2	632	0.2893772893772894	95	0.19308943089430894	90	0.24861878453038674	355	0.6206293706293706	92	0.12137203166226913	C	15.27	2.784993	0.49997	0.191679	0.143434	ENSG00000179023	ENST00000400664;ENST00000540290	T	0.74421	-0.84	5.4	5.4	0.78164	.	2.160560	0.03659	U	0.242324	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	P	0.44877	0.845	B	0.43478	0.421	T	0.33879	-0.9851	9	0.18710	T	0.47	.	16.2414	0.82409	0.0:1.0:0.0:0.0	rs2992754	155	Q5VTJ3	KLD7A_HUMAN	T	155;92	ENSP00000383505:P155T	ENSP00000383505:P155T	P	+	1	0	KLHDC7A	18680525	0.005000	0.15991	0.023000	0.16930	0.269000	0.26545	2.052000	0.41316	2.680000	0.91292	0.591000	0.81541	CCT	C|0.770;A|0.230	0.230	strong		0.652	KLHDC7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006923.3	NM_152375	
HERC2	8924	hgsc.bcm.edu	37	15	28517492	28517492	+	Missense_Mutation	SNP	C	C	A	rs77399744		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:28517492C>A	ENST00000261609.7	-	9	1060	c.952G>T	c.(952-954)Gac>Tac	p.D318Y		NM_004667.5	NP_004658.3			HECT and RLD domain containing E3 ubiquitin protein ligase 2											NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(3)|cervix(3)|endometrium(20)|kidney(11)|large_intestine(33)|lung(95)|ovary(7)|prostate(8)|skin(7)|upper_aerodigestive_tract(8)|urinary_tract(4)	204		all_lung(180;1.3e-11)|Breast(32;0.000194)|Colorectal(260;0.227)		all cancers(64;3.93e-09)|Epithelial(43;9.99e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0271)|GBM - Glioblastoma multiforme(186;0.0497)|Lung(196;0.199)		GCCCCGCTGTCCCACAGCTGA	0.478																																					p.D318Y		Atlas-SNP	.											.	HERC2	501	.	0			c.G952T						PASS	.						49.0	40.0	43.0					15																	28517492		2203	4300	6503	SO:0001583	missense	8924	exon9			CGCTGTCCCACAG	AF071172	CCDS10021.1	15q13	2012-02-23	2012-02-23		ENSG00000128731	ENSG00000128731			4868	protein-coding gene	gene with protein product		605837	"""hect domain and RLD 2"""			9949213	Standard	NM_004667		Approved	jdf2, p528, D15F37S1	uc001zbj.4	O95714	OTTHUMG00000129251	ENST00000261609.7:c.952G>T	15.37:g.28517492C>A	ENSP00000261609:p.Asp318Tyr	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	94	17	0.180851	NM_004667		Missense_Mutation	SNP	ENST00000261609.7	37	CCDS10021.1	.	.	.	.	.	.	.	.	.	.	C	27.1	4.803213	0.90623	.	.	ENSG00000128731	ENST00000261609	T	0.48836	0.8	5.58	5.58	0.84498	.	0.062950	0.64402	D	0.000003	T	0.50718	0.1632	L	0.59436	1.845	0.80722	D	1	P	0.44090	0.826	B	0.41088	0.347	T	0.56884	-0.7905	10	0.72032	D	0.01	.	19.5567	0.95351	0.0:1.0:0.0:0.0	.	318	O95714	HERC2_HUMAN	Y	318	ENSP00000261609:D318Y	ENSP00000261609:D318Y	D	-	1	0	HERC2	26191087	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.761000	0.85260	2.641000	0.89580	0.650000	0.86243	GAC	C|0.500;A|0.500	0.500	weak		0.478	HERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251358.2	NM_004667	
WLS	79971	hgsc.bcm.edu	37	1	68624878	68624878	+	Silent	SNP	C	C	T	rs3748705	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:68624878C>T	ENST00000262348.4	-	3	685	c.432G>A	c.(430-432)gcG>gcA	p.A144A	GNG12-AS1_ENST00000420587.1_RNA|WLS_ENST00000354777.2_Silent_p.A142A|WLS_ENST00000370976.3_Silent_p.A53A|WLS_ENST00000540432.1_Silent_p.A144A|GNG12-AS1_ENST00000413628.1_RNA	NM_024911.6	NP_079187.3	Q5T9L3	WLS_HUMAN	wntless Wnt ligand secretion mediator	144	Interacts with Wnt proteins. {ECO:0000250}.				anterior/posterior axis specification (GO:0009948)|mesoderm formation (GO:0001707)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|Wnt signaling pathway (GO:0016055)	cytoplasmic vesicle (GO:0031410)|early endosome membrane (GO:0031901)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	signal transducer activity (GO:0004871)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(1)|lung(4)|prostate(3)|urinary_tract(1)	20						ACTCAGCAAACGCGTCATCAC	0.468													C|||	1751	0.349641	0.2368	0.4524	5008	,	,		19034	0.4127		0.3648	False		,,,				2504	0.3487				p.A144A		Atlas-SNP	.											.	WLS	97	.	0			c.G432A						PASS	.	C	,,	1114,3292	401.3+/-331.9	170,774,1259	161.0	130.0	141.0		426,159,432	2.0	0.0	1	dbSNP_107	141	2961,5639	460.9+/-365.3	524,1913,1863	no	coding-synonymous,coding-synonymous,coding-synonymous	WLS	NM_001002292.3,NM_001193334.1,NM_024911.6	,,	694,2687,3122	TT,TC,CC		34.4302,25.2837,31.3317	,,	142/544,53/451,144/542	68624878	4075,8931	2203	4300	6503	SO:0001819	synonymous_variant	79971	exon3			AGCAAACGCGTCA	BX538320	CCDS642.1, CCDS30750.1, CCDS53331.1	1p31.2	2013-10-03	2013-10-03	2010-03-02	ENSG00000116729	ENSG00000116729			30238	protein-coding gene	gene with protein product	"""wntless homolog"""	611514	"""chromosome 1 open reading frame 139"", ""G protein-coupled receptor 177"", ""wntless homolog (Drosophila)"""	C1orf139, GPR177		12761501	Standard	NM_024911		Approved	FLJ23091, MRP, wls, EVI, mig-14	uc001dee.3	Q5T9L3	OTTHUMG00000009153	ENST00000262348.4:c.432G>A	1.37:g.68624878C>T		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	92	41	0.445652	NM_024911	B2RNT2|Q5JRS7|Q7Z2Z9|Q8NC43	Silent	SNP	ENST00000262348.4	37	CCDS642.1	811	0.37133699633699635	131	0.266260162601626	172	0.47513812154696133	238	0.4160839160839161	270	0.3562005277044855	C	0.224	-1.026590	0.02045	0.252837	0.344302	ENSG00000116729	ENST00000534713	.	.	.	5.94	1.98	0.26296	.	.	.	.	.	T	0.30039	0.0752	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.09185	-1.0686	3	.	.	.	-3.2332	8.3848	0.32494	0.0:0.6047:0.2134:0.1818	rs3748705;rs17845107;rs17857898;rs52813654;rs59688613;rs3748705	.	.	.	H	47	.	.	R	-	2	0	WLS	68397466	0.000000	0.05858	0.001000	0.08648	0.041000	0.13682	0.049000	0.14099	-0.074000	0.12820	-0.810000	0.03169	CGT	C|0.664;T|0.336	0.336	strong		0.468	WLS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025368.1	NM_024911	
GANAB	23193	hgsc.bcm.edu	37	11	62397114	62397114	+	Missense_Mutation	SNP	T	T	C	rs76572368	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	193	0	0		WXS	Illumina HiSeq	Phase_I	151	29	0.192053	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	
IRAK2	3656	hgsc.bcm.edu	37	3	10264480	10264480	+	Missense_Mutation	SNP	C	C	G	rs3844283	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:10264480C>G	ENST00000256458.4	+	9	1264	c.1174C>G	c.(1174-1176)Ctg>Gtg	p.L392V		NM_001570.3	NP_001561.3	O43187	IRAK2_HUMAN	interleukin-1 receptor-associated kinase 2	392	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		L -> V (in dbSNP:rs3844283). {ECO:0000269|PubMed:17344846}.		activation of MAPK activity (GO:0000187)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interleukin-1-mediated signaling pathway (GO:0070498)|JNK cascade (GO:0007254)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein phosphorylation (GO:0006468)|regulation of cytokine-mediated signaling pathway (GO:0001959)|response to interleukin-1 (GO:0070555)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|endosome membrane (GO:0010008)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)			breast(4)|large_intestine(8)|lung(11)|prostate(1)|stomach(1)	25						GGTGGGGCAGCTGACAAAGCG	0.537													C|||	1443	0.288139	0.2126	0.464	5008	,	,		19517	0.1339		0.4185	False		,,,				2504	0.2904				p.L392V		Atlas-SNP	.											IRAK2_ENST00000256458,caecum,carcinoma,-1,2	IRAK2	113	2	0			c.C1174G						PASS	.	C	VAL/LEU	1026,3380	379.2+/-323.2	115,796,1292	108.0	106.0	107.0		1174	5.1	1.0	3	dbSNP_108	107	3605,4995	521.0+/-379.8	768,2069,1463	yes	missense	IRAK2	NM_001570.3	32	883,2865,2755	GG,GC,CC		41.9186,23.2864,35.6066	probably-damaging	392/626	10264480	4631,8375	2203	4300	6503	SO:0001583	missense	3656	exon9			GGGCAGCTGACAA	AF026273	CCDS33697.1	3p25.2	2008-08-18			ENSG00000134070	ENSG00000134070			6113	protein-coding gene	gene with protein product		603304				9374458	Standard	XR_245126		Approved		uc003bve.1	O43187	OTTHUMG00000155358	ENST00000256458.4:c.1174C>G	3.37:g.10264480C>G	ENSP00000256458:p.Leu392Val	Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	114	60	0.526316	NM_001570	B4DQZ6|Q08AG6|Q5K546	Missense_Mutation	SNP	ENST00000256458.4	37	CCDS33697.1	663	0.30357142857142855	90	0.18292682926829268	158	0.43646408839779005	84	0.14685314685314685	331	0.4366754617414248	C	19.36	3.812335	0.70912	0.232864	0.419186	ENSG00000134070	ENST00000256458	T	0.34667	1.35	5.14	5.14	0.70334	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.38436	N	0.001683	T	0.00012	0.0000	L	0.56199	1.76	0.19300	P	0.9999795581	D	0.89917	1.0	D	0.87578	0.998	T	0.46610	-0.9179	9	0.62326	D	0.03	-15.6131	14.105	0.65083	0.0:1.0:0.0:0.0	rs3844283;rs52790097;rs57169457;rs3844283	392	O43187	IRAK2_HUMAN	V	392	ENSP00000256458:L392V	ENSP00000256458:L392V	L	+	1	2	IRAK2	10239480	1.000000	0.71417	1.000000	0.80357	0.825000	0.46686	1.933000	0.40153	2.369000	0.80426	0.655000	0.94253	CTG	C|0.667;G|0.333	0.333	strong		0.537	IRAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339623.1		
USP35	57558	hgsc.bcm.edu	37	11	77911745	77911745	+	Missense_Mutation	SNP	C	C	T	rs147270370	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:77911745C>T	ENST00000529308.1	+	6	1349	c.1088C>T	c.(1087-1089)tCg>tTg	p.S363L	USP35_ENST00000526425.1_Missense_Mutation_p.S94L|USP35_ENST00000441408.2_5'UTR|USP35_ENST00000530535.1_Intron|USP35_ENST00000530267.1_Intron	NM_020798.2	NP_065849.1	Q9P2H5	UBP35_HUMAN	ubiquitin specific peptidase 35	363					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)			AAGGAGGACTCGAACTCGGGG	0.647													C|||	19	0.00379393	0.0015	0.0014	5008	,	,		17401	0.0		0.008	False		,,,				2504	0.0082				p.S363L		Atlas-SNP	.											USP35_ENST00000263311,rectum,carcinoma,-1,2	USP35	179	2	0			c.C1088T						PASS	.	C	LEU/SER	5,3907		0,5,1951	46.0	52.0	50.0		1088	4.7	1.0	11	dbSNP_134	50	46,8202		0,46,4078	yes	missense	USP35	NM_020798.2	145	0,51,6029	TT,TC,CC		0.5577,0.1278,0.4194	benign	363/1019	77911745	51,12109	1956	4124	6080	SO:0001583	missense	57558	exon6			AGGACTCGAACTC	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.1088C>T	11.37:g.77911745C>T	ENSP00000431876:p.Ser363Leu	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	100	20	0.2	NM_020798		Missense_Mutation	SNP	ENST00000529308.1	37	CCDS41693.1	6	0.0027472527472527475	1	0.0020325203252032522	0	0.0	0	0.0	5	0.006596306068601583	C	13.79	2.343705	0.41498	0.001278	0.005577	ENSG00000118369	ENST00000528910;ENST00000529308;ENST00000526425	T;T;T	0.68181	-0.24;-0.31;3.37	4.73	4.73	0.59995	Armadillo-like helical (1);	0.000000	0.52532	D	0.000071	T	0.40448	0.1117	N	0.19112	0.55	0.80722	D	1	B	0.33739	0.422	B	0.22753	0.041	T	0.43925	-0.9361	10	0.18276	T	0.48	-15.0401	17.9135	0.88942	0.0:1.0:0.0:0.0	.	363	Q9P2H5	UBP35_HUMAN	L	119;363;94	ENSP00000436001:S119L;ENSP00000431876:S363L;ENSP00000434942:S94L	ENSP00000434942:S94L	S	+	2	0	USP35	77589393	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	5.484000	0.66844	2.461000	0.83175	0.561000	0.74099	TCG	C|0.996;T|0.004	0.004	strong		0.647	USP35-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390026.1	XM_290527	
ANKRD35	148741	hgsc.bcm.edu	37	1	145561594	145561594	+	Missense_Mutation	SNP	C	C	T	rs6670984	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:145561594C>T	ENST00000355594.4	+	10	1369	c.1282C>T	c.(1282-1284)Ccc>Tcc	p.P428S		NM_144698.3	NP_653299.4	Q8N283	ANR35_HUMAN	ankyrin repeat domain 35	428			P -> S (in dbSNP:rs6670984). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.							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)					ACAGGGGCCACCCCAGAGCCC	0.547													C|||	2828	0.564696	0.5794	0.5043	5008	,	,		18882	0.7252		0.3797	False		,,,				2504	0.6125				p.P428S	Melanoma(9;127 754 22988 51047)	Atlas-SNP	.											.	ANKRD35	96	.	0			c.C1282T						PASS	.	C	SER/PRO	2326,2080	586.9+/-386.6	613,1100,490	60.0	71.0	67.0		1282	-3.1	0.0	1	dbSNP_116	67	3163,5437	473.4+/-368.6	572,2019,1709	yes	missense	ANKRD35	NM_144698.3	74	1185,3119,2199	TT,TC,CC		36.7791,47.2084,42.2036	benign	428/1002	145561594	5489,7517	2203	4300	6503	SO:0001583	missense	148741	exon10			GGGCCACCCCAGA	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.1282C>T	1.37:g.145561594C>T	ENSP00000347802:p.Pro428Ser	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	117	50	0.42735	NM_144698	A6NEU0|B4DL62|Q3MJ10|Q96LS3	Missense_Mutation	SNP	ENST00000355594.4	37	CCDS919.1	1154	0.5283882783882784	275	0.5589430894308943	169	0.46685082872928174	419	0.7325174825174825	291	0.3839050131926121	C	2.083	-0.410284	0.04799	0.527916	0.367791	ENSG00000198483	ENST00000453670;ENST00000355594	T	0.64991	-0.13	5.21	-3.07	0.05363	.	1.124390	0.06867	N	0.800111	T	0.21674	0.0522	L	0.41027	1.25	0.80722	P	0.0	B	0.06786	0.001	B	0.06405	0.002	T	0.05273	-1.0895	9	0.08837	T	0.75	0.4115	6.7985	0.23738	0.0:0.4134:0.1204:0.4661	rs6670984;rs57708309;rs6670984	428	Q8N283	ANR35_HUMAN	S	337;428	ENSP00000347802:P428S	ENSP00000347802:P428S	P	+	1	0	ANKRD35	144272951	0.000000	0.05858	0.000000	0.03702	0.028000	0.11728	0.280000	0.18790	-0.485000	0.06754	-0.140000	0.14226	CCC	C|0.526;T|0.474	0.474	strong		0.547	ANKRD35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038515.1	NM_144698	
FAM171A1	221061	hgsc.bcm.edu	37	10	15256440	15256440	+	Missense_Mutation	SNP	C	C	T	rs150647132		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:15256440C>T	ENST00000378116.4	-	8	1153	c.1147G>A	c.(1147-1149)Ggc>Agc	p.G383S	FAM171A1_ENST00000477161.1_5'UTR	NM_001010924.1	NP_001010924.1	Q5VUB5	F1711_HUMAN	family with sequence similarity 171, member A1	383						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						TCGGGGCGGCCGTGGCTGGTG	0.597													C|||	1	0.000199681	0.0008	0.0	5008	,	,		15789	0.0		0.0	False		,,,				2504	0.0				p.G383S		Atlas-SNP	.											.	FAM171A1	252	.	0			c.G1147A						PASS	.	C	SER/GLY	0,4406		0,0,2203	39.0	45.0	43.0		1147	-2.7	0.2	10	dbSNP_134	43	10,8590	7.7+/-29.5	0,10,4290	yes	missense	FAM171A1	NM_001010924.1	56	0,10,6493	TT,TC,CC		0.1163,0.0,0.0769	benign	383/891	15256440	10,12996	2203	4300	6503	SO:0001583	missense	221061	exon8			GGCGGCCGTGGCT	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.1147G>A	10.37:g.15256440C>T	ENSP00000367356:p.Gly383Ser	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	73	34	0.465753	NM_001010924	D3DRT9|Q32M49|Q8N4I0	Missense_Mutation	SNP	ENST00000378116.4	37	CCDS31154.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	C	4.340	0.062493	0.08388	0.0	0.001163	ENSG00000148468	ENST00000378116;ENST00000396781	T	0.32023	1.47	4.96	-2.72	0.05968	.	0.300803	0.30695	N	0.009079	T	0.15696	0.0378	N	0.19112	0.55	0.22796	N	0.998728	B	0.15141	0.012	B	0.12156	0.007	T	0.20338	-1.0278	10	0.21014	T	0.42	-16.5191	11.3681	0.49684	0.0:0.4139:0.0:0.5861	.	383	Q5VUB5	F1711_HUMAN	S	383;384	ENSP00000367356:G383S	ENSP00000367356:G383S	G	-	1	0	FAM171A1	15296446	.	.	0.169000	0.22859	0.344000	0.29017	.	.	-0.806000	0.04398	-0.983000	0.02560	GGC	C|0.999;T|0.001	0.001	strong		0.597	FAM171A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046984.1	XM_167709	
ABCA7	10347	hgsc.bcm.edu	37	19	1049305	1049305	+	Silent	SNP	C	C	A	rs4147915	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:1049305C>A	ENST00000263094.6	+	18	2652	c.2421C>A	c.(2419-2421)gtC>gtA	p.V807V	ABCA7_ENST00000435683.2_Silent_p.V669V|ABCA7_ENST00000433129.1_Silent_p.V807V	NM_019112.3	NP_061985.2	Q8IZY2	ABCA7_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 7	807	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				apolipoprotein A-I-mediated signaling pathway (GO:0038027)|ATP catabolic process (GO:0006200)|cholesterol efflux (GO:0033344)|high-density lipoprotein particle assembly (GO:0034380)|memory (GO:0007613)|negative regulation of amyloid precursor protein biosynthetic process (GO:0042985)|negative regulation of ATPase activity (GO:0032780)|negative regulation of beta-amyloid formation (GO:1902430)|peptide cross-linking (GO:0018149)|phagocytosis (GO:0006909)|phospholipid efflux (GO:0033700)|phospholipid scrambling (GO:0017121)|positive regulation of ATPase activity (GO:0032781)|positive regulation of beta-amyloid clearance (GO:1900223)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of engulfment of apoptotic cell (GO:1901076)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of phagocytosis (GO:0050766)|positive regulation of phospholipid efflux (GO:1902995)|protein localization to nucleus (GO:0034504)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|ATP-binding cassette (ABC) transporter complex (GO:0043190)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|phagocytic cup (GO:0001891)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	apolipoprotein A-I receptor activity (GO:0034188)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|phospholipid transporter activity (GO:0005548)|transporter activity (GO:0005215)			NS(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(7)|lung(22)|ovary(1)|pancreas(7)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	65		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GTCCTGGCGTCTCCGTTCGCA	0.667													C|||	1001	0.19988	0.1157	0.2752	5008	,	,		9249	0.371		0.1233	False		,,,				2504	0.1626				p.V807V		Atlas-SNP	.											ABCA7,NS,carcinoma,0,1	ABCA7	174	1	0			c.C2421A						PASS	.	C		539,3865	239.9+/-250.9	34,471,1697	53.0	61.0	59.0		2421	1.7	0.8	19	dbSNP_110	59	1175,7421	238.3+/-269.8	83,1009,3206	no	coding-synonymous	ABCA7	NM_019112.3		117,1480,4903	AA,AC,CC		13.6691,12.2389,13.1846		807/2147	1049305	1714,11286	2202	4298	6500	SO:0001819	synonymous_variant	10347	exon18			TGGCGTCTCCGTT	AF328787	CCDS12055.1	19p13.3	2012-03-14			ENSG00000064687	ENSG00000064687		"""ATP binding cassette transporters / subfamily A"""	37	protein-coding gene	gene with protein product		605414					Standard	NM_019112		Approved	ABCX	uc002lqw.4	Q8IZY2	OTTHUMG00000167547	ENST00000263094.6:c.2421C>A	19.37:g.1049305C>A		Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	160	87	0.54375	NM_019112	Q96S58|Q9BZC4|Q9NR73|Q9UKP8	Silent	SNP	ENST00000263094.6	37	CCDS12055.1																																																																																			C|0.843;A|0.157	0.157	strong		0.667	ABCA7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000394993.1	NM_019112	
TRIM34	53840	hgsc.bcm.edu	37	11	5653866	5653866	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:5653866A>G	ENST00000514226.1	+	2	642	c.305A>G	c.(304-306)gAg>gGg	p.E102G	TRIM6-TRIM34_ENST00000354852.5_Missense_Mutation_p.E456G|TRIM34_ENST00000429814.2_Missense_Mutation_p.E102G|TRIM6-TRIM34_ENST00000457787.2_Missense_Mutation_p.E102G|HBG2_ENST00000380259.2_Intron	NM_001003827.1	NP_001003827.1	Q9BYJ4	TRI34_HUMAN	tripartite motif containing 34	102					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)		CATCATGGAGAGAAACTCCTA	0.502																																					p.E456G		Atlas-SNP	.											.	TRIM6-TRIM34	68	.	0			c.A1367G						PASS	.						75.0	69.0	71.0					11																	5653866		2201	4297	6498	SO:0001583	missense	445372	exon8			ATGGAGAGAAACT	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.305A>G	11.37:g.5653866A>G	ENSP00000422947:p.Glu102Gly	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	90	49	0.544444	NM_001003819	D3DQS7|Q9C016|Q9HCR0|Q9HCR1|Q9HCR2	Missense_Mutation	SNP	ENST00000514226.1	37	CCDS31391.1	.	.	.	.	.	.	.	.	.	.	A	18.93	3.727557	0.69074	.	.	ENSG00000258659;ENSG00000258659;ENSG00000258659;ENSG00000258659;ENSG00000258588	ENST00000337072;ENST00000514226;ENST00000429814;ENST00000457787;ENST00000354852	T;T;T;T	0.47869	0.83;0.83;0.83;0.83	3.53	3.53	0.40419	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, B-box (3);	0.232880	0.22139	N	0.064076	T	0.76321	0.3971	H	0.97051	3.93	0.30699	N	0.750484	D;D;D	0.76494	0.999;0.998;0.983	D;D;P	0.76071	0.984;0.987;0.836	T	0.79257	-0.1878	10	0.87932	D	0	.	10.6794	0.45804	1.0:0.0:0.0:0.0	.	102;102;456	Q9BYJ4-2;Q9BYJ4;B2RNG4	.;TRI34_HUMAN;.	G	456;102;102;102;456	ENSP00000422947:E102G;ENSP00000402595:E102G;ENSP00000395982:E102G;ENSP00000346916:E456G	ENSP00000402595:E102G	E	+	2	0	TRIM34;TRIM6-TRIM34	5610442	1.000000	0.71417	1.000000	0.80357	0.680000	0.39746	8.127000	0.89593	1.847000	0.53656	0.454000	0.30748	GAG	.	.	none		0.502	TRIM34-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143357.2	NM_001003827	
ZNF169	169841	hgsc.bcm.edu	37	9	97062295	97062295	+	Missense_Mutation	SNP	C	C	T	rs34433105	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:97062295C>T	ENST00000395395.2	+	5	545	c.455C>T	c.(454-456)tCa>tTa	p.S152L	ZNF169_ENST00000340911.4_3'UTR	NM_194320.2	NP_919301.2	Q14929	ZN169_HUMAN	zinc finger protein 169	152			S -> L (in dbSNP:rs34433105).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|kidney(2)|large_intestine(3)|lung(8)|ovary(2)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	24		Acute lymphoblastic leukemia(62;0.136)				CCCGACAGCTCATTAAGAAAG	0.483													C|||	341	0.0680911	0.1899	0.0317	5008	,	,		19539	0.0149		0.0348	False		,,,				2504	0.0184				p.S152L		Atlas-SNP	.											.	ZNF169	60	.	0			c.C455T						PASS	.	C	LEU/SER	700,3706	293.6+/-282.7	51,598,1554	50.0	49.0	49.0		455	1.2	0.0	9	dbSNP_126	49	276,8324	103.3+/-164.5	6,264,4030	yes	missense	ZNF169	NM_194320.2	145	57,862,5584	TT,TC,CC		3.2093,15.8874,7.5042	benign	152/604	97062295	976,12030	2203	4300	6503	SO:0001583	missense	169841	exon5			ACAGCTCATTAAG	U28322	CCDS6709.2	9q22.32	2014-07-30			ENSG00000175787	ENSG00000175787		"""Zinc fingers, C2H2-type"", ""-"""	12957	protein-coding gene	gene with protein product		603404				9186526, 9071574	Standard	NM_001301275		Approved	MGC51961	uc004aum.1	Q14929	OTTHUMG00000020264	ENST00000395395.2:c.455C>T	9.37:g.97062295C>T	ENSP00000378792:p.Ser152Leu	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	74	36	0.486486	NM_194320	A2AGP5|A8K127|Q6PI28	Missense_Mutation	SNP	ENST00000395395.2	37	CCDS6709.2	116	0.05311355311355311	74	0.15040650406504066	9	0.024861878453038673	9	0.015734265734265736	24	0.0316622691292876	C	2.861	-0.236154	0.05944	0.158874	0.032093	ENSG00000175787	ENST00000395395	T	0.07114	3.22	2.44	1.24	0.21308	.	.	.	.	.	T	0.00012	0.0000	N	0.00729	-1.24	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.04013	0.001	T	0.46610	-0.9179	8	0.25751	T	0.34	.	1.7342	0.02938	0.2738:0.2088:0.0:0.5173	rs34433105	152	Q14929	ZN169_HUMAN	L	152	ENSP00000378792:S152L	ENSP00000378792:S152L	S	+	2	0	ZNF169	96102116	0.000000	0.05858	0.001000	0.08648	0.032000	0.12392	-0.198000	0.09505	0.317000	0.23160	0.505000	0.49811	TCA	C|0.930;T|0.070	0.070	strong		0.483	ZNF169-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253714.1	NM_194320	
CAMSAP1	157922	hgsc.bcm.edu	37	9	138742077	138742077	+	Silent	SNP	C	C	G	rs35981196	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:138742077C>G	ENST00000389532.4	-	7	1015	c.951G>C	c.(949-951)ccG>ccC	p.P317P	CAMSAP1_ENST00000312405.6_Silent_p.P39P|CAMSAP1_ENST00000409386.3_Silent_p.P328P	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	96	0	0		WXS	Illumina HiSeq	Phase_I	81	45	0.555556	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	
ALPP	250	hgsc.bcm.edu	37	2	233243713	233243713	+	Missense_Mutation	SNP	G	G	C	rs113323105	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:233243713G>C	ENST00000392027.2	+	2	378	c.109G>C	c.(109-111)Gag>Cag	p.E37Q	AC068134.8_ENST00000439072.1_RNA|AC068134.8_ENST00000441266.1_RNA	NM_001632.3	NP_001623.3	P05187	PPB1_HUMAN	alkaline phosphatase, placental	37					dephosphorylation (GO:0016311)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alkaline phosphatase activity (GO:0004035)|magnesium ion binding (GO:0000287)|zinc ion binding (GO:0008270)			NS(1)|biliary_tract(1)|endometrium(1)|kidney(4)|large_intestine(2)|liver(1)|lung(10)|ovary(2)	22		all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0449)|Lung NSC(271;0.132)		Epithelial(121;4.45e-22)|Kidney(3;4.42e-11)|KIRC - Kidney renal clear cell carcinoma(3;1.9e-09)|BRCA - Breast invasive adenocarcinoma(100;0.000767)|Lung(119;0.00566)|LUSC - Lung squamous cell carcinoma(224;0.00746)|STAD - Stomach adenocarcinoma(3;0.0181)|GBM - Glioblastoma multiforme(43;0.196)		CTGGAACCGCGAGGCAGCCGA	0.632													C|||	181	0.0361422	0.0613	0.0058	5008	,	,		15310	0.0397		0.0109	False		,,,				2504	0.046				p.E37Q		Atlas-SNP	.											.	ALPP	53	.	0			c.G109C						PASS	.						66.0	80.0	76.0					2																	233243713		2203	4300	6503	SO:0001583	missense	250	exon2			AACCGCGAGGCAG	M14169	CCDS2490.1	2q37.1	2010-06-24	2010-06-24		ENSG00000163283	ENSG00000163283	3.1.3.1		439	protein-coding gene	gene with protein product	"""Regan isozyme"""	171800	"""alkaline phosphatase, placental (Regan isozyme)"""			3001717, 3461452	Standard	XM_005246439		Approved		uc002vsq.3	P05187	OTTHUMG00000133255	ENST00000392027.2:c.109G>C	2.37:g.233243713G>C	ENSP00000375881:p.Glu37Gln	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	74	38	0.513514	NM_001632	P05188|P06861|Q53S78|Q96DB7	Missense_Mutation	SNP	ENST00000392027.2	37	CCDS2490.1	55	0.025183150183150184	22	0.044715447154471545	1	0.0027624309392265192	24	0.04195804195804196	8	0.010554089709762533	.	0.004	-2.318225	0.00235	.	.	ENSG00000163283	ENST00000392027	T	0.22134	1.97	2.32	-0.812	0.10853	Alkaline phosphatase-like, alpha/beta/alpha (1);Alkaline-phosphatase-like, core domain (1);	0.518247	0.21905	N	0.067388	T	0.00524	0.0017	N	0.00026	-2.67	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.32798	-0.9893	10	0.02654	T	1	.	6.4229	0.21754	0.4732:0.2929:0.2338:0.0	.	37	P05187	PPB1_HUMAN	Q	37	ENSP00000375881:E37Q	ENSP00000375881:E37Q	E	+	1	0	ALPP	232951957	0.000000	0.05858	0.014000	0.15608	0.392000	0.30506	-0.669000	0.05262	-1.013000	0.03383	-0.671000	0.03813	GAG	G|0.974;C|0.026	0.026	strong		0.632	ALPP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257032.3	NM_001632	
LARS	51520	hgsc.bcm.edu	37	5	145506100	145506100	+	Silent	SNP	G	G	A	rs11540216	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:145506100G>A	ENST00000394434.2	-	28	3055	c.2889C>T	c.(2887-2889)aaC>aaT	p.N963N	LARS_ENST00000510191.1_Silent_p.N909N|LARS_ENST00000274562.9_Silent_p.N936N|LARS_ENST00000545646.1_Silent_p.N917N	NM_020117.9	NP_064502.9	Q9P2J5	SYLC_HUMAN	leucyl-tRNA synthetase	963					gene expression (GO:0010467)|leucyl-tRNA aminoacylation (GO:0006429)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	aminoacyl-tRNA editing activity (GO:0002161)|ATP binding (GO:0005524)|leucine-tRNA ligase activity (GO:0004823)			breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(10)|prostate(1)|skin(2)|stomach(8)	34			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		L-Leucine(DB00149)	GCAGTTTTCCGTTATTGGCCT	0.408													G|||	213	0.0425319	0.0582	0.0317	5008	,	,		21246	0.0		0.0726	False		,,,				2504	0.0419				p.N963N		Atlas-SNP	.											.	LARS	100	.	0			c.C2889T						PASS	.	G		244,4162	141.5+/-176.9	4,236,1963	130.0	108.0	116.0		2889	2.8	0.8	5	dbSNP_120	116	641,7957	163.8+/-216.2	32,577,3690	no	coding-synonymous	LARS	NM_020117.9		36,813,5653	AA,AG,GG		7.4552,5.5379,6.8056		963/1177	145506100	885,12119	2203	4299	6502	SO:0001819	synonymous_variant	51520	exon28			TTTTCCGTTATTG	AF151026	CCDS34265.1	5q32	2012-10-02			ENSG00000133706	ENSG00000133706	6.1.1.4	"""Aminoacyl tRNA synthetases / Class I"""	6512	protein-coding gene	gene with protein product	"""leucine tRNA ligase 1, cytoplasmic"""	151350				6933703	Standard	NM_020117		Approved	HSPC192, FLJ10595, FLJ21788, LARS1, LEUS, RNTLS	uc003lnx.1	Q9P2J5	OTTHUMG00000163429	ENST00000394434.2:c.2889C>T	5.37:g.145506100G>A		Somatic	220	0	0		WXS	Illumina HiSeq	Phase_I	160	67	0.41875	NM_020117	A2RRR4|A7E266|B4DJ10|Q2TU79|Q9NSE1	Silent	SNP	ENST00000394434.2	37	CCDS34265.1																																																																																			G|0.767;T|0.009	.	strong		0.408	LARS-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000373367.1	NM_020117	
GNL1	2794	hgsc.bcm.edu	37	6	30515043	30515043	+	Silent	SNP	T	T	C	rs3130247	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:30515043T>C	ENST00000376621.3	-	10	2257	c.1287A>G	c.(1285-1287)gcA>gcG	p.A429A		NM_005275.3	NP_005266.2	P36915	GNL1_HUMAN	guanine nucleotide binding protein-like 1	429					cellular response to DNA damage stimulus (GO:0006974)|GTP catabolic process (GO:0006184)|ribosome biogenesis (GO:0042254)|signal transduction (GO:0007165)|T cell mediated immunity (GO:0002456)	cytosol (GO:0005829)|extracellular space (GO:0005615)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural molecule activity (GO:0005198)			cervix(2)|endometrium(4)|large_intestine(1)|lung(10)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	25						GGTAGATCCCTGCCAGAACCT	0.597													T|||	110	0.0219649	0.0121	0.0216	5008	,	,		19418	0.0		0.0785	False		,,,				2504	0.0				p.A429A		Atlas-SNP	.											.	GNL1	47	.	0			c.A1287G						PASS	.	T		103,2919		1,101,1409	195.0	185.0	189.0		1287	-10.0	0.3	6	dbSNP_103	189	578,4840		35,508,2166	yes	coding-synonymous	GNL1	NM_005275.3		36,609,3575	CC,CT,TT		10.6681,3.4083,8.0687		429/608	30515043	681,7759	1511	2709	4220	SO:0001819	synonymous_variant	2794	exon10			GATCCCTGCCAGA		CCDS4680.1	6p21.3	2010-02-17			ENSG00000204590	ENSG00000204590			4413	protein-coding gene	gene with protein product		143024				8180467	Standard	NM_005275		Approved	HSR1	uc003nqh.3	P36915	OTTHUMG00000031137	ENST00000376621.3:c.1287A>G	6.37:g.30515043T>C		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	96	46	0.479167	NM_005275	B0S838|Q96CT5	Silent	SNP	ENST00000376621.3	37	CCDS4680.1																																																																																			T|0.939;C|0.061	0.061	strong		0.597	GNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076241.2		
PLEKHA5	54477	hgsc.bcm.edu	37	12	19427766	19427766	+	Missense_Mutation	SNP	A	A	G	rs77598867	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:19427766A>G	ENST00000299275.6	+	10	1150	c.1144A>G	c.(1144-1146)Agc>Ggc	p.S382G	PLEKHA5_ENST00000510738.2_3'UTR|PLEKHA5_ENST00000543806.1_Missense_Mutation_p.S274G|PLEKHA5_ENST00000538714.1_Missense_Mutation_p.S382G|PLEKHA5_ENST00000359180.3_Missense_Mutation_p.S382G|PLEKHA5_ENST00000429027.2_Missense_Mutation_p.S388G|PLEKHA5_ENST00000424268.1_Missense_Mutation_p.S274G|PLEKHA5_ENST00000317589.4_Missense_Mutation_p.S382G|PLEKHA5_ENST00000309364.4_Missense_Mutation_p.S382G|PLEKHA5_ENST00000539256.1_Missense_Mutation_p.S140G|PLEKHA5_ENST00000355397.3_Missense_Mutation_p.S382G	NM_019012.5	NP_061885.2	Q9HAU0	PKHA5_HUMAN	pleckstrin homology domain containing, family A member 5	382					reproductive system development (GO:0061458)	cytosol (GO:0005829)|membrane (GO:0016020)	1-phosphatidylinositol binding (GO:0005545)|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)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(14)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	35	Acute lymphoblastic leukemia(4;0.000455)|all_hematologic(4;0.00804)					AGTCAATGTTAGCCTGGCAGA	0.473													A|||	135	0.0269569	0.0015	0.0144	5008	,	,		17985	0.0754		0.0119	False		,,,				2504	0.0358				p.S388G	Pancreas(196;329 2193 11246 14234 19524)	Atlas-SNP	.											.	PLEKHA5	198	.	0			c.A1162G						PASS	.	A	GLY/SER,GLY/SER	10,4396	17.9+/-39.9	0,10,2193	63.0	69.0	67.0		1144,1144	5.8	0.9	12	dbSNP_131	67	76,8524	43.6+/-101.6	1,74,4225	yes	missense,missense	PLEKHA5	NM_001143821.2,NM_019012.5	56,56	1,84,6418	GG,GA,AA		0.8837,0.227,0.6612	benign,benign	382/1175,382/1117	19427766	86,12920	2203	4300	6503	SO:0001583	missense	54477	exon11			AATGTTAGCCTGG	AF302150	CCDS8682.1, CCDS44840.1, CCDS44840.2, CCDS55809.1, CCDS58213.1, CCDS58214.1	12p12	2013-01-10			ENSG00000052126	ENSG00000052126		"""Pleckstrin homology (PH) domain containing"""	30036	protein-coding gene	gene with protein product		607770				11214970, 11001876	Standard	NM_001143821		Approved	PEPP2, KIAA1686, FLJ10667	uc031qgo.1	Q9HAU0	OTTHUMG00000167921	ENST00000299275.6:c.1144A>G	12.37:g.19427766A>G	ENSP00000299275:p.Ser382Gly	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	58	31	0.534483	NM_001256470	A0JP03|B4DGS1|E9PHQ3|F5H0I0|Q6NSF8|Q86ST7|Q8N3K6|Q96DY9|Q9BVR4|Q9C0H7|Q9H924|Q9NVK8	Missense_Mutation	SNP	ENST00000299275.6	37	CCDS8682.1	37	0.01694139194139194	1	0.0020325203252032522	5	0.013812154696132596	21	0.03671328671328671	10	0.013192612137203167	A	10.55	1.381442	0.24944	0.00227	0.008837	ENSG00000052126	ENST00000317589;ENST00000355397;ENST00000359180;ENST00000542828;ENST00000309364;ENST00000429027;ENST00000299275;ENST00000539256;ENST00000538714;ENST00000424268;ENST00000543806;ENST00000536974	T;T;T;T;T;T;T;T;T;T;T	0.14516	2.88;2.91;2.89;2.9;2.91;2.89;2.5;2.91;2.88;2.89;2.88	5.82	5.82	0.92795	.	0.379291	0.33631	N	0.004712	T	0.02929	0.0087	L	0.51422	1.61	0.24644	N	0.993559	B;B;P;P;P;B;P	0.46656	0.007;0.061;0.531;0.659;0.47;0.013;0.882	B;B;B;B;B;B;B	0.44133	0.008;0.027;0.124;0.186;0.129;0.007;0.442	T	0.13602	-1.0503	10	0.10902	T	0.67	-17.2316	9.4509	0.38725	0.9147:0.0:0.0853:0.0	.	382;274;274;388;388;382;382	Q9HAU0-4;F5H0I0;E7EME8;B4DHK5;E9PHQ3;Q9HAU0;Q9HAU0-2	.;.;.;.;.;PKHA5_HUMAN;.	G	382;382;382;389;382;388;382;140;382;274;274;274	ENSP00000325155:S382G;ENSP00000347560:S382G;ENSP00000352104:S382G;ENSP00000311239:S382G;ENSP00000404296:S388G;ENSP00000299275:S382G;ENSP00000440611:S140G;ENSP00000439673:S382G;ENSP00000400411:S274G;ENSP00000439837:S274G;ENSP00000440371:S274G	ENSP00000299275:S382G	S	+	1	0	PLEKHA5	19319033	0.976000	0.34144	0.941000	0.38009	0.621000	0.37620	2.331000	0.43894	2.227000	0.72691	0.455000	0.32223	AGC	A|0.989;G|0.011	0.011	strong		0.473	PLEKHA5-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000397013.1	NM_019012	
ARHGAP9	64333	hgsc.bcm.edu	37	12	57870155	57870155	+	Missense_Mutation	SNP	A	A	C	rs11544238	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:57870155A>C	ENST00000356411.2	-	8	1246	c.1108T>G	c.(1108-1110)Tca>Gca	p.S370A	ARHGAP9_ENST00000424809.2_Missense_Mutation_p.S370A|ARHGAP9_ENST00000550288.1_Missense_Mutation_p.S449A|ARHGAP9_ENST00000393797.2_Missense_Mutation_p.S441A|ARHGAP9_ENST00000430041.2_Missense_Mutation_p.S186A|ARHGAP9_ENST00000550454.1_5'UTR|ARHGAP9_ENST00000393791.3_Missense_Mutation_p.S370A			Q9BRR9	RHG09_HUMAN	Rho GTPase activating protein 9	370	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.		S -> A (in dbSNP:rs11544238). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		positive regulation of GTPase activity (GO:0043547)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)			endometrium(1)|kidney(1)|large_intestine(10)|lung(16)|ovary(1)|prostate(1)	30			GBM - Glioblastoma multiforme(3;3.37e-34)			ACCCAGCCTGAGGAGGGCGCT	0.687													A|||	1854	0.370208	0.1271	0.3919	5008	,	,		15834	0.3254		0.6243	False		,,,				2504	0.4683				p.S370A		Atlas-SNP	.											.	ARHGAP9	79	.	0			c.T1108G						PASS	.	A	ALA/SER,ALA/SER,ALA/SER	902,3504		105,692,1406	26.0	25.0	25.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	556,1108,1108	-3.3	0.0	12	dbSNP_120	25	5463,3137		1743,1977,580	yes	missense,missense,missense	ARHGAP9	NM_001080156.1,NM_001080157.1,NM_032496.2	99,99,99	1848,2669,1986	CC,CA,AA		36.4767,20.4721,48.939	benign,benign,benign	186/548,370/641,370/732	57870155	6365,6641	2203	4300	6503	SO:0001583	missense	64333	exon7			AGCCTGAGGAGGG	AB051853	CCDS8941.2, CCDS44928.1, CCDS44929.1	12q13.3	2013-01-10			ENSG00000123329	ENSG00000123329		"""Rho GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"""	14130	protein-coding gene	gene with protein product		610576				11396949	Standard	NM_032496		Approved	MGC1295, 10C	uc001soc.3	Q9BRR9	OTTHUMG00000150147	ENST00000356411.2:c.1108T>G	12.37:g.57870155A>C	ENSP00000348782:p.Ser370Ala	Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	47	20	0.425532	NM_001080157	B4DVI3|E9PDX9|Q8NAF3|Q8TCJ3|Q8WYR0|Q96EZ2|Q96S74	Missense_Mutation	SNP	ENST00000356411.2	37		907	0.4152930402930403	81	0.16463414634146342	155	0.4281767955801105	203	0.3548951048951049	468	0.6174142480211082	A	12.18	1.860850	0.32884	0.204721	0.635233	ENSG00000123329	ENST00000393791;ENST00000356411;ENST00000423291;ENST00000424809;ENST00000393797;ENST00000340423;ENST00000430041;ENST00000548139	T;T;T;T;T;T	0.47177	3.09;3.06;1.74;3.07;3.0;0.85	4.89	-3.35	0.04928	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.621176	0.15729	N	0.247523	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.06405	0.0;0.001;0.002;0.001	T	0.41928	-0.9481	9	0.38643	T	0.18	.	2.2052	0.03934	0.1941:0.2694:0.3883:0.1482	rs11544238;rs12425852;rs60434946;rs11544238	370;370;370;186	Q9BRR9;Q9BRR9-2;E9PDX9;B4DVI3	RHG09_HUMAN;.;.;.	A	370;370;40;370;441;419;186;186	ENSP00000377380:S370A;ENSP00000348782:S370A;ENSP00000394307:S370A;ENSP00000377386:S441A;ENSP00000397950:S186A;ENSP00000449829:S186A	ENSP00000344852:S419A	S	-	1	0	ARHGAP9	56156422	0.717000	0.27966	0.002000	0.10522	0.042000	0.13812	-0.078000	0.11375	-0.392000	0.07751	0.459000	0.35465	TCA	A|0.557;C|0.443	0.443	strong		0.687	ARHGAP9-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_032496	
PLEKHG5	57449	hgsc.bcm.edu	37	1	6529443	6529443	+	Silent	SNP	A	A	G	rs730600	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:6529443A>G	ENST00000400915.3	-	19	2235	c.2169T>C	c.(2167-2169)agT>agC	p.S723S	PLEKHG5_ENST00000377728.3_Silent_p.S667S|PLEKHG5_ENST00000535355.1_Silent_p.S736S|PLEKHG5_ENST00000544978.1_Silent_p.S667S|PLEKHG5_ENST00000400913.1_Silent_p.S667S|PLEKHG5_ENST00000537245.1_Silent_p.S746S|PLEKHG5_ENST00000377725.1_Silent_p.S667S|PLEKHG5_ENST00000340850.5_Silent_p.S667S|PLEKHG5_ENST00000377740.3_Silent_p.S744S|PLEKHG5_ENST00000377732.1_Silent_p.S704S|PLEKHG5_ENST00000377748.1_Silent_p.S744S|PLEKHG5_ENST00000377737.2_Silent_p.S667S	NM_001042663.1	NP_001036128.1	O94827	PKHG5_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 5	723	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				apoptotic signaling pathway (GO:0097190)|endothelial cell chemotaxis (GO:0035767)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)|signal transducer activity (GO:0004871)			liver(1)	1	Ovarian(185;0.02)|all_lung(157;0.154)	all_cancers(23;1.7e-35)|all_epithelial(116;2.78e-22)|all_lung(118;7.57e-07)|Lung NSC(185;4.26e-06)|Colorectal(325;4.47e-05)|all_hematologic(16;0.00014)|Breast(487;0.000688)|Renal(390;0.0007)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0448)		Epithelial(90;5.51e-35)|GBM - Glioblastoma multiforme(13;3.57e-27)|Colorectal(212;6.23e-08)|COAD - Colon adenocarcinoma(227;1.33e-05)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000894)|BRCA - Breast invasive adenocarcinoma(365;0.00107)|STAD - Stomach adenocarcinoma(132;0.00159)|READ - Rectum adenocarcinoma(331;0.0419)		AGGCCTGGCCACTGGCCTGGA	0.567													N|||	1350	0.269569	0.6778	0.1427	5008	,	,		21856	0.0069		0.1451	False		,,,				2504	0.2065				p.S746S		Atlas-SNP	.											.	PLEKHG5	66	.	0			c.T2238C						PASS	.	G	,,,,	2528,1878	540.8+/-375.6	728,1072,403	134.0	148.0	143.0		2169,2001,2001,2001,2232	-3.5	0.6	1	dbSNP_86	143	1207,7393	763.5+/-407.6	74,1059,3167	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PLEKHG5	NM_001042663.1,NM_001042664.1,NM_001042665.1,NM_020631.3,NM_198681.2	,,,,	802,2131,3570	GG,GA,AA		14.0349,42.6237,28.7175	,,,,	723/1063,667/1007,667/1007,667/1007,744/1084	6529443	3735,9271	2203	4300	6503	SO:0001819	synonymous_variant	57449	exon19			CTGGCCACTGGCC	AK024676	CCDS79.1, CCDS41240.1, CCDS41241.1, CCDS57967.1, CCDS57968.1, CCDS57969.1	1p36.31	2014-09-17		2005-08-09	ENSG00000171680	ENSG00000171680		"""Pleckstrin homology (PH) domain containing"""	29105	protein-coding gene	gene with protein product	"""synectin-binding guanine exchange factor"""	611101				17564964	Standard	NM_001042663		Approved	KIAA0720, Syx, GEF720, Tech	uc010nzr.1	O94827	OTTHUMG00000000905	ENST00000400915.3:c.2169T>C	1.37:g.6529443A>G		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	70	34	0.485714	NM_001265592	B3KU07|B7Z2M3|B7Z5X2|F5GZ21|F5H1I0|Q5SY17|Q5T8W5|Q5T8W9|Q6ZNM0|Q7Z436|Q86YD8|Q96BS1	Silent	SNP	ENST00000400915.3	37	CCDS41241.1																																																																																			A|0.720;G|0.280	0.280	strong		0.567	PLEKHG5-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000002631.1	NM_020631	
MUC4	4585	hgsc.bcm.edu	37	3	195511959	195511959	+	Silent	SNP	G	G	A	rs369770584		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195511959G>A	ENST00000463781.3	-	2	6951	c.6492C>T	c.(6490-6492)acC>acT	p.T2164T	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Silent_p.T2164T	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)		AGGAAGTGTCGGTGACAGGAA	0.577																																					p.T2164T		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,3	MUC4	1505	3	0			c.C6492T						scavenged	.						15.0	15.0	15.0					3																	195511959		676	1556	2232	SO:0001819	synonymous_variant	4585	exon2			AGTGTCGGTGACA	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.6492C>T	3.37:g.195511959G>A		Somatic	113	1	0.00884956		WXS	Illumina HiSeq	Phase_I	66	15	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	Silent	SNP	ENST00000463781.3	37	CCDS54700.1																																																																																			.	.	weak		0.577	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
CD44	960	hgsc.bcm.edu	37	11	35201842	35201842	+	Silent	SNP	C	C	T	rs1071695	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:35201842C>T	ENST00000428726.2	+	3	378	c.255C>T	c.(253-255)caC>caT	p.H85H	CD44_ENST00000526669.2_Silent_p.H85H|CD44_ENST00000352818.4_Silent_p.H85H|CD44_ENST00000360158.4_Silent_p.H85H|CD44_ENST00000437706.2_Silent_p.H85H|CD44_ENST00000278386.6_Intron|CD44_ENST00000449691.2_Silent_p.H85H|CD44_ENST00000433892.2_Silent_p.H85H|CD44_ENST00000415148.2_Silent_p.H85H|CD44_ENST00000434472.2_Silent_p.H85H|CD44_ENST00000433354.2_Silent_p.H85H|CD44_ENST00000263398.6_Silent_p.H85H	NM_000610.3	NP_000601.3	P16070	CD44_HUMAN	CD44 molecule (Indian blood group)	85	Link. {ECO:0000255|PROSITE- ProRule:PRU00323}.				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)	TAGAAGGGCACGTGGTGATTC	0.438													C|||	698	0.139377	0.149	0.2205	5008	,	,		19558	0.0714		0.173	False		,,,				2504	0.1043				p.H85H		Atlas-SNP	.											CD44,colon,carcinoma,0,1	CD44	48	1	0			c.C255T	GRCh37	CM076085	CD44	M	rs1071695	PASS	.	C	,,,,,,,	712,3692	296.7+/-284.4	54,604,1544	168.0	140.0	150.0		255,255,255,255,,255,255,255	-8.2	0.3	11	dbSNP_86	150	1477,7119	280.8+/-294.7	123,1231,2944	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,intron,coding-synonymous,coding-synonymous,coding-synonymous	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	,,,,,,,	177,1835,4488	TT,TC,CC		17.1824,16.1671,16.8385	,,,,,,,	85/743,85/700,85/494,85/362,,85/430,85/341,85/295	35201842	2189,10811	2202	4298	6500	SO:0001819	synonymous_variant	960	exon3			AGGGCACGTGGTG	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.255C>T	11.37:g.35201842C>T		Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	158	121	0.765823	NM_001001391	A5YRN9|B6EAT9|D3DR12|D3DR13|O95370|P22511|Q04858|Q13419|Q13957|Q13958|Q13959|Q13960|Q13961|Q13967|Q13968|Q13980|Q15861|Q16064|Q16065|Q16066|Q16208|Q16522|Q86T72|Q86Z27|Q8N694|Q92493|Q96J24|Q9H5A5|Q9UC28|Q9UC29|Q9UC30|Q9UCB0|Q9UJ36	Silent	SNP	ENST00000428726.2	37	CCDS7897.1	333|333	0.15247252747252749|0.15247252747252749	75|75	0.1524390243902439|0.1524390243902439	79|79	0.21823204419889503|0.21823204419889503	47|47	0.08216783216783216|0.08216783216783216	132|132	0.1741424802110818|0.1741424802110818	C|C	4.473|4.473	0.087625|0.087625	0.08583|0.08583	0.161671|0.161671	0.171824|0.171824	ENSG00000026508|ENSG00000026508	ENST00000442151;ENST00000528455|ENST00000527889;ENST00000531873	.|.	.|.	.|.	5.86|5.86	-8.16|-8.16	0.01061|0.01061	.|.	.|.	.|.	.|.	.|.	T|T	0.00039|0.00039	0.0001|0.0001	.|.	.|.	.|.	0.09310|0.09310	P|P	0.999999831683|0.999999831683	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.18366|0.18366	-1.0339|-1.0339	3|3	.|.	.|.	.|.	-5.8315|-5.8315	17.4346|17.4346	0.87548|0.87548	0.0:0.1989:0.0:0.8011|0.0:0.1989:0.0:0.8011	rs1071695;rs3198437;rs3198804;rs11542696;rs17423178;rs17849845;rs1071695|rs1071695;rs3198437;rs3198804;rs11542696;rs17423178;rs17849845;rs1071695	.|.	.|.	.|.	C|M	85;22|41;6	.|.	.|.	R|T	+|+	1|2	0|0	CD44|CD44	35158418|35158418	0.001000|0.001000	0.12720|0.12720	0.296000|0.296000	0.24974|0.24974	0.509000|0.509000	0.34042|0.34042	-3.037000|-3.037000	0.00634|0.00634	-1.565000|-1.565000	0.01676|0.01676	-0.806000|-0.806000	0.03193|0.03193	CGT|ACG	C|0.835;T|0.165	0.165	strong		0.438	CD44-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000388927.1	NM_000610	
CRIPAK	285464	hgsc.bcm.edu	37	4	1388788	1388788	+	Silent	SNP	C	C	T	rs577053657	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:1388788C>T	ENST00000324803.4	+	1	3449	c.489C>T	c.(487-489)gaC>gaT	p.D163D		NM_175918.3	NP_787114.2	Q8N1N5	CRPAK_HUMAN	cysteine-rich PAK1 inhibitor	163					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)			CACGTGCCGACGTGGAGTGCC	0.687													N|||	91	0.0181709	0.0378	0.0101	5008	,	,		18331	0.004		0.0149	False		,,,				2504	0.0153				p.D163D		Atlas-SNP	.											CRIPAK,extremity,malignant_melanoma,+2,2	CRIPAK	185	2	0			c.C489T						PASS	.						49.0	50.0	49.0					4																	1388788		2123	4040	6163	SO:0001819	synonymous_variant	285464	exon1			TGCCGACGTGGAG	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.489C>T	4.37:g.1388788C>T		Somatic	22	0	0		WXS	Illumina HiSeq	Phase_I	27	7	0.259259	NM_175918	Q8NB03	Silent	SNP	ENST00000324803.4	37	CCDS3349.1	.	.	.	.	.	.	.	.	.	.	t	4.756	0.140533	0.09083	.	.	ENSG00000179979	ENST00000382944	.	.	.	1.25	-0.146	0.13432	.	.	.	.	.	T	0.30541	0.0768	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.26189	-1.0110	5	0.33141	T	0.24	.	5.4055	0.16318	0.0:0.3609:0.0:0.6391	.	.	.	.	C	147	.	ENSP00000372402:R147C	R	+	1	0	CRIPAK	1378788	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.472000	0.06623	-0.595000	0.05828	-1.950000	0.00486	CGT	.	.	none		0.687	CRIPAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241607.2	NM_175918	
GRK4	2868	hgsc.bcm.edu	37	4	3006043	3006043	+	Missense_Mutation	SNP	C	C	T	rs1024323	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:3006043C>T	ENST00000398052.4	+	5	768	c.425C>T	c.(424-426)gCc>gTc	p.A142V	GRK4_ENST00000345167.6_Missense_Mutation_p.A110V|GRK4_ENST00000504933.1_Missense_Mutation_p.A142V|GRK4_ENST00000398051.4_Missense_Mutation_p.A110V	NM_182982.2	NP_892027.2	P32298	GRK4_HUMAN	G protein-coupled receptor kinase 4	142	N-terminal.|RGS. {ECO:0000255|PROSITE- ProRule:PRU00171}.		A -> V (in dbSNP:rs1024323). {ECO:0000269|PubMed:17344846}.		G-protein coupled receptor internalization (GO:0002031)|receptor internalization (GO:0031623)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|signal transduction (GO:0007165)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytosol (GO:0005829)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)	ATP binding (GO:0005524)|G-protein coupled receptor kinase activity (GO:0004703)|rhodopsin kinase activity (GO:0050254)			lung(1)|upper_aerodigestive_tract(1)	2				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)		TCCAAAAAAGCCTTTGAGGAA	0.428													T|||	1869	0.373203	0.6339	0.3833	5008	,	,		20027	0.1895		0.4016	False		,,,				2504	0.1738				p.A142V		Atlas-SNP	.											.	GRK4	72	.	0			c.C425T	GRCh37	CM025430	GRK4	M	rs1024323	PASS	.	T	VAL/ALA,VAL/ALA,VAL/ALA	2631,1775	527.0+/-372.0	794,1043,366	158.0	161.0	160.0		329,425,425	2.1	0.0	4	dbSNP_86	160	3275,5325	648.2+/-400.5	644,1987,1669	yes	missense,missense,missense	GRK4	NM_001004056.1,NM_001004057.1,NM_182982.2	64,64,64	1438,3030,2035	TT,TC,CC		38.0814,40.286,45.4098	benign,benign,benign	110/547,142/533,142/579	3006043	5906,7100	2203	4300	6503	SO:0001583	missense	2868	exon5			AAAAAGCCTTTGA		CCDS33946.1, CCDS33947.1, CCDS47002.1, CCDS68656.1	4p16.3	2008-02-05	2004-02-04	2004-02-06	ENSG00000125388	ENSG00000125388			4543	protein-coding gene	gene with protein product		137026	"""G protein-coupled receptor kinase 2-like (Drosophila)"""	GPRK2L		1338872	Standard	NM_182982		Approved	GPRK4	uc003ggn.1	P32298	OTTHUMG00000159914	ENST00000398052.4:c.425C>T	4.37:g.3006043C>T	ENSP00000381129:p.Ala142Val	Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	111	56	0.504505	NM_182982	O00641|O00642|Q13293|Q13294|Q13295|Q14453|Q14725|Q15313|Q15314|Q15315|Q15316|Q17RH6|Q53EQ8	Missense_Mutation	SNP	ENST00000398052.4	37	CCDS33946.1	860	0.39377289377289376	309	0.6280487804878049	137	0.3784530386740331	103	0.18006993006993008	311	0.4102902374670185	T	6.994	0.553558	0.13374	0.59714	0.380814	ENSG00000125388	ENST00000398051;ENST00000398052;ENST00000345167;ENST00000504933	T;T;T;T	0.01767	4.65;4.65;4.65;4.65	4.65	2.11	0.27256	Regulator of G protein signalling (3);Regulator of G protein signalling superfamily (1);	0.160531	0.42172	N	0.000749	T	0.00012	0.0000	N	0.00841	-1.15	0.58432	P	1.0000000000287557E-6	B;B;B;B	0.06786	0.001;0.0;0.001;0.0	B;B;B;B	0.09377	0.002;0.003;0.004;0.004	T	0.02991	-1.1085	9	0.30854	T	0.27	-4.8717	7.587	0.27998	0.0:0.2523:0.0:0.7477	rs1024323;rs52795674;rs61636656;rs1024323	110;110;142;142	P32298-3;P32298-2;P32298-4;P32298	.;.;.;GRK4_HUMAN	V	110;142;110;142	ENSP00000381128:A110V;ENSP00000381129:A142V;ENSP00000264764:A110V;ENSP00000427445:A142V	ENSP00000264764:A110V	A	+	2	0	GRK4	2975841	0.026000	0.19158	0.042000	0.18584	0.600000	0.36913	0.527000	0.22987	0.052000	0.16007	-0.254000	0.11334	GCC	C|0.576;T|0.424	0.424	strong		0.428	GRK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358176.2	NM_005307	
MYH9	4627	hgsc.bcm.edu	37	22	36684358	36684358	+	Silent	SNP	C	C	A	rs2269530	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:36684358C>A	ENST00000216181.5	-	34	5102	c.4872G>T	c.(4870-4872)gcG>gcT	p.A1624A	MYH9_ENST00000475726.1_5'Flank	NM_002473.4	NP_002464.1	P35579	MYH9_HUMAN	myosin, heavy chain 9, non-muscle	1624					actin cytoskeleton reorganization (GO:0031532)|actin filament-based movement (GO:0030048)|actomyosin structure organization (GO:0031032)|angiogenesis (GO:0001525)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|blood vessel endothelial cell migration (GO:0043534)|cytokinesis (GO:0000910)|establishment of meiotic spindle localization (GO:0051295)|establishment of T cell polarity (GO:0001768)|in utero embryonic development (GO:0001701)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|meiotic spindle organization (GO:0000212)|membrane protein ectodomain proteolysis (GO:0006509)|monocyte differentiation (GO:0030224)|myoblast fusion (GO:0007520)|platelet aggregation (GO:0070527)|platelet formation (GO:0030220)|protein transport (GO:0015031)|regulation of cell shape (GO:0008360)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|uropod organization (GO:0032796)	actin cytoskeleton (GO:0015629)|actomyosin (GO:0042641)|actomyosin contractile ring (GO:0005826)|cell leading edge (GO:0031252)|cell-cell adherens junction (GO:0005913)|cleavage furrow (GO:0032154)|cortical cytoskeleton (GO:0030863)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|immunological synapse (GO:0001772)|membrane (GO:0016020)|myosin II complex (GO:0016460)|myosin II filament (GO:0097513)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|ruffle (GO:0001726)|spindle (GO:0005819)|stress fiber (GO:0001725)|uropod (GO:0001931)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)|motor activity (GO:0003774)|poly(A) RNA binding (GO:0044822)|protein anchor (GO:0043495)|protein homodimerization activity (GO:0042803)			NS(1)|breast(8)|central_nervous_system(3)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(16)|lung(29)|ovary(4)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(6)|urinary_tract(3)	86						AGTCGATGTGCGCCTCCAGGT	0.657			T	ALK	ALCL		"""Deafness, autosomal dominant 17, Epstein syndrome, Fechtner syndrome, May-Hegglin anomaly, Sebastian syndrome"""		Hereditary Macrothrombocytopenia, MYH9-associated				.|||	1471	0.29373	0.0416	0.2118	5008	,	,		16160	0.5952		0.2078	False		,,,				2504	0.4703				p.A1624A		Atlas-SNP	.		Dom	yes		22	22q13.1	4627	"""myosin, heavy polypeptide 9, non-muscle"""	yes	L	.	MYH9	225	.	0			c.G4872T						PASS	.	C		315,4091	166.5+/-197.7	12,291,1900	124.0	99.0	107.0		4872	-10.3	0.4	22	dbSNP_100	107	1703,6897	310.9+/-310.1	195,1313,2792	no	coding-synonymous	MYH9	NM_002473.4		207,1604,4692	AA,AC,CC		19.8023,7.1493,15.5159		1624/1961	36684358	2018,10988	2203	4300	6503	SO:0001819	synonymous_variant	4627	exon34	Familial Cancer Database	MYHIIA syndrome, incl. Fechtner Syndrome, FTNS, and May-Hegglin Anomaly, MHA	GATGTGCGCCTCC		CCDS13927.1	22q13.1	2014-09-17	2006-09-29		ENSG00000100345	ENSG00000100345		"""Myosins / Myosin superfamily : Class II"""	7579	protein-coding gene	gene with protein product	"""nonmuscle myosin heavy chain II-A"""	160775	"""myosin, heavy polypeptide 9, non-muscle"""	DFNA17		1860190, 11023810	Standard	NM_002473		Approved	NMMHCA, NMHC-II-A, MHA, FTNS, EPSTS	uc003apg.3	P35579	OTTHUMG00000030429	ENST00000216181.5:c.4872G>T	22.37:g.36684358C>A		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	90	41	0.455556	NM_002473	A8K6E4|O60805|Q60FE2|Q86T83	Silent	SNP	ENST00000216181.5	37	CCDS13927.1																																																																																			C|0.785;A|0.215	0.215	strong		0.657	MYH9-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000259110.3	NM_002473	
GDF3	9573	hgsc.bcm.edu	37	12	7842932	7842932	+	Missense_Mutation	SNP	C	C	T	rs12819884	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:7842932C>T	ENST00000329913.3	-	2	684	c.637G>A	c.(637-639)Ggg>Agg	p.G213R		NM_020634.1	NP_065685.1	Q9NR23	GDF3_HUMAN	growth differentiation factor 3	213			G -> R (in dbSNP:rs12819884). {ECO:0000269|PubMed:15489334}.		endoderm development (GO:0007492)|eye development (GO:0001654)|formation of anatomical boundary (GO:0048859)|growth (GO:0040007)|in utero embryonic development (GO:0001701)|mesoderm development (GO:0007498)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of epidermal cell differentiation (GO:0045605)|notochord development (GO:0030903)|primitive streak formation (GO:0090009)|regulation of cell fate commitment (GO:0010453)|response to dietary excess (GO:0002021)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)|somite rostral/caudal axis specification (GO:0032525)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	protein kinase binding (GO:0019901)	p.G213R(1)		breast(2)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(5)|lung(7)|ovary(2)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	28						AAATTCACCCCTGAGTCTCTA	0.493													C|||	1128	0.22524	0.1762	0.1671	5008	,	,		-128	0.1488		0.326	False		,,,				2504	0.3078				p.G213R		Atlas-SNP	.											GDF3,NS,adenoma,0,2	GDF3	68	2	1	Substitution - Missense(1)	stomach(1)	c.G637A						PASS	.	C	ARG/GLY	813,3593	322.9+/-297.8	84,645,1474	80.0	81.0	81.0		637	1.6	0.0	12	dbSNP_121	81	2656,5944	427.0+/-355.5	411,1834,2055	yes	missense	GDF3	NM_020634.1	125	495,2479,3529	TT,TC,CC		30.8837,18.4521,26.6723	benign	213/365	7842932	3469,9537	2203	4300	6503	SO:0001583	missense	9573	exon2			TCACCCCTGAGTC	AF263538	CCDS8581.1	12p13.1	2014-01-30			ENSG00000184344	ENSG00000184344		"""Endogenous ligands"""	4218	protein-coding gene	gene with protein product		606522				9467948	Standard	NM_020634		Approved		uc001qte.3	Q9NR23	OTTHUMG00000168433	ENST00000329913.3:c.637G>A	12.37:g.7842932C>T	ENSP00000331745:p.Gly213Arg	Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	152	73	0.480263	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		
BEND2	139105	hgsc.bcm.edu	37	X	18230715	18230715	+	Missense_Mutation	SNP	A	A	C	rs17274127	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:18230715A>C	ENST00000380033.4	-	4	594	c.462T>G	c.(460-462)ttT>ttG	p.F154L	BEND2_ENST00000380030.3_Missense_Mutation_p.F154L	NM_153346.4	NP_699177.2	Q8NDZ0	BEND2_HUMAN	BEN domain containing 2	154			F -> L (in dbSNP:rs17274127).							NS(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(11)|liver(1)|lung(21)|ovary(3)|prostate(1)	49						CTCTTTTTGGAAAATCCACTT	0.348													C|||	770	0.203974	0.1528	0.0807	3775	,	,		12412	0.2599		0.1441	False		,,,				2504	0.1074				p.F154L		Atlas-SNP	.											.	BEND2	108	.	0			c.T462G						PASS	.	C	LEU/PHE,LEU/PHE	736,3099		48,526,114,1058,457	168.0	155.0	159.0		462,462	-0.4	0.0	X	dbSNP_123	159	1295,5433		95,747,358,1586,1514	yes	missense,missense	BEND2	NM_001184767.1,NM_153346.4	22,22	143,1273,472,2644,1971	CC,CA,C,AA,A		19.2479,19.1917,19.2275	benign,benign	154/646,154/800	18230715	2031,8532	2203	4300	6503	SO:0001583	missense	139105	exon4			TTTTGGAAAATCC	AK128155	CCDS14184.1, CCDS55375.1	Xp22.22	2012-11-22	2008-10-03	2008-10-03	ENSG00000177324	ENSG00000177324		"""BEN domain containing"""	28509	protein-coding gene	gene with protein product			"""chromosome X open reading frame 20"""	CXorf20		12477932	Standard	NM_153346		Approved	MGC33653	uc004cyj.4	Q8NDZ0	OTTHUMG00000021211	ENST00000380033.4:c.462T>G	X.37:g.18230715A>C	ENSP00000369372:p.Phe154Leu	Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	93	92	0.989247	NM_001184767	E9PFY2|Q4V9S2|Q5JXE5	Missense_Mutation	SNP	ENST00000380033.4	37	CCDS14184.1	382	0.23025919228450875	63	0.13695652173913042	26	0.07514450867052024	107	0.2296137339055794	72	0.10526315789473684	C	0.006	-2.111741	0.00353	0.191917	0.192479	ENSG00000177324	ENST00000380033;ENST00000380030	T;T	0.26223	1.82;1.75	1.22	-0.388	0.12459	.	1.468090	0.05061	N	0.479850	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	0.21690	-1.0238	9	0.02654	T	1	.	1.6358	0.02742	0.2993:0.3281:0.0:0.3726	rs17274127;rs17274127	154;154	E9PFY2;Q8NDZ0	.;BEND2_HUMAN	L	154	ENSP00000369372:F154L;ENSP00000369369:F154L	ENSP00000369369:F154L	F	-	3	2	BEND2	18140636	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-0.955000	0.03869	-0.791000	0.04486	-0.418000	0.06021	TTT	A|0.766;0|0.015	.	strong		0.348	BEND2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055940.1	NM_153346	
MAGIX	79917	hgsc.bcm.edu	37	X	49021052	49021052	+	Silent	SNP	C	C	T	rs12843494	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:49021052C>T	ENST00000412696.2	+	3	204	c.204C>T	c.(202-204)agC>agT	p.S68S	MAGIX_ENST00000498742.1_3'UTR|MAGIX_ENST00000425661.2_Silent_p.S68S|MAGIX_ENST00000376339.1_5'UTR|MAGIX_ENST00000376338.3_5'UTR	NM_024859.2	NP_079135.3	Q9H6Y5	MAGIX_HUMAN	MAGI family member, X-linked	68																	CAGCTGTTAGCGTGCTGGACT	0.537													C|||	386	0.102252	0.0121	0.0375	3775	,	,		14079	0.0486		0.0805	False		,,,				2504	0.2188				p.S68S		Atlas-SNP	.											.	MAGIX	25	.	0			c.C204T						PASS	.	C	,,,	81,3515		0,63,18,1450,552	153.0	154.0	153.0		48,204,204,204	-7.9	0.0	X	dbSNP_121	153	684,5879		25,439,195,1914,1612	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	MAGIX	NM_001099680.1,NM_001099681.1,NM_001099682.1,NM_024859.2	,,,	25,502,213,3364,2164	TT,TC,T,CC,C		10.4221,2.2525,7.5303	,,,	16/263,68/259,68/254,68/335	49021052	765,9394	2083	4185	6268	SO:0001819	synonymous_variant	79917	exon3			TGTTAGCGTGCTG	AK025340	CCDS48106.1, CCDS48107.1, CCDS75976.1	Xp11.23	2014-05-06			ENSG00000017621	ENSG00000269313			30006	protein-coding gene	gene with protein product							Standard	XM_005278065		Approved	PDZX, JM10, FLJ21687	uc010nin.1	Q9H6Y5	OTTHUMG00000188218	ENST00000412696.2:c.204C>T	X.37:g.49021052C>T		Somatic	245	0	0		WXS	Illumina HiSeq	Phase_I	153	152	0.993464	NM_001099681	A6XND4|A8MSX9|B7WP26|Q14C81	Silent	SNP	ENST00000412696.2	37	CCDS48106.1	107|107	0.0644966847498493|0.0644966847498493	6|6	0.012345679012345678|0.012345679012345678	8|8	0.022598870056497175|0.022598870056497175	16|16	0.028985507246376812|0.028985507246376812	38|38	0.05337078651685393|0.05337078651685393	.|.	7.167|7.167	0.586807|0.586807	0.13749|0.13749	0.022525|0.022525	0.104221|0.104221	ENSG00000017621|ENSG00000017621	ENST00000415364|ENST00000458388	.|.	.|.	.|.	3.95|3.95	-7.9|-7.9	0.01169|0.01169	.|.	.|.	.|.	.|.	.|.	T|T	0.00412|0.00412	0.0013|0.0013	.|.	.|.	.|.	0.58432|0.58432	P|P	1.0000000000287557E-6|1.0000000000287557E-6	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.13845|0.13845	-1.0494|-1.0494	3|3	.|.	.|.	.|.	-11.4604|-11.4604	2.5019|2.5019	0.04636|0.04636	0.1162:0.2925:0.1152:0.4761|0.1162:0.2925:0.1152:0.4761	rs12843494;rs17328035|rs12843494;rs17328035	.|.	.|.	.|.	V|C	52|74	.|.	.|.	A|R	+|+	2|1	0|0	MAGIX|MAGIX	48907996|48907996	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.111000|0.111000	0.19643|0.19643	-1.449000|-1.449000	0.02392|0.02392	-2.019000|-2.019000	0.00942|0.00942	-0.711000|-0.711000	0.03637|0.03637	GCG|CGT	C|0.926;0|0.013	.	strong		0.537	MAGIX-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378832.1	NM_024859	
CCDC168	643677	hgsc.bcm.edu	37	13	103391605	103391605	+	5'Flank	SNP	T	T	C	rs17592480	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:103391605T>C	ENST00000322527.2	-	0	0					NM_001146197.1	NP_001139669.1	Q8NDH2	CC168_HUMAN	coiled-coil domain containing 168																		ATTTCTTTCCTTTCAAAGTGA	0.323													T|||	440	0.0878594	0.0802	0.0706	5008	,	,		21310	0.0139		0.1252	False		,,,				2504	0.1483				p.K3814K		Atlas-SNP	.											.	.	.	.	0			c.A11442G						PASS	.	T		108,1276		6,96,590	95.0	72.0	79.0		11442	0.2	0.0	13	dbSNP_123	79	373,2807		22,329,1239	no	coding-synonymous	CCDC168	NM_001146197.1		28,425,1829	CC,CT,TT		11.7296,7.8035,10.539		3814/7082	103391605	481,4083	692	1590	2282	SO:0001631	upstream_gene_variant	643677	exon4			CTTTCCTTTCAAA		CCDS73596.1	13q33.1	2014-06-17	2011-08-09	2011-08-09	ENSG00000175820	ENSG00000175820			26851	protein-coding gene	gene with protein product			"""chromosome 13 open reading frame 40"""	C13orf40			Standard	NM_001146197		Approved	FLJ40176	uc001vpm.3	Q8NDH2	OTTHUMG00000187287		13.37:g.103391605T>C	Exception_encountered	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	87	42	0.482759	NM_001146197	Q8N800	Silent	SNP	ENST00000322527.2	37																																																																																				T|0.927;C|0.073	0.073	strong		0.323	CCDC168-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001146197	
ARHGAP5	394	hgsc.bcm.edu	37	14	32561296	32561296	+	Missense_Mutation	SNP	T	T	C	rs200111638		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:32561296T>C	ENST00000345122.3	+	2	1736	c.1421T>C	c.(1420-1422)gTa>gCa	p.V474A	ARHGAP5_ENST00000432921.1_Missense_Mutation_p.V474A|ARHGAP5_ENST00000539826.2_Missense_Mutation_p.V474A|ARHGAP5_ENST00000556611.1_Missense_Mutation_p.V474A|ARHGAP5_ENST00000433497.1_Intron|ARHGAP5_ENST00000396582.2_Intron	NM_001030055.1	NP_001025226.1	Q13017	RHG05_HUMAN	Rho GTPase activating protein 5	474	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)		AGCAAAGAGGTATATGGTAGG	0.368																																					p.V474A	NSCLC(9;77 350 3443 29227 41353)	Atlas-SNP	.											ARHGAP5,caecum,carcinoma,0,26	ARHGAP5	166	26	0			c.T1421C						scavenged	.						74.0	77.0	76.0					14																	32561296		2203	4297	6500	SO:0001583	missense	394	exon2			AAGAGGTATATGG	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.1421T>C	14.37:g.32561296T>C	ENSP00000371897:p.Val474Ala	Somatic	87	1	0.0114943		WXS	Illumina HiSeq	Phase_I	71	6	0.084507	NM_001173	A1L375|A1L376|A8KAA1|D3DS89|D3DS90|Q05BE8|Q05BU8|Q59ER0|Q6DHZ3	Missense_Mutation	SNP	ENST00000345122.3	37	CCDS32062.1	.	.	.	.	.	.	.	.	.	.	T	17.13	3.311365	0.60414	.	.	ENSG00000100852	ENST00000556611;ENST00000539826;ENST00000345122;ENST00000432921	T;T;T;T	0.12039	2.72;2.72;2.72;2.72	6.02	6.02	0.97574	FF domain (1);	0.000000	0.85682	D	0.000000	T	0.25457	0.0619	L	0.40543	1.245	0.80722	D	1	P;P	0.49961	0.93;0.885	P;P	0.56042	0.79;0.622	T	0.00254	-1.1874	10	0.56958	D	0.05	.	16.5494	0.84464	0.0:0.0:0.0:1.0	.	474;474	Q13017-2;Q13017	.;RHG05_HUMAN	A	474	ENSP00000452222:V474A;ENSP00000441692:V474A;ENSP00000371897:V474A;ENSP00000393307:V474A	ENSP00000371897:V474A	V	+	2	0	ARHGAP5	31631047	1.000000	0.71417	0.998000	0.56505	0.989000	0.77384	8.040000	0.89188	2.299000	0.77371	0.528000	0.53228	GTA	T|0.999;C|0.001	0.001	weak		0.368	ARHGAP5-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000409735.1	NM_001030055	
TIAM2	26230	hgsc.bcm.edu	37	6	155561796	155561796	+	Missense_Mutation	SNP	C	C	T	rs11751128	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:155561796C>T	ENST00000461783.3	+	18	4574	c.3301C>T	c.(3301-3303)Cgc>Tgc	p.R1101C	TIAM2_ENST00000318981.5_Missense_Mutation_p.R1101C|TIAM2_ENST00000360366.4_Missense_Mutation_p.R1125C|TIAM2_ENST00000275246.7_Missense_Mutation_p.R26C|TIAM2_ENST00000528391.2_Missense_Mutation_p.R437C|TIAM2_ENST00000529824.2_Missense_Mutation_p.R1101C|TIAM2_ENST00000456144.1_Missense_Mutation_p.R1101C|TIAM2_ENST00000456877.2_Missense_Mutation_p.R413C|TIAM2_ENST00000367174.2_Missense_Mutation_p.R477C			Q8IVF5	TIAM2_HUMAN	T-cell lymphoma invasion and metastasis 2	1101	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.		R -> C (in dbSNP:rs11751128).		apoptotic signaling pathway (GO:0097190)|cellular lipid metabolic process (GO:0044255)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	cell projection (GO:0042995)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)|receptor signaling protein activity (GO:0005057)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(20)|lung(21)|ovary(5)|prostate(1)|skin(2)|upper_aerodigestive_tract(4)	65		Ovarian(120;0.196)		OV - Ovarian serous cystadenocarcinoma(155;8.1e-13)|BRCA - Breast invasive adenocarcinoma(81;0.0053)		AGACCGCCTCCGCAAAGTCAT	0.552													C|||	467	0.0932508	0.0144	0.1455	5008	,	,		21462	0.003		0.2773	False		,,,				2504	0.0665				p.R1101C		Atlas-SNP	.											.	TIAM2	161	.	0			c.C3301T						PASS	.	C	CYS/ARG,CYS/ARG	257,4149	147.6+/-182.1	5,247,1951	54.0	52.0	52.0		76,3301	4.1	1.0	6	dbSNP_120	52	2487,6113	406.8+/-348.9	365,1757,2178	yes	missense,missense	TIAM2	NM_001010927.2,NM_012454.3	180,180	370,2004,4129	TT,TC,CC		28.9186,5.833,21.098	probably-damaging,probably-damaging	26/627,1101/1702	155561796	2744,10262	2203	4300	6503	SO:0001583	missense	26230	exon15			CGCCTCCGCAAAG		CCDS34558.1, CCDS34559.1	6q25	2013-01-10			ENSG00000146426	ENSG00000146426		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	11806	protein-coding gene	gene with protein product		604709				10512681	Standard	NM_012454		Approved	STEF	uc003qqe.3	Q8IVF5	OTTHUMG00000015880	ENST00000461783.3:c.3301C>T	6.37:g.155561796C>T	ENSP00000437188:p.Arg1101Cys	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	32	14	0.4375	NM_012454	B2RP56|C9JZV2|Q6NXN9|Q6ZUP9|Q9UFG6|Q9UKV9|Q9UKW0	Missense_Mutation	SNP	ENST00000461783.3	37	CCDS34558.1	283	0.1295787545787546	10	0.02032520325203252	60	0.16574585635359115	2	0.0034965034965034965	211	0.2783641160949868	C	21.9	4.217544	0.79352	0.05833	0.289186	ENSG00000146426	ENST00000461783;ENST00000528928;ENST00000528535;ENST00000456144;ENST00000318981;ENST00000367174;ENST00000360366;ENST00000529824;ENST00000456877;ENST00000528391;ENST00000275246;ENST00000462408	T;T;T;T;T;T;T;T;T;T;T	0.69561	-0.41;-0.41;-0.41;-0.41;-0.41;-0.41;-0.41;-0.41;-0.41;-0.41;1.93	5.09	4.13	0.48395	Dbl homology (DH) domain (3);	0.000000	0.85682	D	0.000000	T	0.79913	0.4528	M	0.89095	3.005	0.09310	P	0.99999826644	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;0.999;0.999;0.997	D	0.83883	0.0280	9	0.87932	D	0	.	12.0581	0.53546	0.2431:0.7569:0.0:0.0	rs11751128;rs56905056;rs11751128	437;1101;1125;1101	E9PKT1;Q8IVF5-2;Q8IVF5-5;Q8IVF5	.;.;.;TIAM2_HUMAN	C	1101;1347;1101;1101;1101;477;1125;1101;413;437;26;39	ENSP00000437188:R1101C;ENSP00000434901:R1101C;ENSP00000407746:R1101C;ENSP00000327315:R1101C;ENSP00000356142:R477C;ENSP00000353528:R1125C;ENSP00000433348:R1101C;ENSP00000407183:R413C;ENSP00000435335:R437C;ENSP00000275246:R26C;ENSP00000431269:R39C	ENSP00000275246:R26C	R	+	1	0	TIAM2	155603488	1.000000	0.71417	0.998000	0.56505	0.995000	0.86356	2.889000	0.48601	2.362000	0.80069	0.491000	0.48974	CGC	C|0.825;T|0.175	0.175	strong		0.552	TIAM2-005	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000387980.2	NM_012454	
MUC4	4585	hgsc.bcm.edu	37	3	195511364	195511364	+	Missense_Mutation	SNP	T	T	A	rs75187745		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195511364T>A	ENST00000463781.3	-	2	7546	c.7087A>T	c.(7087-7089)Aca>Tca	p.T2363S	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.T2363S	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GTGTCACCTGTGGATACTGAG	0.587																																					p.T2363S		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	0			c.A7087T						scavenged	.						23.0	21.0	21.0					3																	195511364		689	1583	2272	SO:0001583	missense	4585	exon2			CACCTGTGGATAC	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.7087A>T	3.37:g.195511364T>A	ENSP00000417498:p.Thr2363Ser	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	71	5	0.0704225	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	T	5.115	0.206928	0.09704	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.49720	0.77;1.01	.	.	.	.	.	.	.	.	T	0.29321	0.0730	N	0.19112	0.55	0.09310	N	1	P	0.34587	0.458	B	0.39152	0.292	T	0.18272	-1.0342	7	.	.	.	.	2.7352	0.05238	0.0:0.3911:0.0:0.6089	.	2363	E7ESK3	.	S	2363	ENSP00000417498:T2363S;ENSP00000420243:T2363S	.	T	-	1	0	MUC4	196995759	0.007000	0.16637	0.008000	0.14137	0.111000	0.19643	-2.023000	0.01438	0.408000	0.25621	0.055000	0.15244	ACA	T|0.500;A|0.500	0.500	weak		0.587	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
EXOSC8	11340	hgsc.bcm.edu	37	13	37577073	37577073	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:37577073T>C	ENST00000389704.3	+	4	386	c.121T>C	c.(121-123)Tca>Cca	p.S41P	ALG5_ENST00000496689.1_5'Flank|EXOSC8_ENST00000489088.1_3'UTR	NM_181503.2	NP_852480.1	Q96B26	EXOS8_HUMAN	exosome component 8	41					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)|rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|exosome (RNase complex) (GO:0000178)|nucleus (GO:0005634)	AU-rich element binding (GO:0017091)			biliary_tract(1)|breast(1)|kidney(2)|pancreas(1)|prostate(1)|skin(1)	7		Lung NSC(96;6.57e-05)|Breast(139;0.0615)|Lung SC(185;0.0743)|Prostate(109;0.184)		all cancers(112;3.67e-07)|Epithelial(112;1.31e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00699)|BRCA - Breast invasive adenocarcinoma(63;0.0117)|GBM - Glioblastoma multiforme(144;0.0411)		CTTTTCAGGTTCAATTAGTAC	0.318																																					p.S41P		Atlas-SNP	.											.	EXOSC8	16	.	0			c.T121C						PASS	.						107.0	102.0	103.0					13																	37577073		2202	4298	6500	SO:0001583	missense	11340	exon4			TCAGGTTCAATTA	AF025438	CCDS31958.1	13q13.1	2010-05-07			ENSG00000120699	ENSG00000120699	3.1.13.-		17035	protein-coding gene	gene with protein product	"""CBP-interacting protein 3"", ""Opa interacting protein 2"""	606019				9466265, 11929972	Standard	NM_181503		Approved	OIP2, RRP43, bA421P11.3, Rrp43p, EAP2, p9, CIP3	uc001uwa.3	Q96B26	OTTHUMG00000016742	ENST00000389704.3:c.121T>C	13.37:g.37577073T>C	ENSP00000374354:p.Ser41Pro	Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	120	5	0.0416667	NM_181503	O43480|Q5TBA5	Missense_Mutation	SNP	ENST00000389704.3	37	CCDS31958.1	.	.	.	.	.	.	.	.	.	.	T	18.46	3.629298	0.67015	.	.	ENSG00000120699	ENST00000389704;ENST00000379809	T	0.63255	-0.03	5.65	4.48	0.54585	Ribosomal protein S5 domain 2-type fold (1);Exoribonuclease, phosphorolytic domain 1 (1);	0.108320	0.64402	D	0.000003	T	0.64405	0.2595	L	0.55017	1.72	0.58432	D	0.999998	P;P	0.46064	0.864;0.872	P;P	0.51229	0.663;0.585	T	0.59941	-0.7359	10	0.24483	T	0.36	-15.5735	11.4062	0.49900	0.0:0.0701:0.0:0.9299	.	41;41	Q5JXM0;Q96B26	.;EXOS8_HUMAN	P	41	ENSP00000374354:S41P	ENSP00000369137:S41P	S	+	1	0	EXOSC8	36475073	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	7.698000	0.84413	1.098000	0.41479	0.533000	0.62120	TCA	.	.	none		0.318	EXOSC8-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044535.2	NM_181503	
ZDHHC4	55146	hgsc.bcm.edu	37	7	6621277	6621277	+	Missense_Mutation	SNP	G	G	A	rs11559146	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:6621277G>A	ENST00000396706.2	+	4	600	c.157G>A	c.(157-159)Gtg>Atg	p.V53M	ZDHHC4_ENST00000396713.2_Missense_Mutation_p.V53M|AC079742.4_ENST00000434951.1_RNA|ZDHHC4_ENST00000405731.3_Missense_Mutation_p.V53M|ZDHHC4_ENST00000335965.6_Missense_Mutation_p.V53M|ZDHHC4_ENST00000396707.2_Missense_Mutation_p.V53M|ZDHHC4_ENST00000396709.1_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	243	0	0		WXS	Illumina HiSeq	Phase_I	174	38	0.218391	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	
BMS1	9790	hgsc.bcm.edu	37	10	43312807	43312807	+	Silent	SNP	C	C	T	rs11239786	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:43312807C>T	ENST00000374518.5	+	15	2508	c.2445C>T	c.(2443-2445)ccC>ccT	p.P815P		NM_014753.3	NP_055568.3	Q14692	BMS1_HUMAN	BMS1 ribosome biogenesis factor	815					ribosome assembly (GO:0042255)	nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(23)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	62						AAATTGACCCCGACGAAGAAG	0.313													C|||	1027	0.205072	0.0333	0.1167	5008	,	,		19710	0.4018		0.1988	False		,,,				2504	0.3037				p.P815P		Atlas-SNP	.											BMS1,NS,carcinoma,0,1	BMS1	132	1	0			c.C2445T						PASS	.						18.0	19.0	19.0					10																	43312807		2179	4257	6436	SO:0001819	synonymous_variant	9790	exon15			TGACCCCGACGAA	BC043345	CCDS7199.1	10q11.21	2013-05-01	2013-05-01	2007-03-20	ENSG00000165733	ENSG00000165733			23505	protein-coding gene	gene with protein product		611448	"""BMS1-like, ribosome assembly protein (yeast)"", ""BMS1 homolog, ribosome assembly protein (yeast)"""	BMS1L		11779832	Standard	NM_014753		Approved	KIAA0187	uc001jaj.3	Q14692	OTTHUMG00000018020	ENST00000374518.5:c.2445C>T	10.37:g.43312807C>T		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	41	22	0.536585	NM_014753	Q5QPT5|Q86XJ9	Silent	SNP	ENST00000374518.5	37	CCDS7199.1																																																																																			C|0.667;T|0.333	0.333	strong		0.313	BMS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047690.2	NM_014753	
OR51F1	256892	hgsc.bcm.edu	37	11	4790396	4790396	+	Missense_Mutation	SNP	G	G	A	rs17324609	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:4790396G>A	ENST00000380383.1	-	1	772	c.773C>T	c.(772-774)gCt>gTt	p.A258V	OR51F1_ENST00000343430.3_Missense_Mutation_p.A251V|MMP26_ENST00000477339.1_Intron|MMP26_ENST00000380390.1_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	165	42	0.254545	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	
UMOD	7369	hgsc.bcm.edu	37	16	20352618	20352618	+	Missense_Mutation	SNP	C	C	A	rs55772253	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:20352618C>A	ENST00000570689.1	-	7	1518	c.1372G>T	c.(1372-1374)Gtg>Ttg	p.V458L	UMOD_ENST00000570331.1_5'UTR|UMOD_ENST00000302509.4_Missense_Mutation_p.V458L|UMOD_ENST00000396138.4_Missense_Mutation_p.V507L|UMOD_ENST00000424589.1_Missense_Mutation_p.V491L|UMOD_ENST00000396134.2_Missense_Mutation_p.V491L|UMOD_ENST00000396142.2_Missense_Mutation_p.V458L			P07911	UROM_HUMAN	uromodulin	458	ZP. {ECO:0000255|PROSITE- ProRule:PRU00375}.		V -> L (in dbSNP:rs55772253).		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						GCCATCCGCACGGTGAACATG	0.597													C|||	69	0.013778	0.0015	0.013	5008	,	,		17370	0.001		0.0209	False		,,,				2504	0.0368				p.V458L		Atlas-SNP	.											UMOD,right_upper_lobe,carcinoma,+2,1	UMOD	128	1	0			c.G1372T						PASS	.	C	LEU/VAL,LEU/VAL	25,4381	31.7+/-61.6	0,25,2178	81.0	68.0	72.0		1372,1372	5.3	1.0	16	dbSNP_129	72	200,8400	87.4+/-149.7	3,194,4103	yes	missense,missense	UMOD	NM_001008389.1,NM_003361.2	32,32	3,219,6281	AA,AC,CC		2.3256,0.5674,1.73	probably-damaging,probably-damaging	458/641,458/641	20352618	225,12781	2203	4300	6503	SO:0001583	missense	7369	exon7			TCCGCACGGTGAA	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.1372G>T	16.37:g.20352618C>A	ENSP00000460548:p.Val458Leu	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	51	37	0.72549	NM_003361	B3KP48|B3KRN9|E9PEA4|Q540J6|Q6ZS84|Q8IYG0	Missense_Mutation	SNP	ENST00000570689.1	37	CCDS10583.1	25	0.011446886446886446	3	0.006097560975609756	6	0.016574585635359115	1	0.0017482517482517483	15	0.01978891820580475	C	22.1	4.245912	0.80024	0.005674	0.023256	ENSG00000169344	ENST00000396138;ENST00000396134;ENST00000424589;ENST00000302509;ENST00000429954;ENST00000396142	D;D;D;D	0.81659	-1.52;-1.52;-1.52;-1.52	5.34	5.34	0.76211	Zona pellucida sperm-binding protein (3);	0.000000	0.47093	D	0.000249	T	0.81987	0.4939	M	0.71206	2.165	0.35001	D	0.756015	D;D	0.76494	0.999;0.998	D;D	0.85130	0.997;0.988	D	0.89089	0.3481	10	0.62326	D	0.03	-31.2931	16.9011	0.86114	0.0:1.0:0.0:0.0	rs55772253	491;458	E9PEA4;P07911	.;UROM_HUMAN	L	458;491;491;458;436;458	ENSP00000379438:V491L;ENSP00000416346:V491L;ENSP00000306279:V458L;ENSP00000379446:V458L	ENSP00000306279:V458L	V	-	1	0	UMOD	20260119	0.968000	0.33430	0.993000	0.49108	0.892000	0.51952	2.911000	0.48774	2.646000	0.89796	0.655000	0.94253	GTG	C|0.983;A|0.017	0.017	strong		0.597	UMOD-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436862.1		
BBS2	583	hgsc.bcm.edu	37	16	56545175	56545175	+	Missense_Mutation	SNP	T	T	C	rs11373	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:56545175T>C	ENST00000245157.5	-	3	787	c.367A>G	c.(367-369)Att>Gtt	p.I123V	BBS2_ENST00000568104.1_Missense_Mutation_p.I123V|BBS2_ENST00000561951.1_5'UTR	NM_031885.3	NP_114091	Q9BXC9	BBS2_HUMAN	Bardet-Biedl syndrome 2	123			I -> V (polymorphism in linkage disequilibrium with G-75 in a Bedouin kindred; dbSNP:rs11373). {ECO:0000269|PubMed:11285252, ECO:0000269|PubMed:15666242, ECO:0000269|PubMed:15770229}.		adult behavior (GO:0030534)|artery smooth muscle contraction (GO:0014824)|brain morphogenesis (GO:0048854)|cartilage development (GO:0051216)|cerebral cortex development (GO:0021987)|cilium morphogenesis (GO:0060271)|fat cell differentiation (GO:0045444)|Golgi to plasma membrane protein transport (GO:0043001)|hippocampus development (GO:0021766)|melanosome transport (GO:0032402)|negative regulation of appetite by leptin-mediated signaling pathway (GO:0038108)|negative regulation of gene expression (GO:0010629)|negative regulation of multicellular organism growth (GO:0040015)|nonmotile primary cilium assembly (GO:0035058)|photoreceptor cell maintenance (GO:0045494)|positive regulation of multicellular organism growth (GO:0040018)|protein localization (GO:0008104)|protein localization to organelle (GO:0033365)|regulation of cilium beat frequency involved in ciliary motility (GO:0060296)|sperm axoneme assembly (GO:0007288)|striatum development (GO:0021756)|vasodilation (GO:0042311)|visual perception (GO:0007601)	BBSome (GO:0034464)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	RNA polymerase II repressing transcription factor binding (GO:0001103)			breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(10)|ovary(1)|skin(3)	26						CCCAGCACAATTGCATTTGCC	0.413									Bardet-Biedl syndrome				T|||	1320	0.263578	0.2458	0.2767	5008	,	,		18413	0.4127		0.1789	False		,,,				2504	0.2117				p.I123V		Atlas-SNP	.											.	BBS2	67	.	0			c.A367G						PASS	.	T	VAL/ILE	994,3402	372.5+/-320.4	102,790,1306	116.0	98.0	104.0		367	0.5	1.0	16	dbSNP_52	104	1546,7054	290.9+/-300.1	138,1270,2892	yes	missense	BBS2	NM_031885.3	29	240,2060,4198	CC,CT,TT		17.9767,22.6115,19.5445	benign	123/722	56545175	2540,10456	2198	4300	6498	SO:0001583	missense	583	exon3	Familial Cancer Database	BBS, Bardet-Biedl syndrome, type 1-12: BBS1-12,Laurence-Moon-Biedl syndrome	GCACAATTGCATT	AF342736	CCDS32451.1	16q21	2013-01-08				ENSG00000125124			967	protein-coding gene	gene with protein product		606151		BBS		11285252	Standard	NM_031885		Approved		uc002ejd.2	Q9BXC9		ENST00000245157.5:c.367A>G	16.37:g.56545175T>C	ENSP00000245157:p.Ile123Val	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	53	36	0.679245	NM_031885	Q96CM0|Q96SN9	Missense_Mutation	SNP	ENST00000245157.5	37	CCDS32451.1	578	0.26465201465201466	110	0.22357723577235772	93	0.2569060773480663	236	0.4125874125874126	139	0.18337730870712401	T	5.499	0.277020	0.10403	0.226115	0.179767	ENSG00000125124	ENST00000245157	D	0.82167	-1.58	5.9	0.542	0.17174	WD40 repeat-like-containing domain (1);	0.376395	0.31976	N	0.006774	T	0.00012	0.0000	N	0.16307	0.4	0.34697	P	0.273659	B;B	0.02656	0.0;0.0	B;B	0.08055	0.003;0.003	T	0.25117	-1.0141	9	0.14656	T	0.56	-3.2293	5.865	0.18771	0.0:0.3239:0.1315:0.5446	rs11373;rs1129878;rs3177663;rs3188184;rs11555777;rs17295965;rs17354402;rs17845410;rs17858274;rs52799276;rs57383601;rs11373	123;123	A8K0N9;Q9BXC9	.;BBS2_HUMAN	V	123	ENSP00000245157:I123V	ENSP00000245157:I123V	I	-	1	0	BBS2	55102676	0.997000	0.39634	0.994000	0.49952	0.608000	0.37181	0.402000	0.20965	-0.180000	0.10637	-0.276000	0.10085	ATT	T|0.778;C|0.222	0.222	strong		0.413	BBS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434386.2	NM_031885	
SCIN	85477	hgsc.bcm.edu	37	7	12610594	12610594	+	Missense_Mutation	SNP	A	A	G	rs2240572	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:12610594A>G	ENST00000297029.5	+	1	283	c.182A>G	c.(181-183)cAc>cGc	p.H61R	AC005281.2_ENST00000433040.1_RNA	NM_001112706.2	NP_001106177.1	Q9Y6U3	ADSV_HUMAN	scinderin	61	Actin-severing. {ECO:0000255}.		H -> R (in dbSNP:rs2240572). {ECO:0000269|PubMed:15489334}.		actin filament capping (GO:0051693)|actin filament severing (GO:0051014)|actin nucleation (GO:0045010)|calcium ion-dependent exocytosis (GO:0017156)|negative regulation of cell proliferation (GO:0008285)|positive regulation of apoptotic process (GO:0043065)|positive regulation of megakaryocyte differentiation (GO:0045654)|positive regulation of secretion (GO:0051047)|regulation of chondrocyte differentiation (GO:0032330)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)	1-phosphatidylinositol binding (GO:0005545)|actin binding (GO:0003779)|actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylserine binding (GO:0001786)			endometrium(3)|kidney(1)|large_intestine(2)|lung(9)|ovary(2)	17				UCEC - Uterine corpus endometrioid carcinoma (126;0.195)		TTCACCTACCACCTGCACTTC	0.692													G|||	2018	0.402955	0.5681	0.3934	5008	,	,		13778	0.244		0.4066	False		,,,				2504	0.3466				p.H61R		Atlas-SNP	.											SCIN_ENST00000297029,NS,carcinoma,0,6	SCIN	105	6	0			c.A182G						PASS	.	G	ARG/HIS	731,653		198,335,159	16.0	26.0	23.0		182	4.9	1.0	7	dbSNP_98	23	1322,1858		289,744,557	yes	missense	SCIN	NM_001112706.2	29	487,1079,716	GG,GA,AA		41.5723,47.1821,44.9825	benign	61/716	12610594	2053,2511	692	1590	2282	SO:0001583	missense	85477	exon1			CCTACCACCTGCA	AF276507	CCDS47545.1, CCDS47546.1	7p21.3	2006-04-25			ENSG00000006747	ENSG00000006747			21695	protein-coding gene	gene with protein product		613416					Standard	NM_033128		Approved	adseverin, KIAA1905	uc003ssn.4	Q9Y6U3	OTTHUMG00000152385	ENST00000297029.5:c.182A>G	7.37:g.12610594A>G	ENSP00000297029:p.His61Arg	Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	113	113	1	NM_001112706	A8K2U8|Q8NBZ6|Q8WU97|Q96JC7|Q96PY2	Missense_Mutation	SNP	ENST00000297029.5	37	CCDS47545.1	851	0.38965201465201466	281	0.5711382113821138	149	0.4116022099447514	121	0.21153846153846154	300	0.39577836411609496	G	12.93	2.086308	0.36855	0.528179	0.415723	ENSG00000006747	ENST00000297029;ENST00000417018	T;T	0.54866	0.55;0.55	4.9	4.9	0.64082	Gelsolin domain (1);	0.223988	0.38005	N	0.001843	T	0.00012	0.0000	N	0.12920	0.275	0.09310	P	0.9999999999999861	B	0.02656	0.0	B	0.04013	0.001	T	0.43988	-0.9357	9	0.40728	T	0.16	-5.212	8.2742	0.31862	0.2373:0.0:0.7627:0.0	rs2240572;rs17856629;rs59501934;rs2240572	61	Q9Y6U3	ADSV_HUMAN	R	61	ENSP00000297029:H61R;ENSP00000404380:H61R	ENSP00000297029:H61R	H	+	2	0	SCIN	12577119	1.000000	0.71417	1.000000	0.80357	0.909000	0.53808	4.277000	0.58939	1.307000	0.44944	-0.215000	0.12644	CAC	A|0.609;G|0.391	0.391	strong		0.692	SCIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326041.1	NM_033128	
WNK2	65268	hgsc.bcm.edu	37	9	95993326	95993326	+	Silent	SNP	T	T	C	rs11787888	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:95993326T>C	ENST00000297954.4	+	3	1011	c.1011T>C	c.(1009-1011)tcT>tcC	p.S337S	WNK2_ENST00000356055.3_5'UTR|WNK2_ENST00000427277.2_5'UTR|WNK2_ENST00000395475.2_Silent_p.S323S|WNK2_ENST00000349097.3_5'UTR|WNK2_ENST00000395477.2_Silent_p.S337S	NM_001282394.1	NP_001269323.1	Q9Y3S1	WNK2_HUMAN	WNK lysine deficient protein kinase 2	337	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				intracellular signal transduction (GO:0035556)|negative regulation of cell proliferation (GO:0008285)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of ion homeostasis (GO:2000021)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(1)|endometrium(11)|kidney(4)|large_intestine(5)|lung(17)|ovary(2)|prostate(3)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)	54						CAACTGGGTCTGTGAAGATTG	0.537													T|||	744	0.148562	0.0983	0.111	5008	,	,		20051	0.0843		0.1541	False		,,,				2504	0.3037				p.S337S		Atlas-SNP	.											WNK2_ENST00000297954,NS,carcinoma,+1,2	WNK2	277	2	0			c.T1011C						PASS	.	T		467,3939	221.0+/-238.3	15,437,1751	184.0	183.0	184.0		1011	-6.7	0.5	9	dbSNP_120	184	1181,7419	242.1+/-272.2	87,1007,3206	no	coding-synonymous	WNK2	NM_006648.3		102,1444,4957	CC,CT,TT		13.7326,10.5992,12.6711		337/2218	95993326	1648,11358	2203	4300	6503	SO:0001819	synonymous_variant	65268	exon3			TGGGTCTGTGAAG	AJ242724	CCDS75858.1	9q22.3	2008-02-05	2003-06-23	2005-01-22	ENSG00000165238	ENSG00000165238			14542	protein-coding gene	gene with protein product		606249	"""serologically defined colon cancer antigen 43"""	SDCCAG43, PRKWNK2		9610721, 11571656	Standard	NM_006648		Approved	NY-CO-43, KIAA1760	uc004atj.3	Q9Y3S1	OTTHUMG00000020247	ENST00000297954.4:c.1011T>C	9.37:g.95993326T>C		Somatic	231	0	0		WXS	Illumina HiSeq	Phase_I	199	98	0.492462	NM_006648	Q5VWF1|Q5VWF2|Q8IY36|Q9C0A3|Q9H3P4	Silent	SNP	ENST00000297954.4	37		247	0.1130952380952381	49	0.09959349593495935	42	0.11602209944751381	38	0.06643356643356643	118	0.15567282321899736	T	10.56	1.385337	0.25031	0.105992	0.137326	ENSG00000165238	ENST00000432730	.	.	.	5.52	-6.68	0.01778	.	.	.	.	.	T	0.00073	0.0002	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.18840	-1.0324	3	.	.	.	.	3.2884	0.06940	0.1033:0.3687:0.2131:0.315	rs11787888;rs11787888	.	.	.	P	333	.	.	L	+	2	0	WNK2	95033147	0.000000	0.05858	0.535000	0.28026	0.976000	0.68499	-1.965000	0.01511	-1.726000	0.01370	0.533000	0.62120	CTG	T|0.881;C|0.119	0.119	strong		0.537	WNK2-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000317359.1	NM_006648	
OR2K2	26248	hgsc.bcm.edu	37	9	114090279	114090279	+	Silent	SNP	A	A	G	rs314452	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:114090279A>G	ENST00000374428.1	-	1	521	c.522T>C	c.(520-522)gcT>gcC	p.A174A	OR2K2_ENST00000302681.1_Silent_p.A145A			Q8NGT1	OR2K2_HUMAN	olfactory receptor, family 2, subfamily K, 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)			breast(1)|central_nervous_system(1)|large_intestine(5)|lung(8)|ovary(1)|prostate(2)|skin(2)	20						AGGAGACCGTAGCCATCCGTG	0.552													G|||	2441	0.48742	0.3162	0.5764	5008	,	,		21213	0.498		0.6302	False		,,,				2504	0.498				p.A145A		Atlas-SNP	.											.	OR2K2	77	.	0			c.T435C						PASS	.	G		1762,2644	644.6+/-398.0	353,1056,794	102.0	81.0	88.0		435	-0.5	0.1	9	dbSNP_79	88	5487,3113	475.3+/-369.1	1754,1979,567	no	coding-synonymous	OR2K2	NM_205859.1		2107,3035,1361	GG,GA,AA		36.1977,39.9909,44.2642		145/317	114090279	7249,5757	2203	4300	6503	SO:0001819	synonymous_variant	26248	exon1			GACCGTAGCCATC	X64977	CCDS6778.1	9q31.3	2012-08-09			ENSG00000171133	ENSG00000171133		"""GPCR / Class A : Olfactory receptors"""	8264	protein-coding gene	gene with protein product				OR2AR1P		1370859, 17010214	Standard	NM_205859		Approved	HTPCRH06, HSHTPCRH06	uc011lwp.2	Q8NGT1	OTTHUMG00000020488	ENST00000374428.1:c.522T>C	9.37:g.114090279A>G		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	63	38	0.603175	NM_205859	Q2TA61|Q5VYK4|Q6IFI5	Silent	SNP	ENST00000374428.1	37																																																																																				A|0.465;G|0.535	0.535	strong		0.552	OR2K2-201	KNOWN	basic	protein_coding	protein_coding		NM_205859	
P2RY11	5032	hgsc.bcm.edu	37	19	10225390	10225390	+	Silent	SNP	C	C	G	rs74462278	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:10225390C>G	ENST00000321826.4	+	2	1285	c.1101C>G	c.(1099-1101)ccC>ccG	p.P367P	PPAN_ENST00000556468.1_Silent_p.P787P|PPAN-P2RY11_ENST00000428358.1_3'UTR|PPAN-P2RY11_ENST00000393796.4_Silent_p.P787P	NM_002566.4	NP_002557.2	Q96G91	P2Y11_HUMAN	purinergic receptor P2Y, G-protein coupled, 11	367					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)			CGTCAGAGCCCCAGTCCCGTG	0.657													C|||	83	0.0165735	0.0	0.0	5008	,	,		18019	0.0228		0.001	False		,,,				2504	0.0603				p.P787P		Atlas-SNP	.											.	PPAN-P2RY11	81	.	0			c.C2361G						PASS	.	C	,,	5,4401	8.1+/-20.4	0,5,2198	44.0	50.0	48.0		2361,,1101	0.5	0.0	19	dbSNP_131	48	0,8596		0,0,4298	no	coding-synonymous,utr-3,coding-synonymous	P2RY11,PPAN-P2RY11	NM_001040664.2,NM_001198690.1,NM_002566.4	,,	0,5,6496	GG,GC,CC		0.0,0.1135,0.0385	,,	787/795,,367/375	10225390	5,12997	2203	4298	6501	SO:0001819	synonymous_variant	692312	exon13			AGAGCCCCAGTCC	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.1101C>G	19.37:g.10225390C>G		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	91	40	0.43956	NM_001040664	B2R8X9|O43190|Q9BYU4|Q9H170	Silent	SNP	ENST00000321826.4	37	CCDS12226.1																																																																																			C|0.997;G|0.003	0.003	strong		0.657	P2RY11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316664.2	NM_002566	
CROCC	9696	hgsc.bcm.edu	37	1	17265560	17265560	+	Missense_Mutation	SNP	C	C	T	rs9435793	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:17265560C>T	ENST00000375541.5	+	12	1600	c.1531C>T	c.(1531-1533)Ccc>Tcc	p.P511S	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)		CCGCCGAGGCCCCTCCCCGGC	0.731																																					p.P511S		Atlas-SNP	.											CROCC,NS,carcinoma,0,1	CROCC	185	1	0			c.C1531T						scavenged	.						6.0	6.0	6.0					1																	17265560		2007	3902	5909	SO:0001583	missense	9696	exon12			CGAGGCCCCTCCC	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.1531C>T	1.37:g.17265560C>T	ENSP00000364691:p.Pro511Ser	Somatic	2	1	0.5		WXS	Illumina HiSeq	Phase_I	11	7	0.636364	NM_014675		Missense_Mutation	SNP	ENST00000375541.5	37	CCDS30616.1	781	0.3576007326007326	171	0.3475609756097561	123	0.3397790055248619	240	0.4195804195804196	247	0.3258575197889182	C	11.08	1.532985	0.27387	.	.	ENSG00000058453	ENST00000375541;ENST00000445545	T	0.09255	3.0	5.39	4.42	0.53409	.	.	.	.	.	T	0.00012	0.0000	N	0.24115	0.695	0.28995	N	0.887822	B;B;P	0.38504	0.007;0.001;0.634	B;B;B	0.41813	0.013;0.002;0.367	T	0.40213	-0.9575	9	0.07644	T	0.81	.	8.3381	0.32228	0.0:0.7587:0.1582:0.0831	rs9435793;rs58724462	374;374;511	A1L0S8;A1L0S9;Q5TZA2	.;.;CROCC_HUMAN	S	511;392	ENSP00000364691:P511S	ENSP00000364691:P511S	P	+	1	0	CROCC	17138147	0.959000	0.32827	1.000000	0.80357	0.963000	0.63663	1.779000	0.38624	2.702000	0.92279	0.561000	0.74099	CCC	C|0.643;T|0.357	0.357	strong		0.731	CROCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006249.2	NM_014675	
IL1RL1	9173	hgsc.bcm.edu	37	2	102955468	102955468	+	Missense_Mutation	SNP	C	C	A	rs1041973	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:102955468C>A	ENST00000233954.1	+	3	504	c.233C>A	c.(232-234)gCa>gAa	p.A78E	IL1RL1_ENST00000393393.3_Missense_Mutation_p.A78E|IL1RL1_ENST00000409584.1_Missense_Mutation_p.A78E|IL1RL1_ENST00000473175.1_3'UTR|IL1RL1_ENST00000311734.2_Missense_Mutation_p.A78E|IL1RL1_ENST00000404917.2_5'UTR	NM_016232.4	NP_057316.3	Q01638	ILRL1_HUMAN	interleukin 1 receptor-like 1	78	Ig-like C2-type 1.		A -> E (in dbSNP:rs1041973). {ECO:0000269|PubMed:10527832, ECO:0000269|PubMed:10936050, ECO:0000269|PubMed:1482686}.		immune response (GO:0006955)|intracellular signal transduction (GO:0035556)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of T-helper 1 type immune response (GO:0002826)|positive regulation of chemokine secretion (GO:0090197)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interleukin-5 production (GO:0032754)|positive regulation of macrophage activation (GO:0043032)|signal transduction (GO:0007165)	external side of plasma membrane (GO:0009897)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)	cytokine receptor activity (GO:0004896)|interleukin-1 receptor activity (GO:0004908)|interleukin-33 receptor activity (GO:0002114)|receptor signaling protein activity (GO:0005057)			NS(1)|central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|skin(3)|urinary_tract(1)	16						CTACCAGCTGCAGTTGCTGAT	0.433													a|||	1412	0.281949	0.5666	0.1988	5008	,	,		17855	0.1518		0.2366	False		,,,				2504	0.137				p.A78E		Atlas-SNP	.											.	IL1RL1	114	.	0			c.C233A						PASS	.	A	GLU/ALA,GLU/ALA	2066,2340	606.1+/-390.7	486,1094,623	166.0	172.0	170.0		233,233	2.3	0.1	2	dbSNP_86	170	2178,6422	712.4+/-405.9	281,1616,2403	yes	missense,missense	IL1RL1	NM_003856.2,NM_016232.4	107,107	767,2710,3026	AA,AC,CC		25.3256,46.8906,32.6311	benign,benign	78/329,78/557	102955468	4244,8762	2203	4300	6503	SO:0001583	missense	9173	exon3			CAGCTGCAGTTGC	D12764	CCDS2057.1, CCDS2058.1, CCDS74548.1	2q12	2013-01-29			ENSG00000115602	ENSG00000115602		"""Interleukins and interleukin receptors"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5998	protein-coding gene	gene with protein product	"""homolog of mouse growth stimulation-expressed"""	601203				1482686, 10191101, 16286016	Standard	NM_016232		Approved	ST2, FIT-1, ST2L, ST2V, DER4, T1, IL33R	uc002tbu.1	Q01638	OTTHUMG00000130782	ENST00000233954.1:c.233C>A	2.37:g.102955468C>A	ENSP00000233954:p.Ala78Glu	Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	140	62	0.442857	NM_016232	A8K6B3|B4E0I3|Q53TU7|Q8NEJ3|Q9ULV7|Q9UQ44	Missense_Mutation	SNP	ENST00000233954.1	37	CCDS2057.1	631	0.2889194139194139	293	0.5955284552845529	75	0.20718232044198895	86	0.15034965034965034	177	0.23350923482849603	A	8.012	0.757800	0.15846	0.468906	0.253256	ENSG00000115602	ENST00000233954;ENST00000393393;ENST00000311734;ENST00000409584	T;T;T;T	0.64991	-0.13;-0.13;-0.13;-0.13	6.03	2.31	0.28768	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	1.353100	0.04451	N	0.372554	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.42498	-0.9448	9	0.02654	T	1	.	2.5349	0.04712	0.4691:0.3123:0.0823:0.1363	rs1041973;rs3171847;rs56665071;rs1041973	78;78	Q01638-2;Q01638	.;ILRL1_HUMAN	E	78	ENSP00000233954:A78E;ENSP00000377052:A78E;ENSP00000310371:A78E;ENSP00000386618:A78E	ENSP00000233954:A78E	A	+	2	0	IL1RL1	102321900	0.000000	0.05858	0.149000	0.22428	0.682000	0.39822	0.110000	0.15437	0.491000	0.27793	-0.256000	0.11100	GCA	C|0.681;A|0.319	0.319	strong		0.433	IL1RL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253296.1	NM_016232	
ROS1	6098	hgsc.bcm.edu	37	6	117686840	117686840	+	Silent	SNP	T	T	C	rs2229078	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:117686840T>C	ENST00000368508.3	-	19	3075	c.2877A>G	c.(2875-2877)gaA>gaG	p.E959E	ROS1_ENST00000368507.3_Silent_p.E954E|GOPC_ENST00000467125.1_Intron	NM_002944.2	NP_002935.2	P08922	ROS1_HUMAN	ROS proto-oncogene 1 , receptor tyrosine kinase	959	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell differentiation (GO:0030154)|cell growth (GO:0016049)|cell proliferation (GO:0008283)|columnar/cuboidal epithelial cell development (GO:0002066)|negative regulation of gene expression (GO:0010629)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein phosphorylation (GO:0006468)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of phosphate transport (GO:0010966)|regulation of TOR signaling (GO:0032006)|spermatogenesis (GO:0007283)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)		TPM3_ENST00000368530/ROS1(4)|LRIG3/ROS1(2)|CD74_ENST00000009530/ROS1(32)|SLC34A2/ROS1(14)|EZR/ROS1(4)|GOPC/ROS1(14)|SDC4/ROS1(7)	NS(2)|breast(7)|central_nervous_system(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(28)|lung(56)|ovary(8)|prostate(5)|skin(19)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	162		all_cancers(87;0.00846)|all_epithelial(87;0.0242)		GBM - Glioblastoma multiforme(226;0.0387)|OV - Ovarian serous cystadenocarcinoma(136;0.0954)|all cancers(137;0.137)		AAGCATTTCCTTCAATCCTAA	0.383			T	"""GOPC, SDC4, SLC34A2, EZR, LRIG3"""	"""glioblastoma, NSCLC"""								T|||	121	0.0241613	0.0	0.0303	5008	,	,		18336	0.001		0.0577	False		,,,				2504	0.0419				p.E959E		Atlas-SNP	.		Dom	yes		6	6q22	6098	v-ros UR2 sarcoma virus oncogene homolog 1 (avian)		"""O, E"""	.	ROS1	728	.	0			c.A2877G						PASS	.	T		48,4358	48.2+/-83.0	0,48,2155	52.0	50.0	51.0		2877	-0.7	1.0	6	dbSNP_98	51	464,8136	135.4+/-192.6	10,444,3846	no	coding-synonymous	ROS1	NM_002944.2		10,492,6001	CC,CT,TT		5.3953,1.0894,3.9366		959/2348	117686840	512,12494	2203	4300	6503	SO:0001819	synonymous_variant	6098	exon19			ATTTCCTTCAATC	M13599	CCDS5116.1	6q21-q22	2014-06-26	2014-06-26		ENSG00000047936	ENSG00000047936		"""Fibronectin type III domain containing"""	10261	protein-coding gene	gene with protein product		165020	"""v-ros avian UR2 sarcoma virus oncogene homolog 1"", ""v-ros UR2 sarcoma virus oncogene homolog 1 (avian)"", ""c-ros oncogene 1 , receptor tyrosine kinase"""			1611909	Standard	NM_002944		Approved	MCF3, ROS, c-ros-1	uc003pxp.1	P08922	OTTHUMG00000016188	ENST00000368508.3:c.2877A>G	6.37:g.117686840T>C		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	125	66	0.528	NM_002944	Q15368|Q5TDB5	Silent	SNP	ENST00000368508.3	37	CCDS5116.1																																																																																			T|0.968;C|0.032	0.032	strong		0.383	ROS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043464.1		
KIAA1683	80726	hgsc.bcm.edu	37	19	18375659	18375659	+	Intron	SNP	C	C	T	rs12608843	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:18375659C>T	ENST00000600328.3	-	3	2810				KIAA1683_ENST00000392413.4_Silent_p.L897L|KIAA1683_ENST00000600359.3_Intron			Q9H0B3	K1683_HUMAN	KIAA1683							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						CTTTGGCCAACAGAGTGCGGA	0.637													C|||	911	0.181909	0.0121	0.3271	5008	,	,		19268	0.2341		0.2704	False		,,,				2504	0.1636				p.L897L		Atlas-SNP	.											.	KIAA1683	190	.	0			c.G2691A						PASS	.	C	,,	76,1308		0,76,616	42.0	45.0	44.0		2691,,	-0.6	0.0	19	dbSNP_120	44	853,2329		114,625,852	no	coding-synonymous,intron,intron	KIAA1683	NM_001145304.1,NM_001145305.1,NM_025249.3	,,	114,701,1468	TT,TC,CC		26.807,5.4913,20.346	,,	897/1368,,	18375659	929,3637	692	1591	2283	SO:0001627	intron_variant	80726	exon3			GGCCAACAGAGTG	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.2616+74G>A	19.37:g.18375659C>T		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	101	51	0.504951	NM_001145304	B4DYH2|E9PDE0|E9PH54|Q2KHR5|Q8N4G8|Q96M14|Q9C0I0	Silent	SNP	ENST00000600328.3	37	CCDS32958.1																																																																																			C|0.805;T|0.195	0.195	strong		0.637	KIAA1683-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000466312.3		
MCCD1	401250	hgsc.bcm.edu	37	6	31496834	31496834	+	Missense_Mutation	SNP	C	C	T	rs146742941	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:31496834C>T	ENST00000376191.2	+	1	341	c.43C>T	c.(43-45)Cgc>Tgc	p.R15C	DDX39B_ENST00000462421.1_5'Flank	NM_001011700.2	NP_001011700.2	P59942	MCCD1_HUMAN	mitochondrial coiled-coil domain 1	15						mitochondrion (GO:0005739)				skin(1)	1						CCATTTCCTTCGCCTCCTTCT	0.627																																					p.R15C		Atlas-SNP	.											MCCD1,NS,carcinoma,-1,1	MCCD1	3	1	0			c.C43T						PASS	.	C	CYS/ARG	0,3022		0,0,1511	173.0	128.0	144.0		43	0.8	0.1	6	dbSNP_134	144	2,5416		0,2,2707	yes	missense	MCCD1	NM_001011700.2	180	0,2,4218	TT,TC,CC		0.0369,0.0,0.0237	probably-damaging	15/120	31496834	2,8438	1511	2709	4220	SO:0001583	missense	401250	exon1			TTCCTTCGCCTCC		CCDS34396.1	6p21.3	2003-10-17				ENSG00000204511			20668	protein-coding gene	gene with protein product		609624				14527716	Standard	NM_001011700		Approved		uc003ntp.1	P59942		ENST00000376191.2:c.43C>T	6.37:g.31496834C>T	ENSP00000365362:p.Arg15Cys	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	46	25	0.543478	NM_001011700	A2AB29|A2RUP7|B0UZB2|Q7RTY2	Missense_Mutation	SNP	ENST00000376191.2	37	CCDS34396.1	.	.	.	.	.	.	.	.	.	.	c	0.103	-1.148811	0.01714	0.0	3.69E-4	ENSG00000204511	ENST00000376191	T	0.25250	1.81	0.748	0.748	0.18376	.	1.197690	0.06338	N	0.707425	T	0.06645	0.0170	N	0.24115	0.695	0.09310	N	1	B	0.10296	0.003	B	0.01281	0.0	T	0.41770	-0.9490	9	0.72032	D	0.01	.	.	.	.	.	15	P59942	MCCD1_HUMAN	C	15	ENSP00000365362:R15C	ENSP00000365362:R15C	R	+	1	0	MCCD1	31604813	0.000000	0.05858	0.062000	0.19696	0.029000	0.11900	-1.047000	0.03521	0.691000	0.31592	0.555000	0.69702	CGC	C|1.000;T|0.000	0.000	strong		0.627	MCCD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259099.1		
GNAT3	346562	hgsc.bcm.edu	37	7	80117993	80117993	+	Splice_Site	SNP	C	C	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:80117993C>A	ENST00000398291.3	-	3	255		c.e3-1		CD36_ENST00000435819.1_Intron	NM_001102386.1	NP_001095856.1	A8MTJ3	GNAT3_HUMAN	guanine nucleotide binding protein, alpha transducing 3						adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|blood coagulation (GO:0007596)|detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|detection of visible light (GO:0009584)|platelet activation (GO:0030168)|response to nicotine (GO:0035094)|sensory perception of sweet taste (GO:0050916)|sensory perception of umami taste (GO:0050917)|synaptic transmission (GO:0007268)	acrosomal vesicle (GO:0001669)|apical plasma membrane (GO:0016324)|axoneme (GO:0005930)|heterotrimeric G-protein complex (GO:0005834)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	G-protein beta/gamma-subunit complex binding (GO:0031683)|G-protein coupled photoreceptor activity (GO:0008020)|G-protein coupled receptor binding (GO:0001664)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(2)|lung(5)|ovary(1)	9						ATGGATGATCCTATAATTTAA	0.318																																					.		Atlas-SNP	.											.	GNAT3	65	.	0			c.162-1G>T						PASS	.						89.0	75.0	80.0					7																	80117993		1830	4083	5913	SO:0001630	splice_region_variant	346562	exon4			ATGATCCTATAAT		CCDS47625.1	7q21.11	2007-06-13			ENSG00000214415	ENSG00000214415			22800	protein-coding gene	gene with protein product		139395					Standard	NM_001102386		Approved	gustducin, GDCA	uc011kgu.2	A8MTJ3	OTTHUMG00000155401	ENST00000398291.3:c.162-1G>T	7.37:g.80117993C>A		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	61	13	0.213115	NM_001102386	A4D1B2|A4D1B3|B9EJG5	Splice_Site	SNP	ENST00000398291.3	37	CCDS47625.1	.	.	.	.	.	.	.	.	.	.	C	23.2	4.390611	0.82902	.	.	ENSG00000214415	ENST00000398291	.	.	.	5.77	5.77	0.91146	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.7634	0.88470	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	GNAT3	79955929	1.000000	0.71417	1.000000	0.80357	0.933000	0.57130	7.127000	0.77210	2.720000	0.93068	0.650000	0.86243	.	.	.	none		0.318	GNAT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339909.3	XM_294370	Intron
TCHH	7062	hgsc.bcm.edu	37	1	152084213	152084213	+	Missense_Mutation	SNP	C	C	G	rs199978168	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:152084213C>G	ENST00000368804.1	-	2	1479	c.1480G>C	c.(1480-1482)Gag>Cag	p.E494Q		NM_007113.2	NP_009044.2	Q07283	TRHY_HUMAN	trichohyalin	494	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)			CGCCTCTCCTCCTCCTCGAGC	0.667																																					p.E494Q		Atlas-SNP	.											.	TCHH	275	.	0			c.G1480C						PASS	.						63.0	71.0	68.0					1																	152084213		2108	4221	6329	SO:0001583	missense	7062	exon3			TCTCCTCCTCCTC	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.1480G>C	1.37:g.152084213C>G	ENSP00000357794:p.Glu494Gln	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	103	16	0.15534	NM_007113	Q5VUI3	Missense_Mutation	SNP	ENST00000368804.1	37	CCDS41396.1	.	.	.	.	.	.	.	.	.	.	c	7.483	0.649136	0.14516	.	.	ENSG00000159450	ENST00000368804	T	0.05199	3.48	3.42	0.2	0.15181	.	.	.	.	.	T	0.00845	0.0028	N	0.08118	0	0.09310	N	1	B	0.26081	0.141	B	0.20767	0.031	T	0.47381	-0.9122	9	0.21014	T	0.42	.	7.1235	0.25458	0.0:0.3768:0.5138:0.1093	.	494	Q07283	TRHY_HUMAN	Q	494	ENSP00000357794:E494Q	ENSP00000357794:E494Q	E	-	1	0	TCHH	150350837	0.000000	0.05858	0.001000	0.08648	0.031000	0.12232	0.016000	0.13377	0.159000	0.19401	-0.742000	0.03525	GAG	C|0.978;G|0.023	0.023	strong		0.667	TCHH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036671.2	NM_007113	
LILRB1	10859	hgsc.bcm.edu	37	19	55143452	55143452	+	Missense_Mutation	SNP	T	T	C	rs1061680	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:55143452T>C	ENST00000396331.1	+	6	782	c.425T>C	c.(424-426)aTc>aCc	p.I142T	LILRB1_ENST00000448689.1_Missense_Mutation_p.I142T|LILRB1_ENST00000396315.1_Missense_Mutation_p.I142T|LILRB1_ENST00000396321.2_Missense_Mutation_p.I142T|LILRB1_ENST00000324602.7_Missense_Mutation_p.I142T|LILRB1_ENST00000427581.2_Missense_Mutation_p.I178T|LILRB1_ENST00000396327.3_Missense_Mutation_p.I142T|LILRB1_ENST00000434867.2_Missense_Mutation_p.I142T|LILRB1_ENST00000396317.1_Missense_Mutation_p.I142T|LILRB1_ENST00000418536.2_Missense_Mutation_p.I142T|AC009892.1_ENST00000578908.1_RNA|LILRB1_ENST00000396332.4_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						PASS	.	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	124	1	0.00806452		WXS	Illumina HiSeq	Phase_I	107	107	1	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		
PLXNA4	91584	hgsc.bcm.edu	37	7	131883311	131883311	+	Missense_Mutation	SNP	C	C	T	rs62622406	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:131883311C>T	ENST00000359827.3	-	13	3633	c.2671G>A	c.(2671-2673)Gcc>Acc	p.A891T	PLXNA4_ENST00000321063.4_Missense_Mutation_p.A891T			Q9HCM2	PLXA4_HUMAN	plexin A4	891	IPT/TIG 1.				anterior commissure morphogenesis (GO:0021960)|axon guidance (GO:0007411)|chemorepulsion of branchiomotor axon (GO:0021793)|facial nerve structural organization (GO:0021612)|glossopharyngeal nerve morphogenesis (GO:0021615)|postganglionic parasympathetic nervous system development (GO:0021784)|regulation of axon extension involved in axon guidance (GO:0048841)|regulation of negative chemotaxis (GO:0050923)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|sympathetic nervous system development (GO:0048485)|trigeminal nerve structural organization (GO:0021637)|vagus nerve morphogenesis (GO:0021644)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)			NS(1)|breast(1)|endometrium(3)|kidney(4)|large_intestine(14)|lung(17)|ovary(1)|prostate(2)|skin(1)|stomach(1)	45						ACATGGGAGGCGATGTCGCGA	0.577													C|||	17	0.00339457	0.0008	0.0014	5008	,	,		19542	0.0		0.0109	False		,,,				2504	0.0041				p.A891T		Atlas-SNP	.											.	PLXNA4	873	.	0			c.G2671A						PASS	.	C	THR/ALA	7,3955		0,7,1974	74.0	76.0	75.0		2671	5.9	1.0	7	dbSNP_129	75	113,8235		0,113,4061	yes	missense	PLXNA4	NM_020911.1	58	0,120,6035	TT,TC,CC		1.3536,0.1767,0.9748	benign	891/1895	131883311	120,12190	1981	4174	6155	SO:0001583	missense	91584	exon13			GGGAGGCGATGTC	AB046770, AK123428	CCDS5826.1, CCDS43646.1, CCDS43647.1	7q32.3	2007-09-26	2007-09-26	2007-09-26	ENSG00000221866	ENSG00000221866		"""Plexins"""	9102	protein-coding gene	gene with protein product		604280	"""plexin A4, A"", ""plexin A4, B"""	PLXNA4A, PLXNA4B			Standard	NM_181775		Approved	KIAA1550, DKFZp434G0625PRO34003, FAYV2820	uc003vra.4	Q9HCM2	OTTHUMG00000155108	ENST00000359827.3:c.2671G>A	7.37:g.131883311C>T	ENSP00000352882:p.Ala891Thr	Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	45	21	0.466667	NM_020911	A4D1N6|E9PAM2|Q6UWC6|Q6ZW89|Q8N969|Q8ND00|Q8NEN3|Q9NTD4	Missense_Mutation	SNP	ENST00000359827.3	37	CCDS43646.1	8	0.003663003663003663	0	0.0	1	0.0027624309392265192	0	0.0	7	0.009234828496042216	C	11.07	1.531317	0.27387	0.001767	0.013536	ENSG00000221866	ENST00000321063;ENST00000359827	T;T	0.75821	-0.97;-0.97	5.94	5.94	0.96194	Cell surface receptor IPT/TIG (2);Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.168437	0.52532	D	0.000077	T	0.60586	0.2280	L	0.43923	1.385	0.36252	D	0.853963	P	0.40250	0.709	B	0.37239	0.244	T	0.66693	-0.5859	10	0.13108	T	0.6	.	20.3658	0.98878	0.0:1.0:0.0:0.0	rs62622406	891	Q9HCM2	PLXA4_HUMAN	T	891	ENSP00000323194:A891T;ENSP00000352882:A891T	ENSP00000323194:A891T	A	-	1	0	PLXNA4	131533851	0.986000	0.35501	0.999000	0.59377	0.242000	0.25591	2.642000	0.46596	2.820000	0.97059	0.650000	0.86243	GCC	C|0.991;T|0.009	0.009	strong		0.577	PLXNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338422.2	NM_181775	
PRAME	23532	hgsc.bcm.edu	37	22	22892449	22892449	+	Missense_Mutation	SNP	T	T	C	rs41277507	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:22892449T>C	ENST00000398741.1	-	5	958	c.652A>G	c.(652-654)Atg>Gtg	p.M218V	PRAME_ENST00000539862.1_Missense_Mutation_p.M202V|PRAME_ENST00000485532.1_5'Flank|PRAME_ENST00000424204.2_Missense_Mutation_p.M202V|PRAME_ENST00000402697.1_Missense_Mutation_p.M218V|PRAME_ENST00000543184.1_Missense_Mutation_p.M218V|PRAME_ENST00000405655.3_Missense_Mutation_p.M218V|PRAME_ENST00000398743.2_Missense_Mutation_p.M218V	NM_206955.1	NP_996838.1	P78395	PRAME_HUMAN	preferentially expressed antigen in melanoma	218			M -> V (in dbSNP:rs41277507).		apoptotic process (GO:0006915)|cell differentiation (GO:0030154)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell differentiation (GO:0045596)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)|regulation of growth (GO:0040008)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|plasma membrane (GO:0005886)	retinoic acid receptor binding (GO:0042974)			autonomic_ganglia(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(17)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	36	all_hematologic(9;0.0135)|Acute lymphoblastic leukemia(84;0.17)	all_hematologic(6;1.74e-30)|Acute lymphoblastic leukemia(6;7.75e-22)|all_lung(157;4.03e-05)		READ - Rectum adenocarcinoma(21;0.0649)		TGCATGGGCATTGCAAAAATC	0.443													T|||	68	0.0135783	0.0068	0.0231	5008	,	,		20377	0.0		0.0388	False		,,,				2504	0.0041				p.M218V	Melanoma(73;1707 1838 15168 27201)	Atlas-SNP	.											.	PRAME	78	.	0			c.A652G						PASS	.	T	VAL/MET,VAL/MET,VAL/MET,VAL/MET,VAL/MET	46,4360		1,44,2158	119.0	117.0	118.0		652,652,652,652,652	-1.5	0.0	22	dbSNP_127	118	410,8190		8,394,3898	yes	missense,missense,missense,missense,missense	PRAME	NM_006115.3,NM_206953.1,NM_206954.1,NM_206955.1,NM_206956.1	21,21,21,21,21	9,438,6056	CC,CT,TT		4.7674,1.044,3.5061	benign,benign,benign,benign,benign	218/510,218/510,218/510,218/510,218/510	22892449	456,12550	2203	4300	6503	SO:0001583	missense	23532	exon5			TGGGCATTGCAAA	U65011	CCDS13801.1	22q11.22	2013-01-17			ENSG00000185686	ENSG00000185686		"""-"""	9336	protein-coding gene	gene with protein product	"""cancer/testis antigen 130"""	606021		MAPE		9047241, 10591208	Standard	XM_006725402		Approved	CT130	uc002zwj.3	P78395	OTTHUMG00000151172	ENST00000398741.1:c.652A>G	22.37:g.22892449T>C	ENSP00000381726:p.Met218Val	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	110	49	0.445455	NM_206954	B2R6Y7|O43481|Q8IXN8	Missense_Mutation	SNP	ENST00000398741.1	37	CCDS13801.1	38	0.0173992673992674	3	0.006097560975609756	9	0.024861878453038673	0	0.0	26	0.03430079155672823	.	0.218	-1.030879	0.02045	0.01044	0.047674	ENSG00000185686	ENST00000398743;ENST00000543184;ENST00000398741;ENST00000405655;ENST00000539862;ENST00000402697;ENST00000424204	T;T;T;T;T;T;T	0.00864	5.6;5.6;5.6;5.6;5.6;5.6;5.6	3.43	-1.54	0.08584	.	0.555420	0.18343	N	0.144137	T	0.00210	0.0006	L	0.43598	1.365	0.09310	N	1	B	0.18461	0.028	B	0.15484	0.013	T	0.45687	-0.9244	10	0.41790	T	0.15	.	7.6549	0.28369	0.0:0.529:0.0:0.471	rs41277507;rs61730837	218	P78395	PRAME_HUMAN	V	218;218;218;218;202;218;202	ENSP00000381728:M218V;ENSP00000445675:M218V;ENSP00000381726:M218V;ENSP00000384343:M218V;ENSP00000445097:M202V;ENSP00000385198:M218V;ENSP00000407342:M202V	ENSP00000381726:M218V	M	-	1	0	PRAME	21222449	0.013000	0.17824	0.012000	0.15200	0.253000	0.25986	-0.506000	0.06359	-0.381000	0.07882	0.459000	0.35465	ATG	T|0.971;C|0.029	0.029	strong		0.443	PRAME-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000321644.1	NM_206953	
ORAI1	84876	hgsc.bcm.edu	37	12	122079441	122079441	+	Silent	SNP	T	T	C	rs3825175	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:122079441T>C	ENST00000330079.7	+	2	997	c.804T>C	c.(802-804)acT>acC	p.T268T		NM_032790.3	NP_116179	Q96D31	CRCM1_HUMAN	ORAI calcium release-activated calcium modulator 1	266					blood coagulation (GO:0007596)|immune system process (GO:0002376)|positive regulation of calcium ion transport (GO:0051928)|regulation of calcium ion transport (GO:0051924)|store-operated calcium entry (GO:0002115)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|protein complex (GO:0043234)	identical protein binding (GO:0042802)|store-operated calcium channel activity (GO:0015279)			breast(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(3)|upper_aerodigestive_tract(1)	11	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)			OV - Ovarian serous cystadenocarcinoma(86;0.000415)|Epithelial(86;0.00148)		GCCATAAGACTGACCGACAGT	0.612													C|||	2783	0.555711	0.7269	0.4755	5008	,	,		19656	0.5823		0.3976	False		,,,				2504	0.5164				p.T268T		Atlas-SNP	.											.	ORAI1	66	.	0			c.T804C						PASS	.	C		2972,1284		1057,858,213	73.0	84.0	81.0		804	-2.2	1.0	12	dbSNP_107	81	3562,4922		746,2070,1426	no	coding-synonymous	ORAI1	NM_032790.3		1803,2928,1639	CC,CT,TT		41.9849,30.1692,48.7127		268/304	122079441	6534,6206	2128	4242	6370	SO:0001819	synonymous_variant	84876	exon2			TAAGACTGACCGA	AK027372		12q24.31	2014-09-17	2007-08-14	2007-08-14	ENSG00000182500	ENSG00000276045		"""ORAI calcium release-activated calcium modulators"""	25896	protein-coding gene	gene with protein product	"""calcium release-activated calcium modulator 1"""	610277	"""transmembrane protein 142A"""	TMEM142A		16582901	Standard	NM_032790		Approved	FLJ14466, CRACM1	uc021rff.1	Q96D31		ENST00000330079.7:c.804T>C	12.37:g.122079441T>C		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	131	131	1	NM_032790	Q3MHV3|Q6DHX2|Q96BP7|Q96K71	Silent	SNP	ENST00000330079.7	37	CCDS41851.1																																																																																			T|0.470;C|0.530	0.530	strong		0.612	ORAI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402151.1	NM_032790	
HLA-A	3105	hgsc.bcm.edu	37	6	29910602	29910602	+	Missense_Mutation	SNP	G	G	T	rs41552219	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:29910602G>T	ENST00000396634.1	+	4	483	c.142G>T	c.(142-144)Gcc>Tcc	p.A48S	HLA-A_ENST00000376802.2_Missense_Mutation_p.A48S|HLA-A_ENST00000376809.5_Missense_Mutation_p.A48S|HLA-A_ENST00000376806.5_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						scavenged	.						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	77	0	0		WXS	Illumina HiSeq	Phase_I	108	12	0.111111	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	
KIAA1024	23251	hgsc.bcm.edu	37	15	79755604	79755604	+	Missense_Mutation	SNP	A	A	G	rs2297773	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:79755604A>G	ENST00000305428.3	+	3	2569	c.2494A>G	c.(2494-2496)Att>Gtt	p.I832V		NM_015206.2	NP_056021.1	Q9UPX6	K1024_HUMAN	KIAA1024	832			I -> V (in dbSNP:rs2297773).			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						TTCTTGGACCATTGAGGAGTA	0.627													A|||	1277	0.254992	0.4962	0.1282	5008	,	,		19903	0.1478		0.2107	False		,,,				2504	0.1748				p.I832V		Atlas-SNP	.											.	KIAA1024	146	.	0			c.A2494G						PASS	.	A	VAL/ILE	1877,2515	541.1+/-375.7	410,1057,729	107.0	96.0	100.0		2494	-10.6	0.0	15	dbSNP_100	100	1699,6887	311.7+/-310.5	164,1371,2758	yes	missense	KIAA1024	NM_015206.2	29	574,2428,3487	GG,GA,AA		19.788,42.7368,27.5543	benign	832/917	79755604	3576,9402	2196	4293	6489	SO:0001583	missense	23251	exon3			TGGACCATTGAGG	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.2494A>G	15.37:g.79755604A>G	ENSP00000307461:p.Ile832Val	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	142	53	0.373239	NM_015206	A7MD43	Missense_Mutation	SNP	ENST00000305428.3	37	CCDS32306.1	546	0.25	238	0.483739837398374	63	0.17403314917127072	82	0.14335664335664336	163	0.21503957783641162	A	7.689	0.690574	0.15039	0.427368	0.19788	ENSG00000169330	ENST00000305428	T	0.40225	1.04	5.32	-10.6	0.00265	.	0.655502	0.15131	N	0.278850	T	0.00012	0.0000	L	0.28344	0.845	0.39727	P	0.028442999999999996	B	0.02656	0.0	B	0.06405	0.002	T	0.31420	-0.9944	8	.	.	.	.	9.3297	0.38014	0.2438:0.4982:0.258:0.0	rs2297773;rs60393750;rs2297773	832	Q9UPX6	K1024_HUMAN	V	832	ENSP00000307461:I832V	.	I	+	1	0	KIAA1024	77542659	1.000000	0.71417	0.001000	0.08648	0.849000	0.48306	1.624000	0.37018	-2.170000	0.00776	-0.313000	0.08912	ATT	A|0.733;G|0.267	0.267	strong		0.627	KIAA1024-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416718.1	NM_015206	
PNPLA7	375775	hgsc.bcm.edu	37	9	140373607	140373607	+	Silent	SNP	C	C	T	rs61747526	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:140373607C>T	ENST00000277531.4	-	23	2775	c.2589G>A	c.(2587-2589)gcG>gcA	p.A863A	PNPLA7_ENST00000371457.1_Silent_p.A469A|PNPLA7_ENST00000492278.1_5'UTR|PNPLA7_ENST00000406427.1_Silent_p.A888A	NM_152286.3	NP_689499.3	Q6ZV29	PLPL7_HUMAN	patatin-like phospholipase domain containing 7	863					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)		CCACGGTGCGCGCTGGCGCCG	0.687													G|||	65	0.0129792	0.0023	0.0159	5008	,	,		15767	0.0		0.0348	False		,,,				2504	0.0164				p.A888A		Atlas-SNP	.											.	PNPLA7	124	.	0			c.G2664A						PASS	.	G	,	25,4331		0,25,2153	14.0	17.0	16.0		2664,2589	2.9	0.5	9	dbSNP_129	16	316,8246		5,306,3970	no	coding-synonymous,coding-synonymous	PNPLA7	NM_001098537.1,NM_152286.3	,	5,331,6123	TT,TC,CC		3.6907,0.5739,2.6397	,	888/1343,863/1318	140373607	341,12577	2178	4281	6459	SO:0001819	synonymous_variant	375775	exon24			GGTGCGCGCTGGC	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.2589G>A	9.37:g.140373607C>T		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	74	49	0.662162	NM_001098537	B5MDD3|Q5T364|Q658X0|Q658Y3|Q6ZTS1|Q86YU8|Q8TAY5|Q96N75|Q9H7N5	Silent	SNP	ENST00000277531.4	37	CCDS7045.1																																																																																			C|0.981;T|0.019	0.019	strong		0.687	PNPLA7-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254787.1	NM_152286	
VARS2	57176	hgsc.bcm.edu	37	6	30893941	30893941	+	Missense_Mutation	SNP	G	G	A	rs4678	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:30893941G>A	ENST00000321897.5	+	29	3778	c.3146G>A	c.(3145-3147)cGg>cAg	p.R1049Q	VARS2_ENST00000542001.1_Missense_Mutation_p.R909Q|VARS2_ENST00000416670.2_Missense_Mutation_p.R1049Q|VARS2_ENST00000541562.1_Missense_Mutation_p.R1079Q|VARS2_ENST00000476162.1_3'UTR			Q5ST30	SYVM_HUMAN	valyl-tRNA synthetase 2, mitochondrial	1049			R -> Q (in dbSNP:rs4678). {ECO:0000269|PubMed:11572484, ECO:0000269|PubMed:14574404, ECO:0000269|PubMed:15489334}.		gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)|valyl-tRNA aminoacylation (GO:0006438)	mitochondrion (GO:0005739)	aminoacyl-tRNA editing activity (GO:0002161)|ATP binding (GO:0005524)|valine-tRNA ligase activity (GO:0004832)			central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(9)|lung(15)|ovary(3)|prostate(3)|skin(4)|urinary_tract(1)	46						TCTCACCTCCGGCAGCTGATG	0.557													G|||	453	0.0904553	0.0968	0.0663	5008	,	,		19166	0.0258		0.1551	False		,,,				2504	0.0992				p.R1079Q		Atlas-SNP	.											.	VARS2	60	.	0			c.G3236A						PASS	.	G	GLN/ARG,GLN/ARG,GLN/ARG	367,2653		15,337,1158	53.0	57.0	56.0		2726,3236,3146	-8.5	0.1	6	dbSNP_52	56	1047,4367		94,859,1754	yes	missense,missense,missense	VARS2	NM_001167733.1,NM_001167734.1,NM_020442.4	43,43,43	109,1196,2912	AA,AG,GG		19.3388,12.1523,16.7655	benign,benign,benign	909/924,1079/1094,1049/1064	30893941	1414,7020	1510	2707	4217	SO:0001583	missense	57176	exon30			ACCTCCGGCAGCT	AB067472	CCDS34387.1, CCDS54980.1	6p21.33	2012-10-26	2012-10-26	2007-02-23	ENSG00000137411	ENSG00000137411	6.1.1.9	"""Aminoacyl tRNA synthetases / Class I"""	21642	protein-coding gene	gene with protein product	"""valine tRNA ligase 2, mitochondrial"""	612802	"""valyl-tRNA synthetase 2-like"", ""valyl-tRNA synthetase like"", ""valyl-tRNA synthetase 2, mitochondrial (putative)"""	VARS2L, VARSL		1898367, 11572484, 18400783	Standard	NM_001167734		Approved	DKFZP434L1435, KIAA1885, G7a	uc011dmz.2	Q5ST30	OTTHUMG00000031263	ENST00000321897.5:c.3146G>A	6.37:g.30893941G>A	ENSP00000316092:p.Arg1049Gln	Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	209	108	0.516746	NM_001167734	A2ABL7|B4DET4|B4E3P5|F5GXJ0|F5H323|Q2M2A0|Q59FI1|Q5SQ96|Q5SS98|Q6DKJ5|Q6ZV24|Q96GN2|Q96H77|Q96Q02|Q9H6R2|Q9UFH7	Missense_Mutation	SNP	ENST00000321897.5	37	CCDS34387.1	246	0.11263736263736264	71	0.1443089430894309	27	0.07458563535911603	20	0.03496503496503497	128	0.16886543535620052	G	4.681	0.126566	0.08931	0.121523	0.193388	ENSG00000137411	ENST00000321897;ENST00000416670;ENST00000542001;ENST00000541562	T;T;T;T	0.31247	1.5;1.5;1.5;1.5	5.8	-8.54	0.00912	.	1.356270	0.04712	N	0.417762	T	0.02929	0.0087	N	0.11845	0.185	0.80722	P	0.0	B;B;B;B	0.22983	0.078;0.0;0.0;0.0	B;B;B;B	0.16722	0.016;0.0;0.001;0.0	T	0.14699	-1.0463	9	0.02654	T	1	-4.8705	8.5559	0.33480	0.3693:0.0:0.5217:0.109	rs4678;rs1043490;rs3173376;rs6929532;rs16898111;rs17189642;rs52796175;rs56648004;rs60218550;rs4678	487;1047;1079;1049	Q5ST30-2;B7ZL25;F5GXJ0;Q5ST30	.;.;.;SYVM_HUMAN	Q	1049;1049;909;1079	ENSP00000316092:R1049Q;ENSP00000394802:R1049Q;ENSP00000438200:R909Q;ENSP00000441000:R1079Q	ENSP00000316092:R1049Q	R	+	2	0	VARS2	31001920	0.057000	0.20700	0.058000	0.19502	0.721000	0.41392	-1.020000	0.03618	-1.624000	0.01556	-0.150000	0.13652	CGG	G|0.856;A|0.144	0.144	strong		0.557	VARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076566.2	NM_020442	
TDRD9	122402	hgsc.bcm.edu	37	14	104394850	104394850	+	Silent	SNP	C	C	T	rs9324066	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:104394850C>T	ENST00000409874.4	+	1	52	c.4C>T	c.(4-6)Ctg>Ttg	p.L2L	C14orf2_ENST00000554880.1_5'Flank|TDRD9_ENST00000339063.5_Silent_p.L2L	NM_153046.2	NP_694591.2	Q8NDG6	TDRD9_HUMAN	tudor domain containing 9	2					cell differentiation (GO:0030154)|DNA methylation involved in gamete generation (GO:0043046)|fertilization (GO:0009566)|gene silencing by RNA (GO:0031047)|male meiosis (GO:0007140)|multicellular organismal development (GO:0007275)|piRNA metabolic process (GO:0034587)|spermatogenesis (GO:0007283)	nucleus (GO:0005634)|piP-body (GO:0071547)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(10)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)	33		all_cancers(154;0.109)|Melanoma(154;0.0525)|all_epithelial(191;0.0768)				CTTGAGGATGCTGCGGAAGCT	0.701													C|||	2308	0.460863	0.5946	0.5216	5008	,	,		5602	0.3869		0.4016	False		,,,				2504	0.3742				p.L2L		Atlas-SNP	.											TDRD9_ENST00000409874,colon,carcinoma,0,1	TDRD9	175	1	0			c.C4T						PASS	.	C		777,607		217,343,132	21.0	25.0	24.0		4	3.6	1.0	14	dbSNP_119	24	1212,1970		225,762,604	yes	coding-synonymous	TDRD9	NM_153046.2		442,1105,736	TT,TC,CC		38.0893,43.8584,43.5611		2/1383	104394850	1989,2577	692	1591	2283	SO:0001819	synonymous_variant	122402	exon1			AGGATGCTGCGGA	AK093483	CCDS9987.2	14q32.33	2013-01-23	2004-04-01	2004-04-02	ENSG00000156414	ENSG00000156414		"""Tudor domain containing"""	20122	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 75"""	C14orf75			Standard	NM_153046		Approved	DKFZp434N0820, FLJ36164, NET54	uc001yom.4	Q8NDG6	OTTHUMG00000152876	ENST00000409874.4:c.4C>T	14.37:g.104394850C>T		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	60	33	0.55	NM_153046	A1A4S7|Q6ZU54|Q8N7T3|Q8N827|Q8N9V5|Q96AS9	Silent	SNP	ENST00000409874.4	37	CCDS9987.2																																																																																			A|0.000;C|0.519;G|0.000;T|0.480	0.480	strong		0.701	TDRD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328325.3	NM_153046	
UTP20	27340	hgsc.bcm.edu	37	12	101776996	101776996	+	Missense_Mutation	SNP	G	G	C	rs1061436	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	55	0	0		WXS	Illumina HiSeq	Phase_I	55	27	0.490909	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	
VPS52	6293	hgsc.bcm.edu	37	6	33236826	33236826	+	Silent	SNP	A	A	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:33236826A>G	ENST00000445902.2	-	6	731	c.513T>C	c.(511-513)ctT>ctC	p.L171L	RPS18_ENST00000439602.2_5'Flank|VPS52_ENST00000436044.2_Silent_p.L46L|VPS52_ENST00000478934.1_5'UTR|VPS52_ENST00000482399.1_3'UTR	NM_022553.4	NP_072047.4	Q8N1B4	VPS52_HUMAN	vacuolar protein sorting 52 homolog (S. cerevisiae)	171					ectodermal cell differentiation (GO:0010668)|embryonic ectodermal digestive tract development (GO:0048611)|protein transport (GO:0015031)	endosome (GO:0005768)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)				endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(1)|lung(8)|ovary(4)|skin(1)|upper_aerodigestive_tract(1)	28						GACCATCAACAAGCTCCCCAA	0.547																																					p.L171L		Atlas-SNP	.											.	VPS52	56	.	0			c.T513C						PASS	.						204.0	179.0	188.0					6																	33236826		1511	2709	4220	SO:0001819	synonymous_variant	6293	exon6			ATCAACAAGCTCC	AJ223319	CCDS4770.2	6p21.3	2010-02-17	2006-12-19	2003-09-05	ENSG00000223501	ENSG00000223501			10518	protein-coding gene	gene with protein product		603443	"""SAC2 suppressor of actin mutations 2-like (yeast)"", ""vacuolar protein sorting 52 (yeast)"""	SACM2L		9790748	Standard	NM_022553		Approved	ARE1	uc003odm.1	Q8N1B4	OTTHUMG00000031276	ENST00000445902.2:c.513T>C	6.37:g.33236826A>G		Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	156	64	0.410256	NM_022553	A2BF38|B0UZZ4|B4DNI9|Q53GR4|Q5JPA0|Q5SQW1|Q8IUN6|Q9NPT5	Silent	SNP	ENST00000445902.2	37	CCDS4770.2																																																																																			.	.	none		0.547	VPS52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076598.2	NM_022553	
CCDC87	55231	hgsc.bcm.edu	37	11	66358126	66358126	+	Silent	SNP	C	C	T	rs486584	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:66358126C>T	ENST00000333861.3	-	1	2428	c.2361G>A	c.(2359-2361)ctG>ctA	p.L787L	CCS_ENST00000310190.4_5'Flank|CCS_ENST00000533244.1_5'Flank	NM_018219.2	NP_060689.2	Q9NVE4	CCD87_HUMAN	coiled-coil domain containing 87	787					cytokinesis (GO:0000910)|microtubule cytoskeleton organization (GO:0000226)					central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(12)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	28						CTATCTCCTCCAGGAGGGAAA	0.507													C|||	2131	0.425519	0.1089	0.6268	5008	,	,		17655	0.4484		0.5129	False		,,,				2504	0.5971				p.L787L		Atlas-SNP	.											.	CCDC87	83	.	0			c.G2361A						PASS	.	C		843,3557	331.0+/-301.8	95,653,1452	134.0	141.0	139.0		2361	-1.6	0.5	11	dbSNP_83	139	4541,4049	596.0+/-393.5	1169,2203,923	no	coding-synonymous	CCDC87	NM_018219.2		1264,2856,2375	TT,TC,CC		47.1362,19.1591,41.4473		787/850	66358126	5384,7606	2200	4295	6495	SO:0001819	synonymous_variant	55231	exon1			CTCCTCCAGGAGG	BC034469	CCDS8145.1	11q13.2	2006-03-15			ENSG00000182791	ENSG00000182791			25579	protein-coding gene	gene with protein product						12477932	Standard	NM_018219		Approved	FLJ10786	uc001oiq.4	Q9NVE4	OTTHUMG00000167237	ENST00000333861.3:c.2361G>A	11.37:g.66358126C>T		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	71	15	0.211268	NM_018219	Q8NE76	Silent	SNP	ENST00000333861.3	37	CCDS8145.1																																																																																			C|0.597;T|0.402	0.402	strong		0.507	CCDC87-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393825.1	NM_018219	
FUT10	84750	hgsc.bcm.edu	37	8	33246538	33246538	+	Silent	SNP	A	A	G	rs16880849	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:33246538A>G	ENST00000327671.5	-	4	1786	c.1155T>C	c.(1153-1155)gaT>gaC	p.D385D	FUT10_ENST00000524021.1_Silent_p.D357D|FUT10_ENST00000518076.1_5'UTR|FUT10_ENST00000335589.3_Silent_p.D323D|FUT10_ENST00000518672.1_Silent_p.D357D	NM_032664.3	NP_116053.3	Q6P4F1	FUT10_HUMAN	fucosyltransferase 10 (alpha (1,3) fucosyltransferase)	385					embryo development (GO:0009790)|fertilization (GO:0009566)|fucosylation (GO:0036065)|hemopoiesis (GO:0030097)|L-fucose catabolic process (GO:0042355)|nervous system development (GO:0007399)|protein folding (GO:0006457)|protein glycosylation (GO:0006486)|protein targeting (GO:0006605)|wound healing (GO:0042060)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	alpha-(1->3)-fucosyltransferase activity (GO:0046920)	p.D385D(1)		cervix(1)|endometrium(1)|large_intestine(7)|liver(1)|lung(9)|ovary(1)|pancreas(1)|prostate(3)|stomach(3)|upper_aerodigestive_tract(2)	29				KIRC - Kidney renal clear cell carcinoma(67;0.129)|Kidney(114;0.154)		ACTCAAATGCATCGATGTAAT	0.498													A|||	1496	0.298722	0.1808	0.17	5008	,	,		22022	0.4692		0.1938	False		,,,				2504	0.4816				p.D385D		Atlas-SNP	.											FUT10,NS,carcinoma,0,1	FUT10	62	1	1	Substitution - coding silent(1)	stomach(1)	c.T1155C						PASS	.	A		916,3490	349.5+/-310.4	76,764,1363	246.0	207.0	220.0		1155	-0.1	0.9	8	dbSNP_123	220	1748,6852	317.0+/-313.0	177,1394,2729	no	coding-synonymous	FUT10	NM_032664.3		253,2158,4092	GG,GA,AA		20.3256,20.7898,20.4829		385/480	33246538	2664,10342	2203	4300	6503	SO:0001819	synonymous_variant	84750	exon4			AAATGCATCGATG	AJ512465	CCDS6088.1	8p12	2013-02-26			ENSG00000172728	ENSG00000172728		"""Fucosyltransferases"""	19234	protein-coding gene	gene with protein product							Standard	NM_032664		Approved		uc003xje.3	Q6P4F1	OTTHUMG00000163954	ENST00000327671.5:c.1155T>C	8.37:g.33246538A>G		Somatic	467	0	0		WXS	Illumina HiSeq	Phase_I	358	355	0.99162	NM_032664	A8KAC8|Q70GG3|Q8IVI6|Q8IVI7|Q8IVJ3|Q8TE43|Q9BSR3	Silent	SNP	ENST00000327671.5	37	CCDS6088.1																																																																																			A|0.769;G|0.231	0.231	strong		0.498	FUT10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376540.1	NM_032664	
CCDC6	8030	hgsc.bcm.edu	37	10	61552763	61552763	+	Missense_Mutation	SNP	G	G	A	rs61740504	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:61552763G>A	ENST00000263102.6	-	9	1568	c.1337C>T	c.(1336-1338)cCg>cTg	p.P446L		NM_005436.4	NP_005427.2	Q16204	CCDC6_HUMAN	coiled-coil domain containing 6	446	Poly-Pro.					cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	structural constituent of cytoskeleton (GO:0005200)		CCDC6/RET(4)	breast(3)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(6)|ovary(3)|stomach(1)	18				Kidney(211;0.0597)		CATGGGTGGCGGAGGTGGAGG	0.622			T	RET	NSCLC								G|||	17	0.00339457	0.0015	0.0029	5008	,	,		16035	0.0		0.0129	False		,,,				2504	0.0				p.P446L		Atlas-SNP	.		Dom	yes		10	10q21	8030	coiled-coil domain containing 6		E	.	CCDC6	44	.	0			c.C1337T						PASS	.	G	LEU/PRO	15,4391	24.3+/-50.5	0,15,2188	149.0	140.0	143.0		1337	5.6	1.0	10	dbSNP_129	143	97,8503	54.0+/-114.7	2,93,4205	yes	missense	CCDC6	NM_005436.4	98	2,108,6393	AA,AG,GG		1.1279,0.3404,0.8611	benign	446/475	61552763	112,12894	2203	4300	6503	SO:0001583	missense	8030	exon9			GGTGGCGGAGGTG	S72869	CCDS7257.1	10q21.2	2006-11-09	2004-01-20		ENSG00000108091	ENSG00000108091			18782	protein-coding gene	gene with protein product	"""DNA segment, single copy, probe pH4 (transforming sequence, thyroid-1"""	601985	"""DNA segment on chromosome 10 (unique) 170"""	TST1, D10S170		8058316, 6745938	Standard	NM_005436		Approved	PTC, TPC, H4	uc001jks.4	Q16204	OTTHUMG00000018284	ENST00000263102.6:c.1337C>T	10.37:g.61552763G>A	ENSP00000263102:p.Pro446Leu	Somatic	237	0	0		WXS	Illumina HiSeq	Phase_I	195	110	0.564103	NM_005436	Q15250|Q6GSG7	Missense_Mutation	SNP	ENST00000263102.6	37	CCDS7257.1	12	0.005494505494505495	0	0.0	2	0.0055248618784530384	0	0.0	10	0.013192612137203167	G	16.55	3.154856	0.57259	0.003404	0.011279	ENSG00000108091	ENST00000263102	T	0.46819	0.86	5.6	5.6	0.85130	.	0.097389	0.64402	D	0.000001	T	0.36413	0.0966	L	0.47716	1.5	0.80722	D	1	B	0.15719	0.014	B	0.08055	0.003	T	0.18304	-1.0341	10	0.23891	T	0.37	-17.8112	19.9854	0.97342	0.0:0.0:1.0:0.0	.	446	Q16204	CCDC6_HUMAN	L	446	ENSP00000263102:P446L	ENSP00000263102:P446L	P	-	2	0	CCDC6	61222769	1.000000	0.71417	0.997000	0.53966	0.936000	0.57629	7.512000	0.81728	2.786000	0.95864	0.563000	0.77884	CCG	G|0.992;A|0.008	0.008	strong		0.622	CCDC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048176.2	NM_005436	
USP42	84132	hgsc.bcm.edu	37	7	6194274	6194274	+	Missense_Mutation	SNP	T	T	C	rs6463529	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:6194274T>C	ENST00000306177.5	+	15	3247	c.3089T>C	c.(3088-3090)cTg>cCg	p.L1030P		NM_032172.2	NP_115548.1	Q9H9J4	UBP42_HUMAN	ubiquitin specific peptidase 42	1030	Arg-rich.		L -> P (in dbSNP:rs6463529).		cell differentiation (GO:0030154)|protein deubiquitination (GO:0016579)|spermatogenesis (GO:0007283)|ubiquitin-dependent protein catabolic process (GO:0006511)		ubiquitin-specific protease activity (GO:0004843)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(2)|lung(14)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	35		Ovarian(82;0.0423)		UCEC - Uterine corpus endometrioid carcinoma (126;0.108)|OV - Ovarian serous cystadenocarcinoma(56;5.77e-14)		GGGGTGGAGCTGGACTGGGTC	0.701													C|||	2360	0.471246	0.6747	0.2767	5008	,	,		7893	0.7282		0.171	False		,,,				2504	0.3783				p.L1030P		Atlas-SNP	.											.	USP42	138	.	0			c.T3089C						PASS	.	C	PRO/LEU	2212,1862		592,1028,417	9.0	11.0	10.0		3089	4.5	0.6	7	dbSNP_116	10	1238,7100		113,1012,3044	yes	missense	USP42	NM_032172.2	98	705,2040,3461	CC,CT,TT		14.8477,45.7045,27.7957	benign	1030/1317	6194274	3450,8962	2037	4169	6206	SO:0001583	missense	84132	exon15			TGGAGCTGGACTG	AK022759	CCDS47535.1	7p22.2	2005-08-08	2005-08-08		ENSG00000106346	ENSG00000106346		"""Ubiquitin-specific peptidases"""	20068	protein-coding gene	gene with protein product			"""ubiquitin specific protease 42"""			12838346	Standard	NM_032172		Approved	FLJ12697	uc011jwp.2	Q9H9J4	OTTHUMG00000151888	ENST00000306177.5:c.3089T>C	7.37:g.6194274T>C	ENSP00000301962:p.Leu1030Pro	Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	26	24	0.923077	NM_032172	A2RUE3|B5MDA5|Q0VIN8|Q3C166|Q6P9B4	Missense_Mutation	SNP	ENST00000306177.5	37	CCDS47535.1	958	0.43864468864468864	302	0.6138211382113821	87	0.24033149171270718	439	0.7674825174825175	130	0.17150395778364116	C	4.103	0.017211	0.07959	0.542955	0.148477	ENSG00000106346	ENST00000306177;ENST00000426246	T;T	0.41065	1.01;1.01	5.66	4.51	0.55191	.	0.264966	0.33327	N	0.005023	T	0.00012	0.0000	N	0.08118	0	0.58432	P	6.999999999979245E-6	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.27400	-1.0075	9	0.26408	T	0.33	.	8.4494	0.32862	0.5191:0.3648:0.0:0.1161	rs6463529;rs9640020;rs9791885;rs10371676;rs6463529	926;1030;1030	A4D2N7;Q9H9J4-2;Q9H9J4	.;.;UBP42_HUMAN	P	1030;876	ENSP00000301962:L1030P;ENSP00000408217:L876P	ENSP00000301962:L1030P	L	+	2	0	USP42	6160799	.	.	0.604000	0.28916	0.007000	0.05969	.	.	0.429000	0.26202	-1.068000	0.02270	CTG	T|0.533;C|0.467	0.467	strong		0.701	USP42-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324262.3	XM_166526	
TH	7054	hgsc.bcm.edu	37	11	2191006	2191006	+	Silent	SNP	C	C	T	rs34510659	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:2191006C>T	ENST00000381178.1	-	3	297	c.279G>A	c.(277-279)tcG>tcA	p.S93S	TH_ENST00000352909.3_Silent_p.S62S|TH_ENST00000333684.5_Silent_p.S66S|TH_ENST00000381175.1_Silent_p.S89S	NM_199292.2	NP_954986.2	P07101	TY3H_HUMAN	tyrosine hydroxylase	93					anatomical structure morphogenesis (GO:0009653)|catecholamine biosynthetic process (GO:0042423)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to drug (GO:0035690)|cellular response to glucose stimulus (GO:0071333)|cellular response to growth factor stimulus (GO:0071363)|cellular response to manganese ion (GO:0071287)|cellular response to nicotine (GO:0071316)|cerebral cortex development (GO:0021987)|circadian sleep/wake cycle (GO:0042745)|dopamine biosynthetic process (GO:0042416)|dopamine biosynthetic process from tyrosine (GO:0006585)|eating behavior (GO:0042755)|embryonic camera-type eye morphogenesis (GO:0048596)|epinephrine biosynthetic process (GO:0042418)|eye photoreceptor cell development (GO:0042462)|fatty acid metabolic process (GO:0006631)|glycoside metabolic process (GO:0016137)|heart development (GO:0007507)|heart morphogenesis (GO:0003007)|isoquinoline alkaloid metabolic process (GO:0033076)|learning (GO:0007612)|locomotory behavior (GO:0007626)|mating behavior (GO:0007617)|memory (GO:0007613)|multicellular organismal aging (GO:0010259)|neurotransmitter biosynthetic process (GO:0042136)|norepinephrine biosynthetic process (GO:0042421)|organ morphogenesis (GO:0009887)|phthalate metabolic process (GO:0018963)|phytoalexin metabolic process (GO:0052314)|pigmentation (GO:0043473)|regulation of heart contraction (GO:0008016)|response to activity (GO:0014823)|response to amphetamine (GO:0001975)|response to corticosterone (GO:0051412)|response to electrical stimulus (GO:0051602)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to ether (GO:0045472)|response to herbicide (GO:0009635)|response to hypoxia (GO:0001666)|response to light stimulus (GO:0009416)|response to lipopolysaccharide (GO:0032496)|response to nutrient levels (GO:0031667)|response to peptide hormone (GO:0043434)|response to pyrethroid (GO:0046684)|response to salt stress (GO:0009651)|response to water deprivation (GO:0009414)|response to zinc ion (GO:0010043)|sensory perception of sound (GO:0007605)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|sphingolipid metabolic process (GO:0006665)|synaptic transmission, dopaminergic (GO:0001963)|synaptic vesicle amine transport (GO:0015842)|terpene metabolic process (GO:0042214)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendrite (GO:0030425)|melanosome membrane (GO:0033162)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|nucleus (GO:0005634)|perikaryon (GO:0043204)|smooth endoplasmic reticulum (GO:0005790)|synaptic vesicle (GO:0008021)|terminal bouton (GO:0043195)	amino acid binding (GO:0016597)|dopamine binding (GO:0035240)|enzyme binding (GO:0019899)|ferric iron binding (GO:0008199)|ferrous iron binding (GO:0008198)|oxygen binding (GO:0019825)|tetrahydrobiopterin binding (GO:0034617)|tyrosine 3-monooxygenase activity (GO:0004511)			NS(1)|endometrium(1)|large_intestine(1)|lung(7)|skin(1)	11		all_epithelial(84;1.46e-23)|Lung NSC(207;4.44e-11)|all_lung(207;1.11e-09)|Ovarian(85;1.78e-06)|Breast(177;1.78e-05)|Medulloblastoma(188;0.0208)|all_neural(188;0.0416)	Colorectal(5;0.00245)|COAD - Colon adenocarcinoma(6;0.0239)	BRCA - Breast invasive adenocarcinoma(625;8.45e-09)|Lung(200;0.000152)|LUSC - Lung squamous cell carcinoma(625;0.00154)	L-Phenylalanine(DB00120)|L-Tyrosine(DB00135)|Metyrosine(DB00765)|Tetrahydrobiopterin(DB00360)	CCCCGGGCTCCGAGGGGACTG	0.711													C|||	122	0.024361	0.0893	0.0058	5008	,	,		13970	0.0		0.0	False		,,,				2504	0.0				p.S93S		Atlas-SNP	.											.	TH	43	.	0			c.G279A						PASS	.	C	,,	343,4043		10,323,1860	17.0	20.0	19.0		186,279,267	-1.0	0.0	11	dbSNP_126	19	6,8586		0,6,4290	no	coding-synonymous,coding-synonymous,coding-synonymous	TH	NM_000360.3,NM_199292.2,NM_199293.2	,,	10,329,6150	TT,TC,CC		0.0698,7.8203,2.6892	,,	62/498,93/529,89/525	2191006	349,12629	2193	4296	6489	SO:0001819	synonymous_variant	7054	exon3			GGGCTCCGAGGGG	X05290	CCDS7730.1, CCDS7731.1, CCDS31338.1	11p15.5	2013-06-03			ENSG00000180176	ENSG00000180176	1.14.16.2		11782	protein-coding gene	gene with protein product	"""tyrosine 3-monooxygenase"""	191290					Standard	NM_199292		Approved	DYT5b	uc001lvq.3	P07101	OTTHUMG00000009559	ENST00000381178.1:c.279G>A	11.37:g.2191006C>T		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	107	90	0.841121	NM_199292	B7ZL70|B7ZL73|Q0PWM2|Q0PWM3|Q15585|Q15588|Q15589|Q2M3B4	Silent	SNP	ENST00000381178.1	37	CCDS7731.1																																																																																			C|0.971;T|0.029	0.029	strong		0.711	TH-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000026597.1	NM_000360	
TMEM200A	114801	hgsc.bcm.edu	37	6	130761804	130761804	+	Silent	SNP	C	C	T	rs12200105	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:130761804C>T	ENST00000296978.3	+	3	1108	c.237C>T	c.(235-237)gcC>gcT	p.A79A	TMEM200A_ENST00000392429.1_Silent_p.A79A|TMEM200A_ENST00000545622.1_Silent_p.A79A	NM_001258276.1|NM_001258277.1|NM_001258278.1	NP_001245205.1|NP_001245206.1|NP_001245207.1	Q86VY9	T200A_HUMAN	transmembrane protein 200A	79						integral component of membrane (GO:0016021)				NS(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(30)|ovary(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	52				GBM - Glioblastoma multiforme(226;0.0139)|OV - Ovarian serous cystadenocarcinoma(155;0.12)		TTGCTATGGCCGTTCTTGGAT	0.418													C|||	1312	0.261981	0.5408	0.2248	5008	,	,		19198	0.1339		0.172	False		,,,				2504	0.136				p.A79A		Atlas-SNP	.											.	TMEM200A	108	.	0			c.C237T						PASS	.	C		2008,2398	562.1+/-380.9	465,1078,660	99.0	100.0	100.0		237	-9.9	0.9	6	dbSNP_120	100	1382,7218	268.3+/-287.8	119,1144,3037	no	coding-synonymous	TMEM200A	NM_052913.2		584,2222,3697	TT,TC,CC		16.0698,45.5742,26.0649		79/492	130761804	3390,9616	2203	4300	6503	SO:0001819	synonymous_variant	114801	exon3			TATGGCCGTTCTT	AB067500	CCDS5140.1	6q23.1	2009-09-04	2007-12-18	2007-12-18	ENSG00000164484	ENSG00000164484			21075	protein-coding gene	gene with protein product			"""KIAA1913"""	KIAA1913		15722956	Standard	NM_001258276		Approved	TTMC	uc010kfh.4	Q86VY9	OTTHUMG00000015557	ENST00000296978.3:c.237C>T	6.37:g.130761804C>T		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	82	34	0.414634	NM_001258277	Q96PX5	Silent	SNP	ENST00000296978.3	37	CCDS5140.1																																																																																			C|0.743;T|0.257	0.257	strong		0.418	TMEM200A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042201.1	NM_052913	
PIGG	54872	hgsc.bcm.edu	37	4	517461	517461	+	Missense_Mutation	SNP	T	T	C	rs7666425	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:517461T>C	ENST00000453061.2	+	9	1934	c.1828T>C	c.(1828-1830)Tgt>Cgt	p.C610R	PIGG_ENST00000383028.4_Missense_Mutation_p.C477R|PIGG_ENST00000296306.7_3'UTR|PIGG_ENST00000504346.1_Missense_Mutation_p.C521R|PIGG_ENST00000310340.5_Missense_Mutation_p.C602R	NM_001127178.1	NP_001120650.1	Q5H8A4	PIGG_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class G	610			C -> R (in dbSNP:rs7666425). {ECO:0000269|PubMed:15489334}.		C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|GPI anchor biosynthetic process (GO:0006506)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	CP2 mannose-ethanolamine phosphotransferase activity (GO:0051267)|phosphotransferase activity, for other substituted phosphate groups (GO:0016780)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(5)|lung(16)|ovary(3)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	39						GTGTGGCCTCTGTGTGGAACA	0.587													t|||	1123	0.224241	0.3956	0.0994	5008	,	,		19535	0.2202		0.1312	False		,,,				2504	0.181				p.C610R		Atlas-SNP	.											.	PIGG	86	.	0			c.T1828C						PASS	.	T	ARG/CYS,ARG/CYS	1505,2901	478.3+/-358.2	271,963,969	95.0	93.0	93.0		1828,1804	1.6	0.0	4	dbSNP_116	93	1051,7549	222.3+/-259.4	69,913,3318	yes	missense,missense	PIGG	NM_001127178.1,NM_017733.3	180,180	340,1876,4287	CC,CT,TT		12.2209,34.158,19.6525	benign,benign	610/984,602/976	517461	2556,10450	2203	4300	6503	SO:0001583	missense	54872	exon9			GGCCTCTGTGTGG		CCDS3336.1, CCDS46992.1, CCDS75080.1, CCDS75081.1, CCDS75082.1, CCDS75083.1	4p16.3	2013-02-26	2006-06-28		ENSG00000174227	ENSG00000174227		"""Phosphatidylinositol glycan anchor biosynthesis"""	25985	protein-coding gene	gene with protein product			"""phosphatidylinositol glycan, class G"""			15632136	Standard	XM_005272287		Approved	FLJ20265, GPI7, LAS21	uc003gak.4	Q5H8A4	OTTHUMG00000112457	ENST00000453061.2:c.1828T>C	4.37:g.517461T>C	ENSP00000415203:p.Cys610Arg	Somatic	191	0	0		WXS	Illumina HiSeq	Phase_I	130	73	0.561538	NM_001127178	B4DKC7|Q2TAK5|Q6UX31|Q7L5Y4|Q8N866|Q8NCC9|Q96SY9|Q9BVT7|Q9NXG5	Missense_Mutation	SNP	ENST00000453061.2	37	CCDS46992.1	482	0.2206959706959707	205	0.4166666666666667	39	0.10773480662983426	139	0.243006993006993	99	0.13060686015831136	t	2.997	-0.206917	0.06180	0.34158	0.122209	ENSG00000174227	ENST00000310340;ENST00000453061;ENST00000504346;ENST00000383028	T;T;T;T	0.08546	3.4;3.4;3.08;3.08	5.45	1.63	0.23807	.	3.818050	0.00769	N	0.001181	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	0.01281	0.0;0.0;0.0	T	0.47249	-0.9132	9	0.15499	T	0.54	.	5.5022	0.16834	0.0:0.5443:0.1359:0.3197	rs7666425;rs61173124;rs7666425	477;610;602	Q5H8A4-3;Q5H8A4;Q5H8A4-2	.;PIGG_HUMAN;.	R	602;610;521;477	ENSP00000311750:C602R;ENSP00000415203:C610R;ENSP00000424800:C521R;ENSP00000372494:C477R	ENSP00000311750:C602R	C	+	1	0	PIGG	507461	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.290000	0.18975	0.371000	0.24564	-0.140000	0.14226	TGT	T|0.785;C|0.215	0.215	strong		0.587	PIGG-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000357494.1	NM_017733	
CIITA	4261	hgsc.bcm.edu	37	16	11000848	11000848	+	Missense_Mutation	SNP	G	G	C	rs4774	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:11000848G>C	ENST00000324288.8	+	11	1632	c.1499G>C	c.(1498-1500)gGc>gCc	p.G500A	CIITA_ENST00000537380.1_Intron|CIITA_ENST00000381835.5_Intron	NM_000246.3	NP_000237	P33076	C2TA_HUMAN	class II, major histocompatibility complex, transactivator	500	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.		G -> A (in dbSNP:rs4774). {ECO:0000269|PubMed:12859996, ECO:0000269|PubMed:7749984, ECO:0000269|PubMed:8402893}.		aging (GO:0007568)|cellular response to electrical stimulus (GO:0071257)|cellular response to exogenous dsRNA (GO:0071360)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|inflammatory response (GO:0006954)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of collagen biosynthetic process (GO:0032966)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of MHC class I biosynthetic process (GO:0045345)|positive regulation of MHC class II biosynthetic process (GO:0045348)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|response to antibiotic (GO:0046677)|response to interferon-gamma (GO:0034341)|transcription, DNA-templated (GO:0006351)	cell surface (GO:0009986)|nucleoplasm (GO:0005654)|PML body (GO:0016605)	activating transcription factor binding (GO:0033613)|ATP binding (GO:0005524)|GTP binding (GO:0005525)|kinase activity (GO:0016301)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)|transferase activity, transferring acyl groups (GO:0016746)			central_nervous_system(1)|large_intestine(7)|ovary(1)|skin(1)|stomach(2)	12						ATCCTAGACGGCTTCGAGGAG	0.647			T	"""FLJ27352, CD274, CD273, RALGDS, RUNDC2A, C16orf75, BCL6"""	"""PMBL, Hodgkin Lymphona, """								C|||	1297	0.258986	0.2663	0.428	5008	,	,		17451	0.1329		0.2724	False		,,,				2504	0.2454				p.G500A		Atlas-SNP	.		Dom	yes		16	16p13	4261	"""class II, major histocompatibility complex, transactivator"""		L	CIITA_ENST00000324288,NS,carcinoma,0,1	CIITA	92	1	0			c.G1499C						PASS	.	C	ALA/GLY	1130,3264		148,834,1215	66.0	70.0	69.0		1499	-0.8	0.0	16	dbSNP_52	69	2514,6086		389,1736,2175	yes	missense	CIITA	NM_000246.3	60	537,2570,3390	CC,CG,GG		29.2326,25.7169,28.0437	benign	500/1131	11000848	3644,9350	2197	4300	6497	SO:0001583	missense	4261	exon11			TAGACGGCTTCGA	U18259	CCDS10544.1, CCDS66943.1, CCDS73826.1	16p13	2014-09-17	2005-08-12	2005-08-12	ENSG00000179583	ENSG00000179583		"""Nucleotide-binding domain and leucine rich repeat containing"""	7067	protein-coding gene	gene with protein product	"""NLR family, acid domain containing"", ""nucleotide-binding oligomerization domain, leucine rich repeat and acid domain containing"""	600005	"""MHC class II transactivator"""	MHC2TA		8402893	Standard	NM_000246		Approved	C2TA, NLRA	uc002dai.4	P33076	OTTHUMG00000129753	ENST00000324288.8:c.1499G>C	16.37:g.11000848G>C	ENSP00000316328:p.Gly500Ala	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	48	43	0.895833	NM_000246	A0N0N9|D3DUG0|E9PFE0|Q29675|Q8SNB8|Q96KL4	Missense_Mutation	SNP	ENST00000324288.8	37	CCDS10544.1	573	0.2623626373626374	139	0.28252032520325204	136	0.3756906077348066	81	0.14160839160839161	217	0.2862796833773087	C	0.011	-1.704285	0.00719	0.257169	0.292326	ENSG00000179583	ENST00000324288;ENST00000388910	T	0.81415	-1.49	5.27	-0.799	0.10901	NACHT nucleoside triphosphatase (1);	0.377447	0.22470	N	0.059640	T	0.00012	0.0000	N	0.25957	0.775	0.58432	P	6.999999999979245E-6	B;B;B	0.13145	0.001;0.007;0.0	B;B;B	0.19148	0.012;0.024;0.005	T	0.37663	-0.9696	9	0.22109	T	0.4	.	24.3173	0.99989	0.0:0.1936:0.8064:0.0	rs4774;rs1135817;rs2228237;rs3198759;rs59312217;rs4774	500;500;452	A0N0N9;P33076;F2Z2G8	.;C2TA_HUMAN;.	A	500;452	ENSP00000316328:G500A	ENSP00000316328:G500A	G	+	2	0	CIITA	10908349	0.872000	0.30054	0.011000	0.14972	0.405000	0.30901	0.706000	0.25690	-0.719000	0.04942	-0.216000	0.12614	GGC	G|0.737;C|0.263	0.263	strong		0.647	CIITA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251966.2	NM_000246	
ANKRD18B	441459	hgsc.bcm.edu	37	9	33548043	33548043	+	Silent	SNP	T	T	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:33548043T>C	ENST00000290943.6	+	9	1167	c.1071T>C	c.(1069-1071)agT>agC	p.S357S		NM_001244752.1	NP_001231681.1	A2A2Z9	AN18B_HUMAN	ankyrin repeat domain 18B	357										NS(1)|breast(1)|endometrium(2)|lung(1)|prostate(1)|stomach(1)	7						AAAATGACAGTCTCAGAAAGG	0.284																																					p.S356S		Atlas-SNP	.											.	ANKRD18B	46	.	0			c.T1068C						PASS	.																																			SO:0001819	synonymous_variant	441459	exon9			TGACAGTCTCAGA			9p13.3	2013-01-10			ENSG00000230453	ENSG00000230453		"""Ankyrin repeat domain containing"""	23644	protein-coding gene	gene with protein product							Standard	NM_001244752		Approved	bA255A11.3	uc010mjw.2	A2A2Z9	OTTHUMG00000019776	ENST00000290943.6:c.1071T>C	9.37:g.33548043T>C		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	106	21	0.198113	NM_001244752		Silent	SNP	ENST00000290943.6	37																																																																																				.	.	none		0.284	ANKRD18B-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000313729.2	XM_001718334	
SEC16A	9919	hgsc.bcm.edu	37	9	139369212	139369212	+	Silent	SNP	G	G	A	rs17567909	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:139369212G>A	ENST00000371706.3	-	1	2355	c.2322C>T	c.(2320-2322)ccC>ccT	p.P774P	SEC16A_ENST00000313050.7_Silent_p.P952P|SEC16A_ENST00000290037.6_Silent_p.P774P|SEC16A_ENST00000431893.2_Silent_p.P774P			O15027	SC16A_HUMAN	SEC16 homolog A (S. cerevisiae)	774					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)		TAGCAAATCCGGGAAGAGCAC	0.507													G|||	464	0.0926518	0.0045	0.0648	5008	,	,		21202	0.004		0.1213	False		,,,				2504	0.2935				p.P952P		Atlas-SNP	.											.	SEC16A	249	.	0			c.C2856T						PASS	.	G		99,3753		5,89,1832	74.0	73.0	73.0		2856	-10.3	0.0	9	dbSNP_123	73	1043,7215		66,911,3152	no	coding-synonymous	SEC16A	NM_014866.1		71,1000,4984	AA,AG,GG		12.6302,2.5701,9.4302		952/2358	139369212	1142,10968	1926	4129	6055	SO:0001819	synonymous_variant	9919	exon3			AAATCCGGGAAGA	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.2322C>T	9.37:g.139369212G>A		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	58	25	0.431034	NM_014866	A1YCA4|Q4G0D7|Q5SXP0|Q5SXP1|Q8N347|Q96HP1	Silent	SNP	ENST00000371706.3	37																																																																																				G|0.926;A|0.074	0.074	strong		0.507	SEC16A-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000055077.1	XM_088459	
SCN10A	6336	hgsc.bcm.edu	37	3	38739494	38739494	+	Silent	SNP	G	G	A	rs116353929	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:38739494G>A	ENST00000449082.2	-	27	5216	c.5217C>T	c.(5215-5217)gaC>gaT	p.D1739D		NM_006514.2	NP_006505.2	Q9Y5Y9	SCNAA_HUMAN	sodium channel, voltage-gated, type X, alpha subunit	1739					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)	TGTCAAAGTCGTCCTCACTCA	0.488													G|||	72	0.014377	0.0	0.0288	5008	,	,		20713	0.001		0.0249	False		,,,				2504	0.0266				p.D1739D		Atlas-SNP	.											.	SCN10A	359	.	0			c.C5217T						PASS	.	G		36,4370	42.3+/-75.8	0,36,2167	95.0	93.0	94.0		5217	-10.8	0.1	3	dbSNP_132	94	265,8335	102.3+/-163.5	3,259,4038	no	coding-synonymous	SCN10A	NM_006514.2		3,295,6205	AA,AG,GG		3.0814,0.8171,2.3143		1739/1957	38739494	301,12705	2203	4300	6503	SO:0001819	synonymous_variant	6336	exon27			AAAGTCGTCCTCA	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.5217C>T	3.37:g.38739494G>A		Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	149	69	0.463087	NM_006514	A6NDQ1	Silent	SNP	ENST00000449082.2	37	CCDS33736.1																																																																																			G|0.979;A|0.021	0.021	strong		0.488	SCN10A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109745.3	NM_006514	
KIAA0368	23392	hgsc.bcm.edu	37	9	114124354	114124354	+	Nonsense_Mutation	SNP	C	C	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:114124354C>A	ENST00000338205.5	-	49	5695	c.5476G>T	c.(5476-5478)Gag>Tag	p.E1826*	KIAA0368_ENST00000374378.3_Intron|KIAA0368_ENST00000259335.4_Nonsense_Mutation_p.E2004*			Q5VYK3	ECM29_HUMAN	KIAA0368	1832					ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)	centrosome (GO:0005813)|cytoplasmic membrane-bounded vesicle (GO:0016023)|early endosome (GO:0005769)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle (GO:0030134)|late endosome (GO:0005770)|membrane (GO:0016020)|multivesicular body (GO:0005771)|nucleus (GO:0005634)|proteasome complex (GO:0000502)				NS(2)|breast(3)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(23)|prostate(3)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	65						GCTGCTTTCTCCTGCAGTTCA	0.428																																					p.E2004X		Atlas-SNP	.											.	KIAA0368	144	.	0			c.G6010T						PASS	.						130.0	133.0	132.0					9																	114124354		1912	4132	6044	SO:0001587	stop_gained	23392	exon51			CTTTCTCCTGCAG	AK025689	CCDS48006.1	9q32	2012-11-29	2006-11-23	2006-11-23	ENSG00000136813	ENSG00000136813			29020	protein-coding gene	gene with protein product	"""ECM29 homolog (S. cerevisiae)"""					9205841, 15496406, 20682791	Standard	NM_001080398		Approved	FLJ22036, ECM29	uc004bfe.1	Q5VYK3	OTTHUMG00000020489	ENST00000338205.5:c.5476G>T	9.37:g.114124354C>A	ENSP00000339889:p.Glu1826*	Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	128	28	0.21875	NM_001080398	O15074|Q8WU82	Nonsense_Mutation	SNP	ENST00000338205.5	37		.	.	.	.	.	.	.	.	.	.	C	47	13.552294	0.99749	.	.	ENSG00000136813	ENST00000338205;ENST00000259335;ENST00000543827	.	.	.	5.93	5.93	0.95920	.	0.090694	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.21540	T	0.41	0.3296	20.3465	0.98790	0.0:1.0:0.0:0.0	.	.	.	.	X	1826;2004;1301	.	ENSP00000259335:E2004X	E	-	1	0	KIAA0368	113164175	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.127000	0.77210	2.798000	0.96311	0.655000	0.94253	GAG	.	.	none		0.428	KIAA0368-001	NOVEL	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000053637.2	NM_014686	
CHAF1A	10036	hgsc.bcm.edu	37	19	4409756	4409756	+	Splice_Site	SNP	A	A	G	rs2230636	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:4409756A>G	ENST00000301280.5	+	3	1061	c.960A>G	c.(958-960)agA>agG	p.R320R		NM_005483.2	NP_005474	Q13111	CAF1A_HUMAN	chromatin assembly factor 1, subunit A (p150)	320					cell cycle (GO:0007049)|chromatin assembly (GO:0031497)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA replication-dependent nucleosome assembly (GO:0006335)|protein complex assembly (GO:0006461)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	CAF-1 complex (GO:0033186)|nuclear chromatin (GO:0000790)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|chromo shadow domain binding (GO:0070087)|identical protein binding (GO:0042802)|unfolded protein binding (GO:0051082)			breast(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(6)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|urinary_tract(1)	27		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0148)|STAD - Stomach adenocarcinoma(1328;0.18)		CCCTCCGCAGAGTGAGTATCT	0.627								Chromatin Structure					A|||	692	0.138179	0.0492	0.3055	5008	,	,		18632	0.0198		0.2406	False		,,,				2504	0.1564				p.R320R		Atlas-SNP	.											.	CHAF1A	69	.	0			c.A960G						PASS	.	A		393,4013	194.3+/-219.2	17,359,1827	50.0	48.0	49.0		960	-2.2	0.8	19	dbSNP_126	49	2129,6471	350.0+/-327.7	262,1605,2433	yes	coding-synonymous-near-splice	CHAF1A	NM_005483.2		279,1964,4260	GG,GA,AA		24.7558,8.9197,19.3911		320/957	4409756	2522,10484	2203	4300	6503	SO:0001630	splice_region_variant	10036	exon3			CCGCAGAGTGAGT	U20979	CCDS32875.1	19p13.3	2008-07-16				ENSG00000167670			1910	protein-coding gene	gene with protein product	"""chromatin assembly factor I (150 kDa)"""	601246				7600578	Standard	NM_005483		Approved	CAF1P150, CAF1B, CAF-1, CAF1, P150, MGC71229	uc002mal.3	Q13111		ENST00000301280.5:c.960+1A>G	19.37:g.4409756A>G		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	34	19	0.558824	NM_005483	Q6NXG5|Q7Z7K3|Q9UJY8	Silent	SNP	ENST00000301280.5	37	CCDS32875.1																																																																																			A|0.809;G|0.191	0.191	strong		0.627	CHAF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458310.2	NM_005483	Silent
FAM114A2	10827	hgsc.bcm.edu	37	5	153413390	153413390	+	Missense_Mutation	SNP	C	C	T	rs2578377	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:153413390C>T	ENST00000351797.4	-	4	440	c.364G>A	c.(364-366)Ggt>Agt	p.G122S	FAM114A2_ENST00000520667.1_Missense_Mutation_p.G122S|FAM114A2_ENST00000522858.1_Missense_Mutation_p.G122S|FAM114A2_ENST00000520313.1_Missense_Mutation_p.G52S	NM_018691.2	NP_061161.2	Q9NRY5	F1142_HUMAN	family with sequence similarity 114, member A2	122				G -> S (in Ref. 1; AAF76523, 2; BAB14952 and 5; AAH11414). {ECO:0000305}.			purine nucleotide binding (GO:0017076)			NS(1)|breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(9)|skin(1)|urinary_tract(1)	18						TCACTGGGACCAGGGATTCCA	0.358													T|||	3587	0.716254	0.6256	0.7161	5008	,	,		20523	0.8581		0.6262	False		,,,				2504	0.7853				p.G122S		Atlas-SNP	.											.	FAM114A2	51	.	0			c.G364A						PASS	.	T	SER/GLY	2859,1547	488.0+/-361.1	932,995,276	84.0	81.0	82.0		364	5.9	1.0	5	dbSNP_100	82	5357,3241	486.7+/-371.9	1670,2017,612	yes	missense	FAM114A2	NM_018691.2	56	2602,3012,888	TT,TC,CC		37.6948,35.1112,36.8194	benign	122/506	153413390	8216,4788	2203	4299	6502	SO:0001583	missense	10827	exon4			TGGGACCAGGGAT	AF159700	CCDS4323.1	5q31-q33	2008-06-13	2008-06-13	2008-06-13	ENSG00000055147	ENSG00000055147			1333	protein-coding gene	gene with protein product			"""chromosome 5 open reading frame 3"""	C5orf3		10843801	Standard	XM_005268359		Approved	133K02	uc003lvc.3	Q9NRY5	OTTHUMG00000130147	ENST00000351797.4:c.364G>A	5.37:g.153413390C>T	ENSP00000341597:p.Gly122Ser	Somatic	233	0	0		WXS	Illumina HiSeq	Phase_I	177	86	0.485876	NM_018691	B2R8D8|Q9H7E0	Missense_Mutation	SNP	ENST00000351797.4	37	CCDS4323.1	1543	0.7065018315018315	317	0.6443089430894309	244	0.6740331491712708	496	0.8671328671328671	486	0.6411609498680739	T	11.13	1.547196	0.27652	0.648888	0.623052	ENSG00000055147	ENST00000351797;ENST00000522858;ENST00000520667;ENST00000433795;ENST00000520313;ENST00000522395;ENST00000523705;ENST00000519808	T;T;T;T;T;T;T	0.37058	1.22;1.22;1.22;1.22;1.22;1.22;1.22	5.93	5.93	0.95920	.	0.044317	0.85682	N	0.000000	T	0.00012	0.0000	N	0.00335	-1.625	0.51482	P	7.999999999996898E-5	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.40117	-0.9580	9	0.02654	T	1	-2.5725	12.1609	0.54103	0.0:0.0665:0.0:0.9335	rs2578377;rs3734082;rs17618347;rs17856351;rs52826751;rs58417947;rs2578377	52;122	E7ESJ7;Q9NRY5	.;F1142_HUMAN	S	122;122;122;122;52;122;122;122	ENSP00000341597:G122S;ENSP00000430489:G122S;ENSP00000430384:G122S;ENSP00000429088:G52S;ENSP00000430186:G122S;ENSP00000428827:G122S;ENSP00000429753:G122S	ENSP00000341597:G122S	G	-	1	0	FAM114A2	153393583	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	5.922000	0.70036	1.074000	0.40909	-0.332000	0.08345	GGT	C|0.344;T|0.656	0.656	strong		0.358	FAM114A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252455.1	NM_018691	
MOB3A	126308	hgsc.bcm.edu	37	19	2078221	2078221	+	Silent	SNP	G	G	C	rs11541046	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:2078221G>C	ENST00000357066.3	-	3	718	c.339C>G	c.(337-339)ctC>ctG	p.L113L	MOB3A_ENST00000592280.1_Silent_p.L113L|MOB3A_ENST00000592143.1_Intron	NM_130807.2	NP_570719.1	Q96BX8	MOB3A_HUMAN	MOB kinase activator 3A	113						intracellular (GO:0005622)	metal ion binding (GO:0046872)										TGGGCGCGGAGAGTGCCGTGG	0.627													G|||	765	0.152756	0.1906	0.1081	5008	,	,		16393	0.0804		0.1352	False		,,,				2504	0.226				p.L113L		Atlas-SNP	.											.	.	.	.	0			c.C339G						PASS	.	G		843,3563	328.8+/-300.7	79,685,1439	83.0	58.0	67.0		339	-2.4	0.0	19	dbSNP_120	67	1289,7311	254.4+/-279.7	95,1099,3106	no	coding-synonymous	MOB3A	NM_130807.2		174,1784,4545	CC,CG,GG		14.9884,19.133,16.3924		113/218	2078221	2132,10874	2203	4300	6503	SO:0001819	synonymous_variant	126308	exon3			CGCGGAGAGTGCC	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.339C>G	19.37:g.2078221G>C		Somatic	244	1	0.00409836		WXS	Illumina HiSeq	Phase_I	223	107	0.479821	NM_130807	B3KTF1|O75249|Q8TF69	Silent	SNP	ENST00000357066.3	37	CCDS12081.1																																																																																			G|0.848;C|0.152	0.152	strong		0.627	MOB3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450893.1	NM_130807	
HOMEZ	57594	hgsc.bcm.edu	37	14	23744932	23744932	+	Missense_Mutation	SNP	C	C	T	rs1055061	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:23744932C>T	ENST00000357460.5	-	2	1669	c.1505G>A	c.(1504-1506)cGa>cAa	p.R502Q	HOMEZ_ENST00000561013.1_Missense_Mutation_p.R504Q|HOMEZ_ENST00000431326.2_Missense_Mutation_p.R504Q	NM_020834.2	NP_065885.2	Q8IX15	HOMEZ_HUMAN	homeobox and leucine zipper encoding	502					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)		CTGAGGTAATCGAGAGTCAAA	0.517													C|||	687	0.137181	0.2496	0.0432	5008	,	,		20026	0.0704		0.0487	False		,,,				2504	0.2117				p.R502Q		Atlas-SNP	.											.	HOMEZ	80	.	0			c.G1505A						PASS	.	C	GLN/ARG	840,3464		78,684,1390	46.0	49.0	48.0		1505	4.2	1.0	14	dbSNP_86	48	399,8123		8,383,3870	yes	missense	HOMEZ	NM_020834.2	43	86,1067,5260	TT,TC,CC		4.682,19.5167,9.6601	probably-damaging	502/551	23744932	1239,11587	2152	4261	6413	SO:0001583	missense	57594	exon2			GGTAATCGAGAGT	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.1505G>A	14.37:g.23744932C>T	ENSP00000350049:p.Arg502Gln	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	89	37	0.41573	NM_020834	A1L445|B4DZ80|F8WCA3|Q6P049|Q86XB6|Q9P2A5	Missense_Mutation	SNP	ENST00000357460.5	37	CCDS45085.1	203	0.09294871794871795	130	0.26422764227642276	15	0.04143646408839779	27	0.0472027972027972	31	0.040897097625329816	C	13.30	2.195416	0.38806	0.195167	0.04682	ENSG00000215271	ENST00000357460;ENST00000431326	D;D	0.93019	-3.15;-3.15	5.96	4.16	0.48862	.	0.284575	0.27375	U	0.019655	T	0.00109	0.0003	L	0.50333	1.59	0.25585	P	0.9867543	B;B	0.29115	0.196;0.233	B;B	0.17722	0.011;0.019	T	0.06267	-1.0836	9	0.66056	D	0.02	-6.0E-4	8.1936	0.31383	0.0:0.759:0.0:0.241	rs1055061;rs3168875;rs60697483;rs1055061	504;502	F8WCA3;Q8IX15	.;HOMEZ_HUMAN	Q	502;504	ENSP00000350049:R502Q;ENSP00000406579:R504Q	ENSP00000350049:R502Q	R	-	2	0	HOMEZ	22814772	0.033000	0.19621	0.999000	0.59377	0.997000	0.91878	1.062000	0.30555	0.870000	0.35726	0.655000	0.94253	CGA	C|0.894;T|0.106	0.106	strong		0.517	HOMEZ-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000416939.2	NM_020834	
C5	727	hgsc.bcm.edu	37	9	123783934	123783934	+	Silent	SNP	T	T	C	rs10985126	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:123783934T>C	ENST00000223642.1	-	11	1184	c.1155A>G	c.(1153-1155)ggA>ggG	p.G385G		NM_001735.2	NP_001726.2	P01031	CO5_HUMAN	complement component 5	385					activation of MAPK activity (GO:0000187)|cell chemotaxis (GO:0060326)|cell surface receptor signaling pathway (GO:0007166)|cellular calcium ion homeostasis (GO:0006874)|chemotaxis (GO:0006935)|complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|complement activation, classical pathway (GO:0006958)|cytolysis (GO:0019835)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|in utero embryonic development (GO:0001701)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|leukocyte migration involved in inflammatory response (GO:0002523)|negative regulation of dopamine secretion (GO:0033602)|negative regulation of macrophage chemotaxis (GO:0010760)|negative regulation of norepinephrine secretion (GO:0010700)|positive regulation of angiogenesis (GO:0045766)|positive regulation of chemokine secretion (GO:0090197)|positive regulation of chemotaxis (GO:0050921)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of complement activation (GO:0030449)|response to stress (GO:0006950)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane attack complex (GO:0005579)	chemokine activity (GO:0008009)|endopeptidase inhibitor activity (GO:0004866)|receptor binding (GO:0005102)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(14)|lung(5)|ovary(2)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	46				OV - Ovarian serous cystadenocarcinoma(323;4.98e-53)|GBM - Glioblastoma multiforme(294;0.0242)	Eculizumab(DB01257)|Intravenous Immunoglobulin(DB00028)	TTACTGGGACTCCTCCTACCA	0.393													C|||	1208	0.241214	0.4418	0.1037	5008	,	,		19524	0.244		0.167	False		,,,				2504	0.1411				p.G385G		Atlas-SNP	.											C5,NS,adenoma,0,1	C5	124	1	0			c.A1155G						PASS	.	C		1677,2729	653.1+/-399.5	318,1041,844	189.0	177.0	181.0		1155	1.9	0.2	9	dbSNP_120	181	1548,7052	745.4+/-407.3	141,1266,2893	no	coding-synonymous	C5	NM_001735.2		459,2307,3737	CC,CT,TT		18.0,38.0617,24.7962		385/1677	123783934	3225,9781	2203	4300	6503	SO:0001819	synonymous_variant	727	exon11			TGGGACTCCTCCT	M57729	CCDS6826.1	9q33-q34	2014-09-17			ENSG00000106804	ENSG00000106804		"""Complement system"", ""Endogenous ligands"""	1331	protein-coding gene	gene with protein product	"""prepro-C5"", ""C5a anaphylatoxin"""	120900					Standard	NM_001735		Approved	CPAMD4, C5a, C5b	uc004bkv.3	P01031	OTTHUMG00000020579	ENST00000223642.1:c.1155A>G	9.37:g.123783934T>C		Somatic	324	1	0.00308642		WXS	Illumina HiSeq	Phase_I	268	130	0.485075	NM_001735	Q14CJ0|Q27I61	Silent	SNP	ENST00000223642.1	37	CCDS6826.1																																																																																			T|0.764;C|0.236	0.236	strong		0.393	C5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053844.1	NM_001735	
TCEB3B	51224	hgsc.bcm.edu	37	18	44560875	44560875	+	Missense_Mutation	SNP	C	C	A	rs2010834	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:44560875C>A	ENST00000332567.4	-	1	1113	c.761G>T	c.(760-762)tGc>tTc	p.C254F	KATNAL2_ENST00000356157.7_Intron|KATNAL2_ENST00000245121.5_Intron|KATNAL2_ENST00000592005.1_Intron	NM_016427.2	NP_057511.2	Q8IYF1	ELOA2_HUMAN	transcription elongation factor B polypeptide 3B (elongin A2)	254			C -> F (in dbSNP:rs2010834). {ECO:0000269|PubMed:10692460}.		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						GCAGGCCCCGCATGATTTCTC	0.582													C|||	2675	0.534145	0.4349	0.6239	5008	,	,		18258	0.6448		0.4433	False		,,,				2504	0.5838				p.C254F		Atlas-SNP	.											.	TCEB3B	141	.	0			c.G761T						PASS	.	C	PHE/CYS,	1950,2456	546.3+/-377.0	448,1054,701	48.0	51.0	50.0		761,	-3.0	0.0	18	dbSNP_92	50	3909,4691	543.9+/-384.5	923,2063,1314	yes	missense,intron	TCEB3B,KATNAL2	NM_016427.2,NM_031303.2	205,	1371,3117,2015	AA,AC,CC		45.4535,44.2578,45.0484	benign,	254/754,	44560875	5859,7147	2203	4300	6503	SO:0001583	missense	51224	exon1			GCCCCGCATGATT	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.761G>T	18.37:g.44560875C>A	ENSP00000331302:p.Cys254Phe	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	117	54	0.461538	NM_016427	Q9P2V9	Missense_Mutation	SNP	ENST00000332567.4	37	CCDS11932.1	1116	0.510989010989011	211	0.42886178861788615	209	0.5773480662983426	362	0.6328671328671329	334	0.44063324538258575	C	0.001	-2.881780	0.00061	0.442578	0.454535	ENSG00000206181	ENST00000332567	T	0.06371	3.31	1.52	-3.04	0.05412	.	2.949720	0.01911	U	0.039898	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.24963	0.115	B	0.20577	0.03	T	0.43988	-0.9357	9	0.20046	T	0.44	.	2.3022	0.04165	0.1451:0.488:0.1529:0.2139	rs2010834;rs3786259;rs16952963;rs59062824;rs2010834	254	Q8IYF1	ELOA2_HUMAN	F	254	ENSP00000331302:C254F	ENSP00000331302:C254F	C	-	2	0	TCEB3B	42814873	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.841000	0.01683	-2.994000	0.00278	-1.569000	0.00873	TGC	C|0.518;A|0.482	0.482	strong		0.582	TCEB3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255900.1	NM_016427	
DGCR14	8220	hgsc.bcm.edu	37	22	19122665	19122665	+	Silent	SNP	C	C	T	rs2240111	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	164	0	0		WXS	Illumina HiSeq	Phase_I	131	69	0.526718	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		
DNAJC9	23234	hgsc.bcm.edu	37	10	75006868	75006868	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:75006868G>A	ENST00000372950.4	-	1	1752	c.80C>T	c.(79-81)tCc>tTc	p.S27F	DNAJC9-AS1_ENST00000440197.2_RNA|DNAJC9-AS1_ENST00000513954.1_RNA|MRPS16_ENST00000416782.2_3'UTR|MRPS16_ENST00000479005.1_5'Flank	NM_015190.3	NP_056005.1	Q8WXX5	DNJC9_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 9	27	J. {ECO:0000255|PROSITE- ProRule:PRU00286}.				social behavior (GO:0035176)	nucleus (GO:0005634)				endometrium(2)|kidney(1)|large_intestine(2)|stomach(1)	6	Prostate(51;0.0119)					CTCGCCGTCGGAGGCCTCGCG	0.697																																					p.S27F		Atlas-SNP	.											.	DNAJC9	19	.	0			c.C80T						PASS	.						13.0	13.0	13.0					10																	75006868		2188	4280	6468	SO:0001583	missense	23234	exon1			CCGTCGGAGGCCT	AF327347	CCDS7322.1	10q22.3	2011-09-02			ENSG00000213551	ENSG00000213551		"""Heat shock proteins / DNAJ (HSP40)"""	19123	protein-coding gene	gene with protein product		611206					Standard	NM_015190		Approved	JDD1, SB73	uc001jtr.3	Q8WXX5	OTTHUMG00000018461	ENST00000372950.4:c.80C>T	10.37:g.75006868G>A	ENSP00000362041:p.Ser27Phe	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	88	42	0.477273	NM_015190	B2RMW6	Missense_Mutation	SNP	ENST00000372950.4	37	CCDS7322.1	.	.	.	.	.	.	.	.	.	.	g	22.8	4.333978	0.81801	.	.	ENSG00000213551	ENST00000372950	T	0.37058	1.22	5.65	4.74	0.60224	Heat shock protein DnaJ, N-terminal (5);	0.527076	0.21432	N	0.074639	T	0.69522	0.3120	H	0.96518	3.835	0.80722	D	1	D	0.60160	0.987	D	0.65684	0.937	T	0.78851	-0.2041	10	0.87932	D	0	-22.6147	12.6301	0.56653	0.0:0.1665:0.8335:0.0	.	27	Q8WXX5	DNJC9_HUMAN	F	27	ENSP00000362041:S27F	ENSP00000362041:S27F	S	-	2	0	DNAJC9	74676874	0.888000	0.30383	0.842000	0.33263	0.371000	0.29859	4.349000	0.59385	1.377000	0.46286	0.586000	0.80456	TCC	.	.	none		0.697	DNAJC9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048643.1	NM_015190	
LILRA6	79168	hgsc.bcm.edu	37	19	54744799	54744799	+	Missense_Mutation	SNP	G	G	C	rs1052975	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:54744799G>C	ENST00000396365.2	-	5	902	c.863C>G	c.(862-864)cCc>cGc	p.P288R	LILRA6_ENST00000245621.5_Missense_Mutation_p.P288R|LILRA6_ENST00000440558.2_Missense_Mutation_p.P288R|LILRA6_ENST00000270464.5_Intron|LILRB3_ENST00000407860.2_Intron|LILRA6_ENST00000419410.2_Missense_Mutation_p.P288R|LILRA6_ENST00000391735.3_3'UTR	NM_024318.2	NP_077294	Q6PI73	LIRA6_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 6	288	Ig-like C2-type 1.		P -> R (in dbSNP:rs1052975).		immune system process (GO:0002376)	integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(20)|ovary(3)|skin(2)|urinary_tract(2)	38	all_cancers(19;0.00723)|all_epithelial(19;0.00389)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		CCCGTGGGAGGGGCTCACAGG	0.657																																					p.P288R		Atlas-SNP	.											.	LILRA6	75	.	0			c.C863G						PASS	.						51.0	62.0	58.0					19																	54744799		2203	4300	6503	SO:0001583	missense	79168	exon5			TGGGAGGGGCTCA	AF041262	CCDS42610.1	19q13.4	2013-01-11	2005-05-17	2005-05-17	ENSG00000244482	ENSG00000244482		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	15495	protein-coding gene	gene with protein product			"""leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 6"""	LILRB6		10941842	Standard	NM_024318		Approved	ILT8, CD85b		Q6PI73	OTTHUMG00000066635	ENST00000396365.2:c.863C>G	19.37:g.54744799G>C	ENSP00000379651:p.Pro288Arg	Somatic	307	0	0		WXS	Illumina HiSeq	Phase_I	245	71	0.289796	NM_024318		Missense_Mutation	SNP	ENST00000396365.2	37	CCDS42610.1	399	0.18269230769230768	67	0.13617886178861788	53	0.1464088397790055	123	0.21503496503496503	156	0.20580474934036938	g	0.021	-1.430762	0.01117	.	.	ENSG00000244482	ENST00000440558;ENST00000419410;ENST00000421123;ENST00000396365;ENST00000245621	T;T;T;T	0.13089	2.62;2.62;2.62;2.62	2.38	-4.75	0.03239	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	5.130160	0.00604	N	0.000395	T	0.00012	0.0000	N	0.10618	0.005	0.09310	N	1	B;D;B;B	0.62365	0.001;0.991;0.002;0.001	B;D;B;B	0.65140	0.02;0.932;0.006;0.006	T	0.48514	-0.9029	10	0.06625	T	0.88	.	3.3196	0.07045	0.1141:0.1581:0.4541:0.2736	rs1052975;rs3193457;rs3745417;rs16989284	288;288;288;288	C9JFH3;Q6PI73;F8WCY4;D3YTC4	.;LIRA6_HUMAN;.;.	R	288	ENSP00000390120:P288R;ENSP00000411227:P288R;ENSP00000379651:P288R;ENSP00000245621:P288R	ENSP00000245621:P288R	P	-	2	0	LILRA6	59436611	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-3.366000	0.00496	-4.910000	0.00027	-2.001000	0.00444	CCC	G|0.816;C|0.184	0.184	strong		0.657	LILRA6-003	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000313725.1	NM_024318	
NUSAP1	51203	hgsc.bcm.edu	37	15	41634587	41634587	+	Missense_Mutation	SNP	A	A	G	rs386783399|rs7178634	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:41634587A>G	ENST00000559596.1	+	2	184	c.97A>G	c.(97-99)Acc>Gcc	p.T33A	NUSAP1_ENST00000560747.1_Missense_Mutation_p.T33A|NUSAP1_ENST00000450592.2_Intron|NUSAP1_ENST00000558123.1_3'UTR|RP11-16O9.2_ENST00000559959.1_RNA|NUSAP1_ENST00000560177.1_Missense_Mutation_p.T33A|NUSAP1_ENST00000450318.1_Missense_Mutation_p.T33A|NUSAP1_ENST00000414849.2_Missense_Mutation_p.T33A|NUSAP1_ENST00000260359.6_Missense_Mutation_p.T33A			Q9BXS6	NUSAP_HUMAN	nucleolar and spindle associated protein 1	33			T -> A (in dbSNP:rs7178634).|T -> N (in dbSNP:rs7178777).	T -> D (in Ref. 6; AL833611). {ECO:0000305}.	establishment of mitotic spindle localization (GO:0040001)|mitotic chromosome condensation (GO:0007076)|mitotic cytokinesis (GO:0000281)|mitotic sister chromatid segregation (GO:0000070)|positive regulation of mitosis (GO:0045840)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)	p.T33A(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(3)|ovary(1)|prostate(2)|urinary_tract(2)	13		all_cancers(109;5.07e-19)|all_epithelial(112;2.43e-16)|Lung NSC(122;1.81e-11)|all_lung(180;4.81e-10)|Melanoma(134;0.0179)|Colorectal(260;0.0946)|Ovarian(310;0.143)		OV - Ovarian serous cystadenocarcinoma(18;9.63e-17)|GBM - Glioblastoma multiforme(113;1.59e-06)|BRCA - Breast invasive adenocarcinoma(123;0.168)		CTTGCAGGCAACCAAGTTGTT	0.338													G|||	1714	0.342252	0.5938	0.2781	5008	,	,		23594	0.1548		0.337	False		,,,				2504	0.2464				p.T33A		Atlas-SNP	.											NUSAP1,NS,carcinoma,0,2	NUSAP1	32	2	1	Substitution - Missense(1)	prostate(1)	c.A97G						PASS	.	G	ALA/THR,ALA/THR,ALA/THR	91,3631		12,67,1782	70.0	66.0	67.0		97,97,97	4.6	1.0	15	dbSNP_116	67	59,8135		7,45,4045	yes	missense,missense,missense	NUSAP1	NM_001129897.1,NM_016359.4,NM_018454.7	58,58,58	19,112,5827	GG,GA,AA		0.72,2.4449,1.2588	benign,benign,benign	33/403,33/442,33/441	41634587	150,11766	1861	4097	5958	SO:0001583	missense	51203	exon2			CAGGCAACCAAGT	AF290612	CCDS45234.1, CCDS45236.1, CCDS58356.1, CCDS58357.1, CCDS58358.1, CCDS73708.1	15q14	2008-02-05				ENSG00000137804			18538	protein-coding gene	gene with protein product		612818				12963707	Standard	NM_016359		Approved	FLJ13421, LNP, ANKT, NuSAP1, SAPL, BM037, PRO0310p1, Q0310	uc001zns.4	Q9BXS6		ENST00000559596.1:c.97A>G	15.37:g.41634587A>G	ENSP00000453403:p.Thr33Ala	Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	107	45	0.420561	NM_018454	B4DDF1|E7ERR5|J3KN21|Q53GW2|Q8TBT4|Q96E58|Q96FJ1|Q9GZM9|Q9NZ85|Q9UI70	Missense_Mutation	SNP	ENST00000559596.1	37	CCDS45234.1	577	0.2641941391941392	222	0.45121951219512196	97	0.26795580110497236	72	0.1258741258741259	186	0.24538258575197888	G	12.08	1.830706	0.32329	0.024449	0.0072	ENSG00000137804	ENST00000260359;ENST00000414849;ENST00000450318	T;T;T	0.30981	1.51;1.51;1.51	5.47	4.56	0.56223	.	0.426017	0.27797	N	0.017808	T	0.00012	0.0000	N	0.08118	0	0.58432	P	1.0000000000287557E-6	B;B;B;B;B	0.12630	0.0;0.006;0.005;0.006;0.005	B;B;B;B;B	0.12837	0.0;0.008;0.006;0.008;0.006	T	0.43048	-0.9415	9	0.72032	D	0.01	.	10.0559	0.42244	0.1593:0.0:0.8407:0.0	rs7178634;rs57619738;rs7178634	33;33;33;33;33	E9PB35;Q9BXS6-3;Q9BXS6-5;Q9BXS6;Q9BXS6-2	.;.;.;NUSAP_HUMAN;.	A	33	ENSP00000260359:T33A;ENSP00000400746:T33A;ENSP00000401351:T33A	ENSP00000260359:T33A	T	+	1	0	NUSAP1	39421879	1.000000	0.71417	0.999000	0.59377	0.229000	0.25112	1.570000	0.36439	0.818000	0.34468	-0.227000	0.12334	ACC	A|0.684;G|0.316	0.316	strong		0.338	NUSAP1-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000419427.1	NM_016359	
ACAN	176	hgsc.bcm.edu	37	15	89402239	89402239	+	Silent	SNP	T	T	C	rs1042631	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:89402239T>C	ENST00000561243.1	+	11	6423	c.6423T>C	c.(6421-6423)ctT>ctC	p.L2141L	ACAN_ENST00000439576.2_Silent_p.L2141L|ACAN_ENST00000559004.1_Silent_p.L2141L|ACAN_ENST00000352105.7_Silent_p.L2141L			P16112	PGCA_HUMAN	aggrecan	2026	CS-2.				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.L2027L(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)			AAGCTAACCTTGAGAGATCCT	0.577													C|||	3688	0.736422	0.854	0.6801	5008	,	,		20188	0.6111		0.7873	False		,,,				2504	0.6943				p.L2141L		Atlas-SNP	.											ACAN,NS,carcinoma,0,1	ACAN	220	1	1	Substitution - coding silent(1)	stomach(1)	c.T6423C						PASS	.	C	,	3526,634		1496,534,50	75.0	80.0	78.0		6423,6423	-10.0	0.0	15	dbSNP_86	78	6738,1698		2687,1364,167	no	coding-synonymous,coding-synonymous	ACAN	NM_001135.3,NM_013227.3	,	4183,1898,217	CC,CT,TT		20.128,15.2404,18.5138	,	2141/2432,2141/2531	89402239	10264,2332	2080	4218	6298	SO:0001819	synonymous_variant	176	exon12			TAACCTTGAGAGA	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.6423T>C	15.37:g.89402239T>C		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	65	65	1	NM_001135	Q13650|Q9UCD3|Q9UCP4|Q9UCP5|Q9UDE0	Silent	SNP	ENST00000561243.1	37	CCDS53970.1																																																																																			T|0.294;C|0.706	0.706	strong		0.577	ACAN-006	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416267.2	NM_001135	
TROAP	10024	hgsc.bcm.edu	37	12	49722793	49722793	+	Silent	SNP	C	C	T	rs2230550	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:49722793C>T	ENST00000257909.3	+	9	1051	c.975C>T	c.(973-975)ccC>ccT	p.P325P	TROAP_ENST00000547923.1_Silent_p.P33P|TROAP_ENST00000551245.1_Silent_p.P325P	NM_005480.3	NP_005471.3	Q12815	TROAP_HUMAN	trophinin associated protein	325					cell adhesion (GO:0007155)	cytoplasm (GO:0005737)				breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(14)|ovary(1)|prostate(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(4)	32						GTCCATCACCCTTTGGACGGG	0.622													C|||	161	0.0321486	0.0605	0.0173	5008	,	,		16094	0.0139		0.0209	False		,,,				2504	0.0348				p.P325P		Atlas-SNP	.											.	TROAP	80	.	0			c.C975T						PASS	.	C		290,4116	158.5+/-191.2	12,266,1925	77.0	72.0	74.0		975	0.8	1.0	12	dbSNP_98	74	125,8475	64.2+/-126.4	0,125,4175	no	coding-synonymous	TROAP	NM_005480.3		12,391,6100	TT,TC,CC		1.4535,6.5819,3.1908		325/779	49722793	415,12591	2203	4300	6503	SO:0001819	synonymous_variant	10024	exon9			ATCACCCTTTGGA	U04810	CCDS8784.1, CCDS41779.1, CCDS61117.1	12q13.12	2012-10-17	2012-10-17		ENSG00000135451	ENSG00000135451			12327	protein-coding gene	gene with protein product	"""tastin"""	603872				7758945	Standard	NM_005480		Approved	TASTIN	uc001rtx.4	Q12815	OTTHUMG00000169486	ENST00000257909.3:c.975C>T	12.37:g.49722793C>T		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	98	50	0.510204	NM_005480	F8VSF9|Q6PJU7|Q8N5B2	Silent	SNP	ENST00000257909.3	37	CCDS8784.1																																																																																			C|0.969;T|0.031	0.031	strong		0.622	TROAP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000404300.1	NM_005480	
MYLIP	29116	hgsc.bcm.edu	37	6	16145473	16145473	+	Silent	SNP	C	C	T	rs1060901	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:16145473C>T	ENST00000356840.3	+	6	1371	c.1173C>T	c.(1171-1173)tgC>tgT	p.C391C	MYLIP_ENST00000349606.4_Silent_p.C210C	NM_013262.3	NP_037394.2	Q8WY64	MYLIP_HUMAN	myosin regulatory light chain interacting protein	391					cellular component movement (GO:0006928)|cholesterol homeostasis (GO:0042632)|negative regulation of low-density lipoprotein particle clearance (GO:0010989)|nervous system development (GO:0007399)|positive regulation of protein catabolic process (GO:0045732)|protein destabilization (GO:0031648)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of low-density lipoprotein particle receptor catabolic process (GO:0032803)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extrinsic component of membrane (GO:0019898)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	cytoskeletal protein binding (GO:0008092)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	28	Breast(50;0.0799)|Ovarian(93;0.103)	all_hematologic(90;0.0895)	Epithelial(50;0.241)			TGGTGTGCTGCGAGGAGGAGA	0.612													C|||	125	0.0249601	0.003	0.0375	5008	,	,		20576	0.001		0.0736	False		,,,				2504	0.0204				p.C391C		Atlas-SNP	.											MYLIP,rectum,carcinoma,0,3	MYLIP	44	3	0			c.C1173T						PASS	.	C		72,4334	63.5+/-100.7	1,70,2132	103.0	89.0	94.0		1173	-5.6	0.6	6	dbSNP_86	94	773,7827	184.6+/-232.5	34,705,3561	no	coding-synonymous	MYLIP	NM_013262.3		35,775,5693	TT,TC,CC		8.9884,1.6341,6.497		391/446	16145473	845,12161	2203	4300	6503	SO:0001819	synonymous_variant	29116	exon6			GTGCTGCGAGGAG	AF187016	CCDS4536.1	6p23-p22.3	2011-11-17			ENSG00000007944	ENSG00000007944			21155	protein-coding gene	gene with protein product	"""E3 ubiquitin ligase-inducible degrader of the low density lipoprotein receptor"""	610082				10593918, 11162443, 19688294	Standard	NM_013262		Approved	MIR, IDOL	uc003nbq.3	Q8WY64	OTTHUMG00000016405	ENST00000356840.3:c.1173C>T	6.37:g.16145473C>T		Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	173	70	0.404624	NM_013262	Q5TIA4|Q9BU73|Q9NRL9|Q9UHE7	Silent	SNP	ENST00000356840.3	37	CCDS4536.1																																																																																			C|0.950;T|0.050	0.050	strong		0.612	MYLIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043864.1	NM_013262	
CCDC110	256309	hgsc.bcm.edu	37	4	186381115	186381115	+	Missense_Mutation	SNP	G	G	T	rs7699687	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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_ENST00000393540.3_Missense_Mutation_p.P172Q|CCDC110_ENST00000507501.1_5'UTR	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	130	0	0		WXS	Illumina HiSeq	Phase_I	85	35	0.411765	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	
TRIM31	11074	hgsc.bcm.edu	37	6	30071330	30071330	+	Missense_Mutation	SNP	C	C	T	rs1116221	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:30071330C>T	ENST00000376734.3	-	9	1386	c.1261G>A	c.(1261-1263)Gag>Aag	p.E421K	TRIM31_ENST00000540829.1_Missense_Mutation_p.E421K|TRIM31-AS1_ENST00000440874.1_RNA|TRIM31_ENST00000485864.1_5'Flank	NM_007028.3	NP_008959.3	Q9BZY9	TRI31_HUMAN	tripartite motif containing 31	421			E -> K (in dbSNP:rs1116221). {ECO:0000269|PubMed:14574404, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.2}.		innate immune response (GO:0045087)|negative regulation of viral entry into host cell (GO:0046597)|negative regulation of viral transcription (GO:0032897)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein ubiquitination (GO:0016567)|regulation of viral release from host cell (GO:1902186)	mitochondrion (GO:0005739)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(5)|ovary(2)|prostate(2)|skin(2)	15						GAAGGAACCTCACAAAACCAA	0.582													C|||	1312	0.261981	0.4115	0.2248	5008	,	,		17945	0.0992		0.2207	False		,,,				2504	0.2965				p.E421K		Atlas-SNP	.											.	TRIM31	40	.	0			c.G1261A						PASS	.	C	LYS/GLU	1136,1884		203,730,577	149.0	166.0	160.0		1261	1.0	0.0	6	dbSNP_86	160	1412,4004		173,1066,1469	yes	missense	TRIM31	NM_007028.3	56	376,1796,2046	TT,TC,CC		26.0709,37.6159,30.2039	possibly-damaging	421/426	30071330	2548,5888	1510	2708	4218	SO:0001583	missense	11074	exon9			GAACCTCACAAAA	AF230386	CCDS34374.1	6p21.3	2013-01-09	2011-01-25		ENSG00000204616	ENSG00000204616		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	16289	protein-coding gene	gene with protein product		609316	"""tripartite motif-containing 31"""			11331580	Standard	XM_006714977		Approved	RNF, HCGI, C6orf13, HCG1	uc003npg.1	Q9BZY9	OTTHUMG00000031064	ENST00000376734.3:c.1261G>A	6.37:g.30071330C>T	ENSP00000365924:p.Glu421Lys	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	45	19	0.422222	NM_007028	A6NLX6|A9R9Q4|Q53H52|Q5RI37|Q5SRJ7|Q5SRJ8|Q5SS28|Q96AK4|Q96AP8|Q99579|Q9BZY8	Missense_Mutation	SNP	ENST00000376734.3	37	CCDS34374.1	544	0.2490842490842491	214	0.4349593495934959	90	0.24861878453038674	63	0.11013986013986014	177	0.23350923482849603	C	9.318	1.057418	0.19907	0.376159	0.260709	ENSG00000204616	ENST00000376734;ENST00000376728;ENST00000540829	T;T	0.70045	-0.45;-0.45	1.99	1.05	0.20165	.	.	.	.	.	T	0.13200	0.0320	N	0.08118	0	0.80722	P	0.0	P	0.41524	0.753	B	0.28991	0.097	T	0.06661	-1.0814	8	0.09084	T	0.74	.	5.5601	0.17140	0.3261:0.6739:0.0:0.0	rs1116221;rs4081515;rs17187903;rs17845513;rs17858403;rs59822889;rs1116221	421	Q9BZY9	TRI31_HUMAN	K	421	ENSP00000365924:E421K;ENSP00000444311:E421K	ENSP00000365918:E421K	E	-	1	0	TRIM31	30179309	0.001000	0.12720	0.000000	0.03702	0.009000	0.06853	0.968000	0.29357	0.371000	0.24564	0.573000	0.79308	GAG	C|0.710;T|0.290	0.290	strong		0.582	TRIM31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076081.2		
FAT2	2196	hgsc.bcm.edu	37	5	150905398	150905398	+	Silent	SNP	C	C	T	rs3734051	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:150905398C>T	ENST00000261800.5	-	17	10449	c.10437G>A	c.(10435-10437)ccG>ccA	p.P3479P		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	3479	Cadherin 31. {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)			GCCATCCATCCGGGGTCACTC	0.577													C|||	872	0.174121	0.2005	0.196	5008	,	,		19464	0.1319		0.2624	False		,,,				2504	0.0757				p.P3479P		Atlas-SNP	.											FAT2,colon,carcinoma,-1,2	FAT2	465	2	0			c.G10437A						scavenged	.	C		900,3506	345.7+/-308.6	90,720,1393	81.0	74.0	76.0		10437	-4.5	1.0	5	dbSNP_107	76	2263,6337	383.8+/-340.9	313,1637,2350	no	coding-synonymous	FAT2	NM_001447.2		403,2357,3743	TT,TC,CC		26.314,20.4267,24.3195		3479/4350	150905398	3163,9843	2203	4300	6503	SO:0001819	synonymous_variant	2196	exon17			TCCATCCGGGGTC	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.10437G>A	5.37:g.150905398C>T		Somatic	76	1	0.0131579		WXS	Illumina HiSeq	Phase_I	78	36	0.461538	NM_001447	O75091|Q9NSR7	Silent	SNP	ENST00000261800.5	37	CCDS4317.1	477	0.2184065934065934	115	0.23373983739837398	82	0.2265193370165746	87	0.1520979020979021	193	0.2546174142480211	C	9.298	1.052233	0.19827	0.204267	0.26314	ENSG00000086570	ENST00000520200	.	.	.	5.11	-4.53	0.03462	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999998391	.	.	.	.	.	.	T	0.38950	-0.9637	3	.	.	.	.	4.0147	0.09639	0.3573:0.2731:0.0:0.3695	rs3734051;rs17404132;rs56590107;rs60495232;rs3734051	.	.	.	R	338	.	.	G	-	1	0	FAT2	150885591	0.296000	0.24398	0.993000	0.49108	0.831000	0.47069	-0.350000	0.07721	-0.238000	0.09724	-1.028000	0.02416	GGA	C|0.776;N|0.000	.	strong		0.577	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447	
MAML1	9794	hgsc.bcm.edu	37	5	179201226	179201226	+	Missense_Mutation	SNP	A	A	C	rs148053500	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:179201226A>C	ENST00000292599.3	+	5	2662	c.2399A>C	c.(2398-2400)aAc>aCc	p.N800T	MAML1_ENST00000503050.1_Intron	NM_014757.4	NP_055572.1			mastermind-like 1 (Drosophila)											central_nervous_system(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(16)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	36	all_cancers(89;0.000197)|all_epithelial(37;6.7e-05)|Renal(175;0.000159)|Lung NSC(126;0.00121)|all_lung(126;0.00218)	all_cancers(40;0.0308)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			TATGGGCAGAACTCTCTGGGA	0.612													A|||	9	0.00179712	0.0015	0.0058	5008	,	,		17029	0.0		0.003	False		,,,				2504	0.0				p.N800T		Atlas-SNP	.											.	MAML1	118	.	0			c.A2399C						PASS	.	A	THR/ASN	4,4402	4.2+/-10.8	0,4,2199	35.0	36.0	35.0		2399	1.3	1.0	5	dbSNP_134	35	27,8573	19.2+/-60.6	0,27,4273	yes	missense	MAML1	NM_014757.4	65	0,31,6472	CC,CA,AA		0.314,0.0908,0.2384	possibly-damaging	800/1017	179201226	31,12975	2203	4300	6503	SO:0001583	missense	9794	exon5			GGCAGAACTCTCT	D83785	CCDS34315.1	5q35	2008-07-18	2001-11-28			ENSG00000161021			13632	protein-coding gene	gene with protein product	"""mastermind homolog"""	605424	"""mastermind (drosophila)-like 1"""			11101851, 11390662	Standard	NM_014757		Approved	KIAA0200, Mam-1	uc003mkm.3	Q92585		ENST00000292599.3:c.2399A>C	5.37:g.179201226A>C	ENSP00000292599:p.Asn800Thr	Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	39	25	0.641026	NM_014757		Missense_Mutation	SNP	ENST00000292599.3	37	CCDS34315.1	7	0.003205128205128205	1	0.0020325203252032522	3	0.008287292817679558	0	0.0	3	0.00395778364116095	A	18.11	3.550143	0.65311	9.08E-4	0.00314	ENSG00000161021	ENST00000292599	T	0.25749	1.78	4.94	1.31	0.21738	.	0.192835	0.45606	D	0.000351	T	0.26085	0.0636	L	0.58101	1.795	0.46901	D	0.999241	D	0.69078	0.997	P	0.59056	0.851	T	0.08911	-1.0699	10	0.17832	T	0.49	-16.6951	8.3868	0.32505	0.6881:0.0:0.3119:0.0	.	800	Q92585	MAML1_HUMAN	T	800	ENSP00000292599:N800T	ENSP00000292599:N800T	N	+	2	0	MAML1	179133832	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	2.050000	0.41297	0.260000	0.21731	0.379000	0.24179	AAC	A|0.997;C|0.003	0.003	strong		0.612	MAML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372316.2	NM_014757	
FAM83C	128876	hgsc.bcm.edu	37	20	33874720	33874720	+	Missense_Mutation	SNP	C	C	T	rs2425049	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:33874720C>T	ENST00000374408.3	-	4	1958	c.1862G>A	c.(1861-1863)cGg>cAg	p.R621Q	EIF6_ENST00000374443.3_5'Flank|EIF6_ENST00000374436.3_5'Flank|FAM83C-AS1_ENST00000429167.1_RNA|EIF6_ENST00000462894.1_5'Flank|EIF6_ENST00000374450.3_5'Flank	NM_178468.5	NP_848563.1	Q9BQN1	FA83C_HUMAN	family with sequence similarity 83, member C	621			R -> Q (in dbSNP:rs2425049).							central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(6)|lung(19)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	40			BRCA - Breast invasive adenocarcinoma(18;0.00252)			ATCTGGTGCCCGTCTGGCAGG	0.627													T|||	1892	0.377796	0.7474	0.1744	5008	,	,		18761	0.2232		0.2028	False		,,,				2504	0.362				p.R621Q		Atlas-SNP	.											.	FAM83C	80	.	0			c.G1862A						PASS	.	T	GLN/ARG	2773,1633	494.6+/-363.0	877,1019,307	52.0	51.0	51.0		1862	2.8	0.3	20	dbSNP_100	51	1871,6729	723.6+/-406.5	218,1435,2647	yes	missense	FAM83C	NM_178468.4	43	1095,2454,2954	TT,TC,CC		21.7558,37.0631,35.7066	benign	621/748	33874720	4644,8362	2203	4300	6503	SO:0001583	missense	128876	exon4			GGTGCCCGTCTGG	AL121753	CCDS13251.1	20q11.22	2011-04-01	2006-03-23	2006-03-23	ENSG00000125998	ENSG00000125998			16121	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 128"""	C20orf128			Standard	NM_178468		Approved	dJ614O4.7	uc021wck.1	Q9BQN1	OTTHUMG00000032332	ENST00000374408.3:c.1862G>A	20.37:g.33874720C>T	ENSP00000363529:p.Arg621Gln	Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	98	38	0.387755	NM_178468	Q14D67|Q5JWN6|Q8N276	Missense_Mutation	SNP	ENST00000374408.3	37	CCDS13251.1	699	0.32005494505494503	352	0.7154471544715447	78	0.2154696132596685	109	0.19055944055944055	160	0.21108179419525067	T	0.005	-2.132108	0.00338	0.629369	0.217558	ENSG00000125998	ENST00000374408	T	0.05580	3.42	4.0	2.85	0.33270	.	0.728390	0.11643	N	0.543528	T	0.00012	0.0000	N	0.00453	-1.485	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.09100	-1.0690	9	0.15952	T	0.53	-25.7861	5.2018	0.15269	0.0:0.0977:0.1806:0.7217	rs2425049;rs3795160;rs56737880;rs2425049	621	Q9BQN1	FA83C_HUMAN	Q	621	ENSP00000363529:R621Q	ENSP00000363529:R621Q	R	-	2	0	FAM83C	33338134	0.088000	0.21588	0.334000	0.25495	0.004000	0.04260	0.401000	0.20948	0.332000	0.23536	-0.361000	0.07541	CGG	C|0.647;T|0.353	0.353	strong		0.627	FAM83C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078854.3		
BIN2	51411	hgsc.bcm.edu	37	12	51695839	51695839	+	Missense_Mutation	SNP	T	T	C	rs143984628		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:51695839T>C	ENST00000267012.4	-	5	434	c.373A>G	c.(373-375)Atg>Gtg	p.M125V	BIN2_ENST00000604560.1_Missense_Mutation_p.M98V|BIN2_ENST00000452142.2_Intron|BIN2_ENST00000544402.1_Missense_Mutation_p.M99V	NM_016293.2	NP_057377.2	Q9UBW5	BIN2_HUMAN	bridging integrator 2	125	BAR. {ECO:0000255|PROSITE- ProRule:PRU00361}.				cell chemotaxis (GO:0060326)|membrane tubulation (GO:0097320)|phagocytosis, engulfment (GO:0006911)|podosome assembly (GO:0071800)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|podosome (GO:0002102)	phospholipid binding (GO:0005543)			NS(2)|breast(1)|endometrium(1)|kidney(4)|large_intestine(4)|lung(12)|ovary(1)|prostate(3)|skin(3)	31						TAGATTTCCATGGTCCTTACA	0.468													T|||	1	0.000199681	0.0	0.0	5008	,	,		19345	0.0		0.001	False		,,,				2504	0.0				p.M125V		Atlas-SNP	.											.	BIN2	58	.	0			c.A373G						PASS	.	T	VAL/MET	0,4406		0,0,2203	152.0	121.0	131.0		373	5.5	1.0	12	dbSNP_134	131	4,8596	3.7+/-12.6	0,4,4296	yes	missense	BIN2	NM_016293.2	21	0,4,6499	CC,CT,TT		0.0465,0.0,0.0308	possibly-damaging	125/566	51695839	4,13002	2203	4300	6503	SO:0001583	missense	51411	exon5			TTTCCATGGTCCT	AF146531	CCDS8811.1	12q13.13	2012-01-23			ENSG00000110934	ENSG00000110934			1053	protein-coding gene	gene with protein product		605936				10903846	Standard	XM_005268957		Approved	BRAP-1	uc001ryg.3	Q9UBW5		ENST00000267012.4:c.373A>G	12.37:g.51695839T>C	ENSP00000267012:p.Met125Val	Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	151	74	0.490066	NM_016293	Q86VV0|Q9NWK4|Q9UKN4	Missense_Mutation	SNP	ENST00000267012.4	37	CCDS8811.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	T	17.72	3.459720	0.63401	0.0	4.65E-4	ENSG00000110934	ENST00000267012;ENST00000544402	T;T	0.58652	0.32;0.32	5.48	5.48	0.80851	BAR (3);	0.000000	0.85682	D	0.000000	T	0.70029	0.3177	L	0.49778	1.585	0.40090	D	0.976241	D;D	0.69078	0.997;0.997	D;D	0.80764	0.99;0.994	T	0.70132	-0.4956	10	0.40728	T	0.16	-11.2107	14.8673	0.70427	0.0:0.0:0.0:1.0	.	99;125	F5H0W4;Q9UBW5	.;BIN2_HUMAN	V	125;99	ENSP00000267012:M125V;ENSP00000445874:M99V	ENSP00000267012:M125V	M	-	1	0	BIN2	49982106	1.000000	0.71417	1.000000	0.80357	0.716000	0.41182	4.698000	0.61789	2.227000	0.72691	0.460000	0.39030	ATG	T|1.000;C|0.000	0.000	strong		0.468	BIN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000469800.1		
FHL3	2275	hgsc.bcm.edu	37	1	38463504	38463504	+	Silent	SNP	C	C	T	rs7366048	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	150	0	0		WXS	Illumina HiSeq	Phase_I	119	119	1	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	
TPST2	8459	hgsc.bcm.edu	37	22	26937321	26937321	+	Silent	SNP	G	G	A	rs17851532	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:26937321G>A	ENST00000338754.4	-	3	546	c.276C>T	c.(274-276)ccC>ccT	p.P92P	TPST2_ENST00000398110.2_Silent_p.P92P|TPST2_ENST00000403880.1_Silent_p.P92P	NM_003595.3	NP_003586.3	O60704	TPST2_HUMAN	tyrosylprotein sulfotransferase 2	92					fusion of sperm to egg plasma membrane (GO:0007342)|peptidyl-tyrosine sulfation (GO:0006478)|prevention of polyspermy (GO:0060468)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	protein-tyrosine sulfotransferase activity (GO:0008476)			central_nervous_system(1)|large_intestine(1)|lung(5)	7						AGCGCACCTCGGGGTGCGCGT	0.677													G|||	151	0.0301518	0.0106	0.036	5008	,	,		17400	0.0		0.1034	False		,,,				2504	0.0082				p.P92P		Atlas-SNP	.											.	TPST2	23	.	0			c.C276T						PASS	.	G	,	74,4324		3,68,2128	37.0	29.0	32.0		276,276	-10.2	0.9	22	dbSNP_123	32	781,7809		41,699,3555	no	coding-synonymous,coding-synonymous	TPST2	NM_001008566.1,NM_003595.3	,	44,767,5683	AA,AG,GG		9.092,1.6826,6.583	,	92/378,92/378	26937321	855,12133	2199	4295	6494	SO:0001819	synonymous_variant	8459	exon3			CACCTCGGGGTGC	AF049891	CCDS13839.1	22q12.1	2012-12-13			ENSG00000128294	ENSG00000128294	2.8.2.20	"""Sulfotransferases, membrane-bound"""	12021	protein-coding gene	gene with protein product	"""transport and golgi organization 13 homolog B (Drosophila)"""	603126				9736702, 9733778	Standard	NM_003595		Approved	TANGO13B	uc003acx.3	O60704	OTTHUMG00000150987	ENST00000338754.4:c.276C>T	22.37:g.26937321G>A		Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	33	16	0.484848	NM_001008566	B3KQA7|Q6FI98|Q9H0V4	Silent	SNP	ENST00000338754.4	37	CCDS13839.1																																																																																			G|0.946;A|0.054	0.054	strong		0.677	TPST2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320820.3	NM_003595	
CHAT	1103	hgsc.bcm.edu	37	10	50824117	50824117	+	Intron	SNP	G	G	A	rs1880676	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:50824117G>A	ENST00000337653.2	+	2	439				CHAT_ENST00000395562.2_Missense_Mutation_p.D7N|CHAT_ENST00000455728.2_Intron|CHAT_ENST00000395559.2_Intron|CHAT_ENST00000339797.1_Intron|CHAT_ENST00000460699.1_Intron|CHAT_ENST00000351556.3_Intron	NM_001142929.1|NM_020549.4	NP_001136401.1|NP_065574	P28329	CLAT_HUMAN	choline O-acetyltransferase						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)	GGAATGCAGAGATGAAGCACT	0.502													G|||	809	0.161542	0.0061	0.1686	5008	,	,		23013	0.1716		0.2316	False		,,,				2504	0.2843				p.D7N		Atlas-SNP	.											CHAT_ENST00000395562,NS,meningioma,0,1	CHAT	162	1	0			c.G19A						PASS	.	G	,ASN/ASP,,,,,	157,2979		6,145,1417	205.0	171.0	181.0		,19,,,,,	3.2	0.0	10	dbSNP_92	181	1775,5389		221,1333,2028	yes	intron,missense,utr-5,intron,intron,intron,intron	CHAT	NM_001142929.1,NM_001142933.1,NM_001142934.1,NM_020549.4,NM_020984.3,NM_020985.3,NM_020986.3	,23,,,,,	227,1478,3445	AA,AG,GG		24.7767,5.0064,18.7573	,,,,,,	,7/667,,,,,	50824117	1932,8368	1568	3582	5150	SO:0001627	intron_variant	1103	exon2			TGCAGAGATGAAG	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.287-431G>A	10.37:g.50824117G>A		Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	157	82	0.522293	NM_001142933	A2BDF4|A2BDF5|Q16488|Q9BQ23|Q9BQ35|Q9BQE1	Missense_Mutation	SNP	ENST00000337653.2	37	CCDS7232.1	334	0.15293040293040294	5	0.01016260162601626	77	0.212707182320442	89	0.1555944055944056	163	0.21503957783641162	G	13.30	2.197365	0.38806	0.050064	0.247767	ENSG00000070748	ENST00000395562	D	0.85088	-1.94	3.16	3.16	0.36331	.	.	.	.	.	T	0.00109	0.0003	.	.	.	0.36813	P	0.11398900000000001	.	.	.	.	.	.	T	0.00984	-1.1491	5	0.87932	D	0	.	10.0691	0.42322	0.0:0.0:1.0:0.0	rs1880676;rs56499801;rs59491670;rs1880676	.	.	.	N	7	ENSP00000378929:D7N	ENSP00000378929:D7N	D	+	1	0	CHAT	50494123	0.004000	0.15560	0.013000	0.15412	0.005000	0.04900	1.413000	0.34725	2.090000	0.63153	0.655000	0.94253	GAT	G|0.836;A|0.164	0.164	strong		0.502	CHAT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047997.1	NM_020549	
SRP72	6731	hgsc.bcm.edu	37	4	57367891	57367891	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:57367891G>T	ENST00000342756.5	+	19	2601	c.1880G>T	c.(1879-1881)aGa>aTa	p.R627I	SRP72_ENST00000510663.1_Missense_Mutation_p.R566I	NM_006947.3	NP_008878.3	O76094	SRP72_HUMAN	signal recognition particle 72kDa	627					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)					ACCTCCCCAAGACCTGGCAGT	0.458																																					p.R627I		Atlas-SNP	.											.	SRP72	59	.	0			c.G1880T						PASS	.						57.0	55.0	56.0					4																	57367891		2203	4300	6503	SO:0001583	missense	6731	exon19			CCCCAAGACCTGG	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.1880G>T	4.37:g.57367891G>T	ENSP00000342181:p.Arg627Ile	Somatic	243	0	0		WXS	Illumina HiSeq	Phase_I	198	43	0.217172	NM_006947	G5E9Z8|Q7Z3C0	Missense_Mutation	SNP	ENST00000342756.5	37	CCDS3506.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	23.6|23.6	4.441168|4.441168	0.83993|0.83993	.|.	.|.	ENSG00000174780|ENSG00000174780	ENST00000537129|ENST00000342756;ENST00000510663	.|T;T	.|0.78481	.|-1.13;-1.18	5.8|5.8	5.8|5.8	0.92144|0.92144	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.87273|0.87273	0.6136|0.6136	M|M	0.69823|0.69823	2.125|2.125	0.80722|0.80722	D|D	1|1	.|D;D	.|0.89917	.|1.0;0.998	.|D;P	.|0.76575	.|0.988;0.896	D|D	0.85985|0.85985	0.1485|0.1485	6|10	0.56958|0.41790	D|T	0.05|0.15	.|.	17.5488|17.5488	0.87870|0.87870	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|566;627	.|G5E9Z8;O76094	.|.;SRP72_HUMAN	Y|I	571|627;566	.|ENSP00000342181:R627I;ENSP00000424576:R566I	ENSP00000445887:D571Y|ENSP00000342181:R627I	D|R	+|+	1|2	0|0	SRP72|SRP72	57062648|57062648	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	6.292000|6.292000	0.72725|0.72725	2.743000|2.743000	0.94032|0.94032	0.455000|0.455000	0.32223|0.32223	GAC|AGA	.	.	none		0.458	SRP72-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250782.7		
ACLY	47	hgsc.bcm.edu	37	17	40065774	40065774	+	Missense_Mutation	SNP	T	T	G	rs2304497	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:40065774T>G	ENST00000352035.2	-	5	655	c.525A>C	c.(523-525)gaA>gaC	p.E175D	ACLY_ENST00000393896.2_Missense_Mutation_p.E175D|ACLY_ENST00000537919.1_Intron|ACLY_ENST00000353196.1_Missense_Mutation_p.E175D|ACLY_ENST00000590151.1_Missense_Mutation_p.E175D	NM_001096.2	NP_001087.2	P53396	ACLY_HUMAN	ATP citrate lyase	175	ATP-grasp.		E -> D (in dbSNP:rs2304497). {ECO:0000269|PubMed:1371749, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:9116495}.		ATP catabolic process (GO:0006200)|cellular carbohydrate metabolic process (GO:0044262)|cellular lipid metabolic process (GO:0044255)|citrate metabolic process (GO:0006101)|coenzyme A metabolic process (GO:0015936)|energy reserve metabolic process (GO:0006112)|lipid biosynthetic process (GO:0008610)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|positive regulation of cellular metabolic process (GO:0031325)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	citrate lyase complex (GO:0009346)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATP citrate synthase activity (GO:0003878)|cofactor binding (GO:0048037)|metal ion binding (GO:0046872)|succinate-CoA ligase (ADP-forming) activity (GO:0004775)		NTN1/ACLY(2)	breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(5)|lung(4)|ovary(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	28		Breast(137;0.000143)				CTTTCTTGTCTTCAGGGGCGT	0.562													T|||	471	0.0940495	0.1089	0.0519	5008	,	,		19799	0.0605		0.1143	False		,,,				2504	0.1176				p.E175D	Colon(64;807 1396 15971 30971)	Atlas-SNP	.											.	ACLY	85	.	0			c.A525C						PASS	.	T	ASP/GLU,ASP/GLU	423,3983	207.8+/-229.1	24,375,1804	117.0	103.0	108.0		525,525	-7.4	0.0	17	dbSNP_100	108	949,7651	208.6+/-250.0	53,843,3404	yes	missense,missense	ACLY	NM_001096.2,NM_198830.1	45,45	77,1218,5208	GG,GT,TT		11.0349,9.6005,10.549	benign,benign	175/1102,175/1092	40065774	1372,11634	2203	4300	6503	SO:0001583	missense	47	exon5			CTTGTCTTCAGGG	X64330	CCDS11412.1, CCDS11413.1	17q21.2	2010-04-27			ENSG00000131473	ENSG00000131473	2.3.3.8		115	protein-coding gene	gene with protein product	"""ATP citrate synthase"""	108728				1371749, 8088842	Standard	NM_001096		Approved	ATPCL, CLATP, ACL	uc002hyg.3	P53396	OTTHUMG00000133507	ENST00000352035.2:c.525A>C	17.37:g.40065774T>G	ENSP00000253792:p.Glu175Asp	Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	159	83	0.522013	NM_001096	B4DIM0|B4E3P0|Q13037|Q9BRL0	Missense_Mutation	SNP	ENST00000352035.2	37	CCDS11412.1	201	0.09203296703296704	52	0.10569105691056911	22	0.06077348066298342	39	0.06818181818181818	88	0.11609498680738786	T	4.556	0.103286	0.08731	0.096005	0.110349	ENSG00000131473	ENST00000352035;ENST00000401700;ENST00000353196;ENST00000393896	T;T;T	0.69685	-0.42;-0.42;-0.42	5.21	-7.37	0.01412	ATP-grasp fold, subdomain 2 (1);ATP-grasp fold, succinyl-CoA synthetase-type (1);	0.761108	0.12996	N	0.422079	T	0.00412	0.0013	N	0.04090	-0.28	0.52099	P	5.999999999994898E-5	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.11518	-1.0584	9	0.11485	T	0.65	.	5.2134	0.15329	0.0861:0.4929:0.1735:0.2476	rs2304497;rs17584309;rs56642660;rs58904106;rs2304497	229;175;175	E7ENH9;G3XAI4;P53396	.;.;ACLY_HUMAN	D	175;229;175;175	ENSP00000253792:E175D;ENSP00000345398:E175D;ENSP00000377474:E175D	ENSP00000253792:E175D	E	-	3	2	ACLY	37319300	0.000000	0.05858	0.026000	0.17262	0.606000	0.37113	-1.122000	0.03267	-0.986000	0.03498	-0.371000	0.07208	GAA	T|0.896;G|0.104	0.104	strong		0.562	ACLY-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257465.1	NM_001096	
MUC20	200958	hgsc.bcm.edu	37	3	195453329	195453329	+	Silent	SNP	C	C	A	rs73203946	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195453329C>A	ENST00000447234.2	+	2	1981	c.1855C>A	c.(1855-1857)Cga>Aga	p.R619R	MUC20_ENST00000436408.1_Silent_p.R619R|MUC20_ENST00000445522.2_Silent_p.R584R|MUC20_ENST00000320736.6_Silent_p.R448R	NM_001282506.1	NP_001269435.1	Q8N307	MUC20_HUMAN	mucin 20, cell surface associated	619	Involved in oligomerization.|Thr-rich.				activation of MAPK activity (GO:0000187)|cellular protein metabolic process (GO:0044267)|hepatocyte growth factor receptor signaling pathway (GO:0048012)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein homooligomerization (GO:0051260)	basal plasma membrane (GO:0009925)|cell projection (GO:0042995)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)		p.R619*(2)|p.R430*(1)		NS(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(4)|skin(4)|stomach(3)|upper_aerodigestive_tract(1)	23	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)	Lung NSC(153;0.191)	Epithelial(36;1e-21)|all cancers(36;9.02e-20)|OV - Ovarian serous cystadenocarcinoma(49;1.6e-18)|Lung(62;0.000104)|LUSC - Lung squamous cell carcinoma(58;0.000128)	GBM - Glioblastoma multiforme(46;1.66e-05)		CAACAGCAGCCGAGGGACGAA	0.622																																					p.R448R		Atlas-SNP	.											MUC20_ENST00000381954,NS,carcinoma,0,5	MUC20	84	5	3	Substitution - Nonsense(3)	lung(2)|upper_aerodigestive_tract(1)	c.C1342A						scavenged	.	C	,	105,4095		0,105,1995	78.0	89.0	86.0		1237,1342	-0.5	0.0	3	dbSNP_130	86	415,8035		0,415,3810	no	coding-synonymous,coding-synonymous	MUC20	NM_001098516.1,NM_152673.2	,	0,520,5805	AA,AC,CC		4.9112,2.5,4.1107	,	413/504,448/539	195453329	520,12130	2100	4225	6325	SO:0001819	synonymous_variant	200958	exon3			AGCAGCCGAGGGA	AB037780	CCDS63877.1	3q29	2008-08-07	2006-03-14		ENSG00000176945	ENSG00000176945		"""Mucins"""	23282	protein-coding gene	gene with protein product		610360				14565953	Standard	NM_001282506		Approved	FLJ14408, KIAA1359	uc010hzo.3	Q8N307	OTTHUMG00000155823	ENST00000447234.2:c.1855C>A	3.37:g.195453329C>A		Somatic	136	1	0.00735294		WXS	Illumina HiSeq	Phase_I	129	43	0.333333	NM_152673	Q6UX97|Q76I83|Q76I85|Q86ST8|Q8NBY6|Q96KA1|Q9P2I8	Silent	SNP	ENST00000447234.2	37		70	0.03205128205128205	12	0.024390243902439025	11	0.03038674033149171	0	0.0	47	0.06200527704485488	C	4.199	0.035688	0.08148	0.025	0.049112	ENSG00000176945	ENST00000423938	.	.	.	4.83	-0.468	0.12146	.	.	.	.	.	T	0.01940	0.0061	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.17107	-1.0380	4	.	.	.	4.3371	0.8336	0.01135	0.3206:0.3364:0.1565:0.1865	.	.	.	.	Q	30	.	.	P	+	2	0	MUC20	196939000	0.001000	0.12720	0.001000	0.08648	0.005000	0.04900	-0.013000	0.12678	0.057000	0.16193	0.655000	0.94253	CCG	C|0.967;A|0.033	0.033	strong		0.622	MUC20-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000341835.1	NM_152673	
PRICKLE4	29964	hgsc.bcm.edu	37	6	41754576	41754576	+	Silent	SNP	C	C	T	rs9381093	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:41754576C>T	ENST00000394260.1	+	5	744	c.744C>T	c.(742-744)ctC>ctT	p.L248L	TOMM6_ENST00000398884.3_5'Flank|PRICKLE4_ENST00000394263.1_Silent_p.L288L|TOMM6_ENST00000398881.3_5'Flank|PRICKLE4_ENST00000458694.1_Silent_p.L288L			Q2TBC4	PRIC4_HUMAN	prickle homolog 4 (Drosophila)	248				L -> LL (in Ref. 5; AAI10460). {ECO:0000305}.		nucleus (GO:0005634)	zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)	13	Ovarian(28;0.0355)|Colorectal(47;0.121)		Epithelial(12;8.38e-05)|STAD - Stomach adenocarcinoma(11;0.000204)|Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)			GAACACTCCTCGCTGCTGCCG	0.637											OREG0017435	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	2812	0.561502	0.3419	0.6945	5008	,	,		13973	0.8304		0.7535	False		,,,				2504	0.2894				p.L288L		Atlas-SNP	.											.	PRICKLE4	29	.	0			c.C864T						PASS	.						76.0	74.0	74.0					6																	41754576		2201	4300	6501	SO:0001819	synonymous_variant	29964	exon8			ACTCCTCGCTGCT	AF216754	CCDS34449.1	6p21.1	2010-08-05	2007-09-18	2007-09-18	ENSG00000124593	ENSG00000124593			16805	protein-coding gene	gene with protein product		611389	"""chromosome 6 open reading frame 49"""	C6orf49		15702247	Standard	NM_013397		Approved	OEBT, DKFZp761H221	uc011duf.1	Q2TBC4	OTTHUMG00000014685	ENST00000394260.1:c.744C>T	6.37:g.41754576C>T		Somatic	68	0	0	903	WXS	Illumina HiSeq	Phase_I	55	33	0.6	NM_013397	A2A3M0|A6PVU1|B3KQ15|Q5T3D4|Q9NSV1	Silent	SNP	ENST00000394260.1	37																																																																																				C|0.588;T|0.412	0.412	strong		0.637	PRICKLE4-007	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000303948.1	NM_013397	
INO80D	54891	hgsc.bcm.edu	37	2	206911228	206911228	+	Splice_Site	SNP	G	G	A	rs2909111	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:206911228G>A	ENST00000403263.1	-	5	1477	c.1073C>T	c.(1072-1074)gCg>gTg	p.A358V		NM_017759.4	NP_060229.3	Q53TQ3	IN80D_HUMAN	INO80 complex subunit D	358			A -> V (in dbSNP:rs2909111). {ECO:0000269|PubMed:14702039}.		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						GAAGACTTACGCATGTCTTTG	0.512													G|||	1955	0.390375	0.236	0.3242	5008	,	,		15885	0.4792		0.3439	False		,,,				2504	0.6022				p.A358V		Atlas-SNP	.											.	INO80D	134	.	0			c.C1073T						PASS	.	G	VAL/ALA	864,2874		98,668,1103	72.0	69.0	70.0		1073	-1.7	1.0	2	dbSNP_101	70	2939,5251		540,1859,1696	yes	missense-near-splice	INO80D	NM_017759.4	64	638,2527,2799	AA,AG,GG		35.8852,23.114,31.883	benign	358/1028	206911228	3803,8125	1869	4095	5964	SO:0001630	splice_region_variant	54891	exon5			ACTTACGCATGTC		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.1073+1C>T	2.37:g.206911228G>A		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	49	25	0.510204	NM_017759	B3KU68|B9EG77|Q6PJC6|Q6PJU1|Q6PKA1|Q9NXD5	Missense_Mutation	SNP	ENST00000403263.1	37	CCDS46500.1	807	0.3695054945054945	136	0.2764227642276423	123	0.3397790055248619	289	0.5052447552447552	259	0.341688654353562	G	13.70	2.316205	0.40996	0.23114	0.358852	ENSG00000114933	ENST00000403263;ENST00000233270;ENST00000424117	T;T	0.42513	0.97;0.97	5.54	-1.7	0.08159	.	0.628168	0.17112	N	0.186596	T	0.00012	0.0000	N	0.08118	0	0.44825	P	0.0021640000000000548	B	0.06786	0.001	B	0.01281	0.0	T	0.46925	-0.9156	8	.	.	.	.	4.9832	0.14176	0.5002:0.0:0.265:0.2348	rs2909111;rs52835029;rs60630711;rs2909111	358	Q53TQ3-2	.	V	358;358;253	ENSP00000384198:A358V;ENSP00000402369:A253V	.	A	-	2	0	INO80D	206619473	0.181000	0.23161	0.984000	0.44739	0.769000	0.43574	-0.045000	0.12003	-0.190000	0.10465	0.655000	0.94253	GCG	G|0.629;A|0.371	0.371	strong		0.512	INO80D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336459.1	NM_017759	Missense_Mutation
EOGT	285203	hgsc.bcm.edu	37	3	69054341	69054341	+	Silent	SNP	T	T	C	rs6781612	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:69054341T>C	ENST00000383701.3	-	7	1207	c.465A>G	c.(463-465)agA>agG	p.R155R	EOGT_ENST00000540764.1_Silent_p.R54R|EOGT_ENST00000540955.1_5'UTR|EOGT_ENST00000295571.5_Silent_p.R155R	NM_001278689.1	NP_001265618.1	Q5NDL2	EOGT_HUMAN	EGF domain-specific O-linked N-acetylglucosamine (GlcNAc) transferase	155					protein O-linked glycosylation (GO:0006493)	endoplasmic reticulum (GO:0005783)	protein N-acetylglucosaminyltransferase activity (GO:0016262)										GATTGGTTGCTCTGCAGTACT	0.353													T|||	1918	0.382987	0.2995	0.3804	5008	,	,		18700	0.5169		0.2873	False		,,,				2504	0.4581				p.R155R		Atlas-SNP	.											.	.	.	.	0			c.A465G						PASS	.	T		1341,3065	444.1+/-347.2	216,909,1078	124.0	124.0	124.0		465	3.7	1.0	3	dbSNP_116	124	2393,6207	398.5+/-346.1	349,1695,2256	no	coding-synonymous	C3orf64	NM_173654.1		565,2604,3334	CC,CT,TT		27.8256,30.4358,28.7098		155/444	69054341	3734,9272	2203	4300	6503	SO:0001819	synonymous_variant	285203	exon7			GGTTGCTCTGCAG	AK091089	CCDS2908.1, CCDS63684.1	3p14.1	2013-10-11	2012-05-21	2012-05-21	ENSG00000163378	ENSG00000163378	2.4.1.255		28526	protein-coding gene	gene with protein product	"""AER61 glycosyltransferase"""	614789	"""chromosome 3 open reading frame 64"""	C3orf64		22310717	Standard	NM_001278689		Approved	AER61, FLJ33770	uc003dnk.3	Q5NDL2	OTTHUMG00000156279	ENST00000383701.3:c.465A>G	3.37:g.69054341T>C		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	57	24	0.421053	NM_173654	A8K2U1|B4DFH5|L7X1M5|Q6MZY0|Q6P985|Q6ZTV0	Silent	SNP	ENST00000383701.3	37																																																																																				T|0.701;C|0.299	0.299	strong		0.353	EOGT-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000343722.1	NM_173654	
HSP90B1	7184	hgsc.bcm.edu	37	12	104341103	104341103	+	Silent	SNP	C	C	T	rs7645	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:104341103C>T	ENST00000299767.5	+	17	2459	c.2277C>T	c.(2275-2277)ccC>ccT	p.P759P	C12orf73_ENST00000543740.2_5'Flank	NM_003299.2	NP_003290.1	P14625	ENPL_HUMAN	heat shock protein 90kDa beta (Grp94), member 1	759					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)	aagaagagcccgaagaagaac	0.383													C|||	2285	0.45627	0.6362	0.4582	5008	,	,		19219	0.4692		0.336	False		,,,				2504	0.3221				p.P759P		Atlas-SNP	.											.	HSP90B1	72	.	0			c.C2277T						PASS	.	C		2585,1821	637.6+/-396.8	766,1053,384	124.0	131.0	129.0		2277	-5.9	0.9	12	dbSNP_52	129	2771,5829	437.2+/-358.5	446,1879,1975	no	coding-synonymous	HSP90B1	NM_003299.1		1212,2932,2359	TT,TC,CC		32.2209,41.33,41.181		759/804	104341103	5356,7650	2203	4300	6503	SO:0001819	synonymous_variant	7184	exon17			AGAGCCCGAAGAA	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.2277C>T	12.37:g.104341103C>T		Somatic	195	0	0		WXS	Illumina HiSeq	Phase_I	186	101	0.543011	NM_003299	Q96A97	Silent	SNP	ENST00000299767.5	37	CCDS9094.1	981	0.4491758241758242	311	0.6321138211382114	154	0.425414364640884	266	0.46503496503496505	250	0.32981530343007914	C	8.541	0.873248	0.17322	0.5867	0.322209	ENSG00000166598	ENST00000550595	T	0.09445	2.98	4.5	-5.92	0.02261	.	0.123738	0.56097	D	0.000037	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999378523	.	.	.	.	.	.	T	0.32348	-0.9910	6	0.51188	T	0.08	.	5.3475	0.16018	0.3908:0.1407:0.0:0.4685	rs7645;rs1131448;rs1185171;rs17161899;rs7645	.	.	.	L	110	ENSP00000450215:P110L	ENSP00000450215:P110L	P	+	2	0	HSP90B1	102865233	0.011000	0.17503	0.888000	0.34837	0.890000	0.51754	-2.780000	0.00773	-1.182000	0.02727	-0.150000	0.13652	CCG	C|0.550;T|0.450	0.450	strong		0.383	HSP90B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407349.1	NM_003299	
QPCTL	54814	hgsc.bcm.edu	37	19	46206262	46206262	+	Silent	SNP	G	G	A	rs17850756	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:46206262G>A	ENST00000012049.5	+	7	1325	c.1104G>A	c.(1102-1104)ttG>ttA	p.L368L	QPCTL_ENST00000366382.4_Silent_p.L274L	NM_017659.3	NP_060129.2	Q9NXS2	QPCTL_HUMAN	glutaminyl-peptide cyclotransferase-like	368					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)	p.L368L(1)		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)		TACACAACTTGTGCCGCATTC	0.612													G|||	1178	0.235224	0.2163	0.1744	5008	,	,		18926	0.2133		0.2853	False		,,,				2504	0.2751				p.L368L		Atlas-SNP	.											QPCTL,NS,carcinoma,0,1	QPCTL	24	1	1	Substitution - coding silent(1)	stomach(1)	c.G1104A						PASS	.	G	,	973,3433	366.4+/-317.8	114,745,1344	171.0	125.0	140.0		822,1104	-8.7	0.8	19	dbSNP_123	140	2781,5819	441.0+/-359.7	472,1837,1991	no	coding-synonymous,coding-synonymous	QPCTL	NM_001163377.1,NM_017659.3	,	586,2582,3335	AA,AG,GG		32.3372,22.0835,28.8636	,	274/289,368/383	46206262	3754,9252	2203	4300	6503	SO:0001819	synonymous_variant	54814	exon7			CAACTTGTGCCGC	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.1104G>A	19.37:g.46206262G>A		Somatic	201	0	0		WXS	Illumina HiSeq	Phase_I	228	125	0.548246	NM_017659	Q53HE4|Q96F74	Silent	SNP	ENST00000012049.5	37	CCDS12672.1																																																																																			G|0.727;A|0.273	0.273	strong		0.612	QPCTL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459656.1	NM_017659	
CD96	10225	hgsc.bcm.edu	37	3	111286403	111286403	+	Missense_Mutation	SNP	T	T	C	rs147832650	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:111286403T>C	ENST00000283285.5	+	3	583	c.452T>C	c.(451-453)aTa>aCa	p.I151T	CD96_ENST00000438817.2_Missense_Mutation_p.I151T|CD96_ENST00000352690.4_Missense_Mutation_p.I151T	NM_198196.2	NP_937839.1	P40200	TACT_HUMAN	CD96 molecule	151					cell adhesion (GO:0007155)|immune response (GO:0006955)|regulation of immune response (GO:0050776)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(4)|liver(2)|lung(14)|skin(5)	35						AACCATACGATAGAAATAGAG	0.348									Opitz Trigonocephaly syndrome																												p.I151T		Atlas-SNP	.											.	CD96	75	.	0			c.T452C						PASS	.	T	THR/ILE,THR/ILE	0,4406		0,0,2203	99.0	90.0	93.0		452,452	4.2	1.0	3	dbSNP_134	93	4,8596	3.7+/-12.6	0,4,4296	yes	missense,missense	CD96	NM_005816.4,NM_198196.2	89,89	0,4,6499	CC,CT,TT		0.0465,0.0,0.0308	possibly-damaging,possibly-damaging	151/570,151/586	111286403	4,13002	2203	4300	6503	SO:0001583	missense	10225	exon3	Familial Cancer Database	C syndrome, Trigonocephaly syndrome	ATACGATAGAAAT	M88282	CCDS2958.1, CCDS2959.1	3p13-q13.2	2013-01-11	2006-03-28		ENSG00000153283	ENSG00000153283		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	16892	protein-coding gene	gene with protein product		606037	"""CD96 antigen"""			1313846	Standard	XR_241462		Approved	TACTILE	uc003dxx.3	P40200	OTTHUMG00000159275	ENST00000283285.5:c.452T>C	3.37:g.111286403T>C	ENSP00000283285:p.Ile151Thr	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	72	43	0.597222	NM_005816	Q5JPB3	Missense_Mutation	SNP	ENST00000283285.5	37	CCDS2959.1	.	.	.	.	.	.	.	.	.	.	T	13.03	2.115390	0.37339	0.0	4.65E-4	ENSG00000153283	ENST00000352690;ENST00000283285;ENST00000438817	T;T;T	0.66995	1.6;-0.24;1.6	5.37	4.19	0.49359	Immunoglobulin subtype (1);	0.297277	0.29587	N	0.011726	T	0.59432	0.2193	L	0.27053	0.805	0.29717	N	0.838913	P;P;P;P	0.51351	0.906;0.944;0.906;0.906	B;P;B;B	0.50617	0.444;0.646;0.444;0.444	T	0.60667	-0.7218	10	0.87932	D	0	-14.79	8.037	0.30499	0.0:0.0921:0.0:0.9079	.	151;151;151;151	E9PEJ1;P40200-2;P40200;Q8WUE2	.;.;TACT_HUMAN;.	T	151	ENSP00000342040:I151T;ENSP00000283285:I151T;ENSP00000389801:I151T	ENSP00000283285:I151T	I	+	2	0	CD96	112769093	1.000000	0.71417	1.000000	0.80357	0.827000	0.46813	1.420000	0.34804	2.262000	0.75019	0.528000	0.53228	ATA	T|1.000;C|0.000	0.000	strong		0.348	CD96-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000354312.2		
BIRC6	57448	hgsc.bcm.edu	37	2	32740138	32740138	+	Silent	SNP	T	T	C	rs34757266	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:32740138T>C	ENST00000421745.2	+	55	10784	c.10650T>C	c.(10648-10650)tgT>tgC	p.C3550C		NM_016252.3	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat containing 6	3550					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)			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)					GCTCAATGTGTCACGTACACC	0.398													T|||	177	0.0353435	0.0045	0.0663	5008	,	,		18142	0.0		0.1093	False		,,,				2504	0.0153				p.C3550C	Pancreas(94;175 1509 16028 18060 45422)	Atlas-SNP	.											.	BIRC6	838	.	0			c.T10650C						PASS	.	T		101,4305	80.9+/-119.3	0,101,2102	114.0	112.0	113.0		10650	0.4	1.0	2	dbSNP_126	113	983,7617	212.5+/-252.8	55,873,3372	no	coding-synonymous	BIRC6	NM_016252.3		55,974,5474	CC,CT,TT		11.4302,2.2923,8.3346		3550/4858	32740138	1084,11922	2203	4300	6503	SO:0001819	synonymous_variant	57448	exon55			AATGTGTCACGTA	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.10650T>C	2.37:g.32740138T>C		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	97	39	0.402062	NM_016252	Q9ULD1	Silent	SNP	ENST00000421745.2	37	CCDS33175.2																																																																																			T|0.927;C|0.073	0.073	strong		0.398	BIRC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318769.3	NM_016252	
DZANK1	55184	hgsc.bcm.edu	37	20	18395988	18395988	+	Missense_Mutation	SNP	C	C	T	rs6035037	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:18395988C>T	ENST00000358866.6	-	10	1082	c.1060G>A	c.(1060-1062)Ggc>Agc	p.G354S	DZANK1_ENST00000329494.5_Missense_Mutation_p.G356S|DZANK1_ENST00000262547.5_Missense_Mutation_p.G354S|DZANK1_ENST00000357236.4_Missense_Mutation_p.G240S|DZANK1_ENST00000487128.1_5'UTR			Q9NVP4	DZAN1_HUMAN	double zinc ribbon and ankyrin repeat domains 1	354							zinc ion binding (GO:0008270)			NS(1)|cervix(1)|endometrium(2)|large_intestine(5)|lung(10)	19						CCACACCAGCCGCAGAAGGAC	0.562													C|||	1251	0.2498	0.1573	0.2983	5008	,	,		15727	0.1696		0.3151	False		,,,				2504	0.3558				p.G354S		Atlas-SNP	.											DZANK1,NS,carcinoma,0,2	DZANK1	65	2	0			c.G1060A						PASS	.	C	SER/GLY	643,3185		54,535,1325	77.0	87.0	84.0		1060	3.5	1.0	20	dbSNP_114	84	2529,5711		368,1793,1959	yes	missense	DZANK1	NM_001099407.1	56	422,2328,3284	TT,TC,CC		30.6917,16.7973,26.2844	benign	354/753	18395988	3172,8896	1914	4120	6034	SO:0001583	missense	55184	exon11			ACCAGCCGCAGAA	AK001462	CCDS46582.1	20p11.23	2013-01-11	2011-10-03	2011-10-03	ENSG00000089091	ENSG00000089091		"""Ankyrin repeat domain containing"""	15858	protein-coding gene	gene with protein product	"""ankyrin repeat domain 64"""		"""chromosome 20 open reading frame 12"""	C20orf84, C20orf12			Standard	NM_001099407		Approved	FLJ10600, dJ568F9.2, FLJ30892, bA189K21.8, ANKRD64	uc002wqq.4	Q9NVP4	OTTHUMG00000031968	ENST00000358866.6:c.1060G>A	20.37:g.18395988C>T	ENSP00000351734:p.Gly354Ser	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	55	23	0.418182	NM_001099407	B7ZLZ4|Q4F7X1|Q5QPD9|Q5QPE0|Q68DN8|Q6ZMX9|Q96NF0|Q9H1E0|Q9H442	Missense_Mutation	SNP	ENST00000358866.6	37	CCDS46582.1	515	0.2358058608058608	77	0.1565040650406504	98	0.27071823204419887	104	0.18181818181818182	236	0.3113456464379947	C	14.53	2.562631	0.45694	0.167973	0.306917	ENSG00000089091	ENST00000377630;ENST00000262547;ENST00000329494;ENST00000414623;ENST00000357236	T;T;T;T	0.61627	0.26;0.09;0.76;0.21	5.57	3.54	0.40534	.	0.634496	0.17261	N	0.180784	T	0.00012	0.0000	N	0.10972	0.075	0.50467	P	1.2199999999995548E-4	B;B;B	0.32031	0.267;0.352;0.063	B;B;B	0.24848	0.056;0.048;0.004	T	0.25467	-1.0131	9	0.46703	T	0.11	-6.1428	8.6331	0.33930	0.0:0.7597:0.1522:0.0881	rs6035037;rs17204022;rs52820643;rs61438457;rs6035037	373;240;354	B7Z631;Q9NVP4-4;Q9NVP4	.;.;DZAN1_HUMAN	S	181;354;356;180;240	ENSP00000366857:G181S;ENSP00000262547:G354S;ENSP00000328866:G356S;ENSP00000349774:G240S	ENSP00000262547:G354S	G	-	1	0	C20orf12	18343988	0.998000	0.40836	0.980000	0.43619	0.858000	0.48976	3.120000	0.50430	0.619000	0.30197	0.313000	0.20887	GGC	C|0.764;T|0.236	0.236	strong		0.562	DZANK1-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000471926.1	NM_001099407	
AIMP1	9255	hgsc.bcm.edu	37	4	107246190	107246190	+	Silent	SNP	G	G	C	rs11544777	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:107246190G>C	ENST00000442366.1	+	2	76	c.24G>C	c.(22-24)ctG>ctC	p.L8L	AIMP1_ENST00000358008.3_Silent_p.L8L|AIMP1_ENST00000394701.4_Silent_p.L32L	NM_001142415.1	NP_001135887.1	Q12904	AIMP1_HUMAN	aminoacyl tRNA synthetase complex-interacting multifunctional protein 1	8	Required for fibroblast proliferation.				angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|chemotaxis (GO:0006935)|gene expression (GO:0010467)|glucose metabolic process (GO:0006006)|inflammatory response (GO:0006954)|leukocyte migration (GO:0050900)|negative regulation of endothelial cell proliferation (GO:0001937)|response to wounding (GO:0009611)|signal transduction (GO:0007165)|tRNA aminoacylation for protein translation (GO:0006418)	aminoacyl-tRNA synthetase multienzyme complex (GO:0017101)|cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)	cytokine activity (GO:0005125)|protein homodimerization activity (GO:0042803)|tRNA binding (GO:0000049)			breast(1)|endometrium(2)|kidney(1)|lung(5)|skin(1)|urinary_tract(1)	11						ATGCTGTTCTGAAGAGACTGG	0.338													G|||	89	0.0177716	0.0045	0.0173	5008	,	,		15705	0.0		0.0646	False		,,,				2504	0.0061				p.L32L		Atlas-SNP	.											.	AIMP1	20	.	0			c.G96C						PASS	.	G	,,	54,4352	53.6+/-89.4	0,54,2149	59.0	59.0	59.0		24,96,24	1.1	1.0	4	dbSNP_120	59	555,8045	151.0+/-205.8	12,531,3757	no	coding-synonymous,coding-synonymous,coding-synonymous	AIMP1	NM_001142415.1,NM_001142416.1,NM_004757.3	,,	12,585,5906	CC,CG,GG		6.4535,1.2256,4.6825	,,	8/313,32/337,8/313	107246190	609,12397	2203	4300	6503	SO:0001819	synonymous_variant	9255	exon2			TGTTCTGAAGAGA	U10117	CCDS3674.1, CCDS47121.1	4q24	2009-05-20	2009-05-20	2009-05-20	ENSG00000164022	ENSG00000164022			10648	protein-coding gene	gene with protein product	"""EMAP II"", ""ARS-interacting multifunctional protein 1"""	603605	"""small inducible cytokine subfamily E, member 1 (endothelial monocyte-activating)"""	SCYE1		7929199, 7545917	Standard	NM_004757		Approved	EMAPII, EMAP-2, p43	uc011cfg.2	Q12904	OTTHUMG00000131217	ENST00000442366.1:c.24G>C	4.37:g.107246190G>C		Somatic	354	0	0		WXS	Illumina HiSeq	Phase_I	279	149	0.53405	NM_001142416	B3KTR2|B4E1S7|Q6FG28|Q96CQ9	Silent	SNP	ENST00000442366.1	37	CCDS3674.1																																																																																			G|0.962;C|0.038	0.038	strong		0.338	AIMP1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253961.1	NM_004757	
FARSA	2193	hgsc.bcm.edu	37	19	13041558	13041558	+	Silent	SNP	G	G	A	rs373756496		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:13041558G>A	ENST00000314606.4	-	2	171	c.153C>T	c.(151-153)atC>atT	p.I51I	CTC-425F1.2_ENST00000592636.1_RNA|FARSA_ENST00000588025.1_Silent_p.I91I|FARSA_ENST00000423140.2_Silent_p.I51I	NM_004461.2	NP_004452.1	Q9Y285	SYFA_HUMAN	phenylalanyl-tRNA synthetase, alpha subunit	51					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)	GTTCAGCCTCGATGACCTAGA	0.622																																					p.I51I		Atlas-SNP	.											.	FARSA	46	.	0			c.C153T						PASS	.	G		1,4405	2.1+/-5.4	0,1,2202	44.0	46.0	45.0		153	-6.0	0.9	19		45	0,8600		0,0,4300	no	coding-synonymous	FARSA	NM_004461.2		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		51/509	13041558	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	2193	exon2			AGCCTCGATGACC	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.153C>T	19.37:g.13041558G>A		Somatic	23	0	0		WXS	Illumina HiSeq	Phase_I	14	9	0.642857	NM_004461	B4E363|Q9NSD8|Q9Y4W8	Silent	SNP	ENST00000314606.4	37	CCDS12287.1																																																																																			.	.	weak		0.622	FARSA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451935.1	NM_004461	
FAM170B	170370	hgsc.bcm.edu	37	10	50339962	50339962	+	Missense_Mutation	SNP	A	A	T	rs75297145	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:50339962A>T	ENST00000311787.5	-	2	637	c.548T>A	c.(547-549)cTg>cAg	p.L183Q	FAM170B-AS1_ENST00000443389.1_RNA|FAM170B-AS1_ENST00000435809.1_RNA|FAM170B-AS1_ENST00000442525.1_RNA	NM_001164484.1	NP_001157956.1	A6NMN3	F170B_HUMAN	family with sequence similarity 170, member B	183										central_nervous_system(1)|endometrium(1)|skin(1)	3						GCAGCACTCCAGCAGGTCTAT	0.652													A|||	442	0.0882588	0.0144	0.1095	5008	,	,		16806	0.003		0.1938	False		,,,				2504	0.1524				p.L183Q		Atlas-SNP	.											.	FAM170B	20	.	0			c.T548A						PASS	.	A	GLN/LEU	55,1329		1,53,638	21.0	23.0	23.0		548	1.9	0.8	10	dbSNP_132	23	662,2520		71,520,1000	no	missense	FAM170B	NM_001164484.1	113	72,573,1638	TT,TA,AA		20.8045,3.974,15.703	benign	183/284	50339962	717,3849	692	1591	2283	SO:0001583	missense	170370	exon2			CACTCCAGCAGGT		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.548T>A	10.37:g.50339962A>T	ENSP00000308292:p.Leu183Gln	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	41	20	0.487805	NM_001164484	Q86WY6|Q8N6K8	Missense_Mutation	SNP	ENST00000311787.5	37	CCDS53536.1	199	0.09111721611721611	9	0.018292682926829267	35	0.09668508287292818	0	0.0	155	0.20448548812664907	A	8.876	0.950364	0.18431	0.03974	0.208045	ENSG00000172538	ENST00000311787	T	0.32515	1.45	5.73	1.93	0.25924	.	0.862135	0.09814	N	0.752387	T	0.00012	0.0000	L	0.54323	1.7	0.80722	P	0.0	B	0.25955	0.138	B	0.21708	0.036	T	0.22103	-1.0226	9	0.51188	T	0.08	-13.7362	2.8237	0.05479	0.6126:0.0:0.2004:0.1869	.	183	A6NMN3	F170B_HUMAN	Q	183	ENSP00000308292:L183Q	ENSP00000308292:L183Q	L	-	2	0	FAM170B	50009968	0.000000	0.05858	0.768000	0.31515	0.115000	0.19883	-0.175000	0.09825	1.011000	0.39340	0.491000	0.48974	CTG	A|0.908;T|0.092	0.092	strong		0.652	FAM170B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047974.1	XM_096317	
SLC22A4	6583	hgsc.bcm.edu	37	5	131670546	131670546	+	Silent	SNP	C	C	G	rs272879	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:131670546C>G	ENST00000200652.3	+	7	1356	c.1182C>G	c.(1180-1182)acC>acG	p.T394T	AC034220.3_ENST00000417795.1_RNA|AC034220.3_ENST00000437091.1_RNA	NM_003059.2	NP_003050.2	Q9H015	S22A4_HUMAN	solute carrier family 22 (organic cation/zwitterion transporter), member 4	394					body fluid secretion (GO:0007589)|carnitine metabolic process (GO:0009437)|carnitine transmembrane transport (GO:1902603)|carnitine transport (GO:0015879)|cation transmembrane transport (GO:0098655)|organic cation transport (GO:0015695)|quaternary ammonium group transport (GO:0015697)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)|triglyceride metabolic process (GO:0006641)	apical plasma membrane (GO:0016324)|integral component of plasma membrane (GO:0005887)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|carnitine transmembrane transporter activity (GO:0015226)|cation:cation antiporter activity (GO:0015491)|nucleotide binding (GO:0000166)|PDZ domain binding (GO:0030165)|quaternary ammonium group transmembrane transporter activity (GO:0015651)|secondary active organic cation transmembrane transporter activity (GO:0008513)|symporter activity (GO:0015293)			endometrium(1)|kidney(3)|large_intestine(2)|lung(8)|ovary(1)|urinary_tract(1)	16		all_cancers(142;0.0752)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)		Amiloride(DB00594)|Aminohippurate(DB00345)|Benzylpenicillin(DB01053)|Choline(DB00122)|Cimetidine(DB00501)|Clonidine(DB00575)|Desipramine(DB01151)|Guanidine(DB00536)|Imipramine(DB00458)|Ipratropium bromide(DB00332)|L-Arginine(DB00125)|L-Carnitine(DB00583)|L-Lysine(DB00123)|Levofloxacin(DB01137)|Mepyramine(DB06691)|Nicotine(DB00184)|Ofloxacin(DB01165)|Procainamide(DB01035)|Quinidine(DB00908)|Quinine(DB00468)|Spermine(DB00127)|Testosterone(DB00624)|Tiotropium(DB01409)|Verapamil(DB00661)	TATTGCGAACCCTGCCCAGGC	0.468													C|||	2605	0.520168	0.6778	0.6729	5008	,	,		19922	0.3304		0.5845	False		,,,				2504	0.3282				p.T394T		Atlas-SNP	.											.	SLC22A4	45	.	0			c.C1182G						PASS	.	C		2892,1514	673.2+/-402.8	942,1008,253	208.0	201.0	204.0		1182	-1.1	0.0	5	dbSNP_79	204	5221,3379	641.6+/-399.7	1599,2023,678	no	coding-synonymous	SLC22A4	NM_003059.2		2541,3031,931	GG,GC,CC		39.2907,34.3622,37.6211		394/552	131670546	8113,4893	2203	4300	6503	SO:0001819	synonymous_variant	6583	exon7			GCGAACCCTGCCC	AB007448	CCDS4153.1	5q23.3	2013-07-18	2013-07-18		ENSG00000197208	ENSG00000197208		"""Solute carriers"""	10968	protein-coding gene	gene with protein product		604190	"""solute carrier family 22 (organic cation/ergothioneine transporter), member 4"""			9426230, 15795384	Standard	NM_003059		Approved	OCTN1, MGC34546	uc003kwq.3	Q9H015	OTTHUMG00000059648	ENST00000200652.3:c.1182C>G	5.37:g.131670546C>G		Somatic	256	0	0		WXS	Illumina HiSeq	Phase_I	185	96	0.518919	NM_003059	O14546	Silent	SNP	ENST00000200652.3	37	CCDS4153.1																																																																																			C|0.395;G|0.605	0.605	strong		0.468	SLC22A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132661.1	NM_003059	
ANKRD6	22881	hgsc.bcm.edu	37	6	90340446	90340446	+	Missense_Mutation	SNP	C	C	T	rs61739327	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:90340446C>T	ENST00000522441.1	+	16	2548	c.1907C>T	c.(1906-1908)cCc>cTc	p.P636L	ANKRD6_ENST00000447838.2_Missense_Mutation_p.P631L|LYRM2_ENST00000520441.1_Intron|ANKRD6_ENST00000520793.1_Missense_Mutation_p.P572L|ANKRD6_ENST00000339746.4_Missense_Mutation_p.P636L|ANKRD6_ENST00000369408.5_Missense_Mutation_p.P601L	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	49	0	0		WXS	Illumina HiSeq	Phase_I	42	18	0.428571	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		
NRCAM	4897	hgsc.bcm.edu	37	7	107838464	107838464	+	Silent	SNP	G	G	T	rs381318	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:107838464G>T	ENST00000425651.2	-	11	1286	c.1287C>A	c.(1285-1287)gtC>gtA	p.V429V	NRCAM_ENST00000351718.4_Silent_p.V423V|NRCAM_ENST00000413765.2_Silent_p.V410V|NRCAM_ENST00000379022.4_Silent_p.V429V|NRCAM_ENST00000379024.4_Silent_p.V410V|NRCAM_ENST00000379028.3_Silent_p.V429V	NM_001037132.2	NP_001032209.1	Q92823	NRCAM_HUMAN	neuronal cell adhesion molecule	429	Ig-like 4.				angiogenesis (GO:0001525)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|axonogenesis (GO:0007409)|central nervous system development (GO:0007417)|clustering of voltage-gated sodium channels (GO:0045162)|heterotypic cell-cell adhesion (GO:0034113)|neuron migration (GO:0001764)|neuronal action potential propagation (GO:0019227)|positive regulation of neuron differentiation (GO:0045666)|protein localization (GO:0008104)|regulation of axon extension (GO:0030516)|retinal ganglion cell axon guidance (GO:0031290)|single organismal cell-cell adhesion (GO:0016337)|synapse assembly (GO:0007416)	axon initial segment (GO:0043194)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|synapse (GO:0045202)	ankyrin binding (GO:0030506)			breast(4)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(8)|liver(1)|lung(36)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(4)	65						TGCACTGATAGACTGCACTTG	0.358													T|||	3312	0.661342	0.388	0.7666	5008	,	,		18079	0.88		0.7416	False		,,,				2504	0.6483				p.V429V		Atlas-SNP	.											.	NRCAM	267	.	0			c.C1287A						PASS	.	T	,,,,	1954,2452	619.0+/-393.3	432,1090,681	97.0	86.0	90.0		1287,1287,1230,1230,1269	-7.8	0.4	7	dbSNP_80	90	6204,2396	397.8+/-345.9	2241,1722,337	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NRCAM	NM_001037132.2,NM_001193582.1,NM_001193583.1,NM_001193584.1,NM_005010.4	,,,,	2673,2812,1018	TT,TG,GG		27.8605,44.3486,37.2751	,,,,	429/1305,429/1212,410/1193,410/1181,423/1184	107838464	8158,4848	2203	4300	6503	SO:0001819	synonymous_variant	4897	exon11			CTGATAGACTGCA		CCDS5751.1, CCDS47686.1, CCDS55153.1, CCDS75652.1	7q31	2013-02-11			ENSG00000091129	ENSG00000091129		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	7994	protein-coding gene	gene with protein product	"""NgCAM-related cell adhesion molecule"""	601581				8812479	Standard	NM_001037132		Approved	KIAA0343, Bravo	uc022aka.1	Q92823	OTTHUMG00000154973	ENST00000425651.2:c.1287C>A	7.37:g.107838464G>T		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	75	75	1	NM_001037132	A4D0S3|E9PDA4|O15051|O15179|Q14BM2|Q9UHI3|Q9UHI4	Silent	SNP	ENST00000425651.2	37	CCDS47686.1																																																																																			G|0.350;T|0.650	0.650	strong		0.358	NRCAM-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337942.2	NM_001037132	
MTOR	2475	hgsc.bcm.edu	37	1	11190646	11190646	+	Silent	SNP	G	G	A	rs2275527	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:11190646G>A	ENST00000361445.4	-	39	5629	c.5553C>T	c.(5551-5553)agC>agT	p.S1851S	MTOR_ENST00000376838.1_Silent_p.S56S|MTOR_ENST00000495435.1_5'Flank	NM_004958.3	NP_004949.1	P42345	MTOR_HUMAN	mechanistic target of rapamycin (serine/threonine kinase)	1851	FAT. {ECO:0000255|PROSITE- ProRule:PRU00534}.				cell growth (GO:0016049)|cellular response to hypoxia (GO:0071456)|cellular response to nutrient levels (GO:0031669)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|germ cell development (GO:0007281)|growth (GO:0040007)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|negative regulation of autophagy (GO:0010507)|negative regulation of cell size (GO:0045792)|negative regulation of macroautophagy (GO:0016242)|negative regulation of NFAT protein import into nucleus (GO:0051534)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|phosphatidylinositol-mediated signaling (GO:0048015)|phosphorylation (GO:0016310)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of gene expression (GO:0010628)|positive regulation of lamellipodium assembly (GO:0010592)|positive regulation of lipid biosynthetic process (GO:0046889)|positive regulation of myotube differentiation (GO:0010831)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein catabolic process (GO:0030163)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of carbohydrate utilization (GO:0043610)|regulation of fatty acid beta-oxidation (GO:0031998)|regulation of glycogen biosynthetic process (GO:0005979)|regulation of protein kinase activity (GO:0045859)|regulation of Rac GTPase activity (GO:0032314)|regulation of response to food (GO:0032095)|response to amino acid (GO:0043200)|response to nutrient (GO:0007584)|response to stress (GO:0006950)|ruffle organization (GO:0031529)|signal transduction (GO:0007165)|T cell costimulation (GO:0031295)|TOR signaling (GO:0031929)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endomembrane system (GO:0012505)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|phosphatidylinositol 3-kinase complex (GO:0005942)|PML body (GO:0016605)|TORC1 complex (GO:0031931)|TORC2 complex (GO:0031932)	ATP binding (GO:0005524)|drug binding (GO:0008144)|kinase activity (GO:0016301)|phosphoprotein binding (GO:0051219)|protein serine/threonine kinase activity (GO:0004674)|ribosome binding (GO:0043022)|RNA polymerase III type 1 promoter DNA binding (GO:0001030)|RNA polymerase III type 2 promoter DNA binding (GO:0001031)|RNA polymerase III type 3 promoter DNA binding (GO:0001032)|TFIIIC-class transcription factor binding (GO:0001156)			breast(5)|central_nervous_system(7)|endometrium(20)|kidney(34)|large_intestine(21)|lung(43)|ovary(9)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	149					Everolimus(DB01590)|Pimecrolimus(DB00337)|Sirolimus(DB00877)|Temsirolimus(DB06287)	TCTCGGCCTCGCTCTCACTGT	0.627													G|||	1145	0.228634	0.4486	0.1542	5008	,	,		17004	0.0794		0.2356	False		,,,				2504	0.1309				p.S1851S		Atlas-SNP	.											.	MTOR	327	.	0			c.C5553T						PASS	.	G		1927,2479	549.0+/-377.7	407,1113,683	107.0	88.0	95.0		5553	-5.7	0.9	1	dbSNP_100	95	2052,6548	356.5+/-330.3	249,1554,2497	no	coding-synonymous	MTOR	NM_004958.3		656,2667,3180	AA,AG,GG		23.8605,43.7358,30.5936		1851/2550	11190646	3979,9027	2203	4300	6503	SO:0001819	synonymous_variant	2475	exon39			GGCCTCGCTCTCA	L34075	CCDS127.1	1p36	2014-09-17	2009-05-29	2009-05-29	ENSG00000198793	ENSG00000198793			3942	protein-coding gene	gene with protein product	"""FK506 binding protein 12-rapamycin associated protein 2"", ""rapamycin target protein"", ""FKBP12-rapamycin complex-associated protein 1"", ""FKBP-rapamycin associated protein"", ""rapamycin associated protein FRAP2"", ""dJ576K7.1 (FK506 binding protein 12-rapamycin associated protein 1)"", ""rapamycin and FKBP12 target 1"", ""mammalian target of rapamycin"""	601231	"""FK506 binding protein 12-rapamycin associated protein 1"""	FRAP, FRAP2, FRAP1		8008069, 8660990	Standard	NM_004958		Approved	RAFT1, RAPT1, FLJ44809	uc001asd.3	P42345	OTTHUMG00000002001	ENST00000361445.4:c.5553C>T	1.37:g.11190646G>A		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	105	49	0.466667	NM_004958	Q4LE76|Q5TER1|Q6LE87|Q96QG3|Q9Y4I3	Silent	SNP	ENST00000361445.4	37	CCDS127.1																																																																																			G|0.716;A|0.284	0.284	strong		0.627	MTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005558.1	NM_004958	
WFDC9	259240	hgsc.bcm.edu	37	20	44238741	44238741	+	Missense_Mutation	SNP	T	T	G	rs2245898	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:44238741T>G	ENST00000326000.1	-	3	297	c.80A>C	c.(79-81)aAc>aCc	p.N27T		NM_147198.3	NP_671731.1	Q8NEX5	WFDC9_HUMAN	WAP four-disulfide core domain 9	27			N -> T (in dbSNP:rs2245898).			extracellular region (GO:0005576)		p.N27T(1)		breast(1)|large_intestine(1)|liver(1)|lung(1)|prostate(1)|stomach(1)	6		Myeloproliferative disorder(115;0.0122)				GGGATCTTTGTTCCAGAAGCT	0.522													G|||	1970	0.393371	0.4175	0.3545	5008	,	,		17994	0.4276		0.325	False		,,,				2504	0.4233				p.N27T		Atlas-SNP	.											WFDC9,NS,carcinoma,0,1	WFDC9	10	1	1	Substitution - Missense(1)	stomach(1)	c.A80C						PASS	.	G	THR/ASN	1736,2670	648.1+/-398.7	334,1068,801	111.0	95.0	101.0		80	-6.1	0.0	20	dbSNP_100	101	2822,5778	675.7+/-403.2	487,1848,1965	yes	missense	WFDC9	NM_147198.3	65	821,2916,2766	GG,GT,TT		32.814,39.4008,35.0454	benign	27/90	44238741	4558,8448	2203	4300	6503	SO:0001583	missense	259240	exon3			TCTTTGTTCCAGA	AL031671	CCDS13362.1	20q13.12	2013-01-21			ENSG00000180205	ENSG00000180205		"""WAP four-disulfide core domain containing"""	20380	protein-coding gene	gene with protein product						12206714	Standard	NM_147198		Approved	WAP9, dJ688G8.2	uc002xoy.3	Q8NEX5	OTTHUMG00000046332	ENST00000326000.1:c.80A>C	20.37:g.44238741T>G	ENSP00000320532:p.Asn27Thr	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	78	52	0.666667	NM_147198	Q3MIX6|Q5TGZ8	Missense_Mutation	SNP	ENST00000326000.1	37	CCDS13362.1	857	0.3923992673992674	232	0.4715447154471545	142	0.39226519337016574	245	0.42832167832167833	238	0.31398416886543534	G	1.900	-0.453305	0.04540	0.394008	0.32814	ENSG00000180205	ENST00000326000	T	0.30714	1.52	4.1	-6.08	0.02151	.	3.200970	0.01266	N	0.009333	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.37842	-0.9688	8	0.11485	T	0.65	.	4.1965	0.10445	0.0899:0.1742:0.1313:0.6046	rs2245898;rs52837047;rs60275083;rs2245898	27	Q8NEX5	WFDC9_HUMAN	T	27	ENSP00000320532:N27T	ENSP00000320532:N27T	N	-	2	0	WFDC9	43672155	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.986000	0.01484	-1.726000	0.01370	-1.935000	0.00506	AAC	T|0.626;G|0.374	0.374	strong		0.522	WFDC9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106945.1		
ZNF749	388567	hgsc.bcm.edu	37	19	57955884	57955884	+	Silent	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:57955884C>T	ENST00000334181.4	+	3	1618	c.1368C>T	c.(1366-1368)caC>caT	p.H456H	AC004076.9_ENST00000596831.1_Intron	NM_001023561.2	NP_001018855.2	O43361	ZN749_HUMAN	zinc finger protein 749	456					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.H369H(1)|p.H456H(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)		TAGTTCAGCACCAGAAAATCC	0.423																																					p.H456H		Atlas-SNP	.											ZNF749,NS,carcinoma,0,2	ZNF749	75	2	2	Substitution - coding silent(2)	endometrium(2)	c.C1368T						scavenged	.						93.0	89.0	91.0					19																	57955884		2203	4300	6503	SO:0001819	synonymous_variant	388567	exon3			TCAGCACCAGAAA	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.1368C>T	19.37:g.57955884C>T		Somatic	175	2	0.0114286		WXS	Illumina HiSeq	Phase_I	180	4	0.0222222	NM_001023561		Silent	SNP	ENST00000334181.4	37	CCDS33132.2																																																																																			.	.	none		0.423	ZNF749-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317879.1	NM_001023561	
KRTAP12-2	353323	hgsc.bcm.edu	37	21	46086758	46086758	+	Missense_Mutation	SNP	C	C	T	rs35163632|rs13046903	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:46086758C>T	ENST00000360770.3	-	1	86	c.46G>A	c.(46-48)Gcg>Acg	p.A16T	TSPEAR_ENST00000323084.4_Intron	NM_181684.2	NP_859012.1	P59991	KR122_HUMAN	keratin associated protein 12-2	16	23 X 5 AA approximate repeats.		A -> T (in dbSNP:rs13046903).|A -> V (in dbSNP:rs7275298).			keratin filament (GO:0045095)				central_nervous_system(1)|endometrium(1)|lung(3)	5						GGGCTGGGCGCGCAGCAGGCT	0.672													T|||	3862	0.771166	0.8608	0.7493	5008	,	,		14620	0.6597		0.7624	False		,,,				2504	0.7894				p.A16T		Atlas-SNP	.											.	KRTAP12-2	10	.	0			c.G46A						PASS	.	T	,THR/ALA	3592,684		1530,532,76	22.0	28.0	26.0		,46	-0.9	0.0	21	dbSNP_121	26	5982,2514		2182,1618,448	no	intron,missense	TSPEAR,KRTAP12-2	NM_144991.2,NM_181684.2	,58	3712,2150,524	TT,TC,CC		29.5904,15.9963,25.0391	,benign	,16/147	46086758	9574,3198	2138	4248	6386	SO:0001583	missense	353323	exon1			TGGGCGCGCAGCA	AJ566389	CCDS42965.1	21q22.3	2006-03-13			ENSG00000221864	ENSG00000221864		"""Keratin associated proteins"""	20530	protein-coding gene	gene with protein product							Standard	NM_181684		Approved	KRTAP12.2, KAP12.2	uc002zfu.3	P59991	OTTHUMG00000057636	ENST00000360770.3:c.46G>A	21.37:g.46086758C>T	ENSP00000354001:p.Ala16Thr	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	113	110	0.973451	NM_181684	A6NIS1|A6NMS9|Q0VAS4	Missense_Mutation	SNP	ENST00000360770.3	37	CCDS42965.1	1494	0.6840659340659341	383	0.7784552845528455	258	0.712707182320442	335	0.5856643356643356	518	0.683377308707124	t	7.155	0.584458	0.13749	0.840037	0.704096	ENSG00000221864	ENST00000360770;ENST00000539483	T	0.03004	4.08	2.82	-0.954	0.10359	.	.	.	.	.	T	0.00012	0.0000	N	0.01228	-0.945	0.80722	P	0.0	B	0.09022	0.002	B	0.10450	0.005	T	0.03576	-1.1023	8	0.27785	T	0.31	.	9.9651	0.41719	0.0:0.7218:0.0:0.2782	rs13046903;rs57325043	16	P59991	KR122_HUMAN	T	16	ENSP00000354001:A16T	ENSP00000354001:A16T	A	-	1	0	KRTAP12-2	44911186	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-4.558000	0.00216	-0.448000	0.07128	-1.898000	0.00530	GCG	C|0.313;T|0.687	0.687	strong		0.672	KRTAP12-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128039.1	NM_181684	
WNK3	65267	hgsc.bcm.edu	37	X	54265469	54265469	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:54265469C>T	ENST00000375159.2	-	17	3714	c.3715G>A	c.(3715-3717)Ggt>Agt	p.G1239S	WNK3_ENST00000375169.3_Missense_Mutation_p.G1239S|WNK3_ENST00000354646.2_Missense_Mutation_p.G1239S			Q9BYP7	WNK3_HUMAN	WNK lysine deficient protein kinase 3	1239					intracellular signal transduction (GO:0035556)|negative regulation of apoptotic process (GO:0043066)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of ion transmembrane transporter activity (GO:0032414)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of rubidium ion transmembrane transporter activity (GO:2000688)|positive regulation of rubidium ion transport (GO:2000682)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|positive regulation of sodium ion transport (GO:0010765)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of ion homeostasis (GO:2000021)	adherens junction (GO:0005912)|cytoplasm (GO:0005737)|tight junction (GO:0005923)	ATP binding (GO:0005524)|chloride channel inhibitor activity (GO:0019869)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			autonomic_ganglia(1)|biliary_tract(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|lung(24)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	80						ATGGCTCCACCGCTTGACACA	0.448																																					p.G1239S		Atlas-SNP	.											.	WNK3	218	.	0			c.G3715A						PASS	.						63.0	59.0	60.0					X																	54265469		2203	4300	6503	SO:0001583	missense	65267	exon18			CTCCACCGCTTGA	AJ409088	CCDS14357.1, CCDS35302.1	Xp11.22	2008-05-14	2005-01-19	2005-01-22	ENSG00000196632	ENSG00000196632			14543	protein-coding gene	gene with protein product		300358	"""protein kinase, lysine deficient 3"""	PRKWNK3			Standard	NM_020922		Approved		uc004dtc.2	Q9BYP7	OTTHUMG00000021626	ENST00000375159.2:c.3715G>A	X.37:g.54265469C>T	ENSP00000364301:p.Gly1239Ser	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	50	34	0.68	NM_001002838	B1AKG2|Q5JRC1|Q6JP76|Q8TCX6|Q9HCK6	Missense_Mutation	SNP	ENST00000375159.2	37	CCDS14357.1	.	.	.	.	.	.	.	.	.	.	C	14.27	2.486242	0.44147	.	.	ENSG00000196632	ENST00000375169;ENST00000354646;ENST00000375159	T;T;T	0.72167	-0.44;-0.63;-0.63	5.02	3.2	0.36748	.	0.584613	0.15074	N	0.282037	T	0.65491	0.2696	L	0.27053	0.805	0.19300	N	0.999975	D;D	0.76494	0.999;0.995	P;P	0.58454	0.839;0.492	T	0.53648	-0.8409	10	0.08837	T	0.75	0.202	8.816	0.34996	0.0:0.7647:0.1477:0.0875	.	1239;1239	Q9BYP7-3;Q9BYP7	.;WNK3_HUMAN	S	1239	ENSP00000364312:G1239S;ENSP00000346667:G1239S;ENSP00000364301:G1239S	ENSP00000346667:G1239S	G	-	1	0	WNK3	54282194	0.002000	0.14202	0.507000	0.27676	0.736000	0.42039	0.569000	0.23638	0.342000	0.23796	0.538000	0.68166	GGT	.	.	none		0.448	WNK3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056799.2	NM_020922	
OGDH	4967	hgsc.bcm.edu	37	7	44747578	44747578	+	Missense_Mutation	SNP	G	G	A	rs2070607	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:44747578G>A	ENST00000222673.5	+	23	3094	c.3052G>A	c.(3052-3054)Gtc>Atc	p.V1018I	OGDH_ENST00000444676.1_Missense_Mutation_p.V1033I|OGDH_ENST00000449767.1_Missense_Mutation_p.V1014I|OGDH_ENST00000439616.2_Missense_Mutation_p.V868I|OGDH_ENST00000543843.1_Missense_Mutation_p.V969I|OGDH_ENST00000447398.1_Missense_Mutation_p.V1029I	NM_002541.3	NP_002532.2	Q02218	ODO1_HUMAN	oxoglutarate (alpha-ketoglutarate) dehydrogenase (lipoamide)	1018			V -> I (in dbSNP:rs2070607).		2-oxoglutarate metabolic process (GO:0006103)|cellular metabolic process (GO:0044237)|cellular nitrogen compound metabolic process (GO:0034641)|cerebellar cortex development (GO:0021695)|generation of precursor metabolites and energy (GO:0006091)|glycolytic process (GO:0006096)|hippocampus development (GO:0021766)|lysine catabolic process (GO:0006554)|NADH metabolic process (GO:0006734)|olfactory bulb mitral cell layer development (GO:0061034)|pyramidal neuron development (GO:0021860)|small molecule metabolic process (GO:0044281)|striatum development (GO:0021756)|succinyl-CoA metabolic process (GO:0006104)|tangential migration from the subventricular zone to the olfactory bulb (GO:0022028)|thalamus development (GO:0021794)|tricarboxylic acid cycle (GO:0006099)	mitochondrial matrix (GO:0005759)|mitochondrial membrane (GO:0031966)|mitochondrion (GO:0005739)|oxoglutarate dehydrogenase complex (GO:0045252)	metal ion binding (GO:0046872)|oxoglutarate dehydrogenase (NAD+) activity (GO:0034602)|oxoglutarate dehydrogenase (succinyl-transferring) activity (GO:0004591)|thiamine pyrophosphate binding (GO:0030976)			breast(2)|endometrium(5)|kidney(2)|large_intestine(6)|lung(13)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(4)	36					Valproic Acid(DB00313)	CGACCTGGACGTCTTCAAGAA	0.607													G|||	239	0.0477236	0.0068	0.0519	5008	,	,		20474	0.0823		0.0417	False		,,,				2504	0.0706				p.V1018I		Atlas-SNP	.											.	OGDH	145	.	0			c.G3052A						PASS	.	G	ILE/VAL,ILE/VAL	79,4327	67.6+/-105.2	1,77,2125	99.0	84.0	89.0		3040,3052	4.1	1.0	7	dbSNP_96	89	471,8129	138.6+/-195.4	10,451,3839	yes	missense,missense	OGDH	NM_001165036.1,NM_002541.3	29,29	11,528,5964	AA,AG,GG		5.4767,1.793,4.2288	benign,benign	1014/1020,1018/1024	44747578	550,12456	2203	4300	6503	SO:0001583	missense	4967	exon23			CTGGACGTCTTCA	D10523	CCDS34627.1, CCDS47580.1, CCDS55107.1	7p13-p11.2	2010-11-23			ENSG00000105953	ENSG00000105953	1.2.4.2		8124	protein-coding gene	gene with protein product		613022				8020988, 1542694	Standard	NM_002541		Approved	E1k	uc003tln.3	Q02218	OTTHUMG00000155304	ENST00000222673.5:c.3052G>A	7.37:g.44747578G>A	ENSP00000222673:p.Val1018Ile	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	66	39	0.590909	NM_002541	B4E2U9|D3DVL0|E9PBM1|Q96DD3|Q9UDX0	Missense_Mutation	SNP	ENST00000222673.5	37	CCDS34627.1	102	0.046703296703296704	2	0.0040650406504065045	23	0.06353591160220995	43	0.07517482517482517	34	0.044854881266490766	G	12.10	1.836875	0.32421	0.01793	0.054767	ENSG00000105953	ENST00000439616;ENST00000449767;ENST00000447398;ENST00000444676;ENST00000222673;ENST00000543843	T;T;T;T;T;T	0.11277	2.79;2.79;2.79;2.79;2.79;2.79	5.0	4.12	0.48240	.	0.177074	0.48767	N	0.000161	T	0.00300	0.0009	N	0.08118	0	0.22199	N	0.999291	B;B;B;B;B	0.28291	0.054;0.206;0.016;0.016;0.016	B;B;B;B;B	0.23716	0.03;0.048;0.018;0.018;0.018	T	0.37709	-0.9694	10	0.62326	D	0.03	-24.1192	7.5713	0.27909	0.0788:0.0:0.6464:0.2748	rs2070607;rs2070607	813;868;1014;1029;1018	B4E3E9;E9PFG7;E9PBM1;E9PDF2;Q02218	.;.;.;.;ODO1_HUMAN	I	868;1014;1029;1033;1018;969	ENSP00000398576:V868I;ENSP00000392878:V1014I;ENSP00000388183:V1029I;ENSP00000414662:V1033I;ENSP00000222673:V1018I;ENSP00000443821:V969I	ENSP00000222673:V1018I	V	+	1	0	OGDH	44714103	1.000000	0.71417	1.000000	0.80357	0.206000	0.24218	3.317000	0.51968	1.242000	0.43836	-0.671000	0.03813	GTC	G|0.955;A|0.045	0.045	strong		0.607	OGDH-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000339391.1		
BDKRB2	624	hgsc.bcm.edu	37	14	96703484	96703484	+	Missense_Mutation	SNP	C	C	T	rs1046248	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:96703484C>T	ENST00000306005.3	+	2	236	c.40C>T	c.(40-42)Cgt>Tgt	p.R14C	BDKRB2_ENST00000539359.1_5'UTR|BDKRB2_ENST00000554311.1_Missense_Mutation_p.R14C|BDKRB2_ENST00000542454.2_5'UTR|RP11-404P21.8_ENST00000553811.1_Missense_Mutation_p.R14C	NM_000623.3	NP_000614.1	P30411	BKRB2_HUMAN	bradykinin receptor B2	14			R -> C (in dbSNP:rs1046248). {ECO:0000269|PubMed:7779090, ECO:0000269|Ref.8}.		arachidonic acid secretion (GO:0050482)|blood circulation (GO:0008015)|cell surface receptor signaling pathway (GO:0007166)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)|metabolic process (GO:0008152)|negative regulation of intrinsic apoptotic signaling pathway in response to osmotic stress by p53 class mediator (GO:1902239)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of vascular permeability (GO:0043114)|regulation of vasoconstriction (GO:0019229)|response to salt stress (GO:0009651)|smooth muscle contraction (GO:0006939)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vasoconstriction (GO:0042310)|vasodilation (GO:0042311)	endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	bradykinin receptor activity (GO:0004947)|phosphatidylinositol phospholipase C activity (GO:0004435)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|type 1 angiotensin receptor binding (GO:0031702)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(5)|lung(7)|ovary(3)|skin(1)	24		all_cancers(154;0.0678)|Melanoma(154;0.155)|all_epithelial(191;0.179)		COAD - Colon adenocarcinoma(157;0.226)	Icatibant(DB06196)	TCTGTCTGTTCGTGAGGACTC	0.527													C|||	213	0.0425319	0.056	0.0548	5008	,	,		21774	0.002		0.0865	False		,,,				2504	0.0123				p.R14C		Atlas-SNP	.											.	BDKRB2	56	.	0			c.C40T						PASS	.	C	CYS/ARG	224,4182	133.3+/-169.7	3,218,1982	200.0	159.0	173.0		40	1.8	0.0	14	dbSNP_86	173	839,7761	191.8+/-238.0	51,737,3512	yes	missense	BDKRB2	NM_000623.3	180	54,955,5494	TT,TC,CC		9.7558,5.084,8.1732	probably-damaging	14/392	96703484	1063,11943	2203	4300	6503	SO:0001583	missense	624	exon2			TCTGTTCGTGAGG	S56772	CCDS9942.1	14q32.1-q32.2	2012-08-08				ENSG00000168398		"""GPCR / Class A : Bradykinin receptors"""	1030	protein-coding gene	gene with protein product		113503				7916737	Standard	NM_000623		Approved	BK-2	uc010avm.1	P30411		ENST00000306005.3:c.40C>T	14.37:g.96703484C>T	ENSP00000307713:p.Arg14Cys	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	149	74	0.496644	NM_000623		Missense_Mutation	SNP	ENST00000306005.3	37	CCDS9942.1	120	0.054945054945054944	30	0.06097560975609756	21	0.058011049723756904	0	0.0	69	0.09102902374670185	C	14.42	2.529529	0.44969	0.05084	0.097558	ENSG00000168398;ENSG00000168398;ENSG00000258691	ENST00000554311;ENST00000306005;ENST00000553811	T;T;T	0.72282	-0.64;-0.64;1.69	3.71	1.77	0.24775	.	2.399830	0.01945	N	0.042183	T	0.01592	0.0051	N	0.08118	0	0.80722	P	0.0	P	0.46277	0.875	B	0.32211	0.142	T	0.24404	-1.0161	9	0.40728	T	0.16	.	5.1894	0.15201	0.0:0.7153:0.0:0.2847	rs1046248;rs1800772;rs3186219;rs17191331;rs52804895;rs57649699;rs1046248	14	P30411	BKRB2_HUMAN	C	14	ENSP00000450482:R14C;ENSP00000307713:R14C;ENSP00000450984:R14C	ENSP00000307713:R14C	R	+	1	0	RP11-404P21.8;BDKRB2	95773237	0.014000	0.17966	0.000000	0.03702	0.006000	0.05464	0.961000	0.29267	0.489000	0.27749	0.655000	0.94253	CGT	C|0.933;T|0.067	0.067	strong		0.527	BDKRB2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413294.1		
AGAP6	414189	hgsc.bcm.edu	37	10	51748684	51748684	+	Missense_Mutation	SNP	G	G	A	rs61848260	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	7	0	0		WXS	Illumina HiSeq	Phase_I	5	5	1	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	
MS4A6E	245802	hgsc.bcm.edu	37	11	60102396	60102396	+	Missense_Mutation	SNP	A	A	G	rs2304934	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:60102396A>G	ENST00000300182.4	+	1	93	c.28A>G	c.(28-30)Acc>Gcc	p.T10A		NM_139249.2	NP_640342.1	Q96DS6	M4A6E_HUMAN	membrane-spanning 4-domains, subfamily A, member 6E	10			T -> A (in dbSNP:rs2304934).			integral component of membrane (GO:0016021)				endometrium(2)|kidney(1)|lung(9)|stomach(1)	13						TTCCAATGAGACCATCATAAT	0.453													A|||	1293	0.258187	0.2269	0.4236	5008	,	,		21278	0.255		0.3111	False		,,,				2504	0.1319				p.T10A		Atlas-SNP	.											MS4A6E,NS,carcinoma,-2,1	MS4A6E	22	1	0			c.A28G						PASS	.	A	ALA/THR	1144,3262	407.8+/-334.4	148,848,1207	166.0	147.0	154.0		28	-2.8	0.0	11	dbSNP_100	154	2888,5712	451.6+/-362.7	507,1874,1919	yes	missense	MS4A6E	NM_139249.2	58	655,2722,3126	GG,GA,AA		33.5814,25.9646,31.0011	possibly-damaging	10/148	60102396	4032,8974	2203	4300	6503	SO:0001583	missense	245802	exon1			AATGAGACCATCA	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.28A>G	11.37:g.60102396A>G	ENSP00000300182:p.Thr10Ala	Somatic	198	0	0		WXS	Illumina HiSeq	Phase_I	188	129	0.68617	NM_139249	Q3MIL2|Q8NE56|Q96PG4|Q96PG5	Missense_Mutation	SNP	ENST00000300182.4	37	CCDS7984.1	651	0.2980769230769231	128	0.2601626016260163	127	0.35082872928176795	149	0.26048951048951047	247	0.3258575197889182	A	12.40	1.927607	0.34002	0.259646	0.335814	ENSG00000166926	ENST00000300182	T	0.10573	2.86	2.4	-2.81	0.05805	.	0.910425	0.09394	N	0.808117	T	0.00012	0.0000	M	0.64404	1.975	0.80722	P	0.0	B	0.24576	0.106	B	0.13407	0.009	T	0.47573	-0.9107	9	0.17832	T	0.49	.	2.2381	0.04013	0.3831:0.0:0.1583:0.4586	rs2304934;rs52829083;rs58112568;rs2304934	10	Q96DS6	M4A6E_HUMAN	A	10	ENSP00000300182:T10A	ENSP00000300182:T10A	T	+	1	0	MS4A6E	59858972	0.000000	0.05858	0.002000	0.10522	0.027000	0.11550	-0.268000	0.08607	-0.804000	0.04410	0.254000	0.18369	ACC	A|0.691;G|0.309	0.309	strong		0.453	MS4A6E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394296.1		
PNPO	55163	hgsc.bcm.edu	37	17	46020698	46020698	+	Silent	SNP	C	C	T	rs11079804	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:46020698C>T	ENST00000225573.4	+	2	270	c.165C>T	c.(163-165)tcC>tcT	p.S55S	PNPO_ENST00000544840.1_Silent_p.S55S|AC003665.1_ENST00000411573.2_RNA|AC003665.1_ENST00000585280.1_RNA|AC003665.1_ENST00000451140.2_RNA|RP11-6N17.9_ENST00000582262.1_RNA|PNPO_ENST00000534893.1_Intron|PNPO_ENST00000434554.2_Silent_p.S55S|AC003665.1_ENST00000433001.1_RNA	NM_018129.3	NP_060599.1	Q9NVS9	PNPO_HUMAN	pyridoxamine 5'-phosphate oxidase	55					pyridoxine biosynthetic process (GO:0008615)|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)	FMN binding (GO:0010181)|pyridoxamine-phosphate oxidase activity (GO:0004733)			endometrium(2)|large_intestine(1)|lung(1)|urinary_tract(1)	5						ATCTGACCTCCCTTGACCCAG	0.463													C|||	814	0.16254	0.0537	0.2176	5008	,	,		20122	0.1617		0.162	False		,,,				2504	0.272				p.S55S		Atlas-SNP	.											PNPO,NS,adenoma,0,1	PNPO	18	1	0			c.C165T						PASS	.	C		330,4076	176.6+/-205.7	19,292,1892	140.0	111.0	120.0		165	-3.7	1.0	17	dbSNP_120	120	1469,7131	279.4+/-293.9	137,1195,2968	no	coding-synonymous	PNPO	NM_018129.3		156,1487,4860	TT,TC,CC		17.0814,7.4898,13.8321		55/262	46020698	1799,11207	2203	4300	6503	SO:0001819	synonymous_variant	55163	exon2			GACCTCCCTTGAC	AF468030	CCDS11522.1	17q21.32	2008-11-27	2006-07-12			ENSG00000108439	1.4.3.5		30260	protein-coding gene	gene with protein product		603287	"""pyridoxine 5'-phosphate oxidase"""			9601034, 15182361	Standard	NM_018129		Approved	PDXPO	uc002imo.3	Q9NVS9		ENST00000225573.4:c.165C>T	17.37:g.46020698C>T		Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	170	83	0.488235	NM_018129	B4E0V0|B4E152|B4E1D7|D3DTT9	Silent	SNP	ENST00000225573.4	37	CCDS11522.1																																																																																			C|0.855;T|0.145	0.145	strong		0.463	PNPO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441407.1	NM_018129	
SIRPG	55423	hgsc.bcm.edu	37	20	1616892	1616892	+	Silent	SNP	A	A	G	rs2277760	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:1616892A>G	ENST00000303415.3	-	3	754	c.690T>C	c.(688-690)caT>caC	p.H230H	SIRPG_ENST00000344103.4_Intron|SIRPG_ENST00000381583.2_Silent_p.H230H|RP11-77C3.3_ENST00000437384.1_RNA|SIRPG_ENST00000381580.1_Silent_p.H197H|SIRPG_ENST00000216927.4_Silent_p.H230H|RP11-77C3.3_ENST00000456177.1_RNA	NM_018556.3	NP_061026.2	Q9P1W8	SIRPG_HUMAN	signal-regulatory protein gamma	230	Ig-like C1-type 1.				blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|intracellular signal transduction (GO:0035556)|leukocyte migration (GO:0050900)|negative regulation of cell proliferation (GO:0008285)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of T cell activation (GO:0050870)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(14)|ovary(1)|prostate(2)|stomach(1)	27						GCAAGGTGACATGGGCCACCT	0.632													a|||	1742	0.347843	0.1135	0.2522	5008	,	,		19002	0.6379		0.2495	False		,,,				2504	0.5348				p.H230H		Atlas-SNP	.											.	SIRPG	61	.	0			c.T690C						PASS	.	A	,,	538,3868		38,462,1703	110.0	100.0	104.0		690,690,	-1.8	0.5	20	dbSNP_100	104	2039,6561		248,1543,2509	no	coding-synonymous,coding-synonymous,intron	SIRPG	NM_001039508.1,NM_018556.3,NM_080816.2	,,	286,2005,4212	GG,GA,AA		23.7093,12.2106,19.8139	,,	230/277,230/388,	1616892	2577,10429	2203	4300	6503	SO:0001819	synonymous_variant	55423	exon3			GGTGACATGGGCC	AB042624	CCDS13020.2, CCDS13021.2, CCDS33434.1	20p13	2013-01-11	2006-02-03	2006-02-03	ENSG00000089012	ENSG00000089012		"""Signal-regulatory proteins"", ""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C1-set domain containing"""	15757	protein-coding gene	gene with protein product		605466	"""signal-regulatory protein beta 2"""	SIRPB2		11185750, 16339511	Standard	XM_005260749		Approved	bA77C3.1, SIRP-B2, SIRPgamma, CD172g	uc002wfm.1	Q9P1W8	OTTHUMG00000031680	ENST00000303415.3:c.690T>C	20.37:g.1616892A>G		Somatic	250	0	0		WXS	Illumina HiSeq	Phase_I	266	126	0.473684	NM_001039508	B1AKP6|Q5D051|Q5JV25|Q5MKL4|Q8WWA5|Q9NQK8	Silent	SNP	ENST00000303415.3	37	CCDS13020.2																																																																																			A|0.764;G|0.236	0.236	strong		0.632	SIRPG-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077566.2	NM_018556	
OR8K1	390157	hgsc.bcm.edu	37	11	56113575	56113575	+	Missense_Mutation	SNP	A	A	G	rs10896271	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:56113575A>G	ENST00000279783.2	+	1	155	c.61A>G	c.(61-63)Atg>Gtg	p.M21V		NM_001002907.1	NP_001002907.1	Q8NGG5	OR8K1_HUMAN	olfactory receptor, family 8, subfamily K, member 1	21			M -> V (in dbSNP:rs10896271).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			large_intestine(8)|liver(2)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	33	Esophageal squamous(21;0.00448)					ATTTATTCTCATGGGGATTAC	0.413										HNSCC(65;0.19)			A|||	2308	0.460863	0.2292	0.6052	5008	,	,		18475	0.6438		0.3708	False		,,,				2504	0.5757				p.M21V		Atlas-SNP	.											.	OR8K1	93	.	0			c.A61G						PASS	.	A	VAL/MET	1111,3291	400.4+/-331.6	149,813,1239	99.0	94.0	95.0		61	-4.6	0.0	11	dbSNP_120	95	3193,5399	483.3+/-371.1	616,1961,1719	yes	missense	OR8K1	NM_001002907.1	21	765,2774,2958	GG,GA,AA		37.1625,25.2385,33.123	benign	21/320	56113575	4304,8690	2201	4296	6497	SO:0001583	missense	390157	exon1			ATTCTCATGGGGA	AB065835	CCDS31528.1	11q11	2012-08-09			ENSG00000150261	ENSG00000150261		"""GPCR / Class A : Olfactory receptors"""	14831	protein-coding gene	gene with protein product							Standard	NM_001002907		Approved		uc010rjg.2	Q8NGG5	OTTHUMG00000166858	ENST00000279783.2:c.61A>G	11.37:g.56113575A>G	ENSP00000279783:p.Met21Val	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	88	19	0.215909	NM_001002907	B9EJB1|Q6IFC3|Q96RC1	Missense_Mutation	SNP	ENST00000279783.2	37	CCDS31528.1	963	0.4409340659340659	108	0.21951219512195122	218	0.6022099447513812	368	0.6433566433566433	269	0.3548812664907652	A	8.032	0.761871	0.15914	0.252385	0.371625	ENSG00000150261	ENST00000279783	T	0.00420	7.47	5.18	-4.56	0.03431	.	0.771273	0.11542	N	0.553627	T	0.00012	0.0000	N	0.13327	0.33	0.80722	P	0.0	B	0.12630	0.006	B	0.11329	0.006	T	0.05582	-1.0876	9	0.11794	T	0.64	-2.9812	7.8372	0.29376	0.2343:0.5844:0.0689:0.1124	rs10896271;rs52795616;rs56517428;rs56995399;rs10896271	21	Q8NGG5	OR8K1_HUMAN	V	21	ENSP00000279783:M21V	ENSP00000279783:M21V	M	+	1	0	OR8K1	55870151	0.000000	0.05858	0.020000	0.16555	0.985000	0.73830	-3.088000	0.00610	-0.806000	0.04398	0.448000	0.29417	ATG	A|0.616;G|0.384	0.384	strong		0.413	OR8K1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391605.1	NM_001002907	
OR8B3	390271	hgsc.bcm.edu	37	11	124266927	124266927	+	Silent	SNP	A	A	G	rs142812088		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:124266927A>G	ENST00000354597.3	-	1	337	c.321T>C	c.(319-321)ttT>ttC	p.F107F		NM_001005467.1	NP_001005467.1	Q8NGG8	OR8B3_HUMAN	olfactory receptor, family 8, subfamily B, member 3	107						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			kidney(1)|large_intestine(2)|lung(7)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	14		Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0277)		CAGAGATGACAAAAAAGAGAA	0.388																																					p.F107F		Atlas-SNP	.											OR8B3,NS,carcinoma,0,1	OR8B3	36	1	0			c.T321C						scavenged	.						78.0	76.0	77.0					11																	124266927		2201	4299	6500	SO:0001819	synonymous_variant	390271	exon1			GATGACAAAAAAG	AB065827	CCDS31709.1	11q24.1	2012-08-09			ENSG00000196661	ENSG00000196661		"""GPCR / Class A : Olfactory receptors"""	8472	protein-coding gene	gene with protein product							Standard	NM_001005467		Approved		uc010saj.2	Q8NGG8	OTTHUMG00000165983	ENST00000354597.3:c.321T>C	11.37:g.124266927A>G		Somatic	297	13	0.043771		WXS	Illumina HiSeq	Phase_I	229	17	0.0742358	NM_001005467	Q6IFQ8|Q8NGH1	Silent	SNP	ENST00000354597.3	37	CCDS31709.1																																																																																			A|1.000;G|0.000	0.000	weak		0.388	OR8B3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387291.1	NM_001005467	
ANO2	57101	hgsc.bcm.edu	37	12	6030405	6030405	+	Missense_Mutation	SNP	A	A	G	rs3741903	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:6030405A>G	ENST00000356134.5	-	3	394	c.323T>C	c.(322-324)gTg>gCg	p.V108A	ANO2_ENST00000546188.1_Missense_Mutation_p.V108A|ANO2_ENST00000327087.8_Missense_Mutation_p.V108A	NM_001278596.1	NP_001265525.1	Q9NQ90	ANO2_HUMAN	anoctamin 2, calcium activated chloride channel	112					chloride transmembrane transport (GO:1902476)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	chloride channel complex (GO:0034707)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	intracellular calcium activated chloride channel activity (GO:0005229)			central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(11)|lung(23)|ovary(4)|pancreas(1)|prostate(1)|skin(5)|stomach(3)|upper_aerodigestive_tract(1)	58						GGCCAGGTGCACCCCGCGTTT	0.607													G|||	784	0.15655	0.0386	0.1441	5008	,	,		18430	0.1915		0.2167	False		,,,				2504	0.227				p.V108A		Atlas-SNP	.											.	ANO2	309	.	0			c.T323C						PASS	.	G	ALA/VAL	292,3824		6,280,1772	56.0	57.0	57.0		323	1.4	0.0	12	dbSNP_107	57	1711,6679		180,1351,2664	yes	missense	ANO2	NM_020373.2	64	186,1631,4436	GG,GA,AA		20.3933,7.0943,16.0163	benign	108/999	6030405	2003,10503	2058	4195	6253	SO:0001583	missense	57101	exon3			AGGTGCACCCCGC	AJ272204	CCDS44807.1, CCDS44807.2	12p13.3	2014-04-09	2014-04-09	2008-08-28		ENSG00000047617		"""Ion channels / Chloride channels : Calcium activated : Anoctamins"""	1183	protein-coding gene	gene with protein product	"""transmembrane protein 16B (eight membrane-spanning domains)"""	610109	"""chromosome 12 open reading frame 3"", ""transmembrane protein 16B"", ""anoctamin 2"""	C12orf3, TMEM16B		12739008, 15067359, 24692353	Standard	NM_001278596		Approved		uc001qnm.2	Q9NQ90		ENST00000356134.5:c.323T>C	12.37:g.6030405A>G	ENSP00000348453:p.Val108Ala	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	92	43	0.467391	NM_020373	C4N787|Q9H847	Missense_Mutation	SNP	ENST00000356134.5	37		344	0.1575091575091575	17	0.034552845528455285	62	0.1712707182320442	102	0.17832167832167833	163	0.21503957783641162	G	0	-2.586289	0.00128	0.070943	0.203933	ENSG00000047617	ENST00000327087;ENST00000356134;ENST00000546188;ENST00000541277	T;T;T	0.66638	-0.22;-0.22;-0.22	4.52	1.37	0.22104	.	0.669254	0.14551	N	0.312671	T	0.00012	0.0000	N	0.02315	-0.6	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.10543	-1.0625	9	0.02654	T	1	.	7.1216	0.25448	0.2452:0.1241:0.6307:0.0	rs3741903;rs17786472;rs58403475;rs3741903	108	Q9NQ90-3	.	A	108;108;108;112	ENSP00000314048:V108A;ENSP00000348453:V108A;ENSP00000440981:V108A	ENSP00000314048:V108A	V	-	2	0	ANO2	5900666	0.000000	0.05858	0.002000	0.10522	0.030000	0.12068	0.524000	0.22940	-0.076000	0.12775	-2.318000	0.00253	GTG	A|0.834;G|0.166	0.166	strong		0.607	ANO2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000399019.4	NM_020373	
OXGR1	27199	hgsc.bcm.edu	37	13	97639827	97639827	+	Silent	SNP	T	T	G	rs9300380	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:97639827T>G	ENST00000298440.1	-	4	430	c.187A>C	c.(187-189)Aga>Cga	p.R63R	OXGR1_ENST00000543457.1_Silent_p.R63R	NM_080818.3	NP_543008.3	Q96P68	OXGR1_HUMAN	oxoglutarate (alpha-ketoglutarate) receptor 1	63					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)			NS(1)|large_intestine(1)|lung(9)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	15	all_neural(89;0.0982)|Medulloblastoma(90;0.163)		BRCA - Breast invasive adenocarcinoma(86;0.186)			TTCCAAGGTCTCATTTTGAAA	0.473													G|||	317	0.0632987	0.2118	0.0288	5008	,	,		21471	0.0		0.0169	False		,,,				2504	0.0				p.R63R		Atlas-SNP	.											.	OXGR1	46	.	0			c.A187C						PASS	.	G		815,3591	747.9+/-411.9	74,667,1462	121.0	113.0	116.0		187	3.3	1.0	13	dbSNP_119	116	83,8517	815.3+/-407.0	0,83,4217	no	coding-synonymous	OXGR1	NM_080818.3		74,750,5679	GG,GT,TT		0.9651,18.4975,6.9045		63/338	97639827	898,12108	2203	4300	6503	SO:0001819	synonymous_variant	27199	exon4			AAGGTCTCATTTT	AF411109	CCDS9482.1	13q32.2	2014-04-09	2004-07-08	2004-07-09	ENSG00000165621	ENSG00000165621		"""GPCR / Class A : Orphans"""	4531	protein-coding gene	gene with protein product	"""2-oxoglutarate receptor 1"", ""alpha-ketoglutarate receptor 1"""	606922	"""G protein-coupled receptor 80"""	GPR99, GPR80		15141213, 12098360	Standard	NM_080818		Approved	P2RY15, P2Y15, aKGR	uc001vmx.1	Q96P68	OTTHUMG00000017236	ENST00000298440.1:c.187A>C	13.37:g.97639827T>G		Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	145	71	0.489655	NM_080818	Q5T5A7|Q86TL1	Silent	SNP	ENST00000298440.1	37	CCDS9482.1																																																																																			T|0.939;G|0.061	0.061	strong		0.473	OXGR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045521.3	NM_080818	
PRR21	643905	hgsc.bcm.edu	37	2	240982116	240982116	+	Missense_Mutation	SNP	C	C	A	rs72993513	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:240982116C>A	ENST00000408934.1	-	1	283	c.284G>T	c.(283-285)cGg>cTg	p.R95L		NM_001080835.1	NP_001074304.1	Q8WXC7	PRR21_HUMAN	proline rich 21	95	Pro-rich.									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						GACGAAGGGCCGTGGGTGAAG	0.617													-|||	1424	0.284345	0.357	0.196	5008	,	,		15582	0.2401		0.2823	False		,,,				2504	0.2965				p.R95L		Atlas-SNP	.											.	PRR21	53	.	0			c.G284T						PASS	.						105.0	100.0	102.0					2																	240982116		2135	4263	6398	SO:0001583	missense	643905	exon1			AAGGGCCGTGGGT	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.284G>T	2.37:g.240982116C>A	ENSP00000386166:p.Arg95Leu	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	88	40	0.454545	NM_001080835		Missense_Mutation	SNP	ENST00000408934.1	37	CCDS33417.1	530	0.24267399267399267	149	0.30284552845528456	71	0.19613259668508287	115	0.20104895104895104	195	0.25725593667546176	-	8.811	0.935251	0.18206	.	.	ENSG00000221961	ENST00000408934;ENST00000486799	T;T	0.28454	1.61;1.61	1.79	-2.88	0.05682	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	P	0.41041	0.736	B	0.40256	0.324	T	0.33059	-0.9883	8	0.49607	T	0.09	.	3.7903	0.08718	0.0:0.4733:0.1957:0.331	.	95	Q8WXC7	PRR21_HUMAN	L	95	ENSP00000386166:R95L;ENSP00000418240:R95L	ENSP00000386166:R95L	R	-	2	0	PRR21	240630789	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.289000	0.02780	-0.793000	0.04475	-0.438000	0.05819	CGG	C|0.741;A|0.259	0.259	strong		0.617	PRR21-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001080835	
GPR98	84059	hgsc.bcm.edu	37	5	90016778	90016778	+	Missense_Mutation	SNP	C	C	T	rs114137750	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:90016778C>T	ENST00000405460.2	+	45	9746	c.9650C>T	c.(9649-9651)gCc>gTc	p.A3217V		NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	3217			A -> V (in dbSNP:rs114137750). {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)		ATCGAAGAAGCCAATAGGACC	0.388													C|||	26	0.00519169	0.0015	0.0058	5008	,	,		14853	0.0		0.0189	False		,,,				2504	0.001				p.A3217V		Atlas-SNP	.											.	GPR98	605	.	0			c.C9650T						PASS	.	C	VAL/ALA	9,3789		1,7,1891	182.0	180.0	181.0		9650	5.8	1.0	5	dbSNP_132	181	84,8184		2,80,4052	yes	missense	GPR98	NM_032119.3	64	3,87,5943	TT,TC,CC		1.016,0.237,0.7708	benign	3217/6307	90016778	93,11973	1899	4134	6033	SO:0001583	missense	84059	exon45			AAGAAGCCAATAG	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.9650C>T	5.37:g.90016778C>T	ENSP00000384582:p.Ala3217Val	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	133	83	0.62406	NM_032119	O75171|Q8TF58|Q9H0X5|Q9UL61	Missense_Mutation	SNP	ENST00000405460.2	37	CCDS47246.1	22|22	0.010073260073260074|0.010073260073260074	0|0	0.0|0.0	4|4	0.011049723756906077|0.011049723756906077	0|0	0.0|0.0	18|18	0.023746701846965697|0.023746701846965697	C|C	12.78|12.78	2.039593|2.039593	0.35989|0.35989	0.00237|0.00237	0.01016|0.01016	ENSG00000164199|ENSG00000164199	ENST00000405460;ENST00000296619|ENST00000509621	T|.	0.28069|.	1.63|.	5.76|5.76	5.76|5.76	0.90799|0.90799	.|.	0.339787|.	0.35151|.	N|.	0.003419|.	T|T	0.45478|0.45478	0.1344|0.1344	L|L	0.43152|0.43152	1.355|1.355	0.80722|0.80722	D|D	1|1	P;B|.	0.44006|.	0.824;0.068|.	B;B|.	0.40982|.	0.345;0.014|.	T|T	0.49341|0.49341	-0.8950|-0.8950	10|5	0.59425|.	D|.	0.04|.	.|.	15.4524|15.4524	0.75282|0.75282	0.0:0.8619:0.1381:0.0|0.0:0.8619:0.1381:0.0	.|.	3217;3217|.	E7ETI5;Q8WXG9|.	.;GPR98_HUMAN|.	V|S	3217|783	ENSP00000384582:A3217V|.	ENSP00000296619:A3217V|.	A|P	+|+	2|1	0|0	GPR98|GPR98	90052534|90052534	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.027000|0.027000	0.11550|0.11550	3.420000|3.420000	0.52735|0.52735	2.718000|2.718000	0.92993|0.92993	0.650000|0.650000	0.86243|0.86243	GCC|CCA	C|0.989;T|0.011	0.011	strong		0.388	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119	
OBSCN	84033	hgsc.bcm.edu	37	1	228562350	228562350	+	Silent	SNP	T	T	C	rs72762068	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:228562350T>C	ENST00000422127.1	+	97	22604	c.22560T>C	c.(22558-22560)ctT>ctC	p.L7520L	OBSCN_ENST00000570156.2_Silent_p.L8477L|OBSCN_ENST00000366707.4_Silent_p.L5154L	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	7520	Ig-like 55.				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)				ACTTCCAGCTTCTGACCATCC	0.622													T|||	26	0.00519169	0.0008	0.0101	5008	,	,		19099	0.0		0.0149	False		,,,				2504	0.0031				p.L8477L		Atlas-SNP	.											.	OBSCN	2142	.	0			c.T25431C						PASS	.	T		18,4188		0,18,2085	84.0	94.0	90.0		22560	-6.1	0.9	1	dbSNP_130	90	236,8192		5,226,3983	no	coding-synonymous	OBSCN	NM_001098623.1		5,244,6068	CC,CT,TT		2.8002,0.428,2.0104		7520/7969	228562350	254,12380	2103	4214	6317	SO:0001819	synonymous_variant	84033	exon108			CCAGCTTCTGACC	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.22560T>C	1.37:g.228562350T>C		Somatic	190	0	0		WXS	Illumina HiSeq	Phase_I	139	60	0.431655	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	15	0.006868131868131868	1	0.0020325203252032522	5	0.013812154696132596	0	0.0	9	0.011873350923482849	T	15.09	2.730454	0.48939	0.00428	0.028002	ENSG00000154358	ENST00000441106	.	.	.	5.43	-6.07	0.02158	.	.	.	.	.	T	0.39172	0.1068	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.62515	-0.6838	4	.	.	.	.	16.0231	0.80512	0.0:0.1194:0.7058:0.1748	.	.	.	.	P	2137	.	.	S	+	1	0	OBSCN	226628973	0.002000	0.14202	0.902000	0.35471	0.929000	0.56500	-1.435000	0.02423	-1.252000	0.02491	-0.488000	0.04728	TCT	T|0.989;C|0.011	0.011	strong		0.622	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
UFL1	23376	hgsc.bcm.edu	37	6	96999725	96999725	+	Silent	SNP	C	C	T	rs1127175	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:96999725C>T	ENST00000369278.4	+	17	1977	c.1911C>T	c.(1909-1911)gaC>gaT	p.D637D		NM_015323.4	NP_056138.1	O94874	UFL1_HUMAN	UFM1-specific ligase 1	637					negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein ubiquitination (GO:0031397)|osteoblast differentiation (GO:0001649)|protein ufmylation (GO:0071569)|regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032434)|response to endoplasmic reticulum stress (GO:0034976)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nucleus (GO:0005634)	UFM1 conjugating enzyme activity (GO:0071568)										GCATAGAAGACTTTATTTCTT	0.299													C|||	1636	0.326677	0.326	0.2911	5008	,	,		16341	0.3075		0.3698	False		,,,				2504	0.3282				p.D637D		Atlas-SNP	.											KIAA0776,NS,carcinoma,0,2	.	.	2	0			c.C1911T						PASS	.	C		1470,2934	455.5+/-351.0	239,992,971	86.0	95.0	92.0		1911	-0.4	1.0	6	dbSNP_86	92	2996,5600	455.3+/-363.7	536,1924,1838	no	coding-synonymous	UFL1	NM_015323.4		775,2916,2809	TT,TC,CC		34.8534,33.3787,34.3538		637/795	96999725	4466,8534	2202	4298	6500	SO:0001819	synonymous_variant	23376	exon17			AGAAGACTTTATT	BC036379	CCDS5034.1	6q16.3	2011-08-18	2011-08-18	2011-08-18	ENSG00000014123	ENSG00000014123			23039	protein-coding gene	gene with protein product	"""novel LZAP-binding protein"", ""Regulator of CDK5RAP3 and DDRGK1"""	613372	"""KIAA0776"""	KIAA0776		20018847, 20164180, 20228063, 20531390	Standard	NM_015323		Approved	NLBP, Maxer, RCAD	uc003por.3	O94874	OTTHUMG00000015238	ENST00000369278.4:c.1911C>T	6.37:g.96999725C>T		Somatic	242	1	0.00413223		WXS	Illumina HiSeq	Phase_I	152	150	0.986842	NM_015323	A0PJ53|B4DJ57|C0H5X5|Q8N765|Q9NTQ0	Silent	SNP	ENST00000369278.4	37	CCDS5034.1																																																																																			C|0.662;T|0.338	0.338	strong		0.299	UFL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041557.1	NM_015323	
GZMH	2999	hgsc.bcm.edu	37	14	25076906	25076906	+	Missense_Mutation	SNP	C	C	T	rs20545	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:25076906C>T	ENST00000216338.4	-	3	295	c.251G>A	c.(250-252)cGg>cAg	p.R84Q	GZMH_ENST00000557220.2_Intron|RP11-104E19.1_ENST00000557736.1_RNA|RP11-104E19.1_ENST00000555300.1_RNA|GZMH_ENST00000382548.4_Missense_Mutation_p.R84Q	NM_033423.4	NP_219491.1	P20718	GRAH_HUMAN	granzyme H (cathepsin G-like 2, protein h-CCPX)	84	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.		R -> Q (in dbSNP:rs20545).		apoptotic process (GO:0006915)|cytolysis (GO:0019835)	membrane (GO:0016020)	serine-type endopeptidase activity (GO:0004252)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(6)|ovary(1)|prostate(1)|skin(1)	12				GBM - Glioblastoma multiforme(265;0.0267)		CTGCTGGGTCCGCTCCTGTTC	0.532													C|||	288	0.057508	0.0303	0.0591	5008	,	,		20942	0.0506		0.1004	False		,,,				2504	0.0562				p.R84Q		Atlas-SNP	.											GZMH,colon,carcinoma,-1,1	GZMH	24	1	0			c.G251A						PASS	.	C	GLN/ARG	221,4185	134.1+/-170.4	3,215,1985	193.0	183.0	187.0		251	-8.6	0.0	14	dbSNP_67	187	770,7830	182.0+/-230.6	39,692,3569	no	missense	GZMH	NM_033423.3	43	42,907,5554	TT,TC,CC		8.9535,5.0159,7.6196	benign	84/247	25076906	991,12015	2203	4300	6503	SO:0001583	missense	2999	exon3			TGGGTCCGCTCCT	M72150	CCDS9632.1, CCDS59243.1	14q11.2	2003-10-20			ENSG00000100450	ENSG00000100450			4710	protein-coding gene	gene with protein product		116831		CTSGL2		2049336	Standard	NM_033423		Approved	CGL-2, CCP-X, CTLA1, CSP-C	uc001wpr.2	P20718	OTTHUMG00000140185	ENST00000216338.4:c.251G>A	14.37:g.25076906C>T	ENSP00000216338:p.Arg84Gln	Somatic	310	0	0		WXS	Illumina HiSeq	Phase_I	326	168	0.515337	NM_033423	G3V2C5|Q6XGZ0|Q6XGZ1	Missense_Mutation	SNP	ENST00000216338.4	37	CCDS9632.1	139	0.06364468864468864	12	0.024390243902439025	22	0.06077348066298342	29	0.050699300699300696	76	0.10026385224274406	c	11.71	1.719133	0.30503	0.050159	0.089535	ENSG00000100450	ENST00000216338;ENST00000382548	D;D	0.88277	-2.36;-2.36	4.7	-8.63	0.00878	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	.	.	.	.	T	0.08223	0.0205	N	0.25094	0.71	0.09310	N	1	B;B	0.30021	0.265;0.043	B;B	0.22753	0.041;0.017	T	0.47368	-0.9123	9	0.40728	T	0.16	.	10.5759	0.45227	0.0:0.1572:0.1088:0.734	rs52812266	84;84	Q6XGZ1;P20718	.;GRAH_HUMAN	Q	84	ENSP00000216338:R84Q;ENSP00000371988:R84Q	ENSP00000216338:R84Q	R	-	2	0	GZMH	24146746	0.000000	0.05858	0.045000	0.18777	0.058000	0.15608	-5.829000	0.00096	-1.513000	0.01789	-0.367000	0.07326	CGG	.	.	weak		0.532	GZMH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276538.2	NM_033423	
LACTB	114294	hgsc.bcm.edu	37	15	63433766	63433766	+	Missense_Mutation	SNP	G	G	A	rs2729835	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:63433766G>A	ENST00000261893.4	+	6	1478	c.1406G>A	c.(1405-1407)aGg>aAg	p.R469K	RPS27L_ENST00000559763.1_Intron	NM_032857.3	NP_116246.2	P83111	LACTB_HUMAN	lactamase, beta	469			R -> K (in dbSNP:rs2729835).			cytoplasm (GO:0005737)|mitochondrion (GO:0005739)	hydrolase activity (GO:0016787)			NS(1)|breast(1)|kidney(1)|large_intestine(3)|lung(3)|prostate(1)|skin(1)|stomach(1)	12						GTTGTGGAAAGGAAACAAACG	0.478													A|||	3555	0.709864	0.5719	0.5749	5008	,	,		20216	0.9891		0.6571	False		,,,				2504	0.7587				p.R469K	Melanoma(85;443 1381 6215 27308 35583)	Atlas-SNP	.											.	LACTB	29	.	0			c.G1406A						PASS	.	A	LYS/ARG	2671,1735	519.1+/-369.9	814,1043,346	79.0	68.0	72.0		1406	4.5	1.0	15	dbSNP_100	72	5765,2835	445.9+/-361.1	1939,1887,474	yes	missense	LACTB	NM_032857.3	26	2753,2930,820	AA,AG,GG		32.9651,39.3781,35.1376	benign	469/548	63433766	8436,4570	2203	4300	6503	SO:0001583	missense	114294	exon6			TGGAAAGGAAACA	AK027808	CCDS10182.1, CCDS45275.1	15q22.1	2012-11-14	2001-12-12	2001-12-14	ENSG00000103642	ENSG00000103642		"""Mitochondrial ribosomal proteins / large subunits"""	16468	protein-coding gene	gene with protein product		608440	"""mitochondrial ribosomal protein L56"""	MRPL56		11707067	Standard	NM_032857		Approved	FLJ14902	uc002alw.3	P83111	OTTHUMG00000132807	ENST00000261893.4:c.1406G>A	15.37:g.63433766G>A	ENSP00000261893:p.Arg469Lys	Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	150	147	0.98	NM_032857	P83096	Missense_Mutation	SNP	ENST00000261893.4	37	CCDS10182.1	1531	0.701007326007326	269	0.5467479674796748	206	0.569060773480663	565	0.9877622377622378	491	0.6477572559366754	A	2.811	-0.246928	0.05867	0.606219	0.670349	ENSG00000103642	ENST00000261893	T	0.38401	1.14	5.64	4.49	0.54785	Beta-lactamase/transpeptidase-like (2);Beta-lactamase-related (1);	0.085601	0.85682	N	0.000000	T	0.00012	0.0000	N	0.00583	-1.355	0.09310	P	1.0	B	0.02656	0.0	B	0.01281	0.0	T	0.40869	-0.9540	9	0.02654	T	1	-9.8763	8.2279	0.31579	0.7965:0.1341:0.0694:0.0	rs2729835;rs52825345;rs56641643;rs57282529;rs2729835	469	P83111	LACTB_HUMAN	K	469	ENSP00000261893:R469K	ENSP00000261893:R469K	R	+	2	0	LACTB	61220819	1.000000	0.71417	1.000000	0.80357	0.529000	0.34654	3.610000	0.54125	0.486000	0.27676	-0.360000	0.07572	AGG	G|0.329;A|0.671	0.671	strong		0.478	LACTB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256224.1	NM_032857	
PDDC1	347862	hgsc.bcm.edu	37	11	771034	771034	+	Silent	SNP	A	A	G	rs7930569	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:771034A>G	ENST00000319863.8	-	7	636	c.615T>C	c.(613-615)acT>acC	p.T205T	PDDC1_ENST00000397472.2_Intron|PDDC1_ENST00000529966.1_5'UTR|PDDC1_ENST00000526325.1_Intron|PDDC1_ENST00000524550.1_Silent_p.T169T|PDDC1_ENST00000442059.2_Silent_p.T155T	NM_182612.2	NP_872418.1	Q8NB37	PDDC1_HUMAN	Parkinson disease 7 domain containing 1	205						extracellular vesicular exosome (GO:0070062)				kidney(1)|lung(3)|urinary_tract(1)	5		all_cancers(49;1.13e-08)|all_epithelial(84;2.95e-05)|Breast(177;0.000286)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.159)|all_lung(207;0.198)		all cancers(45;3.66e-26)|Epithelial(43;2.43e-25)|OV - Ovarian serous cystadenocarcinoma(40;1.33e-19)|BRCA - Breast invasive adenocarcinoma(625;4.29e-05)|Lung(200;0.0582)|LUSC - Lung squamous cell carcinoma(625;0.0703)		CGGCCGGGACAGTGGAGCTGG	0.657													a|||	2166	0.432508	0.3064	0.6037	5008	,	,		15794	0.5605		0.4433	False		,,,				2504	0.3384				p.T205T		Atlas-SNP	.											.	PDDC1	16	.	0			c.T615C						PASS	.	A		1507,2897	469.0+/-355.3	269,969,964	54.0	53.0	53.0		615	-9.1	0.1	11	dbSNP_116	53	4227,4373	563.8+/-388.2	1042,2143,1115	no	coding-synonymous	PDDC1	NM_182612.2		1311,3112,2079	GG,GA,AA		49.1512,34.2189,44.0941		205/221	771034	5734,7270	2202	4300	6502	SO:0001819	synonymous_variant	347862	exon7			CGGGACAGTGGAG	AK128653	CCDS7713.1	11p15.5	2005-10-26			ENSG00000177225	ENSG00000177225			26616	protein-coding gene	gene with protein product							Standard	XM_005252898		Approved	FLJ34283	uc001lrc.3	Q8NB37	OTTHUMG00000133315	ENST00000319863.8:c.615T>C	11.37:g.771034A>G		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	102	22	0.215686	NM_182612	B7ZKW5|Q2NL76|Q6ZQY0|Q8NAE0	Silent	SNP	ENST00000319863.8	37	CCDS7713.1	1074	0.49175824175824173	157	0.31910569105691056	210	0.580110497237569	363	0.6346153846153846	344	0.45382585751978893	A	7.217	0.596652	0.13875	0.342189	0.491512	ENSG00000177225	ENST00000465313	.	.	.	4.55	-9.09	0.00717	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.99999999833531	.	.	.	.	.	.	T	0.34875	-0.9811	3	.	.	.	.	4.568	0.12196	0.2365:0.0898:0.4958:0.1779	rs7930569;rs58747471;rs7930569	.	.	.	R	56	.	.	C	-	1	0	PDDC1	761034	0.000000	0.05858	0.114000	0.21550	0.679000	0.39708	-1.347000	0.02632	-2.024000	0.00936	-0.464000	0.05259	TGT	A|0.556;G|0.444	0.444	strong		0.657	PDDC1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258051.2	NM_182612	
COL6A5	256076	hgsc.bcm.edu	37	3	130110550	130110550	+	Missense_Mutation	SNP	A	A	G	rs11917356	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:130110550A>G	ENST00000432398.2	+	7	3439	c.2945A>G	c.(2944-2946)gAt>gGt	p.D982G	COL6A5_ENST00000265379.6_Missense_Mutation_p.D982G	NM_153264.5	NP_694996.5	A8TX70	CO6A5_HUMAN	collagen, type VI, alpha 5	982	Nonhelical region.|VWFA 5. {ECO:0000255|PROSITE- ProRule:PRU00219}.		D -> G (in dbSNP:rs11917356).		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						AAACTGAAAGATGTTTTCACA	0.363													A|||	1878	0.375	0.3956	0.4323	5008	,	,		22915	0.625		0.1531	False		,,,				2504	0.2771				p.D982G		Atlas-SNP	.											.	COL6A5	205	.	0			c.A2945G						PASS	.	A	GLY/ASP	513,871		90,333,269	21.0	17.0	18.0		2945	5.6	0.7	3	dbSNP_120	18	546,2636		50,446,1095	yes	missense	COL6A5	NM_153264.5	94	140,779,1364	GG,GA,AA		17.159,37.0665,23.1932	benign	982/2527	130110550	1059,3507	692	1591	2283	SO:0001583	missense	256076	exon7			TGAAAGATGTTTT	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.2945A>G	3.37:g.130110550A>G	ENSP00000390895:p.Asp982Gly	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	69	44	0.637681	NM_153264	A9J6L2|A9J6L4|A9J6L6|A9J6L7|A9J6M0|A9J6M1|A9J6M2|B5MEA7|Q6ZW26|Q8NA36	Missense_Mutation	SNP	ENST00000432398.2	37		776	0.3553113553113553	167	0.3394308943089431	136	0.3756906077348066	368	0.6433566433566433	105	0.13852242744063326	A	2.536	-0.307453	0.05458	0.370665	0.17159	ENSG00000172752	ENST00000432398;ENST00000265379	D;D	0.83914	-1.78;-1.78	5.62	5.62	0.85841	.	.	.	.	.	T	0.00012	0.0000	L	0.36672	1.1	0.58432	P	6.999999999979245E-6	B	0.17268	0.021	B	0.17722	0.019	T	0.41945	-0.9480	8	0.15499	T	0.54	.	14.8008	0.69913	1.0:0.0:0.0:0.0	rs11917356;rs56803892;rs11917356	982	A8TX70-2	.	G	982	ENSP00000390895:D982G;ENSP00000265379:D982G	ENSP00000265379:D982G	D	+	2	0	COL6A5	131593240	0.999000	0.42202	0.656000	0.29637	0.014000	0.08584	5.293000	0.65680	2.143000	0.66587	0.477000	0.44152	GAT	A|0.624;G|0.376	0.376	strong		0.363	COL6A5-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_153264	
NQO2	4835	hgsc.bcm.edu	37	6	3015790	3015790	+	Silent	SNP	A	A	G	rs1049115	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:3015790A>G	ENST00000338130.2	+	8	1042	c.330A>G	c.(328-330)ccA>ccG	p.P110P	NQO2_ENST00000380455.4_Silent_p.P110P|NQO2_ENST00000380454.4_Intron|NQO2_ENST00000380441.1_Intron|NQO2_ENST00000380430.1_Silent_p.P110P			P16083	NQO2_HUMAN	NAD(P)H dehydrogenase, quinone 2	110					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)	TCAGCGTGCCAGCCATCCTGA	0.547													G|||	3793	0.757388	0.9312	0.7334	5008	,	,		20068	0.6538		0.7147	False		,,,				2504	0.6902				p.P110P		Atlas-SNP	.											.	NQO2	21	.	0			c.A330G						PASS	.	G		3961,445	213.8+/-233.3	1781,399,23	86.0	81.0	83.0		330	-6.9	0.1	6	dbSNP_86	83	6178,2422	402.2+/-347.4	2209,1760,331	no	coding-synonymous	NQO2	NM_000904.3		3990,2159,354	GG,GA,AA		28.1628,10.0999,22.0437		110/232	3015790	10139,2867	2203	4300	6503	SO:0001819	synonymous_variant	4835	exon5			CGTGCCAGCCATC	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.330A>G	6.37:g.3015790A>G		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	83	83	1	NM_000904	B2R492|Q5TD04	Silent	SNP	ENST00000338130.2	37	CCDS4481.1																																																																																			A|0.232;G|0.768	0.768	strong		0.547	NQO2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039651.1		
POLR2A	5430	hgsc.bcm.edu	37	17	7405937	7405937	+	Silent	SNP	C	C	T	rs2071504	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:7405937C>T	ENST00000322644.6	+	16	3072	c.2673C>T	c.(2671-2673)taC>taT	p.Y891Y		NM_000937.4	NP_000928	P24928	RPB1_HUMAN	polymerase (RNA) II (DNA directed) polypeptide A, 220kDa	891					7-methylguanosine mRNA capping (GO:0006370)|DNA repair (GO:0006281)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|nucleotide-excision repair (GO:0006289)|positive regulation of viral transcription (GO:0050434)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|viral process (GO:0016032)	DNA-directed RNA polymerase II, core complex (GO:0005665)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|RNA-directed RNA polymerase activity (GO:0003968)|ubiquitin protein ligase binding (GO:0031625)			breast(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(8)|lung(17)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	50		Prostate(122;0.173)				AGCTGCGCTACGGCGAAGACG	0.582													C|||	887	0.177117	0.1104	0.2334	5008	,	,		18438	0.1885		0.162	False		,,,				2504	0.2311				p.Y891Y		Atlas-SNP	.											.	POLR2A	157	.	0			c.C2673T						PASS	.	C		588,3818	259.8+/-263.3	47,494,1662	92.0	80.0	84.0		2673	-8.4	0.9	17	dbSNP_96	84	1264,7336	252.1+/-278.3	97,1070,3133	no	coding-synonymous	POLR2A	NM_000937.4		144,1564,4795	TT,TC,CC		14.6977,13.3454,14.2396		891/1971	7405937	1852,11154	2203	4300	6503	SO:0001819	synonymous_variant	5430	exon16			GCGCTACGGCGAA			17p13.1	2013-01-21	2002-08-29		ENSG00000181222	ENSG00000181222	2.7.7.6	"""RNA polymerase subunits"""	9187	protein-coding gene	gene with protein product	"""DNA-directed RNA polymerase II largest subunit, RNA polymerase II 220 kd subunit"", ""RNA polymerase II subunit B1"""	180660	"""polymerase (RNA) II (DNA directed) polypeptide A (220kD)"""	POLR2			Standard	NM_000937		Approved	POLRA, RPB1	uc002ghf.4	P24928	OTTHUMG00000177594	ENST00000322644.6:c.2673C>T	17.37:g.7405937C>T		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	80	36	0.45	NM_000937	A6NN93|B9EH88|Q6NX41	Silent	SNP	ENST00000322644.6	37	CCDS32548.1																																																																																			C|0.849;T|0.151	0.151	strong		0.582	POLR2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437967.1	NM_000937	
KMT2C	58508	hgsc.bcm.edu	37	7	151874498	151874498	+	Silent	SNP	C	C	T	rs10252263	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:151874498C>T	ENST00000262189.6	-	38	8258	c.8040G>A	c.(8038-8040)caG>caA	p.Q2680Q	KMT2C_ENST00000355193.2_Silent_p.Q2680Q	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	2680					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)										CATCAGAAGGCTGGGTGGTTA	0.433													T|||	792	0.158147	0.3442	0.1052	5008	,	,		20439	0.1587		0.0119	False		,,,				2504	0.0941				p.Q2680Q		Atlas-SNP	.											.	MLL3	1564	.	0			c.G8040A						PASS	.	T		1367,3039	687.1+/-404.8	219,929,1055	77.0	76.0	76.0		8040	-1.9	0.0	7	dbSNP_119	76	148,8452	806.1+/-407.2	1,146,4153	no	coding-synonymous	MLL3	NM_170606.2		220,1075,5208	TT,TC,CC		1.7209,31.0259,11.6485		2680/4912	151874498	1515,11491	2203	4300	6503	SO:0001819	synonymous_variant	58508	exon38			AGAAGGCTGGGTG	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.8040G>A	7.37:g.151874498C>T		Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	156	71	0.455128	NM_170606	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Silent	SNP	ENST00000262189.6	37	CCDS5931.1	307	0.14056776556776557	171	0.3475609756097561	35	0.09668508287292818	93	0.16258741258741258	8	0.010554089709762533	T	0.007	-1.998027	0.00435	0.310259	0.017209	ENSG00000055609	ENST00000360104	.	.	.	5.63	-1.92	0.07618	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.58432	P	1.0000000000287557E-6	.	.	.	.	.	.	T	0.31308	-0.9948	3	.	.	.	.	13.3278	0.60469	0.0:0.6024:0.0:0.3976	rs10252263;rs58157666;rs10252263	.	.	.	T	186	.	.	A	-	1	0	MLL3	151505431	0.058000	0.20735	0.003000	0.11579	0.113000	0.19764	-0.070000	0.11523	-0.689000	0.05149	-1.859000	0.00561	GCC	C|0.865;T|0.135	0.135	strong		0.433	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3		
FAM205A	259308	hgsc.bcm.edu	37	9	34726524	34726524	+	Missense_Mutation	SNP	G	G	A	rs1810820	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:34726524G>A	ENST00000378788.3	-	4	752	c.713C>T	c.(712-714)aCg>aTg	p.T238M		NM_001141917.1	NP_001135389.1	Q6ZU69	F205A_HUMAN	family with sequence similarity 205, member A	238						integral component of membrane (GO:0016021)|nucleus (GO:0005634)				breast(1)|endometrium(2)|kidney(1)	4						GTTGCTCTGCGTCATCTCCTC	0.557													A|||	1156	0.230831	0.4123	0.1873	5008	,	,		18475	0.0813		0.17	False		,,,				2504	0.2331				p.T238M		Atlas-SNP	.											.	FAM205A	45	.	0			c.C713T						PASS	.	A	MET/THR	536,848		106,324,262	44.0	40.0	41.0		713	1.4	0.0	9	dbSNP_92	41	555,2627		51,453,1087	no	missense	FAM205A	NM_001141917.1	81	157,777,1349	AA,AG,GG		17.4419,38.7283,23.894	benign	238/1336	34726524	1091,3475	692	1591	2283	SO:0001583	missense	259308	exon4			CTCTGCGTCATCT		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.713C>T	9.37:g.34726524G>A	ENSP00000417711:p.Thr238Met	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	47	20	0.425532	NM_001141917	A8MVW7	Missense_Mutation	SNP	ENST00000378788.3	37	CCDS55305.1	396	0.1813186813186813	165	0.3353658536585366	72	0.19889502762430938	33	0.057692307692307696	126	0.1662269129287599	A	0.083	-1.179611	0.01633	0.387283	0.174419	ENSG00000205108	ENST00000378788	T	0.23552	1.9	3.85	1.37	0.22104	.	728.057000	0.00481	U	0.000125	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	0.43589	-0.9382	9	0.15066	T	0.55	.	6.2973	0.21093	0.662:0.0:0.338:0.0	rs1810820;rs60648957	238	Q6ZU69	F205A_HUMAN	M	238	ENSP00000417711:T238M	ENSP00000417711:T238M	T	-	2	0	RP11-195F19.10	34716524	0.000000	0.05858	0.000000	0.03702	0.018000	0.09664	-0.127000	0.10547	-0.108000	0.12066	-0.381000	0.06696	ACG	G|0.815;A|0.185	0.185	strong		0.557	FAM205A-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001150.2	NM_001141917	
SMIM11	54065	hgsc.bcm.edu	37	21	35757915	35757915	+	Missense_Mutation	SNP	A	A	G	rs34016792	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:35757915A>G	ENST00000399295.2	+	3	522	c.152A>G	c.(151-153)aAg>aGg	p.K51R	SMIM11_ENST00000399292.3_Missense_Mutation_p.K51R|SMIM11_ENST00000481710.1_3'UTR|SMIM11_ENST00000399299.1_Intron			P58511	SIM11_HUMAN	small integral membrane protein 11	51			K -> R (in dbSNP:rs34016792).			integral component of membrane (GO:0016021)											GAAAGGAAGAAGCAATCAGAG	0.433													A|||	81	0.0161741	0.0113	0.0231	5008	,	,		20372	0.002		0.0129	False		,,,				2504	0.0358				p.K51R		Atlas-SNP	.											.	.	.	.	0			c.A152G						PASS	.	A	ARG/LYS	67,4339	61.1+/-98.1	0,67,2136	51.0	47.0	49.0		152	-3.9	0.0	21	dbSNP_126	49	269,8331	100.1+/-161.6	4,261,4035	yes	missense	FAM165B	NM_058182.4	26	4,328,6171	GG,GA,AA		3.1279,1.5207,2.5834	benign	51/59	35757915	336,12670	2203	4300	6503	SO:0001583	missense	54065	exon3			GGAAGAAGCAATC	BC015596	CCDS33550.1	21q22.12	2012-12-03	2012-12-03	2012-12-03	ENSG00000205670	ENSG00000205670			1293	protein-coding gene	gene with protein product			"""chromosome 21 open reading frame 51"", ""family with sequence similarity 165, member B"""	C21orf51, FAM165B			Standard	NM_058182		Approved		uc002ytu.4	P58511	OTTHUMG00000086193	ENST00000399295.2:c.152A>G	21.37:g.35757915A>G	ENSP00000382234:p.Lys51Arg	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	119	49	0.411765	NM_058182		Missense_Mutation	SNP	ENST00000399295.2	37	CCDS33550.1	26	0.011904761904761904	4	0.008130081300813009	12	0.03314917127071823	1	0.0017482517482517483	9	0.011873350923482849	A	10.26	1.300114	0.23650	0.015207	0.031279	ENSG00000205670	ENST00000399292;ENST00000399295	T;T	0.36520	1.25;1.25	5.64	-3.86	0.04230	.	.	.	.	.	T	0.04679	0.0127	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.23691	-1.0181	8	0.15952	T	0.53	.	2.0315	0.03530	0.3294:0.3538:0.2024:0.1144	rs34016792	51	P58511	F165B_HUMAN	R	51	ENSP00000382231:K51R;ENSP00000382234:K51R	ENSP00000382231:K51R	K	+	2	0	FAM165B	34679785	0.000000	0.05858	0.000000	0.03702	0.143000	0.21401	0.555000	0.23422	-0.979000	0.03529	-0.371000	0.07208	AAG	A|0.979;G|0.021	0.021	strong		0.433	SMIM11-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194078.1	NM_058182	
ARHGAP5	394	hgsc.bcm.edu	37	14	32561316	32561316	+	Nonsense_Mutation	SNP	G	G	T	rs200628183	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:32561316G>T	ENST00000345122.3	+	2	1756	c.1441G>T	c.(1441-1443)Gaa>Taa	p.E481*	ARHGAP5_ENST00000432921.1_Nonsense_Mutation_p.E481*|ARHGAP5_ENST00000539826.2_Nonsense_Mutation_p.E481*|ARHGAP5_ENST00000556611.1_Nonsense_Mutation_p.E481*|ARHGAP5_ENST00000433497.1_Intron|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						scavenged	.						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	84	1	0.0119048		WXS	Illumina HiSeq	Phase_I	79	10	0.126582	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	
CCDC67	159989	hgsc.bcm.edu	37	11	93141575	93141575	+	Missense_Mutation	SNP	T	T	C	rs371785641		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:93141575T>C	ENST00000298050.3	+	12	1605	c.1505T>C	c.(1504-1506)gTg>gCg	p.V502A	CCDC67_ENST00000525646.1_Missense_Mutation_p.V244A|AP004242.1_ENST00000408638.1_RNA	NM_181645.3	NP_857596.2	Q05D60	DEUP1_HUMAN	coiled-coil domain containing 67	502					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)				CAAATAAAAGTGGAACAAAAT	0.294																																					p.V502A		Atlas-SNP	.											CCDC67,NS,carcinoma,+1,1	CCDC67	57	1	0			c.T1505C						scavenged	.	T	ALA/VAL	0,3600		0,0,1800	38.0	34.0	35.0		1505	2.2	0.3	11		35	1,8127		0,1,4063	no	missense	CCDC67	NM_181645.3	64	0,1,5863	CC,CT,TT		0.0123,0.0,0.0085	benign	502/605	93141575	1,11727	1800	4064	5864	SO:0001583	missense	159989	exon12			TAAAAGTGGAACA	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.1505T>C	11.37:g.93141575T>C	ENSP00000298050:p.Val502Ala	Somatic	110	1	0.00909091		WXS	Illumina HiSeq	Phase_I	84	19	0.22619	NM_181645	Q8NEF1|Q96LL7	Missense_Mutation	SNP	ENST00000298050.3	37	CCDS44707.1	.	.	.	.	.	.	.	.	.	.	T	14.27	2.485540	0.44147	0.0	1.23E-4	ENSG00000165325	ENST00000534747;ENST00000298050;ENST00000525646	T;T;T	0.16897	2.31;2.31;2.31	5.86	2.18	0.27775	.	0.473884	0.25948	N	0.027261	T	0.07324	0.0185	N	0.08118	0	0.20196	N	0.999929	B;B	0.17465	0.009;0.022	B;B	0.16289	0.009;0.015	T	0.28554	-1.0040	10	0.41790	T	0.15	.	4.9184	0.13858	0.2853:0.0776:0.0:0.6372	.	502;494	Q05D60;Q6ZRU6	CCD67_HUMAN;.	A	502;502;244	ENSP00000432111:V502A;ENSP00000298050:V502A;ENSP00000435079:V244A	ENSP00000298050:V502A	V	+	2	0	CCDC67	92781223	0.992000	0.36948	0.254000	0.24359	0.935000	0.57460	0.381000	0.20619	0.112000	0.17975	0.533000	0.62120	GTG	.	.	weak		0.294	CCDC67-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_181645	
DTNBP1	84062	hgsc.bcm.edu	37	6	15523448	15523448	+	Missense_Mutation	SNP	G	G	A	rs17470454	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:15523448G>A	ENST00000344537.5	-	10	986	c.814C>T	c.(814-816)Cct>Tct	p.P272S	DTNBP1_ENST00000462989.2_Missense_Mutation_p.P116S|DTNBP1_ENST00000355917.3_Missense_Mutation_p.P273S	NM_032122.4	NP_115498.2	Q96EV8	DTBP1_HUMAN	dystrobrevin binding protein 1	272	Dysbindin.		P -> S (in dbSNP:rs17470454).		actin cytoskeleton reorganization (GO:0031532)|anterograde axon cargo transport (GO:0008089)|anterograde synaptic vesicle transport (GO:0048490)|blood coagulation (GO:0007596)|melanosome organization (GO:0032438)|membrane organization (GO:0061024)|neuron projection development (GO:0031175)|neuron projection morphogenesis (GO:0048812)|platelet dense granule organization (GO:0060155)|positive regulation of gene expression (GO:0010628)|positive regulation of neurotransmitter secretion (GO:0001956)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of dopamine receptor signaling pathway (GO:0060159)|regulation of dopamine secretion (GO:0014059)	axon (GO:0030424)|BLOC-1 complex (GO:0031083)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|endoplasmic reticulum membrane (GO:0005789)|endosome (GO:0005768)|growth cone (GO:0030426)|neuron projection (GO:0043005)|nucleus (GO:0005634)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)|synaptic vesicle membrane (GO:0030672)				cervix(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(5)|ovary(1)|skin(2)	14	Breast(50;0.0289)|Ovarian(93;0.103)	all_hematologic(90;0.0895)	Epithelial(50;0.211)			CTGGATTCAGGCCCTGCAAAA	0.483									Hermansky-Pudlak syndrome				G|||	78	0.0155751	0.0045	0.0144	5008	,	,		20489	0.0		0.0586	False		,,,				2504	0.0031				p.P272S		Atlas-SNP	.											.	DTNBP1	56	.	0			c.C814T	GRCh37	CM065138	DTNBP1	M	rs17470454	PASS	.	G	SER/PRO	43,4363	46.0+/-80.4	1,41,2161	99.0	106.0	104.0		814	3.7	0.8	6	dbSNP_123	104	437,8163	133.5+/-191.0	14,409,3877	yes	missense	DTNBP1	NM_032122.4	74	15,450,6038	AA,AG,GG		5.0814,0.9759,3.6906	possibly-damaging	272/352	15523448	480,12526	2203	4300	6503	SO:0001583	missense	84062	exon10	Familial Cancer Database	HPS, HPS1-8	ATTCAGGCCCTGC	AF394226	CCDS4534.1, CCDS4535.1, CCDS75404.1, CCDS75405.1	6p22.3	2013-09-27			ENSG00000047579	ENSG00000047579		"""Biogenesis of lysosomal organelles complex-1 subunits"""	17328	protein-coding gene	gene with protein product	"""dysbindin-1"", ""biogenesis of lysosomal organelles complex-1, subunit 8"""	607145				11316798	Standard	NM_032122		Approved	Dysbindin, My031, HPS7, DBND, BLOC1S8	uc003nbm.3	Q96EV8	OTTHUMG00000014295	ENST00000344537.5:c.814C>T	6.37:g.15523448G>A	ENSP00000341680:p.Pro272Ser	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	58	31	0.534483	NM_032122	A8K3V3|Q5THY3|Q5THY4|Q96NV2|Q9H0U2|Q9H3J5	Missense_Mutation	SNP	ENST00000344537.5	37	CCDS4534.1	65	0.02976190476190476	4	0.008130081300813009	4	0.011049723756906077	0	0.0	57	0.07519788918205805	G	13.90	2.374002	0.42105	0.009759	0.050814	ENSG00000047579	ENST00000344537;ENST00000462989;ENST00000355917;ENST00000397306;ENST00000509674	T;T;T;T	0.31769	1.48;1.48;1.49;1.54	5.48	3.65	0.41850	.	0.639891	0.14625	N	0.308163	T	0.16938	0.0407	M	0.80982	2.52	0.35352	D	0.787468	B	0.25904	0.137	B	0.23018	0.043	T	0.02294	-1.1181	10	0.30078	T	0.28	.	7.6583	0.28388	0.1413:0.0:0.7249:0.1337	rs17470454;rs52793808;rs17470454	272	Q96EV8	DTBP1_HUMAN	S	272;116;273;191;89	ENSP00000341680:P272S;ENSP00000427239:P116S;ENSP00000348183:P273S;ENSP00000421797:P89S	ENSP00000341680:P272S	P	-	1	0	DTNBP1	15631427	1.000000	0.71417	0.813000	0.32504	0.782000	0.44232	3.829000	0.55760	0.632000	0.30432	0.561000	0.74099	CCT	G|0.970;A|0.030	0.030	strong		0.483	DTNBP1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000039933.2	NM_032122	
DOPEY2	9980	hgsc.bcm.edu	37	21	37617724	37617724	+	Missense_Mutation	SNP	C	C	A	rs3746866	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:37617724C>A	ENST00000399151.3	+	19	3531	c.3446C>A	c.(3445-3447)cCc>cAc	p.P1149H		NM_005128.2	NP_005119.2	Q9Y3R5	DOP2_HUMAN	dopey family member 2	1149			P -> H (in dbSNP:rs3746866). {ECO:0000269|PubMed:10950924}.		cognition (GO:0050890)|endoplasmic reticulum organization (GO:0007029)|Golgi to endosome transport (GO:0006895)|multicellular organismal development (GO:0007275)|protein transport (GO:0015031)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)				autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(6)|lung(25)|ovary(2)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58						GCACCCATCCCCATGGGGGGC	0.642													C|||	859	0.171526	0.112	0.1383	5008	,	,		11419	0.2262		0.1372	False		,,,				2504	0.2546				p.P1149H		Atlas-SNP	.											DOPEY2,NS,carcinoma,0,1	DOPEY2	184	1	0			c.C3446A						PASS	.	C	HIS/PRO	477,3929	217.8+/-236.0	26,425,1752	80.0	64.0	70.0		3446	3.8	0.7	21	dbSNP_107	70	1126,7474	227.2+/-262.7	80,966,3254	yes	missense	DOPEY2	NM_005128.2	77	106,1391,5006	AA,AC,CC		13.093,10.8261,12.3251	benign	1149/2299	37617724	1603,11403	2203	4300	6503	SO:0001583	missense	9980	exon19			CCATCCCCATGGG	AJ237839	CCDS13643.1	21q22.2	2013-03-05	2006-02-02	2006-02-02	ENSG00000142197	ENSG00000142197			1291	protein-coding gene	gene with protein product		604803	"""chromosome 21 open reading frame 5"""	C21orf5		16301316, 16303751, 10931277	Standard	NM_005128		Approved	KIAA0933	uc002yvg.3	Q9Y3R5	OTTHUMG00000086619	ENST00000399151.3:c.3446C>A	21.37:g.37617724C>A	ENSP00000382104:p.Pro1149His	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	58	35	0.603448	NM_005128	D3DSG5|Q6PJQ7|Q9UEZ3	Missense_Mutation	SNP	ENST00000399151.3	37	CCDS13643.1	356	0.163003663003663	62	0.12601626016260162	47	0.1298342541436464	138	0.24125874125874125	109	0.1437994722955145	C	9.478	1.097311	0.20552	0.108261	0.13093	ENSG00000142197	ENST00000399151	T	0.39406	1.08	4.7	3.81	0.43845	.	0.546294	0.18501	N	0.139358	T	0.00012	0.0000	L	0.43152	1.355	0.31879	P	0.6187	D;B	0.53885	0.963;0.001	P;B	0.46479	0.518;0.001	T	0.11203	-1.0597	9	0.51188	T	0.08	.	10.9834	0.47508	0.0:0.9128:0.0:0.0872	rs3746866;rs61483860;rs3746866	1149;1149	Q9Y3R5-2;Q9Y3R5	.;DOP2_HUMAN	H	1149	ENSP00000382104:P1149H	ENSP00000382104:P1149H	P	+	2	0	DOPEY2	36539594	0.447000	0.25673	0.739000	0.30968	0.295000	0.27426	4.235000	0.58666	1.341000	0.45600	0.650000	0.86243	CCC	C|0.859;A|0.141	0.141	strong		0.642	DOPEY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194636.1	NM_005128	
SVEP1	79987	hgsc.bcm.edu	37	9	113208250	113208250	+	Missense_Mutation	SNP	T	T	G	rs7863519	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:113208250T>G	ENST00000401783.2	-	26	4666	c.4330A>C	c.(4330-4332)Atg>Ctg	p.M1444L	SVEP1_ENST00000374469.1_Missense_Mutation_p.M1421L|SVEP1_ENST00000302728.8_Missense_Mutation_p.M1444L|SVEP1_ENST00000467821.1_5'UTR	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	154	0	0		WXS	Illumina HiSeq	Phase_I	153	72	0.470588	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			
DEFB127	140850	hgsc.bcm.edu	37	20	139576	139576	+	Missense_Mutation	SNP	C	C	A	rs16995685	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:139576C>A	ENST00000382388.3	+	2	286	c.211C>A	c.(211-213)Cgt>Agt	p.R71S		NM_139074.3	NP_620713.1	Q9H1M4	DB127_HUMAN	defensin, beta 127	71			R -> S (in dbSNP:rs16995685). {ECO:0000269|PubMed:11854508}.		defense response to bacterium (GO:0042742)|innate immune response (GO:0045087)	extracellular region (GO:0005576)				NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(4)	9		all_cancers(10;7.65e-05)|Lung NSC(37;0.0417)|all_epithelial(17;0.0676)|all_lung(30;0.0713)|Breast(17;0.231)	OV - Ovarian serous cystadenocarcinoma(29;0.122)			AAAGCCACCTCGTCCAAAGCC	0.388													C|||	1623	0.324081	0.0431	0.3487	5008	,	,		20057	0.5407		0.3419	False		,,,				2504	0.4448				p.R71S		Atlas-SNP	.											.	DEFB127	15	.	0			c.C211A						PASS	.	C	SER/ARG	399,4007	199.4+/-223.0	18,363,1822	109.0	93.0	98.0		211	1.2	0.0	20	dbSNP_123	98	3030,5570	466.8+/-366.9	519,1992,1789	yes	missense	DEFB127	NM_139074.2	110	537,2355,3611	AA,AC,CC		35.2326,9.0558,26.3648	benign	71/100	139576	3429,9577	2203	4300	6503	SO:0001583	missense	140850	exon2			CCACCTCGTCCAA	AY358796	CCDS12991.1	20p13	2008-02-01	2002-05-09	2002-05-10	ENSG00000088782	ENSG00000088782		"""Defensins, beta"""	16206	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 73"""	C20orf73		11854508	Standard	NM_139074		Approved	bA530N10.2, DEF-27	uc002wcy.2	Q9H1M4	OTTHUMG00000031617	ENST00000382388.3:c.211C>A	20.37:g.139576C>A	ENSP00000371825:p.Arg71Ser	Somatic	232	0	0		WXS	Illumina HiSeq	Phase_I	165	69	0.418182	NM_139074	Q14DW7	Missense_Mutation	SNP	ENST00000382388.3	37	CCDS12991.1	702	0.32142857142857145	19	0.03861788617886179	135	0.3729281767955801	287	0.5017482517482518	261	0.34432717678100266	C	0.491	-0.875449	0.02550	0.090558	0.352326	ENSG00000088782	ENST00000382388	T	0.15256	2.44	3.26	1.24	0.21308	.	0.768263	0.10589	N	0.656961	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.21520	0.057	B	0.20184	0.028	T	0.45512	-0.9256	8	0.26408	T	0.33	-0.2158	4.0324	0.09714	0.2294:0.6438:0.0:0.1268	rs16995685;rs16995685	71	Q9H1M4	DB127_HUMAN	S	71	ENSP00000371825:R71S	ENSP00000371825:R71S	R	+	1	0	DEFB127	87576	0.004000	0.15560	0.003000	0.11579	0.001000	0.01503	0.595000	0.24029	0.367000	0.24454	-0.657000	0.03884	CGT	C|0.718;A|0.282	0.282	strong		0.388	DEFB127-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077429.1	NM_139074	
SLC15A2	6565	hgsc.bcm.edu	37	3	121647286	121647286	+	Missense_Mutation	SNP	C	C	T	rs1143671	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:121647286C>T	ENST00000489711.1	+	15	1613	c.1225C>T	c.(1225-1227)Cca>Tca	p.P409S	SLC15A2_ENST00000295605.2_Missense_Mutation_p.P378S|SLC15A2_ENST00000465060.1_3'UTR	NM_021082.3	NP_066568.3	Q16348	S15A2_HUMAN	solute carrier family 15 (oligopeptide transporter), member 2	409			P -> S (in dbSNP:rs1143671).		drug transport (GO:0015893)|ion transport (GO:0006811)|protein transport (GO:0015031)|proton transport (GO:0015992)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	antibiotic transporter activity (GO:0042895)|dipeptide transporter activity (GO:0042936)|high-affinity oligopeptide transporter activity (GO:0015334)|peptide:proton symporter activity (GO:0015333)			NS(1)|endometrium(1)|kidney(4)|large_intestine(5)|lung(17)|skin(6)|upper_aerodigestive_tract(2)	36				GBM - Glioblastoma multiforme(114;0.0967)	Aminolevulinic acid(DB00855)|Amoxicillin(DB01060)|Ampicillin(DB00415)|Azidocillin(DB08795)|Benazepril(DB00542)|Benzylpenicillin(DB01053)|Cefaclor(DB00833)|Cefadroxil(DB01140)|Cefalotin(DB00456)|Cefdinir(DB00535)|Cefepime(DB01413)|Cefixime(DB00671)|Cefmetazole(DB00274)|Cefotaxime(DB00493)|Cefradine(DB01333)|Ceftazidime(DB00438)|Ceftibuten(DB01415)|Ceftriaxone(DB01212)|Cefuroxime(DB01112)|Cephalexin(DB00567)|Chlorpropamide(DB00672)|Cilazapril(DB01340)|Cloxacillin(DB01147)|Cyclacillin(DB01000)|Dicloxacillin(DB00485)|Fosinopril(DB00492)|Glyburide(DB01016)|Moexipril(DB00691)|Nateglinide(DB00731)|Oxacillin(DB00713)|Perindopril(DB00790)|Quinapril(DB00881)|Ramipril(DB00178)|Spirapril(DB01348)|Tolbutamide(DB01124)|Trandolapril(DB00519)|Tranexamic Acid(DB00302)|Valaciclovir(DB00577)|Valganciclovir(DB01610)	CCCAGCCCAGCCAGGTCCCCA	0.443													T|||	2263	0.451877	0.4834	0.2939	5008	,	,		19560	0.6984		0.4235	False		,,,				2504	0.2965				p.P409S		Atlas-SNP	.											.	SLC15A2	92	.	0			c.C1225T						PASS	.	T	SER/PRO,SER/PRO	2150,2256	595.1+/-388.4	532,1086,585	161.0	165.0	163.0		1132,1225	-0.5	0.0	3	dbSNP_86	163	3905,4695	606.1+/-395.0	880,2145,1275	yes	missense,missense	SLC15A2	NM_001145998.1,NM_021082.3	74,74	1412,3231,1860	TT,TC,CC		45.407,48.7971,46.5554	possibly-damaging,possibly-damaging	378/699,409/730	121647286	6055,6951	2203	4300	6503	SO:0001583	missense	6565	exon15			GCCCAGCCAGGTC	BC044572	CCDS3007.1, CCDS54631.1	3q21.1	2013-07-18	2013-07-18		ENSG00000163406	ENSG00000163406		"""Solute carriers"""	10921	protein-coding gene	gene with protein product		602339	"""solute carrier family 15 (H+/peptide transporter), member 2"""			7756356	Standard	NM_021082		Approved	PEPT2	uc003eep.2	Q16348	OTTHUMG00000159423	ENST00000489711.1:c.1225C>T	3.37:g.121647286C>T	ENSP00000417085:p.Pro409Ser	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	80	41	0.5125	NM_021082	A8K1A5|B4E2A7	Missense_Mutation	SNP	ENST00000489711.1	37	CCDS3007.1	1071	0.49038461538461536	227	0.4613821138211382	100	0.27624309392265195	427	0.7465034965034965	317	0.4182058047493404	T	10.32	1.317079	0.23908	0.487971	0.45407	ENSG00000163406	ENST00000489711;ENST00000542599;ENST00000295605	T;T	0.05447	3.44;3.44	5.61	-0.531	0.11894	.	0.512979	0.23208	N	0.050705	T	0.00012	0.0000	M	0.86097	2.795	0.58432	P	2.9999999999752447E-6	P;D	0.53462	0.809;0.96	P;P	0.59595	0.517;0.86	T	0.41752	-0.9491	9	0.59425	D	0.04	0.0419	2.425	0.04457	0.2192:0.406:0.2314:0.1434	rs1143671;rs1316300;rs3749457;rs52819015;rs59056692;rs1143671	378;409	B4E2A7;Q16348	.;S15A2_HUMAN	S	409;371;378	ENSP00000417085:P409S;ENSP00000295605:P378S	ENSP00000295605:P378S	P	+	1	0	SLC15A2	123129976	0.313000	0.24554	0.004000	0.12327	0.084000	0.17831	-0.176000	0.09811	-0.540000	0.06265	-0.743000	0.03520	CCA	C|0.523;T|0.477	0.477	strong		0.443	SLC15A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355239.1	NM_021082	
IRF7	3665	hgsc.bcm.edu	37	11	613208	613208	+	Missense_Mutation	SNP	T	T	C	rs1131665|rs397786711	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:613208T>C	ENST00000397574.2	-	9	1604	c.1235A>G	c.(1234-1236)cAa>cGa	p.Q412R	IRF7_ENST00000397562.3_Missense_Mutation_p.Q119R|IRF7_ENST00000348655.6_Missense_Mutation_p.Q383R|IRF7_ENST00000397566.1_Missense_Mutation_p.Q425R|IRF7_ENST00000525445.1_Missense_Mutation_p.Q306R|IRF7_ENST00000397570.1_Missense_Mutation_p.Q383R|IRF7_ENST00000330243.5_Missense_Mutation_p.Q425R	NM_001572.3	NP_001563.2	Q92985	IRF7_HUMAN	interferon regulatory factor 7	412			Q -> R (in dbSNP:rs1131665). {ECO:0000269|PubMed:9786932}.		cellular response to DNA damage stimulus (GO:0006974)|cytokine-mediated signaling pathway (GO:0019221)|establishment of viral latency (GO:0019043)|immunoglobulin mediated immune response (GO:0016064)|innate immune response (GO:0045087)|interferon-alpha production (GO:0032607)|interferon-beta production (GO:0032608)|interferon-gamma-mediated signaling pathway (GO:0060333)|MDA-5 signaling pathway (GO:0039530)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of macrophage apoptotic process (GO:2000110)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta production (GO:0032728)|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)|positive regulation of type I interferon-mediated signaling pathway (GO:0060340)|regulation of adaptive immune response (GO:0002819)|regulation of immune response (GO:0050776)|regulation of monocyte differentiation (GO:0045655)|regulation of MyD88-dependent toll-like receptor signaling pathway (GO:0034124)|regulation of MyD88-independent toll-like receptor signaling pathway (GO:0034127)|regulation of type I interferon production (GO:0032479)|response to virus (GO:0009615)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|transcription from RNA polymerase II promoter (GO:0006366)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|type I interferon biosynthetic process (GO:0045351)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome membrane (GO:0010008)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity (GO:0000982)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)			endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	8		all_cancers(49;1.69e-08)|all_epithelial(84;1.65e-05)|Breast(177;0.000231)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.106)|all_lung(207;0.136)		all cancers(45;7.68e-28)|Epithelial(43;7.44e-27)|OV - Ovarian serous cystadenocarcinoma(40;3.53e-21)|BRCA - Breast invasive adenocarcinoma(625;6.96e-05)|Lung(200;0.0375)|LUSC - Lung squamous cell carcinoma(625;0.0703)		TCACTGACCTTGGAAGAAGAC	0.652													C|||	1380	0.275559	0.5847	0.3026	5008	,	,		14882	0.0208		0.2674	False		,,,				2504	0.1094				p.Q425R		Atlas-SNP	.											.	IRF7	23	.	0			c.A1274G						PASS	.	C	ARG/GLN,ARG/GLN,ARG/GLN	2234,2156		583,1068,544	15.0	20.0	18.0		1235,1148,1274	-5.9	0.1	11	dbSNP_86	18	2458,6134		355,1748,2193	yes	missense,missense,missense	IRF7	NM_001572.3,NM_004029.2,NM_004031.2	43,43,43	938,2816,2737	CC,CT,TT		28.608,49.1116,36.1424	benign,benign,benign	412/504,383/475,425/517	613208	4692,8290	2195	4296	6491	SO:0001583	missense	3665	exon7			TGACCTTGGAAGA	U53830	CCDS7703.1, CCDS7704.1, CCDS7705.1	11p15.5	2005-10-10			ENSG00000185507	ENSG00000185507			6122	protein-coding gene	gene with protein product		605047					Standard	XM_005252906		Approved		uc001lqh.3	Q92985	OTTHUMG00000132019	ENST00000397574.2:c.1235A>G	11.37:g.613208T>C	ENSP00000380704:p.Gln412Arg	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	94	62	0.659574	NM_004031	B9EGL3|O00331|O00332|O00333|O75924|Q9UE79	Missense_Mutation	SNP	ENST00000397574.2	37	CCDS7703.1	612	0.2802197802197802	283	0.5752032520325203	124	0.3425414364640884	8	0.013986013986013986	197	0.2598944591029024	C	0	-2.738933	0.00088	0.508884	0.28608	ENSG00000185507	ENST00000525445;ENST00000348655;ENST00000397570;ENST00000397566;ENST00000397574;ENST00000397562;ENST00000330243	D;D;D;D;D;D;D	0.93763	-3.28;-3.28;-3.28;-3.28;-3.28;-3.28;-3.28	4.11	-5.89	0.02282	SMAD domain-like (1);SMAD/FHA domain (1);Interferon regulatory factor-3 (1);	1.525810	0.03842	N	0.270772	T	0.00012	0.0000	N	0.03930	-0.32	0.80722	P	0.0	B;B;B;B	0.09022	0.0;0.002;0.0;0.0	B;B;B;B	0.08055	0.002;0.003;0.001;0.001	T	0.22695	-1.0209	9	0.07990	T	0.79	-27.8167	12.6541	0.56778	0.0:0.1324:0.109:0.7585	rs1131665;rs1802428;rs3088223;rs3178010;rs11544073	306;383;412;425	E9PSE3;Q92985-2;Q92985;Q92985-4	.;.;IRF7_HUMAN;.	R	306;383;383;425;412;119;425	ENSP00000434009:Q306R;ENSP00000331803:Q383R;ENSP00000380700:Q383R;ENSP00000380697:Q425R;ENSP00000380704:Q412R;ENSP00000380693:Q119R;ENSP00000329411:Q425R	ENSP00000329411:Q425R	Q	-	2	0	IRF7	603208	0.158000	0.22850	0.073000	0.20177	0.009000	0.06853	-0.583000	0.05807	-1.746000	0.01335	-3.263000	0.00049	CAA	T|0.719;C|0.281	0.281	strong		0.652	IRF7-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255026.1	NM_001572	
GRIN2C	2905	hgsc.bcm.edu	37	17	72838649	72838649	+	Missense_Mutation	SNP	C	C	A	rs3744215	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:72838649C>A	ENST00000293190.5	-	13	3773	c.3627G>T	c.(3625-3627)agG>agT	p.R1209S		NM_000835.3	NP_000826.2	Q14957	NMDE3_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2C	1209			R -> S (in dbSNP:rs3744215).		directional locomotion (GO:0033058)|glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|negative regulation of protein catabolic process (GO:0042177)|neuromuscular process controlling balance (GO:0050885)|protein localization (GO:0008104)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|response to wounding (GO:0009611)|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)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	cation channel activity (GO:0005261)|extracellular-glutamate-gated ion channel activity (GO:0005234)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(2)|large_intestine(6)|lung(15)|ovary(2)|skin(2)|urinary_tract(1)	33	all_lung(278;0.172)|Lung NSC(278;0.207)				Acamprosate(DB00659)|Atomoxetine(DB00289)|Gabapentin(DB00996)|Glycine(DB00145)|Ketobemidone(DB06738)|Milnacipran(DB04896)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	CACGGGCTACCCTGCTGATCT	0.662													C|||	1450	0.289537	0.2852	0.1931	5008	,	,		15832	0.381		0.2942	False		,,,				2504	0.2648				p.R1209S		Atlas-SNP	.											GRIN2C_ENST00000293190,NS,carcinoma,0,4	GRIN2C	144	4	0			c.G3627T						PASS	.	C	SER/ARG	1356,3050		214,928,1061	22.0	20.0	21.0		3627	-1.4	0.2	17	dbSNP_107	21	2433,6161		337,1759,2201	yes	missense	GRIN2C	NM_000835.3	110	551,2687,3262	AA,AC,CC		28.3104,30.7762,29.1462	possibly-damaging	1209/1234	72838649	3789,9211	2203	4297	6500	SO:0001583	missense	2905	exon13			GGCTACCCTGCTG		CCDS32724.1, CCDS62330.1	17q25.1	2012-08-29			ENSG00000161509	ENSG00000161509		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4587	protein-coding gene	gene with protein product		138254		NMDAR2C		9480759	Standard	NM_001278553		Approved	GluN2C	uc002jlt.1	Q14957	OTTHUMG00000044524	ENST00000293190.5:c.3627G>T	17.37:g.72838649C>A	ENSP00000293190:p.Arg1209Ser	Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	168	100	0.595238	NM_000835	B2RTT1	Missense_Mutation	SNP	ENST00000293190.5	37	CCDS32724.1	681	0.3118131868131868	149	0.30284552845528456	74	0.20441988950276244	229	0.40034965034965037	229	0.3021108179419525	C	14.76	2.631722	0.46944	0.307762	0.283104	ENSG00000161509	ENST00000293190	T	0.10763	2.84	4.74	-1.36	0.09085	.	0.853171	0.10019	N	0.726218	T	0.00012	0.0000	L	0.27053	0.805	0.21290	P	0.999737402	B	0.06786	0.001	B	0.04013	0.001	T	0.47971	-0.9075	9	0.59425	D	0.04	.	3.6082	0.08050	0.4273:0.3215:0.0:0.2511	rs3744215;rs56834934;rs3744215	1209	Q14957	NMDE3_HUMAN	S	1209	ENSP00000293190:R1209S	ENSP00000293190:R1209S	R	-	3	2	GRIN2C	70350244	0.000000	0.05858	0.188000	0.23233	0.666000	0.39218	0.514000	0.22786	-0.045000	0.13468	-0.258000	0.10820	AGG	C|0.689;A|0.311	0.311	strong		0.662	GRIN2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103824.1		
SVEP1	79987	hgsc.bcm.edu	37	9	113168501	113168501	+	Missense_Mutation	SNP	A	A	G	rs41278435	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:113168501A>G	ENST00000401783.2	-	38	9715	c.9379T>C	c.(9379-9381)Tct>Cct	p.S3127P	SVEP1_ENST00000374469.1_Missense_Mutation_p.S3104P|SVEP1_ENST00000297826.5_Missense_Mutation_p.S1053P	NM_153366.3	NP_699197.3	Q4LDE5	SVEP1_HUMAN	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	3127	Sushi 29. {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						TTGGCGACAGACGGTGGGGAC	0.522													A|||	166	0.033147	0.0227	0.0259	5008	,	,		19193	0.0476		0.0467	False		,,,				2504	0.0235				p.S3127P		Atlas-SNP	.											.	SVEP1	326	.	0			c.T9379C						PASS	.	A	PRO/SER	80,3906		0,80,1913	114.0	120.0	118.0		9379	-6.0	0.0	9	dbSNP_127	118	352,7980		8,336,3822	yes	missense	SVEP1	NM_153366.3	74	8,416,5735	GG,GA,AA		4.2247,2.007,3.5071	possibly-damaging	3127/3572	113168501	432,11886	1993	4166	6159	SO:0001583	missense	79987	exon38			CGACAGACGGTGG	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.9379T>C	9.37:g.113168501A>G	ENSP00000384917:p.Ser3127Pro	Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	120	60	0.5	NM_153366	Q0P675|Q5D213|Q5T938|Q5VTE4|Q5VTE5|Q7Z387|Q7Z3G3|Q8NBT9|Q96JU7|Q9H284|Q9H8J9	Missense_Mutation	SNP	ENST00000401783.2	37	CCDS48004.1	82	0.037545787545787544	9	0.018292682926829267	15	0.04143646408839779	20	0.03496503496503497	38	0.05013192612137203	A	4.145	0.025223	0.08054	0.02007	0.042247	ENSG00000165124	ENST00000401783;ENST00000374469;ENST00000297826	T;T;T	0.64085	-0.08;-0.08;-0.08	5.69	-6.0	0.02206	Complement control module (2);Sushi/SCR/CCP (3);	0.882616	0.10320	N	0.688843	T	0.08403	0.0209	L	0.41356	1.27	0.09310	N	1	B	0.09022	0.002	B	0.08055	0.003	T	0.16928	-1.0386	10	0.22706	T	0.39	.	0.9383	0.01350	0.2956:0.2781:0.12:0.3064	rs41278435	3127	Q4LDE5	SVEP1_HUMAN	P	3127;3104;1053	ENSP00000384917:S3127P;ENSP00000363593:S3104P;ENSP00000297826:S1053P	ENSP00000297826:S1053P	S	-	1	0	SVEP1	112208322	0.000000	0.05858	0.000000	0.03702	0.075000	0.17131	-0.035000	0.12205	-0.535000	0.06307	-0.438000	0.05819	TCT	A|0.964;G|0.036	0.036	strong		0.522	SVEP1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
TDRKH	11022	hgsc.bcm.edu	37	1	151751274	151751274	+	Missense_Mutation	SNP	C	C	G	rs17853082	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:151751274C>G	ENST00000368822.1	-	6	1403	c.770G>C	c.(769-771)gGa>gCa	p.G257A	TDRKH_ENST00000368827.6_Missense_Mutation_p.G257A|TDRKH_ENST00000440583.2_Missense_Mutation_p.G33A|TDRKH_ENST00000368825.3_Missense_Mutation_p.G212A|TDRKH_ENST00000368823.1_Missense_Mutation_p.G253A|TDRKH_ENST00000368824.3_Missense_Mutation_p.G257A|TDRKH_ENST00000458431.2_Missense_Mutation_p.G257A|TDRKH_ENST00000484421.1_5'UTR			Q9Y2W6	TDRKH_HUMAN	tudor and KH domain containing	257			G -> A (in dbSNP:rs17853082).		cell differentiation (GO:0030154)|DNA methylation involved in gamete generation (GO:0043046)|fertilization (GO:0009566)|gene silencing by RNA (GO:0031047)|male meiosis (GO:0007140)|piRNA metabolic process (GO:0034587)|spermatogenesis (GO:0007283)	mitochondrion (GO:0005739)|pi-body (GO:0071546)|piP-body (GO:0071547)	RNA binding (GO:0003723)			breast(5)|cervix(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	26	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.14)		LUSC - Lung squamous cell carcinoma(543;0.181)			GTCGCCTCCTCCTTTGGGTGG	0.547													C|||	64	0.0127796	0.0008	0.0058	5008	,	,		19271	0.0		0.0358	False		,,,				2504	0.0235				p.G257A		Atlas-SNP	.											.	TDRKH	45	.	0			c.G770C						PASS	.	C	ALA/GLY,ALA/GLY,ALA/GLY,ALA/GLY	29,3877		1,27,1925	84.0	83.0	83.0		770,635,770,770	5.5	0.9	1	dbSNP_123	83	315,7981		10,295,3843	yes	missense,missense,missense,missense	TDRKH	NM_001083963.1,NM_001083964.1,NM_001083965.1,NM_006862.3	60,60,60,60	11,322,5768	GG,GC,CC		3.797,0.7424,2.8192	probably-damaging,probably-damaging,probably-damaging,probably-damaging	257/562,212/517,257/562,257/562	151751274	344,11858	1953	4148	6101	SO:0001583	missense	11022	exon6			CCTCCTCCTTTGG	AF227192	CCDS41394.1, CCDS41395.1	1q21	2013-01-23	2003-11-07		ENSG00000182134	ENSG00000182134		"""Tudor domain containing"""	11713	protein-coding gene	gene with protein product		609501	"""tudor and KH domain containing"""			10767542	Standard	NM_001083964		Approved	TDRD2	uc001eza.4	Q9Y2W6	OTTHUMG00000013062	ENST00000368822.1:c.770G>C	1.37:g.151751274C>G	ENSP00000357812:p.Gly257Ala	Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	85	43	0.505882	NM_001083965	D3DV24|Q5SZR3|Q5SZR5|Q8N582|Q9NYV5	Missense_Mutation	SNP	ENST00000368822.1	37	CCDS41394.1	37	0.01694139194139194	0	0.0	3	0.008287292817679558	0	0.0	34	0.044854881266490766	C	14.42	2.530449	0.45073	0.007424	0.03797	ENSG00000182134	ENST00000368827;ENST00000368825;ENST00000368824;ENST00000368823;ENST00000368822;ENST00000458431;ENST00000440583	T;T;T;T;T;T;T	0.67865	-0.29;-0.29;-0.29;-0.29;-0.29;-0.29;-0.29	5.48	5.48	0.80851	.	0.743369	0.13380	N	0.392218	T	0.59797	0.2220	L	0.27053	0.805	0.39270	D	0.964376	D;D;D	0.76494	0.999;0.999;0.999	P;D;D	0.83275	0.896;0.923;0.996	T	0.50890	-0.8774	10	0.08179	T	0.78	-19.3116	14.7347	0.69406	0.0:1.0:0.0:0.0	rs17853082;rs52794258	212;253;257	Q5SZR5;Q5SZR4;Q9Y2W6	.;.;TDRKH_HUMAN	A	257;212;257;253;257;257;33	ENSP00000357819:G257A;ENSP00000357817:G212A;ENSP00000357815:G257A;ENSP00000357813:G253A;ENSP00000357812:G257A;ENSP00000395718:G257A;ENSP00000416645:G33A	ENSP00000357812:G257A	G	-	2	0	TDRKH	150017898	0.992000	0.36948	0.865000	0.33974	0.259000	0.26198	2.068000	0.41471	2.861000	0.98227	0.650000	0.86243	GGA	C|0.978;G|0.022	0.022	strong		0.547	TDRKH-005	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000036648.2	NM_006862	
PIM1	5292	hgsc.bcm.edu	37	6	37138412	37138412	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:37138412C>A	ENST00000373509.5	+	1	434	c.61C>A	c.(61-63)Cac>Aac	p.H21N		NM_001243186.1|NM_002648.3	NP_001230115.1|NP_002639.1	P11309	PIM1_HUMAN	Pim-1 proto-oncogene, serine/threonine kinase	112					apoptotic process (GO:0006915)|cell cycle (GO:0007049)|cell proliferation (GO:0008283)|hyaluronan metabolic process (GO:0030212)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|manganese ion binding (GO:0030145)|protein serine/threonine kinase activity (GO:0004674)|ribosomal small subunit binding (GO:0043024)|transcription factor binding (GO:0008134)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(17)|large_intestine(4)|lung(3)|prostate(2)|skin(2)	30			OV - Ovarian serous cystadenocarcinoma(102;0.241)		Adenosine monophosphate(DB00131)	CAACGACCTGCACGCCACCAA	0.726			T	BCL6	NHL																																p.H112N		Atlas-SNP	.		Dom	yes		6	6p21.2	5292	pim-1 oncogene		L	.	PIM1	71	.	0			c.C334A						PASS	.						25.0	27.0	26.0					6																	37138412		2199	4293	6492	SO:0001583	missense	5292	exon1			GACCTGCACGCCA		CCDS4830.1	6p21	2014-06-25	2014-06-25		ENSG00000137193	ENSG00000137193			8986	protein-coding gene	gene with protein product		164960	"""pim-1 oncogene"""	PIM			Standard	NM_002648		Approved		uc003onk.3	P11309	OTTHUMG00000016426	ENST00000373509.5:c.61C>A	6.37:g.37138412C>A	ENSP00000362608:p.His21Asn	Somatic	18	0	0		WXS	Illumina HiSeq	Phase_I	39	11	0.282051	NM_001243186	Q38RT9|Q5T7H7|Q96RG3	Missense_Mutation	SNP	ENST00000373509.5	37	CCDS4830.1	.	.	.	.	.	.	.	.	.	.	C	13.44	2.236939	0.39498	.	.	ENSG00000137193	ENST00000373509	T	0.68479	-0.33	4.2	3.33	0.38152	.	0.432965	0.20921	N	0.083268	T	0.21468	0.0517	N	0.08118	0	0.29891	N	0.825193	P	0.34615	0.459	B	0.32762	0.152	T	0.17899	-1.0354	10	0.10636	T	0.68	.	12.4383	0.55612	0.0:0.915:0.0:0.085	.	112	P11309	PIM1_HUMAN	N	21	ENSP00000362608:H21N	ENSP00000362608:H21N	H	+	1	0	PIM1	37246390	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	2.047000	0.41269	1.080000	0.41073	0.542000	0.68232	CAC	.	.	none		0.726	PIM1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043903.1		
TTLL3	26140	hgsc.bcm.edu	37	3	9876987	9876987	+	Silent	SNP	G	G	A	rs1057281	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:9876987G>A	ENST00000547186.1	+	13	2349	c.2133G>A	c.(2131-2133)agG>agA	p.R711R	TTLL3_ENST00000397241.1_3'UTR|TTLL3_ENST00000455274.1_Intron|TTLL3_ENST00000430793.1_3'UTR|TTLL3_ENST00000426895.4_Silent_p.R854R|ARPC4-TTLL3_ENST00000397256.1_3'UTR|TTLL3_ENST00000383827.1_3'UTR	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	65	0	0		WXS	Illumina HiSeq	Phase_I	39	38	0.974359	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	
SPATA21	374955	hgsc.bcm.edu	37	1	16736132	16736132	+	Missense_Mutation	SNP	T	T	C	rs4661746	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:16736132T>C	ENST00000335496.1	-	6	1033	c.551A>G	c.(550-552)cAg>cGg	p.Q184R	SPATA21_ENST00000466212.1_5'UTR|SPATA21_ENST00000540400.1_Missense_Mutation_p.Q161R	NM_198546.1	NP_940948.1	Q7Z572	SPT21_HUMAN	spermatogenesis associated 21	184			Q -> R (in dbSNP:rs4661746).				calcium ion binding (GO:0005509)			breast(1)|endometrium(2)|lung(8)|ovary(2)|pancreas(3)|stomach(1)|urinary_tract(2)	19		Colorectal(325;0.000147)|Renal(390;0.00145)|Lung NSC(340;0.00215)|Breast(348;0.00224)|all_lung(284;0.00351)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|COAD - Colon adenocarcinoma(227;1.15e-05)|BRCA - Breast invasive adenocarcinoma(304;4.2e-05)|Kidney(64;0.000183)|KIRC - Kidney renal clear cell carcinoma(64;0.00269)|STAD - Stomach adenocarcinoma(313;0.0122)|READ - Rectum adenocarcinoma(331;0.0651)		CTCGCTGCTCTGGTGCAAGAG	0.682													t|||	765	0.152756	0.0159	0.1686	5008	,	,		14091	0.1726		0.3161	False		,,,				2504	0.138				p.Q184R		Atlas-SNP	.											.	SPATA21	47	.	0			c.A551G						PASS	.		ARG/GLN	282,4124	149.2+/-183.4	9,264,1930	27.0	27.0	27.0		551	-1.8	0.0	1	dbSNP_111	27	2822,5778	425.0+/-354.8	512,1798,1990	yes	missense	SPATA21	NM_198546.1	43	521,2062,3920	CC,CT,TT		32.814,6.4004,23.8659	benign	184/470	16736132	3104,9902	2203	4300	6503	SO:0001583	missense	374955	exon6			CTGCTCTGGTGCA		CCDS172.1	1p36.13	2013-01-10			ENSG00000187144	ENSG00000187144		"""EF-hand domain containing"""	28026	protein-coding gene	gene with protein product							Standard	NM_198546		Approved	spergen-2, spergen2	uc001ayn.3	Q7Z572	OTTHUMG00000002312	ENST00000335496.1:c.551A>G	1.37:g.16736132T>C	ENSP00000335612:p.Gln184Arg	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	35	21	0.6	NM_198546	B9EK40|F5GXP5	Missense_Mutation	SNP	ENST00000335496.1	37	CCDS172.1	436	0.19963369963369965	14	0.028455284552845527	72	0.19889502762430938	115	0.20104895104895104	235	0.3100263852242744	t	8.622	0.891646	0.17613	0.064004	0.32814	ENSG00000187144	ENST00000335496;ENST00000540400	T;T	0.65732	-0.17;-0.15	4.03	-1.76	0.08006	.	1.538070	0.03919	N	0.283261	T	0.00012	0.0000	L	0.27053	0.805	0.80722	P	0.0	B;B	0.26195	0.144;0.037	B;B	0.18871	0.023;0.01	T	0.15321	-1.0441	9	0.38643	T	0.18	0.1062	2.3344	0.04243	0.3824:0.2539:0.0:0.3636	rs4661746;rs17453182;rs52812478;rs58066662;rs4661746	161;184	F5GXP5;Q7Z572	.;SPT21_HUMAN	R	184;161	ENSP00000335612:Q184R;ENSP00000440046:Q161R	ENSP00000335612:Q184R	Q	-	2	0	SPATA21	16608719	0.000000	0.05858	0.001000	0.08648	0.036000	0.12997	-0.374000	0.07484	-0.066000	0.12998	0.358000	0.22013	CAG	T|0.794;C|0.206	0.206	strong		0.682	SPATA21-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000006677.2	NM_198546	
TNFRSF10A	8797	hgsc.bcm.edu	37	8	23060256	23060256	+	Missense_Mutation	SNP	T	T	C	rs17620	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:23060256T>C	ENST00000221132.3	-	3	486	c.422A>G	c.(421-423)cAt>cGt	p.H141R		NM_003844.3	NP_003835.3	O00220	TR10A_HUMAN	tumor necrosis factor receptor superfamily, member 10a	141			H -> R (in dbSNP:rs6557634). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:9082980}.		activation of NF-kappaB-inducing kinase activity (GO:0007250)|apoptotic process (GO:0006915)|cellular response to mechanical stimulus (GO:0071260)|extrinsic apoptotic signaling pathway (GO:0097191)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|signal transduction (GO:0007165)|TRAIL-activated apoptotic signaling pathway (GO:0036462)	integral component of membrane (GO:0016021)	death receptor activity (GO:0005035)|protease binding (GO:0002020)|receptor activity (GO:0004872)|TRAIL binding (GO:0045569)|transcription factor binding (GO:0008134)			NS(2)|central_nervous_system(3)|endometrium(2)|large_intestine(3)|lung(1)|ovary(3)|prostate(1)|skin(1)	16		Prostate(55;0.0421)|Breast(100;0.14)		Colorectal(74;0.016)|COAD - Colon adenocarcinoma(73;0.0646)		GGCTCCAGGATGTTCTGATCT	0.483													T|||	2863	0.571685	0.2458	0.6153	5008	,	,		20194	0.9742		0.4553	False		,,,				2504	0.6861				p.H141R		Atlas-SNP	.											.	TNFRSF10A	40	.	0			c.A422G						PASS	.	T	ARG/HIS	1253,3153	428.9+/-342.0	159,935,1109	150.0	136.0	141.0		422	-7.0	0.0	8	dbSNP_116	141	3950,4650	551.3+/-385.9	925,2100,1275	yes	missense	TNFRSF10A	NM_003844.3	29	1084,3035,2384	CC,CT,TT		45.9302,28.4385,40.0046	possibly-damaging	141/469	23060256	5203,7803	2203	4300	6503	SO:0001583	missense	8797	exon3			CCAGGATGTTCTG	U90875	CCDS6039.1	8p21	2006-02-22			ENSG00000104689	ENSG00000104689		"""Tumor necrosis factor receptor superfamily"", ""CD molecules"""	11904	protein-coding gene	gene with protein product		603611				9311998, 9082980	Standard	NM_003844		Approved	DR4, Apo2, TRAILR-1, CD261	uc003xda.3	O00220	OTTHUMG00000097843	ENST00000221132.3:c.422A>G	8.37:g.23060256T>C	ENSP00000221132:p.His141Arg	Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	180	46	0.255556	NM_003844	A8K5I4|Q53Y72|Q96E62	Missense_Mutation	SNP	ENST00000221132.3	37	CCDS6039.1	1233	0.5645604395604396	114	0.23170731707317074	208	0.574585635359116	562	0.9825174825174825	349	0.4604221635883905	T	2.650	-0.282244	0.05642	0.284385	0.459302	ENSG00000104689	ENST00000221132	T	0.41758	0.99	3.48	-6.96	0.01622	.	1.045100	0.07583	U	0.920699	T	0.00012	0.0000	L	0.34521	1.04	0.80722	P	0.0	P	0.44006	0.824	B	0.34180	0.177	T	0.47611	-0.9104	9	0.44086	T	0.13	.	2.0798	0.03632	0.2808:0.3163:0.2827:0.1202	rs6557634;rs11550537;rs17687367;rs59866941;rs6557634	141	O00220	TR10A_HUMAN	R	141	ENSP00000221132:H141R	ENSP00000221132:H141R	H	-	2	0	TNFRSF10A	23116201	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.096000	0.01349	-4.586000	0.00041	-1.400000	0.01143	CAT	T|0.514;C|0.486	0.486	strong		0.483	TNFRSF10A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215133.2	NM_003844	
POTEE	445582	hgsc.bcm.edu	37	2	132021766	132021766	+	Missense_Mutation	SNP	A	A	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:132021766A>C	ENST00000356920.5	+	15	2832	c.2738A>C	c.(2737-2739)aAa>aCa	p.K913T	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	913	Actin-like.				retina homeostasis (GO:0001895)|substantia nigra development (GO:0021762)	blood microparticle (GO:0072562)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)		p.K913T(1)									CGTGACATCAAAGAGAAGCTG	0.602																																					p.K913T		Atlas-SNP	.											ENSG00000188219,rectum,NS,0,1	.	.	1	1	Substitution - Missense(1)	large_intestine(1)	c.A2738C						scavenged	.						73.0	77.0	75.0					2																	132021766		1926	3862	5788	SO:0001583	missense	445582	exon15			ACATCAAAGAGAA	AY462868	CCDS46414.1	2q21.1	2014-04-10	2008-11-26	2008-11-26	ENSG00000188219	ENSG00000188219		"""POTE ankyrin domain containing"", ""Ankyrin repeat domain containing"""	33895	protein-coding gene	gene with protein product	"""cancer/testis antigen family 104, member 2"""	608914	"""ANKRD26-like family C, member 1A"""	A26C1A			Standard	NM_001083538		Approved	POTE2, POTE-2, A26C1, POTE2gamma, CT104.2	uc002tsn.2	Q6S8J3	OTTHUMG00000186974	ENST00000356920.5:c.2738A>C	2.37:g.132021766A>C	ENSP00000439189:p.Lys913Thr	Somatic	157	5	0.0318471		WXS	Illumina HiSeq	Phase_I	144	7	0.0486111	NM_001083538	Q6S8J4|Q6S8J5|Q6S8J8	Missense_Mutation	SNP	ENST00000356920.5	37	CCDS46414.1	.	.	.	.	.	.	.	.	.	.	.	15.85	2.956333	0.53293	.	.	ENSG00000188219	ENST00000356920	D	0.97850	-4.57	.	.	.	.	.	.	.	.	D	0.99177	0.9715	H	0.99884	4.89	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.96111	0.9077	8	0.87932	D	0	.	4.5487	0.12098	0.9994:0.0:6.0E-4:0.0	.	913	Q6S8J3	POTEE_HUMAN	T	913	ENSP00000439189:K913T	ENSP00000439189:K913T	K	+	2	0	AC131180.1	131738236	1.000000	0.71417	0.327000	0.25402	0.329000	0.28539	6.177000	0.71961	0.103000	0.17682	0.102000	0.15555	AAA	.	.	none		0.602	POTEE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001083538	
IQUB	154865	hgsc.bcm.edu	37	7	123119990	123119990	+	Silent	SNP	T	T	C	rs10500091	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:123119990T>C	ENST00000466202.1	-	8	1845	c.1269A>G	c.(1267-1269)caA>caG	p.Q423Q	IQUB_ENST00000434450.1_Silent_p.Q423Q|IQUB_ENST00000324698.6_Silent_p.Q423Q	NM_001282855.1	NP_001269784.1	Q8NA54	IQUB_HUMAN	IQ motif and ubiquitin domain containing	423					cilium morphogenesis (GO:0060271)|smoothened signaling pathway (GO:0007224)	acrosomal vesicle (GO:0001669)|motile cilium (GO:0031514)				breast(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(18)|ovary(3)|prostate(2)|stomach(3)|upper_aerodigestive_tract(1)	45						CAGTAAAAGATTGGTTAATAC	0.378													T|||	1128	0.22524	0.0507	0.2478	5008	,	,		17942	0.3879		0.2853	False		,,,				2504	0.2157				p.Q423Q		Atlas-SNP	.											.	IQUB	117	.	0			c.A1269G						PASS	.	T		445,3961	212.5+/-232.4	22,401,1780	108.0	98.0	101.0		1269	-10.5	0.1	7	dbSNP_119	101	2325,6273	390.1+/-343.2	306,1713,2280	no	coding-synonymous	IQUB	NM_178827.4		328,2114,4060	CC,CT,TT		27.0412,10.0999,21.3011		423/792	123119990	2770,10234	2203	4299	6502	SO:0001819	synonymous_variant	154865	exon8			AAAAGATTGGTTA	AK093153	CCDS5787.1	7q31.32	2010-03-19			ENSG00000164675	ENSG00000164675			21995	protein-coding gene	gene with protein product							Standard	NM_178827		Approved	FLJ35834	uc003vko.3	Q8NA54	OTTHUMG00000157347	ENST00000466202.1:c.1269A>G	7.37:g.123119990T>C		Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	116	48	0.413793	NM_178827	A4D0X0|Q49AL6|Q4G189|Q5BJD9|Q6NUH6|Q8N9Y2	Silent	SNP	ENST00000466202.1	37	CCDS5787.1																																																																																			T|0.782;C|0.218	0.218	strong		0.378	IQUB-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348529.1	NM_178827	
ST6GAL2	84620	hgsc.bcm.edu	37	2	107423188	107423188	+	Silent	SNP	G	G	A	rs1470591	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:107423188G>A	ENST00000409382.3	-	6	2146	c.1536C>T	c.(1534-1536)ccC>ccT	p.P512P	ST6GAL2_ENST00000361686.4_Silent_p.P512P	NM_001142351.1	NP_001135823.1	Q96JF0	SIAT2_HUMAN	ST6 beta-galactosamide alpha-2,6-sialyltranferase 2	512					growth (GO:0040007)|multicellular organismal development (GO:0007275)|oligosaccharide metabolic process (GO:0009311)|protein glycosylation (GO:0006486)|sialylation (GO:0097503)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	beta-galactoside alpha-2,6-sialyltransferase activity (GO:0003835)			autonomic_ganglia(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(8)|liver(1)|lung(30)|ovary(5)|pancreas(6)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	65						CCTGGAAGCCGGGAAGAACCA	0.542													G|||	1094	0.21845	0.1823	0.3285	5008	,	,		18730	0.0377		0.4533	False		,,,				2504	0.1339				p.P512P		Atlas-SNP	.											ST6GAL2,NS,carcinoma,-1,1	ST6GAL2	159	1	0			c.C1536T						PASS	.	G	,	990,3416	370.8+/-319.7	101,788,1314	112.0	101.0	105.0		1536,1536	-11.6	0.0	2	dbSNP_88	105	3968,4632	551.5+/-385.9	900,2168,1232	no	coding-synonymous,coding-synonymous	ST6GAL2	NM_001142351.1,NM_032528.2	,	1001,2956,2546	AA,AG,GG		46.1395,22.4694,38.1209	,	512/530,512/530	107423188	4958,8048	2203	4300	6503	SO:0001819	synonymous_variant	84620	exon6			GAAGCCGGGAAGA	AB059555	CCDS2073.1, CCDS46380.1	2q11-q12	2008-02-05	2005-02-07	2005-02-07	ENSG00000144057	ENSG00000144057	2.4.99.2		10861	protein-coding gene	gene with protein product		608472	"""sialyltransferase 2 (monosialoganglioside sialyltransferase)"""	SIAT2			Standard	NM_032528		Approved	KIAA1877, St6gal2, St6GalII	uc002tdr.3	Q96JF0	OTTHUMG00000130923	ENST00000409382.3:c.1536C>T	2.37:g.107423188G>A		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	99	44	0.444444	NM_032528	D3DVK3|Q53QP4|Q86Y44|Q8IUG7|Q96HE4	Silent	SNP	ENST00000409382.3	37	CCDS2073.1	568	0.2600732600732601	91	0.18495934959349594	119	0.3287292817679558	16	0.027972027972027972	342	0.45118733509234826	G	0.016	-1.537599	0.00942	0.224694	0.461395	ENSG00000144057	ENST00000361803	.	.	.	5.8	-11.6	0.00059	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999995177	.	.	.	.	.	.	T	0.08554	-1.0716	3	.	.	.	-32.3354	5.7615	0.18203	0.1271:0.0587:0.471:0.3432	rs1470591;rs3796113;rs17629922;rs1470591	.	.	.	W	78	.	.	R	-	1	2	ST6GAL2	106789620	0.000000	0.05858	0.002000	0.10522	0.016000	0.09150	-5.699000	0.00104	-5.603000	0.00012	-5.073000	0.00001	CGG	G|0.679;A|0.321	0.321	strong		0.542	ST6GAL2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330065.1	NM_032528	
HOMEZ	57594	hgsc.bcm.edu	37	14	23746340	23746340	+	Missense_Mutation	SNP	C	C	T	rs565379852	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:23746340C>T	ENST00000357460.5	-	2	261	c.97G>A	c.(97-99)Ggt>Agt	p.G33S	HOMEZ_ENST00000561013.1_Missense_Mutation_p.G35S|HOMEZ_ENST00000431326.2_Missense_Mutation_p.G35S	NM_020834.2	NP_065885.2	Q8IX15	HOMEZ_HUMAN	homeobox and leucine zipper encoding	33					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)		CTACTGAGACCGCTGGCCTCT	0.532													C|||	2	0.000399361	0.0	0.0	5008	,	,		17905	0.002		0.0	False		,,,				2504	0.0				p.G33S		Atlas-SNP	.											.	HOMEZ	80	.	0			c.G97A						PASS	.						76.0	71.0	72.0					14																	23746340		1974	4166	6140	SO:0001583	missense	57594	exon2			TGAGACCGCTGGC	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.97G>A	14.37:g.23746340C>T	ENSP00000350049:p.Gly33Ser	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	63	29	0.460317	NM_020834	A1L445|B4DZ80|F8WCA3|Q6P049|Q86XB6|Q9P2A5	Missense_Mutation	SNP	ENST00000357460.5	37	CCDS45085.1	.	.	.	.	.	.	.	.	.	.	C	1.235	-0.622995	0.03636	.	.	ENSG00000215271	ENST00000357460;ENST00000431326	T;T	0.20200	2.09;2.09	5.95	2.18	0.27775	.	0.152484	0.56097	N	0.000023	T	0.07503	0.0189	N	0.08118	0	0.22835	N	0.998674	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.40478	-0.9561	10	0.02654	T	1	-7.3746	7.1207	0.25442	0.0:0.3237:0.0:0.6763	.	35;33	F8WCA3;Q8IX15	.;HOMEZ_HUMAN	S	33;35	ENSP00000350049:G33S;ENSP00000406579:G35S	ENSP00000350049:G33S	G	-	1	0	HOMEZ	22816180	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	0.878000	0.28126	0.494000	0.27859	-0.290000	0.09829	GGT	.	.	none		0.532	HOMEZ-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000416939.2	NM_020834	
HIVEP1	3096	hgsc.bcm.edu	37	6	12124257	12124257	+	Missense_Mutation	SNP	C	C	G	rs372404420		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:12124257C>G	ENST00000379388.2	+	4	4561	c.4229C>G	c.(4228-4230)cCt>cGt	p.P1410R	HIVEP1_ENST00000541134.1_5'Flank	NM_002114.2	NP_002105.2	P15822	ZEP1_HUMAN	human immunodeficiency virus type I enhancer binding protein 1	1410					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)				CCATCTTCACCTTCTCGAGTG	0.488																																					p.P1410R		Atlas-SNP	.											.	HIVEP1	242	.	0			c.C4229G						PASS	.	C	ARG/PRO	0,4074		0,0,2037	113.0	116.0	115.0		4229	4.9	0.3	6		115	1,8369		0,1,4184	no	missense	HIVEP1	NM_002114.2	103	0,1,6221	GG,GC,CC		0.0119,0.0,0.0080	possibly-damaging	1410/2719	12124257	1,12443	2037	4185	6222	SO:0001583	missense	3096	exon4			CTTCACCTTCTCG	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.4229C>G	6.37:g.12124257C>G	ENSP00000368698:p.Pro1410Arg	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	97	36	0.371134	NM_002114	B2RTU3|Q14122|Q5MPB1|Q5VW60	Missense_Mutation	SNP	ENST00000379388.2	37	CCDS43426.1	.	.	.	.	.	.	.	.	.	.	C	20.1	3.931801	0.73442	0.0	1.19E-4	ENSG00000095951	ENST00000379388	T	0.09538	2.97	5.79	4.93	0.64822	.	0.460558	0.16304	N	0.220330	T	0.08044	0.0201	L	0.57536	1.79	0.80722	D	1	D	0.53462	0.96	P	0.46718	0.525	T	0.14227	-1.0480	9	.	.	.	-6.1734	9.7069	0.40220	0.1398:0.79:0.0:0.0702	.	1410	P15822	ZEP1_HUMAN	R	1410	ENSP00000368698:P1410R	.	P	+	2	0	HIVEP1	12232243	0.278000	0.24230	0.260000	0.24451	0.175000	0.22909	3.441000	0.52893	1.454000	0.47793	0.655000	0.94253	CCT	.	.	weak		0.488	HIVEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039870.2	NM_002114	
HLA-DPB1	3115	hgsc.bcm.edu	37	6	33048600	33048600	+	Silent	SNP	T	T	G	rs386699870|rs9277351	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:33048600T>G	ENST00000418931.2	+	2	368	c.252T>G	c.(250-252)gcT>gcG	p.A84A	HLA-DPA1_ENST00000419277.1_5'Flank|HLA-DPB1_ENST00000471184.1_3'UTR|HLA-DPB1_ENST00000535465.1_Silent_p.A84A	NM_002121.5	NP_002112.3	P04440	DPB1_HUMAN	major histocompatibility complex, class II, DP beta 1	84	Beta-1.		A -> D (in allele DPB1*02:01, allele DPB1*03:01, allele DPB1*04:02, allele DPB1*05:02, allele DPB1*06:01, allele DPB1*06:02, allele DPB1*08:01, allele DPB1*09:01, allele DPB1*10:01, allele DPB1*10:02, allele DPB1*11:02, allele DPB1*14:01, allele DPB1*14:02, allele DPB1*16:01, allele DPB1*16:02, allele DPB1*17:01, allele DPB1*18:01, allele DPB1*18:01, allele DPB1*18:02, allele DPB1*19:02, allele DPB1*20:01, allele DPB1*22:02, allele DPB1*25:01, allele DPB1*25:02, allele DPB1*26:02, allele DPB1*28:01, allele DPB1*29:01, allele DPB1*32:01, allele DPB1*35:01, allele DPB1*37:01, allele DPB1*41:01, allele DPB1*44:01, allele DPB1*45:01, allele DPB1*46:01, allele DPB1*48:01, allele DPB1*49:01, allele DPB1*50:01, allele DPB1*51:01, allele DPB1*53:01, allele DPB1*57:01, allele DPB1*59:01, allele DPB1*60:01, allele DPB1*68:01, allele DPB1*69:01, allele DPB1*70:01, allele DPB1*73:01, allele DPB1*75:01, allele DPB1*76:01, allele DPB1*77:01, allele DPB1*78:01, allele DPB1*79:01, allele DPB1*80:01, allele DPB1*81:01, allele DPB1*82:01, allele DPB1*83:01, allele DPB1*86:01, allele DPB1*88:01, allele DPB1*91:01, allele DPB1*92:01, allele DPB1*93:01, allele DPB1*94:01 and allele DPB1*98:01; dbSNP:rs707958).|A -> E (in allele DPB1*01:02, allele DPB1*02:02, allele DPB1*02:03, allele DPB1*05:01, allele DPB1*08:02, allele DPB1*17:02, allele DPB1*19:01, allele DPB1*21:01, allele DPB1*22:01, allele DPB1*24:01, allele DPB1*30:01, allele DPB1*36:01, allele DPB1*38:01, allele DPB1*47:01, allele DPB1*54:01, allele DPB1*84:01 and allele DPB1*97:01).|A -> V (in dbSNP:rs707958).		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell proliferation (GO:0042102)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	peptide antigen binding (GO:0042605)			cervix(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(3)|ovary(1)|skin(1)	11						GGCGGCCTGCTGCGGAGTACT	0.647													.|||	600	0.119808	0.0098	0.0418	5008	,	,		13931	0.498		0.0417	False		,,,				2504	0.0143				p.A84A		Atlas-SNP	.											HLA-DPB1,brain,glioma,+1,1	HLA-DPB1	28	1	0			c.T252G						scavenged	.	T		34,2988		0,34,1477	55.0	57.0	56.0		252	-7.7	0.0	6	dbSNP_118	56	157,5261		2,153,2554	no	coding-synonymous	HLA-DPB1	NM_002121.5		2,187,4031	GG,GT,TT		2.8977,1.1251,2.263		84/259	33048600	191,8249	1511	2709	4220	SO:0001819	synonymous_variant	3115	exon2			GCCTGCTGCGGAG		CCDS4765.1	6p21.3	2013-01-11			ENSG00000223865	ENSG00000223865		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4940	protein-coding gene	gene with protein product		142858		HLA-DP1B			Standard	NM_002121		Approved		uc003ocu.2	P04440	OTTHUMG00000031076	ENST00000418931.2:c.252T>G	6.37:g.33048600T>G		Somatic	57	1	0.0175439		WXS	Illumina HiSeq	Phase_I	49	24	0.489796	NM_002121	A0PFJ7|A5I886|A8YPB3|B5U8B4|B7VF80|B7VF87|B8ZX68|B8ZYT0|B9W5S8|B9W6F7|B9W6F9|C0MPP5|C0MPQ2|C0MPQ3|C0MPQ5|C0MPQ6|C0MPQ7|C4R9J5|C5IZL1|O00259|O19698|O19700|O19702|O19749|O46884|O77952|O98215|O98216|O98217|O98218|O98219|O98222|O98223|P01916|P04232|P13763|P79493|P79608|Q0P0L4|Q0ZFN3|Q14279|Q27S71|Q29682|Q29684|Q29698|Q29714|Q29775|Q29776|Q29778|Q29779|Q29781|Q29827|Q29828|Q29879|Q29880|Q29898|Q29977|Q2MGW3|Q30015|Q30031|Q30032|Q30033|Q30034|Q30050|Q30051|Q30052|Q30053|Q30054|Q30055|Q30174|Q4GY31|Q4JHD8|Q5ENE0|Q5ENE1|Q5ENW3|Q5EP46|Q5EP47|Q5EP49|Q5EP51|Q5EP52|Q5EP53|Q5EP56|Q5I4H8|Q5I4H9|Q5ISH4|Q5ISH5|Q5SQ73|Q5STP2|Q5YLA6|Q6IVX1|Q6LBX2|Q6LBX3|Q6LBX4|Q6LBX5|Q6LBX6|Q6LBX7|Q6PWX6|Q6TAS4|Q714U1|Q714U2|Q7YQ10|Q860Z7|Q8HWL7|Q8HWT5|Q8SNC4|Q95HC1|Q95IT7|Q95IT8|Q9BD13|Q9GIM2|Q9GIM4|Q9GIX6|Q9GJ41|Q9MY67|Q9TNT7|Q9TQE2|Q9XS11|Q9XS12	Silent	SNP	ENST00000418931.2	37	CCDS4765.1	285	0.1304945054945055	4	0.008130081300813009	18	0.049723756906077346	235	0.41083916083916083	28	0.036939313984168866	T	8.246	0.808003	0.16467	0.011251	0.028977	ENSG00000223865	ENST00000416804	.	.	.	4.02	-7.69	0.01263	.	.	.	.	.	T	0.03390	0.0098	.	.	.	0.49915	P	1.6700000000002824E-4	.	.	.	.	.	.	T	0.29792	-1.0000	3	.	.	.	.	1.1463	0.01776	0.2153:0.1326:0.3457:0.3064	rs9277351;rs36072355	.	.	.	R	51	.	.	L	+	2	0	HLA-DPB1	33156578	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.692000	0.00391	-1.519000	0.01775	-1.136000	0.01936	CTG	C|0.004;G|0.058;T|0.937	0.058	strong		0.647	HLA-DPB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076106.2	NM_002121	
EVA1C	59271	hgsc.bcm.edu	37	21	33840095	33840095	+	Silent	SNP	C	C	T	rs8130653	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:33840095C>T	ENST00000300255.2	+	4	1046	c.573C>T	c.(571-573)taC>taT	p.Y191Y	EVA1C_ENST00000382699.3_Silent_p.Y191Y|EVA1C_ENST00000401402.3_Silent_p.Y191Y	NM_058187.3	NP_478067.2	P58658	EVA1C_HUMAN	eva-1 homolog C (C. elegans)	191	SUEL-type lectin 2. {ECO:0000255|PROSITE- ProRule:PRU00260}.					integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)										CTGCGACCTACGGCAGGAGGA	0.502													C|||	327	0.0652955	0.0439	0.062	5008	,	,		13438	0.0149		0.1173	False		,,,				2504	0.0951				p.Y191Y		Atlas-SNP	.											.	.	.	.	0			c.C573T						PASS	.	C		211,4195	129.8+/-166.5	5,201,1997	84.0	68.0	73.0		573	-11.1	0.1	21	dbSNP_116	73	902,7698	201.4+/-244.9	55,792,3453	no	coding-synonymous	C21orf63	NM_058187.3		60,993,5450	TT,TC,CC		10.4884,4.7889,8.5576		191/442	33840095	1113,11893	2203	4300	6503	SO:0001819	synonymous_variant	59271	exon4			GACCTACGGCAGG	AF358258	CCDS13614.1, CCDS68186.1	21q22.11	2012-11-05	2012-11-05	2012-11-05	ENSG00000166979	ENSG00000166979			13239	protein-coding gene	gene with protein product			"""chromosome 21 open reading frame 64"", ""chromosome 21 open reading frame 63"", ""family with sequence similarity 176, member C"""	C21orf64, C21orf63, FAM176C		11707072, 19470522	Standard	NM_058187		Approved	B18, PRED34, B19	uc002ypr.1	P58658	OTTHUMG00000064922	ENST00000300255.2:c.573C>T	21.37:g.33840095C>T		Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	44	29	0.659091	NM_058187	A6ND58|Q8IXZ0	Silent	SNP	ENST00000300255.2	37	CCDS13614.1																																																																																			C|0.917;T|0.083	0.083	strong		0.502	EVA1C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139403.1	NM_058187	
OR51F1	256892	hgsc.bcm.edu	37	11	4790758	4790758	+	Silent	SNP	G	G	A	rs11033796	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:4790758G>A	ENST00000380383.1	-	1	410	c.411C>T	c.(409-411)gaC>gaT	p.D137D	OR51F1_ENST00000343430.3_Silent_p.D130D|MMP26_ENST00000477339.1_Intron|MMP26_ENST00000380390.1_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	142	0	0		WXS	Illumina HiSeq	Phase_I	144	29	0.201389	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	
RADIL	55698	hgsc.bcm.edu	37	7	4841313	4841313	+	Missense_Mutation	SNP	A	A	G	rs6966329	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:4841313A>G	ENST00000399583.3	-	12	3000	c.2813T>C	c.(2812-2814)cTc>cCc	p.L938P	RADIL_ENST00000538469.1_Missense_Mutation_p.L698P|RADIL_ENST00000536091.1_3'UTR	NM_018059.4	NP_060529.4	Q96JH8	RADIL_HUMAN	Ras association and DIL domains	938			L -> P (in dbSNP:rs6966329). {ECO:0000269|PubMed:15489334}.		multicellular organismal development (GO:0007275)|signal transduction (GO:0007165)|substrate adhesion-dependent cell spreading (GO:0034446)	microtubule (GO:0005874)				NS(1)|biliary_tract(2)|breast(1)|central_nervous_system(3)|endometrium(2)|large_intestine(2)|lung(22)|pancreas(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	41		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0986)|OV - Ovarian serous cystadenocarcinoma(56;7.41e-15)		GAGGCCGCTGAGTCCGTTCCT	0.706													G|||	1611	0.321685	0.6929	0.1816	5008	,	,		14142	0.0476		0.1988	False		,,,				2504	0.3282				p.L938P		Atlas-SNP	.											.	RADIL	110	.	0			c.T2813C						PASS	.	G	PRO/LEU	1981,1773		532,917,428	7.0	9.0	8.0		2813	-4.7	0.0	7	dbSNP_116	8	1467,6725		154,1159,2783	no	missense	RADIL	NM_018059.4	98	686,2076,3211	GG,GA,AA		17.9077,47.2296,28.8632	benign	938/1076	4841313	3448,8498	1877	4096	5973	SO:0001583	missense	55698	exon12			CCGCTGAGTCCGT	AB058752	CCDS43544.1	7p22.1	2010-08-27			ENSG00000157927	ENSG00000157927			22226	protein-coding gene	gene with protein product		611491				16051602, 17704304	Standard	NM_018059		Approved	FLJ10324, KIAA1849, RASIP2	uc003snj.1	Q96JH8	OTTHUMG00000151753	ENST00000399583.3:c.2813T>C	7.37:g.4841313A>G	ENSP00000382492:p.Leu938Pro	Somatic	145	1	0.00689655		WXS	Illumina HiSeq	Phase_I	116	116	1	NM_018059	A4D1Z5|A5YM49|B7ZL20|Q0VFZ9|Q75LH3|Q9BSP5|Q9H0M6|Q9NW43|Q9NWC4	Missense_Mutation	SNP	ENST00000399583.3	37	CCDS43544.1	562	0.2573260073260073	321	0.6524390243902439	68	0.1878453038674033	28	0.04895104895104895	145	0.19129287598944592	g	7.674	0.687678	0.14973	0.527704	0.179077	ENSG00000157927	ENST00000399583;ENST00000316919;ENST00000538469	T;T	0.08282	3.19;3.11	4.38	-4.71	0.03279	.	1.741870	0.03289	N	0.187370	T	0.00012	0.0000	N	0.03608	-0.345	0.54753	P	1.3000000000040757E-5	B;B	0.09022	0.0;0.002	B;B	0.04013	0.0;0.001	T	0.37150	-0.9718	9	0.33141	T	0.24	-0.2438	3.9384	0.09316	0.6381:0.1122:0.1292:0.1205	rs6966329;rs10365081;rs59937119	938;246	Q96JH8;Q75LH2	RADIL_HUMAN;.	P	938;909;698	ENSP00000382492:L938P;ENSP00000442966:L698P	ENSP00000320946:L909P	L	-	2	0	RADIL	4807839	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-1.097000	0.03349	-1.885000	0.01118	-2.333000	0.00248	CTC	A|0.744;G|0.256	0.256	strong		0.706	RADIL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323769.2	NM_018059	
PLSCR1	5359	hgsc.bcm.edu	37	3	146234909	146234909	+	Missense_Mutation	SNP	G	G	A	rs343320	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:146234909G>A	ENST00000342435.4	-	8	1194	c.784C>T	c.(784-786)Cac>Tac	p.H262Y	PLSCR1_ENST00000487389.1_Missense_Mutation_p.H255Y|PLSCR1_ENST00000448787.2_Missense_Mutation_p.H181Y|PLSCR1_ENST00000448205.1_5'UTR|PLSCR1_ENST00000484560.1_5'UTR	NM_021105.2	NP_066928.1	O15162	PLS1_HUMAN	phospholipid scramblase 1	262			H -> Y (in dbSNP:rs343320).		acute-phase response (GO:0006953)|apoptotic process (GO:0006915)|defense response to virus (GO:0051607)|negative regulation of viral genome replication (GO:0045071)|phosphatidylserine biosynthetic process (GO:0006659)|phospholipid scrambling (GO:0017121)|platelet activation (GO:0030168)|positive regulation of DNA topoisomerase (ATP-hydrolyzing) activity (GO:2000373)|positive regulation of gene expression (GO:0010628)|positive regulation of innate immune response (GO:0045089)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of Fc receptor mediated stimulatory signaling pathway (GO:0060368)|regulation of mast cell activation (GO:0033003)|response to interferon-beta (GO:0035456)	cytosol (GO:0005829)|extracellular matrix (GO:0031012)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|membrane raft (GO:0045121)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|CD4 receptor binding (GO:0042609)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|epidermal growth factor receptor binding (GO:0005154)|phospholipid scramblase activity (GO:0017128)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|SH3 domain binding (GO:0017124)			breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(5)|ovary(2)|prostate(1)|skin(1)	15						CCAGTCCAGTGCTTGGAAATT	0.333													G|||	148	0.0295527	0.0061	0.0533	5008	,	,		14069	0.0		0.0726	False		,,,				2504	0.0307				p.H262Y		Atlas-SNP	.											.	PLSCR1	35	.	0			c.C784T						PASS	.	G	TYR/HIS	72,4334		0,72,2131	88.0	86.0	87.0		784	4.0	0.6	3	dbSNP_79	87	698,7902		27,644,3629	yes	missense	PLSCR1	NM_021105.2	83	27,716,5760	AA,AG,GG		8.1163,1.6341,5.9203	possibly-damaging	262/319	146234909	770,12236	2203	4300	6503	SO:0001583	missense	5359	exon8			TCCAGTGCTTGGA	AF098642	CCDS3135.1	3q23	2004-02-27			ENSG00000188313	ENSG00000188313			9092	protein-coding gene	gene with protein product		604170				9218461	Standard	NM_021105		Approved	MMTRA1B	uc003evx.4	O15162	OTTHUMG00000159427	ENST00000342435.4:c.784C>T	3.37:g.146234909G>A	ENSP00000345494:p.His262Tyr	Somatic	179	0	0		WXS	Illumina HiSeq	Phase_I	137	74	0.540146	NM_021105	B2R8H8|B4DTE8	Missense_Mutation	SNP	ENST00000342435.4	37	CCDS3135.1	79	0.036172161172161175	6	0.012195121951219513	22	0.06077348066298342	0	0.0	51	0.06728232189973615	.	17.43	3.387636	0.61956	0.016341	0.081163	ENSG00000188313	ENST00000342435;ENST00000487389;ENST00000448787;ENST00000462666	T;T;T;T	0.29142	1.58;1.58;1.58;1.97	4.84	3.95	0.45737	.	1.141540	0.07295	U	0.873100	T	0.01387	0.0045	N	0.11131	0.1	0.80722	D	1	P;P	0.51449	0.945;0.904	P;P	0.47626	0.483;0.552	T	0.06409	-1.0828	10	0.36615	T	0.2	.	14.6731	0.68958	0.0:0.0:0.8534:0.1466	rs343320;rs52835043;rs343320	181;262	B4DTE8;O15162	.;PLS1_HUMAN	Y	262;255;181;238	ENSP00000345494:H262Y;ENSP00000417792:H255Y;ENSP00000411675:H181Y;ENSP00000418103:H238Y	ENSP00000345494:H262Y	H	-	1	0	PLSCR1	147717599	0.998000	0.40836	0.647000	0.29507	0.716000	0.41182	1.823000	0.39062	1.130000	0.42092	0.555000	0.69702	CAC	G|0.948;A|0.052	0.052	strong		0.333	PLSCR1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355257.2	NM_021105	
OR5P2	120065	hgsc.bcm.edu	37	11	7817538	7817538	+	Missense_Mutation	SNP	T	T	C	rs7949771	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:7817538T>C	ENST00000329434.2	-	1	982	c.952A>G	c.(952-954)Aat>Gat	p.N318D	RP11-35J10.5_ENST00000527565.1_lincRNA	NM_153444.1	NP_703145.1	Q8WZ92	OR5P2_HUMAN	olfactory receptor, family 5, subfamily P, member 2	318			N -> D (in dbSNP:rs7949771).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(4)	22				Epithelial(150;8.62e-08)|BRCA - Breast invasive adenocarcinoma(625;0.189)		ATATCATTATTTGAAGTTCTA	0.358													T|||	1185	0.236621	0.3472	0.2911	5008	,	,		18403	0.128		0.2763	False		,,,				2504	0.1196				p.N318D		Atlas-SNP	.											.	OR5P2	68	.	0			c.A952G						PASS	.	T	ASP/ASN	1362,2854		395,572,1141	89.0	125.0	113.0		952	-0.8	0.0	11	dbSNP_116	113	2420,6164		390,1640,2262	yes	missense	OR5P2	NM_153444.1	23	785,2212,3403	CC,CT,TT		28.192,32.3055,29.5469	possibly-damaging	318/323	7817538	3782,9018	2108	4292	6400	SO:0001583	missense	120065	exon1			CATTATTTGAAGT	AF173006	CCDS7782.1	11p15.4	2012-08-09			ENSG00000183303	ENSG00000183303		"""GPCR / Class A : Olfactory receptors"""	14783	protein-coding gene	gene with protein product							Standard	NM_153444		Approved	JCG3	uc001mfp.1	Q8WZ92	OTTHUMG00000165668	ENST00000329434.2:c.952A>G	11.37:g.7817538T>C	ENSP00000331823:p.Asn318Asp	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	79	65	0.822785	NM_153444	Q3MIS8	Missense_Mutation	SNP	ENST00000329434.2	37	CCDS7782.1	587	0.26877289377289376	180	0.36585365853658536	100	0.27624309392265195	85	0.1486013986013986	222	0.2928759894459103	T	1.029	-0.682344	0.03353	0.323055	0.28192	ENSG00000183303	ENST00000329434	T	0.00036	8.86	4.92	-0.787	0.10943	.	1.021990	0.07869	N	0.967611	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.22604	0.072	B	0.14023	0.01	T	0.00068	-1.2139	9	0.30078	T	0.28	-0.4362	6.1083	0.20086	0.3063:0.137:0.0:0.5567	rs7949771;rs7949771	318	Q8WZ92	OR5P2_HUMAN	D	318	ENSP00000331823:N318D	ENSP00000331823:N318D	N	-	1	0	OR5P2	7774114	.	.	0.000000	0.03702	0.002000	0.02628	.	.	0.072000	0.16694	-0.425000	0.05940	AAT	T|0.748;C|0.252	0.252	strong		0.358	OR5P2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385696.1	NM_153444	
GRIN2B	2904	hgsc.bcm.edu	37	12	13764774	13764774	+	Silent	SNP	G	G	A	rs1805482	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:13764774G>A	ENST00000609686.1	-	8	1874	c.1665C>T	c.(1663-1665)agC>agT	p.S555S		NM_000834.3	NP_000825.2	Q13224	NMDE2_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2B	555					behavioral fear response (GO:0001662)|behavioral response to pain (GO:0048266)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|glutamate receptor signaling pathway (GO:0007215)|in utero embryonic development (GO:0001701)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|learning (GO:0007612)|learning or memory (GO:0007611)|memory (GO:0007613)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of synaptic plasticity (GO:0048167)|response to ethanol (GO:0045471)|sensory organ development (GO:0007423)|startle response (GO:0001964)|suckling behavior (GO:0001967)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuron projection (GO:0043005)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|synaptic vesicle (GO:0008021)	calcium channel activity (GO:0005262)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glycine binding (GO:0016594)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|central_nervous_system(5)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(12)|liver(1)|lung(70)|ovary(4)|prostate(6)|skin(10)|upper_aerodigestive_tract(5)|urinary_tract(1)	143					Acamprosate(DB00659)|Acetylcysteine(DB06151)|Atomoxetine(DB00289)|Felbamate(DB00949)|Gabapentin(DB00996)|Haloperidol(DB00502)|Ketobemidone(DB06738)|Memantine(DB01043)|Milnacipran(DB04896)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	ATACGTCAGCGCTGAATGGCT	0.453													g|||	952	0.190096	0.1536	0.3718	5008	,	,		21319	0.0089		0.33	False		,,,				2504	0.1534				p.S555S		Atlas-SNP	.											.	GRIN2B	303	.	0			c.C1665T						PASS	.	A		769,3637	313.6+/-293.2	76,617,1510	120.0	105.0	110.0		1665	-8.0	0.5	12	dbSNP_92	110	2874,5726	451.1+/-362.6	484,1906,1910	no	coding-synonymous	GRIN2B	NM_000834.3		560,2523,3420	AA,AG,GG		33.4186,17.4535,28.0101		555/1485	13764774	3643,9363	2203	4300	6503	SO:0001819	synonymous_variant	2904	exon8			GTCAGCGCTGAAT		CCDS8662.1	12p13.1	2014-07-16			ENSG00000273079			"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4586	protein-coding gene	gene with protein product		138252		NMDAR2B		1350383	Standard	NM_000834		Approved	GluN2B	uc001rbt.2	Q13224	OTTHUMG00000137373	ENST00000609686.1:c.1665C>T	12.37:g.13764774G>A		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	76	29	0.381579	NM_000834	Q12919|Q13220|Q13225|Q14CU4|Q9UM56	Silent	SNP	ENST00000609686.1	37	CCDS8662.1																																																																																			G|0.753;A|0.247	0.247	strong		0.453	GRIN2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268014.2		
IL1A	3552	hgsc.bcm.edu	37	2	113537223	113537223	+	Missense_Mutation	SNP	C	C	A	rs17561	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:113537223C>A	ENST00000263339.3	-	5	495	c.340G>T	c.(340-342)Gca>Tca	p.A114S		NM_000575.3	NP_000566.3	P01583	IL1A_HUMAN	interleukin 1, alpha	114			A -> S (in dbSNP:rs17561). {ECO:0000269|PubMed:2635664, ECO:0000269|PubMed:2994016, ECO:0000269|Ref.10}.		apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|cellular response to heat (GO:0034605)|cytokine-mediated signaling pathway (GO:0019221)|ectopic germ cell programmed cell death (GO:0035234)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|fever generation (GO:0001660)|immune response (GO:0006955)|inflammatory response (GO:0006954)|negative regulation of cell proliferation (GO:0008285)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell division (GO:0051781)|positive regulation of cytokine secretion (GO:0050715)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of mitosis (GO:0045840)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation vascular endothelial growth factor production (GO:0010575)|response to copper ion (GO:0046688)	cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	copper ion binding (GO:0005507)|cytokine activity (GO:0005125)			breast(2)|large_intestine(1)|lung(9)	12					Rilonacept(DB06372)	CTAAAAGGTGCTGACCTAGGC	0.373													C|||	1089	0.217452	0.1672	0.2666	5008	,	,		21276	0.0734		0.2873	False		,,,				2504	0.3272				p.A114S		Atlas-SNP	.											.	IL1A	19	.	0			c.G340T						PASS	.	C	SER/ALA	808,3598	324.0+/-298.4	64,680,1459	119.0	100.0	106.0		340	4.4	0.0	2	dbSNP_63	106	2595,6005	420.3+/-353.3	397,1801,2102	yes	missense	IL1A	NM_000575.3	99	461,2481,3561	AA,AC,CC		30.1744,18.3386,26.1648	possibly-damaging	114/272	113537223	3403,9603	2203	4300	6503	SO:0001583	missense	3552	exon5			AAGGTGCTGACCT	M28983	CCDS2101.1	2q14	2014-01-30			ENSG00000115008	ENSG00000115008		"""Interleukins and interleukin receptors"", ""Endogenous ligands"""	5991	protein-coding gene	gene with protein product	"""preinterleukin 1 alpha"", ""hematopoietin-1"", ""pro-interleukin-1-alpha"""	147760		IL1		8188271, 2989698	Standard	NM_000575		Approved	IL1F1, IL-1A, IL1-ALPHA	uc002tig.3	P01583	OTTHUMG00000131315	ENST00000263339.3:c.340G>T	2.37:g.113537223C>A	ENSP00000263339:p.Ala114Ser	Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	124	62	0.5	NM_000575	Q53QF9|Q7RU02	Missense_Mutation	SNP	ENST00000263339.3	37	CCDS2101.1	443	0.20283882783882784	82	0.16666666666666666	89	0.24585635359116023	48	0.08391608391608392	224	0.2955145118733509	C	17.73	3.461982	0.63513	0.183386	0.301744	ENSG00000115008	ENST00000263339	T	0.17370	2.28	4.44	4.44	0.53790	.	0.521936	0.17528	N	0.170990	T	0.00012	0.0000	L	0.55990	1.75	0.80722	P	0.0	D	0.58268	0.982	P	0.50314	0.637	T	0.47368	-0.9123	9	0.22109	T	0.4	-37.2091	12.8839	0.58032	0.0:1.0:0.0:0.0	rs17561;rs1126753;rs1799942;rs3181980;rs3783542;rs11539014;rs17411697;rs52796584;rs60436142;rs17561	114	P01583	IL1A_HUMAN	S	114	ENSP00000263339:A114S	ENSP00000263339:A114S	A	-	1	0	IL1A	113253694	0.010000	0.17322	0.009000	0.14445	0.005000	0.04900	2.817000	0.48034	2.761000	0.94854	0.650000	0.86243	GCA	C|0.765;A|0.235	0.235	strong		0.373	IL1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254084.1	NM_000575	
FBXO40	51725	hgsc.bcm.edu	37	3	121340536	121340536	+	Missense_Mutation	SNP	T	T	C	rs4676684	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:121340536T>C	ENST00000338040.4	+	3	674	c.260T>C	c.(259-261)gTg>gCg	p.V87A		NM_016298.3	NP_057382.2	Q9UH90	FBX40_HUMAN	F-box protein 40	87			V -> A (in dbSNP:rs4676684).		muscle cell differentiation (GO:0042692)	cytoplasm (GO:0005737)	ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|kidney(1)|large_intestine(11)|lung(19)|ovary(2)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	46				GBM - Glioblastoma multiforme(114;0.189)		CACCTGCAGGTGTGCCCCGCC	0.582													T|||	2192	0.4377	0.382	0.5259	5008	,	,		18771	0.5873		0.2525	False		,,,				2504	0.4867				p.V87A		Atlas-SNP	.											.	FBXO40	108	.	0			c.T260C						PASS	.	T	ALA/VAL	1501,2905	473.5+/-356.7	255,991,957	49.0	54.0	52.0		260	3.1	1.0	3	dbSNP_111	52	2110,6490	361.0+/-332.2	256,1598,2446	yes	missense	FBXO40	NM_016298.3	64	511,2589,3403	CC,CT,TT		24.5349,34.0672,27.7641	benign	87/710	121340536	3611,9395	2203	4300	6503	SO:0001583	missense	51725	exon3			TGCAGGTGTGCCC	AF204674	CCDS33835.1	3q21.1	2004-08-24			ENSG00000163833	ENSG00000163833		"""F-boxes /  ""other"""""	29816	protein-coding gene	gene with protein product		609107				10574462	Standard	NM_016298		Approved	KIAA1195, Fbx40	uc003eeg.2	Q9UH90	OTTHUMG00000159410	ENST00000338040.4:c.260T>C	3.37:g.121340536T>C	ENSP00000337510:p.Val87Ala	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	88	42	0.477273	NM_016298	B2RAX7|Q32M70|Q9ULM5	Missense_Mutation	SNP	ENST00000338040.4	37	CCDS33835.1	884	0.40476190476190477	204	0.4146341463414634	173	0.47790055248618785	311	0.5437062937062938	196	0.25857519788918204	T	10.57	1.387480	0.25031	0.340672	0.245349	ENSG00000163833	ENST00000338040	T	0.41400	1.0	5.47	3.06	0.35304	Zinc finger, TRAF-type (1);Seven In Absentia Homolog-type (1);	0.352897	0.29383	N	0.012307	T	0.00012	0.0000	L	0.46157	1.445	0.26482	P	0.9750886	B	0.31318	0.319	B	0.26416	0.069	T	0.47262	-0.9131	9	0.37606	T	0.19	-4.9402	7.3204	0.26523	0.0:0.1948:0.0:0.8052	rs4676684	87	Q9UH90	FBX40_HUMAN	A	87	ENSP00000337510:V87A	ENSP00000337510:V87A	V	+	2	0	FBXO40	122823226	0.990000	0.36364	0.993000	0.49108	0.977000	0.68977	1.820000	0.39032	0.882000	0.36016	-0.408000	0.06270	GTG	T|0.693;C|0.307	0.307	strong		0.582	FBXO40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355158.1	NM_016298	
MKI67	4288	hgsc.bcm.edu	37	10	129903465	129903465	+	Silent	SNP	A	A	G	rs2857028	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	252	1	0.00396825		WXS	Illumina HiSeq	Phase_I	212	102	0.481132	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	
C1orf68	100129271	hgsc.bcm.edu	37	1	152692512	152692512	+	Missense_Mutation	SNP	G	G	A	rs41268474	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:152692512G>A	ENST00000368775.2	+	1	515	c.515G>A	c.(514-516)tGt>tAt	p.C172Y		NM_001024679.2	NP_001019850.1	Q5T750	XP32_HUMAN	chromosome 1 open reading frame 68	172	Cys-rich.				epidermis development (GO:0008544)	extracellular vesicular exosome (GO:0070062)				NS(1)|breast(1)|lung(2)|prostate(1)|stomach(3)	8						AGCTACTGCTGTCTGGCTCCC	0.577													G|||	500	0.0998403	0.1104	0.0648	5008	,	,		19222	0.1002		0.0974	False		,,,				2504	0.1125				p.C172Y		Atlas-SNP	.											.	C1orf68	19	.	0			c.G515A						PASS	.	G	TYR/CYS	158,1226		13,132,547	70.0	66.0	67.0		515	0.8	1.0	1	dbSNP_127	67	293,2889		13,267,1311	yes	missense	C1orf68	NM_001024679.2	194	26,399,1858	AA,AG,GG		9.208,11.4162,9.8774	benign	172/251	152692512	451,4115	692	1591	2283	SO:0001583	missense	100129271	exon1			ACTGCTGTCTGGC	AF005081	CCDS44226.1	1q21.3	2014-05-30			ENSG00000198854	ENSG00000198854			29468	protein-coding gene	gene with protein product						11698679	Standard	NM_001024679		Approved	LEP7	uc010pdu.2	Q5T750	OTTHUMG00000012401	ENST00000368775.2:c.515G>A	1.37:g.152692512G>A	ENSP00000357764:p.Cys172Tyr	Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	190	79	0.415789	NM_001024679	O14634	Missense_Mutation	SNP	ENST00000368775.2	37	CCDS44226.1	214	0.09798534798534798	54	0.10975609756097561	27	0.07458563535911603	59	0.10314685314685315	74	0.09762532981530343	G	11.17	1.559716	0.27827	0.114162	0.09208	ENSG00000198854	ENST00000362017;ENST00000368775	T;T	0.23950	1.88;1.88	5.1	0.809	0.18725	.	0.174767	0.27986	N	0.017057	T	0.04048	0.0113	N	0.14661	0.345	0.38272	P	0.05782299999999996	B	0.09022	0.002	B	0.10450	0.005	T	0.34403	-0.9830	9	0.30854	T	0.27	-3.4175	5.0103	0.14310	0.1878:0.3318:0.4804:0.0	rs41268474	172	Q5T750	XP32_HUMAN	Y	172	ENSP00000354769:C172Y;ENSP00000357764:C172Y	ENSP00000354769:C172Y	C	+	2	0	C1orf68	150959136	0.804000	0.28969	0.988000	0.46212	0.896000	0.52359	0.483000	0.22292	0.645000	0.30675	0.555000	0.69702	TGT	G|0.900;A|0.100	0.100	strong		0.577	C1orf68-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034521.2	NM_001024679	
ANKRD13A	88455	hgsc.bcm.edu	37	12	110449872	110449872	+	Missense_Mutation	SNP	T	T	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:110449872T>A	ENST00000261739.4	+	2	325	c.159T>A	c.(157-159)caT>caA	p.H53Q	ANKRD13A_ENST00000550404.1_3'UTR	NM_033121.1	NP_149112.1	Q8IZ07	AN13A_HUMAN	ankyrin repeat domain 13A	53						endosome (GO:0005768)|plasma membrane (GO:0005886)				endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(8)|lung(3)|urinary_tract(1)	16						CCTTGGGACATTTGGAATCTG	0.413																																					p.H53Q		Atlas-SNP	.											.	ANKRD13A	39	.	0			c.T159A						PASS	.						129.0	115.0	120.0					12																	110449872		2203	4300	6503	SO:0001583	missense	88455	exon2			GGGACATTTGGAA	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.159T>A	12.37:g.110449872T>A	ENSP00000261739:p.His53Gln	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	72	15	0.208333	NM_033121	O60736	Missense_Mutation	SNP	ENST00000261739.4	37	CCDS9140.1	.	.	.	.	.	.	.	.	.	.	T	25.0	4.594305	0.86953	.	.	ENSG00000076513	ENST00000261739	T	0.66460	-0.21	6.17	1.29	0.21616	Ankyrin repeat-containing domain (3);	0.043066	0.85682	D	0.000000	T	0.64271	0.2583	L	0.39020	1.185	0.80722	D	1	D;D;D	0.61080	0.966;0.989;0.966	P;P;P	0.55055	0.69;0.767;0.69	T	0.63033	-0.6727	10	0.66056	D	0.02	-17.1926	9.0087	0.36129	0.0:0.3655:0.0:0.6345	.	53;53;53	B4DYP5;Q3ZTS7;Q8IZ07	.;.;AN13A_HUMAN	Q	53	ENSP00000261739:H53Q	ENSP00000261739:H53Q	H	+	3	2	ANKRD13A	108934255	0.996000	0.38824	0.984000	0.44739	0.996000	0.88848	0.671000	0.25172	0.199000	0.20427	0.533000	0.62120	CAT	.	.	none		0.413	ANKRD13A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403430.1	NM_033121	
TNFRSF6B	8771	hgsc.bcm.edu	37	20	62328453	62328453	+	Silent	SNP	T	T	C	rs2258056	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:62328453T>C	ENST00000369996.1	+	1	433	c.333T>C	c.(331-333)cgT>cgC	p.R111R	ARFRP1_ENST00000485858.1_5'Flank|RTEL1-TNFRSF6B_ENST00000482936.1_3'UTR	NM_003823.3	NP_003814.1	O95407	TNF6B_HUMAN	tumor necrosis factor receptor superfamily, member 6b, decoy	111					apoptotic process (GO:0006915)|negative regulation of apoptotic process (GO:0043066)	extracellular space (GO:0005615)	receptor activity (GO:0004872)			central_nervous_system(1)|lung(2)|skin(1)	4	all_cancers(38;4.66e-12)|all_epithelial(29;2.56e-13)|Lung NSC(23;1.06e-08)|all_lung(23;3.34e-08)		Epithelial(9;1.78e-08)|all cancers(9;7.89e-08)|OV - Ovarian serous cystadenocarcinoma(5;0.00504)			CCCACAACCGTGCCTGCCGCT	0.662													C|||	1323	0.264177	0.0242	0.2666	5008	,	,		16647	0.6468		0.2048	False		,,,				2504	0.2536				p.R111R		Atlas-SNP	.											TNFRSF6B,NS,carcinoma,0,1	TNFRSF6B	22	1	0			c.T333C						PASS	.	C		294,4036		15,264,1886	11.0	13.0	12.0		333	-5.2	0.1	20	dbSNP_100	12	1841,6681		205,1431,2625	no	coding-synonymous	TNFRSF6B	NM_003823.3		220,1695,4511	CC,CT,TT		21.6029,6.7898,16.6122		111/301	62328453	2135,10717	2165	4261	6426	SO:0001819	synonymous_variant	8771	exon1			CAACCGTGCCTGC	AF104419	CCDS13532.1	20q13.33	2012-06-27						"""Tumor necrosis factor receptor superfamily"""	11921	protein-coding gene	gene with protein product		603361				9872321, 10318773	Standard	NM_003823		Approved	DcR3, DCR3, TR6, M68	uc002yfz.3	O95407	OTTHUMG00000143724	ENST00000369996.1:c.333T>C	20.37:g.62328453T>C		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	52	18	0.346154	NM_003823		Silent	SNP	ENST00000369996.1	37	CCDS13532.1																																																																																			T|0.778;C|0.222	0.222	strong		0.662	TNFRSF6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080182.1		
OR8U1	219417	hgsc.bcm.edu	37	11	56143424	56143424	+	Missense_Mutation	SNP	A	A	G	rs12788990	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:56143424A>G	ENST00000302270.1	+	1	325	c.325A>G	c.(325-327)Ata>Gta	p.I109V		NM_001005204.1	NP_001005204.1	Q8NH10	OR8U1_HUMAN	olfactory receptor, family 8, subfamily U, member 1	109			I -> V (in dbSNP:rs12788990).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.I109V(1)		NS(1)|breast(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(1)|lung(23)|ovary(4)|skin(1)|stomach(1)	39	Esophageal squamous(21;0.00448)					CACCTTCATGATATCAGAATC	0.408													A|||	519	0.103634	0.1725	0.036	5008	,	,		23035	0.0933		0.0934	False		,,,				2504	0.0798				p.I109V		Atlas-SNP	.											OR8U1,NS,carcinoma,0,1	OR8U1	59	1	1	Substitution - Missense(1)	stomach(1)	c.A325G						PASS	.	A	VAL/ILE	597,3563		46,505,1529	175.0	167.0	169.0		325	1.0	0.1	11	dbSNP_121	169	728,7764		31,666,3549	yes	missense	OR8U1	NM_001005204.1	29	77,1171,5078	GG,GA,AA		8.5728,14.351,10.4727	benign	109/310	56143424	1325,11327	2080	4246	6326	SO:0001583	missense	219417	exon1			TTCATGATATCAG	AB065603	CCDS41647.1	11q11	2012-08-09			ENSG00000172199	ENSG00000172199		"""GPCR / Class A : Olfactory receptors"""	19611	protein-coding gene	gene with protein product							Standard	NM_001005204		Approved			Q8NH10	OTTHUMG00000166860	ENST00000302270.1:c.325A>G	11.37:g.56143424A>G	ENSP00000304188:p.Ile109Val	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	53	25	0.471698	NM_001005204		Missense_Mutation	SNP	ENST00000302270.1	37	CCDS41647.1	229	0.10485347985347986	104	0.21138211382113822	19	0.052486187845303865	40	0.06993006993006994	66	0.0870712401055409	A	0.006	-2.037402	0.00406	0.14351	0.085728	ENSG00000172199	ENST00000302270	T	0.02916	4.11	5.78	1.02	0.19986	GPCR, rhodopsin-like superfamily (1);	1.290760	0.05319	N	0.526262	T	0.00012	0.0000	L	0.34521	1.04	0.80722	P	0.0	B	0.02656	0.0	B	0.06405	0.002	T	0.47947	-0.9077	9	0.24483	T	0.36	.	8.9956	0.36050	0.4219:0.0:0.5781:0.0	rs12788990;rs12788990	109	Q8NH10	OR8U1_HUMAN	V	109	ENSP00000304188:I109V	ENSP00000304188:I109V	I	+	1	0	OR8U1	55900000	0.000000	0.05858	0.116000	0.21606	0.003000	0.03518	-3.335000	0.00508	0.146000	0.19002	0.523000	0.50628	ATA	A|0.893;G|0.107	0.107	strong		0.408	OR8U1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391607.1	NM_001005204	
CPXCR1	53336	hgsc.bcm.edu	37	X	88008807	88008807	+	Missense_Mutation	SNP	G	G	A	rs5984611	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	167	0	0		WXS	Illumina HiSeq	Phase_I	82	82	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	
LRP2	4036	hgsc.bcm.edu	37	2	170099473	170099473	+	Silent	SNP	T	T	C	rs386652562|rs831042	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:170099473T>C	ENST00000263816.3	-	24	3945	c.3660A>G	c.(3658-3660)gcA>gcG	p.A1220A	LRP2_ENST00000443831.1_Silent_p.A1083A	NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	1220	LDL-receptor class A 12. {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)"""	TACGACAGCCTGCTTCATCCG	0.413													C|||	2914	0.581869	0.6082	0.6153	5008	,	,		18176	0.4772		0.4612	False		,,,				2504	0.7546				p.A1220A		Atlas-SNP	.											.	LRP2	751	.	0			c.A3660G						PASS	.	C		2681,1725	518.1+/-369.6	832,1017,354	161.0	158.0	159.0		3660	-7.4	0.0	2	dbSNP_86	159	3864,4736	608.9+/-395.5	862,2140,1298	no	coding-synonymous	LRP2	NM_004525.2		1694,3157,1652	CC,CT,TT		44.9302,39.1512,49.6771		1220/4656	170099473	6545,6461	2203	4300	6503	SO:0001819	synonymous_variant	4036	exon24			ACAGCCTGCTTCA		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.3660A>G	2.37:g.170099473T>C		Somatic	213	0	0		WXS	Illumina HiSeq	Phase_I	135	70	0.518519	NM_004525	O00711|Q16215	Silent	SNP	ENST00000263816.3	37	CCDS2232.1																																																																																			T|0.490;C|0.510	0.510	strong		0.413	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525	
MUC17	140453	hgsc.bcm.edu	37	7	100680521	100680521	+	Missense_Mutation	SNP	G	G	A	rs73712043	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:100680521G>A	ENST00000306151.4	+	3	5888	c.5824G>A	c.(5824-5826)Gaa>Aaa	p.E1942K		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	1942	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.E1942*(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)					GGCCAGTTCTGAAATCAACAC	0.488													-|||	164	0.0327476	0.084	0.0072	5008	,	,		26687	0.0278		0.0159	False		,,,				2504	0.0041				p.E1942K		Atlas-SNP	.											.	MUC17	804	.	1	Substitution - Nonsense(1)	lung(1)	c.G5824A						PASS	.	G	LYS/GLU	373,4033	187.4+/-214.1	13,347,1843	239.0	238.0	239.0		5824	-0.0	0.0	7	dbSNP_130	239	93,8507	52.3+/-112.8	0,93,4207	yes	missense	MUC17	NM_001040105.1	56	13,440,6050	AA,AG,GG		1.0814,8.4657,3.583	benign	1942/4494	100680521	466,12540	2203	4300	6503	SO:0001583	missense	140453	exon3			AGTTCTGAAATCA	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.5824G>A	7.37:g.100680521G>A	ENSP00000302716:p.Glu1942Lys	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	45	25	0.555556	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	93	0.042582417582417584	56	0.11382113821138211	4	0.011049723756906077	22	0.038461538461538464	11	0.014511873350923483	g	1.913	-0.450346	0.04572	0.084657	0.010814	ENSG00000169876	ENST00000306151	T	0.02631	4.22	0.932	-0.0248	0.13938	.	.	.	.	.	T	0.00039	0.0001	N	0.24115	0.695	0.09310	N	1	B	0.17038	0.02	B	0.06405	0.002	T	0.46871	-0.9160	9	0.06625	T	0.88	.	3.4997	0.07668	0.2906:0.0:0.7094:0.0	.	1942	Q685J3	MUC17_HUMAN	K	1942	ENSP00000302716:E1942K	ENSP00000302716:E1942K	E	+	1	0	MUC17	100467241	0.002000	0.14202	0.000000	0.03702	0.003000	0.03518	0.200000	0.17257	0.015000	0.14971	-1.411000	0.01122	GAA	G|0.963;A|0.037	0.037	strong		0.488	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
ALOX15	246	hgsc.bcm.edu	37	17	4535314	4535314	+	Missense_Mutation	SNP	G	G	A	rs34210653	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:4535314G>A	ENST00000570836.1	-	14	1775	c.1679C>T	c.(1678-1680)aCg>aTg	p.T560M	ALOX15_ENST00000293761.3_Missense_Mutation_p.T560M|ALOX15_ENST00000574640.1_Missense_Mutation_p.T521M|ALOX15_ENST00000545513.1_Missense_Mutation_p.T582M			P16050	LOX15_HUMAN	arachidonate 15-lipoxygenase	560	Lipoxygenase. {ECO:0000255|PROSITE- ProRule:PRU00726}.		T -> M (loss of catalytic activity; dbSNP:rs34210653). {ECO:0000269|PubMed:17959182}.		apoptotic cell clearance (GO:0043277)|arachidonic acid metabolic process (GO:0019369)|bone mineralization (GO:0030282)|cellular response to calcium ion (GO:0071277)|cellular response to interleukin-13 (GO:0035963)|hepoxilin biosynthetic process (GO:0051122)|inflammatory response (GO:0006954)|leukotriene metabolic process (GO:0006691)|lipoxin A4 biosynthetic process (GO:2001303)|lipoxygenase pathway (GO:0019372)|negative regulation of adaptive immune response (GO:0002820)|ossification (GO:0001503)|phosphatidylethanolamine biosynthetic process (GO:0006646)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|regulation of engulfment of apoptotic cell (GO:1901074)|regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035358)|response to endoplasmic reticulum stress (GO:0034976)|small molecule metabolic process (GO:0044281)|wound healing (GO:0042060)	cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|lipid particle (GO:0005811)|membrane (GO:0016020)|plasma membrane (GO:0005886)	arachidonate 12-lipoxygenase activity (GO:0004052)|arachidonate 15-lipoxygenase activity (GO:0050473)|eoxin A4 synthase activity (GO:0097260)|iron ion binding (GO:0005506)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(10)|ovary(1)|prostate(1)|skin(5)	20				READ - Rectum adenocarcinoma(115;0.0327)		CAGCCGCATCGTGCAGGGTGC	0.607													G|||	63	0.0125799	0.0023	0.0663	5008	,	,		20270	0.0		0.0109	False		,,,				2504	0.0031				p.T560M		Atlas-SNP	.											.	ALOX15	70	.	0			c.C1679T	GRCh37	CM081155	ALOX15	M	rs34210653	PASS	.	G	MET/THR	17,4389	23.3+/-48.9	0,17,2186	59.0	54.0	56.0		1679	3.3	0.9	17	dbSNP_126	56	144,8456	72.0+/-134.6	1,142,4157	yes	missense	ALOX15	NM_001140.3	81	1,159,6343	AA,AG,GG		1.6744,0.3858,1.2379	probably-damaging	560/663	4535314	161,12845	2203	4300	6503	SO:0001583	missense	246	exon13			CGCATCGTGCAGG	M23892	CCDS11049.1	17p13.3	2010-09-24			ENSG00000161905	ENSG00000161905	1.13.11.33	"""Arachidonate lipoxygenases"""	433	protein-coding gene	gene with protein product		152392				1570320	Standard	NM_001140		Approved	15-LOX-1	uc002fyh.3	P16050	OTTHUMG00000090746	ENST00000570836.1:c.1679C>T	17.37:g.4535314G>A	ENSP00000458832:p.Thr560Met	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	63	32	0.507937	NM_001140	A8K2P4|B7ZA11|Q8N6R7|Q99657	Missense_Mutation	SNP	ENST00000570836.1	37	CCDS11049.1	32	0.014652014652014652	2	0.0040650406504065045	20	0.055248618784530384	0	0.0	10	0.013192612137203167	G	18.48	3.632894	0.67015	0.003858	0.016744	ENSG00000161905	ENST00000293761;ENST00000545513	T;T	0.78126	-1.15;-1.15	4.33	3.35	0.38373	Lipoxygenase, C-terminal (3);	0.064395	0.64402	D	0.000011	T	0.51924	0.1703	M	0.85197	2.74	0.35074	D	0.762752	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.998;0.998;0.999	T	0.80529	-0.1342	10	0.87932	D	0	-1.2213	10.1417	0.42738	0.0:0.2025:0.7975:0.0	rs34210653	582;521;560	F5H0G8;B7ZA11;P16050	.;.;LOX15_HUMAN	M	560;582	ENSP00000293761:T560M;ENSP00000439855:T582M	ENSP00000293761:T560M	T	-	2	0	ALOX15	4482063	1.000000	0.71417	0.938000	0.37757	0.976000	0.68499	4.166000	0.58203	1.028000	0.39785	0.655000	0.94253	ACG	G|0.988;A|0.012	0.012	strong		0.607	ALOX15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207487.2		
ZNF587	84914	hgsc.bcm.edu	37	19	58371259	58371259	+	Silent	SNP	A	A	G	rs75951435	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:58371259A>G	ENST00000339656.5	+	3	1661	c.1479A>G	c.(1477-1479)gaA>gaG	p.E493E	ZNF814_ENST00000595295.1_Intron|ZNF587_ENST00000423137.1_Silent_p.E492E|ZNF587_ENST00000419854.1_Silent_p.E450E|ZNF814_ENST00000597342.1_Intron|ZNF814_ENST00000597832.1_Intron|ZNF814_ENST00000596604.1_Intron|ZNF814_ENST00000597652.1_5'Flank	NM_001204817.1|NM_032828.3	NP_001191746.1|NP_116217.1	Q96SQ5	ZN587_HUMAN	zinc finger protein 587	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)	p.E493E(1)		central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(1)|lung(4)|ovary(1)|pancreas(1)|stomach(1)	15		Colorectal(82;0.000256)|all_neural(62;0.0577)|Breast(46;0.147)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0264)		GGCCGTATGAATGCAGTGAAT	0.423																																					p.E493E	Pancreas(59;641 1233 1885 20055 50741)	Atlas-SNP	.											ZNF587,NS,carcinoma,0,1	ZNF587	53	1	1	Substitution - coding silent(1)	stomach(1)	c.A1479G						scavenged	.						145.0	149.0	148.0					19																	58371259		2203	4300	6503	SO:0001819	synonymous_variant	84914	exon3			GTATGAATGCAGT	AF294842	CCDS12964.1, CCDS56110.1	19q13.43	2013-01-08				ENSG00000198466		"""Zinc fingers, C2H2-type"", ""-"""	30955	protein-coding gene	gene with protein product						10520746	Standard	NM_032828		Approved	ZF6, FLJ14710, UBF-fl, FLJ20813	uc002qql.3	Q96SQ5	OTTHUMG00000154901	ENST00000339656.5:c.1479A>G	19.37:g.58371259A>G		Somatic	232	0	0		WXS	Illumina HiSeq	Phase_I	339	56	0.165192	NM_032828	A0AV72|G3V0H5|Q6ZMK8	Silent	SNP	ENST00000339656.5	37	CCDS12964.1																																																																																			A|0.963;G|0.037	0.037	strong		0.423	ZNF587-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337594.2	NM_032828	
GPR112	139378	hgsc.bcm.edu	37	X	135430044	135430044	+	Silent	SNP	T	T	C	rs877761	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:135430044T>C	ENST00000394143.1	+	6	4470	c.4179T>C	c.(4177-4179)acT>acC	p.T1393T	GPR112_ENST00000412101.1_Silent_p.T1188T|GPR112_ENST00000370652.1_Silent_p.T1393T|GPR112_ENST00000287534.4_Silent_p.T1330T|GPR112_ENST00000394141.1_Silent_p.T1188T	NM_153834.3	NP_722576.3	Q8IZF6	GP112_HUMAN	G protein-coupled receptor 112	1393					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(13)|central_nervous_system(2)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(33)|lung(97)|ovary(5)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(2)	199	Acute lymphoblastic leukemia(192;0.000127)					CTCCCAGGACTGTGGAAATGA	0.448													c|||	2014	0.53351	0.5983	0.3847	3775	,	,		16408	0.255		0.3817	False		,,,				2504	0.3221				p.T1393T		Atlas-SNP	.											.	GPR112	459	.	0			c.T4179C						PASS	.			2878,957		910,628,430,94,141	170.0	160.0	163.0		4179	-1.4	0.0	X	dbSNP_86	163	3231,3497		571,1175,914,682,958	no	coding-synonymous	GPR112	NM_153834.3		1481,1803,1344,776,1099	CC,CT,C,TT,T		48.0232,24.9544,42.1661		1393/3081	135430044	6109,4454	2203	4300	6503	SO:0001819	synonymous_variant	139378	exon6			CAGGACTGTGGAA	AY140954	CCDS35409.1	Xq26.3	2014-08-08			ENSG00000156920	ENSG00000156920		"""-"", ""GPCR / Class B : Orphans"""	18992	protein-coding gene	gene with protein product						12435584	Standard	XM_005262367		Approved	RP1-299I16, PGR17	uc004ezu.1	Q8IZF6	OTTHUMG00000022508	ENST00000394143.1:c.4179T>C	X.37:g.135430044T>C		Somatic	215	0	0		WXS	Illumina HiSeq	Phase_I	126	126	1	NM_153834	A2A2J1|A2A2J2|Q5EGP2|Q86SM6	Silent	SNP	ENST00000394143.1	37	CCDS35409.1																																																																																			T|0.432;0|0.003	.	strong		0.448	GPR112-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000286639.1		
PTK2B	2185	hgsc.bcm.edu	37	8	27277537	27277537	+	Silent	SNP	G	G	A	rs1030526	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:27277537G>A	ENST00000397501.1	+	8	1138	c.330G>A	c.(328-330)acG>acA	p.T110T	PTK2B_ENST00000517339.1_Silent_p.T110T|PTK2B_ENST00000346049.5_Silent_p.T110T|PTK2B_ENST00000544172.1_Silent_p.T110T|PTK2B_ENST00000420218.2_Silent_p.T110T|PTK2B_ENST00000338238.4_Silent_p.T110T	NM_173174.2	NP_775266.1	Q14289	FAK2_HUMAN	protein tyrosine kinase 2 beta	110	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				activation of Janus kinase activity (GO:0042976)|activation of Rac GTPase activity (GO:0032863)|apoptotic process (GO:0006915)|blood vessel endothelial cell migration (GO:0043534)|bone resorption (GO:0045453)|cell surface receptor signaling pathway (GO:0007166)|cellular defense response (GO:0006968)|cellular response to retinoic acid (GO:0071300)|chemokine-mediated signaling pathway (GO:0070098)|epidermal growth factor receptor signaling pathway (GO:0007173)|focal adhesion assembly (GO:0048041)|glial cell proliferation (GO:0014009)|integrin-mediated signaling pathway (GO:0007229)|ionotropic glutamate receptor signaling pathway (GO:0035235)|long-term synaptic potentiation (GO:0060291)|MAPK cascade (GO:0000165)|marginal zone B cell differentiation (GO:0002315)|negative regulation of apoptotic process (GO:0043066)|negative regulation of bone mineralization (GO:0030502)|negative regulation of cell proliferation (GO:0008285)|negative regulation of muscle cell apoptotic process (GO:0010656)|negative regulation of myeloid cell differentiation (GO:0045638)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of potassium ion transport (GO:0043267)|neuron projection development (GO:0031175)|oocyte maturation (GO:0001556)|peptidyl-tyrosine autophosphorylation (GO:0038083)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of B cell chemotaxis (GO:2000538)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of JNK cascade (GO:0046330)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of neuron projection development (GO:0010976)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein complex assembly (GO:0006461)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of cell adhesion (GO:0030155)|regulation of cell shape (GO:0008360)|regulation of establishment of cell polarity (GO:2000114)|regulation of inositol trisphosphate biosynthetic process (GO:0032960)|regulation of macrophage chemotaxis (GO:0010758)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000058)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|response to calcium ion (GO:0051592)|response to cAMP (GO:0051591)|response to cocaine (GO:0042220)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to hormone (GO:0009725)|response to hydrogen peroxide (GO:0042542)|response to hypoxia (GO:0001666)|response to lithium ion (GO:0010226)|response to mechanical stimulus (GO:0009612)|response to osmotic stress (GO:0006970)|response to stress (GO:0006950)|signal complex assembly (GO:0007172)|signal transduction (GO:0007165)|sprouting angiogenesis (GO:0002040)|stress fiber assembly (GO:0043149)|tumor necrosis factor-mediated signaling pathway (GO:0033209)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	apical dendrite (GO:0097440)|axon (GO:0030424)|cell body (GO:0044297)|cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|membrane raft (GO:0045121)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|postsynaptic density (GO:0014069)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)|signal transducer activity (GO:0004871)			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)	CACAGATGACGGTGGGTGAGG	0.582													G|||	1936	0.386581	0.4228	0.2738	5008	,	,		19922	0.2718		0.4076	False		,,,				2504	0.5143				p.T110T		Atlas-SNP	.											.	PTK2B	304	.	0			c.G330A						PASS	.	G	,,,	1867,2539	540.1+/-375.4	400,1067,736	100.0	84.0	90.0		330,330,330,330	-10.3	0.2	8	dbSNP_86	90	3484,5116	508.9+/-377.2	727,2030,1543	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PTK2B	NM_004103.4,NM_173174.2,NM_173175.2,NM_173176.2	,,,	1127,3097,2279	AA,AG,GG		40.5116,42.374,41.1425	,,,	110/1010,110/1010,110/968,110/1010	27277537	5351,7655	2203	4300	6503	SO:0001819	synonymous_variant	2185	exon8			GATGACGGTGGGT	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.330G>A	8.37:g.27277537G>A		Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	163	40	0.245399	NM_173174	D3DST0|Q13475|Q14290|Q16709|Q6PID4	Silent	SNP	ENST00000397501.1	37	CCDS6057.1																																																																																			G|0.621;A|0.379	0.379	strong		0.582	PTK2B-009	PUTATIVE	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219916.1	NM_004103	
PCDHA10	56139	hgsc.bcm.edu	37	5	140235875	140235875	+	Missense_Mutation	SNP	G	G	A	rs143002904	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:140235875G>A	ENST00000307360.5	+	1	242	c.242G>A	c.(241-243)gGc>gAc	p.G81D	PCDHA4_ENST00000512229.2_Intron|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|PCDHA5_ENST00000529619.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA10_ENST00000506939.2_Missense_Mutation_p.G81D|PCDHA1_ENST00000504120.2_Intron	NM_018901.2	NP_061724.1	Q9Y5I2	PCDAA_HUMAN	protocadherin alpha 10	81	Cadherin 1. {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)			CTGCAGAATGGCATTTTGTTT	0.622													.|||	19	0.00379393	0.0	0.0029	5008	,	,		17477	0.0		0.0169	False		,,,				2504	0.0				p.G81D		Atlas-SNP	.											.	PCDHA10	358	.	0			c.G242A						PASS	.	G	,ASP/GLY,,,,,,,,,,,ASP/GLY,ASP/GLY	8,4386	11.4+/-27.6	1,6,2190	104.0	113.0	110.0		,242,,,,,,,,,,,242,242	4.3	1.0	5	dbSNP_134	110	49,8493	27.4+/-76.7	2,45,4224	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	,94,,,,,,,,,,,94,94	3,51,6414	AA,AG,GG		0.5736,0.1821,0.4406	,,,,,,,,,,,,,	,81/949,,,,,,,,,,,81/845,81/686	140235875	57,12879	2197	4271	6468	SO:0001583	missense	56139	exon1			AGAATGGCATTTT	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.242G>A	5.37:g.140235875G>A	ENSP00000304234:p.Gly81Asp	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	31	31	1	NM_031859	A1L493|O75280|Q9NRU2	Missense_Mutation	SNP	ENST00000307360.5	37	CCDS54921.1	11	0.005036630036630037	0	0.0	0	0.0	0	0.0	11	0.014511873350923483	G	23.3	4.399977	0.83120	0.001821	0.005736	ENSG00000250120	ENST00000506939;ENST00000307360	T;T	0.40476	1.03;1.03	4.27	4.27	0.50696	Cadherin, N-terminal (1);Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.74876	0.3774	H	0.99590	4.645	0.51012	D	0.999902	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.88448	0.3047	9	0.87932	D	0	.	17.329	0.87258	0.0:0.0:1.0:0.0	.	81;81;81	Q9Y5I2-3;Q9Y5I2;Q9Y5I2-2	.;PCDAA_HUMAN;.	D	81	ENSP00000421030:G81D;ENSP00000304234:G81D	ENSP00000304234:G81D	G	+	2	0	PCDHA10	140216059	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.573000	0.82421	2.391000	0.81399	0.556000	0.70494	GGC	G|0.995;A|0.005	0.005	strong		0.622	PCDHA10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372895.2	NM_018901	
KANK3	256949	hgsc.bcm.edu	37	19	8399272	8399272	+	Silent	SNP	G	G	A	rs8106699	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	115	0	0		WXS	Illumina HiSeq	Phase_I	90	44	0.488889	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	
SLC4A7	9497	hgsc.bcm.edu	37	3	27463229	27463229	+	Silent	SNP	C	C	T	rs79251239	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:27463229C>T	ENST00000295736.5	-	9	1351	c.1281G>A	c.(1279-1281)gaG>gaA	p.E427E	SLC4A7_ENST00000425128.2_Silent_p.E419E|SLC4A7_ENST00000388777.4_Intron|SLC4A7_ENST00000428386.1_Silent_p.E303E|SLC4A7_ENST00000445684.1_Silent_p.E423E|SLC4A7_ENST00000437179.1_Silent_p.E308E|SLC4A7_ENST00000440156.1_Silent_p.E423E|SLC4A7_ENST00000455077.1_Silent_p.E308E|RN7SL859P_ENST00000578725.1_RNA|SLC4A7_ENST00000446700.1_Silent_p.E419E|SLC4A7_ENST00000454389.1_Silent_p.E436E|SLC4A7_ENST00000435667.2_Silent_p.E312E	NM_003615.4	NP_003606.3	Q9Y6M7	S4A7_HUMAN	solute carrier family 4, sodium bicarbonate cotransporter, member 7	427					auditory receptor cell development (GO:0060117)|bicarbonate transport (GO:0015701)|cochlear nucleus development (GO:0021747)|ion transport (GO:0006811)|retina vasculature morphogenesis in camera-type eye (GO:0061299)|retinal cell programmed cell death (GO:0046666)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|cell projection (GO:0042995)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)|sodium:bicarbonate symporter activity (GO:0008510)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(12)|lung(9)|ovary(4)|skin(1)	38					Sodium bicarbonate(DB01390)	CGTTGGATGCCTCAGCACCCG	0.408													C|||	366	0.0730831	0.0068	0.1441	5008	,	,		15100	0.001		0.2306	False		,,,				2504	0.0245				p.E427E		Atlas-SNP	.											.	SLC4A7	119	.	0			c.G1281A						PASS	.	C		193,4213	120.0+/-157.7	4,185,2014	89.0	89.0	89.0		1281	3.4	1.0	3	dbSNP_131	89	1879,6721	332.5+/-320.1	211,1457,2632	no	coding-synonymous	SLC4A7	NM_003615.3		215,1642,4646	TT,TC,CC		21.8488,4.3804,15.9311		427/1215	27463229	2072,10934	2203	4300	6503	SO:0001819	synonymous_variant	9497	exon9			GGATGCCTCAGCA	AB012130	CCDS33721.1, CCDS58819.1, CCDS58820.1	3p24.1	2013-05-22			ENSG00000033867	ENSG00000033867		"""Solute carriers"""	11033	protein-coding gene	gene with protein product		603353		SLC4A6		10198178, 9610397	Standard	NM_003615		Approved	NBC3, SBC2	uc003cdv.4	Q9Y6M7	OTTHUMG00000155679	ENST00000295736.5:c.1281G>A	3.37:g.27463229C>T		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	124	124	1	NM_003615	A6NIA8|B2CI53|B5M449|B5M451|B5M452|B5M453|B6DY52|B6DY53|C9JST9|D3K174|D3K175|O60350|Q6AHZ9|Q9HC88|Q9UIB9	Silent	SNP	ENST00000295736.5	37	CCDS33721.1																																																																																			C|0.855;T|0.145	0.145	strong		0.408	SLC4A7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000341230.2	NM_003615	
TMEM97	27346	hgsc.bcm.edu	37	17	26646320	26646320	+	Missense_Mutation	SNP	C	C	G	rs202198126		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:26646320C>G	ENST00000226230.6	+	1	200	c.55C>G	c.(55-57)Ctc>Gtc	p.L19V	TMEM97_ENST00000583381.1_Intron|TMEM97_ENST00000582113.1_Missense_Mutation_p.L19V|TMEM97_ENST00000336687.6_5'Flank	NM_014573.2	NP_055388.2	Q5BJF2	TMM97_HUMAN	transmembrane protein 97	19					cholesterol homeostasis (GO:0042632)|regulation of cell growth (GO:0001558)	integral component of membrane (GO:0016021)|lysosome (GO:0005764)|nuclear membrane (GO:0031965)|plasma membrane (GO:0005886)|rough endoplasmic reticulum (GO:0005791)				endometrium(1)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	6	all_lung(13;0.000238)|Lung NSC(42;0.000789)			UCEC - Uterine corpus endometrioid carcinoma (53;0.153)		CCTCTACTTCCTCAGCCACAT	0.672																																					p.L19V		Atlas-SNP	.											.	TMEM97	27	.	0			c.C55G						PASS	.	C	VAL/LEU	0,4096		0,0,2048	24.0	31.0	28.0		55	2.1	1.0	17		28	4,8312		0,4,4154	no	missense	TMEM97	NM_014573.2	32	0,4,6202	GG,GC,CC		0.0481,0.0,0.0322	benign	19/177	26646320	4,12408	2048	4158	6206	SO:0001583	missense	27346	exon1			TACTTCCTCAGCC	BC091504	CCDS11226.2	17q11.2	2014-01-28			ENSG00000109084	ENSG00000109084			28106	protein-coding gene	gene with protein product		612912				7694637, 15375745	Standard	NM_014573		Approved	MAC30	uc002hat.3	Q5BJF2	OTTHUMG00000132497	ENST00000226230.6:c.55C>G	17.37:g.26646320C>G	ENSP00000226230:p.Leu19Val	Somatic	210	0	0		WXS	Illumina HiSeq	Phase_I	196	88	0.44898	NM_014573	B4DS02|Q07823	Missense_Mutation	SNP	ENST00000226230.6	37	CCDS11226.2	.	.	.	.	.	.	.	.	.	.	C	0.581	-0.836976	0.02692	0.0	4.81E-4	ENSG00000109084	ENST00000226230	.	.	.	5.41	2.06	0.26882	.	0.329557	0.33534	N	0.004806	T	0.36663	0.0975	L	0.31664	0.95	0.80722	D	1	B	0.10296	0.003	B	0.16289	0.015	T	0.21484	-1.0244	9	0.02654	T	1	-18.6822	9.5507	0.39308	0.0:0.4926:0.4306:0.0767	.	19	Q5BJF2	TMM97_HUMAN	V	19	.	ENSP00000226230:L19V	L	+	1	0	TMEM97	23670447	0.921000	0.31238	1.000000	0.80357	0.020000	0.10135	0.970000	0.29383	0.786000	0.33708	0.561000	0.74099	CTC	C|0.999;G|0.001	0.001	weak		0.672	TMEM97-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255675.2	NM_014573	
KRT27	342574	hgsc.bcm.edu	37	17	38938557	38938557	+	Silent	SNP	G	G	A	rs67771170	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:38938557G>A	ENST00000301656.3	-	1	229	c.189C>T	c.(187-189)ggC>ggT	p.G63G		NM_181537.3	NP_853515.2			keratin 27											NS(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(6)|ovary(1)|prostate(3)|skin(1)|stomach(1)	21		Breast(137;0.000812)				CACTTCCCCCGCCCAGACCTC	0.592													G|||	439	0.0876597	0.0023	0.0605	5008	,	,		16656	0.0704		0.1441	False		,,,				2504	0.182				p.G63G		Atlas-SNP	.											.	KRT27	41	.	0			c.C189T						PASS	.	G		128,4278	93.0+/-131.7	4,120,2079	89.0	78.0	82.0		189	-9.8	0.0	17	dbSNP_130	82	1124,7476	232.6+/-266.2	84,956,3260	no	coding-synonymous	KRT27	NM_181537.3		88,1076,5339	AA,AG,GG		13.0698,2.9051,9.6263		63/460	38938557	1252,11754	2203	4300	6503	SO:0001819	synonymous_variant	342574	exon1			TCCCCCGCCCAGA	AJ564206	CCDS11375.1	17q21.2	2013-01-16	2006-07-17	2006-07-17	ENSG00000171446	ENSG00000171446		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	30841	protein-coding gene	gene with protein product			"""keratin 25C"""	KRT25C		16831889	Standard	NM_181537		Approved		uc002hvg.3	Q7Z3Y8	OTTHUMG00000133371	ENST00000301656.3:c.189C>T	17.37:g.38938557G>A		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	64	28	0.4375	NM_181537		Silent	SNP	ENST00000301656.3	37	CCDS11375.1																																																																																			G|0.899;A|0.101	0.101	strong		0.592	KRT27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257216.1	NM_181537	
SLC1A5	6510	hgsc.bcm.edu	37	19	47291174	47291174	+	Missense_Mutation	SNP	G	G	C	rs3027956	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:47291174G>C	ENST00000542575.2	-	1	677	c.49C>G	c.(49-51)Ccc>Gcc	p.P17A	SLC1A5_ENST00000412532.2_5'Flank	NM_005628.2	NP_005619.1	Q15758	AAAT_HUMAN	solute carrier family 1 (neutral amino acid transporter), member 5	17			P -> A (in dbSNP:rs3027956).		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)	TTGGCGGTGGGCTCCGCCGCT	0.706													G|||	1004	0.200479	0.0257	0.1628	5008	,	,		10929	0.4821		0.2256	False		,,,				2504	0.1472				p.P17A		Atlas-SNP	.											.	SLC1A5	31	.	0			c.C49G						PASS	.	G	ALA/PRO	63,2919		0,63,1428	3.0	4.0	4.0		49	2.1	0.7	19	dbSNP_102	4	595,5831		16,563,2634	no	missense	SLC1A5	NM_005628.2	27	16,626,4062	CC,CG,GG		9.2593,2.1127,6.994	possibly-damaging	17/542	47291174	658,8750	1491	3213	4704	SO:0001583	missense	6510	exon1			CGGTGGGCTCCGC	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.49C>G	19.37:g.47291174G>C	ENSP00000444408:p.Pro17Ala	Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	71	30	0.422535	NM_005628	A8K9H5|B4DR77|B4DWS4|B7ZB81|D0EYG6|E9PC01|O95720|Q96RL9|Q9BWQ3|Q9UNP2	Missense_Mutation	SNP	ENST00000542575.2	37	CCDS12692.1	508	0.2326007326007326	12	0.024390243902439025	54	0.14917127071823205	269	0.47027972027972026	173	0.22823218997361477	G	19.38	3.815594	0.70912	0.021127	0.092593	ENSG00000105281	ENST00000542575;ENST00000306894	T	0.54479	0.57	4.37	2.11	0.27256	.	2.128630	0.01846	N	0.035593	T	0.00012	0.0000	N	0.08118	0	0.09310	P	0.9999999999999963	B	0.24483	0.104	B	0.22386	0.039	T	0.40813	-0.9543	9	0.56958	D	0.05	-24.0782	4.2813	0.10834	0.1935:0.0:0.6254:0.1811	rs3027956	17	Q15758	AAAT_HUMAN	A	17;24	ENSP00000444408:P17A	ENSP00000303623:P24A	P	-	1	0	SLC1A5	51983014	0.002000	0.14202	0.658000	0.29665	0.515000	0.34225	-0.227000	0.09126	0.550000	0.28991	0.313000	0.20887	CCC	G|0.712;C|0.288	0.288	strong		0.706	SLC1A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466630.1		
STAT6	6778	hgsc.bcm.edu	37	12	57496654	57496654	+	Missense_Mutation	SNP	A	A	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:57496654A>T	ENST00000300134.3	-	12	1588	c.1263T>A	c.(1261-1263)aaT>aaA	p.N421K	STAT6_ENST00000537215.2_Missense_Mutation_p.N311K|STAT6_ENST00000454075.3_Missense_Mutation_p.N421K|STAT6_ENST00000543873.2_Missense_Mutation_p.N421K|STAT6_ENST00000556155.1_Missense_Mutation_p.N421K|STAT6_ENST00000538913.2_Missense_Mutation_p.N311K	NM_001178078.1|NM_003153.4	NP_001171549.1|NP_003144.3	P42226	STAT6_HUMAN	signal transducer and activator of transcription 6, interleukin-4 induced	421					cellular response to hydrogen peroxide (GO:0070301)|cellular response to reactive nitrogen species (GO:1902170)|innate immune response (GO:0045087)|interleukin-4-mediated signaling pathway (GO:0035771)|mammary gland epithelial cell proliferation (GO:0033598)|mammary gland morphogenesis (GO:0060443)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of type 2 immune response (GO:0002829)|positive regulation of isotype switching to IgE isotypes (GO:0048295)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|regulation of cell proliferation (GO:0042127)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|signal transduction (GO:0007165)|T-helper 1 cell lineage commitment (GO:0002296)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane raft (GO:0045121)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|protein phosphatase binding (GO:0019903)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)			breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(5)|kidney(2)|large_intestine(2)|lung(8)|ovary(4)|skin(1)	28						TGGCTTTGGCATTGTTGTCTT	0.522																																					p.N421K		Atlas-SNP	.											.	STAT6	69	.	0			c.T1263A						PASS	.						144.0	115.0	125.0					12																	57496654		2203	4300	6503	SO:0001583	missense	6778	exon12			TTTGGCATTGTTG	BC005823, BQ028928	CCDS8931.1, CCDS53804.1	12q13	2013-02-14				ENSG00000166888		"""SH2 domain containing"""	11368	protein-coding gene	gene with protein product		601512				9605853, 8085155	Standard	NM_003153		Approved	D12S1644, IL-4-STAT	uc001sna.3	P42226		ENST00000300134.3:c.1263T>A	12.37:g.57496654A>T	ENSP00000300134:p.Asn421Lys	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	120	14	0.116667	NM_001178079	A8K316|B7ZA27|F5GXI9|Q5FBW5|Q71UP4	Missense_Mutation	SNP	ENST00000300134.3	37	CCDS8931.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	21.7|21.7	4.184980|4.184980	0.78677|0.78677	.|.	.|.	ENSG00000166888|ENSG00000166888	ENST00000553533|ENST00000300134;ENST00000535201;ENST00000538913;ENST00000543873;ENST00000556155;ENST00000537215;ENST00000454075;ENST00000542721;ENST00000542516	.|D;D;D;D;D;D	.|0.87729	.|-2.29;-2.29;-2.29;-2.29;-2.29;-2.29	5.44|5.44	1.65|1.65	0.23941|0.23941	.|STAT transcription factor, DNA-binding (1);p53-like transcription factor, DNA-binding (1);EF-hand-like domain (1);	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.91593|0.91593	0.7344|0.7344	M|M	0.76838|0.76838	2.35|2.35	0.58432|0.58432	D|D	0.999997|0.999997	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.91635	.|0.998;0.999	D|D	0.89559|0.89559	0.3805|0.3805	5|10	.|0.87932	.|D	.|0	-17.2208|-17.2208	8.3744|8.3744	0.32434|0.32434	0.762:0.0:0.238:0.0|0.762:0.0:0.238:0.0	.|.	.|421;421	.|A8K4S9;P42226	.|.;STAT6_HUMAN	S|K	122|421;311;311;421;421;311;421;311;421	.|ENSP00000300134:N421K;ENSP00000445409:N311K;ENSP00000438451:N421K;ENSP00000451742:N421K;ENSP00000444530:N311K;ENSP00000401486:N421K	.|ENSP00000300134:N421K	C|N	-|-	1|3	0|2	STAT6|STAT6	55782921|55782921	0.536000|0.536000	0.26378|0.26378	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	-0.213000|-0.213000	0.09305|0.09305	0.124000|0.124000	0.18369|0.18369	0.528000|0.528000	0.53228|0.53228	TGC|AAT	.	.	none		0.522	STAT6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412248.3	NM_003153	
PTPRB	5787	hgsc.bcm.edu	37	12	70990054	70990054	+	Missense_Mutation	SNP	T	T	C	rs2465811	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:70990054T>C	ENST00000261266.5	-	3	408	c.379A>G	c.(379-381)Agc>Ggc	p.S127G	PTPRB_ENST00000551525.1_Missense_Mutation_p.S344G|PTPRB_ENST00000538174.2_5'UTR|PTPRB_ENST00000550358.1_Missense_Mutation_p.S345G|PTPRB_ENST00000451516.2_Missense_Mutation_p.S127G|PTPRB_ENST00000550857.1_Missense_Mutation_p.S127G|PTPRB_ENST00000538708.1_Missense_Mutation_p.S127G|PTPRB_ENST00000334414.6_Missense_Mutation_p.S345G	NM_002837.4	NP_002828.3	P23467	PTPRB_HUMAN	protein tyrosine phosphatase, receptor type, B	127	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.		S -> G (in dbSNP:rs2465811). {ECO:0000269|PubMed:2170109}.		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)			ACATGCAAGCTGGTTGAAGTC	0.393													T|||	1603	0.320088	0.4402	0.2363	5008	,	,		15448	0.3026		0.2604	False		,,,				2504	0.2965				p.S345G		Atlas-SNP	.											.	PTPRB	676	.	0			c.A1033G	GRCh37	CM086290	PTPRB	M	rs2465811	PASS	.	T	GLY/SER,GLY/SER,GLY/SER,GLY/SER	1481,2253		289,903,675	61.0	59.0	60.0		1033,379,379,379	5.8	0.8	12	dbSNP_100	60	2290,5936		310,1670,2133	yes	missense,missense,missense,missense	PTPRB	NM_001109754.2,NM_001206971.1,NM_001206972.1,NM_002837.4	56,56,56,56	599,2573,2808	CC,CT,TT		27.8386,39.6626,31.5301	benign,benign,benign,benign	345/2216,127/1908,127/1908,127/1998	70990054	3771,8189	1867	4113	5980	SO:0001583	missense	5787	exon5			GCAAGCTGGTTGA	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.379A>G	12.37:g.70990054T>C	ENSP00000261266:p.Ser127Gly	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	75	38	0.506667	NM_001109754	B7ZKS8|B7ZKT0|C9JX87|F5H3G6|Q14D85|Q3MIV7	Missense_Mutation	SNP	ENST00000261266.5	37	CCDS44944.1	669	0.30631868131868134	209	0.4247967479674797	90	0.24861878453038674	175	0.30594405594405594	195	0.25725593667546176	T	10.86	1.471193	0.26423	0.396626	0.278386	ENSG00000127329	ENST00000334414;ENST00000451516;ENST00000550358;ENST00000544694;ENST00000538708;ENST00000550857;ENST00000261266;ENST00000551525;ENST00000548122	T;T;T;T;T;T;T;T	0.62788	0.0;0.0;0.0;0.0;0.0;0.0;0.0;0.0	5.8	5.8	0.92144	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.089006	0.85682	D	0.000000	T	0.00012	0.0000	M	0.70275	2.135	0.25955	P	0.9827042	B;B;B;B;B;B;B;B	0.30482	0.001;0.001;0.008;0.281;0.008;0.007;0.003;0.007	B;B;B;B;B;B;B;B	0.35688	0.008;0.008;0.052;0.208;0.013;0.026;0.03;0.026	T	0.30119	-0.9989	9	0.59425	D	0.04	.	16.1596	0.81693	0.0:0.0:0.0:1.0	rs2465811;rs52801085;rs59164378;rs2465811	127;127;224;345;344;345;127;345	P23467-2;F5H3G6;Q6ZR19;Q6ZTX7;F8VSD5;P23467-3;P23467;F8VU56	.;.;.;.;.;.;PTPRB_HUMAN;.	G	345;127;345;345;127;127;127;344;224	ENSP00000334928:S345G;ENSP00000393028:S127G;ENSP00000448058:S345G;ENSP00000438927:S127G;ENSP00000447302:S127G;ENSP00000261266:S127G;ENSP00000448349:S344G;ENSP00000446982:S224G	ENSP00000261266:S127G	S	-	1	0	PTPRB	69276321	1.000000	0.71417	0.821000	0.32701	0.029000	0.11900	4.003000	0.57061	2.216000	0.71823	0.533000	0.62120	AGC	C|0.325;N|0.000	0.325	strong		0.393	PTPRB-007	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000404439.1		
NOD1	10392	hgsc.bcm.edu	37	7	30491311	30491311	+	Silent	SNP	C	C	T	rs2075821	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:30491311C>T	ENST00000222823.4	-	6	2247	c.1722G>A	c.(1720-1722)gcG>gcA	p.A574A		NM_006092.2	NP_006083.1	Q9Y239	NOD1_HUMAN	nucleotide-binding oligomerization domain containing 1	574					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of MAPK activity (GO:0000187)|apoptotic process (GO:0006915)|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)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interleukin-8 biosynthetic process (GO:0042228)|intracellular signal transduction (GO:0035556)|JNK cascade (GO:0007254)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of dendritic cell antigen processing and presentation (GO:0002606)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of JNK cascade (GO:0046330)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of tumor necrosis factor production (GO:0032760)|protein oligomerization (GO:0051259)|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)	basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|cytosol (GO:0005829)	ATP binding (GO:0005524)|CARD domain binding (GO:0050700)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|identical protein binding (GO:0042802)|peptidoglycan binding (GO:0042834)|protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(17)|ovary(2)|prostate(1)|skin(2)	39						GGTCTTCCCGCGCCGGACCAC	0.602													C|||	1589	0.317292	0.3321	0.1643	5008	,	,		18471	0.3849		0.2366	False		,,,				2504	0.4192				p.A574A		Atlas-SNP	.											.	NOD1	79	.	0			c.G1722A						PASS	.	C		1429,2977	459.6+/-352.3	242,945,1016	54.0	60.0	58.0		1722	-10.6	0.0	7	dbSNP_96	58	2227,6373	377.2+/-338.5	318,1591,2391	no	coding-synonymous	NOD1	NM_006092.2		560,2536,3407	TT,TC,CC		25.8953,32.433,28.1101		574/954	30491311	3656,9350	2203	4300	6503	SO:0001819	synonymous_variant	10392	exon6			TTCCCGCGCCGGA	AF126484	CCDS5427.1	7p15-p14	2006-12-08	2006-12-08	2006-12-08	ENSG00000106100	ENSG00000106100		"""Nucleotide-binding domain and leucine rich repeat containing"""	16390	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 1"", ""NLR family, CARD domain containing 1"""	605980	"""caspase recruitment domain family, member 4"""	CARD4		10224040, 10329646	Standard	NM_006092		Approved	NLRC1, CLR7.1	uc003tav.3	Q9Y239	OTTHUMG00000023923	ENST00000222823.4:c.1722G>A	7.37:g.30491311C>T		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	38	8	0.210526	NM_006092	B4DTU3|Q549U4|Q8IWF5	Silent	SNP	ENST00000222823.4	37	CCDS5427.1																																																																																			C|0.707;T|0.293	0.293	strong		0.602	NOD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250443.2		
OR5D18	219438	hgsc.bcm.edu	37	11	55587914	55587914	+	Missense_Mutation	SNP	A	A	G	rs55832853	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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						PASS	.	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	94	0	0		WXS	Illumina HiSeq	Phase_I	87	26	0.298851	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	
LYPD5	284348	hgsc.bcm.edu	37	19	44303066	44303066	+	Missense_Mutation	SNP	C	C	G	rs11547806	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:44303066C>G	ENST00000377950.3	-	3	348	c.268G>C	c.(268-270)Gcg>Ccg	p.A90P	LYPD5_ENST00000594013.1_Missense_Mutation_p.A47P|LYPD5_ENST00000414615.2_Missense_Mutation_p.A47P	NM_001031749.2	NP_001026919.2	Q6UWN5	LYPD5_HUMAN	LY6/PLAUR domain containing 5	90			A -> P (in dbSNP:rs11547806). {ECO:0000269|PubMed:12975309, ECO:0000269|PubMed:14702039}.			anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)		p.A47P(1)		breast(3)|kidney(1)|large_intestine(1)|lung(1)|prostate(1)|urinary_tract(1)	8		Prostate(69;0.0352)				AGCGCGTCCGCGTTCGATTGC	0.687													c|||	3112	0.621406	0.5772	0.634	5008	,	,		14726	0.5437		0.5765	False		,,,				2504	0.7986				p.A90P		Atlas-SNP	.											LYPD5,NS,carcinoma,0,1	LYPD5	22	1	1	Substitution - Missense(1)	prostate(1)	c.G268C						PASS	.		PRO/ALA,PRO/ALA	2618,1784		797,1024,380	22.0	20.0	21.0		268,139	-4.2	0.0	19	dbSNP_120	21	5027,3569		1477,2073,748	no	missense,missense	LYPD5	NM_001031749.2,NM_182573.2	27,27	2274,3097,1128	GG,GC,CC		41.5193,40.527,41.1833	benign,benign	90/252,47/209	44303066	7645,5353	2201	4298	6499	SO:0001583	missense	284348	exon3			CGTCCGCGTTCGA	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.268G>C	19.37:g.44303066C>G	ENSP00000367185:p.Ala90Pro	Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	174	82	0.471264	NM_001031749	Q6PEX9|Q96DR2	Missense_Mutation	SNP	ENST00000377950.3	37	CCDS46096.1	1248	0.5714285714285714	276	0.5609756097560976	240	0.6629834254143646	304	0.5314685314685315	428	0.5646437994722955	c	9.759	1.169584	0.21621	0.59473	0.584807	ENSG00000159871	ENST00000377950;ENST00000414615	T;D	0.98493	3.22;-4.96	3.3	-4.2	0.03823	.	2.677820	0.02015	N	0.047340	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.11235	0.004	B	0.04013	0.001	T	0.48559	-0.9025	9	0.19590	T	0.45	-0.3627	2.7515	0.05282	0.1087:0.4392:0.2049:0.2471	rs11547806;rs17798417;rs60214634;rs11547806	90	Q6UWN5	LYPD5_HUMAN	P	90;47	ENSP00000367185:A90P;ENSP00000408433:A47P	ENSP00000367185:A90P	A	-	1	0	LYPD5	48994906	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.157000	0.10085	-0.792000	0.04480	-1.579000	0.00862	GCG	C|0.420;G|0.580	0.580	strong		0.687	LYPD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463611.1	NM_182573	
RRP12	23223	hgsc.bcm.edu	37	10	99141484	99141484	+	Silent	SNP	C	C	T	rs12218483	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:99141484C>T	ENST00000370992.4	-	11	1419	c.1308G>A	c.(1306-1308)acG>acA	p.T436T	RRP12_ENST00000315563.6_Silent_p.T336T|RRP12_ENST00000536831.1_Silent_p.T154T|RRP12_ENST00000414986.1_Silent_p.T375T	NM_015179.3	NP_055994.2	Q5JTH9	RRP12_HUMAN	ribosomal RNA processing 12 homolog (S. cerevisiae)	436						integral component of membrane (GO:0016021)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(5)|large_intestine(2)|lung(13)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	37		Colorectal(252;0.162)		Epithelial(162;2.72e-09)|all cancers(201;1.76e-07)		TGAGGCTCTGCGTAGCAGCAG	0.602													C|||	1316	0.26278	0.1377	0.2579	5008	,	,		18072	0.3125		0.2604	False		,,,				2504	0.3865				p.T436T		Atlas-SNP	.											RRP12,colon,carcinoma,0,8	RRP12	97	8	0			c.G1308A						PASS	.	C	,	662,3744	283.4+/-277.1	50,562,1591	67.0	56.0	60.0		1125,1308	1.6	1.0	10	dbSNP_120	60	2179,6421	371.9+/-336.4	281,1617,2402	no	coding-synonymous,coding-synonymous	RRP12	NM_001145114.1,NM_015179.3	,	331,2179,3993	TT,TC,CC		25.3372,15.025,21.8438	,	375/1237,436/1298	99141484	2841,10165	2203	4300	6503	SO:0001819	synonymous_variant	23223	exon11			GCTCTGCGTAGCA		CCDS7457.1, CCDS44467.1, CCDS60605.1	10q24.2	2006-11-06	2006-11-06	2006-11-06	ENSG00000052749	ENSG00000052749			29100	protein-coding gene	gene with protein product			"""KIAA0690"""	KIAA0690		9734811	Standard	NM_015179		Approved		uc001knf.3	Q5JTH9	OTTHUMG00000018855	ENST00000370992.4:c.1308G>A	10.37:g.99141484C>T		Somatic	282	0	0		WXS	Illumina HiSeq	Phase_I	234	119	0.508547	NM_015179	B4DK00|E9PCK7|Q5JTH8|Q69YK4|Q96E87|Q9BUH3|Q9Y4C7	Silent	SNP	ENST00000370992.4	37	CCDS7457.1																																																																																			C|0.769;T|0.231	0.231	strong		0.602	RRP12-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049699.4	NM_015179	
UGT2B11	10720	hgsc.bcm.edu	37	4	70080233	70080233	+	Missense_Mutation	SNP	A	A	G	rs62298957	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:70080233A>G	ENST00000446444.1	-	1	216	c.208T>C	c.(208-210)Tcc>Ccc	p.S70P	RP11-704M14.1_ENST00000504301.1_RNA|RP11-704M14.1_ENST00000505646.1_RNA	NM_001073.1	NP_001064.1	O75310	UDB11_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide B11	70					estrogen metabolic process (GO:0008210)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	glucuronosyltransferase activity (GO:0015020)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(18)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	42						TTAAGAGTGGATGCATCATTG	0.368													.|||	824	0.164537	0.2935	0.1787	5008	,	,		19329	0.0476		0.1064	False		,,,				2504	0.1605				p.S70P		Atlas-SNP	.											UGT2B11,NS,carcinoma,+1,1	UGT2B11	92	1	0			c.T208C						PASS	.	A	PRO/SER	1105,3287		148,809,1239	58.0	67.0	64.0		208	2.0	0.0	4	dbSNP_129	64	808,7768		37,734,3517	no	missense	UGT2B11	NM_001073.1	74	185,1543,4756	GG,GA,AA		9.4216,25.1594,14.7517	benign	70/530	70080233	1913,11055	2196	4288	6484	SO:0001583	missense	10720	exon1			GAGTGGATGCATC	AF016492	CCDS3527.1	4q13.3	2008-02-05	2005-07-20		ENSG00000213759	ENSG00000213759		"""UDP glucuronosyltransferases"""	12545	protein-coding gene	gene with protein product		603064	"""UDP glycosyltransferase 2 family, polypeptide B11"""			9675083	Standard	NM_001073		Approved		uc003heh.3	O75310	OTTHUMG00000129395	ENST00000446444.1:c.208T>C	4.37:g.70080233A>G	ENSP00000387683:p.Ser70Pro	Somatic	261	0	0		WXS	Illumina HiSeq	Phase_I	213	96	0.450704	NM_001073	Q3KNV9	Missense_Mutation	SNP	ENST00000446444.1	37	CCDS3527.1	336	0.15384615384615385	156	0.3170731707317073	66	0.18232044198895028	35	0.06118881118881119	79	0.10422163588390501	-	12.59	1.983954	0.35036	0.251594	0.094216	ENSG00000213759	ENST00000446444	T	0.61392	0.11	1.96	1.96	0.26148	.	0.093181	0.44902	U	0.000403	T	0.00012	0.0000	L	0.31294	0.92	0.80722	P	0.0	B	0.16802	0.019	B	0.20384	0.029	T	0.27739	-1.0065	9	0.29301	T	0.29	.	7.5503	0.27793	1.0:0.0:0.0:0.0	rs62298957	70	O75310	UDB11_HUMAN	P	70	ENSP00000387683:S70P	ENSP00000387683:S70P	S	-	1	0	UGT2B11	70114822	0.000000	0.05858	0.009000	0.14445	0.013000	0.08279	-0.262000	0.08682	0.898000	0.36418	0.155000	0.16302	TCC	A|0.500;G|0.500	0.500	weak		0.368	UGT2B11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251551.2	NM_001073	
TTN	7273	hgsc.bcm.edu	37	2	179403750	179403750	+	Missense_Mutation	SNP	C	C	T	rs4894028	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:179403750C>T	ENST00000591111.1	-	303	94213	c.93989G>A	c.(93988-93990)cGc>cAc	p.R31330H	TTN-AS1_ENST00000438095.1_RNA|TTN-AS1_ENST00000585358.1_RNA|TTN-AS1_ENST00000588804.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.R24031H|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000589391.1_RNA|TTN-AS1_ENST00000588244.1_RNA|TTN-AS1_ENST00000585487.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.R30403H|TTN-AS1_ENST00000592182.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000588716.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.R23906H|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592836.1_RNA|TTN-AS1_ENST00000588257.1_RNA|TTN-AS1_ENST00000589842.1_RNA|TTN-AS1_ENST00000431259.2_RNA|TTN-AS1_ENST00000589434.1_RNA|TTN-AS1_ENST00000415561.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.R32971H|TTN-AS1_ENST00000591867.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000450692.2_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.R24098H|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000591466.1_RNA|RP11-65L3.4_ENST00000604692.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000590040.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590932.1_RNA			Q8WZ42	TITIN_HUMAN	titin	31330	Fibronectin type-III 128. {ECO:0000255|PROSITE-ProRule:PRU00316}.		R -> H. {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)			TGCGATGATGCGGAACTGATA	0.488													C|||	385	0.076877	0.0113	0.1484	5008	,	,		21205	0.0248		0.0477	False		,,,				2504	0.1984				p.R32971H		Atlas-SNP	.											.	TTN	18412	.	0			c.G98912A						PASS	.	C	HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG	67,4169		0,67,2051	204.0	204.0	204.0		71717,91208,72092,72293	6.1	1.0	2	dbSNP_111	204	243,8217		8,227,3995	yes	missense,missense,missense,missense	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	29,29,29,29	8,294,6046	TT,TC,CC		2.8723,1.5817,2.4417	probably-damaging,probably-damaging,probably-damaging,probably-damaging	23906/26927,30403/33424,24031/27052,24098/27119	179403750	310,12386	2118	4230	6348	SO:0001583	missense	7273	exon353			ATGATGCGGAACT	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.93989G>A	2.37:g.179403750C>T	ENSP00000465570:p.Arg31330His	Somatic	203	0	0		WXS	Illumina HiSeq	Phase_I	193	89	0.46114	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		85	0.03891941391941392	4	0.008130081300813009	43	0.11878453038674033	5	0.008741258741258742	33	0.04353562005277045	C	23.5	4.420959	0.83559	0.015817	0.028723	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.60920	0.15;0.15;0.15;0.15	6.06	6.06	0.98353	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.09818	0.0241	H	0.98646	4.29	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;0.999;0.999	T	0.70890	-0.4749	9	0.87932	D	0	.	20.6208	0.99490	0.0:1.0:0.0:0.0	rs4894028;rs52804549;rs4894028	23906;24031;24098;31330	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	H	30403;23906;24098;24031;23903	ENSP00000343764:R30403H;ENSP00000434586:R23906H;ENSP00000340554:R24098H;ENSP00000352154:R24031H	ENSP00000340554:R24098H	R	-	2	0	TTN	179111996	1.000000	0.71417	0.998000	0.56505	0.948000	0.59901	7.818000	0.86416	2.882000	0.98803	0.655000	0.94253	CGC	C|0.965;G|0.000;T|0.035	0.035	strong		0.488	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
IQGAP2	10788	hgsc.bcm.edu	37	5	75996909	75996909	+	Missense_Mutation	SNP	G	G	A	rs34592828	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:75996909G>A	ENST00000274364.6	+	34	4673	c.4376G>A	c.(4375-4377)cGg>cAg	p.R1459Q	IQGAP2_ENST00000502745.1_Missense_Mutation_p.R955Q|CTD-2384B11.2_ENST00000507514.1_RNA|IQGAP2_ENST00000396234.3_Missense_Mutation_p.R955Q|IQGAP2_ENST00000379730.3_Missense_Mutation_p.R961Q	NM_006633.2	NP_006624	Q13576	IQGA2_HUMAN	IQ motif containing GTPase activating protein 2	1459					negative regulation of catalytic activity (GO:0043086)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|microvillus (GO:0005902)	actin binding (GO:0003779)|GTPase inhibitor activity (GO:0005095)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|Ras GTPase activator activity (GO:0005099)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(15)|lung(23)|ovary(6)|prostate(1)|skin(3)|stomach(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	68		all_lung(232;0.000514)|Lung NSC(167;0.00135)|Prostate(461;0.00838)|Ovarian(174;0.0149)		all cancers(79;1.38e-36)		AGAAATACTCGGAGATCAATT	0.443													G|||	70	0.0139776	0.0008	0.0231	5008	,	,		21699	0.0		0.0447	False		,,,				2504	0.0082				p.R1459Q		Atlas-SNP	.											.	IQGAP2	186	.	0			c.G4376A						PASS	.	G	GLN/ARG	37,4369	40.8+/-73.8	1,35,2167	78.0	77.0	77.0		4376	4.6	1.0	5	dbSNP_126	77	370,8230	122.4+/-181.4	7,356,3937	yes	missense	IQGAP2	NM_006633.2	43	8,391,6104	AA,AG,GG		4.3023,0.8398,3.1293	possibly-damaging	1459/1576	75996909	407,12599	2203	4300	6503	SO:0001583	missense	10788	exon34			ATACTCGGAGATC	U51903	CCDS34188.1, CCDS68897.1, CCDS68898.1, CCDS75262.1	5q	2008-07-18			ENSG00000145703	ENSG00000145703			6111	protein-coding gene	gene with protein product		605401				8756646	Standard	XM_005248409		Approved		uc003kek.3	Q13576	OTTHUMG00000162432	ENST00000274364.6:c.4376G>A	5.37:g.75996909G>A	ENSP00000274364:p.Arg1459Gln	Somatic	239	0	0		WXS	Illumina HiSeq	Phase_I	237	88	0.371308	NM_006633	A8K4V1|B7Z8A4|J3KR91	Missense_Mutation	SNP	ENST00000274364.6	37	CCDS34188.1	43	0.019688644688644688	1	0.0020325203252032522	9	0.024861878453038673	0	0.0	33	0.04353562005277045	G	20.9	4.059023	0.76074	0.008398	0.043023	ENSG00000145703	ENST00000274364;ENST00000379730;ENST00000396234;ENST00000502745	T;T;T;T	0.42900	0.96;0.96;0.96;0.96	5.46	4.58	0.56647	RasGAP protein, C-terminal (1);	0.180535	0.45606	D	0.000350	T	0.16854	0.0405	M	0.78049	2.395	0.80722	D	1	B;B;P	0.42039	0.119;0.119;0.769	B;B;B	0.40199	0.034;0.034;0.322	T	0.35351	-0.9792	10	0.49607	T	0.09	-5.5774	15.1468	0.72662	0.0717:0.0:0.9283:0.0	rs34592828	961;955;1459	F5H7S7;Q13576-2;Q13576	.;.;IQGA2_HUMAN	Q	1459;961;955;955	ENSP00000274364:R1459Q;ENSP00000442313:R961Q;ENSP00000379535:R955Q;ENSP00000426027:R955Q	ENSP00000274364:R1459Q	R	+	2	0	IQGAP2	76032665	1.000000	0.71417	0.998000	0.56505	0.482000	0.33219	6.295000	0.72744	2.717000	0.92951	0.655000	0.94253	CGG	A|0.027;G|0.973	0.027	strong		0.443	IQGAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368877.1	NM_006633	
CNOT4	4850	hgsc.bcm.edu	37	7	135047811	135047811	+	Missense_Mutation	SNP	G	G	C	rs200460078	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:135047811G>C	ENST00000451834.1	-	12	2242	c.1959C>G	c.(1957-1959)caC>caG	p.H653Q	CNOT4_ENST00000361528.4_Missense_Mutation_p.H582Q|CNOT4_ENST00000541284.1_Missense_Mutation_p.H656Q|CNOT4_ENST00000473470.1_5'UTR|CNOT4_ENST00000423368.2_Missense_Mutation_p.H585Q			O95628	CNOT4_HUMAN	CCR4-NOT transcription complex, subunit 4	0					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						AGGGGGCGCTGTGGTGGGTCT	0.587													G|||	4	0.000798722	0.0	0.0	5008	,	,		13429	0.0		0.004	False		,,,				2504	0.0				p.H656Q	Ovarian(51;766 1130 5502 35047 50875)	Atlas-SNP	.											CNOT4_ENST00000541284,NS,carcinoma,0,3	CNOT4	146	3	0			c.C1968G						PASS	.	G	GLN/HIS,GLN/HIS,GLN/HIS,GLN/HIS	3,4123		0,3,2060	115.0	129.0	124.0		1755,1959,1968,1746	5.0	1.0	7		124	21,8375		0,21,4177	yes	missense,missense,missense,missense	CNOT4	NM_001190847.1,NM_001190849.1,NM_001190850.1,NM_013316.3	24,24,24,24	0,24,6237	CC,CG,GG		0.2501,0.0727,0.1917	probably-damaging,probably-damaging,probably-damaging,probably-damaging	585/643,653/711,656/714,582/640	135047811	24,12498	2063	4198	6261	SO:0001583	missense	4850	exon12			GGCGCTGTGGTGG	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	ENST00000451834.1:c.1959C>G	7.37:g.135047811G>C	ENSP00000388491:p.His653Gln	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	139	75	0.539568	NM_001190850	B7Z6I4|E7ET38|F8VQP3|O95339|O95627|Q8IYM7|Q8NCL0|Q9NPQ1|Q9NZN6	Missense_Mutation	SNP	ENST00000451834.1	37	CCDS55167.1	4	0.0018315018315018315	0	0.0	0	0.0	0	0.0	4	0.005277044854881266	G	18.61	3.662127	0.67700	7.27E-4	0.002501	ENSG00000080802	ENST00000541284;ENST00000451834;ENST00000423368;ENST00000262563;ENST00000361528	T;T;T;T	0.52295	0.67;0.69;0.68;0.68	5.92	5.04	0.67666	.	0.000000	0.85682	D	0.000000	T	0.45657	0.1353	L	0.29908	0.895	0.80722	D	1	P;D;D;D	0.53462	0.932;0.96;0.96;0.96	D;D;D;D	0.69142	0.917;0.962;0.944;0.944	T	0.41124	-0.9526	10	0.14656	T	0.56	-8.6859	15.0604	0.71947	0.0678:0.0:0.9322:0.0	.	653;656;585;582	E7ET38;F8VQP3;O95628-4;O95628-8	.;.;.;.	Q	656;653;585;656;582	ENSP00000445508:H656Q;ENSP00000388491:H653Q;ENSP00000406777:H585Q;ENSP00000354673:H582Q	ENSP00000262563:H656Q	H	-	3	2	CNOT4	134698351	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.869000	0.99810	1.521000	0.48983	0.557000	0.71058	CAC	G|0.998;C|0.002	0.002	strong		0.587	CNOT4-003	NOVEL	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000340670.1	NM_013316	
PCDHB4	56131	hgsc.bcm.edu	37	5	140503237	140503237	+	Missense_Mutation	SNP	A	A	G	rs246669	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:140503237A>G	ENST00000194152.1	+	1	1657	c.1657A>G	c.(1657-1659)Acc>Gcc	p.T553A	AC005754.8_ENST00000606030.1_lincRNA	NM_018938.2	NP_061761.1	Q9Y5E5	PCDB4_HUMAN	protocadherin beta 4	553	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.		T -> A (in dbSNP:rs246669).		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)			GGTGCTGGACACCAACGACAA	0.701													G|||	1006	0.200879	0.1581	0.2305	5008	,	,		16296	0.1964		0.2276	False		,,,				2504	0.2147				p.T553A		Atlas-SNP	.											.	PCDHB4	177	.	0			c.A1657G						PASS	.						39.0	43.0	42.0					5																	140503237		2197	4288	6485	SO:0001583	missense	56131	exon1			CTGGACACCAACG	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.1657A>G	5.37:g.140503237A>G	ENSP00000194152:p.Thr553Ala	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	77	28	0.363636	NM_018938	Q4V761	Missense_Mutation	SNP	ENST00000194152.1	37	CCDS4246.1	369	0.16895604395604397	72	0.14634146341463414	72	0.19889502762430938	92	0.16083916083916083	133	0.17546174142480211	G	8.414	0.844735	0.16963	.	.	ENSG00000081818	ENST00000194152	T	0.01113	5.32	3.77	1.95	0.26073	Cadherin (4);Cadherin conserved site (1);Cadherin-like (1);	.	.	.	.	T	0.00012	0.0000	N	0.03084	-0.415	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.32508	-0.9904	8	0.07813	T	0.8	.	5.5672	0.17177	0.2653:0.1467:0.588:0.0	rs246669;rs17844415	553	Q9Y5E5	PCDB4_HUMAN	A	553	ENSP00000194152:T553A	ENSP00000194152:T553A	T	+	1	0	PCDHB4	140483421	0.000000	0.05858	0.965000	0.40720	0.981000	0.71138	-0.068000	0.11561	0.404000	0.25506	-0.330000	0.08379	ACC	G|1.000;|0.000	1.000	weak		0.701	PCDHB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251812.2	NM_018938	
HN1	51155	hgsc.bcm.edu	37	17	73143748	73143748	+	Splice_Site	SNP	C	C	G	rs200749518		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:73143748C>G	ENST00000409753.3	-	3	485	c.200G>C	c.(199-201)gGt>gCt	p.G67A	HN1_ENST00000470924.1_Splice_Site_p.G21A|RP11-649A18.4_ENST00000579554.1_RNA|HN1_ENST00000356033.4_Splice_Site_p.G67A|HN1_ENST00000405458.3_Splice_Site_p.G21A|HN1_ENST00000465454.1_5'Flank|HN1_ENST00000476258.1_Splice_Site_p.G21A|HN1_ENST00000481647.1_Splice_Site_p.G21A|HN1_ENST00000392566.2_Splice_Site_p.G21A|HN1_ENST00000482348.1_Splice_Site_p.G21A|Y_RNA_ENST00000516233.1_RNA|HN1_ENST00000581874.1_Splice_Site_p.G67A	NM_016185.2	NP_057269.1	Q9UK76	HN1_HUMAN	hematological and neurological expressed 1	67					developmental process (GO:0032502)	nucleus (GO:0005634)			HN1/USH1G(2)	breast(1)	1	all_lung(278;0.14)|Lung NSC(278;0.168)					AGACTTGGCACCTAAAAATCA	0.453																																					p.G67A		Atlas-SNP	.											.	HN1	17	.	0			c.G200C						PASS	.						58.0	60.0	59.0					17																	73143748		2203	4300	6503	SO:0001630	splice_region_variant	51155	exon3			TTGGCACCTAAAA	AF086910	CCDS32729.1, CCDS45771.1, CCDS45772.1	17q25.1	2013-09-20			ENSG00000189159	ENSG00000189159			14569	protein-coding gene	gene with protein product	"""androgen-regulated protein 2"""					15094197	Standard	NM_001002032		Approved	ARM2, HN1A	uc002jnb.1	Q9UK76	OTTHUMG00000154521	ENST00000409753.3:c.200-1G>C	17.37:g.73143748C>G		Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	24	14	0.583333	NM_016185	B2R6K3|Q53FG7|Q7Z2D2|Q7Z2F0	Missense_Mutation	SNP	ENST00000409753.3	37	CCDS45771.1	.	.	.	.	.	.	.	.	.	.	C	16.21	3.059740	0.55325	.	.	ENSG00000189159	ENST00000405458;ENST00000409753;ENST00000356033;ENST00000409135;ENST00000392566	.	.	.	4.97	4.0	0.46444	.	0.129701	0.52532	D	0.000061	T	0.63745	0.2537	M	0.63843	1.955	0.46954	D	0.99926	D;P;D	0.56035	0.974;0.827;0.971	P;B;P	0.54499	0.754;0.418;0.721	T	0.65479	-0.6158	9	0.59425	D	0.04	.	9.2449	0.37520	0.0:0.8284:0.0:0.1716	.	67;67;67	B8ZZT7;Q9UK76-2;Q9UK76	.;.;HN1_HUMAN	A	21;67;67;67;21	.	ENSP00000348316:G67A	G	-	2	0	HN1	70655343	1.000000	0.71417	0.999000	0.59377	0.671000	0.39405	3.060000	0.49955	1.208000	0.43306	0.467000	0.42956	GGT	C|0.999;G|0.001	0.001	weak		0.453	HN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000335692.1	NM_001002032	Missense_Mutation
HLA-A	3105	hgsc.bcm.edu	37	6	29911213	29911213	+	Nonsense_Mutation	SNP	G	G	A	rs199474545		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:29911213G>A	ENST00000396634.1	+	5	853	c.512G>A	c.(511-513)tGg>tAg	p.W171*	HLA-A_ENST00000376802.2_Nonsense_Mutation_p.W171*|HLA-A_ENST00000376809.5_Nonsense_Mutation_p.W171*|HLA-A_ENST00000376806.5_Nonsense_Mutation_p.W171*			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	171	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						AAGCGCAAGTGGGAGGCGGCC	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)																											p.W171X		Atlas-SNP	.											.	HLA-A	89	.	0			c.G512A						PASS	.						35.0	27.0	30.0					6																	29911213		1509	2705	4214	SO:0001587	stop_gained	3105	exon3	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	GCAAGTGGGAGGC	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.512G>A	6.37:g.29911213G>A	ENSP00000379873:p.Trp171*	Somatic	293	0	0		WXS	Illumina HiSeq	Phase_I	132	32	0.242424	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Nonsense_Mutation	SNP	ENST00000396634.1	37	CCDS34373.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	31|31	5.083642|5.083642	0.94050|0.94050	.|.	.|.	ENSG00000206503|ENSG00000206503	ENST00000355767|ENST00000396634;ENST00000376806;ENST00000376809;ENST00000376802	.|.	.|.	.|.	3.78|3.78	-0.515|-0.515	0.11954|0.11954	.|.	.|0.000000	.|0.36815	.|U	.|0.002400	T|.	0.19644|.	0.0472|.	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.12604|.	-1.0541|.	4|.	0.87932|0.87932	D|D	0|0	.|.	2.0762|2.0762	0.03624|0.03624	0.1916:0.1531:0.4984:0.1569|0.1916:0.1531:0.4984:0.1569	.|.	.|.	.|.	.|.	R|X	146|171	.|.	ENSP00000348012:G146R|ENSP00000365998:W171X	G|W	+|+	1|2	0|0	HLA-A|HLA-A	30019192|30019192	0.184000|0.184000	0.23200|0.23200	0.057000|0.057000	0.19452|0.19452	0.134000|0.134000	0.20937|0.20937	0.137000|0.137000	0.15995|0.15995	-0.240000|-0.240000	0.09696|0.09696	0.485000|0.485000	0.47835|0.47835	GGG|TGG	.	.	weak		0.647	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
WDR46	9277	hgsc.bcm.edu	37	6	33256397	33256397	+	Silent	SNP	G	G	A	rs9277965	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:33256397G>A	ENST00000374617.4	-	3	710	c.354C>T	c.(352-354)tcC>tcT	p.S118S	PFDN6_ENST00000395131.1_5'Flank|PFDN6_ENST00000374606.5_5'Flank|PFDN6_ENST00000374607.1_5'Flank|PFDN6_ENST00000374610.2_5'Flank|PFDN6_ENST00000463584.1_5'Flank|WDR46_ENST00000477718.1_5'UTR	NM_001164267.1|NM_005452.5	NP_001157739.1|NP_005443.3	O15213	WDR46_HUMAN	WD repeat domain 46	118							poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|kidney(1)|large_intestine(6)|lung(9)|prostate(1)	20						TCACCTTTCGGGATTTGTCAA	0.597													G|||	638	0.127396	0.0356	0.134	5008	,	,		18883	0.1071		0.165	False		,,,				2504	0.229				p.S118S		Atlas-SNP	.											.	WDR46	43	.	0			c.C354T						PASS	.	G	,	312,4094	162.5+/-194.5	8,296,1899	44.0	46.0	45.0		192,354	2.6	1.0	6	dbSNP_118	45	1432,7168	273.8+/-290.9	116,1200,2984	yes	coding-synonymous,coding-synonymous	WDR46	NM_001164267.1,NM_005452.5	,	124,1496,4883	AA,AG,GG		16.6512,7.0813,13.4092	,	64/557,118/611	33256397	1744,11262	2203	4300	6503	SO:0001819	synonymous_variant	9277	exon3			CTTTCGGGATTTG	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.354C>T	6.37:g.33256397G>A		Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	147	80	0.544218	NM_005452	A6NDP5|Q5HYZ0|Q5STK5|Q5STR3	Silent	SNP	ENST00000374617.4	37	CCDS4772.1																																																																																			G|0.874;A|0.126	0.126	strong		0.597	WDR46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076382.2	NM_005452	
PDCD2L	84306	hgsc.bcm.edu	37	19	34895647	34895647	+	Missense_Mutation	SNP	G	G	A	rs141960904	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:34895647G>A	ENST00000246535.3	+	2	249	c.202G>A	c.(202-204)Ggc>Agc	p.G68S	PDCD2L_ENST00000587065.2_5'Flank|RP11-618P17.4_ENST00000606020.1_Missense_Mutation_p.G63S	NM_032346.1	NP_115722.1	Q9BRP1	PDD2L_HUMAN	programmed cell death 2-like	68					cell cycle (GO:0007049)	cytoplasm (GO:0005737)|membrane (GO:0016020)				breast(2)|kidney(1)|large_intestine(4)|lung(1)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	11	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.211)			CCCGCTGGAAGGCTCCCCGTT	0.706													G|||	10	0.00199681	0.0	0.0072	5008	,	,		14816	0.0		0.005	False		,,,				2504	0.0				p.G68S		Atlas-SNP	.											.	PDCD2L	27	.	0			c.G202A						PASS	.	G	SER/GLY	2,4400	2.1+/-5.4	0,2,2199	23.0	22.0	22.0		202	4.0	1.0	19	dbSNP_134	22	28,8566	14.0+/-48.4	0,28,4269	yes	missense	PDCD2L	NM_032346.1	56	0,30,6468	AA,AG,GG		0.3258,0.0454,0.2308	probably-damaging	68/359	34895647	30,12966	2201	4297	6498	SO:0001583	missense	84306	exon2			CTGGAAGGCTCCC	BC006146	CCDS12438.1	19q13.11	2008-02-05				ENSG00000126249			28194	protein-coding gene	gene with protein product		615661				16311922	Standard	NM_032346		Approved	MGC13096	uc002nvj.3	Q9BRP1		ENST00000246535.3:c.202G>A	19.37:g.34895647G>A	ENSP00000246535:p.Gly68Ser	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	76	37	0.486842	NM_032346		Missense_Mutation	SNP	ENST00000246535.3	37	CCDS12438.1	4	0.0018315018315018315	0	0.0	2	0.0055248618784530384	0	0.0	2	0.002638522427440633	G	21.4	4.141095	0.77775	4.54E-4	0.003258	ENSG00000126249	ENST00000246535	.	.	.	5.04	4.0	0.46444	.	0.111834	0.64402	N	0.000014	T	0.33818	0.0876	L	0.49640	1.575	0.33769	D	0.622826	D	0.53151	0.958	P	0.45071	0.468	T	0.50825	-0.8782	9	0.16896	T	0.51	-20.8332	11.295	0.49274	0.0866:0.0:0.9134:0.0	.	68	Q9BRP1	PDD2L_HUMAN	S	68	.	ENSP00000246535:G68S	G	+	1	0	PDCD2L	39587487	1.000000	0.71417	0.995000	0.50966	0.337000	0.28794	5.910000	0.69931	1.095000	0.41419	0.313000	0.20887	GGC	G|0.998;A|0.002	0.002	strong		0.706	PDCD2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459251.3	NM_032346	
ARSD	414	hgsc.bcm.edu	37	X	2836047	2836047	+	Missense_Mutation	SNP	C	C	T	rs67359049		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	103	0	0		WXS	Illumina HiSeq	Phase_I	93	8	0.0860215	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		
PCNT	5116	hgsc.bcm.edu	37	21	47836078	47836078	+	Silent	SNP	T	T	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:47836078T>C	ENST00000359568.5	+	30	6353	c.6246T>C	c.(6244-6246)taT>taC	p.Y2082Y	PCNT_ENST00000480896.1_3'UTR	NM_006031.5	NP_006022.3	O95613	PCNT_HUMAN	pericentrin	2082					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)					GTTTGCTGTATTCCATGACCT	0.502																																					p.Y2082Y		Atlas-SNP	.											PCNT,colon,carcinoma,+1,1	PCNT	283	1	0			c.T6246C						scavenged	.						92.0	85.0	87.0					21																	47836078		2203	4300	6503	SO:0001819	synonymous_variant	5116	exon30			GCTGTATTCCATG	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.6246T>C	21.37:g.47836078T>C		Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	158	2	0.0126582	NM_006031	O43152|Q7Z7C9	Silent	SNP	ENST00000359568.5	37	CCDS33592.1																																																																																			.	.	none		0.502	PCNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207336.1	NM_006031	
SRRM4	84530	hgsc.bcm.edu	37	12	119588962	119588962	+	Missense_Mutation	SNP	G	G	A	rs2723880	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:119588962G>A	ENST00000267260.4	+	10	1605	c.1217G>A	c.(1216-1218)cGa>cAa	p.R406Q		NM_194286.3	NP_919262.2	A7MD48	SRRM4_HUMAN	serine/arginine repetitive matrix 4	406	Ser-rich.		R -> Q (in dbSNP:rs2723880).		cell differentiation (GO:0030154)|mRNA processing (GO:0006397)|nervous system development (GO:0007399)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)|sensory perception of sound (GO:0007605)	nucleus (GO:0005634)	mRNA binding (GO:0003729)			breast(2)|central_nervous_system(2)|endometrium(5)|kidney(1)|large_intestine(2)|lung(8)|ovary(3)|upper_aerodigestive_tract(1)	24						CACTCGTCCCGATCCCCAAAT	0.567													G|||	1228	0.245208	0.1641	0.3804	5008	,	,		18490	0.1468		0.3966	False		,,,				2504	0.2045				p.R406Q		Atlas-SNP	.											.	SRRM4	131	.	0			c.G1217A						PASS	.	G	GLN/ARG	689,3221		60,569,1326	78.0	82.0	81.0		1217	2.6	1.0	12	dbSNP_100	81	3203,5087		615,1973,1557	yes	missense	SRRM4	NM_194286.3	43	675,2542,2883	AA,AG,GG		38.6369,17.6215,31.9016	possibly-damaging	406/612	119588962	3892,8308	1955	4145	6100	SO:0001583	missense	84530	exon10			CGTCCCGATCCCC	AB058756	CCDS44994.1	12q24.23	2009-09-22	2009-09-21	2009-09-21	ENSG00000139767	ENSG00000139767			29389	protein-coding gene	gene with protein product	"""neural-specific SR-related protein of 100 kDa"""	613103	"""KIAA1853"""	KIAA1853		19737518	Standard	NM_194286		Approved	nSR100	uc001txa.2	A7MD48	OTTHUMG00000168928	ENST00000267260.4:c.1217G>A	12.37:g.119588962G>A	ENSP00000267260:p.Arg406Gln	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	45	23	0.511111	NM_194286	A8K5P6|B2RZH7|Q7Z5F0|Q96JH4	Missense_Mutation	SNP	ENST00000267260.4	37	CCDS44994.1	602	0.27564102564102566	74	0.15040650406504066	139	0.3839779005524862	80	0.13986013986013987	309	0.4076517150395778	G	22.3	4.265032	0.80358	0.176215	0.386369	ENSG00000139767	ENST00000267260	T	0.25250	1.81	5.58	2.63	0.31362	.	0.488214	0.18593	N	0.136681	T	0.00012	0.0000	L	0.40543	1.245	0.49798	P	1.7500000000003624E-4	B	0.24132	0.098	B	0.12837	0.008	T	0.47169	-0.9138	8	.	.	.	-0.6904	3.8042	0.08770	0.1511:0.1305:0.5842:0.1342	rs2723880;rs52812470;rs59964857;rs2723880	406	A7MD48	SRRM4_HUMAN	Q	406	ENSP00000267260:R406Q	.	R	+	2	0	SRRM4	118073345	0.270000	0.24152	0.970000	0.41538	0.964000	0.63967	0.685000	0.25378	1.489000	0.48450	0.655000	0.94253	CGA	G|0.714;A|0.286	0.286	strong		0.567	SRRM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401640.2	NM_194286	
RNASE9	390443	hgsc.bcm.edu	37	14	21024619	21024619	+	Missense_Mutation	SNP	A	A	G	rs1243647|rs386775312	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:21024619A>G	ENST00000557068.1	-	4	2335	c.610T>C	c.(610-612)Tcg>Ccg	p.S204P	RNASE9_ENST00000338904.3_Missense_Mutation_p.S204P|RNASE9_ENST00000429244.2_Missense_Mutation_p.S204P|RNASE9_ENST00000553541.1_Missense_Mutation_p.S204P|RNASE9_ENST00000555230.1_Missense_Mutation_p.S204P|RNASE9_ENST00000553706.1_Missense_Mutation_p.S209P|RNASE9_ENST00000556208.1_Missense_Mutation_p.S209P|RNASE9_ENST00000554964.1_Missense_Mutation_p.S204P|RNASE9_ENST00000557209.1_Missense_Mutation_p.S209P|RNASE9_ENST00000404716.3_Missense_Mutation_p.S209P			P60153	RNAS9_HUMAN	ribonuclease, RNase A family, 9 (non-active)	204			S -> P (in dbSNP:rs1243647). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:18992174, ECO:0000269|Ref.3}.			extracellular region (GO:0005576)	nucleic acid binding (GO:0003676)			haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|ovary(2)|urinary_tract(1)	8	all_cancers(95;0.00238)		Epithelial(56;3.32e-06)|all cancers(55;2.46e-05)	GBM - Glioblastoma multiforme(265;0.0141)		TGCTAGGGCGATATGACAAAG	0.418													G|||	3771	0.752995	0.8011	0.6931	5008	,	,		23030	0.6607		0.7922	False		,,,				2504	0.7853				p.S209P		Atlas-SNP	.											.	RNASE9	30	.	0			c.T625C						PASS	.	G	PRO/SER,PRO/SER,PRO/SER,PRO/SER,PRO/SER,PRO/SER,PRO/SER	3512,894	345.9+/-308.8	1392,728,83	120.0	101.0	107.0	http://www.ncbi.nlm.nih.gov/pubmed?term	610,610,610,625,625,625,625	-1.1	0.0	14	dbSNP_87	107	6820,1780	321.3+/-315.0	2703,1414,183	yes	missense,missense,missense,missense,missense,missense,missense	RNASE9	NM_001001673.3,NM_001110356.1,NM_001110357.1,NM_001110358.1,NM_001110359.1,NM_001110360.1,NM_001110361.1	74,74,74,74,74,74,74	4095,2142,266	GG,GA,AA	http://www.ncbi.nlm.nih.gov/pubmed?term	20.6977,20.2905,20.5597	benign,benign,benign,benign,benign,benign,benign	204/206,204/206,204/206,209/211,209/211,209/211,209/211	21024619	10332,2674	2203	4300	6503	SO:0001583	missense	390443	exon5			AGGGCGATATGAC	AY665804	CCDS32036.1, CCDS53883.1, CCDS55904.1	14q11.2	2006-10-31				ENSG00000188655		"""Ribonucleases, RNase A"""	20673	protein-coding gene	gene with protein product		614014				15676279, 12920233	Standard	NM_001001673		Approved	h461	uc010ahu.3	P60153		ENST00000557068.1:c.610T>C	14.37:g.21024619A>G	ENSP00000451565:p.Ser204Pro	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	114	59	0.517544	NM_001110359	A2RQR8|A8QJS1|Q5GAN7|Q6KG53	Missense_Mutation	SNP	ENST00000557068.1	37	CCDS32036.1	1615	0.7394688644688645	382	0.7764227642276422	245	0.6767955801104972	388	0.6783216783216783	600	0.7915567282321899	G	0.015	-1.552402	0.00918	0.797095	0.793023	ENSG00000188655	ENST00000338904;ENST00000554964;ENST00000555230;ENST00000557068;ENST00000404716;ENST00000556208;ENST00000553541;ENST00000429244;ENST00000553706;ENST00000557209	T;T;T;T;T;T;T;T;T;T	0.15372	2.45;2.45;2.45;2.45;2.43;2.43;2.45;2.45;2.43;2.43	3.41	-1.08	0.09936	.	.	.	.	.	T	0.00012	0.0000	N	0.01576	-0.805	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.31392	-0.9945	8	0.02654	T	1	-15.5003	3.6608	0.08238	0.2165:0.0:0.2761:0.5074	rs1243647;rs60218735;rs1243647	204;209	P60153;P60153-2	RNAS9_HUMAN;.	P	204;204;204;204;209;209;204;204;209;209	ENSP00000340162:S204P;ENSP00000450599:S204P;ENSP00000450800:S204P;ENSP00000451565:S204P;ENSP00000384683:S209P;ENSP00000451160:S209P;ENSP00000451285:S204P;ENSP00000409504:S204P;ENSP00000450570:S209P;ENSP00000450987:S209P	ENSP00000340162:S204P	S	-	1	0	RNASE9	20094459	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-0.272000	0.08560	-0.514000	0.06488	-0.320000	0.08662	TCG	A|0.233;G|0.767	0.767	strong		0.418	RNASE9-004	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000411094.1	NM_001001673	
ANKRD17	26057	hgsc.bcm.edu	37	4	73942678	73942678	+	Silent	SNP	C	C	T	rs2306058	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:73942678C>T	ENST00000358602.4	-	33	7847	c.7731G>A	c.(7729-7731)acG>acA	p.T2577T	ANKRD17_ENST00000509867.2_Silent_p.T2464T|ANKRD17_ENST00000330838.6_Silent_p.T2326T	NM_032217.3	NP_115593.3	O75179	ANR17_HUMAN	ankyrin repeat domain 17	2577					blood vessel maturation (GO:0001955)|negative regulation of smooth muscle cell differentiation (GO:0051151)|viral process (GO:0016032)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(3)|breast(2)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(39)|ovary(6)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(3)	96	Breast(15;0.000295)		Epithelial(6;8.86e-07)|OV - Ovarian serous cystadenocarcinoma(6;6.22e-06)|all cancers(17;1.51e-05)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			CATTATTTTCCGTGGAGCTGG	0.433													C|||	884	0.176518	0.0136	0.2205	5008	,	,		17906	0.2877		0.165	False		,,,				2504	0.2628				p.T2577T		Atlas-SNP	.											.	ANKRD17	214	.	0			c.G7731A						PASS	.	C	,	171,4235	111.6+/-149.8	4,163,2036	131.0	129.0	130.0		7731,6978	0.0	1.0	4	dbSNP_100	130	1415,7185	273.1+/-290.5	95,1225,2980	no	coding-synonymous,coding-synonymous	ANKRD17	NM_032217.3,NM_198889.1	,	99,1388,5016	TT,TC,CC		16.4535,3.8811,12.1944	,	2577/2604,2326/2353	73942678	1586,11420	2203	4300	6503	SO:0001819	synonymous_variant	26057	exon33			ATTTTCCGTGGAG	AB014597	CCDS34003.1, CCDS34004.1, CCDS68721.1	4q21.1-q21.21	2013-01-10			ENSG00000132466	ENSG00000132466		"""Ankyrin repeat domain containing"""	23575	protein-coding gene	gene with protein product		615929				11165478	Standard	NM_032217		Approved	GTAR, KIAA0697, FLJ22206, NY-BR-16	uc003hgp.3	O75179	OTTHUMG00000160826	ENST00000358602.4:c.7731G>A	4.37:g.73942678C>T		Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	136	71	0.522059	NM_032217	E7EUV3|G5E964|Q6PJ85|Q6PK85|Q6PKA2|Q86XI3|Q8NDR5|Q96I86|Q9H288|Q9H6J9	Silent	SNP	ENST00000358602.4	37	CCDS34004.1																																																																																			C|0.852;T|0.148	0.148	strong		0.433	ANKRD17-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000362475.1	NM_032217	
SPTBN2	6712	hgsc.bcm.edu	37	11	66460527	66460527	+	Silent	SNP	C	C	T	rs639938	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:66460527C>T	ENST00000533211.1	-	25	5230	c.4899G>A	c.(4897-4899)ctG>ctA	p.L1633L	SPTBN2_ENST00000309996.2_Silent_p.L1633L|SPTBN2_ENST00000529997.1_Silent_p.L1633L			O15020	SPTN2_HUMAN	spectrin, beta, non-erythrocytic 2	1633					actin filament capping (GO:0051693)|adult behavior (GO:0030534)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|axon guidance (GO:0007411)|cell death (GO:0008219)|cerebellar Purkinje cell layer morphogenesis (GO:0021692)|multicellular organism growth (GO:0035264)|synapse assembly (GO:0007416)|vesicle-mediated transport (GO:0016192)	apical plasma membrane (GO:0016324)|cytosol (GO:0005829)|extracellular space (GO:0005615)|neuronal cell body (GO:0043025)|spectrin (GO:0008091)	actin binding (GO:0003779)|phospholipid binding (GO:0005543)|structural constituent of cytoskeleton (GO:0005200)			autonomic_ganglia(1)|breast(1)|central_nervous_system(4)|cervix(1)|endometrium(10)|kidney(5)|large_intestine(15)|liver(1)|lung(22)|ovary(2)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	74						GGGCTTGCTCCAGCACCTGGT	0.642													C|||	389	0.0776757	0.056	0.0562	5008	,	,		19218	0.1329		0.0567	False		,,,				2504	0.0869				p.L1633L		Atlas-SNP	.											.	SPTBN2	188	.	0			c.G4899A						PASS	.	C		224,4176	132.1+/-168.6	4,216,1980	91.0	84.0	86.0		4899	1.6	0.8	11	dbSNP_83	86	429,8161	132.0+/-189.7	13,403,3879	no	coding-synonymous	SPTBN2	NM_006946.2		17,619,5859	TT,TC,CC		4.9942,5.0909,5.0269		1633/2391	66460527	653,12337	2200	4295	6495	SO:0001819	synonymous_variant	6712	exon24			TTGCTCCAGCACC	AB008567, AF026487, AF026488, AF079569	CCDS8150.1	11q13.2	2013-01-10			ENSG00000173898	ENSG00000173898		"""Pleckstrin homology (PH) domain containing"""	11276	protein-coding gene	gene with protein product		604985	"""spinocerebellar ataxia 5"""	SCA5		9826670, 16429157	Standard	NM_006946		Approved		uc001ojd.3	O15020	OTTHUMG00000167262	ENST00000533211.1:c.4899G>A	11.37:g.66460527C>T		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	100	76	0.76	NM_006946	O14872|O14873	Silent	SNP	ENST00000533211.1	37	CCDS8150.1																																																																																			C|0.938;T|0.062	0.062	strong		0.642	SPTBN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393892.2	NM_006946	
WDR60	55112	hgsc.bcm.edu	37	7	158672619	158672619	+	Missense_Mutation	SNP	A	A	G	rs2788478	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:158672619A>G	ENST00000407559.3	+	5	976	c.818A>G	c.(817-819)cAa>cGa	p.Q273R		NM_018051.4	NP_060521.4	Q8WVS4	WDR60_HUMAN	WD repeat domain 60	273			Q -> R (in dbSNP:rs2788478).		cell projection organization (GO:0030030)	cilium (GO:0005929)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				NS(3)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(3)|kidney(1)|large_intestine(2)|liver(4)|lung(16)|ovary(2)	35	Ovarian(565;0.152)	all_cancers(7;1.25e-09)|all_epithelial(9;0.000894)|all_hematologic(28;0.00603)	OV - Ovarian serous cystadenocarcinoma(82;0.00174)	UCEC - Uterine corpus endometrioid carcinoma (81;0.19)|STAD - Stomach adenocarcinoma(7;0.18)		GAGAGGCACCAAAGCAACGTG	0.438													G|||	2873	0.573682	0.7368	0.4294	5008	,	,		19248	0.7212		0.3837	False		,,,				2504	0.499				p.Q273R		Atlas-SNP	.											.	WDR60	94	.	0			c.A818G						PASS	.		ARG/GLN	2463,1307		809,845,231	73.0	77.0	76.0		818	0.8	0.0	7	dbSNP_100	76	3004,5188		552,1900,1644	yes	missense	WDR60	NM_018051.4	43	1361,2745,1875	GG,GA,AA		36.6699,34.6684,45.7031	benign	273/1067	158672619	5467,6495	1885	4096	5981	SO:0001583	missense	55112	exon5			GGCACCAAAGCAA		CCDS47757.1	7q36.3	2013-11-15			ENSG00000126870	ENSG00000126870		"""WD repeat domain containing"""	21862	protein-coding gene	gene with protein product		615462				23910462	Standard	NM_018051		Approved	FLJ10300, FAP163	uc003woe.4	Q8WVS4	OTTHUMG00000151443	ENST00000407559.3:c.818A>G	7.37:g.158672619A>G	ENSP00000384290:p.Gln273Arg	Somatic	200	0	0		WXS	Illumina HiSeq	Phase_I	166	85	0.512048	NM_018051	Q9NW58	Missense_Mutation	SNP	ENST00000407559.3	37	CCDS47757.1	1191	0.5453296703296703	354	0.7195121951219512	155	0.4281767955801105	394	0.6888111888111889	288	0.37994722955145116	G	0.033	-1.322301	0.01320	0.653316	0.366699	ENSG00000126870	ENST00000407559	T	0.18016	2.24	4.73	0.795	0.18643	.	0.669254	0.12904	N	0.429496	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	0.36841	-0.9731	9	0.02654	T	1	0.3405	5.0153	0.14333	0.3597:0.1489:0.4914:0.0	rs2788478;rs9654723;rs10349453;rs52836646;rs56855193;rs2788478	273	Q8WVS4	WDR60_HUMAN	R	273	ENSP00000384290:Q273R	ENSP00000384290:Q273R	Q	+	2	0	WDR60	158365380	0.000000	0.05858	0.004000	0.12327	0.000000	0.00434	0.042000	0.13949	-0.043000	0.13513	-0.726000	0.03593	CAA	A|0.435;G|0.565	0.565	strong		0.438	WDR60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322668.1	NM_018051	
SELPLG	6404	hgsc.bcm.edu	37	12	109017674	109017674	+	Missense_Mutation	SNP	A	A	G	rs63748999|rs372173288|rs201851784	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:109017674A>G	ENST00000550948.1	-	2	634	c.410T>C	c.(409-411)gTg>gCg	p.V137A	SELPLG_ENST00000228463.6_Missense_Mutation_p.V153A|SELPLG_ENST00000388962.3_Intron			Q14242	SELPL_HUMAN	selectin P ligand	137	12 X 10 AA tandem repeats.		Missing (in short form; not an alternative splicing; dbSNP:rs63748999). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:7505206}.		blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cellular response to interleukin-6 (GO:0071354)|leukocyte adhesive activation (GO:0050902)|leukocyte migration (GO:0050900)|leukocyte tethering or rolling (GO:0050901)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(3)|prostate(3)|skin(1)	12						CTCCGTGGGCACTGGTTGAGT	0.612													G|||	1010	0.201677	0.1097	0.1412	5008	,	,		19840	0.3413		0.171	False		,,,				2504	0.2566				p.V153A		Atlas-SNP	.											SELPLG_ENST00000550948,NS,carcinoma,0,7	SELPLG	138	7	0			c.T458C						scavenged	.						159.0	124.0	136.0					12																	109017674		2199	4273	6472	SO:0001583	missense	6404	exon2			GTGGGCACTGGTT		CCDS31895.1, CCDS31895.2, CCDS55881.1	12q24	2014-01-30						"""CD molecules"", ""Endogenous ligands"""	10722	protein-coding gene	gene with protein product		600738				7505206	Standard	NM_003006		Approved	PSGL-1, CD162	uc010sxe.2	Q14242		ENST00000550948.1:c.410T>C	12.37:g.109017674A>G	ENSP00000447752:p.Val137Ala	Somatic	117	3	0.025641		WXS	Illumina HiSeq	Phase_I	80	25	0.3125	NM_001206609	A8K2Y0|B4DQC3|B7Z5C7|J3KMX6|Q12775|Q6GTW7|Q8N7J7	Missense_Mutation	SNP	ENST00000550948.1	37	CCDS31895.2	.	.	.	.	.	.	.	.	.	.	G	0.025	-1.376284	0.01214	.	.	ENSG00000110876	ENST00000550948;ENST00000228463	T;T	0.12984	2.63;2.63	3.42	-5.49	0.02584	.	.	.	.	.	T	0.03390	0.0098	N	0.04880	-0.145	0.09310	N	0.999999	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.39251	-0.9623	9	0.02654	T	1	0.1678	0.7612	0.01007	0.3376:0.1925:0.2876:0.1824	.	153;137	B7Z5C7;Q14242	.;SELPL_HUMAN	A	137;153	ENSP00000447752:V137A;ENSP00000228463:V153A	ENSP00000228463:V153A	V	-	2	0	SELPLG	107541803	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.356000	0.02609	-1.321000	0.02281	-1.471000	0.01009	GTG	A|0.896;G|0.104	0.104	strong		0.612	SELPLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403904.1		
DNMT1	1786	hgsc.bcm.edu	37	19	10267077	10267077	+	Silent	SNP	T	T	C	rs2228611	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:10267077T>C	ENST00000340748.4	-	17	1576	c.1341A>G	c.(1339-1341)ccA>ccG	p.P447P	DNMT1_ENST00000359526.4_Silent_p.P463P|DNMT1_ENST00000540357.1_Silent_p.P447P			P26358	DNMT1_HUMAN	DNA (cytosine-5-)-methyltransferase 1	447	DNA replication foci-targeting sequence. {ECO:0000250}.|Homodimerization.|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)	CTTCAAGAGATGGGTCATCAT	0.478													C|||	2674	0.533946	0.5204	0.4539	5008	,	,		15091	0.6488		0.4612	False		,,,				2504	0.5654				p.P463P		Atlas-SNP	.											.	DNMT1	148	.	0			c.A1389G						PASS	.	C	,	2180,2226	591.9+/-387.7	554,1072,577	125.0	113.0	117.0		1389,1341	-11.3	0.0	19	dbSNP_98	117	4208,4392	584.4+/-391.7	1025,2158,1117	no	coding-synonymous,coding-synonymous	DNMT1	NM_001130823.1,NM_001379.2	,	1579,3230,1694	CC,CT,TT		48.9302,49.478,49.1158	,	463/1633,447/1617	10267077	6388,6618	2203	4300	6503	SO:0001819	synonymous_variant	1786	exon18			AAGAGATGGGTCA	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.1341A>G	19.37:g.10267077T>C		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	104	103	0.990385	NM_001130823	A0AV63|B7ZLW6|Q9UHG5|Q9ULA2|Q9UMZ6	Silent	SNP	ENST00000340748.4	37	CCDS12228.1																																																																																			T|0.475;C|0.525	0.525	strong		0.478	DNMT1-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451166.1	NM_001379	
RET	5979	hgsc.bcm.edu	37	10	43610119	43610119	+	Missense_Mutation	SNP	G	G	A	rs1799939	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:43610119G>A	ENST00000355710.3	+	11	2303	c.2071G>A	c.(2071-2073)Ggt>Agt	p.G691S	RET_ENST00000340058.5_Missense_Mutation_p.G691S	NM_020975.4	NP_066124.1	P07949	RET_HUMAN	ret proto-oncogene	691			G -> S (in dbSNP:rs1799939). {ECO:0000269|PubMed:14566559, ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:9223675, ECO:0000269|PubMed:9497256}.		activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|cellular response to retinoic acid (GO:0071300)|embryonic epithelial tube formation (GO:0001838)|enteric nervous system development (GO:0048484)|homophilic cell adhesion (GO:0007156)|innervation (GO:0060384)|lymphocyte migration into lymphoid organs (GO:0097021)|MAPK cascade (GO:0000165)|membrane protein proteolysis (GO:0033619)|neural crest cell migration (GO:0001755)|neuron cell-cell adhesion (GO:0007158)|neuron maturation (GO:0042551)|peptidyl-tyrosine phosphorylation (GO:0018108)|Peyer's patch morphogenesis (GO:0061146)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of cell migration (GO:0030335)|positive regulation of cell size (GO:0045793)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of metanephric glomerulus development (GO:0072300)|positive regulation of neuron maturation (GO:0014042)|positive regulation of neuron projection development (GO:0010976)|positive regulation of transcription, DNA-templated (GO:0045893)|posterior midgut development (GO:0007497)|protein phosphorylation (GO:0006468)|regulation of axonogenesis (GO:0050770)|regulation of cell adhesion (GO:0030155)|response to drug (GO:0042493)|response to pain (GO:0048265)|retina development in camera-type eye (GO:0060041)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|ureter maturation (GO:0035799)|ureteric bud development (GO:0001657)	endosome membrane (GO:0010008)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|protein tyrosine kinase activity (GO:0004713)|receptor activity (GO:0004872)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)		CCDC6/RET(4)|KIF5B/RET(79)	NS(2)|adrenal_gland(26)|breast(5)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(7)|kidney(2)|large_intestine(14)|lung(27)|ovary(5)|prostate(3)|skin(1)|thyroid(504)|upper_aerodigestive_tract(1)|urinary_tract(1)	607		Ovarian(717;0.0423)			Cabozantinib(DB08875)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)	CTCCTCTTCCGGTGCCCGCCG	0.647		1	"""T, Mis, N, F"""	"""H4, PRKAR1A, NCOA4, PCM1, GOLGA5, TRIM33, KTN1, TRIM27, HOOK3, KIF5B, CCDC6"""	"""medullary thyroid,  papillary thyroid, pheochromocytoma, NSCLC"""	"""medullary thyroid,  papillary thyroid, pheochromocytoma"""	Hirschsprung disease		Multiple Endocrine Neoplasia, type 2B;Multiple Endocrine Neoplasia, type 2A;Familial Medullary Thyroid Carcinoma				G|||	847	0.169129	0.0923	0.2565	5008	,	,		18422	0.121		0.1889	False		,,,				2504	0.2403				p.G691S	Melanoma(102;360 522 3376 9752 9881 14372 17251 18341 20876 24662 34807 43144 48149)	Atlas-SNP	.	yes	Dom	yes	Multiple endocrine neoplasia 2A/2B	10	10q11.2	5979	ret proto-oncogene	yes	"""E, O"""	RET_ENST00000340058,adrenal_gland,pheochromocytoma,0,2	RET	916	2	0			c.G2071A	GRCh37	CM023821	RET	M	rs1799939	scavenged	.	G	SER/GLY,SER/GLY	455,3951	216.4+/-235.1	19,417,1767	61.0	55.0	57.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	2071,2071	-1.1	0.0	10	dbSNP_89	57	1587,7013	295.7+/-302.5	155,1277,2868	yes	missense,missense	RET	NM_020630.4,NM_020975.4	56,56	174,1694,4635	AA,AG,GG		18.4535,10.3268,15.7004	possibly-damaging,possibly-damaging	691/1073,691/1115	43610119	2042,10964	2203	4300	6503	SO:0001583	missense	5979	exon11	Familial Cancer Database	MEN2B, Wagenmann-Froboese s.;MEN2A, Sipple disease, incl MEN2C;FMTC	TCTTCCGGTGCCC	BC004257	CCDS7200.1, CCDS53525.1	10q11.2	2014-09-17	2007-02-16		ENSG00000165731	ENSG00000165731		"""Cadherins / Cadherin-related"""	9967	protein-coding gene	gene with protein product	"""cadherin-related family member 16"""	164761	"""multiple endocrine neoplasia and medullary thyroid carcinoma 1"", ""Hirschsprung disease 1"""	HSCR1, MEN2A, MTC1, MEN2B		2687772, 1611909	Standard	NM_020975		Approved	PTC, CDHF12, RET51, CDHR16	uc001jal.3	P07949	OTTHUMG00000018024	ENST00000355710.3:c.2071G>A	10.37:g.43610119G>A	ENSP00000347942:p.Gly691Ser	Somatic	75	1	0.0133333		WXS	Illumina HiSeq	Phase_I	46	20	0.434783	NM_020630	A8K6Z2|Q15250|Q9BTB0|Q9H4A2	Missense_Mutation	SNP	ENST00000355710.3	37	CCDS7200.1	338	0.15476190476190477	45	0.09146341463414634	82	0.2265193370165746	60	0.1048951048951049	151	0.19920844327176782	G	8.525	0.869582	0.17322	0.103268	0.184535	ENSG00000165731	ENST00000355710;ENST00000340058	T;T	0.78246	-1.05;-1.16	4.75	-1.08	0.09936	.	0.349618	0.34603	N	0.003826	T	0.00039	0.0001	N	0.14661	0.345	0.80722	P	0.0	B;B;B	0.24426	0.062;0.062;0.103	B;B;B	0.16722	0.004;0.007;0.016	T	0.04128	-1.0975	9	0.07990	T	0.79	.	9.2584	0.37597	0.7374:0.0:0.2626:0.0	rs1799939;rs3781260;rs17362555;rs17845010;rs17857772;rs1799939	437;691;691	B4DGX8;P07949;P07949-2	.;RET_HUMAN;.	S	691	ENSP00000347942:G691S;ENSP00000344798:G691S	ENSP00000344798:G691S	G	+	1	0	RET	42930125	1.000000	0.71417	0.000000	0.03702	0.411000	0.31082	4.395000	0.59678	-0.060000	0.13132	0.462000	0.41574	GGT	G|0.839;A|0.161	0.161	strong		0.647	RET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047694.2	NM_020975	
FOXS1	2307	hgsc.bcm.edu	37	20	30433139	30433139	+	Silent	SNP	G	G	A	rs6089096	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:30433139G>A	ENST00000375978.3	-	1	281	c.207C>T	c.(205-207)aaC>aaT	p.N69N		NM_004118.3	NP_004109.1	O43638	FOXS1_HUMAN	forkhead box S1	69					blood vessel development (GO:0001568)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription, DNA-templated (GO:0045892)|neuromuscular process controlling balance (GO:0050885)|positive regulation of multicellular organism growth (GO:0040018)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			kidney(1)|large_intestine(3)|lung(3)|ovary(1)|urinary_tract(1)	9						TGAGTGACAGGTTGTGGCGGA	0.627													G|||	254	0.0507188	0.0045	0.0663	5008	,	,		16028	0.001		0.1054	False		,,,				2504	0.0971				p.N69N		Atlas-SNP	.											.	FOXS1	29	.	0			c.C207T						PASS	.	G		98,4308	78.8+/-117.2	1,96,2106	89.0	72.0	78.0		207	3.8	1.0	20	dbSNP_114	78	976,7624	211.7+/-252.2	54,868,3378	no	coding-synonymous	FOXS1	NM_004118.3		55,964,5484	AA,AG,GG		11.3488,2.2242,8.2577		69/331	30433139	1074,11932	2203	4300	6503	SO:0001819	synonymous_variant	2307	exon1			TGACAGGTTGTGG	AF042831	CCDS13192.1	20q11.1-q11.2	2008-04-10	2008-04-10	2008-04-10	ENSG00000179772	ENSG00000179772		"""Forkhead boxes"""	3735	protein-coding gene	gene with protein product		602939	"""forkhead (Drosophila)-like 18"", ""forkhead-like 18 (Drosophila)"""	FKHL18		9325056, 17062144	Standard	NM_004118		Approved	FREAC10	uc002wwt.1	O43638	OTTHUMG00000032183	ENST00000375978.3:c.207C>T	20.37:g.30433139G>A		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	114	56	0.491228	NM_004118	Q96D28	Silent	SNP	ENST00000375978.3	37	CCDS13192.1																																																																																			G|0.929;A|0.071	0.071	strong		0.627	FOXS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078560.2	NM_004118	
STEAP1B	256227	hgsc.bcm.edu	37	7	22478207	22478207	+	Intron	SNP	G	G	T	rs2528843	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:22478207G>T	ENST00000406890.2	-	5	800				STEAP1B_ENST00000404369.4_Silent_p.A310A	NM_207342.2	NP_997225.1	Q6NZ63	STEAL_HUMAN	STEAP family member 1B							integral component of membrane (GO:0016021)				endometrium(1)|kidney(1)|lung(2)	4						ttgaagggctggctgctgata	0.398													T|||	2614	0.521965	0.5832	0.4135	5008	,	,		20390	0.6071		0.4702	False		,,,				2504	0.4816				p.A310A		Atlas-SNP	.											.	STEAP1B	22	.	0			c.C930A						PASS	.	T	,	764,620		218,328,146	155.0	139.0	144.0		930,	0.6	0.0	7	dbSNP_100	144	1397,1785		302,793,496	no	coding-synonymous,intron	STEAP1B	NM_001164460.1,NM_207342.2	,	520,1121,642	TT,TG,GG		43.9032,44.7977,47.3281	,	310/343,	22478207	2161,2405	692	1591	2283	SO:0001627	intron_variant	256227	exon5			AGGGCTGGCTGCT		CCDS55094.1, CCDS56469.1	7p15.3	2011-05-19			ENSG00000105889	ENSG00000105889			41907	protein-coding gene	gene with protein product							Standard	NM_207342		Approved		uc010kum.2	Q6NZ63	OTTHUMG00000152529	ENST00000406890.2:c.706-18752C>A	7.37:g.22478207G>T		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	61	12	0.196721	NM_001164460	B5MCI2	Silent	SNP	ENST00000406890.2	37	CCDS55094.1																																																																																			G|0.488;T|0.512	0.512	strong		0.398	STEAP1B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326617.2		
KRTAP9-1	728318	hgsc.bcm.edu	37	17	39346139	39346139	+	Splice_Site	SNP	A	A	G	rs61743546	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:39346139A>G	ENST00000398470.1	+	1	1	c.1A>G	c.(1-3)Atg>Gtg	p.M1V	KRTAP9-1_ENST00000318329.5_5'Flank|KRTAP9-1_ENST00000377723.3_Intron	NM_001190460.1	NP_001177389.1	A8MXZ3	KRA91_HUMAN	keratin associated protein 9-1	1						keratin filament (GO:0045095)				breast(1)|lung(3)	4						CCCTGACACCATGACCCACTG	0.552													.|||	719	0.14357	0.028	0.1527	5008	,	,		17427	0.0655		0.2058	False		,,,				2504	0.3098				p.M1V		Atlas-SNP	.											.	KRTAP9-1	34	.	0			c.A1G						PASS	.																																			SO:0001630	splice_region_variant	728318	exon1			GACACCATGACCC	AC006070	CCDS56029.1	17q21.2	2010-06-03			ENSG00000240542	ENSG00000240542		"""Keratin associated proteins"""	18912	protein-coding gene	gene with protein product			"""keratin associated protein 9-like 3"""	KRTAP9L3			Standard	NM_001190460		Approved	KAP9.1	uc021txf.1	A8MXZ3	OTTHUMG00000133636	ENST00000398470.1:c.1-1A>G	17.37:g.39346139A>G		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	34	13	0.382353	NM_001190460		Missense_Mutation	SNP	ENST00000398470.1	37	CCDS56029.1	284	0.13003663003663005	14	0.028455284552845527	64	0.17679558011049723	46	0.08041958041958042	160	0.21108179419525067	A	17.09	3.300457	0.60195	.	.	ENSG00000240542	ENST00000398470	T	0.00616	6.2	3.82	3.82	0.43975	.	.	.	.	.	T	0.00012	0.0000	.	.	.	.	.	.	.	.	.	.	.	.	T	0.60480	-0.7255	4	.	.	.	.	9.555	0.39332	1.0:0.0:0.0:0.0	.	.	.	.	V	1	ENSP00000381488:M1V	.	M	+	1	0	KRTAP9-1	36599665	1.000000	0.71417	0.998000	0.56505	0.779000	0.44077	2.519000	0.45546	1.679000	0.50963	0.383000	0.25322	ATG	A|0.854;G|0.146	0.146	strong		0.552	KRTAP9-1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257781.1		Missense_Mutation
TMEM63B	55362	hgsc.bcm.edu	37	6	44115169	44115169	+	Missense_Mutation	SNP	G	G	A	rs4714759	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:44115169G>A	ENST00000259746.9	+	12	1102	c.919G>A	c.(919-921)Gtg>Atg	p.V307M	TMEM63B_ENST00000323267.6_Missense_Mutation_p.V307M			Q5T3F8	CSCL2_HUMAN	transmembrane protein 63B	307			V -> M (in dbSNP:rs4714759). {ECO:0000269|PubMed:17974005}.		ion transport (GO:0006811)	integral component of membrane (GO:0016021)	nucleotide binding (GO:0000166)	p.V307M(1)		breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(8)|ovary(1)|pancreas(2)|prostate(2)|stomach(4)	35	all_cancers(18;1.66e-06)|Lung NSC(15;0.00108)|all_lung(25;0.00278)|Hepatocellular(11;0.00309)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0215)			CAAGGAGAACGTGCCTACCAT	0.607													G|||	521	0.104034	0.0068	0.0965	5008	,	,		20519	0.2252		0.0974	False		,,,				2504	0.1227				p.V307M		Atlas-SNP	.											TMEM63B,NS,carcinoma,0,1	TMEM63B	77	1	1	Substitution - Missense(1)	stomach(1)	c.G919A						PASS	.	G	MET/VAL	110,4296	86.8+/-125.4	2,106,2095	147.0	110.0	122.0		919	2.7	0.9	6	dbSNP_111	122	920,7680	204.5+/-247.2	53,814,3433	yes	missense	TMEM63B	NM_018426.1	21	55,920,5528	AA,AG,GG		10.6977,2.4966,7.9194	benign	307/833	44115169	1030,11976	2203	4300	6503	SO:0001583	missense	55362	exon12			GAGAACGTGCCTA	BC022095	CCDS34461.1	6p21.1	2008-02-05	2005-07-25	2005-07-25	ENSG00000137216	ENSG00000137216			17735	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 110"""	C6orf110			Standard	XM_005249211		Approved	DKFZp434P0531, dJ421H19.2	uc003owr.3	Q5T3F8	OTTHUMG00000014757	ENST00000259746.9:c.919G>A	6.37:g.44115169G>A	ENSP00000259746:p.Val307Met	Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	138	59	0.427536	NM_018426	B9EGU3|Q5T3F9|Q6AHX4|Q6P5A0|Q8N219|Q8NDE1|Q9NSG5	Missense_Mutation	SNP	ENST00000259746.9	37	CCDS34461.1	255	0.11675824175824176	3	0.006097560975609756	38	0.10497237569060773	143	0.25	71	0.09366754617414248	G	12.24	1.879303	0.33162	0.024966	0.106977	ENSG00000137216	ENST00000259746;ENST00000323267	T;T	0.44083	0.93;0.93	4.53	2.74	0.32292	.	0.674800	0.15009	N	0.285696	T	0.10423	0.0255	N	0.22421	0.69	0.58432	P	1.0000000000287557E-6	B;B	0.23058	0.007;0.079	B;B	0.15870	0.006;0.014	T	0.07908	-1.0748	9	0.48119	T	0.1	.	3.4756	0.07583	0.266:0.2077:0.5263:0.0	rs4714759;rs52838417;rs58281604;rs4714759	307;307	Q5T3F8;Q5T3F8-2	TM63B_HUMAN;.	M	307	ENSP00000259746:V307M;ENSP00000327154:V307M	ENSP00000259746:V307M	V	+	1	0	TMEM63B	44223147	0.521000	0.26258	0.941000	0.38009	0.977000	0.68977	2.132000	0.42083	1.254000	0.44035	0.650000	0.86243	GTG	G|0.903;A|0.097	0.097	strong		0.607	TMEM63B-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040712.2	XM_166410	
WDFY4	57705	hgsc.bcm.edu	37	10	50171949	50171949	+	Silent	SNP	C	C	T	rs41283297	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:50171949C>T	ENST00000325239.5	+	53	8313	c.8286C>T	c.(8284-8286)taC>taT	p.Y2762Y	WDFY4_ENST00000465910.1_3'UTR|WDFY4_ENST00000413659.2_3'UTR	NM_020945.1	NP_065996.1	Q6ZS81	WDFY4_HUMAN	WDFY family member 4	2762	BEACH. {ECO:0000255|PROSITE- ProRule:PRU00026}.					integral component of membrane (GO:0016021)				NS(2)|breast(5)|central_nervous_system(4)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|lung(3)|pancreas(2)|prostate(5)|skin(6)|stomach(1)	48						TTTTTGGGTACAAGCAGCAGG	0.507													c|||	104	0.0207668	0.0333	0.0231	5008	,	,		20856	0.0		0.0348	False		,,,				2504	0.0092				p.Y2762Y		Atlas-SNP	.											WDFY4,colon,carcinoma,+1,1	WDFY4	205	1	0			c.C8286T						PASS	.			42,1342		0,42,650	79.0	62.0	67.0		8286	0.0	1.0	10	dbSNP_127	67	99,3083		0,99,1492	no	coding-synonymous	WDFY4	NM_020945.1		0,141,2142	TT,TC,CC		3.1113,3.0347,3.088		2762/3185	50171949	141,4425	692	1591	2283	SO:0001819	synonymous_variant	57705	exon54			TGGGTACAAGCAG	AK074085	CCDS44385.1	10q11.23	2013-01-10			ENSG00000128815	ENSG00000128815		"""WD repeat domain containing"""	29323	protein-coding gene	gene with protein product		613316	"""chromosome 10 open reading frame 64"""	C10orf64		10997877	Standard	NM_020945		Approved	KIAA1607, Em:AC060234.3, FLJ45748	uc001jha.4	Q6ZS81	OTTHUMG00000018180	ENST00000325239.5:c.8286C>T	10.37:g.50171949C>T		Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	162	72	0.444444	NM_020945	B9ZVP2|Q86WZ4|Q8N4A3|Q8TEN7|Q96BE1|Q9H7H8|Q9HCG5	Silent	SNP	ENST00000325239.5	37	CCDS44385.1	46|46	0.021062271062271064|0.021062271062271064	10|10	0.02032520325203252|0.02032520325203252	12|12	0.03314917127071823|0.03314917127071823	0|0	0.0|0.0	24|24	0.0316622691292876|0.0316622691292876	C|C	8.107|8.107	0.777868|0.777868	0.16120|0.16120	0.030347|0.030347	0.031113|0.031113	ENSG00000128815|ENSG00000128815	ENST00000312002|ENST00000265453	.|.	.|.	.|.	5.57|5.57	0.0195|0.0195	0.14121|0.14121	.|.	.|.	.|.	.|.	.|.	.|T	.|0.31544	.|0.0800	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.34950	.|-0.9808	.|4	.|.	.|.	.|.	.|.	9.751|9.751	0.40475|0.40475	0.0:0.5194:0.0:0.4806|0.0:0.5194:0.0:0.4806	rs41283297;rs61733243|rs41283297;rs61733243	.|.	.|.	.|.	X|I	1853|849	.|.	.|.	Q|T	+|+	1|2	0|0	WDFY4|WDFY4	49841955|49841955	0.998000|0.998000	0.40836|0.40836	0.999000|0.999000	0.59377|0.59377	0.916000|0.916000	0.54674|0.54674	0.569000|0.569000	0.23638|0.23638	0.095000|0.095000	0.17434|0.17434	0.655000|0.655000	0.94253|0.94253	CAA|ACA	C|0.972;T|0.028	0.028	strong		0.507	WDFY4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		XM_033379	
ZC3HC1	51530	hgsc.bcm.edu	37	7	129664301	129664301	+	Silent	SNP	T	T	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:129664301T>C	ENST00000358303.4	-	7	906	c.822A>G	c.(820-822)caA>caG	p.Q274Q	ZC3HC1_ENST00000481503.1_Intron|RP11-306G20.1_ENST00000480018.1_RNA|ZC3HC1_ENST00000311873.5_Silent_p.Q253Q|RNA5SP245_ENST00000364239.1_RNA|RP11-306G20.1_ENST00000587038.1_RNA|ZC3HC1_ENST00000360708.5_Silent_p.Q274Q	NM_016478.3	NP_057562.3	Q86WB0	NIPA_HUMAN	zinc finger, C3HC-type containing 1	274					mitotic nuclear division (GO:0007067)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|protein ubiquitination (GO:0016567)	nuclear membrane (GO:0031965)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(6)|large_intestine(10)|lung(2)|prostate(1)|urinary_tract(1)	22	Melanoma(18;0.0435)					TCCTCATACATTGCGAACATG	0.478																																					p.Q274Q	Melanoma(115;540 1606 16325 28853 48167)	Atlas-SNP	.											.	ZC3HC1	45	.	0			c.A822G						PASS	.						73.0	67.0	69.0					7																	129664301		2203	4300	6503	SO:0001819	synonymous_variant	51530	exon7			CATACATTGCGAA	AF151050	CCDS34753.1, CCDS64767.1, CCDS75659.1	7q32.2	2013-01-17			ENSG00000091732	ENSG00000091732		"""Zinc fingers, C3HC-type"""	29913	protein-coding gene	gene with protein product	"""nuclear interaction partner of ALK"""					11042152	Standard	XM_005250403		Approved	NIPA	uc003vpi.3	Q86WB0	OTTHUMG00000157648	ENST00000358303.4:c.822A>G	7.37:g.129664301T>C		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	95	22	0.231579	NM_016478	A6NH66|Q75MF3|Q75MF4|Q8N330|Q96F75|Q9HA34|Q9NVX4|Q9P0R0	Silent	SNP	ENST00000358303.4	37	CCDS34753.1																																																																																			.	.	none		0.478	ZC3HC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349316.1	NM_016478	
CYP4V2	285440	hgsc.bcm.edu	37	4	187118114	187118114	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:187118114C>T	ENST00000378802.4	+	4	738	c.434C>T	c.(433-435)tCc>tTc	p.S145F		NM_207352.3	NP_997235.3	Q6ZWL3	CP4V2_HUMAN	cytochrome P450, family 4, subfamily V, polypeptide 2	145					fatty acid omega-oxidation (GO:0010430)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	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)|endometrium(1)|kidney(1)|large_intestine(5)|lung(9)|skin(1)|stomach(2)	20		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;1.33e-10)|BRCA - Breast invasive adenocarcinoma(30;3.84e-05)|GBM - Glioblastoma multiforme(59;0.000132)|STAD - Stomach adenocarcinoma(60;0.000293)|LUSC - Lung squamous cell carcinoma(40;0.00242)|READ - Rectum adenocarcinoma(43;0.17)		AAATGGCGCTCCAGGAGAAAG	0.323																																					p.S145F		Atlas-SNP	.											.	CYP4V2	49	.	0			c.C434T						PASS	.						65.0	69.0	68.0					4																	187118114		2203	4298	6501	SO:0001583	missense	285440	exon4			GGCGCTCCAGGAG	AK022114	CCDS34119.1	4q35.2	2004-07-05			ENSG00000145476	ENSG00000145476		"""Cytochrome P450s"""	23198	protein-coding gene	gene with protein product		608614				15042513	Standard	NM_207352		Approved	CYP4AH1	uc003iyw.4	Q6ZWL3	OTTHUMG00000160379	ENST00000378802.4:c.434C>T	4.37:g.187118114C>T	ENSP00000368079:p.Ser145Phe	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	55	16	0.290909	NM_207352	B7U6W2|Q6ZTM4	Missense_Mutation	SNP	ENST00000378802.4	37	CCDS34119.1	.	.	.	.	.	.	.	.	.	.	C	15.26	2.780697	0.49891	.	.	ENSG00000145476	ENST00000378802;ENST00000274118	T	0.69806	-0.43	5.42	2.68	0.31781	.	0.512228	0.23803	N	0.044403	T	0.62048	0.2396	L	0.60904	1.88	0.09310	N	1	B	0.27013	0.166	B	0.29267	0.1	T	0.56768	-0.7924	10	0.62326	D	0.03	.	11.3683	0.49686	0.2554:0.6217:0.1229:0.0	.	145	Q6ZWL3	CP4V2_HUMAN	F	145;123	ENSP00000368079:S145F	ENSP00000274118:S123F	S	+	2	0	CYP4V2	187355108	0.014000	0.17966	0.105000	0.21289	0.973000	0.67179	1.809000	0.38922	0.320000	0.23234	-0.182000	0.12963	TCC	.	.	none		0.323	CYP4V2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360398.1	XM_209612	
CBS	875	hgsc.bcm.edu	37	21	44488631	44488631	+	Missense_Mutation	SNP	T	T	G	rs34040148	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:44488631T>G	ENST00000398165.3	-	4	563	c.304A>C	c.(304-306)Aag>Cag	p.K102Q	CBS_ENST00000352178.5_Missense_Mutation_p.K102Q|CBS_ENST00000359624.3_Missense_Mutation_p.K102Q|CBS_ENST00000398158.1_Missense_Mutation_p.K102Q|CBS_ENST00000398168.1_Missense_Mutation_p.K102Q|CBS_ENST00000470912.1_5'UTR|CBS_ENST00000544202.1_Missense_Mutation_p.K14Q	NM_000071.2	NP_000062.1	P35520	CBS_HUMAN	cystathionine-beta-synthase	102			K -> N (in CBSD; 50% of activity). {ECO:0000269|PubMed:7981678}.|K -> Q (in CBSD; severe form; linked with Arg-77; dbSNP:rs34040148). {ECO:0000269|PubMed:11013450}.		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)	AGCTCACACTTCAGGCCGAAC	0.542													T|||	59	0.0117812	0.0446	0.0	5008	,	,		11993	0.0		0.0	False		,,,				2504	0.0				p.K102Q		Atlas-SNP	.											.	CBS	85	.	0			c.A304C	GRCh37	CM994315	CBS	M	rs34040148	PASS	.	T	GLN/LYS,GLN/LYS,GLN/LYS	167,4239	110.8+/-149.0	1,165,2037	96.0	93.0	94.0		304,304,304	4.8	1.0	21	dbSNP_126	94	0,8600		0,0,4300	yes	missense,missense,missense	CBS	NM_000071.2,NM_001178008.1,NM_001178009.1	53,53,53	1,165,6337	GG,GT,TT		0.0,3.7903,1.284	probably-damaging,probably-damaging,probably-damaging	102/552,102/552,102/552	44488631	167,12839	2203	4300	6503	SO:0001583	missense	875	exon4			CACACTTCAGGCC	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.304A>C	21.37:g.44488631T>G	ENSP00000381231:p.Lys102Gln	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	137	51	0.372263	NM_000071	B2R993|D3DSK4|Q99425|Q9BWC5	Missense_Mutation	SNP	ENST00000398165.3	37	CCDS13693.1	24	0.01098901098901099	24	0.04878048780487805	0	0.0	0	0.0	0	0.0	T	15.59	2.878485	0.51801	0.037903	0.0	ENSG00000160200	ENST00000398158;ENST00000398165;ENST00000359624;ENST00000352178;ENST00000398168;ENST00000539520;ENST00000544202;ENST00000441030	D;D;D;D;D;D;D	0.96491	-4.03;-4.03;-4.03;-4.03;-4.03;-4.03;-4.03	4.81	4.81	0.61882	Pyridoxal phosphate-dependent enzyme, beta subunit (2);	0.000000	0.85682	D	0.000000	T	0.80681	0.4669	M	0.66439	2.03	0.48395	D	0.99964	P	0.36495	0.556	B	0.36766	0.232	D	0.84529	0.0632	10	0.38643	T	0.18	-46.6496	12.8977	0.58109	0.0:0.0:0.0:1.0	rs34040148	102	P35520	CBS_HUMAN	Q	102;102;102;102;102;59;14;102	ENSP00000381225:K102Q;ENSP00000381231:K102Q;ENSP00000352643:K102Q;ENSP00000344460:K102Q;ENSP00000381234:K102Q;ENSP00000439332:K14Q;ENSP00000388235:K102Q	ENSP00000344460:K102Q	K	-	1	0	CBS	43361700	1.000000	0.71417	0.998000	0.56505	0.544000	0.35116	3.979000	0.56888	1.917000	0.55516	0.533000	0.62120	AAG	T|0.985;G|0.015	0.015	strong		0.542	CBS-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195525.1	NM_000071	
TMEM71	137835	hgsc.bcm.edu	37	8	133764112	133764112	+	Missense_Mutation	SNP	T	T	C	rs117725783	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:133764112T>C	ENST00000356838.3	-	4	375	c.233A>G	c.(232-234)gAc>gGc	p.D78G	TMEM71_ENST00000517538.1_5'UTR|TMEM71_ENST00000523829.1_Missense_Mutation_p.D78G|TMEM71_ENST00000377901.4_Missense_Mutation_p.D78G	NM_144649.2	NP_653250.2	Q6P5X7	TMM71_HUMAN	transmembrane protein 71	78						integral component of membrane (GO:0016021)				endometrium(2)|kidney(1)|large_intestine(3)|lung(6)|ovary(2)|skin(2)	16	all_neural(3;2.72e-06)|Medulloblastoma(3;7.08e-05)|Ovarian(258;0.00438)|Esophageal squamous(12;0.00507)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;4.46e-05)			CAGGAAGCTGTCTTCAGTCCA	0.473													T|||	26	0.00519169	0.0	0.0072	5008	,	,		18844	0.0		0.0149	False		,,,				2504	0.0061				p.D78G		Atlas-SNP	.											.	TMEM71	55	.	0			c.A233G						PASS	.	T	GLY/ASP,GLY/ASP	17,4389	23.3+/-48.9	0,17,2186	169.0	153.0	158.0		233,233	5.8	1.0	8	dbSNP_132	158	176,8424	80.9+/-143.5	4,168,4128	yes	missense,missense	TMEM71	NM_001145153.1,NM_144649.2	94,94	4,185,6314	CC,CT,TT		2.0465,0.3858,1.4839	probably-damaging,probably-damaging	78/233,78/277	133764112	193,12813	2203	4300	6503	SO:0001583	missense	137835	exon4			AAGCTGTCTTCAG	AK057631	CCDS6366.1, CCDS47921.1	8q24.22	2005-09-02				ENSG00000165071			26572	protein-coding gene	gene with protein product						12477932	Standard	NM_144649		Approved	FLJ33069	uc003ytn.3	Q6P5X7		ENST00000356838.3:c.233A>G	8.37:g.133764112T>C	ENSP00000349296:p.Asp78Gly	Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	145	27	0.186207	NM_144649	Q3KRC2|Q8WVZ4|Q96LX9	Missense_Mutation	SNP	ENST00000356838.3	37	CCDS6366.1	13	0.005952380952380952	0	0.0	2	0.0055248618784530384	0	0.0	11	0.014511873350923483	T	17.79	3.475998	0.63737	0.003858	0.020465	ENSG00000165071	ENST00000523829;ENST00000356838;ENST00000377901;ENST00000519187;ENST00000519304	.	.	.	5.81	5.81	0.92471	.	0.058994	0.64402	D	0.000003	T	0.66858	0.2832	M	0.77103	2.36	0.47245	D	0.999364	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.971;0.998;0.999	T	0.77638	-0.2513	9	0.87932	D	0	-17.5053	13.9131	0.63881	0.0:0.0:0.0:1.0	.	78;78;78	Q6P5X7;Q6P5X7-3;Q6P5X7-2	TMM71_HUMAN;.;.	G	78	.	ENSP00000349296:D78G	D	-	2	0	TMEM71	133833294	1.000000	0.71417	1.000000	0.80357	0.173000	0.22820	6.769000	0.74985	2.214000	0.71695	0.533000	0.62120	GAC	T|0.988;C|0.012	0.012	strong		0.473	TMEM71-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379591.1	NM_144649	
ACKR1	2532	hgsc.bcm.edu	37	1	159175465	159175465	+	Missense_Mutation	SNP	T	T	C	rs141404247		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:159175465T>C	ENST00000368122.2	+	2	915	c.236T>C	c.(235-237)gTc>gCc	p.V79A	CTA-134P22.2_ENST00000609696.1_RNA|DARC_ENST00000368121.2_Missense_Mutation_p.V81A|DARC_ENST00000537147.1_Missense_Mutation_p.V79A	NM_002036.3	NP_002027.2	Q16570	ACKR1_HUMAN		79					chemokine-mediated signaling pathway (GO:0070098)|defense response (GO:0006952)|inflammatory response (GO:0006954)|regulation of chemokine production (GO:0032642)	endosome (GO:0005768)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	C-C chemokine binding (GO:0019957)|G-protein coupled receptor activity (GO:0004930)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			large_intestine(2)|lung(1)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	8	all_hematologic(112;0.0429)					AGCAGCACTGTCCTCTTCATG	0.592																																					p.V81A		Atlas-SNP	.											.	DARC	76	.	0			c.T242C						PASS	.	T	ALA/VAL,ALA/VAL	0,4406		0,0,2203	154.0	140.0	144.0		242,236	2.4	0.4	1	dbSNP_134	144	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	DARC	NM_001122951.2,NM_002036.3	64,64	0,1,6502	CC,CT,TT		0.0116,0.0,0.0077	possibly-damaging,possibly-damaging	81/339,79/337	159175465	1,13005	2203	4300	6503	SO:0001583	missense	2532	exon1			GCACTGTCCTCTT																												ENST00000368122.2:c.236T>C	1.37:g.159175465T>C	ENSP00000357104:p.Val79Ala	Somatic	212	1	0.00471698		WXS	Illumina HiSeq	Phase_I	165	82	0.49697	NM_001122951	A8YPG5|O75898|Q16300|Q8WWE3|Q9UJP0|Q9UKZ5|Q9UKZ6|Q9UQE1	Missense_Mutation	SNP	ENST00000368122.2	37	CCDS1183.1	.	.	.	.	.	.	.	.	.	.	T	7.123	0.578380	0.13686	0.0	1.16E-4	ENSG00000213088	ENST00000368122;ENST00000537147;ENST00000359381;ENST00000435307;ENST00000368121	T;T;T;T	0.48201	0.82;0.82;1.49;0.82	4.96	2.42	0.29668	.	2.278740	0.02794	U	0.122432	T	0.19167	0.0460	L	0.38175	1.15	0.09310	N	1	B;B	0.26876	0.162;0.162	B;B	0.25140	0.058;0.058	T	0.25467	-1.0131	10	0.87932	D	0	-2.2668	4.1077	0.10045	0.1781:0.0985:0.0:0.7234	.	81;79	Q5Y7A1;Q16570	.;DUFFY_HUMAN	A	79;79;79;81;81	ENSP00000357104:V79A;ENSP00000441985:V79A;ENSP00000398406:V81A;ENSP00000357103:V81A	ENSP00000352341:V79A	V	+	2	0	DARC	157442089	0.706000	0.27856	0.391000	0.26233	0.007000	0.05969	1.480000	0.35464	0.818000	0.34468	0.379000	0.24179	GTC	T|1.000;C|0.000	0.000	weak		0.592	DARC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090338.2		
OR6M1	390261	hgsc.bcm.edu	37	11	123676388	123676388	+	Missense_Mutation	SNP	G	G	A	rs76301014	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	74	0	0		WXS	Illumina HiSeq	Phase_I	59	13	0.220339	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	
ACSL5	51703	hgsc.bcm.edu	37	10	114154815	114154815	+	Silent	SNP	C	C	T	rs11195943	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:114154815C>T	ENST00000393081.1	+	2	418	c.111C>T	c.(109-111)ccC>ccT	p.P37P	ACSL5_ENST00000354273.4_Silent_p.P37P|ACSL5_ENST00000433418.1_Silent_p.P37P|ACSL5_ENST00000479936.1_3'UTR|ACSL5_ENST00000356116.1_Silent_p.P93P|ACSL5_ENST00000354655.4_Silent_p.P37P	NM_203380.1	NP_976314.1	Q9ULC5	ACSL5_HUMAN	acyl-CoA synthetase long-chain family member 5	37					cellular lipid metabolic process (GO:0044255)|long-chain fatty acid metabolic process (GO:0001676)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|regulation of extrinsic apoptotic signaling pathway (GO:2001236)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|long-chain fatty acid-CoA ligase activity (GO:0004467)			breast(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(6)|prostate(1)|skin(2)|stomach(1)	21		Colorectal(252;0.117)|Breast(234;0.222)		Epithelial(162;0.0343)|all cancers(201;0.137)		GACCTCAACCCGTCTTACCTC	0.448													C|||	349	0.0696885	0.0166	0.0937	5008	,	,		18354	0.0952		0.0944	False		,,,				2504	0.0726				p.P93P		Atlas-SNP	.											.	ACSL5	51	.	0			c.C279T						PASS	.	C	,,	163,4243	108.6+/-147.0	2,159,2042	123.0	109.0	114.0		279,111,111	-4.4	0.0	10	dbSNP_120	114	979,7621	212.8+/-253.0	60,859,3381	no	coding-synonymous,coding-synonymous,coding-synonymous	ACSL5	NM_016234.3,NM_203379.1,NM_203380.1	,,	62,1018,5423	TT,TC,CC		11.3837,3.6995,8.7806	,,	93/740,37/684,37/684	114154815	1142,11864	2203	4300	6503	SO:0001819	synonymous_variant	51703	exon2			TCAACCCGTCTTA	AB033899	CCDS7572.1, CCDS7573.1	10q25.1-q25.2	2004-06-21	2004-02-19	2004-02-20	ENSG00000197142	ENSG00000197142		"""Acyl-CoA synthetase family"""	16526	protein-coding gene	gene with protein product	"""FACL5 for fatty acid coenzyme A ligase 5"", ""long-chain acyl-CoA synthetase 5"", ""long-chain fatty acid coenzyme A ligase 5"", ""fatty-acid-Coenzyme A ligase, long-chain 5"""	605677	"""fatty-acid-Coenzyme A ligase, long-chain 5"""	FACL5		11127823	Standard	NM_016234		Approved	ACS5, ACS2	uc001kzu.3	Q9ULC5	OTTHUMG00000019060	ENST00000393081.1:c.111C>T	10.37:g.114154815C>T		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	124	67	0.540323	NM_016234	A6GV77|D3DRB3|Q6UX44|Q9UIU4	Silent	SNP	ENST00000393081.1	37	CCDS7573.1																																																																																			C|0.918;T|0.082	0.082	strong		0.448	ACSL5-203	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050386.1	NM_016234	
ABCA13	154664	hgsc.bcm.edu	37	7	48311563	48311563	+	Missense_Mutation	SNP	T	T	G	rs17712293	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:48311563T>G	ENST00000435803.1	+	17	2324	c.2300T>G	c.(2299-2301)aTt>aGt	p.I767S		NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	767			I -> S (in dbSNP:rs17712293).		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						ACAGAGGATATTCTGAATATA	0.378													T|||	974	0.194489	0.1543	0.2709	5008	,	,		12995	0.2153		0.1322	False		,,,				2504	0.2372				p.I767S		Atlas-SNP	.											.	ABCA13	1192	.	0			c.T2300G						PASS	.	T	SER/ILE	588,3046		47,494,1276	52.0	49.0	50.0		2300	3.4	0.0	7	dbSNP_123	50	1161,6985		91,979,3003	yes	missense	ABCA13	NM_152701.3	142	138,1473,4279	GG,GT,TT		14.2524,16.1805,14.8472	benign	767/5059	48311563	1749,10031	1817	4073	5890	SO:0001583	missense	154664	exon17			AGGATATTCTGAA	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.2300T>G	7.37:g.48311563T>G	ENSP00000411096:p.Ile767Ser	Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	80	28	0.35	NM_152701	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Missense_Mutation	SNP	ENST00000435803.1	37	CCDS47584.1	401	0.18360805860805862	84	0.17073170731707318	89	0.24585635359116023	129	0.22552447552447552	99	0.13060686015831136	T	7.752	0.703480	0.15172	0.161805	0.142524	ENSG00000179869	ENST00000435803	D	0.86694	-2.16	5.81	3.42	0.39159	.	1.087280	0.07167	N	0.851812	T	0.00073	0.0002	L	0.40543	1.245	0.80722	P	0.0	B	0.30763	0.294	B	0.24974	0.057	T	0.06092	-1.0846	9	0.72032	D	0.01	.	7.4921	0.27469	0.0:0.2457:0.0:0.7543	rs17712293;rs52795922;rs17712293	767	Q86UQ4	ABCAD_HUMAN	S	767	ENSP00000411096:I767S	ENSP00000411096:I767S	I	+	2	0	ABCA13	48282109	0.000000	0.05858	0.005000	0.12908	0.231000	0.25187	0.606000	0.24194	1.029000	0.39812	0.477000	0.44152	ATT	T|0.817;G|0.183	0.183	strong		0.378	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701	
PSPH	5723	hgsc.bcm.edu	37	7	56088780	56088780	+	Silent	SNP	G	G	A	rs75497420	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:56088780G>A	ENST00000395471.3	-	4	931	c.126C>T	c.(124-126)gaC>gaT	p.D42D	PSPH_ENST00000275605.3_Silent_p.D42D|PSPH_ENST00000459834.1_Intron			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	132	0	0		WXS	Illumina HiSeq	Phase_I	158	27	0.170886	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	
ACAN	176	hgsc.bcm.edu	37	15	89398605	89398605	+	Missense_Mutation	SNP	G	G	T	rs938608	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:89398605G>T	ENST00000561243.1	+	11	2789	c.2789G>T	c.(2788-2790)aGc>aTc	p.S930I	ACAN_ENST00000439576.2_Missense_Mutation_p.S930I|ACAN_ENST00000559004.1_Missense_Mutation_p.S930I|ACAN_ENST00000352105.7_Missense_Mutation_p.S930I			P16112	PGCA_HUMAN	aggrecan	929	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.S930I(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)			GAGTGGCCCAGCACTCCTACG	0.562													G|||	2267	0.452676	0.4463	0.3919	5008	,	,		18902	0.2421		0.6531	False		,,,				2504	0.5153				p.S930I		Atlas-SNP	.											AGC1,NS,carcinoma,-1,3	ACAN	220	3	1	Substitution - Missense(1)	stomach(1)	c.G2789T						PASS	.	G	ILE/SER,ILE/SER	1888,1990		438,1012,489	50.0	55.0	54.0		2789,2789	-3.5	0.0	15	dbSNP_86	54	5358,2904		1726,1906,499	yes	missense,missense	ACAN	NM_001135.3,NM_013227.3	142,142	2164,2918,988	TT,TG,GG		35.1489,48.6849,40.313	probably-damaging,probably-damaging	930/2432,930/2531	89398605	7246,4894	1939	4131	6070	SO:0001583	missense	176	exon12			GGCCCAGCACTCC	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.2789G>T	15.37:g.89398605G>T	ENSP00000453342:p.Ser930Ile	Somatic	108	1	0.00925926		WXS	Illumina HiSeq	Phase_I	87	87	1	NM_001135	Q13650|Q9UCD3|Q9UCP4|Q9UCP5|Q9UDE0	Missense_Mutation	SNP	ENST00000561243.1	37	CCDS53970.1	1003	0.4592490842490842	211	0.42886178861788615	169	0.46685082872928174	117	0.20454545454545456	506	0.6675461741424802	G	10.74	1.434070	0.25813	0.486849	0.648511	ENSG00000157766	ENST00000439576;ENST00000352105;ENST00000268134	T;T	0.02446	4.52;4.29	5.06	-3.45	0.04781	.	0.824660	0.09898	N	0.741404	T	0.00012	0.0000	L	0.59436	1.845	0.80722	P	0.0	D;D	0.54601	0.967;0.967	P;P	0.58520	0.84;0.84	T	0.40308	-0.9570	9	0.20046	T	0.44	0.0066	1.9092	0.03284	0.2907:0.345:0.247:0.1174	rs938608;rs52808766;rs59582752;rs938608	930;930	E7ENV9;E7EX88	.;.	I	930	ENSP00000387356:S930I;ENSP00000341615:S930I	ENSP00000268134:S930I	S	+	2	0	ACAN	87199609	0.000000	0.05858	0.000000	0.03702	0.226000	0.24999	-0.823000	0.04443	-0.466000	0.06943	0.655000	0.94253	AGC	A|0.003;C|0.008	.	strong		0.562	ACAN-006	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416267.2	NM_001135	
MARCH4	57574	hgsc.bcm.edu	37	2	217148417	217148417	+	Silent	SNP	C	C	A	rs876771	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:217148417C>A	ENST00000273067.4	-	2	2318	c.552G>T	c.(550-552)tcG>tcT	p.S184S		NM_020814.2	NP_065865.1	Q9P2E8	MARH4_HUMAN	membrane-associated ring finger (C3HC4) 4, E3 ubiquitin protein ligase	184						Golgi stack (GO:0005795)|integral component of membrane (GO:0016021)|trans-Golgi network (GO:0005802)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|large_intestine(5)|lung(11)|ovary(1)|prostate(1)|skin(1)	20		Renal(323;0.0854)		Epithelial(149;2.19e-05)|all cancers(144;0.00121)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Lung(261;0.0125)		TGCACTTGACCGAGCCATCAC	0.607													C|||	2183	0.435903	0.3147	0.4308	5008	,	,		20032	0.4345		0.493	False		,,,				2504	0.546				p.S184S		Atlas-SNP	.											.	MARCH4	50	.	0			c.G552T						PASS	.	C		1453,2953	469.0+/-355.3	243,967,993	61.0	54.0	56.0		552	-8.5	0.5	2	dbSNP_86	56	4144,4456	565.2+/-388.4	976,2192,1132	no	coding-synonymous	MARCH4	NM_020814.2		1219,3159,2125	AA,AC,CC		48.186,32.9778,43.034		184/411	217148417	5597,7409	2203	4300	6503	SO:0001819	synonymous_variant	57574	exon2			CTTGACCGAGCCA	AB037820	CCDS33376.1	2q35	2013-01-09	2012-02-23		ENSG00000144583	ENSG00000144583		"""MARCH membrane-associated ring fingers"", ""RING-type (C3HC4) zinc fingers"""	29269	protein-coding gene	gene with protein product		608208	"""membrane-associated ring finger (C3HC4) 4"""			10718198, 14722266	Standard	NM_020814		Approved	KIAA1399, MARCH-IV, RNF174	uc002vgb.3	Q9P2E8	OTTHUMG00000154824	ENST00000273067.4:c.552G>T	2.37:g.217148417C>A		Somatic	104	1	0.00961538		WXS	Illumina HiSeq	Phase_I	73	72	0.986301	NM_020814	Q4KMN7|Q86WR8	Silent	SNP	ENST00000273067.4	37	CCDS33376.1																																																																																			C|0.576;A|0.424	0.424	strong		0.607	MARCH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337272.2	NM_020814	
C1orf177	163747	hgsc.bcm.edu	37	1	55280637	55280637	+	Silent	SNP	C	C	T	rs200876449		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:55280637C>T	ENST00000371273.3	+	8	990	c.975C>T	c.(973-975)ccC>ccT	p.P325P	C1orf177_ENST00000358193.3_Silent_p.P325P	NM_001110533.1	NP_001104003	Q3ZCV2	CA177_HUMAN	chromosome 1 open reading frame 177	325								p.P325P(1)		breast(1)|cervix(1)|kidney(1)|large_intestine(6)|lung(6)|prostate(2)	17						AATGCAAACCCGTCAACCAGC	0.547													C|||	1	0.000199681	0.0	0.0014	5008	,	,		20294	0.0		0.0	False		,,,				2504	0.0				p.P325P		Atlas-SNP	.											C1orf177,NS,carcinoma,0,1	C1orf177	36	1	1	Substitution - coding silent(1)	prostate(1)	c.C975T						scavenged	.						113.0	114.0	113.0					1																	55280637		2203	4300	6503	SO:0001819	synonymous_variant	163747	exon8			CAAACCCGTCAAC	AK097520	CCDS599.1, CCDS44153.1	1p32.3	2012-07-25			ENSG00000162398	ENSG00000162398			26854	protein-coding gene	gene with protein product							Standard	NM_152607		Approved	FLJ40201	uc001cyb.4	Q3ZCV2	OTTHUMG00000009986	ENST00000371273.3:c.975C>T	1.37:g.55280637C>T		Somatic	201	1	0.00497512		WXS	Illumina HiSeq	Phase_I	139	2	0.0143885	NM_001110533	B7WPL2|Q8N7Y9	Silent	SNP	ENST00000371273.3	37	CCDS44153.1																																																																																			C|1.000;T|0.000	0.000	strong		0.547	C1orf177-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000027674.1	NM_152607	
HIST1H3J	8356	hgsc.bcm.edu	37	6	27858421	27858421	+	Silent	SNP	A	A	G	rs200973	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:27858421A>G	ENST00000359303.2	-	1	149	c.150T>C	c.(148-150)cgT>cgC	p.R50R	HIST1H2BO_ENST00000303806.4_5'Flank|HIST1H3J_ENST00000479986.1_5'UTR	NM_003535.2	NP_003526.1	P68431	H31_HUMAN	histone cluster 1, H3j	50					blood coagulation (GO:0007596)|chromatin organization (GO:0006325)|DNA replication-dependent nucleosome assembly (GO:0006335)|regulation of gene silencing (GO:0060968)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear chromosome (GO:0000228)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)			central_nervous_system(1)|endometrium(1)|kidney(1)|lung(3)|ovary(1)|prostate(1)	8						GGCGGATCTCACGCAAGGCCA	0.612													G|||	722	0.144169	0.2095	0.1542	5008	,	,		15341	0.0714		0.1461	False		,,,				2504	0.1217				p.R50R		Atlas-SNP	.											.	HIST1H3J	16	.	0			c.T150C						PASS	.	G		883,3523	732.2+/-410.3	90,703,1410	47.0	49.0	48.0		150	3.1	1.0	6	dbSNP_79	48	1387,7213	744.2+/-407.2	114,1159,3027	no	coding-synonymous	HIST1H3J	NM_003535.2		204,1862,4437	GG,GA,AA		16.1279,20.0409,17.4535		50/137	27858421	2270,10736	2203	4300	6503	SO:0001819	synonymous_variant	8356	exon1			GATCTCACGCAAG	Z83737	CCDS4638.1	6p22.1	2011-01-27	2006-10-11	2003-02-14	ENSG00000197153	ENSG00000197153		"""Histones / Replication-dependent"""	4774	protein-coding gene	gene with protein product		602817	"""H3 histone family, member J"", ""histone 1, H3j"""	H3FJ		9439656, 12408966	Standard	NM_003535		Approved	H3/j	uc003nka.3	P68431	OTTHUMG00000016185	ENST00000359303.2:c.150T>C	6.37:g.27858421A>G		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	50	31	0.62	NM_003535	A0PJT7|A5PLR1|P02295|P02296|P16106|Q6ISV8|Q6NWP8|Q6NWP9|Q6NXU4|Q71DJ3|Q93081	Silent	SNP	ENST00000359303.2	37	CCDS4638.1																																																																																			A|0.839;G|0.161	0.161	strong		0.612	HIST1H3J-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043453.2	NM_003535	
ZNF354C	30832	hgsc.bcm.edu	37	5	178506075	178506075	+	Missense_Mutation	SNP	A	A	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:178506075A>T	ENST00000315475.6	+	5	948	c.642A>T	c.(640-642)aaA>aaT	p.K214N		NM_014594.1	NP_055409.1	Q86Y25	Z354C_HUMAN	zinc finger protein 354C	214					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|kidney(1)|large_intestine(10)|lung(13)|ovary(1)|urinary_tract(3)	30	all_cancers(89;0.00065)|all_epithelial(37;0.000153)|Renal(175;0.000159)|Lung NSC(126;0.00175)|all_lung(126;0.00309)	all_cancers(40;0.19)|all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.247)		CAGGAGGAAAACCTCACATCT	0.353																																					p.K214N		Atlas-SNP	.											.	ZNF354C	77	.	0			c.A642T						PASS	.						51.0	53.0	52.0					5																	178506075		2203	4300	6503	SO:0001583	missense	30832	exon5			AGGAAAACCTCAC		CCDS4443.1	5q35	2013-01-08			ENSG00000177932	ENSG00000177932		"""Zinc fingers, C2H2-type"", ""-"""	16736	protein-coding gene	gene with protein product						10786630	Standard	NM_014594		Approved	KID3	uc003mju.3	Q86Y25	OTTHUMG00000130888	ENST00000315475.6:c.642A>T	5.37:g.178506075A>T	ENSP00000324064:p.Lys214Asn	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	71	16	0.225352	NM_014594	Q6P4P9|Q8NFX1	Missense_Mutation	SNP	ENST00000315475.6	37	CCDS4443.1	.	.	.	.	.	.	.	.	.	.	A	13.49	2.254012	0.39896	.	.	ENSG00000177932	ENST00000315475	T	0.35048	1.33	3.94	-4.99	0.03010	Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.36082	0.0954	M	0.80847	2.515	0.09310	N	1	B	0.19073	0.033	B	0.18871	0.023	T	0.44190	-0.9344	9	0.66056	D	0.02	-3.9769	8.2749	0.31866	0.3087:0.1478:0.5435:0.0	.	214	Q86Y25	Z354C_HUMAN	N	214	ENSP00000324064:K214N	ENSP00000324064:K214N	K	+	3	2	ZNF354C	178438681	0.000000	0.05858	0.000000	0.03702	0.291000	0.27294	-0.409000	0.07160	-1.159000	0.02807	0.482000	0.46254	AAA	.	.	none		0.353	ZNF354C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253473.2		
KIAA1551	55196	hgsc.bcm.edu	37	12	32134064	32134064	+	Missense_Mutation	SNP	A	A	G	rs7298803	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:32134064A>G	ENST00000312561.4	+	4	589	c.175A>G	c.(175-177)Att>Gtt	p.I59V	KIAA1551_ENST00000535596.1_Intron	NM_018169.3	NP_060639	Q9HCM1	K1551_HUMAN	KIAA1551	59			I -> V (in dbSNP:rs7298803).														TTCAAATCCAATTTCACAGCC	0.388													A|||	259	0.0517173	0.0371	0.0879	5008	,	,		19909	0.0149		0.0984	False		,,,				2504	0.0358				p.I59V		Atlas-SNP	.											.	.	.	.	0			c.A175G						PASS	.	A	VAL/ILE	224,4182	135.3+/-171.4	5,214,1984	85.0	82.0	83.0		175	-2.2	0.0	12	dbSNP_116	83	1026,7574	219.4+/-257.5	55,916,3329	yes	missense	C12orf35	NM_018169.3	29	60,1130,5313	GG,GA,AA		11.9302,5.084,9.6109	benign	59/1748	32134064	1250,11756	2203	4300	6503	SO:0001583	missense	55196	exon4			AATCCAATTTCAC	AK001514	CCDS8725.2	12p11.21	2012-08-14	2012-08-14	2012-08-14	ENSG00000174718	ENSG00000174718			25559	protein-coding gene	gene with protein product			"""chromosome 12 open reading frame 35"""	C12orf35		10997877	Standard	NM_018169		Approved	FLJ20696, FLJ10652	uc001rks.3	Q9HCM1	OTTHUMG00000128501	ENST00000312561.4:c.175A>G	12.37:g.32134064A>G	ENSP00000310338:p.Ile59Val	Somatic	232	0	0		WXS	Illumina HiSeq	Phase_I	174	94	0.54023	NM_018169	B2RTU5|Q4KN17|Q9NVL6|Q9NWP9	Missense_Mutation	SNP	ENST00000312561.4	37	CCDS8725.2	134	0.06135531135531135	17	0.034552845528455285	30	0.08287292817679558	9	0.015734265734265736	78	0.10290237467018469	A	0.003	-2.451337	0.00175	0.05084	0.119302	ENSG00000174718	ENST00000312561;ENST00000381054	T;T	0.06449	3.3;3.3	5.39	-2.22	0.06952	.	1.509460	0.04410	N	0.365859	T	0.00039	0.0001	N	0.02539	-0.55	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.45891	-0.9230	8	.	.	.	.	7.2192	0.25977	0.4079:0.1179:0.4742:0.0	rs7298803;rs7298803	59	Q9HCM1	CL035_HUMAN	V	59	ENSP00000310338:I59V;ENSP00000370442:I59V	.	I	+	1	0	C12orf35	32025331	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.260000	0.08708	-0.269000	0.09298	-1.839000	0.00587	ATT	A|0.921;G|0.079	0.079	strong		0.388	KIAA1551-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250307.2	NM_018169	
ZNF563	147837	hgsc.bcm.edu	37	19	12429509	12429509	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:12429509T>C	ENST00000293725.5	-	4	1535	c.1330A>G	c.(1330-1332)Acg>Gcg	p.T444A		NM_145276.2	NP_660319.1	Q8TA94	ZN563_HUMAN	zinc finger protein 563	444					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)|kidney(2)|large_intestine(5)|lung(4)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20						CCATCTCCCGTATGCATTACC	0.428																																					p.T444A	GBM(39;623 795 5132 29510 31476)	Atlas-SNP	.											ZNF563,colon,carcinoma,+2,1	ZNF563	77	1	0			c.A1330G						scavenged	.						187.0	173.0	178.0					19																	12429509		2203	4300	6503	SO:0001583	missense	147837	exon4			CTCCCGTATGCAT	BC022523	CCDS12270.1	19p13.2	2013-09-20			ENSG00000188868	ENSG00000188868		"""Zinc fingers, C2H2-type"", ""-"""	30498	protein-coding gene	gene with protein product							Standard	NM_145276		Approved	FLJ34797	uc002mtp.3	Q8TA94	OTTHUMG00000156413	ENST00000293725.5:c.1330A>G	19.37:g.12429509T>C	ENSP00000293725:p.Thr444Ala	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	46	3	0.0652174	NM_145276	B2R9E7|Q8NAT7	Missense_Mutation	SNP	ENST00000293725.5	37	CCDS12270.1	.	.	.	.	.	.	.	.	.	.	T	14.31	2.498724	0.44455	.	.	ENSG00000188868	ENST00000293725	T	0.26518	1.73	0.537	0.537	0.17144	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.41442	0.1159	L	0.58510	1.815	0.20403	N	0.999909	D	0.89917	1.0	D	0.87578	0.998	T	0.13469	-1.0508	9	0.72032	D	0.01	.	6.6537	0.22977	0.0:0.0:0.0:1.0	.	444	Q8TA94	ZN563_HUMAN	A	444	ENSP00000293725:T444A	ENSP00000293725:T444A	T	-	1	0	ZNF563	12290509	0.454000	0.25728	0.020000	0.16555	0.065000	0.16274	1.380000	0.34351	0.454000	0.26884	0.260000	0.18958	ACG	.	.	none		0.428	ZNF563-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344114.1	NM_145276	
ZNF101	94039	hgsc.bcm.edu	37	19	19790159	19790159	+	Missense_Mutation	SNP	A	A	C	rs4808209	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:19790159A>C	ENST00000592502.1	+	4	471	c.361A>C	c.(361-363)Atg>Ctg	p.M121L	ZNF101_ENST00000444249.2_3'UTR|ZNF101_ENST00000415784.2_Start_Codon_SNP_p.M1L			Q8IZC7	ZN101_HUMAN	zinc finger protein 101	121			M -> L (in dbSNP:rs4808209).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(1)|kidney(1)|large_intestine(6)|lung(4)|ovary(2)|prostate(1)	17						GGACAGGCACATGAGAGCTCA	0.498													a|||	314	0.0626997	0.0008	0.0793	5008	,	,		19592	0.1558		0.0298	False		,,,				2504	0.0726				p.M121L		Atlas-SNP	.											.	ZNF101	43	.	0			c.A361C						PASS	.	C	LEU/MET	44,4362	46.0+/-80.4	0,44,2159	104.0	84.0	91.0		361	-0.5	0.2	19	dbSNP_111	91	419,8181	130.2+/-188.1	7,405,3888	yes	missense	ZNF101	NM_033204.2	15	7,449,6047	CC,CA,AA		4.8721,0.9986,3.5599	benign	121/437	19790159	463,12543	2203	4300	6503	SO:0001583	missense	94039	exon4			AGGCACATGAGAG	AK097169	CCDS32971.1	19p13.11	2013-01-08	2004-02-10		ENSG00000181896	ENSG00000181896		"""Zinc fingers, C2H2-type"", ""-"""	12881	protein-coding gene	gene with protein product		603983	"""zinc finger protein 101 (Y2)"""			11441184	Standard	XM_005260165		Approved	HZF12, DKFZp570I0164	uc002nni.2	Q8IZC7	OTTHUMG00000167736	ENST00000592502.1:c.361A>C	19.37:g.19790159A>C	ENSP00000468049:p.Met121Leu	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	71	29	0.408451	NM_033204	C9JU83|Q0VDG9	Missense_Mutation	SNP	ENST00000592502.1	37	CCDS32971.1	138	0.06318681318681318	0	0.0	22	0.06077348066298342	91	0.1590909090909091	25	0.032981530343007916	a	8.494	0.862698	0.17178	0.009986	0.048721	ENSG00000181896	ENST00000318110;ENST00000415440;ENST00000415784	T;T	0.50277	0.75;3.52	0.235	-0.47	0.12131	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00109	0.0003	L	0.35644	1.08	0.09310	P	1.0	B	0.23377	0.084	B	0.21360	0.034	T	0.14062	-1.0486	8	0.27785	T	0.31	.	2.0838	0.03641	0.3507:0.3504:0.2989:0.0	rs4808209;rs52816771;rs4808209	121	Q8IZC7	ZN101_HUMAN	L	121;121;1	ENSP00000319716:M121L;ENSP00000400952:M1L	ENSP00000319716:M121L	M	+	1	0	ZNF101	19651159	0.000000	0.05858	0.155000	0.22561	0.159000	0.22180	-2.318000	0.01121	-0.803000	0.04415	-0.825000	0.03093	ATG	A|0.947;C|0.053	0.053	strong		0.498	ZNF101-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460559.1	NM_033204	
PEPD	5184	hgsc.bcm.edu	37	19	33878837	33878837	+	Missense_Mutation	SNP	G	G	A	rs17570	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:33878837G>A	ENST00000244137.7	-	14	1336	c.1303C>T	c.(1303-1305)Ctt>Ttt	p.L435F	PEPD_ENST00000591968.1_5'UTR|PEPD_ENST00000397032.4_Missense_Mutation_p.L394F|PEPD_ENST00000436370.3_Missense_Mutation_p.L371F	NM_000285.3	NP_000276.2	P12955	PEPD_HUMAN	peptidase D	435			L -> F (in dbSNP:rs17570). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		cellular amino acid metabolic process (GO:0006520)|collagen catabolic process (GO:0030574)|proteolysis (GO:0006508)	extracellular vesicular exosome (GO:0070062)	aminopeptidase activity (GO:0004177)|dipeptidase activity (GO:0016805)|manganese ion binding (GO:0030145)|metallocarboxypeptidase activity (GO:0004181)			endometrium(3)|kidney(3)|large_intestine(2)|lung(7)|ovary(2)	17	Esophageal squamous(110;0.137)					TCGCGGTTAAGGAAGGAGGCG	0.662													A|||	1394	0.278355	0.4932	0.2176	5008	,	,		16600	0.1915		0.2565	False		,,,				2504	0.1431				p.L435F		Atlas-SNP	.											.	PEPD	48	.	0			c.C1303T						PASS	.	A	PHE/LEU,PHE/LEU,PHE/LEU	1543,2345		326,891,727	9.0	14.0	12.0		1303,1180,1111	3.4	1.0	19	dbSNP_63	12	1977,6269		270,1437,2416	yes	missense,missense,missense	PEPD	NM_000285.3,NM_001166056.1,NM_001166057.1	22,22,22	596,2328,3143	AA,AG,GG		23.9753,39.6862,29.0094	benign,benign,benign	435/494,394/453,371/430	33878837	3520,8614	1944	4123	6067	SO:0001583	missense	5184	exon14			GGTTAAGGAAGGA	BC015027	CCDS42544.1, CCDS54244.1, CCDS54245.1	19q13.11	2008-02-05				ENSG00000124299	3.4.13.9		8840	protein-coding gene	gene with protein product	"""prolidase"""	613230				2925654, 1972707	Standard	NM_000285		Approved		uc002nur.4	P12955		ENST00000244137.7:c.1303C>T	19.37:g.33878837G>A	ENSP00000244137:p.Leu435Phe	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	114	59	0.517544	NM_000285	A8K3Z1|A8K416|A8K696|A8MX47|B4DDB7|B4DGJ1|E9PCE8|Q8TBN9|Q9BT75	Missense_Mutation	SNP	ENST00000244137.7	37	CCDS42544.1	646	0.2957875457875458	259	0.5264227642276422	87	0.24033149171270718	100	0.17482517482517482	200	0.2638522427440633	A	4.177	0.031489	0.08101	0.396862	0.239753	ENSG00000124299	ENST00000244137;ENST00000397032;ENST00000436370	T;T;T	0.79749	-1.3;-0.93;-1.29	5.52	3.36	0.38483	Peptidase M24, structural domain (3);	0.090943	0.85682	N	0.000000	T	0.00012	0.0000	N	0.25380	0.74	0.09310	P	1.0	B;B;B;B	0.09022	0.001;0.002;0.001;0.001	B;B;B;B	0.17722	0.019;0.019;0.019;0.019	T	0.43376	-0.9395	9	0.07990	T	0.79	-9.2384	3.6997	0.08378	0.4988:0.0:0.1906:0.3105	rs17570;rs2303102;rs16968055;rs17398453;rs17856803;rs59385819	371;394;435;435	E9PCE8;A8MX47;P12955;A8K3Z1	.;.;PEPD_HUMAN;.	F	435;394;371	ENSP00000244137:L435F;ENSP00000380226:L394F;ENSP00000391890:L371F	ENSP00000244137:L435F	L	-	1	0	PEPD	38570677	1.000000	0.71417	0.996000	0.52242	0.881000	0.50899	2.274000	0.43390	0.388000	0.25054	-0.490000	0.04691	CTT	G|0.706;A|0.294	0.294	strong		0.662	PEPD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451432.3	NM_000285	
ZNF417	147687	hgsc.bcm.edu	37	19	58420699	58420699	+	Missense_Mutation	SNP	C	C	A	rs3745133	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:58420699C>A	ENST00000312026.5	-	3	1111	c.947G>T	c.(946-948)cGt>cTt	p.R316L	ZNF417_ENST00000536263.1_Missense_Mutation_p.R117L|ZNF417_ENST00000595559.1_Missense_Mutation_p.R315L|CTD-2583A14.9_ENST00000602124.1_Intron	NM_152475.2	NP_689688.2	Q8TAU3	ZN417_HUMAN	zinc finger protein 417	316				R -> L (in Ref. 3; AAH25783). {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)	p.R316L(1)		central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|stomach(3)|upper_aerodigestive_tract(1)	18		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0151)		AGTGTGAACACGCTGATGGCT	0.458													C|||	1690	0.33746	0.4153	0.2911	5008	,	,		25205	0.2817		0.3499	False		,,,				2504	0.3098				p.R316L		Atlas-SNP	.											ZNF417,NS,carcinoma,0,1	ZNF417	44	1	1	Substitution - Missense(1)	stomach(1)	c.G947T						PASS	.						167.0	147.0	154.0					19																	58420699		2203	4300	6503	SO:0001583	missense	147687	exon3			TGAACACGCTGAT	BC025783	CCDS12965.1, CCDS74469.1	19q13.43	2013-01-08				ENSG00000173480		"""Zinc fingers, C2H2-type"", ""-"""	20646	protein-coding gene	gene with protein product							Standard	NM_152475		Approved	MGC34079	uc002qqq.3	Q8TAU3		ENST00000312026.5:c.947G>T	19.37:g.58420699C>A	ENSP00000311319:p.Arg316Leu	Somatic	193	0	0		WXS	Illumina HiSeq	Phase_I	209	112	0.535885	NM_152475	B4DEU1	Missense_Mutation	SNP	ENST00000312026.5	37	CCDS12965.1	645	0.29532967032967034	167	0.3394308943089431	107	0.2955801104972376	118	0.2062937062937063	253	0.3337730870712401	.	8.577	0.881369	0.17467	.	.	ENSG00000173480	ENST00000312026;ENST00000536263	T;T	0.25085	1.82;1.82	2.15	-2.01	0.07410	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	L	0.60012	1.86	0.80722	P	0.0	P	0.38335	0.627	B	0.36922	0.236	T	0.32981	-0.9886	8	0.66056	D	0.02	.	7.8865	0.29653	0.0:0.6777:0.0:0.3223	rs3745133;rs17856732	316	Q8TAU3	ZN417_HUMAN	L	316;117	ENSP00000311319:R316L;ENSP00000442760:R117L	ENSP00000311319:R316L	R	-	2	0	ZNF417	63112511	0.000000	0.05858	0.000000	0.03702	0.128000	0.20619	-2.414000	0.01037	-0.691000	0.05135	-1.050000	0.02344	CGT	C|0.500;A|0.500	0.500	weak		0.458	ZNF417-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466860.1	NM_152475	
RLN2	6019	hgsc.bcm.edu	37	9	5300255	5300255	+	Missense_Mutation	SNP	C	C	A	rs61738986	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:5300255C>A	ENST00000381627.3	-	2	789	c.401G>T	c.(400-402)cGc>cTc	p.R134L	RLN2_ENST00000308420.3_3'UTR	NM_134441.2	NP_604390.1	P04090	REL2_HUMAN	relaxin 2	134					female pregnancy (GO:0007565)	extracellular region (GO:0005576)		p.R134H(1)		endometrium(2)|kidney(1)|large_intestine(2)|lung(6)	11	all_hematologic(13;0.137)	Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.0201)|Lung(218;0.0987)		TTGTCTATTGCGAATAAGTTT	0.393													C|||	10	0.00199681	0.0008	0.0029	5008	,	,		18545	0.0		0.006	False		,,,				2504	0.001				p.R134L		Atlas-SNP	.											RLN2,caecum,carcinoma,-1,2	RLN2	22	2	1	Substitution - Missense(1)	lung(1)	c.G401T						PASS	.	C	,LEU/ARG	6,4400	12.9+/-30.5	0,6,2197	115.0	115.0	115.0		,401	-1.6	0.0	9	dbSNP_129	115	85,8515	48.1+/-107.5	0,85,4215	yes	utr-3,missense	RLN2	NM_005059.2,NM_134441.1	,102	0,91,6412	AA,AC,CC		0.9884,0.1362,0.6997	,possibly-damaging	,134/186	5300255	91,12915	2203	4300	6503	SO:0001583	missense	6019	exon2			CTATTGCGAATAA		CCDS6460.1	9p24.1	2013-02-26	2004-11-15		ENSG00000107014	ENSG00000107014		"""Endogenous ligands"""	10027	protein-coding gene	gene with protein product	"""relaxin H2"", ""prorelaxin H2"", ""relaxin, ovarian, of pregnancy"""	179740	"""relaxin 2 (H2)"""			6548703, 6548702	Standard	NM_134441		Approved	H2, RLXH2, bA12D24.1.1, bA12D24.1.2	uc003zja.2	P04090	OTTHUMG00000019496	ENST00000381627.3:c.401G>T	9.37:g.5300255C>A	ENSP00000371040:p.Arg134Leu	Somatic	198	0	0		WXS	Illumina HiSeq	Phase_I	179	49	0.273743	NM_134441	A0AVM0|Q99936|Q9UCX3|Q9UQJ2	Missense_Mutation	SNP	ENST00000381627.3	37	CCDS6460.1	4	0.0018315018315018315	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	C	5.507	0.278499	0.10403	0.001362	0.009884	ENSG00000107014	ENST00000381627	T	0.53640	0.61	3.47	-1.6	0.08426	Insulin-like (3);	2.655290	0.01325	N	0.011073	T	0.22282	0.0537	N	0.21142	0.635	0.09310	N	1	B	0.10296	0.003	B	0.10450	0.005	T	0.05053	-1.0909	10	0.12430	T	0.62	.	3.6846	0.08323	0.2421:0.4304:0.0:0.3275	.	134	P04090	REL2_HUMAN	L	134	ENSP00000371040:R134L	ENSP00000371040:R134L	R	-	2	0	RLN2	5290255	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.454000	0.06770	-0.316000	0.08690	-0.322000	0.08575	CGC	C|0.994;A|0.006	0.006	strong		0.393	RLN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051619.1	NM_134441	
DSPP	1834	hgsc.bcm.edu	37	4	88535868	88535868	+	Missense_Mutation	SNP	A	A	G	rs199719429		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:88535868A>G	ENST00000282478.7	+	4	2087	c.2054A>G	c.(2053-2055)aAc>aGc	p.N685S	RP11-742B18.1_ENST00000506480.1_RNA|DSPP_ENST00000399271.1_Missense_Mutation_p.N685S			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	685	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)		gacagcagcaacagcagtgat	0.483																																					p.N685S		Atlas-SNP	.											DSPP,NS,carcinoma,-1,2	DSPP	174	2	0			c.A2054G						scavenged	.						116.0	132.0	127.0					4																	88535868		1684	3089	4773	SO:0001583	missense	1834	exon5			GCAGCAACAGCAG	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.2054A>G	4.37:g.88535868A>G	ENSP00000282478:p.Asn685Ser	Somatic	133	1	0.0075188		WXS	Illumina HiSeq	Phase_I	94	15	0.159574	NM_014208	A8MUI0|O95815	Missense_Mutation	SNP	ENST00000282478.7	37	CCDS43248.1	.	.	.	.	.	.	.	.	.	.	-	4.290	0.052936	0.08291	.	.	ENSG00000152591	ENST00000399271;ENST00000282478	D;D	0.87809	-2.3;-2.3	1.5	0.247	0.15521	.	.	.	.	.	T	0.69287	0.3094	N	0.17082	0.46	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.54833	-0.8234	9	0.02654	T	1	0.1107	4.5905	0.12304	0.7937:0.0:0.2063:0.0	.	685	Q9NZW4	DSPP_HUMAN	S	685	ENSP00000382213:N685S;ENSP00000282478:N685S	ENSP00000282478:N685S	N	+	2	0	DSPP	88754892	0.003000	0.15002	0.026000	0.17262	0.014000	0.08584	1.419000	0.34793	0.077000	0.16863	0.139000	0.15985	AAC	.	.	weak		0.483	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208	
ZNF695	57116	hgsc.bcm.edu	37	1	247162688	247162688	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:247162688G>T	ENST00000339986.7	-	3	368	c.221C>A	c.(220-222)cCc>cAc	p.P74H	ZNF695_ENST00000487338.2_Missense_Mutation_p.P74H|ZNF695_ENST00000498046.2_Intron	NM_020394.4	NP_065127	Q8IW36	ZN695_HUMAN	zinc finger protein 695	74	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			endometrium(1)|large_intestine(1)|lung(9)|prostate(1)|urinary_tract(1)	13	all_cancers(71;4.01e-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)			CACGTTCCAGGGCTCTTTCCT	0.468																																					p.P74H		Atlas-SNP	.											.	ZNF695	55	.	0			c.C221A						PASS	.						116.0	119.0	118.0					1																	247162688		2046	4248	6294	SO:0001583	missense	57116	exon3			TTCCAGGGCTCTT		CCDS44344.1, CCDS55694.1	1q44	2013-01-08			ENSG00000197472	ENSG00000197472		"""Zinc fingers, C2H2-type"", ""-"""	30954	protein-coding gene	gene with protein product						12477932	Standard	NM_020394		Approved	SBZF3	uc009xgu.3	Q8IW36	OTTHUMG00000040707	ENST00000339986.7:c.221C>A	1.37:g.247162688G>T	ENSP00000341236:p.Pro74His	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	107	29	0.271028	NM_001204221	Q5T0N9|Q5T0P1|Q5T0P3|Q7Z2W8|Q7Z648	Missense_Mutation	SNP	ENST00000339986.7	37	CCDS44344.1	.	.	.	.	.	.	.	.	.	.	G	11.68	1.710105	0.30322	.	.	ENSG00000197472	ENST00000487338;ENST00000391780;ENST00000339986	T;T	0.09911	5.35;2.93	0.149	0.149	0.14863	Krueppel-associated box (2);	.	.	.	.	T	0.35624	0.0938	M	0.91612	3.225	0.09310	N	1	D;D;D	0.89917	0.992;1.0;1.0	P;D;D	0.91635	0.893;0.999;0.983	T	0.06862	-1.0803	8	0.87932	D	0	.	.	.	.	.	74;62;74	Q8IW36;F2Z2N8;Q8IW36-1	ZN695_HUMAN;.;.	H	74	ENSP00000429736:P74H;ENSP00000341236:P74H	ENSP00000428213:P62H	P	-	2	0	ZNF695	245229311	0.448000	0.25681	0.339000	0.25562	0.341000	0.28922	1.086000	0.30853	0.192000	0.20272	0.195000	0.17529	CCC	.	.	none		0.468	ZNF695-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097823.5	NM_020394	
BIN1	274	hgsc.bcm.edu	37	2	127816632	127816632	+	Silent	SNP	G	G	A	rs2276579	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:127816632G>A	ENST00000316724.5	-	11	1368	c.957C>T	c.(955-957)gcC>gcT	p.A319A	BIN1_ENST00000346226.3_Silent_p.A288A|BIN1_ENST00000466111.1_5'UTR|BIN1_ENST00000393040.3_Silent_p.A288A|BIN1_ENST00000351659.3_Silent_p.A319A|BIN1_ENST00000348750.4_Silent_p.A288A|BIN1_ENST00000352848.3_Silent_p.A303A|BIN1_ENST00000376113.2_Silent_p.A303A|BIN1_ENST00000357970.3_Silent_p.A319A|BIN1_ENST00000393041.3_Silent_p.A288A|BIN1_ENST00000409400.1_Silent_p.A288A|BIN1_ENST00000259238.4_Silent_p.A303A	NM_139343.2	NP_647593.1	O00499	BIN1_HUMAN	bridging integrator 1	319					cell proliferation (GO:0008283)|endocytosis (GO:0006897)|lipid tube assembly (GO:0060988)|muscle cell differentiation (GO:0042692)|positive regulation of apoptotic process (GO:0043065)|positive regulation of astrocyte differentiation (GO:0048711)|positive regulation of endocytosis (GO:0045807)|positive regulation of GTPase activity (GO:0043547)|regulation of cell cycle arrest (GO:0071156)|regulation of neuron differentiation (GO:0045664)|viral process (GO:0016032)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|axon initial segment (GO:0043194)|axon terminus (GO:0043679)|cerebellar mossy fiber (GO:0044300)|cytoplasm (GO:0005737)|I band (GO:0031674)|lipid tube (GO:0060987)|node of Ranvier (GO:0033268)|nucleus (GO:0005634)|synaptic vesicle (GO:0008021)|T-tubule (GO:0030315)|varicosity (GO:0043196)|Z disc (GO:0030018)	identical protein binding (GO:0042802)|tau protein binding (GO:0048156)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(3)|lung(6)|ovary(3)|prostate(3)|skin(3)	24	Colorectal(110;0.0831)			BRCA - Breast invasive adenocarcinoma(221;0.073)		tggccccgccggccggcTCTG	0.672													G|||	474	0.0946486	0.0129	0.1859	5008	,	,		10779	0.0486		0.1889	False		,,,				2504	0.091				p.A319A		Atlas-SNP	.											.	BIN1	85	.	0			c.C957T						PASS	.	G	,,,,,,,,,	159,4203		4,151,2026	15.0	19.0	17.0		909,957,957,957,909,864,864,864,864,864	0.0	0.0	2	dbSNP_100	17	1632,6900		159,1314,2793	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	BIN1	NM_004305.3,NM_139343.2,NM_139344.2,NM_139345.2,NM_139346.2,NM_139347.2,NM_139348.2,NM_139349.2,NM_139350.2,NM_139351.2	,,,,,,,,,	163,1465,4819	AA,AG,GG		19.128,3.6451,13.8902	,,,,,,,,,	303/455,319/594,319/551,319/507,303/498,288/519,288/483,288/476,288/440,288/410	127816632	1791,11103	2181	4266	6447	SO:0001819	synonymous_variant	274	exon11			CCCGCCGGCCGGC	U68485	CCDS2137.1, CCDS2138.1, CCDS2139.1, CCDS2140.1, CCDS2141.1, CCDS2142.1, CCDS2143.1, CCDS42743.1, CCDS42744.1, CCDS46403.1	2q14	2014-09-17			ENSG00000136717	ENSG00000136717			1052	protein-coding gene	gene with protein product	"""amphiphysin II"""	601248		AMPHL		8725406, 8782822, 17676042	Standard	NM_004305		Approved	SH3P9, AMPH2	uc002tns.2	O00499	OTTHUMG00000131465	ENST00000316724.5:c.957C>T	2.37:g.127816632G>A		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	43	25	0.581395	NM_139345	O00297|O00545|O43867|O60552|O60553|O60554|O60555|O75514|O75515|O75516|O75517|O75518|Q659B7|Q92944|Q99688	Silent	SNP	ENST00000316724.5	37	CCDS2138.1																																																																																			G|0.886;A|0.114	0.114	strong		0.672	BIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254298.2	NM_139343	
TSNARE1	203062	hgsc.bcm.edu	37	8	143436034	143436034	+	Missense_Mutation	SNP	A	A	G	rs7814359	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:143436034A>G	ENST00000307180.3	-	2	169	c.52T>C	c.(52-54)Ttc>Ctc	p.F18L	TSNARE1_ENST00000519651.1_Missense_Mutation_p.F18L|TSNARE1_ENST00000520166.1_Missense_Mutation_p.F18L|TSNARE1_ENST00000524325.1_Missense_Mutation_p.F18L	NM_145003.3	NP_659440.2	Q96NA8	TSNA1_HUMAN	t-SNARE domain containing 1	18			F -> L (in dbSNP:rs7814359). {ECO:0000269|PubMed:14702039}.		intracellular protein transport (GO:0006886)|synaptic vesicle exocytosis (GO:0016079)	integral component of membrane (GO:0016021)|SNARE complex (GO:0031201)	SNAP receptor activity (GO:0005484)|SNARE binding (GO:0000149)			breast(1)|endometrium(3)|kidney(4)|large_intestine(1)|lung(6)|ovary(2)|stomach(2)|urinary_tract(1)	20	all_cancers(97;7.39e-11)|all_epithelial(106;8.98e-09)|Lung NSC(106;0.000167)|all_lung(105;0.000332)|Ovarian(258;0.0315)|Acute lymphoblastic leukemia(118;0.155)					GGTCCCCCGAAAGGGCCACGG	0.607													A|||	1782	0.355831	0.6278	0.2896	5008	,	,		14925	0.3472		0.1978	False		,,,				2504	0.2065				p.F18L		Atlas-SNP	.											.	TSNARE1	59	.	0			c.T52C						PASS	.	A	LEU/PHE	2416,1990	606.1+/-390.7	674,1068,461	50.0	45.0	47.0		52	2.3	0.0	8	dbSNP_116	47	1803,6797	321.2+/-315.0	183,1437,2680	yes	missense	TSNARE1	NM_145003.3	22	857,2505,3141	GG,GA,AA		20.9651,45.1657,32.4389	benign	18/514	143436034	4219,8787	2203	4300	6503	SO:0001583	missense	203062	exon2			CCCCGAAAGGGCC			8q24.3	2005-08-18							26437	protein-coding gene	gene with protein product						14702039	Standard	XM_005250828		Approved	FLJ31164	uc003ywk.3	Q96NA8		ENST00000307180.3:c.52T>C	8.37:g.143436034A>G	ENSP00000303437:p.Phe18Leu	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	76	19	0.25	NM_145003	B7ZLB0|Q14D03	Missense_Mutation	SNP	ENST00000307180.3	37	CCDS6384.1	723	0.33104395604395603	275	0.5589430894308943	96	0.26519337016574585	214	0.3741258741258741	138	0.1820580474934037	A	11.01	1.512251	0.27036	0.548343	0.209651	ENSG00000171045	ENST00000524325;ENST00000307180;ENST00000520166;ENST00000519651;ENST00000520462;ENST00000518720	T;T;T;T;T;T	0.37584	1.33;1.3;1.33;1.52;1.26;1.19	3.47	2.26	0.28386	.	0.000000	0.34025	U	0.004330	T	0.00012	0.0000	L	0.29908	0.895	0.80722	P	0.0	B;B;B;B	0.30914	0.3;0.043;0.3;0.3	B;B;B;B	0.26202	0.067;0.016;0.067;0.067	T	0.44757	-0.9307	9	0.48119	T	0.1	-0.2963	7.1576	0.25647	0.7708:0.2292:0.0:0.0	rs7814359;rs61501797;rs7814359	18;18;18;18	B7ZLB0;E5RHT3;Q96NA8;A0AVG3	.;.;TSNA1_HUMAN;.	L	18;18;18;18;18;34	ENSP00000428763:F18L;ENSP00000303437:F18L;ENSP00000427770:F18L;ENSP00000429679:F18L;ENSP00000429626:F18L;ENSP00000430789:F34L	ENSP00000303437:F18L	F	-	1	0	TSNARE1	143433941	0.197000	0.23362	0.001000	0.08648	0.491000	0.33493	2.089000	0.41672	0.461000	0.27071	-0.418000	0.06021	TTC	A|0.674;G|0.326	0.326	strong		0.607	TSNARE1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_145003	
PCDHGA8	9708	hgsc.bcm.edu	37	5	140772427	140772427	+	Missense_Mutation	SNP	T	T	G	rs726684	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:140772427T>G	ENST00000398604.2	+	1	47	c.47T>G	c.(46-48)cTg>cGg	p.L16R	PCDHGA3_ENST00000253812.6_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA6_ENST00000517434.1_Intron	NM_032088.1	NP_114477.1	Q9Y5G5	PCDG8_HUMAN	protocadherin gamma subfamily A, 8	16			L -> R (in dbSNP:rs726684).		homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(6)|kidney(6)|large_intestine(6)|lung(30)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	51			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTGATCCTGCTGTGCGCGCTG	0.557													.|||	822	0.164137	0.1021	0.3329	5008	,	,		17243	0.1319		0.1909	False		,,,				2504	0.1339				p.L16R		Atlas-SNP	.											.	PCDHGA8	146	.	0			c.T47G						PASS	.	T	,ARG/LEU,,,,,,,,,,,ARG/LEU	450,3766		27,396,1685	17.0	21.0	20.0		,47,,,,,,,,,,,47	5.0	1.0	5	dbSNP_86	20	1470,7050		116,1238,2906	yes	intron,missense,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,missense	PCDHGB4,PCDHGA8,PCDHGB3,PCDHGB2,PCDHGB1,PCDHGA7,PCDHGA6,PCDHGA5,PCDHGA4,PCDHGA3,PCDHGA2,PCDHGA1	NM_003736.2,NM_014004.2,NM_018912.2,NM_018915.2,NM_018916.3,NM_018917.2,NM_018918.2,NM_018919.2,NM_018920.2,NM_018922.2,NM_018923.2,NM_018924.2,NM_032088.1	,102,,,,,,,,,,,102	143,1634,4591	GG,GT,TT		17.2535,10.6736,15.0754	,,,,,,,,,,,,	,16/821,,,,,,,,,,,16/933	140772427	1920,10816	2108	4260	6368	SO:0001583	missense	9708	exon1			TCCTGCTGTGCGC	AF152515	CCDS47291.1, CCDS75338.1	5q31	2010-01-26			ENSG00000253767	ENSG00000253767		"""Cadherins / Protocadherins : Clustered"""	8706	other	protocadherin		606295				10380929	Standard	NM_014004		Approved	KIAA0327, PCDH-GAMMA-A8		Q9Y5G5	OTTHUMG00000164053	ENST00000398604.2:c.47T>G	5.37:g.140772427T>G	ENSP00000381605:p.Leu16Arg	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	38	38	1	NM_014004	A7MCZ4|O15039	Missense_Mutation	SNP	ENST00000398604.2	37	CCDS47291.1	375	0.1717032967032967	41	0.08333333333333333	112	0.30939226519337015	73	0.12762237762237763	149	0.19656992084432717	.	15.59	2.878362	0.51801	0.106736	0.172535	ENSG00000253767	ENST00000398604	T	0.53206	0.63	5.04	5.04	0.67666	.	.	.	.	.	T	0.00012	0.0000	M	0.89353	3.025	0.39240	P	0.03616600000000003	D;P	0.71674	0.998;0.908	D;P	0.65233	0.933;0.799	T	0.14062	-1.0486	8	0.72032	D	0.01	.	10.3989	0.44218	0.1465:0.0:0.0:0.8535	rs726684;rs17603060;rs58099825;rs726684	16;16	Q9Y5G5;Q9Y5G5-2	PCDG8_HUMAN;.	R	16	ENSP00000381605:L16R	ENSP00000381605:L16R	L	+	2	0	PCDHGA8	140752611	1.000000	0.71417	1.000000	0.80357	0.718000	0.41266	4.361000	0.59461	1.910000	0.55303	0.533000	0.62120	CTG	T|0.847;G|0.153	0.153	strong		0.557	PCDHGA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376972.1	NM_032088	
IL16	3603	hgsc.bcm.edu	37	15	81578139	81578139	+	Missense_Mutation	SNP	C	C	T	rs4072111	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:81578139C>T	ENST00000302987.4	+	9	1300	c.1300C>T	c.(1300-1302)Ccc>Tcc	p.P434S	IL16_ENST00000394660.2_Missense_Mutation_p.P434S			Q14005	IL16_HUMAN	interleukin 16	434	Interaction with GRIN2A.|PDZ 2. {ECO:0000255|PROSITE- ProRule:PRU00143}.		P -> S (in dbSNP:rs4072111).		immune response (GO:0006955)|induction of positive chemotaxis (GO:0050930)|leukocyte chemotaxis (GO:0030595)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.P434S(1)		NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(12)|lung(20)|ovary(3)|skin(3)|stomach(1)|urinary_tract(1)	57						CGGTCCAGTCCCCATCATTGT	0.507													C|||	824	0.164537	0.0431	0.1888	5008	,	,		19338	0.2083		0.1024	False		,,,				2504	0.3303				p.P434S		Atlas-SNP	.											IL16,NS,carcinoma,0,1	IL16	254	1	1	Substitution - Missense(1)	stomach(1)	c.C1300T						PASS	.	C	SER/PRO,SER/PRO	214,3880		6,202,1839	179.0	179.0	179.0		1300,1300	5.2	1.0	15	dbSNP_108	179	886,7490		45,796,3347	yes	missense,missense	IL16	NM_001172128.1,NM_172217.3	74,74	51,998,5186	TT,TC,CC		10.5778,5.2272,8.8212	possibly-damaging,possibly-damaging	434/1332,434/1333	81578139	1100,11370	2047	4188	6235	SO:0001583	missense	3603	exon10			CCAGTCCCCATCA	U82972	CCDS10317.1, CCDS42069.1, CCDS53966.1	15q26.3	2011-07-14	2011-07-14		ENSG00000172349	ENSG00000172349		"""Interleukins and interleukin receptors"""	5980	protein-coding gene	gene with protein product	"""prointerleukin 16"", ""lymphocyte chemoattractant factor"""	603035	"""interleukin 16 (lymphocyte chemoattractant factor)"""			9144227	Standard	NM_004513		Approved	LCF, IL-16, prIL-16, HsT19289, FLJ42735, FLJ16806	uc021ssh.1	Q14005	OTTHUMG00000144186	ENST00000302987.4:c.1300C>T	15.37:g.81578139C>T	ENSP00000302935:p.Pro434Ser	Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	147	55	0.37415	NM_001172128	A6NM20|A8MU65|B5TY35|B9EGR6|H3BVH5|Q16435|Q6VVE6|Q6ZMQ7|Q9UP18	Missense_Mutation	SNP	ENST00000302987.4	37	CCDS42069.1	279	0.12774725274725274	25	0.0508130081300813	59	0.16298342541436464	109	0.19055944055944055	86	0.11345646437994723	C	12.92	2.082011	0.36758	0.052272	0.105778	ENSG00000172349	ENST00000394655;ENST00000394660;ENST00000355368;ENST00000302987	T;T	0.15718	2.4;2.4	5.23	5.23	0.72850	PDZ/DHR/GLGF (2);	0.000000	0.45126	D	0.000386	T	0.00012	0.0000	N	0.01493	-0.835	0.09310	P	1.0	D;D	0.56287	0.958;0.975	P;P	0.51385	0.468;0.668	T	0.29610	-1.0006	9	0.07325	T	0.83	.	13.8975	0.63783	0.1521:0.8479:0.0:0.0	rs4072111;rs17846279;rs17859301;rs52792386;rs58547005;rs4072111	434;434	Q14005;Q14005-2	IL16_HUMAN;.	S	434;434;266;434	ENSP00000378155:P434S;ENSP00000302935:P434S	ENSP00000302935:P434S	P	+	1	0	IL16	79365194	1.000000	0.71417	0.997000	0.53966	0.713000	0.41058	3.714000	0.54889	2.717000	0.92951	0.655000	0.94253	CCC	C|0.870;T|0.130	0.130	strong		0.507	IL16-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000303952.1	NM_172217	
PTPRD	5789	hgsc.bcm.edu	37	9	8497250	8497250	+	Missense_Mutation	SNP	T	T	C	rs72694737	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:8497250T>C	ENST00000381196.4	-	23	2884	c.2341A>G	c.(2341-2343)Act>Gct	p.T781A	PTPRD_ENST00000537002.1_Intron|PTPRD_ENST00000360074.4_Missense_Mutation_p.T768A|PTPRD_ENST00000358503.5_Intron|PTPRD_ENST00000355233.5_Intron|PTPRD_ENST00000397617.3_Intron|PTPRD_ENST00000486161.1_Intron|PTPRD_ENST00000540109.1_Missense_Mutation_p.T781A|PTPRD_ENST00000471274.1_Intron|PTPRD_ENST00000356435.5_Missense_Mutation_p.T781A|PTPRD_ENST00000397606.3_Intron|PTPRD_ENST00000397611.3_Intron	NM_002839.3	NP_002830.1	P23468	PTPRD_HUMAN	protein tyrosine phosphatase, receptor type, D	781	Fibronectin type-III 5. {ECO:0000255|PROSITE-ProRule:PRU00316}.				heterophilic cell-cell adhesion (GO:0007157)|neuron differentiation (GO:0030182)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphate-containing compound metabolic process (GO:0006796)|positive regulation of dendrite morphogenesis (GO:0050775)|presynaptic membrane assembly (GO:0097105)|protein dephosphorylation (GO:0006470)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	cell adhesion molecule binding (GO:0050839)|receptor binding (GO:0005102)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(7)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|liver(1)|lung(83)|ovary(4)|pancreas(1)|prostate(7)|skin(19)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	168		all_cancers(3;3.38e-95)|all_epithelial(3;2.84e-91)|all_lung(3;7.3e-56)|Lung NSC(3;1.82e-52)|Renal(3;3.42e-19)|all_hematologic(3;0.000134)|all_neural(3;0.00409)|Acute lymphoblastic leukemia(23;0.0069)|Melanoma(3;0.0121)|Myeloproliferative disorder(4;0.0122)|Medulloblastoma(3;0.0144)|Lung SC(3;0.0301)|Ovarian(56;0.0694)|Hepatocellular(3;0.0824)		all cancers(1;3.38e-12)|Epithelial(1;2.12e-09)|STAD - Stomach adenocarcinoma(1;1.29e-07)|KIRC - Kidney renal clear cell carcinoma(3;5.49e-07)|Kidney(3;6.36e-07)|GBM - Glioblastoma multiforme(50;9.05e-05)|Lung(1;0.000189)|BRCA - Breast invasive adenocarcinoma(1;0.00178)|LUSC - Lung squamous cell carcinoma(1;0.0115)|LUAD - Lung adenocarcinoma(58;0.119)		ACATGTTCAGTAGTATCATCA	0.338										TSP Lung(15;0.13)			T|||	85	0.0169728	0.0	0.0303	5008	,	,		19450	0.001		0.0388	False		,,,				2504	0.0245				p.T781A		Atlas-SNP	.											.	PTPRD	1348	.	0			c.A2341G						PASS	.	T	,,ALA/THR,,,	24,4382	30.8+/-60.4	0,24,2179	80.0	72.0	75.0		,,2341,,,	4.8	1.0	9	dbSNP_130	75	256,8344	98.8+/-160.4	6,244,4050	yes	intron,intron,missense,intron,intron,intron	PTPRD	NM_001040712.2,NM_001171025.1,NM_002839.3,NM_130391.3,NM_130392.3,NM_130393.3	,,58,,,	6,268,6229	CC,CT,TT		2.9767,0.5447,2.1529	,,benign,,,	,,781/1913,,,	8497250	280,12726	2203	4300	6503	SO:0001583	missense	5789	exon26			GTTCAGTAGTATC	X54133	CCDS6472.1, CCDS43786.1, CCDS6472.2, CCDS55288.1, CCDS55289.1, CCDS55290.1, CCDS75813.1	9p24.1-p23	2013-02-11			ENSG00000153707	ENSG00000153707		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	9668	protein-coding gene	gene with protein product		601598				7896816, 8355697	Standard	NM_002839		Approved	PTPD, HPTP	uc003zkk.3	P23468	OTTHUMG00000021005	ENST00000381196.4:c.2341A>G	9.37:g.8497250T>C	ENSP00000370593:p.Thr781Ala	Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	149	65	0.436242	NM_002839	B1ALA0|F5GWT7|Q3KPJ0|Q3KPJ1|Q3KPJ2	Missense_Mutation	SNP	ENST00000381196.4	37	CCDS43786.1	43	0.019688644688644688	0	0.0	9	0.024861878453038673	1	0.0017482517482517483	33	0.04353562005277045	T	6.679	0.493900	0.12702	0.005447	0.029767	ENSG00000153707	ENST00000381196;ENST00000356435;ENST00000360074;ENST00000540109	T;T;T;T	0.59224	0.28;0.28;0.28;0.28	5.95	4.83	0.62350	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.117593	0.64402	D	0.000020	T	0.12347	0.0300	N	0.25094	0.71	0.50039	D	0.999845	B;B	0.13145	0.007;0.002	B;B	0.14023	0.01;0.01	T	0.06972	-1.0797	9	.	.	.	.	9.6102	0.39659	0.0:0.1292:0.0:0.8708	.	768;781	G3XAE2;P23468	.;PTPRD_HUMAN	A	781;781;768;781	ENSP00000370593:T781A;ENSP00000348812:T781A;ENSP00000353187:T768A;ENSP00000438164:T781A	.	T	-	1	0	PTPRD	8487250	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.616000	0.36933	2.281000	0.76405	0.528000	0.53228	ACT	T|0.979;C|0.021	0.021	strong		0.338	PTPRD-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055395.3		
RGS3	5998	hgsc.bcm.edu	37	9	116346236	116346236	+	Silent	SNP	G	G	A	rs41301525	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:116346236G>A	ENST00000374140.2	+	21	2753	c.2544G>A	c.(2542-2544)gcG>gcA	p.A848A	RGS3_ENST00000350696.5_Silent_p.A848A|RGS3_ENST00000394646.3_Intron|RGS3_ENST00000462143.1_Silent_p.A169A|RP11-168K11.2_ENST00000428429.1_RNA|RGS3_ENST00000342620.5_Intron|RGS3_ENST00000343817.5_Silent_p.A567A|RGS3_ENST00000374134.3_Silent_p.A169A	NM_001282923.1|NM_144488.4	NP_001269852.1|NP_652759.3	P49796	RGS3_HUMAN	regulator of G-protein signaling 3	848					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						ACCCACCTGCGGCCCCCAGGC	0.642													G|||	421	0.0840655	0.18	0.0663	5008	,	,		17005	0.0		0.0974	False		,,,				2504	0.0399				p.A848A		Atlas-SNP	.											.	RGS3	251	.	0			c.G2544A						PASS	.	G	,,,	797,3609	319.1+/-295.9	83,631,1489	48.0	54.0	52.0		507,1701,,2544	0.2	0.1	9	dbSNP_127	52	862,7738	194.8+/-240.1	39,784,3477	no	coding-synonymous,coding-synonymous,intron,coding-synonymous	RGS3	NM_021106.3,NM_130795.2,NM_134427.1,NM_144488.4	,,,	122,1415,4966	AA,AG,GG		10.0233,18.089,12.7557	,,,	169/520,567/918,,848/1199	116346236	1659,11347	2203	4300	6503	SO:0001819	synonymous_variant	5998	exon21			ACCTGCGGCCCCC	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.2544G>A	9.37:g.116346236G>A		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	56	25	0.446429	NM_144488	A6NHA0|A8K0V1|B3KUB2|Q5VXB8|Q5VXC1|Q5VZ05|Q5VZ06|Q6ZRM5|Q8IUQ1|Q8NC47|Q8NFN4|Q8NFN5|Q8NFN6|Q8TD59|Q8TD68|Q8WV02|Q8WXA0	Silent	SNP	ENST00000374140.2	37	CCDS43869.1																																																																																			G|0.886;A|0.114	0.114	strong		0.642	RGS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055561.3	NM_017790	
IGF2BP3	10643	hgsc.bcm.edu	37	7	23357321	23357321	+	Silent	SNP	C	C	T	rs156414	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:23357321C>T	ENST00000258729.3	-	12	1688	c.1332G>A	c.(1330-1332)gcG>gcA	p.A444A		NM_006547.2	NP_006538.2	O00425	IF2B3_HUMAN	insulin-like growth factor 2 mRNA binding protein 3	444	KH 3. {ECO:0000255|PROSITE- ProRule:PRU00117}.				anatomical structure morphogenesis (GO:0009653)|gene expression (GO:0010467)|mRNA transport (GO:0051028)|negative regulation of translation (GO:0017148)|regulation of cytokine biosynthetic process (GO:0042035)|translation (GO:0006412)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	mRNA 3'-UTR binding (GO:0003730)|mRNA 5'-UTR binding (GO:0048027)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|translation regulator activity (GO:0045182)	p.A444A(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(14)|ovary(2)|prostate(2)|skin(4)|stomach(1)	34						CTGGTGCTTCCGCTGGAGCAA	0.463													C|||	1225	0.244609	0.0136	0.2435	5008	,	,		20362	0.3671		0.3946	False		,,,				2504	0.2771				p.A444A		Atlas-SNP	.											IGF2BP3,NS,carcinoma,0,1	IGF2BP3	71	1	1	Substitution - coding silent(1)	stomach(1)	c.G1332A						PASS	.	C		364,4042		37,290,1876	203.0	158.0	173.0		1332	-4.7	1.0	7	dbSNP_79	173	3525,5075		727,2071,1502	no	coding-synonymous	IGF2BP3	NM_006547.2		764,2361,3378	TT,TC,CC		40.9884,8.2615,29.9016		444/580	23357321	3889,9117	2203	4300	6503	SO:0001819	synonymous_variant	10643	exon12			TGCTTCCGCTGGA	AF117108	CCDS5382.1	7p15.3	2014-02-19			ENSG00000136231	ENSG00000136231		"""RNA binding motif (RRM) containing"""	28868	protein-coding gene	gene with protein product	"""IGF II mRNA binding protein 3"", ""cancer/testis antigen 98"""	608259				9891060, 9178771	Standard	NM_006547		Approved	IMP-3, CT98, IMP3	uc003swg.3	O00425	OTTHUMG00000128445	ENST00000258729.3:c.1332G>A	7.37:g.23357321C>T		Somatic	182	0	0		WXS	Illumina HiSeq	Phase_I	163	34	0.208589	NM_006547	A0A4Z5|Q63HM0|Q6MZZ2|Q86VB1	Silent	SNP	ENST00000258729.3	37	CCDS5382.1																																																																																			T|0.301;G|0.001;C|0.698;N|0.000	0.301	strong		0.463	IGF2BP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250243.2	NM_006547	
MTMR7	9108	hgsc.bcm.edu	37	8	17157677	17157677	+	Missense_Mutation	SNP	T	T	G	rs3764796	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:17157677T>G	ENST00000180173.5	-	14	1711	c.1677A>C	c.(1675-1677)caA>caC	p.Q559H	MTMR7_ENST00000398099.3_Missense_Mutation_p.Q150H	NM_004686.4	NP_004677.3	Q9Y216	MTMR7_HUMAN	myotubularin related protein 7	559			Q -> H (in dbSNP:rs3764796). {ECO:0000269|PubMed:14702039}.		inositol phosphate dephosphorylation (GO:0046855)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|protein dephosphorylation (GO:0006470)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|membrane (GO:0016020)	protein tyrosine phosphatase activity (GO:0004725)			breast(1)|endometrium(5)|kidney(2)|large_intestine(5)|liver(1)|lung(8)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)	32				Colorectal(111;0.112)		TGGGCTCACTTTGCTTACTCT	0.403													T|||	529	0.105631	0.0091	0.0951	5008	,	,		18052	0.1062		0.1203	False		,,,				2504	0.228				p.Q559H		Atlas-SNP	.											.	MTMR7	75	.	0			c.A1677C						PASS	.	T	HIS/GLN	102,4304	80.4+/-118.8	1,100,2102	157.0	163.0	161.0		1677	-4.0	0.2	8	dbSNP_107	161	978,7622	210.7+/-251.5	68,842,3390	yes	missense	MTMR7	NM_004686.4	24	69,942,5492	GG,GT,TT		11.3721,2.315,8.3039	possibly-damaging	559/661	17157677	1080,11926	2203	4300	6503	SO:0001583	missense	9108	exon14			CTCACTTTGCTTA	AF073482	CCDS34851.1	8p22	2011-06-09			ENSG00000003987	ENSG00000003987		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"""	7454	protein-coding gene	gene with protein product		603562				9736772, 12890864	Standard	NM_004686		Approved		uc003wxm.3	Q9Y216	OTTHUMG00000163771	ENST00000180173.5:c.1677A>C	8.37:g.17157677T>G	ENSP00000180173:p.Gln559His	Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	130	27	0.207692	NM_004686	A1L4K9|B4DG87|Q68DX4	Missense_Mutation	SNP	ENST00000180173.5	37	CCDS34851.1	214	0.09798534798534798	8	0.016260162601626018	38	0.10497237569060773	75	0.13111888111888112	93	0.12269129287598944	T	11.96	1.795621	0.31777	0.02315	0.113721	ENSG00000003987	ENST00000180173;ENST00000398099	T;T	0.77229	0.63;-1.08	4.76	-3.96	0.04106	.	1.050740	0.07301	N	0.874089	T	0.01061	0.0035	N	0.22421	0.69	0.80722	P	0.0	B	0.32365	0.367	B	0.31751	0.135	T	0.09552	-1.0669	9	0.42905	T	0.14	.	8.4294	0.32748	0.0:0.4513:0.191:0.3577	rs3764796;rs17625520;rs56575510;rs57964925;rs3764796	559	Q9Y216	MTMR7_HUMAN	H	559;150	ENSP00000180173:Q559H;ENSP00000381171:Q150H	ENSP00000180173:Q559H	Q	-	3	2	MTMR7	17202048	0.000000	0.05858	0.210000	0.23637	0.994000	0.84299	-1.732000	0.01851	-0.409000	0.07553	0.482000	0.46254	CAA	T|0.909;G|0.091	0.091	strong		0.403	MTMR7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375311.1	NM_004686	
AAK1	22848	hgsc.bcm.edu	37	2	69709919	69709919	+	Silent	SNP	A	A	G	rs6721259	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	81	0	0		WXS	Illumina HiSeq	Phase_I	68	28	0.411765	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	
PSMB6	5694	hgsc.bcm.edu	37	17	4701402	4701402	+	Silent	SNP	C	C	T	rs7468	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:4701402C>T	ENST00000270586.3	+	5	582	c.531C>T	c.(529-531)taC>taT	p.Y177Y		NM_001270481.1|NM_002798.2	NP_001257410.1|NP_002789.1	P28072	PSB6_HUMAN	proteasome (prosome, macropain) subunit, beta type, 6	177					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						ATGCTACCTACCGGGAAGGCA	0.532													C|||	308	0.0615016	0.0673	0.0202	5008	,	,		19159	0.0942		0.0437	False		,,,				2504	0.0675				p.Y177Y		Atlas-SNP	.											.	PSMB6	20	.	0			c.C531T						PASS	.	C		208,4198	128.2+/-165.1	5,198,2000	110.0	97.0	101.0		531	1.9	1.0	17	dbSNP_52	101	300,8300	110.2+/-170.6	6,288,4006	no	coding-synonymous	PSMB6	NM_002798.1		11,486,6006	TT,TC,CC		3.4884,4.7208,3.9059		177/240	4701402	508,12498	2203	4300	6503	SO:0001819	synonymous_variant	5694	exon5			TACCTACCGGGAA	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.531C>T	17.37:g.4701402C>T		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	125	125	1	NM_002798	Q96J55	Silent	SNP	ENST00000270586.3	37	CCDS11056.1																																																																																			C|0.958;T|0.042	0.042	strong		0.532	PSMB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207559.2	NM_002798	
MEFV	4210	hgsc.bcm.edu	37	16	3297181	3297181	+	Silent	SNP	C	C	T	rs224208	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:3297181C>T	ENST00000219596.1	-	5	1461	c.1422G>A	c.(1420-1422)gaG>gaA	p.E474E	MEFV_ENST00000339854.4_Silent_p.E294E|MEFV_ENST00000541159.1_Silent_p.E263E|MEFV_ENST00000536379.1_Silent_p.E263E	NM_000243.2	NP_000234.1	O15553	MEFV_HUMAN	Mediterranean fever	474	Required for homotrimerization and induction of pyroptosomes.		E -> K (in arFMF). {ECO:0000269|PubMed:16378925}.		inflammatory response (GO:0006954)|innate immune response (GO:0045087)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-1 beta production (GO:0032691)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of macrophage inflammatory protein 1 alpha production (GO:0071641)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of cysteine-type endopeptidase activity (GO:2001056)	cell projection (GO:0042995)|cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|nucleus (GO:0005634)	actin binding (GO:0003779)|zinc ion binding (GO:0008270)			NS(2)|biliary_tract(1)|breast(5)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(6)|lung(19)|ovary(3)|prostate(1)|skin(6)	50						GCTCTTGCTGCTCCAGGAAGT	0.582													C|||	3200	0.638978	0.6407	0.6239	5008	,	,		20588	0.6062		0.5577	False		,,,				2504	0.7648				p.E474E		Atlas-SNP	.											.	MEFV	170	.	0			c.G1422A						PASS	.	C	,	2782,1612	660.9+/-400.8	869,1044,284	157.0	144.0	148.0		1422,789	2.3	0.8	16	dbSNP_79	148	4580,4020	597.8+/-393.8	1248,2084,968	no	coding-synonymous,coding-synonymous	MEFV	NM_000243.2,NM_001198536.1	,	2117,3128,1252	TT,TC,CC		46.7442,36.6864,43.3431	,	474/782,263/446	3297181	7362,5632	2197	4300	6497	SO:0001819	synonymous_variant	4210	exon5			TTGCTGCTCCAGG	AF018080	CCDS10498.1, CCDS55981.1	16p13.3	2014-09-17			ENSG00000103313	ENSG00000103313		"""Tripartite motif containing / Tripartite motif containing"""	6998	protein-coding gene	gene with protein product	"""pyrin"""	608107		MEF		9288094	Standard	NM_000243		Approved	FMF, TRIM20	uc002cun.1	O15553	OTTHUMG00000129324	ENST00000219596.1:c.1422G>A	16.37:g.3297181C>T		Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	182	24	0.131868	NM_000243	D3DUC0|F5H0Q3|Q3MJ84|Q96PN4|Q96PN5	Silent	SNP	ENST00000219596.1	37	CCDS10498.1																																																																																			C|0.414;T|0.586	0.586	strong		0.582	MEFV-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251464.1	NM_000243	
TRPV4	59341	hgsc.bcm.edu	37	12	110238487	110238487	+	Silent	SNP	A	A	G	rs3742034	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:110238487A>G	ENST00000418703.2	-	4	883	c.789T>C	c.(787-789)gaT>gaC	p.D263D	TRPV4_ENST00000536838.1_Silent_p.D229D|TRPV4_ENST00000544971.1_Intron|TRPV4_ENST00000392719.2_Intron|TRPV4_ENST00000541794.1_Intron|TRPV4_ENST00000537083.1_Silent_p.D263D|TRPV4_ENST00000261740.2_Silent_p.D263D|TRPV4_ENST00000346520.2_Silent_p.D263D	NM_001177431.1	NP_001170902.1	Q9HBA0	TRPV4_HUMAN	transient receptor potential cation channel, subfamily V, member 4	263					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						GGGCGTGGACATCAGCTCCCT	0.632													G|||	783	0.15635	0.2693	0.0965	5008	,	,		16826	0.0506		0.0934	False		,,,				2504	0.2198				p.D263D		Atlas-SNP	.											.	TRPV4	88	.	0			c.T789C						PASS	.	G	,,,,	955,3451	735.8+/-410.7	100,755,1348	80.0	64.0	69.0		,687,,789,789	-6.1	0.3	12	dbSNP_107	69	731,7869	786.1+/-407.6	27,677,3596	no	intron,coding-synonymous,intron,coding-synonymous,coding-synonymous	TRPV4	NM_001177428.1,NM_001177431.1,NM_001177433.1,NM_021625.4,NM_147204.2	,,,,	127,1432,4944	GG,GA,AA		8.5,21.675,12.9632	,,,,	,229/838,,263/872,263/812	110238487	1686,11320	2203	4300	6503	SO:0001819	synonymous_variant	59341	exon4			GTGGACATCAGCT	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.789T>C	12.37:g.110238487A>G		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	99	47	0.474747	NM_147204	B7ZKQ6|Q17R79|Q2Y122|Q2Y123|Q2Y124|Q86YZ6|Q8NDY7|Q8NG64|Q96Q92|Q96RS7|Q9HBC0	Silent	SNP	ENST00000418703.2	37	CCDS9134.1																																																																																			A|0.872;G|0.128	0.128	strong		0.632	TRPV4-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403270.1	NM_021625	
C10orf71	118461	hgsc.bcm.edu	37	10	50531549	50531549	+	Missense_Mutation	SNP	G	G	T	rs56206226	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:50531549G>T	ENST00000374144.3	+	3	1247	c.959G>T	c.(958-960)cGc>cTc	p.R320L	C10orf71_ENST00000323868.4_Missense_Mutation_p.R320L			Q711Q0	CJ071_HUMAN	chromosome 10 open reading frame 71	320			R -> L (in dbSNP:rs56206226). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005}.							endometrium(1)	1						CCTCCTGAGCGCACAGTCTCT	0.582													G|||	881	0.175919	0.1021	0.2594	5008	,	,		17968	0.3085		0.1481	False		,,,				2504	0.1084				p.R320L		Atlas-SNP	.											.	C10orf71	179	.	0			c.G959T						PASS	.	G	LEU/ARG,LEU/ARG	520,3564		27,466,1549	59.0	66.0	64.0		959,959	-7.9	0.0	10	dbSNP_129	64	1352,7046		105,1142,2952	yes	missense,missense	C10orf71	NM_001135196.1,NM_199459.3	102,102	132,1608,4501	TT,TG,GG		16.0991,12.7326,14.9976	benign,benign	320/1436,320/720	50531549	1872,10610	2042	4199	6241	SO:0001583	missense	118461	exon3			CTGAGCGCACAGT	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.959G>T	10.37:g.50531549G>T	ENSP00000363259:p.Arg320Leu	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	60	23	0.383333	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	G	0.827	-0.746668	0.03065	0.127326	0.160991	ENSG00000177354	ENST00000323868;ENST00000374144	T;T	0.14766	2.48;3.61	5.4	-7.89	0.01174	.	1.867440	0.02500	N	0.090417	T	0.00012	0.0000	L	0.40543	1.245	0.80722	P	0.0	B	0.06786	0.001	B	0.09377	0.004	T	0.44081	-0.9351	9	0.09338	T	0.73	.	5.0552	0.14529	0.5758:0.143:0.1844:0.0968	rs56206226	320	Q711Q0-3	.	L	320	ENSP00000318713:R320L;ENSP00000363259:R320L	ENSP00000318713:R320L	R	+	2	0	C10orf71	50201555	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-0.855000	0.04295	-1.479000	0.01867	-0.291000	0.09656	CGC	G|0.803;T|0.197	0.197	strong		0.582	C10orf71-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047984.2	NM_199459	
CPO	130749	hgsc.bcm.edu	37	2	207833983	207833983	+	Silent	SNP	A	A	G	rs7582305	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	171	0	0		WXS	Illumina HiSeq	Phase_I	128	69	0.539062	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	
NCEH1	57552	hgsc.bcm.edu	37	3	172365832	172365832	+	Missense_Mutation	SNP	T	T	G	rs2302815	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:172365832T>G	ENST00000475381.1	-	2	444	c.211A>C	c.(211-213)Aaa>Caa	p.K71Q	NCEH1_ENST00000538775.1_Missense_Mutation_p.K103Q|NCEH1_ENST00000273512.3_Missense_Mutation_p.K103Q|NCEH1_ENST00000543711.1_Intron			Q6PIU2	NCEH1_HUMAN	neutral cholesterol ester hydrolase 1	71			K -> Q (in dbSNP:rs2302815).		lipid catabolic process (GO:0016042)|protein dephosphorylation (GO:0006470)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	carboxylic ester hydrolase activity (GO:0052689)|phosphate ion binding (GO:0042301)|serine hydrolase activity (GO:0017171)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(4)|prostate(1)|skin(1)	15						GCGCTTTTTTTGCCAAAAGAA	0.512													T|||	681	0.135982	0.2345	0.1167	5008	,	,		19776	0.0833		0.1054	False		,,,				2504	0.1022				p.K103Q		Atlas-SNP	.											NCEH1,NS,adenoma,0,1	NCEH1	63	1	0			c.A307C						PASS	.	T	,,GLN/LYS,GLN/LYS	926,3480	351.6+/-311.3	110,706,1387	76.0	76.0	76.0		,,307,307	4.8	1.0	3	dbSNP_100	76	806,7794	186.2+/-233.7	48,710,3542	yes	utr-5,intron,missense,missense	NCEH1	NM_001146277.1,NM_001146278.1,NM_020792.4,NM_001146276.1	,,53,53	158,1416,4929	GG,GT,TT		9.3721,21.0168,13.3169	,,benign,benign	,,103/441,103/449	172365832	1732,11274	2203	4300	6503	SO:0001583	missense	57552	exon2			TTTTTTTGCCAAA	AB037784	CCDS54681.1, CCDS54682.1	3q26.31	2009-07-23	2009-07-23	2009-07-23	ENSG00000144959	ENSG00000144959			29260	protein-coding gene	gene with protein product		613234	"""arylacetamide deacetylase-like 1"""	AADACL1		10718198	Standard	NM_001146276		Approved	KIAA1363, NCEH	uc011bpx.2	Q6PIU2	OTTHUMG00000156872	ENST00000475381.1:c.211A>C	3.37:g.172365832T>G	ENSP00000418571:p.Lys71Gln	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	117	65	0.555556	NM_020792	B7Z2K4|B7Z3A1|B7Z5U2|B7Z906|B7ZAW6|F5H7K4|Q86WZ1|Q9P2I4	Missense_Mutation	SNP	ENST00000475381.1	37		275	0.1259157509157509	97	0.19715447154471544	37	0.10220994475138122	60	0.1048951048951049	81	0.10686015831134564	T	10.66	1.413799	0.25465	0.210168	0.093721	ENSG00000144959	ENST00000475381;ENST00000538775;ENST00000273512	T;T;T	0.04454	3.64;3.62;3.62	5.96	4.78	0.61160	.	0.672964	0.16446	N	0.214069	T	0.00012	0.0000	L	0.51422	1.61	0.09310	P	0.999999999938841	B;B	0.26081	0.141;0.017	B;B	0.20577	0.03;0.005	T	0.44862	-0.9300	9	0.25106	T	0.35	-14.7722	12.521	0.56058	0.0:0.0:0.397:0.603	rs2302815;rs59554414;rs2302815	103;71	F5H7K4;Q6PIU2	.;NCEH1_HUMAN	Q	71;103;103	ENSP00000418571:K71Q;ENSP00000442464:K103Q;ENSP00000273512:K103Q	ENSP00000273512:K103Q	K	-	1	0	NCEH1	173848526	1.000000	0.71417	1.000000	0.80357	0.830000	0.47004	2.082000	0.41605	1.039000	0.40074	0.533000	0.62120	AAA	T|0.868;G|0.132	0.132	strong		0.512	NCEH1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000346367.3	NM_020792	
OR8D4	338662	hgsc.bcm.edu	37	11	123777502	123777502	+	Missense_Mutation	SNP	C	C	T	rs61907183	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:123777502C>T	ENST00000321355.2	+	1	394	c.364C>T	c.(364-366)Cgc>Tgc	p.R122C		NM_001005197.1	NP_001005197.1	Q8NGM9	OR8D4_HUMAN	olfactory receptor, family 8, subfamily D, member 4	122						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			large_intestine(1)|lung(16)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	25		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.93e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0409)		GGCCTGCGATCGCTACGTGGC	0.493													C|||	239	0.0477236	0.0469	0.0447	5008	,	,		19419	0.0089		0.1054	False		,,,				2504	0.0317				p.R122C		Atlas-SNP	.											OR8D4,colon,carcinoma,-1,1	OR8D4	62	1	0			c.C364T						PASS	.	C	CYS/ARG	233,4171	138.8+/-174.5	2,229,1971	198.0	183.0	188.0		364	3.8	1.0	11	dbSNP_129	188	734,7864	177.6+/-227.2	36,662,3601	yes	missense	OR8D4	NM_001005197.1	180	38,891,5572	TT,TC,CC		8.5369,5.2906,7.4373	benign	122/315	123777502	967,12035	2202	4299	6501	SO:0001583	missense	338662	exon1			TGCGATCGCTACG	AB065761	CCDS31698.1	11q24.1	2012-08-09			ENSG00000181518	ENSG00000181518		"""GPCR / Class A : Olfactory receptors"""	14840	protein-coding gene	gene with protein product							Standard	NM_001005197		Approved		uc010saa.2	Q8NGM9	OTTHUMG00000165960	ENST00000321355.2:c.364C>T	11.37:g.123777502C>T	ENSP00000325381:p.Arg122Cys	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	73	54	0.739726	NM_001005197	Q6IFE9	Missense_Mutation	SNP	ENST00000321355.2	37	CCDS31698.1	143	0.06547619047619048	39	0.07926829268292683	18	0.049723756906077346	5	0.008741258741258742	81	0.10686015831134564	C	10.68	1.417210	0.25552	0.052906	0.085369	ENSG00000181518	ENST00000321355	T	0.77358	-1.09	5.81	3.81	0.43845	GPCR, rhodopsin-like superfamily (1);	0.136864	0.33732	N	0.004601	T	0.04861	0.0131	M	0.76838	2.35	0.26159	P	0.9800263	B	0.29835	0.258	B	0.20955	0.032	T	0.60219	-0.7306	9	0.66056	D	0.02	.	9.6012	0.39605	0.2689:0.5958:0.1353:0.0	rs61907183	122	Q8NGM9	OR8D4_HUMAN	C	122	ENSP00000325381:R122C	ENSP00000325381:R122C	R	+	1	0	OR8D4	123282712	0.843000	0.29541	1.000000	0.80357	0.039000	0.13416	1.561000	0.36342	1.423000	0.47198	0.655000	0.94253	CGC	C|0.930;T|0.070	0.070	strong		0.493	OR8D4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387262.1	NM_001005197	
HS3ST6	64711	hgsc.bcm.edu	37	16	1962046	1962046	+	Missense_Mutation	SNP	C	C	T	rs386787777|rs1742399	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:1962046C>T	ENST00000293937.3	-	2	573	c.574G>A	c.(574-576)Gcc>Acc	p.A192T	HS3ST6_ENST00000443547.1_Missense_Mutation_p.A161T|HS3ST6_ENST00000454677.2_Missense_Mutation_p.A209T			Q96QI5	HS3S6_HUMAN	heparan sulfate (glucosamine) 3-O-sulfotransferase 6	192				A -> T (in Ref. 1). {ECO:0000305}.	carbohydrate metabolic process (GO:0005975)|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 1 activity (GO:0008467)			endometrium(2)|lung(2)	4						AGCGTCTGGGCGTAGTCGGAG	0.726													c|||	2004	0.40016	0.2345	0.3386	5008	,	,		13827	0.4931		0.3837	False		,,,				2504	0.589				p.A161T		Atlas-SNP	.											.	HS3ST6	26	.	0			c.G481A						PASS	.	T	THR/ALA	964,3418		115,734,1342	17.0	21.0	20.0		481	3.7	0.5	16	dbSNP_89	20	2937,5655		544,1849,1903	no	missense	HS3ST6	NM_001009606.2	58	659,2583,3245	TT,TC,CC		34.183,21.9991,30.0678	benign	161/312	1962046	3901,9073	2191	4296	6487	SO:0001583	missense	64711	exon2			TCTGGGCGTAGTC			16p13.3	2008-10-30	2003-06-11	2003-06-13	ENSG00000162040	ENSG00000162040		"""Sulfotransferases, membrane-bound"""	14178	protein-coding gene	gene with protein product			"""heparan sulfate (glucosamine) 3-O-sulfotransferase 5"""	HS3ST5		11157797	Standard	NM_001009606		Approved		uc002cnf.3	Q96QI5	OTTHUMG00000047860	ENST00000293937.3:c.574G>A	16.37:g.1962046C>T	ENSP00000293937:p.Ala192Thr	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	48	36	0.75	NM_001009606	Q96RX7	Missense_Mutation	SNP	ENST00000293937.3	37		783	0.3585164835164835	100	0.2032520325203252	109	0.3011049723756906	287	0.5017482517482518	287	0.3786279683377309	c	6.931	0.541419	0.13250	0.219991	0.34183	ENSG00000162040	ENST00000293937;ENST00000443547;ENST00000454677	D;D	0.81579	-1.51;-1.51	4.83	3.65	0.41850	Sulfotransferase domain (1);	0.103832	0.64402	D	0.000003	T	0.00012	0.0000	N	0.00382	-1.575	0.33610	P	0.39651000000000003	B	0.23442	0.085	B	0.17098	0.017	T	0.41928	-0.9481	9	0.02654	T	1	.	6.299	0.21101	0.0:0.7313:0.0:0.2687	rs1742399;rs1742399	192	Q96QI5	HS3S6_HUMAN	T	192;161;231	ENSP00000293937:A192T;ENSP00000390354:A161T	ENSP00000293937:A192T	A	-	1	0	HS3ST6	1902047	1.000000	0.71417	0.456000	0.27044	0.919000	0.55068	3.317000	0.51968	2.248000	0.74166	0.500000	0.49745	GCC	C|0.646;T|0.354	0.354	strong		0.726	HS3ST6-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001009606	
KDM2B	84678	hgsc.bcm.edu	37	12	121881848	121881848	+	Silent	SNP	G	G	A	rs10849885	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:121881848G>A	ENST00000377071.4	-	16	2490	c.2418C>T	c.(2416-2418)taC>taT	p.Y806Y	KDM2B_ENST00000542973.1_Silent_p.Y174Y|KDM2B_ENST00000377069.4_Silent_p.Y775Y|KDM2B_ENST00000536437.1_Intron	NM_032590.4	NP_115979.3	Q8NHM5	KDM2B_HUMAN	lysine (K)-specific demethylase 2B	806					embryonic camera-type eye morphogenesis (GO:0048596)|forebrain development (GO:0030900)|fourth ventricle development (GO:0021592)|hindbrain development (GO:0030902)|histone demethylation (GO:0016577)|histone H2A monoubiquitination (GO:0035518)|initiation of neural tube closure (GO:0021993)|lateral ventricle development (GO:0021670)|midbrain development (GO:0030901)|midbrain-hindbrain boundary morphogenesis (GO:0021555)|negative regulation of neural precursor cell proliferation (GO:2000178)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|spermatogenesis (GO:0007283)|third ventricle development (GO:0021678)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone demethylase activity (GO:0032452)|histone demethylase activity (H3-K36 specific) (GO:0051864)|rRNA binding (GO:0019843)|zinc ion binding (GO:0008270)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	19						GGGGCTTCTCGTATTTCCGCT	0.657											OREG0022201	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	1617	0.322883	0.1543	0.3919	5008	,	,		14673	0.4435		0.3956	False		,,,				2504	0.3027				p.Y806Y		Atlas-SNP	.											KDM2B_ENST00000377071,NS,carcinoma,0,2	KDM2B	218	2	0			c.C2418T						PASS	.	G	,	724,3338		72,580,1379	68.0	75.0	73.0		2325,2418	-9.6	0.3	12	dbSNP_120	73	3095,5229		576,1943,1643	no	coding-synonymous,coding-synonymous	KDM2B	NM_001005366.1,NM_032590.4	,	648,2523,3022	AA,AG,GG		37.1816,17.8237,30.8332	,	775/1266,806/1337	121881848	3819,8567	2031	4162	6193	SO:0001819	synonymous_variant	84678	exon16			CTTCTCGTATTTC	AJ459424	CCDS41849.1, CCDS41850.1	12q24.31	2014-02-18	2009-04-06	2009-04-06	ENSG00000089094	ENSG00000089094		"""F-boxes / Leucine-rich repeats"", ""Chromatin-modifying enzymes / K-demethylases"""	13610	protein-coding gene	gene with protein product	"""jumonji C domain-containing histone demethylase 1B"""	609078	"""F-box and leucine-rich repeat protein 10"""	FBXL10		10799292	Standard	NM_032590		Approved	PCCX2, CXXC2, Fbl10, JHDM1B	uc001uat.3	Q8NHM5	OTTHUMG00000169071	ENST00000377071.4:c.2418C>T	12.37:g.121881848G>A		Somatic	74	0	0	1514	WXS	Illumina HiSeq	Phase_I	90	49	0.544444	NM_032590	A8MRS1|Q8NCI2|Q96HC7|Q96SL0|Q96T03|Q9NS96|Q9UF75	Silent	SNP	ENST00000377071.4	37	CCDS41850.1																																																																																			G|0.666;A|0.334	0.334	strong		0.657	KDM2B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000402132.2	NM_032590	
LMF1	64788	hgsc.bcm.edu	37	16	961051	961051	+	Silent	SNP	C	C	T	rs2277893	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:961051C>T	ENST00000262301.11	-	4	561	c.543G>A	c.(541-543)ggG>ggA	p.G181G	LMF1_ENST00000568897.1_5'UTR|LMF1_ENST00000539379.1_3'UTR|LMF1_ENST00000399843.2_Silent_p.G181G|LMF1_ENST00000543238.1_Intron	NM_022773.2	NP_073610.2	Q96S06	LMF1_HUMAN	lipase maturation factor 1	181					chylomicron remnant clearance (GO:0034382)|ER to Golgi vesicle-mediated transport (GO:0006888)|positive regulation of lipoprotein lipase activity (GO:0051006)|protein glycosylation in Golgi (GO:0033578)|protein maturation (GO:0051604)|protein secretion (GO:0009306)|regulation of cholesterol metabolic process (GO:0090181)|regulation of triglyceride metabolic process (GO:0090207)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)		p.G181G(1)		central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|prostate(1)|stomach(2)|urinary_tract(1)	18		Hepatocellular(780;0.00308)				TCCCCAGGAACCCCGTCTCCA	0.532													C|||	1913	0.381989	0.5613	0.3631	5008	,	,		16735	0.3056		0.1769	False		,,,				2504	0.4427				p.G181G		Atlas-SNP	.											LMF1,NS,carcinoma,0,1	LMF1	42	1	1	Substitution - coding silent(1)	stomach(1)	c.G543A						PASS	.	C		1896,2084		473,950,567	46.0	52.0	50.0		543	-9.1	0.5	16	dbSNP_100	50	1512,6772		140,1232,2770	no	coding-synonymous	LMF1	NM_022773.2		613,2182,3337	TT,TC,CC		18.2521,47.6382,27.7886		181/568	961051	3408,8856	1990	4142	6132	SO:0001819	synonymous_variant	64788	exon4			CAGGAACCCCGTC	AK022743	CCDS45373.1	16p13.3	2008-02-05	2007-11-29	2007-11-29	ENSG00000103227	ENSG00000103227			14154	protein-coding gene	gene with protein product		611761	"""chromosome 16 open reading frame 26"", ""transmembrane protein 112"""	C16orf26, TMEM112		11157797, 17994020	Standard	NM_022773		Approved	FLJ12681, JFP11, FLJ22302, TMEM112A	uc021tae.1	Q96S06	OTTHUMG00000047848	ENST00000262301.11:c.543G>A	16.37:g.961051C>T		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	64	19	0.296875	NM_022773	Q68CJ3|Q96FJ4|Q9H6G4|Q9H9K7	Silent	SNP	ENST00000262301.11	37	CCDS45373.1																																																																																			C|0.748;T|0.252	0.252	strong		0.532	LMF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000109071.3	NM_022773	
ARHGAP42	143872	hgsc.bcm.edu	37	11	100665888	100665888	+	Silent	SNP	G	G	A	rs61999341	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:100665888G>A	ENST00000298815.8	+	3	306	c.303G>A	c.(301-303)agG>agA	p.R101R	ARHGAP42_ENST00000524892.2_Silent_p.R101R|AC015600.1_ENST00000577356.1_RNA|ARHGAP42_ENST00000534060.1_3'UTR	NM_152432.2	NP_689645.2	A6NI28	RHG42_HUMAN	Rho GTPase activating protein 42	101	BAR.				signal transduction (GO:0007165)	intracellular (GO:0005622)	GTPase activator activity (GO:0005096)			endometrium(3)|skin(2)	5						AAGAAGAAAGGCGAAGACTGG	0.313													G|||	145	0.0289537	0.0643	0.0086	5008	,	,		15585	0.0		0.0348	False		,,,				2504	0.0194				p.R101R		Atlas-SNP	.											.	ARHGAP42	32	.	0			c.G303A						PASS	.	G		83,1301		1,81,610	120.0	118.0	119.0		303	2.8	1.0	11	dbSNP_129	119	69,3107		0,69,1519	no	coding-synonymous	ARHGAP42	NM_152432.2		1,150,2129	AA,AG,GG		2.1725,5.9971,3.3333		101/875	100665888	152,4408	692	1588	2280	SO:0001819	synonymous_variant	143872	exon3			AGAAAGGCGAAGA			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.303G>A	11.37:g.100665888G>A		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	38	12	0.315789	NM_152432	Q96M56	Silent	SNP	ENST00000298815.8	37																																																																																				G|0.975;A|0.025	0.025	strong		0.313	ARHGAP42-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_152432	
FRG1	2483	hgsc.bcm.edu	37	4	190876283	190876283	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:190876283C>A	ENST00000226798.4	+	5	631	c.409C>A	c.(409-411)Caa>Aaa	p.Q137K	FRG1_ENST00000514482.1_3'UTR	NM_004477.2	NP_004468.1	Q14331	FRG1_HUMAN	FSHD region gene 1	137					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)		ACCAAGAGAACAATGGGAACC	0.353																																					p.Q137K		Atlas-SNP	.											.	FRG1	76	.	0			c.C409A						PASS	.						88.0	87.0	87.0					4																	190876283		2203	4300	6503	SO:0001583	missense	2483	exon5			AGAGAACAATGGG	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.409C>A	4.37:g.190876283C>A	ENSP00000226798:p.Gln137Lys	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	162	9	0.0555556	NM_004477	A8K775	Missense_Mutation	SNP	ENST00000226798.4	37	CCDS34121.1	.	.	.	.	.	.	.	.	.	.	.	16.72	3.202137	0.58234	.	.	ENSG00000109536	ENST00000226798;ENST00000531991	T;T	0.49139	2.03;0.79	4.04	4.04	0.47022	Actin cross-linking (1);	0.103449	0.64402	D	0.000002	T	0.54902	0.1887	M	0.88377	2.95	0.80722	D	1	B	0.11235	0.004	B	0.15484	0.013	T	0.60078	-0.7333	10	0.42905	T	0.14	-3.5101	14.1451	0.65347	0.0:1.0:0.0:0.0	.	137	Q14331	FRG1_HUMAN	K	137;74	ENSP00000226798:Q137K;ENSP00000435943:Q74K	ENSP00000226798:Q137K	Q	+	1	0	FRG1	191113277	1.000000	0.71417	0.998000	0.56505	0.994000	0.84299	7.292000	0.78731	1.964000	0.57103	0.567000	0.79289	CAA	.	.	none		0.353	FRG1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000359622.4	NM_004477	
ACAN	176	hgsc.bcm.edu	37	15	89398825	89398825	+	Silent	SNP	C	C	T	rs4080952	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:89398825C>T	ENST00000561243.1	+	11	3009	c.3009C>T	c.(3007-3009)acC>acT	p.T1003T	ACAN_ENST00000439576.2_Silent_p.T1003T|ACAN_ENST00000559004.1_Silent_p.T1003T|ACAN_ENST00000352105.7_Silent_p.T1003T			P16112	PGCA_HUMAN	aggrecan	1002	29 X 19 AA approximate tandem repeats of E-[IVDG]-[LV]-[EV]-[GTI]-[STA]-[ATV]- [SP]-[GA]-[VIFAD]-[GEDL]-[DE]-[LVI]-[SG]- [GERK]-[LV]-P-S-G.|CS-1.				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|proteolysis (GO:0006508)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)	carbohydrate binding (GO:0030246)|extracellular matrix structural constituent (GO:0005201)|hyaluronic acid binding (GO:0005540)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(4)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(15)|liver(2)|lung(40)|ovary(2)|prostate(5)|skin(5)|stomach(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	93	Lung NSC(78;0.0392)|all_lung(78;0.077)		BRCA - Breast invasive adenocarcinoma(143;0.146)			TTCTAGAGACCACTGCCCCTG	0.562													T|||	1575	0.314497	0.3601	0.2622	5008	,	,		11242	0.2004		0.3966	False		,,,				2504	0.3231				p.T1003T		Atlas-SNP	.											.	ACAN	220	.	0			c.C3009T						PASS	.						3.0	3.0	3.0					15																	89398825		917	2245	3162	SO:0001819	synonymous_variant	176	exon12			AGAGACCACTGCC	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.3009C>T	15.37:g.89398825C>T		Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	34	13	0.382353	NM_001135	Q13650|Q9UCD3|Q9UCP4|Q9UCP5|Q9UDE0	Silent	SNP	ENST00000561243.1	37	CCDS53970.1																																																																																			C|0.250;T|0.750	0.750	strong		0.562	ACAN-006	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416267.2	NM_001135	
IQUB	154865	hgsc.bcm.edu	37	7	123152035	123152035	+	Silent	SNP	T	T	C	rs10270705	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:123152035T>C	ENST00000466202.1	-	2	936	c.360A>G	c.(358-360)gaA>gaG	p.E120E	IQUB_ENST00000488987.1_Intron|IQUB_ENST00000434450.1_Silent_p.E120E|IQUB_ENST00000324698.6_Silent_p.E120E	NM_001282855.1	NP_001269784.1	Q8NA54	IQUB_HUMAN	IQ motif and ubiquitin domain containing	120					cilium morphogenesis (GO:0060271)|smoothened signaling pathway (GO:0007224)	acrosomal vesicle (GO:0001669)|motile cilium (GO:0031514)		p.E120E(1)		breast(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(18)|ovary(3)|prostate(2)|stomach(3)|upper_aerodigestive_tract(1)	45						CTTGCAAAGATTCCTTTACAG	0.353													C|||	1625	0.324481	0.3404	0.2983	5008	,	,		19171	0.369		0.3728	False		,,,				2504	0.226				p.E120E		Atlas-SNP	.											IQUB,middle_lobe,carcinoma,-2,2	IQUB	117	2	1	Substitution - coding silent(1)	stomach(1)	c.A360G						PASS	.	C		1581,2823	665.9+/-401.6	289,1003,910	76.0	75.0	75.0		360	1.1	0.0	7	dbSNP_119	75	2946,5654	666.9+/-402.4	494,1958,1848	no	coding-synonymous	IQUB	NM_178827.4		783,2961,2758	CC,CT,TT		34.2558,35.8992,34.8124		120/792	123152035	4527,8477	2202	4300	6502	SO:0001819	synonymous_variant	154865	exon2			CAAAGATTCCTTT	AK093153	CCDS5787.1	7q31.32	2010-03-19			ENSG00000164675	ENSG00000164675			21995	protein-coding gene	gene with protein product							Standard	NM_178827		Approved	FLJ35834	uc003vko.3	Q8NA54	OTTHUMG00000157347	ENST00000466202.1:c.360A>G	7.37:g.123152035T>C		Somatic	207	0	0		WXS	Illumina HiSeq	Phase_I	95	39	0.410526	NM_178827	A4D0X0|Q49AL6|Q4G189|Q5BJD9|Q6NUH6|Q8N9Y2	Silent	SNP	ENST00000466202.1	37	CCDS5787.1																																																																																			T|0.667;C|0.333	0.333	strong		0.353	IQUB-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348529.1	NM_178827	
FAM114A1	92689	hgsc.bcm.edu	37	4	38879949	38879949	+	Missense_Mutation	SNP	G	G	A	rs11096964	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:38879949G>A	ENST00000358869.2	+	3	426	c.250G>A	c.(250-252)Gga>Aga	p.G84R	FAM114A1_ENST00000515037.1_Intron	NM_138389.2	NP_612398.2	Q8IWE2	NXP20_HUMAN	family with sequence similarity 114, member A1	84			G -> R (in dbSNP:rs11096964). {ECO:0000269|PubMed:15489334}.			cytoplasm (GO:0005737)				haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(8)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	20						CCCTCTCAATGGAGACGTGAC	0.567													G|||	1018	0.203275	0.3192	0.2061	5008	,	,		18604	0.0863		0.2475	False		,,,				2504	0.1196				p.G84R		Atlas-SNP	.											.	FAM114A1	42	.	0			c.G250A						PASS	.	G	ARG/GLY	1377,3029	446.3+/-348.0	219,939,1045	53.0	52.0	53.0		250	1.9	0.2	4	dbSNP_120	53	2352,6248	381.8+/-340.2	349,1654,2297	yes	missense	FAM114A1	NM_138389.2	125	568,2593,3342	AA,AG,GG		27.3488,31.2528,28.6714	possibly-damaging	84/564	38879949	3729,9277	2203	4300	6503	SO:0001583	missense	92689	exon3			CTCAATGGAGACG		CCDS3447.1	4p14	2006-09-21			ENSG00000197712	ENSG00000197712			25087	protein-coding gene	gene with protein product							Standard	NM_138389		Approved	Noxp20	uc003gtn.3	Q8IWE2	OTTHUMG00000128583	ENST00000358869.2:c.250G>A	4.37:g.38879949G>A	ENSP00000351740:p.Gly84Arg	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	112	47	0.419643	NM_138389	A8K9W6|Q6MZV4|Q9BVL6	Missense_Mutation	SNP	ENST00000358869.2	37	CCDS3447.1	496	0.2271062271062271	170	0.34552845528455284	78	0.2154696132596685	46	0.08041958041958042	202	0.26649076517150394	G	14.80	2.643511	0.47258	0.312528	0.273488	ENSG00000197712	ENST00000510213;ENST00000358869	T;T	0.26518	1.73;2.9	4.6	1.88	0.25563	.	0.258181	0.37669	N	0.001981	T	0.00012	0.0000	M	0.63843	1.955	0.38510	P	0.05155399999999999	B	0.23735	0.09	B	0.17433	0.018	T	0.43163	-0.9408	9	0.24483	T	0.36	-4.1098	5.8533	0.18707	0.1696:0.1605:0.67:0.0	rs11096964;rs17853999;rs52823947;rs11096964	84	Q8IWE2	NXP20_HUMAN	R	84	ENSP00000422965:G84R;ENSP00000351740:G84R	ENSP00000351740:G84R	G	+	1	0	FAM114A1	38556344	0.991000	0.36638	0.210000	0.23637	0.640000	0.38277	1.477000	0.35431	0.255000	0.21593	0.484000	0.47621	GGA	G|0.755;A|0.245	0.245	strong		0.567	FAM114A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250436.1	NM_138389	
PCNT	5116	hgsc.bcm.edu	37	21	47863757	47863757	+	Missense_Mutation	SNP	A	A	C	rs2073380	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:47863757A>C	ENST00000359568.5	+	45	9842	c.9735A>C	c.(9733-9735)agA>agC	p.R3245S	PCNT_ENST00000480896.1_3'UTR	NM_006031.5	NP_006022.3	O95613	PCNT_HUMAN	pericentrin	3245	Interaction with NEK2.		R -> S (in dbSNP:rs2073380).		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)					CTCCACCCAGAACCAGAGAGT	0.582													A|||	1033	0.20627	0.056	0.1354	5008	,	,		14631	0.4117		0.2157	False		,,,				2504	0.2382				p.R3245S		Atlas-SNP	.											.	PCNT	283	.	0			c.A9735C						PASS	.	A	SER/ARG	356,4050	179.0+/-207.6	16,324,1863	56.0	67.0	63.0		9735	-3.0	0.0	21	dbSNP_96	63	1849,6751	321.6+/-315.2	193,1463,2644	yes	missense	PCNT	NM_006031.5	110	209,1787,4507	CC,CA,AA		21.5,8.0799,16.9537	benign	3245/3337	47863757	2205,10801	2203	4300	6503	SO:0001583	missense	5116	exon45			ACCCAGAACCAGA	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.9735A>C	21.37:g.47863757A>C	ENSP00000352572:p.Arg3245Ser	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	57	19	0.333333	NM_006031	O43152|Q7Z7C9	Missense_Mutation	SNP	ENST00000359568.5	37	CCDS33592.1	513	0.2348901098901099	31	0.06300813008130081	60	0.16574585635359115	257	0.4493006993006993	165	0.21767810026385223	A	6.196	0.404264	0.11754	0.080799	0.215	ENSG00000160299	ENST00000359568	T	0.01414	4.92	5.0	-2.95	0.05564	.	.	.	.	.	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	B;B	0.14438	0.006;0.01	B;B	0.13407	0.009;0.004	T	0.35574	-0.9783	8	0.08381	T	0.77	.	1.0943	0.01670	0.2612:0.3348:0.2529:0.1511	rs2073380;rs52807129;rs2073380	3048;3245	O95613-2;O95613	.;PCNT_HUMAN	S	3245	ENSP00000352572:R3245S	ENSP00000352572:R3245S	R	+	3	2	PCNT	46688185	0.000000	0.05858	0.000000	0.03702	0.020000	0.10135	-0.016000	0.12613	-0.225000	0.09913	0.533000	0.62120	AGA	A|0.810;C|0.190	0.190	strong		0.582	PCNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207336.1	NM_006031	
MYCBPAP	84073	hgsc.bcm.edu	37	17	48595988	48595988	+	Missense_Mutation	SNP	G	G	C	rs8064455	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	119	0	0		WXS	Illumina HiSeq	Phase_I	88	37	0.420455	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	
OBSCN	84033	hgsc.bcm.edu	37	1	228548197	228548197	+	Intron	SNP	G	G	A	rs10158354	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:228548197G>A	ENST00000422127.1	+	80	18705				OBSCN_ENST00000284548.11_Missense_Mutation_p.R6535H|OBSCN_ENST00000570156.2_Intron|OBSCN_ENST00000366709.4_Missense_Mutation_p.R3654H|OBSCN_ENST00000366707.4_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)				CCTGAGCCCCGTGGGGCGTCA	0.711													G|||	740	0.147764	0.0832	0.0764	5008	,	,		17345	0.3284		0.0984	False		,,,				2504	0.1503				p.R6535H		Atlas-SNP	.											.	OBSCN	2142	.	0			c.G19604A						PASS	.	G	,HIS/ARG	386,3526		18,350,1588	15.0	19.0	18.0		,19604	-5.6	0.0	1	dbSNP_119	18	710,7576		29,652,3462	yes	intron,missense	OBSCN	NM_001098623.1,NM_052843.2	,29	47,1002,5050	AA,AG,GG		8.5687,9.8671,8.9851	,	,6535/6621	228548197	1096,11102	1956	4143	6099	SO:0001627	intron_variant	84033	exon81			AGCCCCGTGGGGC	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"""Rho guanine nucleotide exchange factors"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.18662-2080G>A	1.37:g.228548197G>A		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	34	15	0.441176	NM_052843	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	346	0.15842490842490842	46	0.09349593495934959	35	0.09668508287292818	190	0.3321678321678322	75	0.09894459102902374	G	17.43	3.387211	0.61956	0.098671	0.085687	ENSG00000154358	ENST00000284548;ENST00000366709	T;T	0.56776	0.44;0.58	3.31	-5.62	0.02481	.	.	.	.	.	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	0.30966	-0.9960	8	0.42905	T	0.14	.	5.8246	0.18546	0.6394:0.163:0.1059:0.0917	rs10158354	6535	Q5VST9-3	.	H	6535;3654	ENSP00000284548:R6535H;ENSP00000355670:R3654H	ENSP00000284548:R6535H	R	+	2	0	OBSCN	226614820	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.165000	0.03132	-1.292000	0.02366	-0.194000	0.12790	CGT	G|0.847;A|0.153	0.153	strong		0.711	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
ZNF836	162962	hgsc.bcm.edu	37	19	52658318	52658318	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:52658318C>T	ENST00000322146.8	-	5	3139	c.2618G>A	c.(2617-2619)cGg>cAg	p.R873Q	CTC-471J1.8_ENST00000594362.1_RNA|ZNF836_ENST00000597252.1_Missense_Mutation_p.R873Q	NM_001102657.1	NP_001096127.1	Q6ZNA1	ZN836_HUMAN	zinc finger protein 836	873					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|kidney(2)|large_intestine(9)|lung(10)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	26						GCAAGAAAACCGCCCAAAGGC	0.403																																					p.R873Q		Atlas-SNP	.											ZNF836_ENST00000322146,colon,carcinoma,-1,4	ZNF836	158	4	0			c.G2618A						scavenged	.						104.0	112.0	110.0					19																	52658318		2196	4296	6492	SO:0001583	missense	162962	exon5			GAAAACCGCCCAA	BC011784	CCDS46162.1	19q13.33	2013-01-08			ENSG00000196267	ENSG00000196267		"""Zinc fingers, C2H2-type"", ""-"""	34333	protein-coding gene	gene with protein product							Standard	NM_001102657		Approved	FLJ16287	uc010ydj.2	Q6ZNA1		ENST00000322146.8:c.2618G>A	19.37:g.52658318C>T	ENSP00000325038:p.Arg873Gln	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	132	3	0.0227273	NM_001102657		Missense_Mutation	SNP	ENST00000322146.8	37	CCDS46162.1	.	.	.	.	.	.	.	.	.	.	C	5.705	0.314607	0.10789	.	.	ENSG00000196267	ENST00000322146	T	0.60672	0.17	1.88	-3.76	0.04359	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.30135	0.0755	N	0.03071	-0.42	0.09310	N	1	D	0.76494	0.999	P	0.50896	0.653	T	0.20472	-1.0274	9	0.13470	T	0.59	.	3.3213	0.07052	0.4301:0.1852:0.0:0.3847	.	873	Q6ZNA1	ZN836_HUMAN	Q	873	ENSP00000325038:R873Q	ENSP00000325038:R873Q	R	-	2	0	ZNF836	57350130	0.000000	0.05858	0.000000	0.03702	0.129000	0.20672	-6.399000	0.00067	-0.836000	0.04229	-0.350000	0.07774	CGG	.	.	none		0.403	ZNF836-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462456.1	NM_001102657	
TTN	7273	hgsc.bcm.edu	37	2	179582824	179582824	+	Silent	SNP	C	C	T	rs72648983	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:179582824C>T	ENST00000591111.1	-	84	24182	c.23958G>A	c.(23956-23958)aaG>aaA	p.K7986K	TTN_ENST00000359218.5_Intron|TTN_ENST00000342992.6_Silent_p.K7059K|TTN_ENST00000460472.2_Intron|TTN_ENST00000589042.1_Silent_p.K8303K|TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000585451.1_RNA			Q8WZ42	TITIN_HUMAN	titin	12177	Ig-like 62.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CTGATCGTAGCTTTGTGTGTT	0.383													C|||	118	0.0235623	0.0537	0.013	5008	,	,		21153	0.0109		0.0119	False		,,,				2504	0.0153				p.K8303K		Atlas-SNP	.											.	TTN	18412	.	0			c.G24909A						PASS	.	C	,,,	137,3631		6,125,1753	158.0	146.0	150.0		,21177,,	0.8	1.0	2	dbSNP_130	150	57,8177		0,57,4060	no	intron,coding-synonymous,intron,intron	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	,,,	6,182,5813	TT,TC,CC		0.6923,3.6359,1.6164	,,,	,7059/33424,,	179582824	194,11808	1884	4117	6001	SO:0001819	synonymous_variant	7273	exon86			TCGTAGCTTTGTG	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.23958G>A	2.37:g.179582824C>T		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	64	38	0.59375	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	37																																																																																				C|0.981;T|0.019	0.019	strong		0.383	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
GGT6	124975	hgsc.bcm.edu	37	17	4463713	4463713	+	Missense_Mutation	SNP	A	A	G	rs62066362	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:4463713A>G	ENST00000574154.1	-	1	400	c.104T>C	c.(103-105)cTg>cCg	p.L35P	GGT6_ENST00000573591.1_5'Flank|GGT6_ENST00000301395.3_Missense_Mutation_p.L35P|GGT6_ENST00000381550.3_Missense_Mutation_p.L35P			Q6P531	GGT6_HUMAN	gamma-glutamyltransferase 6	35					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						GTTTAGAACCAGCGCCTCTGA	0.617													A|||	65	0.0129792	0.0015	0.0648	5008	,	,		16130	0.0		0.0139	False		,,,				2504	0.0041				p.L35P		Atlas-SNP	.											.	GGT6	22	.	0			c.T104C						PASS	.	A	PRO/LEU,PRO/LEU	26,4380	32.6+/-62.9	0,26,2177	104.0	94.0	98.0		104,104	3.7	0.0	17	dbSNP_129	98	178,8422	81.2+/-143.8	1,176,4123	yes	missense,missense	GGT6	NM_001122890.1,NM_153338.2	98,98	1,202,6300	GG,GA,AA		2.0698,0.5901,1.5685	possibly-damaging,possibly-damaging	35/494,35/462	4463713	204,12802	2203	4300	6503	SO:0001583	missense	124975	exon1			AGAACCAGCGCCT	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.104T>C	17.37:g.4463713A>G	ENSP00000458307:p.Leu35Pro	Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	33	13	0.393939	NM_001122890	B4DUH4|Q8NCM0	Missense_Mutation	SNP	ENST00000574154.1	37	CCDS45582.1	34	0.015567765567765568	3	0.006097560975609756	18	0.049723756906077346	0	0.0	13	0.017150395778364115	A	15.53	2.862327	0.51482	0.005901	0.020698	ENSG00000167741	ENST00000381550;ENST00000301395	T;T	0.29655	2.36;1.56	4.84	3.67	0.42095	.	0.153909	0.30219	N	0.010135	T	0.08846	0.0219	M	0.62723	1.935	0.20975	N	0.999818	P;P;D	0.53151	0.93;0.838;0.958	P;P;P	0.54312	0.564;0.466;0.748	T	0.02683	-1.1124	10	0.87932	D	0	5.7736	7.2103	0.25929	0.8021:0.0:0.0:0.1979	rs62066362	35;35;35	B4DKN3;Q6P531;Q6P531-2	.;GGT6_HUMAN;.	P	35	ENSP00000370962:L35P;ENSP00000301395:L35P	ENSP00000301395:L35P	L	-	2	0	GGT6	4410462	0.025000	0.19082	0.023000	0.16930	0.012000	0.07955	1.688000	0.37690	2.116000	0.64780	0.533000	0.62120	CTG	A|0.986;G|0.014	0.014	strong		0.617	GGT6-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439122.1	NM_153338	
NUP88	4927	hgsc.bcm.edu	37	17	5290033	5290033	+	Silent	SNP	T	T	C	rs1071705	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:5290033T>C	ENST00000573584.1	-	16	2666	c.2157A>G	c.(2155-2157)aaA>aaG	p.K719K	NUP88_ENST00000573169.1_5'Flank	NM_002532.4	NP_002523.2	Q99567	NUP88_HUMAN	nucleoporin 88kDa	719					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)	cytosol (GO:0005829)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	transporter activity (GO:0005215)			endometrium(4)|kidney(4)|large_intestine(4)|lung(3)	15						CTTACTCCTCTTTCAGGATGG	0.398													C|||	2768	0.552716	0.3994	0.4236	5008	,	,		20862	0.8244		0.4404	False		,,,				2504	0.6871				p.K719K		Atlas-SNP	.											.	NUP88	47	.	0			c.A2157G						PASS	.	C		1852,2554	633.4+/-396.0	411,1030,762	184.0	170.0	175.0		2157	3.5	1.0	17	dbSNP_86	175	3390,5210	639.9+/-399.5	666,2058,1576	no	coding-synonymous	NUP88	NM_002532.4		1077,3088,2338	CC,CT,TT		39.4186,42.0336,40.3045		719/742	5290033	5242,7764	2203	4300	6503	SO:0001819	synonymous_variant	4927	exon16			CTCCTCTTTCAGG	Y08612	CCDS11070.1	17p13	2004-02-18	2002-08-29		ENSG00000108559	ENSG00000108559			8067	protein-coding gene	gene with protein product		602552	"""nucleoporin 88kD"""			9049309	Standard	NM_002532		Approved	MGC8530	uc002gbo.2	Q99567	OTTHUMG00000099453	ENST00000573584.1:c.2157A>G	17.37:g.5290033T>C		Somatic	194	0	0		WXS	Illumina HiSeq	Phase_I	175	71	0.405714	NM_002532	D3DTM2|Q9BWE5	Silent	SNP	ENST00000573584.1	37	CCDS11070.1																																																																																			T|0.566;C|0.434	0.434	strong		0.398	NUP88-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216918.3	NM_002532	
MRPS5	64969	hgsc.bcm.edu	37	2	95775761	95775761	+	Silent	SNP	G	G	A	rs113259652	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:95775761G>A	ENST00000272418.2	-	4	511	c.303C>T	c.(301-303)ggC>ggT	p.G101G		NM_031902.3	NP_114108.1	P82675	RT05_HUMAN	mitochondrial ribosomal protein S5	101					translation (GO:0006412)	mitochondrion (GO:0005739)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			central_nervous_system(1)|kidney(2)|large_intestine(4)|lung(9)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	20						CTGCTAAAGCGCCTTTCCACA	0.398													G|||	66	0.0131789	0.0061	0.0072	5008	,	,		19690	0.001		0.0348	False		,,,				2504	0.0174				p.G101G		Atlas-SNP	.											.	MRPS5	52	.	0			c.C303T						PASS	.	G		41,4365	44.6+/-78.6	1,39,2163	123.0	126.0	125.0		303	-11.5	0.5	2	dbSNP_132	125	462,8138	137.8+/-194.7	25,412,3863	no	coding-synonymous	MRPS5	NM_031902.3		26,451,6026	AA,AG,GG		5.3721,0.9305,3.8674		101/431	95775761	503,12503	2203	4300	6503	SO:0001819	synonymous_variant	64969	exon4			TAAAGCGCCTTTC	AB049940	CCDS2010.1	2p11.2-q11.2	2012-09-13			ENSG00000144029	ENSG00000144029		"""Mitochondrial ribosomal proteins / small subunits"""	14498	protein-coding gene	gene with protein product	"""mitochondrial 28S ribosomal protein S5"""	611972					Standard	NM_031902		Approved	MRP-S5, S5mt	uc002sub.3	P82675	OTTHUMG00000130394	ENST00000272418.2:c.303C>T	2.37:g.95775761G>A		Somatic	334	1	0.00299401		WXS	Illumina HiSeq	Phase_I	311	149	0.4791	NM_031902	Q4ZFY5|Q96LJ6|Q9BWI4|Q9BYC4	Silent	SNP	ENST00000272418.2	37	CCDS2010.1																																																																																			G|0.968;A|0.032	0.032	strong		0.398	MRPS5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252772.1	NM_031902	
KRTAP13-1	140258	hgsc.bcm.edu	37	21	31768539	31768539	+	Silent	SNP	G	G	C	rs9636833	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:31768539G>C	ENST00000355459.2	+	1	148	c.135G>C	c.(133-135)acG>acC	p.T45T		NM_181599.2	NP_853630.2	Q8IUC0	KR131_HUMAN	keratin associated protein 13-1	45						intermediate filament (GO:0005882)				endometrium(1)|kidney(2)|large_intestine(3)|lung(12)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						CTCCCAGCACGTGCCAGCTGG	0.622													C|||	933	0.186302	0.1475	0.0677	5008	,	,		19493	0.4256		0.1272	False		,,,				2504	0.137				p.T45T		Atlas-SNP	.											.	KRTAP13-1	48	.	0			c.G135C						PASS	.	C		657,3749	765.3+/-413.3	48,561,1594	82.0	82.0	82.0		135	1.7	0.1	21	dbSNP_119	82	938,7662	776.2+/-407.7	57,824,3419	no	coding-synonymous	KRTAP13-1	NM_181599.2		105,1385,5013	CC,CG,GG		10.907,14.9115,12.2636		45/173	31768539	1595,11411	2203	4300	6503	SO:0001819	synonymous_variant	140258	exon1			CAGCACGTGCCAG	AJ457066	CCDS13590.2	21q22.11	2013-06-20			ENSG00000198390	ENSG00000198390		"""Keratin associated proteins"""	18924	protein-coding gene	gene with protein product		608718				12359730	Standard	NM_181599		Approved	KAP13.1	uc002yoa.3	Q8IUC0	OTTHUMG00000057800	ENST00000355459.2:c.135G>C	21.37:g.31768539G>C		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	107	42	0.392523	NM_181599	Q14D20|Q3LI79	Silent	SNP	ENST00000355459.2	37	CCDS13590.2																																																																																			G|0.862;C|0.138	0.138	strong		0.622	KRTAP13-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128252.3		
SYT15	83849	hgsc.bcm.edu	37	10	46968665	46968665	+	Silent	SNP	G	G	A	rs200814731	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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|RP11-38L15.3_ENST00000506914.1_RNA|SYT15_ENST00000374323.4_Silent_p.L144L	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	38	0	0		WXS	Illumina HiSeq	Phase_I	42	9	0.214286	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	
SLC25A15	10166	hgsc.bcm.edu	37	13	41373254	41373254	+	Silent	SNP	G	G	A	rs41396747	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:41373254G>A	ENST00000338625.4	+	3	353	c.117G>A	c.(115-117)acG>acA	p.T39T	SLC25A15_ENST00000478827.1_3'UTR	NM_014252.3	NP_055067.1	Q9Y619	ORNT1_HUMAN	solute carrier family 25 (mitochondrial carrier; ornithine transporter) member 15	39					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)			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)	AGATGCAGACGTTCCCTGACC	0.552													G|||	315	0.0628994	0.1006	0.0476	5008	,	,		19648	0.0119		0.0825	False		,,,				2504	0.0552				p.T39T		Atlas-SNP	.											.	SLC25A15	30	.	0			c.G117A						PASS	.	G		388,4018	194.0+/-219.0	16,356,1831	154.0	136.0	142.0		117	-5.6	0.8	13	dbSNP_129	142	803,7797	188.4+/-235.4	35,733,3532	no	coding-synonymous	SLC25A15	NM_014252.3		51,1089,5363	AA,AG,GG		9.3372,8.8062,9.1573		39/302	41373254	1191,11815	2203	4300	6503	SO:0001819	synonymous_variant	10166	exon3			GCAGACGTTCCCT	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.117G>A	13.37:g.41373254G>A		Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	160	85	0.53125	NM_014252	Q5VZD8|Q9HC45	Silent	SNP	ENST00000338625.4	37	CCDS9373.1																																																																																			G|0.923;A|0.077	0.077	strong		0.552	SLC25A15-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276149.2	NM_014252	
REM1	28954	hgsc.bcm.edu	37	20	30064331	30064331	+	Missense_Mutation	SNP	A	A	G	rs1006459	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:30064331A>G	ENST00000201979.2	+	2	376	c.83A>G	c.(82-84)cAc>cGc	p.H28R	DEFB124_ENST00000481595.1_Intron	NM_014012.4	NP_054731.2	O75628	REM1_HUMAN	RAS (RAD and GEM)-like GTP-binding 1	28			H -> R (in dbSNP:rs1006459). {ECO:0000269|PubMed:14702039, ECO:0000269|Ref.3}.		GTP catabolic process (GO:0006184)|small GTPase mediated signal transduction (GO:0007264)	membrane (GO:0016020)	GTP binding (GO:0005525)			kidney(3)|large_intestine(3)|lung(14)|pancreas(2)|upper_aerodigestive_tract(1)	23	all_cancers(5;0.000119)|Lung NSC(7;1.32e-05)|all_lung(7;2.14e-05)|all_hematologic(12;0.158)|Ovarian(7;0.198)		Colorectal(19;0.00254)|COAD - Colon adenocarcinoma(19;0.0347)			CCACGGGGCCACCAGCCTGGC	0.647													G|||	2277	0.454673	0.9024	0.3386	5008	,	,		15593	0.2659		0.3221	False		,,,				2504	0.2628				p.H28R		Atlas-SNP	.											REM1,right_upper_lobe,carcinoma,+1,1	REM1	54	1	0			c.A83G						PASS	.	G	ARG/HIS	3545,861	334.7+/-303.5	1425,695,83	72.0	86.0	81.0		83	0.2	0.7	20	dbSNP_86	81	2700,5900	681.6+/-403.7	411,1878,2011	yes	missense	REM1	NM_014012.4	29	1836,2573,2094	GG,GA,AA		31.3953,19.5415,48.0163	benign	28/299	30064331	6245,6761	2203	4300	6503	SO:0001583	missense	28954	exon2			GGGGCCACCAGCC	AF152863	CCDS13181.1	20q11.21	2014-05-09	2004-04-14	2004-04-16	ENSG00000088320	ENSG00000088320			15922	protein-coding gene	gene with protein product	"""GTPase GES"""	610388	"""RAS (RAD and GEM)-like GTP-binding"""	REM		10831614, 14623965	Standard	NM_014012		Approved	GES	uc002wwa.3	O75628	OTTHUMG00000032168	ENST00000201979.2:c.83A>G	20.37:g.30064331A>G	ENSP00000201979:p.His28Arg	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	95	46	0.484211	NM_014012	E1P5L1|Q5TZR7|Q5TZR8|Q9NP57	Missense_Mutation	SNP	ENST00000201979.2	37	CCDS13181.1	974	0.445970695970696	437	0.8882113821138211	137	0.3784530386740331	163	0.28496503496503495	237	0.31266490765171506	G	3.961	-0.010297	0.07727	0.804585	0.313953	ENSG00000088320	ENST00000201979	T	0.65364	-0.15	4.25	0.213	0.15244	.	1.023970	0.07776	N	0.952480	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	0.31194	-0.9952	9	0.24483	T	0.36	.	5.039	0.14449	0.4557:0.1613:0.383:0.0	rs1006459;rs60259937	28	O75628	REM1_HUMAN	R	28	ENSP00000201979:H28R	ENSP00000201979:H28R	H	+	2	0	REM1	29527992	0.001000	0.12720	0.662000	0.29724	0.712000	0.41017	-0.783000	0.04638	-0.017000	0.14103	-0.119000	0.15052	CAC	A|0.536;C|0.000;G|0.464	0.464	strong		0.647	REM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078508.2	NM_014012	
LILRB1	10859	hgsc.bcm.edu	37	19	55142739	55142739	+	Silent	SNP	A	A	C	rs1985501	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:55142739A>C	ENST00000396331.1	+	4	409	c.52A>C	c.(52-54)Agg>Cgg	p.R18R	LILRB1_ENST00000448689.1_Intron|LILRB1_ENST00000396315.1_Silent_p.R18R|LILRB1_ENST00000396321.2_Intron|LILRB1_ENST00000324602.7_Silent_p.R18R|LILRB1_ENST00000427581.2_Silent_p.R54R|LILRB1_ENST00000396327.3_Silent_p.R18R|LILRB1_ENST00000434867.2_Silent_p.R18R|LILRB1_ENST00000396317.1_Silent_p.R18R|LILRB1_ENST00000418536.2_Intron|AC009892.1_ENST00000578908.1_RNA|LILRB1_ENST00000396332.4_Silent_p.R18R	NM_006669.3	NP_006660.3	Q8NHL6	LIRB1_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 1	18					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)		TCTGGGCCCCAGGACCCACGT	0.667										HNSCC(37;0.09)			a|||	2257	0.450679	0.5537	0.4841	5008	,	,		15896	0.5982		0.3032	False		,,,				2504	0.2873				p.R18R		Atlas-SNP	.											.	LILRB1	140	.	0			c.A52C						PASS	.	A	,,,	2264,2142	571.7+/-383.1	584,1096,523	54.0	65.0	61.0		52,52,52,52	1.5	0.0	19	dbSNP_92	61	2749,5849	425.4+/-354.9	429,1891,1979	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	LILRB1	NM_001081637.1,NM_001081638.1,NM_001081639.1,NM_006669.3	,,,	1013,2987,2502	CC,CA,AA		31.9726,48.6155,38.5497	,,,	18/653,18/652,18/652,18/651	55142739	5013,7991	2203	4299	6502	SO:0001819	synonymous_variant	10859	exon3			GGCCCCAGGACCC	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.52A>C	19.37:g.55142739A>C		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	81	81	1	NM_001081637	A2IXV4|A8MXT0|O75024|O75025|Q8NHJ9|Q8NHK0	Silent	SNP	ENST00000396331.1	37	CCDS42617.1																																																																																			A|0.588;C|0.412	0.412	strong		0.667	LILRB1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000140796.4		
PCDHB8	56128	hgsc.bcm.edu	37	5	140559350	140559350	+	Missense_Mutation	SNP	C	C	T	rs111768595	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:140559350C>T	ENST00000239444.2	+	1	1980	c.1735C>T	c.(1735-1737)Cgg>Tgg	p.R579W	PCDHB16_ENST00000361016.2_5'Flank	NM_019120.3	NP_061993.2	Q9UN66	PCDB8_HUMAN	protocadherin beta 8	579	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(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)			GCTGGTGCCCCGGGCGGCCGA	0.706													C|||	658	0.13139	0.2398	0.1585	5008	,	,		17380	0.0407		0.1103	False		,,,				2504	0.0808				p.R579W		Atlas-SNP	.											PCDHB8,NS,carcinoma,-1,1	PCDHB8	199	1	0			c.C1735T						scavenged	.						7.0	15.0	13.0					5																	140559350		2054	4075	6129	SO:0001583	missense	56128	exon1			GTGCCCCGGGCGG	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.1735C>T	5.37:g.140559350C>T	ENSP00000239444:p.Arg579Trp	Somatic	5	0	0		WXS	Illumina HiSeq	Phase_I	15	7	0.466667	NM_019120	B9EGV1	Missense_Mutation	SNP	ENST00000239444.2	37	CCDS4250.1	282	0.12912087912087913	112	0.22764227642276422	56	0.15469613259668508	26	0.045454545454545456	88	0.11609498680738786	C	16.86	3.238758	0.58995	.	.	ENSG00000120322	ENST00000239444	T	0.68479	-0.33	4.22	-1.7	0.08159	Cadherin (2);Cadherin-like (1);	.	.	.	.	T	0.00073	0.0002	M	0.92691	3.335	0.43317	P	0.004662999999999973	P	0.36587	0.559	P	0.47981	0.563	T	0.40213	-0.9575	8	0.87932	D	0	.	4.9982	0.14251	0.2904:0.5137:0.0772:0.1187	.	579	Q9UN66	PCDB8_HUMAN	W	579	ENSP00000239444:R579W	ENSP00000239444:R579W	R	+	1	2	PCDHB8	140539534	0.000000	0.05858	0.989000	0.46669	0.830000	0.47004	-1.199000	0.03032	-0.636000	0.05524	0.298000	0.19748	CGG	.	.	weak		0.706	PCDHB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251816.2	NM_019120	
LMO7	4008	hgsc.bcm.edu	37	13	76423248	76423248	+	Missense_Mutation	SNP	T	T	C	rs7986131	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:76423248T>C	ENST00000321797.8	+	25	4206	c.3485T>C	c.(3484-3486)aTg>aCg	p.M1162T	LMO7_ENST00000465261.2_Missense_Mutation_p.M1162T|LMO7_ENST00000526202.1_Missense_Mutation_p.M1039T|LMO7_ENST00000341547.4_Missense_Mutation_p.M1113T|LMO7_ENST00000357063.3_Missense_Mutation_p.M1447T|LMO7_ENST00000377534.3_Missense_Mutation_p.M1447T			Q8WWI1	LMO7_HUMAN	LIM domain 7	1447					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)		ATTGGGAACATGACCTCTTCA	0.368													C|||	3440	0.686901	0.6422	0.7651	5008	,	,		21402	0.5377		0.7624	False		,,,				2504	0.7679				p.M1162T		Atlas-SNP	.											LMO7_ENST00000465261,colon,carcinoma,0,3	LMO7	334	3	0			c.T3485C						PASS	.	C	THR/MET,THR/MET	2934,1472	472.2+/-356.3	968,998,237	83.0	72.0	76.0		3338,3485	2.3	0.0	13	dbSNP_116	76	6423,2177	372.5+/-336.7	2404,1615,281	yes	missense,missense	LMO7	NM_005358.5,NM_015842.2	81,81	3372,2613,518	CC,CT,TT		25.314,33.409,28.0563	benign,benign	1113/1350,1162/1386	76423248	9357,3649	2203	4300	6503	SO:0001583	missense	4008	exon24			GGAACATGACCTC	AF092557	CCDS9454.1, CCDS53876.1	13q22.2	2008-02-05	2004-06-15		ENSG00000136153	ENSG00000136153			6646	protein-coding gene	gene with protein product	"""F-box only protein 20"""	604362	"""LIM domain only 7"""	FBXO20		9826547, 10531035	Standard	NM_005358		Approved	FBX20, KIAA0858	uc021rkq.1	Q8WWI1	OTTHUMG00000017093	ENST00000321797.8:c.3485T>C	13.37:g.76423248T>C	ENSP00000317802:p.Met1162Thr	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	58	31	0.534483	NM_015842	E9PLH4|O15462|O95346|Q5TBK6|Q9UKC1|Q9UQM5|Q9Y6A7	Missense_Mutation	SNP	ENST00000321797.8	37		1458	0.6675824175824175	328	0.6666666666666666	278	0.7679558011049724	286	0.5	566	0.7467018469656992	C	0	-2.684288	0.00101	0.66591	0.74686	ENSG00000136153	ENST00000341547;ENST00000357063;ENST00000377534;ENST00000321797;ENST00000526202;ENST00000465261	T;T;T;T;T;T	0.39592	1.65;1.65;1.66;1.08;1.07;1.08	6.02	2.35	0.29111	.	0.814312	0.11576	N	0.550272	T	0.00012	0.0000	N	0.00063	-2.32	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	0.42882	-0.9425	9	0.02654	T	1	-0.2281	8.707	0.34360	0.0:0.4967:0.3251:0.1782	rs7986131;rs52828557;rs61633855;rs7986131	1039;1113;1162	E9PMS6;Q8WWI1-3;E9PLH4	.;.;.	T	1113;1447;1447;1162;1039;1162	ENSP00000342112:M1113T;ENSP00000349571:M1447T;ENSP00000366757:M1447T;ENSP00000317802:M1162T;ENSP00000431129:M1039T;ENSP00000433352:M1162T	ENSP00000317802:M1162T	M	+	2	0	LMO7	75321249	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.870000	0.04228	-0.074000	0.12820	-0.119000	0.15052	ATG	T|0.300;C|0.700	0.700	strong		0.368	LMO7-005	PUTATIVE	alternative_5_UTR|not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000045301.3	NM_005358	
PZP	5858	hgsc.bcm.edu	37	12	9312951	9312951	+	Missense_Mutation	SNP	G	G	A	rs57006764	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:9312951G>A	ENST00000261336.2	-	24	3036	c.3008C>T	c.(3007-3009)aCg>aTg	p.T1003M	PZP_ENST00000539983.1_5'Flank|PZP_ENST00000381997.2_Missense_Mutation_p.T789M	NM_002864.2	NP_002855.2	P20742	PZP_HUMAN	pregnancy-zone protein	1003			T -> M (in dbSNP:rs57006764).		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						GATCTCCTGCGTCAGCTGCTG	0.428													G|||	1356	0.270767	0.1619	0.2695	5008	,	,		-128	0.4762		0.1909	False		,,,				2504	0.2894				p.T1003M	Melanoma(125;1402 1695 4685 34487 38571)	Atlas-SNP	.											PZP_ENST00000381997,NS,carcinoma,+1,2	PZP	422	2	0			c.C3008T						PASS	.	G	MET/THR	710,3696	293.6+/-282.7	68,574,1561	130.0	119.0	123.0		3008	3.7	0.0	12	dbSNP_129	123	1456,7144	278.2+/-293.3	116,1224,2960	yes	missense	PZP	NM_002864.2	81	184,1798,4521	AA,AG,GG		16.9302,16.1144,16.6539	probably-damaging	1003/1483	9312951	2166,10840	2203	4300	6503	SO:0001583	missense	5858	exon24			TCCTGCGTCAGCT	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.3008C>T	12.37:g.9312951G>A	ENSP00000261336:p.Thr1003Met	Somatic	125	1	0.008		WXS	Illumina HiSeq	Phase_I	148	147	0.993243	NM_002864	A6ND27|Q15273|Q2NKL2|Q7M4N7	Missense_Mutation	SNP	ENST00000261336.2	37	CCDS8600.1	577	0.2641941391941392	105	0.21341463414634146	92	0.2541436464088398	253	0.4423076923076923	127	0.16754617414248021	G	11.01	1.514300	0.27123	0.161144	0.169302	ENSG00000126838	ENST00000261336;ENST00000381997	T;T	0.40225	1.04;1.04	4.56	3.67	0.42095	Terpenoid cylases/protein prenyltransferase alpha-alpha toroid (1);	0.075423	0.48286	U	0.000182	T	0.00012	0.0000	M	0.90369	3.11	0.43203	P	0.004940999999999973	D;D	0.89917	1.0;1.0	D;D	0.83275	0.951;0.996	T	0.38090	-0.9677	9	0.87932	D	0	.	8.6441	0.33994	0.0835:0.1509:0.7656:0.0	rs57006764;rs61740800	789;1003	P20742-2;P20742	.;PZP_HUMAN	M	1003;789	ENSP00000261336:T1003M;ENSP00000371427:T789M	ENSP00000261336:T1003M	T	-	2	0	PZP	9204218	0.993000	0.37304	0.031000	0.17742	0.009000	0.06853	2.458000	0.45014	1.044000	0.40200	0.563000	0.77884	ACG	G|0.805;A|0.195	0.195	strong		0.428	PZP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337624.1	NM_002864	
TSC22D1	8848	hgsc.bcm.edu	37	13	45148708	45148708	+	Silent	SNP	C	C	T	rs112613609		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:45148708C>T	ENST00000458659.2	-	1	1993	c.1503G>A	c.(1501-1503)caG>caA	p.Q501Q	TSC22D1_ENST00000501704.2_Silent_p.Q501Q|TSC22D1_ENST00000460842.1_5'Flank	NM_183422.3	NP_904358.2	Q15714	T22D1_HUMAN	TSC22 domain family, member 1	501	Gln-rich.				negative regulation of apoptotic process (GO:0043066)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell proliferation (GO:0008284)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(4)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	27		all_hematologic(4;8.74e-08)|Acute lymphoblastic leukemia(4;1.78e-07)|Lung NSC(96;2.21e-05)|Breast(139;0.000625)|Prostate(109;0.000947)|Hepatocellular(98;0.0202)|Lung SC(185;0.0262)		GBM - Glioblastoma multiforme(144;0.000522)|BRCA - Breast invasive adenocarcinoma(63;0.118)		gttgttgttgctgctgctgct	0.512																																					p.Q501Q		Atlas-SNP	.											TSC22D1,NS,carcinoma,0,4	TSC22D1	88	4	0			c.G1503A						scavenged	.																																			SO:0001819	synonymous_variant	8848	exon1			TTGTTGCTGCTGC	AJ222700	CCDS9392.1, CCDS31966.1, CCDS58291.1, CCDS73565.1	13q14	2008-02-05	2005-03-01	2005-03-03	ENSG00000102804	ENSG00000102804			16826	protein-coding gene	gene with protein product		607715	"""transforming growth factor beta 1 induced transcript 4"""	TGFB1I4		8651929, 9022669	Standard	NM_183422		Approved	TSC22, MGC17597	uc001uzn.4	Q15714	OTTHUMG00000016838	ENST00000458659.2:c.1503G>A	13.37:g.45148708C>T		Somatic	143	2	0.013986		WXS	Illumina HiSeq	Phase_I	142	6	0.0422535	NM_183422	B3KRL7|B9EGI0|O00666|Q6AHX5|Q6IBU1|Q8NCN1|Q96JS5	Silent	SNP	ENST00000458659.2	37	CCDS31966.1																																																																																			.	.	none		0.512	TSC22D1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000044743.2	NM_006022	
WFDC10B	280664	hgsc.bcm.edu	37	20	44314609	44314609	+	Missense_Mutation	SNP	A	A	G	rs232729	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:44314609A>G	ENST00000330523.5	-	3	253	c.23T>C	c.(22-24)cTt>cCt	p.L8P	WFDC10B_ENST00000335769.2_Intron	NM_172006.2	NP_742003.1	Q8IUB3	WF10B_HUMAN	WAP four-disulfide core domain 10B	8			L -> P (in dbSNP:rs232729). {ECO:0000269|PubMed:15489334}.			extracellular region (GO:0005576)	peptidase inhibitor activity (GO:0030414)			lung(2)|ovary(1)|stomach(1)	4		Myeloproliferative disorder(115;0.0122)				AACCAGGACAAGCAGCAGAGT	0.587													G|||	4254	0.849441	0.9697	0.7939	5008	,	,		21003	0.998		0.6113	False		,,,				2504	0.818				p.L8P		Atlas-SNP	.											.	WFDC10B	15	.	0			c.T23C						PASS	.	G	PRO/LEU,	3962,444	212.8+/-232.6	1791,380,32	132.0	106.0	114.0		23,	-0.1	0.0	20	dbSNP_79	114	5181,3419	502.6+/-375.7	1567,2047,686	yes	missense,intron	WFDC10B	NM_172006.2,NM_172131.2	98,	3358,2427,718	GG,GA,AA		39.7558,10.0772,29.7017	benign,	8/74,	44314609	9143,3863	2203	4300	6503	SO:0001583	missense	280664	exon3			AGGACAAGCAGCA	AF454506	CCDS13365.1, CCDS13366.1	20q13.12	2013-01-21			ENSG00000182931	ENSG00000182931		"""WAP four-disulfide core domain containing"""	20479	protein-coding gene	gene with protein product						12206714	Standard	NM_172006		Approved	WAP12	uc002xpb.3	Q8IUB3	OTTHUMG00000130227	ENST00000330523.5:c.23T>C	20.37:g.44314609A>G	ENSP00000327628:p.Leu8Pro	Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	141	140	0.992908	NM_172006	A6PVD7|Q0VAG0|Q0VAG1|Q5TGZ5|Q8IUB4	Missense_Mutation	SNP	ENST00000330523.5	37	CCDS13366.1	1791	0.820054945054945	474	0.9634146341463414	285	0.787292817679558	572	1.0	460	0.6068601583113457	G	0.010	-1.757873	0.00657	0.899228	0.602442	ENSG00000182931	ENST00000330523	T	0.36878	1.23	3.12	-0.113	0.13568	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.38243	-0.9670	7	0.02654	T	1	.	3.4716	0.07569	0.3654:0.1985:0.4361:0.0	rs232729;rs60177823	8	Q8IUB3	WF10B_HUMAN	P	8	ENSP00000327628:L8P	ENSP00000327628:L8P	L	-	2	0	WFDC10B	43748023	0.000000	0.05858	0.001000	0.08648	0.011000	0.07611	-0.403000	0.07214	-0.216000	0.10048	-0.355000	0.07637	CTT	A|0.257;G|0.743	0.743	strong		0.587	WFDC10B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252547.1		
PCDHB7	56129	hgsc.bcm.edu	37	5	140553917	140553917	+	Missense_Mutation	SNP	G	G	A	rs17844455|rs386692906	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:140553917G>A	ENST00000231137.3	+	1	1675	c.1501G>A	c.(1501-1503)Gcc>Acc	p.A501T		NM_018940.2	NP_061763.1	Q9Y5E2	PCDB7_HUMAN	protocadherin beta 7	501	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)			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)			CCTGCCCCTCGCCTCCCTGGT	0.677													G|||	759	0.151558	0.2572	0.1902	5008	,	,		16812	0.0417		0.1531	False		,,,				2504	0.093				p.A501T		Atlas-SNP	.											.	PCDHB7	231	.	0			c.G1501A						PASS	.	G	THR/ALA	1024,3382	361.4+/-315.7	114,796,1293	85.0	88.0	87.0		1501	-1.2	0.0	5	dbSNP_123	87	1416,7184	259.8+/-282.9	120,1176,3004	no	missense	PCDHB7	NM_018940.2	58	234,1972,4297	AA,AG,GG		16.4651,23.241,18.7606	benign	501/794	140553917	2440,10566	2203	4300	6503	SO:0001583	missense	56129	exon1			CCCCTCGCCTCCC	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.1501G>A	5.37:g.140553917G>A	ENSP00000231137:p.Ala501Thr	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	103	51	0.495146	NM_018940	A1L3Y8	Missense_Mutation	SNP	ENST00000231137.3	37	CCDS4249.1	327	0.14972527472527472	121	0.2459349593495935	63	0.17403314917127072	26	0.045454545454545456	117	0.15435356200527706	g	4.524	0.097227	0.08681	0.23241	0.164651	ENSG00000113212	ENST00000231137;ENST00000543636	T	0.03181	4.02	4.34	-1.25	0.09405	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.00012	0.0000	N	0.13003	0.285	0.51482	P	7.40000000000185E-5	B	0.31519	0.327	B	0.24394	0.053	T	0.49293	-0.8955	8	0.38643	T	0.18	.	2.328	0.04228	0.1632:0.1009:0.3896:0.3463	rs17844455	501	Q9Y5E2	PCDB7_HUMAN	T	501;284	ENSP00000231137:A501T	ENSP00000231137:A501T	A	+	1	0	PCDHB7	140534101	0.000000	0.05858	0.009000	0.14445	0.023000	0.10783	-1.352000	0.02619	0.062000	0.16340	-0.261000	0.10672	GCC	G|0.825;A|0.175	0.175	strong		0.677	PCDHB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251803.2	NM_018940	
TACC3	10460	hgsc.bcm.edu	37	4	1730215	1730215	+	Silent	SNP	C	C	G	rs798757	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:1730215C>G	ENST00000313288.4	+	4	1192	c.1086C>G	c.(1084-1086)ggC>ggG	p.G362G		NM_006342.2	NP_006333.1	Q9Y6A5	TACC3_HUMAN	transforming, acidic coiled-coil containing protein 3	362					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)			AGAGGTCCGGCCTCAAGCCTC	0.612													C|||	682	0.136182	0.1914	0.1225	5008	,	,		19034	0.0119		0.1759	False		,,,				2504	0.1585				p.G362G	Ovarian(120;482 2294 11894 35824)	Atlas-SNP	.											.	TACC3	69	.	0			c.C1086G						PASS	.	C		873,3533	335.5+/-303.9	100,673,1430	52.0	61.0	58.0		1086	0.7	0.0	4	dbSNP_86	58	1734,6866	310.2+/-309.8	180,1374,2746	no	coding-synonymous	TACC3	NM_006342.1		280,2047,4176	GG,GC,CC		20.1628,19.8139,20.0446		362/839	1730215	2607,10399	2203	4300	6503	SO:0001819	synonymous_variant	10460	exon4			GTCCGGCCTCAAG	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.1086C>G	4.37:g.1730215C>G		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	121	71	0.586777	NM_006342	Q2NKK4|Q3KQS5|Q9UMQ1	Silent	SNP	ENST00000313288.4	37	CCDS3352.1	275	0.1259157509157509	89	0.18089430894308944	47	0.1298342541436464	8	0.013986013986013986	131	0.17282321899736147	C	3.894	-0.023378	0.07634	0.198139	0.201628	ENSG00000013810	ENST00000470136	.	.	.	4.1	0.669	0.17918	.	.	.	.	.	T	0.00039	0.0001	.	.	.	0.58432	P	2.9999999999752447E-6	.	.	.	.	.	.	T	0.20107	-1.0285	3	.	.	.	-2.1506	3.3079	0.07006	0.29:0.3119:0.0:0.3981	rs798757;rs1665369;rs798757	.	.	.	A	29	.	.	P	+	1	0	TACC3	1700013	0.000000	0.05858	0.010000	0.14722	0.039000	0.13416	0.159000	0.16442	0.190000	0.20209	-0.373000	0.07131	CCT	C|0.830;G|0.170	0.170	strong		0.612	TACC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000203730.2		
ZNF560	147741	hgsc.bcm.edu	37	19	9580305	9580305	+	Splice_Site	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:9580305C>T	ENST00000301480.4	-	8	743		c.e8+1			NM_152476.2	NP_689689.2	Q96MR9	ZN560_HUMAN	zinc finger protein 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)			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						CAAACACTCACCTTGGAGAAC	0.458																																					.		Atlas-SNP	.											.	ZNF560	162	.	0			c.529+1G>A						PASS	.						123.0	103.0	110.0					19																	9580305		2203	4300	6503	SO:0001630	splice_region_variant	147741	exon9			CACTCACCTTGGA	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.529+1G>A	19.37:g.9580305C>T		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	89	4	0.0449438	NM_152476	Q495S9|Q495T1	Splice_Site	SNP	ENST00000301480.4	37	CCDS12214.1	.	.	.	.	.	.	.	.	.	.	C	13.81	2.348351	0.41599	.	.	ENSG00000198028	ENST00000301480	.	.	.	1.87	0.737	0.18314	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	7.3266	0.26560	0.2623:0.7377:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	ZNF560	9441305	0.001000	0.12720	0.544000	0.28141	0.588000	0.36517	0.273000	0.18662	0.301000	0.22738	0.462000	0.41574	.	.	.	none		0.458	ZNF560-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449901.1	NM_152476	Intron
BHLHE40	8553	hgsc.bcm.edu	37	3	5024771	5024771	+	Silent	SNP	T	T	C	rs908078	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	71	0	0		WXS	Illumina HiSeq	Phase_I	64	38	0.59375	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	
IPO4	79711	hgsc.bcm.edu	37	14	24653954	24653954	+	Missense_Mutation	SNP	G	G	A	rs7146310	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:24653954G>A	ENST00000354464.6	-	16	1714	c.1538C>T	c.(1537-1539)gCc>gTc	p.A513V	RP11-468E2.2_ENST00000561419.1_3'UTR	NM_024658.3	NP_078934.3	Q8TEX9	IPO4_HUMAN	importin 4	513			A -> V (in dbSNP:rs7146310). {ECO:0000269|PubMed:11823430, ECO:0000269|PubMed:14702039}.		DNA replication-dependent nucleosome assembly (GO:0006335)|DNA replication-independent nucleosome assembly (GO:0006336)|intracellular protein transport (GO:0006886)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|protein complex (GO:0043234)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|lung(10)|ovary(1)|stomach(2)|urinary_tract(1)	33				GBM - Glioblastoma multiforme(265;0.0087)		CAGCAGCGAGGCCTGGGCAGC	0.622													G|||	1592	0.317891	0.2163	0.2363	5008	,	,		18141	0.4206		0.2654	False		,,,				2504	0.4611				p.A513V		Atlas-SNP	.											IPO4,NS,carcinoma,+1,1	IPO4	74	1	0			c.C1538T						PASS	.	G	VAL/ALA	911,3223		105,701,1261	21.0	26.0	24.0		1538	3.3	1.0	14	dbSNP_116	24	2400,5978		321,1758,2110	yes	missense	IPO4	NM_024658.3	64	426,2459,3371	AA,AG,GG		28.6465,22.0368,26.4626	benign	513/1082	24653954	3311,9201	2067	4189	6256	SO:0001583	missense	79711	exon16			AGCGAGGCCTGGG	AF411122	CCDS9616.1	14q11.2	2003-03-10			ENSG00000196497	ENSG00000196497		"""Importins"""	19426	protein-coding gene	gene with protein product						11823430	Standard	NR_051979		Approved	Imp4, FLJ23338	uc001wmv.1	Q8TEX9	OTTHUMG00000028801	ENST00000354464.6:c.1538C>T	14.37:g.24653954G>A	ENSP00000346453:p.Ala513Val	Somatic	190	0	0		WXS	Illumina HiSeq	Phase_I	224	109	0.486607	NM_024658	B2RN95|Q2NL96|Q86TZ9|Q8NCG8|Q96SJ3|Q9BTI4|Q9H5L0	Missense_Mutation	SNP	ENST00000354464.6	37	CCDS9616.1	648	0.2967032967032967	106	0.21544715447154472	94	0.2596685082872928	249	0.4353146853146853	199	0.262532981530343	G	14.34	2.506634	0.44558	0.220368	0.286465	ENSG00000196497	ENST00000354464;ENST00000399536	T	0.04654	3.58	5.28	3.32	0.38043	Armadillo-like helical (1);Armadillo-type fold (1);	0.612691	0.17322	N	0.178468	T	0.00012	0.0000	N	0.17474	0.49	0.46317	P	0.0010149999999999881	B	0.09022	0.002	B	0.16722	0.016	T	0.43925	-0.9361	9	0.51188	T	0.08	-1.7252	7.6189	0.28173	0.0:0.1498:0.4235:0.4267	rs7146310;rs17256720;rs61234434;rs7146310	513	Q8TEX9	IPO4_HUMAN	V	513;189	ENSP00000346453:A513V	ENSP00000346453:A513V	A	-	2	0	IPO4	23723794	1.000000	0.71417	1.000000	0.80357	0.819000	0.46315	1.072000	0.30678	1.412000	0.46977	0.558000	0.71614	GCC	G|0.693;A|0.307	0.307	strong		0.622	IPO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071931.4	NM_024658	
ENGASE	64772	hgsc.bcm.edu	37	17	77076302	77076302	+	Silent	SNP	G	G	A	rs62063824	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:77076302G>A	ENST00000579016.1	+	5	579	c.579G>A	c.(577-579)acG>acA	p.T193T	ENGASE_ENST00000539857.2_Silent_p.T7T	NM_001042573.2	NP_001036038.1	Q8NFI3	ENASE_HUMAN	endo-beta-N-acetylglucosaminidase	193						cytoplasm (GO:0005737)	mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase activity (GO:0033925)			breast(2)|endometrium(4)|large_intestine(1)|lung(15)|prostate(2)|skin(1)	25						CTTTCATCACGGAGTGGAATG	0.557													G|||	170	0.0339457	0.0182	0.0648	5008	,	,		20091	0.001		0.0795	False		,,,				2504	0.0204				p.T193T		Atlas-SNP	.											.	ENGASE	55	.	0			c.G579A						PASS	.	G		70,3862		0,70,1896	49.0	52.0	51.0		579	-7.9	0.8	17	dbSNP_129	51	596,7722		23,550,3586	no	coding-synonymous	ENGASE	NM_001042573.1		23,620,5482	AA,AG,GG		7.1652,1.7803,5.4367		193/744	77076302	666,11584	1966	4159	6125	SO:0001819	synonymous_variant	64772	exon5			CATCACGGAGTGG	AF512564	CCDS42394.1	17q25.3	2009-03-03			ENSG00000167280	ENSG00000167280	3.2.1.96		24622	protein-coding gene	gene with protein product	"""Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase"", ""Di-N-acetylchitobiosyl beta-N-acetylglucosaminidase"""	611898				12114544, 18586680	Standard	NM_001042573		Approved	FLJ21865	uc002jwv.4	Q8NFI3	OTTHUMG00000167714	ENST00000579016.1:c.579G>A	17.37:g.77076302G>A		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	40	19	0.475	NM_001042573	Q659F0|Q8TB86|Q9H6U4	Silent	SNP	ENST00000579016.1	37	CCDS42394.1																																																																																			G|0.941;A|0.059	0.059	strong		0.557	ENGASE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395807.1	NM_022759	
KCNQ2	3785	hgsc.bcm.edu	37	20	62046278	62046278	+	Silent	SNP	G	G	C	rs1801545	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:62046278G>C	ENST00000359125.2	-	13	1677	c.1503C>G	c.(1501-1503)gcC>gcG	p.A501A	KCNQ2_ENST00000360480.3_Silent_p.A473A|KCNQ2_ENST00000354587.3_Silent_p.A473A|KCNQ2_ENST00000357249.2_Silent_p.A483A|KCNQ2_ENST00000359689.1_Silent_p.A501A|KCNQ2_ENST00000370224.1_Silent_p.A473A|KCNQ2_ENST00000344462.4_Silent_p.A471A	NM_172107.2	NP_742105.1	O43526	KCNQ2_HUMAN	potassium voltage-gated channel, KQT-like subfamily, member 2	501					axon guidance (GO:0007411)|nervous system development (GO:0007399)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)|transmission of nerve impulse (GO:0019226)	axon initial segment (GO:0043194)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	ankyrin binding (GO:0030506)|delayed rectifier potassium channel activity (GO:0005251)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)			biliary_tract(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(4)|liver(1)|lung(30)|ovary(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	65	all_cancers(38;1.24e-11)		BRCA - Breast invasive adenocarcinoma(10;1.04e-05)		Amitriptyline(DB00321)|Diclofenac(DB00586)|Ezogabine(DB04953)|Meclofenamic acid(DB00939)	GCCGTGACGCGGCACCCTTGA	0.672													G|||	347	0.0692891	0.143	0.072	5008	,	,		10683	0.0		0.0905	False		,,,				2504	0.0174				p.A501A		Atlas-SNP	.											.	KCNQ2	201	.	0			c.C1503G						PASS	.	G	,,,	593,3813	255.8+/-260.9	42,509,1652	70.0	79.0	76.0		1419,1449,1503,1413	-6.3	0.4	20	dbSNP_89	76	754,7846	179.0+/-228.3	29,696,3575	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	KCNQ2	NM_004518.4,NM_172106.1,NM_172107.2,NM_172108.3	,,,	71,1205,5227	CC,CG,GG		8.7674,13.4589,10.3568	,,,	473/845,483/855,501/873,471/842	62046278	1347,11659	2203	4300	6503	SO:0001819	synonymous_variant	3785	exon13			TGACGCGGCACCC	AF033348	CCDS13518.1, CCDS13519.1, CCDS13520.1, CCDS13521.1, CCDS46629.1	20q13.33	2012-07-05			ENSG00000075043	ENSG00000075043		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6296	protein-coding gene	gene with protein product		602235		EBN, EBN1		9425895, 16382104	Standard	NM_172107		Approved	Kv7.2, ENB1, BFNC, KCNA11, HNSPC	uc002yex.3	O43526	OTTHUMG00000033049	ENST00000359125.2:c.1503C>G	20.37:g.62046278G>C		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	122	59	0.483607	NM_172107	O43796|O75580|O95845|Q4VXP4|Q4VXR6|Q5VYT8|Q96J59|Q99454	Silent	SNP	ENST00000359125.2	37	CCDS13520.1																																																																																			G|0.911;C|0.089;A|0.000	0.089	strong		0.672	KCNQ2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080353.1	NM_172109	
TEP1	7011	hgsc.bcm.edu	37	14	20850156	20850156	+	Missense_Mutation	SNP	C	C	G	rs1713457	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:20850156C>G	ENST00000262715.5	-	30	4380	c.4340G>C	c.(4339-4341)aGc>aCc	p.S1447T	TEP1_ENST00000545983.1_5'UTR|TEP1_ENST00000556935.1_Missense_Mutation_p.S1339T	NM_007110.4	NP_009041.2	Q99973	TEP1_HUMAN	telomerase-associated protein 1	1447	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.		S -> T (in dbSNP:rs1713457).		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)		TTCTTCCCAGCTCTTAGTCCC	0.592													C|||	446	0.0890575	0.1982	0.0706	5008	,	,		19196	0.0486		0.0268	False		,,,				2504	0.0603				p.S1447T		Atlas-SNP	.											.	TEP1	224	.	0			c.G4340C						PASS	.	C	THR/SER	757,3649	310.5+/-291.6	62,633,1508	162.0	134.0	144.0		4340	-3.7	0.1	14	dbSNP_89	144	275,8325	104.4+/-165.4	1,273,4026	yes	missense	TEP1	NM_007110.4	58	63,906,5534	GG,GC,CC		3.1977,17.1811,7.9348	benign	1447/2628	20850156	1032,11974	2203	4300	6503	SO:0001583	missense	7011	exon30			TCCCAGCTCTTAG		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.4340G>C	14.37:g.20850156C>G	ENSP00000262715:p.Ser1447Thr	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	96	46	0.479167	NM_007110	A0AUV9	Missense_Mutation	SNP	ENST00000262715.5	37	CCDS9548.1	156	0.07142857142857142	90	0.18292682926829268	26	0.0718232044198895	20	0.03496503496503497	20	0.026385224274406333	C	6.723	0.502049	0.12822	0.171811	0.031977	ENSG00000129566	ENST00000262715;ENST00000359243;ENST00000556935	T;T	0.45668	0.93;0.89	5.22	-3.69	0.04450	.	0.753564	0.14050	N	0.344805	T	0.00039	0.0001	N	0.13043	0.29	0.34826	P	0.26081299999999996	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.08055	0.002;0.003;0.001	T	0.28964	-1.0027	9	0.13853	T	0.58	-0.9835	6.3296	0.21262	0.168:0.6276:0.128:0.0764	rs1713457;rs2228031;rs52809808;rs1713457	1339;790;1447	G3V5X7;G3V2A4;Q99973	.;.;TEP1_HUMAN	T	1447;1447;1339	ENSP00000262715:S1447T;ENSP00000452574:S1339T	ENSP00000262715:S1447T	S	-	2	0	TEP1	19919996	0.000000	0.05858	0.057000	0.19452	0.714000	0.41099	-1.161000	0.03144	-0.549000	0.06191	-0.521000	0.04368	AGC	C|0.928;G|0.072	0.072	strong		0.592	TEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073563.2	NM_007110	
OTOL1	131149	hgsc.bcm.edu	37	3	161221705	161221705	+	Missense_Mutation	SNP	A	A	C	rs3921595	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:161221705A>C	ENST00000327928.4	+	4	1409	c.1409A>C	c.(1408-1410)gAg>gCg	p.E470A		NM_001080440.1	NP_001073909.1	A6NHN0	OTOL1_HUMAN	otolin 1	470	C1q. {ECO:0000255|PROSITE- ProRule:PRU00368}.		E -> A (in dbSNP:rs3921595).			collagen trimer (GO:0005581)|extracellular region (GO:0005576)				central_nervous_system(2)|kidney(2)|large_intestine(8)|lung(11)|ovary(1)|prostate(2)|skin(1)	27						TTGTACCCAGAGGAAACTTCT	0.403													A|||	2467	0.492612	0.6475	0.4222	5008	,	,		15058	0.2708		0.4662	False		,,,				2504	0.589				p.E470A		Atlas-SNP	.											.	OTOL1	63	.	0			c.A1409C						PASS	.	A	ALA/GLU	2213,1465		661,891,287	39.0	37.0	38.0		1409	2.9	0.8	3	dbSNP_108	38	3848,4324		952,1944,1190	yes	missense	OTOL1	NM_001080440.1	107	1613,2835,1477	CC,CA,AA		47.0876,39.8314,48.8523	possibly-damaging	470/478	161221705	6061,5789	1839	4086	5925	SO:0001583	missense	131149	exon4			ACCCAGAGGAAAC		CCDS46948.1	3q26.1	2011-05-19	2011-05-19			ENSG00000182447			34071	protein-coding gene	gene with protein product	"""C1q and tumor necrosis factor related protein 15"""		"""otolin 1 homolog (zebrafish)"""			17544811, 15905077	Standard	NM_001080440		Approved	C1QTNF15	uc011bpb.2	A6NHN0		ENST00000327928.4:c.1409A>C	3.37:g.161221705A>C	ENSP00000330808:p.Glu470Ala	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	91	38	0.417582	NM_001080440		Missense_Mutation	SNP	ENST00000327928.4	37	CCDS46948.1	936	0.42857142857142855	296	0.6016260162601627	160	0.4419889502762431	137	0.2395104895104895	343	0.4525065963060686	A	14.38	2.516747	0.44763	0.601686	0.470876	ENSG00000182447	ENST00000327928	D	0.90900	-2.75	5.27	2.86	0.33363	Tumour necrosis factor-like (1);Complement C1q protein (2);	0.110601	0.64402	D	0.000020	T	0.00012	0.0000	L	0.46157	1.445	0.37143	P	0.09820200000000001	D	0.57257	0.979	P	0.49999	0.628	T	0.44236	-0.9341	9	0.66056	D	0.02	.	8.76	0.34669	0.8423:0.0:0.1577:0.0	rs3921595;rs61139900;rs3921595	470	A6NHN0	OTOL1_HUMAN	A	470	ENSP00000330808:E470A	ENSP00000330808:E470A	E	+	2	0	OTOL1	162704399	1.000000	0.71417	0.771000	0.31576	0.810000	0.45777	5.600000	0.67599	0.323000	0.23307	0.456000	0.33151	GAG	A|0.541;C|0.459	0.459	strong		0.403	OTOL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353184.1	NM_001080440	
TRPC4AP	26133	hgsc.bcm.edu	37	20	33587596	33587596	+	IGR	SNP	G	G	A	rs80109502	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:33587596G>A	ENST00000252015.2	-	0	3226				MYH7B_ENST00000262873.7_Silent_p.G1598G			Q8TEL6	TP4AP_HUMAN	transient receptor potential cation channel, subfamily C, member 4 associated protein						calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|protein ubiquitination (GO:0016567)|transmembrane transport (GO:0055085)|ubiquitin-dependent protein catabolic process (GO:0006511)	Cul4A-RING E3 ubiquitin ligase complex (GO:0031464)|plasma membrane (GO:0005886)	phosphatase binding (GO:0019902)			breast(3)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(13)|skin(1)|stomach(1)|urinary_tract(1)	32			BRCA - Breast invasive adenocarcinoma(18;0.00936)			ATCCACAGGGGGCCCTGGAGC	0.652													G|||	403	0.0804712	0.0537	0.0663	5008	,	,		12422	0.0853		0.0875	False		,,,				2504	0.1145				p.G1598G		Atlas-SNP	.											.	MYH7B	145	.	0			c.G4794A						PASS	.	G		198,3606		4,190,1708	36.0	42.0	40.0		4794	1.4	1.0	20	dbSNP_131	40	759,7481		38,683,3399	no	coding-synonymous	MYH7B	NM_020884.3		42,873,5107	AA,AG,GG		9.2112,5.205,7.9459		1598/1984	33587596	957,11087	1902	4120	6022	SO:0001628	intergenic_variant	57644	exon38			ACAGGGGGCCCTG	AF055022	CCDS13246.1, CCDS46591.1	20q11.23	2014-06-13	2003-10-06	2003-10-08	ENSG00000100991	ENSG00000100991			16181	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 158"""	608430	"""chromosome 20 open reading frame 188"""	C20orf188			Standard	NM_015638		Approved	DKFZP727M231, DKFZp586C1223, dJ756N5.2, TRRP4AP, PPP1R158	uc002xbk.3	Q8TEL6	OTTHUMG00000032319		20.37:g.33587596G>A		Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	58	24	0.413793	NM_020884	E1P5Q0|E1P5Q1|Q96H82|Q9BVB8|Q9H429|Q9UFS6	Silent	SNP	ENST00000252015.2	37	CCDS13246.1																																																																																			G|0.921;A|0.079	0.079	strong		0.652	TRPC4AP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078832.2	NM_015638	
SLC38A7	55238	hgsc.bcm.edu	37	16	58713798	58713798	+	Missense_Mutation	SNP	G	G	A	rs7191331	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:58713798G>A	ENST00000570101.1	-	2	1116	c.233C>T	c.(232-234)aCt>aTt	p.T78I	SLC38A7_ENST00000219320.4_Missense_Mutation_p.T78I|SLC38A7_ENST00000564391.1_Missense_Mutation_p.T78I|SLC38A7_ENST00000566953.1_Intron|SLC38A7_ENST00000564010.1_Intron|SLC38A7_ENST00000564100.1_Missense_Mutation_p.T78I			Q9NVC3	S38A7_HUMAN	solute carrier family 38, member 7	78			T -> I (in dbSNP:rs7191331).		sodium ion transport (GO:0006814)	axon (GO:0030424)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)	L-alanine transmembrane transporter activity (GO:0015180)|L-amino acid transmembrane transporter activity (GO:0015179)|L-asparagine transmembrane transporter activity (GO:0015182)|L-aspartate transmembrane transporter activity (GO:0015183)|L-glutamate transmembrane transporter activity (GO:0005313)|L-glutamine transmembrane transporter activity (GO:0015186)|L-histidine transmembrane transporter activity (GO:0005290)|L-leucine transmembrane transporter activity (GO:0015190)|L-methionine transmembrane transporter activity (GO:0015191)|L-serine transmembrane transporter activity (GO:0015194)			endometrium(1)|large_intestine(2)|lung(6)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	13						GCCCCCCGCAGTGCTGAAGGC	0.622													G|||	564	0.11262	0.0998	0.0778	5008	,	,		19815	0.0228		0.1948	False		,,,				2504	0.1626				p.T78I		Atlas-SNP	.											SLC38A7,NS,carcinoma,0,1	SLC38A7	26	1	0			c.C233T						PASS	.	G	ILE/THR	510,3886	234.6+/-247.4	40,430,1728	47.0	44.0	45.0		233	5.9	0.9	16	dbSNP_116	45	1671,6929	304.9+/-307.2	165,1341,2794	yes	missense	SLC38A7	NM_018231.1	89	205,1771,4522	AA,AG,GG		19.4302,11.6015,16.7821	benign	78/463	58713798	2181,10815	2198	4300	6498	SO:0001583	missense	55238	exon3			CCCGCAGTGCTGA	BC001961	CCDS10800.1	16q21	2013-05-22			ENSG00000103042	ENSG00000103042		"""Solute carriers"""	25582	protein-coding gene	gene with protein product		614236					Standard	XM_006721229		Approved	FLJ10815	uc002eod.1	Q9NVC3	OTTHUMG00000133491	ENST00000570101.1:c.233C>T	16.37:g.58713798G>A	ENSP00000454646:p.Thr78Ile	Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	63	25	0.396825	NM_018231	Q53GJ9|Q9H9I5	Missense_Mutation	SNP	ENST00000570101.1	37	CCDS10800.1	253	0.11584249084249085	56	0.11382113821138211	32	0.08839779005524862	13	0.022727272727272728	152	0.20052770448548812	G	10.74	1.434544	0.25813	0.116015	0.194302	ENSG00000103042	ENST00000219320	T	0.02301	4.35	5.91	5.91	0.95273	.	0.257812	0.49916	D	0.000130	T	0.00012	0.0000	N	0.08118	0	0.31568	P	0.656709	B;B	0.12630	0.005;0.006	B;B	0.15870	0.013;0.014	T	0.58137	-0.7689	8	.	.	.	.	12.4954	0.55925	0.0836:0.0:0.9164:0.0	rs7191331;rs17419846;rs57824527;rs7191331	78;78	Q9NVC3;Q9NVC3-2	S38A7_HUMAN;.	I	78	ENSP00000219320:T78I	.	T	-	2	0	SLC38A7	57271299	0.991000	0.36638	0.916000	0.36221	0.010000	0.07245	2.320000	0.43797	2.813000	0.96785	0.655000	0.94253	ACT	G|0.855;A|0.145	0.145	strong		0.622	SLC38A7-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422206.2	NM_018231	
ARHGAP35	2909	hgsc.bcm.edu	37	19	47424071	47424071	+	Silent	SNP	T	T	C	rs2228163	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:47424071T>C	ENST00000404338.3	+	1	2139	c.2139T>C	c.(2137-2139)acT>acC	p.T713T		NM_004491.4	NP_004482.4	Q9NRY4	RHG35_HUMAN	Rho GTPase activating protein 35	713					axon guidance (GO:0007411)|camera-type eye development (GO:0043010)|forebrain development (GO:0030900)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of vascular permeability (GO:0043116)|neural tube closure (GO:0001843)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|transcription, DNA-templated (GO:0006351)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|nucleus (GO:0005634)	DNA binding (GO:0003677)|GTP binding (GO:0005525)|Rho GTPase activator activity (GO:0005100)|transcription corepressor activity (GO:0003714)										GTGGAGAGACTCTGCATAGCT	0.468													T|||	61	0.0121805	0.0	0.0216	5008	,	,		21125	0.0		0.0249	False		,,,				2504	0.0215				p.T713T		Atlas-SNP	.											.	.	.	.	0			c.T2139C						PASS	.	T		18,3976		0,18,1979	51.0	50.0	50.0		2139	-2.5	1.0	19	dbSNP_98	50	251,8085		4,243,3921	no	coding-synonymous	ARHGAP35	NM_004491.4		4,261,5900	CC,CT,TT		3.011,0.4507,2.1817		713/1500	47424071	269,12061	1997	4168	6165	SO:0001819	synonymous_variant	2909	exon1			AGAGACTCTGCAT	M73077	CCDS46127.1	19q13.32	2011-06-29	2011-06-07	2011-06-07	ENSG00000160007	ENSG00000160007		"""Rho GTPase activating proteins"""	4591	protein-coding gene	gene with protein product		605277	"""glucocorticoid receptor DNA binding factor 1"""	GRLF1		1894621, 20675588	Standard	NM_004491		Approved	GRF-1, p190ARhoGAP, P190A, KIAA1722, p190RhoGAP	uc010ekv.3	Q9NRY4		ENST00000404338.3:c.2139T>C	19.37:g.47424071T>C		Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	136	65	0.477941	NM_004491	A7E2A4|Q14452|Q9C0E1	Silent	SNP	ENST00000404338.3	37	CCDS46127.1																																																																																			T|0.985;C|0.015	0.015	strong		0.468	ARHGAP35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466652.1	NM_004491	
CD207	50489	hgsc.bcm.edu	37	2	71060936	71060936	+	Missense_Mutation	SNP	G	G	C	rs17718987	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:71060936G>C	ENST00000410009.3	-	3	451	c.406C>G	c.(406-408)Cag>Gag	p.Q136E		NM_015717.3	NP_056532	Q9UJ71	CLC4K_HUMAN	CD207 molecule, langerin	136			Q -> E (in dbSNP:rs17718987).		antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|defense response to virus (GO:0051607)	clathrin-coated endocytic vesicle membrane (GO:0030669)|early endosome membrane (GO:0031901)|endocytic vesicle (GO:0030139)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|mannose binding (GO:0005537)			endometrium(1)|kidney(2)|large_intestine(2)|lung(13)|ovary(1)|stomach(1)	20						ATCTGGATCTGTGCGTTGGCC	0.453													G|||	662	0.132188	0.0234	0.1873	5008	,	,		19941	0.004		0.3022	False		,,,				2504	0.1973				p.Q136E		Atlas-SNP	.											.	CD207	47	.	0			c.C406G						PASS	.	G	GLU/GLN	285,3627		10,265,1681	129.0	119.0	123.0		406	0.2	0.0	2	dbSNP_123	123	2538,5768		381,1776,1996	yes	missense	CD207	NM_015717.3	29	391,2041,3677	CC,CG,GG		30.5562,7.2853,23.1053	benign	136/329	71060936	2823,9395	1956	4153	6109	SO:0001583	missense	50489	exon3			GGATCTGTGCGTT	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.406C>G	2.37:g.71060936G>C	ENSP00000386378:p.Gln136Glu	Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	155	155	1	NM_015717		Missense_Mutation	SNP	ENST00000410009.3	37		336	0.15384615384615385	19	0.03861788617886179	90	0.24861878453038674	0	0.0	227	0.2994722955145119	G	1.932	-0.445778	0.04604	0.072853	0.305562	ENSG00000116031	ENST00000410009	T	0.24538	1.85	4.23	0.188	0.15114	.	0.565043	0.16340	N	0.218737	T	0.00012	0.0000	L	0.35593	1.075	0.80722	P	0.0	B	0.14438	0.01	B	0.06405	0.002	T	0.40098	-0.9581	9	0.02654	T	1	.	14.0425	0.64684	0.0:0.6296:0.3704:0.0	rs17718987;rs17718987	136	Q9UJ71	CLC4K_HUMAN	E	136	ENSP00000386378:Q136E	ENSP00000386378:Q136E	Q	-	1	0	CD207	70914444	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	0.668000	0.25127	0.021000	0.15133	-0.175000	0.13238	CAG	G|0.841;C|0.159	0.159	strong		0.453	CD207-001	KNOWN	non_canonical_conserved|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000329959.4	NM_015717	
CHGB	1114	hgsc.bcm.edu	37	20	5903323	5903323	+	Missense_Mutation	SNP	G	G	A	rs910122	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:5903323G>A	ENST00000378961.4	+	4	737	c.533G>A	c.(532-534)cGa>cAa	p.R178Q		NM_001819.2	NP_001810.2	P05060	SCG1_HUMAN	chromogranin B (secretogranin 1)	178			R -> Q (in dbSNP:rs910122). {ECO:0000269|PubMed:14702039, ECO:0000269|Ref.4}.			extracellular region (GO:0005576)|secretory granule (GO:0030141)	hormone activity (GO:0005179)			breast(7)|kidney(2)|large_intestine(8)|lung(19)|ovary(1)|pancreas(2)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)	47						AAAGGGGAGCGAGGGGAAGAT	0.473													G|||	2086	0.416534	0.2995	0.4942	5008	,	,		20215	0.5288		0.3489	False		,,,				2504	0.4734				p.R178Q		Atlas-SNP	.											CHGB,colon,carcinoma,+1,1	CHGB	112	1	0			c.G533A						PASS	.	G	GLN/ARG	1478,2928	473.5+/-356.7	260,958,985	88.0	89.0	89.0		533	-11.1	0.0	20	dbSNP_86	89	3075,5525	469.6+/-367.6	549,1977,1774	yes	missense	CHGB	NM_001819.2	43	809,2935,2759	AA,AG,GG		35.7558,33.5452,35.0069	benign	178/678	5903323	4553,8453	2203	4300	6503	SO:0001583	missense	1114	exon4			GGGAGCGAGGGGA		CCDS13092.1	20p12.3	2013-09-19			ENSG00000089199	ENSG00000089199			1930	protein-coding gene	gene with protein product	"""secretogranin B"""	118920		SCG1		3608978	Standard	NM_001819		Approved		uc002wmg.3	P05060	OTTHUMG00000031821	ENST00000378961.4:c.533G>A	20.37:g.5903323G>A	ENSP00000368244:p.Arg178Gln	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	65	34	0.523077	NM_001819	A8K021|Q59EU9|Q6IBS6|Q9BQV6|Q9UC25|Q9UJA6	Missense_Mutation	SNP	ENST00000378961.4	37	CCDS13092.1	886	0.4056776556776557	171	0.3475609756097561	155	0.4281767955801105	295	0.5157342657342657	265	0.3496042216358839	G	5.054	0.195656	0.09599	0.335452	0.357558	ENSG00000089199	ENST00000378961;ENST00000455042	T;T	0.01821	4.62;4.62	5.57	-11.1	0.00147	.	1.782560	0.03085	N	0.159015	T	0.00012	0.0000	L	0.36672	1.1	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.48570	-0.9024	9	0.19147	T	0.46	3.7714	1.6706	0.02810	0.4906:0.1907:0.1291:0.1896	rs910122;rs52803541;rs57501504;rs910122	178	P05060	SCG1_HUMAN	Q	178;158	ENSP00000368244:R178Q;ENSP00000416643:R158Q	ENSP00000368244:R178Q	R	+	2	0	CHGB	5851323	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.898000	0.01602	-4.738000	0.00034	-2.619000	0.00157	CGA	G|0.631;A|0.369	0.369	strong		0.473	CHGB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077897.2	NM_001819	
MTCL1	23255	hgsc.bcm.edu	37	18	8784723	8784723	+	Missense_Mutation	SNP	A	A	G	rs3744979	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:8784723A>G	ENST00000306329.11	+	5	2693	c.2693A>G	c.(2692-2694)gAt>gGt	p.D898G	SOGA2_ENST00000400050.3_Missense_Mutation_p.D538G|SOGA2_ENST00000517570.1_Missense_Mutation_p.D538G|SOGA2_ENST00000359865.3_Missense_Mutation_p.D538G|SOGA2_ENST00000306285.7_5'UTR																							CGCATTGGGGATGGCCTATCC	0.612													A|||	840	0.167732	0.1944	0.0908	5008	,	,		16765	0.2907		0.1451	False		,,,				2504	0.0828				p.D538G		Atlas-SNP	.											.	.	.	.	0			c.A1613G						PASS	.	A	GLY/ASP	775,3631	312.2+/-292.5	75,625,1503	86.0	84.0	85.0		1613	3.8	0.9	18	dbSNP_107	85	1297,7303	255.5+/-280.4	94,1109,3097	yes	missense	CCDC165	NM_015210.3	94	169,1734,4600	GG,GA,AA		15.0814,17.5897,15.9311	possibly-damaging	538/1587	8784723	2072,10934	2203	4300	6503	SO:0001583	missense	23255	exon6			TTGGGGATGGCCT																												ENST00000306329.11:c.2693A>G	18.37:g.8784723A>G	ENSP00000305027:p.Asp898Gly	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	60	30	0.5	NM_015210		Missense_Mutation	SNP	ENST00000306329.11	37		411	0.18818681318681318	93	0.18902439024390244	39	0.10773480662983426	171	0.29895104895104896	108	0.1424802110817942	A	9.424	1.083744	0.20309	0.175897	0.150814	ENSG00000168502	ENST00000306329;ENST00000517570;ENST00000359865;ENST00000400050	T;T;T	0.38722	1.12;1.12;1.12	4.95	3.77	0.43336	.	0.168819	0.28192	N	0.016243	T	0.00012	0.0000	L	0.46157	1.445	0.09310	P	1.0	P;P	0.51653	0.732;0.947	B;P	0.49708	0.325;0.62	T	0.21109	-1.0255	9	0.10902	T	0.67	-14.0025	11.0484	0.47872	0.8439:0.1561:0.0:0.0	rs3744979	559;538	A8MQ54;Q9Y4B5-3	.;.	G	559;538;538;538	ENSP00000429556:D538G;ENSP00000352927:D538G;ENSP00000382924:D538G	ENSP00000305027:D559G	D	+	2	0	CCDC165	8774723	1.000000	0.71417	0.859000	0.33776	0.826000	0.46750	7.404000	0.79996	0.714000	0.32081	0.533000	0.62120	GAT	A|0.838;G|0.162	0.162	strong		0.612	SOGA2-015	PUTATIVE	basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000444141.1		
KRT86	3892	hgsc.bcm.edu	37	12	52695754	52695754	+	Silent	SNP	C	C	T	rs74651927	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:52695754C>T	ENST00000423955.2	+	3	232	c.54C>T	c.(52-54)tgC>tgT	p.C18C	KRT86_ENST00000293525.5_Silent_p.C18C|KRT86_ENST00000544024.1_Silent_p.C18C			O43790	KRT86_HUMAN	keratin 86	18	Head.					extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			breast(1)|cervix(1)|large_intestine(1)|lung(5)|ovary(1)|skin(1)	10				BRCA - Breast invasive adenocarcinoma(357;0.189)		TCTCGGCCTGCGGGCCCCGGC	0.672													c|||	774	0.154553	0.171	0.1326	5008	,	,		11547	0.0883		0.1282	False		,,,				2504	0.2434				p.C18C		Atlas-SNP	.											.	KRT86	33	.	0			c.C54T						PASS	.	C		708,3584		50,608,1488	35.0	42.0	39.0		54	0.4	1.0	12	dbSNP_131	39	1253,7279		104,1045,3117	no	coding-synonymous	KRT86	NM_002284.3		154,1653,4605	TT,TC,CC		14.6859,16.4958,15.2916		18/487	52695754	1961,10863	2146	4266	6412	SO:0001819	synonymous_variant	3892	exon1			GGCCTGCGGGCCC	X99142	CCDS41785.1	12q13	2013-01-16	2006-07-17	2006-07-17		ENSG00000170442		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6463	protein-coding gene	gene with protein product	"""hard keratin type II 6"""	601928	"""keratin, hair, basic, 6 (monilethrix)"""	KRTHB6		9241275, 16831889	Standard	NM_002284		Approved	MNX, Hb6	uc001sad.3	O43790		ENST00000423955.2:c.54C>T	12.37:g.52695754C>T		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	66	37	0.560606	NM_002284	P78387	Silent	SNP	ENST00000423955.2	37	CCDS41785.1																																																																																			C|0.871;T|0.129	0.129	strong		0.672	KRT86-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404911.1	NM_002284	
ASIC4	55515	hgsc.bcm.edu	37	2	220402680	220402680	+	Missense_Mutation	SNP	T	T	C	rs11695248	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:220402680T>C	ENST00000347842.3	+	9	1870	c.1856T>C	c.(1855-1857)gTg>gCg	p.V619A	ASIC4_ENST00000358078.4_Missense_Mutation_p.V638A	NM_182847.2	NP_878267.2	Q96FT7	ASIC4_HUMAN	acid-sensing (proton-gated) ion channel family member 4	619			V -> A (in dbSNP:rs11695248). {ECO:0000269|PubMed:10852210, ECO:0000269|PubMed:11571555, ECO:0000269|PubMed:15489334}.		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)										CGGGGCCGAGTGGAGGGTGGG	0.637													C|||	3064	0.611821	0.5696	0.4697	5008	,	,		15692	0.6706		0.5447	False		,,,				2504	0.7781				p.V619A		Atlas-SNP	.											.	.	.	.	0			c.T1856C						PASS	.	C	ALA/VAL,ALA/VAL	2466,1934		669,1128,403	25.0	26.0	26.0		1913,1856	2.9	0.1	2	dbSNP_120	26	4564,4034		1237,2090,972	yes	missense,missense	ACCN4	NM_018674.4,NM_182847.2	64,64	1906,3218,1375	CC,CT,TT		46.9179,43.9545,45.9148	benign,benign	638/667,619/648	220402680	7030,5968	2200	4299	6499	SO:0001583	missense	55515	exon9			GCCGAGTGGAGGG	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.1856T>C	2.37:g.220402680T>C	ENSP00000326627:p.Val619Ala	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	66	40	0.606061	NM_182847	Q53SB7|Q6GMS1|Q6PIN9|Q9NQA4	Missense_Mutation	SNP	ENST00000347842.3	37	CCDS2442.1	1248	0.5714285714285714	270	0.5487804878048781	191	0.5276243093922652	381	0.666083916083916	406	0.5356200527704486	C	0.003	-2.432321	0.00184	0.560455	0.530821	ENSG00000072182	ENST00000347842;ENST00000358078	T;T	0.61158	0.16;0.13	4.77	2.91	0.33838	.	1.538520	0.03770	N	0.259657	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	0.40683	-0.9550	9	0.02654	T	1	2.5371	6.6559	0.22986	0.0:0.6839:0.1474:0.1687	rs11695248;rs17845260;rs17858089	619;638	Q96FT7;Q96FT7-4	ACCN4_HUMAN;.	A	619;638	ENSP00000326627:V619A;ENSP00000350786:V638A	ENSP00000326627:V619A	V	+	2	0	ACCN4	220110924	0.003000	0.15002	0.061000	0.19648	0.021000	0.10359	0.355000	0.20163	0.311000	0.23014	-0.119000	0.15052	GTG	T|0.438;C|0.562	0.562	strong		0.637	ASIC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000130263.1	NM_018674	
FRYL	285527	hgsc.bcm.edu	37	4	48588742	48588742	+	Silent	SNP	C	C	T	rs34558821	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:48588742C>T	ENST00000503238.1	-	16	1643	c.1644G>A	c.(1642-1644)ggG>ggA	p.G548G	FRYL_ENST00000506685.1_Silent_p.G254G|FRYL_ENST00000264319.7_5'UTR|FRYL_ENST00000358350.4_Silent_p.G548G|FRYL_ENST00000537810.1_Silent_p.G548G|FRYL_ENST00000507711.1_Silent_p.G548G			O94915	FRYL_HUMAN	FRY-like	548					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)					breast(2)|central_nervous_system(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(21)|lung(38)|ovary(1)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	91						GTTTTCTTTCCCCCCTGAAAA	0.368													C|||	2667	0.532548	0.6218	0.353	5008	,	,		14204	0.5288		0.4553	False		,,,				2504	0.6227				p.G548G		Atlas-SNP	.											.	FRYL	242	.	0			c.G1644A						PASS	.	C		2265,1367		715,835,266	90.0	85.0	87.0		1644	-3.4	1.0	4	dbSNP_126	87	3960,4190		984,1992,1099	no	coding-synonymous	FRYL	NM_015030.1		1699,2827,1365	TT,TC,CC		48.589,37.6377,47.1652		548/3014	48588742	6225,5557	1816	4075	5891	SO:0001819	synonymous_variant	285527	exon19			TCTTTCCCCCCTG	AL833170	CCDS43227.1	4p12	2011-08-03	2006-11-17	2005-11-24	ENSG00000075539	ENSG00000075539			29127	protein-coding gene	gene with protein product			"""KIAA0826"", ""furry homolog-like (Drosophila)"""	KIAA0826		10048485	Standard	NM_015030		Approved	DKFZp686E205	uc003gyh.1	O94915	OTTHUMG00000160608	ENST00000503238.1:c.1644G>A	4.37:g.48588742C>T		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	51	21	0.411765	NM_015030	O95640|Q8WTZ5|Q9NT40	Silent	SNP	ENST00000503238.1	37	CCDS43227.1																																																																																			C|0.516;T|0.484	0.484	strong		0.368	FRYL-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000369265.2		
TMC3	342125	hgsc.bcm.edu	37	15	81625552	81625552	+	Silent	SNP	C	C	T	rs530749986		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:81625552C>T	ENST00000359440.5	-	22	2646	c.2511G>A	c.(2509-2511)tcG>tcA	p.S837S	TMC3_ENST00000558726.1_Silent_p.S838S|RP11-761I4.3_ENST00000560973.1_RNA|RP11-761I4.3_ENST00000560851.1_RNA|RP11-761I4.3_ENST00000559781.1_RNA	NM_001080532.1	NP_001074001.1			transmembrane channel-like 3											autonomic_ganglia(2)|breast(1)|endometrium(4)|kidney(1)|large_intestine(7)|liver(1)|lung(11)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	34						TAGGTGTGCGCGATCTGTTCC	0.512													C|||	1	0.000199681	0.0	0.0	5008	,	,		21843	0.0		0.0	False		,,,				2504	0.001				p.S837S		Atlas-SNP	.											TMC3,NS,carcinoma,0,1	TMC3	112	1	0			c.G2511A						scavenged	.						115.0	113.0	114.0					15																	81625552		2039	4210	6249	SO:0001819	synonymous_variant	342125	exon22			TGTGCGCGATCTG	AY263163	CCDS45324.1	15q24.3	2006-11-24				ENSG00000188869			22995	protein-coding gene	gene with protein product						12906855, 12812529	Standard	NM_001080532		Approved		uc021ssk.1	Q7Z5M5		ENST00000359440.5:c.2511G>A	15.37:g.81625552C>T		Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	222	3	0.0135135	NM_001080532		Silent	SNP	ENST00000359440.5	37	CCDS45324.1																																																																																			.	.	none		0.512	TMC3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417795.3	NM_181841	
TCF20	6942	hgsc.bcm.edu	37	22	42606257	42606257	+	Silent	SNP	C	C	T	rs2070116	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:42606257C>T	ENST00000359486.3	-	1	5191	c.5055G>A	c.(5053-5055)tcG>tcA	p.S1685S	TCF20_ENST00000404876.1_5'Flank|TCF20_ENST00000335626.4_Silent_p.S1685S	NM_005650.1	NP_005641.1	Q9UGU0	TCF20_HUMAN	transcription factor 20 (AR1)	1685					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(7)|large_intestine(13)|lung(22)|ovary(5)|prostate(1)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(5)	66						GCATAAAGGACGAGGCCGGGA	0.567													C|||	1138	0.227236	0.115	0.3228	5008	,	,		17784	0.3006		0.2286	False		,,,				2504	0.2342				p.S1685S		Atlas-SNP	.											.	TCF20	164	.	0			c.G5055A						PASS	.	C	,	589,3817	258.9+/-262.7	31,527,1645	71.0	71.0	71.0		5055,5055	-11.9	0.1	22	dbSNP_96	71	1906,6694	337.8+/-322.5	201,1504,2595	no	coding-synonymous,coding-synonymous	TCF20	NM_005650.1,NM_181492.1	,	232,2031,4240	TT,TC,CC		22.1628,13.3681,19.1835	,	1685/1961,1685/1939	42606257	2495,10511	2203	4300	6503	SO:0001819	synonymous_variant	6942	exon1			AAAGGACGAGGCC	U19345	CCDS14032.1, CCDS14033.1	22q13.3	2011-02-08			ENSG00000100207	ENSG00000100207			11631	protein-coding gene	gene with protein product	"""stromelysin-1 platelet-derived growth factor-responsive element binding protein"""	603107				9730594, 10995766	Standard	NM_005650		Approved	AR1, SPBP	uc003bcj.1	Q9UGU0	OTTHUMG00000150920	ENST00000359486.3:c.5055G>A	22.37:g.42606257C>T		Somatic	155	1	0.00645161		WXS	Illumina HiSeq	Phase_I	139	138	0.992806	NM_181492	A9JX12|O14528|Q13078|Q4V353|Q9H4M0	Silent	SNP	ENST00000359486.3	37	CCDS14033.1																																																																																			C|0.788;T|0.212	0.212	strong		0.567	TCF20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320531.1	NM_181492	
WNK2	65268	hgsc.bcm.edu	37	9	96024182	96024182	+	Silent	SNP	G	G	C	rs12000967	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:96024182G>C	ENST00000297954.4	+	12	3153	c.3153G>C	c.(3151-3153)tcG>tcC	p.S1051S	WNK2_ENST00000356055.3_5'UTR|WNK2_ENST00000427277.2_Silent_p.S663S|WNK2_ENST00000395475.2_3'UTR|WNK2_ENST00000349097.3_Silent_p.S663S|WNK2_ENST00000395477.2_Silent_p.S1051S	NM_001282394.1	NP_001269323.1	Q9Y3S1	WNK2_HUMAN	WNK lysine deficient protein kinase 2	1051					intracellular signal transduction (GO:0035556)|negative regulation of cell proliferation (GO:0008285)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of ion homeostasis (GO:2000021)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(1)|endometrium(11)|kidney(4)|large_intestine(5)|lung(17)|ovary(2)|prostate(3)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)	54						CGGTCCTCTCGCCGCCTCTGC	0.692													C|||	665	0.132788	0.2973	0.1124	5008	,	,		13886	0.001		0.1362	False		,,,				2504	0.0573				p.S1051S		Atlas-SNP	.											.	WNK2	277	.	0			c.G3153C						PASS	.	C		1193,3211		166,861,1175	37.0	35.0	36.0		3153	-0.9	1.0	9	dbSNP_120	36	944,7648		60,824,3412	no	coding-synonymous	WNK2	NM_006648.3		226,1685,4587	CC,CG,GG		10.987,27.089,16.4435		1051/2218	96024182	2137,10859	2202	4296	6498	SO:0001819	synonymous_variant	65268	exon12			CCTCTCGCCGCCT	AJ242724	CCDS75858.1	9q22.3	2008-02-05	2003-06-23	2005-01-22	ENSG00000165238	ENSG00000165238			14542	protein-coding gene	gene with protein product		606249	"""serologically defined colon cancer antigen 43"""	SDCCAG43, PRKWNK2		9610721, 11571656	Standard	NM_006648		Approved	NY-CO-43, KIAA1760	uc004atj.3	Q9Y3S1	OTTHUMG00000020247	ENST00000297954.4:c.3153G>C	9.37:g.96024182G>C		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	76	36	0.473684	NM_006648	Q5VWF1|Q5VWF2|Q8IY36|Q9C0A3|Q9H3P4	Silent	SNP	ENST00000297954.4	37		294|294	0.1346153846153846|0.1346153846153846	144|144	0.2926829268292683|0.2926829268292683	46|46	0.1270718232044199|0.1270718232044199	1|1	0.0017482517482517483|0.0017482517482517483	103|103	0.1358839050131926|0.1358839050131926	C|C	6.678|6.678	0.493719|0.493719	0.12702|0.12702	0.27089|0.27089	0.10987|0.10987	ENSG00000165238|ENSG00000165238	ENST00000411624|ENST00000432730	.|.	.|.	.|.	5.17|5.17	-0.945|-0.945	0.10388|0.10388	.|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.09310|0.09310	P|P	0.9999999999999084|0.9999999999999084	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.36138|0.36138	-0.9760|-0.9760	3|3	.|.	.|.	.|.	.|.	2.0839|2.0839	0.03641|0.03641	0.177:0.178:0.1227:0.5223|0.177:0.178:0.1227:0.5223	rs12000967|rs12000967	.|.	.|.	.|.	P|P	655|1047	.|.	.|.	A|R	+|+	1|2	0|0	WNK2|WNK2	95064003|95064003	0.613000|0.613000	0.27009|0.27009	0.957000|0.957000	0.39632|0.39632	0.511000|0.511000	0.34104|0.34104	-0.715000|-0.715000	0.04997|0.04997	-0.302000|-0.302000	0.08869|0.08869	-0.647000|-0.647000	0.03941|0.03941	GCC|CGC	G|0.836;C|0.164	0.164	strong		0.692	WNK2-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000317359.1	NM_006648	
URAD	646625	hgsc.bcm.edu	37	13	28562605	28562605	+	Missense_Mutation	SNP	T	T	G	rs3897926	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:28562605T>G	ENST00000332715.5	-	1	186	c.170A>C	c.(169-171)cAg>cCg	p.Q57P	RN7SL272P_ENST00000487762.2_RNA	NM_001105577.1	NP_001099047.1	A6NGE7	URAD_HUMAN	ureidoimidazoline (2-oxo-4-hydroxy-4-carboxy-5-) decarboxylase	57			Q -> P (in dbSNP:rs3897926).		allantoin biosynthetic process (GO:0019428)|purine nucleobase metabolic process (GO:0006144)|urate catabolic process (GO:0019628)	peroxisome (GO:0005777)	carboxy-lyase activity (GO:0016831)	p.Q57P(1)									CTTACCTGACTGTGCAAGGGC	0.433													T|||	1225	0.244609	0.1626	0.3977	5008	,	,		21544	0.1835		0.3807	False		,,,				2504	0.1697				p.Q57P		Atlas-SNP	.											PRHOXNB,NS,carcinoma,0,1	PRHOXNB	6	1	1	Substitution - Missense(1)	stomach(1)	c.A170C						PASS	.	T	PRO/GLN	725,3027		61,603,1212	71.0	66.0	68.0		170	-2.0	0.0	13	dbSNP_108	68	3213,5015		596,2021,1497	yes	missense	PRHOXNB	NM_001105577.1	76	657,2624,2709	GG,GT,TT		39.0496,19.323,32.8715	benign	57/174	28562605	3938,8042	1876	4114	5990	SO:0001583	missense	646625	exon1			CCTGACTGTGCAA		CCDS45020.1	13q12.2	2014-04-09	2013-06-18	2013-06-18	ENSG00000183463	ENSG00000183463	4.1.1.n1		17785	protein-coding gene	gene with protein product	"""OHCU decarboxylase"""	615804	"""parahox cluster neighbor"""	PRHOXNB		16462750	Standard	NM_001105577		Approved		uc010aan.1	A6NGE7	OTTHUMG00000186217	ENST00000332715.5:c.170A>C	13.37:g.28562605T>G	ENSP00000333490:p.Gln57Pro	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	74	40	0.540541	NM_001105577		Missense_Mutation	SNP	ENST00000332715.5	37	CCDS45020.1	623	0.28525641025641024	99	0.20121951219512196	147	0.40607734806629836	98	0.17132867132867133	279	0.36807387862796836	T	7.262	0.605428	0.14002	0.19323	0.390496	ENSG00000183463	ENST00000332715	T	0.43294	0.95	5.2	-2.01	0.07410	2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase, type 1 (1);Oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase (2);	0.537574	0.18843	N	0.129613	T	0.00012	0.0000	N	0.05230	-0.09	0.80722	P	0.0	B	0.06786	0.001	B	0.11329	0.006	T	0.45745	-0.9240	9	0.28530	T	0.3	-0.8652	3.3162	0.07034	0.405:0.168:0.0:0.427	rs3897926;rs52801559;rs59495031;rs3897926	57	A6NGE7	URAD_HUMAN	P	57	ENSP00000333490:Q57P	ENSP00000333490:Q57P	Q	-	2	0	PRHOXNB	27460605	0.000000	0.05858	0.016000	0.15963	0.713000	0.41058	-0.723000	0.04952	-0.313000	0.08728	0.482000	0.46254	CAG	T|0.723;G|0.277	0.277	strong		0.433	URAD-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000472432.1		
DYNC2LI1	51626	hgsc.bcm.edu	37	2	44004010	44004010	+	Missense_Mutation	SNP	T	T	C	rs2288709	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:44004010T>C	ENST00000260605.8	+	2	198	c.98T>C	c.(97-99)tTt>tCt	p.F33S	DYNC2LI1_ENST00000398823.2_Missense_Mutation_p.F33S|DYNC2LI1_ENST00000406852.3_Missense_Mutation_p.F33S|DYNC2LI1_ENST00000605786.1_Missense_Mutation_p.F33S|DYNC2LI1_ENST00000443170.3_5'UTR|DYNC2LI1_ENST00000489222.2_Intron	NM_001193464.1|NM_016008.3	NP_001180393.1|NP_057092.2	Q8TCX1	DC2L1_HUMAN	dynein, cytoplasmic 2, light intermediate chain 1	33			F -> S (in dbSNP:rs2288709). {ECO:0000269|PubMed:17974005, ECO:0000269|Ref.3}.		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cilium assembly (GO:0042384)|determination of left/right symmetry (GO:0007368)	apical part of cell (GO:0045177)|axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|cytosol (GO:0005829)|intraciliary transport particle (GO:0030990)|microtubule (GO:0005874)|motile primary cilium (GO:0031512)|primary cilium (GO:0072372)	motor activity (GO:0003774)			breast(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(12)|ovary(1)|pancreas(1)|skin(1)	26		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)				GCAGAAAAATTTGTTTTCTTC	0.328													C|||	2570	0.513179	0.8933	0.4942	5008	,	,		14614	0.1696		0.3479	False		,,,				2504	0.5368				p.F33S		Atlas-SNP	.											.	DYNC2LI1	46	.	0			c.T98C						PASS	.	C	SER/PHE,SER/PHE,SER/PHE	3602,804	322.1+/-297.4	1473,656,74	115.0	127.0	123.0		98,98,98	5.4	1.0	2	dbSNP_100	123	3138,5462	656.7+/-401.4	579,1980,1741	yes	missense,missense,missense	DYNC2LI1	NM_001193464.1,NM_015522.3,NM_016008.3	155,155,155	2052,2636,1815	CC,CT,TT		36.4884,18.2478,48.1778	benign,benign,benign	33/353,33/202,33/352	44004010	6740,6266	2203	4300	6503	SO:0001583	missense	51626	exon2			AAAAATTTGTTTT		CCDS1813.1, CCDS46270.1, CCDS62903.1	2p25.1-p24.1	2008-02-05			ENSG00000138036	ENSG00000138036		"""Cytoplasmic dyneins"""	24595	protein-coding gene	gene with protein product						10810093, 11907264	Standard	NM_016008		Approved	D2LIC, LIC3, CGI-60, DKFZP564A033	uc002rtl.3	Q8TCX1	OTTHUMG00000128656	ENST00000260605.8:c.98T>C	2.37:g.44004010T>C	ENSP00000260605:p.Phe33Ser	Somatic	197	0	0		WXS	Illumina HiSeq	Phase_I	357	357	1	NM_016008	A8MVJ5|Q53F57|Q6PDB2|Q8IWA3|Q96B03|Q96J00|Q9Y370|Q9Y3S9	Missense_Mutation	SNP	ENST00000260605.8	37	CCDS1813.1	982	0.44963369963369965	439	0.8922764227642277	183	0.505524861878453	100	0.17482517482517482	260	0.34300791556728233	C	9.980	1.227764	0.22542	0.817522	0.364884	ENSG00000138036	ENST00000260605;ENST00000406852;ENST00000398823	T;T;T	0.28666	1.6;1.6;1.6	5.41	5.41	0.78517	.	0.054487	0.85682	N	0.000000	T	0.00012	0.0000	N	0.00392	-1.555	0.09310	P	1.0	B;B;B;B;B	0.09022	0.0;0.0;0.0;0.002;0.001	B;B;B;B;B	0.06405	0.0;0.0;0.0;0.002;0.002	T	0.32851	-0.9891	9	0.07030	T	0.85	-6.1844	12.3708	0.55254	0.0:0.9213:0.0:0.0787	rs2288709;rs17414745;rs52800670;rs61513437;rs2288709	33;33;33;33;33	Q8TCX1-2;Q8TCX1;Q8TCX1-3;Q8TCX1-5;Q8TCX1-4	.;DC2L1_HUMAN;.;.;.	S	33	ENSP00000260605:F33S;ENSP00000385738:F33S;ENSP00000381804:F33S	ENSP00000260605:F33S	F	+	2	0	DYNC2LI1	43857514	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.034000	0.49751	1.306000	0.44926	-0.119000	0.15052	TTT	T|0.516;C|0.483	0.483	strong		0.328	DYNC2LI1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000250536.2	NM_016008	
GLTSCR2	29997	hgsc.bcm.edu	37	19	48248834	48248834	+	Silent	SNP	T	T	C	rs10404034	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	121	0	0		WXS	Illumina HiSeq	Phase_I	80	38	0.475	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	
RNMTL1	55178	hgsc.bcm.edu	37	17	694847	694847	+	Silent	SNP	T	T	C	rs34081574	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:694847T>C	ENST00000304478.4	+	4	907	c.801T>C	c.(799-801)aaT>aaC	p.N267N	RP11-676J12.8_ENST00000574560.1_RNA	NM_018146.2	NP_060616.1			RNA methyltransferase like 1											breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(1)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	10				UCEC - Uterine corpus endometrioid carcinoma (25;0.0219)		CCATTATCAATAATCTGGAAT	0.517													T|||	23	0.00459265	0.0	0.0144	5008	,	,		19332	0.001		0.0119	False		,,,				2504	0.0				p.N267N		Atlas-SNP	.											.	RNMTL1	25	.	0			c.T801C						PASS	.	T		10,4396	15.5+/-35.6	0,10,2193	84.0	77.0	80.0		801	-0.1	1.0	17	dbSNP_126	80	107,8493	58.3+/-119.8	0,107,4193	no	coding-synonymous	RNMTL1	NM_018146.2		0,117,6386	CC,CT,TT		1.2442,0.227,0.8996		267/421	694847	117,12889	2203	4300	6503	SO:0001819	synonymous_variant	55178	exon4			TATCAATAATCTG	AF177344	CCDS10997.1	17p13.3	2008-02-05			ENSG00000171861	ENSG00000171861			18485	protein-coding gene	gene with protein product		612600				12296377	Standard	NM_018146		Approved	FLJ10581, HC90	uc002frw.3	Q9HC36	OTTHUMG00000090285	ENST00000304478.4:c.801T>C	17.37:g.694847T>C		Somatic	207	0	0		WXS	Illumina HiSeq	Phase_I	178	88	0.494382	NM_018146		Silent	SNP	ENST00000304478.4	37	CCDS10997.1																																																																																			T|0.992;C|0.008	0.008	strong		0.517	RNMTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206611.1	NM_018146	
PSMB9	5698	hgsc.bcm.edu	37	6	32825090	32825090	+	Missense_Mutation	SNP	G	G	A	rs17587	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:32825090G>A	ENST00000374859.2	+	3	248	c.179G>A	c.(178-180)cGc>cAc	p.R60H	PSMB9_ENST00000395330.1_Missense_Mutation_p.R37H|PSMB9_ENST00000453265.2_Intron	NM_002800.4	NP_002791.1	P28065	PSB9_HUMAN	proteasome (prosome, macropain) subunit, beta type, 9	60			R -> H (in dbSNP:rs17587). {ECO:0000269|PubMed:10924276, ECO:0000269|PubMed:1922385}.		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)	cytoplasm (GO:0005737)|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)			large_intestine(4)|lung(4)|skin(1)	9					Carfilzomib(DB08889)	CTGCACGAGCGCATCTACTGT	0.557													G|||	1124	0.224441	0.2322	0.2233	5008	,	,		17369	0.2123		0.2565	False		,,,				2504	0.1943				p.R60H		Atlas-SNP	.											.	PSMB9	16	.	0			c.G179A						PASS	.	G	HIS/ARG	649,2373		81,487,943	109.0	96.0	101.0		179	-3.8	0.4	6	dbSNP_63	101	1444,3972		218,1008,1482	yes	missense	PSMB9	NM_002800.4	29	299,1495,2425	AA,AG,GG		26.6617,21.4758,24.8045	benign	60/220	32825090	2093,6345	1511	2708	4219	SO:0001583	missense	5698	exon3			ACGAGCGCATCTA		CCDS4759.1	6p21.3	2013-03-27	2013-03-27		ENSG00000240065	ENSG00000240065		"""Proteasome (prosome, macropain) subunits"""	9546	protein-coding gene	gene with protein product		177045	"""proteasome (prosome, macropain) subunit, beta type, 9 (large multifunctional protease 2)"", ""large multifunctional peptidase 2"""	LMP2		1922385, 1529427	Standard	NM_002800		Approved	RING12, beta1i, PSMB6i	uc003sga.3	P28065	OTTHUMG00000031287	ENST00000374859.2:c.179G>A	6.37:g.32825090G>A	ENSP00000363993:p.Arg60His	Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	41	21	0.512195	NM_002800	B0V0T1|Q16523|Q5JNW4	Missense_Mutation	SNP	ENST00000374859.2	37	CCDS4759.1	486	0.22252747252747251	95	0.19308943089430894	83	0.2292817679558011	114	0.1993006993006993	194	0.2559366754617414	G	13.16	2.154819	0.38021	0.214758	0.266617	ENSG00000240065	ENST00000395330;ENST00000414474;ENST00000374859	T;T;T	0.19938	2.11;2.11;2.11	5.68	-3.82	0.04281	Proteasome, beta-type subunit, conserved site (1);	0.654017	0.15104	N	0.280372	T	0.05731	0.0150	L	0.37507	1.11	0.32374	P	0.5554250000000001	B	0.06786	0.001	B	0.06405	0.002	T	0.35992	-0.9766	9	0.34782	T	0.22	-7.1336	12.9288	0.58275	0.5927:0.0:0.4073:0.0	rs17587;rs1044244;rs2070254;rs3173317;rs9276814;rs17398467;rs17501771;rs52789962;rs60495382;rs17587	60	P28065	PSB9_HUMAN	H	37;37;60	ENSP00000378739:R37H;ENSP00000394363:R37H;ENSP00000363993:R60H	ENSP00000363993:R60H	R	+	2	0	PSMB9	32933068	0.003000	0.15002	0.413000	0.26509	0.677000	0.39632	0.081000	0.14823	-0.559000	0.06110	-0.154000	0.13518	CGC	G|0.760;A|0.240	0.240	strong		0.557	PSMB9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076624.5	NM_002800	
UBE3B	89910	hgsc.bcm.edu	37	12	109937534	109937534	+	Missense_Mutation	SNP	G	G	A	rs7298565	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:109937534G>A	ENST00000342494.3	+	12	1632	c.1037G>A	c.(1036-1038)cGg>cAg	p.R346Q	UBE3B_ENST00000434735.2_Missense_Mutation_p.R346Q|UBE3B_ENST00000280774.5_Missense_Mutation_p.R346Q	NM_130466.3	NP_569733.2	Q7Z3V4	UBE3B_HUMAN	ubiquitin protein ligase E3B	346			R -> Q (in dbSNP:rs7298565). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005}.		protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			NS(1)|breast(3)|endometrium(6)|kidney(4)|large_intestine(7)|lung(20)|ovary(2)|urinary_tract(2)	45						TGCTACTGTCGGAAGTATGTG	0.537													A|||	2590	0.517173	0.7731	0.4899	5008	,	,		17187	0.3105		0.5417	False		,,,				2504	0.3783				p.R346Q		Atlas-SNP	.											.	UBE3B	116	.	0			c.G1037A						PASS	.	A	GLN/ARG,GLN/ARG	3222,1184	416.5+/-337.6	1171,880,152	153.0	121.0	132.0		1037,1037	5.6	1.0	12	dbSNP_116	132	4578,4022	556.2+/-386.8	1227,2124,949	yes	missense,missense	UBE3B	NM_130466.2,NM_183415.1	43,43	2398,3004,1101	AA,AG,GG		46.7674,26.8724,40.0277	benign,benign	346/1069,346/1069	109937534	7800,5206	2203	4300	6503	SO:0001583	missense	89910	exon12			ACTGTCGGAAGTA	BC032301	CCDS9129.1, CCDS58277.1	12q24.12	2004-03-02			ENSG00000151148	ENSG00000151148			13478	protein-coding gene	gene with protein product		608047					Standard	NM_130466		Approved		uc001toq.4	Q7Z3V4	OTTHUMG00000169254	ENST00000342494.3:c.1037G>A	12.37:g.109937534G>A	ENSP00000340596:p.Arg346Gln	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	133	57	0.428571	NM_130466	A5D8Z3|Q05BX9|Q659F7|Q7Z7Q1|Q9BXZ4	Missense_Mutation	SNP	ENST00000342494.3	37	CCDS9129.1	1132	0.5183150183150184	365	0.741869918699187	183	0.505524861878453	165	0.28846153846153844	419	0.5527704485488126	A	9.788	1.177035	0.21787	0.731276	0.532326	ENSG00000151148	ENST00000434735;ENST00000280774;ENST00000539599;ENST00000342494	T;T;T;T	0.38560	1.43;1.13;1.7;1.43	5.64	5.64	0.86602	.	0.000000	0.85682	N	0.000000	T	0.00012	0.0000	N	0.00082	-2.215	0.47308	P	6.190000000000362E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.39961	-0.9588	9	0.07325	T	0.83	-1.0582	11.0128	0.47673	0.927:0.0:0.073:0.0	rs7298565;rs60248349;rs7298565	346	Q7Z3V4	UBE3B_HUMAN	Q	346	ENSP00000391529:R346Q;ENSP00000280774:R346Q;ENSP00000443131:R346Q;ENSP00000340596:R346Q	ENSP00000280774:R346Q	R	+	2	0	UBE3B	108421917	1.000000	0.71417	1.000000	0.80357	0.762000	0.43233	7.276000	0.78559	0.974000	0.38366	-0.352000	0.07741	CGG	G|0.446;A|0.554	0.554	strong		0.537	UBE3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403119.1	NM_183415	
LY9	4063	hgsc.bcm.edu	37	1	160793560	160793560	+	Missense_Mutation	SNP	A	A	G	rs509749	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:160793560A>G	ENST00000263285.6	+	8	1834	c.1804A>G	c.(1804-1806)Atg>Gtg	p.M602V	LY9_ENST00000392203.4_Missense_Mutation_p.M512V|LY9_ENST00000341032.4_Missense_Mutation_p.M468V|LY9_ENST00000368040.1_Missense_Mutation_p.M240V|LY9_ENST00000368037.5_Missense_Mutation_p.M588V|LY9_ENST00000368041.2_Missense_Mutation_p.M472V			Q9HBG7	LY9_HUMAN	lymphocyte antigen 9	602			M -> V (in dbSNP:rs509749). {ECO:0000269|PubMed:10970093, ECO:0000269|PubMed:8537117}.		cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			autonomic_ganglia(1)|breast(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(17)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	36	all_cancers(52;2.72e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00737)			AGAGAACACCATGTATGCACA	0.527													G|||	3306	0.660144	0.7912	0.6686	5008	,	,		22929	0.7034		0.4503	False		,,,				2504	0.6483				p.M602V		Atlas-SNP	.											.	LY9	115	.	0			c.A1804G						PASS	.	G	VAL/MET	3241,1165	410.6+/-335.4	1187,867,149	146.0	140.0	142.0		1804	2.3	0.0	1	dbSNP_83	142	3625,4975	625.2+/-397.7	758,2109,1433	yes	missense	LY9	NM_002348.2	21	1945,2976,1582	GG,GA,AA		42.1512,26.4412,47.209	benign	602/656	160793560	6866,6140	2203	4300	6503	SO:0001583	missense	4063	exon8			AACACCATGTATG	L42621	CCDS30916.1, CCDS30917.1, CCDS65695.1, CCDS65696.1	1q23.3	2013-01-11			ENSG00000122224	ENSG00000122224		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6730	protein-coding gene	gene with protein product		600684				8537117, 7797269	Standard	NM_001261457		Approved	CD229, mLY9, SLAMF3, hly9	uc001fwu.4	Q9HBG7	OTTHUMG00000024007	ENST00000263285.6:c.1804A>G	1.37:g.160793560A>G	ENSP00000263285:p.Met602Val	Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	133	68	0.511278	NM_002348	A8K7N3|Q14775|Q5VYI3|Q6P2J4|Q9H4N5|Q9NQ24	Missense_Mutation	SNP	ENST00000263285.6	37	CCDS30916.1	1367	0.6259157509157509	390	0.7926829268292683	231	0.638121546961326	408	0.7132867132867133	338	0.44591029023746703	G	0	-2.600850	0.00123	0.735588	0.421512	ENSG00000122224	ENST00000368041;ENST00000341032;ENST00000368040;ENST00000263285;ENST00000392203;ENST00000368037;ENST00000368036;ENST00000368035	T;T;T;T	0.29397	1.66;2.69;1.57;2.69	3.21	2.28	0.28536	.	3.007930	0.01747	N	0.029726	T	0.03053	0.0090	N	0.02247	-0.625	0.80722	P	0.0	B;B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0;0.0	B;B;B;B;B;B	0.01281	0.0;0.0;0.0;0.0;0.0;0.0	T	0.26189	-1.0110	9	0.02654	T	1	-3.2314	8.3708	0.32415	0.2189:0.0:0.7811:0.0	rs509749;rs17386266;rs58983611;rs509749	240;548;472;468;588;602	Q5VYI1;Q5VYH7;Q5VYH9;E7EME5;Q9HBG7-2;Q9HBG7	.;.;.;.;.;LY9_HUMAN	V	602;468;240;602;472;548;370;240	ENSP00000342921:M468V;ENSP00000357019:M240V;ENSP00000263285:M602V;ENSP00000357014:M240V	ENSP00000263285:M602V	M	+	1	0	LY9	159060184	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-0.210000	0.09345	0.061000	0.16311	-3.149000	0.00058	ATG	A|0.404;G|0.596	0.596	strong		0.527	LY9-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000060457.3	NM_002348	
DAAM2	23500	hgsc.bcm.edu	37	6	39865047	39865047	+	Silent	SNP	T	T	C	rs3004067	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:39865047T>C	ENST00000398904.2	+	21	2789	c.2607T>C	c.(2605-2607)gcT>gcC	p.A869A	RP11-61I13.3_ENST00000430595.1_RNA|DAAM2_ENST00000538976.1_Silent_p.A869A|RP11-61I13.3_ENST00000437947.1_RNA|RP11-61I13.3_ENST00000606829.1_RNA|RP11-61I13.3_ENST00000420293.1_RNA|DAAM2_ENST00000274867.4_Silent_p.A869A			Q86T65	DAAM2_HUMAN	dishevelled associated activator of morphogenesis 2	869	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)					TTCCAGAAGCTGCCAAAGTCA	0.453													C|||	3789	0.756589	0.8283	0.611	5008	,	,		21038	0.8671		0.6362	False		,,,				2504	0.773				p.A869A		Atlas-SNP	.											.	DAAM2	101	.	0			c.T2607C						PASS	.	C	,	2972,856		1152,668,94	87.0	86.0	86.0		2607,2607	-4.3	0.8	6	dbSNP_101	86	5098,3202		1564,1970,616	no	coding-synonymous,coding-synonymous	DAAM2	NM_001201427.1,NM_015345.3	,	2716,2638,710	CC,CT,TT		38.5783,22.3615,33.4598	,	869/1069,869/1068	39865047	8070,4058	1914	4150	6064	SO:0001819	synonymous_variant	23500	exon21			AGAAGCTGCCAAA	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.2607T>C	6.37:g.39865047T>C		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	123	64	0.520325	NM_015345	G5EA45|Q5T4T8|Q5T4U0|Q9NQI5|Q9Y4G0	Silent	SNP	ENST00000398904.2	37	CCDS56426.1																																																																																			T|0.269;C|0.731	0.731	strong		0.453	DAAM2-003	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000280648.1		
HPSE	10855	hgsc.bcm.edu	37	4	84222157	84222157	+	Missense_Mutation	SNP	A	A	C	rs145560091	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:84222157A>C	ENST00000405413.2	-	12	1564	c.1428T>G	c.(1426-1428)gaT>gaG	p.D476E	HPSE_ENST00000513463.1_Missense_Mutation_p.D418E|HPSE_ENST00000512196.1_Missense_Mutation_p.D402E|HPSE_ENST00000311412.5_Missense_Mutation_p.D476E	NM_006665.5	NP_006656.2	Q9Y251	HPSE_HUMAN	heparanase	476					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)	GAAGGTATTTATCCACTTGCT	0.348																																					p.D476E		Atlas-SNP	.											.	HPSE	55	.	0			c.T1428G						PASS	.	A	GLU/ASP,GLU/ASP,GLU/ASP,GLU/ASP	0,4406		0,0,2203	114.0	117.0	116.0		1428,1206,1254,1428	-2.4	1.0	4	dbSNP_134	116	17,8581	12.6+/-44.7	0,17,4282	yes	missense,missense,missense,missense	HPSE	NM_001098540.2,NM_001166498.2,NM_001199830.1,NM_006665.5	45,45,45,45	0,17,6485	CC,CA,AA		0.1977,0.0,0.1307	benign,benign,benign,benign	476/544,402/470,418/486,476/544	84222157	17,12987	2203	4299	6502	SO:0001583	missense	10855	exon11			GTATTTATCCACT	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.1428T>G	4.37:g.84222157A>C	ENSP00000384262:p.Asp476Glu	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	133	56	0.421053	NM_001098540	A9JIG7|C7F7I3|C7F7I4|E9PCA9|E9PGR1|Q53GE5|Q9UL39	Missense_Mutation	SNP	ENST00000405413.2	37	CCDS3602.1	.	.	.	.	.	.	.	.	.	.	A	6.169	0.399451	0.11696	0.0	0.001977	ENSG00000173083	ENST00000311412;ENST00000405413;ENST00000512196;ENST00000513463	T;T;T;T	0.38722	1.12;1.12;1.14;1.13	4.56	-2.36	0.06663	.	0.095855	0.64402	D	0.000001	T	0.20981	0.0505	N	0.05199	-0.095	0.35589	D	0.806951	D;B;B;B	0.58620	0.983;0.059;0.097;0.014	P;B;B;B	0.54460	0.753;0.038;0.084;0.009	T	0.44726	-0.9309	10	0.02654	T	1	-21.5243	5.5816	0.17252	0.5796:0.0:0.2952:0.1252	.	402;418;418;476	E9PCA9;A9JIG7;E9PGR1;Q9Y251	.;.;.;HPSE_HUMAN	E	476;476;402;418	ENSP00000308107:D476E;ENSP00000384262:D476E;ENSP00000423265:D402E;ENSP00000421365:D418E	ENSP00000308107:D476E	D	-	3	2	HPSE	84441181	1.000000	0.71417	0.988000	0.46212	0.172000	0.22775	0.482000	0.22276	-0.153000	0.11137	-0.256000	0.11100	GAT	A|0.999;C|0.001	0.001	strong		0.348	HPSE-001	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252812.2	NM_006665	
PIEZO2	63895	hgsc.bcm.edu	37	18	10681711	10681711	+	Missense_Mutation	SNP	C	C	T	rs3748428	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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_ENST00000580640.1_Missense_Mutation_p.V2488I|PIEZO2_ENST00000538948.1_Missense_Mutation_p.V420I|PIEZO2_ENST00000302079.6_Missense_Mutation_p.V2400I	NM_022068.2	NP_071351.2	Q9H5I5	PIEZ2_HUMAN	piezo-type mechanosensitive ion channel component 2	2463			V -> I (in dbSNP:rs3748428). {ECO:0000269|Ref.1}.		cation transport (GO:0006812)|detection of mechanical stimulus involved in sensory perception (GO:0050974)|regulation of membrane potential (GO:0042391)|response to mechanical stimulus (GO:0009612)	integral component of membrane (GO:0016021)	cation channel activity (GO:0005261)|mechanically-gated ion channel activity (GO:0008381)										TGGTCCATAACTTTCAACTGG	0.408													C|||	579	0.115615	0.0219	0.1427	5008	,	,		18706	0.1786		0.1491	False		,,,				2504	0.1237				p.V2463I		Atlas-SNP	.											.	.	.	.	0			c.G7387A						PASS	.	C	ILE/VAL	123,4283	92.0+/-130.7	1,121,2081	157.0	152.0	153.0		7387	5.1	1.0	18	dbSNP_107	153	1124,7476	231.9+/-265.7	69,986,3245	yes	missense	PIEZO2	NM_022068.2	29	70,1107,5326	TT,TC,CC		13.0698,2.7916,9.5879	benign	2463/2753	10681711	1247,11759	2203	4300	6503	SO:0001583	missense	63895	exon47			CCATAACTTTCAA	AK027056		18p11.21	2012-11-19	2011-08-31	2011-08-31	ENSG00000154864	ENSG00000154864			26270	protein-coding gene	gene with protein product		613629	"""chromosome 18 open reading frame 30"", ""chromosome 18 open reading frame 58"", ""family with sequence similarity 38, member B"""	FAM38B2, C18orf30, C18orf58, FAM38B		20813920, 21056836, 21299953	Standard	NM_022068		Approved	FLJ23403, FLJ23144, HsT748, HsT771, FLJ34907	uc002kos.2	Q9H5I5	OTTHUMG00000178507	ENST00000503781.3:c.7387G>A	18.37:g.10681711C>T	ENSP00000421377:p.Val2463Ile	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	121	67	0.553719	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	
LIG4	3981	hgsc.bcm.edu	37	13	108861913	108861913	+	Silent	SNP	A	A	G	rs1805386	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:108861913A>G	ENST00000356922.4	-	2	1976	c.1704T>C	c.(1702-1704)gaT>gaC	p.D568D	LIG4_ENST00000405925.1_Silent_p.D568D|LIG4_ENST00000442234.1_Silent_p.D568D	NM_002312.3|NM_206937.1	NP_002303.2|NP_996820.1	P49917	DNLI4_HUMAN	ligase IV, DNA, ATP-dependent	568					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)					TTTTATACATATCACTGGGTA	0.423								Non-homologous end-joining					A|||	344	0.0686901	0.0507	0.1326	5008	,	,		19957	0.001		0.1481	False		,,,				2504	0.0358				p.D568D		Atlas-SNP	.											.	LIG4	91	.	0			c.T1704C						PASS	.	A	,,	352,4054	182.6+/-210.3	12,328,1863	98.0	91.0	93.0		1704,1704,1704	-11.5	0.1	13	dbSNP_92	93	1581,7019	295.9+/-302.6	145,1291,2864	no	coding-synonymous,coding-synonymous,coding-synonymous	LIG4	NM_001098268.1,NM_002312.3,NM_206937.1	,,	157,1619,4727	GG,GA,AA		18.3837,7.9891,14.8624	,,	568/912,568/912,568/912	108861913	1933,11073	2203	4300	6503	SO:0001819	synonymous_variant	3981	exon3			ATACATATCACTG	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.1704T>C	13.37:g.108861913A>G		Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	112	112	1	NM_206937	Q8IY66|Q8TEU5	Silent	SNP	ENST00000356922.4	37	CCDS9508.1																																																																																			A|0.870;G|0.130	0.130	strong		0.423	LIG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045738.4	NM_002312	
ADPGK	83440	hgsc.bcm.edu	37	15	73044863	73044863	+	Missense_Mutation	SNP	G	G	A	rs34149613	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:73044863G>A	ENST00000311669.8	-	7	1403	c.1310C>T	c.(1309-1311)tCg>tTg	p.S437L	ADPGK_ENST00000456471.2_Missense_Mutation_p.S163L	NM_031284.4	NP_112574.3	Q9BRR6	ADPGK_HUMAN	ADP-dependent glucokinase	438	ADPK. {ECO:0000255|PROSITE- ProRule:PRU00584}.				glycolytic process (GO:0006096)	extracellular region (GO:0005576)|membrane (GO:0016020)	ADP-specific glucokinase activity (GO:0043843)|metal ion binding (GO:0046872)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|lung(2)|skin(1)	7						GCCTGCCTCCGAATGGGAAGT	0.527													G|||	275	0.0549121	0.0484	0.0706	5008	,	,		16699	0.0		0.0934	False		,,,				2504	0.0695				p.S437L		Atlas-SNP	.											.	ADPGK	19	.	0			c.C1310T						PASS	.	G	LEU/SER	189,3627		10,169,1729	94.0	94.0	94.0		1310	2.0	0.0	15	dbSNP_126	94	994,7230		65,864,3183	yes	missense	ADPGK	NM_031284.4	145	75,1033,4912	AA,AG,GG		12.0866,4.9528,9.8256	benign	437/497	73044863	1183,10857	1908	4112	6020	SO:0001583	missense	83440	exon7			GCCTCCGAATGGG	AL136873	CCDS42057.1	15q24.1	2012-07-02			ENSG00000159322	ENSG00000159322			25250	protein-coding gene	gene with protein product		611861				11230166	Standard	NM_031284		Approved	DKFZp434B195, ADP-GK	uc002avf.4	Q9BRR6	OTTHUMG00000172777	ENST00000311669.8:c.1310C>T	15.37:g.73044863G>A	ENSP00000312250:p.Ser437Leu	Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	177	87	0.491525	NM_031284	Q49AU7|Q8NBI1|Q8WZ90|Q96NF8|Q9H0A7	Missense_Mutation	SNP	ENST00000311669.8	37	CCDS42057.1	120	0.054945054945054944	25	0.0508130081300813	25	0.06906077348066299	0	0.0	70	0.09234828496042216	G	8.771	0.926022	0.18056	0.049528	0.120866	ENSG00000159322	ENST00000311669;ENST00000443764;ENST00000456471	T;T	0.40756	1.02;1.02	6.02	1.96	0.26148	.	1.048650	0.07322	N	0.877781	T	0.00412	0.0013	L	0.40543	1.245	0.09310	N	1	B;B;B;B	0.14438	0.003;0.01;0.008;0.005	B;B;B;B	0.09377	0.004;0.004;0.001;0.002	T	0.14282	-1.0478	10	0.13108	T	0.6	-1.8074	5.2284	0.15408	0.3678:0.0:0.5059:0.1263	rs34149613	380;438;437;163	B4DG35;Q9BRR6;Q9BRR6-2;Q9BRR6-4	.;ADPGK_HUMAN;.;.	L	437;357;163	ENSP00000312250:S437L;ENSP00000397694:S163L	ENSP00000312250:S437L	S	-	2	0	ADPGK	70831916	0.000000	0.05858	0.006000	0.13384	0.914000	0.54420	0.312000	0.19397	0.105000	0.17753	0.655000	0.94253	TCG	G|0.922;A|0.078	0.078	strong		0.527	ADPGK-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000420434.1	NM_031284	
MYOZ1	58529	hgsc.bcm.edu	37	10	75394457	75394457	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:75394457C>A	ENST00000359322.4	-	4	651	c.287G>T	c.(286-288)gGa>gTa	p.G96V		NM_021245.3	NP_067068.1			myozenin 1											central_nervous_system(1)|large_intestine(5)|lung(2)|ovary(2)|skin(2)	12	Prostate(51;0.0112)					GCCCAGCTGTCCCCCCACTGT	0.532																																					p.G96V		Atlas-SNP	.											.	MYOZ1	24	.	0			c.G287T						PASS	.						62.0	60.0	60.0					10																	75394457		2203	4300	6503	SO:0001583	missense	58529	exon4			AGCTGTCCCCCCA	AF240633	CCDS7330.1	10q22.1	2008-07-03	2002-01-10	2002-01-11	ENSG00000177791	ENSG00000177791			13752	protein-coding gene	gene with protein product	"""calsarcin-2"""	605603	"""myozenin"""	MYOZ		11171996, 10984498	Standard	NM_021245		Approved	FATZ, CS-2	uc001jur.4	Q9NP98	OTTHUMG00000018466	ENST00000359322.4:c.287G>T	10.37:g.75394457C>A	ENSP00000352272:p.Gly96Val	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	80	29	0.3625	NM_021245		Missense_Mutation	SNP	ENST00000359322.4	37	CCDS7330.1	.	.	.	.	.	.	.	.	.	.	C	22.2	4.251231	0.80135	.	.	ENSG00000177791	ENST00000359322	T	0.66638	-0.22	6.05	6.05	0.98169	.	0.134037	0.64402	D	0.000002	T	0.78027	0.4219	L	0.53249	1.67	0.80722	D	1	D	0.76494	0.999	D	0.73708	0.981	T	0.78455	-0.2197	10	0.72032	D	0.01	-4.7931	14.7834	0.69784	0.0:0.9294:0.0:0.0706	.	96	Q9NP98	MYOZ1_HUMAN	V	96	ENSP00000352272:G96V	ENSP00000352272:G96V	G	-	2	0	MYOZ1	75064463	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.747000	0.62141	2.880000	0.98712	0.655000	0.94253	GGA	.	.	none		0.532	MYOZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048654.1		
OR2D3	120775	hgsc.bcm.edu	37	11	6942726	6942726	+	Missense_Mutation	SNP	G	G	C	rs10839659	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:6942726G>C	ENST00000317834.3	+	1	522	c.494G>C	c.(493-495)tGg>tCg	p.W165S		NM_001004684.1	NP_001004684.1	Q8NGH3	OR2D3_HUMAN	olfactory receptor, family 2, subfamily D, member 3	165			W -> S (in dbSNP:rs10839659).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(2)|large_intestine(7)|lung(12)|prostate(3)|skin(1)|stomach(1)	27		Medulloblastoma(188;0.0523)|all_neural(188;0.236)		Epithelial(150;4.78e-08)|BRCA - Breast invasive adenocarcinoma(625;0.129)		TTCAGGTCCTGGGCCAGTGGG	0.493													G|||	1313	0.262181	0.0545	0.3199	5008	,	,		19557	0.3363		0.3827	False		,,,				2504	0.3016				p.W165S		Atlas-SNP	.											.	OR2D3	51	.	0			c.G494C						PASS	.	G	SER/TRP	454,3948	215.8+/-234.7	30,394,1777	133.0	113.0	120.0		494	5.2	1.0	11	dbSNP_120	120	3214,5378	485.7+/-371.7	603,2008,1685	yes	missense	OR2D3	NM_001004684.1	177	633,2402,3462	CC,CG,GG		37.4069,10.3135,28.2284	probably-damaging	165/331	6942726	3668,9326	2201	4296	6497	SO:0001583	missense	120775	exon1			GGTCCTGGGCCAG	BK004294	CCDS31417.1	11p15.4	2012-08-09			ENSG00000178358	ENSG00000178358		"""GPCR / Class A : Olfactory receptors"""	15146	protein-coding gene	gene with protein product							Standard	NM_001004684		Approved		uc010rav.2	Q8NGH3	OTTHUMG00000165742	ENST00000317834.3:c.494G>C	11.37:g.6942726G>C	ENSP00000320560:p.Trp165Ser	Somatic	322	0	0		WXS	Illumina HiSeq	Phase_I	342	67	0.195906	NM_001004684	B2RP06|Q6IFG8|Q96R51	Missense_Mutation	SNP	ENST00000317834.3	37	CCDS31417.1	619	0.2834249084249084	38	0.07723577235772358	114	0.3149171270718232	186	0.32517482517482516	281	0.370712401055409	G	19.45	3.829810	0.71258	0.103135	0.374069	ENSG00000178358	ENST00000317834	T	0.59502	0.26	5.17	5.17	0.71159	GPCR, rhodopsin-like superfamily (1);	0.000000	0.41938	D	0.000794	T	0.00012	0.0000	H	0.96777	3.88	0.09310	P	0.9999999920009	D	0.89917	1.0	D	0.91635	0.999	T	0.04153	-1.0973	9	0.87932	D	0	-22.9266	16.5766	0.84681	0.0:0.0:1.0:0.0	rs10839659;rs17275979;rs52822521;rs10839659	165	Q8NGH3	OR2D3_HUMAN	S	165	ENSP00000320560:W165S	ENSP00000320560:W165S	W	+	2	0	OR2D3	6899302	0.006000	0.16342	1.000000	0.80357	0.848000	0.48234	0.714000	0.25808	2.865000	0.98341	0.655000	0.94253	TGG	G|0.707;C|0.292	0.292	strong		0.493	OR2D3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385987.1	NM_001004684	
RANBP2	5903	hgsc.bcm.edu	37	2	109368085	109368085	+	Silent	SNP	G	G	A	rs559137643		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:109368085G>A	ENST00000283195.6	+	11	1683	c.1557G>A	c.(1555-1557)gtG>gtA	p.V519V		NM_006267.4	NP_006258.3	P49792	RBP2_HUMAN	RAN binding protein 2	519					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.V519V(2)	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						CCCTTCCTGTGTGTAAACAGC	0.393													G|||	1	0.000199681	0.0	0.0	5008	,	,		17767	0.0		0.0	False		,,,				2504	0.001				p.V519V		Atlas-SNP	.											RANBP2_ENST00000283195,NS,carcinoma,0,2	RANBP2	488	2	2	Substitution - coding silent(2)	kidney(2)	c.G1557A						scavenged	.						29.0	33.0	32.0					2																	109368085		1041	2139	3180	SO:0001819	synonymous_variant	5903	exon11			TCCTGTGTGTAAA	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.1557G>A	2.37:g.109368085G>A		Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	162	5	0.0308642	NM_006267	Q13074|Q15280|Q53TE2|Q59FH7	Silent	SNP	ENST00000283195.6	37	CCDS2079.1																																																																																			ATGTAAACA|0.500;GTGTAAACG|0.500	.	alt		0.393	RANBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253594.1	NM_006267	
MATN2	4147	hgsc.bcm.edu	37	8	99033441	99033441	+	Missense_Mutation	SNP	G	G	A	rs61729731	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:99033441G>A	ENST00000520016.1	+	12	1952	c.1828G>A	c.(1828-1830)Gtc>Atc	p.V610I	MATN2_ENST00000524308.1_Missense_Mutation_p.V569I|MATN2_ENST00000521689.1_Missense_Mutation_p.V610I|MATN2_ENST00000522025.2_Missense_Mutation_p.V326I|MATN2_ENST00000254898.5_Missense_Mutation_p.V610I			O00339	MATN2_HUMAN	matrilin 2	610	EGF-like 10. {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)			AGGGAAGGATGTCTGCAAATC	0.428													G|||	24	0.00479233	0.0	0.0029	5008	,	,		20373	0.001		0.008	False		,,,				2504	0.0133				p.V610I		Atlas-SNP	.											.	MATN2	165	.	0			c.G1828A						PASS	.	G	ILE/VAL,ILE/VAL	2,3804		0,2,1901	100.0	96.0	97.0		1828,1828	1.4	1.0	8	dbSNP_129	97	98,8158		0,98,4030	yes	missense,missense	MATN2	NM_002380.3,NM_030583.2	29,29	0,100,5931	AA,AG,GG		1.187,0.0525,0.829	benign,benign	610/957,610/938	99033441	100,11962	1903	4128	6031	SO:0001583	missense	4147	exon13			AAGGATGTCTGCA	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.1828G>A	8.37:g.99033441G>A	ENSP00000430487:p.Val610Ile	Somatic	152	1	0.00657895		WXS	Illumina HiSeq	Phase_I	112	85	0.758929	NM_002380	A8K106|E7EW74|E9PD48|E9PGL2|Q6UWA5|Q7Z5X1|Q8NDE6|Q96FT5|Q9NSZ1	Missense_Mutation	SNP	ENST00000520016.1	37	CCDS55264.1	10|10	0.004578754578754579|0.004578754578754579	0|0	0.0|0.0	1|1	0.0027624309392265192|0.0027624309392265192	1|1	0.0017482517482517483|0.0017482517482517483	8|8	0.010554089709762533|0.010554089709762533	G|G	13.24|13.24	2.176684|2.176684	0.38413|0.38413	5.25E-4|5.25E-4	0.01187|0.01187	ENSG00000132561|ENSG00000132561	ENST00000518154|ENST00000521689;ENST00000254898;ENST00000378716;ENST00000524308;ENST00000522025;ENST00000520016	.|T;T;D;D;T	.|0.97378	.|1.57;1.57;-4.36;-4.36;1.57	5.7|5.7	1.44|1.44	0.22558|0.22558	.|Epidermal growth factor-like (1);	.|0.631691	.|0.14689	.|N	.|0.304241	D|D	0.89952|0.89952	0.6864|0.6864	L|L	0.33485|0.33485	1.01|1.01	0.32947|0.32947	D|D	0.519229|0.519229	.|B;B;B;B	.|0.09022	.|0.002;0.001;0.001;0.001	.|B;B;B;B	.|0.09377	.|0.004;0.004;0.003;0.002	D|D	0.84084|0.84084	0.0386|0.0386	5|10	.|0.13853	.|T	.|0.58	-11.6395|-11.6395	8.6392|8.6392	0.33968|0.33968	0.3342:0.0:0.6658:0.0|0.3342:0.0:0.6658:0.0	rs61729731|rs61729731	.|569;610;610;610	.|C9JH87;E9PF03;O00339-2;O00339	.|.;.;.;MATN2_HUMAN	Y|I	392|610;610;569;569;326;610	.|ENSP00000429977:V610I;ENSP00000254898:V610I;ENSP00000430221:V569I;ENSP00000429010:V326I;ENSP00000430487:V610I	.|ENSP00000254898:V610I	C|V	+|+	2|1	0|0	MATN2|MATN2	99102617|99102617	0.000000|0.000000	0.05858|0.05858	0.981000|0.981000	0.43875|0.43875	0.800000|0.800000	0.45204|0.45204	-0.184000|-0.184000	0.09698|0.09698	-0.022000|-0.022000	0.13986|0.13986	0.655000|0.655000	0.94253|0.94253	TGT|GTC	G|0.993;A|0.007	0.007	strong		0.428	MATN2-004	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000380332.1		
MTTP	4547	hgsc.bcm.edu	37	4	100518224	100518224	+	Splice_Site	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:100518224C>T	ENST00000265517.5	+	8	1113	c.910C>T	c.(910-912)Ctc>Ttc	p.L304F	MTTP_ENST00000511045.1_Splice_Site_p.L331F|RP11-766F14.1_ENST00000508578.1_RNA|MTTP_ENST00000457717.1_Splice_Site_p.L304F			P55157	MTP_HUMAN	microsomal triglyceride transfer protein	304	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)	TGTTTTGCAGCTCTCGGAGCT	0.498																																					p.L304F		Atlas-SNP	.											.	MTTP	127	.	0			c.C910T						PASS	.						101.0	100.0	101.0					4																	100518224		2203	4300	6503	SO:0001630	splice_region_variant	4547	exon9			TTGCAGCTCTCGG		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.910-1C>T	4.37:g.100518224C>T		Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	33	11	0.333333	NM_000253	A8K428|Q08AM4|Q6P5T3	Missense_Mutation	SNP	ENST00000265517.5	37	CCDS3651.1	.	.	.	.	.	.	.	.	.	.	C	13.84	2.357959	0.41801	.	.	ENSG00000138823	ENST00000511045;ENST00000457717;ENST00000265517;ENST00000538053	T;T;T	0.55052	0.54;0.54;0.54	5.37	4.53	0.55603	Lipid transport protein, N-terminal (3);Vitellinogen, superhelical (1);	0.061492	0.64402	D	0.000003	T	0.74068	0.3668	M	0.77616	2.38	0.58432	D	0.999995	D;D	0.89917	1.0;1.0	D;D	0.91635	0.995;0.999	T	0.75465	-0.3308	9	.	.	.	-28.4593	18.347	0.90326	0.1216:0.8784:0.0:0.0	.	331;304	E9PBP6;P55157	.;MTP_HUMAN	F	331;304;304;304	ENSP00000427679:L331F;ENSP00000400821:L304F;ENSP00000265517:L304F	.	L	+	1	0	MTTP	100737247	1.000000	0.71417	0.903000	0.35520	0.028000	0.11728	3.706000	0.54830	0.646000	0.30693	-0.808000	0.03180	CTC	.	.	none		0.498	MTTP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253662.3		Missense_Mutation
C10orf71	118461	hgsc.bcm.edu	37	10	50531972	50531972	+	Missense_Mutation	SNP	A	A	C	rs45554335	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:50531972A>C	ENST00000374144.3	+	3	1670	c.1382A>C	c.(1381-1383)gAc>gCc	p.D461A	C10orf71_ENST00000323868.4_Missense_Mutation_p.D461A			Q711Q0	CJ071_HUMAN	chromosome 10 open reading frame 71	461			D -> A (in dbSNP:rs45554335). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005}.							endometrium(1)	1						GATTCAGCAGACAGCCAGCCA	0.547													a|||	884	0.176518	0.1029	0.2608	5008	,	,		17159	0.3095		0.1481	False		,,,				2504	0.1084				p.D461A		Atlas-SNP	.											.	C10orf71	179	.	0			c.A1382C						PASS	.	C	ALA/ASP,ALA/ASP	522,3642		25,472,1585	50.0	53.0	52.0		1382,1382	0.2	0.0	10	dbSNP_127	52	1351,7115		107,1137,2989	yes	missense,missense	C10orf71	NM_001135196.1,NM_199459.3	126,126	132,1609,4574	CC,CA,AA		15.9579,12.536,14.8298	benign,benign	461/1436,461/720	50531972	1873,10757	2082	4233	6315	SO:0001583	missense	118461	exon3			CAGCAGACAGCCA	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.1382A>C	10.37:g.50531972A>C	ENSP00000363259:p.Asp461Ala	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	54	25	0.462963	NM_001135196	A0AVL8	Missense_Mutation	SNP	ENST00000374144.3	37	CCDS44387.1	476	0.21794871794871795	68	0.13821138211382114	91	0.2513812154696133	200	0.34965034965034963	117	0.15435356200527706	a	4.399	0.073746	0.08485	0.12536	0.159579	ENSG00000177354	ENST00000323868;ENST00000374144	T;T	0.16597	2.33;3.46	5.3	0.171	0.15026	.	1.161450	0.06649	N	0.762440	T	0.00012	0.0000	L	0.57536	1.79	0.80722	P	0.0	B	0.06786	0.001	B	0.06405	0.002	T	0.42498	-0.9448	9	0.51188	T	0.08	.	6.4363	0.21825	0.5979:0.267:0.135:0.0	rs45554335	461	Q711Q0-3	.	A	461	ENSP00000318713:D461A;ENSP00000363259:D461A	ENSP00000318713:D461A	D	+	2	0	C10orf71	50201978	0.803000	0.28956	0.000000	0.03702	0.001000	0.01503	2.043000	0.41231	-0.215000	0.10063	-0.262000	0.10625	GAC	A|0.802;C|0.198	0.198	strong		0.547	C10orf71-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047984.2	NM_199459	
DROSHA	29102	hgsc.bcm.edu	37	5	31515657	31515657	+	Missense_Mutation	SNP	G	G	A	rs55656741	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:31515657G>A	ENST00000511367.2	-	6	1206	c.962C>T	c.(961-963)tCg>tTg	p.S321L	DROSHA_ENST00000344624.3_Missense_Mutation_p.S321L|DROSHA_ENST00000442743.1_Intron|DROSHA_ENST00000513349.1_Intron	NM_013235.4	NP_037367.3	Q9NRR4	RNC_HUMAN	drosha, ribonuclease type III	321			S -> L (in dbSNP:rs55656741).		defense response to Gram-negative bacterium (GO:0050829)|defense response to Gram-positive bacterium (GO:0050830)|gene expression (GO:0010467)|miRNA metabolic process (GO:0010586)|pre-miRNA processing (GO:0031054)|primary miRNA processing (GO:0031053)|ribosome biogenesis (GO:0042254)|RNA phosphodiester bond hydrolysis (GO:0090501)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|rRNA catabolic process (GO:0016075)	nucleoplasm (GO:0005654)	lipopolysaccharide binding (GO:0001530)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|ribonuclease III activity (GO:0004525)			breast(4)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(19)|lung(33)|ovary(2)|skin(1)	66						aggaacaACCGATAAACCGTA	0.398													G|||	1412	0.281949	0.031	0.3559	5008	,	,		17973	0.1935		0.4513	False		,,,				2504	0.4857				p.S321L		Atlas-SNP	.											.	DROSHA	130	.	0			c.C962T						PASS	.	G	,LEU/SER	196,1682		10,176,753	27.0	30.0	29.0		,962	2.0	0.0	5	dbSNP_129	29	2054,2126		484,1086,520	yes	intron,missense	DROSHA	NM_001100412.1,NM_013235.4	,145	494,1262,1273	AA,AG,GG		49.1388,10.4366,37.141	,benign	,321/1375	31515657	2250,3808	939	2090	3029	SO:0001583	missense	29102	exon6			ACAACCGATAAAC	AF116910	CCDS47194.1, CCDS47195.1	5q11.2	2010-11-17	2010-10-28	2010-10-28	ENSG00000113360	ENSG00000113360	3.1.26.3		17904	protein-coding gene	gene with protein product	"""drosha, ribonuclease type III"", ""drosha, double-stranded RNA-specific endoribonuclease"""	608828	"""ribonuclease type III, nuclear"""	RNASEN		10713462, 10948199	Standard	NM_013235		Approved	RNASE3L, Etohi2, HSA242976, RN3	uc003jhg.2	Q9NRR4	OTTHUMG00000161976	ENST00000511367.2:c.962C>T	5.37:g.31515657G>A	ENSP00000425979:p.Ser321Leu	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	114	40	0.350877	NM_013235	E7EMP9|Q7Z5V2|Q86YH0|Q9NW73|Q9Y2V9|Q9Y4Y0	Missense_Mutation	SNP	ENST00000511367.2	37	CCDS47195.1	611	0.27976190476190477	19	0.03861788617886179	137	0.3784530386740331	111	0.19405594405594406	344	0.45382585751978893	G	4.156	0.027468	0.08054	0.104366	0.491388	ENSG00000113360	ENST00000511367;ENST00000344624;ENST00000512302	T;T;T	0.44482	0.92;0.92;0.92	3.77	1.96	0.26148	.	1.219030	0.05901	N	0.629997	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.46456	-0.9190	9	0.29301	T	0.29	3.4861	6.3598	0.21422	0.2284:0.0:0.7716:0.0	rs55656741;rs61748190	321	Q9NRR4	RNC_HUMAN	L	321;321;88	ENSP00000425979:S321L;ENSP00000339845:S321L;ENSP00000428782:S88L	ENSP00000339845:S321L	S	-	2	0	DROSHA	31551414	0.389000	0.25205	0.005000	0.12908	0.975000	0.68041	0.946000	0.29069	0.557000	0.29117	0.561000	0.74099	TCG	G|0.675;A|0.325	0.325	strong		0.398	DROSHA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366561.3	NM_013235	
CHD8	57680	hgsc.bcm.edu	37	14	21868678	21868678	+	Silent	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:21868678C>T	ENST00000557364.1	-	23	4727	c.4464G>A	c.(4462-4464)gtG>gtA	p.V1488V	CHD8_ENST00000555962.1_Intron|CHD8_ENST00000430710.3_Silent_p.V1209V|CHD8_ENST00000399982.2_Silent_p.V1488V			Q9HCK8	CHD8_HUMAN	chromodomain helicase DNA binding protein 8	1488					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)		GAAGACAGTACACGAGAATGG	0.443																																					p.V1488V		Atlas-SNP	.											.	CHD8	339	.	0			c.G4464A						PASS	.						59.0	58.0	58.0					14																	21868678		1858	4104	5962	SO:0001819	synonymous_variant	57680	exon22			ACAGTACACGAGA	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.4464G>A	14.37:g.21868678C>T		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	54	15	0.277778	NM_001170629	Q4G0D8|Q68DQ0|Q6DKH9|Q6P440|Q6ZNL7|Q8N3Z9|Q8NCY4|Q8TBR9|Q96F26	Silent	SNP	ENST00000557364.1	37	CCDS53885.1	.	.	.	.	.	.	.	.	.	.	C	5.897	0.349646	0.11182	.	.	ENSG00000100888	ENST00000555935	D	0.84660	-1.88	4.82	-4.95	0.03048	.	0.000000	0.85682	D	0.000000	T	0.75117	0.3806	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.61133	-0.7124	6	.	.	.	-7.29	1.8525	0.03172	0.1838:0.1552:0.384:0.277	.	.	.	.	I	714	ENSP00000451442:V714I	.	V	-	1	0	CHD8	20938518	0.000000	0.05858	0.744000	0.31058	0.958000	0.62258	-2.646000	0.00860	-1.016000	0.03371	0.650000	0.86243	GTA	.	.	none		0.443	CHD8-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410436.1	NM_020920	
LARP4	113251	hgsc.bcm.edu	37	12	50821551	50821551	+	Missense_Mutation	SNP	G	G	T	rs146142861	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:50821551G>T	ENST00000398473.2	+	2	137	c.25G>T	c.(25-27)Gca>Tca	p.A9S	LARP4_ENST00000522085.1_Missense_Mutation_p.A9S|LARP4_ENST00000293618.8_Missense_Mutation_p.A9S|LARP4_ENST00000347328.5_Missense_Mutation_p.A9S|LARP4_ENST00000518444.1_Missense_Mutation_p.A8S|LARP4_ENST00000429001.3_Missense_Mutation_p.A9S|LARP4_ENST00000518561.1_5'UTR	NM_052879.4|NM_199188.2	NP_443111.4|NP_954658.2	Q71RC2	LARP4_HUMAN	La ribonucleoprotein domain family, member 4	9					cytoskeleton organization (GO:0007010)|regulation of cell morphogenesis (GO:0022604)	membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(3)|kidney(2)|large_intestine(2)|liver(2)|lung(7)|ovary(1)|skin(2)|urinary_tract(1)	23						TTAGCAGGTAGCATCTAAAGG	0.348													G|||	48	0.00958466	0.0023	0.0245	5008	,	,		13782	0.0		0.0249	False		,,,				2504	0.0031				p.A9S		Atlas-SNP	.											.	LARP4	58	.	0			c.G25T						PASS	.	G	SER/ALA,SER/ALA,SER/ALA,SER/ALA,SER/ALA,SER/ALA	15,3615		0,15,1800	66.0	64.0	65.0		25,25,25,25,22,25	3.2	1.0	12	dbSNP_134	65	215,7943		2,211,3866	yes	missense,missense,missense,missense,missense,missense	LARP4	NM_001170803.1,NM_001170804.1,NM_001170808.1,NM_052879.4,NM_199188.2,NM_199190.2	99,99,99,99,99,99	2,226,5666	TT,TG,GG		2.6354,0.4132,1.9511	benign,benign,benign,benign,benign,benign	9/583,9/446,9/654,9/725,8/724,9/654	50821551	230,11558	1815	4079	5894	SO:0001583	missense	113251	exon2			CAGGTAGCATCTA	AY004310	CCDS41782.1, CCDS44879.1, CCDS44880.1, CCDS44879.2, CCDS53789.1, CCDS53790.1	12q13.12	2005-08-09			ENSG00000161813	ENSG00000161813		"""La ribonucleoprotein domain containing"""	24320	protein-coding gene	gene with protein product						12477932	Standard	NM_052879		Approved	PP13296	uc001rwp.2	Q71RC2	OTTHUMG00000163724	ENST00000398473.2:c.25G>T	12.37:g.50821551G>T	ENSP00000381490:p.Ala9Ser	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	59	32	0.542373	NM_001170808	A8K6T1|E9PDG5|G3XAA8|G5E976|Q5CZ97|Q6ZV14|Q96NF9	Missense_Mutation	SNP	ENST00000398473.2	37	CCDS41782.1	32	0.014652014652014652	3	0.006097560975609756	10	0.027624309392265192	0	0.0	19	0.025065963060686015	G	14.78	2.636835	0.47049	0.004132	0.026354	ENSG00000161813	ENST00000293618;ENST00000429001;ENST00000548174;ENST00000398473;ENST00000522085;ENST00000398464;ENST00000518444;ENST00000551886;ENST00000520064;ENST00000347328;ENST00000550260	T;T;T;T;T;T	0.41065	1.6;1.51;1.62;1.01;1.59;1.58	5.64	3.15	0.36227	.	0.107097	0.64402	D	0.000006	T	0.09069	0.0224	N	0.14661	0.345	0.20926	N	0.999821	B;B;B;B;B	0.29270	0.004;0.003;0.24;0.009;0.015	B;B;B;B;B	0.37091	0.01;0.001;0.241;0.031;0.068	T	0.07558	-1.0766	10	0.39692	T	0.17	.	3.3587	0.07178	0.6494:0.1409:0.0744:0.1354	.	8;9;9;9;9	Q71RC2-3;G3XAA8;G5E976;Q71RC2;Q71RC2-4	.;.;.;LARP4_HUMAN;.	S	9;9;17;9;9;9;8;9;8;9;8	ENSP00000293618:A9S;ENSP00000415464:A9S;ENSP00000381490:A9S;ENSP00000429781:A9S;ENSP00000429077:A8S;ENSP00000340901:A9S	ENSP00000293618:A9S	A	+	1	0	LARP4	49107818	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	4.142000	0.58044	0.961000	0.38030	-0.238000	0.12139	GCA	G|0.983;T|0.017	0.017	strong		0.348	LARP4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000374981.1	NM_052879	
HERC4	26091	hgsc.bcm.edu	37	10	69695974	69695974	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:69695974C>T	ENST00000395198.3	-	23	2861	c.2614G>A	c.(2614-2616)Ggt>Agt	p.G872S	HERC4_ENST00000277817.6_Missense_Mutation_p.G762S|HERC4_ENST00000412272.2_Missense_Mutation_p.G794S|HERC4_ENST00000373700.4_Missense_Mutation_p.G864S|HERC4_ENST00000395187.2_3'UTR	NM_022079.2	NP_071362.1	Q5GLZ8	HERC4_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase 4	872	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				cell differentiation (GO:0030154)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			NS(1)|breast(1)|cervix(1)|endometrium(1)|large_intestine(6)|lung(13)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	27						TCTGTTGCACCAAAGTTTTCA	0.308																																					p.G872S		Atlas-SNP	.											.	HERC4	78	.	0			c.G2614A						PASS	.						138.0	129.0	132.0					10																	69695974		2203	4300	6503	SO:0001583	missense	26091	exon23			TTGCACCAAAGTT	AY221963	CCDS7274.1, CCDS41533.1, CCDS60541.1, CCDS60542.1	10q21.3	2013-09-20	2012-02-23		ENSG00000148634	ENSG00000148634			24521	protein-coding gene	gene with protein product		609248	"""hect domain and RLD 4"""			10997877	Standard	NM_022079		Approved	DKFZP564G092, KIAA1593	uc001jng.4	Q5GLZ8	OTTHUMG00000018343	ENST00000395198.3:c.2614G>A	10.37:g.69695974C>T	ENSP00000378624:p.Gly872Ser	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	62	15	0.241935	NM_022079	Q5GC98|Q5GC99|Q5GCA0|Q8IXP9|Q9HCH9	Missense_Mutation	SNP	ENST00000395198.3	37	CCDS41533.1	.	.	.	.	.	.	.	.	.	.	C	32	5.153248	0.94645	.	.	ENSG00000148634	ENST00000277817;ENST00000412272;ENST00000395198;ENST00000373700	T;T;T;T	0.58210	0.35;0.35;0.35;0.35	5.2	5.2	0.72013	HECT (4);	0.000000	0.85682	D	0.000000	T	0.79587	0.4471	M	0.91872	3.25	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	0.91635	0.999;0.999;0.999;0.999;0.999	D	0.84384	0.0551	10	0.87932	D	0	.	19.1052	0.93291	0.0:1.0:0.0:0.0	.	794;762;722;864;872	Q5GLZ8-3;Q5GLZ8-6;Q5VXS9;Q5GLZ8-2;Q5GLZ8	.;.;.;.;HERC4_HUMAN	S	762;794;872;864	ENSP00000277817:G762S;ENSP00000416504:G794S;ENSP00000378624:G872S;ENSP00000362804:G864S	ENSP00000277817:G762S	G	-	1	0	HERC4	69365980	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.364000	0.79526	2.568000	0.86640	0.460000	0.39030	GGT	.	.	none		0.308	HERC4-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359262.1	NM_015601	
LRGUK	136332	hgsc.bcm.edu	37	7	133906669	133906669	+	Splice_Site	SNP	C	C	T	rs35149449	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:133906669C>T	ENST00000285928.2	+	16	2051	c.1982C>T	c.(1981-1983)gCg>gTg	p.A661V		NM_144648.1	NP_653249.1	Q96M69	LRGUK_HUMAN	leucine-rich repeats and guanylate kinase domain containing	661			A -> V (in dbSNP:rs35149449).			cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|kinase activity (GO:0016301)			breast(1)|endometrium(2)|kidney(2)|large_intestine(12)|lung(23)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	49						AAAACACCAGCGGTAAGAGAG	0.378													C|||	671	0.133986	0.0061	0.1297	5008	,	,		14081	0.3839		0.0706	False		,,,				2504	0.1176				p.A661V		Atlas-SNP	.											.	LRGUK	113	.	0			c.C1982T						PASS	.	C	VAL/ALA	101,4305	79.3+/-117.8	5,91,2107	43.0	45.0	44.0		1982	0.7	0.8	7	dbSNP_126	44	799,7801	185.2+/-233.0	31,737,3532	yes	missense-near-splice	LRGUK	NM_144648.1	64	36,828,5639	TT,TC,CC		9.2907,2.2923,6.9199	benign	661/826	133906669	900,12106	2203	4300	6503	SO:0001630	splice_region_variant	136332	exon16			CACCAGCGGTAAG	AK057348	CCDS5830.1	7q33	2006-10-27			ENSG00000155530	ENSG00000155530			21964	protein-coding gene	gene with protein product							Standard	NM_144648		Approved	FLJ32786	uc003vrm.1	Q96M69	OTTHUMG00000155320	ENST00000285928.2:c.1983+1C>T	7.37:g.133906669C>T		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	30	17	0.566667	NM_144648	Q2M3I1	Missense_Mutation	SNP	ENST00000285928.2	37	CCDS5830.1	313	0.1433150183150183	8	0.016260162601626018	48	0.13259668508287292	213	0.3723776223776224	44	0.05804749340369393	C	0.017	-1.500426	0.01001	0.022923	0.092907	ENSG00000155530	ENST00000285928	T	0.26067	1.76	5.68	0.667	0.17907	.	0.544017	0.17786	N	0.162062	T	0.00012	0.0000	N	0.00841	-1.15	0.42258	P	0.007993999999999946	B	0.09022	0.002	B	0.01281	0.0	T	0.46470	-0.9189	9	0.02654	T	1	-0.5962	7.6851	0.28536	0.0:0.4741:0.0:0.5259	rs35149449;rs61749959	661	Q96M69	LRGUK_HUMAN	V	661	ENSP00000285928:A661V	ENSP00000285928:A661V	A	+	2	0	LRGUK	133557209	0.992000	0.36948	0.826000	0.32828	0.038000	0.13279	-0.101000	0.10973	0.044000	0.15775	-0.225000	0.12378	GCG	C|0.904;T|0.096	0.096	strong		0.378	LRGUK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339442.1	NM_144648	Missense_Mutation
MUC4	4585	hgsc.bcm.edu	37	3	195506555	195506555	+	Missense_Mutation	SNP	C	C	T	rs368695884	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195506555C>T	ENST00000463781.3	-	2	12355	c.11896G>A	c.(11896-11898)Gcc>Acc	p.A3966T	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.A3966T	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.A3966T(2)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		AGAGAGGTGGCGTGACCTGTG	0.592													.|||	176	0.0351438	0.0083	0.0677	5008	,	,		7977	0.0119		0.0915	False		,,,				2504	0.0143				p.A3966T		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	2	Substitution - Missense(2)	endometrium(1)|kidney(1)	c.G11896A						scavenged	.						15.0	10.0	11.0					3																	195506555		666	1488	2154	SO:0001583	missense	4585	exon2			AGGTGGCGTGACC	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.11896G>A	3.37:g.195506555C>T	ENSP00000417498:p.Ala3966Thr	Somatic	76	3	0.0394737		WXS	Illumina HiSeq	Phase_I	33	11	0.333333	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	N	0.905	-0.721125	0.03182	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.48522	1.23;0.81	.	.	.	.	.	.	.	.	T	0.22551	0.0544	N	0.19112	0.55	0.09310	N	1	B	0.18741	0.03	B	0.06405	0.002	T	0.12915	-1.0529	7	.	.	.	-3.1782	2.1866	0.03888	0.0:0.3341:0.3337:0.3322	.	3838	E7ESK3	.	T	3966	ENSP00000417498:A3966T;ENSP00000420243:A3966T	.	A	-	1	0	MUC4	196991334	0.000000	0.05858	0.002000	0.10522	0.002000	0.02628	-0.202000	0.09451	-2.037000	0.00920	-2.088000	0.00374	GCC	.	.	weak		0.592	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
ZNF598	90850	hgsc.bcm.edu	37	16	2050192	2050192	+	Missense_Mutation	SNP	G	G	T	rs11556528	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:2050192G>T	ENST00000563630.1	-	9	1435	c.1193C>A	c.(1192-1194)tCc>tAc	p.S398Y	AC005606.15_ENST00000567515.1_lincRNA|ZNF598_ENST00000431526.1_Missense_Mutation_p.S453Y|ZNF598_ENST00000562103.1_Missense_Mutation_p.S398Y			Q86UK7	ZN598_HUMAN	zinc finger protein 598	453							poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|lung(7)|skin(1)|urinary_tract(1)	16						GCAGGAGGAGGAAGTGGAGGC	0.652													T|||	636	0.126997	0.0061	0.2176	5008	,	,		17001	0.0427		0.1869	False		,,,				2504	0.2515				p.S453Y		Atlas-SNP	.											.	ZNF598	55	.	0			c.C1358A						PASS	.	T	TYR/SER	127,3879		5,117,1881	33.0	41.0	38.0		1360	1.3	0.0	16	dbSNP_120	38	1325,6851		91,1143,2854	yes	missense	ZNF598	NM_178167.2	144	96,1260,4735	TT,TG,GG		16.206,3.1702,11.9192	possibly-damaging	453/905	2050192	1452,10730	2003	4088	6091	SO:0001583	missense	90850	exon11			GAGGAGGAAGTGG	BC029270		16p13.3	2008-05-02				ENSG00000167962		"""Zinc fingers, C2H2-type"""	28079	protein-coding gene	gene with protein product							Standard	NM_178167		Approved	FLJ00086	uc002cof.2	Q86UK7		ENST00000563630.1:c.1193C>A	16.37:g.2050192G>T	ENSP00000455882:p.Ser398Tyr	Somatic	19	0	0		WXS	Illumina HiSeq	Phase_I	24	15	0.625	NM_178167	Q8IW49|Q8N3D9|Q96FG3|Q9H7J3	Missense_Mutation	SNP	ENST00000563630.1	37		227	0.10393772893772894	4	0.008130081300813009	60	0.16574585635359115	21	0.03671328671328671	142	0.18733509234828497	.	0.007	-1.994354	0.00435	0.031702	0.16206	ENSG00000167962	ENST00000431526	T	0.18810	2.19	3.33	1.26	0.21427	.	0.502650	0.20611	N	0.088974	T	0.00039	0.0001	M	0.67953	2.075	0.80722	P	0.0	D	0.59767	0.986	P	0.54100	0.742	T	0.06862	-1.0803	9	0.33940	T	0.23	.	10.8593	0.46817	0.0:0.0:0.6228:0.3772	rs11556528;rs11556528	453	Q86UK7	ZN598_HUMAN	Y	453	ENSP00000411409:S453Y	ENSP00000411409:S453Y	S	-	2	0	ZNF598	1990193	0.871000	0.30034	0.000000	0.03702	0.022000	0.10575	3.120000	0.50430	-0.295000	0.08960	-3.277000	0.00047	TCC	G|0.889;T|0.111	0.111	strong		0.652	ZNF598-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000434439.1	NM_178167	
ZKSCAN2	342357	hgsc.bcm.edu	37	16	25258035	25258035	+	Silent	SNP	A	A	G	rs11649280	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:25258035A>G	ENST00000328086.7	-	5	2285	c.1482T>C	c.(1480-1482)aaT>aaC	p.N494N		NM_001012981.4	NP_001012999.3	Q63HK3	ZKSC2_HUMAN	zinc finger with KRAB and SCAN domains 2	494					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)		TACCACTGAGATTCTGAAACA	0.463													G|||	1682	0.335863	0.4758	0.3026	5008	,	,		23355	0.3294		0.2107	False		,,,				2504	0.3057				p.N494N		Atlas-SNP	.											.	ZKSCAN2	90	.	0			c.T1482C						PASS	.	G		1988,2406	614.6+/-392.4	454,1080,663	110.0	108.0	109.0		1482	2.5	1.0	16	dbSNP_120	109	1787,6813	733.2+/-406.9	181,1425,2694	no	coding-synonymous	ZKSCAN2	NM_001012981.4		635,2505,3357	GG,GA,AA		20.7791,45.2435,29.0519		494/968	25258035	3775,9219	2197	4300	6497	SO:0001819	synonymous_variant	342357	exon5			ACTGAGATTCTGA	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.1482T>C	16.37:g.25258035A>G		Somatic	277	0	0		WXS	Illumina HiSeq	Phase_I	244	97	0.397541	NM_001012981	A1L3B4|Q6ZN77	Silent	SNP	ENST00000328086.7	37	CCDS32410.1																																																																																			A|0.696;G|0.304	0.304	strong		0.463	ZKSCAN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435739.1	NM_001012981	
TLR10	81793	hgsc.bcm.edu	37	4	38776303	38776303	+	Silent	SNP	T	T	C	rs11466652	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:38776303T>C	ENST00000308973.4	-	4	1514	c.909A>G	c.(907-909)aaA>aaG	p.K303K	TLR10_ENST00000506111.1_Silent_p.K303K|TLR10_ENST00000361424.2_Silent_p.K303K|TLR10_ENST00000508334.1_Silent_p.K303K|TLR10_ENST00000507953.1_5'Flank	NM_001017388.2|NM_001195107.1|NM_030956.3	NP_001017388.1|NP_001182036.1|NP_112218.2	Q9BXR5	TLR10_HUMAN	toll-like receptor 10	303					immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of inflammatory response (GO:0050729)|regulation of cytokine secretion (GO:0050707)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor signaling pathway (GO:0002224)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	transmembrane signaling receptor activity (GO:0004888)			breast(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(11)|prostate(1)|urinary_tract(2)	25						CATGCTCCAATTTTATAGTTC	0.343													T|||	1009	0.201478	0.3374	0.0994	5008	,	,		19962	0.122		0.1481	False		,,,				2504	0.227				p.K303K		Atlas-SNP	.											TLR10,NS,carcinoma,-2,1	TLR10	87	1	0			c.A909G						PASS	.	T	,,,,	1253,3153	423.6+/-340.2	167,919,1117	83.0	85.0	85.0		909,909,909,867,909	1.3	0.8	4	dbSNP_120	85	1200,7398	241.4+/-271.8	85,1030,3184	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TLR10	NM_001017388.2,NM_001195106.1,NM_001195107.1,NM_001195108.1,NM_030956.3	,,,,	252,1949,4301	CC,CT,TT		13.9567,28.4385,18.8634	,,,,	303/812,303/812,303/812,289/798,303/812	38776303	2453,10551	2203	4299	6502	SO:0001819	synonymous_variant	81793	exon2			CTCCAATTTTATA	AF296673	CCDS3445.1	4p14	2009-11-23			ENSG00000174123	ENSG00000174123		"""CD molecules"""	15634	protein-coding gene	gene with protein product		606270				11267672	Standard	NM_030956		Approved	CD290	uc003gtk.3	Q9BXR5	OTTHUMG00000128578	ENST00000308973.4:c.909A>G	4.37:g.38776303T>C		Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	159	78	0.490566	NM_001017388	A8K7L1|B3Y668|D1CS21|D1CS22|Q32MI7|Q32MI8|Q5FWG4|Q6UXL3	Silent	SNP	ENST00000308973.4	37	CCDS3445.1																																																																																			T|0.814;C|0.186	0.186	strong		0.343	TLR10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250430.1		
PM20D1	148811	hgsc.bcm.edu	37	1	205801872	205801872	+	Missense_Mutation	SNP	A	A	G	rs1361754	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:205801872A>G	ENST00000367136.4	-	11	1183	c.1139T>C	c.(1138-1140)aTt>aCt	p.I380T	PM20D1_ENST00000460624.1_5'UTR	NM_152491.4	NP_689704.4	Q6GTS8	P20D1_HUMAN	peptidase M20 domain containing 1	380			I -> T (in dbSNP:rs1361754). {ECO:0000269|PubMed:15489334}.		negative regulation of neuron death (GO:1901215)|regulation of defense response to virus by host (GO:0050691)|regulation of viral process (GO:0050792)	extracellular vesicular exosome (GO:0070062)	metal ion binding (GO:0046872)|peptidase activity (GO:0008233)			breast(2)|endometrium(2)|kidney(1)|large_intestine(6)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|stomach(1)	28	Breast(84;0.201)		BRCA - Breast invasive adenocarcinoma(75;0.0252)			ATCAGCCACAATGTTCTTCGT	0.478													A|||	1411	0.281749	0.3487	0.3112	5008	,	,		19562	0.0129		0.5219	False		,,,				2504	0.2004				p.I380T		Atlas-SNP	.											.	PM20D1	56	.	0			c.T1139C						PASS	.	A	THR/ILE	1770,2636	524.4+/-371.3	368,1034,801	107.0	93.0	98.0		1139	-0.1	0.3	1	dbSNP_88	98	4497,4103	591.5+/-392.8	1170,2157,973	yes	missense	PM20D1	NM_152491.4	89	1538,3191,1774	GG,GA,AA		47.7093,40.1725,48.1855	benign	380/503	205801872	6267,6739	2203	4300	6503	SO:0001583	missense	148811	exon11			GCCACAATGTTCT		CCDS1460.1	1q32.1	2008-02-05			ENSG00000162877	ENSG00000162877			26518	protein-coding gene	gene with protein product							Standard	NM_152491		Approved	FLJ32569, Cps1	uc001hdj.3	Q6GTS8	OTTHUMG00000035999	ENST00000367136.4:c.1139T>C	1.37:g.205801872A>G	ENSP00000356104:p.Ile380Thr	Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	119	66	0.554622	NM_152491	Q6P4E3|Q96DM4	Missense_Mutation	SNP	ENST00000367136.4	37	CCDS1460.1	714	0.3269230769230769	173	0.3516260162601626	144	0.39779005524861877	3	0.005244755244755245	394	0.5197889182058048	A	0.003	-2.402190	0.00195	0.401725	0.522907	ENSG00000162877	ENST00000367136	T	0.59364	0.27	4.98	-0.108	0.13588	Peptidase M20, dimerisation (2);	0.238545	0.41001	N	0.000974	T	0.00012	0.0000	N	0.12746	0.255	0.58432	P	4.000000000004E-6	B	0.16166	0.016	B	0.16289	0.015	T	0.47935	-0.9078	9	0.15499	T	0.54	.	7.4869	0.27439	0.5665:0.0:0.4335:0.0	rs1361754;rs17433039;rs59953848;rs1361754	380	Q6GTS8	P20D1_HUMAN	T	380	ENSP00000356104:I380T	ENSP00000356104:I380T	I	-	2	0	PM20D1	204068495	0.852000	0.29690	0.270000	0.24601	0.069000	0.16628	0.906000	0.28517	-0.048000	0.13401	-0.274000	0.10170	ATT	A|0.603;G|0.397	0.397	strong		0.478	PM20D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087736.1	NM_152491	
PCDHB15	56121	hgsc.bcm.edu	37	5	140626855	140626855	+	Missense_Mutation	SNP	C	C	T	rs56840646	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:140626855C>T	ENST00000231173.3	+	1	1709	c.1709C>T	c.(1708-1710)gCg>gTg	p.A570V		NM_018935.2	NP_061758.1	Q9Y5E8	PCDBF_HUMAN	protocadherin beta 15	570	Cadherin 6. {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)			AACGGCTCCGCGCCCTGCACC	0.721													C|||	504	0.100639	0.0726	0.1657	5008	,	,		13489	0.0397		0.1551	False		,,,				2504	0.0992				p.A570V		Atlas-SNP	.											PCDHB15,colon,carcinoma,-1,1	PCDHB15	138	1	0			c.C1709T						scavenged	.						9.0	12.0	11.0					5																	140626855		2116	4166	6282	SO:0001583	missense	56121	exon1			GCTCCGCGCCCTG	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.1709C>T	5.37:g.140626855C>T	ENSP00000231173:p.Ala570Val	Somatic	3	0	0		WXS	Illumina HiSeq	Phase_I	11	5	0.454545	NM_018935	Q8IUX5	Missense_Mutation	SNP	ENST00000231173.3	37	CCDS4257.1	240	0.10989010989010989	48	0.0975609756097561	49	0.13535911602209943	25	0.043706293706293704	118	0.15567282321899736	C	12.09	1.833596	0.32421	.	.	ENSG00000113248	ENST00000231173	T	0.60299	0.2	4.02	2.12	0.27331	Cadherin-like (1);	.	.	.	.	T	0.00328	0.0010	M	0.74647	2.275	0.80722	P	0.0	B	0.28291	0.206	B	0.22753	0.041	T	0.18999	-1.0319	8	0.62326	D	0.03	.	10.7514	0.46211	0.0:0.8242:0.0:0.1758	rs56840646	570	Q9Y5E8	PCDBF_HUMAN	V	570	ENSP00000231173:A570V	ENSP00000231173:A570V	A	+	2	0	PCDHB15	140607039	0.000000	0.05858	0.995000	0.50966	0.756000	0.42949	-0.092000	0.11129	0.794000	0.33899	0.479000	0.44913	GCG	C|0.881;T|0.119	0.119	strong		0.721	PCDHB15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251804.2	NM_018935	
KIF1B	23095	hgsc.bcm.edu	37	1	10318652	10318652	+	Silent	SNP	C	C	G	rs12402052	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:10318652C>G	ENST00000377086.1	+	4	487	c.285C>G	c.(283-285)gcC>gcG	p.A95A	KIF1B_ENST00000377081.1_Silent_p.A95A|KIF1B_ENST00000377093.4_Silent_p.A95A|KIF1B_ENST00000377083.1_Silent_p.A95A|KIF1B_ENST00000263934.6_Silent_p.A95A			O60333	KIF1B_HUMAN	kinesin family member 1B	95	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				anterograde axon cargo transport (GO:0008089)|apoptotic process (GO:0006915)|cytoskeleton-dependent intracellular transport (GO:0030705)|microtubule-based movement (GO:0007018)|mitochondrion transport along microtubule (GO:0047497)|neuromuscular synaptic transmission (GO:0007274)|neuron-neuron synaptic transmission (GO:0007270)|vesicle-mediated transport (GO:0016192)	cytoplasmic vesicle (GO:0031410)|cytoplasmic vesicle membrane (GO:0030659)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|kinesin binding (GO:0019894)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)	p.A95A(2)		breast(2)|endometrium(7)|kidney(8)|large_intestine(9)|lung(29)|ovary(3)|prostate(3)|skin(5)|stomach(3)|upper_aerodigestive_tract(2)	71	Ovarian(185;0.203)	all_lung(284;1.31e-05)|Lung NSC(185;2.2e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0259)|Colorectal(212;9.79e-07)|COAD - Colon adenocarcinoma(227;0.000143)|BRCA - Breast invasive adenocarcinoma(304;0.000413)|Kidney(185;0.00134)|KIRC - Kidney renal clear cell carcinoma(229;0.0037)|STAD - Stomach adenocarcinoma(132;0.0113)|READ - Rectum adenocarcinoma(331;0.0642)		GTATTTTTGCCTATGGGCAGA	0.413													C|||	1152	0.230032	0.056	0.3199	5008	,	,		17615	0.2887		0.3052	False		,,,				2504	0.2638				p.A95A		Atlas-SNP	.											KIF1B_ENST00000377093,NS,carcinoma,0,2	KIF1B	242	2	2	Substitution - coding silent(2)	stomach(2)	c.C285G						scavenged	.	C	,	403,4003	197.4+/-221.5	26,351,1826	143.0	135.0	137.0		285,285	3.8	1.0	1	dbSNP_120	137	2553,6047	415.4+/-351.8	399,1755,2146	no	coding-synonymous,coding-synonymous	KIF1B	NM_015074.3,NM_183416.3	,	425,2106,3972	GG,GC,CC		29.686,9.1466,22.728	,	95/1771,95/1154	10318652	2956,10050	2203	4300	6503	SO:0001819	synonymous_variant	23095	exon4			TTTTGCCTATGGG	AF257176	CCDS111.1, CCDS112.1	1p36.22	2014-09-17			ENSG00000054523	ENSG00000054523		"""Kinesins"", ""Pleckstrin homology (PH) domain containing"""	16636	protein-coding gene	gene with protein product		605995		CMT2A, CMT2		11389829, 10762626	Standard	NM_015074		Approved	KIAA0591, KLP, HMSNII	uc001aqw.4	O60333	OTTHUMG00000001817	ENST00000377086.1:c.285C>G	1.37:g.10318652C>G		Somatic	83	1	0.0120482		WXS	Illumina HiSeq	Phase_I	75	39	0.52	NM_183416	A6NFS8|A6NKQ4|Q4VXC3|Q4VXC4|Q4VXC5|Q4VXC6|Q96Q94|Q9BV80|Q9P280	Silent	SNP	ENST00000377086.1	37																																																																																				C|0.760;G|0.240	0.240	strong		0.413	KIF1B-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000005102.1		
NTRK1	4914	hgsc.bcm.edu	37	1	156848918	156848918	+	Missense_Mutation	SNP	C	C	T	rs6336	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:156848918C>T	ENST00000524377.1	+	15	1851	c.1810C>T	c.(1810-1812)Cat>Tat	p.H604Y	NTRK1_ENST00000392302.2_Missense_Mutation_p.H568Y|NTRK1_ENST00000368196.3_Missense_Mutation_p.H598Y|NTRK1_ENST00000358660.3_Missense_Mutation_p.H601Y	NM_002529.3	NP_002520.2	P04629	NTRK1_HUMAN	neurotrophic tyrosine kinase, receptor, type 1	604	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		H -> Y (in dbSNP:rs6336). {ECO:0000269|PubMed:10330344, ECO:0000269|PubMed:10391209, ECO:0000269|PubMed:10443680, ECO:0000269|PubMed:11310631, ECO:0000269|PubMed:17344846}.		activation of adenylate cyclase activity (GO:0007190)|activation of MAPKK activity (GO:0000186)|activation of phospholipase C activity (GO:0007202)|aging (GO:0007568)|axon guidance (GO:0007411)|axonogenesis involved in innervation (GO:0060385)|B cell differentiation (GO:0030183)|cellular response to nerve growth factor stimulus (GO:1990090)|cellular response to nicotine (GO:0071316)|circadian rhythm (GO:0007623)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|detection of temperature stimulus involved in sensory perception of pain (GO:0050965)|developmental programmed cell death (GO:0010623)|learning or memory (GO:0007611)|mechanoreceptor differentiation (GO:0042490)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|olfactory nerve development (GO:0021553)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of angiogenesis (GO:0045766)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of neuron projection development (GO:0010976)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of programmed cell death (GO:0043068)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of Ras protein signal transduction (GO:0046579)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|Ras protein signal transduction (GO:0007265)|response to activity (GO:0014823)|response to axon injury (GO:0048678)|response to drug (GO:0042493)|response to electrical stimulus (GO:0051602)|response to ethanol (GO:0045471)|response to hydrostatic pressure (GO:0051599)|response to nutrient levels (GO:0031667)|response to radiation (GO:0009314)|Sertoli cell development (GO:0060009)|small GTPase mediated signal transduction (GO:0007264)|sympathetic nervous system development (GO:0048485)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	axon (GO:0030424)|cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|dendrite (GO:0030425)|early endosome (GO:0005769)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|nerve growth factor binding (GO:0048406)|nerve growth factor receptor activity (GO:0010465)|neurotrophin binding (GO:0043121)|protein homodimerization activity (GO:0042803)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(3)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(7)|lung(35)|ovary(8)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	74	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)				Amitriptyline(DB00321)|Imatinib(DB00619)|Regorafenib(DB08896)	TCACAGATCCCATGGACCTGA	0.647			T	"""TPM3, TPR, TFG"""	papillary thyroid					TSP Lung(10;0.080)			C|||	122	0.024361	0.0038	0.0288	5008	,	,		19266	0.0		0.0408	False		,,,				2504	0.0573				p.H604Y		Atlas-SNP	.		Dom	yes		1	1q21-q22	4914	"""neurotrophic tyrosine kinase, receptor, type 1"""		E	.	NTRK1	287	.	0			c.C1810T	GRCh37	CM990977	NTRK1	M	rs6336	PASS	.	C	TYR/HIS,TYR/HIS,TYR/HIS	52,4354	47.5+/-82.1	0,52,2151	29.0	31.0	30.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1702,1792,1810	4.4	1.0	1	dbSNP_52	30	520,8080	143.3+/-199.3	21,478,3801	yes	missense,missense,missense	NTRK1	NM_001007792.1,NM_001012331.1,NM_002529.3	83,83,83	21,530,5952	TT,TC,CC		6.0465,1.1802,4.398	probably-damaging,probably-damaging,probably-damaging	568/761,598/791,604/797	156848918	572,12434	2203	4300	6503	SO:0001583	missense	4914	exon15			AGATCCCATGGAC	Y09028	CCDS1161.1, CCDS30890.1, CCDS30891.1	1q21-q22	2014-09-17			ENSG00000198400	ENSG00000198400	2.7.10.1	"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	8031	protein-coding gene	gene with protein product	"""high affinity nerve growth factor receptor"""	191315				2869410	Standard	NM_001007792		Approved	TRK, TRKA, MTC	uc001fqh.1	P04629	OTTHUMG00000041304	ENST00000524377.1:c.1810C>T	1.37:g.156848918C>T	ENSP00000431418:p.His604Tyr	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	143	59	0.412587	NM_002529	B2R6T5|B7ZM34|P08119|Q15655|Q15656|Q5D056|Q5VZS2|Q7Z5C3|Q9UIU7	Missense_Mutation	SNP	ENST00000524377.1	37	CCDS1161.1	41	0.018772893772893772	0	0.0	10	0.027624309392265192	0	0.0	31	0.040897097625329816	C	22.7	4.323291	0.81580	0.011802	0.060465	ENSG00000198400	ENST00000392302;ENST00000368196;ENST00000524377;ENST00000358660	D;D;D;D	0.83075	-1.68;-1.68;-1.68;-1.68	4.37	4.37	0.52481	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.53938	D	0.000047	D	0.83599	0.5289	L	0.33137	0.985	0.80722	A	1	D;D;D;D	0.76494	0.998;0.993;0.986;0.999	D;P;P;D	0.73708	0.981;0.782;0.808;0.966	D	0.86456	0.1776	9	0.87932	D	0	.	15.9854	0.80147	0.0:1.0:0.0:0.0	rs6336;rs17838190;rs6336	601;598;604;568	A8K3Z4;P04629-2;P04629;A6NF12	.;.;NTRK1_HUMAN;.	Y	568;598;604;601	ENSP00000376120:H568Y;ENSP00000357179:H598Y;ENSP00000431418:H604Y;ENSP00000351486:H601Y	ENSP00000351486:H601Y	H	+	1	0	NTRK1	155115542	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	7.568000	0.82369	2.432000	0.82394	0.561000	0.74099	CAT	C|0.965;T|0.035	0.035	strong		0.647	NTRK1-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000392279.1	NM_002529	
CYP7B1	9420	hgsc.bcm.edu	37	8	65527669	65527669	+	Missense_Mutation	SNP	C	C	T	rs59035258	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:65527669C>T	ENST00000310193.3	-	4	1144	c.971G>A	c.(970-972)cGt>cAt	p.R324H	CYP7B1_ENST00000523954.1_5'UTR	NM_004820.3	NP_004811.1	O75881	CP7B1_HUMAN	cytochrome P450, family 7, subfamily B, polypeptide 1	324				R -> H (in Ref. 1; AAC95426). {ECO:0000305}.	bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|cell death (GO:0008219)|cholesterol metabolic process (GO:0008203)|negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|positive regulation of epithelial cell proliferation (GO:0050679)|prostate gland epithelium morphogenesis (GO:0060740)|small molecule metabolic process (GO:0044281)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	25-hydroxycholesterol 7alpha-hydroxylase activity (GO:0033783)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxysterol 7-alpha-hydroxylase activity (GO:0008396)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(11)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	28		all_cancers(86;0.217)|Lung NSC(129;0.0521)|all_lung(136;0.0906)|all_epithelial(80;0.215)				CTGCAGCAAACGGTCAATTTC	0.463													C|||	89	0.0177716	0.0015	0.0115	5008	,	,		18048	0.001		0.0427	False		,,,				2504	0.0358				p.R324H		Atlas-SNP	.											CYP7B1,caecum,carcinoma,-1,3	CYP7B1	94	3	0			c.G971A						PASS	.	C	HIS/ARG	40,4366	43.8+/-77.6	0,40,2163	115.0	107.0	110.0		971	-4.4	0.8	8	dbSNP_129	110	344,8256	118.3+/-177.8	8,328,3964	yes	missense	CYP7B1	NM_004820.3	29	8,368,6127	TT,TC,CC		4.0,0.9079,2.9525	benign	324/507	65527669	384,12622	2203	4300	6503	SO:0001583	missense	9420	exon4			AGCAAACGGTCAA	AF029403	CCDS6180.1	8q21.3	2008-07-04	2003-01-14		ENSG00000172817	ENSG00000172817		"""Cytochrome P450s"""	2652	protein-coding gene	gene with protein product		603711	"""cytochrome P450, subfamily VIIB (oxysterol 7 alpha-hydroxylase), polypeptide 1"", ""spastic paraplegia 5A (autosomal recessive)"""	SPG5A		9802883, 18252231	Standard	NM_004820		Approved		uc003xvj.2	O75881	OTTHUMG00000164387	ENST00000310193.3:c.971G>A	8.37:g.65527669C>T	ENSP00000310721:p.Arg324His	Somatic	242	0	0		WXS	Illumina HiSeq	Phase_I	190	139	0.731579	NM_004820	B2RN07|Q9UNF5	Missense_Mutation	SNP	ENST00000310193.3	37	CCDS6180.1	42	0.019230769230769232	0	0.0	6	0.016574585635359115	0	0.0	36	0.047493403693931395	C	2.435	-0.329922	0.05314	0.009079	0.04	ENSG00000172817	ENST00000310193	T	0.69926	-0.44	5.93	-4.44	0.03557	.	0.617158	0.19131	N	0.121927	T	0.07593	0.0191	N	0.04018	-0.295	0.22112	N	0.999356	B	0.13145	0.007	B	0.11329	0.006	T	0.09100	-1.0690	10	0.11182	T	0.66	-19.8849	14.5279	0.67902	0.0:0.2062:0.0:0.7938	rs59035258;rs61729537	324	O75881	CP7B1_HUMAN	H	324	ENSP00000310721:R324H	ENSP00000310721:R324H	R	-	2	0	CYP7B1	65690223	1.000000	0.71417	0.763000	0.31416	0.995000	0.86356	0.783000	0.26802	-1.137000	0.02888	-0.140000	0.14226	CGT	C|0.976;T|0.024	0.024	strong		0.463	CYP7B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378550.1		
FAM46C	54855	hgsc.bcm.edu	37	1	118166096	118166096	+	Silent	SNP	C	C	T	rs2884587	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:118166096C>T	ENST00000369448.3	+	2	853	c.606C>T	c.(604-606)atC>atT	p.I202I		NM_017709.3	NP_060179.2	Q5VWP2	FA46C_HUMAN	family with sequence similarity 46, member C	202										endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(1)|lung(7)|ovary(1)|upper_aerodigestive_tract(1)	15	Lung SC(450;0.225)	all_cancers(81;0.000101)|all_lung(203;3.4e-06)|all_epithelial(167;4.98e-06)|Lung NSC(69;2.33e-05)		Lung(183;0.0576)|LUSC - Lung squamous cell carcinoma(189;0.192)|Colorectal(144;0.247)		ATAATCCCATCTCTGAGCACT	0.483			"""Mis, F, O"""		MM					Multiple Myeloma(3;1.13e-06)			C|||	673	0.134385	0.0159	0.2233	5008	,	,		21188	0.1141		0.164	False		,,,				2504	0.2219				p.I202I		Atlas-SNP	.		Rec	yes		1	1p12	54855	"""family with sequence similarity 46, member C"""		L	.	FAM46C	25	.	0			c.C606T						PASS	.	C		211,4195	129.0+/-165.8	10,191,2002	137.0	132.0	134.0		606	1.5	0.9	1	dbSNP_101	134	1423,7177	273.5+/-290.7	121,1181,2998	no	coding-synonymous	FAM46C	NM_017709.3		131,1372,5000	TT,TC,CC		16.5465,4.7889,12.5634		202/392	118166096	1634,11372	2203	4300	6503	SO:0001819	synonymous_variant	54855	exon2			TCCCATCTCTGAG	BC036516	CCDS896.1	1p12	2008-02-05			ENSG00000183508	ENSG00000183508			24712	protein-coding gene	gene with protein product		613952				12477932	Standard	NM_017709		Approved	FLJ20202	uc001ehe.3	Q5VWP2	OTTHUMG00000013703	ENST00000369448.3:c.606C>T	1.37:g.118166096C>T		Somatic	240	0	0		WXS	Illumina HiSeq	Phase_I	227	104	0.45815	NM_017709	A3KMG2|Q8NE25|Q9NXK0	Silent	SNP	ENST00000369448.3	37	CCDS896.1																																																																																			C|0.874;T|0.126	0.126	strong		0.483	FAM46C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038424.1	NM_017709	
GOLGA6C	653641	hgsc.bcm.edu	37	15	75562495	75562495	+	Silent	SNP	G	G	T	rs138154232	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:75562495G>T	ENST00000300576.5	+	18	2037	c.2037G>T	c.(2035-2037)ccG>ccT	p.P679P	RN7SL489P_ENST00000486185.2_RNA	NM_001164404.1	NP_001157876.1	A6NDK9	GOG6C_HUMAN	golgin A6 family, member C	679						Golgi apparatus (GO:0005794)				ovary(1)	1						ACAACCCCCCGGTACAGCAGA	0.602													N|||	184	0.0367412	0.1339	0.0086	5008	,	,		17187	0.0		0.001	False		,,,				2504	0.0				p.P679P		Atlas-SNP	.											GOLGA6C_ENST00000300576,bladder,carcinoma,0,3	GOLGA6C	12	3	0			c.G2037T						scavenged	.						52.0	65.0	61.0					15																	75562495		652	1575	2227	SO:0001819	synonymous_variant	653641	exon18			CCCCCCGGTACAG		CCDS58388.1	15q24.2	2014-02-12	2010-02-12		ENSG00000167195	ENSG00000167195			32206	protein-coding gene	gene with protein product			"""golgi autoantigen, golgin subfamily a, 6C"""				Standard	NM_001164404		Approved		uc002azs.2	A6NDK9	OTTHUMG00000172671	ENST00000300576.5:c.2037G>T	15.37:g.75562495G>T		Somatic	79	5	0.0632911		WXS	Illumina HiSeq	Phase_I	70	9	0.128571	NM_001164404		Silent	SNP	ENST00000300576.5	37	CCDS58388.1																																																																																			.	.	weak		0.602	GOLGA6C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419797.1	NM_001164404	
MYH6	4624	hgsc.bcm.edu	37	14	23859610	23859610	+	Missense_Mutation	SNP	C	C	T	rs28730771	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:23859610C>T	ENST00000356287.3	-	25	3417	c.3388G>A	c.(3388-3390)Gcc>Acc	p.A1130T	MYH6_ENST00000405093.3_Missense_Mutation_p.A1130T|MIR208A_ENST00000362287.1_RNA			P13533	MYH6_HUMAN	myosin, heavy chain 6, cardiac muscle, alpha	1130			A -> T (in dbSNP:rs28730771). {ECO:0000269|PubMed:15998695}.		adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|atrial cardiac muscle tissue morphogenesis (GO:0055009)|BMP signaling pathway (GO:0030509)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle fiber development (GO:0048739)|in utero embryonic development (GO:0001701)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|myofibril assembly (GO:0030239)|regulation of ATPase activity (GO:0043462)|regulation of blood pressure (GO:0008217)|regulation of heart contraction (GO:0008016)|regulation of heart growth (GO:0060420)|regulation of heart rate (GO:0002027)|regulation of the force of heart contraction (GO:0002026)|sarcomere organization (GO:0045214)|striated muscle contraction (GO:0006941)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|visceral muscle development (GO:0007522)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin complex (GO:0016459)|myosin filament (GO:0032982)|nucleus (GO:0005634)|sarcomere (GO:0030017)|stress fiber (GO:0001725)|Z disc (GO:0030018)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)|protein kinase binding (GO:0019901)			breast(4)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(16)|liver(1)|lung(60)|ovary(2)|pancreas(3)|prostate(6)|skin(6)|stomach(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	119	all_cancers(95;2.54e-05)			GBM - Glioblastoma multiforme(265;0.00764)|READ - Rectum adenocarcinoma(4;0.0289)|Colorectal(4;0.0441)		TTAGCCCTGGCGGTGCGCTCG	0.672													C|||	365	0.0728834	0.0098	0.121	5008	,	,		17242	0.0605		0.1352	False		,,,				2504	0.0726				p.A1130T		Atlas-SNP	.											.	MYH6	274	.	0			c.G3388A						PASS	.						11.0	12.0	12.0					14																	23859610		2165	4260	6425	SO:0001583	missense	4624	exon26			CCCTGGCGGTGCG	D00943	CCDS9600.1	14q11.2-q13	2014-09-17	2008-08-01		ENSG00000197616	ENSG00000197616		"""Myosins / Myosin superfamily : Class II"""	7576	protein-coding gene	gene with protein product	"""cardiomyopathy, hypertrophic 1"""	160710	"""myosin, heavy polypeptide 6, cardiac muscle, alpha (cardiomyopathy, hypertrophic 1)"""			2144212	Standard	NM_002471		Approved		uc001wjv.3	P13533	OTTHUMG00000028753	ENST00000356287.3:c.3388G>A	14.37:g.23859610C>T	ENSP00000348634:p.Ala1130Thr	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	102	38	0.372549	NM_002471	A2RTX1|D9YZU2|Q13943|Q14906|Q14907	Missense_Mutation	SNP	ENST00000356287.3	37	CCDS9600.1	195	0.08928571428571429	5	0.01016260162601626	52	0.143646408839779	40	0.06993006993006994	98	0.12928759894459102	c	18.48	3.634015	0.67130	.	.	ENSG00000197616	ENST00000405093;ENST00000356287	D;D	0.82893	-1.66;-1.66	4.25	3.35	0.38373	Myosin tail (1);	.	.	.	.	T	0.03390	0.0098	L	0.61387	1.9	0.24006	P	0.99619363	P	0.47191	0.891	P	0.52909	0.713	T	0.50898	-0.8773	8	0.33141	T	0.24	.	9.869	0.41162	0.2343:0.6364:0.1294:0.0	rs28730771	1130	P13533	MYH6_HUMAN	T	1130	ENSP00000386041:A1130T;ENSP00000348634:A1130T	ENSP00000348634:A1130T	A	-	1	0	MYH6	22929450	0.478000	0.25917	0.861000	0.33841	0.989000	0.77384	1.165000	0.31822	0.888000	0.36160	0.561000	0.74099	GCC	C|0.931;T|0.069	0.069	strong		0.672	MYH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071796.3		
KIAA0368	23392	hgsc.bcm.edu	37	9	114184477	114184477	+	Silent	SNP	C	C	T	rs868405	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:114184477C>T	ENST00000338205.5	-	13	1488	c.1269G>A	c.(1267-1269)cgG>cgA	p.R423R	KIAA0368_ENST00000259335.4_Silent_p.R601R			Q5VYK3	ECM29_HUMAN	KIAA0368	429					ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)	centrosome (GO:0005813)|cytoplasmic membrane-bounded vesicle (GO:0016023)|early endosome (GO:0005769)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle (GO:0030134)|late endosome (GO:0005770)|membrane (GO:0016020)|multivesicular body (GO:0005771)|nucleus (GO:0005634)|proteasome complex (GO:0000502)		p.R601R(1)		NS(2)|breast(3)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(23)|prostate(3)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	65						AATGTGGCATCCGACTGCAAA	0.358													T|||	479	0.095647	0.1861	0.0187	5008	,	,		19517	0.1617		0.0109	False		,,,				2504	0.047				p.R601R		Atlas-SNP	.											KIAA0368,NS,carcinoma,0,1	KIAA0368	144	1	1	Substitution - coding silent(1)	stomach(1)	c.G1803A						scavenged	.	T		546,3132		43,460,1336	69.0	67.0	68.0		1803	2.6	1.0	9	dbSNP_86	68	113,8081		0,113,3984	no	coding-synonymous	KIAA0368	NM_001080398.1		43,573,5320	TT,TC,CC		1.3791,14.845,5.5509		601/2018	114184477	659,11213	1839	4097	5936	SO:0001819	synonymous_variant	23392	exon15			TGGCATCCGACTG	AK025689	CCDS48006.1	9q32	2012-11-29	2006-11-23	2006-11-23	ENSG00000136813	ENSG00000136813			29020	protein-coding gene	gene with protein product	"""ECM29 homolog (S. cerevisiae)"""					9205841, 15496406, 20682791	Standard	NM_001080398		Approved	FLJ22036, ECM29	uc004bfe.1	Q5VYK3	OTTHUMG00000020489	ENST00000338205.5:c.1269G>A	9.37:g.114184477C>T		Somatic	86	1	0.0116279		WXS	Illumina HiSeq	Phase_I	72	47	0.652778	NM_001080398	O15074|Q8WU82	Silent	SNP	ENST00000338205.5	37																																																																																				C|0.909;T|0.091	0.091	strong		0.358	KIAA0368-001	NOVEL	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000053637.2	NM_014686	
BOD1L1	259282	hgsc.bcm.edu	37	4	13601337	13601337	+	Missense_Mutation	SNP	G	G	A	rs3733557	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	89	1	0.011236		WXS	Illumina HiSeq	Phase_I	70	33	0.471429	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	
SSC5D	284297	hgsc.bcm.edu	37	19	56029188	56029188	+	Missense_Mutation	SNP	C	C	G	rs77400028	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:56029188C>G	ENST00000389623.6	+	14	3568	c.3545C>G	c.(3544-3546)aCc>aGc	p.T1182S		NM_001144950.1	NP_001138422.1	A1L4H1	SRCRL_HUMAN	scavenger receptor cysteine rich family, 5 domains	1182	Pro-rich.|Thr-rich.				defense response to Gram-negative bacterium (GO:0050829)|defense response to Gram-positive bacterium (GO:0050830)|detection of bacterial lipoprotein (GO:0042494)|innate immune response (GO:0045087)|multicellular organismal development (GO:0007275)|negative regulation of interleukin-8 secretion (GO:2000483)|receptor-mediated endocytosis (GO:0006898)	cytoplasm (GO:0005737)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|intracellular (GO:0005622)|membrane (GO:0016020)	extracellular matrix binding (GO:0050840)|fibronectin binding (GO:0001968)|laminin binding (GO:0043236)|scavenger receptor activity (GO:0005044)			NS(1)|breast(1)|skin(2)	4						cctcaccccaccacgacccct	0.592													-|||	793	0.158347	0.2814	0.1859	5008	,	,		9379	0.2034		0.0736	False		,,,				2504	0.0133				p.T1182S		Atlas-SNP	.											.	SSC5D	65	.	0			c.C3545G						PASS	.						228.0	215.0	219.0					19																	56029188		692	1591	2283	SO:0001583	missense	284297	exon14			ACCCCACCACGAC		CCDS46196.1, CCDS59424.1	19q13.42	2014-07-09	2014-07-09		ENSG00000179954	ENSG00000179954			26641	protein-coding gene	gene with protein product	"""soluble scavenger with 5 domains"""		"""scavenger receptor cysteine rich domain containing (5 domains)"""			19535143	Standard	NM_001144950		Approved	FLJ35258	uc002qlg.4	A1L4H1		ENST00000389623.6:c.3545C>G	19.37:g.56029188C>G	ENSP00000374274:p.Thr1182Ser	Somatic	188	0	0		WXS	Illumina HiSeq	Phase_I	162	78	0.481481	NM_001144950	B5MDQ5|C7S7T9|C7S7U0|K7EP70	Missense_Mutation	SNP	ENST00000389623.6	37	CCDS46196.1	352	0.16117216117216118	130	0.26422764227642276	52	0.143646408839779	115	0.20104895104895104	55	0.07255936675461741	-	9.773	1.173262	0.21704	.	.	ENSG00000179954	ENST00000389623	T	0.01279	5.06	2.9	0.455	0.16649	.	.	.	.	.	T	0.00012	0.0000	L	0.52759	1.655	0.80722	P	0.0	P	0.40731	0.728	B	0.28991	0.097	T	0.50154	-0.8861	8	0.48119	T	0.1	.	4.1235	0.10116	0.0:0.6051:0.2425:0.1524	.	1182	A1L4H1	SRCRL_HUMAN	S	1182	ENSP00000374274:T1182S	ENSP00000374274:T1182S	T	+	2	0	SSC5D	60721000	0.000000	0.05858	0.000000	0.03702	0.021000	0.10359	-0.136000	0.10405	-0.075000	0.12798	0.282000	0.19409	ACC	C|0.838;G|0.162	0.162	strong		0.592	SSC5D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000453345.2	XM_001718392	
FAM214A	56204	hgsc.bcm.edu	37	15	52901283	52901283	+	Missense_Mutation	SNP	T	T	C	rs61731670|rs386783993	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:52901283T>C	ENST00000261844.7	-	6	1980	c.1828A>G	c.(1828-1830)Act>Gct	p.T610A	FAM214A_ENST00000546305.2_Missense_Mutation_p.T617A	NM_019600.2	NP_062546.2	Q32MH5	F214A_HUMAN	family with sequence similarity 214, member A	610				T -> A (in Ref. 2; BAF85606/BAG57301 and 5; AAI09129). {ECO:0000305}.													ATTGAGGAAGTTGATAAACTA	0.333													T|||	2157	0.430711	0.4402	0.2968	5008	,	,		17056	0.8482		0.167	False		,,,				2504	0.3538				p.T610A		Atlas-SNP	.											.	.	.	.	0			c.A1828G						PASS	.	T	ALA/THR	1334,2336		232,870,733	112.0	119.0	117.0		1828	2.1	0.0	15	dbSNP_129	117	1230,6926		116,998,2964	yes	missense	KIAA1370	NM_019600.2	58	348,1868,3697	CC,CT,TT		15.0809,36.3488,21.681	benign	610/1077	52901283	2564,9262	1835	4078	5913	SO:0001583	missense	56204	exon6			AGGAAGTTGATAA	AB037791	CCDS45263.1, CCDS66773.1	15q21.2-q21.3	2011-12-01	2011-12-01	2011-12-01	ENSG00000047346	ENSG00000047346			25609	protein-coding gene	gene with protein product			"""KIAA1370"""	KIAA1370		10718198	Standard	XM_005254547		Approved	FLJ10980	uc002acg.4	Q32MH5		ENST00000261844.7:c.1828A>G	15.37:g.52901283T>C	ENSP00000261844:p.Thr610Ala	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	83	50	0.60241	NM_019600	A8KA52|B4DEP5|B4DF40|F5H8G0|Q32MH6|Q4G0R7|Q5XJ16|Q6PDA3|Q9NV24|Q9P2H7	Missense_Mutation	SNP	ENST00000261844.7	37	CCDS45263.1	760	0.34798534798534797	156	0.3170731707317073	86	0.23756906077348067	424	0.7412587412587412	94	0.12401055408970976	T	1.003	-0.690316	0.03303	0.363488	0.150809	ENSG00000047346	ENST00000261844;ENST00000399202;ENST00000534964;ENST00000546305	T;T	0.30448	1.53;1.53	5.92	2.07	0.26955	.	0.209202	0.49916	N	0.000136	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B	0.09022	0.002;0.001	B;B	0.14023	0.01;0.004	T	0.20174	-1.0283	9	0.29301	T	0.29	.	5.2861	0.15702	0.1281:0.1543:0.0:0.7176	rs61731670	617;610	F5H8G0;Q32MH5	.;K1370_HUMAN	A	610;610;609;617	ENSP00000261844:T610A;ENSP00000443598:T617A	ENSP00000261844:T610A	T	-	1	0	KIAA1370	50688575	0.807000	0.29009	0.042000	0.18584	0.040000	0.13550	1.242000	0.32755	0.452000	0.26830	0.533000	0.62120	ACT	T|0.697;C|0.303	0.303	strong		0.333	FAM214A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419914.1	NM_019600	
UNC13D	201294	hgsc.bcm.edu	37	17	73824121	73824121	+	Silent	SNP	T	T	C	rs7210574	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:73824121T>C	ENST00000207549.4	-	32	3577	c.3198A>G	c.(3196-3198)gaA>gaG	p.E1066E	UNC13D_ENST00000412096.2_Silent_p.E1066E	NM_199242.2	NP_954712.1	Q70J99	UN13D_HUMAN	unc-13 homolog D (C. elegans)	1066					defense response to virus (GO:0051607)|germinal center formation (GO:0002467)|granuloma formation (GO:0002432)|natural killer cell degranulation (GO:0043320)|phagocytosis (GO:0006909)|positive regulation of exocytosis (GO:0045921)|regulation of mast cell degranulation (GO:0043304)	endosome (GO:0005768)|exocytic vesicle (GO:0070382)|lysosome (GO:0005764)|membrane (GO:0016020)				central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(9)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29			all cancers(21;2.11e-06)|Epithelial(20;2.32e-06)|BRCA - Breast invasive adenocarcinoma(9;0.000618)|LUSC - Lung squamous cell carcinoma(166;0.154)			AGACCTGGGCTTCTCGGTCAC	0.687									Familial Hemophagocytic Lymphohistiocytosis				C|||	2635	0.526158	0.9614	0.3372	5008	,	,		16424	0.4365		0.34	False		,,,				2504	0.3558				p.E1066E		Atlas-SNP	.											.	UNC13D	68	.	0			c.A3198G						PASS	.	C		3743,623		1625,493,65	13.0	15.0	14.0		3198	3.0	1.0	17	dbSNP_116	14	2977,5593		561,1855,1869	no	coding-synonymous	UNC13D	NM_199242.2		2186,2348,1934	CC,CT,TT		34.7375,14.2694,48.0519		1066/1091	73824121	6720,6216	2183	4285	6468	SO:0001819	synonymous_variant	201294	exon32	Familial Cancer Database	FHLH, FHL, Familial Hemophagocytic Reticulosis, FHR	CTGGGCTTCTCGG	AK024474	CCDS11730.1	17q25.3	2014-09-17				ENSG00000092929			23147	protein-coding gene	gene with protein product		608897					Standard	NM_199242		Approved	Munc13-4	uc002jpp.3	Q70J99		ENST00000207549.4:c.3198A>G	17.37:g.73824121T>C		Somatic	205	1	0.00487805		WXS	Illumina HiSeq	Phase_I	223	110	0.493274	NM_199242	B4DWG9|Q9H7K5	Silent	SNP	ENST00000207549.4	37	CCDS11730.1																																																																																			T|0.444;C|0.556	0.556	strong		0.687	UNC13D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448847.2	XM_113950	
CDHR4	389118	hgsc.bcm.edu	37	3	49832788	49832788	+	Missense_Mutation	SNP	G	G	A	rs73079003	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:49832788G>A	ENST00000412678.2	-	8	880	c.872C>T	c.(871-873)aCg>aTg	p.T291M	CDHR4_ENST00000462108.1_5'Flank	NM_001007540.2	NP_001007541.2	A6H8M9	CDHR4_HUMAN	cadherin-related family member 4	291	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(1)|breast(1)|endometrium(3)|large_intestine(3)|lung(3)	11						CTCTAGGGGCGTGGTGGTCCG	0.637													G|||	310	0.061901	0.0038	0.0476	5008	,	,		17886	0.002		0.1272	False		,,,				2504	0.1452				p.T291M		Atlas-SNP	.											CDHR4,NS,carcinoma,+1,1	CDHR4	37	1	0			c.C872T						PASS	.	G	MET/THR	27,1357		0,27,665	59.0	62.0	61.0		872	3.9	0.0	3	dbSNP_130	61	388,2794		17,354,1220	yes	missense	CDHR4	NM_001007540.2	81	17,381,1885	AA,AG,GG		12.1936,1.9509,9.0889	possibly-damaging	291/789	49832788	415,4151	692	1591	2283	SO:0001583	missense	389118	exon8			AGGGGCGTGGTGG		CCDS46829.1	3p21.31	2011-07-01	2010-01-25	2010-01-25	ENSG00000187492	ENSG00000187492		"""Cadherins / Cadherin-related"""	34527	protein-coding gene	gene with protein product			"""cadherin-like 29"""	CDH29			Standard	NM_001007540		Approved	VLLR9392	uc010hkz.3	A6H8M9	OTTHUMG00000158198	ENST00000412678.2:c.872C>T	3.37:g.49832788G>A	ENSP00000391409:p.Thr291Met	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	83	30	0.361446	NM_001007540	Q6UXT0	Missense_Mutation	SNP	ENST00000412678.2	37	CCDS46829.1	122	0.055860805860805864	6	0.012195121951219513	19	0.052486187845303865	1	0.0017482517482517483	96	0.1266490765171504	G	9.184	1.024358	0.19433	0.019509	0.121936	ENSG00000187492	ENST00000412678	D	0.82711	-1.64	5.66	3.89	0.44902	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.01421	0.0046	N	0.14661	0.345	0.09310	N	1	B	0.15141	0.012	B	0.06405	0.002	T	0.07558	-1.0766	9	0.62326	D	0.03	.	3.592	0.07991	0.1498:0.1376:0.5858:0.1268	.	291	A6H8M9	CDHR4_HUMAN	M	291	ENSP00000391409:T291M	ENSP00000391409:T291M	T	-	2	0	CDHR4	49807792	0.000000	0.05858	0.001000	0.08648	0.000000	0.00434	0.209000	0.17435	0.741000	0.32674	-0.355000	0.07637	ACG	G|0.944;A|0.056	0.056	strong		0.637	CDHR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350387.1	NM_001007540	
KRTAP5-5	439915	hgsc.bcm.edu	37	11	1651555	1651555	+	Missense_Mutation	SNP	C	C	A	rs147101544	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:1651555C>A	ENST00000399676.2	+	1	523	c.485C>A	c.(484-486)cCc>cAc	p.P162H		NM_001001480.2	NP_001001480.2	Q701N2	KRA55_HUMAN	keratin associated protein 5-5	162	8 X 4 AA repeats of C-C-X-P.					keratin filament (GO:0045095)				endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(17)|ovary(2)|prostate(5)|urinary_tract(1)	33		all_epithelial(84;0.00018)|Ovarian(85;0.0014)|Breast(177;0.00147)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.000614)|Lung(200;0.0681)|LUSC - Lung squamous cell carcinoma(625;0.082)		TGCTGCAAGCCCTGCTGCTGC	0.642													c|||	375	0.0748802	0.1399	0.0908	5008	,	,		9400	0.003		0.1054	False		,,,				2504	0.0184				p.P162H		Atlas-SNP	.											.	KRTAP5-5	86	.	0			c.C485A						PASS	.	C	HIS/PRO	588,3816		43,502,1657	55.0	71.0	66.0		485	2.9	0.0	11	dbSNP_134	66	852,7740		49,754,3493	no	missense	KRTAP5-5	NM_001001480.2	77	92,1256,5150	AA,AC,CC		9.9162,13.3515,11.0803	probably-damaging	162/238	1651555	1440,11556	2202	4296	6498	SO:0001583	missense	439915	exon1			GCAAGCCCTGCTG	AB125074	CCDS41592.1	11p15.5	2008-10-30			ENSG00000185940	ENSG00000185940		"""Keratin associated proteins"""	23601	protein-coding gene	gene with protein product						15144888	Standard	NM_001001480		Approved	KRTAP5.5, KRTAP5-11	uc001lty.3	Q701N2	OTTHUMG00000057554	ENST00000399676.2:c.485C>A	11.37:g.1651555C>A	ENSP00000382584:p.Pro162His	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	88	70	0.795455	NM_001001480	A8MWN2	Missense_Mutation	SNP	ENST00000399676.2	37	CCDS41592.1	145	0.06639194139194139	46	0.09349593495934959	29	0.08011049723756906	0	0.0	70	0.09234828496042216	c	2.092	-0.408148	0.04832	0.133515	0.099162	ENSG00000185940	ENST00000399676;ENST00000422553	T	0.01252	5.1	3.84	2.89	0.33648	.	.	.	.	.	T	0.00039	0.0001	M	0.85197	2.74	0.80722	P	0.0	D	0.56521	0.976	P	0.44477	0.451	T	0.33650	-0.9860	8	0.87932	D	0	.	6.6355	0.22881	0.2056:0.5946:0.1998:0.0	.	162	Q701N2	KRA55_HUMAN	H	162;133	ENSP00000382584:P162H	ENSP00000382584:P162H	P	+	2	0	KRTAP5-5	1608131	0.002000	0.14202	0.001000	0.08648	0.014000	0.08584	0.883000	0.28200	0.577000	0.29470	0.478000	0.44815	CCC	C|0.928;A|0.072	0.072	strong		0.642	KRTAP5-5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127919.1		
PABPC4L	132430	hgsc.bcm.edu	37	4	135121066	135121066	+	Missense_Mutation	SNP	T	T	G	rs11099273	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	71	0	0		WXS	Illumina HiSeq	Phase_I	52	52	1	NM_001114734		Missense_Mutation	SNP	ENST00000421491.3	37																																																																																				T|0.365;G|0.635	0.635	strong		0.463	PABPC4L-001	KNOWN	upstream_ATG|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000364399.2	NM_001114734	
GAS7	8522	hgsc.bcm.edu	37	17	9846521	9846521	+	Silent	SNP	G	G	C	rs17339499	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:9846521G>C	ENST00000432992.2	-	7	808	c.648C>G	c.(646-648)acC>acG	p.T216T	GAS7_ENST00000323816.4_Silent_p.T156T|GAS7_ENST00000585266.1_Silent_p.T156T|GAS7_ENST00000540214.1_Intron|GAS7_ENST00000542249.1_Silent_p.T152T|GAS7_ENST00000579158.1_Silent_p.T152T|GAS7_ENST00000583882.1_Intron|GAS7_ENST00000437099.2_Silent_p.T152T|GAS7_ENST00000578655.1_5'Flank|GAS7_ENST00000396115.2_Intron|GAS7_ENST00000580865.1_Silent_p.T76T	NM_201433.1	NP_958839.1	O60861	GAS7_HUMAN	growth arrest-specific 7	216	FCH. {ECO:0000255|PROSITE- ProRule:PRU00083}.				actin filament bundle assembly (GO:0051017)|actin filament polymerization (GO:0030041)|cell cycle arrest (GO:0007050)|neuron projection morphogenesis (GO:0048812)|regulation of cell shape (GO:0008360)|regulation of transcription, DNA-templated (GO:0006355)	actin filament (GO:0005884)|cytoplasm (GO:0005737)|ruffle (GO:0001726)	sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(7)|lung(18)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(2)	39						ACCCAGCCACGGTGCCGTTGC	0.532			T	MLL	AML*								A|||	692	0.138179	0.1263	0.1758	5008	,	,		20203	0.005		0.2286	False		,,,				2504	0.1718				p.T216T		Atlas-SNP	.		Dom	yes		17	17p	8522	growth arrest-specific 7		L	.	GAS7	113	.	0			c.C648G						PASS	.	A	,,,	707,3699		58,591,1554	165.0	149.0	154.0		456,228,468,648	-10.7	0.0	17	dbSNP_123	154	1971,6629		214,1543,2543	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	GAS7	NM_001130831.1,NM_003644.2,NM_201432.1,NM_201433.1	,,,	272,2134,4097	CC,CG,GG		22.9186,16.0463,20.5905	,,,	152/413,76/337,156/417,216/477	9846521	2678,10328	2203	4300	6503	SO:0001819	synonymous_variant	8522	exon7			AGCCACGGTGCCG	AB007854	CCDS11152.1, CCDS42263.1, CCDS45611.1, CCDS58518.1	17p13.1	2004-02-18							4169	protein-coding gene	gene with protein product		603127				9736752	Standard	NM_001130831		Approved	KIAA0394, MGC1348	uc002gmg.1	O60861		ENST00000432992.2:c.648C>G	17.37:g.9846521G>C		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	86	46	0.534884	NM_201433	A8KAC2|B2RCK9|O43144|Q53Y77|Q7Z571	Silent	SNP	ENST00000432992.2	37	CCDS11152.1																																																																																			G|0.811;C|0.189	0.189	strong		0.532	GAS7-017	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439883.1	NM_003644, NM_201432, NM_201433	
DST	667	hgsc.bcm.edu	37	6	56420158	56420158	+	Missense_Mutation	SNP	C	C	T	rs62621210	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:56420158C>T	ENST00000361203.3	-	56	14495	c.14488G>A	c.(14488-14490)Gtt>Att	p.V4830I	DST_ENST00000370769.4_Missense_Mutation_p.V4832I|DST_ENST00000244364.6_Missense_Mutation_p.V2418I|DST_ENST00000312431.6_3'UTR|DST_ENST00000446842.2_Missense_Mutation_p.V4506I|DST_ENST00000370754.5_Missense_Mutation_p.V5010I|DST_ENST00000370788.2_Missense_Mutation_p.V2744I|DST_ENST00000421834.2_Missense_Mutation_p.V2744I			Q03001	DYST_HUMAN	dystonin	4830					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)			TTCTGTTCAACATCCTTAAAT	0.363													T|||	213	0.0425319	0.115	0.0245	5008	,	,		21783	0.0		0.0278	False		,,,				2504	0.0164				p.V2418I		Atlas-SNP	.											.	DST	1427	.	0			c.G7252A						PASS	.	T	ILE/VAL	434,3276		22,390,1443	98.0	97.0	97.0		7252	4.8	1.0	6	dbSNP_129	97	356,7848		8,340,3754	yes	missense	DST	NM_015548.4	29	30,730,5197	TT,TC,CC		4.3393,11.6981,6.6309	benign	2418/5172	56420158	790,11124	1855	4102	5957	SO:0001583	missense	667	exon41			GTTCAACATCCTT	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.14488G>A	6.37:g.56420158C>T	ENSP00000354508:p.Val4830Ile	Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	145	72	0.496552	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		88	0.040293040293040296	61	0.12398373983739837	10	0.027624309392265192	0	0.0	17	0.022427440633245383	T	12.33	1.907022	0.33628	0.116981	0.043393	ENSG00000151914	ENST00000244364;ENST00000370754;ENST00000370769;ENST00000421834;ENST00000446842;ENST00000370788;ENST00000361203	T;T;T;T;T;T;T	0.36520	1.25;1.25;1.25;1.25;1.25;1.25;1.25	5.96	4.8	0.61643	.	0.246447	0.28784	N	0.014144	T	0.05640	0.0148	N	0.02802	-0.49	0.09310	N	1.0	B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0	B;B;B;B;B	0.11329	0.0;0.002;0.006;0.0;0.001	T	0.23940	-1.0174	9	0.33141	T	0.24	.	7.9146	0.29810	0.0:0.0664:0.2716:0.662	rs62621210	2744;4832;5010;4830;2418	Q5TBT1;E7ERU2;E9PEB9;Q03001;Q03001-8	.;.;.;DYST_HUMAN;.	I	2418;5010;4832;2744;4506;2744;4830	ENSP00000244364:V2418I;ENSP00000359790:V5010I;ENSP00000359805:V4832I;ENSP00000400883:V2744I;ENSP00000393645:V4506I;ENSP00000359824:V2744I;ENSP00000354508:V4830I	ENSP00000244364:V2418I	V	-	1	0	DST	56528117	1.000000	0.71417	0.997000	0.53966	0.968000	0.65278	2.506000	0.45433	0.505000	0.28104	-0.269000	0.10298	GTT	C|0.959;T|0.041	0.041	strong		0.363	DST-004	NOVEL	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000041021.3	NM_001723	
MUC4	4585	hgsc.bcm.edu	37	3	195506303	195506303	+	Missense_Mutation	SNP	G	G	T	rs192584273	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195506303G>T	ENST00000463781.3	-	2	12607	c.12148C>A	c.(12148-12150)Cct>Act	p.P4050T	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.P4050T	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.P4050T(3)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		TTGGTGACAGGAAGAGGGGTG	0.572													.|||	585	0.116813	0.3132	0.0922	5008	,	,		10067	0.0169		0.0845	False		,,,				2504	0.0051				p.P4050T		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,4	MUC4	1505	4	3	Substitution - Missense(3)	haematopoietic_and_lymphoid_tissue(2)|kidney(1)	c.C12148A						PASS	.						36.0	20.0	25.0					3																	195506303		593	1229	1822	SO:0001583	missense	4585	exon2			TGACAGGAAGAGG	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.12148C>A	3.37:g.195506303G>T	ENSP00000417498:p.Pro4050Thr	Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	136	102	0.75	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	167	0.07646520146520147	97	0.19715447154471544	31	0.0856353591160221	3	0.005244755244755245	36	0.047493403693931395	g	1.949	-0.441794	0.04604	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.32023	1.47;1.53	.	.	.	.	.	.	.	.	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B	0.15141	0.012	B	0.01281	0.0	T	0.37865	-0.9687	6	.	.	.	.	4.7077	0.12858	1.0E-4:0.0:0.6463:0.3536	.	3922	E7ESK3	.	T	4050	ENSP00000417498:P4050T;ENSP00000420243:P4050T	.	P	-	1	0	MUC4	196991082	0.000000	0.05858	0.001000	0.08648	0.060000	0.15804	-0.709000	0.05030	-0.833000	0.04245	0.064000	0.15345	CCT	G|0.925;T|0.075	0.075	strong		0.572	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
SENP5	205564	hgsc.bcm.edu	37	3	196612959	196612959	+	Missense_Mutation	SNP	C	C	T	rs151102982	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:196612959C>T	ENST00000323460.5	+	2	1156	c.907C>T	c.(907-909)Cat>Tat	p.H303Y	SENP5_ENST00000419026.1_Intron|SENP5_ENST00000445299.2_Missense_Mutation_p.H303Y	NM_152699.4	NP_689912.2	Q96HI0	SENP5_HUMAN	SUMO1/sentrin specific peptidase 5	303					cell cycle (GO:0007049)|cell division (GO:0051301)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein sumoylation (GO:0016925)	intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	cysteine-type peptidase activity (GO:0008234)			NS(1)|breast(2)|endometrium(2)|kidney(3)|large_intestine(9)|lung(14)|skin(1)	32	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)|Breast(254;0.135)		Epithelial(36;3.14e-24)|all cancers(36;2.1e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.03e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.004)		TTCTTGTCGGCATCAGCCGTA	0.532													C|||	12	0.00239617	0.0	0.0029	5008	,	,		19282	0.0		0.007	False		,,,				2504	0.0031				p.H303Y	Ovarian(47;891 1095 11174 13858 51271)	Atlas-SNP	.											.	SENP5	68	.	0			c.C907T						PASS	.	C	TYR/HIS	3,4403	6.2+/-15.9	0,3,2200	90.0	86.0	87.0		907	4.5	0.9	3	dbSNP_134	87	68,8532	40.8+/-97.7	1,66,4233	yes	missense	SENP5	NM_152699.4	83	1,69,6433	TT,TC,CC		0.7907,0.0681,0.5459	benign	303/756	196612959	71,12935	2203	4300	6503	SO:0001583	missense	205564	exon2			TGTCGGCATCAGC	BC030705	CCDS3322.1	3q29	2005-08-17	2005-08-17		ENSG00000119231	ENSG00000119231			28407	protein-coding gene	gene with protein product		612845	"""SUMO1/sentrin specific protease 5"""			12477932	Standard	NM_152699		Approved	MGC27076	uc003fwz.4	Q96HI0	OTTHUMG00000155527	ENST00000323460.5:c.907C>T	3.37:g.196612959C>T	ENSP00000327197:p.His303Tyr	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	55	21	0.381818	NM_152699	B4DY82|Q96SA5	Missense_Mutation	SNP	ENST00000323460.5	37	CCDS3322.1	5	0.0022893772893772895	0	0.0	1	0.0027624309392265192	0	0.0	4	0.005277044854881266	C	12.93	2.086414	0.36855	6.81E-4	0.007907	ENSG00000119231	ENST00000323460;ENST00000445299	T;T	0.34275	1.37;1.37	5.37	4.49	0.54785	.	0.432451	0.21815	N	0.068702	T	0.12135	0.0295	N	0.14661	0.345	0.80722	D	1	P;B	0.47350	0.894;0.167	B;B	0.38562	0.276;0.04	T	0.08764	-1.0706	10	0.05351	T	0.99	-0.0265	11.2608	0.49083	0.0:0.9096:0.0:0.0904	.	303;303	B4DY82;Q96HI0	.;SENP5_HUMAN	Y	303	ENSP00000327197:H303Y;ENSP00000390231:H303Y	ENSP00000327197:H303Y	H	+	1	0	SENP5	198097356	0.364000	0.24997	0.863000	0.33907	0.985000	0.73830	2.003000	0.40844	1.381000	0.46364	0.655000	0.94253	CAT	C|0.993;T|0.007	0.007	strong		0.532	SENP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340524.1	NM_152699	
KCNJ15	3772	hgsc.bcm.edu	37	21	39671476	39671476	+	Missense_Mutation	SNP	G	G	A	rs2230033	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:39671476G>A	ENST00000328656.4	+	4	596	c.293G>A	c.(292-294)gGt>gAt	p.G98D	KCNJ15_ENST00000398930.1_Missense_Mutation_p.G98D|KCNJ15_ENST00000398938.2_Missense_Mutation_p.G98D|KCNJ15_ENST00000398934.1_Missense_Mutation_p.G98D|KCNJ15_ENST00000398932.1_Missense_Mutation_p.G98D	NM_001276437.1|NM_001276438.1|NM_001276439.1|NM_002243.3	NP_001263366.1|NP_001263367.1|NP_001263368.1|NP_002234.2	Q99712	KCJ15_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 15	98			G -> D (in dbSNP:rs2230033). {ECO:0000269|PubMed:8995301, ECO:0000269|Ref.3}.		potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	inward rectifier potassium channel activity (GO:0005242)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|kidney(2)|large_intestine(4)|lung(6)|ovary(2)|prostate(2)|skin(3)|urinary_tract(1)	24					Yohimbine(DB01392)	TTAGAACCCGGTGAGCCCATT	0.483													G|||	1446	0.288738	0.0363	0.4625	5008	,	,		20529	0.253		0.497	False		,,,				2504	0.3292				p.L98X		Atlas-SNP	.											KCNJ15,colon,carcinoma,+1,1	KCNJ15	43	1	0			c.T293A						PASS	.	G	ASP/GLY,ASP/GLY,ASP/GLY	533,3873	244.7+/-253.9	32,469,1702	118.0	117.0	117.0		293,293,293	4.2	0.0	21	dbSNP_98	117	4707,3893	606.8+/-395.1	1302,2103,895	yes	missense,missense,missense	KCNJ15	NM_002243.3,NM_170736.1,NM_170737.1	94,94,94	1334,2572,2597	AA,AG,GG		45.2674,12.0971,40.2891	benign,benign,benign	98/376,98/376,98/376	39671476	5240,7766	2203	4300	6503	SO:0001583	missense	3772	exon3			AACCCGGTGAGCC	Y10745	CCDS13656.1	21q22.2	2011-07-05			ENSG00000157551	ENSG00000157551		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Inwardly rectifying"""	6261	protein-coding gene	gene with protein product		602106				9299242, 8995301, 16382105	Standard	NM_170736		Approved	Kir4.2, Kir1.3, IRKK	uc002ywx.4	Q99712	OTTHUMG00000090609	ENST00000328656.4:c.293G>A	21.37:g.39671476G>A	ENSP00000331698:p.Gly98Asp	Somatic	153	1	0.00653595		WXS	Illumina HiSeq	Phase_I	161	160	0.993789	NM_170736	D3DSH5|O00564|Q96L28|Q99446	Nonsense_Mutation	SNP	ENST00000328656.4	37	CCDS13656.1	727	0.33287545787545786	25	0.0508130081300813	167	0.4613259668508287	159	0.27797202797202797	376	0.49604221635883905	G	0.011	-1.728508	0.00694	0.120971	0.547326	ENSG00000157551	ENST00000328656;ENST00000398928;ENST00000398938;ENST00000398932;ENST00000438657;ENST00000398930;ENST00000398934;ENST00000398927;ENST00000419868	D;D;D;D;D;D;D;D;D	0.93712	-3.27;-3.27;-3.27;-3.27;-3.27;-3.27;-3.27;-3.27;-3.27	5.13	4.22	0.49857	Potassium channel, inwardly rectifying, Kir, conserved region 2 (1);	0.593826	0.15252	U	0.272284	T	0.00012	0.0000	N	0.03154	-0.405	0.80722	P	0.0	B	0.23891	0.093	B	0.27380	0.079	T	0.42865	-0.9426	8	.	.	.	.	2.9987	0.06007	0.1131:0.1737:0.5343:0.1789	rs2230033;rs3746877;rs61521838;rs2230033	98	Q99712	IRK15_HUMAN	D	98	ENSP00000331698:G98D;ENSP00000381902:G98D;ENSP00000381911:G98D;ENSP00000381905:G98D;ENSP00000414487:G98D;ENSP00000381904:G98D;ENSP00000381907:G98D;ENSP00000381901:G98D;ENSP00000400849:G98D	.	G	+	2	0	KCNJ15	38593346	0.001000	0.12720	0.005000	0.12908	0.019000	0.09904	1.174000	0.31932	1.249000	0.43950	0.655000	0.94253	GGT	G|0.642;A|0.358	0.358	strong		0.483	KCNJ15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207181.2	NM_002243	
CRIPAK	285464	hgsc.bcm.edu	37	4	1389037	1389037	+	Missense_Mutation	SNP	G	G	A	rs76723438	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:1389037G>A	ENST00000324803.4	+	1	3698	c.738G>A	c.(736-738)atG>atA	p.M246I		NM_175918.3	NP_787114.2	Q8N1N5	CRPAK_HUMAN	cysteine-rich PAK1 inhibitor	246					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)			ACGTGCCCATGTGGAGTGCCC	0.687													g|||	447	0.0892572	0.1672	0.0677	5008	,	,		12586	0.001		0.0924	False		,,,				2504	0.0869				p.M246I		Atlas-SNP	.											.	CRIPAK	185	.	0			c.G738A						PASS	.	G	ILE/MET	707,3697	274.9+/-272.2	56,595,1551	148.0	130.0	136.0		738	-0.3	0.0	4	dbSNP_131	136	875,7719	187.3+/-234.6	47,781,3469	no	missense	CRIPAK	NM_175918.3	10	103,1376,5020	AA,AG,GG		10.1815,16.0536,12.1711	benign	246/447	1389037	1582,11416	2202	4297	6499	SO:0001583	missense	285464	exon1			GCCCATGTGGAGT	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.738G>A	4.37:g.1389037G>A	ENSP00000323978:p.Met246Ile	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	55	23	0.418182	NM_175918	Q8NB03	Missense_Mutation	SNP	ENST00000324803.4	37	CCDS3349.1	.	.	.	.	.	.	.	.	.	.	g	4.357	0.065715	0.08388	0.160536	0.101815	ENSG00000179979	ENST00000324803;ENST00000382944	T	0.17528	2.27	0.815	-0.324	0.12706	Post-SET domain (1);	.	.	.	.	T	0.00039	0.0001	N	0.08118	0	0.09310	N	1	B	0.31174	0.311	B	0.24394	0.053	T	0.37220	-0.9715	9	0.10636	T	0.68	.	2.4029	0.04406	0.2495:0.332:0.4185:0.0	.	246	Q8N1N5	CRPAK_HUMAN	I	246;188	ENSP00000323978:M246I	ENSP00000323978:M246I	M	+	3	0	CRIPAK	1379037	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.205000	0.03014	-0.106000	0.12110	-0.849000	0.03036	ATG	G|0.885;A|0.115	0.115	strong		0.687	CRIPAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241607.2	NM_175918	
KRT32	3882	hgsc.bcm.edu	37	17	39620565	39620565	+	Missense_Mutation	SNP	C	C	T	rs72830046	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:39620565C>T	ENST00000225899.3	-	4	942	c.839G>A	c.(838-840)cGc>cAc	p.R280H		NM_002278.3	NP_002269.3	Q14532	K1H2_HUMAN	keratin 32	280	Coil 2.|Rod.		R -> H (in dbSNP:rs72830046).		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)				CACGTCCCTGCGGTTGGCCTC	0.622													C|||	899	0.179513	0.0431	0.196	5008	,	,		20629	0.1141		0.2724	False		,,,				2504	0.3241				p.R280H		Atlas-SNP	.											.	KRT32	57	.	0			c.G839A						PASS	.	C	HIS/ARG	357,4049	186.0+/-213.0	19,319,1865	146.0	102.0	117.0		839	-2.7	0.9	17	dbSNP_130	117	2610,5990	423.8+/-354.5	384,1842,2074	yes	missense	KRT32	NM_002278.3	29	403,2161,3939	TT,TC,CC		30.3488,8.1026,22.8125	benign	280/449	39620565	2967,10039	2203	4300	6503	SO:0001583	missense	3882	exon4			TCCCTGCGGTTGG	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.839G>A	17.37:g.39620565C>T	ENSP00000225899:p.Arg280His	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	127	64	0.503937	NM_002278		Missense_Mutation	SNP	ENST00000225899.3	37	CCDS11393.1	365	0.1671245421245421	24	0.04878048780487805	85	0.23480662983425415	59	0.10314685314685315	197	0.2598944591029024	C	16.42	3.117464	0.56505	0.081026	0.303488	ENSG00000108759	ENST00000225899	D	0.90004	-2.6	5.22	-2.66	0.06077	Filament (1);	0.678601	0.12184	N	0.491809	T	0.00039	0.0001	M	0.84156	2.68	0.48185	P	3.9800000000000946E-4	B	0.28258	0.205	B	0.34301	0.179	T	0.35699	-0.9778	9	0.56958	D	0.05	.	4.826	0.13416	0.2652:0.4725:0.0:0.2623	.	280	Q14532	K1H2_HUMAN	H	280	ENSP00000225899:R280H	ENSP00000225899:R280H	R	-	2	0	KRT32	36874091	0.000000	0.05858	0.896000	0.35187	0.991000	0.79684	-0.526000	0.06207	-0.710000	0.05001	0.655000	0.94253	CGC	C|0.783;T|0.217	0.217	strong		0.622	KRT32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257293.1	NM_002278	
FCHO2	115548	hgsc.bcm.edu	37	5	72351905	72351905	+	Silent	SNP	A	A	G	rs57213367	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:72351905A>G	ENST00000430046.2	+	16	1340	c.1224A>G	c.(1222-1224)acA>acG	p.T408T	FCHO2_ENST00000512348.1_Silent_p.T375T|FCHO2_ENST00000341845.6_Silent_p.T408T	NM_001146032.1|NM_138782.2	NP_001139504.1|NP_620137.2	Q0JRZ9	FCHO2_HUMAN	FCH domain only 2	408					clathrin coat assembly (GO:0048268)|clathrin-mediated endocytosis (GO:0072583)|membrane invagination (GO:0010324)|protein localization to plasma membrane (GO:0072659)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|plasma membrane (GO:0005886)	phosphatidylinositol binding (GO:0035091)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylserine binding (GO:0001786)			cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(4)|ovary(1)|prostate(1)	17		Lung NSC(167;0.0465)|Ovarian(174;0.0908)|Prostate(461;0.165)		OV - Ovarian serous cystadenocarcinoma(47;4.6e-53)		AGGAGTTAACAAAATCAAAGC	0.254													A|||	693	0.138379	0.0144	0.0951	5008	,	,		15762	0.3879		0.169	False		,,,				2504	0.0481				p.T408T		Atlas-SNP	.											.	FCHO2	96	.	0			c.A1224G						PASS	.	A	,	84,3284		1,82,1601	33.0	33.0	33.0		1125,1224	4.2	1.0	5	dbSNP_129	33	885,6655		40,805,2925	no	coding-synonymous,coding-synonymous	FCHO2	NM_001146032.1,NM_138782.2	,	41,887,4526	GG,GA,AA		11.7374,2.4941,8.8834	,	375/778,408/811	72351905	969,9939	1684	3770	5454	SO:0001819	synonymous_variant	115548	exon16			GTTAACAAAATCA	AL831971	CCDS47230.1, CCDS54868.1	5q13.2	2005-08-15			ENSG00000157107	ENSG00000157107			25180	protein-coding gene	gene with protein product		613438				15254787	Standard	NM_138782		Approved		uc003kcl.3	Q0JRZ9	OTTHUMG00000162413	ENST00000430046.2:c.1224A>G	5.37:g.72351905A>G		Somatic	224	0	0		WXS	Illumina HiSeq	Phase_I	210	136	0.647619	NM_138782	A8K6W7|B2RNQ9|B4DHK0|E9PG79|Q0JTJ3|Q96CF5	Silent	SNP	ENST00000430046.2	37	CCDS47230.1																																																																																			A|0.828;G|0.172	0.172	strong		0.254	FCHO2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000368795.3	XM_291142	
FCN2	2220	hgsc.bcm.edu	37	9	137779026	137779026	+	Missense_Mutation	SNP	C	C	T	rs17549193	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:137779026C>T	ENST00000291744.6	+	8	717	c.707C>T	c.(706-708)aCg>aTg	p.T236M	FCN2_ENST00000350339.2_Missense_Mutation_p.T198M	NM_004108.2	NP_004099.2	Q15485	FCN2_HUMAN	ficolin (collagen/fibrinogen domain containing lectin) 2	236	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.		T -> M (in dbSNP:rs17549193).		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)		GATTCCCTGACGTTCCACAAC	0.468													C|||	1246	0.248802	0.3646	0.2493	5008	,	,		24104	0.0665		0.2753	False		,,,				2504	0.2526				p.T236M		Atlas-SNP	.											.	FCN2	55	.	0			c.C707T	GRCh37	CM051922	FCN2	M	rs17549193	PASS	.	C	MET/THR,MET/THR	1500,2906	479.0+/-358.4	252,996,955	161.0	141.0	148.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	707,593	2.1	0.0	9	dbSNP_123	148	2495,6105	409.4+/-349.8	363,1769,2168	yes	missense,missense	FCN2	NM_004108.2,NM_015837.2	81,81	615,2765,3123	TT,TC,CC		29.0116,34.0445,30.7166	benign,benign	236/314,198/276	137779026	3995,9011	2203	4300	6503	SO:0001583	missense	2220	exon8			CCCTGACGTTCCA	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.707C>T	9.37:g.137779026C>T	ENSP00000291744:p.Thr236Met	Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	109	109	1	NM_004108	A6NFG7|A8K478|Q6IS69|Q7M4P4|Q9UC57	Missense_Mutation	SNP	ENST00000291744.6	37	CCDS6983.1	528	0.24175824175824176	194	0.3943089430894309	93	0.2569060773480663	29	0.050699300699300696	212	0.2796833773087071	C	9.210	1.030738	0.19512	0.340445	0.290116	ENSG00000160339	ENST00000350339;ENST00000291744	T;T	0.79247	-1.25;-1.25	4.05	2.06	0.26882	Fibrinogen, alpha/beta/gamma chain, C-terminal globular (4);Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 (1);	0.557101	0.14767	N	0.299635	T	0.00012	0.0000	M	0.75884	2.315	0.44395	P	0.0026960000000000317	P;P	0.44578	0.838;0.57	B;B	0.30855	0.121;0.1	T	0.11084	-1.0602	9	0.46703	T	0.11	.	6.6263	0.22830	0.1744:0.7225:0.0:0.1031	rs57863140	198;236	Q15485-2;Q15485	.;FCN2_HUMAN	M	198;236	ENSP00000291741:T198M;ENSP00000291744:T236M	ENSP00000291744:T236M	T	+	2	0	FCN2	136918847	0.011000	0.17503	0.023000	0.16930	0.042000	0.13812	0.771000	0.26633	0.628000	0.30357	0.563000	0.77884	ACG	C|0.716;T|0.284	0.284	strong		0.468	FCN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054960.1	NM_004108	
FAM66D	100132923	hgsc.bcm.edu	37	8	11990256	11990256	+	RNA	SNP	G	G	A	rs191378034	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:11990256G>A	ENST00000434078.2	+	0	608					NR_027425.1				family with sequence similarity 66, member D																		CCAAGTGCTCGTCCAACTCGG	0.537													-|||	225	0.0449281	0.0401	0.036	5008	,	,		23065	0.001		0.0726	False		,,,				2504	0.0746				p.D421D		Atlas-SNP	.											.	.	.	.	0			c.C1263T						PASS	.																																					392197	exon1			GTGCTCGTCCAAC			8p23.1	2013-07-05			ENSG00000255052	ENSG00000255052		"""Long non-coding RNAs"""	24159	non-coding RNA	RNA, long non-coding							Standard	NR_027425		Approved				OTTHUMG00000165269		8.37:g.11990256G>A		Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	22	15	0.681818	NM_001256869		Silent	SNP	ENST00000434078.2	37																																																																																				G|0.968;A|0.032	0.032	strong		0.537	FAM66D-201	KNOWN	basic	antisense	antisense		NR_027425	
NHSL1	57224	hgsc.bcm.edu	37	6	138745299	138745299	+	Silent	SNP	G	G	A	rs9495082	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	23	0	0		WXS	Illumina HiSeq	Phase_I	15	7	0.466667	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	
TRPV4	59341	hgsc.bcm.edu	37	12	110252547	110252547	+	Missense_Mutation	SNP	G	G	A	rs3742030	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:110252547G>A	ENST00000418703.2	-	1	149	c.55C>T	c.(55-57)Ccc>Tcc	p.P19S	TRPV4_ENST00000536838.1_Missense_Mutation_p.P19S|TRPV4_ENST00000544971.1_Missense_Mutation_p.P19S|TRPV4_ENST00000392719.2_Missense_Mutation_p.P19S|TRPV4_ENST00000541794.1_Missense_Mutation_p.P19S|TRPV4_ENST00000537083.1_Missense_Mutation_p.P19S|TRPV4_ENST00000261740.2_Missense_Mutation_p.P19S|TRPV4_ENST00000536570.1_5'UTR|TRPV4_ENST00000346520.2_Missense_Mutation_p.P19S	NM_001177431.1	NP_001170902.1	Q9HBA0	TRPV4_HUMAN	transient receptor potential cation channel, subfamily V, member 4	19			P -> S (associated with lower sodium concentraions in serum; shows diminished response to hypotonic stress relative to wild-type; dbSNP:rs3742030).		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						TCATCCCCGGGGAGCTCAGCC	0.682													g|||	218	0.0435304	0.0552	0.0216	5008	,	,		15592	0.0456		0.0348	False		,,,				2504	0.0501				p.P19S		Atlas-SNP	.											.	TRPV4	88	.	0			c.C55T						PASS	.	G	SER/PRO,SER/PRO,SER/PRO,SER/PRO,SER/PRO	176,4200		3,170,2015	14.0	13.0	14.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	55,55,55,55,55	3.6	1.0	12	dbSNP_107	14	199,8367		1,197,4085	yes	missense,missense,missense,missense,missense	TRPV4	NM_001177428.1,NM_001177431.1,NM_001177433.1,NM_021625.4,NM_147204.2	74,74,74,74,74	4,367,6100	AA,AG,GG		2.3231,4.0219,2.8975	benign,benign,benign,benign,benign	19/825,19/838,19/765,19/872,19/812	110252547	375,12567	2188	4283	6471	SO:0001583	missense	59341	exon1			CCCCGGGGAGCTC	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.55C>T	12.37:g.110252547G>A	ENSP00000406191:p.Pro19Ser	Somatic	22	0	0		WXS	Illumina HiSeq	Phase_I	30	13	0.433333	NM_001177433	B7ZKQ6|Q17R79|Q2Y122|Q2Y123|Q2Y124|Q86YZ6|Q8NDY7|Q8NG64|Q96Q92|Q96RS7|Q9HBC0	Missense_Mutation	SNP	ENST00000418703.2	37	CCDS9134.1	97	0.044413919413919416	32	0.06504065040650407	9	0.024861878453038673	27	0.0472027972027972	29	0.03825857519788918	G	13.17	2.156129	0.38021	0.040219	0.023231	ENSG00000111199	ENST00000418703;ENST00000261740;ENST00000392719;ENST00000346520;ENST00000544971;ENST00000537083;ENST00000541794;ENST00000536838	D;D;D;D;D;D;D;D	0.92299	-2.48;-2.48;-2.33;-2.52;-2.35;-2.52;-2.33;-3.01	3.62	3.62	0.41486	.	0.677917	0.14260	U	0.330896	T	0.36690	0.0976	N	0.08118	0	0.27134	N	0.961827	B;B;B;B;B	0.32968	0.0;0.0;0.0;0.002;0.392	B;B;B;B;B	0.36845	0.001;0.001;0.0;0.003;0.234	T	0.60606	-0.7230	10	0.31617	T	0.26	.	13.8858	0.63708	0.0:0.0:1.0:0.0	rs3742030;rs3742030	19;19;19;19;19	Q9HBA0-2;Q9HBA0;Q9HBA0-6;Q9HBA0-4;Q9HBA0-5	.;TRPV4_HUMAN;.;.;.	S	19	ENSP00000406191:P19S;ENSP00000261740:P19S;ENSP00000376480:P19S;ENSP00000319003:P19S;ENSP00000443611:P19S;ENSP00000442738:P19S;ENSP00000442167:P19S;ENSP00000444336:P19S	ENSP00000261740:P19S	P	-	1	0	TRPV4	108736930	0.996000	0.38824	0.962000	0.40283	0.834000	0.47266	1.617000	0.36943	1.586000	0.49944	0.281000	0.19383	CCC	G|0.957;A|0.043	0.043	strong		0.682	TRPV4-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403270.1	NM_021625	
LNPEP	4012	hgsc.bcm.edu	37	5	96350710	96350710	+	Missense_Mutation	SNP	G	G	A	rs2303138	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:96350710G>A	ENST00000231368.5	+	13	2979	c.2287G>A	c.(2287-2289)Gca>Aca	p.A763T	LNPEP_ENST00000395770.3_Missense_Mutation_p.A749T	NM_005575.2	NP_005566.2	Q9UIQ6	LCAP_HUMAN	leucyl/cystinyl aminopeptidase	763			A -> T (in dbSNP:rs2303138).		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-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cell-cell signaling (GO:0007267)|female pregnancy (GO:0007565)|membrane organization (GO:0061024)|protein catabolic process (GO:0030163)|protein polyubiquitination (GO:0000209)|proteolysis (GO:0006508)	cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|early endosome lumen (GO:0031905)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(10)|ovary(3)|skin(1)|urinary_tract(1)	34		all_cancers(142;7e-07)|all_epithelial(76;9.52e-10)|all_lung(232;0.00101)|Lung NSC(167;0.00137)|Ovarian(225;0.024)|Colorectal(57;0.0269)|Breast(839;0.244)		COAD - Colon adenocarcinoma(37;0.072)		GAACCATACTGCACCCATCAC	0.433													G|||	812	0.162141	0.0545	0.1585	5008	,	,		18677	0.3958		0.0636	False		,,,				2504	0.1708				p.A763T		Atlas-SNP	.											.	LNPEP	80	.	0			c.G2287A						PASS	.	G	THR/ALA,THR/ALA	313,4093	167.3+/-198.3	12,289,1902	131.0	124.0	127.0		2287,2245	5.6	1.0	5	dbSNP_100	127	638,7962	163.9+/-216.4	22,594,3684	yes	missense,missense	LNPEP	NM_005575.2,NM_175920.3	58,58	34,883,5586	AA,AG,GG		7.4186,7.1039,7.312	probably-damaging,probably-damaging	763/1026,749/1012	96350710	951,12055	2203	4300	6503	SO:0001583	missense	4012	exon13			CATACTGCACCCA	D50810	CCDS4087.1, CCDS43346.1	5q15	2011-07-25			ENSG00000113441	ENSG00000113441	3.4.11.3		6656	protein-coding gene	gene with protein product	"""cystinyl aminopeptidase"", ""placental leucine aminopeptidase"""	151300				8550619	Standard	NM_175920		Approved	CAP, PLAP, P-LAP	uc003kmw.1	Q9UIQ6	OTTHUMG00000128719	ENST00000231368.5:c.2287G>A	5.37:g.96350710G>A	ENSP00000231368:p.Ala763Thr	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	139	76	0.546763	NM_005575	O00769|Q15145|Q59H76|Q9TNQ2|Q9TNQ3|Q9UIQ7	Missense_Mutation	SNP	ENST00000231368.5	37	CCDS4087.1	372	0.17032967032967034	19	0.03861788617886179	57	0.1574585635359116	243	0.42482517482517484	53	0.06992084432717678	G	18.30	3.594182	0.66219	0.071039	0.074186	ENSG00000113441	ENST00000231368;ENST00000395770	T;T	0.05513	3.43;3.43	5.55	5.55	0.83447	.	0.151494	0.64402	D	0.000017	T	0.00012	0.0000	L	0.45581	1.43	0.09310	P	0.99999856535	P	0.38167	0.621	P	0.48873	0.593	T	0.61729	-0.7003	9	0.27785	T	0.31	.	19.1132	0.93326	0.0:0.0:1.0:0.0	rs2303138;rs17592364;rs60113863;rs2303138	763	Q9UIQ6	LCAP_HUMAN	T	763;749	ENSP00000231368:A763T;ENSP00000379117:A749T	ENSP00000231368:A763T	A	+	1	0	LNPEP	96376466	1.000000	0.71417	0.999000	0.59377	0.762000	0.43233	4.768000	0.62293	2.603000	0.88011	0.655000	0.94253	GCA	G|0.880;A|0.120	0.120	strong		0.433	LNPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250624.1	NM_005575	
MAP2K2	5605	hgsc.bcm.edu	37	19	4117483	4117483	+	Silent	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:4117483G>A	ENST00000262948.5	-	2	490	c.237C>T	c.(235-237)ggC>ggT	p.G79G	MAP2K2_ENST00000599345.1_5'UTR|MAP2K2_ENST00000394867.4_5'UTR	NM_030662.3	NP_109587.1	P36507	MP2K2_HUMAN	mitogen-activated protein kinase kinase 2	79	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|epidermal growth factor receptor signaling pathway (GO:0007173)|ERK1 and ERK2 cascade (GO:0070371)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|MAPK cascade (GO:0000165)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine autophosphorylation (GO:0036289)|positive regulation of cell motility (GO:2000147)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|Ras protein signal transduction (GO:0007265)|regulation of early endosome to late endosome transport (GO:2000641)|regulation of Golgi inheritance (GO:0090170)|regulation of stress-activated MAPK cascade (GO:0032872)|small GTPase mediated signal transduction (GO:0007264)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cell cortex (GO:0005938)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|late endosome (GO:0005770)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|peroxisomal membrane (GO:0005778)	ATP binding (GO:0005524)|MAP kinase kinase activity (GO:0004708)|PDZ domain binding (GO:0030165)|protein serine/threonine kinase activator activity (GO:0043539)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)|scaffold protein binding (GO:0097110)						Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0149)|STAD - Stomach adenocarcinoma(1328;0.18)	Bosutinib(DB06616)|Trametinib(DB08911)	CGTTGCCCGCGCCCAGCTCTG	0.617																																					p.G79G		Atlas-SNP	.											.	MAP2K2	72	.	0			c.C237T						PASS	.						67.0	63.0	64.0					19																	4117483		2203	4300	6503	SO:0001819	synonymous_variant	5605	exon2			GCCCGCGCCCAGC	L11285	CCDS12120.1	19p13.3	2014-09-17			ENSG00000126934	ENSG00000126934	2.7.12.2	"""Mitogen-activated protein kinase cascade / Kinase kinases"""	6842	protein-coding gene	gene with protein product		601263		PRKMK2		8388392	Standard	NM_030662		Approved	MEK2	uc002lzk.3	P36507	OTTHUMG00000134286	ENST00000262948.5:c.237C>T	19.37:g.4117483G>A		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	89	38	0.426966	NM_030662		Silent	SNP	ENST00000262948.5	37	CCDS12120.1																																																																																			.	.	none		0.617	MAP2K2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258957.2		
TCEB3B	51224	hgsc.bcm.edu	37	18	44561100	44561100	+	Missense_Mutation	SNP	C	C	G	rs2571028	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:44561100C>G	ENST00000332567.4	-	1	888	c.536G>C	c.(535-537)cGg>cCg	p.R179P	KATNAL2_ENST00000356157.7_Intron|KATNAL2_ENST00000245121.5_Intron|KATNAL2_ENST00000592005.1_Intron	NM_016427.2	NP_057511.2	Q8IYF1	ELOA2_HUMAN	transcription elongation factor B polypeptide 3B (elongin A2)	179			R -> P (in dbSNP:rs2571028). {ECO:0000269|PubMed:10692460}.		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						CTCGGGCATCCGGAGGGGAGC	0.687													G|||	2825	0.564097	0.4554	0.6643	5008	,	,		13938	0.6518		0.5268	False		,,,				2504	0.5879				p.R179P		Atlas-SNP	.											.	TCEB3B	141	.	0			c.G536C						PASS	.	G	PRO/ARG,	2119,2271		532,1055,608	30.0	37.0	34.0		536,	-5.2	0.0	18	dbSNP_100	34	4495,4083		1218,2059,1012	yes	missense,intron	TCEB3B,KATNAL2	NM_016427.2,NM_031303.2	103,	1750,3114,1620	GG,GC,CC		47.5985,48.2688,48.9975	benign,	179/754,	44561100	6614,6354	2195	4289	6484	SO:0001583	missense	51224	exon1			GGCATCCGGAGGG	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.536G>C	18.37:g.44561100C>G	ENSP00000331302:p.Arg179Pro	Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	28	18	0.642857	NM_016427	Q9P2V9	Missense_Mutation	SNP	ENST00000332567.4	37	CCDS11932.1	1210	0.5540293040293041	219	0.4451219512195122	226	0.6243093922651933	368	0.6433566433566433	397	0.5237467018469657	G	2.378	-0.342720	0.05243	0.482688	0.524015	ENSG00000206181	ENST00000332567	T	0.06933	3.24	2.59	-5.18	0.02840	.	5.029900	0.01017	N	0.003927	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	0.38585	-0.9654	9	0.12430	T	0.62	0.1268	2.6295	0.04940	0.2559:0.4417:0.1273:0.175	rs2571028;rs60264821	179	Q8IYF1	ELOA2_HUMAN	P	179	ENSP00000331302:R179P	ENSP00000331302:R179P	R	-	2	0	TCEB3B	42815098	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.327000	0.01113	-3.593000	0.00135	-1.188000	0.01700	CGG	C|0.467;G|0.533	0.533	strong		0.687	TCEB3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255900.1	NM_016427	
PTPRN2	5799	hgsc.bcm.edu	37	7	157931144	157931144	+	Missense_Mutation	SNP	C	C	T	rs1130499	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:157931144C>T	ENST00000389418.4	-	7	983	c.974G>A	c.(973-975)aGt>aAt	p.S325N	PTPRN2_ENST00000409483.1_Missense_Mutation_p.S287N|PTPRN2_ENST00000389416.4_Missense_Mutation_p.S308N|PTPRN2_ENST00000389413.3_Missense_Mutation_p.S325N|PTPRN2_ENST00000404321.2_Missense_Mutation_p.S348N	NM_002847.3	NP_002838.2	Q92932	PTPR2_HUMAN	protein tyrosine phosphatase, receptor type, N polypeptide 2	325			S -> N (in dbSNP:rs1130499). {ECO:0000269|PubMed:8954911, ECO:0000269|Ref.4}.		negative regulation of GTPase activity (GO:0034260)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	endoplasmic reticulum lumen (GO:0005788)|integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)|secretory granule (GO:0030141)|terminal bouton (GO:0043195)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|liver(1)|lung(42)|ovary(4)|pleura(1)|prostate(2)|skin(10)|upper_aerodigestive_tract(1)	86	all_neural(206;0.181)	all_cancers(7;8.99e-13)|all_epithelial(9;2.4e-06)|all_hematologic(28;0.0155)|Breast(660;0.132)	OV - Ovarian serous cystadenocarcinoma(82;0.00463)	STAD - Stomach adenocarcinoma(7;0.0875)		CTCCAGGCCACTCAGGCCCCT	0.637													C|||	1879	0.3752	0.4387	0.4395	5008	,	,		19314	0.4663		0.2903	False		,,,				2504	0.2372				p.S325N		Atlas-SNP	.											.	PTPRN2	243	.	0			c.G974A						PASS	.		ASN/SER,ASN/SER,ASN/SER	1935,2471	546.4+/-377.0	421,1093,689	65.0	67.0	66.0		974,923,974	2.2	0.0	7	dbSNP_86	66	2540,6060	411.0+/-350.3	362,1816,2122	yes	missense,missense,missense	PTPRN2	NM_002847.3,NM_130842.2,NM_130843.2	46,46,46	783,2909,2811	TT,TC,CC		29.5349,43.9174,34.4072	possibly-damaging,possibly-damaging,possibly-damaging	325/1016,308/999,325/987	157931144	4475,8531	2203	4300	6503	SO:0001583	missense	5799	exon7			AGGCCACTCAGGC	AB002385	CCDS5947.1, CCDS5948.1, CCDS5949.1	7q36	2011-06-09			ENSG00000155093	ENSG00000155093		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"""	9677	protein-coding gene	gene with protein product	"""IAR PTPRP"""	601698				8954911, 9220540	Standard	NM_130842		Approved	KIAA0387, phogrin, ICAAR, IA-2beta	uc003wno.3	Q92932	OTTHUMG00000152646	ENST00000389418.4:c.974G>A	7.37:g.157931144C>T	ENSP00000374069:p.Ser325Asn	Somatic	108	1	0.00925926		WXS	Illumina HiSeq	Phase_I	75	74	0.986667	NM_130843	E9PC57|Q8N4I5|Q92662|Q9Y4F8|Q9Y4I6	Missense_Mutation	SNP	ENST00000389418.4	37	CCDS5947.1	897	0.4107142857142857	237	0.4817073170731707	134	0.3701657458563536	302	0.527972027972028	224	0.2955145118733509	C	9.887	1.203049	0.22121	0.439174	0.295349	ENSG00000155093	ENST00000409483;ENST00000389413;ENST00000389416;ENST00000389418;ENST00000404321	T;T;T;T;T	0.03330	3.98;3.98;3.98;3.98;3.97	4.11	2.21	0.28008	.	.	.	.	.	T	0.00012	0.0000	L	0.29908	0.895	0.80722	P	0.0	B;B;B;B;B	0.16396	0.017;0.01;0.017;0.01;0.01	B;B;B;B;B	0.18561	0.022;0.01;0.022;0.01;0.01	T	0.30707	-0.9969	8	0.41790	T	0.15	.	4.3887	0.11330	0.0:0.5974:0.19:0.2126	rs1130499;rs3189416;rs3752370;rs10434937;rs52826743;rs1130499	348;287;325;308;325	Q92932-3;E7EM83;Q92932-2;E9PC57;Q92932	.;.;.;.;PTPR2_HUMAN	N	287;325;308;325;348	ENSP00000387114:S287N;ENSP00000374064:S325N;ENSP00000374067:S308N;ENSP00000374069:S325N;ENSP00000385464:S348N	ENSP00000374064:S325N	S	-	2	0	PTPRN2	157623905	0.000000	0.05858	0.001000	0.08648	0.004000	0.04260	0.503000	0.22610	0.274000	0.22072	0.650000	0.86243	AGT	C|0.623;T|0.377	0.377	strong		0.637	PTPRN2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000353214.1		
TRIM65	201292	hgsc.bcm.edu	37	17	73888423	73888423	+	Silent	SNP	A	A	G	rs7222755	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:73888423A>G	ENST00000269383.3	-	3	734	c.669T>C	c.(667-669)caT>caC	p.H223H		NM_001256124.1|NM_173547.3	NP_001243053.1|NP_775818.2	Q6PJ69	TRI65_HUMAN	tripartite motif containing 65	223						intracellular (GO:0005622)	zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|lung(5)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	12			Epithelial(20;7.53e-06)|all cancers(21;9.11e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00092)|LUSC - Lung squamous cell carcinoma(166;0.154)			CAGCCTCCAAATGGACCCGCA	0.647													G|||	2044	0.408147	0.7859	0.2709	5008	,	,		16113	0.2212		0.2972	False		,,,				2504	0.3016				p.H223H		Atlas-SNP	.											.	TRIM65	23	.	0			c.T669C						PASS	.	G		3126,1276		1135,856,210	23.0	27.0	26.0		669	3.2	0.9	17	dbSNP_116	26	2536,6062		386,1764,2149	no	coding-synonymous	TRIM65	NM_173547.2		1521,2620,2359	GG,GA,AA		29.4952,28.9868,43.5538		223/518	73888423	5662,7338	2201	4299	6500	SO:0001819	synonymous_variant	201292	exon3			CTCCAAATGGACC	BC006138	CCDS11732.1	17q25.1	2013-01-09	2011-01-25		ENSG00000141569	ENSG00000141569		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	27316	protein-coding gene	gene with protein product			"""tripartite motif-containing 65"""			12477932	Standard	NM_173547		Approved		uc002jpx.4	Q6PJ69	OTTHUMG00000132127	ENST00000269383.3:c.669T>C	17.37:g.73888423A>G		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	47	19	0.404255	NM_001256124	Q4G0F0|Q6DKJ6|Q9BRP6	Silent	SNP	ENST00000269383.3	37	CCDS11732.1	843|843	0.385989010989011|0.385989010989011	374|374	0.7601626016260162|0.7601626016260162	109|109	0.3011049723756906|0.3011049723756906	147|147	0.256993006993007|0.256993006993007	213|213	0.28100263852242746|0.28100263852242746	G|G	0.396|0.396	-0.920654|-0.920654	0.02396|0.02396	0.710132|0.710132	0.294952|0.294952	ENSG00000141569|ENSG00000141569	ENST00000540128|ENST00000543309	.|.	.|.	.|.	4.23|4.23	3.23|3.23	0.37069|0.37069	.|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.09310|0.09310	P|P	0.99999999509411|0.99999999509411	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.24728|0.24728	-1.0152|-1.0152	3|3	.|.	.|.	.|.	.|.	7.3708|7.3708	0.26800|0.26800	0.0908:0.3209:0.5883:0.0|0.0908:0.3209:0.5883:0.0	rs7222755;rs60028486|rs7222755;rs60028486	.|.	.|.	.|.	L|T	215|97	.|.	.|.	F|I	-|-	1|2	0|0	TRIM65|TRIM65	71400018|71400018	0.927000|0.927000	0.31430|0.31430	0.939000|0.939000	0.37840|0.37840	0.013000|0.013000	0.08279|0.08279	0.449000|0.449000	0.21744|0.21744	0.429000|0.429000	0.26202|0.26202	-0.355000|-0.355000	0.07637|0.07637	TTT|ATT	A|0.591;G|0.409	0.409	strong		0.647	TRIM65-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255170.2	NM_173547	
PKHD1L1	93035	hgsc.bcm.edu	37	8	110437384	110437384	+	Missense_Mutation	SNP	A	A	G	rs4735133	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:110437384A>G	ENST00000378402.5	+	24	2872	c.2768A>G	c.(2767-2769)cAt>cGt	p.H923R		NM_177531.4	NP_803875.2	Q86WI1	PKHL1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1	923			H -> R (in dbSNP:rs4735133).		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)			TCAAAAATTCATATTCAAAGA	0.318										HNSCC(38;0.096)			A|||	3068	0.61262	0.7489	0.6585	5008	,	,		15526	0.3968		0.5219	False		,,,				2504	0.7117				p.H923R		Atlas-SNP	.											PKHD1L1,NS,carcinoma,+1,1	PKHD1L1	522	1	0			c.A2768G						PASS	.	A	ARG/HIS	2684,980		990,704,138	44.0	44.0	44.0		2768	1.0	1.0	8	dbSNP_111	44	4442,3734		1221,2000,867	yes	missense	PKHD1L1	NM_177531.4	29	2211,2704,1005	GG,GA,AA		45.6703,26.7467,39.8142	benign	923/4244	110437384	7126,4714	1832	4088	5920	SO:0001583	missense	93035	exon24			AAATTCATATTCA	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.2768A>G	8.37:g.110437384A>G	ENSP00000367655:p.His923Arg	Somatic	205	0	0		WXS	Illumina HiSeq	Phase_I	200	163	0.815	NM_177531	Q567P2|Q9UF27	Missense_Mutation	SNP	ENST00000378402.5	37	CCDS47911.1	1220	0.5586080586080586	363	0.7378048780487805	229	0.6325966850828729	239	0.4178321678321678	389	0.5131926121372031	A	6.282	0.420189	0.11928	0.732533	0.543297	ENSG00000205038	ENST00000378402	D	0.84589	-1.87	5.16	1.04	0.20106	.	0.440867	0.24204	N	0.040590	T	0.00012	0.0000	N	0.00308	-1.67	0.49915	P	1.6899999999997473E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.41627	-0.9498	9	0.07813	T	0.8	.	6.2328	0.20744	0.1824:0.0:0.6675:0.1501	rs4735133;rs52821092;rs57461579;rs4735133	923	Q86WI1	PKHL1_HUMAN	R	923	ENSP00000367655:H923R	ENSP00000367655:H923R	H	+	2	0	PKHD1L1	110506560	0.993000	0.37304	0.999000	0.59377	0.959000	0.62525	0.228000	0.17814	0.270000	0.21984	-1.428000	0.01097	CAT	A|0.427;G|0.573	0.573	strong		0.318	PKHD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381017.1	NM_177531	
PLXNB2	23654	hgsc.bcm.edu	37	22	50726134	50726134	+	Missense_Mutation	SNP	C	C	T	rs375580670		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:50726134C>T	ENST00000449103.1	-	7	1710	c.1570G>A	c.(1570-1572)Gcc>Acc	p.A524T	PLXNB2_ENST00000359337.4_Missense_Mutation_p.A524T|PLXNB2_ENST00000496720.1_5'Flank			O15031	PLXB2_HUMAN	plexin B2	524					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)		TGTGGCTGGGCGCTGGTGACG	0.746																																					p.A524T		Atlas-SNP	.											.	PLXNB2	172	.	0			c.G1570A						PASS	.	C	THR/ALA	0,3290		0,0,1645	3.0	4.0	4.0		1570	2.7	0.0	22		4	2,7290		0,2,3644	no	missense	PLXNB2	NM_012401.3	58	0,2,5289	TT,TC,CC		0.0274,0.0,0.0189	possibly-damaging	524/1839	50726134	2,10580	1645	3646	5291	SO:0001583	missense	23654	exon7			GCTGGGCGCTGGT		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.1570G>A	22.37:g.50726134C>T	ENSP00000409171:p.Ala524Thr	Somatic	21	0	0		WXS	Illumina HiSeq	Phase_I	37	11	0.297297	NM_012401	A6QRH0|Q7KZU3|Q9BSU7	Missense_Mutation	SNP	ENST00000449103.1	37	CCDS43035.1	.	.	.	.	.	.	.	.	.	.	C	9.673	1.147298	0.21288	0.0	2.74E-4	ENSG00000196576	ENST00000449103;ENST00000359337	T;T	0.03272	3.99;3.99	4.84	2.73	0.32206	.	0.106352	0.41712	D	0.000837	T	0.06096	0.0158	M	0.69823	2.125	0.09310	N	0.99999	B	0.13145	0.007	B	0.04013	0.001	T	0.19778	-1.0295	10	0.59425	D	0.04	.	10.3837	0.44127	0.0:0.8373:0.0:0.1627	.	524	O15031	PLXB2_HUMAN	T	524	ENSP00000409171:A524T;ENSP00000352288:A524T	ENSP00000352288:A524T	A	-	1	0	PLXNB2	49068261	0.454000	0.25728	0.005000	0.12908	0.006000	0.05464	0.904000	0.28491	0.759000	0.33084	0.561000	0.74099	GCC	.	.	weak		0.746	PLXNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316874.3	NM_012401	
ADAM21	8747	hgsc.bcm.edu	37	14	70924697	70924697	+	Missense_Mutation	SNP	A	A	G	rs386778613|rs45545935	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:70924697A>G	ENST00000603540.1	+	2	739	c.481A>G	c.(481-483)Ata>Gta	p.I161V	RP11-486O13.4_ENST00000556646.1_lincRNA|ADAM21_ENST00000267499.3_Missense_Mutation_p.I161V	NM_003813.3	NP_003804.2	Q9UKJ8	ADA21_HUMAN	ADAM metallopeptidase domain 21	161				I -> V (in Ref. 1; AAD55255 and 3; AAI09025/AAI09026). {ECO:0000305}.	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.I161V(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)		GGTTTATAAGATAAACAGTAA	0.423													A|||	1254	0.250399	0.3026	0.1297	5008	,	,		19080	0.496		0.1173	False		,,,				2504	0.1493				p.I161V		Atlas-SNP	.											ADAM21_ENST00000267499,NS,carcinoma,0,1	ADAM21	181	1	1	Substitution - Missense(1)	stomach(1)	c.A481G						scavenged	.						39.0	48.0	45.0					14																	70924697		2156	4294	6450	SO:0001583	missense	8747	exon2			TATAAGATAAACA	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.481A>G	14.37:g.70924697A>G	ENSP00000474385:p.Ile161Val	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	67	16	0.238806	NM_003813	O43507|Q2VPC6|Q32MR0	Missense_Mutation	SNP	ENST00000603540.1	37	CCDS9804.1	.	.	.	.	.	.	.	.	.	.	A	0.700	-0.791263	0.02884	.	.	ENSG00000139985	ENST00000267499	T	0.01119	5.31	3.76	-5.66	0.02451	.	0.559418	0.13492	U	0.383910	T	0.00815	0.0027	L	0.41236	1.265	0.09310	N	1	B	0.09022	0.002	B	0.06405	0.002	T	0.48210	-0.9055	10	0.28530	T	0.3	.	0.3958	0.00418	0.2927:0.2858:0.1722:0.2492	rs45545935	161	Q9UKJ8	ADA21_HUMAN	V	161	ENSP00000267499:I161V	ENSP00000267499:I161V	I	+	1	0	ADAM21	69994450	0.000000	0.05858	0.025000	0.17156	0.459000	0.32528	-1.436000	0.02421	-0.597000	0.05813	0.455000	0.32223	ATA	A|0.947;G|0.053	0.053	strong		0.423	ADAM21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413008.3		
KRT84	3890	hgsc.bcm.edu	37	12	52774158	52774158	+	Silent	SNP	G	G	A	rs951772	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:52774158G>A	ENST00000257951.3	-	7	1479	c.1413C>T	c.(1411-1413)ggC>ggT	p.G471G	RP3-416H24.4_ENST00000547174.1_RNA	NM_033045.3	NP_149034.2	Q9NSB2	KRT84_HUMAN	keratin 84	471	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)		GGCTCTCCTCGCCCTCCAGCA	0.577											OREG0021848	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	1657	0.330871	0.6165	0.317	5008	,	,		18924	0.1994		0.2068	False		,,,				2504	0.2178				p.G471G		Atlas-SNP	.											.	KRT84	61	.	0			c.C1413T						PASS	.	G		2449,1953		711,1027,463	37.0	39.0	38.0		1413	0.8	1.0	12	dbSNP_86	38	1798,6800		184,1430,2685	no	coding-synonymous	KRT84	NM_033045.3		895,2457,3148	AA,AG,GG		20.9118,44.3662,32.6692		471/601	52774158	4247,8753	2201	4299	6500	SO:0001819	synonymous_variant	3890	exon7			CTCCTCGCCCTCC	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.1413C>T	12.37:g.52774158G>A		Somatic	67	0	0	987	WXS	Illumina HiSeq	Phase_I	48	24	0.5	NM_033045	B2RA43|Q6ISB0|Q701L6	Silent	SNP	ENST00000257951.3	37	CCDS8825.1																																																																																			G|0.688;A|0.312	0.312	strong		0.577	KRT84-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405187.1	NM_033045	
ARAP3	64411	hgsc.bcm.edu	37	5	141059868	141059868	+	Silent	SNP	T	T	C	rs11167756	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:141059868T>C	ENST00000239440.4	-	2	251	c.186A>G	c.(184-186)ctA>ctG	p.L62L	ARAP3_ENST00000508305.1_5'UTR	NM_022481.5	NP_071926.4	Q8WWN8	ARAP3_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 3	62	SAM. {ECO:0000255|PROSITE- ProRule:PRU00184}.				cytoskeleton organization (GO:0007010)|negative regulation of cell migration (GO:0030336)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of Rho protein signal transduction (GO:0035024)|regulation of ARF GTPase activity (GO:0032312)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	ARF GTPase activator activity (GO:0008060)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|Rho GTPase activator activity (GO:0005100)|zinc ion binding (GO:0008270)			NS(1)|breast(7)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(14)|ovary(1)|prostate(2)|skin(4)|stomach(1)	53						TGCCTGTCTGTAGCAGGCGTA	0.652													C|||	2332	0.465655	0.4493	0.4942	5008	,	,		15776	0.4683		0.4274	False		,,,				2504	0.5041				p.L62L		Atlas-SNP	.											.	ARAP3	139	.	0			c.A186G						PASS	.	C		1957,2449	619.1+/-393.3	439,1079,685	83.0	88.0	87.0		186	0.2	0.9	5	dbSNP_120	87	3613,4987	625.1+/-397.7	778,2057,1465	yes	coding-synonymous	ARAP3	NM_022481.5		1217,3136,2150	CC,CT,TT		42.0116,44.4167,42.8264		62/1545	141059868	5570,7436	2203	4300	6503	SO:0001819	synonymous_variant	64411	exon2			TGTCTGTAGCAGG	AJ310567	CCDS4266.1	5q31.3	2013-01-11	2008-09-22	2008-09-22	ENSG00000120318	ENSG00000120318		"""ADP-ribosylation factor GTPase activating proteins"", ""Sterile alpha motif (SAM) domain containing"", ""Pleckstrin homology (PH) domain containing"", ""Ankyrin repeat domain containing"""	24097	protein-coding gene	gene with protein product		606647	"""centaurin, delta 3"""	CENTD3		11804589, 12015138	Standard	XM_005268497		Approved	FLJ21065, DRAG1	uc003llm.3	Q8WWN8	OTTHUMG00000129610	ENST00000239440.4:c.186A>G	5.37:g.141059868T>C		Somatic	216	1	0.00462963		WXS	Illumina HiSeq	Phase_I	190	96	0.505263	NM_022481	B4DIT1|D3DQE3	Silent	SNP	ENST00000239440.4	37	CCDS4266.1																																																																																			T|0.567;C|0.433	0.433	strong		0.652	ARAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251805.1	NM_022481	
TMIGD2	126259	hgsc.bcm.edu	37	19	4294623	4294623	+	Missense_Mutation	SNP	C	C	A	rs58237134	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:4294623C>A	ENST00000301272.2	-	4	548	c.503G>T	c.(502-504)tGg>tTg	p.W168L	TMIGD2_ENST00000600349.1_Intron|TMIGD2_ENST00000595645.1_Missense_Mutation_p.W168L|TMIGD2_ENST00000600114.1_Missense_Mutation_p.W48L	NM_001169126.1|NM_144615.2	NP_001162597.1|NP_653216.2	Q96BF3	TMIG2_HUMAN	transmembrane and immunoglobulin domain containing 2	168			W -> L (in dbSNP:rs58237134).		positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of cytokine production (GO:0001819)|signal transduction (GO:0007165)|T cell costimulation (GO:0031295)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	coreceptor activity (GO:0015026)			breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(10)|prostate(1)|skin(2)	19				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0339)|STAD - Stomach adenocarcinoma(1328;0.18)		CCAGGCACCCCACACGATCGC	0.637													A|||	894	0.178514	0.1543	0.1931	5008	,	,		13901	0.0873		0.2068	False		,,,				2504	0.2658				p.W168L		Atlas-SNP	.											.	TMIGD2	38	.	0			c.G503T						PASS	.	A	LEU/TRP,LEU/TRP	776,3630	751.6+/-412.2	69,638,1496	119.0	142.0	134.0		503,503	1.9	0.0	19	dbSNP_129	134	1785,6815	732.2+/-406.8	192,1401,2707	yes	missense,missense	TMIGD2	NM_001169126.1,NM_144615.2	61,61	261,2039,4203	AA,AC,CC		20.7558,17.6123,19.6909	benign,benign	168/279,168/283	4294623	2561,10445	2203	4300	6503	SO:0001583	missense	126259	exon4			GCACCCCACACGA	BC015655	CCDS12126.1, CCDS59334.1	19p13.3	2014-02-12	2006-07-05					"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	28324	protein-coding gene	gene with protein product		614715					Standard	NM_144615		Approved	MGC23244	uc002lzx.2	Q96BF3		ENST00000301272.2:c.503G>T	19.37:g.4294623C>A	ENSP00000301272:p.Trp168Leu	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	65	31	0.476923	NM_144615	Q6UW59	Missense_Mutation	SNP	ENST00000301272.2	37	CCDS12126.1	374	0.17124542124542125	92	0.18699186991869918	71	0.19613259668508287	68	0.11888111888111888	143	0.18865435356200527	A	0.011	-1.720885	0.00700	0.176123	0.207558	ENSG00000167664	ENST00000301272	T	0.28454	1.61	2.94	1.86	0.25419	.	.	.	.	.	T	0.00012	0.0000	N	0.01874	-0.695	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.39057	-0.9632	8	0.02654	T	1	.	7.1594	0.25654	0.536:0.464:0.0:0.0	rs58237134;rs61753894	168;168	Q96BF3-2;Q96BF3	.;TMIG2_HUMAN	L	168	ENSP00000301272:W168L	ENSP00000301272:W168L	W	-	2	0	TMIGD2	4245623	0.024000	0.19004	0.032000	0.17829	0.002000	0.02628	0.579000	0.23788	-0.036000	0.13669	-0.384000	0.06662	TGG	C|0.806;A|0.194	0.194	strong		0.637	TMIGD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458088.1	NM_144615	
MYO3B	140469	hgsc.bcm.edu	37	2	171240249	171240249	+	Silent	SNP	C	C	T	rs11675394	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	118	0	0		WXS	Illumina HiSeq	Phase_I	94	57	0.606383	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		
FBXO2	26232	hgsc.bcm.edu	37	1	11710561	11710561	+	Missense_Mutation	SNP	T	T	G	rs9614	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:11710561T>G	ENST00000354287.4	-	2	694	c.353A>C	c.(352-354)aAg>aCg	p.K118T	FBXO2_ENST00000475961.1_5'Flank	NM_012168.5	NP_036300.2	Q9UK22	FBX2_HUMAN	F-box protein 2	118	FBA. {ECO:0000255|PROSITE- ProRule:PRU00482}.		K -> T (in dbSNP:rs9614). {ECO:0000269|Ref.2}.		cellular protein modification process (GO:0006464)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|glycoprotein catabolic process (GO:0006516)|negative regulation of cell proliferation (GO:0008285)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)|regulation of protein ubiquitination (GO:0031396)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)	cytosol (GO:0005829)|dendritic spine (GO:0043197)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|SCF ubiquitin ligase complex (GO:0019005)	beta-amyloid binding (GO:0001540)|carbohydrate binding (GO:0030246)|ubiquitin-protein transferase activity (GO:0004842)			kidney(1)|large_intestine(1)|lung(4)	6	Ovarian(185;0.249)	Lung NSC(185;9.37e-06)|all_lung(284;1.39e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|BRCA - Breast invasive adenocarcinoma(304;1.88e-06)|Colorectal(212;4.88e-06)|COAD - Colon adenocarcinoma(227;0.000241)|Kidney(185;0.000722)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.0072)|Lung(427;0.0146)|LUSC - Lung squamous cell carcinoma(448;0.0228)|READ - Rectum adenocarcinoma(331;0.0649)		GCGGCGCCGCTTGCTCAGGAA	0.687													T|||	1220	0.24361	0.143	0.2565	5008	,	,		14310	0.4494		0.1759	False		,,,				2504	0.228				p.K118T		Atlas-SNP	.											.	FBXO2	25	.	0			c.A353C						PASS	.	T	THR/LYS	730,3668		53,624,1522	20.0	25.0	23.0		353	3.9	1.0	1	dbSNP_52	23	1653,6943		160,1333,2805	yes	missense	FBXO2	NM_012168.5	78	213,1957,4327	GG,GT,TT		19.2299,16.5985,18.3392	probably-damaging	118/297	11710561	2383,10611	2199	4298	6497	SO:0001583	missense	26232	exon2			CGCCGCTTGCTCA	AF174594	CCDS130.1	1p36.21	2010-04-21	2004-06-15		ENSG00000116661	ENSG00000116661		"""F-boxes /  ""other"""""	13581	protein-coding gene	gene with protein product		607112	"""F-box only protein 2"", ""organ of Corti protein 1"""	OCP1		10531035, 10531037	Standard	NM_012168		Approved	FBX2, Nfb42, Fbs1, Fbg1	uc001asj.3	Q9UK22	OTTHUMG00000002072	ENST00000354287.4:c.353A>C	1.37:g.11710561T>G	ENSP00000346240:p.Lys118Thr	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	60	33	0.55	NM_012168	B2R7K7|Q5TGY0|Q6FGJ7|Q8TB29|Q9UKC6	Missense_Mutation	SNP	ENST00000354287.4	37	CCDS130.1	537	0.24587912087912087	73	0.1483739837398374	84	0.23204419889502761	249	0.4353146853146853	131	0.17282321899736147	T	22.7	4.326899	0.81690	0.165985	0.192299	ENSG00000116661	ENST00000354287;ENST00000452872	T	0.32272	1.46	5.06	3.91	0.45181	Galactose-binding domain-like (1);F-box domain, Skp2-like (1);F-box associated (FBA) domain (2);	0.334286	0.29286	N	0.012596	T	0.00012	0.0000	L	0.58101	1.795	0.28577	P	0.9103149	D;D	0.71674	0.986;0.998	D;D	0.87578	0.926;0.998	T	0.47045	-0.9147	9	0.49607	T	0.09	.	9.0059	0.36111	0.0:0.0874:0.0:0.9126	rs9614;rs1055561;rs3170621;rs17342213;rs17349907;rs60441174;rs9614	118;118	A6NNP0;Q9UK22	.;FBX2_HUMAN	T	118	ENSP00000346240:K118T	ENSP00000346240:K118T	K	-	2	0	FBXO2	11633148	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	2.091000	0.41691	1.891000	0.54761	0.459000	0.35465	AAG	T|0.788;G|0.212	0.212	strong		0.687	FBXO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005764.1	NM_012168	
CDK5RAP2	55755	hgsc.bcm.edu	37	9	123220829	123220829	+	Silent	SNP	A	A	G	rs2501727	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:123220829A>G	ENST00000349780.4	-	20	2453	c.2274T>C	c.(2272-2274)gaT>gaC	p.D758D	CDK5RAP2_ENST00000359309.3_Silent_p.D758D|CDK5RAP2_ENST00000360822.3_Silent_p.D726D|CDK5RAP2_ENST00000360190.4_Silent_p.D758D	NM_018249.4	NP_060719.4	Q96SN8	CK5P2_HUMAN	CDK5 regulatory subunit associated protein 2	758					brain development (GO:0007420)|centrosome organization (GO:0051297)|chromosome segregation (GO:0007059)|establishment of mitotic spindle orientation (GO:0000132)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule bundle formation (GO:0001578)|microtubule cytoskeleton organization (GO:0000226)|mitotic cell cycle (GO:0000278)|negative regulation of centriole replication (GO:0046600)|negative regulation of neuron differentiation (GO:0045665)|neurogenesis (GO:0022008)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of neuron differentiation (GO:0045664)|regulation of spindle checkpoint (GO:0090231)	cell junction (GO:0030054)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|pericentriolar material (GO:0000242)|perinuclear region of cytoplasm (GO:0048471)|spindle pole (GO:0000922)	calmodulin binding (GO:0005516)|microtubule binding (GO:0008017)|protein kinase binding (GO:0019901)|transcription regulatory region DNA binding (GO:0044212)|tubulin binding (GO:0015631)			breast(6)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(12)|lung(21)|ovary(2)|prostate(2)|skin(6)|urinary_tract(1)	58						CCCCATCACAATCTGAAATCT	0.423													G|||	1166	0.232827	0.3616	0.1571	5008	,	,		20683	0.3214		0.0984	False		,,,				2504	0.1595				p.D758D		Atlas-SNP	.											.	CDK5RAP2	157	.	0			c.T2274C						PASS	.	G	,	1538,2868	672.2+/-402.6	292,954,957	104.0	102.0	102.0		2274,2274	-2.8	0.0	9	dbSNP_100	102	856,7744	780.2+/-407.7	40,776,3484	no	coding-synonymous,coding-synonymous	CDK5RAP2	NM_001011649.1,NM_018249.4	,	332,1730,4441	GG,GA,AA		9.9535,34.9069,18.4069	,	758/1815,758/1894	123220829	2394,10612	2203	4300	6503	SO:0001819	synonymous_variant	55755	exon20			ATCACAATCTGAA	BK005504	CCDS6823.1, CCDS43871.1, CCDS75888.1	9q33.3	2014-02-21			ENSG00000136861	ENSG00000136861			18672	protein-coding gene	gene with protein product	"""centrosomin"""	608201	"""microcephaly, primary autosomal recessive 3"""	MCPH3		10721722, 17764569, 24466316	Standard	NM_018249		Approved	C48, FLJ10867, CEP215	uc004bkf.4	Q96SN8	OTTHUMG00000021043	ENST00000349780.4:c.2274T>C	9.37:g.123220829A>G		Somatic	211	0	0		WXS	Illumina HiSeq	Phase_I	216	111	0.513889	NM_018249	Q5JV18|Q7Z3L4|Q7Z3U1|Q7Z7I6|Q9BSW0|Q9H6J6|Q9HCD9|Q9NV90|Q9UIW9	Silent	SNP	ENST00000349780.4	37	CCDS6823.1																																																																																			A|0.802;G|0.198	0.198	strong		0.423	CDK5RAP2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055535.1	NM_018249	
ARSD	414	hgsc.bcm.edu	37	X	2836211	2836211	+	Missense_Mutation	SNP	A	A	T	rs73632977	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:2836211A>T	ENST00000381154.1	-	5	572	c.497T>A	c.(496-498)cTg>cAg	p.L166Q	ARSD_ENST00000217890.6_5'UTR	NM_001669.3	NP_001660.2	P51689	ARSD_HUMAN	arylsulfatase D	166					cellular protein metabolic process (GO:0044267)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	arylsulfatase activity (GO:0004065)|metal ion binding (GO:0046872)	p.L166Q(1)		large_intestine(3)|lung(3)	6		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				TCCGTGGTTCAGGGGGTGGTG	0.572																																					p.L166Q		Atlas-SNP	.											.	ARSD	47	.	1	Substitution - Missense(1)	large_intestine(1)	c.T497A						PASS	.						34.0	20.0	25.0					X																	2836211		2200	4289	6489	SO:0001583	missense	414	exon5			TGGTTCAGGGGGT	X83572	CCDS35196.1	Xp22.3	2013-02-14			ENSG00000006756	ENSG00000006756		"""Arylsulfatase family"""	717	protein-coding gene	gene with protein product		300002				7720070	Standard	NM_001669		Approved		uc004cqy.3	P51689	OTTHUMG00000021077	ENST00000381154.1:c.497T>A	X.37:g.2836211A>T	ENSP00000370546:p.Leu166Gln	Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	136	18	0.132353	NM_001669	Q9UHJ8	Missense_Mutation	SNP	ENST00000381154.1	37	CCDS35196.1	142	0.08559373116335142	33	0.07432432432432433	27	0.07988165680473373	33	0.06111111111111111	59	0.081267217630854	a	10.90	1.480007	0.26598	.	.	ENSG00000006756	ENST00000381154;ENST00000217890	D	0.94184	-3.37	3.47	3.47	0.39725	Alkaline phosphatase-like, alpha/beta/alpha (1);Sulfatase (1);Alkaline-phosphatase-like, core domain (1);	0.183165	0.37304	U	0.002147	T	0.65186	0.2667	M	0.79805	2.47	0.80722	P	0.0	D;D	0.61080	0.98;0.989	D;D	0.64877	0.93;0.917	T	0.81662	-0.0831	9	0.62326	D	0.03	.	7.379	0.26845	0.8026:0.0:0.0:0.1974	.	166;166	E9PAW5;P51689	.;ARSD_HUMAN	Q	166	ENSP00000370546:L166Q	ENSP00000217890:L166Q	L	-	2	0	ARSD	2846211	0.026000	0.19158	0.027000	0.17364	0.309000	0.27889	2.195000	0.42677	1.132000	0.42129	0.343000	0.21770	CTG	A|0.913;T|0.087	0.087	strong		0.572	ARSD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055636.1		
PCDHGC5	56097	hgsc.bcm.edu	37	5	140869003	140869003	+	Silent	SNP	T	T	C	rs1002519	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:140869003T>C	ENST00000252087.1	+	1	196	c.196T>C	c.(196-198)Ttg>Ctg	p.L66L	PCDHGA3_ENST00000253812.6_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGC3_ENST00000308177.3_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA10_ENST00000398610.2_Intron|PCDHGA11_ENST00000518882.1_Intron|PCDHGB7_ENST00000398594.2_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA11_ENST00000398587.2_Intron|PCDHGA12_ENST00000252085.3_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGC4_ENST00000306593.1_Intron	NM_018929.2|NM_032403.2|NM_032407.1	NP_061752.1|NP_115779.1|NP_115783.1	Q9Y5F6	PCDGM_HUMAN	protocadherin gamma subfamily C, 5	66	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(2)|endometrium(6)|kidney(4)|large_intestine(4)|lung(10)|ovary(4)|prostate(1)|urinary_tract(2)	35			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCGGCTGCAATTGGGCTCTGA	0.542													T|||	966	0.192891	0.1225	0.366	5008	,	,		17242	0.129		0.2296	False		,,,				2504	0.1933				p.L66L		Atlas-SNP	.											PCDHGC5_ENST00000252087,NS,carcinoma,-1,2	PCDHGC5	199	2	0			c.T196C						PASS	.	T	,,,,,,,,,,,,,,,,,,,,,,,,	625,3781	271.0+/-269.9	43,539,1621	94.0	97.0	96.0		,,,,,,,,,,,,,,,,,,,,196,,,,196	-5.2	0.2	5	dbSNP_86	96	1947,6653	344.7+/-325.5	210,1527,2563	no	intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,coding-synonymous,intron,intron,intron,coding-synonymous	PCDHGC3,PCDHGB4,PCDHGA8,PCDHGA12,PCDHGC5,PCDHGC4,PCDHGB7,PCDHGB6,PCDHGB5,PCDHGB3,PCDHGB2,PCDHGB1,PCDHGA11,PCDHGA10,PCDHGA9,PCDHGA7,PCDHGA6,PCDHGA5,PCDHGA4,PCDHGA3,PCDHGA2,PCDHGA1	NM_002588.2,NM_003735.2,NM_003736.2,NM_018912.2,NM_018913.2,NM_018914.2,NM_018915.2,NM_018916.3,NM_018917.2,NM_018918.2,NM_018919.2,NM_018920.2,NM_018921.2,NM_018922.2,NM_018923.2,NM_018924.2,NM_018925.2,NM_018926.2,NM_018927.3,NM_018928.2,NM_018929.2,NM_032088.1,NM_032092.1,NM_032403.1,NM_032407.1	,,,,,,,,,,,,,,,,,,,,,,,,	253,2066,4184	CC,CT,TT		22.6395,14.1852,19.7755	,,,,,,,,,,,,,,,,,,,,,,,,	,,,,,,,,,,,,,,,,,,,,66/945,,,,66/879	140869003	2572,10434	2203	4300	6503	SO:0001819	synonymous_variant	56097	exon1			CTGCAATTGGGCT	AF152526	CCDS4263.1, CCDS75350.1	5q31	2010-01-26			ENSG00000240764	ENSG00000240764		"""Cadherins / Protocadherins : Clustered"""	8718	other	protocadherin		606306				10380929	Standard	NM_018929		Approved	PCDH-GAMMA-C5	uc003lla.2	Q9Y5F6	OTTHUMG00000129624	ENST00000252087.1:c.196T>C	5.37:g.140869003T>C		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	50	50	1	NM_018929	Q9Y5C2	Silent	SNP	ENST00000252087.1	37	CCDS4263.1																																																																																			T|0.810;C|0.190	0.190	strong		0.542	PCDHGC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251819.1	NM_018929	
HLA-A	3105	hgsc.bcm.edu	37	6	29913042	29913042	+	Silent	SNP	C	C	T	rs14288	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:29913042C>T	ENST00000396634.1	+	9	1418	c.1077C>T	c.(1075-1077)tcC>tcT	p.S359S	HLA-A_ENST00000376802.2_Intron|HLA-A_ENST00000376809.5_Silent_p.S359S|HLA-A_ENST00000376806.5_Silent_p.S365S			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	359					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						CTGATGTGTCCCTCACAGCTT	0.522									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|||	4636	0.925719	0.9342	0.9078	5008	,	,		19201	0.9841		0.8479	False		,,,				2504	0.9468				p.S359S		Atlas-SNP	.											.	HLA-A	89	.	0			c.C1077T						PASS	.	T		3921,485		1834,253,116	108.0	104.0	106.0		1077	2.1	0.0	6	dbSNP_101	106	7053,1547		3114,825,361	no	coding-synonymous	HLA-A	NM_002116.7		4948,1078,477	TT,TC,CC		17.9884,11.0077,15.6236		359/366	29913042	10974,2032	2203	4300	6503	SO:0001819	synonymous_variant	3105	exon7	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	TGTGTCCCTCACA	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.1077C>T	6.37:g.29913042C>T		Somatic	208	1	0.00480769		WXS	Illumina HiSeq	Phase_I	125	125	1	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Silent	SNP	ENST00000396634.1	37	CCDS34373.1																																																																																			C|0.102;T|0.898	0.898	strong		0.522	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
POM121C	100101267	hgsc.bcm.edu	37	7	75050958	75050958	+	Silent	SNP	G	G	A	rs587702156		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:75050958G>A	ENST00000257665.5	-	11	3302	c.3303C>T	c.(3301-3303)agC>agT	p.S1101S	POM121C_ENST00000473168.1_5'Flank|POM121C_ENST00000453279.2_Silent_p.S859S			A8CG34	P121C_HUMAN	POM121 transmembrane nucleoporin C	1101	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						CGGTGGTGGCGCTGGAGCCTG	0.637													.|||	1	0.000199681	0.0	0.0	5008	,	,		17160	0.0		0.001	False		,,,				2504	0.0				p.S859S		Atlas-SNP	.											.	POM121C	46	.	0			c.C2577T						PASS	.						7.0	10.0	9.0					7																	75050958		2158	4253	6411	SO:0001819	synonymous_variant	100101267	exon13			GGTGGCGCTGGAG		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.3303C>T	7.37:g.75050958G>A		Somatic	397	1	0.00251889		WXS	Illumina HiSeq	Phase_I	409	125	0.305623	NM_001099415	O75115|Q9Y2N3|Q9Y4S7	Silent	SNP	ENST00000257665.5	37																																																																																				.	.	none		0.637	POM121C-003	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000343919.2	NM_001099415	
KMT2C	58508	hgsc.bcm.edu	37	7	151878589	151878589	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:151878589G>A	ENST00000262189.6	-	36	6574	c.6356C>T	c.(6355-6357)cCt>cTt	p.P2119L	KMT2C_ENST00000355193.2_Missense_Mutation_p.P2119L	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	2119	Pro-rich.				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)										TATGGTTCCAGGCTGGGAAAA	0.478																																					p.P2119L		Atlas-SNP	.											.	MLL3	1564	.	0			c.C6356T						PASS	.						104.0	107.0	106.0					7																	151878589		2203	4300	6503	SO:0001583	missense	58508	exon36			GTTCCAGGCTGGG	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.6356C>T	7.37:g.151878589G>A	ENSP00000262189:p.Pro2119Leu	Somatic	202	0	0		WXS	Illumina HiSeq	Phase_I	130	74	0.569231	NM_170606	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Missense_Mutation	SNP	ENST00000262189.6	37	CCDS5931.1	.	.	.	.	.	.	.	.	.	.	G	14.04	2.418230	0.42918	.	.	ENSG00000055609	ENST00000262189;ENST00000355193	D;D	0.84800	-1.9;-1.9	5.11	5.11	0.69529	.	0.157447	0.29551	N	0.011839	D	0.87358	0.6157	L	0.56769	1.78	0.80722	D	1	D;D	0.56521	0.961;0.976	P;P	0.51701	0.617;0.677	D	0.85101	0.0957	10	0.23891	T	0.37	.	18.558	0.91091	0.0:0.0:1.0:0.0	.	2119;1180	Q8NEZ4;Q8NEZ4-2	MLL3_HUMAN;.	L	2119	ENSP00000262189:P2119L;ENSP00000347325:P2119L	ENSP00000262189:P2119L	P	-	2	0	MLL3	151509522	1.000000	0.71417	0.999000	0.59377	0.957000	0.61999	5.577000	0.67444	2.390000	0.81377	0.563000	0.77884	CCT	.	.	none		0.478	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3		
FREM2	341640	hgsc.bcm.edu	37	13	39343822	39343822	+	Missense_Mutation	SNP	C	C	T	rs9603422	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:39343822C>T	ENST00000280481.7	+	4	5734	c.5518C>T	c.(5518-5520)Cgg>Tgg	p.R1840W		NM_207361.4	NP_997244.3	Q5SZK8	FREM2_HUMAN	FRAS1 related extracellular matrix protein 2	1840	Calx-beta 1.		R -> W (in dbSNP:rs9603422).		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)		ATGGCGAGTGCGGATCCTGAG	0.542													C|||	710	0.141773	0.2057	0.0591	5008	,	,		14813	0.1617		0.1143	False		,,,				2504	0.1217				p.R1840W		Atlas-SNP	.											.	FREM2	385	.	0			c.C5518T						PASS	.	C	TRP/ARG	949,3457	358.9+/-314.6	100,749,1354	131.0	108.0	116.0		5518	3.3	0.2	13	dbSNP_119	116	1040,7560	220.9+/-258.5	60,920,3320	yes	missense	FREM2	NM_207361.4	101	160,1669,4674	TT,TC,CC		12.093,21.5388,15.2929	probably-damaging	1840/3170	39343822	1989,11017	2203	4300	6503	SO:0001583	missense	341640	exon4			CGAGTGCGGATCC	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.5518C>T	13.37:g.39343822C>T	ENSP00000280481:p.Arg1840Trp	Somatic	235	0	0		WXS	Illumina HiSeq	Phase_I	200	108	0.54	NM_207361	Q4QQG1|Q5H9N8|Q5T6Q1|Q6N057|Q6ZSB4|Q7Z305|Q7Z341	Missense_Mutation	SNP	ENST00000280481.7	37	CCDS31960.1	312	0.14285714285714285	112	0.22764227642276422	24	0.06629834254143646	84	0.14685314685314685	92	0.12137203166226913	C	11.76	1.735572	0.30774	0.215388	0.12093	ENSG00000150893	ENST00000280481	T	0.30981	1.51	5.01	3.29	0.37713	Na-Ca exchanger/integrin-beta4 (2);	0.065177	0.64402	D	0.000008	T	0.00039	0.0001	M	0.87180	2.865	0.19300	P	0.9999752728	D	0.89917	1.0	D	0.76575	0.988	T	0.04440	-1.0951	9	0.38643	T	0.18	.	8.4587	0.32915	0.2741:0.6538:0.0:0.0721	rs9603422;rs52793831;rs9603422	1840	Q5SZK8	FREM2_HUMAN	W	1840	ENSP00000280481:R1840W	ENSP00000280481:R1840W	R	+	1	2	FREM2	38241822	0.972000	0.33761	0.160000	0.22671	0.035000	0.12851	0.845000	0.27668	0.538000	0.28769	-0.942000	0.02676	CGG	C|0.848;T|0.152	0.152	strong		0.542	FREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044599.2	NM_207361	
PIEZO1	9780	hgsc.bcm.edu	37	16	88787704	88787704	+	Silent	SNP	G	G	C	rs8043924	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:88787704G>C	ENST00000301015.9	-	39	5784	c.5538C>G	c.(5536-5538)gcC>gcG	p.A1846A	PIEZO1_ENST00000327397.7_5'Flank|RP5-1142A6.9_ENST00000564984.1_RNA	NM_001142864.2	NP_001136336.2	Q92508	PIEZ1_HUMAN	piezo-type mechanosensitive ion channel component 1	1846					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						GTCCGACCCTGGCTTCCACCT	0.632													C|||	4269	0.852436	0.8464	0.8487	5008	,	,		17373	0.9325		0.8718	False		,,,				2504	0.7607				p.A1846A		Atlas-SNP	.											PIEZO1,NS,carcinoma,0,2	PIEZO1	79	2	0			c.C5538G						PASS	.	C		1185,199		508,169,15	51.0	52.0	52.0		5538	-0.5	0.0	16	dbSNP_116	52	2821,357		1252,317,20	no	coding-synonymous	PIEZO1	NM_001142864.2		1760,486,35	CC,CG,GG		11.2335,14.3786,12.1876		1846/2522	88787704	4006,556	692	1589	2281	SO:0001819	synonymous_variant	9780	exon39			GACCCTGGCTTCC	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.5538C>G	16.37:g.88787704G>C		Somatic	118	1	0.00847458		WXS	Illumina HiSeq	Phase_I	83	82	0.987952	NM_001142864	A6NHT9|A7E2B7|Q0KKZ9	Silent	SNP	ENST00000301015.9	37	CCDS54058.1	1922	0.88003663003663	411	0.8353658536585366	320	0.8839779005524862	532	0.9300699300699301	659	0.8693931398416886	C	6.584	0.476171	0.12521	0.856214	0.887665	ENSG00000103335	ENST00000451779	.	.	.	4.73	-0.508	0.11980	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.16158	-1.0412	3	.	.	.	-5.3024	2.9033	0.05713	0.1587:0.2839:0.3862:0.1712	rs8043924;rs56837082	.	.	.	E	1792	.	.	Q	-	1	0	FAM38A	87315205	0.000000	0.05858	0.000000	0.03702	0.019000	0.09904	-3.648000	0.00404	-0.592000	0.05851	-0.382000	0.06688	CAG	G|0.122;C|0.878	0.878	strong		0.632	PIEZO1-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000345699.4	NM_014745	
BAIAP2	10458	hgsc.bcm.edu	37	17	79009061	79009061	+	Silent	SNP	C	C	T	rs8068528	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:79009061C>T	ENST00000321300.6	+	1	100	c.7C>T	c.(7-9)Ctg>Ttg	p.L3L	BAIAP2_ENST00000435091.3_Silent_p.L3L|BAIAP2_ENST00000321280.7_Silent_p.L3L|BAIAP2-AS1_ENST00000577066.1_lincRNA|BAIAP2_ENST00000392411.3_5'UTR|BAIAP2_ENST00000573894.1_3'UTR|BAIAP2_ENST00000428708.2_Silent_p.L3L|BAIAP2_ENST00000575712.1_Silent_p.L3L|BAIAP2_ENST00000575245.1_Silent_p.L3L	NM_001144888.1|NM_017451.2	NP_001138360.1|NP_059345.1	Q9UQB8	BAIP2_HUMAN	BAI1-associated protein 2	3	IMD. {ECO:0000255|PROSITE- ProRule:PRU00668}.				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)			GACCATGTCTCTGTCTCGCTC	0.687													C|||	691	0.137979	0.0946	0.0865	5008	,	,		4463	0.253		0.0855	False		,,,				2504	0.1687				p.L3L		Atlas-SNP	.											BAIAP2_ENST00000321300,NS,carcinoma,0,2	BAIAP2	74	2	0			c.C7T						PASS	.	C	,,,	419,3971		25,369,1801	19.0	17.0	17.0		7,7,7,7	2.6	1.0	17	dbSNP_116	17	769,7817		33,703,3557	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	BAIAP2	NM_001144888.1,NM_006340.2,NM_017450.2,NM_017451.2	,,,	58,1072,5358	TT,TC,CC		8.9564,9.5444,9.1554	,,,	3/535,3/521,3/522,3/553	79009061	1188,11788	2195	4293	6488	SO:0001819	synonymous_variant	10458	exon1			ATGTCTCTGTCTC	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.7C>T	17.37:g.79009061C>T		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	79	38	0.481013	NM_001144888	O43858|Q53HB1|Q86WC1|Q8N5C0|Q96CR7|Q9UBR3|Q9UQ43	Silent	SNP	ENST00000321300.6	37	CCDS11775.1																																																																																			C|0.889;T|0.111	0.111	strong		0.687	BAIAP2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000438553.1		
MROH7	374977	hgsc.bcm.edu	37	1	55166842	55166842	+	Silent	SNP	C	C	T	rs1065173	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:55166842C>T	ENST00000421030.2	+	19	3417	c.3132C>T	c.(3130-3132)ccC>ccT	p.P1044P	MROH7_ENST00000409996.1_Silent_p.P612P|MROH7-TTC4_ENST00000414150.2_Silent_p.P1044P|MROH7_ENST00000454855.2_Silent_p.P562P	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	96	0	0		WXS	Illumina HiSeq	Phase_I	112	48	0.428571	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	
SLC22A15	55356	hgsc.bcm.edu	37	1	116609185	116609185	+	Silent	SNP	G	G	A	rs3748742	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:116609185G>A	ENST00000369503.4	+	11	1540	c.1410G>A	c.(1408-1410)acG>acA	p.T470T		NM_018420.2	NP_060890.2	Q8IZD6	S22AF_HUMAN	solute carrier family 22, member 15	470					ion transport (GO:0006811)	integral component of membrane (GO:0016021)	transmembrane transporter activity (GO:0022857)			endometrium(1)|large_intestine(2)|lung(12)|prostate(1)|urinary_tract(1)	17	Lung SC(450;0.184)	all_cancers(81;3.17e-06)|all_epithelial(167;2.32e-06)|all_lung(203;9.81e-06)|Lung NSC(69;5.94e-05)		Lung(183;0.0171)|Colorectal(144;0.0686)|LUSC - Lung squamous cell carcinoma(189;0.0903)|all cancers(265;0.108)|COAD - Colon adenocarcinoma(174;0.111)|Epithelial(280;0.12)		TCGGAGCCACGGGTCTGACCT	0.488													C|||	587	0.117212	0.1876	0.0648	5008	,	,		17717	0.1181		0.0835	False		,,,				2504	0.093				p.T470T		Atlas-SNP	.											.	SLC22A15	65	.	0			c.G1410A						PASS	.	C		529,3213		39,451,1381	58.0	52.0	54.0		1410	-11.4	0.0	1	dbSNP_107	54	628,7594		21,586,3504	no	coding-synonymous	SLC22A15	NM_018420.2		60,1037,4885	AA,AG,GG		7.638,14.1368,9.6707		470/548	116609185	1157,10807	1871	4111	5982	SO:0001819	synonymous_variant	55356	exon11			AGCCACGGGTCTG	AY145501	CCDS44198.1	1p12	2013-05-22	2008-01-11		ENSG00000163393	ENSG00000163393		"""Solute carriers"""	20301	protein-coding gene	gene with protein product		608275	"""solute carrier family 22 (organic cation transporter), member 15"""			12372408	Standard	NM_018420		Approved	FLIPT1	uc001egb.4	Q8IZD6	OTTHUMG00000012008	ENST00000369503.4:c.1410G>A	1.37:g.116609185G>A		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	116	60	0.517241	NM_018420	A8MUR3|Q6UXP5|Q8TAL9|Q9NSH5	Silent	SNP	ENST00000369503.4	37	CCDS44198.1																																																																																			G|0.891;A|0.109	0.109	strong		0.488	SLC22A15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033220.2	NM_018420	
DST	667	hgsc.bcm.edu	37	6	56327856	56327856	+	Silent	SNP	C	C	T	rs144012429	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:56327856C>T	ENST00000244364.6	-	82	15324	c.15117G>A	c.(15115-15117)gtG>gtA	p.V5039V	DST_ENST00000370769.4_Intron|DST_ENST00000361203.3_Intron|DST_ENST00000312431.6_3'UTR|DST_ENST00000446842.2_Intron|DST_ENST00000370754.5_Intron|DST_ENST00000370788.2_Intron|DST_ENST00000421834.2_Intron	NM_001144769.2|NM_001144770.1|NM_015548.4|NM_183380.3	NP_001138241.1|NP_001138242.1|NP_056363.2|NP_899236.1	Q03001	DYST_HUMAN	dystonin	7442					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)			CTGCAGATGGCACGGGAAAGT	0.433													C|||	57	0.0113818	0.0015	0.0159	5008	,	,		19060	0.0		0.0268	False		,,,				2504	0.0174				p.V5039V		Atlas-SNP	.											.	DST	1427	.	0			c.G15117A						PASS	.	C		36,3850		0,36,1907	142.0	133.0	136.0		15117	4.0	1.0	6	dbSNP_134	136	348,7958		7,334,3812	yes	coding-synonymous	DST	NM_015548.4		7,370,5719	TT,TC,CC		4.1897,0.9264,3.1496		5039/5172	56327856	384,11808	1943	4153	6096	SO:0001819	synonymous_variant	667	exon82			AGATGGCACGGGA	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	ENST00000244364.6:c.15117G>A	6.37:g.56327856C>T		Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	141	78	0.553191	NM_015548	B7Z3H1|O94833|Q12825|Q13266|Q13267|Q13775|Q5TBT0|Q5TBT2|Q5TF23|Q5TF24|Q8N1T8|Q8N8J3|Q8WXK8|Q8WXK9|Q96AK9|Q96DQ5|Q96J76|Q96QT5|Q9H555|Q9UGD7|Q9UGD8|Q9UN10	Silent	SNP	ENST00000244364.6	37	CCDS47443.1																																																																																			C|0.983;T|0.017	0.017	strong		0.433	DST-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000041022.4	NM_001723	
PLRG1	5356	hgsc.bcm.edu	37	4	155461113	155461113	+	Silent	SNP	T	T	C	rs7671792	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:155461113T>C	ENST00000499023.2	-	11	1158	c.1032A>G	c.(1030-1032)caA>caG	p.Q344Q	PLRG1_ENST00000302078.5_Silent_p.Q335Q|PLRG1_ENST00000393905.2_Silent_p.Q344Q	NM_001201564.1|NM_002669.3	NP_001188493.1|NP_002660.1	O43660	PLRG1_HUMAN	pleiotropic regulator 1	344					mRNA splicing, via spliceosome (GO:0000398)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|protein localization to nucleus (GO:0034504)|regulation of RNA biosynthetic process (GO:2001141)|signal transduction (GO:0007165)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)	signal transducer activity (GO:0004871)|transcription corepressor activity (GO:0003714)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(11)|skin(1)|urinary_tract(1)	22	all_hematologic(180;0.215)	Renal(120;0.0854)				CTGTAATAATTTGTGGTTCTG	0.338													T|||	1160	0.231629	0.1536	0.1888	5008	,	,		18870	0.1438		0.325	False		,,,				2504	0.362				p.Q344Q		Atlas-SNP	.											.	PLRG1	43	.	0			c.A1032G						PASS	.	T	,	788,3618	317.4+/-295.1	72,644,1487	201.0	178.0	186.0		1005,1032	-11.7	0.2	4	dbSNP_116	186	2829,5771	445.7+/-361.0	459,1911,1930	no	coding-synonymous,coding-synonymous	PLRG1	NM_001201564.1,NM_002669.3	,	531,2555,3417	CC,CT,TT		32.8953,17.8847,27.8102	,	335/506,344/515	155461113	3617,9389	2203	4300	6503	SO:0001819	synonymous_variant	5356	exon11			AATAATTTGTGGT	AF044333	CCDS34083.1, CCDS56341.1	4q31.2-q32.1	2013-01-10	2011-05-19		ENSG00000171566	ENSG00000171566		"""WD repeat domain containing"""	9089	protein-coding gene	gene with protein product	"""transport and golgi organization 4 homolog (Drosophila)"""	605961	"""pleiotropic regulator 1 (PRL1, Arabidopsis homolog)"", ""pleiotropic regulator 1 (PRL1 homolog, Arabidopsis)"""				Standard	NM_002669		Approved	PRL1, Prp46, PRPF46, Cwc1, TANGO4	uc003iny.3	O43660	OTTHUMG00000161411	ENST00000499023.2:c.1032A>G	4.37:g.155461113T>C		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	88	88	1	NM_002669	B3KMK4|Q3KQY5|Q8WUD8	Silent	SNP	ENST00000499023.2	37	CCDS34083.1																																																																																			T|0.738;C|0.262	0.262	strong		0.338	PLRG1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364824.1	NM_002669	
MICALL2	79778	hgsc.bcm.edu	37	7	1477844	1477844	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:1477844A>G	ENST00000297508.7	-	12	2375	c.2200T>C	c.(2200-2202)Tac>Cac	p.Y734H	MICALL2_ENST00000405088.4_Missense_Mutation_p.Y522H|MICALL2_ENST00000471899.1_5'UTR	NM_182924.3	NP_891554.1	Q8IY33	MILK2_HUMAN	MICAL-like 2	734	Forms an intramolecular interaction with the N-terminal CH and LIM zinc-binding domains-containing region keeping the protein in a closed conformation. {ECO:0000250}.				actin cytoskeleton reorganization (GO:0031532)|actin filament polymerization (GO:0030041)|endocytic recycling (GO:0032456)|neuron projection development (GO:0031175)|substrate adhesion-dependent cell spreading (GO:0034446)|tight junction assembly (GO:0070830)	cell-cell junction (GO:0005911)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)|stress fiber (GO:0001725)|tight junction (GO:0005923)	actin filament binding (GO:0051015)|filamin binding (GO:0031005)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|endometrium(1)|kidney(2)|lung(8)|ovary(2)|skin(2)	19		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0178)|OV - Ovarian serous cystadenocarcinoma(56;6.01e-15)		GGGGAGAGGTAGTCGGGGTGC	0.706																																					p.Y734H		Atlas-SNP	.											.	MICALL2	63	.	0			c.T2200C						PASS	.						11.0	13.0	12.0					7																	1477844		2179	4274	6453	SO:0001583	missense	79778	exon12			AGAGGTAGTCGGG	BC037988	CCDS5324.1	7p22.3	2006-11-24			ENSG00000164877	ENSG00000164877			29672	protein-coding gene	gene with protein product	"""junctional Rab13-binding protein"""					12110185, 16525024	Standard	NM_182924		Approved	MGC46023, FLJ23471, MICAL-L2, JRAB	uc003skj.4	Q8IY33	OTTHUMG00000119021	ENST00000297508.7:c.2200T>C	7.37:g.1477844A>G	ENSP00000297508:p.Tyr734His	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	129	103	0.79845	NM_182924	D3YTD2|Q7RTP4|Q7Z655|Q8TEQ4|Q9H5F9	Missense_Mutation	SNP	ENST00000297508.7	37	CCDS5324.1	.	.	.	.	.	.	.	.	.	.	A	11.05	1.525674	0.27299	.	.	ENSG00000164877	ENST00000405088;ENST00000297508	T;T	0.72942	2.19;-0.7	3.95	1.41	0.22369	.	0.269934	0.19725	N	0.107484	T	0.77731	0.4174	M	0.70595	2.14	0.09310	N	0.999999	P;D	0.76494	0.481;0.999	B;D	0.75020	0.373;0.985	T	0.65022	-0.6269	10	0.52906	T	0.07	.	4.6281	0.12488	0.6909:0.1929:0.1162:0.0	.	734;522	Q8IY33;D3YTD2	MILK2_HUMAN;.	H	522;734	ENSP00000385928:Y522H;ENSP00000297508:Y734H	ENSP00000297508:Y734H	Y	-	1	0	MICALL2	1444370	0.990000	0.36364	0.011000	0.14972	0.156000	0.22039	2.693000	0.47027	0.116000	0.18110	0.374000	0.22700	TAC	.	.	none		0.706	MICALL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239223.2	NM_182924	
ABCF2	10061	hgsc.bcm.edu	37	7	150915948	150915948	+	Silent	SNP	C	C	T	rs7782699	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:150915948C>T	ENST00000287844.2	-	9	1138	c.1029G>A	c.(1027-1029)gcG>gcA	p.A343A	ABCF2_ENST00000473874.1_5'UTR|ABCF2_ENST00000222388.2_Silent_p.A343A	NM_007189.1	NP_009120.1	Q9UG63	ABCF2_HUMAN	ATP-binding cassette, sub-family F (GCN20), member 2	343					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)		GACCAAACCTCGCAATGTAGT	0.483													C|||	269	0.0537141	0.0363	0.072	5008	,	,		17485	0.0		0.0984	False		,,,				2504	0.0736				p.A343A		Atlas-SNP	.											.	ABCF2	54	.	0			c.G1029A						PASS	.	C	,	257,4149	147.3+/-181.8	6,245,1952	94.0	90.0	92.0		1029,1029	-1.0	1.0	7	dbSNP_116	92	983,7617	213.6+/-253.5	54,875,3371	no	coding-synonymous,coding-synonymous	ABCF2	NM_005692.3,NM_007189.1	,	60,1120,5323	TT,TC,CC		11.4302,5.833,9.5341	,	343/635,343/624	150915948	1240,11766	2203	4300	6503	SO:0001819	synonymous_variant	10061	exon9			AAACCTCGCAATG	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.1029G>A	7.37:g.150915948C>T		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	71	37	0.521127	NM_007189	O60864|Q75MJ0|Q75MJ1|Q96TE8	Silent	SNP	ENST00000287844.2	37	CCDS5923.1																																																																																			C|0.909;T|0.091	0.091	strong		0.483	ABCF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336086.1	NM_005692	
SDK2	54549	hgsc.bcm.edu	37	17	71426670	71426670	+	Silent	SNP	G	G	A	rs1105354	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:71426670G>A	ENST00000392650.3	-	12	1563	c.1563C>T	c.(1561-1563)caC>caT	p.H521H	SDK2_ENST00000388726.3_Silent_p.H521H	NM_001144952.1	NP_001138424.1	Q58EX2	SDK2_HUMAN	sidekick cell adhesion molecule 2	521	Ig-like C2-type 6.				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						CTCGGGGGTCGTGGGTCACTC	0.612													G|||	664	0.132588	0.0431	0.1974	5008	,	,		15367	0.0655		0.2903	False		,,,				2504	0.1145				p.H521H		Atlas-SNP	.											.	SDK2	219	.	0			c.C1563T						PASS	.	G		369,4037	185.0+/-212.2	15,339,1849	51.0	39.0	43.0		1563	-5.9	0.9	17	dbSNP_86	43	2311,6289	373.2+/-336.9	316,1679,2305	no	coding-synonymous	SDK2	NM_001144952.1		331,2018,4154	AA,AG,GG		26.8721,8.3749,20.6059		521/2173	71426670	2680,10326	2203	4300	6503	SO:0001819	synonymous_variant	54549	exon12			GGGGTCGTGGGTC	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.1563C>T	17.37:g.71426670G>A		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	25	16	0.64	NM_001144952	A6NMR8|C9JA57|Q86VY3|Q9NTD2|Q9NVB3|Q9P214	Silent	SNP	ENST00000392650.3	37	CCDS45769.1	370	0.16941391941391942	27	0.054878048780487805	74	0.20441988950276244	42	0.07342657342657342	227	0.2994722955145119	G	1.692	-0.503757	0.04261	0.083749	0.268721	ENSG00000069188	ENST00000416616	.	.	.	4.08	-5.92	0.02261	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	0.9999999999999142	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.5169	0.61545	0.6916:0.0:0.3084:0.0	rs1105354;rs17782278;rs1105354	.	.	.	X	426	.	.	R	-	1	2	SDK2	68938265	0.099000	0.21834	0.945000	0.38365	0.171000	0.22731	-0.479000	0.06567	-1.056000	0.03205	-0.369000	0.07265	CGA	G|0.818;A|0.182	0.182	strong		0.612	SDK2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327598.2	NM_019064	
PFKFB2	5208	hgsc.bcm.edu	37	1	207238419	207238419	+	Silent	SNP	C	C	T	rs72741390	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:207238419C>T	ENST00000367080.3	+	8	670	c.546C>T	c.(544-546)aaC>aaT	p.N182N	PFKFB2_ENST00000545806.1_Silent_p.N149N|PFKFB2_ENST00000411990.2_Silent_p.N84N|PFKFB2_ENST00000367079.2_Silent_p.N182N|PFKFB2_ENST00000541914.1_5'UTR	NM_006212.2	NP_006203.2	O60825	F262_HUMAN	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 2	182	6-phosphofructo-2-kinase.				carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|fructose 2,6-bisphosphate metabolic process (GO:0006003)|fructose metabolic process (GO:0006000)|glucose catabolic process (GO:0006007)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|lactate metabolic process (GO:0006089)|positive regulation of glucokinase activity (GO:0033133)|positive regulation of insulin secretion (GO:0032024)|response to glucose (GO:0009749)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	6-phosphofructo-2-kinase activity (GO:0003873)|ATP binding (GO:0005524)|fructose-2,6-bisphosphate 2-phosphatase activity (GO:0004331)|protein kinase binding (GO:0019901)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(3)|liver(1)|lung(7)|ovary(1)|skin(1)|urinary_tract(1)	20	Prostate(682;0.19)					CTGAAAGGAACAGAGAGAACG	0.458													C|||	555	0.110823	0.0257	0.1542	5008	,	,		16547	0.0079		0.2753	False		,,,				2504	0.1319				p.N182N		Atlas-SNP	.											.	PFKFB2	70	.	0			c.C546T						PASS	.	C	,	257,4149	149.9+/-184.0	7,243,1953	118.0	105.0	109.0		546,546	4.0	1.0	1	dbSNP_130	109	2240,6360	380.1+/-339.5	312,1616,2372	no	coding-synonymous,coding-synonymous	PFKFB2	NM_001018053.1,NM_006212.2	,	319,1859,4325	TT,TC,CC		26.0465,5.833,19.1988	,	182/472,182/506	207238419	2497,10509	2203	4300	6503	SO:0001819	synonymous_variant	5208	exon8			AAGGAACAGAGAG		CCDS31003.1, CCDS31004.1	1q31-q32.2	2012-07-13			ENSG00000123836	ENSG00000123836	2.7.1.105, 3.1.3.46		8873	protein-coding gene	gene with protein product		171835					Standard	XM_005273162		Approved		uc001hfg.3	O60825	OTTHUMG00000036033	ENST00000367080.3:c.546C>T	1.37:g.207238419C>T		Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	115	43	0.373913	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		
TOX	9760	hgsc.bcm.edu	37	8	59739438	59739438	+	Silent	SNP	A	A	C	rs56215946	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:59739438A>C	ENST00000361421.1	-	6	1168	c.948T>G	c.(946-948)gcT>gcG	p.A316A		NM_014729.2	NP_055544.1	O94900	TOX_HUMAN	thymocyte selection-associated high mobility group box	316						nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(13)|prostate(1)|skin(2)|stomach(1)	33		all_cancers(86;0.165)|Myeloproliferative disorder(644;0.00452)|all_lung(136;0.036)|Lung NSC(129;0.0464)|all_epithelial(80;0.0607)				CCTTCTTCGCAGCCTCGGTTT	0.408													A|||	131	0.0261581	0.0023	0.0605	5008	,	,		14781	0.001		0.0686	False		,,,				2504	0.0164				p.A316A	Pancreas(161;610 1969 17913 21374 22725)	Atlas-SNP	.											.	TOX	83	.	0			c.T948G						PASS	.	A		50,4356	54.2+/-90.2	0,50,2153	151.0	119.0	130.0		948	4.6	1.0	8	dbSNP_129	130	655,7945	166.4+/-218.3	30,595,3675	no	coding-synonymous	TOX	NM_014729.2		30,645,5828	CC,CA,AA		7.6163,1.1348,5.4206		316/527	59739438	705,12301	2203	4300	6503	SO:0001819	synonymous_variant	9760	exon6			CTTCGCAGCCTCG		CCDS34897.1	8q12.2-q12.3	2009-04-17			ENSG00000198846	ENSG00000198846			18988	protein-coding gene	gene with protein product		606863				9872452, 11850626	Standard	NM_014729		Approved	KIAA0808, TOX1	uc003xtw.1	O94900	OTTHUMG00000164331	ENST00000361421.1:c.948T>G	8.37:g.59739438A>C		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	91	70	0.769231	NM_014729	Q96AV5	Silent	SNP	ENST00000361421.1	37	CCDS34897.1																																																																																			A|0.950;C|0.050	0.050	strong		0.408	TOX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378307.1	NM_014729	
FAM71A	149647	hgsc.bcm.edu	37	1	212798977	212798977	+	Missense_Mutation	SNP	A	A	G	rs3122712	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:212798977A>G	ENST00000294829.3	+	1	1189	c.758A>G	c.(757-759)aAt>aGt	p.N253S	RP11-338C15.5_ENST00000427949.1_RNA	NM_153606.3	NP_705834.2	Q8IYT1	FA71A_HUMAN	family with sequence similarity 71, member A	253			N -> S (in dbSNP:rs3122712).			nucleus (GO:0005634)				breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(7)|liver(1)|lung(12)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	36				OV - Ovarian serous cystadenocarcinoma(81;0.00631)|all cancers(67;0.00981)|GBM - Glioblastoma multiforme(131;0.0715)|Epithelial(68;0.094)		AAACCCACTAATGTGCTCAAT	0.542													A|||	1267	0.252995	0.4554	0.196	5008	,	,		21770	0.0804		0.2634	False		,,,				2504	0.1871				p.N253S		Atlas-SNP	.											.	FAM71A	87	.	0			c.A758G						PASS	.	A	SER/ASN	1918,2488	547.8+/-377.4	413,1092,698	104.0	112.0	109.0		758	-0.8	0.0	1	dbSNP_103	109	2509,6091	411.1+/-350.4	382,1745,2173	yes	missense	FAM71A	NM_153606.3	46	795,2837,2871	GG,GA,AA		29.1744,43.5315,34.0381	benign	253/595	212798977	4427,8579	2203	4300	6503	SO:0001583	missense	149647	exon1			CCACTAATGTGCT		CCDS1507.1	1q32.3	2008-02-05			ENSG00000162771	ENSG00000162771			26541	protein-coding gene	gene with protein product						12477932	Standard	NM_153606		Approved	FLJ32796	uc010pth.1	Q8IYT1	OTTHUMG00000041084	ENST00000294829.3:c.758A>G	1.37:g.212798977A>G	ENSP00000294829:p.Asn253Ser	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	75	41	0.546667	NM_153606	Q5VTZ1	Missense_Mutation	SNP	ENST00000294829.3	37	CCDS1507.1	569	0.26053113553113555	227	0.4613821138211382	87	0.24033149171270718	55	0.09615384615384616	200	0.2638522427440633	A	4.402	0.074306	0.08485	0.435315	0.291744	ENSG00000162771	ENST00000294829;ENST00000545975	T	0.03272	3.99	3.69	-0.822	0.10819	.	.	.	.	.	T	0.00012	0.0000	N	0.11427	0.14	0.80722	P	0.0	B	0.06786	0.001	B	0.01281	0.0	T	0.38134	-0.9675	8	0.08837	T	0.75	1.1457	1.7677	0.03005	0.2223:0.3327:0.3224:0.1226	rs3122712;rs52808176;rs56594967;rs59779974;rs3122712	253	Q8IYT1	FA71A_HUMAN	S	253;28	ENSP00000294829:N253S	ENSP00000294829:N253S	N	+	2	0	FAM71A	210865600	0.002000	0.14202	0.000000	0.03702	0.000000	0.00434	-0.003000	0.12901	-0.271000	0.09272	-0.290000	0.09829	AAT	A|0.697;G|0.303	0.303	strong		0.542	FAM71A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098529.1	NM_153606	
DISC1	27185	hgsc.bcm.edu	37	1	232144598	232144598	+	Missense_Mutation	SNP	A	A	T	rs821616	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:232144598A>T	ENST00000439617.2	+	11	2163	c.2110A>T	c.(2110-2112)Agc>Tgc	p.S704C	DISC1_ENST00000366637.3_Missense_Mutation_p.S36C|DISC1_ENST00000535983.1_Missense_Mutation_p.R683S|DISC1_ENST00000537876.1_3'UTR|DISC1_ENST00000427560.1_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	108	0	0		WXS	Illumina HiSeq	Phase_I	79	45	0.56962	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	
CABIN1	23523	hgsc.bcm.edu	37	22	24487739	24487739	+	Missense_Mutation	SNP	G	G	A	rs117908385	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:24487739G>A	ENST00000398319.2	+	24	4113	c.3728G>A	c.(3727-3729)cGc>cAc	p.R1243H	CABIN1_ENST00000263119.5_Missense_Mutation_p.R1243H|CABIN1_ENST00000405822.2_Missense_Mutation_p.R1193H	NM_001199281.1	NP_001186210.1	Q9Y6J0	CABIN_HUMAN	calcineurin binding protein 1	1243					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						GAGGCTGCCCGCTACCCCAAG	0.642													G|||	40	0.00798722	0.0015	0.0072	5008	,	,		17045	0.0		0.0328	False		,,,				2504	0.0				p.R1243H		Atlas-SNP	.											.	CABIN1	153	.	0			c.G3728A						PASS	.	G	HIS/ARG,HIS/ARG,HIS/ARG	13,4393	20.2+/-43.8	0,13,2190	69.0	61.0	64.0		3728,3578,3728	5.0	1.0	22	dbSNP_132	64	156,8444	72.9+/-135.5	1,154,4145	yes	missense,missense,missense	CABIN1	NM_001199281.1,NM_001201429.1,NM_012295.3	29,29,29	1,167,6335	AA,AG,GG		1.814,0.2951,1.2994	probably-damaging,probably-damaging,probably-damaging	1243/2221,1193/2171,1243/2221	24487739	169,12837	2203	4300	6503	SO:0001583	missense	23523	exon24			CTGCCCGCTACCC	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.3728G>A	22.37:g.24487739G>A	ENSP00000381364:p.Arg1243His	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	120	60	0.5	NM_001199281	G5E9F3|Q6PHY0|Q9Y460	Missense_Mutation	SNP	ENST00000398319.2	37	CCDS13823.1	32	0.014652014652014652	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	30	0.0395778364116095	G	35	5.482768	0.96307	0.002951	0.01814	ENSG00000099991	ENST00000263119;ENST00000405822;ENST00000398319	T;T;T	0.30182	1.54;1.54;1.54	5.04	5.04	0.67666	Tetratricopeptide-like helical (1);	0.000000	0.85682	D	0.000000	T	0.20170	0.0485	L	0.56769	1.78	0.80722	D	1	D;D	0.89917	1.0;0.999	D;P	0.65773	0.938;0.869	T	0.16571	-1.0398	10	0.52906	T	0.07	.	17.8214	0.88651	0.0:0.0:1.0:0.0	.	1193;1243	G5E9F3;Q9Y6J0	.;CABIN_HUMAN	H	1243;1193;1243	ENSP00000263119:R1243H;ENSP00000384694:R1193H;ENSP00000381364:R1243H	ENSP00000263119:R1243H	R	+	2	0	CABIN1	22817739	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.918000	0.87506	2.531000	0.85337	0.585000	0.79938	CGC	G|0.987;A|0.013	0.013	strong		0.642	CABIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320161.2	NM_012295	
HAVCR1	26762	hgsc.bcm.edu	37	5	156479426	156479426	+	Missense_Mutation	SNP	T	T	C	rs386693988|rs12522248	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:156479426T>C	ENST00000339252.3	-	3	1151	c.619A>G	c.(619-621)Act>Gct	p.T207A	HAVCR1_ENST00000425854.1_Missense_Mutation_p.T207A|HAVCR1_ENST00000523175.1_Missense_Mutation_p.T207A|HAVCR1_ENST00000544197.1_Missense_Mutation_p.T207A|HAVCR1_ENST00000522693.1_Missense_Mutation_p.T207A	NM_012206.2	NP_036338.2	Q96D42	HAVR1_HUMAN	hepatitis A virus cellular receptor 1	0					viral process (GO:0016032)	integral component of membrane (GO:0016021)	virus receptor activity (GO:0001618)			endometrium(3)|large_intestine(2)|lung(17)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	28	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.0999)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			GTAGAGACAGTTGTTGTCACT	0.473													T|||	1133	0.226238	0.1362	0.3386	5008	,	,		25057	0.1478		0.3042	False		,,,				2504	0.2689				p.T207A		Atlas-SNP	.											.	HAVCR1	84	.	0			c.A619G						PASS	.	T	ALA/THR,ALA/THR,ALA/THR	698,3416		51,596,1410	313.0	303.0	306.0		619,619,619	1.0	0.0	5	dbSNP_120	306	2393,6013		348,1697,2158	yes	missense,missense,missense	HAVCR1	NM_012206.2,NM_001173393.1,NM_001099414.1	58,58,58	399,2293,3568	CC,CT,TT		28.4678,16.9665,24.6885	benign,benign,benign	207/365,207/365,207/365	156479426	3091,9429	2057	4203	6260	SO:0001583	missense	26762	exon4			AGACAGTTGTTGT	AF043724	CCDS43392.1	5q33.2	2014-01-14			ENSG00000113249	ENSG00000113249		"""Immunoglobulin superfamily / V-set domain containing"""	17866	protein-coding gene	gene with protein product	"""T-cell immunoglobulin mucin family member 1"""	606518				9658108, 11725301	Standard	NM_012206		Approved	HAVCR-1, TIM-1, TIM1, HAVCR, TIMD1	uc021ygj.1	Q96D42	OTTHUMG00000163466	ENST00000339252.3:c.619A>G	5.37:g.156479426T>C	ENSP00000344844:p.Thr207Ala	Somatic	285	0	0		WXS	Illumina HiSeq	Phase_I	222	103	0.463964	NM_001099414	O43656	Missense_Mutation	SNP	ENST00000339252.3	37	CCDS43392.1	503	0.2303113553113553	63	0.12804878048780488	127	0.35082872928176795	83	0.1451048951048951	230	0.3034300791556728	T	1.618	-0.522318	0.04141	0.169665	0.284678	ENSG00000113249	ENST00000522693;ENST00000523175;ENST00000339252;ENST00000425854;ENST00000544197;ENST00000518745	T;T;T;T;T;T	0.14640	2.49;2.56;2.56;2.49;2.56;2.53	3.51	1.05	0.20165	.	1622.760000	0.00166	N	0.000001	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B;B	0.15930	0.015;0.015;0.015	B;B;B	0.08055	0.002;0.003;0.003	T	0.44544	-0.9321	9	0.07990	T	0.79	-1.1978	0.6206	0.00777	0.211:0.123:0.2184:0.4476	rs12522248;rs61365319;rs12522248	207;202;202	E9PFX0;F1CME6;Q96D42	.;.;HAVR1_HUMAN	A	207	ENSP00000428524:T207A;ENSP00000427898:T207A;ENSP00000344844:T207A;ENSP00000403333:T207A;ENSP00000440258:T207A;ENSP00000428422:T207A	ENSP00000344844:T207A	T	-	1	0	HAVCR1	156412004	0.000000	0.05858	0.003000	0.11579	0.004000	0.04260	-0.117000	0.10708	0.509000	0.28195	0.443000	0.29094	ACT	T|0.756;C|0.244	0.244	strong		0.473	HAVCR1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373698.1		
CD8A	925	hgsc.bcm.edu	37	2	87017575	87017575	+	Silent	SNP	C	C	T	rs2229240	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:87017575C>T	ENST00000409511.2	-	5	1309	c.279G>A	c.(277-279)agG>agA	p.R93R	CD8A_ENST00000538832.1_Silent_p.R134R|CD8A_ENST00000409781.1_Silent_p.R93R|CD8A_ENST00000283635.3_Silent_p.R93R|CD8A_ENST00000456996.2_Silent_p.R93R|CD8A_ENST00000352580.3_Silent_p.R93R	NM_001145873.1	NP_001139345.1	P01732	CD8A_HUMAN	CD8a molecule	93	Ig-like V-type.				antigen processing and presentation (GO:0019882)|cytotoxic T cell differentiation (GO:0045065)|defense response to virus (GO:0051607)|immune response (GO:0006955)|positive regulation of calcium-mediated signaling (GO:0050850)|regulation of immune response (GO:0050776)|T cell activation (GO:0042110)|T cell mediated immunity (GO:0002456)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|T cell receptor complex (GO:0042101)	coreceptor activity (GO:0015026)|MHC class I protein binding (GO:0042288)			lung(4)|ovary(1)|prostate(2)|urinary_tract(1)	8						TGTCCCCCAACCTCTTGCCCG	0.637													C|||	183	0.0365415	0.0696	0.0288	5008	,	,		12826	0.0		0.0626	False		,,,				2504	0.0082				p.R93R		Atlas-SNP	.											.	CD8A	28	.	0			c.G279A						PASS	.	C	,,	349,4057	179.7+/-208.2	15,319,1869	64.0	73.0	70.0		279,279,279	2.9	0.0	2	dbSNP_98	70	656,7944	166.2+/-218.2	26,604,3670	no	coding-synonymous,coding-synonymous,coding-synonymous	CD8A	NM_001145873.1,NM_001768.6,NM_171827.3	,,	41,923,5539	TT,TC,CC		7.6279,7.921,7.7272	,,	93/236,93/236,93/199	87017575	1005,12001	2203	4300	6503	SO:0001819	synonymous_variant	925	exon5			CCCCAACCTCTTG		CCDS1992.1, CCDS1993.1	2p12	2014-09-17	2006-03-28		ENSG00000153563	ENSG00000153563		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"""	1706	protein-coding gene	gene with protein product		186910	"""CD8 antigen, alpha polypeptide (p32)"", ""T-cell surface glycoprotein CD8 alpha chain"""	CD8		1541829	Standard	NM_171827		Approved		uc002sru.3	P01732	OTTHUMG00000130265	ENST00000409511.2:c.279G>A	2.37:g.87017575C>T		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	103	63	0.61165	NM_001145873	B4DT80|D6W5M8|Q13970|Q4ZG17	Silent	SNP	ENST00000409511.2	37	CCDS1992.1																																																																																			C|0.931;T|0.069	0.069	strong		0.637	CD8A-006	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000330784.3	NM_001768	
TANC1	85461	hgsc.bcm.edu	37	2	160086692	160086692	+	Silent	SNP	A	A	G	rs3821296	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:160086692A>G	ENST00000263635.6	+	27	4992	c.4755A>G	c.(4753-4755)acA>acG	p.T1585T	TANC1_ENST00000454300.1_Silent_p.T1479T	NM_001145909.1|NM_033394.2	NP_001139381.1|NP_203752.2	Q9C0D5	TANC1_HUMAN	tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 1	1585					dendritic spine maintenance (GO:0097062)|myoblast fusion (GO:0007520)|visual learning (GO:0008542)	axon terminus (GO:0043679)|cell junction (GO:0030054)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)|postsynaptic membrane (GO:0045211)				breast(3)|central_nervous_system(4)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(9)|lung(25)|ovary(7)|pancreas(1)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(2)	77						TAGAGGGAACAGGTACTTTCA	0.567													A|||	2398	0.478834	0.3495	0.6023	5008	,	,		19188	0.6161		0.3718	False		,,,				2504	0.5348				p.T1585T		Atlas-SNP	.											.	TANC1	157	.	0			c.A4755G						PASS	.	A	,	1375,2531		256,863,834	57.0	63.0	61.0		,4755	-8.6	0.0	2	dbSNP_107	61	2869,5395		511,1847,1774	no	utr-3,coding-synonymous	TANC1	NM_001145909.1,NM_033394.2	,	767,2710,2608	GG,GA,AA		34.7168,35.2023,34.8726	,	,1585/1862	160086692	4244,7926	1953	4132	6085	SO:0001819	synonymous_variant	85461	exon27			GGGAACAGGTACT	AB051515	CCDS42766.1	2q24.2	2013-01-11			ENSG00000115183	ENSG00000115183		"""Ankyrin repeat domain containing"", ""Tetratricopeptide (TTC) repeat domain containing"""	29364	protein-coding gene	gene with protein product	"""rolling pebbles homolog B (Drosophila)"""	611397				15673434	Standard	NM_033394		Approved	KIAA1728, ROLSB	uc002uag.3	Q9C0D5	OTTHUMG00000153945	ENST00000263635.6:c.4755A>G	2.37:g.160086692A>G		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	109	48	0.440367	NM_033394	C9JD88|Q49AI8	Silent	SNP	ENST00000263635.6	37	CCDS42766.1																																																																																			A|0.569;G|0.431	0.431	strong		0.567	TANC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333135.1		
ASB1	51665	hgsc.bcm.edu	37	2	239344412	239344412	+	Silent	SNP	C	C	T	rs3191996	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:239344412C>T	ENST00000264607.4	+	3	499	c.252C>T	c.(250-252)atC>atT	p.I84I	ASB1_ENST00000409297.1_Intron|ASB1_ENST00000469885.1_3'UTR	NM_001040445.1	NP_001035535.1	Q9Y576	ASB1_HUMAN	ankyrin repeat and SOCS box containing 1	84					intracellular signal transduction (GO:0035556)|male genitalia development (GO:0030539)|negative regulation of cytokine biosynthetic process (GO:0042036)|protein ubiquitination (GO:0016567)	intracellular (GO:0005622)				breast(1)|kidney(1)|large_intestine(3)|lung(2)|skin(1)	8		all_epithelial(40;2.65e-14)|Breast(86;7.61e-05)|Renal(207;0.00183)|all_lung(227;0.0283)|Ovarian(221;0.0365)|Lung NSC(271;0.0941)|all_hematologic(139;0.158)|Melanoma(123;0.203)|Hepatocellular(293;0.244)		Epithelial(121;2.04e-26)|OV - Ovarian serous cystadenocarcinoma(60;4.5e-12)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;6.5e-08)|BRCA - Breast invasive adenocarcinoma(100;2.88e-05)|Lung(119;0.000383)|LUSC - Lung squamous cell carcinoma(224;0.00644)		CGTTGCGAATCGCGGCCACTG	0.627													C|||	257	0.0513179	0.003	0.0389	5008	,	,		16702	0.0595		0.1203	False		,,,				2504	0.046				p.I84I		Atlas-SNP	.											ASB1,NS,carcinoma,0,1	ASB1	25	1	0			c.C252T						PASS	.	C		97,4309	76.8+/-115.0	2,93,2108	41.0	38.0	39.0		252	-0.7	0.8	2	dbSNP_105	39	941,7659	205.2+/-247.7	56,829,3415	no	coding-synonymous	ASB1	NM_001040445.1		58,922,5523	TT,TC,CC		10.9419,2.2015,7.9809		84/336	239344412	1038,11968	2203	4300	6503	SO:0001819	synonymous_variant	51665	exon3			GCGAATCGCGGCC	AF156777	CCDS33416.1	2q37	2013-01-10	2011-01-25		ENSG00000065802	ENSG00000065802		"""Ankyrin repeat domain containing"""	16011	protein-coding gene	gene with protein product		605758	"""ankyrin repeat and SOCS box-containing 1"""				Standard	XR_241235		Approved	ASB-1	uc002vyg.3	Q9Y576	OTTHUMG00000152866	ENST00000264607.4:c.252C>T	2.37:g.239344412C>T		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	80	39	0.4875	NM_001040445	A6NL50|Q4ZG29|Q9ULS4	Silent	SNP	ENST00000264607.4	37	CCDS33416.1																																																																																			C|0.925;T|0.075	0.075	strong		0.627	ASB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328294.1	NM_001040445	
CLDN18	51208	hgsc.bcm.edu	37	3	137749839	137749839	+	Silent	SNP	A	A	G	rs16847742	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:137749839A>G	ENST00000183605.5	+	5	868	c.642A>G	c.(640-642)tcA>tcG	p.S214S	CLDN18_ENST00000343735.4_Silent_p.S214S	NM_016369.3	NP_057453.1	P56856	CLD18_HUMAN	claudin 18	214					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)			endometrium(1)|large_intestine(2)|lung(1)|ovary(1)|upper_aerodigestive_tract(1)	6						ATCATGCCTCAGGCCACAGTG	0.453													G|||	540	0.107827	0.1483	0.1138	5008	,	,		20728	0.0288		0.1312	False		,,,				2504	0.1063				p.S214S		Atlas-SNP	.											.	CLDN18	33	.	0			c.A642G						PASS	.	G	,	647,3759	765.3+/-413.3	51,545,1607	144.0	142.0	142.0		642,642	-11.4	0.0	3	dbSNP_123	142	1083,7517	769.4+/-407.6	85,913,3302	no	coding-synonymous,coding-synonymous	CLDN18	NM_001002026.2,NM_016369.3	,	136,1458,4909	GG,GA,AA		12.593,14.6845,13.3016	,	214/262,214/262	137749839	1730,11276	2203	4300	6503	SO:0001819	synonymous_variant	51208	exon5			TGCCTCAGGCCAC	AF221069, AY102073	CCDS3095.1, CCDS33862.1	3q	2008-08-27			ENSG00000066405	ENSG00000066405		"""Claudins"""	2039	protein-coding gene	gene with protein product		609210	"""surfactant associated protein J"""	SFTPJ			Standard	NM_001002026		Approved		uc003ero.1	P56856	OTTHUMG00000159762	ENST00000183605.5:c.642A>G	3.37:g.137749839A>G		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	97	46	0.474227	NM_016369	A5PL21|Q96PH4	Silent	SNP	ENST00000183605.5	37	CCDS3095.1																																																																																			A|0.879;G|0.121	0.121	strong		0.453	CLDN18-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000357199.2	NM_001002026	
CCDC185	164127	hgsc.bcm.edu	37	1	223567401	223567401	+	Missense_Mutation	SNP	T	T	C	rs6689850	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:223567401T>C	ENST00000366875.3	+	1	687	c.584T>C	c.(583-585)gTg>gCg	p.V195A		NM_152610.2	NP_689823.2	Q8N715	CC185_HUMAN		195			V -> A (in dbSNP:rs6689850).							breast(4)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(12)|skin(3)	29				GBM - Glioblastoma multiforme(131;0.0704)		CGGTCTTCTGTGCCCTCGCAA	0.612													T|||	403	0.0804712	0.0825	0.0634	5008	,	,		17152	0.13		0.0408	False		,,,				2504	0.0798				p.V195A		Atlas-SNP	.											.	C1orf65	71	.	0			c.T584C						PASS	.	T	ALA/VAL	359,4047	182.6+/-210.3	19,321,1863	74.0	77.0	76.0		584	-1.3	0.0	1	dbSNP_116	76	331,8269	115.3+/-175.2	6,319,3975	yes	missense	C1orf65	NM_152610.2	64	25,640,5838	CC,CT,TT		3.8488,8.148,5.3052	benign	195/624	223567401	690,12316	2203	4300	6503	SO:0001583	missense	164127	exon1			CTTCTGTGCCCTC																												ENST00000366875.3:c.584T>C	1.37:g.223567401T>C	ENSP00000355840:p.Val195Ala	Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	181	80	0.441989	NM_152610	Q8N746|Q8NA93	Missense_Mutation	SNP	ENST00000366875.3	37	CCDS1537.1	137	0.06272893772893773	26	0.052845528455284556	17	0.04696132596685083	66	0.11538461538461539	28	0.036939313984168866	T	10.92	1.488263	0.26686	0.08148	0.038488	ENSG00000178395	ENST00000366875	T	0.22743	1.94	4.18	-1.26	0.09376	.	.	.	.	.	T	0.00210	0.0006	L	0.56769	1.78	0.80722	P	0.0	B	0.17038	0.02	B	0.15484	0.013	T	0.32079	-0.9920	8	0.28530	T	0.3	.	0.8457	0.01161	0.1603:0.2139:0.3282:0.2976	rs6689850;rs6689850	195	Q8N715	CA065_HUMAN	A	195	ENSP00000355840:V195A	ENSP00000355840:V195A	V	+	2	0	C1orf65	221634024	0.000000	0.05858	0.000000	0.03702	0.154000	0.21943	-0.987000	0.03743	-0.456000	0.07043	0.528000	0.53228	GTG	T|0.940;C|0.060	0.060	strong		0.612	C1orf65-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092718.1		
RCCD1	91433	hgsc.bcm.edu	37	15	91500554	91500554	+	Silent	SNP	C	C	T	rs146488462	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:91500554C>T	ENST00000394258.2	+	3	580	c.378C>T	c.(376-378)gcC>gcT	p.A126A	RCCD1_ENST00000556618.1_Silent_p.A126A|RCCD1_ENST00000555155.1_Silent_p.A126A|RCCD1_ENST00000556774.1_Intron|AC068831.6_ENST00000553321.1_RNA	NM_001017919.1|NM_033544.2	NP_001017919.1|NP_291022.2	A6NED2	RCCD1_HUMAN	RCC1 domain containing 1	126						cytoplasm (GO:0005737)|plasma membrane (GO:0005886)				breast(1)|kidney(1)|large_intestine(2)	4	Lung NSC(78;0.0987)|all_lung(78;0.175)		Lung(145;0.189)			ACGATCCGGCCGGTGAGGCCC	0.721													C|||	21	0.00419329	0.0	0.0086	5008	,	,		10131	0.0		0.0149	False		,,,				2504	0.0				p.A126A		Atlas-SNP	.											.	RCCD1	9	.	0			c.C378T						PASS	.	C	,	11,3977		0,11,1983	10.0	9.0	10.0		378,378	0.5	0.0	15	dbSNP_134	10	130,7772		1,128,3822	no	coding-synonymous,coding-synonymous	RCCD1	NM_001017919.1,NM_033544.2	,	1,139,5805	TT,TC,CC		1.6452,0.2758,1.1859	,	126/377,126/377	91500554	141,11749	1994	3951	5945	SO:0001819	synonymous_variant	91433	exon3			TCCGGCCGGTGAG		CCDS32333.1	15q26.1	2005-10-21	2005-10-21			ENSG00000166965			30457	protein-coding gene	gene with protein product						12477932	Standard	XM_006720763		Approved	MGC14386	uc002bqk.3	A6NED2		ENST00000394258.2:c.378C>T	15.37:g.91500554C>T		Somatic	8	0	0		WXS	Illumina HiSeq	Phase_I	36	19	0.527778	NM_001017919	B2RTP9|Q29RX6	Silent	SNP	ENST00000394258.2	37	CCDS32333.1																																																																																			C|0.994;T|0.006	0.006	strong		0.721	RCCD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000414748.1	NM_033544	
PCDHB11	56125	hgsc.bcm.edu	37	5	140580941	140580941	+	Missense_Mutation	SNP	G	G	A	rs138686663	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	221	0	0		WXS	Illumina HiSeq	Phase_I	229	43	0.187773	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	
BOC	91653	hgsc.bcm.edu	37	3	112997554	112997554	+	Silent	SNP	A	A	G	rs775228	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:112997554A>G	ENST00000495514.1	+	11	2441	c.1737A>G	c.(1735-1737)aaA>aaG	p.K579K	BOC_ENST00000497495.1_3'UTR|BOC_ENST00000355385.3_Silent_p.K579K|BOC_ENST00000273395.4_Silent_p.K580K			Q9BWV1	BOC_HUMAN	BOC cell adhesion associated, oncogene regulated	579					axon guidance (GO:0007411)|cell adhesion (GO:0007155)|muscle cell differentiation (GO:0042692)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of myoblast differentiation (GO:0045663)|smoothened signaling pathway (GO:0007224)	axonal growth cone (GO:0044295)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)				NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(17)|lung(18)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	68			Epithelial(53;0.227)			TGGCCAGCAAAGAGCAGCAGA	0.632													G|||	3107	0.620407	0.7663	0.5418	5008	,	,		15121	0.7183		0.4781	False		,,,				2504	0.5245				p.K579K		Atlas-SNP	.											.	BOC	139	.	0			c.A1737G						PASS	.	G		3220,1152		1217,786,183	40.0	42.0	41.0		1737	4.0	1.0	3	dbSNP_86	41	3844,4684		919,2006,1339	no	coding-synonymous	BOC	NM_033254.2		2136,2792,1522	GG,GA,AA		45.075,26.3495,45.2403		579/1115	112997554	7064,5836	2186	4264	6450	SO:0001819	synonymous_variant	91653	exon11			CAGCAAAGAGCAG	AY027658	CCDS2971.1	3q13.2	2013-02-11	2012-12-07		ENSG00000144857	ENSG00000144857		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	17173	protein-coding gene	gene with protein product	"""brother of CDO"", ""brother of CDON"", ""cell adhesion associated, oncogene regulated 2"""	608708	"""Boc homolog (mouse)"""			11782431	Standard	NM_033254		Approved	CDON2	uc003dzy.3	Q9BWV1	OTTHUMG00000159305	ENST00000495514.1:c.1737A>G	3.37:g.112997554A>G		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	87	87	1	NM_033254	A6NJ30|B2RMS8|D3DN70|Q6UXJ5|Q8N2P7|Q8NF26	Silent	SNP	ENST00000495514.1	37	CCDS2971.1																																																																																			A|0.404;G|0.596	0.596	strong		0.632	BOC-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000354485.3	NM_033254	
EXOC4	60412	hgsc.bcm.edu	37	7	133749164	133749164	+	Silent	SNP	G	G	A	rs6953296	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:133749164G>A	ENST00000253861.4	+	18	2837	c.2808G>A	c.(2806-2808)caG>caA	p.Q936Q	EXOC4_ENST00000545148.1_Silent_p.Q546Q|EXOC4_ENST00000539845.1_Silent_p.Q835Q|EXOC4_ENST00000541309.1_Silent_p.Q224Q	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	66	0	0		WXS	Illumina HiSeq	Phase_I	52	27	0.519231	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	
ZNF317	57693	hgsc.bcm.edu	37	19	9267319	9267319	+	Missense_Mutation	SNP	G	G	T	rs3752199	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	53	0	0		WXS	Illumina HiSeq	Phase_I	73	32	0.438356	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	
C1orf85	112770	hgsc.bcm.edu	37	1	156264000	156264000	+	Missense_Mutation	SNP	G	G	A	rs10908496	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:156264000G>A	ENST00000362007.1	-	4	633	c.607C>T	c.(607-609)Cca>Tca	p.P203S	C1orf85_ENST00000482579.1_5'Flank	NM_001256604.1|NM_001256609.1|NM_144580.2	NP_001243533.1|NP_001243538.1|NP_653181.1	Q8WWB7	NCUG1_HUMAN	chromosome 1 open reading frame 85	203			P -> S (in dbSNP:rs10908496). {ECO:0000269|PubMed:15489334}.		intracellular receptor signaling pathway (GO:0030522)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|nucleus (GO:0005634)	ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|endometrium(2)|large_intestine(1)|lung(2)|ovary(2)|prostate(2)|skin(3)	14	Hepatocellular(266;0.158)					GGTTGGGCTGGTCGGCTGGAC	0.592													G|||	998	0.199281	0.0681	0.2738	5008	,	,		19636	0.2272		0.2694	False		,,,				2504	0.2229				p.P203S		Atlas-SNP	.											.	C1orf85	41	.	0			c.C607T						PASS	.	G	SER/PRO	423,3983	206.2+/-227.9	22,379,1802	42.0	43.0	43.0		607	4.6	0.8	1	dbSNP_120	43	2519,6081	408.6+/-349.5	381,1757,2162	yes	missense	C1orf85	NM_144580.1	74	403,2136,3964	AA,AG,GG		29.2907,9.6005,22.6203	probably-damaging	203/407	156264000	2942,10064	2203	4300	6503	SO:0001583	missense	112770	exon4			GGGCTGGTCGGCT	BC011575	CCDS1139.1, CCDS72947.1, CCDS72948.1, CCDS72949.1	1q22	2014-08-07			ENSG00000198715	ENSG00000198715			29436	protein-coding gene	gene with protein product	"""kidney lysosomal membrane protein"""					12975309, 18021396, 19489740	Standard	NM_144580		Approved	MGC31963, NCU-G1	uc001foh.4	Q8WWB7	OTTHUMG00000019789	ENST00000362007.1:c.607C>T	1.37:g.156264000G>A	ENSP00000354553:p.Pro203Ser	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	72	35	0.486111	NM_001256608	A6NH16|B4DJN4|Q5SZX4|Q6UX96|Q8IV07|Q96F65	Missense_Mutation	SNP	ENST00000362007.1	37	CCDS1139.1	455	0.20833333333333334	33	0.06707317073170732	82	0.2265193370165746	135	0.23601398601398602	205	0.2704485488126649	G	11.35	1.612711	0.28712	0.096005	0.292907	ENSG00000198715	ENST00000362007;ENST00000368264	T;T	0.19806	2.12;2.12	5.53	4.59	0.56863	.	0.284991	0.32987	N	0.005403	T	0.16938	0.0407	M	0.67953	2.075	0.54753	P	1.799999999996249E-5	D;D	0.53312	0.959;0.959	P;P	0.51615	0.675;0.675	T	0.08764	-1.0706	9	0.12103	T	0.63	-0.8596	12.4594	0.55723	0.0:0.3244:0.6756:0.0	rs10908496;rs60798557;rs10908496	122;203	Q8WWB7-2;Q8WWB7	.;NCUG1_HUMAN	S	203;117	ENSP00000354553:P203S;ENSP00000357247:P117S	ENSP00000354553:P203S	P	-	1	0	C1orf85	154530624	0.890000	0.30428	0.777000	0.31699	0.989000	0.77384	1.928000	0.40104	1.277000	0.44412	0.462000	0.41574	CCA	G|0.796;A|0.204	0.204	strong		0.592	C1orf85-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052108.1	NM_144580	
ATAD5	79915	hgsc.bcm.edu	37	17	29159404	29159404	+	Silent	SNP	G	G	C	rs999796|rs372459410	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:29159404G>C	ENST00000321990.4	+	1	417	c.39G>C	c.(37-39)ccG>ccC	p.P13P	CTD-2349P21.11_ENST00000580873.1_RNA	NM_024857.3	NP_079133.3	Q96QE3	ATAD5_HUMAN	ATPase family, AAA domain containing 5	13					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)				CAGCTGCTCCGCCTCCCGTGA	0.627													C|||	1441	0.28774	0.5681	0.2305	5008	,	,		16614	0.1349		0.1173	False		,,,				2504	0.2822				p.P13P		Atlas-SNP	.											ATAD5,NS,carcinoma,0,1	ATAD5	150	1	0			c.G39C						PASS	.	C		2118,2288	595.7+/-388.5	507,1104,592	67.0	73.0	71.0		39	2.8	1.0	17	dbSNP_86	71	961,7639	773.6+/-407.7	45,871,3384	yes	coding-synonymous	ATAD5	NM_024857.3		552,1975,3976	CC,CG,GG		11.1744,48.0708,23.6737		13/1845	29159404	3079,9927	2203	4300	6503	SO:0001819	synonymous_variant	79915	exon1			TGCTCCGCCTCCC		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.39G>C	17.37:g.29159404G>C		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	48	25	0.520833	NM_024857	Q05DH0|Q69YR6|Q9H9I1	Silent	SNP	ENST00000321990.4	37	CCDS11260.1																																																																																			G|0.765;C|0.235	0.235	strong		0.627	ATAD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256206.2	NM_024857	
KRTAP4-8	728224	hgsc.bcm.edu	37	17	39253960	39253960	+	Missense_Mutation	SNP	C	C	T	rs144672535	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:39253960C>T	ENST00000333822.4	-	1	433	c.377G>A	c.(376-378)cGc>cAc	p.R126H		NM_031960.2	NP_114166.1	Q9BYQ9	KRA48_HUMAN	keratin associated protein 4-8	126	25 X 5 AA repeats of C-C-[IKRQVHEC]- [SPRT]-[STCVQPR].			R -> H (in Ref. 2; CAC27579). {ECO:0000305}.	aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)				endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(1)|prostate(1)	11						gcagctggggcggcagcagtt	0.672													T|||	1899	0.379193	0.4198	0.3948	5008	,	,		14996	0.2292		0.4543	False		,,,				2504	0.3906				p.R126H		Atlas-SNP	.											KRTAP4-8,right_lower_lobe,carcinoma,0,2	KRTAP4-8	57	2	0			c.G377A						scavenged	.						3.0	5.0	4.0					17																	39253960		568	1364	1932	SO:0001583	missense	728224	exon1			CTGGGGCGGCAGC	AJ406940	CCDS45674.1	17q21.2	2013-06-25			ENSG00000204880	ENSG00000204880		"""Keratin associated proteins"""	17230	protein-coding gene	gene with protein product						11279113	Standard	NM_031960		Approved	KAP4.8	uc010wfo.2	Q9BYQ9	OTTHUMG00000133580	ENST00000333822.4:c.377G>A	17.37:g.39253960C>T	ENSP00000328444:p.Arg126His	Somatic	61	1	0.0163934		WXS	Illumina HiSeq	Phase_I	30	10	0.333333	NM_031960	A8MSH3	Missense_Mutation	SNP	ENST00000333822.4	37	CCDS45674.1	686	0.3141025641025641	142	0.2886178861788618	131	0.36187845303867405	103	0.18006993006993008	310	0.40897097625329815	.	14.80	2.642678	0.47153	.	.	ENSG00000204880	ENST00000333822;ENST00000332991	T	0.01548	4.78	3.36	-2.03	0.07365	.	1.816570	0.03571	U	0.228564	T	0.00012	0.0000	L	0.46614	1.455	0.80722	P	0.0	D	0.54207	0.965	P	0.46389	0.515	T	0.42258	-0.9462	9	0.32370	T	0.25	.	4.6421	0.12555	0.1571:0.5787:0.0:0.2642	.	126	Q9BYQ9	KRA48_HUMAN	H	126;111	ENSP00000328444:R126H	ENSP00000414561:R111H	R	-	2	0	KRTAP4-8	36507486	0.000000	0.05858	0.052000	0.19188	0.698000	0.40448	-0.965000	0.03829	-0.703000	0.05049	-0.384000	0.06662	CGC	C|0.500;T|0.500	0.500	strong		0.672	KRTAP4-8-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257684.1	NM_031960	
HIPK1	204851	hgsc.bcm.edu	37	1	114514543	114514543	+	Silent	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:114514543G>A	ENST00000369558.1	+	15	3343	c.3111G>A	c.(3109-3111)ggG>ggA	p.G1037G	HIPK1_ENST00000426820.2_Silent_p.G1037G|HIPK1_ENST00000369553.1_Silent_p.G643G|HIPK1_ENST00000369555.2_Silent_p.G992G|HIPK1_ENST00000340480.4_Silent_p.G663G|HIPK1_ENST00000369559.4_Silent_p.G1037G|HIPK1_ENST00000369554.2_Silent_p.G992G|HIPK1_ENST00000406344.1_Silent_p.G643G|HIPK1_ENST00000369561.4_Silent_p.G1003G			Q86Z02	HIPK1_HUMAN	homeodomain interacting protein kinase 1	1037	Interaction with TP53.				anterior/posterior pattern specification (GO:0009952)|definitive hemopoiesis (GO:0060216)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|endothelial cell apoptotic process (GO:0072577)|extrinsic apoptotic signaling pathway (GO:0097191)|eye development (GO:0001654)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|iris morphogenesis (GO:0061072)|lens induction in camera-type eye (GO:0060235)|neuron differentiation (GO:0030182)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell proliferation (GO:0008284)|regulation of transcription, DNA-templated (GO:0006355)|regulation of tumor necrosis factor-mediated signaling pathway (GO:0010803)|retina layer formation (GO:0010842)|smoothened signaling pathway (GO:0007224)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|PML body (GO:0016605)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(9)|lung(15)|ovary(4)|prostate(2)	39	Lung SC(450;0.184)	all_cancers(81;4.5e-08)|all_epithelial(167;1.09e-07)|all_lung(203;1.53e-05)|Lung NSC(69;2.76e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		AACGCGGGGGGACCAGTGCAG	0.542																																					p.G1037G		Atlas-SNP	.											.	HIPK1	195	.	0			c.G3111A						PASS	.						176.0	143.0	154.0					1																	114514543		2203	4300	6503	SO:0001819	synonymous_variant	204851	exon15			CGGGGGGACCAGT	AB089957	CCDS867.1, CCDS868.1, CCDS869.1, CCDS41370.1	1p13.1	2008-02-05			ENSG00000163349	ENSG00000163349			19006	protein-coding gene	gene with protein product		608003					Standard	NM_198268		Approved	KIAA0630, Myak, MGC26642, Nbak2, MGC33446, MGC33548	uc001eem.3	Q86Z02	OTTHUMG00000011983	ENST00000369558.1:c.3111G>A	1.37:g.114514543G>A		Somatic	222	1	0.0045045		WXS	Illumina HiSeq	Phase_I	182	94	0.516484	NM_198268	A6NJ34|O75125|Q5SQL2|Q5SQL4|Q5SQL5|Q8IYD7|Q8NDN5|Q8NEB6|Q8TBZ1	Silent	SNP	ENST00000369558.1	37	CCDS867.1	.	.	.	.	.	.	.	.	.	.	G	0.089	-1.170955	0.01660	.	.	ENSG00000163349	ENST00000361587	.	.	.	5.89	0.0782	0.14411	.	.	.	.	.	T	0.25344	0.0616	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.20706	-1.0267	4	.	.	.	.	1.851	0.03169	0.2593:0.1094:0.4096:0.2218	.	.	.	.	N	318	.	.	D	+	1	0	HIPK1	114316066	0.060000	0.20803	0.994000	0.49952	0.168000	0.22595	-0.497000	0.06428	0.095000	0.17434	0.563000	0.77884	GAC	.	.	none		0.542	HIPK1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000033127.1	NM_198268	
ZNF701	55762	hgsc.bcm.edu	37	19	53085659	53085659	+	Missense_Mutation	SNP	C	C	T	rs366793	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:53085659C>T	ENST00000540331.1	+	5	770	c.545C>T	c.(544-546)aCc>aTc	p.T182I	ZNF701_ENST00000391785.3_Missense_Mutation_p.T116I|CTD-3099C6.7_ENST00000599222.1_RNA|ZNF701_ENST00000301093.2_Missense_Mutation_p.T182I	NM_001172655.1	NP_001166126.1	Q9NV72	ZN701_HUMAN	zinc finger protein 701	182			T -> I (in dbSNP:rs366793). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(5)|kidney(1)|large_intestine(2)|lung(6)	14				OV - Ovarian serous cystadenocarcinoma(262;0.0105)|GBM - Glioblastoma multiforme(134;0.0402)		ATGACAAAAACCAAAAAGTTG	0.388													T|||	3226	0.644169	0.6694	0.6182	5008	,	,		20083	0.497		0.7117	False		,,,				2504	0.7106				p.T182I	NSCLC(89;451 1475 9611 20673 52284)	Atlas-SNP	.											.	ZNF701	44	.	0			c.C545T						PASS	.	T	ILE/THR,ILE/THR	2945,1461		996,953,254	110.0	109.0	109.0		545,347	-1.3	0.0	19	dbSNP_80	109	6247,2353		2292,1663,345	yes	missense,missense	ZNF701	NM_001172655.1,NM_018260.2	89,89	3288,2616,599	TT,TC,CC		27.3605,33.1593,29.3249	benign,benign	182/532,116/466	53085659	9192,3814	2203	4300	6503	SO:0001583	missense	55762	exon5			CAAAAACCAAAAA	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.545C>T	19.37:g.53085659C>T	ENSP00000444339:p.Thr182Ile	Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	101	101	1	NM_001172655	A2RRM8|B9EGF2|F5GZM6|Q66K42	Missense_Mutation	SNP	ENST00000540331.1	37	CCDS54311.1	1418	0.6492673992673993	347	0.7052845528455285	235	0.649171270718232	289	0.5052447552447552	547	0.7216358839050132	N	0.470	-0.884709	0.02530	0.668407	0.726395	ENSG00000167562	ENST00000391785;ENST00000301093;ENST00000540331	T;T;T	0.05199	3.48;3.51;3.51	1.81	-1.3	0.09259	.	.	.	.	.	T	0.00012	0.0000	N	0.00960	-1.095	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.07009	-1.0795	8	0.25751	T	0.34	.	3.692	0.08350	0.4315:0.3672:0.0:0.2012	rs366793;rs577807;rs3745100;rs16983985;rs52822021;rs366793	182;116	F5GZM6;Q9NV72	.;ZN701_HUMAN	I	116;182;182	ENSP00000375662:T116I;ENSP00000301093:T182I;ENSP00000444339:T182I	ENSP00000301093:T182I	T	+	2	0	ZNF701	57777471	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.077000	0.14738	-0.539000	0.06273	-0.848000	0.03037	ACC	C|0.309;T|0.691	0.691	strong		0.388	ZNF701-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000463467.1	NM_018260	
DUSP4	1846	hgsc.bcm.edu	37	8	29197672	29197672	+	Silent	SNP	A	A	G	rs583034	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:29197672A>G	ENST00000240100.2	-	2	911	c.522T>C	c.(520-522)agT>agC	p.S174S	DUSP4_ENST00000240101.2_Silent_p.S83S	NM_001394.6	NP_001385.1	Q13115	DUS4_HUMAN	dual specificity phosphatase 4	174					endoderm formation (GO:0001706)|innate immune response (GO:0045087)|MAPK cascade (GO:0000165)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|neurotrophin TRK receptor signaling pathway (GO:0048011)|protein dephosphorylation (GO:0006470)|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)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	MAP kinase tyrosine/serine/threonine phosphatase activity (GO:0017017)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)|protein tyrosine/threonine phosphatase activity (GO:0008330)			endometrium(1)|large_intestine(1)|lung(4)	6				KIRC - Kidney renal clear cell carcinoma(542;0.094)|Kidney(114;0.113)		GCTCTGTGGCACTGGGGGGAA	0.617											OREG0018686	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	3117	0.622404	0.8147	0.6455	5008	,	,		14166	0.6617		0.4533	False		,,,				2504	0.4796				p.S174S		Atlas-SNP	.											.	DUSP4	58	.	0			c.T522C						PASS	.	G	,	3306,1098		1252,802,148	16.0	21.0	19.0		522,249	-2.5	0.0	8	dbSNP_83	19	3636,4962		755,2126,1418	no	coding-synonymous,coding-synonymous	DUSP4	NM_001394.6,NM_057158.3	,	2007,2928,1566	GG,GA,AA		42.2889,24.9319,46.6082	,	174/395,83/304	29197672	6942,6060	2202	4299	6501	SO:0001819	synonymous_variant	1846	exon2			TGTGGCACTGGGG	U21108	CCDS6072.1, CCDS6073.1	8p12-p11	2011-06-09			ENSG00000120875	ENSG00000120875		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : MAP kinase phosphatases"""	3070	protein-coding gene	gene with protein product	"""VH1 homologous phosphatase 2"", ""MAP kinase phosphatase 2"""	602747				7535768, 9205128	Standard	NM_001394		Approved	HVH2, MKP-2, TYP	uc003xhm.3	Q13115	OTTHUMG00000133395	ENST00000240100.2:c.522T>C	8.37:g.29197672A>G		Somatic	33	0	0	807	WXS	Illumina HiSeq	Phase_I	35	23	0.657143	NM_001394	B2RBU5|D3DSU4|G5E930|Q13524	Silent	SNP	ENST00000240100.2	37	CCDS6072.1																																																																																			A|0.447;G|0.553	0.553	strong		0.617	DUSP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257249.1	NM_001394	
C14orf39	317761	hgsc.bcm.edu	37	14	60903757	60903757	+	Missense_Mutation	SNP	G	G	A	rs1254319	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:60903757G>A	ENST00000321731.3	-	18	1729	c.1570C>T	c.(1570-1572)Ctt>Ttt	p.L524F		NM_174978.2	NP_777638	Q8N1H7	S6OS1_HUMAN	chromosome 14 open reading frame 39	524				L -> F (in Ref. 1; BAC05253). {ECO:0000305}.	multicellular organismal development (GO:0007275)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)					breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(5)|lung(7)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	30				OV - Ovarian serous cystadenocarcinoma(108;0.0448)		GGCTTCTCAAGTAAGTTTCCT	0.299													A|||	2338	0.466853	0.5182	0.2406	5008	,	,		16553	0.6944		0.3012	False		,,,				2504	0.4939				p.L524F		Atlas-SNP	.											.	C14orf39	79	.	0			c.C1570T						PASS	.	A	PHE/LEU	2181,2225	580.0+/-385.0	541,1099,563	102.0	114.0	110.0		1570	4.0	1.0	14	dbSNP_87	110	2535,6063	688.6+/-404.3	362,1811,2126	yes	missense	C14orf39	NM_174978.2	22	903,2910,2689	AA,AG,GG		29.4836,49.5007,36.2658	benign	524/588	60903757	4716,8288	2203	4299	6502	SO:0001583	missense	317761	exon18			TCTCAAGTAAGTT	AK098187	CCDS9746.1	14q23.1	2012-11-05	2012-11-05	2012-11-05	ENSG00000179008	ENSG00000179008			19849	protein-coding gene	gene with protein product							Standard	NM_174978		Approved	SIX6OS1	uc001xez.4	Q8N1H7	OTTHUMG00000140332	ENST00000321731.3:c.1570C>T	14.37:g.60903757G>A	ENSP00000324920:p.Leu524Phe	Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	141	72	0.510638	NM_174978	Q08AQ4	Missense_Mutation	SNP	ENST00000321731.3	37	CCDS9746.1	954	0.4368131868131868	243	0.49390243902439024	107	0.2955801104972376	385	0.6730769230769231	219	0.28891820580474936	A	0.031	-1.331798	0.01298	0.495007	0.294836	ENSG00000179008	ENST00000321731	T	0.15372	2.43	5.17	4.03	0.46877	.	0.103898	0.43260	N	0.000594	T	0.00012	0.0000	N	0.00104	-2.125	0.39087	P	0.03897099999999998	B	0.02656	0.0	B	0.01281	0.0	T	0.43278	-0.9401	9	0.02654	T	1	-4.4151	8.9267	0.35646	0.8474:0.0:0.1526:0.0	rs1254319;rs57641575;rs1254319	524	Q8N1H7	S6OS1_HUMAN	F	524	ENSP00000324920:L524F	ENSP00000324920:L524F	L	-	1	0	C14orf39	59973510	1.000000	0.71417	0.998000	0.56505	0.458000	0.32498	4.268000	0.58883	0.307000	0.22880	-1.266000	0.01441	CTT	G|0.588;A|0.412	0.412	strong		0.299	C14orf39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276948.1	NM_174978	
C17orf97	400566	hgsc.bcm.edu	37	17	260299	260299	+	Missense_Mutation	SNP	G	G	A	rs4581766	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:260299G>A	ENST00000571106.1	+	1	172	c.166G>A	c.(166-168)Gag>Aag	p.E56K	AC108004.3_ENST00000599026.1_RNA|C17orf97_ENST00000360127.6_Missense_Mutation_p.E56K|AC108004.3_ENST00000466740.2_RNA			Q6ZQX7	CQ097_HUMAN	chromosome 17 open reading frame 97	56	Poly-Glu.		E -> K (in dbSNP:rs4581766). {ECO:0000269|PubMed:15489334}.							breast(1)|kidney(2)|large_intestine(4)|lung(4)|ovary(1)|prostate(1)|skin(1)	14						CGGCGAGGAGGAGGAGCGGGA	0.731													g|||	992	0.198083	0.2905	0.1657	5008	,	,		11861	0.2073		0.1093	False		,,,				2504	0.1779				p.E56K		Atlas-SNP	.											C17orf97_ENST00000360127,NS,carcinoma,0,4	C17orf97	76	4	0			c.G166A						PASS	.		LYS/GLU	562,2470		32,498,986	2.0	4.0	4.0		166	3.6	0.9	17	dbSNP_111	4	498,5448		18,462,2493	yes	missense	C17orf97	NM_001013672.4	56	50,960,3479	AA,AG,GG		8.3754,18.5356,11.8066	benign	56/424	260299	1060,7918	1516	2973	4489	SO:0001583	missense	400566	exon1			GAGGAGGAGGAGC	AK128660, BC057385	CCDS32519.2	17p13.3	2008-08-15			ENSG00000187624	ENSG00000187624			33800	protein-coding gene	gene with protein product						12477932	Standard	NM_001013672		Approved	LOC400566	uc021tna.1	Q6ZQX7	OTTHUMG00000132479	ENST00000571106.1:c.166G>A	17.37:g.260299G>A	ENSP00000458320:p.Glu56Lys	Somatic	6	0	0		WXS	Illumina HiSeq	Phase_I	14	9	0.642857	NM_001013672	A5D8T6|Q6NSI2|Q6PFW9	Missense_Mutation	SNP	ENST00000571106.1	37		437	0.2000915750915751	157	0.31910569105691056	59	0.16298342541436464	135	0.23601398601398602	86	0.11345646437994723	g	22.1	4.246429	0.80024	0.185356	0.083754	ENSG00000187624	ENST00000360127;ENST00000491373	T;T	0.54279	0.93;0.58	3.56	3.56	0.40772	.	0.000000	0.42548	D	0.000690	T	0.00012	0.0000	L	0.27053	0.805	0.38502	P	0.05175099999999999	D	0.76494	0.999	D	0.80764	0.994	T	0.15723	-1.0427	9	0.49607	T	0.09	-0.156	10.9491	0.47319	0.0:0.0:1.0:0.0	rs4581766;rs60466803	56	Q6ZQX7-4	.	K	56;50	ENSP00000353245:E56K;ENSP00000419482:E50K	ENSP00000353245:E56K	E	+	1	0	C17orf97	260615	0.992000	0.36948	0.855000	0.33649	0.658000	0.38924	2.263000	0.43293	2.299000	0.77371	0.556000	0.70494	GAG	G|0.798;A|0.202	0.202	strong		0.731	C17orf97-003	PUTATIVE	basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000436874.1	NM_001013672	
CYP4B1	1580	hgsc.bcm.edu	37	1	47280859	47280859	+	Missense_Mutation	SNP	G	G	A	rs2297810	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:47280859G>A	ENST00000271153.4	+	8	1029	c.993G>A	c.(991-993)atG>atA	p.M331I	CYP4B1_ENST00000371919.4_Missense_Mutation_p.M317I|CYP4B1_ENST00000452782.2_Missense_Mutation_p.M169I|CYP4B1_ENST00000371923.4_Missense_Mutation_p.M332I			P13584	CP4B1_HUMAN	cytochrome P450, family 4, subfamily B, polypeptide 1	331			M -> I (in allele CYP4B1*2, allele CYP4B1*7 and allele CYP4B1*5; dbSNP:rs2297810). {ECO:0000269|PubMed:12142726, ECO:0000269|Ref.5}.		biphenyl metabolic process (GO:0018879)|exogenous drug catabolic process (GO:0042738)|fluorene metabolic process (GO:0018917)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	aromatase activity (GO:0070330)|drug binding (GO:0008144)|fluorene oxygenase activity (GO:0018585)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxygen binding (GO:0019825)			NS(2)|breast(1)|endometrium(2)|kidney(1)|large_intestine(12)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	36	Acute lymphoblastic leukemia(166;0.155)				Midazolam(DB00683)|Phenobarbital(DB01174)|Thiamine(DB00152)	TCTACTGCATGGCCCTGTACC	0.562													g|||	1356	0.270767	0.4614	0.2334	5008	,	,		20608	0.2808		0.1312	False		,,,				2504	0.1728				p.M332I		Atlas-SNP	.											.	CYP4B1	81	.	0			c.G996A						PASS	.	G	ILE/MET,ILE/MET	1819,2587	533.4+/-373.7	380,1059,764	126.0	100.0	109.0		993,996	4.0	1.0	1	dbSNP_100	109	1265,7335	253.3+/-279.0	98,1069,3133	yes	missense,missense	CYP4B1	NM_000779.3,NM_001099772.1	10,10	478,2128,3897	AA,AG,GG		14.7093,41.2846,23.7121	benign,benign	331/512,332/513	47280859	3084,9922	2203	4300	6503	SO:0001583	missense	1580	exon8			CTGCATGGCCCTG	BC017758	CCDS542.1, CCDS41328.1	1p33	2013-11-11	2003-01-14		ENSG00000142973	ENSG00000142973		"""Cytochrome P450s"""	2644	protein-coding gene	gene with protein product		124075	"""cytochrome P450, subfamily IVB, polypeptide 1"""				Standard	NM_000779		Approved		uc001cqn.4	P13584	OTTHUMG00000007984	ENST00000271153.4:c.993G>A	1.37:g.47280859G>A	ENSP00000271153:p.Met331Ile	Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	126	61	0.484127	NM_001099772	Q1HBI2|Q8TD85|Q8WWF2|Q8WWU9|Q8WWV0	Missense_Mutation	SNP	ENST00000271153.4	37	CCDS542.1	626	0.2866300366300366	246	0.5	79	0.21823204419889503	194	0.33916083916083917	107	0.14116094986807387	g	34	5.379942	0.95945	0.412846	0.147093	ENSG00000142973	ENST00000371923;ENST00000271153;ENST00000371919;ENST00000452782;ENST00000468637	T;T;T;T;T	0.79033	-1.23;-1.23;-0.26;-1.23;-1.23	5.85	3.95	0.45737	.	0.099034	0.64402	D	0.000001	T	0.00012	0.0000	N	0.12920	0.275	0.22389	P	0.999143936	B;B;B	0.26577	0.153;0.032;0.018	B;B;B	0.27262	0.078;0.03;0.05	T	0.43294	-0.9400	9	0.54805	T	0.06	.	12.1686	0.54144	0.0655:0.1195:0.815:0.0	rs2297810;rs12724127;rs17102584;rs56573458;rs58421583;rs2297810	317;332;331	Q8IZB0;P13584-2;P13584	.;.;CP4B1_HUMAN	I	332;331;317;169;168	ENSP00000360991:M332I;ENSP00000271153:M331I;ENSP00000360987:M317I;ENSP00000400413:M169I;ENSP00000437670:M168I	ENSP00000271153:M331I	M	+	3	0	CYP4B1	47053446	1.000000	0.71417	1.000000	0.80357	0.851000	0.48451	7.945000	0.87732	1.475000	0.48197	0.643000	0.83706	ATG	G|0.736;A|0.264	0.264	strong		0.562	CYP4B1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000021911.1	NM_000779	
PLIN4	729359	hgsc.bcm.edu	37	19	4512945	4512945	+	Missense_Mutation	SNP	C	C	T	rs75031432	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:4512945C>T	ENST00000301286.3	-	3	984	c.985G>A	c.(985-987)Ggt>Agt	p.G329S		NM_001080400.1	NP_001073869.1	Q96Q06	PLIN4_HUMAN	perilipin 4	329	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						TTCATGGCACCAGTCACCCCA	0.567													C|||	840	0.167732	0.4539	0.1037	5008	,	,		18994	0.0119		0.0934	False		,,,				2504	0.0634				p.G329S		Atlas-SNP	.											PLIN4_ENST00000301286,NS,carcinoma,0,2	PLIN4	191	2	0			c.G985A						scavenged	.						39.0	40.0	39.0					19																	4512945		1862	4105	5967	SO:0001583	missense	729359	exon3			TGGCACCAGTCAC	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.985G>A	19.37:g.4512945C>T	ENSP00000301286:p.Gly329Ser	Somatic	267	1	0.00374532		WXS	Illumina HiSeq	Phase_I	153	21	0.137255	NM_001080400	A6NEI2	Missense_Mutation	SNP	ENST00000301286.3	37	CCDS45927.1	.	.	.	.	.	.	.	.	.	.	C	15.24	2.776204	0.49786	.	.	ENSG00000167676	ENST00000301286	T	0.13901	2.55	4.53	1.21	0.21127	.	0.420915	0.19796	N	0.105865	T	0.13543	0.0328	L	0.46157	1.445	0.80722	P	0.0	D	0.54397	0.966	P	0.45794	0.493	T	0.19353	-1.0308	9	0.87932	D	0	-15.096	7.3812	0.26856	0.0:0.7112:0.0:0.2888	rs56366613	329	Q96Q06	PLIN4_HUMAN	S	329	ENSP00000301286:G329S	ENSP00000301286:G329S	G	-	1	0	PLIN4	4463945	0.091000	0.21658	0.003000	0.11579	0.001000	0.01503	0.810000	0.27183	0.906000	0.36621	0.407000	0.27541	GGT	C|0.826;T|0.174	0.174	strong		0.567	PLIN4-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395095.1	XM_170901	
CBX2	84733	hgsc.bcm.edu	37	17	77758484	77758484	+	Silent	SNP	G	G	A	rs3751956	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:77758484G>A	ENST00000310942.4	+	5	1346	c.1242G>A	c.(1240-1242)ctG>ctA	p.L414L		NM_005189.2	NP_005180.1	Q14781	CBX2_HUMAN	chromobox homolog 2	414					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)			GTGAGAAGCTGGCTTCCAGAG	0.677													G|||	1024	0.204473	0.0287	0.2334	5008	,	,		3668	0.1806		0.4443	False		,,,				2504	0.1994				p.L414L		Atlas-SNP	.											CBX2,NS,carcinoma,0,2	CBX2	50	2	0			c.G1242A						PASS	.	G		388,4014		16,356,1829	17.0	19.0	19.0		1242	3.1	0.8	17	dbSNP_107	19	3567,5033		731,2105,1464	no	coding-synonymous	CBX2	NM_005189.2		747,2461,3293	AA,AG,GG		41.4767,8.8142,30.4184		414/533	77758484	3955,9047	2201	4300	6501	SO:0001819	synonymous_variant	84733	exon5			GAAGCTGGCTTCC	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.1242G>A	17.37:g.77758484G>A		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	82	42	0.512195	NM_005189	Q0VDA5|Q9BTB1	Silent	SNP	ENST00000310942.4	37	CCDS32757.1																																																																																			G|0.744;A|0.256	0.256	strong		0.677	CBX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437040.1	NM_032647	
COL24A1	255631	hgsc.bcm.edu	37	1	86512536	86512536	+	Missense_Mutation	SNP	C	C	T	rs60891279	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:86512536C>T	ENST00000370571.2	-	12	2288	c.1922G>A	c.(1921-1923)cGt>cAt	p.R641H	COL24A1_ENST00000436319.1_Missense_Mutation_p.R641H	NM_152890.5	NP_690850.2	Q17RW2	COOA1_HUMAN	collagen, type XXIV, alpha 1	641			R -> H (in dbSNP:rs60891279).		extracellular matrix organization (GO:0030198)|hematopoietic progenitor cell differentiation (GO:0002244)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)			NS(3)|central_nervous_system(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(9)|liver(1)|lung(56)|ovary(4)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	101				all cancers(265;0.0627)|Epithelial(280;0.0689)		cttctttccacggatcccagg	0.313													C|||	921	0.183906	0.1097	0.2651	5008	,	,		17486	0.2788		0.1322	False		,,,				2504	0.182				p.R641H		Atlas-SNP	.											COL24A1,NS,carcinoma,-1,1	COL24A1	202	1	0			c.G1922A						PASS	.	C	HIS/ARG	404,3202		20,364,1419	114.0	114.0	114.0		1922	4.2	1.0	1	dbSNP_129	114	1200,6924		77,1046,2939	yes	missense	COL24A1	NM_152890.5	29	97,1410,4358	TT,TC,CC		14.771,11.2035,13.6743	benign	641/1715	86512536	1604,10126	1803	4062	5865	SO:0001583	missense	255631	exon12			TTTCCACGGATCC	AF410793	CCDS41353.1	1p22.3-p22.2	2013-01-16			ENSG00000171502	ENSG00000171502		"""Collagens"""	20821	protein-coding gene	gene with protein product		610025					Standard	NM_152890		Approved		uc001dlj.3	Q17RW2	OTTHUMG00000010629	ENST00000370571.2:c.1922G>A	1.37:g.86512536C>T	ENSP00000359603:p.Arg641His	Somatic	198	0	0		WXS	Illumina HiSeq	Phase_I	128	126	0.984375	NM_152890	C9J1X6|Q14BD7|Q59EX5|Q5VY50|Q7Z5L5	Missense_Mutation	SNP	ENST00000370571.2	37	CCDS41353.1	402	0.18406593406593408	59	0.11991869918699187	84	0.23204419889502761	161	0.28146853146853146	98	0.12928759894459102	C	11.28	1.591078	0.28357	0.112035	0.14771	ENSG00000171502	ENST00000370571;ENST00000436319	D;D	0.95035	-3.59;-3.59	4.22	4.22	0.49857	.	0.000000	0.38272	N	0.001752	D	0.86171	0.5869	L	0.38953	1.18	0.35679	P	0.18606299999999998	B;B	0.18013	0.025;0.004	B;B	0.13407	0.009;0.002	T	0.83293	-0.0032	9	0.41790	T	0.15	.	12.3912	0.55360	0.0:1.0:0.0:0.0	rs60891279	641;641	F8WDM8;Q17RW2	.;COOA1_HUMAN	H	641	ENSP00000359603:R641H;ENSP00000392531:R641H	ENSP00000359603:R641H	R	-	2	0	COL24A1	86285124	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.707000	0.37888	2.616000	0.88540	0.655000	0.94253	CGT	C|0.832;T|0.168	0.168	strong		0.313	COL24A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029335.4	NM_152890	
ARHGEF10	9639	hgsc.bcm.edu	37	8	1833801	1833801	+	Missense_Mutation	SNP	G	G	C	rs9657362	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:1833801G>C	ENST00000398564.1	+	11	1185	c.1185G>C	c.(1183-1185)ttG>ttC	p.L395F	ARHGEF10_ENST00000398560.1_Missense_Mutation_p.L356F|ARHGEF10_ENST00000518288.1_Missense_Mutation_p.L395F|ARHGEF10_ENST00000349830.3_Missense_Mutation_p.L370F|ARHGEF10_ENST00000520359.1_Missense_Mutation_p.L332F|ARHGEF10_ENST00000262112.6_Missense_Mutation_p.L395F			O15013	ARHGA_HUMAN	Rho guanine nucleotide exchange factor (GEF) 10	395				L -> F (in Ref. 5; AAI12927). {ECO:0000305}.	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)	p.L395F(1)|p.L147F(1)		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)		AACAGAATTTGTTCATTGATG	0.418													G|||	843	0.168331	0.0091	0.1239	5008	,	,		16560	0.2907		0.1352	False		,,,				2504	0.3231				p.L370F		Atlas-SNP	.											ARHGEF10_ENST00000398564,NS,carcinoma,0,2	ARHGEF10	255	2	2	Substitution - Missense(2)	stomach(2)	c.G1110C						PASS	.	G	PHE/LEU	164,4242	109.1+/-147.4	5,154,2044	88.0	83.0	85.0		1110	-4.8	0.0	8	dbSNP_119	85	1242,7358	248.6+/-276.2	98,1046,3156	yes	missense	ARHGEF10	NM_014629.2	22	103,1200,5200	CC,CG,GG		14.4419,3.7222,10.8104	possibly-damaging	370/1345	1833801	1406,11600	2203	4300	6503	SO:0001583	missense	9639	exon11			GAATTTGTTCATT	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.1185G>C	8.37:g.1833801G>C	ENSP00000381571:p.Leu395Phe	Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	44	15	0.340909	NM_014629	O14665|Q2KHR8|Q68D55|Q8IWD9|Q8IY77	Missense_Mutation	SNP	ENST00000398564.1	37		296	0.13553113553113552	3	0.006097560975609756	45	0.12430939226519337	152	0.26573426573426573	96	0.1266490765171504	g	8.974	0.973589	0.18736	0.037222	0.144419	ENSG00000104728	ENST00000349830;ENST00000520359;ENST00000518288;ENST00000398560;ENST00000398564;ENST00000262112;ENST00000522435	T;T;T;T;T;T;T	0.65732	0.09;0.19;0.09;-0.17;0.08;0.08;0.29	5.12	-4.8	0.03190	.	2.405150	0.02296	N	0.070730	T	0.00012	0.0000	L	0.48642	1.525	0.35344	P	0.21322200000000002	D;P;D;P	0.57257	0.964;0.715;0.979;0.708	P;B;P;P	0.61800	0.802;0.342;0.894;0.543	T	0.16571	-1.0398	9	0.21014	T	0.42	-4.3658	8.8816	0.35378	0.5809:0.3162:0.1029:0.0	rs9657362;rs52817136;rs57380468;rs9657362	395;356;332;370	O15013;E9PB39;O15013-7;O15013-5	ARHGA_HUMAN;.;.;.	F	370;332;395;356;395;395;43	ENSP00000340297:L370F;ENSP00000427909:L332F;ENSP00000431012:L395F;ENSP00000381568:L356F;ENSP00000381571:L395F;ENSP00000262112:L395F;ENSP00000427768:L43F	ENSP00000262112:L395F	L	+	3	2	ARHGEF10	1821208	0.999000	0.42202	0.013000	0.15412	0.012000	0.07955	0.685000	0.25378	-1.240000	0.02529	-0.740000	0.03531	TTG	G|0.884;C|0.116	0.116	strong		0.418	ARHGEF10-203	KNOWN	basic	protein_coding	protein_coding			
TTC3	7267	hgsc.bcm.edu	37	21	38534308	38534308	+	Missense_Mutation	SNP	C	C	G	rs377155188		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:38534308C>G	ENST00000399017.2	+	31	5860	c.3113C>G	c.(3112-3114)tCt>tGt	p.S1038C	TTC3_ENST00000479930.1_3'UTR|TTC3_ENST00000354749.2_Missense_Mutation_p.S1038C|TTC3_ENST00000355666.1_Missense_Mutation_p.S1038C	NM_003316.3	NP_003307.3	P53804	TTC3_HUMAN	tetratricopeptide repeat domain 3	1038					negative regulation of cell morphogenesis involved in differentiation (GO:0010771)|negative regulation of neuron differentiation (GO:0045665)|protein K48-linked ubiquitination (GO:0070936)|ubiquitin-dependent protein catabolic process (GO:0006511)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|vacuole (GO:0005773)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(5)|endometrium(7)|kidney(5)|large_intestine(17)|liver(1)|lung(18)|ovary(4)|prostate(2)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(5)	75		Myeloproliferative disorder(46;0.0412)				TTAGTTGGGTCTGGAACAACT	0.279																																					p.S1038C	Ovarian(38;194 1649 35661)	Atlas-SNP	.											.	TTC3	182	.	0			c.C3113G						PASS	.	C	CYS/SER,CYS/SER	0,4404		0,0,2202	50.0	47.0	48.0		3113,3113	5.1	1.0	21		48	1,8573		0,1,4286	no	missense,missense	TTC3	NM_001001894.1,NM_003316.3	112,112	0,1,6488	GG,GC,CC		0.0117,0.0,0.0077	probably-damaging,probably-damaging	1038/2026,1038/2026	38534308	1,12977	2202	4287	6489	SO:0001583	missense	7267	exon31			TTGGGTCTGGAAC	D84296	CCDS13651.1	21q22.2	2013-01-11			ENSG00000182670	ENSG00000182670		"""RING-type (C3HC4) zinc fingers"", ""Tetratricopeptide (TTC) repeat domain containing"""	12393	protein-coding gene	gene with protein product		602259				8947847	Standard	NM_003316		Approved	TPRD, TPRDI, DCRR1, TPRDII, TPRDIII, RNF105	uc002yvz.3	P53804	OTTHUMG00000086654	ENST00000399017.2:c.3113C>G	21.37:g.38534308C>G	ENSP00000381981:p.Ser1038Cys	Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	145	79	0.544828	NM_001001894	A8K7H7|B2RPA7|D3DSG9|D3DSH2|D3DSH3|O60767|P78476|P78477|Q569I2|Q6P578|Q9UEK4	Missense_Mutation	SNP	ENST00000399017.2	37	CCDS13651.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	17.86|17.86	3.493015|3.493015	0.64186|0.64186	0.0|0.0	1.17E-4|1.17E-4	ENSG00000182670|ENSG00000182670	ENST00000411496|ENST00000418766;ENST00000438055;ENST00000355666;ENST00000399017;ENST00000354749	.|T;T;T;T;T	.|0.15834	.|2.39;2.39;2.68;2.68;2.68	5.06|5.06	5.06|5.06	0.68205|0.68205	.|.	.|0.000000	.|0.64402	.|D	.|0.000013	T|T	0.40222|0.40222	0.1108|0.1108	M|M	0.66939|0.66939	2.045|2.045	0.80722|0.80722	D|D	1|1	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.87578	.|0.998;0.996	T|T	0.19679|0.19679	-1.0298|-1.0298	5|10	.|0.87932	.|D	.|0	-23.3456|-23.3456	14.2622|14.2622	0.66092|0.66092	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|96;1038	.|Q5GIT6;P53804	.|.;TTC3_HUMAN	V|C	194|1038;1020;1038;1038;1038	.|ENSP00000403943:S1038C;ENSP00000391891:S1020C;ENSP00000347889:S1038C;ENSP00000381981:S1038C;ENSP00000346791:S1038C	.|ENSP00000346791:S1038C	L|S	+|+	1|2	2|0	TTC3|TTC3	37456178|37456178	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.964000|0.964000	0.63967|0.63967	3.437000|3.437000	0.52863|0.52863	2.502000|2.502000	0.84385|0.84385	0.557000|0.557000	0.71058|0.71058	CTG|TCT	.	.	weak		0.279	TTC3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194776.1		
NKX1-2	390010	hgsc.bcm.edu	37	10	126136112	126136112	+	Silent	SNP	A	A	G	rs7075981|rs386748536	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:126136112A>G	ENST00000451024.3	-	2	1059	c.819T>C	c.(817-819)aaT>aaC	p.N273N	RP13-238F13.3_ENST00000604581.1_RNA|NKX1-2_ENST00000440536.2_Silent_p.N295N|RP13-238F13.5_ENST00000602332.1_lincRNA	NM_001146340.1	NP_001139812.1	Q9UD57	NKX12_HUMAN	NK1 homeobox 2	273					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)										GGAAGAGGACATTGGCCGCGG	0.741													G|||	937	0.187101	0.3154	0.1167	5008	,	,		9188	0.1012		0.173	False		,,,				2504	0.1667				p.N273N		Atlas-SNP	.											NKX1-2_ENST00000440536,NS,carcinoma,0,2	NKX1-2	6	2	0			c.T819C						PASS	.	G		385,999		58,269,365	42.0	66.0	59.0		819	2.1	1.0	10	dbSNP_116	59	438,2744		33,372,1186	no	coding-synonymous	NKX1-2	NM_001146340.1		91,641,1551	GG,GA,AA		13.7649,27.8179,18.0245		273/311	126136112	823,3743	692	1591	2283	SO:0001819	synonymous_variant	390010	exon2			GAGGACATTGGCC	CN285329	CCDS59221.1	10q26.13	2012-03-09	2007-07-09	2006-06-29		ENSG00000229544		"""Homeoboxes / ANTP class : NKL subclass"""	31652	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 121"", ""NK1 transcription factor related, locus 2 (Drosophila)"""	C10orf121		10681422	Standard	NM_001146340		Approved	bB238F13.2	uc010quf.2	Q9UD57		ENST00000451024.3:c.819T>C	10.37:g.126136112A>G		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	43	14	0.325581	NM_001146340		Silent	SNP	ENST00000451024.3	37	CCDS59221.1																																																																																			A|0.824;G|0.176	0.176	strong		0.741	NKX1-2-001	PUTATIVE	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050861.3	XM_372331	
KLHL33	123103	hgsc.bcm.edu	37	14	20897064	20897064	+	Missense_Mutation	SNP	C	C	T	rs7145318	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	140	0	0		WXS	Illumina HiSeq	Phase_I	136	135	0.992647	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	
CRLF3	51379	hgsc.bcm.edu	37	17	29113016	29113016	+	Silent	SNP	A	A	G	rs34756112	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:29113016A>G	ENST00000324238.6	-	7	1117	c.993T>C	c.(991-993)gaT>gaC	p.D331D	CRLF3_ENST00000544695.1_Silent_p.D215D|CRLF3_ENST00000577725.1_Intron	NM_015986.3	NP_057070.3	Q8IUI8	CRLF3_HUMAN	cytokine receptor-like factor 3	331					G1/S transition of mitotic cell cycle (GO:0000082)|negative regulation of cell growth (GO:0030308)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)	cytoplasm (GO:0005737)				endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(7)|prostate(1)|upper_aerodigestive_tract(1)	17		all_hematologic(16;0.014)|Acute lymphoblastic leukemia(14;0.0236)|Myeloproliferative disorder(56;0.0255)				CTCCTATGCTATCTCTTCTGT	0.378													a|||	810	0.161741	0.1354	0.1902	5008	,	,		15663	0.1359		0.1074	False		,,,				2504	0.2597				p.D331D	Pancreas(30;346 881 29244 33464 41299)	Atlas-SNP	.											.	CRLF3	36	.	0			c.T993C						PASS	.	G		614,3792	266.8+/-267.5	36,542,1625	194.0	173.0	180.0		993	1.9	1.0	17	dbSNP_126	180	994,7606	214.5+/-254.1	62,870,3368	no	coding-synonymous	CRLF3	NM_015986.3		98,1412,4993	GG,GA,AA		11.5581,13.9355,12.3635		331/443	29113016	1608,11398	2203	4300	6503	SO:0001819	synonymous_variant	51379	exon7			TATGCTATCTCTT	AF120151	CCDS32607.1	17q11.2	2008-05-02				ENSG00000176390			17177	protein-coding gene	gene with protein product		614853					Standard	NM_015986		Approved	CREME9, CYTOR4	uc002hfr.4	Q8IUI8		ENST00000324238.6:c.993T>C	17.37:g.29113016A>G		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	81	38	0.469136	NM_015986	A6NJF3|B2R8C3|Q2MLY7|Q9UNI3|Q9Y6M8	Silent	SNP	ENST00000324238.6	37	CCDS32607.1																																																																																			A|0.868;G|0.132	0.132	strong		0.378	CRLF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444354.1		
DST	667	hgsc.bcm.edu	37	6	56481632	56481632	+	Silent	SNP	T	T	C	rs115542549	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:56481632T>C	ENST00000370765.6	-	24	6740	c.6633A>G	c.(6631-6633)gcA>gcG	p.A2211A	DST_ENST00000370769.4_Intron|DST_ENST00000361203.3_Intron|DST_ENST00000244364.6_Intron|DST_ENST00000312431.6_Intron|DST_ENST00000446842.2_Intron|DST_ENST00000370754.5_Intron|DST_ENST00000370788.2_Intron|DST_ENST00000421834.2_Intron	NM_001723.5	NP_001714.1	Q03001	DYST_HUMAN	dystonin	1627					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)			CTGCCTTCTCTGCCTCAAGAA	0.373													T|||	51	0.0101837	0.0015	0.0101	5008	,	,		20122	0.0		0.0258	False		,,,				2504	0.0164				p.A2211A		Atlas-SNP	.											.	DST	1427	.	0			c.A6633G						PASS	.	T	,	35,4371	38.4+/-70.7	0,35,2168	62.0	65.0	64.0		6633,	3.2	1.0	6	dbSNP_132	64	366,8234	119.5+/-178.9	10,346,3944	no	coding-synonymous,intron	DST	NM_001723.5,NM_015548.4	,	10,381,6112	CC,CT,TT		4.2558,0.7944,3.0832	,	2211/2650,	56481632	401,12605	2203	4300	6503	SO:0001819	synonymous_variant	667	exon24			CTTCTCTGCCTCA	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.6633A>G	6.37:g.56481632T>C		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	90	37	0.411111	NM_001723	B7Z3H1|O94833|Q12825|Q13266|Q13267|Q13775|Q5TBT0|Q5TBT2|Q5TF23|Q5TF24|Q8N1T8|Q8N8J3|Q8WXK8|Q8WXK9|Q96AK9|Q96DQ5|Q96J76|Q96QT5|Q9H555|Q9UGD7|Q9UGD8|Q9UN10	Silent	SNP	ENST00000370765.6	37	CCDS4959.1																																																																																			T|0.974;C|0.026	0.026	strong		0.373	DST-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000041027.2	NM_001723	
DOCK5	80005	hgsc.bcm.edu	37	8	25265651	25265651	+	Missense_Mutation	SNP	C	C	A	rs34067851	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:25265651C>A	ENST00000276440.7	+	49	5290	c.5246C>A	c.(5245-5247)gCa>gAa	p.A1749E		NM_024940.6	NP_079216.4	Q9H7D0	DOCK5_HUMAN	dedicator of cytokinesis 5	1749					positive regulation of GTPase activity (GO:0043547)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	guanyl-nucleotide exchange factor activity (GO:0005085)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(12)|kidney(9)|large_intestine(13)|lung(20)|ovary(3)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	72		all_cancers(63;0.0361)|Ovarian(32;0.000711)|all_epithelial(46;0.0153)|Hepatocellular(4;0.115)|Prostate(55;0.13)|Breast(100;0.143)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0267)|Epithelial(17;1.07e-11)|Colorectal(74;0.0276)|COAD - Colon adenocarcinoma(73;0.0828)		GCAGAGAAAGCACCAGAACCC	0.483													C|||	86	0.0171725	0.0	0.0159	5008	,	,		17337	0.001		0.0258	False		,,,				2504	0.0491				p.A1749E	Pancreas(145;34 1887 3271 10937 30165)	Atlas-SNP	.											.	DOCK5	167	.	0			c.C5246A						PASS	.	C	GLU/ALA	18,4388		0,18,2185	36.0	35.0	35.0		5246	1.8	0.1	8	dbSNP_126	35	187,8413		2,183,4115	yes	missense	DOCK5	NM_024940.6	107	2,201,6300	AA,AC,CC		2.1744,0.4085,1.5762	benign	1749/1871	25265651	205,12801	2203	4300	6503	SO:0001583	missense	80005	exon49			AGAAAGCACCAGA		CCDS6047.1	8p21.2	2009-04-17			ENSG00000147459	ENSG00000147459			23476	protein-coding gene	gene with protein product						12432077	Standard	NM_024940		Approved	FLJ21034	uc003xeg.3	Q9H7D0	OTTHUMG00000131991	ENST00000276440.7:c.5246C>A	8.37:g.25265651C>A	ENSP00000276440:p.Ala1749Glu	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	85	68	0.8	NM_024940	B2RNY0|Q5XKD5|Q6AI11|Q6PJS6|Q6ZTS6	Missense_Mutation	SNP	ENST00000276440.7	37	CCDS6047.1	25	0.011446886446886446	0	0.0	6	0.016574585635359115	0	0.0	19	0.025065963060686015	C	5.640	0.302670	0.10678	0.004085	0.021744	ENSG00000147459	ENST00000276440	T	0.03689	3.84	5.92	1.81	0.25067	.	0.620356	0.16710	N	0.202737	T	0.00580	0.0019	N	0.08118	0	0.09310	N	0.999998	B	0.02656	0.0	B	0.01281	0.0	T	0.49204	-0.8964	10	0.11794	T	0.64	.	4.2551	0.10714	0.2285:0.5115:0.0:0.26	rs34067851	1749	Q9H7D0	DOCK5_HUMAN	E	1749	ENSP00000276440:A1749E	ENSP00000276440:A1749E	A	+	2	0	DOCK5	25321568	0.340000	0.24792	0.146000	0.22360	0.865000	0.49528	0.821000	0.27338	0.848000	0.35191	0.655000	0.94253	GCA	C|0.986;A|0.014	0.014	strong		0.483	DOCK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254955.2	NM_024940	
METTL20	254013	hgsc.bcm.edu	37	12	31815167	31815167	+	Missense_Mutation	SNP	G	G	T	rs61736289	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:31815167G>T	ENST00000357721.3	+	2	495	c.280G>T	c.(280-282)Gca>Tca	p.A94S	METTL20_ENST00000412352.2_Missense_Mutation_p.A94S|METTL20_ENST00000395763.3_Missense_Mutation_p.A94S|METTL20_ENST00000538391.1_Missense_Mutation_p.A94S|METTL20_ENST00000538463.1_Missense_Mutation_p.A94S	NM_001135863.1	NP_001129335.1	Q8IXQ9	MET20_HUMAN	methyltransferase like 20	94						cytoplasm (GO:0005737)	protein methyltransferase activity (GO:0008276)			lung(2)|stomach(1)	3						TCCTTACTGGGCAATCTACTG	0.527													G|||	113	0.0225639	0.0023	0.0504	5008	,	,		19695	0.001		0.0596	False		,,,				2504	0.0143				p.A94S		Atlas-SNP	.											.	METTL20	23	.	0			c.G280T						PASS	.	G	SER/ALA,SER/ALA,SER/ALA	40,4366	43.1+/-76.7	0,40,2163	64.0	67.0	66.0		280,280,280	4.4	1.0	12	dbSNP_129	66	438,8162	133.5+/-191.0	10,418,3872	yes	missense,missense,missense	METTL20	NM_001135863.1,NM_001135864.1,NM_173802.3	99,99,99	10,458,6035	TT,TG,GG		5.093,0.9079,3.6752	probably-damaging,probably-damaging,probably-damaging	94/263,94/263,94/263	31815167	478,12528	2203	4300	6503	SO:0001583	missense	254013	exon2			TACTGGGCAATCT	BC039535	CCDS8724.1	12p11.21	2011-03-03	2011-03-03	2011-03-03	ENSG00000139160	ENSG00000139160			28739	protein-coding gene	gene with protein product		615256	"""chromosome 12 open reading frame 72"""	C12orf72			Standard	NM_173802		Approved	DKFZp451L235, MGC50559	uc001rkm.3	Q8IXQ9		ENST00000357721.3:c.280G>T	12.37:g.31815167G>T	ENSP00000350353:p.Ala94Ser	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	48	23	0.479167	NM_173802	D3DUW3	Missense_Mutation	SNP	ENST00000357721.3	37	CCDS8724.1	61	0.027930402930402932	1	0.0020325203252032522	16	0.04419889502762431	1	0.0017482517482517483	43	0.05672823218997362	G	26.6	4.751076	0.89753	0.009079	0.05093	ENSG00000139160	ENST00000412352;ENST00000395763;ENST00000538463;ENST00000357721;ENST00000538391	.	.	.	4.4	4.4	0.53042	.	0.000000	0.85682	D	0.000000	T	0.22666	0.0547	M	0.73962	2.25	0.80722	D	1	D	0.54397	0.966	P	0.49140	0.601	T	0.55964	-0.8057	9	0.37606	T	0.19	-10.4463	17.1676	0.86821	0.0:0.0:1.0:0.0	rs61736289	94	Q8IXQ9	MET20_HUMAN	S	94	.	ENSP00000350353:A94S	A	+	1	0	METTL20	31706434	1.000000	0.71417	0.999000	0.59377	0.996000	0.88848	8.907000	0.92634	2.277000	0.76020	0.561000	0.74099	GCA	G|0.968;T|0.032	0.032	strong		0.527	METTL20-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402196.1	NM_173802	
AKNAD1	254268	hgsc.bcm.edu	37	1	109363232	109363232	+	Silent	SNP	T	T	C	rs1333130	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:109363232T>C	ENST00000370001.3	-	14	2452	c.2184A>G	c.(2182-2184)aaA>aaG	p.K728K	AKNAD1_ENST00000477908.1_5'Flank	NM_152763.4	NP_689976.2	Q5T1N1	AKND1_HUMAN	AKNA domain containing 1	728						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						AACAGATCCGTTTGGGTTTTA	0.328													T|||	1935	0.386382	0.2617	0.3919	5008	,	,		5833	0.6974		0.2565	False		,,,				2504	0.364				p.K728K		Atlas-SNP	.											.	AKNAD1	83	.	0			c.A2184G						PASS	.	T		1216,3190	414.6+/-336.9	178,860,1165	89.0	93.0	92.0		2184	2.9	0.0	1	dbSNP_88	92	1983,6617	345.0+/-325.6	220,1543,2537	no	coding-synonymous	AKNAD1	NM_152763.3		398,2403,3702	CC,CT,TT		23.0581,27.5987,24.5963		728/837	109363232	3199,9807	2203	4300	6503	SO:0001819	synonymous_variant	254268	exon14			GATCCGTTTGGGT	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.2184A>G	1.37:g.109363232T>C		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	60	60	1	NM_152763	B9EK62|Q5T1N0|Q8N990|Q8NCN9	Silent	SNP	ENST00000370001.3	37	CCDS791.2																																																																																			T|0.694;C|0.306	0.306	strong		0.328	AKNAD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030923.2	NM_152763	
TTC21A	199223	hgsc.bcm.edu	37	3	39156124	39156124	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:39156124G>A	ENST00000431162.2	+	6	741	c.607G>A	c.(607-609)Gtg>Atg	p.V203M	TTC21A_ENST00000301819.6_Missense_Mutation_p.V203M|TTC21A_ENST00000440121.1_Missense_Mutation_p.V162M			Q8NDW8	TT21A_HUMAN	tetratricopeptide repeat domain 21A	203										NS(1)|breast(2)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(9)|lung(23)|ovary(1)|prostate(1)|skin(3)	50				KIRC - Kidney renal clear cell carcinoma(284;0.0588)|Kidney(284;0.0738)		CCTGGAGGTGGTGAACCAGAT	0.552																																					p.V203M		Atlas-SNP	.											.	TTC21A	96	.	0			c.G607A						PASS	.						136.0	133.0	134.0					3																	39156124		2028	4185	6213	SO:0001583	missense	199223	exon6			GAGGTGGTGAACC	AJ487015	CCDS43068.1, CCDS46800.1, CCDS43068.2	3p22.2	2014-09-04			ENSG00000168026	ENSG00000168026		"""Tetratricopeptide (TTC) repeat domain containing"""	30761	protein-coding gene	gene with protein product		611430					Standard	NM_145755		Approved	STI2	uc003cjc.2	Q8NDW8	OTTHUMG00000155973	ENST00000431162.2:c.607G>A	3.37:g.39156124G>A	ENSP00000398211:p.Val203Met	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	128	19	0.148438	NM_145755	A1L388|B4DYF6|B4DYJ3|D3YTE7|D4PHA5|Q6P5W8|Q8N7G5|Q8NA02	Missense_Mutation	SNP	ENST00000431162.2	37	CCDS46800.1	.	.	.	.	.	.	.	.	.	.	G	19.00	3.742688	0.69418	.	.	ENSG00000168026	ENST00000301819;ENST00000424305;ENST00000431162;ENST00000440121	T;T;T	0.64618	-0.11;-0.11;2.27	5.0	5.0	0.66597	Tetratricopeptide-like helical (1);	0.183014	0.35615	N	0.003092	T	0.73690	0.3619	M	0.72118	2.19	0.28282	N	0.923935	D;D;D;D;D	0.61080	0.967;0.989;0.989;0.981;0.989	P;D;D;P;D	0.63192	0.805;0.912;0.912;0.819;0.912	T	0.69439	-0.5145	10	0.54805	T	0.06	-18.6922	10.7065	0.45958	0.0894:0.0:0.9106:0.0	.	162;203;203;203;203	Q8NDW8-6;Q8NDW8-5;Q8NDW8-7;Q8NDW8;F5H6V8	.;.;.;TT21A_HUMAN;.	M	203;203;203;162	ENSP00000301819:V203M;ENSP00000398211:V203M;ENSP00000410882:V162M	ENSP00000301819:V203M	V	+	1	0	TTC21A	39131128	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	3.201000	0.51059	2.316000	0.78162	0.561000	0.74099	GTG	.	.	none		0.552	TTC21A-021	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000377829.1	NM_145755	
OR10H5	284433	hgsc.bcm.edu	37	19	15905206	15905206	+	Silent	SNP	T	T	C	rs4808380	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:15905206T>C	ENST00000308940.8	+	1	446	c.348T>C	c.(346-348)acT>acC	p.T116T		NM_001004466.1	NP_001004466.1	Q8NGA6	O10H5_HUMAN	olfactory receptor, family 10, subfamily H, member 5	116						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(1)|lung(9)|ovary(1)	20						TCCTGCTCACTGTCATGGGCT	0.642													.|||	754	0.150559	0.143	0.1167	5008	,	,		20394	0.1071		0.162	False		,,,				2504	0.2178				p.T116T		Atlas-SNP	.											.	OR10H5	49	.	0			c.T348C						PASS	.	T		636,3770		55,526,1622	146.0	121.0	130.0		348	-6.9	0.0	19	dbSNP_111	130	1451,7149		149,1153,2998	no	coding-synonymous	OR10H5	NM_001004466.1		204,1679,4620	CC,CT,TT		16.8721,14.4349,16.0464		116/316	15905206	2087,10919	2203	4300	6503	SO:0001819	synonymous_variant	284433	exon1			GCTCACTGTCATG	AC011537	CCDS32940.1	19p13.12	2013-09-24			ENSG00000172519	ENSG00000172519		"""GPCR / Class A : Olfactory receptors"""	15389	protein-coding gene	gene with protein product							Standard	NM_001004466		Approved		uc010xos.2	Q8NGA6	OTTHUMG00000182284	ENST00000308940.8:c.348T>C	19.37:g.15905206T>C		Somatic	206	0	0		WXS	Illumina HiSeq	Phase_I	146	63	0.431507	NM_001004466	Q6IFJ0|Q96R60	Silent	SNP	ENST00000308940.8	37	CCDS32940.1																																																																																			T|0.250;C|0.750	0.750	strong		0.642	OR10H5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460363.1		
CD48	962	hgsc.bcm.edu	37	1	160654786	160654786	+	Silent	SNP	G	G	A	rs1980606	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:160654786G>A	ENST00000368046.3	-	2	363	c.276C>T	c.(274-276)ggC>ggT	p.G92G	RP11-404F10.2_ENST00000443928.2_RNA|RP11-404F10.2_ENST00000598917.2_RNA|RP11-404F10.2_ENST00000588034.1_RNA|CD48_ENST00000368045.3_Silent_p.G92G	NM_001778.3	NP_001769.2	P09326	CD48_HUMAN	CD48 molecule	92	Ig-like C2-type 1.				blood coagulation (GO:0007596)|defense response (GO:0006952)|leukocyte migration (GO:0050900)|mast cell activation (GO:0045576)|signal transduction (GO:0007165)|T cell activation (GO:0042110)	anchored component of plasma membrane (GO:0046658)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	antigen binding (GO:0003823)|receptor activity (GO:0004872)			breast(2)|endometrium(1)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)|stomach(1)	10	all_cancers(52;2.18e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.0175)			TGTACAGTGCGCCACTCTGAG	0.423													A|||	1174	0.234425	0.3253	0.2637	5008	,	,		21242	0.1448		0.1859	False		,,,				2504	0.2331				p.G92G		Atlas-SNP	.											.	CD48	31	.	0			c.C276T						PASS	.	A		1309,3097	697.3+/-406.2	195,919,1089	164.0	163.0	163.0		276	-7.2	0.0	1	dbSNP_92	163	1915,6685	726.7+/-406.6	202,1511,2587	no	coding-synonymous	CD48	NM_001778.2		397,2430,3676	AA,AG,GG		22.2674,29.7095,24.7886		92/244	160654786	3224,9782	2203	4300	6503	SO:0001819	synonymous_variant	962	exon2			CAGTGCGCCACTC	BC016182	CCDS1208.1, CCDS72955.1	1q21.3-q22	2013-01-29	2006-03-31		ENSG00000117091	ENSG00000117091		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	1683	protein-coding gene	gene with protein product		109530	"""CD48 antigen (B-cell membrane protein)"", ""CD48 molecule """	BCM1		2828034	Standard	NM_001256030		Approved	BLAST, mCD48, hCD48, SLAMF2	uc001fwo.2	P09326	OTTHUMG00000024009	ENST00000368046.3:c.276C>T	1.37:g.160654786G>A		Somatic	233	0	0		WXS	Illumina HiSeq	Phase_I	146	144	0.986301	NM_001256030	Q5U055|Q8MGR0	Silent	SNP	ENST00000368046.3	37	CCDS1208.1																																																																																			G|0.772;A|0.228	0.228	strong		0.423	CD48-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060471.1	NM_001778	
PHF2	5253	hgsc.bcm.edu	37	9	96415482	96415482	+	Silent	SNP	A	A	T	rs56134753	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:96415482A>T	ENST00000359246.4	+	6	991	c.624A>T	c.(622-624)ccA>ccT	p.P208P	PHF2_ENST00000375376.4_Intron	NM_005392.3	NP_005383.3	O75151	PHF2_HUMAN	PHD finger protein 2	208	JmjC. {ECO:0000255|PROSITE- ProRule:PRU00538}.				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)		TCGTGGAGCCACCTGACATTG	0.502													A|||	102	0.0203674	0.0008	0.0216	5008	,	,		20636	0.0456		0.0139	False		,,,				2504	0.0266				p.P208P		Atlas-SNP	.											.	PHF2	113	.	0			c.A624T						PASS	.	A		14,4392	21.2+/-45.6	0,14,2189	89.0	74.0	79.0		624	-9.4	0.0	9	dbSNP_129	79	156,8444	76.0+/-138.7	4,148,4148	no	coding-synonymous	PHF2	NM_005392.3		4,162,6337	TT,TA,AA		1.814,0.3177,1.3071		208/1097	96415482	170,12836	2203	4300	6503	SO:0001819	synonymous_variant	5253	exon6			GGAGCCACCTGAC	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.624A>T	9.37:g.96415482A>T		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	54	24	0.444444	NM_005392	Q4VXG0|Q8N3K2|Q9Y6N4	Silent	SNP	ENST00000359246.4	37	CCDS35069.1																																																																																			A|0.985;T|0.015	0.015	strong		0.502	PHF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053162.1	NM_005392	
RABEP1	9135	hgsc.bcm.edu	37	17	5284719	5284719	+	Silent	SNP	T	T	C	rs1065482	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:5284719T>C	ENST00000546142.2	+	17	2593	c.2406T>C	c.(2404-2406)aaT>aaC	p.N802N	RABEP1_ENST00000537505.1_Silent_p.N759N|RABEP1_ENST00000408982.2_Silent_p.N769N|RABEP1_ENST00000341923.6_Silent_p.N769N|NUP88_ENST00000573169.1_Intron|RABEP1_ENST00000262477.6_Silent_p.N802N			Q15276	RABE1_HUMAN	rabaptin, RAB GTPase binding effector protein 1	802					apoptotic process (GO:0006915)|endocytosis (GO:0006897)|membrane fusion (GO:0061025)|protein transport (GO:0015031)	early endosome (GO:0005769)|endocytic vesicle (GO:0030139)|endosome (GO:0005768)|intracellular membrane-bounded organelle (GO:0043231)	GTPase activator activity (GO:0005096)|protein homodimerization activity (GO:0042803)			NS(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|ovary(2)|stomach(1)|upper_aerodigestive_tract(1)	8						AAGAGAAGAATAAAGCTCAGA	0.393													C|||	2765	0.552117	0.3964	0.4251	5008	,	,		21936	0.8254		0.4394	False		,,,				2504	0.6871				p.N802N		Atlas-SNP	.											.	RABEP1	59	.	0			c.T2406C						PASS	.	C	,	1531,2177		327,877,650	86.0	85.0	85.0		2307,2406	1.4	1.0	17	dbSNP_86	85	3199,4993		619,1961,1516	no	coding-synonymous,coding-synonymous	RABEP1	NM_001083585.1,NM_004703.4	,	946,2838,2166	CC,CT,TT		39.0503,41.2891,39.7479	,	769/830,802/863	5284719	4730,7170	1854	4096	5950	SO:0001819	synonymous_variant	9135	exon17			GAAGAATAAAGCT	AF098638	CCDS42243.1, CCDS45592.1	17p13.2	2008-02-05				ENSG00000029725			17677	protein-coding gene	gene with protein product		603616				8521472	Standard	NM_001291582		Approved	neurocrescin, RAB5EP, RABPT5, rabaptin-5	uc002gbm.4	Q15276		ENST00000546142.2:c.2406T>C	17.37:g.5284719T>C		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	69	35	0.507246	NM_004703	B2RAG7|O95369|Q8IVX3	Silent	SNP	ENST00000546142.2	37	CCDS45592.1																																																																																			T|0.500;C|0.500	0.500	strong		0.393	RABEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439349.1	NM_004703	
DSPP	1834	hgsc.bcm.edu	37	4	88536457	88536457	+	Silent	SNP	T	T	C	rs141186173|rs111205177|rs199994008	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:88536457T>C	ENST00000282478.7	+	4	2676	c.2643T>C	c.(2641-2643)gaT>gaC	p.D881D	RP11-742B18.1_ENST00000506480.1_RNA|DSPP_ENST00000399271.1_Silent_p.D881D			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	881	Asp/Ser-rich.				biomineral tissue development (GO:0031214)|cellular response to cell-matrix adhesion (GO:0071460)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)	p.D881_S882insSSD(1)		breast(2)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|skin(3)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Hepatocellular(203;0.114)|all_hematologic(202;0.236)		OV - Ovarian serous cystadenocarcinoma(123;0.000508)		acagcagtgatagcagtgaca	0.498																																					p.D881D		Atlas-SNP	.											.	DSPP	174	.	1	Insertion - In frame(1)	ovary(1)	c.T2643C						PASS	.						73.0	87.0	82.0					4																	88536457		1618	2922	4540	SO:0001819	synonymous_variant	1834	exon5			CAGTGATAGCAGT	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.2643T>C	4.37:g.88536457T>C		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	66	18	0.272727	NM_014208	A8MUI0|O95815	Silent	SNP	ENST00000282478.7	37	CCDS43248.1																																																																																			.	.	weak		0.498	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208	
SRPX	8406	hgsc.bcm.edu	37	X	38009121	38009121	+	Missense_Mutation	SNP	G	G	A	rs35318931	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:38009121G>A	ENST00000378533.3	-	10	1344	c.1238C>T	c.(1237-1239)tCc>tTc	p.S413F	SRPX_ENST00000343800.6_Missense_Mutation_p.S400F|SRPX_ENST00000479015.1_5'UTR|TM4SF2_ENST00000465127.1_Intron|SRPX_ENST00000544439.1_Missense_Mutation_p.S393F|SRPX_ENST00000538295.1_Silent_p.L372L|SRPX_ENST00000432886.2_Missense_Mutation_p.S354F	NM_006307.4	NP_006298.1	P78539	SRPX_HUMAN	sushi-repeat containing protein, X-linked	413			S -> F (in dbSNP:rs35318931). {ECO:0000269|PubMed:8634709}.		autophagy (GO:0006914)|cell adhesion (GO:0007155)|negative regulation of cell proliferation involved in contact inhibition (GO:0060244)|phagolysosome assembly (GO:0001845)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|response to endoplasmic reticulum stress (GO:0034976)	autophagic vacuole (GO:0005776)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)				autonomic_ganglia(1)|breast(2)|endometrium(5)|large_intestine(5)|lung(10)|prostate(2)	25						CATACTGAAGGAGTAGAGTGG	0.517													G|||	81	0.021457	0.0038	0.0216	3775	,	,		15156	0.0		0.0537	False		,,,				2504	0.0072				p.S413F		Atlas-SNP	.											.	SRPX	53	.	0			c.C1238T						PASS	.	G	PHE/SER,PHE/SER,,PHE/SER	45,3788		0,37,8,1594,563	113.0	70.0	84.0		1178,1061,1116,1238	5.2	1.0	X	dbSNP_126	84	531,6197		13,348,157,2067,1715	yes	missense,missense,coding-synonymous,missense	SRPX	NM_001170750.1,NM_001170751.1,NM_001170752.1,NM_006307.4	155,155,,155	13,385,165,3661,2278	AA,AG,A,GG,G		7.8924,1.174,5.454	possibly-damaging,possibly-damaging,,possibly-damaging	393/445,354/406,372/380,413/465	38009121	576,9985	2202	4300	6502	SO:0001583	missense	8406	exon10			CTGAAGGAGTAGA	U78093	CCDS14245.1, CCDS55400.1, CCDS55401.1, CCDS55402.1	Xp21.1	2011-01-25	2011-01-25		ENSG00000101955	ENSG00000101955			11309	protein-coding gene	gene with protein product		300187	"""sushi-repeat-containing protein, X chromosome"", ""sushi-repeat-containing protein, X-linked"""			8634708, 8634709	Standard	NM_006307		Approved	ETX1	uc004ddy.2	P78539	OTTHUMG00000021362	ENST00000378533.3:c.1238C>T	X.37:g.38009121G>A	ENSP00000367794:p.Ser413Phe	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	73	72	0.986301	NM_006307	A8K065|B3KWP8|B4DDB8|B4DQH5|F5H4D7|G3V1L0|Q4VX66|Q99652|Q99913	Missense_Mutation	SNP	ENST00000378533.3	37	CCDS14245.1	60	0.03616636528028933	4	0.008130081300813009	8	0.02247191011235955	0	0.0	23	0.03221288515406162	G	15.46	2.838926	0.51057	0.01174	0.078924	ENSG00000101955	ENST00000544439;ENST00000432886;ENST00000378533;ENST00000343800	T;T;T;T	0.46451	0.87;0.87;0.87;0.87	6.03	5.17	0.71159	.	0.279150	0.41500	D	0.000872	T	0.03136	0.0092	L	0.40543	1.245	0.09310	P	0.9999999999997803	D;P;P	0.60575	0.988;0.925;0.939	P;P;P	0.57960	0.83;0.568;0.694	T	0.30149	-0.9988	9	0.15952	T	0.53	-20.0451	7.6485	0.28334	0.0825:0.0:0.6356:0.2818	rs35318931	354;393;413	B4DQH5;G3V1L0;P78539	.;.;SRPX_HUMAN	F	393;354;413;400	ENSP00000440758:S393F;ENSP00000411165:S354F;ENSP00000367794:S413F;ENSP00000339211:S400F	ENSP00000339211:S400F	S	-	2	0	SRPX	37894065	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.242000	0.51384	1.301000	0.44836	0.600000	0.82982	TCC	G|0.935;0|0.016	.	strong		0.517	SRPX-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056243.1	NM_006307	
PTPRM	5797	hgsc.bcm.edu	37	18	8253407	8253407	+	Missense_Mutation	SNP	T	T	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:8253407T>A	ENST00000332175.8	+	17	3747	c.2710T>A	c.(2710-2712)Tac>Aac	p.Y904N	PTPRM_ENST00000580170.1_Missense_Mutation_p.Y917N|PTPRM_ENST00000400060.4_Missense_Mutation_p.Y918N|PTPRM_ENST00000400053.4_Missense_Mutation_p.Y842N|PTPRM_ENST00000444013.1_Missense_Mutation_p.Y691N	NM_002845.3	NP_002836.3	P28827	PTPRM_HUMAN	protein tyrosine phosphatase, receptor type, M	904	Tyrosine-protein phosphatase 1. {ECO:0000255|PROSITE-ProRule:PRU00160}.				homophilic cell adhesion (GO:0007156)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|neuron projection development (GO:0031175)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of vasodilation (GO:0045909)|protein dephosphorylation (GO:0006470)|response to drug (GO:0042493)|retina layer formation (GO:0010842)|retinal ganglion cell axon guidance (GO:0031290)|signal transduction (GO:0007165)	cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|perinuclear region of cytoplasm (GO:0048471)	cadherin binding (GO:0045296)|identical protein binding (GO:0042802)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(3)|central_nervous_system(1)|cervix(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(32)|lung(25)|ovary(2)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	90		Colorectal(10;0.234)				CAAGGAGGAATACGAGGTGAG	0.557																																					p.Y917N		Atlas-SNP	.											.	PTPRM	185	.	0			c.T2749A						PASS	.						43.0	30.0	34.0					18																	8253407		2203	4300	6503	SO:0001583	missense	5797	exon19			GAGGAATACGAGG	X58288	CCDS11840.1, CCDS58613.1	18p11.2	2013-02-11			ENSG00000173482	ENSG00000173482		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	9675	protein-coding gene	gene with protein product		176888		PTPRL1		1655529, 8404049	Standard	NM_002845		Approved	RPTPU, hR-PTPu	uc010dkv.3	P28827	OTTHUMG00000131575	ENST00000332175.8:c.2710T>A	18.37:g.8253407T>A	ENSP00000331418:p.Tyr904Asn	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	86	19	0.22093	NM_001105244	A7MBN1|D3DUH8|J3QL11	Missense_Mutation	SNP	ENST00000332175.8	37	CCDS11840.1	.	.	.	.	.	.	.	.	.	.	T	22.1	4.243448	0.79912	.	.	ENSG00000173482	ENST00000332175;ENST00000400060;ENST00000400053;ENST00000444013	T;T;T;T	0.34072	1.38;1.38;1.38;1.38	5.93	5.93	0.95920	Protein-tyrosine phosphatase, receptor/non-receptor type (2);	0.000000	0.85682	D	0.000000	T	0.72170	0.3427	H	0.95679	3.705	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.85130	0.992;0.997;0.997	T	0.81466	-0.0920	10	0.87932	D	0	.	16.3695	0.83350	0.0:0.0:0.0:1.0	.	691;917;904	E7EVX9;A7MBN1;P28827	.;.;PTPRM_HUMAN	N	904;918;842;691	ENSP00000331418:Y904N;ENSP00000382933:Y918N;ENSP00000382927:Y842N;ENSP00000387608:Y691N	ENSP00000331418:Y904N	Y	+	1	0	PTPRM	8243407	1.000000	0.71417	0.693000	0.30195	0.951000	0.60555	8.033000	0.88852	2.261000	0.74972	0.459000	0.35465	TAC	.	.	none		0.557	PTPRM-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254456.1		
LAMB3	3914	hgsc.bcm.edu	37	1	209796329	209796329	+	Missense_Mutation	SNP	T	T	A	rs12748250	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:209796329T>A	ENST00000356082.4	-	17	2688	c.2554A>T	c.(2554-2556)Atg>Ttg	p.M852L	MIR4260_ENST00000583107.1_RNA|LAMB3_ENST00000391911.1_Missense_Mutation_p.M852L|LAMB3_ENST00000367030.3_Missense_Mutation_p.M852L	NM_000228.2	NP_000219.2	Q13751	LAMB3_HUMAN	laminin, beta 3	852	Domain I.		M -> L (in dbSNP:rs12748250). {ECO:0000269|Ref.6}.		brown fat cell differentiation (GO:0050873)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	extracellular region (GO:0005576)|laminin-5 complex (GO:0005610)	structural molecule activity (GO:0005198)			NS(1)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(11)|lung(13)|ovary(1)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	45				OV - Ovarian serous cystadenocarcinoma(81;0.0519)		GCACTTACCATCTGCCTGGTC	0.632													T|||	513	0.102436	0.0439	0.0865	5008	,	,		15100	0.001		0.159	False		,,,				2504	0.2393				p.M852L		Atlas-SNP	.											.	LAMB3	136	.	0			c.A2554T						PASS	.	T	LEU/MET,LEU/MET,LEU/MET	236,4168		4,228,1970	78.0	91.0	86.0		2554,2554,2554	5.2	1.0	1	dbSNP_121	86	1313,7283		104,1105,3089	yes	missense,missense,missense	LAMB3	NM_000228.2,NM_001017402.1,NM_001127641.1	15,15,15	108,1333,5059	AA,AT,TT		15.2745,5.3588,11.9154	benign,benign,benign	852/1173,852/1173,852/1173	209796329	1549,11451	2202	4298	6500	SO:0001583	missense	3914	exon17			TTACCATCTGCCT	D37766	CCDS1487.1	1q32	2013-03-01	2002-08-29		ENSG00000196878	ENSG00000196878		"""Laminins"""	6490	protein-coding gene	gene with protein product		150310	"""laminin, beta 3 (nicein (125kD), kalinin (140kD), BM600 (125kD))"""	LAMNB1		8088808, 7774918	Standard	NM_001127641		Approved	nicein-125kDa, kalinin-140kDa, BM600-125kDa	uc001hhh.3	Q13751	OTTHUMG00000036360	ENST00000356082.4:c.2554A>T	1.37:g.209796329T>A	ENSP00000348384:p.Met852Leu	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	82	37	0.451219	NM_000228	D3DT88|O14947|Q14733|Q9UJK4|Q9UJL1	Missense_Mutation	SNP	ENST00000356082.4	37	CCDS1487.1	174	0.07967032967032966	20	0.04065040650406504	31	0.0856353591160221	1	0.0017482517482517483	122	0.16094986807387862	T	11.55	1.673222	0.29693	0.053588	0.152745	ENSG00000196878	ENST00000391911;ENST00000356082;ENST00000367030	T;T;T	0.19394	2.15;2.15;2.15	5.21	5.21	0.72293	.	0.142994	0.64402	D	0.000011	T	0.00073	0.0002	M	0.61703	1.905	0.32625	P	0.522823	B	0.18610	0.029	B	0.17433	0.018	T	0.10064	-1.0646	9	0.28530	T	0.3	.	11.6693	0.51391	0.0:0.0:0.1479:0.8521	rs12748250;rs17388506	852	Q13751	LAMB3_HUMAN	L	852	ENSP00000375778:M852L;ENSP00000348384:M852L;ENSP00000355997:M852L	ENSP00000348384:M852L	M	-	1	0	LAMB3	207862952	1.000000	0.71417	1.000000	0.80357	0.600000	0.36913	1.767000	0.38501	1.992000	0.58205	0.374000	0.22700	ATG	T|0.890;A|0.110	0.110	strong		0.632	LAMB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088525.2	NM_000228	
CYP2B6	1555	hgsc.bcm.edu	37	19	41512841	41512841	+	Missense_Mutation	SNP	G	G	T	rs3745274	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:41512841G>T	ENST00000324071.4	+	4	523	c.516G>T	c.(514-516)caG>caT	p.Q172H	CYP2B6_ENST00000593831.1_Intron|CYP2B6_ENST00000330446.5_Intron|CYP2B6_ENST00000598834.1_3'UTR	NM_000767.4	NP_000758.1	P20813	CP2B6_HUMAN	cytochrome P450, family 2, subfamily B, polypeptide 6	172			Q -> H (in allele CYP2B6*6, allele CYP2B6*7, allele CYP2B6*9 and allele CYP2B6*13; dbSNP:rs3745274). {ECO:0000269|PubMed:11243870, ECO:0000269|PubMed:11470993, ECO:0000269|PubMed:12721789, ECO:0000269|PubMed:14551287, ECO:0000269|PubMed:15469410, ECO:0000269|Ref.2, ECO:0000269|Ref.4}.		cellular ketone metabolic process (GO:0042180)|drug metabolic process (GO:0017144)|exogenous drug catabolic process (GO:0042738)|oxidation-reduction process (GO:0055114)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen (GO:0016712)			NS(1)|breast(1)|endometrium(5)|kidney(1)|lung(14)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	28			LUSC - Lung squamous cell carcinoma(20;0.00322)		Amitriptyline(DB00321)|Amlodipine(DB00381)|Amprenavir(DB00701)|Antipyrine(DB01435)|Artemether(DB06697)|Atorvastatin(DB01076)|Azelastine(DB00972)|Benzphetamine(DB00865)|Benzyl alcohol(DB06770)|Bifonazole(DB04794)|Brompheniramine(DB00835)|Bupropion(DB01156)|Carbamazepine(DB00564)|Carbinoxamine(DB00748)|Cholecalciferol(DB00169)|Cinnarizine(DB00568)|Cisapride(DB00604)|Cisplatin(DB00515)|Citalopram(DB00215)|Clobazam(DB00349)|Clofibrate(DB00636)|Clopidogrel(DB00758)|Clotiazepam(DB01559)|Clotrimazole(DB00257)|Colchicine(DB01394)|Cyclophosphamide(DB00531)|Desipramine(DB01151)|Dexamethasone(DB01234)|Dextromethorphan(DB00514)|Diazepam(DB00829)|Diclofenac(DB00586)|Diphenhydramine(DB01075)|Domperidone(DB01184)|Doxorubicin(DB00997)|Efavirenz(DB00625)|Enzalutamide(DB08899)|Epinastine(DB00751)|Erythromycin(DB00199)|Estrone(DB00655)|Ethanol(DB00898)|Ethylmorphine(DB01466)|Flunarizine(DB04841)|Flunitrazepam(DB01544)|Fluoxetine(DB00472)|Fluvastatin(DB01095)|Fluvoxamine(DB00176)|Fosphenytoin(DB01320)|Halothane(DB01159)|Ifosfamide(DB01181)|Imipramine(DB00458)|Irinotecan(DB00762)|Isoflurane(DB00753)|Itraconazole(DB01167)|Ketamine(DB01221)|Ketobemidone(DB06738)|Ketoconazole(DB01026)|Lidocaine(DB00281)|Loperamide(DB00836)|Lopinavir(DB01601)|Lorcaserin(DB04871)|Malathion(DB00772)|Memantine(DB01043)|Methadone(DB00333)|Methimazole(DB00763)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyltestosterone(DB06710)|Mexiletine(DB00379)|Mianserin(DB06148)|Miconazole(DB01110)|Midazolam(DB00683)|Modafinil(DB00745)|Nelfinavir(DB00220)|Nevirapine(DB00238)|Nicardipine(DB00622)|Nicotine(DB00184)|Nifedipine(DB01115)|Nilotinib(DB04868)|Nitric Oxide(DB00435)|Orphenadrine(DB01173)|Ospemifene(DB04938)|Paroxetine(DB00715)|Perhexiline(DB01074)|Permethrin(DB04930)|Perphenazine(DB00850)|Pethidine(DB00454)|Phenobarbital(DB01174)|Phenytoin(DB00252)|Prasugrel(DB06209)|Primidone(DB00794)|Promethazine(DB01069)|Propofol(DB00818)|Quinidine(DB00908)|Raloxifene(DB00481)|Regorafenib(DB08896)|Rifampicin(DB01045)|Rilpivirine(DB08864)|Ritonavir(DB00503)|Ropivacaine(DB00296)|Roxithromycin(DB00778)|Selegiline(DB01037)|Sertraline(DB01104)|Sevoflurane(DB01236)|Simvastatin(DB00641)|Sorafenib(DB00398)|Sulfaphenazole(DB06729)|Sulfinpyrazone(DB01138)|Tamoxifen(DB00675)|Temazepam(DB00231)|Testosterone(DB00624)|Thiotepa(DB04572)|Ticlopidine(DB00208)|Tramadol(DB00193)|Tretinoin(DB00755)|Valproic Acid(DB00313)|Venlafaxine(DB00285)|Verapamil(DB00661)	TCCTCTTCCAGTCCATTACCG	0.507													g|||	1581	0.315695	0.3744	0.3732	5008	,	,		19726	0.2153		0.2356	False		,,,				2504	0.3814				p.Q172H		Atlas-SNP	.											.	CYP2B6	79	.	0			c.G516T	GRCh37	CS080663	CYP2B6	S	rs3745274	PASS	.	G	HIS/GLN	1629,2777		311,1007,885	87.0	77.0	81.0		516	-9.0	0.0	19	dbSNP_107	81	2148,6452		267,1614,2419	yes	missense	CYP2B6	NM_000767.4	24	578,2621,3304	TT,TG,GG		24.9767,36.9723,29.0404	benign	172/492	41512841	3777,9229	2203	4300	6503	SO:0001583	missense	1555	exon4			CTTCCAGTCCATT	AF182277	CCDS12570.1	19q13.2	2013-07-25	2003-01-14		ENSG00000197408	ENSG00000197408		"""Cytochrome P450s"""	2615	protein-coding gene	gene with protein product		123930	"""cytochrome P450, subfamily IIB (phenobarbital-inducible), polypeptide 6"", ""cytochrome P450, family 2, subfamily B"", ""cytochrome P450, subfamily IIB (phenobarbital-inducible)"""	CYP2B		7668294, 15128046	Standard	NM_000767		Approved	CPB6, CYPIIB6	uc002opr.1	P20813	OTTHUMG00000182714	ENST00000324071.4:c.516G>T	19.37:g.41512841G>T	ENSP00000324648:p.Gln172His	Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	149	76	0.510067	NM_000767	B4DWP3|Q2V565|Q9UK46	Missense_Mutation	SNP	ENST00000324071.4	37	CCDS12570.1	583	0.26694139194139194	174	0.35365853658536583	131	0.36187845303867405	102	0.17832167832167833	176	0.23218997361477572	.	7.755	0.704176	0.15172	0.369723	0.249767	ENSG00000197408	ENST00000324071	T	0.69561	-0.41	4.48	-8.96	0.00761	.	0.221834	0.44285	N	0.000465	T	0.00012	0.0000	N	0.17838	0.53	0.80722	P	0.0	B	0.06786	0.001	B	0.10450	0.005	T	0.18493	-1.0335	9	0.45353	T	0.12	.	1.071	0.01621	0.199:0.1663:0.3402:0.2946	rs3745274;rs57685583;rs3745274	172	P20813	CP2B6_HUMAN	H	172	ENSP00000324648:Q172H	ENSP00000324648:Q172H	Q	+	3	2	CYP2B6	46204681	0.000000	0.05858	0.000000	0.03702	0.012000	0.07955	-1.320000	0.02700	-1.641000	0.01523	-1.412000	0.01120	CAG	.	.	weak		0.507	CYP2B6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463260.1	NM_000767	
TH	7054	hgsc.bcm.edu	37	11	2188238	2188238	+	Silent	SNP	C	C	T	rs6357	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:2188238C>T	ENST00000381178.1	-	8	831	c.813G>A	c.(811-813)aaG>aaA	p.K271K	TH_ENST00000352909.3_Silent_p.K240K|TH_ENST00000333684.5_Intron|TH_ENST00000381175.1_Silent_p.K267K	NM_199292.2	NP_954986.2	P07101	TY3H_HUMAN	tyrosine hydroxylase	271					anatomical structure morphogenesis (GO:0009653)|catecholamine biosynthetic process (GO:0042423)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to drug (GO:0035690)|cellular response to glucose stimulus (GO:0071333)|cellular response to growth factor stimulus (GO:0071363)|cellular response to manganese ion (GO:0071287)|cellular response to nicotine (GO:0071316)|cerebral cortex development (GO:0021987)|circadian sleep/wake cycle (GO:0042745)|dopamine biosynthetic process (GO:0042416)|dopamine biosynthetic process from tyrosine (GO:0006585)|eating behavior (GO:0042755)|embryonic camera-type eye morphogenesis (GO:0048596)|epinephrine biosynthetic process (GO:0042418)|eye photoreceptor cell development (GO:0042462)|fatty acid metabolic process (GO:0006631)|glycoside metabolic process (GO:0016137)|heart development (GO:0007507)|heart morphogenesis (GO:0003007)|isoquinoline alkaloid metabolic process (GO:0033076)|learning (GO:0007612)|locomotory behavior (GO:0007626)|mating behavior (GO:0007617)|memory (GO:0007613)|multicellular organismal aging (GO:0010259)|neurotransmitter biosynthetic process (GO:0042136)|norepinephrine biosynthetic process (GO:0042421)|organ morphogenesis (GO:0009887)|phthalate metabolic process (GO:0018963)|phytoalexin metabolic process (GO:0052314)|pigmentation (GO:0043473)|regulation of heart contraction (GO:0008016)|response to activity (GO:0014823)|response to amphetamine (GO:0001975)|response to corticosterone (GO:0051412)|response to electrical stimulus (GO:0051602)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to ether (GO:0045472)|response to herbicide (GO:0009635)|response to hypoxia (GO:0001666)|response to light stimulus (GO:0009416)|response to lipopolysaccharide (GO:0032496)|response to nutrient levels (GO:0031667)|response to peptide hormone (GO:0043434)|response to pyrethroid (GO:0046684)|response to salt stress (GO:0009651)|response to water deprivation (GO:0009414)|response to zinc ion (GO:0010043)|sensory perception of sound (GO:0007605)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|sphingolipid metabolic process (GO:0006665)|synaptic transmission, dopaminergic (GO:0001963)|synaptic vesicle amine transport (GO:0015842)|terpene metabolic process (GO:0042214)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendrite (GO:0030425)|melanosome membrane (GO:0033162)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|nucleus (GO:0005634)|perikaryon (GO:0043204)|smooth endoplasmic reticulum (GO:0005790)|synaptic vesicle (GO:0008021)|terminal bouton (GO:0043195)	amino acid binding (GO:0016597)|dopamine binding (GO:0035240)|enzyme binding (GO:0019899)|ferric iron binding (GO:0008199)|ferrous iron binding (GO:0008198)|oxygen binding (GO:0019825)|tetrahydrobiopterin binding (GO:0034617)|tyrosine 3-monooxygenase activity (GO:0004511)			NS(1)|endometrium(1)|large_intestine(1)|lung(7)|skin(1)	11		all_epithelial(84;1.46e-23)|Lung NSC(207;4.44e-11)|all_lung(207;1.11e-09)|Ovarian(85;1.78e-06)|Breast(177;1.78e-05)|Medulloblastoma(188;0.0208)|all_neural(188;0.0416)	Colorectal(5;0.00245)|COAD - Colon adenocarcinoma(6;0.0239)	BRCA - Breast invasive adenocarcinoma(625;8.45e-09)|Lung(200;0.000152)|LUSC - Lung squamous cell carcinoma(625;0.00154)	L-Phenylalanine(DB00120)|L-Tyrosine(DB00135)|Metyrosine(DB00765)|Tetrahydrobiopterin(DB00360)	CGTAGAGGCCCTTCAGCGTGG	0.662													C|||	774	0.154553	0.1165	0.1931	5008	,	,		14280	0.0486		0.3032	False		,,,				2504	0.135				p.K271K		Atlas-SNP	.											.	TH	43	.	0			c.G813A						PASS	.	C	,,	547,3807		33,481,1663	19.0	20.0	20.0		720,813,801	2.2	0.1	11	dbSNP_52	20	2647,5923		433,1781,2071	yes	coding-synonymous,coding-synonymous,coding-synonymous	TH	NM_000360.3,NM_199292.2,NM_199293.2	,,	466,2262,3734	TT,TC,CC		30.8868,12.5632,24.7137	,,	240/498,271/529,267/525	2188238	3194,9730	2177	4285	6462	SO:0001819	synonymous_variant	7054	exon8			GAGGCCCTTCAGC	X05290	CCDS7730.1, CCDS7731.1, CCDS31338.1	11p15.5	2013-06-03			ENSG00000180176	ENSG00000180176	1.14.16.2		11782	protein-coding gene	gene with protein product	"""tyrosine 3-monooxygenase"""	191290					Standard	NM_199292		Approved	DYT5b	uc001lvq.3	P07101	OTTHUMG00000009559	ENST00000381178.1:c.813G>A	11.37:g.2188238C>T		Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	147	21	0.142857	NM_199292	B7ZL70|B7ZL73|Q0PWM2|Q0PWM3|Q15585|Q15588|Q15589|Q2M3B4	Silent	SNP	ENST00000381178.1	37	CCDS7731.1																																																																																			C|0.798;T|0.202	0.202	strong		0.662	TH-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000026597.1	NM_000360	
C2orf61	285051	hgsc.bcm.edu	37	2	47357129	47357129	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:47357129C>T	ENST00000445927.2	-	5	596	c.470G>A	c.(469-471)tGt>tAt	p.C157Y	RP11-761B3.1_ENST00000422269.1_3'UTR|C2orf61_ENST00000294947.2_Missense_Mutation_p.C157Y	NM_001163561.1	NP_001157033.1	Q8N801	CB061_HUMAN	chromosome 2 open reading frame 61	157										endometrium(1)|kidney(1)|lung(2)	4		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)	Lung(47;0.0792)|LUSC - Lung squamous cell carcinoma(58;0.114)			GCGAAATACACAGCTCCTATA	0.259																																					p.C157Y		Atlas-SNP	.											.	C2orf61	31	.	0			c.G470A						PASS	.						77.0	81.0	80.0					2																	47357129		2203	4300	6503	SO:0001583	missense	285051	exon5			AATACACAGCTCC	AK097491	CCDS1831.1, CCDS54356.1	2p21	2008-02-05			ENSG00000239605	ENSG00000239605			26850	protein-coding gene	gene with protein product							Standard	NM_173649		Approved	FLJ40172	uc010yog.2	Q8N801	OTTHUMG00000128851	ENST00000445927.2:c.470G>A	2.37:g.47357129C>T	ENSP00000408527:p.Cys157Tyr	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	186	27	0.145161	NM_173649	H7C2Z2	Missense_Mutation	SNP	ENST00000445927.2	37	CCDS54356.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	7.371|7.371	0.626725|0.626725	0.14257|0.14257	.|.	.|.	ENSG00000239605|ENSG00000239605	ENST00000445927;ENST00000294947|ENST00000449846	T;T|.	0.29397|.	1.57;1.6|.	5.07|5.07	0.0874|0.0874	0.14450|0.14450	.|.	0.377447|.	0.22845|.	N|.	0.054930|.	T|T	0.16171|0.16171	0.0389|0.0389	N|N	0.14661|0.14661	0.345|0.345	0.09310|0.09310	N|N	0.999995|0.999995	B|.	0.02656|.	0.0|.	B|.	0.01281|.	0.0|.	T|T	0.21552|0.21552	-1.0242|-1.0242	10|5	0.02654|.	T|.	1|.	-5.7694|-5.7694	0.8202|0.8202	0.01110|0.01110	0.4569:0.1806:0.1051:0.2573|0.4569:0.1806:0.1051:0.2573	.|.	157|.	Q8N801|.	CB061_HUMAN|.	Y|M	157|37	ENSP00000408527:C157Y;ENSP00000294947:C157Y|.	ENSP00000294947:C157Y|.	C|V	-|-	2|1	0|0	C2orf61|C2orf61	47210633|47210633	0.159000|0.159000	0.22864|0.22864	0.705000|0.705000	0.30386|0.30386	0.479000|0.479000	0.33129|0.33129	0.539000|0.539000	0.23175|0.23175	0.794000|0.794000	0.33899|0.33899	-0.521000|-0.521000	0.04368|0.04368	TGT|GTG	.	.	none		0.259	C2orf61-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_173649	
MANEA	79694	hgsc.bcm.edu	37	6	96034560	96034560	+	Missense_Mutation	SNP	C	C	T	rs62417812	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:96034560C>T	ENST00000358812.4	+	2	379	c.245C>T	c.(244-246)aCt>aTt	p.T82I	MANEA_ENST00000369293.1_Missense_Mutation_p.T82I	NM_024641.3	NP_078917.2	Q5SRI9	MANEA_HUMAN	mannosidase, endo-alpha	82	Catalytic. {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)		GTTGAAATCACTATGAAACCT	0.328													C|||	251	0.0501198	0.0605	0.0346	5008	,	,		17245	0.003		0.1103	False		,,,				2504	0.0337				p.T82I		Atlas-SNP	.											.	MANEA	58	.	0			c.C245T						PASS	.	C	ILE/THR	314,4092	164.0+/-195.7	13,288,1902	97.0	100.0	99.0		245	2.9	0.2	6	dbSNP_129	99	984,7616	210.3+/-251.2	68,848,3384	yes	missense	MANEA	NM_024641.3	89	81,1136,5286	TT,TC,CC		11.4419,7.1266,9.98	benign	82/463	96034560	1298,11708	2203	4300	6503	SO:0001583	missense	79694	exon2			AAATCACTATGAA	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.245C>T	6.37:g.96034560C>T	ENSP00000351669:p.Thr82Ile	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	62	25	0.403226	NM_024641	A6H8M6|Q5SRJ0|Q6MZV0|Q70JE9|Q7Z3V7|Q8WWX5|Q9H9D2	Missense_Mutation	SNP	ENST00000358812.4	37	CCDS5032.1	136	0.06227106227106227	27	0.054878048780487805	12	0.03314917127071823	2	0.0034965034965034965	95	0.12532981530343007	C	10.52	1.372093	0.24857	0.071266	0.114419	ENSG00000172469	ENST00000358812;ENST00000369293;ENST00000542500	.	.	.	5.82	2.87	0.33458	.	0.440545	0.27563	N	0.018819	T	0.29524	0.0736	M	0.67953	2.075	0.80722	P	0.0	B;B	0.24823	0.091;0.112	B;B	0.23716	0.022;0.048	T	0.13926	-1.0491	8	0.34782	T	0.22	-10.0816	7.6663	0.28432	0.1285:0.6836:0.1141:0.0738	rs62417812	82;82	Q5SRI9;Q8WWX4	MANEA_HUMAN;.	I	82	.	ENSP00000351669:T82I	T	+	2	0	MANEA	96141281	0.018000	0.18449	0.174000	0.22961	0.996000	0.88848	-0.000000	0.12993	1.459000	0.47892	0.650000	0.86243	ACT	C|0.917;T|0.083	0.083	strong		0.328	MANEA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043644.1	NM_024641	
MUC5B	727897	hgsc.bcm.edu	37	11	1263687	1263687	+	Silent	SNP	C	C	T	rs55933911	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:1263687C>T	ENST00000529681.1	+	31	5635	c.5577C>T	c.(5575-5577)aaC>aaT	p.N1859N	MUC5B_ENST00000447027.1_Silent_p.N1862N|RP11-532E4.2_ENST00000532061.2_RNA	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	1859	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)		CCTGCAAGAACGAAGACCAGA	0.597													c|||	72	0.014377	0.0008	0.0216	5008	,	,		19578	0.0		0.0477	False		,,,				2504	0.0082				p.N1859N		Atlas-SNP	.											.	MUC5B	473	.	0			c.C5577T						PASS	.	C		49,4315		0,49,2133	57.0	74.0	68.0		5577	0.5	0.0	11	dbSNP_129	68	430,8122		15,400,3861	no	coding-synonymous	MUC5B	NM_002458.2		15,449,5994	TT,TC,CC		5.0281,1.1228,3.7086		1859/5763	1263687	479,12437	2182	4276	6458	SO:0001819	synonymous_variant	727897	exon31			CAAGAACGAAGAC	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.5577C>T	11.37:g.1263687C>T		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	142	115	0.809859	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Silent	SNP	ENST00000529681.1	37	CCDS44515.2																																																																																			C|0.973;G|0.000;T|0.026	0.026	strong		0.597	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
ZNF627	199692	hgsc.bcm.edu	37	19	11725413	11725413	+	Silent	SNP	G	G	A	rs12151212	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:11725413G>A	ENST00000361113.5	+	2	283	c.75G>A	c.(73-75)caG>caA	p.Q25Q	ZNF627_ENST00000588174.1_Silent_p.Q25Q	NM_145295.3	NP_660338.1	Q7L945	ZN627_HUMAN	zinc finger protein 627	25	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)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(6)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	14						ATCCTTCCCAGAAGAATCTCT	0.498													G|||	610	0.121805	0.0832	0.1167	5008	,	,		16866	0.0258		0.169	False		,,,				2504	0.228				p.Q25Q	Melanoma(112;173 1614 10731 17751 23322)	Atlas-SNP	.											ZNF627,NS,carcinoma,0,1	ZNF627	43	1	0			c.G75A						PASS	.	G		422,3984	203.8+/-226.2	17,388,1798	107.0	112.0	110.0		75	-0.9	0.5	19	dbSNP_120	110	1689,6911	306.1+/-307.8	164,1361,2775	no	coding-synonymous	ZNF627	NM_145295.3		181,1749,4573	AA,AG,GG		19.6395,9.5778,16.231		25/462	11725413	2111,10895	2203	4300	6503	SO:0001819	synonymous_variant	199692	exon2			TTCCCAGAAGAAT	AK074846	CCDS42502.1	19p13.2	2013-01-08				ENSG00000198551		"""Zinc fingers, C2H2-type"", ""-"""	30570	protein-coding gene	gene with protein product		612248				12477932	Standard	NM_145295		Approved	FLJ90365	uc002msk.2	Q7L945		ENST00000361113.5:c.75G>A	19.37:g.11725413G>A		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	61	27	0.442623	NM_145295	O14846|Q4KMP9|Q6NT81|Q9BRG4	Silent	SNP	ENST00000361113.5	37	CCDS42502.1																																																																																			G|0.865;A|0.135	0.135	strong		0.498	ZNF627-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458875.1	NM_145295	
ERCC8	1161	hgsc.bcm.edu	37	5	60200665	60200665	+	Silent	SNP	A	A	G	rs4647100	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:60200665A>G	ENST00000265038.5	-	5	477	c.435T>C	c.(433-435)taT>taC	p.Y145Y	ERCC8_ENST00000426742.2_Silent_p.Y87Y|ERCC8_ENST00000543101.1_Intron|ERCC8_ENST00000462279.1_5'UTR	NM_000082.3	NP_000073.1	Q13216	ERCC8_HUMAN	excision repair cross-complementation group 8	145					cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|nucleotide-excision repair (GO:0006289)|positive regulation of DNA repair (GO:0045739)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein autoubiquitination (GO:0051865)|protein polyubiquitination (GO:0000209)|response to oxidative stress (GO:0006979)|response to UV (GO:0009411)|response to X-ray (GO:0010165)|transcription-coupled nucleotide-excision repair (GO:0006283)	Cul4A-RING E3 ubiquitin ligase complex (GO:0031464)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleotide-excision repair complex (GO:0000109)|nucleus (GO:0005634)|protein complex (GO:0043234)	protein complex binding (GO:0032403)			breast(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|upper_aerodigestive_tract(1)	14		Lung NSC(810;1.51e-06)|Prostate(74;0.0322)|Ovarian(174;0.0481)|Breast(144;0.077)				TATGATGACTATAAACTGTTT	0.308													A|||	680	0.135783	0.0666	0.1686	5008	,	,		8590	0.002		0.2704	False		,,,				2504	0.2055				p.Y145Y		Atlas-SNP	.											.	ERCC8	31	.	0			c.T435C						PASS	.	A		397,4009	197.1+/-221.3	15,367,1821	110.0	111.0	111.0		435	3.5	1.0	5	dbSNP_111	111	2258,6338	381.7+/-340.1	282,1694,2322	no	coding-synonymous	ERCC8	NM_000082.3		297,2061,4143	GG,GA,AA		26.268,9.0104,20.4199		145/397	60200665	2655,10347	2203	4298	6501	SO:0001819	synonymous_variant	1161	exon5			ATGACTATAAACT	U28413	CCDS3978.1	5q12.1	2014-09-17	2014-03-07		ENSG00000049167	ENSG00000049167		"""WD repeat domain containing"""	3439	protein-coding gene	gene with protein product		609412	"""Cockayne syndrome 1 (classical)"", ""excision repair cross-complementing rodent repair deficiency, complementation group 8"""	CKN1		8596535	Standard	NM_000082		Approved	CSA	uc003jsm.3	Q13216	OTTHUMG00000097741	ENST00000265038.5:c.435T>C	5.37:g.60200665A>G		Somatic	237	1	0.00421941		WXS	Illumina HiSeq	Phase_I	216	124	0.574074	NM_000082	B2RB64|Q6FHX5|Q96GB9	Silent	SNP	ENST00000265038.5	37	CCDS3978.1																																																																																			A|0.820;G|0.180	0.180	strong		0.308	ERCC8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214971.2	NM_000082	
TNNI2	7136	hgsc.bcm.edu	37	11	1861760	1861760	+	Silent	SNP	T	T	C	rs17845989|rs907610	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:1861760T>C	ENST00000381906.1	+	5	129	c.60T>C	c.(58-60)agT>agC	p.S20S	TNNI2_ENST00000381911.1_Silent_p.S20S|TNNI2_ENST00000252898.7_Silent_p.S20S|TNNI2_ENST00000381905.3_Silent_p.S20S	NM_001145829.1	NP_001139301.1	P48788	TNNI2_HUMAN	troponin I type 2 (skeletal, fast)	20	Involved in binding TNC.				muscle filament sliding (GO:0030049)|positive regulation of transcription, DNA-templated (GO:0045893)|skeletal muscle contraction (GO:0003009)	cytosol (GO:0005829)|nucleus (GO:0005634)|troponin complex (GO:0005861)	troponin T binding (GO:0031014)			lung(8)|prostate(1)|urinary_tract(1)	10		all_epithelial(84;0.000138)|Breast(177;0.000962)|Ovarian(85;0.0014)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00136)|Lung(200;0.0681)|LUSC - Lung squamous cell carcinoma(625;0.082)		CACCGCAGAGTGTGATGCTGC	0.682													C|||	4145	0.827676	0.612	0.8703	5008	,	,		13507	0.9861		0.8847	False		,,,				2504	0.8671				p.S20S		Atlas-SNP	.											.	TNNI2	24	.	0			c.T60C						PASS	.	C	,,	2931,1453		996,939,257	17.0	22.0	21.0		60,60,60	-1.4	1.0	11	dbSNP_86	21	7479,1097		3266,947,75	no	coding-synonymous,coding-synonymous,coding-synonymous	TNNI2	NM_001145829.1,NM_001145841.1,NM_003282.3	,,	4262,1886,332	CC,CT,TT		12.7915,33.1432,19.6759	,,	20/183,20/183,20/183	1861760	10410,2550	2192	4288	6480	SO:0001819	synonymous_variant	7136	exon3			GCAGAGTGTGATG	L21715	CCDS31333.1, CCDS53594.1	11p15.5	2014-09-17	2005-09-12		ENSG00000130598	ENSG00000130598			11946	protein-coding gene	gene with protein product	"""troponin I, fast-twitch skeletal muscle isoform"", ""troponin I fast twitch 2"""	191043	"""troponin I, skeletal, fast"", ""arthrogryposis multiplex congenita, distal, type 2B"""	AMCD2B		9016781, 12592607	Standard	NM_001145829		Approved	FSSV, DA2B	uc010qxe.1	P48788	OTTHUMG00000012253	ENST00000381906.1:c.60T>C	11.37:g.1861760T>C		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	76	75	0.986842	NM_001145841	A6NIV8|A6NJU5	Silent	SNP	ENST00000381906.1	37	CCDS31333.1																																																																																			A|0.000;C|0.810;G|0.000;T|0.189	0.810	strong		0.682	TNNI2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000034046.2	NM_003282	
GGT6	124975	hgsc.bcm.edu	37	17	4463716	4463716	+	Missense_Mutation	SNP	G	G	A	rs62066363	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:4463716G>A	ENST00000574154.1	-	1	397	c.101C>T	c.(100-102)gCg>gTg	p.A34V	GGT6_ENST00000573591.1_5'Flank|GGT6_ENST00000301395.3_Missense_Mutation_p.A34V|GGT6_ENST00000381550.3_Missense_Mutation_p.A34V			Q6P531	GGT6_HUMAN	gamma-glutamyltransferase 6	34					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						TAGAACCAGCGCCTCTGATGT	0.617													A|||	65	0.0129792	0.0015	0.0648	5008	,	,		16173	0.0		0.0139	False		,,,				2504	0.0041				p.A34V		Atlas-SNP	.											.	GGT6	22	.	0			c.C101T						PASS	.	A	VAL/ALA,VAL/ALA	27,4379	823.8+/-416.5	0,27,2176	105.0	95.0	98.0		101,101	-7.0	0.0	17	dbSNP_129	98	177,8423	811.3+/-407.1	1,175,4124	no	missense,missense	GGT6	NM_001122890.1,NM_153338.2	64,64	1,202,6300	AA,AG,GG		2.0581,0.6128,1.5685	benign,benign	34/494,34/462	4463716	204,12802	2203	4300	6503	SO:0001583	missense	124975	exon1			ACCAGCGCCTCTG	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.101C>T	17.37:g.4463716G>A	ENSP00000458307:p.Ala34Val	Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	36	13	0.361111	NM_001122890	B4DUH4|Q8NCM0	Missense_Mutation	SNP	ENST00000574154.1	37	CCDS45582.1	34	0.015567765567765568	3	0.006097560975609756	18	0.049723756906077346	0	0.0	13	0.017150395778364115	A	1.145	-0.648519	0.03506	0.006128	0.020581	ENSG00000167741	ENST00000381550;ENST00000301395	T;T	0.23348	2.55;1.91	4.84	-6.97	0.01616	.	1.589900	0.03776	N	0.260554	T	0.01454	0.0047	N	0.14661	0.345	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	0.27331	-1.0077	10	0.02654	T	1	-25.4271	6.244	0.20807	0.4293:0.0:0.3732:0.1975	rs62066363	34;34;34	B4DKN3;Q6P531;Q6P531-2	.;GGT6_HUMAN;.	V	34	ENSP00000370962:A34V;ENSP00000301395:A34V	ENSP00000301395:A34V	A	-	2	0	GGT6	4410465	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.515000	0.06290	-1.883000	0.01120	-1.974000	0.00461	GCG	G|0.986;A|0.014	0.014	strong		0.617	GGT6-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439122.1	NM_153338	
PIWIL3	440822	hgsc.bcm.edu	37	22	25145471	25145471	+	Missense_Mutation	SNP	A	A	G	rs1892722	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:25145471A>G	ENST00000332271.5	-	11	1650	c.1234T>C	c.(1234-1236)Tgt>Cgt	p.C412R	PIWIL3_ENST00000527701.1_Missense_Mutation_p.C303R|PIWIL3_ENST00000533313.1_Missense_Mutation_p.C303R|PIWIL3_ENST00000532537.2_5'UTR	NM_001008496.3|NM_001255975.1	NP_001008496.2|NP_001242904.1	Q7Z3Z3	PIWL3_HUMAN	piwi-like RNA-mediated gene silencing 3	412			C -> R (in dbSNP:rs1892722).		cell differentiation (GO:0030154)|gene silencing by RNA (GO:0031047)|meiotic nuclear division (GO:0007126)|multicellular organismal development (GO:0007275)|regulation of translation (GO:0006417)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)	RNA binding (GO:0003723)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(14)|lung(15)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	50						TAATCTTTACATATTTCATCT	0.323													G|||	3370	0.672923	0.6831	0.7061	5008	,	,		22331	0.7312		0.5696	False		,,,				2504	0.682				p.C412R		Atlas-SNP	.											.	PIWIL3	115	.	0			c.T1234C						PASS	.	G	ARG/CYS	2893,1513	481.4+/-359.1	946,1001,256	82.0	74.0	77.0		1234	-5.0	0.0	22	dbSNP_92	77	5136,3464	507.2+/-376.8	1535,2066,699	yes	missense	PIWIL3	NM_001008496.2	180	2481,3067,955	GG,GA,AA		40.2791,34.3395,38.267	benign	412/883	25145471	8029,4977	2203	4300	6503	SO:0001583	missense	440822	exon11			CTTTACATATTTC	AB079368	CCDS33623.1	22q11.23	2013-02-15	2013-02-15		ENSG00000184571	ENSG00000184571		"""Argonaute/PIWI family"""	18443	protein-coding gene	gene with protein product		610314	"""piwi-like 3 (Drosophila)"""			12906857	Standard	NM_001008496		Approved	HIWI3	uc003abd.2	Q7Z3Z3	OTTHUMG00000150788	ENST00000332271.5:c.1234T>C	22.37:g.25145471A>G	ENSP00000330031:p.Cys412Arg	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	59	35	0.59322	NM_001008496		Missense_Mutation	SNP	ENST00000332271.5	37	CCDS33623.1	1408	0.6446886446886447	328	0.6666666666666666	247	0.6823204419889503	419	0.7325174825174825	414	0.5461741424802111	G	0.007	-1.989360	0.00439	0.656605	0.597209	ENSG00000184571	ENST00000332271;ENST00000533313;ENST00000527701	T;T;T	0.05382	3.45;3.45;3.45	2.81	-4.97	0.03029	Argonaute/Dicer protein, PAZ (3);	0.231987	0.34700	N	0.003758	T	0.00012	0.0000	N	0.00006	-3.205	0.80722	P	0.0	B;B;B	0.06786	0.001;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.42783	-0.9431	9	0.02654	T	1	0.0803	0.4211	0.00456	0.3247:0.1297:0.1763:0.3693	rs1892722;rs57690624;rs1892722	303;412;412	E9PIP6;B4DYF7;Q7Z3Z3	.;.;PIWL3_HUMAN	R	412;303;303	ENSP00000330031:C412R;ENSP00000431843:C303R;ENSP00000435718:C303R	ENSP00000330031:C412R	C	-	1	0	PIWIL3	23475471	0.022000	0.18835	0.000000	0.03702	0.266000	0.26442	-0.216000	0.09266	-1.121000	0.02949	-0.684000	0.03749	TGT	A|0.368;G|0.632	0.632	strong		0.323	PIWIL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320084.2	NM_001008496	
ZNF804A	91752	hgsc.bcm.edu	37	2	185803364	185803364	+	Missense_Mutation	SNP	C	C	G	rs3731834	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:185803364C>G	ENST00000302277.6	+	4	3835	c.3241C>G	c.(3241-3243)Ctg>Gtg	p.L1081V		NM_194250.1	NP_919226.1	Q7Z570	Z804A_HUMAN	zinc finger protein 804A	1081			L -> V (in dbSNP:rs3731834).				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						TAGCACACCTCTGCAGCCTTT	0.532													C|||	773	0.154353	0.034	0.1239	5008	,	,		20558	0.2044		0.1819	False		,,,				2504	0.2587				p.L1081V		Atlas-SNP	.											.	ZNF804A	322	.	0			c.C3241G						PASS	.	C	VAL/LEU	296,4110	161.4+/-193.6	7,282,1914	92.0	88.0	90.0		3241	3.2	1.0	2	dbSNP_107	90	1517,7083	286.5+/-297.7	128,1261,2911	yes	missense	ZNF804A	NM_194250.1	32	135,1543,4825	GG,GC,CC		17.6395,6.7181,13.9397	possibly-damaging	1081/1210	185803364	1813,11193	2203	4300	6503	SO:0001583	missense	91752	exon4			ACACCTCTGCAGC	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.3241C>G	2.37:g.185803364C>G	ENSP00000303252:p.Leu1081Val	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	123	121	0.98374	NM_194250	A7E253|Q6ZN26	Missense_Mutation	SNP	ENST00000302277.6	37	CCDS2291.1	338	0.15476190476190477	13	0.026422764227642278	49	0.13535911602209943	133	0.23251748251748253	143	0.18865435356200527	C	1.870	-0.460565	0.04508	0.067181	0.176395	ENSG00000170396	ENST00000302277	T	0.07444	3.19	5.07	3.23	0.37069	.	0.206931	0.24072	N	0.041817	T	0.00012	0.0000	N	0.20530	0.585	0.40134	P	0.023241999999999985	B	0.27882	0.192	B	0.25987	0.065	T	0.48340	-0.9044	9	0.35671	T	0.21	-1.1323	4.7089	0.12863	0.0:0.5724:0.1716:0.256	rs3731834;rs52819327;rs56895785;rs3731834	1081	Q7Z570	Z804A_HUMAN	V	1081	ENSP00000303252:L1081V	ENSP00000303252:L1081V	L	+	1	2	ZNF804A	185511609	0.686000	0.27661	0.953000	0.39169	0.683000	0.39861	1.039000	0.30266	0.502000	0.28037	-0.657000	0.03884	CTG	C|0.853;G|0.147	0.147	strong		0.532	ZNF804A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255871.1	NM_194250	
PRR21	643905	hgsc.bcm.edu	37	2	240981375	240981375	+	Missense_Mutation	SNP	T	T	A	rs6732185	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:240981375T>A	ENST00000408934.1	-	1	1024	c.1025A>T	c.(1024-1026)aAg>aTg	p.K342M		NM_001080835.1	NP_001074304.1	Q8WXC7	PRR21_HUMAN	proline rich 21	342			K -> M (in dbSNP:rs6732185).							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						ATGAAGAGACTTGGATGAAGA	0.587													N|||	3630	0.72484	0.9251	0.5879	5008	,	,		21941	0.7817		0.6312	False		,,,				2504	0.589				p.K342M		Atlas-SNP	.											.	PRR21	53	.	0			c.A1025T						PASS	.	A	MET/LYS	3878,528		1700,478,25	161.0	143.0	149.0		1025	-1.2	0.0	2	dbSNP_116	149	5530,3070		1781,1968,551	yes	missense	PRR21	NM_001080835.1	95	3481,2446,576	AA,AT,TT		35.6977,11.9837,27.6642	possibly-damaging	342/390	240981375	9408,3598	2203	4300	6503	SO:0001583	missense	643905	exon1			AGAGACTTGGATG	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.1025A>T	2.37:g.240981375T>A	ENSP00000386166:p.Lys342Met	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	60	24	0.4	NM_001080835		Missense_Mutation	SNP	ENST00000408934.1	37	CCDS33417.1	1598	0.7316849816849816	458	0.9308943089430894	218	0.6022099447513812	431	0.7534965034965035	491	0.6477572559366754	N	0.792	-0.758439	0.03019	0.880163	0.643023	ENSG00000221961	ENST00000408934;ENST00000486799	T;T	0.28454	1.61;1.61	0.612	-1.22	0.09494	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.30236	0.274	B	0.08055	0.003	T	0.44787	-0.9305	8	0.54805	T	0.06	.	0.9984	0.01472	0.1999:0.3912:0.2111:0.1977	rs6732185;rs52797090;rs59866356;rs6732185	342	Q8WXC7	PRR21_HUMAN	M	342	ENSP00000386166:K342M;ENSP00000418240:K342M	ENSP00000386166:K342M	K	-	2	0	PRR21	240630048	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-4.269000	0.00262	-3.326000	0.00186	-2.852000	0.00102	AAG	T|0.277;A|0.723	0.723	strong		0.587	PRR21-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001080835	
RUFY1	80230	hgsc.bcm.edu	37	5	179025789	179025789	+	Silent	SNP	G	G	A	rs72824522	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:179025789G>A	ENST00000319449.4	+	14	1740	c.1728G>A	c.(1726-1728)agG>agA	p.R576R	RUFY1_ENST00000393438.2_Silent_p.R468R|RP11-1379J22.2_ENST00000500262.1_RNA|RUFY1_ENST00000377001.2_3'UTR|RUFY1_ENST00000437570.2_Silent_p.R468R	NM_025158.4	NP_079434.3	Q96T51	RUFY1_HUMAN	RUN and FYVE domain containing 1	576					endocytosis (GO:0006897)|regulation of endocytosis (GO:0030100)	cytoplasm (GO:0005737)|endosome (GO:0005768)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)	lipid binding (GO:0008289)|protein transporter activity (GO:0008565)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(11)|ovary(4)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	26	all_cancers(89;0.00018)|all_epithelial(37;8.37e-05)|Renal(175;0.000159)|Lung NSC(126;0.00108)|all_lung(126;0.00195)	all_cancers(40;0.0322)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CTCTACTCAGGATGGAGCTGC	0.522										HNSCC(44;0.11)			G|||	361	0.0720847	0.0378	0.0764	5008	,	,		19945	0.0853		0.1064	False		,,,				2504	0.0665				p.R576R		Atlas-SNP	.											.	RUFY1	101	.	0			c.G1728A						PASS	.	G	,,	194,4212	122.9+/-160.3	6,182,2015	113.0	110.0	111.0		1404,1404,1728	-2.1	0.0	5	dbSNP_130	111	956,7644	208.4+/-249.9	60,836,3404	no	coding-synonymous,coding-synonymous,coding-synonymous	RUFY1	NM_001040451.1,NM_001040452.1,NM_025158.3	,,	66,1018,5419	AA,AG,GG		11.1163,4.4031,8.8421	,,	468/601,468/601,576/709	179025789	1150,11856	2203	4300	6503	SO:0001819	synonymous_variant	80230	exon14			ACTCAGGATGGAG	AF361055	CCDS4445.2, CCDS34312.1	5q35.3	2008-02-05			ENSG00000176783	ENSG00000176783		"""Zinc fingers, FYVE domain containing"""	19760	protein-coding gene	gene with protein product		610327				11877430	Standard	NM_001040451		Approved	FLJ22251, ZFYVE12, RABIP4	uc003mka.2	Q96T51	OTTHUMG00000130913	ENST00000319449.4:c.1728G>A	5.37:g.179025789G>A		Somatic	211	0	0		WXS	Illumina HiSeq	Phase_I	229	125	0.545852	NM_025158	Q59FF3|Q71S93|Q9H6I3	Silent	SNP	ENST00000319449.4	37	CCDS4445.2	173	0.07921245421245421	23	0.046747967479674794	28	0.07734806629834254	47	0.08216783216783216	75	0.09894459102902374	G	0.032	-1.325400	0.01309	0.044031	0.111163	ENSG00000176783	ENST00000502434	.	.	.	4.98	-2.1	0.07210	.	.	.	.	.	T	0.00608	0.0020	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.21143	-1.0254	3	.	.	.	-1.642	6.3823	0.21542	0.4772:0.1314:0.3914:0.0	.	.	.	.	N	254	.	.	D	+	1	0	RUFY1	178958395	0.235000	0.23794	0.001000	0.08648	0.019000	0.09904	0.424000	0.21330	-0.693000	0.05121	-0.459000	0.05422	GAT	G|0.912;A|0.088	0.088	strong		0.522	RUFY1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000253505.2	NM_001040451	
DPF3	8110	hgsc.bcm.edu	37	14	73220020	73220020	+	Silent	SNP	A	A	G	rs3742836	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:73220020A>G	ENST00000556509.1	-	3	252	c.253T>C	c.(253-255)Ttg>Ctg	p.L85L	DPF3_ENST00000541685.1_Silent_p.L85L|DPF3_ENST00000546183.1_Silent_p.L95L	NM_001280542.1	NP_001267471.1	Q92784	DPF3_HUMAN	D4, zinc and double PHD fingers, family 3	85					chromatin modification (GO:0016568)|nervous system development (GO:0007399)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)	zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(13)|ovary(1)	22				BRCA - Breast invasive adenocarcinoma(234;0.00649)|OV - Ovarian serous cystadenocarcinoma(108;0.0654)		GGTGGGTGCAATCGTCTCTTC	0.562													A|||	1118	0.223243	0.0764	0.2205	5008	,	,		19283	0.2907		0.2744	False		,,,				2504	0.3016				p.L85L		Atlas-SNP	.											.	DPF3	117	.	0			c.T253C						PASS	.	A		401,3395		29,343,1526	58.0	59.0	59.0		253	3.2	1.0	14	dbSNP_107	59	2312,5912		328,1656,2128	yes	coding-synonymous	DPF3	NM_012074.3		357,1999,3654	GG,GA,AA		28.1128,10.5638,22.5707		85/358	73220020	2713,9307	1898	4112	6010	SO:0001819	synonymous_variant	8110	exon3			GGTGCAATCGTCT	U43919	CCDS45133.1, CCDS61495.1, CCDS61496.1, CCDS61497.1	14q24.2	2014-05-13			ENSG00000205683	ENSG00000205683		"""Zinc fingers, PHD-type"""	17427	protein-coding gene	gene with protein product		601672				11845289, 8812431	Standard	NM_012074		Approved	cer-d4, Cerd4, FLJ14079, BAF45c	uc010ari.1	Q92784		ENST00000556509.1:c.253T>C	14.37:g.73220020A>G		Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	35	16	0.457143	NM_012074	A8MSI3|B7Z276|F5H575|Q32UJ0|Q6P9E6|Q6ZT41|Q9H7Y5	Silent	SNP	ENST00000556509.1	37																																																																																				A|0.773;G|0.227	0.227	strong		0.562	DPF3-004	NOVEL	basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000413152.2		
OR1S2	219958	hgsc.bcm.edu	37	11	57971478	57971478	+	Missense_Mutation	SNP	A	A	G	rs11229281	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:57971478A>G	ENST00000302592.6	-	1	175	c.176T>C	c.(175-177)aTt>aCt	p.I59T		NM_001004459.1	NP_001004459.1	Q8NGQ3	OR1S2_HUMAN	olfactory receptor, family 1, subfamily S, member 2	59			I -> T (in dbSNP:rs11229281).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(11)|kidney(1)|large_intestine(4)|lung(23)|ovary(2)|skin(2)|stomach(2)|urinary_tract(1)	46		Breast(21;0.0589)				GATAGCCACAATGATGAGCCC	0.473													A|||	438	0.0874601	0.056	0.1095	5008	,	,		21576	0.0417		0.1083	False		,,,				2504	0.1401				p.I59T		Atlas-SNP	.											.	OR1S2	119	.	0			c.T176C						PASS	.	A	THR/ILE	230,4172	137.3+/-173.1	6,218,1977	207.0	192.0	197.0		176	4.3	0.9	11	dbSNP_120	197	834,7758	192.1+/-238.2	46,742,3508	yes	missense	OR1S2	NM_001004459.1	89	52,960,5485	GG,GA,AA		9.7067,5.2249,8.1884	probably-damaging	59/326	57971478	1064,11930	2201	4296	6497	SO:0001583	missense	219958	exon1			GCCACAATGATGA	BK004297	CCDS31545.1	11q12.1	2012-08-09			ENSG00000197887	ENSG00000197887		"""GPCR / Class A : Olfactory receptors"""	15141	protein-coding gene	gene with protein product							Standard	NM_001004459		Approved		uc010rkb.2	Q8NGQ3	OTTHUMG00000167541	ENST00000302592.6:c.176T>C	11.37:g.57971478A>G	ENSP00000305469:p.Ile59Thr	Somatic	293	0	0		WXS	Illumina HiSeq	Phase_I	239	46	0.192469	NM_001004459	Q6IFG5|Q96R85	Missense_Mutation	SNP	ENST00000302592.6	37	CCDS31545.1	171	0.0782967032967033	38	0.07723577235772358	33	0.09116022099447514	22	0.038461538461538464	78	0.10290237467018469	A	11.87	1.767166	0.31320	0.052249	0.097067	ENSG00000197887	ENST00000302592	T	0.03124	4.04	4.26	4.26	0.50523	GPCR, rhodopsin-like superfamily (1);	0.274748	0.25552	N	0.029897	T	0.00384	0.0012	M	0.89414	3.03	0.44985	P	0.0019970000000000265	D	0.62365	0.991	P	0.56700	0.804	T	0.02860	-1.1101	9	0.87932	D	0	.	9.5868	0.39521	0.8241:0.1759:0.0:0.0	rs11229281	59	Q8NGQ3	OR1S2_HUMAN	T	59	ENSP00000305469:I59T	ENSP00000305469:I59T	I	-	2	0	OR1S2	57728054	0.574000	0.26684	0.928000	0.36995	0.353000	0.29299	4.177000	0.58276	1.921000	0.55644	0.533000	0.62120	ATT	A|0.913;G|0.087	0.087	strong		0.473	OR1S2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394703.2	NM_001004459	
GMPR	2766	hgsc.bcm.edu	37	6	16290761	16290761	+	Missense_Mutation	SNP	T	T	A	rs1042391	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:16290761T>A	ENST00000259727.4	+	8	880	c.766T>A	c.(766-768)Ttt>Att	p.F256I	GMPR_ENST00000544145.1_3'UTR	NM_006877.3	NP_006868.3	P36959	GMPR1_HUMAN	guanosine monophosphate reductase	256			F -> I (in dbSNP:rs1042391). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:1757097}.		nucleobase-containing small molecule metabolic process (GO:0055086)|nucleotide metabolic process (GO:0009117)|purine nucleobase metabolic process (GO:0006144)|purine-containing compound salvage (GO:0043101)|response to cold (GO:0009409)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|GMP reductase complex (GO:1902560)	GMP reductase activity (GO:0003920)|metal ion binding (GO:0046872)			NS(1)|breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(5)|ovary(1)	20	Breast(50;0.0427)|Ovarian(93;0.103)	all_hematologic(90;0.0895)				TGGAGAAGTGTTTGAGAGGAA	0.532													A|||	3537	0.70627	0.8835	0.5576	5008	,	,		18799	0.874		0.3986	False		,,,				2504	0.7157				p.F256I		Atlas-SNP	.											.	GMPR	44	.	0			c.T766A						PASS	.	A	ILE/PHE	3623,783	314.7+/-293.7	1496,631,76	248.0	232.0	237.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	766	5.2	1.0	6	dbSNP_86	237	3366,5234	642.0+/-399.8	655,2056,1589	yes	missense	GMPR	NM_006877.3	21	2151,2687,1665	AA,AT,TT		39.1395,17.7712,46.2633	benign	256/346	16290761	6989,6017	2203	4300	6503	SO:0001583	missense	2766	exon8			GAAGTGTTTGAGA		CCDS4537.1	6p23	2009-07-10			ENSG00000137198	ENSG00000137198	1.7.1.7		4376	protein-coding gene	gene with protein product		139265				2194676	Standard	NM_006877		Approved		uc003nbs.3	P36959	OTTHUMG00000014302	ENST00000259727.4:c.766T>A	6.37:g.16290761T>A	ENSP00000259727:p.Phe256Ile	Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	137	62	0.452555	NM_006877	Q96HQ6	Missense_Mutation	SNP	ENST00000259727.4	37	CCDS4537.1	1410	0.6456043956043956	417	0.8475609756097561	195	0.5386740331491713	504	0.8811188811188811	294	0.38786279683377306	A	2.686	-0.274157	0.05679	0.822288	0.391395	ENSG00000137198	ENST00000259727	T	0.76839	-1.05	5.22	5.22	0.72569	Aldolase-type TIM barrel (1);IMP dehydrogenase/GMP reductase (1);	0.100527	0.64402	N	0.000003	T	0.16642	0.0400	N	0.00217	-1.83	0.54753	P	1.0999999999983245E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.09574	-1.0668	9	0.02654	T	1	-2.6838	11.563	0.50788	0.866:0.0:0.0:0.134	rs1042391;rs3181849;rs17649286;rs17845156;rs17857961;rs60468552;rs1042391	256	P36959	GMPR1_HUMAN	I	256	ENSP00000259727:F256I	ENSP00000259727:F256I	F	+	1	0	GMPR	16398740	1.000000	0.71417	1.000000	0.80357	0.227000	0.25037	4.307000	0.59123	0.810000	0.34279	-0.257000	0.10917	TTT	A|0.579;N|0.000	0.579	strong		0.532	GMPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039942.2		
DUOX2	50506	hgsc.bcm.edu	37	15	45400296	45400296	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:45400296A>G	ENST00000603300.1	-	13	1725	c.1523T>C	c.(1522-1524)tTt>tCt	p.F508S	DUOX2_ENST00000389039.6_Missense_Mutation_p.F508S	NM_014080.4	NP_054799.4	Q9NRD8	DUOX2_HUMAN	dual oxidase 2	508	Peroxidase-like; mediates peroxidase activity. {ECO:0000250}.				adenohypophysis morphogenesis (GO:0048855)|bone mineralization (GO:0030282)|cuticle development (GO:0042335)|cytokine-mediated signaling pathway (GO:0019221)|fertilization (GO:0009566)|hormone biosynthetic process (GO:0042446)|hydrogen peroxide catabolic process (GO:0042744)|inner ear development (GO:0048839)|multicellular organism growth (GO:0035264)|oxidation-reduction process (GO:0055114)|response to cAMP (GO:0051591)|response to virus (GO:0009615)|thyroid gland development (GO:0030878)|thyroid hormone generation (GO:0006590)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|heme binding (GO:0020037)|NAD(P)H oxidase activity (GO:0016174)|peroxidase activity (GO:0004601)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(28)|ovary(3)|pancreas(1)|prostate(4)|skin(7)|urinary_tract(1)	63		all_cancers(109;3.79e-11)|all_epithelial(112;2.92e-09)|Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;1.05e-18)|GBM - Glioblastoma multiforme(94;4.23e-07)|COAD - Colon adenocarcinoma(120;0.0668)|Colorectal(133;0.068)		CAGCCGTACAAACTGGTCGAG	0.612																																					p.F508S		Atlas-SNP	.											.	DUOX2	137	.	0			c.T1523C						PASS	.						86.0	87.0	87.0					15																	45400296		2198	4298	6496	SO:0001583	missense	50506	exon13			CGTACAAACTGGT	AF181972	CCDS10117.1	15q15.3-q21	2013-01-10			ENSG00000140279	ENSG00000140279		"""EF-hand domain containing"""	13273	protein-coding gene	gene with protein product	"""dual oxidase-like domains 2"", ""nicotinamide adenine dinucleotide phosphate oxidase"", ""flavoprotein NADPH oxidase"", ""NADPH thyroid oxidase 2"", ""NADH/NADPH thyroid oxidase p138-tox"", ""NADPH oxidase/peroxidase DUOX2"""	606759				10601291, 10806195	Standard	NM_014080		Approved	P138-TOX, P138(TOX), THOX2, LNOX2	uc010bea.3	Q9NRD8	OTTHUMG00000131355	ENST00000603300.1:c.1523T>C	15.37:g.45400296A>G	ENSP00000475084:p.Phe508Ser	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	109	73	0.669725	NM_014080	A8MQ13|D2XI64|Q9NR02|Q9UHF9	Missense_Mutation	SNP	ENST00000603300.1	37	CCDS10117.1	.	.	.	.	.	.	.	.	.	.	A	25.0	4.593116	0.86953	.	.	ENSG00000140279	ENST00000389039	.	.	.	5.47	5.47	0.80525	.	0.000000	0.85682	D	0.000000	D	0.86892	0.6042	H	0.95745	3.715	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.90760	0.4664	9	0.87932	D	0	-8.369	14.7402	0.69448	1.0:0.0:0.0:0.0	.	508;70	Q9NRD8;Q59GU9	DUOX2_HUMAN;.	S	508	.	ENSP00000373691:F508S	F	-	2	0	DUOX2	43187588	1.000000	0.71417	1.000000	0.80357	0.742000	0.42306	9.106000	0.94253	2.080000	0.62538	0.533000	0.62120	TTT	.	.	none		0.612	DUOX2-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_014080	
MYO9B	4650	hgsc.bcm.edu	37	19	17306031	17306031	+	Silent	SNP	T	T	C	rs2279003	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:17306031T>C	ENST00000594824.1	+	22	3942	c.3795T>C	c.(3793-3795)ccT>ccC	p.P1265P	MYO9B_ENST00000595618.1_Silent_p.P1265P|MYO9B_ENST00000397274.2_Silent_p.P1265P			Q13459	MYO9B_HUMAN	myosin IXB	1265	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						CACCGGCCCCTGGCAGCGCCC	0.682													C|||	3802	0.759185	0.9705	0.8012	5008	,	,		12611	0.745		0.5676	False		,,,				2504	0.6554				p.P1265P		Atlas-SNP	.											.	MYO9B	264	.	0			c.T3795C						PASS	.	C	,	3431,307		1583,265,21	13.0	18.0	16.0		3795,3795	-0.8	0.0	19	dbSNP_100	16	4781,3383		1431,1919,732	no	coding-synonymous,coding-synonymous	MYO9B	NM_001130065.1,NM_004145.3	,	3014,2184,753	CC,CT,TT		41.438,8.2129,31.0032	,	1265/2023,1265/2158	17306031	8212,3690	1869	4082	5951	SO:0001819	synonymous_variant	4650	exon22			GGCCCCTGGCAGC		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.3795T>C	19.37:g.17306031T>C		Somatic	21	0	0		WXS	Illumina HiSeq	Phase_I	27	26	0.962963	NM_001130065	O75314|Q9NUJ2|Q9UHN0	Silent	SNP	ENST00000594824.1	37																																																																																				T|0.284;C|0.716	0.716	strong		0.682	MYO9B-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000463236.1		
DSG1	1828	hgsc.bcm.edu	37	18	28919911	28919911	+	Missense_Mutation	SNP	A	A	G	rs61730306|rs386802123	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:28919911A>G	ENST00000257192.4	+	11	1822	c.1610A>G	c.(1609-1611)aAa>aGa	p.K537R		NM_001942.2	NP_001933.2	Q02413	DSG1_HUMAN	desmoglein 1	537					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)			AACGGAGCCAAAGATTTGTTA	0.418													a|||	745	0.148762	0.2428	0.0994	5008	,	,		16748	0.0645		0.0845	False		,,,				2504	0.2096				p.K537R		Atlas-SNP	.											.	DSG1	176	.	0			c.A1610G						PASS	.	G	ARG/LYS	12,4394		2,8,2193	97.0	97.0	97.0		1610	-2.2	0.0	18	dbSNP_129	97	2,8598		1,0,4299	yes	missense	DSG1	NM_001942.2	26	3,8,6492	GG,GA,AA		0.0233,0.2724,0.1076	benign	537/1050	28919911	14,12992	2203	4300	6503	SO:0001583	missense	1828	exon11			GAGCCAAAGATTT	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.1610A>G	18.37:g.28919911A>G	ENSP00000257192:p.Lys537Arg	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	102	45	0.441176	NM_001942	B7Z845	Missense_Mutation	SNP	ENST00000257192.4	37	CCDS11896.1	250	0.11446886446886446	119	0.241869918699187	40	0.11049723756906077	33	0.057692307692307696	58	0.07651715039577836	a	0.011	-1.713122	0.00706	0.002724	2.33E-4	ENSG00000134760	ENST00000257192	T	0.56275	0.47	1.12	-2.24	0.06909	.	1.652450	0.04589	N	0.396400	T	0.00012	0.0000	N	0.12182	0.205	0.47547	P	5.460000000000464E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.07271	-1.0781	9	0.11794	T	0.64	.	4.5681	0.12196	0.5075:0.0:0.4925:0.0	rs61730306	537	Q02413	DSG1_HUMAN	R	537	ENSP00000257192:K537R	ENSP00000257192:K537R	K	+	2	0	DSG1	27173909	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.976000	0.03786	-1.292000	0.02366	-1.322000	0.01289	AAA	A|0.893;G|0.107	0.107	strong		0.418	DSG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254947.1	NM_001942	
IRAK1BP1	134728	hgsc.bcm.edu	37	6	79595097	79595097	+	Silent	SNP	A	A	G	rs6908105	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:79595097A>G	ENST00000369940.2	+	2	423	c.318A>G	c.(316-318)gcA>gcG	p.A106A	IRAK1BP1_ENST00000607739.1_Silent_p.A19A	NM_001010844.2	NP_001010844.1	Q5VVH5	IKBP1_HUMAN	interleukin-1 receptor-associated kinase 1 binding protein 1	106					I-kappaB kinase/NF-kappaB signaling (GO:0007249)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(2)|kidney(3)|large_intestine(3)|liver(1)|lung(3)	12		all_cancers(76;0.0398)|Acute lymphoblastic leukemia(125;1.24e-05)|all_hematologic(105;0.00223)		BRCA - Breast invasive adenocarcinoma(397;0.21)		TGTTTCAGGCAGAAAATATAA	0.303													a|||	1330	0.265575	0.292	0.3112	5008	,	,		15573	0.1855		0.3668	False		,,,				2504	0.1759				p.A106A		Atlas-SNP	.											.	IRAK1BP1	18	.	0			c.A318G						PASS	.	A		1361,3045	445.3+/-347.6	198,965,1040	93.0	101.0	98.0		318	5.3	1.0	6	dbSNP_116	98	2994,5604	458.5+/-364.6	528,1938,1833	no	coding-synonymous	IRAK1BP1	NM_001010844.1		726,2903,2873	GG,GA,AA		34.8221,30.8897,33.4897		106/261	79595097	4355,8649	2203	4299	6502	SO:0001819	synonymous_variant	134728	exon2			TCAGGCAGAAAAT	AI478629	CCDS34488.1	6q14-q15	2006-04-12				ENSG00000146243			17368	protein-coding gene	gene with protein product		615375				11096118	Standard	XM_005248654		Approved	AIP70, SIMPL	uc003pim.4	Q5VVH5		ENST00000369940.2:c.318A>G	6.37:g.79595097A>G		Somatic	224	1	0.00446429		WXS	Illumina HiSeq	Phase_I	151	151	1	NM_001010844		Silent	SNP	ENST00000369940.2	37	CCDS34488.1																																																																																			A|0.684;G|0.316	0.316	strong		0.303	IRAK1BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041296.2	XM_059729	
C1orf189	388701	hgsc.bcm.edu	37	1	154178079	154178079	+	Silent	SNP	G	G	A	rs74957241	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:154178079G>A	ENST00000368525.3	-	2	94	c.69C>T	c.(67-69)gtC>gtT	p.V23V	C1orf43_ENST00000483282.1_5'Flank	NM_001010979.1	NP_001010979.1	Q5VU69	CA189_HUMAN	chromosome 1 open reading frame 189	23										kidney(1)|large_intestine(3)|lung(1)|skin(2)	7	all_lung(78;9.35e-31)|Lung NSC(65;1.33e-28)|Hepatocellular(266;0.0877)|Melanoma(130;0.128)					ATTACCTGTCGACCGTCTTCT	0.473													G|||	192	0.0383387	0.003	0.0677	5008	,	,		18138	0.001		0.1163	False		,,,				2504	0.0235				p.V23V		Atlas-SNP	.											C1orf189,NS,carcinoma,-2,1	C1orf189	17	1	0			c.C69T						PASS	.	G		82,4324	71.4+/-109.4	2,78,2123	166.0	148.0	154.0		69	-2.7	0.1	1	dbSNP_132	154	926,7674	205.1+/-247.6	55,816,3429	no	coding-synonymous	C1orf189	NM_001010979.1		57,894,5552	AA,AG,GG		10.7674,1.8611,7.7503		23/102	154178079	1008,11998	2203	4300	6503	SO:0001819	synonymous_variant	388701	exon2			CCTGTCGACCGTC		CCDS30876.1	1q21.3	2012-07-27			ENSG00000163263	ENSG00000163263			32305	protein-coding gene	gene with protein product							Standard	NM_001010979		Approved		uc001fee.2	Q5VU69	OTTHUMG00000035982	ENST00000368525.3:c.69C>T	1.37:g.154178079G>A		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	83	35	0.421687	NM_001010979	A1L4E3	Silent	SNP	ENST00000368525.3	37	CCDS30876.1																																																																																			G|0.926;A|0.074	0.074	strong		0.473	C1orf189-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087672.1	NM_001010979	
DNAH9	1770	hgsc.bcm.edu	37	17	11543610	11543610	+	Missense_Mutation	SNP	A	A	G	rs61740059	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:11543610A>G	ENST00000262442.4	+	10	1878	c.1810A>G	c.(1810-1812)Atg>Gtg	p.M604V	DNAH9_ENST00000454412.2_Missense_Mutation_p.M604V	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	604	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)		GCACAAGAACATGCCCACCGT	0.602													A|||	67	0.0133786	0.0015	0.0216	5008	,	,		18384	0.0		0.0219	False		,,,				2504	0.0286				p.M604V		Atlas-SNP	.											.	DNAH9	695	.	0			c.A1810G						PASS	.	A	VAL/MET	16,4390	24.3+/-50.5	0,16,2187	130.0	123.0	125.0		1810	5.4	1.0	17	dbSNP_129	125	277,8323	104.2+/-165.2	5,267,4028	yes	missense	DNAH9	NM_001372.3	21	5,283,6215	GG,GA,AA		3.2209,0.3631,2.2528	possibly-damaging	604/4487	11543610	293,12713	2203	4300	6503	SO:0001583	missense	1770	exon10			AAGAACATGCCCA	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.1810A>G	17.37:g.11543610A>G	ENSP00000262442:p.Met604Val	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	66	28	0.424242	NM_001372	A2VCQ8|O15064|O95494|Q9NQ28	Missense_Mutation	SNP	ENST00000262442.4	37	CCDS11160.1	23	0.010531135531135532	1	0.0020325203252032522	5	0.013812154696132596	0	0.0	17	0.022427440633245383	A	18.65	3.669200	0.67814	0.003631	0.032209	ENSG00000007174	ENST00000262442;ENST00000454412	T;T	0.55930	0.49;0.49	5.4	5.4	0.78164	Dynein heavy chain, domain-1 (1);	0.554792	0.19401	N	0.115180	T	0.47358	0.1441	M	0.86268	2.805	0.80722	D	1	P	0.52316	0.952	P	0.56127	0.792	T	0.66352	-0.5945	10	0.52906	T	0.07	.	13.6437	0.62267	1.0:0.0:0.0:0.0	rs61740059	604	Q9NYC9	DYH9_HUMAN	V	604	ENSP00000262442:M604V;ENSP00000414874:M604V	ENSP00000262442:M604V	M	+	1	0	DNAH9	11484335	1.000000	0.71417	1.000000	0.80357	0.861000	0.49209	5.050000	0.64251	2.049000	0.60858	0.528000	0.53228	ATG	A|0.981;G|0.019	0.019	strong		0.602	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372	
SPICE1	152185	hgsc.bcm.edu	37	3	113187675	113187675	+	Missense_Mutation	SNP	G	G	C	rs16861032	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:113187675G>C	ENST00000295872.4	-	9	1082	c.823C>G	c.(823-825)Cta>Gta	p.L275V		NM_144718.3	NP_653319.1	Q8N0Z3	SPICE_HUMAN	spindle and centriole associated protein 1	275			L -> V (in dbSNP:rs16861032).		metaphase plate congression (GO:0051310)|regulation of centriole replication (GO:0046599)|spindle assembly involved in mitosis (GO:0090307)	centriole (GO:0005814)|centrosome (GO:0005813)|spindle (GO:0005819)				NS(1)|autonomic_ganglia(1)|breast(4)|endometrium(3)|large_intestine(9)|lung(10)|ovary(2)|skin(2)|urinary_tract(1)	33						CTTGAGTCTAGAGTCTCAGTA	0.403													G|||	310	0.061901	0.0575	0.0216	5008	,	,		20377	0.1071		0.0427	False		,,,				2504	0.0695				p.L275V		Atlas-SNP	.											.	SPICE1	130	.	0			c.C823G						PASS	.	G	VAL/LEU	234,4172	138.4+/-174.2	7,220,1976	102.0	91.0	95.0		823	0.6	0.3	3	dbSNP_123	95	315,8285	112.7+/-172.9	5,305,3990	yes	missense	SPICE1	NM_144718.3	32	12,525,5966	CC,CG,GG		3.6628,5.3109,4.2211	benign	275/856	113187675	549,12457	2203	4300	6503	SO:0001583	missense	152185	exon9			AGTCTAGAGTCTC	AY099107	CCDS2973.1	3q13.2	2010-09-01	2010-09-01	2010-09-01	ENSG00000163611	ENSG00000163611			25083	protein-coding gene	gene with protein product	"""spindle and centriole protein"""	613447	"""coiled-coil domain containing 52"""	CCDC52		20736305	Standard	NM_144718		Approved	SPICE	uc003eag.4	Q8N0Z3	OTTHUMG00000159261	ENST00000295872.4:c.823C>G	3.37:g.113187675G>C	ENSP00000295872:p.Leu275Val	Somatic	199	0	0		WXS	Illumina HiSeq	Phase_I	193	93	0.481865	NM_144718	D3DN72|Q8WUX6	Missense_Mutation	SNP	ENST00000295872.4	37	CCDS2973.1	133	0.060897435897435896	36	0.07317073170731707	10	0.027624309392265192	54	0.0944055944055944	33	0.04353562005277045	G	0.013	-1.612637	0.00835	0.053109	0.036628	ENSG00000163611	ENST00000295872	T	0.28454	1.61	5.05	0.647	0.17796	.	0.784257	0.11562	N	0.551597	T	0.00496	0.0016	N	0.04508	-0.205	0.09310	N	1	B;B	0.06786	0.001;0.0	B;B	0.09377	0.004;0.001	T	0.23655	-1.0182	10	0.18710	T	0.47	-2.1757	11.6844	0.51476	0.0827:0.5149:0.4024:0.0	rs16861032;rs56471661;rs16861032	171;275	B3KX77;Q8N0Z3	.;SPICE_HUMAN	V	275	ENSP00000295872:L275V	ENSP00000295872:L275V	L	-	1	2	SPICE1	114670365	0.504000	0.26123	0.340000	0.25575	0.065000	0.16274	0.030000	0.13688	0.167000	0.19631	-0.216000	0.12614	CTA	G|0.946;C|0.054	0.054	strong		0.403	SPICE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354177.2	NM_144718	
RXFP3	51289	hgsc.bcm.edu	37	5	33937601	33937601	+	Silent	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:33937601G>A	ENST00000330120.3	+	1	1111	c.756G>A	c.(754-756)ccG>ccA	p.P252P		NM_016568.3	NP_057652.1	Q9NSD7	RL3R1_HUMAN	relaxin/insulin-like family peptide receptor 3	252					G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of cytokinesis (GO:0032467)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled peptide receptor activity (GO:0008528)|G-protein coupled receptor activity (GO:0004930)			endometrium(4)|large_intestine(9)|lung(24)|ovary(1)|skin(1)|upper_aerodigestive_tract(3)	42						TGCGTTTCCCGGACAAGTTGC	0.627																																					p.P252P		Atlas-SNP	.											RXFP3,NS,carcinoma,+2,1	RXFP3	114	1	0			c.G756A						scavenged	.						47.0	39.0	42.0					5																	33937601		2202	4299	6501	SO:0001819	synonymous_variant	51289	exon1			TTTCCCGGACAAG	D88437	CCDS3900.1	5p15.1-p14	2012-08-08	2006-05-09	2006-03-15	ENSG00000182631	ENSG00000182631		"""GPCR / Class A : Relaxin family peptide receptors"""	24883	protein-coding gene	gene with protein product		609445	"""relaxin 3 receptor 1"", ""relaxin family peptide receptor 3"""	RLN3R1		15956688, 16507880	Standard	NM_016568		Approved	SALPR, GPCR135, RXFPR3	uc003jic.2	Q9NSD7	OTTHUMG00000090685	ENST00000330120.3:c.756G>A	5.37:g.33937601G>A		Somatic	209	0	0		WXS	Illumina HiSeq	Phase_I	209	3	0.0143541	NM_016568	Q14DA5	Silent	SNP	ENST00000330120.3	37	CCDS3900.1																																																																																			.	.	none		0.627	RXFP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207369.1	NM_016568	
CCDC185	164127	hgsc.bcm.edu	37	1	223567531	223567531	+	Silent	SNP	G	G	A	rs2298063	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:223567531G>A	ENST00000366875.3	+	1	817	c.714G>A	c.(712-714)ccG>ccA	p.P238P		NM_152610.2	NP_689823.2	Q8N715	CC185_HUMAN		238										breast(4)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(12)|skin(3)	29				GBM - Glioblastoma multiforme(131;0.0704)		TGCGGAGCCCGCACACCCAGG	0.627													G|||	403	0.0804712	0.0825	0.0634	5008	,	,		16355	0.13		0.0408	False		,,,				2504	0.0798				p.P238P		Atlas-SNP	.											C1orf65,colon,carcinoma,+1,1	C1orf65	71	1	0			c.G714A						PASS	.	G		359,4047	179.4+/-207.9	19,321,1863	42.0	43.0	43.0		714	0.5	0.0	1	dbSNP_100	43	331,8269	114.6+/-174.5	6,319,3975	no	coding-synonymous	C1orf65	NM_152610.2		25,640,5838	AA,AG,GG		3.8488,8.148,5.3052		238/624	223567531	690,12316	2203	4300	6503	SO:0001819	synonymous_variant	164127	exon1			GAGCCCGCACACC																												ENST00000366875.3:c.714G>A	1.37:g.223567531G>A		Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	180	82	0.455556	NM_152610	Q8N746|Q8NA93	Silent	SNP	ENST00000366875.3	37	CCDS1537.1																																																																																			G|0.940;A|0.060	0.060	strong		0.627	C1orf65-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092718.1		
CAPN11	11131	hgsc.bcm.edu	37	6	44147821	44147821	+	Missense_Mutation	SNP	A	A	G	rs34710081	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:44147821A>G	ENST00000398776.1	+	14	1599	c.1561A>G	c.(1561-1563)Att>Gtt	p.I521V	CAPN11_ENST00000542245.1_Missense_Mutation_p.I521V	NM_007058.3	NP_008989.2	Q9UMQ6	CAN11_HUMAN	calpain 11	521	Domain III.		I -> V (in dbSNP:rs34710081).		proteolysis (GO:0006508)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|peptidase activity (GO:0008233)			breast(3)|endometrium(5)|kidney(1)|large_intestine(5)|lung(17)|ovary(1)|pancreas(1)|prostate(2)|stomach(1)	36	all_cancers(18;3.19e-06)|Lung NSC(15;0.00108)|all_lung(25;0.00278)|Hepatocellular(11;0.00908)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			GGAATATATCATTATTCCCTC	0.547													a|||	929	0.185503	0.149	0.2133	5008	,	,		13686	0.1349		0.2028	False		,,,				2504	0.2495				p.I521V		Atlas-SNP	.											.	CAPN11	66	.	0			c.A1561G						PASS	.	A	VAL/ILE	561,3545		32,497,1524	55.0	57.0	57.0		1561	5.0	0.9	6	dbSNP_126	57	1843,6577		201,1441,2568	yes	missense	CAPN11	NM_007058.3	29	233,1938,4092	GG,GA,AA		21.8884,13.6629,19.1921	probably-damaging	521/740	44147821	2404,10122	2053	4210	6263	SO:0001583	missense	11131	exon14			TATATCATTATTC	AJ242832	CCDS47436.1	6p12	2013-01-10			ENSG00000137225	ENSG00000137225		"""EF-hand domain containing"""	1478	protein-coding gene	gene with protein product		604822				10409436	Standard	NM_007058		Approved		uc003owt.1	Q9UMQ6	OTTHUMG00000014758	ENST00000398776.1:c.1561A>G	6.37:g.44147821A>G	ENSP00000381758:p.Ile521Val	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	63	37	0.587302	NM_007058	B2RA64|Q5T3G1|Q8N4R5	Missense_Mutation	SNP	ENST00000398776.1	37	CCDS47436.1	385	0.1762820512820513	63	0.12804878048780488	88	0.2430939226519337	82	0.14335664335664336	152	0.20052770448548812	A	11.34	1.610849	0.28712	0.136629	0.218884	ENSG00000137225	ENST00000398776;ENST00000542245	D;D	0.88124	-2.34;-2.34	4.97	4.97	0.65823	Peptidase C2, calpain, large subunit, domain III (2);Peptidase C2, calpain, domain III (1);	0.000000	0.48286	D	0.000198	T	0.75961	0.3921	L	0.49778	1.585	0.32223	P	0.5749230000000001	P;P	0.41978	0.767;0.767	B;B	0.43331	0.416;0.416	T	0.75039	-0.3458	9	0.29301	T	0.29	.	7.5215	0.27631	0.8365:0.0:0.1635:0.0	rs34710081	175;521	B4DT90;Q9UMQ6	.;CAN11_HUMAN	V	521	ENSP00000381758:I521V;ENSP00000441078:I521V	ENSP00000381758:I521V	I	+	1	0	CAPN11	44255799	1.000000	0.71417	0.936000	0.37596	0.492000	0.33523	1.646000	0.37249	2.105000	0.64084	0.496000	0.49642	ATT	A|0.815;G|0.185	0.185	strong		0.547	CAPN11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040714.3		
PABPN1L	390748	hgsc.bcm.edu	37	16	88931274	88931274	+	Missense_Mutation	SNP	C	C	T	rs76267236	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:88931274C>T	ENST00000419291.2	-	5	652	c.641G>A	c.(640-642)gGc>gAc	p.G214D	PABPN1L_ENST00000378358.4_Missense_Mutation_p.G214D|PABPN1L_ENST00000411789.2_Intron|PABPN1L_ENST00000427766.1_Silent_p.G178G	NM_001080487.2	NP_001073956.2	A6NDY0	EPAB2_HUMAN	poly(A) binding protein, nuclear 1-like (cytoplasmic)	214	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.					cytoplasm (GO:0005737)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			kidney(1)	1						GATGACCCGGCCCCGGAAGAG	0.682													.|||	103	0.0205671	0.0038	0.0187	5008	,	,		14223	0.001		0.0726	False		,,,				2504	0.0112				p.G214D		Atlas-SNP	.											PABPN1L_ENST00000419291,colon,carcinoma,0,2	PABPN1L	25	2	0			c.G641A						scavenged	.	C	ASP/GLY	56,3896		0,56,1920	14.0	19.0	17.0		641	4.5	0.5	16	dbSNP_131	17	588,7688		18,552,3568	yes	missense	PABPN1L	NM_001080487.2	94	18,608,5488	TT,TC,CC		7.1049,1.417,5.2666	possibly-damaging	214/279	88931274	644,11584	1976	4138	6114	SO:0001583	missense	390748	exon5			ACCCGGCCCCGGA		CCDS45547.1, CCDS45547.2, CCDS73925.1	16q24.3	2013-02-12	2009-12-17		ENSG00000205022	ENSG00000205022		"""RNA binding motif (RRM) containing"""	37237	protein-coding gene	gene with protein product	"""embryonic poly(A) binding protein 2"""					18483763	Standard	NM_001080487		Approved	ePABP2	uc010vpe.2	A6NDY0		ENST00000419291.2:c.641G>A	16.37:g.88931274C>T	ENSP00000408598:p.Gly214Asp	Somatic	206	1	0.00485437		WXS	Illumina HiSeq	Phase_I	222	85	0.382883	NM_001080487	A1L3B3|A2VDI2	Missense_Mutation	SNP	ENST00000419291.2	37	CCDS45547.2	70	0.03205128205128205	0	0.0	8	0.022099447513812154	0	0.0	62	0.08179419525065963	C	20.9	4.063480	0.76187	0.01417	0.071049	ENSG00000205022	ENST00000378358;ENST00000419291	D;D	0.81821	-1.54;-1.54	5.41	4.46	0.54185	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.099305	0.64402	N	0.000001	T	0.39600	0.1084	M	0.85373	2.75	0.80722	D	1	D;P	0.60160	0.987;0.622	D;B	0.66351	0.943;0.097	T	0.70691	-0.4802	10	0.54805	T	0.06	4.3894	11.22	0.48848	0.0:0.8482:0.0:0.1518	.	214;214	A6NDY0;A6NDY0-4	EPAB2_HUMAN;.	D	214	ENSP00000367609:G214D;ENSP00000408598:G214D	ENSP00000367609:G214D	G	-	2	0	PABPN1L	87458775	1.000000	0.71417	0.538000	0.28064	0.814000	0.46013	3.555000	0.53727	1.273000	0.44346	0.511000	0.50034	GGC	C|0.965;T|0.035	0.035	strong		0.682	PABPN1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407502.1	NM_001080487	
HLA-A	3105	hgsc.bcm.edu	37	6	29911218	29911218	+	Missense_Mutation	SNP	G	G	A	rs1059526	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:29911218G>A	ENST00000396634.1	+	5	858	c.517G>A	c.(517-519)Gcg>Acg	p.A173T	HLA-A_ENST00000376802.2_Missense_Mutation_p.A173T|HLA-A_ENST00000376809.5_Missense_Mutation_p.A173T|HLA-A_ENST00000376806.5_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	284	0	0		WXS	Illumina HiSeq	Phase_I	132	61	0.462121	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	
POM121C	100101267	hgsc.bcm.edu	37	7	75053499	75053499	+	Missense_Mutation	SNP	G	G	A	rs113744930	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:75053499G>A	ENST00000257665.5	-	10	1606	c.1607C>T	c.(1606-1608)tCg>tTg	p.S536L	POM121C_ENST00000473168.1_5'UTR|POM121C_ENST00000453279.2_Missense_Mutation_p.S294L			A8CG34	P121C_HUMAN	POM121 transmembrane nucleoporin C	536	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						GACAGAGTTCGAGGCAGCATC	0.562													.|||	752	0.15016	0.3169	0.098	5008	,	,		19287	0.002		0.1183	False		,,,				2504	0.1472				p.S294L		Atlas-SNP	.											POM121C,NS,carcinoma,+1,1	POM121C	46	1	0			c.C881T						scavenged	.	G	LEU/SER	1149,3257	409.5+/-335.0	165,819,1219	241.0	265.0	257.0		881	1.7	0.0	7	dbSNP_132	257	1073,7527	223.7+/-260.4	60,953,3287	no	missense	POM121C	NM_001099415.1	145	225,1772,4506	AA,AG,GG		12.4767,26.0781,17.0844	benign	294/988	75053499	2222,10784	2203	4300	6503	SO:0001583	missense	100101267	exon12			GAGTTCGAGGCAG		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.1607C>T	7.37:g.75053499G>A	ENSP00000257665:p.Ser536Leu	Somatic	228	1	0.00438596		WXS	Illumina HiSeq	Phase_I	279	104	0.37276	NM_001099415	O75115|Q9Y2N3|Q9Y4S7	Missense_Mutation	SNP	ENST00000257665.5	37		270	0.12362637362637363	151	0.30691056910569103	39	0.10773480662983426	1	0.0017482517482517483	79	0.10422163588390501	G	9.798	1.179694	0.21787	0.260781	0.124767	ENSG00000135213	ENST00000257665;ENST00000453279	T;T	0.20069	3.62;2.1	3.57	1.71	0.24356	.	0.422937	0.17553	N	0.170085	T	0.00012	0.0000	M	0.71581	2.175	0.80722	P	0.0	B	0.15473	0.013	B	0.14023	0.01	T	0.21690	-1.0238	9	0.62326	D	0.03	.	7.0486	0.25061	0.2201:0.0:0.7799:0.0	.	536	A8CG34	P121C_HUMAN	L	536;294	ENSP00000257665:S536L;ENSP00000414208:S294L	ENSP00000257665:S536L	S	-	2	0	POM121C	74891435	0.139000	0.22563	0.015000	0.15790	0.411000	0.31082	2.461000	0.45040	0.161000	0.19458	0.195000	0.17529	TCG	G|0.881;A|0.119	0.119	strong		0.562	POM121C-003	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000343919.2	NM_001099415	
UBR3	130507	hgsc.bcm.edu	37	2	170917648	170917648	+	Silent	SNP	A	A	G	rs10203212	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:170917648A>G	ENST00000272793.5	+	34	4895	c.4845A>G	c.(4843-4845)ctA>ctG	p.L1615L	UBR3_ENST00000392631.1_Silent_p.L436L|UBR3_ENST00000418381.1_Silent_p.L1615L			Q6ZT12	UBR3_HUMAN	ubiquitin protein ligase E3 component n-recognin 3 (putative)	1615					embryo development (GO:0009790)|in utero embryonic development (GO:0001701)|olfactory behavior (GO:0042048)|sensory perception of smell (GO:0007608)|suckling behavior (GO:0001967)|ubiquitin-dependent protein catabolic process (GO:0006511)	integral component of membrane (GO:0016021)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(9)|liver(1)|lung(8)|ovary(1)|prostate(3)|stomach(1)	33						TAAGTGAACTATTTAAAGGAA	0.313													A|||	1663	0.332069	0.3185	0.1945	5008	,	,		16483	0.4077		0.2525	False		,,,				2504	0.4519				p.L1615L		Atlas-SNP	.											.	UBR3	182	.	0			c.A4845G						PASS	.	A		1437,2969	452.2+/-349.9	229,979,995	78.0	84.0	82.0		4845	-10.7	0.5	2	dbSNP_119	82	2198,6398	370.9+/-336.0	287,1624,2387	no	coding-synonymous	UBR3	NM_172070.3		516,2603,3382	GG,GA,AA		25.57,32.6146,27.9572		1615/1889	170917648	3635,9367	2203	4298	6501	SO:0001819	synonymous_variant	130507	exon34			TGAACTATTTAAA	AL834144	CCDS2238.2	2q31.1	2008-06-23	2008-06-23	2007-11-29	ENSG00000144357	ENSG00000144357		"""Ubiquitin protein ligase E3 component n-recognins"""	30467	protein-coding gene	gene with protein product		613831	"""zinc finger protein 650"""	ZNF650		17462990	Standard	NM_172070		Approved	KIAA2024, DKFZp434P117, FLJ37422	uc010zdi.2	Q6ZT12	OTTHUMG00000132229	ENST00000272793.5:c.4845A>G	2.37:g.170917648A>G		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	105	46	0.438095	NM_172070	B4DZR7|Q2KHN5|Q6ZR55|Q6ZSC2|Q8IVE7|Q8ND96	Silent	SNP	ENST00000272793.5	37		662	0.3031135531135531	168	0.34146341463414637	80	0.22099447513812154	219	0.38286713286713286	195	0.25725593667546176	A	7.125	0.578734	0.13686	0.326146	0.2557	ENSG00000144357	ENST00000392632	.	.	.	6.06	-10.7	0.00240	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.99999999070877	.	.	.	.	.	.	T	0.24012	-1.0172	3	.	.	.	.	6.0718	0.19893	0.2412:0.2378:0.4365:0.0844	rs10203212;rs61612763;rs10203212	.	.	.	C	677	.	.	Y	+	2	0	UBR3	170625894	0.049000	0.20398	0.451000	0.26982	0.929000	0.56500	-0.900000	0.04097	-2.018000	0.00943	-1.237000	0.01550	TAT	A|0.719;G|0.281	0.281	strong		0.313	UBR3-001	KNOWN	non_canonical_conserved|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000255290.2	NM_172070	
ARSD	414	hgsc.bcm.edu	37	X	2833643	2833643	+	Missense_Mutation	SNP	C	C	A	rs115332247		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	143	0	0		WXS	Illumina HiSeq	Phase_I	107	13	0.121495	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		
FIGNL1	63979	hgsc.bcm.edu	37	7	50513721	50513721	+	Missense_Mutation	SNP	A	A	C	rs146680091	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:50513721A>C	ENST00000419119.1	-	2	2818	c.1265T>G	c.(1264-1266)tTg>tGg	p.L422W	FIGNL1_ENST00000433017.1_Missense_Mutation_p.L422W|FIGNL1_ENST00000356889.4_Missense_Mutation_p.L422W|FIGNL1_ENST00000395556.2_Missense_Mutation_p.L422W			Q6PIW4	FIGL1_HUMAN	fidgetin-like 1	422					ATP metabolic process (GO:0046034)|cellular response to ionizing radiation (GO:0071479)|negative regulation of apoptotic process (GO:0043066)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|osteoblast differentiation (GO:0001649)|osteoblast proliferation (GO:0033687)|regulation of cell cycle (GO:0051726)|regulation of double-strand break repair via homologous recombination (GO:0010569)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nuclear chromosome (GO:0000228)|nucleus (GO:0005634)	ATP binding (GO:0005524)|hydrolase activity (GO:0016787)|magnesium ion binding (GO:0000287)			endometrium(3)|kidney(1)|large_intestine(5)|lung(13)|ovary(3)|prostate(3)|upper_aerodigestive_tract(1)	29	Glioma(55;0.08)|all_neural(89;0.245)	Acute lymphoblastic leukemia(4;3.73e-08)|all_hematologic(4;7.51e-06)				GTCTGGCCTCAACATGGGCCA	0.433													A|||	4	0.000798722	0.0	0.0014	5008	,	,		21003	0.0		0.003	False		,,,				2504	0.0				p.L422W		Atlas-SNP	.											.	FIGNL1	73	.	0			c.T1265G						PASS	.	A	TRP/LEU,TRP/LEU	3,4403	6.2+/-15.9	0,3,2200	82.0	89.0	86.0		1265,1265	6.0	1.0	7	dbSNP_134	86	33,8567	19.8+/-62.0	0,33,4267	yes	missense,missense	FIGNL1	NM_001042762.1,NM_022116.3	61,61	0,36,6467	CC,CA,AA		0.3837,0.0681,0.2768	probably-damaging,probably-damaging	422/675,422/675	50513721	36,12970	2203	4300	6503	SO:0001583	missense	63979	exon4			GGCCTCAACATGG	AK023142	CCDS5510.1	7p12.2	2010-04-21			ENSG00000132436	ENSG00000132436		"""ATPases / AAA-type"""	13286	protein-coding gene	gene with protein product		615383					Standard	XM_005271783		Approved		uc003tpc.3	Q6PIW4	OTTHUMG00000022866	ENST00000419119.1:c.1265T>G	7.37:g.50513721A>C	ENSP00000410811:p.Leu422Trp	Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	110	75	0.681818	NM_001042762	D3DVM6|Q86V18|Q8ND59|Q9H8P1|Q9H917	Missense_Mutation	SNP	ENST00000419119.1	37	CCDS5510.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	A	22.2	4.262784	0.80358	6.81E-4	0.003837	ENSG00000132436	ENST00000356889;ENST00000395556;ENST00000433017;ENST00000419119	D;D;D;D	0.95238	-3.65;-3.65;-3.65;-3.65	5.99	5.99	0.97316	.	0.227384	0.36740	N	0.002426	D	0.95652	0.8586	L	0.47190	1.495	0.80722	D	1	D	0.71674	0.998	D	0.65874	0.939	D	0.95189	0.8306	10	0.41790	T	0.15	-3.4226	15.6754	0.77316	1.0:0.0:0.0:0.0	.	422	Q6PIW4	FIGL1_HUMAN	W	422	ENSP00000349356:L422W;ENSP00000378924:L422W;ENSP00000399997:L422W;ENSP00000410811:L422W	ENSP00000349356:L422W	L	-	2	0	FIGNL1	50481215	1.000000	0.71417	0.994000	0.49952	0.995000	0.86356	9.339000	0.96797	2.291000	0.77112	0.533000	0.62120	TTG	A|0.997;C|0.003	0.003	strong		0.433	FIGNL1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342579.1	NM_001042762	
FOLH1B	219595	hgsc.bcm.edu	37	11	89420607	89420607	+	RNA	SNP	G	G	A	rs61905507	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:89420607G>A	ENST00000532352.1	+	0	1421							Q9HBA9	FOH1B_HUMAN	folate hydrolase 1B							cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	dipeptidase activity (GO:0016805)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(26)|ovary(4)|skin(4)|urinary_tract(2)	48						GCATGCCCAGGTAAATAAATG	0.343													G|||	157	0.0313498	0.0023	0.0432	5008	,	,		15419	0.0		0.0656	False		,,,				2504	0.0593				.		Atlas-SNP	.											.	FOLH1B	93	.	0			c.608+1G>A						PASS	.	G		61,4341	58.1+/-94.6	1,59,2141	66.0	67.0	67.0			4.2	1.0	11	dbSNP_129	67	653,7945	165.5+/-217.6	23,607,3669	yes	splice-5	FOLH1B	NM_153696.2		24,666,5810	AA,AG,GG		7.5948,1.3857,5.4923			89420607	714,12286	2201	4299	6500			219595	exon9			GCCCAGGTAAATA	AF261715		11q14.3	2014-03-18			ENSG00000134612	ENSG00000134612			13636	protein-coding gene	gene with protein product	"""prostate specific membrane antigen like protein"", ""Cell growth-inhibiting gene 26 protein"", ""glutamate carboxypeptidase III"""	609020	"""folate hydrolase 2"""	FOLH2, FOLHP		9838072, 14716746	Standard	NM_153696		Approved	PSMAL, GCPIII	uc001pda.3	Q9HBA9	OTTHUMG00000167376		11.37:g.89420607G>A		Somatic	301	0	0		WXS	Illumina HiSeq	Phase_I	270	65	0.240741	NM_153696		Splice_Site	SNP	ENST00000532352.1	37																																																																																				G|0.947;A|0.053	0.053	strong		0.343	FOLH1B-004	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000395421.1	NM_153696	
GOLGA3	2802	hgsc.bcm.edu	37	12	133378440	133378440	+	Silent	SNP	C	C	T	rs2291258	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:133378440C>T	ENST00000450791.2	-	7	1896	c.1713G>A	c.(1711-1713)ctG>ctA	p.L571L	GOLGA3_ENST00000204726.3_Silent_p.L571L|GOLGA3_ENST00000456883.2_Silent_p.L571L|GOLGA3_ENST00000537452.1_Silent_p.L571L|GOLGA3_ENST00000545875.1_Silent_p.L571L			Q08378	GOGA3_HUMAN	golgin A3	571	Gln-rich.				intra-Golgi vesicle-mediated transport (GO:0006891)	cytosol (GO:0005829)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extrinsic component of Golgi membrane (GO:0090498)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi transport complex (GO:0017119)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	transporter activity (GO:0005215)			breast(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(4)|lung(33)|ovary(3)|pancreas(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	64	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0176)|Lung NSC(355;0.204)		OV - Ovarian serous cystadenocarcinoma(86;2.27e-08)|Epithelial(86;3.34e-07)|all cancers(50;9.4e-06)		GGACACTCTGCAGGGACGAGA	0.652													C|||	2080	0.415335	0.5098	0.451	5008	,	,		17103	0.5159		0.2833	False		,,,				2504	0.2945				p.L571L		Atlas-SNP	.											.	GOLGA3	234	.	0			c.G1713A						PASS	.	C	,	2095,2309	568.8+/-382.5	515,1065,622	87.0	79.0	81.0		1713,1713	3.9	1.0	12	dbSNP_100	81	2233,6367	375.7+/-337.9	302,1629,2369	no	coding-synonymous,coding-synonymous	GOLGA3	NM_001172557.1,NM_005895.3	,	817,2694,2991	TT,TC,CC		25.9651,47.5704,33.2821	,	571/1135,571/1499	133378440	4328,8676	2202	4300	6502	SO:0001819	synonymous_variant	2802	exon8			ACTCTGCAGGGAC	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.1713G>A	12.37:g.133378440C>T		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	44	43	0.977273	NM_001172557	A5PKX6|O43241|Q6P9C7|Q86XW3|Q8TDA9|Q8WZA3	Silent	SNP	ENST00000450791.2	37	CCDS9281.1																																																																																			C|0.621;T|0.379	0.379	strong		0.652	GOLGA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397569.2	NM_005895	
LGR6	59352	hgsc.bcm.edu	37	1	202287537	202287537	+	Silent	SNP	G	G	A	rs788794	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:202287537G>A	ENST00000367278.3	+	18	2195	c.2106G>A	c.(2104-2106)gcG>gcA	p.A702A	LGR6_ENST00000439764.2_Silent_p.A563A|LGR6_ENST00000255432.7_Silent_p.A650A	NM_001017403.1	NP_001017403.1	Q9HBX8	LGR6_HUMAN	leucine-rich repeat containing G protein-coupled receptor 6	702					G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell migration (GO:0030335)|positive regulation of Wnt signaling pathway (GO:0030177)|Wnt signaling pathway (GO:0016055)	integral component of plasma membrane (GO:0005887)|trans-Golgi network membrane (GO:0032588)|vesicle (GO:0031982)	transmembrane signaling receptor activity (GO:0004888)			breast(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(16)|ovary(3)|pancreas(1)|prostate(3)|skin(3)	36						TGGCCGCCGCGCTGCCCCTGG	0.711													G|||	2644	0.527955	0.2791	0.6182	5008	,	,		14115	0.7163		0.5268	False		,,,				2504	0.6074				p.A702A		Atlas-SNP	.											.	LGR6	102	.	0			c.G2106A						PASS	.	G	,,	1383,3019		216,951,1034	16.0	18.0	18.0		2106,1689,1950	-5.4	0.6	1	dbSNP_86	18	4113,4481		990,2133,1174	no	coding-synonymous,coding-synonymous,coding-synonymous	LGR6	NM_001017403.1,NM_001017404.1,NM_021636.2	,,	1206,3084,2208	AA,AG,GG		47.859,31.4175,42.2899	,,	702/968,563/829,650/916	202287537	5496,7500	2201	4297	6498	SO:0001819	synonymous_variant	59352	exon18			CGCCGCGCTGCCC	AF190501	CCDS1424.1, CCDS30971.1, CCDS30972.1	1q32.1	2012-08-21	2011-01-25		ENSG00000133067	ENSG00000133067		"""GPCR / Class A : Orphans"""	19719	protein-coding gene	gene with protein product		606653	"""leucine-rich repeat-containing G protein-coupled receptor 6"""			10935549	Standard	XM_005245404		Approved	FLJ14471	uc001gxu.3	Q9HBX8	OTTHUMG00000041383	ENST00000367278.3:c.2106G>A	1.37:g.202287537G>A		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	65	38	0.584615	NM_001017403	Q5T509|Q5T512|Q6UY15|Q86VU0|Q96K69|Q9BYD7	Silent	SNP	ENST00000367278.3	37	CCDS30971.1																																																																																			G|0.538;A|0.462	0.462	strong		0.711	LGR6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099143.1	NM_021636	
C19orf71	100128569	hgsc.bcm.edu	37	19	3543980	3543980	+	Missense_Mutation	SNP	C	C	T	rs190228213	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:3543980C>T	ENST00000329493.5	+	4	626	c.602C>T	c.(601-603)cCg>cTg	p.P201L	MFSD12_ENST00000398558.4_Intron|MFSD12_ENST00000389395.3_Intron|AC005786.7_ENST00000589360.1_RNA	NM_001135580.1	NP_001129052.1	A6NCJ1	CS071_HUMAN	chromosome 19 open reading frame 71	201										endometrium(2)	2						CAGCGGTCCCCGCCTTCCCTC	0.667													C|||	13	0.00259585	0.0	0.0	5008	,	,		16688	0.0		0.0109	False		,,,				2504	0.002				p.P201L		Atlas-SNP	.											.	C19orf71	12	.	0			c.C602T						PASS	.	C	,LEU/PRO,	1,1383		0,1,691	71.0	84.0	80.0		,602,	-4.0	0.0	19		80	42,3140		0,42,1549	yes	intron,missense,intron	C19orf28,C19orf71	NM_001042680.1,NM_001135580.1,NM_021731.2	,98,	0,43,2240	TT,TC,CC		1.3199,0.0723,0.9417	,benign,	,201/210,	3543980	43,4523	692	1591	2283	SO:0001583	missense	100128569	exon4			GGTCCCCGCCTTC		CCDS45918.1	19p13.3	2012-10-26			ENSG00000183397	ENSG00000183397			34496	protein-coding gene	gene with protein product							Standard	NM_001135580		Approved	LOC100128569	uc010xhm.2	A6NCJ1		ENST00000329493.5:c.602C>T	19.37:g.3543980C>T	ENSP00000327950:p.Pro201Leu	Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	160	77	0.48125	NM_001135580		Missense_Mutation	SNP	ENST00000329493.5	37	CCDS45918.1	8	0.003663003663003663	0	0.0	0	0.0	0	0.0	8	0.010554089709762533	C	4.283	0.051674	0.08291	7.23E-4	0.013199	ENSG00000183397	ENST00000329493	T	0.28895	1.59	4.71	-4.0	0.04057	.	0.227463	0.22628	N	0.057620	T	0.12860	0.0312	L	0.43701	1.375	0.18873	N	0.999989	B	0.15719	0.014	B	0.08055	0.003	T	0.11842	-1.0571	10	0.36615	T	0.2	.	5.6363	0.17538	0.0:0.3681:0.3651:0.2668	.	201	A6NCJ1	CS071_HUMAN	L	201	ENSP00000327950:P201L	ENSP00000327950:P201L	P	+	2	0	C19orf71	3494980	0.000000	0.05858	0.010000	0.14722	0.004000	0.04260	-0.768000	0.04715	-0.158000	0.11040	-1.225000	0.01585	CCG	C|0.995;T|0.005	0.005	strong		0.667	C19orf71-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452943.1	NM_001135580	
CACNA1B	774	hgsc.bcm.edu	37	9	141008876	141008876	+	Silent	SNP	C	C	T	rs2229948	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:141008876C>T	ENST00000371372.1	+	41	5728	c.5583C>T	c.(5581-5583)ttC>ttT	p.F1861F	CACNA1B_ENST00000371355.4_Silent_p.F1862F|CACNA1B_ENST00000277549.5_Silent_p.F1055F|CACNA1B_ENST00000277551.2_Silent_p.F1861F|CACNA1B_ENST00000371363.1_Silent_p.F1859F|CACNA1B_ENST00000371357.1_Silent_p.F1860F	NM_000718.3|NM_001243812.1	NP_000709.1|NP_001230741.1	Q00975	CAC1B_HUMAN	calcium channel, voltage-dependent, N type, alpha 1B subunit	1861					calcium ion import (GO:0070509)|locomotory behavior (GO:0007626)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|neurotransmitter secretion (GO:0007269)|regulation of blood pressure (GO:0008217)|regulation of calcium ion transport (GO:0051924)|regulation of heart contraction (GO:0008016)|response to pain (GO:0048265)|synaptic transmission (GO:0007268)|transport (GO:0006810)	dendrite (GO:0030425)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|protein C-terminus binding (GO:0008022)|voltage-gated calcium channel activity (GO:0005245)			NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(17)|lung(31)|ovary(1)|prostate(1)|skin(2)|stomach(2)|urinary_tract(2)	80	all_cancers(76;0.166)			OV - Ovarian serous cystadenocarcinoma(145;1.16e-05)|Epithelial(140;0.000476)	Amlodipine(DB00381)|Gabapentin(DB00996)|Levetiracetam(DB01202)|Spironolactone(DB00421)|Verapamil(DB00661)	TGATGATATTCGACTTCTACA	0.527													C|||	2527	0.504593	0.2269	0.745	5008	,	,		18751	0.2748		0.7773	False		,,,				2504	0.6656				p.F1861F		Atlas-SNP	.											.	CACNA1B	266	.	0			c.C5583T						PASS	.	C		1391,2499		267,857,821	56.0	52.0	53.0		5583	-4.1	0.9	9	dbSNP_98	53	6251,2029		2339,1573,228	no	coding-synonymous	CACNA1B	NM_000718.3		2606,2430,1049	TT,TC,CC		24.5048,35.7584,37.2062		1861/2340	141008876	7642,4528	1945	4140	6085	SO:0001819	synonymous_variant	774	exon40			GATATTCGACTTC	AB209467	CCDS59522.1, CCDS59523.1	9q34	2013-01-10	2007-02-16		ENSG00000148408	ENSG00000148408		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"", ""EF-hand domain containing"""	1389	protein-coding gene	gene with protein product		601012		CACNL1A5		8825650, 16382099	Standard	NM_000718		Approved	Cav2.2, CACNN	uc004cog.3	Q00975	OTTHUMG00000021002	ENST00000371372.1:c.5583C>T	9.37:g.141008876C>T		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	58	58	1	NM_001243812	B1AQK5	Silent	SNP	ENST00000371372.1	37	CCDS59522.1																																																																																			C|0.503;T|0.497	0.497	strong		0.527	CACNA1B-001	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055380.1	NM_000718	
SYNPO2	171024	hgsc.bcm.edu	37	4	119948046	119948046	+	Missense_Mutation	SNP	A	A	C	rs17263971	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:119948046A>C	ENST00000429713.2	+	3	704	c.522A>C	c.(520-522)caA>caC	p.Q174H	SYNPO2_ENST00000434046.2_Missense_Mutation_p.Q174H|SYNPO2_ENST00000448416.2_Intron|SYNPO2_ENST00000307142.4_Missense_Mutation_p.Q174H	NM_001128933.1	NP_001122405.1	Q9UMS6	SYNP2_HUMAN	synaptopodin 2	174			Q -> H (in dbSNP:rs17263971).			actin cytoskeleton (GO:0015629)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|Z disc (GO:0030018)	14-3-3 protein binding (GO:0071889)|muscle alpha-actinin binding (GO:0051371)			breast(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(20)|lung(18)|ovary(2)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	64						CTGACTCCCAAAGAGGACGCG	0.557													A|||	1110	0.221645	0.2133	0.219	5008	,	,		18571	0.1577		0.2644	False		,,,				2504	0.2566				p.Q174H		Atlas-SNP	.											.	SYNPO2	353	.	0			c.A522C						PASS	.	A	HIS/GLN,HIS/GLN,HIS/GLN	1006,3400	342.8+/-307.3	115,776,1312	36.0	41.0	40.0		522,522,522	-1.5	0.0	4	dbSNP_123	40	2140,6460	354.8+/-329.6	264,1612,2424	yes	missense,missense,missense	SYNPO2	NM_001128933.1,NM_001128934.1,NM_133477.2	24,24,24	379,2388,3736	CC,CA,AA		24.8837,22.8325,24.1888	benign,benign,benign	174/1094,174/1110,174/1262	119948046	3146,9860	2203	4300	6503	SO:0001583	missense	171024	exon3			CTCCCAAAGAGGA	AJ010482	CCDS34054.1, CCDS47128.1, CCDS47129.1, CCDS75185.1, CCDS75186.1	4q26	2008-08-29			ENSG00000172403	ENSG00000172403			17732	protein-coding gene	gene with protein product						11673475, 17828378	Standard	NM_133477		Approved	MYOPODIN	uc010inb.3	Q9UMS6	OTTHUMG00000161165	ENST00000429713.2:c.522A>C	4.37:g.119948046A>C	ENSP00000395143:p.Gln174His	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	97	44	0.453608	NM_001128934	B2RWP6|B2Y8J9|Q9UK89|S5XAM4	Missense_Mutation	SNP	ENST00000429713.2	37	CCDS47129.1	463|463	0.211996336996337|0.211996336996337	87|87	0.17682926829268292|0.17682926829268292	88|88	0.2430939226519337|0.2430939226519337	90|90	0.15734265734265734|0.15734265734265734	198|198	0.2612137203166227|0.2612137203166227	A|A	6.546|6.546	0.469035|0.469035	0.12461|0.12461	0.228325|0.228325	0.248837|0.248837	ENSG00000172403|ENSG00000172403	ENST00000504178|ENST00000307142;ENST00000429713;ENST00000434046	.|T;T;T	.|0.09073	.|3.02;3.03;3.02	5.24|5.24	-1.52|-1.52	0.08637|0.08637	.|.	.|1.114660	.|0.06829	.|N	.|0.793679	T|T	0.00012|0.00012	0.0000|0.0000	L|L	0.53249|0.53249	1.67|1.67	0.80722|0.80722	P|P	0.0|0.0	.|P;B;B	.|0.41569	.|0.755;0.0;0.0	.|B;B;B	.|0.37346	.|0.247;0.001;0.001	T|T	0.44143|0.44143	-0.9347|-0.9347	4|9	.|0.30854	.|T	.|0.27	0.4447|0.4447	5.7472|5.7472	0.18126|0.18126	0.4363:0.2693:0.2945:0.0|0.4363:0.2693:0.2945:0.0	rs17263971;rs17263971|rs17263971;rs17263971	.|174;174;174	.|Q9UMS6-2;E9PEM2;Q9UMS6	.|.;.;SYNP2_HUMAN	Q|H	126|174	.|ENSP00000306015:Q174H;ENSP00000395143:Q174H;ENSP00000390965:Q174H	.|ENSP00000306015:Q174H	K|Q	+|+	1|3	0|2	SYNPO2|SYNPO2	120167494|120167494	0.000000|0.000000	0.05858|0.05858	0.001000|0.001000	0.08648|0.08648	0.201000|0.201000	0.24016|0.24016	-0.045000|-0.045000	0.12003|0.12003	-0.240000|-0.240000	0.09696|0.09696	0.455000|0.455000	0.32223|0.32223	AAG|CAA	A|0.774;C|0.226	0.226	strong		0.557	SYNPO2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000364020.1		
ZNF136	7695	hgsc.bcm.edu	37	19	12298164	12298164	+	Missense_Mutation	SNP	G	G	A	rs200700405		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:12298164G>A	ENST00000343979.4	+	4	1111	c.971G>A	c.(970-972)cGa>cAa	p.R324Q	ZNF136_ENST00000398616.2_Missense_Mutation_p.R258Q	NM_003437.3	NP_003428.1	P52737	ZN136_HUMAN	zinc finger protein 136	324					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|transcription corepressor activity (GO:0003714)			NS(1)|biliary_tract(1)|kidney(3)|large_intestine(2)|lung(6)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)	18						CCCTCCCTTCGACTACATGAA	0.428																																					p.R324Q		Atlas-SNP	.											ZNF136,colon,carcinoma,+1,1	ZNF136	57	1	0			c.G971A						PASS	.						92.0	93.0	92.0					19																	12298164		2203	4300	6503	SO:0001583	missense	7695	exon4			CCCTTCGACTACA	U09367	CCDS32916.1	19p13.2	2013-01-08	2006-06-13		ENSG00000196646	ENSG00000196646		"""Zinc fingers, C2H2-type"", ""-"""	12920	protein-coding gene	gene with protein product		604078	"""zinc finger protein 136 (clone pHZ-20)"""			7557990	Standard	NM_003437		Approved	pHZ-20	uc002mti.3	P52737	OTTHUMG00000156429	ENST00000343979.4:c.971G>A	19.37:g.12298164G>A	ENSP00000344162:p.Arg324Gln	Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	39	22	0.564103	NM_003437		Missense_Mutation	SNP	ENST00000343979.4	37	CCDS32916.1	.	.	.	.	.	.	.	.	.	.	G	11.56	1.676518	0.29783	.	.	ENSG00000196646	ENST00000343979;ENST00000398616	T;T	0.07444	3.19;3.19	1.25	0.00598	0.14064	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.02571	0.0078	N	0.10685	0.025	0.09310	N	1	B	0.33857	0.429	B	0.15052	0.012	T	0.42292	-0.9460	8	.	.	.	.	1.9912	0.03447	0.4876:0.0:0.254:0.2584	.	324	P52737	ZN136_HUMAN	Q	324;258	ENSP00000344162:R324Q;ENSP00000381617:R258Q	.	R	+	2	0	ZNF136	12159164	0.000000	0.05858	0.007000	0.13788	0.997000	0.91878	-1.017000	0.03630	-0.007000	0.14345	0.655000	0.94253	CGA	G|0.999;A|0.001	0.001	weak		0.428	ZNF136-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344151.2	NM_003437	
OR10H2	26538	hgsc.bcm.edu	37	19	15839081	15839081	+	Silent	SNP	C	C	T	rs2067083	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:15839081C>T	ENST00000305899.3	+	1	248	c.228C>T	c.(226-228)gcC>gcT	p.A76A		NM_013939.2	NP_039227.1	O60403	O10H2_HUMAN	olfactory receptor, family 10, subfamily H, member 2	76						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(2)|skin(3)|stomach(1)	27	all_hematologic(1;0.0517)|Acute lymphoblastic leukemia(2;0.074)					ACACCGTGGCCATCATCCCGC	0.617													C|||	1287	0.256989	0.4198	0.2709	5008	,	,		23430	0.0119		0.3111	False		,,,				2504	0.2239				p.A76A		Atlas-SNP	.											.	OR10H2	59	.	0			c.C228T						PASS	.	C		1763,2643		337,1089,777	149.0	122.0	131.0		228	2.3	0.8	19	dbSNP_96	131	2449,6151		356,1737,2207	no	coding-synonymous	OR10H2	NM_013939.2		693,2826,2984	TT,TC,CC		28.4767,40.0136,32.3851		76/316	15839081	4212,8794	2203	4300	6503	SO:0001819	synonymous_variant	26538	exon1			CGTGGCCATCATC	AC004597	CCDS12333.1	19p13.1	2012-08-09				ENSG00000171942		"""GPCR / Class A : Olfactory receptors"""	8173	protein-coding gene	gene with protein product							Standard	NM_013939		Approved		uc002nbm.2	O60403		ENST00000305899.3:c.228C>T	19.37:g.15839081C>T		Somatic	208	0	0		WXS	Illumina HiSeq	Phase_I	250	66	0.264	NM_013939	Q6IFQ1|Q96R58	Silent	SNP	ENST00000305899.3	37	CCDS12333.1																																																																																			C|0.708;T|0.292	0.292	strong		0.617	OR10H2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460917.1		
SLC25A15	10166	hgsc.bcm.edu	37	13	41379272	41379272	+	Silent	SNP	C	C	T	rs9577152	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	88	0	0		WXS	Illumina HiSeq	Phase_I	72	37	0.513889	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	
CNKSR3	154043	hgsc.bcm.edu	37	6	154763401	154763401	+	Silent	SNP	G	G	A	rs6557351	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	90	0	0		WXS	Illumina HiSeq	Phase_I	41	31	0.756098	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	
CCDC8	83987	hgsc.bcm.edu	37	19	46914921	46914921	+	Missense_Mutation	SNP	G	G	A	rs34186470	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:46914921G>A	ENST00000307522.3	-	1	1920	c.1147C>T	c.(1147-1149)Cac>Tac	p.H383Y		NM_032040.4	NP_114429.2	Q9H0W5	CCDC8_HUMAN	coiled-coil domain containing 8	383			H -> Y (in dbSNP:rs34186470).		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)		TCTTCCCTGTGGTTATCTGTG	0.577													G|||	1158	0.23123	0.0998	0.1225	5008	,	,		17813	0.4048		0.1312	False		,,,				2504	0.41				p.H383Y		Atlas-SNP	.											.	CCDC8	56	.	0			c.C1147T						PASS	.	G	TYR/HIS	419,3987	204.5+/-226.7	21,377,1805	129.0	124.0	126.0		1147	2.8	0.2	19	dbSNP_126	126	1169,7431	239.3+/-270.5	83,1003,3214	yes	missense	CCDC8	NM_032040.3	83	104,1380,5019	AA,AG,GG		13.593,9.5098,12.2097	benign	383/539	46914921	1588,11418	2203	4300	6503	SO:0001583	missense	83987	exon1			CCCTGTGGTTATC	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.1147C>T	19.37:g.46914921G>A	ENSP00000303158:p.His383Tyr	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	84	46	0.547619	NM_032040	Q8TB26	Missense_Mutation	SNP	ENST00000307522.3	37	CCDS12685.1	432	0.1978021978021978	46	0.09349593495934959	40	0.11049723756906077	238	0.4160839160839161	108	0.1424802110817942	G	11.61	1.689855	0.29962	0.095098	0.13593	ENSG00000169515	ENST00000307522	T	0.11604	2.76	2.79	2.79	0.32731	.	1.910480	0.03066	N	0.156491	T	0.00012	0.0000	N	0.22421	0.69	0.58432	P	2.9999999999752447E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.43845	-0.9366	9	0.72032	D	0.01	0.0649	11.7523	0.51855	0.0:0.0:1.0:0.0	rs34186470	383	Q9H0W5	CCDC8_HUMAN	Y	383	ENSP00000303158:H383Y	ENSP00000303158:H383Y	H	-	1	0	CCDC8	51606761	0.007000	0.16637	0.232000	0.24009	0.066000	0.16364	1.530000	0.36007	1.847000	0.53656	0.313000	0.20887	CAC	A|0.146;C|0.000;G|0.854	0.146	strong		0.577	CCDC8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368598.1	NM_032040	
PCNT	5116	hgsc.bcm.edu	37	21	47786524	47786524	+	Missense_Mutation	SNP	A	A	G	rs2839227	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:47786524A>G	ENST00000359568.5	+	15	2742	c.2635A>G	c.(2635-2637)Acc>Gcc	p.T879A	PCNT_ENST00000480896.1_3'UTR	NM_006031.5	NP_006022.3	O95613	PCNT_HUMAN	pericentrin	879			T -> A (in dbSNP:rs2839227). {ECO:0000269|PubMed:11171385}.		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)					TAAAGAGATCACCGAGAAATT	0.522													A|||	1586	0.316693	0.5787	0.2464	5008	,	,		20280	0.2014		0.1521	False		,,,				2504	0.3006				p.T879A		Atlas-SNP	.											.	PCNT	283	.	0			c.A2635G						PASS	.	A	ALA/THR	2199,2189		545,1109,540	63.0	60.0	61.0		2635	1.8	0.0	21	dbSNP_100	61	1168,7408		82,1004,3202	yes	missense	PCNT	NM_006031.5	58	627,2113,3742	GG,GA,AA		13.6194,49.8861,25.9719	possibly-damaging	879/3337	47786524	3367,9597	2194	4288	6482	SO:0001583	missense	5116	exon15			GAGATCACCGAGA	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.2635A>G	21.37:g.47786524A>G	ENSP00000352572:p.Thr879Ala	Somatic	295	0	0		WXS	Illumina HiSeq	Phase_I	345	115	0.333333	NM_006031	O43152|Q7Z7C9	Missense_Mutation	SNP	ENST00000359568.5	37	CCDS33592.1	584	0.2673992673992674	275	0.5589430894308943	71	0.19613259668508287	121	0.21153846153846154	117	0.15435356200527706	A	7.766	0.706433	0.15239	0.501139	0.136194	ENSG00000160299	ENST00000359568	T	0.01560	4.77	5.61	1.81	0.25067	.	0.919056	0.08883	N	0.879765	T	0.00012	0.0000	L	0.54323	1.7	0.80722	P	0.0	B;B	0.29988	0.264;0.172	B;B	0.17722	0.019;0.009	T	0.12760	-1.0535	9	0.19590	T	0.45	.	4.1456	0.10214	0.689:0.0:0.1615:0.1495	rs2839227;rs59744350;rs2839227	761;879	O95613-2;O95613	.;PCNT_HUMAN	A	879	ENSP00000352572:T879A	ENSP00000352572:T879A	T	+	1	0	PCNT	46610952	0.044000	0.20184	0.002000	0.10522	0.099000	0.18886	2.418000	0.44662	0.438000	0.26450	0.533000	0.62120	ACC	A|0.704;C|0.002	.	strong		0.522	PCNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207336.1	NM_006031	
RAD51AP2	729475	hgsc.bcm.edu	37	2	17696573	17696573	+	Missense_Mutation	SNP	C	C	T	rs834514	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:17696573C>T	ENST00000399080.2	-	1	3133	c.3110G>A	c.(3109-3111)gGt>gAt	p.G1037D		NM_001099218.2	NP_001092688.1	Q09MP3	R51A2_HUMAN	RAD51 associated protein 2	1037			G -> D (in dbSNP:rs834514).							endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(10)|liver(1)|lung(17)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	49	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)					CATATTAGGACCTGCTATAGT	0.358													C|||	2908	0.580671	0.1339	0.6326	5008	,	,		19259	0.8849		0.6183	False		,,,				2504	0.7955				p.G1037D		Atlas-SNP	.											.	RAD51AP2	134	.	0			c.G3110A						PASS	.	C	ASP/GLY	955,2719		136,683,1018	151.0	138.0	142.0		3110	2.3	0.0	2	dbSNP_86	142	5110,3072		1605,1900,586	yes	missense	RAD51AP2	NM_001099218.2	94	1741,2583,1604	TT,TC,CC		37.5458,25.9935,48.8445	probably-damaging	1037/1160	17696573	6065,5791	1837	4091	5928	SO:0001583	missense	729475	exon1			TTAGGACCTGCTA	AK310498	CCDS42656.1	2p24.2	2009-01-13			ENSG00000214842	ENSG00000214842			34417	protein-coding gene	gene with protein product						16990250	Standard	NM_001099218		Approved	FLJ17540	uc002rcl.1	Q09MP3	OTTHUMG00000151761	ENST00000399080.2:c.3110G>A	2.37:g.17696573C>T	ENSP00000382030:p.Gly1037Asp	Somatic	262	1	0.00381679		WXS	Illumina HiSeq	Phase_I	265	265	1	NM_001099218		Missense_Mutation	SNP	ENST00000399080.2	37	CCDS42656.1	1264	0.5787545787545788	85	0.17276422764227642	220	0.6077348066298343	500	0.8741258741258742	459	0.6055408970976254	C	8.123	0.781475	0.16120	0.259935	0.624542	ENSG00000214842	ENST00000399080	T	0.32515	1.45	5.15	2.29	0.28610	.	.	.	.	.	T	0.00012	0.0000	N	0.12182	0.205	0.80722	P	0.0	B	0.23540	0.087	B	0.25759	0.063	T	0.08700	-1.0709	8	0.30078	T	0.28	-0.2348	5.6724	0.17729	0.0:0.5727:0.1336:0.2937	rs834514;rs1619596;rs2139384;rs17380198;rs52804587;rs834514	1037	Q09MP3	R51A2_HUMAN	D	1037	ENSP00000382030:G1037D	ENSP00000382030:G1037D	G	-	2	0	RAD51AP2	17560054	0.000000	0.05858	0.002000	0.10522	0.043000	0.13939	0.320000	0.19540	0.246000	0.21394	0.655000	0.94253	GGT	C|0.409;T|0.591	0.591	strong		0.358	RAD51AP2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323801.3	NM_001099218	
TNKS1BP1	85456	hgsc.bcm.edu	37	11	57080938	57080938	+	Silent	SNP	C	C	A	rs145901431	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:57080938C>A	ENST00000532437.1	-	4	1535	c.1224G>T	c.(1222-1224)ggG>ggT	p.G408G	TNKS1BP1_ENST00000530920.1_5'Flank|TNKS1BP1_ENST00000358252.3_Silent_p.G408G			Q9C0C2	TB182_HUMAN	tankyrase 1 binding protein 1, 182kDa	408	Acidic.|Pro-rich.				gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|RNA metabolic process (GO:0016070)|telomere maintenance via telomerase (GO:0007004)	CCR4-NOT complex (GO:0030014)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|nuclear telomeric heterochromatin (GO:0005724)|nucleus (GO:0005634)	ankyrin binding (GO:0030506)|enzyme binding (GO:0019899)			breast(3)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(11)|lung(24)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	64		all_epithelial(135;0.21)				CCTCCTCCTCCCCGCCAGATG	0.647													C|||	7	0.00139776	0.0	0.0029	5008	,	,		16354	0.0		0.004	False		,,,				2504	0.001				p.G408G		Atlas-SNP	.											.	TNKS1BP1	148	.	0			c.G1224T						PASS	.	C		0,4398		0,0,2199	23.0	24.0	24.0		1224	0.8	0.0	11	dbSNP_134	24	27,8561		0,27,4267	yes	coding-synonymous	TNKS1BP1	NM_033396.2		0,27,6466	AA,AC,CC		0.3144,0.0,0.2079		408/1730	57080938	27,12959	2199	4294	6493	SO:0001819	synonymous_variant	85456	exon5			CTCCTCCCCGCCA	AB051528	CCDS7951.1	11q12.2	2008-07-21			ENSG00000149115	ENSG00000149115			19081	protein-coding gene	gene with protein product		607104				11854288	Standard	NM_033396		Approved	TAB182, KIAA1741, FLJ45975	uc001njs.3	Q9C0C2	OTTHUMG00000167022	ENST00000532437.1:c.1224G>T	11.37:g.57080938C>A		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	50	41	0.82	NM_033396	A7E2F8|Q6PJ35|Q6ZV74	Silent	SNP	ENST00000532437.1	37	CCDS7951.1																																																																																			C|0.998;A|0.002	0.002	strong		0.647	TNKS1BP1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392455.1	NM_033396	
SERPIND1	3053	hgsc.bcm.edu	37	22	21133831	21133831	+	Missense_Mutation	SNP	C	C	A	rs5903	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:21133831C>A	ENST00000215727.5	+	2	514	c.231C>A	c.(229-231)gaC>gaA	p.D77E	PI4KA_ENST00000466162.1_Intron|PI4KA_ENST00000255882.6_Intron|SERPIND1_ENST00000406799.1_Missense_Mutation_p.D77E|PI4KA_ENST00000572273.1_Intron	NM_000185.3	NP_000176.2	P05546	HEP2_HUMAN	serpin peptidase inhibitor, clade D (heparin cofactor), member 1	77	2 X 11 AA approximate repeats, Asp/Glu- rich (acidic) (hirudin-like).|Chemotactic activity.				blood coagulation (GO:0007596)|chemotaxis (GO:0006935)|negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	endopeptidase inhibitor activity (GO:0004866)|heparin binding (GO:0008201)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(2)|endometrium(3)|kidney(1)|large_intestine(2)|lung(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	13	all_cancers(11;6.16e-25)|all_epithelial(7;1.02e-22)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0332)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.000536)|Lung(15;0.0108)|Epithelial(17;0.196)		Ardeparin(DB00407)|Sulodexide(DB06271)	AGGAGGACGACGACTATCTGG	0.507													C|||	17	0.00339457	0.0	0.0043	5008	,	,		20196	0.0		0.0119	False		,,,				2504	0.002				p.D77E		Atlas-SNP	.											.	SERPIND1	92	.	0			c.C231A						PASS	.	C	GLU/ASP,	10,4396	16.8+/-37.8	0,10,2193	79.0	69.0	72.0		231,	-11.5	0.4	22	dbSNP_52	72	83,8517	48.5+/-108.0	0,83,4217	yes	missense,intron	SERPIND1,PI4KA	NM_000185.3,NM_058004.3	45,	0,93,6410	AA,AC,CC		0.9651,0.227,0.7151	benign,	77/500,	21133831	93,12913	2203	4300	6503	SO:0001583	missense	3053	exon2			GGACGACGACTAT	M12849	CCDS13783.1	22q11.21	2014-02-18	2005-08-18		ENSG00000099937	ENSG00000099937		"""Serine (or cysteine) peptidase inhibitors"""	4838	protein-coding gene	gene with protein product	"""heparin cofactor II"""	142360	"""serine (or cysteine) proteinase inhibitor, clade D (heparin cofactor), member 1"""	HCF2		1671335, 24172014	Standard	XM_005261597		Approved	HC-II, HLS2, HC2, D22S673	uc002ztb.1	P05546	OTTHUMG00000150755	ENST00000215727.5:c.231C>A	22.37:g.21133831C>A	ENSP00000215727:p.Asp77Glu	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	133	65	0.488722	NM_000185	B2RAI1|D3DX34|Q6IBZ5	Missense_Mutation	SNP	ENST00000215727.5	37	CCDS13783.1	.	.	.	.	.	.	.	.	.	.	C	4.885	0.164489	0.09287	0.00227	0.009651	ENSG00000099937	ENST00000215727;ENST00000406799	D;D	0.81739	-1.53;-1.53	5.75	-11.5	0.00074	.	0.295809	0.41500	N	0.000877	T	0.34135	0.0887	N	0.04018	-0.295	0.22034	N	0.999407	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.55579	-0.8119	10	0.02654	T	1	.	7.576	0.27937	0.0539:0.4378:0.3104:0.1979	.	77;77	Q8IVC0;P05546	.;HEP2_HUMAN	E	77	ENSP00000215727:D77E;ENSP00000384050:D77E	ENSP00000215727:D77E	D	+	3	2	SERPIND1	19463831	0.000000	0.05858	0.378000	0.26068	0.923000	0.55619	-2.171000	0.01267	-1.815000	0.01222	-1.021000	0.02439	GAC	A|0.004;C|0.984;T|0.013	0.004	strong		0.507	SERPIND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319961.1	NM_000185	
FAM222B	55731	hgsc.bcm.edu	37	17	27085564	27085564	+	Silent	SNP	A	A	G	rs2043031	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:27085564A>G	ENST00000341217.5	-	3	1628	c.1413T>C	c.(1411-1413)ctT>ctC	p.L471L	FAM222B_ENST00000582266.1_3'UTR|FAM222B_ENST00000581407.1_Silent_p.L471L|FAM222B_ENST00000452648.3_Silent_p.L471L	NM_018182.2	NP_060652.2	Q8WU58	F222B_HUMAN	family with sequence similarity 222, member B	471			L -> S (in dbSNP:rs2043031).														ACGGCATGGCAAGGTCCTGAG	0.657													G|||	1064	0.21246	0.1422	0.2349	5008	,	,		17804	0.1786		0.1938	False		,,,				2504	0.3456				p.L471L		Atlas-SNP	.											.	.	.	.	0			c.T1413C						PASS	.	G	,	557,3407		54,449,1479	40.0	41.0	41.0		1413,1413	0.7	0.3	17	dbSNP_94	41	1603,6699		152,1299,2700	no	coding-synonymous,coding-synonymous	C17orf63	NM_001077498.1,NM_018182.2	,	206,1748,4179	GG,GA,AA		19.3086,14.0515,17.6097	,	471/563,471/563	27085564	2160,10106	1982	4151	6133	SO:0001819	synonymous_variant	55731	exon4			CATGGCAAGGTCC	AK001562	CCDS45637.1, CCDS74022.1	17q11.2	2012-04-27	2012-04-27	2012-04-27	ENSG00000173065	ENSG00000173065			25563	protein-coding gene	gene with protein product			"""chromosome 17 open reading frame 63"""	C17orf63			Standard	NM_001288631		Approved	FLJ10700	uc010way.1	Q8WU58		ENST00000341217.5:c.1413T>C	17.37:g.27085564A>G		Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	35	35	1	NM_018182	Q9H6F3|Q9NVJ4|Q9NXN6	Silent	SNP	ENST00000341217.5	37	CCDS45637.1																																																																																			A|0.808;G|0.192	0.192	strong		0.657	FAM222B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446703.1	NM_018182	
PSD4	23550	hgsc.bcm.edu	37	2	113940207	113940207	+	Silent	SNP	T	T	A	rs3738908	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:113940207T>A	ENST00000245796.6	+	2	369	c.174T>A	c.(172-174)ccT>ccA	p.P58P	PSD4_ENST00000441564.3_Silent_p.P58P|PSD4_ENST00000465917.1_3'UTR	NM_012455.2	NP_036587.2	Q8NDX1	PSD4_HUMAN	pleckstrin and Sec7 domain containing 4	58					neuron differentiation (GO:0030182)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)	cell junction (GO:0030054)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|phospholipid binding (GO:0005543)			cervix(1)|endometrium(2)|large_intestine(4)|lung(13)|ovary(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						CTCCTGAACCTACCAGACAAA	0.627													T|||	216	0.043131	0.0	0.0101	5008	,	,		18830	0.0813		0.0308	False		,,,				2504	0.0982				p.P58P		Atlas-SNP	.											.	PSD4	74	.	0			c.T174A						PASS	.	T		26,4380	32.6+/-62.9	0,26,2177	82.0	79.0	80.0		174	-6.4	0.0	2	dbSNP_107	80	158,8442	75.1+/-137.7	0,158,4142	no	coding-synonymous	PSD4	NM_012455.2		0,184,6319	AA,AT,TT		1.8372,0.5901,1.4147		58/1057	113940207	184,12822	2203	4300	6503	SO:0001819	synonymous_variant	23550	exon2			TGAACCTACCAGA	U63127	CCDS33276.1	2q13	2013-01-10			ENSG00000125637	ENSG00000125637		"""Pleckstrin homology (PH) domain containing"""	19096	protein-coding gene	gene with protein product		614442				12082148	Standard	XM_005263634		Approved	TIC, EFA6B	uc002tjc.3	Q8NDX1	OTTHUMG00000153339	ENST00000245796.6:c.174T>A	2.37:g.113940207T>A		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	125	64	0.512	NM_012455	A6NEG7|A8K1Y0|O95621|Q4ZG34|Q6GPH8|Q8IYP4	Silent	SNP	ENST00000245796.6	37	CCDS33276.1																																																																																			T|0.982;A|0.018	0.018	strong		0.627	PSD4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000330789.1	NM_012455	
FBXW10	10517	hgsc.bcm.edu	37	17	18671961	18671961	+	Missense_Mutation	SNP	C	C	T	rs144931466	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:18671961C>T	ENST00000395665.4	+	10	2040	c.1819C>T	c.(1819-1821)Cgc>Tgc	p.R607C	FBXW10_ENST00000308799.4_Missense_Mutation_p.R636C|FBXW10_ENST00000395667.1_Missense_Mutation_p.R607C|FBXW10_ENST00000301938.4_Missense_Mutation_p.R607C			Q5XX13	FBW10_HUMAN	F-box and WD repeat domain containing 10	607										NS(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(13)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	42						GAAGTACGAGCGCTGCCTGAT	0.572													C|||	350	0.0698882	0.1067	0.1095	5008	,	,		17668	0.003		0.0825	False		,,,				2504	0.0481				p.R607C		Atlas-SNP	.											.	FBXW10	82	.	0			c.C1819T						PASS	.	C	CYS/ARG	586,3820	257.4+/-261.8	47,492,1664	92.0	82.0	85.0		1819	1.9	1.0	17	dbSNP_134	85	627,7969	162.6+/-215.3	23,581,3694	no	missense	FBXW10	NM_031456.3	180	70,1073,5358	TT,TC,CC		7.2941,13.3,9.3293	probably-damaging	607/1052	18671961	1213,11789	2203	4298	6501	SO:0001583	missense	10517	exon10			TACGAGCGCTGCC	BC028364	CCDS11199.2, CCDS11199.3, CCDS58524.1	17p11	2013-01-09	2007-02-08	2004-07-21	ENSG00000171931	ENSG00000171931		"""F-boxes / WD-40 domains"", ""WD repeat domain containing"""	1211	protein-coding gene	gene with protein product		611679	"""chromosome 17 open reading frame 1A"", ""F-box and WD-40 domain protein 10"""	C17orf1, C17orf1A		9787083, 7586531	Standard	NM_001267585		Approved	SM2SH2, HREP, Fbw10	uc002guk.3	Q5XX13	OTTHUMG00000059048	ENST00000395665.4:c.1819C>T	17.37:g.18671961C>T	ENSP00000379025:p.Arg607Cys	Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	169	74	0.43787	NM_001267585	C9JRY8|C9JZD7|Q8TC00|Q9H0F0	Missense_Mutation	SNP	ENST00000395665.4	37	CCDS11199.3	157	0.07188644688644688	56	0.11382113821138211	39	0.10773480662983426	3	0.005244755244755245	59	0.07783641160949868	C	11.68	1.709898	0.30322	0.133	0.072941	ENSG00000171931	ENST00000395667;ENST00000308799;ENST00000301938;ENST00000395665	T;T;T;T	0.19938	2.11;2.11;2.11;2.11	2.97	1.93	0.25924	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.435434	0.15519	U	0.258126	T	0.00468	0.0015	M	0.72894	2.215	0.42668	D	0.993509	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.995;0.999;0.993;0.994	T	0.00068	-1.2141	10	0.87932	D	0	.	7.6577	0.28386	0.4858:0.5141:0.0:0.0	.	607;636;607;607	Q5XX13-3;Q5XX13-2;Q5XX13;Q5XX13-4	.;.;FBW10_HUMAN;.	C	607;636;607;607	ENSP00000379026:R607C;ENSP00000310382:R636C;ENSP00000306937:R607C;ENSP00000379025:R607C	ENSP00000306937:R607C	R	+	1	0	FBXW10	18612686	1.000000	0.71417	0.967000	0.41034	0.366000	0.29705	1.060000	0.30530	0.527000	0.28560	0.194000	0.17425	CGC	.	.	weak		0.572	FBXW10-003	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313531.2	NM_031456	
NPAS2	4862	hgsc.bcm.edu	37	2	101587455	101587455	+	Silent	SNP	C	C	T	rs1562313	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:101587455C>T	ENST00000335681.5	+	12	1344	c.1059C>T	c.(1057-1059)taC>taT	p.Y353Y	AC016738.3_ENST00000439150.1_RNA|AC016738.3_ENST00000446644.1_RNA|NPAS2_ENST00000542504.1_Silent_p.Y418Y	NM_002518.3	NP_002509.2	Q99743	NPAS2_HUMAN	neuronal PAS domain protein 2	353	PAC.				cellular lipid metabolic process (GO:0044255)|cellular response to DNA damage stimulus (GO:0006974)|central nervous system development (GO:0007417)|circadian regulation of gene expression (GO:0032922)|circadian sleep/wake cycle (GO:0042745)|locomotor rhythm (GO:0045475)|negative regulation of cell death (GO:0060548)|positive regulation of DNA repair (GO:0045739)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of response to DNA damage stimulus (GO:2001020)|response to redox state (GO:0051775)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	core promoter binding (GO:0001047)|DNA binding (GO:0003677)|Hsp90 protein binding (GO:0051879)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)			cervix(1)|endometrium(3)|large_intestine(7)|lung(9)|ovary(3)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						TGTACAGTTACGCAGATGTCC	0.567													C|||	1185	0.236621	0.3033	0.1095	5008	,	,		16076	0.2808		0.2256	False		,,,				2504	0.2025				p.Y353Y		Atlas-SNP	.											.	NPAS2	88	.	0			c.C1059T						PASS	.	C		1190,3216	417.6+/-338.0	152,886,1165	90.0	88.0	89.0		1059	-8.2	0.1	2	dbSNP_88	89	1787,6813	321.3+/-315.0	184,1419,2697	no	coding-synonymous	NPAS2	NM_002518.3		336,2305,3862	TT,TC,CC		20.7791,27.0086,22.8894		353/825	101587455	2977,10029	2203	4300	6503	SO:0001819	synonymous_variant	4862	exon12			CAGTTACGCAGAT	U77970	CCDS2048.1	2q11.2	2013-05-21			ENSG00000170485	ENSG00000170485		"""Basic helix-loop-helix proteins"""	7895	protein-coding gene	gene with protein product		603347				9012850, 9079689	Standard	NM_002518		Approved	MOP4, PASD4, bHLHe9	uc002tap.1	Q99743	OTTHUMG00000130675	ENST00000335681.5:c.1059C>T	2.37:g.101587455C>T		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	98	39	0.397959	NM_002518	Q4ZFV9|Q53SQ3|Q86V96|Q99629	Silent	SNP	ENST00000335681.5	37	CCDS2048.1	518	0.23717948717948717	152	0.3089430894308943	43	0.11878453038674033	144	0.2517482517482518	179	0.23614775725593667	C	0.085	-1.177368	0.01633	0.270086	0.207791	ENSG00000170485	ENST00000448812	.	.	.	6.06	-8.22	0.01037	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.99999999888017	.	.	.	.	.	.	T	0.25082	-1.0142	3	.	.	.	.	20.7068	0.99706	0.0:0.2374:0.0:0.7626	rs1562313;rs3739007;rs58016169;rs1562313	.	.	.	C	240	.	.	R	+	1	0	NPAS2	100953887	0.018000	0.18449	0.083000	0.20561	0.032000	0.12392	-1.204000	0.03017	-2.172000	0.00774	-2.084000	0.00378	CGC	C|0.766;T|0.234	0.234	strong		0.567	NPAS2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253168.3		
SNX18	112574	hgsc.bcm.edu	37	5	53815219	53815219	+	Silent	SNP	G	G	A	rs35241631	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:53815219G>A	ENST00000326277.3	+	1	1627	c.1437G>A	c.(1435-1437)gaG>gaA	p.E479E	SNX18_ENST00000381410.4_Silent_p.E479E|SNX18_ENST00000343017.6_Silent_p.E479E	NM_052870.2	NP_443102.2	Q96RF0	SNX18_HUMAN	sorting nexin 18	479	BAR.				cleavage furrow formation (GO:0036089)|endocytosis (GO:0006897)|endosomal transport (GO:0016197)|intracellular protein transport (GO:0006886)|mitotic cytokinesis (GO:0000281)|mitotic nuclear division (GO:0007067)|positive regulation of GTPase activity (GO:0043547)	cytoplasmic membrane-bounded vesicle (GO:0016023)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|growth cone (GO:0030426)|neuronal cell body (GO:0043025)	phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)			endometrium(3)|kidney(1)|large_intestine(3)|lung(6)|prostate(2)|stomach(1)|upper_aerodigestive_tract(2)	18		Lung NSC(810;3.46e-05)|Breast(144;0.102)				AGGCCTTTGAGCTGGACCAGC	0.632													g|||	97	0.019369	0.0045	0.0216	5008	,	,		19624	0.0		0.0497	False		,,,				2504	0.0266				p.E479E		Atlas-SNP	.											.	SNX18	102	.	0			c.G1437A						PASS	.	G	,,	31,4375	37.6+/-69.7	0,31,2172	42.0	41.0	42.0		1437,1437,1437	1.2	1.0	5	dbSNP_126	42	379,8221	123.6+/-182.4	9,361,3930	no	coding-synonymous,coding-synonymous,coding-synonymous	SNX18	NM_001102575.1,NM_001145427.1,NM_052870.2	,,	9,392,6102	AA,AG,GG		4.407,0.7036,3.1524	,,	479/625,479/592,479/629	53815219	410,12596	2203	4300	6503	SO:0001819	synonymous_variant	112574	exon1			CTTTGAGCTGGAC	AF395536	CCDS3962.1, CCDS43317.1, CCDS54851.1	5q11.2	2010-05-12	2008-03-11	2008-03-11	ENSG00000178996	ENSG00000178996		"""Sorting nexins"""	19245	protein-coding gene	gene with protein product			"""sorting nexin associated golgi protein 1"""	SNAG1		16782399, 17761170	Standard	NM_052870		Approved	SH3PX2, SH3PXD3B	uc003jpi.4	Q96RF0	OTTHUMG00000096994	ENST00000326277.3:c.1437G>A	5.37:g.53815219G>A		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	59	24	0.40678	NM_052870	B4E2B3|H7BXX3|Q05BB3|Q0VG02	Silent	SNP	ENST00000326277.3	37	CCDS3962.1																																																																																			G|0.969;A|0.031	0.031	strong		0.632	SNX18-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000214072.2		
C9orf66	157983	hgsc.bcm.edu	37	9	214864	214864	+	Missense_Mutation	SNP	C	C	T	rs2236547	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:214864C>T	ENST00000382387.2	-	1	1029	c.533G>A	c.(532-534)cGg>cAg	p.R178Q	DOCK8_ENST00000453981.1_5'Flank|DOCK8_ENST00000432829.2_5'Flank	NM_152569.2	NP_689782.2	Q5T8R8	CI066_HUMAN	chromosome 9 open reading frame 66	178			R -> Q (in dbSNP:rs2236547).							central_nervous_system(1)|cervix(1)|kidney(1)|skin(1)	4	all_lung(41;0.218)	all_cancers(5;2.09e-12)|all_epithelial(5;6.16e-09)|all_lung(10;1.15e-08)|Lung NSC(10;1.91e-08)|Acute lymphoblastic leukemia(5;0.00457)|all_hematologic(5;0.0332)|Breast(48;0.0646)|Prostate(43;0.137)	Kidney(42;0.112)|KIRC - Kidney renal clear cell carcinoma(5;0.157)	all cancers(5;0.000704)|Lung(218;0.00755)|GBM - Glioblastoma multiforme(5;0.0149)|Epithelial(6;0.0154)		CAGCGCCGACCGACAGACGAG	0.692													T|||	1630	0.325479	0.326	0.3213	5008	,	,		11784	0.4117		0.2048	False		,,,				2504	0.363				p.R178Q		Atlas-SNP	.											C9orf66,rectum,carcinoma,0,1	C9orf66	16	1	0			c.G533A						PASS	.	T	GLN/ARG	1030,2672		136,758,957	20.0	17.0	18.0		533	3.5	0.4	9	dbSNP_98	18	1388,6106		127,1134,2486	yes	missense	C9orf66	NM_152569.2	43	263,1892,3443	TT,TC,CC		18.5215,27.8228,21.597	benign	178/296	214864	2418,8778	1851	3747	5598	SO:0001583	missense	157983	exon1			GCCGACCGACAGA	AK055720	CCDS6439.1	9p24.3	2008-02-05			ENSG00000183784	ENSG00000183784			26436	protein-coding gene	gene with protein product							Standard	NM_152569		Approved	FLJ31158	uc003zge.4	Q5T8R8	OTTHUMG00000021017	ENST00000382387.2:c.533G>A	9.37:g.214864C>T	ENSP00000371824:p.Arg178Gln	Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	51	21	0.411765	NM_152569	Q96NB0	Missense_Mutation	SNP	ENST00000382387.2	37	CCDS6439.1	646	0.2957875457875458	174	0.35365853658536583	101	0.27900552486187846	211	0.3688811188811189	160	0.21108179419525067	.	9.102	1.004339	0.19199	0.278228	0.185215	ENSG00000183784	ENST00000382387	T	0.21031	2.03	4.63	3.46	0.39613	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.09310	P	0.999999999980934	B	0.02656	0.0	B	0.01281	0.0	T	0.45862	-0.9232	8	0.87932	D	0	.	4.0571	0.09821	0.18:0.1005:0.0:0.7195	rs2236547;rs2236547	178	Q5T8R8	CI066_HUMAN	Q	178	ENSP00000371824:R178Q	ENSP00000371824:R178Q	R	-	2	0	C9orf66	204864	0.139000	0.22563	0.407000	0.26434	0.054000	0.15201	0.094000	0.15107	0.146000	0.19002	-0.524000	0.04348	CGG	C|0.737;T|0.263	0.263	strong		0.692	C9orf66-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055436.1	NM_152569	
ULK3	25989	hgsc.bcm.edu	37	15	75131661	75131661	+	Silent	SNP	A	A	G	rs4886615	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:75131661A>G	ENST00000440863.2	-	8	997	c.906T>C	c.(904-906)gcT>gcC	p.A302A	ULK3_ENST00000568667.1_Silent_p.A313A|ULK3_ENST00000569437.1_Silent_p.A302A	NM_001099436.1	NP_001092906	Q6PHR2	ULK3_HUMAN	unc-51 like kinase 3	302	MIT 1.				autophagic vacuole assembly (GO:0000045)|autophagy (GO:0006914)|cellular senescence (GO:0090398)|negative regulation of smoothened signaling pathway (GO:0045879)|positive regulation of smoothened signaling pathway (GO:0045880)|protein autophosphorylation (GO:0046777)|regulation of autophagy (GO:0010506)	ATG1/UKL1 signaling complex (GO:0034273)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|pre-autophagosomal structure (GO:0000407)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.A302A(1)		breast(2)	2						GTGATAAGGCAGCTGCTGAAT	0.612													G|||	3402	0.679313	0.6021	0.7133	5008	,	,		14709	0.7351		0.6909	False		,,,				2504	0.6902				p.A302A		Atlas-SNP	.											ULK3_ENST00000440863,NS,carcinoma,0,1	ULK3	30	1	1	Substitution - coding silent(1)	prostate(1)	c.T906C						PASS	.	G		2456,1424		795,866,279	45.0	47.0	46.0		906	-5.5	0.0	15	dbSNP_111	46	5875,2353		2134,1607,373	no	coding-synonymous	ULK3	NM_001099436.1		2929,2473,652	GG,GA,AA		28.5975,36.701,31.1943		302/473	75131661	8331,3777	1940	4114	6054	SO:0001819	synonymous_variant	25989	exon8			TAAGGCAGCTGCT	BC048289		15q24.1	2013-07-02	2013-07-02			ENSG00000140474			19703	protein-coding gene	gene with protein product		613472	"""unc-51-like kinase 3 (C. elegans)"""				Standard	XM_005254289		Approved	DKFZP434C131, FLJ90566	uc010bkf.1	Q6PHR2		ENST00000440863.2:c.906T>C	15.37:g.75131661A>G		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	157	157	1	NM_001099436	B2RXK3|B4DRQ7|D3DW68|Q9NPN5|Q9UFS4	Silent	SNP	ENST00000440863.2	37	CCDS45305.1																																																																																			A|0.331;G|0.669	0.669	strong		0.612	ULK3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000421734.4	NM_015518	
SKA3	221150	hgsc.bcm.edu	37	13	21742311	21742311	+	Missense_Mutation	SNP	C	C	T	rs61950353	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:21742311C>T	ENST00000314759.5	-	4	683	c.559G>A	c.(559-561)Gta>Ata	p.V187I	SKA3_ENST00000400018.3_Missense_Mutation_p.V187I	NM_145061.5	NP_659498.4	Q8IX90	SKA3_HUMAN	spindle and kinetochore associated complex subunit 3	187					chromosome segregation (GO:0007059)|mitotic nuclear division (GO:0007067)|regulation of microtubule polymerization or depolymerization (GO:0031110)	condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|spindle microtubule (GO:0005876)				breast(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	19						GTTACAATTACGGGCTCTTCC	0.398																																					p.V187I		Atlas-SNP	.											.	SKA3	76	.	0			c.G559A						PASS	.	C	ILE/VAL,ILE/VAL	172,4234		0,172,2031	187.0	201.0	196.0		559,559	-11.5	0.0	13	dbSNP_129	196	1012,7588		0,1012,3288	yes	missense,missense	SKA3	NM_001166017.1,NM_145061.5	29,29	0,1184,5319	TT,TC,CC		11.7674,3.9038,9.1035	benign,benign	187/389,187/413	21742311	1184,11822	2203	4300	6503	SO:0001583	missense	221150	exon4			CAATTACGGGCTC	AF361358	CCDS31946.1, CCDS53856.1	13q11	2013-01-17	2009-08-19	2009-08-19	ENSG00000165480	ENSG00000165480			20262	protein-coding gene	gene with protein product			"""chromosome 13 open reading frame 3"""	C13orf3		19387489, 19289083, 19646878, 19360002	Standard	NM_145061		Approved	MGC4832, RAMA1	uc001unt.3	Q8IX90	OTTHUMG00000016539	ENST00000314759.5:c.559G>A	13.37:g.21742311C>T	ENSP00000319417:p.Val187Ile	Somatic	563	0	0		WXS	Illumina HiSeq	Phase_I	471	88	0.186837	NM_145061	A2A330|A2A331|B2RBY2|Q5VZV5|Q86WR2|Q8NBG1|Q96D22	Missense_Mutation	SNP	ENST00000314759.5	37	CCDS31946.1	310	0.14194139194139194	15	0.03048780487804878	59	0.16298342541436464	128	0.22377622377622378	108	0.1424802110817942	C	11.24	1.580771	0.28180	0.039038	0.117674	ENSG00000165480	ENST00000314759;ENST00000400018	T;T	0.22743	1.95;1.94	5.88	-11.5	0.00074	.	1.396020	0.04148	N	0.320754	T	0.00012	0.0000	N	0.22421	0.69	0.09310	N	1	B;B	0.21753	0.06;0.001	B;B	0.08055	0.003;0.001	T	0.16988	-1.0384	10	0.27785	T	0.31	1.2613	19.3159	0.94213	0.0:0.5809:0.0:0.4191	rs61950353	187;187	Q8IX90-3;Q8IX90	.;SKA3_HUMAN	I	187	ENSP00000319417:V187I;ENSP00000382896:V187I	ENSP00000319417:V187I	V	-	1	0	SKA3	20640311	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.018000	0.00644	-2.167000	0.00779	-2.097000	0.00363	GTA	C|0.893;T|0.107	0.107	strong		0.398	SKA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000272912.1	NM_145061	
C14orf39	317761	hgsc.bcm.edu	37	14	60945066	60945066	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:60945066T>C	ENST00000321731.3	-	5	434	c.275A>G	c.(274-276)tAt>tGt	p.Y92C		NM_174978.2	NP_777638	Q8N1H7	S6OS1_HUMAN	chromosome 14 open reading frame 39	92					multicellular organismal development (GO:0007275)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)					breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(5)|lung(7)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	30				OV - Ovarian serous cystadenocarcinoma(108;0.0448)		GTCCTGCATATAATCTTCATG	0.279																																					p.Y92C		Atlas-SNP	.											.	C14orf39	79	.	0			c.A275G						PASS	.						78.0	76.0	77.0					14																	60945066		2201	4294	6495	SO:0001583	missense	317761	exon5			TGCATATAATCTT	AK098187	CCDS9746.1	14q23.1	2012-11-05	2012-11-05	2012-11-05	ENSG00000179008	ENSG00000179008			19849	protein-coding gene	gene with protein product							Standard	NM_174978		Approved	SIX6OS1	uc001xez.4	Q8N1H7	OTTHUMG00000140332	ENST00000321731.3:c.275A>G	14.37:g.60945066T>C	ENSP00000324920:p.Tyr92Cys	Somatic	200	0	0		WXS	Illumina HiSeq	Phase_I	166	90	0.542169	NM_174978	Q08AQ4	Missense_Mutation	SNP	ENST00000321731.3	37	CCDS9746.1	.	.	.	.	.	.	.	.	.	.	T	12.70	2.016056	0.35606	.	.	ENSG00000179008	ENST00000321731;ENST00000555476	T;T	0.59364	1.7;0.27	5.56	5.56	0.83823	.	0.000000	0.64402	D	0.000006	T	0.71187	0.3310	M	0.69823	2.125	0.35794	D	0.822654	D	0.89917	1.0	D	0.73380	0.98	T	0.77770	-0.2463	10	0.44086	T	0.13	-10.7904	9.2845	0.37749	0.1605:0.0:0.0:0.8395	.	92	Q8N1H7	S6OS1_HUMAN	C	92;63	ENSP00000324920:Y92C;ENSP00000451665:Y63C	ENSP00000324920:Y92C	Y	-	2	0	C14orf39	60014819	1.000000	0.71417	0.997000	0.53966	0.107000	0.19398	2.294000	0.43567	2.237000	0.73441	0.528000	0.53228	TAT	.	.	none		0.279	C14orf39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276948.1	NM_174978	
ZNF880	400713	hgsc.bcm.edu	37	19	52887904	52887904	+	Silent	SNP	T	T	C	rs2042913	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:52887904T>C	ENST00000422689.2	+	4	1086	c.1071T>C	c.(1069-1071)tgT>tgC	p.C357C		NM_001145434.1	NP_001138906.1	Q6PDB4	ZN880_HUMAN	zinc finger protein 880	357					regulation of transcription, DNA-templated (GO:0006355)	intracellular (GO:0005622)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(2)|skin(1)	10						GTAATAAATGTGGCAAGGTCT	0.403																																					p.C357C		Atlas-SNP	.											ZNF880,colon,carcinoma,0,1	ZNF880	45	1	0			c.T1071C						PASS	.						41.0	38.0	39.0					19																	52887904		1568	3582	5150	SO:0001819	synonymous_variant	400713	exon4			TAAATGTGGCAAG	BC058819	CCDS46164.1	19q13.41	2013-01-08			ENSG00000221923	ENSG00000221923		"""Zinc fingers, C2H2-type"", ""-"""	37249	protein-coding gene	gene with protein product							Standard	NM_001145434		Approved		uc002pzc.3	Q6PDB4	OTTHUMG00000167972	ENST00000422689.2:c.1071T>C	19.37:g.52887904T>C		Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	25	24	0.96	NM_001145434	B4DNA6	Silent	SNP	ENST00000422689.2	37	CCDS46164.1																																																																																			T|0.637;C|0.363	0.363	strong		0.403	ZNF880-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397374.1	NM_001145434	
ZNF611	81856	hgsc.bcm.edu	37	19	53209553	53209553	+	Missense_Mutation	SNP	G	G	A	rs4085566|rs34846371	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:53209553G>A	ENST00000319783.1	-	7	1071	c.755C>T	c.(754-756)cCc>cTc	p.P252L	ZNF611_ENST00000602162.1_Missense_Mutation_p.P183L|ZNF611_ENST00000595798.1_Missense_Mutation_p.P183L|ZNF611_ENST00000540744.1_Missense_Mutation_p.P252L|ZNF611_ENST00000602046.1_5'Flank|ZNF611_ENST00000453741.2_Missense_Mutation_p.P183L|ZNF611_ENST00000543227.1_Missense_Mutation_p.P252L	NM_030972.3	NP_112234.3	Q8N823	ZN611_HUMAN	zinc finger protein 611	252			P -> I (requires 2 nucleotide substitutions; dbSNP:rs34846371). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:17974005}.|P -> L (in dbSNP:rs4085566).|P -> T (in dbSNP:rs4085565).		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.P252L(1)		breast(1)|endometrium(4)|kidney(4)|large_intestine(10)|lung(12)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	36				OV - Ovarian serous cystadenocarcinoma(262;0.0233)|GBM - Glioblastoma multiforme(134;0.04)		TCCTAAATGGGGTATCTGGTG	0.378													-|||	2197	0.438698	0.7012	0.3285	5008	,	,		21198	0.3681		0.4105	False		,,,				2504	0.2638				p.P252L		Atlas-SNP	.											ZNF611,NS,carcinoma,0,1	ZNF611	72	1	1	Substitution - Missense(1)	stomach(1)	c.C755T						PASS	.	A	LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO	2860,1546		1004,852,347	137.0	145.0	142.0		755,755,548,755	1.2	0.0	19	dbSNP_108	142	3194,5400		725,1744,1828	no	missense,missense,missense,missense	ZNF611	NM_001161499.1,NM_001161500.1,NM_001161501.1,NM_030972.3	98,98,98,98	1729,2596,2175	AA,AG,GG		37.1655,35.0885,46.5692	benign,benign,benign,benign	252/706,252/706,183/637,252/706	53209553	6054,6946	2203	4297	6500	SO:0001583	missense	81856	exon7			AAATGGGGTATCT	AK091389	CCDS12855.1, CCDS54312.1	19q13.42	2013-01-08			ENSG00000213020	ENSG00000213020		"""Zinc fingers, C2H2-type"", ""-"""	28766	protein-coding gene	gene with protein product						12477932	Standard	NM_030972		Approved	MGC5384	uc010ydq.2	Q8N823	OTTHUMG00000154908	ENST00000319783.1:c.755C>T	19.37:g.53209553G>A	ENSP00000322427:p.Pro252Leu	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	92	37	0.402174	NM_030972	B3KRD5|Q69YG9	Missense_Mutation	SNP	ENST00000319783.1	37	CCDS12855.1	940	0.43040293040293043	322	0.6544715447154471	126	0.34806629834254144	215	0.3758741258741259	277	0.3654353562005277	.	5.048	0.194555	0.09599	0.649115	0.371655	ENSG00000213020	ENST00000543227;ENST00000540744;ENST00000453741;ENST00000319783	T;T;T;T	0.13657	2.57;2.57;2.57;2.57	1.2	1.2	0.21068	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	N	0.01729	-0.75	0.80722	P	0.0	B	0.02656	0.0	B	0.06405	0.002	T	0.25328	-1.0135	8	0.59425	D	0.04	.	2.3777	0.04346	0.5844:0.0:0.1773:0.2382	rs4085566;rs58003344	252	Q8N823	ZN611_HUMAN	L	252;252;183;252	ENSP00000437616:P252L;ENSP00000439211:P252L;ENSP00000443505:P183L;ENSP00000322427:P252L	ENSP00000322427:P252L	P	-	2	0	ZNF611	57901365	0.000000	0.05858	0.025000	0.17156	0.006000	0.05464	-1.050000	0.03510	-0.303000	0.08856	-1.220000	0.01600	CCC	.	.	weak		0.378	ZNF611-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337612.1	NM_030972	
OR11H12	440153	hgsc.bcm.edu	37	14	19378322	19378322	+	Missense_Mutation	SNP	G	G	A	rs201485834		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	518	4	0.00772201		WXS	Illumina HiSeq	Phase_I	433	12	0.0277136	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	
CCDC148	130940	hgsc.bcm.edu	37	2	159195562	159195562	+	Silent	SNP	A	A	G	rs61746487	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:159195562A>G	ENST00000283233.5	-	6	835	c.522T>C	c.(520-522)ttT>ttC	p.F174F	CCDC148_ENST00000409187.1_Silent_p.F183F|CCDC148_ENST00000536771.1_Silent_p.F88F|CCDC148_ENST00000409889.1_Silent_p.F174F	NM_138803.3	NP_620158.3	Q8NFR7	CC148_HUMAN	coiled-coil domain containing 148	174										endometrium(2)|kidney(2)|large_intestine(6)|lung(9)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	23						TAAGTCTTTCAAAGACAGTTT	0.313													A|||	113	0.0225639	0.0023	0.0331	5008	,	,		18042	0.002		0.0785	False		,,,				2504	0.0061				p.F174F		Atlas-SNP	.											.	CCDC148	64	.	0			c.T522C						PASS	.	A	,	71,4333	64.7+/-102.0	0,71,2131	117.0	117.0	117.0		264,522	3.6	1.0	2	dbSNP_129	117	702,7898	172.3+/-223.0	35,632,3633	no	coding-synonymous,coding-synonymous	CCDC148	NM_001171637.1,NM_138803.3	,	35,703,5764	GG,GA,AA		8.1628,1.6122,5.9443	,	88/300,174/592	159195562	773,12231	2202	4300	6502	SO:0001819	synonymous_variant	130940	exon6			TCTTTCAAAGACA		CCDS33304.1	2q24.1	2007-12-07			ENSG00000153237	ENSG00000153237			25191	protein-coding gene	gene with protein product							Standard	NM_138803		Approved	MGC125588	uc002tzq.3	Q8NFR7	OTTHUMG00000153973	ENST00000283233.5:c.522T>C	2.37:g.159195562A>G		Somatic	201	0	0		WXS	Illumina HiSeq	Phase_I	146	64	0.438356	NM_138803	F5H839|Q3B7I3|Q3B7I4|Q3KR41|Q4ZG12|Q4ZG23|Q53TM6|Q96BN5|Q96LM2	Silent	SNP	ENST00000283233.5	37	CCDS33304.1																																																																																			A|0.948;G|0.052	0.052	strong		0.313	CCDC148-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333270.1	NM_138803	
C3	718	hgsc.bcm.edu	37	19	6718146	6718146	+	Missense_Mutation	SNP	T	T	G	rs147859257	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:6718146T>G	ENST00000245907.6	-	4	555	c.463A>C	c.(463-465)Aag>Cag	p.K155Q		NM_000064.2	NP_000055.2	P01024	CO3_HUMAN	complement component 3	155			K -> Q (in ARMD9; results in resistance to proteolytic inactivation by CFH and CFI). {ECO:0000269|PubMed:24036952}.		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)	GGTAGCAGCTTGTGGTTGACG	0.652													T|||	2	0.000399361	0.0	0.0	5008	,	,		18237	0.0		0.002	False		,,,				2504	0.0				p.K155Q		Atlas-SNP	.											.	C3	192	.	0			c.A463C						PASS	.	T	GLN/LYS	1,4405	2.1+/-5.4	0,1,2202	94.0	88.0	90.0		463	1.3	0.4	19	dbSNP_134	90	37,8563	25.1+/-72.6	0,37,4263	yes	missense	C3	NM_000064.2	53	0,38,6465	GG,GT,TT		0.4302,0.0227,0.2922	possibly-damaging	155/1664	6718146	38,12968	2203	4300	6503	SO:0001583	missense	718	exon4			GCAGCTTGTGGTT	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.463A>C	19.37:g.6718146T>G	ENSP00000245907:p.Lys155Gln	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	87	47	0.54023	NM_000064	A7E236	Missense_Mutation	SNP	ENST00000245907.6	37	CCDS32883.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	T	9.992	1.231149	0.22626	2.27E-4	0.004302	ENSG00000125730	ENST00000245907	T	0.73681	-0.77	4.56	1.27	0.21489	Alpha-2-macroglobulin, N-terminal (1);	0.839580	0.11137	N	0.595772	T	0.69305	0.3096	L	0.58354	1.805	0.20074	N	0.999934	B	0.25235	0.121	B	0.32022	0.139	T	0.57359	-0.7825	10	0.33940	T	0.23	.	7.5787	0.27952	0.0:0.2731:0.0:0.7269	.	155	P01024	CO3_HUMAN	Q	155	ENSP00000245907:K155Q	ENSP00000245907:K155Q	K	-	1	0	C3	6669146	0.002000	0.14202	0.358000	0.25811	0.607000	0.37147	-0.429000	0.06982	-0.030000	0.13804	0.248000	0.18094	AAG	T|0.998;G|0.002	0.002	strong		0.652	C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317636.2	NM_000064	
OR7A17	26333	hgsc.bcm.edu	37	19	14991963	14991963	+	Missense_Mutation	SNP	C	C	A	rs10404119	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	93	0	0		WXS	Illumina HiSeq	Phase_I	50	20	0.4	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	
CRTC1	23373	hgsc.bcm.edu	37	19	18876309	18876309	+	Missense_Mutation	SNP	A	A	G	rs3746266	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:18876309A>G	ENST00000321949.8	+	9	1008	c.982A>G	c.(982-984)Acc>Gcc	p.T328A	CRTC1_ENST00000594658.1_Missense_Mutation_p.T287A|CRTC1_ENST00000338797.6_Missense_Mutation_p.T344A|CRTC1_ENST00000601916.1_Missense_Mutation_p.T253A	NM_015321.2	NP_056136.2			CREB regulated transcription coactivator 1										CRTC1/MAML2(516)	NS(1)|breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(6)|ovary(1)|skin(1)	19						GGCATCGCCCACCCTGTCCCC	0.652													A|||	635	0.126797	0.0484	0.1153	5008	,	,		15774	0.1726		0.17	False		,,,				2504	0.1493				p.T344A		Atlas-SNP	.											.	CRTC1	88	.	0			c.A1030G						PASS	.	A	ALA/THR,ALA/THR	333,4073	175.1+/-204.6	22,289,1892	61.0	56.0	58.0		1030,982	3.3	0.9	19	dbSNP_107	58	1367,7233	264.9+/-285.8	112,1143,3045	yes	missense,missense	CRTC1	NM_001098482.1,NM_015321.2	58,58	134,1432,4937	GG,GA,AA		15.8953,7.5579,13.0709	probably-damaging,probably-damaging	344/651,328/635	18876309	1700,11306	2203	4300	6503	SO:0001583	missense	23373	exon10			TCGCCCACCCTGT	AY040323	CCDS32963.1, CCDS42525.1	19p13	2012-07-31	2005-11-24	2005-11-24					16062	protein-coding gene	gene with protein product	"""transducer of regulated cAMP response element-binding protein"""	607536	"""mucoepidermoid carcinoma translocated 1"""	MECT1		12539049, 14536081, 14506290	Standard	NM_015321		Approved	KIAA0616, FLJ14027, TORC1	uc010ebv.3	Q6UUV9		ENST00000321949.8:c.982A>G	19.37:g.18876309A>G	ENSP00000323332:p.Thr328Ala	Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	44	16	0.363636	NM_001098482		Missense_Mutation	SNP	ENST00000321949.8	37	CCDS32963.1	311	0.1423992673992674	26	0.052845528455284556	53	0.1464088397790055	104	0.18181818181818182	128	0.16886543535620052	A	16.49	3.138666	0.56936	0.075579	0.158953	ENSG00000105662	ENST00000262813;ENST00000338797;ENST00000321949	T;T	0.13089	2.62;2.64	4.38	3.31	0.37934	.	2.007280	0.02221	N	0.064026	T	0.00039	0.0001	L	0.43152	1.355	0.24039	P	0.99608583	D;B;P	0.57257	0.979;0.155;0.687	P;B;B	0.50934	0.654;0.047;0.257	T	0.10917	-1.0609	9	0.37606	T	0.19	-13.8054	9.9087	0.41392	0.8278:0.1722:0.0:0.0	rs3746266;rs17852482;rs17858423	328;344;328	Q6UUV9-3;Q6UUV9-2;Q6UUV9	.;.;CRTC1_HUMAN	A	328;344;328	ENSP00000345001:T344A;ENSP00000323332:T328A	ENSP00000262813:T328A	T	+	1	0	CRTC1	18737309	1.000000	0.71417	0.925000	0.36789	0.854000	0.48673	5.595000	0.67563	0.611000	0.30052	0.459000	0.35465	ACC	A|0.865;G|0.135	0.135	strong		0.652	CRTC1-002	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465151.3	NM_025021	
FFAR3	2865	hgsc.bcm.edu	37	19	35850408	35850408	+	Missense_Mutation	SNP	C	C	T	rs138920343	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:35850408C>T	ENST00000327809.4	+	2	817	c.616C>T	c.(616-618)Cgc>Tgc	p.R206C	FFAR3_ENST00000594310.1_Missense_Mutation_p.R206C	NM_005304.3	NP_005295.1	O14843	FFAR3_HUMAN	free fatty acid receptor 3	206					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to fatty acid (GO:0071398)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)|mucosal immune response (GO:0002385)|negative regulation of blood pressure (GO:0045776)|positive regulation of acute inflammatory response to non-antigenic stimulus (GO:0002879)|positive regulation of chemokine production (GO:0032722)|positive regulation of cytokine production involved in immune response (GO:0002720)|positive regulation of glucose import in response to insulin stimulus (GO:2001275)|regulation of hormone biosynthetic process (GO:0046885)|regulation of norepinephrine secretion (GO:0014061)|regulation of peptide hormone secretion (GO:0090276)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|lipid binding (GO:0008289)			endometrium(3)|large_intestine(2)|lung(9)|ovary(1)|skin(1)|stomach(1)	17	all_lung(56;9.78e-09)|Lung NSC(56;1.46e-08)|Esophageal squamous(110;0.162)		Epithelial(14;1.29e-19)|OV - Ovarian serous cystadenocarcinoma(14;4.63e-18)|all cancers(14;5.19e-17)|LUSC - Lung squamous cell carcinoma(66;0.0221)			CTGCTACAGCCGCCTGGTGTG	0.652																																					p.R206C	Esophageal Squamous(185;1742 2042 21963 24215 27871)	Atlas-SNP	.											.	FFAR3	40	.	0			c.C616T						PASS	.	C	CYS/ARG	7,4375		0,7,2184	14.0	13.0	13.0		616	5.1	1.0	19	dbSNP_134	13	61,8409		0,61,4174	no	missense	FFAR3	NM_005304.3	180	0,68,6358	TT,TC,CC		0.7202,0.1597,0.5291	probably-damaging	206/347	35850408	68,12784	2191	4235	6426	SO:0001583	missense	2865	exon2			TACAGCCGCCTGG	AF024688	CCDS12459.1	19q13.1	2012-08-08	2006-02-15	2006-02-15	ENSG00000185897	ENSG00000185897		"""GPCR / Class A : Fatty acid receptors"""	4499	protein-coding gene	gene with protein product		603821	"""G protein-coupled receptor 41"""	GPR41		9344866, 22493486	Standard	NM_005304		Approved	FFA3R	uc002nzd.3	O14843	OTTHUMG00000172514	ENST00000327809.4:c.616C>T	19.37:g.35850408C>T	ENSP00000328230:p.Arg206Cys	Somatic	417	0	0		WXS	Illumina HiSeq	Phase_I	405	113	0.279012	NM_005304	B2RWM8|Q14CM7	Missense_Mutation	SNP	ENST00000327809.4	37	CCDS12459.1	.	.	.	.	.	.	.	.	.	.	C	18.48	3.633388	0.67015	0.001597	0.007202	ENSG00000185897	ENST00000327809	T	0.39592	1.07	5.13	5.13	0.70059	GPCR, rhodopsin-like superfamily (1);	0.264721	0.41001	U	0.000964	T	0.49558	0.1564	M	0.71581	2.175	0.18873	N	0.999988	D	0.76494	0.999	D	0.63033	0.91	T	0.49570	-0.8926	10	0.37606	T	0.19	-16.7142	11.2036	0.48756	0.1836:0.8164:0.0:0.0	.	206	O14843	FFAR3_HUMAN	C	206	ENSP00000328230:R206C	ENSP00000328230:R206C	R	+	1	0	FFAR3	40542248	0.097000	0.21791	1.000000	0.80357	0.990000	0.78478	2.128000	0.42045	2.385000	0.81259	0.455000	0.32223	CGC	C|0.997;T|0.003	0.003	strong		0.652	FFAR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418873.2	NM_005304	
PRG4	10216	hgsc.bcm.edu	37	1	186273994	186273994	+	Missense_Mutation	SNP	C	C	T	rs2273779	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:186273994C>T	ENST00000445192.2	+	6	583	c.538C>T	c.(538-540)Cgg>Tgg	p.R180W	PRG4_ENST00000367486.3_Intron|PRG4_ENST00000367485.4_Intron|PRG4_ENST00000367483.4_Missense_Mutation_p.R139W|PRG4_ENST00000367484.3_Missense_Mutation_p.R139W	NM_005807.3	NP_005798.2	Q92954	PRG4_HUMAN	proteoglycan 4	180	Ser-rich.		R -> W (in dbSNP:rs2273779). {ECO:0000269|Ref.1}.		cell proliferation (GO:0008283)|hematopoietic stem cell proliferation (GO:0071425)|immune response (GO:0006955)|negative regulation of interleukin-6 biosynthetic process (GO:0045409)|regulation of cell proliferation (GO:0042127)	extracellular space (GO:0005615)	polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(33)|prostate(7)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(1)	102						ttcAACAATTCGGAAAATCAA	0.358													C|||	1160	0.231629	0.149	0.4063	5008	,	,		16449	0.129		0.33	False		,,,				2504	0.2239				p.R180W		Atlas-SNP	.											.	PRG4	259	.	0			c.C538T						PASS	.	C	TRP/ARG,TRP/ARG,,	822,3576	293.6+/-282.7	79,664,1456	41.0	44.0	43.0		415,538,,	4.3	1.0	1	dbSNP_100	43	3031,5567	451.4+/-362.6	537,1957,1805	yes	missense,missense,intron,intron	PRG4	NM_001127708.1,NM_005807.3,NM_001127709.1,NM_001127710.1	101,101,,	616,2621,3261	TT,TC,CC		35.2524,18.6903,29.6476	possibly-damaging,possibly-damaging,,	139/1364,180/1405,,	186273994	3853,9143	2199	4299	6498	SO:0001583	missense	10216	exon6			ACAATTCGGAAAA	U70136	CCDS1369.1, CCDS44287.1, CCDS44288.1	1q25-q31	2008-07-18	2004-11-15		ENSG00000116690	ENSG00000116690			9364	protein-coding gene	gene with protein product	"""lubricin"", ""megakaryocyte stimulating factor"", ""articular superficial zone protein"", ""Jacobs camptodactyly-arthropathy-pericarditis syndrome"", ""camptodactyly, arthropathy, coxa vara, pericarditis syndrome"", ""bG174L6.2 (MSF: megakaryocyte stimulating factor )"""	604283	"""proteoglycan 4, (megakaryocyte stimulating factor, articular superficial zone protein, camptodactyly, arthropathy, coxa vara, pericarditis syndrome)"""	CACP		10545950, 9920774	Standard	NM_005807		Approved	JCAP, SZP, MSF, HAPO, bG174L6.2, FLJ32635	uc001gru.4	Q92954	OTTHUMG00000035574	ENST00000445192.2:c.538C>T	1.37:g.186273994C>T	ENSP00000399679:p.Arg180Trp	Somatic	185	1	0.00540541		WXS	Illumina HiSeq	Phase_I	162	162	1	NM_005807	Q6DNC4|Q6DNC5|Q6ZMZ5|Q9BX49	Missense_Mutation	SNP	ENST00000445192.2	37	CCDS1369.1	550	0.2518315018315018	65	0.13211382113821138	145	0.4005524861878453	77	0.1346153846153846	263	0.3469656992084433	C	18.69	3.677565	0.68042	0.186903	0.352524	ENSG00000116690	ENST00000367484;ENST00000533951;ENST00000367483;ENST00000445192	T;T;T;T	0.50548	2.96;0.74;2.87;2.92	5.17	4.26	0.50523	.	0.199396	0.25081	U	0.033299	T	0.00012	0.0000	N	0.19112	0.55	0.41286	P	0.013051999999999953	P;D	0.55172	0.949;0.97	B;P	0.46850	0.329;0.529	T	0.42085	-0.9472	9	0.62326	D	0.03	-4.2039	9.7397	0.40411	0.0:0.9046:0.0:0.0954	rs2273779;rs52813784;rs58219930;rs2273779	180;139	Q92954;Q92954-2	PRG4_HUMAN;.	W	139;89;139;180	ENSP00000356454:R139W;ENSP00000431330:R89W;ENSP00000356453:R139W;ENSP00000399679:R180W	ENSP00000356453:R139W	R	+	1	2	PRG4	184540617	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.402000	0.34600	1.188000	0.43014	0.650000	0.86243	CGG	C|0.726;T|0.274	0.274	strong		0.358	PRG4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000086346.1	NM_005807	
NEUROD6	63974	hgsc.bcm.edu	37	7	31378795	31378795	+	Nonsense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:31378795G>A	ENST00000297142.3	-	2	410	c.88C>T	c.(88-90)Caa>Taa	p.Q30*		NM_022728.2	NP_073565.2	Q96NK8	NDF6_HUMAN	neuronal differentiation 6	30					cell differentiation (GO:0030154)|dentate gyrus development (GO:0021542)	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)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(18)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	32						TTCTTAATTTGCTTCTGGTCC	0.433																																					p.Q30X		Atlas-SNP	.											.	NEUROD6	84	.	0			c.C88T						PASS	.						136.0	148.0	144.0					7																	31378795		2203	4300	6503	SO:0001587	stop_gained	63974	exon2			TAATTTGCTTCTG	AF248954	CCDS5434.1	7p15.1	2013-05-21	2012-02-22		ENSG00000164600	ENSG00000164600		"""Basic helix-loop-helix proteins"""	13804	protein-coding gene	gene with protein product		611513	"""neurogenic differentiation 6"""			12357074	Standard	NM_022728		Approved	Atoh2, NEX1M, Math-2, bHLHa2, Nex1	uc003tch.4	Q96NK8	OTTHUMG00000022865	ENST00000297142.3:c.88C>T	7.37:g.31378795G>A	ENSP00000297142:p.Gln30*	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	61	12	0.196721	NM_022728	Q548T9|Q9H3H6	Nonsense_Mutation	SNP	ENST00000297142.3	37	CCDS5434.1	.	.	.	.	.	.	.	.	.	.	G	37	6.007479	0.97195	.	.	ENSG00000164600	ENST00000297142	.	.	.	5.28	5.28	0.74379	.	0.240470	0.36101	N	0.002799	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.05436	T	0.98	-2.4487	18.9485	0.92632	0.0:0.0:1.0:0.0	.	.	.	.	X	30	.	ENSP00000297142:Q30X	Q	-	1	0	NEUROD6	31345320	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.750000	0.62162	2.485000	0.83878	0.650000	0.86243	CAA	.	.	none		0.433	NEUROD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215050.1	NM_022728	
ATP6V1B1	525	hgsc.bcm.edu	37	2	71170807	71170807	+	Silent	SNP	C	C	T	rs2266918	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:71170807C>T	ENST00000234396.4	+	2	211	c.138C>T	c.(136-138)agC>agT	p.S46S	AC007040.11_ENST00000606025.1_Intron|AC007040.7_ENST00000447639.1_RNA|ATP6V1B1_ENST00000412314.1_Silent_p.S46S|AC007040.7_ENST00000422761.1_RNA	NM_001692.3	NP_001683.2	P15313	VATB1_HUMAN	ATPase, H+ transporting, lysosomal 56/58kDa, V1 subunit B1	46					ATP hydrolysis coupled proton transport (GO:0015991)|ATP metabolic process (GO:0046034)|calcium ion homeostasis (GO:0055074)|cellular iron ion homeostasis (GO:0006879)|excretion (GO:0007588)|inner ear morphogenesis (GO:0042472)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|ossification (GO:0001503)|pH reduction (GO:0045851)|phagosome maturation (GO:0090382)|proton transport (GO:0015992)|regulation of pH (GO:0006885)|sensory perception of sound (GO:0007605)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|lateral plasma membrane (GO:0016328)|microvillus (GO:0005902)|proton-transporting V-type ATPase, V1 domain (GO:0033180)|vacuolar proton-transporting V-type ATPase complex (GO:0016471)	ATP binding (GO:0005524)|hydrogen ion transmembrane transporter activity (GO:0015078)|hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances (GO:0016820)			endometrium(5)|kidney(1)|large_intestine(5)|liver(1)|lung(5)|prostate(1)|skin(1)	19						CTGTGTGCAGCGTGAACGGGC	0.642													C|||	1400	0.279553	0.1029	0.1744	5008	,	,		14726	0.5258		0.2087	False		,,,				2504	0.4121				p.S46S		Atlas-SNP	.											.	ATP6V1B1	66	.	0			c.C138T						PASS	.	C		506,3900	233.3+/-246.5	24,458,1721	92.0	81.0	85.0		138	-1.3	1.0	2	dbSNP_100	85	1533,7067	287.1+/-298.1	129,1275,2896	no	coding-synonymous	ATP6V1B1	NM_001692.3		153,1733,4617	TT,TC,CC		17.8256,11.4843,15.6774		46/514	71170807	2039,10967	2203	4300	6503	SO:0001819	synonymous_variant	525	exon2			GTGCAGCGTGAAC	AF107466	CCDS1912.1	2p13	2010-04-21	2008-07-31	2002-05-10	ENSG00000116039	ENSG00000116039	3.6.3.14	"""ATPases / V-type"""	853	protein-coding gene	gene with protein product	"""Renal tubular acidosis with deafness"""	192132	"""vacuolar proton pump 3"""	VPP3, ATP6B1		9916796, 2527371	Standard	XM_005264368		Approved	VATB, RTA1B, Vma2	uc002shj.3	P15313	OTTHUMG00000129711	ENST00000234396.4:c.138C>T	2.37:g.71170807C>T		Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	29	29	1	NM_001692	Q53FY0|Q6P4H6	Silent	SNP	ENST00000234396.4	37	CCDS1912.1																																																																																			C|0.801;T|0.199	0.199	strong		0.642	ATP6V1B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251920.2	NM_001692	
FUCA2	2519	hgsc.bcm.edu	37	6	143816859	143816859	+	Silent	SNP	C	C	T	rs8161	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:143816859C>T	ENST00000002165.6	-	7	1444	c.1389G>A	c.(1387-1389)ctG>ctA	p.L463L	RP1-20N2.6_ENST00000589563.1_RNA|RP1-20N2.6_ENST00000591892.1_RNA|RP1-20N2.6_ENST00000610068.1_RNA	NM_032020.4	NP_114409.2	Q9BTY2	FUCO2_HUMAN	fucosidase, alpha-L- 2, plasma	463					fucose metabolic process (GO:0006004)|glycoside catabolic process (GO:0016139)|regulation of entry of bacterium into host cell (GO:2000535)|response to bacterium (GO:0009617)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	alpha-L-fucosidase activity (GO:0004560)|fucose binding (GO:0042806)	p.L463L(1)		endometrium(1)|large_intestine(1)|lung(2)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	9				OV - Ovarian serous cystadenocarcinoma(155;7.45e-06)|GBM - Glioblastoma multiforme(68;0.0142)		TCACATTAGTCAGGGCTAGAG	0.448													T|||	2116	0.422524	0.4796	0.438	5008	,	,		18597	0.4821		0.339	False		,,,				2504	0.3589				p.L463L		Atlas-SNP	.											FUCA2,NS,carcinoma,0,1	FUCA2	28	1	1	Substitution - coding silent(1)	stomach(1)	c.G1389A						PASS	.	T		2070,2336	605.8+/-390.6	486,1098,619	88.0	74.0	79.0		1389	-1.4	0.0	6	dbSNP_52	79	2938,5662	668.3+/-402.5	523,1892,1885	yes	coding-synonymous	FUCA2	NM_032020.4		1009,2990,2504	TT,TC,CC		34.1628,46.9814,38.5053		463/468	143816859	5008,7998	2203	4300	6503	SO:0001819	synonymous_variant	2519	exon7			ATTAGTCAGGGCT	BC003060	CCDS5200.1	6q24	2012-10-02			ENSG00000001036	ENSG00000001036	3.2.1.51		4008	protein-coding gene	gene with protein product		136820				6590153	Standard	NM_032020		Approved	MGC1314, dJ20N2.5	uc003qjm.3	Q9BTY2	OTTHUMG00000015728	ENST00000002165.6:c.1389G>A	6.37:g.143816859C>T		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	75	75	1	NM_032020	E9PEB6|Q7Z6V1|Q7Z6Y2|Q8NBK4	Silent	SNP	ENST00000002165.6	37	CCDS5200.1																																																																																			C|0.585;T|0.415	0.415	strong		0.448	FUCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042521.2	NM_032020	
MYOM1	8736	hgsc.bcm.edu	37	18	3067278	3067278	+	Silent	SNP	A	A	G	rs2230164	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:3067278A>G	ENST00000356443.4	-	38	5373	c.5040T>C	c.(5038-5040)ggT>ggC	p.G1680G	MYOM1_ENST00000400569.3_Silent_p.G1680G|MYOM1_ENST00000261606.7_Silent_p.G1584G	NM_003803.3|NM_019856.1	NP_003794.3|NP_062830.1	P52179	MYOM1_HUMAN	myomesin 1	1680					muscle contraction (GO:0006936)	M band (GO:0031430)|striated muscle myosin thick filament (GO:0005863)	identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|structural constituent of muscle (GO:0008307)			NS(2)|autonomic_ganglia(1)|central_nervous_system(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(20)|ovary(4)|pancreas(1)|prostate(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	77						CCTTCTTGCCACCTTTCAGGG	0.567													G|||	2977	0.594449	0.8533	0.4207	5008	,	,		16407	0.5308		0.4652	False		,,,				2504	0.5665				p.G1680G		Atlas-SNP	.											MYOM1,colon,carcinoma,0,1	MYOM1	192	1	0			c.T5040C						PASS	.	G	,	3376,978		1313,750,114	19.0	26.0	24.0		5040,4752	-2.1	0.0	18	dbSNP_98	24	3990,4564		936,2118,1223	no	coding-synonymous,coding-synonymous	MYOM1	NM_003803.3,NM_019856.1	,	2249,2868,1337	GG,GA,AA		46.6448,22.4621,42.9346	,	1680/1686,1584/1590	3067278	7366,5542	2177	4277	6454	SO:0001819	synonymous_variant	8736	exon38			CTTGCCACCTTTC	AF185573	CCDS45823.1, CCDS45824.1	18p11.31	2014-09-17	2012-10-17		ENSG00000101605	ENSG00000101605		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	7613	protein-coding gene	gene with protein product	"""skelemin"""	603508	"""myomesin 1 (skelemin) (185kD)"", ""myomesin 1 (skelemin) 185kDa"", ""myomesin 1, 185kDa"""			9806852	Standard	NM_019856		Approved		uc002klp.3	P52179	OTTHUMG00000178209	ENST00000356443.4:c.5040T>C	18.37:g.3067278A>G		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	49	19	0.387755	NM_003803	Q14BD6|Q6H969|Q6ZUU0	Silent	SNP	ENST00000356443.4	37	CCDS45824.1																																																																																			A|0.424;G|0.576	0.576	strong		0.567	MYOM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441037.2	NM_003803	
SLC45A3	85414	hgsc.bcm.edu	37	1	205628616	205628616	+	Missense_Mutation	SNP	C	C	T	rs137949511	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:205628616C>T	ENST00000367145.3	-	5	1703	c.1408G>A	c.(1408-1410)Gta>Ata	p.V470I	SLC45A3_ENST00000460934.1_5'UTR	NM_033102.2	NP_149093.1	Q96JT2	S45A3_HUMAN	solute carrier family 45, member 3	470					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)			SLC45A3/BRAF(2)|SLC45A3/ELK4(18)|SLC45A3/ETV1(3)|SLC45A3/ETV5_ENST00000306376(2)|SLC45A3/ERG(50)	cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|liver(1)|lung(7)|ovary(3)|prostate(5)	21	Breast(84;0.07)		BRCA - Breast invasive adenocarcinoma(75;0.0194)			ACCACACGTACGGAGACATCA	0.677			T	"""ETV1, ETV5, ELK4, ERG"""	prostate						OREG0014161	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	21	0.00419329	0.0	0.0043	5008	,	,		18353	0.0		0.0119	False		,,,				2504	0.0061				p.V470I		Atlas-SNP	.		Dom	yes		1	1q32	85414	"""solute carrier family 45, member 3"""		E	.	SLC45A3	54	.	0			c.G1408A						PASS	.	C	ILE/VAL	8,4396	14.3+/-33.2	0,8,2194	38.0	38.0	38.0		1408	-1.4	0.4	1	dbSNP_134	38	78,8520	44.5+/-102.8	0,78,4221	yes	missense	SLC45A3	NM_033102.2	29	0,86,6415	TT,TC,CC		0.9072,0.1817,0.6614	benign	470/554	205628616	86,12916	2202	4299	6501	SO:0001583	missense	85414	exon5			CACGTACGGAGAC	AF109301	CCDS1458.1	1q32.1	2013-05-22	2005-10-04	2005-10-04	ENSG00000158715	ENSG00000158715		"""Solute carriers"""	8642	protein-coding gene	gene with protein product		605097	"""prostate cancer associated protein 6"", ""prostate cancer associated protein 2"", ""prostate cancer associated protein 8"""	PCANAP6, PCANAP2, PCANAP8		10613842, 11245466	Standard	XM_005245556		Approved	IPCA-6, prostein, IPCA-2, IPCA-8	uc001hda.1	Q96JT2	OTTHUMG00000037223	ENST00000367145.3:c.1408G>A	1.37:g.205628616C>T	ENSP00000356113:p.Val470Ile	Somatic	115	0	0	2153	WXS	Illumina HiSeq	Phase_I	128	71	0.554688	NM_033102	A8K2U9	Missense_Mutation	SNP	ENST00000367145.3	37	CCDS1458.1	8	0.003663003663003663	0	0.0	1	0.0027624309392265192	0	0.0	7	0.009234828496042216	C	2.983	-0.209897	0.06140	0.001817	0.009072	ENSG00000158715	ENST00000367145	T	0.44482	0.92	5.48	-1.36	0.09085	.	0.387498	0.26341	N	0.024935	T	0.13072	0.0317	N	0.14661	0.345	0.09310	N	1	B	0.22211	0.066	B	0.13407	0.009	T	0.20538	-1.0272	10	0.14656	T	0.56	-17.1135	7.4464	0.27213	0.0:0.4405:0.1634:0.3962	.	470	Q96JT2	S45A3_HUMAN	I	470	ENSP00000356113:V470I	ENSP00000356113:V470I	V	-	1	0	SLC45A3	203895239	0.023000	0.18921	0.369000	0.25952	0.167000	0.22549	-0.027000	0.12371	-0.144000	0.11314	-0.339000	0.08088	GTA	C|0.994;T|0.006	0.006	strong		0.677	SLC45A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090619.1	NM_033102	
TRAPPC12	51112	hgsc.bcm.edu	37	2	3469463	3469463	+	Silent	SNP	G	G	C	rs4971514	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:3469463G>C	ENST00000324266.5	+	9	1968	c.1773G>C	c.(1771-1773)ctG>ctC	p.L591L	TRAPPC12_ENST00000469147.1_3'UTR|TRAPPC12_ENST00000382110.2_Silent_p.L591L	NM_016030.5	NP_057114.5	Q8WVT3	TPC12_HUMAN	trafficking protein particle complex 12	591					vesicle-mediated transport (GO:0016192)												GGATTTCCCTGCAGGTACCTG	0.488													G|||	2080	0.415335	0.4826	0.3285	5008	,	,		18864	0.3601		0.4473	False		,,,				2504	0.41				p.L591L		Atlas-SNP	.											.	.	.	.	0			c.G1773C						PASS	.	G		2006,2400	560.5+/-380.5	459,1088,656	74.0	75.0	75.0		1773	-10.7	0.4	2	dbSNP_111	75	3586,5014	519.3+/-379.4	751,2084,1465	no	coding-synonymous	TTC15	NM_016030.5		1210,3172,2121	CC,CG,GG		41.6977,45.5288,42.9955		591/736	3469463	5592,7414	2203	4300	6503	SO:0001819	synonymous_variant	51112	exon9			TTCCCTGCAGGTA	BC017475	CCDS1652.1	2p25.3	2013-01-10	2011-12-12	2011-12-12	ENSG00000171853	ENSG00000171853		"""Trafficking protein particle complex"", ""Tetratricopeptide (TTC) repeat domain containing"""	24284	protein-coding gene	gene with protein product		614139	"""tetratricopeptide repeat domain 15"""	TTC15		10810093, 21525244, 20562859	Standard	NM_016030		Approved	CGI-87, TTC-15	uc002qxm.1	Q8WVT3	OTTHUMG00000090328	ENST00000324266.5:c.1773G>C	2.37:g.3469463G>C		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	92	26	0.282609	NM_016030	B3KV01|D6W4Y2|Q8WVW1|Q9Y395	Silent	SNP	ENST00000324266.5	37	CCDS1652.1	932|932	0.4267399267399267|0.4267399267399267	244|244	0.4959349593495935|0.4959349593495935	134|134	0.3701657458563536|0.3701657458563536	213|213	0.3723776223776224|0.3723776223776224	341|341	0.449868073878628|0.449868073878628	G|G	13.50|13.50	2.257146|2.257146	0.39896|0.39896	0.455288|0.455288	0.416977|0.416977	ENSG00000171853|ENSG00000171853	ENST00000433382|ENST00000416918	.|.	.|.	.|.	5.65|5.65	-10.7|-10.7	0.00240|0.00240	.|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.09310|0.09310	P|P	1.0|1.0	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.32640|0.32640	-0.9899|-0.9899	3|3	.|.	.|.	.|.	.|.	2.9671|2.9671	0.05911|0.05911	0.165:0.3251:0.3618:0.1481|0.165:0.3251:0.3618:0.1481	rs4971514;rs17851116;rs57881176;rs4971514|rs4971514;rs17851116;rs57881176;rs4971514	.|.	.|.	.|.	P|S	137|7	.|.	.|.	A|C	+|+	1|2	0|0	TTC15|TTC15	3448470|3448470	0.166000|0.166000	0.22962|0.22962	0.430000|0.430000	0.26722|0.26722	0.957000|0.957000	0.61999|0.61999	-0.650000|-0.650000	0.05378|0.05378	-2.368000|-2.368000	0.00604|0.00604	0.655000|0.655000	0.94253|0.94253	GCA|TGC	G|0.566;C|0.434	0.434	strong		0.488	TRAPPC12-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206693.2	NM_016030	
C9orf3	84909	hgsc.bcm.edu	37	9	97717527	97717527	+	Missense_Mutation	SNP	C	C	T	rs143555020		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:97717527C>T	ENST00000375315.2	+	7	1730	c.1730C>T	c.(1729-1731)cCg>cTg	p.P577L	C9orf3_ENST00000297979.5_Missense_Mutation_p.P478L	NM_001193329.1	NP_001180258.1	Q8N6M6	AMPO_HUMAN	chromosome 9 open reading frame 3	577					leukotriene biosynthetic process (GO:0019370)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(12)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	23				OV - Ovarian serous cystadenocarcinoma(323;0.000275)		GGACTTAATCCGGAGAAGATC	0.398													C|||	1	0.000199681	0.0008	0.0	5008	,	,		20468	0.0		0.0	False		,,,				2504	0.0				p.P577L		Atlas-SNP	.											.	C9orf3	100	.	0			c.C1730T						PASS	.	C	LEU/PRO,LEU/PRO	1,4405	2.1+/-5.4	0,1,2202	125.0	110.0	115.0		1730,1433	4.1	1.0	9	dbSNP_134	115	0,8600		0,0,4300	no	missense,missense	C9orf3	NM_001193329.1,NM_032823.5	98,98	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging,probably-damaging	577/820,478/721	97717527	1,13005	2203	4300	6503	SO:0001583	missense	84909	exon7			TTAATCCGGAGAA	AF043896	CCDS6713.1, CCDS55327.1, CCDS55328.1	9q22	2013-06-27			ENSG00000148120	ENSG00000148120			1361	protein-coding gene	gene with protein product	aminopeptidase O					15687497	Standard	NM_001193329		Approved	C90RF3, FLJ14675, APO, AOPEP, AP-O	uc004ava.3	Q8N6M6	OTTHUMG00000020276	ENST00000375315.2:c.1730C>T	9.37:g.97717527C>T	ENSP00000364464:p.Pro577Leu	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	32	7	0.21875	NM_001193329	Q5T9B1|Q5T9B3|Q5T9B4|Q8WUL6|Q96M23|Q96SS1	Missense_Mutation	SNP	ENST00000375315.2	37	CCDS55328.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	10.54	1.377611	0.24944	2.27E-4	0.0	ENSG00000148120	ENST00000297979;ENST00000375315;ENST00000424143;ENST00000428313	T;T;T;T	0.05199	3.48;3.48;3.48;3.48	5.0	4.11	0.48088	.	0.210223	0.39759	N	0.001269	T	0.22781	0.0550	M	0.84082	2.675	0.80722	D	1	D;P;D	0.76494	0.998;0.848;0.999	P;B;P	0.62435	0.835;0.361;0.902	T	0.01508	-1.1337	10	0.87932	D	0	-10.1413	11.284	0.49212	0.0:0.9136:0.0:0.0864	.	577;478;478	Q8N6M6;Q8N6M6-4;Q8N6M6-2	AMPO_HUMAN;.;.	L	478;577;301;359	ENSP00000297979:P478L;ENSP00000364464:P577L;ENSP00000402171:P301L;ENSP00000401854:P359L	ENSP00000297979:P478L	P	+	2	0	C9orf3	96757348	0.442000	0.25633	0.980000	0.43619	0.172000	0.22775	2.770000	0.47662	1.483000	0.48342	-0.126000	0.14955	CCG	C|1.000;T|0.000	0.000	strong		0.398	C9orf3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_032823	
SF3B4	10262	hgsc.bcm.edu	37	1	149898292	149898292	+	Silent	SNP	A	A	G	rs115070660	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:149898292A>G	ENST00000271628.8	-	3	1266	c.682T>C	c.(682-684)Ttg>Ctg	p.L228L	MTMR11_ENST00000492824.1_5'Flank	NM_005850.4	NP_005841.1	Q15427	SF3B4_HUMAN	splicing factor 3b, subunit 4, 49kDa	228					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)			CCAGACCCCAATGATGATACC	0.517													A|||	57	0.0113818	0.0008	0.0072	5008	,	,		19003	0.0		0.0348	False		,,,				2504	0.0164				p.L228L		Atlas-SNP	.											.	SF3B4	37	.	0			c.T682C						PASS	.	A		26,4380	31.7+/-61.6	0,26,2177	51.0	50.0	50.0		682	-8.7	0.0	1	dbSNP_132	50	201,8399	86.3+/-148.7	2,197,4101	no	coding-synonymous	SF3B4	NM_005850.4		2,223,6278	GG,GA,AA		2.3372,0.5901,1.7453		228/425	149898292	227,12779	2203	4300	6503	SO:0001819	synonymous_variant	10262	exon3			ACCCCAATGATGA	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.682T>C	1.37:g.149898292A>G		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	72	43	0.597222	NM_005850	Q5SZ63	Silent	SNP	ENST00000271628.8	37	CCDS941.1																																																																																			A|0.985;G|0.015	0.015	strong		0.517	SF3B4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033753.1	NM_005850	
SH3BP4	23677	hgsc.bcm.edu	37	2	235949920	235949920	+	Silent	SNP	A	A	G	rs3731645	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:235949920A>G	ENST00000409212.1	+	4	1014	c.507A>G	c.(505-507)ccA>ccG	p.P169P	SH3BP4_ENST00000344528.4_Silent_p.P169P|SH3BP4_ENST00000392011.2_Silent_p.P169P			Q9P0V3	SH3B4_HUMAN	SH3-domain binding protein 4	169					cellular response to amino acid stimulus (GO:0071230)|endocytosis (GO:0006897)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of GTPase activity (GO:0034260)|negative regulation of TOR signaling (GO:0032007)|positive regulation of autophagy (GO:0010508)|protein localization to lysosome (GO:0061462)|regulation of catalytic activity (GO:0050790)	coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	GDP-dissociation inhibitor activity (GO:0005092)|identical protein binding (GO:0042802)|Ras GTPase binding (GO:0017016)	p.P169P(1)		central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(6)|lung(13)|ovary(4)|prostate(2)|skin(6)|stomach(3)|urinary_tract(2)	44		Breast(86;0.000332)|Renal(207;0.00339)|all_lung(227;0.00458)|all_hematologic(139;0.0296)|Lung NSC(271;0.0419)		Epithelial(121;7.66e-20)|BRCA - Breast invasive adenocarcinoma(100;0.000402)|Lung(119;0.00299)|LUSC - Lung squamous cell carcinoma(224;0.00645)|GBM - Glioblastoma multiforme(43;0.237)		AGACCAATCCATTTCTGAATG	0.502													G|||	1657	0.330871	0.4002	0.3372	5008	,	,		21045	0.4127		0.0915	False		,,,				2504	0.3947				p.P169P		Atlas-SNP	.											SH3BP4,NS,carcinoma,0,1	SH3BP4	109	1	1	Substitution - coding silent(1)	stomach(1)	c.A507G						PASS	.	G		1615,2791	662.3+/-401.0	311,993,899	114.0	115.0	115.0		507	-11.2	0.0	2	dbSNP_107	115	895,7705	778.2+/-407.7	44,807,3449	no	coding-synonymous	SH3BP4	NM_014521.2		355,1800,4348	GG,GA,AA		10.407,36.6546,19.2988		169/964	235949920	2510,10496	2203	4300	6503	SO:0001819	synonymous_variant	23677	exon4			CAATCCATTTCTG	AF147747	CCDS2513.1	2q37.1-q37.2	2008-05-15			ENSG00000130147	ENSG00000130147			10826	protein-coding gene	gene with protein product		605611				10644451	Standard	NM_014521		Approved		uc002vvp.3	Q9P0V3	OTTHUMG00000133292	ENST00000409212.1:c.507A>G	2.37:g.235949920A>G		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	38	18	0.473684	NM_014521	O95082|Q309A3|Q53QD0|Q53TD1	Silent	SNP	ENST00000409212.1	37	CCDS2513.1																																																																																			A|0.760;G|0.240	0.240	strong		0.502	SH3BP4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329763.1		
SSC5D	284297	hgsc.bcm.edu	37	19	56029191	56029191	+	Missense_Mutation	SNP	C	C	T	rs76172483	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:56029191C>T	ENST00000389623.6	+	14	3571	c.3548C>T	c.(3547-3549)aCg>aTg	p.T1183M		NM_001144950.1	NP_001138422.1	A1L4H1	SRCRL_HUMAN	scavenger receptor cysteine rich family, 5 domains	1183	Pro-rich.|Thr-rich.				defense response to Gram-negative bacterium (GO:0050829)|defense response to Gram-positive bacterium (GO:0050830)|detection of bacterial lipoprotein (GO:0042494)|innate immune response (GO:0045087)|multicellular organismal development (GO:0007275)|negative regulation of interleukin-8 secretion (GO:2000483)|receptor-mediated endocytosis (GO:0006898)	cytoplasm (GO:0005737)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|intracellular (GO:0005622)|membrane (GO:0016020)	extracellular matrix binding (GO:0050840)|fibronectin binding (GO:0001968)|laminin binding (GO:0043236)|scavenger receptor activity (GO:0005044)			NS(1)|breast(1)|skin(2)	4						caccccaccacgacccctcac	0.592													-|||	797	0.159145	0.2837	0.1859	5008	,	,		9314	0.2044		0.0736	False		,,,				2504	0.0133				p.T1183M		Atlas-SNP	.											.	SSC5D	65	.	0			c.C3548T						PASS	.						231.0	217.0	221.0					19																	56029191		692	1591	2283	SO:0001583	missense	284297	exon14			CCACCACGACCCC		CCDS46196.1, CCDS59424.1	19q13.42	2014-07-09	2014-07-09		ENSG00000179954	ENSG00000179954			26641	protein-coding gene	gene with protein product	"""soluble scavenger with 5 domains"""		"""scavenger receptor cysteine rich domain containing (5 domains)"""			19535143	Standard	NM_001144950		Approved	FLJ35258	uc002qlg.4	A1L4H1		ENST00000389623.6:c.3548C>T	19.37:g.56029191C>T	ENSP00000374274:p.Thr1183Met	Somatic	190	0	0		WXS	Illumina HiSeq	Phase_I	162	77	0.475309	NM_001144950	B5MDQ5|C7S7T9|C7S7U0|K7EP70	Missense_Mutation	SNP	ENST00000389623.6	37	CCDS46196.1	360	0.16483516483516483	138	0.2804878048780488	52	0.143646408839779	115	0.20104895104895104	55	0.07255936675461741	-	6.828	0.521990	0.13005	.	.	ENSG00000179954	ENST00000389623	T	0.01335	5.0	3.2	2.13	0.27403	.	.	.	.	.	T	0.00012	0.0000	L	0.54323	1.7	0.80722	P	0.0	D	0.56035	0.974	P	0.46362	0.514	T	0.54695	-0.8255	8	0.38643	T	0.18	.	6.8708	0.24119	0.0:0.856:0.0:0.144	.	1183	A1L4H1	SRCRL_HUMAN	M	1183	ENSP00000374274:T1183M	ENSP00000374274:T1183M	T	+	2	0	SSC5D	60721003	0.000000	0.05858	0.002000	0.10522	0.014000	0.08584	-1.740000	0.01839	0.461000	0.27071	-0.760000	0.03462	ACG	C|0.835;T|0.165	0.165	strong		0.592	SSC5D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000453345.2	XM_001718392	
HSDL2	84263	hgsc.bcm.edu	37	9	115167994	115167994	+	Missense_Mutation	SNP	A	A	T	rs41280175	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:115167994A>T	ENST00000398805.3	+	3	499	c.272A>T	c.(271-273)aAa>aTa	p.K91I	HSDL2_ENST00000488101.1_3'UTR|HSDL2_ENST00000262542.7_5'UTR|HSDL2_ENST00000539114.1_5'UTR|HSDL2_ENST00000398803.1_Missense_Mutation_p.K91I	NM_032303.4	NP_115679.2	Q6YN16	HSDL2_HUMAN	hydroxysteroid dehydrogenase like 2	91						membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisome (GO:0005777)	oxidoreductase activity (GO:0016491)			NS(1)|breast(2)|cervix(2)|endometrium(1)|large_intestine(2)|lung(2)|prostate(1)|upper_aerodigestive_tract(2)	13						GCCATCAAGAAATTTGGAGGT	0.318													A|||	10	0.00199681	0.0008	0.0058	5008	,	,		16111	0.0		0.005	False		,,,				2504	0.0				p.K91I		Atlas-SNP	.											.	HSDL2	24	.	0			c.A272T						PASS	.	A	ILE/LYS,ILE/LYS	7,3743		0,7,1868	128.0	126.0	126.0		272,272	3.2	1.0	9	dbSNP_127	126	107,8109		1,105,4002	yes	missense,missense	HSDL2	NM_001195822.1,NM_032303.4	102,102	1,112,5870	TT,TA,AA		1.3023,0.1867,0.9527	benign,benign	91/346,91/419	115167994	114,11852	1875	4108	5983	SO:0001583	missense	84263	exon3			TCAAGAAATTTGG	AY093428	CCDS43864.1, CCDS56582.1	9q32	2011-09-14			ENSG00000119471	ENSG00000119471		"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"""	18572	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 13C, member 1"""		"""chromosome 9 open reading frame 99"""	C9orf99		12834046, 19027726	Standard	NM_032303		Approved	SDR13C1	uc004bga.2	Q6YN16	OTTHUMG00000020504	ENST00000398805.3:c.272A>T	9.37:g.115167994A>T	ENSP00000381785:p.Lys91Ile	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	43	26	0.604651	NM_032303	A8K1L4|A8K8X1|A8MSV3|Q658M8|Q9BT58	Missense_Mutation	SNP	ENST00000398805.3	37	CCDS43864.1	8	0.003663003663003663	0	0.0	3	0.008287292817679558	0	0.0	5	0.006596306068601583	A	12.14	1.848888	0.32699	0.001867	0.013023	ENSG00000119471	ENST00000398805;ENST00000398803	D;D	0.88431	-2.38;-2.38	5.57	3.15	0.36227	NAD(P)-binding domain (1);	0.456598	0.25677	N	0.029030	D	0.82296	0.5006	M	0.69823	2.125	0.80722	D	1	P;B	0.45902	0.868;0.064	B;B	0.42138	0.377;0.159	T	0.79027	-0.1971	10	0.39692	T	0.17	.	6.4508	0.21902	0.6281:0.2284:0.1434:0.0	rs41280175	91;91	Q6YN16-2;Q6YN16	.;HSDL2_HUMAN	I	91	ENSP00000381785:K91I;ENSP00000381783:K91I	ENSP00000381783:K91I	K	+	2	0	HSDL2	114207815	0.922000	0.31269	0.991000	0.47740	0.021000	0.10359	0.964000	0.29306	0.369000	0.24510	0.260000	0.18958	AAA	A|0.995;T|0.005	0.005	strong		0.318	HSDL2-002	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053681.1	NM_032303	
RBM27	54439	hgsc.bcm.edu	37	5	145650597	145650597	+	Silent	SNP	A	A	G	rs17104362	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:145650597A>G	ENST00000265271.5	+	18	2938	c.2772A>G	c.(2770-2772)aaA>aaG	p.K924K	RBM27_ENST00000506502.1_Silent_p.K869K	NM_018989.1	NP_061862.1	Q9P2N5	RBM27_HUMAN	RNA binding motif protein 27	924					mRNA processing (GO:0006397)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(2)|breast(1)|central_nervous_system(3)|endometrium(4)|kidney(5)|large_intestine(7)|liver(2)|lung(10)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	39			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			AATTACGGAAAAAACTCAGTC	0.448													A|||	812	0.162141	0.4962	0.062	5008	,	,		18170	0.0		0.0716	False		,,,				2504	0.0419				p.K924K		Atlas-SNP	.											.	RBM27	119	.	0			c.A2772G						PASS	.	A		1272,1864		263,746,559	83.0	74.0	76.0		2772	-1.4	1.0	5	dbSNP_123	76	554,6610		32,490,3060	no	coding-synonymous	RBM27	NM_018989.1		295,1236,3619	GG,GA,AA		7.7331,40.5612,17.7282		924/1061	145650597	1826,8474	1568	3582	5150	SO:0001819	synonymous_variant	54439	exon18			ACGGAAAAAACTC	AL833706	CCDS43378.1	5q32	2013-01-09				ENSG00000091009		"""Zinc fingers, CCCH-type domain containing"", ""RNA binding motif (RRM) containing"""	29243	protein-coding gene	gene with protein product	"""acidic rich RS domain containing 1"""					10718198, 15741184	Standard	NM_018989		Approved	KIAA1311, ARRS1, Psc1, ZC3H18	uc003lnz.4	Q9P2N5		ENST00000265271.5:c.2772A>G	5.37:g.145650597A>G		Somatic	187	0	0		WXS	Illumina HiSeq	Phase_I	177	92	0.519774	NM_018989	Q8IYW9	Silent	SNP	ENST00000265271.5	37	CCDS43378.1																																																																																			A|0.836;G|0.164	0.164	strong		0.448	RBM27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373420.1	XM_291128	
ZKSCAN8	7745	hgsc.bcm.edu	37	6	28120898	28120898	+	Silent	SNP	G	G	A	rs17774663	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:28120898G>A	ENST00000330236.6	+	6	1024	c.840G>A	c.(838-840)caG>caA	p.Q280Q	ZKSCAN8_ENST00000457389.2_Silent_p.Q280Q	NM_001278119.1|NM_001278121.1|NM_001278122.1|NM_006298.2	NP_001265048.1|NP_001265050.1|NP_001265051.1|NP_006289.2	Q15776	ZKSC8_HUMAN	zinc finger with KRAB and SCAN domains 8	280	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)										CTGGAATCCAGCCACATGGAG	0.468													a|||	1100	0.219649	0.2958	0.2608	5008	,	,		20259	0.1875		0.1968	False		,,,				2504	0.1442				p.Q280Q		Atlas-SNP	.											ZNF192,NS,carcinoma,+1,1	.	.	1	0			c.G840A						PASS	.	T		1223,3183	707.1+/-407.5	174,875,1154	83.0	84.0	83.0		840	-11.2	0.1	6	dbSNP_123	83	1897,6703	728.3+/-406.7	216,1465,2619	no	coding-synonymous	ZNF192	NM_006298.2		390,2340,3773	AA,AG,GG		22.0581,27.7576,23.9889		280/579	28120898	3120,9886	2203	4300	6503	SO:0001819	synonymous_variant	7745	exon6			AATCCAGCCACAT		CCDS4645.1	6p21	2013-01-09	2013-01-09	2013-01-09	ENSG00000198315	ENSG00000198315		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	12983	protein-coding gene	gene with protein product		602240	"""zinc finger protein 192"""	ZNF192			Standard	NM_001278119		Approved	LD5-1, ZSCAN40	uc003nkn.2	Q15776	OTTHUMG00000014510	ENST00000330236.6:c.840G>A	6.37:g.28120898G>A		Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	119	60	0.504202	NM_006298	A1L3D4|B4DYF1|Q4VAR1|Q4VAR2|Q4VAR3|Q9H4T1	Silent	SNP	ENST00000330236.6	37	CCDS4645.1																																																																																			G|0.765;A|0.235	0.235	strong		0.468	ZKSCAN8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040178.2		
NUP62CL	54830	hgsc.bcm.edu	37	X	106396402	106396402	+	Splice_Site	SNP	A	A	G	rs1298577	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:106396402A>G	ENST00000372466.4	-	7	781	c.530T>C	c.(529-531)aTc>aCc	p.I177T	NUP62CL_ENST00000372461.3_3'UTR	NM_017681.2	NP_060151.2	Q9H1M0	N62CL_HUMAN	nucleoporin 62kDa C-terminal like	177			I -> T (in dbSNP:rs1298577). {ECO:0000269|PubMed:14702039, ECO:0000269|Ref.3}.		protein transport (GO:0015031)	nuclear pore (GO:0005643)	structural constituent of nuclear pore (GO:0017056)			lung(4)	4						AGTTACTTACATCTCCACATG	0.438													G|||	1812	0.48	0.6566	0.3213	3775	,	,		14275	0.3333		0.1521	False		,,,				2504	0.2372				p.I177T		Atlas-SNP	.											.	NUP62CL	10	.	0			c.T530C						PASS	.	G	THR/ILE	2886,949		925,604,432,103,139	194.0	212.0	206.0		530	-4.0	0.0	X	dbSNP_87	206	1226,5502		66,739,355,1623,1517	yes	missense-near-splice	NUP62CL	NM_017681.2	89	991,1343,787,1726,1656	GG,GA,G,AA,A		18.2224,24.7458,38.9283	benign	177/185	106396402	4112,6451	2203	4300	6503	SO:0001630	splice_region_variant	54830	exon7			ACTTACATCTCCA	AK000137	CCDS14527.1	Xq22.3	2008-02-05			ENSG00000198088	ENSG00000198088			25960	protein-coding gene	gene with protein product						12477932	Standard	NM_017681		Approved	FLJ20130	uc004ena.3	Q9H1M0	OTTHUMG00000022159	ENST00000372466.4:c.530+1T>C	X.37:g.106396402A>G		Somatic	266	1	0.0037594		WXS	Illumina HiSeq	Phase_I	143	143	1	NM_017681	D3DUX4|Q8WVL6|Q9NXP2	Missense_Mutation	SNP	ENST00000372466.4	37	CCDS14527.1	738	0.4448462929475588	217	0.7138157894736842	67	0.23591549295774647	137	0.315668202764977	77	0.11290322580645161	G	1.065	-0.671578	0.03403	0.752542	0.182224	ENSG00000198088	ENST00000372466;ENST00000372465	T	0.48836	0.8	5.44	-4.01	0.04045	Nucleoporin, NSP1-like, C-terminal (1);	0.153986	0.56097	N	0.000021	T	0.00012	0.0000	N	0.01505	-0.83	0.09310	P	0.9999999999999784	B	0.02656	0.0	B	0.01281	0.0	T	0.27872	-1.0061	8	.	.	.	0.0386	9.0347	0.36280	0.6223:0.1049:0.2727:0.0	rs1298577;rs52826101;rs61274773;rs1298577	177	Q9H1M0	N62CL_HUMAN	T	177	ENSP00000361544:I177T	.	I	-	2	0	NUP62CL	106283058	1.000000	0.71417	0.001000	0.08648	0.038000	0.13279	1.926000	0.40084	-2.277000	0.00677	-0.396000	0.06452	ATC;ATT	A|0.540;0|0.011	.	strong		0.438	NUP62CL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057828.1	NM_017681	Missense_Mutation
SYCE1L	100130958	hgsc.bcm.edu	37	16	77245139	77245139	+	Missense_Mutation	SNP	T	T	C	rs61746433	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:77245139T>C	ENST00000378644.4	+	7	444	c.389T>C	c.(388-390)cTg>cCg	p.L130P	RP11-538I12.2_ENST00000569032.1_RNA	NM_001129979.1	NP_001123451.1	A8MT33	SYC1L_HUMAN	synaptonemal complex central element protein 1-like	130					synaptonemal complex assembly (GO:0007130)	synaptonemal complex (GO:0000795)				breast(1)|prostate(1)	2						CTGGAGGATCTGATGGGCCAG	0.567													T|||	182	0.0363419	0.0628	0.0274	5008	,	,		18650	0.0179		0.0229	False		,,,				2504	0.0399				p.L130P		Atlas-SNP	.											.	SYCE1L	10	.	0			c.T389C						PASS	.	T	PRO/LEU	70,1314		3,64,625	167.0	156.0	159.0		389	1.5	0.0	16	dbSNP_129	159	88,3094		1,86,1504	yes	missense	SYCE1L	NM_001129979.1	98	4,150,2129	CC,CT,TT		2.7656,5.0578,3.4604	probably-damaging	130/243	77245139	158,4408	692	1591	2283	SO:0001583	missense	100130958	exon7			AGGATCTGATGGG		CCDS45533.1	16q23.1	2009-10-06			ENSG00000205078	ENSG00000205078			37236	protein-coding gene	gene with protein product	"""meiosis-related protein"""					16328886	Standard	NM_001129979		Approved	MRP2	uc010vnh.1	A8MT33		ENST00000378644.4:c.389T>C	16.37:g.77245139T>C	ENSP00000367911:p.Leu130Pro	Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	156	101	0.647436	NM_001129979	A6NF23	Missense_Mutation	SNP	ENST00000378644.4	37	CCDS45533.1	72	0.03296703296703297	33	0.06707317073170732	8	0.022099447513812154	10	0.017482517482517484	21	0.027704485488126648	T	15.25	2.777605	0.49786	0.050578	0.027656	ENSG00000205078	ENST00000378644	T	0.35973	1.28	3.82	1.5	0.22942	.	0.238102	0.20238	U	0.096343	T	0.02571	0.0078	M	0.65975	2.015	0.09310	N	0.999993	B	0.23735	0.09	B	0.23419	0.046	T	0.16276	-1.0408	10	0.87932	D	0	.	3.9775	0.09481	0.0:0.1142:0.214:0.6718	rs61746433	130	A8MT33	SYC1L_HUMAN	P	130	ENSP00000367911:L130P	ENSP00000367911:L130P	L	+	2	0	SYCE1L	75802640	0.009000	0.17119	0.003000	0.11579	0.475000	0.33008	0.120000	0.15647	0.282000	0.22254	0.460000	0.39030	CTG	T|0.970;C|0.030	0.030	strong		0.567	SYCE1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433889.1	NM_001129979	
NIPSNAP1	8508	hgsc.bcm.edu	37	22	29957570	29957570	+	Silent	SNP	G	G	A	rs1058642	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:29957570G>A	ENST00000216121.7	-	6	758	c.504C>T	c.(502-504)ctC>ctT	p.L168L		NM_001202502.1|NM_003634.3	NP_001189431.1|NP_003625.2	Q9BPW8	NIPS1_HUMAN	nipsnap homolog 1 (C. elegans)	168					sensory perception of pain (GO:0019233)	mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|synaptic membrane (GO:0097060)	neurotransmitter binding (GO:0042165)	p.?(1)		large_intestine(2)|lung(2)|skin(1)	5						AGCTGAACTCGAGGAGCAGCT	0.577													G|||	911	0.181909	0.2133	0.1571	5008	,	,		20245	0.1468		0.2744	False		,,,				2504	0.0982				p.L168L		Atlas-SNP	.											.	NIPSNAP1	17	.	1	Unknown(1)	lung(1)	c.C504T						PASS	.	G	,	955,3451	362.9+/-316.3	106,743,1354	101.0	96.0	98.0		444,504	-9.7	0.0	22	dbSNP_86	98	2351,6249	393.1+/-344.2	300,1751,2249	yes	coding-synonymous,coding-synonymous	NIPSNAP1	NM_001202502.1,NM_003634.3	,	406,2494,3603	AA,AG,GG		27.3372,21.675,25.419	,	148/265,168/285	29957570	3306,9700	2203	4300	6503	SO:0001819	synonymous_variant	8508	exon6			GAACTCGAGGAGC	AJ001258	CCDS13860.1	22q12	2013-09-12	2001-11-28		ENSG00000184117	ENSG00000184117			7827	protein-coding gene	gene with protein product	"""4-nitrophenylphosphatase domain and non-neuronal SNAP25-like 1"""	603249	"""NIPSNAP, C. elegans, homolog 1"""			9661659	Standard	NM_003634		Approved		uc003afx.4	Q9BPW8	OTTHUMG00000151294	ENST00000216121.7:c.504C>T	22.37:g.29957570G>A		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	74	34	0.459459	NM_003634	B2RAY3|O43800	Silent	SNP	ENST00000216121.7	37	CCDS13860.1	480	0.21978021978021978	117	0.23780487804878048	73	0.20165745856353592	89	0.1555944055944056	201	0.26517150395778366	G	7.620	0.676691	0.14841	0.21675	0.273372	ENSG00000184117	ENST00000415100	.	.	.	4.83	-9.67	0.00531	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	.	.	.	.	.	.	.	-7.6728	9.0159	0.36170	0.3038:0.5436:0.0921:0.0606	rs1058642;rs3199284;rs17420578	.	.	.	X	185	.	.	R	-	1	2	NIPSNAP1	28287570	0.061000	0.20836	0.028000	0.17463	0.818000	0.46254	-0.643000	0.05421	-2.274000	0.00680	-1.244000	0.01528	CGA	G|0.757;A|0.243	0.243	strong		0.577	NIPSNAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322117.1		
LSP1	4046	hgsc.bcm.edu	37	11	1902771	1902771	+	Silent	SNP	T	T	C	rs147746785	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:1902771T>C	ENST00000311604.3	+	3	476	c.301T>C	c.(301-303)Ttg>Ctg	p.L101L	LSP1_ENST00000405957.2_Silent_p.L39L|LSP1_ENST00000485341.1_3'UTR|LSP1_ENST00000381775.1_Silent_p.L229L|LSP1_ENST00000406638.2_Silent_p.L39L	NM_002339.2	NP_002330.1	P33241	LSP1_HUMAN	lymphocyte-specific protein 1	101				Missing (in Ref. 3; AAB29545). {ECO:0000305}.	cellular component movement (GO:0006928)|cellular defense response (GO:0006968)|chemotaxis (GO:0006935)	actin cytoskeleton (GO:0015629)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|signal transducer activity (GO:0004871)			haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(9)|prostate(1)|skin(1)	16		all_epithelial(84;0.000138)|Breast(177;0.000962)|Ovarian(85;0.0014)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00147)|Lung(200;0.0729)|LUSC - Lung squamous cell carcinoma(625;0.0856)		GCAGGGCGCCTTGGACAGCGG	0.706													T|||	43	0.00858626	0.003	0.0058	5008	,	,		14079	0.0		0.0318	False		,,,				2504	0.0031				p.L229L		Atlas-SNP	.											.	LSP1	59	.	0			c.T685C						PASS	.	T	,,,	24,4298		0,24,2137	14.0	16.0	15.0		115,115,115,301	-6.3	0.0	11	dbSNP_134	15	214,8202		4,206,3998	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	LSP1	NM_001013253.1,NM_001013254.1,NM_001013255.1,NM_002339.2	,,,	4,230,6135	CC,CT,TT		2.5428,0.5553,1.8684	,,,	39/278,39/278,39/278,101/340	1902771	238,12500	2161	4208	6369	SO:0001819	synonymous_variant	4046	exon4			GGCGCCTTGGACA	M33552	CCDS31334.1, CCDS31335.1, CCDS58110.1	11p15.5	2008-02-05			ENSG00000130592	ENSG00000130592			6707	protein-coding gene	gene with protein product		153432				2174784	Standard	NM_001242932		Approved	WP34	uc001luj.3	P33241	OTTHUMG00000012252	ENST00000311604.3:c.301T>C	11.37:g.1902771T>C		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	190	37	0.194737	NM_001242932	B3KPP1|B3KRR6|E9PBV6|E9PFP3|Q16096|Q53H48|Q6FHM3|Q9BUY8	Silent	SNP	ENST00000311604.3	37	CCDS31334.1																																																																																			T|0.982;C|0.018	0.018	strong		0.706	LSP1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000034045.3	NM_002339	
KIAA1549	57670	hgsc.bcm.edu	37	7	138602916	138602916	+	Missense_Mutation	SNP	G	G	C	rs2718131	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	67	0	0		WXS	Illumina HiSeq	Phase_I	72	24	0.333333	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		
UBR3	130507	hgsc.bcm.edu	37	2	170762566	170762566	+	Silent	SNP	A	A	T	rs10194785	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:170762566A>T	ENST00000272793.5	+	10	1721	c.1671A>T	c.(1669-1671)ctA>ctT	p.L557L	UBR3_ENST00000418381.1_Silent_p.L557L			Q6ZT12	UBR3_HUMAN	ubiquitin protein ligase E3 component n-recognin 3 (putative)	557					embryo development (GO:0009790)|in utero embryonic development (GO:0001701)|olfactory behavior (GO:0042048)|sensory perception of smell (GO:0007608)|suckling behavior (GO:0001967)|ubiquitin-dependent protein catabolic process (GO:0006511)	integral component of membrane (GO:0016021)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(9)|liver(1)|lung(8)|ovary(1)|prostate(3)|stomach(1)	33						AGCGAGAACTAAACGAGCATG	0.408													A|||	1388	0.277157	0.2663	0.1945	5008	,	,		16538	0.376		0.1581	False		,,,				2504	0.3712				p.L557L		Atlas-SNP	.											.	UBR3	182	.	0			c.A1671T						PASS	.	A		383,1001		58,267,367	119.0	103.0	108.0		1671	1.6	1.0	2	dbSNP_119	108	545,2637		49,447,1095	no	coding-synonymous	UBR3	NM_172070.3		107,714,1462	TT,TA,AA		17.1276,27.6734,20.3241		557/1889	170762566	928,3638	692	1591	2283	SO:0001819	synonymous_variant	130507	exon10			AGAACTAAACGAG	AL834144	CCDS2238.2	2q31.1	2008-06-23	2008-06-23	2007-11-29	ENSG00000144357	ENSG00000144357		"""Ubiquitin protein ligase E3 component n-recognins"""	30467	protein-coding gene	gene with protein product		613831	"""zinc finger protein 650"""	ZNF650		17462990	Standard	NM_172070		Approved	KIAA2024, DKFZp434P117, FLJ37422	uc010zdi.2	Q6ZT12	OTTHUMG00000132229	ENST00000272793.5:c.1671A>T	2.37:g.170762566A>T		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	82	38	0.463415	NM_172070	B4DZR7|Q2KHN5|Q6ZR55|Q6ZSC2|Q8IVE7|Q8ND96	Silent	SNP	ENST00000272793.5	37																																																																																				A|0.748;T|0.252	0.252	strong		0.408	UBR3-001	KNOWN	non_canonical_conserved|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000255290.2	NM_172070	
LIPM	340654	hgsc.bcm.edu	37	10	90580144	90580144	+	Silent	SNP	C	C	T	rs10788615	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:90580144C>T	ENST00000404743.4	+	9	1325	c.1158C>T	c.(1156-1158)caC>caT	p.H386H	ANKRD22_ENST00000476963.1_5'Flank|LIPM_ENST00000539337.1_Silent_p.H346H	NM_001128215.1	NP_001121687.1	Q5VYY2	LIPM_HUMAN	lipase, family member M	386					lipid catabolic process (GO:0016042)	extracellular region (GO:0005576)	hydrolase activity, acting on ester bonds (GO:0016788)			breast(1)|central_nervous_system(1)|endometrium(1)|lung(2)|pancreas(1)|skin(1)	7						AATGGGCTCACGTGGATTTCA	0.493													c|||	1480	0.295527	0.0598	0.3141	5008	,	,		21390	0.4375		0.336	False		,,,				2504	0.4131				p.H386H		Atlas-SNP	.											.	LIPM	17	.	0			c.C1158T						PASS	.	T	,	136,1248		6,124,562	178.0	142.0	153.0		1158,	-6.2	0.3	10	dbSNP_120	153	1002,2180		164,674,753	yes	coding-synonymous,utr-3	ANKRD22,LIPM	NM_001128215.1,NM_144590.2	,	170,798,1315	TT,TC,CC		31.4896,9.8266,24.9233	,	386/424,	90580144	1138,3428	692	1591	2283	SO:0001819	synonymous_variant	340654	exon9			GGCTCACGTGGAT		CCDS44457.1	10q23.31	2008-02-04	2007-02-27	2007-02-27	ENSG00000173239	ENSG00000173239			23455	protein-coding gene	gene with protein product		613923	"""lipase-like, ab-hydrolase domain containing 3"""	LIPL3			Standard	NM_001128215		Approved	bA304I5.1	uc009xtm.1	Q5VYY2	OTTHUMG00000018698	ENST00000404743.4:c.1158C>T	10.37:g.90580144C>T		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	92	50	0.543478	NM_001128215	A6PVS3|B2RXK7|B5MCR3	Silent	SNP	ENST00000404743.4	37	CCDS44457.1																																																																																			C|0.705;N|0.000	.	strong		0.493	LIPM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049261.3	XM_291663	
GNRH2	2797	hgsc.bcm.edu	37	20	3025107	3025107	+	Missense_Mutation	SNP	C	C	T	rs6051545	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:3025107C>T	ENST00000245983.2	+	2	98	c.47C>T	c.(46-48)gCc>gTc	p.A16V	GNRH2_ENST00000359100.2_Missense_Mutation_p.A16V|GNRH2_ENST00000380347.2_Missense_Mutation_p.A16V|MRPS26_ENST00000380325.3_5'Flank|GNRH2_ENST00000359987.1_Missense_Mutation_p.A16V|GNRH2_ENST00000380346.2_Missense_Mutation_p.A16V	NM_001501.1	NP_001492.1	O43555	GON2_HUMAN	gonadotropin-releasing hormone 2	16			A -> V (in dbSNP:rs6051545).		multicellular organismal development (GO:0007275)|signal transduction (GO:0007165)	extracellular region (GO:0005576)	hormone activity (GO:0005179)			ovary(1)|upper_aerodigestive_tract(1)	2						CTGCTGACTGCCCACCTTGGA	0.617													C|||	1203	0.240216	0.1104	0.281	5008	,	,		18857	0.372		0.173	False		,,,				2504	0.32				p.A16V		Atlas-SNP	.											.	GNRH2	15	.	0			c.C47T						PASS	.	C	VAL/ALA,VAL/ALA,VAL/ALA	584,3822	258.6+/-262.5	36,512,1655	70.0	69.0	70.0		47,47,47	1.3	0.0	20	dbSNP_114	70	1374,7226	267.1+/-287.1	103,1168,3029	yes	missense,missense,missense	GNRH2	NM_001501.1,NM_178331.1,NM_178332.1	64,64,64	139,1680,4684	TT,TC,CC		15.9767,13.2547,15.0546	probably-damaging,probably-damaging,probably-damaging	16/121,16/114,16/113	3025107	1958,11048	2203	4300	6503	SO:0001583	missense	2797	exon2			TGACTGCCCACCT	AF036329	CCDS13040.1, CCDS13041.1, CCDS13042.1	20p13	2013-02-26			ENSG00000125787	ENSG00000125787		"""Endogenous ligands"""	4420	protein-coding gene	gene with protein product		602352				9419371, 12447356	Standard	NM_178331		Approved		uc002whr.1	O43555	OTTHUMG00000031723	ENST00000245983.2:c.47C>T	20.37:g.3025107C>T	ENSP00000245983:p.Ala16Val	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	95	52	0.547368	NM_001501	Q14C68|Q14C69|Q9BYN9|Q9BYP0	Missense_Mutation	SNP	ENST00000245983.2	37	CCDS13040.1	509	0.23305860805860806	62	0.12601626016260162	103	0.2845303867403315	207	0.3618881118881119	137	0.18073878627968337	C	14.43	2.533369	0.45073	0.132547	0.159767	ENSG00000125787	ENST00000245983;ENST00000359100;ENST00000359987;ENST00000380347;ENST00000380346	T;T;T;T;T	0.41400	1.0;1.0;1.0;1.0;1.0	3.32	1.34	0.21922	.	.	.	.	.	T	0.00012	0.0000	N	0.10664	0.02	0.80722	P	0.0	B;B;B	0.20550	0.027;0.046;0.046	B;B;B	0.17433	0.008;0.018;0.018	T	0.46610	-0.9179	8	0.13853	T	0.58	.	6.8688	0.24108	0.0:0.7646:0.0:0.2353	rs6051545;rs6051545	16;16;16	O43555;O43555-2;O43555-3	GON2_HUMAN;.;.	V	16	ENSP00000245983:A16V;ENSP00000352003:A16V;ENSP00000353077:A16V;ENSP00000369705:A16V;ENSP00000369704:A16V	ENSP00000245983:A16V	A	+	2	0	GNRH2	2973107	0.000000	0.05858	0.000000	0.03702	0.023000	0.10783	0.193000	0.17116	0.407000	0.25591	0.563000	0.77884	GCC	C|0.815;T|0.185	0.185	strong		0.617	GNRH2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077694.2	NM_001501	
VAPA	9218	hgsc.bcm.edu	37	18	9944956	9944956	+	Intron	SNP	T	T	C	rs29133	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:9944956T>C	ENST00000400000.2	+	5	672				VAPA_ENST00000340541.4_Silent_p.T151T|VAPA_ENST00000584796.1_Intron	NM_003574.5|NM_194434.2	NP_003565.4|NP_919415.2	Q9P0L0	VAPA_HUMAN	VAMP (vesicle-associated membrane protein)-associated protein A, 33kDa						cell death (GO:0008219)|membrane fusion (GO:0061025)|neuron projection development (GO:0031175)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|protein localization to endoplasmic reticulum (GO:0070972)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|microtubule cytoskeleton (GO:0015630)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	protein heterodimerization activity (GO:0046982)|signal transducer activity (GO:0004871)|structural molecule activity (GO:0005198)			breast(1)|lung(2)|prostate(1)	4						CGACTGTCACTTCAATGAGCA	0.468													T|||	422	0.0842652	0.1263	0.1052	5008	,	,		19105	0.0774		0.0537	False		,,,				2504	0.0511				p.T151T		Atlas-SNP	.											.	VAPA	28	.	0			c.T453C						PASS	.	T	,	510,3490		29,452,1519	114.0	105.0	108.0		453,	-5.6	0.0	18	dbSNP_76	108	448,7910		16,416,3747	no	coding-synonymous,intron	VAPA	NM_003574.5,NM_194434.2	,	45,868,5266	CC,CT,TT		5.3601,12.75,7.7521	,	151/295,	9944956	958,11400	2000	4179	6179	SO:0001627	intron_variant	9218	exon5			TGTCACTTCAATG		CCDS11847.2, CCDS11848.2	18p11.2	2008-07-28	2002-08-29		ENSG00000101558	ENSG00000101558			12648	protein-coding gene	gene with protein product		605703	"""VAMP (vesicle-associated membrane protein)-associated protein A (33kD)"""			9920726, 9657962	Standard	NM_003574		Approved	hVAP-33, VAP-A	uc002koj.3	Q9P0L0	OTTHUMG00000131603	ENST00000400000.2:c.418-5436T>C	18.37:g.9944956T>C		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	92	48	0.521739	NM_003574	A6NDZ0|D3DUI3|O75453|Q5U0E7|Q9UBZ2	Silent	SNP	ENST00000400000.2	37	CCDS11848.2																																																																																			T|0.931;C|0.069	0.069	strong		0.468	VAPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254490.1		
MYO7B	4648	hgsc.bcm.edu	37	2	128388437	128388437	+	Missense_Mutation	SNP	A	A	C	rs138651379	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:128388437A>C	ENST00000409816.2	+	34	4845	c.4813A>C	c.(4813-4815)Aag>Cag	p.K1605Q	MYO7B_ENST00000428314.1_Missense_Mutation_p.K1605Q|MYO7B_ENST00000389524.4_Missense_Mutation_p.K1605Q|MYO7B_ENST00000409090.1_Missense_Mutation_p.K458Q			Q6PIF6	MYO7B_HUMAN	myosin VIIB	1605						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)		GGAGCCACCCAAGGAAAAGCT	0.632													A|||	143	0.0285543	0.0008	0.0115	5008	,	,		14729	0.002		0.0219	False		,,,				2504	0.1125				p.K1605Q		Atlas-SNP	.											MYO7B_ENST00000428314,NS,haematopoietic_neoplasm,0,2	MYO7B	359	2	0			c.A4813C						PASS	.	A	GLN/LYS	14,3926		0,14,1956	32.0	39.0	36.0		4813	-4.9	0.0	2	dbSNP_134	36	203,8063		7,189,3937	yes	missense	MYO7B	NM_001080527.1	53	7,203,5893	CC,CA,AA		2.4558,0.3553,1.7778	benign	1605/2117	128388437	217,11989	1970	4133	6103	SO:0001583	missense	4648	exon35			CCACCCAAGGAAA		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.4813A>C	2.37:g.128388437A>C	ENSP00000386461:p.Lys1605Gln	Somatic	297	1	0.003367		WXS	Illumina HiSeq	Phase_I	254	128	0.503937	NM_001080527	Q14786|Q8TEE1	Missense_Mutation	SNP	ENST00000409816.2	37	CCDS46405.1	28	0.01282051282051282	1	0.0020325203252032522	6	0.016574585635359115	1	0.0017482517482517483	20	0.026385224274406333	N	5.664	0.307102	0.10733	0.003553	0.024558	ENSG00000169994	ENST00000389524;ENST00000428314;ENST00000272666;ENST00000409816;ENST00000409090	T;T;T;T	0.68181	-0.31;-0.31;-0.31;-0.31	5.19	-4.88	0.03113	.	0.540372	0.18467	N	0.140348	T	0.16342	0.0393	N	0.11756	0.17	0.09310	N	1	B	0.14012	0.009	B	0.12837	0.008	T	0.10291	-1.0636	10	0.25751	T	0.34	.	7.877	0.29599	0.2389:0.5204:0.2407:0.0	.	1605	Q6PIF6	MYO7B_HUMAN	Q	1605;1605;700;1605;458	ENSP00000374175:K1605Q;ENSP00000415090:K1605Q;ENSP00000386461:K1605Q;ENSP00000386850:K458Q	ENSP00000272666:K700Q	K	+	1	0	MYO7B	128104907	0.000000	0.05858	0.001000	0.08648	0.004000	0.04260	0.077000	0.14738	-0.700000	0.05070	-0.394000	0.06481	AAG	A|0.987;C|0.013	0.013	strong		0.632	MYO7B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000331124.3	XM_291001	
PCDHA8	56140	hgsc.bcm.edu	37	5	140222138	140222138	+	Missense_Mutation	SNP	G	G	C	rs144906391	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:140222138G>C	ENST00000531613.1	+	1	1232	c.1232G>C	c.(1231-1233)aGc>aCc	p.S411T	PCDHA4_ENST00000512229.2_Intron|PCDHA8_ENST00000378123.3_Missense_Mutation_p.S411T|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|PCDHA5_ENST00000529619.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA1_ENST00000504120.2_Intron	NM_018911.2	NP_061734.1	Q9Y5H6	PCDA8_HUMAN	protocadherin alpha 8	411	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(2)|breast(3)|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)			GTGCTGGACAGCGCCCTGGAC	0.627													.|||	13	0.00259585	0.003	0.0043	5008	,	,		16977	0.002		0.004	False		,,,				2504	0.0				p.S411T		Atlas-SNP	.											PCDHA8_ENST00000531613,middle_lobe,carcinoma,-1,2	PCDHA8	366	2	0			c.G1232C						scavenged	.						130.0	113.0	119.0					5																	140222138		2202	4290	6492	SO:0001583	missense	56140	exon1			TGGACAGCGCCCT	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.1232G>C	5.37:g.140222138G>C	ENSP00000434655:p.Ser411Thr	Somatic	299	0	0		WXS	Illumina HiSeq	Phase_I	134	3	0.0223881	NM_031856	B9EGT7|O75281	Missense_Mutation	SNP	ENST00000531613.1	37	CCDS54919.1	.	.	.	.	.	.	.	.	.	.	G	7.775	0.708334	0.15239	.	.	ENSG00000204962	ENST00000531613;ENST00000378123	T;T	0.52057	0.68;0.68	3.57	2.68	0.31781	Cadherin (4);Cadherin-like (1);	0.343970	0.20583	U	0.089491	T	0.27832	0.0685	N	0.16066	0.365	0.09310	N	1	B;B	0.28900	0.227;0.092	B;B	0.29785	0.107;0.094	T	0.15065	-1.0450	10	0.44086	T	0.13	.	7.0255	0.24938	0.2939:0.0:0.7061:0.0	.	411;411	Q9Y5H6;Q9Y5H6-2	PCDA8_HUMAN;.	T	411	ENSP00000434655:S411T;ENSP00000367363:S411T	ENSP00000367363:S411T	S	+	2	0	PCDHA8	140202322	0.000000	0.05858	0.893000	0.35052	0.373000	0.29922	-0.036000	0.12185	0.610000	0.30035	0.306000	0.20318	AGC	.	.	weak		0.627	PCDHA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372830.2	NM_018911	
SNTB2	6645	hgsc.bcm.edu	37	16	69318149	69318149	+	Splice_Site	SNP	T	T	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:69318149T>C	ENST00000336278.4	+	5	1383		c.e5+2			NM_006750.3	NP_006741.1	Q13425	SNTB2_HUMAN	syntrophin, beta 2 (dystrophin-associated protein A1, 59kDa, basic component 2)							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)		TCTCTCTAGGTAGAGATGCTG	0.423																																					.	NSCLC(58;1458 1722 3262 39967)|Melanoma(111;1698 2173 25379 28738)	Atlas-SNP	.											.	SNTB2	22	.	0			c.1345+2T>C						PASS	.						70.0	64.0	66.0					16																	69318149		2198	4300	6498	SO:0001630	splice_region_variant	6645	exon5			TCTAGGTAGAGAT	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.1345+2T>C	16.37:g.69318149T>C		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	88	4	0.0454545	NM_006750	Q9BY09	Splice_Site	SNP	ENST00000336278.4	37	CCDS10873.1	.	.	.	.	.	.	.	.	.	.	T	22.9	4.346898	0.82022	.	.	ENSG00000168807	ENST00000336278;ENST00000467311	.	.	.	5.23	5.23	0.72850	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.7976	0.69889	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	SNTB2	67875650	1.000000	0.71417	1.000000	0.80357	0.901000	0.52897	7.857000	0.86963	1.975000	0.57531	0.533000	0.62120	.	.	.	none		0.423	SNTB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268945.1		Intron
VCX2	51480	hgsc.bcm.edu	37	X	8138182	8138182	+	Missense_Mutation	SNP	A	A	G	rs41305169		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:8138182A>G	ENST00000317103.4	-	3	617	c.311T>C	c.(310-312)cTg>cCg	p.L104P		NM_016378.2	NP_057462.2	Q9H322	VCX2_HUMAN	variable charge, X-linked 2	104	2 X 10 AA tandem repeats of L-S-Q-E-S- [EQ]-V-E-E-P.		L -> P (in dbSNP:rs41305169). {ECO:0000269|PubMed:10607842, ECO:0000269|PubMed:10903929, ECO:0000269|PubMed:15489334}.							endometrium(1)	1		Colorectal(8;0.0136)|Medulloblastoma(8;0.184)				CTCCTGACTCAGGGGGTCGTG	0.667																																					p.L104P		Atlas-SNP	.											.	VCX2	16	.	0			c.T311C						PASS	.						27.0	34.0	32.0					X																	8138182		2157	4235	6392	SO:0001583	missense	51480	exon3			TGACTCAGGGGGT	AF159127	CCDS35200.1	Xp22.32	2008-02-05			ENSG00000177504	ENSG00000177504			18158	protein-coding gene	gene with protein product		300532				10607842	Standard	NM_016378		Approved	VCX-2r, VCX-2R	uc004csb.3	Q9H322	OTTHUMG00000021105	ENST00000317103.4:c.311T>C	X.37:g.8138182A>G	ENSP00000321309:p.Leu104Pro	Somatic	233	2	0.00858369		WXS	Illumina HiSeq	Phase_I	95	85	0.894737	NM_016378	A3KPB6|Q4V9T2|Q9P0H5	Missense_Mutation	SNP	ENST00000317103.4	37	CCDS35200.1	798	0.4810126582278481	89	0.21394230769230768	103	0.3759124087591241	195	0.5158730158730159	169	0.2725806451612903	A	3.519	-0.098106	0.07010	.	.	ENSG00000177504	ENST00000317103	T	0.34859	1.34	0.0465	0.0465	0.14256	.	.	.	.	.	T	0.00012	0.0000	L	0.61218	1.895	0.09310	N	0.999999	D	0.54397	0.966	P	0.61070	0.883	T	0.47649	-0.9101	8	0.51188	T	0.08	.	.	.	.	rs41305169	104	Q9H322	VCX2_HUMAN	P	104	ENSP00000321309:L104P	ENSP00000321309:L104P	L	-	2	0	VCX2	8098182	0.001000	0.12720	0.014000	0.15608	0.015000	0.08874	-0.143000	0.10296	0.105000	0.17753	0.104000	0.15600	CTG	A|0.518;G|0.482	0.482	strong		0.667	VCX2-001	KNOWN	non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055690.1	NM_016378	
DOK7	285489	hgsc.bcm.edu	37	4	3491504	3491504	+	Silent	SNP	G	G	A	rs59932476|rs373384998	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:3491504G>A	ENST00000340083.5	+	6	818	c.753G>A	c.(751-753)gcG>gcA	p.A251A	DOK7_ENST00000389653.2_Silent_p.A251A|DOK7_ENST00000507039.1_Missense_Mutation_p.G248R	NM_173660.4	NP_775931.3	Q18PE1	DOK7_HUMAN	docking protein 7	251					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)		TCTCACATGCGGGCAGGCCGG	0.667													.|||	334	0.0666933	0.121	0.0764	5008	,	,		13871	0.0288		0.0338	False		,,,				2504	0.0593				p.G248R		Atlas-SNP	.											.	DOK7	44	.	0			c.G742A						PASS	.		ARG/GLY,	382,3972		11,360,1806	20.0	19.0	19.0		742,753	-1.9	0.0	4	dbSNP_129	19	275,8281		5,265,4008	yes	missense,coding-synonymous	DOK7	NM_001164673.1,NM_173660.4	125,	16,625,5814	AA,AG,GG		3.2141,8.7735,5.0891	,	248/256,251/505	3491504	657,12253	2177	4278	6455	SO:0001819	synonymous_variant	285489	exon6			ACATGCGGGCAGG	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.753G>A	4.37:g.3491504G>A		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	87	40	0.45977	NM_001164673	A2A499|A2RRD4|E9PB56|Q6P6A6|Q86XG5|Q8N2J3|Q8NBC1	Missense_Mutation	SNP	ENST00000340083.5	37	CCDS3370.2	103	0.04716117216117216	42	0.08536585365853659	27	0.07458563535911603	12	0.02097902097902098	22	0.029023746701846966	G	0.063	-1.219582	0.01542	0.087735	0.032141	ENSG00000175920	ENST00000507039	D	0.93488	-3.23	3.97	-1.91	0.07641	.	.	.	.	.	T	0.35682	0.0940	.	.	.	0.28812	N	0.898182	.	.	.	.	.	.	T	0.70421	-0.4876	6	0.87932	D	0	-18.4194	3.9601	0.09407	0.2597:0.1187:0.5133:0.1083	rs59932476;rs61740390	.	.	.	R	248	ENSP00000423614:G248R	ENSP00000423614:G248R	G	+	1	0	DOK7	3461302	0.000000	0.05858	0.010000	0.14722	0.002000	0.02628	-2.607000	0.00887	-1.075000	0.03129	-1.634000	0.00779	GGG	G|0.946;A|0.054	0.054	strong		0.667	DOK7-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000313538.1	NM_173660	
MKNK1	8569	hgsc.bcm.edu	37	1	47028362	47028362	+	Missense_Mutation	SNP	C	C	T	rs55791614	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:47028362C>T	ENST00000371946.4	-	11	1085	c.922G>A	c.(922-924)Gac>Aac	p.D308N	MKNK1-AS1_ENST00000602433.1_RNA|MKNK1_ENST00000371944.4_Missense_Mutation_p.D172N|MKNK1_ENST00000428112.2_Missense_Mutation_p.D267N|MKNK1_ENST00000371945.4_Missense_Mutation_p.D267N|MKNK1_ENST00000341183.5_Missense_Mutation_p.D267N	NM_003684.5	NP_003675.2	Q9BUB5	MKNK1_HUMAN	MAP kinase interacting serine/threonine kinase 1	308	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		D -> N (in dbSNP:rs55791614). {ECO:0000269|PubMed:17344846}.		extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|fibroblast growth factor receptor signaling pathway (GO:0008543)|intracellular signal transduction (GO:0035556)|peptidyl-serine phosphorylation (GO:0018105)|protein phosphorylation (GO:0006468)|regulation of translation (GO:0006417)|response to salt stress (GO:0009651)	cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|skin(1)	13	Acute lymphoblastic leukemia(166;0.155)					CAGCCACAGTCGGCCCCGCAG	0.662													C|||	10	0.00199681	0.0	0.0043	5008	,	,		16040	0.0		0.005	False		,,,				2504	0.002				p.D308N		Atlas-SNP	.											.	MKNK1	36	.	0			c.G922A						PASS	.	C	ASN/ASP,ASN/ASP,ASN/ASP	11,4385		0,11,2187	27.0	24.0	25.0		799,922,799	4.5	1.0	1	dbSNP_129	25	60,8500		1,58,4221	no	missense,missense,missense	MKNK1	NM_001135553.1,NM_003684.4,NM_198973.2	23,23,23	1,69,6408	TT,TC,CC		0.7009,0.2502,0.548	benign,benign,benign	267/425,308/466,267/348	47028362	71,12885	2198	4280	6478	SO:0001583	missense	8569	exon11			CACAGTCGGCCCC	AB000409	CCDS538.1, CCDS30705.1, CCDS44134.1	1p33	2008-02-05			ENSG00000079277	ENSG00000079277			7110	protein-coding gene	gene with protein product		606724				9155018	Standard	NM_003684		Approved	MNK1	uc001cqb.4	Q9BUB5	OTTHUMG00000007983	ENST00000371946.4:c.922G>A	1.37:g.47028362C>T	ENSP00000361014:p.Asp308Asn	Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	171	104	0.608187	NM_003684	D3DQ20|D3DQ21|O00312|Q5TC06|Q5TC07|Q6V0N6	Missense_Mutation	SNP	ENST00000371946.4	37	CCDS538.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	C	15.55	2.866573	0.51588	0.002502	0.007009	ENSG00000079277	ENST00000371946;ENST00000371945;ENST00000371944;ENST00000341183;ENST00000428112	T;T;T;T;T	0.20598	2.06;2.06;2.06;2.06;2.06	5.42	4.49	0.54785	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.086825	0.85682	D	0.000000	T	0.08358	0.0208	N	0.12502	0.225	0.80722	D	1	B;B;B;B;B;P	0.42649	0.102;0.245;0.102;0.083;0.193;0.786	B;B;B;B;B;B	0.37888	0.031;0.054;0.031;0.018;0.09;0.26	T	0.09596	-1.0667	10	0.32370	T	0.25	.	13.8642	0.63578	0.0:0.9252:0.0:0.0748	rs55791614	172;172;267;267;267;308	B4DQK5;Q7Z319;A8K341;Q9BUB5-3;Q9BUB5-2;Q9BUB5	.;.;.;.;.;MKNK1_HUMAN	N	308;267;172;267;267	ENSP00000361014:D308N;ENSP00000361013:D267N;ENSP00000361012:D172N;ENSP00000339573:D267N;ENSP00000411135:D267N	ENSP00000339573:D267N	D	-	1	0	MKNK1	46800949	0.994000	0.37717	0.977000	0.42913	0.672000	0.39443	3.119000	0.50422	2.826000	0.97356	0.563000	0.77884	GAC	C|0.996;T|0.004	0.004	strong		0.662	MKNK1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000021897.2	NM_003684	
RNF111	54778	hgsc.bcm.edu	37	15	59323048	59323048	+	Missense_Mutation	SNP	C	C	G	rs2899642	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:59323048C>G	ENST00000557998.1	+	2	314	c.27C>G	c.(25-27)aaC>aaG	p.N9K	RNF111_ENST00000561186.1_Missense_Mutation_p.N9K|RNF111_ENST00000434298.1_Missense_Mutation_p.N9K|RNF111_ENST00000559209.1_Missense_Mutation_p.N9K|RNF111_ENST00000348370.4_Missense_Mutation_p.N9K	NM_001270530.1	NP_001257459.1	Q6ZNA4	RN111_HUMAN	ring finger protein 111	9			N -> K (in dbSNP:rs2899642). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005}.		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)		CTGAATATAACGAGCTCTACA	0.363													C|||	1160	0.231629	0.0212	0.2925	5008	,	,		12701	0.1399		0.4781	False		,,,				2504	0.3139				p.N9K	NSCLC(72;983 1365 10746 34387 47081)	Atlas-SNP	.											.	RNF111	179	.	0			c.C27G						PASS	.	C	LYS/ASN	392,3990		26,340,1825	54.0	54.0	54.0		27	3.7	1.0	15	dbSNP_101	54	3897,4685		917,2063,1311	yes	missense	RNF111	NM_017610.6	94	943,2403,3136	GG,GC,CC		45.409,8.9457,33.0839	possibly-damaging	9/987	59323048	4289,8675	2191	4291	6482	SO:0001583	missense	54778	exon2			ATATAACGAGCTC	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.27C>G	15.37:g.59323048C>G	ENSP00000452732:p.Asn9Lys	Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	159	65	0.408805	NM_017610	C9JUS4|H0YN55|Q6P9A4|Q6ZMU2|Q7L428|Q7Z346|Q8N1P9|Q8WUA3|Q9NSR1	Missense_Mutation	SNP	ENST00000557998.1	37	CCDS58366.1	561	0.25686813186813184	16	0.032520325203252036	125	0.3453038674033149	70	0.12237762237762238	350	0.46174142480211083	C	11.13	1.548288	0.27652	0.089457	0.45409	ENSG00000157450	ENST00000348370;ENST00000434298	T;T	0.17213	2.29;2.31	5.58	3.7	0.42460	.	0.088685	0.49305	N	0.000160	T	0.00012	0.0000	L	0.36672	1.1	0.40775	P	0.016878999999999977	B;B;B	0.32396	0.05;0.253;0.369	B;B;B	0.35182	0.05;0.097;0.197	T	0.47249	-0.9132	9	0.54805	T	0.06	-4.5618	5.9476	0.19227	0.0:0.535:0.2994:0.1656	rs2899642;rs17190757;rs17846585;rs17859666;rs52829460;rs2899642	9;9;9	Q6ZNA4-3;Q6ZNA4;Q6ZNA4-2	.;RN111_HUMAN;.	K	9	ENSP00000288199:N9K;ENSP00000393641:N9K	ENSP00000288199:N9K	N	+	3	2	RNF111	57110340	1.000000	0.71417	0.998000	0.56505	0.964000	0.63967	0.738000	0.26158	0.716000	0.32124	0.491000	0.48974	AAC	C|0.704;G|0.296	0.296	strong		0.363	RNF111-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000416012.1	NM_017610	
CRIPAK	285464	hgsc.bcm.edu	37	4	1388379	1388379	+	Missense_Mutation	SNP	G	G	A	rs56109734	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	129	2	0.0155039		WXS	Illumina HiSeq	Phase_I	90	20	0.222222	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	
HLA-A	3105	hgsc.bcm.edu	37	6	29912333	29912333	+	Missense_Mutation	SNP	C	C	T	rs3179982	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:29912333C>T	ENST00000396634.1	+	7	1293	c.952C>T	c.(952-954)Ctt>Ttt	p.L318F	HLA-A_ENST00000376802.2_Intron|HLA-A_ENST00000376809.5_Missense_Mutation_p.L318F|HLA-A_ENST00000376806.5_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	207	0	0		WXS	Illumina HiSeq	Phase_I	149	58	0.389262	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	
ATF4	468	hgsc.bcm.edu	37	22	39917515	39917515	+	Missense_Mutation	SNP	A	A	C	rs4894	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:39917515A>C	ENST00000337304.2	+	1	947	c.65A>C	c.(64-66)cAg>cCg	p.Q22P	ATF4_ENST00000404241.2_Missense_Mutation_p.Q22P|ATF4_ENST00000396680.1_Missense_Mutation_p.Q22P	NM_001675.2	NP_001666.2	P18848	ATF4_HUMAN	activating transcription factor 4	22			Q -> P (in dbSNP:rs4894). {ECO:0000269|PubMed:1534408, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:1847461}.		activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular amino acid metabolic process (GO:0006520)|cellular protein metabolic process (GO:0044267)|circadian regulation of gene expression (GO:0032922)|endoplasmic reticulum unfolded protein response (GO:0030968)|gamma-aminobutyric acid signaling pathway (GO:0007214)|gluconeogenesis (GO:0006094)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|negative regulation of oxidative stress-induced neuron death (GO:1903204)|negative regulation of potassium ion transport (GO:0043267)|positive regulation of apoptotic process (GO:0043065)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to endoplasmic reticulum stress (GO:1990440)|positive regulation of transcription from RNA polymerase II promoter in response to oxidative stress (GO:0036091)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|response to endoplasmic reticulum stress (GO:0034976)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dendrite membrane (GO:0032590)|Lewy body core (GO:1990037)|neuron projection (GO:0043005)|nuclear periphery (GO:0034399)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	core promoter sequence-specific DNA binding (GO:0001046)|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 RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|endometrium(2)|large_intestine(2)|lung(5)|skin(1)	11	Melanoma(58;0.04)				Pseudoephedrine(DB00852)	CCCTTCGACCAGTCGGGTTTG	0.537													A|||	1371	0.273762	0.2557	0.2507	5008	,	,		20063	0.2024		0.3171	False		,,,				2504	0.3436				p.Q22P		Atlas-SNP	.											.	ATF4	27	.	0			c.A65C						PASS	.	A	PRO/GLN,PRO/GLN	1190,3216	404.6+/-333.2	167,856,1180	64.0	64.0	64.0		65,65	3.3	1.0	22	dbSNP_52	64	2741,5859	420.8+/-353.5	460,1821,2019	no	missense,missense	ATF4	NM_001675.2,NM_182810.1	76,76	627,2677,3199	CC,CA,AA		31.8721,27.0086,30.2245	benign,benign	22/352,22/352	39917515	3931,9075	2203	4300	6503	SO:0001583	missense	468	exon1			TCGACCAGTCGGG	D90209	CCDS13996.1	22q13.1	2013-05-23	2013-05-23		ENSG00000128272	ENSG00000128272		"""basic leucine zipper proteins"""	786	protein-coding gene	gene with protein product	"""tax-responsive enhancer element B67"""	604064	"""activating transcription factor 4 (tax-responsive enhancer element B67)"""	TXREB		1847461, 1534408	Standard	NM_182810		Approved	TAXREB67, CREB-2	uc003axz.3	P18848	OTTHUMG00000151099	ENST00000337304.2:c.65A>C	22.37:g.39917515A>C	ENSP00000336790:p.Gln22Pro	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	111	110	0.990991	NM_001675	Q9UH31	Missense_Mutation	SNP	ENST00000337304.2	37	CCDS13996.1	553	0.2532051282051282	129	0.2621951219512195	95	0.26243093922651933	90	0.15734265734265734	239	0.3153034300791557	A	12.20	1.867018	0.32977	0.270086	0.318721	ENSG00000128272	ENST00000404241;ENST00000337304;ENST00000396680	T;T;T	0.52983	0.64;0.64;0.64	4.37	3.29	0.37713	.	0.062472	0.64402	N	0.000003	T	0.00012	0.0000	L	0.45137	1.4	0.21220	P	0.999754168	B	0.06786	0.001	B	0.06405	0.002	T	0.18713	-1.0328	9	0.87932	D	0	-10.5758	10.646	0.45621	0.8385:0.1615:0.0:0.0	rs4894;rs3175832;rs3859851;rs11556098;rs17850300;rs17850840;rs17852243	22	P18848	ATF4_HUMAN	P	22	ENSP00000384587:Q22P;ENSP00000336790:Q22P;ENSP00000379912:Q22P	ENSP00000336790:Q22P	Q	+	2	0	ATF4	38247461	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.075000	0.30716	0.504000	0.28082	0.459000	0.35465	CAG	A|0.706;C|0.294	0.294	strong		0.537	ATF4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321305.1	NM_001675	
DHRS9	10170	hgsc.bcm.edu	37	2	169952233	169952233	+	Silent	SNP	T	T	C	rs1059261	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:169952233T>C	ENST00000327239.4	+	8	2420	c.916T>C	c.(916-918)Ttg>Ctg	p.L306L	DHRS9_ENST00000602501.1_Silent_p.L306L|DHRS9_ENST00000428522.1_Silent_p.L306L|DHRS9_ENST00000412271.1_Silent_p.L306L|DHRS9_ENST00000436483.2_Silent_p.L306L|DHRS9_ENST00000432060.2_Silent_p.L366L|DHRS9_ENST00000421653.1_Silent_p.L159L|DHRS9_ENST00000357546.2_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	155	0	0		WXS	Illumina HiSeq	Phase_I	144	68	0.472222	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	
EGFL7	51162	hgsc.bcm.edu	37	9	139564668	139564668	+	Missense_Mutation	SNP	G	G	A	rs2297538	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:139564668G>A	ENST00000371699.1	+	7	1368	c.457G>A	c.(457-459)Gtc>Atc	p.V153I	EGFL7_ENST00000492002.1_3'UTR|MIR126_ENST00000362291.1_RNA|EGFL7_ENST00000308874.7_Missense_Mutation_p.V153I|EGFL7_ENST00000371698.3_Missense_Mutation_p.V153I|EGFL7_ENST00000406555.3_Missense_Mutation_p.V153I			Q9UHF1	EGFL7_HUMAN	EGF-like-domain, multiple 7	153	EGF-like 2; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.		V -> I (in dbSNP:rs2297538). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.2}.		angiogenesis (GO:0001525)|blood vessel development (GO:0001568)|cell adhesion (GO:0007155)|negative regulation of cell migration (GO:0030336)|negative regulation of Notch signaling pathway (GO:0045746)|positive regulation of endothelial cell proliferation (GO:0001938)|vasculogenesis (GO:0001570)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	calcium ion binding (GO:0005509)			kidney(2)|ovary(1)|prostate(2)|urinary_tract(1)	6	all_cancers(76;0.109)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;9.87e-06)|Epithelial(140;0.000123)		CCAGCGCTGCGTCAACACCGC	0.672													g|||	843	0.168331	0.2073	0.1945	5008	,	,		17073	0.1349		0.2087	False		,,,				2504	0.09				p.V153I		Atlas-SNP	.											.	EGFL7	11	.	0			c.G457A						PASS	.	G	ILE/VAL,ILE/VAL	967,3427		108,751,1338	35.0	38.0	37.0		457,457	0.5	0.9	9	dbSNP_100	37	1757,6825		169,1419,2703	yes	missense,missense	EGFL7	NM_016215.4,NM_201446.2	29,29	277,2170,4041	AA,AG,GG		20.4731,22.0073,20.9926	benign,benign	153/274,153/274	139564668	2724,10252	2197	4291	6488	SO:0001583	missense	51162	exon8			CGCTGCGTCAACA	AF186111	CCDS7002.1	9q34.3	2008-02-05			ENSG00000172889	ENSG00000172889			20594	protein-coding gene	gene with protein product		608582					Standard	NM_016215		Approved	ZNEU1	uc004cih.3	Q9UHF1	OTTHUMG00000020938	ENST00000371699.1:c.457G>A	9.37:g.139564668G>A	ENSP00000360764:p.Val153Ile	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	77	38	0.493506	NM_016215	B3KRP0|M9VTX9|Q5M7Y5|Q5VUD5|Q96EG0	Missense_Mutation	SNP	ENST00000371699.1	37	CCDS7002.1	407	0.18635531135531136	118	0.23983739837398374	66	0.18232044198895028	68	0.11888111888111888	155	0.20448548812664907	G	6.763	0.509711	0.12883	0.220073	0.204731	ENSG00000172889	ENST00000371699;ENST00000308874;ENST00000406555;ENST00000371698	T;T;T;T	0.31247	1.5;1.5;1.5;1.5	5.05	0.508	0.16972	EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (2);	0.447530	0.23342	N	0.049234	T	0.00012	0.0000	N	0.05230	-0.09	0.26060	P	0.9813663	B	0.15473	0.013	B	0.12837	0.008	T	0.40384	-0.9566	9	0.27082	T	0.32	-17.081	9.6192	0.39710	0.4213:0.0:0.5787:0.0	rs2297538;rs17850906;rs61338841;rs2297538	153	Q9UHF1	EGFL7_HUMAN	I	153	ENSP00000360764:V153I;ENSP00000307843:V153I;ENSP00000385639:V153I;ENSP00000360763:V153I	ENSP00000307843:V153I	V	+	1	0	EGFL7	138684489	0.020000	0.18652	0.857000	0.33713	0.266000	0.26442	-0.001000	0.12947	0.173000	0.19788	-0.254000	0.11334	GTC	G|0.800;A|0.200	0.200	strong		0.672	EGFL7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055094.1	NM_016215	
STRC	161497	hgsc.bcm.edu	37	15	43892847	43892847	+	Silent	SNP	G	G	C	rs12438025	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:43892847G>C	ENST00000450892.2	-	26	4955	c.4878C>G	c.(4876-4878)ctC>ctG	p.L1626L	RNU6-554P_ENST00000410466.1_RNA|STRC_ENST00000541030.1_Silent_p.L853L	NM_153700.2	NP_714544.1	Q7RTU9	STRC_HUMAN	stereocilin	1626					auditory receptor cell stereocilium organization (GO:0060088)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)	kinocilium (GO:0060091)|stereocilium bundle tip (GO:0032426)				skin(4)	4		all_cancers(109;3.26e-15)|all_epithelial(112;1.48e-12)|Lung NSC(122;2.76e-08)|all_lung(180;3.1e-07)|Melanoma(134;0.027)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;3.56e-07)		CAGAGCACTGGAGATGCAGGG	0.532													G|||	1475	0.294529	0.556	0.2032	5008	,	,		20056	0.2718		0.0994	False		,,,				2504	0.2301				p.L1626L		Atlas-SNP	.											STRC_ENST00000450892,colon,carcinoma,0,1	STRC	58	1	0			c.C4878G						PASS	.	G		2041,2359	541.9+/-375.9	485,1071,644	55.0	64.0	61.0		4878	2.9	1.0	15	dbSNP_120	61	846,7748	189.1+/-236.0	50,746,3501	no	coding-synonymous	STRC	NM_153700.2		535,1817,4145	CC,CG,GG		9.8441,46.3864,22.2179		1626/1776	43892847	2887,10107	2200	4297	6497	SO:0001819	synonymous_variant	161497	exon26			GCACTGGAGATGC	BK000138	CCDS10098.1	15q15.3	2010-02-26			ENSG00000242866	ENSG00000242866			16035	protein-coding gene	gene with protein product		606440		DFNB16		11687802, 9429146	Standard	NM_153700		Approved		uc001zsf.3	Q7RTU9	OTTHUMG00000059899	ENST00000450892.2:c.4878C>G	15.37:g.43892847G>C		Somatic	235	0	0		WXS	Illumina HiSeq	Phase_I	219	69	0.315068	NM_153700		Silent	SNP	ENST00000450892.2	37	CCDS10098.1																																																																																			G|0.784;C|0.216	0.216	strong		0.532	STRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133140.1	NM_153700	
OR5T2	219464	hgsc.bcm.edu	37	11	56000600	56000600	+	Missense_Mutation	SNP	G	G	T	rs3919907	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	92	0	0		WXS	Illumina HiSeq	Phase_I	71	20	0.28169	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	
MSH3	4437	hgsc.bcm.edu	37	5	79966029	79966029	+	Silent	SNP	G	G	A	rs1805355	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	204	0	0		WXS	Illumina HiSeq	Phase_I	202	100	0.49505	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	
TOP2A	7153	hgsc.bcm.edu	37	17	38548586	38548586	+	Silent	SNP	T	T	G	rs34270904	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:38548586T>G	ENST00000423485.1	-	31	4130	c.3972A>C	c.(3970-3972)acA>acC	p.T1324T	Y_RNA_ENST00000410949.1_RNA	NM_001067.3	NP_001058.2	P11388	TOP2A_HUMAN	topoisomerase (DNA) II alpha 170kDa	1324			T -> K (in dbSNP:rs28969502).		apoptotic chromosome condensation (GO:0030263)|ATP catabolic process (GO:0006200)|cellular response to DNA damage stimulus (GO:0006974)|chromosome segregation (GO:0007059)|DNA ligation (GO:0006266)|DNA topological change (GO:0006265)|DNA unwinding involved in DNA replication (GO:0006268)|embryonic cleavage (GO:0040016)|hematopoietic progenitor cell differentiation (GO:0002244)|mitotic cell cycle (GO:0000278)|mitotic DNA integrity checkpoint (GO:0044774)|mitotic recombination (GO:0006312)|positive regulation of apoptotic process (GO:0043065)|positive regulation of single stranded viral RNA replication via double stranded DNA intermediate (GO:0045870)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of viral genome replication (GO:0045070)|resolution of meiotic recombination intermediates (GO:0000712)|sister chromatid segregation (GO:0000819)	condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|DNA topoisomerase complex (ATP-hydrolyzing) (GO:0009330)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA binding, bending (GO:0008301)|DNA topoisomerase type II (ATP-hydrolyzing) activity (GO:0003918)|DNA-dependent ATPase activity (GO:0008094)|drug binding (GO:0008144)|enzyme binding (GO:0019899)|histone deacetylase binding (GO:0042826)|magnesium ion binding (GO:0000287)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase C binding (GO:0005080)|ubiquitin binding (GO:0043130)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(9)|ovary(5)|pancreas(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)	39		Breast(137;0.00328)	STAD - Stomach adenocarcinoma(5;0.00183)		Amsacrine(DB00276)|Ciprofloxacin(DB00537)|Dactinomycin(DB00970)|Daunorubicin(DB00694)|Dexrazoxane(DB00380)|Doxorubicin(DB00997)|Enoxacin(DB00467)|Epirubicin(DB00445)|Etoposide(DB00773)|Fleroxacin(DB04576)|Idarubicin(DB01177)|Levofloxacin(DB01137)|Lomefloxacin(DB00978)|Lucanthone(DB04967)|Mitoxantrone(DB01204)|Moxifloxacin(DB00218)|Norfloxacin(DB01059)|Ofloxacin(DB01165)|Pefloxacin(DB00487)|Podofilox(DB01179)|Sparfloxacin(DB01208)|Teniposide(DB00444)|Trovafloxacin(DB00685)|Valrubicin(DB00385)	TTGTGAATTTTGTTTTTGCTA	0.299													G|||	171	0.0341454	0.0998	0.0173	5008	,	,		17564	0.0		0.0209	False		,,,				2504	0.0061				p.T1324T		Atlas-SNP	.											.	TOP2A	124	.	0			c.A3972C						PASS	.	G		270,3318		10,250,1534	41.0	35.0	37.0		3972	2.6	1.0	17	dbSNP_126	37	171,7941		3,165,3888	no	coding-synonymous	TOP2A	NM_001067.3		13,415,5422	GG,GT,TT		2.108,7.5251,3.7692		1324/1532	38548586	441,11259	1794	4056	5850	SO:0001819	synonymous_variant	7153	exon31			GAATTTTGTTTTT		CCDS45672.1	17q21-q22	2008-08-06	2002-08-29		ENSG00000131747	ENSG00000131747	5.99.1.2		11989	protein-coding gene	gene with protein product		126430	"""topoisomerase (DNA) II alpha (170kD)"""	TOP2			Standard	NM_001067		Approved		uc002huq.3	P11388	OTTHUMG00000155008	ENST00000423485.1:c.3972A>C	17.37:g.38548586T>G		Somatic	321	0	0		WXS	Illumina HiSeq	Phase_I	232	108	0.465517	NM_001067	B2RTS1|Q71UN1|Q71UQ5|Q9HB24|Q9HB25|Q9HB26|Q9UP44|Q9UQP9	Silent	SNP	ENST00000423485.1	37	CCDS45672.1																																																																																			T|0.966;G|0.034	0.034	strong		0.299	TOP2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338035.1		
CDC20B	166979	hgsc.bcm.edu	37	5	54424381	54424381	+	Silent	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:54424381G>A	ENST00000381375.2	-	7	907	c.762C>T	c.(760-762)taC>taT	p.Y254Y	CDC20B_ENST00000334206.5_Silent_p.Y254Y|CDC20B_ENST00000296733.1_Silent_p.Y254Y|CDC20B_ENST00000322374.6_Silent_p.Y254Y			Q86Y33	CD20B_HUMAN	cell division cycle 20B	254										kidney(1)|large_intestine(5)|lung(7)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)	19		Lung NSC(810;0.000744)|Breast(144;0.159)|Prostate(74;0.194)	LUSC - Lung squamous cell carcinoma(15;0.225)			CATTCCAGATGTATACAGCAG	0.383																																					p.Y254Y		Atlas-SNP	.											.	CDC20B	61	.	0			c.C762T						PASS	.						145.0	151.0	149.0					5																	54424381		2203	4300	6503	SO:0001819	synonymous_variant	166979	exon7			CCAGATGTATACA	AB086378	CCDS3966.1, CCDS47207.1, CCDS54852.1	5q11.2	2013-01-17	2013-01-17		ENSG00000164287	ENSG00000164287		"""WD repeat domain containing"""	24222	protein-coding gene	gene with protein product			"""CDC20 cell division cycle 20 homolog B (S. cerevisiae)"", ""cell division cycle 20 homolog B (S. cerevisiae)"""				Standard	NM_152623		Approved	FLJ37927	uc003jpo.2	Q86Y33	OTTHUMG00000131185	ENST00000381375.2:c.762C>T	5.37:g.54424381G>A		Somatic	199	0	0		WXS	Illumina HiSeq	Phase_I	184	64	0.347826	NM_001170402	B7WNV8|B9EGL8|C9J6X8|C9JHE9|C9JKL5|Q86Y31|Q86Y32|Q8IUZ8|Q8N1S1|Q8NG56	Silent	SNP	ENST00000381375.2	37	CCDS54852.1																																																																																			.	.	none		0.383	CDC20B-004	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000369715.1	NM_152623	
EPHB4	2050	hgsc.bcm.edu	37	7	100410597	100410597	+	Silent	SNP	G	G	A	rs2230585	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:100410597G>A	ENST00000358173.3	-	12	2358	c.1890C>T	c.(1888-1890)tgC>tgT	p.C630C	EPHB4_ENST00000477446.1_5'Flank|EPHB4_ENST00000360620.3_Silent_p.C630C	NM_004444.4	NP_004435.3	P54760	EPHB4_HUMAN	EPH receptor B4	630	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|cell migration involved in sprouting angiogenesis (GO:0002042)|ephrin receptor signaling pathway (GO:0048013)|heart morphogenesis (GO:0003007)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein autophosphorylation (GO:0046777)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(1)|central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(7)|lung(20)|ovary(3)|prostate(2)|skin(3)|stomach(3)	47	Lung NSC(181;0.041)|all_lung(186;0.0581)					GCCGCCCCCGGCACACCTCGC	0.647													G|||	1380	0.275559	0.1641	0.2867	5008	,	,		16499	0.3115		0.3668	False		,,,				2504	0.2873				p.C630C	GBM(200;2113 3072 25865 52728)	Atlas-SNP	.											.	EPHB4	106	.	0			c.C1890T						PASS	.	G		924,3482	354.9+/-312.8	91,742,1370	101.0	106.0	105.0		1890	2.9	1.0	7	dbSNP_98	105	3324,5276	494.2+/-373.8	632,2060,1608	no	coding-synonymous	EPHB4	NM_004444.4		723,2802,2978	AA,AG,GG		38.6512,20.9714,32.6618		630/988	100410597	4248,8758	2203	4300	6503	SO:0001819	synonymous_variant	2050	exon12			CCCCCGGCACACC	AY056047	CCDS5706.1	7q22	2013-02-11	2004-10-28		ENSG00000196411	ENSG00000196411		"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3395	protein-coding gene	gene with protein product		600011	"""EphB4"""	HTK		8188704	Standard	NM_004444		Approved	Tyro11	uc003uwn.1	P54760	OTTHUMG00000157040	ENST00000358173.3:c.1890C>T	7.37:g.100410597G>A		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	84	45	0.535714	NM_004444	B5A970|B5A971|B5A972|Q7Z635|Q9BTA5|Q9BXP0	Silent	SNP	ENST00000358173.3	37	CCDS5706.1																																																																																			G|0.683;A|0.317	0.317	strong		0.647	EPHB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347222.1	NM_004444	
PPP6R3	55291	hgsc.bcm.edu	37	11	68377475	68377475	+	Missense_Mutation	SNP	A	A	G	rs79540432	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:68377475A>G	ENST00000393800.2	+	23	2808	c.2554A>G	c.(2554-2556)Agc>Ggc	p.S852G	PPP6R3_ENST00000393799.2_Missense_Mutation_p.S858G|PPP6R3_ENST00000265636.5_Missense_Mutation_p.S772G|PPP6R3_ENST00000529710.1_Missense_Mutation_p.S772G|PPP6R3_ENST00000265637.4_Missense_Mutation_p.S806G|PPP6R3_ENST00000524904.1_Missense_Mutation_p.S846G|PPP6R3_ENST00000527403.2_Missense_Mutation_p.S817G|PPP6R3_ENST00000534534.1_Missense_Mutation_p.S620G|PPP6R3_ENST00000393801.3_Missense_Mutation_p.S858G|PPP6R3_ENST00000524845.1_Missense_Mutation_p.S823G	NM_001164161.1|NM_001164162.1|NM_001164163.1	NP_001157633.1|NP_001157634.1|NP_001157635.1	Q5H9R7	PP6R3_HUMAN	protein phosphatase 6, regulatory subunit 3	852					regulation of phosphoprotein phosphatase activity (GO:0043666)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein phosphatase binding (GO:0019903)			breast(2)|endometrium(6)|kidney(3)|large_intestine(10)|liver(2)|lung(9)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	37						GCCTCCCAGCAGCAGTCCCGA	0.622													A|||	19	0.00379393	0.0008	0.0086	5008	,	,		18142	0.0		0.0119	False		,,,				2504	0.0				p.S858G		Atlas-SNP	.											.	PPP6R3	159	.	0			c.A2572G						PASS	.	A	GLY/SER,GLY/SER,GLY/SER,GLY/SER,GLY/SER,GLY/SER	10,4390	17.9+/-39.9	0,10,2190	53.0	52.0	52.0		2572,2554,2536,2467,2314,2314	3.8	1.0	11	dbSNP_131	52	111,8477	58.3+/-119.8	3,105,4186	yes	missense,missense,missense,missense,missense,missense	PPP6R3	NM_001164160.1,NM_001164161.1,NM_001164162.1,NM_001164163.1,NM_001164164.1,NM_018312.4	56,56,56,56,56,56	3,115,6376	GG,GA,AA		1.2925,0.2273,0.9316	benign,benign,benign,benign,benign,benign	858/880,852/874,846/868,823/845,772/792,772/794	68377475	121,12867	2200	4294	6494	SO:0001583	missense	55291	exon24			CCCAGCAGCAGTC	AF264779	CCDS8182.1, CCDS53671.1, CCDS53672.1, CCDS53673.1, CCDS53674.1, CCDS53675.1	11q13	2012-04-17	2010-06-28	2010-06-28	ENSG00000110075	ENSG00000110075		"""Serine/threonine phosphatases / Protein phosphatase 6, regulatory subunits"""	1173	protein-coding gene	gene with protein product	"""sporulation-induced transcript 4-associated protein"""	610879	"""chromosome 11 open reading frame 23"", ""SAPS domain family, member 3"""	C11orf23, SAPS3		11401438, 16769727	Standard	NM_018312		Approved	SAPLa, DKFZp781E2374, DKFZp781O2362, DKFZp781E17107, SAP190, SAPL, PP6R3, FLJ11058, FLJ43065, KIAA1558, MGC125711, MGC125712	uc001onv.3	Q5H9R7		ENST00000393800.2:c.2554A>G	11.37:g.68377475A>G	ENSP00000377389:p.Ser852Gly	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	58	41	0.706897	NM_001164160	Q3B7I1|Q3I4Y0|Q3KR35|Q68CR3|Q7L4R8|Q8N3B2|Q96MB2|Q9H2K5|Q9H2K6|Q9HCL4|Q9NUY3	Missense_Mutation	SNP	ENST00000393800.2	37	CCDS53672.1	12	0.005494505494505495	0	0.0	4	0.011049723756906077	0	0.0	8	0.010554089709762533	A	11.52	1.663897	0.29515	0.002273	0.012925	ENSG00000110075	ENST00000393799;ENST00000393800;ENST00000534534;ENST00000524845;ENST00000265637;ENST00000524904;ENST00000393801;ENST00000265636;ENST00000529710;ENST00000527403;ENST00000534190	T;T;T;T;T;T;T;T;T;T;T	0.54279	0.58;0.58;0.58;0.58;0.58;0.58;0.58;0.58;0.58;0.58;0.58	4.96	3.76	0.43208	.	0.236035	0.35207	N	0.003362	T	0.38241	0.1033	L	0.47716	1.5	0.38584	D	0.950242	B;B;B;B;B;B;B;B	0.19200	0.031;0.034;0.0;0.0;0.001;0.0;0.0;0.0	B;B;B;B;B;B;B;B	0.24006	0.05;0.011;0.002;0.001;0.004;0.002;0.003;0.001	T	0.48681	-0.9014	10	0.44086	T	0.13	.	12.9887	0.58606	0.8559:0.1441:0.0:0.0	.	535;620;772;823;846;852;858;772	B4DYU6;E9PQP7;Q5H9R7-3;Q5H9R7-6;Q5H9R7-2;Q5H9R7;Q5H9R7-5;Q5H9R7-4	.;.;.;.;.;PP6R3_HUMAN;.;.	G	858;852;620;823;806;846;858;772;772;817;559	ENSP00000377388:S858G;ENSP00000377389:S852G;ENSP00000434429:S620G;ENSP00000431415:S823G;ENSP00000265637:S806G;ENSP00000433058:S846G;ENSP00000377390:S858G;ENSP00000265636:S772G;ENSP00000437329:S772G;ENSP00000433565:S817G;ENSP00000436209:S559G	ENSP00000265636:S772G	S	+	1	0	PPP6R3	68134051	1.000000	0.71417	0.997000	0.53966	0.357000	0.29423	4.276000	0.58933	1.861000	0.53984	0.459000	0.35465	AGC	A|0.992;G|0.008	0.008	strong		0.622	PPP6R3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395275.1	NM_018312	
SLC9C1	285335	hgsc.bcm.edu	37	3	111981924	111981924	+	Missense_Mutation	SNP	T	T	C	rs9809404	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:111981924T>C	ENST00000305815.5	-	10	1296	c.1044A>G	c.(1042-1044)atA>atG	p.I348M	SLC9C1_ENST00000487372.1_Missense_Mutation_p.I300M	NM_183061.1	NP_898884.1	Q4G0N8	SL9C1_HUMAN	solute carrier family 9, subfamily C (Na+-transporting carboxylic acid decarboxylase), member 1	348			I -> M (in dbSNP:rs9809404). {ECO:0000269|PubMed:14702039}.		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)										AAACAGGGCTTATTAAAAGAA	0.353													C|||	3220	0.642971	0.4849	0.7118	5008	,	,		17388	0.7738		0.5964	False		,,,				2504	0.7209				p.I348M		Atlas-SNP	.											.	.	.	.	0			c.A1044G						PASS	.	C	MET/ILE	2217,2189	583.1+/-385.7	536,1145,522	91.0	89.0	90.0		1044	3.0	0.7	3	dbSNP_119	90	5329,3271	488.7+/-372.4	1658,2013,629	yes	missense	SLC9A10	NM_183061.1	10	2194,3158,1151	CC,CT,TT		38.0349,49.6823,41.9806	benign	348/1178	111981924	7546,5460	2203	4300	6503	SO:0001583	missense	285335	exon10			AGGGCTTATTAAA	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.1044A>G	3.37:g.111981924T>C	ENSP00000306627:p.Ile348Met	Somatic	261	0	0		WXS	Illumina HiSeq	Phase_I	184	182	0.98913	NM_183061	Q6ZRP4|Q7RTP2	Missense_Mutation	SNP	ENST00000305815.5	37	CCDS33817.1	1405	0.6433150183150184	247	0.5020325203252033	242	0.6685082872928176	455	0.7954545454545454	461	0.6081794195250659	C	1.218	-0.627820	0.03610	0.503177	0.619651	ENSG00000172139	ENST00000305815;ENST00000487372	T;T	0.16597	2.34;2.33	5.68	2.95	0.34219	Cation/H+ exchanger (1);	0.444819	0.23265	N	0.050087	T	0.00012	0.0000	N	0.01048	-1.04	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.10894	-1.0610	9	0.22109	T	0.4	-14.0259	7.9213	0.29848	0.0:0.6783:0.0:0.3217	rs9809404;rs52818029;rs58741493;rs9809404	300;348	Q4G0N8-2;Q4G0N8	.;S9A10_HUMAN	M	348;300	ENSP00000306627:I348M;ENSP00000420688:I300M	ENSP00000306627:I348M	I	-	3	3	SLC9A10	113464614	0.985000	0.35326	0.706000	0.30403	0.236000	0.25371	0.609000	0.24238	0.086000	0.17137	-0.246000	0.11932	ATA	T|0.395;C|0.605	0.605	strong		0.353	SLC9C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354066.1	NM_183061	
C1QC	714	hgsc.bcm.edu	37	1	22970642	22970642	+	Silent	SNP	C	C	T	rs15940	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:22970642C>T	ENST00000374639.3	+	2	244	c.126C>T	c.(124-126)ccC>ccT	p.P42P	C1QC_ENST00000374637.1_Silent_p.P42P|C1QC_ENST00000374640.4_Silent_p.P42P	NM_001114101.1	NP_001107573.1	P02747	C1QC_HUMAN	complement component 1, q subcomponent, C chain	42	Collagen-like.				complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|immune response (GO:0006955)|innate immune response (GO:0045087)|negative regulation of granulocyte differentiation (GO:0030853)|negative regulation of macrophage differentiation (GO:0045650)	blood microparticle (GO:0072562)|collagen trimer (GO:0005581)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				endometrium(2)|kidney(1)|large_intestine(3)|lung(4)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	15		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;6.21e-27)|Colorectal(126;1.5e-07)|COAD - Colon adenocarcinoma(152;1.12e-05)|GBM - Glioblastoma multiforme(114;1.61e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000538)|KIRC - Kidney renal clear cell carcinoma(1967;0.00269)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.196)	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)	CCGGCCTGCCCGGGGCACCAG	0.692													C|||	1499	0.299321	0.3722	0.2522	5008	,	,		15469	0.2927		0.2475	False		,,,				2504	0.2945				p.P42P	Ovarian(26;671 750 8290 29071 43278)	Atlas-SNP	.											.	C1QC	35	.	0			c.C126T						PASS	.	C	,	1552,2828		297,958,935	15.0	16.0	16.0		126,126	-10.5	0.3	1	dbSNP_131	16	2200,6360		304,1592,2384	no	coding-synonymous,coding-synonymous	C1QC	NM_001114101.1,NM_172369.3	,	601,2550,3319	TT,TC,CC		25.7009,35.4338,28.9954	,	42/246,42/246	22970642	3752,9188	2190	4280	6470	SO:0001819	synonymous_variant	714	exon2			CCTGCCCGGGGCA	AK057792	CCDS227.1	1p36.11	2014-09-17	2006-02-09	2006-02-09	ENSG00000159189	ENSG00000159189		"""Complement system"""	1245	protein-coding gene	gene with protein product		120575	"""complement component 1, q subcomponent, gamma polypeptide"""	C1QG		1706597	Standard	NM_001114101		Approved		uc001bga.4	P02747	OTTHUMG00000002891	ENST00000374639.3:c.126C>T	1.37:g.22970642C>T		Somatic	188	0	0		WXS	Illumina HiSeq	Phase_I	160	78	0.4875	NM_001114101	Q7Z502|Q96DL2|Q96H05	Silent	SNP	ENST00000374639.3	37	CCDS227.1																																																																																			C|0.703;T|0.297	0.297	strong		0.692	C1QC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008083.1	NM_172369	
CACNB4	785	hgsc.bcm.edu	37	2	152955482	152955482	+	Missense_Mutation	SNP	G	G	C	rs200662010	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:152955482G>C	ENST00000539935.1	-	1	111	c.44C>G	c.(43-45)cCg>cGg	p.P15R	AC079790.2_ENST00000420365.1_RNA|CACNB4_ENST00000427385.1_5'Flank|CACNB4_ENST00000201943.5_Missense_Mutation_p.P15R	NM_000726.3|NM_001145798.1	NP_000717.2|NP_001139270.1	O00305	CACB4_HUMAN	calcium channel, voltage-dependent, beta 4 subunit	15					adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|calcium ion transmembrane transport (GO:0070588)|cAMP metabolic process (GO:0046058)|cellular calcium ion homeostasis (GO:0006874)|detection of light stimulus involved in visual perception (GO:0050908)|gamma-aminobutyric acid secretion (GO:0014051)|gamma-aminobutyric acid signaling pathway (GO:0007214)|membrane depolarization (GO:0051899)|muscle fiber development (GO:0048747)|neuromuscular junction development (GO:0007528)|neuronal action potential propagation (GO:0019227)|Peyer's patch development (GO:0048541)|regulation of voltage-gated calcium channel activity (GO:1901385)|spleen development (GO:0048536)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|T cell receptor signaling pathway (GO:0050852)|thymus development (GO:0048538)|transport (GO:0006810)	cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|plasma membrane (GO:0005886)|synapse (GO:0045202)|voltage-gated calcium channel complex (GO:0005891)	voltage-gated calcium channel activity (GO:0005245)			endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(2)	11				BRCA - Breast invasive adenocarcinoma(221;0.156)	Dronedarone(DB04855)|Nimodipine(DB00393)|Spironolactone(DB00421)|Verapamil(DB00661)	GGGGGAGTGCGGCCCGTCCGC	0.721													G|||	2	0.000399361	0.0	0.0029	5008	,	,		9469	0.0		0.0	False		,,,				2504	0.0				p.P15R		Atlas-SNP	.											.	CACNB4	108	.	0			c.C44G						PASS	.	G	ARG/PRO,ARG/PRO	4,3898		0,4,1947	11.0	16.0	14.0		44,44	-0.1	1.0	2		14	26,8102		0,26,4038	yes	missense,missense	CACNB4	NM_000726.3,NM_001145798.1	103,103	0,30,5985	CC,CG,GG		0.3199,0.1025,0.2494	benign,benign	15/521,15/459	152955482	30,12000	1951	4064	6015	SO:0001583	missense	785	exon1			GAGTGCGGCCCGT	AF038852	CCDS46426.1, CCDS46427.1, CCDS46428.1, CCDS54409.1	2q22-q23	2009-09-04			ENSG00000182389	ENSG00000182389		"""Calcium channel subunits"""	1404	protein-coding gene	gene with protein product		601949				9628818	Standard	NM_000726		Approved	EJM4	uc002tya.3	O00305	OTTHUMG00000155091	ENST00000539935.1:c.44C>G	2.37:g.152955482G>C	ENSP00000438949:p.Pro15Arg	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	124	61	0.491935	NM_001145798	A7BJ74|A8K1Y4|B4DG40|O60515|Q6B000|Q96L40	Missense_Mutation	SNP	ENST00000539935.1	37	CCDS46426.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	G	4.250	0.045444	0.08196	0.001025	0.003199	ENSG00000182389	ENST00000539935;ENST00000201943;ENST00000339254	T;T	0.71461	-0.57;-0.57	4.55	-0.0829	0.13696	.	0.952431	0.08719	N	0.903787	T	0.49321	0.1550	N	0.14661	0.345	0.80722	D	1	B;B	0.20671	0.0;0.047	B;B	0.19148	0.0;0.024	T	0.36962	-0.9726	10	0.52906	T	0.07	-4.6977	4.2846	0.10848	0.0937:0.2947:0.4771:0.1345	.	15;15	A7BJ74;O00305	.;CACB4_HUMAN	R	15	ENSP00000438949:P15R;ENSP00000201943:P15R	ENSP00000201943:P15R	P	-	2	0	CACNB4	152663728	0.980000	0.34600	0.997000	0.53966	0.024000	0.10985	-0.208000	0.09371	0.025000	0.15241	-0.176000	0.13171	CCG	G|1.000;C|0.000	0.000	strong		0.721	CACNB4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000338385.4	NM_000726.3	
LRRFIP1	9208	hgsc.bcm.edu	37	2	238668802	238668802	+	Silent	SNP	A	A	G	rs3213868	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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_ENST00000244815.5_Silent_p.T257T|LRRFIP1_ENST00000289175.6_Silent_p.T225T	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	102	0	0		WXS	Illumina HiSeq	Phase_I	74	48	0.648649	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	
KIAA1549	57670	hgsc.bcm.edu	37	7	138602417	138602417	+	Missense_Mutation	SNP	G	G	A	rs2774960	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	66	0	0		WXS	Illumina HiSeq	Phase_I	49	24	0.489796	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		
ZNF431	170959	hgsc.bcm.edu	37	19	21326358	21326358	+	Missense_Mutation	SNP	A	A	G	rs17445374	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:21326358A>G	ENST00000311048.7	+	2	152	c.8A>G	c.(7-9)gAc>gGc	p.D3G	ZNF431_ENST00000599296.1_Missense_Mutation_p.D3G|ZNF431_ENST00000594425.1_Missense_Mutation_p.D3G|ZNF431_ENST00000600692.1_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	73	0	0		WXS	Illumina HiSeq	Phase_I	70	30	0.428571	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	
CCL4	6351	hgsc.bcm.edu	37	17	34432663	34432663	+	Silent	SNP	A	A	G	rs1049807|rs386796798	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:34432663A>G	ENST00000250151.4	+	3	553	c.237A>G	c.(235-237)gaA>gaG	p.E79E	CCL4_ENST00000394495.1_Missense_Mutation_p.N41S	NM_002984.2	NP_002975.1	P13236	CCL4_HUMAN	chemokine (C-C motif) ligand 4	79					cell adhesion (GO:0007155)|cell chemotaxis (GO:0060326)|cell-cell signaling (GO:0007267)|cellular component movement (GO:0006928)|establishment or maintenance of cell polarity (GO:0007163)|immune response (GO:0006955)|inflammatory response (GO:0006954)|negative regulation by host of viral transcription (GO:0043922)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of natural killer cell chemotaxis (GO:2000503)|response to toxic substance (GO:0009636)|response to virus (GO:0009615)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	CCR1 chemokine receptor binding (GO:0031726)|CCR5 chemokine receptor binding (GO:0031730)|chemokine activity (GO:0008009)|cytokine activity (GO:0005125)|identical protein binding (GO:0042802)			endometrium(1)|large_intestine(1)|lung(2)	4		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		ATCCCAGTGAATCCTGGGTCC	0.498													G|||	1096	0.21885	0.1732	0.1254	5008	,	,		21052	0.3036		0.2485	False		,,,				2504	0.229				p.E79E	Colon(139;824 1752 21188 21615 24765)	Atlas-SNP	.											.	CCL4	14	.	0			c.A237G						PASS	.	G		480,3926		54,372,1777	200.0	184.0	190.0		237	-10.1	0.0	17	dbSNP_86	190	278,8322		96,86,4118	no	coding-synonymous	CCL4	NM_002984.2		150,458,5895	GG,GA,AA		3.2326,10.8942,5.8281		79/93	34432663	758,12248	2203	4300	6503	SO:0001819	synonymous_variant	6351	exon3			CAGTGAATCCTGG	M23502	CCDS11308.1	17q21-q23	2014-05-06	2002-08-22	2002-08-23	ENSG00000129277	ENSG00000275302		"""Chemokine ligands"", ""Endogenous ligands"""	10630	protein-coding gene	gene with protein product		182284	"""small inducible cytokine A4 (homologous to mouse Mip-1b)"""	LAG1, SCYA4		1972563	Standard	NM_002984		Approved	MIP-1-beta, Act-2, AT744.1	uc002hkw.1	P13236	OTTHUMG00000188414	ENST00000250151.4:c.237A>G	17.37:g.34432663A>G		Somatic	413	0	0		WXS	Illumina HiSeq	Phase_I	389	209	0.537275	NM_002984	P22617|Q13704|Q3SXL8|Q6FGI8	Silent	SNP	ENST00000250151.4	37	CCDS11308.1	380	0.17399267399267399	58	0.11788617886178862	48	0.13259668508287292	137	0.2395104895104895	137	0.18073878627968337	.	0.859	-0.736020	0.03111	0.108942	0.032326	ENSG00000129277	ENST00000394495	T	0.71222	-0.55	5.03	-10.1	0.00402	.	.	.	.	.	T	0.00039	0.0001	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.29822	-0.9999	5	0.87932	D	0	.	2.3631	0.04312	0.1849:0.3061:0.1036:0.4054	rs1049807;rs1719151;rs52827317;rs56801182;rs1049807	.	.	.	S	41	ENSP00000378004:N41S	ENSP00000378004:N41S	N	+	2	0	CCL4	31456776	0.000000	0.05858	0.000000	0.03702	0.025000	0.11179	-2.376000	0.01070	-3.251000	0.00204	-0.768000	0.03414	AAT	A|0.816;G|0.184	0.184	strong		0.498	CCL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256592.2	NM_002984	
MUC4	4585	hgsc.bcm.edu	37	3	195515413	195515413	+	Missense_Mutation	SNP	C	C	T	rs55868431	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195515413C>T	ENST00000463781.3	-	2	3497	c.3038G>A	c.(3037-3039)aGc>aAc	p.S1013N	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.S1013N	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	448	Repeat.|Ser-rich.				cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.S1013_T1028delSPSSVSTGHTTPLPVT(4)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		TGAGGAAGGGCTGGTGACAGG	0.572													.|||	808	0.161342	0.152	0.1124	5008	,	,		17298	0.2321		0.1352	False		,,,				2504	0.1626				p.S1013N		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,-1,2	MUC4	1505	2	4	Deletion - In frame(4)	stomach(4)	c.G3038A						PASS	.						55.0	29.0	37.0					3																	195515413		688	1591	2279	SO:0001583	missense	4585	exon2			GAAGGGCTGGTGA	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.3038G>A	3.37:g.195515413C>T	ENSP00000417498:p.Ser1013Asn	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	72	41	0.569444	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	-	4.515	0.095618	0.08681	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.33438	1.42;1.41	0.814	-1.63	0.08345	.	.	.	.	.	T	0.14960	0.0361	N	0.19112	0.55	0.09310	N	1	B	0.17667	0.023	B	0.11329	0.006	T	0.15809	-1.0424	8	.	.	.	.	3.4557	0.07514	0.0:0.2084:0.4437:0.3479	rs55868431	1013	E7ESK3	.	N	1013	ENSP00000417498:S1013N;ENSP00000420243:S1013N	.	S	-	2	0	MUC4	196999808	.	.	0.000000	0.03702	0.010000	0.07245	.	.	-3.282000	0.00197	-2.088000	0.00374	AGC	C|0.963;T|0.037	0.037	strong		0.572	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
SDC4	6385	hgsc.bcm.edu	37	20	43976991	43976991	+	Missense_Mutation	SNP	A	A	G	rs2228384	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:43976991A>G	ENST00000372733.3	-	1	73	c.34T>C	c.(34-36)Ttc>Ctc	p.F12L	SDC4_ENST00000537976.1_5'UTR	NM_002999.3	NP_002990.2	P31431	SDC4_HUMAN	syndecan 4	12			F -> L (in dbSNP:rs4458268). {ECO:0000269|PubMed:1500433, ECO:0000269|Ref.6}.		carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|extracellular matrix organization (GO:0030198)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|phototransduction, visible light (GO:0007603)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of stress fiber assembly (GO:0051496)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|ureteric bud development (GO:0001657)	cell surface (GO:0009986)|costamere (GO:0043034)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	thrombospondin receptor activity (GO:0070053)		SDC4/ROS1(7)	NS(1)|breast(1)|endometrium(1)|large_intestine(2)	5		Myeloproliferative disorder(115;0.0122)				CCTACGAAGAACAGCAGCAGC	0.736			T	ROS1	NSCLC								G|||	1564	0.3123	0.1324	0.3012	5008	,	,		7892	0.4216		0.3807	False		,,,				2504	0.3804				p.F12L		Atlas-SNP	.		Dom	yes		20	20q12	6385	syndecan 4		E	SDC4,NS,carcinoma,0,1	SDC4	16	1	0			c.T34C						PASS	.	G	LEU/PHE	704,3632		68,568,1532	14.0	16.0	16.0		34	1.9	0.7	20	dbSNP_111	16	2893,5617		542,1809,1904	yes	missense	SDC4	NM_002999.3	22	610,2377,3436	GG,GA,AA		33.9953,16.2362,28.0009	benign	12/199	43976991	3597,9249	2168	4255	6423	SO:0001583	missense	6385	exon1			CGAAGAACAGCAG	X67016, D13292	CCDS13350.1	20q12	2010-03-25	2007-02-15		ENSG00000124145	ENSG00000124145		"""Proteoglycans / Cell Surface : Syndecans"""	10661	protein-coding gene	gene with protein product	"""syndecan proteoglycan 4"""	600017	"""syndecan 4 (amphiglycan, ryudocan)"""			7916598, 1500433	Standard	NM_002999		Approved	SYND4, amphiglycan, ryudocan	uc002xnu.3	P31431	OTTHUMG00000033083	ENST00000372733.3:c.34T>C	20.37:g.43976991A>G	ENSP00000361818:p.Phe12Leu	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	54	54	1	NM_002999	O00773|Q16833|Q53FN9|Q6FGN3	Missense_Mutation	SNP	ENST00000372733.3	37	CCDS13350.1	735	0.33653846153846156	49	0.09959349593495935	128	0.35359116022099446	262	0.458041958041958	296	0.39050131926121373	G	11.74	1.727977	0.30593	0.162362	0.339953	ENSG00000124145	ENST00000372733	T	0.26660	1.72	3.88	1.9	0.25705	.	1.457070	0.04340	N	0.353868	T	0.00012	0.0000	N	0.00210	-1.845	0.09310	P	0.99999838508	B	0.02656	0.0	B	0.01281	0.0	T	0.44314	-0.9336	9	0.09590	T	0.72	-1.4689	5.8347	0.18601	0.3534:0.0:0.6466:0.0	rs4458268;rs17173359;rs60954343;rs4458268	12	P31431	SDC4_HUMAN	L	12	ENSP00000361818:F12L	ENSP00000361818:F12L	F	-	1	0	SDC4	43410405	0.991000	0.36638	0.736000	0.30914	0.806000	0.45545	0.205000	0.17356	0.091000	0.17302	-0.186000	0.12905	TTC	A|0.686;G|0.314	0.314	strong		0.736	SDC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080515.1	NM_002999	
WBSCR27	155368	hgsc.bcm.edu	37	7	73254812	73254812	+	Missense_Mutation	SNP	T	T	C	rs13241921	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:73254812T>C	ENST00000297873.4	-	4	369	c.320A>G	c.(319-321)cAg>cGg	p.Q107R		NM_152559.2	NP_689772.2	Q8N6F8	WBS27_HUMAN	Williams Beuren syndrome chromosome region 27	107			Q -> R (in dbSNP:rs13241921). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:18398435, ECO:0000269|Ref.1}.							NS(1)|central_nervous_system(1)|lung(2)|prostate(1)	5		Lung NSC(55;0.159)				GCCGGGGGCCTGGGCCTGTTC	0.677													C|||	2911	0.58127	0.4637	0.6124	5008	,	,		14538	0.5813		0.7256	False		,,,				2504	0.5695				p.Q107R		Atlas-SNP	.											WBSCR27,colon,carcinoma,0,2	WBSCR27	21	2	0			c.A320G						PASS	.	C	ARG/GLN	2252,2114		611,1030,542	11.0	12.0	12.0		320	-3.0	0.0	7	dbSNP_121	12	6266,2262		2350,1566,348	yes	missense	WBSCR27	NM_152559.2	43	2961,2596,890	CC,CT,TT		26.5244,48.4196,33.9383	benign	107/246	73254812	8518,4376	2183	4264	6447	SO:0001583	missense	155368	exon4			GGGGCCTGGGCCT	AF534110	CCDS5561.1	7q11.23	2004-07-05			ENSG00000165171	ENSG00000165171			19068	protein-coding gene	gene with protein product		612546					Standard	NM_152559		Approved		uc003tzj.2	Q8N6F8	OTTHUMG00000130033	ENST00000297873.4:c.320A>G	7.37:g.73254812T>C	ENSP00000297873:p.Gln107Arg	Somatic	132	1	0.00757576		WXS	Illumina HiSeq	Phase_I	119	119	1	NM_152559		Missense_Mutation	SNP	ENST00000297873.4	37	CCDS5561.1	1328	0.608058608058608	228	0.4634146341463415	218	0.6022099447513812	328	0.5734265734265734	554	0.7308707124010554	C	0.004	-2.292375	0.00245	0.515804	0.734756	ENSG00000165171	ENST00000297873	T	0.63255	-0.03	4.69	-3.02	0.05446	.	0.498360	0.21142	N	0.079474	T	0.00012	0.0000	N	0.01656	-0.775	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.37526	-0.9702	9	0.02654	T	1	-9.0478	12.2327	0.54497	0.0:0.3346:0.0:0.6654	rs13241921;rs17856861;rs13241921	107	Q8N6F8	WBS27_HUMAN	R	107	ENSP00000297873:Q107R	ENSP00000297873:Q107R	Q	-	2	0	WBSCR27	72892748	0.000000	0.05858	0.001000	0.08648	0.005000	0.04900	-1.422000	0.02453	-1.055000	0.03209	-0.355000	0.07637	CAG	T|0.385;C|0.615	0.615	strong		0.677	WBSCR27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252312.1	NM_152559	
SATL1	340562	hgsc.bcm.edu	37	X	84363140	84363140	+	Missense_Mutation	SNP	A	A	G	rs10126146	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:84363140A>G	ENST00000395409.3	-	1	834	c.274T>C	c.(274-276)Tgg>Cgg	p.W92R	SATL1_ENST00000332921.5_Missense_Mutation_p.W92R|SATL1_ENST00000509231.1_Missense_Mutation_p.W279R			Q86VE3	SATL1_HUMAN	spermidine/spermine N1-acetyl transferase-like 1	92	Gln-rich.		W -> R (in dbSNP:rs10126146). {ECO:0000269|PubMed:15489334}.				N-acetyltransferase activity (GO:0008080)			NS(1)|breast(5)|endometrium(2)|large_intestine(3)|lung(13)|skin(3)|stomach(1)|urinary_tract(1)	29						CTTGCACTCCATTGGTTCATG	0.433													G|||	2858	0.757086	0.6006	0.572	3775	,	,		17880	0.4841		0.5477	False		,,,				2504	0.6421				p.W279R		Atlas-SNP	.											.	SATL1	70	.	0			c.T835C						PASS	.	G	ARG/TRP	2972,863		993,560,426,79,145	265.0	214.0	231.0		835	-5.4	0.0	X	dbSNP_119	231	4591,2137		1119,1059,1294,250,578	yes	missense	SATL1	NM_001012980.2	101	2112,1619,1720,329,723	GG,GA,G,AA,A		31.7628,22.5033,28.401	benign	279/633	84363140	7563,3000	2203	4300	6503	SO:0001583	missense	340562	exon1			CACTCCATTGGTT	BC043215	CCDS35343.1, CCDS35343.2	Xq21	2008-02-05			ENSG00000184788	ENSG00000184788			27992	protein-coding gene	gene with protein product						12477932	Standard	NM_001012980		Approved		uc004een.3	Q86VE3	OTTHUMG00000021931	ENST00000395409.3:c.274T>C	X.37:g.84363140A>G	ENSP00000378804:p.Trp92Arg	Somatic	595	1	0.00168067		WXS	Illumina HiSeq	Phase_I	393	388	0.987277	NM_001012980	A0AVK7|E9PB72|Q5H8V9	Missense_Mutation	SNP	ENST00000395409.3	37		1213	0.731163351416516	213	0.696078431372549	143	0.5860655737704918	190	0.5	293	0.5813492063492064	G	0.011	-1.726338	0.00694	0.774967	0.682372	ENSG00000184788	ENST00000395409;ENST00000332921;ENST00000509231	T;T;T	0.37235	1.21;1.21;1.21	2.7	-5.39	0.02664	.	3.270730	0.01318	N	0.010859	T	0.00012	0.0000	N	0.03608	-0.345	0.80722	P	0.0	B;B	0.16396	0.0;0.017	B;B	0.09377	0.0;0.004	T	0.23190	-1.0195	9	0.15066	T	0.55	-0.0923	4.4697	0.11706	0.5825:0.1033:0.2097:0.1045	rs10126146;rs41380046;rs10126146	92;279	Q86VE3;E9PB72	SATL1_HUMAN;.	R	92;92;279	ENSP00000378804:W92R;ENSP00000329115:W92R;ENSP00000425421:W279R	ENSP00000329115:W92R	W	-	1	0	SATL1	84249796	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.336000	0.07863	-3.898000	0.00093	-3.007000	0.00075	TGG	A|0.262;0|0.014	.	strong		0.433	SATL1-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		XM_291339	
SCIN	85477	hgsc.bcm.edu	37	7	12620804	12620804	+	Silent	SNP	C	C	T	rs17283717	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:12620804C>T	ENST00000297029.5	+	3	575	c.474C>T	c.(472-474)gaC>gaT	p.D158D		NM_001112706.2	NP_001106177.1	Q9Y6U3	ADSV_HUMAN	scinderin	158	Actin-severing. {ECO:0000255}.				actin filament capping (GO:0051693)|actin filament severing (GO:0051014)|actin nucleation (GO:0045010)|calcium ion-dependent exocytosis (GO:0017156)|negative regulation of cell proliferation (GO:0008285)|positive regulation of apoptotic process (GO:0043065)|positive regulation of megakaryocyte differentiation (GO:0045654)|positive regulation of secretion (GO:0051047)|regulation of chondrocyte differentiation (GO:0032330)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)	1-phosphatidylinositol binding (GO:0005545)|actin binding (GO:0003779)|actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylserine binding (GO:0001786)			endometrium(3)|kidney(1)|large_intestine(2)|lung(9)|ovary(2)	17				UCEC - Uterine corpus endometrioid carcinoma (126;0.195)		TTAGCTGGGACAGTTTCAACA	0.443													C|||	1275	0.254593	0.1778	0.3386	5008	,	,		19419	0.2123		0.3598	False		,,,				2504	0.2342				p.D158D		Atlas-SNP	.											.	SCIN	105	.	0			c.C474T						PASS	.	C		269,1115		30,209,453	146.0	114.0	124.0		474	2.2	1.0	7	dbSNP_123	124	1186,1996		227,732,632	no	coding-synonymous	SCIN	NM_001112706.2		257,941,1085	TT,TC,CC		37.2722,19.4364,31.866		158/716	12620804	1455,3111	692	1591	2283	SO:0001819	synonymous_variant	85477	exon3			CTGGGACAGTTTC	AF276507	CCDS47545.1, CCDS47546.1	7p21.3	2006-04-25			ENSG00000006747	ENSG00000006747			21695	protein-coding gene	gene with protein product		613416					Standard	NM_033128		Approved	adseverin, KIAA1905	uc003ssn.4	Q9Y6U3	OTTHUMG00000152385	ENST00000297029.5:c.474C>T	7.37:g.12620804C>T		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	73	73	1	NM_001112706	A8K2U8|Q8NBZ6|Q8WU97|Q96JC7|Q96PY2	Silent	SNP	ENST00000297029.5	37	CCDS47545.1																																																																																			C|0.733;T|0.267	0.267	strong		0.443	SCIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326041.1	NM_033128	
ZNF260	339324	hgsc.bcm.edu	37	19	37005298	37005298	+	Silent	SNP	A	A	G	rs76808668	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:37005298A>G	ENST00000523638.1	-	3	1964	c.843T>C	c.(841-843)tgT>tgC	p.C281C	ZNF260_ENST00000588993.1_Silent_p.C281C|ZNF260_ENST00000592282.1_Silent_p.C281C|ZNF260_ENST00000593142.1_Silent_p.C281C	NM_001166036.1|NM_001166037.1|NM_001166038.1	NP_001159508.1|NP_001159509.1|NP_001159510.1	Q3ZCT1	ZN260_HUMAN	zinc finger protein 260	281					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(8)	15	Esophageal squamous(110;0.162)					AGATTGTTCCACATTCATTAC	0.378													A|||	273	0.0545128	0.0098	0.1297	5008	,	,		22585	0.003		0.1103	False		,,,				2504	0.0573				p.C281C		Atlas-SNP	.											.	ZNF260	34	.	0			c.T843C						PASS	.	A	,,,	133,4273	94.8+/-133.5	1,131,2071	141.0	135.0	137.0		843,843,843,843	3.5	1.0	19	dbSNP_132	137	1057,7543	222.9+/-259.8	67,923,3310	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ZNF260	NM_001012756.2,NM_001166036.1,NM_001166037.1,NM_001166038.1	,,,	68,1054,5381	GG,GA,AA		12.2907,3.0186,9.1496	,,,	281/413,281/413,281/413,281/413	37005298	1190,11816	2203	4300	6503	SO:0001819	synonymous_variant	339324	exon3			TGTTCCACATTCA	AK122854	CCDS33003.1	19q13.12	2013-01-08				ENSG00000254004		"""Zinc fingers, C2H2-type"""	13499	protein-coding gene	gene with protein product		613749					Standard	NM_001166036		Approved	ozrf1, Zfp260	uc002oed.2	Q3ZCT1		ENST00000523638.1:c.843T>C	19.37:g.37005298A>G		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	59	25	0.423729	NM_001166038	Q0VF43	Silent	SNP	ENST00000523638.1	37	CCDS33003.1																																																																																			A|0.915;G|0.085	0.085	strong		0.378	ZNF260-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109564.2	NM_001012756	
ARHGAP23	57636	hgsc.bcm.edu	37	17	36636008	36636008	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:36636008C>T	ENST00000431231.2	+	14	2581	c.2513C>T	c.(2512-2514)cCc>cTc	p.P838L	ARHGAP23_ENST00000437668.3_Missense_Mutation_p.P838L|ARHGAP23_ENST00000443378.1_Missense_Mutation_p.P744L	NM_001199417.1	NP_001186346.1	Q9P227	RHG23_HUMAN	Rho GTPase activating protein 23	838					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	GTPase activator activity (GO:0005096)	p.P1163L(5)		breast(2)|endometrium(8)|kidney(6)|lung(1)|skin(1)|stomach(2)	20						AGCTCTGGGCCCAAAGCTGAT	0.642																																					p.P838L		Atlas-SNP	.											ARHGAP23,NS,carcinoma,0,5	ARHGAP23	48	5	5	Substitution - Missense(5)	endometrium(5)	c.C2513T						scavenged	.						3.0	3.0	3.0					17																	36636008		635	1447	2082	SO:0001583	missense	57636	exon14			CTGGGCCCAAAGC	AB040934	CCDS56027.1	17q12	2014-05-06			ENSG00000225485	ENSG00000275832		"""Rho GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"""	29293	protein-coding gene	gene with protein product		610590				10819331, 15254754	Standard	NM_001199417		Approved	KIAA1501	uc021twd.1	Q9P227	OTTHUMG00000188547	ENST00000431231.2:c.2513C>T	17.37:g.36636008C>T	ENSP00000393539:p.Pro838Leu	Somatic	345	0	0		WXS	Illumina HiSeq	Phase_I	382	35	0.091623	NM_001199417		Missense_Mutation	SNP	ENST00000431231.2	37	CCDS56027.1	.	.	.	.	.	.	.	.	.	.	C	16.59	3.166506	0.57476	.	.	ENSG00000225485	ENST00000437668;ENST00000431231;ENST00000443378	T;T;T	0.15718	2.4;2.77;2.73	4.88	4.88	0.63580	.	0.339007	0.31358	N	0.007798	T	0.12050	0.0293	N	0.22421	0.69	0.53688	D	0.999976	B;P	0.34587	0.288;0.458	B;B	0.31869	0.122;0.137	T	0.10268	-1.0637	10	0.38643	T	0.18	.	13.4088	0.60931	0.0:1.0:0.0:0.0	.	838;838	Q9P227;Q9P227-2	RHG23_HUMAN;.	L	838;838;744	ENSP00000394153:P838L;ENSP00000393539:P838L;ENSP00000407333:P744L	ENSP00000393539:P838L	P	+	2	0	ARHGAP23	33889534	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	3.077000	0.50089	2.544000	0.85801	0.650000	0.86243	CCC	.	.	none		0.642	ARHGAP23-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441789.1	XM_290799	
ITIH1	3697	hgsc.bcm.edu	37	3	52825912	52825912	+	Silent	SNP	C	C	A	rs7549	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:52825912C>A	ENST00000273283.2	+	22	2745	c.2721C>A	c.(2719-2721)gtC>gtA	p.V907V	ITIH1_ENST00000542827.1_3'UTR|ITIH3_ENST00000416872.2_5'Flank|ITIH1_ENST00000540715.1_Silent_p.V765V|ITIH3_ENST00000449956.2_5'Flank|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	178	0	0		WXS	Illumina HiSeq	Phase_I	195	87	0.446154	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	
ACHE	43	hgsc.bcm.edu	37	7	100488658	100488658	+	Intron	SNP	G	G	C	rs1799806	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:100488658G>C	ENST00000412389.1	-	3	1879				ACHE_ENST00000241069.5_Intron|ACHE_ENST00000411582.1_Missense_Mutation_p.P592R|UFSP1_ENST00000388761.2_5'Flank|ACHE_ENST00000419336.2_Intron|ACHE_ENST00000428317.1_Intron|ACHE_ENST00000302913.4_Missense_Mutation_p.P592R			P22303	ACES_HUMAN	acetylcholinesterase (Yt blood group)						acetylcholine catabolic process (GO:0006581)|acetylcholine catabolic process in synaptic cleft (GO:0001507)|amyloid precursor protein metabolic process (GO:0042982)|cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|choline metabolic process (GO:0019695)|DNA replication (GO:0006260)|glycerophospholipid biosynthetic process (GO:0046474)|muscle organ development (GO:0007517)|negative regulation of synaptic transmission, cholinergic (GO:0032223)|nervous system development (GO:0007399)|neurotransmitter biosynthetic process (GO:0042136)|neurotransmitter receptor biosynthetic process (GO:0045212)|osteoblast development (GO:0002076)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|positive regulation of protein secretion (GO:0050714)|protein tetramerization (GO:0051262)|receptor internalization (GO:0031623)|regulation of axonogenesis (GO:0050770)|regulation of dendrite morphogenesis (GO:0048814)|regulation of receptor recycling (GO:0001919)|response to wounding (GO:0009611)|retina development in camera-type eye (GO:0060041)|small molecule metabolic process (GO:0044281)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic transmission, cholinergic (GO:0007271)	anchored component of membrane (GO:0031225)|axon (GO:0030424)|basal lamina (GO:0005605)|cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|synapse (GO:0045202)	acetylcholine binding (GO:0042166)|acetylcholinesterase activity (GO:0003990)|beta-amyloid binding (GO:0001540)|cholinesterase activity (GO:0004104)|collagen binding (GO:0005518)|hydrolase activity (GO:0016787)|laminin binding (GO:0043236)|protein homodimerization activity (GO:0042803)|serine hydrolase activity (GO:0017171)			large_intestine(3)|lung(7)|skin(3)|urinary_tract(3)	16	Lung NSC(181;0.041)|all_lung(186;0.0581)				Ambenonium(DB01122)|Choline(DB00122)|Decamethonium(DB01245)|Demecarium(DB00944)|Dipivefrin(DB00449)|Donepezil(DB00843)|Edrophonium(DB01010)|Ephedrine(DB01364)|Galantamine(DB00674)|Gallamine Triethiodide(DB00483)|Isoflurophate(DB00677)|Mefloquine(DB00358)|Minaprine(DB00805)|Neostigmine(DB01400)|Physostigmine(DB00981)|Pralidoxime(DB00733)|Pyridostigmine(DB00545)|Rivastigmine(DB00989)|Tubocurarine(DB01199)	gCCGGGCCTCGGAGCAGCCTC	0.697													G|||	1349	0.269369	0.174	0.2795	5008	,	,		13043	0.125		0.4533	False		,,,				2504	0.3507				p.P592R		Atlas-SNP	.											ACHE,NS,carcinoma,0,1	ACHE	80	1	0			c.C1775G						scavenged	.	G	,ARG/PRO	771,3151		119,533,1309	6.0	5.0	5.0		,1775	1.9	1.0	7	dbSNP_89	5	3296,4702		821,1654,1524	yes	intron,missense	ACHE	NM_000665.3,NM_015831.2	,103	940,2187,2833	CC,CG,GG		41.2103,19.6583,34.1191	,benign	,592/618	100488658	4067,7853	1961	3999	5960	SO:0001627	intron_variant	43	exon5			GGCCTCGGAGCAG		CCDS5709.1, CCDS5710.1, CCDS64736.1	7q22	2014-07-19	2014-01-02		ENSG00000087085	ENSG00000087085	3.1.1.7	"""Blood group antigens"""	108	protein-coding gene	gene with protein product	"""Yt blood group"""	100740	"""acetylcholinesterase (YT blood group)"", ""acetylcholinesterase (Yt blood group)"", ""acetylcholinesterase"""	YT		1380483	Standard	XM_005250357		Approved		uc003uxe.3	P22303	OTTHUMG00000157033	ENST00000412389.1:c.1723+131C>G	7.37:g.100488658G>C		Somatic	147	2	0.0136054		WXS	Illumina HiSeq	Phase_I	122	52	0.42623	NM_015831	A4D2E2|B7ZKZ0|D6W5X7|Q16169|Q29S23|Q2M324|Q504V3|Q53F46|Q86TM9|Q86YX9|Q9BXP7	Missense_Mutation	SNP	ENST00000412389.1	37	CCDS5709.1	613	0.2806776556776557	90	0.18292682926829268	114	0.3149171270718232	66	0.11538461538461539	343	0.4525065963060686	G	15.21	2.764618	0.49574	0.196583	0.412103	ENSG00000087085	ENST00000302913;ENST00000411582	T;T	0.64618	-0.11;-0.11	3.8	1.92	0.25849	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.42341	P	0.007662999999999975	B	0.06786	0.001	B	0.08055	0.003	T	0.43972	-0.9358	7	0.24483	T	0.36	.	5.4585	0.16604	0.115:0.2026:0.6824:0.0	rs1799806;rs17235003;rs17296925;rs17883536	592	P22303-2	.	R	592	ENSP00000303211:P592R;ENSP00000404865:P592R	ENSP00000303211:P592R	P	-	2	0	ACHE	100326594	0.995000	0.38212	0.996000	0.52242	0.965000	0.64279	0.337000	0.19841	0.367000	0.24454	0.448000	0.29417	CCG	G|0.724;C|0.276	0.276	strong		0.697	ACHE-013	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347201.1	NM_015831	
ECE1	1889	hgsc.bcm.edu	37	1	21573722	21573722	+	Silent	SNP	G	G	A	rs2229450	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:21573722G>A	ENST00000374893.6	-	9	1229	c.1155C>T	c.(1153-1155)acC>acT	p.T385T	ECE1_ENST00000415912.2_Silent_p.T369T|ECE1_ENST00000264205.6_Silent_p.T382T|ECE1_ENST00000357071.4_Silent_p.T373T|ECE1_ENST00000528294.1_5'UTR|ECE1_ENST00000436918.2_Silent_p.T385T	NM_001397.2	NP_001388.1	P42892	ECE1_HUMAN	endothelin converting enzyme 1	385					bradykinin catabolic process (GO:0010815)|calcitonin catabolic process (GO:0010816)|ear development (GO:0043583)|embryonic digit morphogenesis (GO:0042733)|endothelin maturation (GO:0034959)|heart development (GO:0007507)|hormone catabolic process (GO:0042447)|peptide hormone processing (GO:0016486)|pharyngeal system development (GO:0060037)|positive regulation of receptor recycling (GO:0001921)|protein processing (GO:0016485)|regulation of systemic arterial blood pressure by endothelin (GO:0003100)|regulation of vasoconstriction (GO:0019229)|substance P catabolic process (GO:0010814)	early endosome (GO:0005769)|endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intrinsic component of endosome membrane (GO:0031302)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|vesicle (GO:0031982)|Weibel-Palade body (GO:0033093)	endopeptidase activity (GO:0004175)|metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)|peptide hormone binding (GO:0017046)|protein homodimerization activity (GO:0042803)			endometrium(5)|kidney(1)|large_intestine(7)|lung(8)|ovary(2)|prostate(1)|skin(1)	25		Lung NSC(340;1.14e-05)|all_lung(284;1.23e-05)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00147)|Ovarian(437;0.00432)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0183)|OV - Ovarian serous cystadenocarcinoma(117;4.83e-27)|COAD - Colon adenocarcinoma(152;1.36e-06)|GBM - Glioblastoma multiforme(114;1.47e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000162)|STAD - Stomach adenocarcinoma(196;0.00326)|KIRC - Kidney renal clear cell carcinoma(1967;0.00755)|READ - Rectum adenocarcinoma(331;0.0678)|Lung(427;0.206)		ACCATCTGTCGGTGGTGTTGA	0.552													G|||	735	0.146765	0.0144	0.2709	5008	,	,		17950	0.128		0.2535	False		,,,				2504	0.1472				p.T385T		Atlas-SNP	.											.	ECE1	76	.	0			c.C1155T						PASS	.	G	,,,	253,4153	145.7+/-180.5	10,233,1960	157.0	127.0	137.0		1119,1107,1146,1155	-11.0	0.0	1	dbSNP_98	137	2309,6291	387.6+/-342.3	286,1737,2277	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ECE1	NM_001113347.1,NM_001113348.1,NM_001113349.1,NM_001397.2	,,,	296,1970,4237	AA,AG,GG		26.8488,5.7422,19.6986	,,,	373/759,369/755,382/768,385/771	21573722	2562,10444	2203	4300	6503	SO:0001819	synonymous_variant	1889	exon9			TCTGTCGGTGGTG	D49471	CCDS215.1, CCDS44081.1, CCDS44082.1, CCDS44083.1	1p36.1	2008-02-05			ENSG00000117298	ENSG00000117298			3146	protein-coding gene	gene with protein product		600423		ECE		7805846, 7864876, 17592116	Standard	NM_001397		Approved		uc001bei.2	P42892	OTTHUMG00000002625	ENST00000374893.6:c.1155C>T	1.37:g.21573722G>A		Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	123	64	0.520325	NM_001397	A8K3P1|B4E291|Q14217|Q17RN5|Q2Z2K8|Q58GE7|Q5THM5|Q5THM7|Q5THM8|Q9UJQ6|Q9UPF4|Q9UPM4|Q9Y501	Silent	SNP	ENST00000374893.6	37	CCDS215.1																																																																																			G|0.817;N|0.000;A|0.183	0.183	strong		0.552	ECE1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000007470.2	NM_001397	
BUB1B	701	hgsc.bcm.edu	37	15	40488851	40488851	+	Silent	SNP	G	G	A	rs1047130	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:40488851G>A	ENST00000287598.6	+	9	1359	c.1164G>A	c.(1162-1164)gcG>gcA	p.A388A	BUB1B_ENST00000412359.3_Silent_p.A402A	NM_001211.5	NP_001202	O60566	BUB1B_HUMAN	BUB1 mitotic checkpoint serine/threonine kinase B	388					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|protein localization to chromosome, centromeric region (GO:0071459)|protein localization to kinetochore (GO:0034501)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|condensed chromosome kinetochore (GO:0000777)|condensed chromosome outer kinetochore (GO:0000940)|condensed nuclear chromosome kinetochore (GO:0000778)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|perinuclear region of cytoplasm (GO:0048471)|spindle midzone (GO:0051233)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|endometrium(1)|kidney(2)|large_intestine(7)|liver(2)|lung(17)|ovary(1)|stomach(2)|urinary_tract(2)	36		all_cancers(109;1.12e-18)|all_epithelial(112;1.61e-15)|Lung NSC(122;5.63e-11)|all_lung(180;1.4e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;1.83e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0556)		ATCAGCAAGCGTCTGAGGAGA	0.428			"""Mis, N, F, S"""			rhabdomyosarcoma			Mosaic Variegated Aneuploidy Syndrome				G|||	955	0.190695	0.0182	0.3242	5008	,	,		18833	0.1627		0.327	False		,,,				2504	0.2178				p.A388A		Atlas-SNP	.	yes	Rec		Mosaic variegated aneuploidy	15	15q15	701	BUB1 budding uninhibited by benzimidazoles 1 homolog beta (yeast)		M	.	BUB1B	71	.	0			c.G1164A						PASS	.	G		315,4091	168.0+/-198.9	12,291,1900	103.0	104.0	103.0		1164	-2.8	0.4	15	dbSNP_86	103	2630,5970	424.6+/-354.7	409,1812,2079	no	coding-synonymous	BUB1B	NM_001211.5		421,2103,3979	AA,AG,GG		30.5814,7.1493,22.6434		388/1051	40488851	2945,10061	2203	4300	6503	SO:0001819	synonymous_variant	701	exon9	Familial Cancer Database	MVA, MVA syndrome, VMA syndrome, variegated mosaic aneuploidy syndrome, premature centromere division	GCAAGCGTCTGAG	AF107297	CCDS10053.1	15q15	2014-09-17	2013-01-17		ENSG00000156970	ENSG00000156970			1149	protein-coding gene	gene with protein product		602860	"""budding uninhibited by benzimidazoles 1 (yeast homolog), beta"", ""budding uninhibited by benzimidazoles 1 homolog beta (yeast)"""			9889005	Standard	NM_001211		Approved	BUBR1, MAD3L, Bub1A, SSK1	uc001zkx.4	O60566	OTTHUMG00000129877	ENST00000287598.6:c.1164G>A	15.37:g.40488851G>A		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	126	65	0.515873	NM_001211	B2R6U0|B4DL09|B4DLG3|O60501|O60627|O60758|O75389|Q59HH6|Q8WV50|Q96KM4	Silent	SNP	ENST00000287598.6	37	CCDS10053.1																																																																																			G|0.793;A|0.207	0.207	strong		0.428	BUB1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252122.4		
SIGLEC9	27180	hgsc.bcm.edu	37	19	51630482	51630482	+	Missense_Mutation	SNP	C	C	A	rs2258983	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:51630482C>A	ENST00000250360.3	+	4	1011	c.944C>A	c.(943-945)gCa>gAa	p.A315E	SIGLEC9_ENST00000440804.3_Missense_Mutation_p.A315E	NM_014441.2	NP_055256.1	Q9Y336	SIGL9_HUMAN	sialic acid binding Ig-like lectin 9	315	Ig-like C2-type 2.		A -> E (in dbSNP:rs2258983). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.4}.		cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)	integral component of plasma membrane (GO:0005887)	carbohydrate binding (GO:0030246)			NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(6)|liver(3)|lung(25)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	45		all_neural(266;0.0529)		GBM - Glioblastoma multiforme(134;0.000826)|OV - Ovarian serous cystadenocarcinoma(262;0.00295)		CTGAGGGATGCAGCTGAATTC	0.637													.|||	3380	0.67492	0.913	0.5086	5008	,	,		20662	0.5744		0.5845	False		,,,				2504	0.6677				p.A315E		Atlas-SNP	.											.	SIGLEC9	85	.	0			c.C944A						PASS	.	A	GLU/ALA,GLU/ALA	3737,669		1589,559,55	41.0	41.0	41.0		944,944	-0.4	0.0	19	dbSNP_100	41	4940,3660		1442,2056,802	no	missense,missense	SIGLEC9	NM_001198558.1,NM_014441.2	107,107	3031,2615,857	AA,AC,CC		42.5581,15.1838,33.2846	benign,benign	315/480,315/464	51630482	8677,4329	2203	4300	6503	SO:0001583	missense	27180	exon4			GGGATGCAGCTGA	AF135027	CCDS12825.1, CCDS56100.1	19q13.3-q13.4	2013-01-29			ENSG00000129450	ENSG00000129450		"""Sialic acid binding Ig-like lectins"", ""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	10878	protein-coding gene	gene with protein product		605640				10903842	Standard	NM_014441		Approved	CD329	uc002pvu.3	Q9Y336		ENST00000250360.3:c.944C>A	19.37:g.51630482C>A	ENSP00000250360:p.Ala315Glu	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	99	37	0.373737	NM_001198558	Q6GTU4|Q9BYI9	Missense_Mutation	SNP	ENST00000250360.3	37	CCDS12825.1	1383	0.6332417582417582	433	0.8800813008130082	195	0.5386740331491713	314	0.548951048951049	441	0.5817941952506597	.	0.007	-1.957070	0.00465	0.848162	0.574419	ENSG00000129450	ENST00000440804;ENST00000250360	T;T	0.14516	2.5;2.5	2.3	-0.399	0.12415	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.638986	0.12823	N	0.436262	T	0.00012	0.0000	N	0.00230	-1.795	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.22382	-1.0218	9	0.02654	T	1	.	3.0571	0.06188	0.3731:0.2525:0.3745:0.0	rs2258983;rs17846137;rs17859145;rs52811663;rs58493370;rs2258983	315	Q9Y336	SIGL9_HUMAN	E	315	ENSP00000413861:A315E;ENSP00000250360:A315E	ENSP00000250360:A315E	A	+	2	0	SIGLEC9	56322294	0.000000	0.05858	0.001000	0.08648	0.002000	0.02628	-0.534000	0.06150	-0.421000	0.07416	-0.694000	0.03704	GCA	C|0.349;A|0.651	0.651	strong		0.637	SIGLEC9-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464224.1	NM_014441	
DIP2A	23181	hgsc.bcm.edu	37	21	47961711	47961711	+	Silent	SNP	G	G	A	rs2070435	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:47961711G>A	ENST00000417564.2	+	18	2100	c.2079G>A	c.(2077-2079)ctG>ctA	p.L693L	DIP2A_ENST00000318711.7_Silent_p.L694L|DIP2A_ENST00000427143.2_Silent_p.L629L|DIP2A_ENST00000457905.3_Silent_p.L693L|DIP2A_ENST00000400274.1_Silent_p.L689L|DIP2A_ENST00000466639.1_Silent_p.L650L|DIP2A_ENST00000435722.3_Silent_p.L693L			Q14689	DIP2A_HUMAN	DIP2 disco-interacting protein 2 homolog A (Drosophila)	693					multicellular organismal development (GO:0007275)|negative regulation of gene expression (GO:0010629)|regulation of apoptotic process (GO:0042981)	cell surface (GO:0009986)|nucleus (GO:0005634)	catalytic activity (GO:0003824)			cervix(1)|endometrium(7)|kidney(2)|large_intestine(6)|lung(22)|ovary(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	43	Breast(49;0.0933)			Epithelial(3;3.12e-06)|OV - Ovarian serous cystadenocarcinoma(3;5.68e-06)|all cancers(3;4.08e-05)|Colorectal(79;0.0129)|COAD - Colon adenocarcinoma(84;0.0824)		AAGCAGTCCTGTCGATGAACG	0.478													A|||	1940	0.38738	0.5408	0.2147	5008	,	,		21409	0.4058		0.3439	False		,,,				2504	0.3282				p.L693L		Atlas-SNP	.											.	DIP2A	332	.	0			c.G2079A						PASS	.	A	,,,,,,	1869,2021		443,983,519	126.0	126.0	126.0		1887,1950,2067,2079,2079,2079,2079	-2.5	0.7	21	dbSNP_96	126	2643,5651		423,1797,1927	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	DIP2A	NM_001146114.1,NM_001146115.1,NM_001146116.1,NM_015151.3,NM_206889.2,NM_206890.2,NM_206891.2	,,,,,,	866,2780,2446	AA,AG,GG		31.8664,48.0463,37.0322	,,,,,,	629/1111,650/799,689/1568,693/1572,693/890,693/842,693/813	47961711	4512,7672	1945	4147	6092	SO:0001819	synonymous_variant	23181	exon18			AGTCCTGTCGATG	AF490768	CCDS46655.1, CCDS46656.1, CCDS46657.1, CCDS54490.1, CCDS54491.1	21q22.3	2010-08-20	2006-01-13	2006-01-13	ENSG00000160305	ENSG00000160305			17217	protein-coding gene	gene with protein product		607711	"""chromosome 21 open reading frame 106"""	C21orf106			Standard	NM_015151		Approved	Dip2, KIAA0184	uc002zjo.2	Q14689	OTTHUMG00000090717	ENST00000417564.2:c.2079G>A	21.37:g.47961711G>A		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	77	27	0.350649	NM_206891	A6P4T3|B4E0F0|E7EMA5|Q8IVA3|Q8N4S2|Q8TD89|Q96ML9	Silent	SNP	ENST00000417564.2	37	CCDS46655.1																																																																																			G|0.580;A|0.420	0.420	strong		0.478	DIP2A-012	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000376736.1	NM_015151	
NCOA7	135112	hgsc.bcm.edu	37	6	126249914	126249914	+	Missense_Mutation	SNP	T	T	G	rs1567|rs386705611	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:126249914T>G	ENST00000368357.3	+	17	3178	c.2826T>G	c.(2824-2826)gaT>gaG	p.D942E	NCOA7_ENST00000392477.2_Missense_Mutation_p.D942E|NCOA7_ENST00000229634.9_Missense_Mutation_p.D827E	NM_001199619.1|NM_001199620.1	NP_001186548.1|NP_001186549.1	Q8NI08	NCOA7_HUMAN	nuclear receptor coactivator 7	942	TLD.		D -> E (in dbSNP:rs1567).		positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	intracellular (GO:0005622)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)			NS(1)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(6)|lung(16)|ovary(1)|skin(1)|soft_tissue(1)|urinary_tract(2)	39				UCEC - Uterine corpus endometrioid carcinoma (4;0.0803)|GBM - Glioblastoma multiforme(226;0.0193)|all cancers(137;0.237)		GGGCATTTGATTGAAATTCAG	0.433													G|||	827	0.165136	0.2617	0.0764	5008	,	,		16628	0.2401		0.1153	False		,,,				2504	0.0716				p.D942E		Atlas-SNP	.											.	NCOA7	92	.	0			c.T2826G						PASS	.	G	GLU/ASP,GLU/ASP,GLU/ASP,GLU/ASP,GLU/ASP,GLU/ASP	1109,3297	715.1+/-408.4	152,805,1246	76.0	78.0	77.0		2793,2826,2826,2481,657,2826	4.1	1.0	6	dbSNP_36	77	1106,7494	768.0+/-407.6	64,978,3258	yes	missense,missense,missense,missense,missense,missense	NCOA7	NM_001122842.2,NM_001199619.1,NM_001199620.1,NM_001199621.1,NM_001199622.1,NM_181782.4	45,45,45,45,45,45	216,1783,4504	GG,GT,TT		12.8605,25.1702,17.0306	benign,benign,benign,benign,benign,benign	931/932,942/943,942/943,827/828,219/220,942/943	126249914	2215,10791	2203	4300	6503	SO:0001583	missense	135112	exon17			ATTTGATTGAAAT	AJ420542	CCDS5132.1, CCDS56448.1	6q22.33	2013-03-14			ENSG00000111912	ENSG00000111912			21081	protein-coding gene	gene with protein product	"""TBC/LysM-associated domain containing 4"""	609752				11971969	Standard	NM_001199619		Approved	ERAP140, dJ187J11.3, TLDC4	uc003qai.3	Q8NI08	OTTHUMG00000015513	ENST00000368357.3:c.2826T>G	6.37:g.126249914T>G	ENSP00000357341:p.Asp942Glu	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	46	46	1	NM_001199619	B2RNS2|B7Z2C4|B9EH71|G8JL91|Q3LID6|Q4G0V1|Q5TF95|Q6IPQ4|Q6NE83|Q86T89|Q8N1W4	Missense_Mutation	SNP	ENST00000368357.3	37	CCDS5132.1	343|343	0.15705128205128205|0.15705128205128205	116|116	0.23577235772357724|0.23577235772357724	24|24	0.06629834254143646|0.06629834254143646	115|115	0.20104895104895104|0.20104895104895104	88|88	0.11609498680738786|0.11609498680738786	G|G	1.772|1.772	-0.484123|-0.484123	0.04383|0.04383	0.251702|0.251702	0.128605|0.128605	ENSG00000111912|ENSG00000111912	ENST00000368357;ENST00000392477;ENST00000229634|ENST00000438495	T;T;T|.	0.06933|.	3.26;3.26;3.24|.	6.17|6.17	4.1|4.1	0.47936|0.47936	TLDc (1);|.	0.000000|.	0.85682|.	N|.	0.000000|.	T|T	0.03305|0.03305	0.0096|0.0096	N|N	0.01202|0.01202	-0.96|-0.96	0.58432|0.58432	P|P	1.0000000000287557E-6|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;0.001;0.0;0.0|.	T|T	0.38265|0.38265	-0.9669|-0.9669	9|4	0.02654|.	T|.	1|.	.|.	6.2777|6.2777	0.20989|0.20989	0.2432:0.0:0.6121:0.1447|0.2432:0.0:0.6121:0.1447	rs1567;rs52814580;rs59469171;rs1567|rs1567;rs52814580;rs59469171;rs1567	931;236;931;942|.	B3KXK4;Q5JVL0;Q8NI08-2;Q8NI08|.	.;.;.;NCOA7_HUMAN|.	E|V	942;942;827|237	ENSP00000357341:D942E;ENSP00000376269:D942E;ENSP00000229634:D827E|.	ENSP00000229634:D827E|.	D|L	+|+	3|1	2|2	NCOA7|NCOA7	126291607|126291607	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.734000|0.734000	0.41952|0.41952	1.200000|1.200000	0.32247|0.32247	0.952000|0.952000	0.37798|0.37798	-0.121000|-0.121000	0.15023|0.15023	GAT|TTG	T|0.829;G|0.171	0.171	strong		0.433	NCOA7-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042083.4	XM_059748	
HAUS4	54930	hgsc.bcm.edu	37	14	23421593	23421593	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:23421593G>A	ENST00000206474.7	-	4	526	c.274C>T	c.(274-276)Ctt>Ttt	p.L92F	RP11-298I3.1_ENST00000548322.1_RNA|RP11-298I3.1_ENST00000548819.1_RNA|HAUS4_ENST00000541587.1_Missense_Mutation_p.L92F|HAUS4_ENST00000342454.8_Missense_Mutation_p.L92F|HAUS4_ENST00000397409.4_Missense_Mutation_p.L92F|HAUS4_ENST00000555367.1_Missense_Mutation_p.L92F|HAUS4_ENST00000555986.1_Missense_Mutation_p.L92F|RP11-298I3.5_ENST00000555074.1_Intron|HAUS4_ENST00000554446.1_5'UTR|HAUS4_ENST00000490506.1_5'UTR|HAUS4_ENST00000347758.2_Missense_Mutation_p.L92F			Q9H6D7	HAUS4_HUMAN	HAUS augmin-like complex, subunit 4	92					centrosome organization (GO:0051297)|mitotic nuclear division (GO:0007067)|spindle assembly (GO:0051225)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|HAUS complex (GO:0070652)|microtubule (GO:0005874)				breast(3)|cervix(1)|endometrium(2)|lung(6)|ovary(1)|skin(1)	14						TAGTCCACAAGCAACTCTTGA	0.433																																					p.L92F		Atlas-SNP	.											.	HAUS4	34	.	0			c.C274T						PASS	.						229.0	218.0	222.0					14																	23421593		2203	4300	6503	SO:0001583	missense	54930	exon4			CCACAAGCAACTC	AK000431	CCDS9580.1, CCDS53886.1	14q11.1	2011-10-24	2009-04-20	2009-04-20	ENSG00000092036	ENSG00000092036		"""HAUS augmin-like complex subunits"""	20163	protein-coding gene	gene with protein product		613431	"""chromosome 14 open reading frame 94"""	C14orf94		19427217	Standard	NM_017815		Approved	FLJ20424	uc001wht.3	Q9H6D7	OTTHUMG00000028710	ENST00000206474.7:c.274C>T	14.37:g.23421593G>A	ENSP00000206474:p.Leu92Phe	Somatic	206	0	0		WXS	Illumina HiSeq	Phase_I	183	97	0.530055	NM_001166270	B7WP17|D3DS34|Q86T15|Q86T16|Q86U43|Q9NX59	Missense_Mutation	SNP	ENST00000206474.7	37	CCDS9580.1	.	.	.	.	.	.	.	.	.	.	G	22.2	4.260380	0.80246	.	.	ENSG00000092036	ENST00000206474;ENST00000541587;ENST00000342454;ENST00000347758;ENST00000397409;ENST00000555367;ENST00000555986;ENST00000555040;ENST00000556915;ENST00000554516;ENST00000557591	.	.	.	5.71	5.71	0.89125	.	0.124104	0.53938	D	0.000054	T	0.69214	0.3086	L	0.59436	1.845	0.32357	N	0.557748	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.85130	0.997;0.996;0.997	T	0.75453	-0.3312	9	0.72032	D	0.01	-7.2977	15.3637	0.74503	0.0:0.0:1.0:0.0	.	92;92;92	Q9H6D7-4;Q9H6D7-2;Q9H6D7	.;.;HAUS4_HUMAN	F	92	.	ENSP00000206474:L92F	L	-	1	0	HAUS4	22491433	1.000000	0.71417	1.000000	0.80357	0.938000	0.57974	3.932000	0.56537	2.694000	0.91930	0.655000	0.94253	CTT	.	.	none		0.433	HAUS4-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071680.3		
KRTAP10-4	386672	hgsc.bcm.edu	37	21	45994302	45994302	+	Missense_Mutation	SNP	T	T	C	rs200473430|rs201123486		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:45994302T>C	ENST00000400374.3	+	1	697	c.667T>C	c.(667-669)Tcc>Ccc	p.S223P	TSPEAR_ENST00000397916.1_5'Flank|TSPEAR_ENST00000323084.4_Intron	NM_198687.1	NP_941960.1	P60372	KR104_HUMAN	keratin associated protein 10-4	223	36 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				NS(1)|endometrium(4)|kidney(1)|large_intestine(1)|lung(9)|pancreas(1)|prostate(1)	18						CACCTCCTCCTCCTGCCAGCA	0.637																																					p.S223P		Atlas-SNP	.											KRTAP10-4,NS,carcinoma,0,1	KRTAP10-4	44	1	0			c.T667C						scavenged	.						59.0	65.0	63.0					21																	45994302		2203	4299	6502	SO:0001583	missense	386672	exon1			TCCTCCTCCTGCC	AB076351	CCDS42957.1	21q22.3	2006-03-13	2004-07-12	2004-07-14	ENSG00000215454	ENSG00000215454		"""Keratin associated proteins"""	20521	protein-coding gene	gene with protein product			"""keratin associated protein 18-4"""	KRTAP18-4			Standard	NM_198687		Approved	KRTAP18.4, KAP10.4	uc002zfk.1	P60372	OTTHUMG00000057641	ENST00000400374.3:c.667T>C	21.37:g.45994302T>C	ENSP00000383225:p.Ser223Pro	Somatic	202	17	0.0841584		WXS	Illumina HiSeq	Phase_I	234	20	0.0854701	NM_198687	Q08AS0	Missense_Mutation	SNP	ENST00000400374.3	37	CCDS42957.1	.	.	.	.	.	.	.	.	.	.	N	8.649	0.897850	0.17686	.	.	ENSG00000215454	ENST00000400374	T	0.01388	4.95	2.9	-3.25	0.05079	.	.	.	.	.	T	0.00440	0.0014	N	0.00368	-1.59	0.20926	N	0.999826	B	0.02656	0.0	B	0.04013	0.001	T	0.45425	-0.9262	9	0.18276	T	0.48	.	4.3087	0.10960	0.0:0.2984:0.1843:0.5173	.	223	P60372	KR104_HUMAN	P	223	ENSP00000383225:S223P	ENSP00000383225:S223P	S	+	1	0	KRTAP10-4	44818730	0.000000	0.05858	0.609000	0.28983	0.851000	0.48451	-2.984000	0.00661	-0.677000	0.05231	-0.552000	0.04208	TCC	.	.	weak		0.637	KRTAP10-4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128045.1	NM_198687	
ENG	2022	hgsc.bcm.edu	37	9	130605385	130605385	+	Silent	SNP	C	C	T	rs45605432|rs11545664	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	47	0	0		WXS	Illumina HiSeq	Phase_I	26	10	0.384615	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		
ODF2L	57489	hgsc.bcm.edu	37	1	86818572	86818572	+	Silent	SNP	T	T	C	rs272496	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:86818572T>C	ENST00000359242.3	-	17	2144	c.1863A>G	c.(1861-1863)gaA>gaG	p.E621E	ODF2L_ENST00000370566.3_Silent_p.E539E|ODF2L_ENST00000394731.1_Silent_p.E461E|ODF2L_ENST00000294678.2_Silent_p.E605E|ODF2L_ENST00000370567.1_Silent_p.E592E|ODF2L_ENST00000317336.7_Silent_p.E621E	NM_001007022.2	NP_001007023.2	Q9ULJ1	ODF2L_HUMAN	outer dense fiber of sperm tails 2-like	621						centrosome (GO:0005813)				endometrium(2)|kidney(2)|large_intestine(10)|lung(6)|ovary(1)|pancreas(1)|skin(1)|stomach(1)	24				all cancers(265;0.0313)|Epithelial(280;0.0611)		GTTGATTTTGTTCTTCATTTT	0.284													T|||	3712	0.741214	0.7557	0.6585	5008	,	,		16896	0.8284		0.6451	False		,,,				2504	0.7894				p.E621E		Atlas-SNP	.											.	ODF2L	53	.	0			c.A1863G						PASS	.	T	,,,	3335,1063	712.9+/-408.2	1275,785,139	109.0	107.0	108.0		1863,1704,1617,1815	2.2	1.0	1	dbSNP_79	108	5583,3009	657.4+/-401.5	1805,1973,518	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ODF2L	NM_001007022.2,NM_001184765.1,NM_001184766.1,NM_020729.2	,,,	3080,2758,657	CC,CT,TT		35.0209,24.1701,31.3472	,,,	621/637,568/621,539/592,605/621	86818572	8918,4072	2199	4296	6495	SO:0001819	synonymous_variant	57489	exon17			ATTTTGTTCTTCA		CCDS30763.1, CCDS41354.1, CCDS30763.2, CCDS41354.2, CCDS53339.1	1p22.3	2008-02-05			ENSG00000122417	ENSG00000122417			29225	protein-coding gene	gene with protein product						10574462	Standard	NM_020729		Approved	KIAA1229	uc001dll.2	Q9ULJ1	OTTHUMG00000010080	ENST00000359242.3:c.1863A>G	1.37:g.86818572T>C		Somatic	434	0	0		WXS	Illumina HiSeq	Phase_I	379	177	0.467018	NM_001007022	A8MU56|B4E037|Q05C40|Q5BJG5|Q5TBX3|Q5TBX4|Q86X31	Silent	SNP	ENST00000359242.3	37	CCDS41354.2	1587	0.7266483516483516	376	0.7642276422764228	235	0.649171270718232	490	0.8566433566433567	486	0.6411609498680739	T	8.365	0.833928	0.16820	0.758299	0.649791	ENSG00000122417	ENST00000459999	.	.	.	5.84	2.2	0.27929	.	.	.	.	.	T	0.33206	0.0855	.	.	.	0.09310	P	0.9999999999994298	.	.	.	.	.	.	T	0.10543	-1.0625	3	.	.	.	-18.9514	9.1594	0.37012	0.0:0.3005:0.0:0.6995	rs272496;rs1048900;rs3188946;rs3765510;rs17359491;rs17412686;rs59037625	.	.	.	S	388	.	.	N	-	2	0	ODF2L	86591160	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	0.452000	0.21795	0.539000	0.28788	-0.417000	0.06048	AAC	T|0.315;C|0.685	0.685	strong		0.284	ODF2L-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000027873.2		
SCIN	85477	hgsc.bcm.edu	37	7	12617727	12617727	+	Missense_Mutation	SNP	A	A	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:12617727A>C	ENST00000297029.5	+	2	339	c.238A>C	c.(238-240)Atc>Ctc	p.I80L		NM_001112706.2	NP_001106177.1	Q9Y6U3	ADSV_HUMAN	scinderin	80	Actin-severing. {ECO:0000255}.				actin filament capping (GO:0051693)|actin filament severing (GO:0051014)|actin nucleation (GO:0045010)|calcium ion-dependent exocytosis (GO:0017156)|negative regulation of cell proliferation (GO:0008285)|positive regulation of apoptotic process (GO:0043065)|positive regulation of megakaryocyte differentiation (GO:0045654)|positive regulation of secretion (GO:0051047)|regulation of chondrocyte differentiation (GO:0032330)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)	1-phosphatidylinositol binding (GO:0005545)|actin binding (GO:0003779)|actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylserine binding (GO:0001786)			endometrium(3)|kidney(1)|large_intestine(2)|lung(9)|ovary(2)	17				UCEC - Uterine corpus endometrioid carcinoma (126;0.195)		AGCTGCTGCCATCTTCACTGT	0.418																																					p.I80L		Atlas-SNP	.											.	SCIN	105	.	0			c.A238C						PASS	.						116.0	98.0	104.0					7																	12617727		692	1591	2283	SO:0001583	missense	85477	exon2			GCTGCCATCTTCA	AF276507	CCDS47545.1, CCDS47546.1	7p21.3	2006-04-25			ENSG00000006747	ENSG00000006747			21695	protein-coding gene	gene with protein product		613416					Standard	NM_033128		Approved	adseverin, KIAA1905	uc003ssn.4	Q9Y6U3	OTTHUMG00000152385	ENST00000297029.5:c.238A>C	7.37:g.12617727A>C	ENSP00000297029:p.Ile80Leu	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	148	64	0.432432	NM_001112706	A8K2U8|Q8NBZ6|Q8WU97|Q96JC7|Q96PY2	Missense_Mutation	SNP	ENST00000297029.5	37	CCDS47545.1	.	.	.	.	.	.	.	.	.	.	A	22.3	4.275863	0.80580	.	.	ENSG00000006747	ENST00000297029;ENST00000417018	T;T	0.51574	0.7;0.7	4.93	3.76	0.43208	Gelsolin domain (1);	0.000000	0.85682	D	0.000000	T	0.59032	0.2164	M	0.67953	2.075	0.80722	D	1	B	0.26708	0.157	P	0.46026	0.501	T	0.61705	-0.7008	10	0.72032	D	0.01	-9.0734	11.05	0.47880	0.8607:0.0:0.0:0.1393	.	80	Q9Y6U3	ADSV_HUMAN	L	80;107	ENSP00000297029:I80L;ENSP00000404380:I107L	ENSP00000297029:I80L	I	+	1	0	SCIN	12584252	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	7.286000	0.78671	0.884000	0.36064	-0.481000	0.04817	ATC	.	.	none		0.418	SCIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326041.1	NM_033128	
AHNAK2	113146	hgsc.bcm.edu	37	14	105415433	105415433	+	Missense_Mutation	SNP	T	T	C	rs199970974	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:105415433T>C	ENST00000333244.5	-	7	6474	c.6355A>G	c.(6355-6357)Atg>Gtg	p.M2119V	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	2119						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)			TCCACCTCCATGCTGGGCAGA	0.597																																					p.M2119V		Atlas-SNP	.											AHNAK2_ENST00000333244,NS,carcinoma,0,2	AHNAK2	719	2	0			c.A6355G						scavenged	.						150.0	106.0	124.0					14																	105415433		1955	2967	4922	SO:0001583	missense	113146	exon7			CCTCCATGCTGGG	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.6355A>G	14.37:g.105415433T>C	ENSP00000353114:p.Met2119Val	Somatic	0	0	.		WXS	Illumina HiSeq	Phase_I	95	22	0.231579	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	.	.	.	.	.	.	.	.	.	.	N	0.010	-1.792568	0.00623	.	.	ENSG00000185567	ENST00000333244	T	0.00666	5.91	4.31	-2.8	0.05823	.	.	.	.	.	T	0.00328	0.0010	N	0.01464	-0.85	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.38607	-0.9653	9	0.07813	T	0.8	.	3.0364	0.06123	0.1064:0.1654:0.2303:0.4979	.	2119	Q8IVF2	AHNK2_HUMAN	V	2119	ENSP00000353114:M2119V	ENSP00000353114:M2119V	M	-	1	0	AHNAK2	104486478	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-1.481000	0.02323	-1.184000	0.02720	-1.803000	0.00618	ATG	T|0.962;C|0.038	0.038	strong		0.597	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
C3orf30	152405	hgsc.bcm.edu	37	3	118867047	118867047	+	Missense_Mutation	SNP	C	C	G	rs9289122	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:118867047C>G	ENST00000295622.1	+	2	1459	c.1419C>G	c.(1417-1419)gaC>gaG	p.D473E	IGSF11_ENST00000354673.2_5'Flank|IGSF11_ENST00000441144.2_5'Flank|RP11-484M3.5_ENST00000490594.1_Intron|IGSF11_ENST00000425327.2_5'Flank	NM_152539.2	NP_689752.2	Q96M34	CC030_HUMAN	chromosome 3 open reading frame 30	473			D -> E (in dbSNP:rs9289122).							NS(1)|breast(1)|cervix(1)|endometrium(1)|large_intestine(6)|lung(20)|ovary(2)|prostate(1)|urinary_tract(1)	34				GBM - Glioblastoma multiforme(114;0.222)		CAGAAATTGACCAAGGAAAGG	0.363													G|||	2352	0.469649	0.4818	0.4856	5008	,	,		18727	0.5119		0.4404	False		,,,				2504	0.4284				p.D473E		Atlas-SNP	.											.	C3orf30	64	.	0			c.C1419G						PASS	.	G	GLU/ASP	2098,2308	595.5+/-388.5	494,1110,599	81.0	88.0	86.0		1419	-2.6	0.0	3	dbSNP_119	86	4077,4523	590.5+/-392.7	984,2109,1207	yes	missense	C3orf30	NM_152539.2	45	1478,3219,1806	GG,GC,CC		47.407,47.6169,47.4781	benign	473/537	118867047	6175,6831	2203	4300	6503	SO:0001583	missense	152405	exon2			AATTGACCAAGGA	AK057421	CCDS2984.1	3q13.32	2011-08-09			ENSG00000163424	ENSG00000163424			26553	protein-coding gene	gene with protein product							Standard	NM_152539		Approved	FLJ32859	uc003ecb.1	Q96M34	OTTHUMG00000159349	ENST00000295622.1:c.1419C>G	3.37:g.118867047C>G	ENSP00000295622:p.Asp473Glu	Somatic	288	0	0		WXS	Illumina HiSeq	Phase_I	234	232	0.991453	NM_152539	A1L4B7	Missense_Mutation	SNP	ENST00000295622.1	37	CCDS2984.1	1084	0.49633699633699635	256	0.5203252032520326	176	0.4861878453038674	303	0.5297202797202797	349	0.4604221635883905	G	0.041	-1.283573	0.01398	0.476169	0.47407	ENSG00000163424	ENST00000295622;ENST00000470341	T	0.11495	2.77	4.74	-2.61	0.06171	.	1.523470	0.04778	N	0.429264	T	0.00012	0.0000	N	0.01352	-0.895	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.45629	-0.9248	9	0.02654	T	1	3.0155	0.727	0.00950	0.41:0.1284:0.2103:0.2513	rs9289122;rs52829346;rs9289122	473;473	E9PFE5;Q96M34	.;CC030_HUMAN	E	473	ENSP00000295622:D473E	ENSP00000295622:D473E	D	+	3	2	C3orf30	120349737	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.870000	0.01641	-0.718000	0.04949	-0.120000	0.15030	GAC	C|0.521;G|0.479	0.479	strong		0.363	C3orf30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354838.1	NM_152539	
PPFIA3	8541	hgsc.bcm.edu	37	19	49641651	49641651	+	Silent	SNP	C	C	T	rs117880896	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:49641651C>T	ENST00000334186.4	+	16	2392	c.2043C>T	c.(2041-2043)ccC>ccT	p.P681P	PPFIA3_ENST00000602351.1_Silent_p.P681P	NM_003660.2	NP_003651.1	O75145	LIPA3_HUMAN	protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 3	681					cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|presynaptic active zone (GO:0048786)				NS(1)|breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(2)|lung(16)|pancreas(1)|prostate(1)|skin(4)|urinary_tract(1)	35		all_lung(116;3.16e-06)|Lung NSC(112;6.25e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392)		all cancers(93;2.36e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.000203)|GBM - Glioblastoma multiforme(486;0.00307)|Epithelial(262;0.00677)		GCCTGGCACCCCCTAGCCCTG	0.687													C|||	57	0.0113818	0.0	0.0159	5008	,	,		12555	0.0		0.0417	False		,,,				2504	0.0041				p.P681P		Atlas-SNP	.											.	PPFIA3	71	.	0			c.C2043T						PASS	.	C		31,4373		0,31,2171	29.0	32.0	31.0		2043	-6.4	1.0	19	dbSNP_132	31	392,8200		7,378,3911	no	coding-synonymous	PPFIA3	NM_003660.2		7,409,6082	TT,TC,CC		4.5624,0.7039,3.2548		681/1195	49641651	423,12573	2202	4296	6498	SO:0001819	synonymous_variant	8541	exon16			GGCACCCCCTAGC	AF034800	CCDS12758.1	19q13.33	2013-09-23			ENSG00000177380	ENSG00000177380		"""Sterile alpha motif (SAM) domain containing"""	9247	protein-coding gene	gene with protein product	"""protein tyrosine phosphatase, receptor type, f polypeptide, alpha 3"", ""liprin-alpha 3"", ""liprin"""	603144				9624153, 9734811	Standard	NM_003660		Approved	KIAA0654, LPNA3, MGC126567, MGC126569	uc002pmr.3	O75145	OTTHUMG00000183213	ENST00000334186.4:c.2043C>T	19.37:g.49641651C>T		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	53	27	0.509434	NM_003660	A8K142|Q3MJA0|Q9H8B5|Q9UEW4	Silent	SNP	ENST00000334186.4	37	CCDS12758.1																																																																																			C|0.974;T|0.026	0.026	strong		0.687	PPFIA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465688.1	NM_003660	
ARAP3	64411	hgsc.bcm.edu	37	5	141036337	141036337	+	Silent	SNP	A	A	G	rs7703648	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:141036337A>G	ENST00000239440.4	-	26	3668	c.3603T>C	c.(3601-3603)gcT>gcC	p.A1201A	ARAP3_ENST00000512390.1_5'UTR|ARAP3_ENST00000513878.1_Silent_p.A863A|ARAP3_ENST00000508305.1_Silent_p.A1032A	NM_022481.5	NP_071926.4	Q8WWN8	ARAP3_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 3	1201	Ras-associating. {ECO:0000255|PROSITE- ProRule:PRU00166}.				cytoskeleton organization (GO:0007010)|negative regulation of cell migration (GO:0030336)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of Rho protein signal transduction (GO:0035024)|regulation of ARF GTPase activity (GO:0032312)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	ARF GTPase activator activity (GO:0008060)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|Rho GTPase activator activity (GO:0005100)|zinc ion binding (GO:0008270)	p.A1201A(1)		NS(1)|breast(7)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(14)|ovary(1)|prostate(2)|skin(4)|stomach(1)	53						AGAGCAGGGAAGCTGAGCAGG	0.577													G|||	2411	0.48143	0.7065	0.4885	5008	,	,		18041	0.3889		0.4314	False		,,,				2504	0.319				p.A1201A		Atlas-SNP	.											ARAP3,NS,carcinoma,0,1	ARAP3	139	1	1	Substitution - coding silent(1)	stomach(1)	c.T3603C						PASS	.	G		2873,1533	476.8+/-357.7	935,1003,265	40.0	40.0	40.0		3603	-0.1	1.0	5	dbSNP_116	40	3475,5125	626.4+/-397.8	733,2009,1558	no	coding-synonymous	ARAP3	NM_022481.5		1668,3012,1823	GG,GA,AA		40.407,34.7935,48.8082		1201/1545	141036337	6348,6658	2203	4300	6503	SO:0001819	synonymous_variant	64411	exon26			CAGGGAAGCTGAG	AJ310567	CCDS4266.1	5q31.3	2013-01-11	2008-09-22	2008-09-22	ENSG00000120318	ENSG00000120318		"""ADP-ribosylation factor GTPase activating proteins"", ""Sterile alpha motif (SAM) domain containing"", ""Pleckstrin homology (PH) domain containing"", ""Ankyrin repeat domain containing"""	24097	protein-coding gene	gene with protein product		606647	"""centaurin, delta 3"""	CENTD3		11804589, 12015138	Standard	XM_005268497		Approved	FLJ21065, DRAG1	uc003llm.3	Q8WWN8	OTTHUMG00000129610	ENST00000239440.4:c.3603T>C	5.37:g.141036337A>G		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	86	33	0.383721	NM_022481	B4DIT1|D3DQE3	Silent	SNP	ENST00000239440.4	37	CCDS4266.1																																																																																			A|0.497;G|0.503	0.503	strong		0.577	ARAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251805.1	NM_022481	
RPTOR	57521	hgsc.bcm.edu	37	17	78935197	78935197	+	Silent	SNP	C	C	T	rs9899178	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:78935197C>T	ENST00000306801.3	+	31	3971	c.3609C>T	c.(3607-3609)cgC>cgT	p.R1203R	RPTOR_ENST00000544334.2_Silent_p.R1045R|CTD-2561B21.3_ENST00000571591.1_RNA|RPTOR_ENST00000575542.1_3'UTR	NM_020761.2	NP_065812.1	Q8N122	RPTOR_HUMAN	regulatory associated protein of MTOR, complex 1	1203					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						CCTACAGCCGCGTCATGACGT	0.672													C|||	1550	0.309505	0.0862	0.3415	5008	,	,		15561	0.5546		0.3479	False		,,,				2504	0.2965				p.R1203R		Atlas-SNP	.											.	RPTOR	122	.	0			c.C3609T						PASS	.	C	,	512,3812		39,434,1689	69.0	41.0	50.0		3135,3609	-3.8	1.0	17	dbSNP_119	50	2659,5691		428,1803,1944	no	coding-synonymous,coding-synonymous	RPTOR	NM_001163034.1,NM_020761.2	,	467,2237,3633	TT,TC,CC		31.8443,11.8409,25.0197	,	1045/1178,1203/1336	78935197	3171,9503	2162	4175	6337	SO:0001819	synonymous_variant	57521	exon31			CAGCCGCGTCATG		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.3609C>T	17.37:g.78935197C>T		Somatic	19	0	0		WXS	Illumina HiSeq	Phase_I	34	33	0.970588	NM_020761	B2RN36|C6KEF2|F5H7J5|Q8N4V9|Q8TB32|Q9P2P3	Silent	SNP	ENST00000306801.3	37	CCDS11773.1																																																																																			C|0.703;T|0.297	0.297	strong		0.672	RPTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438125.1	NM_020761	
SYNGAP1	8831	hgsc.bcm.edu	37	6	33405994	33405994	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:33405994G>A	ENST00000418600.2	+	8	1413	c.1312G>A	c.(1312-1314)Gcc>Acc	p.A438T	MIR5004_ENST00000579078.1_RNA|SYNGAP1_ENST00000293748.5_Missense_Mutation_p.A438T|SYNGAP1_ENST00000496374.1_3'UTR|SYNGAP1_ENST00000428982.2_Missense_Mutation_p.A379T	NM_006772.2	NP_006763.2	Q96PV0	SYGP1_HUMAN	synaptic Ras GTPase activating protein 1	438					dendrite development (GO:0016358)|negative regulation of axonogenesis (GO:0050771)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of Ras protein signal transduction (GO:0046580)|pattern specification process (GO:0007389)|positive regulation of Ras GTPase activity (GO:0032320)|Ras protein signal transduction (GO:0007265)|receptor clustering (GO:0043113)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of MAPK cascade (GO:0043408)|regulation of synapse structure and activity (GO:0050803)|regulation of synaptic plasticity (GO:0048167)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)	Rab GTPase activator activity (GO:0005097)|Ras GTPase activator activity (GO:0005099)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(15)|ovary(7)|pancreas(1)|stomach(1)|urinary_tract(1)	43						CTTGGAGCCCGCCCTGAATGT	0.512																																					p.A438T		Atlas-SNP	.											SYNGAP1_ENST00000293748,right_lower_lobe,carcinoma,0,2	SYNGAP1	202	2	0			c.G1312A						scavenged	.						160.0	155.0	157.0					6																	33405994		2203	4300	6503	SO:0001583	missense	8831	exon8			GAGCCCGCCCTGA	AB067525	CCDS34434.2	6p21.3	2010-06-25	2010-06-25		ENSG00000197283	ENSG00000197283			11497	protein-coding gene	gene with protein product		603384	"""synaptic Ras GTPase activating protein 1 homolog (rat)"""			9581761, 18323856	Standard	NM_006772		Approved	SYNGAP, RASA5, KIAA1938	uc011dri.2	Q96PV0	OTTHUMG00000031096	ENST00000418600.2:c.1312G>A	6.37:g.33405994G>A	ENSP00000403636:p.Ala438Thr	Somatic	276	2	0.00724638		WXS	Illumina HiSeq	Phase_I	285	149	0.522807	NM_006772	A2AB17|A2BEL6|A2BEL7|A8MQC4|Q8TCS2|Q9UGE2	Missense_Mutation	SNP	ENST00000418600.2	37	CCDS34434.2	.	.	.	.	.	.	.	.	.	.	G	14.39	2.522340	0.44866	.	.	ENSG00000197283	ENST00000293748;ENST00000418600;ENST00000449372;ENST00000428982	T;T;T	0.16457	2.34;2.43;2.43	4.86	3.99	0.46301	Rho GTPase activation protein (1);Ras GTPase-activating protein (1);	0.246616	0.33712	N	0.004627	T	0.03095	0.0091	N	0.14661	0.345	0.31709	N	0.639723	B;P;P;B	0.36660	0.428;0.564;0.564;0.026	B;B;B;B	0.19666	0.011;0.026;0.026;0.003	T	0.27502	-1.0072	10	0.72032	D	0.01	.	11.1118	0.48237	0.0904:0.0:0.9096:0.0	.	438;438;438;438	Q96PV0;Q96PV0-2;Q96PV0-4;B7ZCA0	SYGP1_HUMAN;.;.;.	T	438;438;438;379	ENSP00000293748:A438T;ENSP00000403636:A438T;ENSP00000412475:A379T	ENSP00000293748:A438T	A	+	1	0	SYNGAP1	33513972	0.968000	0.33430	0.858000	0.33744	0.950000	0.60333	1.961000	0.40432	1.255000	0.44051	0.650000	0.86243	GCC	.	.	none		0.512	SYNGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076151.4	XM_166407	
PER3	8863	hgsc.bcm.edu	37	1	7890024	7890024	+	Missense_Mutation	SNP	T	T	G	rs201662971|rs57875989		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:7890024T>G	ENST00000361923.2	+	18	3165	c.2990T>G	c.(2989-2991)aTg>aGg	p.M997R	RP3-467L1.4_ENST00000451646.1_RNA|PER3_ENST00000377532.3_Missense_Mutation_p.M1006R	NM_016831.1	NP_058515.1	P56645	PER3_HUMAN	period circadian clock 3	997	5 X 18 AA tandem repeats of S-[HP]-[AP]- T-[AT]-[GST]-[ATV]-L-S-[MT]-G-[LS]-P-P- [MRS]-[EKR]-[NST]-P.|Ser-rich.				circadian regulation of gene expression (GO:0032922)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of circadian sleep/wake cycle, sleep (GO:0045187)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	signal transducer activity (GO:0004871)	p.M997R(1)		breast(4)|central_nervous_system(3)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(9)|lung(8)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	39	Ovarian(185;0.0634)|all_lung(157;0.178)	all_epithelial(116;9.35e-21)|all_lung(118;7.57e-07)|Lung NSC(185;4.52e-06)|Renal(390;0.000147)|Breast(487;0.00086)|Colorectal(325;0.000959)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0234)|all cancers(8;8.58e-70)|GBM - Glioblastoma multiforme(8;1.81e-35)|Colorectal(212;2.06e-07)|COAD - Colon adenocarcinoma(227;1.92e-05)|Kidney(185;7.18e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000472)|STAD - Stomach adenocarcinoma(132;0.00118)|KIRC - Kidney renal clear cell carcinoma(229;0.00122)|READ - Rectum adenocarcinoma(331;0.0649)		TCGCCTCCCATGAAGAATCCA	0.582																																					p.M997R		Atlas-SNP	.											PER3,NS,carcinoma,0,3	PER3	95	3	1	Substitution - Missense(1)	central_nervous_system(1)	c.T2990G						PASS	.						85.0	70.0	75.0					1																	7890024		2001	3894	5895	SO:0001583	missense	8863	exon18			CTCCCATGAAGAA	BC026102	CCDS89.1, CCDS72695.1	1p36.23	2012-12-13	2012-12-13		ENSG00000049246	ENSG00000049246			8847	protein-coding gene	gene with protein product		603427	"""period (Drosophila) homolog 3"", ""period homolog 3 (Drosophila)"""			9427249	Standard	XM_005263520		Approved		uc001aoo.3	P56645	OTTHUMG00000001216	ENST00000361923.2:c.2990T>G	1.37:g.7890024T>G	ENSP00000355031:p.Met997Arg	Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	85	14	0.164706	NM_016831	Q5H8X4|Q5H8X5|Q969K6|Q96S77|Q96S78|Q9C0J3|Q9NSP9|Q9UGU8	Missense_Mutation	SNP	ENST00000361923.2	37	CCDS89.1	.	.	.	.	.	.	.	.	.	.	T	0.033	-1.321421	0.01320	.	.	ENSG00000049246	ENST00000377532;ENST00000361923	T;T	0.14640	2.49;2.49	.	.	.	Period circadian-like, C-terminal (1);	31.945600	0.01768	N	0.031022	T	0.04861	0.0131	N	0.04508	-0.205	0.09310	N	1	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.25152	-1.0140	8	0.11485	T	0.65	.	.	.	.	.	997;1006;1006;997	A2I2N5;A6H8X0;P56645-2;P56645	.;.;.;PER3_HUMAN	R	1006;997	ENSP00000366755:M1006R;ENSP00000355031:M997R	ENSP00000355031:M997R	M	+	2	0	PER3	7812611	0.004000	0.15560	0.012000	0.15200	0.013000	0.08279	-1.043000	0.03535	-1.402000	0.02056	-1.459000	0.01027	ATG	.	.	weak		0.582	PER3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000003607.1	NM_016831	
ZC3H4	23211	hgsc.bcm.edu	37	19	47571039	47571039	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:47571039G>A	ENST00000253048.5	-	15	2523	c.2486C>T	c.(2485-2487)tCc>tTc	p.S829F	ZC3H4_ENST00000594019.1_Intron	NM_015168.1	NP_055983.1	Q9UPT8	ZC3H4_HUMAN	zinc finger CCCH-type containing 4	829							metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(13)|ovary(4)|prostate(2)|skin(7)|upper_aerodigestive_tract(1)	41		all_cancers(25;3.3e-08)|all_epithelial(76;2.28e-06)|all_lung(116;7.86e-06)|Lung NSC(112;2.31e-05)|all_neural(266;0.026)|Ovarian(192;0.0392)|Breast(70;0.0889)		OV - Ovarian serous cystadenocarcinoma(262;5.76e-05)|all cancers(93;7.69e-05)|Epithelial(262;0.00354)|GBM - Glioblastoma multiforme(486;0.0372)		GGGTCGGCTGGACGTCTGCTG	0.622																																					p.S829F		Atlas-SNP	.											.	ZC3H4	96	.	0			c.C2486T						PASS	.						17.0	19.0	18.0					19																	47571039		2045	4167	6212	SO:0001583	missense	23211	exon15			CGGCTGGACGTCT	AB028987	CCDS42582.1	19q13.33	2012-07-05	2007-10-18	2007-10-18		ENSG00000130749		"""Zinc fingers, CCCH-type domain containing"""	17808	protein-coding gene	gene with protein product			"""chromosome 19 open reading frame 7"""	C19orf7			Standard	NM_015168		Approved	KIAA1064	uc002pga.4	Q9UPT8		ENST00000253048.5:c.2486C>T	19.37:g.47571039G>A	ENSP00000253048:p.Ser829Phe	Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	33	6	0.181818	NM_015168	Q9Y420	Missense_Mutation	SNP	ENST00000253048.5	37	CCDS42582.1	.	.	.	.	.	.	.	.	.	.	G	16.11	3.029641	0.54790	.	.	ENSG00000130749	ENST00000253048	T	0.19532	2.14	5.58	5.58	0.84498	.	0.329705	0.30201	N	0.010169	T	0.41650	0.1168	L	0.47716	1.5	0.51233	D	0.999918	D	0.71674	0.998	D	0.71870	0.975	T	0.12604	-1.0541	10	0.66056	D	0.02	.	18.3514	0.90339	0.0:0.0:1.0:0.0	.	829	Q9UPT8	ZC3H4_HUMAN	F	829	ENSP00000253048:S829F	ENSP00000253048:S829F	S	-	2	0	ZC3H4	52262879	1.000000	0.71417	0.103000	0.21229	0.293000	0.27360	5.684000	0.68197	2.642000	0.89623	0.655000	0.94253	TCC	.	.	none		0.622	ZC3H4-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466667.1		
SLCO1C1	53919	hgsc.bcm.edu	37	12	20876168	20876168	+	Missense_Mutation	SNP	C	C	T	rs144285413	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:20876168C>T	ENST00000266509.2	+	9	1534	c.1166C>T	c.(1165-1167)tCc>tTc	p.S389F	SLCO1C1_ENST00000545102.1_Missense_Mutation_p.S271F|SLCO1C1_ENST00000540354.1_Missense_Mutation_p.S340F|SLCO1C1_ENST00000545604.1_Missense_Mutation_p.S389F|SLCO1C1_ENST00000381552.1_Missense_Mutation_p.S389F	NM_017435.4	NP_059131.1	Q9NYB5	SO1C1_HUMAN	solute carrier organic anion transporter family, member 1C1	389					sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			NS(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(9)|liver(1)|lung(28)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	60	Esophageal squamous(101;0.149)				Conjugated Estrogens(DB00286)|Dextrothyroxine(DB00509)|Diclofenac(DB00586)|Digoxin(DB00390)|Dinoprostone(DB00917)|Estradiol(DB00783)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Liotrix(DB01583)|Meclofenamic acid(DB00939)|Methotrexate(DB00563)|Ouabain(DB01092)|Phenytoin(DB00252)|Probenecid(DB01032)	CAGTCATCCTCCAGGGCCAAC	0.443													C|||	20	0.00399361	0.0008	0.0058	5008	,	,		19476	0.0		0.0139	False		,,,				2504	0.001				p.S389F		Atlas-SNP	.											.	SLCO1C1	216	.	0			c.C1166T						PASS	.	C	PHE/SER,PHE/SER,PHE/SER,PHE/SER	8,4398	14.3+/-33.2	0,8,2195	159.0	138.0	145.0		812,1019,1166,1166	4.5	0.9	12	dbSNP_134	145	59,8541	35.9+/-90.5	0,59,4241	yes	missense,missense,missense,missense	SLCO1C1	NM_001145944.1,NM_001145945.1,NM_001145946.1,NM_017435.4	155,155,155,155	0,67,6436	TT,TC,CC		0.686,0.1816,0.5151	probably-damaging,probably-damaging,probably-damaging,probably-damaging	271/613,340/664,389/731,389/713	20876168	67,12939	2203	4300	6503	SO:0001583	missense	53919	exon9			CATCCTCCAGGGC	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.1166C>T	12.37:g.20876168C>T	ENSP00000266509:p.Ser389Phe	Somatic	296	0	0		WXS	Illumina HiSeq	Phase_I	213	111	0.521127	NM_017435	B7Z251|B7Z3Q3|B7Z8P1|F5GZD6|Q5JPA4	Missense_Mutation	SNP	ENST00000266509.2	37	CCDS8683.1	12	0.005494505494505495	0	0.0	1	0.0027624309392265192	0	0.0	11	0.014511873350923483	C	21.6	4.166506	0.78339	0.001816	0.00686	ENSG00000139155	ENST00000545604;ENST00000540354;ENST00000266509;ENST00000381552;ENST00000545102	T;T;T;T;T	0.49139	0.79;0.79;0.79;0.79;0.79	4.54	4.54	0.55810	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.85682	D	0.000000	T	0.69387	0.3105	M	0.92026	3.265	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.997;0.999;0.997;0.997	T	0.80690	-0.1270	10	0.87932	D	0	.	17.8397	0.88712	0.0:1.0:0.0:0.0	.	271;340;389;389	F5GZD6;B7Z3Q3;Q5JPA4;Q9NYB5	.;.;.;SO1C1_HUMAN	F	389;340;389;389;271	ENSP00000444149:S389F;ENSP00000438665:S340F;ENSP00000266509:S389F;ENSP00000370964:S389F;ENSP00000444527:S271F	ENSP00000266509:S389F	S	+	2	0	SLCO1C1	20767435	1.000000	0.71417	0.949000	0.38748	0.767000	0.43475	7.278000	0.78587	2.510000	0.84645	0.561000	0.74099	TCC	C|0.994;T|0.006	0.006	strong		0.443	SLCO1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401765.1	NM_017435	
TTN	7273	hgsc.bcm.edu	37	2	179643775	179643775	+	Missense_Mutation	SNP	C	C	T	rs36021856	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:179643775C>T	ENST00000591111.1	-	24	4258	c.4034G>A	c.(4033-4035)gGc>gAc	p.G1345D	TTN_ENST00000359218.5_Missense_Mutation_p.G1299D|RP11-88L24.4_ENST00000582038.2_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.G1345D|TTN_ENST00000460472.2_Missense_Mutation_p.G1299D|TTN_ENST00000589042.1_Missense_Mutation_p.G1345D|TTN_ENST00000342175.6_Missense_Mutation_p.G1299D|TTN_ENST00000360870.5_Missense_Mutation_p.G1345D			Q8WZ42	TITIN_HUMAN	titin	33541	Ig-like 5.		G -> D (in dbSNP:rs36021856). {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)			ACTAGCTCTGCCATCTTGTAG	0.398													C|||	19	0.00379393	0.0	0.0043	5008	,	,		21020	0.0		0.0159	False		,,,				2504	0.0				p.G1345D		Atlas-SNP	.											.	TTN	18412	.	0			c.G4034A						PASS	.	C	ASP/GLY,ASP/GLY,ASP/GLY,ASP/GLY,ASP/GLY	3,4403	6.2+/-15.9	0,3,2200	136.0	120.0	125.0		3896,4034,4034,3896,3896	5.7	1.0	2	dbSNP_126	125	63,8537	38.8+/-94.9	1,61,4238	yes	missense,missense,missense,missense,missense	TTN	NM_003319.4,NM_133378.4,NM_133379.3,NM_133432.3,NM_133437.3	94,94,94,94,94	1,64,6438	TT,TC,CC		0.7326,0.0681,0.5075	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	1299/26927,1345/33424,1345/5605,1299/27052,1299/27119	179643775	66,12940	2203	4300	6503	SO:0001583	missense	7273	exon24			GCTCTGCCATCTT	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.4034G>A	2.37:g.179643775C>T	ENSP00000465570:p.Gly1345Asp	Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	144	76	0.527778	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		17	0.007783882783882784	0	0.0	3	0.008287292817679558	0	0.0	14	0.018469656992084433	C	17.13	3.311645	0.60414	6.81E-4	0.007326	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127;ENST00000360870	T;T;T;T;T	0.66995	-0.24;-0.24;-0.24;-0.24;-0.24	5.72	5.72	0.89469	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.73194	0.3556	M	0.77616	2.38	0.49389	D	0.999784	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0	T	0.80845	-0.1200	9	0.87932	D	0	.	19.8946	0.96949	0.0:1.0:0.0:0.0	rs36021856	1299;1299;1299;1345;1345	D3DPF9;E7EQE6;E7ET18;Q8WZ42;Q8WZ42-6	.;.;.;TITIN_HUMAN;.	D	1345;1299;1299;1299;1299;1345	ENSP00000343764:G1345D;ENSP00000434586:G1299D;ENSP00000340554:G1299D;ENSP00000352154:G1299D;ENSP00000354117:G1345D	ENSP00000340554:G1299D	G	-	2	0	TTN	179352020	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.781000	0.85668	2.711000	0.92665	0.655000	0.94253	GGC	C|0.993;T|0.007	0.007	strong		0.398	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
SPATA22	84690	hgsc.bcm.edu	37	17	3352294	3352294	+	Missense_Mutation	SNP	A	A	G	rs1488689	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:3352294A>G	ENST00000573128.1	-	6	962	c.479T>C	c.(478-480)aTa>aCa	p.I160T	SPATA22_ENST00000575375.1_Missense_Mutation_p.I160T|SPATA22_ENST00000355380.4_Missense_Mutation_p.I117T|SPATA22_ENST00000541913.1_Missense_Mutation_p.I144T|SPATA22_ENST00000572969.1_Missense_Mutation_p.I160T|SPATA22_ENST00000268981.5_Missense_Mutation_p.I160T|SPATA22_ENST00000397168.3_Missense_Mutation_p.I160T			Q8NHS9	SPT22_HUMAN	spermatogenesis associated 22	160			I -> T (in dbSNP:rs1488689). {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						AGGTTCAGGTATTCTTAATTG	0.383													a|||	1337	0.266973	0.2209	0.3501	5008	,	,		15352	0.4187		0.1809	False		,,,				2504	0.2025				p.I160T		Atlas-SNP	.											.	SPATA22	49	.	0			c.T479C						PASS	.	A	THR/ILE,THR/ILE,THR/ILE,THR/ILE,THR/ILE,THR/ILE	1088,3318	393.5+/-328.9	136,816,1251	268.0	258.0	261.0		479,350,479,479,479,479	2.8	0.0	17	dbSNP_88	261	1586,7014	296.9+/-303.1	144,1298,2858	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	89,89,89,89,89,89	280,2114,4109	GG,GA,AA		18.4419,24.6936,20.5597	benign,benign,benign,benign,benign,benign	160/364,117/321,160/364,160/364,160/270,160/364	3352294	2674,10332	2203	4300	6503	SO:0001583	missense	84690	exon6			TCAGGTATTCTTA	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.479T>C	17.37:g.3352294A>G	ENSP00000459580:p.Ile160Thr	Somatic	321	1	0.00311526		WXS	Illumina HiSeq	Phase_I	247	128	0.518219	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	a	0.254	-1.004215	0.02112	0.246936	0.184419	ENSG00000141255	ENST00000355380;ENST00000397168;ENST00000268981;ENST00000541913	T;T;T;T	0.17370	2.28;2.3;2.31;2.29	3.87	2.79	0.32731	.	1.568880	0.03690	N	0.246975	T	0.00012	0.0000	N	0.12182	0.205	0.80722	P	0.0	B;B;B;B	0.13145	0.001;0.0;0.007;0.001	B;B;B;B	0.08055	0.003;0.002;0.003;0.003	T	0.44651	-0.9314	9	0.19590	T	0.45	-1.2633	6.7352	0.23405	0.8841:0.0:0.1159:0.0	rs1488689;rs17845887;rs17858862;rs61019090;rs1488689	144;160;117;160	F5GWB9;B4DXB1;Q8NHS9-2;Q8NHS9	.;.;.;SPT22_HUMAN	T	117;160;160;144	ENSP00000347541:I117T;ENSP00000380354:I160T;ENSP00000268981:I160T;ENSP00000441920:I144T	ENSP00000268981:I160T	I	-	2	0	SPATA22	3299044	0.025000	0.19082	0.003000	0.11579	0.010000	0.07245	0.736000	0.26130	0.851000	0.35264	0.454000	0.30748	ATA	A|0.769;G|0.231	0.231	strong		0.383	SPATA22-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438067.2	NM_032598	
DOCK1	1793	hgsc.bcm.edu	37	10	129216658	129216658	+	Silent	SNP	T	T	C	rs2229600	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:129216658T>C	ENST00000280333.6	+	45	4591	c.4482T>C	c.(4480-4482)atT>atC	p.I1494I		NM_001380.3	NP_001371.1	Q14185	DOCK1_HUMAN	dedicator of cytokinesis 1	1494	DHR-2.				apoptotic process (GO:0006915)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell migration (GO:0016477)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|hematopoietic progenitor cell differentiation (GO:0002244)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|phagocytosis, engulfment (GO:0006911)|positive regulation of GTPase activity (GO:0043547)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)			NS(2)|breast(1)|central_nervous_system(7)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(10)|lung(15)|ovary(4)|prostate(3)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	72		all_epithelial(44;2.3e-07)|all_lung(145;0.00466)|Lung NSC(174;0.00685)|Colorectal(57;0.0107)|Renal(717;0.0113)|Breast(234;0.0492)|all_neural(114;0.108)|all_hematologic(284;0.14)		BRCA - Breast invasive adenocarcinoma(275;0.0221)|Colorectal(40;0.115)		AGAATGCCATTGAGACCATGC	0.597													C|||	1597	0.31889	0.2247	0.4222	5008	,	,		15912	0.4296		0.2575	False		,,,				2504	0.3221				p.I1494I		Atlas-SNP	.											.	DOCK1	188	.	0			c.T4482C						PASS	.	C		1055,3329		158,739,1295	52.0	62.0	59.0		4437	-1.7	1.0	10	dbSNP_98	59	2232,6364		304,1624,2370	no	coding-synonymous	DOCK1	NM_001380.3		462,2363,3665	CC,CT,TT		25.9656,24.0648,25.3236		1479/1851	129216658	3287,9693	2192	4298	6490	SO:0001819	synonymous_variant	1793	exon45			TGCCATTGAGACC	D50857	CCDS73222.1	10q26.13-q26.3	2009-10-28			ENSG00000150760	ENSG00000150760			2987	protein-coding gene	gene with protein product	"""DOwnstream of CrK"""	601403	"""dedicator of cyto-kinesis 1"""			8657152, 8661160	Standard	XM_006717681		Approved	DOCK180, ced5	uc001ljt.3	Q14185	OTTHUMG00000019249	ENST00000280333.6:c.4482T>C	10.37:g.129216658T>C		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	56	27	0.482143	NM_001380	A9Z1Z5	Silent	SNP	ENST00000280333.6	37																																																																																				A|0.000;C|0.325;G|0.000;T|0.674	0.325	strong		0.597	DOCK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050979.2	NM_001380	
KRTAP10-3	386682	hgsc.bcm.edu	37	21	45978592	45978592	+	Missense_Mutation	SNP	T	T	C	rs452472	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:45978592T>C	ENST00000391620.1	-	1	51	c.7A>G	c.(7-9)Acg>Gcg	p.T3A	TSPEAR_ENST00000397916.1_Intron|TSPEAR_ENST00000323084.4_Intron	NM_198696.2	NP_941969.2	P60369	KR103_HUMAN	keratin associated protein 10-3	3			T -> A (in dbSNP:rs452472). {ECO:0000269|PubMed:15489334}.			keratin filament (GO:0045095)				kidney(1)|lung(4)|prostate(1)|skin(1)	7						ATGGTAGACGTGGCCATGCTG	0.642													.|||	1067	0.213059	0.1483	0.2594	5008	,	,		17698	0.1964		0.337	False		,,,				2504	0.1575				p.T3A		Atlas-SNP	.											KRTAP10-3,rectum,carcinoma,0,1	KRTAP10-3	17	1	0			c.A7G						PASS	.	T	,ALA/THR	730,3676	732.5+/-410.4	60,610,1533	59.0	59.0	59.0		,7	-3.7	0.0	21	dbSNP_80	59	2840,5760	661.1+/-401.8	475,1890,1935	no	intron,missense	TSPEAR,KRTAP10-3	NM_144991.2,NM_198696.2	,58	535,2500,3468	CC,CT,TT		33.0233,16.5683,27.4489	,benign	,3/222	45978592	3570,9436	2203	4300	6503	SO:0001583	missense	386682	exon1			TAGACGTGGCCAT	AJ566383	CCDS42956.1	21q22.3	2007-10-05			ENSG00000212935	ENSG00000212935		"""Keratin associated proteins"""	22968	protein-coding gene	gene with protein product				KRTAP18-3			Standard	NM_198696		Approved	KAP10.3, KAP18.3	uc002zfj.1	P60369	OTTHUMG00000057628	ENST00000391620.1:c.7A>G	21.37:g.45978592T>C	ENSP00000375478:p.Thr3Ala	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	116	48	0.413793	NM_198696	A3KN67|Q70LJ4	Missense_Mutation	SNP	ENST00000391620.1	37	CCDS42956.1	482	0.2206959706959707	65	0.13211382113821138	91	0.2513812154696133	102	0.17832167832167833	224	0.2955145118733509	c	0.001	-2.986087	0.00046	0.165683	0.330233	ENSG00000212935	ENST00000391620	T	0.02863	4.13	3.32	-3.69	0.04450	.	.	.	.	.	T	0.00012	0.0000	N	0.00128	-2.045	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.36720	-0.9736	8	0.02654	T	1	.	3.4126	0.07364	0.1224:0.5648:0.1215:0.1914	rs452472	3	P60369	KR103_HUMAN	A	3	ENSP00000375478:T3A	ENSP00000375478:T3A	T	-	1	0	KRTAP10-3	44803020	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.871000	0.04223	-1.132000	0.02907	-2.541000	0.00179	ACG	T|0.735;C|0.265	0.265	strong		0.642	KRTAP10-3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128031.1		
RPH3A	22895	hgsc.bcm.edu	37	12	113325629	113325629	+	Silent	SNP	T	T	C	rs4141253	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:113325629T>C	ENST00000389385.4	+	17	1961	c.1464T>C	c.(1462-1464)ttT>ttC	p.F488F	RPH3A_ENST00000549913.2_3'UTR|RPH3A_ENST00000551052.1_Silent_p.F484F|RPH3A_ENST00000548866.1_Silent_p.F439F|RPH3A_ENST00000447659.2_Silent_p.F439F|RPH3A_ENST00000420983.2_Silent_p.F488F|RPH3A_ENST00000543106.2_Silent_p.F488F|RPH3A_ENST00000415485.3_Silent_p.F488F	NM_001143854.1|NM_014954.3	NP_001137326.1|NP_055769.2	Q9Y2J0	RP3A_HUMAN	rabphilin 3A	488	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.				intracellular protein transport (GO:0006886)	cell junction (GO:0030054)|membrane (GO:0016020)|synaptic vesicle (GO:0008021)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|phosphatidylinositol phosphate binding (GO:1901981)|transporter activity (GO:0005215)			breast(1)|central_nervous_system(3)|cervix(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(16)|ovary(3)|prostate(4)|skin(6)|urinary_tract(1)	47				BRCA - Breast invasive adenocarcinoma(302;0.00453)		AGGACAAATTTGGCCACAATG	0.468													T|||	2612	0.521565	0.5446	0.5735	5008	,	,		19581	0.623		0.4165	False		,,,				2504	0.4571				p.F488F		Atlas-SNP	.											.	RPH3A	98	.	0			c.T1464C						PASS	.	T	,	2210,2196	591.0+/-387.5	558,1094,551	157.0	159.0	159.0		1464,1452	1.6	1.0	12	dbSNP_110	159	3390,5210	500.6+/-375.3	724,1942,1634	yes	coding-synonymous,coding-synonymous	RPH3A	NM_001143854.1,NM_014954.3	,	1282,3036,2185	CC,CT,TT		39.4186,49.8411,43.0571	,	488/695,484/691	113325629	5600,7406	2203	4300	6503	SO:0001819	synonymous_variant	22895	exon17			CAAATTTGGCCAC	AB023202	CCDS31904.1, CCDS44979.1	12q24.13	2014-07-02	2014-07-02		ENSG00000089169	ENSG00000089169		"""Synaptotagmins"""	17056	protein-coding gene	gene with protein product		612159	"""rabphilin 3A homolog (mouse)"""			10231032, 7822236	Standard	NM_014954		Approved	KIAA0985, rabphilin, exophilin-1	uc001ttz.3	Q9Y2J0	OTTHUMG00000169713	ENST00000389385.4:c.1464T>C	12.37:g.113325629T>C		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	68	35	0.514706	NM_001143854	B7Z3C3|Q96AE0	Silent	SNP	ENST00000389385.4	37	CCDS44979.1																																																																																			T|0.535;C|0.465	0.465	strong		0.468	RPH3A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000405561.1	NM_014954	
PPP6R1	22870	hgsc.bcm.edu	37	19	55756980	55756980	+	Silent	SNP	A	A	G	rs3745920	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:55756980A>G	ENST00000412770.2	-	3	860	c.294T>C	c.(292-294)gcT>gcC	p.A98A	PPP6R1_ENST00000587283.1_Silent_p.A98A	NM_014931.3	NP_055746.3	Q9UPN7	PP6R1_HUMAN	protein phosphatase 6, regulatory subunit 1	98	Interaction with PPP6C.				regulation of phosphoprotein phosphatase activity (GO:0043666)	cytoplasm (GO:0005737)	protein phosphatase binding (GO:0019903)			breast(1)	1						GGGACTCATCAGCACCCAGGG	0.622													A|||	1022	0.204073	0.0635	0.2738	5008	,	,		13837	0.1111		0.336	False		,,,				2504	0.3047				p.A98A		Atlas-SNP	.											PPP6R1_ENST00000412770,NS,carcinoma,0,2	PPP6R1	63	2	0			c.T294C						PASS	.	A		414,3694		24,366,1664	44.0	47.0	46.0		294	-10.3	0.0	19	dbSNP_107	46	2881,5509		503,1875,1817	no	coding-synonymous	PPP6R1	NM_014931.3		527,2241,3481	GG,GA,AA		34.3385,10.0779,26.3642		98/882	55756980	3295,9203	2054	4195	6249	SO:0001819	synonymous_variant	22870	exon3			CTCATCAGCACCC	AB029038	CCDS46186.1	19q13.42	2012-04-17	2010-06-28	2010-06-28	ENSG00000105063	ENSG00000105063		"""Serine/threonine phosphatases / Protein phosphatase 6, regulatory subunits"""	29195	protein-coding gene	gene with protein product		610875	"""KIAA1115"", ""SAPS domain family, member 1"""	KIAA1115, SAPS1		16769727	Standard	NM_014931		Approved	SAP190	uc002qjw.4	Q9UPN7		ENST00000412770.2:c.294T>C	19.37:g.55756980A>G		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	72	71	0.986111	NM_014931	Q2M2H3|Q504V2|Q6NVJ6|Q9BU97	Silent	SNP	ENST00000412770.2	37	CCDS46186.1																																																																																			A|0.789;G|0.211	0.211	strong		0.622	PPP6R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452663.1	NM_014931	
CES1	1066	hgsc.bcm.edu	37	16	55862720	55862720	+	Silent	SNP	T	T	C	rs74019278	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:55862720T>C	ENST00000361503.4	-	2	346	c.216A>G	c.(214-216)gaA>gaG	p.E72E	CES1_ENST00000360526.3_Silent_p.E73E|CES1_ENST00000422046.2_Silent_p.E72E|CES1_ENST00000566555.1_5'Flank			P23141	EST1_HUMAN	carboxylesterase 1	72					epithelial cell differentiation (GO:0030855)|metabolic process (GO:0008152)|response to toxic substance (GO:0009636)	endoplasmic reticulum (GO:0005783)	carboxylic ester hydrolase activity (GO:0052689)|methylumbelliferyl-acetate deacetylase activity (GO:0047374)								all cancers(182;0.13)|Epithelial(162;0.137)	Benzocaine(DB01086)|Capecitabine(DB01101)|Ciclesonide(DB01410)|Clopidogrel(DB00758)|Cyclandelate(DB04838)|Dabigatran etexilate(DB06695)|Indomethacin(DB00328)|Irinotecan(DB00762)|L-Carnitine(DB00583)|Mycophenolate mofetil(DB00688)|Oseltamivir(DB00198)|Probucol(DB01599)|Rufinamide(DB06201)|Tamoxifen(DB00675)|Trandolapril(DB00519)	AGCTCCATGGTTCTGCAGGCT	0.532																																					p.E73E	NSCLC(162;1801 2756 42904 52896)	Atlas-SNP	.											CES1_ENST00000360526,caecum,carcinoma,0,2	CES1	78	2	0			c.A219G						PASS	.						108.0	108.0	108.0					16																	55862720		2198	4300	6498	SO:0001819	synonymous_variant	1066	exon2			CCATGGTTCTGCA	BC012418	CCDS32450.1, CCDS45488.1, CCDS45489.1	16q22.2	2010-10-12	2010-10-12		ENSG00000198848	ENSG00000198848	3.1.1.1	"""Carboxylesterases"""	1863	protein-coding gene	gene with protein product	"""human monocyte/macrophage serine esterase 1"""	114835	"""carboxylesterase 1 (monocyte/macrophage serine esterase 1)"""			2070086, 20931200	Standard	XM_005255774		Approved	HMSE, CES2, HMSE1, SES1, CEH, CES1A1, CES1A2	uc002eil.3	P23141		ENST00000361503.4:c.216A>G	16.37:g.55862720T>C		Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	107	25	0.233645	NM_001025195	A6NIM1|A8K3K8|A8K844|E9PAU8|P82127|Q00015|Q13657|Q14062|Q16737|Q16788|Q549X7|Q549X8|Q86UK2|Q96EE8|Q9UC52|Q9UDG8|Q9UK77|Q9ULY2	Silent	SNP	ENST00000361503.4	37	CCDS45488.1																																																																																			T|0.634;C|0.366	0.366	strong		0.532	CES1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000433285.1	NM_001266	
PASK	23178	hgsc.bcm.edu	37	2	242063448	242063448	+	Silent	SNP	G	G	A	rs2302052	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:242063448G>A	ENST00000405260.1	-	11	3518	c.2820C>T	c.(2818-2820)gcC>gcT	p.A940A	PASK_ENST00000403638.3_Silent_p.A940A|PASK_ENST00000358649.4_Silent_p.A940A|PASK_ENST00000234040.4_Silent_p.A940A|PASK_ENST00000544142.1_Silent_p.A754A|PASK_ENST00000539818.1_Silent_p.A724A	NM_001252120.1	NP_001239049.1	Q96RG2	PASK_HUMAN	PAS domain containing serine/threonine kinase	940					negative regulation of glycogen biosynthetic process (GO:0045719)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of energy homeostasis (GO:2000505)|regulation of glucagon secretion (GO:0070092)|regulation of respiratory gaseous exchange (GO:0043576)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	ATP binding (GO:0005524)|phosphatidylinositol binding (GO:0035091)|protein serine/threonine kinase activity (GO:0004674)|signal transducer activity (GO:0004871)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(6)|lung(20)|ovary(4)|prostate(4)|skin(1)|stomach(1)|urinary_tract(2)	53		all_cancers(19;4.46e-39)|all_epithelial(40;1.34e-17)|Breast(86;1.53e-05)|Renal(207;0.00179)|all_lung(227;0.00481)|Lung NSC(271;0.017)|Ovarian(221;0.0228)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;1.34e-31)|all cancers(36;1e-28)|OV - Ovarian serous cystadenocarcinoma(60;3.53e-14)|Kidney(56;4.31e-09)|KIRC - Kidney renal clear cell carcinoma(57;4.35e-08)|BRCA - Breast invasive adenocarcinoma(100;5.64e-06)|Lung(119;0.000596)|LUSC - Lung squamous cell carcinoma(224;0.00481)|Colorectal(34;0.014)|COAD - Colon adenocarcinoma(134;0.0968)		GGGTCCTGGCGGCTGAGTCGC	0.632													G|||	474	0.0946486	0.1369	0.0951	5008	,	,		11317	0.131		0.0606	False		,,,				2504	0.0348				p.A940A		Atlas-SNP	.											.	PASK	230	.	0			c.C2820T						PASS	.	G		627,3779	269.2+/-268.9	51,525,1627	45.0	48.0	47.0		2820	0.3	0.0	2	dbSNP_100	47	566,8034	151.9+/-206.6	18,530,3752	no	coding-synonymous	PASK	NM_015148.2		69,1055,5379	AA,AG,GG		6.5814,14.2306,9.1727		940/1324	242063448	1193,11813	2203	4300	6503	SO:0001819	synonymous_variant	23178	exon11			CCTGGCGGCTGAG	U79240	CCDS2545.1, CCDS58758.1, CCDS58759.1	2q37.3	2008-05-23			ENSG00000115687	ENSG00000115687			17270	protein-coding gene	gene with protein product		607505				11688972, 11459942, 15148392	Standard	NM_001252119		Approved	PASKIN, KIAA0135, STK37	uc010fzl.2	Q96RG2	OTTHUMG00000133392	ENST00000405260.1:c.2820C>T	2.37:g.242063448G>A		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	72	25	0.347222	NM_015148	G5E9F1|Q05BE4|Q68DY3|Q6GSJ5|Q86XH6|Q99763|Q9UFR7	Silent	SNP	ENST00000405260.1	37	CCDS2545.1																																																																																			G|0.898;A|0.102	0.102	strong		0.632	PASK-003	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000323753.1	NM_015148	
MUC20	200958	hgsc.bcm.edu	37	3	195452689	195452689	+	Silent	SNP	C	C	T	rs141077164	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195452689C>T	ENST00000447234.2	+	2	1341	c.1215C>T	c.(1213-1215)gaC>gaT	p.D405D	MUC20_ENST00000436408.1_Silent_p.D405D|MUC20_ENST00000445522.2_Silent_p.D370D|MUC20_ENST00000320736.6_Silent_p.D234D	NM_001282506.1	NP_001269435.1	Q8N307	MUC20_HUMAN	mucin 20, cell surface associated	405					activation of MAPK activity (GO:0000187)|cellular protein metabolic process (GO:0044267)|hepatocyte growth factor receptor signaling pathway (GO:0048012)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein homooligomerization (GO:0051260)	basal plasma membrane (GO:0009925)|cell projection (GO:0042995)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)				NS(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(4)|skin(4)|stomach(3)|upper_aerodigestive_tract(1)	23	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)	Lung NSC(153;0.191)	Epithelial(36;1e-21)|all cancers(36;9.02e-20)|OV - Ovarian serous cystadenocarcinoma(49;1.6e-18)|Lung(62;0.000104)|LUSC - Lung squamous cell carcinoma(58;0.000128)	GBM - Glioblastoma multiforme(46;1.66e-05)		CGGGATCTGACGTCACTCTCC	0.582																																					p.D234D		Atlas-SNP	.											MUC20,NS,carcinoma,0,1	MUC20	84	1	0			c.C702T						scavenged	.						6.0	4.0	5.0					3																	195452689		1717	3830	5547	SO:0001819	synonymous_variant	200958	exon3			ATCTGACGTCACT	AB037780	CCDS63877.1	3q29	2008-08-07	2006-03-14		ENSG00000176945	ENSG00000176945		"""Mucins"""	23282	protein-coding gene	gene with protein product		610360				14565953	Standard	NM_001282506		Approved	FLJ14408, KIAA1359	uc010hzo.3	Q8N307	OTTHUMG00000155823	ENST00000447234.2:c.1215C>T	3.37:g.195452689C>T		Somatic	829	1	0.00120627		WXS	Illumina HiSeq	Phase_I	814	443	0.544226	NM_152673	Q6UX97|Q76I83|Q76I85|Q86ST8|Q8NBY6|Q96KA1|Q9P2I8	Silent	SNP	ENST00000447234.2	37																																																																																				T|1.000;|0.000	1.000	weak		0.582	MUC20-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000341835.1	NM_152673	
CAMKK2	10645	hgsc.bcm.edu	37	12	121691088	121691088	+	Silent	SNP	G	G	T	rs3815990	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:121691088G>T	ENST00000324774.5	-	10	1923	c.1095C>A	c.(1093-1095)atC>atA	p.I365I	CAMKK2_ENST00000337174.3_Silent_p.I365I|CAMKK2_ENST00000545538.1_Silent_p.I152I|CAMKK2_ENST00000535524.1_5'UTR|CAMKK2_ENST00000392473.2_Silent_p.I365I|CAMKK2_ENST00000404169.3_Silent_p.I365I|CAMKK2_ENST00000412367.2_Silent_p.I365I|CAMKK2_ENST00000538733.1_Silent_p.I365I|CAMKK2_ENST00000402834.4_Silent_p.I365I|CAMKK2_ENST00000392474.2_Silent_p.I365I|CAMKK2_ENST00000347034.2_Silent_p.I365I|CAMKK2_ENST00000446440.2_Silent_p.I365I	NM_006549.3	NP_006540.3	Q96RR4	KKCC2_HUMAN	calcium/calmodulin-dependent protein kinase kinase 2, beta	365	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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)					TCCCAGAGAAGATCTTGCGGG	0.572													G|||	308	0.0615016	0.003	0.0115	5008	,	,		20371	0.1071		0.0616	False		,,,				2504	0.1288				p.I365I		Atlas-SNP	.											.	CAMKK2	87	.	0			c.C1095A						PASS	.	G	,,,,,,	44,4362	47.5+/-82.1	1,42,2160	96.0	71.0	79.0		1095,1095,1095,1095,1095,1095,1095	3.5	1.0	12	dbSNP_107	79	451,8149	135.6+/-192.8	11,429,3860	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CAMKK2	NM_006549.3,NM_153499.2,NM_153500.1,NM_172214.2,NM_172215.2,NM_172216.1,NM_172226.2	,,,,,,	12,471,6020	TT,TG,GG		5.2442,0.9986,3.8059	,,,,,,	365/589,365/542,365/499,365/534,365/491,365/546,365/542	121691088	495,12511	2203	4300	6503	SO:0001819	synonymous_variant	10645	exon10			AGAGAAGATCTTG	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.1095C>A	12.37:g.121691088G>T		Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	174	97	0.557471	NM_153500	A8K7Q7|O94883|Q8IUG2|Q8IUG3|Q8N3I4|Q8WY03|Q8WY04|Q8WY05|Q8WY06|Q96RP1|Q96RP2|Q96RR3|Q9BWE9|Q9UER3|Q9UES2|Q9Y5N2	Silent	SNP	ENST00000324774.5	37	CCDS9216.1																																																																																			G|0.958;T|0.042	0.042	strong		0.572	CAMKK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000402563.1	NM_172226	
PRG4	10216	hgsc.bcm.edu	37	1	186276661	186276661	+	Missense_Mutation	SNP	A	A	G	rs61831150	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:186276661A>G	ENST00000445192.2	+	7	1855	c.1810A>G	c.(1810-1812)Act>Gct	p.T604A	PRG4_ENST00000367486.3_Missense_Mutation_p.T561A|PRG4_ENST00000367485.4_Missense_Mutation_p.T511A|PRG4_ENST00000367483.4_Missense_Mutation_p.T563A|PRG4_ENST00000367484.3_Intron	NM_005807.3	NP_005798.2	Q92954	PRG4_HUMAN	proteoglycan 4	604	59 X 8 AA repeats of K-X-P-X-P-T-T-X.			T -> A (in Ref. 1; AAB09089). {ECO:0000305}.	cell proliferation (GO:0008283)|hematopoietic stem cell proliferation (GO:0071425)|immune response (GO:0006955)|negative regulation of interleukin-6 biosynthetic process (GO:0045409)|regulation of cell proliferation (GO:0042127)	extracellular space (GO:0005615)	polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(33)|prostate(7)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(1)	102						TGCACCCACCACTCCCAAAGA	0.657													-|||	1149	0.229433	0.1415	0.4078	5008	,	,		8224	0.125		0.33	False		,,,				2504	0.226				p.T604A		Atlas-SNP	.											PRG4,brain,glioma,0,1	PRG4	259	1	0			c.A1810G						PASS	.	A	ALA/THR,ALA/THR,ALA/THR,ALA/THR	826,3580	322.6+/-297.7	75,676,1452	77.0	74.0	75.0		1810,1408,1531,1687	-7.0	0.0	1	dbSNP_129	75	3037,5563	461.6+/-365.5	537,1963,1800	no	missense,missense,missense,missense	PRG4	NM_005807.3,NM_001127710.1,NM_001127709.1,NM_001127708.1	58,58,58,58	612,2639,3252	GG,GA,AA		35.314,18.7472,29.7017	benign,benign,benign,benign	604/1405,470/1271,511/1312,563/1364	186276661	3863,9143	2203	4300	6503	SO:0001583	missense	10216	exon7			CCCACCACTCCCA	U70136	CCDS1369.1, CCDS44287.1, CCDS44288.1	1q25-q31	2008-07-18	2004-11-15		ENSG00000116690	ENSG00000116690			9364	protein-coding gene	gene with protein product	"""lubricin"", ""megakaryocyte stimulating factor"", ""articular superficial zone protein"", ""Jacobs camptodactyly-arthropathy-pericarditis syndrome"", ""camptodactyly, arthropathy, coxa vara, pericarditis syndrome"", ""bG174L6.2 (MSF: megakaryocyte stimulating factor )"""	604283	"""proteoglycan 4, (megakaryocyte stimulating factor, articular superficial zone protein, camptodactyly, arthropathy, coxa vara, pericarditis syndrome)"""	CACP		10545950, 9920774	Standard	NM_005807		Approved	JCAP, SZP, MSF, HAPO, bG174L6.2, FLJ32635	uc001gru.4	Q92954	OTTHUMG00000035574	ENST00000445192.2:c.1810A>G	1.37:g.186276661A>G	ENSP00000399679:p.Thr604Ala	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	54	50	0.925926	NM_005807	Q6DNC4|Q6DNC5|Q6ZMZ5|Q9BX49	Missense_Mutation	SNP	ENST00000445192.2	37	CCDS1369.1	533	0.24404761904761904	57	0.11585365853658537	143	0.39502762430939226	73	0.12762237762237763	260	0.34300791556728233	A	6.871	0.530050	0.13127	0.187472	0.35314	ENSG00000116690	ENST00000367486;ENST00000367482;ENST00000367483;ENST00000367485;ENST00000445192	T;T;T;T	0.05996	3.36;3.45;3.39;3.46	3.74	-6.98	0.01611	.	0.224316	0.21263	U	0.077456	T	0.00012	0.0000	L	0.55990	1.75	0.80722	P	0.0	B;B;B;B	0.17268	0.021;0.021;0.012;0.021	B;B;B;B	0.11329	0.006;0.006;0.003;0.006	T	0.46596	-0.9180	8	.	.	.	.	2.0325	0.03532	0.2526:0.1179:0.3962:0.2333	rs61831150	470;511;604;563	Q92954-4;Q92954-3;Q92954;Q92954-2	.;.;PRG4_HUMAN;.	A	561;470;563;511;604	ENSP00000356456:T561A;ENSP00000356453:T563A;ENSP00000356455:T511A;ENSP00000399679:T604A	.	T	+	1	0	PRG4	184543284	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.345000	0.19979	-1.252000	0.02491	-0.486000	0.04755	ACT	A|0.713;G|0.287	0.287	strong		0.657	PRG4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000086346.1	NM_005807	
RANBP3	8498	hgsc.bcm.edu	37	19	5915300	5915300	+	IGR	SNP	C	C	A	rs147363394	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:5915300C>A	ENST00000340578.6	-	0	3233				AC104532.4_ENST00000591109.1_RNA|CAPS_ENST00000452990.2_Missense_Mutation_p.F152L|CAPS_ENST00000222125.5_Missense_Mutation_p.F179L|CAPS_ENST00000588776.1_Missense_Mutation_p.F265L	NM_003624.2|NM_007320.2|NM_007322.2	NP_003615.2|NP_015559.2|NP_015561.1	Q9H6Z4	RANB3_HUMAN	RAN binding protein 3						intracellular transport (GO:0046907)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	R-SMAD binding (GO:0070412)|Ran GTPase binding (GO:0008536)			breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|ovary(3)|upper_aerodigestive_tract(1)	18						ATGAGGAGTTCGTGGCCATGA	0.657													C|||	5	0.000998403	0.0	0.0043	5008	,	,		16061	0.0		0.002	False		,,,				2504	0.0				p.F179L		Atlas-SNP	.											.	CAPS	14	.	0			c.C537A						PASS	.	C	LEU/PHE,LEU/PHE	1,4401	2.1+/-5.4	0,1,2200	74.0	59.0	64.0		537,456	-10.0	0.5	19	dbSNP_134	64	11,8589	7.7+/-29.5	0,11,4289	yes	missense,missense	CAPS	NM_004058.3,NM_080590.2	22,22	0,12,6489	AA,AC,CC		0.1279,0.0227,0.0923	probably-damaging,probably-damaging	179/190,152/163	5915300	12,12990	2201	4300	6501	SO:0001628	intergenic_variant	828	exon5			GGAGTTCGTGGCC	Y08698	CCDS42477.1, CCDS42478.1, CCDS45935.1, CCDS74268.1	19p13.3	2008-02-05							9850	protein-coding gene	gene with protein product		603327				9637251	Standard	NM_007322		Approved		uc002mdw.3	Q9H6Z4			19.37:g.5915300C>A		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	111	57	0.513514	NM_004058	B2RAT8|O60405|O75759|O75760|Q9BT47|Q9UG74	Missense_Mutation	SNP	ENST00000340578.6	37	CCDS42478.1	3	0.0013736263736263737	0	0.0	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	C	22.2	4.252906	0.80135	2.27E-4	0.001279	ENSG00000105519	ENST00000394521;ENST00000222125;ENST00000452990	T;T	0.69175	-0.25;-0.38	5.3	-10.0	0.00425	EF-hand-like domain (1);	0.000000	0.64402	D	0.000007	T	0.80374	0.4611	M	0.90425	3.115	0.34295	D	0.683746	D;D	0.89917	1.0;1.0	D;D	0.97110	0.992;1.0	D	0.88488	0.3073	10	0.87932	D	0	-13.7929	17.3435	0.87304	0.0:0.6317:0.0:0.3683	.	312;179	Q8NF12;Q13938	.;CAYP1_HUMAN	L	312;179;152	ENSP00000222125:F179L;ENSP00000403263:F152L	ENSP00000222125:F179L	F	+	3	2	CAPS	5866300	0.002000	0.14202	0.526000	0.27913	0.946000	0.59487	-2.224000	0.01213	-2.213000	0.00735	-1.036000	0.02392	TTC	C|0.999;A|0.001	0.001	strong		0.657	RANBP3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000452304.1	NM_007322	
LILRB2	10288	hgsc.bcm.edu	37	19	54783836	54783836	+	Silent	SNP	G	G	A	rs111453734	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:54783836G>A	ENST00000391749.4	-	4	436	c.165C>T	c.(163-165)gcC>gcT	p.A55A	LILRB2_ENST00000434421.1_Intron|LILRB2_ENST00000314446.5_Silent_p.A55A|MIR4752_ENST00000579672.1_RNA|LILRB2_ENST00000391746.1_Silent_p.A55A|LILRB2_ENST00000471216.1_5'UTR|LILRB2_ENST00000391748.1_Silent_p.A55A	NM_001278406.1	NP_001265335.1	Q8N423	LIRB2_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 2	55	Ig-like C2-type 1.				cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|cellular defense response (GO:0006968)|cellular response to lipopolysaccharide (GO:0071222)|Fc receptor mediated inhibitory signaling pathway (GO:0002774)|heterotypic cell-cell adhesion (GO:0034113)|immune response (GO:0006955)|immune response-inhibiting cell surface receptor signaling pathway (GO:0002767)|negative regulation of antigen processing and presentation (GO:0002578)|negative regulation of calcium ion transport (GO:0051926)|negative regulation of T cell proliferation (GO:0042130)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of regulatory T cell differentiation (GO:0045591)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of T cell tolerance induction (GO:0002666)|regulation of dendritic cell differentiation (GO:2001198)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cell adhesion molecule binding (GO:0050839)|inhibitory MHC class I receptor activity (GO:0032396)|MHC class I protein binding (GO:0042288)|MHC class Ib protein binding (GO:0023029)|protein phosphatase 1 binding (GO:0008157)|receptor activity (GO:0004872)			breast(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(30)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	44	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		GGTACTCCTGGGCTTCAAGGC	0.547													.|||	8	0.00159744	0.0008	0.0072	5008	,	,		19344	0.0		0.002	False		,,,				2504	0.0				p.A55A		Atlas-SNP	.											.	LILRB2	94	.	0			c.C165T						PASS	.	G	,	6,4400	9.9+/-24.2	0,6,2197	173.0	172.0	172.0		165,165	-4.8	0.0	19	dbSNP_132	172	26,8574	17.9+/-57.8	0,26,4274	no	coding-synonymous,coding-synonymous	LILRB2	NM_001080978.2,NM_005874.3	,	0,32,6471	AA,AG,GG		0.3023,0.1362,0.246	,	55/598,55/599	54783836	32,12974	2203	4300	6503	SO:0001819	synonymous_variant	10288	exon4			CTCCTGGGCTTCA	AF000574	CCDS12886.1, CCDS42612.1, CCDS62791.1, CCDS62792.1	19q13.4	2013-01-11			ENSG00000131042	ENSG00000131042		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6606	protein-coding gene	gene with protein product		604815				9151699, 9079806	Standard	XM_006722966		Approved	LIR-2, ILT4, MIR-10, LIR2, CD85d, MIR10	uc002qfb.3	Q8N423	OTTHUMG00000064896	ENST00000391749.4:c.165C>T	19.37:g.54783836G>A		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	84	49	0.583333	NM_005874	A8MU67|C9JF29|O75017|Q8NHJ7|Q8NHJ8	Silent	SNP	ENST00000391749.4	37	CCDS12886.1																																																																																			G|0.997;A|0.003	0.003	strong		0.547	LILRB2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139510.1		
MFF	56947	hgsc.bcm.edu	37	2	228197238	228197238	+	Silent	SNP	G	G	A	rs11557342	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:228197238G>A	ENST00000353339.3	+	5	804	c.363G>A	c.(361-363)acG>acA	p.T121T	MFF_ENST00000337110.7_Silent_p.T95T|MFF_ENST00000409616.1_Silent_p.T95T|MFF_ENST00000349901.7_Silent_p.T95T|MFF_ENST00000476924.1_3'UTR|MFF_ENST00000304593.9_Silent_p.T95T|MFF_ENST00000354503.6_Silent_p.T95T|MFF_ENST00000409565.1_Silent_p.T95T|MFF_ENST00000392059.1_Silent_p.T121T|MFF_ENST00000524634.1_De_novo_Start_InFrame	NM_001277061.1	NP_001263990.1	Q9GZY8	MFF_HUMAN	mitochondrial fission factor	121					mitochondrial fission (GO:0000266)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|mitochondrial fusion (GO:0008053)|mitochondrion morphogenesis (GO:0070584)|peroxisome fission (GO:0016559)|positive regulation of mitochondrial fission (GO:0090141)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|protein homooligomerization (GO:0051260)|protein targeting to mitochondrion (GO:0006626)|regulation of mitochondrion organization (GO:0010821)|regulation of peroxisome organization (GO:1900063)|release of cytochrome c from mitochondria (GO:0001836)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|integral component of mitochondrial membrane (GO:0032592)|mitochondrial outer membrane (GO:0005741)|peroxisome (GO:0005777)|synapse (GO:0045202)	protein homodimerization activity (GO:0042803)	p.T121T(1)		breast(3)|endometrium(2)|kidney(3)|large_intestine(7)|lung(4)|stomach(2)	21						GTGTACTTACGCTGAGTGAAA	0.393													G|||	446	0.0890575	0.0741	0.1081	5008	,	,		17428	0.1022		0.0716	False		,,,				2504	0.1002				p.T121T		Atlas-SNP	.											MFF,NS,carcinoma,0,1	MFF	48	1	1	Substitution - coding silent(1)	stomach(1)	c.G363A						PASS	.	G		328,4078	171.6+/-201.8	4,320,1879	259.0	254.0	256.0		363	-10.2	0.5	2	dbSNP_120	256	749,7851	179.6+/-228.7	30,689,3581	no	coding-synonymous	MFF	NM_020194.4		34,1009,5460	AA,AG,GG		8.7093,7.4444,8.2808		121/343	228197238	1077,11929	2203	4300	6503	SO:0001819	synonymous_variant	56947	exon5			ACTTACGCTGAGT	AF258660	CCDS2465.1, CCDS63139.1, CCDS63140.1, CCDS63141.1, CCDS63142.1, CCDS74662.1	2q36	2008-05-29	2008-05-29	2008-05-29	ENSG00000168958	ENSG00000168958			24858	protein-coding gene	gene with protein product		614785	"""chromosome 2 open reading frame 33"""	C2orf33		18353969	Standard	NM_001277061		Approved	GL004	uc002voy.4	Q9GZY8	OTTHUMG00000133180	ENST00000353339.3:c.363G>A	2.37:g.228197238G>A		Somatic	243	0	0		WXS	Illumina HiSeq	Phase_I	211	91	0.43128	NM_020194	Q567U1|Q658R6|Q9BVZ1|Q9H690|Q9NRG8	Silent	SNP	ENST00000353339.3	37	CCDS2465.1																																																																																			G|0.922;A|0.078	0.078	strong		0.393	MFF-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256887.2	NM_020194	
PLA2G7	7941	hgsc.bcm.edu	37	6	46672943	46672943	+	Missense_Mutation	SNP	A	A	G	rs1051931	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	119	1	0.00840336		WXS	Illumina HiSeq	Phase_I	87	85	0.977012	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		
PDE1C	5137	hgsc.bcm.edu	37	7	31855569	31855569	+	Silent	SNP	G	G	A	rs2302450	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:31855569G>A	ENST00000396191.1	-	15	2237	c.1782C>T	c.(1780-1782)gcC>gcT	p.A594A	PDE1C_ENST00000321453.7_Silent_p.A594A|PDE1C_ENST00000396193.1_Silent_p.A654A|PDE1C_ENST00000396184.3_Silent_p.A594A|PDE1C_ENST00000479980.1_5'UTR|PDE1C_ENST00000396182.2_Silent_p.A594A	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	269	0	0		WXS	Illumina HiSeq	Phase_I	209	156	0.746412	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		
WNT9A	7483	hgsc.bcm.edu	37	1	228113046	228113046	+	Silent	SNP	C	C	T	rs8192629	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:228113046C>T	ENST00000272164.5	-	2	280	c.270G>A	c.(268-270)gcG>gcA	p.A90A		NM_003395.2	NP_003386.1	O14904	WNT9A_HUMAN	wingless-type MMTV integration site family, member 9A	90					canonical Wnt signaling pathway (GO:0060070)|cell fate commitment (GO:0045165)|cell-cell signaling (GO:0007267)|cellular response to retinoic acid (GO:0071300)|cornea development in camera-type eye (GO:0061303)|embryonic forelimb morphogenesis (GO:0035115)|embryonic skeletal joint development (GO:0072498)|embryonic skeletal system morphogenesis (GO:0048704)|iris morphogenesis (GO:0061072)|mitotic cell cycle checkpoint (GO:0007093)|multicellular organismal development (GO:0007275)|negative regulation of cartilage development (GO:0061037)|negative regulation of cell death (GO:0060548)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|neuron differentiation (GO:0030182)|positive regulation of cell differentiation (GO:0045597)|positive regulation of smoothened signaling pathway (GO:0045880)|Wnt signaling pathway (GO:0016055)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	frizzled binding (GO:0005109)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(5)|ovary(2)|pancreas(1)|prostate(2)|skin(1)	19		Prostate(94;0.0405)				GGCACTCGAGCGCACTCATGC	0.697													C|||	414	0.0826677	0.0613	0.0576	5008	,	,		15553	0.0992		0.0696	False		,,,				2504	0.1258				p.A90A		Atlas-SNP	.											.	WNT9A	39	.	0			c.G270A						PASS	.	C		281,4117		5,271,1923	18.0	18.0	18.0		270	-10.2	0.0	1	dbSNP_117	18	803,7789		36,731,3529	no	coding-synonymous	WNT9A	NM_003395.2		41,1002,5452	TT,TC,CC		9.3459,6.3893,8.3449		90/366	228113046	1084,11906	2199	4296	6495	SO:0001819	synonymous_variant	7483	exon2			CTCGAGCGCACTC	AB060283	CCDS31045.1	1q42	2008-02-05	2003-03-11	2003-03-14	ENSG00000143816	ENSG00000143816		"""Wingless-type MMTV integration sites"""	12778	protein-coding gene	gene with protein product		602863	"""wingless-type MMTV integration site family, member 14"""	WNT14		9441749	Standard	NM_003395		Approved		uc001hri.2	O14904	OTTHUMG00000037592	ENST00000272164.5:c.270G>A	1.37:g.228113046C>T		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	124	60	0.483871	NM_003395	A6NLW2|Q2M2J3|Q5VWU0|Q96S50	Silent	SNP	ENST00000272164.5	37	CCDS31045.1																																																																																			C|0.927;T|0.073	0.073	strong		0.697	WNT9A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091646.1	NM_003395	
DDX11	1663	hgsc.bcm.edu	37	12	31244716	31244716	+	Silent	SNP	C	C	T	rs35588475	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:31244716C>T	ENST00000407793.2	+	10	1404	c.1153C>T	c.(1153-1155)Ctg>Ttg	p.L385L	DDX11_ENST00000350437.4_Silent_p.L385L|DDX11_ENST00000228264.6_Silent_p.L359L|DDX11_ENST00000545668.1_Silent_p.L385L|DDX11_ENST00000542838.1_Silent_p.L385L|DDX11_ENST00000251758.5_3'UTR	NM_030653.3|NM_152438.1	NP_085911.2|NP_689651.1	Q96FC9	DDX11_HUMAN	DEAD/H (Asp-Glu-Ala-Asp/His) box helicase 11	385	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|ATP catabolic process (GO:0006200)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|sister chromatid cohesion (GO:0007062)|viral process (GO:0016032)	midbody (GO:0030496)|nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle pole (GO:0000922)	4 iron, 4 sulfur cluster binding (GO:0051539)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA-dependent ATPase activity (GO:0008094)|double-stranded DNA binding (GO:0003690)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(11)|large_intestine(5)|lung(23)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	57	all_cancers(9;1.77e-11)|all_lung(12;6.21e-11)|all_epithelial(9;6.49e-11)|Lung NSC(12;1.06e-08)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Lung SC(12;0.0592)|Esophageal squamous(101;0.233)					GGGCATCCGGCTGCAGGACCA	0.677										Multiple Myeloma(12;0.14)																											p.L385L		Atlas-SNP	.											.	DDX11	188	.	0			c.C1153T						PASS	.						43.0	42.0	42.0					12																	31244716		2203	4298	6501	SO:0001819	synonymous_variant	1663	exon10			ATCCGGCTGCAGG	U75969	CCDS8721.1, CCDS41767.1, CCDS44856.1, CCDS58224.1	12p11.21	2012-02-23	2012-02-23		ENSG00000013573	ENSG00000013573		"""DEAD-boxes"""	2736	protein-coding gene	gene with protein product	"""CHL1-like helicase homolog (S. cerevisiae)"""	601150	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 11 (S.cerevisiae CHL1-like helicase)"", ""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 11"""				Standard	NM_030653		Approved	CHLR1, KRG2, CHL1, ChlR1, WABS	uc001rjv.2	Q96FC9	OTTHUMG00000168435	ENST00000407793.2:c.1153C>T	12.37:g.31244716C>T		Somatic	454	0	0		WXS	Illumina HiSeq	Phase_I	414	126	0.304348	NM_030653	Q13333|Q86VQ4|Q86W62|Q92498|Q92770|Q92998|Q92999	Silent	SNP	ENST00000407793.2	37	CCDS44856.1																																																																																			T|1.000;|0.000	1.000	weak		0.677	DDX11-202	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000399728.1	NM_030653	
HHLA2	11148	hgsc.bcm.edu	37	3	108081247	108081247	+	Silent	SNP	G	G	A	rs16854512	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:108081247G>A	ENST00000357759.5	+	7	1476	c.1062G>A	c.(1060-1062)gcG>gcA	p.A354A	HHLA2_ENST00000491820.1_Silent_p.A354A|HHLA2_ENST00000467562.1_Silent_p.A290A|HHLA2_ENST00000489514.2_Silent_p.A354A|HHLA2_ENST00000467761.1_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	80	0	0		WXS	Illumina HiSeq	Phase_I	58	27	0.465517	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	
BCAS3	54828	hgsc.bcm.edu	37	17	58952044	58952044	+	Silent	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:58952044G>A	ENST00000390652.5	+	9	637	c.606G>A	c.(604-606)caG>caA	p.Q202Q	BCAS3_ENST00000407086.3_Silent_p.Q202Q|BCAS3_ENST00000408905.3_Silent_p.Q202Q|BCAS3_ENST00000589222.1_Silent_p.Q202Q|BCAS3_ENST00000588462.1_Silent_p.Q202Q	NM_001099432.1	NP_001092902.1			breast carcinoma amplified sequence 3											NS(1)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(24)|ovary(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	44			BRCA - Breast invasive adenocarcinoma(1;3.11e-12)|Epithelial(12;8.2e-07)|all cancers(12;5.33e-06)			TAGTCTTGCAGGAGAAAATTG	0.328																																					p.Q202Q		Atlas-SNP	.											.	BCAS3	90	.	0			c.G606A						PASS	.						110.0	101.0	104.0					17																	58952044		1820	4081	5901	SO:0001819	synonymous_variant	54828	exon9			CTTGCAGGAGAAA	AF361219	CCDS11626.1, CCDS45749.1	17q23.2	2013-06-25			ENSG00000141376	ENSG00000141376		"""WD repeat domain containing"""	14347	protein-coding gene	gene with protein product		607470				12378525	Standard	NM_017679		Approved	FLJ20128	uc002iyv.4	Q9H6U6	OTTHUMG00000180064	ENST00000390652.5:c.606G>A	17.37:g.58952044G>A		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	49	25	0.510204	NM_001099432		Silent	SNP	ENST00000390652.5	37	CCDS45749.1																																																																																			.	.	none		0.328	BCAS3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000449578.1	NM_017679	
AGRN	375790	hgsc.bcm.edu	37	1	986732	986732	+	Missense_Mutation	SNP	G	G	A	rs144245019	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:986732G>A	ENST00000379370.2	+	31	5403	c.5353G>A	c.(5353-5355)Gac>Aac	p.D1785N		NM_198576.3	NP_940978.2	O00468	AGRIN_HUMAN	agrin	1789	Laminin G-like 2. {ECO:0000255|PROSITE- ProRule:PRU00122}.				axon guidance (GO:0007411)|carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|clustering of voltage-gated sodium channels (GO:0045162)|extracellular matrix organization (GO:0030198)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|neuromuscular junction development (GO:0007528)|neurotransmitter receptor metabolic process (GO:0045213)|phototransduction, visible light (GO:0007603)|plasma membrane organization (GO:0007009)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of synaptic growth at neuromuscular junction (GO:0045887)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|receptor clustering (GO:0043113)|retinoid metabolic process (GO:0001523)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synapse organization (GO:0050808)	basal lamina (GO:0005605)|cell junction (GO:0030054)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)|synapse (GO:0045202)	acetylcholine receptor regulator activity (GO:0030548)|calcium ion binding (GO:0005509)|chondroitin sulfate binding (GO:0035374)|dystroglycan binding (GO:0002162)|heparan sulfate proteoglycan binding (GO:0043395)|laminin binding (GO:0043236)|sialic acid binding (GO:0033691)|structural constituent of cytoskeleton (GO:0005200)			breast(1)|central_nervous_system(2)|endometrium(8)|kidney(3)|large_intestine(2)|lung(20)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	42	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		UCEC - Uterine corpus endometrioid carcinoma (11;0.00462)|Epithelial(90;5.98e-38)|OV - Ovarian serous cystadenocarcinoma(86;5.43e-23)|Colorectal(212;5.97e-05)|COAD - Colon adenocarcinoma(227;0.000201)|Kidney(185;0.0024)|BRCA - Breast invasive adenocarcinoma(365;0.00246)|STAD - Stomach adenocarcinoma(132;0.00645)|KIRC - Kidney renal clear cell carcinoma(229;0.0354)|Lung(427;0.201)		CTCTGGCTTCGACGGTGCCAT	0.711													G|||	9	0.00179712	0.0008	0.0058	5008	,	,		10485	0.0		0.002	False		,,,				2504	0.002				p.D1785N		Atlas-SNP	.											.	AGRN	110	.	0			c.G5353A						PASS	.	G	ASN/ASP	10,4338		0,10,2164	14.0	14.0	14.0		5353	-2.1	0.0	1	dbSNP_134	14	99,8417		0,99,4159	yes	missense	AGRN	NM_198576.3	23	0,109,6323	AA,AG,GG		1.1625,0.23,0.8473	possibly-damaging	1785/2046	986732	109,12755	2174	4258	6432	SO:0001583	missense	375790	exon31			GGCTTCGACGGTG	XM_372195	CCDS30551.1	1p36.33	2014-09-17		2007-02-16	ENSG00000188157	ENSG00000188157		"""Proteoglycans / Extracellular Matrix : Other"""	329	protein-coding gene	gene with protein product	"""agrin proteoglycan"""	103320				1851019, 12270958	Standard	NM_198576		Approved	AGRIN	uc001ack.2	O00468	OTTHUMG00000040778	ENST00000379370.2:c.5353G>A	1.37:g.986732G>A	ENSP00000368678:p.Asp1785Asn	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	74	56	0.756757	NM_198576	Q5SVA1|Q5SVA2|Q60FE1|Q7KYS8|Q8N4J5|Q96IC1|Q9BTD4	Missense_Mutation	SNP	ENST00000379370.2	37	CCDS30551.1	9|9	0.004120879120879121|0.004120879120879121	0|0	0.0|0.0	4|4	0.011049723756906077|0.011049723756906077	0|0	0.0|0.0	5|5	0.006596306068601583|0.006596306068601583	g|g	6.846|6.846	0.525419|0.525419	0.13066|0.13066	0.0023|0.0023	0.011625|0.011625	ENSG00000188157|ENSG00000188157	ENST00000379370;ENST00000379364|ENST00000419249	T|.	0.76316|.	-1.01|.	5.06|5.06	-2.07|-2.07	0.07276|0.07276	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 1 (1);|.	0.530450|.	0.17293|.	N|.	0.179547|.	T|T	0.10937|0.10937	0.0267|0.0267	N|N	0.11427|0.11427	0.14|0.14	0.09310|0.09310	N|N	1|1	B|.	0.09022|.	0.002|.	B|.	0.04013|.	0.001|.	T|T	0.26883|0.26883	-1.0090|-1.0090	10|5	0.16896|.	T|.	0.51|.	-10.2792|-10.2792	4.5587|4.5587	0.12149|0.12149	0.2551:0.0972:0.5487:0.099|0.2551:0.0972:0.5487:0.099	.|.	1785|.	O00468|.	AGRIN_HUMAN|.	N|Q	1785;128|87	ENSP00000368678:D1785N|.	ENSP00000368671:D128N|.	D|R	+|+	1|2	0|0	AGRN|AGRN	976595|976595	0.001000|0.001000	0.12720|0.12720	0.000000|0.000000	0.03702|0.03702	0.001000|0.001000	0.01503|0.01503	0.308000|0.308000	0.19314|0.19314	-0.235000|-0.235000	0.09767|0.09767	-1.333000|-1.333000	0.01266|0.01266	GAC|CGA	G|0.993;A|0.007	0.007	strong		0.711	AGRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097990.2	NM_198576	
CASZ1	54897	hgsc.bcm.edu	37	1	10703243	10703243	+	Missense_Mutation	SNP	T	T	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:10703243T>A	ENST00000377022.3	-	19	4311	c.3994A>T	c.(3994-3996)Aac>Tac	p.N1332Y	RP4-734G22.3_ENST00000606802.1_RNA	NM_001079843.2	NP_001073312.1	Q86V15	CASZ1_HUMAN	castor zinc finger 1	1332					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)		CGGTCGAAGTTCTTCCCCAGC	0.662																																					p.N1332Y		Atlas-SNP	.											.	CASZ1	150	.	0			c.A3994T						PASS	.						52.0	60.0	57.0					1																	10703243		2085	4210	6295	SO:0001583	missense	54897	exon19			CGAAGTTCTTCCC	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.3994A>T	1.37:g.10703243T>A	ENSP00000366221:p.Asn1332Tyr	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	51	16	0.313726	NM_001079843	Q078S9|Q2EN02|Q5T9S1|Q6ZNM8|Q8WX49|Q8WX50|Q9BT16|Q9NXC6	Missense_Mutation	SNP	ENST00000377022.3	37	CCDS41246.1	.	.	.	.	.	.	.	.	.	.	T	25.7	4.666405	0.88251	.	.	ENSG00000130940	ENST00000377022	.	.	.	4.77	4.77	0.60923	.	0.000000	0.49305	U	0.000149	T	0.68705	0.3030	L	0.43152	1.355	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.71523	-0.4567	9	0.62326	D	0.03	-26.2009	14.3215	0.66489	0.0:0.0:0.0:1.0	.	1332	Q86V15	CASZ1_HUMAN	Y	1332	.	ENSP00000366221:N1332Y	N	-	1	0	CASZ1	10625830	1.000000	0.71417	1.000000	0.80357	0.942000	0.58702	7.530000	0.81962	1.783000	0.52377	0.459000	0.35465	AAC	.	.	none		0.662	CASZ1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005673.2	NM_017766	
KRTAP10-2	386679	hgsc.bcm.edu	37	21	45971299	45971299	+	Missense_Mutation	SNP	T	T	C	rs233240	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:45971299T>C	ENST00000391621.1	-	1	89	c.43A>G	c.(43-45)Aac>Gac	p.N15D	TSPEAR_ENST00000397916.1_Intron|TSPEAR_ENST00000323084.4_Intron|KRTAP10-2_ENST00000498210.1_5'UTR	NM_198693.2	NP_941966.1	P60368	KR102_HUMAN	keratin associated protein 10-2	15			N -> D (in dbSNP:rs233240). {ECO:0000269|PubMed:15028290}.			keratin filament (GO:0045095)		p.N15D(1)		large_intestine(1)|lung(4)|skin(1)	6						TGCCAGGAGTTGGTGCAGGCG	0.667													T|||	1085	0.216653	0.1725	0.1527	5008	,	,		17203	0.371		0.2068	False		,,,				2504	0.1728				p.N15D		Atlas-SNP	.											KRTAP10-2,bladder,carcinoma,0,3	KRTAP10-2	21	3	1	Substitution - Missense(1)	large_intestine(1)	c.A43G						PASS	.	T	,ASP/ASN	761,3645	309.4+/-291.0	65,631,1507	81.0	86.0	84.0		,43	-1.0	0.0	21	dbSNP_79	84	1692,6908	310.1+/-309.7	158,1376,2766	no	intron,missense	TSPEAR,KRTAP10-2	NM_144991.2,NM_198693.2	,23	223,2007,4273	CC,CT,TT		19.6744,17.2719,18.8605	,benign	,15/256	45971299	2453,10553	2203	4300	6503	SO:0001583	missense	386679	exon1			AGGAGTTGGTGCA	AJ566381	CCDS42955.1	21q22.3	2007-10-05			ENSG00000205445	ENSG00000205445		"""Keratin associated proteins"""	22967	protein-coding gene	gene with protein product				KRTAP18-2			Standard	NM_198693		Approved	KAP10.2, KAP18.2	uc002zfi.1	P60368	OTTHUMG00000057625	ENST00000391621.1:c.43A>G	21.37:g.45971299T>C	ENSP00000375479:p.Asn15Asp	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	109	33	0.302752	NM_198693	Q70LJ5	Missense_Mutation	SNP	ENST00000391621.1	37	CCDS42955.1	531	0.24313186813186813	81	0.16463414634146342	60	0.16574585635359115	218	0.3811188811188811	172	0.22691292875989447	t	0.005	-2.231254	0.00280	0.172719	0.196744	ENSG00000205445	ENST00000391621	T	0.14640	2.49	3.46	-1.05	0.10036	.	.	.	.	.	T	0.00012	0.0000	N	0.00355	-1.605	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.38457	-0.9660	8	0.02654	T	1	.	3.6264	0.08114	0.0:0.4225:0.1919:0.3855	rs233240;rs620443;rs59814995	15	P60368	KR102_HUMAN	D	15	ENSP00000375479:N15D	ENSP00000375479:N15D	N	-	1	0	KRTAP10-2	44795727	0.000000	0.05858	0.001000	0.08648	0.064000	0.16182	0.100000	0.15231	-0.801000	0.04427	-0.814000	0.03130	AAC	T|0.767;C|0.233	0.233	strong		0.667	KRTAP10-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128027.1		
KIFC3	3801	hgsc.bcm.edu	37	16	57795343	57795343	+	Silent	SNP	G	G	A	rs12920931	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:57795343G>A	ENST00000379655.4	-	14	2111	c.1854C>T	c.(1852-1854)agC>agT	p.S618S	KIFC3_ENST00000562903.1_Silent_p.S479S|KIFC3_ENST00000543930.1_Silent_p.S476S|KIFC3_ENST00000541240.1_Silent_p.S640S|KIFC3_ENST00000540079.2_Silent_p.S516S|KIFC3_ENST00000421376.2_Silent_p.S479S|KIFC3_ENST00000539578.1_Silent_p.S560S|KIFC3_ENST00000445690.2_Silent_p.S618S|KIFC3_ENST00000465878.2_Silent_p.S479S	NM_005550.3	NP_005541.3	Q9BVG8	KIFC3_HUMAN	kinesin family member C3	618	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|epithelial cell-cell adhesion (GO:0090136)|Golgi organization (GO:0007030)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|visual perception (GO:0007601)|zonula adherens maintenance (GO:0045218)	centrosome (GO:0005813)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)|zonula adherens (GO:0005915)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(2)|central_nervous_system(3)|endometrium(4)|large_intestine(3)|lung(6)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	23		all_neural(199;0.224)				TGTCGTCCACGCTCTGCACTT	0.572													G|||	77	0.0153754	0.0023	0.0346	5008	,	,		20029	0.0		0.0467	False		,,,				2504	0.0031				p.S618S		Atlas-SNP	.											.	KIFC3	55	.	0			c.C1854T						PASS	.	G	,,	40,4356	43.8+/-77.6	0,40,2158	126.0	109.0	114.0		1437,1854,1854	-2.5	1.0	16	dbSNP_121	114	441,8159	134.1+/-191.5	11,419,3870	no	coding-synonymous,coding-synonymous,coding-synonymous	KIFC3	NM_001130099.1,NM_001130100.1,NM_005550.3	,,	11,459,6028	AA,AG,GG		5.1279,0.9099,3.7011	,,	479/688,618/827,618/834	57795343	481,12515	2198	4300	6498	SO:0001819	synonymous_variant	3801	exon14			GTCCACGCTCTGC	BC001211	CCDS10789.2, CCDS45493.1, CCDS45494.1	16q13-q21	2008-02-05			ENSG00000140859	ENSG00000140859		"""Kinesins"""	6326	protein-coding gene	gene with protein product		604535				9782090	Standard	NM_001130099		Approved		uc002emp.3	Q9BVG8	OTTHUMG00000133455	ENST00000379655.4:c.1854C>T	16.37:g.57795343G>A		Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	223	127	0.569507	NM_001130100	A8K6S2|B7Z484|O75299|Q49A29|Q49AQ0|Q59G19|Q8IUT3|Q96HW6	Silent	SNP	ENST00000379655.4	37	CCDS10789.2																																																																																			G|0.970;A|0.030	0.030	strong		0.572	KIFC3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257329.2	NM_005550	
TTN	7273	hgsc.bcm.edu	37	2	179554305	179554305	+	Missense_Mutation	SNP	C	C	T	rs2244492	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:179554305C>T	ENST00000591111.1	-	121	31137	c.30913G>A	c.(30913-30915)Gga>Aga	p.G10305R	TTN_ENST00000359218.5_Intron|TTN-AS1_ENST00000589830.1_RNA|TTN-AS1_ENST00000589487.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.G9378R|TTN_ENST00000460472.2_Intron|TTN_ENST00000589042.1_Missense_Mutation_p.G10622R|TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000431752.1_RNA			Q8WZ42	TITIN_HUMAN	titin	0	Glu-rich.|Pro-rich.			G -> R (in Ref. 3; CAD12456). {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)			GTCACAACTCCCTTCTGTACT	0.358													T|||	2070	0.413339	0.6067	0.3501	5008	,	,		19129	0.1677		0.3827	False		,,,				2504	0.4816				p.G10622R		Atlas-SNP	.											.	TTN	18412	.	0			c.G31864A						PASS	.	T	,,,ARG/GLY	2207,1503		654,899,302	229.0	224.0	225.0		,,,28132	5.3	1.0	2	dbSNP_100	225	2955,5243		514,1927,1658	yes	intron,intron,intron,missense	TTN	NM_003319.4,NM_133432.3,NM_133437.3,NM_133378.4	,,,125	1168,2826,1960	TT,TC,CC		36.0454,40.5121,43.349	,,,benign	,,,9378/33424	179554305	5162,6746	1855	4099	5954	SO:0001583	missense	7273	exon123			CAACTCCCTTCTG	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.30913G>A	2.37:g.179554305C>T	ENSP00000465570:p.Gly10305Arg	Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	161	159	0.987578	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		812	0.3717948717948718	292	0.5934959349593496	139	0.3839779005524862	84	0.14685314685314685	297	0.391820580474934	T	10.60	1.396903	0.25205	0.594879	0.360454	ENSG00000155657	ENST00000342992;ENST00000414766	T;T	0.63913	-0.07;-0.07	5.34	5.34	0.76211	.	.	.	.	.	T	0.00012	0.0000	N	0.03608	-0.345	0.09310	P	0.9999999999991834	.	.	.	.	.	.	T	0.41980	-0.9478	6	0.87932	D	0	.	10.226	0.43225	0.0:0.0756:0.0:0.9244	rs2244492;rs17355152;rs2244492	.	.	.	R	9378;500	ENSP00000343764:G9378R;ENSP00000401501:G500R	ENSP00000343764:G9378R	G	-	1	0	TTN	179262550	0.313000	0.24554	0.960000	0.40013	0.986000	0.74619	3.252000	0.51461	0.971000	0.38288	-0.254000	0.11334	GGA	C|0.624;T|0.376	0.376	strong		0.358	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
BTBD16	118663	hgsc.bcm.edu	37	10	124089075	124089075	+	Missense_Mutation	SNP	G	G	A	rs986178|rs58204486	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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						PASS	.	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	29	0	0		WXS	Illumina HiSeq	Phase_I	48	21	0.4375	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	
SHPRH	257218	hgsc.bcm.edu	37	6	146267376	146267376	+	Silent	SNP	T	T	C	rs201477770	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:146267376T>C	ENST00000367505.2	-	7	1578	c.1314A>G	c.(1312-1314)caA>caG	p.Q438Q	SHPRH_ENST00000367503.3_Silent_p.Q438Q|SHPRH_ENST00000275233.7_Silent_p.Q438Q|SHPRH_ENST00000438092.2_Silent_p.Q438Q			Q149N8	SHPRH_HUMAN	SNF2 histone linker PHD RING helicase, E3 ubiquitin protein ligase	438	H15. {ECO:0000255|PROSITE- ProRule:PRU00837}.		Q -> R (in an ovarian cancer cell line). {ECO:0000269|PubMed:12837266}.		DNA repair (GO:0006281)|nucleosome assembly (GO:0006334)|protein polyubiquitination (GO:0000209)	nucleosome (GO:0000786)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(15)|lung(33)|ovary(3)|pancreas(2)|prostate(7)|skin(1)|urinary_tract(1)	79		Ovarian(120;0.0365)		OV - Ovarian serous cystadenocarcinoma(155;1.47e-07)|GBM - Glioblastoma multiforme(68;0.0124)		TACGAGGGCATTGAACTTTTT	0.313													T|||	2	0.000399361	0.0015	0.0	5008	,	,		16466	0.0		0.0	False		,,,				2504	0.0				p.Q438Q		Atlas-SNP	.											.	SHPRH	169	.	0			c.A1314G						PASS	.	T	,	0,3650		0,0,1825	165.0	146.0	152.0		1314,1314	-6.0	0.9	6	dbSNP_134	152	1,8145		0,1,4072	no	coding-synonymous,coding-synonymous	SHPRH	NM_001042683.2,NM_173082.3	,	0,1,5897	CC,CT,TT		0.0123,0.0,0.0085	,	438/1684,438/1660	146267376	1,11795	1825	4073	5898	SO:0001819	synonymous_variant	257218	exon7			AGGGCATTGAACT	AB095943	CCDS43513.1, CCDS47496.1, CCDS43513.2	6q24.2	2012-02-23	2012-02-23		ENSG00000146414	ENSG00000146414		"""RING-type (C3HC4) zinc fingers"""	19336	protein-coding gene	gene with protein product		608048	"""SNF2 histone linker PHD RING helicase"""			12837266	Standard	NM_001042683		Approved	FLJ90837, KIAA2023, bA545I5.2	uc003qlf.3	Q149N8	OTTHUMG00000015750	ENST00000367505.2:c.1314A>G	6.37:g.146267376T>C		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	20	10	0.5	NM_173082	Q149N9|Q5VV79|Q68DS5|Q7Z5J5|Q8IVE8|Q8IWQ9|Q8N1S8|Q8NBR7	Silent	SNP	ENST00000367505.2	37	CCDS43513.2																																																																																			T|1.000;C|0.000	0.000	strong		0.313	SHPRH-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000042571.2	NM_173082	
MUC4	4585	hgsc.bcm.edu	37	3	195511526	195511526	+	Missense_Mutation	SNP	C	C	T	rs200787582	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195511526C>T	ENST00000463781.3	-	2	7384	c.6925G>A	c.(6925-6927)Gac>Aac	p.D2309N	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.D2309N	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.D2309N(3)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GAGGAAGCGTCGGTGACATGA	0.587													.|||	2473	0.49381	0.3926	0.4438	5008	,	,		11151	0.6607		0.5229	False		,,,				2504	0.4642				p.D2309N		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,+1,5	MUC4	1505	5	3	Substitution - Missense(3)	stomach(2)|kidney(1)	c.G6925A						scavenged	.																																			SO:0001583	missense	4585	exon2			AAGCGTCGGTGAC	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.6925G>A	3.37:g.195511526C>T	ENSP00000417498:p.Asp2309Asn	Somatic	57	2	0.0350877		WXS	Illumina HiSeq	Phase_I	20	9	0.45	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	6.620	0.482774	0.12581	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.30448	1.54;1.53	.	.	.	.	0.310550	0.14023	U	0.346674	T	0.12732	0.0309	N	0.19112	0.55	0.09310	N	1	B	0.26975	0.165	B	0.04013	0.001	T	0.18713	-1.0328	8	.	.	.	.	2.1447	0.03784	0.0:0.3304:0.3444:0.3251	.	2309	E7ESK3	.	N	2309	ENSP00000417498:D2309N;ENSP00000420243:D2309N	.	D	-	1	0	MUC4	196995921	0.000000	0.05858	0.004000	0.12327	0.069000	0.16628	-0.548000	0.06048	-0.417000	0.07461	0.064000	0.15345	GAC	C|0.823;T|0.177	0.177	strong		0.587	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
APH1B	83464	hgsc.bcm.edu	37	15	63594660	63594660	+	Missense_Mutation	SNP	G	G	T	rs61751105	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:63594660G>T	ENST00000261879.5	+	5	665	c.595G>T	c.(595-597)Gtg>Ttg	p.V199L	APH1B_ENST00000560716.1_3'UTR|APH1B_ENST00000380343.4_Missense_Mutation_p.V158L	NM_001145646.1|NM_031301.3	NP_001139118.1|NP_112591.2	Q8WW43	APH1B_HUMAN	APH1B gamma secretase subunit	199					apoptotic signaling pathway (GO:0097190)|membrane protein intracellular domain proteolysis (GO:0031293)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|positive regulation of apoptotic process (GO:0043065)|positive regulation of catalytic activity (GO:0043085)|protein processing (GO:0016485)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|transport vesicle (GO:0030133)	peptidase activity (GO:0008233)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|stomach(1)|upper_aerodigestive_tract(1)	12						CCACCTGCTGGTGTCAGCCCA	0.448													G|||	40	0.00798722	0.0008	0.0115	5008	,	,		19588	0.0		0.0258	False		,,,				2504	0.0051				p.V199L		Atlas-SNP	.											.	APH1B	27	.	0			c.G595T						PASS	.	G	LEU/VAL,LEU/VAL	11,4395	19.1+/-41.9	0,11,2192	150.0	139.0	143.0		472,595	4.9	1.0	15	dbSNP_129	143	115,8485	61.0+/-122.8	3,109,4188	yes	missense,missense	APH1B	NM_001145646.1,NM_031301.3	32,32	3,120,6380	TT,TG,GG		1.3372,0.2497,0.9688	probably-damaging,probably-damaging	158/217,199/258	63594660	126,12880	2203	4300	6503	SO:0001583	missense	83464	exon5			CTGCTGGTGTCAG	AY358698	CCDS10184.1, CCDS45276.1	15q22.2	2013-05-01	2013-05-01		ENSG00000138613	ENSG00000138613			24080	protein-coding gene	gene with protein product		607630	"""anterior pharynx defective 1 homolog B (C. elegans)"""			12110170, 11230166	Standard	NM_031301		Approved	PSFL, APH-1B, DKFZp564D0372	uc002ama.3	Q8WW43	OTTHUMG00000132863	ENST00000261879.5:c.595G>T	15.37:g.63594660G>T	ENSP00000261879:p.Val199Leu	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	166	67	0.403614	NM_031301	A8K589|Q564N3|Q6UWQ1|Q9H0S0	Missense_Mutation	SNP	ENST00000261879.5	37	CCDS10184.1	23	0.010531135531135532	0	0.0	2	0.0055248618784530384	0	0.0	21	0.027704485488126648	G	17.68	3.448351	0.63178	0.002497	0.013372	ENSG00000138613	ENST00000380343;ENST00000261879	T;T	0.48836	0.8;0.8	4.94	4.94	0.65067	.	0.000000	0.64402	D	0.000001	T	0.20820	0.0501	L	0.53617	1.68	0.58432	D	0.999999	B;B	0.25048	0.117;0.02	B;B	0.22601	0.04;0.04	T	0.15867	-1.0422	10	0.45353	T	0.12	-9.7136	14.3914	0.66981	0.0:0.0:1.0:0.0	rs61751105	158;199	Q564N3;Q8WW43	.;APH1B_HUMAN	L	158;199	ENSP00000369700:V158L;ENSP00000261879:V199L	ENSP00000261879:V199L	V	+	1	0	APH1B	61381713	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.536000	0.82023	2.663000	0.90544	0.655000	0.94253	GTG	G|0.990;T|0.010	0.010	strong		0.448	APH1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256337.1	NM_031301	
ZFP69	339559	hgsc.bcm.edu	37	1	40961449	40961449	+	Silent	SNP	T	T	C	rs3795348	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:40961449T>C	ENST00000372706.1	+	6	2305	c.1299T>C	c.(1297-1299)caT>caC	p.H433H	RP11-656D10.3_ENST00000450713.1_RNA|ZFP69_ENST00000372705.3_Silent_p.H433H			Q49AA0	ZFP69_HUMAN	ZFP69 zinc finger protein	433					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)										AGAGAATCCATACTGGGGAGA	0.413													T|||	220	0.0439297	0.0598	0.0331	5008	,	,		21816	0.0218		0.0328	False		,,,				2504	0.0644				p.H433H		Atlas-SNP	.											.	.	.	.	0			c.T1299C						PASS	.	T		247,4159	143.1+/-178.2	9,229,1965	73.0	75.0	75.0		1299	-3.9	1.0	1	dbSNP_107	75	300,8300	109.0+/-169.6	5,290,4005	no	coding-synonymous	ZNF642	NM_198494.2		14,519,5970	CC,CT,TT		3.4884,5.606,4.2058		433/527	40961449	547,12459	2203	4300	6503	SO:0001819	synonymous_variant	339559	exon6			AATCCATACTGGG	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.1299T>C	1.37:g.40961449T>C		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	66	37	0.560606	NM_198494	Q5SWM5|Q6ZWK8	Silent	SNP	ENST00000372706.1	37	CCDS30686.1																																																																																			T|0.960;C|0.040	0.040	strong		0.413	ZFP69-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019082.1	NM_198494	
ALCAM	214	hgsc.bcm.edu	37	3	105266331	105266331	+	Silent	SNP	A	A	G	rs9855810	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:105266331A>G	ENST00000306107.5	+	11	1838	c.1338A>G	c.(1336-1338)caA>caG	p.Q446Q	ALCAM_ENST00000389927.4_Silent_p.Q168Q|ALCAM_ENST00000486979.2_Silent_p.Q395Q|ALCAM_ENST00000472644.2_Silent_p.Q446Q	NM_001627.3	NP_001618.2	Q13740	CD166_HUMAN	activated leukocyte cell adhesion molecule	446	Ig-like C2-type 3.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|motor neuron axon guidance (GO:0008045)|signal transduction (GO:0007165)	axon (GO:0030424)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)	receptor binding (GO:0005102)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(14)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	28						CAGCCATTCAATGGACAATTA	0.398													A|||	258	0.0515176	0.0091	0.049	5008	,	,		19951	0.0437		0.1074	False		,,,				2504	0.0613				p.Q446Q		Atlas-SNP	.											.	ALCAM	71	.	0			c.A1338G						PASS	.	A		125,4281	92.0+/-130.7	3,119,2081	103.0	99.0	101.0		1338	-0.6	1.0	3	dbSNP_119	101	1010,7588	215.5+/-254.8	67,876,3356	no	coding-synonymous	ALCAM	NM_001627.3		70,995,5437	GG,GA,AA		11.7469,2.837,8.7281		446/584	105266331	1135,11869	2203	4299	6502	SO:0001819	synonymous_variant	214	exon11			CATTCAATGGACA	AK054632	CCDS33810.1, CCDS58841.1	3q13.1	2013-01-29	2002-08-08		ENSG00000170017	ENSG00000170017		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	400	protein-coding gene	gene with protein product		601662	"""activated leucocyte cell adhesion molecule"""			7760007	Standard	NM_001627		Approved	CD166, MEMD	uc003dvx.3	Q13740	OTTHUMG00000159192	ENST00000306107.5:c.1338A>G	3.37:g.105266331A>G		Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	183	99	0.540984	NM_001627	B2RNS3|B4DTU0|O60892|Q1HGM8|Q1HGM9|Q6PEY4|Q6ZS95	Silent	SNP	ENST00000306107.5	37	CCDS33810.1	133	0.060897435897435896	4	0.008130081300813009	23	0.06353591160220995	26	0.045454545454545456	80	0.10554089709762533	A	0.743	-0.775577	0.02951	0.02837	0.117469	ENSG00000170017	ENST00000465413	.	.	.	5.77	-0.614	0.11590	.	.	.	.	.	T	0.00356	0.0011	.	.	.	0.09310	P	0.9999999999986332	.	.	.	.	.	.	T	0.15407	-1.0438	3	.	.	.	-0.6385	1.9517	0.03368	0.3429:0.2099:0.3404:0.1068	rs9855810;rs17189333;rs56585623;rs9855810	.	.	.	V	207	.	.	M	+	1	0	ALCAM	106749021	0.999000	0.42202	0.995000	0.50966	0.182000	0.23217	0.379000	0.20585	-0.146000	0.11274	-1.039000	0.02377	ATG	A|0.924;G|0.076	0.076	strong		0.398	ALCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353764.1	NM_001627	
ANO7	50636	hgsc.bcm.edu	37	2	242147054	242147054	+	Nonsense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:242147054G>A	ENST00000274979.8	+	11	1311	c.1208G>A	c.(1207-1209)tGg>tAg	p.W403*	ANO7_ENST00000402430.3_Nonsense_Mutation_p.W402*	NM_001001891.3	NP_001001891.2	Q6IWH7	ANO7_HUMAN	anoctamin 7	403					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						TGCCCTTTCTGGCTGCTCTCC	0.617																																					p.W403X		Atlas-SNP	.											.	ANO7	136	.	0			c.G1208A						PASS	.						108.0	102.0	104.0					2																	242147054		2203	4300	6503	SO:0001587	stop_gained	50636	exon11			CTTTCTGGCTGCT	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.1208G>A	2.37:g.242147054G>A	ENSP00000274979:p.Trp403*	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	49	11	0.22449	NM_001001891	Q6IWH6	Nonsense_Mutation	SNP	ENST00000274979.8	37	CCDS33423.1	.	.	.	.	.	.	.	.	.	.	G	19.35	3.809907	0.70797	.	.	ENSG00000146205	ENST00000274979;ENST00000402430	.	.	.	2.49	2.49	0.30216	.	0.451423	0.21800	U	0.068929	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	12.4445	0.55643	0.0:0.0:1.0:0.0	.	.	.	.	X	403;402	.	ENSP00000274979:W403X	W	+	2	0	ANO7	241795727	1.000000	0.71417	1.000000	0.80357	0.400000	0.30750	6.347000	0.73004	1.315000	0.45114	0.313000	0.20887	TGG	.	.	none		0.617	ANO7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323509.1	NM_001001891	
ARL10	285598	hgsc.bcm.edu	37	5	175793532	175793532	+	Silent	SNP	C	C	T	rs2303666	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:175793532C>T	ENST00000310389.5	+	2	429	c.333C>T	c.(331-333)ggC>ggT	p.G111G	MIR1271_ENST00000408537.1_RNA	NM_173664.4	NP_775935.1	Q8N8L6	ARL10_HUMAN	ADP-ribosylation factor-like 10	111					small GTPase mediated signal transduction (GO:0007264)	intracellular (GO:0005622)	GTP binding (GO:0005525)			endometrium(2)|lung(1)|ovary(1)	4	all_cancers(89;0.0064)|Renal(175;0.000269)|Lung NSC(126;0.0105)|all_lung(126;0.0168)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)|all_hematologic(541;0.214)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	Kidney(146;0.0965)		CCACCTGGGGCTTCAACTCCG	0.637													C|||	574	0.114617	0.0628	0.1585	5008	,	,		17243	0.1121		0.1272	False		,,,				2504	0.1431				p.G111G		Atlas-SNP	.											.	ARL10	19	.	0			c.C333T						PASS	.	C		336,4070	175.5+/-204.9	12,312,1879	76.0	80.0	79.0		333	2.2	1.0	5	dbSNP_100	79	1136,7464	234.7+/-267.5	73,990,3237	no	coding-synonymous	ARL10	NM_173664.4		85,1302,5116	TT,TC,CC		13.2093,7.626,11.3179		111/245	175793532	1472,11534	2203	4300	6503	SO:0001819	synonymous_variant	285598	exon2			CTGGGGCTTCAAC	BK001673	CCDS4400.1	5q35.3	2014-05-09	2005-11-03	2005-11-03	ENSG00000175414	ENSG00000175414		"""ADP-ribosylation factors-like"", ""ADP-ribosylation factors"""	22042	protein-coding gene	gene with protein product			"""ADP-ribosylation factor-like 10A"""	ARL10A			Standard	NM_173664		Approved		uc003mec.1	Q8N8L6	OTTHUMG00000130655	ENST00000310389.5:c.333C>T	5.37:g.175793532C>T		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	100	44	0.44	NM_173664		Silent	SNP	ENST00000310389.5	37	CCDS4400.1																																																																																			C|0.894;T|0.106	0.106	strong		0.637	ARL10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253145.2	NM_173664	
JSRP1	126306	hgsc.bcm.edu	37	19	2253687	2253687	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:2253687G>A	ENST00000300961.6	-	5	432	c.368C>T	c.(367-369)tCg>tTg	p.S123L	MIR4321_ENST00000592276.1_RNA|JSRP1_ENST00000586471.2_Missense_Mutation_p.S123L	NM_144616.3	NP_653217.1	Q96MG2	JSPR1_HUMAN	junctional sarcoplasmic reticulum protein 1	123	Pro-rich.				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)		CTTGTTGAGCGACAGGTCTCC	0.756																																					p.S123L		Atlas-SNP	.											.	JSRP1	18	.	0			c.C368T						PASS	.						7.0	10.0	9.0					19																	2253687		1985	3928	5913	SO:0001583	missense	126306	exon5			TTGAGCGACAGGT	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.368C>T	19.37:g.2253687G>A	ENSP00000300961:p.Ser123Leu	Somatic	15	0	0		WXS	Illumina HiSeq	Phase_I	20	9	0.45	NM_144616		Missense_Mutation	SNP	ENST00000300961.6	37	CCDS12086.1	.	.	.	.	.	.	.	.	.	.	G	20.8	4.051013	0.75960	.	.	ENSG00000167476	ENST00000300961	T	0.42513	0.97	4.89	4.89	0.63831	.	1.031560	0.07762	N	0.950312	T	0.30070	0.0753	N	0.19112	0.55	0.09310	N	1	B	0.28584	0.216	B	0.21546	0.035	T	0.12993	-1.0526	10	0.72032	D	0.01	-7.5515	9.2315	0.37439	0.1:0.0:0.9:0.0	.	123	Q96MG2	JSPR1_HUMAN	L	123	ENSP00000300961:S123L	ENSP00000300961:S123L	S	-	2	0	JSRP1	2204687	0.687000	0.27671	0.017000	0.16124	0.777000	0.43975	4.762000	0.62250	2.251000	0.74343	0.561000	0.74099	TCG	.	.	none		0.756	JSRP1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451266.2	NM_144616	
KRTAP4-3	85290	hgsc.bcm.edu	37	17	39324104	39324104	+	Silent	SNP	A	A	G	rs368619075		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:39324104A>G	ENST00000391356.2	-	1	320	c.321T>C	c.(319-321)tcT>tcC	p.S107S		NM_033187.1	NP_149443.1	Q9BYR4	KRA43_HUMAN	keratin associated protein 4-3	107	29 X 5 AA repeats of C-C-[GIKRQVH]-[SPT]- [STA].		Missing (in allele KAP3-v2). {ECO:0000269|PubMed:15955084}.		aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)		p.S107S(1)		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)			TGCAGCAACTAGAAATGCAGC	0.597																																					p.S107S		Atlas-SNP	.											KRTAP4-3,colon,carcinoma,0,1	KRTAP4-3	40	1	1	Substitution - coding silent(1)	large_intestine(1)	c.T321C						scavenged	.						18.0	23.0	21.0					17																	39324104		2109	4252	6361	SO:0001819	synonymous_variant	85290	exon1			GCAACTAGAAATG	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.321T>C	17.37:g.39324104A>G		Somatic	247	4	0.0161943		WXS	Illumina HiSeq	Phase_I	192	2	0.0104167	NM_033187		Silent	SNP	ENST00000391356.2	37	CCDS42331.1																																																																																			.	.	weak		0.597	KRTAP4-3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257784.1		
ZNF880	400713	hgsc.bcm.edu	37	19	52888050	52888050	+	Missense_Mutation	SNP	A	A	G	rs76053634	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:52888050A>G	ENST00000422689.2	+	4	1232	c.1217A>G	c.(1216-1218)cAa>cGa	p.Q406R		NM_001145434.1	NP_001138906.1	Q6PDB4	ZN880_HUMAN	zinc finger protein 880	406					regulation of transcription, DNA-templated (GO:0006355)	intracellular (GO:0005622)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(2)|skin(1)	10						ACGGGAGAGCAACCTTACAAA	0.398																																					p.Q406R		Atlas-SNP	.											ZNF880,colon,carcinoma,0,2	ZNF880	45	2	0			c.A1217G						PASS	.						70.0	64.0	66.0					19																	52888050		1568	3582	5150	SO:0001583	missense	400713	exon4			GAGAGCAACCTTA	BC058819	CCDS46164.1	19q13.41	2013-01-08			ENSG00000221923	ENSG00000221923		"""Zinc fingers, C2H2-type"", ""-"""	37249	protein-coding gene	gene with protein product							Standard	NM_001145434		Approved		uc002pzc.3	Q6PDB4	OTTHUMG00000167972	ENST00000422689.2:c.1217A>G	19.37:g.52888050A>G	ENSP00000406318:p.Gln406Arg	Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	7	7	1	NM_001145434	B4DNA6	Missense_Mutation	SNP	ENST00000422689.2	37	CCDS46164.1	.	.	.	.	.	.	.	.	.	.	A	4.567	0.105370	0.08731	.	.	ENSG00000221923	ENST00000422689	T	0.15718	2.4	1.84	1.84	0.25277	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.04182	0.0116	N	0.00392	-1.555	0.19775	N	0.999952	B	0.17667	0.023	B	0.23150	0.044	T	0.43360	-0.9396	8	.	.	.	.	8.4442	0.32833	1.0:0.0:0.0:0.0	.	406	Q6PDB4	ZN880_HUMAN	R	406	ENSP00000406318:Q406R	.	Q	+	2	0	ZNF880	57579862	0.002000	0.14202	0.418000	0.26571	0.177000	0.22998	0.149000	0.16243	0.834000	0.34852	0.450000	0.29827	CAA	A|0.867;G|0.133	0.133	strong		0.398	ZNF880-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397374.1	NM_001145434	
NSA2	10412	hgsc.bcm.edu	37	5	74069863	74069863	+	Silent	SNP	A	A	G	rs6874609	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:74069863A>G	ENST00000296802.5	+	5	1062	c.693A>G	c.(691-693)acA>acG	p.T231T		NM_014886.3	NP_055701.1	O95478	NSA2_HUMAN	NSA2 ribosome biogenesis homolog (S. cerevisiae)	231					rRNA processing (GO:0006364)	nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(2)|kidney(1)|lung(1)|ovary(1)|skin(1)	7						GCCTTGTGACACAAGGAGGCA	0.378													G|||	1907	0.380791	0.7481	0.3357	5008	,	,		16898	0.2063		0.2416	False		,,,				2504	0.2393				p.T231T		Atlas-SNP	.											NSA2,NS,carcinoma,+1,1	NSA2	18	1	0			c.A693G						PASS	.	G		2961,1445	466.6+/-354.6	1000,961,242	96.0	92.0	94.0		693	-3.0	1.0	5	dbSNP_116	94	1912,6688	726.4+/-406.6	204,1504,2592	yes	coding-synonymous	NSA2	NM_014886.3		1204,2465,2834	GG,GA,AA		22.2326,32.7962,37.4673		231/261	74069863	4873,8133	2203	4300	6503	SO:0001819	synonymous_variant	10412	exon5			TGTGACACAAGGA	AF077615	CCDS4025.1, CCDS75260.1	5q13.3	2010-01-18			ENSG00000164346	ENSG00000164346			30728	protein-coding gene	gene with protein product	"""hairy cell leukemia protein 1"", ""TGF beta-inducible nuclear protein 1"""	612497				11124703, 10486207	Standard	NM_014886		Approved	HUSSY-29, HCLG1, FLJ94393, TINP1	uc003kdk.2	O95478	OTTHUMG00000131273	ENST00000296802.5:c.693A>G	5.37:g.74069863A>G		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	95	62	0.652632	NM_014886		Silent	SNP	ENST00000296802.5	37	CCDS4025.1																																																																																			A|0.624;G|0.376	0.376	strong		0.378	NSA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254041.3	NM_014886	
C5orf52	100190949	hgsc.bcm.edu	37	5	157102159	157102159	+	Missense_Mutation	SNP	G	G	A	rs10051838	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:157102159G>A	ENST00000409999.3	+	2	334	c.272G>A	c.(271-273)cGg>cAg	p.R91Q		NM_001145132.1	NP_001138604.1	A6NGY3	CE052_HUMAN	chromosome 5 open reading frame 52	91										endometrium(2)|lung(1)	3						CATTTATCTCGGGTGATTATT	0.448													.|||	913	0.182308	0.3071	0.111	5008	,	,		19662	0.119		0.1252	False		,,,				2504	0.1881				p.R91Q		Atlas-SNP	.											C5orf52,NS,carcinoma,+1,1	C5orf52	17	1	0			c.G272A						PASS	.	G	GLN/ARG	412,972		53,306,333	123.0	111.0	115.0		272	2.2	1.0	5	dbSNP_119	115	431,2751		32,367,1192	yes	missense	C5orf52	NM_001145132.1	43	85,673,1525	AA,AG,GG		13.5449,29.7688,18.4625	probably-damaging	91/160	157102159	843,3723	692	1591	2283	SO:0001583	missense	100190949	exon2			TATCTCGGGTGAT	BG721329	CCDS47329.1	5q33.3	2012-02-24			ENSG00000187658	ENSG00000187658			35121	protein-coding gene	gene with protein product							Standard	NM_001145132		Approved		uc011ddt.2	A6NGY3	OTTHUMG00000154518	ENST00000409999.3:c.272G>A	5.37:g.157102159G>A	ENSP00000387027:p.Arg91Gln	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	102	44	0.431373	NM_001145132		Missense_Mutation	SNP	ENST00000409999.3	37	CCDS47329.1	355	0.16254578754578755	148	0.3008130081300813	39	0.10773480662983426	74	0.12937062937062938	94	0.12401055408970976	G	11.63	1.697086	0.30142	0.297688	0.135449	ENSG00000187658	ENST00000409999	T	0.36878	1.23	2.22	2.22	0.28083	.	.	.	.	.	T	0.00012	0.0000	L	0.32530	0.975	0.39575	P	0.030656000000000017	P	0.46952	0.887	B	0.32211	0.142	T	0.37753	-0.9692	8	0.66056	D	0.02	-17.8701	7.8836	0.29637	0.0:0.0:1.0:0.0	rs10051838;rs52825189;rs61469151;rs10051838	91	A6NGY3	CE052_HUMAN	Q	91	ENSP00000387027:R91Q	ENSP00000387027:R91Q	R	+	2	0	C5orf52	157034737	0.989000	0.36119	0.998000	0.56505	0.581000	0.36288	0.228000	0.17814	1.235000	0.43724	0.313000	0.20887	CGG	G|0.823;A|0.177	0.177	strong		0.448	C5orf52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335664.1	NM_001145132	
OR56B1	387748	hgsc.bcm.edu	37	11	5757785	5757785	+	Silent	SNP	C	C	T	rs12792180	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:5757785C>T	ENST00000317121.3	+	1	105	c.39C>T	c.(37-39)agC>agT	p.S13S	TRIM5_ENST00000380027.1_Intron	NM_001005180.2	NP_001005180.1	Q8NGI3	O56B1_HUMAN	olfactory receptor, family 56, subfamily B, member 1	13						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(2)|lung(7)|prostate(1)|skin(1)	13		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.086)		Epithelial(150;1.74e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)|LUSC - Lung squamous cell carcinoma(625;0.184)		TCTCCAATAGCTCCAAATTCC	0.443													C|||	566	0.113019	0.09	0.1268	5008	,	,		18374	0.1399		0.1133	False		,,,				2504	0.1063				p.S13S		Atlas-SNP	.											.	OR56B1	38	.	0			c.C39T						PASS	.	C		405,3997	200.1+/-223.5	18,369,1814	77.0	77.0	77.0		39	0.7	1.0	11	dbSNP_121	77	868,7726	196.8+/-241.6	45,778,3474	no	coding-synonymous	OR56B1	NM_001005180.2		63,1147,5288	TT,TC,CC		10.1001,9.2004,9.7953		13/325	5757785	1273,11723	2201	4297	6498	SO:0001819	synonymous_variant	387748	exon1			CAATAGCTCCAAA	BK004386	CCDS31395.1	11p15.4	2012-08-09		2004-03-10	ENSG00000181023	ENSG00000181023		"""GPCR / Class A : Olfactory receptors"""	15245	protein-coding gene	gene with protein product				OR56B1P			Standard	NM_001005180		Approved		uc001mbt.2	Q8NGI3	OTTHUMG00000066891	ENST00000317121.3:c.39C>T	11.37:g.5757785C>T		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	122	101	0.827869	NM_001005180	B2RNY6|B3KV42|Q6IF76	Silent	SNP	ENST00000317121.3	37	CCDS31395.1																																																																																			C|0.895;T|0.105	0.105	strong		0.443	OR56B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143354.1	NM_001005180	
IGSF10	285313	hgsc.bcm.edu	37	3	151162998	151162998	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:151162998C>T	ENST00000282466.3	-	4	4770	c.4771G>A	c.(4771-4773)Gaa>Aaa	p.E1591K		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	1591					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)			ATGCTTACTTCTGGCTTTTTG	0.413																																					p.E1591K		Atlas-SNP	.											IGSF10,NS,carcinoma,+2,1	IGSF10	279	1	0			c.G4771A						scavenged	.						165.0	157.0	160.0					3																	151162998		2203	4300	6503	SO:0001583	missense	285313	exon4			TTACTTCTGGCTT	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.4771G>A	3.37:g.151162998C>T	ENSP00000282466:p.Glu1591Lys	Somatic	178	1	0.00561798		WXS	Illumina HiSeq	Phase_I	149	2	0.0134228	NM_178822	Q86YJ9|Q8N772|Q8NA84	Missense_Mutation	SNP	ENST00000282466.3	37	CCDS3160.1	.	.	.	.	.	.	.	.	.	.	C	2.189	-0.385787	0.04966	.	.	ENSG00000152580	ENST00000282466;ENST00000544042	T	0.67698	-0.28	5.32	1.5	0.22942	.	2.708520	0.01530	N	0.018769	T	0.39759	0.1090	N	0.08118	0	0.09310	N	1	B	0.13594	0.008	B	0.09377	0.004	T	0.38134	-0.9675	10	0.06099	T	0.92	.	0.866	0.01203	0.175:0.4051:0.1701:0.2498	.	1591	Q6WRI0	IGS10_HUMAN	K	1591;218	ENSP00000282466:E1591K	ENSP00000282466:E1591K	E	-	1	0	IGSF10	152645688	0.000000	0.05858	0.001000	0.08648	0.018000	0.09664	-0.864000	0.04254	0.236000	0.21180	0.650000	0.86243	GAA	.	.	none		0.413	IGSF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357782.1	NM_178822	
UGT2B7	7364	hgsc.bcm.edu	37	4	69972952	69972952	+	Silent	SNP	C	C	T	rs4348159	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:69972952C>T	ENST00000508661.1	+	4	1089	c.1062C>T	c.(1060-1062)taC>taT	p.Y354Y	UGT2B7_ENST00000305231.7_Silent_p.Y354Y|UGT2B7_ENST00000509763.1_3'UTR			P16662	UD2B7_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide B7	354					androgen metabolic process (GO:0008209)|cellular glucuronidation (GO:0052695)|lipid metabolic process (GO:0006629)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	glucuronosyltransferase activity (GO:0015020)			autonomic_ganglia(1)|endometrium(3)|kidney(4)|large_intestine(6)|lung(16)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	38					Atorvastatin(DB01076)|Carbamazepine(DB00564)|Chenodeoxycholic acid(DB06777)|Codeine(DB00318)|Dabigatran etexilate(DB06695)|Dapagliflozin(DB06292)|Diclofenac(DB00586)|Epirubicin(DB00445)|Etodolac(DB00749)|Ezetimibe(DB00973)|Flunitrazepam(DB01544)|Flurbiprofen(DB00712)|Fluvastatin(DB01095)|Ibuprofen(DB01050)|Indomethacin(DB00328)|Losartan(DB00678)|Lovastatin(DB00227)|Mitiglinide(DB01252)|Morphine(DB00295)|Mycophenolate mofetil(DB00688)|Mycophenolic acid(DB01024)|Naproxen(DB00788)|Oxazepam(DB00842)|Pitavastatin(DB08860)|Silodosin(DB06207)|Simvastatin(DB00641)|Suprofen(DB00870)|Tapentadol(DB06204)|Valproic Acid(DB00313)|Zidovudine(DB00495)	CTCGGCTCTACAAGTGGATAC	0.353													c|||	856	0.170927	0.2368	0.3271	5008	,	,		16261	0.0437		0.1551	False		,,,				2504	0.1186				p.Y354Y		Atlas-SNP	.											.	UGT2B7	79	.	0			c.C1062T	GRCh37	CS086287	UGT2B7	S	rs4348159	PASS	.	C		945,3461	352.6+/-311.8	100,745,1358	130.0	129.0	129.0		1062	-5.4	0.0	4	dbSNP_111	129	1178,7422	237.6+/-269.4	86,1006,3208	yes	coding-synonymous	UGT2B7	NM_001074.2		186,1751,4566	TT,TC,CC		13.6977,21.448,16.3232		354/530	69972952	2123,10883	2203	4300	6503	SO:0001819	synonymous_variant	7364	exon4			GCTCTACAAGTGG	BC030974	CCDS3526.1	4q13	2008-02-05	2005-07-20		ENSG00000171234	ENSG00000171234		"""UDP glucuronosyltransferases"""	12554	protein-coding gene	gene with protein product		600068	"""UDP glycosyltransferase 2 family, polypeptide B7"""			2159463, 7835904	Standard	NM_001074		Approved	UGT2B9	uc003heg.4	P16662	OTTHUMG00000129404	ENST00000508661.1:c.1062C>T	4.37:g.69972952C>T		Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	108	43	0.398148	NM_001074	B2R810|Q6GTW0	Silent	SNP	ENST00000508661.1	37																																																																																				C|0.845;T|0.155	0.155	strong		0.353	UGT2B7-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000362103.1	NM_001074	
MEP1B	4225	hgsc.bcm.edu	37	18	29797921	29797921	+	Missense_Mutation	SNP	C	C	T	rs616114	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:29797921C>T	ENST00000269202.6	+	14	2131	c.2084C>T	c.(2083-2085)cCg>cTg	p.P695L	MEP1B_ENST00000581447.1_Missense_Mutation_p.P695L	NM_005925.2	NP_005916.2	Q16820	MEP1B_HUMAN	meprin A, beta	695			P -> L (in dbSNP:rs616114). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9288916}.		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						AATTTGACTCCGCAAAATGTA	0.393													C|||	1782	0.355831	0.4251	0.2882	5008	,	,		22256	0.255		0.3648	False		,,,				2504	0.4049				p.P695L		Atlas-SNP	.											.	MEP1B	54	.	0			c.C2084T	GRCh37	CM065309	MEP1B	M	rs616114	PASS	.	C	LEU/PRO	1534,2324		321,892,716	103.0	101.0	101.0		2084	0.4	0.0	18	dbSNP_83	101	3220,5040		638,1944,1548	yes	missense	MEP1B	NM_005925.2	98	959,2836,2264	TT,TC,CC		38.9831,39.7615,39.2309	benign	695/702	29797921	4754,7364	1929	4130	6059	SO:0001583	missense	4225	exon14			TGACTCCGCAAAA	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.2084C>T	18.37:g.29797921C>T	ENSP00000269202:p.Pro695Leu	Somatic	191	0	0		WXS	Illumina HiSeq	Phase_I	179	72	0.402235	NM_005925	B7ZM35|B9EGL6|Q670J1	Missense_Mutation	SNP	ENST00000269202.6	37	CCDS45846.1	778	0.35622710622710624	225	0.4573170731707317	109	0.3011049723756906	160	0.27972027972027974	284	0.37467018469656993	C	0.016	-1.529447	0.00951	0.397615	0.389831	ENSG00000141434	ENST00000269202	T	0.17854	2.25	5.68	0.414	0.16406	.	2.205680	0.01512	N	0.017988	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	0.45512	-0.9256	9	0.02654	T	1	5.6145	9.8349	0.40963	0.0:0.3279:0.0:0.6721	rs616114;rs17663247;rs616114	695	Q16820	MEP1B_HUMAN	L	695	ENSP00000269202:P695L	ENSP00000269202:P695L	P	+	2	0	MEP1B	28051919	0.005000	0.15991	0.004000	0.12327	0.028000	0.11728	0.916000	0.28651	-0.149000	0.11215	-0.600000	0.04104	CCG	C|0.631;T|0.368	0.368	strong		0.393	MEP1B-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447755.1	NM_005925	
KIAA0100	9703	hgsc.bcm.edu	37	17	26938651	26938651	+	IGR	SNP	C	C	T	rs34026109	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:26938651C>T	ENST00000528896.2	-	0	7407				RP11-192H23.4_ENST00000577790.1_Intron|SGK494_ENST00000469832.3_5'Flank|RP11-192H23.6_ENST00000579019.2_RNA|SPAG5-AS1_ENST00000414744.1_RNA|RP11-192H23.4_ENST00000534850.1_3'UTR|SGK494_ENST00000301037.5_Missense_Mutation_p.G249S|SPAG5-AS1_ENST00000554154.1_RNA|SPAG5-AS1_ENST00000424210.1_RNA	NM_014680.3	NP_055495.2	Q14667	K0100_HUMAN	KIAA0100							extracellular region (GO:0005576)				breast(3)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(13)|lung(23)|ovary(2)|prostate(2)|skin(6)|stomach(2)|urinary_tract(3)	68	Lung NSC(42;0.00431)					CGGGACAGACCAAAGTCTGTC	0.498													C|||	47	0.00938498	0.0008	0.0187	5008	,	,		17084	0.001		0.0278	False		,,,				2504	0.0041				p.G249S		Atlas-SNP	.											.	.	.	.	0			c.G745A						PASS	.	C	SER/GLY	20,4386	28.1+/-56.4	0,20,2183	146.0	126.0	133.0		745	5.4	1.0	17	dbSNP_126	133	271,8329	102.9+/-164.1	4,263,4033	yes	missense	SGK494	NM_001174103.1	56	4,283,6216	TT,TC,CC		3.1512,0.4539,2.2374		249/411	26938651	291,12715	2203	4300	6503	SO:0001628	intergenic_variant	0	exon9			ACAGACCAAAGTC	D43947	CCDS32595.1	17q11.2	2012-11-29			ENSG00000007202	ENSG00000007202			28960	protein-coding gene	gene with protein product	"""cancer/testis antigen 101"", ""breast cancer overexpressed gene 1"""	610664				16289875	Standard	NM_014680		Approved	DKFZp686M0843, MGC111488, BCOX1, CT101, BCOX	uc002hbu.3	Q14667	OTTHUMG00000166587		17.37:g.26938651C>T		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	67	36	0.537313	NM_001174103	A6NCX3|Q3SYN5|Q49A07|Q5H9T4|Q6WG74|Q6ZP51|Q96HH8	Missense_Mutation	SNP	ENST00000528896.2	37	CCDS32595.1	33	0.01510989010989011	0	0.0	8	0.022099447513812154	0	0.0	25	0.032981530343007916	C	26.0	4.694340	0.88830	0.004539	0.031512	ENSG00000167524	ENST00000301037	T	0.61392	0.11	5.45	5.45	0.79879	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.65749	0.2721	M	0.93808	3.46	0.58432	D	0.999993	D	0.76494	0.999	D	0.83275	0.996	T	0.82218	-0.0566	10	0.87932	D	0	-7.9003	18.2718	0.90070	0.0:1.0:0.0:0.0	rs34026109;rs34026109	249	Q96LW2	SG494_HUMAN	S	249	ENSP00000301037:G249S	ENSP00000301037:G249S	G	-	1	0	AC005726.6	23962778	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	5.156000	0.64905	2.566000	0.86566	0.467000	0.42956	GGT	C|0.980;T|0.020	0.020	strong		0.498	KIAA0100-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390571.3	NM_014680	
TMEM151A	256472	hgsc.bcm.edu	37	11	66062014	66062014	+	Silent	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:66062014G>A	ENST00000327259.4	+	2	441	c.297G>A	c.(295-297)ctG>ctA	p.L99L		NM_153266.3	NP_694998.1	Q8N4L1	T151A_HUMAN	transmembrane protein 151A	99						integral component of membrane (GO:0016021)				central_nervous_system(1)|kidney(4)|lung(6)	11						ATGGCTACCTGTACATCCCGC	0.731																																					p.L99L		Atlas-SNP	.											.	TMEM151A	39	.	0			c.G297A						PASS	.						66.0	47.0	53.0					11																	66062014		2197	4291	6488	SO:0001819	synonymous_variant	256472	exon2			CTACCTGTACATC	BC033898	CCDS8133.1	11q13.2	2007-10-25	2007-10-25	2007-10-25	ENSG00000179292	ENSG00000179292			28497	protein-coding gene	gene with protein product			"""transmembrane protein 151"""	TMEM151		12477932	Standard	NM_153266		Approved	MGC33486	uc001ohl.3	Q8N4L1	OTTHUMG00000166920	ENST00000327259.4:c.297G>A	11.37:g.66062014G>A		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	68	38	0.558824	NM_153266	Q8ND14	Silent	SNP	ENST00000327259.4	37	CCDS8133.1																																																																																			.	.	none		0.731	TMEM151A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391897.1	NM_153266	
SLC7A13	157724	hgsc.bcm.edu	37	8	87235273	87235273	+	Missense_Mutation	SNP	C	C	T	rs2976189	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:87235273C>T	ENST00000297524.3	-	2	848	c.745G>A	c.(745-747)Gtg>Atg	p.V249M	SLC7A13_ENST00000520624.1_5'UTR|SLC7A13_ENST00000419776.2_Missense_Mutation_p.V240M	NM_138817.2	NP_620172.2	Q8TCU3	S7A13_HUMAN	solute carrier family 7 (anionic amino acid transporter), member 13	249			V -> M (in dbSNP:rs2976189). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.			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						ACTACAGTCACCAGAGGTAAC	0.388													C|||	480	0.0958466	0.1286	0.0749	5008	,	,		15430	0.0179		0.1491	False		,,,				2504	0.092				p.V249M		Atlas-SNP	.											.	SLC7A13	97	.	0			c.G745A						PASS	.	C	MET/VAL	628,3778	271.6+/-270.3	49,530,1624	160.0	163.0	162.0		745	2.5	0.1	8	dbSNP_101	162	1290,7310	255.9+/-280.6	99,1092,3109	yes	missense	SLC7A13	NM_138817.2	21	148,1622,4733	TT,TC,CC		15.0,14.2533,14.747	probably-damaging	249/471	87235273	1918,11088	2203	4300	6503	SO:0001583	missense	157724	exon2			CAGTCACCAGAGG	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.745G>A	8.37:g.87235273C>T	ENSP00000297524:p.Val249Met	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	113	112	0.99115	NM_138817	Q05C37|Q08AH9|Q96N84	Missense_Mutation	SNP	ENST00000297524.3	37	CCDS34917.1	223	0.1021062271062271	69	0.1402439024390244	34	0.09392265193370165	1	0.0017482517482517483	119	0.15699208443271767	C	15.75	2.925452	0.52759	0.142533	0.15	ENSG00000164893	ENST00000297524;ENST00000419776	D;D	0.91686	-2.89;-2.89	4.36	2.49	0.30216	Amino acid permease domain (1);	0.119417	0.37136	N	0.002240	T	0.11623	0.0283	M	0.93150	3.385	0.58432	P	5.999999999950489E-6	D;D	0.89917	1.0;1.0	D;D	0.87578	0.997;0.998	T	0.57734	-0.7760	9	0.87932	D	0	.	7.8039	0.29191	0.0:0.7398:0.165:0.0952	rs2976189;rs17606419;rs52826324;rs59401360;rs2976189	240;249	Q8TCU3-2;Q8TCU3	.;S7A13_HUMAN	M	249;240	ENSP00000297524:V249M;ENSP00000410982:V240M	ENSP00000297524:V249M	V	-	1	0	SLC7A13	87304389	0.697000	0.27767	0.085000	0.20634	0.348000	0.29142	0.698000	0.25571	1.038000	0.40049	-0.182000	0.12963	GTG	C|0.874;T|0.126	0.126	strong		0.388	SLC7A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374704.1	NM_138817	
MYO10	4651	hgsc.bcm.edu	37	5	16794780	16794780	+	Missense_Mutation	SNP	G	G	A	rs7737765	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:16794780G>A	ENST00000513610.1	-	4	896	c.442C>T	c.(442-444)Cac>Tac	p.H148Y		NM_012334.2	NP_036466.2	Q9HD67	MYO10_HUMAN	myosin X	148	Myosin motor.		H -> Y (in dbSNP:rs7737765). {ECO:0000269|PubMed:11278607}.		ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cytoskeleton-dependent intracellular transport (GO:0030705)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|metabolic process (GO:0008152)|positive regulation of cell-cell adhesion (GO:0022409)|regulation of cell shape (GO:0008360)|regulation of filopodium assembly (GO:0051489)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|plus-end directed microfilament motor activity (GO:0060002)|spectrin binding (GO:0030507)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|lung(28)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	86						TGGTTGTCGTGGCGCTTCCAC	0.667													G|||	968	0.193291	0.2496	0.1282	5008	,	,		14999	0.1845		0.1183	False		,,,				2504	0.2495				p.H148Y		Atlas-SNP	.											.	MYO10	198	.	0			c.C442T						PASS	.	G	TYR/HIS	921,3395		100,721,1337	30.0	36.0	34.0		442	4.8	0.9	5	dbSNP_116	34	978,7530		58,862,3334	yes	missense	MYO10	NM_012334.2	83	158,1583,4671	AA,AG,GG		11.4951,21.3392,14.8082	benign	148/2059	16794780	1899,10925	2158	4254	6412	SO:0001583	missense	4651	exon4			TGTCGTGGCGCTT	AF247457	CCDS54834.1	5p15.1-p14.3	2013-01-10				ENSG00000145555		"""Myosins / Myosin superfamily : Class X"", ""Pleckstrin homology (PH) domain containing"""	7593	protein-coding gene	gene with protein product		601481				8884266	Standard	NM_012334		Approved	KIAA0799	uc003jft.4	Q9HD67		ENST00000513610.1:c.442C>T	5.37:g.16794780G>A	ENSP00000421280:p.His148Tyr	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	130	56	0.430769	NM_012334	A7E2D1|O94893|Q8IVX5|Q9NYM7|Q9P110|Q9P111|Q9UHF6	Missense_Mutation	SNP	ENST00000513610.1	37	CCDS54834.1	365	0.1671245421245421	116	0.23577235772357724	60	0.16574585635359115	99	0.17307692307692307	90	0.11873350923482849	G	17.66	3.444144	0.63067	0.213392	0.114951	ENSG00000145555	ENST00000513610;ENST00000513882;ENST00000502436	T;T;T	0.71934	-0.61;-0.61;-0.61	4.76	4.76	0.60689	Myosin head, motor domain (2);	.	.	.	.	T	0.00073	0.0002	M	0.71920	2.185	0.09310	P	1.0	B;P	0.38642	0.355;0.641	B;P	0.44359	0.393;0.447	T	0.01084	-1.1457	8	0.62326	D	0.03	.	18.153	0.89682	0.0:0.0:1.0:0.0	rs7737765;rs59339492	115;148	E9PCN3;Q9HD67	.;MYO10_HUMAN	Y	148;159;115	ENSP00000421280:H148Y;ENSP00000421309:H159Y;ENSP00000426783:H115Y	ENSP00000426783:H115Y	H	-	1	0	MYO10	16847780	0.993000	0.37304	0.932000	0.37286	0.849000	0.48306	6.606000	0.74159	2.342000	0.79632	0.561000	0.74099	CAC	G|0.839;A|0.161	0.161	strong		0.667	MYO10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366167.1	NM_012334	
SIRT3	23410	hgsc.bcm.edu	37	11	233067	233067	+	Missense_Mutation	SNP	C	C	T	rs11246020	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:233067C>T	ENST00000382743.4	-	3	724	c.622G>A	c.(622-624)Gtc>Atc	p.V208I	SIRT3_ENST00000528702.1_5'UTR|SIRT3_ENST00000532956.1_Missense_Mutation_p.V208I|SIRT3_ENST00000529382.1_Missense_Mutation_p.V66I|SIRT3_ENST00000525319.1_Missense_Mutation_p.V127I|SIRT3_ENST00000524564.1_Missense_Mutation_p.V144I	NM_001017524.2|NM_012239.5	NP_001017524.1|NP_036371.1	Q9NTG7	SIR3_HUMAN	sirtuin 3	208	Deacetylase sirtuin-type. {ECO:0000255|PROSITE-ProRule:PRU00236}.		V -> I (in dbSNP:rs11246020).		aerobic respiration (GO:0009060)|peptidyl-lysine deacetylation (GO:0034983)|protein ADP-ribosylation (GO:0006471)|protein deacetylation (GO:0006476)	membrane (GO:0016020)|mitochondrion (GO:0005739)	NAD+ ADP-ribosyltransferase activity (GO:0003950)|NAD+ binding (GO:0070403)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|zinc ion binding (GO:0008270)			endometrium(1)|lung(5)|urinary_tract(1)	7		all_cancers(49;1.58e-09)|all_epithelial(84;2.71e-06)|Breast(177;0.000162)|Ovarian(85;0.000626)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.0538)|all_lung(207;0.0713)		all cancers(45;3.66e-27)|Epithelial(43;2.02e-26)|OV - Ovarian serous cystadenocarcinoma(40;2.9e-21)|BRCA - Breast invasive adenocarcinoma(625;3.88e-05)|Lung(200;0.111)|LUSC - Lung squamous cell carcinoma(625;0.129)		TAGTGAGTGACGTTGGGCTTG	0.532													c|||	575	0.114816	0.0151	0.1484	5008	,	,		17968	0.0942		0.2048	False		,,,				2504	0.1544				p.V208I		Atlas-SNP	.											.	SIRT3	28	.	0			c.G622A						PASS	.		ILE/VAL,ILE/VAL	191,4215	120.0+/-157.7	6,179,2018	109.0	104.0	106.0		196,622	-3.3	0.0	11	dbSNP_120	106	1831,6769	328.2+/-318.2	179,1473,2648	yes	missense,missense	SIRT3	NM_001017524.2,NM_012239.5	29,29	185,1652,4666	TT,TC,CC		21.2907,4.335,15.5467	benign,benign	66/258,208/400	233067	2022,10984	2203	4300	6503	SO:0001583	missense	23410	exon3			GAGTGACGTTGGG	AF083108	CCDS7691.1, CCDS53590.1	11p15.5	2010-06-25	2010-06-25		ENSG00000142082	ENSG00000142082			14931	protein-coding gene	gene with protein product		604481	"""sirtuin (silent mating type information regulation 2, S.cerevisiae, homolog) 3"", ""sirtuin (silent mating type information regulation 2 homolog) 3 (S. cerevisiae)"""			10381378, 18215119	Standard	NM_012239		Approved	SIR2L3	uc001lok.4	Q9NTG7	OTTHUMG00000119074	ENST00000382743.4:c.622G>A	11.37:g.233067C>T	ENSP00000372191:p.Val208Ile	Somatic	278	0	0		WXS	Illumina HiSeq	Phase_I	289	229	0.792388	NM_012239	B7Z5U6|Q9Y6E8	Missense_Mutation	SNP	ENST00000382743.4	37	CCDS7691.1	279	0.12774725274725274	12	0.024390243902439025	54	0.14917127071823205	66	0.11538461538461539	147	0.19393139841688653	c	0.008	-1.872500	0.00542	0.04335	0.212907	ENSG00000142082	ENST00000382743;ENST00000525319;ENST00000524564;ENST00000532956;ENST00000529382;ENST00000528469	T;T;T;T;T;T	0.16897	2.31;2.31;2.31;2.31;2.31;2.31	5.37	-3.33	0.04958	.	1.847400	0.03050	N	0.154442	T	0.00012	0.0000	N	0.10685	0.025	0.80722	P	0.0	B;B;B;B;B	0.25609	0.13;0.002;0.001;0.004;0.002	B;B;B;B;B	0.15484	0.013;0.001;0.001;0.003;0.001	T	0.34551	-0.9824	9	0.21540	T	0.41	-5.4653	1.3502	0.02171	0.2453:0.2876:0.093:0.3741	rs11246020;rs52815403;rs61432625;rs11246020	208;208;127;144;208	E9PM75;B7Z7G4;E9PK80;E9PN58;Q9NTG7	.;.;.;.;SIRT3_HUMAN	I	208;127;144;208;66;66	ENSP00000372191:V208I;ENSP00000435464:V127I;ENSP00000432937:V144I;ENSP00000433077:V208I;ENSP00000437216:V66I;ENSP00000432857:V66I	ENSP00000372191:V208I	V	-	1	0	SIRT3	223067	0.000000	0.05858	0.000000	0.03702	0.194000	0.23727	-0.858000	0.04281	-0.565000	0.06061	-0.810000	0.03169	GTC	T|0.146;C|0.854	0.146	strong		0.532	SIRT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239288.3		
AHNAK2	113146	hgsc.bcm.edu	37	14	105418638	105418638	+	Silent	SNP	A	A	G	rs78353106|rs386781104	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:105418638A>G	ENST00000333244.5	-	7	3269	c.3150T>C	c.(3148-3150)ccT>ccC	p.P1050P	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	1050						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)			CAGTAGAAGCAGGCTGAATGC	0.617													.|||	1021	0.203874	0.3041	0.0807	5008	,	,		19172	0.2887		0.0477	False		,,,				2504	0.229				p.P1050P		Atlas-SNP	.											.	AHNAK2	719	.	0			c.T3150C						PASS	.	G		1056,2922		167,722,1100	106.0	119.0	115.0		3150	-3.6	0.0	14	dbSNP_131	115	359,7931		10,339,3796	no	coding-synonymous	AHNAK2	NM_138420.2		177,1061,4896	GG,GA,AA		4.3305,26.546,11.5341		1050/5796	105418638	1415,10853	1989	4145	6134	SO:0001819	synonymous_variant	113146	exon7			AGAAGCAGGCTGA	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.3150T>C	14.37:g.105418638A>G		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	178	67	0.376404	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Silent	SNP	ENST00000333244.5	37	CCDS45177.1																																																																																			A|0.849;G|0.151	0.151	strong		0.617	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
AGO2	27161	hgsc.bcm.edu	37	8	141566311	141566311	+	Silent	SNP	C	C	T	rs2271738	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:141566311C>T	ENST00000220592.5	-	9	1213	c.1101G>A	c.(1099-1101)gcG>gcA	p.A367A	AGO2_ENST00000519980.1_Silent_p.A367A	NM_012154.3	NP_036286.2	Q9UKV8	AGO2_HUMAN	argonaute RISC catalytic component 2	367					epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|innate immune response (GO:0045087)|mRNA cleavage involved in gene silencing by miRNA (GO:0035279)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|negative regulation of translational initiation (GO:0045947)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|post-embryonic development (GO:0009791)|pre-miRNA processing (GO:0031054)|regulation of transcription, DNA-templated (GO:0006355)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|transcription, DNA-templated (GO:0006351)|translation (GO:0006412)|translational initiation (GO:0006413)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|membrane (GO:0016020)|micro-ribonucleoprotein complex (GO:0035068)|mRNA cap binding complex (GO:0005845)|nucleus (GO:0005634)|polysome (GO:0005844)|ribonucleoprotein complex (GO:0030529)|RISC complex (GO:0016442)	endoribonuclease activity (GO:0004521)|endoribonuclease activity, cleaving siRNA-paired mRNA (GO:0070551)|metal ion binding (GO:0046872)|miRNA binding (GO:0035198)|mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|RNA 7-methylguanosine cap binding (GO:0000340)|siRNA binding (GO:0035197)|translation initiation factor activity (GO:0003743)										ACCTAGCAGTCGCTCTGATCA	0.527													C|||	2250	0.449281	0.2897	0.5807	5008	,	,		17424	0.6389		0.332	False		,,,				2504	0.4969				p.A367A		Atlas-SNP	.											.	.	.	.	0			c.G1101A						PASS	.	C	,	1329,3077	445.5+/-347.7	199,931,1073	102.0	95.0	97.0		1101,1101	-5.7	0.7	8	dbSNP_100	97	3191,5409	483.0+/-371.0	600,1991,1709	no	coding-synonymous,coding-synonymous	EIF2C2	NM_001164623.1,NM_012154.3	,	799,2922,2782	TT,TC,CC		37.1047,30.1634,34.7532	,	367/826,367/860	141566311	4520,8486	2203	4300	6503	SO:0001819	synonymous_variant	27161	exon9			AGCAGTCGCTCTG	AF121255	CCDS6380.1, CCDS55279.1	8q24.3	2013-02-15	2013-02-15	2013-02-15	ENSG00000123908	ENSG00000123908		"""Argonaute/PIWI family"""	3263	protein-coding gene	gene with protein product	"""argonaute 2"""	606229	"""eukaryotic translation initiation factor 2C, 2"""	EIF2C2		10534406, 12906857	Standard	NM_012154		Approved	hAGO2, Q10	uc003yvn.3	Q9UKV8	OTTHUMG00000164232	ENST00000220592.5:c.1101G>A	8.37:g.141566311C>T		Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	125	104	0.832	NM_012154	Q8TCZ5|Q8WV58|Q96ID1	Silent	SNP	ENST00000220592.5	37	CCDS6380.1																																																																																			C|0.623;T|0.377	0.377	strong		0.527	AGO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377866.4		
DDX60L	91351	hgsc.bcm.edu	37	4	169369862	169369862	+	Missense_Mutation	SNP	A	A	T	rs10029536	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:169369862A>T	ENST00000511577.1	-	9	1312	c.1065T>A	c.(1063-1065)aaT>aaA	p.N355K	DDX60L_ENST00000505890.1_Missense_Mutation_p.N355K|DDX60L_ENST00000260184.7_Missense_Mutation_p.N355K			Q5H9U9	DDX6L_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60-like	355			N -> K (in dbSNP:rs10029536).				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)		CAGAAACATGATTTAAATTCA	0.289													A|||	481	0.0960463	0.2496	0.0288	5008	,	,		17532	0.002		0.0209	False		,,,				2504	0.1104				p.N355K		Atlas-SNP	.											.	DDX60L	116	.	0			c.T1065A						PASS	.	A	LYS/ASN	839,2797		101,637,1080	55.0	51.0	52.0		1065	2.5	0.4	4	dbSNP_119	52	206,7942		3,200,3871	yes	missense	DDX60L	NM_001012967.1	94	104,837,4951	TT,TA,AA		2.5282,23.0748,8.868	benign	355/1707	169369862	1045,10739	1818	4074	5892	SO:0001583	missense	91351	exon9			AACATGATTTAAA	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.1065T>A	4.37:g.169369862A>T	ENSP00000422423:p.Asn355Lys	Somatic	338	0	0		WXS	Illumina HiSeq	Phase_I	255	116	0.454902	NM_001012967	Q96ND6	Missense_Mutation	SNP	ENST00000511577.1	37		145	0.06639194139194139	119	0.241869918699187	9	0.024861878453038673	1	0.0017482517482517483	16	0.021108179419525065	A	5.533	0.283307	0.10458	0.230748	0.025282	ENSG00000181381	ENST00000260184;ENST00000511577;ENST00000505890;ENST00000505863	T;T;T;T	0.16196	2.36;2.36;2.36;3.04	2.55	2.55	0.30701	.	0.631973	0.12106	U	0.499050	T	0.00012	0.0000	L	0.34521	1.04	0.50171	P	1.4899999999995472E-4	B;B;B	0.17268	0.012;0.021;0.012	B;B;B	0.15484	0.004;0.013;0.004	T	0.38178	-0.9673	9	0.23891	T	0.37	.	8.0632	0.30646	1.0:0.0:0.0:0.0	rs10029536;rs52797809;rs58298392;rs10029536	355;355;355	E9PAP8;D6R906;Q5H9U9	.;.;DDX6L_HUMAN	K	355;355;355;83	ENSP00000260184:N355K;ENSP00000422423:N355K;ENSP00000422202:N355K;ENSP00000421026:N83K	ENSP00000260184:N355K	N	-	3	2	DDX60L	169606437	0.553000	0.26513	0.420000	0.26596	0.455000	0.32408	2.703000	0.47110	1.147000	0.42369	0.383000	0.25322	AAT	A|0.918;T|0.082	0.082	strong		0.289	DDX60L-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000364839.1	NM_001012967	
CDH5	1003	hgsc.bcm.edu	37	16	66432424	66432424	+	Silent	SNP	C	C	T	rs3826229|rs386791725	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	112	0	0		WXS	Illumina HiSeq	Phase_I	105	105	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	
TTN	7273	hgsc.bcm.edu	37	2	179477717	179477717	+	Silent	SNP	A	A	G	rs2115558	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:179477717A>G	ENST00000591111.1	-	215	45032	c.44808T>C	c.(44806-44808)caT>caC	p.H14936H	TTN_ENST00000359218.5_Silent_p.H7637H|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000589830.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000589487.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000589234.1_RNA|TTN_ENST00000342992.6_Silent_p.H14009H|TTN_ENST00000460472.2_Silent_p.H7512H|TTN_ENST00000589042.1_Silent_p.H16577H|TTN_ENST00000342175.6_Silent_p.H7704H|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000592630.1_RNA			Q8WZ42	TITIN_HUMAN	titin	14936	Fibronectin type-III 8. {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)			CACCTCCATCATGTTCTGGTT	0.463													A|||	369	0.0736821	0.0885	0.0231	5008	,	,		19169	0.1577		0.0209	False		,,,				2504	0.0573				p.H16577H		Atlas-SNP	.											.	TTN	18412	.	0			c.T49731C						PASS	.	A	,,,	267,3667		8,251,1708	97.0	96.0	96.0		22536,42027,22911,23112	-6.7	0.7	2	dbSNP_96	96	108,8206		1,106,4050	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	,,,	9,357,5758	GG,GA,AA		1.299,6.787,3.0617	,,,	7512/26927,14009/33424,7637/27052,7704/27119	179477717	375,11873	1967	4157	6124	SO:0001819	synonymous_variant	7273	exon265			TCCATCATGTTCT	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.44808T>C	2.37:g.179477717A>G		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	136	58	0.426471	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|0.929;G|0.071	0.071	strong		0.463	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
TNN	63923	hgsc.bcm.edu	37	1	175087885	175087885	+	Missense_Mutation	SNP	A	A	G	rs6694078|rs386636935	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:175087885A>G	ENST00000239462.4	+	11	2688	c.2575A>G	c.(2575-2577)Atg>Gtg	p.M859V		NM_022093.1	NP_071376.1	Q9UQP3	TENN_HUMAN	tenascin N	859	Fibronectin type-III 7. {ECO:0000255|PROSITE-ProRule:PRU00316}.		M -> V (in dbSNP:rs6694078).		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)		p.M859V(1)		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)		GAGGCCGGGCATGGAGTACAC	0.592													G|||	866	0.172923	0.0424	0.17	5008	,	,		18400	0.3462		0.1292	False		,,,				2504	0.2178				p.M859V		Atlas-SNP	.											TNN,NS,carcinoma,0,1	TNN	297	1	1	Substitution - Missense(1)	stomach(1)	c.A2575G						scavenged	.	G	VAL/MET	222,4184		5,212,1986	85.0	71.0	76.0		2575	1.0	0.1	1	dbSNP_116	76	1065,7535		84,897,3319	no	missense	TNN	NM_022093.1	21	89,1109,5305	GG,GA,AA		12.3837,5.0386,9.8954	benign	859/1300	175087885	1287,11719	2203	4300	6503	SO:0001583	missense	63923	exon11			CCGGGCATGGAGT	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.2575A>G	1.37:g.175087885A>G	ENSP00000239462:p.Met859Val	Somatic	159	1	0.00628931		WXS	Illumina HiSeq	Phase_I	155	77	0.496774	NM_022093	B9EGP3|Q5R360	Missense_Mutation	SNP	ENST00000239462.4	37	CCDS30943.1	335	0.1533882783882784	22	0.044715447154471545	51	0.1408839779005525	177	0.3094405594405594	85	0.11213720316622691	G	0.011	-1.693923	0.00731	0.050386	0.123837	ENSG00000120332	ENST00000239462;ENST00000539081	T	0.56444	0.46	5.01	0.971	0.19698	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.458670	0.23196	N	0.050851	T	0.00012	0.0000	N	0.10760	0.04	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.38478	-0.9659	9	0.16896	T	0.51	.	9.4554	0.38751	0.5833:0.0:0.4167:0.0	rs6694078	859	Q9UQP3	TENN_HUMAN	V	859;682	ENSP00000239462:M859V	ENSP00000239462:M859V	M	+	1	0	TNN	173354508	0.069000	0.21087	0.096000	0.21009	0.072000	0.16883	0.342000	0.19926	0.011000	0.14865	-0.642000	0.03964	ATG	A|0.852;G|0.148	0.148	strong		0.592	TNN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084422.1	XM_040527	
GRK7	131890	hgsc.bcm.edu	37	3	141497368	141497368	+	Missense_Mutation	SNP	G	G	A	rs34429284		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:141497368G>A	ENST00000264952.2	+	1	379	c.242G>A	c.(241-243)cGc>cAc	p.R81H		NM_139209.2	NP_631948.1	Q8WTQ7	GRK7_HUMAN	G protein-coupled receptor kinase 7	81	RGS. {ECO:0000255|PROSITE- ProRule:PRU00171}.		R -> H (in dbSNP:rs34429284). {ECO:0000269|PubMed:17344846}.		protein autophosphorylation (GO:0046777)|signal transduction (GO:0007165)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|visual perception (GO:0007601)	membrane (GO:0016020)	ATP binding (GO:0005524)|G-protein coupled receptor kinase activity (GO:0004703)|rhodopsin kinase activity (GO:0050254)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(14)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	26						CCCACGTTCCGCAAGGCGGCA	0.647													G|||	1	0.000199681	0.0	0.0	5008	,	,		18091	0.0		0.0	False		,,,				2504	0.001				p.R81H		Atlas-SNP	.											.	GRK7	65	.	0			c.G242A						PASS	.	G	HIS/ARG	3,4401		0,3,2199	27.0	26.0	27.0		242	-4.7	0.0	3	dbSNP_126	27	26,8568		0,26,4271	yes	missense	GRK7	NM_139209.2	29	0,29,6470	AA,AG,GG		0.3025,0.0681,0.2231	possibly-damaging	81/554	141497368	29,12969	2202	4297	6499	SO:0001583	missense	131890	exon1			CGTTCCGCAAGGC		CCDS3120.1	3q24	2004-02-04	2004-02-04	2004-02-04	ENSG00000114124	ENSG00000114124			17031	protein-coding gene	gene with protein product		606987		GPRK7		11717351, 11754336	Standard	NM_139209		Approved		uc011bnd.2	Q8WTQ7	OTTHUMG00000159068	ENST00000264952.2:c.242G>A	3.37:g.141497368G>A	ENSP00000264952:p.Arg81His	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	108	46	0.425926	NM_139209		Missense_Mutation	SNP	ENST00000264952.2	37	CCDS3120.1	.	.	.	.	.	.	.	.	.	.	G	3.233	-0.157014	0.06544	6.81E-4	0.003025	ENSG00000114124	ENST00000264952	T	0.02236	4.38	4.33	-4.7	0.03288	Regulator of G protein signalling (3);Regulator of G protein signalling superfamily (1);	0.921148	0.09093	N	0.849577	T	0.01222	0.0040	N	0.08118	0	0.09310	N	1	P	0.45594	0.862	B	0.39562	0.303	T	0.47886	-0.9082	10	0.35671	T	0.21	1.776	7.5979	0.28058	0.3685:0.0:0.4911:0.1404	rs34429284	81	Q8WTQ7	GRK7_HUMAN	H	81	ENSP00000264952:R81H	ENSP00000264952:R81H	R	+	2	0	GRK7	142980058	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.737000	0.04877	-1.006000	0.03412	-0.982000	0.02568	CGC	G|0.998;A|0.002	0.002	strong		0.647	GRK7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353168.1	NM_139209	
CTAGE15	441294	hgsc.bcm.edu	37	7	143270172	143270172	+	Missense_Mutation	SNP	A	A	G	rs62484910		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:143270172A>G	ENST00000420911.2	+	1	1279	c.1262A>G	c.(1261-1263)gAa>gGa	p.E421G	RNU6-162P_ENST00000516228.1_RNA	NM_001008747.1	NP_001008747.1	A4D2H0	CTGEF_HUMAN	CTAGE family, member 15	421						integral component of membrane (GO:0016021)											AGAGTGGAAGAAAAGCTCAGC	0.383																																					p.E421G		Atlas-SNP	.											.	.	.	.	0			c.A1262G						PASS	.						80.0	84.0	83.0					7																	143270172		1760	3756	5516	SO:0001583	missense	441294	exon1			TGGAAGAAAAGCT		CCDS64788.1	7q35	2013-02-25	2013-02-25	2013-02-25	ENSG00000176227	ENSG00000271079			37295	protein-coding gene	gene with protein product			"""CTAGE family, member 15, pseudogene"""	CTAGE15P			Standard	NM_001008747		Approved		uc011kth.3	A4D2H0	OTTHUMG00000153233	ENST00000420911.2:c.1262A>G	7.37:g.143270172A>G	ENSP00000474204:p.Glu421Gly	Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	210	183	0.871429	NM_001008747	A6H8Z8	Missense_Mutation	SNP	ENST00000420911.2	37																																																																																				A|0.440;G|0.560	0.560	strong		0.383	CTAGE15-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000330280.2	NM_001008747	
SLC25A27	9481	hgsc.bcm.edu	37	6	46623698	46623698	+	Silent	SNP	T	T	C	rs3757241	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:46623698T>C	ENST00000371347.5	+	2	477	c.225T>C	c.(223-225)gcT>gcC	p.A75A	SLC25A27_ENST00000411689.2_Silent_p.A75A|SLC25A27_ENST00000452689.2_5'UTR	NM_001204051.1|NM_004277.4	NP_001190980.1|NP_004268.3	O95847	UCP4_HUMAN	solute carrier family 25, member 27	75					cellular triglyceride homeostasis (GO:0035356)|generation of precursor metabolites and energy (GO:0006091)|inner ear development (GO:0048839)|negative regulation of apoptotic process (GO:0043066)|negative regulation of mitochondrial calcium ion concentration (GO:0051562)|negative regulation of mitochondrial membrane potential (GO:0010917)|neuron death (GO:0070997)|positive regulation of cell proliferation (GO:0008284)|regulation of glucose import (GO:0046324)|transport (GO:0006810)	apical part of cell (GO:0045177)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)				central_nervous_system(1)|kidney(1)|lung(4)|prostate(1)|urinary_tract(1)	8			Lung(136;0.192)			TGCGCACAGCTCTAGGGATCA	0.488													C|||	4434	0.885383	0.9705	0.8631	5008	,	,		14769	0.9097		0.7575	False		,,,				2504	0.8926				p.A75A		Atlas-SNP	.											.	SLC25A27	22	.	0			c.T225C						PASS	.	C	,,	3611,183		1722,167,8	124.0	128.0	126.0		225,225,225	4.4	1.0	6	dbSNP_107	126	6687,1557		2716,1255,151	no	coding-synonymous,coding-synonymous,coding-synonymous	SLC25A27	NM_001204051.1,NM_001204052.1,NM_004277.4	,,	4438,1422,159	CC,CT,TT		18.8865,4.8234,14.4542	,,	75/301,75/246,75/324	46623698	10298,1740	1897	4122	6019	SO:0001819	synonymous_variant	9481	exon2			CACAGCTCTAGGG	AK090871	CCDS43470.1, CCDS56431.1	6p12.3	2013-05-22			ENSG00000153291	ENSG00000153291		"""Solute carriers"""	21065	protein-coding gene	gene with protein product		613725				10025957, 10772343	Standard	NM_004277		Approved	UCP4, FLJ33552	uc003oyh.3	O95847	OTTHUMG00000014786	ENST00000371347.5:c.225T>C	6.37:g.46623698T>C		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	106	106	1	NM_001204051	F5GWR4|Q5VTS9|Q8N518	Silent	SNP	ENST00000371347.5	37	CCDS43470.1																																																																																			T|0.141;C|0.859	0.859	strong		0.488	SLC25A27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040791.1	NM_004277	
KRTAP10-2	386679	hgsc.bcm.edu	37	21	45970718	45970718	+	Silent	SNP	C	C	T	rs233238	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:45970718C>T	ENST00000391621.1	-	1	670	c.624G>A	c.(622-624)ccG>ccA	p.P208P	TSPEAR_ENST00000397916.1_Intron|TSPEAR_ENST00000323084.4_Intron|KRTAP10-2_ENST00000498210.1_Intron	NM_198693.2	NP_941966.1	P60368	KR102_HUMAN	keratin associated protein 10-2	208	22 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				large_intestine(1)|lung(4)|skin(1)	6						GCTGGCAGCACGGAGAGGAAG	0.642													C|||	1331	0.265775	0.357	0.1715	5008	,	,		20976	0.3641		0.2068	False		,,,				2504	0.1687				p.P208P		Atlas-SNP	.											.	KRTAP10-2	21	.	0			c.G624A						PASS	.	C	,	1465,2941	472.6+/-356.4	247,971,985	119.0	126.0	124.0		,624	-5.0	0.0	21	dbSNP_79	124	1696,6904	311.7+/-310.5	158,1380,2762	no	intron,coding-synonymous	TSPEAR,KRTAP10-2	NM_144991.2,NM_198693.2	,	405,2351,3747	TT,TC,CC		19.7209,33.2501,24.3042	,	,208/256	45970718	3161,9845	2203	4300	6503	SO:0001819	synonymous_variant	386679	exon1			GCAGCACGGAGAG	AJ566381	CCDS42955.1	21q22.3	2007-10-05			ENSG00000205445	ENSG00000205445		"""Keratin associated proteins"""	22967	protein-coding gene	gene with protein product				KRTAP18-2			Standard	NM_198693		Approved	KAP10.2, KAP18.2	uc002zfi.1	P60368	OTTHUMG00000057625	ENST00000391621.1:c.624G>A	21.37:g.45970718C>T		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	78	20	0.25641	NM_198693	Q70LJ5	Silent	SNP	ENST00000391621.1	37	CCDS42955.1																																																																																			C|0.742;T|0.258	0.258	strong		0.642	KRTAP10-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128027.1		
CCDC158	339965	hgsc.bcm.edu	37	4	77305346	77305346	+	Silent	SNP	A	A	G	rs17001890	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:77305346A>G	ENST00000388914.3	-	5	773	c.621T>C	c.(619-621)caT>caC	p.H207H	CCDC158_ENST00000434846.2_Silent_p.H207H	NM_001042784.1	NP_001036249.1	Q5M9N0	CD158_HUMAN	coiled-coil domain containing 158	207										breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(28)|ovary(3)|pancreas(1)|prostate(1)|skin(6)|stomach(1)	56						ACATGCTGTCATGTTCACATA	0.393													G|||	1136	0.226837	0.3427	0.1585	5008	,	,		15743	0.0724		0.2565	False		,,,				2504	0.2474				p.H207H		Atlas-SNP	.											.	CCDC158	114	.	0			c.T621C						PASS	.	G		1124,2614		162,800,907	100.0	92.0	94.0		621	-10.8	0.1	4	dbSNP_123	94	2060,6160		270,1520,2320	no	coding-synonymous	CCDC158	NM_001042784.1		432,2320,3227	GG,GA,AA		25.0608,30.0696,26.6265		207/1114	77305346	3184,8774	1869	4110	5979	SO:0001819	synonymous_variant	339965	exon5			GCTGTCATGTTCA	BC035224	CCDS43242.1	4q21.1	2009-04-06			ENSG00000163749	ENSG00000163749			26374	protein-coding gene	gene with protein product						12477932	Standard	NM_001042784		Approved	FLJ25770	uc003hkb.4	Q5M9N0	OTTHUMG00000160916	ENST00000388914.3:c.621T>C	4.37:g.77305346A>G		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	91	41	0.450549	NM_001042784	Q8IYQ1|Q8N7D4|Q8N7E3	Silent	SNP	ENST00000388914.3	37	CCDS43242.1																																																																																			A|0.776;G|0.224	0.224	strong		0.393	CCDC158-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362694.2	NM_001042784	
SPATA19	219938	hgsc.bcm.edu	37	11	133714522	133714522	+	Missense_Mutation	SNP	G	G	A	rs2282602	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:133714522G>A	ENST00000299140.3	-	3	203	c.149C>T	c.(148-150)gCt>gTt	p.A50V	SPATA19_ENST00000532889.1_Missense_Mutation_p.A50V	NM_174927.1	NP_777587.1	Q7Z5L4	SPT19_HUMAN	spermatogenesis associated 19	50			A -> V (in dbSNP:rs2282602). {ECO:0000269|PubMed:12688595}.		cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	mitochondrial outer membrane (GO:0005741)				cervix(1)|endometrium(2)|large_intestine(2)|lung(5)|prostate(1)	11	all_hematologic(175;0.127)	all_cancers(12;5.59e-17)|all_epithelial(12;2.65e-12)|all_lung(97;0.00045)|Lung NSC(97;0.000861)|Breast(109;0.000873)|Medulloblastoma(222;0.0425)|Esophageal squamous(93;0.0844)|all_neural(223;0.117)		Epithelial(10;4.36e-10)|all cancers(11;7.1e-09)|BRCA - Breast invasive adenocarcinoma(10;8.45e-09)|OV - Ovarian serous cystadenocarcinoma(99;0.00286)|Lung(977;0.207)		GCCCCGAGAAGCCTCTTCTTC	0.498													G|||	1700	0.339457	0.1044	0.317	5008	,	,		20435	0.6022		0.3926	False		,,,				2504	0.3476				p.A50V		Atlas-SNP	.											.	SPATA19	36	.	0			c.C149T						PASS	.	G	VAL/ALA	741,3661	305.5+/-289.0	65,611,1525	100.0	102.0	101.0		149	5.0	1.0	11	dbSNP_100	101	3216,5378	485.9+/-371.8	616,1984,1697	yes	missense	SPATA19	NM_174927.1	64	681,2595,3222	AA,AG,GG		37.4215,16.8333,30.4478	possibly-damaging	50/168	133714522	3957,9039	2201	4297	6498	SO:0001583	missense	219938	exon3			CGAGAAGCCTCTT	AK098717	CCDS8493.1	11q25	2010-04-23				ENSG00000166118			30614	protein-coding gene	gene with protein product	"""spergen 1"", ""cancer/testis antigen 132"""	609805				12477932	Standard	XM_005271448		Approved	FLJ25851, spergen1, SPAS1, CT132	uc001qgv.1	Q7Z5L4		ENST00000299140.3:c.149C>T	11.37:g.133714522G>A	ENSP00000299140:p.Ala50Val	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	68	50	0.735294	NM_174927	Q8N7A9	Missense_Mutation	SNP	ENST00000299140.3	37	CCDS8493.1	796	0.36446886446886445	48	0.0975609756097561	120	0.3314917127071823	329	0.5751748251748252	299	0.3944591029023747	G	20.4	3.990884	0.74703	0.168333	0.374215	ENSG00000166118	ENST00000299140;ENST00000532889	T;T	0.56611	0.45;0.45	5.02	5.02	0.67125	.	0.000000	0.56097	D	0.000029	T	0.00012	0.0000	L	0.34521	1.04	0.26466	P	0.9753572	D	0.76494	0.999	D	0.80764	0.994	T	0.50734	-0.8793	9	0.52906	T	0.07	-6.9761	14.1925	0.65646	0.0:0.0:1.0:0.0	rs2282602;rs61530072;rs2282602	50	Q7Z5L4	SPT19_HUMAN	V	50	ENSP00000299140:A50V;ENSP00000435248:A50V	ENSP00000299140:A50V	A	-	2	0	SPATA19	133219732	1.000000	0.71417	1.000000	0.80357	0.774000	0.43823	3.306000	0.51881	2.493000	0.84123	0.655000	0.94253	GCT	G|0.673;A|0.327	0.327	strong		0.498	SPATA19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393281.1	NM_174927	
MON1A	84315	hgsc.bcm.edu	37	3	49949071	49949071	+	Silent	SNP	A	A	G	rs868891	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:49949071A>G	ENST00000417270.1	-	4	1218	c.525T>C	c.(523-525)ccT>ccC	p.P175P	MON1A_ENST00000483022.1_5'UTR|CTD-2330K9.3_ENST00000419183.1_Intron|MON1A_ENST00000455683.2_Intron|MON1A_ENST00000296473.3_Silent_p.P264P			Q86VX9	MON1A_HUMAN	MON1 secretory trafficking family member A	167										breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(3)|ovary(2)|prostate(1)	13				BRCA - Breast invasive adenocarcinoma(193;4.62e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.00551)|Kidney(197;0.00621)		GGGAGTACACAGGCTTCCCTG	0.612													A|||	1250	0.249601	0.2542	0.3012	5008	,	,		20663	0.122		0.4215	False		,,,				2504	0.1616				p.P264P		Atlas-SNP	.											MON1A,NS,carcinoma,0,1	MON1A	41	1	0			c.T792C						PASS	.	A	,	1209,3197	419.6+/-338.7	169,871,1163	91.0	79.0	83.0		,792	-10.2	0.6	3	dbSNP_86	83	3678,4922	527.8+/-381.2	763,2152,1385	yes	intron,coding-synonymous	MON1A	NM_001142501.1,NM_032355.3	,	932,3023,2548	GG,GA,AA		42.7674,27.4399,37.575	,	,264/653	49949071	4887,8119	2203	4300	6503	SO:0001819	synonymous_variant	84315	exon3			GTACACAGGCTTC	AK074404	CCDS2808.2, CCDS46830.1	3p21.31	2013-08-21	2013-08-21		ENSG00000164077	ENSG00000164077			28207	protein-coding gene	gene with protein product		611464	"""MON1 homolog A (yeast)"""			12477932	Standard	NM_032355		Approved	MGC13272, SAND1	uc003cxz.3	Q86VX9	OTTHUMG00000156737	ENST00000417270.1:c.525T>C	3.37:g.49949071A>G		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	79	50	0.632911	NM_032355	B2RDQ1|G5E9N1|Q8NAV7|Q9BRF3	Silent	SNP	ENST00000417270.1	37																																																																																				A|0.671;G|0.329	0.329	strong		0.612	MON1A-005	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000345538.2	NM_032355	
INHBA	3624	hgsc.bcm.edu	37	7	41729843	41729843	+	Missense_Mutation	SNP	C	C	T	rs138819536	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:41729843C>T	ENST00000242208.4	-	3	932	c.686G>A	c.(685-687)cGg>cAg	p.R229Q	AC005027.3_ENST00000416150.1_RNA|INHBA_ENST00000464515.1_5'UTR|INHBA_ENST00000442711.1_Missense_Mutation_p.R229Q	NM_002192.2	NP_002183.1	P08476	INHBA_HUMAN	inhibin, beta A	229					activin receptor signaling pathway (GO:0032924)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|cellular response to cholesterol (GO:0071397)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|defense response (GO:0006952)|endodermal cell differentiation (GO:0035987)|erythrocyte differentiation (GO:0030218)|extrinsic apoptotic signaling pathway (GO:0097191)|eyelid development in camera-type eye (GO:0061029)|G1/S transition of mitotic cell cycle (GO:0000082)|growth (GO:0040007)|hair follicle development (GO:0001942)|hematopoietic progenitor cell differentiation (GO:0002244)|hemoglobin biosynthetic process (GO:0042541)|male gonad development (GO:0008584)|mesodermal cell differentiation (GO:0048333)|negative regulation of B cell differentiation (GO:0045578)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of follicle-stimulating hormone secretion (GO:0046882)|negative regulation of interferon-gamma biosynthetic process (GO:0045077)|negative regulation of macrophage differentiation (GO:0045650)|negative regulation of phosphorylation (GO:0042326)|nervous system development (GO:0007399)|odontogenesis (GO:0042476)|ovarian follicle development (GO:0001541)|palate development (GO:0060021)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of follicle-stimulating hormone secretion (GO:0046881)|positive regulation of ovulation (GO:0060279)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|progesterone secretion (GO:0042701)|regulation of follicle-stimulating hormone secretion (GO:0046880)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to drug (GO:0042493)	activin A complex (GO:0043509)|extracellular region (GO:0005576)|inhibin A complex (GO:0043512)	cytokine activity (GO:0005125)|growth factor activity (GO:0008083)|hormone activity (GO:0005179)|identical protein binding (GO:0042802)|peptide hormone binding (GO:0017046)|type II activin receptor binding (GO:0070699)			biliary_tract(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(15)|lung(26)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	55						GTCCAGCAACCGCTGGATGCT	0.572										TSP Lung(11;0.080)			C|||	3	0.000599042	0.0008	0.0	5008	,	,		18089	0.0		0.002	False		,,,				2504	0.0				p.R229Q		Atlas-SNP	.											INHBA,NS,carcinoma,0,1	INHBA	118	1	0			c.G686A						PASS	.	C	GLN/ARG	4,4402		0,4,2199	52.0	50.0	51.0		686	6.1	1.0	7	dbSNP_134	51	30,8570		0,30,4270	yes	missense	INHBA	NM_002192.2	43	0,34,6469	TT,TC,CC		0.3488,0.0908,0.2614	possibly-damaging	229/427	41729843	34,12972	2203	4300	6503	SO:0001583	missense	3624	exon3			AGCAACCGCTGGA		CCDS5464.1	7p15-p13	2014-01-30	2007-07-30		ENSG00000122641	ENSG00000122641		"""Endogenous ligands"""	6066	protein-coding gene	gene with protein product		147290	"""inhibin, beta A (activin A, activin AB alpha polypeptide)"""			3345731	Standard	NM_002192		Approved		uc003thr.3	P08476	OTTHUMG00000023574	ENST00000242208.4:c.686G>A	7.37:g.41729843C>T	ENSP00000242208:p.Arg229Gln	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	54	43	0.796296	NM_002192	Q14599	Missense_Mutation	SNP	ENST00000242208.4	37	CCDS5464.1	2	9.157509157509158E-4	1	0.0020325203252032522	0	0.0	0	0.0	1	0.0013192612137203166	.	18.81	3.702318	0.68501	9.08E-4	0.003488	ENSG00000122641	ENST00000242208;ENST00000442711	T;T	0.68025	-0.3;-0.3	6.06	6.06	0.98353	Transforming growth factor-beta, N-terminal (1);	0.420201	0.27686	N	0.018263	T	0.61248	0.2332	L	0.43152	1.355	0.43714	D	0.996185	P	0.44478	0.836	B	0.39503	0.301	T	0.56902	-0.7902	10	0.19147	T	0.46	-17.7159	20.6208	0.99490	0.0:1.0:0.0:0.0	.	229	P08476	INHBA_HUMAN	Q	229	ENSP00000242208:R229Q;ENSP00000397197:R229Q	ENSP00000242208:R229Q	R	-	2	0	INHBA	41696368	0.946000	0.32159	0.988000	0.46212	0.992000	0.81027	2.752000	0.47516	2.882000	0.98803	0.655000	0.94253	CGG	C|0.998;T|0.002	0.002	strong		0.572	INHBA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250793.1		
GPR149	344758	hgsc.bcm.edu	37	3	154147336	154147336	+	Silent	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:154147336C>T	ENST00000389740.2	-	1	168	c.69G>A	c.(67-69)acG>acA	p.T23T		NM_001038705.1	NP_001033794.1	Q86SP6	GP149_HUMAN	G protein-coupled receptor 149	23					antral ovarian follicle growth (GO:0001547)|estrous cycle phase (GO:0060206)|negative regulation of ovulation (GO:0060280)|preantral ovarian follicle growth (GO:0001546)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			autonomic_ganglia(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(22)|ovary(7)|prostate(1)|skin(1)|urinary_tract(2)	47			LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.173)			TTAAAAGGTCCGTAGAATTAT	0.363																																					p.T23T		Atlas-SNP	.											GPR149,NS,carcinoma,-1,1	GPR149	134	1	0			c.G69A						PASS	.						77.0	77.0	77.0					3																	154147336		1836	4087	5923	SO:0001819	synonymous_variant	344758	exon1			AAGGTCCGTAGAA	AY255534	CCDS43162.1	3q25.2	2012-08-21			ENSG00000174948	ENSG00000174948		"""GPCR / Class A : Orphans"""	23627	protein-coding gene	gene with protein product						12679517	Standard	NM_001038705		Approved	PGR10, IEDA	uc003faa.3	Q86SP6	OTTHUMG00000159131	ENST00000389740.2:c.69G>A	3.37:g.154147336C>T		Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	146	33	0.226027	NM_001038705		Silent	SNP	ENST00000389740.2	37	CCDS43162.1																																																																																			.	.	none		0.363	GPR149-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353430.1	XM_293580	
CCDC169	728591	hgsc.bcm.edu	37	13	36801415	36801415	+	Missense_Mutation	SNP	C	C	T	rs9546785	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:36801415C>T	ENST00000503173.1	-	8	678	c.649G>A	c.(649-651)Gga>Aga	p.G217R	CCDC169_ENST00000239860.6_Missense_Mutation_p.G117R|CCDC169_ENST00000491049.2_Missense_Mutation_p.G115R|SOHLH2_ENST00000554962.1_Intron|CCDC169_ENST00000379864.2_Missense_Mutation_p.G115R|CCDC169-SOHLH2_ENST00000511166.1_Intron	NM_001198908.1	NP_001185837.1	A6NNP5	CC169_HUMAN	coiled-coil domain containing 169	0										breast(1)|endometrium(1)	2						GCTTTTTGTCCGAGGCATGTC	0.493													C|||	1891	0.377596	0.2231	0.4755	5008	,	,		14885	0.3819		0.4712	False		,,,				2504	0.4162				p.G217R		Atlas-SNP	.											.	CCDC169	20	.	0			c.G649A						PASS	.	C	ARG/GLY,ARG/GLY,ARG/GLY,ARG/GLY,	368,1016		51,266,375	96.0	81.0	86.0		343,343,349,649,	0.2	0.0	13	dbSNP_119	86	1513,1669		358,797,436	yes	missense,missense,missense,missense,intron	CCDC169,CCDC169-SOHLH2	NM_001144982.2,NM_001144983.2,NM_001144984.2,NM_001198908.1,NM_001198910.1	125,125,125,125,	409,1063,811	TT,TC,CC		47.5487,26.5896,41.1958	,,,,	115/140,115/140,117/142,217/242,	36801415	1881,2685	692	1591	2283	SO:0001583	missense	728591	exon8			TTTGTCCGAGGCA		CCDS45027.1, CCDS45028.1, CCDS45029.1, CCDS53863.1, CCDS55897.1	13q13.3	2011-08-09	2011-08-09	2011-08-09	ENSG00000242715	ENSG00000242715			34361	protein-coding gene	gene with protein product			"""chromosome 13 open reading frame 38"""	C13orf38			Standard	NM_001144981		Approved	RP11-251J8.1, LOC728591		A6NNP5	OTTHUMG00000016731	ENST00000503173.1:c.649G>A	13.37:g.36801415C>T	ENSP00000426174:p.Gly217Arg	Somatic	265	0	0		WXS	Illumina HiSeq	Phase_I	180	176	0.977778	NM_001198908	A6NC13|A6NCT2|B7ZW45|B7ZW49|B9EJF2|Q9H1T4|Q9H1T5	Missense_Mutation	SNP	ENST00000503173.1	37	CCDS55897.1	830	0.38003663003663	110	0.22357723577235772	166	0.4585635359116022	207	0.3618881118881119	347	0.4577836411609499	C	6.816	0.519730	0.13005	0.265896	0.475487	ENSG00000242715	ENST00000491049;ENST00000503173;ENST00000239860;ENST00000379864	T;T;T;T	0.59083	0.33;0.48;0.29;0.33	0.235	0.235	0.15431	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.73380	0.98;0.98;0.98	T	0.46484	-0.9188	7	0.87932	D	0	.	.	.	.	rs9546785;rs52798169;rs9546785	217;117;115	A6NNP5-4;B7ZW49;A6NNP5-3	.;.;.	R	115;217;117;115	ENSP00000425252:G115R;ENSP00000426174:G217R;ENSP00000239860:G117R;ENSP00000369193:G115R	ENSP00000239860:G117R	G	-	1	0	CCDC169	35699415	0.002000	0.14202	0.004000	0.12327	0.004000	0.04260	0.305000	0.19254	0.308000	0.22923	0.313000	0.20887	GGA	C|0.624;T|0.376	0.376	strong		0.493	CCDC169-012	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000368253.1	NM_001144981	
ADAMTSL3	57188	hgsc.bcm.edu	37	15	84651185	84651185	+	Silent	SNP	C	C	A	rs8031704	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:84651185C>A	ENST00000286744.5	+	21	3029	c.2805C>A	c.(2803-2805)ccC>ccA	p.P935P	ADAMTSL3_ENST00000567476.1_Silent_p.P935P	NM_207517.2	NP_997400.2	P82987	ATL3_HUMAN	ADAMTS-like 3	935	Ig-like C2-type 1.					proteinaceous extracellular matrix (GO:0005578)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.P935P(1)		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)			TTAAGTGCCCCGTGCGACGAT	0.493													A|||	1883	0.375998	0.5681	0.2536	5008	,	,		18791	0.38		0.3419	False		,,,				2504	0.2342				p.P935P		Atlas-SNP	.											ADAMTSL3,NS,adenoma,0,2	ADAMTSL3	290	2	1	Substitution - coding silent(1)	stomach(1)	c.C2805A						PASS	.	A		2372,2034	563.1+/-381.1	649,1074,480	148.0	137.0	141.0		2805	-2.1	1.0	15	dbSNP_116	141	2959,5641	666.8+/-402.4	512,1935,1853	no	coding-synonymous	ADAMTSL3	NM_207517.2		1161,3009,2333	AA,AC,CC		34.407,46.1643,40.9888		935/1692	84651185	5331,7675	2203	4300	6503	SO:0001819	synonymous_variant	57188	exon21			GTGCCCCGTGCGA	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.2805C>A	15.37:g.84651185C>A		Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	197	196	0.994924	NM_207517	A1A566|A1A567|Q9ULI7	Silent	SNP	ENST00000286744.5	37	CCDS10326.1																																																																																			C|0.593;A|0.407	0.407	strong		0.493	ADAMTSL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304007.2	NM_207517	
TMEM9B	56674	hgsc.bcm.edu	37	11	8977830	8977830	+	Silent	SNP	A	A	G	rs2568068	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:8977830A>G	ENST00000534025.1	-	3	672	c.213T>C	c.(211-213)gtT>gtC	p.V71V	TMEM9B_ENST00000528117.1_5'UTR|TMEM9B_ENST00000309134.5_5'UTR|TMEM9B_ENST00000525069.1_5'UTR	NM_020644.1	NP_065695.1	Q9NQ34	TMM9B_HUMAN	TMEM9 domain family, member B	71					positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	signal transducer activity (GO:0004871)			breast(1)|lung(1)|prostate(1)	3				Epithelial(150;4.39e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0237)		TGGGCTCCACAACATGAAGGC	0.423													A|||	1677	0.334864	0.4395	0.2363	5008	,	,		19737	0.4494		0.2097	False		,,,				2504	0.274				p.V71V		Atlas-SNP	.											.	TMEM9B	6	.	0			c.T213C						PASS	.	A		1667,2735	509.1+/-367.1	301,1065,835	84.0	78.0	80.0		213	-2.3	1.0	11	dbSNP_100	80	1789,6803	320.4+/-314.6	181,1427,2688	no	coding-synonymous	TMEM9B	NM_020644.1		482,2492,3523	GG,GA,AA		20.8217,37.8692,26.5969		71/199	8977830	3456,9538	2201	4296	6497	SO:0001819	synonymous_variant	56674	exon3			CTCCACAACATGA	AJ400877	CCDS7796.1, CCDS66021.1	11p15.3	2008-02-05	2005-10-06	2005-10-06	ENSG00000175348	ENSG00000175348			1168	protein-coding gene	gene with protein product			"""chromosome 11 open reading frame 15"""	C11orf15		11528127	Standard	NM_001286095		Approved		uc001mhe.1	Q9NQ34	OTTHUMG00000165676	ENST00000534025.1:c.213T>C	11.37:g.8977830A>G		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	54	6	0.111111	NM_020644	Q7Z649	Silent	SNP	ENST00000534025.1	37	CCDS7796.1																																																																																			T|0.006;G|0.283	0.283	strong		0.423	TMEM9B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385722.1		
RADIL	55698	hgsc.bcm.edu	37	7	4856904	4856904	+	Missense_Mutation	SNP	T	T	C	rs201312293	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:4856904T>C	ENST00000399583.3	-	7	1881	c.1694A>G	c.(1693-1695)tAc>tGc	p.Y565C	RADIL_ENST00000538469.1_Missense_Mutation_p.Y325C|RADIL_ENST00000536091.1_Silent_p.V511V	NM_018059.4	NP_060529.4	Q96JH8	RADIL_HUMAN	Ras association and DIL domains	565	Dilute. {ECO:0000255|PROSITE- ProRule:PRU00503}.				multicellular organismal development (GO:0007275)|signal transduction (GO:0007165)|substrate adhesion-dependent cell spreading (GO:0034446)	microtubule (GO:0005874)				NS(1)|biliary_tract(2)|breast(1)|central_nervous_system(3)|endometrium(2)|large_intestine(2)|lung(22)|pancreas(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	41		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0986)|OV - Ovarian serous cystadenocarcinoma(56;7.41e-15)		CTGGAAGGCGTACAGCACCAC	0.632													T|||	7	0.00139776	0.0	0.0058	5008	,	,		16847	0.0		0.003	False		,,,				2504	0.0				p.Y565C		Atlas-SNP	.											RADIL,right_upper_lobe,carcinoma,0,1	RADIL	110	1	0			c.A1694G						PASS	.	T	CYS/TYR	9,4395	12.9+/-30.5	0,9,2193	67.0	74.0	71.0		1694	4.5	0.9	7		71	48,8550	30.7+/-82.3	0,48,4251	yes	missense	RADIL	NM_018059.4	194	0,57,6444	CC,CT,TT		0.5583,0.2044,0.4384	probably-damaging	565/1076	4856904	57,12945	2202	4299	6501	SO:0001583	missense	55698	exon7			AAGGCGTACAGCA	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.1694A>G	7.37:g.4856904T>C	ENSP00000382492:p.Tyr565Cys	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	100	65	0.65	NM_018059	A4D1Z5|A5YM49|B7ZL20|Q0VFZ9|Q75LH3|Q9BSP5|Q9H0M6|Q9NW43|Q9NWC4	Missense_Mutation	SNP	ENST00000399583.3	37	CCDS43544.1	4	0.0018315018315018315	0	0.0	2	0.0055248618784530384	0	0.0	2	0.002638522427440633	t	18.25	3.583364	0.65992	0.002044	0.005583	ENSG00000157927	ENST00000399583;ENST00000316919;ENST00000544486;ENST00000538469	T;T	0.42900	0.96;0.96	5.7	4.54	0.55810	Dilute (1);	0.000000	0.85682	D	0.000000	T	0.49321	0.1550	L	0.60455	1.87	0.80722	D	1	D	0.89917	1.0	D	0.77557	0.99	T	0.52660	-0.8546	10	0.46703	T	0.11	-18.0204	10.6794	0.45804	0.0:0.0759:0.0:0.9241	.	565	Q96JH8	RADIL_HUMAN	C	565;536;299;325	ENSP00000382492:Y565C;ENSP00000442966:Y325C	ENSP00000320946:Y536C	Y	-	2	0	RADIL	4823430	1.000000	0.71417	0.867000	0.34043	0.958000	0.62258	2.542000	0.45744	0.987000	0.38709	0.375000	0.23000	TAC	T|0.997;C|0.003	0.003	strong		0.632	RADIL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323769.2	NM_018059	
AMPD2	271	hgsc.bcm.edu	37	1	110170896	110170896	+	Silent	SNP	T	T	C	rs863978	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:110170896T>C	ENST00000256578.3	+	10	1794	c.1434T>C	c.(1432-1434)caT>caC	p.H478H	RP5-1160K1.6_ENST00000369843.3_RNA|AMPD2_ENST00000342115.4_Silent_p.H397H|AMPD2_ENST00000526301.1_3'UTR|AMPD2_ENST00000358729.4_Silent_p.H403H|AMPD2_ENST00000528667.1_Silent_p.H478H|AMPD2_ENST00000393688.3_Silent_p.H359H|AMPD2_ENST00000528454.1_Silent_p.H360H	NM_004037.7	NP_004028.3	Q01433	AMPD2_HUMAN	adenosine monophosphate deaminase 2	478					cell death (GO:0008219)|cyclic purine nucleotide metabolic process (GO:0052652)|energy homeostasis (GO:0097009)|IMP biosynthetic process (GO:0006188)|IMP salvage (GO:0032264)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase metabolic process (GO:0006144)|purine-containing compound salvage (GO:0043101)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	AMP deaminase activity (GO:0003876)|metal ion binding (GO:0046872)			breast(1)|large_intestine(3)|ovary(2)|skin(1)	7		all_epithelial(167;2.5e-05)|all_lung(203;0.000135)|Lung NSC(277;0.000269)|Breast(1374;0.244)		Lung(183;0.0425)|all cancers(265;0.0884)|Colorectal(144;0.109)|Epithelial(280;0.111)|LUSC - Lung squamous cell carcinoma(189;0.228)		TGGATGTGCATGCGGTCTGTG	0.622													T|||	4045	0.807708	0.7337	0.7695	5008	,	,		19104	0.9802		0.6769	False		,,,				2504	0.8916				p.H478H		Atlas-SNP	.											.	AMPD2	75	.	0			c.T1434C						PASS	.	T	,,	3331,1075	722.3+/-409.3	1256,819,128	76.0	71.0	73.0		1434,1191,1077	-1.8	1.0	1	dbSNP_86	73	5568,3032	663.0+/-402.0	1798,1972,530	no	coding-synonymous,coding-synonymous,coding-synonymous	AMPD2	NM_004037.6,NM_139156.2,NM_203404.1	,,	3054,2791,658	CC,CT,TT		35.2558,24.3985,31.5777	,,	478/880,397/799,359/761	110170896	8899,4107	2203	4300	6503	SO:0001819	synonymous_variant	271	exon10			TGTGCATGCGGTC	S47833	CCDS804.1, CCDS805.1, CCDS30796.1, CCDS58016.1	1p13.3	2014-03-03	2010-02-10		ENSG00000116337	ENSG00000116337	3.5.4.6		469	protein-coding gene	gene with protein product	"""AMPD isoform L"""	102771	"""adenosine monophosphate deaminase 2 (isoform L)"""			1400401, 24482476	Standard	NM_004037		Approved	SPG63	uc009wfh.2	Q01433	OTTHUMG00000011649	ENST00000256578.3:c.1434T>C	1.37:g.110170896T>C		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	70	69	0.985714	NM_004037	B4DK50|B4DZI5|E9PNG0|Q14856|Q14857|Q16686|Q16687|Q16688|Q16729|Q5T693|Q5T695|Q96IA1|Q9UDX8|Q9UDX9|Q9UMU4	Silent	SNP	ENST00000256578.3	37	CCDS805.1	1713	0.7843406593406593	371	0.7540650406504065	270	0.7458563535911602	563	0.9842657342657343	509	0.6715039577836411	T	7.305	0.613917	0.14066	0.756015	0.647442	ENSG00000116337	ENST00000369840	.	.	.	5.04	-1.77	0.07982	.	.	.	.	.	T	0.24084	0.0583	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.20338	-1.0278	3	.	.	.	-42.0812	10.0817	0.42393	0.0:0.3024:0.0:0.6976	rs863978;rs2228425;rs11556215;rs60258788;rs863978	.	.	.	R	449	.	.	C	+	1	0	AMPD2	109972419	0.042000	0.20092	0.994000	0.49952	0.692000	0.40212	-0.772000	0.04694	-0.169000	0.10834	-0.441000	0.05720	TGC	T|0.265;C|0.735	0.735	strong		0.622	AMPD2-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390615.1		
ABCA7	10347	hgsc.bcm.edu	37	19	1047161	1047161	+	Silent	SNP	A	A	G	rs3752237	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:1047161A>G	ENST00000263094.6	+	15	2082	c.1851A>G	c.(1849-1851)ggA>ggG	p.G617G	ABCA7_ENST00000435683.2_Silent_p.G479G|ABCA7_ENST00000533574.1_3'UTR|ABCA7_ENST00000433129.1_Silent_p.G617G	NM_019112.3	NP_061985.2	Q8IZY2	ABCA7_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 7	617					apolipoprotein A-I-mediated signaling pathway (GO:0038027)|ATP catabolic process (GO:0006200)|cholesterol efflux (GO:0033344)|high-density lipoprotein particle assembly (GO:0034380)|memory (GO:0007613)|negative regulation of amyloid precursor protein biosynthetic process (GO:0042985)|negative regulation of ATPase activity (GO:0032780)|negative regulation of beta-amyloid formation (GO:1902430)|peptide cross-linking (GO:0018149)|phagocytosis (GO:0006909)|phospholipid efflux (GO:0033700)|phospholipid scrambling (GO:0017121)|positive regulation of ATPase activity (GO:0032781)|positive regulation of beta-amyloid clearance (GO:1900223)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of engulfment of apoptotic cell (GO:1901076)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of phagocytosis (GO:0050766)|positive regulation of phospholipid efflux (GO:1902995)|protein localization to nucleus (GO:0034504)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|ATP-binding cassette (ABC) transporter complex (GO:0043190)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|phagocytic cup (GO:0001891)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	apolipoprotein A-I receptor activity (GO:0034188)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|phospholipid transporter activity (GO:0005548)|transporter activity (GO:0005215)			NS(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(7)|lung(22)|ovary(1)|pancreas(7)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	65		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CACAGCTGGGAGACATCCTCC	0.672													G|||	3482	0.695288	0.6089	0.7695	5008	,	,		13710	0.8056		0.6004	False		,,,				2504	0.7434				p.G617G		Atlas-SNP	.											.	ABCA7	174	.	0			c.A1851G						PASS	.			2848,1554		936,976,289	39.0	36.0	37.0		1851	-2.8	1.0	19	dbSNP_107	37	5259,3329		1651,1957,686	no	coding-synonymous	ABCA7	NM_019112.3		2587,2933,975	GG,GA,AA		38.7634,35.3021,37.5905		617/2147	1047161	8107,4883	2201	4294	6495	SO:0001819	synonymous_variant	10347	exon15			GCTGGGAGACATC	AF328787	CCDS12055.1	19p13.3	2012-03-14			ENSG00000064687	ENSG00000064687		"""ATP binding cassette transporters / subfamily A"""	37	protein-coding gene	gene with protein product		605414					Standard	NM_019112		Approved	ABCX	uc002lqw.4	Q8IZY2	OTTHUMG00000167547	ENST00000263094.6:c.1851A>G	19.37:g.1047161A>G		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	55	28	0.509091	NM_019112	Q96S58|Q9BZC4|Q9NR73|Q9UKP8	Silent	SNP	ENST00000263094.6	37	CCDS12055.1																																																																																			A|0.347;G|0.653	0.653	strong		0.672	ABCA7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000394993.1	NM_019112	
CCDC148	130940	hgsc.bcm.edu	37	2	159201754	159201754	+	Missense_Mutation	SNP	T	T	C	rs4664950	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:159201754T>C	ENST00000283233.5	-	3	537	c.224A>G	c.(223-225)cAg>cGg	p.Q75R	CCDC148_ENST00000409187.1_Missense_Mutation_p.Q84R|CCDC148_ENST00000536771.1_Intron|CCDC148_ENST00000409889.1_Missense_Mutation_p.Q75R	NM_138803.3	NP_620158.3	Q8NFR7	CC148_HUMAN	coiled-coil domain containing 148	75			Q -> R (in dbSNP:rs4664950).							endometrium(2)|kidney(2)|large_intestine(6)|lung(9)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	23						CTGGTATTCCTGCCACCACAC	0.383													T|||	127	0.0253594	0.0023	0.0346	5008	,	,		16655	0.0248		0.0288	False		,,,				2504	0.047				p.Q75R		Atlas-SNP	.											.	CCDC148	64	.	0			c.A224G						PASS	.	T	,ARG/GLN	26,4380	35.2+/-66.4	0,26,2177	301.0	276.0	284.0		,224	5.9	1.0	2	dbSNP_111	284	178,8422	81.2+/-143.8	2,174,4124	yes	intron,missense	CCDC148	NM_001171637.1,NM_138803.3	,43	2,200,6301	CC,CT,TT		2.0698,0.5901,1.5685	,benign	,75/592	159201754	204,12802	2203	4300	6503	SO:0001583	missense	130940	exon3			TATTCCTGCCACC		CCDS33304.1	2q24.1	2007-12-07			ENSG00000153237	ENSG00000153237			25191	protein-coding gene	gene with protein product							Standard	NM_138803		Approved	MGC125588	uc002tzq.3	Q8NFR7	OTTHUMG00000153973	ENST00000283233.5:c.224A>G	2.37:g.159201754T>C	ENSP00000283233:p.Gln75Arg	Somatic	269	0	0		WXS	Illumina HiSeq	Phase_I	240	117	0.4875	NM_138803	F5H839|Q3B7I3|Q3B7I4|Q3KR41|Q4ZG12|Q4ZG23|Q53TM6|Q96BN5|Q96LM2	Missense_Mutation	SNP	ENST00000283233.5	37	CCDS33304.1	52	0.023809523809523808	1	0.0020325203252032522	16	0.04419889502762431	15	0.026223776223776224	20	0.026385224274406333	T	11.35	1.613110	0.28712	0.005901	0.020698	ENSG00000153237	ENST00000283233;ENST00000409187;ENST00000409889	T;T;T	0.48836	0.8;0.8;0.8	5.88	5.88	0.94601	.	.	.	.	.	T	0.23492	0.0568	L	0.57536	1.79	0.80722	D	1	P	0.50156	0.932	P	0.53450	0.726	T	0.24905	-1.0147	9	0.27785	T	0.31	-15.0859	12.6933	0.56988	0.0:0.0:0.0:1.0	rs4664950;rs52814321;rs4664950	75	Q8NFR7	CC148_HUMAN	R	75;84;75	ENSP00000283233:Q75R;ENSP00000386674:Q84R;ENSP00000386583:Q75R	ENSP00000283233:Q75R	Q	-	2	0	CCDC148	158910000	0.998000	0.40836	1.000000	0.80357	0.998000	0.95712	2.423000	0.44705	2.239000	0.73571	0.533000	0.62120	CAG	C|0.020;G|0.000;T|0.980	0.020	strong		0.383	CCDC148-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333270.1	NM_138803	
C19orf45	374877	hgsc.bcm.edu	37	19	7573301	7573301	+	Silent	SNP	C	C	T	rs1133380|rs113917984	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:7573301C>T	ENST00000361664.2	+	9	1644	c.1503C>T	c.(1501-1503)tgC>tgT	p.C501C	CTD-2207O23.12_ENST00000599312.1_Intron	NM_198534.2	NP_940936.2	Q8NA69	CS045_HUMAN	chromosome 19 open reading frame 45	501										endometrium(1)|kidney(1)|liver(1)|lung(2)|ovary(2)|stomach(1)	8						TGTACCTGTGCCCCAGCCAGC	0.607													C|||	1199	0.239417	0.1725	0.3285	5008	,	,		17982	0.1756		0.337	False		,,,				2504	0.2321				p.C501C		Atlas-SNP	.											.	C19orf45	36	.	0			c.C1503T						PASS	.	C		814,3590		90,634,1478	25.0	24.0	24.0		1503	1.5	1.0	19	dbSNP_86	24	2762,5838		459,1844,1997	no	coding-synonymous	C19orf45	NM_198534.2		549,2478,3475	TT,TC,CC		32.1163,18.4832,27.4992		501/506	7573301	3576,9428	2202	4300	6502	SO:0001819	synonymous_variant	374877	exon9			CCTGTGCCCCAGC	BC029824	CCDS12179.2	19p13.2	2008-02-05			ENSG00000198723	ENSG00000198723			24745	protein-coding gene	gene with protein product						12477932	Standard	NM_198534		Approved	FLJ35784	uc002mgm.2	Q8NA69	OTTHUMG00000157183	ENST00000361664.2:c.1503C>T	19.37:g.7573301C>T		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	99	34	0.343434	NM_198534	Q8N115	Silent	SNP	ENST00000361664.2	37	CCDS12179.2																																																																																			.	.	weak		0.607	C19orf45-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347808.1	NM_198534	
POF1B	79983	hgsc.bcm.edu	37	X	84563135	84563135	+	Missense_Mutation	SNP	T	T	A	rs363774	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:84563135T>A	ENST00000262753.4	-	10	1190	c.1045A>T	c.(1045-1047)Atg>Ttg	p.M349L	POF1B_ENST00000373145.3_Missense_Mutation_p.M349L	NM_024921.3	NP_079197.3	Q8WVV4	POF1B_HUMAN	premature ovarian failure, 1B	349			M -> L (in dbSNP:rs363774). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15459172, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.4}.			tight junction (GO:0005923)				central_nervous_system(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|liver(2)|lung(17)|ovary(1)|prostate(1)	35						CTTACTGTCATATCATTTTGA	0.348													A|||	3443	0.912053	0.7284	0.6643	3775	,	,		11209	0.7173		0.6163	False		,,,				2504	0.6912				p.M349L		Atlas-SNP	.											.	POF1B	77	.	0			c.A1045T						PASS	.	A	LEU/MET	3577,258		1419,205,534,8,37	76.0	69.0	71.0		1045	3.5	1.0	X	dbSNP_79	71	5196,1532		1452,836,1456,140,416	yes	missense	POF1B	NM_024921.3	15	2871,1041,1990,148,453	AA,AT,A,TT,T		22.7705,6.7275,16.9459	benign	349/590	84563135	8773,1790	2203	4300	6503	SO:0001583	missense	79983	exon10			CTGTCATATCATT	BC017500	CCDS14452.1	Xq21.2	2008-02-05			ENSG00000124429	ENSG00000124429			13711	protein-coding gene	gene with protein product		300603				11299520	Standard	NM_024921		Approved	POF, FLJ22792	uc004eer.2	Q8WVV4	OTTHUMG00000021934	ENST00000262753.4:c.1045A>T	X.37:g.84563135T>A	ENSP00000262753:p.Met349Leu	Somatic	246	0	0		WXS	Illumina HiSeq	Phase_I	151	150	0.993378	NM_024921	A8K2U5|Q5H9E9|Q5H9F0|Q8NG12|Q9H5Y2|Q9H738|Q9H744	Missense_Mutation	SNP	ENST00000262753.4	37	CCDS14452.1	1486	0.8957203134418324	252	0.9333333333333333	165	0.7638888888888888	276	0.9517241379310345	323	0.6931330472103004	A	3.511	-0.099866	0.07010	0.932725	0.772295	ENSG00000124429	ENST00000262753;ENST00000373145	D;D	0.81908	-1.55;-1.55	5.86	3.52	0.40303	.	0.000000	0.85682	N	0.000000	T	0.00012	0.0000	N	0.00210	-1.845	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.42103	-0.9471	9	0.02654	T	1	.	4.7834	0.13213	0.7001:0.0:0.1572:0.1427	rs363774;rs17318017;rs17856541;rs60469476;rs363774	349;349	Q8WVV4-1;Q8WVV4	.;POF1B_HUMAN	L	349	ENSP00000262753:M349L;ENSP00000362238:M349L	ENSP00000262753:M349L	M	-	1	0	POF1B	84449791	1.000000	0.71417	0.996000	0.52242	0.941000	0.58515	1.108000	0.31123	0.330000	0.23485	-0.315000	0.08773	ATG	T|0.137;0|0.004	.	strong		0.348	POF1B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000057391.2	NM_024921	
KIF21B	23046	hgsc.bcm.edu	37	1	200978027	200978027	+	Missense_Mutation	SNP	G	G	A	rs140589352	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:200978027G>A	ENST00000422435.2	-	3	633	c.317C>T	c.(316-318)tCg>tTg	p.S106L	KIF21B_ENST00000461742.2_Missense_Mutation_p.S106L|KIF21B_ENST00000360529.5_Missense_Mutation_p.S106L|KIF21B_ENST00000332129.2_Missense_Mutation_p.S106L	NM_001252100.1	NP_001239029.1	O75037	KI21B_HUMAN	kinesin family member 21B	106	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				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						CTCCTCCTCCGACGTTGCCAT	0.642													G|||	42	0.00838658	0.0	0.013	5008	,	,		20340	0.0		0.0179	False		,,,				2504	0.0153				p.S106L		Atlas-SNP	.											.	KIF21B	208	.	0			c.C317T						PASS	.	G	LEU/SER	13,4393	20.2+/-43.8	0,13,2190	118.0	103.0	108.0		317	4.7	0.0	1	dbSNP_134	108	193,8407	85.0+/-147.5	3,187,4110	yes	missense	KIF21B	NM_017596.2	145	3,200,6300	AA,AG,GG		2.2442,0.2951,1.5839	benign	106/1625	200978027	206,12800	2203	4300	6503	SO:0001583	missense	23046	exon3			TCCTCCGACGTTG	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.317C>T	1.37:g.200978027G>A	ENSP00000411831:p.Ser106Leu	Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	51	26	0.509804	NM_017596	B2RP62|B7ZMI0|Q5T4J3	Missense_Mutation	SNP	ENST00000422435.2	37	CCDS58056.1	19	0.0086996336996337	0	0.0	4	0.011049723756906077	0	0.0	15	0.01978891820580475	G	10.10	1.257053	0.22965	0.002951	0.022442	ENSG00000116852	ENST00000332129;ENST00000360529;ENST00000461742;ENST00000422435;ENST00000539858	T;T;T;T	0.74315	-0.83;-0.83;-0.83;-0.83	5.57	4.66	0.58398	Kinesin, motor domain (4);	0.322422	0.29073	N	0.013235	T	0.52208	0.1720	M	0.68952	2.095	0.09310	N	0.999999	P;P;B;P	0.42248	0.774;0.774;0.0;0.733	B;B;B;B	0.31869	0.094;0.137;0.002;0.131	T	0.55296	-0.8163	10	0.27082	T	0.32	.	14.3505	0.66699	0.0714:0.0:0.9286:0.0	.	106;106;106;106	B7ZMI0;B2RP62;O75037;O75037-2	.;.;KI21B_HUMAN;.	L	106	ENSP00000328494:S106L;ENSP00000353724:S106L;ENSP00000433808:S106L;ENSP00000411831:S106L	ENSP00000328494:S106L	S	-	2	0	KIF21B	199244650	0.791000	0.28800	0.014000	0.15608	0.324000	0.28378	4.731000	0.62022	1.348000	0.45733	0.650000	0.86243	TCG	G|0.987;A|0.013	0.013	strong		0.642	KIF21B-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382635.1	XM_371332	
TNKS1BP1	85456	hgsc.bcm.edu	37	11	57081197	57081197	+	Missense_Mutation	SNP	G	G	C	rs4939134	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:57081197G>C	ENST00000532437.1	-	4	1276	c.965C>G	c.(964-966)aCt>aGt	p.T322S	TNKS1BP1_ENST00000530920.1_5'Flank|TNKS1BP1_ENST00000358252.3_Missense_Mutation_p.T322S			Q9C0C2	TB182_HUMAN	tankyrase 1 binding protein 1, 182kDa	322	Acidic.|Pro-rich.		T -> S (in dbSNP:rs4939134). {ECO:0000269|PubMed:11854288}.		gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|RNA metabolic process (GO:0016070)|telomere maintenance via telomerase (GO:0007004)	CCR4-NOT complex (GO:0030014)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|nuclear telomeric heterochromatin (GO:0005724)|nucleus (GO:0005634)	ankyrin binding (GO:0030506)|enzyme binding (GO:0019899)			breast(3)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(11)|lung(24)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	64		all_epithelial(135;0.21)				AGCTTCAGGAGTCTGGGCTTC	0.662													g|||	2438	0.486821	0.0711	0.6268	5008	,	,		14414	0.7063		0.5457	False		,,,				2504	0.6626				p.T322S		Atlas-SNP	.											.	TNKS1BP1	148	.	0			c.C965G						PASS	.	G	SER/THR	648,3744		59,530,1607	19.0	25.0	23.0		965	2.2	0.8	11	dbSNP_111	23	4530,4062		1212,2106,978	yes	missense	TNKS1BP1	NM_033396.2	58	1271,2636,2585	CC,CG,GG		47.2765,14.7541,39.8799	benign	322/1730	57081197	5178,7806	2196	4296	6492	SO:0001583	missense	85456	exon5			TCAGGAGTCTGGG	AB051528	CCDS7951.1	11q12.2	2008-07-21			ENSG00000149115	ENSG00000149115			19081	protein-coding gene	gene with protein product		607104				11854288	Standard	NM_033396		Approved	TAB182, KIAA1741, FLJ45975	uc001njs.3	Q9C0C2	OTTHUMG00000167022	ENST00000532437.1:c.965C>G	11.37:g.57081197G>C	ENSP00000437271:p.Thr322Ser	Somatic	211	1	0.00473934		WXS	Illumina HiSeq	Phase_I	168	168	1	NM_033396	A7E2F8|Q6PJ35|Q6ZV74	Missense_Mutation	SNP	ENST00000532437.1	37	CCDS7951.1	1091	0.49954212454212454	50	0.1016260162601626	211	0.5828729281767956	397	0.6940559440559441	433	0.5712401055408971	g	2.298	-0.360917	0.05103	0.147541	0.527235	ENSG00000149115	ENST00000358252;ENST00000532437	T;T	0.26810	1.71;1.71	4.11	2.23	0.28157	.	.	.	.	.	T	0.00012	0.0000	N	0.01352	-0.895	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.41556	-0.9502	8	0.02654	T	1	-0.9643	3.5604	0.07880	0.157:0.4422:0.3082:0.0926	rs4939134	322	Q9C0C2	TB182_HUMAN	S	322	ENSP00000350990:T322S;ENSP00000437271:T322S	ENSP00000350990:T322S	T	-	2	0	TNKS1BP1	56837773	0.001000	0.12720	0.786000	0.31890	0.504000	0.33889	0.130000	0.15850	0.348000	0.23949	-0.364000	0.07487	ACT	G|0.586;C|0.414	0.414	strong		0.662	TNKS1BP1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392455.1	NM_033396	
DNAH14	127602	hgsc.bcm.edu	37	1	225555512	225555512	+	Intron	SNP	C	C	T	rs11578981	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:225555512C>T	ENST00000445597.2	+	53	9205				DNAH14_ENST00000439375.2_Silent_p.A3939A|DNAH14_ENST00000430092.1_Silent_p.A3939A			Q0VDD8	DYH14_HUMAN	dynein, axonemal, heavy chain 14						microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			NS(2)|breast(3)|central_nervous_system(3)|endometrium(8)|kidney(4)|large_intestine(2)|lung(2)|skin(2)|stomach(1)	27						TCAAGATTGCCGTGGAATCTC	0.433													C|||	1628	0.32508	0.1876	0.4366	5008	,	,		18169	0.2321		0.5696	False		,,,				2504	0.2761				p.A3939A		Atlas-SNP	.											.	DNAH14	300	.	0			c.C11817T						PASS	.	C		347,1037		48,251,393	121.0	101.0	107.0		11817	-2.8	0.0	1	dbSNP_120	107	1772,1410		474,824,293	no	coding-synonymous	DNAH14	NM_001373.1		522,1075,686	TT,TC,CC		44.3118,25.0723,46.4082		3939/4516	225555512	2119,2447	692	1591	2283	SO:0001627	intron_variant	127602	exon75			GATTGCCGTGGAA	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.9205+9158C>T	1.37:g.225555512C>T		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	43	21	0.488372	NM_001373	A6NG62|A6NNL2|Q0VDD9|Q4VXC7|Q4VXG4|Q4VXG5|Q5VU33|Q5VU34	Silent	SNP	ENST00000445597.2	37																																																																																				C|0.637;T|0.363	0.363	strong		0.433	DNAH14-007	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000331217.3	XM_059166	
KCNJ2	3759	hgsc.bcm.edu	37	17	68172326	68172326	+	Silent	SNP	C	C	T	rs173135	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:68172326C>T	ENST00000243457.3	+	2	1529	c.1146C>T	c.(1144-1146)ctC>ctT	p.L382L	KCNJ2_ENST00000535240.1_Silent_p.L382L	NM_000891.2	NP_000882.1	P63252	KCNJ2_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 2	382					cardiac muscle cell action potential involved in contraction (GO:0086002)|cellular potassium ion homeostasis (GO:0030007)|cellular response to mechanical stimulus (GO:0071260)|magnesium ion transport (GO:0015693)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|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 import (GO:0010107)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|protein homotetramerization (GO:0051289)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of membrane repolarization (GO:0060306)|regulation of resting membrane potential (GO:0060075)|regulation of skeletal muscle contraction via regulation of action potential (GO:0014861)|relaxation of cardiac muscle (GO:0055119)|relaxation of skeletal muscle (GO:0090076)|synaptic transmission (GO:0007268)	dendritic spine (GO:0043197)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|intrinsic component of membrane (GO:0031224)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|rough endoplasmic reticulum (GO:0005791)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|voltage-gated potassium channel complex (GO:0008076)	inward rectifier potassium channel activity (GO:0005242)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|voltage-gated potassium channel activity involved in cardiac muscle cell action potential repolarization (GO:0086008)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(13)|skin(1)|urinary_tract(1)	25	Breast(10;1.64e-08)					AAGTTGCCCTCACAAGCAAAG	0.448													C|||	771	0.153954	0.1551	0.2392	5008	,	,		20815	0.131		0.1203	False		,,,				2504	0.1503				p.L382L		Atlas-SNP	.											.	KCNJ2	74	.	0			c.C1146T						PASS	.	C		574,3832	251.8+/-258.4	35,504,1664	121.0	123.0	122.0		1146	3.0	1.0	17	dbSNP_79	122	1020,7580	214.9+/-254.4	63,894,3343	no	coding-synonymous	KCNJ2	NM_000891.2		98,1398,5007	TT,TC,CC		11.8605,13.0277,12.2559		382/428	68172326	1594,11412	2203	4300	6503	SO:0001819	synonymous_variant	3759	exon2			TGCCCTCACAAGC	AF011904	CCDS11688.1	17q24.3	2014-09-17				ENSG00000123700		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Inwardly rectifying"""	6263	protein-coding gene	gene with protein product		600681				7696590, 11240146, 16382105	Standard	NM_000891		Approved	Kir2.1, IRK1, LQT7	uc002jir.3	P63252		ENST00000243457.3:c.1146C>T	17.37:g.68172326C>T		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	49	23	0.469388	NM_000891	O15110|P48049	Silent	SNP	ENST00000243457.3	37	CCDS11688.1																																																																																			C|0.867;T|0.133	0.133	strong		0.448	KCNJ2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450889.1	NM_000891	
SHROOM3	57619	hgsc.bcm.edu	37	4	77661017	77661017	+	Missense_Mutation	SNP	A	A	C	rs76656494	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:77661017A>C	ENST00000296043.6	+	5	2644	c.1691A>C	c.(1690-1692)gAa>gCa	p.E564A		NM_020859.3	NP_065910.3	Q8TF72	SHRM3_HUMAN	shroom family member 3	564					actin cytoskeleton organization (GO:0030036)|apical protein localization (GO:0045176)|cell morphogenesis (GO:0000902)|cellular pigment accumulation (GO:0043482)|columnar/cuboidal epithelial cell development (GO:0002066)|neural tube closure (GO:0001843)|pattern specification process (GO:0007389)|regulation of cell shape (GO:0008360)	adherens junction (GO:0005912)|apical junction complex (GO:0043296)|apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|microtubule (GO:0005874)				NS(3)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(10)|kidney(2)|large_intestine(6)|lung(29)|ovary(1)|skin(5)|upper_aerodigestive_tract(1)	60			Lung(101;0.0903)			TCAGTGCCTGAAAATGAGGAG	0.502													A|||	33	0.00658946	0.0	0.013	5008	,	,		21550	0.0		0.0229	False		,,,				2504	0.001				p.E564A		Atlas-SNP	.											.	SHROOM3	134	.	0			c.A1691C						PASS	.	A	ALA/GLU	14,4392	22.3+/-47.3	0,14,2189	168.0	168.0	168.0		1691	4.4	1.0	4	dbSNP_131	168	145,8455	70.7+/-133.2	2,141,4157	yes	missense	SHROOM3	NM_020859.3	107	2,155,6346	CC,CA,AA		1.686,0.3177,1.2225	probably-damaging	564/1997	77661017	159,12847	2203	4300	6503	SO:0001583	missense	57619	exon5			TGCCTGAAAATGA	AB055660	CCDS3579.2	4q21.1	2009-11-25			ENSG00000138771	ENSG00000138771			30422	protein-coding gene	gene with protein product		604570				10589677, 16615870	Standard	NM_020859		Approved	ShrmL, SHRM, KIAA1481, APXL3	uc011cbx.2	Q8TF72	OTTHUMG00000157075	ENST00000296043.6:c.1691A>C	4.37:g.77661017A>C	ENSP00000296043:p.Glu564Ala	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	50	26	0.52	NM_020859	Q5QTQ3|Q6ZRW3|Q96IR9|Q9P247	Missense_Mutation	SNP	ENST00000296043.6	37	CCDS3579.2	23	0.010531135531135532	1	0.0020325203252032522	5	0.013812154696132596	0	0.0	17	0.022427440633245383	A	15.10	2.733513	0.48939	0.003177	0.01686	ENSG00000138771	ENST00000296043	T	0.26660	1.72	5.59	4.39	0.52855	.	0.093877	0.44902	D	0.000410	T	0.31009	0.0783	M	0.71581	2.175	0.35431	D	0.794093	D;P;P	0.76494	0.999;0.89;0.8	D;B;B	0.65987	0.94;0.382;0.153	T	0.57688	-0.7768	10	0.72032	D	0.01	-7.8779	12.7677	0.57401	0.8629:0.1371:0.0:0.0	.	388;564;342	B4E244;Q8TF72;B3KY47	.;SHRM3_HUMAN;.	A	564	ENSP00000296043:E564A	ENSP00000296043:E564A	E	+	2	0	SHROOM3	77880041	1.000000	0.71417	1.000000	0.80357	0.414000	0.31173	1.907000	0.39897	0.925000	0.37094	0.460000	0.39030	GAA	A|0.988;C|0.012	0.012	strong		0.502	SHROOM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252408.2	NM_020859	
TTLL3	26140	hgsc.bcm.edu	37	3	9876919	9876919	+	Missense_Mutation	SNP	G	G	A	rs1057278	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:9876919G>A	ENST00000547186.1	+	13	2281	c.2065G>A	c.(2065-2067)Gct>Act	p.A689T	TTLL3_ENST00000397241.1_3'UTR|TTLL3_ENST00000455274.1_Intron|TTLL3_ENST00000430793.1_3'UTR|TTLL3_ENST00000426895.4_Missense_Mutation_p.A832T|ARPC4-TTLL3_ENST00000397256.1_3'UTR|TTLL3_ENST00000383827.1_3'UTR	NM_001025930.3	NP_001021100.3	Q9Y4R7	TTLL3_HUMAN	tubulin tyrosine ligase-like family, member 3	689			A -> T (in dbSNP:rs1057278).		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)					CAAACCCAGGGCTGAGGCCTG	0.577													G|||	675	0.134784	0.2572	0.1081	5008	,	,		19877	0.0565		0.1243	False		,,,				2504	0.0798				p.A832T		Atlas-SNP	.											.	TTLL3	51	.	0			c.G2494A						PASS	.	G	THR/ALA,	910,3038		89,732,1153	61.0	66.0	65.0		2494,	0.9	0.6	3	dbSNP_86	65	1329,6977		115,1099,2939	yes	missense,utr-3	TTLL3,ARPC4-TTLL3	NM_001025930.3,NM_001198793.1	58,	204,1831,4092	AA,AG,GG		16.0005,23.0496,18.2716	benign,	832/916,	9876919	2239,10015	1974	4153	6127	SO:0001583	missense	26140	exon13			CCCAGGGCTGAGG		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.2065G>A	3.37:g.9876919G>A	ENSP00000446659:p.Ala689Thr	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	48	48	1	NM_001025930	Q4KMS8|Q6AWA3|Q6ZU95|Q8NDN8|Q96GG8|Q9H876|Q9UI99	Missense_Mutation	SNP	ENST00000547186.1	37		321	0.14697802197802198	144	0.2926829268292683	43	0.11878453038674033	34	0.05944055944055944	100	0.13192612137203166	G	13.18	2.159321	0.38119	0.230496	0.160005	ENSG00000214021	ENST00000426895;ENST00000547186	T;T	0.05855	3.38;3.51	3.72	0.904	0.19302	.	687.911000	0.01247	N	0.008766	T	0.00012	0.0000	N	0.08118	0	0.21147	P	0.999772258	B	0.14012	0.009	B	0.09377	0.004	T	0.45977	-0.9224	9	0.44086	T	0.13	.	6.0331	0.19690	0.3402:0.0:0.6598:0.0	rs1057278;rs3172413;rs52789940;rs60101267;rs1057278	689	Q9Y4R7	TTLL3_HUMAN	T	832;689	ENSP00000392549:A832T;ENSP00000446659:A689T	ENSP00000392549:A832T	A	+	1	0	TTLL3	9851919	0.951000	0.32395	0.631000	0.29282	0.287000	0.27160	0.599000	0.24089	0.184000	0.20083	0.561000	0.74099	GCT	G|0.859;A|0.141	0.141	strong		0.577	TTLL3-203	KNOWN	basic	protein_coding	protein_coding		NM_001025930.2	
CES1	1066	hgsc.bcm.edu	37	16	55862883	55862883	+	Splice_Site	SNP	C	C	A	rs3826190		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:55862883C>A	ENST00000361503.4	-	2	183	c.53G>T	c.(52-54)gGg>gTg	p.G18V	CES1_ENST00000360526.3_Missense_Mutation_p.G19V|CES1_ENST00000422046.2_Splice_Site_p.G18V|CES1_ENST00000566555.1_5'Flank			P23141	EST1_HUMAN	carboxylesterase 1	18			G -> GA.		epithelial cell differentiation (GO:0030855)|metabolic process (GO:0008152)|response to toxic substance (GO:0009636)	endoplasmic reticulum (GO:0005783)	carboxylic ester hydrolase activity (GO:0052689)|methylumbelliferyl-acetate deacetylase activity (GO:0047374)	p.G19V(1)							all cancers(182;0.13)|Epithelial(162;0.137)	Benzocaine(DB01086)|Capecitabine(DB01101)|Ciclesonide(DB01410)|Clopidogrel(DB00758)|Cyclandelate(DB04838)|Dabigatran etexilate(DB06695)|Indomethacin(DB00328)|Irinotecan(DB00762)|L-Carnitine(DB00583)|Mycophenolate mofetil(DB00688)|Oseltamivir(DB00198)|Probucol(DB01599)|Rufinamide(DB06201)|Tamoxifen(DB00675)|Trandolapril(DB00519)	GGACGGATGCCCTGCTGGACA	0.522																																					p.G19V	NSCLC(162;1801 2756 42904 52896)	Atlas-SNP	.											CES1_ENST00000360526,NS,carcinoma,0,1	CES1	78	1	1	Substitution - Missense(1)	prostate(1)	c.G56T						scavenged	.						38.0	29.0	32.0					16																	55862883		2198	4300	6498	SO:0001630	splice_region_variant	1066	exon2			GGATGCCCTGCTG	BC012418	CCDS32450.1, CCDS45488.1, CCDS45489.1	16q22.2	2010-10-12	2010-10-12		ENSG00000198848	ENSG00000198848	3.1.1.1	"""Carboxylesterases"""	1863	protein-coding gene	gene with protein product	"""human monocyte/macrophage serine esterase 1"""	114835	"""carboxylesterase 1 (monocyte/macrophage serine esterase 1)"""			2070086, 20931200	Standard	XM_005255774		Approved	HMSE, CES2, HMSE1, SES1, CEH, CES1A1, CES1A2	uc002eil.3	P23141		ENST00000361503.4:c.53-1G>T	16.37:g.55862883C>A		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	44	6	0.136364	NM_001025195	A6NIM1|A8K3K8|A8K844|E9PAU8|P82127|Q00015|Q13657|Q14062|Q16737|Q16788|Q549X7|Q549X8|Q86UK2|Q96EE8|Q9UC52|Q9UDG8|Q9UK77|Q9ULY2	Missense_Mutation	SNP	ENST00000361503.4	37	CCDS45488.1	804	0.36813186813186816	220	0.44715447154471544	142	0.39226519337016574	112	0.1958041958041958	330	0.43535620052770446	.	18.35	3.604104	0.66445	.	.	ENSG00000198848	ENST00000360526;ENST00000361503;ENST00000422046	T;T;T	0.66995	-0.24;-0.17;-0.17	4.48	3.52	0.40303	Carboxylesterase, type B (1);	8.429180	0.00357	N	0.000020	T	0.00012	0.0000	M	0.64080	1.96	0.58432	D	0.999993	D;D;D	0.63046	0.992;0.992;0.972	D;D;P	0.70487	0.969;0.958;0.891	T	0.53556	-0.8422	10	0.72032	D	0.01	.	9.5301	0.39189	0.0:0.8943:0.0:0.1057	rs3826190	18;18;19	E9PAU8;P23141;P23141-2	.;EST1_HUMAN;.	V	19;18;18	ENSP00000353720:G19V;ENSP00000355193:G18V;ENSP00000390492:G18V	ENSP00000353720:G19V	G	-	2	0	CES1	54420384	0.940000	0.31905	0.780000	0.31762	0.099000	0.18886	1.881000	0.39638	2.051000	0.60960	0.393000	0.25936	GGG	C|0.632;A|0.368	0.368	strong		0.522	CES1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000433285.1	NM_001266	Missense_Mutation
MUC4	4585	hgsc.bcm.edu	37	3	195511780	195511780	+	Missense_Mutation	SNP	G	G	A	rs391928|rs71291863	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195511780G>A	ENST00000463781.3	-	2	7130	c.6671C>T	c.(6670-6672)cCt>cTt	p.P2224L	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.P2224L	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.P2224L(1)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GACAAGAAGAGGGATGGCGTG	0.592																																					p.P2224L		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,3	MUC4	1505	3	1	Substitution - Missense(1)	prostate(1)	c.C6671T						PASS	.						34.0	32.0	33.0					3																	195511780		654	1584	2238	SO:0001583	missense	4585	exon2			AGAAGAGGGATGG	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.6671C>T	3.37:g.195511780G>A	ENSP00000417498:p.Pro2224Leu	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	83	17	0.204819	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	G	4.046	0.006276	0.07866	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.36699	1.24;1.25	.	.	.	.	.	.	.	.	T	0.19927	0.0479	N	0.19112	0.55	0.09310	N	1	B	0.09022	0.002	B	0.01281	0.0	T	0.24548	-1.0157	6	.	.	.	.	.	.	.	.	2224	E7ESK3	.	L	2224	ENSP00000417498:P2224L;ENSP00000420243:P2224L	.	P	-	2	0	MUC4	196996175	0.116000	0.22171	0.001000	0.08648	0.003000	0.03518	0.211000	0.17474	0.488000	0.27723	0.064000	0.15345	CCT	G|0.789;A|0.211	0.211	strong		0.592	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
ARSD	414	hgsc.bcm.edu	37	X	2836181	2836181	+	Missense_Mutation	SNP	A	A	T	rs73632975	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:2836181A>T	ENST00000381154.1	-	5	602	c.527T>A	c.(526-528)aTg>aAg	p.M176K	ARSD_ENST00000217890.6_5'UTR	NM_001669.3	NP_001660.2	P51689	ARSD_HUMAN	arylsulfatase D	176					cellular protein metabolic process (GO:0044267)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	arylsulfatase activity (GO:0004065)|metal ion binding (GO:0046872)			large_intestine(3)|lung(3)	6		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				CGTGAAGGGCATGCCGTAGAA	0.602																																					p.M176K		Atlas-SNP	.											.	ARSD	47	.	0			c.T527A						PASS	.						36.0	23.0	27.0					X																	2836181		2202	4298	6500	SO:0001583	missense	414	exon5			AAGGGCATGCCGT	X83572	CCDS35196.1	Xp22.3	2013-02-14			ENSG00000006756	ENSG00000006756		"""Arylsulfatase family"""	717	protein-coding gene	gene with protein product		300002				7720070	Standard	NM_001669		Approved		uc004cqy.3	P51689	OTTHUMG00000021077	ENST00000381154.1:c.527T>A	X.37:g.2836181A>T	ENSP00000370546:p.Met176Lys	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	133	17	0.12782	NM_001669	Q9UHJ8	Missense_Mutation	SNP	ENST00000381154.1	37	CCDS35196.1	143	0.0861965039180229	34	0.07727272727272727	32	0.09302325581395349	35	0.06433823529411764	60	0.0821917808219178	a	16.17	3.048099	0.55110	.	.	ENSG00000006756	ENST00000381154;ENST00000217890	D	0.93763	-3.28	3.47	3.47	0.39725	Alkaline phosphatase-like, alpha/beta/alpha (1);Sulfatase (1);Alkaline-phosphatase-like, core domain (1);	0.071270	0.64402	U	0.000010	T	0.52125	0.1715	M	0.90252	3.1	0.23186	P	0.99815953	B;B	0.31227	0.314;0.097	B;B	0.37387	0.248;0.114	T	0.80901	-0.1175	9	0.62326	D	0.03	.	11.4758	0.50297	1.0:0.0:0.0:0.0	.	176;176	E9PAW5;P51689	.;ARSD_HUMAN	K	176	ENSP00000370546:M176K	ENSP00000217890:M176K	M	-	2	0	ARSD	2846181	1.000000	0.71417	0.287000	0.24848	0.868000	0.49771	5.800000	0.69108	1.132000	0.42129	0.343000	0.21770	ATG	A|0.913;T|0.087	0.087	strong		0.602	ARSD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055636.1		
TTN	7273	hgsc.bcm.edu	37	2	179435337	179435337	+	Silent	SNP	T	T	G	rs6732060	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:179435337T>G	ENST00000591111.1	-	276	70823	c.70599A>C	c.(70597-70599)gcA>gcC	p.A23533A	TTN-AS1_ENST00000438095.1_RNA|TTN_ENST00000359218.5_Silent_p.A16234A|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN_ENST00000342992.6_Silent_p.A22606A|TTN-AS1_ENST00000586452.1_RNA|TTN_ENST00000460472.2_Silent_p.A16109A|TTN-AS1_ENST00000591332.1_RNA|TTN_ENST00000589042.1_Silent_p.A25174A|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN_ENST00000342175.6_Silent_p.A16301A|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590932.1_RNA			Q8WZ42	TITIN_HUMAN	titin	23533	Ig-like 119.				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)			CGACACGTACTGCATCTTTTA	0.438													T|||	717	0.143171	0.2405	0.1801	5008	,	,		22705	0.0258		0.0527	False		,,,				2504	0.1994				p.A25174A		Atlas-SNP	.											.	TTN	18412	.	0			c.A75522C						PASS	.	T	,,,	826,3038		99,628,1205	125.0	114.0	117.0		48327,67818,48702,48903	1.9	0.6	2	dbSNP_116	117	270,7992		9,252,3870	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	,,,	108,880,5075	GG,GT,TT		3.268,21.3768,9.0384	,,,	16109/26927,22606/33424,16234/27052,16301/27119	179435337	1096,11030	1932	4131	6063	SO:0001819	synonymous_variant	7273	exon326			ACGTACTGCATCT	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.70599A>C	2.37:g.179435337T>G		Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	159	74	0.465409	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																																																																																				T|0.892;G|0.108	0.108	strong		0.438	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
KRT84	3890	hgsc.bcm.edu	37	12	52778829	52778829	+	Missense_Mutation	SNP	C	C	A	rs140632920	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:52778829C>A	ENST00000257951.3	-	1	607	c.541G>T	c.(541-543)Gac>Tac	p.D181Y	RP3-416H24.4_ENST00000547174.1_RNA	NM_033045.3	NP_149034.2	Q9NSB2	KRT84_HUMAN	keratin 84	181	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)		GGTACCTTGTCAATGAAGGAG	0.488													C|||	7	0.00139776	0.0	0.0	5008	,	,		22209	0.0		0.006	False		,,,				2504	0.001				p.D181Y		Atlas-SNP	.											.	KRT84	61	.	0			c.G541T						PASS	.	C	TYR/ASP	3,4403	6.2+/-15.9	0,3,2200	216.0	219.0	218.0		541	5.0	1.0	12	dbSNP_134	218	22,8578	16.0+/-53.3	0,22,4278	yes	missense	KRT84	NM_033045.3	160	0,25,6478	AA,AC,CC		0.2558,0.0681,0.1922	probably-damaging	181/601	52778829	25,12981	2203	4300	6503	SO:0001583	missense	3890	exon1			CCTTGTCAATGAA	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.541G>T	12.37:g.52778829C>A	ENSP00000257951:p.Asp181Tyr	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	98	55	0.561224	NM_033045	B2RA43|Q6ISB0|Q701L6	Missense_Mutation	SNP	ENST00000257951.3	37	CCDS8825.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	C	21.2	4.119953	0.77323	6.81E-4	0.002558	ENSG00000161849	ENST00000257951	D	0.92299	-3.01	5.03	5.03	0.67393	Filament (1);	0.000000	0.52532	D	0.000066	D	0.97695	0.9244	H	0.97315	3.98	0.58432	D	0.999998	D	0.76494	0.999	D	0.77004	0.989	D	0.98708	1.0703	10	0.87932	D	0	.	18.9362	0.92586	0.0:1.0:0.0:0.0	.	181	Q9NSB2	KRT84_HUMAN	Y	181	ENSP00000257951:D181Y	ENSP00000257951:D181Y	D	-	1	0	KRT84	51065096	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	7.612000	0.82975	2.790000	0.95986	0.609000	0.83330	GAC	C|0.998;A|0.002	0.002	strong		0.488	KRT84-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405187.1	NM_033045	
SLC25A39	51629	hgsc.bcm.edu	37	17	42398052	42398052	+	Missense_Mutation	SNP	A	A	G	rs2011951	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:42398052A>G	ENST00000377095.5	-	9	858	c.739T>C	c.(739-741)Ttc>Ctc	p.F247L	SLC25A39_ENST00000225308.8_Missense_Mutation_p.F239L|SLC25A39_ENST00000586016.1_Missense_Mutation_p.F115L|SLC25A39_ENST00000537904.2_Missense_Mutation_p.F224L|SLC25A39_ENST00000590194.1_Missense_Mutation_p.F239L	NM_001143780.1	NP_001137252.1	Q9BZJ4	S2539_HUMAN	solute carrier family 25, member 39	247			F -> L (in dbSNP:rs2011951). {ECO:0000269|PubMed:11139402, ECO:0000269|PubMed:11230166, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.5, ECO:0000269|Ref.7}.		heme biosynthetic process (GO:0006783)|transport (GO:0006810)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)				endometrium(2)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	7		Prostate(33;0.0233)		BRCA - Breast invasive adenocarcinoma(366;0.189)		TTCGGCCTGAACCCATTGAGC	0.602													G|||	3411	0.68111	0.7791	0.5764	5008	,	,		18046	0.9266		0.4036	False		,,,				2504	0.6554				p.F247L		Atlas-SNP	.											.	SLC25A39	24	.	0			c.T739C						PASS	.	G	LEU/PHE,LEU/PHE	3223,1183	415.2+/-337.1	1198,827,178	114.0	121.0	118.0		739,715	0.7	0.0	17	dbSNP_92	118	3331,5269	644.4+/-400.0	638,2055,1607	yes	missense,missense	SLC25A39	NM_001143780.1,NM_016016.2	22,22	1836,2882,1785	GG,GA,AA		38.7326,26.8498,49.6079	benign,benign	247/360,239/352	42398052	6554,6452	2203	4300	6503	SO:0001583	missense	51629	exon9			GCCTGAACCCATT	BC096819	CCDS11482.1, CCDS45700.1	17q12	2013-05-22			ENSG00000013306	ENSG00000013306		"""Solute carriers"""	24279	protein-coding gene	gene with protein product		610820				16949250	Standard	NM_001143780		Approved	FLJ22407, CGI-69	uc002ign.2	Q9BZJ4	OTTHUMG00000132628	ENST00000377095.5:c.739T>C	17.37:g.42398052A>G	ENSP00000366299:p.Phe247Leu	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	94	45	0.478723	NM_001143780	A8JZZ2|D3DX51|D3DX54|Q4V9M1|Q9P182|Q9UF66|Q9Y379	Missense_Mutation	SNP	ENST00000377095.5	37	CCDS45700.1	1421	0.6506410256410257	377	0.766260162601626	206	0.569060773480663	525	0.9178321678321678	313	0.4129287598944591	G	2.061	-0.415327	0.04766	0.731502	0.387326	ENSG00000013306	ENST00000225308;ENST00000377095;ENST00000537904	T;T;T	0.79247	-1.25;-1.1;-1.22	5.18	0.7	0.18099	Mitochondrial carrier domain (2);	2.312390	0.01561	N	0.020130	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	0.37384	-0.9708	9	0.09084	T	0.74	-5.109	5.6686	0.17709	0.3855:0.0:0.4808:0.1337	rs2011951;rs3200280;rs17424083;rs17856304;rs57988364;rs2011951	224;247;239	B4DFG5;Q9BZJ4;Q9BZJ4-2	.;S2539_HUMAN;.	L	239;247;224	ENSP00000225308:F239L;ENSP00000366299:F247L;ENSP00000444540:F224L	ENSP00000225308:F239L	F	-	1	0	SLC25A39	39753578	0.000000	0.05858	0.000000	0.03702	0.207000	0.24258	0.161000	0.16481	0.094000	0.17404	-0.119000	0.15052	TTC	A|0.426;G|0.574	0.574	strong		0.602	SLC25A39-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457745.1	NM_016016	
AP5Z1	9907	hgsc.bcm.edu	37	7	4830971	4830971	+	Silent	SNP	G	G	T	rs77393809	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:4830971G>T	ENST00000348624.4	+	17	2473	c.2379G>T	c.(2377-2379)acG>acT	p.T793T	AP5Z1_ENST00000490487.1_3'UTR|MIR4656_ENST00000579503.1_RNA	NM_014855.2	NP_055670.1	O43299	AP5Z1_HUMAN	adaptor-related protein complex 5, zeta 1 subunit	793					cell death (GO:0008219)|double-strand break repair via homologous recombination (GO:0000724)|endosomal transport (GO:0016197)|protein transport (GO:0015031)	AP-5 adaptor complex (GO:0044599)|AP-type membrane coat adaptor complex (GO:0030119)|cytoplasm (GO:0005737)|nucleus (GO:0005634)											CCCTGCGCACGGTCAGCCGGC	0.677													G|||	62	0.0123802	0.0015	0.0187	5008	,	,		17357	0.0		0.0239	False		,,,				2504	0.0235				p.T793T		Atlas-SNP	.											.	.	.	.	0			c.G2379T						PASS	.	G		12,4080		0,12,2034	15.0	20.0	18.0		2379	-9.4	0.0	7	dbSNP_133	18	204,8148		4,196,3976	no	coding-synonymous	KIAA0415	NM_014855.2		4,208,6010	TT,TG,GG		2.4425,0.2933,1.7358		793/808	4830971	216,12228	2046	4176	6222	SO:0001819	synonymous_variant	9907	exon17			GCGCACGGTCAGC	AB007875	CCDS47528.1	7p22.1	2012-03-20	2012-03-20	2012-03-20	ENSG00000242802	ENSG00000242802			22197	protein-coding gene	gene with protein product		613653	"""KIAA0415"""	KIAA0415		20613862, 22022230	Standard	NM_014855		Approved	SPG48, zeta	uc003sne.3	O43299	OTTHUMG00000151754	ENST00000348624.4:c.2379G>T	7.37:g.4830971G>T		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	153	39	0.254902	NM_014855	Q8N3X2|Q96H80	Silent	SNP	ENST00000348624.4	37	CCDS47528.1																																																																																			G|0.985;T|0.015	0.015	strong		0.677	AP5Z1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323771.1		
PDLIM5	10611	hgsc.bcm.edu	37	4	95496940	95496940	+	Silent	SNP	G	G	A	rs115743950	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:95496940G>A	ENST00000317968.4	+	5	601	c.465G>A	c.(463-465)gcG>gcA	p.A155A	PDLIM5_ENST00000542407.1_Silent_p.A33A|PDLIM5_ENST00000437932.1_Intron|PDLIM5_ENST00000380180.3_Intron|PDLIM5_ENST00000450793.1_Intron|PDLIM5_ENST00000538141.1_Intron|PDLIM5_ENST00000508216.1_Intron|PDLIM5_ENST00000514743.1_Intron|PDLIM5_ENST00000318007.5_Intron	NM_001256428.1|NM_006457.4	NP_001243357.1|NP_006448	Q96HC4	PDLI5_HUMAN	PDZ and LIM domain 5	155					regulation of dendritic spine morphogenesis (GO:0061001)|regulation of synapse assembly (GO:0051963)	actin cytoskeleton (GO:0015629)|cell junction (GO:0030054)|cytosol (GO:0005829)|membrane (GO:0016020)|neuron projection (GO:0043005)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	actin binding (GO:0003779)|actinin binding (GO:0042805)|protein kinase C binding (GO:0005080)|zinc ion binding (GO:0008270)	p.A155A(1)		central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(3)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	22		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;1.84e-09)		CAGCCCATGCGACCACCTCAT	0.552													G|||	20	0.00399361	0.0023	0.0043	5008	,	,		20003	0.0		0.0089	False		,,,				2504	0.0051				p.A155A		Atlas-SNP	.											PDLIM5,NS,carcinoma,+1,2	PDLIM5	76	2	1	Substitution - coding silent(1)	kidney(1)	c.G465A						PASS	.	G	,,,	16,4390	24.3+/-50.5	0,16,2187	295.0	249.0	265.0		,,,465	2.9	1.0	4	dbSNP_132	265	140,8460	70.0+/-132.6	0,140,4160	no	intron,intron,intron,coding-synonymous	PDLIM5	NM_001011513.2,NM_001011515.1,NM_001011516.1,NM_006457.3	,,,	0,156,6347	AA,AG,GG		1.6279,0.3631,1.1994	,,,	,,,155/597	95496940	156,12850	2203	4300	6503	SO:0001819	synonymous_variant	10611	exon5			CCATGCGACCACC	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.465G>A	4.37:g.95496940G>A		Somatic	203	0	0		WXS	Illumina HiSeq	Phase_I	205	115	0.560976	NM_006457	A8K6F9|D6RB78|E9PBF5|O60705|Q56VN4|Q5UW38|Q8WVK0	Silent	SNP	ENST00000317968.4	37	CCDS3641.1																																																																																			G|0.991;A|0.009	0.009	strong		0.552	PDLIM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253586.1		
AMPD1	270	hgsc.bcm.edu	37	1	115236057	115236057	+	Splice_Site	SNP	G	G	A	rs17602729	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:115236057G>A	ENST00000520113.2	-	2	148	c.133C>T	c.(133-135)Caa>Taa	p.Q45*	AMPD1_ENST00000369538.3_Intron|AMPD1_ENST00000353928.6_Splice_Site_p.Q12*			P23109	AMPD1_HUMAN	adenosine monophosphate deaminase 1	45					IMP salvage (GO:0032264)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase metabolic process (GO:0006144)|purine-containing compound salvage (GO:0043101)|response to organic substance (GO:0010033)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	AMP deaminase activity (GO:0003876)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(17)|ovary(3)|pancreas(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	45	all_epithelial(7;7.83e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;4.64e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)	Adenosine monophosphate(DB00131)	CAATACTCACGTTTCTCTTCA	0.323													G|||	191	0.038139	0.0045	0.0576	5008	,	,		12866	0.001		0.1233	False		,,,				2504	0.0204				p.Q45X		Atlas-SNP	.											AMPD1_ENST00000520113,NS,carcinoma,0,2	AMPD1	223	2	0			c.C133T	GRCh37	CM920025	AMPD1	M	rs17602729	PASS	.	G	stop/GLN,	104,4302	81.9+/-120.4	2,100,2101	85.0	90.0	89.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	133,	2.8	1.0	1	dbSNP_123	89	1126,7472	232.6+/-266.2	89,948,3262	yes	stop-gained-near-splice,intron	AMPD1	NM_000036.2,NM_001172626.1	,	91,1048,5363	AA,AG,GG		13.0961,2.3604,9.4586	,	45/781,	115236057	1230,11774	2203	4299	6502	SO:0001630	splice_region_variant	270	exon2			ACTCACGTTTCTC	M60092	CCDS876.1, CCDS876.2, CCDS53349.1	1p13	2010-02-10	2010-02-10		ENSG00000116748	ENSG00000116748	3.5.4.6		468	protein-coding gene	gene with protein product	"""AMPD isoform M"", ""skeletal muscle AMPD"""	102770	"""adenosine monophosphate deaminase 1 (isoform M)"""			1400401	Standard	NM_001172626		Approved	MAD, MADA	uc001efe.2	P23109	OTTHUMG00000011892	ENST00000520113.2:c.133+1C>T	1.37:g.115236057G>A		Somatic	216	1	0.00462963		WXS	Illumina HiSeq	Phase_I	162	79	0.487654	NM_000036	A8K5N4|B2RAM1|F2Z3B3|Q5TF00|Q5TF02	Nonsense_Mutation	SNP	ENST00000520113.2	37	CCDS876.2	117	0.05357142857142857	3	0.006097560975609756	30	0.08287292817679558	0	0.0	84	0.11081794195250659	G	29.9	5.043403	0.93685	0.023604	0.130961	ENSG00000116748	ENST00000520113;ENST00000353928	.	.	.	4.91	2.84	0.33178	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.6038	0.62035	0.0:0.2934:0.7066:0.0	rs17602729;rs52833197;rs17602729	.	.	.	X	45;12	.	.	Q	-	1	0	AMPD1	115037580	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	2.265000	0.43311	1.143000	0.42306	0.650000	0.86243	CAA	G|0.923;A|0.077	0.077	strong		0.323	AMPD1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000032860.4		Nonsense_Mutation
DHX9	1660	hgsc.bcm.edu	37	1	182845346	182845346	+	Silent	SNP	C	C	T	rs35533583	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:182845346C>T	ENST00000367549.3	+	17	2087	c.1977C>T	c.(1975-1977)ggC>ggT	p.G659G		NM_001357.4	NP_001348.2	Q08211	DHX9_HUMAN	DEAH (Asp-Glu-Ala-His) box helicase 9	659	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				ATP catabolic process (GO:0006200)|cellular response to heat (GO:0034605)|circadian rhythm (GO:0007623)|CRD-mediated mRNA stabilization (GO:0070934)|DNA duplex unwinding (GO:0032508)|gene expression (GO:0010467)|innate immune response (GO:0045087)|mRNA splicing, via spliceosome (GO:0000398)|osteoblast differentiation (GO:0001649)|positive regulation of type I interferon production (GO:0032481)|RNA splicing (GO:0008380)	centrosome (GO:0005813)|CRD-mediated mRNA stability complex (GO:0070937)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|ATP-dependent RNA helicase activity (GO:0004004)|DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|RNA helicase activity (GO:0003724)|RNA polymerase II transcription factor binding (GO:0001085)			NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(10)|kidney(3)|large_intestine(7)|liver(1)|lung(19)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	49						TTTTGCCTGGCTGGAATCTGA	0.358													C|||	91	0.0181709	0.0204	0.0461	5008	,	,		18919	0.0		0.0219	False		,,,				2504	0.0102				p.G659G	Colon(69;210 1162 3697 13559 39565)	Atlas-SNP	.											.	DHX9	114	.	0			c.C1977T						PASS	.	C		87,3629		0,87,1771	165.0	151.0	155.0		1977	4.7	1.0	1	dbSNP_126	155	258,7926		2,254,3836	no	coding-synonymous	DHX9	NM_001357.4		2,341,5607	TT,TC,CC		3.1525,2.3412,2.8992		659/1271	182845346	345,11555	1858	4092	5950	SO:0001819	synonymous_variant	1660	exon17			GCCTGGCTGGAAT	L13848	CCDS41444.1	1q25	2013-05-13	2013-05-13	2003-06-20	ENSG00000135829	ENSG00000135829		"""DEAH-boxes"""	2750	protein-coding gene	gene with protein product	"""NDH II"", ""RNA helicase A"""	603115	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 9 (RNA helicase A, nuclear DNA helicase II; leukophysin)"", ""DEAH (Asp-Glu-Ala-His) box polypeptide 9"""	LKP, DDX9		8344961, 9111062	Standard	NM_001357		Approved	RHA	uc001gpr.3	Q08211	OTTHUMG00000035337	ENST00000367549.3:c.1977C>T	1.37:g.182845346C>T		Somatic	235	0	0		WXS	Illumina HiSeq	Phase_I	195	95	0.487179	NM_001357	B2RNV4|Q05CI5|Q12803|Q32Q22|Q5VY62|Q6PD69|Q99556	Silent	SNP	ENST00000367549.3	37	CCDS41444.1																																																																																			C|0.976;T|0.024	0.024	strong		0.358	DHX9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085522.2	NM_030588	
HIST1H3G	8355	hgsc.bcm.edu	37	6	26271208	26271208	+	Silent	SNP	T	T	C	rs141036055	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:26271208T>C	ENST00000305910.3	-	1	404	c.405A>G	c.(403-405)agA>agG	p.R135R	HIST1H2BI_ENST00000377733.2_5'Flank	NM_003534.2	NP_003525.1	P68431	H31_HUMAN	histone cluster 1, H3g	135				Missing (in Ref. 2; AAA52651). {ECO:0000305}.	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)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(4)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	12						ACCTCTACGCTCTCTCCCCAC	0.483													T|||	2	0.000399361	0.0	0.0	5008	,	,		17707	0.0		0.0	False		,,,				2504	0.002				p.R135R		Atlas-SNP	.											.	HIST1H3G	20	.	0			c.A405G						PASS	.	T		0,4406		0,0,2203	61.0	64.0	63.0		405	1.5	1.0	6	dbSNP_134	63	11,8589		0,11,4289	no	coding-synonymous	HIST1H3G	NM_003534.2		0,11,6492	CC,CT,TT		0.1279,0.0,0.0846		135/137	26271208	11,12995	2203	4300	6503	SO:0001819	synonymous_variant	8355	exon1			CTACGCTCTCTCC	Z80785	CCDS4602.1	6p22.1	2011-07-22	2006-10-11	2003-03-14	ENSG00000256018			"""Histones / Replication-dependent"""	4772	protein-coding gene	gene with protein product		602815	"""H3 histone family, member H"", ""histone 1, H3g"""	H3FH		9119399, 12408966	Standard	NM_003534		Approved	H3/h	uc003nhi.3	P68431	OTTHUMG00000014436	ENST00000305910.3:c.405A>G	6.37:g.26271208T>C		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	50	22	0.44	NM_003534	A0PJT7|A5PLR1|P02295|P02296|P16106|Q6ISV8|Q6NWP8|Q6NWP9|Q6NXU4|Q71DJ3|Q93081	Silent	SNP	ENST00000305910.3	37	CCDS4602.1																																																																																			T|0.999;C|0.001	0.001	strong		0.483	HIST1H3G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040099.2	NM_003534	
BPIFA3	128861	hgsc.bcm.edu	37	20	31812923	31812923	+	Missense_Mutation	SNP	G	G	A	rs3818222	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:31812923G>A	ENST00000375454.3	+	4	616	c.406G>A	c.(406-408)Gta>Ata	p.V136I	BPIFA3_ENST00000375452.3_Missense_Mutation_p.V100I|BPIFA3_ENST00000490499.1_3'UTR	NM_178466.3	NP_848561.2	Q9BQP9	BPIA3_HUMAN	BPI fold containing family A, member 3	136			V -> I (in dbSNP:rs3818222).			extracellular region (GO:0005576)	lipid binding (GO:0008289)										TAACAACATCGTAAAGATGTG	0.507													A|||	3327	0.664337	0.789	0.428	5008	,	,		22625	0.8115		0.5229	False		,,,				2504	0.6575				p.V136I		Atlas-SNP	.											.	.	.	.	0			c.G406A						PASS	.	A	ILE/VAL,ILE/VAL	3204,1202	419.1+/-338.5	1169,866,168	165.0	157.0	160.0		298,406	-5.5	0.0	20	dbSNP_107	160	4382,4218	571.0+/-389.5	1122,2138,1040	yes	missense,missense	BPIFA3	NM_001042439.1,NM_178466.3	29,29	2291,3004,1208	AA,AG,GG		49.0465,27.281,41.6731	benign,benign	100/219,136/255	31812923	7586,5420	2203	4300	6503	SO:0001583	missense	128861	exon4			AACATCGTAAAGA		CCDS13216.2, CCDS42865.1	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000131059	ENSG00000131059		"""BPI fold containing"""	16204	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 71"""	C20orf71		11971875, 21787333	Standard	XR_244132		Approved	bA49G10.4, SPLUNC3	uc002wyr.3	Q9BQP9	OTTHUMG00000032245	ENST00000375454.3:c.406G>A	20.37:g.31812923G>A	ENSP00000364603:p.Val136Ile	Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	141	75	0.531915	NM_178466	Q5JWG8|Q6NZ38	Missense_Mutation	SNP	ENST00000375454.3	37	CCDS13216.2	1412	0.6465201465201466	381	0.774390243902439	167	0.4613259668508287	465	0.8129370629370629	399	0.5263852242744064	A	0.188	-1.055829	0.01965	0.72719	0.509535	ENSG00000131059	ENST00000375454;ENST00000375452	T;T	0.04809	3.55;3.55	3.49	-5.46	0.02608	.	1.231100	0.05853	N	0.621586	T	0.00012	0.0000	N	0.02539	-0.55	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.30060	-0.9991	9	0.02654	T	1	-0.0358	4.4607	0.11665	0.2017:0.1397:0.5209:0.1376	rs3818222;rs13041676;rs61303950;rs3818222	100;136	Q9BQP9-2;Q9BQP9	.;BPIA3_HUMAN	I	136;100	ENSP00000364603:V136I;ENSP00000364601:V100I	ENSP00000364601:V100I	V	+	1	0	BPIFA3	31276584	0.000000	0.05858	0.000000	0.03702	0.018000	0.09664	-1.653000	0.01986	-1.846000	0.01175	-0.521000	0.04368	GTA	G|0.380;A|0.620	0.620	strong		0.507	BPIFA3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078672.1	NM_178466	
DENND5A	23258	hgsc.bcm.edu	37	11	9225486	9225486	+	Missense_Mutation	SNP	C	C	G	rs952374	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:9225486C>G	ENST00000328194.3	-	4	990	c.670G>C	c.(670-672)Gag>Cag	p.E224Q	DENND5A_ENST00000530044.1_Missense_Mutation_p.E224Q	NM_001243254.1|NM_015213.3	NP_001230183.1|NP_056028.2	Q6IQ26	DEN5A_HUMAN	DENN/MADD domain containing 5A	224	DENN. {ECO:0000255|PROSITE- ProRule:PRU00304}.		E -> Q (in dbSNP:rs952374). {ECO:0000269|PubMed:10470851, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		positive regulation of Rab GTPase activity (GO:0032851)	Golgi apparatus (GO:0005794)|membrane (GO:0016020)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(1)|endometrium(7)|kidney(2)|large_intestine(8)|liver(1)|lung(16)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	39						TGGAGTTGCTCCAGCACGCTC	0.552													C|||	1879	0.3752	0.2103	0.464	5008	,	,		20880	0.4573		0.2773	False		,,,				2504	0.5511				p.E224Q		Atlas-SNP	.											.	DENND5A	84	.	0			c.G670C						PASS	.	C	GLN/GLU	973,3429	366.6+/-317.9	119,735,1347	95.0	80.0	85.0		670	4.5	1.0	11	dbSNP_86	85	2407,6185	400.1+/-346.7	368,1671,2257	yes	missense	DENND5A	NM_015213.3	29	487,2406,3604	GG,GC,CC		28.0144,22.1036,26.012	benign	224/1288	9225486	3380,9614	2201	4296	6497	SO:0001583	missense	23258	exon4			GTTGCTCCAGCAC	AB029014	CCDS31423.1, CCDS58119.1	11p15.3	2012-10-03	2008-08-14	2008-08-14	ENSG00000184014	ENSG00000184014		"""DENN/MADD domain containing"""	19344	protein-coding gene	gene with protein product			"""RAB6 interacting protein 1"""	RAB6IP1		10470851	Standard	NM_015213		Approved	KIAA1091, FLJ22354, FLJ33829, FLJ43455	uc001mhl.3	Q6IQ26	OTTHUMG00000165716	ENST00000328194.3:c.670G>C	11.37:g.9225486C>G	ENSP00000328524:p.Glu224Gln	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	101	81	0.80198	NM_015213	B4DJ15|E9PS91|Q96GN3|Q9H6U7|Q9UFV0|Q9UPR1	Missense_Mutation	SNP	ENST00000328194.3	37	CCDS31423.1	744	0.34065934065934067	111	0.22560975609756098	160	0.4419889502762431	268	0.46853146853146854	205	0.2704485488126649	C	8.966	0.971813	0.18736	0.221036	0.280144	ENSG00000184014	ENST00000328194;ENST00000530044	T;T	0.11712	2.75;2.75	5.42	4.49	0.54785	DENN (3);	0.159837	0.56097	N	0.000030	T	0.00012	0.0000	N	0.10874	0.06	0.09310	P	1.0	B;B	0.20550	0.046;0.002	B;B	0.19148	0.024;0.014	T	0.45585	-0.9251	9	0.15066	T	0.55	.	15.7483	0.77965	0.0:0.8585:0.1415:0.0	rs952374;rs3813397;rs52811808;rs952374	224;224	E9PS91;Q6IQ26	.;DEN5A_HUMAN	Q	224	ENSP00000328524:E224Q;ENSP00000435866:E224Q	ENSP00000328524:E224Q	E	-	1	0	DENND5A	9182062	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.220000	0.42908	1.233000	0.43693	0.650000	0.86243	GAG	C|0.715;G|0.285	0.285	strong		0.552	DENND5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385910.2	NM_015213	
ZNF804A	91752	hgsc.bcm.edu	37	2	185801871	185801871	+	Missense_Mutation	SNP	A	A	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:185801871A>T	ENST00000302277.6	+	4	2342	c.1748A>T	c.(1747-1749)aAa>aTa	p.K583I		NM_194250.1	NP_919226.1	Q7Z570	Z804A_HUMAN	zinc finger protein 804A	583							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						ATAAGGTTGAAAGAGACCCAT	0.294																																					p.K583I		Atlas-SNP	.											.	ZNF804A	322	.	0			c.A1748T						PASS	.						34.0	41.0	39.0					2																	185801871		2180	4278	6458	SO:0001583	missense	91752	exon4			GGTTGAAAGAGAC	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.1748A>T	2.37:g.185801871A>T	ENSP00000303252:p.Lys583Ile	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	60	20	0.333333	NM_194250	A7E253|Q6ZN26	Missense_Mutation	SNP	ENST00000302277.6	37	CCDS2291.1	.	.	.	.	.	.	.	.	.	.	A	18.55	3.647690	0.67358	.	.	ENSG00000170396	ENST00000302277	T	0.10005	2.92	5.5	5.5	0.81552	.	0.097775	0.44902	D	0.000416	T	0.29491	0.0735	L	0.58101	1.795	0.34076	D	0.659021	D	0.89917	1.0	D	0.73380	0.98	T	0.40459	-0.9562	10	0.87932	D	0	-23.4158	14.793	0.69857	1.0:0.0:0.0:0.0	.	583	Q7Z570	Z804A_HUMAN	I	583	ENSP00000303252:K583I	ENSP00000303252:K583I	K	+	2	0	ZNF804A	185510116	1.000000	0.71417	0.489000	0.27452	0.972000	0.66771	3.815000	0.55651	2.083000	0.62718	0.528000	0.53228	AAA	.	.	none		0.294	ZNF804A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255871.1	NM_194250	
UGT1A5	54579	hgsc.bcm.edu	37	2	234621661	234621661	+	Silent	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:234621661C>T	ENST00000373414.3	+	1	24	c.24C>T	c.(22-24)ccC>ccT	p.P8P	UGT1A6_ENST00000480628.1_Intron|UGT1A1_ENST00000373450.4_Intron|UGT1A10_ENST00000373445.1_Intron|UGT1A9_ENST00000354728.4_Intron|UGT1A10_ENST00000344644.5_Intron|UGT1A7_ENST00000373426.3_Intron|UGT1A6_ENST00000406651.1_Intron|UGT1A1_ENST00000609637.1_Intron|UGT1A6_ENST00000305139.6_Intron|UGT1A1_ENST00000608381.1_Silent_p.P8P|UGT1A6_ENST00000373424.1_Intron			P35504	UD15_HUMAN	UDP glucuronosyltransferase 1 family, polypeptide A5	8						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	glucuronosyltransferase activity (GO:0015020)			cervix(1)|endometrium(3)|large_intestine(4)|lung(9)|ovary(1)|skin(3)|urinary_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;4.51e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000523)|Lung(119;0.00271)|LUSC - Lung squamous cell carcinoma(224;0.00645)		TCCAGGTTCCCCTGCCGCAGC	0.602																																					p.P8P		Atlas-SNP	.											UGT1A5,NS,malignant_melanoma,+2,1	UGT1A5	66	1	0			c.C24T						scavenged	.						52.0	46.0	48.0					2																	234621661		2203	4300	6503	SO:0001819	synonymous_variant	54579	exon1			GGTTCCCCTGCCG	M84129	CCDS33404.1	2q37	2010-03-05	2005-07-20		ENSG00000240224	ENSG00000240224		"""UDP glucuronosyltransferases"""	12537	other	complex locus constituent		606430	"""UDP glycosyltransferase 1 family, polypeptide A5"""			9295054, 1339448	Standard	NM_019078		Approved	UGT1E		P35504	OTTHUMG00000059120	ENST00000373414.3:c.24C>T	2.37:g.234621661C>T		Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	150	2	0.0133333	NM_019078	B8K294	Silent	SNP	ENST00000373414.3	37	CCDS33404.1																																																																																			.	.	none		0.602	UGT1A5-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000130985.1	NM_019078	
NSMAF	8439	hgsc.bcm.edu	37	8	59508166	59508166	+	Silent	SNP	A	A	G	rs149564750	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:59508166A>G	ENST00000038176.3	-	22	2057	c.1845T>C	c.(1843-1845)aaT>aaC	p.N615N	NSMAF_ENST00000427130.2_Silent_p.N646N	NM_003580.3	NP_003571.2	Q92636	FAN_HUMAN	neutral sphingomyelinase (N-SMase) activation associated factor	615					ceramide metabolic process (GO:0006672)|intracellular signal transduction (GO:0035556)|positive regulation of apoptotic process (GO:0043065)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)	receptor signaling protein activity (GO:0005057)|sphingomyelin phosphodiesterase activator activity (GO:0016230)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(7)|lung(11)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|urinary_tract(1)	38		all_lung(136;0.174)|Lung NSC(129;0.2)				TGGTGATGTTATTCCAGGCCA	0.403													A|||	24	0.00479233	0.0	0.0101	5008	,	,		18010	0.0		0.0139	False		,,,				2504	0.0031				p.N646N		Atlas-SNP	.											.	NSMAF	156	.	0			c.T1938C						PASS	.	A	,	6,4400	11.4+/-27.6	0,6,2197	196.0	181.0	186.0		1938,1845	1.1	0.8	8	dbSNP_134	186	79,8521	44.9+/-103.4	1,77,4222	no	coding-synonymous,coding-synonymous	NSMAF	NM_001144772.1,NM_003580.3	,	1,83,6419	GG,GA,AA		0.9186,0.1362,0.6535	,	646/949,615/918	59508166	85,12921	2203	4300	6503	SO:0001819	synonymous_variant	8439	exon22			GATGTTATTCCAG	X96586	CCDS6173.1, CCDS47864.1	8q12-q13	2013-01-10			ENSG00000035681	ENSG00000035681		"""WD repeat domain containing"""	8017	protein-coding gene	gene with protein product		603043				8808629, 10640829	Standard	NM_003580		Approved	FAN	uc011lee.2	Q92636	OTTHUMG00000164352	ENST00000038176.3:c.1845T>C	8.37:g.59508166A>G		Somatic	270	0	0		WXS	Illumina HiSeq	Phase_I	185	41	0.221622	NM_001144772	B4DFB0|E9PCH0|Q8IW26	Silent	SNP	ENST00000038176.3	37	CCDS6173.1																																																																																			A|0.994;G|0.006	0.006	strong		0.403	NSMAF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378384.1	NM_003580	
LPP	4026	hgsc.bcm.edu	37	3	188590446	188590446	+	Silent	SNP	A	A	G	rs1136644	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:188590446A>G	ENST00000312675.4	+	10	1851	c.1605A>G	c.(1603-1605)cgA>cgG	p.R535R	LPP_ENST00000543006.1_Silent_p.R535R	NM_001167672.1|NM_005578.3	NP_001161144.1|NP_005569.1	Q93052	LPP_HUMAN	LIM domain containing preferred translocation partner in lipoma	535	LIM zinc-binding 3. {ECO:0000255|PROSITE- ProRule:PRU00125}.				cell adhesion (GO:0007155)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	zinc ion binding (GO:0008270)		HMGA2/LPP(161)	NS(1)|breast(1)|large_intestine(3)|lung(2)|ovary(1)|upper_aerodigestive_tract(2)	10	all_cancers(143;1.37e-09)|all_hematologic(3;0.0429)|Ovarian(172;0.088)	all_lung(153;0.00139)|Lung NSC(153;0.00202)		GBM - Glioblastoma multiforme(93;0.00602)		TTGCCCCGCGATGTTCTGTGT	0.522			T	"""HMGA2, MLL, C12orf9"""	"""lipoma, leukemia"""								A|||	2005	0.400359	0.2602	0.3919	5008	,	,		21140	0.4345		0.5298	False		,,,				2504	0.4274				p.R535R		Atlas-SNP	.		Dom	yes		3	3q28	4026	LIM domain containing preferred translocation partner in lipoma		"""L, M"""	LPP_ENST00000312675,NS,carcinoma,+1,1	LPP	72	1	0			c.A1605G						PASS	.	A	,,	1244,3162	429.5+/-342.2	184,876,1143	139.0	128.0	132.0		1605,1164,1605	0.0	1.0	3	dbSNP_86	132	4360,4240	582.0+/-391.3	1118,2124,1058	no	coding-synonymous,coding-synonymous,coding-synonymous	LPP	NM_001167671.1,NM_001167672.1,NM_005578.3	,,	1302,3000,2201	GG,GA,AA		49.3023,28.2342,43.0878	,,	535/613,388/466,535/613	188590446	5604,7402	2203	4300	6503	SO:0001819	synonymous_variant	4026	exon10			CCCGCGATGTTCT	AL833171	CCDS3291.1	3q27-q28	2004-03-02	2002-01-14		ENSG00000145012	ENSG00000145012			6679	protein-coding gene	gene with protein product		600700	"""LIM domain-containing preferred translocation partner in lipoma"""			8812423	Standard	XM_005247453		Approved		uc003frs.2	Q93052	OTTHUMG00000156387	ENST00000312675.4:c.1605A>G	3.37:g.188590446A>G		Somatic	212	0	0		WXS	Illumina HiSeq	Phase_I	183	95	0.519126	NM_005578	A1L4L6|D3DNV6|Q8NFX5	Silent	SNP	ENST00000312675.4	37	CCDS3291.1																																																																																			A|0.579;G|0.421	0.421	strong		0.522	LPP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344030.1	NM_005578	
ARHGAP6	395	hgsc.bcm.edu	37	X	11682921	11682921	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:11682921C>A	ENST00000337414.4	-	1	900	c.28G>T	c.(28-30)Gtc>Ttc	p.V10F	ARHGAP6_ENST00000380718.1_Missense_Mutation_p.V10F|ARHGAP6_ENST00000380732.3_Missense_Mutation_p.V10F	NM_013427.2	NP_038286.2	O43182	RHG06_HUMAN	Rho GTPase activating protein 6	10					actin filament polymerization (GO:0030041)|activation of phospholipase C activity (GO:0007202)|focal adhesion assembly (GO:0048041)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of stress fiber assembly (GO:0051497)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of signal transduction (GO:0009967)|regulation of GTPase activity (GO:0043087)|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)|actin filament (GO:0005884)|cytoplasm (GO:0005737)|cytosol (GO:0005829)	phospholipase activator activity (GO:0016004)|phospholipase binding (GO:0043274)|Rho GTPase activator activity (GO:0005100)|SH3/SH2 adaptor activity (GO:0005070)			cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(19)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	38						CAGGAGAAGACGCTGTGGAGC	0.677																																					p.V10F		Atlas-SNP	.											.	ARHGAP6	130	.	0			c.G28T						PASS	.						8.0	10.0	10.0					X																	11682921		1777	3411	5188	SO:0001583	missense	395	exon1			AGAAGACGCTGTG	AF012272	CCDS14140.1, CCDS14141.1, CCDS14142.1	Xp22.3	2008-02-05			ENSG00000047648	ENSG00000047648		"""Rho GTPase activating proteins"""	676	protein-coding gene	gene with protein product		300118				9417914	Standard	XM_005274507		Approved	rhoGAPX-1	uc004cup.1	O43182	OTTHUMG00000021134	ENST00000337414.4:c.28G>T	X.37:g.11682921C>A	ENSP00000338967:p.Val10Phe	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	110	37	0.336364	NM_006125	B2RWQ0|O43437|Q9P1B3|Q9UK81|Q9UK82	Missense_Mutation	SNP	ENST00000337414.4	37	CCDS14140.1	.	.	.	.	.	.	.	.	.	.	C	25.4	4.634288	0.87660	.	.	ENSG00000047648	ENST00000337414;ENST00000380718;ENST00000380732	T;T;T	0.44881	1.35;1.19;0.91	4.82	4.82	0.62117	.	.	.	.	.	T	0.50548	0.1622	N	0.24115	0.695	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.91635	0.999;0.997	T	0.56595	-0.7953	9	0.87932	D	0	.	14.4354	0.67277	0.0:1.0:0.0:0.0	.	10;10	O43182-2;O43182	.;RHG06_HUMAN	F	10	ENSP00000338967:V10F;ENSP00000370094:V10F;ENSP00000370108:V10F	ENSP00000338967:V10F	V	-	1	0	ARHGAP6	11592842	1.000000	0.71417	1.000000	0.80357	0.888000	0.51559	3.516000	0.53436	1.987000	0.57996	0.594000	0.82650	GTC	.	.	none		0.677	ARHGAP6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055760.2	NM_013427	
ALOXE3	59344	hgsc.bcm.edu	37	17	8021608	8021608	+	5'UTR	SNP	G	G	C	rs3027229	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:8021608G>C	ENST00000448843.2	-	0	41				ALOXE3_ENST00000380149.1_Missense_Mutation_p.P57A|ALOXE3_ENST00000318227.3_Missense_Mutation_p.P33A	NM_021628.2	NP_067641.2	Q9BYJ1	LOXE3_HUMAN	arachidonate lipoxygenase 3						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						TGGATATCAGGAGCCTGGGTT	0.582											OREG0024155	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	719	0.14357	0.3018	0.0908	5008	,	,		19267	0.0407		0.0974	False		,,,				2504	0.1207				p.P33A		Atlas-SNP	.											.	ALOXE3	145	.	0			c.C97G						PASS	.						11.0	10.0	10.0					17																	8021608		692	1589	2281	SO:0001623	5_prime_UTR_variant	59344	exon2			TATCAGGAGCCTG	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.-300C>G	17.37:g.8021608G>C		Somatic	89	0	0	646	WXS	Illumina HiSeq	Phase_I	65	31	0.476923	NM_001165960	B2R981|B7Z3W0|Q3ZB74|Q9H4F2|Q9HC22	Missense_Mutation	SNP	ENST00000448843.2	37	CCDS11130.1	280	0.1282051282051282	134	0.27235772357723576	38	0.10497237569060773	34	0.05944055944055944	74	0.09762532981530343	G	4.403	0.074380	0.08485	.	.	ENSG00000179148	ENST00000380149;ENST00000318227	T;T	0.75154	-0.91;-0.86	4.09	-1.02	0.10135	.	1.450200	0.04702	N	0.416035	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.12013	0.005	B	0.18263	0.021	T	0.04767	-1.0928	9	0.51188	T	0.08	-0.6437	7.1612	0.25664	0.5798:0.0:0.4202:0.0	rs3027229;rs3809880	33	B7Z3W0	.	A	57;33	ENSP00000369494:P57A;ENSP00000314879:P33A	ENSP00000314879:P33A	P	-	1	0	ALOXE3	7962333	0.787000	0.28750	0.007000	0.13788	0.042000	0.13812	0.392000	0.20801	-0.160000	0.11002	0.655000	0.94253	CCT	G|0.877;C|0.123	0.123	strong		0.582	ALOXE3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441475.1		
TMPRSS13	84000	hgsc.bcm.edu	37	11	117779305	117779305	+	Missense_Mutation	SNP	C	C	A	rs80264810	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:117779305C>A	ENST00000526090.1	-	9	1455	c.1304G>T	c.(1303-1305)cGc>cTc	p.R435L	TMPRSS13_ENST00000528626.1_Intron|TMPRSS13_ENST00000524993.1_Intron|TMPRSS13_ENST00000445164.2_Intron|TMPRSS13_ENST00000430170.2_Intron	NM_001206790.1	NP_001193719.1	Q9BYE2	TMPSD_HUMAN	transmembrane protease, serine 13	0	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					blood microparticle (GO:0072562)|integral component of membrane (GO:0016021)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)			endometrium(1)|kidney(3)|large_intestine(6)|lung(7)|pancreas(1)|prostate(1)|urinary_tract(1)	20	all_hematologic(175;0.0487)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.78e-05)|Epithelial(105;0.00106)		GGCAGGAGAGCGGGGAGTGCA	0.602													C|||	98	0.0195687	0.0023	0.0303	5008	,	,		15493	0.001		0.0547	False		,,,				2504	0.0184				p.R435L		Atlas-SNP	.											.	TMPRSS13	75	.	0			c.G1304T						PASS	.	C	,,LEU/ARG	60,4008		0,60,1974	19.0	21.0	20.0		,,1304	-6.7	0.0	11	dbSNP_132	20	531,7773		20,491,3641	yes	intron,intron,missense	TMPRSS13	NM_001077263.2,NM_001206789.1,NM_001206790.1	,,102	20,551,5615	AA,AC,CC		6.3945,1.4749,4.7769	,,	,,435/492	117779305	591,11781	2034	4152	6186	SO:0001583	missense	84000	exon9			GGAGAGCGGGGAG	AB048796	CCDS41721.1, CCDS55788.1, CCDS55789.1, CCDS58185.1	11q23	2010-04-13	2005-03-11	2005-03-12	ENSG00000137747	ENSG00000137747		"""Serine peptidases / Transmembrane"""	29808	protein-coding gene	gene with protein product		610050	"""transmembrane protease, serine 11"""	TMPRSS11		11267681	Standard	NM_001077263		Approved	MSPL	uc001prs.2	Q9BYE2	OTTHUMG00000166992	ENST00000526090.1:c.1304G>T	11.37:g.117779305C>A	ENSP00000436502:p.Arg435Leu	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	32	8	0.25	NM_001206790	B4DTM9|E9PIJ5|F8WAJ3|Q86YM4|Q96JY8|Q9BYE1	Missense_Mutation	SNP	ENST00000526090.1	37	CCDS55789.1	61	0.027930402930402932	1	0.0020325203252032522	14	0.03867403314917127	0	0.0	46	0.06068601583113457	C	4.101	0.016804	0.07959	0.014749	0.063945	ENSG00000137747	ENST00000526090	D	0.88896	-2.44	3.34	-6.69	0.01772	.	.	.	.	.	T	0.26846	0.0657	.	.	.	0.09310	N	1	B	0.17465	0.022	B	0.17722	0.019	T	0.51521	-0.8695	8	0.18276	T	0.48	.	3.6166	0.08079	0.1116:0.3185:0.4182:0.1516	.	430	Q9BYE2-4	.	L	435	ENSP00000436502:R435L	ENSP00000436502:R435L	R	-	2	0	TMPRSS13	117284515	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.386000	0.02537	-1.208000	0.02634	-0.463000	0.05309	CGC	C|0.971;A|0.029	0.029	strong		0.602	TMPRSS13-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000392320.1	NM_032046	
HIST1H1E	3008	hgsc.bcm.edu	37	6	26156817	26156817	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:26156817G>A	ENST00000304218.3	+	1	259	c.199G>A	c.(199-201)Gca>Aca	p.A67T	HIST1H2BD_ENST00000289316.2_5'Flank|HIST1H2BD_ENST00000377777.4_5'Flank	NM_005321.2	NP_005312.1	P10412	H14_HUMAN	histone cluster 1, H1e	67	H15. {ECO:0000255|PROSITE- ProRule:PRU00837}.				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						GAAAGCGCTGGCAGCCGCTGG	0.617																																					p.A67T		Atlas-SNP	.											.	HIST1H1E	69	.	0			c.G199A						PASS	.						35.0	38.0	37.0					6																	26156817		2203	4300	6503	SO:0001583	missense	3008	exon1			GCGCTGGCAGCCG	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.199G>A	6.37:g.26156817G>A	ENSP00000307705:p.Ala67Thr	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	72	10	0.138889	NM_005321	Q4VB25	Missense_Mutation	SNP	ENST00000304218.3	37	CCDS4586.1	.	.	.	.	.	.	.	.	.	.	.	19.26	3.794164	0.70452	.	.	ENSG00000168298	ENST00000304218	T	0.10477	2.87	5.11	5.11	0.69529	Histone H1/H5 (3);Winged helix-turn-helix transcription repressor DNA-binding (1);	0.416196	0.25863	N	0.027820	T	0.15089	0.0364	L	0.60957	1.885	0.53688	D	0.999973	B	0.33379	0.41	P	0.47528	0.549	T	0.01643	-1.1305	10	0.42905	T	0.14	-2.9473	17.8759	0.88825	0.0:0.0:1.0:0.0	.	67	P10412	H14_HUMAN	T	67	ENSP00000307705:A67T	ENSP00000307705:A67T	A	+	1	0	HIST1H1E	26264796	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	5.534000	0.67167	2.542000	0.85734	0.561000	0.74099	GCA	.	.	none		0.617	HIST1H1E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040084.1	NM_005321	
SIGLEC1	6614	hgsc.bcm.edu	37	20	3672836	3672836	+	Silent	SNP	G	G	A	rs910653	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:3672836G>A	ENST00000344754.4	-	16	4043	c.4044C>T	c.(4042-4044)gaC>gaT	p.D1348D	SIGLEC1_ENST00000202578.4_Silent_p.D1348D	NM_023068.3	NP_075556.1	Q9BZZ2	SN_HUMAN	sialic acid binding Ig-like lectin 1, sialoadhesin	1348					cell-matrix adhesion (GO:0007160)|endocytosis (GO:0006897)|inflammatory response (GO:0006954)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of T cell apoptotic process (GO:0070234)|single organismal cell-cell adhesion (GO:0016337)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)			NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(4)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(5)|liver(2)|lung(24)|ovary(3)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)	70						ACAGGACAGCGTCCTGAGGGG	0.612													G|||	1905	0.380391	0.2352	0.5043	5008	,	,		21871	0.4038		0.3479	False		,,,				2504	0.498				p.D1348D		Atlas-SNP	.											.	SIGLEC1	210	.	0			c.C4044T						PASS	.	G		1100,3306	393.1+/-328.7	147,806,1250	41.0	42.0	42.0		4044	-10.3	0.0	20	dbSNP_86	42	3138,5462	470.3+/-367.8	568,2002,1730	no	coding-synonymous	SIGLEC1	NM_023068.3		715,2808,2980	AA,AG,GG		36.4884,24.966,32.585		1348/1710	3672836	4238,8768	2203	4300	6503	SO:0001819	synonymous_variant	6614	exon16			GACAGCGTCCTGA	AF230073	CCDS13060.1	20p13	2013-01-29	2006-01-19	2006-01-19	ENSG00000088827	ENSG00000088827		"""CD molecules"", ""Sialic acid binding Ig-like lectins"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	11127	protein-coding gene	gene with protein product		600751	"""sialoadhesin"""	SN		8530048	Standard	XM_006723610		Approved	SIGLEC-1, CD169, FLJ00051, FLJ00055, FLJ00073, FLJ32150, dJ1009E24.1, sialoadhesin	uc002wja.3	Q9BZZ2	OTTHUMG00000031757	ENST00000344754.4:c.4044C>T	20.37:g.3672836G>A		Somatic	19	0	0		WXS	Illumina HiSeq	Phase_I	22	10	0.454545	NM_023068	Q96DL4|Q9GZS5|Q9H1H6|Q9H1H7|Q9H7L7	Silent	SNP	ENST00000344754.4	37	CCDS13060.1	780	0.35714285714285715	120	0.24390243902439024	158	0.43646408839779005	235	0.41083916083916083	267	0.35224274406332456	G	0.012	-1.649729	0.00785	0.24966	0.364884	ENSG00000088827	ENST00000419548	.	.	.	5.2	-10.3	0.00346	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.45607	P	0.0014560000000000128	.	.	.	.	.	.	T	0.03717	-1.1010	3	.	.	.	.	16.1564	0.81670	0.4084:0.0:0.5916:0.0	rs910653;rs3746635	.	.	.	C	162	.	.	R	-	1	0	SIGLEC1	3620836	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.909000	0.01586	-2.116000	0.00830	-2.052000	0.00405	CGC	G|0.663;A|0.337	0.337	strong		0.612	SIGLEC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077761.2	NM_023068	
ADAMTS7	11173	hgsc.bcm.edu	37	15	79067099	79067099	+	Silent	SNP	G	G	C	rs142017909	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	102	0	0		WXS	Illumina HiSeq	Phase_I	113	13	0.115044	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	
DAAM2	23500	hgsc.bcm.edu	37	6	39851818	39851818	+	Silent	SNP	G	G	A	rs3003929	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:39851818G>A	ENST00000398904.2	+	15	2108	c.1926G>A	c.(1924-1926)aaG>aaA	p.K642K	DAAM2_ENST00000538976.1_Silent_p.K642K|RP11-61I13.3_ENST00000607675.1_RNA|RP11-61I13.3_ENST00000607215.1_RNA|DAAM2_ENST00000274867.4_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	127	0	0		WXS	Illumina HiSeq	Phase_I	99	40	0.40404	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		
BRWD1	54014	hgsc.bcm.edu	37	21	40608530	40608530	+	Silent	SNP	A	A	C	rs143020455		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:40608530A>C	ENST00000333229.2	-	23	3084	c.2757T>G	c.(2755-2757)ccT>ccG	p.P919P	BRWD1_ENST00000380800.3_Silent_p.P919P|BRWD1_ENST00000342449.3_Silent_p.P919P	NM_018963.4	NP_061836.2	Q9NSI6	BRWD1_HUMAN	bromodomain and WD repeat domain containing 1	919					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)				CCTCCTTCTTAGGCTTATTTT	0.328													A|||	1	0.000199681	0.0008	0.0	5008	,	,		21667	0.0		0.0	False		,,,				2504	0.0				p.P919P	Melanoma(170;988 1986 4794 16843 39731)	Atlas-SNP	.											.	BRWD1	325	.	0			c.T2757G						PASS	.	A	,	0,4406		0,0,2203	122.0	110.0	114.0		2757,2757	4.2	1.0	21	dbSNP_134	114	8,8592	6.4+/-24.3	0,8,4292	no	coding-synonymous,coding-synonymous	BRWD1	NM_018963.4,NM_033656.3	,	0,8,6495	CC,CA,AA		0.093,0.0,0.0615	,	919/2321,919/2270	40608530	8,12998	2203	4300	6503	SO:0001819	synonymous_variant	54014	exon23			CTTCTTAGGCTTA	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.2757T>G	21.37:g.40608530A>C		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	115	56	0.486957	NM_018963	C9JK25|O43721|Q5R2V0|Q5R2V1|Q6P2D1|Q8TCV3|Q96QG9|Q96QH0|Q9NUK1	Silent	SNP	ENST00000333229.2	37	CCDS13662.1																																																																																			A|0.999;C|0.001	0.001	strong		0.328	BRWD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141398.3	NM_033656	
MUC4	4585	hgsc.bcm.edu	37	3	195477791	195477791	+	Silent	SNP	G	G	A	rs2291652	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195477791G>A	ENST00000346145.4	-	22	3171	c.3132C>T	c.(3130-3132)atC>atT	p.I1044I	MUC4_ENST00000349607.4_Silent_p.I993I|MUC4_ENST00000463781.3_Silent_p.I5280I|MUC4_ENST00000475231.1_Silent_p.I5228I	NM_004532.5	NP_004523.3	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	2037					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		CTTCCCCGGAGATGGGCTGGA	0.637													.|||	2034	0.40615	0.0787	0.4179	5008	,	,		11844	0.7679		0.4583	False		,,,				2504	0.4141				p.I5280I		Atlas-SNP	.											.	MUC4	1505	.	0			c.C15840T						PASS	.	G	,,	658,3748	276.6+/-273.2	54,550,1599	64.0	57.0	60.0		3132,15840,2979	3.0	0.9	3	dbSNP_100	60	3871,4729	540.4+/-383.8	868,2135,1297	no	coding-synonymous,coding-synonymous,coding-synonymous	MUC4	NM_004532.5,NM_018406.6,NM_138297.4	,,	922,2685,2896	AA,AG,GG		45.0116,14.9342,34.8224	,,	1044/1177,5280/5413,993/1126	195477791	4529,8477	2203	4300	6503	SO:0001819	synonymous_variant	4585	exon23			CCCGGAGATGGGC	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000346145.4:c.3132C>T	3.37:g.195477791G>A		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	34	15	0.441176	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Silent	SNP	ENST00000346145.4	37	CCDS3310.1																																																																																			G|0.628;A|0.372	0.372	strong		0.637	MUC4-015	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341862.1	NM_018406	
ADAMTSL4	54507	hgsc.bcm.edu	37	1	150526406	150526406	+	Silent	SNP	C	C	T	rs6681639	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:150526406C>T	ENST00000369038.2	+	4	1140	c.939C>T	c.(937-939)ggC>ggT	p.G313G	RP11-54A4.2_ENST00000442435.2_RNA|ADAMTSL4_ENST00000271643.4_Silent_p.G313G|MIR4257_ENST00000581735.1_RNA|ADAMTSL4_ENST00000369039.5_Silent_p.G313G|ADAMTSL4_ENST00000369041.5_Silent_p.G313G			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	85	0	0		WXS	Illumina HiSeq	Phase_I	67	40	0.597015	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	
SNPH	9751	hgsc.bcm.edu	37	20	1285549	1285549	+	Silent	SNP	G	G	A	rs35467629	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:1285549G>A	ENST00000381873.3	+	6	572	c.336G>A	c.(334-336)acG>acA	p.T112T	SNPH_ENST00000381867.1_Silent_p.T156T	NM_014723.2	NP_055538.2	O15079	SNPH_HUMAN	syntaphilin	112					brain development (GO:0007420)|neuron differentiation (GO:0030182)|neurotransmitter secretion (GO:0007269)|synaptic vesicle docking involved in exocytosis (GO:0016081)	cell junction (GO:0030054)|cytoplasmic microtubule (GO:0005881)|integral component of membrane (GO:0016021)|mitochondrial membrane (GO:0031966)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|presynaptic membrane (GO:0042734)	syntaxin-1 binding (GO:0017075)			endometrium(2)|large_intestine(4)|lung(10)|ovary(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	23						ACCTGAAGACGCAGCTGTCAC	0.622													G|||	139	0.0277556	0.0	0.0389	5008	,	,		17994	0.001		0.0567	False		,,,				2504	0.0552				p.T112T		Atlas-SNP	.											.	SNPH	89	.	0			c.G336A						PASS	.	G		34,4372	40.0+/-72.8	0,34,2169	74.0	70.0	71.0		336	-3.0	0.9	20	dbSNP_126	71	420,8180	129.2+/-187.3	6,408,3886	no	coding-synonymous	SNPH	NM_014723.2		6,442,6055	AA,AG,GG		4.8837,0.7717,3.4907		112/495	1285549	454,12552	2203	4300	6503	SO:0001819	synonymous_variant	9751	exon6			GAAGACGCAGCTG		CCDS13012.1	20p13	2008-07-02			ENSG00000101298	ENSG00000101298			15931	protein-coding gene	gene with protein product		604942				10707983	Standard	NM_014723		Approved	bA314N13.5	uc002wes.3	O15079	OTTHUMG00000031662	ENST00000381873.3:c.336G>A	20.37:g.1285549G>A		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	73	33	0.452055	NM_014723	Q8IYI3	Silent	SNP	ENST00000381873.3	37	CCDS13012.1																																																																																			G|0.965;A|0.035	0.035	strong		0.622	SNPH-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000145240.2	NM_014723	
KRT15	3866	hgsc.bcm.edu	37	17	39671724	39671724	+	Splice_Site	SNP	T	T	C	rs2305556	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:39671724T>C	ENST00000254043.3	-	6	4832	c.1247A>G	c.(1246-1248)aAg>aGg	p.K416R	KRT15_ENST00000393974.3_Splice_Site_p.K251R|KRT15_ENST00000393981.3_Missense_Mutation_p.K251R|KRT15_ENST00000393976.2_Splice_Site_p.K416R	NM_002275.3	NP_002266	P19012	K1C15_HUMAN	keratin 15	416	Tail.		K -> R (in dbSNP:rs2305556). {ECO:0000269|PubMed:14702039}.		epidermis development (GO:0008544)	extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	scaffold protein binding (GO:0097110)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|lung(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	16		Breast(137;0.000286)				AGGCGCCTACTTGGCATCCTG	0.587													T|||	668	0.133387	0.2012	0.1354	5008	,	,		20443	0.0565		0.2107	False		,,,				2504	0.0399				p.K416R		Atlas-SNP	.											.	KRT15	60	.	0			c.A1247G						PASS	.	T	ARG/LYS	945,3461	356.9+/-313.7	96,753,1354	83.0	73.0	76.0		1247	2.5	1.0	17	dbSNP_100	76	1940,6660	339.5+/-323.2	225,1490,2585	yes	missense-near-splice	KRT15	NM_002275.3	26	321,2243,3939	CC,CT,TT		22.5581,21.448,22.1821	benign	416/457	39671724	2885,10121	2203	4300	6503	SO:0001630	splice_region_variant	3866	exon6			GCCTACTTGGCAT		CCDS11398.1	17q21.2	2013-06-20			ENSG00000171346	ENSG00000171346		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6421	protein-coding gene	gene with protein product	"""keratin-15, basic"", ""keratin-15, beta"", ""type I cytoskeletal 15"", ""cytokeratin 15"""	148030				16831889	Standard	NM_002275		Approved	K15, CK15, K1CO	uc002hwy.3	P19012	OTTHUMG00000133435	ENST00000254043.3:c.1247+1A>G	17.37:g.39671724T>C		Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	34	16	0.470588	NM_002275	B3KQY1|B3KRA2|E0CX14|Q53XV8|Q9BUG4	Missense_Mutation	SNP	ENST00000254043.3	37	CCDS11398.1	345	0.15796703296703296	99	0.20121951219512196	58	0.16022099447513813	27	0.0472027972027972	161	0.21240105540897097	T	15.25	2.776876	0.49786	0.21448	0.225581	ENSG00000171346	ENST00000254043;ENST00000393974;ENST00000393976;ENST00000393981	D;T;D;T	0.81499	-1.5;-0.96;-1.5;-1.44	4.71	2.51	0.30379	.	0.124418	0.35805	N	0.002962	T	0.00039	0.0001	L	0.33093	0.98	0.41345	P	0.012674999999999992	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.15484	0.013;0.012;0.012	T	0.03555	-1.1025	8	.	.	.	.	1.9768	0.03418	0.161:0.0973:0.1665:0.5752	rs2305556;rs17581965;rs58310507;rs2305556	251;416;416	A8MT21;B3KVF5;P19012	.;.;K1C15_HUMAN	R	416;251;416;251	ENSP00000254043:K416R;ENSP00000377544:K251R;ENSP00000377546:K416R;ENSP00000377550:K251R	.	K	-	2	0	KRT15	36925250	0.090000	0.21635	0.997000	0.53966	0.973000	0.67179	0.036000	0.13819	0.356000	0.24157	0.533000	0.62120	AAG	T|0.806;C|0.194	0.194	strong		0.587	KRT15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257301.1	NM_002275	Missense_Mutation
TBL3	10607	hgsc.bcm.edu	37	16	2025604	2025604	+	Missense_Mutation	SNP	G	G	C	rs8052713	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:2025604G>C	ENST00000568546.1	+	10	1008	c.880G>C	c.(880-882)Gag>Cag	p.E294Q		NM_006453.2	NP_006444.2	Q12788	TBL3_HUMAN	transducin (beta)-like 3	294			E -> Q (in dbSNP:rs8052713).		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						CCCTGGGCAGGAGCTGACCCA	0.701													G|||	573	0.114417	0.0038	0.1873	5008	,	,		17024	0.0397		0.1312	False		,,,				2504	0.272				p.E294Q	Melanoma(118;616 1651 35077 38081 48633)	Atlas-SNP	.											TBL3,NS,carcinoma,0,1	TBL3	54	1	0			c.G880C						PASS	.	G	GLN/GLU	115,4271		4,107,2082	20.0	22.0	21.0		880	5.2	0.8	16	dbSNP_116	21	1032,7554		57,918,3318	no	missense	TBL3	NM_006453.2	29	61,1025,5400	CC,CG,GG		12.0196,2.622,8.8421	benign	294/809	2025604	1147,11825	2193	4293	6486	SO:0001583	missense	10607	exon10			GGGCAGGAGCTGA	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.880G>C	16.37:g.2025604G>C	ENSP00000454836:p.Glu294Gln	Somatic	15	0	0		WXS	Illumina HiSeq	Phase_I	8	6	0.75	NM_006453	Q59GD6|Q8IVB7|Q96A78	Missense_Mutation	SNP	ENST00000568546.1	37	CCDS10453.1	169	0.07738095238095238	3	0.006097560975609756	50	0.13812154696132597	21	0.03671328671328671	95	0.12532981530343007	G	10.55	1.382302	0.24944	0.02622	0.120196	ENSG00000183751	ENST00000332704	.	.	.	5.17	5.17	0.71159	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.607646	0.14343	N	0.325608	T	0.00356	0.0011	L	0.47716	1.5	0.27465	P	0.9530353	B;P	0.37176	0.008;0.586	B;B	0.27608	0.005;0.081	T	0.22243	-1.0222	8	0.10377	T	0.69	-13.4403	17.6351	0.88120	0.0:0.0:1.0:0.0	rs8052713	56;294	A0JLS5;Q12788	.;TBL3_HUMAN	Q	294	.	ENSP00000331815:E294Q	E	+	1	0	TBL3	1965605	1.000000	0.71417	0.809000	0.32408	0.510000	0.34073	4.016000	0.57159	2.415000	0.81967	0.655000	0.94253	GAG	G|0.921;C|0.079	0.079	strong		0.701	TBL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250615.3	NM_006453	
ACSS1	84532	hgsc.bcm.edu	37	20	25038484	25038484	+	Silent	SNP	G	G	T	rs66817095	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:25038484G>T	ENST00000323482.4	-	1	334	c.255C>A	c.(253-255)acC>acA	p.T85T	ACSS1_ENST00000376726.3_Silent_p.T85T|ACSS1_ENST00000432802.2_Silent_p.T85T	NM_001252675.1|NM_032501.3	NP_001239604.1|NP_115890.2	Q9NUB1	ACS2L_HUMAN	acyl-CoA synthetase short-chain family member 1	85					acetate biosynthetic process (GO:0019413)|acetyl-CoA biosynthetic process (GO:0006085)|acetyl-CoA biosynthetic process from acetate (GO:0019427)|ethanol oxidation (GO:0006069)|propionate biosynthetic process (GO:0019542)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	mitochondrial matrix (GO:0005759)	acetate-CoA ligase activity (GO:0003987)|AMP binding (GO:0016208)|ATP binding (GO:0005524)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(11)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	26					Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)	TGTGGTAGGGGGTGTCCCACA	0.662													G|||	959	0.191494	0.0098	0.2032	5008	,	,		10301	0.4812		0.1829	False		,,,				2504	0.1391				p.T85T		Atlas-SNP	.											.	ACSS1	46	.	0			c.C255A						PASS	.	G		158,4248	101.6+/-140.2	2,154,2047	42.0	47.0	45.0		255	1.5	1.0	20	dbSNP_130	45	1447,7153	267.5+/-287.3	106,1235,2959	no	coding-synonymous	ACSS1	NM_032501.2		108,1389,5006	TT,TG,GG		16.8256,3.586,12.3405		85/690	25038484	1605,11401	2203	4300	6503	SO:0001819	synonymous_variant	84532	exon1			GTAGGGGGTGTCC		CCDS13167.1, CCDS58764.1, CCDS58765.1	20p11.23-p11.21	2012-07-13	2005-09-08	2005-09-08	ENSG00000154930	ENSG00000154930	6.2.1.1	"""Acyl-CoA synthetase family"""	16091	protein-coding gene	gene with protein product		614355	"""acetyl-Coenzyme A synthetase 2 (AMP forming)-like"""	ACAS2L			Standard	NM_032501		Approved	dJ568C11.3, AceCS2L, MGC33843	uc002wub.3	Q9NUB1	OTTHUMG00000032112	ENST00000323482.4:c.255C>A	20.37:g.25038484G>T		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	131	57	0.435115	NM_001252677	B3KXL2|B4DJZ3|D3DW48|F5H6F4|F8W7Y1|Q5TF42|Q8IV99|Q8N234|Q96JI1|Q96JX6|Q9NU28	Silent	SNP	ENST00000323482.4	37	CCDS13167.1																																																																																			G|0.845;T|0.155	0.155	strong		0.662	ACSS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078386.2	NM_032501	
NBPF10	100132406	hgsc.bcm.edu	37	1	145368461	145368461	+	Missense_Mutation	SNP	A	A	C	rs12128680	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:145368461A>C	ENST00000369339.3	+	17	2046	c.1793A>C	c.(1792-1794)gAa>gCa	p.E598A	NBPF10_ENST00000369338.1_Missense_Mutation_p.E596A|NBPF10_ENST00000342960.5_Missense_Mutation_p.E3480A			Q6P3W6	NBPFA_HUMAN	neuroblastoma breakpoint family, member 10	775	NBPF 3. {ECO:0000255|PROSITE- ProRule:PRU00647}.					cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)			NS(3)|breast(1)|central_nervous_system(3)|endometrium(12)|kidney(23)|lung(15)|ovary(1)|prostate(7)|skin(6)|urinary_tract(2)	73	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		GTGCTGATGGAAGTGGAAGAG	0.468																																					p.E3480A		Atlas-SNP	.											.	NBPF10	221	.	0			c.A10439C						PASS	.																																			SO:0001583	missense	100132406	exon84			TGATGGAAGTGGA	BC021111		1q21.1	2013-01-17			ENSG00000163386	ENSG00000271425		"""neuroblastoma breakpoint family"""	31992	protein-coding gene	gene with protein product		614000				16079250	Standard	NM_001039703		Approved	AG1		Q6P3W6	OTTHUMG00000013757	ENST00000369339.3:c.1793A>C	1.37:g.145368461A>C	ENSP00000358345:p.Glu598Ala	Somatic	204	0	0		WXS	Illumina HiSeq	Phase_I	197	36	0.182741	NM_001039703	Q5RHC0|Q9NWN6	Missense_Mutation	SNP	ENST00000369339.3	37		.	.	.	.	.	.	.	.	.	.	.	6.133	0.392687	0.11638	.	.	ENSG00000163386	ENST00000369339;ENST00000369338;ENST00000342960	T;T	0.09817	2.94;2.94	0.732	-1.11	0.09840	.	.	.	.	.	T	0.04679	0.0127	M	0.83603	2.65	0.09310	N	1	B	0.02656	0.0	B	0.09377	0.004	T	0.38178	-0.9673	9	0.66056	D	0.02	.	2.7049	0.05159	0.5769:0.0:0.0:0.4231	rs12128680;rs57717963;rs12128680	544	Q4VC10	.	A	600;596;3480	ENSP00000358344:E596A;ENSP00000345684:E3480A	ENSP00000345684:E3480A	E	+	2	0	NBPF10	144079818	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	0.155000	0.16362	-0.323000	0.08602	0.316000	0.21350	GAA	A|0.899;C|0.101	0.101	strong		0.468	NBPF10-001	KNOWN	not_best_in_genome_evidence|basic	protein_coding	protein_coding	OTTHUMT00000038550.3	NM_001039703	
SNRNP48	154007	hgsc.bcm.edu	37	6	7601720	7601720	+	Silent	SNP	C	C	T	rs3734586	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:7601720C>T	ENST00000342415.5	+	5	617	c.558C>T	c.(556-558)agC>agT	p.S186S		NM_152551.3	NP_689764.3	Q6IEG0	SNR48_HUMAN	small nuclear ribonucleoprotein 48kDa (U11/U12)	186					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	U12-type spliceosomal complex (GO:0005689)	metal ion binding (GO:0046872)			kidney(2)|lung(5)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	10						AAAATGACAGCGATCTCTTTG	0.358													C|||	1523	0.304113	0.1747	0.3401	5008	,	,		17437	0.4841		0.17	False		,,,				2504	0.4059				p.S186S		Atlas-SNP	.											.	SNRNP48	32	.	0			c.C558T						PASS	.	C		799,3607	317.7+/-295.3	70,659,1474	78.0	78.0	78.0		558	1.8	1.0	6	dbSNP_107	78	1459,7141	279.8+/-294.2	131,1197,2972	no	coding-synonymous	SNRNP48	NM_152551.3		201,1856,4446	TT,TC,CC		16.9651,18.1344,17.3612		186/340	7601720	2258,10748	2203	4300	6503	SO:0001819	synonymous_variant	154007	exon5			TGACAGCGATCTC	AK056796	CCDS4502.1	6p24.3	2011-10-11	2008-10-29	2008-10-29	ENSG00000168566	ENSG00000168566			21368	protein-coding gene	gene with protein product	"""U11/U12 snRNP 48K"""		"""chromosome 6 open reading frame 151"""	C6orf151		15146077	Standard	XR_427825		Approved	FLJ32234, dJ512B11.2, dJ336K20B.1	uc003mxr.3	Q6IEG0	OTTHUMG00000014213	ENST00000342415.5:c.558C>T	6.37:g.7601720C>T		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	101	40	0.39604	NM_152551	A8K8P4|Q14C91|Q5T339|Q5THM1|Q5THM2|Q96MK1	Silent	SNP	ENST00000342415.5	37	CCDS4502.1																																																																																			C|0.776;T|0.224	0.224	strong		0.358	SNRNP48-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039787.3	NM_152551	
XPC	7508	hgsc.bcm.edu	37	3	14199908	14199908	+	Missense_Mutation	SNP	C	C	T	rs2227999	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:14199908C>T	ENST00000285021.7	-	9	1689	c.1475G>A	c.(1474-1476)cGt>cAt	p.R492H	XPC_ENST00000449060.2_Missense_Mutation_p.R455H	NM_001145769.1|NM_004628.4	NP_001139241.1|NP_004619.3	Q01831	XPC_HUMAN	xeroderma pigmentosum, complementation group C	492	Arg/Lys-rich (basic).		R -> H (in dbSNP:rs2227999). {ECO:0000269|Ref.4}.		DNA repair (GO:0006281)|intra-S DNA damage checkpoint (GO:0031573)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage recognition (GO:0000715)|nucleotide-excision repair, DNA damage removal (GO:0000718)|regulation of mitotic cell cycle phase transition (GO:1901990)|response to drug (GO:0042493)|response to UV-B (GO:0010224)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|XPC complex (GO:0071942)	bubble DNA binding (GO:0000405)|damaged DNA binding (GO:0003684)|heteroduplex DNA loop binding (GO:0000404)|single-stranded DNA binding (GO:0003697)			NS(1)|breast(2)|endometrium(1)|kidney(3)|large_intestine(4)|lung(5)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						TGGGTCCTTACGATGGCTCCC	0.547			"""Mis, N, F, S"""			"""skin basal cell, skin squamous cell, melanoma"""		Nucleotide excision repair (NER)	Xeroderma Pigmentosum				T|||	116	0.0231629	0.0076	0.0216	5008	,	,		19988	0.001		0.0557	False		,,,				2504	0.0348				p.R492H		Atlas-SNP	.	yes	Rec		Xeroderma pigmentosum (C)	3	3p25	7508	"""xeroderma pigmentosum, complementation group C"""		E	.	XPC	60	.	0			c.G1475A	GRCh37	CM068096	XPC	M	rs2227999	PASS	.	T	HIS/ARG,HIS/ARG	40,3096		1,38,1529	55.0	51.0	52.0		1364,1475	-4.5	0.0	3	dbSNP_98	52	439,6725		17,405,3160	yes	missense,missense	XPC	NM_001145769.1,NM_004628.4	29,29	18,443,4689	TT,TC,CC		6.1279,1.2755,4.6505	benign,benign	455/904,492/941	14199908	479,9821	1568	3582	5150	SO:0001583	missense	7508	exon9	Familial Cancer Database	incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV	TCCTTACGATGGC		CCDS46763.1	3p25.1	2014-09-17			ENSG00000154767	ENSG00000154767			12816	protein-coding gene	gene with protein product	"""xeroderma pigmentosum group C protein"""	613208				1522891	Standard	NM_004628		Approved	XPCC, RAD4	uc011ave.2	Q01831	OTTHUMG00000155526	ENST00000285021.7:c.1475G>A	3.37:g.14199908C>T	ENSP00000285021:p.Arg492His	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	45	25	0.555556	NM_004628	B4DIP3|E9PB96|E9PH69|Q53GT7|Q96AX0	Missense_Mutation	SNP	ENST00000285021.7	37	CCDS46763.1	62	0.028388278388278388	6	0.012195121951219513	13	0.03591160220994475	1	0.0017482517482517483	42	0.055408970976253295	T	9.872	1.199153	0.22121	0.012755	0.061279	ENSG00000154767	ENST00000285021;ENST00000449060	T;T	0.36699	1.24;1.26	5.52	-4.51	0.03483	.	2.165560	0.01300	N	0.010264	T	0.02083	0.0065	N	0.14661	0.345	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.09250	-1.0683	10	0.34782	T	0.22	3.2709	5.9024	0.18974	0.118:0.5607:0.0818:0.2395	rs2227999;rs3731129;rs17621236;rs52800264;rs2227999	455;492	E9PH69;Q01831	.;XPC_HUMAN	H	492;455	ENSP00000285021:R492H;ENSP00000404002:R455H	ENSP00000285021:R492H	R	-	2	0	XPC	14174910	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.502000	0.06390	-1.099000	0.03034	-3.250000	0.00050	CGT	C|0.969;T|0.031	0.031	strong		0.547	XPC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000340517.3	NM_004628	
POM121L12	285877	hgsc.bcm.edu	37	7	53103946	53103946	+	Silent	SNP	G	G	C	rs12113170	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:53103946G>C	ENST00000408890.4	+	1	598	c.582G>C	c.(580-582)ggG>ggC	p.G194G		NM_182595.3	NP_872401.3	Q8N7R1	P1L12_HUMAN	POM121 transmembrane nucleoporin-like 12	194										endometrium(5)|kidney(1)|large_intestine(5)|lung(44)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	61						GGTTCGACGGGCCGTTGTGGT	0.682													G|||	1647	0.328874	0.1725	0.4308	5008	,	,		12550	0.3026		0.4871	False		,,,				2504	0.3323				p.G194G		Atlas-SNP	.											.	POM121L12	146	.	0			c.G582C						PASS	.	G		802,3142		90,622,1260	48.0	55.0	53.0		582	-4.4	0.0	7	dbSNP_120	53	4189,4093		1054,2081,1006	no	coding-synonymous	POM121L12	NM_182595.3		1144,2703,2266	CC,CG,GG		49.4204,20.3347,40.8228		194/297	53103946	4991,7235	1972	4141	6113	SO:0001819	synonymous_variant	285877	exon1			CGACGGGCCGTTG		CCDS43584.1	7p12.1	2012-03-13	2012-03-13		ENSG00000221900	ENSG00000221900			25369	protein-coding gene	gene with protein product			"""POM121 membrane glycoprotein-like 12"""				Standard	NM_182595		Approved	DKFZp564N2472	uc003tpz.3	Q8N7R1	OTTHUMG00000155995	ENST00000408890.4:c.582G>C	7.37:g.53103946G>C		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	41	12	0.292683	NM_182595	Q8NDI9	Silent	SNP	ENST00000408890.4	37	CCDS43584.1																																																																																			G|0.631;C|0.369	0.369	strong		0.682	POM121L12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342656.1	NM_182595	
AHNAK2	113146	hgsc.bcm.edu	37	14	105415333	105415333	+	Missense_Mutation	SNP	T	T	C	rs201240658	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:105415333T>C	ENST00000333244.5	-	7	6574	c.6455A>G	c.(6454-6456)aAg>aGg	p.K2152R	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	2152						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)			CATTTTGAACTTGCTGTCTTT	0.592													.|||	437	0.0872604	0.1142	0.0605	5008	,	,		14688	0.0516		0.0447	False		,,,				2504	0.1503				p.K2152R		Atlas-SNP	.											AHNAK2_ENST00000333244,NS,carcinoma,0,1	AHNAK2	719	1	0			c.A6455G						scavenged	.	T	ARG/LYS	99,3871		15,69,1901	228.0	151.0	179.0		6455	3.2	1.0	14		179	12,7048		2,8,3520	yes	missense	AHNAK2	NM_138420.2	26	17,77,5421	CC,CT,TT		0.17,2.4937,1.0063	benign	2152/5796	105415333	111,10919	1985	3530	5515	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.6455A>G	14.37:g.105415333T>C	ENSP00000353114:p.Lys2152Arg	Somatic	2	0	0		WXS	Illumina HiSeq	Phase_I	101	9	0.0891089	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	77	0.035256410256410256	48	0.0975609756097561	4	0.011049723756906077	18	0.03146853146853147	7	0.009234828496042216	N	13.10	2.136869	0.37728	0.024937	0.0017	ENSG00000185567	ENST00000333244	T	0.00882	5.58	4.35	3.2	0.36748	.	.	.	.	.	T	0.00178	0.0005	M	0.90814	3.15	0.20703	N	0.999862	D	0.71674	0.998	D	0.87578	0.998	T	0.25293	-1.0136	9	0.62326	D	0.03	.	7.8725	0.29573	0.0:0.1733:0.0:0.8267	.	2152	Q8IVF2	AHNK2_HUMAN	R	2152	ENSP00000353114:K2152R	ENSP00000353114:K2152R	K	-	2	0	AHNAK2	104486378	0.833000	0.29383	0.972000	0.41901	0.091000	0.18340	2.383000	0.44354	0.563000	0.29222	0.254000	0.18369	AAG	T|0.965;C|0.035	0.035	strong		0.592	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
HMCN1	83872	hgsc.bcm.edu	37	1	186121996	186121996	+	Missense_Mutation	SNP	C	C	T	rs114629728	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:186121996C>T	ENST00000271588.4	+	96	15240	c.15011C>T	c.(15010-15012)aCt>aTt	p.T5004I	HMCN1_ENST00000367492.2_Missense_Mutation_p.T5004I	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	5004	Nidogen G2 beta-barrel. {ECO:0000255|PROSITE-ProRule:PRU00348}.				response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						GCTGAAGTCACTGTAAAGGTA	0.433													C|||	10	0.00199681	0.0	0.0014	5008	,	,		18553	0.0		0.008	False		,,,				2504	0.001				p.T5004I		Atlas-SNP	.											.	HMCN1	797	.	0			c.C15011T						PASS	.	C	ILE/THR	4,4402	2.1+/-5.4	0,4,2199	196.0	170.0	179.0		15011	2.9	0.0	1	dbSNP_133	179	29,8571	9.1+/-34.3	1,27,4272	yes	missense	HMCN1	NM_031935.2	89	1,31,6471	TT,TC,CC		0.3372,0.0908,0.2537	benign	5004/5636	186121996	33,12973	2203	4300	6503	SO:0001583	missense	83872	exon96			AAGTCACTGTAAA	AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"""Fibulins"", ""Immunoglobulin superfamily / I-set domain containing"""	19194	protein-coding gene	gene with protein product	"""fibulin 6"""	608548	"""age-related macular degeneration 1 (senile macular degeneration)"""	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.15011C>T	1.37:g.186121996C>T	ENSP00000271588:p.Thr5004Ile	Somatic	215	0	0		WXS	Illumina HiSeq	Phase_I	170	88	0.517647	NM_031935	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Missense_Mutation	SNP	ENST00000271588.4	37	CCDS30956.1	6	0.0027472527472527475	0	0.0	0	0.0	0	0.0	6	0.0079155672823219	C	8.698	0.909113	0.17833	9.08E-4	0.003372	ENSG00000143341	ENST00000271588;ENST00000367492	T;T	0.31510	1.49;1.49	5.9	2.9	0.33743	G2 nidogen/fibulin G2F (2);Green fluorescent protein-like (1);	0.929918	0.09308	N	0.819936	T	0.12603	0.0306	N	0.08118	0	0.09310	N	1	B	0.27316	0.175	B	0.30855	0.121	T	0.34601	-0.9822	10	0.29301	T	0.29	.	9.0753	0.36517	0.4557:0.2514:0.2928:0.0	.	5004	Q96RW7	HMCN1_HUMAN	I	5004	ENSP00000271588:T5004I;ENSP00000356462:T5004I	ENSP00000271588:T5004I	T	+	2	0	HMCN1	184388619	0.000000	0.05858	0.026000	0.17262	0.758000	0.43043	0.220000	0.17660	0.314000	0.23086	0.650000	0.86243	ACT	C|0.996;T|0.004	0.004	strong		0.433	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935	
ZNF85	7639	hgsc.bcm.edu	37	19	21132453	21132453	+	Missense_Mutation	SNP	C	C	G	rs146063134	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:21132453C>G	ENST00000328178.8	+	4	1246	c.1133C>G	c.(1132-1134)gCc>gGc	p.A378G	ZNF85_ENST00000601023.1_Missense_Mutation_p.A319G|ZNF85_ENST00000345030.6_Missense_Mutation_p.A345G	NM_001256173.1|NM_003429.4	NP_001243102.1|NP_003420.2	Q03923	ZNF85_HUMAN	zinc finger protein 85	378					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						TGTGGAAAAGCCTTTAATCAT	0.348													.|||	2	0.000399361	0.0	0.0	5008	,	,		19410	0.0		0.001	False		,,,				2504	0.001				p.A408G		Atlas-SNP	.											.	ZNF85	72	.	0			c.C1223G						PASS	.	C	GLY/ALA	0,4394		0,0,2197	39.0	42.0	41.0		1133	1.4	0.0	19	dbSNP_134	41	6,8586		0,6,4290	no	missense	ZNF85	NM_003429.4	60	0,6,6487	GG,GC,CC		0.0698,0.0,0.0462	possibly-damaging	378/596	21132453	6,12980	2197	4296	6493	SO:0001583	missense	7639	exon5			GAAAAGCCTTTAA	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.1133C>G	19.37:g.21132453C>G	ENSP00000329793:p.Ala378Gly	Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	18	8	0.444444	NM_001256171	B9ZVP4|Q6NVI0	Missense_Mutation	SNP	ENST00000328178.8	37	CCDS32977.1	.	.	.	.	.	.	.	.	.	.	.	12.01	1.809319	0.31961	0.0	6.98E-4	ENSG00000105750	ENST00000328178;ENST00000345030;ENST00000421385	T;T	0.19669	2.13;2.13	1.35	1.35	0.21983	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.31071	0.0785	L	0.41573	1.285	0.58432	D	0.999999	B;D;P	0.63046	0.289;0.992;0.898	B;D;P	0.77004	0.17;0.989;0.808	T	0.05632	-1.0873	9	0.66056	D	0.02	.	6.8304	0.23907	0.0:0.4775:0.5225:0.0	.	345;319;378	Q03923-2;Q49A12;Q03923	.;.;ZNF85_HUMAN	G	378;345;253	ENSP00000329793:A378G;ENSP00000342340:A345G	ENSP00000329793:A378G	A	+	2	0	ZNF85	20924293	0.001000	0.12720	0.039000	0.18376	0.129000	0.20672	0.077000	0.14738	0.681000	0.31386	0.462000	0.41574	GCC	C|0.999;G|0.001	0.001	strong		0.348	ZNF85-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463430.1	NM_003429	
FHL5	9457	hgsc.bcm.edu	37	6	97063522	97063522	+	Missense_Mutation	SNP	C	C	G	rs9373985	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:97063522C>G	ENST00000326771.2	+	7	1109	c.729C>G	c.(727-729)agC>agG	p.S243R	FHL5_ENST00000541107.1_Missense_Mutation_p.S243R	NM_020482.4	NP_065228.4	Q5TD97	FHL5_HUMAN	four and a half LIM domains 5	243	LIM zinc-binding 4. {ECO:0000255|PROSITE- ProRule:PRU00125}.		S -> R (in dbSNP:rs9373985).		positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(4)|lung(17)|ovary(2)|urinary_tract(1)	27		all_cancers(76;1.57e-07)|Acute lymphoblastic leukemia(125;4.93e-10)|all_hematologic(75;3.55e-07)|all_epithelial(107;0.00266)|Colorectal(196;0.0341)|Lung NSC(302;0.204)		BRCA - Breast invasive adenocarcinoma(108;0.0948)		TTCAAGACAGCCAGTGGCATA	0.438													C|||	1913	0.381989	0.497	0.2997	5008	,	,		20721	0.3502		0.3479	False		,,,				2504	0.3528				p.S243R		Atlas-SNP	.											.	FHL5	73	.	0			c.C729G						PASS	.	C	ARG/SER,ARG/SER	2137,2269	579.2+/-384.9	517,1103,583	111.0	109.0	109.0		729,729	3.9	1.0	6	dbSNP_119	109	2868,5732	450.2+/-362.3	476,1916,1908	yes	missense,missense	FHL5	NM_001170807.1,NM_020482.4	110,110	993,3019,2491	GG,GC,CC		33.3488,48.502,38.4822	benign,benign	243/285,243/285	97063522	5005,8001	2203	4300	6503	SO:0001583	missense	9457	exon7			AGACAGCCAGTGG	AF278541	CCDS5035.1	6q16.1-q16.3	2008-02-05			ENSG00000112214	ENSG00000112214			17371	protein-coding gene	gene with protein product		605126					Standard	NM_020482		Approved	FLJ33049, ACT, dJ393D12.2	uc003pot.2	Q5TD97	OTTHUMG00000015239	ENST00000326771.2:c.729C>G	6.37:g.97063522C>G	ENSP00000326022:p.Ser243Arg	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	116	115	0.991379	NM_020482	B2RBD1|E1P526|Q5TD98|Q8WW21|Q9NQU2	Missense_Mutation	SNP	ENST00000326771.2	37	CCDS5035.1	837	0.38324175824175827	259	0.5264227642276422	123	0.3397790055248619	200	0.34965034965034963	255	0.33641160949868076	C	2.233	-0.375731	0.05034	0.48502	0.333488	ENSG00000112214	ENST00000541107;ENST00000326771	D;D	0.87029	-2.2;-2.2	5.66	3.9	0.45041	Zinc finger, LIM-type (5);	0.179999	0.27362	N	0.019718	T	0.30792	0.0776	N	0.00227	-1.8	0.33206	P	0.44715099999999997	B	0.02656	0.0	B	0.04013	0.001	T	0.17868	-1.0355	9	0.02654	T	1	.	8.5385	0.33377	0.0:0.6902:0.0:0.3098	rs9373985;rs52808781;rs9373985	243	Q5TD97	FHL5_HUMAN	R	243	ENSP00000442357:S243R;ENSP00000326022:S243R	ENSP00000326022:S243R	S	+	3	2	FHL5	97170243	0.906000	0.30813	1.000000	0.80357	0.989000	0.77384	0.065000	0.14466	0.750000	0.32877	-0.136000	0.14681	AGC	C|0.612;G|0.388	0.388	strong		0.438	FHL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041559.1	NM_020482	
NELL1	4745	hgsc.bcm.edu	37	11	20805286	20805286	+	Missense_Mutation	SNP	G	G	A	rs8176785	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:20805286G>A	ENST00000357134.5	+	3	397	c.245G>A	c.(244-246)cGg>cAg	p.R82Q	NELL1_ENST00000325319.5_Missense_Mutation_p.R82Q|NELL1_ENST00000532434.1_Missense_Mutation_p.R82Q|NELL1_ENST00000298925.5_Missense_Mutation_p.R110Q	NM_006157.3|NM_201551.1	NP_006148.2|NP_963845.1	Q92832	NELL1_HUMAN	NEL-like 1 (chicken)	82	Laminin G-like.		R -> Q (in dbSNP:rs8176785). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:8975702, ECO:0000269|Ref.3}.		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						CAGCTGTTCCGGAACAAGAGT	0.453													g|||	3191	0.637181	0.2269	0.8256	5008	,	,		19124	0.8393		0.7396	False		,,,				2504	0.7444				p.R82Q		Atlas-SNP	.											.	NELL1	179	.	0			c.G245A	GRCh37	CM074381	NELL1	M	rs8176785	PASS	.	A	GLN/ARG,GLN/ARG	1331,3075	446.1+/-347.9	220,891,1092	115.0	105.0	109.0		245,245	3.1	1.0	11	dbSNP_117	109	6504,2096	716.7+/-406.1	2461,1582,257	yes	missense,missense	NELL1	NM_006157.3,NM_201551.1	43,43	2681,2473,1349	AA,AG,GG		24.3721,30.2088,39.7586	benign,benign	82/811,82/764	20805286	7835,5171	2203	4300	6503	SO:0001583	missense	4745	exon3			TGTTCCGGAACAA	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.245G>A	11.37:g.20805286G>A	ENSP00000349654:p.Arg82Gln	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	64	50	0.78125	NM_006157	B2CKC1|Q4VB90|Q4VB91|Q6NSY8|Q9Y472	Missense_Mutation	SNP	ENST00000357134.5	37	CCDS7855.1	1499	0.6863553113553114	143	0.29065040650406504	299	0.8259668508287292	489	0.8548951048951049	568	0.7493403693931399	g	15.15	2.746657	0.49257	0.302088	0.756279	ENSG00000165973	ENST00000298925;ENST00000357134;ENST00000325319;ENST00000532434	T;T;T;T	0.02177	4.41;4.41;4.41;4.41	5.9	3.07	0.35406	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (1);Laminin G, thrombospondin-type, N-terminal (1);	0.255913	0.36002	N	0.002855	T	0.00012	0.0000	M	0.65975	2.015	0.44162	P	0.0030360000000000387	B;B;B	0.24675	0.007;0.109;0.004	B;B;B	0.25987	0.004;0.065;0.002	T	0.04281	-1.0963	9	0.59425	D	0.04	-0.4969	11.2438	0.48985	0.1963:0.0:0.8037:0.0	rs8176785;rs52837466;rs58991519;rs8176785	82;82;82	F5H6I3;Q92832-2;Q92832	.;.;NELL1_HUMAN	Q	110;82;82;82	ENSP00000298925:R110Q;ENSP00000349654:R82Q;ENSP00000317837:R82Q;ENSP00000437170:R82Q	ENSP00000298925:R110Q	R	+	2	0	NELL1	20761862	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	3.332000	0.52083	0.423000	0.26033	-0.119000	0.15052	CGG	G|0.367;A|0.633	0.633	strong		0.453	NELL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387588.1	NM_006157	
CRIPAK	285464	hgsc.bcm.edu	37	4	1388786	1388786	+	Missense_Mutation	SNP	G	G	C	rs146249377	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:1388786G>C	ENST00000324803.4	+	1	3447	c.487G>C	c.(487-489)Gac>Cac	p.D163H		NM_175918.3	NP_787114.2	Q8N1N5	CRPAK_HUMAN	cysteine-rich PAK1 inhibitor	163					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.D163H(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)			CACACGTGCCGACGTGGAGTG	0.687													N|||	88	0.0175719	0.0371	0.0101	5008	,	,		19055	0.002		0.0149	False		,,,				2504	0.0153				p.D163H		Atlas-SNP	.											CRIPAK,extremity,malignant_melanoma,0,2	CRIPAK	185	2	1	Substitution - Missense(1)	skin(1)	c.G487C						PASS	.						176.0	124.0	142.0					4																	1388786		2202	4288	6490	SO:0001583	missense	285464	exon1			CGTGCCGACGTGG	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.487G>C	4.37:g.1388786G>C	ENSP00000323978:p.Asp163His	Somatic	21	0	0		WXS	Illumina HiSeq	Phase_I	25	4	0.16	NM_175918	Q8NB03	Missense_Mutation	SNP	ENST00000324803.4	37	CCDS3349.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	c|c	0.022|0.022	-1.413360|-1.413360	0.01145|0.01145	.|.	.|.	ENSG00000179979|ENSG00000179979	ENST00000324803|ENST00000382944	T|.	0.18657|.	2.2|.	1.25|1.25	-2.49|-2.49	0.06403|0.06403	.|.	.|.	.|.	.|.	.|.	T|T	0.13200|0.13200	0.0320|0.0320	N|N	0.08118|0.08118	0|0	0.09310|0.09310	N|N	1|1	B|.	0.14012|.	0.009|.	B|.	0.08055|.	0.003|.	T|T	0.05500|0.05500	-1.0881|-1.0881	9|6	0.45353|0.34782	T|T	0.12|0.22	.|.	0.6983|0.6983	0.00903|0.00903	0.1675:0.2958:0.1729:0.3639|0.1675:0.2958:0.1729:0.3639	.|.	163|.	Q8N1N5|.	CRPAK_HUMAN|.	H|P	163|146	ENSP00000323978:D163H|.	ENSP00000323978:D163H|ENSP00000372402:R146P	D|R	+|+	1|2	0|0	CRIPAK|CRIPAK	1378786|1378786	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.008000|0.008000	0.06430|0.06430	-2.475000|-2.475000	0.00987|0.00987	-3.363000|-3.363000	0.00178|0.00178	-1.824000|-1.824000	0.00597|0.00597	GAC|CGA	.	.	weak		0.687	CRIPAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241607.2	NM_175918	
LIMS1	3987	hgsc.bcm.edu	37	2	109276110	109276110	+	Missense_Mutation	SNP	G	G	A	rs146149508	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:109276110G>A	ENST00000393310.1	+	2	213	c.46G>A	c.(46-48)Ggc>Agc	p.G16S	LIMS1_ENST00000332345.6_Missense_Mutation_p.G16S|LIMS1_ENST00000393314.2_Missense_Mutation_p.G78S|LIMS1_ENST00000338045.3_Missense_Mutation_p.G16S|LIMS1_ENST00000409441.1_Missense_Mutation_p.G53S|LIMS1_ENST00000542845.1_Missense_Mutation_p.G78S|LIMS1_ENST00000544547.1_Missense_Mutation_p.G28S|LIMS1_ENST00000462817.1_3'UTR|LIMS1_ENST00000410093.1_Missense_Mutation_p.G20S	NM_001193488.1	NP_001180417.1	P48059	LIMS1_HUMAN	LIM and senescent cell antigen-like domains 1	16	LIM zinc-binding 1. {ECO:0000255|PROSITE- ProRule:PRU00125}.				cell aging (GO:0007569)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|cell-matrix adhesion (GO:0007160)|cellular response to transforming growth factor beta stimulus (GO:0071560)|chordate embryonic development (GO:0043009)|establishment or maintenance of cell polarity (GO:0007163)|negative regulation of apoptotic process (GO:0043066)|negative regulation of hepatocyte proliferation (GO:2000346)|negative regulation of neural precursor cell proliferation (GO:2000178)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of integrin-mediated signaling pathway (GO:2001046)|protein heterooligomerization (GO:0051291)|single organismal cell-cell adhesion (GO:0016337)	cytosol (GO:0005829)|focal adhesion (GO:0005925)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	zinc ion binding (GO:0008270)			breast(2)|endometrium(2)|kidney(1)|large_intestine(1)|lung(4)	10						CTGCAAGGGCGGCTTTGCGCC	0.572													G|||	11	0.00219649	0.0	0.0043	5008	,	,		24021	0.0		0.008	False		,,,				2504	0.0				p.G78S		Atlas-SNP	.											.	LIMS1	38	.	0			c.G232A						PASS	.	G	SER/GLY,SER/GLY,SER/GLY,SER/GLY,SER/GLY,SER/GLY	9,4397	14.3+/-33.2	0,9,2194	117.0	90.0	99.0		58,82,157,232,46,46	4.6	0.8	2	dbSNP_134	99	93,8507	52.3+/-112.8	0,93,4207	no	missense,missense,missense,missense,missense,missense	LIMS1	NM_001193482.1,NM_001193483.2,NM_001193484.1,NM_001193485.2,NM_001193488.1,NM_004987.5	56,56,56,56,56,56	0,102,6401	AA,AG,GG		1.0814,0.2043,0.7843	benign,benign,benign,benign,benign,benign	20/330,28/338,53/363,78/388,16/326,16/326	109276110	102,12904	2203	4300	6503	SO:0001583	missense	3987	exon2			AAGGGCGGCTTTG		CCDS2078.1, CCDS54382.1, CCDS54383.1, CCDS54384.1, CCDS54385.1	2q12.3	2008-05-23			ENSG00000169756	ENSG00000169756			6616	protein-coding gene	gene with protein product		602567				7517666, 10022929	Standard	NM_001193482		Approved	PINCH, PINCH1	uc002tek.4	P48059	OTTHUMG00000130983	ENST00000393310.1:c.46G>A	2.37:g.109276110G>A	ENSP00000376987:p.Gly16Ser	Somatic	630	0	0		WXS	Illumina HiSeq	Phase_I	859	303	0.352736	NM_001193485	B2RAJ4|B7Z483|B7Z7R3|B7Z907|Q53TE0|Q9BS44	Missense_Mutation	SNP	ENST00000393310.1	37	CCDS2078.1	.	.	.	.	.	.	.	.	.	.	G	20.6	4.017490	0.75161	0.002043	0.010814	ENSG00000169756	ENST00000544547;ENST00000428064;ENST00000332345;ENST00000393310;ENST00000410093;ENST00000409441;ENST00000338045;ENST00000542845;ENST00000393314	D;D;D;D;D;D;D;D;D	0.87256	-2.23;-2.23;-2.23;-2.23;-2.23;-2.23;-2.23;-2.23;-2.23	4.63	4.63	0.57726	Zinc finger, LIM-type (5);	0.160833	0.41605	D	0.000860	T	0.81978	0.4937	L	0.45744	1.44	0.80722	D	1	P;P;B;B	0.44946	0.846;0.53;0.377;0.377	P;B;B;B	0.45195	0.473;0.124;0.087;0.087	T	0.83289	-0.0034	10	0.33141	T	0.24	.	17.6679	0.88208	0.0:0.0:1.0:0.0	.	78;53;16;28	B7Z7R3;B7Z907;P48059;B7Z483	.;.;LIMS1_HUMAN;.	S	28;28;16;16;20;53;16;78;78	ENSP00000437912:G28S;ENSP00000390862:G28S;ENSP00000331775:G16S;ENSP00000376987:G16S;ENSP00000386926:G20S;ENSP00000387264:G53S;ENSP00000337598:G16S;ENSP00000446121:G78S;ENSP00000376990:G78S	ENSP00000331775:G16S	G	+	1	0	LIMS1	108642542	1.000000	0.71417	0.842000	0.33263	0.932000	0.56968	6.498000	0.73679	2.392000	0.81423	0.563000	0.77884	GGC	G|0.994;A|0.006	0.006	strong		0.572	LIMS1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000253596.1	NM_004987	
R3HDM1	23518	hgsc.bcm.edu	37	2	136467084	136467084	+	Silent	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:136467084G>A	ENST00000264160.4	+	21	2806	c.2436G>A	c.(2434-2436)caG>caA	p.Q812Q	R3HDM1_ENST00000409606.1_Silent_p.Q813Q|R3HDM1_ENST00000329971.3_Silent_p.Q683Q|R3HDM1_ENST00000410054.1_Silent_p.Q757Q|R3HDM1_ENST00000409478.1_Silent_p.Q684Q	NM_001282798.1|NM_015361.2	NP_001269727.1|NP_056176.2	Q15032	R3HD1_HUMAN	R3H domain containing 1	812							poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(6)|kidney(5)|large_intestine(3)|lung(14)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(3)	38				BRCA - Breast invasive adenocarcinoma(221;0.127)		GTTCCCAGCAGCTTCAAGGCC	0.383																																					p.Q812Q		Atlas-SNP	.											.	R3HDM1	84	.	0			c.G2436A						PASS	.						123.0	107.0	112.0					2																	136467084		2203	4300	6503	SO:0001819	synonymous_variant	23518	exon21			CCAGCAGCTTCAA	D21852	CCDS2177.1, CCDS63024.1, CCDS63025.1, CCDS63026.1	2q21.3	2012-09-20	2005-09-02	2005-09-02	ENSG00000048991	ENSG00000048991			9757	protein-coding gene	gene with protein product			"""R3H domain (binds single-stranded nucleic acids) containing"""	R3HDM		7584026	Standard	NM_001282798		Approved	KIAA0029	uc002tuo.3	Q15032	OTTHUMG00000131740	ENST00000264160.4:c.2436G>A	2.37:g.136467084G>A		Somatic	425	1	0.00235294		WXS	Illumina HiSeq	Phase_I	307	149	0.485342	NM_015361	A8K1V0|B3KXQ9|E9PBB4|E9PG42|G5E9G8|Q8IW32	Silent	SNP	ENST00000264160.4	37	CCDS2177.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	8.684|8.684	0.905766|0.905766	0.17760|0.17760	.|.	.|.	ENSG00000048991|ENSG00000048991	ENST00000429703|ENST00000445855	.|.	.|.	.|.	5.61|5.61	4.72|4.72	0.59763|0.59763	.|.	.|.	.|.	.|.	.|.	T|T	0.60612|0.60612	0.2282|0.2282	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.57329|0.57329	-0.7830|-0.7830	4|4	.|.	.|.	.|.	0.2051|0.2051	9.5268|9.5268	0.39169|0.39169	0.0734:0.0:0.7872:0.1394|0.0734:0.0:0.7872:0.1394	.|.	.|.	.|.	.|.	T|N	536|108	.|.	.|.	A|S	+|+	1|2	0|0	R3HDM1|R3HDM1	136183554|136183554	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.988000|0.988000	0.76386|0.76386	2.615000|2.615000	0.46368|0.46368	2.647000|2.647000	0.89833|0.89833	0.644000|0.644000	0.83932|0.83932	GCT|AGC	.	.	none		0.383	R3HDM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254659.1	NM_015361	
PELI3	246330	hgsc.bcm.edu	37	11	66240882	66240882	+	Silent	SNP	T	T	C	rs2277302	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:66240882T>C	ENST00000320740.7	+	6	787	c.627T>C	c.(625-627)gaT>gaC	p.D209D	CTD-3074O7.5_ENST00000533502.1_RNA|CTD-3074O7.5_ENST00000602951.1_RNA|PELI3_ENST00000531856.1_Intron|PELI3_ENST00000349459.6_Silent_p.D185D|PELI3_ENST00000524466.1_Silent_p.D209D|CTD-3074O7.5_ENST00000527092.1_RNA	NM_001243136.1|NM_145065.2	NP_001230065.1|NP_659502.2	Q8N2H9	PELI3_HUMAN	pellino E3 ubiquitin protein ligase family member 3	209					defense response to Gram-negative bacterium (GO:0050829)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of Toll signaling pathway (GO:0045751)|negative regulation of tumor necrosis factor-mediated signaling pathway (GO:0010804)|negative regulation of type I interferon production (GO:0032480)|positive regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway (GO:0070434)|protein K63-linked ubiquitination (GO:0070534)|regulation of nucleotide-binding oligomerization domain containing 1 signaling pathway (GO:0070428)|Toll signaling pathway (GO:0008063)	cytosol (GO:0005829)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(2)|large_intestine(4)|lung(4)|ovary(2)|prostate(1)|skin(1)	15						CTGGCTTCGATGCCTCTAGCA	0.602													t|||	1327	0.264976	0.3623	0.1801	5008	,	,		19279	0.2877		0.2425	False		,,,				2504	0.1933				p.D209D		Atlas-SNP	.											.	PELI3	36	.	0			c.T627C						PASS	.	T	,	1435,2965	464.0+/-353.7	243,949,1008	57.0	44.0	48.0		555,627	-3.3	1.0	11	dbSNP_100	48	2015,6575	351.1+/-328.1	227,1561,2507	yes	coding-synonymous,coding-synonymous	PELI3	NM_001098510.1,NM_145065.2	,	470,2510,3515	CC,CT,TT		23.4575,32.6136,26.5589	,	185/446,209/470	66240882	3450,9540	2200	4295	6495	SO:0001819	synonymous_variant	246330	exon6			CTTCGATGCCTCT	AL834395	CCDS31615.1, CCDS41675.1, CCDS73328.1	11q13.2	2012-02-23	2012-02-23		ENSG00000174516	ENSG00000174516		"""Pellino homologs"""	30010	protein-coding gene	gene with protein product		609827	"""pellino homolog 3 (Drosophila)"""			12874243, 15917247	Standard	NM_145065		Approved	MGC35521	uc001oic.4	Q8N2H9	OTTHUMG00000167109	ENST00000320740.7:c.627T>C	11.37:g.66240882T>C		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	51	39	0.764706	NM_145065	Q8N3E1|Q8N9Q6|Q8TAW7|Q8TED5	Silent	SNP	ENST00000320740.7	37	CCDS31615.1																																																																																			T|0.739;C|0.261	0.261	strong		0.602	PELI3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000393226.1	NM_145065	
UGT1A10	54575	hgsc.bcm.edu	37	2	234545861	234545861	+	Silent	SNP	C	C	T	rs17854828	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:234545861C>T	ENST00000344644.5	+	1	762	c.693C>T	c.(691-693)gcC>gcT	p.A231A	UGT1A1_ENST00000373450.4_Intron|UGT1A10_ENST00000373445.1_Silent_p.A231A	NM_019075.2	NP_061948.1	Q9HAW8	UD110_HUMAN	UDP glucuronosyltransferase 1 family, polypeptide A10	231					cellular glucuronidation (GO:0052695)|flavone metabolic process (GO:0051552)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	enzyme binding (GO:0019899)|glucuronosyltransferase activity (GO:0015020)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase C binding (GO:0005080)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(15)|ovary(2)|skin(3)	32		Breast(86;0.000766)|all_lung(227;0.00271)|Renal(207;0.00339)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0334)|Lung NSC(271;0.0461)|Lung SC(224;0.128)		Epithelial(121;1.96e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000468)|Lung(119;0.00381)|LUSC - Lung squamous cell carcinoma(224;0.008)	Acetaminophen(DB00316)|Etodolac(DB00749)|Losartan(DB00678)|Mycophenolate mofetil(DB00688)|Valproic Acid(DB00313)	TAGAAATAGCCTCTGAAATTC	0.438													-|||	557	0.111222	0.1467	0.0663	5008	,	,		20270	0.1071		0.1571	False		,,,				2504	0.0521				p.A231A		Atlas-SNP	.											.	UGT1A10	71	.	0			c.C693T						PASS	.	C	,	633,3773	276.9+/-273.4	48,537,1618	230.0	245.0	240.0		693,	-5.1	0.9	2	dbSNP_123	240	1324,7276	258.6+/-282.2	106,1112,3082	no	coding-synonymous,intron	UGT1A10,UGT1A8	NM_019075.2,NM_019076.4	,	154,1649,4700	TT,TC,CC		15.3953,14.3668,15.0469	,	231/531,	234545861	1957,11049	2203	4300	6503	SO:0001819	synonymous_variant	54575	exon1			AATAGCCTCTGAA	U39550	CCDS33403.1	2q37	2010-03-05	2005-07-20		ENSG00000242515	ENSG00000242515		"""UDP glucuronosyltransferases"""	12531	other	complex locus constituent		606435	"""UDP glycosyltransferase 1 family, polypeptide A10"""			9295054, 9325166	Standard	NM_019075		Approved	UGT1J		Q9HAW8	OTTHUMG00000059121	ENST00000344644.5:c.693C>T	2.37:g.234545861C>T		Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	176	108	0.613636	NM_019075	O00474|Q6NT91|Q7Z6H8	Silent	SNP	ENST00000344644.5	37	CCDS33403.1																																																																																			C|0.868;T|0.132	0.132	strong		0.438	UGT1A10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130986.1	NM_019075	
MUC5B	727897	hgsc.bcm.edu	37	11	1265987	1265987	+	Missense_Mutation	SNP	C	C	G	rs3021158	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:1265987C>G	ENST00000529681.1	+	31	7935	c.7877C>G	c.(7876-7878)aCg>aGg	p.T2626R	MUC5B_ENST00000447027.1_Missense_Mutation_p.T2629R|RP11-532E4.2_ENST00000532061.2_RNA	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	256	0	0		WXS	Illumina HiSeq	Phase_I	253	44	0.173913	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	
CAMKK2	10645	hgsc.bcm.edu	37	12	121701681	121701681	+	Silent	SNP	G	G	A	rs2230776	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:121701681G>A	ENST00000324774.5	-	6	1515	c.687C>T	c.(685-687)ccC>ccT	p.P229P	CAMKK2_ENST00000337174.3_Silent_p.P229P|CAMKK2_ENST00000535524.1_Intron|CAMKK2_ENST00000392473.2_Silent_p.P229P|CAMKK2_ENST00000404169.3_Silent_p.P229P|CAMKK2_ENST00000412367.2_Silent_p.P229P|CAMKK2_ENST00000538733.1_Silent_p.P229P|CAMKK2_ENST00000402834.4_Silent_p.P229P|CAMKK2_ENST00000392474.2_Silent_p.P229P|CAMKK2_ENST00000347034.2_Silent_p.P229P|CAMKK2_ENST00000446440.2_Silent_p.P229P	NM_006549.3	NP_006540.3	Q96RR4	KKCC2_HUMAN	calcium/calmodulin-dependent protein kinase kinase 2, beta	229	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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)					CCTGCTCAATGGGGCCCCTGG	0.612													G|||	498	0.0994409	0.0552	0.0793	5008	,	,		16720	0.2669		0.0765	False		,,,				2504	0.0245				p.P229P		Atlas-SNP	.											.	CAMKK2	87	.	0			c.C687T						PASS	.	G	,,,,,,	246,4160	143.1+/-178.2	6,234,1963	46.0	44.0	45.0		687,687,687,687,687,687,687	3.1	1.0	12	dbSNP_98	45	686,7914	170.3+/-221.5	23,640,3637	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CAMKK2	NM_006549.3,NM_153499.2,NM_153500.1,NM_172214.2,NM_172215.2,NM_172216.1,NM_172226.2	,,,,,,	29,874,5600	AA,AG,GG		7.9767,5.5833,7.1659	,,,,,,	229/589,229/542,229/499,229/534,229/491,229/546,229/542	121701681	932,12074	2203	4300	6503	SO:0001819	synonymous_variant	10645	exon6			CTCAATGGGGCCC	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.687C>T	12.37:g.121701681G>A		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	84	39	0.464286	NM_153500	A8K7Q7|O94883|Q8IUG2|Q8IUG3|Q8N3I4|Q8WY03|Q8WY04|Q8WY05|Q8WY06|Q96RP1|Q96RP2|Q96RR3|Q9BWE9|Q9UER3|Q9UES2|Q9Y5N2	Silent	SNP	ENST00000324774.5	37	CCDS9216.1																																																																																			G|0.911;A|0.089	0.089	strong		0.612	CAMKK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000402563.1	NM_172226	
P2RX3	5024	hgsc.bcm.edu	37	11	57137371	57137371	+	Silent	SNP	G	G	A	rs2276039	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	151	0	0		WXS	Illumina HiSeq	Phase_I	128	128	1	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	
CRIPAK	285464	hgsc.bcm.edu	37	4	1388508	1388508	+	Missense_Mutation	SNP	T	T	C	rs55703801		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:1388508T>C	ENST00000324803.4	+	1	3169	c.209T>C	c.(208-210)gTc>gCc	p.V70A		NM_175918.3	NP_787114.2	Q8N1N5	CRPAK_HUMAN	cysteine-rich PAK1 inhibitor	70					negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of protein kinase activity (GO:0006469)|regulation of cytoskeleton organization (GO:0051493)|response to estrogen (GO:0043627)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(3)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(11)|ovary(1)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(1)	35			OV - Ovarian serous cystadenocarcinoma(23;0.0106)			CACACACGTGTCCATGTGGAG	0.632																																					p.V70A		Atlas-SNP	.											CRIPAK,rectum,carcinoma,0,1	CRIPAK	185	1	0			c.T209C						scavenged	.						283.0	245.0	257.0					4																	1388508		2203	4300	6503	SO:0001583	missense	285464	exon1			CACGTGTCCATGT	AK096209	CCDS3349.1	4p16.3	2011-02-10	2006-09-04		ENSG00000179979	ENSG00000179979			26619	protein-coding gene	gene with protein product		610203	"""cysteine-rich PAK1inhibitor"""			16278681	Standard	NM_175918		Approved	FLJ34443	uc003gdf.2	Q8N1N5	OTTHUMG00000121131	ENST00000324803.4:c.209T>C	4.37:g.1388508T>C	ENSP00000323978:p.Val70Ala	Somatic	125	2	0.016		WXS	Illumina HiSeq	Phase_I	122	27	0.221311	NM_175918	Q8NB03	Missense_Mutation	SNP	ENST00000324803.4	37	CCDS3349.1	.	.	.	.	.	.	.	.	.	.	t	8.717	0.913380	0.17907	.	.	ENSG00000179979	ENST00000324803;ENST00000382944	T	0.24350	1.86	1.09	-2.19	0.07015	.	.	.	.	.	T	0.08714	0.0216	N	0.08118	0	0.09310	N	1	B	0.12630	0.006	B	0.06405	0.002	T	0.25257	-1.0137	9	0.16896	T	0.51	.	0.4342	0.00476	0.19:0.3247:0.1898:0.2955	rs55703801	70	Q8N1N5	CRPAK_HUMAN	A	70;63	ENSP00000323978:V70A	ENSP00000323978:V70A	V	+	2	0	CRIPAK	1378508	0.002000	0.14202	0.000000	0.03702	0.003000	0.03518	-1.991000	0.01478	-2.302000	0.00657	-1.823000	0.00598	GTC	.	.	weak		0.632	CRIPAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241607.2	NM_175918	
MYO18B	84700	hgsc.bcm.edu	37	22	26247456	26247456	+	Silent	SNP	G	G	A	rs5996988	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:26247456G>A	ENST00000407587.2	+	21	3967	c.3798G>A	c.(3796-3798)ggG>ggA	p.G1266G	MYO18B_ENST00000335473.7_Silent_p.G1265G|MYO18B_ENST00000536101.1_Silent_p.G1265G			Q8IUG5	MY18B_HUMAN	myosin XVIIIB	1265	Myosin motor.					cytoplasm (GO:0005737)|nucleus (GO:0005634)|unconventional myosin complex (GO:0016461)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(2)|breast(6)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(27)|liver(2)|lung(60)|ovary(7)|prostate(8)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	146						ACCACATGGGGCTCACTCGCT	0.572													G|||	1212	0.242013	0.171	0.3559	5008	,	,		18680	0.0833		0.3946	False		,,,				2504	0.2638				p.G1265G		Atlas-SNP	.											MYO18B,NS,carcinoma,0,1	MYO18B	322	1	0			c.G3795A						PASS	.	G		861,3479		87,687,1396	31.0	32.0	32.0		3795	-0.6	1.0	22	dbSNP_114	32	3217,5271		641,1935,1668	no	coding-synonymous	MYO18B	NM_032608.5		728,2622,3064	AA,AG,GG		37.9006,19.8387,31.7898		1265/2568	26247456	4078,8750	2170	4244	6414	SO:0001819	synonymous_variant	84700	exon21			CATGGGGCTCACT	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.3798G>A	22.37:g.26247456G>A		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	56	30	0.535714	NM_032608	B2RWP3|F5GYU7|Q8NDI8|Q8TE65|Q8WWS0|Q96KH2|Q96KR8|Q96KR9	Silent	SNP	ENST00000407587.2	37																																																																																				G|0.748;A|0.252	0.252	strong		0.572	MYO18B-006	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000400691.1	NM_032608	
SORCS1	114815	hgsc.bcm.edu	37	10	108380256	108380256	+	Missense_Mutation	SNP	G	G	A	rs144056795	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:108380256G>A	ENST00000263054.6	-	20	2733	c.2726C>T	c.(2725-2727)gCg>gTg	p.A909V	SORCS1_ENST00000344440.6_Missense_Mutation_p.A909V|SORCS1_ENST00000478809.2_5'Flank|SORCS1_ENST00000369698.1_Missense_Mutation_p.A444V	NM_001206570.1|NM_052918.4	NP_001193499.1|NP_443150.3	Q8WY21	SORC1_HUMAN	sortilin-related VPS10 domain containing receptor 1	909					neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	neuropeptide receptor activity (GO:0008188)	p.A909V(2)		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)		CACTGCCGTCGCATTGACCTC	0.562													G|||	5	0.000998403	0.0038	0.0	5008	,	,		19875	0.0		0.0	False		,,,				2504	0.0				p.A909V		Atlas-SNP	.											SORCS1_ENST00000344440,right_upper_lobe,carcinoma,+1,3	SORCS1	534	3	2	Substitution - Missense(2)	endometrium(2)	c.C2726T						PASS	.	G	VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA	18,4388	25.3+/-52.1	0,18,2185	166.0	135.0	146.0		2726,2726,2726,2726,2726,2726	5.8	0.7	10	dbSNP_134	146	0,8600		0,0,4300	yes	missense,missense,missense,missense,missense,missense	SORCS1	NM_001013031.2,NM_001206569.1,NM_001206570.1,NM_001206571.1,NM_001206572.1,NM_052918.4	64,64,64,64,64,64	0,18,6485	AA,AG,GG		0.0,0.4085,0.1384	benign,benign,benign,benign,benign,benign	909/1199,909/1180,909/1131,909/1160,909/1180,909/1169	108380256	18,12988	2203	4300	6503	SO:0001583	missense	114815	exon20			GCCGTCGCATTGA	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.2726C>T	10.37:g.108380256G>A	ENSP00000263054:p.Ala909Val	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	112	25	0.223214	NM_001206572	A2RRF4|Q59GG7|Q5JVT7|Q5JVT8|Q5VY14|Q86WQ1|Q86WQ2|Q9H1Y1|Q9H1Y2	Missense_Mutation	SNP	ENST00000263054.6	37	CCDS7559.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	G	11.29	1.594477	0.28445	0.004085	0.0	ENSG00000108018	ENST00000369698;ENST00000263054;ENST00000344440	T;T;T	0.40476	1.03;1.03;1.03	5.75	5.75	0.90469	PKD/Chitinase domain (1);PKD domain (1);	0.224860	0.40728	N	0.001035	T	0.29556	0.0737	N	0.13043	0.29	0.45962	D	0.998782	B;B;B;B;B	0.19445	0.021;0.036;0.036;0.021;0.036	B;B;B;B;B	0.14023	0.005;0.01;0.01;0.005;0.01	T	0.08576	-1.0715	9	.	.	.	-18.823	19.9548	0.97216	0.0:0.0:1.0:0.0	.	909;909;909;909;909	A8K182;Q8WY21-4;Q8WY21-3;Q8WY21;Q8WY21-2	.;.;.;SORC1_HUMAN;.	V	444;909;909	ENSP00000358712:A444V;ENSP00000263054:A909V;ENSP00000345964:A909V	.	A	-	2	0	SORCS1	108370246	1.000000	0.71417	0.676000	0.29932	0.232000	0.25224	5.920000	0.70017	2.714000	0.92807	0.655000	0.94253	GCG	G|0.999;A|0.001	0.001	strong		0.562	SORCS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050232.4	NM_052918	
TTLL6	284076	hgsc.bcm.edu	37	17	46847364	46847364	+	Missense_Mutation	SNP	C	C	A	rs2032844	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	275	0	0		WXS	Illumina HiSeq	Phase_I	218	104	0.477064	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	
IL2RA	3559	hgsc.bcm.edu	37	10	6067969	6067969	+	Silent	SNP	C	C	T	rs2228150	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:6067969C>T	ENST00000379959.3	-	2	257	c.84G>A	c.(82-84)ccG>ccA	p.P28P	RP11-536K7.5_ENST00000440436.1_RNA|IL2RA_ENST00000256876.6_Silent_p.P28P|IL2RA_ENST00000379954.1_Silent_p.P28P	NM_000417.2	NP_000408.1	P01589	IL2RA_HUMAN	interleukin 2 receptor, alpha	28	Sushi 1. {ECO:0000255|PROSITE- ProRule:PRU00302}.				activation-induced cell death of T cells (GO:0006924)|apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|immune response (GO:0006955)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-2-mediated signaling pathway (GO:0038110)|negative regulation of defense response to virus (GO:0050687)|negative regulation of immune response (GO:0050777)|negative regulation of inflammatory response (GO:0050728)|negative regulation of T cell proliferation (GO:0042130)|Notch signaling pathway (GO:0007219)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of T cell differentiation (GO:0045582)|regulation of T cell homeostatic proliferation (GO:0046013)	external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	drug binding (GO:0008144)|interleukin-2 receptor activity (GO:0004911)			endometrium(1)|kidney(3)|large_intestine(3)|lung(7)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	17					Aldesleukin(DB00041)|Basiliximab(DB00074)|Daclizumab(DB00111)|Denileukin diftitox(DB00004)	GGATCTCTGGCGGGTCATCGT	0.463													C|||	410	0.081869	0.2322	0.0317	5008	,	,		18681	0.001		0.0229	False		,,,				2504	0.0583				p.P28P		Atlas-SNP	.											.	IL2RA	37	.	0			c.G84A						PASS	.	C		900,3506	348.5+/-309.9	88,724,1391	101.0	88.0	92.0		84	-7.8	0.0	10	dbSNP_98	92	236,8364	95.4+/-157.2	4,228,4068	no	coding-synonymous	IL2RA	NM_000417.2		92,952,5459	TT,TC,CC		2.7442,20.4267,8.7344		28/273	6067969	1136,11870	2203	4300	6503	SO:0001819	synonymous_variant	3559	exon2			CTCTGGCGGGTCA	X01057	CCDS7076.1	10p15-p14	2014-09-17			ENSG00000134460	ENSG00000134460		"""Interleukins and interleukin receptors"", ""CD molecules"""	6008	protein-coding gene	gene with protein product		147730	"""insulin-dependent diabetes mellitus 10"""	IL2R, IDDM10		3925551, 17676041	Standard	NM_000417		Approved	CD25	uc001iiz.2	P01589	OTTHUMG00000017616	ENST00000379959.3:c.84G>A	10.37:g.6067969C>T		Somatic	220	1	0.00454545		WXS	Illumina HiSeq	Phase_I	158	73	0.462025	NM_000417	Q5W007	Silent	SNP	ENST00000379959.3	37	CCDS7076.1																																																																																			T|0.080;G|0.006	0.080	strong		0.463	IL2RA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046627.1	NM_000417	
TTBK1	84630	hgsc.bcm.edu	37	6	43251880	43251880	+	Silent	SNP	C	C	G	rs45564136	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:43251880C>G	ENST00000259750.4	+	14	3485	c.3402C>G	c.(3400-3402)ccC>ccG	p.P1134P		NM_032538.1	NP_115927.1	Q5TCY1	TTBK1_HUMAN	tau tubulin kinase 1	1134					substantia nigra development (GO:0021762)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(10)|liver(1)|lung(21)|ovary(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	53			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0125)|OV - Ovarian serous cystadenocarcinoma(102;0.0399)			AGGACACGCCCGCCTCTGAGC	0.711													C|||	233	0.0465256	0.003	0.0965	5008	,	,		13420	0.001		0.0845	False		,,,				2504	0.0777				p.P1134P		Atlas-SNP	.											.	TTBK1	124	.	0			c.C3402G						PASS	.	C		46,3406		1,44,1681	3.0	3.0	3.0		3402	-10.6	0.3	6	dbSNP_127	3	590,6584		19,552,3016	no	coding-synonymous	TTBK1	NM_032538.1		20,596,4697	GG,GC,CC		8.2241,1.3326,5.9853		1134/1322	43251880	636,9990	1726	3587	5313	SO:0001819	synonymous_variant	84630	exon14			CACGCCCGCCTCT	AB058758	CCDS34455.1	6p21.1	2008-02-05			ENSG00000146216	ENSG00000146216			19140	protein-coding gene	gene with protein product						11347906	Standard	XM_006715229		Approved	KIAA1855	uc003ouq.1	Q5TCY1	OTTHUMG00000014725	ENST00000259750.4:c.3402C>G	6.37:g.43251880C>G		Somatic	14	0	0		WXS	Illumina HiSeq	Phase_I	11	6	0.545455	NM_032538	A2A2U5|Q2L6C6|Q6ZNH0|Q8N444|Q96JH2	Silent	SNP	ENST00000259750.4	37	CCDS34455.1																																																																																			C|0.952;G|0.048	0.048	strong		0.711	TTBK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040584.3		
PRB3	5544	hgsc.bcm.edu	37	12	11420563	11420563	+	Missense_Mutation	SNP	G	G	T	rs200902635		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:11420563G>T	ENST00000279573.7	-	3	755	c.620C>A	c.(619-621)cCa>cAa	p.P207Q	PRB3_ENST00000440870.3_Intron|PRB3_ENST00000538488.1_Missense_Mutation_p.P186Q|PRB3_ENST00000381842.3_Intron			Q04118	PRB3_HUMAN	proline-rich protein BstNI subfamily 3	207	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.		Missing (in allele S).		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)			TTGTGGGGGTGGTCCTTCTGG	0.632																																					p.P207Q		Atlas-SNP	.											PRB3_ENST00000538488,NS,carcinoma,0,1	PRB3	84	1	0			c.C620A						scavenged	.						67.0	93.0	85.0					12																	11420563		1603	3645	5248	SO:0001583	missense	5544	exon3			GGGGGTGGTCCTT			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.620C>A	12.37:g.11420563G>T	ENSP00000279573:p.Pro207Gln	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	94	3	0.0319149	NM_006249	Q15188|Q4VAY3|Q4VAY4|Q7M4M9|Q9UCT9	Missense_Mutation	SNP	ENST00000279573.7	37		.	.	.	.	.	.	.	.	.	.	.	0.001	-3.098522	0.00033	.	.	ENSG00000197870	ENST00000538488	T	0.09445	2.98	1.25	-2.5	0.06384	.	0.000000	0.30302	U	0.009922	T	0.07279	0.0184	.	.	.	0.09310	N	1	B	0.27166	0.17	B	0.17979	0.02	T	0.18335	-1.0340	9	0.59425	D	0.04	.	6.227	0.20714	0.0:0.1573:0.2128:0.6299	.	207	Q04118	PRB3_HUMAN	Q	186	ENSP00000442626:P186Q	ENSP00000279573:P207Q	P	-	2	0	PRB3	11311830	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-2.685000	0.00834	-3.567000	0.00140	-2.957000	0.00083	CCA	.	.	weak		0.632	PRB3-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000402119.5	NM_006249	
SCNN1G	6340	hgsc.bcm.edu	37	16	23226787	23226787	+	Silent	SNP	C	C	G	rs5723	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:23226787C>G	ENST00000300061.2	+	13	2090	c.1947C>G	c.(1945-1947)ctC>ctG	p.L649L	CTC-391G2.1_ENST00000563471.1_RNA	NM_001039.3	NP_001030.2	P51170	SCNNG_HUMAN	sodium channel, non-voltage-gated 1, gamma subunit	649					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)	TGGATGAGCTCTGAGGCAGGG	0.587													C|||	776	0.154952	0.2542	0.1441	5008	,	,		17469	0.0585		0.2227	False		,,,				2504	0.0583				p.L649L		Atlas-SNP	.											.	SCNN1G	82	.	0			c.C1947G						PASS	.	C		1107,3283	374.6+/-321.3	144,819,1232	47.0	51.0	50.0		1947	-0.1	0.0	16	dbSNP_52	50	1922,6678	326.9+/-317.6	229,1464,2607	no	coding-synonymous	SCNN1G	NM_001039.3		373,2283,3839	GG,GC,CC		22.3488,25.2164,23.3179		649/650	23226787	3029,9961	2195	4300	6495	SO:0001819	synonymous_variant	6340	exon13			TGAGCTCTGAGGC	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.1947C>G	16.37:g.23226787C>G		Somatic	13	0	0		WXS	Illumina HiSeq	Phase_I	16	9	0.5625	NM_001039	P78437|Q6PCC2|Q93023|Q93024|Q93025|Q93026|Q93027|Q96TD2	Silent	SNP	ENST00000300061.2	37	CCDS10608.1																																																																																			C|0.788;G|0.212	0.212	strong		0.587	SCNN1G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254496.1	NM_001039	
ATAD5	79915	hgsc.bcm.edu	37	17	29162173	29162173	+	Silent	SNP	T	T	C	rs11655623	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:29162173T>C	ENST00000321990.4	+	2	1452	c.1074T>C	c.(1072-1074)ccT>ccC	p.P358P	CTD-2349P21.11_ENST00000580873.1_RNA	NM_024857.3	NP_079133.3	Q96QE3	ATAD5_HUMAN	ATPase family, AAA domain containing 5	358					cellular response to DNA damage stimulus (GO:0006974)	nucleus (GO:0005634)	ATP binding (GO:0005524)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(3)|large_intestine(18)|lung(13)|ovary(3)|pancreas(1)	51		all_hematologic(16;0.0202)|Acute lymphoblastic leukemia(14;0.0238)|Myeloproliferative disorder(56;0.0393)				TATCTGATCCTGAGAATGAAC	0.373													t|||	902	0.180112	0.2027	0.1931	5008	,	,		19186	0.1359		0.1083	False		,,,				2504	0.2597				p.P358P		Atlas-SNP	.											.	ATAD5	150	.	0			c.T1074C						PASS	.	C		781,3613		69,643,1485	46.0	49.0	48.0		1074	1.1	1.0	17	dbSNP_120	48	899,7701		39,821,3440	no	coding-synonymous	ATAD5	NM_024857.3		108,1464,4925	CC,CT,TT		10.4535,17.7742,12.929		358/1845	29162173	1680,11314	2197	4300	6497	SO:0001819	synonymous_variant	79915	exon2			TGATCCTGAGAAT		CCDS11260.1	17q11.2	2010-04-21	2007-02-08	2007-02-08	ENSG00000176208	ENSG00000176208		"""ATPases / AAA-type"""	25752	protein-coding gene	gene with protein product	"""enhanced level of genomic instability 1 homolog (S. cerevisiae)"""	609534	"""chromosome 17 open reading frame 41"""	C17orf41		15983387, 11468690, 19755857	Standard	NM_024857		Approved	FLJ12735, FRAG1, ELG1	uc002hfs.1	Q96QE3	OTTHUMG00000132794	ENST00000321990.4:c.1074T>C	17.37:g.29162173T>C		Somatic	207	0	0		WXS	Illumina HiSeq	Phase_I	146	64	0.438356	NM_024857	Q05DH0|Q69YR6|Q9H9I1	Silent	SNP	ENST00000321990.4	37	CCDS11260.1																																																																																			T|0.859;C|0.141	0.141	strong		0.373	ATAD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256206.2	NM_024857	
WNK2	65268	hgsc.bcm.edu	37	9	96026243	96026243	+	Silent	SNP	G	G	A	rs55981123	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:96026243G>A	ENST00000297954.4	+	15	3624	c.3624G>A	c.(3622-3624)acG>acA	p.T1208T	WNK2_ENST00000356055.3_5'UTR|WNK2_ENST00000427277.2_Silent_p.T820T|WNK2_ENST00000395475.2_3'UTR|WNK2_ENST00000349097.3_Silent_p.T820T|WNK2_ENST00000395477.2_Silent_p.T1208T	NM_001282394.1	NP_001269323.1	Q9Y3S1	WNK2_HUMAN	WNK lysine deficient protein kinase 2	1208					intracellular signal transduction (GO:0035556)|negative regulation of cell proliferation (GO:0008285)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of ion homeostasis (GO:2000021)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(1)|endometrium(11)|kidney(4)|large_intestine(5)|lung(17)|ovary(2)|prostate(3)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)	54						AGCTGGAGACGCACAACCACA	0.607													G|||	514	0.102636	0.1762	0.1124	5008	,	,		10483	0.001		0.1431	False		,,,				2504	0.0593				p.T1208T		Atlas-SNP	.											WNK2_ENST00000297954,caecum,carcinoma,0,4	WNK2	277	4	0			c.G3624A						PASS	.	G		726,3680	298.1+/-285.1	58,610,1535	132.0	96.0	108.0		3624	-10.3	0.4	9	dbSNP_129	108	1025,7575	218.4+/-256.8	66,893,3341	no	coding-synonymous	WNK2	NM_006648.3		124,1503,4876	AA,AG,GG		11.9186,16.4775,13.463		1208/2218	96026243	1751,11255	2203	4300	6503	SO:0001819	synonymous_variant	65268	exon15			GGAGACGCACAAC	AJ242724	CCDS75858.1	9q22.3	2008-02-05	2003-06-23	2005-01-22	ENSG00000165238	ENSG00000165238			14542	protein-coding gene	gene with protein product		606249	"""serologically defined colon cancer antigen 43"""	SDCCAG43, PRKWNK2		9610721, 11571656	Standard	NM_006648		Approved	NY-CO-43, KIAA1760	uc004atj.3	Q9Y3S1	OTTHUMG00000020247	ENST00000297954.4:c.3624G>A	9.37:g.96026243G>A		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	78	36	0.461538	NM_006648	Q5VWF1|Q5VWF2|Q8IY36|Q9C0A3|Q9H3P4	Silent	SNP	ENST00000297954.4	37		242|242	0.1108058608058608|0.1108058608058608	90|90	0.18292682926829268|0.18292682926829268	45|45	0.12430939226519337|0.12430939226519337	1|1	0.0017482517482517483|0.0017482517482517483	106|106	0.13984168865435356|0.13984168865435356	G|G	9.325|9.325	1.058954|1.058954	0.19987|0.19987	0.164775|0.164775	0.119186|0.119186	ENSG00000165238|ENSG00000165238	ENST00000411624|ENST00000432730;ENST00000448251	.|.	.|.	.|.	5.15|5.15	-10.3|-10.3	0.00346|0.00346	.|.	.|.	.|.	.|.	.|.	T|T	0.00039|0.00039	0.0001|0.0001	.|.	.|.	.|.	0.09310|0.09310	P|P	0.9999999999999997|0.9999999999999997	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.08086|0.08086	-1.0739|-1.0739	3|3	.|.	.|.	.|.	.|.	4.5012|4.5012	0.11865|0.11865	0.5339:0.2285:0.0848:0.1528|0.5339:0.2285:0.0848:0.1528	rs55981123|rs55981123	.|.	.|.	.|.	T|H	812|1204;5	.|.	.|.	A|R	+|+	1|2	0|0	WNK2|WNK2	95066064|95066064	0.000000|0.000000	0.05858|0.05858	0.410000|0.410000	0.26471|0.26471	0.988000|0.988000	0.76386|0.76386	-1.789000|-1.789000	0.01761|0.01761	-2.243000|-2.243000	0.00707|0.00707	-0.251000|-0.251000	0.11542|0.11542	GCA|CGC	G|0.870;A|0.130	0.130	strong		0.607	WNK2-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000317359.1	NM_006648	
TRPC1	7220	hgsc.bcm.edu	37	3	142524858	142524858	+	Silent	SNP	G	G	A	rs1132030	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:142524858G>A	ENST00000476941.1	+	13	2649	c.2163G>A	c.(2161-2163)agG>agA	p.R721R	TRPC1_ENST00000273482.6_Silent_p.R687R	NM_001251845.1	NP_001238774.1	P48995	TRPC1_HUMAN	transient receptor potential cation channel, subfamily C, member 1	721					axon guidance (GO:0007411)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|response to calcium ion (GO:0051592)|saliva secretion (GO:0046541)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|costamere (GO:0043034)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|sarcomere (GO:0030017)	calcium channel activity (GO:0005262)|cation channel activity (GO:0005261)|inositol 1,4,5 trisphosphate binding (GO:0070679)|ion channel binding (GO:0044325)|store-operated calcium channel activity (GO:0015279)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(18)|ovary(2)|skin(2)|stomach(3)|urinary_tract(1)	37						AGGAATGGAGGAATTTGAAAC	0.348													A|||	1832	0.365815	0.736	0.1772	5008	,	,		17698	0.3552		0.2058	False		,,,				2504	0.1748				p.R721R		Atlas-SNP	.											.	TRPC1	82	.	0			c.G2163A						PASS	.	A		2808,1598	492.0+/-362.3	898,1012,293	91.0	102.0	98.0		2061	3.0	1.0	3	dbSNP_86	98	1606,6994	741.3+/-407.1	168,1270,2862	no	coding-synonymous	TRPC1	NM_003304.4		1066,2282,3155	AA,AG,GG		18.6744,36.2687,33.9382		687/760	142524858	4414,8592	2203	4300	6503	SO:0001819	synonymous_variant	7220	exon13			ATGGAGGAATTTG	X89066	CCDS3126.1, CCDS58856.1	3q23	2011-12-14			ENSG00000144935	ENSG00000144935		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	12333	protein-coding gene	gene with protein product		602343				7568191, 16382100	Standard	NM_001251845		Approved	HTRP-1	uc003evc.3	P48995	OTTHUMG00000159301	ENST00000476941.1:c.2163G>A	3.37:g.142524858G>A		Somatic	203	0	0		WXS	Illumina HiSeq	Phase_I	169	73	0.431953	NM_001251845	Q14CE4	Silent	SNP	ENST00000476941.1	37	CCDS58856.1																																																																																			A|0.353;G|0.647;T|0.000	0.353	strong		0.348	TRPC1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354520.1	NM_003304	
AMBN	258	hgsc.bcm.edu	37	4	71469006	71469006	+	Silent	SNP	C	C	T	rs113360877	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:71469006C>T	ENST00000322937.6	+	10	781	c.678C>T	c.(676-678)caC>caT	p.H226H	AMBN_ENST00000449493.2_Silent_p.H211H	NM_016519.5	NP_057603.1	Q9NP70	AMBN_HUMAN	ameloblastin (enamel matrix protein)	226					biomineral tissue development (GO:0031214)|cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|odontogenesis of dentin-containing tooth (GO:0042475)	proteinaceous extracellular matrix (GO:0005578)	growth factor activity (GO:0008083)|structural constituent of tooth enamel (GO:0030345)			NS(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(12)|ovary(3)|prostate(2)|skin(1)	29			Lung(101;0.235)			TGATTTCTCACGGACCAATGC	0.318													C|||	29	0.00579073	0.0008	0.0086	5008	,	,		14320	0.001		0.0179	False		,,,				2504	0.0031				p.H226H		Atlas-SNP	.											.	AMBN	73	.	0			c.C678T						PASS	.	C		14,4390	21.2+/-45.6	0,14,2188	77.0	74.0	75.0		678	1.8	1.0	4	dbSNP_132	75	186,8406	84.2+/-146.7	1,184,4111	no	coding-synonymous	AMBN	NM_016519.5		1,198,6299	TT,TC,CC		2.1648,0.3179,1.5389		226/448	71469006	200,12796	2202	4296	6498	SO:0001819	synonymous_variant	258	exon10			TTCTCACGGACCA	AF209780	CCDS3543.1	4q21	2006-11-28	2006-04-27		ENSG00000178522	ENSG00000178522			452	protein-coding gene	gene with protein product		601259	"""ameloblastin, enamel matrix protein"""			9126491	Standard	NM_016519		Approved		uc003hfl.3	Q9NP70	OTTHUMG00000129913	ENST00000322937.6:c.678C>T	4.37:g.71469006C>T		Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	149	65	0.436242	NM_016519	Q3B862|Q9H2X1|Q9H4L1	Silent	SNP	ENST00000322937.6	37	CCDS3543.1																																																																																			C|0.987;T|0.013	0.013	strong		0.318	AMBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252165.1	NM_016519	
GSG2	83903	hgsc.bcm.edu	37	17	3628362	3628362	+	Missense_Mutation	SNP	T	T	C	rs3809806	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:3628362T>C	ENST00000325418.4	+	1	1152	c.1133T>C	c.(1132-1134)gTc>gCc	p.V378A	ITGAE_ENST00000263087.4_Intron|CTD-3195I5.3_ENST00000571741.1_RNA|ITGAE_ENST00000571185.1_Intron	NM_031965.2	NP_114171.2	Q8TF76	HASP_HUMAN	germ cell associated 2 (haspin)	378			V -> A (in dbSNP:rs3809806). {ECO:0000269|PubMed:11311556, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17344846}.		histone H3-T3 phosphorylation involved in chromosome passenger complex localization to kinetochore (GO:2000751)|intracellular signal transduction (GO:0035556)|mitotic sister chromatid cohesion (GO:0007064)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|protein localization to chromosome, centromeric region (GO:0071459)|protein phosphorylation (GO:0006468)|regulation of spindle checkpoint (GO:0090231)	centrosome (GO:0005813)|chromosome (GO:0005694)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|spindle (GO:0005819)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|histone kinase activity (H3-T3 specific) (GO:0072354)|protein kinase activity (GO:0004672)	p.V378A(2)									TTACAGAATGTCTGCTTTTGG	0.483													C|||	2661	0.53135	0.6838	0.3473	5008	,	,		20813	0.3353		0.5477	False		,,,				2504	0.6411				p.V378A		Atlas-SNP	.											GSG2_ENST00000325418,NS,carcinoma,0,1	GSG2	48	1	2	Substitution - Missense(2)	prostate(2)	c.T1133C						PASS	.	C	,ALA/VAL	2807,1599	495.0+/-363.1	893,1021,289	74.0	74.0	74.0		,1133	1.0	0.0	17	dbSNP_107	74	4674,3926	547.8+/-385.2	1274,2126,900	yes	intron,missense	ITGAE,GSG2	NM_002208.4,NM_031965.2	,64	2167,3147,1189	CC,CT,TT		45.6512,36.2914,42.4804	,benign	,378/799	3628362	7481,5525	2203	4300	6503	SO:0001583	missense	83903	exon1			AGAATGTCTGCTT	AB039834	CCDS11036.1	17p13	2005-01-19			ENSG00000177602	ENSG00000177602			19682	protein-coding gene	gene with protein product		609240					Standard	NM_031965		Approved	haspin	uc002fwp.3	Q8TF76	OTTHUMG00000090703	ENST00000325418.4:c.1133T>C	17.37:g.3628362T>C	ENSP00000325290:p.Val378Ala	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	81	43	0.530864	NM_031965	Q5U5K3|Q96MN1|Q9BXS7	Missense_Mutation	SNP	ENST00000325418.4	37	CCDS11036.1	1087	0.4977106227106227	333	0.676829268292683	140	0.3867403314917127	197	0.34440559440559443	417	0.5501319261213721	C	1.283	-0.609872	0.03690	0.637086	0.543488	ENSG00000177602	ENST00000325418	T	0.05258	3.47	4.23	0.989	0.19802	.	1.426380	0.05004	N	0.469640	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	0.35822	-0.9773	9	0.87932	D	0	-32.5476	4.2491	0.10686	0.1734:0.5639:0.0:0.2627	rs3809806;rs56614897;rs59995636;rs3809806	378	Q8TF76	HASP_HUMAN	A	378	ENSP00000325290:V378A	ENSP00000325290:V378A	V	+	2	0	GSG2	3575111	0.000000	0.05858	0.000000	0.03702	0.316000	0.28119	-0.223000	0.09177	-0.105000	0.12132	-0.726000	0.03593	GTC	T|0.447;C|0.553	0.553	strong		0.483	GSG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207391.1	NM_031965	
LRRC37A3	374819	hgsc.bcm.edu	37	17	62856646	62856646	+	Silent	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:62856646G>A	ENST00000584306.1	-	11	4148	c.3618C>T	c.(3616-3618)ctC>ctT	p.L1206L	LRRC37A3_ENST00000339474.5_Silent_p.L324L|LRRC37A3_ENST00000400877.3_Silent_p.L244L|LRRC37A3_ENST00000334962.5_Silent_p.L183L|LRRC37A3_ENST00000319651.5_Silent_p.L1206L	NM_199340.2	NP_955372.2	O60309	L37A3_HUMAN	leucine rich repeat containing 37, member A3	1206						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						CTGGACTTCCGAGCCTTTTTT	0.562																																					p.L1206L		Atlas-SNP	.											.	LRRC37A3	75	.	0			c.C3618T						PASS	.																																			SO:0001819	synonymous_variant	374819	exon11			ACTTCCGAGCCTT	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.3618C>T	17.37:g.62856646G>A		Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	38	21	0.552632	NM_199340	Q49A01|Q49A80|Q8NB33	Silent	SNP	ENST00000584306.1	37	CCDS32708.1																																																																																			.	.	none		0.562	LRRC37A3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445377.1	NM_199340	
FAM102A	399665	hgsc.bcm.edu	37	9	130742271	130742271	+	Splice_Site	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:130742271C>T	ENST00000373095.1	-	1	521	c.146G>A	c.(145-147)aGg>aAg	p.R49K		NM_001035254.2	NP_001030331.1	Q5T9C2	F102A_HUMAN	family with sequence similarity 102, member A	49										breast(1)|cervix(1)|large_intestine(3)|lung(1)|ovary(4)	10						CAGCTCCTACCTTGACGACAA	0.632																																					p.R49K		Atlas-SNP	.											.	FAM102A	32	.	0			c.G146A						PASS	.						63.0	67.0	66.0					9																	130742271		2203	4300	6503	SO:0001630	splice_region_variant	399665	exon1			TCCTACCTTGACG		CCDS6888.1, CCDS35150.1	9q34.11	2012-11-05	2005-11-17	2005-11-17	ENSG00000167106	ENSG00000167106			31419	protein-coding gene	gene with protein product	"""sym-3 homolog A (C. elegans)"""	610891	"""chromosome 9 open reading frame 132"""	C9orf132			Standard	NM_001035254		Approved	Eeig1, bA203J24.7, SYM-3A	uc004bsx.2	Q5T9C2	OTTHUMG00000020720	ENST00000373095.1:c.146+1G>A	9.37:g.130742271C>T		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	72	17	0.236111	NM_001035254	A2A329|Q8TEL4	Missense_Mutation	SNP	ENST00000373095.1	37	CCDS35150.1	.	.	.	.	.	.	.	.	.	.	C	36	5.857711	0.97030	.	.	ENSG00000167106	ENST00000373095	T	0.39787	1.06	4.87	4.87	0.63330	.	0.000000	0.85682	D	0.000000	T	0.52075	0.1712	M	0.79011	2.435	0.80722	D	1	P	0.45634	0.863	P	0.45538	0.484	T	0.57946	-0.7723	9	.	.	.	-30.8032	16.9987	0.86376	0.0:1.0:0.0:0.0	.	49	Q5T9C2	F102A_HUMAN	K	49	ENSP00000362187:R49K	.	R	-	2	0	FAM102A	129782092	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	7.487000	0.81328	2.244000	0.73946	0.462000	0.41574	AGG	.	.	none		0.632	FAM102A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054298.2		Missense_Mutation
SH3BGR	6450	hgsc.bcm.edu	37	21	40871810	40871810	+	Missense_Mutation	SNP	T	T	C	rs9974333	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:40871810T>C	ENST00000333634.4	+	4	641	c.563T>C	c.(562-564)gTg>gCg	p.V188A	SH3BGR_ENST00000380631.1_Missense_Mutation_p.V77A|SH3BGR_ENST00000380634.1_Missense_Mutation_p.V77A|SH3BGR_ENST00000458295.1_Intron|SH3BGR_ENST00000380637.3_Missense_Mutation_p.V77A	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						PASS	.	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	104	0	0		WXS	Illumina HiSeq	Phase_I	97	97	1	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	
OR4C16	219428	hgsc.bcm.edu	37	11	55339798	55339798	+	Silent	SNP	C	C	T	rs557667	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:55339798C>T	ENST00000314634.3	+	1	195	c.195C>T	c.(193-195)tcC>tcT	p.S65S		NM_001004701.2	NP_001004701.2	Q8NGL9	OR4CG_HUMAN	olfactory receptor, family 4, subfamily C, member 16 (gene/pseudogene)	65						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)				TCTACTTATCCTTATCTGATA	0.413													c|||	1288	0.257188	0.1188	0.3242	5008	,	,		19752	0.3909		0.2843	False		,,,				2504	0.2311				p.S65S		Atlas-SNP	.											.	OR4C16	104	.	0			c.C195T						PASS	.	C		621,3781	270.1+/-269.4	36,549,1616	274.0	249.0	257.0		195	0.8	0.3	11	dbSNP_83	257	2289,6303	385.8+/-341.6	329,1631,2336	no	coding-synonymous	OR4C16	NM_001004701.2		365,2180,3952	TT,TC,CC		26.6411,14.1072,22.395		65/311	55339798	2910,10084	2201	4296	6497	SO:0001819	synonymous_variant	219428	exon1			CTTATCCTTATCT	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.195C>T	11.37:g.55339798C>T		Somatic	191	0	0		WXS	Illumina HiSeq	Phase_I	176	39	0.221591	NM_001004701	Q6IEV8	Silent	SNP	ENST00000314634.3	37	CCDS31502.1																																																																																			C|0.755;T|0.245	0.245	strong		0.413	OR4C16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382627.1	NM_001004701	
ASB10	136371	hgsc.bcm.edu	37	7	150878260	150878260	+	Silent	SNP	C	C	G	rs2253592	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:150878260C>G	ENST00000420175.2	-	3	894	c.870G>C	c.(868-870)gcG>gcC	p.A290A	ASB10_ENST00000275838.1_Silent_p.A290A|ASB10_ENST00000377867.3_Silent_p.A275A|ASB10_ENST00000422024.1_Silent_p.A335A|ASB10_ENST00000434669.1_Silent_p.A335A			Q8WXI3	ASB10_HUMAN	ankyrin repeat and SOCS box containing 10	290					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)		TGTCCTGGTCCGCAGCATCAG	0.667													G|||	2523	0.503794	0.7791	0.4467	5008	,	,		17782	0.5486		0.3757	False		,,,				2504	0.2577				p.A290A		Atlas-SNP	.											.	ASB10	99	.	0			c.G870C						PASS	.	G	,,	3117,1285		1106,905,190	28.0	28.0	28.0		870,870,825	-6.1	0.2	7	dbSNP_100	28	3163,5427		615,1933,1747	no	coding-synonymous,coding-synonymous,coding-synonymous	ASB10	NM_001142459.1,NM_001142460.1,NM_080871.3	,,	1721,2838,1937	GG,GC,CC		36.8219,29.1913,48.3374	,,	290/468,290/430,275/453	150878260	6280,6712	2201	4295	6496	SO:0001819	synonymous_variant	136371	exon3			CTGGTCCGCAGCA	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.870G>C	7.37:g.150878260C>G		Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	169	79	0.467456	NM_001142459	A0AVH0|Q6ZUL6	Silent	SNP	ENST00000420175.2	37	CCDS47750.2																																																																																			C|0.485;G|0.515	0.515	strong		0.667	ASB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347096.3	NM_080871	
GCNT1	2650	hgsc.bcm.edu	37	9	79117751	79117751	+	Missense_Mutation	SNP	A	A	G	rs2282683	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:79117751A>G	ENST00000376730.4	+	4	937	c.454A>G	c.(454-456)Att>Gtt	p.I152V	GCNT1_ENST00000442371.1_Missense_Mutation_p.I152V|GCNT1_ENST00000444201.2_Missense_Mutation_p.I152V|GCNT1_ENST00000536223.1_Missense_Mutation_p.I152V	NM_001097636.1|NM_001490.4	NP_001091105.1|NP_001481.2	Q02742	GCNT1_HUMAN	glucosaminyl (N-acetyl) transferase 1, core 2	152	Catalytic. {ECO:0000250}.		I -> V (in dbSNP:rs2282683). {ECO:0000269|PubMed:1329093, ECO:0000269|PubMed:7579796}.		cell adhesion molecule production (GO:0060352)|cellular protein metabolic process (GO:0044267)|glycoprotein biosynthetic process (GO:0009101)|kidney morphogenesis (GO:0060993)|leukocyte tethering or rolling (GO:0050901)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|response to insulin (GO:0032868)|tissue morphogenesis (GO:0048729)	extracellular space (GO:0005615)|Golgi cisterna (GO:0031985)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|trans-Golgi network (GO:0005802)	beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase activity (GO:0003829)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(6)|lung(11)|prostate(2)|urinary_tract(1)	30						TTTCTATTGCATTCATGTGGA	0.443													A|||	1180	0.235623	0.239	0.2478	5008	,	,		19763	0.1974		0.2276	False		,,,				2504	0.2699				p.I152V		Atlas-SNP	.											.	GCNT1	52	.	0			c.A454G						PASS	.	A	VAL/ILE,VAL/ILE,VAL/ILE,VAL/ILE,VAL/ILE	970,3436	361.6+/-315.8	126,718,1359	70.0	71.0	71.0		454,454,454,454,454	4.9	1.0	9	dbSNP_100	71	1852,6748	328.0+/-318.1	193,1466,2641	yes	missense,missense,missense,missense,missense	GCNT1	NM_001097633.1,NM_001097634.1,NM_001097635.1,NM_001097636.1,NM_001490.4	29,29,29,29,29	319,2184,4000	GG,GA,AA		21.5349,22.0154,21.6977	benign,benign,benign,benign,benign	152/429,152/429,152/429,152/429,152/429	79117751	2822,10184	2203	4300	6503	SO:0001583	missense	2650	exon4			TATTGCATTCATG	L41415	CCDS6653.1	9q13	2013-02-25	2010-03-16		ENSG00000187210	ENSG00000187210	2.4.1.102	"""Glucosaminyl (N-acetyl) transferase and xylosyltransferase family"""	4203	protein-coding gene	gene with protein product	"""core 2 beta1,6 N-acetylglucosaminyltransferase-I"", ""beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N--acetylglucosaminyltransferase"""	600391	"""glucosaminyl (N-acetyl) transferase 1, core 2 (beta-1,6-N-acetylglucosaminyltransferase)"""	NACGT2		8449405, 9915862	Standard	NM_001490		Approved	C2GNT, NAGCT2	uc004akf.4	Q02742	OTTHUMG00000020044	ENST00000376730.4:c.454A>G	9.37:g.79117751A>G	ENSP00000365920:p.Ile152Val	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	98	52	0.530612	NM_001490	Q6DJZ4	Missense_Mutation	SNP	ENST00000376730.4	37	CCDS6653.1	505	0.23122710622710624	113	0.22967479674796748	91	0.2513812154696133	125	0.21853146853146854	176	0.23218997361477572	a	8.141	0.785332	0.16189	0.220154	0.215349	ENSG00000187210	ENST00000536223;ENST00000442371;ENST00000444201;ENST00000376730	T;T;T;T	0.11063	2.81;2.81;2.81;2.81	6.07	4.94	0.65067	.	0.163576	0.53938	N	0.000049	T	0.00012	0.0000	L	0.31294	0.92	0.28431	P	0.9172873	B	0.22480	0.07	B	0.39185	0.293	T	0.50651	-0.8803	8	.	.	.	.	11.9491	0.52944	0.9329:0.0:0.0671:0.0	rs2282683;rs52805917;rs61476015;rs2282683	152	Q02742	GCNT1_HUMAN	V	152	ENSP00000440883:I152V;ENSP00000415454:I152V;ENSP00000390703:I152V;ENSP00000365920:I152V	.	I	+	1	0	GCNT1	78307571	1.000000	0.71417	1.000000	0.80357	0.730000	0.41778	2.458000	0.45014	1.128000	0.42052	0.533000	0.62120	ATT	A|0.773;G|0.227	0.227	strong		0.443	GCNT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052725.1	NM_001097634	
C5	727	hgsc.bcm.edu	37	9	123716103	123716103	+	Silent	SNP	T	T	C	rs41258306	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:123716103T>C	ENST00000223642.1	-	40	4835	c.4806A>G	c.(4804-4806)aaA>aaG	p.K1602K		NM_001735.2	NP_001726.2	P01031	CO5_HUMAN	complement component 5	1602	NTR. {ECO:0000255|PROSITE- ProRule:PRU00295}.				activation of MAPK activity (GO:0000187)|cell chemotaxis (GO:0060326)|cell surface receptor signaling pathway (GO:0007166)|cellular calcium ion homeostasis (GO:0006874)|chemotaxis (GO:0006935)|complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|complement activation, classical pathway (GO:0006958)|cytolysis (GO:0019835)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|in utero embryonic development (GO:0001701)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|leukocyte migration involved in inflammatory response (GO:0002523)|negative regulation of dopamine secretion (GO:0033602)|negative regulation of macrophage chemotaxis (GO:0010760)|negative regulation of norepinephrine secretion (GO:0010700)|positive regulation of angiogenesis (GO:0045766)|positive regulation of chemokine secretion (GO:0090197)|positive regulation of chemotaxis (GO:0050921)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of complement activation (GO:0030449)|response to stress (GO:0006950)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane attack complex (GO:0005579)	chemokine activity (GO:0008009)|endopeptidase inhibitor activity (GO:0004866)|receptor binding (GO:0005102)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(14)|lung(5)|ovary(2)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	46				OV - Ovarian serous cystadenocarcinoma(323;4.98e-53)|GBM - Glioblastoma multiforme(294;0.0242)	Eculizumab(DB01257)|Intravenous Immunoglobulin(DB00028)	AGGTTACCTTTTTAATGAAGG	0.373													T|||	262	0.0523163	0.0711	0.0389	5008	,	,		22368	0.002		0.0606	False		,,,				2504	0.0798				p.K1602K		Atlas-SNP	.											.	C5	124	.	0			c.A4806G						PASS	.	T		293,4113	160.7+/-193.0	8,277,1918	113.0	105.0	108.0		4806	0.6	1.0	9	dbSNP_127	108	602,7998	159.7+/-212.9	32,538,3730	no	coding-synonymous	C5	NM_001735.2		40,815,5648	CC,CT,TT		7.0,6.65,6.8814		1602/1677	123716103	895,12111	2203	4300	6503	SO:0001819	synonymous_variant	727	exon40			TACCTTTTTAATG	M57729	CCDS6826.1	9q33-q34	2014-09-17			ENSG00000106804	ENSG00000106804		"""Complement system"", ""Endogenous ligands"""	1331	protein-coding gene	gene with protein product	"""prepro-C5"", ""C5a anaphylatoxin"""	120900					Standard	NM_001735		Approved	CPAMD4, C5a, C5b	uc004bkv.3	P01031	OTTHUMG00000020579	ENST00000223642.1:c.4806A>G	9.37:g.123716103T>C		Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	170	84	0.494118	NM_001735	Q14CJ0|Q27I61	Silent	SNP	ENST00000223642.1	37	CCDS6826.1																																																																																			T|0.939;C|0.061	0.061	strong		0.373	C5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053844.1	NM_001735	
ETFB	2109	hgsc.bcm.edu	37	19	51857774	51857774	+	Intron	SNP	T	T	G	rs143144671	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:51857774T>G	ENST00000309244.4	-	2	149				ETFB_ENST00000354232.4_Missense_Mutation_p.E40A|CTD-2616J11.9_ENST00000600974.1_RNA|CTD-2616J11.11_ENST00000600067.1_Intron	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)		ATCCAGCCATTCCTGGGTACC	0.522													t|||	4	0.000798722	0.0	0.0029	5008	,	,		18122	0.0		0.002	False		,,,				2504	0.0				p.E40A		Atlas-SNP	.											.	ETFB	46	.	0			c.A119C						PASS	.	T	ALA/GLU,	3,4403	6.2+/-15.9	0,3,2200	88.0	83.0	85.0		119,	-3.9	0.0	19	dbSNP_134	85	31,8569	21.6+/-65.8	0,31,4269	yes	missense,intron	ETFB	NM_001014763.1,NM_001985.2	107,	0,34,6469	GG,GT,TT		0.3605,0.0681,0.2614	possibly-damaging,	40/347,	51857774	34,12972	2203	4300	6503	SO:0001627	intron_variant	2109	exon1			AGCCATTCCTGGG	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.58-212A>C	19.37:g.51857774T>G		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	94	65	0.691489	NM_001014763	A8K766|B3KNY2|Q6IBH7|Q71RF6|Q9Y3S7	Missense_Mutation	SNP	ENST00000309244.4	37	CCDS12828.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	t	12.37	1.918726	0.33908	6.81E-4	0.003605	ENSG00000105379	ENST00000354232	D	0.85339	-1.97	2.49	-3.88	0.04205	.	.	.	.	.	T	0.68430	0.3000	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.50558	-0.8814	7	.	.	.	.	4.1225	0.10112	0.0:0.1914:0.3562:0.4524	.	40	P38117-2	.	A	40	ENSP00000346173:E40A	.	E	-	2	0	ETFB	56549586	0.000000	0.05858	0.000000	0.03702	0.054000	0.15201	-0.697000	0.05098	-1.056000	0.03205	-0.319000	0.08680	GAA	T|0.998;G|0.002	0.002	strong		0.522	ETFB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464273.1		
ALCAM	214	hgsc.bcm.edu	37	3	105260520	105260520	+	Missense_Mutation	SNP	C	C	T	rs1044243	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:105260520C>T	ENST00000306107.5	+	8	1402	c.902C>T	c.(901-903)aCg>aTg	p.T301M	ALCAM_ENST00000389927.4_Intron|ALCAM_ENST00000486979.2_Missense_Mutation_p.T250M|ALCAM_ENST00000472644.2_Missense_Mutation_p.T301M|ALCAM_ENST00000481337.1_3'UTR	NM_001627.3	NP_001618.2	Q13740	CD166_HUMAN	activated leukocyte cell adhesion molecule	301	Ig-like C2-type 1.		T -> M (in dbSNP:rs1044243). {ECO:0000269|PubMed:7760007}.		axon guidance (GO:0007411)|cell adhesion (GO:0007155)|motor neuron axon guidance (GO:0008045)|signal transduction (GO:0007165)	axon (GO:0030424)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)	receptor binding (GO:0005102)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(14)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	28						TACACACTGACGGATGTGAGG	0.423													C|||	261	0.0521166	0.0091	0.049	5008	,	,		19991	0.0466		0.1074	False		,,,				2504	0.0613				p.T301M		Atlas-SNP	.											.	ALCAM	71	.	0			c.C902T						PASS	.	C	MET/THR	125,4281	92.0+/-130.7	3,119,2081	164.0	132.0	143.0		902	5.3	1.0	3	dbSNP_86	143	1012,7588	216.4+/-255.5	67,878,3355	no	missense	ALCAM	NM_001627.3	81	70,997,5436	TT,TC,CC		11.7674,2.837,8.7421	probably-damaging	301/584	105260520	1137,11869	2203	4300	6503	SO:0001583	missense	214	exon8			CACTGACGGATGT	AK054632	CCDS33810.1, CCDS58841.1	3q13.1	2013-01-29	2002-08-08		ENSG00000170017	ENSG00000170017		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	400	protein-coding gene	gene with protein product		601662	"""activated leucocyte cell adhesion molecule"""			7760007	Standard	NM_001627		Approved	CD166, MEMD	uc003dvx.3	Q13740	OTTHUMG00000159192	ENST00000306107.5:c.902C>T	3.37:g.105260520C>T	ENSP00000305988:p.Thr301Met	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	72	37	0.513889	NM_001627	B2RNS3|B4DTU0|O60892|Q1HGM8|Q1HGM9|Q6PEY4|Q6ZS95	Missense_Mutation	SNP	ENST00000306107.5	37	CCDS33810.1	133	0.060897435897435896	4	0.008130081300813009	23	0.06353591160220995	26	0.045454545454545456	80	0.10554089709762533	C	15.03	2.711023	0.48517	0.02837	0.117674	ENSG00000170017	ENST00000306107;ENST00000472644;ENST00000486979	T;T;T	0.12879	2.64;2.64;2.64	6.17	5.3	0.74995	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.286912	0.43747	D	0.000532	T	0.00210	0.0006	L	0.59912	1.85	0.09310	P	0.9999999999999829	B;B	0.27951	0.195;0.195	B;B	0.24541	0.054;0.054	T	0.02933	-1.1092	9	0.59425	D	0.04	-3.6835	12.1962	0.54298	0.0:0.8715:0.0:0.1285	rs1044243;rs17189213;rs1044243	301;301	B4DTU0;Q13740	.;CD166_HUMAN	M	301;301;250	ENSP00000305988:T301M;ENSP00000419236:T301M;ENSP00000418213:T250M	ENSP00000305988:T301M	T	+	2	0	ALCAM	106743210	1.000000	0.71417	0.999000	0.59377	0.992000	0.81027	2.804000	0.47931	2.941000	0.99782	0.655000	0.94253	ACG	C|0.920;T|0.080	0.080	strong		0.423	ALCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353764.1	NM_001627	
MUC2	4583	hgsc.bcm.edu	37	11	1092948	1092948	+	Silent	SNP	C	C	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:1092948C>G	ENST00000441003.2	+	30	4794	c.4767C>G	c.(4765-4767)acC>acG	p.T1589T	MUC2_ENST00000359061.5_Silent_p.T1590T|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.T1590T(2)|p.T1589T(2)		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)	tcaccaccaccactacggtga	0.627																																					p.T1589T		Atlas-SNP	.											MUC2_ENST00000441003,NS,carcinoma,+1,12	MUC2	614	12	4	Substitution - coding silent(4)	endometrium(2)|kidney(2)	c.C4767G						scavenged	.																																			SO:0001819	synonymous_variant	4583	exon30			CACCACCACTACG	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.4767C>G	11.37:g.1092948C>G		Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	56	4	0.0714286	NM_002457	Q14878	Silent	SNP	ENST00000441003.2	37																																																																																				.	.	none		0.627	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
OR4C15	81309	hgsc.bcm.edu	37	11	55322211	55322211	+	Silent	SNP	A	A	G	rs9804659	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:55322211A>G	ENST00000314644.2	+	1	429	c.429A>G	c.(427-429)aaA>aaG	p.K143K		NM_001001920.1	NP_001001920.1	Q8NGM1	OR4CF_HUMAN	olfactory receptor, family 4, subfamily C, member 15	89						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|lung(31)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(5)	56						ATGTGACAAAAACCATCTCTT	0.478										HNSCC(20;0.049)			a|||	1265	0.252596	0.1014	0.3242	5008	,	,		19759	0.3919		0.2833	False		,,,				2504	0.2311				p.K143K		Atlas-SNP	.											.	OR4C15	145	.	0			c.A429G						PASS	.	A		561,3841	252.1+/-258.6	27,507,1667	159.0	140.0	146.0		429	2.8	1.0	11	dbSNP_119	146	2288,6304	385.5+/-341.5	329,1630,2337	no	coding-synonymous	OR4C15	NM_001001920.1		356,2137,4004	GG,GA,AA		26.6294,12.7442,21.9255		143/371	55322211	2849,10145	2201	4296	6497	SO:0001819	synonymous_variant	81309	exon1			GACAAAAACCATC	BK004319	CCDS31501.1	11q11	2012-08-09			ENSG00000181939	ENSG00000181939		"""GPCR / Class A : Olfactory receptors"""	15171	protein-coding gene	gene with protein product							Standard	NM_001001920		Approved		uc010rig.2	Q8NGM1	OTTHUMG00000166714	ENST00000314644.2:c.429A>G	11.37:g.55322211A>G		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	59	19	0.322034	NM_001001920	Q6IFE2	Silent	SNP	ENST00000314644.2	37	CCDS31501.1																																																																																			A|0.760;G|0.240	0.240	strong		0.478	OR4C15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391164.1	NM_001001920	
BCAR1	9564	hgsc.bcm.edu	37	16	75269477	75269477	+	Silent	SNP	A	A	C	rs61729595	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:75269477A>C	ENST00000162330.5	-	5	1446	c.1320T>G	c.(1318-1320)tcT>tcG	p.S440S	BCAR1_ENST00000546196.1_Silent_p.S411S|BCAR1_ENST00000393422.2_Silent_p.S458S|BCAR1_ENST00000418647.3_Silent_p.S486S|BCAR1_ENST00000566982.1_5'UTR|BCAR1_ENST00000420641.3_Silent_p.S458S|BCAR1_ENST00000535626.2_Silent_p.S292S|BCAR1_ENST00000542031.2_Silent_p.S438S|BCAR1_ENST00000538440.2_Silent_p.S440S|BCAR1_ENST00000393420.6_Silent_p.S458S	NM_001170717.1|NM_014567.3	NP_001164188.1|NP_055382.2	P56945	BCAR1_HUMAN	breast cancer anti-estrogen resistance 1	440	Ser-rich.				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)	p.S458S(1)|p.S440S(1)		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)		AGGAGGACGCAGACTGGCTGC	0.701													A|||	169	0.033746	0.003	0.0375	5008	,	,		15021	0.001		0.0855	False		,,,				2504	0.0532				p.S486S		Atlas-SNP	.											BCAR1_ENST00000393420,NS,carcinoma,0,2	BCAR1	184	2	2	Substitution - coding silent(2)	prostate(2)	c.T1458G						PASS	.	A	,,,,,,,,	69,4303		0,69,2117	10.0	15.0	13.0		1458,1374,1374,1374,1320,1314,876,690,1320	-7.5	0.0	16	dbSNP_129	13	590,7978		14,562,3708	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	,,,,,,,,	14,631,5825	CC,CA,AA		6.8861,1.5782,5.0927	,,,,,,,,	486/917,458/889,458/889,458/889,440/871,438/869,292/723,230/661,440/871	75269477	659,12281	2186	4284	6470	SO:0001819	synonymous_variant	9564	exon6			GGACGCAGACTGG	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.1320T>G	16.37:g.75269477A>C		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	85	19	0.223529	NM_001170714	B3KWD7|B4DEV4|B4DGB5|B4DIW5|B7Z7X7|E9PCL5|E9PCV2|F5GXA2|F5GXV6|F5H7Z0|F8WA69|Q6QEF7	Silent	SNP	ENST00000162330.5	37	CCDS10915.1																																																																																			A|0.962;C|0.038	0.038	strong		0.701	BCAR1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000269017.1	NM_014567	
PSPH	5723	hgsc.bcm.edu	37	7	56088902	56088902	+	Missense_Mutation	SNP	C	C	T	rs77329757	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:56088902C>T	ENST00000395471.3	-	4	809	c.4G>A	c.(4-6)Gtc>Atc	p.V2I	PSPH_ENST00000275605.3_Missense_Mutation_p.V2I|PSPH_ENST00000459834.1_Intron			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						scavenged	.						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	145	0	0		WXS	Illumina HiSeq	Phase_I	131	17	0.129771	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	
AHNAK2	113146	hgsc.bcm.edu	37	14	105415431	105415431	+	Missense_Mutation	SNP	C	C	G	rs199873247	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:105415431C>G	ENST00000333244.5	-	7	6476	c.6357G>C	c.(6355-6357)atG>atC	p.M2119I	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	2119						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)			CGTCCACCTCCATGCTGGGCA	0.592																																					p.M2119I		Atlas-SNP	.											AHNAK2_ENST00000333244,NS,carcinoma,-2,2	AHNAK2	719	2	0			c.G6357C						scavenged	.						151.0	107.0	124.0					14																	105415431		1958	2981	4939	SO:0001583	missense	113146	exon7			CACCTCCATGCTG	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.6357G>C	14.37:g.105415431C>G	ENSP00000353114:p.Met2119Ile	Somatic	0	0	.		WXS	Illumina HiSeq	Phase_I	96	22	0.229167	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	.	.	.	.	.	.	.	.	.	.	N	4.775	0.144115	0.09134	.	.	ENSG00000185567	ENST00000333244	T	0.00672	5.89	4.31	2.38	0.29361	.	.	.	.	.	T	0.00695	0.0023	L	0.39020	1.185	0.09310	N	1	B	0.10296	0.003	B	0.14023	0.01	T	0.47861	-0.9084	9	0.15066	T	0.55	.	3.1626	0.06525	0.205:0.4504:0.2466:0.0979	.	2119	Q8IVF2	AHNK2_HUMAN	I	2119	ENSP00000353114:M2119I	ENSP00000353114:M2119I	M	-	3	0	AHNAK2	104486476	0.003000	0.15002	0.051000	0.19133	0.018000	0.09664	0.196000	0.17176	0.821000	0.34540	0.306000	0.20318	ATG	C|0.965;G|0.036	0.036	strong		0.592	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
ZNF675	171392	hgsc.bcm.edu	37	19	23837195	23837195	+	Silent	SNP	T	T	C	rs77385655	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:23837195T>C	ENST00000359788.4	-	4	708	c.540A>G	c.(538-540)tcA>tcG	p.S180S	ZNF675_ENST00000601935.1_Intron|ZNF675_ENST00000596211.1_Intron|ZNF675_ENST00000600313.1_Intron	NM_138330.2	NP_612203.2	Q8TD23	ZN675_HUMAN	zinc finger protein 675	180					bone resorption (GO:0045453)|cytokine-mediated signaling pathway (GO:0019221)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|negative regulation of interleukin-1-mediated signaling pathway (GO:2000660)|negative regulation of JNK cascade (GO:0046329)|negative regulation of JUN kinase activity (GO:0043508)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription regulatory region DNA binding (GO:2000678)|negative regulation of tumor necrosis factor-mediated signaling pathway (GO:0010804)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	DNA binding (GO:0003677)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)			endometrium(3)|kidney(2)|large_intestine(8)|lung(11)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	27		all_lung(12;0.11)|Lung NSC(12;0.163)|all_epithelial(12;0.206)				GCATGCAAAATGATCTGCCAC	0.294													T|||	648	0.129393	0.1135	0.0504	5008	,	,		18094	0.2133		0.1034	False		,,,				2504	0.1472				p.S180S		Atlas-SNP	.											.	ZNF675	88	.	0			c.A540G						PASS	.	T		467,3937		22,423,1757	56.0	55.0	55.0		540	-1.4	0.0	19	dbSNP_131	55	694,7900		26,642,3629	no	coding-synonymous	ZNF675	NM_138330.2		48,1065,5386	CC,CT,TT		8.0754,10.604,8.9321		180/569	23837195	1161,11837	2202	4297	6499	SO:0001819	synonymous_variant	171392	exon4			GCAAAATGATCTG		CCDS32981.1	19p12	2013-01-08						"""Zinc fingers, C2H2-type"", ""-"""	30768	protein-coding gene	gene with protein product	"""TRAF6 inhibitory zinc finger"""					11751921	Standard	NM_138330		Approved	TIZ, TBZF	uc002nri.3	Q8TD23		ENST00000359788.4:c.540A>G	19.37:g.23837195T>C		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	98	49	0.5	NM_138330	Q8N211	Silent	SNP	ENST00000359788.4	37	CCDS32981.1																																																																																			T|0.900;C|0.100	0.100	strong		0.294	ZNF675-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466433.1	NM_138330	
KANK4	163782	hgsc.bcm.edu	37	1	62739198	62739198	+	Silent	SNP	G	G	A	rs17855078	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:62739198G>A	ENST00000371153.4	-	3	1956	c.1578C>T	c.(1576-1578)agC>agT	p.S526S	KANK4_ENST00000354381.3_Intron|KANK4_ENST00000371150.1_5'Flank	NM_181712.4	NP_859063.3	Q5T7N3	KANK4_HUMAN	KN motif and ankyrin repeat domains 4	526						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						TCTTTCTGTCGCTGCCCCACA	0.607													G|||	1255	0.250599	0.1641	0.2291	5008	,	,		20578	0.1121		0.341	False		,,,				2504	0.4325				p.S526S		Atlas-SNP	.											.	KANK4	135	.	0			c.C1578T						PASS	.	G		828,3578	328.0+/-300.3	82,664,1457	54.0	55.0	55.0		1578	-10.0	0.0	1	dbSNP_123	55	2846,5754	446.7+/-361.3	496,1854,1950	no	coding-synonymous	KANK4	NM_181712.4		578,2518,3407	AA,AG,GG		33.093,18.7926,28.2485		526/996	62739198	3674,9332	2203	4300	6503	SO:0001819	synonymous_variant	163782	exon3			TCTGTCGCTGCCC	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.1578C>T	1.37:g.62739198G>A		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	126	55	0.436508	NM_181712	B1ALP7|Q6P9A0|Q86T71|Q86VE6|Q8NAX3	Silent	SNP	ENST00000371153.4	37	CCDS620.1																																																																																			G|0.724;A|0.276	0.276	strong		0.607	KANK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024877.1	NM_181712	
OR5B3	441608	hgsc.bcm.edu	37	11	58170469	58170469	+	Silent	SNP	C	C	A	rs11229412	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:58170469C>A	ENST00000309403.2	-	1	413	c.414G>T	c.(412-414)gtG>gtT	p.V138V		NM_001005469.1	NP_001005469.1	Q8NH48	OR5B3_HUMAN	olfactory receptor, family 5, subfamily B, member 3	138						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.V138V(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(17)|ovary(1)|prostate(1)|skin(2)|stomach(6)|upper_aerodigestive_tract(1)	34	Esophageal squamous(5;0.0027)	Breast(21;0.0778)				GACGAGCACACACAGTTGTTG	0.493													c|||	1453	0.290136	0.3525	0.2695	5008	,	,		20988	0.1448		0.3638	False		,,,				2504	0.2945				p.V138V		Atlas-SNP	.											OR5B3,NS,carcinoma,0,1	OR5B3	65	1	1	Substitution - coding silent(1)	stomach(1)	c.G414T						PASS	.	C		1442,2960	467.9+/-355.0	229,984,988	121.0	109.0	113.0		414	-0.8	0.3	11	dbSNP_120	113	3094,5496	473.5+/-368.6	550,1994,1751	no	coding-synonymous	OR5B3	NM_001005469.1		779,2978,2739	AA,AC,CC		36.0186,32.7578,34.9138		138/315	58170469	4536,8456	2201	4295	6496	SO:0001819	synonymous_variant	441608	exon1			AGCACACACAGTT	AB065545	CCDS31549.1	11q12.1	2012-08-09			ENSG00000172769	ENSG00000172769		"""GPCR / Class A : Olfactory receptors"""	8324	protein-coding gene	gene with protein product				OR5B13			Standard	NM_001005469		Approved	OST129	uc010rkf.2	Q8NH48	OTTHUMG00000167516	ENST00000309403.2:c.414G>T	11.37:g.58170469C>A		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	107	80	0.747664	NM_001005469	Q6IEV6	Silent	SNP	ENST00000309403.2	37	CCDS31549.1																																																																																			C|0.672;A|0.328	0.328	strong		0.493	OR5B3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394886.1	NM_001005469	
UMODL1	89766	hgsc.bcm.edu	37	21	43531345	43531345	+	Intron	SNP	G	G	A	rs76618631	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:43531345G>A	ENST00000408910.2	+	11	1899				UMODL1_ENST00000400427.1_Silent_p.A599A|UMODL1_ENST00000400424.2_Intron|UMODL1_ENST00000408989.2_Silent_p.A671A|C21orf128_ENST00000329015.2_5'Flank	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						CCAGCCAGGCGAGCCCCAGCC	0.726													G|||	104	0.0207668	0.0734	0.0072	5008	,	,		10161	0.0		0.002	False		,,,				2504	0.0				p.A671A	Pancreas(122;680 807 13940 14411 22888 25505 31742 36028 36332 38435)	Atlas-SNP	.											.	UMODL1	186	.	0			c.G2013A						PASS	.	G	,,,	161,3347		2,157,1595	4.0	7.0	6.0		,1797,,2013	0.1	0.0	21	dbSNP_131	6	1,7635		0,1,3817	no	intron,coding-synonymous,intron,coding-synonymous	UMODL1	NM_001004416.2,NM_001199527.1,NM_001199528.2,NM_173568.3	,,,	2,158,5412	AA,AG,GG		0.0131,4.5895,1.4537	,,,	,599/1375,,671/1447	43531345	162,10982	1754	3818	5572	SO:0001627	intron_variant	89766	exon11			CCAGGCGAGCCCC		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+114G>A	21.37:g.43531345G>A		Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	35	14	0.4	NM_173568	C9JCE6|Q5DIC9|Q6LA40|Q6LA41|Q8N216	Silent	SNP	ENST00000408910.2	37	CCDS42936.1																																																																																			G|0.983;A|0.017	0.017	strong		0.726	UMODL1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195292.2		
PABPC1	26986	hgsc.bcm.edu	37	8	101721785	101721785	+	Missense_Mutation	SNP	T	T	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:101721785T>A	ENST00000318607.5	-	8	2275	c.1147A>T	c.(1147-1149)Atg>Ttg	p.M383L	AP001205.1_ENST00000579868.1_RNA|PABPC1_ENST00000522387.1_Missense_Mutation_p.M351L|PABPC1_ENST00000519596.1_5'UTR|PABPC1_ENST00000519004.1_Missense_Mutation_p.M338L	NM_002568.3	NP_002559.2	P11940	PABP1_HUMAN	poly(A) binding protein, cytoplasmic 1	383					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA metabolic process (GO:0016071)|mRNA polyadenylation (GO:0006378)|mRNA splicing, via spliceosome (GO:0000398)|mRNA stabilization (GO:0048255)|negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:2000623)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|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)|positive regulation of translation (GO:0045727)|RNA metabolic process (GO:0016070)|translation (GO:0006412)|translational initiation (GO:0006413)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytoplasmic stress granule (GO:0010494)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) binding (GO:0008143)|poly(A) RNA binding (GO:0044822)|poly(U) RNA binding (GO:0008266)|protein C-terminus binding (GO:0008022)|translation activator activity (GO:0008494)			breast(2)|endometrium(4)|kidney(15)|large_intestine(4)|lung(13)|prostate(1)|skin(1)	40	all_cancers(14;6.8e-05)|all_epithelial(15;3.16e-07)|Lung NSC(17;0.000453)|all_lung(17;0.00125)		Epithelial(11;6.37e-11)|all cancers(13;1.11e-08)|OV - Ovarian serous cystadenocarcinoma(57;3.91e-05)|STAD - Stomach adenocarcinoma(118;0.206)			ATTCTCTGCATATACTGGTTA	0.493																																					p.M383L		Atlas-SNP	.											.	PABPC1	76	.	0			c.A1147T						PASS	.						168.0	142.0	151.0					8																	101721785		2203	4300	6503	SO:0001583	missense	26986	exon8			TCTGCATATACTG	Y00345	CCDS6289.1	8q22.2-q23	2013-02-12	2004-04-20		ENSG00000070756	ENSG00000070756		"""RNA binding motif (RRM) containing"""	8554	protein-coding gene	gene with protein product		604679	"""poly(A)-binding protein, cytoplasmic 2"""	PAB1, PABPC2		2885805	Standard	XM_005250861		Approved	PABP1, PABPL1	uc003yjs.1	P11940	OTTHUMG00000164779	ENST00000318607.5:c.1147A>T	8.37:g.101721785T>A	ENSP00000313007:p.Met383Leu	Somatic	256	0	0		WXS	Illumina HiSeq	Phase_I	220	73	0.331818	NM_002568	Q15097|Q93004	Missense_Mutation	SNP	ENST00000318607.5	37	CCDS6289.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	19.08|19.08	3.757792|3.757792	0.69648|0.69648	.|.	.|.	ENSG00000070756|ENSG00000070756	ENST00000318607;ENST00000347137;ENST00000519004;ENST00000522387|ENST00000519596	T;T;T|.	0.32023|.	1.52;1.47;2.53|.	5.19|5.19	5.19|5.19	0.71726|0.71726	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.76601|0.76601	0.4010|0.4010	M|M	0.84846|0.84846	2.72|2.72	0.58432|0.58432	D|D	0.999995|0.999995	B;B;B|.	0.21452|.	0.043;0.056;0.025|.	B;B;B|.	0.23150|.	0.033;0.044;0.019|.	T|T	0.75736|0.75736	-0.3213|-0.3213	10|6	0.48119|0.23891	T|T	0.1|0.37	.|.	15.3415|15.3415	0.74300|0.74300	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	351;383;383|.	E7ERJ7;B3KT93;P11940|.	.;.;PABP1_HUMAN|.	L|F	383;383;338;351|215	ENSP00000313007:M383L;ENSP00000429594:M338L;ENSP00000429395:M351L|.	ENSP00000313007:M383L|ENSP00000430068:Y215F	M|Y	-|-	1|2	0|0	PABPC1|PABPC1	101790961|101790961	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	7.968000|7.968000	0.87980|0.87980	2.083000|2.083000	0.62718|0.62718	0.533000|0.533000	0.62120|0.62120	ATG|TAT	.	.	none		0.493	PABPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380217.1	NM_002568	
TSSK1B	83942	hgsc.bcm.edu	37	5	112770027	112770027	+	Silent	SNP	T	T	G	rs26980	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:112770027T>G	ENST00000390666.3	-	1	701	c.510A>C	c.(508-510)gcA>gcC	p.A170A	MCC_ENST00000408903.3_Intron|CTD-2201G3.1_ENST00000510381.2_RNA|CTD-2201G3.1_ENST00000416046.2_RNA|CTD-2201G3.1_ENST00000383058.4_RNA	NM_032028.3	NP_114417.1	Q9BXA7	TSSK1_HUMAN	testis-specific serine kinase 1B	170	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)		TCTTGCTTAATGCCATTCGAC	0.562													T|||	257	0.0513179	0.0204	0.0317	5008	,	,		20598	0.0288		0.1243	False		,,,				2504	0.0552				p.A170A		Atlas-SNP	.											.	TSSK1B	89	.	0			c.A510C						PASS	.	T	,	152,4252	101.6+/-140.2	2,148,2052	75.0	72.0	73.0		,510	-0.0	0.6	5	dbSNP_76	73	1022,7578	218.0+/-256.5	46,930,3324	no	intron,coding-synonymous	MCC,TSSK1B	NM_001085377.1,NM_032028.3	,	48,1078,5376	GG,GT,TT		11.8837,3.4514,9.028	,	,170/368	112770027	1174,11830	2202	4300	6502	SO:0001819	synonymous_variant	83942	exon1			GCTTAATGCCATT	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.510A>C	5.37:g.112770027T>G		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	58	30	0.517241	NM_032028	B2R8D9	Silent	SNP	ENST00000390666.3	37	CCDS4112.1																																																																																			T|0.931;G|0.069	0.069	strong		0.562	TSSK1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250774.2	NM_032028	
TRIOBP	11078	hgsc.bcm.edu	37	22	38121152	38121152	+	Missense_Mutation	SNP	C	C	A	rs9610841	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	176	0	0		WXS	Illumina HiSeq	Phase_I	151	71	0.470199	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		
NBAS	51594	hgsc.bcm.edu	37	2	15607853	15607853	+	Silent	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:15607853G>A	ENST00000281513.5	-	18	1978	c.1953C>T	c.(1951-1953)gcC>gcT	p.A651A	NBAS_ENST00000441750.1_Silent_p.A651A	NM_015909.3	NP_056993.2	A2RRP1	NBAS_HUMAN	neuroblastoma amplified sequence	651					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						TTTTATTCTTGGCAGGCTCTT	0.343																																					p.A651A		Atlas-SNP	.											.	NBAS	246	.	0			c.C1953T						PASS	.						106.0	99.0	101.0					2																	15607853		2202	4299	6501	SO:0001819	synonymous_variant	51594	exon18			ATTCTTGGCAGGC	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.1953C>T	2.37:g.15607853G>A		Somatic	211	1	0.00473934		WXS	Illumina HiSeq	Phase_I	246	136	0.552846	NM_015909	O95790|Q2VPJ7|Q53TK6|Q86V39|Q8NFY8|Q9Y3W5	Silent	SNP	ENST00000281513.5	37	CCDS1685.1																																																																																			.	.	none		0.343	NBAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241638.1	NM_015909	
MMP14	4323	hgsc.bcm.edu	37	14	23312923	23312923	+	Silent	SNP	T	T	C	rs2236307	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:23312923T>C	ENST00000311852.6	+	6	1116	c.855T>C	c.(853-855)ggT>ggC	p.G285G	MMP14_ENST00000548162.1_3'UTR	NM_004995.2	NP_004986.1	P50281	MMP14_HUMAN	matrix metallopeptidase 14 (membrane-inserted)	285					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)	CCCCAGGGGGTGAGTCAGGGT	0.572													T|||	1360	0.271565	0.3313	0.1671	5008	,	,		16355	0.3562		0.2018	False		,,,				2504	0.2495				p.G285G		Atlas-SNP	.											.	MMP14	40	.	0			c.T855C						PASS	.	T		1343,3063	447.5+/-348.4	189,965,1049	100.0	111.0	108.0		855	0.8	0.8	14	dbSNP_98	108	1816,6784	326.7+/-317.5	197,1422,2681	no	coding-synonymous	MMP14	NM_004995.2		386,2387,3730	CC,CT,TT		21.1163,30.4812,24.2888		285/583	23312923	3159,9847	2203	4300	6503	SO:0001819	synonymous_variant	4323	exon6			AGGGGGTGAGTCA		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.855T>C	14.37:g.23312923T>C		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	70	28	0.4	NM_004995	A8K5L0|Q6GSF3|Q92678	Silent	SNP	ENST00000311852.6	37	CCDS9577.1																																																																																			A|0.000;C|0.247;G|0.000;T|0.753	0.247	strong		0.572	MMP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071660.3	NM_004995	
TMEM132A	54972	hgsc.bcm.edu	37	11	60698054	60698054	+	Silent	SNP	G	G	A	rs2074416	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:60698054G>A	ENST00000453848.2	+	5	1097	c.939G>A	c.(937-939)ctG>ctA	p.L313L	TMEM132A_ENST00000005286.4_Silent_p.L313L			Q24JP5	T132A_HUMAN	transmembrane protein 132A	313						endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				breast(1)|cervix(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(14)|ovary(3)|prostate(1)|skin(3)	32						CTGCCAAGCTGGACCGCTTCA	0.622													G|||	1483	0.296126	0.0961	0.3862	5008	,	,		16514	0.3204		0.3897	False		,,,				2504	0.3814				p.L313L		Atlas-SNP	.											.	TMEM132A	135	.	0			c.G939A						PASS	.	G	,	661,3745	282.5+/-276.6	47,567,1589	80.0	84.0	82.0		939,939	0.6	1.0	11	dbSNP_96	82	3446,5152	506.7+/-376.6	694,2058,1547	no	coding-synonymous,coding-synonymous	TMEM132A	NM_017870.3,NM_178031.2	,	741,2625,3136	AA,AG,GG		40.0791,15.0023,31.5826	,	313/1025,313/1024	60698054	4107,8897	2203	4299	6502	SO:0001819	synonymous_variant	54972	exon5			CAAGCTGGACCGC	AK000546	CCDS7997.1, CCDS44618.1	11q12.2	2006-03-02	2006-03-02	2006-03-02	ENSG00000006118	ENSG00000006118			31092	protein-coding gene	gene with protein product			"""heat shock 70kDa protein 5 (glucose-regulated protein, 78kDa) binding protein 1"""	HSPA5BP1		12514190, 10997877	Standard	NM_017870		Approved	GBP, FLJ20539	uc001nqi.3	Q24JP5	OTTHUMG00000167803	ENST00000453848.2:c.939G>A	11.37:g.60698054G>A		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	45	45	1	NM_178031	Q69YU7|Q86VZ8|Q86W97|Q9H8K3|Q9HCI9|Q9NWY0	Silent	SNP	ENST00000453848.2	37	CCDS44618.1																																																																																			G|0.692;A|0.308	0.308	strong		0.622	TMEM132A-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000396352.1	NM_017870	
ADAMTS10	81794	hgsc.bcm.edu	37	19	8669931	8669931	+	Missense_Mutation	SNP	G	G	C	rs7255721	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:8669931G>C	ENST00000597188.1	-	4	671	c.401C>G	c.(400-402)aCc>aGc	p.T134S	ADAMTS10_ENST00000596709.1_5'UTR|ADAMTS10_ENST00000270328.4_Missense_Mutation_p.T134S	NM_030957.2	NP_112219.3	Q9H324	ATS10_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 10	134			T -> S (in dbSNP:rs7255721). {ECO:0000269|PubMed:15355968}.			extracellular matrix (GO:0031012)|microfibril (GO:0001527)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(16)|large_intestine(5)|lung(9)|ovary(1)|pancreas(2)|prostate(3)|skin(10)|urinary_tract(1)	53						CACATGGGAGGTGCTGGCCTG	0.622													C|||	4477	0.89397	0.9766	0.8516	5008	,	,		15683	0.9702		0.7048	False		,,,				2504	0.9284				p.T134S		Atlas-SNP	.											.	ADAMTS10	132	.	0			c.C401G						PASS	.	C	SER/THR	4069,273		1906,257,8	8.0	10.0	9.0		401	5.2	1.0	19	dbSNP_116	9	5979,2533		2139,1701,416	yes	missense	ADAMTS10	NM_030957.2	58	4045,1958,424	CC,CG,GG		29.758,6.2874,21.8298	benign	134/1104	8669931	10048,2806	2171	4256	6427	SO:0001583	missense	81794	exon4			TGGGAGGTGCTGG	AF163762	CCDS12206.1, CCDS62529.1	19p13.2	2014-08-12	2005-08-19		ENSG00000142303	ENSG00000142303		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	13201	protein-coding gene	gene with protein product		608990	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 10"""				Standard	XM_005272499		Approved	ADAM-TS10	uc002mkj.1	Q9H324	OTTHUMG00000182216	ENST00000597188.1:c.401C>G	19.37:g.8669931G>C	ENSP00000471851:p.Thr134Ser	Somatic	106	1	0.00943396		WXS	Illumina HiSeq	Phase_I	93	91	0.978495	NM_030957	M0QZE4	Missense_Mutation	SNP	ENST00000597188.1	37	CCDS12206.1	1862	0.8525641025641025	478	0.9715447154471545	297	0.8204419889502762	552	0.965034965034965	535	0.7058047493403694	C	3.922	-0.017841	0.07681	0.937126	0.70242	ENSG00000142303	ENST00000270328	T	0.58060	0.36	5.24	5.24	0.73138	Peptidase M12B, propeptide (1);	0.190363	0.46758	N	0.000276	T	0.00012	0.0000	N	0.00471	-1.455	0.80722	P	0.0	B	0.02656	0.0	B	0.06405	0.002	T	0.41179	-0.9523	9	0.02654	T	1	.	10.455	0.44546	0.0:0.789:0.1357:0.0753	rs7255721;rs7255721	134	Q9H324	ATS10_HUMAN	S	134	ENSP00000270328:T134S	ENSP00000270328:T134S	T	-	2	0	ADAMTS10	8575931	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	0.951000	0.29135	1.228000	0.43614	-0.322000	0.08575	ACC	G|0.152;C|0.848	0.848	strong		0.622	ADAMTS10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460085.3	NM_030957	
SERPINA5	5104	hgsc.bcm.edu	37	14	95053891	95053891	+	Silent	SNP	C	C	T	rs6111|rs386780205	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:95053891C>T	ENST00000554866.1	+	2	306	c.192C>T	c.(190-192)agC>agT	p.S64S	SERPINA5_ENST00000554276.1_Silent_p.S64S|SERPINA5_ENST00000553780.1_Silent_p.S64S|SERPINA5_ENST00000329597.7_Silent_p.S64S			P05154	IPSP_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 5	64			S -> N (in dbSNP:rs6115). {ECO:0000269|PubMed:10391209, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:1714450, ECO:0000269|PubMed:17974005, ECO:0000269|PubMed:2173165, ECO:0000269|PubMed:3027058, ECO:0000269|PubMed:8471250, ECO:0000269|PubMed:8713781, ECO:0000269|Ref.6}.		fusion of sperm to egg plasma membrane (GO:0007342)|lipid transport (GO:0006869)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of proteolysis (GO:0045861)|regulation of proteolysis (GO:0030162)|spermatogenesis (GO:0007283)	acrosomal membrane (GO:0002080)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|platelet alpha granule (GO:0031091)|platelet dense tubular network (GO:0031094)|protein C inhibitor-coagulation factor V complex (GO:0097181)|protein C inhibitor-coagulation factor Xa complex (GO:0097182)|protein C inhibitor-coagulation factor XI complex (GO:0097183)|protein C inhibitor-KLK3 complex (GO:0036029)|protein C inhibitor-plasma kallikrein complex (GO:0036030)|protein C inhibitor-PLAT complex (GO:0036026)|protein C inhibitor-PLAU complex (GO:0036027)|protein C inhibitor-thrombin complex (GO:0036028)|protein C inhibitor-TMPRSS11E complex (GO:0036025)|protein C inhibitor-TMPRSS7 complex (GO:0036024)|protein complex (GO:0043234)	acrosin binding (GO:0032190)|glycosaminoglycan binding (GO:0005539)|heparin binding (GO:0008201)|phosphatidylcholine binding (GO:0031210)|protease binding (GO:0002020)|retinoic acid binding (GO:0001972)|serine-type endopeptidase inhibitor activity (GO:0004867)			endometrium(3)|large_intestine(5)|lung(18)|ovary(2)|skin(5)|upper_aerodigestive_tract(3)	36				COAD - Colon adenocarcinoma(157;0.21)	Drotrecogin alfa(DB00055)|Urokinase(DB00013)	CCAGCCAGAGCATCTTCTTCT	0.622													C|||	1366	0.272764	0.612	0.1167	5008	,	,		18414	0.2748		0.0905	False		,,,				2504	0.1104				p.S64S		Atlas-SNP	.											.	SERPINA5	69	.	0			c.C192T						PASS	.	C		2148,2258		574,1000,629	34.0	35.0	35.0		192	1.2	0.3	14	dbSNP_52	35	751,7849		41,669,3590	no	coding-synonymous	SERPINA5	NM_000624.4		615,1669,4219	TT,TC,CC		8.7326,48.7517,22.2897		64/407	95053891	2899,10107	2203	4300	6503	SO:0001819	synonymous_variant	5104	exon3			CCAGAGCATCTTC	M68516	CCDS9928.1	14q32.1	2014-02-18	2005-08-18		ENSG00000188488	ENSG00000188488		"""Serine (or cysteine) peptidase inhibitors"""	8723	protein-coding gene	gene with protein product		601841	"""serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 5"""	PLANH3, PCI		1714450, 8381582, 24172014	Standard	NM_000624		Approved	PAI3, PROCI	uc001ydm.3	P05154	OTTHUMG00000170860	ENST00000554866.1:c.192C>T	14.37:g.95053891C>T		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	41	16	0.390244	NM_000624	Q07616|Q9UG30	Silent	SNP	ENST00000554866.1	37	CCDS9928.1																																																																																			C|0.783;T|0.217	0.217	strong		0.622	SERPINA5-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410726.1	NM_000624	
NOLC1	9221	hgsc.bcm.edu	37	10	103920475	103920475	+	Missense_Mutation	SNP	T	T	C	rs1049455	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:103920475T>C	ENST00000605788.1	+	10	1601	c.1366T>C	c.(1366-1368)Tct>Cct	p.S456P	NOLC1_ENST00000405356.1_Missense_Mutation_p.S466P|NOLC1_ENST00000488254.2_Missense_Mutation_p.S457P|NOLC1_ENST00000603742.1_Missense_Mutation_p.S175P	NM_001284389.1|NM_004741.3	NP_001271318.1|NP_004732.2	Q14978	NOLC1_HUMAN	nucleolar and coiled-body phosphoprotein 1	456	11 X 12 AA approximate repeats of an acidic serine cluster.		S -> P (in dbSNP:rs1049455). {ECO:0000269|PubMed:7584026}.		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)		AGCAGCTCTATCTCTGCCTGC	0.557													C|||	916	0.182907	0.5477	0.1052	5008	,	,		20309	0.001		0.0815	False		,,,				2504	0.0368				p.S456P		Atlas-SNP	.											.	NOLC1	61	.	0			c.T1366C						PASS	.	C	PRO/SER	2015,2389	604.0+/-390.2	459,1097,646	59.0	58.0	58.0		1366	-0.5	0.0	10	dbSNP_86	58	729,7871	775.3+/-407.7	33,663,3604	yes	missense	NOLC1	NM_004741.3	74	492,1760,4250	CC,CT,TT		8.4767,45.7539,21.1012	benign	456/700	103920475	2744,10260	2202	4300	6502	SO:0001583	missense	9221	exon10			GCTCTATCTCTGC	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.1366T>C	10.37:g.103920475T>C	ENSP00000474710:p.Ser456Pro	Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	118	53	0.449153	NM_004741	Q15030|Q5VV70|Q9BUV3	Missense_Mutation	SNP	ENST00000605788.1	37	CCDS7530.1	355	0.16254578754578755	241	0.4898373983739837	44	0.12154696132596685	0	0.0	70	0.09234828496042216	C	2.603	-0.292553	0.05568	0.457539	0.084767	ENSG00000166197	ENST00000405356;ENST00000370007	T	0.49720	0.77	5.94	-0.492	0.12041	.	0.538227	0.18818	N	0.130321	T	0.00012	0.0000	L	0.31526	0.94	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	0.47923	-0.9079	9	0.22109	T	0.4	0.0149	5.2759	0.15649	0.0:0.3173:0.2697:0.413	rs1049455;rs3189626;rs1049455	457;466;456	Q14978-3;Q14978-2;Q14978	.;.;NOLC1_HUMAN	P	466;456	ENSP00000385410:S466P	ENSP00000359024:S456P	S	+	1	0	NOLC1	103910465	0.000000	0.05858	0.005000	0.12908	0.016000	0.09150	-0.550000	0.06034	-0.348000	0.08286	-1.073000	0.02249	TCT	T|0.797;C|0.203	0.203	strong		0.557	NOLC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000050012.2	NM_004741	
PDIA4	9601	hgsc.bcm.edu	37	7	148709061	148709061	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:148709061G>A	ENST00000286091.4	-	6	1088	c.856C>T	c.(856-858)Ccc>Tcc	p.P286S		NM_004911.4	NP_004902.1	P13667	PDIA4_HUMAN	protein disulfide isomerase family A, member 4	286	Thioredoxin 2. {ECO:0000255|PROSITE- ProRule:PRU00691}.				cell redox homeostasis (GO:0045454)|chaperone-mediated protein folding (GO:0061077)|protein folding (GO:0006457)|protein secretion (GO:0009306)|response to endoplasmic reticulum stress (GO:0034976)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)	poly(A) RNA binding (GO:0044822)|protein disulfide isomerase activity (GO:0003756)			large_intestine(6)|lung(15)|ovary(2)|prostate(1)	24	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00385)			TCCTTGGAGGGAGGCCCGGAC	0.577																																					p.P286S		Atlas-SNP	.											.	PDIA4	57	.	0			c.C856T						PASS	.						80.0	76.0	77.0					7																	148709061		2203	4300	6503	SO:0001583	missense	9601	exon6			TGGAGGGAGGCCC	BC001928	CCDS5893.1	7q35	2009-11-20	2005-06-29		ENSG00000155660	ENSG00000155660	5.3.4.1	"""Protein disulfide isomerases"""	30167	protein-coding gene	gene with protein product			"""protein disulfide isomerase-associated 4"""			2549034, 2002068	Standard	NM_004911		Approved	ERP70, ERP72	uc003wff.2	P13667	OTTHUMG00000150248	ENST00000286091.4:c.856C>T	7.37:g.148709061G>A	ENSP00000286091:p.Pro286Ser	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	60	10	0.166667	NM_004911	A8K4K6|Q549T6	Missense_Mutation	SNP	ENST00000286091.4	37	CCDS5893.1	.	.	.	.	.	.	.	.	.	.	g	12.18	1.862013	0.32884	.	.	ENSG00000155660	ENST00000286091	T	0.19394	2.15	5.14	5.14	0.70334	Thioredoxin-like fold (2);	0.100995	0.64402	D	0.000001	T	0.13114	0.0318	N	0.21583	0.68	0.80722	D	1	P	0.36282	0.546	B	0.22386	0.039	T	0.11567	-1.0582	10	0.16896	T	0.51	.	18.7073	0.91643	0.0:0.0:1.0:0.0	.	286	P13667	PDIA4_HUMAN	S	286	ENSP00000286091:P286S	ENSP00000286091:P286S	P	-	1	0	PDIA4	148339994	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	6.052000	0.71080	2.423000	0.82170	0.639000	0.83563	CCC	.	.	none		0.577	PDIA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317077.1	NM_004911	
KIF25	3834	hgsc.bcm.edu	37	6	168442765	168442765	+	Missense_Mutation	SNP	G	G	A	rs2073634	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:168442765G>A	ENST00000443060.2	+	8	1154	c.763G>A	c.(763-765)Gca>Aca	p.A255T	KIF25_ENST00000354419.2_Missense_Mutation_p.A255T|KIF25_ENST00000351261.3_Missense_Mutation_p.A255T			Q9UIL4	KIF25_HUMAN	kinesin family member 25	255	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.		A -> T (in dbSNP:rs2073634).		ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic sister chromatid segregation (GO:0000070)|negative regulation of autophagy (GO:0010507)|organelle organization (GO:0006996)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(2)|breast(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	29		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)		TGGGAACCCCGCAGGGCATGC	0.672													G|||	570	0.113818	0.0091	0.085	5008	,	,		17441	0.2133		0.0805	False		,,,				2504	0.2076				p.A255T		Atlas-SNP	.											.	KIF25	75	.	0			c.G763A						PASS	.	G	THR/ALA,THR/ALA	93,4165		5,83,2041	25.0	24.0	24.0		763,763	-2.5	0.0	6	dbSNP_96	24	672,7712		22,628,3542	yes	missense,missense	KIF25	NM_005355.3,NM_030615.2	58,58	27,711,5583	AA,AG,GG		8.0153,2.1841,6.0513	benign,benign	255/333,255/385	168442765	765,11877	2129	4192	6321	SO:0001583	missense	3834	exon7			AACCCCGCAGGGC	AB012722	CCDS5305.1, CCDS43530.1	6q27	2008-02-05	2003-01-09	2003-01-10	ENSG00000125337	ENSG00000125337		"""Kinesins"""	6390	protein-coding gene	gene with protein product		603815	"""kinesin-like 3"""	KNSL3		9925910	Standard	NM_030615		Approved		uc003qwk.1	Q9UIL4	OTTHUMG00000016035	ENST00000443060.2:c.763G>A	6.37:g.168442765G>A	ENSP00000388878:p.Ala255Thr	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	104	28	0.269231	NM_030615	O94775|Q5SZU9	Missense_Mutation	SNP	ENST00000443060.2	37	CCDS5305.1	225	0.10302197802197802	7	0.014227642276422764	34	0.09392265193370165	123	0.21503496503496503	61	0.08047493403693931	G	6.328	0.428658	0.11987	0.021841	0.080153	ENSG00000125337	ENST00000443060;ENST00000354419;ENST00000351261	T;T;T	0.72394	-0.65;-0.65;-0.01	3.16	-2.49	0.06403	Kinesin, motor domain (3);	8.679060	0.00166	N	0.000008	T	0.16041	0.0386	N	0.02854	-0.475	0.80722	P	0.0	B;P	0.35745	0.142;0.518	B;B	0.23574	0.033;0.047	T	0.15549	-1.0433	9	0.46703	T	0.11	-1.071	0.4999	0.00578	0.3585:0.1778:0.283:0.1807	rs2073634;rs59155379;rs2073634	255;255	Q9UIL4-2;Q9UIL4	.;KIF25_HUMAN	T	255	ENSP00000388878:A255T;ENSP00000346401:A255T;ENSP00000252688:A255T	ENSP00000252688:A255T	A	+	1	0	KIF25	168185614	0.000000	0.05858	0.000000	0.03702	0.026000	0.11368	-0.340000	0.07821	-0.443000	0.07180	-0.474000	0.04947	GCA	G|0.927;A|0.073	0.073	strong		0.672	KIF25-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362509.1		
IDUA	3425	hgsc.bcm.edu	37	4	994414	994414	+	Missense_Mutation	SNP	G	G	A	rs3755955	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	193	1	0.00518135		WXS	Illumina HiSeq	Phase_I	185	97	0.524324	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	
UMODL1	89766	hgsc.bcm.edu	37	21	43510514	43510514	+	Silent	SNP	C	C	G	rs2839464	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:43510514C>G	ENST00000408910.2	+	6	897	c.897C>G	c.(895-897)gcC>gcG	p.A299A	UMODL1_ENST00000400427.1_Silent_p.A227A|UMODL1_ENST00000400424.2_Silent_p.A227A|UMODL1_ENST00000408989.2_Silent_p.A299A	NM_001004416.2	NP_001004416	Q5DID0	UROL1_HUMAN	uromodulin-like 1	299	EGF-like 1; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				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						AAGCTCCAGCCACGTCTCCAC	0.547													C|||	1429	0.285343	0.4576	0.2046	5008	,	,		21305	0.1022		0.2833	False		,,,				2504	0.3006				p.A299A	Pancreas(122;680 807 13940 14411 22888 25505 31742 36028 36332 38435)	Atlas-SNP	.											.	UMODL1	186	.	0			c.C897G						PASS	.	C	,,,	1795,2383		420,955,714	94.0	98.0	96.0		897,681,681,897	-2.3	0.0	21	dbSNP_100	96	2455,5957		363,1729,2114	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	UMODL1	NM_001004416.2,NM_001199527.1,NM_001199528.2,NM_173568.3	,,,	783,2684,2828	GG,GC,CC		29.1845,42.9631,33.7569	,,,	299/1319,227/1375,227/1247,299/1447	43510514	4250,8340	2089	4206	6295	SO:0001819	synonymous_variant	89766	exon6			TCCAGCCACGTCT		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.897C>G	21.37:g.43510514C>G		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	97	50	0.515464	NM_173568	C9JCE6|Q5DIC9|Q6LA40|Q6LA41|Q8N216	Silent	SNP	ENST00000408910.2	37	CCDS42936.1	572	0.2619047619047619	228	0.4634146341463415	82	0.2265193370165746	64	0.11188811188811189	198	0.2612137203166227	C	2.076	-0.411831	0.04799	0.429631	0.291845	ENSG00000177398	ENST00000423139	.	.	.	3.8	-2.29	0.06805	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.47711	-0.9096	3	.	.	.	-0.6178	0.6453	0.00817	0.1709:0.335:0.1678:0.3264	rs2839464;rs58566425;rs2839464	.	.	.	R	72	.	.	P	+	2	0	UMODL1	42383583	0.000000	0.05858	0.000000	0.03702	0.065000	0.16274	-0.303000	0.08210	-0.242000	0.09667	0.313000	0.20887	CCA	C|0.733;G|0.267	0.267	strong		0.547	UMODL1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195292.2		
BTN3A1	11119	hgsc.bcm.edu	37	6	26409890	26409890	+	Missense_Mutation	SNP	G	G	C	rs41266839	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:26409890G>C	ENST00000289361.6	+	5	1213	c.845G>C	c.(844-846)aGa>aCa	p.R282T	BTN3A1_ENST00000476549.2_Missense_Mutation_p.R282T|BTN3A1_ENST00000414912.2_Missense_Mutation_p.R230T|BTN3A1_ENST00000425234.2_Missense_Mutation_p.R282T	NM_001145008.1|NM_001145009.1|NM_007048.5	NP_001138480.1|NP_001138481.1|NP_008979.3	O00481	BT3A1_HUMAN	butyrophilin, subfamily 3, member A1	282			R -> T (in dbSNP:rs41266839). {ECO:0000269|PubMed:14702039}.		activated T cell proliferation (GO:0050798)|cytokine secretion (GO:0050663)|interferon-gamma secretion (GO:0072643)|T cell receptor signaling pathway (GO:0050852)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(5)|kidney(3)|large_intestine(6)|lung(8)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	28						ACTCAGTTCAGAAAGAAAAAG	0.512													G|||	91	0.0181709	0.003	0.0288	5008	,	,		18500	0.0		0.0666	False		,,,				2504	0.0				p.R282T		Atlas-SNP	.											.	BTN3A1	80	.	0			c.G845C						PASS	.	G	THR/ARG,THR/ARG,THR/ARG,THR/ARG	79,4327		1,77,2125	106.0	118.0	114.0		689,845,845,845	-1.3	0.0	6	dbSNP_127	114	701,7899		29,643,3628	yes	missense,missense,missense,missense	BTN3A1	NM_001145008.1,NM_001145009.1,NM_007048.5,NM_194441.2	71,71,71,71	30,720,5753	CC,CG,GG		8.1512,1.793,5.9972	benign,benign,benign,benign	230/462,282/379,282/514,282/353	26409890	780,12226	2203	4300	6503	SO:0001583	missense	11119	exon5			AGTTCAGAAAGAA	U90552	CCDS4608.1, CCDS4609.1, CCDS47388.1, CCDS47389.1	6p22.1	2014-01-14			ENSG00000026950	ENSG00000026950		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Butyrophilins"""	1138	protein-coding gene	gene with protein product		613593				9149941	Standard	NM_007048		Approved	BT3.1, BTF5, CD277, BTN3.1	uc003nhv.3	O00481	OTTHUMG00000014449	ENST00000289361.6:c.845G>C	6.37:g.26409890G>C	ENSP00000289361:p.Arg282Thr	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	26	8	0.307692	NM_007048	A2A278|A8K2C8|B4DIQ1|B4DRM2|E9PGB4|E9PHG8|Q0P515|Q147X5|Q53F15|Q99420|Q9HCY1	Missense_Mutation	SNP	ENST00000289361.6	37	CCDS4608.1	69	0.03159340659340659	4	0.008130081300813009	9	0.024861878453038673	0	0.0	56	0.07387862796833773	.	2.133	-0.398534	0.04865	0.01793	0.081512	ENSG00000026950	ENST00000476549;ENST00000289361;ENST00000425234;ENST00000414912	T;T;T;T	0.46819	3.92;1.2;3.93;0.86	1.06	-1.33	0.09172	.	.	.	.	.	T	0.12944	0.0314	L	0.53249	1.67	0.09310	N	1	P;B;B;B	0.35328	0.495;0.008;0.0;0.0	B;B;B;B	0.25987	0.065;0.007;0.002;0.001	T	0.13415	-1.0510	9	0.27082	T	0.32	.	2.4299	0.04469	0.2529:0.3251:0.422:0.0	rs41266839	230;282;282;282	E9PGB4;O00481-3;O00481-2;O00481	.;.;.;BT3A1_HUMAN	T	282;282;282;230	ENSP00000420010:R282T;ENSP00000289361:R282T;ENSP00000396684:R282T;ENSP00000406667:R230T	ENSP00000289361:R282T	R	+	2	0	BTN3A1	26517869	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-4.252000	0.00266	-0.510000	0.06523	-0.199000	0.12753	AGA	G|0.951;C|0.049	0.049	strong		0.512	BTN3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040112.3		
MUC4	4585	hgsc.bcm.edu	37	3	195511358	195511358	+	Missense_Mutation	SNP	C	C	G	rs77614482	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195511358C>G	ENST00000463781.3	-	2	7552	c.7093G>C	c.(7093-7095)Gac>Cac	p.D2365H	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.D2365H	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)		GGGGTGGTGTCACCTGTGGAT	0.587																																					p.D2365H		Atlas-SNP	.											.	MUC4	1505	.	0			c.G7093C						PASS	.						26.0	24.0	24.0					3																	195511358		689	1585	2274	SO:0001583	missense	4585	exon2			TGGTGTCACCTGT	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.7093G>C	3.37:g.195511358C>G	ENSP00000417498:p.Asp2365His	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	69	8	0.115942	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	C	2.131	-0.399179	0.04865	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.45668	0.89;0.99	.	.	.	.	.	.	.	.	T	0.18425	0.0442	N	0.19112	0.55	0.09310	N	1	B	0.31077	0.307	B	0.15870	0.014	T	0.13098	-1.0522	7	.	.	.	.	2.1447	0.03784	0.0:0.3304:0.3444:0.3251	.	2365	E7ESK3	.	H	2365	ENSP00000417498:D2365H;ENSP00000420243:D2365H	.	D	-	1	0	MUC4	196995753	0.000000	0.05858	0.002000	0.10522	0.113000	0.19764	-2.917000	0.00695	-0.417000	0.07461	0.064000	0.15345	GAC	C|0.991;G|0.009	0.009	weak		0.587	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
CLCF1	23529	hgsc.bcm.edu	37	11	67132804	67132804	+	Missense_Mutation	SNP	G	G	A	rs78755659	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:67132804G>A	ENST00000312438.7	-	3	678	c.481C>T	c.(481-483)Ccg>Tcg	p.P161S	CLCF1_ENST00000528474.1_Missense_Mutation_p.P151S|RN7SKP239_ENST00000364814.1_RNA|AP003419.11_ENST00000543494.1_RNA|CLCF1_ENST00000533438.1_Missense_Mutation_p.P151S	NM_013246.2	NP_037378.1	Q9UBD9	CLCF1_HUMAN	cardiotrophin-like cytokine factor 1	161					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)			CCAGGCAGCGGCTGGGGCAGT	0.657													g|||	64	0.0127796	0.0	0.0058	5008	,	,		17140	0.0		0.0179	False		,,,				2504	0.0429				p.P161S		Atlas-SNP	.											.	CLCF1	15	.	0			c.C481T						PASS	.		SER/PRO,SER/PRO	9,4389		0,9,2190	20.0	21.0	21.0		451,481	4.3	1.0	11	dbSNP_131	21	91,8483		1,89,4197	yes	missense,missense	CLCF1	NM_001166212.1,NM_013246.2	74,74	1,98,6387	AA,AG,GG		1.0613,0.2046,0.7709	benign,benign	151/216,161/226	67132804	100,12872	2199	4287	6486	SO:0001583	missense	23529	exon3			GCAGCGGCTGGGG	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.481C>T	11.37:g.67132804G>A	ENSP00000309338:p.Pro161Ser	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	81	20	0.246914	NM_013246	B4DNT4|Q6NZA4	Missense_Mutation	SNP	ENST00000312438.7	37	CCDS31617.1	18	0.008241758241758242	0	0.0	2	0.0055248618784530384	0	0.0	16	0.021108179419525065	g	11.26	1.587561	0.28268	0.002046	0.010613	ENSG00000175505	ENST00000312438;ENST00000533438;ENST00000528474	T;T;T	0.75260	-0.92;-0.92;-0.92	4.27	4.27	0.50696	Four-helical cytokine-like, core (1);Four-helical cytokine, core (1);	0.000000	0.64402	D	0.000001	T	0.58409	0.2120	L	0.29908	0.895	0.30105	N	0.807084	P	0.45212	0.853	P	0.52109	0.69	T	0.68981	-0.5266	10	0.87932	D	0	-7.0213	13.0463	0.58928	0.0:0.1625:0.8375:0.0	.	161	Q9UBD9	CLCF1_HUMAN	S	161;151;151	ENSP00000309338:P161S;ENSP00000434122:P151S;ENSP00000432553:P151S	ENSP00000309338:P161S	P	-	1	0	CLCF1	66889380	1.000000	0.71417	1.000000	0.80357	0.907000	0.53573	3.795000	0.55499	2.320000	0.78422	0.556000	0.70494	CCG	G|0.992;A|0.008	0.008	strong		0.657	CLCF1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395478.1	NM_013246	
ST3GAL1	6482	hgsc.bcm.edu	37	8	134488007	134488007	+	Silent	SNP	G	G	A	rs2230542	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:134488007G>A	ENST00000319914.5	-	4	1288	c.261C>T	c.(259-261)acC>acT	p.T87T	ST3GAL1_ENST00000522652.1_Silent_p.T87T|ST3GAL1_ENST00000521180.1_Silent_p.T87T|ST3GAL1_ENST00000519435.1_5'Flank|ST3GAL1_ENST00000399640.2_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	132	0	0		WXS	Illumina HiSeq	Phase_I	80	15	0.1875	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	
KIF18A	81930	hgsc.bcm.edu	37	11	28045367	28045367	+	Silent	SNP	G	G	A	rs35440657	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:28045367G>A	ENST00000263181.6	-	16	2825	c.2535C>T	c.(2533-2535)gaC>gaT	p.D845D		NM_031217.3	NP_112494.3	Q8NI77	KI18A_HUMAN	kinesin family member 18A	845					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|metabolic process (GO:0008152)|microtubule depolymerization (GO:0007019)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic metaphase plate congression (GO:0007080)|protein transport (GO:0015031)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|kinetochore microtubule (GO:0005828)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)|ruffle (GO:0001726)	actin binding (GO:0003779)|ATP binding (GO:0005524)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|plus-end-directed microtubule motor activity (GO:0008574)|tubulin-dependent ATPase activity (GO:0070463)|ubiquitin binding (GO:0043130)	p.D845D(1)		breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(10)|ovary(3)|prostate(1)|skin(1)|urinary_tract(2)	36						CAGAATTTACGTCTGCAGTTA	0.318													G|||	13	0.00259585	0.0	0.0029	5008	,	,		17656	0.0		0.0089	False		,,,				2504	0.002				p.D845D		Atlas-SNP	.											KIF18A,caecum,carcinoma,0,1	KIF18A	92	1	1	Substitution - coding silent(1)	large_intestine(1)	c.C2535T						PASS	.	G		3,4399	6.2+/-15.9	0,3,2198	127.0	115.0	119.0		2535	-5.2	0.0	11	dbSNP_126	119	66,8532	40.3+/-97.0	0,66,4233	no	coding-synonymous	KIF18A	NM_031217.3		0,69,6431	AA,AG,GG		0.7676,0.0682,0.5308		845/899	28045367	69,12931	2201	4299	6500	SO:0001819	synonymous_variant	81930	exon16			ATTTACGTCTGCA	AL136819	CCDS7867.1	11p14.1	2014-06-12			ENSG00000121621	ENSG00000121621		"""Kinesins"""	29441	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 99"""	611271				11230166	Standard	NM_031217		Approved	DKFZP434G2226, PPP1R99	uc001msc.2	Q8NI77	OTTHUMG00000166195	ENST00000263181.6:c.2535C>T	11.37:g.28045367G>A		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	115	20	0.173913	NM_031217	Q4VPE3|Q86VS5|Q9H0F3	Silent	SNP	ENST00000263181.6	37	CCDS7867.1																																																																																			G|0.995;A|0.005	0.005	strong		0.318	KIF18A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388328.3	NM_031217	
HEG1	57493	hgsc.bcm.edu	37	3	124731485	124731485	+	Missense_Mutation	SNP	C	C	G	rs10804567	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	159	0	0		WXS	Illumina HiSeq	Phase_I	152	75	0.493421	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	
BMS1	9790	hgsc.bcm.edu	37	10	43281089	43281089	+	Silent	SNP	T	T	C	rs7074877	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:43281089T>C	ENST00000374518.5	+	3	399	c.336T>C	c.(334-336)acT>acC	p.T112T		NM_014753.3	NP_055568.3	Q14692	BMS1_HUMAN	BMS1 ribosome biogenesis factor	112	Bms1-type G.				ribosome assembly (GO:0042255)	nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(23)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	62						AGAAGTTGACTGAGATCAGAG	0.512													C|||	2810	0.561102	0.6293	0.4899	5008	,	,		15419	0.6359		0.4185	False		,,,				2504	0.589				p.T112T		Atlas-SNP	.											.	BMS1	132	.	0			c.T336C						PASS	.	C		2628,1778		783,1062,358	136.0	140.0	139.0		336	-7.2	0.8	10	dbSNP_116	139	3363,5237		651,2061,1588	no	coding-synonymous	BMS1	NM_014753.3		1434,3123,1946	CC,CT,TT		39.1047,40.3541,46.0634		112/1283	43281089	5991,7015	2203	4300	6503	SO:0001819	synonymous_variant	9790	exon3			GTTGACTGAGATC	BC043345	CCDS7199.1	10q11.21	2013-05-01	2013-05-01	2007-03-20	ENSG00000165733	ENSG00000165733			23505	protein-coding gene	gene with protein product		611448	"""BMS1-like, ribosome assembly protein (yeast)"", ""BMS1 homolog, ribosome assembly protein (yeast)"""	BMS1L		11779832	Standard	NM_014753		Approved	KIAA0187	uc001jaj.3	Q14692	OTTHUMG00000018020	ENST00000374518.5:c.336T>C	10.37:g.43281089T>C		Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	86	44	0.511628	NM_014753	Q5QPT5|Q86XJ9	Silent	SNP	ENST00000374518.5	37	CCDS7199.1																																																																																			T|0.503;C|0.497	0.497	strong		0.512	BMS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047690.2	NM_014753	
ANGPTL2	23452	hgsc.bcm.edu	37	9	129870763	129870763	+	Missense_Mutation	SNP	C	C	T	rs370920897		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:129870763C>T	ENST00000373425.3	-	2	865	c.248G>A	c.(247-249)cGa>cAa	p.R83Q	RALGPS1_ENST00000373436.1_Intron|RALGPS1_ENST00000373434.1_Intron|RALGPS1_ENST00000424082.2_Intron|RALGPS1_ENST00000259351.5_Intron|ANGPTL2_ENST00000373417.1_Intron|RALGPS1_ENST00000394022.3_Intron|ANGPTL2_ENST00000491991.1_5'Flank	NM_012098.2	NP_036230.1	Q9UKU9	ANGL2_HUMAN	angiopoietin-like 2	83					multicellular organismal development (GO:0007275)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	receptor binding (GO:0005102)			breast(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(4)|ovary(1)|urinary_tract(1)	18						CTTATGCACTCGGTTCTCCAG	0.592																																					p.R83Q		Atlas-SNP	.											ANGPTL2,colon,carcinoma,-1,1	ANGPTL2	46	1	0			c.G248A						PASS	.	C	,,,GLN/ARG,	1,4405	2.1+/-5.4	0,1,2202	63.0	53.0	56.0		,,,248,	4.9	1.0	9		56	0,8600		0,0,4300	no	intron,intron,intron,missense,intron	RALGPS1,ANGPTL2	NM_001190728.1,NM_001190729.1,NM_001190730.1,NM_012098.2,NM_014636.2	,,,43,	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	,,,probably-damaging,	,,,83/494,	129870763	1,13005	2203	4300	6503	SO:0001583	missense	23452	exon2			TGCACTCGGTTCT	AF125175	CCDS6868.1	9q34	2013-02-06			ENSG00000136859	ENSG00000136859		"""Fibrinogen C domain containing"""	490	protein-coding gene	gene with protein product		605001				10473614	Standard	NM_012098		Approved	ARP2, HARP	uc004bqr.1	Q9UKU9	OTTHUMG00000020695	ENST00000373425.3:c.248G>A	9.37:g.129870763C>T	ENSP00000362524:p.Arg83Gln	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	63	14	0.222222	NM_012098	Q5JT58|Q8NCH7	Missense_Mutation	SNP	ENST00000373425.3	37	CCDS6868.1	.	.	.	.	.	.	.	.	.	.	C	22.5	4.291664	0.80914	2.27E-4	0.0	ENSG00000136859	ENST00000373425	T	0.40225	1.04	4.87	4.87	0.63330	.	0.119965	0.52532	D	0.000062	T	0.47060	0.1425	M	0.70275	2.135	0.80722	D	1	D	0.53885	0.963	P	0.45660	0.489	T	0.47898	-0.9081	10	0.12103	T	0.63	.	18.0259	0.89269	0.0:1.0:0.0:0.0	.	83	Q9UKU9	ANGL2_HUMAN	Q	83	ENSP00000362524:R83Q	ENSP00000362524:R83Q	R	-	2	0	ANGPTL2	128910584	1.000000	0.71417	0.995000	0.50966	0.749000	0.42624	7.818000	0.86416	2.259000	0.74868	0.655000	0.94253	CGA	.	.	weak		0.592	ANGPTL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054129.1	NM_012098	
RRP1	8568	hgsc.bcm.edu	37	21	45220483	45220483	+	Missense_Mutation	SNP	A	A	G	rs915770	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:45220483A>G	ENST00000497547.1	+	10	1094	c.977A>G	c.(976-978)aAa>aGa	p.K326R	RRP1_ENST00000471909.1_3'UTR	NM_003683.5	NP_003674.1	P05386	RLA1_HUMAN	ribosomal RNA processing 1	0					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)	RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)	p.K326R(1)		central_nervous_system(1)|kidney(1)|lung(4)|stomach(2)	8				COAD - Colon adenocarcinoma(84;0.00753)|Colorectal(79;0.0157)|STAD - Stomach adenocarcinoma(101;0.171)		CGTCTCTACAAAGTGATCCGG	0.537													A|||	1310	0.261581	0.3366	0.3012	5008	,	,		19266	0.2292		0.1581	False		,,,				2504	0.272				p.K326R		Atlas-SNP	.											RRP1,NS,carcinoma,0,1	RRP1	23	1	1	Substitution - Missense(1)	stomach(1)	c.A977G						PASS	.	A	ARG/LYS	1270,2840		202,866,987	53.0	56.0	55.0		977	5.2	1.0	21	dbSNP_86	55	1478,6904		139,1200,2852	yes	missense	RRP1	NM_003683.5	26	341,2066,3839	GG,GA,AA		17.633,30.9002,21.9981	possibly-damaging	326/462	45220483	2748,9744	2055	4191	6246	SO:0001583	missense	8568	exon10			TCTACAAAGTGAT	U79775	CCDS42951.1	21q22.3	2013-07-02	2013-07-02		ENSG00000160214	ENSG00000160214			18785	protein-coding gene	gene with protein product	"""DNA segment on chromosome 21 (unique) 2056 expressed sequence"", ""Nnp1 homolog, nucleolar protein (Drosophila)"""	610653	"""ribosomal RNA processing 1 homolog (S. cerevisiae)"""			10830953, 10341208	Standard	NM_003683		Approved	NNP-1, Nop52, NOP52, RRP1A, D21S2056E	uc002zds.2	P56182	OTTHUMG00000086884	ENST00000497547.1:c.977A>G	21.37:g.45220483A>G	ENSP00000417464:p.Lys326Arg	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	128	45	0.351562	NM_003683	A6NIB2	Missense_Mutation	SNP	ENST00000497547.1	37	CCDS42951.1	500	0.22893772893772893	163	0.3313008130081301	86	0.23756906077348067	134	0.23426573426573427	117	0.15435356200527706	A	17.93	3.509174	0.64410	0.309002	0.17633	ENSG00000160214	ENST00000497547;ENST00000400387	T	0.01215	5.16	5.2	5.2	0.72013	.	0.469084	0.25256	N	0.031994	T	0.00012	0.0000	L	0.52823	1.66	0.23906	P	0.99650116	D;D	0.89917	1.0;0.999	D;D	0.83275	0.996;0.994	T	0.56751	-0.7927	9	0.87932	D	0	.	11.4934	0.50394	1.0:0.0:0.0:0.0	rs915770;rs58923119;rs915770	326;326	B4DZM3;P56182	.;RRP1_HUMAN	R	326	ENSP00000417464:K326R	ENSP00000383237:K326R	K	+	2	0	RRP1	44044911	0.998000	0.40836	1.000000	0.80357	0.979000	0.70002	1.606000	0.36826	1.964000	0.57103	0.533000	0.62120	AAA	A|0.767;G|0.233	0.233	strong		0.537	RRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195680.1	NM_003683	
TAS2R14	50840	hgsc.bcm.edu	37	12	11091693	11091693	+	Silent	SNP	T	T	A	rs7138535	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:11091693T>A	ENST00000537503.1	-	1	169	c.114A>T	c.(112-114)ggA>ggT	p.G38G	PRR4_ENST00000536668.1_Intron|TAS2R14_ENST00000381852.4_Intron	NM_023922.1	NP_076411.1	Q9NYV8	T2R14_HUMAN	taste receptor, type 2, member 14	38					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|G-protein coupled receptor signaling pathway (GO:0007186)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)|taste receptor activity (GO:0008527)			central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(3)|upper_aerodigestive_tract(1)	8						AGATCTTTCTTCCCTTGACCC	0.378													T|||	1117	0.223043	0.2337	0.2911	5008	,	,		20154	0.2073		0.2147	False		,,,				2504	0.1851				p.G38G		Atlas-SNP	.											.	TAS2R14	26	.	0			c.A114T						PASS	.	T		984,3422	364.6+/-317.1	116,752,1335	68.0	67.0	67.0		114	-1.9	0.0	12	dbSNP_116	67	2072,6528	352.1+/-328.5	259,1554,2487	no	coding-synonymous	TAS2R14	NM_023922.1		375,2306,3822	AA,AT,TT		24.093,22.3332,23.4968		38/318	11091693	3056,9950	2203	4300	6503	SO:0001819	synonymous_variant	50840	exon1			CTTTCTTCCCTTG	AF227138	CCDS8637.1	12p13	2012-08-22			ENSG00000212127	ENSG00000212127		"""Taste receptors / Type 2"", ""GPCR / Unclassified : Taste receptors"""	14920	protein-coding gene	gene with protein product		604790				10761934, 10766242	Standard	NM_023922		Approved	T2R14, TRB1	uc010shi.2	Q9NYV8	OTTHUMG00000162720	ENST00000537503.1:c.114A>T	12.37:g.11091693T>A		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	73	39	0.534247	NM_023922	Q645X3	Silent	SNP	ENST00000537503.1	37	CCDS8637.1																																																																																			T|0.766;A|0.234	0.234	strong		0.378	TAS2R14-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370194.4	NM_023922	
HERC3	8916	hgsc.bcm.edu	37	4	89625427	89625427	+	Missense_Mutation	SNP	G	G	C	rs1804080	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:89625427G>C	ENST00000402738.1	+	24	3075	c.2836G>C	c.(2836-2838)Gaa>Caa	p.E946Q	HERC3_ENST00000543130.1_Missense_Mutation_p.E390Q|HERC3_ENST00000264345.3_Missense_Mutation_p.E946Q	NM_001271602.1|NM_014606.1	NP_001258531.1|NP_055421.1	Q15034	HERC3_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase 3	946			E -> Q (in dbSNP:rs1804080).		protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasmic vesicle (GO:0031410)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(10)|lung(14)|prostate(2)|skin(2)	45				OV - Ovarian serous cystadenocarcinoma(123;0.000319)		GGAAGAACTGGAAGAGGTAAG	0.512													G|||	933	0.186302	0.1906	0.2017	5008	,	,		17767	0.2381		0.166	False		,,,				2504	0.137				p.E946Q		Atlas-SNP	.											.	HERC3	82	.	0			c.G2836C						PASS	.	G	GLN/GLU	851,3555	334.4+/-303.4	81,689,1433	150.0	147.0	148.0		2836	3.5	0.9	4	dbSNP_89	148	1331,7269	261.6+/-283.9	107,1117,3076	yes	missense	HERC3	NM_014606.1	29	188,1806,4509	CC,CG,GG		15.4767,19.3146,16.7769	probably-damaging	946/1051	89625427	2182,10824	2203	4300	6503	SO:0001583	missense	8916	exon24			GAACTGGAAGAGG	D25215	CCDS34028.1	4q21	2012-02-23	2012-02-23		ENSG00000138641	ENSG00000138641			4876	protein-coding gene	gene with protein product		605200	"""hect domain and RLD 3"""			10702688	Standard	NM_014606		Approved	KIAA0032	uc003hrw.2	Q15034	OTTHUMG00000150436	ENST00000402738.1:c.2836G>C	4.37:g.89625427G>C	ENSP00000385684:p.Glu946Gln	Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	126	52	0.412698	NM_014606	A8K1S5|Q8IXX3	Missense_Mutation	SNP	ENST00000402738.1	37	CCDS34028.1	421	0.19276556776556777	88	0.17886178861788618	67	0.1850828729281768	134	0.23426573426573427	132	0.1741424802110818	G	19.18	3.776833	0.70107	0.193146	0.154767	ENSG00000138641	ENST00000402738;ENST00000264345;ENST00000543130	T;T;T	0.57907	0.37;0.37;0.37	5.26	3.51	0.40186	HECT (4);	0.000000	0.85682	D	0.000000	T	0.00039	0.0001	L	0.41079	1.255	0.09310	P	0.99999808362	D	0.89917	1.0	D	0.97110	1.0	T	0.03684	-1.1013	9	0.39692	T	0.17	.	10.8765	0.46915	0.0704:0.1307:0.7989:0.0	rs1804080;rs3737486;rs52837068;rs3737486	946	Q15034	HERC3_HUMAN	Q	946;946;390	ENSP00000385684:E946Q;ENSP00000264345:E946Q;ENSP00000441703:E390Q	ENSP00000264345:E946Q	E	+	1	0	HERC3	89844450	1.000000	0.71417	0.873000	0.34254	0.932000	0.56968	6.588000	0.74076	0.763000	0.33175	0.655000	0.94253	GAA	G|0.801;C|0.199	0.199	strong		0.512	HERC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318081.2	NM_014606	
CGN	57530	hgsc.bcm.edu	37	1	151501841	151501841	+	Missense_Mutation	SNP	C	C	G	rs12044926	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:151501841C>G	ENST00000271636.7	+	11	2045	c.1912C>G	c.(1912-1914)Cag>Gag	p.Q638E	SNORA44_ENST00000517031.1_RNA	NM_020770.2	NP_065821.1	Q9P2M7	CING_HUMAN	cingulin	632	Glu-rich.				transforming growth factor beta receptor signaling pathway (GO:0007179)	cell junction (GO:0030054)|myosin complex (GO:0016459)|tight junction (GO:0005923)	actin binding (GO:0003779)|motor activity (GO:0003774)			NS(1)|central_nervous_system(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|liver(1)|lung(14)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	45	Ovarian(49;0.0273)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		LUSC - Lung squamous cell carcinoma(543;0.181)			GCTCCGGACACAGGAGGAGCT	0.592													C|||	504	0.100639	0.0272	0.0908	5008	,	,		17642	0.2063		0.0258	False		,,,				2504	0.1748				p.Q638E		Atlas-SNP	.											.	CGN	106	.	0			c.C1912G						PASS	.	C	GLU/GLN	122,4284	86.8+/-125.4	3,116,2084	39.0	43.0	42.0		1912	3.5	0.9	1	dbSNP_120	42	329,8271	108.0+/-168.7	11,307,3982	yes	missense	CGN	NM_020770.2	29	14,423,6066	GG,GC,CC		3.8256,2.769,3.4676	possibly-damaging	638/1204	151501841	451,12555	2203	4300	6503	SO:0001583	missense	57530	exon11			CGGACACAGGAGG	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.1912C>G	1.37:g.151501841C>G	ENSP00000271636:p.Gln638Glu	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	63	36	0.571429	NM_020770	A6H8L3|A7MD22|Q5T386|Q9NR25	Missense_Mutation	SNP	ENST00000271636.7	37	CCDS999.1	195	0.08928571428571429	10	0.02032520325203252	27	0.07458563535911603	133	0.23251748251748253	25	0.032981530343007916	C	11.36	1.614831	0.28712	0.02769	0.038256	ENSG00000143375	ENST00000271636	T	0.64618	-0.11	4.43	3.49	0.39957	.	0.340826	0.32608	N	0.005877	T	0.46151	0.1378	M	0.67953	2.075	0.35170	P	0.228557	P	0.43788	0.817	B	0.41764	0.366	T	0.50250	-0.8850	9	0.42905	T	0.14	-19.8897	10.9793	0.47483	0.187:0.813:0.0:0.0	rs12044926;rs12044926	632	Q9P2M7	CING_HUMAN	E	638	ENSP00000271636:Q638E	ENSP00000271636:Q638E	Q	+	1	0	CGN	149768465	0.968000	0.33430	0.914000	0.36105	0.013000	0.08279	2.324000	0.43831	1.182000	0.42928	0.655000	0.94253	CAG	C|0.943;G|0.057	0.057	strong		0.592	CGN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034900.3	NM_020770	
PLEKHA8	84725	hgsc.bcm.edu	37	7	30113706	30113706	+	Silent	SNP	A	A	G	rs11977829	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:30113706A>G	ENST00000449726.1	+	13	1670	c.1320A>G	c.(1318-1320)acA>acG	p.T440T	PLEKHA8_ENST00000258679.7_Intron|PLEKHA8_ENST00000396259.1_Intron|AC007285.7_ENST00000433088.1_RNA|PLEKHA8_ENST00000396257.2_Silent_p.T440T	NM_001197027.1	NP_001183956.1	Q96JA3	PKHA8_HUMAN	pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 8	440	Glycolipid transfer protein homology domain.				ER to Golgi ceramide transport (GO:0035621)|lipid transport (GO:0006869)|protein transport (GO:0015031)	membrane (GO:0016020)|trans-Golgi network (GO:0005802)	ceramide binding (GO:0097001)|glycolipid binding (GO:0051861)|glycolipid transporter activity (GO:0017089)|phosphatidylinositol-4-phosphate binding (GO:0070273)			breast(4)|large_intestine(3)|lung(8)|ovary(1)|prostate(1)	17						ATGGTAAAACATTGCGGCAAC	0.378													G|||	1244	0.248403	0.4228	0.2378	5008	,	,		18953	0.1141		0.2396	False		,,,				2504	0.1677				p.T440T		Atlas-SNP	.											PLEKHA8_ENST00000449726,NS,carcinoma,0,2	PLEKHA8	68	2	0			c.A1320G						scavenged	.	G	,,	722,1030		155,412,309	72.0	68.0	69.0		1320,1320,	-11.5	0.0	7	dbSNP_120	69	942,3040		107,728,1156	no	coding-synonymous,coding-synonymous,intron	PLEKHA8	NM_001197026.1,NM_001197027.1,NM_032639.3	,,	262,1140,1465	GG,GA,AA		23.6565,41.21,29.0199	,,	440/520,440/460,	30113706	1664,4070	876	1991	2867	SO:0001819	synonymous_variant	84725	exon13			TAAAACATTGCGG	BC053990	CCDS5424.1, CCDS56473.1, CCDS75574.1	7p21-p11.2	2013-01-10			ENSG00000106086	ENSG00000106086		"""Pleckstrin homology (PH) domain containing"""	30037	protein-coding gene	gene with protein product		608639				11001876	Standard	NM_001197027		Approved	FAPP2, MGC3358	uc003taq.3	Q96JA3	OTTHUMG00000097751	ENST00000449726.1:c.1320A>G	7.37:g.30113706A>G		Somatic	329	1	0.00303951		WXS	Illumina HiSeq	Phase_I	261	64	0.245211	NM_001197027	B4DH00|Q7Z5V8|Q9BU78|Q9H274|Q9H8Z7	Silent	SNP	ENST00000449726.1	37	CCDS56473.1																																																																																			A|0.748;G|0.252	0.252	strong		0.378	PLEKHA8-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_032639	
IQUB	154865	hgsc.bcm.edu	37	7	123152019	123152019	+	Missense_Mutation	SNP	C	C	T	rs10255061	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:123152019C>T	ENST00000466202.1	-	2	952	c.376G>A	c.(376-378)Gtg>Atg	p.V126M	IQUB_ENST00000488987.1_Intron|IQUB_ENST00000434450.1_Missense_Mutation_p.V126M|IQUB_ENST00000324698.6_Missense_Mutation_p.V126M	NM_001282855.1	NP_001269784.1	Q8NA54	IQUB_HUMAN	IQ motif and ubiquitin domain containing	126			V -> M (in dbSNP:rs10255061). {ECO:0000269|PubMed:15489334}.		cilium morphogenesis (GO:0060271)|smoothened signaling pathway (GO:0007224)	acrosomal vesicle (GO:0001669)|motile cilium (GO:0031514)		p.V126M(1)		breast(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(18)|ovary(3)|prostate(2)|stomach(3)|upper_aerodigestive_tract(1)	45						GAATCTTCCACTGATTCTTGC	0.353													T|||	1342	0.267971	0.2194	0.2637	5008	,	,		19187	0.369		0.2863	False		,,,				2504	0.2137				p.V126M		Atlas-SNP	.											IQUB,NS,adenoma,0,2	IQUB	117	2	1	Substitution - Missense(1)	stomach(1)	c.G376A						PASS	.	T	MET/VAL	1048,3356	723.4+/-409.4	131,786,1285	64.0	64.0	64.0		376	-4.5	0.0	7	dbSNP_119	64	2296,6304	703.7+/-405.4	298,1700,2302	yes	missense	IQUB	NM_178827.4	21	429,2486,3587	TT,TC,CC		26.6977,23.7965,25.7152	benign	126/792	123152019	3344,9660	2202	4300	6502	SO:0001583	missense	154865	exon2			CTTCCACTGATTC	AK093153	CCDS5787.1	7q31.32	2010-03-19			ENSG00000164675	ENSG00000164675			21995	protein-coding gene	gene with protein product							Standard	NM_178827		Approved	FLJ35834	uc003vko.3	Q8NA54	OTTHUMG00000157347	ENST00000466202.1:c.376G>A	7.37:g.123152019C>T	ENSP00000417769:p.Val126Met	Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	87	36	0.413793	NM_178827	A4D0X0|Q49AL6|Q4G189|Q5BJD9|Q6NUH6|Q8N9Y2	Missense_Mutation	SNP	ENST00000466202.1	37	CCDS5787.1	634	0.2902930402930403	104	0.21138211382113822	109	0.3011049723756906	202	0.3531468531468531	219	0.28891820580474936	T	7.972	0.749246	0.15710	0.237965	0.266977	ENSG00000164675	ENST00000466202;ENST00000324698;ENST00000434450	T;T;T	0.42513	0.97;0.97;0.97	5.41	-4.47	0.03525	.	1.448530	0.04416	N	0.366878	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B;B;B	0.09022	0.0;0.002;0.001	B;B;B	0.08055	0.001;0.003;0.001	T	0.33752	-0.9856	9	0.14252	T	0.57	.	11.0952	0.48141	0.1213:0.676:0.0:0.2027	rs10255061;rs56649278;rs59485939;rs10255061	126;126;126	A1A4Z1;Q8NA54-2;Q8NA54	.;.;IQUB_HUMAN	M	126	ENSP00000417769:V126M;ENSP00000324882:V126M;ENSP00000388498:V126M	ENSP00000324882:V126M	V	-	1	0	IQUB	122939255	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.742000	0.01835	-1.087000	0.03081	-0.254000	0.11334	GTG	C|0.741;T|0.259	0.259	strong		0.353	IQUB-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348529.1	NM_178827	
SPNS1	83985	hgsc.bcm.edu	37	16	28995211	28995211	+	Silent	SNP	C	C	T	rs113165798	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:28995211C>T	ENST00000311008.11	+	11	1802	c.1425C>T	c.(1423-1425)ggC>ggT	p.G475G	LAT_ENST00000564277.1_5'Flank|SPNS1_ENST00000323081.8_Silent_p.G402G|RP11-264B17.3_ENST00000569969.1_RNA|LAT_ENST00000395456.2_5'Flank|LAT_ENST00000454369.2_5'Flank|LAT_ENST00000360872.5_5'Flank|SPNS1_ENST00000565975.1_Silent_p.G520G|LAT_ENST00000395461.3_5'Flank|LAT_ENST00000566177.1_5'Flank|LAT_ENST00000354453.4_5'Flank|SPNS1_ENST00000334536.8_Silent_p.G423G|SPNS1_ENST00000352260.7_Silent_p.G401G	NM_032038.2	NP_114427.1	Q9H2V7	SPNS1_HUMAN	spinster homolog 1 (Drosophila)	475					lipid transport (GO:0006869)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|mitochondrial inner membrane (GO:0005743)				cervix(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(9)|prostate(1)|skin(2)|urinary_tract(1)	21						CACTGGGCGGCGCAGCCTTCC	0.672													C|||	9	0.00179712	0.0	0.0014	5008	,	,		18700	0.0		0.008	False		,,,				2504	0.0				p.G475G		Atlas-SNP	.											.	SPNS1	47	.	0			c.C1425T						PASS	.	C	,,,,	7,4387	12.9+/-30.5	0,7,2190	48.0	51.0	50.0		1425,1203,1206,1269,1425	-9.2	0.1	16	dbSNP_132	50	74,8526	44.0+/-102.2	1,72,4227	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SPNS1	NM_001142448.1,NM_001142449.1,NM_001142450.1,NM_001142451.1,NM_032038.2	,,,,	1,79,6417	TT,TC,CC		0.8605,0.1593,0.6234	,,,,	475/529,401/455,402/456,423/477,475/529	28995211	81,12913	2197	4300	6497	SO:0001819	synonymous_variant	83985	exon12			GGGCGGCGCAGCC	BC006156	CCDS10646.1, CCDS45452.1, CCDS45453.1, CCDS45454.1	16p11.2	2007-04-12			ENSG00000169682	ENSG00000169682			30621	protein-coding gene	gene with protein product		612583				11340170, 12815463	Standard	NM_032038		Approved	HSpin1, nrs, SPINL, PP2030, SPIN1, LAT	uc010vdi.1	Q9H2V7	OTTHUMG00000131762	ENST00000311008.11:c.1425C>T	16.37:g.28995211C>T		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	65	33	0.507692	NM_001142448	B5MDM9|Q6P182|Q71RB5|Q7L541|Q86VU7|Q8N953|Q8TCS5|Q9BRN5	Silent	SNP	ENST00000311008.11	37	CCDS10646.1																																																																																			C|0.995;T|0.005	0.005	strong		0.672	SPNS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254690.2	NM_032038	
MYO1F	4542	hgsc.bcm.edu	37	19	8616999	8616999	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:8616999C>T	ENST00000338257.8	-	7	821	c.554G>A	c.(553-555)gGc>gAc	p.G185D	AC092316.1_ENST00000598703.1_RNA	NM_012335.3	NP_036467.2	O00160	MYO1F_HUMAN	myosin IF	185	Myosin motor.				defense response to Gram-positive bacterium (GO:0050830)|negative regulation of cell adhesion (GO:0007162)|neutrophil degranulation (GO:0043312)|positive regulation of cell migration (GO:0030335)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of innate immune response (GO:0045088)	cortical actin cytoskeleton (GO:0030864)|filamentous actin (GO:0031941)|unconventional myosin complex (GO:0016461)	actin binding (GO:0003779)|ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(7)|lung(13)|ovary(3)|prostate(3)|skin(3)|urinary_tract(1)	42						GGAGATCTTGCCCCCATCTGG	0.562																																					p.G185D		Atlas-SNP	.											.	MYO1F	128	.	0			c.G554A						PASS	.						100.0	102.0	102.0					19																	8616999		1977	4203	6180	SO:0001583	missense	4542	exon7			ATCTTGCCCCCAT	X98411	CCDS42494.1	19p13.3-p13.2	2011-09-27			ENSG00000142347	ENSG00000142347		"""Myosins / Myosin superfamily : Class I"""	7600	protein-coding gene	gene with protein product		601480				9119401, 8884266	Standard	NM_012335		Approved		uc002mkg.3	O00160	OTTHUMG00000156005	ENST00000338257.8:c.554G>A	19.37:g.8616999C>T	ENSP00000344871:p.Gly185Asp	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	102	23	0.22549	NM_012335	Q8WWN7	Missense_Mutation	SNP	ENST00000338257.8	37	CCDS42494.1	.	.	.	.	.	.	.	.	.	.	C	22.6	4.316297	0.81469	.	.	ENSG00000142347	ENST00000305795;ENST00000338257	D	0.95885	-3.84	3.93	3.93	0.45458	Myosin head, motor domain (2);	0.064498	0.64402	D	0.000010	D	0.98695	0.9562	H	0.98721	4.31	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	D	0.99301	1.0901	10	0.87932	D	0	.	15.1284	0.72500	0.0:1.0:0.0:0.0	.	185;185;185	B4DVP3;B0I1T1;O00160	.;.;MYO1F_HUMAN	D	230;185	ENSP00000344871:G185D	ENSP00000304899:G230D	G	-	2	0	MYO1F	8522999	1.000000	0.71417	0.986000	0.45419	0.850000	0.48378	7.651000	0.83577	2.048000	0.60808	0.460000	0.39030	GGC	.	.	none		0.562	MYO1F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342716.2		
PDE1C	5137	hgsc.bcm.edu	37	7	31855577	31855577	+	Missense_Mutation	SNP	A	A	C	rs2230175	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:31855577A>C	ENST00000396191.1	-	15	2229	c.1774T>G	c.(1774-1776)Tcc>Gcc	p.S592A	PDE1C_ENST00000321453.7_Missense_Mutation_p.S592A|PDE1C_ENST00000396193.1_Missense_Mutation_p.S652A|PDE1C_ENST00000396184.3_Missense_Mutation_p.S592A|PDE1C_ENST00000479980.1_5'UTR|PDE1C_ENST00000396182.2_Missense_Mutation_p.S592A	NM_001191057.1	NP_001177986.1	Q14123	PDE1C_HUMAN	phosphodiesterase 1C, calmodulin-dependent 70kDa	592					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)			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)	TCGGCTTTGGAGTTTTTCCCA	0.453													A|||	7	0.00139776	0.0	0.0	5008	,	,		22053	0.0		0.007	False		,,,				2504	0.0				p.S652A		Atlas-SNP	.											.	PDE1C	465	.	0			c.T1954G						PASS	.						236.0	229.0	231.0					7																	31855577		2203	4300	6503	SO:0001583	missense	5137	exon16			CTTTGGAGTTTTT	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.1774T>G	7.37:g.31855577A>C	ENSP00000379494:p.Ser592Ala	Somatic	267	0	0		WXS	Illumina HiSeq	Phase_I	207	52	0.251208	NM_001191058	B3KPC6|E9PE92|Q14124|Q8NB10	Missense_Mutation	SNP	ENST00000396191.1	37	CCDS55099.1	.	.	.	.	.	.	.	.	.	.	A	4.602	0.111870	0.08831	.	.	ENSG00000154678	ENST00000396193;ENST00000396191;ENST00000321453;ENST00000396184;ENST00000396182	T;T;T;T;T	0.71817	-0.6;-0.59;-0.59;-0.56;-0.56	5.34	-3.43	0.04810	.	1.780330	0.02694	N	0.110987	T	0.53818	0.1820	N	0.19112	0.55	0.18873	N	0.999987	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.38415	-0.9662	10	0.38643	T	0.18	.	7.2612	0.26203	0.3059:0.2468:0.4473:0.0	.	592;652;592	Q14123-2;E9PE92;Q14123	.;.;PDE1C_HUMAN	A	652;592;592;592;592	ENSP00000379496:S652A;ENSP00000379494:S592A;ENSP00000318105:S592A;ENSP00000379487:S592A;ENSP00000379485:S592A	ENSP00000318105:S592A	S	-	1	0	PDE1C	31822102	0.011000	0.17503	0.438000	0.26821	0.046000	0.14306	-0.007000	0.12810	-0.794000	0.04468	-0.290000	0.09829	TCC	A|0.990;C|0.010	0.010	strong		0.453	PDE1C-006	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000328458.1		
RFX6	222546	hgsc.bcm.edu	37	6	117246719	117246719	+	Silent	SNP	C	C	T	rs4946206	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:117246719C>T	ENST00000332958.2	+	16	1798	c.1782C>T	c.(1780-1782)caC>caT	p.H594H		NM_173560.3	NP_775831.2	Q8HWS3	RFX6_HUMAN	regulatory factor X, 6	594					endocrine pancreas development (GO:0031018)|glucose homeostasis (GO:0042593)|pancreatic A cell differentiation (GO:0003310)|pancreatic D cell differentiation (GO:0003311)|pancreatic epsilon cell differentiation (GO:0090104)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of insulin secretion (GO:0050796)|transcription, DNA-templated (GO:0006351)|type B pancreatic cell differentiation (GO:0003309)	nucleus (GO:0005634)	transcription regulatory region DNA binding (GO:0044212)			cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(29)|ovary(1)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	59						ATGAAAGCCACGTGGAGACAA	0.542													T|||	1707	0.340855	0.2958	0.2911	5008	,	,		17024	0.4236		0.2286	False		,,,				2504	0.4673				p.H594H		Atlas-SNP	.											.	RFX6	141	.	0			c.C1782T						PASS	.	T		1252,3154	704.5+/-407.1	187,878,1138	119.0	112.0	114.0		1782	-11.9	0.1	6	dbSNP_111	114	1530,7070	747.0+/-407.3	143,1244,2913	no	coding-synonymous	RFX6	NM_173560.3		330,2122,4051	TT,TC,CC		17.7907,28.4158,21.3901		594/929	117246719	2782,10224	2203	4300	6503	SO:0001819	synonymous_variant	222546	exon16			AAGCCACGTGGAG	BC039248	CCDS5113.1	6q22.31	2008-08-04	2008-08-04	2008-08-04	ENSG00000185002	ENSG00000185002			21478	protein-coding gene	gene with protein product		612659	"""regulatory factor X domain containing 1"""	RFXDC1			Standard	NM_173560		Approved	MGC33442, dJ955L16.1	uc003pxm.3	Q8HWS3	OTTHUMG00000015449	ENST00000332958.2:c.1782C>T	6.37:g.117246719C>T		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	93	35	0.376344	NM_173560	Q5T6B3	Silent	SNP	ENST00000332958.2	37	CCDS5113.1																																																																																			C|0.744;T|0.256	0.256	strong		0.542	RFX6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041970.2	NM_173560	
GOLGB1	2804	hgsc.bcm.edu	37	3	121413362	121413362	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:121413362T>C	ENST00000340645.5	-	13	6118	c.5993A>G	c.(5992-5994)cAg>cGg	p.Q1998R	GOLGB1_ENST00000393667.3_Missense_Mutation_p.Q2003R	NM_001256487.1|NM_001256488.1|NM_004487.4	NP_001243416.1|NP_001243417.1|NP_004478.3	Q14789	GOGB1_HUMAN	golgin B1	1998					Golgi organization (GO:0007030)	cis-Golgi network (GO:0005801)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(2)|cervix(2)|endometrium(12)|kidney(3)|large_intestine(26)|liver(2)|lung(36)|ovary(7)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(13)	119				GBM - Glioblastoma multiforme(114;0.0989)		GGGTTCTTTCTGAGCACCTTG	0.378																																					p.Q2003R		Atlas-SNP	.											.	GOLGB1	319	.	0			c.A6008G						PASS	.						166.0	176.0	172.0					3																	121413362		2203	4300	6503	SO:0001583	missense	2804	exon13			TCTTTCTGAGCAC	X75304	CCDS3004.1, CCDS58847.1, CCDS74989.1	3q13	2010-02-12	2010-02-12	2007-07-27	ENSG00000173230	ENSG00000173230			4429	protein-coding gene	gene with protein product	"""macrogolgin"", ""golgi integral membrane protein 1"""	602500	"""golgi autoantigen, golgin subfamily b, macrogolgin (with transmembrane signal), 1"", ""golgin B1, golgi integral membrane protein"""			7691276, 15004235	Standard	NM_001256486		Approved	GCP, GCP372, giantin, GOLIM1	uc010hrc.4	Q14789	OTTHUMG00000159411	ENST00000340645.5:c.5993A>G	3.37:g.121413362T>C	ENSP00000341848:p.Gln1998Arg	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	87	41	0.471264	NM_001256486	B2ZZ91|D3DN92|E7EP74|Q14398	Missense_Mutation	SNP	ENST00000340645.5	37	CCDS3004.1	.	.	.	.	.	.	.	.	.	.	T	13.84	2.356523	0.41700	.	.	ENSG00000173230	ENST00000340645;ENST00000393667	T;T	0.25912	1.81;1.77	5.21	5.21	0.72293	.	0.130327	0.35525	N	0.003143	T	0.46444	0.1393	M	0.72894	2.215	0.45837	D	0.998705	D;D;D;D	0.76494	0.996;0.996;0.959;0.999	D;D;P;D	0.75484	0.922;0.986;0.564;0.953	T	0.35549	-0.9784	10	0.17832	T	0.49	.	13.0741	0.59077	0.0:0.0:0.0:1.0	.	1923;2003;2003;1998	F1T0J2;E7EP74;B2ZZ91;Q14789	.;.;.;GOGB1_HUMAN	R	1998;2003	ENSP00000341848:Q1998R;ENSP00000377275:Q2003R	ENSP00000341848:Q1998R	Q	-	2	0	GOLGB1	122896052	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.173000	0.50839	2.174000	0.68829	0.533000	0.62120	CAG	.	.	none		0.378	GOLGB1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000355159.1	NM_004487	
SHISA9	729993	hgsc.bcm.edu	37	16	13297254	13297254	+	Missense_Mutation	SNP	C	C	G	rs112510263	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:13297254C>G	ENST00000424107.3	+	3	1140	c.695C>G	c.(694-696)gCc>gGc	p.A232G	AC009134.1_ENST00000571939.1_RNA|SHISA9_ENST00000558583.1_Missense_Mutation_p.A273G			B4DS77	SHSA9_HUMAN	shisa family member 9	232					regulation of short-term neuronal synaptic plasticity (GO:0048172)	cell junction (GO:0030054)|dendritic spine membrane (GO:0032591)|ionotropic glutamate receptor complex (GO:0008328)|synapse (GO:0045202)				breast(1)|endometrium(2)|kidney(1)|lung(2)|prostate(1)|skin(2)	9						CTTCCAGATGCCACCCAGATG	0.547													C|||	43	0.00858626	0.0008	0.0202	5008	,	,		17596	0.0		0.0219	False		,,,				2504	0.0061				p.A232G		Atlas-SNP	.											.	SHISA9	33	.	0			c.C695G						PASS	.	C	GLY/ALA	6,1378		0,6,686	145.0	130.0	135.0		695	4.8	0.2	16	dbSNP_132	135	48,3134		1,46,1544	yes	missense	SHISA9	NM_001145204.2	60	1,52,2230	GG,GC,CC		1.5085,0.4335,1.1827	benign	232/425	13297254	54,4512	692	1591	2283	SO:0001583	missense	729993	exon3			CAGATGCCACCCA		CCDS45417.1, CCDS45418.1, CCDS45417.2, CCDS45418.2	16p13.12	2013-07-31	2013-07-31		ENSG00000237515	ENSG00000237515		"""Shisa homologs"""	37231	protein-coding gene	gene with protein product		613346	"""shisa homolog 9 (Xenopus laevis)"""				Standard	NM_001145205		Approved		uc010uyy.2	B4DS77	OTTHUMG00000154258	ENST00000424107.3:c.695C>G	16.37:g.13297254C>G	ENSP00000407958:p.Ala232Gly	Somatic	26	0	0		WXS	Illumina HiSeq	Phase_I	33	28	0.848485	NM_001145204	C9J314|C9JCE9	Missense_Mutation	SNP	ENST00000424107.3	37	CCDS45417.2	27	0.012362637362637362	2	0.0040650406504065045	7	0.019337016574585635	0	0.0	18	0.023746701846965697	C	16.16	3.045295	0.55110	0.004335	0.015085	ENSG00000237515	ENST00000424107	.	.	.	5.76	4.8	0.61643	.	.	.	.	.	T	0.20618	0.0496	N	0.22421	0.69	0.23981	N	0.996275	B	0.02656	0.0	B	0.08055	0.003	T	0.07829	-1.0752	8	0.21014	T	0.42	.	15.5168	0.75830	0.0:0.8612:0.1388:0.0	.	232	B4DS77	SHSA9_HUMAN	G	273	.	ENSP00000407958:A273G	A	+	2	0	SHISA9	13204755	0.018000	0.18449	0.159000	0.22649	0.716000	0.41182	2.651000	0.46674	1.411000	0.46957	0.551000	0.68910	GCC	C|0.987;G|0.013	0.013	strong		0.547	SHISA9-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334564.5	NM_001145204	
SPECC1	92521	hgsc.bcm.edu	37	17	20108184	20108184	+	Missense_Mutation	SNP	C	C	G	rs9908032	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:20108184C>G	ENST00000261503.5	+	4	873	c.822C>G	c.(820-822)agC>agG	p.S274R	SPECC1_ENST00000395530.2_Missense_Mutation_p.S193R|SPECC1_ENST00000395529.3_Missense_Mutation_p.S274R|SPECC1_ENST00000395527.4_Missense_Mutation_p.S274R|SPECC1_ENST00000395525.3_Missense_Mutation_p.S193R|SPECC1_ENST00000395522.2_Missense_Mutation_p.S193R|SPECC1_ENST00000472876.1_Intron|SPECC1_ENST00000584527.1_5'Flank|AC004702.2_ENST00000580225.1_lincRNA|SPECC1_ENST00000536879.1_Intron	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	76	0	0		WXS	Illumina HiSeq	Phase_I	58	31	0.534483	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	
ZNF169	169841	hgsc.bcm.edu	37	9	97055310	97055310	+	Missense_Mutation	SNP	C	C	T	rs1536690	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:97055310C>T	ENST00000395395.2	+	4	305	c.215C>T	c.(214-216)cCt>cTt	p.P72L	ZNF169_ENST00000481550.2_Missense_Mutation_p.P72L|ZNF169_ENST00000480716.1_Missense_Mutation_p.P72L|ZNF169_ENST00000340911.4_Missense_Mutation_p.P72L|ZNF169_ENST00000375354.4_Missense_Mutation_p.P72L	NM_194320.2	NP_919301.2	Q14929	ZN169_HUMAN	zinc finger protein 169	72	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.		P -> L (in dbSNP:rs1536690).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|kidney(2)|large_intestine(3)|lung(8)|ovary(2)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	24		Acute lymphoblastic leukemia(62;0.136)				GGCGACGAACCTTGGAGAGAG	0.507													c|||	919	0.183506	0.2526	0.1571	5008	,	,		21689	0.0565		0.1759	False		,,,				2504	0.2474				p.P72L		Atlas-SNP	.											ZNF169,NS,carcinoma,+1,1	ZNF169	60	1	0			c.C215T						PASS	.	C	LEU/PRO	1085,3321	387.2+/-326.4	135,815,1253	95.0	70.0	79.0		215	3.1	1.0	9	dbSNP_88	79	1578,7022	289.7+/-299.4	164,1250,2886	yes	missense	ZNF169	NM_194320.2	98	299,2065,4139	TT,TC,CC		18.3488,24.6255,20.4752	probably-damaging	72/604	97055310	2663,10343	2203	4300	6503	SO:0001583	missense	169841	exon4			ACGAACCTTGGAG	U28322	CCDS6709.2	9q22.32	2014-07-30			ENSG00000175787	ENSG00000175787		"""Zinc fingers, C2H2-type"", ""-"""	12957	protein-coding gene	gene with protein product		603404				9186526, 9071574	Standard	NM_001301275		Approved	MGC51961	uc004aum.1	Q14929	OTTHUMG00000020264	ENST00000395395.2:c.215C>T	9.37:g.97055310C>T	ENSP00000378792:p.Pro72Leu	Somatic	204	0	0		WXS	Illumina HiSeq	Phase_I	171	84	0.491228	NM_194320	A2AGP5|A8K127|Q6PI28	Missense_Mutation	SNP	ENST00000395395.2	37	CCDS6709.2	356	0.163003663003663	128	0.2601626016260163	58	0.16022099447513813	44	0.07692307692307693	126	0.1662269129287599	c	11.02	1.516372	0.27123	0.246255	0.183488	ENSG00000175787	ENST00000395395;ENST00000375354	T;T	0.09911	2.93;5.45	3.09	3.09	0.35607	Krueppel-associated box (2);	.	.	.	.	T	0.00012	0.0000	L	0.58510	1.815	0.22435	P	0.999106679	D;P;D	0.69078	0.997;0.908;0.97	P;P;P	0.60886	0.88;0.642;0.629	T	0.27606	-1.0069	8	0.87932	D	0	.	9.8219	0.40887	0.0:1.0:0.0:0.0	rs1536690;rs52799007;rs56559953;rs59771324;rs1536690	72;72;72	Q6PIG1;Q7Z761;Q14929	.;.;ZN169_HUMAN	L	72	ENSP00000378792:P72L;ENSP00000364503:P72L	ENSP00000364503:P72L	P	+	2	0	ZNF169	96095131	0.004000	0.15560	0.982000	0.44146	0.127000	0.20565	1.624000	0.37018	1.754000	0.51921	0.543000	0.68304	CCT	C|0.805;T|0.195	0.195	strong		0.507	ZNF169-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253714.1	NM_194320	
LRP3	4037	hgsc.bcm.edu	37	19	33696621	33696621	+	Silent	SNP	C	C	T	rs3745975	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:33696621C>T	ENST00000253193.7	+	5	1147	c.945C>T	c.(943-945)ggC>ggT	p.G315G	CTD-2540B15.13_ENST00000609744.1_RNA	NM_002333.3	NP_002324.2	O75074	LRP3_HUMAN	low density lipoprotein receptor-related protein 3	315	CUB 2. {ECO:0000255|PROSITE- ProRule:PRU00059}.				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)					AGGGCCTGGGCGAGCGCGGGG	0.701													C|||	252	0.0503195	0.0098	0.0764	5008	,	,		10950	0.12		0.0447	False		,,,				2504	0.0204				p.G315G		Atlas-SNP	.											.	LRP3	46	.	0			c.C945T						PASS	.	C		105,4263		1,103,2080	11.0	15.0	14.0		945	-1.7	1.0	19	dbSNP_107	14	454,8084		16,422,3831	no	coding-synonymous	LRP3	NM_002333.3		17,525,5911	TT,TC,CC		5.3174,2.4038,4.3313		315/771	33696621	559,12347	2184	4269	6453	SO:0001819	synonymous_variant	4037	exon5			CCTGGGCGAGCGC	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.945C>T	19.37:g.33696621C>T		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	54	37	0.685185	NM_002333	B3KQD6|B4DKF2	Silent	SNP	ENST00000253193.7	37	CCDS12430.1																																																																																			C|0.956;T|0.044	0.044	strong		0.701	LRP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450842.4		
MTUS1	57509	hgsc.bcm.edu	37	8	17611916	17611916	+	Silent	SNP	C	C	T	rs61740538	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:17611916C>T	ENST00000262102.6	-	2	1625	c.1401G>A	c.(1399-1401)tcG>tcA	p.S467S	MTUS1_ENST00000519263.1_Silent_p.S467S|MTUS1_ENST00000381862.3_Silent_p.S467S|MTUS1_ENST00000381869.3_Silent_p.S467S	NM_001001924.2	NP_001001924.1	Q9ULD2	MTUS1_HUMAN	microtubule associated tumor suppressor 1	467					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)		GTGCCTCCTTCGAGTCTGGTA	0.398													C|||	34	0.00678914	0.0015	0.0086	5008	,	,		19744	0.0		0.0229	False		,,,				2504	0.0031				p.S467S		Atlas-SNP	.											.	MTUS1	144	.	0			c.G1401A						PASS	.	C	,	9,3729		0,9,1860	154.0	146.0	149.0		1401,1401	2.8	0.0	8	dbSNP_129	149	219,8015		4,211,3902	no	coding-synonymous,coding-synonymous	MTUS1	NM_001001924.2,NM_001001925.2	,	4,220,5762	TT,TC,CC		2.6597,0.2408,1.9044	,	467/1271,467/1217	17611916	228,11744	1869	4117	5986	SO:0001819	synonymous_variant	57509	exon2			CTCCTTCGAGTCT	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.1401G>A	8.37:g.17611916C>T		Somatic	214	0	0		WXS	Illumina HiSeq	Phase_I	145	26	0.17931	NM_001001924	A8K135|B2RBJ6|B3KWJ9|B4DH03|B9EGA1|D3DSP8|Q63HJ6|Q659F4|Q6PK49|Q6URW7|Q8N4M6|Q8WTT9|Q9H7T2	Silent	SNP	ENST00000262102.6	37	CCDS43717.1																																																																																			C|0.982;T|0.018	0.018	strong		0.398	MTUS1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000375247.1	XM_372031	
RBPJL	11317	hgsc.bcm.edu	37	20	43944958	43944958	+	Silent	SNP	G	G	T	rs2741500	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:43944958G>T	ENST00000343694.3	+	10	1224	c.1152G>T	c.(1150-1152)ccG>ccT	p.P384P	RBPJL_ENST00000372743.1_Silent_p.P384P|RBPJL_ENST00000464504.1_3'UTR|RBPJL_ENST00000372741.3_Silent_p.P384P	NM_001281448.1|NM_001281449.1|NM_014276.2	NP_001268377.1|NP_001268378.1|NP_055091.2	Q9UBG7	RBPJL_HUMAN	recombination signal binding protein for immunoglobulin kappa J region-like	384					positive regulation of transcription, DNA-templated (GO:0045893)|signal transduction (GO:0007165)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity (GO:0000982)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(2)|kidney(1)|large_intestine(5)|lung(3)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19		Myeloproliferative disorder(115;0.0122)				CGGTCACTCCGGTGCCTCTCA	0.637													G|||	557	0.111222	0.0961	0.1297	5008	,	,		17481	0.0169		0.1988	False		,,,				2504	0.1258				p.P384P		Atlas-SNP	.											.	RBPJL	67	.	0			c.G1152T						PASS	.	G		489,3917	227.2+/-242.5	25,439,1739	48.0	45.0	46.0		1152	-9.4	0.0	20	dbSNP_100	46	1843,6757	329.6+/-318.8	192,1459,2649	no	coding-synonymous	RBPJL	NM_014276.2		217,1898,4388	TT,TG,GG		21.4302,11.0985,17.9302		384/518	43944958	2332,10674	2203	4300	6503	SO:0001819	synonymous_variant	11317	exon10			CACTCCGGTGCCT	AB024964	CCDS13349.1, CCDS63283.1, CCDS63284.1	20q13.12	2013-10-18	2007-02-26	2007-02-26	ENSG00000124232	ENSG00000124232			13761	protein-coding gene	gene with protein product			"""recombining binding protein suppressor of hairless (Drosophila)-like"""	RBPSUHL		9929984	Standard	NM_014276		Approved	RBP-L, SUH, SUHL	uc002xns.3	Q9UBG7	OTTHUMG00000033055	ENST00000343694.3:c.1152G>T	20.37:g.43944958G>T		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	100	48	0.48	NM_014276	O95723|Q5QPU9|Q5QPV0|Q9ULV9	Silent	SNP	ENST00000343694.3	37	CCDS13349.1																																																																																			G|0.853;T|0.147	0.147	strong		0.637	RBPJL-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080391.1	NM_014276	
IFITM3	10410	hgsc.bcm.edu	37	11	320649	320649	+	Silent	SNP	G	G	A	rs11553885	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:320649G>A	ENST00000399808.4	-	1	401	c.165C>T	c.(163-165)ccC>ccT	p.P55P	RP11-326C3.10_ENST00000534271.1_RNA|RP11-326C3.11_ENST00000508004.2_RNA|RP11-326C3.11_ENST00000602429.1_RNA|RP11-326C3.14_ENST00000602809.1_lincRNA|RP11-326C3.11_ENST00000602756.1_RNA|IFITM3_ENST00000602735.1_Silent_p.P34P|IFITM3_ENST00000526811.1_Silent_p.P34P	NM_021034.2	NP_066362.2	Q01628	IFM3_HUMAN	interferon induced transmembrane protein 3	55					cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|immune response (GO:0006955)|negative regulation of viral entry into host cell (GO:0046597)|negative regulation of viral genome replication (GO:0045071)|negative regulation of viral transcription (GO:0032897)|response to interferon-alpha (GO:0035455)|response to interferon-beta (GO:0035456)|response to interferon-gamma (GO:0034341)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|plasma membrane (GO:0005886)		p.P55P(5)		central_nervous_system(7)|endometrium(7)|kidney(2)|large_intestine(1)|lung(1)	18		all_cancers(49;2e-09)|all_epithelial(84;3.36e-06)|Breast(177;0.000162)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.0538)|all_lung(207;0.0713)		all cancers(45;8.85e-28)|Epithelial(43;5.52e-27)|OV - Ovarian serous cystadenocarcinoma(40;1.11e-20)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0327)|LUSC - Lung squamous cell carcinoma(625;0.122)		CGACATGGTCGGGCACGGAGG	0.637																																					p.P55P		Atlas-SNP	.											IFITM3,caecum,carcinoma,0,23	IFITM3	132	23	5	Substitution - coding silent(5)	endometrium(4)|central_nervous_system(1)	c.C165T						scavenged	.						93.0	98.0	96.0					11																	320649		2062	4173	6235	SO:0001819	synonymous_variant	10410	exon1			ATGGTCGGGCACG	X57352	CCDS41585.1	11p15.5	2011-05-24	2011-05-24		ENSG00000142089	ENSG00000142089			5414	protein-coding gene	gene with protein product		605579	"""interferon induced transmembrane protein 3 (1-8U)"""			1906403, 16326387	Standard	NM_021034		Approved	1-8U	uc001lpa.2	Q01628		ENST00000399808.4:c.165C>T	11.37:g.320649G>A		Somatic	67	1	0.0149254		WXS	Illumina HiSeq	Phase_I	83	9	0.108434	NM_021034	Q53Y76|Q96HK8|Q96J15	Silent	SNP	ENST00000399808.4	37	CCDS41585.1																																																																																			G|0.946;A|0.054	0.054	strong		0.637	IFITM3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384765.1	NM_021034	
FAM153B	202134	hgsc.bcm.edu	37	5	175528119	175528119	+	Splice_Site	SNP	T	T	C	rs199710353		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:175528119T>C	ENST00000253490.4	+	11	689	c.632T>C	c.(631-633)aTg>aCg	p.M211T	FAM153B_ENST00000515817.1_Splice_Site_p.M134T|FAM153B_ENST00000510151.1_Splice_Site_p.M134T|FAM153B_ENST00000512862.1_Intron			P0C7A2	F153B_HUMAN	family with sequence similarity 153, member B	211								p.M211T(4)		endometrium(3)|kidney(2)|large_intestine(1)|lung(8)|ovary(1)|prostate(1)	16	all_cancers(89;0.00406)|Renal(175;0.000269)|Lung NSC(126;0.0103)|all_lung(126;0.0164)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)|all_hematologic(541;0.214)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)	Kidney(146;0.0965)		GAAGTTCACATGGTAAAGTCG	0.433													N|||	1	0.000199681	0.0	0.0014	5008	,	,		30376	0.0		0.0	False		,,,				2504	0.0				p.M134T		Atlas-SNP	.											FAM153B,NS,carcinoma,0,4	FAM153B	28	4	4	Substitution - Missense(4)	endometrium(3)|kidney(1)	c.T401C						scavenged	.						258.0	307.0	289.0					5																	175528119		1510	2708	4218	SO:0001630	splice_region_variant	202134	exon10			TTCACATGGTAAA	AK055006	CCDS43401.1, CCDS43401.2	5q35.2	2010-05-12			ENSG00000182230	ENSG00000182230			27323	protein-coding gene	gene with protein product							Standard	NM_001265615		Approved		uc031smb.1	P0C7A2	OTTHUMG00000163181	ENST00000253490.4:c.633+1T>C	5.37:g.175528119T>C		Somatic	551	1	0.00181488		WXS	Illumina HiSeq	Phase_I	554	7	0.0126354	NM_001265615	A8MTI1	Missense_Mutation	SNP	ENST00000253490.4	37		.	.	.	.	.	.	.	.	.	.	T	0.008	-1.861446	0.00552	.	.	ENSG00000182230	ENST00000515817;ENST00000253490	.	.	.	0.917	-0.575	0.11734	.	.	.	.	.	T	0.20292	0.0488	N	0.24115	0.695	0.09310	N	1	B	0.33528	0.416	B	0.35470	0.203	T	0.18618	-1.0331	8	0.35671	T	0.21	.	2.9058	0.05720	0.5811:0.0:0.0:0.4189	.	211	P0C7A2	F153B_HUMAN	T	134;211	.	ENSP00000253490:M211T	M	+	2	0	FAM153B	175460725	0.015000	0.18098	0.001000	0.08648	0.003000	0.03518	-0.418000	0.07080	-0.147000	0.11254	-0.935000	0.02700	ATG	T|0.500;C|0.500	0.500	weak		0.433	FAM153B-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_001079529	Missense_Mutation
PRRC2B	84726	hgsc.bcm.edu	37	9	134371165	134371165	+	Silent	SNP	C	C	T	rs41296113	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:134371165C>T	ENST00000357304.4	+	31	6649	c.6594C>T	c.(6592-6594)gcC>gcT	p.A2198A	PRRC2B_ENST00000372249.1_Missense_Mutation_p.P268L|PRRC2B_ENST00000405995.1_Silent_p.A1504A|PRRC2B_ENST00000465931.1_3'UTR|PRRC2B_ENST00000458550.1_Silent_p.A1504A	NM_013318.3	NP_037450.2	Q5JSZ5	PRC2B_HUMAN	proline-rich coiled-coil 2B	2198							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						GCCTGGGAGCCGTGAAGCTGC	0.547													C|||	296	0.0591054	0.0492	0.1412	5008	,	,		18174	0.0526		0.0577	False		,,,				2504	0.0225				p.A2198A		Atlas-SNP	.											.	PRRC2B	266	.	0			c.C6594T						PASS	.	C		191,3711		2,187,1762	45.0	50.0	48.0		6594	1.6	1.0	9	dbSNP_127	48	390,7898		11,368,3765	no	coding-synonymous	PRRC2B	NM_013318.3		13,555,5527	TT,TC,CC		4.7056,4.8949,4.7662		2198/2230	134371165	581,11609	1951	4144	6095	SO:0001819	synonymous_variant	84726	exon31			GGGAGCCGTGAAG	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.6594C>T	9.37:g.134371165C>T		Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	22	4	0.181818	NM_013318	O60270|Q5JSZ7|Q66VZ2|Q68CR0|Q96EI9|Q9H683	Silent	SNP	ENST00000357304.4	37	CCDS48044.1	141	0.06456043956043957	29	0.05894308943089431	39	0.10773480662983426	30	0.05244755244755245	43	0.05672823218997362	C	19.23	3.786569	0.70337	0.048949	0.047056	ENSG00000130723	ENST00000372249	.	.	.	4.75	1.56	0.23342	.	.	.	.	.	T	0.00784	0.0026	.	.	.	0.28068	N	0.93271	.	.	.	.	.	.	T	0.08806	-1.0704	5	0.87932	D	0	-16.5039	4.0105	0.09621	0.177:0.4296:0.0:0.3935	rs41296113;rs61742042	.	.	.	L	268	.	ENSP00000361323:P268L	P	+	2	0	PRRC2B	133360986	0.958000	0.32768	0.998000	0.56505	0.995000	0.86356	-0.042000	0.12063	0.161000	0.19458	0.557000	0.71058	CCG	C|0.936;T|0.064	0.064	strong		0.547	PRRC2B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
QRSL1	55278	hgsc.bcm.edu	37	6	107113715	107113715	+	Silent	SNP	G	G	A	rs2015205	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	155	0	0		WXS	Illumina HiSeq	Phase_I	107	55	0.514019	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	
NDOR1	27158	hgsc.bcm.edu	37	9	140110555	140110555	+	Missense_Mutation	SNP	G	G	A	rs62587579	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:140110555G>A	ENST00000344894.5	+	13	1647	c.1564G>A	c.(1564-1566)Gta>Ata	p.V522I	NDOR1_ENST00000458322.2_Missense_Mutation_p.V515I|NDOR1_ENST00000427047.2_Missense_Mutation_p.V488I|NDOR1_ENST00000371521.4_Missense_Mutation_p.V531I	NM_001144028.1|NM_014434.2	NP_001137500.1|NP_055249.1			NADPH dependent diflavin oxidoreductase 1											breast(1)|endometrium(5)|large_intestine(1)|lung(5)|prostate(1)|skin(1)|urinary_tract(1)	15	all_cancers(76;0.0926)		STAD - Stomach adenocarcinoma(284;0.0698)	OV - Ovarian serous cystadenocarcinoma(145;6.37e-05)|Epithelial(140;0.00057)		GGAGCAGAAAGTATATGTGCA	0.637													G|||	87	0.0173722	0.0023	0.0447	5008	,	,		17550	0.001		0.0398	False		,,,				2504	0.0123				p.V531I		Atlas-SNP	.											.	NDOR1	71	.	0			c.G1591A	GRCh37	CM056012	NDOR1	M	rs62587579	PASS	.	G	ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL	45,4361	46.0+/-80.4	0,45,2158	50.0	57.0	54.0		1591,1462,1543,1564	2.0	0.1	9	dbSNP_129	54	468,8132	137.6+/-194.5	14,440,3846	yes	missense,missense,missense,missense	NDOR1	NM_001144026.1,NM_001144027.1,NM_001144028.1,NM_014434.2	29,29,29,29	14,485,6004	AA,AG,GG		5.4419,1.0213,3.9443	benign,benign,benign,benign	531/607,488/522,515/591,522/598	140110555	513,12493	2203	4300	6503	SO:0001583	missense	27158	exon13			CAGAAAGTATATG	BC015735	CCDS7036.1, CCDS48061.1, CCDS48062.1, CCDS48063.1	9q34.3	2008-02-05			ENSG00000188566	ENSG00000188566			29838	protein-coding gene	gene with protein product	"""NADPH dependent FMN and FAD containing oxidoreductase"""	606073				10625700, 12631275	Standard	XM_005266066		Approved	NR1, bA350O14.9	uc004clx.3	Q9UHB4	OTTHUMG00000020986	ENST00000344894.5:c.1564G>A	9.37:g.140110555G>A	ENSP00000343344:p.Val522Ile	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	70	26	0.371429	NM_001144026		Missense_Mutation	SNP	ENST00000344894.5	37	CCDS7036.1	51	0.023351648351648352	2	0.0040650406504065045	18	0.049723756906077346	1	0.0017482517482517483	30	0.0395778364116095	G	8.357	0.832158	0.16820	0.010213	0.054419	ENSG00000188566	ENST00000458322;ENST00000427047;ENST00000371521;ENST00000344894	D;D;D;D	0.86694	-2.16;-2.16;-2.16;-2.16	4.06	2.0	0.26442	Oxidoreductase FAD/NAD(P)-binding (1);Flavoprotein pyridine nucleotide cytochrome reductase (1);	0.152913	0.43747	N	0.000522	T	0.38665	0.1049	N	0.20574	0.59	0.54753	D	0.999985	B;B;B;B	0.18166	0.026;0.003;0.021;0.011	B;B;B;B	0.30495	0.116;0.042;0.071;0.075	T	0.53265	-0.8463	10	0.24483	T	0.36	-6.0513	7.5162	0.27602	0.2428:0.0:0.7572:0.0	rs62587579	515;488;531;522	D3YTG6;D3YTH9;Q9UHB4-2;Q9UHB4	.;.;.;NDOR1_HUMAN	I	515;488;531;522	ENSP00000389905:V515I;ENSP00000394309:V488I;ENSP00000360576:V531I;ENSP00000343344:V522I	ENSP00000343344:V522I	V	+	1	0	NDOR1	139230376	0.986000	0.35501	0.146000	0.22360	0.589000	0.36550	1.232000	0.32636	0.927000	0.37143	0.561000	0.74099	GTA	G|0.962;A|0.038	0.038	strong		0.637	NDOR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254704.1	NM_014434	
MUC4	4585	hgsc.bcm.edu	37	3	195507062	195507062	+	Missense_Mutation	SNP	C	C	T	rs199822551	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195507062C>T	ENST00000463781.3	-	2	11848	c.11389G>A	c.(11389-11391)Gac>Aac	p.D3797N	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.D3797N	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)		GAGGAAGTGTCGGTGACAGGA	0.607													.|||	549	0.109625	0.0575	0.1239	5008	,	,		9468	0.0556		0.2028	False		,,,				2504	0.1299				p.D3797N		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	0			c.G11389A						scavenged	.						7.0	7.0	7.0					3																	195507062		641	1482	2123	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.11389G>A	3.37:g.195507062C>T	ENSP00000417498:p.Asp3797Asn	Somatic	27	3	0.111111		WXS	Illumina HiSeq	Phase_I	82	43	0.52439	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	8.329	0.826143	0.16749	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.31247	1.51;1.5	.	.	.	.	0.282130	0.14041	U	0.345384	T	0.13586	0.0329	N	0.19112	0.55	0.09310	N	0.999991	B	0.26975	0.165	B	0.06405	0.002	T	0.19516	-1.0303	8	.	.	.	.	3.5985	0.08016	2.0E-4:0.5013:0.4982:2.0E-4	.	3669	E7ESK3	.	N	3797	ENSP00000417498:D3797N;ENSP00000420243:D3797N	.	D	-	1	0	MUC4	196991841	0.000000	0.05858	0.054000	0.19295	0.055000	0.15305	0.157000	0.16402	0.064000	0.16427	0.064000	0.15345	GAC	.	.	weak		0.607	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
SLC2A9	56606	hgsc.bcm.edu	37	4	9922130	9922130	+	Missense_Mutation	SNP	C	C	T	rs3733591	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:9922130C>T	ENST00000264784.3	-	7	934	c.881G>A	c.(880-882)cGc>cAc	p.R294H	SLC2A9_ENST00000309065.3_Missense_Mutation_p.R265H|RP13-560N11.1_ENST00000504249.1_RNA|SLC2A9_ENST00000506583.1_Missense_Mutation_p.R265H	NM_020041.2	NP_064425.2	Q9NRM0	GTR9_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 9	294			R -> H (in dbSNP:rs3733591).		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)	CCTCTGCACGCGGCTCTCAGC	0.592													C|||	1473	0.294129	0.0393	0.2075	5008	,	,		20053	0.6845		0.1909	False		,,,				2504	0.4039				p.R294H		Atlas-SNP	.											.	SLC2A9	158	.	0			c.G881A						PASS	.	C	HIS/ARG,HIS/ARG	314,4092	170.5+/-200.9	9,296,1898	60.0	53.0	55.0		794,881	1.6	0.2	4	dbSNP_107	55	1629,6971	301.7+/-305.6	145,1339,2816	yes	missense,missense	SLC2A9	NM_001001290.1,NM_020041.2	29,29	154,1635,4714	TT,TC,CC		18.9419,7.1266,14.9393	probably-damaging,probably-damaging	265/512,294/541	9922130	1943,11063	2203	4300	6503	SO:0001583	missense	56606	exon7			TGCACGCGGCTCT	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.881G>A	4.37:g.9922130C>T	ENSP00000264784:p.Arg294His	Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	154	76	0.493506	NM_020041	Q0VGC4|Q4W5D1|Q8WV30|Q96P00	Missense_Mutation	SNP	ENST00000264784.3	37	CCDS3407.1	640	0.29304029304029305	23	0.046747967479674794	64	0.17679558011049723	393	0.6870629370629371	160	0.21108179419525067	C	13.80	2.345619	0.41498	0.071266	0.189419	ENSG00000109667	ENST00000506583;ENST00000264784;ENST00000309065	T;T;T	0.74106	-0.81;-0.81;-0.81	5.2	1.57	0.23409	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	1.450200	0.04268	N	0.341597	T	0.00012	0.0000	M	0.78049	2.395	0.43896	P	0.003475000000000006	D;D	0.89917	1.0;1.0	D;D	0.85130	0.989;0.997	T	0.48559	-0.9025	8	.	.	.	.	9.2553	0.37579	0.0:0.704:0.0:0.296	rs3733591;rs52832215;rs59677463;rs3733591	265;294	Q9NRM0-2;Q9NRM0	.;GTR9_HUMAN	H	265;294;265	ENSP00000422209:R265H;ENSP00000264784:R294H;ENSP00000311383:R265H	.	R	-	2	0	SLC2A9	9531228	0.012000	0.17670	0.178000	0.23040	0.122000	0.20287	0.218000	0.17622	-0.019000	0.14055	0.650000	0.86243	CGC	C|0.781;T|0.219	0.219	strong		0.592	SLC2A9-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207055.1		
EPPK1	83481	hgsc.bcm.edu	37	8	144940290	144940290	+	Missense_Mutation	SNP	C	C	G	rs201976887		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:144940290C>G	ENST00000525985.1	-	2	7203	c.7132G>C	c.(7132-7134)Gac>Cac	p.D2378H				P58107	EPIPL_HUMAN	epiplakin 1	2378						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(5)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(2)|lung(30)|ovary(2)|pancreas(1)|prostate(10)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	71	all_cancers(97;1.42e-10)|all_epithelial(106;1.99e-09)|Lung NSC(106;0.000126)|all_lung(105;0.000354)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;2.88e-40)|all cancers(56;1.82e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			TCGCTGGGGTCGGCCAGGACG	0.682																																					p.D2378H		Atlas-SNP	.											EPPK1,NS,carcinoma,0,5	EPPK1	199	5	0			c.G7132C						PASS	.	C	HIS/ASP	51,4341	20.2+/-43.8	0,51,2145	315.0	292.0	300.0		7132	3.6	0.8	8		300	22,8530	7.1+/-27.0	0,22,4254	no	missense	EPPK1	NM_031308.1	81	0,73,6399	GG,GC,CC		0.2572,1.1612,0.564	probably-damaging	2378/2420	144940290	73,12871	2196	4276	6472	SO:0001583	missense	83481	exon1			TGGGGTCGGCCAG	AB051895	CCDS75800.1	8q24.3	2014-09-17				ENSG00000261150			15577	protein-coding gene	gene with protein product	"""epidermal autoantigen 450K"""	607553				11278896, 15671067	Standard	NM_031308		Approved	EPIPL1	uc003zaa.1	P58107		ENST00000525985.1:c.7132G>C	8.37:g.144940290C>G	ENSP00000436337:p.Asp2378His	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	118	22	0.186441	NM_031308	Q76E58|Q9NSU9	Missense_Mutation	SNP	ENST00000525985.1	37		.	.	.	.	.	.	.	.	.	.	C	22.4	4.279155	0.80692	0.011612	0.002572	ENSG00000227184	ENST00000525985	T	0.74737	-0.87	4.43	3.56	0.40772	.	.	.	.	.	D	0.83133	0.5188	M	0.89785	3.06	0.42176	D	0.991666	D	0.89917	1.0	D	0.91635	0.999	D	0.86316	0.1689	9	0.62326	D	0.03	.	10.4012	0.44231	0.0:0.9038:0.0:0.0962	.	2378	E9PPU0	.	H	2378	ENSP00000436337:D2378H	ENSP00000436337:D2378H	D	-	1	0	EPPK1	145012278	1.000000	0.71417	0.773000	0.31616	0.942000	0.58702	7.555000	0.82223	1.223000	0.43536	0.591000	0.81541	GAC	.	.	weak		0.682	EPPK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000382675.1	NM_031308	
APMAP	57136	hgsc.bcm.edu	37	20	24954303	24954303	+	Silent	SNP	G	G	C	rs148400044	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:24954303G>C	ENST00000217456.2	-	4	689	c.399C>G	c.(397-399)gcC>gcG	p.A133A	RNU6-1257P_ENST00000384625.1_RNA|APMAP_ENST00000447138.1_Silent_p.A133A	NM_020531.2	NP_065392.1	Q9HDC9	APMAP_HUMAN	adipocyte plasma membrane associated protein	133					biosynthetic process (GO:0009058)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	arylesterase activity (GO:0004064)|strictosidine synthase activity (GO:0016844)										AACCAAACCGGGCAATGGTCT	0.448													G|||	3	0.000599042	0.0	0.0	5008	,	,		19675	0.0		0.001	False		,,,				2504	0.002				p.A133A		Atlas-SNP	.											.	APMAP	3	.	0			c.C399G						PASS	.	G		2,4404	4.2+/-10.8	0,2,2201	107.0	92.0	97.0		399	0.0	1.0	20	dbSNP_134	97	11,8589	9.1+/-34.3	0,11,4289	no	coding-synonymous	C20orf3	NM_020531.2		0,13,6490	CC,CG,GG		0.1279,0.0454,0.1		133/417	24954303	13,12993	2203	4300	6503	SO:0001819	synonymous_variant	57136	exon4			AAACCGGGCAATG	AB033767	CCDS13166.1	20p11.2	2012-07-20	2012-07-20	2012-07-20	ENSG00000101474	ENSG00000101474			13238	protein-coding gene	gene with protein product		615884	"""chromosome 20 open reading frame 3"""	C20orf3		10945474, 11583587, 20552250	Standard	NM_020531		Approved	BSCv	uc002wty.3	Q9HDC9	OTTHUMG00000032107	ENST00000217456.2:c.399C>G	20.37:g.24954303G>C		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	116	62	0.534483	NM_020531	A8K514|B4DXG1|Q6UVZ8|Q9GZS8|Q9NUB2	Silent	SNP	ENST00000217456.2	37	CCDS13166.1	.	.	.	.	.	.	.	.	.	.	G	9.501	1.103322	0.20632	4.54E-4	0.001279	ENSG00000101474	ENST00000451442	.	.	.	5.43	0.0444	0.14225	.	.	.	.	.	T	0.50360	0.1611	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.33752	-0.9856	4	.	.	.	-17.6727	5.067	0.14587	0.3047:0.2599:0.4354:0.0	.	.	.	.	R	118	.	.	P	-	2	0	C20orf3	24902303	0.804000	0.28969	0.963000	0.40424	0.854000	0.48673	-0.233000	0.09041	-0.200000	0.10300	-0.150000	0.13652	CCC	G|0.998;C|0.002	0.002	strong		0.448	APMAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078380.2	NM_020531	
CDH8	1006	hgsc.bcm.edu	37	16	61689493	61689493	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:61689493A>G	ENST00000577390.1	-	11	2741	c.1787T>C	c.(1786-1788)gTc>gCc	p.V596A	CDH8_ENST00000577730.1_Missense_Mutation_p.V596A|CDH8_ENST00000299345.6_Missense_Mutation_p.V596A	NM_001796.4	NP_001787.2	P55286	CADH8_HUMAN	cadherin 8, type 2	596	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|response to cold (GO:0009409)|synaptic transmission, glutamatergic (GO:0035249)	axon terminus (GO:0043679)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synaptic cleft (GO:0043083)	calcium ion binding (GO:0005509)			biliary_tract(1)|breast(3)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(22)|liver(2)|lung(49)|ovary(6)|pancreas(2)|prostate(5)|skin(4)|urinary_tract(4)	112		Ovarian(137;0.0799)|Melanoma(118;0.16)		UCEC - Uterine corpus endometrioid carcinoma (183;0.196)|Epithelial(162;0.0155)|all cancers(182;0.0305)|OV - Ovarian serous cystadenocarcinoma(108;0.0499)|BRCA - Breast invasive adenocarcinoma(181;0.249)		GCAGCCACAGACCCTGATTGT	0.468																																					p.V596A		Atlas-SNP	.											CDH8,rectum,carcinoma,+1,1	CDH8	273	1	0			c.T1787C						scavenged	.						159.0	135.0	143.0					16																	61689493		2203	4300	6503	SO:0001583	missense	1006	exon11			CCACAGACCCTGA	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.1787T>C	16.37:g.61689493A>G	ENSP00000462701:p.Val596Ala	Somatic	150	1	0.00666667		WXS	Illumina HiSeq	Phase_I	220	5	0.0227273	NM_001796	B3KWC1|Q14DC6|Q9ULB2	Missense_Mutation	SNP	ENST00000577390.1	37	CCDS10802.1	.	.	.	.	.	.	.	.	.	.	A	32	5.110342	0.94292	.	.	ENSG00000150394	ENST00000299345	T	0.68181	-0.31	5.52	5.52	0.82312	Cadherin (4);Cadherin-like (1);	0.000000	0.85682	D	0.000000	D	0.86310	0.5902	H	0.95260	3.645	0.80722	D	1	D	0.65815	0.995	D	0.67382	0.951	D	0.90285	0.4318	10	0.72032	D	0.01	.	14.82	0.70065	1.0:0.0:0.0:0.0	.	596	P55286	CADH8_HUMAN	A	596	ENSP00000299345:V596A	ENSP00000299345:V596A	V	-	2	0	CDH8	60246994	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	8.904000	0.92590	2.101000	0.63845	0.459000	0.35465	GTC	.	.	none		0.468	CDH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268754.3	NM_001796	
VWA5A	4013	hgsc.bcm.edu	37	11	124015994	124015994	+	Silent	SNP	C	C	T	rs1056615	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:124015994C>T	ENST00000456829.2	+	18	2456	c.2205C>T	c.(2203-2205)caC>caT	p.H735H	VWA5A_ENST00000392748.1_Silent_p.H735H|VWA5A_ENST00000360334.4_3'UTR	NM_001130142.1	NP_001123614.1	O00534	VMA5A_HUMAN	von Willebrand factor A domain containing 5A	735										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						TCTGGCTGCACAGCAATGGTA	0.562													T|||	3028	0.604633	0.7821	0.5403	5008	,	,		20325	0.7093		0.5229	False		,,,				2504	0.3865				p.H735H		Atlas-SNP	.											VWA5A,colon,carcinoma,+1,1	VWA5A	102	1	0			c.C2205T						PASS	.	T	,	3119,1283	436.4+/-344.6	1090,939,172	125.0	117.0	120.0		2205,2205	-3.9	0.0	11	dbSNP_86	120	4500,4098	562.1+/-387.9	1178,2144,977	no	coding-synonymous,coding-synonymous	VWA5A	NM_001130142.1,NM_014622.4	,	2268,3083,1149	TT,TC,CC		47.6622,29.1458,41.3923	,	735/787,735/787	124015994	7619,5381	2201	4299	6500	SO:0001819	synonymous_variant	4013	exon17			GCTGCACAGCAAT	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.2205C>T	11.37:g.124015994C>T		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	75	24	0.32	NM_014622	Q6UN19|Q6UN20|Q9BVF8	Silent	SNP	ENST00000456829.2	37	CCDS8444.1																																																																																			C|0.391;T|0.609	0.609	strong		0.562	VWA5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387273.1	NM_014622	
ESPL1	9700	hgsc.bcm.edu	37	12	53680011	53680011	+	Missense_Mutation	SNP	T	T	G	rs111320105	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:53680011T>G	ENST00000257934.4	+	18	3582	c.3491T>G	c.(3490-3492)gTa>gGa	p.V1164G	ESPL1_ENST00000552462.1_Missense_Mutation_p.V1164G	NM_012291.4	NP_036423.4	Q14674	ESPL1_HUMAN	extra spindle pole bodies homolog 1 (S. cerevisiae)	1164					apoptotic process (GO:0006915)|cytokinesis (GO:0000910)|establishment of mitotic spindle localization (GO:0040001)|homologous chromosome segregation (GO:0045143)|meiotic spindle organization (GO:0000212)|mitotic cell cycle (GO:0000278)|mitotic sister chromatid segregation (GO:0000070)|negative regulation of sister chromatid cohesion (GO:0045875)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)	centrosome (GO:0005813)|cytosol (GO:0005829)|nucleus (GO:0005634)	catalytic activity (GO:0003824)|cysteine-type peptidase activity (GO:0008234)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(10)|large_intestine(12)|lung(21)|ovary(2)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(8)	70						CTGCGCTGGGTATTGGTCACG	0.642													T|||	42	0.00838658	0.0015	0.0101	5008	,	,		18919	0.0		0.0249	False		,,,				2504	0.0082				p.V1164G	Colon(53;1069 1201 2587 5382)	Atlas-SNP	.											.	ESPL1	158	.	0			c.T3491G						PASS	.	T	GLY/VAL	26,4380	32.6+/-62.9	0,26,2177	80.0	81.0	80.0		3491	-0.6	0.1	12	dbSNP_132	80	209,8391	88.1+/-150.5	1,207,4092	yes	missense	ESPL1	NM_012291.4	109	1,233,6269	GG,GT,TT		2.4302,0.5901,1.8069	benign	1164/2121	53680011	235,12771	2203	4300	6503	SO:0001583	missense	9700	exon18			GCTGGGTATTGGT	D79987	CCDS8852.1	12q13.13	2014-08-04	2013-05-03		ENSG00000135476	ENSG00000135476	3.4.22.49		16856	protein-coding gene	gene with protein product	"""separin"", ""separase"", ""separin, cysteine protease"""	604143	"""extra spindle poles like 1 (S. cerevisiae)"""			8724849, 16258266	Standard	NM_012291		Approved	KIAA0165, ESP1, SEPA	uc001sck.2	Q14674	OTTHUMG00000169674	ENST00000257934.4:c.3491T>G	12.37:g.53680011T>G	ENSP00000257934:p.Val1164Gly	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	48	23	0.479167	NM_012291		Missense_Mutation	SNP	ENST00000257934.4	37	CCDS8852.1	24	0.01098901098901099	0	0.0	7	0.019337016574585635	0	0.0	17	0.022427440633245383	T	11.01	1.513753	0.27123	0.005901	0.024302	ENSG00000135476	ENST00000257934;ENST00000552671;ENST00000552462	T;T	0.13196	2.61;2.61	5.65	-0.569	0.11756	.	0.468437	0.24920	N	0.034549	T	0.04407	0.0121	L	0.36672	1.1	0.28116	N	0.930819	B	0.25441	0.126	B	0.21360	0.034	T	0.19745	-1.0296	10	0.35671	T	0.21	.	10.7181	0.46023	0.0:0.1493:0.0:0.8507	.	1164	Q14674	ESPL1_HUMAN	G	1164;839;1164	ENSP00000257934:V1164G;ENSP00000449831:V1164G	ENSP00000257934:V1164G	V	+	2	0	ESPL1	51966278	0.002000	0.14202	0.114000	0.21550	0.688000	0.40055	-0.007000	0.12810	0.019000	0.15079	0.533000	0.62120	GTA	T|0.983;G|0.017	0.017	strong		0.642	ESPL1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406899.2	NM_012291	
PCDH18	54510	hgsc.bcm.edu	37	4	138452706	138452706	+	Missense_Mutation	SNP	A	A	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:138452706A>T	ENST00000344876.4	-	1	923	c.537T>A	c.(535-537)aaT>aaA	p.N179K	PCDH18_ENST00000412923.2_Missense_Mutation_p.N179K|PCDH18_ENST00000510305.1_Intron|PCDH18_ENST00000507846.1_5'UTR|PCDH18_ENST00000511115.1_Intron	NM_019035.3	NP_061908.1	Q9HCL0	PCD18_HUMAN	protocadherin 18	179	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				brain development (GO:0007420)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(27)|lung(21)|ovary(2)|pancreas(4)|prostate(3)|skin(12)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	86	all_hematologic(180;0.24)					TAAAAAAATCATTGGCAGAGA	0.483																																					p.N179K		Atlas-SNP	.											.	PCDH18	229	.	0			c.T537A						PASS	.						60.0	59.0	60.0					4																	138452706		2203	4300	6503	SO:0001583	missense	54510	exon1			AAAATCATTGGCA	AL137471	CCDS34064.1, CCDS75193.1	4q28.3	2010-01-26			ENSG00000189184	ENSG00000189184		"""Cadherins / Protocadherins : Non-clustered"""	14268	protein-coding gene	gene with protein product		608287				10835267, 11549318	Standard	XM_005263070		Approved	KIAA1562, PCDH68L	uc003ihe.4	Q9HCL0	OTTHUMG00000161348	ENST00000344876.4:c.537T>A	4.37:g.138452706A>T	ENSP00000355082:p.Asn179Lys	Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	119	31	0.260504	NM_019035	A8K7K3|B7ZKT1|Q52LS2	Missense_Mutation	SNP	ENST00000344876.4	37	CCDS34064.1	.	.	.	.	.	.	.	.	.	.	A	12.89	2.072697	0.36566	.	.	ENSG00000189184	ENST00000344876;ENST00000412923	T;T	0.50813	0.73;0.73	5.89	0.536	0.17138	Cadherin (4);Cadherin-like (1);	0.000000	0.46145	D	0.000304	T	0.65544	0.2701	M	0.87827	2.91	0.80722	D	1	D;D	0.71674	0.998;0.992	P;P	0.61201	0.885;0.739	T	0.69476	-0.5135	10	0.87932	D	0	.	10.9316	0.47222	0.5396:0.0:0.4604:0.0	.	179;179	Q9HCL0-2;Q9HCL0	.;PCD18_HUMAN	K	179	ENSP00000355082:N179K;ENSP00000390688:N179K	ENSP00000355082:N179K	N	-	3	2	PCDH18	138672156	1.000000	0.71417	0.930000	0.37139	0.304000	0.27724	1.063000	0.30567	0.078000	0.16900	0.455000	0.32223	AAT	.	.	none		0.483	PCDH18-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364614.1	NM_019035	
ZNF598	90850	hgsc.bcm.edu	37	16	2048796	2048796	+	Silent	SNP	C	C	T	rs1058474	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:2048796C>T	ENST00000563630.1	-	11	2345	c.2103G>A	c.(2101-2103)agG>agA	p.R701R	AC005606.15_ENST00000567515.1_lincRNA|ZNF598_ENST00000431526.1_Silent_p.R756R|ZNF598_ENST00000562103.1_Silent_p.R701R			Q86UK7	ZN598_HUMAN	zinc finger protein 598	756	Pro-rich.						poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|lung(7)|skin(1)|urinary_tract(1)	16						GCTGAAGGTTCCTCTCCCGGA	0.617													C|||	633	0.126398	0.0061	0.2176	5008	,	,		13578	0.0427		0.1849	False		,,,				2504	0.2505				p.R756R		Atlas-SNP	.											.	ZNF598	55	.	0			c.G2268A						PASS	.	C		131,3771		4,123,1824	27.0	30.0	29.0		2270	4.5	1.0	16	dbSNP_86	29	1403,6887		112,1179,2854	yes	coding-synonymous	ZNF598	NM_178167.2		116,1302,4678	TT,TC,CC		16.924,3.3573,12.582		756/905	2048796	1534,10658	1951	4145	6096	SO:0001819	synonymous_variant	90850	exon13			AAGGTTCCTCTCC	BC029270		16p13.3	2008-05-02				ENSG00000167962		"""Zinc fingers, C2H2-type"""	28079	protein-coding gene	gene with protein product							Standard	NM_178167		Approved	FLJ00086	uc002cof.2	Q86UK7		ENST00000563630.1:c.2103G>A	16.37:g.2048796C>T		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	107	82	0.766355	NM_178167	Q8IW49|Q8N3D9|Q96FG3|Q9H7J3	Silent	SNP	ENST00000563630.1	37																																																																																				C|0.885;T|0.115	0.115	strong		0.617	ZNF598-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000434439.1	NM_178167	
GAD1	2571	hgsc.bcm.edu	37	2	171716266	171716266	+	Missense_Mutation	SNP	G	G	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:171716266G>C	ENST00000358196.3	+	17	2209	c.1659G>C	c.(1657-1659)atG>atC	p.M553I		NM_000817.2	NP_000808.2	Q99259	DCE1_HUMAN	glutamate decarboxylase 1 (brain, 67kDa)	553					gamma-aminobutyric acid biosynthetic process (GO:0009449)|glutamate catabolic process (GO:0006538)|glutamate decarboxylation to succinate (GO:0006540)|neurotransmitter biosynthetic process (GO:0042136)|neurotransmitter secretion (GO:0007269)|protein-pyridoxal-5-phosphate linkage (GO:0018352)|response to drug (GO:0042493)|synaptic transmission (GO:0007268)	clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane (GO:0061202)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|vesicle membrane (GO:0012506)	glutamate binding (GO:0016595)|glutamate decarboxylase activity (GO:0004351)|pyridoxal phosphate binding (GO:0030170)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(11)|lung(15)|ovary(1)|urinary_tract(2)	35						GTACGACCATGGTTGGCTACC	0.493																																					p.M553I		Atlas-SNP	.											.	GAD1	79	.	0			c.G1659C						PASS	.						78.0	71.0	73.0					2																	171716266		2203	4300	6503	SO:0001583	missense	2571	exon17			GACCATGGTTGGC		CCDS2239.1, CCDS2240.1	2q31	2008-02-05	2002-08-29		ENSG00000128683	ENSG00000128683	4.1.1.15		4092	protein-coding gene	gene with protein product		605363	"""glutamate decarboxylase 1 (brain, 67kD)"""	GAD		1549570	Standard	XM_005246443		Approved		uc002ugi.3	Q99259	OTTHUMG00000044175	ENST00000358196.3:c.1659G>C	2.37:g.171716266G>C	ENSP00000350928:p.Met553Ile	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	90	19	0.211111	NM_000817	Q49AK1|Q53TQ7|Q9BU91|Q9UHH4	Missense_Mutation	SNP	ENST00000358196.3	37	CCDS2239.1	.	.	.	.	.	.	.	.	.	.	G	26.9	4.785893	0.90282	.	.	ENSG00000128683	ENST00000358196	T	0.36520	1.25	5.47	5.47	0.80525	Pyridoxal phosphate-dependent transferase, major region, subdomain 2 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.000000	0.85682	D	0.000000	T	0.63803	0.2542	M	0.93328	3.405	0.80722	D	1	P	0.50528	0.936	P	0.51016	0.656	T	0.74914	-0.3502	10	0.87932	D	0	-23.7109	19.6956	0.96023	0.0:0.0:1.0:0.0	.	553	Q99259	DCE1_HUMAN	I	553	ENSP00000350928:M553I	ENSP00000350928:M553I	M	+	3	0	GAD1	171424512	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.420000	0.97426	2.729000	0.93468	0.585000	0.79938	ATG	.	.	none		0.493	GAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102664.2		
TNS1	7145	hgsc.bcm.edu	37	2	218713282	218713282	+	Missense_Mutation	SNP	G	G	A	rs3796033	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:218713282G>A	ENST00000171887.4	-	17	2035	c.1583C>T	c.(1582-1584)aCc>aTc	p.T528I	TNS1_ENST00000419504.1_Missense_Mutation_p.T528I|TNS1_ENST00000480665.1_5'UTR|TNS1_ENST00000430930.1_Missense_Mutation_p.T528I	NM_022648.4	NP_072174.3	Q9HBL0	TENS1_HUMAN	tensin 1	528			T -> I (in dbSNP:rs3796033).		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)		CCCCTCACTGGTGTTGGTGAC	0.602													G|||	2070	0.413339	0.5983	0.3055	5008	,	,		18412	0.2937		0.3459	False		,,,				2504	0.4325				p.T528I		Atlas-SNP	.											.	TNS1	251	.	0			c.C1583T						PASS	.	G	ILE/THR	2378,2028	608.6+/-391.2	661,1056,486	69.0	73.0	72.0		1583	2.4	1.0	2	dbSNP_107	72	2631,5969	420.5+/-353.4	419,1793,2088	yes	missense	TNS1	NM_022648.4	89	1080,2849,2574	AA,AG,GG		30.593,46.0281,38.513	possibly-damaging	528/1736	218713282	5009,7997	2203	4300	6503	SO:0001583	missense	7145	exon17			TCACTGGTGTTGG	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.1583C>T	2.37:g.218713282G>A	ENSP00000171887:p.Thr528Ile	Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	150	61	0.406667	NM_022648	Q4ZG71|Q6IPI5	Missense_Mutation	SNP	ENST00000171887.4	37	CCDS2407.1	839	0.3841575091575092	304	0.6178861788617886	109	0.3011049723756906	176	0.3076923076923077	250	0.32981530343007914	G	12.43	1.934427	0.34096	0.539719	0.30593	ENSG00000079308	ENST00000171887;ENST00000419504;ENST00000430930;ENST00000446903	D;D;D;D	0.94184	-2.86;-2.86;-2.87;-3.37	4.49	2.37	0.29283	.	0.460849	0.24620	N	0.036961	T	0.00012	0.0000	L	0.40543	1.245	0.09310	P	0.9999999999841128	B;P;P;P	0.40578	0.013;0.722;0.666;0.483	B;B;B;B	0.33454	0.008;0.164;0.162;0.122	T	0.48198	-0.9056	9	0.30854	T	0.27	.	7.2402	0.26092	0.3097:0.0:0.6903:0.0	rs3796033;rs56992876;rs3796033	528;528;528;528	B2RU35;Q9HBL0;E9PGF5;E9PF55	.;TENS1_HUMAN;.;.	I	528;528;528;653	ENSP00000171887:T528I;ENSP00000408724:T528I;ENSP00000406016:T528I;ENSP00000405460:T653I	ENSP00000171887:T528I	T	-	2	0	TNS1	218421527	0.997000	0.39634	1.000000	0.80357	0.978000	0.69477	2.711000	0.47177	0.447000	0.26695	0.561000	0.74099	ACC	G|0.602;A|0.398	0.398	strong		0.602	TNS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256672.2	NM_022648	
TYW1	55253	hgsc.bcm.edu	37	7	66660242	66660242	+	Missense_Mutation	SNP	A	A	G	rs2949097		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	198	1	0.00505051		WXS	Illumina HiSeq	Phase_I	135	32	0.237037	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	
CUBN	8029	hgsc.bcm.edu	37	10	17147521	17147521	+	Missense_Mutation	SNP	G	G	T	rs1801224	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:17147521G>T	ENST00000377833.4	-	11	1230	c.1165C>A	c.(1165-1167)Cca>Aca	p.P389T		NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)	389			P -> T (in dbSNP:rs1801224). {ECO:0000269|PubMed:10080186}.		cholesterol metabolic process (GO:0008203)|cobalamin metabolic process (GO:0009235)|cobalamin transport (GO:0015889)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|tissue homeostasis (GO:0001894)|vitamin D metabolic process (GO:0042359)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|Golgi apparatus (GO:0005794)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|cobalamin binding (GO:0031419)|protein homodimerization activity (GO:0042803)|receptor activity (GO:0004872)|transporter activity (GO:0005215)			breast(8)|central_nervous_system(4)|cervix(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(42)|liver(1)|lung(107)|ovary(9)|pancreas(2)|prostate(3)|skin(9)|stomach(3)|upper_aerodigestive_tract(11)|urinary_tract(8)	241					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	CATCCATTTGGCCCATAACCA	0.448													G|||	2676	0.534345	0.3676	0.6009	5008	,	,		18892	0.6558		0.5875	False		,,,				2504	0.5327				p.P389T		Atlas-SNP	.											.	CUBN	515	.	0			c.C1165A						PASS	.	G	THR/PRO	1819,2587	533.3+/-373.7	371,1077,755	146.0	126.0	133.0		1165	1.4	0.5	10	dbSNP_89	133	5823,2777	678.5+/-403.5	1983,1857,460	yes	missense	CUBN	NM_001081.3	38	2354,2934,1215	TT,TG,GG		32.2907,41.2846,41.2425	possibly-damaging	389/3624	17147521	7642,5364	2203	4300	6503	SO:0001583	missense	8029	exon11			CATTTGGCCCATA	AF034611	CCDS7113.1	10p12	2014-09-17			ENSG00000107611	ENSG00000107611			2548	protein-coding gene	gene with protein product		602997		MGA1		9572993, 9478979	Standard	NM_001081		Approved	IFCR, gp280	uc001ioo.3	O60494	OTTHUMG00000017741	ENST00000377833.4:c.1165C>A	10.37:g.17147521G>T	ENSP00000367064:p.Pro389Thr	Somatic	196	0	0		WXS	Illumina HiSeq	Phase_I	152	71	0.467105	NM_001081	B0YIZ4|Q5VTA6|Q96RU9	Missense_Mutation	SNP	ENST00000377833.4	37	CCDS7113.1	1225	0.5608974358974359	205	0.4166666666666667	220	0.6077348066298343	365	0.6381118881118881	435	0.5738786279683378	G	14.04	2.415303	0.42817	0.412846	0.677093	ENSG00000107611	ENST00000377833	T	0.40756	1.02	5.65	1.37	0.22104	Growth factor, receptor (1);Epidermal growth factor-like (1);	0.670270	0.13115	N	0.412718	T	0.00012	0.0000	L	0.53249	1.67	0.09310	P	0.999999999795783	P	0.39282	0.666	B	0.35859	0.212	T	0.37384	-0.9708	9	0.66056	D	0.02	.	5.4646	0.16635	0.0693:0.1251:0.5467:0.2588	rs1801224;rs2228052;rs10795446;rs41538725;rs41538899;rs41539425;rs52807320;rs61727981;rs10795446	389	O60494	CUBN_HUMAN	T	389	ENSP00000367064:P389T	ENSP00000367064:P389T	P	-	1	0	CUBN	17187527	0.991000	0.36638	0.490000	0.27465	0.703000	0.40648	3.034000	0.49751	0.296000	0.22592	-0.282000	0.10007	CCA	T|0.469;G|0.343;C|0.092;A|0.097	0.469	strong		0.448	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047009.1	NM_001081	
XRCC6	2547	hgsc.bcm.edu	37	22	42059768	42059768	+	Silent	SNP	G	G	T	rs132788	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:42059768G>T	ENST00000359308.4	+	12	2434	c.1779G>T	c.(1777-1779)ggG>ggT	p.G593G	XRCC6_ENST00000405878.1_Silent_p.G593G|XRCC6_ENST00000402580.3_Silent_p.G552G|XRCC6_ENST00000360079.3_Silent_p.G593G|XRCC6_ENST00000405506.1_Silent_p.G543G|XRCC6_ENST00000428575.2_Silent_p.G460G			P12956	XRCC6_HUMAN	X-ray repair complementing defective repair in Chinese hamster cells 6	593	Interaction with DEAF1.|SAP. {ECO:0000255|PROSITE- ProRule:PRU00186}.				brain development (GO:0007420)|cellular hyperosmotic salinity response (GO:0071475)|cellular response to X-ray (GO:0071481)|DNA duplex unwinding (GO:0032508)|DNA ligation (GO:0006266)|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)|innate immune response (GO:0045087)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of neurogenesis (GO:0050769)|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)|telomere maintenance (GO:0000723)|transcription, DNA-templated (GO:0006351)|V(D)J recombination (GO:0033151)|viral process (GO:0016032)	cytosol (GO:0005829)|Ku70:Ku80 complex (GO:0043564)|membrane (GO:0016020)|nonhomologous end joining complex (GO:0070419)|nuclear telomere cap complex (GO:0000783)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	5'-deoxyribose-5-phosphate lyase activity (GO:0051575)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)|telomeric DNA binding (GO:0042162)|transcription regulatory region DNA binding (GO:0044212)			central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(4)|liver(2)|lung(12)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	31						TGAAGAGTGGGCTGAAGAAGC	0.622								Non-homologous end-joining					G|||	1047	0.209065	0.034	0.2089	5008	,	,		19059	0.2331		0.3628	False		,,,				2504	0.2628				p.G593G		Atlas-SNP	.											.	XRCC6	64	.	0			c.G1779T						PASS	.	G		405,4001	190.9+/-216.7	25,355,1823	50.0	49.0	50.0		1779	1.6	0.2	22	dbSNP_78	50	3082,5518	449.5+/-362.1	553,1976,1771	no	coding-synonymous	XRCC6	NM_001469.3		578,2331,3594	TT,TG,GG		35.8372,9.192,26.8107		593/610	42059768	3487,9519	2203	4300	6503	SO:0001819	synonymous_variant	2547	exon13			GAGTGGGCTGAAG	J04607	CCDS14021.1, CCDS74870.1, CCDS74871.1	22q13.2	2011-09-12	2008-07-31	2005-05-06	ENSG00000196419	ENSG00000196419			4055	protein-coding gene	gene with protein product	"""Ku autoantigen, 70kDa"""	152690	"""thyroid autoantigen 70kD (Ku antigen)"", ""thyroid autoantigen 70kDa (Ku antigen)"""	G22P1		9200330, 9223317	Standard	NM_001469		Approved	D22S731, D22S671, KU70, ML8	uc003bao.1	P12956	OTTHUMG00000151190	ENST00000359308.4:c.1779G>T	22.37:g.42059768G>T		Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	164	72	0.439024	NM_001469	B1AHC8|Q6FG89|Q9UCQ2|Q9UCQ3	Silent	SNP	ENST00000359308.4	37	CCDS14021.1																																																																																			.	.	weak		0.622	XRCC6-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321688.1	NM_001469	
OR10H5	284433	hgsc.bcm.edu	37	19	15905431	15905431	+	Silent	SNP	T	T	C	rs4808381	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:15905431T>C	ENST00000308940.8	+	1	671	c.573T>C	c.(571-573)gaT>gaC	p.D191D		NM_001004466.1	NP_001004466.1	Q8NGA6	O10H5_HUMAN	olfactory receptor, family 10, subfamily H, member 5	191						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(1)|lung(9)|ovary(1)	20						CCTGTGGAGATGATGTGCTGG	0.572													.|||	2284	0.45607	0.3359	0.4784	5008	,	,		22330	0.7897		0.3052	False		,,,				2504	0.4141				p.D191D		Atlas-SNP	.											.	OR10H5	49	.	0			c.T573C						PASS	.	T		1488,2918		260,968,975	165.0	130.0	142.0		573	-5.6	0.0	19	dbSNP_111	142	2843,5757		509,1825,1966	no	coding-synonymous	OR10H5	NM_001004466.1		769,2793,2941	CC,CT,TT		33.0581,33.7721,33.3		191/316	15905431	4331,8675	2203	4300	6503	SO:0001819	synonymous_variant	284433	exon1			TGGAGATGATGTG	AC011537	CCDS32940.1	19p13.12	2013-09-24			ENSG00000172519	ENSG00000172519		"""GPCR / Class A : Olfactory receptors"""	15389	protein-coding gene	gene with protein product							Standard	NM_001004466		Approved		uc010xos.2	Q8NGA6	OTTHUMG00000182284	ENST00000308940.8:c.573T>C	19.37:g.15905431T>C		Somatic	279	0	0		WXS	Illumina HiSeq	Phase_I	206	103	0.5	NM_001004466	Q6IFJ0|Q96R60	Silent	SNP	ENST00000308940.8	37	CCDS32940.1																																																																																			T|0.623;C|0.377	0.377	strong		0.572	OR10H5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460363.1		
ARHGEF1	9138	hgsc.bcm.edu	37	19	42409189	42409189	+	Splice_Site	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:42409189G>A	ENST00000354532.3	+	23	2397		c.e23+1		ARHGEF1_ENST00000378152.4_Splice_Site|ARHGEF1_ENST00000347545.4_Splice_Site|ARHGEF1_ENST00000599846.1_Splice_Site|ARHGEF1_ENST00000337665.4_Splice_Site	NM_004706.3	NP_004697.2	Q92888	ARHG1_HUMAN	Rho guanine nucleotide exchange factor (GEF) 1						cell proliferation (GO:0008283)|negative regulation of axonogenesis (GO:0050771)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of axonogenesis (GO:0050770)|Rho protein signal transduction (GO:0007266)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)|poly(A) RNA binding (GO:0044822)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(2)|endometrium(8)|large_intestine(6)|lung(9)|ovary(3)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	37		Renal(1328;0.000518)|Hepatocellular(1079;0.0046)|Medulloblastoma(540;0.0425)		Epithelial(262;5.89e-46)|GBM - Glioblastoma multiforme(1328;2.49e-12)|STAD - Stomach adenocarcinoma(1328;0.00644)		AGCGGAAAAAGTGAGGGGGGG	0.602																																					.		Atlas-SNP	.											ARHGEF1,NS,carcinoma,+1,1	ARHGEF1	95	1	0			c.2249+1G>A						PASS	.						46.0	45.0	45.0					19																	42409189		2203	4300	6503	SO:0001630	splice_region_variant	9138	exon23			GAAAAAGTGAGGG	U64105	CCDS12590.1, CCDS12591.1, CCDS12592.1	19q13.13	2014-06-19			ENSG00000076928	ENSG00000076928		"""Rho guanine nucleotide exchange factors"""	681	protein-coding gene	gene with protein product		601855				8810315, 9135076	Standard	NM_004706		Approved	P115-RHOGEF, SUB1.5, LBCL2	uc002osa.3	Q92888	OTTHUMG00000182679	ENST00000354532.3:c.2249+1G>A	19.37:g.42409189G>A		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	78	16	0.205128	NM_004706	O00513|Q8N4J4|Q96BF4|Q96F17|Q9BSB1	Splice_Site	SNP	ENST00000354532.3	37	CCDS12591.1	.	.	.	.	.	.	.	.	.	.	G	15.82	2.946544	0.53186	.	.	ENSG00000076928	ENST00000354532;ENST00000347545;ENST00000337665;ENST00000378152	.	.	.	4.53	4.53	0.55603	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.1593	0.72771	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	ARHGEF1	47101029	1.000000	0.71417	0.160000	0.22671	0.018000	0.09664	5.579000	0.67457	2.229000	0.72834	0.585000	0.79938	.	.	.	none		0.602	ARHGEF1-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000463360.1	NM_199002	Intron
MCEE	84693	hgsc.bcm.edu	37	2	71351403	71351403	+	Missense_Mutation	SNP	C	C	A	rs6748672	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:71351403C>A	ENST00000244217.5	-	2	328	c.311G>T	c.(310-312)cGt>cTt	p.R104L	AC007881.1_ENST00000578636.1_RNA	NM_032601.3	NP_115990.3	Q96PE7	MCEE_HUMAN	methylmalonyl CoA epimerase	104			R -> L (in dbSNP:rs6748672). {ECO:0000269|PubMed:15489334}.		cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|L-methylmalonyl-CoA metabolic process (GO:0046491)|short-chain fatty acid catabolic process (GO:0019626)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)	metal ion binding (GO:0046872)|methylmalonyl-CoA epimerase activity (GO:0004493)			kidney(1)|large_intestine(2)|lung(3)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	9						TGGACTGTCACGTCCCAATGG	0.428													C|||	1009	0.201478	0.2277	0.1729	5008	,	,		17794	0.2282		0.1342	False		,,,				2504	0.228				p.R104L		Atlas-SNP	.											MCEE,NS,carcinoma,-1,1	MCEE	19	1	0			c.G311T						scavenged	.	C	LEU/ARG	1003,3403	373.4+/-320.8	113,777,1313	80.0	76.0	77.0		311	-4.6	0.0	2	dbSNP_116	77	1449,7151	277.2+/-292.7	121,1207,2972	yes	missense	MCEE	NM_032601.3	102	234,1984,4285	AA,AC,CC		16.8488,22.7644,18.8528	benign	104/177	71351403	2452,10554	2203	4300	6503	SO:0001583	missense	84693	exon2			CTGTCACGTCCCA	AF364547	CCDS1915.1	2p13.3	2011-05-12			ENSG00000124370	ENSG00000124370	5.1.99.1		16732	protein-coding gene	gene with protein product	"""glyoxalase domain containing 2"""	608419				16697227, 16752391, 16843692	Standard	NM_032601		Approved	GLOD2	uc002shs.2	Q96PE7	OTTHUMG00000129709	ENST00000244217.5:c.311G>T	2.37:g.71351403C>A	ENSP00000244217:p.Arg104Leu	Somatic	167	2	0.011976		WXS	Illumina HiSeq	Phase_I	101	55	0.544554	NM_032601	Q53TP1|Q8WW63	Missense_Mutation	SNP	ENST00000244217.5	37	CCDS1915.1	377	0.17261904761904762	108	0.21951219512195122	61	0.1685082872928177	102	0.17832167832167833	106	0.13984168865435356	C	10.04	1.241494	0.22711	0.227644	0.168488	ENSG00000124370	ENST00000244217;ENST00000494660;ENST00000486135	T;T;T	0.64438	-0.1;-0.1;-0.1	5.38	-4.61	0.03380	Glyoxalase/fosfomycin resistance/dioxygenase (1);	0.710167	0.14406	N	0.321551	T	0.00012	0.0000	N	0.12746	0.255	0.80722	P	0.0	B	0.14438	0.01	B	0.10450	0.005	T	0.06698	-1.0812	9	0.62326	D	0.03	-12.157	6.8041	0.23768	0.1109:0.3619:0.0:0.5272	rs6748672;rs17851835;rs52804383;rs58491237;rs6748672	104	Q96PE7	MCEE_HUMAN	L	104;9;9	ENSP00000244217:R104L;ENSP00000437361:R9L;ENSP00000441569:R9L	ENSP00000244217:R104L	R	-	2	0	MCEE	71204911	0.658000	0.27402	0.000000	0.03702	0.217000	0.24651	0.803000	0.27083	-1.053000	0.03218	-0.259000	0.10710	CGT	C|0.817;A|0.183	0.183	strong		0.428	MCEE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251917.3	NM_032601	
TTC22	55001	hgsc.bcm.edu	37	1	55266797	55266797	+	Missense_Mutation	SNP	G	G	C	rs671108	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:55266797G>C	ENST00000371276.4	-	1	143	c.40C>G	c.(40-42)Ctc>Gtc	p.L14V	TTC22_ENST00000371274.4_Missense_Mutation_p.L14V	NM_001114108.1	NP_001107580.1	Q5TAA0	TTC22_HUMAN	tetratricopeptide repeat domain 22	14			L -> V (in dbSNP:rs671108).							kidney(1)|large_intestine(1)|lung(7)|skin(1)	10						TCGTCGATGAGGGCGTCTAGA	0.662													G|||	769	0.153554	0.0265	0.2334	5008	,	,		13377	0.2639		0.2356	False		,,,				2504	0.0706				p.L14V		Atlas-SNP	.											.	TTC22	40	.	0			c.C40G						PASS	.	G	VAL/LEU,VAL/LEU	251,4141		11,229,1956	28.0	26.0	27.0		40,40	4.1	1.0	1	dbSNP_83	27	1735,6841		178,1379,2731	yes	missense,missense	TTC22	NM_001114108.1,NM_017904.3	32,32	189,1608,4687	CC,CG,GG		20.2309,5.7149,15.3146	probably-damaging,probably-damaging	14/570,14/373	55266797	1986,10982	2196	4288	6484	SO:0001583	missense	55001	exon1			CGATGAGGGCGTC	AK000626	CCDS598.1, CCDS44152.1	1p32.3	2013-01-11			ENSG00000006555	ENSG00000006555		"""Tetratricopeptide (TTC) repeat domain containing"""	26067	protein-coding gene	gene with protein product							Standard	NM_017904		Approved	FLJ20619	uc009vzt.1	Q5TAA0	OTTHUMG00000009916	ENST00000371276.4:c.40C>G	1.37:g.55266797G>C	ENSP00000360323:p.Leu14Val	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	118	53	0.449153	NM_001114108	Q9NWT4	Missense_Mutation	SNP	ENST00000371276.4	37	CCDS44152.1	435	0.19917582417582416	24	0.04878048780487805	87	0.24033149171270718	157	0.2744755244755245	167	0.22031662269129287	G	15.92	2.974554	0.53720	0.057149	0.202309	ENSG00000006555	ENST00000371276;ENST00000371274	T;T	0.60920	0.17;0.15	4.13	4.13	0.48395	.	0.000000	0.64402	D	0.000001	T	0.00012	0.0000	M	0.61703	1.905	0.20489	P	0.999899774	D;D	0.76494	0.999;0.996	D;D	0.80764	0.987;0.994	T	0.01015	-1.1480	9	0.56958	D	0.05	-10.3499	15.6739	0.77300	0.0:0.0:1.0:0.0	rs671108;rs671108	14;14	Q5TAA0;Q5TAA0-2	TTC22_HUMAN;.	V	14	ENSP00000360323:L14V;ENSP00000360321:L14V	ENSP00000360321:L14V	L	-	1	0	TTC22	55039385	1.000000	0.71417	1.000000	0.80357	0.910000	0.53928	2.057000	0.41365	2.279000	0.76181	0.491000	0.48974	CTC	G|0.830;C|0.170	0.170	strong		0.662	TTC22-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027438.1	NM_017904	
RRN3	54700	hgsc.bcm.edu	37	16	15165103	15165103	+	Silent	SNP	G	G	A	rs73491931	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:15165103G>A	ENST00000198767.6	-	13	1217	c.1134C>T	c.(1132-1134)ttC>ttT	p.F378F	RRN3_ENST00000327307.7_Silent_p.F345F|RRN3_ENST00000540462.1_Silent_p.F196F|RRN3_ENST00000429751.2_Silent_p.F348F|PDXDC1_ENST00000535621.2_Intron|RRN3_ENST00000563559.1_Silent_p.F378F	NM_018427.3	NP_060897.3	Q9NYV6	RRN3_HUMAN	RRN3 RNA polymerase I transcription factor homolog (S. cerevisiae)	378					cell proliferation (GO:0008283)|cytoplasm organization (GO:0007028)|gene expression (GO:0010467)|homeostasis of number of cells (GO:0048872)|in utero embryonic development (GO:0001701)|negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator (GO:1902254)|nucleolus organization (GO:0007000)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of DNA-templated transcription, initiation (GO:2000142)|ribosome biogenesis (GO:0042254)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				NS(2)|central_nervous_system(3)|endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(2)|prostate(2)	20						ATGCCTCTGCGAATCCCTATA	0.408													.|||	324	0.0646965	0.1498	0.0317	5008	,	,		15604	0.0615		0.0298	False		,,,				2504	0.0123				p.F378F		Atlas-SNP	.											.	RRN3	36	.	0			c.C1134T						PASS	.	G		527,3867		32,463,1702	74.0	83.0	80.0		1134	-5.8	0.7	16	dbSNP_131	80	252,8348		3,246,4051	no	coding-synonymous	RRN3	NM_018427.3		35,709,5753	AA,AG,GG		2.9302,11.9936,5.9951		378/652	15165103	779,12215	2197	4300	6497	SO:0001819	synonymous_variant	54700	exon13			CTCTGCGAATCCC	AF227156	CCDS10559.1, CCDS73833.1	16p13.11	2009-10-26	2006-04-04		ENSG00000085721	ENSG00000085721			30346	protein-coding gene	gene with protein product		605121	"""RRN3 RNA polymerase I transcription factor homolog (yeast)"""			10758157, 11250903	Standard	XM_005255375		Approved	DKFZp566E104	uc002dde.3	Q9NYV6	OTTHUMG00000129847	ENST00000198767.6:c.1134C>T	16.37:g.15165103G>A		Somatic	359	0	0		WXS	Illumina HiSeq	Phase_I	331	71	0.214502	NM_018427	A2RTY9|B4E0J7|B4E3T2|Q3MHU9|Q6IPL4|Q9H4F0	Silent	SNP	ENST00000198767.6	37	CCDS10559.1																																																																																			G|0.945;A|0.055	0.055	strong		0.408	RRN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252087.2	NM_018427	
COBL	23242	hgsc.bcm.edu	37	7	51097216	51097216	+	Missense_Mutation	SNP	G	G	A	rs17656599	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:51097216G>A	ENST00000265136.7	-	10	1742	c.1577C>T	c.(1576-1578)cCa>cTa	p.P526L	COBL_ENST00000395542.2_Missense_Mutation_p.P608L	NM_015198.3	NP_056013.2	O75128	COBL_HUMAN	cordon-bleu WH2 repeat protein	526			P -> L (in dbSNP:rs17656599). {ECO:0000269|PubMed:17974005}.		actin filament network formation (GO:0051639)|actin filament polymerization (GO:0030041)|collateral sprouting in absence of injury (GO:0048669)|digestive tract development (GO:0048565)|embryonic axis specification (GO:0000578)|floor plate development (GO:0033504)|liver development (GO:0001889)|neural tube closure (GO:0001843)|notochord development (GO:0030903)|positive regulation of dendrite development (GO:1900006)|somite specification (GO:0001757)	actin filament (GO:0005884)|axon (GO:0030424)|axonal growth cone (GO:0044295)|cell cortex (GO:0005938)|dendrite (GO:0030425)|dendritic growth cone (GO:0044294)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	actin monomer binding (GO:0003785)			NS(2)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(26)|ovary(3)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	65	Glioma(55;0.08)					GGCATCCTGTGGGCAGTGGTT	0.493													G|||	228	0.0455272	0.0053	0.0865	5008	,	,		19243	0.0		0.1302	False		,,,				2504	0.0307				p.P526L	NSCLC(189;2119 2138 12223 30818 34679)	Atlas-SNP	.											.	COBL	167	.	0			c.C1577T						PASS	.	G	LEU/PRO	110,4296	84.4+/-122.9	5,100,2098	117.0	113.0	114.0		1577	0.5	0.0	7	dbSNP_123	114	1057,7543	223.3+/-260.1	77,903,3320	yes	missense	COBL	NM_015198.3	98	82,1003,5418	AA,AG,GG		12.2907,2.4966,8.9728	benign	526/1262	51097216	1167,11839	2203	4300	6503	SO:0001583	missense	23242	exon10			TCCTGTGGGCAGT	AB014533	CCDS34637.1, CCDS75601.1, CCDS75602.1	7p12.2-p12.1	2012-12-07	2012-12-07		ENSG00000106078	ENSG00000106078			22199	protein-coding gene	gene with protein product		610317	"""cordon-bleu homolog (mouse)"""				Standard	NM_015198		Approved	KIAA0633	uc003tpr.4	O75128	OTTHUMG00000155999	ENST00000265136.7:c.1577C>T	7.37:g.51097216G>A	ENSP00000265136:p.Pro526Leu	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	79	21	0.265823	NM_015198	A4D257|A7E2B0|B7ZLW9|B9EGF8|Q2T9J3|Q504Y4|Q86XA7|Q8N304|Q8TCM1	Missense_Mutation	SNP	ENST00000265136.7	37	CCDS34637.1	138	0.06318681318681318	5	0.01016260162601626	39	0.10773480662983426	0	0.0	94	0.12401055408970976	G	7.611	0.674869	0.14841	0.024966	0.122907	ENSG00000106078	ENST00000265136;ENST00000445054;ENST00000431948;ENST00000395542;ENST00000457306	T;T;T;T	0.20463	2.07;2.07;2.07;2.07	5.6	0.527	0.17084	.	2.250440	0.02046	N	0.049656	T	0.00144	0.0004	N	0.03608	-0.345	0.80722	P	0.0	B;B;B;B;B	0.06786	0.0;0.0;0.0;0.0;0.001	B;B;B;B;B	0.06405	0.001;0.001;0.0;0.001;0.002	T	0.22521	-1.0214	9	0.27785	T	0.31	.	5.7387	0.18081	0.4638:0.1479:0.3883:0.0	rs17656599;rs52804892;rs17656599	526;583;526;608;68	O75128-3;O75128-7;O75128;O75128-2;O75128-6	.;.;COBL_HUMAN;.;.	L	526;418;411;608;24	ENSP00000265136:P526L;ENSP00000401204:P418L;ENSP00000413498:P411L;ENSP00000378912:P608L	ENSP00000265136:P526L	P	-	2	0	COBL	51064710	0.000000	0.05858	0.004000	0.12327	0.010000	0.07245	-1.240000	0.02914	0.447000	0.26695	0.655000	0.94253	CCA	G|0.919;A|0.081	0.081	strong		0.493	COBL-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000342682.1	NM_015198	
PPP1R18	170954	hgsc.bcm.edu	37	6	30652781	30652781	+	Missense_Mutation	SNP	C	C	T	rs9262143	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:30652781C>T	ENST00000274853.3	-	1	2891	c.1015G>A	c.(1015-1017)Ggg>Agg	p.G339R	PPP1R18_ENST00000399199.3_Missense_Mutation_p.G339R|PPP1R18_ENST00000488324.1_Intron	NM_133471.3	NP_597728.1	Q6NYC8	PPR18_HUMAN	protein phosphatase 1, regulatory subunit 18	339			G -> R (in dbSNP:rs9262143). {ECO:0000269|PubMed:14574404}.			cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)											CGAGCCTTCCCGGAGTTCAGG	0.567													C|||	97	0.019369	0.0023	0.0202	5008	,	,		14981	0.0		0.0795	False		,,,				2504	0.0				p.G339R		Atlas-SNP	.											.	.	.	.	0			c.G1015A						PASS	.	C	ARG/GLY,ARG/GLY	54,2818		1,52,1383	120.0	143.0	135.0		1015,1015	5.1	1.0	6	dbSNP_118	135	551,4765		32,487,2139	yes	missense,missense	KIAA1949	NM_001134870.1,NM_133471.3	125,125	33,539,3522	TT,TC,CC		10.3649,1.8802,7.3889	probably-damaging,probably-damaging	339/614,339/614	30652781	605,7583	1436	2658	4094	SO:0001583	missense	170954	exon2			CCTTCCCGGAGTT	AK097089	CCDS43444.1	6p21.3	2012-04-17	2011-10-11	2011-10-11	ENSG00000146112	ENSG00000146112		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	29413	protein-coding gene	gene with protein product	"""protein phosphatase 1 F-actin cytoskeleton targeting subunit"""	610990	"""KIAA1949"""	KIAA1949		11853319	Standard	NM_001134870		Approved	phostensin	uc003nra.3	Q6NYC8	OTTHUMG00000031237	ENST00000274853.3:c.1015G>A	6.37:g.30652781C>T	ENSP00000274853:p.Gly339Arg	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	97	53	0.546392	NM_001134870	A2AB01|A2AIB8|A4UBI6|A6NCB7|A8MSS7|B7ZCV7|Q68CK8|Q6ZTV1|Q6ZUJ6|Q8NDQ4|Q8TF52|Q9BRL9	Missense_Mutation	SNP	ENST00000274853.3	37	CCDS43444.1	79	0.036172161172161175	2	0.0040650406504065045	11	0.03038674033149171	0	0.0	66	0.0870712401055409	C	20.5	4.006971	0.74932	0.018802	0.103649	ENSG00000146112	ENST00000274853;ENST00000399199	T;T	0.55588	0.51;0.51	5.1	5.1	0.69264	.	0.378221	0.21808	N	0.068801	T	0.50837	0.1639	L	0.32530	0.975	0.38584	D	0.950265	D	0.76494	0.999	D	0.64595	0.927	T	0.45101	-0.9284	10	0.28530	T	0.3	-24.1078	17.2657	0.87086	0.0:1.0:0.0:0.0	rs9262143;rs17189267;rs52821119;rs57338511;rs9262143	339	Q6NYC8	PPR18_HUMAN	R	339	ENSP00000274853:G339R;ENSP00000382150:G339R	ENSP00000274853:G339R	G	-	1	0	KIAA1949	30760760	0.995000	0.38212	1.000000	0.80357	0.967000	0.64934	3.624000	0.54231	2.369000	0.80426	0.561000	0.74099	GGG	C|0.942;T|0.058	0.058	strong		0.567	PPP1R18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076498.2	NM_133471	
ARHGAP8	23779	hgsc.bcm.edu	37	22	45221423	45221423	+	Silent	SNP	A	A	T	rs3209476	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:45221423A>T	ENST00000389774.2	+	8	780	c.639A>T	c.(637-639)ccA>ccT	p.P213P	PRR5-ARHGAP8_ENST00000352766.7_Silent_p.P392P|ARHGAP8_ENST00000356099.6_Silent_p.P182P|PRR5-ARHGAP8_ENST00000361473.5_Silent_p.P313P|ARHGAP8_ENST00000517296.3_Silent_p.P392P|ARHGAP8_ENST00000336963.4_Silent_p.P182P|ARHGAP8_ENST00000389773.5_Silent_p.P304P	NM_001017526.1	NP_001017526.1	P85298	RHG08_HUMAN	Rho GTPase activating protein 8	213					positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho GTPase activator activity (GO:0005100)			breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(7)|lung(9)|prostate(1)|skin(7)	29		all_neural(38;0.00409)|Ovarian(80;0.00976)|Glioma(61;0.0649)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0204)		CCAAGACACCACCGCCGCGGC	0.652													a|||	732	0.146166	0.1914	0.085	5008	,	,		13154	0.0099		0.1948	False		,,,				2504	0.2188				p.P304P		Atlas-SNP	.											PRR5-ARHGAP8,colon,carcinoma,+1,2	PRR5-ARHGAP8	53	2	0			c.A912T						PASS	.	A	,,,	846,3558	315.2+/-294.0	65,716,1421	31.0	33.0	33.0		639,546,912,546	-8.8	0.0	22	dbSNP_105	33	1678,6920	290.7+/-299.9	164,1350,2785	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ARHGAP8,PRR5-ARHGAP8	NM_001017526.1,NM_001198726.1,NM_181334.4,NM_181335.2	,,,	229,2066,4206	TT,TA,AA		19.5162,19.2098,19.4124	,,,	213/465,182/306,304/556,182/434	45221423	2524,10478	2202	4299	6501	SO:0001819	synonymous_variant	553158	exon10			GACACCACCGCCG	AF177331	CCDS14060.2, CCDS33664.1, CCDS56233.1	22q13.3	2010-05-11			ENSG00000241484	ENSG00000241484		"""Rho GTPase activating proteins"""	677	protein-coding gene	gene with protein product		609405				10591208	Standard	NM_001198726		Approved	FLJ20185, BPGAP1		P85298	OTTHUMG00000030234	ENST00000389774.2:c.639A>T	22.37:g.45221423A>T		Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	163	79	0.484663	NM_181334	A6ZJ79|A6ZJ80|O75983|O95695|Q96RW1|Q96RW2|Q9HA49|Q9HC46|Q9NSG0|Q9NVX8|Q9NXL1|Q9UH20	Silent	SNP	ENST00000389774.2	37	CCDS33664.1	268	0.1227106227106227	92	0.18699186991869918	29	0.08011049723756906	1	0.0017482517482517483	146	0.19261213720316622	a	6.831	0.522414	0.13066	0.192098	0.195162	ENSG00000248405	ENST00000515632	.	.	.	4.39	-8.78	0.00824	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.33833	P	0.36955499999999997	.	.	.	.	.	.	T	0.17837	-1.0356	3	.	.	.	.	1.066	0.01611	0.3899:0.2635:0.1256:0.2211	rs3209476;rs17410467	.	.	.	L	236	.	.	H	+	2	0	PRR5-ARHGAP8	43600087	0.000000	0.05858	0.002000	0.10522	0.001000	0.01503	-6.362000	0.00069	-2.852000	0.00330	-0.771000	0.03389	CAC	A|0.825;T|0.175	0.175	strong		0.652	ARHGAP8-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000075088.4	NM_017701	
CNTNAP4	85445	hgsc.bcm.edu	37	16	76461498	76461498	+	Splice_Site	SNP	T	T	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:76461498T>G	ENST00000476707.1	+	3	686		c.e3+2		CNTNAP4_ENST00000377504.4_Splice_Site|CNTNAP4_ENST00000478060.1_Splice_Site|CNTNAP4_ENST00000307431.8_Splice_Site|CNTNAP4_ENST00000469589.1_Splice_Site			Q9C0A0	CNTP4_HUMAN	contactin associated protein-like 4						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						GTGCATACAGTAAGTGTTTGT	0.388																																					.		Atlas-SNP	.											.	CNTNAP4	600	.	0			c.537+2T>G						PASS	.						76.0	71.0	73.0					16																	76461498		2198	4300	6498	SO:0001630	splice_region_variant	85445	exon4			ATACAGTAAGTGT	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.547+2T>G	16.37:g.76461498T>G		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	168	74	0.440476	NM_033401	E9PFZ6|Q86YZ7	Splice_Site	SNP	ENST00000476707.1	37		.	.	.	.	.	.	.	.	.	.	T	24.5	4.533056	0.85812	.	.	ENSG00000152910	ENST00000307431;ENST00000377504;ENST00000478060;ENST00000476707	.	.	.	4.98	4.98	0.66077	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.8097	0.69985	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	CNTNAP4	75018999	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.720000	0.84759	2.232000	0.73038	0.533000	0.62120	.	.	.	none		0.388	CNTNAP4-005	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000348216.1	NM_033401	Intron
CDHR3	222256	hgsc.bcm.edu	37	7	105615406	105615406	+	Missense_Mutation	SNP	G	G	A	rs35008315	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:105615406G>A	ENST00000317716.9	+	2	243	c.163G>A	c.(163-165)Gtg>Atg	p.V55M	CDHR3_ENST00000478080.1_Intron|CDHR3_ENST00000542731.1_Missense_Mutation_p.V55M|CDHR3_ENST00000470188.1_3'UTR|CDHR3_ENST00000541203.1_Missense_Mutation_p.V55M|CDHR3_ENST00000343407.5_5'UTR	NM_152750.4	NP_689963.2	Q6ZTQ4	CDHR3_HUMAN	cadherin-related family member 3	55	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.		V -> M (in dbSNP:rs35008315).		homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|cervix(3)|endometrium(1)|kidney(1)|large_intestine(1)|lung(15)|ovary(1)	23						ATTGTCACCTGTGATCCCAGG	0.458													G|||	805	0.160743	0.062	0.2133	5008	,	,		22290	0.2609		0.1789	False		,,,				2504	0.135				p.V55M		Atlas-SNP	.											.	CDHR3	153	.	0			c.G163A						PASS	.	G	MET/VAL	344,3432		18,308,1562	190.0	177.0	181.0		163	4.6	1.0	7	dbSNP_126	181	1637,6615		162,1313,2651	yes	missense	CDHR3	NM_152750.4	21	180,1621,4213	AA,AG,GG		19.8376,9.1102,16.4699	probably-damaging	55/886	105615406	1981,10047	1888	4126	6014	SO:0001583	missense	222256	exon2			TCACCTGTGATCC	AK126338	CCDS47684.1, CCDS75651.1	7q22.2	2011-07-01			ENSG00000128536	ENSG00000128536		"""Cadherins / Cadherin-related"""	26308	protein-coding gene	gene with protein product		615610					Standard	NM_152750		Approved	FLJ44366, FLJ23834, CDH28	uc003vdl.4	Q6ZTQ4	OTTHUMG00000157520	ENST00000317716.9:c.163G>A	7.37:g.105615406G>A	ENSP00000325954:p.Val55Met	Somatic	254	0	0		WXS	Illumina HiSeq	Phase_I	221	104	0.470588	NM_152750	Q8TCI7	Missense_Mutation	SNP	ENST00000317716.9	37	CCDS47684.1	383	0.17536630036630035	36	0.07317073170731707	85	0.23480662983425415	126	0.2202797202797203	136	0.17941952506596306	G	18.28	3.590200	0.66105	0.091102	0.198376	ENSG00000128536	ENST00000542731;ENST00000317716;ENST00000541203	T;T;T	0.15487	2.42;2.42;2.42	5.46	4.56	0.56223	Cadherin (2);	0.088554	0.47455	D	0.000221	T	0.00012	0.0000	M	0.68317	2.08	0.09310	P	1.0	D;D	0.53619	0.961;0.961	P;P	0.52646	0.705;0.705	T	0.08597	-1.0714	9	0.56958	D	0.05	-9.0937	15.1633	0.72801	0.0:0.1419:0.8581:0.0	rs35008315;rs58776450;rs62481264	42;55	B3KYA0;Q6ZTQ4	.;CDHR3_HUMAN	M	55	ENSP00000439766:V55M;ENSP00000325954:V55M;ENSP00000443733:V55M	ENSP00000325954:V55M	V	+	1	0	CDHR3	105402642	1.000000	0.71417	0.997000	0.53966	0.708000	0.40852	2.616000	0.46376	1.491000	0.48482	0.655000	0.94253	GTG	G|0.824;A|0.176	0.176	strong		0.458	CDHR3-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000349025.2	NM_152750	
AGBL1	123624	hgsc.bcm.edu	37	15	86702241	86702241	+	Missense_Mutation	SNP	C	C	T	rs79814209	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:86702241C>T	ENST00000441037.2	+	4	429	c.334C>T	c.(334-336)Cgc>Tgc	p.R112C	AGBL1_ENST00000421325.2_Missense_Mutation_p.R112C	NM_152336.2	NP_689549.2	Q96MI9	CBPC4_HUMAN	ATP/GTP binding protein-like 1	112					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						CACCCGAAAGCGCACCCAAGC	0.438													C|||	73	0.0145767	0.0	0.0086	5008	,	,		20806	0.0		0.0408	False		,,,				2504	0.0266				p.R112C		Atlas-SNP	.											.	AGBL1	151	.	0			c.C334T						PASS	.	C	CYS/ARG	35,3831		0,35,1898	126.0	116.0	119.0		334	4.1	0.0	15	dbSNP_131	119	347,7925		5,337,3794	yes	missense	AGBL1	NM_152336.2	180	5,372,5692	TT,TC,CC		4.1949,0.9053,3.1471	probably-damaging	112/1067	86702241	382,11756	1933	4136	6069	SO:0001583	missense	123624	exon4			CGAAAGCGCACCC	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.334C>T	15.37:g.86702241C>T	ENSP00000413001:p.Arg112Cys	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	98	48	0.489796	NM_152336	A1A4X5|A6NJH6|C9JHL5	Missense_Mutation	SNP	ENST00000441037.2	37	CCDS58398.1	31	0.014194139194139194	0	0.0	1	0.0027624309392265192	0	0.0	30	0.0395778364116095	C	8.492	0.862235	0.17178	0.009053	0.041949	ENSG00000166748	ENST00000441037;ENST00000421325	T	0.35236	1.32	5.01	4.08	0.47627	Armadillo-like helical (1);Armadillo-type fold (1);	.	.	.	.	T	0.11879	0.0289	L	0.47716	1.5	0.23070	N	0.998347	D	0.64830	0.994	P	0.47744	0.556	T	0.02774	-1.1112	9	0.54805	T	0.06	-2.3402	11.7532	0.51859	0.0:0.8222:0.1778:0.0	.	112	Q96MI9	CBPC4_HUMAN	C	141;112	ENSP00000397173:R112C	ENSP00000397173:R112C	R	+	1	0	AGBL1	84503245	0.718000	0.27976	0.019000	0.16419	0.054000	0.15201	1.328000	0.33758	1.218000	0.43458	0.655000	0.94253	CGC	C|0.980;T|0.020	0.020	strong		0.438	AGBL1-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000314929.5	NM_152336	
ZCWPW2	152098	hgsc.bcm.edu	37	3	28454627	28454627	+	Missense_Mutation	SNP	A	A	G	rs148504648	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:28454627A>G	ENST00000383768.2	+	3	256	c.68A>G	c.(67-69)aAc>aGc	p.N23S	ZCWPW2_ENST00000421010.1_Missense_Mutation_p.N23S			Q504Y3	ZCPW2_HUMAN	zinc finger, CW type with PWWP domain 2	23							zinc ion binding (GO:0008270)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(6)|ovary(2)	17						TCAGTGGAAAACATGTATGTA	0.323													A|||	2	0.000399361	0.0	0.0	5008	,	,		19875	0.0		0.002	False		,,,				2504	0.0				p.N23S		Atlas-SNP	.											.	ZCWPW2	49	.	0			c.A68G						PASS	.	A	SER/ASN	6,4400	9.9+/-24.2	0,6,2197	109.0	107.0	108.0		68	0.1	0.0	3	dbSNP_134	108	25,8575	17.3+/-56.4	0,25,4275	yes	missense	ZCWPW2	NM_001040432.1	46	0,31,6472	GG,GA,AA		0.2907,0.1362,0.2384	benign	23/357	28454627	31,12975	2203	4300	6503	SO:0001583	missense	152098	exon2			TGGAAAACATGTA	BC065764	CCDS33723.1	3p23	2005-08-22			ENSG00000206559	ENSG00000206559			23574	protein-coding gene	gene with protein product						14607086	Standard	XM_005264892		Approved	ZCW2	uc003cei.3	Q504Y3	OTTHUMG00000155705	ENST00000383768.2:c.68A>G	3.37:g.28454627A>G	ENSP00000373278:p.Asn23Ser	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	83	28	0.337349	NM_001040432		Missense_Mutation	SNP	ENST00000383768.2	37	CCDS33723.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	A	16.03	3.007777	0.54361	0.001362	0.002907	ENSG00000206559	ENST00000420223;ENST00000383768;ENST00000421010	T;T	0.32988	1.43;1.43	5.37	0.0559	0.14317	.	0.328394	0.26474	N	0.024175	T	0.18383	0.0441	L	0.29908	0.895	0.09310	N	1	B	0.09022	0.002	B	0.08055	0.003	T	0.15350	-1.0440	10	0.36615	T	0.2	-2.9798	7.7479	0.28879	0.5196:0.0:0.4804:0.0	.	23	Q504Y3	ZCPW2_HUMAN	S	23	ENSP00000373278:N23S;ENSP00000412386:N23S	ENSP00000373278:N23S	N	+	2	0	ZCWPW2	28429631	0.001000	0.12720	0.033000	0.17914	0.962000	0.63368	-0.160000	0.10041	0.000000	0.14550	0.482000	0.46254	AAC	A|0.998;G|0.002	0.002	strong		0.323	ZCWPW2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341318.1	XM_087384	
OR10H5	284433	hgsc.bcm.edu	37	19	15905639	15905639	+	Silent	SNP	C	C	T	rs3746151	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:15905639C>T	ENST00000308940.8	+	1	879	c.781C>T	c.(781-783)Ctg>Ttg	p.L261L		NM_001004466.1	NP_001004466.1	Q8NGA6	O10H5_HUMAN	olfactory receptor, family 10, subfamily H, member 5	261						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(1)|lung(9)|ovary(1)	20						CGTCATTTACCTGAAGCCCAA	0.567													.|||	764	0.152556	0.1422	0.1153	5008	,	,		17530	0.122		0.161	False		,,,				2504	0.2157				p.L261L		Atlas-SNP	.											.	OR10H5	49	.	0			c.C781T						PASS	.	C		680,3726		54,572,1577	108.0	86.0	94.0		781	3.9	1.0	19	dbSNP_107	94	1549,7051		150,1249,2901	no	coding-synonymous	OR10H5	NM_001004466.1		204,1821,4478	TT,TC,CC		18.0116,15.4335,17.1382		261/316	15905639	2229,10777	2203	4300	6503	SO:0001819	synonymous_variant	284433	exon1			ATTTACCTGAAGC	AC011537	CCDS32940.1	19p13.12	2013-09-24			ENSG00000172519	ENSG00000172519		"""GPCR / Class A : Olfactory receptors"""	15389	protein-coding gene	gene with protein product							Standard	NM_001004466		Approved		uc010xos.2	Q8NGA6	OTTHUMG00000182284	ENST00000308940.8:c.781C>T	19.37:g.15905639C>T		Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	144	63	0.4375	NM_001004466	Q6IFJ0|Q96R60	Silent	SNP	ENST00000308940.8	37	CCDS32940.1																																																																																			C|0.841;T|0.159	0.159	strong		0.567	OR10H5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460363.1		
LRP2	4036	hgsc.bcm.edu	37	2	170103336	170103336	+	Silent	SNP	T	T	C	rs831043	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:170103336T>C	ENST00000263816.3	-	21	3354	c.3069A>G	c.(3067-3069)acA>acG	p.T1023T	LRP2_ENST00000443831.1_Silent_p.T886T	NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	1023					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)"""	CACACTGCTCTGTGGGTGGTT	0.493													C|||	3098	0.61861	0.7201	0.6369	5008	,	,		17744	0.4792		0.4622	False		,,,				2504	0.773				p.T1023T		Atlas-SNP	.											.	LRP2	751	.	0			c.A3069G						PASS	.	C		3047,1359	452.6+/-350.1	1064,919,220	143.0	131.0	135.0		3069	-1.9	0.0	2	dbSNP_86	135	3921,4679	604.9+/-394.9	890,2141,1269	no	coding-synonymous	LRP2	NM_004525.2		1954,3060,1489	CC,CT,TT		45.593,30.8443,46.4247		1023/4656	170103336	6968,6038	2203	4300	6503	SO:0001819	synonymous_variant	4036	exon21			CTGCTCTGTGGGT		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.3069A>G	2.37:g.170103336T>C		Somatic	205	0	0		WXS	Illumina HiSeq	Phase_I	191	92	0.481675	NM_004525	O00711|Q16215	Silent	SNP	ENST00000263816.3	37	CCDS2232.1																																																																																			T|0.456;C|0.544	0.544	strong		0.493	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525	
PGAP1	80055	hgsc.bcm.edu	37	2	197711870	197711870	+	Silent	SNP	G	G	A	rs149815494	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:197711870G>A	ENST00000354764.4	-	22	2121	c.2007C>T	c.(2005-2007)gcC>gcT	p.A669A		NM_024989.3	NP_079265.2	Q75T13	PGAP1_HUMAN	post-GPI attachment to proteins 1	669					anterior/posterior axis specification (GO:0009948)|attachment of GPI anchor to protein (GO:0016255)|C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|embryonic pattern specification (GO:0009880)|forebrain regionalization (GO:0021871)|head development (GO:0060322)|intracellular protein transport (GO:0006886)|myo-inositol transport (GO:0015798)|post-translational protein modification (GO:0043687)|sensory perception of sound (GO:0007605)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	nuclease activity (GO:0004518)|phosphoric ester hydrolase activity (GO:0042578)			breast(4)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(9)|lung(11)|ovary(6)|stomach(1)|urinary_tract(1)	40						TTAAAATGACGGCATCTAATT	0.373													G|||	17	0.00339457	0.0	0.0	5008	,	,		16262	0.0		0.0169	False		,,,				2504	0.0				p.A669A		Atlas-SNP	.											.	PGAP1	84	.	0			c.C2007T						PASS	.	G		10,4396	16.8+/-37.8	0,10,2193	138.0	143.0	141.0		2007	3.1	1.0	2	dbSNP_134	141	87,8513	49.8+/-109.6	1,85,4214	no	coding-synonymous	PGAP1	NM_024989.3		1,95,6407	AA,AG,GG		1.0116,0.227,0.7458		669/923	197711870	97,12909	2203	4300	6503	SO:0001819	synonymous_variant	80055	exon22			AATGACGGCATCT		CCDS2318.1	2q33.1	2014-03-03			ENSG00000197121	ENSG00000197121			25712	protein-coding gene	gene with protein product	"""GPI inositol-deacylase"""	611655				14734546, 17711852, 24482476	Standard	XM_005246866		Approved	FLJ12377, Bst1, SPG67	uc002utw.3	Q75T13	OTTHUMG00000132743	ENST00000354764.4:c.2007C>T	2.37:g.197711870G>A		Somatic	204	0	0		WXS	Illumina HiSeq	Phase_I	147	59	0.401361	NM_024989	Q4G0R8|Q4ZG47|Q53SM0|Q6AW92|Q6UWV4|Q9HA24	Silent	SNP	ENST00000354764.4	37	CCDS2318.1																																																																																			G|0.993;A|0.007	0.007	strong		0.373	PGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256103.5	NM_024989	
C17orf97	400566	hgsc.bcm.edu	37	17	263643	263643	+	Missense_Mutation	SNP	C	C	A	rs71369083|rs71145728		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:263643C>A	ENST00000360127.6	+	2	1025	c.1009C>A	c.(1009-1011)Ccc>Acc	p.P337T	AC108004.3_ENST00000466740.2_RNA|C17orf97_ENST00000571106.1_Intron	NM_001013672.4	NP_001013694.4	Q6ZQX7	CQ097_HUMAN	chromosome 17 open reading frame 97	367	20 X 10 AA approximative tandem repeat of A-L-K-G-F-H-P-D-P-E.									breast(1)|kidney(2)|large_intestine(4)|lung(4)|ovary(1)|prostate(1)|skin(1)	14						GGGCTTCCACCCCGACCCCGA	0.697																																					p.P337T		Atlas-SNP	.											C17orf97_ENST00000360127,NS,carcinoma,0,2	C17orf97	76	2	0			c.C1009A						scavenged	.																																			SO:0001583	missense	400566	exon2			TTCCACCCCGACC	AK128660, BC057385	CCDS32519.2	17p13.3	2008-08-15			ENSG00000187624	ENSG00000187624			33800	protein-coding gene	gene with protein product						12477932	Standard	NM_001013672		Approved	LOC400566	uc021tna.1	Q6ZQX7	OTTHUMG00000132479	ENST00000360127.6:c.1009C>A	17.37:g.263643C>A	ENSP00000353245:p.Pro337Thr	Somatic	207	3	0.0144928		WXS	Illumina HiSeq	Phase_I	114	2	0.0175439	NM_001013672	A5D8T6|Q6NSI2|Q6PFW9	Missense_Mutation	SNP	ENST00000360127.6	37	CCDS32519.2	.	.	.	.	.	.	.	.	.	.	c	0.001	-3.987809	0.00002	.	.	ENSG00000187624	ENST00000360127	T	0.31247	1.5	2.05	-4.1	0.03940	.	.	.	.	.	T	0.13329	0.0323	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.35400	-0.9790	9	0.13853	T	0.58	.	10.5042	0.44823	0.1779:0.7067:0.1154:0.0	.	337	Q6ZQX7-4	.	T	337	ENSP00000353245:P337T	ENSP00000353245:P337T	P	+	1	0	C17orf97	263989	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-4.281000	0.00260	-5.715000	0.00010	-5.246000	0.00001	CCC	C|0.981;A|0.019	0.019	strong		0.697	C17orf97-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255648.4	NM_001013672	
NHLRC2	374354	hgsc.bcm.edu	37	10	115644040	115644040	+	Missense_Mutation	SNP	G	G	A	rs7913176	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:115644040G>A	ENST00000369301.3	+	5	1152	c.940G>A	c.(940-942)Gta>Ata	p.V314I		NM_198514.3	NP_940916.2	Q8NBF2	NHLC2_HUMAN	NHL repeat containing 2	314			V -> I (in dbSNP:rs7913176).							breast(1)|endometrium(2)|kidney(4)|large_intestine(3)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	15				Epithelial(162;0.017)|all cancers(201;0.0187)		GGTGAGCACTGTAGCTGGTAT	0.388													G|||	1119	0.223442	0.121	0.2291	5008	,	,		15051	0.3125		0.2932	False		,,,				2504	0.1943				p.V314I		Atlas-SNP	.											NHLRC2,NS,carcinoma,0,1	NHLRC2	56	1	0			c.G940A						PASS	.	G	ILE/VAL	684,3722	289.8+/-280.6	64,556,1583	137.0	126.0	130.0		940	5.0	1.0	10	dbSNP_116	130	2422,6178	400.6+/-346.9	361,1700,2239	yes	missense	NHLRC2	NM_198514.3	29	425,2256,3822	AA,AG,GG		28.1628,15.5243,23.8813	benign	314/727	115644040	3106,9900	2203	4300	6503	SO:0001583	missense	374354	exon5			AGCACTGTAGCTG	AK090631	CCDS7585.1	10q26.11	2006-03-31			ENSG00000196865	ENSG00000196865			24731	protein-coding gene	gene with protein product						12477932	Standard	NM_198514		Approved	FLJ25621, FLJ20147, FLJ33312, MGC45492, DKFZp779F115	uc001lax.2	Q8NBF2	OTTHUMG00000019078	ENST00000369301.3:c.940G>A	10.37:g.115644040G>A	ENSP00000358307:p.Val314Ile	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	105	57	0.542857	NM_198514	Q8N1H1|Q8N5A6	Missense_Mutation	SNP	ENST00000369301.3	37	CCDS7585.1	525	0.2403846153846154	59	0.11991869918699187	71	0.19613259668508287	178	0.3111888111888112	217	0.2862796833773087	G	13.78	2.338147	0.41398	0.155243	0.281628	ENSG00000196865	ENST00000369301	D	0.89939	-2.59	5.03	5.03	0.67393	Six-bladed beta-propeller, TolB-like (1);	0.155986	0.44285	D	0.000462	T	0.00012	0.0000	L	0.35723	1.085	0.27849	P	0.9408216	P	0.36412	0.552	B	0.25884	0.064	T	0.33599	-0.9862	9	0.07990	T	0.79	-18.5562	16.5886	0.84759	0.0:0.0:1.0:0.0	rs7913176;rs52796392;rs56430477;rs61476386;rs7913176	314	Q8NBF2	NHLC2_HUMAN	I	314	ENSP00000358307:V314I	ENSP00000358307:V314I	V	+	1	0	NHLRC2	115634030	1.000000	0.71417	1.000000	0.80357	0.940000	0.58332	2.574000	0.46016	2.345000	0.79718	0.479000	0.44913	GTA	G|0.771;A|0.229	0.229	strong		0.388	NHLRC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050446.1	NM_198514	
CCDC168	643677	hgsc.bcm.edu	37	13	103385534	103385534	+	Missense_Mutation	SNP	C	C	T	rs17592438	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:103385534C>T	ENST00000322527.2	-	1	3625	c.3626G>A	c.(3625-3627)cGa>cAa	p.R1209Q		NM_001146197.1	NP_001139669.1	Q8NDH2	CC168_HUMAN	coiled-coil domain containing 168	1209			R -> Q (in dbSNP:rs17592438).														TTCACACCGTCGGATCACTTG	0.433													C|||	514	0.102636	0.0416	0.1066	5008	,	,		20905	0.0159		0.1471	False		,,,				2504	0.226				p.R5838Q		Atlas-SNP	.											.	.	.	.	0			c.G17513A						PASS	.	C	GLN/ARG	67,1317		5,57,630	232.0	177.0	194.0		17513	-6.2	0.0	13	dbSNP_123	194	505,2677		37,431,1123	yes	missense	CCDC168	NM_001146197.1	43	42,488,1753	TT,TC,CC		15.8705,4.841,12.5274	benign	5838/7082	103385534	572,3994	692	1591	2283	SO:0001583	missense	643677	exon4			CACCGTCGGATCA		CCDS73596.1	13q33.1	2014-06-17	2011-08-09	2011-08-09	ENSG00000175820	ENSG00000175820			26851	protein-coding gene	gene with protein product			"""chromosome 13 open reading frame 40"""	C13orf40			Standard	NM_001146197		Approved	FLJ40176	uc001vpm.3	Q8NDH2	OTTHUMG00000187287	ENST00000322527.2:c.3626G>A	13.37:g.103385534C>T	ENSP00000320232:p.Arg1209Gln	Somatic	223	0	0		WXS	Illumina HiSeq	Phase_I	172	72	0.418605	NM_001146197	Q8N800	Missense_Mutation	SNP	ENST00000322527.2	37		181	0.08287545787545787	14	0.028455284552845527	44	0.12154696132596685	4	0.006993006993006993	119	0.15699208443271767	C	3.053	-0.195003	0.06259	0.04841	0.158705	ENSG00000175820	ENST00000322527	T	0.03772	3.81	3.09	-6.18	0.02085	.	.	.	.	.	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	0.45264	-0.9273	8	0.54805	T	0.06	.	1.1016	0.01685	0.21:0.3099:0.1239:0.3562	rs17592438;rs52826073;rs58195593;rs17592438	1209	Q8NDH2	CC168_HUMAN	Q	1209	ENSP00000320232:R1209Q	ENSP00000320232:R1209Q	R	-	2	0	CCDC168	102183535	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.307000	0.02733	-3.139000	0.00234	-2.611000	0.00159	CGA	C|0.926;T|0.074	0.074	strong		0.433	CCDC168-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001146197	
B4GALT4	8702	hgsc.bcm.edu	37	3	118945796	118945796	+	Missense_Mutation	SNP	G	G	C	rs3764779	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:118945796G>C	ENST00000483209.1	-	4	987	c.346C>G	c.(346-348)Cag>Gag	p.Q116E	B4GALT4_ENST00000393765.2_Missense_Mutation_p.Q116E|B4GALT4-AS1_ENST00000470790.1_RNA|B4GALT4_ENST00000471675.1_Intron|B4GALT4_ENST00000460321.1_5'UTR|B4GALT4_ENST00000359213.3_Missense_Mutation_p.Q116E|B4GALT4_ENST00000467604.1_Missense_Mutation_p.Q116E			O60513	B4GT4_HUMAN	UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 4	116			Q -> E (in dbSNP:rs3764779). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005, ECO:0000269|Ref.4}.		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)|membrane lipid metabolic process (GO:0006643)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	galactosyltransferase activity (GO:0008378)|metal ion binding (GO:0046872)|N-acetyllactosamine synthase activity (GO:0003945)	p.Q116E(1)		breast(2)|endometrium(1)|large_intestine(1)|lung(6)|skin(2)|stomach(2)	14				GBM - Glioblastoma multiforme(114;0.222)	N-Acetyl-D-glucosamine(DB00141)	TTACATTCCTGAGGGCGATAC	0.512													C|||	1487	0.296925	0.3064	0.353	5008	,	,		20833	0.3333		0.1978	False		,,,				2504	0.3088				p.Q116E		Atlas-SNP	.											B4GALT4,NS,carcinoma,0,1	B4GALT4	30	1	1	Substitution - Missense(1)	stomach(1)	c.C346G						PASS	.	C	GLU/GLN,GLU/GLN	1409,2997	687.5+/-404.9	214,981,1008	124.0	110.0	115.0		346,346	5.1	0.6	3	dbSNP_107	115	2123,6477	715.3+/-406.0	247,1629,2424	yes	missense,missense	B4GALT4	NM_003778.3,NM_212543.1	29,29	461,2610,3432	CC,CG,GG		24.686,31.9791,27.1567	benign,benign	116/345,116/345	118945796	3532,9474	2203	4300	6503	SO:0001583	missense	8702	exon5			ATTCCTGAGGGCG	AF022367	CCDS2986.1	3q13.3	2013-02-19			ENSG00000121578	ENSG00000121578		"""Beta 4-glycosyltransferases"""	927	protein-coding gene	gene with protein product		604015				9597550	Standard	NM_003778		Approved	beta4Gal-T4	uc003eci.3	O60513	OTTHUMG00000159358	ENST00000483209.1:c.346C>G	3.37:g.118945796G>C	ENSP00000420161:p.Gln116Glu	Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	156	96	0.615385	NM_212543	Q68D68|Q9BSW3|Q9C078	Missense_Mutation	SNP	ENST00000483209.1	37	CCDS2986.1	612	0.2802197802197802	147	0.29878048780487804	120	0.3314917127071823	194	0.33916083916083917	151	0.19920844327176782	C	0.008	-1.883719	0.00532	0.319791	0.24686	ENSG00000121578	ENST00000483209;ENST00000467604;ENST00000359213;ENST00000393765;ENST00000475803;ENST00000479150	T;T;T;T;T;T	0.38887	2.05;2.05;2.05;2.05;2.05;1.11	6.02	5.1	0.69264	.	0.263318	0.44285	N	0.000479	T	0.00012	0.0000	N	0.00252	-1.77	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.33111	-0.9881	9	0.02654	T	1	-21.8622	10.8754	0.46909	0.0:0.6856:0.2468:0.0676	rs3764779;rs17845026;rs17857795;rs17859691;rs52792113;rs60499237;rs3764779	116	O60513	B4GT4_HUMAN	E	116	ENSP00000420161:Q116E;ENSP00000417226:Q116E;ENSP00000352144:Q116E;ENSP00000377360:Q116E;ENSP00000417188:Q116E;ENSP00000417958:Q116E	ENSP00000352144:Q116E	Q	-	1	0	B4GALT4	120428486	0.000000	0.05858	0.644000	0.29465	0.010000	0.07245	-0.256000	0.08757	1.578000	0.49821	-0.120000	0.15030	CAG	G|0.722;C|0.278	0.278	strong		0.512	B4GALT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354925.2	NM_003778	
FBN3	84467	hgsc.bcm.edu	37	19	8203328	8203328	+	Missense_Mutation	SNP	G	G	A	rs7246376	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:8203328G>A	ENST00000600128.1	-	9	1400	c.986C>T	c.(985-987)cCg>cTg	p.P329L	FBN3_ENST00000270509.2_Missense_Mutation_p.P329L|FBN3_ENST00000601739.1_Missense_Mutation_p.P329L			Q75N90	FBN3_HUMAN	fibrillin 3	329	TB 2.		P -> L (in dbSNP:rs7246376).			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						CTCAGGGACCGGGCCAGCTGC	0.682													G|||	1639	0.327276	0.2685	0.2709	5008	,	,		14964	0.4712		0.2018	False		,,,				2504	0.4274				p.P329L		Atlas-SNP	.											FBN3,NS,carcinoma,+1,1	FBN3	300	1	0			c.C986T						PASS	.	G	LEU/PRO	1120,3286		149,822,1232	28.0	31.0	30.0		986	2.0	0.0	19	dbSNP_116	30	1579,7017		174,1231,2893	yes	missense	FBN3	NM_032447.3	98	323,2053,4125	AA,AG,GG		18.369,25.4199,20.7583	benign	329/2810	8203328	2699,10303	2203	4298	6501	SO:0001583	missense	84467	exon8			GGGACCGGGCCAG		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.986C>T	19.37:g.8203328G>A	ENSP00000470498:p.Pro329Leu	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	114	114	1	NM_032447	Q75N91|Q75N92|Q75N93|Q86SJ5|Q96JP8	Missense_Mutation	SNP	ENST00000600128.1	37	CCDS12196.1	634	0.2902930402930403	129	0.2621951219512195	97	0.26795580110497236	258	0.45104895104895104	150	0.19788918205804748	g	8.130	0.782882	0.16189	0.254199	0.18369	ENSG00000142449	ENST00000270509	D	0.92299	-3.01	4.21	2.05	0.26809	Matrix fibril-associated (3);TGF-beta binding (1);	0.306666	0.30329	N	0.009873	T	0.00012	0.0000	M	0.71581	2.175	0.80722	P	0.0	B	0.18863	0.031	B	0.14578	0.011	T	0.20273	-1.0280	9	0.28530	T	0.3	.	4.415	0.11452	0.1921:0.0:0.5135:0.2944	rs7246376;rs7246376	329	Q75N90	FBN3_HUMAN	L	329	ENSP00000270509:P329L	ENSP00000270509:P329L	P	-	2	0	FBN3	8109328	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	-0.036000	0.12185	0.357000	0.24183	-0.258000	0.10820	CCG	G|0.739;A|0.260	0.260	strong		0.682	FBN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461428.2	NM_032447	
KIF26B	55083	hgsc.bcm.edu	37	1	245850095	245850095	+	Silent	SNP	C	C	T	rs871840	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:245850095C>T	ENST00000407071.2	+	12	4250	c.3810C>T	c.(3808-3810)gaC>gaT	p.D1270D	KIF26B_ENST00000366518.4_Silent_p.D889D	NM_018012.3	NP_060482.2	Q2KJY2	KI26B_HUMAN	kinesin family member 26B	1270					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)			AGGCCCAGGACGCAGGGAGCA	0.617													C|||	729	0.145567	0.2307	0.1571	5008	,	,		18948	0.0179		0.2425	False		,,,				2504	0.0542				p.D1270D		Atlas-SNP	.											.	KIF26B	343	.	0			c.C3810T						PASS	.	C		960,3346		116,728,1309	34.0	40.0	38.0		3810	-4.6	0.1	1	dbSNP_86	38	2168,6316		283,1602,2357	no	coding-synonymous	KIF26B	NM_018012.3		399,2330,3666	TT,TC,CC		25.554,22.2945,24.4566		1270/2109	245850095	3128,9662	2153	4242	6395	SO:0001819	synonymous_variant	55083	exon12			CCAGGACGCAGGG	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.3810C>T	1.37:g.245850095C>T		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	79	47	0.594937	NM_018012	Q6ZQR9|Q6ZUZ0|Q8IUN3|Q8IVR1|Q9NWB4	Silent	SNP	ENST00000407071.2	37	CCDS44342.1																																																																																			C|0.808;T|0.192	0.192	strong		0.617	KIF26B-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381037.1	XM_371354	
GNRHR	2798	hgsc.bcm.edu	37	4	68619601	68619601	+	Silent	SNP	G	G	A	rs4986942	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:68619601G>A	ENST00000226413.4	-	1	477	c.453C>T	c.(451-453)agC>agT	p.S151S	UBA6-AS1_ENST00000500538.2_RNA|GNRHR_ENST00000420975.2_Silent_p.S151S|UBA6-AS1_ENST00000502758.1_RNA	NM_000406.2	NP_000397.1	P30968	GNRHR_HUMAN	gonadotropin-releasing hormone receptor	151					cellular response to gonadotropin-releasing hormone (GO:0097211)|G-protein coupled receptor signaling pathway (GO:0007186)|multicellular organismal development (GO:0007275)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	gonadotropin-releasing hormone receptor activity (GO:0004968)			endometrium(2)|large_intestine(4)|liver(1)|lung(4)|ovary(1)|urinary_tract(1)	13					Abarelix(DB00106)|Buserelin(DB06719)|Cetrorelix(DB00050)|Danazol(DB01406)|Degarelix(DB06699)|Gonadorelin(DB00644)|Goserelin(DB00014)|Leuprolide(DB00007)|Nafarelin(DB00666)	CTTTGCTGTTGCTTTTCAAAG	0.498													G|||	333	0.0664936	0.087	0.0908	5008	,	,		19267	0.0069		0.0815	False		,,,				2504	0.0675				p.S151S		Atlas-SNP	.											.	GNRHR	31	.	0			c.C453T						PASS	.	G	,	466,3940	221.7+/-238.7	27,412,1764	64.0	62.0	62.0		453,453	5.3	0.2	4	dbSNP_118	62	853,7747	194.4+/-239.8	40,773,3487	no	coding-synonymous,coding-synonymous	GNRHR	NM_000406.2,NM_001012763.1	,	67,1185,5251	AA,AG,GG		9.9186,10.5765,10.1415	,	151/329,151/250	68619601	1319,11687	2203	4300	6503	SO:0001819	synonymous_variant	2798	exon1			GCTGTTGCTTTTC		CCDS3517.1, CCDS47064.1	4q21.2	2012-08-08			ENSG00000109163	ENSG00000109163		"""GPCR / Class A : Gonadotropin-releasing hormone receptors"""	4421	protein-coding gene	gene with protein product		138850		GRHR		8386108	Standard	NM_000406		Approved	LHRHR	uc003hdn.3	P30968	OTTHUMG00000129302	ENST00000226413.4:c.453C>T	4.37:g.68619601G>A		Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	132	50	0.378788	NM_000406	O75793|Q14D13|Q92644	Silent	SNP	ENST00000226413.4	37	CCDS3517.1																																																																																			G|0.914;A|0.086	0.086	strong		0.498	GNRHR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251432.2		
FAM170B	170370	hgsc.bcm.edu	37	10	50339925	50339925	+	Silent	SNP	G	G	A	rs12765281	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:50339925G>A	ENST00000311787.5	-	2	674	c.585C>T	c.(583-585)gaC>gaT	p.D195D	FAM170B-AS1_ENST00000443389.1_RNA|FAM170B-AS1_ENST00000435809.1_RNA|FAM170B-AS1_ENST00000442525.1_RNA	NM_001164484.1	NP_001157956.1	A6NMN3	F170B_HUMAN	family with sequence similarity 170, member B	195										central_nervous_system(1)|endometrium(1)|skin(1)	3						TGACCAGCCAGTCCGGCGGCT	0.687													G|||	1228	0.245208	0.118	0.3444	5008	,	,		15830	0.3075		0.2684	False		,,,				2504	0.2587				p.D195D		Atlas-SNP	.											.	FAM170B	20	.	0			c.C585T						PASS	.						7.0	11.0	10.0					10																	50339925		684	1579	2263	SO:0001819	synonymous_variant	170370	exon2			CAGCCAGTCCGGC		CCDS53536.1	10q11.23	2008-11-06	2008-06-12	2008-06-12	ENSG00000172538	ENSG00000172538			19736	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 73"""	C10orf73			Standard	NM_001164484		Approved	Em:AC084727.4	uc001jhj.3	A6NMN3	OTTHUMG00000018187	ENST00000311787.5:c.585C>T	10.37:g.50339925G>A		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	37	20	0.540541	NM_001164484	Q86WY6|Q8N6K8	Silent	SNP	ENST00000311787.5	37	CCDS53536.1																																																																																			G|0.768;A|0.232	0.232	strong		0.687	FAM170B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047974.1	XM_096317	
B3GNTL1	146712	hgsc.bcm.edu	37	17	80923536	80923536	+	Silent	SNP	C	C	T	rs4986144	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:80923536C>T	ENST00000320865.3	-	7	604	c.591G>A	c.(589-591)gaG>gaA	p.E197E	B3GNTL1_ENST00000571954.1_5'UTR|B3GNTL1_ENST00000576599.1_Silent_p.E86E	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	46	0	0		WXS	Illumina HiSeq	Phase_I	57	27	0.473684	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	
RRP1	8568	hgsc.bcm.edu	37	21	45219524	45219524	+	Silent	SNP	T	T	C	rs4566449	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:45219524T>C	ENST00000497547.1	+	9	1002	c.885T>C	c.(883-885)gtT>gtC	p.V295V	RRP1_ENST00000471909.1_3'UTR	NM_003683.5	NP_003674.1	P05386	RLA1_HUMAN	ribosomal RNA processing 1	0					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)	RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			central_nervous_system(1)|kidney(1)|lung(4)|stomach(2)	8				COAD - Colon adenocarcinoma(84;0.00753)|Colorectal(79;0.0157)|STAD - Stomach adenocarcinoma(101;0.171)		GCGGCCCCGTTCTCCAGGTGG	0.642													C|||	1747	0.348842	0.4213	0.3415	5008	,	,		14283	0.3175		0.2078	False		,,,				2504	0.4335				p.V295V		Atlas-SNP	.											.	RRP1	23	.	0			c.T885C						PASS	.	C		1553,2591		300,953,819	48.0	65.0	59.0		885	-3.6	0.0	21	dbSNP_111	59	1989,6443		252,1485,2479	no	coding-synonymous	RRP1	NM_003683.5		552,2438,3298	CC,CT,TT		23.5887,37.4759,28.1648		295/462	45219524	3542,9034	2072	4216	6288	SO:0001819	synonymous_variant	8568	exon9			CCCCGTTCTCCAG	U79775	CCDS42951.1	21q22.3	2013-07-02	2013-07-02		ENSG00000160214	ENSG00000160214			18785	protein-coding gene	gene with protein product	"""DNA segment on chromosome 21 (unique) 2056 expressed sequence"", ""Nnp1 homolog, nucleolar protein (Drosophila)"""	610653	"""ribosomal RNA processing 1 homolog (S. cerevisiae)"""			10830953, 10341208	Standard	NM_003683		Approved	NNP-1, Nop52, NOP52, RRP1A, D21S2056E	uc002zds.2	P56182	OTTHUMG00000086884	ENST00000497547.1:c.885T>C	21.37:g.45219524T>C		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	102	34	0.333333	NM_003683	A6NIB2	Silent	SNP	ENST00000497547.1	37	CCDS42951.1																																																																																			T|0.688;C|0.312	0.312	strong		0.642	RRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195680.1	NM_003683	
MUC4	4585	hgsc.bcm.edu	37	3	195509331	195509331	+	Silent	SNP	C	C	A	rs369416005		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195509331C>A	ENST00000463781.3	-	2	9579	c.9120G>T	c.(9118-9120)ccG>ccT	p.P3040P	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Silent_p.P3040P	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	981					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.P3040P(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)		TGACAGGAAGCGGGGTGGCGT	0.607																																					p.P3040P		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	1	Substitution - coding silent(1)	endometrium(1)	c.G9120T						scavenged	.						9.0	7.0	7.0					3																	195509331		602	1470	2072	SO:0001819	synonymous_variant	4585	exon2			AGGAAGCGGGGTG	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.9120G>T	3.37:g.195509331C>A		Somatic	47	3	0.0638298		WXS	Illumina HiSeq	Phase_I	89	12	0.134831	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		0.607	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
C14orf37	145407	hgsc.bcm.edu	37	14	58605043	58605043	+	Missense_Mutation	SNP	G	G	A	rs61741199	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:58605043G>A	ENST00000267485.7	-	2	1228	c.1034C>T	c.(1033-1035)aCa>aTa	p.T345I	C14orf37_ENST00000334342.5_5'UTR	NM_001001872.2	NP_001001872.2	Q86TY3	CN037_HUMAN	chromosome 14 open reading frame 37	345						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						TACTTGTGCTGTCTGAGACAT	0.547													G|||	351	0.0700879	0.1437	0.0432	5008	,	,		20918	0.0		0.0577	False		,,,				2504	0.0746				p.T345I		Atlas-SNP	.											.	C14orf37	87	.	0			c.C1034T						PASS	.	G	ILE/THR	516,3890	237.1+/-249.0	31,454,1718	155.0	152.0	153.0		1034	3.7	0.2	14	dbSNP_129	153	483,8117	140.1+/-196.7	12,459,3829	yes	missense	C14orf37	NM_001001872.2	89	43,913,5547	AA,AG,GG		5.6163,11.7113,7.6811	benign	345/775	58605043	999,12007	2203	4300	6503	SO:0001583	missense	145407	exon2			TGTGCTGTCTGAG		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.1034C>T	14.37:g.58605043G>A	ENSP00000267485:p.Thr345Ile	Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	112	112	1	NM_001001872	A8K8Z8|Q6P5Q1|Q86TY1	Missense_Mutation	SNP	ENST00000267485.7	37	CCDS32089.1	123	0.05631868131868132	62	0.12601626016260162	15	0.04143646408839779	0	0.0	46	0.06068601583113457	G	11.64	1.698404	0.30142	0.117113	0.056163	ENSG00000139971	ENST00000267485;ENST00000438670	T	0.21191	2.02	5.6	3.72	0.42706	.	0.558344	0.18393	N	0.142606	T	0.00144	0.0004	L	0.46157	1.445	0.58432	P	9.000000000036756E-6	B;P;B;B	0.38597	0.084;0.639;0.084;0.084	B;B;B;B	0.32928	0.066;0.155;0.066;0.066	T	0.12400	-1.0549	9	0.11794	T	0.64	-0.2219	6.3844	0.21552	0.1574:0.1953:0.6473:0.0	.	383;345;345;345	B4DMS4;Q86TY3-2;A8K990;Q86TY3	.;.;.;CN037_HUMAN	I	345;383	ENSP00000267485:T345I	ENSP00000267485:T345I	T	-	2	0	C14orf37	57674796	0.050000	0.20438	0.200000	0.23457	0.367000	0.29736	0.079000	0.14782	1.302000	0.44855	0.655000	0.94253	ACA	G|0.928;A|0.072	0.072	strong		0.547	C14orf37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412059.1	NM_001001872	
PNPLA1	285848	hgsc.bcm.edu	37	6	36260858	36260858	+	Silent	SNP	C	C	T	rs2239795	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:36260858C>T	ENST00000394571.2	+	3	459	c.459C>T	c.(457-459)ttC>ttT	p.F153F	PNPLA1_ENST00000312917.5_Silent_p.F58F|PNPLA1_ENST00000388715.3_Silent_p.F58F	NM_001145717.1	NP_001139189.2	Q8N8W4	PLPL1_HUMAN	patatin-like phospholipase domain containing 1	153	Patatin.				lipid catabolic process (GO:0016042)	cytoplasm (GO:0005737)	hydrolase activity (GO:0016787)			breast(1)|kidney(1)|large_intestine(4)|lung(9)|pancreas(1)|skin(4)|upper_aerodigestive_tract(2)	22						GCAGCTGCTTCGTCCCGGTGT	0.662													C|||	2095	0.418331	0.5703	0.3213	5008	,	,		17655	0.3472		0.4155	False		,,,				2504	0.3579				p.F153F		Atlas-SNP	.											PNPLA1_ENST00000394571,NS,carcinoma,+2,2	PNPLA1	92	2	0			c.C459T						PASS	.	C	,,	2278,2128	598.9+/-389.2	596,1086,521	116.0	96.0	103.0		174,459,174	-5.1	0.9	6	dbSNP_98	103	3346,5254	497.8+/-374.6	654,2038,1608	no	coding-synonymous,coding-synonymous,coding-synonymous	PNPLA1	NM_001145716.1,NM_001145717.1,NM_173676.2	,,	1250,3124,2129	TT,TC,CC		38.907,48.2978,43.2416	,,	58/447,153/533,58/438	36260858	5624,7382	2203	4300	6503	SO:0001819	synonymous_variant	285848	exon3			CTGCTTCGTCCCG		CCDS34438.1, CCDS47416.1, CCDS54997.1	6p21.31	2009-01-12			ENSG00000180316	ENSG00000180316		"""Patatin-like phospholipase domain containing"""	21246	protein-coding gene	gene with protein product		612121				16799181, 19029121	Standard	NM_001145717		Approved	FLJ38755, dJ50J22.1	uc010jwf.2	Q8N8W4	OTTHUMG00000014590	ENST00000394571.2:c.459C>T	6.37:g.36260858C>T		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	63	33	0.52381	NM_001145717	A3RMU3|J3JS20|Q2A6N1|Q3SY95|Q3SY96|Q5R3L2	Silent	SNP	ENST00000394571.2	37	CCDS54997.1																																																																																			C|0.568;T|0.432	0.432	strong		0.662	PNPLA1-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_173676	
TNFRSF19	55504	hgsc.bcm.edu	37	13	24167505	24167505	+	Missense_Mutation	SNP	T	T	A	rs9550987	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:24167505T>A	ENST00000382258.4	+	3	295	c.91T>A	c.(91-93)Tca>Aca	p.S31T	TNFRSF19_ENST00000248484.4_Missense_Mutation_p.S31T|TNFRSF19_ENST00000403372.2_Intron|TNFRSF19_ENST00000382263.3_Missense_Mutation_p.S31T|TNFRSF19_ENST00000464735.1_3'UTR	NM_018647.3	NP_061117.2	Q9NS68	TNR19_HUMAN	tumor necrosis factor receptor superfamily, member 19	31			S -> T (in dbSNP:rs9550987). {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)			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)		GACTTGTGAATCAGGAGACTG	0.358													A|||	1378	0.27516	0.413	0.1888	5008	,	,		18697	0.2421		0.2217	False		,,,				2504	0.2393				p.S31T		Atlas-SNP	.											.	TNFRSF19	52	.	0			c.T91A						PASS	.	A	THR/SER,,THR/SER,THR/SER	1624,2782	661.6+/-400.9	295,1034,874	121.0	123.0	122.0		91,,91,91	5.3	1.0	13	dbSNP_119	122	1862,6738	730.4+/-406.8	211,1440,2649	yes	missense,intron,missense,missense	TNFRSF19	NM_001204458.1,NM_001204459.1,NM_018647.3,NM_148957.3	58,,58,58	506,2474,3523	AA,AT,TT		21.6512,36.8588,26.803	benign,,benign,benign	31/418,,31/424,31/418	24167505	3486,9520	2203	4300	6503	SO:0001583	missense	55504	exon3			TGTGAATCAGGAG	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.91T>A	13.37:g.24167505T>A	ENSP00000371693:p.Ser31Thr	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	48	27	0.5625	NM_018647	A8KA09|A8KA26|B1AM40|B1AM41|B4E2I6|Q9BXZ9|Q9BY00|Q9NZV2	Missense_Mutation	SNP	ENST00000382258.4	37	CCDS9302.1	562	0.2573260073260073	169	0.3434959349593496	73	0.20165745856353592	155	0.270979020979021	165	0.21767810026385223	A	6.120	0.390465	0.11581	0.368588	0.216512	ENSG00000127863	ENST00000248484;ENST00000382258;ENST00000382263	T;T;T	0.22134	1.97;1.97;1.97	5.3	5.3	0.74995	TNFR/CD27/30/40/95 cysteine-rich region (1);	0.224065	0.45606	N	0.000358	T	0.00012	0.0000	N	0.00327	-1.64	0.09310	P	0.9999999999999999	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.43718	-0.9374	9	0.02654	T	1	-16.2659	9.7956	0.40733	0.8463:0.0:0.0:0.1537	rs9550987;rs9550987	31;31;31	Q9NS68;A8KA09;Q9NS68-2	TNR19_HUMAN;.;.	T	31	ENSP00000248484:S31T;ENSP00000371693:S31T;ENSP00000371698:S31T	ENSP00000248484:S31T	S	+	1	0	TNFRSF19	23065505	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	3.731000	0.55013	0.962000	0.38057	-0.336000	0.08194	TCA	A|0.272;N|0.000	0.272	strong		0.358	TNFRSF19-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000044156.2	NM_018647	
TNK1	8711	hgsc.bcm.edu	37	17	7286326	7286326	+	Silent	SNP	T	T	A	rs1554948	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:7286326T>A	ENST00000576812.1	+	2	450	c.81T>A	c.(79-81)ctT>ctA	p.L27L	TNK1_ENST00000311668.2_Silent_p.L27L|TNK1_ENST00000570896.1_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	74	0	0		WXS	Illumina HiSeq	Phase_I	98	98	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	
FAM154B	283726	hgsc.bcm.edu	37	15	82563991	82563991	+	Missense_Mutation	SNP	C	C	T	rs16973457	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:82563991C>T	ENST00000339465.5	+	2	170	c.101C>T	c.(100-102)cCa>cTa	p.P34L	FAM154B_ENST00000427381.2_Missense_Mutation_p.P19L|FAM154B_ENST00000565432.1_Missense_Mutation_p.P47L|FAM154B_ENST00000565501.1_3'UTR	NM_001008226.1	NP_001008227.1	Q658L1	F154B_HUMAN	family with sequence similarity 154, member B	34			P -> L (in dbSNP:rs16973457).							autonomic_ganglia(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(9)|skin(2)	19						CGCCATGTGCCAGAAGAATAT	0.373													C|||	1872	0.373802	0.3154	0.317	5008	,	,		17232	0.1994		0.5497	False		,,,				2504	0.4918				p.P34L		Atlas-SNP	.											.	FAM154B	50	.	0			c.C101T						PASS	.	C	LEU/PRO	1585,2821	492.9+/-362.5	299,987,917	81.0	75.0	77.0		101	3.9	0.9	15	dbSNP_123	77	4433,4167	586.9+/-392.1	1156,2121,1023	yes	missense	FAM154B	NM_001008226.1	98	1455,3108,1940	TT,TC,CC		48.4535,35.9737,46.271	possibly-damaging	34/399	82563991	6018,6988	2203	4300	6503	SO:0001583	missense	283726	exon2			ATGTGCCAGAAGA	AL833762	CCDS32310.1	15q25.2	2008-02-21				ENSG00000188659			33727	protein-coding gene	gene with protein product							Standard	XM_005254317		Approved	DKFZp666G057	uc002bgv.3	Q658L1		ENST00000339465.5:c.101C>T	15.37:g.82563991C>T	ENSP00000340445:p.Pro34Leu	Somatic	243	0	0		WXS	Illumina HiSeq	Phase_I	288	113	0.392361	NM_001008226	B4E2M2	Missense_Mutation	SNP	ENST00000339465.5	37	CCDS32310.1	800	0.3663003663003663	142	0.2886178861788618	130	0.35911602209944754	108	0.1888111888111888	420	0.554089709762533	C	14.95	2.687880	0.48097	0.359737	0.515465	ENSG00000188659	ENST00000339465;ENST00000427381	T;T	0.21361	2.01;2.01	4.98	3.93	0.45458	.	0.253294	0.32273	N	0.006323	T	0.00012	0.0000	M	0.62723	1.935	0.26411	P	0.9762506	P;P	0.50528	0.936;0.867	P;P	0.52627	0.704;0.652	T	0.48068	-0.9067	9	0.28530	T	0.3	-0.1202	7.2589	0.26191	0.3677:0.5027:0.1296:0.0	rs16973457;rs56537957;rs61145947;rs16973457	19;34	B4E2M2;Q658L1	.;F154B_HUMAN	L	34;19	ENSP00000340445:P34L;ENSP00000403743:P19L	ENSP00000340445:P34L	P	+	2	0	FAM154B	80351046	1.000000	0.71417	0.950000	0.38849	0.943000	0.58893	3.564000	0.53791	2.481000	0.83766	0.591000	0.81541	CCA	C|0.582;T|0.418	0.418	strong		0.373	FAM154B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000419644.1	NM_001008226	
ZNF304	57343	hgsc.bcm.edu	37	19	57868483	57868483	+	Missense_Mutation	SNP	G	G	A	rs45612632	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:57868483G>A	ENST00000282286.5	+	3	1419	c.1246G>A	c.(1246-1248)Gca>Aca	p.A416T	ZNF304_ENST00000598744.1_Missense_Mutation_p.A374T|ZNF304_ENST00000391705.3_Missense_Mutation_p.A416T|ZNF304_ENST00000443917.2_Missense_Mutation_p.A463T			Q9HCX3	ZN304_HUMAN	zinc finger protein 304	416					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)		TCATACCGGGGCAAGGCCCTA	0.443													G|||	65	0.0129792	0.0015	0.0101	5008	,	,		21870	0.0		0.0358	False		,,,				2504	0.0204				p.A416T		Atlas-SNP	.											.	ZNF304	74	.	0			c.G1246A						PASS	.	G	THR/ALA	19,4387	25.3+/-52.1	1,17,2185	50.0	53.0	52.0		1246	3.0	0.9	19	dbSNP_127	52	261,8339	99.9+/-161.4	4,253,4043	yes	missense	ZNF304	NM_020657.2	58	5,270,6228	AA,AG,GG		3.0349,0.4312,2.1529	possibly-damaging	416/660	57868483	280,12726	2203	4300	6503	SO:0001583	missense	57343	exon3			ACCGGGGCAAGGC	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.1246G>A	19.37:g.57868483G>A	ENSP00000282286:p.Ala416Thr	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	73	50	0.684932	NM_020657		Missense_Mutation	SNP	ENST00000282286.5	37	CCDS12950.1	30	0.013736263736263736	0	0.0	3	0.008287292817679558	0	0.0	27	0.03562005277044855	G	20.5	3.996773	0.74818	0.004312	0.030349	ENSG00000131845	ENST00000282286;ENST00000391705;ENST00000443917	T;T;T	0.17213	2.29;2.29;2.29	4.03	2.96	0.34315	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.02230	0.0069	N	0.11364	0.135	0.25176	N	0.990242	P;P	0.35272	0.493;0.493	B;B	0.35413	0.202;0.202	T	0.21042	-1.0257	9	0.87932	D	0	.	12.651	0.56761	0.0:0.0:0.8326:0.1674	rs45612632	416;463	Q9HCX3;E7EQD3	ZN304_HUMAN;.	T	416;416;463	ENSP00000282286:A416T;ENSP00000375586:A416T;ENSP00000401642:A463T	ENSP00000282286:A416T	A	+	1	0	ZNF304	62560295	0.976000	0.34144	0.873000	0.34254	0.992000	0.81027	4.167000	0.58209	1.234000	0.43709	0.650000	0.86243	GCA	G|0.981;A|0.019	0.019	strong		0.443	ZNF304-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000465785.1		
HMBS	3145	hgsc.bcm.edu	37	11	118962230	118962230	+	Silent	SNP	G	G	T	rs1131488	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:118962230G>T	ENST00000278715.3	+	9	757	c.606G>T	c.(604-606)gtG>gtT	p.V202V	HMBS_ENST00000537841.1_Silent_p.V185V|HMBS_ENST00000543090.1_Silent_p.V184V|HMBS_ENST00000542729.1_Silent_p.V185V|HMBS_ENST00000392841.1_Silent_p.V185V|HMBS_ENST00000442944.2_Silent_p.V185V|HMBS_ENST00000544387.1_Silent_p.V202V|HMBS_ENST00000534956.1_Intron	NM_000190.3	NP_000181.2	P08397	HEM3_HUMAN	hydroxymethylbilane synthase	202			V -> L (in AIP). {ECO:0000269|PubMed:10657149}.		heme biosynthetic process (GO:0006783)|peptidyl-pyrromethane cofactor linkage (GO:0018160)|porphyrin-containing compound metabolic process (GO:0006778)|protoporphyrinogen IX biosynthetic process (GO:0006782)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	hydroxymethylbilane synthase activity (GO:0004418)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|urinary_tract(1)	15	all_hematologic(175;0.0977)	Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.72e-05)		ACAACCGGGTGGGGCAGGTAG	0.562													G|||	923	0.184305	0.1286	0.1931	5008	,	,		17883	0.1558		0.2952	False		,,,				2504	0.1687				p.V202V		Atlas-SNP	.											.	HMBS	27	.	0			c.G606T						PASS	.	G	,	516,3152		45,426,1363	30.0	24.0	26.0		606,555	2.0	1.0	11	dbSNP_86	26	1650,5172		199,1252,1960	no	coding-synonymous,coding-synonymous	HMBS	NM_000190.3,NM_001024382.1	,	244,1678,3323	TT,TG,GG		24.1865,14.0676,20.6482	,	202/362,185/345	118962230	2166,8324	1834	3411	5245	SO:0001819	synonymous_variant	3145	exon9			CCGGGTGGGGCAG	X04808	CCDS8409.1, CCDS41726.1, CCDS58186.1, CCDS58187.1	11q23.3	2013-07-10			ENSG00000256269	ENSG00000256269	2.5.1.61		4982	protein-coding gene	gene with protein product		609806	"""uroporphyrinogen I synthase"", ""porphobilinogen deaminase"", ""porphyria, acute; Chester type"""	PBGD, UPS, PORC		8432552, 17298217	Standard	NM_001258208		Approved		uc001puz.1	P08397	OTTHUMG00000168295	ENST00000278715.3:c.606G>T	11.37:g.118962230G>T		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	111	76	0.684685	NM_000190	A8K2L0|G3V1P4|G5EA58|P08396|Q16012	Silent	SNP	ENST00000278715.3	37	CCDS8409.1																																																																																			G|0.792;T|0.208	0.208	strong		0.562	HMBS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399188.1	NM_000190	
ELP2	55250	hgsc.bcm.edu	37	18	33750046	33750046	+	Silent	SNP	C	C	T	rs8299	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:33750046C>T	ENST00000358232.6	+	20	2160	c.2097C>T	c.(2095-2097)tgC>tgT	p.C699C	ELP2_ENST00000351393.6_Silent_p.C673C|ELP2_ENST00000423854.2_Silent_p.C629C|ELP2_ENST00000350494.6_Silent_p.C694C|ELP2_ENST00000442325.2_Silent_p.C764C|ELP2_ENST00000542824.1_Silent_p.C629C	NM_018255.2	NP_060725.1	Q6IA86	ELP2_HUMAN	elongator acetyltransferase complex subunit 2	699					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						GGGGTGAGTGCGACTCCACTG	0.527													C|||	1621	0.323682	0.3812	0.3948	5008	,	,		17714	0.2014		0.3907	False		,,,				2504	0.2526				p.C764C		Atlas-SNP	.											ELP2,colon,carcinoma,0,2	ELP2	70	2	0			c.C2292T						PASS	.	C	,,,,,	1624,2782	503.0+/-365.4	304,1016,883	186.0	136.0	153.0		2292,2082,2019,1887,1887,2097	-7.2	0.1	18	dbSNP_52	153	3306,5294	494.0+/-373.7	624,2058,1618	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ELP2	NM_001242875.1,NM_001242876.1,NM_001242877.1,NM_001242878.1,NM_001242879.1,NM_018255.2	,,,,,	928,3074,2501	TT,TC,CC		38.4419,36.8588,37.9056	,,,,,	764/892,694/822,673/801,629/757,629/757,699/827	33750046	4930,8076	2203	4300	6503	SO:0001819	synonymous_variant	55250	exon21			TGAGTGCGACTCC	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.2097C>T	18.37:g.33750046C>T		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	143	70	0.48951	NM_001242875	A8KAI6|B4DTG0|B4DXP0|E7EP23|E9PCX0|Q53GZ0|Q687Y8|Q8N5C2|Q96GV4|Q96PI7|Q9H9N0|Q9NV81	Silent	SNP	ENST00000358232.6	37	CCDS11918.1																																																																																			C|0.645;T|0.355	0.355	strong		0.527	ELP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255800.2	NM_018255	
WDR93	56964	hgsc.bcm.edu	37	15	90260145	90260145	+	Missense_Mutation	SNP	T	T	A	rs7163367	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:90260145T>A	ENST00000268130.7	+	7	861	c.760T>A	c.(760-762)Tcc>Acc	p.S254T	RNU6-132P_ENST00000383863.1_RNA|WDR93_ENST00000560294.1_Missense_Mutation_p.S254T	NM_020212.1	NP_064597.1	Q6P2C0	WDR93_HUMAN	WD repeat domain 93	254			S -> T (in dbSNP:rs7163367).		electron transport chain (GO:0022900)		oxidoreductase activity, acting on NAD(P)H (GO:0016651)			NS(1)|breast(3)|endometrium(2)|kidney(4)|large_intestine(5)|liver(2)|lung(8)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	33	Lung NSC(78;0.0237)|all_lung(78;0.0478)		KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|BRCA - Breast invasive adenocarcinoma(143;0.128)			TTCTCAGAACTCCCTTGGTCC	0.338													A|||	1879	0.3752	0.4766	0.3112	5008	,	,		15609	0.2044		0.3956	False		,,,				2504	0.4387				p.S254T		Atlas-SNP	.											WDR93,NS,carcinoma,-1,2	WDR93	63	2	0			c.T760A						PASS	.	A	THR/SER	2074,2326	603.5+/-390.1	483,1108,609	100.0	100.0	100.0		760	-2.3	0.0	15	dbSNP_116	100	3788,4810	613.1+/-396.1	816,2156,1327	yes	missense	WDR93	NM_020212.1	58	1299,3264,1936	AA,AT,TT		44.0568,47.1364,45.0992	benign	254/687	90260145	5862,7136	2200	4299	6499	SO:0001583	missense	56964	exon7			CAGAACTCCCTTG		CCDS32326.1, CCDS66862.1, CCDS73779.1	15q26.1	2012-11-02						"""WD repeat domain containing"""	26924	protein-coding gene	gene with protein product							Standard	NM_020212		Approved		uc002boj.3	Q6P2C0		ENST00000268130.7:c.760T>A	15.37:g.90260145T>A	ENSP00000268130:p.Ser254Thr	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	71	35	0.492958	NM_020212	Q8N7Y8|Q9NP89	Missense_Mutation	SNP	ENST00000268130.7	37	CCDS32326.1	757	0.3466117216117216	201	0.40853658536585363	125	0.3453038674033149	132	0.23076923076923078	299	0.3944591029023747	A	0.011	-1.739211	0.00681	0.471364	0.440568	ENSG00000140527	ENST00000268130	T	0.21361	2.01	3.21	-2.28	0.06826	WD40 repeat-like-containing domain (1);	0.687039	0.13286	N	0.399397	T	0.00012	0.0000	N	0.00237	-1.79	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.32798	-0.9893	9	0.02654	T	1	-0.901	0.9508	0.01376	0.2657:0.319:0.1032:0.3121	rs7163367;rs52812393;rs7163367	254;254	Q6P2C0-2;Q6P2C0	.;WDR93_HUMAN	T	254	ENSP00000268130:S254T	ENSP00000268130:S254T	S	+	1	0	WDR93	88061149	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.435000	0.06931	-0.913000	0.03832	-0.336000	0.08194	TCC	A|0.415;N|0.000	0.415	strong		0.338	WDR93-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000416369.1	NM_020212	
PLIN4	729359	hgsc.bcm.edu	37	19	4512890	4512890	+	Missense_Mutation	SNP	G	G	A	rs199944112	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:4512890G>A	ENST00000301286.3	-	3	1039	c.1040C>T	c.(1039-1041)aCt>aTt	p.T347I		NM_001080400.1	NP_001073869.1	Q96Q06	PLIN4_HUMAN	perilipin 4	347	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						AGTTAGGACAGTCTTGGTGGT	0.577													G|||	613	0.122404	0.3404	0.0735	5008	,	,		19607	0.001		0.0765	False		,,,				2504	0.0348				p.T347I		Atlas-SNP	.											.	PLIN4	191	.	0			c.C1040T						PASS	.						45.0	88.0	76.0					19																	4512890		1706	4160	5866	SO:0001583	missense	729359	exon3			AGGACAGTCTTGG	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.1040C>T	19.37:g.4512890G>A	ENSP00000301286:p.Thr347Ile	Somatic	241	0	0		WXS	Illumina HiSeq	Phase_I	127	13	0.102362	NM_001080400	A6NEI2	Missense_Mutation	SNP	ENST00000301286.3	37	CCDS45927.1	.	.	.	.	.	.	.	.	.	.	G	15.18	2.756798	0.49362	.	.	ENSG00000167676	ENST00000301286	T	0.05319	3.46	4.58	-2.82	0.05787	.	0.834705	0.10002	U	0.728326	T	0.06735	0.0172	M	0.63428	1.95	0.09310	N	1	P	0.49185	0.92	B	0.42386	0.386	T	0.29852	-0.9998	10	0.39692	T	0.17	-0.7204	3.5654	0.07897	0.0837:0.1338:0.3723:0.4103	.	347	Q96Q06	PLIN4_HUMAN	I	347	ENSP00000301286:T347I	ENSP00000301286:T347I	T	-	2	0	PLIN4	4463890	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.482000	0.22276	0.054000	0.16065	-0.373000	0.07131	ACT	G|0.996;A|0.004	0.004	weak		0.577	PLIN4-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395095.1	XM_170901	
ICAM3	3385	hgsc.bcm.edu	37	19	10445806	10445806	+	Silent	SNP	C	C	T	rs3181047	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:10445806C>T	ENST00000160262.5	-	4	1081	c.873G>A	c.(871-873)gaG>gaA	p.E291E	ICAM3_ENST00000589261.1_Silent_p.E214E|RAVER1_ENST00000293677.6_5'Flank	NM_002162.3	NP_002153.2	P32942	ICAM3_HUMAN	intercellular adhesion molecule 3	291	Ig-like C2-type 3.				extracellular matrix organization (GO:0030198)|regulation of immune response (GO:0050776)|single organismal cell-cell adhesion (GO:0016337)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	integrin binding (GO:0005178)|receptor binding (GO:0005102)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(7)|ovary(1)|upper_aerodigestive_tract(2)	13			OV - Ovarian serous cystadenocarcinoma(20;6.13e-09)|Epithelial(33;9.69e-06)|all cancers(31;2.05e-05)			TGCAGACGATCTCCCGGGCAC	0.662													C|||	45	0.00898562	0.0	0.0	5008	,	,		14325	0.0377		0.004	False		,,,				2504	0.0031				p.E291E		Atlas-SNP	.											.	ICAM3	29	.	0			c.G873A						PASS	.	C		3,4403	6.2+/-15.9	0,3,2200	106.0	113.0	110.0		873	-4.6	0.0	19	dbSNP_105	110	6,8594	5.0+/-18.6	0,6,4294	no	coding-synonymous	ICAM3	NM_002162.3		0,9,6494	TT,TC,CC		0.0698,0.0681,0.0692		291/548	10445806	9,12997	2203	4300	6503	SO:0001819	synonymous_variant	3385	exon4			GACGATCTCCCGG		CCDS12235.1	19p13.3-p13.2	2013-01-11				ENSG00000076662		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5346	protein-coding gene	gene with protein product		146631				1448174	Standard	NM_002162		Approved	CDW50, ICAM-R, CD50	uc002mob.2	P32942		ENST00000160262.5:c.873G>A	19.37:g.10445806C>T		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	90	47	0.522222	NM_002162	Q6PD68	Silent	SNP	ENST00000160262.5	37	CCDS12235.1																																																																																			C|0.995;T|0.005	0.005	strong		0.662	ICAM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451234.1		
OTOP3	347741	hgsc.bcm.edu	37	17	72937851	72937851	+	Missense_Mutation	SNP	G	G	A	rs9890664	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:72937851G>A	ENST00000328801.4	+	2	437	c.437G>A	c.(436-438)cGa>cAa	p.R146Q		NM_178233.1	NP_839947.1	Q7RTS5	OTOP3_HUMAN	otopetrin 3	146			R -> Q (in dbSNP:rs9890664).			integral component of membrane (GO:0016021)	metal ion binding (GO:0046872)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(5)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	23	all_lung(278;0.151)|Lung NSC(278;0.185)					ACCACCCGCCGACCACACGCC	0.662													G|||	3274	0.653754	0.4947	0.7695	5008	,	,		13828	0.7341		0.6948	False		,,,				2504	0.6616				p.R146Q		Atlas-SNP	.											.	OTOP3	64	.	0			c.G437A						PASS	.	G	GLN/ARG	2430,1976	610.9+/-391.7	664,1102,437	50.0	41.0	44.0		437	-6.3	0.0	17	dbSNP_119	44	5788,2812	666.8+/-402.4	1954,1880,466	yes	missense	OTOP3	NM_178233.1	43	2618,2982,903	AA,AG,GG		32.6977,44.8479,36.8138	benign	146/597	72937851	8218,4788	2203	4300	6503	SO:0001583	missense	347741	exon2			CCCGCCGACCACA	BK000568	CCDS11709.1	17q25	2004-01-19				ENSG00000182938			19658	protein-coding gene	gene with protein product		607828				12651873	Standard	NM_178233		Approved		uc010wrr.3	Q7RTS5		ENST00000328801.4:c.437G>A	17.37:g.72937851G>A	ENSP00000328090:p.Arg146Gln	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	76	30	0.394737	NM_178233		Missense_Mutation	SNP	ENST00000328801.4	37	CCDS11709.1	1456	0.6666666666666666	238	0.483739837398374	267	0.7375690607734806	401	0.701048951048951	550	0.7255936675461742	G	0.731	-0.780058	0.02929	0.551521	0.673023	ENSG00000182938	ENST00000328801	T	0.07688	3.17	4.71	-6.34	0.01982	.	0.989339	0.08203	N	0.981934	T	0.00012	0.0000	N	0.11255	0.115	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.28235	-1.0050	9	0.15952	T	0.53	-12.3028	9.6546	0.39919	0.6685:0.0:0.2258:0.1058	rs9890664;rs52799712;rs60871048;rs9890664	146	Q7RTS5	OTOP3_HUMAN	Q	146	ENSP00000328090:R146Q	ENSP00000328090:R146Q	R	+	2	0	OTOP3	70449446	0.004000	0.15560	0.000000	0.03702	0.005000	0.04900	-0.031000	0.12287	-0.910000	0.03847	-0.448000	0.05591	CGA	G|0.360;A|0.640	0.640	strong		0.662	OTOP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445308.1	NM_178233	
CD207	50489	hgsc.bcm.edu	37	2	71062648	71062648	+	Missense_Mutation	SNP	G	G	A	rs10489990	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	128	0	0		WXS	Illumina HiSeq	Phase_I	91	35	0.384615	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	
HCN4	10021	hgsc.bcm.edu	37	15	73621946	73621946	+	Silent	SNP	G	G	A	rs12909882	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:73621946G>A	ENST00000261917.3	-	4	2551	c.1558C>T	c.(1558-1560)Ctg>Ttg	p.L520L		NM_005477.2	NP_005468.1	Q9Y3Q4	HCN4_HUMAN	hyperpolarization activated cyclic nucleotide-gated potassium channel 4	520					blood circulation (GO:0008015)|cation transport (GO:0006812)|cellular response to cAMP (GO:0071320)|cellular response to cGMP (GO:0071321)|in utero embryonic development (GO:0001701)|muscle contraction (GO:0006936)|potassium ion transmembrane transport (GO:0071805)|regulation of heart rate (GO:0002027)|regulation of membrane potential (GO:0042391)|sodium ion transmembrane transport (GO:0035725)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|intrinsic component of plasma membrane (GO:0031226)|plasma membrane (GO:0005886)|terminal bouton (GO:0043195)	cAMP binding (GO:0030552)|cation channel activity (GO:0005261)|identical protein binding (GO:0042802)|intracellular cAMP activated cation channel activity (GO:0005222)|voltage-gated potassium channel activity (GO:0005249)|voltage-gated sodium channel activity (GO:0005248)			NS(2)|biliary_tract(1)|breast(1)|endometrium(4)|kidney(1)|large_intestine(13)|liver(1)|lung(18)|ovary(6)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	55				COAD - Colon adenocarcinoma(1;0.142)		GAGGAGTCCAGGGACTGGATG	0.632													G|||	266	0.053115	0.0446	0.0576	5008	,	,		18042	0.003		0.0815	False		,,,				2504	0.0838				p.L520L		Atlas-SNP	.											.	HCN4	150	.	0			c.C1558T						PASS	.	G		179,4217	116.7+/-154.6	4,171,2023	74.0	66.0	69.0		1558	4.2	1.0	15	dbSNP_121	69	782,7812	184.2+/-232.2	37,708,3552	no	coding-synonymous	HCN4	NM_005477.2		41,879,5575	AA,AG,GG		9.0994,4.0719,7.398		520/1204	73621946	961,12029	2198	4297	6495	SO:0001819	synonymous_variant	10021	exon4			AGTCCAGGGACTG	AJ132429	CCDS10248.1	15q24.1	2011-07-05			ENSG00000138622	ENSG00000138622		"""Voltage-gated ion channels / Cyclic nucleotide-regulated channels"""	16882	protein-coding gene	gene with protein product		605206				10228147, 10430953, 16382102	Standard	NM_005477		Approved		uc002avp.3	Q9Y3Q4	OTTHUMG00000137563	ENST00000261917.3:c.1558C>T	15.37:g.73621946G>A		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	122	47	0.385246	NM_005477	Q9UMQ7	Silent	SNP	ENST00000261917.3	37	CCDS10248.1																																																																																			G|0.929;A|0.071	0.071	strong		0.632	HCN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268900.2	NM_005477	
KRT81	3887	hgsc.bcm.edu	37	12	52681080	52681080	+	Silent	SNP	G	G	A	rs4761784	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	121	0	0		WXS	Illumina HiSeq	Phase_I	114	44	0.385965	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	
TSEN54	283989	hgsc.bcm.edu	37	17	73518328	73518328	+	Missense_Mutation	SNP	A	A	C	rs77247739	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:73518328A>C	ENST00000333213.6	+	8	1202	c.1166A>C	c.(1165-1167)cAg>cCg	p.Q389P		NM_207346.2	NP_997229.2	Q7Z6J9	SEN54_HUMAN	TSEN54 tRNA splicing endonuclease subunit	389					mRNA processing (GO:0006397)|tRNA splicing, via endonucleolytic cleavage and ligation (GO:0006388)	nucleus (GO:0005634)				endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(1)|lung(5)|ovary(2)	13	all_cancers(13;3.15e-09)|all_epithelial(9;5.78e-10)|Breast(9;5.8e-10)|all_lung(278;0.246)		all cancers(21;4.57e-07)|Epithelial(20;2.92e-06)|Lung(188;0.0809)|LUSC - Lung squamous cell carcinoma(166;0.154)			CAGCGGCGGCAGGTGCAGAGG	0.716													A|||	354	0.0706869	0.0976	0.0648	5008	,	,		13683	0.0		0.0984	False		,,,				2504	0.0828				p.Q389P		Atlas-SNP	.											.	TSEN54	27	.	0			c.A1166C						PASS	.	A	PRO/GLN	290,3664		11,268,1698	5.0	5.0	5.0		1166	-0.1	0.0	17	dbSNP_131	5	522,7188		9,504,3342	no	missense	TSEN54	NM_207346.2	76	20,772,5040	CC,CA,AA		6.7704,7.3343,6.9616	benign	389/527	73518328	812,10852	1977	3855	5832	SO:0001583	missense	283989	exon8			GGCGGCAGGTGCA	AK097583	CCDS11724.1	17q25.1	2013-08-06	2013-08-06		ENSG00000182173	ENSG00000182173		"""tRNA splicing endonuclease subunits"""	27561	protein-coding gene	gene with protein product		608755	"""tRNA splicing endonuclease 54 homolog (SEN54, S. cerevisiae)"", ""tRNA splicing endonuclease 54 homolog (S. cerevisiae)"""			15109492	Standard	NM_207346		Approved	SEN54, SEN54L	uc002jof.1	Q7Z6J9		ENST00000333213.6:c.1166A>C	17.37:g.73518328A>C	ENSP00000327487:p.Gln389Pro	Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	23	9	0.391304	NM_207346	Q86WV3|Q86XE4|Q8N9H2	Missense_Mutation	SNP	ENST00000333213.6	37	CCDS11724.1	162	0.07417582417582418	55	0.11178861788617886	36	0.09944751381215469	0	0.0	71	0.09366754617414248	A	3.847	-0.032674	0.07543	0.073343	0.067704	ENSG00000182173	ENST00000333213	T	0.58060	0.36	5.47	-0.0634	0.13777	.	0.913377	0.09679	N	0.770042	T	0.00936	0.0031	L	0.43152	1.355	0.80722	P	0.0	B	0.25609	0.13	B	0.22601	0.04	T	0.12528	-1.0544	9	0.33141	T	0.24	-2.0841	9.9457	0.41607	0.3984:0.0:0.6016:0.0	.	389	Q7Z6J9	SEN54_HUMAN	P	389	ENSP00000327487:Q389P	ENSP00000327487:Q389P	Q	+	2	0	TSEN54	71029923	0.000000	0.05858	0.004000	0.12327	0.007000	0.05969	0.306000	0.19279	0.036000	0.15547	0.533000	0.62120	CAG	A|0.926;C|0.074	0.074	strong		0.716	TSEN54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447618.1	NM_207346	
MUC4	4585	hgsc.bcm.edu	37	3	195507349	195507349	+	Missense_Mutation	SNP	A	A	C	rs200575589	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195507349A>C	ENST00000463781.3	-	2	11561	c.11102T>G	c.(11101-11103)aTc>aGc	p.I3701S	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.I3701S	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	0.572													.|||	6	0.00119808	0.003	0.0	5008	,	,		10020	0.0		0.002	False		,,,				2504	0.0				p.I3701S		Atlas-SNP	.											.	MUC4	1505	.	0			c.T11102G						PASS	.						53.0	45.0	48.0					3																	195507349		649	1589	2238	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.11102T>G	3.37:g.195507349A>C	ENSP00000417498:p.Ile3701Ser	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	67	10	0.149254	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	2.741	-0.262273	0.05791	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.26957	1.76;1.7	.	.	.	.	.	.	.	.	T	0.11024	0.0269	N	0.14661	0.345	0.20926	N	0.999828	B	0.15141	0.012	B	0.01281	0.0	T	0.32561	-0.9902	7	.	.	.	.	2.1384	0.03768	0.5016:0.0:0.0:0.4984	.	3573	E7ESK3	.	S	3701	ENSP00000417498:I3701S;ENSP00000420243:I3701S	.	I	-	2	0	MUC4	196992128	0.000000	0.05858	0.025000	0.17156	0.025000	0.11179	-2.950000	0.00678	0.056000	0.16144	0.055000	0.15244	ATC	.	.	weak		0.572	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
TRPT1	83707	hgsc.bcm.edu	37	11	63993287	63993287	+	Missense_Mutation	SNP	C	C	T	rs11549691	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:63993287C>T	ENST00000317459.6	-	2	214	c.46G>A	c.(46-48)Ggt>Agt	p.G16S	TRPT1_ENST00000541278.1_Missense_Mutation_p.G16S|TRPT1_ENST00000394547.3_Intron|TRPT1_ENST00000540472.1_Intron|TRPT1_ENST00000546133.1_5'Flank|TRPT1_ENST00000546089.1_5'UTR|NUDT22_ENST00000441250.2_5'Flank|NUDT22_ENST00000279206.3_5'Flank|TRPT1_ENST00000394546.2_Missense_Mutation_p.G16S			Q86TN4	TRPT1_HUMAN	tRNA phosphotransferase 1	16					regulation of protein kinase activity (GO:0045859)|tRNA splicing, via endonucleolytic cleavage and ligation (GO:0006388)		tRNA 2'-phosphotransferase activity (GO:0000215)			lung(2)|skin(1)	3						GCCCTTCTACCCCTGGACCCT	0.657													C|||	370	0.0738818	0.0182	0.1297	5008	,	,		16345	0.0526		0.0636	False		,,,				2504	0.1421				p.G16S		Atlas-SNP	.											.	TRPT1	14	.	0			c.G46A						PASS	.	C	SER/GLY,SER/GLY,SER/GLY,SER/GLY,SER/GLY,	115,4185		2,111,2037	37.0	28.0	31.0		46,46,46,46,46,	1.7	0.1	11	dbSNP_120	31	520,7942		13,494,3724	yes	missense,missense,missense,missense,missense,intron	TRPT1	NM_001033678.3,NM_001160389.1,NM_001160390.1,NM_001160392.1,NM_001160393.1,NM_031472.3	56,56,56,56,56,	15,605,5761	TT,TC,CC		6.1451,2.6744,4.9757	benign,benign,benign,benign,benign,	16/254,16/256,16/254,16/217,16/255,	63993287	635,12127	2150	4231	6381	SO:0001583	missense	83707	exon2			TTCTACCCCTGGA		CCDS31595.1, CCDS44639.1, CCDS53652.1, CCDS53653.1	11q13	2012-05-03			ENSG00000149743	ENSG00000149743			20316	protein-coding gene	gene with protein product	"""tRNA splicing 2' phosphotransferase 1"""	610470				14504659	Standard	NM_001160389		Approved	MGC11134	uc010rnc.2	Q86TN4	OTTHUMG00000167844	ENST00000317459.6:c.46G>A	11.37:g.63993287C>T	ENSP00000314073:p.Gly16Ser	Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	42	35	0.833333	NM_001033678	A8MU17|A8MYC9|F5H2B2|Q9BSB9	Missense_Mutation	SNP	ENST00000317459.6	37	CCDS31595.1	134	0.06135531135531135	7	0.014227642276422764	50	0.13812154696132597	29	0.050699300699300696	48	0.0633245382585752	C	11.05	1.524767	0.27299	0.026744	0.061451	ENSG00000149743	ENST00000394546;ENST00000541278;ENST00000317459;ENST00000545812	T;T;T;T	0.35605	1.65;1.3;1.65;1.31	4.73	1.74	0.24563	.	0.448580	0.24725	N	0.036111	T	0.00241	0.0007	L	0.56769	1.78	0.43187	P	0.00498299999999996	B;B;B	0.27013	0.01;0.166;0.084	B;B;B	0.32624	0.01;0.149;0.042	T	0.07366	-1.0776	9	0.32370	T	0.25	-4.9742	5.0742	0.14622	0.0:0.6345:0.1718:0.1937	rs11549691	16;16;16	F5H2B2;A8MU17;Q86TN4	.;.;TRPT1_HUMAN	S	16	ENSP00000378050:G16S;ENSP00000438683:G16S;ENSP00000314073:G16S;ENSP00000442066:G16S	ENSP00000314073:G16S	G	-	1	0	TRPT1	63749863	0.000000	0.05858	0.098000	0.21074	0.236000	0.25371	-0.365000	0.07573	0.150000	0.19136	0.561000	0.74099	GGT	C|0.947;T|0.053	0.053	strong		0.657	TRPT1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000396579.1	NM_031472	
DPP6	1804	hgsc.bcm.edu	37	7	154667643	154667643	+	Silent	SNP	G	G	A	rs2230064	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:154667643G>A	ENST00000377770.3	+	20	2052	c.1911G>A	c.(1909-1911)gtG>gtA	p.V637V	DPP6_ENST00000332007.3_Silent_p.V575V|DPP6_ENST00000427557.1_Silent_p.V530V|DPP6_ENST00000404039.1_Silent_p.V573V			P42658	DPP6_HUMAN	dipeptidyl-peptidase 6	637					cell death (GO:0008219)|neuronal action potential (GO:0019228)|positive regulation of potassium ion transmembrane transport (GO:1901381)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	dipeptidyl-peptidase activity (GO:0008239)|serine-type peptidase activity (GO:0008236)			NS(3)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(4)|lung(35)|pancreas(4)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	71	all_neural(206;0.181)	all_hematologic(28;0.0044)|all_lung(21;0.0176)|Lung NSC(21;0.0204)	OV - Ovarian serous cystadenocarcinoma(82;0.0562)			GCCAGAGTGTGGCTGAGAAGT	0.652													G|||	889	0.177516	0.1369	0.2133	5008	,	,		16015	0.0159		0.3459	False		,,,				2504	0.2004				p.V637V	NSCLC(125;1384 1783 2490 7422 34254)	Atlas-SNP	.											.	DPP6	383	.	0			c.G1911A						PASS	.	G	,,	694,3458		57,580,1439	28.0	34.0	32.0		1365,1284,1284	4.0	0.9	7	dbSNP_98	32	2941,5447		526,1889,1779	no	coding-synonymous,coding-synonymous,coding-synonymous	DPP6	NM_001039350.1,NM_001936.3,NM_130797.2	,,	583,2469,3218	AA,AG,GG		35.062,16.7148,28.9872	,,	455/684,428/657,428/657	154667643	3635,8905	2076	4194	6270	SO:0001819	synonymous_variant	1804	exon20			GAGTGTGGCTGAG	M96859	CCDS75682.1, CCDS75683.1, CCDS75684.1	7q36.2	2006-08-07	2006-01-12		ENSG00000130226	ENSG00000130226			3010	protein-coding gene	gene with protein product		126141	"""dipeptidylpeptidase VI"", ""dipeptidylpeptidase 6"""			1729689	Standard	XM_006715871		Approved	DPPX	uc003wlk.3	P42658	OTTHUMG00000151511	ENST00000377770.3:c.1911G>A	7.37:g.154667643G>A		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	82	31	0.378049	NM_130797		Silent	SNP	ENST00000377770.3	37																																																																																				G|0.805;A|0.195	0.195	strong		0.652	DPP6-003	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000322932.1	NM_130797	
KRTAP4-2	85291	hgsc.bcm.edu	37	17	39334241	39334241	+	Missense_Mutation	SNP	G	G	C	rs62067292	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:39334241G>C	ENST00000377726.2	-	1	219	c.176C>G	c.(175-177)aCc>aGc	p.T59S		NM_033062.3	NP_149051	Q9BYR5	KRA42_HUMAN	keratin associated protein 4-2	59	20 X 5 AA repeats OF C-C-[GRQVS]-[SPT]- [VSTQ].					keratin filament (GO:0045095)				kidney(2)|lung(4)|upper_aerodigestive_tract(1)	7		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000449)			GCTGCAGCAGGTGGGCTGGCA	0.667													G|||	96	0.0191693	0.0023	0.0173	5008	,	,		18091	0.0		0.0716	False		,,,				2504	0.0092				p.T59S		Atlas-SNP	.											.	KRTAP4-2	93	.	0			c.C176G						PASS	.	G	SER/THR	58,4344		0,58,2143	39.0	45.0	43.0		176	-9.3	0.0	17	dbSNP_129	43	512,8082		11,490,3796	no	missense	KRTAP4-2	NM_033062.3	58	11,548,5939	CC,CG,GG		5.9576,1.3176,4.386	benign	59/137	39334241	570,12426	2201	4297	6498	SO:0001583	missense	85291	exon1			CAGCAGGTGGGCT	AJ406934	CCDS11384.1	17q21.2	2013-06-25			ENSG00000244537	ENSG00000244537		"""Keratin associated proteins"""	18900	protein-coding gene	gene with protein product						11279113	Standard	NM_033062		Approved	KAP4.2	uc002hwd.3	Q9BYR5	OTTHUMG00000133437	ENST00000377726.2:c.176C>G	17.37:g.39334241G>C	ENSP00000366955:p.Thr59Ser	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	43	23	0.534884	NM_033062	A0JP64	Missense_Mutation	SNP	ENST00000377726.2	37	CCDS11384.1	62	0.028388278388278388	0	0.0	7	0.019337016574585635	0	0.0	55	0.07255936675461741	.	6.408	0.443409	0.12164	0.013176	0.059576	ENSG00000244537	ENST00000377726;ENST00000458321	T	0.01335	5.0	4.67	-9.33	0.00639	.	1.425970	0.05105	N	0.487923	T	0.00178	0.0005	N	0.21373	0.66	0.09310	N	1	B	0.34329	0.449	B	0.41988	0.372	T	0.42699	-0.9436	10	0.06891	T	0.86	.	23.9875	0.99987	0.0:0.7515:0.2485:0.0	rs62067292	59	Q9BYR5	KRA42_HUMAN	S	59;176	ENSP00000366955:T59S	ENSP00000366955:T59S	T	-	2	0	KRTAP4-2	36587767	0.000000	0.05858	0.003000	0.11579	0.043000	0.13939	-5.132000	0.00148	-1.635000	0.01535	-0.414000	0.06135	ACC	G|0.941;C|0.059	0.059	strong		0.667	KRTAP4-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257305.1		
SART1	9092	hgsc.bcm.edu	37	11	65732651	65732651	+	Silent	SNP	G	G	A	rs550435	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:65732651G>A	ENST00000312397.5	+	4	608	c.516G>A	c.(514-516)gcG>gcA	p.A172A		NM_005146.4	NP_005137.1	O43290	SNUT1_HUMAN	squamous cell carcinoma antigen recognized by T cells	172					cell cycle arrest (GO:0007050)|intrinsic apoptotic signaling pathway (GO:0097193)|mRNA splicing, via spliceosome (GO:0000398)|positive regulation of cytotoxic T cell differentiation (GO:0045585)|spliceosomal snRNP assembly (GO:0000387)	Cajal body (GO:0015030)|catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(1)|large_intestine(1)|lung(5)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	11						AGAAGCTGGCGGCTGCCAAGG	0.662													G|||	2201	0.439497	0.3079	0.6023	5008	,	,		8297	0.5218		0.4364	False		,,,				2504	0.4202				p.A172A		Atlas-SNP	.											.	SART1	41	.	0			c.G516A						PASS	.	G		1470,2932		249,972,980	23.0	30.0	28.0		516	-7.3	0.2	11	dbSNP_83	28	3877,4713		867,2143,1285	no	coding-synonymous	SART1	NM_005146.4		1116,3115,2265	AA,AG,GG		45.1339,33.3939,41.1561		172/801	65732651	5347,7645	2201	4295	6496	SO:0001819	synonymous_variant	9092	exon4			GCTGGCGGCTGCC	AB006198	CCDS31611.1	11q13.1	2009-01-06	2006-12-07		ENSG00000175467	ENSG00000175467			10538	protein-coding gene	gene with protein product	"""small nuclear ribonucleoprotein 110kDa (U4/U6.U5)"""	605941	"""squamous cell carcinoma antigen recognised by T cells"""			9449708	Standard	NM_005146		Approved	Ara1, Snu66, SNRNP110	uc001ogl.3	O43290	OTTHUMG00000166771	ENST00000312397.5:c.516G>A	11.37:g.65732651G>A		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	92	92	1	NM_005146	A6NDN1|Q53GB5	Silent	SNP	ENST00000312397.5	37	CCDS31611.1																																																																																			G|0.565;A|0.435	0.435	strong		0.662	SART1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391409.1		
ACTN1	87	hgsc.bcm.edu	37	14	69341653	69341653	+	Missense_Mutation	SNP	T	T	A	rs11557769	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:69341653T>A	ENST00000193403.6	-	21	2985	c.2602A>T	c.(2602-2604)Acc>Tcc	p.T868S	ACTN1_ENST00000438964.2_Missense_Mutation_p.T863S|ACTN1_ENST00000394419.4_Missense_Mutation_p.T890S|ACTN1_ENST00000538545.2_Missense_Mutation_p.T906S|ACTN1_ENST00000376839.3_Missense_Mutation_p.T798S	NM_001102.3	NP_001093.1	P12814	ACTN1_HUMAN	actinin, alpha 1	868			T -> S (in dbSNP:rs11557769).		actin crosslink formation (GO:0051764)|actin filament bundle assembly (GO:0051017)|blood coagulation (GO:0007596)|cell junction assembly (GO:0034329)|extracellular matrix organization (GO:0030198)|focal adhesion assembly (GO:0048041)|negative regulation of cellular component movement (GO:0051271)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of apoptotic process (GO:0042981)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)|pseudopodium (GO:0031143)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|double-stranded RNA binding (GO:0003725)|integrin binding (GO:0005178)|ion channel binding (GO:0044325)|vinculin binding (GO:0017166)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|lung(9)|prostate(2)|urinary_tract(1)	27				BRCA - Breast invasive adenocarcinoma(234;0.00605)|all cancers(60;0.00846)|OV - Ovarian serous cystadenocarcinoma(108;0.0654)		TCGGGGCCGGTGTAGGGGGCC	0.662													t|||	31	0.0061901	0.0	0.0159	5008	,	,		14509	0.0		0.0189	False		,,,				2504	0.001				p.T890S		Atlas-SNP	.											ACTN1,NS,carcinoma,+2,1	ACTN1	77	1	0			c.A2668T						PASS	.	T	SER/THR,SER/THR,SER/THR	16,4390	25.3+/-52.1	0,16,2187	42.0	41.0	41.0		2602,2668,2587	-2.7	0.9	14	dbSNP_120	41	142,8458	70.3+/-132.9	0,142,4158	yes	missense,missense,missense	ACTN1	NM_001102.3,NM_001130004.1,NM_001130005.1	58,58,58	0,158,6345	AA,AT,TT		1.6512,0.3631,1.2148	benign,benign,benign	868/893,890/915,863/888	69341653	158,12848	2203	4300	6503	SO:0001583	missense	87	exon22			GGCCGGTGTAGGG	M95178	CCDS9792.1, CCDS45129.1, CCDS45130.1	14q24.1	2014-08-08			ENSG00000072110	ENSG00000072110		"""EF-hand domain containing"""	163	protein-coding gene	gene with protein product		102575				2349951	Standard	NM_001102		Approved		uc001xkm.3	P12814	OTTHUMG00000171386	ENST00000193403.6:c.2602A>T	14.37:g.69341653T>A	ENSP00000193403:p.Thr868Ser	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	42	15	0.357143	NM_001130004	B3V8S3|B4DHH3|B7TY16|Q1HE25|Q9BTN1	Missense_Mutation	SNP	ENST00000193403.6	37	CCDS9792.1	18	0.008241758241758242	0	0.0	8	0.022099447513812154	0	0.0	10	0.013192612137203167	T	9.571	1.121108	0.20877	0.003631	0.016512	ENSG00000072110	ENST00000193403;ENST00000394419;ENST00000438964;ENST00000376839;ENST00000538545	T;T;T;T;T	0.39229	1.6;1.09;1.09;1.09;1.09	4.68	-2.72	0.05968	EF-hand, Ca insensitive (1);EF-hand-like domain (1);	0.656003	0.15664	N	0.250756	T	0.09642	0.0237	L	0.28556	0.865	0.22185	N	0.999308	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.04013	0.001;0.001;0.001;0.001	T	0.21690	-1.0238	10	0.08381	T	0.77	.	2.1866	0.03888	0.1289:0.3501:0.1331:0.3879	rs11557769	863;890;868;510	P12814-2;Q1HE25;P12814;B4DFY0	.;.;ACTN1_HUMAN;.	S	868;890;863;798;906	ENSP00000193403:T868S;ENSP00000377941:T890S;ENSP00000414272:T863S;ENSP00000366035:T798S;ENSP00000439828:T906S	ENSP00000193403:T868S	T	-	1	0	ACTN1	68411406	0.003000	0.15002	0.930000	0.37139	0.998000	0.95712	-0.007000	0.12810	-0.578000	0.05959	0.528000	0.53228	ACC	T|0.988;A|0.012	0.012	strong		0.662	ACTN1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000413233.3	NM_001102	
TAS2R20	259295	hgsc.bcm.edu	37	12	11150240	11150240	+	Missense_Mutation	SNP	T	T	C	rs7135018	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:11150240T>C	ENST00000538986.1	-	1	234	c.235A>G	c.(235-237)Aaa>Gaa	p.K79E	PRR4_ENST00000536668.1_Intron|TAS2R14_ENST00000381852.4_Intron	NM_176889.2	NP_795370.2	P59543	T2R20_HUMAN	taste receptor, type 2, member 20	79			K -> E (in dbSNP:rs7135018). {ECO:0000269|PubMed:15489334}.		sensory perception of taste (GO:0050909)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(1)|endometrium(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	13						ATTATTACTTTTAAATTAGAT	0.358													T|||	1039	0.207468	0.2171	0.2392	5008	,	,		17782	0.1964		0.2068	False		,,,				2504	0.184				p.K79E		Atlas-SNP	.											.	TAS2R20	17	.	0			c.A235G						PASS	.	T	GLU/LYS	889,3419		102,685,1367	36.0	40.0	39.0		235	-4.2	0.0	12	dbSNP_116	39	1950,6604		238,1474,2565	yes	missense	TAS2R20	NM_176889.2	56	340,2159,3932	CC,CT,TT		22.7964,20.636,22.0728	benign	79/310	11150240	2839,10023	2154	4277	6431	SO:0001583	missense	259295	exon1			TTACTTTTAAATT	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.235A>G	12.37:g.11150240T>C	ENSP00000441624:p.Lys79Glu	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	84	44	0.52381	NM_176889	P59549|Q2HIZ4|Q496D8|Q645X9	Missense_Mutation	SNP	ENST00000538986.1	37	CCDS8639.1	465	0.2129120879120879	94	0.1910569105691057	76	0.20994475138121546	126	0.2202797202797203	169	0.22295514511873352	T	0.007	-2.002581	0.00431	0.20636	0.227964	ENSG00000255837	ENST00000538986	T	0.00737	5.76	2.65	-4.21	0.03812	.	2.421730	0.02456	N	0.086115	T	0.00012	0.0000	N	0.01705	-0.755	0.80722	P	0.0	B	0.06786	0.001	B	0.13407	0.009	T	0.41805	-0.9488	9	0.02654	T	1	.	1.285	0.02049	0.1643:0.1796:0.1642:0.4919	rs7135018;rs60271229;rs7135018	79	P59543	T2R20_HUMAN	E	79	ENSP00000441624:K79E	ENSP00000441624:K79E	K	-	1	0	TAS2R20	11041507	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.986000	0.00660	-0.881000	0.03992	-1.251000	0.01509	AAA	T|0.779;C|0.221	0.221	strong		0.358	TAS2R20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370130.2	NM_176889	
GPATCH1	55094	hgsc.bcm.edu	37	19	33605300	33605300	+	Missense_Mutation	SNP	A	A	G	rs10416265	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	126	0	0		WXS	Illumina HiSeq	Phase_I	112	51	0.455357	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	
ZNF320	162967	hgsc.bcm.edu	37	19	53384197	53384197	+	Silent	SNP	A	A	G	rs61745485	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:53384197A>G	ENST00000595635.1	-	8	1683	c.1182T>C	c.(1180-1182)ttT>ttC	p.F394F	ZNF320_ENST00000597909.1_Intron|ZNF320_ENST00000391781.2_Silent_p.F394F|ZNF320_ENST00000600930.1_Intron	NM_207333.2	NP_997216.2	A2RRD8	ZN320_HUMAN	zinc finger protein 320	394					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|endometrium(2)|kidney(4)|large_intestine(5)|liver(1)|lung(10)|urinary_tract(1)	24				GBM - Glioblastoma multiforme(134;0.0534)		CTTTTGTACTAAAAACCTTGC	0.403													.|||	334	0.0666933	0.143	0.0288	5008	,	,		23267	0.0437		0.0487	False		,,,				2504	0.0327				p.F394F		Atlas-SNP	.											.	ZNF320	67	.	0			c.T1182C						PASS	.	A		569,3837		26,517,1660	91.0	87.0	88.0		1182	-0.3	0.0	19	dbSNP_129	88	353,8247		5,343,3952	no	coding-synonymous	ZNF320	NM_207333.2		31,860,5612	GG,GA,AA		4.1047,12.9142,7.089		394/510	53384197	922,12084	2203	4300	6503	SO:0001819	synonymous_variant	162967	exon4			TGTACTAAAAACC	AF086262	CCDS33095.1	19q13.41	2014-09-04			ENSG00000182986	ENSG00000182986		"""Zinc fingers, C2H2-type"", ""-"""	13842	protein-coding gene	gene with protein product		606427				11536051	Standard	XM_006723059		Approved	ZFPL, DKFZp686G16228	uc002qag.3	A2RRD8	OTTHUMG00000182797	ENST00000595635.1:c.1182T>C	19.37:g.53384197A>G		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	47	18	0.382979	NM_207333	Q8NDR6	Silent	SNP	ENST00000595635.1	37	CCDS33095.1																																																																																			A|0.933;G|0.067	0.067	strong		0.403	ZNF320-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463771.1	NM_207333	
MEIOB	254528	hgsc.bcm.edu	37	16	1894961	1894961	+	Missense_Mutation	SNP	A	A	G	rs9806945	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:1894961A>G	ENST00000397344.3	-	10	976	c.782T>C	c.(781-783)aTa>aCa	p.I261T	MEIOB_ENST00000452149.2_Missense_Mutation_p.I261T|LA16c-429E7.1_ENST00000570247.1_RNA|MEIOB_ENST00000470044.1_Missense_Mutation_p.I54T|MEIOB_ENST00000412554.2_Missense_Mutation_p.I261T|MEIOB_ENST00000325962.3_Missense_Mutation_p.I261T	NM_152764.2	NP_689977.2	Q8N635	MEIOB_HUMAN	meiosis specific with OB domains	261			I -> T (in dbSNP:rs9806945).		double-strand break repair via homologous recombination (GO:0000724)|female meiosis I (GO:0007144)|fertilization (GO:0009566)|male meiosis (GO:0007140)|male meiosis I (GO:0007141)|resolution of meiotic recombination intermediates (GO:0000712)|synapsis (GO:0007129)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|single-stranded DNA 3'-5' exodeoxyribonuclease activity (GO:0008310)|single-stranded DNA binding (GO:0003697)										AGCTTCTGGTATATCTTAAAT	0.249													G|||	1010	0.201677	0.1831	0.2262	5008	,	,		16259	0.1736		0.1819	False		,,,				2504	0.2587				p.I261T		Atlas-SNP	.											.	.	.	.	0			c.T782C						PASS	.	G	THR/ILE,THR/ILE	789,3597	726.1+/-409.7	80,629,1484	38.0	38.0	38.0		782,782	4.9	1.0	16	dbSNP_119	38	1319,7251	738.4+/-407.1	109,1101,3075	yes	missense,missense	C16orf73	NM_001163560.2,NM_152764.2	89,89	189,1730,4559	GG,GA,AA		15.3909,17.9891,16.2705	benign,benign	261/472,261/443	1894961	2108,10848	2193	4285	6478	SO:0001583	missense	254528	exon10			TCTGGTATATCTT	BC029829	CCDS10449.2, CCDS53983.1	16p13.3	2012-08-13	2012-08-13	2012-08-13	ENSG00000162039	ENSG00000162039			28569	protein-coding gene	gene with protein product			"""chromosome 16 open reading frame 73"""	C16orf73		12477932	Standard	NM_152764		Approved	MGC35212	uc010uvq.1	Q8N635	OTTHUMG00000128683	ENST00000397344.3:c.782T>C	16.37:g.1894961A>G	ENSP00000380504:p.Ile261Thr	Somatic	178	1	0.00561798		WXS	Illumina HiSeq	Phase_I	126	91	0.722222	NM_001163560	B1AK39|C9J0S1|Q96RY0	Missense_Mutation	SNP	ENST00000397344.3	37	CCDS10449.2	396	0.1813186813186813	91	0.18495934959349594	62	0.1712707182320442	101	0.17657342657342656	142	0.18733509234828497	G	0.037	-1.303042	0.01353	0.179891	0.153909	ENSG00000162039	ENST00000412554;ENST00000452149;ENST00000325962;ENST00000397344	T;T;T;T	0.04502	3.61;3.61;3.61;3.61	5.98	4.91	0.64330	Nucleic acid-binding, OB-fold-like (1);Nucleic acid-binding, OB-fold (1);	0.166727	0.53938	N	0.000054	T	0.00012	0.0000	N	0.00069	-2.28	0.53005	P	3.2999999999949736E-5	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.34527	-0.9825	9	0.10377	T	0.69	.	10.2088	0.43128	0.1842:0.0:0.8158:0.0	rs9806945;rs52797208;rs59366262;rs9806945	261;261	C9J0S1;Q8N635	.;CP073_HUMAN	T	261	ENSP00000390778:I261T;ENSP00000391033:I261T;ENSP00000314484:I261T;ENSP00000380504:I261T	ENSP00000314484:I261T	I	-	2	0	C16orf73	1834962	1.000000	0.71417	0.972000	0.41901	0.134000	0.20937	2.440000	0.44855	0.686000	0.31488	-0.186000	0.12905	ATA	A|0.839;G|0.161	0.161	strong		0.249	MEIOB-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250580.1	NM_152764	
MYCBP2	23077	hgsc.bcm.edu	37	13	77632470	77632470	+	Silent	SNP	C	C	T	rs2285386	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:77632470C>T	ENST00000544440.2	-	78	13115	c.13098G>A	c.(13096-13098)gaG>gaA	p.E4366E	MYCBP2_ENST00000357337.6_Silent_p.E4366E|MYCBP2_ENST00000407578.2_Silent_p.E4404E					MYC binding protein 2, E3 ubiquitin protein ligase											NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|lung(51)|ovary(5)|pancreas(2)|prostate(5)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	118		Breast(118;0.212)|Acute lymphoblastic leukemia(28;0.22)		GBM - Glioblastoma multiforme(99;0.109)		GCAGACAGTGCTCTTCGTTTT	0.483													C|||	543	0.108427	0.0772	0.1772	5008	,	,		16705	0.121		0.0865	False		,,,				2504	0.1115				p.E4404E		Atlas-SNP	.											.	MYCBP2	1029	.	0			c.G13212A						PASS	.	C		401,4005	200.8+/-224.0	23,355,1825	165.0	132.0	143.0		13212	-1.0	1.0	13	dbSNP_100	143	826,7774	191.5+/-237.7	42,742,3516	no	coding-synonymous	MYCBP2	NM_015057.4		65,1097,5341	TT,TC,CC		9.6047,9.1012,9.4341		4404/4679	77632470	1227,11779	2203	4300	6503	SO:0001819	synonymous_variant	23077	exon78			ACAGTGCTCTTCG	AB020723		13q22	2012-02-23	2012-02-23		ENSG00000005810	ENSG00000005810			23386	protein-coding gene	gene with protein product		610392	"""MYC binding protein 2"""			9689053, 15057823	Standard	NM_015057		Approved	PAM, KIAA0916, FLJ10106	uc021rks.1	O75592	OTTHUMG00000017105	ENST00000544440.2:c.13098G>A	13.37:g.77632470C>T		Somatic	201	0	0		WXS	Illumina HiSeq	Phase_I	164	71	0.432927	NM_015057		Silent	SNP	ENST00000544440.2	37		223	0.1021062271062271	40	0.08130081300813008	55	0.15193370165745856	62	0.10839160839160839	66	0.0870712401055409	C	9.759	1.169521	0.21621	0.091012	0.096047	ENSG00000005810	ENST00000429715	.	.	.	5.42	-1.01	0.10169	.	.	.	.	.	T	0.00210	0.0006	.	.	.	0.09310	P	0.9999999999976027	.	.	.	.	.	.	T	0.18023	-1.0350	3	.	.	.	.	6.7158	0.23302	0.0:0.4793:0.2113:0.3094	rs2285386;rs2285386	.	.	.	T	787	.	.	A	-	1	0	MYCBP2	76530471	0.189000	0.23263	0.997000	0.53966	0.991000	0.79684	-0.397000	0.07269	0.080000	0.16959	0.585000	0.79938	GCA	C|0.903;T|0.097	0.097	strong		0.483	MYCBP2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000045326.1	NM_015057	
DSC1	1823	hgsc.bcm.edu	37	18	28710615	28710615	+	Silent	SNP	C	C	A	rs1816634	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:28710615C>A	ENST00000257198.5	-	16	2808	c.2547G>T	c.(2545-2547)tcG>tcT	p.S849S	DSC1_ENST00000257197.3_3'UTR|RP11-408H20.2_ENST00000581836.1_RNA|RP11-408H20.3_ENST00000582307.1_RNA	NM_024421.2	NP_077739.1	Q08554	DSC1_HUMAN	desmocollin 1	849					homophilic cell adhesion (GO:0007156)	desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|gap junction (GO:0005921)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(20)|ovary(3)|skin(10)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	53			OV - Ovarian serous cystadenocarcinoma(10;0.00778)			CATAGTTATACGAACAAACGT	0.418													C|||	465	0.0928514	0.2542	0.0533	5008	,	,		18467	0.0		0.0467	False		,,,				2504	0.046				p.S849S		Atlas-SNP	.											.	DSC1	240	.	0			c.G2547T						PASS	.	C	,	886,3520	344.1+/-307.9	88,710,1405	133.0	134.0	134.0		,2547	-12.3	0.0	18	dbSNP_92	134	344,8256	118.1+/-177.6	6,332,3962	no	utr-3,coding-synonymous	DSC1	NM_004948.3,NM_024421.2	,	94,1042,5367	AA,AC,CC		4.0,20.1089,9.4572	,	,849/895	28710615	1230,11776	2203	4300	6503	SO:0001819	synonymous_variant	1823	exon16			GTTATACGAACAA	AF293358	CCDS11894.1, CCDS11895.1	18q12.1	2010-01-26			ENSG00000134765	ENSG00000134765		"""Cadherins / Major cadherins"""	3035	protein-coding gene	gene with protein product		125643				8486729	Standard	NM_024421		Approved	CDHF1	uc002kwn.3	Q08554	OTTHUMG00000131982	ENST00000257198.5:c.2547G>T	18.37:g.28710615C>A		Somatic	246	0	0		WXS	Illumina HiSeq	Phase_I	201	85	0.422886	NM_024421	Q9HB01	Silent	SNP	ENST00000257198.5	37	CCDS11894.1																																																																																			C|0.914;A|0.086	0.086	strong		0.418	DSC1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254946.1	NM_004948, NM_024421	
SSTR5	6755	hgsc.bcm.edu	37	16	1129872	1129872	+	Missense_Mutation	SNP	C	C	T	rs169068	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:1129872C>T	ENST00000293897.4	+	1	1092	c.1004C>T	c.(1003-1005)cCg>cTg	p.P335L	SSTR5_ENST00000397547.2_Missense_Mutation_p.P335L|SSTR5-AS1_ENST00000569832.1_RNA|SSTR5_ENST00000562758.1_Intron	NM_001053.3	NP_001044.1	P35346	SSR5_HUMAN	somatostatin receptor 5	335			P -> L (in dbSNP:rs169068). {ECO:0000269|PubMed:11157797, ECO:0000269|PubMed:15616553}.		G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|glucose homeostasis (GO:0042593)|negative regulation of cell proliferation (GO:0008285)|positive regulation of cytokinesis (GO:0032467)|regulation of insulin secretion (GO:0050796)|somatostatin signaling pathway (GO:0038170)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	somatostatin receptor activity (GO:0004994)			endometrium(2)|lung(5)|prostate(1)|skin(1)	9		Hepatocellular(780;0.00369)			Octreotide(DB00104)|Pasireotide(DB06663)|Vapreotide(DB04894)	GCCACGGAGCCGCGTCCAGAC	0.657													C|||	2595	0.518171	0.3366	0.5562	5008	,	,		15310	0.8085		0.5427	False		,,,				2504	0.4121				p.P335L		Atlas-SNP	.											.	SSTR5	36	.	0			c.C1004T						PASS	.	C	LEU/PRO,LEU/PRO	1671,2691	488.8+/-361.3	321,1029,831	31.0	29.0	30.0		1004,1004	2.2	0.6	16	dbSNP_79	30	4627,3955	576.5+/-390.4	1266,2095,930	yes	missense,missense	SSTR5	NM_001053.3,NM_001172560.1	98,98	1587,3124,1761	TT,TC,CC		46.0848,38.3081,48.6557	benign,benign	335/365,335/365	1129872	6298,6646	2181	4291	6472	SO:0001583	missense	6755	exon2			CGGAGCCGCGTCC	D16827	CCDS10429.1	16p13.3	2012-08-08			ENSG00000162009	ENSG00000162009		"""GPCR / Class A : Somatostatin receptors"""	11334	protein-coding gene	gene with protein product		182455				7607700	Standard	NM_001053		Approved		uc021taf.1	P35346	OTTHUMG00000047842	ENST00000293897.4:c.1004C>T	16.37:g.1129872C>T	ENSP00000293897:p.Pro335Leu	Somatic	23	0	0		WXS	Illumina HiSeq	Phase_I	33	9	0.272727	NM_001172560	P34988|Q541E0|Q9UJI5	Missense_Mutation	SNP	ENST00000293897.4	37	CCDS10429.1	1229	0.5627289377289377	149	0.30284552845528456	197	0.5441988950276243	463	0.8094405594405595	420	0.554089709762533	C	3.347	-0.133417	0.06711	0.383081	0.539152	ENSG00000162009	ENST00000397547;ENST00000293897	T;T	0.71698	-0.59;-0.59	4.49	2.24	0.28232	.	0.636775	0.16012	N	0.233745	T	0.00012	0.0000	M	0.65975	2.015	0.80722	P	0.0	B	0.21381	0.055	B	0.14578	0.011	T	0.37641	-0.9697	9	0.23891	T	0.37	.	6.5926	0.22656	0.2905:0.6025:0.0:0.107	rs169068;rs642192;rs169068	335	P35346	SSR5_HUMAN	L	335	ENSP00000380680:P335L;ENSP00000293897:P335L	ENSP00000293897:P335L	P	+	2	0	SSTR5	1069873	0.045000	0.20229	0.589000	0.28718	0.066000	0.16364	0.488000	0.22371	0.883000	0.36040	0.561000	0.74099	CCG	C|0.484;T|0.516	0.516	strong		0.657	SSTR5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000420836.1		
OR8K1	390157	hgsc.bcm.edu	37	11	56113593	56113593	+	Missense_Mutation	SNP	C	C	A	rs10896272	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:56113593C>A	ENST00000279783.2	+	1	173	c.79C>A	c.(79-81)Cct>Act	p.P27T		NM_001002907.1	NP_001002907.1	Q8NGG5	OR8K1_HUMAN	olfactory receptor, family 8, subfamily K, member 1	27			P -> T (in dbSNP:rs10896272).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			large_intestine(8)|liver(2)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	33	Esophageal squamous(21;0.00448)					TACAGACAACCCTGGGCTGCA	0.453										HNSCC(65;0.19)			C|||	2282	0.455671	0.2133	0.598	5008	,	,		17747	0.6438		0.3708	False		,,,				2504	0.5757				p.P27T		Atlas-SNP	.											.	OR8K1	93	.	0			c.C79A						PASS	.	C	THR/PRO	1092,3310	395.1+/-329.5	141,810,1250	115.0	106.0	109.0		79	4.3	0.1	11	dbSNP_120	109	3194,5398	483.4+/-371.1	616,1962,1718	yes	missense	OR8K1	NM_001002907.1	38	757,2772,2968	AA,AC,CC		37.1741,24.8069,32.9845	benign	27/320	56113593	4286,8708	2201	4296	6497	SO:0001583	missense	390157	exon1			GACAACCCTGGGC	AB065835	CCDS31528.1	11q11	2012-08-09			ENSG00000150261	ENSG00000150261		"""GPCR / Class A : Olfactory receptors"""	14831	protein-coding gene	gene with protein product							Standard	NM_001002907		Approved		uc010rjg.2	Q8NGG5	OTTHUMG00000166858	ENST00000279783.2:c.79C>A	11.37:g.56113593C>A	ENSP00000279783:p.Pro27Thr	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	100	24	0.24	NM_001002907	B9EJB1|Q6IFC3|Q96RC1	Missense_Mutation	SNP	ENST00000279783.2	37	CCDS31528.1	946	0.43315018315018317	94	0.1910569105691057	215	0.5939226519337016	368	0.6433566433566433	269	0.3548812664907652	C	16.53	3.150464	0.57151	0.248069	0.371741	ENSG00000150261	ENST00000279783	T	0.00428	7.44	5.18	4.26	0.50523	.	0.135624	0.33834	N	0.004503	T	0.00012	0.0000	M	0.78637	2.42	0.80722	P	0.0	B	0.28820	0.224	B	0.28385	0.089	T	0.04153	-1.0973	9	0.66056	D	0.02	-9.85	8.9442	0.35749	0.1452:0.7789:0.0:0.0759	rs10896272;rs52806840;rs60301163;rs10896272	27	Q8NGG5	OR8K1_HUMAN	T	27	ENSP00000279783:P27T	ENSP00000279783:P27T	P	+	1	0	OR8K1	55870169	0.000000	0.05858	0.065000	0.19835	0.756000	0.42949	-0.062000	0.11674	2.387000	0.81309	0.549000	0.68633	CCT	C|0.621;A|0.379	0.379	strong		0.453	OR8K1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391605.1	NM_001002907	
CCDC102A	92922	hgsc.bcm.edu	37	16	57555076	57555076	+	Silent	SNP	C	C	T	rs28446687	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:57555076C>T	ENST00000258214.2	-	4	1071	c.825G>A	c.(823-825)gcG>gcA	p.A275A		NM_033212.3	NP_149989.2	Q96A19	C102A_HUMAN	coiled-coil domain containing 102A	275										endometrium(1)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)	8						TCCTGCTCAACGCCAGTTTAT	0.582													c|||	926	0.184904	0.3162	0.134	5008	,	,		17816	0.0298		0.2366	False		,,,				2504	0.1503				p.A275A		Atlas-SNP	.											.	CCDC102A	22	.	0			c.G825A						PASS	.	T		1326,3070	446.5+/-348.0	206,914,1078	137.0	114.0	122.0		825	-6.7	0.9	16	dbSNP_125	122	1908,6692	337.3+/-322.2	210,1488,2602	no	coding-synonymous	CCDC102A	NM_033212.3		416,2402,3680	TT,TC,CC		22.186,30.1638,24.8846		275/551	57555076	3234,9762	2198	4300	6498	SO:0001819	synonymous_variant	92922	exon4			GCTCAACGCCAGT	BC008285	CCDS10784.1	16q13	2008-02-05			ENSG00000135736	ENSG00000135736			28097	protein-coding gene	gene with protein product						12477932	Standard	NM_033212		Approved	MGC10992	uc002elw.3	Q96A19	OTTHUMG00000133472	ENST00000258214.2:c.825G>A	16.37:g.57555076C>T		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	122	72	0.590164	NM_033212	Q9BT74	Silent	SNP	ENST00000258214.2	37	CCDS10784.1																																																																																			C|0.768;T|0.232	0.232	strong		0.582	CCDC102A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257348.1	NM_033212	
OR5R1	219479	hgsc.bcm.edu	37	11	56184888	56184888	+	Missense_Mutation	SNP	G	G	A	rs998544	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:56184888G>A	ENST00000312253.1	-	1	820	c.821C>T	c.(820-822)gCt>gTt	p.A274V		NM_001004744.1	NP_001004744.1	Q8NH85	OR5R1_HUMAN	olfactory receptor, family 5, subfamily R, member 1	274			A -> V (in dbSNP:rs998544).			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(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|liver(1)|lung(17)|ovary(2)|prostate(3)|stomach(1)|upper_aerodigestive_tract(1)	37	Esophageal squamous(21;0.00448)					AAATACAGAAGCCATCTTGTC	0.413													G|||	2238	0.446885	0.1838	0.5922	5008	,	,		17733	0.6429		0.3708	False		,,,				2504	0.5757				p.A274V		Atlas-SNP	.											.	OR5R1	83	.	0			c.C821T						PASS	.	G	VAL/ALA	950,3452	361.4+/-315.7	113,724,1364	174.0	164.0	168.0		821	1.5	0.6	11	dbSNP_86	168	3189,5403	483.4+/-371.1	617,1955,1724	yes	missense	OR5R1	NM_001004744.1	64	730,2679,3088	AA,AG,GG		37.1159,21.5811,31.8532	probably-damaging	274/325	56184888	4139,8855	2201	4296	6497	SO:0001583	missense	219479	exon1			ACAGAAGCCATCT	AB065504	CCDS31530.1	11q11	2012-08-09		2004-03-10	ENSG00000174942	ENSG00000174942		"""GPCR / Class A : Olfactory receptors"""	14841	protein-coding gene	gene with protein product				OR5R1P			Standard	NM_001004744		Approved		uc010rji.2	Q8NH85	OTTHUMG00000154219	ENST00000312253.1:c.821C>T	11.37:g.56184888G>A	ENSP00000308595:p.Ala274Val	Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	168	28	0.166667	NM_001004744		Missense_Mutation	SNP	ENST00000312253.1	37	CCDS31530.1	933	0.4271978021978022	85	0.17276422764227642	211	0.5828729281767956	368	0.6433566433566433	269	0.3548812664907652	G	10.26	1.300901	0.23650	0.215811	0.371159	ENSG00000174942	ENST00000312253	T	0.34275	1.37	5.52	1.53	0.23141	GPCR, rhodopsin-like superfamily (1);	0.000000	0.32593	U	0.005885	T	0.00012	0.0000	L	0.33668	1.02	0.80722	P	0.0	D	0.76494	0.999	D	0.75484	0.986	T	0.40079	-0.9582	9	0.26408	T	0.33	-11.0225	4.9356	0.13939	0.359:0.2515:0.3895:0.0	rs998544;rs52811598;rs61607512;rs998544	274	Q8NH85	OR5R1_HUMAN	V	274	ENSP00000308595:A274V	ENSP00000308595:A274V	A	-	2	0	OR5R1	55941464	0.000000	0.05858	0.634000	0.29324	0.078000	0.17371	0.518000	0.22847	0.691000	0.31592	-0.152000	0.13540	GCT	G|0.630;N|0.000	.	strong		0.413	OR5R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334444.1	NM_001004744	
AKR1C1	1645	hgsc.bcm.edu	37	10	5014935	5014935	+	Missense_Mutation	SNP	C	C	A	rs142200840	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:5014935C>A	ENST00000380872.4	+	7	1032	c.840C>A	c.(838-840)aaC>aaA	p.N280K	AKR1C1_ENST00000477661.1_3'UTR|AKR1C1_ENST00000434459.2_Missense_Mutation_p.N280K	NM_001353.5	NP_001344.2	Q04828	AK1C1_HUMAN	aldo-keto reductase family 1, member C1	280					bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|cellular response to jasmonic acid stimulus (GO:0071395)|cholesterol homeostasis (GO:0042632)|daunorubicin metabolic process (GO:0044597)|digestion (GO:0007586)|doxorubicin metabolic process (GO:0044598)|epithelial cell differentiation (GO:0030855)|intestinal cholesterol absorption (GO:0030299)|oxidation-reduction process (GO:0055114)|phototransduction, visible light (GO:0007603)|progesterone metabolic process (GO:0042448)|protein homooligomerization (GO:0051260)|response to organophosphorus (GO:0046683)|retinal metabolic process (GO:0042574)|retinoid metabolic process (GO:0001523)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	17-alpha,20-alpha-dihydroxypregn-4-en-3-one dehydrogenase activity (GO:0047006)|alditol:NADP+ 1-oxidoreductase activity (GO:0004032)|aldo-keto reductase (NADP) activity (GO:0004033)|androsterone dehydrogenase (B-specific) activity (GO:0047042)|bile acid binding (GO:0032052)|carboxylic acid binding (GO:0031406)|indanol dehydrogenase activity (GO:0047718)|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)|trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity (GO:0047115)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|lung(2)|ovary(3)|prostate(1)	13					Acetylsalicylic acid(DB00945)|Salicylic acid(DB00936)	TCAGACAGAACGTGCAGGTGA	0.607													C|||	38	0.00758786	0.0008	0.0173	5008	,	,		21995	0.0		0.0239	False		,,,				2504	0.001				p.N280K	Colon(130;2054 2316 13360 15380)	Atlas-SNP	.											.	AKR1C1	39	.	0			c.C840A						PASS	.	C	LYS/ASN	14,4272		0,14,2129	28.0	26.0	27.0		840	-1.2	0.0	10	dbSNP_134	27	127,8277		2,123,4077	no	missense	AKR1C1	NM_001353.5	94	2,137,6206	AA,AC,CC		1.5112,0.3266,1.1111		280/324	5014935	141,12549	2143	4202	6345	SO:0001583	missense	1645	exon7			ACAGAACGTGCAG	D26124	CCDS7061.1	10p15-p14	2012-12-04	2012-12-04		ENSG00000187134	ENSG00000187134	1.3.1.20, 1.1.1.149, 1.1.1.112	"""Aldo-keto reductases"""	384	protein-coding gene	gene with protein product	"""dihydrodiol dehydrogenase 1; 20-alpha (3-alpha)-hydroxysteroid dehydrogenase"""	600449	"""aldo-keto reductase family 1, member C1 (dihydrodiol dehydrogenase 1; 20-alpha (3-alpha)-hydroxysteroid dehydrogenase)"""	DDH1		8011662	Standard	NM_001353		Approved	DDH, MBAB, DD1, HAKRC		Q04828	OTTHUMG00000017580	ENST00000380872.4:c.840C>A	10.37:g.5014935C>A	ENSP00000370254:p.Asn280Lys	Somatic	358	0	0		WXS	Illumina HiSeq	Phase_I	329	131	0.398176	NM_001353	P52896|Q5SR15|Q7M4N2|Q9UCX2	Missense_Mutation	SNP	ENST00000380872.4	37	CCDS7061.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	13.54|13.54	2.267700|2.267700	0.40095|0.40095	0.003266|0.003266	0.015112|0.015112	ENSG00000187134|ENSG00000187134	ENST00000434459;ENST00000380872|ENST00000442997	T;T|.	0.60424|.	0.19;0.19|.	1.98|1.98	-1.22|-1.22	0.09494|0.09494	Aldo/keto reductase, conserved site (1);NADP-dependent oxidoreductase domain (3);|.	0.000000|.	0.64402|.	D|.	0.000004|.	T|T	0.65291|0.65291	0.2677|0.2677	H|H	0.94847|0.94847	3.59|3.59	0.38716|0.38716	D|D	0.953321|0.953321	D|.	0.89917|.	1.0|.	D|.	0.97110|.	1.0|.	T|T	0.73990|0.73990	-0.3808|-0.3808	10|5	0.87932|.	D|.	0|.	.|.	6.6077|6.6077	0.22734|0.22734	0.0:0.5882:0.0:0.4118|0.0:0.5882:0.0:0.4118	.|.	280|.	Q04828|.	AK1C1_HUMAN|.	K|K	280|247	ENSP00000412248:N280K;ENSP00000370254:N280K|.	ENSP00000370254:N280K|.	N|T	+|+	3|2	2|0	AKR1C1|AKR1C1	5004935|5004935	0.189000|0.189000	0.23263|0.23263	0.003000|0.003000	0.11579|0.11579	0.003000|0.003000	0.03518|0.03518	0.540000|0.540000	0.23191|0.23191	-0.344000|-0.344000	0.08338|0.08338	0.313000|0.313000	0.20887|0.20887	AAC|ACG	C|0.990;A|0.010	0.010	strong		0.607	AKR1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046523.2	NM_001353	
SLC38A10	124565	hgsc.bcm.edu	37	17	79225330	79225330	+	Missense_Mutation	SNP	C	C	A	rs55872261	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:79225330C>A	ENST00000374759.3	-	14	2411	c.2028G>T	c.(2026-2028)gaG>gaT	p.E676D	SLC38A10_ENST00000288439.5_Missense_Mutation_p.E676D	NM_001037984.1	NP_001033073.1	Q9HBR0	S38AA_HUMAN	solute carrier family 38, member 10	676					amino acid transport (GO:0006865)|bone development (GO:0060348)|sodium ion transport (GO:0006814)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				NS(1)|breast(2)|endometrium(4)|kidney(2)|large_intestine(2)|lung(7)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	23	all_neural(118;0.0804)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0272)|OV - Ovarian serous cystadenocarcinoma(97;0.117)			CACCCGCTCGCTCCACGTCCC	0.731													C|||	228	0.0455272	0.0272	0.0922	5008	,	,		12374	0.0298		0.0487	False		,,,				2504	0.0501				p.E676D		Atlas-SNP	.											.	SLC38A10	133	.	0			c.G2028T						PASS	.	C	ASP/GLU,ASP/GLU	159,4153		6,147,2003	8.0	11.0	10.0		2028,2028	1.4	0.0	17	dbSNP_129	10	380,8098		10,360,3869	no	missense,missense	SLC38A10	NM_001037984.1,NM_138570.2	45,45	16,507,5872	AA,AC,CC		4.4822,3.6874,4.2142	probably-damaging,probably-damaging	676/1120,676/781	79225330	539,12251	2156	4239	6395	SO:0001583	missense	124565	exon14			CGCTCGCTCCACG	BC014642	CCDS11780.1, CCDS42397.1	17q25.3	2013-05-22			ENSG00000157637	ENSG00000157637		"""Solute carriers"""	28237	protein-coding gene	gene with protein product							Standard	XM_005257019		Approved	MGC15523, PP1744	uc002jzz.1	Q9HBR0	OTTHUMG00000168049	ENST00000374759.3:c.2028G>T	17.37:g.79225330C>A	ENSP00000363891:p.Glu676Asp	Somatic	21	0	0		WXS	Illumina HiSeq	Phase_I	41	27	0.658537	NM_001037984	Q6ZRC5|Q8NA99|Q96C66	Missense_Mutation	SNP	ENST00000374759.3	37	CCDS42397.1	99	0.04532967032967033	14	0.028455284552845527	27	0.07458563535911603	21	0.03671328671328671	37	0.048812664907651716	C	13.90	2.375314	0.42105	0.036874	0.044822	ENSG00000157637	ENST00000374759;ENST00000540966;ENST00000288439	T;T;T	0.56103	2.7;0.48;2.3	3.38	1.36	0.22044	.	2.052620	0.02743	N	0.116476	T	0.08447	0.0210	L	0.61218	1.895	0.09310	N	0.999999	P;B	0.50156	0.932;0.262	P;B	0.44561	0.453;0.115	T	0.28364	-1.0046	10	0.66056	D	0.02	-17.4629	7.8236	0.29303	0.0:0.7806:0.0:0.2194	rs55872261;rs61740867	676;676	Q9HBR0-2;Q9HBR0	.;S38AA_HUMAN	D	676;54;676	ENSP00000363891:E676D;ENSP00000437601:E54D;ENSP00000288439:E676D	ENSP00000288439:E676D	E	-	3	2	SLC38A10	76839925	0.794000	0.28838	0.029000	0.17559	0.267000	0.26476	1.166000	0.31834	0.768000	0.33290	0.453000	0.30009	GAG	C|0.955;A|0.045	0.045	strong		0.731	SLC38A10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397747.1	NM_138570	
C2orf16	84226	hgsc.bcm.edu	37	2	27801418	27801418	+	Missense_Mutation	SNP	C	C	A	rs1919126	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:27801418C>A	ENST00000408964.2	+	1	2030	c.1979C>A	c.(1978-1980)gCa>gAa	p.A660E		NM_032266.3	NP_115642.3	Q68DN1	CB016_HUMAN	chromosome 2 open reading frame 16	660			A -> E (in dbSNP:rs1919126).			extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(33)|urinary_tract(1)	47	Acute lymphoblastic leukemia(172;0.155)					GTGAAGTCTGCAGAATTAACC	0.393													A|||	3303	0.659545	0.7368	0.6888	5008	,	,		21677	0.8462		0.498	False		,,,				2504	0.5082				p.A660E		Atlas-SNP	.											.	C2orf16	357	.	0			c.C1979A						PASS	.	A	GLU/ALA	2621,1157		901,819,169	97.0	94.0	95.0		1979	-3.1	0.6	2	dbSNP_92	95	4093,4147		1033,2027,1060	yes	missense	C2orf16	NM_032266.3	107	1934,2846,1229	AA,AC,CC		49.6723,30.6247,44.1338	benign	660/1985	27801418	6714,5304	1889	4120	6009	SO:0001583	missense	84226	exon1			AGTCTGCAGAATT	AL136898	CCDS42666.1	2p23.3	2013-09-20			ENSG00000221843	ENSG00000221843			25275	protein-coding gene	gene with protein product	"""P-S-E-R-S-H-H-S repeats containing"""						Standard	NM_032266		Approved	DKFZp434G118	uc002rkz.4	Q68DN1	OTTHUMG00000159099	ENST00000408964.2:c.1979C>A	2.37:g.27801418C>A	ENSP00000386190:p.Ala660Glu	Somatic	314	1	0.00318471		WXS	Illumina HiSeq	Phase_I	325	324	0.996923	NM_032266	B9EIQ4|Q53S01|Q8ND64|Q9H088	Missense_Mutation	SNP	ENST00000408964.2	37	CCDS42666.1	1446	0.6620879120879121	359	0.7296747967479674	228	0.6298342541436464	490	0.8566433566433567	369	0.4868073878627968	A	3.617	-0.078286	0.07184	0.693753	0.496723	ENSG00000221843	ENST00000408964	T	0.08807	3.05	4.83	-3.09	0.05331	.	.	.	.	.	T	0.00012	0.0000	L	0.27053	0.805	0.58432	P	2.9999999999752447E-6	B	0.02656	0.0	B	0.04013	0.001	T	0.10064	-1.0646	8	0.33141	T	0.24	.	1.8543	0.03175	0.3285:0.3785:0.1261:0.1669	rs1919126;rs17705292;rs56730508;rs1919126	660	Q68DN1	CB016_HUMAN	E	660	ENSP00000386190:A660E	ENSP00000386190:A660E	A	+	2	0	C2orf16	27654922	0.755000	0.28372	0.604000	0.28916	0.421000	0.31385	-1.056000	0.03489	-1.023000	0.03342	-0.363000	0.07495	GCA	C|0.365;A|0.635	0.635	strong		0.393	C2orf16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353292.1	NM_032266	
MORC3	23515	hgsc.bcm.edu	37	21	37736413	37736413	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:37736413G>A	ENST00000400485.1	+	14	1551	c.1475G>A	c.(1474-1476)cGg>cAg	p.R492Q	MORC3_ENST00000487909.1_3'UTR|AP000692.9_ENST00000397184.2_RNA	NM_015358.2	NP_056173.1	Q14149	MORC3_HUMAN	MORC family CW-type zinc finger 3	492					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)	p.R492Q(1)		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						CTGTTGTTTCGGCCAACTGCT	0.383																																					p.R492Q		Atlas-SNP	.											MORC3,NS,carcinoma,0,1	MORC3	78	1	1	Substitution - Missense(1)	kidney(1)	c.G1475A						scavenged	.						129.0	117.0	120.0					21																	37736413		1861	4096	5957	SO:0001583	missense	23515	exon14			TGTTTCGGCCAAC	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.1475G>A	21.37:g.37736413G>A	ENSP00000383333:p.Arg492Gln	Somatic	269	0	0		WXS	Illumina HiSeq	Phase_I	381	5	0.0131234	NM_015358	A8KA92|Q9UEZ2	Missense_Mutation	SNP	ENST00000400485.1	37	CCDS42924.1	.	.	.	.	.	.	.	.	.	.	G	5.361	0.251920	0.10185	.	.	ENSG00000159256	ENST00000400485	T	0.13420	2.59	5.38	1.19	0.21007	.	0.831221	0.10244	N	0.698016	T	0.04634	0.0126	N	0.03115	-0.41	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.44081	-0.9351	10	0.18710	T	0.47	-0.6205	2.3788	0.04348	0.172:0.2945:0.3986:0.135	.	492	Q14149	MORC3_HUMAN	Q	492	ENSP00000383333:R492Q	ENSP00000383333:R492Q	R	+	2	0	MORC3	36658283	0.001000	0.12720	0.002000	0.10522	0.764000	0.43329	0.461000	0.21940	0.311000	0.23014	0.561000	0.74099	CGG	.	.	none		0.383	MORC3-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000194640.1	NM_015358	
MDGA1	266727	hgsc.bcm.edu	37	6	37631768	37631768	+	Missense_Mutation	SNP	A	A	G	rs10947690	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:37631768A>G	ENST00000434837.3	-	2	1360	c.182T>C	c.(181-183)cTt>cCt	p.L61P	MDGA1_ENST00000505425.1_Missense_Mutation_p.L61P|MDGA1_ENST00000297153.7_Missense_Mutation_p.L61P	NM_153487.3	NP_705691.1	Q8NFP4	MDGA1_HUMAN	MAM domain containing glycosylphosphatidylinositol anchor 1	61	Ig-like 1.		L -> P (in dbSNP:rs10947690).		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						CCCTGTTACAAGGCACTGCAG	0.607													A|||	425	0.0848642	0.0068	0.1412	5008	,	,		19734	0.006		0.2147	False		,,,				2504	0.0982				p.L61P		Atlas-SNP	.											.	MDGA1	104	.	0			c.T182C						PASS	.	A	PRO/LEU	183,4065		7,169,1948	70.0	72.0	72.0		182	5.2	1.0	6	dbSNP_120	72	1997,6447		254,1489,2479	yes	missense	MDGA1	NM_153487.3	98	261,1658,4427	GG,GA,AA		23.6499,4.3079,17.1762	probably-damaging	61/956	37631768	2180,10512	2124	4222	6346	SO:0001583	missense	266727	exon2			GTTACAAGGCACT	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.182T>C	6.37:g.37631768A>G	ENSP00000402584:p.Leu61Pro	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	84	34	0.404762	NM_153487	A6NHG0|Q8NBE3	Missense_Mutation	SNP	ENST00000434837.3	37	CCDS47417.1	213	0.09752747252747253	6	0.012195121951219513	55	0.15193370165745856	2	0.0034965034965034965	150	0.19788918205804748	A	22.5	4.294354	0.81025	0.043079	0.236499	ENSG00000112139	ENST00000434837;ENST00000297153;ENST00000505425;ENST00000515437;ENST00000508399	T;T;T;T;T	0.66638	0.3;0.3;0.3;-0.22;-0.22	5.25	5.25	0.73442	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.40908	D	0.000981	T	0.60183	0.2249	N	0.21508	0.67	0.09310	P	0.999999999653738	D	0.69078	0.997	D	0.68621	0.959	T	0.63395	-0.6647	9	0.31617	T	0.26	.	14.3559	0.66738	1.0:0.0:0.0:0.0	rs10947690;rs60791866;rs10947690	61	Q8NFP4	MDGA1_HUMAN	P	61;61;61;5;5	ENSP00000402584:L61P;ENSP00000297153:L61P;ENSP00000422042:L61P;ENSP00000421510:L5P;ENSP00000427645:L5P	ENSP00000297153:L61P	L	-	2	0	MDGA1	37739746	1.000000	0.71417	0.994000	0.49952	0.993000	0.82548	9.339000	0.96797	1.994000	0.58287	0.533000	0.62120	CTT	A|0.894;G|0.106	0.106	strong		0.607	MDGA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040419.3		
MUC5B	727897	hgsc.bcm.edu	37	11	1270647	1270647	+	Missense_Mutation	SNP	G	G	C	rs185838223	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:1270647G>C	ENST00000529681.1	+	31	12595	c.12537G>C	c.(12535-12537)caG>caC	p.Q4179H	MUC5B_ENST00000447027.1_Missense_Mutation_p.Q4182H|RP11-532E4.2_ENST00000532061.2_RNA	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	4179	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)		CCCAGGCCCAGCCTGGTGTCC	0.667													G|||	246	0.0491214	0.0598	0.1066	5008	,	,		16942	0.003		0.0497	False		,,,				2504	0.0409				p.Q4179H		Atlas-SNP	.											.	MUC5B	473	.	0			c.G12537C						PASS	.	G	HIS/GLN	237,3547		17,203,1672	44.0	53.0	50.0		12537	-7.2	0.0	11		50	432,7746		13,406,3670	no	missense	MUC5B	NM_002458.2	24	30,609,5342	CC,CG,GG		5.2825,6.2632,5.5927	benign	4179/5763	1270647	669,11293	1892	4089	5981	SO:0001583	missense	727897	exon31			GGCCCAGCCTGGT	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.12537G>C	11.37:g.1270647G>C	ENSP00000436812:p.Gln4179His	Somatic	731	0	0		WXS	Illumina HiSeq	Phase_I	732	153	0.209016	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Missense_Mutation	SNP	ENST00000529681.1	37	CCDS44515.2	96	0.04395604395604396	20	0.04065040650406504	33	0.09116022099447514	0	0.0	43	0.05672823218997362	g	7.941	0.742802	0.15642	0.062632	0.052825	ENSG00000117983	ENST00000529681;ENST00000447027;ENST00000349637;ENST00000406844	T;T	0.17370	2.28;2.28	3.62	-7.25	0.01470	.	.	.	.	.	T	0.00412	0.0013	N	0.05441	-0.05	0.09310	N	1	B;B	0.09022	0.002;0.002	B;B	0.10450	0.005;0.005	T	0.16041	-1.0416	9	0.87932	D	0	.	24.3801	0.99989	0.0:0.8733:0.1267:0.0	.	4652;4182	A7Y9J9;E9PBJ0	.;.	H	4179;4182;4123;4029	ENSP00000436812:Q4179H;ENSP00000415793:Q4182H	ENSP00000343037:Q4123H	Q	+	3	2	MUC5B	1227223	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.783000	0.04638	-1.952000	0.01027	0.393000	0.25936	CAG	G|0.952;C|0.048	0.048	strong		0.667	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
FGF6	2251	hgsc.bcm.edu	37	12	4554630	4554630	+	Missense_Mutation	SNP	A	A	G	rs11613495	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:4554630A>G	ENST00000228837.2	-	1	150	c.107T>C	c.(106-108)gTg>gCg	p.V36A		NM_020996.1	NP_066276.2	P10767	FGF6_HUMAN	fibroblast growth factor 6	36			V -> A (in dbSNP:rs11613495). {ECO:0000269|Ref.2}.		angiogenesis (GO:0001525)|cartilage condensation (GO:0001502)|cell proliferation (GO:0008283)|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)|myoblast differentiation (GO:0045445)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|sarcolemma (GO:0042383)	growth factor activity (GO:0008083)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	20			Colorectal(7;0.00165)|COAD - Colon adenocarcinoma(12;0.0229)			AGGCGAGGGCACCACCATGCC	0.642													A|||	467	0.0932508	0.09	0.0994	5008	,	,		16764	0.0139		0.1461	False		,,,				2504	0.1207				p.V36A		Atlas-SNP	.											.	FGF6	40	.	0			c.T107C						PASS	.	A	ALA/VAL	466,3940	219.7+/-237.4	38,390,1775	71.0	78.0	76.0		107	3.3	1.0	12	dbSNP_120	76	1399,7201	271.1+/-289.3	134,1131,3035	yes	missense	FGF6	NM_020996.1	64	172,1521,4810	GG,GA,AA		16.2674,10.5765,14.3395	benign	36/209	4554630	1865,11141	2203	4300	6503	SO:0001583	missense	2251	exon1			GAGGGCACCACCA	X63454	CCDS8527.1	12p13	2014-01-30				ENSG00000111241		"""Endogenous ligands"""	3684	protein-coding gene	gene with protein product		134921				16597617	Standard	NM_020996		Approved		uc001qmr.1	P10767		ENST00000228837.2:c.107T>C	12.37:g.4554630A>G	ENSP00000228837:p.Val36Ala	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	46	22	0.478261	NM_020996	Q0VAE1	Missense_Mutation	SNP	ENST00000228837.2	37	CCDS8527.1	210	0.09615384615384616	50	0.1016260162601626	30	0.08287292817679558	9	0.015734265734265736	121	0.15963060686015831	A	5.776	0.327498	0.10956	0.105765	0.162674	ENSG00000111241	ENST00000228837	T	0.24723	1.84	4.47	3.3	0.37823	.	0.307478	0.36002	N	0.002841	T	0.00039	0.0001	N	0.19112	0.55	0.40264	P	0.021788999999999947	B	0.02656	0.0	B	0.01281	0.0	T	0.29119	-1.0022	9	0.06365	T	0.9	.	5.7882	0.18345	0.7595:0.0:0.0889:0.1516	rs11613495;rs17183522;rs57277343;rs11613495	36	P10767	FGF6_HUMAN	A	36	ENSP00000228837:V36A	ENSP00000228837:V36A	V	-	2	0	FGF6	4424891	0.984000	0.35163	1.000000	0.80357	0.657000	0.38888	1.317000	0.33631	0.840000	0.34995	0.459000	0.35465	GTG	A|0.879;G|0.121	0.121	strong		0.642	FGF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398939.1	NM_020996	
ADAMTS7	11173	hgsc.bcm.edu	37	15	79092750	79092750	+	Silent	SNP	G	G	C	rs7173267	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:79092750G>C	ENST00000388820.4	-	2	450	c.240C>G	c.(238-240)gcC>gcG	p.A80A	ADAMTS7_ENST00000566303.1_5'UTR	NM_014272.3	NP_055087.2	Q9UKP4	ATS7_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 7	80					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						GCTCGTAGAAGGCGGGCGCGT	0.692													G|||	1245	0.248602	0.1044	0.2968	5008	,	,		12618	0.1518		0.4284	False		,,,				2504	0.3241				p.A80A		Atlas-SNP	.											.	ADAMTS7	142	.	0			c.C240G						PASS	.	G		628,3716		55,518,1599	11.0	12.0	11.0		240	1.1	0.9	15	dbSNP_116	11	3580,4914		781,2018,1448	no	coding-synonymous	ADAMTS7	NM_014272.3		836,2536,3047	CC,CG,GG		42.1474,14.4567,32.7777		80/1687	79092750	4208,8630	2172	4247	6419	SO:0001819	synonymous_variant	11173	exon2			GTAGAAGGCGGGC	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.240C>G	15.37:g.79092750G>C		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	68	29	0.426471	NM_014272	Q14F51|Q6P7J9	Silent	SNP	ENST00000388820.4	37	CCDS32303.1																																																																																			G|0.752;C|0.248	0.248	strong		0.692	ADAMTS7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421331.1	NM_014272	
ADAMTS19	171019	hgsc.bcm.edu	37	5	128796860	128796860	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:128796860C>A	ENST00000274487.4	+	2	284	c.139C>A	c.(139-141)Ccg>Acg	p.P47T	ADAMTS19-AS1_ENST00000502827.1_RNA	NM_133638.3	NP_598377.3	Q8TE59	ATS19_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 19	47						proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|endometrium(10)|kidney(9)|large_intestine(14)|lung(34)|ovary(6)|pancreas(1)|prostate(6)|skin(6)	91		all_cancers(142;0.0148)|Prostate(80;0.0494)|Breast(839;0.238)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	OV - Ovarian serous cystadenocarcinoma(64;0.222)		GCGCCGGGAGCCGGTGGACCC	0.761																																					p.P47T		Atlas-SNP	.											.	ADAMTS19	216	.	0			c.C139A						PASS	.						1.0	1.0	1.0					5																	128796860		985	2022	3007	SO:0001583	missense	171019	exon2			CGGGAGCCGGTGG	AJ311904	CCDS4146.1	5q23.3	2009-04-27	2005-08-19		ENSG00000145808	ENSG00000145808		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	17111	protein-coding gene	gene with protein product		607513	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 19"""			11867212	Standard	NM_133638		Approved		uc003kvb.1	Q8TE59	OTTHUMG00000128990	ENST00000274487.4:c.139C>A	5.37:g.128796860C>A	ENSP00000274487:p.Pro47Thr	Somatic	8	0	0		WXS	Illumina HiSeq	Phase_I	14	13	0.928571	NM_133638		Missense_Mutation	SNP	ENST00000274487.4	37	CCDS4146.1	.	.	.	.	.	.	.	.	.	.	C	13.54	2.266920	0.40095	.	.	ENSG00000145808	ENST00000274487	T	0.64618	-0.11	3.54	2.64	0.31445	.	0.215910	0.23754	N	0.044896	T	0.35566	0.0936	N	0.08118	0	0.24389	N	0.994758	B	0.24186	0.099	B	0.17098	0.017	T	0.16041	-1.0416	9	.	.	.	.	8.9587	0.35834	0.0:0.8863:0.0:0.1137	.	47	Q8TE59	ATS19_HUMAN	T	47	ENSP00000274487:P47T	.	P	+	1	0	ADAMTS19	128824759	1.000000	0.71417	1.000000	0.80357	0.554000	0.35429	1.324000	0.33712	1.043000	0.40175	0.455000	0.32223	CCG	.	.	none		0.761	ADAMTS19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250979.2	NM_133638	
OR10H3	26532	hgsc.bcm.edu	37	19	15853080	15853080	+	Missense_Mutation	SNP	G	G	A	rs2240229	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:15853080G>A	ENST00000305892.1	+	1	878	c.878G>A	c.(877-879)aGt>aAt	p.S293N		NM_013938.1	NP_039226.1	O60404	O10H3_HUMAN	olfactory receptor, family 10, subfamily H, member 3	293			S -> N (in dbSNP:rs2240229).			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)|kidney(2)|large_intestine(1)|liver(1)|lung(6)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	17						ATCATTTTCAGTCTAAGGAAC	0.443													g|||	788	0.157348	0.1505	0.111	5008	,	,		21377	0.122		0.169	False		,,,				2504	0.2239				p.S293N		Atlas-SNP	.											.	OR10H3	53	.	0			c.G878A						PASS	.	G	ASN/SER	766,3640		64,638,1501	154.0	148.0	150.0		878	2.4	1.0	19	dbSNP_98	150	1623,6977		169,1285,2846	yes	missense	OR10H3	NM_013938.1	46	233,1923,4347	AA,AG,GG		18.8721,17.3854,18.3684	probably-damaging	293/317	15853080	2389,10617	2203	4300	6503	SO:0001583	missense	26532	exon1			TTTTCAGTCTAAG		CCDS12334.1	19p13.1	2012-08-09				ENSG00000171936		"""GPCR / Class A : Olfactory receptors"""	8174	protein-coding gene	gene with protein product							Standard	NM_013938		Approved		uc010xoq.2	O60404		ENST00000305892.1:c.878G>A	19.37:g.15853080G>A	ENSP00000307130:p.Ser293Asn	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	63	30	0.47619	NM_013938	Q2HIZ3|Q6IFQ0	Missense_Mutation	SNP	ENST00000305892.1	37	CCDS12334.1	323	0.1478937728937729	79	0.16056910569105692	36	0.09944751381215469	79	0.1381118881118881	129	0.17018469656992086	.	11.25	1.582703	0.28180	0.173854	0.188721	ENSG00000171936	ENST00000305892	T	0.39056	1.1	2.37	2.37	0.29283	.	0.274240	0.25439	U	0.030667	T	0.00241	0.0007	M	0.93197	3.39	0.38547	P	0.050629000000000035	D	0.89917	1.0	D	0.91635	0.999	T	0.32214	-0.9915	9	0.72032	D	0.01	.	10.3915	0.44171	0.0:0.0:1.0:0.0	rs2240229;rs17682603;rs60748494;rs2240229	293	O60404	O10H3_HUMAN	N	293	ENSP00000307130:S293N	ENSP00000307130:S293N	S	+	2	0	OR10H3	15714080	0.017000	0.18338	0.996000	0.52242	0.017000	0.09413	0.941000	0.29005	1.330000	0.45394	0.205000	0.17691	AGT	G|0.833;A|0.167	0.167	strong		0.443	OR10H3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460918.1		
PCDHB4	56131	hgsc.bcm.edu	37	5	140503017	140503017	+	Silent	SNP	G	G	A	rs144689137	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:140503017G>A	ENST00000194152.1	+	1	1437	c.1437G>A	c.(1435-1437)tcG>tcA	p.S479S	AC005754.8_ENST00000606030.1_lincRNA	NM_018938.2	NP_061761.1	Q9Y5E5	PCDB4_HUMAN	protocadherin beta 4	479	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)			ACAGAGACTCGGGCACCAACG	0.667													g|||	133	0.0265575	0.0862	0.0159	5008	,	,		14724	0.0		0.008	False		,,,				2504	0.0				p.S479S		Atlas-SNP	.											PCDHB4,right_upper_lobe,carcinoma,+1,1	PCDHB4	177	1	0			c.G1437A						scavenged	.						42.0	48.0	46.0					5																	140503017		2202	4295	6497	SO:0001819	synonymous_variant	56131	exon1			AGACTCGGGCACC	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.1437G>A	5.37:g.140503017G>A		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	84	4	0.047619	NM_018938	Q4V761	Silent	SNP	ENST00000194152.1	37	CCDS4246.1																																																																																			G|0.216;A|0.784	0.784	strong		0.667	PCDHB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251812.2	NM_018938	
ZNF717	100131827	hgsc.bcm.edu	37	3	75786440	75786440	+	Silent	SNP	C	C	T	rs145944373	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:75786440C>T	ENST00000478296.1	-	4	2460	c.2184G>A	c.(2182-2184)ggG>ggA	p.G728G	ZNF717_ENST00000477374.1_Intron|ZNF717_ENST00000422325.1_Silent_p.G778G|ZNF717_ENST00000491507.1_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	21	1	0.047619		WXS	Illumina HiSeq	Phase_I	23	21	0.913043	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	
MUC4	4585	hgsc.bcm.edu	37	3	195510062	195510062	+	Missense_Mutation	SNP	G	G	C	rs200366897		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195510062G>C	ENST00000463781.3	-	2	8848	c.8389C>G	c.(8389-8391)Cac>Gac	p.H2797D	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.H2797D	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.H2797D(1)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GGGGTGGTGTGACCTGTGGAT	0.587																																					p.H2797D		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	1	Substitution - Missense(1)	kidney(1)	c.C8389G						scavenged	.						62.0	36.0	44.0					3																	195510062		687	1519	2206	SO:0001583	missense	4585	exon2			TGGTGTGACCTGT	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.8389C>G	3.37:g.195510062G>C	ENSP00000417498:p.His2797Asp	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	90	8	0.0888889	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	.	.	.	.	.	.	.	.	.	.	-	2.270	-0.367202	0.05069	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.30448	1.53;1.53	0.918	0.918	0.19386	.	.	.	.	.	T	0.15609	0.0376	N	0.19112	0.55	0.18873	N	0.999985	P	0.47604	0.898	B	0.37550	0.253	T	0.12218	-1.0556	8	.	.	.	.	7.3741	0.26818	0.0:0.0:1.0:0.0	.	2669	E7ESK3	.	D	2797	ENSP00000417498:H2797D;ENSP00000420243:H2797D	.	H	-	1	0	MUC4	196994841	0.000000	0.05858	0.213000	0.23690	0.036000	0.12997	0.296000	0.19083	0.432000	0.26286	0.074000	0.15403	CAC	.	.	weak		0.587	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
SYK	6850	hgsc.bcm.edu	37	9	93606309	93606309	+	Silent	SNP	G	G	A	rs35758162	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:93606309G>A	ENST00000375754.4	+	2	277	c.129G>A	c.(127-129)caG>caA	p.Q43Q	SYK_ENST00000375746.1_Silent_p.Q43Q|SYK_ENST00000375747.1_Silent_p.Q43Q|SYK_ENST00000476708.1_3'UTR|SYK_ENST00000375751.4_Silent_p.Q43Q	NM_003177.5	NP_003168.2	P43405	KSYK_HUMAN	spleen tyrosine kinase	43	SH2 1. {ECO:0000255|PROSITE- ProRule:PRU00191}.				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						TGCTGCGCCAGAGCCGCAACT	0.612			T	"""ETV6, ITK"""	"""MDS, peripheral T-cell lymphoma"""								G|||	556	0.111022	0.1067	0.1138	5008	,	,		18957	0.0159		0.168	False		,,,				2504	0.1544				p.Q43Q		Atlas-SNP	.		Dom	yes		9	9q22	6850	spleen tyrosine kinase		L	.	SYK	132	.	0			c.G129A						PASS	.	G	,,,	529,3877	232.6+/-246.1	36,457,1710	60.0	41.0	48.0		129,129,129,129	4.1	1.0	9	dbSNP_126	48	1795,6805	313.7+/-311.4	181,1433,2686	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SYK	NM_001135052.2,NM_001174167.1,NM_001174168.1,NM_003177.5	,,,	217,1890,4396	AA,AG,GG		20.8721,12.0064,17.8687	,,,	43/613,43/636,43/613,43/636	93606309	2324,10682	2203	4300	6503	SO:0001819	synonymous_variant	6850	exon2			GCGCCAGAGCCGC	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.129G>A	9.37:g.93606309G>A		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	77	40	0.519481	NM_003177		Silent	SNP	ENST00000375754.4	37	CCDS6688.1																																																																																			G|0.847;A|0.153	0.153	strong		0.612	SYK-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053018.1		
HRNR	388697	hgsc.bcm.edu	37	1	152192327	152192327	+	Missense_Mutation	SNP	T	T	A	rs369151727		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:152192327T>A	ENST00000368801.2	-	3	1853	c.1778A>T	c.(1777-1779)cAg>cTg	p.Q593L	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_001009931.1	NP_001009931.1	Q86YZ3	HORN_HUMAN	hornerin	593					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)			GCCAGAGGACTGTCCTGAGCG	0.557																																					p.Q593L		Atlas-SNP	.											HRNR,bladder,carcinoma,0,1	HRNR	403	1	0			c.A1778T						scavenged	.						267.0	246.0	253.0					1																	152192327		2203	4300	6503	SO:0001583	missense	388697	exon3			GAGGACTGTCCTG	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.1778A>T	1.37:g.152192327T>A	ENSP00000357791:p.Gln593Leu	Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	162	2	0.0123457	NM_001009931	Q5DT20|Q5U1F4	Missense_Mutation	SNP	ENST00000368801.2	37	CCDS30859.1	.	.	.	.	.	.	.	.	.	.	-	7.751	0.703241	0.15172	.	.	ENSG00000197915	ENST00000368801	T	0.01613	4.73	3.93	2.76	0.32466	.	.	.	.	.	T	0.00524	0.0017	N	0.24115	0.695	0.09310	N	1	P	0.43477	0.808	B	0.38156	0.266	T	0.51671	-0.8676	9	0.27785	T	0.31	.	8.5385	0.33377	0.0:0.0:0.1964:0.8036	.	593	Q86YZ3	HORN_HUMAN	L	593	ENSP00000357791:Q593L	ENSP00000357791:Q593L	Q	-	2	0	HRNR	150458951	0.030000	0.19436	0.000000	0.03702	0.000000	0.00434	3.483000	0.53194	0.540000	0.28808	-0.457000	0.05445	CAG	.	.	none		0.557	HRNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034016.1	XM_373868	
LRIT3	345193	hgsc.bcm.edu	37	4	110791273	110791273	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:110791273G>T	ENST00000594814.1	+	4	1368	c.1368G>T	c.(1366-1368)aaG>aaT	p.K456N	LRIT3_ENST00000379920.3_Missense_Mutation_p.K411N|LRIT3_ENST00000409621.2_Missense_Mutation_p.K273N|LRIT3_ENST00000327908.3_Missense_Mutation_p.K273N	NM_198506.3	NP_940908.3	Q3SXY7	LRIT3_HUMAN	leucine-rich repeat, immunoglobulin-like and transmembrane domains 3	456					regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				cervix(1)|kidney(1)|large_intestine(3)|lung(8)|prostate(2)|skin(1)	16				OV - Ovarian serous cystadenocarcinoma(123;0.0011)		AGGTGGCAAAGAATGGAAGTA	0.463																																					p.K456N		Atlas-SNP	.											.	LRIT3	107	.	0			c.G1368T						PASS	.						69.0	71.0	70.0					4																	110791273		2203	4300	6503	SO:0001583	missense	345193	exon4			GGCAAAGAATGGA	AK126648	CCDS3688.2, CCDS3688.3	4q25	2014-01-28	2007-06-19		ENSG00000183423	ENSG00000183423		"""Immunoglobulin superfamily / I-set domain containing"""	24783	protein-coding gene	gene with protein product	"""fibronectin type III, immunoglobulin and leucine rich repeat domains 4"""	615004					Standard	NM_198506		Approved	FLJ44691, FIGLER4, CSNB1F	uc031sgv.1	Q3SXY7	OTTHUMG00000132043	ENST00000594814.1:c.1368G>T	4.37:g.110791273G>T	ENSP00000469759:p.Lys456Asn	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	73	37	0.506849	NM_198506	C9J1C2|Q6ZTG1	Missense_Mutation	SNP	ENST00000594814.1	37	CCDS3688.3	.	.	.	.	.	.	.	.	.	.	G	0.029	-1.351036	0.01256	.	.	ENSG00000183423	ENST00000327908;ENST00000379920;ENST00000409621	T;T;T	0.58506	0.33;0.5;0.33	5.06	2.14	0.27477	.	0.790373	0.11066	N	0.603446	T	0.38639	0.1048	L	0.29908	0.895	0.09310	N	1	B;B	0.29805	0.097;0.257	B;B	0.26416	0.023;0.069	T	0.17592	-1.0364	10	0.18276	T	0.48	.	6.0052	0.19542	0.2318:0.2504:0.5178:0.0	.	411;273	Q3SXY7;Q3SXY7-2	LRIT3_HUMAN;.	N	273;411;273	ENSP00000328222:K273N;ENSP00000369252:K411N;ENSP00000386734:K273N	ENSP00000328222:K273N	K	+	3	2	LRIT3	111010722	0.000000	0.05858	0.004000	0.12327	0.008000	0.06430	0.171000	0.16685	1.118000	0.41863	0.655000	0.94253	AAG	.	.	none		0.463	LRIT3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335270.2	NM_198506	
C7orf26	79034	hgsc.bcm.edu	37	7	6639953	6639953	+	Silent	SNP	G	G	A	rs34300529	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:6639953G>A	ENST00000344417.5	+	4	1341	c.1074G>A	c.(1072-1074)gtG>gtA	p.V358V	C7orf26_ENST00000472693.1_3'UTR|C7orf26_ENST00000359073.5_Silent_p.V261V	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	58	0	0		WXS	Illumina HiSeq	Phase_I	40	12	0.3	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	
CDON	50937	hgsc.bcm.edu	37	11	125871721	125871721	+	Missense_Mutation	SNP	G	G	C	rs145983470	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:125871721G>C	ENST00000392693.3	-	11	2178	c.2051C>G	c.(2050-2052)aCc>aGc	p.T684S	CDON_ENST00000531738.1_Missense_Mutation_p.T61S|CDON_ENST00000263577.7_Missense_Mutation_p.T684S	NM_001243597.1|NM_016952.4	NP_001230526.1|NP_058648.4	Q4KMG0	CDON_HUMAN	cell adhesion associated, oncogene regulated	684			T -> S (in HPE11; dbSNP:rs145983470). {ECO:0000269|PubMed:21802063}.		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.T684I(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)		GGATGCCTGGGTGTTTTTTGA	0.393													G|||	9	0.00179712	0.0	0.0	5008	,	,		16120	0.0		0.008	False		,,,				2504	0.001				p.T684S		Atlas-SNP	.											CDON,right_lower_lobe,carcinoma,0,1	CDON	137	1	1	Substitution - Missense(1)	skin(1)	c.C2051G						PASS	.	G	SER/THR	12,4390	19.1+/-41.9	0,12,2189	121.0	121.0	121.0		2051	5.8	1.0	11	dbSNP_134	121	76,8522	44.9+/-103.4	0,76,4223	yes	missense	CDON	NM_016952.4	58	0,88,6412	CC,CG,GG		0.8839,0.2726,0.6769	benign	684/1265	125871721	88,12912	2201	4299	6500	SO:0001583	missense	50937	exon11			GCCTGGGTGTTTT	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.2051C>G	11.37:g.125871721G>C	ENSP00000376458:p.Thr684Ser	Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	101	77	0.762376	NM_016952	O14631	Missense_Mutation	SNP	ENST00000392693.3	37	CCDS58192.1	8	0.003663003663003663	0	0.0	0	0.0	0	0.0	8	0.010554089709762533	G	13.73	2.323686	0.41096	0.002726	0.008839	ENSG00000064309	ENST00000392693;ENST00000531738;ENST00000263577	T;T;T	0.69040	-0.36;0.25;-0.37	5.78	5.78	0.91487	.	0.231330	0.30383	N	0.009752	T	0.52158	0.1717	L	0.32530	0.975	0.41753	D	0.989675	B;P;B	0.36974	0.44;0.576;0.018	B;B;B	0.36845	0.118;0.234;0.016	T	0.56347	-0.7994	10	0.37606	T	0.19	-9.5924	20.3668	0.98882	0.0:0.0:1.0:0.0	.	684;684;61	Q4KMG0;Q4KMG0-2;E9PN78	CDON_HUMAN;.;.	S	684;61;684	ENSP00000376458:T684S;ENSP00000432901:T61S;ENSP00000263577:T684S	ENSP00000263577:T684S	T	-	2	0	CDON	125376931	1.000000	0.71417	0.971000	0.41717	0.478000	0.33099	4.745000	0.62125	2.894000	0.99253	0.655000	0.94253	ACC	G|0.994;C|0.006	0.006	strong		0.393	CDON-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386749.2	NM_016952	
GJA8	2703	hgsc.bcm.edu	37	1	147380460	147380460	+	Silent	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:147380460G>A	ENST00000369235.1	+	1	378	c.378G>A	c.(376-378)caG>caA	p.Q126Q	GJA8_ENST00000240986.4_Silent_p.Q126Q			P48165	CXA8_HUMAN	gap junction protein, alpha 8, 50kDa	126					cell-cell signaling (GO:0007267)|lens development in camera-type eye (GO:0002088)|protein homooligomerization (GO:0051260)|transmembrane transport (GO:0055085)|transport (GO:0006810)|visual perception (GO:0007601)	connexon complex (GO:0005922)|integral component of plasma membrane (GO:0005887)	channel activity (GO:0015267)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(12)|ovary(2)|pancreas(1)|prostate(3)|skin(1)|stomach(1)	37	all_hematologic(923;0.0276)					GCCCGGACCAGGGCAGCGTCA	0.647																																					p.Q126Q	Melanoma(76;1255 1795 8195 52096)	Atlas-SNP	.											GJA8,NS,carcinoma,+2,1	GJA8	108	1	0			c.G378A						PASS	.						46.0	55.0	52.0					1																	147380460		2203	4300	6503	SO:0001819	synonymous_variant	2703	exon2			GGACCAGGGCAGC	U34802	CCDS30834.1	1q21.1	2008-02-05	2007-01-16		ENSG00000121634	ENSG00000121634		"""Ion channels / Gap junction proteins (connexins)"""	4281	protein-coding gene	gene with protein product	"""connexin 50"""	600897	"""gap junction protein, alpha 8, 50kD (connexin 50)"", ""gap junction protein, alpha 8, 50kDa (connexin 50)"""	CAE1, CZP1, CAE		9497259, 7796604	Standard	NM_005267		Approved	CX50	uc001epu.2	P48165	OTTHUMG00000024085	ENST00000369235.1:c.378G>A	1.37:g.147380460G>A		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	42	11	0.261905	NM_005267	A7L5M5|Q5VVN9|Q9NP25	Silent	SNP	ENST00000369235.1	37	CCDS30834.1																																																																																			.	.	none		0.647	GJA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060647.1	NM_005267	
SLAMF1	6504	hgsc.bcm.edu	37	1	160580549	160580549	+	Missense_Mutation	SNP	G	G	T	rs3796504	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	278	0	0		WXS	Illumina HiSeq	Phase_I	181	57	0.314917	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		
MUC15	143662	hgsc.bcm.edu	37	11	26586801	26586801	+	Missense_Mutation	SNP	G	G	A	rs15783	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:26586801G>A	ENST00000455601.2	-	2	723	c.605C>T	c.(604-606)aCc>aTc	p.T202I	MUC15_ENST00000281268.8_Missense_Mutation_p.T229I|MUC15_ENST00000529533.1_Missense_Mutation_p.T229I|MUC15_ENST00000527569.1_Missense_Mutation_p.T229I|ANO3_ENST00000525139.1_Intron|MUC15_ENST00000436318.2_Missense_Mutation_p.T229I|ANO3_ENST00000537978.1_Intron|ANO3_ENST00000256737.3_Intron|ANO3_ENST00000531568.1_Intron	NM_145650.3	NP_663625.2	Q8N387	MUC15_HUMAN	mucin 15, cell surface associated	202			T -> I (in dbSNP:rs15783). {ECO:0000269|PubMed:12047385, ECO:0000269|PubMed:15489334}.		cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(7)|ovary(1)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	25						TTGATAAGGGGTAAACCCAGT	0.398													G|||	2816	0.5623	0.4887	0.7421	5008	,	,		19290	0.4425		0.6581	False		,,,				2504	0.5593				p.T229I		Atlas-SNP	.											MUC15,colon,carcinoma,0,1	MUC15	88	1	0			c.C686T						PASS	.	G	ILE/THR,ILE/THR,,ILE/THR	2268,2138	593.9+/-388.1	576,1116,511	134.0	135.0	134.0		686,686,,605	2.1	0.0	11	dbSNP_52	134	5573,3027	662.3+/-402.0	1782,2009,509	yes	missense,missense,intron,missense	ANO3,MUC15	NM_001135091.1,NM_001135092.1,NM_031418.2,NM_145650.3	89,89,,89	2358,3125,1020	AA,AG,GG		35.1977,48.5247,39.7124	probably-damaging,probably-damaging,,probably-damaging	229/362,229/312,,202/335	26586801	7841,5165	2203	4300	6503	SO:0001583	missense	143662	exon3			TAAGGGGTAAACC	AJ417818	CCDS7859.1, CCDS44556.1, CCDS44557.1	11p14.3	2007-01-17	2006-03-14					"""Mucins"""	14956	protein-coding gene	gene with protein product		608566				12047385	Standard	NM_145650		Approved		uc001mqw.3	Q8N387		ENST00000455601.2:c.605C>T	11.37:g.26586801G>A	ENSP00000397339:p.Thr202Ile	Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	102	79	0.77451	NM_001135092	B3KY00|E9PII6|F8W945|Q6UWS3|Q8IXI8|Q8WW41	Missense_Mutation	SNP	ENST00000455601.2	37	CCDS7859.1	1239	0.5673076923076923	249	0.5060975609756098	254	0.7016574585635359	240	0.4195804195804196	496	0.6543535620052771	G	13.71	2.319766	0.41096	0.514753	0.648023	ENSG00000169550	ENST00000455601;ENST00000436318;ENST00000281268;ENST00000529533;ENST00000527569	T;T;T;T;T	0.30448	1.55;1.53;1.56;1.53;1.56	4.2	2.12	0.27331	.	0.258612	0.27176	N	0.020570	T	0.00012	0.0000	L	0.46157	1.445	0.80722	P	0.0	P;P;P	0.44816	0.844;0.492;0.844	B;B;B	0.43809	0.432;0.121;0.292	T	0.26883	-1.0090	9	0.62326	D	0.03	-6.2717	4.1989	0.10457	0.1192:0.0:0.6518:0.229	rs15783;rs293981;rs3191114;rs17845625;rs17858556;rs17859636;rs52800238;rs57603196;rs15783	229;202;229	F8W945;Q8N387;E9PII6	.;MUC15_HUMAN;.	I	202;229;229;229;229	ENSP00000397339:T202I;ENSP00000416753:T229I;ENSP00000281268:T229I;ENSP00000431983:T229I;ENSP00000431945:T229I	ENSP00000281268:T229I	T	-	2	0	MUC15	26543377	0.478000	0.25917	0.020000	0.16555	0.027000	0.11550	1.067000	0.30616	1.060000	0.40578	0.650000	0.86243	ACC	G|0.424;A|0.576	0.576	strong		0.398	MUC15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387866.1	NM_145650	
KXD1	79036	hgsc.bcm.edu	37	19	18679379	18679379	+	Missense_Mutation	SNP	C	C	G	rs7648	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:18679379C>G	ENST00000602094.1	+	5	1929	c.469C>G	c.(469-471)Cct>Gct	p.P157A	KXD1_ENST00000540691.1_Missense_Mutation_p.P157A|KXD1_ENST00000539106.1_Missense_Mutation_p.P157A|KXD1_ENST00000222307.4_Missense_Mutation_p.P157A|KXD1_ENST00000599319.1_Missense_Mutation_p.P157A|KXD1_ENST00000601630.1_Missense_Mutation_p.P176A|AC005253.4_ENST00000593791.1_RNA|KXD1_ENST00000595073.1_Missense_Mutation_p.P157A			Q9BQD3	KXDL1_HUMAN	KxDL motif containing 1	157			P -> A (in dbSNP:rs7648). {ECO:0000269|PubMed:15489334}.		vesicle-mediated transport (GO:0016192)	BLOC-1 complex (GO:0031083)											CCATGTCCAGCCTGGCTCCCC	0.662													C|||	2316	0.46246	0.146	0.5533	5008	,	,		16763	0.6895		0.5606	False		,,,				2504	0.4908				p.P157A		Atlas-SNP	.											.	.	.	.	0			c.C469G						PASS	.	C	ALA/PRO,ALA/PRO,ALA/PRO	886,3520	342.3+/-307.1	93,700,1410	94.0	87.0	89.0		469,469,469	2.4	0.0	19	dbSNP_52	89	4849,3751	616.3+/-396.5	1356,2137,807	yes	missense,missense,missense	C19orf50	NM_001171948.1,NM_001171949.1,NM_024069.3	27,27,27	1449,2837,2217	GG,GC,CC		43.6163,20.1089,44.095	benign,benign,benign	157/177,157/177,157/177	18679379	5735,7271	2203	4300	6503	SO:0001583	missense	79036	exon6			GTCCAGCCTGGCT	AK098346	CCDS12381.1	19p13.11	2011-11-24	2011-11-24	2011-11-24	ENSG00000105700	ENSG00000105700			28420	protein-coding gene	gene with protein product		615178	"""chromosome 19 open reading frame 50"""	C19orf50		21159114	Standard	NM_001171948		Approved	FLJ25480, MGC2749, KXDL	uc002njo.3	Q9BQD3		ENST00000602094.1:c.469C>G	19.37:g.18679379C>G	ENSP00000472836:p.Pro157Ala	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	37	17	0.459459	NM_001171948	O76098	Missense_Mutation	SNP	ENST00000602094.1	37	CCDS12381.1	1101	0.5041208791208791	83	0.16869918699186992	190	0.5248618784530387	391	0.6835664335664335	437	0.5765171503957783	C	2.533	-0.308095	0.05458	0.201089	0.563837	ENSG00000105700	ENST00000540691;ENST00000539106;ENST00000222307	T;T;T	0.41400	1.0;1.0;1.0	4.6	2.41	0.29592	.	0.417725	0.27645	N	0.018454	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	B	0.25667	0.131	B	0.22386	0.039	T	0.40156	-0.9578	9	0.10111	T	0.7	-6.4712	6.6392	0.22899	0.0:0.5966:0.0:0.4034	rs7648;rs3170472;rs17844882;rs17857599;rs17857882;rs60515468	157	Q9BQD3	CS050_HUMAN	A	157	ENSP00000443549:P157A;ENSP00000438903:P157A;ENSP00000222307:P157A	ENSP00000222307:P157A	P	+	1	0	C19orf50	18540379	0.000000	0.05858	0.003000	0.11579	0.038000	0.13279	0.467000	0.22035	0.346000	0.23899	0.561000	0.74099	CCT	C|0.536;G|0.464	0.464	strong		0.662	KXD1-003	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465107.1	NM_024069	
NBPF10	100132406	hgsc.bcm.edu	37	1	145293469	145293469	+	Missense_Mutation	SNP	G	G	C	rs6671324		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:145293469G>C	ENST00000369339.3	+	3	317	c.64G>C	c.(64-66)Gag>Cag	p.E22Q	RP11-458D21.5_ENST00000468030.1_3'UTR|NBPF10_ENST00000369338.1_Intron|NBPF10_ENST00000342960.5_Missense_Mutation_p.E22Q			Q6P3W6	NBPFA_HUMAN	neuroblastoma breakpoint family, member 10	293						cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)			NS(3)|breast(1)|central_nervous_system(3)|endometrium(12)|kidney(23)|lung(15)|ovary(1)|prostate(7)|skin(6)|urinary_tract(2)	73	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		AGAAATCAACGAGACATTGCG	0.517																																					p.E22Q		Atlas-SNP	.											.	NBPF10	221	.	0			c.G64C						PASS	.																																			SO:0001583	missense	100132406	exon1			ATCAACGAGACAT	BC021111		1q21.1	2013-01-17			ENSG00000163386	ENSG00000271425		"""neuroblastoma breakpoint family"""	31992	protein-coding gene	gene with protein product		614000				16079250	Standard	NM_001039703		Approved	AG1		Q6P3W6	OTTHUMG00000013757	ENST00000369339.3:c.64G>C	1.37:g.145293469G>C	ENSP00000358345:p.Glu22Gln	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	75	8	0.106667	NM_001039703	Q5RHC0|Q9NWN6	Missense_Mutation	SNP	ENST00000369339.3	37		.	.	.	.	.	.	.	.	.	.	.	0.003	-2.490659	0.00161	.	.	ENSG00000163386	ENST00000369339;ENST00000342960	T	0.03181	4.02	1.21	-1.37	0.09056	.	.	.	.	.	T	0.00845	0.0028	N	0.26042	0.785	0.09310	N	1	P	0.46621	0.881	B	0.43990	0.438	T	0.36261	-0.9755	9	0.09084	T	0.74	.	6.6617	0.23018	0.0:0.4052:0.5948:0.0	rs6671324	22	A8MQ30	.	Q	22	ENSP00000345684:E22Q	ENSP00000345684:E22Q	E	+	1	0	NBPF10	144004826	0.000000	0.05858	0.002000	0.10522	0.002000	0.02628	-1.862000	0.01653	-0.414000	0.07495	-1.406000	0.01132	GAG	.	.	weak		0.517	NBPF10-001	KNOWN	not_best_in_genome_evidence|basic	protein_coding	protein_coding	OTTHUMT00000038550.3	NM_001039703	
ADAMTSL4	54507	hgsc.bcm.edu	37	1	150531905	150531905	+	Missense_Mutation	SNP	C	C	A	rs150225445	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:150531905C>A	ENST00000369038.2	+	15	3107	c.2906C>A	c.(2905-2907)gCc>gAc	p.A969D	RP11-54A4.2_ENST00000442435.2_RNA|ADAMTSL4_ENST00000271643.4_Missense_Mutation_p.A969D|ADAMTSL4_ENST00000369039.5_Missense_Mutation_p.A992D			Q6UY14	ATL4_HUMAN	ADAMTS-like 4	969	TSP type-1 5. {ECO:0000255|PROSITE- ProRule:PRU00210}.				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)			CAAGGGCAGGCCTGCCAGGAC	0.642											OREG0013787	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	15	0.00299521	0.0008	0.0058	5008	,	,		16910	0.0		0.0089	False		,,,				2504	0.001				p.A969D		Atlas-SNP	.											.	ADAMTSL4	101	.	0			c.C2906A						PASS	.	C	ASP/ALA	12,4394	19.1+/-41.9	0,12,2191	59.0	53.0	55.0		2906	-0.1	1.0	1	dbSNP_134	55	132,8468	65.3+/-127.6	4,124,4172	yes	missense	ADAMTSL4	NM_019032.4	126	4,136,6363	AA,AC,CC		1.5349,0.2724,1.1072	benign	969/1075	150531905	144,12862	2203	4300	6503	SO:0001583	missense	54507	exon17			GGCAGGCCTGCCA	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.2906C>A	1.37:g.150531905C>A	ENSP00000358034:p.Ala969Asp	Somatic	119	0	0	1733	WXS	Illumina HiSeq	Phase_I	101	42	0.415842	NM_019032	B2RTT0|F8WAD0|Q5T5F7|Q6IPM6|Q8N643|Q9HBS6	Missense_Mutation	SNP	ENST00000369038.2	37	CCDS955.1	8	0.003663003663003663	0	0.0	1	0.0027624309392265192	0	0.0	7	0.009234828496042216	C	7.526	0.657648	0.14645	0.002724	0.015349	ENSG00000143382	ENST00000271643;ENST00000369039;ENST00000369038	T;T;T	0.53423	0.62;0.62;0.62	5.52	-0.118	0.13547	.	.	.	.	.	T	0.08670	0.0215	N	0.12637	0.245	0.23162	N	0.998196	B;B;B	0.09022	0.002;0.001;0.001	B;B;B	0.14023	0.01;0.005;0.007	T	0.29912	-0.9996	9	0.35671	T	0.21	.	2.075	0.03622	0.2698:0.3971:0.2201:0.113	.	930;992;969	B7ZMJ3;F8WAD0;Q6UY14	.;.;ATL4_HUMAN	D	969;992;969	ENSP00000271643:A969D;ENSP00000358035:A992D;ENSP00000358034:A969D	ENSP00000271643:A969D	A	+	2	0	ADAMTSL4	148798529	0.004000	0.15560	0.978000	0.43139	0.969000	0.65631	0.193000	0.17116	-0.067000	0.12976	0.462000	0.41574	GCC	C|0.993;A|0.007	0.007	strong		0.642	ADAMTSL4-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084395.4	NM_019032	
CWF19L1	55280	hgsc.bcm.edu	37	10	101995477	101995477	+	Silent	SNP	T	T	G	rs139693285		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:101995477T>G	ENST00000354105.4	-	13	1505	c.1419A>C	c.(1417-1419)acA>acC	p.T473T	SNORA12_ENST00000391162.1_RNA|CWF19L1_ENST00000370379.1_Silent_p.T188T|RP11-316M21.6_ENST00000444359.1_RNA|CWF19L1_ENST00000478047.1_5'UTR	NM_018294.4	NP_060764.3	Q69YN2	C19L1_HUMAN	CWF19-like 1, cell cycle control (S. pombe)	473							catalytic activity (GO:0003824)			cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(1)|lung(4)|pancreas(1)|prostate(1)|stomach(2)	17		Colorectal(252;0.117)		Epithelial(162;3.78e-10)|all cancers(201;3.1e-08)		GCTTTTCTCCTGTGTCAAGTT	0.328													T|||	1	0.000199681	0.0	0.0	5008	,	,		20611	0.0		0.001	False		,,,				2504	0.0				p.T473T		Atlas-SNP	.											.	CWF19L1	39	.	0			c.A1419C						PASS	.	T		0,4406		0,0,2203	77.0	79.0	78.0		1419	1.6	1.0	10	dbSNP_134	78	24,8574	17.3+/-56.4	0,24,4275	no	coding-synonymous	CWF19L1	NM_018294.4		0,24,6478	GG,GT,TT		0.2791,0.0,0.1846		473/539	101995477	24,12980	2203	4299	6502	SO:0001819	synonymous_variant	55280	exon13			TTCTCCTGTGTCA	AK001860	CCDS7489.1	10q24.31	2008-11-24			ENSG00000095485	ENSG00000095485			25613	protein-coding gene	gene with protein product						14702039	Standard	NM_018294		Approved	FLJ10998	uc001kqq.1	Q69YN2	OTTHUMG00000018901	ENST00000354105.4:c.1419A>C	10.37:g.101995477T>G		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	38	16	0.421053	NM_018294	B4DHX1|D3DR66|Q5W0I3|Q96HC3|Q9H865|Q9NV13	Silent	SNP	ENST00000354105.4	37	CCDS7489.1																																																																																			T|0.999;G|0.001	0.001	strong		0.328	CWF19L1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_018294	
MLC1	23209	hgsc.bcm.edu	37	22	50515270	50515270	+	Splice_Site	SNP	T	T	C	rs267607236|rs6010164	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:50515270T>C	ENST00000311597.5	-	7	1203	c.597A>G	c.(595-597)tcA>tcG	p.S199S	MLC1_ENST00000535444.1_Splice_Site_p.S120S|MLC1_ENST00000450140.2_Splice_Site_p.S147S|MLC1_ENST00000538737.1_Splice_Site_p.S165S|MLC1_ENST00000431262.2_Splice_Site_p.S169S|MLC1_ENST00000395876.2_Splice_Site_p.S199S	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	64	0	0		WXS	Illumina HiSeq	Phase_I	51	23	0.45098	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
HLA-A	3105	hgsc.bcm.edu	37	6	29912087	29912087	+	Missense_Mutation	SNP	G	G	T	rs1059632	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:29912087G>T	ENST00000396634.1	+	6	1149	c.808G>T	c.(808-810)Gct>Tct	p.A270S	HLA-A_ENST00000376802.2_Missense_Mutation_p.A270S|HLA-A_ENST00000376809.5_Missense_Mutation_p.A270S|HLA-A_ENST00000376806.5_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	146	0	0		WXS	Illumina HiSeq	Phase_I	125	41	0.328	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	
SBSPON	157869	hgsc.bcm.edu	37	8	74005131	74005131	+	Missense_Mutation	SNP	A	A	G	rs59331088	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:74005131A>G	ENST00000297354.6	-	1	376	c.172T>C	c.(172-174)Ttc>Ctc	p.F58L	SBSPON_ENST00000519697.1_Intron	NM_153225.3	NP_694957.3	Q8IVN8	SBSPO_HUMAN	somatomedin B and thrombospondin, type 1 domain containing	58	SMB. {ECO:0000255|PROSITE- ProRule:PRU00350}.		F -> L (in dbSNP:rs59331088). {ECO:0000269|PubMed:12107410}.		immune response (GO:0006955)	proteinaceous extracellular matrix (GO:0005578)	polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)										TCCCCGGTGAAGCGACAGGCT	0.711													G|||	1839	0.367212	0.649	0.2738	5008	,	,		9492	0.2966		0.2873	False		,,,				2504	0.2076				p.F58L		Atlas-SNP	.											.	.	.	.	0			c.T172C						PASS	.	G	LEU/PHE	2242,1716		657,928,394	26.0	38.0	34.0		172	3.2	1.0	8	dbSNP_129	34	2237,6025		307,1623,2201	yes	missense	C8orf84	NM_153225.3	22	964,2551,2595	GG,GA,AA		27.0758,43.3552,36.653	benign	58/265	74005131	4479,7741	1979	4131	6110	SO:0001583	missense	157869	exon1			CGGTGAAGCGACA		CCDS43747.2	8q21.11	2013-08-07	2012-05-15	2012-05-15	ENSG00000164764	ENSG00000164764			30362	protein-coding gene	gene with protein product	"""RPE spondin"", ""rpe-spondin"""		"""chromosome 8 open reading frame 84"""	C8orf84		12107410	Standard	NM_153225		Approved	RPESP	uc003xzf.3	Q8IVN8	OTTHUMG00000157144	ENST00000297354.6:c.172T>C	8.37:g.74005131A>G	ENSP00000297354:p.Phe58Leu	Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	156	122	0.782051	NM_153225	A8KAA5|Q96J64	Missense_Mutation	SNP	ENST00000297354.6	37	CCDS43747.2	800	0.3663003663003663	324	0.6585365853658537	111	0.30662983425414364	163	0.28496503496503495	202	0.26649076517150394	G	10.70	1.423153	0.25639	0.566448	0.270758	ENSG00000164764	ENST00000297354	T	0.20738	2.05	5.15	3.25	0.37280	Somatomedin B domain (2);	0.526255	0.19119	N	0.122227	T	0.00012	0.0000	N	0.00707	-1.245	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.35351	-0.9792	9	0.07990	T	0.79	-14.5554	7.5784	0.27950	0.1573:0.1376:0.7051:0.0	rs59331088;rs62510382	58	Q8IVN8	RPESP_HUMAN	L	58	ENSP00000297354:F58L	ENSP00000297354:F58L	F	-	1	0	C8orf84	74167685	0.163000	0.22920	0.998000	0.56505	0.992000	0.81027	0.807000	0.27140	1.175000	0.42826	-0.220000	0.12472	TTC	A|0.660;G|0.340	0.340	strong		0.711	SBSPON-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347584.2	NM_153225	
IGFBP3	3486	hgsc.bcm.edu	37	7	45956969	45956969	+	Missense_Mutation	SNP	T	T	G	rs9282734	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:45956969T>G	ENST00000275521.6	-	2	606	c.473A>C	c.(472-474)cAc>cCc	p.H158P	IGFBP3_ENST00000465642.1_5'UTR|IGFBP3_ENST00000381083.4_Missense_Mutation_p.H164P|IGFBP3_ENST00000381086.5_Missense_Mutation_p.H61P	NM_000598.4|NM_001013398.1	NP_000589.2|NP_001013416.1	P17936	IBP3_HUMAN	insulin-like growth factor binding protein 3	158	Ser/Thr-rich.		H -> P (in dbSNP:rs9282734).		apoptotic process (GO:0006915)|cellular protein metabolic process (GO:0044267)|negative regulation of cell proliferation (GO:0008285)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of signal transduction (GO:0009968)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of smooth muscle cell proliferation (GO:0048662)|osteoblast differentiation (GO:0001649)|positive regulation of apoptotic process (GO:0043065)|positive regulation of catalytic activity (GO:0043085)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of myoblast differentiation (GO:0045663)|protein phosphorylation (GO:0006468)|regulation of cell growth (GO:0001558)|regulation of glucose metabolic process (GO:0010906)|type B pancreatic cell proliferation (GO:0044342)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|insulin-like growth factor binding protein complex (GO:0016942)|nucleus (GO:0005634)	insulin-like growth factor binding (GO:0005520)|insulin-like growth factor I binding (GO:0031994)|metal ion binding (GO:0046872)|protein tyrosine phosphatase activator activity (GO:0008160)			large_intestine(6)|lung(7)|pancreas(1)|prostate(3)	17					Mecasermin(DB01277)	AGACACCCGGTGCGTGCTGGA	0.532											OREG0018049	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	T|||	144	0.028754	0.0348	0.0101	5008	,	,		16600	0.0685		0.006	False		,,,				2504	0.0164				p.H164P		Atlas-SNP	.											.	IGFBP3	40	.	0			c.A491C						PASS	.	T	PRO/HIS,PRO/HIS	180,4226	112.9+/-151.0	2,176,2025	84.0	80.0	81.0		473,491	1.8	0.0	7	dbSNP_118	81	47,8553	30.1+/-81.4	0,47,4253	yes	missense,missense	IGFBP3	NM_000598.4,NM_001013398.1	77,77	2,223,6278	GG,GT,TT		0.5465,4.0853,1.7453	benign,benign	158/292,164/298	45956969	227,12779	2203	4300	6503	SO:0001583	missense	3486	exon2			ACCCGGTGCGTGC		CCDS5505.1, CCDS34632.1	7p12.3	2014-09-17			ENSG00000146674	ENSG00000146674			5472	protein-coding gene	gene with protein product	"""growth hormone-dependent binding protein"", ""acid stable subunit of the 140 K IGF complex"", ""binding protein 53"", ""binding protein 29"", ""IGF-binding protein 3"""	146732				1695633	Standard	NM_000598		Approved	IBP3, BP-53	uc003tnr.3	P17936	OTTHUMG00000023769	ENST00000275521.6:c.473A>C	7.37:g.45956969T>G	ENSP00000275521:p.His158Pro	Somatic	109	0	0	935	WXS	Illumina HiSeq	Phase_I	68	25	0.367647	NM_001013398	A4D2F5|D3DVM0|Q2V509|Q6P1M6|Q9UCL4	Missense_Mutation	SNP	ENST00000275521.6	37	CCDS5505.1	75|75	0.034340659340659344|0.034340659340659344	18|18	0.036585365853658534|0.036585365853658534	2|2	0.0055248618784530384|0.0055248618784530384	49|49	0.08566433566433566|0.08566433566433566	6|6	0.0079155672823219|0.0079155672823219	T|T	7.282|7.282	0.609326|0.609326	0.14066|0.14066	0.040853|0.040853	0.005465|0.005465	ENSG00000146674|ENSG00000146674	ENST00000545032;ENST00000275521;ENST00000381086;ENST00000438491;ENST00000442142;ENST00000381083;ENST00000433047;ENST00000448817|ENST00000428530	T;T;T;T|.	0.25749|.	2.43;1.78;2.44;1.87|.	5.55|5.55	1.8|1.8	0.24995|0.24995	.|.	5.052270|.	0.00766|.	N|.	0.001165|.	T|T	0.01661|0.01661	0.0053|0.0053	L|L	0.41573|0.41573	1.285|1.285	0.09310|0.09310	N|N	0.999999|0.999999	B;B;B|.	0.12013|.	0.004;0.002;0.005|.	B;B;B|.	0.12837|.	0.003;0.008;0.006|.	T|T	0.02925|0.02925	-1.1093|-1.1093	10|5	0.30854|.	T|.	0.27|.	-57.9071|-57.9071	11.208|11.208	0.48782|0.48782	0.0:0.0:0.593:0.407|0.0:0.0:0.593:0.407	rs9282734;rs52829675;rs9282734|rs9282734;rs52829675;rs9282734	61;158;143|.	B3KWK7;P17936;B4DN53|.	.;IBP3_HUMAN;.|.	P|P	135;158;61;144;56;164;130;48|10	ENSP00000275521:H158P;ENSP00000370476:H61P;ENSP00000370473:H164P;ENSP00000389668:H48P|.	ENSP00000275521:H158P|.	H|T	-|-	2|1	0|0	IGFBP3|IGFBP3	45923494|45923494	0.998000|0.998000	0.40836|0.40836	0.022000|0.022000	0.16811|0.16811	0.048000|0.048000	0.14542|0.14542	0.303000|0.303000	0.19210|0.19210	0.347000|0.347000	0.23924|0.23924	-0.313000|-0.313000	0.08912|0.08912	CAC|ACC	T|0.974;G|0.026	0.026	strong		0.532	IGFBP3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251356.3	NM_001013398	
CES1	1066	hgsc.bcm.edu	37	16	55862762	55862762	+	Silent	SNP	C	C	G	rs3826194	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:55862762C>G	ENST00000361503.4	-	2	304	c.174G>C	c.(172-174)ccG>ccC	p.P58P	CES1_ENST00000360526.3_Silent_p.P59P|CES1_ENST00000422046.2_Silent_p.P58P|CES1_ENST00000566555.1_5'Flank			P23141	EST1_HUMAN	carboxylesterase 1	58					epithelial cell differentiation (GO:0030855)|metabolic process (GO:0008152)|response to toxic substance (GO:0009636)	endoplasmic reticulum (GO:0005783)	carboxylic ester hydrolase activity (GO:0052689)|methylumbelliferyl-acetate deacetylase activity (GO:0047374)								all cancers(182;0.13)|Epithelial(162;0.137)	Benzocaine(DB01086)|Capecitabine(DB01101)|Ciclesonide(DB01410)|Clopidogrel(DB00758)|Cyclandelate(DB04838)|Dabigatran etexilate(DB06695)|Indomethacin(DB00328)|Irinotecan(DB00762)|L-Carnitine(DB00583)|Mycophenolate mofetil(DB00688)|Oseltamivir(DB00198)|Probucol(DB01599)|Rufinamide(DB06201)|Tamoxifen(DB00675)|Trandolapril(DB00519)	GTCCAAGAGGCGGCTTGGCAA	0.552																																					p.P59P	NSCLC(162;1801 2756 42904 52896)	Atlas-SNP	.											CES1_ENST00000360526,caecum,carcinoma,0,2	CES1	78	2	0			c.G177C						scavenged	.						100.0	93.0	95.0					16																	55862762		2198	4300	6498	SO:0001819	synonymous_variant	1066	exon2			AAGAGGCGGCTTG	BC012418	CCDS32450.1, CCDS45488.1, CCDS45489.1	16q22.2	2010-10-12	2010-10-12		ENSG00000198848	ENSG00000198848	3.1.1.1	"""Carboxylesterases"""	1863	protein-coding gene	gene with protein product	"""human monocyte/macrophage serine esterase 1"""	114835	"""carboxylesterase 1 (monocyte/macrophage serine esterase 1)"""			2070086, 20931200	Standard	XM_005255774		Approved	HMSE, CES2, HMSE1, SES1, CEH, CES1A1, CES1A2	uc002eil.3	P23141		ENST00000361503.4:c.174G>C	16.37:g.55862762C>G		Somatic	152	1	0.00657895		WXS	Illumina HiSeq	Phase_I	95	15	0.157895	NM_001025195	A6NIM1|A8K3K8|A8K844|E9PAU8|P82127|Q00015|Q13657|Q14062|Q16737|Q16788|Q549X7|Q549X8|Q86UK2|Q96EE8|Q9UC52|Q9UDG8|Q9UK77|Q9ULY2	Silent	SNP	ENST00000361503.4	37	CCDS45488.1																																																																																			C|0.766;G|0.234	0.234	strong		0.552	CES1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000433285.1	NM_001266	
HLA-DPA1	3113	hgsc.bcm.edu	37	6	33036977	33036977	+	Silent	SNP	G	G	A	rs2308927	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:33036977G>A	ENST00000419277.1	-	4	576	c.447C>T	c.(445-447)aaC>aaT	p.N149N	HLA-DPA1_ENST00000428995.1_Silent_p.N149N|HLA-DPA1_ENST00000463066.1_5'UTR	NM_001242524.1|NM_001242525.1	NP_001229453.1|NP_001229454.1	P20036	DPA1_HUMAN	major histocompatibility complex, class II, DP alpha 1	149	Alpha-2.|Ig-like C1-type.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cellular response to interferon-gamma (GO:0071346)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell proliferation (GO:0042102)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			kidney(5)|large_intestine(1)|lung(6)|prostate(1)|skin(2)	15						GCCACGTGACGTTGAGCACTG	0.572													.|||	856	0.170927	0.1815	0.0288	5008	,	,		19187	0.5298		0.0239	False		,,,				2504	0.0389				p.N149N		Atlas-SNP	.											.	HLA-DPA1	20	.	0			c.C447T						PASS	.	G	,,	463,2555		19,425,1065	139.0	161.0	153.0		447,447,447	-5.8	0.9	6	dbSNP_126	153	129,5287		0,129,2579	no	coding-synonymous,coding-synonymous,coding-synonymous	HLA-DPA1	NM_001242524.1,NM_001242525.1,NM_033554.3	,,	19,554,3644	AA,AG,GG		2.3818,15.3413,7.0192	,,	149/261,149/261,149/261	33036977	592,7842	1509	2708	4217	SO:0001819	synonymous_variant	3113	exon3			CGTGACGTTGAGC	X00457	CCDS4764.1	6p21.3	2013-01-11			ENSG00000231389	ENSG00000231389		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4938	protein-coding gene	gene with protein product		142880		HLA-DP1A		6584734	Standard	NM_033554		Approved		uc003ocs.2	P20036	OTTHUMG00000031058	ENST00000419277.1:c.447C>T	6.37:g.33036977G>A		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	49	19	0.387755	NM_033554	A9YWH7|B9UKH4|O19722|O46883|P01905|P79554|Q2Q060|Q2Q061|Q5EY03|Q5STP1|Q6DQK4|Q9BCQ1|Q9TPX3|Q9XS10	Silent	SNP	ENST00000419277.1	37	CCDS4764.1	411	0.18818681318681318	106	0.21544715447154472	6	0.016574585635359115	283	0.49475524475524474	16	0.021108179419525065	G	4.697	0.129537	0.08981	0.153413	0.023818	ENSG00000231389	ENST00000437811	.	.	.	3.4	-5.84	0.02318	.	.	.	.	.	T	0.27798	0.0684	.	.	.	0.09310	P	0.99999999607824	.	.	.	.	.	.	T	0.32268	-0.9913	3	.	.	.	.	12.6047	0.56516	0.2374:0.0:0.7626:0.0	rs2308927	.	.	.	C	17	.	.	R	-	1	0	HLA-DPA1	33144955	0.000000	0.05858	0.882000	0.34594	0.507000	0.33981	-1.620000	0.02046	-0.859000	0.04105	-0.824000	0.03097	CGT	G|0.903;A|0.097	0.097	strong		0.572	HLA-DPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076071.3	NM_033554	
ZNF628	89887	hgsc.bcm.edu	37	19	55995272	55995272	+	Silent	SNP	G	G	A	rs11550705	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:55995272G>A	ENST00000598519.1	+	3	3265	c.2712G>A	c.(2710-2712)ccG>ccA	p.P904P	NAT14_ENST00000205194.4_5'Flank|NAT14_ENST00000591590.1_5'Flank|NAT14_ENST00000587400.1_5'Flank|ZNF628_ENST00000391718.2_Silent_p.P900P			Q5EBL2	ZN628_HUMAN	zinc finger protein 628	904					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(4)|kidney(1)|lung(2)	7	Breast(117;0.155)		BRCA - Breast invasive adenocarcinoma(297;0.18)|LUSC - Lung squamous cell carcinoma(43;0.193)	GBM - Glioblastoma multiforme(193;0.0531)		TCACTGGCCCGGGCCCCGGGG	0.662													g|||	1181	0.235823	0.0825	0.2781	5008	,	,		13382	0.0149		0.4404	False		,,,				2504	0.4305				p.P904P		Atlas-SNP	.											.	ZNF628	75	.	0			c.G2712A						PASS	.	G		544,3850		32,480,1685	17.0	19.0	18.0		2700	-7.0	0.0	19	dbSNP_120	18	3972,4614		924,2124,1245	no	coding-synonymous	ZNF628	NM_033113.2		956,2604,2930	AA,AG,GG		46.2614,12.3805,34.792		900/1056	55995272	4516,8464	2197	4293	6490	SO:0001819	synonymous_variant	89887	exon3			TGGCCCGGGCCCC	AF367249	CCDS33116.3	19q13.43	2013-01-08			ENSG00000197483	ENSG00000197483		"""Zinc fingers, C2H2-type"""	28054	protein-coding gene	gene with protein product	"""Zinc finger expressed in Embryonal cells and Certain adult organs"""	610671					Standard	NM_033113		Approved	ZEC, Zfp628	uc002qld.3	Q5EBL2	OTTHUMG00000150396	ENST00000598519.1:c.2712G>A	19.37:g.55995272G>A		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	67	67	1	NM_033113	Q86X34	Silent	SNP	ENST00000598519.1	37	CCDS33116.3																																																																																			G|0.723;A|0.277	0.277	strong		0.662	ZNF628-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317934.2	XM_058964	
REST	5978	hgsc.bcm.edu	37	4	57798174	57798174	+	Silent	SNP	C	C	G	rs3796528	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:57798174C>G	ENST00000309042.7	+	4	3464	c.3150C>G	c.(3148-3150)gcC>gcG	p.A1050A		NM_001193508.1|NM_005612.4	NP_001180437.1|NP_005603.3	Q13127	REST_HUMAN	RE1-silencing transcription factor	1050	Interaction with RCOR1.				cardiac muscle cell myoblast differentiation (GO:0060379)|cellular response to drug (GO:0035690)|cellular response to electrical stimulus (GO:0071257)|cellular response to glucocorticoid stimulus (GO:0071385)|hematopoietic progenitor cell differentiation (GO:0002244)|histone H4 deacetylation (GO:0070933)|negative regulation by host of viral transcription (GO:0043922)|negative regulation of aldosterone biosynthetic process (GO:0032348)|negative regulation of amniotic stem cell differentiation (GO:2000798)|negative regulation of calcium ion-dependent exocytosis (GO:0045955)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cortisol biosynthetic process (GO:2000065)|negative regulation of dense core granule biogenesis (GO:2000706)|negative regulation of gene expression (GO:0010629)|negative regulation of insulin secretion (GO:0046676)|negative regulation of mesenchymal stem cell differentiation (GO:2000740)|negative regulation of neurogenesis (GO:0050768)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of transcription, DNA-templated (GO:0045893)|potassium ion transmembrane transport (GO:0071805)|regulation of transcription, DNA-templated (GO:0006355)	cytosol (GO:0005829)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|core promoter binding (GO:0001047)|core promoter sequence-specific DNA binding (GO:0001046)|metal ion binding (GO:0046872)|outward rectifier potassium channel activity (GO:0015271)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.A1050A(1)		central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(2)|lung(22)|ovary(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	50	Glioma(25;0.08)|all_neural(26;0.181)					CAAAGGAAGCCTTGGCAGTCA	0.448													C|||	596	0.11901	0.1256	0.2522	5008	,	,		20562	0.2024		0.0328	False		,,,				2504	0.0184				p.A1050A		Atlas-SNP	.											REST,NS,carcinoma,0,1	REST	104	1	1	Substitution - coding silent(1)	stomach(1)	c.C3150G						PASS	.	C	,	531,3875	241.5+/-251.9	29,473,1701	78.0	74.0	75.0		3150,3150	-1.1	0.0	4	dbSNP_107	75	351,8249	117.6+/-177.1	9,333,3958	yes	coding-synonymous,coding-synonymous	REST	NM_001193508.1,NM_005612.4	,	38,806,5659	GG,GC,CC		4.0814,12.0517,6.7815	,	1050/1098,1050/1098	57798174	882,12124	2203	4300	6503	SO:0001819	synonymous_variant	5978	exon4			GGAAGCCTTGGCA	U13879	CCDS3509.1	4q12	2008-02-05			ENSG00000084093	ENSG00000084093			9966	protein-coding gene	gene with protein product		600571				7871435, 7697725	Standard	NM_005612		Approved	NRSF, XBR	uc003hci.3	Q13127	OTTHUMG00000128770	ENST00000309042.7:c.3150C>G	4.37:g.57798174C>G		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	135	67	0.496296	NM_001193508	A2RUE0|B9EGJ0|Q12956|Q12957|Q13134|Q59ER1|Q8IWI3	Silent	SNP	ENST00000309042.7	37	CCDS3509.1																																																																																			C|0.914;G|0.086	0.086	strong		0.448	REST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250691.2	NM_005612	
RRN3	54700	hgsc.bcm.edu	37	16	15178499	15178499	+	Splice_Site	SNP	G	G	A	rs76732059	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:15178499G>A	ENST00000198767.6	-	7	679	c.596C>T	c.(595-597)tCg>tTg	p.S199L	RRN3_ENST00000327307.7_Splice_Site_p.S166L|RRN3_ENST00000540462.1_Splice_Site_p.S50L|RRN3_ENST00000564131.1_Splice_Site_p.S199L|RRN3_ENST00000429751.2_Splice_Site_p.S169L|PDXDC1_ENST00000535621.2_Intron|RRN3_ENST00000563559.1_Splice_Site_p.S199L	NM_018427.3	NP_060897.3	Q9NYV6	RRN3_HUMAN	RRN3 RNA polymerase I transcription factor homolog (S. cerevisiae)	199					cell proliferation (GO:0008283)|cytoplasm organization (GO:0007028)|gene expression (GO:0010467)|homeostasis of number of cells (GO:0048872)|in utero embryonic development (GO:0001701)|negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator (GO:1902254)|nucleolus organization (GO:0007000)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of DNA-templated transcription, initiation (GO:2000142)|ribosome biogenesis (GO:0042254)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				NS(2)|central_nervous_system(3)|endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(2)|prostate(2)	20						GTATACTCACGATGGTACATA	0.294																																					p.S199L		Atlas-SNP	.											.	RRN3	36	.	0			c.C596T						PASS	.						65.0	55.0	59.0					16																	15178499		2197	4300	6497	SO:0001630	splice_region_variant	54700	exon7			ACTCACGATGGTA	AF227156	CCDS10559.1, CCDS73833.1	16p13.11	2009-10-26	2006-04-04		ENSG00000085721	ENSG00000085721			30346	protein-coding gene	gene with protein product		605121	"""RRN3 RNA polymerase I transcription factor homolog (yeast)"""			10758157, 11250903	Standard	XM_005255375		Approved	DKFZp566E104	uc002dde.3	Q9NYV6	OTTHUMG00000129847	ENST00000198767.6:c.596+1C>T	16.37:g.15178499G>A		Somatic	300	0	0		WXS	Illumina HiSeq	Phase_I	335	90	0.268657	NM_018427	A2RTY9|B4E0J7|B4E3T2|Q3MHU9|Q6IPL4|Q9H4F0	Missense_Mutation	SNP	ENST00000198767.6	37	CCDS10559.1	.	.	.	.	.	.	.	.	.	.	.	10.85	1.465668	0.26335	.	.	ENSG00000085721	ENST00000198767;ENST00000429751;ENST00000327307;ENST00000540462	T;T;T;T	0.42900	1.14;1.14;1.14;0.96	3.86	3.86	0.44501	.	0.193609	0.33980	U	0.004372	T	0.30324	0.0761	L	0.39514	1.22	0.58432	D	0.999998	B;B;B;P	0.35348	0.08;0.192;0.107;0.496	B;B;B;B	0.29176	0.017;0.041;0.05;0.099	T	0.09684	-1.0663	9	.	.	.	.	12.516	0.56032	0.0:0.0:1.0:0.0	.	169;100;199;199	F5H148;B4DZL9;Q3MHU9;Q9NYV6	.;.;.;RRN3_HUMAN	L	199;169;166;50	ENSP00000198767:S199L;ENSP00000402027:S169L;ENSP00000318484:S166L;ENSP00000437963:S50L	.	S	-	2	0	RRN3	15086000	1.000000	0.71417	1.000000	0.80357	0.614000	0.37383	4.366000	0.59492	1.700000	0.51204	0.313000	0.20887	TCG	G|0.960;A|0.040	0.040	strong		0.294	RRN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252087.2	NM_018427	Missense_Mutation
THSD7A	221981	hgsc.bcm.edu	37	7	11675855	11675855	+	Silent	SNP	C	C	T	rs61996273	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:11675855C>T	ENST00000423059.4	-	2	1175	c.924G>A	c.(922-924)agG>agA	p.R308R	THSD7A_ENST00000480061.1_5'Flank	NM_015204.2	NP_056019.1	Q9UPZ6	THS7A_HUMAN	thrombospondin, type I, domain containing 7A	308					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)		GTCTGTTCTGCCTGTTTCTGT	0.448										HNSCC(18;0.044)			T|||	795	0.158746	0.1891	0.0634	5008	,	,		19201	0.25		0.0696	False		,,,				2504	0.183				p.R308R		Atlas-SNP	.											.	THSD7A	219	.	0			c.G924A						PASS	.	T		614,3164		54,506,1329	148.0	145.0	146.0		924	-0.6	1.0	7	dbSNP_129	146	630,7594		21,588,3503	no	coding-synonymous	THSD7A	NM_015204.2		75,1094,4832	TT,TC,CC		7.6605,16.252,10.3649		308/1658	11675855	1244,10758	1889	4112	6001	SO:0001819	synonymous_variant	221981	exon2			GTTCTGCCTGTTT		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.924G>A	7.37:g.11675855C>T		Somatic	226	1	0.00442478		WXS	Illumina HiSeq	Phase_I	217	216	0.995392	NM_015204		Silent	SNP	ENST00000423059.4	37	CCDS47543.1																																																																																			C|0.880;T|0.120	0.120	strong		0.448	THSD7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325944.4	XM_928187.2	
CNPY3	10695	hgsc.bcm.edu	37	6	42906384	42906384	+	Missense_Mutation	SNP	G	G	T	rs9471969	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:42906384G>T	ENST00000372836.4	+	6	1063	c.692G>T	c.(691-693)aGc>aTc	p.S231I	RP3-475N16.1_ENST00000450671.1_RNA|CNPY3_ENST00000394142.3_3'UTR	NM_006586.3	NP_006577.2	Q9BT09	CNPY3_HUMAN	canopy FGF signaling regulator 3	231	Saposin B-type.		S -> I (in dbSNP:rs9471969).		innate immune response (GO:0045087)|toll-like receptor signaling pathway (GO:0002224)	endoplasmic reticulum lumen (GO:0005788)				central_nervous_system(1)|endometrium(1)|lung(3)|ovary(1)	6	Colorectal(47;0.196)		all cancers(41;0.000954)|Colorectal(64;0.00237)|COAD - Colon adenocarcinoma(64;0.00473)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|OV - Ovarian serous cystadenocarcinoma(102;0.0218)|Kidney(15;0.0388)			AAGAAGAGCAGCAGGGCCAAG	0.622													G|||	1071	0.213858	0.3328	0.2075	5008	,	,		19202	0.0149		0.2744	False		,,,				2504	0.2004				p.S231I		Atlas-SNP	.											.	CNPY3	25	.	0			c.G692T						PASS	.	G	ILE/SER	1419,2987	449.8+/-349.2	230,959,1014	79.0	80.0	80.0		692	5.0	0.6	6	dbSNP_119	80	2199,6399	362.9+/-332.9	263,1673,2363	yes	missense	CNPY3	NM_006586.3	142	493,2632,3377	TT,TG,GG		25.5757,32.2061,27.8222	benign	231/279	42906384	3618,9386	2203	4299	6502	SO:0001583	missense	10695	exon6			AGAGCAGCAGGGC	U80744	CCDS4875.1	6p21.1	2013-09-19	2013-07-23	2007-10-22	ENSG00000137161	ENSG00000137161		"""Trinucleotide (CAG) repeat containing"""	11968	protein-coding gene	gene with protein product		610774	"""trinucleotide repeat containing 5"", ""canopy 3 homolog (zebrafish)"""	TNRC5		9225980	Standard	NM_006586		Approved	CAG4A	uc003ota.4	Q9BT09	OTTHUMG00000014708	ENST00000372836.4:c.692G>T	6.37:g.42906384G>T	ENSP00000361926:p.Ser231Ile	Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	103	46	0.446602	NM_006586	O15412|Q0P6I2|Q8NF54|Q8WTU8|Q9P0F2	Missense_Mutation	SNP	ENST00000372836.4	37	CCDS4875.1	463	0.211996336996337	158	0.32113821138211385	81	0.22375690607734808	13	0.022727272727272728	211	0.2783641160949868	G	16.53	3.149626	0.57151	0.322061	0.255757	ENSG00000137161	ENST00000372836	T	0.24723	1.84	5.02	5.02	0.67125	.	0.433550	0.25747	N	0.028570	T	0.06690	0.0171	N	0.08118	0	0.09310	P	1.0	B	0.32693	0.38	B	0.28011	0.085	T	0.15607	-1.0431	9	0.39692	T	0.17	-13.8584	15.6126	0.76737	0.0:0.0:1.0:0.0	rs9471969;rs52835372;rs58234738;rs9471969	231	Q9BT09	CNPY3_HUMAN	I	231	ENSP00000361926:S231I	ENSP00000361926:S231I	S	+	2	0	CNPY3	43014362	1.000000	0.71417	0.631000	0.29282	0.974000	0.67602	4.641000	0.61375	2.504000	0.84457	0.462000	0.41574	AGC	G|0.754;T|0.246	0.246	strong		0.622	CNPY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040564.1	NM_006586	
WBSCR28	135886	hgsc.bcm.edu	37	7	73280020	73280020	+	Silent	SNP	C	C	T	rs1136647	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:73280020C>T	ENST00000320531.2	+	3	651	c.615C>T	c.(613-615)acC>acT	p.T205T		NM_182504.3	NP_872310.2	Q6UE05	WBS28_HUMAN	Williams-Beuren syndrome chromosome region 28	205						integral component of membrane (GO:0016021)				breast(2)|kidney(2)|lung(6)|skin(1)	11		Lung NSC(55;0.159)				ATCTCATCACCTGGACCACCT	0.617													C|||	2117	0.422724	0.2625	0.4928	5008	,	,		18551	0.4335		0.5726	False		,,,				2504	0.4243				p.T205T		Atlas-SNP	.											WBSCR28,NS,carcinoma,+1,1	WBSCR28	24	1	0			c.C615T						PASS	.	C		1402,2984	414.6+/-336.9	227,948,1018	151.0	160.0	157.0		615	0.0	1.0	7	dbSNP_86	157	4981,3577	610.4+/-395.7	1456,2069,754	no	coding-synonymous	WBSCR28	NM_182504.3		1683,3017,1772	TT,TC,CC		41.7971,31.9653,49.3124		205/266	73280020	6383,6561	2193	4279	6472	SO:0001819	synonymous_variant	135886	exon3			CATCACCTGGACC	BC030643	CCDS43597.1	7q11.23	2006-07-04			ENSG00000175877	ENSG00000175877			23018	protein-coding gene	gene with protein product		612547				8812460	Standard	NM_182504		Approved	MGC26719	uc003tzk.2	Q6UE05	OTTHUMG00000157243	ENST00000320531.2:c.615C>T	7.37:g.73280020C>T		Somatic	207	1	0.00483092		WXS	Illumina HiSeq	Phase_I	162	160	0.987654	NM_182504	Q6UE04|Q8NHP4	Silent	SNP	ENST00000320531.2	37	CCDS43597.1																																																																																			C|0.529;T|0.471	0.471	strong		0.617	WBSCR28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348130.1	NM_182504	
PDLIM7	9260	hgsc.bcm.edu	37	5	176917897	176917897	+	Silent	SNP	C	C	T	rs1132445	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:176917897C>T	ENST00000355841.2	-	7	612	c.546G>A	c.(544-546)ccG>ccA	p.P182P	PDLIM7_ENST00000393551.1_Silent_p.P182P|PDLIM7_ENST00000355572.2_Silent_p.P182P|PDLIM7_ENST00000356618.4_Silent_p.P182P|PDLIM7_ENST00000359895.2_Silent_p.P148P	NM_005451.3	NP_005442.2	Q9NR12	PDLI7_HUMAN	PDZ and LIM domain 7 (enigma)	182					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)			GCTCCTCATCCGGGTCTTGCA	0.602													C|||	118	0.0235623	0.0061	0.0375	5008	,	,		14772	0.001		0.0646	False		,,,				2504	0.0184				p.P182P		Atlas-SNP	.											.	PDLIM7	32	.	0			c.G546A						PASS	.	C	,,	69,4337	62.9+/-100.1	0,69,2134	59.0	59.0	59.0		546,444,546	1.5	1.0	5	dbSNP_131	59	656,7944	167.3+/-219.0	29,598,3673	no	coding-synonymous,coding-synonymous,coding-synonymous	PDLIM7	NM_005451.3,NM_203352.1,NM_213636.1	,,	29,667,5807	TT,TC,CC		7.6279,1.566,5.5744	,,	182/458,148/424,182/223	176917897	725,12281	2203	4300	6503	SO:0001819	synonymous_variant	9260	exon7			CTCATCCGGGTCT	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.546G>A	5.37:g.176917897C>T		Somatic	288	0	0		WXS	Illumina HiSeq	Phase_I	313	132	0.421725	NM_213636	Q14250|Q5XG82|Q6NVZ5|Q96C91|Q9BXB8|Q9BXB9	Silent	SNP	ENST00000355841.2	37	CCDS4422.1																																																																																			T|0.049;G|0.000;C|0.951	0.049	strong		0.602	PDLIM7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253423.1	NM_005451	
ZNF831	128611	hgsc.bcm.edu	37	20	57768399	57768399	+	Silent	SNP	T	T	C	rs442091	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:57768399T>C	ENST00000371030.2	+	1	2325	c.2325T>C	c.(2323-2325)gcT>gcC	p.A775A		NM_178457.1	NP_848552.1	Q5JPB2	ZN831_HUMAN	zinc finger protein 831	775							metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(15)|lung(71)|ovary(2)|pancreas(1)|prostate(4)|skin(16)|upper_aerodigestive_tract(2)|urinary_tract(3)	125	all_lung(29;0.0085)					ATGTAGAGGCTCCCAGGCCAG	0.652													.|||	1808	0.361022	0.5643	0.3141	5008	,	,		16119	0.372		0.2356	False		,,,				2504	0.2372				p.A775A		Atlas-SNP	.											ZNF831,NS,carcinoma,+2,1	ZNF831	287	1	0			c.T2325C						PASS	.	C		1847,1895		445,957,469	22.0	29.0	27.0		2325	-1.1	0.0	20	dbSNP_80	27	1835,6361		198,1439,2461	yes	coding-synonymous	ZNF831	NM_178457.1		643,2396,2930	CC,CT,TT		22.389,49.3586,30.8427		775/1678	57768399	3682,8256	1871	4098	5969	SO:0001819	synonymous_variant	128611	exon1			AGAGGCTCCCAGG	AL121919	CCDS42894.1	20q13.32	2008-10-20	2008-03-25	2008-03-25	ENSG00000124203	ENSG00000124203			16167	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 174"""	C20orf174			Standard	NM_178457		Approved	dJ492J12.1	uc002yan.3	Q5JPB2	OTTHUMG00000032864	ENST00000371030.2:c.2325T>C	20.37:g.57768399T>C		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	74	32	0.432432	NM_178457	Q5TDR4|Q8TCP0	Silent	SNP	ENST00000371030.2	37	CCDS42894.1																																																																																			T|0.666;C|0.334	0.334	strong		0.652	ZNF831-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000079916.2	NM_178457	
SELPLG	6404	hgsc.bcm.edu	37	12	109017673	109017673	+	Silent	SNP	C	C	T	rs63748999|rs558357966|rs372173288	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:109017673C>T	ENST00000550948.1	-	2	635	c.411G>A	c.(409-411)gtG>gtA	p.V137V	SELPLG_ENST00000228463.6_Silent_p.V153V|SELPLG_ENST00000388962.3_Intron			Q14242	SELPL_HUMAN	selectin P ligand	137	12 X 10 AA tandem repeats.		Missing (in short form; not an alternative splicing; dbSNP:rs63748999). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:7505206}.		blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cellular response to interleukin-6 (GO:0071354)|leukocyte adhesive activation (GO:0050902)|leukocyte migration (GO:0050900)|leukocyte tethering or rolling (GO:0050901)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(3)|prostate(3)|skin(1)	12						CCTCCGTGGGCACTGGTTGAG	0.617													c|||	441	0.0880591	0.0272	0.0504	5008	,	,		19600	0.2034		0.0795	False		,,,				2504	0.0869				p.V153V		Atlas-SNP	.											SELPLG_ENST00000550948,NS,carcinoma,-1,7	SELPLG	138	7	0			c.G459A						scavenged	.						159.0	124.0	136.0					12																	109017673		2199	4274	6473	SO:0001819	synonymous_variant	6404	exon2			CGTGGGCACTGGT		CCDS31895.1, CCDS31895.2, CCDS55881.1	12q24	2014-01-30						"""CD molecules"", ""Endogenous ligands"""	10722	protein-coding gene	gene with protein product		600738				7505206	Standard	NM_003006		Approved	PSGL-1, CD162	uc010sxe.2	Q14242		ENST00000550948.1:c.411G>A	12.37:g.109017673C>T		Somatic	117	4	0.034188		WXS	Illumina HiSeq	Phase_I	85	25	0.294118	NM_001206609	A8K2Y0|B4DQC3|B7Z5C7|J3KMX6|Q12775|Q6GTW7|Q8N7J7	Silent	SNP	ENST00000550948.1	37	CCDS31895.2																																																																																			.	.	none		0.617	SELPLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403904.1		
GREB1	9687	hgsc.bcm.edu	37	2	11727507	11727507	+	Intron	SNP	G	G	A	rs13394619	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:11727507G>A	ENST00000381486.2	+	10	1459				RN7SL674P_ENST00000463397.2_RNA|GREB1_ENST00000381483.2_Intron|GREB1_ENST00000263834.5_Splice_Site|GREB1_ENST00000234142.5_Intron	NM_014668.3	NP_055483.2	Q4ZG55	GREB1_HUMAN	growth regulation by estrogen in breast cancer 1							integral component of membrane (GO:0016021)		p.?(1)		breast(3)|central_nervous_system(2)|endometrium(2)|kidney(4)|large_intestine(9)|lung(9)|ovary(1)	30	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.115)|OV - Ovarian serous cystadenocarcinoma(76;0.186)		GCCCACTGCAGTATTTGTAAA	0.498													A|||	3101	0.619209	0.916	0.5893	5008	,	,		19435	0.4881		0.5278	False		,,,				2504	0.4683				.	Ovarian(39;850 945 2785 23371 33093)	Atlas-SNP	.											GREB1_ENST00000263834,NS,carcinoma,0,1	GREB1	308	1	1	Unknown(1)	stomach(1)	c.1160-1G>A						PASS	.	A	,,	3700,704	294.4+/-283.1	1552,596,54	137.0	136.0	136.0		,,	-0.7	0.0	2	dbSNP_121	136	4294,4306	578.4+/-390.7	1057,2180,1063	yes	intron,intron,splice-3	GREB1	NM_014668.3,NM_033090.2,NM_148903.2	,,	2609,2776,1117	AA,AG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	49.9302,15.9855,38.5266	,,	,,	11727507	7994,5010	2202	4300	6502	SO:0001627	intron_variant	9687	exon10			ACTGCAGTATTTG		CCDS33146.1, CCDS33147.1, CCDS42655.1	2p25.1	2010-02-17	2009-09-10		ENSG00000196208	ENSG00000196208			24885	protein-coding gene	gene with protein product	"""gene regulated by estrogen in breast cancer"""	611736				11103799	Standard	NM_014668		Approved	KIAA0575	uc002rbk.1	Q4ZG55	OTTHUMG00000141276	ENST00000381486.2:c.1160-1365G>A	2.37:g.11727507G>A		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	65	26	0.4	NM_148903	A6NHD0|A6NKN0|B5MDA9|O60321|Q7Z5S2|Q9H2Q6|Q9H2Q7|Q9H2Q8	Splice_Site	SNP	ENST00000381486.2	37	CCDS42655.1	1362	0.6236263736263736	454	0.9227642276422764	216	0.5966850828729282	303	0.5297202797202797	389	0.5131926121372031	A	1.031	-0.681773	0.03353	0.840145	0.499302	ENSG00000196208	ENST00000263834	.	.	.	2.02	-0.7	0.11273	.	.	.	.	.	.	.	.	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	6.295	0.21081	0.4356:0.0:0.5644:0.0	rs13394619;rs17529763;rs58035934;rs13394619	.	.	.	.	-1	.	.	.	+	.	.	GREB1	11644958	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.639000	0.05446	-0.592000	0.05851	-1.246000	0.01523	.	G|0.377;A|0.623	0.623	strong		0.498	GREB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280490.1	NM_014668	
RPAP1	26015	hgsc.bcm.edu	37	15	41813279	41813279	+	Silent	SNP	C	C	T	rs3743031	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:41813279C>T	ENST00000304330.4	-	22	3221	c.3105G>A	c.(3103-3105)agG>agA	p.R1035R	RPAP1_ENST00000561603.1_Intron	NM_015540.2	NP_056355.2	Q9BWH6	RPAP1_HUMAN	RNA polymerase II associated protein 1	1035	Leu-rich.					nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)			NS(1)|breast(1)|cervix(2)|endometrium(4)|kidney(4)|large_intestine(6)|lung(16)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	45		all_cancers(109;6.59e-20)|all_epithelial(112;7.67e-17)|Lung NSC(122;5.34e-11)|all_lung(180;4.17e-10)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.173)		OV - Ovarian serous cystadenocarcinoma(18;2.84e-17)|GBM - Glioblastoma multiforme(113;1.68e-06)|Colorectal(105;0.0163)|BRCA - Breast invasive adenocarcinoma(123;0.117)		ACCGAGGGACCCTGCTGCTTC	0.602													C|||	1495	0.298522	0.1256	0.3285	5008	,	,		17963	0.2758		0.4324	False		,,,				2504	0.3967				p.R1035R		Atlas-SNP	.											RPAP1,NS,carcinoma,0,1	RPAP1	111	1	0			c.G3105A						PASS	.	C		794,3612		79,636,1488	45.0	49.0	47.0		3105	3.9	0.0	15	dbSNP_107	47	3684,4914		816,2052,1431	no	coding-synonymous	RPAP1	NM_015540.2		895,2688,2919	TT,TC,CC		42.8472,18.0209,34.4356		1035/1394	41813279	4478,8526	2203	4299	6502	SO:0001819	synonymous_variant	26015	exon22			AGGGACCCTGCTG	BC000246	CCDS10079.1	15q14	2004-03-16			ENSG00000103932	ENSG00000103932			24567	protein-coding gene	gene with protein product		611475				10718198	Standard	XM_005254297		Approved	DKFZP727M111, KIAA1403, MGC858, FLJ12732	uc001zod.3	Q9BWH6	OTTHUMG00000130342	ENST00000304330.4:c.3105G>A	15.37:g.41813279C>T		Somatic	198	0	0		WXS	Illumina HiSeq	Phase_I	158	64	0.405063	NM_015540	Q9H9I2|Q9NSQ5|Q9P2E4|Q9UFS7	Silent	SNP	ENST00000304330.4	37	CCDS10079.1																																																																																			C|0.680;T|0.320	0.320	strong		0.602	RPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252694.2	NM_015540	
PCSK5	5125	hgsc.bcm.edu	37	9	78936358	78936358	+	Missense_Mutation	SNP	G	G	A	rs1110222	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:78936358G>A	ENST00000545128.1	+	30	4362	c.3824G>A	c.(3823-3825)gGc>gAc	p.G1275D		NM_001190482.1	NP_001177411.1	Q92824	PCSK5_HUMAN	proprotein convertase subtilisin/kexin type 5	1275	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						GCAGAAGACGGCATATGTGAA	0.527													G|||	1598	0.319089	0.4592	0.2378	5008	,	,		15572	0.1369		0.341	False		,,,				2504	0.3528				p.G1275D		Atlas-SNP	.											.	PCSK5	329	.	0			c.G3824A						PASS	.	G	ASP/GLY	775,977		182,411,283	174.0	138.0	149.0		3824	4.6	0.0	9	dbSNP_86	149	1314,2668		221,872,898	yes	missense	PCSK5	NM_001190482.1	94	403,1283,1181	AA,AG,GG		32.9985,44.2352,36.4318	benign	1275/1861	78936358	2089,3645	876	1991	2867	SO:0001583	missense	5125	exon30			AAGACGGCATATG		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.3824G>A	9.37:g.78936358G>A	ENSP00000446280:p.Gly1275Asp	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	40	24	0.6	NM_001190482	F5H2G7|Q13527|Q96EP4	Missense_Mutation	SNP	ENST00000545128.1	37	CCDS55320.1	670	0.3067765567765568	234	0.47560975609756095	99	0.27348066298342544	76	0.13286713286713286	261	0.34432717678100266	G	8.856	0.945778	0.18356	0.442352	0.329985	ENSG00000099139	ENST00000545128;ENST00000376754;ENST00000424854	T;T	0.32023	1.52;1.47	5.5	4.61	0.57282	.	0.338727	0.30732	N	0.008997	T	0.00012	0.0000	M	0.70595	2.14	0.80722	P	0.0	.	.	.	.	.	.	T	0.50250	-0.8850	7	0.21014	T	0.42	-7.5297	8.5591	0.33501	0.1743:0.0:0.8257:0.0	rs1110222;rs2803425;rs60377265;rs1110222	.	.	.	D	1275;1005;975	ENSP00000446280:G1275D;ENSP00000411654:G975D	ENSP00000365945:G1005D	G	+	2	0	PCSK5	78126178	0.005000	0.15991	0.002000	0.10522	0.004000	0.04260	0.922000	0.28734	1.334000	0.45468	0.561000	0.74099	GGC	G|0.679;A|0.321	0.321	strong		0.527	PCSK5-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
MYO9B	4650	hgsc.bcm.edu	37	19	17317955	17317955	+	Silent	SNP	A	A	G	rs8110964	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:17317955A>G	ENST00000594824.1	+	35	5673	c.5526A>G	c.(5524-5526)tcA>tcG	p.S1842S	MYO9B_ENST00000595618.1_Silent_p.S1842S|MYO9B_ENST00000397274.2_Silent_p.S1842S|CTD-3032J10.3_ENST00000601929.1_RNA			Q13459	MYO9B_HUMAN	myosin IXB	1842	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.|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						ACCGCATGTCACCTGGGGCGC	0.637													G|||	3162	0.63139	0.7073	0.6772	5008	,	,		14431	0.746		0.3926	False		,,,				2504	0.6237				p.S1842S		Atlas-SNP	.											MYO9B_ENST00000319396,NS,carcinoma,0,2	MYO9B	264	2	0			c.A5526G						PASS	.	G	,	2827,1549		936,955,297	33.0	38.0	37.0		5526,5526	-8.3	0.1	19	dbSNP_116	37	3377,5189		705,1967,1611	no	coding-synonymous,coding-synonymous	MYO9B	NM_001130065.1,NM_004145.3	,	1641,2922,1908	GG,GA,AA		39.4233,35.3976,47.9369	,	1842/2023,1842/2158	17317955	6204,6738	2188	4283	6471	SO:0001819	synonymous_variant	4650	exon35			CATGTCACCTGGG		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.5526A>G	19.37:g.17317955A>G		Somatic	221	0	0		WXS	Illumina HiSeq	Phase_I	188	102	0.542553	NM_001130065	O75314|Q9NUJ2|Q9UHN0	Silent	SNP	ENST00000594824.1	37																																																																																				A|0.384;G|0.616	0.616	strong		0.637	MYO9B-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000463236.1		
TMEM63B	55362	hgsc.bcm.edu	37	6	44119676	44119676	+	Silent	SNP	A	A	G	rs3734697	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:44119676A>G	ENST00000259746.9	+	19	1950	c.1767A>G	c.(1765-1767)ccA>ccG	p.P589P	TMEM63B_ENST00000323267.6_Silent_p.P589P			Q5T3F8	CSCL2_HUMAN	transmembrane protein 63B	589					ion transport (GO:0006811)	integral component of membrane (GO:0016021)	nucleotide binding (GO:0000166)	p.P589P(1)		breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(8)|ovary(1)|pancreas(2)|prostate(2)|stomach(4)	35	all_cancers(18;1.66e-06)|Lung NSC(15;0.00108)|all_lung(25;0.00278)|Hepatocellular(11;0.00309)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0215)			TGCGCATCCCAGGCCTGCTCA	0.667											OREG0017465	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	A|||	525	0.104832	0.0068	0.0965	5008	,	,		15711	0.2262		0.0994	False		,,,				2504	0.1237				p.P589P		Atlas-SNP	.											TMEM63B,NS,carcinoma,0,1	TMEM63B	77	1	1	Substitution - coding silent(1)	stomach(1)	c.A1767G						PASS	.	A		107,4299	84.8+/-123.5	2,103,2098	79.0	55.0	63.0		1767	-9.3	0.5	6	dbSNP_107	63	917,7683	200.6+/-244.3	52,813,3435	no	coding-synonymous	TMEM63B	NM_018426.1		54,916,5533	GG,GA,AA		10.6628,2.4285,7.8733		589/833	44119676	1024,11982	2203	4300	6503	SO:0001819	synonymous_variant	55362	exon19			CATCCCAGGCCTG	BC022095	CCDS34461.1	6p21.1	2008-02-05	2005-07-25	2005-07-25	ENSG00000137216	ENSG00000137216			17735	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 110"""	C6orf110			Standard	XM_005249211		Approved	DKFZp434P0531, dJ421H19.2	uc003owr.3	Q5T3F8	OTTHUMG00000014757	ENST00000259746.9:c.1767A>G	6.37:g.44119676A>G		Somatic	108	0	0	921	WXS	Illumina HiSeq	Phase_I	132	62	0.469697	NM_018426	B9EGU3|Q5T3F9|Q6AHX4|Q6P5A0|Q8N219|Q8NDE1|Q9NSG5	Silent	SNP	ENST00000259746.9	37	CCDS34461.1	255	0.11675824175824176	3	0.006097560975609756	38	0.10497237569060773	143	0.25	71	0.09366754617414248	A	11.02	1.514920	0.27123	0.024285	0.106628	ENSG00000137216	ENST00000371893	.	.	.	5.14	-9.26	0.00662	.	.	.	.	.	T	0.10165	0.0249	.	.	.	0.09310	P	0.9999999999999982	.	.	.	.	.	.	T	0.10451	-1.0629	3	.	.	.	.	8.3418	0.32247	0.1371:0.0914:0.5774:0.194	rs3734697	.	.	.	R	518	.	.	Q	+	2	0	TMEM63B	44227654	0.000000	0.05858	0.513000	0.27749	0.994000	0.84299	-3.661000	0.00400	-2.162000	0.00784	-0.385000	0.06624	CAG	A|0.910;G|0.090	0.090	strong		0.667	TMEM63B-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040712.2	XM_166410	
DDX52	11056	hgsc.bcm.edu	37	17	35984410	35984410	+	Missense_Mutation	SNP	T	T	C	rs7216445	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:35984410T>C	ENST00000349699.2	-	9	1250	c.1207A>G	c.(1207-1209)Atg>Gtg	p.M403V	DDX52_ENST00000394367.3_Missense_Mutation_p.M295V	NM_007010.3	NP_008941.2	Q9Y2R4	DDX52_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 52	403	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.		M -> V (in dbSNP:rs7216445). {ECO:0000269|PubMed:11124703, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.1}.			membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)			biliary_tract(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(5)|ovary(1)|skin(3)	17		Breast(25;0.00637)|Ovarian(249;0.15)				AGTTCTCTCATGGCCAGAAGT	0.368													T|||	2877	0.574481	0.4002	0.7205	5008	,	,		17075	0.5605		0.7604	False		,,,				2504	0.5297				p.M403V		Atlas-SNP	.											.	DDX52	40	.	0			c.A1207G						PASS	.	T	VAL/MET	2168,2238	582.8+/-385.7	548,1072,583	103.0	102.0	102.0		1207	4.7	1.0	17	dbSNP_116	102	6901,1699	738.1+/-407.0	2768,1365,167	yes	missense	DDX52	NM_007010.3	21	3316,2437,750	CC,CT,TT		19.7558,49.2056,30.2706	benign	403/600	35984410	9069,3937	2203	4300	6503	SO:0001583	missense	11056	exon9			CTCTCATGGCCAG	AF077033	CCDS11323.1	17q21.1	2014-05-06			ENSG00000141141	ENSG00000278053		"""DEAD-boxes"""	20038	protein-coding gene	gene with protein product		612500				11124703	Standard	XM_006721650		Approved	ROK1	uc002hoi.2	Q9Y2R4	OTTHUMG00000188475	ENST00000349699.2:c.1207A>G	17.37:g.35984410T>C	ENSP00000268854:p.Met403Val	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	55	24	0.436364	NM_007010	Q86YG1|Q8N213|Q9NVE0|Q9Y482	Missense_Mutation	SNP	ENST00000349699.2	37	CCDS11323.1	1368	0.6263736263736264	208	0.42276422764227645	265	0.7320441988950276	322	0.5629370629370629	573	0.7559366754617414	T	12.42	1.931580	0.34096	0.492056	0.802442	ENSG00000141141	ENST00000349699;ENST00000394367	T;T	0.04015	3.73;3.73	5.8	4.73	0.59995	Helicase, C-terminal (1);	0.084250	0.85682	D	0.000000	T	0.00012	0.0000	N	0.02296	-0.605	0.22001	P	0.999428028	B	0.11235	0.004	B	0.13407	0.009	T	0.04128	-1.0975	9	0.38643	T	0.18	-18.4889	11.0562	0.47920	0.0:0.0722:0.0:0.9278	rs7216445;rs17854150;rs52820328;rs59452890;rs7216445	403	Q9Y2R4	DDX52_HUMAN	V	403;295	ENSP00000268854:M403V;ENSP00000377893:M295V	ENSP00000268854:M403V	M	-	1	0	DDX52	33058523	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	3.268000	0.51585	1.027000	0.39758	-0.263000	0.10527	ATG	C|0.654;T|0.346	0.654	strong		0.368	DDX52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256795.1	NM_152300	
BTN3A2	11118	hgsc.bcm.edu	37	6	26373507	26373507	+	Missense_Mutation	SNP	G	G	A	rs13216828	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:26373507G>A	ENST00000356386.2	+	7	1108	c.920G>A	c.(919-921)aGc>aAc	p.S307N	BTN3A2_ENST00000396948.1_Missense_Mutation_p.S307N|BTN3A2_ENST00000396934.3_Missense_Mutation_p.S284N|BTN3A2_ENST00000527422.1_Missense_Mutation_p.S307N|BTN3A2_ENST00000508906.2_Missense_Mutation_p.S265N|BTN3A2_ENST00000377708.2_Missense_Mutation_p.S307N	NM_001197246.2|NM_001197247.1|NM_007047.3	NP_001184175.1|NP_001184176.1|NP_008978.2	P78410	BT3A2_HUMAN	butyrophilin, subfamily 3, member A2	307			S -> N (in dbSNP:rs13216828). {ECO:0000269|PubMed:14702039}.		interferon-gamma secretion (GO:0072643)|T cell mediated immunity (GO:0002456)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(5)	10						TTTCCAGAGAGCCTCCAGGAG	0.403													G|||	406	0.0810703	0.0287	0.0389	5008	,	,		10942	0.0992		0.1103	False		,,,				2504	0.1329				p.S307N		Atlas-SNP	.											.	BTN3A2	44	.	0			c.G920A						PASS	.	G	ASN/SER,ASN/SER,ASN/SER,ASN/SER,ASN/SER	166,4240	110.4+/-148.6	2,162,2039	120.0	112.0	115.0		920,920,851,794,920	-4.6	0.0	6	dbSNP_121	115	929,7671	204.7+/-247.3	50,829,3421	yes	missense,missense,missense,missense,missense	BTN3A2	NM_001197246.1,NM_001197247.1,NM_001197248.1,NM_001197249.1,NM_007047.3	46,46,46,46,46	52,991,5460	AA,AG,GG		10.8023,3.7676,8.4192	benign,benign,benign,benign,benign	307/335,307/335,284/312,265/293,307/335	26373507	1095,11911	2203	4300	6503	SO:0001583	missense	11118	exon5			CAGAGAGCCTCCA	U90546	CCDS4605.1, CCDS56399.1, CCDS56400.1	6p22.1	2014-01-14			ENSG00000186470	ENSG00000186470		"""Immunoglobulin superfamily / V-set domain containing"", ""Butyrophilins"""	1139	protein-coding gene	gene with protein product		613594				9149941	Standard	NM_007047		Approved	BTN3.2	uc010jqi.2	P78410	OTTHUMG00000014450	ENST00000356386.2:c.920G>A	6.37:g.26373507G>A	ENSP00000348751:p.Ser307Asn	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	56	55	0.982143	NM_001197246	B4DRT7|B4E103|F5H791|F8W6E0|O00477|O15338|O75658|Q76PA0|Q9BU81|Q9NR44	Missense_Mutation	SNP	ENST00000356386.2	37	CCDS4605.1	157	0.07188644688644688	22	0.044715447154471545	13	0.03591160220994475	40	0.06993006993006994	82	0.10817941952506596	g	11.08	1.534478	0.27475	0.037676	0.108023	ENSG00000186470	ENST00000535620;ENST00000527422;ENST00000356386;ENST00000396934;ENST00000377708;ENST00000396948;ENST00000508906	T;T;T;T;T;T	0.03413	4.09;4.09;3.94;4.09;4.09;4.5	2.55	-4.61	0.03380	.	.	.	.	.	T	0.00695	0.0023	N	0.22421	0.69	0.80722	P	0.0	B;B	0.22211	0.066;0.039	B;B	0.24006	0.05;0.01	T	0.48559	-0.9025	8	0.56958	D	0.05	.	0.4235	0.00460	0.3467:0.1904:0.2757:0.1872	rs13216828;rs52811297;rs13216828	284;307	F8W6E0;P78410	.;BT3A2_HUMAN	N	307;307;307;284;307;307;265	ENSP00000432138:S307N;ENSP00000348751:S307N;ENSP00000380140:S284N;ENSP00000366937:S307N;ENSP00000380152:S307N;ENSP00000442687:S265N	ENSP00000348751:S307N	S	+	2	0	BTN3A2	26481486	0.025000	0.19082	0.008000	0.14137	0.627000	0.37826	0.231000	0.17872	-1.164000	0.02790	-0.474000	0.04947	AGC	G|0.922;A|0.078	0.078	strong		0.403	BTN3A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040113.2		
ANKRD18B	441459	hgsc.bcm.edu	37	9	33566234	33566234	+	Silent	SNP	C	C	T	rs62559879	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:33566234C>T	ENST00000290943.6	+	13	2388	c.2292C>T	c.(2290-2292)gcC>gcT	p.A764A		NM_001244752.1	NP_001231681.1	A2A2Z9	AN18B_HUMAN	ankyrin repeat domain 18B	764										NS(1)|breast(1)|endometrium(2)|lung(1)|prostate(1)|stomach(1)	7						ATCTTATGGCCGAGAAGGAAG	0.328													.|||	799	0.159545	0.0121	0.196	5008	,	,		17645	0.2083		0.2455	False		,,,				2504	0.1943				p.A763A		Atlas-SNP	.											.	ANKRD18B	46	.	0			c.C2289T						PASS	.																																			SO:0001819	synonymous_variant	441459	exon13			TATGGCCGAGAAG			9p13.3	2013-01-10			ENSG00000230453	ENSG00000230453		"""Ankyrin repeat domain containing"""	23644	protein-coding gene	gene with protein product							Standard	NM_001244752		Approved	bA255A11.3	uc010mjw.2	A2A2Z9	OTTHUMG00000019776	ENST00000290943.6:c.2292C>T	9.37:g.33566234C>T		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	91	91	1	NM_001244752		Silent	SNP	ENST00000290943.6	37																																																																																				T|1.000;|0.000	1.000	weak		0.328	ANKRD18B-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000313729.2	XM_001718334	
CYYR1	116159	hgsc.bcm.edu	37	21	27852724	27852724	+	Silent	SNP	A	A	G	rs966410	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:27852724A>G	ENST00000299340.4	-	3	544	c.201T>C	c.(199-201)gtT>gtC	p.V67V	AP001597.1_ENST00000357401.3_RNA|CYYR1_ENST00000400043.3_Silent_p.V67V|AP001597.1_ENST00000414486.1_RNA|CYYR1_ENST00000435845.2_3'UTR	NM_052954.2	NP_443186.1	Q96J86	CYYR1_HUMAN	cysteine/tyrosine-rich 1	67						integral component of membrane (GO:0016021)				large_intestine(2)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|skin(2)	15						CTATTCCAAAAACAATGCCCG	0.443													A|||	2287	0.456669	0.6021	0.3444	5008	,	,		17962	0.3353		0.4483	False		,,,				2504	0.4734				p.V67V		Atlas-SNP	.											.	CYYR1	38	.	0			c.T201C						PASS	.	A		2463,1943	622.6+/-394.0	684,1095,424	121.0	110.0	114.0		201	0.2	1.0	21	dbSNP_86	114	3925,4675	548.1+/-385.3	882,2161,1257	no	coding-synonymous	CYYR1	NM_052954.2		1566,3256,1681	GG,GA,AA		45.6395,44.099,49.1158		67/155	27852724	6388,6618	2203	4300	6503	SO:0001819	synonymous_variant	116159	exon3			TCCAAAAACAATG	AY061853	CCDS13578.1	21q21.2	2014-07-04	2005-07-24		ENSG00000166265	ENSG00000166265			16274	protein-coding gene	gene with protein product			"""cysteine and tyrosine-rich 1"""	C21orf95		12036297, 12062809, 24981926	Standard	NM_052954		Approved		uc002ymd.3	Q96J86	OTTHUMG00000078689	ENST00000299340.4:c.201T>C	21.37:g.27852724A>G		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	64	41	0.640625	NM_052954	A0A059TD09|A8MTU9|B2R845|Q53ER3|Q5JPD0|Q96NV7|R9QAJ4|W8CQB3	Silent	SNP	ENST00000299340.4	37	CCDS13578.1																																																																																			A|0.549;G|0.451	0.451	strong		0.443	CYYR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171654.2	NM_052954	
SMARCA2	6595	hgsc.bcm.edu	37	9	2191309	2191309	+	Missense_Mutation	SNP	C	C	G	rs2296212	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:2191309C>G	ENST00000382203.1	+	33	4847	c.4638C>G	c.(4636-4638)gaC>gaG	p.D1546E	SMARCA2_ENST00000357248.2_Missense_Mutation_p.D1528E|SMARCA2_ENST00000382194.1_Missense_Mutation_p.D1528E|SMARCA2_ENST00000349721.2_Missense_Mutation_p.D1546E|SMARCA2_ENST00000324954.5_Missense_Mutation_p.D192E|SMARCA2_ENST00000382186.1_Missense_Mutation_p.D210E|SMARCA2_ENST00000382185.1_Missense_Mutation_p.D192E|SMARCA2_ENST00000302401.3_Missense_Mutation_p.D234E			P51531	SMCA2_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2	1546			D -> E (in dbSNP:rs2296212).		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)		AAAAAGATGACAAAGGCCGGG	0.413													G|||	1120	0.223642	0.3071	0.2061	5008	,	,		20895	0.2163		0.0984	False		,,,				2504	0.2597				p.D1546E		Atlas-SNP	.											.	SMARCA2	313	.	0			c.C4638G						PASS	.	G	GLU/ASP,GLU/ASP	1187,3219	710.9+/-407.9	149,889,1165	111.0	95.0	100.0	http://omim.org/entry/600014	4584,4638	3.8	1.0	9	dbSNP_100	100	962,7638	775.6+/-407.7	53,856,3391	yes	missense,missense	SMARCA2	NM_139045.2,NM_003070.3	45,45	202,1745,4556	GG,GC,CC		11.186,26.9405,16.5231	benign,benign	1528/1573,1546/1591	2191309	2149,10857	2203	4300	6503	SO:0001583	missense	6595	exon33			AGATGACAAAGGC	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.4638C>G	9.37:g.2191309C>G	ENSP00000371638:p.Asp1546Glu	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	143	88	0.615385	NM_003070	B1ALG3|B1ALG4|D3DRH4|D3DRH5	Missense_Mutation	SNP	ENST00000382203.1	37	CCDS34977.1	397	0.18177655677655677	143	0.29065040650406504	70	0.19337016574585636	115	0.20104895104895104	69	0.09102902374670185	G	5.237	0.229183	0.09916	0.269405	0.11186	ENSG00000080503	ENST00000349721;ENST00000357248;ENST00000382203;ENST00000382194;ENST00000302401;ENST00000324954;ENST00000382186;ENST00000417599;ENST00000382185;ENST00000382183;ENST00000382182	D;D;D;D;T;T;T;T;T;T	0.86956	-2.19;-2.13;-2.19;-2.13;3.19;3.34;3.12;3.35;3.34;3.34	5.71	3.76	0.43208	.	0.232312	0.35466	N	0.003181	T	0.00012	0.0000	N	0.03115	-0.41	0.49798	P	1.7100000000003224E-4	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.04090	-1.0978	9	0.02654	T	1	-24.9	12.6243	0.56620	0.0717:0.5959:0.3323:0.0	rs2296212;rs2296212	232;234;1528;1546	B4DNT1;B1ALF6;P51531-2;P51531	.;.;.;SMCA2_HUMAN	E	1546;1528;1546;1528;234;192;210;232;192;192;75	ENSP00000265773:D1546E;ENSP00000349788:D1528E;ENSP00000371638:D1546E;ENSP00000371629:D1528E;ENSP00000305411:D234E;ENSP00000324770:D192E;ENSP00000371621:D210E;ENSP00000387486:D232E;ENSP00000371620:D192E;ENSP00000371618:D192E	ENSP00000305411:D234E	D	+	3	2	SMARCA2	2181309	0.982000	0.34865	1.000000	0.80357	0.994000	0.84299	0.094000	0.15107	0.742000	0.32697	-0.127000	0.14921	GAC	C|0.831;G|0.169	0.169	strong		0.413	SMARCA2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000051505.1	NM_003070	
LRIG1	26018	hgsc.bcm.edu	37	3	66434643	66434643	+	Missense_Mutation	SNP	T	T	C	rs2306272	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:66434643T>C	ENST00000273261.3	-	14	2367	c.1843A>G	c.(1843-1845)Atg>Gtg	p.M615V	SLC25A26_ENST00000536651.1_Intron|LRIG1_ENST00000496559.2_5'UTR|LRIG1_ENST00000383703.3_Missense_Mutation_p.M639V	NM_015541.2	NP_056356.2	Q96JA1	LRIG1_HUMAN	leucine-rich repeats and immunoglobulin-like domains 1	615	Ig-like C2-type 2.		M -> V (in dbSNP:rs2306272). {ECO:0000269|PubMed:11414704, ECO:0000269|PubMed:17974005}.		innervation (GO:0060384)|otolith morphogenesis (GO:0032474)|sensory perception of sound (GO:0007605)	integral component of membrane (GO:0016021)				NS(2)|breast(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(12)|ovary(3)|prostate(1)|skin(4)|stomach(4)|urinary_tract(1)	42		Lung NSC(201;0.0101)		BRCA - Breast invasive adenocarcinoma(55;0.00047)		AGGCGGGCCATGGTGGTGGTC	0.577													T|||	1814	0.36222	0.1513	0.2435	5008	,	,		17527	0.7341		0.2922	False		,,,				2504	0.4202				p.M615V		Atlas-SNP	.											.	LRIG1	138	.	0			c.A1843G						PASS	.	T	VAL/MET	637,3769	274.6+/-272.0	45,547,1611	192.0	184.0	186.0		1843	5.0	1.0	3	dbSNP_100	186	2358,6242	394.7+/-344.8	337,1684,2279	yes	missense	LRIG1	NM_015541.2	21	382,2231,3890	CC,CT,TT		27.4186,14.4576,23.0278	benign	615/1094	66434643	2995,10011	2203	4300	6503	SO:0001583	missense	26018	exon14			GGGCCATGGTGGT	AB050468	CCDS33783.1	3p14	2013-01-14			ENSG00000144749	ENSG00000144749		"""Immunoglobulin superfamily / I-set domain containing"""	17360	protein-coding gene	gene with protein product	"""ortholog of mouse integral membrane glycoprotein LIG-1"", ""leucine-rich repeat protein LRIG1"""	608868				11414704, 12234026	Standard	NM_015541		Approved	LIG-1, DKFZP586O1624, LIG1	uc003dmx.3	Q96JA1	OTTHUMG00000158727	ENST00000273261.3:c.1843A>G	3.37:g.66434643T>C	ENSP00000273261:p.Met615Val	Somatic	256	1	0.00390625		WXS	Illumina HiSeq	Phase_I	234	94	0.401709	NM_015541	Q6IQ51|Q96CF9|Q9BYB8|Q9UFI4	Missense_Mutation	SNP	ENST00000273261.3	37	CCDS33783.1	830	0.38003663003663	82	0.16666666666666666	106	0.292817679558011	418	0.7307692307692307	224	0.2955145118733509	T	8.389	0.839336	0.16891	0.144576	0.274186	ENSG00000144749	ENST00000273261;ENST00000383703;ENST00000383702	T;T	0.65916	1.06;-0.18	6.17	5.0	0.66597	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.379169	0.31936	N	0.006822	T	0.00012	0.0000	N	0.05467	-0.045	0.34993	P	0.24476699999999996	B;B	0.13145	0.006;0.007	B;B	0.19666	0.015;0.026	T	0.37596	-0.9699	9	0.27082	T	0.32	.	12.8497	0.57850	0.1223:0.0:0.0:0.8776	rs2306272;rs52808080;rs59543444;rs2306272	639;615	Q96JA1-2;Q96JA1	.;LRIG1_HUMAN	V	615;639;518	ENSP00000273261:M615V;ENSP00000373208:M639V	ENSP00000273261:M615V	M	-	1	0	LRIG1	66517333	0.990000	0.36364	0.989000	0.46669	0.306000	0.27790	6.232000	0.72313	1.126000	0.42016	0.533000	0.62120	ATG	T|0.707;C|0.293	0.293	strong		0.577	LRIG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351930.1	NM_015541	
SVIL	6840	hgsc.bcm.edu	37	10	29747417	29747417	+	Silent	SNP	C	C	T	rs1887465	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:29747417C>T	ENST00000355867.4	-	37	7256	c.6504G>A	c.(6502-6504)ccG>ccA	p.P2168P	SVIL_ENST00000375400.3_Silent_p.P1742P|PTCHD3P1_ENST00000446807.1_RNA|SVIL_ENST00000535393.1_Silent_p.P1082P|PTCHD3P1_ENST00000423223.1_RNA|SVIL_ENST00000375398.2_Silent_p.P2168P|PTCHD3P1_ENST00000455774.1_RNA|PTCHD3P1_ENST00000445521.1_RNA|PTCHD3P1_ENST00000413405.1_RNA|PTCHD3P1_ENST00000414457.1_RNA|PTCHD3P1_ENST00000430295.1_RNA|PTCHD3P1_ENST00000438202.1_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	79	0	0		WXS	Illumina HiSeq	Phase_I	66	34	0.515152	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		
MTTP	4547	hgsc.bcm.edu	37	4	100504664	100504664	+	Missense_Mutation	SNP	T	T	C	rs3816873	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:100504664T>C	ENST00000265517.5	+	3	586	c.383T>C	c.(382-384)aTc>aCc	p.I128T	MTTP_ENST00000511045.1_Missense_Mutation_p.I155T|MTTP_ENST00000422897.2_Missense_Mutation_p.I128T|MTTP_ENST00000457717.1_Missense_Mutation_p.I128T			P55157	MTP_HUMAN	microsomal triglyceride transfer protein	128	Vitellogenin. {ECO:0000255|PROSITE- ProRule:PRU00557}.		I -> T (in dbSNP:rs3816873). {ECO:0000269|PubMed:11792722, ECO:0000269|PubMed:14732481}.		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)	p.I128T(1)		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)	CTTCATCTAATCCATGGAAAG	0.383													T|||	1251	0.2498	0.261	0.1787	5008	,	,		16406	0.1359		0.2604	False		,,,				2504	0.3916				p.I128T		Atlas-SNP	.											MTTP,NS,carcinoma,0,1	MTTP	127	1	1	Substitution - Missense(1)	prostate(1)	c.T383C	GRCh37	CM062884	MTTP	M	rs3816873	scavenged	.	T	THR/ILE	1197,3205	397.4+/-330.4	162,873,1166	77.0	83.0	81.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	383	4.1	0.8	4	dbSNP_107	81	2218,6382	370.2+/-335.8	298,1622,2380	yes	missense	MTTP	NM_000253.2	89	460,2495,3546	CC,CT,TT		25.7907,27.1922,26.2652	benign	128/895	100504664	3415,9587	2201	4300	6501	SO:0001583	missense	4547	exon4			ATCTAATCCATGG		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.383T>C	4.37:g.100504664T>C	ENSP00000265517:p.Ile128Thr	Somatic	311	3	0.0096463		WXS	Illumina HiSeq	Phase_I	259	123	0.474903	NM_000253	A8K428|Q08AM4|Q6P5T3	Missense_Mutation	SNP	ENST00000265517.5	37	CCDS3651.1	471	0.21565934065934067	134	0.27235772357723576	73	0.20165745856353592	76	0.13286713286713286	188	0.24802110817941952	T	4.371	0.068340	0.08436	0.271922	0.257907	ENSG00000138823	ENST00000506883;ENST00000511045;ENST00000457717;ENST00000265517;ENST00000422897;ENST00000538053	T;T;T;T;T	0.38560	1.13;1.13;1.13;1.13;1.13	5.48	4.1	0.47936	Lipid transport protein, beta-sheet shell (1);Lipid transport protein, N-terminal (3);Vitellinogen, beta-sheet N-terminal (1);	0.871593	0.10491	N	0.668429	T	0.00012	0.0000	N	0.20685	0.6	0.80722	P	0.0	B;B;B	0.13145	0.002;0.0;0.007	B;B;B	0.12837	0.003;0.001;0.008	T	0.22417	-1.0217	8	.	.	.	-27.8047	10.3303	0.43818	0.0:0.0885:0.0:0.9115	rs3816873;rs17532657;rs58329270;rs3816873	155;128;128	E9PBP6;P55157;Q6P5T3	.;MTP_HUMAN;.	T	138;155;128;128;128;128	ENSP00000426755:I138T;ENSP00000427679:I155T;ENSP00000400821:I128T;ENSP00000265517:I128T;ENSP00000407350:I128T	.	I	+	2	0	MTTP	100723687	0.001000	0.12720	0.810000	0.32431	0.979000	0.70002	0.992000	0.29667	2.081000	0.62600	0.533000	0.62120	ATC	T|0.748;C|0.252	0.252	strong		0.383	MTTP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253662.3		
CDH1	999	hgsc.bcm.edu	37	16	68862165	68862165	+	Silent	SNP	C	C	T	rs33964119	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:68862165C>T	ENST00000261769.5	+	14	2444	c.2253C>T	c.(2251-2253)aaC>aaT	p.N751N	CDH1_ENST00000562836.1_3'UTR|CDH1_ENST00000422392.2_Silent_p.N690N	NM_004360.3	NP_004351.1	P12830	CADH1_HUMAN	cadherin 1, type 1, E-cadherin (epithelial)	751		Cleavage; by caspase-3.			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.N751N(1)		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)		CCCGGGACAACGTTTATTACT	0.507			"""Mis, N, F, S"""		"""lobular breast, gastric"""	gastric			Hereditary Diffuse Gastric Cancer				C|||	273	0.0545128	0.0582	0.0692	5008	,	,		19674	0.0694		0.0348	False		,,,				2504	0.044				p.N751N		Atlas-SNP	.	yes	Rec	yes	Familial gastric carcinoma	16	16q22.1	999	"""cadherin 1, type 1, E-cadherin (epithelial) (ECAD)"""		E	CDH1,colon,carcinoma,0,3	CDH1	535	3	1	Substitution - coding silent(1)	stomach(1)	c.C2253T						PASS	.	C		215,4181	132.1+/-168.6	5,205,1988	98.0	94.0	95.0		2253	-12.1	0.0	16	dbSNP_126	95	273,8327	104.4+/-165.4	2,269,4029	no	coding-synonymous	CDH1	NM_004360.3		7,474,6017	TT,TC,CC		3.1744,4.8908,3.755		751/883	68862165	488,12508	2198	4300	6498	SO:0001819	synonymous_variant	999	exon14	Familial Cancer Database	HDGC	GGACAACGTTTAT	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.2253C>T	16.37:g.68862165C>T		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	84	34	0.404762	NM_004360	A8K1U7|Q13799|Q14216|Q15855|Q16194|Q4PJ14|Q9UII8	Silent	SNP	ENST00000261769.5	37	CCDS10869.1																																																																																			A|0.000;C|0.956;G|0.000;T|0.043	0.043	strong		0.507	CDH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268897.2	NM_004360	
MTAP	4507	hgsc.bcm.edu	37	9	21816758	21816758	+	Missense_Mutation	SNP	G	G	A	rs7023954	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:21816758G>A	ENST00000460874.2	+	3	442	c.217G>A	c.(217-219)Gtc>Atc	p.V73I	MTAP_ENST00000580900.1_Missense_Mutation_p.V56I|RP11-145E5.5_ENST00000404796.2_Missense_Mutation_p.V56I|MTAP_ENST00000427788.2_3'UTR|MTAP_ENST00000380172.4_Missense_Mutation_p.V56I					methylthioadenosine phosphorylase									p.0(1)|p.0?(1)		central_nervous_system(1)|endometrium(2)|kidney(3)|lung(3)|pancreas(1)	10		all_cancers(5;0)|Hepatocellular(5;0.00162)|Colorectal(97;0.173)		GBM - Glioblastoma multiforme(3;0)|Lung(24;2.24e-57)|LUSC - Lung squamous cell carcinoma(38;1.97e-36)|STAD - Stomach adenocarcinoma(4;3.26e-05)|OV - Ovarian serous cystadenocarcinoma(39;0.00931)|COAD - Colon adenocarcinoma(8;0.15)		TGTTGATTGCGTCCTCCTTGC	0.313													G|||	1944	0.388179	0.4334	0.4438	5008	,	,		18888	0.4375		0.3946	False		,,,				2504	0.2301				p.V56I		Atlas-SNP	.											.	MTAP	23	.	2	Whole gene deletion(2)	lung(2)	c.G166A						PASS	.	G	ILE/VAL	1916,2490	547.2+/-377.2	407,1102,694	233.0	228.0	230.0		166	5.4	1.0	9	dbSNP_116	230	3569,5031	518.1+/-379.2	735,2099,1466	yes	missense	MTAP	NM_002451.3	29	1142,3201,2160	AA,AG,GG		41.5,43.4862,42.1728	benign	56/284	21816758	5485,7521	2203	4300	6503	SO:0001583	missense	4507	exon3			GATTGCGTCCTCC	AB062485	CCDS6509.1	9p21	2013-05-29			ENSG00000099810	ENSG00000099810	2.4.2.28		7413	protein-coding gene	gene with protein product	"""S-methyl-5'-thioadenosine phosphorylase"""	156540				11126361	Standard	NM_002451		Approved	MSAP, c86fus	uc003zph.3	Q13126	OTTHUMG00000019690	ENST00000460874.2:c.217G>A	9.37:g.21816758G>A	ENSP00000461932:p.Val73Ile	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	72	33	0.458333	NM_002451		Missense_Mutation	SNP	ENST00000460874.2	37		897	0.4107142857142857	218	0.44308943089430897	149	0.4116022099447514	230	0.4020979020979021	300	0.39577836411609496	G	17.50	3.405531	0.62288	0.434862	0.415	ENSG00000099810	ENST00000380172	D	0.90004	-2.6	5.44	5.44	0.79542	Nucleoside phosphorylase domain (1);	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	M	0.77616	2.38	0.09310	P	0.999999999893112	B;B;B	0.27450	0.179;0.052;0.006	B;B;B	0.34418	0.182;0.072;0.027	T	0.01956	-1.1240	9	0.49607	T	0.09	-17.3118	18.3922	0.90487	0.0:0.0:1.0:0.0	rs7023954;rs11555745;rs17755881;rs17852350;rs52809882;rs56427578;rs56666707;rs7023954	73;56;56	B4DUC8;F2Z2F3;Q13126	.;.;MTAP_HUMAN	I	56	ENSP00000369519:V56I	ENSP00000369519:V56I	V	+	1	0	MTAP	21806758	1.000000	0.71417	1.000000	0.80357	0.926000	0.56050	6.620000	0.74224	2.711000	0.92665	0.561000	0.74099	GTC	G|0.589;A|0.411	0.411	strong		0.313	MTAP-003	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000051929.2	NM_002451	
CDHR3	222256	hgsc.bcm.edu	37	7	105621512	105621512	+	Silent	SNP	G	G	T	rs193795	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:105621512G>T	ENST00000317716.9	+	3	428	c.348G>T	c.(346-348)ctG>ctT	p.L116L	CDHR3_ENST00000478080.1_Silent_p.L28L|CDHR3_ENST00000542731.1_Silent_p.L116L|CDHR3_ENST00000470188.1_3'UTR|CDHR3_ENST00000541203.1_Silent_p.L116L|CDHR3_ENST00000343407.5_5'UTR	NM_152750.4	NP_689963.2	Q6ZTQ4	CDHR3_HUMAN	cadherin-related family member 3	116	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(1)|cervix(3)|endometrium(1)|kidney(1)|large_intestine(1)|lung(15)|ovary(1)	23						TCACAGACCTGCAAGTCCTGA	0.473													G|||	2294	0.458067	0.2776	0.562	5008	,	,		20439	0.4901		0.4433	False		,,,				2504	0.6104				p.L116L		Atlas-SNP	.											.	CDHR3	153	.	0			c.G348T						PASS	.	G		1185,2801		188,809,996	91.0	84.0	86.0		348	-4.3	0.6	7	dbSNP_79	86	3659,4679		826,2007,1336	no	coding-synonymous	CDHR3	NM_152750.4		1014,2816,2332	TT,TG,GG		43.8834,29.7291,39.3054		116/886	105621512	4844,7480	1993	4169	6162	SO:0001819	synonymous_variant	222256	exon3			AGACCTGCAAGTC	AK126338	CCDS47684.1, CCDS75651.1	7q22.2	2011-07-01			ENSG00000128536	ENSG00000128536		"""Cadherins / Cadherin-related"""	26308	protein-coding gene	gene with protein product		615610					Standard	NM_152750		Approved	FLJ44366, FLJ23834, CDH28	uc003vdl.4	Q6ZTQ4	OTTHUMG00000157520	ENST00000317716.9:c.348G>T	7.37:g.105621512G>T		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	121	120	0.991736	NM_152750	Q8TCI7	Silent	SNP	ENST00000317716.9	37	CCDS47684.1																																																																																			G|0.578;T|0.422	0.422	strong		0.473	CDHR3-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000349025.2	NM_152750	
OR3A2	4995	hgsc.bcm.edu	37	17	3181384	3181384	+	Silent	SNP	C	C	T	rs769434	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	106	0	0		WXS	Illumina HiSeq	Phase_I	101	41	0.405941	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		
HAUS8	93323	hgsc.bcm.edu	37	19	17170885	17170885	+	Missense_Mutation	SNP	C	C	T	rs1130222	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:17170885C>T	ENST00000253669.5	-	5	437	c.247G>A	c.(247-249)Gga>Aga	p.G83R	HAUS8_ENST00000593360.1_Missense_Mutation_p.G22R|HAUS8_ENST00000448593.2_Missense_Mutation_p.G82R			Q9BT25	HAUS8_HUMAN	HAUS augmin-like complex, subunit 8	83			G -> R (in dbSNP:rs1130222). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:18362163}.		centrosome organization (GO:0051297)|mitotic nuclear division (GO:0007067)|spindle assembly (GO:0051225)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|HAUS complex (GO:0070652)|microtubule (GO:0005874)				endometrium(1)|kidney(2)|large_intestine(4)|lung(4)|ovary(1)	12						TCACCCTTTCCGACCCCACTG	0.502													C|||	2360	0.471246	0.4539	0.5187	5008	,	,		16301	0.4058		0.3996	False		,,,				2504	0.6022				p.G83R		Atlas-SNP	.											.	HAUS8	31	.	0			c.G247A						PASS	.	C	ARG/GLY,ARG/GLY	1960,2446	552.7+/-378.6	415,1130,658	101.0	87.0	92.0		244,247	1.1	0.0	19	dbSNP_86	92	3661,4939	525.0+/-380.7	798,2065,1437	yes	missense,missense	HAUS8	NM_001011699.1,NM_033417.1	125,125	1213,3195,2095	TT,TC,CC		42.5698,44.4848,43.2185	possibly-damaging,possibly-damaging	82/410,83/411	17170885	5621,7385	2203	4300	6503	SO:0001583	missense	93323	exon5			CCTTTCCGACCCC	BC004398	CCDS32948.1, CCDS46009.1	19p13.11	2013-10-11	2009-04-20	2009-04-20	ENSG00000131351	ENSG00000131351		"""HAUS augmin-like complex subunits"""	30532	protein-coding gene	gene with protein product		613434	"""HEC1/NDC80 interacting, centrosome associated 1"""	HICE1		19427217	Standard	XM_005260154		Approved	MGC20533, NY-SAR-48	uc002nfe.3	Q9BT25		ENST00000253669.5:c.247G>A	19.37:g.17170885C>T	ENSP00000253669:p.Gly83Arg	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	30	14	0.466667	NM_033417	B4DJA7|C9JBZ4|Q49AC4|Q86WF0|Q96FX3	Missense_Mutation	SNP	ENST00000253669.5	37	CCDS32948.1	934	0.42765567765567764	229	0.4654471544715447	174	0.48066298342541436	239	0.4178321678321678	292	0.38522427440633245	C	14.40	2.524794	0.44969	0.444848	0.425698	ENSG00000131351	ENST00000253669;ENST00000448593	T;T	0.41400	1.0;1.0	4.43	1.07	0.20283	.	0.712150	0.13389	N	0.391533	T	0.00012	0.0000	L	0.55481	1.735	0.80722	P	0.0	B;B;B	0.21905	0.062;0.025;0.025	B;B;B	0.10450	0.005;0.005;0.005	T	0.41770	-0.9490	9	0.56958	D	0.05	-10.6702	5.9279	0.19122	0.0:0.6594:0.0:0.3406	rs1130222;rs3177737;rs3188898;rs11550295;rs12459084;rs17412666;rs17845018;rs17857785;rs52803931;rs57637244;rs12459084	22;82;83	Q9BT25-2;C9JBZ4;Q9BT25	.;.;HAUS8_HUMAN	R	83;82	ENSP00000253669:G83R;ENSP00000395298:G82R	ENSP00000253669:G83R	G	-	1	0	HAUS8	17031885	0.003000	0.15002	0.001000	0.08648	0.166000	0.22503	1.777000	0.38604	0.427000	0.26145	0.561000	0.74099	GGA	T|0.368;G|0.076;C|0.484;A|0.072	0.368	strong		0.502	HAUS8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000463015.1	NM_001011699	
RIF1	55183	hgsc.bcm.edu	37	2	152311612	152311612	+	Missense_Mutation	SNP	A	A	G	rs61750444	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:152311612A>G	ENST00000243326.5	+	21	3031	c.2548A>G	c.(2548-2550)Atg>Gtg	p.M850V	RIF1_ENST00000430328.2_Missense_Mutation_p.M850V|RIF1_ENST00000453091.2_Missense_Mutation_p.M850V|RIF1_ENST00000444746.2_Missense_Mutation_p.M850V|RIF1_ENST00000428287.2_Missense_Mutation_p.M850V			Q9Y581	INSL6_HUMAN	replication timing regulatory factor 1	0					fertilization (GO:0009566)|male gonad development (GO:0008584)|negative regulation of apoptotic process (GO:0043066)|sperm motility (GO:0030317)|spermatid development (GO:0007286)	extracellular region (GO:0005576)	hormone activity (GO:0005179)			NS(2)|breast(8)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(19)|liver(1)|lung(34)|ovary(6)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	97				BRCA - Breast invasive adenocarcinoma(221;0.0429)		TTTGCCTTCTATGATCCGAAA	0.353													A|||	85	0.0169728	0.0371	0.0072	5008	,	,		17680	0.0		0.0268	False		,,,				2504	0.0041				p.M850V		Atlas-SNP	.											RIF1,NS,carcinoma,-2,1	RIF1	244	1	0			c.A2548G						scavenged	.	A	VAL/MET,VAL/MET,VAL/MET,VAL/MET	156,4250	106.0+/-144.5	5,146,2052	109.0	108.0	108.0		2548,2548,2548,2548	-1.1	1.0	2	dbSNP_129	108	167,8433	78.4+/-141.0	2,163,4135	yes	missense,missense,missense,missense	RIF1	NM_001177663.1,NM_001177664.1,NM_001177665.1,NM_018151.4	21,21,21,21	7,309,6187	GG,GA,AA		1.9419,3.5406,2.4835	benign,benign,benign,benign	850/2447,850/2447,850/2447,850/2473	152311612	323,12683	2203	4300	6503	SO:0001583	missense	55183	exon22			CCTTCTATGATCC	AK022932	CCDS2194.1, CCDS54406.1	2q23.3	2014-06-02	2014-06-02		ENSG00000080345	ENSG00000080345			23207	protein-coding gene	gene with protein product		608952	"""RAP1 interacting factor homolog (yeast)"""			15342490, 15042697, 22850674	Standard	NM_018151		Approved	FLJ12870, FLJ10599	uc002txm.3	Q5UIP0	OTTHUMG00000131886	ENST00000243326.5:c.2548A>G	2.37:g.152311612A>G	ENSP00000243326:p.Met850Val	Somatic	179	1	0.00558659		WXS	Illumina HiSeq	Phase_I	143	76	0.531469	NM_018151	A0AVS0|Q9NS16	Missense_Mutation	SNP	ENST00000243326.5	37	CCDS2194.1	48|48	0.02197802197802198|0.02197802197802198	22|22	0.044715447154471545|0.044715447154471545	2|2	0.0055248618784530384|0.0055248618784530384	0|0	0.0|0.0	24|24	0.0316622691292876|0.0316622691292876	A|A	1.477|1.477	-0.558248|-0.558248	0.03967|0.03967	0.035406|0.035406	0.019419|0.019419	ENSG00000080345|ENSG00000080345	ENST00000444746;ENST00000453091;ENST00000428287;ENST00000243326;ENST00000430328|ENST00000414861	T;T;T;T;T|.	0.63744|.	-0.06;-0.06;-0.06;-0.06;-0.06|.	5.55|5.55	-1.09|-1.09	0.09904|0.09904	.|.	0.463720|.	0.26324|.	N|.	0.025028|.	T|T	0.19644|0.19644	0.0472|0.0472	L|L	0.38838|0.38838	1.175|1.175	0.80722|0.80722	D|D	1|1	B;B|.	0.06786|.	0.001;0.001|.	B;B|.	0.04013|.	0.001;0.001|.	T|T	0.16012|0.16012	-1.0417|-1.0417	10|5	0.11794|.	T|.	0.64|.	-3.1534|-3.1534	11.2086|11.2086	0.48784|0.48784	0.4305:0.0:0.5695:0.0|0.4305:0.0:0.5695:0.0	rs61750444|rs61750444	850;850|.	Q5UIP0;Q5UIP0-2|.	RIF1_HUMAN;.|.	V|C	850|841	ENSP00000390181:M850V;ENSP00000414615:M850V;ENSP00000415691:M850V;ENSP00000243326:M850V;ENSP00000416123:M850V|.	ENSP00000243326:M850V|.	M|Y	+|+	1|2	0|0	RIF1|RIF1	152019858|152019858	0.939000|0.939000	0.31865|0.31865	0.997000|0.997000	0.53966|0.53966	0.982000|0.982000	0.71751|0.71751	0.435000|0.435000	0.21510|0.21510	-0.136000|-0.136000	0.11475|0.11475	0.533000|0.533000	0.62120|0.62120	ATG|TAT	A|0.976;G|0.024	0.024	strong		0.353	RIF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254836.3		
ARHGEF12	23365	hgsc.bcm.edu	37	11	120317168	120317168	+	Missense_Mutation	SNP	A	A	G	rs201670344		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:120317168A>G	ENST00000397843.2	+	17	1568	c.1402A>G	c.(1402-1404)Atg>Gtg	p.M468V	ARHGEF12_ENST00000532993.1_Missense_Mutation_p.M365V|ARHGEF12_ENST00000356641.3_Missense_Mutation_p.M449V	NM_015313.2	NP_056128.1	Q9NZN5	ARHGC_HUMAN	Rho guanine nucleotide exchange factor (GEF) 12	468	RGSL.				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)		TATCCAAACTATGCAAGAAAG	0.343			T	MLL	AML																																p.M468V		Atlas-SNP	.		Dom	yes		11	11q23.3	23365	RHO guanine nucleotide exchange factor (GEF) 12 (LARG)		L	.	ARHGEF12	133	.	0			c.A1402G						PASS	.	A	VAL/MET,VAL/MET	0,3754		0,0,1877	95.0	90.0	91.0		1402,1345	6.2	1.0	11		91	2,8250		0,2,4124	no	missense,missense	ARHGEF12	NM_015313.2,NM_001198665.1	21,21	0,2,6001	GG,GA,AA		0.0242,0.0,0.0167	benign,benign	468/1545,449/1526	120317168	2,12004	1877	4126	6003	SO:0001583	missense	23365	exon17			CAAACTATGCAAG	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.1402A>G	11.37:g.120317168A>G	ENSP00000380942:p.Met468Val	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	59	12	0.20339	NM_015313	O15086|Q6P526	Missense_Mutation	SNP	ENST00000397843.2	37	CCDS41727.1	.	.	.	.	.	.	.	.	.	.	A	11.62	1.692691	0.30052	0.0	2.42E-4	ENSG00000196914	ENST00000397843;ENST00000356641;ENST00000532993	D;D;D	0.81579	-1.51;-1.51;-1.51	6.17	6.17	0.99709	Regulator of G protein signalling superfamily (1);Regulator of G protein signalling-like fold (1);	0.000000	0.64402	D	0.000011	T	0.69860	0.3158	N	0.13043	0.29	0.45837	D	0.998706	B;B;B	0.23442	0.005;0.069;0.085	B;B;B	0.33960	0.012;0.108;0.173	T	0.65084	-0.6254	10	0.09843	T	0.71	-14.5224	16.8222	0.85835	1.0:0.0:0.0:0.0	.	365;449;468	B4DGW2;Q9NZN5-2;Q9NZN5	.;.;ARHGC_HUMAN	V	468;449;365	ENSP00000380942:M468V;ENSP00000349056:M449V;ENSP00000432984:M365V	ENSP00000349056:M449V	M	+	1	0	ARHGEF12	119822378	1.000000	0.71417	0.999000	0.59377	0.993000	0.82548	3.005000	0.49521	2.371000	0.80710	0.533000	0.62120	ATG	A|1.000;C|0.000	.	strong		0.343	ARHGEF12-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388052.1	NM_015313	
FUK	197258	hgsc.bcm.edu	37	16	70515355	70515355	+	IGR	SNP	C	C	T	rs11054	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:70515355C>T	ENST00000288078.6	+	0	4081				COG4_ENST00000323786.5_Silent_p.S714S	NM_145059.2	NP_659496.2	Q8N0W3	FUK_HUMAN	fucokinase							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)				AGGCAATGAGCGACCTCAGCT	0.592													T|||	1872	0.373802	0.5083	0.3847	5008	,	,		18714	0.2222		0.4692	False		,,,				2504	0.2423				p.S714S		Atlas-SNP	.											.	COG4	64	.	0			c.G2142A						PASS	.	T	,	2275,2121	575.9+/-384.1	574,1127,497	91.0	83.0	86.0		2079,2142	-2.1	1.0	16	dbSNP_52	86	4016,4584	597.2+/-393.7	944,2128,1228	no	coding-synonymous,coding-synonymous	COG4	NM_001195139.1,NM_015386.2	,	1518,3255,1725	TT,TC,CC		46.6977,48.2484,48.4072	,	693/769,714/790	70515355	6291,6705	2198	4300	6498	SO:0001628	intergenic_variant	25839	exon18			AATGAGCGACCTC		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		16.37:g.70515355C>T		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	51	29	0.568627	NM_015386	Q5PSM3|Q5XKL6|Q6ZRA0|Q96MT9	Silent	SNP	ENST00000288078.6	37	CCDS10891.2																																																																																			C|0.538;A|0.002	.	strong		0.592	FUK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157291.2	NM_145059	
PSPH	5723	hgsc.bcm.edu	37	7	56088825	56088825	+	Missense_Mutation	SNP	T	T	A	rs74445297	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:56088825T>A	ENST00000395471.3	-	4	886	c.81A>T	c.(79-81)agA>agT	p.R27S	PSPH_ENST00000275605.3_Missense_Mutation_p.R27S|PSPH_ENST00000459834.1_Intron			P78330	SERB_HUMAN	phosphoserine phosphatase	27					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)			TTCCTTCTTCTCTGATGACCG	0.448																																					p.R27S		Atlas-SNP	.											.	PSPH	23	.	0			c.A81T						PASS	.						133.0	99.0	110.0					7																	56088825		2203	4300	6503	SO:0001583	missense	5723	exon4			TTCTTCTCTGATG	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.81A>T	7.37:g.56088825T>A	ENSP00000378854:p.Arg27Ser	Somatic	195	0	0		WXS	Illumina HiSeq	Phase_I	197	29	0.147208	NM_004577	B2RCR5|Q7Z3S5	Missense_Mutation	SNP	ENST00000395471.3	37	CCDS5522.1	702	0.32142857142857145	240	0.4878048780487805	94	0.2596685082872928	224	0.3916083916083916	144	0.18997361477572558	T	8.101	0.776745	0.16120	.	.	ENSG00000146733	ENST00000275605;ENST00000395471;ENST00000421626;ENST00000419984;ENST00000421312	D;D;D;D;D	0.83992	-1.58;-1.58;-1.58;-1.79;-1.79	5.6	0.722	0.18225	Haloacid dehalogenase-like hydrolase (1);HAD-like domain (2);	0.155391	0.64402	D	0.000020	T	0.00012	0.0000	L	0.48362	1.52	0.58432	D	0.999996	B;B	0.06786	0.001;0.001	B;B	0.14023	0.006;0.01	T	0.43327	-0.9398	10	0.27082	T	0.32	-15.084	8.7161	0.34411	0.0:0.4041:0.0:0.5959	.	27;27	Q53EY1;P78330	.;SERB_HUMAN	S	27	ENSP00000275605:R27S;ENSP00000378854:R27S;ENSP00000398653:R27S;ENSP00000399660:R27S;ENSP00000390952:R27S	ENSP00000275605:R27S	R	-	3	2	PSPH	56056319	0.997000	0.39634	0.998000	0.56505	0.198000	0.23893	0.542000	0.23222	0.108000	0.17862	0.482000	0.46254	AGA	T|0.752;A|0.248	0.248	strong		0.448	PSPH-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343304.1	NM_004577	
MRPL28	10573	hgsc.bcm.edu	37	16	419092	419092	+	Silent	SNP	A	A	G	rs3830160	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:419092A>G	ENST00000199706.8	-	3	452	c.417T>C	c.(415-417)taT>taC	p.Y139Y	MRPL28_ENST00000389675.2_Silent_p.Y139Y|MRPL28_ENST00000429738.1_Intron	NM_006428.4	NP_006419.2	Q13084	RM28_HUMAN	mitochondrial ribosomal protein L28	139					translation (GO:0006412)	cytoplasm (GO:0005737)|mitochondrial ribosome (GO:0005761)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			breast(1)|kidney(1)|lung(1)|ovary(1)|prostate(1)	5		Hepatocellular(16;0.000105)|Lung NSC(18;0.0324)|all_lung(18;0.064)				AGTCGAGCCCATAAGCCTCAT	0.577													G|||	3412	0.68131	0.8858	0.6383	5008	,	,		19336	0.5317		0.5487	False		,,,				2504	0.726				p.Y139Y		Atlas-SNP	.											.	MRPL28	15	.	0			c.T417C						PASS	.	G		3712,694	291.3+/-281.4	1568,576,59	155.0	115.0	128.0		417	-3.3	0.8	16	dbSNP_107	128	4982,3618	522.6+/-380.1	1468,2046,786	no	coding-synonymous	MRPL28	NM_006428.4		3036,2622,845	GG,GA,AA		42.0698,15.7512,33.1539		139/257	419092	8694,4312	2203	4300	6503	SO:0001819	synonymous_variant	10573	exon3			GAGCCCATAAGCC	U19796	CCDS32349.1	16p13.12	2012-09-26	2002-11-13		ENSG00000086504	ENSG00000086504		"""Mitochondrial ribosomal proteins / large subunits"""	14484	protein-coding gene	gene with protein product		604853	"""melanoma-associated antigen recognised by cytotoxic T lymphocytes"""	MAAT1		11551941, 19753307	Standard	NM_006428		Approved	p15	uc002cgs.2	Q13084	OTTHUMG00000047994	ENST00000199706.8:c.417T>C	16.37:g.419092A>G		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	100	99	0.99	NM_006428	B2RCM4|D3DU46|Q4TT39|Q96S26|Q9BQD8|Q9BR04	Silent	SNP	ENST00000199706.8	37	CCDS32349.1																																																																																			A|0.346;G|0.654	0.654	strong		0.577	MRPL28-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139285.2		
SH3TC1	54436	hgsc.bcm.edu	37	4	8238151	8238151	+	Silent	SNP	C	C	T	rs11603	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:8238151C>T	ENST00000245105.3	+	16	3619	c.3552C>T	c.(3550-3552)acC>acT	p.T1184T	SH3TC1_ENST00000539824.1_Silent_p.T1108T	NM_018986.3	NP_061859	Q8TE82	S3TC1_HUMAN	SH3 domain and tetratricopeptide repeats 1	1184										NS(1)|breast(3)|endometrium(4)|kidney(4)|large_intestine(6)|lung(10)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	33						TCAGCATCACCCTGGGTAAGC	0.647													C|||	1407	0.28095	0.2073	0.3026	5008	,	,		17382	0.2431		0.4095	False		,,,				2504	0.272				p.T1184T	NSCLC(145;2298 2623 35616 37297)	Atlas-SNP	.											.	SH3TC1	105	.	0			c.C3552T						PASS	.	C		843,3261		90,663,1299	30.0	26.0	28.0		3552	2.9	1.0	4	dbSNP_52	28	2674,5232		458,1758,1737	no	coding-synonymous	SH3TC1	NM_018986.3		548,2421,3036	TT,TC,CC		33.8224,20.5409,29.2839		1184/1337	8238151	3517,8493	2052	3953	6005	SO:0001819	synonymous_variant	54436	exon16			CATCACCCTGGGT	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.3552C>T	4.37:g.8238151C>T		Somatic	306	0	0		WXS	Illumina HiSeq	Phase_I	265	129	0.486792	NM_018986	Q4W5G5	Silent	SNP	ENST00000245105.3	37	CCDS3399.1																																																																																			C|0.684;T|0.316	0.316	strong		0.647	SH3TC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206991.2	NM_018986	
EXOC3	11336	hgsc.bcm.edu	37	5	453567	453567	+	Silent	SNP	G	G	A	rs2672722	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:453567G>A	ENST00000512944.1	+	4	636	c.447G>A	c.(445-447)gaG>gaA	p.E149E	EXOC3_ENST00000315013.5_Silent_p.E149E	NM_007277.4	NP_009208.2	O60645	EXOC3_HUMAN	exocyst complex component 3	160					cellular protein metabolic process (GO:0044267)|exocytosis (GO:0006887)|membrane organization (GO:0061024)|protein transport (GO:0015031)	exocyst (GO:0000145)|secretory granule membrane (GO:0030667)				breast(2)|cervix(1)|endometrium(4)|large_intestine(1)|lung(13)|ovary(1)|urinary_tract(1)	23		Ovarian(839;0.0563)	Epithelial(17;0.000529)|OV - Ovarian serous cystadenocarcinoma(19;0.00153)|all cancers(22;0.00186)|Lung(60;0.0863)			TGGACCTGGAGTGCTCCCGGG	0.597													G|||	2900	0.579073	0.8048	0.4928	5008	,	,		20497	0.5337		0.4533	False		,,,				2504	0.5112				p.E149E		Atlas-SNP	.											.	EXOC3	54	.	0			c.G447A						PASS	.	G		3118,992		1201,716,138	32.0	34.0	33.0		447	4.5	1.0	5	dbSNP_100	33	4088,4282		1012,2064,1109	no	coding-synonymous	EXOC3	NM_007277.4		2213,2780,1247	AA,AG,GG		48.8411,24.1363,42.2596		149/746	453567	7206,5274	2055	4185	6240	SO:0001819	synonymous_variant	11336	exon4			CCTGGAGTGCTCC	BC034427	CCDS54830.1	5p15.33	2013-01-22	2005-11-01	2005-11-01	ENSG00000180104	ENSG00000180104			30378	protein-coding gene	gene with protein product		608186	"""SEC6-like 1 (S. cerevisiae)"""	SEC6L1		8619474	Standard	XM_005248238		Approved	Sec6p	uc003jba.3	O60645	OTTHUMG00000162205	ENST00000512944.1:c.447G>A	5.37:g.453567G>A		Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	139	138	0.992806	NM_007277	Q6P2E8|Q8TEN6|Q8WUW0|Q96DI4	Silent	SNP	ENST00000512944.1	37	CCDS54830.1																																																																																			G|0.438;A|0.562	0.562	strong		0.597	EXOC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367882.1	NM_007277	
RADIL	55698	hgsc.bcm.edu	37	7	4839882	4839882	+	Missense_Mutation	SNP	T	T	C	rs3816854	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:4839882T>C	ENST00000399583.3	-	13	3089	c.2902A>G	c.(2902-2904)Acc>Gcc	p.T968A	RADIL_ENST00000538469.1_Missense_Mutation_p.T728A|RADIL_ENST00000536091.1_3'UTR	NM_018059.4	NP_060529.4	Q96JH8	RADIL_HUMAN	Ras association and DIL domains	968					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)		AAGTCCTCGGTGCTGGAGCTG	0.687													T|||	560	0.111821	0.1452	0.0317	5008	,	,		16208	0.0506		0.0666	False		,,,				2504	0.2331				p.T968A		Atlas-SNP	.											.	RADIL	110	.	0			c.A2902G						PASS	.	T	ALA/THR	471,3497		13,445,1526	15.0	19.0	18.0		2902	0.5	0.4	7	dbSNP_107	18	486,7838		16,454,3692	yes	missense	RADIL	NM_018059.4	58	29,899,5218	CC,CT,TT		5.8385,11.87,7.7856	benign	968/1076	4839882	957,11335	1984	4162	6146	SO:0001583	missense	55698	exon13			CCTCGGTGCTGGA	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.2902A>G	7.37:g.4839882T>C	ENSP00000382492:p.Thr968Ala	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	110	87	0.790909	NM_018059	A4D1Z5|A5YM49|B7ZL20|Q0VFZ9|Q75LH3|Q9BSP5|Q9H0M6|Q9NW43|Q9NWC4	Missense_Mutation	SNP	ENST00000399583.3	37	CCDS43544.1	165	0.07554945054945054	72	0.14634146341463414	14	0.03867403314917127	31	0.05419580419580419	48	0.0633245382585752	T	4.931	0.173060	0.09391	0.1187	0.058385	ENSG00000157927	ENST00000399583;ENST00000316919;ENST00000538469	T;T	0.37584	1.19;1.19	4.7	0.484	0.16825	PDZ/DHR/GLGF (1);	0.458963	0.23045	N	0.052563	T	0.00144	0.0004	M	0.66939	2.045	0.09310	P	0.9999999999816251	B;B	0.23185	0.001;0.081	B;B	0.15052	0.003;0.012	T	0.20773	-1.0265	9	0.10377	T	0.69	-2.2677	5.0034	0.14275	0.0:0.1824:0.1959:0.6218	rs3816854;rs58037322	968;276	Q96JH8;Q75LH2	RADIL_HUMAN;.	A	968;939;728	ENSP00000382492:T968A;ENSP00000442966:T728A	ENSP00000320946:T939A	T	-	1	0	RADIL	4806408	0.974000	0.33945	0.417000	0.26559	0.197000	0.23852	-0.037000	0.12164	-0.101000	0.12219	0.459000	0.35465	ACC	T|0.926;C|0.074	0.074	strong		0.687	RADIL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323769.2	NM_018059	
SERPINA11	256394	hgsc.bcm.edu	37	14	94912799	94912799	+	Silent	SNP	G	G	A	rs12888805	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:94912799G>A	ENST00000334708.3	-	3	850	c.786C>T	c.(784-786)acC>acT	p.T262T	RP11-349I1.2_ENST00000536735.1_RNA	NM_001080451.1	NP_001073920.1	Q86U17	SPA11_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 11	262					negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	extracellular space (GO:0005615)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(14)|skin(1)|upper_aerodigestive_tract(1)	24				COAD - Colon adenocarcinoma(157;0.211)		TCTGGAGGACGGTGCAAGCCA	0.532													G|||	1301	0.259784	0.0605	0.2695	5008	,	,		20967	0.1815		0.4513	False		,,,				2504	0.4059				p.T262T		Atlas-SNP	.											SERPINA11,right_lower_lobe,carcinoma,-1,1	SERPINA11	53	1	0			c.C786T						PASS	.	G		587,3819	258.6+/-262.5	46,495,1662	138.0	122.0	127.0		786	-10.8	0.1	14	dbSNP_121	127	3525,5075	515.2+/-378.5	701,2123,1476	no	coding-synonymous	SERPINA11	NM_001080451.1		747,2618,3138	AA,AG,GG		40.9884,13.3227,31.6162		262/423	94912799	4112,8894	2203	4300	6503	SO:0001819	synonymous_variant	256394	exon3			GAGGACGGTGCAA	BX248259	CCDS32149.1	14q32.13	2014-02-18	2005-08-18		ENSG00000186910	ENSG00000186910		"""Serine (or cysteine) peptidase inhibitors"""	19193	protein-coding gene	gene with protein product			"""serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 11"""			15014966, 24172014	Standard	NM_001080451		Approved		uc001ydd.1	Q86U17	OTTHUMG00000171348	ENST00000334708.3:c.786C>T	14.37:g.94912799G>A		Somatic	193	0	0		WXS	Illumina HiSeq	Phase_I	179	75	0.418994	NM_001080451	B2RV07	Silent	SNP	ENST00000334708.3	37	CCDS32149.1																																																																																			G|0.707;A|0.293	0.293	strong		0.532	SERPINA11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413091.1	NM_001080451	
TG	7038	hgsc.bcm.edu	37	8	133980076	133980076	+	Silent	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:133980076G>A	ENST00000220616.4	+	31	5764	c.5724G>A	c.(5722-5724)gaG>gaA	p.E1908E	TG_ENST00000542445.1_Silent_p.E278E|TG_ENST00000519543.1_Silent_p.E62E|TG_ENST00000377869.1_Silent_p.E1851E	NM_003235.4	NP_003226.4	P01266	THYG_HUMAN	thyroglobulin	1908					hormone biosynthetic process (GO:0042446)|iodide transport (GO:0015705)|regulation of myelination (GO:0031641)|signal transduction (GO:0007165)|thyroid gland development (GO:0030878)|thyroid hormone generation (GO:0006590)	extracellular region (GO:0005576)|extracellular space (GO:0005615)		p.E1908E(1)		NS(1)|breast(11)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(34)|liver(2)|lung(59)|ovary(9)|pancreas(2)|prostate(6)|skin(7)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(8)	168	Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)	Myeloproliferative disorder(644;0.00878)|Acute lymphoblastic leukemia(644;0.0559)|Breast(495;0.0735)	BRCA - Breast invasive adenocarcinoma(115;0.000701)	KIRC - Kidney renal clear cell carcinoma(542;0.0546)		AGCTCGCAGAGATAACAGAGA	0.498																																					p.E1908E		Atlas-SNP	.											TG,colon,carcinoma,0,1	TG	416	1	1	Substitution - coding silent(1)	large_intestine(1)	c.G5724A						PASS	.						83.0	66.0	72.0					8																	133980076		2203	4300	6503	SO:0001819	synonymous_variant	7038	exon31			CGCAGAGATAACA	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.5724G>A	8.37:g.133980076G>A		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	78	43	0.551282	NM_003235	O15274|O43899|Q15593|Q15948|Q9NYR1|Q9NYR2|Q9UMZ0|Q9UNY3	Silent	SNP	ENST00000220616.4	37	CCDS34944.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	0.014|0.014	-1.571920|-1.571920	0.00895|0.00895	.|.	.|.	ENSG00000042832|ENSG00000042832	ENST00000519178|ENST00000518058	.|.	.|.	.|.	5.87|5.87	0.802|0.802	0.18686|0.18686	.|.	.|.	.|.	.|.	.|.	T|T	0.24470|0.24470	0.0593|0.0593	.|.	.|.	.|.	0.09310|0.09310	N|N	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.24657|0.24657	-1.0154|-1.0154	4|4	.|.	.|.	.|.	.|.	4.5777|4.5777	0.12241|0.12241	0.1434:0.2262:0.5202:0.1102|0.1434:0.2262:0.5202:0.1102	.|.	.|.	.|.	.|.	N|K	364|40	.|.	.|.	D|R	+|+	1|2	0|0	TG|TG	134049258|134049258	0.111000|0.111000	0.22076|0.22076	0.038000|0.038000	0.18304|0.18304	0.021000|0.021000	0.10359|0.10359	0.030000|0.030000	0.13688|0.13688	-0.039000|-0.039000	0.13602|0.13602	-0.797000|-0.797000	0.03246|0.03246	GAT|AGA	.	.	none		0.498	TG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379606.1	NM_003235	
HJURP	55355	hgsc.bcm.edu	37	2	234761225	234761225	+	Missense_Mutation	SNP	C	C	T	rs2286430	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:234761225C>T	ENST00000411486.2	-	3	291	c.226G>A	c.(226-228)Gaa>Aaa	p.E76K	HJURP_ENST00000441687.1_Missense_Mutation_p.E76K|HJURP_ENST00000432087.1_Missense_Mutation_p.E76K	NM_018410.3	NP_060880.3	Q8NCD3	HJURP_HUMAN	Holliday junction recognition protein	76			E -> K (in dbSNP:rs2286430). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17823411, ECO:0000269|Ref.2}.		cell cycle (GO:0007049)|CENP-A containing nucleosome assembly (GO:0034080)|chromosome segregation (GO:0007059)|nucleosome assembly (GO:0006334)|regulation of DNA binding (GO:0051101)|regulation of protein complex assembly (GO:0043254)	chromosome, centromeric region (GO:0000775)|condensed chromosome kinetochore (GO:0000777)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone binding (GO:0042393)|identical protein binding (GO:0042802)			NS(2)|breast(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(3)|lung(11)|ovary(2)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	38		Breast(86;0.00204)|all_lung(227;0.00433)|Renal(207;0.00685)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0719)|Lung SC(224;0.128)		Epithelial(121;2.01e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000186)|Lung(119;0.00521)|LUSC - Lung squamous cell carcinoma(224;0.00829)		ATCTCTCCTTCGTTTCTTTCC	0.383													C|||	1733	0.346046	0.1029	0.5086	5008	,	,		19534	0.3938		0.5159	False		,,,				2504	0.3354				p.E76K		Atlas-SNP	.											.	HJURP	72	.	0			c.G226A						PASS	.	C	LYS/GLU	717,3689	295.3+/-283.6	64,589,1550	158.0	128.0	138.0		226	-5.3	0.0	2	dbSNP_100	138	4395,4205	580.7+/-391.1	1123,2149,1028	yes	missense	HJURP	NM_018410.3	56	1187,2738,2578	TT,TC,CC		48.8953,16.2733,39.3049	benign	76/749	234761225	5112,7894	2203	4300	6503	SO:0001583	missense	55355	exon3			CTCCTTCGTTTCT		CCDS33406.1, CCDS63166.1, CCDS63167.1	2q37.1	2007-12-06			ENSG00000123485	ENSG00000123485			25444	protein-coding gene	gene with protein product		612667				17823411	Standard	NM_001282962		Approved	DKFZp762E1312, URLC9, hFLEG1, FAKTS	uc002vvg.3	Q8NCD3	OTTHUMG00000059125	ENST00000411486.2:c.226G>A	2.37:g.234761225C>T	ENSP00000414109:p.Glu76Lys	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	67	67	1	NM_018410	A8IRH5|B4DWR0|B4DZV4|Q9BUT2|Q9NSL8	Missense_Mutation	SNP	ENST00000411486.2	37	CCDS33406.1	871|871	0.39880952380952384|0.39880952380952384	52|52	0.10569105691056911|0.10569105691056911	177|177	0.4889502762430939|0.4889502762430939	235|235	0.41083916083916083|0.41083916083916083	407|407	0.5369393139841688|0.5369393139841688	C|C	1.323|1.323	-0.598848|-0.598848	0.03744|0.03744	0.162733|0.162733	0.511047|0.511047	ENSG00000123485|ENSG00000123485	ENST00000411486;ENST00000432087;ENST00000441687;ENST00000414924|ENST00000454020	T;T;T;T|T	0.48201|0.36157	0.82;0.82;0.82;0.82|1.27	3.55|3.55	-5.31|-5.31	0.02730|0.02730	Centromere protein Scm3, N-terminal (1);|.	1.405580|.	0.04824|.	N|.	0.437524|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.08118|0.08118	0|0	0.80722|0.80722	P|P	0.0|0.0	B;B;B|.	0.17268|.	0.017;0.006;0.021|.	B;B;B|.	0.12156|.	0.003;0.002;0.007|.	T|T	0.45629|0.45629	-0.9248|-0.9248	9|6	0.05620|0.87932	T|D	0.96|0	-0.0036|-0.0036	5.8643|5.8643	0.18767|0.18767	0.0:0.4239:0.3121:0.264|0.0:0.4239:0.3121:0.264	rs2286430;rs11546250;rs61495737;rs2286430|rs2286430;rs11546250;rs61495737;rs2286430	76;76;76|.	Q8NCD3-3;Q8NCD3-2;Q8NCD3|.	.;.;HJURP_HUMAN|.	K|Q	76|67	ENSP00000414109:E76K;ENSP00000407208:E76K;ENSP00000401944:E76K;ENSP00000393253:E76K|ENSP00000414051:R67Q	ENSP00000414109:E76K|ENSP00000414051:R67Q	E|R	-|-	1|2	0|0	HJURP|HJURP	234425964|234425964	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.461000|0.461000	0.32589|0.32589	-3.158000|-3.158000	0.00579|0.00579	-1.191000|-1.191000	0.02695|0.02695	-0.302000|-0.302000	0.09304|0.09304	GAA|CGA	C|0.621;T|0.379	0.379	strong		0.383	HJURP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000130996.6	NM_018410	
LMF1	64788	hgsc.bcm.edu	37	16	1004554	1004554	+	Silent	SNP	C	C	T	rs3751667	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:1004554C>T	ENST00000262301.11	-	2	324	c.306G>A	c.(304-306)acG>acA	p.T102T	LMF1_ENST00000568897.1_5'UTR|LMF1_ENST00000539379.1_Silent_p.T95T|LMF1_ENST00000399843.2_Silent_p.T102T|LMF1_ENST00000543238.1_Intron	NM_022773.2	NP_073610.2	Q96S06	LMF1_HUMAN	lipase maturation factor 1	102					chylomicron remnant clearance (GO:0034382)|ER to Golgi vesicle-mediated transport (GO:0006888)|positive regulation of lipoprotein lipase activity (GO:0051006)|protein glycosylation in Golgi (GO:0033578)|protein maturation (GO:0051604)|protein secretion (GO:0009306)|regulation of cholesterol metabolic process (GO:0090181)|regulation of triglyceride metabolic process (GO:0090207)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|prostate(1)|stomach(2)|urinary_tract(1)	18		Hepatocellular(780;0.00308)				CTTCCCAGCTCGTCCTGTCCT	0.557													C|||	1807	0.360823	0.4274	0.2608	5008	,	,		20519	0.4127		0.2078	False		,,,				2504	0.4458				p.T102T		Atlas-SNP	.											LMF1,NS,carcinoma,-1,3	LMF1	42	3	0			c.G306A						PASS	.	C		1550,2552		292,966,793	51.0	53.0	53.0		306	-11.1	0.0	16	dbSNP_107	53	1918,6470		220,1478,2496	no	coding-synonymous	LMF1	NM_022773.2		512,2444,3289	TT,TC,CC		22.866,37.7864,27.7662		102/568	1004554	3468,9022	2051	4194	6245	SO:0001819	synonymous_variant	64788	exon2			CCAGCTCGTCCTG	AK022743	CCDS45373.1	16p13.3	2008-02-05	2007-11-29	2007-11-29	ENSG00000103227	ENSG00000103227			14154	protein-coding gene	gene with protein product		611761	"""chromosome 16 open reading frame 26"", ""transmembrane protein 112"""	C16orf26, TMEM112		11157797, 17994020	Standard	NM_022773		Approved	FLJ12681, JFP11, FLJ22302, TMEM112A	uc021tae.1	Q96S06	OTTHUMG00000047848	ENST00000262301.11:c.306G>A	16.37:g.1004554C>T		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	85	17	0.2	NM_022773	Q68CJ3|Q96FJ4|Q9H6G4|Q9H9K7	Silent	SNP	ENST00000262301.11	37	CCDS45373.1																																																																																			C|0.674;T|0.326	0.326	strong		0.557	LMF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000109071.3	NM_022773	
CHGB	1114	hgsc.bcm.edu	37	20	5904040	5904040	+	Missense_Mutation	SNP	G	G	A	rs742711	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:5904040G>A	ENST00000378961.4	+	4	1454	c.1250G>A	c.(1249-1251)cGc>cAc	p.R417H		NM_001819.2	NP_001810.2	P05060	SCG1_HUMAN	chromogranin B (secretogranin 1)	417			R -> H (in dbSNP:rs742711). {ECO:0000269|PubMed:14702039, ECO:0000269|Ref.4}.			extracellular region (GO:0005576)|secretory granule (GO:0030141)	hormone activity (GO:0005179)	p.R417H(1)		breast(7)|kidney(2)|large_intestine(8)|lung(19)|ovary(1)|pancreas(2)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)	47						GGAAAGGGACGCCATCACAGA	0.527													G|||	1158	0.23123	0.0734	0.2334	5008	,	,		20807	0.379		0.2584	False		,,,				2504	0.2628				p.R417H		Atlas-SNP	.											CHGB,NS,carcinoma,0,1	CHGB	112	1	1	Substitution - Missense(1)	stomach(1)	c.G1250A	GRCh37	CM043991	CHGB	M	rs742711	PASS	.	G	HIS/ARG	521,3885	238.4+/-249.8	37,447,1719	80.0	80.0	80.0		1250	-10.8	0.0	20	dbSNP_86	80	2277,6323	378.7+/-339.0	302,1673,2325	yes	missense	CHGB	NM_001819.2	29	339,2120,4044	AA,AG,GG		26.4767,11.8248,21.5131	benign	417/678	5904040	2798,10208	2203	4300	6503	SO:0001583	missense	1114	exon4			AGGGACGCCATCA		CCDS13092.1	20p12.3	2013-09-19			ENSG00000089199	ENSG00000089199			1930	protein-coding gene	gene with protein product	"""secretogranin B"""	118920		SCG1		3608978	Standard	NM_001819		Approved		uc002wmg.3	P05060	OTTHUMG00000031821	ENST00000378961.4:c.1250G>A	20.37:g.5904040G>A	ENSP00000368244:p.Arg417His	Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	43	19	0.44186	NM_001819	A8K021|Q59EU9|Q6IBS6|Q9BQV6|Q9UC25|Q9UJA6	Missense_Mutation	SNP	ENST00000378961.4	37	CCDS13092.1	529	0.24221611721611722	49	0.09959349593495935	77	0.212707182320442	206	0.36013986013986016	197	0.2598944591029024	G	1.700	-0.501792	0.04261	0.118248	0.264767	ENSG00000089199	ENST00000378961	T	0.01963	4.53	5.4	-10.8	0.00216	.	2.054640	0.02189	N	0.061130	T	0.00012	0.0000	L	0.38175	1.15	0.80722	P	0.0	B	0.15473	0.013	B	0.06405	0.002	T	0.48536	-0.9027	9	0.10902	T	0.67	1.7578	6.6545	0.22981	0.2912:0.3742:0.2747:0.0599	rs742711;rs52814619;rs61667157;rs742711	417	P05060	SCG1_HUMAN	H	417	ENSP00000368244:R417H	ENSP00000368244:R417H	R	+	2	0	CHGB	5852040	0.000000	0.05858	0.000000	0.03702	0.022000	0.10575	-2.806000	0.00758	-2.864000	0.00326	-1.788000	0.00630	CGC	G|0.775;A|0.225	0.225	strong		0.527	CHGB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077897.2	NM_001819	
SPP1	6696	hgsc.bcm.edu	37	4	88902692	88902692	+	Silent	SNP	T	T	C	rs4754	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:88902692T>C	ENST00000395080.3	+	6	409	c.282T>C	c.(280-282)gaT>gaC	p.D94D	SPP1_ENST00000237623.7_Silent_p.D80D|SPP1_ENST00000360804.4_Silent_p.D67D|SPP1_ENST00000509659.1_3'UTR	NM_001040058.1|NM_001251830.1	NP_001035147.1|NP_001238759.1	P10451	OSTP_HUMAN	secreted phosphoprotein 1	94					biomineral tissue development (GO:0031214)|cell adhesion (GO:0007155)|decidualization (GO:0046697)|embryo implantation (GO:0007566)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|inflammatory response (GO:0006954)|negative regulation of collateral sprouting of intact axon in response to injury (GO:0048685)|neutrophil chemotaxis (GO:0030593)|osteoblast differentiation (GO:0001649)|positive regulation of bone resorption (GO:0045780)|positive regulation of cell-substrate adhesion (GO:0010811)|response to steroid hormone (GO:0048545)|response to vitamin D (GO:0033280)	apical part of cell (GO:0045177)|cell projection (GO:0042995)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|perinuclear region of cytoplasm (GO:0048471)	extracellular matrix binding (GO:0050840)	p.D94D(1)		NS(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|prostate(3)|skin(1)	13		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;9.87e-05)		AAGATGATGATGACCATGTGG	0.433													T|||	1808	0.361022	0.1543	0.3775	5008	,	,		19176	0.7054		0.2813	False		,,,				2504	0.3558				p.D107D		Atlas-SNP	.											SPP1,NS,carcinoma,0,1	SPP1	35	1	1	Substitution - coding silent(1)	prostate(1)	c.T321C	GRCh37	CM033816	SPP1	M	rs4754	PASS	.	T	,,	784,3622	315.5+/-294.2	59,666,1478	269.0	248.0	255.0		240,282,201	-9.9	0.0	4	dbSNP_52	255	2339,6261	391.6+/-343.7	348,1643,2309	no	coding-synonymous,coding-synonymous,coding-synonymous	SPP1	NM_000582.2,NM_001040058.1,NM_001040060.1	,,	407,2309,3787	CC,CT,TT		27.1977,17.7939,24.012	,,	80/301,94/315,67/288	88902692	3123,9883	2203	4300	6503	SO:0001819	synonymous_variant	6696	exon7			TGATGATGACCAT		CCDS3626.1, CCDS34027.1, CCDS43250.1	4q22.1	2014-01-30	2008-07-31		ENSG00000118785	ENSG00000118785		"""Endogenous ligands"""	11255	protein-coding gene	gene with protein product	"""early T-lymphocyte activation 1"""	166490	"""osteopontin"", ""bone sialoprotein I"""	BNSP, OPN		1575754	Standard	NM_001251829		Approved	BSPI, ETA-1	uc003hra.3	P10451	OTTHUMG00000130599	ENST00000395080.3:c.282T>C	4.37:g.88902692T>C		Somatic	200	0	0		WXS	Illumina HiSeq	Phase_I	174	174	1	NM_001251830	B2RDA1|Q15681|Q15682|Q15683|Q4W597|Q567T5|Q8NBK2|Q96IZ1	Silent	SNP	ENST00000395080.3	37	CCDS43250.1																																																																																			T|0.713;C|0.287	0.287	strong		0.433	SPP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253048.3		
ZNF83	55769	hgsc.bcm.edu	37	19	53117531	53117531	+	Missense_Mutation	SNP	C	C	T	rs1056185	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:53117531C>T	ENST00000597597.1	-	2	2540	c.287G>A	c.(286-288)aGt>aAt	p.S96N	ZNF83_ENST00000601257.1_Intron|ZNF83_ENST00000545872.1_Missense_Mutation_p.S96N|ZNF83_ENST00000600714.1_Intron|ZNF83_ENST00000541777.2_Missense_Mutation_p.S96N|ZNF83_ENST00000391789.4_Missense_Mutation_p.S96N|ZNF83_ENST00000594682.2_3'UTR|ZNF83_ENST00000536937.1_Missense_Mutation_p.S96N|ZNF83_ENST00000301096.3_Missense_Mutation_p.S96N|ZNF83_ENST00000544146.1_Missense_Mutation_p.S96N			P51522	ZNF83_HUMAN	zinc finger protein 83	96			S -> N (in dbSNP:rs1056185). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:2505992}.		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(3)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	18				OV - Ovarian serous cystadenocarcinoma(262;0.00841)|GBM - Glioblastoma multiforme(134;0.0244)		GCCACGCTCACTACATTTGTA	0.338													T|||	3570	0.712859	0.885	0.7435	5008	,	,		20580	0.7063		0.6431	False		,,,				2504	0.5368				p.S96N		Atlas-SNP	.											.	ZNF83	73	.	0			c.G287A						PASS	.	T	ASN/SER,ASN/SER,ASN/SER,ASN/SER,ASN/SER,ASN/SER,ASN/SER,ASN/SER,ASN/SER	3572,834		1453,666,84	72.0	74.0	73.0		287,287,287,287,287,287,287,287,287	-2.4	0.0	19	dbSNP_86	73	5117,3483		1529,2059,712	yes	missense,missense,missense,missense,missense,missense,missense,missense,missense	ZNF83	NM_001105549.1,NM_001105550.1,NM_001105551.1,NM_001105552.1,NM_001105553.1,NM_001105554.1,NM_001242531.1,NM_001242538.1,NM_018300.3	46,46,46,46,46,46,46,46,46	2982,2725,796	TT,TC,CC		40.5,18.9287,33.1924	benign,benign,benign,benign,benign,benign,benign,benign,benign	96/517,96/517,96/517,96/517,96/489,96/489,96/489,96/489,96/517	53117531	8689,4317	2203	4300	6503	SO:0001583	missense	55769	exon3			CGCTCACTACATT	M27877	CCDS12854.1	19q13.3	2013-01-08	2006-05-12			ENSG00000167766		"""Zinc fingers, C2H2-type"""	13158	protein-coding gene	gene with protein product		194558	"""zinc finger protein 83 (HPF1)"", ""zinc finger protein 816B"""	ZNF816B		8088807	Standard	NM_018300		Approved	FLJ11015, HPF1	uc010epy.3	P51522		ENST00000597597.1:c.287G>A	19.37:g.53117531C>T	ENSP00000472619:p.Ser96Asn	Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	126	124	0.984127	NM_018300	A8MT75|Q3ZCX0|Q6PI08	Missense_Mutation	SNP	ENST00000597597.1	37	CCDS12854.1	1584	0.7252747252747253	423	0.8597560975609756	257	0.7099447513812155	414	0.7237762237762237	490	0.6464379947229552	N	0.004	-2.251714	0.00268	0.810713	0.595	ENSG00000167766	ENST00000536937;ENST00000301096;ENST00000544146;ENST00000434535;ENST00000545872;ENST00000541777;ENST00000391789	T;T;T;T;T;T	0.28454	1.61;1.61;1.61;1.61;1.61;3.07	1.87	-2.41	0.06562	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	N	0.10837	0.055	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.35076	-0.9803	8	0.02654	T	1	.	7.568	0.27890	0.0:0.2272:0.5906:0.1822	rs1056185;rs3786489;rs17633306;rs17846458;rs17859510;rs17859703;rs57819939;rs1056185	96;96	P51522-2;P51522	.;ZNF83_HUMAN	N	96	ENSP00000445993:S96N;ENSP00000301096:S96N;ENSP00000445470:S96N;ENSP00000440713:S96N;ENSP00000439681:S96N;ENSP00000375666:S96N	ENSP00000301096:S96N	S	-	2	0	ZNF83	57809343	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-1.362000	0.02595	-1.441000	0.01958	-1.411000	0.01122	AGT	C|0.299;T|0.700	0.700	strong		0.338	ZNF83-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463700.1	NM_018300	
SSX7	280658	hgsc.bcm.edu	37	X	52674514	52674514	+	Missense_Mutation	SNP	G	G	T	rs112382781		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:52674514G>T	ENST00000298181.5	-	7	704	c.546C>A	c.(544-546)gaC>gaA	p.D182E		NM_173358.2	NP_775494.1	Q7RTT5	SSX7_HUMAN	synovial sarcoma, X breakpoint 7	182					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleic acid binding (GO:0003676)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(11)|skin(1)	16	Ovarian(276;0.236)					CTTCTTCAGGGTCGCTGATCT	0.498													.|||	213	0.0564238	0.0053	0.0447	3775	,	,		13809	0.0218		0.1064	False		,,,				2504	0.047				p.D182E		Atlas-SNP	.											.	SSX7	34	.	0			c.C546A						PASS	.	G	GLU/ASP	74,3759		4,52,14,1575,557	85.0	69.0	74.0		546	-0.7	0.0	X	dbSNP_134	74	841,5854		40,512,249,1863,1616	no	missense	SSX7	NM_173358.2	45	44,564,263,3438,2173	TT,TG,T,GG,G		12.5616,1.9306,8.6911	probably-damaging	182/189	52674514	915,9613	2202	4280	6482	SO:0001583	missense	280658	exon7			TTCAGGGTCGCTG	BK000687	CCDS14343.1	Xp11.23	2011-02-10			ENSG00000187754	ENSG00000187754			19653	protein-coding gene	gene with protein product		300542				12216073	Standard	NM_173358		Approved		uc004dqx.1	Q7RTT5	OTTHUMG00000021572	ENST00000298181.5:c.546C>A	X.37:g.52674514G>T	ENSP00000298181:p.Asp182Glu	Somatic	926	1	0.00107991		WXS	Illumina HiSeq	Phase_I	647	434	0.670788	NM_173358		Missense_Mutation	SNP	ENST00000298181.5	37	CCDS14343.1	111	0.06690777576853527	6	0.012195121951219513	13	0.03672316384180791	7	0.012455516014234875	61	0.08567415730337079	g	12.49	1.953243	0.34471	0.019306	0.125616	ENSG00000187754	ENST00000298181	T	0.09723	2.95	0.541	-0.687	0.11320	SSXRD motif (1);	0.424262	0.20161	N	0.097952	T	0.00210	0.0006	L	0.58101	1.795	0.80722	P	0.0	D	0.89917	1.0	D	0.91635	0.999	T	0.10613	-1.0622	8	0.15952	T	0.53	.	.	.	.	.	182	Q7RTT5	SSX7_HUMAN	E	182	ENSP00000298181:D182E	ENSP00000298181:D182E	D	-	3	2	SSX7	52691239	0.016000	0.18221	0.008000	0.14137	0.369000	0.29798	-0.783000	0.04638	-0.355000	0.08199	0.164000	0.16699	GAC	G|0.933;T|0.067	0.067	strong		0.498	SSX7-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056671.1	NM_173358	
CEP192	55125	hgsc.bcm.edu	37	18	13116432	13116432	+	Missense_Mutation	SNP	G	G	T	rs1786263	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:13116432G>T	ENST00000325971.8	+	41	7151	c.5558G>T	c.(5557-5559)cGg>cTg	p.R1853L	CEP192_ENST00000430049.2_Missense_Mutation_p.R1974L|CEP192_ENST00000540847.2_3'UTR|CEP192_ENST00000506447.1_Missense_Mutation_p.R2449L			Q8TEP8	CE192_HUMAN	centrosomal protein 192kDa	1853			R -> L (in dbSNP:rs1786263). {ECO:0000269|PubMed:11230166, ECO:0000269|PubMed:12693554, ECO:0000269|PubMed:14702039}.		centrosome duplication (GO:0051298)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|negative regulation of phosphatase activity (GO:0010923)|spindle assembly (GO:0051225)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)	phosphatase binding (GO:0019902)			NS(1)|breast(4)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(36)|ovary(4)|pancreas(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	71						TACAGGTTCCGGCCGACTAGT	0.428													T|||	3884	0.775559	0.9788	0.6441	5008	,	,		15909	0.8075		0.6113	False		,,,				2504	0.7301				p.R2449L		Atlas-SNP	.											.	CEP192	340	.	0			c.G7346T						PASS	.	T	LEU/ARG	4056,350	180.1+/-208.5	1868,320,15	96.0	90.0	92.0		7346	4.8	1.0	18	dbSNP_89	92	5297,3303	493.6+/-373.6	1642,2013,645	yes	missense	CEP192	NM_032142.3	102	3510,2333,660	TT,TG,GG		38.407,7.9437,28.087	benign	2449/2538	13116432	9353,3653	2203	4300	6503	SO:0001583	missense	55125	exon43			GGTTCCGGCCGAC	AK074074	CCDS32792.1, CCDS32792.2	18p11.21	2014-02-20				ENSG00000101639		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	25515	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 62"""					11230166, 14654843	Standard	NM_032142		Approved	KIAA1569, FLJ10352, PPP1R62	uc010xac.2	Q8TEP8		ENST00000325971.8:c.5558G>T	18.37:g.13116432G>T	ENSP00000317156:p.Arg1853Leu	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	93	42	0.451613	NM_032142	A0A060A9S4|E9PF99|Q8WYT8|Q9H0F4|Q9NW27	Missense_Mutation	SNP	ENST00000325971.8	37		1642	0.7518315018315018	476	0.967479674796748	237	0.6546961325966851	462	0.8076923076923077	467	0.6160949868073878	T	2.675	-0.276722	0.05679	0.920563	0.61593	ENSG00000101639	ENST00000506447;ENST00000325971;ENST00000399863;ENST00000430049;ENST00000540847	T;T;T	0.04862	3.54;3.54;3.54	4.76	4.76	0.60689	.	0.077542	0.53938	N	0.000042	T	0.00012	0.0000	N	0.00128	-2.045	0.53688	P	2.8000000000028002E-5	B;B;B;B	0.06786	0.0;0.001;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.29822	-0.9999	9	0.02654	T	1	-2.2435	4.8966	0.13753	0.0:0.159:0.1629:0.6781	rs1786263;rs17661484;rs52836864;rs61351048;rs1786263	1974;2449;453;1052	C9JT09;E9PF99;F5GZ47;Q9HCK3	.;.;.;.	L	2449;1853;1853;1974;453	ENSP00000427550:R2449L;ENSP00000317156:R1853L;ENSP00000389190:R1974L	ENSP00000317156:R1853L	R	+	2	0	CEP192	13106432	1.000000	0.71417	1.000000	0.80357	0.285000	0.27093	0.755000	0.26405	0.785000	0.33685	-0.520000	0.04383	CGG	G|0.251;T|0.749	0.749	strong		0.428	CEP192-201	KNOWN	basic	protein_coding	protein_coding		NM_032142	
DAOA	267012	hgsc.bcm.edu	37	13	106142235	106142235	+	Intron	SNP	C	C	T	rs778294	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:106142235C>T	ENST00000375936.3	+	4	327				DAOA-AS1_ENST00000448407.1_RNA|DAOA_ENST00000329625.5_Intron	NM_001161812.1|NM_172370.3	NP_001155284.1|NP_758958.3	P59103	DAOA_HUMAN	D-amino acid oxidase activator						negative regulation of D-amino-acid oxidase activity (GO:1900758)|positive regulation of catalytic activity (GO:0043085)	Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)|perinuclear region of cytoplasm (GO:0048471)	enzyme activator activity (GO:0008047)|enzyme binding (GO:0019899)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(5)|skin(1)	13	Lung NSC(43;0.01)|all_neural(89;0.0741)|Lung SC(71;0.14)|Medulloblastoma(90;0.169)					caactgagaccggatctcctt	0.498													c|||	1087	0.217053	0.2405	0.2507	5008	,	,		17670	0.1081		0.2763	False		,,,				2504	0.2127				p.T61T		Atlas-SNP	.											.	DAOA	26	.	0			c.C183T						PASS	.	T	,,	957,3427	319.3+/-296.1	117,723,1352	78.0	84.0	82.0		183,,	-4.4	0.0	13	dbSNP_86	82	2447,6137	391.3+/-343.6	344,1759,2189	no	coding-synonymous,intron,intron	DAOA	NM_001161812.1,NM_001161814.1,NM_172370.3	,,	461,2482,3541	TT,TC,CC		28.5065,21.8294,26.2492	,,	61/126,,	106142235	3404,9564	2192	4292	6484	SO:0001627	intron_variant	267012	exon4			TGAGACCGGATCT	AY138547	CCDS41905.1, CCDS53880.1, CCDS59242.1	13q33.2	2011-08-01			ENSG00000182346	ENSG00000182346			21191	protein-coding gene	gene with protein product	"""G72 transcript"""	607408				12364586, 15057823	Standard	NM_001161814		Approved	G72	uc010tjg.2	P59103	OTTHUMG00000041333	ENST00000375936.3:c.282-15C>T	13.37:g.106142235C>T		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	72	31	0.430556	NM_001161812	A6NKG7|Q0VAE6|Q5VX59|Q86Y17|Q8IWM4	Silent	SNP	ENST00000375936.3	37	CCDS41905.1																																																																																			C|0.763;T|0.237	0.237	strong		0.498	DAOA-005	KNOWN	NMD_exception|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000099040.2	NM_172370	
DYNC2LI1	51626	hgsc.bcm.edu	37	2	44028013	44028013	+	Missense_Mutation	SNP	A	A	T	rs11556157	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:44028013A>T	ENST00000260605.8	+	9	788	c.688A>T	c.(688-690)Ata>Tta	p.I230L	DYNC2LI1_ENST00000605786.1_Missense_Mutation_p.I231L|DYNC2LI1_ENST00000443170.3_Missense_Mutation_p.I104L|DYNC2LI1_ENST00000489222.2_3'UTR	NM_001193464.1|NM_016008.3	NP_001180393.1|NP_057092.2	Q8TCX1	DC2L1_HUMAN	dynein, cytoplasmic 2, light intermediate chain 1	230			I -> L (in dbSNP:rs11556157). {ECO:0000269|PubMed:17974005, ECO:0000269|Ref.3}.		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cilium assembly (GO:0042384)|determination of left/right symmetry (GO:0007368)	apical part of cell (GO:0045177)|axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|cytosol (GO:0005829)|intraciliary transport particle (GO:0030990)|microtubule (GO:0005874)|motile primary cilium (GO:0031512)|primary cilium (GO:0072372)	motor activity (GO:0003774)			breast(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(12)|ovary(1)|pancreas(1)|skin(1)	26		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)				ATTACTAAAAATACGTGGAGT	0.303													A|||	1177	0.235024	0.3427	0.1844	5008	,	,		12055	0.0258		0.2386	False		,,,				2504	0.3374				p.I231L		Atlas-SNP	.											.	DYNC2LI1	46	.	0			c.A691T						PASS	.	A	LEU/ILE,LEU/ILE	1423,2983	460.2+/-352.5	247,929,1027	90.0	95.0	94.0		691,688	3.9	1.0	2	dbSNP_120	94	2100,6498	359.4+/-331.5	266,1568,2465	yes	missense,missense	DYNC2LI1	NM_001193464.1,NM_016008.3	5,5	513,2497,3492	TT,TA,AA		24.4243,32.2969,27.0917	benign,benign	231/353,230/352	44028013	3523,9481	2203	4299	6502	SO:0001583	missense	51626	exon9			CTAAAAATACGTG		CCDS1813.1, CCDS46270.1, CCDS62903.1	2p25.1-p24.1	2008-02-05			ENSG00000138036	ENSG00000138036		"""Cytoplasmic dyneins"""	24595	protein-coding gene	gene with protein product						10810093, 11907264	Standard	NM_016008		Approved	D2LIC, LIC3, CGI-60, DKFZP564A033	uc002rtl.3	Q8TCX1	OTTHUMG00000128656	ENST00000260605.8:c.688A>T	2.37:g.44028013A>T	ENSP00000260605:p.Ile230Leu	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	138	40	0.289855	NM_001193464	A8MVJ5|Q53F57|Q6PDB2|Q8IWA3|Q96B03|Q96J00|Q9Y370|Q9Y3S9	Missense_Mutation	SNP	ENST00000260605.8	37	CCDS1813.1	432|432	0.1978021978021978|0.1978021978021978	163|163	0.3313008130081301|0.3313008130081301	81|81	0.22375690607734808|0.22375690607734808	16|16	0.027972027972027972|0.027972027972027972	172|172	0.22691292875989447|0.22691292875989447	A|A	7.886|7.886	0.731358|0.731358	0.15507|0.15507	0.322969|0.322969	0.244243|0.244243	ENSG00000138036|ENSG00000138036	ENST00000260605;ENST00000443170|ENST00000378587	T;T|T	0.05319|0.15834	3.46;3.46|2.39	5.09|5.09	3.94|3.94	0.45596|0.45596	.|.	0.315054|.	0.36703|.	N|.	0.002460|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.04297|0.04297	-0.235|-0.235	0.40481|0.40481	P|P	0.019550999999999985|0.019550999999999985	B;B;B|.	0.06786|.	0.001;0.001;0.001|.	B;B;B|.	0.06405|.	0.002;0.001;0.002|.	T|T	0.49485|0.49485	-0.8935|-0.8935	9|6	0.02654|0.25106	T|T	1|0.35	-8.7008|-8.7008	8.7254|8.7254	0.34467|0.34467	0.8337:0.0:0.1663:0.0|0.8337:0.0:0.1663:0.0	rs11556157;rs52837792;rs56458012;rs11556157|rs11556157;rs52837792;rs56458012;rs11556157	231;230;230|.	Q8TCX1-2;Q8TCX1;Q8TCX1-3|.	.;DC2L1_HUMAN;.|.	L|N	230;104|213	ENSP00000260605:I230L;ENSP00000388941:I104L|ENSP00000367850:K213N	ENSP00000260605:I230L|ENSP00000367850:K213N	I|K	+|+	1|3	0|2	DYNC2LI1|DYNC2LI1	43881517|43881517	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.991000|0.991000	0.79684|0.79684	2.364000|2.364000	0.44187|0.44187	0.952000|0.952000	0.37798|0.37798	0.477000|0.477000	0.44152|0.44152	ATA|AAA	A|0.758;T|0.242	0.242	strong		0.303	DYNC2LI1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000250536.2	NM_016008	
PDE10A	10846	hgsc.bcm.edu	37	6	165832227	165832227	+	Silent	SNP	C	C	T	rs220740	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:165832227C>T	ENST00000366882.1	-	12	1018	c.864G>A	c.(862-864)gcG>gcA	p.A288A	PDE10A_ENST00000354448.4_Silent_p.A288A|PDE10A_ENST00000539869.2_Silent_p.A298A			Q9Y233	PDE10_HUMAN	phosphodiesterase 10A	288	GAF 2.				blood coagulation (GO:0007596)|cAMP catabolic process (GO:0006198)|cGMP catabolic process (GO:0046069)|regulation of cAMP-mediated signaling (GO:0043949)|regulation of protein kinase A signaling (GO:0010738)|signal transduction (GO:0007165)	cytosol (GO:0005829)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|cAMP binding (GO:0030552)|cGMP binding (GO:0030553)|cGMP-stimulated cyclic-nucleotide phosphodiesterase activity (GO:0004118)|metal ion binding (GO:0046872)			breast(4)|endometrium(5)|kidney(1)|large_intestine(13)|liver(1)|lung(39)|ovary(3)|skin(4)|upper_aerodigestive_tract(1)	71		Breast(66;0.000425)|Prostate(117;0.104)|Ovarian(120;0.221)		OV - Ovarian serous cystadenocarcinoma(33;1.5e-17)|BRCA - Breast invasive adenocarcinoma(81;1.8e-06)|GBM - Glioblastoma multiforme(31;1.92e-05)	Caffeine(DB00201)|Dipyridamole(DB00975)|Papaverine(DB01113)|Tofisopam(DB08811)|Triflusal(DB08814)	CCTGGAAAAGCGCACAACGAT	0.383													T|||	1222	0.24401	0.4236	0.1916	5008	,	,		16569	0.0813		0.2475	False		,,,				2504	0.2025				p.A298A	Esophageal Squamous(22;308 615 5753 12038 40624)	Atlas-SNP	.											.	PDE10A	154	.	0			c.G894A						PASS	.	T	,	1768,2638	645.1+/-398.1	354,1060,789	93.0	85.0	88.0		894,864	-7.8	0.9	6	dbSNP_79	88	2509,6091	694.5+/-404.7	362,1785,2153	no	coding-synonymous,coding-synonymous	PDE10A	NM_001130690.1,NM_006661.2	,	716,2845,2942	TT,TC,CC		29.1744,40.1271,32.8848	,	298/790,288/780	165832227	4277,8729	2203	4300	6503	SO:0001819	synonymous_variant	10846	exon11			GAAAAGCGCACAA	AB020593	CCDS47513.1	6q26	2008-03-18			ENSG00000112541	ENSG00000112541	3.1.4.17	"""Phosphodiesterases"""	8772	protein-coding gene	gene with protein product		610652				10373451	Standard	NM_001130690		Approved		uc003quo.3	Q9Y233	OTTHUMG00000015986	ENST00000366882.1:c.864G>A	6.37:g.165832227C>T		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	21	9	0.428571	NM_001130690	Q6FHX1|Q9HCP9|Q9NTV4|Q9ULW9|Q9Y5T1	Silent	SNP	ENST00000366882.1	37																																																																																				C|0.710;T|0.290	0.290	strong		0.383	PDE10A-001	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000043031.1		
ESPN	83715	hgsc.bcm.edu	37	1	6500762	6500762	+	Missense_Mutation	SNP	G	G	A	rs200602012		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:6500762G>A	ENST00000377828.1	+	4	920	c.752G>A	c.(751-753)gGc>gAc	p.G251D	RP1-202O8.2_ENST00000419034.1_RNA	NM_031475.2	NP_113663.2	B1AK53	ESPN_HUMAN	espin	251					locomotory behavior (GO:0007626)|negative regulation of cytoskeleton organization (GO:0051494)|parallel actin filament bundle assembly (GO:0030046)|positive regulation of filopodium assembly (GO:0051491)|sensory perception of sound (GO:0007605)	brush border (GO:0005903)|cytoplasm (GO:0005737)|filamentous actin (GO:0031941)|microvillus (GO:0005902)|stereocilium bundle tip (GO:0032426)	actin filament binding (GO:0051015)|SH3 domain binding (GO:0017124)			NS(1)|breast(2)|cervix(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|prostate(1)|skin(1)	17	Ovarian(185;0.0386)|all_lung(157;0.154)	all_cancers(23;3.6e-37)|all_epithelial(116;2.56e-22)|all_lung(118;7.57e-07)|Lung NSC(185;4.26e-06)|all_hematologic(16;6.92e-06)|Colorectal(325;4.47e-05)|Acute lymphoblastic leukemia(12;4.92e-05)|Breast(487;7.61e-05)|Renal(390;0.0007)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0392)		Epithelial(90;1.82e-35)|GBM - Glioblastoma multiforme(13;3e-28)|Kidney(185;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(229;5.63e-08)|Colorectal(212;7e-08)|COAD - Colon adenocarcinoma(227;1.41e-05)|BRCA - Breast invasive adenocarcinoma(365;0.000109)|STAD - Stomach adenocarcinoma(132;0.00167)|Lung(427;0.0108)|LUSC - Lung squamous cell carcinoma(448;0.0253)|READ - Rectum adenocarcinoma(331;0.0419)		GCGAGCCGCGGCCACACCAAG	0.726																																					p.G251D		Atlas-SNP	.											.	ESPN	32	.	0			c.G752A						PASS	.						5.0	6.0	5.0					1																	6500762		1942	3927	5869	SO:0001583	missense	83715	exon4			GCCGCGGCCACAC	AF134401	CCDS70.1	1p36.31	2013-01-10			ENSG00000187017	ENSG00000187017		"""Ankyrin repeat domain containing"""	13281	protein-coding gene	gene with protein product		606351	"""deafness, autosomal recessive 36"""	DFNB36		10975527, 15286153	Standard	NM_031475		Approved		uc001amy.3	B1AK53	OTTHUMG00000000753	ENST00000377828.1:c.752G>A	1.37:g.6500762G>A	ENSP00000367059:p.Gly251Asp	Somatic	12	0	0		WXS	Illumina HiSeq	Phase_I	35	13	0.371429	NM_031475	Q6XYB2|Q9H0A2|Q9Y329	Missense_Mutation	SNP	ENST00000377828.1	37	CCDS70.1	.	.	.	.	.	.	.	.	.	.	G	25.6	4.650081	0.87958	.	.	ENSG00000187017	ENST00000377828;ENST00000418286	T;T	0.72394	-0.65;0.89	3.84	3.84	0.44239	Ankyrin repeat-containing domain (5);	0.233607	0.34959	N	0.003544	T	0.81772	0.4893	M	0.80982	2.52	0.80722	D	1	D	0.65815	0.995	D	0.63283	0.913	D	0.83857	0.0266	10	0.54805	T	0.06	-5.9744	12.6418	0.56714	0.0:0.0:1.0:0.0	.	251	B1AK53	ESPN_HUMAN	D	251;36	ENSP00000367059:G251D;ENSP00000401793:G36D	ENSP00000367059:G251D	G	+	2	0	ESPN	6423349	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	8.972000	0.93424	1.989000	0.58080	0.430000	0.28490	GGC	G|0.991;A|0.010	0.010	weak		0.726	ESPN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001887.3	NM_031475	
TLR10	81793	hgsc.bcm.edu	37	4	38775794	38775794	+	Missense_Mutation	SNP	A	A	G	rs11466657	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:38775794A>G	ENST00000308973.4	-	4	2023	c.1418T>C	c.(1417-1419)aTt>aCt	p.I473T	TLR10_ENST00000506111.1_Missense_Mutation_p.I473T|TLR10_ENST00000361424.2_Missense_Mutation_p.I473T|TLR10_ENST00000508334.1_Missense_Mutation_p.I473T|TLR10_ENST00000507953.1_5'Flank	NM_001017388.2|NM_001195107.1|NM_030956.3	NP_001017388.1|NP_001182036.1|NP_112218.2	Q9BXR5	TLR10_HUMAN	toll-like receptor 10	473			I -> T (in dbSNP:rs11466657). {ECO:0000269|PubMed:15489334}.		immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of inflammatory response (GO:0050729)|regulation of cytokine secretion (GO:0050707)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor signaling pathway (GO:0002224)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	transmembrane signaling receptor activity (GO:0004888)			breast(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(11)|prostate(1)|urinary_tract(2)	25						ATTAAATGCAATATTTAGTTC	0.358													A|||	93	0.0185703	0.0023	0.0331	5008	,	,		21007	0.0		0.0527	False		,,,				2504	0.0143				p.I473T		Atlas-SNP	.											.	TLR10	87	.	0			c.T1418C						PASS	.	A	THR/ILE,THR/ILE,THR/ILE,THR/ILE,THR/ILE	30,4374	34.3+/-65.2	0,30,2172	87.0	93.0	91.0		1418,1418,1418,1376,1418	4.1	0.1	4	dbSNP_120	91	321,8279	112.9+/-173.0	6,309,3985	yes	missense,missense,missense,missense,missense	TLR10	NM_001017388.2,NM_001195106.1,NM_001195107.1,NM_001195108.1,NM_030956.3	89,89,89,89,89	6,339,6157	GG,GA,AA		3.7326,0.6812,2.6992	benign,benign,benign,benign,benign	473/812,473/812,473/812,459/798,473/812	38775794	351,12653	2202	4300	6502	SO:0001583	missense	81793	exon2			AATGCAATATTTA	AF296673	CCDS3445.1	4p14	2009-11-23			ENSG00000174123	ENSG00000174123		"""CD molecules"""	15634	protein-coding gene	gene with protein product		606270				11267672	Standard	NM_030956		Approved	CD290	uc003gtk.3	Q9BXR5	OTTHUMG00000128578	ENST00000308973.4:c.1418T>C	4.37:g.38775794A>G	ENSP00000308925:p.Ile473Thr	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	90	41	0.455556	NM_001017388	A8K7L1|B3Y668|D1CS21|D1CS22|Q32MI7|Q32MI8|Q5FWG4|Q6UXL3	Missense_Mutation	SNP	ENST00000308973.4	37	CCDS3445.1	50	0.022893772893772892	1	0.0020325203252032522	16	0.04419889502762431	0	0.0	33	0.04353562005277045	A	8.336	0.827600	0.16749	0.006812	0.037326	ENSG00000174123	ENST00000308973;ENST00000506111;ENST00000361424;ENST00000508334	T;T;T;T	0.27557	1.66;1.66;1.66;1.66	5.32	4.11	0.48088	.	0.538513	0.14501	N	0.315746	T	0.09992	0.0245	L	0.60067	1.865	0.30811	N	0.738872	B	0.30973	0.302	B	0.35182	0.197	T	0.17592	-1.0364	10	0.87932	D	0	.	11.4547	0.50173	0.8649:0.0:0.0:0.1351	rs11466657;rs52835680;rs60306705;rs11466657	473	Q9BXR5	TLR10_HUMAN	T	473	ENSP00000308925:I473T;ENSP00000421483:I473T;ENSP00000354459:I473T;ENSP00000424923:I473T	ENSP00000308925:I473T	I	-	2	0	TLR10	38452189	0.985000	0.35326	0.067000	0.19924	0.286000	0.27126	5.112000	0.64634	0.827000	0.34685	0.477000	0.44152	ATT	A|0.970;G|0.030	0.030	strong		0.358	TLR10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250430.1		
ENDOD1	23052	hgsc.bcm.edu	37	11	94862577	94862577	+	Missense_Mutation	SNP	G	G	T	rs3740861	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:94862577G>T	ENST00000278505.4	+	2	1455	c.1337G>T	c.(1336-1338)gGc>gTc	p.G446V		NM_015036.2	NP_055851.1	O94919	ENDD1_HUMAN	endonuclease domain containing 1	446			G -> V (in dbSNP:rs3740861).			extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			breast(1)|endometrium(2)|large_intestine(3)|lung(4)|upper_aerodigestive_tract(1)	11		Acute lymphoblastic leukemia(157;2.33e-05)|all_hematologic(158;0.00824)				TACACCATGGGCGCTATTCCA	0.532													G|||	1002	0.20008	0.087	0.196	5008	,	,		19140	0.122		0.2684	False		,,,				2504	0.3661				p.G446V		Atlas-SNP	.											ENDOD1,NS,carcinoma,-1,1	ENDOD1	26	1	0			c.G1337T						PASS	.	G	VAL/GLY	488,3592		31,426,1583	189.0	180.0	183.0		1337	6.0	0.1	11	dbSNP_107	183	2329,6089		319,1691,2199	yes	missense	ENDOD1	NM_015036.2	109	350,2117,3782	TT,TG,GG		27.6669,11.9608,22.5396	probably-damaging	446/501	94862577	2817,9681	2040	4209	6249	SO:0001583	missense	23052	exon2			CCATGGGCGCTAT	BC026191	CCDS41699.1	11q21	2010-03-19			ENSG00000149218	ENSG00000149218			29129	protein-coding gene	gene with protein product						10048485	Standard	NM_015036		Approved	KIAA0830	uc001pfh.3	O94919	OTTHUMG00000167835	ENST00000278505.4:c.1337G>T	11.37:g.94862577G>T	ENSP00000278505:p.Gly446Val	Somatic	424	2	0.00471698		WXS	Illumina HiSeq	Phase_I	322	239	0.742236	NM_015036	A8K6K8|Q6GQY5|Q8TAQ8	Missense_Mutation	SNP	ENST00000278505.4	37	CCDS41699.1	392	0.1794871794871795	53	0.10772357723577236	68	0.1878453038674033	66	0.11538461538461539	205	0.2704485488126649	G	13.52	2.261585	0.39995	0.119608	0.276669	ENSG00000149218	ENST00000278505	T	0.36699	1.24	5.97	5.97	0.96955	.	0.532850	0.21869	N	0.067907	T	0.00012	0.0000	M	0.65975	2.015	0.36868	P	0.11124599999999996	D	0.65815	0.995	P	0.58172	0.834	T	0.00163	-1.1969	9	0.46703	T	0.11	-10.5144	20.4301	0.99081	0.0:0.0:1.0:0.0	rs3740861;rs17693261;rs52803898;rs58207096;rs3740861	446	O94919	ENDD1_HUMAN	V	446	ENSP00000278505:G446V	ENSP00000278505:G446V	G	+	2	0	ENDOD1	94502225	0.981000	0.34729	0.067000	0.19924	0.018000	0.09664	6.268000	0.72552	2.834000	0.97654	0.557000	0.71058	GGC	G|0.794;T|0.206	0.206	strong		0.532	ENDOD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396545.1	NM_015036	
SERPINE2	5270	hgsc.bcm.edu	37	2	224862842	224862842	+	Silent	SNP	A	A	G	rs12457	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:224862842A>G	ENST00000258405.4	-	3	719	c.477T>C	c.(475-477)aaT>aaC	p.N159N	SERPINE2_ENST00000409304.1_Silent_p.N159N|SERPINE2_ENST00000409840.3_Silent_p.N159N|SERPINE2_ENST00000447280.2_Silent_p.N171N	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	159				N -> D (in Ref. 4; BAG35401). {ECO:0000305}.	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)		CCCTGGTTTCATTTTTAACCC	0.453													G|||	1272	0.253994	0.4826	0.2161	5008	,	,		20707	0.129		0.1909	False		,,,				2504	0.1656				p.N171N		Atlas-SNP	.											.	SERPINE2	103	.	0			c.T513C						PASS	.	G	,,	1957,2449	621.9+/-393.8	440,1077,686	71.0	66.0	68.0		477,513,477	-1.8	0.5	2	dbSNP_116	68	1679,6921	739.8+/-407.1	161,1357,2782	no	coding-synonymous,coding-synonymous,coding-synonymous	SERPINE2	NM_001136528.1,NM_001136530.1,NM_006216.3	,,	601,2434,3468	GG,GA,AA		19.5233,44.4167,27.9563	,,	159/398,171/410,159/399	224862842	3636,9370	2203	4300	6503	SO:0001819	synonymous_variant	5270	exon3			GGTTTCATTTTTA	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.477T>C	2.37:g.224862842A>G		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	93	35	0.376344	NM_001136530	B2R6A4|B4DIF2|Q53S15|Q5D0C4	Silent	SNP	ENST00000258405.4	37	CCDS2460.1																																																																																			A|0.718;G|0.282	0.282	strong		0.453	SERPINE2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256865.2	NM_006216	
KIF1B	23095	hgsc.bcm.edu	37	1	10435324	10435324	+	Silent	SNP	C	C	A	rs11121552	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:10435324C>A	ENST00000377086.1	+	48	5503	c.5301C>A	c.(5299-5301)acC>acA	p.T1767T	KIF1B_ENST00000377081.1_Silent_p.T1767T|KIF1B_ENST00000263934.6_Silent_p.T1721T			O60333	KIF1B_HUMAN	kinesin family member 1B	1767	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				anterograde axon cargo transport (GO:0008089)|apoptotic process (GO:0006915)|cytoskeleton-dependent intracellular transport (GO:0030705)|microtubule-based movement (GO:0007018)|mitochondrion transport along microtubule (GO:0047497)|neuromuscular synaptic transmission (GO:0007274)|neuron-neuron synaptic transmission (GO:0007270)|vesicle-mediated transport (GO:0016192)	cytoplasmic vesicle (GO:0031410)|cytoplasmic vesicle membrane (GO:0030659)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|kinesin binding (GO:0019894)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)	p.T1721T(1)		breast(2)|endometrium(7)|kidney(8)|large_intestine(9)|lung(29)|ovary(3)|prostate(3)|skin(5)|stomach(3)|upper_aerodigestive_tract(2)	71	Ovarian(185;0.203)	all_lung(284;1.31e-05)|Lung NSC(185;2.2e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0259)|Colorectal(212;9.79e-07)|COAD - Colon adenocarcinoma(227;0.000143)|BRCA - Breast invasive adenocarcinoma(304;0.000413)|Kidney(185;0.00134)|KIRC - Kidney renal clear cell carcinoma(229;0.0037)|STAD - Stomach adenocarcinoma(132;0.0113)|READ - Rectum adenocarcinoma(331;0.0642)		CACCAAACACCTTTGCTGTCT	0.478													C|||	1160	0.231629	0.0575	0.3199	5008	,	,		21284	0.2827		0.3091	False		,,,				2504	0.272				p.T1721T		Atlas-SNP	.											KIF1B,NS,carcinoma,0,1	KIF1B	242	1	1	Substitution - coding silent(1)	stomach(1)	c.C5163A						PASS	.	C		413,3993	200.8+/-224.0	28,357,1818	97.0	93.0	94.0		5163	0.1	1.0	1	dbSNP_120	94	2585,6015	419.1+/-353.0	409,1767,2124	no	coding-synonymous	KIF1B	NM_015074.3		437,2124,3942	AA,AC,CC		30.0581,9.3736,23.0509		1721/1771	10435324	2998,10008	2203	4300	6503	SO:0001819	synonymous_variant	23095	exon46			AAACACCTTTGCT	AF257176	CCDS111.1, CCDS112.1	1p36.22	2014-09-17			ENSG00000054523	ENSG00000054523		"""Kinesins"", ""Pleckstrin homology (PH) domain containing"""	16636	protein-coding gene	gene with protein product		605995		CMT2A, CMT2		11389829, 10762626	Standard	NM_015074		Approved	KIAA0591, KLP, HMSNII	uc001aqw.4	O60333	OTTHUMG00000001817	ENST00000377086.1:c.5301C>A	1.37:g.10435324C>A		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	82	44	0.536585	NM_015074	A6NFS8|A6NKQ4|Q4VXC3|Q4VXC4|Q4VXC5|Q4VXC6|Q96Q94|Q9BV80|Q9P280	Silent	SNP	ENST00000377086.1	37																																																																																				C|0.759;A|0.241	0.241	strong		0.478	KIF1B-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000005102.1		
CHRNA5	1138	hgsc.bcm.edu	37	15	78882925	78882925	+	Missense_Mutation	SNP	G	G	A	rs16969968	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:78882925G>A	ENST00000299565.5	+	5	1392	c.1192G>A	c.(1192-1194)Gat>Aat	p.D398N	CHRNA5_ENST00000559554.1_Intron|RP11-650L12.2_ENST00000567141.1_RNA	NM_000745.3	NP_000736.2	P30532	ACHA5_HUMAN	cholinergic receptor, nicotinic, alpha 5 (neuronal)	398			D -> N (associated with susceptibility to lung cancer; dbSNP:rs16969968). {ECO:0000269|PubMed:8906617, ECO:0000269|Ref.4}.		behavioral response to nicotine (GO:0035095)|cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|ion transmembrane transport (GO:0034220)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transport (GO:0006810)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|ligand-gated ion channel activity (GO:0015276)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(1)|ovary(1)|prostate(1)|skin(3)	15					Galantamine(DB00674)|Nicotine(DB00184)	AGCTGCGCTCGATTCTATTCG	0.398													G|||	749	0.149561	0.0234	0.2089	5008	,	,		20833	0.0268		0.3658	False		,,,				2504	0.182				p.D398N		Atlas-SNP	.											.	CHRNA5	48	.	0			c.G1192A	GRCh37	CM081554	CHRNA5	M	rs16969968	PASS	.	G	ASN/ASP	274,4118	151.8+/-185.6	16,242,1938	71.0	68.0	69.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1192	3.9	0.0	15	dbSNP_123	69	2993,5593	459.1+/-364.8	550,1893,1850	yes	missense	CHRNA5	NM_000745.3	23	566,2135,3788	AA,AG,GG		34.8591,6.2386,25.1734	benign	398/469	78882925	3267,9711	2196	4293	6489	SO:0001583	missense	1138	exon5			GCGCTCGATTCTA		CCDS10304.1	15q24	2012-02-11	2012-02-07		ENSG00000169684	ENSG00000169684		"""Cholinergic receptors"", ""Ligand-gated ion channels / Acetylcholine receptors, nicotinic"""	1959	protein-coding gene	gene with protein product	"""acetylcholine receptor, nicotinic, alpha 5 (neuronal)"""	118505	"""cholinergic receptor, nicotinic, alpha polypeptide 5"""			2004777	Standard	NM_000745		Approved		uc002bdy.3	P30532	OTTHUMG00000143858	ENST00000299565.5:c.1192G>A	15.37:g.78882925G>A	ENSP00000299565:p.Asp398Asn	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	131	131	1	NM_000745	Q15824|Q99554	Missense_Mutation	SNP	ENST00000299565.5	37	CCDS10304.1	383	0.17536630036630035	11	0.022357723577235773	85	0.23480662983425415	16	0.027972027972027972	271	0.3575197889182058	G	10.45	1.352305	0.24512	0.062386	0.348591	ENSG00000169684	ENST00000299565	T	0.69806	-0.43	4.79	3.88	0.44766	Neurotransmitter-gated ion-channel transmembrane domain (2);	0.605324	0.18104	N	0.151590	T	0.00012	0.0000	L	0.60957	1.885	0.09310	P	1.0	B	0.20459	0.045	B	0.14578	0.011	T	0.15607	-1.0431	9	0.38643	T	0.18	.	10.8638	0.46842	0.1543:0.0:0.8457:0.0	rs16969968;rs17486705;rs52821477;rs16969968	398	P30532	ACHA5_HUMAN	N	398	ENSP00000299565:D398N	ENSP00000299565:D398N	D	+	1	0	CHRNA5	76669980	1.000000	0.71417	0.042000	0.18584	0.027000	0.11550	6.622000	0.74233	1.166000	0.42689	-0.229000	0.12294	GAT	G|0.771;A|0.229	0.229	strong		0.398	CHRNA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000290106.1		
KCNJ12	3768	hgsc.bcm.edu	37	17	21318773	21318773	+	Missense_Mutation	SNP	G	G	A	rs3752034	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:21318773G>A	ENST00000583088.1	+	3	1014	c.119G>A	c.(118-120)cGc>cAc	p.R40H	KCNJ12_ENST00000331718.5_Missense_Mutation_p.R40H	NM_021012.4	NP_066292.2	Q14500	KCJ12_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 12	40					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)	CACACGCGGCGCAGGTGCCGC	0.612										Prostate(3;0.18)			.|||	1734	0.346246	0.1505	0.366	5008	,	,		36495	0.4812		0.3559	False		,,,				2504	0.4479				p.R40H		Atlas-SNP	.											KCNJ12,NS,carcinoma,+1,1	.	.	1	0			c.G119A						PASS	.	G	HIS/ARG	626,3780		0,626,1577	122.0	91.0	101.0		119	5.3	1.0	17	dbSNP_107	101	2643,5957		0,2643,1657	yes	missense	KCNJ12	NM_021012.4	29	0,3269,3234	AA,AG,GG		30.7326,14.2079,25.1346	benign	40/434	21318773	3269,9737	2203	4300	6503	SO:0001583	missense	100134444	exon3			CGCGGCGCAGGTG	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.119G>A	17.37:g.21318773G>A	ENSP00000463778:p.Arg40His	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	117	27	0.230769	NM_001194958	O43401|Q15756|Q8NG63	Missense_Mutation	SNP	ENST00000583088.1	37	CCDS11219.1	717	0.3282967032967033	78	0.15853658536585366	120	0.3314917127071823	270	0.47202797202797203	249	0.32849604221635886	G	17.23	3.337271	0.60963	0.142079	0.307326	ENSG00000184185	ENST00000331718	T	0.36699	1.24	5.33	5.33	0.75918	Potassium channel, inwardly rectifying, Kir, N-terminal (1);	0.175986	0.42964	N	0.000638	T	0.00012	0.0000	L	0.47716	1.5	0.53005	D	0.999968	B	0.20780	0.048	B	0.21546	0.035	T	0.50056	-0.8872	10	0.62326	D	0.03	.	19.026	0.92932	0.0:0.0:1.0:0.0	rs3752034;rs3752034	40	Q14500	IRK12_HUMAN	H	40	ENSP00000328150:R40H	ENSP00000328150:R40H	R	+	2	0	KCNJ12	21259366	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	6.619000	0.74219	2.506000	0.84524	0.591000	0.81541	CGC	G|0.744;A|0.256	0.256	strong		0.612	KCNJ12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255060.2	NM_021012	
PODXL	5420	hgsc.bcm.edu	37	7	131196062	131196062	+	Silent	SNP	C	C	T	rs17744792	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:131196062C>T	ENST00000378555.3	-	2	478	c.231G>A	c.(229-231)tcG>tcA	p.S77S	PODXL_ENST00000537928.1_Silent_p.S77S|PODXL_ENST00000322985.9_Silent_p.S77S|PODXL_ENST00000465001.1_5'UTR|PODXL_ENST00000541194.1_Silent_p.S79S			O00592	PODXL_HUMAN	podocalyxin-like	77	Thr-rich.				cell adhesion (GO:0007155)|cell migration (GO:0016477)|epithelial tube formation (GO:0072175)|glomerular visceral epithelial cell development (GO:0072015)|leukocyte migration (GO:0050900)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell-cell adhesion (GO:0022408)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-cell adhesion mediated by integrin (GO:0033634)|regulation of microvillus assembly (GO:0032534)	apical plasma membrane (GO:0016324)|cell body (GO:0044297)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|microvillus membrane (GO:0031528)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|slit diaphragm (GO:0036057)				NS(1)|breast(3)|endometrium(3)|kidney(3)|large_intestine(4)|lung(4)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	24	Melanoma(18;0.162)					TCGCCTTGACCGAGGCCAAGA	0.572													C|||	502	0.10024	0.0567	0.1369	5008	,	,		18838	0.0099		0.1849	False		,,,				2504	0.1391				p.S77S		Atlas-SNP	.											.	PODXL	53	.	0			c.G231A						PASS	.	C	,	334,4072	175.5+/-204.9	14,306,1883	174.0	167.0	169.0		231,231	-5.2	0.0	7	dbSNP_123	169	1477,7123	280.6+/-294.6	129,1219,2952	no	coding-synonymous,coding-synonymous	PODXL	NM_001018111.2,NM_005397.3	,	143,1525,4835	TT,TC,CC		17.1744,7.5806,13.9243	,	77/559,77/527	131196062	1811,11195	2203	4300	6503	SO:0001819	synonymous_variant	5420	exon2			CTTGACCGAGGCC		CCDS34755.1, CCDS47714.1	7q32-q33	2008-07-18			ENSG00000128567	ENSG00000128567			9171	protein-coding gene	gene with protein product		602632					Standard	NM_001018111		Approved	PCLP, Gp200, PC	uc003vqx.4	O00592	OTTHUMG00000154918	ENST00000378555.3:c.231G>A	7.37:g.131196062C>T		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	101	40	0.39604	NM_001018111	A6NHX8|Q52LZ7|Q53ER6	Silent	SNP	ENST00000378555.3	37	CCDS34755.1																																																																																			C|0.871;T|0.129	0.129	strong		0.572	PODXL-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000337627.2	NM_001018111	
EXOSC6	118460	hgsc.bcm.edu	37	16	70285780	70285780	+	Missense_Mutation	SNP	G	G	C	rs543954936		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:70285780G>C	ENST00000435634.1	-	1	53	c.24C>G	c.(22-24)atC>atG	p.I8M		NM_058219.2	NP_478126.1	Q5RKV6	EXOS6_HUMAN	exosome component 6	8					DNA deamination (GO:0045006)|exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|isotype switching (GO:0045190)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|RNA metabolic process (GO:0016070)|rRNA processing (GO:0006364)	cytosol (GO:0005829)|exosome (RNase complex) (GO:0000178)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)										CAGGGCCGCGGATGCGGCGGT	0.697													G|||	1	0.000199681	0.0	0.0	5008	,	,		8098	0.0		0.0	False		,,,				2504	0.001				p.I8M		Atlas-SNP	.											.	EXOSC6	1	.	0			c.C24G						PASS	.						4.0	4.0	4.0					16																	70285780		1337	2762	4099	SO:0001583	missense	118460	exon1			GCCGCGGATGCGG	BC052252	CCDS10887.1	16q22.1	2008-02-05			ENSG00000223496	ENSG00000223496			19055	protein-coding gene	gene with protein product	"""Mtr3 (mRNA transport regulator 3)-homolog (yeast)"""	606490				11719186, 12419256	Standard	NM_058219		Approved	MTR3, hMtr3p, Mtr3p, EAP4, p11	uc002eym.1	Q5RKV6	OTTHUMG00000137578	ENST00000435634.1:c.24C>G	16.37:g.70285780G>C	ENSP00000398597:p.Ile8Met	Somatic	5	0	0		WXS	Illumina HiSeq	Phase_I	18	9	0.5	NM_058219		Missense_Mutation	SNP	ENST00000435634.1	37	CCDS10887.1	.	.	.	.	.	.	.	.	.	.	N	10.08	1.251763	0.22880	.	.	ENSG00000223496	ENST00000435634	D	0.87412	-2.25	4.4	0.827	0.18835	.	0.086932	0.45126	U	0.000398	D	0.88518	0.6458	L	0.54323	1.7	0.29321	N	0.867386	D	0.61080	0.989	D	0.69654	0.965	T	0.80921	-0.1166	10	0.72032	D	0.01	-0.6466	5.5934	0.17313	0.0993:0.0:0.4371:0.4636	.	8	Q5RKV6	EXOS6_HUMAN	M	8	ENSP00000398597:I8M	ENSP00000398597:I8M	I	-	3	3	EXOSC6	68843281	0.895000	0.30542	1.000000	0.80357	0.026000	0.11368	-0.143000	0.10296	0.824000	0.34613	-0.823000	0.03104	ATC	.	.	none		0.697	EXOSC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268966.1	NM_058219	
BCL10	8915	hgsc.bcm.edu	37	1	85742012	85742012	+	Silent	SNP	G	G	C	rs11576939	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:85742012G>C	ENST00000370580.1	-	1	761	c.24C>G	c.(22-24)ctC>ctG	p.L8L	RP11-131L23.1_ENST00000426125.1_RNA|RP11-131L23.1_ENST00000427819.1_RNA	NM_003921.4	NP_003912.1	O95999	BCL10_HUMAN	B-cell CLL/lymphoma 10	8					adaptive immune response (GO:0002250)|B cell apoptotic process (GO:0001783)|cell death (GO:0008219)|cellular defense response (GO:0006968)|cellular response to mechanical stimulus (GO:0071260)|Fc-epsilon receptor signaling pathway (GO:0038095)|immunoglobulin mediated immune response (GO:0016064)|innate immune response (GO:0045087)|interleukin-6 biosynthetic process (GO:0042226)|lymphotoxin A biosynthetic process (GO:0042109)|negative regulation of mature B cell apoptotic process (GO:0002906)|neural tube closure (GO:0001843)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-8 biosynthetic process (GO:0045416)|positive regulation of mast cell cytokine production (GO:0032765)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of T cell activation (GO:0050870)|positive regulation of transcription, DNA-templated (GO:0045893)|protein homooligomerization (GO:0051260)|protein oligomerization (GO:0051259)|regulation of T cell receptor signaling pathway (GO:0050856)|response to food (GO:0032094)|response to fungus (GO:0009620)|response to molecule of bacterial origin (GO:0002237)|T cell apoptotic process (GO:0070231)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor signaling pathway (GO:0002224)	CBM complex (GO:0032449)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|immunological synapse (GO:0001772)|lysosome (GO:0005764)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	enzyme binding (GO:0019899)|kinase binding (GO:0019900)|NF-kappaB binding (GO:0051059)|protease binding (GO:0002020)|protein C-terminus binding (GO:0008022)|protein kinase B binding (GO:0043422)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|ubiquitin binding (GO:0043130)|ubiquitin protein ligase binding (GO:0031625)			haematopoietic_and_lymphoid_tissue(7)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|stomach(1)|urinary_tract(1)	19				all cancers(265;0.0114)|Epithelial(280;0.0311)		CCTCCTCGGTGAGGGACGGTG	0.716			T	IGH@	MALT								G|||	1143	0.228235	0.2663	0.2032	5008	,	,		15363	0.0744		0.3111	False		,,,				2504	0.2679				p.L8L	NSCLC(34;993 1034 12176 32621 50182)	Atlas-SNP	.		Dom	yes		1	1p22	8915	B-cell CLL/lymphoma 10		L	.	BCL10	39	.	0			c.C24G	GRCh37	CM062460	BCL10	M	rs11576939	PASS	.	G		1093,3313	394.7+/-329.4	144,805,1254	66.0	60.0	62.0		24	2.2	1.0	1	dbSNP_120	62	2637,5963	422.6+/-354.1	399,1839,2062	no	coding-synonymous	BCL10	NM_003921.4		543,2644,3316	CC,CG,GG		30.6628,24.8071,28.6791		8/234	85742012	3730,9276	2203	4300	6503	SO:0001819	synonymous_variant	8915	exon1			CTCGGTGAGGGAC	AJ006288	CCDS704.1	1p22	2008-07-18			ENSG00000142867	ENSG00000142867			989	protein-coding gene	gene with protein product	"""CARD-like apoptotic protein"", ""CARD-containing apoptotic signaling protein"", ""CARD containing molecule enhancing NF-kB"", ""caspase-recruiting domain-containing protein"", ""CARD-containing proapoptotic protein"""	603517				9989495	Standard	NM_003921		Approved	CARMEN, CIPER, mE10, c-E10, CLAP	uc021opd.1	O95999	OTTHUMG00000009965	ENST00000370580.1:c.24C>G	1.37:g.85742012G>C		Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	108	53	0.490741	NM_003921	Q5VUF1	Silent	SNP	ENST00000370580.1	37	CCDS704.1																																																																																			G|0.735;C|0.265	0.265	strong		0.716	BCL10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027612.1	NM_003921	
MUC4	4585	hgsc.bcm.edu	37	3	195513515	195513515	+	Missense_Mutation	SNP	C	C	T	rs201194776	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195513515C>T	ENST00000463781.3	-	2	5395	c.4936G>A	c.(4936-4938)Gcc>Acc	p.A1646T	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.A1646T	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0	VWFD. {ECO:0000255|PROSITE- ProRule:PRU00580}.				cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.N1637_T1652delNASSLSTGHATPLHVT(2)|p.A1646T(1)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		AGAGGGGTGGCGTGACCTGTG	0.587													.|||	3	0.000599042	0.0008	0.0014	5008	,	,		15070	0.0		0.001	False		,,,				2504	0.0				p.A1646T		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	3	Deletion - In frame(2)|Substitution - Missense(1)	stomach(2)|endometrium(1)	c.G4936A						scavenged	.						29.0	35.0	33.0					3																	195513515		689	1579	2268	SO:0001583	missense	4585	exon2			GGGTGGCGTGACC	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.4936G>A	3.37:g.195513515C>T	ENSP00000417498:p.Ala1646Thr	Somatic	190	3	0.0157895		WXS	Illumina HiSeq	Phase_I	253	42	0.166008	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	-	6.077	0.382480	0.11524	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.32272	1.46;1.47	0.605	-1.21	0.09524	.	.	.	.	.	T	0.14399	0.0348	N	0.19112	0.55	0.09310	N	1	B	0.12013	0.005	B	0.01281	0.0	T	0.21655	-1.0239	8	.	.	.	.	2.184	0.03881	0.2468:0.2138:0.0:0.5394	.	1646	E7ESK3	.	T	1646	ENSP00000417498:A1646T;ENSP00000420243:A1646T	.	A	-	1	0	MUC4	196997910	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.394000	0.07296	-2.601000	0.00451	-2.041000	0.00417	GCC	C|0.965;T|0.036	0.036	strong		0.587	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
REEP4	80346	hgsc.bcm.edu	37	8	21997738	21997738	+	Silent	SNP	A	A	T	rs35574275	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:21997738A>T	ENST00000306306.3	-	3	597	c.129T>A	c.(127-129)atT>atA	p.I43I	REEP4_ENST00000334530.5_Silent_p.I43I|REEP4_ENST00000523293.1_Silent_p.I43I	NM_025232.2	NP_079508.2	Q9H6H4	REEP4_HUMAN	receptor accessory protein 4	43					mitotic nuclear division (GO:0007067)|mitotic nuclear envelope reassembly (GO:0007084)|nuclear envelope organization (GO:0006998)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|microtubule (GO:0005874)	microtubule binding (GO:0008017)			kidney(1)|lung(3)|ovary(1)|skin(1)|urinary_tract(1)	7				Colorectal(74;0.00187)|COAD - Colon adenocarcinoma(73;0.061)|READ - Rectum adenocarcinoma(644;0.0993)		GTGCAAAAACAATCCAGTACA	0.592													A|||	220	0.0439297	0.0076	0.0346	5008	,	,		18355	0.0437		0.1133	False		,,,				2504	0.0286				p.I43I		Atlas-SNP	.											REEP4,NS,carcinoma,0,1	REEP4	13	1	0			c.T129A						PASS	.	A		103,4303	80.9+/-119.3	1,101,2101	74.0	66.0	69.0		129	-4.9	1.0	8	dbSNP_126	69	973,7627	213.4+/-253.3	60,853,3387	no	coding-synonymous	REEP4	NM_025232.2		61,954,5488	TT,TA,AA		11.314,2.3377,8.2731		43/258	21997738	1076,11930	2203	4300	6503	SO:0001819	synonymous_variant	80346	exon3			AAAAACAATCCAG	BC013048	CCDS6024.1	8p21.3	2008-05-02	2006-02-07	2006-02-07	ENSG00000168476	ENSG00000168476		"""Receptor accessory proteins"""	26176	protein-coding gene	gene with protein product		609349	"""chromosome 8 open reading frame 20"""	C8orf20		16271481, 15550249	Standard	NM_025232		Approved	FLJ22246, FLJ22277, PP432	uc003xau.1	Q9H6H4	OTTHUMG00000131491	ENST00000306306.3:c.129T>A	8.37:g.21997738A>T		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	102	78	0.764706	NM_025232	D3DSQ9|Q86VL1|Q9H6I5|Q9HBP4	Silent	SNP	ENST00000306306.3	37	CCDS6024.1																																																																																			A|0.923;T|0.077	0.077	strong		0.592	REEP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254337.2	NM_025232	
LBP	3929	hgsc.bcm.edu	37	20	37001761	37001761	+	Missense_Mutation	SNP	T	T	C	rs2232618	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:37001761T>C	ENST00000217407.2	+	13	1467	c.1306T>C	c.(1306-1308)Ttc>Ctc	p.F436L		NM_004139.3	NP_004130.2	P18428	LBP_HUMAN	lipopolysaccharide binding protein	436			F -> L (in dbSNP:rs2232618). {ECO:0000269|PubMed:2402637, ECO:0000269|PubMed:9240454, ECO:0000269|Ref.5}.		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)				CCTTAACACCTTCTACCCCAA	0.463													C|||	629	0.125599	0.2201	0.0591	5008	,	,		19471	0.0565		0.0726	False		,,,				2504	0.1708				p.F436L		Atlas-SNP	.											.	LBP	60	.	0			c.T1306C						PASS	.	C	LEU/PHE	843,3563	746.2+/-411.7	82,679,1442	112.0	102.0	106.0		1306	-1.0	0.0	20	dbSNP_98	106	774,7826	784.1+/-407.6	25,724,3551	yes	missense	LBP	NM_004139.2	22	107,1403,4993	CC,CT,TT		9.0,19.133,12.4327	benign	436/482	37001761	1617,11389	2203	4300	6503	SO:0001583	missense	3929	exon13			AACACCTTCTACC		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.1306T>C	20.37:g.37001761T>C	ENSP00000217407:p.Phe436Leu	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	55	29	0.527273	NM_004139	B2R938|O43438|Q92672|Q9H403|Q9UD66	Missense_Mutation	SNP	ENST00000217407.2	37	CCDS13304.1	188	0.08608058608058608	81	0.16463414634146342	26	0.0718232044198895	33	0.057692307692307696	48	0.0633245382585752	C	0.006	-2.060426	0.00386	0.19133	0.09	ENSG00000129988	ENST00000217407;ENST00000538599	T	0.05925	3.37	4.82	-0.996	0.10218	Lipid-binding serum glycoprotein, C-terminal (2);Bactericidal permeability-increasing protein, alpha/beta domain (1);	0.415593	0.22646	N	0.057383	T	0.00012	0.0000	N	0.00459	-1.475	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.41360	-0.9513	9	0.18276	T	0.48	-12.5231	1.2193	0.01921	0.2711:0.3029:0.2646:0.1614	rs2232618;rs3197421;rs17422694;rs52812841;rs58745877;rs2232618	436	P18428	LBP_HUMAN	L	436	ENSP00000217407:F436L	ENSP00000217407:F436L	F	+	1	0	LBP	36435175	0.002000	0.14202	0.005000	0.12908	0.001000	0.01503	-0.516000	0.06282	-0.466000	0.06943	-1.473000	0.01005	TTC	T|0.884;C|0.116	0.116	strong		0.463	LBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079174.2	NM_004139	
INCENP	3619	hgsc.bcm.edu	37	11	61895741	61895741	+	Silent	SNP	A	A	G	rs1675131	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:61895741A>G	ENST00000394818.3	+	2	310	c.108A>G	c.(106-108)gaA>gaG	p.E36E	INCENP_ENST00000278849.4_Silent_p.E36E	NM_001040694.1	NP_001035784.1	Q9NQS7	INCE_HUMAN	inner centromere protein antigens 135/155kDa	36					chromosome segregation (GO:0007059)|cytokinesis (GO:0000910)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	central element (GO:0000801)|chromocenter (GO:0010369)|chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lateral element (GO:0000800)|microtubule (GO:0005874)|midbody (GO:0030496)|pericentric heterochromatin (GO:0005721)|protein complex (GO:0043234)|spindle (GO:0005819)				breast(1)|endometrium(1)|kidney(6)|large_intestine(2)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	19						GGCTTGAGGAAATCCAAGAGG	0.572													G|||	1760	0.351438	0.329	0.3818	5008	,	,		15645	0.131		0.6859	False		,,,				2504	0.2434				p.E36E		Atlas-SNP	.											.	INCENP	122	.	0			c.A108G						PASS	.	G	,	1620,2784	662.7+/-401.1	317,986,899	83.0	76.0	78.0		108,108	2.9	1.0	11	dbSNP_89	78	5907,2691	431.8+/-356.9	2041,1825,433	no	coding-synonymous,coding-synonymous	INCENP	NM_001040694.1,NM_020238.2	,	2358,2811,1332	GG,GA,AA		31.298,36.7847,42.1089	,	36/919,36/915	61895741	7527,5475	2202	4299	6501	SO:0001819	synonymous_variant	3619	exon2			TGAGGAAATCCAA	AF282265	CCDS31582.1, CCDS44624.1	11q12.3	2013-01-17	2002-08-29		ENSG00000149503	ENSG00000149503			6058	protein-coding gene	gene with protein product		604411	"""inner centromere protein antigens (135kD, 155kD)"""			1860899, 11453556	Standard	NM_001040694		Approved	FLJ31633	uc001nsw.1	Q9NQS7	OTTHUMG00000167470	ENST00000394818.3:c.108A>G	11.37:g.61895741A>G		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	69	49	0.710145	NM_001040694	A8MQD2|Q5Y192	Silent	SNP	ENST00000394818.3	37	CCDS44624.1																																																																																			A|0.521;G|0.478	0.478	strong		0.572	INCENP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000394723.2	NM_020238	
COL6A6	131873	hgsc.bcm.edu	37	3	130361856	130361856	+	Missense_Mutation	SNP	G	G	A	rs16830494	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:130361856G>A	ENST00000358511.6	+	30	5247	c.5216G>A	c.(5215-5217)cGa>cAa	p.R1739Q	COL6A6_ENST00000453409.2_Missense_Mutation_p.R1739Q	NM_001102608.1	NP_001096078.1	A6NMZ7	CO6A6_HUMAN	collagen, type VI, alpha 6	1739	Nonhelical region.		R -> Q (in dbSNP:rs16830494).		cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				NS(2)|breast(5)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(30)|lung(57)|ovary(8)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	134						CAGTATGTGCGAGACCGCAGT	0.388													G|||	607	0.121206	0.0461	0.1614	5008	,	,		18958	0.1855		0.0934	False		,,,				2504	0.1564				p.R1739Q		Atlas-SNP	.											COL6A6_ENST00000358511,colon,carcinoma,+1,2	COL6A6	497	2	0			c.G5216A						PASS	.	G	GLN/ARG	232,3518		5,222,1648	114.0	100.0	104.0		5216	3.1	1.0	3	dbSNP_123	104	803,7421		40,723,3349	yes	missense	COL6A6	NM_001102608.1	43	45,945,4997	AA,AG,GG		9.7641,6.1867,8.6437	probably-damaging	1739/2264	130361856	1035,10939	1875	4112	5987	SO:0001583	missense	131873	exon30			ATGTGCGAGACCG	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.5216G>A	3.37:g.130361856G>A	ENSP00000351310:p.Arg1739Gln	Somatic	272	0	0		WXS	Illumina HiSeq	Phase_I	219	117	0.534247	NM_001102608	A7DZQ0|A7DZQ1|A7DZQ2|Q69YT0	Missense_Mutation	SNP	ENST00000358511.6	37	CCDS46911.1	260	0.11904761904761904	23	0.046747967479674794	58	0.16022099447513813	107	0.18706293706293706	72	0.09498680738786279	G	15.35	2.808812	0.50421	0.061867	0.097641	ENSG00000206384	ENST00000358511;ENST00000453409	D;D	0.90504	-2.63;-2.68	5.77	3.06	0.35304	.	.	.	.	.	T	0.00637	0.0021	L	0.53249	1.67	0.34767	P	0.26665000000000005	B	0.30193	0.272	B	0.20955	0.032	T	0.32214	-0.9915	8	0.59425	D	0.04	.	9.6965	0.40161	0.2159:0.0:0.7841:0.0	rs16830494;rs56471849;rs16830494	1739	A6NMZ7	CO6A6_HUMAN	Q	1739	ENSP00000351310:R1739Q;ENSP00000399236:R1739Q	ENSP00000351310:R1739Q	R	+	2	0	COL6A6	131844546	0.995000	0.38212	0.990000	0.47175	0.931000	0.56810	1.703000	0.37846	0.387000	0.25024	-0.219000	0.12488	CGA	G|0.887;A|0.113	0.113	strong		0.388	COL6A6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356705.5	NM_001102608	
MUC4	4585	hgsc.bcm.edu	37	3	195511412	195511412	+	Missense_Mutation	SNP	T	T	A	rs199878638		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195511412T>A	ENST00000463781.3	-	2	7498	c.7039A>T	c.(7039-7041)Aca>Tca	p.T2347S	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.T2347S	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)		GCGTGACCTGTGGATGCTGAG	0.587																																					p.T2347S		Atlas-SNP	.											.	MUC4	1505	.	0			c.A7039T						PASS	.						8.0	10.0	9.0					3																	195511412		608	1542	2150	SO:0001583	missense	4585	exon2			GACCTGTGGATGC	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.7039A>T	3.37:g.195511412T>A	ENSP00000417498:p.Thr2347Ser	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	51	22	0.431373	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	T	5.227	0.227355	0.09916	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.35048	1.37;1.33	.	.	.	.	.	.	.	.	T	0.16727	0.0402	N	0.19112	0.55	0.09310	N	1	B	0.28820	0.224	B	0.18263	0.021	T	0.18429	-1.0337	7	.	.	.	.	2.6594	0.05021	0.0:0.4962:0.0:0.5038	.	2347	E7ESK3	.	S	2347	ENSP00000417498:T2347S;ENSP00000420243:T2347S	.	T	-	1	0	MUC4	196995807	0.011000	0.17503	0.023000	0.16930	0.050000	0.14768	0.288000	0.18939	0.056000	0.16144	0.055000	0.15244	ACA	.	.	weak		0.587	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
TMCO3	55002	hgsc.bcm.edu	37	13	114156093	114156093	+	Silent	SNP	C	C	T	rs2260080	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:114156093C>T	ENST00000434316.2	+	5	1202	c.843C>T	c.(841-843)tcC>tcT	p.S281S	TMCO3_ENST00000375391.1_Silent_p.S281S|TMCO3_ENST00000474393.1_3'UTR	NM_017905.4	NP_060375.4	Q6UWJ1	TMCO3_HUMAN	transmembrane and coiled-coil domains 3	281						integral component of membrane (GO:0016021)	solute:proton antiporter activity (GO:0015299)	p.S281S(1)		NS(1)|endometrium(4)|large_intestine(9)|liver(1)|lung(8)|prostate(1)|stomach(1)	25	Lung NSC(43;0.0161)|all_neural(89;0.0337)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0145)|all_epithelial(44;0.00286)|all_lung(25;0.0273)|Breast(118;0.0411)|Lung NSC(25;0.0983)	all cancers(43;0.0317)			GAATGCTGTCCTTGCCTTGTG	0.408													.|||	1207	0.241014	0.4107	0.147	5008	,	,		22189	0.2708		0.1581	False		,,,				2504	0.1329				p.S281S		Atlas-SNP	.											TMCO3,NS,carcinoma,0,1	TMCO3	77	1	1	Substitution - coding silent(1)	stomach(1)	c.C843T						PASS	.	C		1535,2871	486.2+/-360.5	264,1007,932	167.0	164.0	165.0		843	-3.1	0.1	13	dbSNP_100	165	1275,7325	252.3+/-278.5	90,1095,3115	no	coding-synonymous	TMCO3	NM_017905.4		354,2102,4047	TT,TC,CC		14.8256,34.8389,21.6054		281/678	114156093	2810,10196	2203	4300	6503	SO:0001819	synonymous_variant	55002	exon5			GCTGTCCTTGCCT	BC012564	CCDS9537.1	13q34	2008-02-05	2005-07-22	2005-07-22	ENSG00000150403	ENSG00000150403			20329	protein-coding gene	gene with protein product			"""chromosome 13 open reading frame 11"""	C13orf11			Standard	NM_017905		Approved	FLJ20623	uc001vtu.4	Q6UWJ1	OTTHUMG00000017389	ENST00000434316.2:c.843C>T	13.37:g.114156093C>T		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	101	47	0.465347	NM_017905	Q5JSB1|Q6NUN1|Q8NG29|Q8TCI6|Q96EA6|Q9NWT2	Silent	SNP	ENST00000434316.2	37	CCDS9537.1																																																																																			C|0.772;T|0.228	0.228	strong		0.408	TMCO3-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045931.3	NM_017905	
UBXN11	91544	hgsc.bcm.edu	37	1	26608879	26608879	+	Missense_Mutation	SNP	C	C	T	rs1134581|rs140364749		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:26608879C>T	ENST00000374222.1	-	16	1938	c.1474G>A	c.(1474-1476)Ggc>Agc	p.G492S	UBXN11_ENST00000314675.7_Missense_Mutation_p.G372S|UBXN11_ENST00000374221.3_Missense_Mutation_p.G492S|UBXN11_ENST00000374217.2_Missense_Mutation_p.G459S|UBXN11_ENST00000357089.4_Missense_Mutation_p.G459S|UBXN11_ENST00000374223.1_Missense_Mutation_p.G249S			Q5T124	UBX11_HUMAN	UBX domain protein 11	492	3 X 8 AA tandem repeats of P-G-P-G-P-G-P- S.|Pro-rich.		Missing.|Missing. {ECO:0000269|PubMed:14702039, ECO:0000269|Ref.2}.			cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)		p.G490_P515delGPGPSPGPGPGPSPGPGPGPSPCPGP(1)		endometrium(3)|kidney(2)|large_intestine(4)|lung(6)|ovary(2)|prostate(3)|upper_aerodigestive_tract(3)	23						ggactggggccgggaccggga	0.716																																					p.G492S		Atlas-SNP	.											UBXN11,NS,carcinoma,+2,2	UBXN11	54	2	1	Deletion - In frame(1)	ovary(1)	c.G1474A						scavenged	.						29.0	36.0	34.0					1																	26608879		1760	4012	5772	SO:0001583	missense	91544	exon16			TGGGGCCGGGACC	AF521017	CCDS41286.1, CCDS41287.1, CCDS41288.1	1p36.11	2008-07-25	2008-07-25	2008-07-25	ENSG00000158062	ENSG00000158062		"""UBX domain containing"""	30600	protein-coding gene	gene with protein product	"""socius"""	609151	"""UBX domain containing 5"""	UBXD5		11940653	Standard	NM_183008		Approved	SOC, SOCI	uc001blw.3	Q5T124	OTTHUMG00000003382	ENST00000374222.1:c.1474G>A	1.37:g.26608879C>T	ENSP00000363339:p.Gly492Ser	Somatic	29	3	0.103448		WXS	Illumina HiSeq	Phase_I	25	10	0.4	NM_183008	D3DPK6|Q5T117|Q5T120|Q5T125|Q5T126|Q5T129|Q5T131|Q5T133|Q63HM6|Q71RB3|Q8IY27|Q8N1L6|Q8N9M4|Q8NA18|Q8NFE3|Q8NFE4|Q8NFE6	Missense_Mutation	SNP	ENST00000374222.1	37	CCDS41288.1	.	.	.	.	.	.	.	.	.	.	C	0.123	-1.123266	0.01770	.	.	ENSG00000158062	ENST00000314675;ENST00000374223;ENST00000357089;ENST00000374221;ENST00000374222;ENST00000374217	T;T;T;T;T;T	0.19669	2.2;2.13;2.57;2.55;2.55;2.57	1.27	-2.55	0.06288	.	.	.	.	.	T	0.05686	0.0149	N	0.02011	-0.69	0.19575	N	0.999966	B;B;B;B	0.18461	0.028;0.015;0.028;0.016	B;B;B;B	0.06405	0.001;0.001;0.002;0.001	T	0.32188	-0.9916	9	0.16896	T	0.51	.	3.7345	0.08506	0.0:0.3022:0.1997:0.4981	rs1134581;rs3196813	459;454;372;492	Q5T124-2;Q5T124-4;Q5T124-3;Q5T124	.;.;.;UBX11_HUMAN	S	372;249;459;492;492;459	ENSP00000324721:G372S;ENSP00000363340:G249S;ENSP00000349601:G459S;ENSP00000363338:G492S;ENSP00000363339:G492S;ENSP00000363334:G459S	ENSP00000324721:G372S	G	-	1	0	UBXN11	26481466	0.000000	0.05858	0.001000	0.08648	0.012000	0.07955	-1.484000	0.02316	-1.758000	0.01315	-0.582000	0.04134	GGC	C|1.000;|0.000	.	weak		0.716	UBXN11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000009500.1	NM_145345	
PCYOX1	51449	hgsc.bcm.edu	37	2	70488470	70488470	+	Missense_Mutation	SNP	C	C	T	rs2706762	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:70488470C>T	ENST00000433351.2	+	3	474	c.446C>T	c.(445-447)tCc>tTc	p.S149F	PCYOX1_ENST00000505044.2_Missense_Mutation_p.S72F|PCYOX1_ENST00000264441.5_Missense_Mutation_p.S149F|PCYOX1_ENST00000545138.1_Missense_Mutation_p.S71F	NM_016297.3	NP_057381.3	Q9UHG3	PCYOX_HUMAN	prenylcysteine oxidase 1	149			S -> F (in dbSNP:rs2706762). {ECO:0000269|PubMed:10048485}.		prenylated protein catabolic process (GO:0030327)|prenylcysteine catabolic process (GO:0030328)|prenylcysteine metabolic process (GO:0030329)	extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	chloride-transporting ATPase activity (GO:0008555)|prenylcysteine oxidase activity (GO:0001735)			breast(1)|central_nervous_system(3)|endometrium(1)|kidney(1)|large_intestine(3)|lung(6)	15						GGATTTCAATCCCTCCGTATG	0.373													C|||	261	0.0521166	0.0083	0.0749	5008	,	,		19929	0.0		0.1362	False		,,,				2504	0.0624				p.S149F		Atlas-SNP	.											.	PCYOX1	34	.	0			c.C446T						PASS	.	C	PHE/SER	138,4268	97.1+/-135.8	6,126,2071	189.0	173.0	178.0		446	4.6	1.0	2	dbSNP_100	178	1309,7291	259.8+/-282.9	95,1119,3086	yes	missense	PCYOX1	NM_016297.3	155	101,1245,5157	TT,TC,CC		15.2209,3.1321,11.1256	benign	149/506	70488470	1447,11559	2203	4300	6503	SO:0001583	missense	51449	exon3			TTCAATCCCTCCG	AB020715	CCDS1902.1	2p13.3	2008-02-05			ENSG00000116005	ENSG00000116005	1.8.3.5		20588	protein-coding gene	gene with protein product		610995				10585463, 12186880	Standard	NM_016297		Approved	KIAA0908, PCL1	uc002sgn.4	Q9UHG3	OTTHUMG00000129671	ENST00000433351.2:c.446C>T	2.37:g.70488470C>T	ENSP00000387654:p.Ser149Phe	Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	150	72	0.48	NM_016297	B2RB14|B7Z9P8|O94982|Q8N4N5|Q96QM8	Missense_Mutation	SNP	ENST00000433351.2	37	CCDS1902.1	139	0.06364468864468864	7	0.014227642276422764	29	0.08011049723756906	0	0.0	103	0.1358839050131926	C	2.209	-0.381192	0.05000	0.031321	0.152209	ENSG00000116005	ENST00000422380;ENST00000505044;ENST00000414812;ENST00000433351;ENST00000264441;ENST00000451279;ENST00000545138	T;T;T;T;T;T;T	0.14391	2.51;2.87;2.51;2.87;2.87;2.51;2.87	5.53	4.58	0.56647	Prenylcysteine lyase (1);	0.294882	0.42420	N	0.000702	T	0.00039	0.0001	N	0.02158	-0.66	0.30738	P	0.7464919999999999	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.002	T	0.36578	-0.9742	9	0.09338	T	0.73	-2.2309	6.6505	0.22959	0.0:0.7307:0.0:0.2693	rs2706762;rs17500206;rs52827540;rs56507972;rs57406768;rs2706762	131;149	B7Z8A2;Q9UHG3	.;PCYOX_HUMAN	F	72;72;72;149;149;72;71	ENSP00000404327:S72F;ENSP00000441566:S72F;ENSP00000413178:S72F;ENSP00000387654:S149F;ENSP00000264441:S149F;ENSP00000408751:S72F;ENSP00000439916:S71F	ENSP00000264441:S149F	S	+	2	0	PCYOX1	70341974	1.000000	0.71417	1.000000	0.80357	0.820000	0.46376	2.746000	0.47467	1.448000	0.47680	0.655000	0.94253	TCC	C|0.912;T|0.088	0.088	strong		0.373	PCYOX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251872.3	NM_016297	
DNAH1	25981	hgsc.bcm.edu	37	3	52428988	52428988	+	Silent	SNP	C	C	A	rs11708581	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:52428988C>A	ENST00000420323.2	+	68	11142	c.10881C>A	c.(10879-10881)gtC>gtA	p.V3627V		NM_015512.4	NP_056327	Q9P2D7	DYH1_HUMAN	dynein, axonemal, heavy chain 1	3692					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)		AGCTGCTAGTCCTCCGCTGCC	0.597													C|||	207	0.0413339	0.0015	0.0692	5008	,	,		19827	0.0		0.1014	False		,,,				2504	0.0562				p.V3627V		Atlas-SNP	.											DNAH1_ENST00000420323,NS,carcinoma,0,2	DNAH1	534	2	0			c.C10881A						PASS	.	C		75,4057		2,71,1993	50.0	55.0	54.0		10881	-2.4	1.0	3	dbSNP_120	54	1027,7381		64,899,3241	no	coding-synonymous	DNAH1	NM_015512.4		66,970,5234	AA,AC,CC		12.2146,1.8151,8.7879		3627/4266	52428988	1102,11438	2066	4204	6270	SO:0001819	synonymous_variant	25981	exon68			GCTAGTCCTCCGC	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.10881C>A	3.37:g.52428988C>A		Somatic	268	1	0.00373134		WXS	Illumina HiSeq	Phase_I	233	101	0.433476	NM_015512	B0I1R6|O00436|O15435|O95491|Q6ZU48|Q86YK7|Q8TEJ4|Q92863|Q9H8E6|Q9UFW6|Q9Y4Z7	Silent	SNP	ENST00000420323.2	37	CCDS46842.1																																																																																			C|0.940;A|0.060	0.060	strong		0.597	DNAH1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350816.1	NM_015512	
PIGG	54872	hgsc.bcm.edu	37	4	520853	520853	+	Missense_Mutation	SNP	G	G	A	rs13114026	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:520853G>A	ENST00000453061.2	+	10	2201	c.2095G>A	c.(2095-2097)Gtc>Atc	p.V699I	PIGG_ENST00000383028.4_Missense_Mutation_p.V566I|PIGG_ENST00000296306.7_3'UTR|PIGG_ENST00000504346.1_Missense_Mutation_p.V610I|PIGG_ENST00000310340.5_Missense_Mutation_p.V691I	NM_001127178.1	NP_001120650.1	Q5H8A4	PIGG_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class G	699			V -> I (in dbSNP:rs13114026). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|GPI anchor biosynthetic process (GO:0006506)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	CP2 mannose-ethanolamine phosphotransferase activity (GO:0051267)|phosphotransferase activity, for other substituted phosphate groups (GO:0016780)	p.L689_A694delLSVLAA(1)		breast(1)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(5)|lung(16)|ovary(3)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	39						CGAGCTCTCTGTCCTGGCTGC	0.552													G|||	893	0.178315	0.2413	0.0908	5008	,	,		14770	0.2054		0.1292	False		,,,				2504	0.1779				p.V699I		Atlas-SNP	.											.	PIGG	86	.	1	Deletion - In frame(1)	ovary(1)	c.G2095A						PASS	.	G	ILE/VAL,ILE/VAL	1003,3403	370.8+/-319.7	117,769,1317	62.0	49.0	53.0		2095,2071	3.4	0.0	4	dbSNP_121	53	1035,7565	219.7+/-257.6	66,903,3331	yes	missense,missense	PIGG	NM_001127178.1,NM_017733.3	29,29	183,1672,4648	AA,AG,GG		12.0349,22.7644,15.6697	benign,benign	699/984,691/976	520853	2038,10968	2203	4300	6503	SO:0001583	missense	54872	exon10			CTCTCTGTCCTGG		CCDS3336.1, CCDS46992.1, CCDS75080.1, CCDS75081.1, CCDS75082.1, CCDS75083.1	4p16.3	2013-02-26	2006-06-28		ENSG00000174227	ENSG00000174227		"""Phosphatidylinositol glycan anchor biosynthesis"""	25985	protein-coding gene	gene with protein product			"""phosphatidylinositol glycan, class G"""			15632136	Standard	XM_005272287		Approved	FLJ20265, GPI7, LAS21	uc003gak.4	Q5H8A4	OTTHUMG00000112457	ENST00000453061.2:c.2095G>A	4.37:g.520853G>A	ENSP00000415203:p.Val699Ile	Somatic	215	0	0		WXS	Illumina HiSeq	Phase_I	226	107	0.473451	NM_001127178	B4DKC7|Q2TAK5|Q6UX31|Q7L5Y4|Q8N866|Q8NCC9|Q96SY9|Q9BVT7|Q9NXG5	Missense_Mutation	SNP	ENST00000453061.2	37	CCDS46992.1	396	0.1813186813186813	132	0.2682926829268293	37	0.10220994475138122	130	0.22727272727272727	97	0.1279683377308707	G	2.896	-0.228623	0.06022	0.227644	0.120349	ENSG00000174227	ENST00000310340;ENST00000453061;ENST00000504346;ENST00000383028	T;T;T;T	0.09255	3.32;3.33;3.0;3.0	6.06	3.39	0.38822	.	0.669240	0.16139	N	0.227810	T	0.00012	0.0000	L	0.52011	1.625	0.58432	P	1.0000000000287557E-6	B;B;B	0.30236	0.274;0.022;0.169	B;B;B	0.30401	0.115;0.01;0.086	T	0.42932	-0.9422	9	0.12766	T	0.61	-2.4778	5.1107	0.14808	0.1524:0.0:0.5552:0.2924	rs13114026;rs59899952;rs13114026	566;699;691	Q5H8A4-3;Q5H8A4;Q5H8A4-2	.;PIGG_HUMAN;.	I	691;699;610;566	ENSP00000311750:V691I;ENSP00000415203:V699I;ENSP00000424800:V610I;ENSP00000372494:V566I	ENSP00000311750:V691I	V	+	1	0	PIGG	510853	0.063000	0.20901	0.004000	0.12327	0.216000	0.24613	0.374000	0.20501	0.437000	0.26423	-0.145000	0.13849	GTC	G|0.827;A|0.173	0.173	strong		0.552	PIGG-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000357494.1	NM_017733	
RAD51AP1	10635	hgsc.bcm.edu	37	12	4662210	4662210	+	Silent	SNP	T	T	C	rs17850028	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:4662210T>C	ENST00000544927.1	+	7	628	c.618T>C	c.(616-618)tcT>tcC	p.S206S	RAD51AP1_ENST00000228843.9_Silent_p.S223S|RAD51AP1_ENST00000321524.7_Silent_p.S223S|RAD51AP1_ENST00000543041.1_Silent_p.S88S|RAD51AP1_ENST00000544931.1_3'UTR|RAD51AP1_ENST00000352618.4_Silent_p.S206S					RAD51 associated protein 1											breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(5)|upper_aerodigestive_tract(1)	13			Colorectal(7;0.00306)|COAD - Colon adenocarcinoma(12;0.0389)			AAGACTTCTCTATGAGAAAAA	0.303													T|||	256	0.0511182	0.0045	0.1816	5008	,	,		18859	0.001		0.0746	False		,,,				2504	0.0491				p.S223S		Atlas-SNP	.											.	RAD51AP1	30	.	0			c.T669C						PASS	.	T	,	70,4336	58.1+/-94.6	3,64,2136	69.0	73.0	72.0		669,618	1.2	0.1	12	dbSNP_123	72	636,7962	162.9+/-215.5	18,600,3681	no	coding-synonymous,coding-synonymous	RAD51AP1	NM_001130862.1,NM_006479.4	,	21,664,5817	CC,CT,TT		7.3971,1.5887,5.4291	,	223/353,206/336	4662210	706,12298	2203	4299	6502	SO:0001819	synonymous_variant	10635	exon8			CTTCTCTATGAGA	AF006259	CCDS8529.1, CCDS44805.1	12p13.2-p13.1	2004-09-16			ENSG00000111247	ENSG00000111247			16956	protein-coding gene	gene with protein product		603070				9396801	Standard	NM_001130862		Approved	PIR51	uc001qmw.3	Q96B01	OTTHUMG00000168125	ENST00000544927.1:c.618T>C	12.37:g.4662210T>C		Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	110	47	0.427273	NM_001130862		Silent	SNP	ENST00000544927.1	37		117	0.05357142857142857	3	0.006097560975609756	52	0.143646408839779	0	0.0	62	0.08179419525065963	T	7.243	0.601593	0.13939	0.015887	0.073971	ENSG00000111247	ENST00000536117	.	.	.	5.14	1.21	0.21127	.	.	.	.	.	T	0.00210	0.0006	.	.	.	0.53005	P	3.6000000000036E-5	.	.	.	.	.	.	T	0.12889	-1.0530	3	.	.	.	-6.5864	3.1192	0.06385	0.1766:0.1947:0.0:0.6287	rs17850028	.	.	.	H	201	.	.	Y	+	1	0	RAD51AP1	4532471	0.006000	0.16342	0.109000	0.21407	0.863000	0.49368	0.278000	0.18753	0.377000	0.24735	0.533000	0.62120	TAT	T|0.944;C|0.056	0.056	strong		0.303	RAD51AP1-012	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000399208.1	NM_006479	
CYP4F2	8529	hgsc.bcm.edu	37	19	15990431	15990431	+	Missense_Mutation	SNP	C	C	T	rs2108622	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:15990431C>T	ENST00000221700.6	-	11	1392	c.1297G>A	c.(1297-1299)Gtg>Atg	p.V433M		NM_001082.3	NP_001073.3			cytochrome P450, family 4, subfamily F, polypeptide 2											NS(2)|breast(1)|endometrium(6)|kidney(2)|large_intestine(9)|liver(1)|lung(18)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	46						TCCGGCCACACAGCTGGGTTG	0.577													.|||	1186	0.236821	0.0825	0.2378	5008	,	,		18423	0.2143		0.2903	False		,,,				2504	0.4131				p.V433M		Atlas-SNP	.											.	CYP4F2	97	.	0			c.G1297A	GRCh37	CM074767	CYP4F2	M	rs2108622	PASS	.	C	MET/VAL	428,3978	208.5+/-229.5	23,382,1798	110.0	118.0	115.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1297	1.7	0.9	19	dbSNP_96	115	2504,6096	410.8+/-350.3	379,1746,2175	yes	missense	CYP4F2	NM_001082.3	21	402,2128,3973	TT,TC,CC	http://www.ncbi.nlm.nih.gov/pubmed?term	29.1163,9.714,22.5434	probably-damaging	433/521	15990431	2932,10074	2203	4300	6503	SO:0001583	missense	8529	exon11			GCCACACAGCTGG	U02388	CCDS12336.1	19p13.12	2013-11-11	2003-01-14		ENSG00000186115	ENSG00000186115		"""Cytochrome P450s"""	2645	protein-coding gene	gene with protein product		604426	"""cytochrome P450, subfamily IVF, polypeptide 2"""			8424651, 8026587	Standard	NM_001082		Approved		uc002nbs.1	P78329	OTTHUMG00000185995	ENST00000221700.6:c.1297G>A	19.37:g.15990431C>T	ENSP00000221700:p.Val433Met	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	69	26	0.376812	NM_001082		Missense_Mutation	SNP	ENST00000221700.6	37	CCDS12336.1	470	0.21520146520146521	42	0.08536585365853659	103	0.2845303867403315	118	0.2062937062937063	207	0.27308707124010556	c	14.01	2.407803	0.42715	0.09714	0.291163	ENSG00000186115	ENST00000221700;ENST00000392846	T	0.70749	-0.51	2.78	1.72	0.24424	.	0.000000	0.56097	U	0.000026	T	0.00039	0.0001	M	0.90019	3.08	0.09310	P	1.0	D	0.89917	1.0	D	0.73380	0.98	T	0.02156	-1.1204	9	0.72032	D	0.01	.	7.54	0.27733	0.0:0.8612:0.0:0.1388	rs2108622;rs52819608;rs57319528;rs2108622	433	P78329	CP4F2_HUMAN	M	433;284	ENSP00000221700:V433M	ENSP00000221700:V433M	V	-	1	0	CYP4F2	15851431	0.942000	0.31987	0.926000	0.36857	0.526000	0.34562	1.995000	0.40767	0.476000	0.27440	0.491000	0.48974	GTG	C|0.779;T|0.221	0.221	strong		0.577	CYP4F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460372.3	NM_001082	
SLC9C1	285335	hgsc.bcm.edu	37	3	111921116	111921116	+	Missense_Mutation	SNP	C	C	A	rs9288938	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:111921116C>A	ENST00000305815.5	-	18	2555	c.2303G>T	c.(2302-2304)aGt>aTt	p.S768I	SLC9C1_ENST00000487372.1_Missense_Mutation_p.S720I	NM_183061.1	NP_898884.1	Q4G0N8	SL9C1_HUMAN	solute carrier family 9, subfamily C (Na+-transporting carboxylic acid decarboxylase), member 1	768			S -> I (in dbSNP:rs9288938). {ECO:0000269|PubMed:14702039}.		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)										CTGTTTAGAACTTGTAATCTG	0.353													C|||	1680	0.335463	0.3699	0.4049	5008	,	,		17677	0.3393		0.2376	False		,,,				2504	0.3364				p.S768I		Atlas-SNP	.											.	.	.	.	0			c.G2303T						PASS	.	C	ILE/SER	1601,2805	495.5+/-363.3	302,997,904	116.0	119.0	118.0		2303	2.0	1.0	3	dbSNP_119	118	2330,6268	388.5+/-342.6	322,1686,2291	yes	missense	SLC9A10	NM_183061.1	142	624,2683,3195	AA,AC,CC		27.0993,36.3368,30.2292	benign	768/1178	111921116	3931,9073	2203	4299	6502	SO:0001583	missense	285335	exon18			TTAGAACTTGTAA	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.2303G>T	3.37:g.111921116C>A	ENSP00000306627:p.Ser768Ile	Somatic	182	1	0.00549451		WXS	Illumina HiSeq	Phase_I	158	155	0.981013	NM_183061	Q6ZRP4|Q7RTP2	Missense_Mutation	SNP	ENST00000305815.5	37	CCDS33817.1	689	0.31547619047619047	181	0.3678861788617886	138	0.3812154696132597	185	0.32342657342657344	185	0.24406332453825857	C	15.44	2.835271	0.50951	0.363368	0.270993	ENSG00000172139	ENST00000305815;ENST00000487372	T;T	0.78364	-1.17;-1.17	5.78	1.96	0.26148	.	0.273276	0.33127	N	0.005256	T	0.00012	0.0000	M	0.62723	1.935	0.43076	P	0.005272000000000054	P;P	0.48162	0.906;0.893	P;B	0.54270	0.747;0.387	T	0.12400	-1.0549	9	0.32370	T	0.25	.	6.0804	0.19938	0.0:0.5468:0.2926:0.1606	rs9288938;rs61474261;rs9288938	720;768	Q4G0N8-2;Q4G0N8	.;S9A10_HUMAN	I	768;720	ENSP00000306627:S768I;ENSP00000420688:S720I	ENSP00000306627:S768I	S	-	2	0	SLC9A10	113403806	0.996000	0.38824	0.998000	0.56505	0.760000	0.43138	0.167000	0.16602	0.072000	0.16694	0.609000	0.83330	AGT	C|0.676;A|0.324	0.324	strong		0.353	SLC9C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354066.1	NM_183061	
GTPBP10	85865	hgsc.bcm.edu	37	7	90001496	90001496	+	Missense_Mutation	SNP	G	G	C	rs35001814	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	86	0	0		WXS	Illumina HiSeq	Phase_I	68	25	0.367647	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	
CSNK1G2	1455	hgsc.bcm.edu	37	19	1979386	1979386	+	Silent	SNP	C	C	T	rs11550450	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:1979386C>T	ENST00000255641.8	+	8	1332	c.837C>T	c.(835-837)ctC>ctT	p.L279L		NM_001319.6	NP_001310.3	P78368	KC1G2_HUMAN	casein kinase 1, gamma 2	279	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|peptide binding (GO:0042277)|protein serine/threonine kinase activity (GO:0004674)			endometrium(1)|kidney(1)|lung(3)|prostate(1)|skin(1)|stomach(1)	8		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)		TCGAGGTGCTCTGCGAGAACT	0.726													c|||	904	0.180511	0.4221	0.0605	5008	,	,		3701	0.0843		0.0875	False		,,,				2504	0.1339				p.L279L	Ovarian(91;880 1392 21236 36928 37598)	Atlas-SNP	.											.	CSNK1G2	28	.	0			c.C837T						PASS	.	C		1571,2779		263,1045,867	14.0	13.0	13.0		837	-4.3	1.0	19	dbSNP_120	13	713,7855		31,651,3602	no	coding-synonymous	CSNK1G2	NM_001319.6		294,1696,4469	TT,TC,CC		8.3217,36.1149,17.6808		279/416	1979386	2284,10634	2175	4284	6459	SO:0001819	synonymous_variant	1455	exon8			GGTGCTCTGCGAG	AF001177	CCDS12077.1	19p13.3	2013-01-17			ENSG00000133275	ENSG00000133275			2455	protein-coding gene	gene with protein product		602214				9403068	Standard	NM_001319		Approved	CK1g2	uc002lul.4	P78368		ENST00000255641.8:c.837C>T	19.37:g.1979386C>T		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	47	24	0.510638	NM_001319	B5BU42|O00704|Q8WUB1	Silent	SNP	ENST00000255641.8	37	CCDS12077.1																																																																																			C|0.820;T|0.180	0.180	strong		0.726	CSNK1G2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449287.1	NM_001319	
CFAP57	149465	hgsc.bcm.edu	37	1	43675499	43675499	+	Missense_Mutation	SNP	C	C	T	rs41301054	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:43675499C>T	ENST00000372492.4	+	11	2165	c.1841C>T	c.(1840-1842)tCg>tTg	p.S614L	WDR65_ENST00000528956.1_Missense_Mutation_p.S614L	NM_001195831.2	NP_001182760.2	Q96MR6	WDR65_HUMAN		614										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)				GTGGGCACCTCGGTGGGAACC	0.547													c|||	83	0.0165735	0.0045	0.0548	5008	,	,		19710	0.0		0.0348	False		,,,				2504	0.0041				p.S614L		Atlas-SNP	.											.	WDR65	76	.	0			c.C1841T						PASS	.	C	LEU/SER,LEU/SER,LEU/SER	44,4362	46.7+/-81.2	0,44,2159	173.0	139.0	151.0		1841,1841,1841	5.8	1.0	1	dbSNP_127	151	318,8282	112.3+/-172.5	7,304,3989	yes	missense,missense,missense	WDR65	NM_001167965.1,NM_001167966.1,NM_152498.3	145,145,145	7,348,6148	TT,TC,CC		3.6977,0.9986,2.7833	possibly-damaging,possibly-damaging,possibly-damaging	614/699,614/699,614/699	43675499	362,12644	2203	4300	6503	SO:0001583	missense	149465	exon11			GCACCTCGGTGGG																												ENST00000372492.4:c.1841C>T	1.37:g.43675499C>T	ENSP00000361570:p.Ser614Leu	Somatic	188	0	0		WXS	Illumina HiSeq	Phase_I	115	65	0.565217	NM_152498	A6NKQ3|Q17RI9|Q5TAI0	Missense_Mutation	SNP	ENST00000372492.4	37		53	0.024267399267399268	3	0.006097560975609756	26	0.0718232044198895	0	0.0	24	0.0316622691292876	c	26.1	4.707641	0.89018	0.009986	0.036977	ENSG00000243710	ENST00000372492;ENST00000528956	T;T	0.40476	1.03;3.57	5.75	5.75	0.90469	WD40/YVTN repeat-like-containing domain (1);Quinonprotein alcohol dehydrogenase-like (1);	0.150646	0.45126	D	0.000392	T	0.06142	0.0159	M	0.78456	2.415	0.53688	D	0.999976	P;P	0.42296	0.531;0.775	B;B	0.39217	0.11;0.294	T	0.07271	-1.0781	10	0.28530	T	0.3	.	19.9425	0.97170	0.0:1.0:0.0:0.0	rs41301054	614;614	Q96MR6;Q96MR6-2	WDR65_HUMAN;.	L	614	ENSP00000361570:S614L;ENSP00000435310:S614L	ENSP00000361570:S614L	S	+	2	0	WDR65	43448086	0.999000	0.42202	0.963000	0.40424	0.847000	0.48162	7.262000	0.78410	2.721000	0.93114	0.543000	0.68304	TCG	C|0.972;T|0.028	0.028	strong		0.547	WDR65-002	NOVEL	not_organism_supported|basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000384325.1		
NRXN1	9378	hgsc.bcm.edu	37	2	50779939	50779939	+	Silent	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:50779939G>A	ENST00000406316.2	-	9	3021	c.1545C>T	c.(1543-1545)ggC>ggT	p.G515G	NRXN1_ENST00000331040.5_5'UTR|NRXN1_ENST00000404971.1_Silent_p.G555G|NRXN1_ENST00000405472.3_Silent_p.G507G|NRXN1_ENST00000406859.3_Silent_p.G515G|NRXN1_ENST00000401669.2_Silent_p.G515G|NRXN1_ENST00000402717.3_Silent_p.G507G	NM_004801.4	NP_004792.1	Q9ULB1	NRX1A_HUMAN	neurexin 1	515	Laminin G-like 3. {ECO:0000255|PROSITE- ProRule:PRU00122}.				adult behavior (GO:0030534)|axon guidance (GO:0007411)|calcium-dependent cell-cell adhesion (GO:0016339)|cerebellar granule cell differentiation (GO:0021707)|establishment of protein localization (GO:0045184)|extracellular matrix organization (GO:0030198)|gamma-aminobutyric acid receptor clustering (GO:0097112)|gephyrin clustering (GO:0097116)|guanylate kinase-associated protein clustering (GO:0097117)|heterophilic cell-cell adhesion (GO:0007157)|learning (GO:0007612)|N-methyl-D-aspartate receptor clustering (GO:0097114)|negative regulation of filopodium assembly (GO:0051490)|neuroligin clustering (GO:0097118)|neuromuscular process controlling balance (GO:0050885)|neuron cell-cell adhesion (GO:0007158)|neuron maturation (GO:0042551)|neurotransmitter secretion (GO:0007269)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|postsynaptic density protein 95 clustering (GO:0097119)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|receptor localization to synapse (GO:0097120)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic vesicle clustering (GO:0097091)|vocal learning (GO:0042297)|vocalization behavior (GO:0071625)	axonal growth cone (GO:0044295)|cell junction (GO:0030054)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	acetylcholine receptor binding (GO:0033130)|calcium channel regulator activity (GO:0005246)|calcium ion binding (GO:0005509)|cell adhesion molecule binding (GO:0050839)|neuroligin family protein binding (GO:0097109)|receptor activity (GO:0004872)			breast(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(33)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	58		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.192)	Lung(47;0.0813)|LUSC - Lung squamous cell carcinoma(58;0.116)			ATAAGATGAGGCCATTTGGCT	0.433																																					p.G555G		Atlas-SNP	.											NRXN1_ENST00000536085,rectum,carcinoma,0,6	NRXN1	1118	6	0			c.C1665T						PASS	.						162.0	151.0	154.0					2																	50779939		1904	4114	6018	SO:0001819	synonymous_variant	9378	exon10			GATGAGGCCATTT	AB011150	CCDS1845.1, CCDS46282.1, CCDS54360.1	2p16.3	2008-05-15			ENSG00000179915	ENSG00000179915			8008	protein-coding gene	gene with protein product		600565					Standard	NM_001135659		Approved	KIAA0578, Hs.22998	uc021vhj.1	P58400	OTTHUMG00000129263	ENST00000406316.2:c.1545C>T	2.37:g.50779939G>A		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	261	55	0.210728	NM_001135659	A7KRL9|O60323|Q53TJ9|Q53TQ1|Q9C079|Q9C080|Q9C081|Q9H3M2|Q9UDM6	Silent	SNP	ENST00000406316.2	37	CCDS54360.1																																																																																			.	.	none		0.433	NRXN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000325291.2		
TNR	7143	hgsc.bcm.edu	37	1	175375469	175375469	+	Missense_Mutation	SNP	C	C	A	rs2239819	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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						PASS	.	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	195	0	0		WXS	Illumina HiSeq	Phase_I	190	92	0.484211	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	
E4F1	1877	hgsc.bcm.edu	37	16	2278509	2278509	+	Silent	SNP	G	G	A	rs2241070	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:2278509G>A	ENST00000301727.4	+	2	342	c.294G>A	c.(292-294)gcG>gcA	p.A98A	E4F1_ENST00000565090.1_Silent_p.A98A|E4F1_ENST00000564139.1_Silent_p.A98A	NM_004424.3	NP_004415.2	Q66K89	E4F1_HUMAN	E4F transcription factor 1	98					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						CCACCACAGCGTTGCTGGGCC	0.662													G|||	185	0.0369409	0.0038	0.0245	5008	,	,		14785	0.0625		0.0586	False		,,,				2504	0.0419				p.A98A		Atlas-SNP	.											.	E4F1	53	.	0			c.G294A						PASS	.	G		64,4328	53.6+/-89.4	1,62,2133	21.0	24.0	23.0		294	-9.6	0.0	16	dbSNP_98	23	485,8109	132.3+/-190.0	12,461,3824	no	coding-synonymous	E4F1	NM_004424.3		13,523,5957	AA,AG,GG		5.6435,1.4572,4.2276		98/785	2278509	549,12437	2196	4297	6493	SO:0001819	synonymous_variant	1877	exon2			CACAGCGTTGCTG	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.294G>A	16.37:g.2278509G>A		Somatic	213	0	0		WXS	Illumina HiSeq	Phase_I	207	42	0.202899	NM_004424	A8K2R4|O00146	Silent	SNP	ENST00000301727.4	37	CCDS32370.1																																																																																			G|0.959;A|0.041	0.041	strong		0.662	E4F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435225.1	NM_004424	
PCED1A	64773	hgsc.bcm.edu	37	20	2816821	2816821	+	Silent	SNP	C	C	T	rs2274669	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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						PASS	.	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	134	0	0		WXS	Illumina HiSeq	Phase_I	123	114	0.926829	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	
ANKIB1	54467	hgsc.bcm.edu	37	7	92027537	92027537	+	Silent	SNP	C	C	G	rs1861635	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:92027537C>G	ENST00000265742.3	+	20	2920	c.2544C>G	c.(2542-2544)tcC>tcG	p.S848S		NM_019004.1	NP_061877.1	Q9P2G1	AKIB1_HUMAN	ankyrin repeat and IBR domain containing 1	848							zinc ion binding (GO:0008270)			cervix(1)|endometrium(7)|kidney(3)|large_intestine(10)|lung(19)|skin(1)	41	all_cancers(62;2.06e-09)|all_epithelial(64;9.24e-09)|Breast(17;0.0034)|all_lung(186;0.0509)|Lung NSC(181;0.0692)		STAD - Stomach adenocarcinoma(171;6.16e-05)|all cancers(6;0.00183)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)			CTCTGAGTTCCTTGGATGAAG	0.398													C|||	775	0.154752	0.0643	0.1167	5008	,	,		16849	0.3413		0.0845	False		,,,				2504	0.184				p.S848S		Atlas-SNP	.											.	ANKIB1	92	.	0			c.C2544G						PASS	.	C		219,3475		1,217,1629	66.0	60.0	61.0		2544	5.0	1.0	7	dbSNP_92	61	788,7438		46,696,3371	no	coding-synonymous	ANKIB1	NM_019004.1		47,913,5000	GG,GC,CC		9.5794,5.9285,8.448		848/1090	92027537	1007,10913	1847	4113	5960	SO:0001819	synonymous_variant	54467	exon20			GAGTTCCTTGGAT	AB037807	CCDS47639.1	7q21.3	2013-01-10			ENSG00000001629	ENSG00000001629		"""Ankyrin repeat domain containing"""	22215	protein-coding gene	gene with protein product							Standard	NM_019004		Approved	DKFZP434A0225, KIAA1386	uc003ulw.2	Q9P2G1	OTTHUMG00000155859	ENST00000265742.3:c.2544C>G	7.37:g.92027537C>G		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	97	52	0.536082	NM_019004	Q6GMS4|Q6P3S9|Q9NTD7|Q9NW49	Silent	SNP	ENST00000265742.3	37	CCDS47639.1																																																																																			C|0.845;G|0.155	0.155	strong		0.398	ANKIB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342018.1		
CNTNAP3	79937	hgsc.bcm.edu	37	9	39085764	39085764	+	Silent	SNP	G	G	A	rs2150942		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:39085764G>A	ENST00000297668.6	-	21	3484	c.3411C>T	c.(3409-3411)gcC>gcT	p.A1137A	CNTNAP3_ENST00000358144.2_3'UTR|CNTNAP3_ENST00000377656.2_Silent_p.A1056A	NM_033655.3	NP_387504.2	Q9BZ76	CNTP3_HUMAN	contactin associated protein-like 3	1137	Laminin G-like 4. {ECO:0000255|PROSITE- ProRule:PRU00122}.				cell adhesion (GO:0007155)|cell recognition (GO:0008037)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(3)|kidney(2)|large_intestine(5)|liver(2)|lung(8)|ovary(1)|upper_aerodigestive_tract(2)	24				GBM - Glioblastoma multiforme(29;0.02)|Lung(182;0.0681)		GAGATTTGACGGCGTTGAATT	0.398																																					p.A1137A		Atlas-SNP	.											CNTNAP3,NS,carcinoma,-1,1	CNTNAP3	82	1	0			c.C3411T						scavenged	.						66.0	84.0	78.0					9																	39085764		2168	4238	6406	SO:0001819	synonymous_variant	79937	exon21			TTTGACGGCGTTG	AF333769	CCDS6616.1	9q12	2008-02-05			ENSG00000106714	ENSG00000106714			13834	protein-coding gene	gene with protein product	"""cell recognition molecule CASPR3 (FLJ14195, KIAA1714)"""	610517				12093160	Standard	NM_033655		Approved	CASPR3, KIAA1714, FLJ14195, CNTNAP3A	uc004abi.3	Q9BZ76	OTTHUMG00000019954	ENST00000297668.6:c.3411C>T	9.37:g.39085764G>A		Somatic	889	3	0.00337458		WXS	Illumina HiSeq	Phase_I	99	94	0.949495	NM_033655	B1AMA0|Q9C0E9	Silent	SNP	ENST00000297668.6	37	CCDS6616.1																																																																																			.	.	weak		0.398	CNTNAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052511.1	NM_033655	
OR1J2	26740	hgsc.bcm.edu	37	9	125273574	125273574	+	Missense_Mutation	SNP	G	G	A	rs4836891	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:125273574G>A	ENST00000335302.5	+	1	494	c.494G>A	c.(493-495)cGg>cAg	p.R165Q		NM_054107.1	NP_473448.1	Q8NGS2	OR1J2_HUMAN	olfactory receptor, family 1, subfamily J, member 2	165			R -> Q (in dbSNP:rs4836891).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.R165Q(1)		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						CTCCTGACCCGGCTGTCTTTC	0.527													G|||	561	0.112021	0.0023	0.0951	5008	,	,		20482	0.2411		0.0726	False		,,,				2504	0.18				p.R165Q		Atlas-SNP	.											OR1J2,NS,carcinoma,-1,2	OR1J2	64	2	1	Substitution - Missense(1)	stomach(1)	c.G494A						PASS	.	G	GLN/ARG	80,4326	69.8+/-107.6	1,78,2124	181.0	150.0	161.0		494	-9.2	0.0	9	dbSNP_111	161	675,7925	170.0+/-221.2	29,617,3654	yes	missense	OR1J2	NM_054107.1	43	30,695,5778	AA,AG,GG		7.8488,1.8157,5.805	benign	165/314	125273574	755,12251	2203	4300	6503	SO:0001583	missense	26740	exon1			TGACCCGGCTGTC		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.494G>A	9.37:g.125273574G>A	ENSP00000335575:p.Arg165Gln	Somatic	202	0	0		WXS	Illumina HiSeq	Phase_I	176	84	0.477273	NM_054107	A3KFL9|Q6IF14|Q96R90|Q9NZP1	Missense_Mutation	SNP	ENST00000335302.5	37	CCDS35121.1	222	0.10164835164835165	3	0.006097560975609756	27	0.07458563535911603	132	0.23076923076923078	60	0.079155672823219	G	8.495	0.862979	0.17178	0.018157	0.078488	ENSG00000197233	ENST00000335302;ENST00000444856	T	0.00145	8.67	4.68	-9.23	0.00672	GPCR, rhodopsin-like superfamily (1);	0.456810	0.15936	N	0.237439	T	0.00012	0.0000	N	0.03891	-0.335	0.80722	P	0.0	B	0.15473	0.013	B	0.12156	0.007	T	0.23084	-1.0198	9	0.18276	T	0.48	.	3.8883	0.09108	0.553:0.0908:0.1724:0.1838	rs4836891;rs4836891	165	Q8NGS2	OR1J2_HUMAN	Q	165	ENSP00000335575:R165Q	ENSP00000335575:R165Q	R	+	2	0	OR1J2	124313395	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.720000	0.00812	-1.803000	0.01242	-2.518000	0.00185	CGG	G|0.918;A|0.082	0.082	strong		0.527	OR1J2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053932.1		
OR10G2	26534	hgsc.bcm.edu	37	14	22102293	22102293	+	Missense_Mutation	SNP	C	C	T	rs41307110	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	379	3	0.00791557		WXS	Illumina HiSeq	Phase_I	143	8	0.0559441	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		
OPA3	80207	hgsc.bcm.edu	37	19	46057081	46057081	+	Silent	SNP	A	A	G	rs3826860	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:46057081A>G	ENST00000263275.4	-	2	285	c.231T>C	c.(229-231)gcT>gcC	p.A77A	OPA3_ENST00000544371.1_Silent_p.A24A|OPA3_ENST00000323060.3_Intron	NM_025136.3	NP_079412.1	Q9H6K4	OPA3_HUMAN	optic atrophy 3 (autosomal recessive, with chorea and spastic paraplegia)	77					growth (GO:0040007)|mitochondrion morphogenesis (GO:0070584)|neuromuscular process (GO:0050905)|regulation of lipid metabolic process (GO:0019216)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	mitochondrion (GO:0005739)				cervix(1)|large_intestine(1)|lung(2)	4		Ovarian(192;0.051)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.00778)|GBM - Glioblastoma multiforme(486;0.0976)|Epithelial(262;0.242)		CGCCCAGCTCAGCTGCCGCCT	0.662													G|||	3841	0.766973	0.7806	0.8055	5008	,	,		16229	0.8869		0.664	False		,,,				2504	0.7035				p.A77A		Atlas-SNP	.											OPA3_ENST00000263275,NS,carcinoma,0,1	OPA3	19	1	0			c.T231C						PASS	.		,	3339,1053		1291,757,148	17.0	20.0	19.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	,231	-5.2	0.8	19	dbSNP_107	19	5522,3068		1813,1896,586	no	intron,coding-synonymous	OPA3	NM_001017989.2,NM_025136.3	,	3104,2653,734	GG,GA,AA		35.7159,23.9754,31.744	,	,77/180	46057081	8861,4121	2196	4295	6491	SO:0001819	synonymous_variant	80207	exon2			CAGCTCAGCTGCC	AK025840	CCDS12668.1, CCDS33052.1	19q13.2-q13.3	2014-01-28				ENSG00000125741			8142	protein-coding gene	gene with protein product		606580				9097959, 11668429	Standard	NM_001017989		Approved	FLJ22187, MGA3	uc002pcj.4	Q9H6K4		ENST00000263275.4:c.231T>C	19.37:g.46057081A>G		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	50	49	0.98	NM_025136	Q6P384|Q8N784	Silent	SNP	ENST00000263275.4	37	CCDS12668.1																																																																																			A|0.295;G|0.705	0.705	strong		0.662	OPA3-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000459601.1		
SHROOM1	134549	hgsc.bcm.edu	37	5	132159393	132159393	+	Silent	SNP	G	G	A	rs33935150	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:132159393G>A	ENST00000378679.3	-	8	2679	c.1875C>T	c.(1873-1875)aaC>aaT	p.N625N	SHROOM1_ENST00000378676.1_Silent_p.N556N|SHROOM1_ENST00000488072.1_5'UTR|SHROOM1_ENST00000319854.3_Silent_p.N625N	NM_001172700.1	NP_001166171.1	Q2M3G4	SHRM1_HUMAN	shroom family member 1	625	ASD2. {ECO:0000255|PROSITE- ProRule:PRU00638}.				actin filament bundle assembly (GO:0051017)|cell morphogenesis (GO:0000902)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|myosin II complex (GO:0016460)	actin filament binding (GO:0051015)			endometrium(1)|kidney(4)|large_intestine(2)|lung(4)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	17			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			GGGTGGCAGGGTTTTCAAGCC	0.597													G|||	379	0.0756789	0.1664	0.0144	5008	,	,		17766	0.1349		0.0119	False		,,,				2504	0.001				p.N625N		Atlas-SNP	.											.	SHROOM1	35	.	0			c.C1875T						PASS	.	G	,	690,3716	281.4+/-275.9	51,588,1564	52.0	53.0	52.0		1875,1875	-0.4	0.0	5	dbSNP_126	52	21,8579	15.3+/-51.7	0,21,4279	no	coding-synonymous,coding-synonymous	SHROOM1	NM_001172700.1,NM_133456.2	,	51,609,5843	AA,AG,GG		0.2442,15.6605,5.4667	,	625/853,625/848	132159393	711,12295	2203	4300	6503	SO:0001819	synonymous_variant	134549	exon5			GGCAGGGTTTTCA	AF314142	CCDS4161.1, CCDS54902.1	5q31.1	2007-05-03			ENSG00000164403	ENSG00000164403			24084	protein-coding gene	gene with protein product		611179				11853319, 16615870	Standard	NM_133456		Approved	APXL2, KIAA1960	uc003kxy.2	Q2M3G4	OTTHUMG00000059835	ENST00000378679.3:c.1875C>T	5.37:g.132159393G>A		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	65	30	0.461538	NM_133456	B7WP40|B7ZL01|Q8TDP0|Q8TF41	Silent	SNP	ENST00000378679.3	37	CCDS54902.1																																																																																			G|0.939;A|0.061	0.061	strong		0.597	SHROOM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000133033.1	NM_133456	
MURC	347273	hgsc.bcm.edu	37	9	103348634	103348634	+	Silent	SNP	G	G	A	rs2780956	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:103348634G>A	ENST00000307584.5	+	2	1061	c.996G>A	c.(994-996)agG>agA	p.R332R		NM_001018116.1	NP_001018126.1	Q5BKX8	MURC_HUMAN	muscle-related coiled-coil protein	332					cell differentiation (GO:0030154)|muscle organ development (GO:0007517)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	Z disc (GO:0030018)				endometrium(1)|kidney(1)|large_intestine(6)|lung(7)|ovary(1)	16		Acute lymphoblastic leukemia(62;0.0461)				ATGAAGGAAGGGAAATCCCCA	0.483													G|||	1469	0.293331	0.2405	0.4784	5008	,	,		15010	0.0804		0.4254	False		,,,				2504	0.317				p.R332R		Atlas-SNP	.											.	MURC	43	.	0			c.G996A						PASS	.	G		1353,3053	445.9+/-347.8	209,935,1059	48.0	51.0	50.0		996	3.4	0.2	9	dbSNP_100	50	3583,5017	516.7+/-378.9	729,2125,1446	no	coding-synonymous	MURC	NM_001018116.1		938,3060,2505	AA,AG,GG		41.6628,30.7081,37.9517		332/365	103348634	4936,8070	2203	4300	6503	SO:0001819	synonymous_variant	347273	exon2			AGGAAGGGAAATC	BC090888	CCDS35083.1	9q31.1	2014-09-17			ENSG00000170681	ENSG00000170681			33742	protein-coding gene	gene with protein product	"""muscle-restricted coiled-coil protein"""					18508909, 18332105	Standard	NM_001018116		Approved	cavin-4, CAVIN4	uc004bba.3	Q5BKX8	OTTHUMG00000020368	ENST00000307584.5:c.996G>A	9.37:g.103348634G>A		Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	33	17	0.515152	NM_001018116	B1PRL3|B4DT88	Silent	SNP	ENST00000307584.5	37	CCDS35083.1																																																																																			G|0.649;A|0.351	0.351	strong		0.483	MURC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053419.2	NM_001018116	
SUMF1	285362	hgsc.bcm.edu	37	3	4403837	4403837	+	Silent	SNP	A	A	G	rs2633852	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:4403837A>G	ENST00000272902.5	-	9	1151	c.1116T>C	c.(1114-1116)acT>acC	p.T372T	SUMF1_ENST00000458465.2_Silent_p.T240T|SUMF1_ENST00000405420.2_Silent_p.T352T|SUMF1_ENST00000383843.5_Silent_p.T347T|SUMF1_ENST00000534863.1_Intron	NM_182760.3	NP_877437.2	Q8NBK3	SUMF1_HUMAN	sulfatase modifying factor 1	372					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)	metal ion binding (GO:0046872)|oxidoreductase activity (GO:0016491)			breast(1)|endometrium(1)|large_intestine(2)|lung(5)|prostate(1)|upper_aerodigestive_tract(3)	13		Melanoma(143;0.068)|Colorectal(144;0.233)		Epithelial(13;0.0147)|OV - Ovarian serous cystadenocarcinoma(96;0.0444)|all cancers(10;0.0549)		GTCAGTCCATAGTGGGCAGGC	0.522													G|||	3808	0.760383	0.9206	0.6945	5008	,	,		20130	0.7609		0.5905	False		,,,				2504	0.7648				p.T372T		Atlas-SNP	.											.	SUMF1	23	.	0			c.T1116C						PASS	.	G	,,	3754,652	277.2+/-273.6	1603,548,52	64.0	62.0	63.0		1041,1056,1116	0.6	0.0	3	dbSNP_100	63	4747,3853	541.5+/-384.0	1316,2115,869	no	coding-synonymous,coding-synonymous,coding-synonymous	SUMF1	NM_001164674.1,NM_001164675.1,NM_182760.3	,,	2919,2663,921	GG,GA,AA		44.8023,14.798,34.6379	,,	347/350,352/355,372/375	4403837	8501,4505	2203	4300	6503	SO:0001819	synonymous_variant	285362	exon9			GTCCATAGTGGGC	BC017005	CCDS2564.1, CCDS54548.1, CCDS54549.1	3p26.1	2009-07-23			ENSG00000144455	ENSG00000144455			20376	protein-coding gene	gene with protein product		607939				12757705, 12757706	Standard	NM_182760		Approved	FGE, UNQ3037	uc003bpz.2	Q8NBK3	OTTHUMG00000090269	ENST00000272902.5:c.1116T>C	3.37:g.4403837A>G		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	63	63	1	NM_182760	B4DXK5|B7XD05|E9PGL0|G5E9B0|Q0VAC6|Q0VAC7|Q2NL78|Q53ZE4|Q6UY39|Q96AK5|Q96DK8	Silent	SNP	ENST00000272902.5	37	CCDS2564.1																																																																																			A|0.307;G|0.693	0.693	strong		0.522	SUMF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206591.2	NM_182760	
ABCA13	154664	hgsc.bcm.edu	37	7	48313949	48313949	+	Silent	SNP	C	C	T	rs6583483	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:48313949C>T	ENST00000435803.1	+	17	4710	c.4686C>T	c.(4684-4686)taC>taT	p.Y1562Y		NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	1562					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						AAGGTATTTACTTTAACATCC	0.313													c|||	634	0.126597	0.0522	0.17	5008	,	,		18245	0.1518		0.1074	False		,,,				2504	0.1902				p.Y1562Y		Atlas-SNP	.											.	ABCA13	1192	.	0			c.C4686T						PASS	.	T		219,3379		7,205,1587	61.0	62.0	62.0		4686	-3.7	0.0	7	dbSNP_116	62	884,7240		51,782,3229	no	coding-synonymous	ABCA13	NM_152701.3		58,987,4816	TT,TC,CC		10.8813,6.0867,9.4097		1562/5059	48313949	1103,10619	1799	4062	5861	SO:0001819	synonymous_variant	154664	exon17			TATTTACTTTAAC	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.4686C>T	7.37:g.48313949C>T		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	24	4	0.166667	NM_152701	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Silent	SNP	ENST00000435803.1	37	CCDS47584.1																																																																																			C|0.878;T|0.122	0.122	strong		0.313	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701	
ZFYVE27	118813	hgsc.bcm.edu	37	10	99504630	99504630	+	Missense_Mutation	SNP	G	G	T	rs10882993	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:99504630G>T	ENST00000393677.4	+	4	617	c.413G>T	c.(412-414)gGt>gTt	p.G138V	ZFYVE27_ENST00000356257.4_Missense_Mutation_p.G138V|ZFYVE27_ENST00000357540.4_Intron|ZFYVE27_ENST00000370610.3_Missense_Mutation_p.G40V|ZFYVE27_ENST00000359980.3_Missense_Mutation_p.G138V|ZFYVE27_ENST00000370613.3_Intron|ZFYVE27_ENST00000337540.7_Missense_Mutation_p.G106V|ZFYVE27_ENST00000453958.2_Missense_Mutation_p.G138V	NM_144588.6	NP_653189.3	Q5T4F4	ZFY27_HUMAN	zinc finger, FYVE domain containing 27	138			G -> V (in dbSNP:rs10882993). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005}.		cell death (GO:0008219)|neuron projection development (GO:0031175)|neurotrophin TRK receptor signaling pathway (GO:0048011)|protein localization to plasma membrane (GO:0072659)	axon (GO:0030424)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|growth cone membrane (GO:0032584)|integral component of membrane (GO:0016021)|recycling endosome membrane (GO:0055038)	metal ion binding (GO:0046872)			endometrium(1)|kidney(2)|large_intestine(1)|lung(1)|ovary(1)|prostate(1)|urinary_tract(1)	8		Colorectal(252;0.0846)		Epithelial(162;7.08e-10)|all cancers(201;5.18e-08)		CTGCAGAGAGGTCGCCTGTCT	0.602													T|||	3488	0.696486	0.7761	0.6023	5008	,	,		17951	0.5427		0.7962	False		,,,				2504	0.7117				p.G138V		Atlas-SNP	.											.	ZFYVE27	31	.	0			c.G413T						PASS	.	T	VAL/GLY,VAL/GLY,VAL/GLY,,VAL/GLY,,VAL/GLY	3380,1024	359.9+/-315.0	1312,756,134	42.0	36.0	38.0		413,413,317,,119,,413	4.5	0.5	10	dbSNP_120	38	6553,2047	341.2+/-323.9	2493,1567,240	yes	missense,missense,missense,intron,missense,intron,missense	ZFYVE27	NM_001002261.3,NM_001002262.3,NM_001174119.1,NM_001174120.1,NM_001174121.1,NM_001174122.1,NM_144588.6	109,109,109,,109,,109	3805,2323,374	TT,TG,GG		23.8023,23.2516,23.6158	benign,benign,benign,,benign,,benign	138/417,138/405,106/373,,40/312,,138/412	99504630	9933,3071	2202	4300	6502	SO:0001583	missense	118813	exon3			AGAGAGGTCGCCT	BC030621	CCDS31263.1, CCDS31264.1, CCDS53562.1, CCDS53563.1, CCDS53564.1, CCDS53565.1	10q24.2	2013-09-11			ENSG00000155256	ENSG00000155256		"""Zinc fingers, FYVE domain containing"""	26559	protein-coding gene	gene with protein product	"""protrudin"""	610243				14702039	Standard	NM_144588		Approved	FLJ32919, SPG33	uc001kol.2	Q5T4F4	OTTHUMG00000018867	ENST00000393677.4:c.413G>T	10.37:g.99504630G>T	ENSP00000377282:p.Gly138Val	Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	36	36	1	NM_001002261	B7Z3S0|B7Z404|B7Z626|G8JLC3|G8JLF0|J3KP98|Q5T4F1|Q5T4F2|Q5T4F3|Q8N1K0|Q8N6D6|Q8NCA0|Q8NDE4|Q96M08	Missense_Mutation	SNP	ENST00000393677.4	37	CCDS31263.1	1554	0.7115384615384616	391	0.7947154471544715	241	0.6657458563535912	325	0.5681818181818182	597	0.787598944591029	T	0.013	-1.617960	0.00828	0.767484	0.761977	ENSG00000155256	ENST00000337540;ENST00000370610;ENST00000393677;ENST00000453958;ENST00000359980;ENST00000356257;ENST00000423811	T;T;T;T;T;T;T	0.29142	1.58;1.58;1.85;1.86;1.85;1.85;1.84	5.65	4.53	0.55603	.	0.055638	0.64402	N	0.000001	T	0.00012	0.0000	N	0.01168	-0.975	0.34919	P	0.251795	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.41840	-0.9486	9	0.02654	T	1	-8.6616	8.6274	0.33897	0.0:0.0669:0.1304:0.8027	rs10882993;rs17845922;rs17858899;rs52795542;rs59456783;rs10882993	138;138;138	Q5T4F4-3;Q5T4F4-2;Q5T4F4	.;.;ZFY27_HUMAN	V	106;40;138;138;138;138;116	ENSP00000337993:G106V;ENSP00000359642:G40V;ENSP00000377282:G138V;ENSP00000401580:G138V;ENSP00000353069:G138V;ENSP00000348593:G138V;ENSP00000409594:G116V	ENSP00000337993:G106V	G	+	2	0	ZFYVE27	99494620	1.000000	0.71417	0.509000	0.27700	0.049000	0.14656	3.331000	0.52075	0.428000	0.26173	-1.182000	0.01712	GGT	G|0.267;N|0.000	.	strong		0.602	ZFYVE27-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000049745.2	NM_144588	
TGM4	7047	hgsc.bcm.edu	37	3	44943389	44943389	+	Missense_Mutation	SNP	G	G	A	rs1995641	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:44943389G>A	ENST00000296125.4	+	8	1005	c.937G>A	c.(937-939)Gag>Aag	p.E313K	RP11-272D20.2_ENST00000427258.1_RNA	NM_003241.3	NP_003232.2	P49221	TGM4_HUMAN	transglutaminase 4	313			E -> K (in dbSNP:rs1995641). {ECO:0000269|PubMed:8645175}.		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)	TGAGAATGGCGAGAAAATCAC	0.502													G|||	2780	0.555112	0.475	0.5072	5008	,	,		20918	0.7996		0.4026	False		,,,				2504	0.6022				p.E313K		Atlas-SNP	.											.	TGM4	82	.	0			c.G937A						PASS	.	G	LYS/GLU	2047,2359	567.1+/-382.1	459,1129,615	129.0	125.0	126.0		937	-3.6	0.0	3	dbSNP_92	126	3584,5016	518.5+/-379.3	737,2110,1453	yes	missense	TGM4	NM_003241.3	56	1196,3239,2068	AA,AG,GG		41.6744,46.4594,43.2954	benign	313/685	44943389	5631,7375	2203	4300	6503	SO:0001583	missense	7047	exon8			AATGGCGAGAAAA	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.937G>A	3.37:g.44943389G>A	ENSP00000296125:p.Glu313Lys	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	77	44	0.571429	NM_003241	Q16707|Q96QN4	Missense_Mutation	SNP	ENST00000296125.4	37	CCDS2723.1	1168	0.5347985347985348	221	0.4491869918699187	169	0.46685082872928174	474	0.8286713286713286	304	0.40105540897097625	G	2.365	-0.345692	0.05208	0.464594	0.416744	ENSG00000163810	ENST00000296125	T	0.50813	0.73	2.99	-3.6	0.04570	Transglutaminase-like (2);	0.318920	0.19959	N	0.102256	T	0.00012	0.0000	N	0.11698	0.16	0.80722	P	0.0	P	0.37101	0.582	B	0.31442	0.13	T	0.29792	-1.0000	9	0.35671	T	0.21	.	8.3409	0.32243	0.1763:0.1618:0.6619:0.0	rs1995641;rs60793956;rs1995641	313	P49221	TGM4_HUMAN	K	313	ENSP00000296125:E313K	ENSP00000296125:E313K	E	+	1	0	TGM4	44918393	0.508000	0.26154	0.000000	0.03702	0.006000	0.05464	0.881000	0.28173	-0.402000	0.07633	-0.471000	0.05019	GAG	G|0.521;A|0.479	0.479	strong		0.502	TGM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256755.2	NM_003241	
SLC38A10	124565	hgsc.bcm.edu	37	17	79226264	79226264	+	Missense_Mutation	SNP	T	T	C	rs35546507	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:79226264T>C	ENST00000374759.3	-	13	2059	c.1676A>G	c.(1675-1677)aAg>aGg	p.K559R	SLC38A10_ENST00000288439.5_Missense_Mutation_p.K559R	NM_001037984.1	NP_001033073.1	Q9HBR0	S38AA_HUMAN	solute carrier family 38, member 10	559			K -> R (in dbSNP:rs35546507).		amino acid transport (GO:0006865)|bone development (GO:0060348)|sodium ion transport (GO:0006814)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				NS(1)|breast(2)|endometrium(4)|kidney(2)|large_intestine(2)|lung(7)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	23	all_neural(118;0.0804)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0272)|OV - Ovarian serous cystadenocarcinoma(97;0.117)			TCCAGGCCTCTTCCCAACCTC	0.632													t|||	229	0.0457268	0.028	0.0922	5008	,	,		17467	0.0298		0.0487	False		,,,				2504	0.0501				p.K559R		Atlas-SNP	.											.	SLC38A10	133	.	0			c.A1676G						PASS	.		ARG/LYS,ARG/LYS	172,4234		7,158,2038	51.0	58.0	55.0		1676,1676	-0.2	0.0	17	dbSNP_126	55	402,8198		10,382,3908	yes	missense,missense	SLC38A10	NM_001037984.1,NM_138570.2	26,26	17,540,5946	CC,CT,TT		4.6744,3.9038,4.4133	probably-damaging,probably-damaging	559/1120,559/781	79226264	574,12432	2203	4300	6503	SO:0001583	missense	124565	exon13			GGCCTCTTCCCAA	BC014642	CCDS11780.1, CCDS42397.1	17q25.3	2013-05-22			ENSG00000157637	ENSG00000157637		"""Solute carriers"""	28237	protein-coding gene	gene with protein product							Standard	XM_005257019		Approved	MGC15523, PP1744	uc002jzz.1	Q9HBR0	OTTHUMG00000168049	ENST00000374759.3:c.1676A>G	17.37:g.79226264T>C	ENSP00000363891:p.Lys559Arg	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	73	34	0.465753	NM_001037984	Q6ZRC5|Q8NA99|Q96C66	Missense_Mutation	SNP	ENST00000374759.3	37	CCDS42397.1	100	0.045787545787545784	14	0.028455284552845527	28	0.07734806629834254	21	0.03671328671328671	37	0.048812664907651716	T	15.67	2.900984	0.52227	0.039038	0.046744	ENSG00000157637	ENST00000374759;ENST00000288439	T;T	0.11063	2.98;2.81	2.37	-0.197	0.13228	.	7739.210000	0.00166	N	0.000000	T	0.01124	0.0037	L	0.44542	1.39	0.09310	N	1	P;D	0.61697	0.763;0.99	B;D	0.69824	0.229;0.966	T	0.05599	-1.0875	10	0.46703	T	0.11	-7.9173	3.9561	0.09390	0.1948:0.4694:0.0:0.3357	rs35546507	559;559	Q9HBR0-2;Q9HBR0	.;S38AA_HUMAN	R	559	ENSP00000363891:K559R;ENSP00000288439:K559R	ENSP00000288439:K559R	K	-	2	0	SLC38A10	76840859	0.001000	0.12720	0.000000	0.03702	0.511000	0.34104	0.242000	0.18087	-0.189000	0.10482	0.248000	0.18094	AAG	T|0.957;C|0.043	0.043	strong		0.632	SLC38A10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397747.1	NM_138570	
INO80	54617	hgsc.bcm.edu	37	15	41277551	41277551	+	Silent	SNP	T	T	C	rs61757083	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:41277551T>C	ENST00000361937.3	-	32	4330	c.3906A>G	c.(3904-3906)gaA>gaG	p.E1302E	INO80_ENST00000401393.3_Silent_p.E1302E|INO80_ENST00000561244.1_5'UTR			Q9ULG1	INO80_HUMAN	INO80 complex subunit	1302	Assembles INO80 complex module consisting of conserved components INO80B, INO80C, ACTR5, RVBL1, RVBL2.				ATP catabolic process (GO:0006200)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|chromatin remodeling (GO:0006338)|DNA duplex unwinding (GO:0032508)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|mitotic sister chromatid segregation (GO:0000070)|positive regulation of cell growth (GO:0030307)|positive regulation of nuclear cell cycle DNA replication (GO:0010571)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of G1/S transition of mitotic cell cycle (GO:2000045)|spindle assembly (GO:0051225)|UV-damage excision repair (GO:0070914)	Ino80 complex (GO:0031011)|microtubule (GO:0005874)|nucleus (GO:0005634)	alpha-tubulin binding (GO:0043014)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)			NS(1)|breast(4)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(10)|ovary(3)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	49						CTGCATACTTTTCCCGCTTCC	0.502													T|||	15	0.00299521	0.0008	0.0029	5008	,	,		19721	0.0		0.0089	False		,,,				2504	0.0031				p.E1302E		Atlas-SNP	.											.	INO80	122	.	0			c.A3906G						PASS	.	T		4,4402	8.1+/-20.4	0,4,2199	229.0	179.0	196.0		3906	-0.1	1.0	15	dbSNP_129	196	94,8506	53.6+/-114.3	0,94,4206	no	coding-synonymous	INO80	NM_017553.1		0,98,6405	CC,CT,TT		1.093,0.0908,0.7535		1302/1557	41277551	98,12908	2203	4300	6503	SO:0001819	synonymous_variant	54617	exon32			ATACTTTTCCCGC	AB033085	CCDS10071.1	15q15.1	2013-08-21	2013-08-21	2008-08-07	ENSG00000128908	ENSG00000128908	3.6.1.3	"""INO80 complex subunits"""	26956	protein-coding gene	gene with protein product	"""INO80 complex subunit A"""	610169	"""INO80 complex homolog 1 (S. cerevisiae)"", ""INO80 homolog (S. cerevisiae)"""	INOC1		16298340, 16230350, 20237820	Standard	NM_017553		Approved	KIAA1259, Ino80, hINO80, INO80A	uc001zni.3	Q9ULG1	OTTHUMG00000130209	ENST00000361937.3:c.3906A>G	15.37:g.41277551T>C		Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	99	50	0.50505	NM_017553	A6H8X4|Q9NTG6	Silent	SNP	ENST00000361937.3	37	CCDS10071.1																																																																																			T|0.992;C|0.008	0.008	strong		0.502	INO80-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252527.2	NM_017553	
HLA-C	3107	hgsc.bcm.edu	37	6	31239613	31239613	+	Missense_Mutation	SNP	C	C	T	rs2308538	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:31239613C>T	ENST00000376228.5	-	2	120	c.106G>A	c.(106-108)Gtg>Atg	p.V36M	HLA-C_ENST00000383329.3_Missense_Mutation_p.V36M	NM_002117.5	NP_002108.4	Q95604	1C17_HUMAN	major histocompatibility complex, class I, C	36	Alpha-1.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	peptide antigen binding (GO:0042605)	p.V36M(2)		central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(4)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	17						GGCCGGGACACGGCGGTGTCG	0.721																																					p.V36M		Atlas-SNP	.											HLA-C_ENST00000383329,NS,carcinoma,0,2	HLA-C	92	2	2	Substitution - Missense(2)	prostate(2)	c.G106A						scavenged	.						19.0	19.0	19.0					6																	31239613		1490	2687	4177	SO:0001583	missense	3107	exon2			GGGACACGGCGGT	M11886	CCDS34393.1	6p21.3	2014-01-30			ENSG00000204525	ENSG00000204525		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4933	protein-coding gene	gene with protein product		142840	"""psoriasis susceptibility 1"""	HLA-JY3, D6S204, PSORS1		3863816, 16642438	Standard	NM_001243042		Approved		uc003nsy.3	P04222	OTTHUMG00000031154	ENST00000376228.5:c.106G>A	6.37:g.31239613C>T	ENSP00000365402:p.Val36Met	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	55	11	0.2	NM_002117	O02864|O02958|Q29643|Q9MY30	Missense_Mutation	SNP	ENST00000376228.5	37	CCDS34393.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	N|N	13.07|13.07	2.127655|2.127655	0.37533|0.37533	.|.	.|.	ENSG00000204525|ENSG00000204525	ENST00000415537|ENST00000376228;ENST00000383329;ENST00000396254;ENST00000539307	.|T;T	.|0.01092	.|5.35;5.35	2.16|2.16	2.16|2.16	0.27623|0.27623	.|MHC class I, alpha chain, alpha1/alpha2 (1);MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);	.|0.224693	.|0.20953	.|U	.|0.082710	T|T	0.01661|0.01661	0.0053|0.0053	M|M	0.63843|0.63843	1.955|1.955	0.23747|0.23747	N|N	0.996957|0.996957	.|D;D;D;D	.|0.89917	.|1.0;1.0;1.0;1.0	.|D;D;D;D	.|0.97110	.|0.999;0.999;0.999;1.0	T|T	0.53236|0.53236	-0.8467|-0.8467	5|10	.|0.30854	.|T	.|0.27	.|.	7.8706|7.8706	0.29563|0.29563	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|36;36;36;36	.|A2AEA4;A6H578;A2AEA2;P10321	.|.;.;.;1C07_HUMAN	H|M	35|36;36;36;73	.|ENSP00000365402:V36M;ENSP00000372819:V36M	.|ENSP00000365402:V36M	R|V	-|-	2|1	0|0	HLA-C|HLA-C	31347592|31347592	0.000000|0.000000	0.05858|0.05858	0.780000|0.780000	0.31762|0.31762	0.007000|0.007000	0.05969|0.05969	0.465000|0.465000	0.22004|0.22004	1.524000|1.524000	0.49035|0.49035	0.305000|0.305000	0.20034|0.20034	CGT|GTG	T|0.155;C|0.845	0.155	strong		0.721	HLA-C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076281.3	NM_002117	
AHNAK2	113146	hgsc.bcm.edu	37	14	105415264	105415264	+	Missense_Mutation	SNP	G	G	A	rs201041268	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:105415264G>A	ENST00000333244.5	-	7	6643	c.6524C>T	c.(6523-6525)tCg>tTg	p.S2175L	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	2175						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)			CACATCCACCGAGGCCTCGAT	0.582													.|||	481	0.0960463	0.1573	0.0432	5008	,	,		17715	0.0734		0.0258	False		,,,				2504	0.1462				p.S2175L		Atlas-SNP	.											AHNAK2_ENST00000333244,NS,carcinoma,0,1	AHNAK2	719	1	0			c.C6524T						scavenged	.						173.0	120.0	137.0					14																	105415264		1942	4093	6035	SO:0001583	missense	113146	exon7			TCCACCGAGGCCT	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.6524C>T	14.37:g.105415264G>A	ENSP00000353114:p.Ser2175Leu	Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	114	20	0.175439	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	.	.	.	.	.	.	.	.	.	.	N	15.11	2.736935	0.49045	.	.	ENSG00000185567	ENST00000333244	T	0.00940	5.52	3.99	3.99	0.46301	.	.	.	.	.	T	0.02727	0.0082	M	0.71920	2.185	0.09310	N	1	D	0.54601	0.967	P	0.50825	0.651	T	0.47368	-0.9123	9	0.33940	T	0.23	.	13.0355	0.58867	0.0:0.1629:0.8371:0.0	.	2175	Q8IVF2	AHNK2_HUMAN	L	2175	ENSP00000353114:S2175L	ENSP00000353114:S2175L	S	-	2	0	AHNAK2	104486309	0.000000	0.05858	0.002000	0.10522	0.032000	0.12392	0.550000	0.23345	2.082000	0.62665	0.485000	0.47835	TCG	G|0.980;A|0.019	0.019	strong		0.582	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
PSMA4	5685	hgsc.bcm.edu	37	15	78841220	78841220	+	Silent	SNP	T	T	C	rs8053	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:78841220T>C	ENST00000044462.7	+	9	870	c.720T>C	c.(718-720)caT>caC	p.H240H	PSMA4_ENST00000560217.1_Silent_p.H209H|PSMA4_ENST00000558094.1_3'UTR|PSMA4_ENST00000559082.1_Silent_p.H240H|PSMA4_ENST00000558341.1_Nonstop_Mutation_p.*126R|PSMA4_ENST00000558281.1_3'UTR|PSMA4_ENST00000413382.2_Silent_p.H169H	NM_002789.4	NP_002780.1	P25789	PSA4_HUMAN	proteasome (prosome, macropain) subunit, alpha type, 4	240					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)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome complex (GO:0000502)|proteasome core complex (GO:0005839)|proteasome core complex, alpha-subunit complex (GO:0019773)	threonine-type endopeptidase activity (GO:0004298)			kidney(2)|large_intestine(2)|lung(2)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	9						TCAAAAAACATGAGGAAGAAG	0.353													C|||	3768	0.752396	0.8389	0.7781	5008	,	,		18985	0.8522		0.6282	False		,,,				2504	0.6421				p.H240H		Atlas-SNP	.											.	PSMA4	17	.	0			c.T720C						PASS	.	C	,,	3333,1059	387.5+/-326.5	1280,773,143	74.0	75.0	75.0		720,507,720	-7.6	0.5	15	dbSNP_52	75	5001,3585	518.6+/-379.3	1472,2057,764	no	coding-synonymous,coding-synonymous,coding-synonymous	PSMA4	NM_001102667.1,NM_001102668.1,NM_002789.4	,,	2752,2830,907	CC,CT,TT		41.754,24.112,35.7836	,,	240/262,169/191,240/262	78841220	8334,4644	2196	4293	6489	SO:0001819	synonymous_variant	5685	exon9			AAAACATGAGGAA	BC005361	CCDS10303.1, CCDS45319.1	15q24.1	2004-01-19			ENSG00000041357	ENSG00000041357		"""Proteasome (prosome, macropain) subunits"""	9533	protein-coding gene	gene with protein product		176846				2025653	Standard	NM_002789		Approved	HC9, HsT17706	uc010blf.3	P25789	OTTHUMG00000143859	ENST00000044462.7:c.720T>C	15.37:g.78841220T>C		Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	170	168	0.988235	NM_001102667	D3DW86|Q53XP2|Q567Q5|Q8TBD1	Silent	SNP	ENST00000044462.7	37	CCDS10303.1																																																																																			T|0.307;C|0.693	0.693	strong		0.353	PSMA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000290107.5	NM_002789	
DYNC1H1	1778	hgsc.bcm.edu	37	14	102446161	102446161	+	Silent	SNP	G	G	A	rs3818188	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:102446161G>A	ENST00000360184.4	+	4	788	c.624G>A	c.(622-624)ccG>ccA	p.P208P		NM_001376.4	NP_001367.2	Q14204	DYHC1_HUMAN	dynein, cytoplasmic 1, heavy chain 1	208	Stem. {ECO:0000250}.				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						TCAGCCTGCCGATTCATCCAA	0.408													G|||	1044	0.208466	0.0242	0.3357	5008	,	,		19557	0.4405		0.1958	False		,,,				2504	0.1411				p.P208P		Atlas-SNP	.											.	DYNC1H1	395	.	0			c.G624A						PASS	.	G		218,4188	132.1+/-168.6	6,206,1991	129.0	136.0	134.0		624	-9.8	0.0	14	dbSNP_107	134	1642,6958	304.2+/-306.8	177,1288,2835	no	coding-synonymous	DYNC1H1	NM_001376.4		183,1494,4826	AA,AG,GG		19.093,4.9478,14.3011		208/4647	102446161	1860,11146	2203	4300	6503	SO:0001819	synonymous_variant	1778	exon4			CCTGCCGATTCAT	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.624G>A	14.37:g.102446161G>A		Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	137	72	0.525547	NM_001376	B0I1R0|Q6DKQ7|Q8WU28|Q92814|Q9Y4G5	Silent	SNP	ENST00000360184.4	37	CCDS9966.1																																																																																			G|0.812;A|0.188	0.188	strong		0.408	DYNC1H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414574.1	NM_001376	
OR51B5	282763	hgsc.bcm.edu	37	11	5364742	5364742	+	Missense_Mutation	SNP	C	C	T	rs11036913	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:5364742C>T	ENST00000300773.2	-	1	67	c.13G>A	c.(13-15)Ggc>Agc	p.G5S	HBG2_ENST00000380252.1_Intron|HBG2_ENST00000380259.2_Intron|HBE1_ENST00000380237.1_Intron|AC104389.28_ENST00000415970.1_RNA	NM_001005567.2	NP_001005567.2	Q9H339	O51B5_HUMAN	olfactory receptor, family 51, subfamily B, member 5	5			G -> S (in dbSNP:rs11036913). {ECO:0000269|PubMed:11121057, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.3}.		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)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(13)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	28		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;3.05e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TGGGAGCTGCCGCTGGACGAC	0.418													C|||	1491	0.297724	0.0847	0.438	5008	,	,		20107	0.2391		0.4304	False		,,,				2504	0.41				p.G5S		Atlas-SNP	.											.	OR51B5	60	.	0			c.G13A						PASS	.	C	SER/GLY	660,3676		80,500,1588	22.0	26.0	25.0		13	0.8	0.0	11	dbSNP_120	25	3832,4736		906,2020,1358	yes	missense	OR51B5	NM_001005567.2	56	986,2520,2946	TT,TC,CC		44.7246,15.2214,34.8109	benign	5/313	5364742	4492,8412	2168	4284	6452	SO:0001583	missense	282763	exon5			AGCTGCCGCTGGA	BK004430	CCDS31378.1	11p15.4	2012-08-09			ENSG00000242180	ENSG00000242180		"""GPCR / Class A : Olfactory receptors"""	19599	protein-coding gene	gene with protein product							Standard	NM_001005567		Approved		uc001maq.2	Q9H339	OTTHUMG00000066676	ENST00000300773.2:c.13G>A	11.37:g.5364742C>T	ENSP00000300773:p.Gly5Ser	Somatic	20	0	0		WXS	Illumina HiSeq	Phase_I	20	17	0.85	NM_001005567	B2RN59	Missense_Mutation	SNP	ENST00000300773.2	37	CCDS31378.1	659	0.3017399267399267	42	0.08536585365853659	150	0.4143646408839779	147	0.256993006993007	320	0.42216358839050133	C	5.541	0.284717	0.10513	0.152214	0.447246	ENSG00000242180	ENST00000300773	T	0.00848	5.62	4.63	0.753	0.18404	.	1.123250	0.06820	N	0.792149	T	0.00012	0.0000	N	0.00750	-1.22	0.80722	P	0.0	B	0.06786	0.001	B	0.04013	0.001	T	0.31110	-0.9955	9	0.02654	T	1	.	7.4483	0.27223	0.0:0.2764:0.0:0.7236	rs11036913;rs58626646;rs11036913	5	Q9H339	O51B5_HUMAN	S	5	ENSP00000300773:G5S	ENSP00000300773:G5S	G	-	1	0	OR51B5	5321318	0.000000	0.05858	0.002000	0.10522	0.072000	0.16883	-0.508000	0.06344	0.005000	0.14708	-0.303000	0.09236	GGC	C|0.671;T|0.329	0.329	strong		0.418	OR51B5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142975.1	NM_001005567	
RP1L1	94137	hgsc.bcm.edu	37	8	10468172	10468172	+	Missense_Mutation	SNP	G	G	A	rs4840502	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:10468172G>A	ENST00000382483.3	-	4	3659	c.3436C>T	c.(3436-3438)Cgg>Tgg	p.R1146W		NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	1146			R -> W (in dbSNP:rs4840502). {ECO:0000269|PubMed:12724644}.		cell projection organization (GO:0030030)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|visual perception (GO:0007601)	axoneme (GO:0005930)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|photoreceptor connecting cilium (GO:0032391)|photoreceptor outer segment (GO:0001750)				breast(5)|central_nervous_system(2)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(16)|lung(82)|ovary(8)|prostate(5)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(3)	148				COAD - Colon adenocarcinoma(149;0.0811)		TCCTGGTACCGAGGGGAGTCT	0.582													G|||	3546	0.708067	0.6528	0.755	5008	,	,		20051	0.5962		0.7346	False		,,,				2504	0.8374				p.R1146W		Atlas-SNP	.											RP1L1,colon,carcinoma,0,1	RP1L1	453	1	0			c.C3436T						PASS	.	G	TRP/ARG	2775,1323		933,909,207	55.0	63.0	61.0		3436	-0.2	0.0	8	dbSNP_111	61	6066,2340		2182,1702,319	yes	missense	RP1L1	NM_178857.5	101	3115,2611,526	AA,AG,GG		27.8373,32.284,29.2946	probably-damaging	1146/2401	10468172	8841,3663	2049	4203	6252	SO:0001583	missense	94137	exon4			GGTACCGAGGGGA	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.3436C>T	8.37:g.10468172G>A	ENSP00000371923:p.Arg1146Trp	Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	122	122	1	NM_178857	Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	Missense_Mutation	SNP	ENST00000382483.3	37	CCDS43708.1	1478	0.6767399267399268	308	0.6260162601626016	265	0.7320441988950276	343	0.5996503496503497	562	0.741424802110818	G	13.89	2.371741	0.42003	0.67716	0.721627	ENSG00000183638	ENST00000382483	T	0.06218	3.33	4.64	-0.17	0.13335	.	1.288700	0.06092	N	0.663905	T	0.00012	0.0000	L	0.29908	0.895	0.80722	P	0.0	D	0.89917	1.0	D	0.67548	0.952	T	0.40001	-0.9586	9	0.40728	T	0.16	-4.0825	8.7622	0.34680	0.0:0.111:0.2505:0.6386	rs4840502;rs58404957;rs4840502	1146	A6NKC6	.	W	1146	ENSP00000371923:R1146W	ENSP00000371923:R1146W	R	-	1	2	RP1L1	10505582	0.016000	0.18221	0.001000	0.08648	0.537000	0.34900	1.424000	0.34848	0.100000	0.17581	0.561000	0.74099	CGG	G|0.311;A|0.689	0.689	strong		0.582	RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375673.1		
KANK4	163782	hgsc.bcm.edu	37	1	62740065	62740065	+	Silent	SNP	A	A	G	rs12127930	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:62740065A>G	ENST00000371153.4	-	3	1089	c.711T>C	c.(709-711)ggT>ggC	p.G237G	KANK4_ENST00000354381.3_Intron|KANK4_ENST00000371150.1_5'Flank	NM_181712.4	NP_859063.3	Q5T7N3	KANK4_HUMAN	KN motif and ankyrin repeat domains 4	237	Pro-rich.					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						CCTTCACCACACCCTCTGGAG	0.537													G|||	2415	0.482228	0.6437	0.3948	5008	,	,		19899	0.248		0.4394	False		,,,				2504	0.6115				p.G237G		Atlas-SNP	.											.	KANK4	135	.	0			c.T711C						PASS	.	G		2678,1728	518.0+/-369.6	803,1072,328	48.0	45.0	46.0		711	-2.5	0.0	1	dbSNP_120	46	3673,4927	622.1+/-397.3	822,2029,1449	no	coding-synonymous	KANK4	NM_181712.4		1625,3101,1777	GG,GA,AA		42.7093,39.2192,48.8313		237/996	62740065	6351,6655	2203	4300	6503	SO:0001819	synonymous_variant	163782	exon3			CACCACACCCTCT	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.711T>C	1.37:g.62740065A>G		Somatic	220	0	0		WXS	Illumina HiSeq	Phase_I	171	78	0.45614	NM_181712	B1ALP7|Q6P9A0|Q86T71|Q86VE6|Q8NAX3	Silent	SNP	ENST00000371153.4	37	CCDS620.1																																																																																			A|0.524;G|0.476	0.476	strong		0.537	KANK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024877.1	NM_181712	
OR52L1	338751	hgsc.bcm.edu	37	11	6007899	6007899	+	Missense_Mutation	SNP	C	C	T	rs4501959	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:6007899C>T	ENST00000332249.4	-	1	316	c.262G>A	c.(262-264)Gac>Aac	p.D88N		NM_001005173.2	NP_001005173.2	Q8NGH7	O52L1_HUMAN	olfactory receptor, family 52, subfamily L, member 1	88			D -> N (in dbSNP:rs4501959). {ECO:0000269|PubMed:15489334}.			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(6)|lung(11)|pancreas(1)|skin(3)|soft_tissue(1)	30		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)		Epithelial(150;1.98e-08)|BRCA - Breast invasive adenocarcinoma(625;0.135)		AGAACCAGGTCGATGGCAGCT	0.522													.|||	838	0.167332	0.0121	0.2954	5008	,	,		22990	0.3264		0.1879	False		,,,				2504	0.1012				p.D88N	Melanoma(121;653 1666 10547 22796 51255)	Atlas-SNP	.											.	OR52L1	100	.	0			c.G262A						PASS	.	C	ASN/ASP	184,4030		2,180,1925	72.0	76.0	75.0		262	2.7	1.0	11	dbSNP_111	75	1634,6846		146,1342,2752	no	missense	OR52L1	NM_001005173.2	23	148,1522,4677	TT,TC,CC		19.2689,4.3664,14.3217	probably-damaging	88/330	6007899	1818,10876	2107	4240	6347	SO:0001583	missense	338751	exon1			CCAGGTCGATGGC	AB065819	CCDS44529.1	11p15.4	2012-08-09			ENSG00000183313	ENSG00000183313		"""GPCR / Class A : Olfactory receptors"""	14785	protein-coding gene	gene with protein product							Standard	NM_001005173		Approved		uc001mcd.2	Q8NGH7	OTTHUMG00000165374	ENST00000332249.4:c.262G>A	11.37:g.6007899C>T	ENSP00000330338:p.Asp88Asn	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	94	93	0.989362	NM_001005173	B2RPA6|Q6IFK9	Missense_Mutation	SNP	ENST00000332249.4	37	CCDS44529.1	423	0.1936813186813187	10	0.02032520325203252	91	0.2513812154696133	178	0.3111888111888112	144	0.18997361477572558	C	19.27	3.795375	0.70452	0.043664	0.192689	ENSG00000183313	ENST00000332249	T	0.66280	-0.2	3.64	2.7	0.31948	GPCR, rhodopsin-like superfamily (1);	0.000000	0.40818	N	0.001011	T	0.00012	0.0000	M	0.91249	3.19	0.25768	P	0.9848787	D	0.89917	1.0	D	0.77557	0.99	T	0.02789	-1.1110	9	0.72032	D	0.01	.	9.4286	0.38595	0.0:0.8881:0.0:0.1119	rs4501959;rs4501959	88	Q8NGH7	O52L1_HUMAN	N	88	ENSP00000330338:D88N	ENSP00000330338:D88N	D	-	1	0	OR52L1	5964475	0.928000	0.31464	0.996000	0.52242	0.752000	0.42762	1.845000	0.39279	1.747000	0.51819	0.313000	0.20887	GAC	C|0.822;T|0.178	0.178	strong		0.522	OR52L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383754.1	NM_001005173	
SDC3	9672	hgsc.bcm.edu	37	1	31351513	31351513	+	Silent	SNP	G	G	A	rs1891419	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:31351513G>A	ENST00000339394.6	-	2	387	c.213C>T	c.(211-213)ccC>ccT	p.P71P	SDC3_ENST00000336798.7_5'UTR|SDC3_ENST00000471567.1_5'UTR	NM_014654.3	NP_055469.3	O75056	SDC3_HUMAN	syndecan 3	71					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)		GTTCATCATCGGGAAAGGAGT	0.617													G|||	891	0.177915	0.0295	0.2795	5008	,	,		19140	0.1111		0.3042	False		,,,				2504	0.2454				p.P71P		Atlas-SNP	.											.	SDC3	45	.	0			c.C213T						PASS	.	G		334,4072	175.5+/-204.9	16,302,1885	130.0	115.0	120.0		213	-9.2	0.7	1	dbSNP_92	120	2428,6172	402.5+/-347.5	332,1764,2204	no	coding-synonymous	SDC3	NM_014654.3		348,2066,4089	AA,AG,GG		28.2326,7.5806,21.2364		71/443	31351513	2762,10244	2203	4300	6503	SO:0001819	synonymous_variant	9672	exon2			ATCATCGGGAAAG	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.213C>T	1.37:g.31351513G>A		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	82	39	0.47561	NM_014654	Q5T1Z6|Q5T1Z7|Q96CT3|Q96PR8	Silent	SNP	ENST00000339394.6	37	CCDS30661.1																																																																																			G|0.818;A|0.182	0.182	strong		0.617	SDC3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102017.1	NM_014654	
FAM170B	170370	hgsc.bcm.edu	37	10	50340304	50340304	+	Missense_Mutation	SNP	C	C	A	rs17773851	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:50340304C>A	ENST00000311787.5	-	2	295	c.206G>T	c.(205-207)cGg>cTg	p.R69L	FAM170B-AS1_ENST00000443389.1_RNA|FAM170B-AS1_ENST00000435809.1_RNA|FAM170B-AS1_ENST00000442525.1_RNA	NM_001164484.1	NP_001157956.1	A6NMN3	F170B_HUMAN	family with sequence similarity 170, member B	69			R -> L (in dbSNP:rs17773851).							central_nervous_system(1)|endometrium(1)|skin(1)	3						GCTCCAGTCCCGCATCCCCCG	0.632													A|||	1228	0.245208	0.118	0.3444	5008	,	,		17030	0.3075		0.2684	False		,,,				2504	0.2587				p.R69L		Atlas-SNP	.											.	FAM170B	20	.	0			c.G206T						PASS	.	A	LEU/ARG	223,1161		20,183,489	38.0	43.0	42.0		206	3.9	1.0	10	dbSNP_123	42	922,2260		148,626,817	yes	missense	FAM170B	NM_001164484.1	102	168,809,1306	AA,AC,CC		28.9755,16.1127,25.0767	benign	69/284	50340304	1145,3421	692	1591	2283	SO:0001583	missense	170370	exon2			CAGTCCCGCATCC		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.206G>T	10.37:g.50340304C>A	ENSP00000308292:p.Arg69Leu	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	71	30	0.422535	NM_001164484	Q86WY6|Q8N6K8	Missense_Mutation	SNP	ENST00000311787.5	37	CCDS53536.1	527	0.2413003663003663	61	0.12398373983739837	117	0.32320441988950277	148	0.25874125874125875	201	0.26517150395778366	A	0.262	-0.998912	0.02128	0.161127	0.289755	ENSG00000172538	ENST00000311787	T	0.27557	1.66	5.12	3.93	0.45458	.	0.372809	0.19801	N	0.105742	T	0.00012	0.0000	N	0.00237	-1.79	0.48830	P	2.889999999999837E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.41520	-0.9504	9	0.16896	T	0.51	-16.088	5.9475	0.19227	0.6642:0.1716:0.0:0.1642	rs17773851;rs52836194;rs17773851	69	A6NMN3	F170B_HUMAN	L	69	ENSP00000308292:R69L	ENSP00000308292:R69L	R	-	2	0	FAM170B	50010310	0.838000	0.29461	0.986000	0.45419	0.043000	0.13939	1.760000	0.38430	0.970000	0.38263	-0.262000	0.10625	CGG	C|0.765;A|0.235	0.235	strong		0.632	FAM170B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047974.1	XM_096317	
MCTP1	79772	hgsc.bcm.edu	37	5	94278129	94278129	+	Silent	SNP	T	T	C	rs293035	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:94278129T>C	ENST00000515393.1	-	4	983	c.984A>G	c.(982-984)gtA>gtG	p.V328V	MCTP1_ENST00000312216.8_Silent_p.V107V|MCTP1_ENST00000505208.1_Silent_p.V107V|MCTP1_ENST00000429576.2_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	70	0	0		WXS	Illumina HiSeq	Phase_I	78	34	0.435897	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	
SPTBN4	57731	hgsc.bcm.edu	37	19	41012190	41012190	+	Silent	SNP	C	C	T	rs7258094	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:41012190C>T	ENST00000352632.3	+	13	1799	c.1713C>T	c.(1711-1713)gaC>gaT	p.D571D	SPTBN4_ENST00000338932.3_Silent_p.D571D|SPTBN4_ENST00000344104.3_Silent_p.D571D|SPTBN4_ENST00000595535.1_Silent_p.D571D|SPTBN4_ENST00000598249.1_Silent_p.D571D			Q9H254	SPTN4_HUMAN	spectrin, beta, non-erythrocytic 4	571					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)			TGGAGGCAGACGACCTGTTGC	0.657													C|||	946	0.188898	0.27	0.1614	5008	,	,		18530	0.0833		0.2167	False		,,,				2504	0.1789				p.D571D		Atlas-SNP	.											.	SPTBN4	213	.	0			c.C1713T						PASS	.	C		1135,3271	403.7+/-332.8	153,829,1221	86.0	79.0	81.0		1713	-3.0	0.9	19	dbSNP_116	81	2051,6549	356.4+/-330.3	235,1581,2484	no	coding-synonymous	SPTBN4	NM_020971.2		388,2410,3705	TT,TC,CC		23.8488,25.7603,24.4964		571/2565	41012190	3186,9820	2203	4300	6503	SO:0001819	synonymous_variant	57731	exon13			GGCAGACGACCTG	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.1713C>T	19.37:g.41012190C>T		Somatic	224	0	0		WXS	Illumina HiSeq	Phase_I	190	96	0.505263	NM_020971	E9PGQ5|Q9H1K7|Q9H1K8|Q9H1K9|Q9H253|Q9H3G8|Q9HCD0	Silent	SNP	ENST00000352632.3	37	CCDS12559.1																																																																																			C|0.772;T|0.228	0.228	strong		0.657	SPTBN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462559.2		
ZFP42	132625	hgsc.bcm.edu	37	4	188924523	188924523	+	Missense_Mutation	SNP	A	A	G	rs138176771		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:188924523A>G	ENST00000326866.4	+	4	970	c.562A>G	c.(562-564)Atc>Gtc	p.I188V	ZFP42_ENST00000509524.1_Missense_Mutation_p.I188V	NM_174900.3	NP_777560.2	Q96MM3	ZFP42_HUMAN	ZFP42 zinc finger protein	188					female gonad development (GO:0008585)|in utero embryonic development (GO:0001701)|male gonad development (GO:0008584)|meiotic nuclear division (GO:0007126)|regulation of genetic imprinting (GO:2000653)|spermatid development (GO:0007286)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|protein complex (GO:0043234)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(15)|ovary(1)|skin(2)|stomach(1)	27		all_cancers(14;6.2e-52)|all_epithelial(14;7.36e-37)|all_lung(41;2.29e-15)|Lung NSC(41;6.7e-15)|Breast(6;1.53e-05)|Melanoma(20;3.01e-05)|Hepatocellular(41;0.00335)|all_hematologic(60;0.014)|Renal(120;0.0183)|Prostate(90;0.0421)|Colorectal(36;0.227)		OV - Ovarian serous cystadenocarcinoma(60;1.54e-11)|BRCA - Breast invasive adenocarcinoma(30;4.21e-06)|GBM - Glioblastoma multiforme(59;8.93e-05)|STAD - Stomach adenocarcinoma(60;0.000279)|LUSC - Lung squamous cell carcinoma(40;0.00902)|READ - Rectum adenocarcinoma(43;0.157)		TCTGAGCGCAATCGCTTGTCC	0.488													A|||	1	0.000199681	0.0	0.0	5008	,	,		17143	0.0		0.001	False		,,,				2504	0.0				p.I188V		Atlas-SNP	.											ZFP42,NS,carcinoma,-2,1	ZFP42	87	1	0			c.A562G						PASS	.	A	VAL/ILE	2,4404	4.2+/-10.8	0,2,2201	107.0	113.0	111.0		562	-7.3	0.0	4	dbSNP_134	111	5,8595	4.3+/-15.6	0,5,4295	yes	missense	ZFP42	NM_174900.3	29	0,7,6496	GG,GA,AA		0.0581,0.0454,0.0538	benign	188/311	188924523	7,12999	2203	4300	6503	SO:0001583	missense	132625	exon4			AGCGCAATCGCTT	AK056719	CCDS3849.1	4q35.2	2014-09-04	2012-11-27		ENSG00000179059	ENSG00000179059		"""Zinc fingers, C2H2-type"""	30949	protein-coding gene	gene with protein product		614572	"""zinc finger protein 42 homolog (mouse)"", ""zinc finger protein 42"""			12110702	Standard	NM_174900		Approved	REX1, ZNF754	uc003izh.1	Q96MM3	OTTHUMG00000160235	ENST00000326866.4:c.562A>G	4.37:g.188924523A>G	ENSP00000317686:p.Ile188Val	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	87	46	0.528736	NM_174900	D3DP65|Q8WXE2	Missense_Mutation	SNP	ENST00000326866.4	37	CCDS3849.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	A	6.125	0.391354	0.11581	4.54E-4	5.81E-4	ENSG00000179059	ENST00000326866;ENST00000509524	T;T	0.61742	0.08;0.08	3.64	-7.28	0.01456	Zinc finger, C2H2-like (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.115814	0.53938	D	0.000048	T	0.24044	0.0582	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.04427	-1.0952	10	0.35671	T	0.21	.	3.1416	0.06457	0.1935:0.4611:0.1484:0.197	.	188	Q96MM3	ZFP42_HUMAN	V	188	ENSP00000317686:I188V;ENSP00000424662:I188V	ENSP00000317686:I188V	I	+	1	0	ZFP42	189161517	0.000000	0.05858	0.000000	0.03702	0.026000	0.11368	-0.764000	0.04735	-3.402000	0.00170	0.533000	0.62120	ATC	A|0.999;G|0.001	0.001	strong		0.488	ZFP42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359794.1	NM_174900	
TM4SF20	79853	hgsc.bcm.edu	37	2	228230945	228230945	+	Missense_Mutation	SNP	G	G	A	rs76547437	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:228230945G>A	ENST00000304568.3	-	3	302	c.265C>T	c.(265-267)Ctt>Ttt	p.L89F		NM_024795.3	NP_079071.2	Q53R12	T4S20_HUMAN	transmembrane 4 L six family member 20	89				L -> F (in Ref. 1; AAQ89034 and 4; AAH35754). {ECO:0000305}.		integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.L89F(1)		breast(1)|kidney(2)|large_intestine(1)|lung(4)|stomach(2)	10		Renal(207;0.025)|all_lung(227;0.123)|Esophageal squamous(248;0.23)|all_hematologic(139;0.248)		Epithelial(121;3.8e-11)|all cancers(144;2.57e-08)|Lung(261;0.00942)|LUSC - Lung squamous cell carcinoma(224;0.0115)		ACACTGAAAAGTGATGAAAGA	0.383													G|||	369	0.0736821	0.0076	0.0836	5008	,	,		20917	0.0873		0.1481	False		,,,				2504	0.0654				p.L89F		Atlas-SNP	.											TM4SF20,NS,carcinoma,0,1	TM4SF20	24	1	1	Substitution - Missense(1)	stomach(1)	c.C265T						PASS	.	G	PHE/LEU	126,4280	93.0+/-131.7	4,118,2081	106.0	103.0	104.0		265	-2.0	0.0	2	dbSNP_131	104	1337,7263	261.3+/-283.8	108,1121,3071	yes	missense	TM4SF20	NM_024795.3	22	112,1239,5152	AA,AG,GG		15.5465,2.8597,11.2487	benign	89/230	228230945	1463,11543	2203	4300	6503	SO:0001583	missense	79853	exon3			TGAAAAGTGATGA	AK026453	CCDS2466.1	2q36.3	2008-02-05			ENSG00000168955	ENSG00000168955			26230	protein-coding gene	gene with protein product		615404				12975309	Standard	NM_024795		Approved	FLJ22800, TCCE518	uc002vpb.2	Q53R12	OTTHUMG00000133187	ENST00000304568.3:c.265C>T	2.37:g.228230945G>A	ENSP00000303028:p.Leu89Phe	Somatic	206	0	0		WXS	Illumina HiSeq	Phase_I	176	95	0.539773	NM_024795	B2RP42|Q5U609|Q6UWS1|Q9H5X9	Missense_Mutation	SNP	ENST00000304568.3	37	CCDS2466.1	219	0.10027472527472528	10	0.02032520325203252	32	0.08839779005524862	71	0.12412587412587413	106	0.13984168865435356	G	5.841	0.339381	0.11069	0.028597	0.155465	ENSG00000168955	ENST00000304568	T	0.41758	0.99	6.03	-1.95	0.07548	.	0.387117	0.24485	N	0.038110	T	0.00109	0.0003	L	0.50333	1.59	0.80722	P	0.0	B	0.18166	0.026	B	0.19946	0.027	T	0.05733	-1.0867	9	0.32370	T	0.25	-7.9097	0.947	0.01368	0.4163:0.1354:0.2617:0.1865	.	89	Q53R12	T4S20_HUMAN	F	89	ENSP00000303028:L89F	ENSP00000303028:L89F	L	-	1	0	TM4SF20	227939189	0.031000	0.19500	0.007000	0.13788	0.135000	0.20990	0.320000	0.19540	0.010000	0.14839	-0.136000	0.14681	CTT	G|0.895;A|0.105	0.105	strong		0.383	TM4SF20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256896.2	NM_024795	
MYBPC1	4604	hgsc.bcm.edu	37	12	102045163	102045163	+	Missense_Mutation	SNP	C	C	G	rs3817552	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:102045163C>G	ENST00000550270.1	+	14	1443	c.1443C>G	c.(1441-1443)caC>caG	p.H481Q	MYBPC1_ENST00000551300.1_Missense_Mutation_p.H382Q|MYBPC1_ENST00000549145.1_Missense_Mutation_p.H494Q|MYBPC1_ENST00000360610.2_Missense_Mutation_p.H481Q|MYBPC1_ENST00000441232.1_Missense_Mutation_p.H481Q|MYBPC1_ENST00000547405.1_Missense_Mutation_p.H455Q|RP11-755O11.2_ENST00000552081.1_RNA|MYBPC1_ENST00000541119.1_Missense_Mutation_p.H469Q|MYBPC1_ENST00000452455.2_Missense_Mutation_p.H481Q|MYBPC1_ENST00000545503.2_Missense_Mutation_p.H481Q|MYBPC1_ENST00000361466.2_Missense_Mutation_p.H506Q|MYBPC1_ENST00000553190.1_Missense_Mutation_p.H481Q|MYBPC1_ENST00000361685.2_Missense_Mutation_p.H506Q|MYBPC1_ENST00000392934.3_Missense_Mutation_p.H468Q|RP11-755O11.2_ENST00000547027.1_RNA|MYBPC1_ENST00000547509.1_Missense_Mutation_p.H467Q|MYBPC1_ENST00000536007.1_Missense_Mutation_p.H462Q|MYBPC1_ENST00000550501.1_Intron			Q00872	MYPC1_HUMAN	myosin binding protein C, slow type	481	Ig-like C2-type 4.		H -> Q (in dbSNP:rs3817552).		cell adhesion (GO:0007155)|muscle filament sliding (GO:0030049)	cytosol (GO:0005829)|myofibril (GO:0030016)|myosin filament (GO:0032982)	structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|liver(1)|lung(22)|ovary(4)|prostate(1)|skin(4)|urinary_tract(2)	57						AGGTGGTTCACAAGGGAAGGT	0.428													C|||	857	0.171126	0.1278	0.0893	5008	,	,		20876	0.2986		0.1501	False		,,,				2504	0.1779				p.H506Q		Atlas-SNP	.											.	MYBPC1	235	.	0			c.C1518G	GRCh37	CM065330	MYBPC1	M	rs3817552	PASS	.	C	GLN/HIS,GLN/HIS,GLN/HIS,GLN/HIS	571,3835	253.7+/-259.5	31,509,1663	112.0	115.0	114.0		1518,1518,1443,1443	3.6	1.0	12	dbSNP_107	114	1273,7327	253.7+/-279.3	101,1071,3128	yes	missense,missense,missense,missense	MYBPC1	NM_002465.2,NM_206819.1,NM_206820.1,NM_206821.1	24,24,24,24	132,1580,4791	GG,GC,CC		14.8023,12.9596,14.1781	probably-damaging,probably-damaging,probably-damaging,probably-damaging	506/1172,506/1149,481/1142,481/1124	102045163	1844,11162	2203	4300	6503	SO:0001583	missense	4604	exon16			GGTTCACAAGGGA		CCDS9083.1, CCDS9084.1, CCDS9085.1, CCDS55877.1, CCDS58268.1, CCDS58269.1, CCDS58270.1, CCDS58271.1, CCDS58272.1, CCDS58273.1	12q23.2	2013-02-11	2001-11-28		ENSG00000196091	ENSG00000196091		"""Myosin binding proteins"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	7549	protein-coding gene	gene with protein product		160794	"""myosin-binding protein C, slow-type"""			8375400, 16918501	Standard	NM_002465		Approved		uc010svs.2	Q00872	OTTHUMG00000170274	ENST00000550270.1:c.1443C>G	12.37:g.102045163C>G	ENSP00000449702:p.His481Gln	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	96	44	0.458333	NM_206819	B4DKR5|B7Z8G8|B7ZL02|B7ZL09|B7ZL10|E7ESM5|E7EWS6|G3XAE8|Q15497|Q17RR7|Q569K7|Q86T48|Q86TC8|Q8N3L2	Missense_Mutation	SNP	ENST00000550270.1	37	CCDS9085.1	385	0.1762820512820513	63	0.12804878048780488	36	0.09944751381215469	167	0.291958041958042	119	0.15699208443271767	C	16.76	3.211904	0.58452	0.129596	0.148023	ENSG00000196091	ENST00000547405;ENST00000452455;ENST00000441232;ENST00000360610;ENST00000392934;ENST00000547509;ENST00000361685;ENST00000549145;ENST00000553190;ENST00000540770;ENST00000545503;ENST00000536007;ENST00000541119;ENST00000361466;ENST00000551300;ENST00000550270	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.65916	-0.18;-0.18;-0.18;-0.18;-0.18;-0.18;-0.18;-0.18;-0.18;-0.18;-0.18;-0.18;-0.18;-0.18;-0.18	5.48	3.63	0.41609	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like fold (1);	0.000000	0.53938	D	0.000059	T	0.00012	0.0000	L	0.48986	1.54	0.19575	P	0.9999645718	P;D;D;D;D;D;D;D;D;D;D	0.89917	0.947;1.0;1.0;0.999;0.999;0.976;0.999;0.999;0.997;0.999;0.999	D;D;D;D;D;D;D;D;D;D;D	0.91635	0.93;0.999;0.998;0.998;0.997;0.949;0.997;0.999;0.986;0.998;0.999	T	0.15206	-1.0445	9	0.87932	D	0	.	5.075	0.14626	0.158:0.6341:0.0:0.2079	rs3817552;rs52790499;rs3817552	462;469;481;481;468;455;481;481;506;506;494	B7ZL02;B7ZL10;E7EWS6;B7ZL09;E7ESM5;Q17RR7;Q00872-3;Q00872;G3XAE8;Q00872-2;F8VZY0	.;.;.;.;.;.;.;MYPC1_HUMAN;.;.;.	Q	455;481;481;481;468;467;506;494;481;506;481;462;469;506;382;481	ENSP00000448175:H455Q;ENSP00000400908:H481Q;ENSP00000388989:H481Q;ENSP00000353822:H481Q;ENSP00000376665:H468Q;ENSP00000447362:H467Q;ENSP00000354845:H506Q;ENSP00000447660:H494Q;ENSP00000447900:H481Q;ENSP00000440034:H481Q;ENSP00000446128:H462Q;ENSP00000442847:H469Q;ENSP00000354849:H506Q;ENSP00000447116:H382Q;ENSP00000449702:H481Q	ENSP00000353822:H481Q	H	+	3	2	MYBPC1	100569294	1.000000	0.71417	1.000000	0.80357	0.722000	0.41435	2.317000	0.43770	1.289000	0.44618	0.655000	0.94253	CAC	C|0.844;G|0.156	0.156	strong		0.428	MYBPC1-024	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000408806.1		
C7orf71	285941	hgsc.bcm.edu	37	7	26678856	26678856	+	Silent	SNP	A	A	G	rs57000259	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:26678856A>G	ENST00000409974.3	+	2	809	c.93A>G	c.(91-93)agA>agG	p.R31R		NM_001145531.1	NP_001139003.1	A4D174	CG071_HUMAN	chromosome 7 open reading frame 71	31																	cagagacaagacacatgagga	0.547													G|||	1990	0.397364	0.7526	0.2536	5008	,	,		17132	0.3393		0.2763	False		,,,				2504	0.2035				p.R31R		Atlas-SNP	.											.	C7orf71	6	.	0			c.A93G						PASS	.	G		943,441		314,315,63	69.0	85.0	80.0		93	0.4	0.1	7	dbSNP_129	80	965,2217		150,665,776	no	coding-synonymous	C7orf71	NM_001145531.1		464,980,839	GG,GA,AA		30.3268,31.8642,41.7871		31/170	26678856	1908,2658	692	1591	2283	SO:0001819	synonymous_variant	285941	exon2			GACAAGACACATG		CCDS47565.1	7p15.2	2009-09-11			ENSG00000222004	ENSG00000222004			22364	protein-coding gene	gene with protein product							Standard	NM_001145531		Approved		uc003syb.3	A4D174	OTTHUMG00000152860	ENST00000409974.3:c.93A>G	7.37:g.26678856A>G		Somatic	10	0	0		WXS	Illumina HiSeq	Phase_I	18	13	0.722222	NM_001145531		Silent	SNP	ENST00000409974.3	37	CCDS47565.1																																																																																			A|0.601;G|0.399	0.399	strong		0.547	C7orf71-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328272.1	NM_001145531	
RAI1	10743	hgsc.bcm.edu	37	17	17698901	17698901	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:17698901G>A	ENST00000353383.1	+	3	3108	c.2639G>A	c.(2638-2640)aGc>aAc	p.S880N	RAI1_ENST00000261641.6_Missense_Mutation_p.S880N	NM_030665.3	NP_109590.3	Q7Z5J4	RAI1_HUMAN	retinoic acid induced 1	880					circadian regulation of gene expression (GO:0032922)|negative regulation of multicellular organism growth (GO:0040015)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	enhancer binding (GO:0035326)|zinc ion binding (GO:0008270)	p.S880N(1)		breast(1)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(14)|ovary(1)|prostate(1)|skin(5)|urinary_tract(7)	48				READ - Rectum adenocarcinoma(1115;0.0276)		CTCCTGGGCAGCCCCGAGCAG	0.662																																					p.S880N		Atlas-SNP	.											RAI1,NS,carcinoma,0,1	RAI1	121	1	1	Substitution - Missense(1)	endometrium(1)	c.G2639A						scavenged	.						28.0	26.0	27.0					17																	17698901		2203	4298	6501	SO:0001583	missense	10743	exon3			TGGGCAGCCCCGA	AJ230819	CCDS11188.1	17p11.2	2011-02-08			ENSG00000108557	ENSG00000108557			9834	protein-coding gene	gene with protein product		607642	"""Smith-Magenis syndrome chromosome region"""	SMCR		10036180	Standard	NM_030665		Approved	DKFZP434A139, SMS, KIAA1820, MGC12824	uc002grm.3	Q7Z5J4	OTTHUMG00000059314	ENST00000353383.1:c.2639G>A	17.37:g.17698901G>A	ENSP00000323074:p.Ser880Asn	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	86	2	0.0232558	NM_030665	Q8N3B4|Q8ND08|Q8WU64|Q96JK5|Q9H1C1|Q9H1C2|Q9UF69	Missense_Mutation	SNP	ENST00000353383.1	37	CCDS11188.1	.	.	.	.	.	.	.	.	.	.	G	20.9	4.061642	0.76187	.	.	ENSG00000108557	ENST00000353383;ENST00000395774;ENST00000395776;ENST00000355970;ENST00000261641;ENST00000315321	T;T;T	0.70045	-0.45;2.29;0.15	5.03	5.03	0.67393	.	0.165679	0.43919	D	0.000513	T	0.67869	0.2939	L	0.51422	1.61	0.34892	D	0.745652	D	0.57257	0.979	P	0.47528	0.549	T	0.79475	-0.1788	10	0.72032	D	0.01	.	16.5548	0.84482	0.0:0.0:1.0:0.0	.	880	Q7Z5J4	RAI1_HUMAN	N	880;880;880;880;880;832	ENSP00000323074:S880N;ENSP00000379120:S880N;ENSP00000261641:S880N	ENSP00000261641:S880N	S	+	2	0	RAI1	17639626	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	6.525000	0.73795	2.356000	0.79943	0.561000	0.74099	AGC	.	.	none		0.662	RAI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131775.1	NM_030665	
TRIT1	54802	hgsc.bcm.edu	37	1	40349131	40349131	+	Silent	SNP	G	G	A	rs3845570	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:40349131G>A	ENST00000316891.5	-	1	47	c.33C>T	c.(31-33)ccC>ccT	p.P11P	Y_RNA_ENST00000365352.1_RNA|TRIT1_ENST00000491865.1_5'UTR|TRIT1_ENST00000544981.1_Silent_p.P11P|TRIT1_ENST00000545233.1_5'Flank|TRIT1_ENST00000372818.1_Silent_p.P11P|TRIT1_ENST00000541099.1_5'Flank|TRIT1_ENST00000441669.2_Silent_p.P11P|TRIT1_ENST00000537223.1_5'Flank|TRIT1_ENST00000537440.1_5'Flank	NM_017646.4	NP_060116.2	Q9H3H1	MOD5_HUMAN	tRNA isopentenyltransferase 1	11					tRNA processing (GO:0008033)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|tRNA dimethylallyltransferase activity (GO:0052381)			breast(1)|large_intestine(5)|liver(1)|lung(3)|ovary(2)|pancreas(1)|stomach(1)|urinary_tract(1)	15	all_cancers(7;4.55e-14)|all_lung(5;1.23e-16)|all_epithelial(6;2.17e-16)|Lung NSC(20;7.03e-07)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)	OV - Ovarian serous cystadenocarcinoma(33;3.29e-18)|Epithelial(16;3.07e-17)|all cancers(16;6.21e-16)|LUSC - Lung squamous cell carcinoma(16;0.000261)|Lung(16;0.000457)			CACTGCCCACGGGAACTGCTC	0.662													A|||	2547	0.508586	0.6157	0.4107	5008	,	,		13891	0.5933		0.3946	False		,,,				2504	0.4632				p.P11P		Atlas-SNP	.											TRIT1,NS,carcinoma,0,2	TRIT1	40	2	0			c.C33T						PASS	.	A		2498,1908		718,1062,423	22.0	27.0	26.0		33	-1.0	0.0	1	dbSNP_108	26	3379,5219		654,2071,1574	no	coding-synonymous	TRIT1	NM_017646.4		1372,3133,1997	AA,AG,GG		39.2998,43.3046,45.1938		11/468	40349131	5877,7127	2203	4299	6502	SO:0001819	synonymous_variant	54802	exon1			GCCCACGGGAACT	AF074918	CCDS30681.1	1p34.2	2012-10-05			ENSG00000043514	ENSG00000043514	2.5.1.8		20286	protein-coding gene	gene with protein product						11111046, 15870694	Standard	NM_017646		Approved	FLJ20061, IPT	uc021olz.1	Q9H3H1	OTTHUMG00000009245	ENST00000316891.5:c.33C>T	1.37:g.40349131G>A		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	71	71	1	NM_017646	A1A4X7|Q3T7B5|Q5QPK5|Q5QPK6|Q6IAC9|Q96FJ3|Q96L45|Q9NXT7	Silent	SNP	ENST00000316891.5	37	CCDS30681.1																																																																																			G|0.541;A|0.459	0.459	strong		0.662	TRIT1-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025627.2	NM_017646	
FGFRL1	53834	hgsc.bcm.edu	37	4	1006333	1006333	+	Silent	SNP	G	G	A	rs4647942	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:1006333G>A	ENST00000398484.2	+	3	640	c.60G>A	c.(58-60)ccG>ccA	p.P20P	FGFRL1_ENST00000264748.6_Silent_p.P20P|FGFRL1_ENST00000510644.1_Silent_p.P20P|FGFRL1_ENST00000504138.1_Silent_p.P20P			Q8N441	FGRL1_HUMAN	fibroblast growth factor receptor-like 1	20					diaphragm development (GO:0060539)|heart valve morphogenesis (GO:0003179)|negative regulation of cell proliferation (GO:0008285)|skeletal system development (GO:0001501)|ventricular septum morphogenesis (GO:0060412)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	fibroblast growth factor-activated receptor activity (GO:0005007)|heparin binding (GO:0008201)			endometrium(1)|lung(9)|ovary(1)|prostate(1)|skin(1)	13			OV - Ovarian serous cystadenocarcinoma(23;0.0158)			GGGCCTTcccgccggccgccg	0.771													G|||	2551	0.509385	0.7375	0.4135	5008	,	,		8101	0.4583		0.492	False		,,,				2504	0.3395				p.P20P		Atlas-SNP	.											.	FGFRL1	77	.	0			c.G60A						PASS	.	G	,,	3010,1068		1128,754,157	7.0	9.0	8.0		60,60,60	1.5	0.9	4	dbSNP_111	8	4170,3724		1222,1726,999	no	coding-synonymous,coding-synonymous,coding-synonymous	FGFRL1	NM_001004356.2,NM_001004358.1,NM_021923.3	,,	2350,2480,1156	AA,AG,GG		47.1751,26.1893,40.0267	,,	20/505,20/505,20/505	1006333	7180,4792	2039	3947	5986	SO:0001819	synonymous_variant	53834	exon2			CTTCCCGCCGGCC		CCDS3344.1	4p16	2013-01-11			ENSG00000127418	ENSG00000127418		"""Immunoglobulin superfamily / I-set domain containing"""	3693	protein-coding gene	gene with protein product		605830					Standard	NM_021923		Approved		uc003gcg.3	Q8N441	OTTHUMG00000118998	ENST00000398484.2:c.60G>A	4.37:g.1006333G>A		Somatic	1	0	0		WXS	Illumina HiSeq	Phase_I	9	9	1	NM_001004356	B2RAU9|Q6PJN1|Q9BXN7|Q9H4D7	Silent	SNP	ENST00000398484.2	37	CCDS3344.1																																																																																			G|0.475;A|0.525	0.525	strong		0.771	FGFRL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239195.2	NM_021923	
AOC1	26	hgsc.bcm.edu	37	7	150557665	150557665	+	Missense_Mutation	SNP	C	C	G	rs1049793	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:150557665C>G	ENST00000493429.1	+	6	2517	c.1933C>G	c.(1933-1935)Cac>Gac	p.H645D	AOC1_ENST00000360937.4_Missense_Mutation_p.H645D|AOC1_ENST00000416793.2_Missense_Mutation_p.H664D|AOC1_ENST00000467291.1_Missense_Mutation_p.H645D|AOC1_ENST00000480582.1_3'UTR			P19801	AOC1_HUMAN	amine oxidase, copper containing 1	645			H -> D (in dbSNP:rs1049793). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:2217167, ECO:0000269|PubMed:8595053, ECO:0000269|Ref.4}.		amine metabolic process (GO:0009308)|cellular response to azide (GO:0097185)|cellular response to copper ion (GO:0071280)|cellular response to copper ion starvation (GO:0035874)|cellular response to heparin (GO:0071504)|cellular response to histamine (GO:0071420)|oxidation-reduction process (GO:0055114)|response to antibiotic (GO:0046677)|response to drug (GO:0042493)|sodium ion transmembrane transport (GO:0035725)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|peroxisome (GO:0005777)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	calcium ion binding (GO:0005509)|cation channel activity (GO:0005261)|copper ion binding (GO:0005507)|diamine oxidase activity (GO:0052597)|drug binding (GO:0008144)|heparin binding (GO:0008201)|histamine oxidase activity (GO:0052598)|methylputrescine oxidase activity (GO:0052599)|primary amine oxidase activity (GO:0008131)|propane-1,3-diamine oxidase activity (GO:0052600)|protein complex binding (GO:0032403)|protein homodimerization activity (GO:0042803)|quinone binding (GO:0048038)|receptor activity (GO:0004872)|sodium channel activity (GO:0005272)|zinc ion binding (GO:0008270)	p.H645D(1)								Amiloride(DB00594)	CGACCCCTGGCACCCGCCCGT	0.617													G|||	2270	0.453275	0.5446	0.3991	5008	,	,		18854	0.4792		0.2694	False		,,,				2504	0.5307				p.H664D		Atlas-SNP	.											ABP1,NS,carcinoma,0,1	ABP1	92	1	1	Substitution - Missense(1)	stomach(1)	c.C1990G	GRCh37	CM073993	ABP1	M	rs1049793	PASS	.	G	ASP/HIS	1945,2241		479,987,627	95.0	109.0	105.0		1933	3.1	1.0	7	dbSNP_86	105	2531,5897		402,1727,2085	yes	missense	ABP1	NM_001091.2	81	881,2714,2712	GG,GC,CC		30.0308,46.4644,35.4844	benign	645/752	150557665	4476,8138	2093	4214	6307	SO:0001583	missense	26	exon4			CCCTGGCACCCGC	AK092514	CCDS43679.1, CCDS64797.1	7q36.1	2013-06-19	2013-06-19	2013-06-19	ENSG00000002726	ENSG00000002726	1.4.3.22		80	protein-coding gene	gene with protein product	"""diamine oxidase"""	104610	"""amiloride binding protein 1 (amine oxidase (copper-containing))"""	ABP1		8182053	Standard	NM_001091		Approved	DAO	uc003wia.2	P19801	OTTHUMG00000158306	ENST00000493429.1:c.1933C>G	7.37:g.150557665C>G	ENSP00000418614:p.His645Asp	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	55	29	0.527273	NM_001272072	C9J690|Q16683|Q16684|Q56II4|Q6GU42	Missense_Mutation	SNP	ENST00000493429.1	37	CCDS43679.1	922	0.42216117216117216	267	0.5426829268292683	148	0.4088397790055249	291	0.5087412587412588	216	0.2849604221635884	G	1.200	-0.632801	0.03584	0.464644	0.300308	ENSG00000002726	ENST00000493429;ENST00000467291;ENST00000360937;ENST00000487631;ENST00000416793;ENST00000437714	T;T;T;T	0.02916	4.11;4.11;4.11;4.11	5.05	3.07	0.35406	Copper amine oxidase, C-terminal (3);	0.101712	0.64402	N	0.000003	T	0.00012	0.0000	N	0.00042	-2.48	0.40518	P	0.01919800000000005	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.42899	-0.9424	9	0.02654	T	1	-7.9873	13.8505	0.63494	0.0:0.4414:0.5586:0.0	rs1049793;rs3177802;rs17416505;rs17845408;rs17858269;rs1049793	664;645	C9J690;P19801	.;ABP1_HUMAN	D	645;645;645;171;664;521	ENSP00000418614:H645D;ENSP00000418328:H645D;ENSP00000354193:H645D;ENSP00000411613:H664D	ENSP00000354193:H645D	H	+	1	0	ABP1	150188598	0.141000	0.22595	1.000000	0.80357	0.567000	0.35839	0.377000	0.20552	0.521000	0.28445	-0.322000	0.08575	CAC	C|0.600;G|0.400	0.400	strong		0.617	AOC1-009	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350628.1	NM_001091	
PKHD1	5314	hgsc.bcm.edu	37	6	51768466	51768466	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:51768466C>T	ENST00000371117.3	-	43	7200	c.6925G>A	c.(6925-6927)Gag>Aag	p.E2309K	PKHD1_ENST00000340994.4_Missense_Mutation_p.E2309K	NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	2309					cellular calcium ion homeostasis (GO:0006874)|cilium assembly (GO:0042384)|homeostatic process (GO:0042592)|kidney development (GO:0001822)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular component movement (GO:0051271)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein kinase B signaling (GO:0051898)|positive regulation of cell proliferation (GO:0008284)|regulation of centrosome duplication (GO:0010824)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of TOR signaling (GO:0032006)|single organismal cell-cell adhesion (GO:0016337)	anchored component of external side of plasma membrane (GO:0031362)|apical plasma membrane (GO:0016324)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitotic spindle (GO:0072686)|perinuclear region of cytoplasm (GO:0048471)|primary cilium (GO:0072372)	receptor activity (GO:0004872)	p.E2309K(1)		NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(5)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(59)|lung(139)|ovary(16)|prostate(8)|skin(20)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(7)|urinary_tract(5)	304	Lung NSC(77;0.0605)					GAGAGTCCCTCGGCACCAGAA	0.428																																					p.E2309K		Atlas-SNP	.											PKHD1,colon,carcinoma,0,1	PKHD1	927	1	1	Substitution - Missense(1)	large_intestine(1)	c.G6925A						PASS	.						192.0	174.0	180.0					6																	51768466		2203	4300	6503	SO:0001583	missense	5314	exon43			GTCCCTCGGCACC	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.6925G>A	6.37:g.51768466C>T	ENSP00000360158:p.Glu2309Lys	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	98	34	0.346939	NM_170724	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Missense_Mutation	SNP	ENST00000371117.3	37	CCDS4935.1	.	.	.	.	.	.	.	.	.	.	C	19.41	3.822784	0.71028	.	.	ENSG00000170927	ENST00000371117;ENST00000340994;ENST00000393616	T;T	0.80304	-1.36;-1.36	5.87	5.87	0.94306	Pectin lyase fold/virulence factor (1);Pectin lyase fold (1);	0.376162	0.25619	N	0.029438	D	0.85066	0.5612	M	0.71581	2.175	0.40270	D	0.978272	D;D;D	0.71674	0.998;0.992;0.998	P;P;P	0.60609	0.837;0.585;0.877	T	0.83066	-0.0145	10	0.35671	T	0.21	.	17.3804	0.87403	0.0:1.0:0.0:0.0	.	2309;2309;2309	A8MVM9;P08F94-2;P08F94	.;.;PKHD1_HUMAN	K	2309	ENSP00000360158:E2309K;ENSP00000341097:E2309K	ENSP00000341097:E2309K	E	-	1	0	PKHD1	51876425	0.984000	0.35163	0.965000	0.40720	0.368000	0.29767	4.428000	0.59894	2.770000	0.95276	0.650000	0.86243	GAG	.	.	none		0.428	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694	
KIF24	347240	hgsc.bcm.edu	37	9	34310927	34310927	+	Missense_Mutation	SNP	T	T	C	rs10972048	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:34310927T>C	ENST00000402558.2	-	1	442	c.418A>G	c.(418-420)Atg>Gtg	p.M140V	KIF24_ENST00000379166.2_Missense_Mutation_p.M140V|KIF24_ENST00000379174.3_Missense_Mutation_p.M140V|KIF24_ENST00000345050.2_Missense_Mutation_p.M140V			Q5T7B8	KIF24_HUMAN	kinesin family member 24	140			M -> V (in dbSNP:rs10972048).		ATP catabolic process (GO:0006200)|cilium assembly (GO:0042384)|metabolic process (GO:0008152)|microtubule depolymerization (GO:0007019)|microtubule-based movement (GO:0007018)	centriole (GO:0005814)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|protein complex (GO:0043234)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(1)|endometrium(5)|large_intestine(4)|liver(1)|lung(13)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	32			LUSC - Lung squamous cell carcinoma(29;0.0107)			TCTGGTAGCATGTGTTCTAGC	0.398													T|||	2058	0.410942	0.1059	0.5	5008	,	,		20677	0.3353		0.6223	False		,,,				2504	0.6207				p.M140V		Atlas-SNP	.											.	KIF24	64	.	0			c.A418G						PASS	.	T	VAL/MET	691,3101		66,559,1271	179.0	170.0	173.0		418	1.9	0.9	9	dbSNP_120	173	5160,3120		1604,1952,584	yes	missense	KIF24	NM_194313.2	21	1670,2511,1855	CC,CT,TT		37.6812,18.2226,48.4675	benign	140/1369	34310927	5851,6221	1896	4140	6036	SO:0001583	missense	347240	exon2			GTAGCATGTGTTC	AK001795	CCDS6551.2	9p13.3	2013-01-10			ENSG00000186638	ENSG00000186638		"""Kinesins"", ""Sterile alpha motif (SAM) domain containing"""	19916	protein-coding gene	gene with protein product		613747	"""chromosome 9 open reading frame 48"""	C9orf48		12477932	Standard	NM_194313		Approved	bA571F15.4, FLJ10933, FLJ43884	uc003zua.4	Q5T7B8	OTTHUMG00000019810	ENST00000402558.2:c.418A>G	9.37:g.34310927T>C	ENSP00000384433:p.Met140Val	Somatic	382	1	0.0026178		WXS	Illumina HiSeq	Phase_I	335	138	0.41194	NM_194313	Q2TB93|Q5T7B5|Q5T7B7|Q6ZU97|Q6ZUZ2|Q86XZ0|Q9NV43	Missense_Mutation	SNP	ENST00000402558.2	37	CCDS6551.2	913	0.41804029304029305	51	0.10365853658536585	200	0.5524861878453039	185	0.32342657342657344	477	0.6292875989445911	T	0.005	-2.128481	0.00342	0.182226	0.623188	ENSG00000186638	ENST00000402558;ENST00000379174;ENST00000379166;ENST00000345050;ENST00000420188	T;T;T;T	0.70045	-0.28;-0.45;-0.28;-0.45	5.48	1.9	0.25705	.	0.406548	0.21334	N	0.076241	T	0.00012	0.0000	L	0.45581	1.43	0.80722	P	0.0	B;B	0.09022	0.002;0.0	B;B	0.06405	0.002;0.001	T	0.44050	-0.9353	9	0.28530	T	0.3	.	4.2329	0.10611	0.1386:0.2167:0.0:0.6446	rs10972048;rs17259557;rs52797474;rs56911205;rs10972048	140;140	Q5T7B8-4;Q5T7B8	.;KIF24_HUMAN	V	140	ENSP00000384433:M140V;ENSP00000368472:M140V;ENSP00000368464:M140V;ENSP00000340179:M140V	ENSP00000340179:M140V	M	-	1	0	KIF24	34300927	0.420000	0.25457	0.874000	0.34290	0.231000	0.25187	0.035000	0.13797	0.383000	0.24910	0.528000	0.53228	ATG	T|0.590;C|0.410	0.410	strong		0.398	KIF24-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052150.5		
FCHSD1	89848	hgsc.bcm.edu	37	5	141030640	141030640	+	Silent	SNP	C	C	T	rs17287002	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:141030640C>T	ENST00000435817.2	-	2	116	c.66G>A	c.(64-66)ctG>ctA	p.L22L	ARAP3_ENST00000512390.1_5'Flank|FCHSD1_ENST00000519800.1_Silent_p.L22L|FCHSD1_ENST00000522126.1_5'UTR|FCHSD1_ENST00000522783.1_Silent_p.L22L	NM_033449.2	NP_258260.1	Q86WN1	FCSD1_HUMAN	FCH and double SH3 domains 1	22	FCH. {ECO:0000255|PROSITE- ProRule:PRU00083}.								FCHSD1/BRAF(2)	central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(8)|lung(5)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	24			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GAAGGATGCTCAGCTGTTCCA	0.582													C|||	132	0.0263578	0.003	0.0519	5008	,	,		12042	0.0		0.0805	False		,,,				2504	0.0112				p.L22L		Atlas-SNP	.											.	FCHSD1	51	.	0			c.G66A						PASS	.	C		67,3993		0,67,1963	26.0	28.0	28.0		66	1.9	1.0	5	dbSNP_123	28	616,7746		21,574,3586	no	coding-synonymous	FCHSD1	NM_033449.2		21,641,5549	TT,TC,CC		7.3667,1.6502,5.4983		22/691	141030640	683,11739	2030	4181	6211	SO:0001819	synonymous_variant	89848	exon2			GATGCTCAGCTGT	AK027281	CCDS47295.1	5q31.3	2008-02-05			ENSG00000197948	ENSG00000197948			25463	protein-coding gene	gene with protein product						11214971, 15067381	Standard	NM_033449		Approved	FLJ00007	uc003llk.3	Q86WN1	OTTHUMG00000163762	ENST00000435817.2:c.66G>A	5.37:g.141030640C>T		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	74	32	0.432432	NM_033449	Q6UX75|Q86Y77|Q9NXX8	Silent	SNP	ENST00000435817.2	37	CCDS47295.1																																																																																			C|0.962;T|0.038	0.038	strong		0.582	FCHSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375282.2	NM_033449	
ZNF536	9745	hgsc.bcm.edu	37	19	31039939	31039939	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:31039939A>G	ENST00000355537.3	+	4	3560	c.3413A>G	c.(3412-3414)aAg>aGg	p.K1138R		NM_014717.1	NP_055532.1	O15090	ZN536_HUMAN	zinc finger protein 536	1138					negative regulation of neuron differentiation (GO:0045665)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|retinoic acid-responsive element binding (GO:0044323)			NS(3)|breast(6)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(22)|lung(119)|ovary(7)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(3)	182	Esophageal squamous(110;0.0834)					CCTGATGGAAAGGCCCACTCT	0.532																																					p.K1138R		Atlas-SNP	.											.	ZNF536	424	.	0			c.A3413G						PASS	.						74.0	72.0	73.0					19																	31039939		2203	4300	6503	SO:0001583	missense	9745	exon4			ATGGAAAGGCCCA		CCDS32984.1	19q13.11	2013-01-08				ENSG00000198597		"""Zinc fingers, C2H2-type"""	29025	protein-coding gene	gene with protein product						9205841	Standard	XM_005259445		Approved	KIAA0390	uc002nsu.1	O15090		ENST00000355537.3:c.3413A>G	19.37:g.31039939A>G	ENSP00000347730:p.Lys1138Arg	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	93	4	0.0430108	NM_014717	A2RU18	Missense_Mutation	SNP	ENST00000355537.3	37	CCDS32984.1	.	.	.	.	.	.	.	.	.	.	A	9.828	1.187633	0.21870	.	.	ENSG00000198597	ENST00000355537	T	0.09445	2.98	5.59	4.57	0.56435	.	0.454568	0.26428	N	0.024436	T	0.07863	0.0197	L	0.29908	0.895	0.28208	N	0.927077	B;P	0.44734	0.001;0.842	B;B	0.36922	0.001;0.236	T	0.13818	-1.0495	10	0.30078	T	0.28	-26.8781	11.4985	0.50424	0.9295:0.0:0.0705:0.0	.	1138;1138	A7E228;O15090	.;ZN536_HUMAN	R	1138	ENSP00000347730:K1138R	ENSP00000347730:K1138R	K	+	2	0	ZNF536	35731779	0.971000	0.33674	0.989000	0.46669	0.505000	0.33919	3.797000	0.55514	0.940000	0.37473	0.533000	0.62120	AAG	.	.	none		0.532	ZNF536-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459667.2	NM_014717	
ZNF469	84627	hgsc.bcm.edu	37	16	88501034	88501034	+	Missense_Mutation	SNP	G	G	C	rs12598474	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:88501034G>C	ENST00000437464.1	+	2	7072	c.7072G>C	c.(7072-7074)Ggg>Cgg	p.G2358R	ZNF469_ENST00000565624.1_Missense_Mutation_p.G2386R	NM_001127464.1	NP_001120936.1	Q96JG9	ZN469_HUMAN	zinc finger protein 469	2358			G -> R (in dbSNP:rs12598474). {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)	p.G2358R(1)		breast(4)|endometrium(6)|kidney(3)|large_intestine(1)|skin(6)	20						CCCTGAGACCGGGCGCTCTGG	0.662													g|||	1478	0.295128	0.2231	0.2997	5008	,	,		15260	0.377		0.3807	False		,,,				2504	0.2168				p.G2358R		Atlas-SNP	.											ZNF469,NS,carcinoma,0,1	ZNF469	121	1	1	Substitution - Missense(1)	kidney(1)	c.G7072C						PASS	.						27.0	36.0	33.0					16																	88501034		692	1590	2282	SO:0001583	missense	84627	exon2			GAGACCGGGCGCT	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.7072G>C	16.37:g.88501034G>C	ENSP00000402343:p.Gly2358Arg	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	77	35	0.454545	NM_001127464		Missense_Mutation	SNP	ENST00000437464.1	37	CCDS45544.1	682	0.31227106227106227	104	0.21138211382113822	99	0.27348066298342544	195	0.3409090909090909	284	0.37467018469656993	g	7.137	0.581006	0.13686	.	.	ENSG00000225614	ENST00000437464	T	0.05513	3.43	3.66	-2.17	0.07059	.	.	.	.	.	T	0.00012	0.0000	N	0.12182	0.205	0.80722	P	0.0	B	0.32781	0.384	B	0.25884	0.064	T	0.47873	-0.9083	8	0.30078	T	0.28	.	4.2493	0.10686	0.4349:0.1731:0.392:0.0	rs12598474	2358	Q96JG9	ZN469_HUMAN	R	2358	ENSP00000402343:G2358R	ENSP00000402343:G2358R	G	+	1	0	ZNF469	87028535	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.132000	0.03235	-0.239000	0.09710	-0.320000	0.08662	GGG	G|0.685;C|0.315	0.315	strong		0.662	ZNF469-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NG_012236	
PCSK9	255738	hgsc.bcm.edu	37	1	55505647	55505647	+	Missense_Mutation	SNP	G	G	T	rs11591147	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:55505647G>T	ENST00000302118.5	+	1	427	c.137G>T	c.(136-138)cGt>cTt	p.R46L	PCSK9_ENST00000543384.1_5'Flank|PCSK9_ENST00000452118.2_Missense_Mutation_p.R46L	NM_174936.3	NP_777596.2	Q8NBP7	PCSK9_HUMAN	proprotein convertase subtilisin/kexin type 9	46			R -> L (polymorphism associated with lower plasma levels of low-density lipoprotein cholesterol and reduced phosphorylation at Ser-47; dbSNP:rs11591147). {ECO:0000269|PubMed:12730697, ECO:0000269|PubMed:16465619, ECO:0000269|PubMed:22095935, ECO:0000269|Ref.4}.		apoptotic process (GO:0006915)|cellular response to insulin stimulus (GO:0032869)|cellular response to starvation (GO:0009267)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|kidney development (GO:0001822)|lipoprotein metabolic process (GO:0042157)|liver development (GO:0001889)|low-density lipoprotein particle receptor catabolic process (GO:0032802)|lysosomal transport (GO:0007041)|negative regulation of low-density lipoprotein particle clearance (GO:0010989)|negative regulation of receptor recycling (GO:0001920)|neurogenesis (GO:0022008)|neuron differentiation (GO:0030182)|phospholipid metabolic process (GO:0006644)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of receptor internalization (GO:0002092)|protein autoprocessing (GO:0016540)|proteolysis (GO:0006508)|regulation of low-density lipoprotein particle receptor catabolic process (GO:0032803)|regulation of neuron apoptotic process (GO:0043523)|regulation of receptor activity (GO:0010469)|triglyceride metabolic process (GO:0006641)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle (GO:0030134)|extracellular space (GO:0005615)|extrinsic component of external side of plasma membrane (GO:0031232)|Golgi apparatus (GO:0005794)|late endosome (GO:0005770)|lysosome (GO:0005764)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|rough endoplasmic reticulum (GO:0005791)	apolipoprotein binding (GO:0034185)|apolipoprotein receptor binding (GO:0034190)|low-density lipoprotein particle binding (GO:0030169)|low-density lipoprotein particle receptor binding (GO:0050750)|poly(A) RNA binding (GO:0044822)|protein self-association (GO:0043621)|serine-type endopeptidase activity (GO:0004252)|sodium channel inhibitor activity (GO:0019871)|very-low-density lipoprotein particle binding (GO:0034189)|very-low-density lipoprotein particle receptor binding (GO:0070326)			NS(2)|breast(2)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(1)|liver(2)|lung(4)|ovary(3)|prostate(3)|skin(1)|urinary_tract(1)	32						CTAGCCTTGCGTTCCGAGGAG	0.711													G|||	32	0.00638978	0.0	0.0159	5008	,	,		14712	0.0		0.0209	False		,,,				2504	0.0				p.R46L	Pancreas(137;1454 1827 5886 22361 42375)	Atlas-SNP	.											.	PCSK9	76	.	0			c.G137T	GRCh37	CM061163	PCSK9	M	rs11591147	PASS	.	G	LEU/ARG	13,4359		0,13,2173	35.0	28.0	31.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	137	-0.3	0.0	1	dbSNP_120	31	114,8428		1,112,4158	yes	missense	PCSK9	NM_174936.3	102	1,125,6331	TT,TG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	1.3346,0.2973,0.9834	benign	46/693	55505647	127,12787	2186	4271	6457	SO:0001583	missense	255738	exon1			CCTTGCGTTCCGA	AX207686	CCDS603.1	1p34.1-p32	2014-09-17	2003-05-13		ENSG00000169174	ENSG00000169174			20001	protein-coding gene	gene with protein product		607786	"""hypercholesterolemia, autosomal dominant 3"""	HCHOLA3		12552133, 12730697	Standard	NM_174936		Approved	NARC-1, FH3	uc001cyf.2	Q8NBP7	OTTHUMG00000008136	ENST00000302118.5:c.137G>T	1.37:g.55505647G>T	ENSP00000303208:p.Arg46Leu	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	97	46	0.474227	NM_174936	A8T640|C0JYY9|Q5PSM5|Q5SZQ2	Missense_Mutation	SNP	ENST00000302118.5	37	CCDS603.1	19	0.0086996336996337	0	0.0	6	0.016574585635359115	0	0.0	13	0.017150395778364115	G	11.46	1.644247	0.29246	0.002973	0.013346	ENSG00000169174	ENST00000302118;ENST00000452118	T;T	0.71103	-0.47;-0.54	3.39	-0.263	0.12954	.	2.195950	0.03739	N	0.254722	T	0.33206	0.0855	N	0.14661	0.345	0.09310	N	0.999996	B	0.06786	0.001	B	0.06405	0.002	T	0.18085	-1.0348	10	0.09843	T	0.71	0.3635	5.9343	0.19156	0.0:0.5014:0.3708:0.1278	rs11591147;rs11591147	46	Q8NBP7	PCSK9_HUMAN	L	46	ENSP00000303208:R46L;ENSP00000401598:R46L	ENSP00000303208:R46L	R	+	2	0	PCSK9	55278235	0.000000	0.05858	0.000000	0.03702	0.916000	0.54674	-0.910000	0.04054	-0.290000	0.09025	0.313000	0.20887	CGT	G|0.990;T|0.010	0.010	strong		0.711	PCSK9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022280.1	NM_174936	
GRM3	2913	hgsc.bcm.edu	37	7	86415987	86415987	+	Silent	SNP	C	C	T	rs2228595	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:86415987C>T	ENST00000361669.2	+	3	1978	c.879C>T	c.(877-879)gcC>gcT	p.A293A	GRM3_ENST00000439827.1_Silent_p.A293A|GRM3_ENST00000394720.2_Silent_p.A291A|GRM3_ENST00000536043.1_Silent_p.A165A|AC005009.2_ENST00000452471.1_RNA|GRM3_ENST00000546348.1_Intron|AC005009.2_ENST00000418031.1_RNA	NM_000840.2	NP_000831.2	Q14832	GRM3_HUMAN	glutamate receptor, metabotropic 3	293					adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|negative regulation of adenylate cyclase activity (GO:0007194)|regulation of synaptic transmission, glutamatergic (GO:0051966)|synaptic transmission (GO:0007268)	astrocyte projection (GO:0097449)|axon (GO:0030424)|dendritic spine (GO:0043197)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)	calcium channel regulator activity (GO:0005246)|G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)|group II metabotropic glutamate receptor activity (GO:0001641)			NS(2)|breast(6)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(43)|ovary(3)|pancreas(2)|prostate(4)|skin(25)|upper_aerodigestive_tract(5)	109	Esophageal squamous(14;0.0058)|all_lung(186;0.132)|Lung NSC(181;0.142)					GCGCCAATGCCTCCTTCACCT	0.672													C|||	290	0.0579073	0.003	0.0706	5008	,	,		17533	0.0516		0.0706	False		,,,				2504	0.1166				p.A293A	GBM(52;969 1098 3139 52280)	Atlas-SNP	.											.	GRM3	237	.	0			c.C879T						PASS	.	C		41,4361		0,41,2160	33.0	38.0	36.0		879	1.7	1.0	7	dbSNP_98	36	532,8048		16,500,3774	no	coding-synonymous	GRM3	NM_000840.2		16,541,5934	TT,TC,CC		6.2005,0.9314,4.4138		293/880	86415987	573,12409	2201	4290	6491	SO:0001819	synonymous_variant	2913	exon3			CAATGCCTCCTTC		CCDS5600.1	7q21.1-q21.2	2012-08-29			ENSG00000198822	ENSG00000198822		"""GPCR / Class C : Glutamate receptors, metabotropic"", ""Glutamate receptors"""	4595	protein-coding gene	gene with protein product		601115				8824806	Standard	NM_000840		Approved	GPRC1C, mGlu3, MGLUR3	uc003uid.3	Q14832	OTTHUMG00000022884	ENST00000361669.2:c.879C>T	7.37:g.86415987C>T		Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	35	19	0.542857	NM_000840	Q2PNZ6|Q75MV4|Q75N17|Q86YG6|Q8TBH9	Silent	SNP	ENST00000361669.2	37	CCDS5600.1																																																																																			C|0.946;T|0.054	0.054	strong		0.672	GRM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253362.2		
ACOT11	26027	hgsc.bcm.edu	37	1	55064980	55064980	+	Missense_Mutation	SNP	G	G	A	rs2304303	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:55064980G>A	ENST00000371316.3	+	8	858	c.776G>A	c.(775-777)cGt>cAt	p.R259H	ACOT11_ENST00000481208.1_3'UTR|ACOT11_ENST00000343744.2_Missense_Mutation_p.R259H	NM_015547.3	NP_056362.1	Q8WXI4	ACO11_HUMAN	acyl-CoA thioesterase 11	259	Acyl coenzyme A hydrolase 2.				fatty acid metabolic process (GO:0006631)|intracellular signal transduction (GO:0035556)|response to cold (GO:0009409)|response to temperature stimulus (GO:0009266)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	acyl-CoA hydrolase activity (GO:0047617)|carboxylic ester hydrolase activity (GO:0052689)|lipid binding (GO:0008289)			NS(1)|central_nervous_system(1)|endometrium(6)|large_intestine(3)|lung(5)|ovary(1)	17						CGGCTCTGCCGTGCCCACCCT	0.547													G|||	404	0.0806709	0.0295	0.1412	5008	,	,		8222	0.1706		0.0348	False		,,,				2504	0.0613				p.R259H	Ovarian(148;1440 1861 22015 32453 51933)	Atlas-SNP	.											ACOT11_ENST00000371316,caecum,carcinoma,0,2	ACOT11	105	2	0			c.G776A						PASS	.	G	HIS/ARG,HIS/ARG	153,4253	104.3+/-142.8	2,149,2052	80.0	78.0	79.0		776,776	-1.6	0.1	1	dbSNP_100	79	236,8364	95.2+/-157.0	5,226,4069	yes	missense,missense	ACOT11	NM_015547.3,NM_147161.3	29,29	7,375,6121	AA,AG,GG		2.7442,3.4725,2.9909	benign,benign	259/608,259/595	55064980	389,12617	2203	4300	6503	SO:0001583	missense	26027	exon8			TCTGCCGTGCCCA	AB014607	CCDS592.1, CCDS593.1	1p32.3	2011-09-13	2005-09-08	2005-09-08	ENSG00000162390	ENSG00000162390	3.1.2.-	"""Acyl CoA thioesterases"", ""StAR-related lipid transfer (START) domain containing"""	18156	protein-coding gene	gene with protein product	"""StAR-related lipid transfer (START) domain containing 14"""	606803	"""thioesterase, adipose associated"""	THEA		11696000, 16103133, 16940157	Standard	NM_015547		Approved	STARD14, BFIT, KIAA0707, BFIT1, THEM1	uc001cxl.2	Q8WXI4	OTTHUMG00000009891	ENST00000371316.3:c.776G>A	1.37:g.55064980G>A	ENSP00000360366:p.Arg259His	Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	124	63	0.508065	NM_147161	B1AQ22|D3DQ50|O75187|Q52LP1|Q53ER9|Q96DI1|Q9H883	Missense_Mutation	SNP	ENST00000371316.3	37	CCDS592.1	188	0.08608058608058608	13	0.026422764227642278	48	0.13259668508287292	99	0.17307692307692307	28	0.036939313984168866	G	12.41	1.928244	0.34002	0.034725	0.027442	ENSG00000162390	ENST00000343744;ENST00000371316	T;T	0.31510	1.49;1.49	5.27	-1.58	0.08479	Thioesterase superfamily (1);	0.518159	0.21888	N	0.067627	T	0.00039	0.0001	L	0.48642	1.525	0.53688	P	2.199999999996649E-5	B;B	0.14805	0.011;0.002	B;B	0.15870	0.014;0.005	T	0.23476	-1.0187	9	0.20046	T	0.44	-9.6805	6.4701	0.22003	0.5971:0.1422:0.2607:0.0	rs2304303	259;259	Q8WXI4;Q8WXI4-2	ACO11_HUMAN;.	H	259	ENSP00000340260:R259H;ENSP00000360366:R259H	ENSP00000340260:R259H	R	+	2	0	ACOT11	54837568	0.348000	0.24861	0.096000	0.21009	0.952000	0.60782	1.950000	0.40323	-0.026000	0.13895	0.561000	0.74099	CGT	G|0.956;A|0.044	0.044	strong		0.547	ACOT11-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000027356.1	NM_015547	
ZNF100	163227	hgsc.bcm.edu	37	19	21909948	21909948	+	Missense_Mutation	SNP	G	G	A	rs7246400	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:21909948G>A	ENST00000358296.6	-	5	1364	c.1166C>T	c.(1165-1167)aCt>aTt	p.T389I	ZNF100_ENST00000305570.6_Missense_Mutation_p.T325I	NM_173531.3	NP_775802.2	Q8IYN0	ZN100_HUMAN	zinc finger protein 100	389			T -> I (in dbSNP:rs7246400). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:1740334}.		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						CTTATGTTTAGTAAGGTATGA	0.388													N|||	2550	0.509185	0.3699	0.6614	5008	,	,		21187	0.621		0.5616	False		,,,				2504	0.4202				p.T389I		Atlas-SNP	.											.	ZNF100	62	.	0			c.C1166T						PASS	.	G	ILE/THR	1638,2718		310,1018,850	52.0	57.0	55.0		1166	0.8	0.0	19	dbSNP_116	55	4838,3726		1352,2134,796	no	missense	ZNF100	NM_173531.3	89	1662,3152,1646	AA,AG,GG		43.5077,37.6033,49.8762	possibly-damaging	389/543	21909948	6476,6444	2178	4282	6460	SO:0001583	missense	163227	exon5			TGTTTAGTAAGGT	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.1166C>T	19.37:g.21909948G>A	ENSP00000351042:p.Thr389Ile	Somatic	22	0	0		WXS	Illumina HiSeq	Phase_I	19	19	1	NM_173531	Q7M4M0	Missense_Mutation	SNP	ENST00000358296.6	37	CCDS42538.1	1201	0.549908424908425	180	0.36585365853658536	233	0.643646408839779	363	0.6346153846153846	425	0.5606860158311345	.	2.552	-0.303828	0.05495	0.376033	0.564923	ENSG00000197020	ENST00000358296	T	0.35605	1.3	0.841	0.841	0.18918	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	N	0.26130	0.795	0.58432	P	5.999999999950489E-6	P;P	0.43352	0.719;0.804	B;P	0.44394	0.41;0.448	T	0.36768	-0.9734	8	0.33141	T	0.24	.	1.79	0.03049	0.2538:0.0:0.4232:0.323	rs7246400;rs17853437;rs57140346	389;443	Q8IYN0;Q4G131	ZN100_HUMAN;.	I	389	ENSP00000351042:T389I	ENSP00000351042:T389I	T	-	2	0	ZNF100	21701788	0.000000	0.05858	0.029000	0.17559	0.029000	0.11900	-0.000000	0.12993	0.182000	0.20032	0.185000	0.17295	ACT	G|0.451;A|0.549	0.549	strong		0.388	ZNF100-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464087.1	NM_173531	
TMPRSS15	5651	hgsc.bcm.edu	37	21	19713821	19713821	+	Silent	SNP	C	C	T	rs2824751	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:19713821C>T	ENST00000284885.3	-	13	1506	c.1473G>A	c.(1471-1473)gcG>gcA	p.A491A		NM_002772.2	NP_002763	P98073	ENTK_HUMAN	transmembrane protease, serine 15	491	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)			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						TGTCATCCAACGCAATATCAC	0.393													t|||	920	0.183706	0.1551	0.1499	5008	,	,		21084	0.1101		0.2505	False		,,,				2504	0.2536				p.A491A		Atlas-SNP	.											TMPRSS15,NS,carcinoma,-1,1	TMPRSS15	189	1	0			c.G1473A						PASS	.	G		721,3685	758.0+/-412.8	61,599,1543	159.0	147.0	151.0		1473	-4.6	0.1	21	dbSNP_100	151	2132,6468	715.2+/-406.0	275,1582,2443	no	coding-synonymous	TMPRSS15	NM_002772.2		336,2181,3986	TT,TC,CC		24.7907,16.364,21.936		491/1020	19713821	2853,10153	2203	4300	6503	SO:0001819	synonymous_variant	5651	exon13			ATCCAACGCAATA		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.1473G>A	21.37:g.19713821C>T		Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	102	102	1	NM_002772	Q2NKL7	Silent	SNP	ENST00000284885.3	37	CCDS13571.1																																																																																			C|0.811;T|0.189	0.189	strong		0.393	TMPRSS15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000158231.2	NM_002772	
LY9	4063	hgsc.bcm.edu	37	1	160793442	160793442	+	Silent	SNP	A	A	G	rs474131	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:160793442A>G	ENST00000263285.6	+	8	1716	c.1686A>G	c.(1684-1686)gtA>gtG	p.V562V	LY9_ENST00000392203.4_Silent_p.V472V|LY9_ENST00000341032.4_Silent_p.V428V|LY9_ENST00000368040.1_Silent_p.V200V|LY9_ENST00000368037.5_Silent_p.V548V|LY9_ENST00000368041.2_Silent_p.V432V			Q9HBG7	LY9_HUMAN	lymphocyte antigen 9	562					cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			autonomic_ganglia(1)|breast(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(17)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	36	all_cancers(52;2.72e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00737)			GATATGAGGTATTTGACCAGG	0.557													G|||	3166	0.632188	0.6884	0.6643	5008	,	,		21651	0.7034		0.4493	False		,,,				2504	0.6483				p.V562V		Atlas-SNP	.											.	LY9	115	.	0			c.A1686G						PASS	.	G		2805,1601	496.5+/-363.6	887,1031,285	142.0	128.0	133.0		1686	-1.5	0.0	1	dbSNP_83	133	3625,4975	625.2+/-397.7	758,2109,1433	no	coding-synonymous	LY9	NM_002348.2		1645,3140,1718	GG,GA,AA		42.1512,36.3368,49.4387		562/656	160793442	6430,6576	2203	4300	6503	SO:0001819	synonymous_variant	4063	exon8			TGAGGTATTTGAC	L42621	CCDS30916.1, CCDS30917.1, CCDS65695.1, CCDS65696.1	1q23.3	2013-01-11			ENSG00000122224	ENSG00000122224		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6730	protein-coding gene	gene with protein product		600684				8537117, 7797269	Standard	NM_001261457		Approved	CD229, mLY9, SLAMF3, hly9	uc001fwu.4	Q9HBG7	OTTHUMG00000024007	ENST00000263285.6:c.1686A>G	1.37:g.160793442A>G		Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	164	96	0.585366	NM_002348	A8K7N3|Q14775|Q5VYI3|Q6P2J4|Q9H4N5|Q9NQ24	Silent	SNP	ENST00000263285.6	37	CCDS30916.1																																																																																			A|0.447;G|0.553	0.553	strong		0.557	LY9-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000060457.3	NM_002348	
C2orf81	388963	hgsc.bcm.edu	37	2	74641624	74641624	+	Silent	SNP	G	G	C	rs2240444	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:74641624G>C	ENST00000517883.1	-	1	2086	c.1395C>G	c.(1393-1395)ccC>ccG	p.P465P	C2orf81_ENST00000290390.5_Silent_p.P533P			A6NN90	CB081_HUMAN	chromosome 2 open reading frame 81	526										endometrium(3)|kidney(1)	4						GCAGCAACACGGGCTTCCACA	0.622													C|||	2730	0.545128	0.91	0.3271	5008	,	,		16936	0.8244		0.1412	False		,,,				2504	0.3344				p.P533P		Atlas-SNP	.											.	C2orf81	23	.	0			c.C1599G						PASS	.	C		1103,281		439,225,28	39.0	46.0	44.0		1599	-1.6	0.0	2	dbSNP_98	44	423,2759		31,361,1199	no	coding-synonymous	C2orf81	NM_001145054.1		470,586,1227	CC,CG,GG		13.2935,20.3035,33.4209		533/589	74641624	1526,3040	692	1591	2283	SO:0001819	synonymous_variant	388963	exon4			CAACACGGGCTTC	AC005041, CH471053		2p13.1	2012-08-07			ENSG00000159239	ENSG00000159239			34350	protein-coding gene	gene with protein product						15815621	Standard	NM_001145054		Approved	LOC388963, hCG40743	uc010yrq.1	A6NN90	OTTHUMG00000164184	ENST00000517883.1:c.1395C>G	2.37:g.74641624G>C		Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	130	54	0.415385	NM_001145054		Silent	SNP	ENST00000517883.1	37																																																																																				G|0.496;C|0.504	0.504	strong		0.622	C2orf81-002	PUTATIVE	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000377683.1	NM_001145054	
MLLT6	4302	hgsc.bcm.edu	37	17	36873149	36873149	+	Silent	SNP	C	C	T	rs9892493	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:36873149C>T	ENST00000325718.7	+	10	1657	c.1566C>T	c.(1564-1566)tcC>tcT	p.S522S	CTB-58E17.9_ENST00000579499.1_RNA|MIR4726_ENST00000577947.1_RNA	NM_005937.3	NP_005928	P55198	AF17_HUMAN	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 6	522					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)					TGGTCAGCTCCGGCCTGGGAG	0.657			T	MLL	AL								C|||	707	0.141174	0.2821	0.0821	5008	,	,		17704	0.0308		0.0457	False		,,,				2504	0.2045				p.S522S		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.C1566T						PASS	.	C		987,3419	350.0+/-310.6	119,749,1335	24.0	25.0	24.0		1566	-10.3	0.4	17	dbSNP_119	24	511,8089	141.2+/-197.6	22,467,3811	no	coding-synonymous	MLLT6	NM_005937.3		141,1216,5146	TT,TC,CC		5.9419,22.4013,11.5178		522/1094	36873149	1498,11508	2203	4300	6503	SO:0001819	synonymous_variant	4302	exon10			CAGCTCCGGCCTG		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.1566C>T	17.37:g.36873149C>T		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	100	45	0.45	NM_005937	Q59F28|Q96IU3|Q9H5F6|Q9UF49	Silent	SNP	ENST00000325718.7	37	CCDS11327.1																																																																																			C|0.869;T|0.131	0.131	strong		0.657	MLLT6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256799.1	NM_005937	
TMEM8A	58986	hgsc.bcm.edu	37	16	426432	426432	+	Missense_Mutation	SNP	T	T	C	rs2071915	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:426432T>C	ENST00000431232.2	-	6	1088	c.928A>G	c.(928-930)Atc>Gtc	p.I310V	TMEM8A_ENST00000476735.1_5'Flank|TMEM8A_ENST00000250930.3_Missense_Mutation_p.I117V	NM_021259.2	NP_067082.2	Q9HCN3	TMM8A_HUMAN	transmembrane protein 8A	310			I -> V (in dbSNP:rs2071915). {ECO:0000269|PubMed:11006113, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		cell adhesion (GO:0007155)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)				central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|pancreas(1)|prostate(1)	14						AGGGGCTGGATGGTCACGCTC	0.647													C|||	2667	0.532548	0.6188	0.4712	5008	,	,		16721	0.3036		0.5378	False		,,,				2504	0.6902				p.I310V		Atlas-SNP	.											.	TMEM8A	49	.	0			c.A928G						PASS	.	C	VAL/ILE	2746,1652		848,1050,301	25.0	27.0	27.0		928	-9.1	0.0	16	dbSNP_96	27	4870,3724		1411,2048,838	yes	missense	TMEM8A	NM_021259.2	29	2259,3098,1139	CC,CT,TT		43.3326,37.5625,41.3793	benign	310/772	426432	7616,5376	2199	4297	6496	SO:0001583	missense	58986	exon6			GCTGGATGGTCAC	AB045292	CCDS10407.1	16p13.3	2009-06-12	2009-06-12	2009-06-12	ENSG00000129925	ENSG00000129925			17205	protein-coding gene	gene with protein product			"""transmembrane protein 6"", ""transmembrane protein 8 (five membrane-spanning domains)"""	TMEM6, TMEM8		11006113	Standard	NM_021259		Approved	M83	uc002cgu.4	Q9HCN3	OTTHUMG00000047996	ENST00000431232.2:c.928A>G	16.37:g.426432T>C	ENSP00000401338:p.Ile310Val	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	54	54	1	NM_021259	D3DU49|Q4TT35|Q8WU24|Q96S25|Q9BR03|Q9BT97|Q9H7B9	Missense_Mutation	SNP	ENST00000431232.2	37	CCDS10407.1	1086	0.49725274725274726	335	0.6808943089430894	179	0.494475138121547	163	0.28496503496503495	409	0.5395778364116095	C	0.012	-1.684225	0.00745	0.624375	0.566674	ENSG00000129925	ENST00000431232;ENST00000250930	T;T	0.28666	2.01;1.6	4.57	-9.13	0.00704	.	3.050000	0.00628	N	0.000477	T	0.00012	0.0000	N	0.00926	-1.1	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.26985	-1.0087	9	0.22109	T	0.4	-13.6961	4.298	0.10911	0.0755:0.2978:0.203:0.4237	rs2071915;rs17797276;rs17845651;rs17858585;rs56985763;rs2071915	310	Q9HCN3	TMM8A_HUMAN	V	310;117	ENSP00000401338:I310V;ENSP00000250930:I117V	ENSP00000250930:I117V	I	-	1	0	TMEM8A	366433	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.095000	0.01350	-5.232000	0.00018	-4.127000	0.00010	ATC	C|0.542;N|0.001	0.542	strong		0.647	TMEM8A-001	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000109257.2	NM_021259	
PCDH18	54510	hgsc.bcm.edu	37	4	138449683	138449683	+	Silent	SNP	A	A	G	rs10018837	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:138449683A>G	ENST00000344876.4	-	3	3075	c.2689T>C	c.(2689-2691)Ttg>Ctg	p.L897L	PCDH18_ENST00000412923.2_Silent_p.L896L|PCDH18_ENST00000510305.1_Silent_p.L108L|PCDH18_ENST00000507846.1_Silent_p.L676L|PCDH18_ENST00000511115.1_Silent_p.L77L	NM_019035.3	NP_061908.1	Q9HCL0	PCD18_HUMAN	protocadherin 18	897	Interaction with DAB1. {ECO:0000250}.				brain development (GO:0007420)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(27)|lung(21)|ovary(2)|pancreas(4)|prostate(3)|skin(12)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	86	all_hematologic(180;0.24)					CCTTCACCCAACAGCCTATCT	0.453													G|||	2857	0.570487	0.8994	0.4496	5008	,	,		14896	0.5079		0.4155	False		,,,				2504	0.4356				p.L897L		Atlas-SNP	.											.	PCDH18	229	.	0			c.T2689C						PASS	.	G		3535,871	340.2+/-306.1	1428,679,96	188.0	205.0	199.0		2689	4.7	1.0	4	dbSNP_119	199	3628,4972	625.0+/-397.7	782,2064,1454	no	coding-synonymous	PCDH18	NM_019035.3		2210,2743,1550	GG,GA,AA		42.186,19.7685,44.9254		897/1136	138449683	7163,5843	2203	4300	6503	SO:0001819	synonymous_variant	54510	exon3			CACCCAACAGCCT	AL137471	CCDS34064.1, CCDS75193.1	4q28.3	2010-01-26			ENSG00000189184	ENSG00000189184		"""Cadherins / Protocadherins : Non-clustered"""	14268	protein-coding gene	gene with protein product		608287				10835267, 11549318	Standard	XM_005263070		Approved	KIAA1562, PCDH68L	uc003ihe.4	Q9HCL0	OTTHUMG00000161348	ENST00000344876.4:c.2689T>C	4.37:g.138449683A>G		Somatic	205	0	0		WXS	Illumina HiSeq	Phase_I	152	62	0.407895	NM_019035	A8K7K3|B7ZKT1|Q52LS2	Silent	SNP	ENST00000344876.4	37	CCDS34064.1																																																																																			A|0.443;G|0.557	0.557	strong		0.453	PCDH18-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364614.1	NM_019035	
UTP18	51096	hgsc.bcm.edu	37	17	49338257	49338257	+	Silent	SNP	C	C	T	rs14180	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:49338257C>T	ENST00000225298.7	+	1	369	c.312C>T	c.(310-312)gaC>gaT	p.D104D	MBTD1_ENST00000376381.2_5'Flank|MBTD1_ENST00000586178.1_5'Flank	NM_016001.2	NP_057085.2	Q9Y5J1	UTP18_HUMAN	UTP18 small subunit (SSU) processome component homolog (yeast)	104					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)			ACGACGAGGACGCGTTGCTGC	0.751													C|||	291	0.058107	0.0091	0.0576	5008	,	,		11043	0.0873		0.1004	False		,,,				2504	0.0511				p.D104D		Atlas-SNP	.											.	UTP18	28	.	0			c.C312T						PASS	.	C		81,3593		1,79,1757	8.0	11.0	10.0		312	0.1	1.0	17	dbSNP_52	10	818,7116		39,740,3188	no	coding-synonymous	UTP18	NM_016001.2		40,819,4945	TT,TC,CC		10.3101,2.2047,7.7447		104/557	49338257	899,10709	1837	3967	5804	SO:0001819	synonymous_variant	51096	exon1			CGAGGACGCGTTG	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.312C>T	17.37:g.49338257C>T		Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	48	48	1	NM_016001	Q9H4N6	Silent	SNP	ENST00000225298.7	37	CCDS42362.1																																																																																			C|0.927;T|0.073	0.073	strong		0.751	UTP18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368654.1	NM_016001	
PCDHGA12	26025	hgsc.bcm.edu	37	5	140871425	140871425	+	Intron	SNP	A	A	G	rs17208425	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:140871425A>G	ENST00000252085.3	+	2	2566				PCDHGA3_ENST00000253812.6_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGC3_ENST00000308177.3_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGC5_ENST00000252087.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA10_ENST00000398610.2_Intron|PCDHGA11_ENST00000518882.1_Intron|PCDHGB7_ENST00000398594.2_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA11_ENST00000398587.2_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGC4_ENST00000306593.1_Intron	NM_003735.2|NM_032094.1	NP_003726.1|NP_115265.1	O60330	PCDGC_HUMAN	protocadherin gamma subfamily A, 12						homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|cervix(1)|endometrium(7)|kidney(1)|large_intestine(10)|lung(23)|ovary(5)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)	58			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CGTTTGCGCGAAACCAGAGTG	0.632													G|||	936	0.186901	0.1437	0.3545	5008	,	,		13778	0.129		0.2127	False		,,,				2504	0.1595				p.E873G		Atlas-SNP	.											.	PCDHGC5	199	.	0			c.A2618G						PASS	.	G	,,,,,,,,,,,,,,,,,,,,,,,,GLY/GLU	292,1890		24,244,823	12.0	16.0	15.0		,,,,,,,,,,,,,,,,,,,,,,,,2618	-1.0	0.0	5	dbSNP_123	15	770,3534		74,622,1456	yes	intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,missense	PCDHGC3,PCDHGB4,PCDHGA8,PCDHGA12,PCDHGC5,PCDHGC4,PCDHGB7,PCDHGB6,PCDHGB5,PCDHGB3,PCDHGB2,PCDHGB1,PCDHGA11,PCDHGA10,PCDHGA9,PCDHGA7,PCDHGA6,PCDHGA5,PCDHGA4,PCDHGA3,PCDHGA2,PCDHGA1	NM_002588.2,NM_003735.2,NM_003736.2,NM_018912.2,NM_018913.2,NM_018914.2,NM_018915.2,NM_018916.3,NM_018917.2,NM_018918.2,NM_018919.2,NM_018920.2,NM_018921.2,NM_018922.2,NM_018923.2,NM_018924.2,NM_018925.2,NM_018926.2,NM_018927.3,NM_018928.2,NM_018929.2,NM_032088.1,NM_032092.1,NM_032403.1,NM_032407.1	,,,,,,,,,,,,,,,,,,,,,,,,98	98,866,2279	GG,GA,AA		17.8903,13.3822,16.3737	,,,,,,,,,,,,,,,,,,,,,,,,	,,,,,,,,,,,,,,,,,,,,,,,,873/879	140871425	1062,5424	1091	2152	3243	SO:0001627	intron_variant	56097	exon1			TGCGCGAAACCAG	AF152506	CCDS4260.1, CCDS75346.1	5q31	2010-01-26	2002-05-23		ENSG00000253159	ENSG00000253159		"""Cadherins / Protocadherins : Clustered"""	8699	other	protocadherin	"""fibroblast cadherin FIB3"""	603059	"""cadherin 21"""	CDH21		10380929	Standard	NM_003735		Approved	KIAA0588, FIB3, PCDH-GAMMA-A12		O60330	OTTHUMG00000129611	ENST00000252085.3:c.2425-2949A>G	5.37:g.140871425A>G		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	103	103	1	NM_032407	O15100|Q6UW70|Q9Y5D7	Missense_Mutation	SNP	ENST00000252085.3	37	CCDS4260.1																																																																																			A|0.821;G|0.179	0.179	strong		0.632	PCDHGA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251806.2	NM_003735	
NUP210	23225	hgsc.bcm.edu	37	3	13399786	13399786	+	Missense_Mutation	SNP	G	G	A	rs6795271	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	126	0	0		WXS	Illumina HiSeq	Phase_I	119	51	0.428571	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	
WBSCR27	155368	hgsc.bcm.edu	37	7	73249165	73249165	+	Missense_Mutation	SNP	T	T	A	rs13246460	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:73249165T>A	ENST00000297873.4	-	6	695	c.646A>T	c.(646-648)Agg>Tgg	p.R216W		NM_152559.2	NP_689772.2	Q8N6F8	WBS27_HUMAN	Williams Beuren syndrome chromosome region 27	216				R -> W (in Ref. 1; AAN63884, 2; AAQ55828 and 4; AAH30295). {ECO:0000305}.						NS(1)|central_nervous_system(1)|lung(2)|prostate(1)	5		Lung NSC(55;0.159)				GGATACCACCTCCAGCTCGGA	0.627													T|||	2910	0.58107	0.4629	0.6124	5008	,	,		15582	0.5813		0.7256	False		,,,				2504	0.5695				p.R216W		Atlas-SNP	.											.	WBSCR27	21	.	0			c.A646T						PASS	.	T	TRP/ARG	2290,2116	597.0+/-388.8	593,1104,506	67.0	61.0	63.0		646	5.2	0.1	7	dbSNP_121	63	6384,2216	708.8+/-405.7	2371,1642,287	yes	missense	WBSCR27	NM_152559.2	101	2964,2746,793	AA,AT,TT		25.7674,48.0254,33.3077	probably-damaging	216/246	73249165	8674,4332	2203	4300	6503	SO:0001583	missense	155368	exon6			ACCACCTCCAGCT	AF534110	CCDS5561.1	7q11.23	2004-07-05			ENSG00000165171	ENSG00000165171			19068	protein-coding gene	gene with protein product		612546					Standard	NM_152559		Approved		uc003tzj.2	Q8N6F8	OTTHUMG00000130033	ENST00000297873.4:c.646A>T	7.37:g.73249165T>A	ENSP00000297873:p.Arg216Trp	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	77	75	0.974026	NM_152559		Missense_Mutation	SNP	ENST00000297873.4	37	CCDS5561.1	1327	0.6076007326007326	227	0.4613821138211382	218	0.6022099447513812	328	0.5734265734265734	554	0.7308707124010554	T	23.8	4.463481	0.84425	0.519746	0.742326	ENSG00000165171	ENST00000297873	T	0.69685	-0.42	5.25	5.25	0.73442	.	1.356490	0.04448	N	0.372109	T	0.00012	0.0000	N	0.22421	0.69	0.46131	P	0.0011200000000000099	D	0.55800	0.973	B	0.43754	0.43	T	0.38972	-0.9636	9	0.37606	T	0.19	-8.7324	11.6685	0.51387	0.0:0.0:0.0:1.0	rs13246460;rs17845919;rs17858895	216	Q8N6F8	WBS27_HUMAN	W	216	ENSP00000297873:R216W	ENSP00000297873:R216W	R	-	1	2	WBSCR27	72887101	0.999000	0.42202	0.106000	0.21319	0.330000	0.28571	5.701000	0.68325	2.013000	0.59113	0.449000	0.29647	AGG	T|0.351;A|0.649	0.649	strong		0.627	WBSCR27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252312.1	NM_152559	
NEGR1	257194	hgsc.bcm.edu	37	1	72748169	72748169	+	Missense_Mutation	SNP	C	C	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:72748169C>G	ENST00000357731.5	-	1	248	c.9G>C	c.(7-9)atG>atC	p.M3I	NEGR1_ENST00000434200.1_Start_Codon_SNP_p.M1I	NM_173808.2	NP_776169.2	Q7Z3B1	NEGR1_HUMAN	neuronal growth regulator 1	3					feeding behavior (GO:0007631)|locomotory behavior (GO:0007626)|positive regulation of neuron projection development (GO:0010976)|single organismal cell-cell adhesion (GO:0016337)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)				endometrium(1)|kidney(4)|large_intestine(7)|lung(16)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	32		all_cancers(4;1.26e-06)|Renal(4;1.32e-08)|all_epithelial(4;5.39e-07)|Hepatocellular(141;0.117)		KIRC - Kidney renal clear cell carcinoma(4;0.00529)|Kidney(4;0.00609)|all cancers(265;0.022)|GBM - Glioblastoma multiforme(62;0.0382)|Epithelial(280;0.242)		CCAACAGCATCATGTCCATCC	0.662																																					p.M3I		Atlas-SNP	.											.	NEGR1	60	.	0			c.G9C						PASS	.						89.0	68.0	76.0					1																	72748169		2203	4300	6503	SO:0001583	missense	257194	exon1			CAGCATCATGTCC	AK092307	CCDS661.1	1p31.1	2013-01-11			ENSG00000172260	ENSG00000172260		"""Immunoglobulin superfamily / I-set domain containing"""	17302	protein-coding gene	gene with protein product	"""a kindred of IgLON"", ""neurotractin"", ""IgLON family member 4"""	613173				10075727	Standard	NM_173808		Approved	KILON, MGC46680, Ntra, IGLON4	uc001dfw.3	Q7Z3B1	OTTHUMG00000009698	ENST00000357731.5:c.9G>C	1.37:g.72748169C>G	ENSP00000350364:p.Met3Ile	Somatic	295	0	0		WXS	Illumina HiSeq	Phase_I	273	76	0.278388	NM_173808	Q5VT21|Q6UY06|Q8N440|Q8NAQ3	Missense_Mutation	SNP	ENST00000357731.5	37	CCDS661.1	.	.	.	.	.	.	.	.	.	.	C	7.644	0.681557	0.14907	.	.	ENSG00000172260	ENST00000357731;ENST00000434200	T;T	0.69806	0.85;-0.43	5.14	4.17	0.49024	.	0.093449	0.64402	D	0.000001	T	0.23846	0.0577	N	0.04508	-0.205	0.29795	N	0.832905	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.03887	-1.0995	10	0.15499	T	0.54	-14.4855	14.7993	0.69900	0.0:0.8412:0.1588:0.0	.	1;3	B4DI94;Q7Z3B1	.;NEGR1_HUMAN	I	3;1	ENSP00000350364:M3I;ENSP00000413294:M1I	ENSP00000350364:M3I	M	-	3	0	NEGR1	72520757	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	2.185000	0.42584	2.385000	0.81259	0.561000	0.74099	ATG	.	.	none		0.662	NEGR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026722.4	NM_173808	
WDR88	126248	hgsc.bcm.edu	37	19	33635761	33635761	+	Silent	SNP	C	C	T	rs3848596	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:33635761C>T	ENST00000355868.3	+	3	475	c.399C>T	c.(397-399)gaC>gaT	p.D133D	WDR88_ENST00000592765.1_Silent_p.D133D|WDR88_ENST00000361680.2_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	179	0	0		WXS	Illumina HiSeq	Phase_I	165	81	0.490909	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	
ARHGEF37	389337	hgsc.bcm.edu	37	5	149001551	149001551	+	Missense_Mutation	SNP	A	A	C	rs4629585	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:149001551A>C	ENST00000333677.6	+	9	1424	c.1261A>C	c.(1261-1263)Atg>Ctg	p.M421L		NM_001001669.2	NP_001001669.2	A1IGU5	ARH37_HUMAN	Rho guanine nucleotide exchange factor (GEF) 37	421	BAR. {ECO:0000255|PROSITE- ProRule:PRU00361}.		M -> L (in dbSNP:rs4629585).			cytoplasm (GO:0005737)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			large_intestine(5)|lung(6)|ovary(1)|prostate(2)|stomach(3)	17						GGGCCAGATCATGTGCACATT	0.597													C|||	2188	0.436901	0.3797	0.4769	5008	,	,		20370	0.5		0.34	False		,,,				2504	0.5204				p.M421L		Atlas-SNP	.											.	ARHGEF37	45	.	0			c.A1261C						PASS	.	C	LEU/MET	1617,2629		330,957,836	38.0	47.0	44.0		1261	4.1	1.0	5	dbSNP_111	44	3010,5458		529,1952,1753	yes	missense	ARHGEF37	NM_001001669.2	15	859,2909,2589	CC,CA,AA		35.5456,38.0829,36.393	benign	421/676	149001551	4627,8087	2123	4234	6357	SO:0001583	missense	389337	exon9			CAGATCATGTGCA	BC041325	CCDS43385.1	5q33.1	2012-07-24			ENSG00000183111	ENSG00000183111		"""Rho guanine nucleotide exchange factors"""	34430	protein-coding gene	gene with protein product							Standard	XM_005268448		Approved	FLJ41603	uc003lra.1	A1IGU5	OTTHUMG00000163491	ENST00000333677.6:c.1261A>C	5.37:g.149001551A>C	ENSP00000328083:p.Met421Leu	Somatic	226	1	0.00442478		WXS	Illumina HiSeq	Phase_I	203	91	0.448276	NM_001001669	Q6ZW51	Missense_Mutation	SNP	ENST00000333677.6	37	CCDS43385.1	891	0.40796703296703296	176	0.35772357723577236	151	0.4171270718232044	305	0.5332167832167832	259	0.341688654353562	C	0.062	-1.222824	0.01530	0.380829	0.355456	ENSG00000183111	ENST00000333677	T	0.47177	0.85	6.17	4.1	0.47936	BAR (2);	0.071421	0.56097	N	0.000024	T	0.00012	0.0000	N	0.00088	-2.19	0.58432	P	2.9999999999752447E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.46775	-0.9167	9	0.02654	T	1	-1.3808	8.8224	0.35034	0.1207:0.6947:0.0:0.1846	rs4629585;rs52811837;rs57716052;rs4629585	421	A1IGU5	ARH37_HUMAN	L	421	ENSP00000328083:M421L	ENSP00000328083:M421L	M	+	1	0	ARHGEF37	148981744	0.017000	0.18338	1.000000	0.80357	0.242000	0.25591	0.122000	0.15687	0.956000	0.37904	-0.121000	0.15023	ATG	A|0.596;C|0.404	0.404	strong		0.597	ARHGEF37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373763.1	NM_001001669	
OR51A2	401667	hgsc.bcm.edu	37	11	4976447	4976447	+	Missense_Mutation	SNP	C	C	G	rs77497717	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:4976447C>G	ENST00000380371.1	-	1	496	c.497G>C	c.(496-498)aGa>aCa	p.R166T	MMP26_ENST00000477339.1_Intron|MMP26_ENST00000380390.1_Intron	NM_001004748.1	NP_001004748.1	Q8NGJ7	O51A2_HUMAN	olfactory receptor, family 51, subfamily A, member 2	166						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(4)|kidney(1)|large_intestine(3)|lung(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	17		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;3.22e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0284)|LUSC - Lung squamous cell carcinoma(625;0.19)		TCTCAAGCTTCTTAAAGTGAA	0.418													C|||	435	0.086861	0.112	0.0865	5008	,	,		14020	0.0069		0.1243	False		,,,				2504	0.0971				p.R166T		Atlas-SNP	.											.	OR51A2	40	.	0			c.G497C						PASS	.		THR/ARG	642,3510		222,198,1656	152.0	132.0	139.0		497	-0.6	0.0	11	dbSNP_131	139	1811,6107		680,451,2828	no	missense	OR51A2	NM_001004748.1	71	902,649,4484	GG,GC,CC		22.8719,15.4624,20.3231	possibly-damaging	166/314	4976447	2453,9617	2076	3959	6035	SO:0001583	missense	401667	exon1			AAGCTTCTTAAAG	AB065797	CCDS31368.1	11p15.4	2012-08-09			ENSG00000205496	ENSG00000205496		"""GPCR / Class A : Olfactory receptors"""	14764	protein-coding gene	gene with protein product							Standard	NM_001004748		Approved		uc010qyt.2	Q8NGJ7	OTTHUMG00000066602	ENST00000380371.1:c.497G>C	11.37:g.4976447C>G	ENSP00000369729:p.Arg166Thr	Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	623	621	0.99679	NM_001004748		Missense_Mutation	SNP	ENST00000380371.1	37	CCDS31368.1	213	0.09752747252747253	40	0.08130081300813008	46	0.1270718232044199	3	0.005244755244755245	124	0.16358839050131926	-	7.414	0.635312	0.14322	0.154624	0.228719	ENSG00000205496	ENST00000380371	T	0.71817	-0.6	3.13	-0.611	0.11601	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00039	0.0001	L	0.45051	1.395	0.80722	P	0.0	B	0.23249	0.082	B	0.24701	0.055	T	0.09400	-1.0676	8	0.66056	D	0.02	.	7.4986	0.27505	0.0:0.3281:0.0:0.6719	.	166	Q8NGJ7	O51A2_HUMAN	T	166	ENSP00000369729:R166T	ENSP00000369729:R166T	R	-	2	0	OR51A2	4933023	0.000000	0.05858	0.007000	0.13788	0.007000	0.05969	-2.709000	0.00819	0.017000	0.15025	-0.512000	0.04463	AGA	C|0.897;G|0.103	0.103	strong		0.418	OR51A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142809.1	NM_001004748	
ACTR3B	57180	hgsc.bcm.edu	37	7	152520490	152520490	+	Missense_Mutation	SNP	C	C	T	rs140327402	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:152520490C>T	ENST00000256001.8	+	8	882	c.748C>T	c.(748-750)Cgg>Tgg	p.R250W	ACTR3B_ENST00000377776.3_Missense_Mutation_p.R250W|ACTR3B_ENST00000537264.1_Missense_Mutation_p.R162W|ACTR3B_ENST00000397282.2_Missense_Mutation_p.R162W	NM_020445.5	NP_065178.1	Q9P1U1	ARP3B_HUMAN	ARP3 actin-related protein 3 homolog B (yeast)	250			R -> Q (in dbSNP:rs2260545).			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)		TGTGGATCCCCGGAAGTGGAT	0.418																																					p.R250W		Atlas-SNP	.											ACTR3B,NS,haematopoietic_neoplasm,0,1	ACTR3B	50	1	0			c.C748T						scavenged	.						239.0	179.0	199.0					7																	152520490		2203	4300	6503	SO:0001583	missense	57180	exon8			GATCCCCGGAAGT		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.748C>T	7.37:g.152520490C>T	ENSP00000256001:p.Arg250Trp	Somatic	197	0	0		WXS	Illumina HiSeq	Phase_I	232	60	0.258621	NM_020445	A8MTG1|B4DFW4|Q7Z526|Q96BT2	Missense_Mutation	SNP	ENST00000256001.8	37	CCDS5934.1	37	0.01694139194139194	2	0.0040650406504065045	4	0.011049723756906077	2	0.0034965034965034965	29	0.03825857519788918	C	10.03	1.238713	0.22711	.	.	ENSG00000133627	ENST00000377776;ENST00000256001;ENST00000397282;ENST00000537264	T;T;T;T	0.09163	3.01;3.01;3.01;3.01	3.88	3.88	0.44766	.	0.115245	0.35708	U	0.003040	T	0.01800	0.0057	L	0.29908	0.895	0.09310	N	1	B;B	0.06786	0.0;0.001	B;B	0.04013	0.0;0.001	T	0.20273	-1.0280	10	0.87932	D	0	.	11.2938	0.49267	0.0:0.8151:0.1849:0.0	.	250;250	Q9P1U1-3;Q9P1U1	.;ARP3B_HUMAN	W	250;250;162;162	ENSP00000367007:R250W;ENSP00000256001:R250W;ENSP00000380452:R162W;ENSP00000446157:R162W	ENSP00000256001:R250W	R	+	1	2	ACTR3B	152151423	0.002000	0.14202	0.921000	0.36526	0.839000	0.47603	0.523000	0.22925	1.879000	0.54435	0.491000	0.48974	CGG	C|0.500;T|0.500	0.500	weak		0.418	ACTR3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322803.1	NM_020445	
BMP6	654	hgsc.bcm.edu	37	6	7862631	7862631	+	Silent	SNP	G	G	C	rs17557	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:7862631G>C	ENST00000283147.6	+	4	1263	c.1104G>C	c.(1102-1104)gtG>gtC	p.V368V		NM_001718.4	NP_001709.1	P22004	BMP6_HUMAN	bone morphogenetic protein 6	368					BMP signaling pathway (GO:0030509)|cartilage development (GO:0051216)|cellular response to mechanical stimulus (GO:0071260)|endochondral ossification (GO:0001958)|eye development (GO:0001654)|growth (GO:0040007)|immune response (GO:0006955)|inflammatory response (GO:0006954)|kidney development (GO:0001822)|male genitalia development (GO:0030539)|osteoblast differentiation (GO:0001649)|positive regulation of aldosterone biosynthetic process (GO:0032349)|positive regulation of aldosterone secretion (GO:2000860)|positive regulation of bone mineralization (GO:0030501)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of DNA-dependent DNA replication (GO:2000105)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of protein secretion (GO:0050714)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to activity (GO:0014823)|response to glucocorticoid (GO:0051384)|response to iron ion (GO:0010039)|response to magnesium ion (GO:0032026)|response to retinoic acid (GO:0032526)|skeletal system development (GO:0001501)|SMAD protein signal transduction (GO:0060395)|type B pancreatic cell development (GO:0003323)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|membrane-bounded vesicle (GO:0031988)	BMP receptor binding (GO:0070700)|protein heterodimerization activity (GO:0046982)			breast(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(6)|ovary(1)|prostate(1)	23	Ovarian(93;0.0721)					TGAGTGAGGTGCACGTGCGCA	0.637													C|||	2993	0.597644	0.7481	0.6095	5008	,	,		17438	0.7411		0.3917	False		,,,				2504	0.4499				p.V368V		Atlas-SNP	.											.	BMP6	67	.	0			c.G1104C						PASS	.	C		3050,1356	449.8+/-349.2	1082,886,235	77.0	77.0	77.0		1104	0.1	1.0	6	dbSNP_63	77	3224,5376	651.1+/-400.8	590,2044,1666	no	coding-synonymous	BMP6	NM_001718.4		1672,2930,1901	CC,CG,GG		37.4884,30.7762,48.2393		368/514	7862631	6274,6732	2203	4300	6503	SO:0001819	synonymous_variant	654	exon4			TGAGGTGCACGTG	AF083030	CCDS4503.1	6p24-p23	2014-01-30	2003-10-06		ENSG00000153162	ENSG00000153162		"""Bone morphogenetic proteins"", ""Endogenous ligands"""	1073	protein-coding gene	gene with protein product		112266	"""vegetal related growth factor (TGFB-related)"""	VGR		1427904, 1453478	Standard	NM_001718		Approved	VGR1	uc003mxu.4	P22004	OTTHUMG00000014217	ENST00000283147.6:c.1104G>C	6.37:g.7862631G>C		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	87	33	0.37931	NM_001718	Q5TCP3	Silent	SNP	ENST00000283147.6	37	CCDS4503.1																																																																																			G|0.489;C|0.511	0.511	strong		0.637	BMP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039794.1	NM_001718	
MFHAS1	9258	hgsc.bcm.edu	37	8	8748148	8748148	+	Silent	SNP	A	A	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:8748148A>C	ENST00000276282.6	-	1	3007	c.2421T>G	c.(2419-2421)ctT>ctG	p.L807L		NM_004225.2	NP_004216.2	Q9Y4C4	MFHA1_HUMAN	malignant fibrous histiocytoma amplified sequence 1	807										endometrium(1)|kidney(3)|large_intestine(7)|lung(6)|ovary(1)|prostate(2)|stomach(1)	21		Hepatocellular(245;0.217)		COAD - Colon adenocarcinoma(149;0.124)		CATGAGGCTTAAGCAGCAACC	0.572																																					p.L807L	Melanoma(103;1201 2045 17515 28966)	Atlas-SNP	.											.	MFHAS1	58	.	0			c.T2421G						PASS	.						67.0	66.0	66.0					8																	8748148		2203	4300	6503	SO:0001819	synonymous_variant	9258	exon1			AGGCTTAAGCAGC	AB016816	CCDS34844.1	8p23.1	2014-03-07			ENSG00000147324	ENSG00000147324			16982	protein-coding gene	gene with protein product	"""leucine rich repeat containing 65"", ""malignant fibrous histiocytoma-amplified sequences with leucine-rich tandem repeats 1"""	605352				9973190	Standard	NM_004225		Approved	MASL1, LRRC65	uc003wsj.1	Q9Y4C4	OTTHUMG00000163676	ENST00000276282.6:c.2421T>G	8.37:g.8748148A>C		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	61	35	0.57377	NM_004225	Q96CI0	Silent	SNP	ENST00000276282.6	37	CCDS34844.1																																																																																			.	.	none		0.572	MFHAS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374724.2	NM_004225	
SPON2	10417	hgsc.bcm.edu	37	4	1165748	1165748	+	Missense_Mutation	SNP	T	T	C	rs6836335	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:1165748T>C	ENST00000290902.5	-	2	444	c.112A>G	c.(112-114)Aga>Gga	p.R38G	SPON2_ENST00000431380.1_Missense_Mutation_p.R38G	NM_012445.3	NP_036577	Q9BUD6	SPON2_HUMAN	spondin 2, extracellular matrix protein	38	Spondin. {ECO:0000255|PROSITE- ProRule:PRU00364}.		R -> G (in dbSNP:rs6836335).		axon guidance (GO:0007411)|cell adhesion (GO:0007155)|innate immune response (GO:0045087)	extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|pancreas(1)|skin(1)	9			OV - Ovarian serous cystadenocarcinoma(23;0.00805)	UCEC - Uterine corpus endometrioid carcinoma (64;0.139)|Colorectal(103;0.19)		GCCAGGGCTCTGGCGGAACAG	0.692													T|||	690	0.13778	0.2943	0.0994	5008	,	,		12371	0.001		0.1312	False		,,,				2504	0.1012				p.R38G		Atlas-SNP	.											.	SPON2	22	.	0			c.A112G						PASS	.	T	GLY/ARG,GLY/ARG,GLY/ARG	1280,3118		190,900,1109	36.0	49.0	45.0		112,112,112	0.2	0.0	4	dbSNP_116	45	1039,7541		64,911,3315	yes	missense,missense,missense	SPON2	NM_001128325.2,NM_001199021.1,NM_012445.3	125,125,125	254,1811,4424	CC,CT,TT		12.1096,29.1041,17.8687	benign,benign,benign	38/332,38/332,38/332	1165748	2319,10659	2199	4290	6489	SO:0001583	missense	10417	exon2			GGGCTCTGGCGGA	AB027466	CCDS3347.1	4p16.3	2008-07-29			ENSG00000159674	ENSG00000159674			11253	protein-coding gene	gene with protein product	"""Mindin"", ""M-spondin"""	605918				10512675, 15094111	Standard	NM_012445		Approved	DIL1	uc003gco.4	Q9BUD6	OTTHUMG00000089002	ENST00000290902.5:c.112A>G	4.37:g.1165748T>C	ENSP00000290902:p.Arg38Gly	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	151	67	0.443709	NM_012445	D3DVN9|Q4W5N4|Q9ULW1	Missense_Mutation	SNP	ENST00000290902.5	37	CCDS3347.1	280	0.1282051282051282	139	0.28252032520325204	42	0.11602209944751381	1	0.0017482517482517483	98	0.12928759894459102	T	12.21	1.868543	0.32977	0.291041	0.121096	ENSG00000159674	ENST00000290902;ENST00000431380;ENST00000503765;ENST00000515004;ENST00000502483	T;T;T;T;T	0.32515	2.95;2.95;1.52;1.46;1.45	4.74	0.199	0.15175	Spondin, N-terminal (1);	0.838802	0.10780	N	0.634936	T	0.00012	0.0000	L	0.53249	1.67	0.54753	P	1.0999999999983245E-5	P;P;B	0.37688	0.605;0.459;0.28	B;B;B	0.36464	0.225;0.017;0.019	T	0.32079	-0.9920	9	0.25751	T	0.34	.	2.1123	0.03706	0.1008:0.322:0.2969:0.2803	rs6836335;rs6836335	38;38;38	D6RB12;D3DVN9;Q9BUD6	.;.;SPON2_HUMAN	G	38	ENSP00000290902:R38G;ENSP00000394832:R38G;ENSP00000424542:R38G;ENSP00000425871:R38G;ENSP00000422516:R38G	ENSP00000290902:R38G	R	-	1	2	SPON2	1155748	0.792000	0.28813	0.001000	0.08648	0.067000	0.16453	1.458000	0.35223	-0.012000	0.14223	0.334000	0.21626	AGA	T|0.847;C|0.153	0.153	strong		0.692	SPON2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000202080.2		
GLI3	2737	hgsc.bcm.edu	37	7	42007201	42007201	+	Missense_Mutation	SNP	T	T	C	rs62622373	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:42007201T>C	ENST00000395925.3	-	14	2508	c.2424A>G	c.(2422-2424)atA>atG	p.I808M	GLI3_ENST00000479210.1_5'UTR	NM_000168.5	NP_000159.3	P10071	GLI3_HUMAN	GLI family zinc finger 3	808			I -> M (in GCPS; dbSNP:rs62622373). {ECO:0000269|PubMed:10441342}.		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						CACCATTTCCTATGAGAGGAG	0.443									Pallister-Hall syndrome;Greig Cephalopolysyndactyly				T|||	3	0.000599042	0.0	0.0014	5008	,	,		18932	0.0		0.002	False		,,,				2504	0.0				p.I808M		Atlas-SNP	.											.	GLI3	312	.	0			c.A2424G	GRCh37	CM990707	GLI3	M	rs62622373	PASS	.	T	MET/ILE	3,4403	6.2+/-15.9	0,3,2200	197.0	214.0	208.0		2424	4.2	1.0	7	dbSNP_129	208	26,8574	16.6+/-54.9	0,26,4274	yes	missense	GLI3	NM_000168.5	10	0,29,6474	CC,CT,TT		0.3023,0.0681,0.223	possibly-damaging	808/1581	42007201	29,12977	2203	4300	6503	SO:0001583	missense	2737	exon14	Familial Cancer Database	;	ATTTCCTATGAGA		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.2424A>G	7.37:g.42007201T>C	ENSP00000379258:p.Ile808Met	Somatic	226	1	0.00442478		WXS	Illumina HiSeq	Phase_I	182	132	0.725275	NM_000168	A4D1W1|O75219|Q17RW4|Q75MT0|Q75MU9|Q9UDT5|Q9UJ39	Missense_Mutation	SNP	ENST00000395925.3	37	CCDS5465.1	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	T	15.74	2.921346	0.52653	6.81E-4	0.003023	ENSG00000106571	ENST00000395925	D	0.92545	-3.06	5.31	4.15	0.48705	.	0.203242	0.52532	D	0.000066	D	0.90428	0.7003	L	0.57536	1.79	0.80722	D	1	D	0.54397	0.966	P	0.48873	0.593	D	0.87818	0.2636	10	0.46703	T	0.11	.	6.3136	0.21178	0.1403:0.0746:0.0:0.7851	rs62622373	808	P10071	GLI3_HUMAN	M	808	ENSP00000379258:I808M	ENSP00000379258:I808M	I	-	3	3	GLI3	41973726	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.344000	0.44010	0.861000	0.35504	0.533000	0.62120	ATA	T|0.999;C|0.001	0.001	strong		0.443	GLI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250806.3	NM_000168	
BTN3A2	11118	hgsc.bcm.edu	37	6	26370707	26370707	+	Silent	SNP	T	T	C	rs9379862	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:26370707T>C	ENST00000356386.2	+	5	779	c.591T>C	c.(589-591)gaT>gaC	p.D197D	BTN3A2_ENST00000396948.1_Silent_p.D197D|BTN3A2_ENST00000396934.3_Silent_p.D174D|BTN3A2_ENST00000532994.1_3'UTR|BTN3A2_ENST00000527422.1_Silent_p.D197D|BTN3A2_ENST00000508906.2_Silent_p.D155D|BTN3A2_ENST00000377708.2_Silent_p.D197D	NM_001197246.2|NM_001197247.1|NM_007047.3	NP_001184175.1|NP_001184176.1|NP_008978.2	P78410	BT3A2_HUMAN	butyrophilin, subfamily 3, member A2	197					interferon-gamma secretion (GO:0072643)|T cell mediated immunity (GO:0002456)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(5)	10						TGGTTGCAGATGGAGTGGGCC	0.567													t|||	1182	0.236022	0.3109	0.1931	5008	,	,		18947	0.124		0.2396	False		,,,				2504	0.2771				p.D197D		Atlas-SNP	.											.	BTN3A2	44	.	0			c.T591C						PASS	.	C	,,,,	1355,3051		203,949,1051	153.0	143.0	146.0		591,591,522,465,591	-4.6	0.0	6	dbSNP_119	146	2112,6488		249,1614,2437	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	BTN3A2	NM_001197246.1,NM_001197247.1,NM_001197248.1,NM_001197249.1,NM_007047.3	,,,,	452,2563,3488	CC,CT,TT		24.5581,30.7535,26.6569	,,,,	197/335,197/335,174/312,155/293,197/335	26370707	3467,9539	2203	4300	6503	SO:0001819	synonymous_variant	11118	exon3			TGCAGATGGAGTG	U90546	CCDS4605.1, CCDS56399.1, CCDS56400.1	6p22.1	2014-01-14			ENSG00000186470	ENSG00000186470		"""Immunoglobulin superfamily / V-set domain containing"", ""Butyrophilins"""	1139	protein-coding gene	gene with protein product		613594				9149941	Standard	NM_007047		Approved	BTN3.2	uc010jqi.2	P78410	OTTHUMG00000014450	ENST00000356386.2:c.591T>C	6.37:g.26370707T>C		Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	127	126	0.992126	NM_001197246	B4DRT7|B4E103|F5H791|F8W6E0|O00477|O15338|O75658|Q76PA0|Q9BU81|Q9NR44	Silent	SNP	ENST00000356386.2	37	CCDS4605.1																																																																																			T|0.752;C|0.248	0.248	strong		0.567	BTN3A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040113.2		
PPWD1	23398	hgsc.bcm.edu	37	5	64881936	64881936	+	Silent	SNP	A	A	G	rs27141	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:64881936A>G	ENST00000261308.5	+	10	1797	c.1725A>G	c.(1723-1725)ccA>ccG	p.P575P	PPWD1_ENST00000535264.1_Silent_p.P545P|PPWD1_ENST00000538977.1_Silent_p.P419P	NM_015342.3	NP_056157.1	Q96BP3	PPWD1_HUMAN	peptidylprolyl isomerase domain and WD repeat containing 1	575	PPIase cyclophilin-type. {ECO:0000255|PROSITE-ProRule:PRU00156}.				mRNA splicing, via spliceosome (GO:0000398)|protein folding (GO:0006457)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)	peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)	19		Lung NSC(167;7.21e-05)|Prostate(74;0.0174)|Ovarian(174;0.186)		Lung(70;0.00451)		ATGACAGGCCATACACACTCA	0.413													G|||	2897	0.578474	0.6309	0.5115	5008	,	,		20230	0.4137		0.6203	False		,,,				2504	0.682				p.P575P		Atlas-SNP	.											.	PPWD1	47	.	0			c.A1725G						PASS	.	G		2741,1665	507.6+/-366.7	852,1037,314	145.0	130.0	135.0		1725	-5.6	0.8	5	dbSNP_76	135	5584,3016	465.8+/-366.6	1800,1984,516	yes	coding-synonymous	PPWD1	NM_015342.2		2652,3021,830	GG,GA,AA		35.0698,37.7894,35.9911		575/647	64881936	8325,4681	2203	4300	6503	SO:0001819	synonymous_variant	23398	exon10			CAGGCCATACACA	AK025679	CCDS3985.1, CCDS64161.1, CCDS64162.1	5q12.3	2013-01-09			ENSG00000113593	ENSG00000113593		"""WD repeat domain containing"""	28954	protein-coding gene	gene with protein product						7584044	Standard	NM_015342		Approved	KIAA0073	uc003jtv.5	Q96BP3	OTTHUMG00000131226	ENST00000261308.5:c.1725A>G	5.37:g.64881936A>G		Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	186	185	0.994624	NM_015342	B4DWR9|Q15002|Q7KZ89	Silent	SNP	ENST00000261308.5	37	CCDS3985.1																																																																																			A|0.396;G|0.604	0.604	strong		0.413	PPWD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253970.2	NM_015342	
ZNF417	147687	hgsc.bcm.edu	37	19	58421128	58421128	+	Missense_Mutation	SNP	C	C	T	rs201944488	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:58421128C>T	ENST00000312026.5	-	3	682	c.518G>A	c.(517-519)cGc>cAc	p.R173H	ZNF417_ENST00000536263.1_5'UTR|ZNF417_ENST00000595559.1_Missense_Mutation_p.R172H|CTD-2583A14.9_ENST00000602124.1_Intron	NM_152475.2	NP_689688.2	Q8TAU3	ZN417_HUMAN	zinc finger protein 417	173				R -> H (in Ref. 3; AAH25783). {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)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|stomach(3)|upper_aerodigestive_tract(1)	18		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0151)		CCCAAACTCGCGGAAGACAAA	0.478													c|||	1646	0.328674	0.2496	0.3069	5008	,	,		19752	0.3631		0.3708	False		,,,				2504	0.3722				p.R173H		Atlas-SNP	.											ZNF417,NS,carcinoma,+1,1	ZNF417	44	1	0			c.G518A						scavenged	.	C	HIS/ARG	938,2814		296,346,1234	50.0	52.0	51.0		518	-3.3	0.0	19	dbSNP_134	51	3014,4976		1034,946,2015	no	missense	ZNF417	NM_152475.2	29	1330,1292,3249	TT,TC,CC		37.7222,25.0,33.657	benign	173/576	58421128	3952,7790	1876	3995	5871	SO:0001583	missense	147687	exon3			AACTCGCGGAAGA	BC025783	CCDS12965.1, CCDS74469.1	19q13.43	2013-01-08				ENSG00000173480		"""Zinc fingers, C2H2-type"", ""-"""	20646	protein-coding gene	gene with protein product							Standard	NM_152475		Approved	MGC34079	uc002qqq.3	Q8TAU3		ENST00000312026.5:c.518G>A	19.37:g.58421128C>T	ENSP00000311319:p.Arg173His	Somatic	396	1	0.00252525		WXS	Illumina HiSeq	Phase_I	492	345	0.701219	NM_152475	B4DEU1	Missense_Mutation	SNP	ENST00000312026.5	37	CCDS12965.1	554	0.25366300366300365	111	0.22560975609756098	90	0.24861878453038674	138	0.24125874125874125	215	0.2836411609498681	.	0.284	-0.984691	0.02180	0.25	0.377222	ENSG00000173480	ENST00000312026	T	0.06294	3.32	1.86	-3.31	0.04988	.	.	.	.	.	T	0.00012	0.0000	N	0.16201	0.385	0.53688	P	2.999999999997449E-5	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.47086	-0.9144	8	0.41790	T	0.15	.	7.2829	0.26322	0.0:0.4727:0.0:0.5273	.	173;173	F5H0M9;Q8TAU3	.;ZN417_HUMAN	H	173	ENSP00000311319:R173H	ENSP00000311319:R173H	R	-	2	0	ZNF417	63112940	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.558000	0.05978	-0.695000	0.05105	-2.164000	0.00325	CGC	C|0.500;T|0.500	0.500	weak		0.478	ZNF417-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466860.1	NM_152475	
FRMD3	257019	hgsc.bcm.edu	37	9	85863091	85863091	+	Silent	SNP	A	A	G	rs10114696	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:85863091A>G	ENST00000304195.3	-	14	1742	c.1536T>C	c.(1534-1536)taT>taC	p.Y512Y	FRMD3_ENST00000328788.1_Silent_p.Y169Y|FRMD3_ENST00000376438.1_Silent_p.Y512Y|FRMD3_ENST00000465485.1_5'UTR|FRMD3_ENST00000376434.1_Silent_p.Y318Y	NM_001244960.1|NM_174938.5	NP_001231889.1|NP_777598.3	A2A2Y4	FRMD3_HUMAN	FERM domain containing 3	512						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extrinsic component of membrane (GO:0019898)|integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|liver(1)|lung(15)|ovary(1)|upper_aerodigestive_tract(1)	30						TCAGAATGTCATAGCTCCACG	0.507													.|||	1404	0.280351	0.1415	0.2767	5008	,	,		19160	0.2014		0.3936	False		,,,				2504	0.4356				p.Y512Y		Atlas-SNP	.											.	FRMD3	96	.	0			c.T1536C						PASS	.	A		696,3268		61,574,1347	80.0	83.0	82.0		1536	4.6	1.0	9	dbSNP_119	82	3451,4897		728,1995,1451	no	coding-synonymous	FRMD3	NM_174938.4		789,2569,2798	GG,GA,AA		41.3392,17.558,33.6826		512/598	85863091	4147,8165	1982	4174	6156	SO:0001819	synonymous_variant	257019	exon14			AATGTCATAGCTC	AK094281	CCDS43840.1, CCDS59131.1, CCDS59132.1, CCDS59133.1, CCDS75852.1	9q21.33	2008-02-05			ENSG00000172159	ENSG00000172159			24125	protein-coding gene	gene with protein product		607619				12601556	Standard	NM_174938		Approved	EPB41L4O, MGC20553	uc004ams.2	A2A2Y4	OTTHUMG00000020103	ENST00000304195.3:c.1536T>C	9.37:g.85863091A>G		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	75	29	0.386667	NM_174938	A8MQB0|B4DN14|Q53EP2|Q5JV59|Q5VZA1|Q86WP8|Q8IZ44|Q8N3Y5|Q8N9L2	Silent	SNP	ENST00000304195.3	37	CCDS43840.1																																																																																			A|0.685;G|0.315	0.315	strong		0.507	FRMD3-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157355.1	NM_174938	
OR52H1	390067	hgsc.bcm.edu	37	11	5566076	5566076	+	Silent	SNP	G	G	A	rs139835065	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:5566076G>A	ENST00000322653.4	-	1	703	c.678C>T	c.(676-678)taC>taT	p.Y226Y	HBG2_ENST00000380259.2_Intron	NM_001005289.1	NP_001005289.1	Q8NGJ2	O52H1_HUMAN	olfactory receptor, family 52, subfamily H, member 1	226						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(5)|ovary(1)|prostate(1)|skin(2)	20		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;5.33e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		GGATGTGTGCGTAGGAAACAG	0.502													G|||	6	0.00119808	0.0	0.0	5008	,	,		23186	0.001		0.003	False		,,,				2504	0.002				p.Y226Y		Atlas-SNP	.											.	OR52H1	46	.	0			c.C678T						PASS	.	G		0,4402		0,0,2201	120.0	99.0	106.0		678	0.2	0.0	11	dbSNP_134	106	32,8562	22.8+/-68.1	0,32,4265	no	coding-synonymous	OR52H1	NM_001005289.1		0,32,6466	AA,AG,GG		0.3724,0.0,0.2462		226/321	5566076	32,12964	2201	4297	6498	SO:0001819	synonymous_variant	390067	exon1			GTGTGCGTAGGAA	AB065802	CCDS31386.1	11p15.4	2012-08-09			ENSG00000181616	ENSG00000181616		"""GPCR / Class A : Olfactory receptors"""	15218	protein-coding gene	gene with protein product							Standard	NM_001005289		Approved		uc010qzh.2	Q8NGJ2	OTTHUMG00000066909	ENST00000322653.4:c.678C>T	11.37:g.5566076G>A		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	123	108	0.878049	NM_001005289	B9EH26|Q6IF79	Silent	SNP	ENST00000322653.4	37	CCDS31386.1																																																																																			G|0.998;A|0.002	0.002	strong		0.502	OR52H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143400.1	NM_001005289	
ACACB	32	hgsc.bcm.edu	37	12	109644616	109644616	+	Silent	SNP	C	C	T	rs17848814	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:109644616C>T	ENST00000338432.7	+	20	3134	c.3015C>T	c.(3013-3015)aaC>aaT	p.N1005N	ACACB_ENST00000377848.3_Silent_p.N1005N|ACACB_ENST00000377854.5_Silent_p.N1005N			O00763	ACACB_HUMAN	acetyl-CoA carboxylase beta	1005					acetyl-CoA metabolic process (GO:0006084)|biotin metabolic process (GO:0006768)|carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|malonyl-CoA biosynthetic process (GO:2001295)|positive regulation of cellular metabolic process (GO:0031325)|protein homotetramerization (GO:0051289)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	acetyl-CoA carboxylase activity (GO:0003989)|ATP binding (GO:0005524)|biotin binding (GO:0009374)|biotin carboxylase activity (GO:0004075)|metal ion binding (GO:0046872)	p.N1005N(1)		NS(1)|breast(2)|endometrium(9)|kidney(5)|large_intestine(20)|lung(40)|ovary(6)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95					Adenine(DB00173)|Biotin(DB00121)	ACCTCACCAACGTCATGAGTG	0.542													C|||	450	0.0898562	0.289	0.0432	5008	,	,		16239	0.0099		0.0258	False		,,,				2504	0.002				p.N1005N		Atlas-SNP	.											ACACB,NS,carcinoma,0,1	ACACB	330	1	1	Substitution - coding silent(1)	stomach(1)	c.C3015T						PASS	.	C		1078,3328	391.2+/-328.0	119,840,1244	145.0	136.0	139.0		3015	-4.6	0.4	12	dbSNP_123	139	138,8462	69.0+/-131.5	0,138,4162	no	coding-synonymous	ACACB	NM_001093.3		119,978,5406	TT,TC,CC		1.6047,24.4666,9.3495		1005/2459	109644616	1216,11790	2203	4300	6503	SO:0001819	synonymous_variant	32	exon19			CACCAACGTCATG	U89344	CCDS31898.1	12q24.1	2010-05-07	2010-04-30		ENSG00000076555	ENSG00000076555	6.4.1.2		85	protein-coding gene	gene with protein product	"""acetyl-CoA carboxylase 2"""	601557	"""acetyl-Coenzyme A carboxylase beta"""			8670171	Standard	NM_001093		Approved	HACC275, ACC2, ACCB	uc001toc.3	O00763	OTTHUMG00000169250	ENST00000338432.7:c.3015C>T	12.37:g.109644616C>T		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	114	46	0.403509	NM_001093	A6NK36|Q16852|Q1HEC1|Q6KE87|Q6KE89|Q6TY48	Silent	SNP	ENST00000338432.7	37	CCDS31898.1																																																																																			C|0.914;T|0.086	0.086	strong		0.542	ACACB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403077.1	NM_001093	
GPATCH1	55094	hgsc.bcm.edu	37	19	33602757	33602757	+	Silent	SNP	C	C	T	rs10420258	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	145	0	0		WXS	Illumina HiSeq	Phase_I	98	42	0.428571	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	
PDE4DIP	9659	hgsc.bcm.edu	37	1	145021150	145021150	+	Missense_Mutation	SNP	T	T	C	rs11538401	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:145021150T>C	ENST00000530740.1	-	2	289	c.251A>G	c.(250-252)gAt>gGt	p.D84G	PDE4DIP_ENST00000369359.4_Missense_Mutation_p.D84G|PDE4DIP_ENST00000493130.2_Missense_Mutation_p.D13G|RP11-326G21.1_ENST00000610119.1_RNA|PDE4DIP_ENST00000313382.9_Missense_Mutation_p.D13G|PDE4DIP_ENST00000478649.2_Missense_Mutation_p.D13G|PDE4DIP_ENST00000369348.3_Missense_Mutation_p.D84G			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	0					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.D84G(1)		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)		CTCCCCATCATCCTCTGCAAA	0.448			T	PDGFRB	MPD																																p.D84G		Atlas-SNP	.		Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	PDE4DIP_ENST00000369348,NS,carcinoma,0,1	PDE4DIP	817	1	1	Substitution - Missense(1)	kidney(1)	c.A251G						PASS	.	T	GLY/ASP,GLY/ASP	50,4356	36.8+/-68.6	0,50,2153	210.0	192.0	198.0		38,251	4.3	1.0	1	dbSNP_131	198	41,8559	16.0+/-53.3	0,41,4259	yes	missense,missense	PDE4DIP	NM_001198832.1,NM_022359.5	94,94	0,91,6412	CC,CT,TT		0.4767,1.1348,0.6997	,	13/2241,84/311	145021150	91,12915	2203	4300	6503	SO:0001583	missense	9659	exon2			CCATCATCCTCTG	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	ENST00000530740.1:c.251A>G	1.37:g.145021150T>C	ENSP00000435654:p.Asp84Gly	Somatic	234	0	0		WXS	Illumina HiSeq	Phase_I	224	26	0.116071	NM_022359	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	ENST00000530740.1	37		.	.	.	.	.	.	.	.	.	.	T	15.15	2.746559	0.49257	0.011348	0.004767	ENSG00000178104	ENST00000313382;ENST00000530740;ENST00000369359;ENST00000532801;ENST00000530078;ENST00000369348;ENST00000531369;ENST00000493130;ENST00000478649	T;T;T;T;T;T	0.58940	3.99;3.96;3.94;0.3;2.45;1.35	4.33	4.33	0.51752	.	.	.	.	.	T	0.40094	0.1103	L	0.27053	0.805	0.80722	D	1	P;P;P	0.46784	0.877;0.884;0.884	P;P;P	0.49829	0.623;0.516;0.516	T	0.47774	-0.9091	9	0.72032	D	0.01	.	9.8293	0.40932	0.0:0.0:0.0:1.0	.	13;84;13	Q5VU43-3;E9PJ64;E9PQH9	.;.;.	G	13;84;84;13;13;84;14;13;13	ENSP00000327209:D13G;ENSP00000435654:D84G;ENSP00000358366:D84G;ENSP00000436751:D13G;ENSP00000358354:D84G;ENSP00000435616:D14G	ENSP00000327209:D13G	D	-	2	0	PDE4DIP	143732507	1.000000	0.71417	0.997000	0.53966	0.973000	0.67179	3.601000	0.54059	1.820000	0.53075	0.533000	0.62120	GAT	T|0.979;C|0.021	0.021	strong		0.448	PDE4DIP-036	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000384663.2	NM_022359	
TJP2	9414	hgsc.bcm.edu	37	9	71862975	71862975	+	Silent	SNP	C	C	T	rs2282336	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:71862975C>T	ENST00000377245.4	+	19	2923	c.2715C>T	c.(2713-2715)acC>acT	p.T905T	TJP2_ENST00000453658.2_Silent_p.T882T|TJP2_ENST00000535702.1_Silent_p.T909T|TJP2_ENST00000265384.7_Silent_p.T905T|TJP2_ENST00000348208.4_Silent_p.T905T|TJP2_ENST00000498204.1_3'UTR|TJP2_ENST00000539225.1_Silent_p.T936T	NM_004817.3	NP_004808.2	Q9UDY2	ZO2_HUMAN	tight junction protein 2	905					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						CCTACTTAACCGCCATGGGCG	0.557													C|||	1423	0.284145	0.1664	0.451	5008	,	,		18768	0.4514		0.2197	False		,,,				2504	0.2188				p.T936T		Atlas-SNP	.											.	TJP2	120	.	0			c.C2808T						PASS	.	C	,,,,,	754,3652	307.5+/-290.0	78,598,1527	94.0	84.0	87.0		2646,2727,2808,2715,2715,2715	-3.0	1.0	9	dbSNP_100	87	1815,6785	323.8+/-316.2	197,1421,2682	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	,,,,,	275,2019,4209	TT,TC,CC		21.1047,17.113,19.7524	,,,,,	882/1021,909/1158,936/1222,905/994,905/1191,905/1044	71862975	2569,10437	2203	4300	6503	SO:0001819	synonymous_variant	9414	exon19			CTTAACCGCCATG	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.2715C>T	9.37:g.71862975C>T		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	55	33	0.6	NM_001170416	A2A3H9|B7Z2R8|B7Z7T6|F5H301|F5H886|Q15883|Q5VXL0|Q5VXL1|Q8N756|Q8NI14|Q99839|Q9UDY0|Q9UDY1	Silent	SNP	ENST00000377245.4	37	CCDS6627.1																																																																																			C|0.770;T|0.230	0.230	strong		0.557	TJP2-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000052572.2	NM_201629	
MUC5B	727897	hgsc.bcm.edu	37	11	1268955	1268955	+	Silent	SNP	C	C	T	rs2943523	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:1268955C>T	ENST00000529681.1	+	31	10903	c.10845C>T	c.(10843-10845)ctC>ctT	p.L3615L	MUC5B_ENST00000447027.1_Silent_p.L3618L|RP11-532E4.2_ENST00000532061.2_RNA	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	3615	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)		CCCTGGGCCTCGAGTGCCGTG	0.677													-|||	648	0.129393	0.0862	0.2378	5008	,	,		12284	0.0645		0.1491	False		,,,				2504	0.1575				p.L3615L		Atlas-SNP	.											MUC5AC,colon,carcinoma,+1,1	MUC5B	473	1	0			c.C10845T						scavenged	.	T		348,3338		63,222,1558	30.0	32.0	31.0		10845	-8.0	0.0	11	dbSNP_134	31	1209,6841		266,677,3082	no	coding-synonymous	MUC5B	NM_002458.2		329,899,4640	TT,TC,CC		15.0186,9.4411,13.2669		3615/5763	1268955	1557,10179	1843	4025	5868	SO:0001819	synonymous_variant	727897	exon31			GGGCCTCGAGTGC	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.10845C>T	11.37:g.1268955C>T		Somatic	471	0	0		WXS	Illumina HiSeq	Phase_I	830	135	0.162651	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Silent	SNP	ENST00000529681.1	37	CCDS44515.2																																																																																			.	.	weak		0.677	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
OR6K3	391114	hgsc.bcm.edu	37	1	158687896	158687896	+	Missense_Mutation	SNP	C	C	T	rs857705	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	94	47	0.5	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			
PKD1L2	114780	hgsc.bcm.edu	37	16	81253917	81253917	+	RNA	SNP	A	A	G	rs533693628|rs9924530	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:81253917A>G	ENST00000525539.1	-	0	58				PKD1L2_ENST00000337114.4_RNA	NM_052892.3	NP_443124.3	Q7Z442	PK1L2_HUMAN	polycystic kidney disease 1-like 2						ion transport (GO:0006811)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(20)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44						CTCTGGCTTAACAGTGGTGGC	0.567													G|||	2680	0.535144	0.6014	0.562	5008	,	,		20950	0.4405		0.6501	False		,,,				2504	0.4059				p.V20A		Atlas-SNP	.											.	PKD1L2	361	.	0			c.T59C						PASS	.	G	ALA/VAL,ALA/VAL	2630,1446		865,900,273	69.0	69.0	69.0		59,59	3.2	0.0	16	dbSNP_119	69	5299,3093		1657,1985,554	yes	missense,missense	PKD1L2	NM_052892.3,NM_001076780.1	64,64	2522,2885,827	GG,GA,AA		36.8565,35.476,36.4052	benign,benign	20/2460,20/992	81253917	7929,4539	2038	4196	6234			114780	exon1			GGCTTAACAGTGG	AY164483	CCDS61998.1, CCDS61999.1	16q23.2	2014-09-11			ENSG00000166473	ENSG00000166473			21715	protein-coding gene	gene with protein product		607894				12782129	Standard	NM_052892		Approved	KIAA1879	uc002fgf.1	Q7Z442	OTTHUMG00000166126		16.37:g.81253917A>G		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	188	188	1	NM_001076780	Q6UEE1|Q6ZN46|Q6ZSP2|Q8N1H9|Q96CL2|Q96Q08	Missense_Mutation	SNP	ENST00000525539.1	37		1251	0.5728021978021978	301	0.6117886178861789	226	0.6243093922651933	233	0.40734265734265734	491	0.6477572559366754	G	0.019	-1.453081	0.01071	0.64524	0.631435	ENSG00000166473	ENST00000337114	T	0.16196	2.36	4.17	3.22	0.36961	.	0.335569	0.23343	N	0.049204	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.43861	-0.9365	8	0.02654	T	1	-0.5748	3.3619	0.07189	0.2937:0.0:0.5103:0.196	rs9924530;rs52790816;rs61536671;rs9924530	20;20	Q7Z442-3;Q7Z442	.;PK1L2_HUMAN	A	20	ENSP00000337397:V20A	ENSP00000337397:V20A	V	-	2	0	PKD1L2	79811418	0.009000	0.17119	0.001000	0.08648	0.013000	0.08279	1.062000	0.30555	0.426000	0.26116	-0.213000	0.12676	GTT	A|0.429;G|0.571	0.571	strong		0.567	PKD1L2-001	KNOWN	non_canonical_polymorphism|basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000387972.2		
NAV2	89797	hgsc.bcm.edu	37	11	19901632	19901632	+	Silent	SNP	G	G	A	rs11025310	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:19901632G>A	ENST00000396087.3	+	5	828	c.729G>A	c.(727-729)gcG>gcA	p.A243A	NAV2_ENST00000527559.2_Silent_p.A172A|NAV2_ENST00000540292.1_Silent_p.A174A|NAV2_ENST00000534229.1_3'UTR|NAV2_ENST00000360655.4_Silent_p.A179A|NAV2_ENST00000349880.4_Silent_p.A243A|NAV2_ENST00000396085.1_Silent_p.A243A	NM_001244963.1	NP_001231892.1	Q8IVL1	NAV2_HUMAN	neuron navigator 2	243	Gln-rich.				glossopharyngeal nerve development (GO:0021563)|locomotory behavior (GO:0007626)|optic nerve development (GO:0021554)|regulation of systemic arterial blood pressure by baroreceptor feedback (GO:0003025)|sensory perception of smell (GO:0007608)|sensory perception of sound (GO:0007605)|vagus nerve development (GO:0021564)	interstitial matrix (GO:0005614)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|heparin binding (GO:0008201)			NS(1)|breast(2)|central_nervous_system(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(26)|lung(38)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	116						ACCAGCCAGCGCCACATCAGC	0.632													G|||	1562	0.311901	0.1702	0.3199	5008	,	,		16911	0.3274		0.4871	False		,,,				2504	0.3016				p.A243A		Atlas-SNP	.											NAV2,caecum,carcinoma,+1,1	NAV2	255	1	0			c.G729A						PASS	.	G	,,	777,3619	303.2+/-287.8	77,623,1498	35.0	32.0	33.0		537,729,729	-2.3	0.9	11	dbSNP_120	33	3817,4769	525.6+/-380.8	857,2103,1333	no	coding-synonymous,coding-synonymous,coding-synonymous	NAV2	NM_001111018.1,NM_145117.4,NM_182964.5	,,	934,2726,2831	AA,AG,GG		44.4561,17.6752,35.3875	,,	179/2366,243/2430,243/2433	19901632	4594,8388	2198	4293	6491	SO:0001819	synonymous_variant	89797	exon5			GCCAGCGCCACAT	AB037840	CCDS7850.1, CCDS7851.2, CCDS44552.1, CCDS53612.1, CCDS58126.1	11p15.1	2008-07-18			ENSG00000166833	ENSG00000166833	3.6.1.1		15997	protein-coding gene	gene with protein product	"""pore membrane and/or filament interacting like protein 2"", ""retinoic acid inducible gene in neuroblastoma 1"", ""helicase, APC down-regulated 1"""	607026				12079279, 12062803	Standard	NM_145117		Approved	FLJ10633, FLJ11030, HELAD1, KIAA1419, POMFIL2, RAINB1, FLJ23707	uc010rdm.2	Q8IVL1	OTTHUMG00000151837	ENST00000396087.3:c.729G>A	11.37:g.19901632G>A		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	85	64	0.752941	NM_145117	A6NEC1|Q8IVK3|Q8IVK4|Q8IVK5|Q8IVK6|Q8IVK7|Q8IVK8|Q8NHC9|Q8NHD0|Q8TDE9|Q8TDF0|Q8TEB3|Q96B30|Q9NUZ6|Q9NVM7|Q9P2C8	Silent	SNP	ENST00000396087.3	37	CCDS58126.1																																																																																			G|0.645;A|0.355	0.355	strong		0.632	NAV2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324112.1	NM_145117	
FCGBP	8857	hgsc.bcm.edu	37	19	40363020	40363020	+	Missense_Mutation	SNP	G	G	A	rs741143	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:40363020G>A	ENST00000221347.6	-	32	15057	c.15050C>T	c.(15049-15051)gCg>gTg	p.A5017V		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	5017	VWFD 12. {ECO:0000255|PROSITE- ProRule:PRU00580}.		A -> V (in dbSNP:rs741143). {ECO:0000269|PubMed:9182547}.			extracellular vesicular exosome (GO:0070062)				NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(5)|endometrium(13)|kidney(9)|large_intestine(27)|lung(49)|ovary(8)|pancreas(3)|prostate(13)|skin(9)|stomach(9)|upper_aerodigestive_tract(6)|urinary_tract(3)	165	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			GGAGCCGGGCGCCCGCCATGC	0.652													G|||	1380	0.275559	0.1868	0.1571	5008	,	,		14056	0.5367		0.1988	False		,,,				2504	0.2894				p.A5017V		Atlas-SNP	.											FCGBP,NS,carcinoma,-1,1	FCGBP	416	1	0			c.C15050T						PASS	.	G	VAL/ALA	854,3550		89,676,1437	15.0	19.0	18.0		15050	-1.2	0.0	19	dbSNP_86	18	1820,6778		205,1410,2684	yes	missense	FCGBP	NM_003890.2	64	294,2086,4121	AA,AG,GG		21.1677,19.3915,20.5661	benign	5017/5406	40363020	2674,10328	2202	4299	6501	SO:0001583	missense	8857	exon32			CCGGGCGCCCGCC	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.15050C>T	19.37:g.40363020G>A	ENSP00000221347:p.Ala5017Val	Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	37	19	0.513514	NM_003890	O95784	Missense_Mutation	SNP	ENST00000221347.6	37	CCDS12546.1	618	0.28296703296703296	88	0.17886178861788618	62	0.1712707182320442	316	0.5524475524475524	152	0.20052770448548812	G	2.898	-0.228255	0.06022	0.193915	0.211677	ENSG00000090920	ENST00000221347	T	0.14022	2.54	4.9	-1.24	0.09435	von Willebrand factor, type D domain (1);	0.202030	0.29638	U	0.011593	T	0.00012	0.0000	N	0.02751	-0.505	0.80722	P	0.0	P	0.38729	0.644	B	0.37304	0.246	T	0.25572	-1.0128	9	0.02654	T	1	.	4.4927	0.11820	0.4089:0.0:0.444:0.1471	rs741143;rs1053685;rs741143	5017	Q9Y6R7	FCGBP_HUMAN	V	5017	ENSP00000221347:A5017V	ENSP00000221347:A5017V	A	-	2	0	FCGBP	45054860	0.000000	0.05858	0.029000	0.17559	0.467000	0.32768	-0.017000	0.12590	0.005000	0.14708	0.313000	0.20887	GCG	G|0.749;A|0.251	0.251	strong		0.652	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890	
SASS6	163786	hgsc.bcm.edu	37	1	100575933	100575933	+	Missense_Mutation	SNP	G	G	A	rs13375867	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:100575933G>A	ENST00000287482.5	-	8	916	c.776C>T	c.(775-777)gCg>gTg	p.A259V	SASS6_ENST00000462159.1_5'UTR|SASS6_ENST00000535161.1_Missense_Mutation_p.A92V	NM_194292.1	NP_919268.1	Q6UVJ0	SAS6_HUMAN	spindle assembly 6 homolog (C. elegans)	259			A -> V (in dbSNP:rs13375867).		centriole replication (GO:0007099)|centrosome duplication (GO:0051298)	centriole (GO:0005814)|centrosome (GO:0005813)|deuterosome (GO:0098536)				breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(2)|lung(6)|ovary(1)|upper_aerodigestive_tract(2)	19		all_epithelial(167;4.58e-06)|all_lung(203;0.00125)|Lung NSC(277;0.00131)		Epithelial(280;0.085)|all cancers(265;0.139)|COAD - Colon adenocarcinoma(174;0.15)|Lung(183;0.197)		TTTATTAGCCGCTTCTAACTC	0.353													G|||	1754	0.35024	0.0658	0.5562	5008	,	,		15563	0.5813		0.3867	False		,,,				2504	0.3129				p.A259V		Atlas-SNP	.											.	SASS6	61	.	0			c.C776T						PASS	.	G	VAL/ALA	576,3830	256.1+/-261.0	43,490,1670	155.0	145.0	148.0		776	3.4	0.8	1	dbSNP_121	148	3410,5190	502.1+/-375.6	671,2068,1561	yes	missense	SASS6	NM_194292.1	64	714,2558,3231	AA,AG,GG		39.6512,13.0731,30.6474	benign	259/658	100575933	3986,9020	2203	4300	6503	SO:0001583	missense	163786	exon8			TTAGCCGCTTCTA	AL834265	CCDS764.1	1p21.3	2008-02-05			ENSG00000156876	ENSG00000156876			25403	protein-coding gene	gene with protein product		609321				15665853, 14654843	Standard	NM_194292		Approved	DKFZp761A078, SAS-6, FLJ22097, SAS6	uc001dsu.3	Q6UVJ0	OTTHUMG00000010754	ENST00000287482.5:c.776C>T	1.37:g.100575933G>A	ENSP00000287482:p.Ala259Val	Somatic	240	0	0		WXS	Illumina HiSeq	Phase_I	227	105	0.462555	NM_194292	D3DT55|Q8N3K0	Missense_Mutation	SNP	ENST00000287482.5	37	CCDS764.1	874	0.4001831501831502	42	0.08536585365853659	190	0.5248618784530387	353	0.6171328671328671	289	0.3812664907651715	G	10.82	1.456932	0.26161	0.130731	0.396512	ENSG00000156876	ENST00000287482;ENST00000539329;ENST00000535161	T;T	0.78246	-1.16;-1.16	5.31	3.41	0.39046	.	0.419300	0.28877	N	0.013853	T	0.36524	0.0970	N	0.10874	0.06	0.80722	P	0.0	B	0.16603	0.018	B	0.13407	0.009	T	0.11131	-1.0600	9	0.27785	T	0.31	-4.242	5.2703	0.15620	0.1664:0.3446:0.489:0.0	rs13375867;rs52830638;rs58236074;rs13375867	259	Q6UVJ0	SAS6_HUMAN	V	259;232;92	ENSP00000287482:A259V;ENSP00000440169:A92V	ENSP00000287482:A259V	A	-	2	0	SASS6	100348521	0.010000	0.17322	0.768000	0.31515	0.785000	0.44390	1.271000	0.33098	2.474000	0.83562	0.655000	0.94253	GCG	G|0.659;A|0.341	0.341	strong		0.353	SASS6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029656.2	NM_194292	
DNAH6	1768	hgsc.bcm.edu	37	2	84924823	84924823	+	Missense_Mutation	SNP	T	T	C	rs78190897	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:84924823T>C	ENST00000237449.6	+	46	7657	c.7649T>C	c.(7648-7650)gTa>gCa	p.V2550A	DNAH6_ENST00000389394.3_Missense_Mutation_p.V2550A|DNAH6_ENST00000398278.2_Missense_Mutation_p.V2501A|DNAH6_ENST00000602588.1_Missense_Mutation_p.V522A			Q9C0G6	DYH6_HUMAN	dynein, axonemal, heavy chain 6	2550	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						GCAAAAGAAGTAGGAATTTCT	0.398													T|||	585	0.116813	0.1067	0.1715	5008	,	,		17291	0.0893		0.1382	False		,,,				2504	0.0982				p.V2550A		Atlas-SNP	.											.	DNAH6	194	.	0			c.T7649C						PASS	.	T	ALA/VAL	175,1209		12,151,529	121.0	116.0	118.0		7649	-10.6	0.0	2	dbSNP_131	118	528,2654		42,444,1105	yes	missense	DNAH6	NM_001370.1	64	54,595,1634	CC,CT,TT		16.5933,12.6445,15.3964	benign	2550/4159	84924823	703,3863	692	1591	2283	SO:0001583	missense	1768	exon47			AAGAAGTAGGAAT	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.7649T>C	2.37:g.84924823T>C	ENSP00000237449:p.Val2550Ala	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	66	32	0.484848	NM_001370	A0PJN9|B5MEE0|B7ZL99|O95493|Q53QZ1|Q53TE5|Q8N1W6|Q92861|Q96BL6|Q9H030|Q9H5E1	Missense_Mutation	SNP	ENST00000237449.6	37	CCDS46348.1	266	0.12179487179487179	43	0.08739837398373984	58	0.16022099447513813	51	0.08916083916083917	114	0.1503957783641161	T	5.764	0.325432	0.10900	0.126445	0.165933	ENSG00000115423	ENST00000389394;ENST00000398278;ENST00000237449	T;T;T	0.42131	0.98;0.98;0.98	5.67	-10.6	0.00265	Dynein heavy chain, P-loop containing D4 domain (1);ATPase, AAA+ type, core (1);	.	.	.	.	T	0.00039	0.0001	N	0.00034	-2.565	0.48696	P	3.1000000000003247E-4	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.48536	-0.9027	8	0.06494	T	0.89	.	23.5218	0.99983	0.0:0.7727:0.0:0.2273	.	2550;2501	Q9C0G6;Q9C0G6-4	DYH6_HUMAN;.	A	2550;2501;2550	ENSP00000374045:V2550A;ENSP00000381326:V2501A;ENSP00000237449:V2550A	ENSP00000237449:V2550A	V	+	2	0	DNAH6	84778334	0.000000	0.05858	0.012000	0.15200	0.814000	0.46013	-1.615000	0.02055	-2.303000	0.00656	-0.425000	0.05940	GTA	T|0.868;C|0.132	0.132	strong		0.398	DNAH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328537.2	NM_001370	
ARHGEF19	128272	hgsc.bcm.edu	37	1	16534646	16534646	+	Missense_Mutation	SNP	C	C	G	rs221058	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:16534646C>G	ENST00000270747.3	-	3	623	c.487G>C	c.(487-489)Ggc>Cgc	p.G163R	ARHGEF19_ENST00000478117.1_5'Flank	NM_153213.3	NP_694945.2	Q8IW93	ARHGJ_HUMAN	Rho guanine nucleotide exchange factor (GEF) 19	163			G -> R (in dbSNP:rs221058). {ECO:0000269|PubMed:14702039}.		regulation of actin cytoskeleton organization (GO:0032956)|wound healing (GO:0042060)		GTPase activator activity (GO:0005096)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			cervix(1)|endometrium(1)|lung(3)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	12		Colorectal(325;0.000147)|Renal(390;0.00145)|Breast(348;0.00224)|Lung NSC(340;0.00566)|all_lung(284;0.00831)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.018)|Colorectal(212;3.48e-07)|COAD - Colon adenocarcinoma(227;2.19e-05)|BRCA - Breast invasive adenocarcinoma(304;9.46e-05)|Kidney(64;0.000171)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(313;0.0117)|READ - Rectum adenocarcinoma(331;0.0649)		ACTACCTGGCCAGGCTCTAGG	0.657													C|||	1222	0.24401	0.0862	0.3948	5008	,	,		16480	0.1528		0.2654	False		,,,				2504	0.4223				p.G163R		Atlas-SNP	.											ARHGEF19,colon,carcinoma,0,1	ARHGEF19	49	1	0			c.G487C						PASS	.	C	ARG/GLY	453,3953	209.2+/-230.0	35,383,1785	56.0	61.0	59.0		487	2.1	1.0	1	dbSNP_79	59	2233,6367	370.2+/-335.8	295,1643,2362	yes	missense	ARHGEF19	NM_153213.3	125	330,2026,4147	GG,GC,CC		25.9651,10.2814,20.652	benign	163/803	16534646	2686,10320	2203	4300	6503	SO:0001583	missense	128272	exon3			CCTGGCCAGGCTC	BC012982	CCDS170.1	1p36.13	2011-11-16			ENSG00000142632	ENSG00000142632		"""Rho guanine nucleotide exchange factors"""	26604	protein-coding gene	gene with protein product		612496				12477932	Standard	NM_153213		Approved	FLJ33962, WGEF	uc001ayc.1	Q8IW93	OTTHUMG00000002219	ENST00000270747.3:c.487G>C	1.37:g.16534646C>G	ENSP00000270747:p.Gly163Arg	Somatic	232	0	0		WXS	Illumina HiSeq	Phase_I	196	82	0.418367	NM_153213	A6NJ04|Q5TEV2|Q6PJQ4|Q8N244	Missense_Mutation	SNP	ENST00000270747.3	37	CCDS170.1	450	0.20604395604395603	47	0.09552845528455285	118	0.3259668508287293	74	0.12937062937062938	211	0.2783641160949868	C	10.83	1.459937	0.26248	0.102814	0.259651	ENSG00000142632	ENST00000270747;ENST00000421561;ENST00000375607	T;T	0.50001	0.76;0.76	5.21	2.13	0.27403	.	1.238380	0.05817	N	0.615075	T	0.00012	0.0000	L	0.32530	0.975	0.45390	P	0.001623000000000041	B	0.15719	0.014	B	0.14578	0.011	T	0.31138	-0.9954	9	0.30078	T	0.28	.	6.6718	0.23072	0.0:0.6669:0.0:0.3331	rs221058;rs221058	163	Q8IW93	ARHGJ_HUMAN	R	163	ENSP00000270747:G163R;ENSP00000396001:G163R	ENSP00000270747:G163R	G	-	1	0	ARHGEF19	16407233	0.296000	0.24398	0.967000	0.41034	0.118000	0.20060	0.673000	0.25203	0.220000	0.20860	0.561000	0.74099	GGC	C|0.794;G|0.206	0.206	strong		0.657	ARHGEF19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006289.1	NM_153213	
CMYA5	202333	hgsc.bcm.edu	37	5	79095417	79095417	+	Missense_Mutation	SNP	C	C	T	rs10043986	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	124	62	0.5	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	
P2RY11	5032	hgsc.bcm.edu	37	19	10225060	10225060	+	Silent	SNP	C	C	T	rs77496977	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:10225060C>T	ENST00000321826.4	+	2	955	c.771C>T	c.(769-771)taC>taT	p.Y257Y	PPAN_ENST00000556468.1_Silent_p.Y677Y|PPAN-P2RY11_ENST00000428358.1_3'UTR|PPAN-P2RY11_ENST00000393796.4_Silent_p.Y677Y	NM_002566.4	NP_002557.2	Q96G91	P2Y11_HUMAN	purinergic receptor P2Y, G-protein coupled, 11	257					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)			TGGCCCTCTACGCCAGCTCCT	0.677													c|||	83	0.0165735	0.0	0.0	5008	,	,		18173	0.0228		0.001	False		,,,				2504	0.0603				p.Y677Y		Atlas-SNP	.											.	PPAN-P2RY11	81	.	0			c.C2031T						PASS	.	T	,,	5,4401	8.1+/-20.4	0,5,2198	66.0	62.0	63.0		2031,,771	-5.5	0.0	19	dbSNP_131	63	0,8596		0,0,4298	no	coding-synonymous,utr-3,coding-synonymous	P2RY11,PPAN-P2RY11	NM_001040664.2,NM_001198690.1,NM_002566.4	,,	0,5,6496	TT,TC,CC		0.0,0.1135,0.0385	,,	677/795,,257/375	10225060	5,12997	2203	4298	6501	SO:0001819	synonymous_variant	692312	exon13			CCTCTACGCCAGC	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.771C>T	19.37:g.10225060C>T		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	55	32	0.581818	NM_001040664	B2R8X9|O43190|Q9BYU4|Q9H170	Silent	SNP	ENST00000321826.4	37	CCDS12226.1																																																																																			C|0.997;T|0.003	0.003	strong		0.677	P2RY11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316664.2	NM_002566	
LDLR	3949	hgsc.bcm.edu	37	19	11227602	11227602	+	Silent	SNP	C	C	T	rs688	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:11227602C>T	ENST00000558518.1	+	12	1960	c.1773C>T	c.(1771-1773)aaC>aaT	p.N591N	LDLR_ENST00000557933.1_Silent_p.N591N|LDLR_ENST00000455727.2_Silent_p.N423N|LDLR_ENST00000558013.1_Silent_p.N591N|LDLR_ENST00000545707.1_Silent_p.N464N|LDLR_ENST00000535915.1_Silent_p.N550N	NM_000527.4|NM_001195798.1	NP_000518.1|NP_001182727.1	P01130	LDLR_HUMAN	low density lipoprotein receptor	591					cholesterol homeostasis (GO:0042632)|cholesterol import (GO:0070508)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|endocytosis (GO:0006897)|intestinal cholesterol absorption (GO:0030299)|lipid metabolic process (GO:0006629)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|low-density lipoprotein particle clearance (GO:0034383)|phospholipid transport (GO:0015914)|phototransduction, visible light (GO:0007603)|positive regulation of triglyceride biosynthetic process (GO:0010867)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol homeostasis (GO:2000188)|regulation of phosphatidylcholine catabolic process (GO:0010899)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|coated pit (GO:0005905)|early endosome (GO:0005769)|endosome membrane (GO:0010008)|external side of plasma membrane (GO:0009897)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|low-density lipoprotein particle (GO:0034362)|lysosome (GO:0005764)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|glycoprotein binding (GO:0001948)|low-density lipoprotein particle binding (GO:0030169)|low-density lipoprotein receptor activity (GO:0005041)|very-low-density lipoprotein particle receptor activity (GO:0030229)	p.?(1)		breast(2)|endometrium(2)|large_intestine(5)|lung(8)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	26		Lung NSC(9;0.000245)|Renal(1328;0.0007)|Hepatocellular(1079;0.0524)		GBM - Glioblastoma multiforme(1328;1.36e-05)|STAD - Stomach adenocarcinoma(1328;0.000766)|Lung(535;0.197)	Porfimer(DB00707)	TCGATGTCAACGGGGGCAACC	0.542													C|||	1381	0.275759	0.0439	0.4582	5008	,	,		17670	0.1835		0.4414	False		,,,				2504	0.3845				p.N591N	GBM(18;201 575 7820 21545)	Atlas-SNP	.											.	LDLR	72	.	1	Unknown(1)	lung(1)	c.C1773T	GRCh37	CM984053	LDLR	M	rs688	PASS	.	C	,,,,,	486,3920	227.5+/-242.7	36,414,1753	234.0	208.0	217.0		1773,1773,1650,1269,1410,1392	-6.7	0.0	19	dbSNP_36	217	3874,4726	543.7+/-384.4	847,2180,1273	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	LDLR	NM_000527.4,NM_001195798.1,NM_001195799.1,NM_001195800.1,NM_001195802.1,NM_001195803.1	,,,,,	883,2594,3026	TT,TC,CC		45.0465,11.0304,33.523	,,,,,	591/861,591/859,550/820,423/693,470/740,464/683	11227602	4360,8646	2203	4300	6503	SO:0001819	synonymous_variant	3949	exon12			TGTCAACGGGGGC	AY114155	CCDS12254.1, CCDS56083.1, CCDS56084.1, CCDS56085.1, CCDS58651.1	19p13.2	2014-09-17	2008-08-01		ENSG00000130164	ENSG00000130164		"""Low density lipoprotein receptors"""	6547	protein-coding gene	gene with protein product	"""familial hypercholesterolemia"""	606945					Standard	NM_000527		Approved	LDLCQ2	uc002mqk.4	P01130		ENST00000558518.1:c.1773C>T	19.37:g.11227602C>T		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	137	69	0.50365	NM_001195798	B4DII3|B4DJZ8|B4DR00|B4DTQ3|C0JYY8|H0YLU8|H0YNT7|Q53ZD9|Q59FQ1|Q9UDH7	Silent	SNP	ENST00000558518.1	37	CCDS12254.1																																																																																			C|0.717;N|0.000	.	strong		0.542	LDLR-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000415973.2		
ATP4A	495	hgsc.bcm.edu	37	19	36048741	36048741	+	Silent	SNP	G	G	T	rs2230181	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:36048741G>T	ENST00000262623.3	-	11	1537	c.1509C>A	c.(1507-1509)atC>atA	p.I503I		NM_000704.2	NP_000695.2	P20648	ATP4A_HUMAN	ATPase, H+/K+ exchanging, alpha polypeptide	503					ATP biosynthetic process (GO:0006754)|ATP hydrolysis coupled proton transport (GO:0015991)|ion transmembrane transport (GO:0034220)|pH reduction (GO:0045851)|regulation of proton transport (GO:0010155)|response to drug (GO:0042493)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|hydrogen:potassium-exchanging ATPase activity (GO:0008900)|magnesium ion binding (GO:0000287)			breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(26)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	53	all_lung(56;1.05e-07)|Lung NSC(56;1.63e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)		Esomeprazole(DB00736)|Lansoprazole(DB00448)|Omeprazole(DB00338)|Pantoprazole(DB00213)|Rabeprazole(DB01129)	CCAGCGTATGGATGGACAGCT	0.721													G|||	1406	0.280751	0.174	0.2277	5008	,	,		8328	0.2659		0.4105	False		,,,				2504	0.3446				p.I503I		Atlas-SNP	.											.	ATP4A	123	.	0			c.C1509A						PASS	.	G		705,3255		72,561,1347	7.0	8.0	8.0		1509	1.5	1.0	19	dbSNP_98	8	2729,5079		474,1781,1649	no	coding-synonymous	ATP4A	NM_000704.2		546,2342,2996	TT,TG,GG		34.9513,17.803,29.1808		503/1036	36048741	3434,8334	1980	3904	5884	SO:0001819	synonymous_variant	495	exon11			CGTATGGATGGAC		CCDS12467.1	19q13.1	2010-04-20			ENSG00000105675	ENSG00000105675	3.6.3.10	"""ATPases / P-type"""	819	protein-coding gene	gene with protein product	"""gastric H,K-ATPase alpha subunit"", ""H(+)-K(+)-ATPase alpha subunit"", ""proton pump"""	137216				1330887	Standard	NM_000704		Approved	ATP6A	uc002oal.1	P20648	OTTHUMG00000048106	ENST00000262623.3:c.1509C>A	19.37:g.36048741G>T		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	96	48	0.5	NM_000704	O00738	Silent	SNP	ENST00000262623.3	37	CCDS12467.1																																																																																			G|0.705;T|0.295	0.295	strong		0.721	ATP4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109470.2	NM_000704	
ABCB5	340273	hgsc.bcm.edu	37	7	20698270	20698270	+	Missense_Mutation	SNP	A	A	G	rs2301641	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:20698270A>G	ENST00000404938.2	+	14	2330	c.1678A>G	c.(1678-1680)Aag>Gag	p.K560E	ABCB5_ENST00000443026.2_Missense_Mutation_p.K115E|ABCB5_ENST00000406935.1_Missense_Mutation_p.K115E|ABCB5_ENST00000258738.6_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	118	0	0		WXS	Illumina HiSeq	Phase_I	79	79	1	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	
RUNDC3B	154661	hgsc.bcm.edu	37	7	87445520	87445520	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:87445520C>T	ENST00000338056.3	+	11	1630	c.1219C>T	c.(1219-1221)Cca>Tca	p.P407S	RUNDC3B_ENST00000394654.3_Missense_Mutation_p.P390S|RUNDC3B_ENST00000493037.1_Missense_Mutation_p.P341S	NM_001134405.1|NM_138290.2	NP_001127877.1|NP_612147.1	Q96NL0	RUN3B_HUMAN	RUN domain containing 3B	407										breast(2)|endometrium(3)|kidney(2)|large_intestine(7)|lung(8)|ovary(1)|prostate(1)|skin(2)	26	Esophageal squamous(14;0.00164)					TTCACTAGATCCAGGCCAGTC	0.348																																					p.P407S		Atlas-SNP	.											RUNDC3B,NS,carcinoma,-1,1	RUNDC3B	63	1	0			c.C1219T						scavenged	.						77.0	72.0	73.0					7																	87445520		2203	4300	6503	SO:0001583	missense	154661	exon11			CTAGATCCAGGCC		CCDS5609.1, CCDS47635.1, CCDS47636.1	7q21.12	2009-01-14			ENSG00000105784	ENSG00000105784			30286	protein-coding gene	gene with protein product						12645870	Standard	NM_138290		Approved	RPIP9, RPIB9	uc003ujb.3	Q96NL0	OTTHUMG00000131035	ENST00000338056.3:c.1219C>T	7.37:g.87445520C>T	ENSP00000337732:p.Pro407Ser	Somatic	267	0	0		WXS	Illumina HiSeq	Phase_I	233	3	0.0128755	NM_138290	B4DFD0|E9PBR4|Q8IWW5|Q8NB55|Q8TBG7	Missense_Mutation	SNP	ENST00000338056.3	37	CCDS5609.1	.	.	.	.	.	.	.	.	.	.	C	23.1	4.370170	0.82573	.	.	ENSG00000105784	ENST00000338056;ENST00000493037;ENST00000394654	T;T;T	0.14640	2.61;2.49;2.6	5.44	5.44	0.79542	.	0.158832	0.56097	D	0.000023	T	0.18341	0.0440	N	0.08118	0	0.53688	D	0.999973	P;P;P;D;P	0.67145	0.799;0.799;0.728;0.996;0.655	B;B;B;D;B	0.75484	0.343;0.343;0.349;0.986;0.165	T	0.21552	-1.0242	10	0.09084	T	0.74	-12.6693	19.6271	0.95682	0.0:1.0:0.0:0.0	.	390;390;263;341;407	E9PBR4;B4DFD0;Q96NL0-2;Q96NL0-4;Q96NL0	.;.;.;.;RUN3B_HUMAN	S	407;341;390	ENSP00000337732:P407S;ENSP00000420394:P341S;ENSP00000378149:P390S	ENSP00000337732:P407S	P	+	1	0	RUNDC3B	87283456	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	5.966000	0.70395	2.712000	0.92718	0.650000	0.86243	CCA	.	.	none		0.348	RUNDC3B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000253679.1	NM_138290	
DMXL2	23312	hgsc.bcm.edu	37	15	51748564	51748564	+	Silent	SNP	A	A	G	rs76659258	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:51748564A>G	ENST00000251076.5	-	37	8561	c.8274T>C	c.(8272-8274)ctT>ctC	p.L2758L	RP11-707P17.2_ENST00000559173.1_RNA|RP11-707P17.2_ENST00000560727.1_RNA|RP11-707P17.1_ENST00000561007.1_RNA|DMXL2_ENST00000543779.2_Silent_p.L2759L|DMXL2_ENST00000449909.3_Silent_p.L2122L|RP11-707P17.2_ENST00000559977.1_RNA	NM_001174116.1|NM_015263.3	NP_001167587.1|NP_056078.2	Q8TDJ6	DMXL2_HUMAN	Dmx-like 2	2758						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)		TCCTTTTCATAAGCtttaaaa	0.299													A|||	70	0.0139776	0.003	0.0231	5008	,	,		18765	0.0		0.0298	False		,,,				2504	0.0204				p.L2759L		Atlas-SNP	.											DMXL2,NS,carcinoma,0,1	DMXL2	262	1	0			c.T8277C						PASS	.	A	,,	35,4347	35.2+/-66.4	0,35,2156	43.0	45.0	45.0		8277,6366,8274	-1.2	1.0	15	dbSNP_131	45	310,8266	109.0+/-169.6	4,302,3982	no	coding-synonymous,coding-synonymous,coding-synonymous	DMXL2	NM_001174116.1,NM_001174117.1,NM_015263.3	,,	4,337,6138	GG,GA,AA		3.6147,0.7987,2.6624	,,	2759/3038,2122/2401,2758/3037	51748564	345,12613	2191	4288	6479	SO:0001819	synonymous_variant	23312	exon37			TTTCATAAGCTTT	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.8274T>C	15.37:g.51748564A>G		Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	146	58	0.39726	NM_001174116	B2RTR3|B7ZMH3|F5GWF1|O94938	Silent	SNP	ENST00000251076.5	37	CCDS10141.1																																																																																			A|0.975;G|0.025	0.025	strong		0.299	DMXL2-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254671.2	NM_015263	
TNS1	7145	hgsc.bcm.edu	37	2	218712306	218712306	+	Silent	SNP	C	C	T	rs1004814	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:218712306C>T	ENST00000171887.4	-	17	3011	c.2559G>A	c.(2557-2559)gcG>gcA	p.A853A	TNS1_ENST00000419504.1_Silent_p.A853A|TNS1_ENST00000480665.1_5'Flank|TNS1_ENST00000430930.1_Silent_p.A853A	NM_022648.4	NP_072174.3	Q9HBL0	TENS1_HUMAN	tensin 1	853					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)		GGTCTGAAGTCGCTTCCTTTG	0.602													C|||	2176	0.434505	0.6218	0.3141	5008	,	,		17071	0.3442		0.3499	False		,,,				2504	0.4468				p.A853A		Atlas-SNP	.											.	TNS1	251	.	0			c.G2559A						PASS	.	C		2473,1933	623.5+/-394.1	696,1081,426	70.0	77.0	75.0		2559	-5.7	0.0	2	dbSNP_86	75	2695,5905	431.2+/-356.7	437,1821,2042	no	coding-synonymous	TNS1	NM_022648.4		1133,2902,2468	TT,TC,CC		31.3372,43.872,39.7355		853/1736	218712306	5168,7838	2203	4300	6503	SO:0001819	synonymous_variant	7145	exon17			TGAAGTCGCTTCC	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.2559G>A	2.37:g.218712306C>T		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	66	31	0.469697	NM_022648	Q4ZG71|Q6IPI5	Silent	SNP	ENST00000171887.4	37	CCDS2407.1																																																																																			C|0.594;T|0.406	0.406	strong		0.602	TNS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256672.2	NM_022648	
KRTAP16-1	100505753	hgsc.bcm.edu	37	17	39464487	39464487	+	Missense_Mutation	SNP	G	G	C	rs2074285	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:39464487G>C	ENST00000391352.1	-	1	1018	c.1019C>G	c.(1018-1020)cCt>cGt	p.P340R		NM_001146182.1	NP_001139654.1	A8MUX0	KR161_HUMAN	keratin associated protein 16-1	340						keratin filament (GO:0045095)				haematopoietic_and_lymphoid_tissue(1)	1						GCAGACAGAAGGACAGCGCTT	0.567													C|||	1899	0.379193	0.6135	0.2435	5008	,	,		22005	0.3968		0.2992	False		,,,				2504	0.2229				p.P340R		Atlas-SNP	.											.	KRTAP16-1	12	.	0			c.C1019G						PASS	.																																			SO:0001583	missense	100505753	exon1			ACAGAAGGACAGC	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.1019C>G	17.37:g.39464487G>C	ENSP00000375147:p.Pro340Arg	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	70	36	0.514286	NM_001146182		Missense_Mutation	SNP	ENST00000391352.1	37	CCDS56032.1	833	0.3814102564102564	290	0.5894308943089431	99	0.27348066298342544	216	0.3776223776223776	228	0.3007915567282322	C	0.001	-2.912640	0.00056	.	.	ENSG00000212657	ENST00000391352	T	0.00646	6.0	5.26	-3.19	0.05171	.	.	.	.	.	T	0.00012	0.0000	N	0.00583	-1.355	0.80722	P	0.0	.	.	.	.	.	.	T	0.02214	-1.1194	6	0.14656	T	0.56	.	7.4869	0.27439	0.0:0.2194:0.1205:0.66	rs2074285;rs2074285	.	.	.	R	340	ENSP00000375147:P340R	ENSP00000375147:P340R	P	-	2	0	KRTAP16-1	36718013	0.000000	0.05858	0.003000	0.11579	0.049000	0.14656	-1.700000	0.01905	-0.730000	0.04869	-0.322000	0.08575	CCT	G|0.614;C|0.386	0.386	strong		0.567	KRTAP16-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257785.1	NM_001146182	
C10orf71	118461	hgsc.bcm.edu	37	10	50533386	50533386	+	Silent	SNP	C	C	T	rs41306409	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:50533386C>T	ENST00000374144.3	+	3	3084	c.2796C>T	c.(2794-2796)aaC>aaT	p.N932N	C10orf71_ENST00000323868.4_Intron			Q711Q0	CJ071_HUMAN	chromosome 10 open reading frame 71	932										endometrium(1)	1						GCATGGCCAACGAGGTCATGG	0.597													C|||	26	0.00519169	0.0023	0.0043	5008	,	,		19318	0.0		0.0189	False		,,,				2504	0.001				p.N932N		Atlas-SNP	.											.	C10orf71	179	.	0			c.C2796T						PASS	.	C	,	3,1381		0,3,689	11.0	12.0	12.0		2796,	-2.6	0.0	10	dbSNP_127	12	70,3108		0,70,1519	no	coding-synonymous,intron	C10orf71	NM_001135196.1,NM_199459.3	,	0,73,2208	TT,TC,CC		2.2026,0.2168,1.6002	,	932/1436,	50533386	73,4489	692	1589	2281	SO:0001819	synonymous_variant	118461	exon3			GGCCAACGAGGTC	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.2796C>T	10.37:g.50533386C>T		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	94	48	0.510638	NM_001135196	A0AVL8	Silent	SNP	ENST00000374144.3	37	CCDS44387.1																																																																																			C|0.988;T|0.012	0.012	strong		0.597	C10orf71-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047984.2	NM_199459	
DFNB31	25861	hgsc.bcm.edu	37	9	117166311	117166311	+	Silent	SNP	G	G	A	rs34963246	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:117166311G>A	ENST00000362057.3	-	10	2451	c.2283C>T	c.(2281-2283)agC>agT	p.S761S	DFNB31_ENST00000374059.3_Silent_p.S410S|DFNB31_ENST00000265134.6_Silent_p.S378S	NM_001173425.1|NM_015404.3	NP_001166896.1|NP_056219	Q9P202	WHRN_HUMAN	deafness, autosomal recessive 31	761					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						CACTGTCCTCGCTTAGAGTCT	0.622													G|||	463	0.0924521	0.1921	0.147	5008	,	,		19778	0.001		0.0905	False		,,,				2504	0.0153				p.S761S		Atlas-SNP	.											.	DFNB31	100	.	0			c.C2283T						PASS	.	G	,,	849,3557	329.9+/-301.2	82,685,1436	58.0	53.0	55.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1134,2280,2283	-4.2	0.3	9	dbSNP_126	55	755,7845	179.9+/-228.9	31,693,3576	no	coding-synonymous,coding-synonymous,coding-synonymous	DFNB31	NM_001083885.2,NM_001173425.1,NM_015404.3	,,	113,1378,5012	AA,AG,GG		8.7791,19.2692,12.3328	,,	378/525,760/907,761/908	117166311	1604,11402	2203	4300	6503	SO:0001819	synonymous_variant	25861	exon10			GTCCTCGCTTAGA	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.2283C>T	9.37:g.117166311G>A		Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	67	23	0.343284	NM_015404	A5PKU1|A5PKZ9|Q5TAU9|Q5TAV0|Q5TAV1|Q5TAV2|Q96MZ9|Q9H9F4|Q9UFZ3	Silent	SNP	ENST00000362057.3	37	CCDS6806.1																																																																																			A|0.112;G|0.887;T|0.000	0.112	strong		0.622	DFNB31-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053776.2	NM_015404	
MYH4	4622	hgsc.bcm.edu	37	17	10360854	10360854	+	Missense_Mutation	SNP	C	C	T	rs12949680	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:10360854C>T	ENST00000255381.2	-	16	1890	c.1780G>A	c.(1780-1782)Gcc>Acc	p.A594T	CTC-297N7.11_ENST00000587182.2_RNA|RP11-799N11.1_ENST00000399342.2_RNA|RP11-799N11.1_ENST00000581304.1_RNA	NM_017533.2	NP_060003.2	Q9Y623	MYH4_HUMAN	myosin, heavy chain 4, skeletal muscle	594	Myosin motor.		A -> T (in dbSNP:rs12949680).		actin filament-based movement (GO:0030048)|ATP catabolic process (GO:0006200)|membrane organization (GO:0061024)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|response to activity (GO:0014823)	muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin filament (GO:0032982)|sarcomere (GO:0030017)	ATP binding (GO:0005524)|double-stranded RNA binding (GO:0003725)|microfilament motor activity (GO:0000146)			NS(4)|breast(8)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(13)|lung(72)|ovary(10)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	149						AGCCAGCCGGCGATGTTGTAG	0.552													C|||	288	0.057508	0.0401	0.0346	5008	,	,		19095	0.0308		0.0517	False		,,,				2504	0.1309				p.A594T		Atlas-SNP	.											.	MYH4	349	.	0			c.G1780A						PASS	.	C	THR/ALA	195,4211	122.1+/-159.5	4,187,2012	107.0	106.0	107.0		1780	-1.3	0.0	17	dbSNP_121	107	526,8074	146.9+/-202.4	16,494,3790	no	missense	MYH4	NM_017533.2	58	20,681,5802	TT,TC,CC		6.1163,4.4258,5.5436	benign	594/1940	10360854	721,12285	2203	4300	6503	SO:0001583	missense	4622	exon16			AGCCGGCGATGTT		CCDS11154.1	17p13.1	2013-09-19	2006-09-29		ENSG00000264424	ENSG00000264424		"""Myosins / Myosin superfamily : Class II"""	7574	protein-coding gene	gene with protein product		160742	"""myosin, heavy polypeptide 4, skeletal muscle"""			8518795	Standard	NM_017533		Approved	MYH2B, MyHC-2B, MyHC-IIb	uc002gmn.3	Q9Y623	OTTHUMG00000130365	ENST00000255381.2:c.1780G>A	17.37:g.10360854C>T	ENSP00000255381:p.Ala594Thr	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	112	52	0.464286	NM_017533		Missense_Mutation	SNP	ENST00000255381.2	37	CCDS11154.1	103	0.04716117216117216	21	0.042682926829268296	16	0.04419889502762431	20	0.03496503496503497	46	0.06068601583113457	C	0.007	-1.979767	0.00448	0.044258	0.061163	ENSG00000141048	ENST00000255381	D	0.86432	-2.12	5.01	-1.26	0.09376	Myosin head, motor domain (2);	1.090020	0.07356	U	0.883241	T	0.10895	0.0266	N	0.00282	-1.705	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.48536	-0.9027	10	0.02654	T	1	.	5.3299	0.15926	0.2266:0.211:0.0:0.5624	rs12949680	594	Q9Y623	MYH4_HUMAN	T	594	ENSP00000255381:A594T	ENSP00000255381:A594T	A	-	1	0	MYH4	10301579	0.000000	0.05858	0.002000	0.10522	0.009000	0.06853	-0.206000	0.09398	-0.060000	0.13132	-0.291000	0.09656	GCC	C|0.945;T|0.055	0.055	strong		0.552	MYH4-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252731.1	NM_017533	
RFFL	117584	hgsc.bcm.edu	37	17	33348541	33348541	+	Missense_Mutation	SNP	C	C	T	rs34747500	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:33348541C>T	ENST00000315249.7	-	3	662	c.440G>A	c.(439-441)cGt>cAt	p.R147H	RAD51L3-RFFL_ENST00000593039.1_Intron|RFFL_ENST00000378516.2_Missense_Mutation_p.R147H|RFFL_ENST00000415395.2_Missense_Mutation_p.R147H|RFFL_ENST00000394597.2_Missense_Mutation_p.R147H|RFFL_ENST00000413582.2_Missense_Mutation_p.R147H|RFFL_ENST00000447669.2_Missense_Mutation_p.R147H|RFFL_ENST00000584655.1_Missense_Mutation_p.R147H|RFFL_ENST00000268850.7_Missense_Mutation_p.R147H					ring finger and FYVE-like domain containing E3 ubiquitin protein ligase											kidney(1)|large_intestine(2)|lung(3)	6		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0227)		GGTGGAGGCACGAGTCCTGTC	0.582													C|||	68	0.0135783	0.0356	0.0029	5008	,	,		19710	0.0188		0.0	False		,,,				2504	0.0				p.R147H		Atlas-SNP	.											.	RFFL	27	.	0			c.G440A						PASS	.	C	HIS/ARG	124,4282	91.6+/-130.3	3,118,2082	81.0	65.0	70.0		440	-4.3	0.4	17	dbSNP_126	70	1,8599	1.2+/-3.3	0,1,4299	yes	missense	RFFL	NM_001017368.1	29	3,119,6381	TT,TC,CC		0.0116,2.8143,0.9611	benign	147/364	33348541	125,12881	2203	4300	6503	SO:0001583	missense	117584	exon3			GAGGCACGAGTCC	AF434816	CCDS11286.1	17q12	2012-02-23	2012-02-23		ENSG00000092871	ENSG00000092871		"""RING-type (C3HC4) zinc fingers"""	24821	protein-coding gene	gene with protein product		609735	"""ring finger and FYVE-like domain containing"""			15229288	Standard	NR_037713		Approved	rififylin, fring, RNF189, RNF34L	uc002hin.1	Q8WZ73	OTTHUMG00000132933	ENST00000315249.7:c.440G>A	17.37:g.33348541C>T	ENSP00000326170:p.Arg147His	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	91	4	0.043956	NM_001017368		Missense_Mutation	SNP	ENST00000315249.7	37	CCDS11286.1	31	0.014194139194139194	16	0.032520325203252036	1	0.0027624309392265192	14	0.024475524475524476	0	0.0	C	7.587	0.669935	0.14776	0.028143	1.16E-4	ENSG00000092871	ENST00000315249;ENST00000394597;ENST00000378516;ENST00000268850;ENST00000413582;ENST00000415395	T;T;T;T;T;T	0.46451	0.87;0.87;0.89;0.91;0.89;0.87	5.65	-4.35	0.03656	.	1.494590	0.03679	N	0.245226	T	0.14184	0.0343	L	0.46157	1.445	0.19300	N	0.999975	B;B;B;B	0.10296	0.003;0.003;0.002;0.003	B;B;B;B	0.10450	0.005;0.003;0.001;0.001	T	0.33497	-0.9866	10	0.45353	T	0.12	-0.0021	7.6995	0.28615	0.1025:0.4344:0.0:0.4631	rs34747500	147;147;147;147	C9JN73;Q8WZ73-3;Q8WZ73;Q8WZ73-2	.;.;RFFL_HUMAN;.	H	147	ENSP00000326170:R147H;ENSP00000378096:R147H;ENSP00000367777:R147H;ENSP00000268850:R147H;ENSP00000408513:R147H;ENSP00000412322:R147H	ENSP00000268850:R147H	R	-	2	0	RFFL	30372654	0.000000	0.05858	0.450000	0.26969	0.123000	0.20343	-1.166000	0.03129	-0.526000	0.06383	-0.940000	0.02684	CGT	C|0.986;T|0.014	0.014	strong		0.582	RFFL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256460.2	NM_057178	
BTN3A2	11118	hgsc.bcm.edu	37	6	26370657	26370657	+	Missense_Mutation	SNP	A	A	G	rs71544290|rs9358936	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:26370657A>G	ENST00000356386.2	+	5	729	c.541A>G	c.(541-543)Aac>Gac	p.N181D	BTN3A2_ENST00000396948.1_Missense_Mutation_p.N181D|BTN3A2_ENST00000396934.3_Missense_Mutation_p.N158D|BTN3A2_ENST00000532994.1_3'UTR|BTN3A2_ENST00000527422.1_Missense_Mutation_p.N181D|BTN3A2_ENST00000508906.2_Missense_Mutation_p.N139D|BTN3A2_ENST00000377708.2_Missense_Mutation_p.N181D	NM_001197246.2|NM_001197247.1|NM_007047.3	NP_001184175.1|NP_001184176.1|NP_008978.2	P78410	BT3A2_HUMAN	butyrophilin, subfamily 3, member A2	181			N -> D (in dbSNP:rs9358936). {ECO:0000269|PubMed:14702039}.		interferon-gamma secretion (GO:0072643)|T cell mediated immunity (GO:0002456)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(5)	10						ACAGTGGAGCAACGCCAAGGG	0.542													G|||	409	0.0816693	0.0287	0.0403	5008	,	,		18132	0.0992		0.1123	False		,,,				2504	0.1329				p.N181D		Atlas-SNP	.											.	BTN3A2	44	.	0			c.A541G						PASS	.	G	ASP/ASN,ASP/ASN,ASP/ASN,ASP/ASN,ASP/ASN	168,4238		2,164,2037	130.0	115.0	120.0		541,541,472,415,541	-4.1	0.0	6	dbSNP_119	120	940,7660		51,838,3411	no	missense,missense,missense,missense,missense	BTN3A2	NM_001197246.1,NM_001197247.1,NM_001197248.1,NM_001197249.1,NM_007047.3	23,23,23,23,23	53,1002,5448	GG,GA,AA		10.9302,3.813,8.5191	benign,benign,benign,benign,benign	181/335,181/335,158/312,139/293,181/335	26370657	1108,11898	2203	4300	6503	SO:0001583	missense	11118	exon3			TGGAGCAACGCCA	U90546	CCDS4605.1, CCDS56399.1, CCDS56400.1	6p22.1	2014-01-14			ENSG00000186470	ENSG00000186470		"""Immunoglobulin superfamily / V-set domain containing"", ""Butyrophilins"""	1139	protein-coding gene	gene with protein product		613594				9149941	Standard	NM_007047		Approved	BTN3.2	uc010jqi.2	P78410	OTTHUMG00000014450	ENST00000356386.2:c.541A>G	6.37:g.26370657A>G	ENSP00000348751:p.Asn181Asp	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	110	110	1	NM_001197246	B4DRT7|B4E103|F5H791|F8W6E0|O00477|O15338|O75658|Q76PA0|Q9BU81|Q9NR44	Missense_Mutation	SNP	ENST00000356386.2	37	CCDS4605.1	158	0.07234432234432235	22	0.044715447154471545	14	0.03867403314917127	40	0.06993006993006994	82	0.10817941952506596	N	0.006	-2.031555	0.00410	0.03813	0.109302	ENSG00000186470	ENST00000532865;ENST00000535620;ENST00000527422;ENST00000356386;ENST00000396934;ENST00000377708;ENST00000396948;ENST00000508906	T;T;T;T;T;T;T	0.75260	-0.92;4.32;4.32;4.16;4.32;4.32;4.73	2.31	-4.07	0.03975	Immunoglobulin-like fold (1);	.	.	.	.	T	0.11324	0.0276	N	0.01109	-1.01	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.01393	-1.1366	8	0.02654	T	1	.	5.8415	0.18637	0.5502:0.1453:0.3045:0.0	rs9358936	158;181	F8W6E0;P78410	.;BT3A2_HUMAN	D	139;181;181;181;158;181;181;139	ENSP00000435952:N139D;ENSP00000432138:N181D;ENSP00000348751:N181D;ENSP00000380140:N158D;ENSP00000366937:N181D;ENSP00000380152:N181D;ENSP00000442687:N139D	ENSP00000348751:N181D	N	+	1	0	BTN3A2	26478636	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-2.022000	0.01439	-2.079000	0.00871	-2.510000	0.00188	AAC	A|0.926;G|0.074	0.074	strong		0.542	BTN3A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040113.2		
DCDC2	51473	hgsc.bcm.edu	37	6	24291203	24291203	+	Missense_Mutation	SNP	T	T	C	rs2274305	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:24291203T>C	ENST00000378454.3	-	5	962	c.661A>G	c.(661-663)Agt>Ggt	p.S221G		NM_001195610.1|NM_016356.3	NP_001182539.1|NP_057440.2	Q9UHG0	DCDC2_HUMAN	doublecortin domain containing 2	221	Doublecortin 2. {ECO:0000255|PROSITE- ProRule:PRU00072}.		S -> G (in dbSNP:rs2274305). {ECO:0000269|PubMed:10574461, ECO:0000269|PubMed:10601354, ECO:0000269|PubMed:15489334}.		cellular defense response (GO:0006968)|dendrite morphogenesis (GO:0048813)|intracellular signal transduction (GO:0035556)|neuron migration (GO:0001764)|visual learning (GO:0008542)					breast(1)|endometrium(2)|kidney(3)|large_intestine(8)|lung(12)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	32		Ovarian(999;0.101)				AGTAACTCACTGTAAGGCAGT	0.403													T|||	2589	0.516973	0.0537	0.6671	5008	,	,		15873	0.7827		0.668	False		,,,				2504	0.6074				p.S221G		Atlas-SNP	.											.	DCDC2	53	.	0			c.A661G						PASS	.	T	GLY/SER,GLY/SER	678,3728	284.9+/-277.9	65,548,1590	126.0	117.0	120.0		661,661	1.8	1.0	6	dbSNP_100	120	5597,3003	664.5+/-402.2	1817,1963,520	yes	missense,missense	DCDC2	NM_001195610.1,NM_016356.3	56,56	1882,2511,2110	CC,CT,TT		34.9186,15.3881,48.247	benign,benign	221/477,221/477	24291203	6275,6731	2203	4300	6503	SO:0001583	missense	51473	exon6			ACTCACTGTAAGG	AB032980	CCDS4550.1	6p22.1	2008-02-05			ENSG00000146038	ENSG00000146038			18141	protein-coding gene	gene with protein product		605755				10601354, 10574461	Standard	NM_001195610		Approved	RU2, KIAA1154, DCDC2A	uc003ndx.3	Q9UHG0	OTTHUMG00000016275	ENST00000378454.3:c.661A>G	6.37:g.24291203T>C	ENSP00000367715:p.Ser221Gly	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	104	40	0.384615	NM_001195610	Q5VTR8|Q5VTR9|Q86W35|Q9UFD1|Q9UHG1|Q9ULR6	Missense_Mutation	SNP	ENST00000378454.3	37	CCDS4550.1	1201	0.549908424908425	27	0.054878048780487805	241	0.6657458563535912	420	0.7342657342657343	513	0.6767810026385225	T	11.75	1.731498	0.30684	0.153881	0.650814	ENSG00000146038	ENST00000378454	D	0.93659	-3.26	5.48	1.8	0.24995	Doublecortin domain (4);	0.345140	0.33496	N	0.004848	T	0.67822	0.2934	N	0.05230	-0.09	0.09310	P	0.999999999770654	B	0.02656	0.0	B	0.01281	0.0	T	0.45948	-0.9226	9	0.12766	T	0.61	-24.4174	9.4015	0.38435	0.0:0.2796:0.0:0.7204	rs2274305;rs17243473;rs58797242;rs2274305	221	Q9UHG0	DCDC2_HUMAN	G	221	ENSP00000367715:S221G	ENSP00000367715:S221G	S	-	1	0	DCDC2	24399182	1.000000	0.71417	0.979000	0.43373	0.693000	0.40251	1.221000	0.32503	0.136000	0.18733	-0.256000	0.11100	AGT	T|0.493;C|0.507	0.507	strong		0.403	DCDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043604.1	NM_016356	
AKAP7	9465	hgsc.bcm.edu	37	6	131520655	131520655	+	Missense_Mutation	SNP	G	G	A	rs1190788	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:131520655G>A	ENST00000431975.2	+	6	742	c.644G>A	c.(643-645)aGt>aAt	p.S215N	AKAP7_ENST00000368123.4_Missense_Mutation_p.S193N|AKAP7_ENST00000263050.3_5'Flank|AKAP7_ENST00000541650.1_Missense_Mutation_p.S214N|AKAP7_ENST00000537868.1_5'Flank	NM_016377.3	NP_057461.2	Q9P0M2	AKA7G_HUMAN	A kinase (PRKA) anchor protein 7	215			S -> N (in dbSNP:rs1190788).			cytosol (GO:0005829)|nucleus (GO:0005634)	catalytic activity (GO:0003824)|nucleotide binding (GO:0000166)|protein kinase A binding (GO:0051018)			endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(2)|prostate(1)|stomach(1)	13	Breast(56;0.152)			GBM - Glioblastoma multiforme(226;0.0184)|OV - Ovarian serous cystadenocarcinoma(155;0.0345)		GAGAGCAGAAGTTTTAAACCT	0.393													G|||	969	0.19349	0.1407	0.2262	5008	,	,		21588	0.0536		0.3479	False		,,,				2504	0.227				p.S215N		Atlas-SNP	.											.	AKAP7	61	.	0			c.G644A						PASS	.	G	ASN/SER	801,3605	321.0+/-296.9	66,669,1468	139.0	120.0	126.0		644	0.2	0.1	6	dbSNP_87	126	3047,5553	470.0+/-367.7	533,1981,1786	yes	missense	AKAP7	NM_016377.3	46	599,2650,3254	AA,AG,GG		35.4302,18.1798,29.5863	benign	215/349	131520655	3848,9158	2203	4300	6503	SO:0001583	missense	9465	exon6			GCAGAAGTTTTAA	AF047715	CCDS5142.1, CCDS5143.1, CCDS5144.1, CCDS5142.2	6q23.2	2012-10-24			ENSG00000118507	ENSG00000118507		"""A-kinase anchor proteins"""	377	protein-coding gene	gene with protein product		604693				9545239	Standard	NM_016377		Approved	AKAP18, AKAP15	uc003qck.4	O43687	OTTHUMG00000015563	ENST00000431975.2:c.644G>A	6.37:g.131520655G>A	ENSP00000405252:p.Ser215Asn	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	94	22	0.234043	NM_016377	B4DUC3|Q9HCZ8	Missense_Mutation	SNP	ENST00000431975.2	37	CCDS5142.2	433	0.19826007326007325	84	0.17073170731707318	94	0.2596685082872928	10	0.017482517482517484	245	0.3232189973614776	G	13.52	2.260534	0.39995	0.181798	0.354302	ENSG00000118507	ENST00000431975;ENST00000541650;ENST00000368123	T;T;T	0.42513	0.97;0.97;0.97	5.36	0.182	0.15077	RNA ligase/cyclic nucleotide phosphodiesterase (1);Protein kinase A anchor protein, nuclear localisation signal domain (1);	0.691962	0.14573	N	0.311309	T	0.12732	0.0309	L	0.54323	1.7	0.50632	P	1.1099999999997223E-4	P;P	0.44344	0.646;0.833	B;B	0.36666	0.23;0.229	T	0.11867	-1.0570	9	0.21540	T	0.41	-10.0413	5.3228	0.15891	0.0822:0.4471:0.3407:0.13	rs1190788;rs1729536;rs17788100;rs58901183;rs1190788	214;215	F5GXD1;Q9P0M2	.;AKA7G_HUMAN	N	215;214;193	ENSP00000405252:S215N;ENSP00000441048:S214N;ENSP00000357105:S193N	ENSP00000357105:S193N	S	+	2	0	AKAP7	131562348	1.000000	0.71417	0.109000	0.21407	0.983000	0.72400	0.811000	0.27198	-0.190000	0.10465	0.655000	0.94253	AGT	G|0.752;A|0.248	0.248	strong		0.393	AKAP7-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042209.2	NM_004842	
MUC4	4585	hgsc.bcm.edu	37	3	195508343	195508343	+	Missense_Mutation	SNP	A	A	T	rs555793435|rs396680		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195508343A>T	ENST00000463781.3	-	2	10567	c.10108T>A	c.(10108-10110)Tcc>Acc	p.S3370T	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.S3370T	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)		TCACCTGTGGAAGCTGAGGAA	0.587																																					p.S3370T		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	0			c.T10108A						scavenged	.						36.0	31.0	33.0					3																	195508343		686	1582	2268	SO:0001583	missense	4585	exon2			CTGTGGAAGCTGA	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.10108T>A	3.37:g.195508343A>T	ENSP00000417498:p.Ser3370Thr	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	154	24	0.155844	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	a	3.051	-0.195478	0.06259	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.38401	1.29;1.14	0.423	-0.846	0.10734	.	.	.	.	.	T	0.15046	0.0363	N	0.19112	0.55	0.09310	N	1	P	0.38110	0.618	B	0.25759	0.063	T	0.13818	-1.0495	8	.	.	.	.	4.4467	0.11600	0.3383:0.0:0.6617:0.0	.	3242	E7ESK3	.	T	3370	ENSP00000417498:S3370T;ENSP00000420243:S3370T	.	S	-	1	0	MUC4	196993122	0.001000	0.12720	0.001000	0.08648	0.005000	0.04900	-2.391000	0.01057	-0.409000	0.07553	0.076000	0.15429	TCC	.	.	none		0.587	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
SHCBP1	79801	hgsc.bcm.edu	37	16	46642286	46642286	+	Silent	SNP	G	G	A	rs34559393	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:46642286G>A	ENST00000303383.3	-	5	878	c.612C>T	c.(610-612)aaC>aaT	p.N204N		NM_024745.4	NP_079021	Q8NEM2	SHCBP_HUMAN	SHC SH2-domain binding protein 1	204					fibroblast growth factor receptor signaling pathway (GO:0008543)|regulation of neural precursor cell proliferation (GO:2000177)					breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(7)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	28		all_cancers(37;0.00404)|all_epithelial(9;0.00527)|all_lung(18;0.0413)|Lung NSC(13;0.213)				TCCTCCAAATGTTTTGGTAGA	0.358													G|||	509	0.101637	0.0008	0.0937	5008	,	,		19408	0.4008		0.0258	False		,,,				2504	0.0133				p.N204N		Atlas-SNP	.											.	SHCBP1	54	.	0			c.C612T						PASS	.	G		31,4375		0,31,2172	111.0	101.0	104.0		612	-0.3	1.0	16	dbSNP_126	104	161,8437		2,157,4140	no	coding-synonymous	SHCBP1	NM_024745.4		2,188,6312	AA,AG,GG		1.8725,0.7036,1.4765		204/673	46642286	192,12812	2203	4299	6502	SO:0001819	synonymous_variant	79801	exon5			CCAAATGTTTTGG	AK055931	CCDS10720.1	16q11	2008-02-05			ENSG00000171241	ENSG00000171241			29547	protein-coding gene	gene with protein product		611027				10086341	Standard	NM_024745		Approved	FLJ22009	uc002eec.4	Q8NEM2	OTTHUMG00000132540	ENST00000303383.3:c.612C>T	16.37:g.46642286G>A		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	92	31	0.336957	NM_024745	Q96N60|Q9BVS0|Q9H6P6	Silent	SNP	ENST00000303383.3	37	CCDS10720.1																																																																																			G|0.955;A|0.045	0.045	strong		0.358	SHCBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255740.1	NM_024745	
PHRF1	57661	hgsc.bcm.edu	37	11	609068	609068	+	Silent	SNP	G	G	A	rs7928902	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:609068G>A	ENST00000264555.5	+	14	3740	c.3612G>A	c.(3610-3612)gcG>gcA	p.A1204A	PHRF1_ENST00000533464.1_Silent_p.A1200A|PHRF1_ENST00000413872.2_Silent_p.A1202A|PHRF1_ENST00000416188.2_Silent_p.A1203A	NM_020901.2	NP_065952.2	Q9P1Y6	PHRF1_HUMAN	PHD and ring finger domains 1	1204					mRNA processing (GO:0006397)|transcription from RNA polymerase II promoter (GO:0006366)	membrane (GO:0016020)	RNA polymerase binding (GO:0070063)|zinc ion binding (GO:0008270)			breast(1)|cervix(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(13)|urinary_tract(2)	28						CTTCCCCAGCGCCCCTTGCAC	0.701													G|||	940	0.1877	0.3359	0.2522	5008	,	,		15187	0.0198		0.2147	False		,,,				2504	0.0869				p.A1203A		Atlas-SNP	.											PHRF1_ENST00000264555,rectum,carcinoma,0,4	PHRF1	188	4	0			c.G3609A						scavenged	.	G		1208,2732		183,842,945	9.0	11.0	10.0		3609	-9.3	0.0	11	dbSNP_116	10	1939,6289		225,1489,2400	no	coding-synonymous	PHRF1	NM_020901.2		408,2331,3345	AA,AG,GG		23.5659,30.6599,25.8629		1203/1649	609068	3147,9021	1970	4114	6084	SO:0001819	synonymous_variant	57661	exon14			CCCAGCGCCCCTT	BC004950	CCDS44507.1, CCDS65987.1, CCDS65988.1, CCDS65989.1	11p15.5	2014-06-13			ENSG00000070047	ENSG00000070047		"""RING-type (C3HC4) zinc fingers"", ""Zinc fingers, PHD-type"""	24351	protein-coding gene	gene with protein product	"""CTD binding SR like protein rA9"", ""protein phosphatase 1, regulatory subunit 125"""	611780		RNF221			Standard	XM_005253027		Approved	KIAA1542, PPP1R125	uc010qwc.2	Q9P1Y6	OTTHUMG00000165141	ENST00000264555.5:c.3612G>A	11.37:g.609068G>A		Somatic	37	1	0.027027		WXS	Illumina HiSeq	Phase_I	41	34	0.829268	NM_020901	A6H8W1|B7ZM64|B9EGP0|C9JS82|Q6PJP2|Q8IVY2|Q8N2Y7|Q9BSM2	Silent	SNP	ENST00000264555.5	37																																																																																				G|0.799;A|0.201	0.201	strong		0.701	PHRF1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000382133.1	NM_020901	
OR2D3	120775	hgsc.bcm.edu	37	11	6942952	6942952	+	Silent	SNP	T	T	C	rs2035844	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:6942952T>C	ENST00000317834.3	+	1	748	c.720T>C	c.(718-720)acT>acC	p.T240T		NM_001004684.1	NP_001004684.1	Q8NGH3	OR2D3_HUMAN	olfactory receptor, family 2, subfamily D, member 3	240						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(2)|large_intestine(7)|lung(12)|prostate(3)|skin(1)|stomach(1)	27		Medulloblastoma(188;0.0523)|all_neural(188;0.236)		Epithelial(150;4.78e-08)|BRCA - Breast invasive adenocarcinoma(625;0.129)		TTATCTCCACTGTTATCCAGA	0.463													T|||	2040	0.407348	0.6241	0.3329	5008	,	,		20687	0.4464		0.1948	False		,,,				2504	0.3456				p.T240T		Atlas-SNP	.											.	OR2D3	51	.	0			c.T720C						PASS	.	T		2479,1923	626.0+/-394.6	692,1095,414	110.0	98.0	102.0		720	-0.1	1.0	11	dbSNP_94	102	1701,6891	310.0+/-309.6	172,1357,2767	no	coding-synonymous	OR2D3	NM_001004684.1		864,2452,3181	CC,CT,TT		19.7975,43.6847,32.1687		240/331	6942952	4180,8814	2201	4296	6497	SO:0001819	synonymous_variant	120775	exon1			CTCCACTGTTATC	BK004294	CCDS31417.1	11p15.4	2012-08-09			ENSG00000178358	ENSG00000178358		"""GPCR / Class A : Olfactory receptors"""	15146	protein-coding gene	gene with protein product							Standard	NM_001004684		Approved		uc010rav.2	Q8NGH3	OTTHUMG00000165742	ENST00000317834.3:c.720T>C	11.37:g.6942952T>C		Somatic	295	1	0.00338983		WXS	Illumina HiSeq	Phase_I	261	208	0.796935	NM_001004684	B2RP06|Q6IFG8|Q96R51	Silent	SNP	ENST00000317834.3	37	CCDS31417.1																																																																																			T|0.667;C|0.333	0.333	strong		0.463	OR2D3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385987.1	NM_001004684	
GRID1	2894	hgsc.bcm.edu	37	10	88126072	88126072	+	Splice_Site	SNP	G	G	A	rs61856638	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:88126072G>A	ENST00000327946.7	-	1	163	c.78C>T	c.(76-78)atC>atT	p.I26I		NM_017551.2	NP_060021.1	Q9ULK0	GRID1_HUMAN	glutamate receptor, ionotropic, delta 1	26					ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|social behavior (GO:0035176)|synaptic transmission, glutamatergic (GO:0035249)	cell junction (GO:0030054)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|ionotropic glutamate receptor complex (GO:0008328)|postsynaptic membrane (GO:0045211)	extracellular-glutamate-gated ion channel activity (GO:0005234)|ionotropic glutamate receptor activity (GO:0004970)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(24)|lung(46)|ovary(5)|prostate(4)|skin(5)|stomach(4)|upper_aerodigestive_tract(5)	106						CGCGCTTACCGATGTGGATGA	0.716										Multiple Myeloma(13;0.14)			G|||	1721	0.34365	0.5219	0.1398	5008	,	,		6767	0.5218		0.172	False		,,,				2504	0.2403				p.I26I		Atlas-SNP	.											.	GRID1	204	.	0			c.C78T						PASS	.	G		1885,2343		423,1039,652	10.0	9.0	10.0		78	2.2	1.0	10	dbSNP_129	10	1203,7105		112,979,3063	yes	coding-synonymous-near-splice	GRID1	NM_017551.2		535,2018,3715	AA,AG,GG		14.48,44.5837,24.6331		26/1010	88126072	3088,9448	2114	4154	6268	SO:0001630	splice_region_variant	2894	exon1			CTTACCGATGTGG	AB033046	CCDS31236.1	10q22	2012-08-29			ENSG00000182771	ENSG00000182771		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4575	protein-coding gene	gene with protein product		610659					Standard	NM_017551		Approved	GluD1, KIAA1220	uc001kdl.1	Q9ULK0	OTTHUMG00000018650	ENST00000327946.7:c.79+1C>T	10.37:g.88126072G>A		Somatic	8	0	0		WXS	Illumina HiSeq	Phase_I	21	9	0.428571	NM_017551	B3KXD5|B7Z7L0|Q8IXT3	Silent	SNP	ENST00000327946.7	37	CCDS31236.1																																																																																			G|0.654;A|0.346	0.346	strong		0.716	GRID1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049148.3	XM_043613	Silent
CFAP46	54777	hgsc.bcm.edu	37	10	134726272	134726272	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:134726272T>C	ENST00000368586.5	-	19	2486	c.2386A>G	c.(2386-2388)Atc>Gtc	p.I796V	TTC40_ENST00000368582.2_Missense_Mutation_p.I796V	NM_001200049.2	NP_001186978.2														breast(1)|endometrium(5)|lung(19)|urinary_tract(3)	28						ATCCAGCTGATGATCAGGCCT	0.607																																					p.I796V		Atlas-SNP	.											.	TTC40	100	.	0			c.A2386G						PASS	.																																			SO:0001583	missense	54777	exon19			AGCTGATGATCAG																												ENST00000368586.5:c.2386A>G	10.37:g.134726272T>C	ENSP00000357575:p.Ile796Val	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	63	34	0.539683	NM_001200049		Missense_Mutation	SNP	ENST00000368586.5	37	CCDS58101.1	.	.	.	.	.	.	.	.	.	.	T	0.985	-0.695708	0.03279	.	.	ENSG00000171811	ENST00000368586;ENST00000368582	T;T	0.41400	2.98;1.0	4.63	2.34	0.29019	.	.	.	.	.	T	0.27419	0.0673	.	.	.	0.09310	N	0.999994	B	0.29432	0.244	B	0.28638	0.092	T	0.17137	-1.0379	8	0.33141	T	0.24	.	5.6138	0.17420	0.1401:0.0:0.4971:0.3628	.	796	Q5SR76	CJ093_HUMAN	V	796	ENSP00000357575:I796V;ENSP00000357571:I796V	ENSP00000357571:I796V	I	-	1	0	C10orf93	134576262	0.003000	0.15002	0.157000	0.22605	0.022000	0.10575	0.082000	0.14847	0.631000	0.30412	0.443000	0.29094	ATC	.	.	none		0.607	TTC40-001	PUTATIVE	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000051095.3		
FKBP9	11328	hgsc.bcm.edu	37	7	33028165	33028165	+	Missense_Mutation	SNP	G	G	A	rs150348129	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:33028165G>A	ENST00000242209.4	+	6	1109	c.940G>A	c.(940-942)Gtg>Atg	p.V314M	AVL9_ENST00000404479.1_Intron|FKBP9_ENST00000538336.1_Missense_Mutation_p.V367M|FKBP9_ENST00000538443.1_Missense_Mutation_p.V176M|FKBP9_ENST00000489038.1_3'UTR|FKBP9_ENST00000490776.2_Missense_Mutation_p.V82M	NM_001284343.1|NM_007270.3	NP_001271272.1|NP_009201.2	O95302	FKBP9_HUMAN	FK506 binding protein 9, 63 kDa	314	PPIase FKBP-type 3. {ECO:0000255|PROSITE- ProRule:PRU00277}.				chaperone-mediated protein folding (GO:0061077)|protein folding (GO:0006457)|protein peptidyl-prolyl isomerization (GO:0000413)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)	calcium ion binding (GO:0005509)|FK506 binding (GO:0005528)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			central_nervous_system(13)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(6)|lung(9)|ovary(2)|upper_aerodigestive_tract(1)	39			GBM - Glioblastoma multiforme(11;0.0156)			GCAGGGCTACGTGATTCCTGG	0.517													G|||	53	0.0105831	0.0008	0.0086	5008	,	,		21623	0.0		0.0159	False		,,,				2504	0.0307				p.V314M		Atlas-SNP	.											FKBP9_ENST00000490776,NS,carcinoma,0,2	FKBP9	335	2	0			c.G940A						PASS	.	G	MET/VAL	14,4392	21.2+/-45.6	0,14,2189	149.0	131.0	137.0		940	4.5	1.0	7	dbSNP_134	137	154,8446	74.2+/-136.8	2,150,4148	no	missense	FKBP9	NM_007270.3	21	2,164,6337	AA,AG,GG		1.7907,0.3177,1.2917	possibly-damaging	314/571	33028165	168,12838	2203	4300	6503	SO:0001583	missense	11328	exon6			GGCTACGTGATTC	AF089745	CCDS5439.1, CCDS64622.1, CCDS64623.1	7p11.1	2013-01-10	2002-08-29		ENSG00000122642	ENSG00000122642		"""EF-hand domain containing"""	3725	protein-coding gene	gene with protein product			"""FK506-binding protein 9 (63 kD)"""			12036304	Standard	NM_007270		Approved	FKBP60, FKBP63	uc003tdh.3	O95302	OTTHUMG00000097847	ENST00000242209.4:c.940G>A	7.37:g.33028165G>A	ENSP00000242209:p.Val314Met	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	63	37	0.587302	NM_007270	B3KY35|B7Z1G9|B7Z6H3|Q2M2A1|Q3MIR7|Q6IN76|Q6P2N1|Q96EX5|Q96IJ9	Missense_Mutation	SNP	ENST00000242209.4	37	CCDS5439.1	13	0.005952380952380952	0	0.0	2	0.0055248618784530384	0	0.0	11	0.014511873350923483	G	23.8	4.458487	0.84317	0.003177	0.017907	ENSG00000122642	ENST00000242209;ENST00000538336;ENST00000538443;ENST00000418354;ENST00000490776	D;D;D;D;D	0.88586	-2.4;-2.4;-2.4;-2.4;-2.4	4.47	4.47	0.54385	Peptidyl-prolyl cis-trans isomerase, FKBP-type, domain (2);	0.000000	0.85682	D	0.000000	D	0.89083	0.6614	M	0.66439	2.03	0.80722	D	1	D;D;D;D	0.89917	0.999;1.0;0.971;0.999	D;D;P;D	0.79784	0.966;0.993;0.74;0.984	D	0.90825	0.4712	10	0.62326	D	0.03	-27.5046	17.5068	0.87748	0.0:0.0:1.0:0.0	.	82;367;314;314	B7Z1G9;B7Z6H3;O95302;B3KQQ0	.;.;FKBP9_HUMAN;.	M	314;367;176;82;82	ENSP00000242209:V314M;ENSP00000439250:V367M;ENSP00000437504:V176M;ENSP00000391034:V82M;ENSP00000441317:V82M	ENSP00000242209:V314M	V	+	1	0	FKBP9	32994690	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.901000	0.87382	2.211000	0.71520	0.555000	0.69702	GTG	G|0.988;A|0.012	0.012	strong		0.517	FKBP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215137.1	NM_007270	
GRIA1	2890	hgsc.bcm.edu	37	5	153078582	153078582	+	Silent	SNP	A	A	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:153078582A>C	ENST00000285900.5	+	10	1744	c.1401A>C	c.(1399-1401)cgA>cgC	p.R467R	GRIA1_ENST00000518783.1_Silent_p.R477R|GRIA1_ENST00000340592.5_Silent_p.R467R|GRIA1_ENST00000518142.1_Silent_p.R387R|GRIA1_ENST00000521843.2_Silent_p.R398R|GRIA1_ENST00000448073.4_Silent_p.R477R	NM_000827.3|NM_001258019.1	NP_000818.2|NP_001244948.1	P42261	GRIA1_HUMAN	glutamate receptor, ionotropic, AMPA 1	467					ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|long-term memory (GO:0007616)|receptor internalization (GO:0031623)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|axonal spine (GO:0044308)|cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|dendrite membrane (GO:0032590)|dendritic spine (GO:0043197)|endocytic vesicle membrane (GO:0030666)|endoplasmic reticulum (GO:0005783)|neuron spine (GO:0044309)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|synaptic vesicle (GO:0008021)	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:0004971)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glutamate receptor activity (GO:0008066)|PDZ domain binding (GO:0030165)			NS(1)|breast(4)|endometrium(7)|kidney(3)|large_intestine(24)|liver(2)|lung(23)|ovary(4)|pancreas(1)|prostate(5)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	81		Medulloblastoma(196;0.0391)|all_neural(177;0.16)|all_hematologic(541;0.21)	Kidney(363;0.000173)|KIRC - Kidney renal clear cell carcinoma(527;0.000785)		Desflurane(DB01189)|Enflurane(DB00228)|Isoflurane(DB00753)|Methoxyflurane(DB01028)|Perampanel(DB08883)|Sevoflurane(DB01236)	ACGGAGCCCGAGACCCTGACA	0.562																																					p.R477R		Atlas-SNP	.											GRIA1_ENST00000544403,NS,carcinoma,+1,2	GRIA1	321	2	0			c.A1431C						PASS	.						66.0	63.0	64.0					5																	153078582		2203	4300	6503	SO:0001819	synonymous_variant	2890	exon10			AGCCCGAGACCCT		CCDS4322.1, CCDS47318.1, CCDS58986.1, CCDS58987.1, CCDS58988.1, CCDS58989.1	5q33	2012-08-29			ENSG00000155511	ENSG00000155511		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4571	protein-coding gene	gene with protein product		138248		GLUR1		1652753, 1319477	Standard	NM_000827		Approved	GluA1, GLURA	uc011dcy.2	P42261	OTTHUMG00000130148	ENST00000285900.5:c.1401A>C	5.37:g.153078582A>C		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	104	25	0.240385	NM_001258021	B7Z2S0|B7Z2W8|B7Z3F6|B7Z9G9|D3DQI4|E7ESV8|Q2NKM6	Silent	SNP	ENST00000285900.5	37	CCDS4322.1																																																																																			.	.	none		0.562	GRIA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252456.3		
TNRC6A	27327	hgsc.bcm.edu	37	16	24801979	24801979	+	Silent	SNP	C	C	T	rs13336754	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:24801979C>T	ENST00000395799.3	+	6	2145	c.2016C>T	c.(2014-2016)agC>agT	p.S672S	TNRC6A_ENST00000315183.7_Silent_p.S672S	NM_014494.2	NP_055309.2	Q8NDV7	TNR6A_HUMAN	trinucleotide repeat containing 6A	672	Interaction with argonaute family proteins.|Sufficient for interaction with AGO1 and AGO4.|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)			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)		CAGTGGAGAGCGATGGTAGTA	0.463													C|||	833	0.166334	0.2693	0.1427	5008	,	,		21662	0.002		0.2763	False		,,,				2504	0.1002				p.S672S		Atlas-SNP	.											.	TNRC6A	171	.	0			c.C2016T						PASS	.	C		1312,3082	441.4+/-346.4	193,926,1078	94.0	86.0	89.0		2016	-5.2	0.9	16	dbSNP_121	89	2304,6296	388.9+/-342.7	325,1654,2321	no	coding-synonymous	TNRC6A	NM_014494.2		518,2580,3399	TT,TC,CC		26.7907,29.8589,27.8282		672/1963	24801979	3616,9378	2197	4300	6497	SO:0001819	synonymous_variant	27327	exon6			GGAGAGCGATGGT	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.2016C>T	16.37:g.24801979C>T		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	153	108	0.705882	NM_014494	C9JAR8|O15408|Q658L5|Q6NVB5|Q8NEZ0|Q8TBT8|Q8TCR0|Q9NV59|Q9P268	Silent	SNP	ENST00000395799.3	37	CCDS10624.2																																																																																			C|0.763;T|0.237	0.237	strong		0.463	TNRC6A-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214081.1	NM_020847	
CYP4F2	8529	hgsc.bcm.edu	37	19	16008388	16008388	+	Missense_Mutation	SNP	A	A	C	rs3093105	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:16008388A>C	ENST00000221700.6	-	2	129	c.34T>G	c.(34-36)Tgg>Ggg	p.W12G	CYP4F2_ENST00000011989.7_5'UTR	NM_001082.3	NP_001073.3			cytochrome P450, family 4, subfamily F, polypeptide 2											NS(2)|breast(1)|endometrium(6)|kidney(2)|large_intestine(9)|liver(1)|lung(18)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	46						GCCACTGGCCAGAGGCCCAGC	0.667													.|||	787	0.157149	0.239	0.1326	5008	,	,		15950	0.0585		0.1759	False		,,,				2504	0.1462				p.W12G		Atlas-SNP	.											.	CYP4F2	97	.	0			c.T34G						PASS	.	C	GLY/TRP	1034,3368		131,772,1298	33.0	35.0	34.0		34	-4.3	0.0	19	dbSNP_103	34	1468,7118		126,1216,2951	no	missense	CYP4F2	NM_001082.3	184	257,1988,4249	CC,CA,AA		17.0976,23.4893,19.2639	benign	12/521	16008388	2502,10486	2201	4293	6494	SO:0001583	missense	8529	exon2			CTGGCCAGAGGCC	U02388	CCDS12336.1	19p13.12	2013-11-11	2003-01-14		ENSG00000186115	ENSG00000186115		"""Cytochrome P450s"""	2645	protein-coding gene	gene with protein product		604426	"""cytochrome P450, subfamily IVF, polypeptide 2"""			8424651, 8026587	Standard	NM_001082		Approved		uc002nbs.1	P78329	OTTHUMG00000185995	ENST00000221700.6:c.34T>G	19.37:g.16008388A>C	ENSP00000221700:p.Trp12Gly	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	58	26	0.448276	NM_001082		Missense_Mutation	SNP	ENST00000221700.6	37	CCDS12336.1	343	0.15705128205128205	118	0.23983739837398374	64	0.17679558011049723	41	0.07167832167832168	120	0.158311345646438	N	0.011	-1.718931	0.00700	0.234893	0.170976	ENSG00000186115	ENST00000221700	D	0.87729	-2.29	2.99	-4.3	0.03710	.	0.324812	0.22983	N	0.053290	T	0.00012	0.0000	N	0.00230	-1.795	0.58432	P	8.000000000008E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.24083	-1.0170	9	0.02654	T	1	.	3.6498	0.08199	0.3407:0.1881:0.0:0.4712	rs3093105	12	P78329	CP4F2_HUMAN	G	12	ENSP00000221700:W12G	ENSP00000221700:W12G	W	-	1	0	CYP4F2	15869388	0.000000	0.05858	0.000000	0.03702	0.104000	0.19210	-0.868000	0.04236	-1.196000	0.02676	-0.346000	0.07831	TGG	A|0.824;C|0.176	0.176	strong		0.667	CYP4F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460372.3	NM_001082	
PIK3IP1	113791	hgsc.bcm.edu	37	22	31679110	31679110	+	Missense_Mutation	SNP	G	G	C	rs2040533	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:31679110G>C	ENST00000215912.5	-	6	935	c.752C>G	c.(751-753)aCc>aGc	p.T251S	PIK3IP1_ENST00000441972.1_3'UTR|PIK3IP1_ENST00000487265.2_Missense_Mutation_p.T172S	NM_052880.4	NP_443112.2	Q96FE7	P3IP1_HUMAN	phosphoinositide-3-kinase interacting protein 1	251			T -> S (in dbSNP:rs2040533). {ECO:0000269|PubMed:15461802, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.1}.		negative regulation of phosphatidylinositol 3-kinase activity (GO:0043553)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	phosphatidylinositol 3-kinase catalytic subunit binding (GO:0036313)			large_intestine(2)|lung(1)|ovary(1)	4						AAGGGGGGTGGTGCCCTCCTG	0.642													C|||	4232	0.845048	0.9856	0.7478	5008	,	,		17270	0.876		0.7266	False		,,,				2504	0.8139				p.T251S		Atlas-SNP	.											.	PIK3IP1	20	.	0			c.C752G						PASS	.	C	,SER/THR	4164,242	141.1+/-176.5	1970,224,9	53.0	40.0	45.0		,752	1.3	0.5	22	dbSNP_94	45	6233,2367	390.0+/-343.1	2259,1715,326	yes	utr-3,missense	PIK3IP1	NM_001135911.1,NM_052880.4	,58	4229,1939,335	CC,CG,GG		27.5233,5.4925,20.06	,benign	,251/264	31679110	10397,2609	2203	4300	6503	SO:0001583	missense	113791	exon6			GGGGTGGTGCCCT	BC011049	CCDS13893.1, CCDS46690.1	22q12.2	2007-04-13			ENSG00000100100	ENSG00000100100			24942	protein-coding gene	gene with protein product						12477932	Standard	NM_052880		Approved	HGFL, MGC17330	uc003akm.3	Q96FE7	OTTHUMG00000151256	ENST00000215912.5:c.752C>G	22.37:g.31679110G>C	ENSP00000215912:p.Thr251Ser	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	68	36	0.529412	NM_052880	B4DRR9|D1MEI0|O00318|Q49A94|Q86YW2|Q8NCJ9	Missense_Mutation	SNP	ENST00000215912.5	37	CCDS13893.1	1797	0.8228021978021978	484	0.983739837398374	275	0.7596685082872928	498	0.8706293706293706	540	0.712401055408971	C	0.005	-2.192325	0.00302	0.945075	0.724767	ENSG00000100100	ENST00000215912;ENST00000416925;ENST00000487265	T;T	0.42131	0.98;0.98	5.67	1.32	0.21799	.	0.557605	0.22422	N	0.060270	T	0.00012	0.0000	N	0.00289	-1.7	0.43902	P	0.0034610000000000474	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.34104	-0.9842	9	0.02654	T	1	-11.371	2.2271	0.03987	0.1251:0.4863:0.1217:0.267	rs2040533;rs17760782;rs17845282;rs17858115;rs59901552;rs2040533	172;251	D1MEI0;Q96FE7	.;P3IP1_HUMAN	S	251;229;172	ENSP00000215912:T251S;ENSP00000441361:T172S	ENSP00000215912:T251S	T	-	2	0	PIK3IP1	30009110	0.006000	0.16342	0.473000	0.27253	0.033000	0.12548	0.236000	0.17967	0.357000	0.24183	-0.978000	0.02582	ACC	G|0.183;C|0.817	0.817	strong		0.642	PIK3IP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321939.1	NM_052880	
LAMA2	3908	hgsc.bcm.edu	37	6	129635800	129635800	+	Splice_Site	SNP	G	G	A	rs2306942	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:129635800G>A	ENST00000421865.2	+	24	3461	c.3412G>A	c.(3412-3414)Gtg>Atg	p.V1138M		NM_000426.3|NM_001079823.1	NP_000417|NP_001073291.1	P24043	LAMA2_HUMAN	laminin, alpha 2	1138	Laminin EGF-like 13. {ECO:0000255|PROSITE-ProRule:PRU00460}.		V -> M (in dbSNP:rs2306942).		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)		CTTTCCTCAGGTGAATGTGGA	0.478													G|||	601	0.120008	0.2186	0.0562	5008	,	,		16729	0.1111		0.0427	False		,,,				2504	0.1207				p.V1138M		Atlas-SNP	.											.	LAMA2	481	.	0			c.G3412A						PASS	.	G	MET/VAL,MET/VAL	782,3624	314.7+/-293.7	76,630,1497	52.0	51.0	51.0		3412,3412	4.7	1.0	6	dbSNP_100	51	403,8197	126.7+/-185.1	11,381,3908	yes	missense-near-splice,missense-near-splice	LAMA2	NM_000426.3,NM_001079823.1	21,21	87,1011,5405	AA,AG,GG		4.686,17.7485,9.1112	possibly-damaging,possibly-damaging	1138/3123,1138/3119	129635800	1185,11821	2203	4300	6503	SO:0001630	splice_region_variant	3908	exon24			CCTCAGGTGAATG	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.3412-1G>A	6.37:g.129635800G>A		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	41	14	0.341463	NM_000426	Q14736|Q5VUM2|Q93022	Missense_Mutation	SNP	ENST00000421865.2	37	CCDS5138.1	231	0.10576923076923077	94	0.1910569105691057	21	0.058011049723756904	83	0.1451048951048951	33	0.04353562005277045	G	13.57	2.277729	0.40294	0.177485	0.04686	ENSG00000196569	ENST00000358023;ENST00000354729;ENST00000421865	T	0.54866	0.55	5.59	4.72	0.59763	EGF-like, laminin (3);	0.313651	0.30347	N	0.009831	T	0.28067	0.0692	L	0.53617	1.68	0.23221	P	0.99809855	B;B	0.16603	0.018;0.018	B;B	0.23716	0.048;0.048	T	0.12889	-1.0530	8	.	.	.	.	8.9207	0.35610	0.2224:0.0:0.7776:0.0	rs2306942;rs56723955;rs2306942	1138;1138	A6NF00;P24043	.;LAMA2_HUMAN	M	1138	ENSP00000400365:V1138M	.	V	+	1	0	LAMA2	129677493	1.000000	0.71417	1.000000	0.80357	0.837000	0.47467	3.073000	0.50057	1.378000	0.46305	0.655000	0.94253	GTG	G|0.896;A|0.104	0.104	strong		0.478	LAMA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042180.1		Missense_Mutation
KRTAP10-11	386678	hgsc.bcm.edu	37	21	46067194	46067194	+	Silent	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:46067194C>T	ENST00000334670.8	+	1	864	c.819C>T	c.(817-819)tgC>tgT	p.C273C	TSPEAR_ENST00000323084.4_Intron	NM_198692.2	NP_941965.2	P60412	KR10B_HUMAN	keratin associated protein 10-11	273						keratin filament (GO:0045095)				NS(1)|endometrium(1)|large_intestine(1)|lung(6)|ovary(2)|prostate(1)	12						CGGCCTCCTGCGTGTCCCTCC	0.677																																					p.C273C		Atlas-SNP	.											KRTAP10-11,NS,carcinoma,0,1	KRTAP10-11	36	1	0			c.C819T						scavenged	.						41.0	52.0	48.0					21																	46067194		2199	4293	6492	SO:0001819	synonymous_variant	386678	exon1			CTCCTGCGTGTCC	AB076359	CCDS42962.1	21q22.3	2006-03-13	2004-07-12	2004-07-14	ENSG00000243489	ENSG00000243489		"""Keratin associated proteins"""	20528	protein-coding gene	gene with protein product			"""keratin associated protein 10-11"""	KRTAP18-11			Standard	NM_198692		Approved	KRTAP18.11, KAP18.11, KAP10.11	uc002zfr.4	P60412	OTTHUMG00000057626	ENST00000334670.8:c.819C>T	21.37:g.46067194C>T		Somatic	88	1	0.0113636		WXS	Illumina HiSeq	Phase_I	108	5	0.0462963	NM_198692	A2RRF9	Silent	SNP	ENST00000334670.8	37	CCDS42962.1																																																																																			.	.	none		0.677	KRTAP10-11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128029.1	NM_198692	
CCDC27	148870	hgsc.bcm.edu	37	1	3679775	3679775	+	Missense_Mutation	SNP	C	C	T	rs10910024	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:3679775C>T	ENST00000294600.2	+	7	1142	c.1058C>T	c.(1057-1059)aCg>aTg	p.T353M		NM_152492.2	NP_689705.2	Q2M243	CCD27_HUMAN	coiled-coil domain containing 27	353	Glu-rich.		T -> M (in dbSNP:rs10910024). {ECO:0000269|PubMed:15489334}.							breast(1)|endometrium(2)|kidney(1)|large_intestine(8)|liver(2)|lung(17)|prostate(1)|skin(2)|urinary_tract(2)	36	all_cancers(77;0.0385)|Ovarian(185;0.0634)|Lung NSC(156;0.21)|all_lung(157;0.218)	all_epithelial(116;5.52e-17)|all_lung(118;1.04e-06)|Lung NSC(185;0.000214)|Renal(390;0.00357)|Breast(487;0.00446)|Hepatocellular(190;0.0218)|Lung SC(97;0.0367)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.127)		Epithelial(90;1.11e-38)|OV - Ovarian serous cystadenocarcinoma(86;1.35e-22)|GBM - Glioblastoma multiforme(42;3.46e-16)|Colorectal(212;1.17e-05)|COAD - Colon adenocarcinoma(227;5.76e-05)|Kidney(185;0.00036)|BRCA - Breast invasive adenocarcinoma(365;0.000696)|KIRC - Kidney renal clear cell carcinoma(229;0.00558)|STAD - Stomach adenocarcinoma(132;0.00645)|Lung(427;0.203)		GTGGAGGACACGGGTGCCTGG	0.667													C|||	744	0.148562	0.1074	0.2738	5008	,	,		16229	0.003		0.2435	False		,,,				2504	0.1677				p.T353M		Atlas-SNP	.											.	CCDC27	79	.	0			c.C1058T						PASS	.	C	MET/THR	547,3823		32,483,1670	57.0	57.0	57.0		1058	-5.1	0.0	1	dbSNP_120	57	2072,6486		256,1560,2463	yes	missense	CCDC27	NM_152492.2	81	288,2043,4133	TT,TC,CC		24.2113,12.5172,20.2584	probably-damaging	353/657	3679775	2619,10309	2185	4279	6464	SO:0001583	missense	148870	exon7			AGGACACGGGTGC		CCDS50.1	1p36.32	2008-02-05			ENSG00000162592	ENSG00000162592			26546	protein-coding gene	gene with protein product							Standard	NM_152492		Approved	FLJ32825	uc001akv.2	Q2M243	OTTHUMG00000003504	ENST00000294600.2:c.1058C>T	1.37:g.3679775C>T	ENSP00000294600:p.Thr353Met	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	36	21	0.583333	NM_152492	Q5TBV3|Q96M50	Missense_Mutation	SNP	ENST00000294600.2	37	CCDS50.1	323	0.1478937728937729	48	0.0975609756097561	87	0.24033149171270718	0	0.0	188	0.24802110817941952	C	5.949	0.359090	0.11239	0.125172	0.242113	ENSG00000162592	ENST00000294600	T	0.18960	2.18	2.93	-5.07	0.02938	.	3.906960	0.00575	N	0.000301	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.19583	0.037	B	0.12156	0.007	T	0.28267	-1.0049	9	0.41790	T	0.15	.	1.2646	0.02008	0.1856:0.2133:0.1286:0.4725	rs10910024;rs57282654;rs10910024	353	Q2M243	CCD27_HUMAN	M	353	ENSP00000294600:T353M	ENSP00000294600:T353M	T	+	2	0	CCDC27	3669635	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-4.171000	0.00281	-1.283000	0.02393	-1.406000	0.01132	ACG	C|0.836;T|0.164	0.164	strong		0.667	CCDC27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009740.1	NM_152492	
CEACAM6	4680	hgsc.bcm.edu	37	19	42265889	42265889	+	Missense_Mutation	SNP	G	G	T	rs11548735	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:42265889G>T	ENST00000199764.6	+	4	934	c.716G>T	c.(715-717)gGc>gTc	p.G239V	AC011513.4_ENST00000601409.1_RNA	NM_002483.4	NP_002474.3	P40199	CEAM6_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 6 (non-specific cross reacting antigen)	239	Ig-like C2-type 2.		G -> V (in dbSNP:rs11548735). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:18318008, ECO:0000269|PubMed:3337731, ECO:0000269|Ref.4}.		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)				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)		GGCCCAGATGGCCCCACCATT	0.547													t|||	2751	0.549321	0.7526	0.536	5008	,	,		18314	0.5625		0.4056	False		,,,				2504	0.4182				p.G239V		Atlas-SNP	.											.	CEACAM6	52	.	0			c.G716T						PASS	.	T	VAL/GLY	3013,1393	458.0+/-351.8	1031,951,221	80.0	82.0	81.0		716	-1.6	0.0	19	dbSNP_120	81	3542,5058	631.5+/-398.5	714,2114,1472	yes	missense	CEACAM6	NM_002483.4	109	1745,3065,1693	TT,TG,GG		41.186,31.616,49.6002	benign	239/345	42265889	6555,6451	2203	4300	6503	SO:0001583	missense	4680	exon4			CAGATGGCCCCAC	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.716G>T	19.37:g.42265889G>T	ENSP00000199764:p.Gly239Val	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	71	31	0.43662	NM_002483	Q13774|Q14920|Q53XP7	Missense_Mutation	SNP	ENST00000199764.6	37	CCDS12585.1	1192	0.5457875457875457	364	0.7398373983739838	181	0.5	332	0.5804195804195804	315	0.4155672823218997	T	1.048	-0.676735	0.03378	0.68384	0.41186	ENSG00000086548	ENST00000199764	T	0.09723	2.95	1.72	-1.6	0.08426	.	.	.	.	.	T	0.00012	0.0000	N	0.03115	-0.41	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.11916	-1.0568	8	0.32370	T	0.25	.	4.1838	0.10388	0.0:0.3614:0.4645:0.1741	rs11548735;rs16975588;rs17856125;rs52790104;rs61656290;rs11548735	239	P40199	CEAM6_HUMAN	V	239	ENSP00000199764:G239V	ENSP00000199764:G239V	G	+	2	0	CEACAM6	46957729	0.000000	0.05858	0.002000	0.10522	0.125000	0.20455	-0.235000	0.09016	-1.295000	0.02357	-2.494000	0.00193	GGC	G|0.489;T|0.511	0.511	strong		0.547	CEACAM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321147.1		
TPX2	22974	hgsc.bcm.edu	37	20	30381758	30381758	+	Silent	SNP	G	G	C	rs1062794	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:30381758G>C	ENST00000300403.6	+	14	2145	c.1617G>C	c.(1615-1617)tcG>tcC	p.S539S	TPX2_ENST00000340513.4_Silent_p.S575S	NM_012112.4	NP_036244.2	Q9ULW0	TPX2_HUMAN	TPX2, microtubule-associated	539					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)			GCCCTTTCTCGTTTGATTCTC	0.438													C|||	1461	0.291733	0.6778	0.2435	5008	,	,		18940	0.001		0.3161	False		,,,				2504	0.0787				p.S539S		Atlas-SNP	.											.	TPX2	61	.	0			c.G1617C						PASS	.	C		2598,1808	531.2+/-373.1	757,1084,362	144.0	144.0	144.0		1617	3.8	1.0	20	dbSNP_86	144	2500,6100	694.3+/-404.7	358,1784,2158	no	coding-synonymous	TPX2	NM_012112.4		1115,2868,2520	CC,CG,GG		29.0698,41.035,39.1973		539/748	30381758	5098,7908	2203	4300	6503	SO:0001819	synonymous_variant	22974	exon14			TTTCTCGTTTGAT	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.1617G>C	20.37:g.30381758G>C		Somatic	191	0	0		WXS	Illumina HiSeq	Phase_I	150	61	0.406667	NM_012112	Q9H1R4|Q9NRA3|Q9UFN9|Q9UL00|Q9Y2M1	Silent	SNP	ENST00000300403.6	37	CCDS13190.1																																																																																			G|0.637;C|0.363	0.363	strong		0.438	TPX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078569.2		
MUC4	4585	hgsc.bcm.edu	37	3	195509443	195509443	+	Missense_Mutation	SNP	A	A	G	rs74585045		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195509443A>G	ENST00000463781.3	-	2	9467	c.9008T>C	c.(9007-9009)aTa>aCa	p.I3003T	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.I3003T	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)		GGCGTGACCTATGGATGCTGA	0.582																																					p.I3003T		Atlas-SNP	.											.	MUC4	1505	.	0			c.T9008C						PASS	.						15.0	11.0	12.0					3																	195509443		628	1543	2171	SO:0001583	missense	4585	exon2			TGACCTATGGATG	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.9008T>C	3.37:g.195509443A>G	ENSP00000417498:p.Ile3003Thr	Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	51	13	0.254902	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	0.314	-0.966155	0.02232	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.30448	1.53;1.58	.	.	.	.	.	.	.	.	T	0.12050	0.0293	N	0.08118	0	0.09310	N	1	B	0.10296	0.003	B	0.01281	0.0	T	0.31558	-0.9939	7	.	.	.	.	4.3667	0.11228	0.5198:0.0:0.4802:0.0	.	2875	E7ESK3	.	T	3003	ENSP00000417498:I3003T;ENSP00000420243:I3003T	.	I	-	2	0	MUC4	196994222	.	.	0.024000	0.17045	0.000000	0.00434	.	.	-0.437000	0.07243	0.000000	0.15137	ATA	A|0.250;G|0.750	0.750	weak		0.582	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
HPS1	3257	hgsc.bcm.edu	37	10	100190920	100190920	+	Silent	SNP	G	G	A	rs1801287	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:100190920G>A	ENST00000325103.6	-	7	869	c.636C>T	c.(634-636)ctC>ctT	p.L212L	HPS1_ENST00000338546.5_Silent_p.L212L|HPS1_ENST00000467246.1_5'UTR|MIR4685_ENST00000578185.1_RNA|HPS1_ENST00000361490.4_Silent_p.L212L	NM_000195.3	NP_000186.2	Q92902	HPS1_HUMAN	Hermansky-Pudlak syndrome 1	212					blood coagulation (GO:0007596)|eye pigmentation (GO:0048069)|lysosome organization (GO:0007040)|melanocyte differentiation (GO:0030318)|positive regulation of natural killer cell activation (GO:0032816)|retina development in camera-type eye (GO:0060041)|secretion of lysosomal enzymes (GO:0033299)|visual perception (GO:0007601)	BLOC-3 complex (GO:0031085)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)	protein dimerization activity (GO:0046983)			breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|liver(1)|lung(9)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	23		Colorectal(252;0.234)		Epithelial(162;3.87e-12)|all cancers(201;5.63e-10)		TGGAGTGCACGAGCAGGAAGG	0.622									Hermansky-Pudlak syndrome				G|||	1417	0.282947	0.1369	0.2911	5008	,	,		20397	0.3442		0.2952	False		,,,				2504	0.3988				p.L212L		Atlas-SNP	.											HPS1,NS,carcinoma,0,1	HPS1	65	1	0			c.C636T						PASS	.	G	,	592,3814	258.9+/-262.7	45,502,1656	64.0	56.0	59.0		636,636	-10.6	0.2	10	dbSNP_89	59	2515,6085	408.7+/-349.6	385,1745,2170	no	coding-synonymous,coding-synonymous	HPS1	NM_000195.3,NM_182639.2	,	430,2247,3826	AA,AG,GG		29.2442,13.4362,23.889	,	212/701,212/325	100190920	3107,9899	2203	4300	6503	SO:0001819	synonymous_variant	3257	exon7	Familial Cancer Database	HPS, HPS1-8	GTGCACGAGCAGG	U79136	CCDS7475.1, CCDS7476.1	10q23.1-q23.3	2014-06-18		2002-05-01	ENSG00000107521	ENSG00000107521			5163	protein-coding gene	gene with protein product		604982	"""Hermansky-Pudlak syndrome"""	HPS		8541858, 7573033	Standard	NM_182639		Approved		uc021pwv.1	Q92902	OTTHUMG00000018876	ENST00000325103.6:c.636C>T	10.37:g.100190920G>A		Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	163	79	0.484663	NM_000195	A8MRT2|O15402|O15502|Q5TAA3|Q8WXE5	Silent	SNP	ENST00000325103.6	37	CCDS7475.1	601	0.2751831501831502	68	0.13821138211382114	104	0.287292817679558	202	0.3531468531468531	227	0.2994722955145119	G	7.097	0.573403	0.13623	0.134362	0.292442	ENSG00000107521	ENST00000414009	.	.	.	5.3	-10.6	0.00265	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.99999999561151	.	.	.	.	.	.	T	0.12218	-1.0556	3	.	.	.	.	8.2338	0.31614	0.3875:0.4577:0.0859:0.0689	rs1801287;rs17535258;rs1801287	.	.	.	C	80	.	.	R	-	1	0	HPS1	100180910	0.000000	0.05858	0.235000	0.24058	0.788000	0.44548	-1.746000	0.01829	-2.442000	0.00549	-2.005000	0.00442	CGT	G|0.745;A|0.255	0.255	strong		0.622	HPS1-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049776.1	NM_000195, NM_182637, NM_182638, NM_182639	
ABCA4	24	hgsc.bcm.edu	37	1	94466659	94466659	+	Silent	SNP	A	A	G	rs1801555	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:94466659A>G	ENST00000370225.3	-	46	6371	c.6285T>C	c.(6283-6285)gaT>gaC	p.D2095D	ABCA4_ENST00000535881.1_Silent_p.D214D|ABCA4_ENST00000536513.1_Silent_p.D365D|ABCA4_ENST00000465352.1_5'Flank	NM_000350.2	NP_000341.2	P78363	ABCA4_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 4	2095	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				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)		TGGTGGGCTCATCCTGGGGGG	0.632													G|||	1508	0.301118	0.733	0.1297	5008	,	,		18222	0.1567		0.1193	False		,,,				2504	0.1748				p.D2095D		Atlas-SNP	.											.	ABCA4	275	.	0			c.T6285C						PASS	.	G		2788,1618	499.5+/-364.4	873,1042,288	49.0	48.0	48.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	6285	2.6	1.0	1	dbSNP_89	48	1099,7501	764.2+/-407.6	87,925,3288	no	coding-synonymous	ABCA4	NM_000350.2		960,1967,3576	GG,GA,AA		12.7791,36.7227,29.8862		2095/2274	94466659	3887,9119	2203	4300	6503	SO:0001819	synonymous_variant	24	exon46			GGGCTCATCCTGG	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.6285T>C	1.37:g.94466659A>G		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	51	24	0.470588	NM_000350	O15112|O60438|O60915|Q0QD48|Q4LE31	Silent	SNP	ENST00000370225.3	37	CCDS747.1																																																																																			A|0.712;G|0.288	0.288	strong		0.632	ABCA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029320.1	NM_000350	
ORM1	5004	hgsc.bcm.edu	37	9	117087412	117087412	+	Missense_Mutation	SNP	G	G	A	rs1126801	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:117087412G>A	ENST00000259396.8	+	5	598	c.520G>A	c.(520-522)Gtg>Atg	p.V174M	ORM1_ENST00000477456.1_3'UTR	NM_000607.2	NP_000598.2	P02763	A1AG1_HUMAN	orosomucoid 1	174			V -> M (in allele ORM1*F2; dbSNP:rs1126801). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9050929}.		acute-phase response (GO:0006953)|inflammatory response (GO:0006954)|regulation of immune system process (GO:0002682)|transport (GO:0006810)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				endometrium(2)|large_intestine(4)|lung(2)	8		Myeloproliferative disorder(63;0.163)			Abiraterone(DB05812)|Acenocoumarol(DB01418)|Ajmaline(DB01426)|Alfentanil(DB00802)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Aprindine(DB01429)|Bupropion(DB01156)|Canagliflozin(DB08907)|Celecoxib(DB00482)|Chlorpromazine(DB00477)|Desipramine(DB01151)|Disopyramide(DB00280)|Doxazosin(DB00590)|Doxepin(DB01142)|Erlotinib(DB00530)|Fluoxetine(DB00472)|Gefitinib(DB00317)|Imatinib(DB00619)|Imipramine(DB00458)|Ivacaftor(DB08820)|Maprotiline(DB00934)|Mirabegron(DB08893)|Nateglinide(DB00731)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Oxycodone(DB00497)|Penbutolol(DB01359)|Pethidine(DB00454)|Phenprocoumon(DB00946)|Pitavastatin(DB08860)|Prazosin(DB00457)|Propranolol(DB00571)|Quinidine(DB00908)|Saquinavir(DB01232)|Tacrolimus(DB00864)|Tamsulosin(DB00706)|Telaprevir(DB05521)|Thalidomide(DB01041)|Trazodone(DB00656)|Vandetanib(DB05294)|Vemurafenib(DB08881)|Vismodegib(DB08828)|Warfarin(DB00682)	GTCAGATGTCGTGTACACCGA	0.572													-|||	111	0.0221645	0.0408	0.0187	5008	,	,		23206	0.001		0.0328	False		,,,				2504	0.0102				p.V174M		Atlas-SNP	.											.	ORM1	20	.	0			c.G520A						PASS	.	A	MET/VAL	183,4223		0,183,2020	128.0	141.0	136.0		520	-8.5	0.0	9	dbSNP_86	136	191,8409		2,187,4111	no	missense	ORM1	NM_000607.2	21	2,370,6131	AA,AG,GG		2.2209,4.1534,2.8756	benign	174/202	117087412	374,12632	2203	4300	6503	SO:0001583	missense	5004	exon5			GATGTCGTGTACA		CCDS6803.1	9q32	2013-09-19			ENSG00000229314	ENSG00000229314		"""Lipocalins"""	8498	protein-coding gene	gene with protein product		138600					Standard	NM_000607		Approved		uc004bik.4	P02763	OTTHUMG00000021012	ENST00000259396.8:c.520G>A	9.37:g.117087412G>A	ENSP00000259396:p.Val174Met	Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	128	67	0.523438	NM_000607	B7ZKQ5|Q5T539|Q5U067|Q8TC16	Missense_Mutation	SNP	ENST00000259396.8	37	CCDS6803.1	51	0.023351648351648352	18	0.036585365853658534	8	0.022099447513812154	1	0.0017482517482517483	24	0.0316622691292876	-	3.977	-0.007207	0.07773	0.041534	0.022209	ENSG00000229314	ENST00000259396	T	0.10099	2.91	4.23	-8.47	0.00939	Calycin-like (1);Lipocalin/cytosolic fatty-acid binding protein domain (1);Calycin (1);	1.390010	0.04077	N	0.308987	T	0.00524	0.0017	N	0.02916	-0.46	0.09310	N	0.999999	P	0.37525	0.598	B	0.18263	0.021	T	0.40905	-0.9538	10	0.12103	T	0.63	-0.9597	2.7473	0.05271	0.3979:0.2169:0.2939:0.0913	rs1126801;rs1803078;rs3182058;rs11552134;rs17412027	174	P02763	A1AG1_HUMAN	M	174	ENSP00000259396:V174M	ENSP00000259396:V174M	V	+	1	0	ORM1	116127233	0.000000	0.05858	0.000000	0.03702	0.020000	0.10135	-1.459000	0.02370	-2.210000	0.00738	0.197000	0.17608	GTG	G|0.972;A|0.028	0.028	strong		0.572	ORM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055426.1		
PROCR	10544	hgsc.bcm.edu	37	20	33764554	33764554	+	Missense_Mutation	SNP	A	A	G	rs867186	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:33764554A>G	ENST00000216968.4	+	4	737	c.655A>G	c.(655-657)Agt>Ggt	p.S219G	EDEM2_ENST00000540582.1_Intron	NM_006404.3	NP_006395.2	Q9UNN8	EPCR_HUMAN	protein C receptor, endothelial	219			S -> G (in dbSNP:rs867186). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.6}.		antigen processing and presentation (GO:0019882)|blood coagulation (GO:0007596)|immune response (GO:0006955)|negative regulation of coagulation (GO:0050819)	cell surface (GO:0009986)|centrosome (GO:0005813)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)	receptor activity (GO:0004872)			breast(1)|kidney(2)|large_intestine(1)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)	10			BRCA - Breast invasive adenocarcinoma(18;0.0152)		Drotrecogin alfa(DB00055)	CCTGGTGGGCAGTTTCATCAT	0.567													A|||	481	0.0960463	0.1044	0.0519	5008	,	,		19296	0.0883		0.0875	False		,,,				2504	0.1329				p.S219G		Atlas-SNP	.											.	PROCR	26	.	0			c.A655G	GRCh37	CM052909	PROCR	M	rs867186	PASS	.	A	GLY/SER	425,3981	205.5+/-227.4	22,381,1800	106.0	84.0	91.0	http://www.ncbi.nlm.nih.gov/pubmed?term	655	-2.6	1.0	20	dbSNP_86	91	865,7735	196.2+/-241.2	52,761,3487	yes	missense	PROCR	NM_006404.3	56	74,1142,5287	GG,GA,AA	http://www.ncbi.nlm.nih.gov/pubmed?term	10.0581,9.6459,9.9185	benign	219/239	33764554	1290,11716	2203	4300	6503	SO:0001583	missense	10544	exon4			GTGGGCAGTTTCA	L35545	CCDS13248.1	20q11.2	2010-05-04	2010-05-04		ENSG00000101000	ENSG00000101000		"""CD molecules"""	9452	protein-coding gene	gene with protein product		600646				7929370, 10518938	Standard	NM_006404		Approved	EPCR, CCD41, CD201	uc002xbt.3	Q9UNN8	OTTHUMG00000032323	ENST00000216968.4:c.655A>G	20.37:g.33764554A>G	ENSP00000216968:p.Ser219Gly	Somatic	211	0	0		WXS	Illumina HiSeq	Phase_I	182	91	0.5	NM_006404	B2RC04|Q14218|Q6IB56|Q96CB3|Q9ULX1	Missense_Mutation	SNP	ENST00000216968.4	37	CCDS13248.1	183	0.08379120879120878	46	0.09349593495934959	28	0.07734806629834254	35	0.06118881118881119	74	0.09762532981530343	A	15.74	2.924137	0.52653	0.096459	0.100581	ENSG00000101000	ENST00000374477;ENST00000216968	T	0.05258	3.47	5.75	-2.58	0.06228	.	0.828884	0.11137	N	0.595761	T	0.00109	0.0003	N	0.14661	0.345	0.44754	P	0.002242999999999995	B	0.28128	0.201	B	0.26770	0.073	T	0.41893	-0.9483	9	0.52906	T	0.07	-7.7927	7.1489	0.25599	0.2988:0.0:0.0833:0.6179	rs867186;rs1051021;rs3177976;rs17321376;rs17851161;rs56568720;rs59257071;rs867186	219	Q9UNN8	EPCR_HUMAN	G	219	ENSP00000216968:S219G	ENSP00000216968:S219G	S	+	1	0	PROCR	33228215	0.976000	0.34144	0.995000	0.50966	0.940000	0.58332	0.206000	0.17375	-0.358000	0.08162	-0.301000	0.09380	AGT	A|0.909;G|0.091	0.091	strong		0.567	PROCR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078843.3		
RBBP6	5930	hgsc.bcm.edu	37	16	24583406	24583406	+	Silent	SNP	A	A	G	rs7593	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:24583406A>G	ENST00000319715.4	+	18	5451	c.5019A>G	c.(5017-5019)gcA>gcG	p.A1673A	RBBP6_ENST00000381039.3_Silent_p.A833A|RBBP6_ENST00000348022.2_Silent_p.A1639A	NM_006910.4	NP_008841.2	Q7Z6E9	RBBP6_HUMAN	retinoblastoma binding protein 6	1673					embryonic organ development (GO:0048568)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|somite development (GO:0061053)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(17)|ovary(4)|pancreas(1)|prostate(2)|urinary_tract(1)	46				GBM - Glioblastoma multiforme(48;0.0518)		TGGAGAAAGCAAAAGAGAGCC	0.458													G|||	1559	0.311302	0.3464	0.3343	5008	,	,		18720	0.0893		0.4095	False		,,,				2504	0.3753				p.A1673A		Atlas-SNP	.											.	RBBP6	158	.	0			c.A5019G						PASS	.	G	,	1613,2781	658.3+/-400.4	291,1031,875	59.0	67.0	64.0		5019,4917	-4.5	0.9	16	dbSNP_52	64	3431,5169	632.8+/-398.7	689,2053,1558	no	coding-synonymous,coding-synonymous	RBBP6	NM_006910.4,NM_018703.3	,	980,3084,2433	GG,GA,AA		39.8953,36.7091,38.8179	,	1673/1793,1639/1759	24583406	5044,7950	2197	4300	6497	SO:0001819	synonymous_variant	5930	exon18			GAAAGCAAAAGAG		CCDS10621.1, CCDS10622.1, CCDS45444.1	16p12.2	2008-08-04	2001-11-28		ENSG00000122257	ENSG00000122257			9889	protein-coding gene	gene with protein product	"""proliferation potential-related protein"""	600938	"""retinoblastoma-binding protein 6"""			8595913, 16396680	Standard	NM_006910		Approved	P2P-R, PACT, SNAMA	uc002dmh.3	Q7Z6E9	OTTHUMG00000096991	ENST00000319715.4:c.5019A>G	16.37:g.24583406A>G		Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	131	131	1	NM_006910	Q147T5|Q15290|Q6DKH4|Q6P4C2|Q6YNC9|Q7Z6E8|Q8N0V2|Q96PH3|Q9H3I8|Q9H5M5|Q9NPX4	Silent	SNP	ENST00000319715.4	37	CCDS10621.1																																																																																			A|0.650;G|0.350	0.350	strong		0.458	RBBP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214067.2	NM_006910	
FAM207A	85395	hgsc.bcm.edu	37	21	46387078	46387078	+	Missense_Mutation	SNP	G	G	T	rs2294168	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:46387078G>T	ENST00000291634.6	+	4	530	c.482G>T	c.(481-483)aGc>aTc	p.S161I	FAM207A_ENST00000397826.3_Missense_Mutation_p.S146I|FAM207A_ENST00000479127.1_3'UTR	NM_058190.2	NP_478070.1	Q9NSI2	F207A_HUMAN	family with sequence similarity 207, member A	161																	GAGGCTGGCAGCCGGCGCCAA	0.711													G|||	547	0.109225	0.0991	0.2003	5008	,	,		13190	0.1121		0.1282	False		,,,				2504	0.0358				p.S161I		Atlas-SNP	.											C21orf70,NS,carcinoma,-1,1	.	.	1	0			c.G482T						PASS	.	G	ILE/SER	491,3883		35,421,1731	14.0	19.0	17.0		482	1.5	0.0	21	dbSNP_100	17	1032,7520		80,872,3324	no	missense	FAM207A	NM_058190.2	142	115,1293,5055	TT,TG,GG		12.0674,11.2254,11.7825	benign	161/231	46387078	1523,11403	2187	4276	6463	SO:0001583	missense	85395	exon4			CTGGCAGCCGGCG		CCDS13718.1	21q22.3	2011-08-15	2011-08-15	2011-08-15	ENSG00000160256	ENSG00000160256			15811	protein-coding gene	gene with protein product			"""chromosome 21 open reading frame 70"""	C21orf70			Standard	NM_058190		Approved	PRED56	uc002zgl.3	Q9NSI2	OTTHUMG00000090293	ENST00000291634.6:c.482G>T	21.37:g.46387078G>T	ENSP00000291634:p.Ser161Ile	Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	34	24	0.705882	NM_058190		Missense_Mutation	SNP	ENST00000291634.6	37	CCDS13718.1	275	0.1259157509157509	56	0.11382113821138211	56	0.15469613259668508	67	0.11713286713286714	96	0.1266490765171504	G	12.01	1.809550	0.31961	0.112254	0.120674	ENSG00000160256	ENST00000291634;ENST00000397826;ENST00000458015	T;T;T	0.47177	1.01;1.01;0.85	3.44	1.53	0.23141	.	0.895789	0.09616	N	0.778288	T	0.00271	0.0008	L	0.38531	1.155	0.80722	P	0.0	P;P	0.44380	0.73;0.834	B;P	0.45506	0.316;0.483	T	0.06716	-1.0811	9	0.39692	T	0.17	-0.0034	9.4412	0.38670	0.0:0.4286:0.5714:0.0	rs2294168	146;161	Q9NSI2-2;Q9NSI2	.;F207A_HUMAN	I	161;146;146	ENSP00000291634:S161I;ENSP00000380926:S146I;ENSP00000404964:S146I	ENSP00000291634:S161I	S	+	2	0	C21orf70	45211506	0.000000	0.05858	0.006000	0.13384	0.015000	0.08874	0.202000	0.17295	0.405000	0.25532	0.563000	0.77884	AGC	G|0.887;T|0.113	0.113	strong		0.711	FAM207A-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000206639.1	NM_058190	
KIF26A	26153	hgsc.bcm.edu	37	14	104643650	104643650	+	Missense_Mutation	SNP	C	C	T	rs372336742		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:104643650C>T	ENST00000423312.2	+	12	4525	c.4525C>T	c.(4525-4527)Cgg>Tgg	p.R1509W	KIF26A_ENST00000315264.7_Missense_Mutation_p.R1370W	NM_015656.1	NP_056471.1	Q9ULI4	KI26A_HUMAN	kinesin family member 26A	1509					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)	p.R1509W(1)		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)		TGGTGGGTCGCGGGCTCTGGG	0.736																																					p.R1509W		Atlas-SNP	.											KIF26A,NS,carcinoma,0,1	KIF26A	84	1	1	Substitution - Missense(1)	endometrium(1)	c.C4525T						PASS	.	C	TRP/ARG	0,3588		0,0,1794	8.0	11.0	10.0		4525	-0.3	0.0	14		10	1,7821		0,1,3910	no	missense	KIF26A	NM_015656.1	101	0,1,5704	TT,TC,CC		0.0128,0.0,0.0088	probably-damaging	1509/1883	104643650	1,11409	1794	3911	5705	SO:0001583	missense	26153	exon12			GGGTCGCGGGCTC	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.4525C>T	14.37:g.104643650C>T	ENSP00000388241:p.Arg1509Trp	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	97	58	0.597938	NM_015656	Q8TAZ7|Q96GK3|Q9UFL3	Missense_Mutation	SNP	ENST00000423312.2	37	CCDS45171.1	.	.	.	.	.	.	.	.	.	.	C	12.07	1.828514	0.32329	0.0	1.28E-4	ENSG00000066735	ENST00000423312;ENST00000315264	T;T	0.80824	-1.42;-1.42	4.09	-0.307	0.12777	.	.	.	.	.	D	0.82393	0.5027	L	0.47716	1.5	0.09310	N	1	D	0.76494	0.999	P	0.62014	0.897	T	0.71629	-0.4535	9	0.87932	D	0	.	8.6301	0.33915	0.5422:0.3597:0.098:0.0	.	1509	Q9ULI4	KI26A_HUMAN	W	1509;1370	ENSP00000388241:R1509W;ENSP00000325452:R1370W	ENSP00000325452:R1370W	R	+	1	2	KIF26A	103713403	0.964000	0.33143	0.001000	0.08648	0.002000	0.02628	2.357000	0.44125	0.113000	0.18004	0.462000	0.41574	CGG	.	.	weak		0.736	KIF26A-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414356.1		
CCDC33	80125	hgsc.bcm.edu	37	15	74625175	74625175	+	Missense_Mutation	SNP	C	C	A	rs200735867		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:74625175C>A	ENST00000398814.3	+	16	2358	c.1927C>A	c.(1927-1929)Cag>Aag	p.Q643K	CCDC33_ENST00000268082.4_Missense_Mutation_p.Q236K|CCDC33_ENST00000321288.5_Missense_Mutation_p.Q846K|CCDC33_ENST00000558821.1_Missense_Mutation_p.Q236K	NM_025055.3	NP_079331.3	Q8N5R6	CCD33_HUMAN	coiled-coil domain containing 33	846										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						TCTGCAGCAACAGGCCCTGCC	0.592																																					p.Q643K		Atlas-SNP	.											.	CCDC33	160	.	0			c.C1927A						PASS	.	C	LYS/GLN,LYS/GLN	0,3826		0,0,1913	34.0	41.0	39.0		1927,706	5.0	1.0	15		39	3,8237		0,3,4117	yes	missense,missense	CCDC33	NM_025055.3,NM_182791.2	53,53	0,3,6030	AA,AC,CC		0.0364,0.0,0.0249	probably-damaging,probably-damaging	643/756,236/368	74625175	3,12063	1913	4120	6033	SO:0001583	missense	80125	exon16			CAGCAACAGGCCC	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.1927C>A	15.37:g.74625175C>A	ENSP00000381795:p.Gln643Lys	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	66	36	0.545455	NM_025055	A8K3U4|A8MPQ6|A8MV61|A8MVU9|B3KQ49|Q8TAX6|Q9H5Q6	Missense_Mutation	SNP	ENST00000398814.3	37	CCDS42058.1	.	.	.	.	.	.	.	.	.	.	C	17.67	3.446257	0.63178	0.0	3.64E-4	ENSG00000140481	ENST00000321288;ENST00000398814;ENST00000321374;ENST00000268082	T;T;T;T	0.34472	1.36;2.14;1.81;1.73	5.04	5.04	0.67666	.	0.277119	0.26126	N	0.026198	T	0.52996	0.1769	M	0.73962	2.25	0.30582	N	0.762407	P;B;P;D	0.64830	0.936;0.29;0.69;0.994	P;B;B;P	0.58013	0.554;0.081;0.292;0.831	T	0.55425	-0.8143	10	0.20046	T	0.44	.	15.3817	0.74661	0.0:1.0:0.0:0.0	.	236;236;846;643	Q8N5R6-4;Q8N5R6-5;C9JFX2;Q8N5R6-6	.;.;.;.	K	846;643;236;236	ENSP00000325012:Q846K;ENSP00000381795:Q643K;ENSP00000325661:Q236K;ENSP00000268082:Q236K	ENSP00000268082:Q236K	Q	+	1	0	CCDC33	72412228	1.000000	0.71417	1.000000	0.80357	0.837000	0.47467	4.670000	0.61583	2.354000	0.79902	0.543000	0.68304	CAG	.	.	weak		0.592	CCDC33-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000419491.2	NM_182791	
IMPACT	55364	hgsc.bcm.edu	37	18	22020467	22020467	+	Missense_Mutation	SNP	T	T	A	rs582234	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	101	0	0		WXS	Illumina HiSeq	Phase_I	99	51	0.515152	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	
EIF2AK3	9451	hgsc.bcm.edu	37	2	88926536	88926536	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:88926536T>C	ENST00000303236.3	-	1	558	c.257A>G	c.(256-258)gAg>gGg	p.E86G	AC062029.1_ENST00000606164.1_RNA|EIF2AK3_ENST00000419748.1_5'Flank|AC062029.1_ENST00000453008.2_RNA	NM_004836.5	NP_004827.4	Q9NZJ5	E2AK3_HUMAN	eukaryotic translation initiation factor 2-alpha kinase 3	86					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of signaling protein activity involved in unfolded protein response (GO:0006987)|bone mineralization (GO:0030282)|calcium-mediated signaling (GO:0019722)|cellular protein metabolic process (GO:0044267)|chondrocyte development (GO:0002063)|endocrine pancreas development (GO:0031018)|endoplasmic reticulum organization (GO:0007029)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER overload response (GO:0006983)|fat cell differentiation (GO:0045444)|insulin secretion (GO:0030073)|insulin-like growth factor receptor signaling pathway (GO:0048009)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|lactation (GO:0007595)|negative regulation of apoptotic process (GO:0043066)|negative regulation of gene expression (GO:0010629)|negative regulation of myelination (GO:0031642)|negative regulation of translation (GO:0017148)|negative regulation of translational initiation in response to stress (GO:0032057)|ossification (GO:0001503)|positive regulation of protein binding (GO:0032092)|positive regulation of signal transduction (GO:0009967)|protein autophosphorylation (GO:0046777)|protein homooligomerization (GO:0051260)|protein phosphorylation (GO:0006468)|regulation of fatty acid metabolic process (GO:0019217)|response to endoplasmic reticulum stress (GO:0034976)|skeletal system development (GO:0001501)|SREBP signaling pathway (GO:0032933)|translation (GO:0006412)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|eukaryotic translation initiation factor 2alpha kinase activity (GO:0004694)|identical protein binding (GO:0042802)|protein kinase activity (GO:0004672)|protein phosphatase binding (GO:0019903)|protein serine/threonine kinase activity (GO:0004674)			ovary(3)	3						ACCCCGAGGCTCCTGCTCTCc	0.731																																					p.E86G	GBM(138;671 1851 16235 39058 45249)	Atlas-SNP	.											.	EIF2AK3	160	.	0			c.A257G						PASS	.						11.0	14.0	13.0					2																	88926536		1978	4004	5982	SO:0001583	missense	9451	exon1			CGAGGCTCCTGCT	AF110146	CCDS33241.1	2p12	2008-05-21			ENSG00000172071	ENSG00000172071			3255	protein-coding gene	gene with protein product		604032				10026192, 10575235	Standard	NM_004836		Approved	PEK, PERK	uc002stc.4	Q9NZJ5	OTTHUMG00000155046	ENST00000303236.3:c.257A>G	2.37:g.88926536T>C	ENSP00000307235:p.Glu86Gly	Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	55	19	0.345455	NM_004836	A0AVH1|A0AVH2|B2RCU9|O95846|Q53QY0|Q53SB1	Missense_Mutation	SNP	ENST00000303236.3	37	CCDS33241.1	.	.	.	.	.	.	.	.	.	.	T	9.820	1.185631	0.21870	.	.	ENSG00000172071	ENST00000303236	T	0.73258	-0.73	3.67	3.67	0.42095	.	0.229807	0.30011	N	0.010633	T	0.57932	0.2087	L	0.44542	1.39	0.20074	N	0.999937	B	0.31318	0.319	B	0.29440	0.102	T	0.48163	-0.9059	10	0.29301	T	0.29	-6.3314	8.8508	0.35199	0.0:0.0:0.0:1.0	.	86	Q9NZJ5	E2AK3_HUMAN	G	86	ENSP00000307235:E86G	ENSP00000307235:E86G	E	-	2	0	EIF2AK3	88707651	0.289000	0.24334	0.051000	0.19133	0.018000	0.09664	3.014000	0.49590	1.651000	0.50673	0.459000	0.35465	GAG	.	.	none		0.731	EIF2AK3-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000338233.2	NM_004836	
MST1R	4486	hgsc.bcm.edu	37	3	49924940	49924940	+	Missense_Mutation	SNP	T	T	C	rs1062633	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:49924940T>C	ENST00000296474.3	-	20	4030	c.4003A>G	c.(4003-4005)Aga>Gga	p.R1335G	MST1R_ENST00000344206.4_Missense_Mutation_p.R1286G	NM_002447.2	NP_002438	Q04912	RON_HUMAN	macrophage stimulating 1 receptor (c-met-related tyrosine kinase)	1335	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		R -> G (in dbSNP:rs1062633). {ECO:0000269|PubMed:17344846}.		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)		ACTAGTACTCTGAAGGTGGGT	0.562													C|||	2099	0.419129	0.7443	0.3761	5008	,	,		22571	0.1438		0.498	False		,,,				2504	0.2127				p.R1335G		Atlas-SNP	.											.	MST1R	205	.	0			c.A4003G						PASS	.	C	GLY/ARG	2969,1437	466.4+/-354.5	1020,929,254	81.0	76.0	78.0		4003	-4.2	0.0	3	dbSNP_86	78	4352,4248	573.1+/-389.8	1102,2148,1050	yes	missense	MST1R	NM_002447.2	125	2122,3077,1304	CC,CT,TT		49.3953,32.6146,43.7106	benign	1335/1401	49924940	7321,5685	2203	4300	6503	SO:0001583	missense	4486	exon20			GTACTCTGAAGGT	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.4003A>G	3.37:g.49924940T>C	ENSP00000296474:p.Arg1335Gly	Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	66	42	0.636364	NM_002447	B5A944|B5A945|B5A946|B5A947	Missense_Mutation	SNP	ENST00000296474.3	37	CCDS2807.1	921	0.4217032967032967	345	0.7012195121951219	132	0.36464088397790057	82	0.14335664335664336	362	0.47757255936675463	C	0.012	-1.688274	0.00738	0.673854	0.506047	ENSG00000164078	ENST00000296474;ENST00000344206	D;D	0.83075	-1.68;-1.68	5.91	-4.24	0.03777	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.698574	0.15223	N	0.273810	T	0.00012	0.0000	N	0.21240	0.645	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.37798	-0.9690	9	0.27785	T	0.31	0.726	4.1631	0.10293	0.1918:0.1396:0.0948:0.5738	rs1062633;rs3203637;rs17657515;rs52829115;rs1062633	1335	Q04912	RON_HUMAN	G	1335;1286	ENSP00000296474:R1335G;ENSP00000341325:R1286G	ENSP00000296474:R1335G	R	-	1	2	MST1R	49899944	0.000000	0.05858	0.000000	0.03702	0.029000	0.11900	-3.031000	0.00637	-1.356000	0.02183	-0.119000	0.15052	AGA	T|0.500;C|0.499	0.499	strong		0.562	MST1R-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000345403.1		
FLT3LG	2323	hgsc.bcm.edu	37	19	49983673	49983673	+	Silent	SNP	C	C	T	rs1042120	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:49983673C>T	ENST00000594009.1	+	6	679	c.600C>T	c.(598-600)gcC>gcT	p.A200A	FLT3LG_ENST00000600429.1_Silent_p.A200A|CTD-3148I10.9_ENST00000599536.1_Intron|FLT3LG_ENST00000204637.2_Silent_p.A118A|FLT3LG_ENST00000595510.1_Silent_p.A118A|FLT3LG_ENST00000597551.1_Silent_p.A200A|FLT3LG_ENST00000596435.1_Silent_p.A182A|CTD-3148I10.15_ENST00000595815.1_RNA	NM_001204503.1	NP_001191432.1	P49771	FLT3L_HUMAN	fms-related tyrosine kinase 3 ligand	200					embryonic hemopoiesis (GO:0035162)|lymphocyte differentiation (GO:0030098)|positive regulation of cell proliferation (GO:0008284)|positive regulation of natural killer cell differentiation (GO:0032825)|positive regulation of protein phosphorylation (GO:0001934)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|intrinsic component of external side of plasma membrane (GO:0031233)|membrane (GO:0016020)	receptor binding (GO:0005102)			large_intestine(2)|lung(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	10		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)		TGCTGCTGGCCGCTGCCTGGT	0.746													C|||	973	0.194289	0.4531	0.1124	5008	,	,		14283	0.0694		0.1243	False		,,,				2504	0.1033				p.A200A		Atlas-SNP	.											.	FLT3LG	22	.	0			c.C600T						PASS	.	C	,,	1600,2746		303,994,876	12.0	13.0	12.0		600,600,600	-1.3	0.0	19	dbSNP_86	12	795,7713		42,711,3501	no	coding-synonymous,coding-synonymous,coding-synonymous	FLT3LG	NM_001204502.1,NM_001204503.1,NM_001459.3	,,	345,1705,4377	TT,TC,CC		9.3441,36.8155,18.6323	,,	200/236,200/236,200/236	49983673	2395,10459	2173	4254	6427	SO:0001819	synonymous_variant	2323	exon6			GCTGGCCGCTGCC	U04806	CCDS12767.1, CCDS62753.1	19q13.3	2014-01-30				ENSG00000090554		"""Endogenous ligands"""	3766	protein-coding gene	gene with protein product		600007				8145851, 7824267	Standard	NM_001204502		Approved		uc010yau.2	P49771		ENST00000594009.1:c.600C>T	19.37:g.49983673C>T		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	46	30	0.652174	NM_001204503	A0AVC2|B9EGH2|Q05C96	Silent	SNP	ENST00000594009.1	37	CCDS12767.1																																																																																			C|0.820;T|0.180	0.180	strong		0.746	FLT3LG-007	KNOWN	alternative_3_UTR|alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465305.1		
RNF213	57674	hgsc.bcm.edu	37	17	78293189	78293189	+	Intron	SNP	A	A	T	rs55996424	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:78293189A>T	ENST00000582970.1	+	17	3167				CTD-2047H16.2_ENST00000576808.1_RNA|RNF213_ENST00000456466.1_Intron|RNF213_ENST00000508628.2_Intron|RNF213_ENST00000319921.4_Missense_Mutation_p.K1034M	NM_001256071.1	NP_001243000.1	Q63HN8	RN213_HUMAN	ring finger protein 213						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)			AGGGCTATGAAGCACCCGCTG	0.587													a|||	1651	0.329673	0.2663	0.3588	5008	,	,		19655	0.6121		0.1451	False		,,,				2504	0.2935				p.K1034M		Atlas-SNP	.											.	RNF213	766	.	0			c.A3101T						PASS	.		,MET/LYS	1071,3335	388.6+/-327.0	135,801,1267	88.0	77.0	81.0		,3101	1.4	0.0	17	dbSNP_129	81	1393,7207	269.6+/-288.5	104,1185,3011	yes	intron,missense	RNF213	NM_020914.4,NM_020954.2	,95	239,1986,4278	TT,TA,AA		16.1977,24.3078,18.9451	,	,1034/1064	78293189	2464,10542	2203	4300	6503	SO:0001627	intron_variant	57674	exon17			CTATGAAGCACCC	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.3024+77A>T	17.37:g.78293189A>T		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	87	42	0.482759	NM_020954	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	739	0.3383699633699634	153	0.31097560975609756	123	0.3397790055248619	360	0.6293706293706294	103	0.1358839050131926	a	12.53	1.964889	0.34659	0.243078	0.161977	ENSG00000173821	ENST00000319921	.	.	.	2.43	1.35	0.21983	.	0.427242	0.19832	N	0.105078	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	D	0.52996	0.957	B	0.40375	0.327	T	0.39210	-0.9625	7	.	.	.	.	4.0068	0.09605	0.8234:0.0:0.1766:0.0	rs55996424	1034	Q9HCF4-2	.	M	1034	.	.	K	+	2	0	RNF213	75907784	0.000000	0.05858	0.001000	0.08648	0.009000	0.06853	0.150000	0.16263	0.381000	0.24851	0.373000	0.22412	AAG	A|0.768;T|0.232	0.232	strong		0.587	RNF213-020	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443298.1	NM_020914	
HECA	51696	hgsc.bcm.edu	37	6	139487836	139487836	+	Silent	SNP	T	T	C	rs3173082	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:139487836T>C	ENST00000367658.2	+	2	972	c.687T>C	c.(685-687)aaT>aaC	p.N229N	RP1-225E12.2_ENST00000591102.1_RNA|RP1-225E12.2_ENST00000415194.2_RNA|RP1-225E12.2_ENST00000590679.1_RNA|RP1-225E12.2_ENST00000589192.1_RNA|RP1-225E12.2_ENST00000588638.1_RNA|RP1-225E12.3_ENST00000585874.1_RNA|RP1-225E12.2_ENST00000587577.1_RNA|RP1-225E12.2_ENST00000586229.1_RNA|RP1-225E12.2_ENST00000586266.1_RNA|RP1-225E12.2_ENST00000588529.1_RNA	NM_016217.2	NP_057301.1	Q9UBI9	HDC_HUMAN	headcase homolog (Drosophila)	229					respiratory tube development (GO:0030323)	membrane (GO:0016020)				endometrium(4)|kidney(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)|skin(1)	15				GBM - Glioblastoma multiforme(68;0.000252)|OV - Ovarian serous cystadenocarcinoma(155;0.000387)		GGCCCCCAAATAAGCCCCAGA	0.627													T|||	3147	0.628395	0.8661	0.7248	5008	,	,		12940	0.2183		0.6948	False		,,,				2504	0.593				p.N229N		Atlas-SNP	.											.	HECA	45	.	0			c.T687C						PASS	.	T		3756,646		1601,554,46	16.0	22.0	20.0		687	2.1	0.8	6	dbSNP_105	20	5737,2861		1921,1895,483	no	coding-synonymous	HECA	NM_016217.2		3522,2449,529	CC,CT,TT		33.2752,14.6751,26.9769		229/544	139487836	9493,3507	2201	4299	6500	SO:0001819	synonymous_variant	51696	exon2			CCCAAATAAGCCC	AB033492	CCDS5194.1	6q23-q24	2010-11-25			ENSG00000112406	ENSG00000112406			21041	protein-coding gene	gene with protein product		607977				11696983, 19643820	Standard	NM_016217		Approved	HDCL, hHDC, HDC, dJ225E12.1	uc003qin.3	Q9UBI9	OTTHUMG00000015686	ENST00000367658.2:c.687T>C	6.37:g.139487836T>C		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	50	28	0.56	NM_016217		Silent	SNP	ENST00000367658.2	37	CCDS5194.1																																																																																			T|0.328;C|0.672	0.672	strong		0.627	HECA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042456.1	NM_016217	
GAA	2548	hgsc.bcm.edu	37	17	78083791	78083791	+	Silent	SNP	C	C	T	rs1800305	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:78083791C>T	ENST00000302262.3	+	9	1593	c.1374C>T	c.(1372-1374)taC>taT	p.Y458Y	GAA_ENST00000390015.3_Silent_p.Y458Y	NM_000152.3	NP_000143.2	P10253	LYAG_HUMAN	glucosidase, alpha; acid	458			Y -> C. {ECO:0000269|PubMed:22644586}.		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)			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)	ACAGGCCCTACGACGAGGGTC	0.657													C|||	492	0.0982428	0.2284	0.0533	5008	,	,		15097	0.0		0.0736	False		,,,				2504	0.0808				p.Y458Y		Atlas-SNP	.											.	GAA	66	.	0			c.C1374T						PASS	.	C	,,	809,3597	304.9+/-288.7	73,663,1467	40.0	46.0	44.0		1374,1374,1374	-8.6	0.6	17	dbSNP_89	44	615,7985	158.0+/-211.6	28,559,3713	no	coding-synonymous,coding-synonymous,coding-synonymous	GAA	NM_000152.3,NM_001079803.1,NM_001079804.1	,,	101,1222,5180	TT,TC,CC		7.1512,18.3613,10.9488	,,	458/953,458/953,458/953	78083791	1424,11582	2203	4300	6503	SO:0001819	synonymous_variant	2548	exon10			GCCCTACGACGAG		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.1374C>T	17.37:g.78083791C>T		Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	117	66	0.564103	NM_001079803	Q09GN4|Q14351|Q16302|Q8IWE7	Silent	SNP	ENST00000302262.3	37	CCDS32760.1																																																																																			C|0.902;T|0.098	0.098	strong		0.657	GAA-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437441.1		
EFHC2	80258	hgsc.bcm.edu	37	X	44094685	44094685	+	Missense_Mutation	SNP	G	G	T	rs2208592	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:44094685G>T	ENST00000420999.1	-	9	1372	c.1289C>A	c.(1288-1290)tCc>tAc	p.S430Y		NM_025184.3	NP_079460.2	Q5JST6	EFHC2_HUMAN	EF-hand domain (C-terminal) containing 2	430			S -> Y (in dbSNP:rs2208592). {ECO:0000269|PubMed:16112844}.				calcium ion binding (GO:0005509)			NS(1)|breast(7)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(6)|ovary(2)|skin(1)|urinary_tract(1)	29						ATTGCTTTTGGAGCCATAGCT	0.338													G|||	322	0.085298	0.0393	0.2147	3775	,	,		13855	0.0308		0.0338	False		,,,				2504	0.0573				p.S430Y		Atlas-SNP	.											.	EFHC2	81	.	0			c.C1289A						PASS	.	G	TYR/SER	196,2893		4,161,27,1095,542	50.0	44.0	46.0		1289	-3.6	0.0	X	dbSNP_96	46	531,5849		11,369,140,1924,1632	yes	missense	EFHC2	NM_025184.3	144	15,530,167,3019,2174	TT,TG,T,GG,G		8.3229,6.3451,7.6777	benign	430/750	44094685	727,8742	1829	4076	5905	SO:0001583	missense	80258	exon9			CTTTTGGAGCCAT	AK026254	CCDS55405.1	Xp11	2014-01-31			ENSG00000183690	ENSG00000183690		"""EF-hand domain containing"""	26233	protein-coding gene	gene with protein product		300817	"""mental retardation, X-linked 74"""	MRX74		17221867	Standard	NM_025184		Approved	FLJ22843	uc004dgb.4	Q5JST6	OTTHUMG00000021393	ENST00000420999.1:c.1289C>A	X.37:g.44094685G>T	ENSP00000404232:p.Ser430Tyr	Somatic	131	1	0.00763359		WXS	Illumina HiSeq	Phase_I	120	117	0.975	NM_025184	Q5JST8|Q68DK4|Q8NEI0|Q9H653	Missense_Mutation	SNP	ENST00000420999.1	37	CCDS55405.1	120	0.07233273056057866	16	0.03292181069958848	40	0.12738853503184713	9	0.01607142857142857	14	0.018867924528301886	g	0.001	-3.189711	0.00026	0.063451	0.083229	ENSG00000183690	ENST00000333807;ENST00000420999;ENST00000378056	T;T	0.68181	-0.3;-0.31	5.61	-3.6	0.04570	.	1.365940	0.04957	N	0.461435	T	0.00412	0.0013	N	0.16478	0.41	0.80722	P	0.0	B	0.09022	0.002	B	0.04013	0.001	T	0.07539	-1.0767	9	0.02654	T	1	-0.1202	0.3082	0.00283	0.3419:0.2498:0.2015:0.2068	rs2208592;rs3788866;rs61203808;rs2208592	430	Q5JST6	EFHC2_HUMAN	Y	430;458;234	ENSP00000333823:S430Y;ENSP00000404232:S458Y	ENSP00000333823:S430Y	S	-	2	0	EFHC2	43979629	0.117000	0.22190	0.000000	0.03702	0.000000	0.00434	0.672000	0.25187	-0.611000	0.05709	-3.481000	0.00034	TCC	G|0.910;0|0.026	.	strong		0.338	EFHC2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056312.2	NM_025184	
ZDHHC11	79844	hgsc.bcm.edu	37	5	825297	825297	+	Silent	SNP	A	A	G	rs1808545	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:825297A>G	ENST00000283441.8	-	8	1388	c.1005T>C	c.(1003-1005)gaT>gaC	p.D335D	ZDHHC11_ENST00000503758.2_5'UTR|ZDHHC11_ENST00000424784.2_Silent_p.D335D	NM_024786.2	NP_079062.1	Q9H8X9	ZDH11_HUMAN	zinc finger, DHHC-type containing 11	335						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)			TCGAATCCCCATCCTGGTTTA	0.547																																					p.D335D		Atlas-SNP	.											.	ZDHHC11	97	.	0			c.T1005C						PASS	.						191.0	137.0	155.0					5																	825297		2203	4296	6499	SO:0001819	synonymous_variant	79844	exon8			ATCCCCATCCTGG	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.1005T>C	5.37:g.825297A>G		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	120	20	0.166667	NM_024786	Q6UWR9	Silent	SNP	ENST00000283441.8	37	CCDS3857.1																																																																																			A|0.977;G|0.023	0.023	strong		0.547	ZDHHC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206681.3	NM_024786	
XIRP1	165904	hgsc.bcm.edu	37	3	39228043	39228043	+	Missense_Mutation	SNP	T	T	G	rs11711871	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:39228043T>G	ENST00000340369.3	-	2	3122	c.2894A>C	c.(2893-2895)cAc>cCc	p.H965P	XIRP1_ENST00000396251.1_Missense_Mutation_p.H965P|XIRP1_ENST00000421646.1_Intron	NM_194293.2	NP_919269.2	Q702N8	XIRP1_HUMAN	xin actin-binding repeat containing 1	965			H -> P (in dbSNP:rs11711871).		cardiac muscle cell development (GO:0055013)|negative regulation of cell proliferation (GO:0008285)|regulation of membrane potential (GO:0042391)|sarcomere organization (GO:0045214)	fascia adherens (GO:0005916)	poly(A) RNA binding (GO:0044822)			breast(4)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(14)|lung(22)|ovary(4)|pancreas(1)|prostate(2)|skin(6)	71				KIRC - Kidney renal clear cell carcinoma(284;0.0517)|Kidney(284;0.065)		CTCAGTTGGGTGCAGGCTCTG	0.647													G|||	508	0.101438	0.0091	0.1023	5008	,	,		17152	0.0615		0.2008	False		,,,				2504	0.1646				p.H965P		Atlas-SNP	.											XIRP1,NS,carcinoma,+1,1	XIRP1	173	1	0			c.A2894C						scavenged	.	G	PRO/HIS,PRO/HIS	170,4236		5,160,2038	46.0	47.0	46.0		2894,2894	3.2	0.0	3	dbSNP_120	46	1626,6974		177,1272,2851	yes	missense,missense	XIRP1	NM_001198621.1,NM_194293.2	77,77	182,1432,4889	GG,GT,TT		18.907,3.8584,13.809	benign,benign	965/1122,965/1844	39228043	1796,11210	2203	4300	6503	SO:0001583	missense	165904	exon2			GTTGGGTGCAGGC	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.2894A>C	3.37:g.39228043T>G	ENSP00000343140:p.His965Pro	Somatic	97	2	0.0206186		WXS	Illumina HiSeq	Phase_I	83	40	0.481928	NM_001198621	A0JP25|A4QPE2|Q68DF2|Q6ZTR3|Q702N9|Q8IVN7|Q8N1N3|Q8N904|Q8TCG7	Missense_Mutation	SNP	ENST00000340369.3	37	CCDS2683.1	250	0.11446886446886446	7	0.014227642276422764	40	0.11049723756906077	45	0.07867132867132867	158	0.20844327176781002	G	0.003	-2.541499	0.00142	0.038584	0.18907	ENSG00000168334	ENST00000396251;ENST00000340369	T;T	0.04275	3.66;4.09	5.02	3.2	0.36748	.	0.438328	0.18642	N	0.135270	T	0.00012	0.0000	N	0.00246	-1.78	0.58432	P	9.000000000036756E-6	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.41502	-0.9505	9	0.02654	T	1	.	4.125	0.10123	0.1909:0.0:0.6224:0.1867	rs11711871;rs11711871	965;965	Q702N8;Q702N8-2	XIRP1_HUMAN;.	P	965	ENSP00000379550:H965P;ENSP00000343140:H965P	ENSP00000343140:H965P	H	-	2	0	XIRP1	39203047	0.864000	0.29904	0.031000	0.17742	0.062000	0.15995	0.284000	0.18864	0.668000	0.31126	-0.127000	0.14921	CAC	T|0.872;G|0.128	0.128	strong		0.647	XIRP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254065.1	XM_093522	
FOXA3	3171	hgsc.bcm.edu	37	19	46376217	46376217	+	Silent	SNP	C	C	A	rs3810327	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:46376217C>A	ENST00000302177.2	+	2	1151	c.954C>A	c.(952-954)ccC>ccA	p.P318P		NM_004497.2	NP_004488.2	P55318	FOXA3_HUMAN	forkhead box A3	318					cell differentiation (GO:0030154)|cellular glucose homeostasis (GO:0001678)|cellular response to starvation (GO:0009267)|chromatin modification (GO:0016568)|endocrine pancreas development (GO:0031018)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|endometrium(2)|large_intestine(2)|lung(4)|ovary(2)|pancreas(1)|prostate(1)	13		Ovarian(192;0.0308)|all_neural(266;0.0476)		OV - Ovarian serous cystadenocarcinoma(262;0.00453)|GBM - Glioblastoma multiforme(486;0.0518)|Epithelial(262;0.236)		CAGCACCTCCCAAACTGGACG	0.577													c|||	349	0.0696885	0.0174	0.0591	5008	,	,		15652	0.0714		0.1113	False		,,,				2504	0.1033				p.P318P		Atlas-SNP	.											.	FOXA3	19	.	0			c.C954A						PASS	.	A		144,4262	93.9+/-132.6	1,142,2060	49.0	42.0	44.0		954	2.2	1.0	19	dbSNP_107	44	812,7788	178.3+/-227.7	37,738,3525	no	coding-synonymous	FOXA3	NM_004497.2		38,880,5585	AA,AC,CC		9.4419,3.2683,7.3505		318/351	46376217	956,12050	2203	4300	6503	SO:0001819	synonymous_variant	3171	exon2			ACCTCCCAAACTG	L12141	CCDS12677.1	19q13.32	2014-09-11		2002-09-20	ENSG00000170608	ENSG00000170608		"""Forkhead boxes"""	5023	protein-coding gene	gene with protein product		602295	"""hepatocyte nuclear factor 3, gamma"""	HNF3G		9119385	Standard	NM_004497		Approved		uc002pdr.3	P55318	OTTHUMG00000182484	ENST00000302177.2:c.954C>A	19.37:g.46376217C>A		Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	111	57	0.513514	NM_004497	A9LYI5|Q53F16|Q9UMW9	Silent	SNP	ENST00000302177.2	37	CCDS12677.1																																																																																			C|0.927;A|0.073	0.073	strong		0.577	FOXA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461682.1		
ZNF679	168417	hgsc.bcm.edu	37	7	63726645	63726645	+	Missense_Mutation	SNP	T	T	C	rs1830035	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:63726645T>C	ENST00000421025.1	+	5	903	c.634T>C	c.(634-636)Tac>Cac	p.Y212H	ZNF679_ENST00000255746.4_Missense_Mutation_p.Y212H	NM_001159524.1|NM_153363.2	NP_001152996.1|NP_699194.2	Q8IYX0	ZN679_HUMAN	zinc finger protein 679	212			Y -> H (in dbSNP:rs1830035).		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						GGAGAATTCCTACCAATGTGA	0.358													.|||	701	0.139976	0.3003	0.1369	5008	,	,		20732	0.0685		0.0378	False		,,,				2504	0.1043				p.Y212H		Atlas-SNP	.											.	ZNF679	80	.	0			c.T634C						PASS	.	T	HIS/TYR	337,1047		48,241,403	63.0	63.0	63.0		634	0.8	0.0	7	dbSNP_92	63	146,3036		8,130,1453	yes	missense	ZNF679	NM_153363.2	83	56,371,1856	CC,CT,TT		4.5883,24.3497,10.5782	benign	212/412	63726645	483,4083	692	1591	2283	SO:0001583	missense	168417	exon5			AATTCCTACCAAT	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.634T>C	7.37:g.63726645T>C	ENSP00000416809:p.Tyr212His	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	38	13	0.342105	NM_153363		Missense_Mutation	SNP	ENST00000421025.1	37	CCDS47592.1	225	0.10302197802197802	127	0.258130081300813	33	0.09116022099447514	42	0.07342657342657342	23	0.030343007915567283	T	9.124	1.009721	0.19277	0.243497	0.045883	ENSG00000197123	ENST00000421025;ENST00000255746	T;T	0.03889	3.77;3.77	0.819	0.819	0.18785	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	L	0.28649	0.875	0.54753	P	1.2000000000012001E-5	B	0.06786	0.001	B	0.14578	0.011	T	0.45264	-0.9273	8	0.54805	T	0.06	.	5.4486	0.16550	0.0:0.0:0.0:1.0	rs1830035;rs58865316;rs1830035	212	Q8IYX0	ZN679_HUMAN	H	212	ENSP00000416809:Y212H;ENSP00000255746:Y212H	ENSP00000255746:Y212H	Y	+	1	0	ZNF679	63364080	0.000000	0.05858	0.045000	0.18777	0.045000	0.14185	0.803000	0.27083	0.165000	0.19558	0.163000	0.16589	TAC	T|0.900;C|0.100	0.100	strong		0.358	ZNF679-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344317.2	NM_153363	
EPHA3	2042	hgsc.bcm.edu	37	3	89391215	89391215	+	Silent	SNP	G	G	A	rs56112995	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:89391215G>A	ENST00000336596.2	+	5	1506	c.1281G>A	c.(1279-1281)gcG>gcA	p.A427A	EPHA3_ENST00000494014.1_Silent_p.A427A|EPHA3_ENST00000452448.2_Silent_p.A427A	NM_005233.5	NP_005224.2	P29320	EPHA3_HUMAN	EPH receptor A3	427	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|cell migration (GO:0016477)|cellular response to retinoic acid (GO:0071300)|ephrin receptor signaling pathway (GO:0048013)|fasciculation of motor neuron axon (GO:0097156)|fasciculation of sensory neuron axon (GO:0097155)|positive regulation of neuron projection development (GO:0010976)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of epithelial to mesenchymal transition (GO:0010717)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule cytoskeleton organization (GO:0070507)|regulation of Rho GTPase activity (GO:0032319)	early endosome (GO:0005769)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|GPI-linked ephrin receptor activity (GO:0005004)			NS(1)|breast(4)|central_nervous_system(4)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(26)|liver(3)|lung(67)|ovary(7)|pancreas(1)|prostate(4)|skin(8)|stomach(1)|upper_aerodigestive_tract(5)	139	all_cancers(8;0.0406)|Melanoma(1;0.00142)|all_epithelial(1;0.0612)	Lung NSC(201;0.0782)		LUSC - Lung squamous cell carcinoma(29;0.00344)|Lung(72;0.00942)		AGTTTGCTGCGGTCAGCATCA	0.458										TSP Lung(6;0.00050)			G|||	16	0.00319489	0.0	0.0	5008	,	,		18214	0.0		0.008	False		,,,				2504	0.0082				p.A427A		Atlas-SNP	.											EPHA3_ENST00000452448,caecum,carcinoma,0,4	EPHA3	501	4	0			c.G1281A						PASS	.	G	,	3,4403	6.2+/-15.9	0,3,2200	65.0	54.0	57.0		1281,1281	-11.1	0.5	3	dbSNP_129	57	55,8545	33.8+/-87.4	1,53,4246	no	coding-synonymous,coding-synonymous	EPHA3	NM_005233.5,NM_182644.2	,	1,56,6446	AA,AG,GG		0.6395,0.0681,0.4459	,	427/984,427/540	89391215	58,12948	2203	4300	6503	SO:0001819	synonymous_variant	2042	exon5			TGCTGCGGTCAGC	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.1281G>A	3.37:g.89391215G>A		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	72	31	0.430556	NM_005233	Q9H2V3|Q9H2V4	Silent	SNP	ENST00000336596.2	37	CCDS2922.1																																																																																			G|0.995;A|0.005	0.005	strong		0.458	EPHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352995.1	NM_005233	
ZPLD1	131368	hgsc.bcm.edu	37	3	102157417	102157417	+	Missense_Mutation	SNP	A	A	G	rs6784389	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:102157417A>G	ENST00000491959.1	+	9	968	c.86A>G	c.(85-87)aAc>aGc	p.N29S	ZPLD1_ENST00000306176.1_Missense_Mutation_p.N45S|ZPLD1_ENST00000466937.1_Missense_Mutation_p.N29S			Q8TCW7	ZPLD1_HUMAN	zona pellucida-like domain containing 1	29			N -> S (in dbSNP:rs6784389).			integral component of membrane (GO:0016021)				central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(18)|ovary(2)|skin(3)	35						TGTGATGCCAACCTCCACAGT	0.393													A|||	484	0.0966454	0.09	0.1599	5008	,	,		18199	0.0357		0.1372	False		,,,				2504	0.0818				p.N45S		Atlas-SNP	.											.	ZPLD1	82	.	0			c.A134G						PASS	.	A	SER/ASN	405,4001	200.8+/-224.0	18,369,1816	109.0	98.0	102.0		134	1.5	1.0	3	dbSNP_116	102	1330,7270	260.2+/-283.1	94,1142,3064	yes	missense	ZPLD1	NM_175056.1	46	112,1511,4880	GG,GA,AA		15.4651,9.192,13.34	benign	45/432	102157417	1735,11271	2203	4300	6503	SO:0001583	missense	131368	exon2			ATGCCAACCTCCA	AY090780	CCDS2947.1	3q12.3	2009-03-25			ENSG00000170044	ENSG00000170044			27022	protein-coding gene	gene with protein product		615915				18632209	Standard	NM_175056		Approved		uc003dvt.1	Q8TCW7	OTTHUMG00000159229	ENST00000491959.1:c.86A>G	3.37:g.102157417A>G	ENSP00000420265:p.Asn29Ser	Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	120	50	0.416667	NM_175056	Q49AS1|Q8WU36	Missense_Mutation	SNP	ENST00000491959.1	37		219	0.10027472527472528	40	0.08130081300813008	58	0.16022099447513813	16	0.027972027972027972	105	0.13852242744063326	A	10.91	1.483079	0.26598	0.09192	0.154651	ENSG00000170044	ENST00000491959;ENST00000306176;ENST00000466937	T;T;T	0.81078	-1.43;-1.45;-1.43	5.26	1.48	0.22813	.	0.088124	0.85682	N	0.000000	T	0.00468	0.0015	L	0.36672	1.1	0.20638	P	0.999875443	B;B	0.20671	0.047;0.01	B;B	0.16289	0.015;0.007	T	0.05115	-1.0905	9	0.19147	T	0.46	-27.4424	5.8196	0.18520	0.6608:0.1299:0.2093:0.0	rs6784389;rs52799816;rs59422592;rs6784389	45;29	Q8TCW7-2;Q8TCW7	.;ZPLD1_HUMAN	S	29;45;29	ENSP00000420265:N29S;ENSP00000307801:N45S;ENSP00000418253:N29S	ENSP00000307801:N45S	N	+	2	0	ZPLD1	103640107	1.000000	0.71417	0.999000	0.59377	0.972000	0.66771	2.667000	0.46808	0.019000	0.15079	-1.453000	0.01033	AAC	A|0.882;G|0.118	0.118	strong		0.393	ZPLD1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000353984.1	NM_175056	
VEGFB	7423	hgsc.bcm.edu	37	11	64004692	64004692	+	Silent	SNP	C	C	T	rs11558381|rs12366035	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:64004692C>T	ENST00000309422.2	+	5	704	c.408C>T	c.(406-408)gaC>gaT	p.D136D	VEGFB_ENST00000426086.2_Silent_p.D136D|RP11-783K16.14_ENST00000539963.1_RNA|RP11-783K16.14_ENST00000534988.1_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	147	0	0		WXS	Illumina HiSeq	Phase_I	116	18	0.155172	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	
VWF	7450	hgsc.bcm.edu	37	12	6173433	6173433	+	Missense_Mutation	SNP	C	C	T	rs1800377	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:6173433C>T	ENST00000261405.5	-	12	1665	c.1411G>A	c.(1411-1413)Gtc>Atc	p.V471I		NM_000552.3	NP_000543	P04275	VWF_HUMAN	von Willebrand factor	471	VWFD 2. {ECO:0000255|PROSITE- ProRule:PRU00580}.		V -> I (in dbSNP:rs1800377). {ECO:0000269|PubMed:2584182}.		blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|cell adhesion (GO:0007155)|cell-substrate adhesion (GO:0031589)|extracellular matrix organization (GO:0030198)|hemostasis (GO:0007599)|liver development (GO:0001889)|placenta development (GO:0001890)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|protein homooligomerization (GO:0051260)|response to wounding (GO:0009611)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|proteinaceous extracellular matrix (GO:0005578)|Weibel-Palade body (GO:0033093)	chaperone binding (GO:0051087)|collagen binding (GO:0005518)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|immunoglobulin binding (GO:0019865)|integrin binding (GO:0005178)|protease binding (GO:0002020)|protein homodimerization activity (GO:0042803)|protein N-terminus binding (GO:0047485)			NS(1)|breast(6)|central_nervous_system(5)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(25)|lung(41)|ovary(7)|pancreas(2)|prostate(6)|skin(15)|stomach(1)|upper_aerodigestive_tract(5)	129					Antihemophilic Factor(DB00025)	GGGAGCTGGACGTCCTGGCCA	0.632													C|||	681	0.135982	0.1346	0.0749	5008	,	,		18977	0.1885		0.0934	False		,,,				2504	0.1708				p.V471I		Atlas-SNP	.											.	VWF	338	.	0			c.G1411A						PASS	.	C	ILE/VAL	611,3795	266.5+/-267.3	45,521,1637	102.0	69.0	81.0		1411	-2.9	0.0	12	dbSNP_89	81	948,7652	207.2+/-249.0	60,828,3412	yes	missense	VWF	NM_000552.3	29	105,1349,5049	TT,TC,CC		11.0233,13.8675,11.9868	benign	471/2814	6173433	1559,11447	2203	4300	6503	SO:0001583	missense	7450	exon12			GCTGGACGTCCTG		CCDS8539.1	12p13.3	2014-09-17			ENSG00000110799	ENSG00000110799		"""Endogenous ligands"""	12726	protein-coding gene	gene with protein product		613160		F8VWF		2251280	Standard	NM_000552		Approved		uc001qnn.1	P04275	OTTHUMG00000168265	ENST00000261405.5:c.1411G>A	12.37:g.6173433C>T	ENSP00000261405:p.Val471Ile	Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	147	147	1	NM_000552	Q8TCE8|Q99806	Missense_Mutation	SNP	ENST00000261405.5	37	CCDS8539.1	255	0.11675824175824176	47	0.09552845528455285	29	0.08011049723756906	99	0.17307692307692307	80	0.10554089709762533	C	3.103	-0.184309	0.06340	0.138675	0.110233	ENSG00000110799	ENST00000261405	T	0.62639	0.01	4.43	-2.9	0.05648	von Willebrand factor, type D domain (3);	0.886756	0.09321	N	0.818225	T	0.00109	0.0003	N	0.11845	0.185	0.09310	P	0.9999999095414	B;B	0.16802	0.016;0.019	B;B	0.18263	0.021;0.02	T	0.17776	-1.0358	9	0.06236	T	0.91	.	11.6795	0.51448	0.0:0.1896:0.0:0.8104	rs1800377	471;471	B4DNX0;P04275	.;VWF_HUMAN	I	471	ENSP00000261405:V471I	ENSP00000261405:V471I	V	-	1	0	VWF	6043694	0.417000	0.25432	0.013000	0.15412	0.962000	0.63368	0.002000	0.13061	-0.454000	0.07066	0.561000	0.74099	GTC	C|0.886;T|0.114	0.114	strong		0.632	VWF-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399020.1	NM_000552	
PTPRD	5789	hgsc.bcm.edu	37	9	8485834	8485834	+	Missense_Mutation	SNP	G	G	A	rs35929428	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:8485834G>A	ENST00000381196.4	-	25	3526	c.2983C>T	c.(2983-2985)Cgt>Tgt	p.R995C	PTPRD_ENST00000537002.1_Intron|PTPRD_ENST00000360074.4_Missense_Mutation_p.R982C|PTPRD_ENST00000358503.5_Missense_Mutation_p.R973C|PTPRD_ENST00000355233.5_Intron|PTPRD_ENST00000397617.3_Intron|PTPRD_ENST00000486161.1_Intron|PTPRD_ENST00000540109.1_Missense_Mutation_p.R995C|PTPRD_ENST00000471274.1_5'UTR|PTPRD_ENST00000356435.5_Missense_Mutation_p.R995C|PTPRD_ENST00000397606.3_Intron|PTPRD_ENST00000397611.3_Intron	NM_002839.3	NP_002830.1	P23468	PTPRD_HUMAN	protein tyrosine phosphatase, receptor type, D	995	Fibronectin type-III 7. {ECO:0000255|PROSITE-ProRule:PRU00316}.		R -> C (in dbSNP:rs35929428).		heterophilic cell-cell adhesion (GO:0007157)|neuron differentiation (GO:0030182)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphate-containing compound metabolic process (GO:0006796)|positive regulation of dendrite morphogenesis (GO:0050775)|presynaptic membrane assembly (GO:0097105)|protein dephosphorylation (GO:0006470)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	cell adhesion molecule binding (GO:0050839)|receptor binding (GO:0005102)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(7)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|liver(1)|lung(83)|ovary(4)|pancreas(1)|prostate(7)|skin(19)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	168		all_cancers(3;3.38e-95)|all_epithelial(3;2.84e-91)|all_lung(3;7.3e-56)|Lung NSC(3;1.82e-52)|Renal(3;3.42e-19)|all_hematologic(3;0.000134)|all_neural(3;0.00409)|Acute lymphoblastic leukemia(23;0.0069)|Melanoma(3;0.0121)|Myeloproliferative disorder(4;0.0122)|Medulloblastoma(3;0.0144)|Lung SC(3;0.0301)|Ovarian(56;0.0694)|Hepatocellular(3;0.0824)		all cancers(1;3.38e-12)|Epithelial(1;2.12e-09)|STAD - Stomach adenocarcinoma(1;1.29e-07)|KIRC - Kidney renal clear cell carcinoma(3;5.49e-07)|Kidney(3;6.36e-07)|GBM - Glioblastoma multiforme(50;9.05e-05)|Lung(1;0.000189)|BRCA - Breast invasive adenocarcinoma(1;0.00178)|LUSC - Lung squamous cell carcinoma(1;0.0115)|LUAD - Lung adenocarcinoma(58;0.119)		GTATGAGCACGTACTTTTACA	0.507										TSP Lung(15;0.13)			G|||	388	0.077476	0.0053	0.0951	5008	,	,		17541	0.0784		0.0964	False		,,,				2504	0.1421				p.R995C		Atlas-SNP	.											.	PTPRD	1348	.	0			c.C2983T						PASS	.	G	,,CYS/ARG,,,	101,4305	80.4+/-118.8	1,99,2103	123.0	106.0	112.0		,,2983,,,	4.5	1.0	9	dbSNP_126	112	794,7806	185.9+/-233.5	40,714,3546	yes	intron,intron,missense,intron,intron,intron	PTPRD	NM_001040712.2,NM_001171025.1,NM_002839.3,NM_130391.3,NM_130392.3,NM_130393.3	,,180,,,	41,813,5649	AA,AG,GG		9.2326,2.2923,6.8814	,,benign,,,	,,995/1913,,,	8485834	895,12111	2203	4300	6503	SO:0001583	missense	5789	exon28			GAGCACGTACTTT	X54133	CCDS6472.1, CCDS43786.1, CCDS6472.2, CCDS55288.1, CCDS55289.1, CCDS55290.1, CCDS75813.1	9p24.1-p23	2013-02-11			ENSG00000153707	ENSG00000153707		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	9668	protein-coding gene	gene with protein product		601598				7896816, 8355697	Standard	NM_002839		Approved	PTPD, HPTP	uc003zkk.3	P23468	OTTHUMG00000021005	ENST00000381196.4:c.2983C>T	9.37:g.8485834G>A	ENSP00000370593:p.Arg995Cys	Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	116	54	0.465517	NM_002839	B1ALA0|F5GWT7|Q3KPJ0|Q3KPJ1|Q3KPJ2	Missense_Mutation	SNP	ENST00000381196.4	37	CCDS43786.1	152	0.0695970695970696	6	0.012195121951219513	30	0.08287292817679558	47	0.08216783216783216	69	0.09102902374670185	G	12.34	1.907638	0.33721	0.022923	0.092326	ENSG00000153707	ENST00000381196;ENST00000356435;ENST00000360074;ENST00000358503;ENST00000540109	T;T;T;T;T	0.58940	0.3;0.3;0.3;0.3;0.3	5.38	4.49	0.54785	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.048728	0.85682	D	0.000000	T	0.03348	0.0097	M	0.62209	1.925	0.09310	P	0.999999688693	B;B;B	0.31383	0.321;0.007;0.001	B;B;B	0.26614	0.071;0.002;0.001	T	0.38802	-0.9644	8	.	.	.	.	14.648	0.68774	0.0702:0.0:0.9298:0.0	rs35929428;rs62534029	982;995;995	G3XAE2;Q2HXI4;P23468	.;.;PTPRD_HUMAN	C	995;995;982;973;995	ENSP00000370593:R995C;ENSP00000348812:R995C;ENSP00000353187:R982C;ENSP00000351293:R973C;ENSP00000438164:R995C	.	R	-	1	0	PTPRD	8475834	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.342000	0.59341	1.432000	0.47375	-0.119000	0.15052	CGT	G|0.929;A|0.071	0.071	strong		0.507	PTPRD-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055395.3		
GPR112	139378	hgsc.bcm.edu	37	X	135480126	135480126	+	Silent	SNP	T	T	C	rs5974595	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:135480126T>C	ENST00000394143.1	+	20	8562	c.8271T>C	c.(8269-8271)ttT>ttC	p.F2757F	GPR112_ENST00000412101.1_Silent_p.F2552F|GPR112_ENST00000370652.1_Silent_p.F2757F|GPR112_ENST00000287534.4_Silent_p.F2510F|GPR112_ENST00000394141.1_Silent_p.F2552F	NM_153834.3	NP_722576.3	Q8IZF6	GP112_HUMAN	G protein-coupled receptor 112	2757					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(13)|central_nervous_system(2)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(33)|lung(97)|ovary(5)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(2)	199	Acute lymphoblastic leukemia(192;0.000127)					CCTCCATTTTTCTGGGAGTTG	0.393													C|||	2899	0.767947	0.6029	0.5994	3775	,	,		15704	0.7024		0.4821	False		,,,				2504	0.5041				p.F2757F		Atlas-SNP	.											.	GPR112	459	.	0			c.T8271C						PASS	.	C		2993,842		988,565,452,79,119	173.0	141.0	152.0		8271	0.8	1.0	X	dbSNP_114	152	4083,2645		896,1155,1136,377,736	no	coding-synonymous	GPR112	NM_153834.3		1884,1720,1588,456,855	CC,CT,C,TT,T		39.3133,21.9557,33.0115		2757/3081	135480126	7076,3487	2203	4300	6503	SO:0001819	synonymous_variant	139378	exon20			CATTTTTCTGGGA	AY140954	CCDS35409.1	Xq26.3	2014-08-08			ENSG00000156920	ENSG00000156920		"""-"", ""GPCR / Class B : Orphans"""	18992	protein-coding gene	gene with protein product						12435584	Standard	XM_005262367		Approved	RP1-299I16, PGR17	uc004ezu.1	Q8IZF6	OTTHUMG00000022508	ENST00000394143.1:c.8271T>C	X.37:g.135480126T>C		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	105	105	1	NM_153834	A2A2J1|A2A2J2|Q5EGP2|Q86SM6	Silent	SNP	ENST00000394143.1	37	CCDS35409.1																																																																																			T|0.287;C|0.713	0.713	strong		0.393	GPR112-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000286639.1		
GJD3	125111	hgsc.bcm.edu	37	17	38519831	38519831	+	Silent	SNP	G	G	T	rs141158879	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:38519831G>T	ENST00000578689.1	-	1	236	c.237C>A	c.(235-237)ctC>ctA	p.L79L	GJD3_ENST00000337376.4_Silent_p.L79L|CTD-2267D19.3_ENST00000578774.1_Nonsense_Mutation_p.E215*	NM_152219.3	NP_689343.3	Q8N144	CXD3_HUMAN	gap junction protein, delta 3, 31.9kDa	79					cell communication (GO:0007154)|gap junction assembly (GO:0016264)	cell surface (GO:0009986)|connexon complex (GO:0005922)|integral component of plasma membrane (GO:0005887)	ion channel activity (GO:0005216)						Breast(137;0.00328)	STAD - Stomach adenocarcinoma(5;0.00143)			GGATGTGGAAGAGCCAGAAGC	0.682													G|||	29	0.00579073	0.0008	0.0086	5008	,	,		10470	0.0		0.0159	False		,,,				2504	0.0061				p.L79L		Atlas-SNP	.											.	GJD3	2	.	0			c.C237A						PASS	.	G		19,4233		0,19,2107	24.0	34.0	31.0		237	0.9	1.0	17	dbSNP_134	31	170,8320		2,166,4077	no	coding-synonymous	GJD3	NM_152219.3		2,185,6184	TT,TG,GG		2.0024,0.4468,1.4833		79/295	38519831	189,12553	2126	4245	6371	SO:0001819	synonymous_variant	125111	exon1			GTGGAAGAGCCAG	AF514298	CCDS58547.1	17q21.1	2012-04-19	2007-11-06	2007-11-06	ENSG00000183153	ENSG00000183153		"""Ion channels / Gap junction proteins (connexins)"""	19147	protein-coding gene	gene with protein product	"""connexin 31.9"""	607425	"""gap junction protein, chi 1, 31.9kDa"""	GJC1		12176752	Standard	NM_152219		Approved	CX31.9, GJA11, Cx30.2	uc010cwz.3	Q8N144		ENST00000578689.1:c.237C>A	17.37:g.38519831G>T		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	58	26	0.448276	NM_152219	Q6ZUW6	Silent	SNP	ENST00000578689.1	37	CCDS58547.1																																																																																			G|0.992;T|0.008	0.008	strong		0.682	GJD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447449.1	NM_152219	
NLRP5	126206	hgsc.bcm.edu	37	19	56572832	56572832	+	Missense_Mutation	SNP	G	G	A	rs10409555	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	209	0	0		WXS	Illumina HiSeq	Phase_I	165	69	0.418182	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	
IGLL5	100423062	hgsc.bcm.edu	37	22	23230348	23230348	+	Missense_Mutation	SNP	C	C	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:23230348C>G	ENST00000526893.1	+	1	389	c.115C>G	c.(115-117)Ctg>Gtg	p.L39V	IGLL5_ENST00000531372.1_Missense_Mutation_p.L39V|IGLL5_ENST00000532223.2_Missense_Mutation_p.L39V|hsa-mir-5571_ENST00000577998.1_RNA	NM_001178126.1	NP_001171597.1	B9A064	IGLL5_HUMAN	immunoglobulin lambda-like polypeptide 5	39						extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|urinary_tract(1)	7						CCATGGCCTGCTGCGCCCAAT	0.687																																					p.L39V		Atlas-SNP	.											.	IGLL5	26	.	0			c.C115G						PASS	.																																			SO:0001583	missense	100423062	exon1			GGCCTGCTGCGCC	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.115C>G	22.37:g.23230348C>G	ENSP00000431254:p.Leu39Val	Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	143	28	0.195804	NM_001178126		Missense_Mutation	SNP	ENST00000526893.1	37	CCDS54506.1	.	.	.	.	.	.	.	.	.	.	C	10.65	1.410199	0.25465	.	.	ENSG00000254709	ENST00000532223;ENST00000526893;ENST00000531372	T;T	0.00717	5.79;5.8	3.92	-2.91	0.05631	.	.	.	.	.	T	0.00608	0.0020	L	0.29908	0.895	0.09310	N	1	B	0.21821	0.061	B	0.13407	0.009	T	0.47509	-0.9112	9	0.51188	T	0.08	.	0.7315	0.00958	0.1663:0.3182:0.1632:0.3524	.	39	B9A064	IGLL5_HUMAN	V	39	ENSP00000436353:L39V;ENSP00000431254:L39V	ENSP00000431254:L39V	L	+	1	2	IGLL5	21560348	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.230000	0.09083	-0.436000	0.07254	0.643000	0.83706	CTG	.	.	none		0.687	IGLL5-002	KNOWN	basic|appris_candidate|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000385699.1	NM_001178126	
COL28A1	340267	hgsc.bcm.edu	37	7	7514293	7514293	+	Missense_Mutation	SNP	T	T	C	rs199518824		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:7514293T>C	ENST00000399429.3	-	15	1381	c.1241A>G	c.(1240-1242)aAa>aGa	p.K414R		NM_001037763.2	NP_001032852.2	Q2UY09	COSA1_HUMAN	collagen, type XXVIII, alpha 1	414					cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(23)|prostate(1)|skin(4)|stomach(1)|urinary_tract(1)	42		Ovarian(82;0.0789)		UCEC - Uterine corpus endometrioid carcinoma (126;0.228)		TTCAGAACCTTTTTCACCCTG	0.393																																					p.K414R		Atlas-SNP	.											.	COL28A1	113	.	0			c.A1241G						PASS	.	T	ARG/LYS	0,3672		0,0,1836	121.0	117.0	118.0		1241	4.7	1.0	7		118	4,8194		0,4,4095	yes	missense	COL28A1	NM_001037763.2	26	0,4,5931	CC,CT,TT		0.0488,0.0,0.0337	possibly-damaging	414/1126	7514293	4,11866	1836	4099	5935	SO:0001583	missense	340267	exon15			GAACCTTTTTCAC	AJ890451	CCDS43553.1	7p21.3	2013-01-16			ENSG00000215018	ENSG00000215018		"""Collagens"""	22442	protein-coding gene	gene with protein product		609996				16330543	Standard	NM_001037763		Approved		uc003src.1	Q2UY09	OTTHUMG00000150034	ENST00000399429.3:c.1241A>G	7.37:g.7514293T>C	ENSP00000382356:p.Lys414Arg	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	81	63	0.777778	NM_001037763	A4D101|A4D106|A4D107|A8MVR2|B9EGX9|Q2UY07|Q2UY08	Missense_Mutation	SNP	ENST00000399429.3	37	CCDS43553.1	.	.	.	.	.	.	.	.	.	.	T	12.72	2.022978	0.35701	0.0	4.88E-4	ENSG00000215018	ENST00000399429;ENST00000399419	D	0.90004	-2.6	4.7	4.7	0.59300	.	0.106321	0.35805	U	0.002969	D	0.88100	0.6346	N	0.25332	0.735	0.32928	D	0.516805	D;D	0.64830	0.994;0.993	D;D	0.72982	0.979;0.968	D	0.84976	0.0885	10	0.10902	T	0.67	-7.2148	10.7486	0.46196	0.0:0.0:0.0:1.0	.	414;414	Q2UY09-2;Q2UY09	.;COSA1_HUMAN	R	414	ENSP00000382356:K414R	ENSP00000382347:K414R	K	-	2	0	COL28A1	7480818	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.768000	0.47645	2.108000	0.64289	0.528000	0.53228	AAA	.	.	weak		0.393	COL28A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315899.1	NM_001037763	
MED24	9862	hgsc.bcm.edu	37	17	38189328	38189328	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:38189328G>A	ENST00000394128.2	-	8	884	c.803C>T	c.(802-804)aCg>aTg	p.T268M	MED24_ENST00000394127.2_Missense_Mutation_p.T255M|MED24_ENST00000501516.3_Missense_Mutation_p.T287M|MED24_ENST00000394126.1_Missense_Mutation_p.T293M|MED24_ENST00000356271.3_Missense_Mutation_p.T255M|MED24_ENST00000479829.1_5'Flank	NM_014815.3	NP_055630.2	O75448	MED24_HUMAN	mediator complex subunit 24	268					androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of transcription, DNA-templated (GO:0045893)|protein heterooligomerization (GO:0051291)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|receptor activity (GO:0004872)|RNA polymerase II transcription cofactor activity (GO:0001104)|thyroid hormone receptor binding (GO:0046966)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			autonomic_ganglia(1)|breast(2)|endometrium(9)|large_intestine(10)|lung(14)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	41	Colorectal(19;0.000442)					CTTCACCATCGTCAGCTGCTC	0.637																																					p.T268M		Atlas-SNP	.											.	MED24	89	.	0			c.C803T						PASS	.						51.0	43.0	46.0					17																	38189328		2203	4300	6503	SO:0001583	missense	9862	exon8			ACCATCGTCAGCT	AF055995	CCDS11359.1, CCDS42315.1	17q21.2	2007-07-30	2007-07-30	2007-07-30	ENSG00000008838	ENSG00000008838			22963	protein-coding gene	gene with protein product		607000	"""thyroid hormone receptor associated protein 4"", ""cofactor required for Sp1 transcriptional activation, subunit 4, 100kDa"""	THRAP4, CRSP4			Standard	NM_001079518		Approved	TRAP100, KIAA0130, DRIP100, CRSP100	uc002htt.3	O75448	OTTHUMG00000133329	ENST00000394128.2:c.803C>T	17.37:g.38189328G>A	ENSP00000377686:p.Thr268Met	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	48	10	0.208333	NM_014815	A8K4S5|B3KMR9|Q14143|Q9NNY5	Missense_Mutation	SNP	ENST00000394128.2	37	CCDS11359.1	.	.	.	.	.	.	.	.	.	.	G	9.996	1.232071	0.22626	.	.	ENSG00000008838	ENST00000394126;ENST00000356271;ENST00000394128;ENST00000535071;ENST00000394127;ENST00000536318;ENST00000543759;ENST00000431269;ENST00000428757	T;T;T;T	0.48836	0.8;1.02;1.02;1.02	5.58	3.38	0.38709	Mediator complex, subunit Med24, N-terminal (1);	0.164448	0.64402	N	0.000003	T	0.14098	0.0341	N	0.00436	-1.5	0.25784	N	0.984692	B;B;B;B;B;B;B;B	0.13594	0.0;0.001;0.0;0.001;0.0;0.0;0.0;0.008	B;B;B;B;B;B;B;B	0.08055	0.001;0.003;0.0;0.001;0.001;0.0;0.001;0.001	T	0.22487	-1.0215	10	0.22109	T	0.4	-22.9865	8.1246	0.30990	0.8066:0.0:0.0711:0.1223	.	255;218;197;218;178;255;268;210	B9TX65;B4DV99;B4DDR8;F5H5K2;F8W9R9;O75448-2;O75448;F5H0K1	.;.;.;.;.;.;MED24_HUMAN;.	M	268;268;268;218;255;210;242;178;287	ENSP00000377684:T268M;ENSP00000377686:T268M;ENSP00000443344:T218M;ENSP00000377685:T255M	ENSP00000348610:T268M	T	-	2	0	MED24	35442854	1.000000	0.71417	1.000000	0.80357	0.710000	0.40934	5.178000	0.65037	0.416000	0.25844	-1.099000	0.02127	ACG	.	.	none		0.637	MED24-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257147.2	NM_014815	
FHAD1	114827	hgsc.bcm.edu	37	1	15599025	15599025	+	Splice_Site	SNP	G	G	A	rs75432354	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:15599025G>A	ENST00000375998.4	+	2	300	c.300G>A	c.(298-300)ccG>ccA	p.P100P	FHAD1_ENST00000417793.1_Splice_Site_p.P100P|FHAD1_ENST00000375999.3_Splice_Site_p.P100P|FHAD1_ENST00000358897.4_Splice_Site_p.P100P			B1AJZ9	FHAD1_HUMAN	forkhead-associated (FHA) phosphopeptide binding domain 1	100	Pro-rich.									skin(1)|stomach(1)	2						ATCCACCTCCGGTGAGTCCGG	0.592											OREG0013125	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	639	0.127596	0.0234	0.1571	5008	,	,		17268	0.1409		0.164	False		,,,				2504	0.1963				p.P100P		Atlas-SNP	.											.	FHAD1	78	.	0			c.G300A						PASS	.	G		51,1333		1,49,642	28.0	26.0	27.0		300	3.3	0.9	1	dbSNP_131	27	513,2669		48,417,1126	yes	coding-synonymous-near-splice	FHAD1	NM_052929.1		49,466,1768	AA,AG,GG		16.1219,3.685,12.3522		100/1413	15599025	564,4002	692	1591	2283	SO:0001630	splice_region_variant	114827	exon3			ACCTCCGGTGAGT	AK093300		1p36.21	2012-04-19			ENSG00000142621	ENSG00000142621			29408	protein-coding gene	gene with protein product						11572484	Standard	NM_052929		Approved	KIAA1937	uc001awb.2	B1AJZ9	OTTHUMG00000002088	ENST00000375998.4:c.300+1G>A	1.37:g.15599025G>A		Somatic	71	0	0	704	WXS	Illumina HiSeq	Phase_I	87	38	0.436782	NM_052929	Q0P6F5|Q8N8D3|Q8N9T6|Q8NA05	Silent	SNP	ENST00000375998.4	37																																																																																				G|0.874;A|0.126	0.126	strong		0.592	FHAD1-026	PUTATIVE	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000393400.2	NM_052929	Silent
PXDNL	137902	hgsc.bcm.edu	37	8	52321238	52321238	+	Silent	SNP	G	G	A	rs141024159	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:52321238G>A	ENST00000356297.4	-	17	3046	c.2946C>T	c.(2944-2946)gcC>gcT	p.A982A	PXDNL_ENST00000543296.1_Silent_p.A982A	NM_144651.4	NP_653252	A1KZ92	PXDNL_HUMAN	peroxidasin homolog (Drosophila)-like	982					hydrogen peroxide catabolic process (GO:0042744)|oxidation-reduction process (GO:0055114)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	endonuclease activity (GO:0004519)|heme binding (GO:0020037)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)			NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(6)|lung(25)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	48		all_cancers(86;0.107)|Lung NSC(129;0.00641)|all_epithelial(80;0.00716)|all_lung(136;0.015)				ACAGCTCCGTGGCCATCCTGT	0.647													G|||	29	0.00579073	0.0008	0.0058	5008	,	,		16344	0.0		0.0219	False		,,,				2504	0.002				p.A982A		Atlas-SNP	.											.	PXDNL	414	.	0			c.C2946T						PASS	.	G		9,4085		0,9,2038	17.0	20.0	19.0		2946	-2.5	0.0	8	dbSNP_134	19	127,8265		1,125,4070	no	coding-synonymous	PXDNL	NM_144651.4		1,134,6108	AA,AG,GG		1.5133,0.2198,1.0892		982/1464	52321238	136,12350	2047	4196	6243	SO:0001819	synonymous_variant	137902	exon17			CTCCGTGGCCATC		CCDS47855.1	8q11.21-q11.22	2013-02-18	2007-01-12		ENSG00000147485	ENSG00000147485		"""Immunoglobulin superfamily / I-set domain containing"""	26359	protein-coding gene	gene with protein product	"""polysomal ribonuclease 1 homolog (Xenopus)"""	615904	"""peroxidasin homolog-like (Drosophila)"""			22543864	Standard	NM_144651		Approved	FLJ25471, PMR1	uc003xqu.4	A1KZ92	OTTHUMG00000164244	ENST00000356297.4:c.2946C>T	8.37:g.52321238G>A		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	67	46	0.686567	NM_144651	B5ME43|B6CGZ3|H0YBM9|Q6ZMR2|Q96LH9	Silent	SNP	ENST00000356297.4	37	CCDS47855.1	23	0.010531135531135532	0	0.0	4	0.011049723756906077	0	0.0	19	0.025065963060686015	G	0.093	-1.164305	0.01673	0.002198	0.015133	ENSG00000147485	ENST00000522933	.	.	.	4.47	-2.51	0.06365	.	.	.	.	.	T	0.16085	0.0387	.	.	.	0.52501	D	0.99995	.	.	.	.	.	.	T	0.21484	-1.0244	4	.	.	.	.	0.455	0.00507	0.3332:0.127:0.2814:0.2584	.	.	.	.	L	101	.	.	P	-	2	0	PXDNL	52483791	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.056000	0.03489	-1.110000	0.02992	-0.175000	0.13238	CCA	G|0.989;A|0.011	0.011	strong		0.647	PXDNL-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377905.1	NM_144651	
LY75	4065	hgsc.bcm.edu	37	2	160746800	160746800	+	Silent	SNP	T	T	C	rs34592866	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:160746800T>C	ENST00000263636.4	-	4	753	c.726A>G	c.(724-726)gaA>gaG	p.E242E	LY75_ENST00000554112.1_Silent_p.E242E|LY75_ENST00000553424.1_Silent_p.E242E|LY75-CD302_ENST00000504764.1_Silent_p.E242E|LY75-CD302_ENST00000505052.1_Silent_p.E242E	NM_002349.3	NP_002340.2	O60449	LY75_HUMAN	lymphocyte antigen 75	242	C-type lectin 1. {ECO:0000255|PROSITE- ProRule:PRU00040}.				endocytosis (GO:0006897)|immune response (GO:0006955)|inflammatory response (GO:0006954)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)			NS(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(22)|prostate(7)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	59				COAD - Colon adenocarcinoma(177;0.132)		AAACATAAGCTTCTTTCCAAG	0.368													T|||	94	0.01877	0.0023	0.0288	5008	,	,		20298	0.0		0.0517	False		,,,				2504	0.0194				p.E242E		Atlas-SNP	.											.	LY75	151	.	0			c.A726G						PASS	.	T	,,	49,4357	48.9+/-83.8	2,45,2156	100.0	104.0	103.0		726,726,726	3.2	1.0	2	dbSNP_126	103	571,8029	153.7+/-208.1	21,529,3750	no	coding-synonymous,coding-synonymous,coding-synonymous	LY75,LY75-CD302	NM_001198759.1,NM_001198760.1,NM_002349.3	,,	23,574,5906	CC,CT,TT		6.6395,1.1121,4.767	,,	242/1874,242/1818,242/1723	160746800	620,12386	2203	4300	6503	SO:0001819	synonymous_variant	4065	exon4			ATAAGCTTCTTTC	AF011333	CCDS2211.1	2q24	2011-08-30			ENSG00000054219	ENSG00000054219		"""CD molecules"", ""C-type lectin domain containing"""	6729	protein-coding gene	gene with protein product		604524				9553150	Standard	NM_002349		Approved	DEC-205, CLEC13B, CD205		O60449	OTTHUMG00000132025	ENST00000263636.4:c.726A>G	2.37:g.160746800T>C		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	127	58	0.456693	NM_002349	O75913|Q53R46|Q53TF5|Q7Z575|Q7Z577	Silent	SNP	ENST00000263636.4	37	CCDS2211.1																																																																																			T|0.962;C|0.038	0.038	strong		0.368	LY75-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255035.1		
OLFM2	93145	hgsc.bcm.edu	37	19	9964946	9964946	+	Silent	SNP	G	G	A	rs11556088	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:9964946G>A	ENST00000264833.4	-	6	1466	c.1281C>T	c.(1279-1281)cgC>cgT	p.R427R	AC008752.3_ENST00000582439.1_RNA|OLFM2_ENST00000590841.1_Silent_p.R349R	NM_058164.2	NP_477512.1	O95897	NOE2_HUMAN	olfactomedin 2	427	Olfactomedin-like. {ECO:0000255|PROSITE- ProRule:PRU00446}.				protein secretion (GO:0009306)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|extracellular region (GO:0005576)|synapse (GO:0045202)				breast(1)|cervix(1)|endometrium(3)|large_intestine(8)|lung(9)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)	31						TATAGAGGGCGCGCTCCCGGG	0.562													G|||	417	0.0832668	0.0393	0.0562	5008	,	,		16913	0.0923		0.1123	False		,,,				2504	0.1227				p.R427R		Atlas-SNP	.											.	OLFM2	42	.	0			c.C1281T	GRCh37	CM066939	OLFM2	M	rs11556088	PASS	.	G		264,4142	150.3+/-184.3	9,246,1948	98.0	88.0	91.0		1281	-3.5	1.0	19	dbSNP_120	91	1049,7551	223.1+/-260.0	63,923,3314	no	coding-synonymous	OLFM2	NM_058164.2		72,1169,5262	AA,AG,GG		12.1977,5.9918,10.0953		427/455	9964946	1313,11693	2203	4300	6503	SO:0001819	synonymous_variant	93145	exon6			GAGGGCGCGCTCC	AF131839	CCDS12221.1	19p13.2	2008-07-03				ENSG00000105088			17189	protein-coding gene	gene with protein product	"""noelin 2"""						Standard	NM_058164		Approved	OlfC, NOE2	uc002mmp.3	O95897		ENST00000264833.4:c.1281C>T	19.37:g.9964946G>A		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	113	54	0.477876	NM_058164	Q6IMJ3|Q96FC2	Silent	SNP	ENST00000264833.4	37	CCDS12221.1																																																																																			G|0.905;A|0.095	0.095	strong		0.562	OLFM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451119.1		
PCDHB6	56130	hgsc.bcm.edu	37	5	140530852	140530852	+	Silent	SNP	G	G	C	rs246708	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:140530852G>C	ENST00000231136.1	+	1	1014	c.1014G>C	c.(1012-1014)gtG>gtC	p.V338V	PCDHB6_ENST00000543635.1_Silent_p.V202V	NM_018939.2	NP_061762.1	Q9Y5E3	PCDB6_HUMAN	protocadherin beta 6	338	Cadherin 3. {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)			TCCTGGACGTGAATGACAATG	0.468													G|||	1122	0.224042	0.4909	0.2406	5008	,	,		18488	0.0407		0.169	False		,,,				2504	0.0971				p.V338V		Atlas-SNP	.											PCDHB6,NS,carcinoma,+2,1	PCDHB6	161	1	0			c.G1014C						PASS	.	G		1871,2535	542.4+/-376.0	393,1085,725	102.0	98.0	99.0		1014	0.0	0.9	5	dbSNP_79	99	1580,7020	295.5+/-302.4	152,1276,2872	no	coding-synonymous	PCDHB6	NM_018939.2		545,2361,3597	CC,CG,GG		18.3721,42.4648,26.5339		338/795	140530852	3451,9555	2203	4300	6503	SO:0001819	synonymous_variant	56130	exon1			GGACGTGAATGAC	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.1014G>C	5.37:g.140530852G>C		Somatic	224	1	0.00446429		WXS	Illumina HiSeq	Phase_I	192	93	0.484375	NM_018939	B2R8R9	Silent	SNP	ENST00000231136.1	37	CCDS4248.1																																																																																			G|0.747;C|0.253	0.253	strong		0.468	PCDHB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251818.2	NM_018939	
NPHS1	4868	hgsc.bcm.edu	37	19	36340009	36340009	+	Missense_Mutation	SNP	G	G	A	rs113825926	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:36340009G>A	ENST00000378910.5	-	8	880	c.881C>T	c.(880-882)aCc>aTc	p.T294I	NPHS1_ENST00000353632.6_Missense_Mutation_p.T294I|NPHS1_ENST00000591817.1_5'Flank	NM_004646.3	NP_004637.1	O60500	NPHN_HUMAN	nephrosis 1, congenital, Finnish type (nephrin)	294	Ig-like C2-type 3.				cell adhesion (GO:0007155)|excretion (GO:0007588)|glomerular basement membrane development (GO:0032836)|glomerular visceral epithelial cell development (GO:0072015)|JNK cascade (GO:0007254)|myoblast fusion (GO:0007520)|positive regulation of actin filament polymerization (GO:0030838)|regulation of excretion (GO:0044062)|skeletal muscle tissue development (GO:0007519)	cell projection (GO:0042995)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|slit diaphragm (GO:0036057)	myosin binding (GO:0017022)			NS(2)|breast(1)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(16)|liver(1)|lung(26)|ovary(5)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	74	all_lung(56;7.14e-07)|Lung NSC(56;1.12e-06)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			CACCGCCTGGGTGTGCTCTGT	0.677													G|||	18	0.00359425	0.0008	0.0029	5008	,	,		18085	0.0		0.0109	False		,,,				2504	0.0041				p.T294I		Atlas-SNP	.											.	NPHS1	165	.	0			c.C881T	GRCh37	CM044680	NPHS1	M	rs113825926	PASS	.	G	ILE/THR	17,4389	23.3+/-48.9	0,17,2186	45.0	42.0	43.0		881	-1.0	0.0	19	dbSNP_132	43	102,8496	56.4+/-117.6	1,100,4198	yes	missense	NPHS1	NM_004646.3	89	1,117,6384	AA,AG,GG		1.1863,0.3858,0.9151	benign	294/1242	36340009	119,12885	2203	4299	6502	SO:0001583	missense	4868	exon8			GCCTGGGTGTGCT		CCDS32996.1	19q12-q13.1	2014-09-17				ENSG00000161270		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	7908	protein-coding gene	gene with protein product		602716				9915943, 9660941	Standard	NM_004646		Approved	CNF, NPHN	uc002oby.3	O60500		ENST00000378910.5:c.881C>T	19.37:g.36340009G>A	ENSP00000368190:p.Thr294Ile	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	48	19	0.395833	NM_004646	A6NDH2|C3RX61	Missense_Mutation	SNP	ENST00000378910.5	37	CCDS32996.1	10	0.004578754578754579	0	0.0	2	0.0055248618784530384	0	0.0	8	0.010554089709762533	G	11.76	1.734293	0.30774	0.003858	0.011863	ENSG00000161270	ENST00000378910;ENST00000353632	T;T	0.76578	-1.03;-1.03	5.17	-1.04	0.10068	Immunoglobulin subtype (1);CD80-like, immunoglobulin C2-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	1.458410	0.04145	N	0.320188	T	0.54191	0.1843	N	0.21583	0.68	0.09310	N	1	B	0.24092	0.097	B	0.27076	0.076	T	0.43702	-0.9375	10	0.24483	T	0.36	-0.2874	3.5633	0.07890	0.373:0.0:0.4437:0.1832	.	294	O60500	NPHN_HUMAN	I	294	ENSP00000368190:T294I;ENSP00000343634:T294I	ENSP00000343634:T294I	T	-	2	0	NPHS1	41031849	0.000000	0.05858	0.011000	0.14972	0.862000	0.49288	0.089000	0.15002	0.224000	0.20940	0.467000	0.42956	ACC	G|0.992;A|0.008	0.008	strong		0.677	NPHS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452553.1		
PCDHGB4	8641	hgsc.bcm.edu	37	5	140769334	140769334	+	Missense_Mutation	SNP	G	G	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:140769334G>C	ENST00000519479.1	+	1	1883	c.1883G>C	c.(1882-1884)cGt>cCt	p.R628P	PCDHGA3_ENST00000253812.6_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA6_ENST00000517434.1_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	628	Cadherin 6. {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)			CGCACAGCGCGTGCCTTAGGC	0.692																																					p.R628P		Atlas-SNP	.											.	PCDHGB4	125	.	0			c.G1883C						PASS	.						36.0	41.0	39.0					5																	140769334		2128	4243	6371	SO:0001583	missense	8641	exon1			CAGCGCGTGCCTT	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.1883G>C	5.37:g.140769334G>C	ENSP00000428288:p.Arg628Pro	Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	36	11	0.305556	NM_032098	O15099|Q2M267|Q9UN64	Missense_Mutation	SNP	ENST00000519479.1	37	CCDS54928.1	.	.	.	.	.	.	.	.	.	.	.	15.68	2.906359	0.52333	.	.	ENSG00000253953	ENST00000519479	T	0.54279	0.58	5.05	5.05	0.67936	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.78528	0.4297	H	0.94345	3.525	0.28002	N	0.935256	D;D	0.56521	0.97;0.976	P;P	0.57911	0.793;0.829	T	0.76838	-0.2811	9	0.87932	D	0	.	18.4161	0.90571	0.0:0.0:1.0:0.0	.	628;628	Q9UN71-2;Q9UN71	.;PCDGG_HUMAN	P	628	ENSP00000428288:R628P	ENSP00000428288:R628P	R	+	2	0	PCDHGB4	140749518	0.784000	0.28713	0.057000	0.19452	0.031000	0.12232	4.360000	0.59455	2.503000	0.84419	0.563000	0.77884	CGT	.	.	none		0.692	PCDHGB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374745.1	NM_003736	
ZNRD1	30834	hgsc.bcm.edu	37	6	30030057	30030057	+	Silent	SNP	G	G	A	rs10745	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:30030057G>A	ENST00000332435.5	+	3	574	c.303G>A	c.(301-303)caG>caA	p.Q101Q	ZNRD1-AS1_ENST00000421692.1_RNA|ZNRD1_ENST00000359374.4_Silent_p.Q101Q|ZNRD1-AS1_ENST00000431012.1_RNA|ZNRD1-AS1_ENST00000420251.1_RNA|ZNRD1_ENST00000463141.1_3'UTR|ZNRD1-AS1_ENST00000425604.1_RNA|ZNRD1-AS1_ENST00000437417.1_RNA|ZNRD1-AS1_ENST00000452229.1_RNA|ZNRD1-AS1_ENST00000376797.3_RNA|ZNRD1_ENST00000376785.2_Silent_p.Q101Q|ZNRD1-AS1_ENST00000448093.1_RNA|ZNRD1_ENST00000376782.2_Silent_p.Q101Q	NM_170783.2	NP_740753.1	Q9P1U0	RPA12_HUMAN	zinc ribbon domain containing 1	101					nucleobase-containing compound metabolic process (GO:0006139)|termination of RNA polymerase I transcription (GO:0006363)	DNA-directed RNA polymerase I complex (GO:0005736)	DNA-directed RNA polymerase activity (GO:0003899)|nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)										ACACCAGACAGATGCGTTCAG	0.517													G|||	207	0.0413339	0.0499	0.0403	5008	,	,		18366	0.0357		0.0507	False		,,,				2504	0.0266				p.Q101Q		Atlas-SNP	.											.	.	.	.	0			c.G303A						PASS	.	G	,	155,2867		3,149,1359	185.0	123.0	145.0		303,303	3.4	1.0	6	dbSNP_52	145	315,5103		10,295,2404	no	coding-synonymous,coding-synonymous	ZNRD1	NM_014596.4,NM_170783.2	,	13,444,3763	AA,AG,GG		5.814,5.1291,5.5687	,	101/127,101/127	30030057	470,7970	1511	2709	4220	SO:0001819	synonymous_variant	30834	exon3			CAGACAGATGCGT	AF024617	CCDS4670.1	6p21	2011-02-18	2006-04-04		ENSG00000066379	ENSG00000066379			13182	protein-coding gene	gene with protein product		607525	"""zinc ribbon domain containing, 1"""			8938444, 10662553	Standard	NM_170783		Approved	hZR14, HTEX-6, tctex-6, RPA12	uc003npa.3	Q9P1U0	OTTHUMG00000031149	ENST00000332435.5:c.303G>A	6.37:g.30030057G>A		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	71	25	0.352113	NM_170783		Silent	SNP	ENST00000332435.5	37	CCDS4670.1																																																																																			G|0.942;A|0.058	0.058	strong		0.517	ZNRD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076272.2		
ARMC4	55130	hgsc.bcm.edu	37	10	28250610	28250610	+	Missense_Mutation	SNP	C	C	A	rs147175768	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:28250610C>A	ENST00000305242.5	-	10	1365	c.1273G>T	c.(1273-1275)Gat>Tat	p.D425Y	ARMC4_ENST00000239715.3_Missense_Mutation_p.D282Y|ARMC4_ENST00000537576.1_Missense_Mutation_p.D117Y|ARMC4_ENST00000480504.1_5'UTR|ARMC4_ENST00000545014.1_5'UTR	NM_018076.2	NP_060546.2	Q5T2S8	ARMC4_HUMAN	armadillo repeat containing 4	425					cell projection organization (GO:0030030)|cilium movement (GO:0003341)|left/right axis specification (GO:0070986)|outer dynein arm assembly (GO:0036158)|ventricular system development (GO:0021591)	axoneme (GO:0005930)|ciliary base (GO:0097546)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)		p.D425Y(3)		NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(17)|liver(1)|lung(17)|ovary(5)|prostate(3)|skin(8)|stomach(2)|urinary_tract(3)	75						GAGGAGCTATCGCTAACAGTT	0.413																																					p.D425Y		Atlas-SNP	.											ARMC4,NS,malignant_melanoma,0,3	ARMC4	177	3	3	Substitution - Missense(3)	skin(2)|NS(1)	c.G1273T						scavenged	.						68.0	63.0	65.0					10																	28250610		2203	4295	6498	SO:0001583	missense	55130	exon10			AGCTATCGCTAAC	AL136859	CCDS7157.1	10p12.1-p11.23	2014-02-03			ENSG00000169126	ENSG00000169126		"""Armadillo repeat containing"""	25583	protein-coding gene	gene with protein product		615408				11230166	Standard	XM_005252485		Approved	FLJ10817, FLJ10376, DKFZP434P1735, CILD23	uc001itz.3	Q5T2S8	OTTHUMG00000017867	ENST00000305242.5:c.1273G>T	10.37:g.28250610C>A	ENSP00000306410:p.Asp425Tyr	Somatic	216	1	0.00462963		WXS	Illumina HiSeq	Phase_I	165	19	0.115152	NM_018076	A8K906|B7Z7I1|Q9H0C0	Missense_Mutation	SNP	ENST00000305242.5	37	CCDS7157.1	90	0.04120879120879121	20	0.04065040650406504	16	0.04419889502762431	10	0.017482517482517484	44	0.05804749340369393	C	12.66	2.005911	0.35415	.	.	ENSG00000169126	ENST00000537576;ENST00000305242;ENST00000537573;ENST00000434029;ENST00000239715	T;T;T;T	0.26223	1.75;1.75;1.75;1.75	5.4	5.4	0.78164	.	0.268930	0.40640	N	0.001048	T	0.02970	0.0088	L	0.50333	1.59	0.50813	D	0.999894	P	0.45569	0.861	B	0.37267	0.245	T	0.00956	-1.1501	10	0.72032	D	0.01	-9.8277	18.3066	0.90184	0.0:1.0:0.0:0.0	.	425	Q5T2S8	ARMC4_HUMAN	Y	117;425;117;319;282	ENSP00000443208:D117Y;ENSP00000306410:D425Y;ENSP00000398155:D319Y;ENSP00000239715:D282Y	ENSP00000239715:D282Y	D	-	1	0	ARMC4	28290616	1.000000	0.71417	0.912000	0.35992	0.024000	0.10985	5.087000	0.64480	2.677000	0.91161	0.650000	0.86243	GAT	.	.	weak		0.413	ARMC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047339.1	NM_018076	
LSS	4047	hgsc.bcm.edu	37	21	47614443	47614443	+	Silent	SNP	A	A	G	rs2254522	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:47614443A>G	ENST00000397728.3	-	20	2028	c.1950T>C	c.(1948-1950)caT>caC	p.H650H	LSS_ENST00000522411.1_Silent_p.H639H|AP001468.1_ENST00000594486.1_5'Flank|LSS_ENST00000457828.2_Silent_p.H570H|LSS_ENST00000356396.4_Silent_p.H650H	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	75	0	0		WXS	Illumina HiSeq	Phase_I	87	30	0.344828	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		
MUC5B	727897	hgsc.bcm.edu	37	11	1268481	1268481	+	Silent	SNP	G	G	A	rs186744090	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:1268481G>A	ENST00000529681.1	+	31	10429	c.10371G>A	c.(10369-10371)cgG>cgA	p.R3457R	MUC5B_ENST00000447027.1_Silent_p.R3460R|RP11-532E4.2_ENST00000532061.2_RNA	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	3457	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)		CACACGGGCGGTCCCTGCCCC	0.677																																					p.R3457R		Atlas-SNP	.											MUC5B,NS,haematopoietic_neoplasm,0,4	MUC5B	473	4	0			c.G10371A						scavenged	.						99.0	137.0	124.0					11																	1268481		2117	4240	6357	SO:0001819	synonymous_variant	727897	exon31			CGGGCGGTCCCTG	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.10371G>A	11.37:g.1268481G>A		Somatic	454	0	0		WXS	Illumina HiSeq	Phase_I	436	29	0.0665138	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Silent	SNP	ENST00000529681.1	37	CCDS44515.2																																																																																			G|0.973;A|0.027	0.027	strong		0.677	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
PCNXL3	399909	hgsc.bcm.edu	37	11	65387378	65387378	+	Silent	SNP	T	T	A	rs61744384	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:65387378T>A	ENST00000355703.3	+	8	2522	c.1983T>A	c.(1981-1983)gcT>gcA	p.A661A		NM_032223.2	NP_115599.2	Q9H6A9	PCX3_HUMAN	pecanex-like 3 (Drosophila)	661						integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(6)|prostate(1)	13						CTGAGGGTGCTGTGCACTATT	0.612													T|||	2062	0.411741	0.2065	0.3228	5008	,	,		19233	0.4355		0.4672	False		,,,				2504	0.6708				p.A661A		Atlas-SNP	.											.	PCNXL3	140	.	0			c.T1983A						PASS	.	T		1012,3214		128,756,1229	53.0	52.0	52.0		1983	-3.8	0.6	11	dbSNP_129	52	3728,4694		836,2056,1319	no	coding-synonymous	PCNXL3	NM_032223.2		964,2812,2548	AA,AT,TT		44.265,23.947,37.4763		661/2035	65387378	4740,7908	2113	4211	6324	SO:0001819	synonymous_variant	399909	exon8			GGGTGCTGTGCAC	BX640978	CCDS44650.1	11q12.1	2008-07-21			ENSG00000197136	ENSG00000197136			18760	protein-coding gene	gene with protein product						15146197	Standard	NM_032223		Approved	FLJ22427	uc001oey.2	Q9H6A9	OTTHUMG00000166539	ENST00000355703.3:c.1983T>A	11.37:g.65387378T>A		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	70	18	0.257143	NM_032223	Q6MZN8	Silent	SNP	ENST00000355703.3	37	CCDS44650.1																																																																																			T|0.604;A|0.396	0.396	strong		0.612	PCNXL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390321.1	NM_032223	
ANXA9	8416	hgsc.bcm.edu	37	1	150958836	150958836	+	Missense_Mutation	SNP	A	A	G	rs267733	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:150958836A>G	ENST00000368947.4	+	8	973	c.497A>G	c.(496-498)gAc>gGc	p.D166G		NM_003568.2	NP_003559.2	O76027	ANXA9_HUMAN	annexin A9	166			D -> G (in dbSNP:rs267733). {ECO:0000269|PubMed:10899159, ECO:0000269|PubMed:9742942, ECO:0000269|Ref.5}.		single organismal cell-cell adhesion (GO:0016337)|synaptic transmission (GO:0007268)	cell surface (GO:0009986)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	acetylcholine receptor activity (GO:0015464)|calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|phosphatidylserine binding (GO:0001786)|phospholipid binding (GO:0005543)|protein homodimerization activity (GO:0042803)			endometrium(1)|large_intestine(1)|lung(4)|skin(2)	8	all_lung(15;1.09e-34)|Lung NSC(24;1.1e-30)|Lung SC(34;0.00202)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.211)			GCTGTGGATGACATCACATCT	0.567													A|||	318	0.0634984	0.0424	0.0735	5008	,	,		19507	0.0258		0.1382	False		,,,				2504	0.047				p.D166G		Atlas-SNP	.											.	ANXA9	28	.	0			c.A497G						PASS	.	A	GLY/ASP	271,4135	152.9+/-186.6	5,261,1937	81.0	69.0	73.0		497	5.1	1.0	1	dbSNP_79	73	1332,7268	261.3+/-283.8	112,1108,3080	yes	missense	ANXA9	NM_003568.2	94	117,1369,5017	GG,GA,AA		15.4884,6.1507,12.3251	probably-damaging	166/346	150958836	1603,11403	2203	4300	6503	SO:0001583	missense	8416	exon8			TGGATGACATCAC	AJ009985	CCDS975.2	1q21.2	2008-02-05			ENSG00000143412	ENSG00000143412		"""Annexins"""	547	protein-coding gene	gene with protein product		603319		ANX31		9742942, 9931420	Standard	NM_003568		Approved		uc001ewa.2	O76027	OTTHUMG00000035063	ENST00000368947.4:c.497A>G	1.37:g.150958836A>G	ENSP00000357943:p.Asp166Gly	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	101	100	0.990099	NM_003568	Q5SZF1|Q6FI55|Q9BS00|Q9HBJ6	Missense_Mutation	SNP	ENST00000368947.4	37	CCDS975.2	173	0.07921245421245421	21	0.042682926829268296	29	0.08011049723756906	19	0.033216783216783216	104	0.13720316622691292	A	14.34	2.507144	0.44558	0.061507	0.154884	ENSG00000143412	ENST00000368947	T	0.08634	3.07	5.1	5.1	0.69264	.	0.061224	0.64402	D	0.000005	T	0.24160	0.0585	M	0.91300	3.195	0.23589	P	0.99734447	D	0.61697	0.99	D	0.67231	0.95	T	0.27262	-1.0079	9	0.72032	D	0.01	.	11.5488	0.50708	1.0:0.0:0.0:0.0	rs267733;rs579783;rs17356291;rs17610363;rs61138212;rs267733	166	O76027	ANXA9_HUMAN	G	166	ENSP00000357943:D166G	ENSP00000357943:D166G	D	+	2	0	ANXA9	149225460	1.000000	0.71417	1.000000	0.80357	0.134000	0.20937	5.151000	0.64875	2.049000	0.60858	0.379000	0.24179	GAC	A|0.906;G|0.094	0.094	strong		0.567	ANXA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084895.2	NM_003568	
TROAP	10024	hgsc.bcm.edu	37	12	49723963	49723963	+	Silent	SNP	A	A	G	rs4243545	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:49723963A>G	ENST00000257909.3	+	13	1411	c.1335A>G	c.(1333-1335)gaA>gaG	p.E445E	TROAP_ENST00000547923.1_Silent_p.E153E|TROAP_ENST00000551245.1_Silent_p.E445E	NM_005480.3	NP_005471.3	Q12815	TROAP_HUMAN	trophinin associated protein	445					cell adhesion (GO:0007155)	cytoplasm (GO:0005737)		p.E445E(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(14)|ovary(1)|prostate(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(4)	32						TGAGACAGGAAGTAGAGGGGC	0.532													G|||	972	0.194089	0.4123	0.1138	5008	,	,		19065	0.0407		0.1531	False		,,,				2504	0.1564				p.E445E		Atlas-SNP	.											TROAP,NS,carcinoma,0,1	TROAP	80	1	1	Substitution - coding silent(1)	stomach(1)	c.A1335G						PASS	.	G		1686,2720	629.2+/-395.2	314,1058,831	105.0	110.0	108.0		1335	1.6	0.8	12	dbSNP_111	108	1408,7188	725.2+/-406.5	122,1164,3012	no	coding-synonymous	TROAP	NM_005480.3		436,2222,3843	GG,GA,AA		16.3797,38.266,23.7963		445/779	49723963	3094,9908	2203	4298	6501	SO:0001819	synonymous_variant	10024	exon13			ACAGGAAGTAGAG	U04810	CCDS8784.1, CCDS41779.1, CCDS61117.1	12q13.12	2012-10-17	2012-10-17		ENSG00000135451	ENSG00000135451			12327	protein-coding gene	gene with protein product	"""tastin"""	603872				7758945	Standard	NM_005480		Approved	TASTIN	uc001rtx.4	Q12815	OTTHUMG00000169486	ENST00000257909.3:c.1335A>G	12.37:g.49723963A>G		Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	158	79	0.5	NM_005480	F8VSF9|Q6PJU7|Q8N5B2	Silent	SNP	ENST00000257909.3	37	CCDS8784.1																																																																																			A|0.789;G|0.211	0.211	strong		0.532	TROAP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000404300.1	NM_005480	
VCX3B	425054	hgsc.bcm.edu	37	X	8434367	8434367	+	Silent	SNP	C	C	T	rs139169782		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:8434367C>T	ENST00000381032.1	+	3	991	c.684C>T	c.(682-684)agC>agT	p.S228S	VCX3B_ENST00000444481.1_Silent_p.S198S|VCX3B_ENST00000453306.1_Intron|VCX3B_ENST00000381029.4_Silent_p.S196S|VCX3B_ENST00000440654.2_Intron	NM_001001888.3	NP_001001888.3	Q9H321	VCX3B_HUMAN	variable charge, X-linked 3B	228	14 X 10 AA tandem repeats of L-S-Q-E-S- [EQ]-V-E-E-P.					nucleolus (GO:0005730)|nucleus (GO:0005634)				NS(1)|large_intestine(1)|lung(2)|prostate(1)|skin(3)|urinary_tract(3)	11						GTCAGGAGAGCGAGATGGAAG	0.557													-|||	923	0.244503	0.0968	0.147	3775	,	,		6423	0.2887		0.1173	False		,,,				2504	0.2904				p.S228S		Atlas-SNP	.											.	VCX3B	34	.	0			c.C684T						PASS	.	C		600,2579		158,223,61,977,402	108.0	222.0	187.0		684	-0.6	0.0	X	dbSNP_134	187	808,5694		89,402,228,1896,1500	no	coding-synonymous	VCX3B	NM_001001888.3		247,625,289,2873,1902	TT,TC,T,CC,C		12.4269,18.8739,14.544		228/247	8434367	1408,8273	1821	4115	5936	SO:0001819	synonymous_variant	425054	exon3			GGAGAGCGAGATG		CCDS48077.1, CCDS48077.2	Xp22.31	2009-01-14			ENSG00000205642	ENSG00000205642			31838	protein-coding gene	gene with protein product							Standard	NM_001001888		Approved	VCX-C	uc011mht.2	Q9H321	OTTHUMG00000021106	ENST00000381032.1:c.684C>T	X.37:g.8434367C>T		Somatic	873	0	0		WXS	Illumina HiSeq	Phase_I	514	489	0.951362	NM_001001888	C9JS46|Q4KN12	Silent	SNP	ENST00000381032.1	37	CCDS48077.2																																																																																			C|0.777;T|0.223	0.223	strong		0.557	VCX3B-001	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055691.1		
GLI1	2735	hgsc.bcm.edu	37	12	57865321	57865321	+	Missense_Mutation	SNP	G	G	A	rs2228224	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:57865321G>A	ENST00000228682.2	+	12	2889	c.2798G>A	c.(2797-2799)gGt>gAt	p.G933D	GLI1_ENST00000543426.1_Missense_Mutation_p.G805D|GLI1_ENST00000546141.1_Missense_Mutation_p.G892D	NM_005269.2	NP_005260.1	P08151	GLI1_HUMAN	GLI family zinc finger 1	933			G -> D (in dbSNP:rs2228224). {ECO:0000269|PubMed:10951255, ECO:0000269|Ref.2}.		cerebellar cortex morphogenesis (GO:0021696)|digestive tract morphogenesis (GO:0048546)|dorsal/ventral pattern formation (GO:0009953)|epidermal cell differentiation (GO:0009913)|lung development (GO:0030324)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|notochord regression (GO:0060032)|osteoblast differentiation (GO:0001649)|pituitary gland development (GO:0021983)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA replication (GO:0045740)|positive regulation of smoothened signaling pathway (GO:0045880)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|proximal/distal pattern formation (GO:0009954)|regulation of smoothened signaling pathway (GO:0008589)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in regulation of cerebellar granule cell precursor cell proliferation (GO:0021938)|spermatogenesis (GO:0007283)|ventral midline development (GO:0007418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|primary cilium (GO:0072372)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(8)|lung(22)|ovary(6)|pancreas(2)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	69			GBM - Glioblastoma multiforme(3;3.99e-32)			TTTCTGGGGGGTTCCCAGGTT	0.552													G|||	1823	0.364018	0.1626	0.3934	5008	,	,		16722	0.3036		0.6252	False		,,,				2504	0.409				p.G933D	Pancreas(157;841 1936 10503 41495 50368)	Atlas-SNP	.											.	GLI1	141	.	0			c.G2798A						PASS	.	G	ASP/GLY,ASP/GLY,ASP/GLY	1073,3333	369.3+/-319.0	137,799,1267	40.0	43.0	42.0		2414,2675,2798	0.6	0.9	12	dbSNP_98	42	5406,3194	627.3+/-398.0	1711,1984,605	yes	missense,missense,missense	GLI1	NM_001160045.1,NM_001167609.1,NM_005269.2	94,94,94	1848,2783,1872	AA,AG,GG		37.1395,24.3532,49.8155	probably-damaging,probably-damaging,probably-damaging	805/979,892/1066,933/1107	57865321	6479,6527	2203	4300	6503	SO:0001583	missense	2735	exon12			TGGGGGGTTCCCA		CCDS8940.1, CCDS53806.1, CCDS53807.1	12q13.2-q13.3	2013-01-25	2009-03-05	2005-01-14		ENSG00000111087		"""Zinc fingers, C2H2-type"""	4317	protein-coding gene	gene with protein product		165220	"""glioma-associated oncogene homolog 1 (zinc finger protein)"", ""glioma-associated oncogene family zinc finger 1"""	GLI		2850480	Standard	NM_005269		Approved		uc001snx.3	P08151		ENST00000228682.2:c.2798G>A	12.37:g.57865321G>A	ENSP00000228682:p.Gly933Asp	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	43	16	0.372093	NM_005269	D0EUY3|E9PQQ9|F5H6H8|Q8TDN9	Missense_Mutation	SNP	ENST00000228682.2	37	CCDS8940.1	911	0.41712454212454214	94	0.1910569105691057	158	0.43646408839779005	190	0.3321678321678322	469	0.6187335092348285	G	10.70	1.424561	0.25639	0.243532	0.628605	ENSG00000111087	ENST00000543426;ENST00000228682;ENST00000546141;ENST00000528467;ENST00000443131	T;T;T;T	0.13901	2.65;2.55;2.63;2.63	4.53	0.557	0.17260	.	0.160493	0.29783	N	0.011202	T	0.00012	0.0000	L	0.36672	1.1	0.46609	P	8.789999999999631E-4	B	0.24258	0.1	B	0.24541	0.054	T	0.29088	-1.0023	9	0.36615	T	0.2	.	1.9411	0.03347	0.1663:0.2936:0.3897:0.1505	rs2228224;rs3741412;rs58230115;rs2228224	933	P08151	GLI1_HUMAN	D	805;933;892;892;401	ENSP00000437607:G805D;ENSP00000228682:G933D;ENSP00000441006:G892D;ENSP00000434408:G892D	ENSP00000228682:G933D	G	+	2	0	GLI1	56151588	0.921000	0.31238	0.935000	0.37517	0.993000	0.82548	0.370000	0.20433	-0.001000	0.14495	0.555000	0.69702	GGT	G|0.547;A|0.452	0.452	strong		0.552	GLI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394197.1	NM_005269	
KRT17	3872	hgsc.bcm.edu	37	17	39775870	39775870	+	Silent	SNP	C	C	T	rs117941474	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:39775870C>T	ENST00000311208.8	-	8	1342	c.1275G>A	c.(1273-1275)gaG>gaA	p.E425E	JUP_ENST00000540235.1_Silent_p.E584E	NM_000422.2	NP_000413.1	Q04695	K1C17_HUMAN	keratin 17	425	Tail.				epidermis development (GO:0008544)|intermediate filament organization (GO:0045109)|keratinization (GO:0031424)|morphogenesis of an epithelium (GO:0002009)|positive regulation of cell growth (GO:0030307)|positive regulation of hair follicle development (GO:0051798)|positive regulation of translation (GO:0045727)|signal transduction (GO:0007165)	cell periphery (GO:0071944)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	MHC class II protein binding (GO:0042289)|MHC class II receptor activity (GO:0032395)|structural constituent of cytoskeleton (GO:0005200)			central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(5)|ovary(1)|skin(1)	12		Breast(137;0.000307)				GGTGGACCTGCTCGCGGGAGG	0.652													c|||	59	0.0117812	0.0015	0.0317	5008	,	,		17027	0.0		0.0338	False		,,,				2504	0.001				p.E425E	Pancreas(92;1242 2086 39193 50508)	Atlas-SNP	.											.	KRT17	57	.	0			c.G1275A						PASS	.	C		25,4381	31.7+/-61.6	0,25,2178	92.0	91.0	92.0		1275	2.4	1.0	17	dbSNP_132	92	273,8327	104.0+/-165.0	3,267,4030	yes	coding-synonymous	KRT17	NM_000422.2		3,292,6208	TT,TC,CC		3.1744,0.5674,2.2913		425/433	39775870	298,12708	2203	4300	6503	SO:0001819	synonymous_variant	3872	exon8			GACCTGCTCGCGG	X62571	CCDS11402.1	17q21.2	2014-06-12			ENSG00000128422	ENSG00000128422		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6427	protein-coding gene	gene with protein product		148069		PCHC1		7539673, 1281771, 16831889	Standard	NM_000422		Approved		uc002hxh.2	Q04695	OTTHUMG00000133505	ENST00000311208.8:c.1275G>A	17.37:g.39775870C>T		Somatic	607	0	0		WXS	Illumina HiSeq	Phase_I	551	274	0.497278	NM_000422	A5Z1M9|A5Z1N0|A5Z1N1|A5Z1N2|A6NDV6|A6NKQ2|Q6IP98|Q8N1P6	Silent	SNP	ENST00000311208.8	37	CCDS11402.1																																																																																			C|0.977;T|0.023	0.023	strong		0.652	KRT17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257460.1	NM_000422	
CLEC18C	283971	hgsc.bcm.edu	37	16	70211218	70211218	+	Silent	SNP	G	G	A	rs149087931	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:70211218G>A	ENST00000569347.2	+	3	545	c.291G>A	c.(289-291)gcG>gcA	p.A97A	CLEC18C_ENST00000536907.2_Silent_p.A97A|CLEC18C_ENST00000541793.2_Silent_p.A97A|CLEC18C_ENST00000561612.1_Intron|CLEC18C_ENST00000314151.8_Silent_p.A97A	NM_173619.2	NP_775890.2	Q8NCF0	CL18C_HUMAN	C-type lectin domain family 18, member C	97	SCP.					extracellular region (GO:0005576)	carbohydrate binding (GO:0030246)			endometrium(3)|large_intestine(6)|lung(1)	10						CGAGCCTGGCGTCCGGCCTGT	0.637																																					p.A97A		Atlas-SNP	.											CLEC18C,NS,carcinoma,0,1	CLEC18C	15	1	0			c.G291A						scavenged	.						4.0	7.0	6.0					16																	70211218		1856	3689	5545	SO:0001819	synonymous_variant	283971	exon3			CCTGGCGTCCGGC	AL833339	CCDS32473.1	16q22.1	2010-04-27	2009-03-10	2009-03-10		ENSG00000157335		"""C-type lectin domain containing"""	28538	protein-coding gene	gene with protein product						12477932	Standard	XM_005255906		Approved	MGC34761		Q8NCF0		ENST00000569347.2:c.291G>A	16.37:g.70211218G>A		Somatic	779	2	0.00256739		WXS	Illumina HiSeq	Phase_I	1057	159	0.150426	NM_173619	Q8IUW8	Silent	SNP	ENST00000569347.2	37	CCDS32473.1	.	.	.	.	.	.	.	.	.	.	N	4.212	0.038195	0.08148	.	.	ENSG00000157335	ENST00000539438	.	.	.	3.67	-7.35	0.01422	.	.	.	.	.	T	0.29684	0.0741	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.31943	-0.9925	5	0.34782	T	0.22	.	7.4304	0.27124	0.5189:0.3372:0.1439:0.0	.	.	.	.	I	95	.	ENSP00000445424:V95I	V	+	1	0	CLEC18C	68768719	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-3.589000	0.00422	-2.515000	0.00501	-0.701000	0.03672	GTC	G|0.925;A|0.075	0.075	strong		0.637	CLEC18C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000434588.2	NM_173619	
GOLGA1	2800	hgsc.bcm.edu	37	9	127643456	127643456	+	Silent	SNP	T	T	C	rs687434	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:127643456T>C	ENST00000373555.4	-	22	2550	c.2217A>G	c.(2215-2217)gaA>gaG	p.E739E		NM_002077.3	NP_002068	Q92805	GOGA1_HUMAN	golgin A1	739					protein targeting to Golgi (GO:0000042)	Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|trans-Golgi network (GO:0005802)				NS(1)|endometrium(5)|kidney(2)|large_intestine(3)|lung(7)|ovary(1)|stomach(1)	20						CTACCTTATATTCCAGAGTTT	0.448													T|||	1512	0.301917	0.2148	0.3242	5008	,	,		20094	0.3433		0.4036	False		,,,				2504	0.2566				p.E739E		Atlas-SNP	.											.	GOLGA1	60	.	0			c.A2217G						PASS	.	T		1040,3366	383.5+/-324.9	130,780,1293	167.0	149.0	155.0		2217	3.7	1.0	9	dbSNP_83	155	3487,5113	511.0+/-377.6	749,1989,1562	no	coding-synonymous	GOLGA1	NM_002077.3		879,2769,2855	CC,CT,TT		40.5465,23.6042,34.807		739/768	127643456	4527,8479	2203	4300	6503	SO:0001819	synonymous_variant	2800	exon22			CTTATATTCCAGA	U51587	CCDS6860.1	9q34.11	2010-02-12	2010-02-12		ENSG00000136935	ENSG00000136935			4424	protein-coding gene	gene with protein product		602502	"""golgi autoantigen, golgin subfamily a, 1"""			9324025	Standard	NM_002077		Approved	golgin-97, MGC33154	uc004bpc.3	Q92805	OTTHUMG00000020665	ENST00000373555.4:c.2217A>G	9.37:g.127643456T>C		Somatic	203	1	0.00492611		WXS	Illumina HiSeq	Phase_I	185	100	0.540541	NM_002077	Q5T164|Q8IYZ9	Silent	SNP	ENST00000373555.4	37	CCDS6860.1																																																																																			T|0.661;C|0.339	0.339	strong		0.448	GOLGA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054049.1	NM_002077	
AIFM2	84883	hgsc.bcm.edu	37	10	71874734	71874734	+	Silent	SNP	G	G	A	rs2271695	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:71874734G>A	ENST00000307864.1	-	8	1125	c.912C>T	c.(910-912)atC>atT	p.I304I	AIFM2_ENST00000373248.1_Silent_p.I304I|AIFM2_ENST00000482166.1_5'UTR	NM_001198696.1|NM_032797.5	NP_001185625.1|NP_116186.1	Q9BRQ8	AIFM2_HUMAN	apoptosis-inducing factor, mitochondrion-associated, 2	304					apoptotic mitochondrial changes (GO:0008637)|positive regulation of apoptotic process (GO:0043065)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|lipid particle (GO:0005811)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	DNA binding (GO:0003677)|electron-transferring-flavoprotein dehydrogenase activity (GO:0004174)|flavin adenine dinucleotide binding (GO:0050660)|NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(3)|prostate(1)|skin(2)|urinary_tract(2)	16						TGGCCACGGCGATGTTGGCGT	0.587													G|||	709	0.141573	0.2088	0.232	5008	,	,		19291	0.1677		0.0606	False		,,,				2504	0.0429				p.I304I		Atlas-SNP	.											.	AIFM2	33	.	0			c.C912T						PASS	.	G	,	799,3607	318.2+/-295.5	65,669,1469	70.0	56.0	61.0		912,912	-6.2	0.0	10	dbSNP_100	61	557,8043	151.9+/-206.6	21,515,3764	no	coding-synonymous,coding-synonymous	AIFM2	NM_001198696.1,NM_032797.5	,	86,1184,5233	AA,AG,GG		6.4767,18.1344,10.426	,	304/374,304/374	71874734	1356,11650	2203	4300	6503	SO:0001819	synonymous_variant	84883	exon8			CACGGCGATGTTG	AK027403	CCDS7297.1	10q22.2	2006-11-16	2006-11-16	2006-11-16	ENSG00000042286	ENSG00000042286			21411	protein-coding gene	gene with protein product		605159	"""apoptosis-inducing factor (AIF)-like mitochondrion-associated inducer of death"""	AMID		12135761, 11980907, 15958387	Standard	NM_001198696		Approved	FLJ14497, PRG3	uc001jqp.2	Q9BRQ8	OTTHUMG00000018398	ENST00000307864.1:c.912C>T	10.37:g.71874734G>A		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	46	24	0.521739	NM_001198696	B3KXI0|Q63Z39	Silent	SNP	ENST00000307864.1	37	CCDS7297.1																																																																																			G|0.880;A|0.120	0.120	strong		0.587	AIFM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048487.1	NM_032797	
CACNA1S	779	hgsc.bcm.edu	37	1	201058530	201058530	+	Silent	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:201058530G>A	ENST00000362061.3	-	6	982	c.756C>T	c.(754-756)cgC>cgT	p.R252R	CACNA1S_ENST00000367338.3_Silent_p.R252R	NM_000069.2	NP_000060.2	Q13698	CAC1S_HUMAN	calcium channel, voltage-dependent, L type, alpha 1S subunit	252					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)	TGGTGCACCGGCGCCCTGAGC	0.617																																					p.R252R		Atlas-SNP	.											CACNA1S,colon,carcinoma,-2,1	CACNA1S	249	1	0			c.C756T						PASS	.						50.0	45.0	47.0					1																	201058530		2203	4300	6503	SO:0001819	synonymous_variant	779	exon6			GCACCGGCGCCCT	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.756C>T	1.37:g.201058530G>A		Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	117	72	0.615385	NM_000069	A4IF51|B1ALM2|Q12896|Q13934	Silent	SNP	ENST00000362061.3	37	CCDS1407.1																																																																																			.	.	none		0.617	CACNA1S-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087049.1	NM_000069	
PDZRN4	29951	hgsc.bcm.edu	37	12	41967677	41967677	+	Silent	SNP	G	G	A	rs3747556	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:41967677G>A	ENST00000402685.2	+	10	3104	c.3096G>A	c.(3094-3096)tcG>tcA	p.S1032S	PDZRN4_ENST00000298919.7_Silent_p.S772S|PDZRN4_ENST00000539469.2_Silent_p.S774S	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	116	0	0		WXS	Illumina HiSeq	Phase_I	101	53	0.524752	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	
MAP3K6	9064	hgsc.bcm.edu	37	1	27686373	27686373	+	Silent	SNP	G	G	A	rs138787990		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:27686373G>A	ENST00000493901.1	-	18	2534	c.2295C>T	c.(2293-2295)aaC>aaT	p.N765N	MAP3K6_ENST00000357582.2_Silent_p.N765N|MAP3K6_ENST00000374040.3_Silent_p.N757N	NM_004672.3	NP_004663.3	O95382	M3K6_HUMAN	mitogen-activated protein kinase kinase kinase 6	765	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of JUN kinase activity (GO:0007257)|activation of MAPKK activity (GO:0000186)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)		ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|MAP kinase kinase kinase activity (GO:0004709)			breast(4)|central_nervous_system(2)|lung(3)|ovary(1)	10		all_lung(284;1.6e-05)|Lung NSC(340;2.92e-05)|Colorectal(325;3.46e-05)|Renal(390;0.0007)|Breast(348;0.0021)|Ovarian(437;0.0175)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0416)|OV - Ovarian serous cystadenocarcinoma(117;1.69e-27)|Colorectal(126;1.24e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00132)|KIRC - Kidney renal clear cell carcinoma(1967;0.00163)|STAD - Stomach adenocarcinoma(196;0.00303)|READ - Rectum adenocarcinoma(331;0.0419)		GCACGATGTGGTTGTCGTGCA	0.612																																					p.N765N		Atlas-SNP	.											.	MAP3K6	134	.	0			c.C2295T						PASS	.	G		1,4405	2.1+/-5.4	0,1,2202	115.0	105.0	108.0		2295	2.2	1.0	1	dbSNP_134	108	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	MAP3K6	NM_004672.3		0,2,6501	AA,AG,GG		0.0116,0.0227,0.0154		765/1289	27686373	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	9064	exon17			GATGTGGTTGTCG	AF100318	CCDS299.1, CCDS72738.1	1p36.11	2011-06-09			ENSG00000142733	ENSG00000142733		"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	6858	protein-coding gene	gene with protein product	"""apoptosis signal regulating kinase 2"""	604468				9875215	Standard	XM_005246029		Approved	MAPKKK6, ASK2, MEKK6	uc001bny.1	O95382	OTTHUMG00000004631	ENST00000493901.1:c.2295C>T	1.37:g.27686373G>A		Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	183	89	0.486339	NM_004672	A2ACE8|A2VDG4|A2VDG5|Q59HF4|Q5SSD4|Q75PK3|Q96B75	Silent	SNP	ENST00000493901.1	37	CCDS299.1	.	.	.	.	.	.	.	.	.	.	G	3.628	-0.076203	0.07184	2.27E-4	1.16E-4	ENSG00000142733	ENST00000472410	.	.	.	5.03	2.16	0.27623	.	.	.	.	.	T	0.58004	0.2092	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.50625	-0.8806	4	.	.	.	.	9.1199	0.36780	0.243:0.0:0.757:0.0	.	.	.	.	I	489	.	.	T	-	2	0	MAP3K6	27558960	1.000000	0.71417	0.989000	0.46669	0.380000	0.30137	1.262000	0.32992	0.309000	0.22966	0.561000	0.74099	ACC	G|1.000;A|0.000	0.000	weak		0.612	MAP3K6-001	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000013469.2	NM_004672	
AKAP6	9472	hgsc.bcm.edu	37	14	33004975	33004975	+	Silent	SNP	G	G	A	rs35436895	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:33004975G>A	ENST00000280979.4	+	3	710	c.540G>A	c.(538-540)acG>acA	p.T180T	AKAP6_ENST00000557272.1_Silent_p.T180T|AKAP6_ENST00000557354.1_Silent_p.T180T	NM_004274.4	NP_004265.3	Q13023	AKAP6_HUMAN	A kinase (PRKA) anchor protein 6	180					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)		CTAGGCAGACGGACATTCTGC	0.493													G|||	328	0.0654952	0.1483	0.0533	5008	,	,		21839	0.001		0.0606	False		,,,				2504	0.0337				p.T180T	Melanoma(49;821 1200 7288 13647 42351)	Atlas-SNP	.											.	AKAP6	308	.	0			c.G540A						PASS	.	G		629,3777	272.5+/-270.8	37,555,1611	87.0	86.0	87.0		540	-8.7	0.8	14	dbSNP_126	87	499,8101	143.1+/-199.2	13,473,3814	no	coding-synonymous	AKAP6	NM_004274.4		50,1028,5425	AA,AG,GG		5.8023,14.276,8.6729		180/2320	33004975	1128,11878	2203	4300	6503	SO:0001819	synonymous_variant	9472	exon3			GCAGACGGACATT	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.540G>A	14.37:g.33004975G>A		Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	145	143	0.986207	NM_004274	A7E242|A7E2D4|O15028	Silent	SNP	ENST00000280979.4	37	CCDS9644.1																																																																																			G|0.924;A|0.076	0.076	strong		0.493	AKAP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276617.2	NM_004274	
MARCH10	162333	hgsc.bcm.edu	37	17	60814632	60814632	+	Silent	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:60814632C>T	ENST00000311269.5	-	6	871	c.597G>A	c.(595-597)gaG>gaA	p.E199E	RP11-156L14.1_ENST00000582564.1_RNA|MARCH10_ENST00000544856.2_Silent_p.E198E|MARCH10_ENST00000583600.1_Silent_p.E237E|RP11-156L14.1_ENST00000577270.1_RNA|RP11-156L14.1_ENST00000584597.1_RNA|MARCH10_ENST00000456609.2_Silent_p.E199E|RP11-156L14.1_ENST00000579201.1_RNA	NM_152598.2	NP_689811.2	Q8NA82	MARHA_HUMAN	membrane-associated ring finger (C3HC4) 10, E3 ubiquitin protein ligase	199					protein ubiquitination (GO:0016567)		ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(11)|liver(1)|lung(15)	38						AGTTTCTTCTCTCTTGATTTG	0.463																																					p.E199E		Atlas-SNP	.											MARCH10,NS,carcinoma,-2,1	MARCH10	102	1	0			c.G597A						scavenged	.						272.0	257.0	262.0					17																	60814632		2203	4300	6503	SO:0001819	synonymous_variant	162333	exon6			TCTTCTCTCTTGA	AK093076	CCDS11635.1, CCDS74122.1, CCDS74123.1	17q23.3	2013-01-09	2012-02-23	2007-08-20		ENSG00000173838		"""RING-type (C3HC4) zinc fingers"", ""MARCH membrane-associated ring fingers"""	26655	protein-coding gene	gene with protein product		613337	"""ring finger protein 190"", ""membrane-associated ring finger (C3HC4) 10"""	RNF190		17604280	Standard	XM_005257103		Approved	FLJ35757, MARCH-X	uc002jag.4	Q8NA82		ENST00000311269.5:c.597G>A	17.37:g.60814632C>T		Somatic	388	1	0.00257732		WXS	Illumina HiSeq	Phase_I	277	3	0.0108303	NM_001100875	D3DU09|Q8IYS7|Q8N7Z7	Silent	SNP	ENST00000311269.5	37	CCDS11635.1																																																																																			.	.	none		0.463	MARCH10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000445252.1	NM_152598	
WDR45B	56270	hgsc.bcm.edu	37	17	80585094	80585094	+	Silent	SNP	C	C	T	rs2291393	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:80585094C>T	ENST00000392325.4	-	4	512	c.318G>A	c.(316-318)aaG>aaA	p.K106K	WDR45B_ENST00000571835.1_5'UTR	NM_019613.3	NP_062559.2	Q5MNZ6	WIPI3_HUMAN	WD repeat domain 45B	106																	CTCGCCGCAGCTTGACTGCCT	0.348													T|||	1005	0.200679	0.0991	0.304	5008	,	,		20262	0.1548		0.2535	False		,,,				2504	0.2577				p.K106K		Atlas-SNP	.											.	.	.	.	0			c.G318A						PASS	.	T		493,3913	780.2+/-414.4	35,423,1745	164.0	164.0	164.0		318	-2.7	0.1	17	dbSNP_100	164	2164,6436	713.8+/-406.0	260,1644,2396	no	coding-synonymous	WDR45L	NM_019613.3		295,2067,4141	TT,TC,CC		25.1628,11.1893,20.429		106/345	80585094	2657,10349	2203	4300	6503	SO:0001819	synonymous_variant	56270	exon4			CCGCAGCTTGACT	AF091083	CCDS11815.2	17q25.3	2013-01-11	2013-01-11	2013-01-11	ENSG00000141580	ENSG00000141580		"""WD repeat domain containing"""	25072	protein-coding gene	gene with protein product		609226	"""WDR45-like"""	WDR45L		12477932	Standard	NM_019613		Approved	WIPI3	uc002kfq.3	Q5MNZ6	OTTHUMG00000150146	ENST00000392325.4:c.318G>A	17.37:g.80585094C>T		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	66	24	0.363636	NM_019613	O95328|Q2MCP6|Q6IBN2	Silent	SNP	ENST00000392325.4	37	CCDS11815.2																																																																																			C|0.797;T|0.203	0.203	strong		0.348	WDR45B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316536.1	NM_019613	
PROM1	8842	hgsc.bcm.edu	37	4	16077475	16077475	+	Missense_Mutation	SNP	A	A	C	rs189108830	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:16077475A>C	ENST00000510224.1	-	2	303	c.55T>G	c.(55-57)Tca>Gca	p.S19A	PROM1_ENST00000505450.1_Missense_Mutation_p.S19A|PROM1_ENST00000540805.1_Missense_Mutation_p.S19A|PROM1_ENST00000543373.1_Missense_Mutation_p.S19A|PROM1_ENST00000508167.1_Missense_Mutation_p.S19A|PROM1_ENST00000447510.2_Missense_Mutation_p.S19A|PROM1_ENST00000539194.1_Missense_Mutation_p.S19A			O43490	PROM1_HUMAN	prominin 1	19					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						TGCCCTCCTGAAAAGGAGTTC	0.522													A|||	34	0.00678914	0.0008	0.0375	5008	,	,		18283	0.0		0.005	False		,,,				2504	0.002				p.S19A		Atlas-SNP	.											PROM1,NS,carcinoma,+1,1	PROM1	91	1	0			c.T55G						PASS	.	A	ALA/SER,ALA/SER,ALA/SER,ALA/SER,ALA/SER,ALA/SER,ALA/SER	9,3995		0,9,1993	45.0	46.0	45.0		55,55,55,55,55,55,55	2.0	0.0	4		45	75,8271		1,73,4099	yes	missense,missense,missense,missense,missense,missense,missense	PROM1	NM_006017.2,NM_001145852.1,NM_001145851.1,NM_001145850.1,NM_001145849.1,NM_001145848.1,NM_001145847.1	99,99,99,99,99,99,99	1,82,6092	CC,CA,AA		0.8986,0.2248,0.6802	benign,benign,benign,benign,benign,benign,benign	19/866,19/826,19/834,19/835,19/843,19/857,19/857	16077475	84,12266	2002	4173	6175	SO:0001583	missense	8842	exon2			CTCCTGAAAAGGA	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.55T>G	4.37:g.16077475A>C	ENSP00000426809:p.Ser19Ala	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	63	36	0.571429	NM_001145847	Q6SV49|Q6SV50|Q6SV51|Q6SV52|Q6SV53|Q96EN6	Missense_Mutation	SNP	ENST00000510224.1	37	CCDS47029.1	22	0.010073260073260074	1	0.0020325203252032522	16	0.04419889502762431	0	0.0	5	0.006596306068601583	A	11.03	1.518361	0.27211	0.002248	0.008986	ENSG00000007062	ENST00000447510;ENST00000540805;ENST00000539194;ENST00000505450;ENST00000508167;ENST00000510224;ENST00000543373;ENST00000508322;ENST00000508940	T;T;T;T;T;T;T;T;T	0.56275	0.99;0.99;0.99;0.99;0.99;0.99;0.99;0.99;0.47	5.76	2.0	0.26442	.	0.495123	0.20303	N	0.094990	T	0.11750	0.0286	L	0.45137	1.4	0.09310	N	1	B;B;B;B;B;B	0.28971	0.192;0.192;0.192;0.192;0.192;0.229	B;B;B;B;B;B	0.28385	0.031;0.031;0.054;0.054;0.054;0.089	T	0.06698	-1.0812	10	0.34782	T	0.22	-4.4321	5.3181	0.15866	0.6934:0.1501:0.1565:0.0	.	19;19;19;19;19;19	O43490-5;O43490-6;O43490-4;O43490-7;O43490-2;O43490	.;.;.;.;.;PROM1_HUMAN	A	19	ENSP00000415481:S19A;ENSP00000438045:S19A;ENSP00000443620:S19A;ENSP00000426090:S19A;ENSP00000427346:S19A;ENSP00000426809:S19A;ENSP00000445526:S19A;ENSP00000425927:S19A;ENSP00000422704:S19A	ENSP00000415481:S19A	S	-	1	0	PROM1	15686573	0.612000	0.27000	0.001000	0.08648	0.009000	0.06853	1.114000	0.31196	0.427000	0.26145	0.454000	0.30748	TCA	A|0.990;C|0.010	0.010	strong		0.522	PROM1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000359595.2	NM_006017	
HSP90B1	7184	hgsc.bcm.edu	37	12	104327979	104327979	+	Silent	SNP	C	C	T	rs6615	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:104327979C>T	ENST00000299767.5	+	5	839	c.657C>T	c.(655-657)acC>acT	p.T219T		NM_003299.2	NP_003290.1	P14625	ENPL_HUMAN	heat shock protein 90kDa beta (Grp94), member 1	219					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)	ACAACGATACCCAGCACATCT	0.438													C|||	620	0.123802	0.0053	0.1859	5008	,	,		20983	0.2808		0.1153	False		,,,				2504	0.0869				p.T219T		Atlas-SNP	.											.	HSP90B1	72	.	0			c.C657T						PASS	.	C		111,4295	85.8+/-124.5	1,109,2093	90.0	85.0	87.0		657	5.0	1.0	12	dbSNP_52	87	1044,7556	222.4+/-259.5	76,892,3332	no	coding-synonymous	HSP90B1	NM_003299.1		77,1001,5425	TT,TC,CC		12.1395,2.5193,8.8805		219/804	104327979	1155,11851	2203	4300	6503	SO:0001819	synonymous_variant	7184	exon5			CGATACCCAGCAC	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.657C>T	12.37:g.104327979C>T		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	95	47	0.494737	NM_003299	Q96A97	Silent	SNP	ENST00000299767.5	37	CCDS9094.1																																																																																			C|0.892;T|0.108	0.108	strong		0.438	HSP90B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407349.1	NM_003299	
AHNAK2	113146	hgsc.bcm.edu	37	14	105410417	105410417	+	Silent	SNP	G	G	A	rs200284292	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:105410417G>A	ENST00000333244.5	-	7	11490	c.11371C>T	c.(11371-11373)Ctg>Ttg	p.L3791L	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	3791						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)			TTGTCGGCCAGGGACAGGTCC	0.582													.|||	177	0.0353435	0.053	0.0231	5008	,	,		20409	0.0417		0.004	False		,,,				2504	0.046				p.L3791L		Atlas-SNP	.											.	AHNAK2	719	.	0			c.C11371T						PASS	.						216.0	217.0	217.0					14																	105410417		1998	4162	6160	SO:0001819	synonymous_variant	113146	exon7			CGGCCAGGGACAG	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.11371C>T	14.37:g.105410417G>A		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	117	9	0.0769231	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Silent	SNP	ENST00000333244.5	37	CCDS45177.1																																																																																			G|0.993;A|0.007	0.007	strong		0.582	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
SRD5A1	6715	hgsc.bcm.edu	37	5	6651970	6651970	+	Silent	SNP	A	A	G	rs3822430	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:6651970A>G	ENST00000274192.5	+	2	543	c.309A>G	c.(307-309)ccA>ccG	p.P103P	SRD5A1_ENST00000504286.1_3'UTR|SRD5A1_ENST00000537411.1_3'UTR|SRD5A1_ENST00000538824.1_Intron	NM_001047.2	NP_001038.1	P18405	S5A1_HUMAN	steroid-5-alpha-reductase, alpha polypeptide 1 (3-oxo-5 alpha-steroid delta 4-dehydrogenase alpha 1)	103					androgen biosynthetic process (GO:0006702)|cell differentiation (GO:0030154)|sex determination (GO:0007530)|sex differentiation (GO:0007548)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	3-oxo-5-alpha-steroid 4-dehydrogenase activity (GO:0003865)|cholestenone 5-alpha-reductase activity (GO:0047751)|electron carrier activity (GO:0009055)	p.P103P(1)		endometrium(3)|kidney(1)|large_intestine(1)|lung(8)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	19					Dutasteride(DB01126)|Finasteride(DB01216)|Levonorgestrel(DB00367)|Spironolactone(DB00421)	TAATTTACCCATTTCTGATGC	0.368													A|||	1451	0.289736	0.3321	0.3919	5008	,	,		13397	0.1587		0.3897	False		,,,				2504	0.1922				p.P103P		Atlas-SNP	.											SRD5A1,NS,carcinoma,0,1	SRD5A1	31	1	1	Substitution - coding silent(1)	stomach(1)	c.A309G						PASS	.	A		1441,2965	467.7+/-354.9	242,957,1004	126.0	113.0	118.0		309	-11.4	0.0	5	dbSNP_107	118	3219,5381	486.1+/-371.8	610,1999,1691	no	coding-synonymous	SRD5A1	NM_001047.2		852,2956,2695	GG,GA,AA		37.4302,32.7054,35.8296		103/260	6651970	4660,8346	2203	4300	6503	SO:0001819	synonymous_variant	6715	exon2			TTACCCATTTCTG	M32313	CCDS3870.1	5p15.31	2008-02-05			ENSG00000145545	ENSG00000145545	1.3.99.5		11284	protein-coding gene	gene with protein product		184753				1686016	Standard	XR_427663		Approved		uc003jdw.3	P18405	OTTHUMG00000090456	ENST00000274192.5:c.309A>G	5.37:g.6651970A>G		Somatic	191	0	0		WXS	Illumina HiSeq	Phase_I	138	62	0.449275	NM_001047	B2R7Q1|Q9UHY4|Q9UP36|Q9UP37	Silent	SNP	ENST00000274192.5	37	CCDS3870.1																																																																																			A|0.667;G|0.333	0.333	strong		0.368	SRD5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206903.1	NM_001047	
KRT6C	286887	hgsc.bcm.edu	37	12	52866060	52866060	+	Missense_Mutation	SNP	C	C	T	rs11608915	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:52866060C>T	ENST00000252250.6	-	2	592	c.545G>A	c.(544-546)cGg>cAg	p.R182Q		NM_173086.4	NP_775109.2	P48668	K2C6C_HUMAN	keratin 6C	182	Coil 1A.|Rod.		R -> Q (in dbSNP:rs11608915). {ECO:0000269|PubMed:15489334}.		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)		CTCTAGGAACCGCACCTGGAA	0.547													C|||	2006	0.400559	0.1997	0.3271	5008	,	,		17211	0.506		0.4682	False		,,,				2504	0.546				p.R182Q		Atlas-SNP	.											.	KRT6C	55	.	0			c.G545A						PASS	.	C	GLN/ARG	1118,3284		196,726,1279	63.0	41.0	49.0		545	2.1	0.9	12	dbSNP_120	49	4107,4245		1573,961,1642	yes	missense	KRT6C	NM_173086.4	43	1769,1687,2921	TT,TC,CC		49.1739,25.3975,40.9675	probably-damaging	182/565	52866060	5225,7529	2201	4176	6377	SO:0001583	missense	286887	exon2			AGGAACCGCACCT	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.545G>A	12.37:g.52866060C>T	ENSP00000252250:p.Arg182Gln	Somatic	18	0	0		WXS	Illumina HiSeq	Phase_I	201	87	0.432836	NM_173086	A1L4L5|P48666|Q2TAZ9|Q7RTN9	Missense_Mutation	SNP	ENST00000252250.6	37	CCDS8829.1	826	0.3782051282051282	111	0.22560975609756098	119	0.3287292817679558	242	0.4230769230769231	354	0.46701846965699206	C	17.53	3.412329	0.62511	0.253975	0.491739	ENSG00000170465	ENST00000252250;ENST00000411979	D	0.92099	-2.97	3.03	2.12	0.27331	Filament (1);	0.000000	0.56097	D	0.000035	T	0.00012	0.0000	M	0.88105	2.93	0.23227	P	0.99808916	D	0.71674	0.998	P	0.62184	0.899	T	0.00001	-1.2726	9	0.62326	D	0.03	.	11.1947	0.48707	0.0:0.9042:0.0:0.0958	rs11608915;rs11608915	182	P48668	K2C6C_HUMAN	Q	182;167	ENSP00000252250:R182Q	ENSP00000252250:R182Q	R	-	2	0	KRT6C	51152327	1.000000	0.71417	0.924000	0.36721	0.495000	0.33615	5.704000	0.68347	0.814000	0.34374	0.407000	0.27541	CGG	C|0.677;T|0.323	0.323	strong		0.547	KRT6C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404976.1	NM_173086	
PAIP2B	400961	hgsc.bcm.edu	37	2	71417134	71417134	+	Silent	SNP	C	C	T	rs357776	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:71417134C>T	ENST00000244221.8	-	3	322	c.156G>A	c.(154-156)caG>caA	p.Q52Q		NM_020459.1	NP_065192.1	Q9ULR5	PAI2B_HUMAN	poly(A) binding protein interacting protein 2B	52					negative regulation of translational initiation (GO:0045947)	cytoplasm (GO:0005737)	translation repressor activity, nucleic acid binding (GO:0000900)			large_intestine(1)|lung(1)	2						AGTCTTGCTCCTGCAGTTCCT	0.522													C|||	1686	0.336661	0.3343	0.2205	5008	,	,		19581	0.3343		0.2326	False		,,,				2504	0.5317				p.Q52Q		Atlas-SNP	.											.	PAIP2B	7	.	0			c.G156A						PASS	.	C		1251,2695		196,859,918	44.0	43.0	43.0		156	3.9	1.0	2	dbSNP_79	43	2155,6173		296,1563,2305	no	coding-synonymous	PAIP2B	NM_020459.1		492,2422,3223	TT,TC,CC		25.8766,31.703,27.7497		52/124	71417134	3406,8868	1973	4164	6137	SO:0001819	synonymous_variant	400961	exon3			TTGCTCCTGCAGT		CCDS46322.1	2p13.3	2007-07-16			ENSG00000124374	ENSG00000124374			29200	protein-coding gene	gene with protein product		611018				16804161	Standard	NM_020459		Approved	KIAA1155	uc002shu.2	Q9ULR5	OTTHUMG00000153284	ENST00000244221.8:c.156G>A	2.37:g.71417134C>T		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	60	27	0.45	NM_020459		Silent	SNP	ENST00000244221.8	37	CCDS46322.1																																																																																			C|0.699;T|0.301	0.301	strong		0.522	PAIP2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330547.2	XM_376062	
SLC39A13	91252	hgsc.bcm.edu	37	11	47434986	47434986	+	Silent	SNP	G	G	A	rs2293576	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:47434986G>A	ENST00000362021.4	+	5	615	c.573G>A	c.(571-573)gcG>gcA	p.A191A	SLC39A13_ENST00000533076.1_Silent_p.A191A|SLC39A13_ENST00000354884.4_Silent_p.A191A|SLC39A13_ENST00000529740.1_3'UTR|SLC39A13_ENST00000524928.1_Silent_p.A191A	NM_001128225.2	NP_001121697	Q96H72	S39AD_HUMAN	solute carrier family 39 (zinc transporter), member 13	191	Poly-Ala.				cellular zinc ion homeostasis (GO:0006882)|connective tissue development (GO:0061448)|zinc ion transmembrane transport (GO:0071577)	Golgi apparatus (GO:0005794)|integral component of Golgi membrane (GO:0030173)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)	protein homodimerization activity (GO:0042803)|zinc ion transmembrane transporter activity (GO:0005385)			breast(1)|kidney(1)|lung(1)|prostate(1)	4				Lung(87;0.0936)		CTGCCGCCGCGCTCAATGGAG	0.667													G|||	1355	0.270567	0.0136	0.2147	5008	,	,		15354	0.3988		0.3111	False		,,,				2504	0.4836				p.A191A		Atlas-SNP	.											SLC39A13,NS,carcinoma,+2,1	SLC39A13	18	1	0			c.G573A						PASS	.	G	,	306,4096	159.2+/-191.8	12,282,1907	29.0	32.0	31.0		573,573	-1.7	0.0	11	dbSNP_100	31	2889,5707	430.6+/-356.6	464,1961,1873	no	coding-synonymous,coding-synonymous	SLC39A13	NM_001128225.2,NM_152264.4	,	476,2243,3780	AA,AG,GG		33.6087,6.9514,24.5807	,	191/372,191/365	47434986	3195,9803	2201	4298	6499	SO:0001819	synonymous_variant	91252	exon5			CGCCGCGCTCAAT		CCDS7934.1, CCDS44592.1	11p11.2	2013-05-22			ENSG00000165915	ENSG00000165915		"""Solute carriers"""	20859	protein-coding gene	gene with protein product		608735	"""solute carrier family 39 (metal ion transporter), member 13"""			12659941	Standard	NM_001128225		Approved	FLJ25785	uc009ylq.3	Q96H72	OTTHUMG00000166890	ENST00000362021.4:c.573G>A	11.37:g.47434986G>A		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	107	86	0.803738	NM_152264	D3DQR6|D3DQR7|E9PLY1|E9PQV3|Q659D9|Q8N7C9|Q8WV10	Silent	SNP	ENST00000362021.4	37	CCDS44592.1																																																																																			G|0.756;A|0.244	0.244	strong		0.667	SLC39A13-012	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000395652.1	NM_152264	
NCK1	4690	hgsc.bcm.edu	37	3	136664737	136664737	+	Missense_Mutation	SNP	C	C	T	rs13320485	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:136664737C>T	ENST00000481752.1	+	3	703	c.539C>T	c.(538-540)gCa>gTa	p.A180V	NCK1_ENST00000288986.2_Missense_Mutation_p.A180V|NCK1_ENST00000469404.1_Missense_Mutation_p.A116V			P16333	NCK1_HUMAN	NCK adaptor protein 1	180			A -> V (in dbSNP:rs13320485).		actin filament organization (GO:0007015)|axon guidance (GO:0007411)|cell migration (GO:0016477)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|lamellipodium assembly (GO:0030032)|negative regulation of cell death (GO:0060548)|negative regulation of protein kinase activity (GO:0006469)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of translation (GO:0006417)|response to other organism (GO:0051707)|signal complex assembly (GO:0007172)|T cell activation (GO:0042110)|T cell receptor signaling pathway (GO:0050852)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|vesicle membrane (GO:0012506)	cytoskeletal adaptor activity (GO:0008093)|protein kinase inhibitor activity (GO:0004860)|receptor binding (GO:0005102)|receptor signaling complex scaffold activity (GO:0030159)|receptor tyrosine kinase binding (GO:0030971)			cervix(1)|endometrium(1)|large_intestine(2)|lung(6)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	13						GAGAAATTAGCAGCAGTCGTC	0.423													C|||	43	0.00858626	0.0023	0.0274	5008	,	,		20979	0.0		0.0179	False		,,,				2504	0.0031				p.A180V		Atlas-SNP	.											.	NCK1	26	.	0			c.C539T						PASS	.	C	VAL/ALA,VAL/ALA	12,4394	19.1+/-41.9	0,12,2191	203.0	199.0	200.0		347,539	6.2	1.0	3	dbSNP_121	200	143,8457	70.3+/-132.9	1,141,4158	yes	missense,missense	NCK1	NM_001190796.1,NM_006153.4	64,64	1,153,6349	TT,TC,CC		1.6628,0.2724,1.1918	benign,benign	116/314,180/378	136664737	155,12851	2203	4300	6503	SO:0001583	missense	4690	exon3			AATTAGCAGCAGT	X17576	CCDS3092.1, CCDS54644.1	3q21	2013-02-14			ENSG00000158092	ENSG00000158092		"""SH2 domain containing"""	7664	protein-coding gene	gene with protein product		600508		NCK		7806213, 9737977	Standard	XM_005247498		Approved	NCKalpha	uc003erh.3	P16333	OTTHUMG00000159781	ENST00000481752.1:c.539C>T	3.37:g.136664737C>T	ENSP00000417273:p.Ala180Val	Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	122	59	0.483607	NM_006153	B7Z751|D3DNE3	Missense_Mutation	SNP	ENST00000481752.1	37	CCDS3092.1	24	0.01098901098901099	3	0.006097560975609756	10	0.027624309392265192	0	0.0	11	0.014511873350923483	C	27.5	4.836165	0.91117	0.002724	0.016628	ENSG00000158092	ENST00000288986;ENST00000481752;ENST00000469404	T;T;T	0.69175	-0.32;-0.32;-0.38	6.16	6.16	0.99307	.	0.000000	0.85682	D	0.000000	T	0.42449	0.1203	M	0.64997	1.995	0.80722	D	1	B;B	0.33512	0.415;0.243	B;B	0.30716	0.119;0.09	T	0.59112	-0.7515	10	0.54805	T	0.06	-5.3209	18.3537	0.90348	0.0:1.0:0.0:0.0	rs13320485;rs13320485	116;180	B7Z751;P16333	.;NCK1_HUMAN	V	180;180;116	ENSP00000288986:A180V;ENSP00000417273:A180V;ENSP00000419631:A116V	ENSP00000288986:A180V	A	+	2	0	NCK1	138147427	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.451000	0.60047	2.937000	0.99478	0.650000	0.86243	GCA	C|0.989;T|0.011	0.011	strong		0.423	NCK1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357307.1	NM_006153	
PLIN4	729359	hgsc.bcm.edu	37	19	4512636	4512636	+	Missense_Mutation	SNP	A	A	C	rs140230284|rs386806138	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:4512636A>C	ENST00000301286.3	-	3	1293	c.1294T>G	c.(1294-1296)Ttg>Gtg	p.L432V		NM_001080400.1	NP_001073869.1	Q96Q06	PLIN4_HUMAN	perilipin 4	432	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						CCTCTGGCCAAATTCATGGCA	0.552																																					p.L432V		Atlas-SNP	.											PLIN4_ENST00000301286,caecum,carcinoma,0,4	PLIN4	191	4	0			c.T1294G						PASS	.	A	VAL/LEU	240,3794		55,130,1832	122.0	147.0	139.0		1294	-9.5	0.0	19	dbSNP_134	139	165,8197		33,99,4049	no	missense	PLIN4	NM_001080400.1	32	88,229,5881	CC,CA,AA		1.9732,5.9494,3.2672	benign	432/1358	4512636	405,11991	2017	4181	6198	SO:0001583	missense	729359	exon3			TGGCCAAATTCAT	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.1294T>G	19.37:g.4512636A>C	ENSP00000301286:p.Leu432Val	Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	82	13	0.158537	NM_001080400	A6NEI2	Missense_Mutation	SNP	ENST00000301286.3	37	CCDS45927.1	56	0.02564102564102564	36	0.07317073170731707	6	0.016574585635359115	0	0.0	14	0.018469656992084433	C	0.046	-1.266936	0.01433	0.059494	0.019732	ENSG00000167676	ENST00000301286	T	0.03065	4.06	4.73	-9.46	0.00597	.	0.585786	0.15154	N	0.277551	T	0.00073	0.0002	N	0.00135	-2.02	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.20706	-1.0267	10	0.02654	T	1	-14.0824	6.7295	0.23375	0.1975:0.1757:0.0:0.6268	.	432	Q96Q06	PLIN4_HUMAN	V	432	ENSP00000301286:L432V	ENSP00000301286:L432V	L	-	1	2	PLIN4	4463636	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	-4.177000	0.00279	-1.887000	0.01115	-2.171000	0.00323	TTG	A|0.966;C|0.034	0.034	strong		0.552	PLIN4-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395095.1	XM_170901	
CASP5	838	hgsc.bcm.edu	37	11	104877927	104877927	+	Missense_Mutation	SNP	T	T	C	rs507879	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:104877927T>C	ENST00000260315.3	-	3	315	c.316A>G	c.(316-318)Acc>Gcc	p.T106A	CASP5_ENST00000531367.1_Intron|CASP5_ENST00000418434.1_Intron|CASP5_ENST00000393139.2_Missense_Mutation_p.T73A|CASP5_ENST00000444749.2_Missense_Mutation_p.T48A|CASP5_ENST00000393141.2_Missense_Mutation_p.T119A|CASP5_ENST00000526056.1_Missense_Mutation_p.T119A			P51878	CASP5_HUMAN	caspase 5, apoptosis-related cysteine peptidase	106	CARD. {ECO:0000255|PROSITE- ProRule:PRU00046}.		T -> A (in dbSNP:rs507879). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:16893518, ECO:0000269|PubMed:7797592, ECO:0000269|PubMed:8617266, ECO:0000269|Ref.7, ECO:0000269|Ref.8}.		apoptotic process (GO:0006915)|cellular response to mechanical stimulus (GO:0071260)|execution phase of apoptosis (GO:0097194)|proteolysis (GO:0006508)|regulation of apoptotic process (GO:0042981)|regulation of inflammatory response (GO:0050727)|substantia nigra development (GO:0021762)	cytoplasm (GO:0005737)|NLRP1 inflammasome complex (GO:0072558)	cysteine-type endopeptidase activity (GO:0004197)|cysteine-type peptidase activity (GO:0008234)			NS(1)|breast(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(15)|ovary(3)|skin(1)|urinary_tract(1)	35		Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Melanoma(852;0.0047)		BRCA - Breast invasive adenocarcinoma(274;0.000943)|Epithelial(105;0.0104)|all cancers(92;0.042)		TCAATTTTGGTATCATAATAT	0.373													C|||	2230	0.445288	0.646	0.4683	5008	,	,		18435	0.2341		0.4443	False		,,,				2504	0.3763				p.T119A		Atlas-SNP	.											.	CASP5	213	.	0			c.A355G						PASS	.	C	ALA/THR,,ALA/THR,ALA/THR	2704,1700		857,990,355	135.0	133.0	134.0		142,,355,316	2.5	0.1	11	dbSNP_83	134	3788,4810		831,2126,1342	yes	missense,intron,missense,missense	CASP5	NM_001136109.1,NM_001136110.1,NM_001136112.1,NM_004347.3	58,,58,58	1688,3116,1697	CC,CT,TT		44.0568,38.6013,49.9308	benign,,benign,benign	48/377,,119/448,106/435	104877927	6492,6510	2202	4299	6501	SO:0001583	missense	838	exon3			TTTTGGTATCATA		CCDS8328.2, CCDS44718.1, CCDS44719.1, CCDS44720.1	11q22.2-q22.3	2006-02-17	2005-08-17		ENSG00000137757	ENSG00000137757		"""Caspases"""	1506	protein-coding gene	gene with protein product		602665	"""caspase 5, apoptosis-related cysteine protease"""			7797592, 9250871	Standard	NM_004347		Approved	ICE(rel)III	uc010ruz.1	P51878	OTTHUMG00000048073	ENST00000260315.3:c.316A>G	11.37:g.104877927T>C	ENSP00000260315:p.Thr106Ala	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	76	75	0.986842	NM_001136112	B4DKP5|Q0QVY7|Q0QVY8|Q0QVZ0|Q0QVZ1|Q0QVZ2|Q14DD6|Q1HBJ3|Q6DJV7	Missense_Mutation	SNP	ENST00000260315.3	37	CCDS8328.2	939	0.42994505494505497	308	0.6260162601626016	170	0.4696132596685083	138	0.24125874125874125	323	0.4261213720316623	.	0.020	-1.433602	0.01108	0.613987	0.440568	ENSG00000137757	ENST00000393141;ENST00000393139;ENST00000260315;ENST00000444749;ENST00000526056;ENST00000456094	T;T;T;T;T;T	0.20738	2.05;2.05;2.05;2.05;2.05;2.05	4.42	2.54	0.30619	DEATH-like (2);Caspase Recruitment (3);	0.662303	0.14946	N	0.289191	T	0.00012	0.0000	N	0.00446	-1.495	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	0.43212	-0.9405	9	0.02654	T	1	.	5.9798	0.19401	0.0:0.6777:0.0:0.3223	rs507879;rs1042883;rs1212543;rs3167687;rs52811301;rs59825138;rs507879	48;106;119	P51878-2;P51878;P51878-5	.;CASP5_HUMAN;.	A	119;73;106;48;119;90	ENSP00000376849:T119A;ENSP00000376847:T73A;ENSP00000260315:T106A;ENSP00000388365:T48A;ENSP00000436877:T119A;ENSP00000415241:T90A	ENSP00000260315:T106A	T	-	1	0	CASP5	104383137	0.000000	0.05858	0.051000	0.19133	0.007000	0.05969	0.167000	0.16602	0.617000	0.30160	-0.898000	0.02899	ACC	T|0.536;G|0.002	.	strong		0.373	CASP5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000109397.2	NM_004347	
ATXN1	6310	hgsc.bcm.edu	37	6	16327909	16327909	+	Missense_Mutation	SNP	A	A	C	rs59310777	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	43	0	0		WXS	Illumina HiSeq	Phase_I	41	15	0.365854	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	
RNF17	56163	hgsc.bcm.edu	37	13	25378476	25378476	+	Missense_Mutation	SNP	A	A	G	rs9511451	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:25378476A>G	ENST00000255324.5	+	15	2052	c.2000A>G	c.(1999-2001)cAc>cGc	p.H667R	RNF17_ENST00000255325.6_Intron|RNF17_ENST00000381921.1_Missense_Mutation_p.H667R	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	104	0	0		WXS	Illumina HiSeq	Phase_I	108	48	0.444444	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	
CIB4	130106	hgsc.bcm.edu	37	2	26804247	26804247	+	Missense_Mutation	SNP	T	T	C	rs935172	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:26804247T>C	ENST00000288861.4	-	7	595	c.542A>G	c.(541-543)cAc>cGc	p.H181R	CIB4_ENST00000405346.3_5'UTR	NM_001029881.1	NP_001025052.1	A0PJX0	CIB4_HUMAN	calcium and integrin binding family member 4	181			H -> R (in dbSNP:rs935172). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.1}.				calcium ion binding (GO:0005509)			endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|ovary(1)	10	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TCCCCAGAAGTGAATCCGAAA	0.582													T|||	2930	0.585064	0.5363	0.6326	5008	,	,		4379	0.6855		0.504	False		,,,				2504	0.5971				p.H181R		Atlas-SNP	.											.	CIB4	15	.	0			c.A542G						PASS	.	T	ARG/HIS	2339,2067	606.5+/-390.8	616,1107,480	76.0	67.0	70.0		542	2.5	1.0	2	dbSNP_86	70	4282,4318	575.3+/-390.2	1088,2106,1106	yes	missense	CIB4	NM_001029881.1	29	1704,3213,1586	CC,CT,TT		49.7907,46.9133,49.0927	benign	181/186	26804247	6621,6385	2203	4300	6503	SO:0001583	missense	130106	exon7			CAGAAGTGAATCC		CCDS33160.1	2p23.3	2013-01-10			ENSG00000157884	ENSG00000157884		"""EF-hand domain containing"""	33703	protein-coding gene	gene with protein product		610646				15574431	Standard	NM_001029881		Approved		uc002rhm.3	A0PJX0	OTTHUMG00000151993	ENST00000288861.4:c.542A>G	2.37:g.26804247T>C	ENSP00000288861:p.His181Arg	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	56	22	0.392857	NM_001029881	B2RU18	Missense_Mutation	SNP	ENST00000288861.4	37	CCDS33160.1	1262	0.5778388278388278	274	0.556910569105691	208	0.574585635359116	385	0.6730769230769231	395	0.521108179419525	T	3.634	-0.074965	0.07184	0.530867	0.497907	ENSG00000157884	ENST00000288861;ENST00000403670;ENST00000405346	T	0.66099	-0.19	3.81	2.54	0.30619	.	0.115244	0.38959	N	0.001506	T	0.00012	0.0000	N	0.00165	-1.945	0.38552	P	0.05052800000000002	B	0.06786	0.001	B	0.01281	0.0	T	0.47611	-0.9104	9	0.02654	T	1	.	6.7041	0.23240	0.0:0.0:0.2433:0.7567	rs935172;rs1142729;rs3206254;rs11547941;rs17408222;rs56556656;rs58929580;rs935172	181	A0PJX0	CIB4_HUMAN	R	181;136;183	ENSP00000288861:H181R	ENSP00000288861:H181R	H	-	2	0	CIB4	26657751	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	1.870000	0.39529	1.727000	0.51537	0.533000	0.62120	CAC	C|0.532;N|0.000	0.532	strong		0.582	CIB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324709.1		
ZFC3H1	196441	hgsc.bcm.edu	37	12	72008421	72008421	+	Missense_Mutation	SNP	T	T	C	rs11541286	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:72008421T>C	ENST00000378743.3	-	30	5778	c.5420A>G	c.(5419-5421)aAa>aGa	p.K1807R		NM_144982.4	NP_659419.3	O60293	ZC3H1_HUMAN	zinc finger, C3H1-type containing	1807			K -> R (in dbSNP:rs11541286).		RNA processing (GO:0006396)	extracellular space (GO:0005615)|intracellular (GO:0005622)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(12)|lung(31)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	69						AGTAAAAAATTTGAATTCTTG	0.333													T|||	207	0.0413339	0.0113	0.0562	5008	,	,		15627	0.003		0.0606	False		,,,				2504	0.091				p.K1807R		Atlas-SNP	.											.	ZFC3H1	172	.	0			c.A5420G						PASS	.	T	ARG/LYS	73,3539		1,71,1734	111.0	112.0	112.0		5420	0.0	1.0	12	dbSNP_120	112	615,7523		17,581,3471	yes	missense	ZFC3H1	NM_144982.4	26	18,652,5205	CC,CT,TT		7.5571,2.021,5.8553	probably-damaging	1807/1990	72008421	688,11062	1806	4069	5875	SO:0001583	missense	196441	exon30			AAAAATTTGAATT	AB011118	CCDS41813.1	12q21.1	2013-01-25	2008-10-01	2008-10-01		ENSG00000133858		"""Zinc finger, C3H1-type containing"""	28328	protein-coding gene	gene with protein product			"""proline/serine-rich coiled-coil 2"", ""coiled-coil domain containing 131"""	PSRC2, CCDC131		9628581	Standard	NM_144982		Approved	MGC23401, KIAA0546	uc001swo.2	O60293	OTTHUMG00000169545	ENST00000378743.3:c.5420A>G	12.37:g.72008421T>C	ENSP00000368017:p.Lys1807Arg	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	59	27	0.457627	NM_144982	Q6GMU1|Q6P2S9|Q6ZV36|Q96BE7	Missense_Mutation	SNP	ENST00000378743.3	37	CCDS41813.1	76	0.0347985347985348	3	0.006097560975609756	24	0.06629834254143646	1	0.0017482517482517483	48	0.0633245382585752	T	12.11	1.840561	0.32513	0.02021	0.075571	ENSG00000133858	ENST00000378743	T	0.34072	1.38	5.35	0.0229	0.14135	.	0.161807	0.53938	N	0.000047	T	0.00998	0.0033	L	0.27053	0.805	0.80722	D	1	B	0.15141	0.012	B	0.12156	0.007	T	0.08310	-1.0728	10	0.48119	T	0.1	.	5.3631	0.16099	0.1189:0.2036:0.0:0.6775	rs11541286;rs52822945;rs59889096;rs11541286	1807	O60293	ZC3H1_HUMAN	R	1807	ENSP00000368017:K1807R	ENSP00000368017:K1807R	K	-	2	0	ZFC3H1	70294688	1.000000	0.71417	0.993000	0.49108	0.997000	0.91878	0.659000	0.24994	-0.238000	0.09724	0.455000	0.32223	AAA	T|0.956;C|0.044	0.044	strong		0.333	ZFC3H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404751.1	NM_144982	
MYH7B	57644	hgsc.bcm.edu	37	20	33585437	33585437	+	Silent	SNP	C	C	T	rs55734215	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:33585437C>T	ENST00000262873.7	+	30	3959	c.3867C>T	c.(3865-3867)cgC>cgT	p.R1289R		NM_020884.3	NP_065935.2	A7E2Y1	MYH7B_HUMAN	myosin, heavy chain 7B, cardiac muscle, beta	1247						membrane (GO:0016020)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(2)|breast(5)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(19)|ovary(5)|prostate(3)|upper_aerodigestive_tract(2)|urinary_tract(3)	54			BRCA - Breast invasive adenocarcinoma(18;0.00691)			CTCTGACCCGCGCCAAGGTGT	0.612													C|||	402	0.0802716	0.0537	0.0663	5008	,	,		14026	0.0853		0.0875	False		,,,				2504	0.1135				p.R1289R		Atlas-SNP	.											.	MYH7B	145	.	0			c.C3867T						PASS	.	C		240,4166	140.4+/-175.9	3,234,1966	65.0	71.0	69.0		3867	-9.0	0.2	20	dbSNP_129	69	810,7790	187.7+/-234.9	43,724,3533	no	coding-synonymous	MYH7B	NM_020884.3		46,958,5499	TT,TC,CC		9.4186,5.4471,8.0732		1289/1984	33585437	1050,11956	2203	4300	6503	SO:0001819	synonymous_variant	57644	exon32			GACCCGCGCCAAG	AB040945	CCDS42869.1	20q11	2011-09-27	2006-09-29		ENSG00000078814	ENSG00000078814		"""Myosins / Myosin superfamily : Class II"""	15906	protein-coding gene	gene with protein product		609928	"""myosin, heavy polypeptide 7B, cardiac muscle, beta"""			11919279, 15014174	Standard	XM_006723839		Approved	KIAA1512, dJ756N5.1, MYH14, MHC14	uc002xbi.2	A7E2Y1	OTTHUMG00000032320	ENST00000262873.7:c.3867C>T	20.37:g.33585437C>T		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	90	38	0.422222	NM_020884	Q5JVW7|Q6NT44|Q6NT57|Q6WG75|Q96I57|Q9NWE2|Q9P216	Silent	SNP	ENST00000262873.7	37	CCDS42869.1																																																																																			C|0.922;T|0.078	0.078	strong		0.612	MYH7B-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000078833.2	NM_020884	
EAF1	85403	hgsc.bcm.edu	37	3	15477861	15477861	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:15477861A>G	ENST00000396842.2	+	5	964	c.539A>G	c.(538-540)gAa>gGa	p.E180G	EAF1_ENST00000432764.2_Missense_Mutation_p.E79G|EAF1-AS1_ENST00000593876.1_RNA|EAF1-AS1_ENST00000494875.3_RNA|EAF1-AS1_ENST00000597949.1_RNA|EAF1-AS1_ENST00000608780.1_RNA|EAF1-AS1_ENST00000596371.1_RNA|EAF1-AS1_ENST00000595627.1_RNA|EAF1-AS1_ENST00000594820.1_RNA|EAF1-AS1_ENST00000609310.1_RNA|EAF1-AS1_ENST00000595975.1_RNA	NM_033083.6	NP_149074.3	Q96JC9	EAF1_HUMAN	ELL associated factor 1	180					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|ELL-EAF complex (GO:0032783)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)				central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(1)|prostate(1)|urinary_tract(1)	7						CTGAGGGCTGAAGTTGACATT	0.473																																					p.E180G		Atlas-SNP	.											.	EAF1	16	.	0			c.A539G						PASS	.						45.0	46.0	45.0					3																	15477861		2203	4300	6503	SO:0001583	missense	85403	exon5			GGGCTGAAGTTGA	AF272973	CCDS2626.1	3p25.1	2011-06-10			ENSG00000144597	ENSG00000144597			20907	protein-coding gene	gene with protein product		608315				11418481	Standard	NM_033083		Approved		uc003bzu.3	Q96JC9	OTTHUMG00000162544	ENST00000396842.2:c.539A>G	3.37:g.15477861A>G	ENSP00000380054:p.Glu180Gly	Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	161	32	0.198758	NM_033083	B4E3F5|Q8IW10	Missense_Mutation	SNP	ENST00000396842.2	37	CCDS2626.1	.	.	.	.	.	.	.	.	.	.	A	24.4	4.523059	0.85600	.	.	ENSG00000144597	ENST00000396842;ENST00000432764	.	.	.	5.65	5.65	0.86999	.	0.000000	0.85682	D	0.000000	T	0.78848	0.4348	M	0.78637	2.42	0.80722	D	1	D;D	0.71674	0.989;0.998	D;D	0.70487	0.969;0.968	T	0.81678	-0.0824	9	0.72032	D	0.01	-27.7472	14.8502	0.70292	1.0:0.0:0.0:0.0	.	79;180	B4E3F5;Q96JC9	.;EAF1_HUMAN	G	180;79	.	ENSP00000380054:E180G	E	+	2	0	EAF1	15452865	1.000000	0.71417	0.898000	0.35279	0.924000	0.55760	8.962000	0.93254	2.150000	0.67090	0.397000	0.26171	GAA	.	.	none		0.473	EAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252100.4	NM_033083	
MICB	4277	hgsc.bcm.edu	37	6	31473561	31473561	+	Missense_Mutation	SNP	A	A	G	rs1065075	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:31473561A>G	ENST00000252229.6	+	2	317	c.238A>G	c.(238-240)Aag>Gag	p.K80E	MICB_ENST00000538442.1_Missense_Mutation_p.K48E|MICB_ENST00000399150.3_Missense_Mutation_p.K80E	NM_005931.3	NP_005922.2			MHC class I polypeptide-related sequence B											NS(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|prostate(1)	13						CCTGGGAGCTAAGACCTGGGA	0.572													a|||	1417	0.282947	0.3835	0.1902	5008	,	,		20308	0.2748		0.2634	False		,,,				2504	0.2413				p.K80E		Atlas-SNP	.											.	MICB	26	.	0			c.A238G						PASS	.	G	GLU/LYS	926,1650		172,582,534	39.0	43.0	41.0		238	-5.3	0.0	6	dbSNP_86	41	1565,3539		242,1081,1229	yes	missense	MICB	NM_005931.3	56	414,1663,1763	GG,GA,AA		30.6622,35.9472,32.4349	benign	80/384	31473561	2491,5189	1288	2552	3840	SO:0001583	missense	4277	exon2			GGAGCTAAGACCT		CCDS43449.1, CCDS75422.1, CCDS75423.1	6p21.3	2013-01-11			ENSG00000204516	ENSG00000204516		"""Immunoglobulin superfamily / C1-set domain containing"""	7091	protein-coding gene	gene with protein product		602436				8022771	Standard	NM_005931		Approved	PERB11.2	uc003ntn.4	Q29980	OTTHUMG00000031074	ENST00000252229.6:c.238A>G	6.37:g.31473561A>G	ENSP00000252229:p.Lys80Glu	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	50	34	0.68	NM_005931		Missense_Mutation	SNP	ENST00000252229.6	37	CCDS43449.1	614	0.28113553113553114	198	0.4024390243902439	77	0.212707182320442	130	0.22727272727272727	209	0.2757255936675462	N	0.009	-1.797801	0.00617	0.359472	0.306622	ENSG00000204516	ENST00000538442;ENST00000399150;ENST00000252229	T;T;T	0.01335	5.0;5.0;5.0	2.64	-5.29	0.02747	MHC class I, alpha chain, alpha1/alpha2 (1);MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);	0.673345	0.12089	N	0.500570	T	0.00109	0.0003	N	0.01152	-0.98	0.80722	P	0.0	B;B;B	0.09022	0.0;0.002;0.0	B;B;B	0.13407	0.004;0.009;0.001	T	0.32771	-0.9894	9	0.02654	T	1	.	3.1138	0.06367	0.1191:0.3073:0.4311:0.1425	rs1065075;rs3175107;rs16897483;rs59872907	48;80;80	F5H7Q8;A2AC57;Q29980	.;.;MICB_HUMAN	E	48;80;80	ENSP00000442345:K48E;ENSP00000382103:K80E;ENSP00000252229:K80E	ENSP00000252229:K80E	K	+	1	0	MICB	31581540	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.679000	0.05203	-1.442000	0.01955	-2.116000	0.00351	AAG	A|0.712;G|0.288	0.288	strong		0.572	MICB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076102.3	NM_005931	
ZNF254	9534	hgsc.bcm.edu	37	19	24310032	24310032	+	Missense_Mutation	SNP	A	A	T	rs61737180	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	39	0	0		WXS	Illumina HiSeq	Phase_I	19	6	0.315789	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	
RPGRIP1	57096	hgsc.bcm.edu	37	14	21770730	21770730	+	Missense_Mutation	SNP	A	A	G	rs6571751	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:21770730A>G	ENST00000400017.2	+	4	574	c.574A>G	c.(574-576)Aaa>Gaa	p.K192E	RPGRIP1_ENST00000206660.6_Missense_Mutation_p.K192E|RPGRIP1_ENST00000556336.1_Missense_Mutation_p.K192E|RPGRIP1_ENST00000557771.1_Missense_Mutation_p.K192E	NM_020366.3	NP_065099.3	Q96KN7	RPGR1_HUMAN	retinitis pigmentosa GTPase regulator interacting protein 1	192			K -> E (in dbSNP:rs6571751). {ECO:0000269|PubMed:18682808}.		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)		AGTAGCCAGTAAACCCAGTGA	0.423													G|||	2390	0.477236	0.472	0.5101	5008	,	,		16887	0.3224		0.501	False		,,,				2504	0.5961				p.K192E		Atlas-SNP	.											.	RPGRIP1	213	.	0			c.A574G						PASS	.	G	GLU/LYS	1697,2091		377,943,574	44.0	45.0	44.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	574	3.1	0.1	14	dbSNP_116	44	4112,4140		1050,2012,1064	yes	missense	RPGRIP1	NM_020366.3	56	1427,2955,1638	GG,GA,AA		49.8303,44.7994,48.2475	benign	192/1287	21770730	5809,6231	1894	4126	6020	SO:0001583	missense	57096	exon4			GCCAGTAAACCCA	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.574A>G	14.37:g.21770730A>G	ENSP00000382895:p.Lys192Glu	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	99	36	0.363636	NM_020366	Q7Z2W6|Q8IXV5|Q96QA8|Q9HB94|Q9HB95|Q9HBK6|Q9NR40	Missense_Mutation	SNP	ENST00000400017.2	37	CCDS45080.1	991	0.45375457875457875	243	0.49390243902439024	182	0.5027624309392266	187	0.3269230769230769	379	0.5	G	0.004	-2.347412	0.00219	0.447994	0.498303	ENSG00000092200	ENST00000556336;ENST00000557771;ENST00000400017;ENST00000206660	T;T;T;T	0.30981	1.51;1.51;1.51;1.51	4.0	3.11	0.35812	.	1.683130	0.02576	N	0.098365	T	0.00012	0.0000	N	0.00729	-1.24	0.58432	P	5.999999999950489E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.44314	-0.9336	9	0.02654	T	1	-0.7479	6.5573	0.22468	0.2168:0.0:0.7832:0.0	rs6571751;rs52798683;rs59879033;rs6571751	192	Q96KN7	RPGR1_HUMAN	E	192	ENSP00000450445:K192E;ENSP00000451219:K192E;ENSP00000382895:K192E;ENSP00000206660:K192E	ENSP00000206660:K192E	K	+	1	0	RPGRIP1	20840570	0.027000	0.19231	0.062000	0.19696	0.004000	0.04260	1.415000	0.34748	0.668000	0.31126	-0.128000	0.14901	AAA	A|0.546;G|0.454	0.454	strong		0.423	RPGRIP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410258.1	NM_020366	
MUC5B	727897	hgsc.bcm.edu	37	11	1270691	1270691	+	Missense_Mutation	SNP	G	G	C	rs201822010		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:1270691G>C	ENST00000529681.1	+	31	12639	c.12581G>C	c.(12580-12582)aGc>aCc	p.S4194T	MUC5B_ENST00000447027.1_Missense_Mutation_p.S4197T|RP11-532E4.2_ENST00000532061.2_RNA	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	4194	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)		GTGGAATGCAGCCTGGACTTT	0.637													G|||	1	0.000199681	0.0	0.0	5008	,	,		18430	0.0		0.001	False		,,,				2504	0.0				p.S4194T		Atlas-SNP	.											.	MUC5B	473	.	0			c.G12581C						PASS	.	G	THR/SER	1,3771		0,1,1885	35.0	44.0	41.0		12581	-0.3	0.0	11		41	14,8120		0,14,4053	no	missense	MUC5B	NM_002458.2	58	0,15,5938	CC,CG,GG		0.1721,0.0265,0.126	possibly-damaging	4194/5763	1270691	15,11891	1886	4067	5953	SO:0001583	missense	727897	exon31			AATGCAGCCTGGA	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.12581G>C	11.37:g.1270691G>C	ENSP00000436812:p.Ser4194Thr	Somatic	882	1	0.00113379		WXS	Illumina HiSeq	Phase_I	1023	155	0.151515	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Missense_Mutation	SNP	ENST00000529681.1	37	CCDS44515.2	.	.	.	.	.	.	.	.	.	.	g	5.081	0.200521	0.09652	2.65E-4	0.001721	ENSG00000117983	ENST00000529681;ENST00000447027;ENST00000349637;ENST00000406844	T;T	0.18810	2.19;2.19	3.69	-0.352	0.12598	.	.	.	.	.	T	0.23330	0.0564	M	0.74467	2.265	0.09310	N	1	P;P	0.42123	0.771;0.771	B;B	0.38562	0.216;0.276	T	0.12268	-1.0554	9	0.87932	D	0	.	8.4625	0.32936	0.6517:0.0:0.3483:0.0	.	4667;4197	A7Y9J9;E9PBJ0	.;.	T	4194;4197;4138;4044	ENSP00000436812:S4194T;ENSP00000415793:S4197T	ENSP00000343037:S4138T	S	+	2	0	MUC5B	1227267	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-1.695000	0.01913	-0.269000	0.09298	-0.515000	0.04445	AGC	G|0.996;C|0.004	0.004	strong		0.637	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
CATIP	375307	hgsc.bcm.edu	37	2	219221846	219221846	+	Silent	SNP	G	G	A	rs4324314	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	71	0	0		WXS	Illumina HiSeq	Phase_I	63	24	0.380952	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		
METTL21B	25895	hgsc.bcm.edu	37	12	58176614	58176614	+	IGR	SNP	T	T	C	rs10747783	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:58176614T>C	ENST00000300209.8	+	0	2563				RP11-571M6.15_ENST00000553083.1_Intron|TSFM_ENST00000540550.1_Silent_p.F10F|TSFM_ENST00000323833.8_Silent_p.F10F|TSFM_ENST00000548851.1_Silent_p.F10F|TSFM_ENST00000454289.3_Silent_p.F10F|TSFM_ENST00000543727.1_Silent_p.F10F|TSFM_ENST00000350762.5_5'UTR|TSFM_ENST00000550559.1_Silent_p.F10F|RP11-571M6.15_ENST00000471530.1_Intron	NM_015433.2	NP_056248.2	Q96AZ1	MT21B_HUMAN	methyltransferase like 21B							cytoplasm (GO:0005737)|intracellular (GO:0005622)	methyltransferase activity (GO:0008168)			endometrium(1)|lung(1)	2						TGCGCGTGTTTCTGGTCGCGC	0.652											OREG0021954	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	1818	0.363019	0.0681	0.2594	5008	,	,		18192	0.6468		0.3191	False		,,,				2504	0.5879				p.F10F		Atlas-SNP	.											.	TSFM	26	.	0			c.T30C						PASS	.	C	,,,	487,3913		32,423,1745	39.0	35.0	37.0		30,30,30,30	3.2	0.0	12	dbSNP_120	37	2717,5873		458,1801,2036	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TSFM	NM_001172695.1,NM_001172696.1,NM_001172697.1,NM_005726.5	,,,	490,2224,3781	CC,CT,TT		31.6298,11.0682,24.6651	,,,	10/168,10/347,10/216,10/326	58176614	3204,9786	2200	4295	6495	SO:0001628	intergenic_variant	10102	exon1			CGTGTTTCTGGTC	AL050100, AF455816	CCDS8957.1, CCDS31848.1	12q14.1	2011-03-03	2011-03-03	2011-03-03	ENSG00000123427	ENSG00000123427			24936	protein-coding gene	gene with protein product		615258	"""family with sequence similarity 119, member B"""	FAM119B		12477932	Standard	NM_015433		Approved	DKFZP586D0919	uc001sqg.3	Q96AZ1	OTTHUMG00000170459		12.37:g.58176614T>C		Somatic	70	0	0	1028	WXS	Illumina HiSeq	Phase_I	55	30	0.545455	NM_005726	Q9H749|Q9Y3W2	Silent	SNP	ENST00000300209.8	37	CCDS8957.1																																																																																			T|0.714;C|0.286	0.286	strong		0.652	METTL21B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409268.1	NM_015433	
CAND2	23066	hgsc.bcm.edu	37	3	12858028	12858028	+	Missense_Mutation	SNP	T	T	C	rs3732675	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:12858028T>C	ENST00000456430.2	+	10	1638	c.1597T>C	c.(1597-1599)Tct>Cct	p.S533P	CAND2_ENST00000295989.5_Missense_Mutation_p.S440P	NM_001162499.1	NP_001155971.1	O75155	CAND2_HUMAN	cullin-associated and neddylation-dissociated 2 (putative)	533			S -> P (in dbSNP:rs3732675).		positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	intracellular (GO:0005622)|nucleus (GO:0005634)				breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(8)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	37						TGTGGCTGACTCTTTCTACAA	0.637													C|||	3025	0.604034	0.9584	0.4914	5008	,	,		18601	0.4365		0.6243	False		,,,				2504	0.3569				p.S533P	GBM(43;676 868 1633 6395 37496)	Atlas-SNP	.											CAND2_ENST00000456430,NS,carcinoma,0,2	CAND2	138	2	0			c.T1597C						scavenged	.	C	PRO/SER,PRO/SER	3700,460		1648,404,28	39.0	44.0	43.0		1597,1318	4.2	1.0	3	dbSNP_107	43	4931,3475		1439,2053,711	yes	missense,missense	CAND2	NM_001162499.1,NM_012298.2	74,74	3087,2457,739	CC,CT,TT		41.3395,11.0577,31.3147	benign,benign	533/1237,440/1120	12858028	8631,3935	2080	4203	6283	SO:0001583	missense	23066	exon10			GCTGACTCTTTCT		CCDS43053.1, CCDS54554.1	3p25.2	2008-02-05			ENSG00000144712	ENSG00000144712			30689	protein-coding gene	gene with protein product	"""TBP interacting protein"""	610403				9734811, 10441524	Standard	NM_012298		Approved	TIP120B, KIAA0667, Tp120b	uc003bxk.2	O75155	OTTHUMG00000155397	ENST00000456430.2:c.1597T>C	3.37:g.12858028T>C	ENSP00000387641:p.Ser533Pro	Somatic	126	1	0.00793651		WXS	Illumina HiSeq	Phase_I	103	46	0.446602	NM_001162499	B9EGM9|E9KL24	Missense_Mutation	SNP	ENST00000456430.2	37	CCDS54554.1	1331	0.6094322344322345	468	0.9512195121951219	173	0.47790055248618785	226	0.3951048951048951	464	0.6121372031662269	C	1.795	-0.478506	0.04414	0.889423	0.586605	ENSG00000144712	ENST00000295989;ENST00000456430	T;T	0.63744	-0.06;-0.06	5.12	4.25	0.50352	Armadillo-like helical (1);Armadillo-type fold (1);	0.204228	0.42682	N	0.000667	T	0.00012	0.0000	N	0.01086	-1.025	0.09310	P	1.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.42103	-0.9471	9	0.02654	T	1	-27.0988	7.3268	0.26560	0.0:0.7304:0.0:0.2696	rs3732675;rs17825071;rs60814914;rs3732675	533;440	O75155;O75155-2	CAND2_HUMAN;.	P	440;533	ENSP00000295989:S440P;ENSP00000387641:S533P	ENSP00000295989:S440P	S	+	1	0	CAND2	12833028	1.000000	0.71417	1.000000	0.80357	0.828000	0.46876	1.701000	0.37825	0.577000	0.29470	-0.215000	0.12644	TCT	C|0.609;G|0.000;T|0.391	0.609	strong		0.637	CAND2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339856.4	XM_371617	
SSPO	23145	hgsc.bcm.edu	37	7	149484798	149484798	+	RNA	SNP	C	C	T	rs62490656	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	78	0	0		WXS	Illumina HiSeq	Phase_I	46	19	0.413043	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			
DNAH5	1767	hgsc.bcm.edu	37	5	13716796	13716796	+	Missense_Mutation	SNP	C	C	T	rs138045391	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:13716796C>T	ENST00000265104.4	-	74	12813	c.12709G>A	c.(12709-12711)Gtc>Atc	p.V4237I		NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	4237					cilium movement (GO:0003341)|lateral ventricle development (GO:0021670)|left/right axis specification (GO:0070986)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(6)|breast(14)|central_nervous_system(4)|cervix(2)|endometrium(23)|haematopoietic_and_lymphoid_tissue(8)|kidney(11)|large_intestine(85)|liver(1)|lung(129)|ovary(16)|pancreas(2)|prostate(5)|skin(48)|stomach(5)|upper_aerodigestive_tract(11)|urinary_tract(8)	378	Lung NSC(4;0.00476)					GTCCAGGAGACACCCTGGGAA	0.403									Kartagener syndrome				C|||	2	0.000399361	0.0015	0.0	5008	,	,		16991	0.0		0.0	False		,,,				2504	0.0				p.V4237I		Atlas-SNP	.											.	DNAH5	868	.	0			c.G12709A						PASS	.																																			SO:0001583	missense	1767	exon74	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	AGGAGACACCCTG	AJ132090	CCDS3882.1	5p15.2	2008-07-18	2006-09-04		ENSG00000039139	ENSG00000039139		"""Axonemal dyneins"""	2950	protein-coding gene	gene with protein product	"""dynein heavy chain 5"""	603335	"""dynein, axonemal, heavy polypeptide 5"""			9256245, 11788826	Standard	NM_001369		Approved	Dnahc5, HL1, PCD, CILD3, KTGNR	uc003jfd.2	Q8TE73	OTTHUMG00000090533	ENST00000265104.4:c.12709G>A	5.37:g.13716796C>T	ENSP00000265104:p.Val4237Ile	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	103	43	0.417476	NM_001369	Q92860|Q96L74|Q9H5S7|Q9HCG9	Missense_Mutation	SNP	ENST00000265104.4	37	CCDS3882.1	.	.	.	.	.	.	.	.	.	.	C	7.699	0.692759	0.15039	.	.	ENSG00000039139	ENST00000265104	T	0.09538	2.97	5.53	4.67	0.58626	Dynein heavy chain (1);	0.128288	0.51477	N	0.000093	T	0.08537	0.0212	N	0.25426	0.745	0.58432	D	0.999996	B	0.09022	0.002	B	0.23574	0.047	T	0.23619	-1.0183	10	0.20046	T	0.44	.	11.2865	0.49224	0.0:0.8422:0.0:0.1578	.	4237	Q8TE73	DYH5_HUMAN	I	4237	ENSP00000265104:V4237I	ENSP00000265104:V4237I	V	-	1	0	DNAH5	13769796	0.996000	0.38824	0.686000	0.30086	0.589000	0.36550	3.359000	0.52292	1.348000	0.45733	-0.157000	0.13467	GTC	A|0.001;C|0.999	.	weak		0.403	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369	
TMEM194B	100131211	hgsc.bcm.edu	37	2	191379268	191379268	+	Silent	SNP	G	G	A	rs4586658	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:191379268G>A	ENST00000409150.3	-	7	930	c.864C>T	c.(862-864)gcC>gcT	p.A288A		NM_001142645.1	NP_001136117.1	A6NFY4	T194B_HUMAN	transmembrane protein 194B	288						integral component of membrane (GO:0016021)											ACTGAGGCACGGCCACACCAG	0.522													G|||	2667	0.532548	0.3321	0.696	5008	,	,		16189	0.5833		0.5765	False		,,,				2504	0.59				p.A288A		Atlas-SNP	.											.	TMEM194B	18	.	0			c.C864T						PASS	.	G		473,911		86,301,305	73.0	73.0	73.0		864	-0.5	0.0	2	dbSNP_111	73	1822,1360		520,782,289	no	coding-synonymous	TMEM194B	NM_001142645.1		606,1083,594	AA,AG,GG		42.7404,34.1763,49.7372		288/418	191379268	2295,2271	692	1591	2283	SO:0001819	synonymous_variant	100131211	exon7			AGGCACGGCCACA		CCDS46476.1	2q32.2	2008-06-10			ENSG00000189362	ENSG00000189362			33700	protein-coding gene	gene with protein product							Standard	NM_001142645		Approved		uc010zgf.2	A6NFY4	OTTHUMG00000154454	ENST00000409150.3:c.864C>T	2.37:g.191379268G>A		Somatic	341	2	0.0058651		WXS	Illumina HiSeq	Phase_I	288	285	0.989583	NM_001142645	B4DYG6	Silent	SNP	ENST00000409150.3	37	CCDS46476.1																																																																																			G|0.492;A|0.508	0.508	strong		0.522	TMEM194B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335299.1	XM_001723498	
PPAN	56342	hgsc.bcm.edu	37	19	10217248	10217248	+	Silent	SNP	C	C	T	rs11559190	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:10217248C>T	ENST00000253107.7	+	2	196	c.90C>T	c.(88-90)caC>caT	p.H30H	PPAN_ENST00000556468.1_Silent_p.H30H|PPAN-P2RY11_ENST00000428358.1_Silent_p.H30H|PPAN-P2RY11_ENST00000393796.4_Silent_p.H30H|SNORD105_ENST00000386910.1_RNA|PPAN_ENST00000393793.1_5'UTR	NM_020230.5	NP_064615.3	Q9NQ55	SSF1_HUMAN	peter pan homolog (Drosophila)	30	Brix. {ECO:0000255|PROSITE- ProRule:PRU00034}.				RNA splicing (GO:0008380)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(3)|liver(2)|lung(7)|prostate(1)|skin(1)|urinary_tract(1)	15			OV - Ovarian serous cystadenocarcinoma(20;2.19e-08)|Epithelial(33;1.76e-05)|all cancers(31;3.54e-05)			CGAACCCGCACTCGTTCGTGT	0.701													C|||	82	0.0163738	0.0	0.0	5008	,	,		10898	0.0218		0.001	False		,,,				2504	0.0603				p.H30H		Atlas-SNP	.											.	PPAN	43	.	0			c.C90T						PASS	.	C	,,	5,4305		0,5,2150	9.0	12.0	11.0		90,90,90	3.1	1.0	19	dbSNP_120	11	0,8446		0,0,4223	no	coding-synonymous,coding-synonymous,coding-synonymous	PPAN,PPAN-P2RY11	NM_001040664.2,NM_001198690.1,NM_020230.5	,,	0,5,6373	TT,TC,CC		0.0,0.116,0.0392	,,	30/795,30/521,30/474	10217248	5,12751	2155	4223	6378	SO:0001819	synonymous_variant	56342	exon2			CCCGCACTCGTTC	BC033202	CCDS12225.1	19p13.2	2008-02-05	2001-11-28		ENSG00000130810	ENSG00000130810			9227	protein-coding gene	gene with protein product		607793	"""peter pan (Drosophila) homolog"""			10873382	Standard	NM_020230		Approved	SSF1, SSF2, SSF, BXDC3		Q9NQ55	OTTHUMG00000156826	ENST00000253107.7:c.90C>T	19.37:g.10217248C>T		Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	47	19	0.404255	NM_020230	C9J3F9|Q9BW97|Q9H170	Silent	SNP	ENST00000253107.7	37	CCDS12225.1																																																																																			C|0.992;T|0.008	0.008	strong		0.701	PPAN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316658.1	NM_020230	
NRCAM	4897	hgsc.bcm.edu	37	7	107824889	107824889	+	Silent	SNP	C	C	G	rs401433	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:107824889C>G	ENST00000425651.2	-	18	2204	c.2205G>C	c.(2203-2205)gcG>gcC	p.A735A	NRCAM_ENST00000351718.4_Silent_p.A719A|NRCAM_ENST00000413765.2_Silent_p.A716A|NRCAM_ENST00000379022.4_Silent_p.A735A|NRCAM_ENST00000379024.4_Silent_p.A716A|NRCAM_ENST00000379028.3_Silent_p.A735A	NM_001037132.2	NP_001032209.1	Q92823	NRCAM_HUMAN	neuronal cell adhesion molecule	735	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				angiogenesis (GO:0001525)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|axonogenesis (GO:0007409)|central nervous system development (GO:0007417)|clustering of voltage-gated sodium channels (GO:0045162)|heterotypic cell-cell adhesion (GO:0034113)|neuron migration (GO:0001764)|neuronal action potential propagation (GO:0019227)|positive regulation of neuron differentiation (GO:0045666)|protein localization (GO:0008104)|regulation of axon extension (GO:0030516)|retinal ganglion cell axon guidance (GO:0031290)|single organismal cell-cell adhesion (GO:0016337)|synapse assembly (GO:0007416)	axon initial segment (GO:0043194)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|synapse (GO:0045202)	ankyrin binding (GO:0030506)			breast(4)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(8)|liver(1)|lung(36)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(4)	65						ACTGCTCAGACGCCTCGCTGG	0.502													C|||	3451	0.689097	0.348	0.7983	5008	,	,		16957	0.9554		0.7644	False		,,,				2504	0.7209				p.A735A		Atlas-SNP	.											.	NRCAM	267	.	0			c.G2205C						PASS	.	C	,,,,	1945,2461	551.2+/-378.2	431,1083,689	83.0	75.0	78.0		2205,2205,2148,2148,2157	-10.9	0.0	7	dbSNP_80	78	6620,1980	723.2+/-406.4	2553,1514,233	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NRCAM	NM_001037132.2,NM_001193582.1,NM_001193583.1,NM_001193584.1,NM_005010.4	,,,,	2984,2597,922	GG,GC,CC		23.0233,44.1443,34.1458	,,,,	735/1305,735/1212,716/1193,716/1181,719/1184	107824889	8565,4441	2203	4300	6503	SO:0001819	synonymous_variant	4897	exon18			CTCAGACGCCTCG		CCDS5751.1, CCDS47686.1, CCDS55153.1, CCDS75652.1	7q31	2013-02-11			ENSG00000091129	ENSG00000091129		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	7994	protein-coding gene	gene with protein product	"""NgCAM-related cell adhesion molecule"""	601581				8812479	Standard	NM_001037132		Approved	KIAA0343, Bravo	uc022aka.1	Q92823	OTTHUMG00000154973	ENST00000425651.2:c.2205G>C	7.37:g.107824889C>G		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	85	84	0.988235	NM_001037132	A4D0S3|E9PDA4|O15051|O15179|Q14BM2|Q9UHI3|Q9UHI4	Silent	SNP	ENST00000425651.2	37	CCDS47686.1																																																																																			C|0.317;G|0.683	0.683	strong		0.502	NRCAM-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337942.2	NM_001037132	
TMC8	147138	hgsc.bcm.edu	37	17	76131070	76131070	+	Silent	SNP	G	G	A	rs12452890	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:76131070G>A	ENST00000318430.5	+	9	1481	c.1107G>A	c.(1105-1107)gaG>gaA	p.E369E	TMC8_ENST00000589691.1_Silent_p.E146E|TMC6_ENST00000322914.3_5'Flank	NM_152468.4	NP_689681.2	Q8IU68	TMC8_HUMAN	transmembrane channel-like 8	369					ion transport (GO:0006811)|negative regulation of protein binding (GO:0032091)|negative regulation of protein oligomerization (GO:0032460)|regulation of cell growth (GO:0001558)|regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902041)|zinc ion homeostasis (GO:0055069)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear membrane (GO:0031965)	receptor binding (GO:0005102)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	12			BRCA - Breast invasive adenocarcinoma(99;0.00269)|Lung(188;0.0973)|OV - Ovarian serous cystadenocarcinoma(97;0.192)			CCAACACGGAGGTCAACCTCA	0.572													G|||	2706	0.540335	0.7231	0.6268	5008	,	,		20489	0.3938		0.5288	False		,,,				2504	0.3947				p.E369E		Atlas-SNP	.											.	TMC8	44	.	0			c.G1107A						PASS	.	G		3021,1385	687.4+/-404.8	1044,933,226	96.0	80.0	86.0		1107	2.5	1.0	17	dbSNP_120	86	4477,4123	591.2+/-392.8	1203,2071,1026	no	coding-synonymous	TMC8	NM_152468.4		2247,3004,1252	AA,AG,GG		47.9419,31.4344,42.3497		369/727	76131070	7498,5508	2203	4300	6503	SO:0001819	synonymous_variant	147138	exon9			CACGGAGGTCAAC	AY057380	CCDS32749.1	17q25.3	2014-09-17	2005-11-10	2005-11-10	ENSG00000167895	ENSG00000167895			20474	protein-coding gene	gene with protein product		605829	"""epidermodysplasia verruciformis 2"""	EVER2		12426567	Standard	NM_152468		Approved	EVIN2	uc002jup.2	Q8IU68		ENST00000318430.5:c.1107G>A	17.37:g.76131070G>A		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	93	49	0.526882	NM_152468	Q2YDC0|Q8IWU7|Q8N358|Q8NF04	Silent	SNP	ENST00000318430.5	37	CCDS32749.1																																																																																			G|0.421;A|0.579	0.579	strong		0.572	TMC8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436900.3		
ZNF93	81931	hgsc.bcm.edu	37	19	20044886	20044886	+	Silent	SNP	T	T	C	rs10401345	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:20044886T>C	ENST00000343769.5	+	4	1150	c.1122T>C	c.(1120-1122)tgT>tgC	p.C374C	AC007204.2_ENST00000592245.1_lincRNA	NM_031218.3	NP_112495.2	P35789	ZNF93_HUMAN	zinc finger protein 93	374					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)	p.C374C(1)		endometrium(6)|kidney(2)|large_intestine(4)|lung(8)|pancreas(1)|prostate(1)|skin(1)|stomach(1)	24						GTGAAGAATGTGGCAAAGCCT	0.388													t|||	601	0.120008	0.2534	0.0447	5008	,	,		22657	0.0506		0.0437	False		,,,				2504	0.1431				p.C374C		Atlas-SNP	.											ZNF93,NS,carcinoma,0,1	ZNF93	81	1	1	Substitution - coding silent(1)	stomach(1)	c.T1122C						PASS	.	T		928,3478	355.1+/-312.9	98,732,1373	89.0	89.0	89.0		1122	0.9	0.5	19	dbSNP_119	89	281,8319	105.4+/-166.3	2,277,4021	no	coding-synonymous	ZNF93	NM_031218.3		100,1009,5394	CC,CT,TT		3.2674,21.0622,9.2957		374/621	20044886	1209,11797	2203	4300	6503	SO:0001819	synonymous_variant	81931	exon4			AGAATGTGGCAAA	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.1122T>C	19.37:g.20044886T>C		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	36	36	1	NM_031218	A6NMY2|B9EGT2|Q8N8Q4|Q9H9X5|Q9Y2N8	Silent	SNP	ENST00000343769.5	37	CCDS32973.1																																																																																			T|0.908;C|0.092	0.092	strong		0.388	ZNF93-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460808.2	NM_031218	
GRIN3A	116443	hgsc.bcm.edu	37	9	104433235	104433235	+	Missense_Mutation	SNP	C	C	T	rs10989589	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:104433235C>T	ENST00000361820.3	-	3	2059	c.1459G>A	c.(1459-1461)Gga>Aga	p.G487R		NM_133445.2	NP_597702.2	Q8TCU5	NMD3A_HUMAN	glutamate receptor, ionotropic, N-methyl-D-aspartate 3A	487			G -> R (in dbSNP:rs10989589). {ECO:0000269|PubMed:11735224, ECO:0000269|PubMed:11880201}.		calcium ion transport (GO:0006816)|dendrite development (GO:0016358)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|prepulse inhibition (GO:0060134)|response to ethanol (GO:0045471)|rhythmic process (GO:0048511)|synaptic transmission, glutamatergic (GO:0035249)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	calcium channel activity (GO:0005262)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glycine binding (GO:0016594)|identical protein binding (GO:0042802)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|neurotransmitter binding (GO:0042165)|protein phosphatase 2A binding (GO:0051721)			breast(2)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(12)|lung(44)|ovary(4)|pancreas(1)|skin(7)|upper_aerodigestive_tract(1)	80		Acute lymphoblastic leukemia(62;0.0568)			Acamprosate(DB00659)|Acetylcysteine(DB06151)|Amantadine(DB00915)|Atomoxetine(DB00289)|Chloroprocaine(DB01161)|Dextromethorphan(DB00514)|Ethanol(DB00898)|Ethopropazine(DB00392)|Felbamate(DB00949)|Gabapentin(DB00996)|Halothane(DB01159)|Ketamine(DB01221)|Ketobemidone(DB06738)|Memantine(DB01043)|Methadone(DB00333)|Milnacipran(DB04896)|Orphenadrine(DB01173)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Procaine(DB00721)|Secobarbital(DB00418)|Tramadol(DB00193)	ACAATCTTTCCCCCCTGCCAG	0.498													C|||	1329	0.265375	0.1097	0.3617	5008	,	,		18574	0.2262		0.4076	False		,,,				2504	0.3016				p.G487R		Atlas-SNP	.											GRIN3A,caecum,carcinoma,+1,1	GRIN3A	186	1	0			c.G1459A						PASS	.	C	ARG/GLY	741,3665	303.0+/-287.7	64,613,1526	166.0	161.0	163.0		1459	5.8	0.3	9	dbSNP_120	163	3549,5051	515.9+/-378.7	726,2097,1477	yes	missense	GRIN3A	NM_133445.2	125	790,2710,3003	TT,TC,CC		41.2674,16.818,32.9848	possibly-damaging	487/1116	104433235	4290,8716	2203	4300	6503	SO:0001583	missense	116443	exon3			TCTTTCCCCCCTG		CCDS6758.1	9q31.1	2012-08-29			ENSG00000198785	ENSG00000198785		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	16767	protein-coding gene	gene with protein product		606650					Standard	NM_133445		Approved	GluN3A	uc004bbp.2	Q8TCU5	OTTHUMG00000020387	ENST00000361820.3:c.1459G>A	9.37:g.104433235C>T	ENSP00000355155:p.Gly487Arg	Somatic	237	1	0.00421941		WXS	Illumina HiSeq	Phase_I	214	109	0.509346	NM_133445	B3DLF9|Q5VTR3|Q8TF29|Q8WXI6	Missense_Mutation	SNP	ENST00000361820.3	37	CCDS6758.1	618	0.28296703296703296	54	0.10975609756097561	147	0.40607734806629836	115	0.20104895104895104	302	0.39841688654353563	C	14.17	2.454432	0.43634	0.16818	0.412674	ENSG00000198785	ENST00000361820	T	0.11277	2.79	5.76	5.76	0.90799	.	0.135566	0.49305	D	0.000160	T	0.00012	0.0000	L	0.56396	1.775	0.09310	P	0.99999884003	P	0.52842	0.956	P	0.56474	0.799	T	0.52697	-0.8541	9	0.48119	T	0.1	.	13.5255	0.61593	0.0:0.9287:0.0:0.0713	rs10989589;rs52814301;rs10989589	487	Q8TCU5	NMD3A_HUMAN	R	487	ENSP00000355155:G487R	ENSP00000355155:G487R	G	-	1	0	GRIN3A	103473056	1.000000	0.71417	0.252000	0.24328	0.990000	0.78478	5.989000	0.70587	2.882000	0.98803	0.655000	0.94253	GGA	C|0.670;T|0.330	0.330	strong		0.498	GRIN3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053453.1		
PTCHD2	57540	hgsc.bcm.edu	37	1	11579504	11579504	+	Missense_Mutation	SNP	G	G	C	rs2072993	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:11579504G>C	ENST00000294484.6	+	8	2120	c.1982G>C	c.(1981-1983)gGc>gCc	p.G661A	PTCHD2_ENST00000389575.3_Missense_Mutation_p.G661A	NM_020780.1	NP_065831.1	Q9P2K9	PTHD2_HUMAN	patched domain containing 2	661			G -> A (in dbSNP:rs2072993).		cholesterol homeostasis (GO:0042632)|regulation of lipid transport (GO:0032368)|smoothened signaling pathway (GO:0007224)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nuclear membrane (GO:0031965)	hedgehog receptor activity (GO:0008158)			NS(3)|breast(2)|endometrium(9)|kidney(4)|large_intestine(5)|lung(34)|ovary(3)|pancreas(1)|prostate(6)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	76	Ovarian(185;0.249)	Lung NSC(185;4.16e-05)|all_lung(284;4.76e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.13e-07)|COAD - Colon adenocarcinoma(227;4.83e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000325)|Kidney(185;0.000877)|KIRC - Kidney renal clear cell carcinoma(229;0.00273)|STAD - Stomach adenocarcinoma(313;0.00766)|READ - Rectum adenocarcinoma(331;0.0549)		CCTGCCCAGGGCCCCATACCC	0.642													g|||	951	0.189896	0.0908	0.0951	5008	,	,		18219	0.4444		0.1054	False		,,,				2504	0.2157				p.G661A		Atlas-SNP	.											.	PTCHD2	193	.	0			c.G1982C						PASS	.		ALA/GLY	424,3620		24,376,1622	136.0	150.0	145.0		1982	3.7	0.8	1	dbSNP_96	145	1209,7169		79,1051,3059	yes	missense	PTCHD2	NM_020780.1	60	103,1427,4681	CC,CG,GG		14.4307,10.4847,13.146	benign	661/1393	11579504	1633,10789	2022	4189	6211	SO:0001583	missense	57540	exon8			CCCAGGGCCCCAT	AB037758	CCDS41247.1	1p36.22	2010-02-17			ENSG00000204624	ENSG00000204624			29251	protein-coding gene	gene with protein product		611251				15738394	Standard	NM_020780		Approved	KIAA1337, DISP3	uc001ash.4	Q9P2K9	OTTHUMG00000002074	ENST00000294484.6:c.1982G>C	1.37:g.11579504G>C	ENSP00000294484:p.Gly661Ala	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	53	31	0.584906	NM_020780	Q5VTU9|Q9UJD6	Missense_Mutation	SNP	ENST00000294484.6	37	CCDS41247.1	406	0.1858974358974359	50	0.1016260162601626	32	0.08839779005524862	244	0.42657342657342656	80	0.10554089709762533	g	10.91	1.484304	0.26598	0.104847	0.144307	ENSG00000204624	ENST00000294484;ENST00000389575	D;D	0.89552	-2.53;-2.53	5.52	3.67	0.42095	.	0.314529	0.34223	N	0.004143	T	0.00012	0.0000	N	0.22421	0.69	0.42777	P	0.0061430000000000096	P	0.35684	0.515	B	0.37601	0.254	T	0.16512	-1.0400	9	0.24483	T	0.36	-26.0355	9.88	0.41227	0.1646:0.0:0.8354:0.0	rs2072993;rs52804559;rs59951833;rs2072993	661	Q9P2K9	PTHD2_HUMAN	A	661	ENSP00000294484:G661A;ENSP00000374226:G661A	ENSP00000294484:G661A	G	+	2	0	PTCHD2	11502091	1.000000	0.71417	0.779000	0.31741	0.119000	0.20118	4.385000	0.59613	0.717000	0.32145	-0.141000	0.14075	GGC	G|0.811;C|0.189	0.189	strong		0.642	PTCHD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000005770.2	XM_052561	
DSP	1832	hgsc.bcm.edu	37	6	7581636	7581636	+	Missense_Mutation	SNP	G	G	A	rs6929069	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:7581636G>A	ENST00000379802.3	+	23	5554	c.5213G>A	c.(5212-5214)cGa>cAa	p.R1738Q	DSP_ENST00000418664.2_Intron	NM_004415.2	NP_004406.2	P15924	DESP_HUMAN	desmoplakin	1738	Central fibrous rod domain.		R -> Q (in dbSNP:rs6929069). {ECO:0000269|PubMed:19863551, ECO:0000269|PubMed:20031617}.		adherens junction organization (GO:0034332)|apoptotic process (GO:0006915)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|desmosome organization (GO:0002934)|epidermis development (GO:0008544)|intermediate filament organization (GO:0045109)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)|protein localization to adherens junction (GO:0071896)|regulation of heart rate by cardiac conduction (GO:0086091)|single organismal cell-cell adhesion (GO:0016337)|ventricular cardiac muscle cell action potential (GO:0086005)|ventricular compact myocardium morphogenesis (GO:0003223)|wound healing (GO:0042060)	basolateral plasma membrane (GO:0016323)|cornified envelope (GO:0001533)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|intercalated disc (GO:0014704)|intermediate filament (GO:0005882)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)|protein binding, bridging (GO:0030674)|protein kinase C binding (GO:0005080)|scaffold protein binding (GO:0097110)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)	p.R1738Q(1)		biliary_tract(1)|breast(6)|central_nervous_system(7)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(16)|liver(2)|lung(27)|ovary(4)|prostate(1)|skin(8)|stomach(3)|upper_aerodigestive_tract(7)|urinary_tract(5)	101	Ovarian(93;0.0584)	all_hematologic(90;0.236)		OV - Ovarian serous cystadenocarcinoma(45;0.000508)		AGGAGAGGACGAAGCGAAGCG	0.517													G|||	1204	0.240415	0.379	0.1859	5008	,	,		17459	0.1944		0.1352	False		,,,				2504	0.2474				p.R1738Q		Atlas-SNP	.											DSP,NS,carcinoma,0,2	DSP	306	2	1	Substitution - Missense(1)	stomach(1)	c.G5213A						PASS	.	G	,GLN/ARG	1444,2962	469.4+/-355.4	230,984,989	124.0	128.0	126.0		,5213	3.2	0.1	6	dbSNP_116	126	1081,7519	227.1+/-262.6	70,941,3289	yes	intron,missense	DSP	NM_001008844.1,NM_004415.2	,43	300,1925,4278	AA,AG,GG		12.5698,32.7735,19.4141	,benign	,1738/2872	7581636	2525,10481	2203	4300	6503	SO:0001583	missense	1832	exon23			GAGGACGAAGCGA	J05211	CCDS4501.1, CCDS47368.1	6p24.3	2014-09-17	2003-05-20		ENSG00000096696	ENSG00000096696			3052	protein-coding gene	gene with protein product		125647	"""desmoplakin (DPI, DPII)"""			1889810	Standard	NM_004415		Approved	KPPS2, PPKS2, DPI, DPII	uc003mxp.1	P15924	OTTHUMG00000014212	ENST00000379802.3:c.5213G>A	6.37:g.7581636G>A	ENSP00000369129:p.Arg1738Gln	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	116	37	0.318966	NM_004415	B2RTT2|D7RX09|O75993|Q14189|Q9UHN4	Missense_Mutation	SNP	ENST00000379802.3	37	CCDS4501.1	485	0.22206959706959706	193	0.39227642276422764	71	0.19613259668508287	113	0.19755244755244755	108	0.1424802110817942	G	5.922	0.354153	0.11182	0.327735	0.125698	ENSG00000096696	ENST00000379802	T	0.72051	-0.62	5.98	3.24	0.37175	.	0.192746	0.35349	N	0.003267	T	0.30230	0.0758	N	0.14661	0.345	0.58432	P	9.000000000036756E-6	B	0.10296	0.003	B	0.04013	0.001	T	0.04796	-1.0926	9	0.25106	T	0.35	.	9.2173	0.37355	0.334:0.0:0.666:0.0	rs6929069;rs52837086;rs61346221;rs6929069	1738	P15924	DESP_HUMAN	Q	1738	ENSP00000369129:R1738Q	ENSP00000369129:R1738Q	R	+	2	0	DSP	7526635	0.195000	0.23338	0.054000	0.19295	0.329000	0.28539	0.611000	0.24268	0.885000	0.36088	0.650000	0.86243	CGA	G|0.792;A|0.208	0.208	strong		0.517	DSP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039786.2	NM_004415	
SNED1	25992	hgsc.bcm.edu	37	2	242003487	242003487	+	Silent	SNP	C	C	T	rs17852471	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:242003487C>T	ENST00000310397.8	+	19	2544	c.2544C>T	c.(2542-2544)ggC>ggT	p.G848G	SNED1_ENST00000342631.6_Silent_p.G848G|SNED1_ENST00000401884.1_Silent_p.G848G|AC005237.4_ENST00000458377.1_RNA|SNED1_ENST00000405547.3_Silent_p.G848G	NM_001080437.1	NP_001073906.1	Q8TER0	SNED1_HUMAN	sushi, nidogen and EGF-like domains 1	848	EGF-like 13. {ECO:0000255|PROSITE- ProRule:PRU00076}.				cell-matrix adhesion (GO:0007160)	extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|central_nervous_system(3)|kidney(2)|large_intestine(6)|lung(4)|ovary(3)|prostate(3)|upper_aerodigestive_tract(1)	24		all_cancers(19;7.48e-31)|all_epithelial(40;1.35e-12)|Breast(86;0.000148)|Renal(207;0.00528)|Ovarian(221;0.104)|Esophageal squamous(248;0.131)|all_lung(227;0.17)|all_hematologic(139;0.182)|Melanoma(123;0.238)		Epithelial(32;6.46e-32)|all cancers(36;6.23e-29)|OV - Ovarian serous cystadenocarcinoma(60;2.1e-14)|Kidney(56;6.35e-09)|KIRC - Kidney renal clear cell carcinoma(57;5.98e-08)|BRCA - Breast invasive adenocarcinoma(100;3.66e-06)|Lung(119;0.00072)|LUSC - Lung squamous cell carcinoma(224;0.00553)|Colorectal(34;0.0162)|COAD - Colon adenocarcinoma(134;0.109)		AGAGCGGCGGCGGGGCCTACC	0.697													C|||	1282	0.25599	0.2179	0.2478	5008	,	,		9290	0.4048		0.1829	False		,,,				2504	0.2352				p.G848G		Atlas-SNP	.											.	SNED1	76	.	0			c.C2544T						PASS	.	C		642,3114		71,500,1307	8.0	12.0	11.0		2544	-4.5	0.7	2	dbSNP_123	11	1180,6876		101,978,2949	no	coding-synonymous	SNED1	NM_001080437.1		172,1478,4256	TT,TC,CC		14.6475,17.0927,15.425		848/1414	242003487	1822,9990	1878	4028	5906	SO:0001819	synonymous_variant	25992	exon19			CGGCGGCGGGGCC	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.2544C>T	2.37:g.242003487C>T		Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	155	70	0.451613	NM_001080437	B5MDC3|B7WNK6|B7WPM0|Q336F4|Q336F5|Q8N369|Q8TEP7	Silent	SNP	ENST00000310397.8	37	CCDS46562.1																																																																																			C|0.733;T|0.267	0.267	strong		0.697	SNED1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323935.2	XM_059482	
SH2D4A	63898	hgsc.bcm.edu	37	8	19221700	19221700	+	Missense_Mutation	SNP	G	G	A	rs34608771	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:19221700G>A	ENST00000265807.3	+	7	1235	c.824G>A	c.(823-825)aGc>aAc	p.S275N	SH2D4A_ENST00000519207.1_Missense_Mutation_p.S275N|SH2D4A_ENST00000518040.1_Missense_Mutation_p.S230N	NM_001174160.1|NM_022071.3	NP_001167631.1|NP_071354.2	Q9H788	SH24A_HUMAN	SH2 domain containing 4A	275			S -> N (in dbSNP:rs34608771). {ECO:0000269|PubMed:15489334}.		negative regulation of phosphatase activity (GO:0010923)	cytoplasm (GO:0005737)	phosphatase binding (GO:0019902)			endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|stomach(1)	16				Colorectal(111;0.0732)		AGGCTGCAAAGCCCCTTGCGT	0.527													G|||	891	0.177915	0.0946	0.2378	5008	,	,		14052	0.0595		0.3072	False		,,,				2504	0.2372				p.S275N		Atlas-SNP	.											.	SH2D4A	49	.	0			c.G824A						PASS	.	G	ASN/SER,ASN/SER,ASN/SER	556,3850	249.0+/-256.6	36,484,1683	81.0	82.0	81.0		824,689,824	3.9	0.0	8	dbSNP_126	81	2669,5931	427.8+/-355.7	416,1837,2047	yes	missense,missense,missense	SH2D4A	NM_001174159.1,NM_001174160.1,NM_022071.3	46,46,46	452,2321,3730	AA,AG,GG		31.0349,12.6192,24.7962	benign,benign,benign	275/455,230/410,275/455	19221700	3225,9781	2203	4300	6503	SO:0001583	missense	63898	exon7			TGCAAAGCCCCTT	AY190323	CCDS6009.1, CCDS55206.1	8p21	2013-02-14			ENSG00000104611	ENSG00000104611		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""SH2 domain containing"""	26102	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 38"""	614968					Standard	NM_022071		Approved	FLJ20967, SH2A, PPP1R38	uc003wzc.3	Q9H788	OTTHUMG00000097005	ENST00000265807.3:c.824G>A	8.37:g.19221700G>A	ENSP00000265807:p.Ser275Asn	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	69	11	0.15942	NM_022071	B4DDR1|Q5XKC1|Q6NXE9|Q86YM2|Q96C88|Q9H7F7	Missense_Mutation	SNP	ENST00000265807.3	37	CCDS6009.1	401	0.18360805860805862	40	0.08130081300813008	95	0.26243093922651933	32	0.055944055944055944	234	0.3087071240105541	G	11.29	1.596322	0.28445	0.126192	0.310349	ENSG00000104611	ENST00000265807;ENST00000518040;ENST00000519207	T;D;T	0.94537	2.62;-3.45;2.62	5.75	3.94	0.45596	.	0.730267	0.13855	N	0.358071	T	0.00012	0.0000	L	0.28344	0.845	0.80722	P	0.0	B;B	0.10296	0.003;0.001	B;B	0.08055	0.003;0.002	T	0.07481	-1.0770	9	0.13853	T	0.58	.	7.9302	0.29897	0.1895:0.0:0.8105:0.0	rs34608771	230;275	B4DDR1;Q9H788	.;SH24A_HUMAN	N	275;230;275	ENSP00000265807:S275N;ENSP00000429482:S230N;ENSP00000428684:S275N	ENSP00000265807:S275N	S	+	2	0	SH2D4A	19265980	0.001000	0.12720	0.006000	0.13384	0.008000	0.06430	0.087000	0.14958	0.754000	0.32968	0.563000	0.77884	AGC	G|0.764;A|0.236	0.236	strong		0.527	SH2D4A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214094.1	NM_022071	
HLA-DPA1	3113	hgsc.bcm.edu	37	6	33037639	33037639	+	Missense_Mutation	SNP	G	G	A	rs1126534|rs386699859	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:33037639G>A	ENST00000419277.1	-	3	254	c.125C>T	c.(124-126)gCg>gTg	p.A42V	HLA-DPA1_ENST00000428995.1_Missense_Mutation_p.A42V|HLA-DPA1_ENST00000463066.1_5'UTR	NM_001242524.1|NM_001242525.1	NP_001229453.1|NP_001229454.1	P20036	DPA1_HUMAN	major histocompatibility complex, class II, DP alpha 1	42	Alpha-1.		A -> M (in allele DPA1*02:02, allele DPA1*02:04, allele DPA1*03:01, allele DPA1*03:02 and allele DPA1*03:03; requires 2 nucleotide substitutions).|A -> T (in dbSNP:rs1126533).|A -> V (in dbSNP:rs1126534).		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cellular response to interferon-gamma (GO:0071346)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell proliferation (GO:0042102)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)	p.A42V(4)		kidney(5)|large_intestine(1)|lung(6)|prostate(1)|skin(2)	15						CTGTACAAACGCGGCATAAGT	0.418													.|||	1189	0.23742	0.351	0.062	5008	,	,		20498	0.5496		0.0318	False		,,,				2504	0.0982				p.A42V		Atlas-SNP	.											HLA-DPA1,NS,carcinoma,0,4	HLA-DPA1	20	4	4	Substitution - Missense(4)	kidney(4)	c.C125T						scavenged	.	G	VAL/ALA,VAL/ALA,VAL/ALA	595,2425		107,381,1022	53.0	76.0	68.0		125,125,125	-6.1	0.0	6	dbSNP_86	68	69,5347		2,65,2641	yes	missense,missense,missense	HLA-DPA1	NM_001242524.1,NM_001242525.1,NM_033554.3	64,64,64	109,446,3663	AA,AG,GG		1.274,19.702,7.871	benign,benign,benign	42/261,42/261,42/261	33037639	664,7772	1510	2708	4218	SO:0001583	missense	3113	exon2			ACAAACGCGGCAT	X00457	CCDS4764.1	6p21.3	2013-01-11			ENSG00000231389	ENSG00000231389		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4938	protein-coding gene	gene with protein product		142880		HLA-DP1A		6584734	Standard	NM_033554		Approved		uc003ocs.2	P20036	OTTHUMG00000031058	ENST00000419277.1:c.125C>T	6.37:g.33037639G>A	ENSP00000393566:p.Ala42Val	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	75	22	0.293333	NM_033554	A9YWH7|B9UKH4|O19722|O46883|P01905|P79554|Q2Q060|Q2Q061|Q5EY03|Q5STP1|Q6DQK4|Q9BCQ1|Q9TPX3|Q9XS10	Missense_Mutation	SNP	ENST00000419277.1	37	CCDS4764.1	483	0.22115384615384615	170	0.34552845528455284	20	0.055248618784530384	273	0.4772727272727273	20	0.026385224274406333	G	0.014	-1.597863	0.00857	0.19702	0.01274	ENSG00000231389	ENST00000419277;ENST00000428995;ENST00000448544;ENST00000453337	T;T;T	0.00711	5.8;5.8;5.8	3.04	-6.08	0.02151	MHC class II, alpha/beta chain, N-terminal (1);MHC classes I/II-like antigen recognition protein (1);MHC class II, alpha chain, N-terminal (2);	1.357570	0.05045	U	0.477012	T	0.00109	0.0003	N	0.16903	0.455	0.80722	P	0.0	B	0.13594	0.008	B	0.09377	0.004	T	0.48581	-0.9023	9	0.02654	T	1	.	5.3357	0.15957	0.2685:0.0:0.3496:0.3819	rs1126534;rs2308904;rs3176949;rs3181626;rs60270851	42	P20036	DPA1_HUMAN	V	42	ENSP00000393566:A42V;ENSP00000402872:A42V;ENSP00000390929:A42V	ENSP00000393566:A42V	A	-	2	0	HLA-DPA1	33145617	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.174000	0.01264	-3.564000	0.00140	-3.054000	0.00069	GCG	G|0.875;A|0.125	0.125	strong		0.418	HLA-DPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076071.3	NM_033554	
KRTAP10-11	386678	hgsc.bcm.edu	37	21	46067180	46067180	+	Missense_Mutation	SNP	C	C	T	rs462007	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:46067180C>T	ENST00000334670.8	+	1	850	c.805C>T	c.(805-807)Cgc>Tgc	p.R269C	TSPEAR_ENST00000323084.4_Intron	NM_198692.2	NP_941965.2	P60412	KR10B_HUMAN	keratin associated protein 10-11	269	25 X 5 AA repeats of C-C-X(3).			R -> C (in Ref. 1; BAD01546 and 3; AAI31612). {ECO:0000305}.		keratin filament (GO:0045095)				NS(1)|endometrium(1)|large_intestine(1)|lung(6)|ovary(2)|prostate(1)	12						CAGCTGCTGCCGCCCGGCCTC	0.682													T|||	4087	0.816094	0.9887	0.7954	5008	,	,		19081	0.6796		0.8062	False		,,,				2504	0.7485				p.R269C		Atlas-SNP	.											.	KRTAP10-11	36	.	0			c.C805T						PASS	.	T	,CYS/ARG	4211,193	107.3+/-145.7	2012,187,3	42.0	54.0	50.0		,805	3.0	0.3	21	dbSNP_80	50	6723,1865	319.0+/-313.9	2635,1453,206	no	intron,missense	TSPEAR,KRTAP10-11	NM_144991.2,NM_198692.2	,180	4647,1640,209	TT,TC,CC		21.7163,4.3824,15.8405	,probably-damaging	,269/299	46067180	10934,2058	2202	4294	6496	SO:0001583	missense	386678	exon1			TGCTGCCGCCCGG	AB076359	CCDS42962.1	21q22.3	2006-03-13	2004-07-12	2004-07-14	ENSG00000243489	ENSG00000243489		"""Keratin associated proteins"""	20528	protein-coding gene	gene with protein product			"""keratin associated protein 10-11"""	KRTAP18-11			Standard	NM_198692		Approved	KRTAP18.11, KAP18.11, KAP10.11	uc002zfr.4	P60412	OTTHUMG00000057626	ENST00000334670.8:c.805C>T	21.37:g.46067180C>T	ENSP00000334197:p.Arg269Cys	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	109	107	0.981651	NM_198692	A2RRF9	Missense_Mutation	SNP	ENST00000334670.8	37	CCDS42962.1	1775	0.8127289377289377	480	0.975609756097561	298	0.8232044198895028	383	0.6695804195804196	614	0.8100263852242744	t	8.562	0.877898	0.17395	0.956176	0.782837	ENSG00000243489	ENST00000334670	T	0.00686	5.85	3.93	3.04	0.35103	.	.	.	.	.	T	0.00012	0.0000	M	0.63843	1.955	0.37916	P	0.06845500000000004	D	0.89917	1.0	P	0.61874	0.895	T	0.43410	-0.9393	8	0.54805	T	0.06	.	6.258	0.20884	0.1641:0.725:0.0:0.1109	rs462007;rs58847266	269	P60412	KR10B_HUMAN	C	269	ENSP00000334197:R269C	ENSP00000334197:R269C	R	+	1	0	KRTAP10-11	44891608	0.000000	0.05858	0.334000	0.25495	0.053000	0.15095	-1.248000	0.02890	0.187000	0.20147	-1.295000	0.01343	CGC	C|0.202;T|0.798	0.798	strong		0.682	KRTAP10-11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128029.1	NM_198692	
TMEM173	340061	hgsc.bcm.edu	37	5	138857925	138857925	+	Missense_Mutation	SNP	C	C	G	rs78233829	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:138857925C>G	ENST00000330794.4	-	6	1022	c.689G>C	c.(688-690)gGt>gCt	p.G230A	TMEM173_ENST00000511850.1_5'Flank	NM_198282.2	NP_938023.1	Q86WV6	STING_HUMAN	transmembrane protein 173	230	c-di-GMP-binding domain (CBD).				activation of innate immune response (GO:0002218)|apoptotic process (GO:0006915)|cellular response to exogenous dsRNA (GO:0071360)|cellular response to interferon-beta (GO:0035458)|defense response to virus (GO:0051607)|innate immune response (GO:0045087)|interferon-beta production (GO:0032608)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of protein binding (GO:0032092)|positive regulation of protein import into nucleus, translocation (GO:0033160)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|regulation of type I interferon production (GO:0032479)	cytoplasmic vesicle membrane (GO:0030659)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)|perinuclear region of cytoplasm (GO:0048471)|peroxisome (GO:0005777)|plasma membrane (GO:0005886)	cyclic-di-GMP binding (GO:0035438)|cyclic-GMP-AMP binding (GO:0061507)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|transcription factor binding (GO:0008134)			endometrium(1)|kidney(1)|lung(6)|upper_aerodigestive_tract(1)	9			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			AGCATGGTCACCGGTCTGCTG	0.557													G|||	1342	0.267971	0.2368	0.2983	5008	,	,		19260	0.4058		0.1541	False		,,,				2504	0.2638				p.G230A		Atlas-SNP	.											.	TMEM173	19	.	0			c.G689C						PASS	.	G	ALA/GLY	1046,3360	725.9+/-409.7	118,810,1275	114.0	106.0	109.0		689	1.0	0.0	5	dbSNP_131	109	1218,7382	762.7+/-407.6	91,1036,3173	yes	missense	TMEM173	NM_198282.2	60	209,1846,4448	GG,GC,CC		14.1628,23.7404,17.4074	benign	230/380	138857925	2264,10742	2203	4300	6503	SO:0001583	missense	340061	exon6			TGGTCACCGGTCT		CCDS4215.1	5q31.2	2009-11-06			ENSG00000184584	ENSG00000184584			27962	protein-coding gene	gene with protein product		612374				12477932	Standard	XM_005268445		Approved	FLJ38577, NET23	uc003lep.3	Q86WV6	OTTHUMG00000129239	ENST00000330794.4:c.689G>C	5.37:g.138857925C>G	ENSP00000331288:p.Gly230Ala	Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	119	57	0.478992	NM_198282	A8K3P6|B6EB35|D6RBX0|D6RE01|D6RID9	Missense_Mutation	SNP	ENST00000330794.4	37	CCDS4215.1	551	0.2522893772893773	108	0.21951219512195122	91	0.2513812154696133	238	0.4160839160839161	114	0.1503957783641161	G	5.562	0.288555	0.10513	0.237404	0.141628	ENSG00000184584	ENST00000330794;ENST00000510817	T;T	0.20598	2.06;2.06	5.79	0.964	0.19655	.	1.017410	0.07828	N	0.960847	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	0.45731	-0.9241	9	0.22109	T	0.4	0.8351	5.5191	0.16923	0.4359:0.1359:0.4282:0.0	.	230	Q86WV6	TM173_HUMAN	A	230	ENSP00000331288:G230A;ENSP00000427455:G230A	ENSP00000331288:G230A	G	-	2	0	TMEM173	138838109	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	0.501000	0.22578	-0.103000	0.12175	-0.998000	0.02512	GGT	C|0.807;G|0.193	0.193	strong		0.557	TMEM173-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251338.1	NM_198282	
TRIM31	11074	hgsc.bcm.edu	37	6	30075864	30075864	+	Silent	SNP	A	A	G	rs2023472	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:30075864A>G	ENST00000376734.3	-	6	974	c.849T>C	c.(847-849)caT>caC	p.H283H	TRIM31_ENST00000540829.1_Silent_p.H283H|TRIM31-AS1_ENST00000440874.1_RNA|TRIM31_ENST00000485864.1_5'UTR	NM_007028.3	NP_008959.3	Q9BZY9	TRI31_HUMAN	tripartite motif containing 31	283					innate immune response (GO:0045087)|negative regulation of viral entry into host cell (GO:0046597)|negative regulation of viral transcription (GO:0032897)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein ubiquitination (GO:0016567)|regulation of viral release from host cell (GO:1902186)	mitochondrion (GO:0005739)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)	p.H283H(1)		central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(5)|ovary(2)|prostate(2)|skin(2)	15						TGATGGAGTCATGTCTTGATT	0.438													A|||	3694	0.73762	0.6346	0.7104	5008	,	,		20070	0.869		0.6362	False		,,,				2504	0.865				p.H283H		Atlas-SNP	.											TRIM31,NS,carcinoma,0,1	TRIM31	40	1	1	Substitution - coding silent(1)	prostate(1)	c.T849C						PASS	.	A		1983,1039		647,689,175	75.0	74.0	74.0		849	0.7	0.4	6	dbSNP_94	74	3328,2090		1018,1292,399	yes	coding-synonymous	TRIM31	NM_007028.3		1665,1981,574	GG,GA,AA		38.5751,34.3812,37.0735		283/426	30075864	5311,3129	1511	2709	4220	SO:0001819	synonymous_variant	11074	exon6			GGAGTCATGTCTT	AF230386	CCDS34374.1	6p21.3	2013-01-09	2011-01-25		ENSG00000204616	ENSG00000204616		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	16289	protein-coding gene	gene with protein product		609316	"""tripartite motif-containing 31"""			11331580	Standard	XM_006714977		Approved	RNF, HCGI, C6orf13, HCG1	uc003npg.1	Q9BZY9	OTTHUMG00000031064	ENST00000376734.3:c.849T>C	6.37:g.30075864A>G		Somatic	224	0	0		WXS	Illumina HiSeq	Phase_I	138	68	0.492754	NM_007028	A6NLX6|A9R9Q4|Q53H52|Q5RI37|Q5SRJ7|Q5SRJ8|Q5SS28|Q96AK4|Q96AP8|Q99579|Q9BZY8	Silent	SNP	ENST00000376734.3	37	CCDS34374.1																																																																																			A|0.348;G|0.652	0.652	strong		0.438	TRIM31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076081.2		
LCE1F	353137	hgsc.bcm.edu	37	1	152749091	152749091	+	Missense_Mutation	SNP	C	C	T	rs41268480	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:152749091C>T	ENST00000334371.2	+	1	244	c.244C>T	c.(244-246)Cgg>Tgg	p.R82W		NM_178354.2	NP_848131.1	Q5T754	LCE1F_HUMAN	late cornified envelope 1F	82	Poly-Arg.				keratinization (GO:0031424)					kidney(1)|large_intestine(2)|lung(7)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	15	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)			CCACCACAGACGGCGTAGGTC	0.706													.|||	455	0.0908546	0.0053	0.1311	5008	,	,		13505	0.0278		0.2117	False		,,,				2504	0.1186				p.R82W		Atlas-SNP	.											LCE1F,right_lower_lobe,carcinoma,-1,1	LCE1F	42	1	0			c.C244T						PASS	.	C	TRP/ARG	161,4241		5,151,2045	22.0	26.0	25.0		244	4.4	1.0	1	dbSNP_127	25	1846,6746		213,1420,2663	no	missense	LCE1F	NM_178354.2	101	218,1571,4708	TT,TC,CC		21.4851,3.6574,15.4456	probably-damaging	82/119	152749091	2007,10987	2201	4296	6497	SO:0001583	missense	353137	exon1			CACAGACGGCGTA		CCDS1023.1	1q21.3	2008-02-05			ENSG00000240386	ENSG00000240386		"""Late cornified envelopes"""	29467	protein-coding gene	gene with protein product		612608				11698679	Standard	NM_178354		Approved	LEP6	uc010pdv.2	Q5T754	OTTHUMG00000012403	ENST00000334371.2:c.244C>T	1.37:g.152749091C>T	ENSP00000334187:p.Arg82Trp	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	63	36	0.571429	NM_178354		Missense_Mutation	SNP	ENST00000334371.2	37	CCDS1023.1	229	0.10485347985347986	3	0.006097560975609756	43	0.11878453038674033	14	0.024475524475524476	169	0.22295514511873352	C	10.38	1.333655	0.24167	0.036574	0.214851	ENSG00000240386	ENST00000334371	T	0.03831	3.79	4.45	4.45	0.53987	.	.	.	.	.	T	0.03011	0.0089	L	0.50333	1.59	0.40610	P	0.01833600000000002	D	0.54772	0.968	B	0.40636	0.335	T	0.35176	-0.9799	8	0.87932	D	0	.	12.7727	0.57429	0.0:1.0:0.0:0.0	rs41268480	82	Q5T754	LCE1F_HUMAN	W	82	ENSP00000334187:R82W	ENSP00000334187:R82W	R	+	1	2	LCE1F	151015715	0.032000	0.19561	0.964000	0.40570	0.487000	0.33371	0.406000	0.21032	2.445000	0.82738	0.557000	0.71058	CGG	C|0.867;T|0.133	0.133	strong		0.706	LCE1F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034523.2	NM_178354	
DOCK2	1794	hgsc.bcm.edu	37	5	169435713	169435713	+	Silent	SNP	A	A	C	rs2287727	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:169435713A>C	ENST00000256935.8	+	32	3275	c.3195A>C	c.(3193-3195)ctA>ctC	p.L1065L	DOCK2_ENST00000520908.1_Silent_p.L557L|DOCK2_ENST00000523351.1_3'UTR|DOCK2_ENST00000540750.1_Silent_p.L126L	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	242	0	0		WXS	Illumina HiSeq	Phase_I	241	240	0.995851	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	
VCX3A	51481	hgsc.bcm.edu	37	X	6451834	6451834	+	Silent	SNP	C	C	T	rs146638597		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:6451834C>T	ENST00000381089.3	-	3	819	c.513G>A	c.(511-513)gaG>gaA	p.E171E	VCX3A_ENST00000398729.1_Silent_p.E151E	NM_016379.3	NP_057463.2	Q9NNX9	VCX3_HUMAN	variable charge, X-linked 3A	171	8 X 10 AA tandem repeats of L-S-Q-E-S- [EQ]-V-E-E-P.|Glu-rich.				brain development (GO:0007420)	nucleolus (GO:0005730)|nucleus (GO:0005634)				NS(1)|lung(2)|pancreas(1)	4						TCAGTGGTTCCTCCACCTGGC	0.587																																					p.E171E		Atlas-SNP	.											.	VCX3A	17	.	0			c.G513A						PASS	.						230.0	203.0	212.0					X																	6451834		2203	4296	6499	SO:0001819	synonymous_variant	51481	exon3			TGGTTCCTCCACC	AF159128	CCDS35199.1	Xp22.31	2008-02-05	2005-01-11	2005-01-12	ENSG00000169059	ENSG00000169059			18159	protein-coding gene	gene with protein product		300533	"""variable charge, X-linked 3"""	VCX3		10607842	Standard	NM_016379		Approved	VCX-8r, VCX-8R, VCX-A	uc004crs.3	Q9NNX9	OTTHUMG00000021097	ENST00000381089.3:c.513G>A	X.37:g.6451834C>T		Somatic	1050	0	0		WXS	Illumina HiSeq	Phase_I	927	82	0.0884574	NM_016379	Q9P0H4	Silent	SNP	ENST00000381089.3	37	CCDS35199.1																																																																																			.	.	weak		0.587	VCX3A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055679.1	NM_016379	
PCSK1N	27344	hgsc.bcm.edu	37	X	48690749	48690749	+	Silent	SNP	C	C	T	rs11538178		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:48690749C>T	ENST00000218230.5	-	2	217	c.117G>A	c.(115-117)gaG>gaA	p.E39E	PCSK1N_ENST00000478242.1_5'UTR	NM_013271.2	NP_037403.1	Q9UHG2	PCSK1_HUMAN	proprotein convertase subtilisin/kexin type 1 inhibitor	39	ProSAAS(1-180). {ECO:0000250}.				neuropeptide signaling pathway (GO:0007218)|peptide hormone processing (GO:0016486)|response to cold (GO:0009409)|response to dietary excess (GO:0002021)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|secretory granule (GO:0030141)|trans-Golgi network (GO:0005802)	endopeptidase inhibitor activity (GO:0004866)|receptor binding (GO:0005102)|serine-type endopeptidase inhibitor activity (GO:0004867)										GGCCGCGGGGCTCCTGCGGGA	0.682													c|||	1198	0.317351	0.5234	0.0807	3775	,	,		6872	0.1151		0.0666	False		,,,				2504	0.273				p.E39E		Atlas-SNP	.											.	PCSK1N	6	.	0			c.G117A						PASS	.			1039,1413		118,601,202,343,126	2.0	2.0	2.0		117	0.3	0.9	X	dbSNP_120	2	346,4094		11,224,100,1486,898	yes	coding-synonymous	PCSK1N	NM_013271.2		129,825,302,1829,1024	TT,TC,T,CC,C		7.7928,42.3736,20.0958		39/261	48690749	1385,5507	1390	2719	4109	SO:0001819	synonymous_variant	27344	exon2			GCGGGGCTCCTGC	AF181562	CCDS14307.1	Xp11.23	2008-07-28			ENSG00000102109	ENSG00000102109			17301	protein-coding gene	gene with protein product		300399				10632593	Standard	NM_013271		Approved	SAAS	uc004dkz.4	Q9UHG2	OTTHUMG00000034502	ENST00000218230.5:c.117G>A	X.37:g.48690749C>T		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	34	31	0.911765	NM_013271	Q4VC04	Silent	SNP	ENST00000218230.5	37	CCDS14307.1																																																																																			C|0.763;T|0.237	0.237	strong		0.682	PCSK1N-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083444.1	NM_013271	
OBSCN	84033	hgsc.bcm.edu	37	1	228468244	228468244	+	Silent	SNP	G	G	A	rs12061320	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:228468244G>A	ENST00000422127.1	+	30	7988	c.7944G>A	c.(7942-7944)gtG>gtA	p.V2648V	OBSCN_ENST00000284548.11_Silent_p.V2648V|OBSCN_ENST00000359599.6_Silent_p.V1495V|OBSCN_ENST00000570156.2_Silent_p.V3077V|OBSCN_ENST00000366709.4_5'UTR|OBSCN_ENST00000366707.4_5'UTR	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	2648	Ig-like 26.				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)				AGCCGGTGGTGTTCCTGAAGG	0.642													g|||	569	0.113618	0.115	0.0173	5008	,	,		16189	0.3185		0.0268	False		,,,				2504	0.0583				p.V3077V		Atlas-SNP	.											.	OBSCN	2142	.	0			c.G9231A						PASS	.		,	452,3880		24,404,1738	46.0	54.0	51.0		7944,7944	2.2	1.0	1	dbSNP_120	51	156,8368		0,156,4106	no	coding-synonymous,coding-synonymous	OBSCN	NM_001098623.1,NM_052843.2	,	24,560,5844	AA,AG,GG		1.8301,10.434,4.7293	,	2648/7969,2648/6621	228468244	608,12248	2166	4262	6428	SO:0001819	synonymous_variant	84033	exon35			GGTGGTGTTCCTG	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.7944G>A	1.37:g.228468244G>A		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	128	64	0.5	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|0.865;A|0.135	0.135	strong		0.642	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
YTHDF1	54915	hgsc.bcm.edu	37	20	61834092	61834092	+	Silent	SNP	G	G	A	rs41282994	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:61834092G>A	ENST00000370339.3	-	4	1541	c.1200C>T	c.(1198-1200)gaC>gaT	p.D400D	YTHDF1_ENST00000370334.4_Intron|YTHDF1_ENST00000370333.4_Silent_p.D350D	NM_017798.3	NP_060268.2	Q9BYJ9	YTHD1_HUMAN	YTH domain family, member 1	400	YTH. {ECO:0000255|PROSITE- ProRule:PRU00225}.						N6-methyladenosine-containing RNA binding (GO:1990247)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|endometrium(6)|kidney(1)|large_intestine(5)|lung(7)|ovary(2)	24						GGTGGATGTCGTCCTCAGAGT	0.542													G|||	281	0.0561102	0.0038	0.0648	5008	,	,		18268	0.001		0.1153	False		,,,				2504	0.1166				p.D400D		Atlas-SNP	.											.	YTHDF1	66	.	0			c.C1200T						PASS	.	G		93,4313	76.2+/-114.5	2,89,2112	99.0	87.0	91.0		1200	-7.2	0.1	20	dbSNP_127	91	886,7714	199.4+/-243.5	43,800,3457	no	coding-synonymous	YTHDF1	NM_017798.3		45,889,5569	AA,AG,GG		10.3023,2.1108,7.5273		400/560	61834092	979,12027	2203	4300	6503	SO:0001819	synonymous_variant	54915	exon4			GATGTCGTCCTCA	AK000398	CCDS13511.1	20q13.33	2010-03-15	2004-11-16	2004-06-04	ENSG00000149658	ENSG00000149658			15867	protein-coding gene	gene with protein product			"""YTH domain family 1"""	C20orf21			Standard	NM_017798		Approved	FLJ20391	uc002yeh.3	Q9BYJ9	OTTHUMG00000032955	ENST00000370339.3:c.1200C>T	20.37:g.61834092G>A		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	62	26	0.419355	NM_017798	Q8N3G5|Q8TBT1|Q96AN4|Q96S57|Q9BTI7|Q9NX79	Silent	SNP	ENST00000370339.3	37	CCDS13511.1																																																																																			G|0.930;A|0.070	0.070	strong		0.542	YTHDF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080110.2	NM_017798	
GIGYF1	64599	hgsc.bcm.edu	37	7	100281768	100281768	+	Silent	SNP	T	T	C	rs221794	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:100281768T>C	ENST00000275732.5	-	15	2952	c.1743A>G	c.(1741-1743)ccA>ccG	p.P581P	GIGYF1_ENST00000471340.2_5'Flank	NM_022574.4	NP_072096.2	O75420	PERQ1_HUMAN	GRB10 interacting GYF protein 1	581	Gln-rich.				insulin-like growth factor receptor signaling pathway (GO:0048009)					central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(6)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	23	Lung NSC(181;0.035)|all_lung(186;0.0509)|Esophageal squamous(72;0.0817)					GCGCGCACTGTGGGAGCTGGC	0.692													C|||	4315	0.861621	0.8812	0.902	5008	,	,		11029	0.9206		0.8231	False		,,,				2504	0.7853				p.P581P		Atlas-SNP	.											GIGYF1_ENST00000539430,NS,carcinoma,0,2	GIGYF1	113	2	0			c.A1743G						PASS	.	C		3847,553		1684,479,37	21.0	26.0	25.0		1743	-2.8	0.2	7	dbSNP_79	25	7278,1320		3093,1092,114	no	coding-synonymous	GIGYF1	NM_022574.4		4777,1571,151	CC,CT,TT		15.3524,12.5682,14.4099		581/1036	100281768	11125,1873	2200	4299	6499	SO:0001819	synonymous_variant	64599	exon15			GCACTGTGGGAGC	AF053356	CCDS34708.1	7q22	2008-02-11	2008-02-11	2008-02-11	ENSG00000146830	ENSG00000146830			9126	protein-coding gene	gene with protein product	"""GYF domain containing 1"""	612064	"""PERQ amino acid rich, with GYF domain 1"""	PERQ1		9799793, 12771153	Standard	NM_022574		Approved	GYF1	uc003uwg.1	O75420	OTTHUMG00000157036	ENST00000275732.5:c.1743A>G	7.37:g.100281768T>C		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	111	53	0.477477	NM_022574	Q6Y7W7|Q8WZ38	Silent	SNP	ENST00000275732.5	37	CCDS34708.1																																																																																			T|0.141;C|0.859	0.859	strong		0.692	GIGYF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347205.2	NM_022574	
NUP210	23225	hgsc.bcm.edu	37	3	13364836	13364836	+	Missense_Mutation	SNP	C	C	T	rs199752879		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:13364836C>T	ENST00000254508.5	-	34	4823	c.4741G>A	c.(4741-4743)Gtg>Atg	p.V1581M		NM_024923.2	NP_079199.2	Q8TEM1	PO210_HUMAN	nucleoporin 210kDa	1581					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)		p.V1581M(1)		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)					CTGTCTCCCACGGCAACAATC	0.582																																					p.V1581M		Atlas-SNP	.											NUP210,NS,carcinoma,0,1	NUP210	182	1	1	Substitution - Missense(1)	liver(1)	c.G4741A						PASS	.	C	MET/VAL	0,4406		0,0,2203	138.0	139.0	139.0		4741	-4.2	0.0	3		139	5,8595	4.3+/-15.6	0,5,4295	yes	missense	NUP210	NM_024923.2	21	0,5,6498	TT,TC,CC		0.0581,0.0,0.0384	possibly-damaging	1581/1888	13364836	5,13001	2203	4300	6503	SO:0001583	missense	23225	exon34			CTCCCACGGCAAC	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.4741G>A	3.37:g.13364836C>T	ENSP00000254508:p.Val1581Met	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	64	23	0.359375	NM_024923	A6NN56|O94980|Q6NXG6|Q8NBJ1|Q9H6C8|Q9UFP3	Missense_Mutation	SNP	ENST00000254508.5	37	CCDS33704.1	.	.	.	.	.	.	.	.	.	.	C	11.56	1.674605	0.29693	0.0	5.81E-4	ENSG00000132182	ENST00000254508	T	0.04970	3.52	5.54	-4.17	0.03857	.	0.660669	0.15319	N	0.268660	T	0.04182	0.0116	L	0.46157	1.445	0.09310	N	1	B	0.17268	0.021	B	0.08055	0.003	T	0.36212	-0.9757	10	0.48119	T	0.1	-10.586	0.6247	0.00784	0.3136:0.1703:0.125:0.3911	.	1581	Q8TEM1	PO210_HUMAN	M	1581	ENSP00000254508:V1581M	ENSP00000254508:V1581M	V	-	1	0	NUP210	13339836	0.028000	0.19301	0.020000	0.16555	0.749000	0.42624	-0.160000	0.10041	-0.685000	0.05177	-0.137000	0.14449	GTG	.	.	weak		0.582	NUP210-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340085.1	NM_024923	
AP3B1	8546	hgsc.bcm.edu	37	5	77412011	77412011	+	Silent	SNP	A	A	G	rs42360	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:77412011A>G	ENST00000255194.6	-	18	2191	c.2016T>C	c.(2014-2016)gcT>gcC	p.A672A	AP3B1_ENST00000519295.1_Silent_p.A623A	NM_001271769.1	NP_001258698.1	O00203	AP3B1_HUMAN	adaptor-related protein complex 3, beta 1 subunit	672					anterograde axon cargo transport (GO:0008089)|anterograde synaptic vesicle transport (GO:0048490)|antigen processing and presentation, exogenous lipid antigen via MHC class Ib (GO:0048007)|blood coagulation (GO:0007596)|intracellular protein transport (GO:0006886)|melanosome organization (GO:0032438)|positive regulation of NK T cell differentiation (GO:0051138)|protein targeting to lysosome (GO:0006622)	AP-3 adaptor complex (GO:0030123)|cytoplasmic vesicle (GO:0031410)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	GTP-dependent protein binding (GO:0030742)|protein phosphatase binding (GO:0019903)			breast(5)|central_nervous_system(2)|cervix(1)|endometrium(3)|large_intestine(12)|lung(12)|prostate(1)|skin(2)|urinary_tract(1)	39		all_lung(232;0.000397)|Lung NSC(167;0.00106)|Ovarian(174;0.0105)|Prostate(461;0.215)		OV - Ovarian serous cystadenocarcinoma(54;8.23e-47)|Epithelial(54;2.74e-41)|all cancers(79;4.8e-36)		AAAACTTCTTAGCAGAATTCT	0.338									Hermansky-Pudlak syndrome				A|||	946	0.188898	0.2383	0.3271	5008	,	,		16072	0.0754		0.2127	False		,,,				2504	0.1166				p.A672A		Atlas-SNP	.											AP3B1,NS,carcinoma,0,1	AP3B1	94	1	0			c.T2016C						PASS	.	A		1135,3271	401.5+/-332.0	163,809,1231	87.0	91.0	89.0		2016	3.6	0.8	5	dbSNP_76	89	2013,6587	351.2+/-328.2	249,1515,2536	no	coding-synonymous	AP3B1	NM_003664.3		412,2324,3767	GG,GA,AA		23.407,25.7603,24.2042		672/1095	77412011	3148,9858	2203	4300	6503	SO:0001819	synonymous_variant	8546	exon18	Familial Cancer Database	HPS, HPS1-8	CTTCTTAGCAGAA	U81504	CCDS4041.1, CCDS64186.1	5q14.1	2014-09-17			ENSG00000132842	ENSG00000132842			566	protein-coding gene	gene with protein product		603401				9182526, 9151686	Standard	NM_003664		Approved	ADTB3A, HPS2	uc003kfj.4	O00203	OTTHUMG00000106919	ENST00000255194.6:c.2016T>C	5.37:g.77412011A>G		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	120	77	0.641667	NM_003664	E5RJ68|O00580|Q7Z393|Q9HD66	Silent	SNP	ENST00000255194.6	37	CCDS4041.1																																																																																			A|0.776;C|0.001	.	strong		0.338	AP3B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000225548.2		
ABCA7	10347	hgsc.bcm.edu	37	19	1047537	1047537	+	Missense_Mutation	SNP	A	A	C	rs3752239	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:1047537A>C	ENST00000263094.6	+	16	2384	c.2153A>C	c.(2152-2154)aAc>aCc	p.N718T	ABCA7_ENST00000435683.2_Missense_Mutation_p.N580T|ABCA7_ENST00000533574.1_3'UTR|ABCA7_ENST00000433129.1_Missense_Mutation_p.N718T	NM_019112.3	NP_061985.2	Q8IZY2	ABCA7_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 7	718			N -> T (in dbSNP:rs3752239). {ECO:0000269|PubMed:12111378}.		apolipoprotein A-I-mediated signaling pathway (GO:0038027)|ATP catabolic process (GO:0006200)|cholesterol efflux (GO:0033344)|high-density lipoprotein particle assembly (GO:0034380)|memory (GO:0007613)|negative regulation of amyloid precursor protein biosynthetic process (GO:0042985)|negative regulation of ATPase activity (GO:0032780)|negative regulation of beta-amyloid formation (GO:1902430)|peptide cross-linking (GO:0018149)|phagocytosis (GO:0006909)|phospholipid efflux (GO:0033700)|phospholipid scrambling (GO:0017121)|positive regulation of ATPase activity (GO:0032781)|positive regulation of beta-amyloid clearance (GO:1900223)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of engulfment of apoptotic cell (GO:1901076)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of phagocytosis (GO:0050766)|positive regulation of phospholipid efflux (GO:1902995)|protein localization to nucleus (GO:0034504)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|ATP-binding cassette (ABC) transporter complex (GO:0043190)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|phagocytic cup (GO:0001891)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	apolipoprotein A-I receptor activity (GO:0034188)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|phospholipid transporter activity (GO:0005548)|transporter activity (GO:0005215)			NS(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(7)|lung(22)|ovary(1)|pancreas(7)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	65		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CAGTGGCACAACGTGGGCACC	0.701													A|||	296	0.0591054	0.0023	0.0086	5008	,	,		11114	0.1855		0.0408	False		,,,				2504	0.0603				p.N718T		Atlas-SNP	.											.	ABCA7	174	.	0			c.A2153C						PASS	.		THR/ASN	30,4350		0,30,2160	17.0	21.0	20.0		2153	3.7	0.7	19	dbSNP_107	20	320,8262		4,312,3975	yes	missense	ABCA7	NM_019112.3	65	4,342,6135	CC,CA,AA		3.7287,0.6849,2.7002	benign	718/2147	1047537	350,12612	2190	4291	6481	SO:0001583	missense	10347	exon16			GGCACAACGTGGG	AF328787	CCDS12055.1	19p13.3	2012-03-14			ENSG00000064687	ENSG00000064687		"""ATP binding cassette transporters / subfamily A"""	37	protein-coding gene	gene with protein product		605414					Standard	NM_019112		Approved	ABCX	uc002lqw.4	Q8IZY2	OTTHUMG00000167547	ENST00000263094.6:c.2153A>C	19.37:g.1047537A>C	ENSP00000263094:p.Asn718Thr	Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	69	30	0.434783	NM_019112	Q96S58|Q9BZC4|Q9NR73|Q9UKP8	Missense_Mutation	SNP	ENST00000263094.6	37	CCDS12055.1	127	0.05815018315018315	2	0.0040650406504065045	3	0.008287292817679558	91	0.1590909090909091	31	0.040897097625329816	a	18.21	3.573161	0.65765	0.006849	0.037287	ENSG00000064687	ENST00000263094;ENST00000433129	D;D	0.86097	-2.07;-2.07	4.69	3.67	0.42095	.	.	.	.	.	T	0.01800	0.0057	L	0.60012	1.86	0.34310	P	0.314682	P;P	0.35944	0.475;0.529	B;P	0.48524	0.182;0.58	T	0.47169	-0.9138	8	0.33141	T	0.24	.	8.5128	0.33229	0.904:0.0:0.096:0.0	rs3752239	580;718	Q8IZY2-2;Q8IZY2	.;ABCA7_HUMAN	T	718	ENSP00000263094:N718T;ENSP00000414062:N718T	ENSP00000263094:N718T	N	+	2	0	ABCA7	998537	1.000000	0.71417	0.717000	0.30585	0.779000	0.44077	5.181000	0.65054	0.638000	0.30545	0.330000	0.21533	AAC	A|0.934;C|0.066	0.066	strong		0.701	ABCA7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000394993.1	NM_019112	
PPIC	5480	hgsc.bcm.edu	37	5	122359640	122359640	+	Missense_Mutation	SNP	T	T	C	rs451195	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:122359640T>C	ENST00000306442.4	-	5	684	c.569A>G	c.(568-570)aAc>aGc	p.N190S	RN7SL689P_ENST00000577215.1_RNA	NM_000943.4	NP_000934.1	P45877	PPIC_HUMAN	peptidylprolyl isomerase C (cyclophilin C)	190	PPIase cyclophilin-type. {ECO:0000255|PROSITE-ProRule:PRU00156}.		N -> S (in dbSNP:rs451195). {ECO:0000269|Ref.2}.		protein folding (GO:0006457)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	cyclosporin A binding (GO:0016018)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			endometrium(1)|kidney(1)|large_intestine(1)|lung(1)|ovary(1)|urinary_tract(1)	6		all_cancers(142;0.0168)|Prostate(80;0.0322)|Lung NSC(810;0.102)|all_lung(232;0.163)	KIRC - Kidney renal clear cell carcinoma(527;0.0897)|Kidney(363;0.137)	OV - Ovarian serous cystadenocarcinoma(64;0.000331)|Epithelial(69;0.000553)|all cancers(49;0.00505)	L-Proline(DB00172)	GATCGAGCAGTTGGTGAGTGG	0.473													T|||	707	0.141174	0.0348	0.1902	5008	,	,		16612	0.0129		0.339	False		,,,				2504	0.1789				p.N190S	Ovarian(99;690 1502 20765 45543 49568)	Atlas-SNP	.											.	PPIC	18	.	0			c.A569G						PASS	.	T	SER/ASN	378,4028	189.9+/-215.9	14,350,1839	270.0	241.0	250.0		569	4.7	1.0	5	dbSNP_80	250	2982,5618	461.9+/-365.5	509,1964,1827	yes	missense	PPIC	NM_000943.4	46	523,2314,3666	CC,CT,TT		34.6744,8.5792,25.8342	benign	190/213	122359640	3360,9646	2203	4300	6503	SO:0001583	missense	5480	exon5			GAGCAGTTGGTGA	S71018	CCDS4133.1	5q23.2	2008-02-05			ENSG00000168938	ENSG00000168938	5.2.1.8		9256	protein-coding gene	gene with protein product		123842				1383094, 8031755	Standard	NM_000943		Approved	CYPC	uc003kth.3	P45877	OTTHUMG00000128921	ENST00000306442.4:c.569A>G	5.37:g.122359640T>C	ENSP00000303057:p.Asn190Ser	Somatic	240	0	0		WXS	Illumina HiSeq	Phase_I	240	107	0.445833	NM_000943	A4LBB5	Missense_Mutation	SNP	ENST00000306442.4	37	CCDS4133.1	344	0.1575091575091575	16	0.032520325203252036	71	0.19613259668508287	5	0.008741258741258742	252	0.3324538258575198	T	16.06	3.015510	0.54468	0.085792	0.346744	ENSG00000168938	ENST00000306442	T	0.35421	1.31	5.93	4.74	0.60224	Peptidyl-prolyl cis-trans isomerase, cyclophilin-type (3);Cyclophilin-like (1);	0.087968	0.85682	D	0.000000	T	0.00012	0.0000	N	0.10837	0.055	0.35742	P	0.18126399999999998	B	0.06786	0.001	B	0.04013	0.001	T	0.38672	-0.9650	9	0.39692	T	0.17	.	13.2054	0.59793	0.0:0.0:0.133:0.867	rs451195;rs17388196;rs52837765;rs60389846;rs451195	190	P45877	PPIC_HUMAN	S	190	ENSP00000303057:N190S	ENSP00000303057:N190S	N	-	2	0	PPIC	122387539	1.000000	0.71417	0.998000	0.56505	0.958000	0.62258	4.760000	0.62235	1.035000	0.39972	0.533000	0.62120	AAC	A|0.005;C|0.208	0.208	strong		0.473	PPIC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250898.2	NM_000943	
SCFD2	152579	hgsc.bcm.edu	37	4	54218834	54218834	+	Missense_Mutation	SNP	G	G	A	rs147606542	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:54218834G>A	ENST00000401642.3	-	2	1071	c.938C>T	c.(937-939)gCg>gTg	p.A313V	SCFD2_ENST00000388940.4_Missense_Mutation_p.A313V	NM_152540.3	NP_689753.2	Q8WU76	SCFD2_HUMAN	sec1 family domain containing 2	313					protein transport (GO:0015031)|vesicle docking involved in exocytosis (GO:0006904)			p.A313V(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)			TGCAGTGAGCGCTATCATGTT	0.428													G|||	64	0.0127796	0.0008	0.0	5008	,	,		19473	0.0		0.001	False		,,,				2504	0.0634				p.A313V		Atlas-SNP	.											SCFD2,NS,NS,0,1	SCFD2	78	1	1	Substitution - Missense(1)	pancreas(1)	c.C938T						scavenged	.	G	VAL/ALA	2,4404	4.2+/-10.8	0,2,2201	182.0	157.0	166.0		938	4.2	0.9	4	dbSNP_134	166	21,8579	16.0+/-53.3	0,21,4279	yes	missense	SCFD2	NM_152540.3	64	0,23,6480	AA,AG,GG		0.2442,0.0454,0.1768	benign	313/685	54218834	23,12983	2203	4300	6503	SO:0001583	missense	152579	exon2			GTGAGCGCTATCA	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.938C>T	4.37:g.54218834G>A	ENSP00000384182:p.Ala313Val	Somatic	207	1	0.00483092		WXS	Illumina HiSeq	Phase_I	196	90	0.459184	NM_152540	Q8N5F3|Q8N8H0|Q96ED3	Missense_Mutation	SNP	ENST00000401642.3	37	CCDS33984.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	9.740	1.164726	0.21538	4.54E-4	0.002442	ENSG00000184178	ENST00000401642;ENST00000388940;ENST00000503450	D;D	0.85629	-2.01;-2.01	5.33	4.15	0.48705	.	0.060828	0.64402	D	0.000005	T	0.70081	0.3183	N	0.08118	0	0.21553	N	0.999646	B;B	0.13594	0.008;0.005	B;B	0.12837	0.008;0.003	T	0.56890	-0.7904	10	0.30078	T	0.28	.	11.6001	0.50997	0.0:0.0:0.1497:0.8503	.	313;313	Q8WU76-2;Q8WU76	.;SCFD2_HUMAN	V	313;313;6	ENSP00000384182:A313V;ENSP00000373592:A313V	ENSP00000373592:A313V	A	-	2	0	SCFD2	53913591	0.999000	0.42202	0.921000	0.36526	0.006000	0.05464	3.548000	0.53670	0.849000	0.35215	-0.357000	0.07601	GCG	G|0.998;A|0.002	0.002	strong		0.428	SCFD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361311.3	NM_152540	
CFHR3	10878	hgsc.bcm.edu	37	1	196759282	196759282	+	Missense_Mutation	SNP	C	C	T	rs138675433		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:196759282C>T	ENST00000367425.4	+	5	813	c.721C>T	c.(721-723)Ccc>Tcc	p.P241S	CFHR3_ENST00000391985.3_Missense_Mutation_p.P180S	NM_021023.5	NP_066303.2	Q02985	FHR3_HUMAN	complement factor H-related 3	241	Sushi 4. {ECO:0000255|PROSITE- ProRule:PRU00302}.			P -> S (in Ref. 1; CAA48639). {ECO:0000305}.		blood microparticle (GO:0072562)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)		p.P241S(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(4)|lung(6)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	18						CCAATGCCAGCCCTACTATGA	0.428																																					p.P241S		Atlas-SNP	.											CFHR3,NS,carcinoma,0,1	CFHR3	52	1	1	Substitution - Missense(1)	prostate(1)	c.C721T						scavenged	.						101.0	148.0	134.0					1																	196759282		1754	4010	5764	SO:0001583	missense	10878	exon5			TGCCAGCCCTACT	X68679	CCDS30958.1, CCDS53453.1	1q32	2014-09-17		2006-02-28	ENSG00000116785	ENSG00000116785		"""Complement system"""	16980	protein-coding gene	gene with protein product	"""complement factor H related 3"""	605336		CFHL3		8428964, 10380701	Standard	NM_021023		Approved	FHR-3, HLF4, FHR3, DOWN16	uc001gtl.3	Q02985	OTTHUMG00000035929	ENST00000367425.4:c.721C>T	1.37:g.196759282C>T	ENSP00000356395:p.Pro241Ser	Somatic	327	3	0.00917431		WXS	Illumina HiSeq	Phase_I	9	7	0.777778	NM_021023	B4DPR0|Q9UJ16	Missense_Mutation	SNP	ENST00000367425.4	37	CCDS30958.1	487	0.222985347985348	102	0.2073170731707317	61	0.1685082872928177	231	0.40384615384615385	93	0.12269129287598944	T	0.008	-1.884513	0.00532	.	.	ENSG00000116785	ENST00000367425;ENST00000391985	T;T	0.65178	-0.14;-0.14	3.27	-6.54	0.01860	Complement control module (2);Sushi/SCR/CCP (3);	.	.	.	.	T	0.00012	0.0000	N	0.01668	-0.77	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.09377	0.002;0.004	T	0.02398	-1.1165	8	0.06757	T	0.87	.	1.7706	0.03011	0.5551:0.1977:0.1048:0.1423	.	180;241	B4DPR0;Q02985	.;FHR3_HUMAN	S	241;180	ENSP00000356395:P241S;ENSP00000375845:P180S	ENSP00000356395:P241S	P	+	1	0	CFHR3	195025905	0.000000	0.05858	0.001000	0.08648	0.042000	0.13812	-3.343000	0.00504	-3.939000	0.00089	-1.461000	0.01025	CCC	T|0.236;G|0.236	0.236	strong		0.428	CFHR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087505.2	NM_021023	
ADAMDEC1	27299	hgsc.bcm.edu	37	8	24256470	24256470	+	Silent	SNP	C	C	T	rs2291577	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:24256470C>T	ENST00000256412.4	+	9	1066	c.846C>T	c.(844-846)agC>agT	p.S282S	RP11-624C23.1_ENST00000519689.1_RNA|RP11-624C23.1_ENST00000523578.1_RNA|ADAMDEC1_ENST00000522298.1_Silent_p.S203S|ADAMDEC1_ENST00000538205.1_Silent_p.S203S	NM_014479.3	NP_055294.1	O15204	ADEC1_HUMAN	ADAM-like, decysin 1	282	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				immune response (GO:0006955)|negative regulation of cell adhesion (GO:0007162)	extracellular region (GO:0005576)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|large_intestine(4)|skin(2)|stomach(1)	9		Prostate(55;0.0181)		Colorectal(74;0.016)|COAD - Colon adenocarcinoma(73;0.0646)|BRCA - Breast invasive adenocarcinoma(99;0.168)		TGGTGCCCAGCGCAAGCACCA	0.483													C|||	1467	0.292931	0.0968	0.4539	5008	,	,		19362	0.2034		0.4235	False		,,,				2504	0.4018				p.S282S	Ovarian(147;687 1849 3699 25981 31337)	Atlas-SNP	.											.	ADAMDEC1	69	.	0			c.C846T						PASS	.	C	,,	674,3732	286.3+/-278.7	52,570,1581	118.0	110.0	113.0		609,609,846	-0.4	0.0	8	dbSNP_100	113	3783,4817	536.6+/-383.0	826,2131,1343	no	coding-synonymous,coding-synonymous,coding-synonymous	ADAMDEC1	NM_001145271.1,NM_001145272.1,NM_014479.3	,,	878,2701,2924	TT,TC,CC		43.9884,15.2973,34.2688	,,	203/392,203/392,282/471	24256470	4457,8549	2203	4300	6503	SO:0001819	synonymous_variant	27299	exon9			GCCCAGCGCAAGC	Y13323	CCDS6044.1, CCDS55212.1	8p12	2008-08-07			ENSG00000134028	ENSG00000134028			16299	protein-coding gene	gene with protein product		606393				9271581, 12037602	Standard	NM_001145271		Approved	M12.219	uc003xdz.2	O15204	OTTHUMG00000097858	ENST00000256412.4:c.846C>T	8.37:g.24256470C>T		Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	159	111	0.698113	NM_014479	B7ZAK5	Silent	SNP	ENST00000256412.4	37	CCDS6044.1																																																																																			C|0.670;T|0.330	0.330	strong		0.483	ADAMDEC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215149.2	NM_014479	
DNAH14	127602	hgsc.bcm.edu	37	1	225237950	225237950	+	Missense_Mutation	SNP	A	A	G	rs78320839	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:225237950A>G	ENST00000445597.2	+	12	1864	c.1864A>G	c.(1864-1866)Atc>Gtc	p.I622V	DNAH14_ENST00000439375.2_Missense_Mutation_p.I651V|DNAH14_ENST00000430092.1_Missense_Mutation_p.I651V			Q0VDD8	DYH14_HUMAN	dynein, axonemal, heavy chain 14	622					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						CCAGCTGTCTATCTTCATTGA	0.343													A|||	43	0.00858626	0.0008	0.0101	5008	,	,		16907	0.0129		0.007	False		,,,				2504	0.0153				p.I651V		Atlas-SNP	.											.	DNAH14	300	.	0			c.A1951G						PASS	.	A	VAL/ILE	2,1382		0,2,690	169.0	139.0	148.0		1951	-4.1	0.0	1	dbSNP_131	148	58,3124		1,56,1534	yes	missense	DNAH14	NM_001373.1	29	1,58,2224	GG,GA,AA		1.8228,0.1445,1.3141	benign	651/4516	225237950	60,4506	692	1591	2283	SO:0001583	missense	127602	exon16			CTGTCTATCTTCA	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.1864A>G	1.37:g.225237950A>G	ENSP00000409472:p.Ile622Val	Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	181	80	0.441989	NM_001373	A6NG62|A6NNL2|Q0VDD9|Q4VXC7|Q4VXG4|Q4VXG5|Q5VU33|Q5VU34	Missense_Mutation	SNP	ENST00000445597.2	37		20	0.009157509157509158	1	0.0020325203252032522	6	0.016574585635359115	9	0.015734265734265736	4	0.005277044854881266	A	14.53	2.563703	0.45694	0.001445	0.018228	ENSG00000185842	ENST00000445597;ENST00000430092;ENST00000439375	T;T;T	0.27890	2.61;1.64;1.64	5.49	-4.13	0.03904	.	.	.	.	.	T	0.06050	0.0157	N	0.08118	0	0.09310	N	0.999998	B	0.10296	0.003	B	0.12156	0.007	T	0.32134	-0.9918	9	0.21014	T	0.42	.	7.8316	0.29347	0.4385:0.1253:0.4362:0.0	.	651	Q0VDD8-4	.	V	622;651;651	ENSP00000409472:I622V;ENSP00000414402:I651V;ENSP00000392061:I651V	ENSP00000414402:I651V	I	+	1	0	DNAH14	223304573	0.000000	0.05858	0.005000	0.12908	0.439000	0.31926	-1.628000	0.02031	-0.704000	0.05042	0.338000	0.21704	ATC	A|0.991;G|0.009	0.009	strong		0.343	DNAH14-007	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000331217.3	XM_059166	
GBF1	8729	hgsc.bcm.edu	37	10	104140350	104140350	+	Missense_Mutation	SNP	G	G	A	rs11191274	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:104140350G>A	ENST00000369983.3	+	38	5337	c.5077G>A	c.(5077-5079)Ggc>Agc	p.G1693S		NM_001199378.1|NM_001199379.1|NM_004193.2	NP_001186307.1|NP_001186308.1|NP_004184.1	Q92538	GBF1_HUMAN	golgi brefeldin A resistant guanine nucleotide exchange factor 1	1693			G -> S (in dbSNP:rs11191274).		COPI coating of Golgi vesicle (GO:0048205)|membrane organization (GO:0061024)|positive regulation of GTPase activity (GO:0043547)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of ARF protein signal transduction (GO:0032012)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|vesicle-mediated transport (GO:0016192)|viral process (GO:0016032)	cis-Golgi network (GO:0005801)|endoplasmic reticulum lumen (GO:0005788)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisome (GO:0005777)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(14)|kidney(8)|large_intestine(15)|lung(19)|ovary(1)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	71		Colorectal(252;0.0236)		Epithelial(162;5.16e-08)|all cancers(201;1.19e-06)		ACGGGGAGGCGGCCCCTCGGC	0.577													G|||	259	0.0517173	0.003	0.0749	5008	,	,		20003	0.0456		0.1213	False		,,,				2504	0.0358				p.G1693S		Atlas-SNP	.											.	GBF1	142	.	0			c.G5077A						PASS	.	G	SER/GLY,SER/GLY,SER/GLY	107,4299	82.4+/-120.9	3,101,2099	242.0	265.0	257.0		5068,5065,5077	-3.7	0.0	10	dbSNP_120	257	1117,7483	232.1+/-265.8	62,993,3245	yes	missense,missense,missense	GBF1	NM_001199378.1,NM_001199379.1,NM_004193.2	56,56,56	65,1094,5344	AA,AG,GG		12.9884,2.4285,9.411	probably-damaging,probably-damaging,probably-damaging	1690/1857,1689/1856,1693/1860	104140350	1224,11782	2203	4300	6503	SO:0001583	missense	8729	exon38			GGAGGCGGCCCCT	D87435	CCDS7533.1	10q24	2010-02-12	2010-02-12		ENSG00000107862	ENSG00000107862			4181	protein-coding gene	gene with protein product		603698	"""golgi-specific brefeldin A resistance factor 1"""			9828135	Standard	NM_004193		Approved	KIAA0248, ARF1GEF	uc001kux.2	Q92538	OTTHUMG00000018955	ENST00000369983.3:c.5077G>A	10.37:g.104140350G>A	ENSP00000359000:p.Gly1693Ser	Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	113	56	0.495575	NM_004193	Q5VXX3|Q96CK6|Q96HZ3|Q9H473	Missense_Mutation	SNP	ENST00000369983.3	37	CCDS7533.1	152	0.0695970695970696	2	0.0040650406504065045	32	0.08839779005524862	23	0.04020979020979021	95	0.12532981530343007	G	0.008	-1.878389	0.00537	0.024285	0.129884	ENSG00000107862	ENST00000369983	T	0.08634	3.07	5.91	-3.65	0.04502	.	0.390538	0.32147	N	0.006510	T	0.00039	0.0001	L	0.40543	1.245	0.58432	P	4.000000000004E-6	P;P;B	0.40107	0.703;0.703;0.01	B;B;B	0.30401	0.115;0.115;0.008	T	0.48525	-0.9028	9	0.08837	T	0.75	-0.1049	8.0024	0.30304	0.3925:0.1192:0.4883:0.0	rs11191274;rs52831419;rs59539666;rs11191274	1689;1689;1693	Q149P1;Q149P0;Q92538	.;.;GBF1_HUMAN	S	1693	ENSP00000359000:G1693S	ENSP00000359000:G1693S	G	+	1	0	GBF1	104130340	0.000000	0.05858	0.031000	0.17742	0.082000	0.17680	-0.664000	0.05292	-0.640000	0.05495	-1.058000	0.02302	GGC	G|0.918;A|0.082	0.082	strong		0.577	GBF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050051.1		
C11orf84	144097	hgsc.bcm.edu	37	11	63585804	63585804	+	Silent	SNP	C	C	A	rs643634	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:63585804C>A	ENST00000294244.4	+	3	873	c.574C>A	c.(574-576)Cgg>Agg	p.R192R		NM_138471.1	NP_612480.1	Q9BUA3	CK084_HUMAN	chromosome 11 open reading frame 84	192	Pro-rich.									endometrium(3)|kidney(1)|lung(3)|skin(1)	8						TAAAAGGAGCCGGCCCAGGGG	0.612													C|||	1966	0.392572	0.0734	0.6354	5008	,	,		14644	0.6944		0.4225	False		,,,				2504	0.3098				p.R192R		Atlas-SNP	.											.	C11orf84	33	.	0			c.C574A						PASS	.	C		609,3793	263.8+/-265.7	46,517,1638	51.0	62.0	58.0		574	5.5	1.0	11	dbSNP_83	58	4008,4588	554.1+/-386.4	935,2138,1225	no	coding-synonymous	C11orf84	NM_138471.1		981,2655,2863	AA,AC,CC		46.6263,13.8346,35.5208		192/382	63585804	4617,8381	2201	4298	6499	SO:0001819	synonymous_variant	144097	exon3			AGGAGCCGGCCCA	BC007540	CCDS31594.1	11q13.1	2014-02-10			ENSG00000168005	ENSG00000168005			25115	protein-coding gene	gene with protein product						12477932	Standard	NM_138471		Approved		uc001nxt.3	Q9BUA3	OTTHUMG00000167746	ENST00000294244.4:c.574C>A	11.37:g.63585804C>A		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	42	10	0.238095	NM_138471	Q68CV7|Q6PHS2|Q96IH0	Silent	SNP	ENST00000294244.4	37	CCDS31594.1																																																																																			C|0.623;A|0.377	0.377	strong		0.612	C11orf84-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396084.1	NM_138471	
PAPPA	5069	hgsc.bcm.edu	37	9	119028233	119028233	+	Missense_Mutation	SNP	A	A	C	rs117124330	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:119028233A>C	ENST00000328252.3	+	8	3199	c.2830A>C	c.(2830-2832)Agt>Cgt	p.S944R	PAPPA_ENST00000534838.1_5'UTR	NM_002581.3	NP_002572.2	Q13219	PAPP1_HUMAN	pregnancy-associated plasma protein A, pappalysin 1	944			S -> R (in dbSNP:rs117124330). {ECO:0000269|PubMed:7508748, ECO:0000269|PubMed:8620868}.		cell differentiation (GO:0030154)|cellular protein metabolic process (GO:0044267)|female pregnancy (GO:0007565)|response to follicle-stimulating hormone (GO:0032354)|response to glucocorticoid (GO:0051384)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)	endopeptidase activity (GO:0004175)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|endometrium(9)|kidney(2)|large_intestine(23)|lung(33)|ovary(4)|pancreas(2)|prostate(5)|skin(7)|stomach(1)|upper_aerodigestive_tract(6)|urinary_tract(1)	98						CATCCATGGAAGTGGGTACTG	0.438													A|||	48	0.00958466	0.0	0.0159	5008	,	,		19890	0.0		0.0169	False		,,,				2504	0.0204				p.S944R		Atlas-SNP	.											.	PAPPA	243	.	0			c.A2830C						PASS	.	A	ARG/SER	17,4389	25.3+/-52.1	0,17,2186	103.0	94.0	97.0		2830	2.9	1.0	9	dbSNP_132	97	154,8446	73.8+/-136.5	1,152,4147	yes	missense	PAPPA	NM_002581.3	110	1,169,6333	CC,CA,AA		1.7907,0.3858,1.3148	possibly-damaging	944/1628	119028233	171,12835	2203	4300	6503	SO:0001583	missense	5069	exon8			CATGGAAGTGGGT		CCDS6813.1	9q33.1	2014-03-05			ENSG00000182752	ENSG00000182752			8602	protein-coding gene	gene with protein product	"""insulin-like growth factor-dependent IGF binding protein-4 protease"", ""aspecific BCL2 ARE-binding protein 2"", ""differentially placenta 1 expressed protein"""	176385				7679961	Standard	NM_002581		Approved	PAPP-A, PAPPA1, IGFBP-4ase, PAPA, ASBABP2, DIPLA1	uc004bjn.3	Q13219	OTTHUMG00000021045	ENST00000328252.3:c.2830A>C	9.37:g.119028233A>C	ENSP00000330658:p.Ser944Arg	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	68	39	0.573529	NM_002581	B1AMF9|Q08371|Q68G52|Q9UDK7	Missense_Mutation	SNP	ENST00000328252.3	37	CCDS6813.1	15	0.006868131868131868	0	0.0	4	0.011049723756906077	0	0.0	11	0.014511873350923483	A	12.44	1.939319	0.34189	0.003858	0.017907	ENSG00000182752	ENST00000328252;ENST00000443904	T	0.42513	0.97	5.28	2.88	0.33553	.	0.277336	0.47093	D	0.000259	T	0.29882	0.0747	L	0.45698	1.435	0.80722	D	1	D;P	0.59357	0.985;0.918	P;P	0.56916	0.809;0.475	T	0.06127	-1.0844	10	0.30078	T	0.28	-1.3511	8.9684	0.35890	0.8425:0.0:0.1575:0.0	.	388;944	E7EMD3;Q13219	.;PAPP1_HUMAN	R	944;388	ENSP00000330658:S944R	ENSP00000330658:S944R	S	+	1	0	PAPPA	118068054	1.000000	0.71417	0.995000	0.50966	0.969000	0.65631	1.669000	0.37492	0.306000	0.22856	0.455000	0.32223	AGT	A|0.988;C|0.012	0.012	strong		0.438	PAPPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055546.1	NM_002581	
SLC25A38	54977	hgsc.bcm.edu	37	3	39431081	39431081	+	Silent	SNP	G	G	A	rs2270770	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:39431081G>A	ENST00000273158.4	+	2	542	c.165G>A	c.(163-165)ctG>ctA	p.L55L		NM_017875.2	NP_060345.2			solute carrier family 25, member 38											breast(1)|endometrium(1)|large_intestine(1)|lung(6)|skin(1)|stomach(1)	11				KIRC - Kidney renal clear cell carcinoma(284;0.0525)|Kidney(284;0.0661)		AAACACGCCTGCAAACCCTCC	0.498													G|||	2084	0.416134	0.0825	0.5	5008	,	,		20316	0.6141		0.508	False		,,,				2504	0.5092				p.L55L		Atlas-SNP	.											.	SLC25A38	25	.	0			c.G165A						PASS	.	G		638,3768	273.4+/-271.3	49,540,1614	140.0	128.0	132.0		165	1.3	1.0	3	dbSNP_100	132	4171,4429	568.4+/-389.0	1040,2091,1169	no	coding-synonymous	SLC25A38	NM_017875.2		1089,2631,2783	AA,AG,GG		48.5,14.4803,36.9752		55/305	39431081	4809,8197	2203	4300	6503	SO:0001819	synonymous_variant	54977	exon2			ACGCCTGCAAACC	BC013194	CCDS2685.1	3p22.1	2013-05-22			ENSG00000144659	ENSG00000144659		"""Solute carriers"""	26054	protein-coding gene	gene with protein product		610819				16949250	Standard	NM_017875		Approved	FLJ20551	uc003cjo.2	Q96DW6	OTTHUMG00000131289	ENST00000273158.4:c.165G>A	3.37:g.39431081G>A		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	122	58	0.47541	NM_017875		Silent	SNP	ENST00000273158.4	37	CCDS2685.1																																																																																			G|0.592;A|0.408	0.408	strong		0.498	SLC25A38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254057.3	NM_017875	
ZNF91	7644	hgsc.bcm.edu	37	19	23545004	23545004	+	Silent	SNP	G	G	A	rs296092	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:23545004G>A	ENST00000300619.7	-	4	982	c.777C>T	c.(775-777)atC>atT	p.I259I	ZNF91_ENST00000599743.1_Intron|ZNF91_ENST00000397082.2_Silent_p.I227I	NM_003430.2	NP_003421.2	Q05481	ZNF91_HUMAN	zinc finger protein 91	259					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)				CTTTAGCACAGATTATTTTAT	0.368													A|||	1561	0.311701	0.4062	0.1571	5008	,	,		18337	0.369		0.2495	False		,,,				2504	0.2986				p.I259I		Atlas-SNP	.											.	ZNF91	349	.	0			c.C777T						PASS	.	A		1627,2737		317,993,872	109.0	121.0	117.0		777	-3.9	0.0	19	dbSNP_79	117	2290,6302		285,1720,2291	no	coding-synonymous	ZNF91	NM_003430.2		602,2713,3163	AA,AG,GG		26.6527,37.2823,30.2331		259/1192	23545004	3917,9039	2182	4296	6478	SO:0001819	synonymous_variant	7644	exon4			AGCACAGATTATT	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.777C>T	19.37:g.23545004G>A		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	59	21	0.355932	NM_003430	A8K5E1|B7Z6G6	Silent	SNP	ENST00000300619.7	37	CCDS42541.1																																																																																			G|0.682;A|0.318	0.318	strong		0.368	ZNF91-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465891.1	NM_003430	
HLA-A	3105	hgsc.bcm.edu	37	6	29912068	29912068	+	Silent	SNP	A	A	G	rs145353606	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:29912068A>G	ENST00000396634.1	+	6	1130	c.789A>G	c.(787-789)ggA>ggG	p.G263G	HLA-A_ENST00000376802.2_Silent_p.G263G|HLA-A_ENST00000376809.5_Silent_p.G263G|HLA-A_ENST00000376806.5_Silent_p.G263G			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	263	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						CAGGGGATGGAACCTTCCAGA	0.632									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.G263G		Atlas-SNP	.											.	HLA-A	89	.	0			c.A789G						PASS	.						28.0	31.0	30.0					6																	29912068		1509	2698	4207	SO:0001819	synonymous_variant	3105	exon4	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	GGATGGAACCTTC	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.789A>G	6.37:g.29912068A>G		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	122	36	0.295082	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Silent	SNP	ENST00000396634.1	37	CCDS34373.1																																																																																			A|0.951;G|0.049	0.049	strong		0.632	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
CRIPAK	285464	hgsc.bcm.edu	37	4	1388429	1388429	+	Missense_Mutation	SNP	G	G	A	rs79298048	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:1388429G>A	ENST00000324803.4	+	1	3090	c.130G>A	c.(130-132)Gcc>Acc	p.A44T		NM_175918.3	NP_787114.2	Q8N1N5	CRPAK_HUMAN	cysteine-rich PAK1 inhibitor	44					negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of protein kinase activity (GO:0006469)|regulation of cytoskeleton organization (GO:0051493)|response to estrogen (GO:0043627)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(3)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(11)|ovary(1)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(1)	35			OV - Ovarian serous cystadenocarcinoma(23;0.0106)			CGGAGTGCCCGCCTGCTCACA	0.662													N|||	944	0.188498	0.062	0.2853	5008	,	,		16920	0.0536		0.3797	False		,,,				2504	0.2331				p.A44T		Atlas-SNP	.											CRIPAK,colon,carcinoma,0,2	CRIPAK	185	2	0			c.G130A						PASS	.	G	THR/ALA	508,3898		29,450,1724	219.0	210.0	213.0		130	-1.5	0.0	4	dbSNP_131	213	3442,5158		673,2096,1531	no	missense	CRIPAK	NM_175918.3	58	702,2546,3255	AA,AG,GG		40.0233,11.5297,30.3706	benign	44/447	1388429	3950,9056	2203	4300	6503	SO:0001583	missense	285464	exon1			GTGCCCGCCTGCT	AK096209	CCDS3349.1	4p16.3	2011-02-10	2006-09-04		ENSG00000179979	ENSG00000179979			26619	protein-coding gene	gene with protein product		610203	"""cysteine-rich PAK1inhibitor"""			16278681	Standard	NM_175918		Approved	FLJ34443	uc003gdf.2	Q8N1N5	OTTHUMG00000121131	ENST00000324803.4:c.130G>A	4.37:g.1388429G>A	ENSP00000323978:p.Ala44Thr	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	88	40	0.454545	NM_175918	Q8NB03	Missense_Mutation	SNP	ENST00000324803.4	37	CCDS3349.1	438	0.20054945054945056	28	0.056910569105691054	99	0.27348066298342544	38	0.06643356643356643	273	0.36015831134564646	-	6.138	0.393672	0.11638	0.115297	0.400233	ENSG00000179979	ENST00000324803;ENST00000382944	T	0.24350	1.86	1.11	-1.54	0.08584	Post-SET domain (1);	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	P	0.39748	0.686	B	0.17722	0.019	T	0.47484	-0.9114	8	0.36615	T	0.2	.	3.7735	0.08650	0.1991:0.2527:0.5481:0.0	.	44	Q8N1N5	CRPAK_HUMAN	T	44;37	ENSP00000323978:A44T	ENSP00000323978:A44T	A	+	1	0	CRIPAK	1378429	0.001000	0.12720	0.000000	0.03702	0.001000	0.01503	-0.619000	0.05572	-0.466000	0.06943	0.413000	0.27773	GCC	G|0.725;A|0.275	0.275	strong		0.662	CRIPAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241607.2	NM_175918	
TMPRSS2	7113	hgsc.bcm.edu	37	21	42852497	42852497	+	Missense_Mutation	SNP	C	C	T	rs12329760	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:42852497C>T	ENST00000332149.5	-	6	612	c.478G>A	c.(478-480)Gtg>Atg	p.V160M	TMPRSS2_ENST00000458356.1_Missense_Mutation_p.V160M|TMPRSS2_ENST00000398585.3_Missense_Mutation_p.V197M	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	120	0	0		WXS	Illumina HiSeq	Phase_I	121	121	1	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		
TGIF1	7050	hgsc.bcm.edu	37	18	3457776	3457776	+	Silent	SNP	T	T	G	rs2229336	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:3457776T>G	ENST00000330513.5	+	3	1347	c.1044T>G	c.(1042-1044)acT>acG	p.T348T	TGIF1_ENST00000551541.1_Silent_p.T199T|TGIF1_ENST00000401449.1_Silent_p.T199T|TGIF1_ENST00000405385.3_Silent_p.T199T|TGIF1_ENST00000400167.2_Silent_p.T199T|TGIF1_ENST00000548489.2_Silent_p.T233T|TGIF1_ENST00000407501.2_Silent_p.T219T|TGIF1_ENST00000345133.5_Silent_p.T199T|TGIF1_ENST00000472042.1_Silent_p.T199T|TGIF1_ENST00000343820.5_Silent_p.T219T	NM_170695.2	NP_733796.2	Q15583	TGIF1_HUMAN	TGFB-induced factor homeobox 1	348					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)				CAGAGGACACTTGTAAATCTG	0.498													A|||	270	0.0539137	0.177	0.0231	5008	,	,		17791	0.003		0.0129	False		,,,				2504	0.0041				p.T348T		Atlas-SNP	.											.	TGIF1	41	.	0			c.T1044G						PASS	.	A	,,,,,,,	747,3659		62,623,1518	133.0	121.0	125.0		657,1044,699,657,597,597,597,597	-10.5	0.0	18	dbSNP_98	125	55,8545		0,55,4245	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TGIF1	NM_003244.2,NM_170695.2,NM_173207.1,NM_173208.1,NM_173209.1,NM_173210.1,NM_173211.1,NM_174886.1	,,,,,,,	62,678,5763	GG,GT,TT		0.6395,16.9542,6.1664	,,,,,,,	219/273,348/402,233/287,219/273,199/253,199/253,199/253,199/253	3457776	802,12204	2203	4300	6503	SO:0001819	synonymous_variant	7050	exon3			GGACACTTGTAAA	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.1044T>G	18.37:g.3457776T>G		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	45	23	0.511111	NM_170695	A6NE42|A6NLU7|F8VZB6|Q6ICR0|Q8N5X9|Q9NRS0	Silent	SNP	ENST00000330513.5	37	CCDS11834.1																																																																																			T|0.941;G|0.059	0.059	strong		0.498	TGIF1-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254368.4	NM_170695	
ODF2L	57489	hgsc.bcm.edu	37	1	86847955	86847955	+	Silent	SNP	G	G	A	rs272516	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:86847955G>A	ENST00000359242.3	-	7	875	c.594C>T	c.(592-594)gcC>gcT	p.A198A	ODF2L_ENST00000370566.3_Silent_p.A198A|ODF2L_ENST00000394731.1_Silent_p.A67A|ODF2L_ENST00000294678.2_Silent_p.A198A|ODF2L_ENST00000370567.1_Silent_p.A198A|ODF2L_ENST00000317336.7_Silent_p.A198A	NM_001007022.2	NP_001007023.2	Q9ULJ1	ODF2L_HUMAN	outer dense fiber of sperm tails 2-like	198						centrosome (GO:0005813)				endometrium(2)|kidney(2)|large_intestine(10)|lung(6)|ovary(1)|pancreas(1)|skin(1)|stomach(1)	24				all cancers(265;0.0313)|Epithelial(280;0.0611)		TATCGTTCTCGGCTTCCCTTT	0.313													G|||	1943	0.387979	0.5371	0.3977	5008	,	,		15255	0.2897		0.326	False		,,,				2504	0.3446				p.A198A		Atlas-SNP	.											.	ODF2L	53	.	0			c.C594T						PASS	.	G	,,,	2205,2199	585.7+/-386.3	557,1091,554	110.0	108.0	109.0		594,594,594,594	-2.5	1.0	1	dbSNP_79	109	2671,5925	427.6+/-355.6	425,1821,2052	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ODF2L	NM_001007022.2,NM_001184765.1,NM_001184766.1,NM_020729.2	,,,	982,2912,2606	AA,AG,GG		31.0726,49.9319,37.5077	,,,	198/637,198/621,198/592,198/621	86847955	4876,8124	2202	4298	6500	SO:0001819	synonymous_variant	57489	exon7			GTTCTCGGCTTCC		CCDS30763.1, CCDS41354.1, CCDS30763.2, CCDS41354.2, CCDS53339.1	1p22.3	2008-02-05			ENSG00000122417	ENSG00000122417			29225	protein-coding gene	gene with protein product						10574462	Standard	NM_020729		Approved	KIAA1229	uc001dll.2	Q9ULJ1	OTTHUMG00000010080	ENST00000359242.3:c.594C>T	1.37:g.86847955G>A		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	84	37	0.440476	NM_001184766	A8MU56|B4E037|Q05C40|Q5BJG5|Q5TBX3|Q5TBX4|Q86X31	Silent	SNP	ENST00000359242.3	37	CCDS41354.2	813	0.37225274725274726	267	0.5426829268292683	132	0.36464088397790057	177	0.3094405594405594	237	0.31266490765171506	G	2.751	-0.259949	0.05791	0.500681	0.310726	ENSG00000122417	ENST00000459999	.	.	.	5.4	-2.5	0.06384	.	.	.	.	.	T	0.06234	0.0161	.	.	.	0.09310	P	0.99999999406726	.	.	.	.	.	.	T	0.34650	-0.9820	3	.	.	.	-0.5509	0.2343	0.00184	0.3341:0.1795:0.1447:0.3416	rs272516;rs9433467;rs57934963;rs272516	.	.	.	L	47	.	.	P	-	2	0	ODF2L	86620543	0.523000	0.26274	0.995000	0.50966	0.162000	0.22319	-0.809000	0.04510	-0.131000	0.11578	-0.474000	0.04947	CCG	G|0.619;A|0.381	0.381	strong		0.313	ODF2L-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000027873.2		
PAQR6	79957	hgsc.bcm.edu	37	1	156213921	156213921	+	Silent	SNP	C	C	T	rs7513351	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:156213921C>T	ENST00000292291.5	-	8	1192	c.1034G>A	c.(1033-1035)tGa>tAa	p.*345*	PAQR6_ENST00000335852.1_Missense_Mutation_p.E263K|PAQR6_ENST00000492619.1_5'UTR|PAQR6_ENST00000368270.1_Silent_p.*321*|PAQR6_ENST00000540423.1_Silent_p.*342*|PAQR6_ENST00000356983.2_Missense_Mutation_p.E263K	NM_001272104.1|NM_001272105.1|NM_198406.2	NP_001259033.1|NP_001259034.1|NP_940798.1	Q6TCH4	PAQR6_HUMAN	progestin and adipoQ receptor family member VI	0						integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			lung(4)|ovary(1)	5	Hepatocellular(266;0.158)					GATGGGGCCTCACTGTTGTTT	0.637													C|||	1098	0.219249	0.1604	0.3026	5008	,	,		19101	0.256		0.1481	False		,,,				2504	0.2751				p.E263K	GBM(16;219 398 12385 32425 38531)	Atlas-SNP	.											.	PAQR6	23	.	0			c.G787A						PASS	.	C	LYS/GLU,	698,3708	293.6+/-282.7	63,572,1568	67.0	70.0	69.0		787,1034	-3.6	0.3	1	dbSNP_116	69	1413,7187	273.1+/-290.5	114,1185,3001	yes	missense,coding-synonymous	PAQR6	NM_024897.2,NM_198406.1	56,	177,1757,4569	TT,TC,CC		16.4302,15.842,16.231	,	263/352,345/345	156213921	2111,10895	2203	4300	6503	SO:0001819	synonymous_variant	79957	exon7			GGGCCTCACTGTT	AF455045	CCDS1135.1, CCDS1136.1, CCDS60301.1, CCDS72945.1, CCDS72946.1	1q23	2008-02-05			ENSG00000160781	ENSG00000160781			30132	protein-coding gene	gene with protein product		614579				12477932	Standard	NM_024897		Approved	FLJ22672	uc010phh.2	Q6TCH4	OTTHUMG00000017490	ENST00000292291.5:c.1034G>A	1.37:g.156213921C>T		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	104	50	0.480769	NM_024897	B7Z9R9|D3DVB4|D3DVB6|Q5TCK9|Q6PDU0|Q7Z4Q7|Q7Z4Q9|Q8N121|Q8N3M2|Q9H621	Missense_Mutation	SNP	ENST00000292291.5	37	CCDS1136.1	436	0.19963369963369965	76	0.15447154471544716	116	0.32044198895027626	138	0.24125874125874125	106	0.13984168865435356	C	17.16	3.319012	0.60524	0.15842	0.164302	ENSG00000160781	ENST00000360733;ENST00000335852;ENST00000356983	T;T;T	0.38240	1.15;1.15;1.15	5.24	-3.56	0.04626	.	.	.	.	.	T	0.08492	0.0211	.	.	.	0.49130	P	2.4299999999999322E-4	B;B;B	0.26602	0.154;0.154;0.006	B;B;B	0.23716	0.048;0.048;0.016	T	0.35943	-0.9768	7	0.87932	D	0	.	2.5753	0.04805	0.1144:0.4297:0.1128:0.3431	rs7513351;rs58089457;rs7513351	195;123;263	B4DJ42;Q7Z4Q8;Q6TCH4-2	.;.;.	K	263	ENSP00000353961:E263K;ENSP00000338330:E263K;ENSP00000349474:E263K	ENSP00000338330:E263K	E	-	1	0	PAQR6	154480545	0.958000	0.32768	0.268000	0.24571	0.091000	0.18340	0.235000	0.17948	-0.222000	0.09958	0.462000	0.41574	GAG	C|0.818;T|0.182	0.182	strong		0.637	PAQR6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000046297.2	NM_024897	
MUC4	4585	hgsc.bcm.edu	37	3	195510073	195510073	+	Missense_Mutation	SNP	G	G	A	rs200663432	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195510073G>A	ENST00000463781.3	-	2	8837	c.8378C>T	c.(8377-8379)gCa>gTa	p.A2793V	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.A2793V	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		ACCTGTGGATGCTGAGGAAGG	0.587													.|||	15	0.00299521	0.0113	0.0	5008	,	,		6295	0.0		0.0	False		,,,				2504	0.0				p.A2793V		Atlas-SNP	.											.	MUC4	1505	.	0			c.C8378T						PASS	.						57.0	33.0	41.0					3																	195510073		689	1521	2210	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.8378C>T	3.37:g.195510073G>A	ENSP00000417498:p.Ala2793Val	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	92	14	0.152174	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	.	.	.	.	.	.	.	.	.	.	-	2.540	-0.306588	0.05458	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.30448	1.53;1.54	0.918	-0.419	0.12340	.	.	.	.	.	T	0.12689	0.0308	N	0.08118	0	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.30090	-0.9990	8	.	.	.	.	5.3055	0.15801	0.579:0.0:0.421:0.0	.	2665	E7ESK3	.	V	2793	ENSP00000417498:A2793V;ENSP00000420243:A2793V	.	A	-	2	0	MUC4	196994852	0.000000	0.05858	0.034000	0.17996	0.015000	0.08874	0.293000	0.19029	-1.755000	0.01320	-1.973000	0.00462	GCA	G|0.756;A|0.244	0.244	strong		0.587	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
TTC28	23331	hgsc.bcm.edu	37	22	28389453	28389453	+	Silent	SNP	T	T	C	rs470101	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:28389453T>C	ENST00000397906.2	-	18	5439	c.5298A>G	c.(5296-5298)acA>acG	p.T1766T	TTC28-AS1_ENST00000430525.1_RNA|TTC28-AS1_ENST00000453632.1_RNA|TTC28-AS1_ENST00000454741.1_RNA|TTC28-AS1_ENST00000417497.1_RNA|TTC28-AS1_ENST00000433317.1_RNA|TTC28-AS1_ENST00000428584.1_RNA|TTC28-AS1_ENST00000424161.1_RNA|TTC28-AS1_ENST00000452612.1_RNA|TTC28-AS1_ENST00000430853.1_RNA|TTC28-AS1_ENST00000434221.1_RNA|TTC28-AS1_ENST00000435348.1_RNA	NM_001145418.1	NP_001138890.1	Q96AY4	TTC28_HUMAN	tetratricopeptide repeat domain 28	1766					mitotic nuclear division (GO:0007067)|regulation of mitotic cell cycle (GO:0007346)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|midbody (GO:0030496)				endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)	12						TCTGCTGGGATGTGTACATGG	0.637													C|||	395	0.0788738	0.0991	0.0937	5008	,	,		19292	0.0069		0.1034	False		,,,				2504	0.09				p.T1766T		Atlas-SNP	.											.	TTC28	84	.	0			c.A5298G						PASS	.	C		144,1240		7,130,555	69.0	66.0	67.0		5298	-8.9	0.5	22	dbSNP_80	67	381,2801		26,329,1236	no	coding-synonymous	TTC28	NM_001145418.1		33,459,1791	CC,CT,TT		11.9736,10.4046,11.498		1766/2482	28389453	525,4041	692	1591	2283	SO:0001819	synonymous_variant	23331	exon18			CTGGGATGTGTAC	AB028966	CCDS46678.1	22q12.1	2013-01-10			ENSG00000100154	ENSG00000100154		"""Tetratricopeptide (TTC) repeat domain containing"""	29179	protein-coding gene	gene with protein product		615098				10470851	Standard	NM_001145418		Approved	KIAA1043	uc003adp.4	Q96AY4	OTTHUMG00000151006	ENST00000397906.2:c.5298A>G	22.37:g.28389453T>C		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	113	67	0.59292	NM_001145418	K7ZRV2|O95928|O95929|Q5W189|Q9NTE4|Q9UG31|Q9UGG5|Q9UPV8|Q9Y3S5	Silent	SNP	ENST00000397906.2	37	CCDS46678.1																																																																																			T|0.926;C|0.074	0.074	strong		0.637	TTC28-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000320930.2	XM_929318	
FHL5	9457	hgsc.bcm.edu	37	6	97058567	97058567	+	Silent	SNP	A	A	G	rs2273622	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:97058567A>G	ENST00000326771.2	+	6	1004	c.624A>G	c.(622-624)ccA>ccG	p.P208P	FHL5_ENST00000541107.1_Silent_p.P208P	NM_020482.4	NP_065228.4	Q5TD97	FHL5_HUMAN	four and a half LIM domains 5	208	LIM zinc-binding 3. {ECO:0000255|PROSITE- ProRule:PRU00125}.				positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(4)|lung(17)|ovary(2)|urinary_tract(1)	27		all_cancers(76;1.57e-07)|Acute lymphoblastic leukemia(125;4.93e-10)|all_hematologic(75;3.55e-07)|all_epithelial(107;0.00266)|Colorectal(196;0.0341)|Lung NSC(302;0.204)		BRCA - Breast invasive adenocarcinoma(108;0.0948)		ACGACTATCCATTCTGCGTGG	0.428													A|||	689	0.13758	0.115	0.183	5008	,	,		18288	0.0357		0.2117	False		,,,				2504	0.1646				p.P208P		Atlas-SNP	.											FHL5,NS,malignant_melanoma,+2,1	FHL5	73	1	0			c.A624G						PASS	.	A	,	492,3914	228.1+/-243.1	25,442,1736	245.0	225.0	232.0		624,624	-3.3	1.0	6	dbSNP_100	232	1673,6927	307.0+/-308.2	175,1323,2802	no	coding-synonymous,coding-synonymous	FHL5	NM_001170807.1,NM_020482.4	,	200,1765,4538	GG,GA,AA		19.4535,11.1666,16.6462	,	208/285,208/285	97058567	2165,10841	2203	4300	6503	SO:0001819	synonymous_variant	9457	exon6			CTATCCATTCTGC	AF278541	CCDS5035.1	6q16.1-q16.3	2008-02-05			ENSG00000112214	ENSG00000112214			17371	protein-coding gene	gene with protein product		605126					Standard	NM_020482		Approved	FLJ33049, ACT, dJ393D12.2	uc003pot.2	Q5TD97	OTTHUMG00000015239	ENST00000326771.2:c.624A>G	6.37:g.97058567A>G		Somatic	246	0	0		WXS	Illumina HiSeq	Phase_I	198	84	0.424242	NM_020482	B2RBD1|E1P526|Q5TD98|Q8WW21|Q9NQU2	Silent	SNP	ENST00000326771.2	37	CCDS5035.1																																																																																			A|0.841;G|0.159	0.159	strong		0.428	FHL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041559.1	NM_020482	
NAGLU	4669	hgsc.bcm.edu	37	17	40696122	40696122	+	Missense_Mutation	SNP	A	A	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:40696122A>C	ENST00000225927.2	+	6	2199	c.2098A>C	c.(2098-2100)Aat>Cat	p.N700H	RP11-400F19.8_ENST00000585572.1_RNA	NM_000263.3	NP_000254.2	P54802	ANAG_HUMAN	N-acetylglucosaminidase, alpha	700					carbohydrate metabolic process (GO:0005975)|cerebellar Purkinje cell layer development (GO:0021680)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|inner ear receptor cell development (GO:0060119)|locomotor rhythm (GO:0045475)|lysosome organization (GO:0007040)|middle ear morphogenesis (GO:0042474)|nervous system development (GO:0007399)|retinal rod cell development (GO:0046548)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)	alpha-N-acetylglucosaminidase activity (GO:0004561)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(1)|ovary(2)|skin(1)	12		all_cancers(22;1.58e-05)|Breast(137;0.000153)|all_epithelial(22;0.000344)		BRCA - Breast invasive adenocarcinoma(366;0.13)	N-Acetyl-D-glucosamine(DB00141)	GTTTGACAAAAATGTCTTCCA	0.577																																					p.N700H		Atlas-SNP	.											.	NAGLU	36	.	0			c.A2098C						PASS	.						50.0	47.0	48.0					17																	40696122		2203	4300	6503	SO:0001583	missense	4669	exon6			GACAAAAATGTCT		CCDS11427.1	17q21.2	2010-07-27	2010-07-27		ENSG00000108784	ENSG00000108784	3.2.1.50		7632	protein-coding gene	gene with protein product	"""Sanfilippo disease IIIB"""	609701					Standard	XM_006721920		Approved	NAG	uc002hzv.3	P54802		ENST00000225927.2:c.2098A>C	17.37:g.40696122A>C	ENSP00000225927:p.Asn700His	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	54	18	0.333333	NM_000263		Missense_Mutation	SNP	ENST00000225927.2	37	CCDS11427.1	.	.	.	.	.	.	.	.	.	.	A	11.71	1.720488	0.30503	.	.	ENSG00000108784	ENST00000225927;ENST00000377405	D	0.98649	-5.05	5.03	1.08	0.20341	Alpha-N-acetylglucosaminidase, C-terminal (1);	0.878057	0.10023	N	0.725727	D	0.95868	0.8655	L	0.42245	1.32	0.20074	N	0.999938	B	0.09022	0.002	B	0.08055	0.003	D	0.90986	0.4831	10	0.52906	T	0.07	0.2904	3.5341	0.07788	0.3663:0.2592:0.3745:0.0	.	700	P54802	ANAG_HUMAN	H	700;376	ENSP00000225927:N700H	ENSP00000225927:N700H	N	+	1	0	NAGLU	37949648	0.991000	0.36638	0.010000	0.14722	0.865000	0.49528	3.225000	0.51246	0.354000	0.24105	0.454000	0.30748	AAT	.	.	none		0.577	NAGLU-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450385.1	NM_000263	
DHFRL1	200895	hgsc.bcm.edu	37	3	93779860	93779860	+	Missense_Mutation	SNP	C	C	T	rs17855824	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:93779860C>T	ENST00000394221.2	-	2	945	c.496G>A	c.(496-498)Gtt>Att	p.V166I	NSUN3_ENST00000314622.4_5'Flank|DHFRL1_ENST00000481631.1_Intron|DHFRL1_ENST00000314636.2_Missense_Mutation_p.V166I	NM_001195643.1	NP_001182572.1	Q86XF0	DYRL1_HUMAN	dihydrofolate reductase-like 1	166	DHFR. {ECO:0000255|PROSITE- ProRule:PRU00660}.		V -> I (in dbSNP:rs17855824). {ECO:0000269|PubMed:15489334}.		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)			kidney(1)|large_intestine(2)|lung(3)|skin(1)|stomach(1)	8						TCAGAGAGAACACCTGGGTAT	0.373													C|||	387	0.0772764	0.003	0.0764	5008	,	,		18827	0.0863		0.1103	False		,,,				2504	0.135				p.V166I		Atlas-SNP	.											.	DHFRL1	25	.	0			c.G496A						PASS	.	C	ILE/VAL,ILE/VAL	98,4308	80.4+/-118.8	0,98,2105	120.0	118.0	119.0		496,496	0.3	1.0	3	dbSNP_123	119	1014,7586	217.6+/-256.2	60,894,3346	yes	missense,missense	DHFRL1	NM_001195643.1,NM_176815.4	29,29	60,992,5451	TT,TC,CC		11.7907,2.2242,8.5499	possibly-damaging,possibly-damaging	166/188,166/188	93779860	1112,11894	2203	4300	6503	SO:0001583	missense	200895	exon2			AGAGAACACCTGG	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.496G>A	3.37:g.93779860C>T	ENSP00000377768:p.Val166Ile	Somatic	196	0	0		WXS	Illumina HiSeq	Phase_I	172	82	0.476744	NM_001195643	D3DN30|Q6P4I9	Missense_Mutation	SNP	ENST00000394221.2	37	CCDS2926.1	161	0.07371794871794872	3	0.006097560975609756	31	0.0856353591160221	50	0.08741258741258741	77	0.10158311345646438	C	9.878	1.200708	0.22121	0.022242	0.117907	ENSG00000178700	ENST00000314636;ENST00000394221	T;T	0.71461	-0.57;-0.57	1.25	0.311	0.15831	Dihydrofolate reductase domain (2);Dihydrofolate reductase-like domain (2);	0.247728	0.32416	U	0.006131	T	0.01124	0.0037	L	0.38838	1.175	0.31602	P	0.6526339999999999	P	0.39443	0.674	B	0.40825	0.341	T	0.07501	-1.0769	9	0.34782	T	0.22	-10.0577	3.8637	0.09007	0.0:0.5428:0.0:0.4572	rs17855824	166	Q86XF0	DYRL1_HUMAN	I	166	ENSP00000319170:V166I;ENSP00000377768:V166I	ENSP00000319170:V166I	V	-	1	0	DHFRL1	95262550	0.044000	0.20184	0.982000	0.44146	0.795000	0.44927	0.383000	0.20651	0.106000	0.17784	0.449000	0.29647	GTT	C|0.915;T|0.085	0.085	strong		0.373	DHFRL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352910.1	NM_176815	
HHIPL1	84439	hgsc.bcm.edu	37	14	100129327	100129327	+	Silent	SNP	G	G	A	rs34890784	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	171	0	0		WXS	Illumina HiSeq	Phase_I	142	58	0.408451	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	
MUC4	4585	hgsc.bcm.edu	37	3	195506775	195506775	+	Silent	SNP	G	G	A	rs79609066	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195506775G>A	ENST00000463781.3	-	2	12135	c.11676C>T	c.(11674-11676)acC>acT	p.T3892T	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Silent_p.T3892T	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.T3892T(1)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		AGGAAGTGTCGGTGACAGGAA	0.592													.|||	23	0.00459265	0.0	0.0014	5008	,	,		8217	0.0		0.0	False		,,,				2504	0.0225				p.T3892T		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	1	Substitution - coding silent(1)	kidney(1)	c.C11676T						PASS	.						11.0	9.0	10.0					3																	195506775		565	1303	1868	SO:0001819	synonymous_variant	4585	exon2			AGTGTCGGTGACA	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.11676C>T	3.37:g.195506775G>A		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	91	11	0.120879	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Silent	SNP	ENST00000463781.3	37	CCDS54700.1																																																																																			G|0.767;A|0.233	0.233	strong		0.592	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
GABRB3	2562	hgsc.bcm.edu	37	15	26825545	26825545	+	Silent	SNP	G	G	A	rs75965657	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:26825545G>A	ENST00000311550.5	-	6	714	c.603C>T	c.(601-603)acC>acT	p.T201T	GABRB3_ENST00000400188.3_Silent_p.T130T|GABRB3_ENST00000299267.4_Silent_p.T201T|GABRB3_ENST00000545868.1_Silent_p.T116T|GABRB3_ENST00000541819.2_Silent_p.T257T	NM_000814.5|NM_001278631.1	NP_000805.1|NP_001265560.1	P28472	GBRB3_HUMAN	gamma-aminobutyric acid (GABA) A receptor, beta 3	201					cellular response to histamine (GO:0071420)|chloride transmembrane transport (GO:1902476)|cochlea development (GO:0090102)|inner ear receptor cell development (GO:0060119)|innervation (GO:0060384)|ion transmembrane transport (GO:0034220)|negative regulation of neuron apoptotic process (GO:0043524)|palate development (GO:0060021)|sensory perception of sound (GO:0007605)|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)|GABA-gated chloride ion channel activity (GO:0022851)			NS(2)|breast(1)|central_nervous_system(1)|cervix(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(11)|liver(1)|lung(41)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	68		all_cancers(20;1.89e-22)|all_lung(180;6.35e-15)|Breast(32;0.000279)|Colorectal(260;0.232)		all cancers(64;1.46e-07)|Epithelial(43;2.89e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0251)|COAD - Colon adenocarcinoma(236;0.235)|Lung(196;0.243)	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)|Fospropofol(DB06716)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Ivermectin(DB00602)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Piperazine(DB00592)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	TTTCCACTCCGGTAACAGCCT	0.537													G|||	90	0.0179712	0.0643	0.0058	5008	,	,		18278	0.0		0.001	False		,,,				2504	0.0				p.T201T		Atlas-SNP	.											.	GABRB3	338	.	0			c.C603T						PASS	.	G	,,,	275,4131	154.8+/-188.1	7,261,1935	122.0	105.0	111.0		603,348,390,603	-10.2	0.0	15	dbSNP_131	111	18,8582	11.9+/-42.8	0,18,4282	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	GABRB3	NM_000814.5,NM_001191320.1,NM_001191321.1,NM_021912.4	,,,	7,279,6217	AA,AG,GG		0.2093,6.2415,2.2528	,,,	201/474,116/389,130/403,201/474	26825545	293,12713	2203	4300	6503	SO:0001819	synonymous_variant	2562	exon6			CACTCCGGTAACA		CCDS10018.1, CCDS10019.1, CCDS53920.1, CCDS53921.1	15q12	2012-06-22			ENSG00000166206	ENSG00000166206		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	4083	protein-coding gene	gene with protein product	"""GABA(A) receptor, beta 3"""	137192					Standard	NM_000814		Approved		uc001zaz.3	P28472	OTTHUMG00000129231	ENST00000311550.5:c.603C>T	15.37:g.26825545G>A		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	90	43	0.477778	NM_021912	B7Z2W1|B7Z825|F5H3D2|H7BYV8|Q14352|Q96FM5	Silent	SNP	ENST00000311550.5	37	CCDS10019.1																																																																																			G|0.982;A|0.018	0.018	strong		0.537	GABRB3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251352.2		
CREB3L3	84699	hgsc.bcm.edu	37	19	4154910	4154910	+	Silent	SNP	C	C	T	rs35474881	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:4154910C>T	ENST00000078445.2	+	2	189	c.42C>T	c.(40-42)gcC>gcT	p.A14A	CREB3L3_ENST00000595923.1_Silent_p.A14A|CREB3L3_ENST00000602147.1_Silent_p.A14A|CREB3L3_ENST00000252587.3_Silent_p.A5A|CREB3L3_ENST00000602257.1_Silent_p.A14A	NM_001271995.1|NM_001271996.1|NM_032607.1	NP_001258924.1|NP_001258925.1|NP_115996.1	Q68CJ9	CR3L3_HUMAN	cAMP responsive element binding protein 3-like 3	14					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to unfolded protein (GO:0006986)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|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)			breast(2)|kidney(1)|large_intestine(3)|lung(12)|ovary(1)|skin(2)|urinary_tract(3)	24				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0232)|STAD - Stomach adenocarcinoma(1328;0.18)		CTTCTGCTGCCTGCTCCATGG	0.622													C|||	429	0.0856629	0.0855	0.0821	5008	,	,		18561	0.0308		0.1431	False		,,,				2504	0.0859				p.A14A		Atlas-SNP	.											CREB3L3,NS,carcinoma,+1,2	CREB3L3	53	2	0			c.C42T						PASS	.	C		403,4003	199.4+/-223.0	24,355,1824	96.0	79.0	85.0		42	0.7	0.0	19	dbSNP_126	85	1175,7425	239.0+/-270.3	90,995,3215	no	coding-synonymous	CREB3L3	NM_032607.1		114,1350,5039	TT,TC,CC		13.6628,9.1466,12.1329		14/462	4154910	1578,11428	2203	4300	6503	SO:0001819	synonymous_variant	84699	exon2			TGCTGCCTGCTCC		CCDS12121.1, CCDS62498.1, CCDS62499.1, CCDS62500.1	19p13.3	2013-01-10				ENSG00000060566		"""basic leucine zipper proteins"""	18855	protein-coding gene	gene with protein product		611998				11353085	Standard	NM_032607		Approved	CREB-H	uc002lzl.4	Q68CJ9		ENST00000078445.2:c.42C>T	19.37:g.4154910C>T		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	85	43	0.505882	NM_001271997	B2R7S6|B7ZL69|M0QYW7|Q6ZMC5|Q96TB9	Silent	SNP	ENST00000078445.2	37	CCDS12121.1																																																																																			C|0.881;T|0.119	0.119	strong		0.622	CREB3L3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457922.1	NM_032607	
ZNF680	340252	hgsc.bcm.edu	37	7	63986829	63986829	+	Intron	SNP	G	G	C	rs73128772	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:63986829G>C	ENST00000309683.6	-	4	405				ZNF680_ENST00000476563.1_Intron|ZNF680_ENST00000447137.2_Missense_Mutation_p.S107C	NM_178558.4	NP_848653.2	Q8NEM1	ZN680_HUMAN	zinc finger protein 680						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)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(11)|ovary(1)|prostate(1)	27		Lung NSC(55;0.118)|all_lung(88;0.243)				catctttagggaggccaaggc	0.408													G|||	1059	0.211462	0.1914	0.2233	5008	,	,		15089	0.0833		0.2475	False		,,,				2504	0.3252				p.S107C		Atlas-SNP	.											.	ZNF680	58	.	0			c.C320G						PASS	.						142.0	135.0	137.0					7																	63986829		692	1591	2283	SO:0001627	intron_variant	340252	exon4			TTTAGGGAGGCCA	AK074911	CCDS34644.1, CCDS47594.1	7q11.21	2013-01-08			ENSG00000173041	ENSG00000173041		"""Zinc fingers, C2H2-type"", ""-"""	26897	protein-coding gene	gene with protein product	"""hypothetical protein FLJ90430"""					12477932	Standard	NM_178558		Approved	FLJ90430	uc003tta.2	Q8NEM1	OTTHUMG00000156542	ENST00000309683.6:c.254-3951C>G	7.37:g.63986829G>C		Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	26	9	0.346154	NM_001130022	B3KVJ4|Q6ZNF3|Q8NC79	Missense_Mutation	SNP	ENST00000309683.6	37	CCDS34644.1	446	0.2042124542124542	107	0.21747967479674796	85	0.23480662983425415	53	0.09265734265734266	201	0.26517150395778366	g	7.725	0.697958	0.15106	.	.	ENSG00000173041	ENST00000447137	T	0.00840	5.63	0.158	0.158	0.14942	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.47245	P	6.340000000000234E-4	P	0.46578	0.88	P	0.52481	0.7	T	0.53746	-0.8395	6	0.72032	D	0.01	.	.	.	.	.	107	Q6ZNF3	.	C	107	ENSP00000393506:S107C	ENSP00000393506:S107C	S	-	2	0	ZNF680	63624264	0.988000	0.35896	0.246000	0.24233	0.247000	0.25773	1.068000	0.30629	0.202000	0.20498	0.205000	0.17691	TCC	G|0.795;C|0.205	0.205	strong		0.408	ZNF680-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344568.1	NM_178558	
HLA-G	3135	hgsc.bcm.edu	37	6	29797639	29797639	+	Silent	SNP	C	C	T	rs1049033	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:29797639C>T	ENST00000360323.6	+	5	966	c.942C>T	c.(940-942)ggC>ggT	p.G314G	HLA-G_ENST00000376818.3_Silent_p.G222G|HLA-G_ENST00000376815.3_Silent_p.G130G|HLA-G_ENST00000428701.1_Silent_p.G314G|HLA-G_ENST00000376828.2_Silent_p.G319G			P17693	HLAG_HUMAN	major histocompatibility complex, class I, G	314					antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular defense response (GO:0006968)|cytokine-mediated signaling pathway (GO:0019221)|immune response-inhibiting cell surface receptor signaling pathway (GO:0002767)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of dendritic cell differentiation (GO:2001199)|negative regulation of T cell proliferation (GO:0042130)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of regulatory T cell differentiation (GO:0045591)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|positive regulation of T cell tolerance induction (GO:0002666)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)	early endosome membrane (GO:0031901)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|membrane (GO:0016020)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	peptide antigen binding (GO:0042605)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)			central_nervous_system(1)|endometrium(1)|large_intestine(5)|lung(4)|ovary(3)|pancreas(1)|prostate(5)|skin(1)	21						TCGTTGCTGGCCTGGTTGTCC	0.597													N|||	1161	0.231829	0.2504	0.245	5008	,	,		20908	0.1091		0.2555	False		,,,				2504	0.2996				p.G314G		Atlas-SNP	.											.	HLA-G	90	.	0			c.C942T						PASS	.	C		1182,3224		158,866,1179	109.0	90.0	96.0		942	-0.2	0.0	6	dbSNP_86	96	2541,6059		367,1807,2126	no	coding-synonymous	HLA-G	NM_002127.5		525,2673,3305	TT,TC,CC		29.5465,26.8271,28.6252		314/339	29797639	3723,9283	2203	4300	6503	SO:0001819	synonymous_variant	3135	exon6			TGCTGGCCTGGTT		CCDS4668.1	6p21.3	2013-01-11	2007-12-12		ENSG00000204632	ENSG00000204632		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4964	protein-coding gene	gene with protein product	"""b2 microglobulin"""	142871	"""HLA-G histocompatibility antigen, class I, G"""				Standard	NM_002127		Approved		uc003nnw.2	P17693	OTTHUMG00000031157	ENST00000360323.6:c.942C>T	6.37:g.29797639C>T		Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	119	117	0.983193	NM_002127		Silent	SNP	ENST00000360323.6	37	CCDS4668.1																																																																																			C|0.738;T|0.262	0.262	strong		0.597	HLA-G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076286.2	NM_002127	
AXDND1	126859	hgsc.bcm.edu	37	1	179347832	179347832	+	Silent	SNP	T	T	C	rs10798674	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:179347832T>C	ENST00000367618.3	+	5	822	c.435T>C	c.(433-435)gtT>gtC	p.V145V	AXDND1_ENST00000461179.2_3'UTR|AXDND1_ENST00000457238.2_Silent_p.V145V	NM_144696.4	NP_653297.3	Q5T1B0	AXDN1_HUMAN	axonemal dynein light chain domain containing 1	145										NS(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(27)|ovary(1)|pancreas(1)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)	59						AGAAGGCAGTTTGTCCCCCAC	0.363													T|||	2563	0.511781	0.2799	0.5274	5008	,	,		14205	0.6974		0.5159	False		,,,				2504	0.6186				p.V145V		Atlas-SNP	.											.	AXDND1	142	.	0			c.T435C						PASS	.	T		1413,2993	460.7+/-352.7	230,953,1020	128.0	105.0	113.0		435	-1.6	0.3	1	dbSNP_120	113	3991,4609	553.1+/-386.2	933,2125,1242	no	coding-synonymous	AXDND1	NM_144696.4		1163,3078,2262	CC,CT,TT		46.407,32.0699,41.5501		145/1013	179347832	5404,7602	2203	4300	6503	SO:0001819	synonymous_variant	126859	exon5			GGCAGTTTGTCCC	BX647935	CCDS30948.1	1q25.2	2011-02-18	2011-02-18	2011-02-18	ENSG00000162779	ENSG00000162779			26564	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 125"""	C1orf125		14702039	Standard	NM_144696		Approved	FLJ32940	uc001gmo.3	Q5T1B0	OTTHUMG00000035266	ENST00000367618.3:c.435T>C	1.37:g.179347832T>C		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	96	56	0.583333	NM_144696	Q6AWB2|Q96LJ3|Q96M01	Silent	SNP	ENST00000367618.3	37	CCDS30948.1																																																																																			T|0.546;C|0.454	0.454	strong		0.363	AXDND1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085312.1	NM_144696	
ZNF461	92283	hgsc.bcm.edu	37	19	37130419	37130419	+	Silent	SNP	G	G	A	rs61746298	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:37130419G>A	ENST00000588268.1	-	6	1055	c.828C>T	c.(826-828)aaC>aaT	p.N276N	ZNF461_ENST00000360357.4_Silent_p.N253N|ZNF461_ENST00000540605.2_5'UTR	NM_153257.2	NP_694989.2	Q8TAF7	ZN461_HUMAN	zinc finger protein 461	276					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(1)|large_intestine(4)|lung(17)|prostate(1)|urinary_tract(2)	29	Esophageal squamous(110;0.198)		COAD - Colon adenocarcinoma(19;0.0454)|Colorectal(19;0.065)			TCCCACATTCGTTACATTCAT	0.368													G|||	73	0.0145767	0.0	0.0317	5008	,	,		20302	0.001		0.0398	False		,,,				2504	0.0102				p.N276N		Atlas-SNP	.											.	ZNF461	73	.	0			c.C828T						PASS	.	G		18,4354	22.3+/-47.3	1,16,2169	56.0	60.0	59.0		828	1.0	1.0	19	dbSNP_129	59	265,8305	97.5+/-159.1	5,255,4025	no	coding-synonymous	ZNF461	NM_153257.2		6,271,6194	AA,AG,GG		3.0922,0.4117,2.1867		276/564	37130419	283,12659	2186	4285	6471	SO:0001819	synonymous_variant	92283	exon6			ACATTCGTTACAT	BX649031	CCDS54257.1, CCDS74348.1	19q13.13	2013-01-08				ENSG00000197808		"""Zinc fingers, C2H2-type"", ""-"""	21629	protein-coding gene	gene with protein product		608640				11579202, 15004467	Standard	XM_005259402		Approved	GIOT-1, MGC33911	uc002oem.3	Q8TAF7		ENST00000588268.1:c.828C>T	19.37:g.37130419G>A		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	81	39	0.481481	NM_153257	A8K9W9|Q6VSF7|Q9ULZ8	Silent	SNP	ENST00000588268.1	37	CCDS54257.1																																																																																			G|0.980;A|0.020	0.020	strong		0.368	ZNF461-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000453202.1	NM_153257	
HLA-DPB1	3115	hgsc.bcm.edu	37	6	33048599	33048599	+	Missense_Mutation	SNP	C	C	A	rs707958|rs386699870	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:33048599C>A	ENST00000418931.2	+	2	367	c.251C>A	c.(250-252)gCt>gAt	p.A84D	HLA-DPA1_ENST00000419277.1_5'Flank|HLA-DPB1_ENST00000471184.1_3'UTR|HLA-DPB1_ENST00000535465.1_Missense_Mutation_p.A84D	NM_002121.5	NP_002112.3	P04440	DPB1_HUMAN	major histocompatibility complex, class II, DP beta 1	84	Beta-1.		A -> D (in allele DPB1*02:01, allele DPB1*03:01, allele DPB1*04:02, allele DPB1*05:02, allele DPB1*06:01, allele DPB1*06:02, allele DPB1*08:01, allele DPB1*09:01, allele DPB1*10:01, allele DPB1*10:02, allele DPB1*11:02, allele DPB1*14:01, allele DPB1*14:02, allele DPB1*16:01, allele DPB1*16:02, allele DPB1*17:01, allele DPB1*18:01, allele DPB1*18:01, allele DPB1*18:02, allele DPB1*19:02, allele DPB1*20:01, allele DPB1*22:02, allele DPB1*25:01, allele DPB1*25:02, allele DPB1*26:02, allele DPB1*28:01, allele DPB1*29:01, allele DPB1*32:01, allele DPB1*35:01, allele DPB1*37:01, allele DPB1*41:01, allele DPB1*44:01, allele DPB1*45:01, allele DPB1*46:01, allele DPB1*48:01, allele DPB1*49:01, allele DPB1*50:01, allele DPB1*51:01, allele DPB1*53:01, allele DPB1*57:01, allele DPB1*59:01, allele DPB1*60:01, allele DPB1*68:01, allele DPB1*69:01, allele DPB1*70:01, allele DPB1*73:01, allele DPB1*75:01, allele DPB1*76:01, allele DPB1*77:01, allele DPB1*78:01, allele DPB1*79:01, allele DPB1*80:01, allele DPB1*81:01, allele DPB1*82:01, allele DPB1*83:01, allele DPB1*86:01, allele DPB1*88:01, allele DPB1*91:01, allele DPB1*92:01, allele DPB1*93:01, allele DPB1*94:01 and allele DPB1*98:01; dbSNP:rs707958).|A -> E (in allele DPB1*01:02, allele DPB1*02:02, allele DPB1*02:03, allele DPB1*05:01, allele DPB1*08:02, allele DPB1*17:02, allele DPB1*19:01, allele DPB1*21:01, allele DPB1*22:01, allele DPB1*24:01, allele DPB1*30:01, allele DPB1*36:01, allele DPB1*38:01, allele DPB1*47:01, allele DPB1*54:01, allele DPB1*84:01 and allele DPB1*97:01).|A -> V (in dbSNP:rs707958).		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell proliferation (GO:0042102)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	peptide antigen binding (GO:0042605)			cervix(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(3)|ovary(1)|skin(1)	11						GGGCGGCCTGCTGCGGAGTAC	0.647													.|||	2933	0.585663	0.4985	0.6398	5008	,	,		13901	0.8393		0.499	False		,,,				2504	0.4928				p.A84D		Atlas-SNP	.											HLA-DPB1,brain,glioma,0,1	HLA-DPB1	28	1	0			c.C251A						PASS	.	C	ASP/ALA	1507,1515		348,811,352	56.0	57.0	56.0		251	-8.0	0.0	6	dbSNP_86	56	2546,2872		573,1400,736	no	missense	HLA-DPB1	NM_002121.5	126	921,2211,1088	AA,AC,CC		46.9915,49.8676,48.0213	benign	84/259	33048599	4053,4387	1511	2709	4220	SO:0001583	missense	3115	exon2			GGCCTGCTGCGGA		CCDS4765.1	6p21.3	2013-01-11			ENSG00000223865	ENSG00000223865		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4940	protein-coding gene	gene with protein product		142858		HLA-DP1B			Standard	NM_002121		Approved		uc003ocu.2	P04440	OTTHUMG00000031076	ENST00000418931.2:c.251C>A	6.37:g.33048599C>A	ENSP00000408146:p.Ala84Asp	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	50	47	0.94	NM_002121	A0PFJ7|A5I886|A8YPB3|B5U8B4|B7VF80|B7VF87|B8ZX68|B8ZYT0|B9W5S8|B9W6F7|B9W6F9|C0MPP5|C0MPQ2|C0MPQ3|C0MPQ5|C0MPQ6|C0MPQ7|C4R9J5|C5IZL1|O00259|O19698|O19700|O19702|O19749|O46884|O77952|O98215|O98216|O98217|O98218|O98219|O98222|O98223|P01916|P04232|P13763|P79493|P79608|Q0P0L4|Q0ZFN3|Q14279|Q27S71|Q29682|Q29684|Q29698|Q29714|Q29775|Q29776|Q29778|Q29779|Q29781|Q29827|Q29828|Q29879|Q29880|Q29898|Q29977|Q2MGW3|Q30015|Q30031|Q30032|Q30033|Q30034|Q30050|Q30051|Q30052|Q30053|Q30054|Q30055|Q30174|Q4GY31|Q4JHD8|Q5ENE0|Q5ENE1|Q5ENW3|Q5EP46|Q5EP47|Q5EP49|Q5EP51|Q5EP52|Q5EP53|Q5EP56|Q5I4H8|Q5I4H9|Q5ISH4|Q5ISH5|Q5SQ73|Q5STP2|Q5YLA6|Q6IVX1|Q6LBX2|Q6LBX3|Q6LBX4|Q6LBX5|Q6LBX6|Q6LBX7|Q6PWX6|Q6TAS4|Q714U1|Q714U2|Q7YQ10|Q860Z7|Q8HWL7|Q8HWT5|Q8SNC4|Q95HC1|Q95IT7|Q95IT8|Q9BD13|Q9GIM2|Q9GIM4|Q9GIX6|Q9GJ41|Q9MY67|Q9TNT7|Q9TQE2|Q9XS11|Q9XS12	Missense_Mutation	SNP	ENST00000418931.2	37	CCDS4765.1	1331|1331	0.6094322344322345|0.6094322344322345	257|257	0.5223577235772358|0.5223577235772358	225|225	0.6215469613259669|0.6215469613259669	473|473	0.8269230769230769|0.8269230769230769	376|376	0.49604221635883905|0.49604221635883905	c|c	1.258|1.258	-0.616560|-0.616560	0.03663|0.03663	0.498676|0.498676	0.469915|0.469915	ENSG00000223865|ENSG00000223865	ENST00000418931;ENST00000535465;ENST00000411942;ENST00000428835|ENST00000416804	T;T;T|.	0.00249|.	8.44;8.44;8.44|.	4.02|4.02	-8.04|-8.04	0.01110|0.01110	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);|.	39.927600|.	0.00166|.	N|.	0.000000|.	T|T	0.00524|0.00524	0.0017|0.0017	N|N	0.00082|0.00082	-2.215|-2.215	0.80722|0.80722	P|P	0.0|0.0	B|.	0.02656|.	0.0|.	B|.	0.04013|.	0.001|.	T|T	0.36480|0.36480	-0.9746|-0.9746	9|4	0.02654|.	T|.	1|.	.|.	2.1334|2.1334	0.03755|0.03755	0.2119:0.383:0.2233:0.1818|0.2119:0.383:0.2233:0.1818	rs707958;rs2567285;rs3173296;rs3200322;rs3208224;rs9277350;rs17214727|rs707958;rs2567285;rs3173296;rs3200322;rs3208224;rs9277350;rs17214727	84|.	P04440|.	DPB1_HUMAN|.	D|M	84;84;84;61|51	ENSP00000408146:A84D;ENSP00000439674:A84D;ENSP00000412654:A61D|.	ENSP00000389210:A84D|.	A|L	+|+	2|1	0|2	HLA-DPB1|HLA-DPB1	33156577|33156577	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.000000|0.000000	0.00434|0.00434	-3.571000|-3.571000	0.00427|0.00427	-3.980000|-3.980000	0.00085|0.00085	-2.361000|-2.361000	0.00239|0.00239	GCT|CTG	A|0.527;C|0.473	0.527	strong		0.647	HLA-DPB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076106.2	NM_002121	
SERPINA5	5104	hgsc.bcm.edu	37	14	95053863	95053863	+	Missense_Mutation	SNP	C	C	T	rs6118	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:95053863C>T	ENST00000554866.1	+	2	278	c.164C>T	c.(163-165)gCc>gTc	p.A55V	SERPINA5_ENST00000554276.1_Missense_Mutation_p.A55V|SERPINA5_ENST00000553780.1_Missense_Mutation_p.A55V|SERPINA5_ENST00000329597.7_Missense_Mutation_p.A55V			P05154	IPSP_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 5	55			A -> V (in allele PCI*B; dbSNP:rs6118). {ECO:0000269|PubMed:10391209, ECO:0000269|PubMed:8713781, ECO:0000269|Ref.6}.		fusion of sperm to egg plasma membrane (GO:0007342)|lipid transport (GO:0006869)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of proteolysis (GO:0045861)|regulation of proteolysis (GO:0030162)|spermatogenesis (GO:0007283)	acrosomal membrane (GO:0002080)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|platelet alpha granule (GO:0031091)|platelet dense tubular network (GO:0031094)|protein C inhibitor-coagulation factor V complex (GO:0097181)|protein C inhibitor-coagulation factor Xa complex (GO:0097182)|protein C inhibitor-coagulation factor XI complex (GO:0097183)|protein C inhibitor-KLK3 complex (GO:0036029)|protein C inhibitor-plasma kallikrein complex (GO:0036030)|protein C inhibitor-PLAT complex (GO:0036026)|protein C inhibitor-PLAU complex (GO:0036027)|protein C inhibitor-thrombin complex (GO:0036028)|protein C inhibitor-TMPRSS11E complex (GO:0036025)|protein C inhibitor-TMPRSS7 complex (GO:0036024)|protein complex (GO:0043234)	acrosin binding (GO:0032190)|glycosaminoglycan binding (GO:0005539)|heparin binding (GO:0008201)|phosphatidylcholine binding (GO:0031210)|protease binding (GO:0002020)|retinoic acid binding (GO:0001972)|serine-type endopeptidase inhibitor activity (GO:0004867)			endometrium(3)|large_intestine(5)|lung(18)|ovary(2)|skin(5)|upper_aerodigestive_tract(3)	36				COAD - Colon adenocarcinoma(157;0.21)	Drotrecogin alfa(DB00055)|Urokinase(DB00013)	CTCTACAGGGCCTTGGCTTCC	0.617													C|||	1382	0.275958	0.6157	0.1196	5008	,	,		18490	0.2758		0.0905	False		,,,				2504	0.1186				p.A55V		Atlas-SNP	.											.	SERPINA5	69	.	0			c.C164T						PASS	.	C	VAL/ALA	2242,2164	582.4+/-385.6	573,1096,534	42.0	40.0	41.0		164	0.8	1.0	14	dbSNP_52	41	818,7782	188.4+/-235.4	41,736,3523	yes	missense	SERPINA5	NM_000624.4	64	614,1832,4057	TT,TC,CC		9.5116,49.1148,23.5276	possibly-damaging	55/407	95053863	3060,9946	2203	4300	6503	SO:0001583	missense	5104	exon3			ACAGGGCCTTGGC	M68516	CCDS9928.1	14q32.1	2014-02-18	2005-08-18		ENSG00000188488	ENSG00000188488		"""Serine (or cysteine) peptidase inhibitors"""	8723	protein-coding gene	gene with protein product		601841	"""serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 5"""	PLANH3, PCI		1714450, 8381582, 24172014	Standard	NM_000624		Approved	PAI3, PROCI	uc001ydm.3	P05154	OTTHUMG00000170860	ENST00000554866.1:c.164C>T	14.37:g.95053863C>T	ENSP00000451126:p.Ala55Val	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	43	18	0.418605	NM_000624	Q07616|Q9UG30	Missense_Mutation	SNP	ENST00000554866.1	37	CCDS9928.1	551	0.2522893772893773	291	0.5914634146341463	48	0.13259668508287292	142	0.24825174825174826	70	0.09234828496042216	C	2.095	-0.407466	0.04832	0.508852	0.095116	ENSG00000188488	ENST00000554220;ENST00000553780;ENST00000554760;ENST00000554866;ENST00000329597;ENST00000556775;ENST00000553511;ENST00000554633;ENST00000555681;ENST00000554276;ENST00000557598	D;D;D;D;D;D;D;D;D;D;D	0.85339	-1.97;-1.97;-1.97;-1.97;-1.97;-1.97;-1.97;-1.97;-1.97;-1.97;-1.97	4.11	0.813	0.18749	Serpin domain (3);	0.357145	0.22789	N	0.055621	T	0.00012	0.0000	L	0.42686	1.345	0.80722	P	0.0	P;P	0.43885	0.784;0.82	B;B	0.33339	0.153;0.162	T	0.48547	-0.9026	9	0.40728	T	0.16	.	6.2696	0.20947	0.343:0.3768:0.2802:0.0	rs6118;rs933176;rs60797362;rs6118	55;55	G3V5Q9;P05154	.;IPSP_HUMAN	V	55	ENSP00000450484:A55V;ENSP00000450837:A55V;ENSP00000452469:A55V;ENSP00000451126:A55V;ENSP00000333203:A55V;ENSP00000450745:A55V;ENSP00000451215:A55V;ENSP00000451697:A55V;ENSP00000451650:A55V;ENSP00000451610:A55V;ENSP00000450485:A55V	ENSP00000333203:A55V	A	+	2	0	SERPINA5	94123616	0.000000	0.05858	0.996000	0.52242	0.121000	0.20230	0.741000	0.26202	0.442000	0.26555	0.561000	0.74099	GCC	C|0.764;T|0.236	0.236	strong		0.617	SERPINA5-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410726.1	NM_000624	
CELSR1	9620	hgsc.bcm.edu	37	22	46805772	46805772	+	Missense_Mutation	SNP	C	C	T	rs11704506	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:46805772C>T	ENST00000262738.3	-	8	4938	c.4939G>A	c.(4939-4941)Gct>Act	p.A1647T		NM_014246.1	NP_055061.1	Q9NYQ6	CELR1_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 1	1647					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)		CTCCGAGCAGCGCAGCCTGGC	0.627													C|||	48	0.00958466	0.0015	0.013	5008	,	,		17743	0.0		0.0348	False		,,,				2504	0.002				p.A1647T		Atlas-SNP	.											.	CELSR1	242	.	0			c.G4939A						PASS	.	C	THR/ALA	39,4367	43.8+/-77.6	1,37,2165	126.0	107.0	114.0		4939	0.8	0.0	22	dbSNP_120	114	295,8305	109.0+/-169.6	6,283,4011	yes	missense	CELSR1	NM_014246.1	58	7,320,6176	TT,TC,CC		3.4302,0.8852,2.568	benign	1647/3015	46805772	334,12672	2203	4300	6503	SO:0001583	missense	9620	exon8			GAGCAGCGCAGCC	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.4939G>A	22.37:g.46805772C>T	ENSP00000262738:p.Ala1647Thr	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	43	21	0.488372	NM_014246	O95722|Q5TH47|Q9BWQ5|Q9Y506|Q9Y526	Missense_Mutation	SNP	ENST00000262738.3	37	CCDS14076.1	35	0.016025641025641024	2	0.0040650406504065045	7	0.019337016574585635	0	0.0	26	0.03430079155672823	C	8.987	0.976677	0.18812	0.008852	0.034302	ENSG00000075275	ENST00000262738	T	0.78246	-1.16	4.41	0.781	0.18561	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);	0.295815	0.25964	U	0.027179	T	0.30324	0.0761	N	0.13003	0.285	0.18873	N	0.999988	B	0.24675	0.109	B	0.14578	0.011	T	0.29792	-1.0000	10	0.44086	T	0.13	.	5.6632	0.17680	0.2461:0.5904:0.0:0.1635	rs11704506	1647	Q9NYQ6	CELR1_HUMAN	T	1647	ENSP00000262738:A1647T	ENSP00000262738:A1647T	A	-	1	0	CELSR1	45184436	0.000000	0.05858	0.033000	0.17914	0.653000	0.38743	-0.276000	0.08514	0.415000	0.25817	0.655000	0.94253	GCT	C|0.979;T|0.021	0.021	strong		0.627	CELSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318037.1	NM_014246	
SSBP4	170463	hgsc.bcm.edu	37	19	18538742	18538742	+	Silent	SNP	A	A	C	rs10405636	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:18538742A>C	ENST00000270061.7	+	4	523	c.229A>C	c.(229-231)Aga>Cga	p.R77R	SSBP4_ENST00000348495.6_Silent_p.R77R|SSBP4_ENST00000598159.2_3'UTR	NM_032627.4	NP_116016.1	Q9BWG4	SSBP4_HUMAN	single stranded DNA binding protein 4	77						nucleus (GO:0005634)	single-stranded DNA binding (GO:0003697)			endometrium(2)|kidney(1)|skin(1)	4						GGCGCCTGACAGAAGAGAGGC	0.662													C|||	2357	0.470647	0.8283	0.3689	5008	,	,		14038	0.2153		0.3469	False		,,,				2504	0.4499				p.R77R		Atlas-SNP	.											.	SSBP4	19	.	0			c.A229C						PASS	.	C	,	3306,1100	393.5+/-328.9	1249,808,146	65.0	61.0	63.0		229,229	3.7	1.0	19	dbSNP_119	63	2944,5654	666.5+/-402.4	539,1866,1894	no	coding-synonymous,coding-synonymous	SSBP4	NM_001009998.3,NM_032627.4	,	1788,2674,2040	CC,CA,AA		34.2405,24.966,48.0621	,	77/364,77/386	18538742	6250,6754	2203	4299	6502	SO:0001819	synonymous_variant	170463	exon4			CCTGACAGAAGAG		CCDS12378.1, CCDS32960.1	19p13.1	2008-02-05				ENSG00000130511			15676	protein-coding gene	gene with protein product		607391				12079286	Standard	NM_032627		Approved		uc002niy.3	Q9BWG4		ENST00000270061.7:c.229A>C	19.37:g.18538742A>C		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	113	113	1	NM_001009998	Q9BWW5	Silent	SNP	ENST00000270061.7	37	CCDS12378.1																																																																																			A|0.545;C|0.455	0.455	strong		0.662	SSBP4-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000466348.3	NM_032627	
SLC37A2	219855	hgsc.bcm.edu	37	11	124953735	124953735	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:124953735G>A	ENST00000403796.2	+	11	1302	c.1001G>A	c.(1000-1002)gGg>gAg	p.G334E	SLC37A2_ENST00000298280.5_Missense_Mutation_p.G334E|SLC37A2_ENST00000308074.4_Missense_Mutation_p.G334E|SLC37A2_ENST00000525837.1_3'UTR|SLC37A2_ENST00000407458.1_Missense_Mutation_p.G334E	NM_001145290.1	NP_001138762.1	Q8TED4	SPX2_HUMAN	solute carrier family 37 (glucose-6-phosphate transporter), member 2	334					carbohydrate transport (GO:0008643)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	transporter activity (GO:0005215)			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)		AAGGAGGCTGGGGACCTGTCT	0.557																																					p.G334E	Melanoma(11;373 620 21213 26083 47768)	Atlas-SNP	.											.	SLC37A2	105	.	0			c.G1001A						PASS	.						150.0	116.0	127.0					11																	124953735		2201	4299	6500	SO:0001583	missense	219855	exon11			AGGCTGGGGACCT	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.1001G>A	11.37:g.124953735G>A	ENSP00000384407:p.Gly334Glu	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	98	4	0.0408163	NM_001145290	A8K2P9|Q6P599|Q7Z7P8|Q8TEM2	Missense_Mutation	SNP	ENST00000403796.2	37	CCDS44757.1	.	.	.	.	.	.	.	.	.	.	G	27.3	4.818168	0.90790	.	.	ENSG00000134955	ENST00000403796;ENST00000407458;ENST00000298280;ENST00000308074	T;T;T;T	0.66099	0.02;0.02;-0.19;0.02	4.97	4.97	0.65823	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.85682	D	0.000000	D	0.84188	0.5417	M	0.92970	3.365	0.80722	D	1	D;D	0.76494	0.999;0.996	D;D	0.83275	0.996;0.979	D	0.88033	0.2776	10	0.72032	D	0.01	-19.5454	18.0204	0.89253	0.0:0.0:1.0:0.0	.	334;334	Q8TED4-2;Q8TED4	.;SPX2_HUMAN	E	334	ENSP00000384407:G334E;ENSP00000385126:G334E;ENSP00000298280:G334E;ENSP00000311833:G334E	ENSP00000298280:G334E	G	+	2	0	SLC37A2	124458945	1.000000	0.71417	0.998000	0.56505	0.959000	0.62525	9.214000	0.95140	2.583000	0.87209	0.655000	0.94253	GGG	.	.	none		0.557	SLC37A2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000386837.1	XM_166184	
TMCO3	55002	hgsc.bcm.edu	37	13	114152755	114152755	+	Silent	SNP	C	C	T	rs2260218	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:114152755C>T	ENST00000434316.2	+	3	902	c.543C>T	c.(541-543)gaC>gaT	p.D181D	TMCO3_ENST00000375391.1_Silent_p.D181D|TMCO3_ENST00000474393.1_3'UTR	NM_017905.4	NP_060375.4	Q6UWJ1	TMCO3_HUMAN	transmembrane and coiled-coil domains 3	181						integral component of membrane (GO:0016021)	solute:proton antiporter activity (GO:0015299)			NS(1)|endometrium(4)|large_intestine(9)|liver(1)|lung(8)|prostate(1)|stomach(1)	25	Lung NSC(43;0.0161)|all_neural(89;0.0337)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0145)|all_epithelial(44;0.00286)|all_lung(25;0.0273)|Breast(118;0.0411)|Lung NSC(25;0.0983)	all cancers(43;0.0317)			CCATGCTTGACGAGATTCTTG	0.398													.|||	1019	0.203474	0.4092	0.1369	5008	,	,		19525	0.1488		0.1292	False		,,,				2504	0.1053				p.D181D		Atlas-SNP	.											.	TMCO3	77	.	0			c.C543T						PASS	.	C		1511,2895	481.5+/-359.1	256,999,948	133.0	130.0	131.0		543	-3.9	0.0	13	dbSNP_100	131	1089,7511	226.6+/-262.3	62,965,3273	no	coding-synonymous	TMCO3	NM_017905.4		318,1964,4221	TT,TC,CC		12.6628,34.2941,19.9908		181/678	114152755	2600,10406	2203	4300	6503	SO:0001819	synonymous_variant	55002	exon3			GCTTGACGAGATT	BC012564	CCDS9537.1	13q34	2008-02-05	2005-07-22	2005-07-22	ENSG00000150403	ENSG00000150403			20329	protein-coding gene	gene with protein product			"""chromosome 13 open reading frame 11"""	C13orf11			Standard	NM_017905		Approved	FLJ20623	uc001vtu.4	Q6UWJ1	OTTHUMG00000017389	ENST00000434316.2:c.543C>T	13.37:g.114152755C>T		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	48	25	0.520833	NM_017905	Q5JSB1|Q6NUN1|Q8NG29|Q8TCI6|Q96EA6|Q9NWT2	Silent	SNP	ENST00000434316.2	37	CCDS9537.1																																																																																			C|0.795;T|0.205	0.205	strong		0.398	TMCO3-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045931.3	NM_017905	
BARX2	8538	hgsc.bcm.edu	37	11	129321066	129321066	+	Silent	SNP	C	C	T	rs10791011	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:129321066C>T	ENST00000281437.4	+	4	705	c.609C>T	c.(607-609)ccC>ccT	p.P203P	BARX2_ENST00000526127.1_Silent_p.P58P|BARX2_ENST00000531946.1_Silent_p.P81P	NM_003658.4	NP_003649.2	Q9UMQ3	BARX2_HUMAN	BARX homeobox 2	203					cartilage condensation (GO:0001502)|catagen (GO:0042637)|myotube differentiation (GO:0014902)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|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)			breast(1)|central_nervous_system(1)|large_intestine(4)|lung(7)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	20	all_hematologic(175;0.0749)	Lung NSC(97;0.000383)|all_lung(97;0.000824)|Breast(109;0.000962)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)		OV - Ovarian serous cystadenocarcinoma(99;0.00929)|Lung(977;0.0245)|LUSC - Lung squamous cell carcinoma(976;0.0253)		CCACAAAACCCAAAGGTCGCC	0.483													C|||	1499	0.299321	0.2224	0.1902	5008	,	,		17671	0.4048		0.1968	False		,,,				2504	0.4775				p.P203P		Atlas-SNP	.											.	BARX2	40	.	0			c.C609T						PASS	.	C		981,3421	366.8+/-318.0	105,771,1325	74.0	66.0	69.0		609	2.1	1.0	11	dbSNP_120	69	1707,6887	309.0+/-309.2	164,1379,2754	no	coding-synonymous	BARX2	NM_003658.4		269,2150,4079	TT,TC,CC		19.8627,22.2853,20.6833		203/280	129321066	2688,10308	2201	4297	6498	SO:0001819	synonymous_variant	8538	exon4			AAAACCCAAAGGT	AF031924	CCDS8481.1	11q24.3	2011-06-20	2007-07-09		ENSG00000043039	ENSG00000043039		"""Homeoboxes / ANTP class : NKL subclass"""	956	protein-coding gene	gene with protein product		604823	"""BarH-like homeobox 2"""			10644443	Standard	NM_003658		Approved		uc001qfc.4	Q9UMQ3	OTTHUMG00000165776	ENST00000281437.4:c.609C>T	11.37:g.129321066C>T		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	81	62	0.765432	NM_003658	O43518|Q6NT51	Silent	SNP	ENST00000281437.4	37	CCDS8481.1																																																																																			C|0.769;T|0.231	0.231	strong		0.483	BARX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386153.1	NM_003658	
PTCHD3	374308	hgsc.bcm.edu	37	10	27687437	27687437	+	Missense_Mutation	SNP	C	C	A	rs139600575	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:27687437C>A	ENST00000438700.3	-	4	2207	c.2090G>T	c.(2089-2091)tGg>tTg	p.W697L		NM_001034842.3	NP_001030014.2	Q3KNS1	PTHD3_HUMAN	patched domain containing 3	697					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						TGCATCTAACCAAAACTCTGT	0.284																																					p.W697L		Atlas-SNP	.											.	PTCHD3	140	.	0			c.G2090T						PASS	.	C	LEU/TRP	0,4404		0,0,2202	39.0	41.0	41.0		2090	4.2	1.0	10	dbSNP_134	41	5,8569	3.7+/-12.6	0,5,4282	yes	missense	PTCHD3	NM_001034842.3	61	0,5,6484	AA,AC,CC		0.0583,0.0,0.0385	probably-damaging	697/768	27687437	5,12973	2202	4287	6489	SO:0001583	missense	374308	exon4			TCTAACCAAAACT	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.2090G>T	10.37:g.27687437C>A	ENSP00000417658:p.Trp697Leu	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	76	35	0.460526	NM_001034842	I3L499|Q6ZU28	Missense_Mutation	SNP	ENST00000438700.3	37	CCDS31173.1	.	.	.	.	.	.	.	.	.	.	C	15.65	2.895630	0.52121	0.0	5.83E-4	ENSG00000182077	ENST00000438700	D	0.89746	-2.56	4.18	4.18	0.49190	.	0.183449	0.51477	D	0.000085	D	0.94548	0.8244	M	0.84326	2.69	0.49130	D	0.999753	D	0.89917	1.0	D	0.87578	0.998	D	0.95493	0.8571	10	0.87932	D	0	-7.4899	16.2851	0.82714	0.0:1.0:0.0:0.0	.	697	Q3KNS1	PTHD3_HUMAN	L	697	ENSP00000417658:W697L	ENSP00000417658:W697L	W	-	2	0	PTCHD3	27727443	1.000000	0.71417	1.000000	0.80357	0.422000	0.31414	3.467000	0.53078	2.169000	0.68431	0.542000	0.68232	TGG	C|0.999;A|0.001	0.001	strong		0.284	PTCHD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047325.3	XM_370541	
DGKI	9162	hgsc.bcm.edu	37	7	137128830	137128830	+	Silent	SNP	T	T	C	rs1918837	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:137128830T>C	ENST00000288490.5	-	29	2778	c.2778A>G	c.(2776-2778)gaA>gaG	p.E926E	DGKI_ENST00000494390.1_5'UTR|DGKI_ENST00000453654.2_Silent_p.E595E|DGKI_ENST00000446122.1_Silent_p.E908E|DGKI_ENST00000424189.2_Silent_p.E939E	NM_004717.2	NP_004708.1	O75912	DGKI_HUMAN	diacylglycerol kinase, iota	926					blood coagulation (GO:0007596)|intracellular signal transduction (GO:0035556)|platelet activation (GO:0030168)|positive regulation of Ras protein signal transduction (GO:0046579)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of Rap GTPase activity (GO:0032317)	cytoplasm (GO:0005737)|guanyl-nucleotide exchange factor complex (GO:0032045)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|diacylglycerol kinase activity (GO:0004143)|GTPase inhibitor activity (GO:0005095)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)			breast(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(46)|ovary(2)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	84						TACCATGATCTTCTGAAGAGA	0.299													T|||	2228	0.444888	0.2057	0.5274	5008	,	,		16450	0.6627		0.3598	False		,,,				2504	0.5726				p.E926E		Atlas-SNP	.											.	DGKI	335	.	0			c.A2778G						PASS	.	T		1016,3384	366.4+/-317.8	112,792,1296	58.0	56.0	57.0		2778	5.5	1.0	7	dbSNP_92	57	3044,5556	455.4+/-363.8	548,1948,1804	no	coding-synonymous	DGKI	NM_004717.2		660,2740,3100	CC,CT,TT		35.3953,23.0909,31.2308		926/1066	137128830	4060,8940	2200	4300	6500	SO:0001819	synonymous_variant	9162	exon29			ATGATCTTCTGAA	AF061936	CCDS5845.1	7q32.3-q33	2013-01-10			ENSG00000157680	ENSG00000157680		"""Ankyrin repeat domain containing"""	2855	protein-coding gene	gene with protein product		604072				9830018	Standard	NM_004717		Approved	DGK-IOTA	uc003vtt.3	O75912	OTTHUMG00000155697	ENST00000288490.5:c.2778A>G	7.37:g.137128830T>C		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	103	47	0.456311	NM_004717	A4D1Q9|Q9NZ49	Silent	SNP	ENST00000288490.5	37	CCDS5845.1																																																																																			T|0.641;C|0.359	0.359	strong		0.299	DGKI-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341286.3	NM_004717	
MUC4	4585	hgsc.bcm.edu	37	3	195509676	195509676	+	Missense_Mutation	SNP	C	C	G	rs372419355		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195509676C>G	ENST00000463781.3	-	2	9234	c.8775G>C	c.(8773-8775)caG>caC	p.Q2925H	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.Q2925H	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.Q2925H(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)		GAGGGGTGGCCTGACCTGTGG	0.582																																					p.Q2925H		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	1	Substitution - Missense(1)	stomach(1)	c.G8775C						scavenged	.						9.0	7.0	8.0					3																	195509676		655	1521	2176	SO:0001583	missense	4585	exon2			GGTGGCCTGACCT	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.8775G>C	3.37:g.195509676C>G	ENSP00000417498:p.Gln2925His	Somatic	57	1	0.0175439		WXS	Illumina HiSeq	Phase_I	120	60	0.5	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	0.030	-1.340469	0.01277	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.34472	1.42;1.36	.	.	.	.	.	.	.	.	T	0.15652	0.0377	N	0.08118	0	0.09310	N	1	B	0.17852	0.024	B	0.21546	0.035	T	0.31420	-0.9944	7	.	.	.	.	4.6597	0.12636	0.0:1.0:0.0:0.0	.	2797	E7ESK3	.	H	2925	ENSP00000417498:Q2925H;ENSP00000420243:Q2925H	.	Q	-	3	2	MUC4	196994455	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.474000	0.06607	-0.000000	0.14550	0.000000	0.15137	CAG	.	.	weak		0.582	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
CCP110	9738	hgsc.bcm.edu	37	16	19548290	19548290	+	Silent	SNP	G	G	A	rs7191012	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:19548290G>A	ENST00000381396.5	+	4	1546	c.1299G>A	c.(1297-1299)gcG>gcA	p.A433A	CCP110_ENST00000396208.2_Silent_p.A433A|CCP110_ENST00000396212.2_Silent_p.A433A	NM_001199022.1	NP_001185951	O43303	CP110_HUMAN	centriolar coiled coil protein 110kDa	433	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						CTGATTTAGCGGGAGTTTGTT	0.368													G|||	776	0.154952	0.1702	0.1844	5008	,	,		22792	0.1577		0.1581	False		,,,				2504	0.1074				p.A433A		Atlas-SNP	.											.	CCP110	57	.	0			c.G1299A						PASS	.	G	,	696,3698	288.7+/-280.0	49,598,1550	97.0	96.0	96.0		1299,1299	0.5	0.1	16	dbSNP_116	96	1344,7256	261.4+/-283.8	101,1142,3057	no	coding-synonymous,coding-synonymous	CCP110	NM_001199022.1,NM_014711.4	,	150,1740,4607	AA,AG,GG		15.6279,15.8398,15.6996	,	433/1013,433/992	19548290	2040,10954	2197	4300	6497	SO:0001819	synonymous_variant	9738	exon4			TTTAGCGGGAGTT	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.1299G>A	16.37:g.19548290G>A		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	177	69	0.38983	NM_001199022	B7WP23|O43335|Q68DV9|Q8NE13	Silent	SNP	ENST00000381396.5	37	CCDS55992.1																																																																																			G|0.843;A|0.157	0.157	strong		0.368	CCP110-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254284.2	NM_014711	
CYFIP2	26999	hgsc.bcm.edu	37	5	156741411	156741411	+	Silent	SNP	C	C	T	rs139943836	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:156741411C>T	ENST00000521420.1	+	11	1183	c.1092C>T	c.(1090-1092)ttC>ttT	p.F364F	CYFIP2_ENST00000318218.6_Silent_p.F390F|CYFIP2_ENST00000442283.2_5'UTR|CYFIP2_ENST00000522463.1_Silent_p.F194F|CYFIP2_ENST00000541131.1_Silent_p.F315F|CYFIP2_ENST00000435847.2_Silent_p.F64F|CYFIP2_ENST00000347377.6_Silent_p.F390F|CYFIP2_ENST00000377576.3_Silent_p.F390F					cytoplasmic FMR1 interacting protein 2											breast(1)|endometrium(12)|kidney(2)|lung(23)	38	Renal(175;0.00212)	Medulloblastoma(196;0.0306)|all_neural(177;0.0897)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			GCGAGCTCTTCGACCTAGCCC	0.597													C|||	4	0.000798722	0.0	0.0014	5008	,	,		16212	0.0		0.003	False		,,,				2504	0.0				p.F390F		Atlas-SNP	.											.	CYFIP2	354	.	0			c.C1170T						PASS	.	C	,,	1,4071		0,1,2035	100.0	104.0	103.0		1170,1170,1170	-0.7	1.0	5	dbSNP_134	103	27,8355		0,27,4164	no	coding-synonymous,coding-synonymous,coding-synonymous	CYFIP2	NM_001037332.2,NM_001037333.1,NM_014376.2	,,	0,28,6199	TT,TC,CC		0.3221,0.0246,0.2248	,,	390/1254,390/1254,390/1254	156741411	28,12426	2036	4191	6227	SO:0001819	synonymous_variant	26999	exon12			GCTCTTCGACCTA	AF160973	CCDS75364.1	5q34	2008-07-18				ENSG00000055163			13760	protein-coding gene	gene with protein product	"""p53 inducible protein"""	606323				11438699	Standard	NM_001037333		Approved	PIR121	uc021ygm.1	Q96F07		ENST00000521420.1:c.1092C>T	5.37:g.156741411C>T		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	71	38	0.535211	NM_001037332		Silent	SNP	ENST00000521420.1	37																																																																																				C|0.999;T|0.001	0.001	strong		0.597	CYFIP2-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000373710.1	NM_001037332	
CCDC110	256309	hgsc.bcm.edu	37	4	186380515	186380515	+	Missense_Mutation	SNP	G	G	A	rs11132306	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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_ENST00000393540.3_Missense_Mutation_p.S372F|CCDC110_ENST00000507501.1_5'Flank	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	157	0	0		WXS	Illumina HiSeq	Phase_I	122	56	0.459016	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	
SLC6A17	388662	hgsc.bcm.edu	37	1	110709719	110709719	+	Silent	SNP	T	T	C	rs35600013|rs7527375	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:110709719T>C	ENST00000331565.4	+	2	653	c.168T>C	c.(166-168)gaT>gaC	p.D56D	RP5-1028L10.1_ENST00000430098.1_RNA|RP5-1028L10.1_ENST00000443008.1_RNA|RP5-1028L10.1_ENST00000418579.1_RNA	NM_001010898.2	NP_001010898.1	Q9H1V8	S6A17_HUMAN	solute carrier family 6 (neutral amino acid transporter), member 17	56					alanine transport (GO:0032328)|glycine transport (GO:0015816)|leucine transport (GO:0015820)|neutral amino acid transport (GO:0015804)|proline transport (GO:0015824)	cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|synaptic vesicle (GO:0008021)	neurotransmitter:sodium symporter activity (GO:0005328)			breast(1)|endometrium(4)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	37		all_cancers(81;9.9e-06)|all_epithelial(167;3.24e-06)|all_lung(203;0.000116)|Lung NSC(277;0.000233)		Lung(183;0.0282)|Epithelial(280;0.0372)|all cancers(265;0.0378)|Colorectal(144;0.0438)|LUSC - Lung squamous cell carcinoma(189;0.151)|COAD - Colon adenocarcinoma(174;0.151)		AGGAGCTGGATGCAGAGGACC	0.607													C|||	1968	0.392971	0.4652	0.353	5008	,	,		14134	0.2143		0.5249	False		,,,				2504	0.3722				p.D56D		Atlas-SNP	.											.	SLC6A17	86	.	0			c.T168C						PASS	.	C	,VAL/ILE	2258,2148		577,1104,522	72.0	58.0	63.0		168,292	-7.0	0.0	1	dbSNP_116	63	4519,4081		1273,1973,1054	no	coding-synonymous,missense	SLC6A17,LOC100130800	NM_001010898.2,XM_001719118.1	,29	1850,3077,1576	CC,CT,TT		47.4535,48.7517,47.8933	,	56/728,98/154	110709719	6777,6229	2203	4300	6503	SO:0001819	synonymous_variant	388662	exon2			GCTGGATGCAGAG		CCDS30799.1	1p13.2	2013-07-19	2013-07-19		ENSG00000197106	ENSG00000197106		"""Solute carriers"""	31399	protein-coding gene	gene with protein product		610299	"""solute carrier family 6 (neurotransmitter transporter), member 17"", ""solute carrier family 6, member 17"""				Standard	NM_001010898		Approved		uc009wfq.3	Q9H1V8	OTTHUMG00000011761	ENST00000331565.4:c.168T>C	1.37:g.110709719T>C		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	90	44	0.488889	NM_001010898	A6NEA8|A8K1R7|B9EIR5|Q5T5Q9	Silent	SNP	ENST00000331565.4	37	CCDS30799.1																																																																																			T|0.518;C|0.482	0.482	strong		0.607	SLC6A17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032550.2	XM_371280	
CCDC102B	79839	hgsc.bcm.edu	37	18	66513615	66513615	+	Missense_Mutation	SNP	A	A	G	rs2187094	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:66513615A>G	ENST00000360242.5	+	4	1010	c.893A>G	c.(892-894)aAg>aGg	p.K298R	CCDC102B_ENST00000577772.1_3'UTR|CCDC102B_ENST00000358653.5_Splice_Site_p.E312E|CCDC102B_ENST00000584156.1_Missense_Mutation_p.K298R|CCDC102B_ENST00000319445.6_Missense_Mutation_p.K298R	NM_024781.2	NP_079057	Q68D86	C102B_HUMAN	coiled-coil domain containing 102B	298			K -> R (in dbSNP:rs2187094). {ECO:0000269|PubMed:17974005}.					p.K298R(1)		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)				TGGAAGTGGAAGTATGAAGAA	0.358													A|||	1842	0.367812	0.0703	0.4467	5008	,	,		12915	0.6438		0.4006	False		,,,				2504	0.3957				p.K298R		Atlas-SNP	.											CCDC102B,NS,carcinoma,0,2	CCDC102B	92	2	1	Substitution - Missense(1)	stomach(1)	c.A893G						PASS	.	A	ARG/LYS,ARG/LYS	561,3845	245.3+/-254.3	37,487,1679	70.0	70.0	70.0		893,893	4.4	1.0	18	dbSNP_96	70	3289,5311	486.0+/-371.8	639,2011,1650	yes	missense,missense	CCDC102B	NM_001093729.1,NM_024781.2	26,26	676,2498,3329	GG,GA,AA		38.2442,12.7326,29.6017	benign,benign	298/514,298/514	66513615	3850,9156	2203	4300	6503	SO:0001583	missense	79839	exon6			AGTGGAAGTATGA	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.893A>G	18.37:g.66513615A>G	ENSP00000353377:p.Lys298Arg	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	125	125	1	NM_001093729	Q7Z467|Q8NDK7|Q9H5C1	Missense_Mutation	SNP	ENST00000360242.5	37	CCDS11996.2	850	0.3891941391941392	37	0.07520325203252033	156	0.430939226519337	359	0.6276223776223776	298	0.39313984168865435	A	8.901	0.956416	0.18507	0.127326	0.382442	ENSG00000150636	ENST00000319445;ENST00000360242	T;T	0.15256	2.44;2.44	5.56	4.4	0.53042	.	0.000000	0.64402	D	0.000011	T	0.00012	0.0000	L	0.37697	1.125	0.09310	P	1.0	P	0.47034	0.889	B	0.42827	0.399	T	0.11155	-1.0599	9	0.18710	T	0.47	-26.3717	9.5041	0.39035	0.9196:0.0:0.0804:0.0	rs2187094;rs52829798;rs58141486;rs2187094	298	Q68D86	C102B_HUMAN	R	298	ENSP00000316237:K298R;ENSP00000353377:K298R	ENSP00000316237:K298R	K	+	2	0	CCDC102B	64664595	1.000000	0.71417	0.998000	0.56505	0.313000	0.28021	2.635000	0.46537	1.043000	0.40175	0.528000	0.53228	AAG	A|0.674;G|0.326	0.326	strong		0.358	CCDC102B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256225.2	NM_024781	
ZNF419	79744	hgsc.bcm.edu	37	19	58002964	58002964	+	Splice_Site	SNP	G	G	C	rs1135692	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:58002964G>C	ENST00000221735.7	+	3	384	c.198G>C	c.(196-198)ctG>ctC	p.L66L	ZNF419_ENST00000424930.2_Splice_Site_p.L67L|AC003005.4_ENST00000601674.1_Splice_Site_p.L53L|ZNF419_ENST00000347466.6_Splice_Site_p.L67L|ZNF419_ENST00000415379.2_Splice_Site_p.L53L|ZNF419_ENST00000354197.4_Splice_Site_p.L54L|ZNF419_ENST00000518999.1_Splice_Site_p.L67L|ZNF419_ENST00000520540.1_Splice_Site_p.L54L|ZNF419_ENST00000442920.2_Splice_Site_p.L53L|ZNF419_ENST00000426954.2_Splice_Site_p.L54L			Q96HQ0	ZN419_HUMAN	zinc finger protein 419	66	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(10)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	26		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0694)|Breast(46;0.0848)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0252)|Lung(386;0.171)		TGGCCTCTCTGGGTAAGGTTC	0.542													G|||	1310	0.261581	0.2761	0.2608	5008	,	,		20364	0.1181		0.3638	False		,,,				2504	0.2853				p.L67L		Atlas-SNP	.											.	ZNF419	134	.	0			c.G201C						PASS	.	G	,,,,,,	1262,3144	428.7+/-342.0	179,904,1120	67.0	69.0	69.0		201,162,159,201,162,159,198	-0.9	0.2	19	dbSNP_116	69	3010,5588	464.4+/-366.2	498,2014,1787	no	coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice	ZNF419	NM_001098491.1,NM_001098492.1,NM_001098493.1,NM_001098494.1,NM_001098495.1,NM_001098496.1,NM_024691.3	,,,,,,	677,2918,2907	CC,CG,GG		35.0081,28.6428,32.8514	,,,,,,	67/512,54/499,53/498,67/479,54/466,53/465,66/511	58002964	4272,8732	2203	4299	6502	SO:0001630	splice_region_variant	79744	exon3			CTCTCTGGGTAAG	AK026886	CCDS42637.1, CCDS46211.1, CCDS54325.1, CCDS54326.1, CCDS54327.1, CCDS54328.1	19q13.43	2013-01-08	2006-12-15	2006-12-15	ENSG00000105136	ENSG00000105136		"""Zinc fingers, C2H2-type"", ""-"""	20648	protein-coding gene	gene with protein product			"""zinc finger protein 419A"""	ZNF419A			Standard	NM_001098492		Approved		uc010ety.1	Q96HQ0	OTTHUMG00000037073	ENST00000221735.7:c.199+1G>C	19.37:g.58002964G>C		Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	253	67	0.264822	NM_001098494	B4DXU7|B4E348|B7ZA41|E9PCP4|E9PED0|E9PET3|E9PFX9|Q9H5P0	Silent	SNP	ENST00000221735.7	37	CCDS54326.1																																																																																			G|0.730;C|0.270	0.270	strong		0.542	ZNF419-006	KNOWN	NAGNAG_splice_site|non_canonical_polymorphism|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000378506.1	NM_024691	Silent
EPHA3	2042	hgsc.bcm.edu	37	3	89521693	89521693	+	Missense_Mutation	SNP	T	T	C	rs35124509	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:89521693T>C	ENST00000336596.2	+	16	2995	c.2770T>C	c.(2770-2772)Tgg>Cgg	p.W924R	EPHA3_ENST00000494014.1_Intron	NM_005233.5	NP_005224.2	P29320	EPHA3_HUMAN	EPH receptor A3	924	SAM. {ECO:0000255|PROSITE- ProRule:PRU00184}.		W -> R (in dbSNP:rs35124509). {ECO:0000269|PubMed:1311845, ECO:0000269|PubMed:17344846}.		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)		TAATGGTGTCTGGACAGCACA	0.423										TSP Lung(6;0.00050)			C|||	1959	0.391174	0.674	0.3732	5008	,	,		19697	0.2163		0.3976	False		,,,				2504	0.1953				p.W924R		Atlas-SNP	.											EPHA3,NS,carcinoma,-2,2	EPHA3	501	2	0			c.T2770C						scavenged	.	C	ARG/TRP	2721,1685	510.6+/-367.6	839,1043,321	149.0	139.0	143.0		2770	3.8	1.0	3	dbSNP_126	143	3370,5230	641.9+/-399.7	662,2046,1592	yes	missense	EPHA3	NM_005233.5	101	1501,3089,1913	CC,CT,TT		39.186,38.2433,46.8322	benign	924/984	89521693	6091,6915	2203	4300	6503	SO:0001583	missense	2042	exon16			GGTGTCTGGACAG	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.2770T>C	3.37:g.89521693T>C	ENSP00000337451:p.Trp924Arg	Somatic	172	3	0.0174419		WXS	Illumina HiSeq	Phase_I	102	101	0.990196	NM_005233	Q9H2V3|Q9H2V4	Missense_Mutation	SNP	ENST00000336596.2	37	CCDS2922.1	881	0.4033882783882784	321	0.6524390243902439	147	0.40607734806629836	115	0.20104895104895104	298	0.39313984168865435	C	11.95	1.790698	0.31685	0.617567	0.39186	ENSG00000044524	ENST00000336596	D	0.83506	-1.73	5.72	3.84	0.44239	Sterile alpha motif domain (2);Sterile alpha motif/pointed domain (2);Sterile alpha motif, type 2 (1);	0.000000	0.85682	N	0.000000	T	0.00012	0.0000	N	0.00308	-1.67	0.09310	P	0.9999999999999999	B	0.02656	0.0	B	0.01281	0.0	T	0.47058	-0.9146	8	.	.	.	.	9.5719	0.39433	0.2609:0.6726:0.0:0.0665	rs35124509;rs61735548;rs35124509	924	P29320	EPHA3_HUMAN	R	924	ENSP00000337451:W924R	.	W	+	1	0	EPHA3	89604383	0.996000	0.38824	0.992000	0.48379	0.964000	0.63967	1.947000	0.40293	0.296000	0.22592	-0.128000	0.14901	TGG	T|0.563;C|0.437	0.437	strong		0.423	EPHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352995.1	NM_005233	
TAF2	6873	hgsc.bcm.edu	37	8	120803654	120803654	+	Silent	SNP	C	C	T	rs11996390	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:120803654C>T	ENST00000378164.2	-	11	1621	c.1323G>A	c.(1321-1323)ctG>ctA	p.L441L		NM_003184.3	NP_003175	Q6P1X5	TAF2_HUMAN	TAF2 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 150kDa	441					G2/M transition of mitotic cell cycle (GO:0000086)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to organic cyclic compound (GO:0014070)|transcription initiation from RNA polymerase II promoter (GO:0006367)	transcription factor TFIID complex (GO:0005669)|transcription factor TFTC complex (GO:0033276)	metallopeptidase activity (GO:0008237)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			NS(2)|breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(21)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	49	Lung NSC(37;9.35e-07)|Ovarian(258;0.011)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00185)			ATTCCCAGGACAGTGTATGTG	0.328													C|||	879	0.175519	0.3079	0.1427	5008	,	,		18326	0.0268		0.1968	False		,,,				2504	0.1513				p.L441L		Atlas-SNP	.											.	TAF2	204	.	0			c.G1323A						PASS	.	C		1341,3065	449.0+/-348.9	214,913,1076	108.0	102.0	104.0		1323	-9.6	0.0	8	dbSNP_120	104	1966,6632	344.2+/-325.2	203,1560,2536	no	coding-synonymous	TAF2	NM_003184.3		417,2473,3612	TT,TC,CC		22.8658,30.4358,25.4306		441/1200	120803654	3307,9697	2203	4299	6502	SO:0001819	synonymous_variant	6873	exon11			CCAGGACAGTGTA	AF040701	CCDS34937.1	8q24	2012-07-18	2002-08-29	2001-12-07	ENSG00000064313	ENSG00000064313			11536	protein-coding gene	gene with protein product		604912	"""TATA box binding protein (TBP)-associated factor, RNA polymerase II, B, 150kD"""	TAF2B		9774672, 9418870	Standard	NM_003184		Approved	TAFII150, CIF150	uc003you.3	Q6P1X5	OTTHUMG00000165009	ENST00000378164.2:c.1323G>A	8.37:g.120803654C>T		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	126	24	0.190476	NM_003184	B2RE82|O43487|O43604|O60668|Q86WW7|Q8IWK4	Silent	SNP	ENST00000378164.2	37	CCDS34937.1	381	0.17445054945054944	168	0.34146341463414637	51	0.1408839779005525	13	0.022727272727272728	149	0.19656992084432717	C	4.330	0.060658	0.08339	0.304358	0.228658	ENSG00000064313	ENST00000523904	.	.	.	4.79	-9.59	0.00556	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.999999999670865	.	.	.	.	.	.	T	0.17561	-1.0365	3	.	.	.	-39.2558	13.4587	0.61214	0.2386:0.6286:0.0746:0.0582	rs11996390;rs57077905;rs11996390	.	.	.	Y	134	.	.	C	-	2	0	TAF2	120872835	0.001000	0.12720	0.002000	0.10522	0.717000	0.41224	-1.603000	0.02077	-3.771000	0.00109	-0.499000	0.04595	TGT	C|0.777;T|0.223	0.223	strong		0.328	TAF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381436.1	NM_003184	
PRKCI	5584	hgsc.bcm.edu	37	3	169988286	169988286	+	Silent	SNP	C	C	T	rs56257047	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:169988286C>T	ENST00000295797.4	+	6	833	c.528C>T	c.(526-528)ctC>ctT	p.L176L		NM_002740.5	NP_002731.4	P41743	KPCI_HUMAN	protein kinase C, iota	176	Regulatory domain.				actin filament organization (GO:0007015)|cell junction assembly (GO:0034329)|cell migration (GO:0016477)|cell-cell junction organization (GO:0045216)|cellular response to insulin stimulus (GO:0032869)|cytoskeleton organization (GO:0007010)|establishment of apical/basal cell polarity (GO:0035089)|establishment or maintenance of epithelial cell apical/basal polarity (GO:0045197)|eye photoreceptor cell development (GO:0042462)|Golgi vesicle budding (GO:0048194)|intracellular signal transduction (GO:0035556)|membrane organization (GO:0061024)|negative regulation of apoptotic process (GO:0043066)|negative regulation of glial cell apoptotic process (GO:0034351)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of endothelial cell apoptotic process (GO:2000353)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of glial cell proliferation (GO:0060252)|positive regulation of glucose import (GO:0046326)|positive regulation of neuron projection development (GO:0010976)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein phosphorylation (GO:0006468)|protein targeting to membrane (GO:0006612)|response to interleukin-1 (GO:0070555)|secretion (GO:0046903)|tight junction assembly (GO:0070830)|vesicle-mediated transport (GO:0016192)	apical plasma membrane (GO:0016324)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|intercellular bridge (GO:0045171)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|Schmidt-Lanterman incisure (GO:0043220)	ATP binding (GO:0005524)|phospholipid binding (GO:0005543)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)|zinc ion binding (GO:0008270)			breast(2)|endometrium(5)|kidney(1)|large_intestine(4)|lung(16)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	36	all_cancers(22;6.45e-23)|all_epithelial(15;8.52e-28)|all_lung(20;6.31e-17)|Lung NSC(18;2.61e-16)|Ovarian(172;0.000337)|Breast(254;0.169)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.197)		Tamoxifen(DB00675)	ACTGCAAACTCTTGGTTCATA	0.403													C|||	378	0.0754792	0.0204	0.1225	5008	,	,		19057	0.0645		0.1541	False		,,,				2504	0.047				p.L176L		Atlas-SNP	.											.	PRKCI	82	.	0			c.C528T						PASS	.	C		176,4230	116.3+/-154.2	5,166,2032	115.0	106.0	109.0		528	-3.1	0.6	3	dbSNP_129	109	1299,7301	256.8+/-281.1	102,1095,3103	no	coding-synonymous	PRKCI	NM_002740.5		107,1261,5135	TT,TC,CC		15.1047,3.9946,11.3409		176/597	169988286	1475,11531	2203	4300	6503	SO:0001819	synonymous_variant	5584	exon6			CAAACTCTTGGTT		CCDS3212.2	3q26.3	2008-07-18			ENSG00000163558	ENSG00000163558	2.7.11.13		9404	protein-coding gene	gene with protein product		600539		DXS1179E		7607695, 11978974	Standard	NM_002740		Approved	PKCI	uc003fgs.2	P41743	OTTHUMG00000150214	ENST00000295797.4:c.528C>T	3.37:g.169988286C>T		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	96	47	0.489583	NM_002740	D3DNQ4|Q8WW06	Silent	SNP	ENST00000295797.4	37	CCDS3212.2																																																																																			C|0.886;T|0.114	0.114	strong		0.403	PRKCI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316866.3	NM_002740	
PLEKHH1	57475	hgsc.bcm.edu	37	14	68035879	68035879	+	Missense_Mutation	SNP	A	A	G	rs3825725	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:68035879A>G	ENST00000329153.5	+	8	1420	c.1288A>G	c.(1288-1290)Aca>Gca	p.T430A		NM_020715.2	NP_065766.1	Q9ULM0	PKHH1_HUMAN	pleckstrin homology domain containing, family H (with MyTH4 domain) member 1	430			T -> A (in dbSNP:rs3825725).			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)		TGCTGTGGCCACATCGGGCAT	0.577													A|||	1060	0.211661	0.1437	0.2896	5008	,	,		17453	0.1468		0.2903	False		,,,				2504	0.2342				p.T430A		Atlas-SNP	.											PLEKHH1_ENST00000329153,NS,carcinoma,0,2	PLEKHH1	118	2	0			c.A1288G						PASS	.	A	ALA/THR	629,3279		59,511,1384	73.0	76.0	75.0		1288	3.2	0.9	14	dbSNP_107	75	2294,5982		319,1656,2163	yes	missense	PLEKHH1	NM_020715.2	58	378,2167,3547	GG,GA,AA		27.7187,16.0952,23.9905	benign	430/1365	68035879	2923,9261	1954	4138	6092	SO:0001583	missense	57475	exon8			GTGGCCACATCGG	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.1288A>G	14.37:g.68035879A>G	ENSP00000330278:p.Thr430Ala	Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	48	47	0.979167	NM_020715	A6H8X6|Q6PJL4|Q6ZWC7	Missense_Mutation	SNP	ENST00000329153.5	37	CCDS45128.1	494	0.2261904761904762	70	0.14227642276422764	105	0.2900552486187845	101	0.17657342657342656	218	0.287598944591029	A	12.44	1.939829	0.34189	0.160952	0.277187	ENSG00000054690	ENST00000329153	T	0.21543	2.0	4.45	3.23	0.37069	.	0.242027	0.40064	N	0.001187	T	0.00012	0.0000	L	0.51422	1.61	0.09310	P	0.9999999999996754	B	0.11235	0.004	B	0.09377	0.004	T	0.35475	-0.9787	9	0.28530	T	0.3	.	9.8029	0.40775	0.8354:0.0:0.0:0.1645	rs3825725;rs58796727;rs3825725	430	Q9ULM0	PKHH1_HUMAN	A	430	ENSP00000330278:T430A	ENSP00000330278:T430A	T	+	1	0	PLEKHH1	67105632	0.999000	0.42202	0.855000	0.33649	0.767000	0.43475	3.886000	0.56190	1.845000	0.53610	0.459000	0.35465	ACA	A|0.789;G|0.211	0.211	strong		0.577	PLEKHH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412730.3	XM_031054	
RGPD8	727851	hgsc.bcm.edu	37	2	113147666	113147666	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:113147666C>A	ENST00000302558.3	-	20	3047	c.2856G>T	c.(2854-2856)agG>agT	p.R952S	RGPD8_ENST00000409750.1_Missense_Mutation_p.R812S	NM_001164463.1	NP_001157935.1	O14715	RGPD8_HUMAN	RANBP2-like and GRIP domain containing 8	952					protein targeting to Golgi (GO:0000042)	nuclear pore (GO:0005643)	Ran GTPase binding (GO:0008536)			endometrium(4)|kidney(1)|lung(1)|prostate(3)|urinary_tract(1)	10						TCTTCCGGCCCCTAATATCCT	0.413																																					p.R952S		Atlas-SNP	.											RGPD8_ENST00000302558,NS,carcinoma,-1,2	RGPD8	81	2	0			c.G2856T						scavenged	.						170.0	130.0	143.0					2																	113147666		688	1572	2260	SO:0001583	missense	727851	exon20			CCGGCCCCTAATA	AF012086	CCDS46394.1	2q13	2013-01-10	2005-12-20	2005-12-20	ENSG00000169629	ENSG00000169629		"""Tetratricopeptide (TTC) repeat domain containing"""	9849	protein-coding gene	gene with protein product		602752	"""RAN binding protein 2-like 1"""	RANBP2L1		9480752	Standard	NM_001164463		Approved	RanBP2alpha	uc002ths.2	O14715	OTTHUMG00000153289	ENST00000302558.3:c.2856G>T	2.37:g.113147666C>A	ENSP00000306637:p.Arg952Ser	Somatic	858	0	0		WXS	Illumina HiSeq	Phase_I	188	178	0.946809	NM_001164463	Q5CZA8	Missense_Mutation	SNP	ENST00000302558.3	37	CCDS46394.1	.	.	.	.	.	.	.	.	.	.	-	0.001	-3.797847	0.00004	.	.	ENSG00000169629	ENST00000302558;ENST00000409750	T;T	0.36340	1.26;1.26	2.33	2.33	0.28932	.	.	.	.	.	T	0.05410	0.0143	N	0.00067	-2.295	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.36089	-0.9762	9	0.05525	T	0.97	-3.6976	3.1911	0.06618	0.5145:0.2459:0.0:0.2395	.	952	O14715	RGPD8_HUMAN	S	952;812	ENSP00000306637:R952S;ENSP00000386511:R812S	ENSP00000306637:R952S	R	-	3	2	RGPD8	112864137	0.000000	0.05858	0.012000	0.15200	0.011000	0.07611	0.325000	0.19628	0.153000	0.19213	-1.882000	0.00544	AGG	C|0.500;A|0.500	0.500	weak		0.413	RGPD8-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375951.1	XM_001722279	
KLHL23	151230	hgsc.bcm.edu	37	2	170592709	170592709	+	Silent	SNP	A	A	G	rs2288331	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:170592709A>G	ENST00000392647.2	+	2	1429	c.1185A>G	c.(1183-1185)aaA>aaG	p.K395K	KLHL23_ENST00000272797.4_Silent_p.K395K|KLHL23_ENST00000602521.1_Intron	NM_144711.5	NP_653312.2	Q8NBE8	KLH23_HUMAN	kelch-like family member 23	395										breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(4)|skin(1)|urinary_tract(1)	16						TAAAAGAGAAATGGATTCCTA	0.413													A|||	783	0.15635	0.1831	0.1369	5008	,	,		20251	0.1766		0.1581	False		,,,				2504	0.1115				p.K395K		Atlas-SNP	.											.	KLHL23	52	.	0			c.A1185G						PASS	.	A	,	677,3729	284.3+/-277.5	58,561,1584	95.0	102.0	100.0		1185,1185	-2.5	1.0	2	dbSNP_100	100	1393,7207	267.5+/-287.3	126,1141,3033	no	coding-synonymous,coding-synonymous	KLHL23,PHOSPHO2-KLHL23	NM_001199290.1,NM_144711.5	,	184,1702,4617	GG,GA,AA		16.1977,15.3654,15.9157	,	395/559,395/559	170592709	2070,10936	2203	4300	6503	SO:0001819	synonymous_variant	151230	exon2			AGAGAAATGGATT	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.1185A>G	2.37:g.170592709A>G		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	42	19	0.452381	NM_144711	Q8N9B9|Q96FT8	Silent	SNP	ENST00000392647.2	37	CCDS2236.1																																																																																			A|0.835;G|0.165	0.165	strong		0.413	KLHL23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255271.2	NM_144711	
CDNF	441549	hgsc.bcm.edu	37	10	14862082	14862082	+	Missense_Mutation	SNP	C	C	G	rs61738953	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:14862082C>G	ENST00000378442.1	-	6	658	c.155G>C	c.(154-156)tGg>tCg	p.W52S	CDNF_ENST00000378441.2_5'UTR			Q49AH0	CDNF_HUMAN	cerebral dopamine neurotrophic factor	154						extracellular region (GO:0005576)				breast(2)|large_intestine(2)|lung(1)	5						CTCCTCCCCCCAGCTATGCAG	0.502													C|||	68	0.0135783	0.0008	0.0259	5008	,	,		17873	0.0		0.0408	False		,,,				2504	0.0082				p.W154S		Atlas-SNP	.											.	CDNF	19	.	0			c.G461C						PASS	.	C	SER/TRP	39,4367	43.1+/-76.7	0,39,2164	138.0	138.0	138.0		461	5.9	1.0	10	dbSNP_129	138	350,8250	118.3+/-177.8	4,342,3954	yes	missense	CDNF	NM_001029954.2	177	4,381,6118	GG,GC,CC		4.0698,0.8852,2.9909	probably-damaging	154/188	14862082	389,12617	2203	4300	6503	SO:0001583	missense	441549	exon4			TCCCCCCAGCTAT	BC037872	CCDS31148.1	10p13	2009-06-04	2009-06-04	2009-06-04	ENSG00000185267	ENSG00000185267			24913	protein-coding gene	gene with protein product	"""conserved dopamine neurotrophic factor"""	611233	"""arginine-rich, mutated in early stage tumors-like 1"""	ARMETL1		17611540	Standard	NM_001029954		Approved		uc001inb.1	Q49AH0	OTTHUMG00000017713	ENST00000378442.1:c.155G>C	10.37:g.14862082C>G	ENSP00000367703:p.Trp52Ser	Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	123	64	0.520325	NM_001029954	A2RUU0|B4DVW3	Missense_Mutation	SNP	ENST00000378442.1	37		45	0.020604395604395604	1	0.0020325203252032522	12	0.03314917127071823	0	0.0	32	0.04221635883905013	C	26.0	4.693187	0.88735	0.008852	0.040698	ENSG00000185267	ENST00000378442;ENST00000465530	.	.	.	5.9	5.9	0.94986	.	0.000000	0.85682	D	0.000000	T	0.62551	0.2437	M	0.87269	2.87	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.78999	-0.1982	9	0.72032	D	0.01	-19.457	19.0536	0.93054	0.0:1.0:0.0:0.0	rs61738953	154	Q49AH0	CDNF_HUMAN	S	52;154	.	ENSP00000367703:W52S	W	-	2	0	CDNF	14902088	1.000000	0.71417	1.000000	0.80357	0.910000	0.53928	6.699000	0.74613	2.806000	0.96561	0.655000	0.94253	TGG	C|0.964;G|0.036	0.036	strong		0.502	CDNF-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000046919.1	NM_001029954	
AXIN2	8313	hgsc.bcm.edu	37	17	63554591	63554591	+	Missense_Mutation	SNP	G	G	A	rs2240308	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:63554591G>A	ENST00000375702.5	-	1	256	c.148C>T	c.(148-150)Cct>Tct	p.P50S	CTD-2535L24.2_ENST00000577662.1_3'UTR|AXIN2_ENST00000307078.5_Missense_Mutation_p.P50S			Q9Y2T1	AXIN2_HUMAN	axin 2	50			S -> P (in polymorphism associated with increased risk of lung cancer; dbSNP:rs2240308). {ECO:0000269|PubMed:16820935}.	QPGVGKGQVTKPMSVSSNTRRNEDGL -> HHGGQGPGHQT HVCLFQHQAERRWV (in Ref. 2; AAF22799). {ECO:0000305}.	bone mineralization (GO:0030282)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to organic cyclic compound (GO:0071407)|chondrocyte differentiation involved in endochondral bone morphogenesis (GO:0003413)|dorsal/ventral axis specification (GO:0009950)|intramembranous ossification (GO:0001957)|maintenance of DNA repeat elements (GO:0043570)|mRNA stabilization (GO:0048255)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catenin import into nucleus (GO:0035414)|negative regulation of cell proliferation (GO:0008285)|negative regulation of osteoblast differentiation (GO:0045668)|odontogenesis (GO:0042476)|positive regulation of cell death (GO:0010942)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of GTPase activity (GO:0043547)|positive regulation of protein phosphorylation (GO:0001934)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of chondrocyte development (GO:0061181)|regulation of mismatch repair (GO:0032423)|secondary heart field specification (GO:0003139)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|Wnt signaling pathway involved in somitogenesis (GO:0090244)	beta-catenin destruction complex (GO:0030877)|cell cortex (GO:0005938)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoplasmic microtubule (GO:0005881)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	armadillo repeat domain binding (GO:0070016)|beta-catenin binding (GO:0008013)|enzyme binding (GO:0019899)|GTPase activator activity (GO:0005096)|protein kinase binding (GO:0019901)|ubiquitin protein ligase binding (GO:0031625)			NS(1)|central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(10)|lung(10)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	34						GAAGAGACAGGCATGGGTTTG	0.662									Oligodontia, Ectodermal Dysplasia and Colorectal Polyp syndrome				G|||	1691	0.33766	0.0666	0.5159	5008	,	,		15989	0.3234		0.4702	False		,,,				2504	0.456				p.P50S		Atlas-SNP	.											.	AXIN2	92	.	0			c.C148T	GRCh37	CM066739	AXIN2	M	rs2240308	PASS	.	G	SER/PRO	596,3810	261.6+/-264.4	46,504,1653	54.0	56.0	55.0		148	2.8	0.8	17	dbSNP_98	55	4539,4061	590.3+/-392.6	1195,2149,956	yes	missense	AXIN2	NM_004655.3	74	1241,2653,2609	AA,AG,GG		47.2209,13.527,39.4818	benign	50/844	63554591	5135,7871	2203	4300	6503	SO:0001583	missense	8313	exon2	Familial Cancer Database	Oligodontia-Colorectal Cancer syndrome, Tooth Agenesis-Colorectal Cancer Syndrome	AGACAGGCATGGG	AF078165	CCDS11662.1	17q24.1	2014-09-17	2008-08-01		ENSG00000168646				904	protein-coding gene	gene with protein product	"""conductin"", ""axil"""	604025				10049590	Standard	NM_004655		Approved	MGC126582, DKFZp781B0869	uc002jfi.3	Q9Y2T1	OTTHUMG00000179353	ENST00000375702.5:c.148C>T	17.37:g.63554591G>A	ENSP00000364854:p.Pro50Ser	Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	36	13	0.361111	NM_004655	Q3MJ88|Q9H3M6|Q9UH84	Missense_Mutation	SNP	ENST00000375702.5	37		759	0.3475274725274725	42	0.08536585365853659	171	0.4723756906077348	176	0.3076923076923077	370	0.48812664907651715	G	1.053	-0.675392	0.03378	0.13527	0.527791	ENSG00000168646	ENST00000307078;ENST00000544103;ENST00000375702	T;T;T	0.76578	-0.05;-1.03;-0.04	4.74	2.75	0.32379	.	0.600804	0.16571	N	0.208652	T	0.00012	0.0000	.	.	.	0.22330	P	0.999193277	B	0.02656	0.0	B	0.01281	0.0	T	0.36480	-0.9746	8	0.05620	T	0.96	-7.6866	7.627	0.28218	0.2676:0.0:0.7324:0.0	rs2240308;rs52824132;rs60904566;rs2240308	50	E7ES00	.	S	50	ENSP00000302625:P50S;ENSP00000441151:P50S;ENSP00000364854:P50S	ENSP00000302625:P50S	P	-	1	0	AXIN2	60985053	0.999000	0.42202	0.834000	0.33040	0.020000	0.10135	0.923000	0.28757	0.980000	0.38523	0.561000	0.74099	CCT	G|0.641;A|0.359	0.359	strong		0.662	AXIN2-004	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000445901.1	NM_004655	
PAK6	56924	hgsc.bcm.edu	37	15	40564576	40564576	+	Missense_Mutation	SNP	C	C	T	rs3743137	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:40564576C>T	ENST00000542403.2	+	4	1121	c.1010C>T	c.(1009-1011)cCg>cTg	p.P337L	PAK6_ENST00000560346.1_Missense_Mutation_p.P337L|PAK6_ENST00000455577.2_Missense_Mutation_p.P337L|PAK6_ENST00000453867.1_Missense_Mutation_p.P337L|PAK6_ENST00000441369.1_Missense_Mutation_p.P337L|PAK6_ENST00000260404.4_Missense_Mutation_p.P337L|RP11-133K1.2_ENST00000558658.1_3'UTR	NM_001276717.1	NP_001263646.1	Q9NQU5	PAK6_HUMAN	p21 protein (Cdc42/Rac)-activated kinase 6	337	Linker.		P -> L (in dbSNP:rs3743137). {ECO:0000269|PubMed:17344846}.		apoptotic process (GO:0006915)|cytoskeleton organization (GO:0007010)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|cervix(1)|endometrium(3)|large_intestine(2)|liver(1)|lung(11)|ovary(2)|prostate(1)|skin(2)	24		all_cancers(109;1.13e-18)|all_epithelial(112;1.62e-15)|Lung NSC(122;5.67e-11)|all_lung(180;1.41e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0823)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;1.51e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0544)		CGCACAGCCCCGGCCACAGGC	0.697													C|||	471	0.0940495	0.0348	0.0663	5008	,	,		15740	0.119		0.1252	False		,,,				2504	0.136				p.P337L		Atlas-SNP	.											.	PAK6	49	.	0			c.C1010T						PASS	.	C	LEU/PRO,LEU/PRO,LEU/PRO	206,4200	128.2+/-165.1	5,196,2002	44.0	51.0	49.0		1010,1010,1010	3.0	0.1	15	dbSNP_107	49	960,7640	205.9+/-248.2	47,866,3387	yes	missense,missense,missense	PAK6	NM_001128628.1,NM_001128629.1,NM_020168.4	98,98,98	52,1062,5389	TT,TC,CC		11.1628,4.6754,8.9651	benign,benign,benign	337/682,337/682,337/682	40564576	1166,11840	2203	4300	6503	SO:0001583	missense	56924	exon5			CAGCCCCGGCCAC	AF276893	CCDS10054.1, CCDS61590.1	15q14	2008-06-17	2008-06-17		ENSG00000137843	ENSG00000137843			16061	protein-coding gene	gene with protein product		608110	"""p21(CDKN1A)-activated kinase 6"""			11278661	Standard	NM_020168		Approved	PAK5	uc001zlb.3	Q9NQU5	OTTHUMG00000129921	ENST00000542403.2:c.1010C>T	15.37:g.40564576C>T	ENSP00000439597:p.Pro337Leu	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	85	35	0.411765	NM_001128629	A8K2G2|B3KYB0|G5E9R2	Missense_Mutation	SNP	ENST00000542403.2	37	CCDS10054.1	238	0.10897435897435898	32	0.06504065040650407	31	0.0856353591160221	70	0.12237762237762238	105	0.13852242744063326	C	10.65	1.408476	0.25378	0.046754	0.111628	ENSG00000137843	ENST00000441369;ENST00000453867;ENST00000455577;ENST00000260404;ENST00000542403	T;T;T;T;T	0.76448	-0.92;-0.92;-1.02;-0.92;-0.92	3.97	3.04	0.35103	.	0.411806	0.28393	N	0.015516	T	0.00754	0.0025	L	0.27053	0.805	0.20074	P	0.9999341805	P;P	0.39920	0.569;0.695	B;B	0.32928	0.074;0.155	T	0.20538	-1.0272	9	0.25106	T	0.35	.	13.2801	0.60210	0.1596:0.8404:0.0:0.0	rs3743137;rs3743137	337;337	Q9NQU5;G5E9R2	PAK6_HUMAN;.	L	337	ENSP00000406873:P337L;ENSP00000401153:P337L;ENSP00000409465:P337L;ENSP00000260404:P337L;ENSP00000439597:P337L	ENSP00000260404:P337L	P	+	2	0	PAK6	38351868	0.368000	0.25031	0.132000	0.22025	0.036000	0.12997	2.667000	0.46808	0.996000	0.38943	0.555000	0.69702	CCG	C|0.904;T|0.096	0.096	strong		0.697	PAK6-004	NOVEL	alternative_3_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000418355.1		
TOR3A	64222	hgsc.bcm.edu	37	1	179064145	179064145	+	Missense_Mutation	SNP	T	T	C	rs138598531	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:179064145T>C	ENST00000367627.3	+	6	1738	c.986T>C	c.(985-987)aTt>aCt	p.I329T	TOR3A_ENST00000352445.6_Intron	NM_022371.3	NP_071766.2	Q9H497	TOR3A_HUMAN	torsin family 3, member A	329					ATP catabolic process (GO:0006200)|chaperone mediated protein folding requiring cofactor (GO:0051085)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			endometrium(1)|kidney(2)|large_intestine(4)|lung(4)|pancreas(1)|urinary_tract(1)	13						GAAAACCTGATTGACTACTTC	0.502													T|||	3	0.000599042	0.0	0.0	5008	,	,		20059	0.0		0.003	False		,,,				2504	0.0				p.I329T		Atlas-SNP	.											.	TOR3A	28	.	0			c.T986C						PASS	.	T	THR/ILE	1,4405	2.1+/-5.4	0,1,2202	207.0	183.0	191.0		986	5.6	1.0	1	dbSNP_134	191	8,8592	6.4+/-24.3	0,8,4292	yes	missense	TOR3A	NM_022371.3	89	0,9,6494	CC,CT,TT		0.093,0.0227,0.0692	possibly-damaging	329/398	179064145	9,12997	2203	4300	6503	SO:0001583	missense	64222	exon6			ACCTGATTGACTA	BC001085	CCDS1329.1	1q25.2	2008-02-05	2003-04-02		ENSG00000186283	ENSG00000186283			11997	protein-coding gene	gene with protein product		607555	"""ATP-dependant interferon responsive"""	ADIR		10644435	Standard	NM_022371		Approved	FLJ22345, ADIR2	uc001gmd.3	Q9H497	OTTHUMG00000035077	ENST00000367627.3:c.986T>C	1.37:g.179064145T>C	ENSP00000356599:p.Ile329Thr	Somatic	213	0	0		WXS	Illumina HiSeq	Phase_I	192	98	0.510417	NM_022371	B4DSY0|B7ZB65|Q5M7Y7|Q8WVA7|Q8WWM2|Q9H495|Q9H6E7	Missense_Mutation	SNP	ENST00000367627.3	37	CCDS1329.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	T	23.6	4.433498	0.83776	2.27E-4	9.3E-4	ENSG00000186283	ENST00000367627	T	0.60797	0.16	5.62	5.62	0.85841	.	0.102990	0.64402	D	0.000005	T	0.67998	0.2953	M	0.90650	3.135	0.80722	D	1	P	0.46706	0.883	B	0.42827	0.399	T	0.76567	-0.2912	10	0.62326	D	0.03	-9.8442	15.0006	0.71469	0.0:0.0:0.0:1.0	.	329	Q9H497	TOR3A_HUMAN	T	329	ENSP00000356599:I329T	ENSP00000356599:I329T	I	+	2	0	TOR3A	177330768	1.000000	0.71417	1.000000	0.80357	0.943000	0.58893	7.662000	0.83803	2.134000	0.65973	0.496000	0.49642	ATT	T|0.999;C|0.001	0.001	strong		0.502	TOR3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084927.1	NM_022371	
RIN1	9610	hgsc.bcm.edu	37	11	66099987	66099987	+	Silent	SNP	C	C	T	rs1784029	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:66099987C>T	ENST00000311320.4	-	10	2238	c.2112G>A	c.(2110-2112)gcG>gcA	p.A704A	RP11-867G23.12_ENST00000526655.1_RNA|RIN1_ENST00000424433.2_Intron|RIN1_ENST00000530056.1_Silent_p.A538A|RIN1_ENST00000524804.1_5'Flank	NM_004292.2	NP_004283.2	Q13671	RIN1_HUMAN	Ras and Rab interactor 1	704	Ras and 14-3-3 protein binding region.|Ras-associating. {ECO:0000255|PROSITE- ProRule:PRU00166}.				associative learning (GO:0008306)|endocytosis (GO:0006897)|memory (GO:0007613)|negative regulation of synaptic plasticity (GO:0031914)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)			breast(1)|central_nervous_system(3)|haematopoietic_and_lymphoid_tissue(1)|lung(8)|ovary(1)	14						CAGGCCACTCCGCCCGGCGGT	0.682													C|||	2808	0.560703	0.2209	0.7334	5008	,	,		15942	0.5595		0.662	False		,,,				2504	0.7945				p.A704A		Atlas-SNP	.											.	RIN1	64	.	0			c.G2112A						PASS	.	C		1295,3105	435.9+/-344.5	213,869,1118	83.0	92.0	89.0		2112	-3.0	1.0	11	dbSNP_89	89	5932,2658	682.8+/-403.8	2058,1816,421	no	coding-synonymous	RIN1	NM_004292.2		2271,2685,1539	TT,TC,CC		30.943,29.4318,44.3649		704/784	66099987	7227,5763	2200	4295	6495	SO:0001819	synonymous_variant	9610	exon10			CCACTCCGCCCGG	L36463	CCDS31614.1	11q13.2	2005-09-18				ENSG00000174791			18749	protein-coding gene	gene with protein product		605965				9144171, 1849280	Standard	NM_004292		Approved		uc001ohn.1	Q13671		ENST00000311320.4:c.2112G>A	11.37:g.66099987C>T		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	77	27	0.350649	NM_004292	O15010|Q00427|Q96CC8	Silent	SNP	ENST00000311320.4	37	CCDS31614.1																																																																																			C|0.445;T|0.555	0.555	strong		0.682	RIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392980.2	NM_004292	
KPTN	11133	hgsc.bcm.edu	37	19	47978739	47978739	+	Silent	SNP	C	C	T	rs1046273	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:47978739C>T	ENST00000338134.3	-	12	1352	c.1245G>A	c.(1243-1245)agG>agA	p.R415R	KPTN_ENST00000536339.1_Silent_p.R175R	NM_007059.2	NP_008990.2	Q9Y664	KPTN_HUMAN	kaptin (actin binding protein)	415					actin filament organization (GO:0007015)|cellular component movement (GO:0006928)|sensory perception of sound (GO:0007605)	actin cytoskeleton (GO:0015629)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|microtubule organizing center (GO:0005815)|nucleus (GO:0005634)	actin binding (GO:0003779)			breast(1)|lung(3)|ovary(2)|pancreas(2)	8		all_cancers(25;1.55e-10)|all_epithelial(76;3.4e-08)|all_lung(116;1.73e-07)|Lung NSC(112;3.95e-07)|Ovarian(192;0.0139)|all_neural(266;0.026)|Breast(70;0.0503)		OV - Ovarian serous cystadenocarcinoma(262;0.000428)|all cancers(93;0.000631)|Epithelial(262;0.0153)|GBM - Glioblastoma multiforme(486;0.0694)		GCCGACGTCTCCTCTGCTCCA	0.612													C|||	92	0.0183706	0.0008	0.062	5008	,	,		19204	0.0		0.0249	False		,,,				2504	0.0235				p.R415R		Atlas-SNP	.											.	KPTN	34	.	0			c.G1245A						PASS	.	C		13,4085		0,13,2036	35.0	37.0	36.0		1245	2.5	0.9	19	dbSNP_86	36	166,8212		3,160,4026	no	coding-synonymous	KPTN	NM_007059.2		3,173,6062	TT,TC,CC		1.9814,0.3172,1.4348		415/437	47978739	179,12297	2049	4189	6238	SO:0001819	synonymous_variant	11133	exon12			ACGTCTCCTCTGC	AF105369	CCDS42583.1	19q13.32	2014-08-13	2001-11-28		ENSG00000118162	ENSG00000118162			6404	protein-coding gene	gene with protein product		615620	"""kaptin (actin-binding protein)"""			10099934	Standard	XM_005258467		Approved	2E4	uc002pgy.3	Q9Y664	OTTHUMG00000183443	ENST00000338134.3:c.1245G>A	19.37:g.47978739C>T		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	95	31	0.326316	NM_007059	B3KN86|B4DQ76|Q96GT1	Silent	SNP	ENST00000338134.3	37	CCDS42583.1																																																																																			C|0.982;T|0.018	0.018	strong		0.612	KPTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466672.2		
OR2D2	120776	hgsc.bcm.edu	37	11	6913243	6913243	+	Missense_Mutation	SNP	T	T	C	rs1965207|rs386750330	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:6913243T>C	ENST00000299459.2	-	1	587	c.489A>G	c.(487-489)atA>atG	p.I163M		NM_003700.1	NP_003691.1	Q9H210	OR2D2_HUMAN	olfactory receptor, family 2, subfamily D, member 2	163			I -> M (in dbSNP:rs1965207).|I -> T (in dbSNP:rs1965208). {ECO:0000269|PubMed:11416212, ECO:0000269|PubMed:12213199, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9787077, ECO:0000269|Ref.3}.		detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|cervix(1)|large_intestine(3)|lung(9)|ovary(1)|skin(2)	18		Medulloblastoma(188;0.0523)|all_neural(188;0.236)		Epithelial(150;4.68e-08)|BRCA - Breast invasive adenocarcinoma(625;0.129)		GTAGCCTCAGTATGAAGGTGG	0.502													T|||	668	0.133387	0.1293	0.0937	5008	,	,		20670	0.0764		0.162	False		,,,				2504	0.1963				p.I163M		Atlas-SNP	.											.	OR2D2	52	.	0			c.A489G						PASS	.		MET/ILE	603,3799		33,537,1631	113.0	86.0	95.0		489	-10.2	0.0	11	dbSNP_92	95	1190,7402		99,992,3205	yes	missense	OR2D2	NM_003700.1	10	132,1529,4836	CC,CT,TT		13.8501,13.6983,13.7987	benign	163/309	6913243	1793,11201	2201	4296	6497	SO:0001583	missense	120776	exon1			CCTCAGTATGAAG	AB065824	CCDS31416.1	11p15.4	2012-08-09			ENSG00000166368	ENSG00000166368		"""GPCR / Class A : Olfactory receptors"""	8244	protein-coding gene	gene with protein product		608494		OR2D1		9787077	Standard	NM_003700		Approved	OR11-610, hg27	uc010rau.2	Q9H210	OTTHUMG00000165741	ENST00000299459.2:c.489A>G	11.37:g.6913243T>C	ENSP00000299459:p.Ile163Met	Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	167	125	0.748503	NM_003700	B9EIL5|O95224|Q6IF28|Q8NGH4|Q96R52	Missense_Mutation	SNP	ENST00000299459.2	37	CCDS31416.1	236	0.10805860805860806	61	0.12398373983739837	35	0.09668508287292818	39	0.06818181818181818	101	0.13324538258575197	t	12.79	2.042140	0.35989	0.136983	0.138501	ENSG00000166368	ENST00000299459	T	0.00107	8.72	5.12	-10.2	0.00374	GPCR, rhodopsin-like superfamily (1);	0.126744	0.36034	N	0.002839	T	0.00012	0.0000	L	0.41124	1.26	0.80722	P	0.0	B	0.33044	0.395	P	0.47162	0.54	T	0.46261	-0.9204	9	0.59425	D	0.04	-13.1389	4.3554	0.11176	0.3217:0.0604:0.4446:0.1732	rs1965207;rs1965207	163	Q9H210	OR2D2_HUMAN	M	163	ENSP00000299459:I163M	ENSP00000299459:I163M	I	-	3	3	OR2D2	6869819	0.000000	0.05858	0.003000	0.11579	0.790000	0.44656	-2.769000	0.00780	-2.599000	0.00452	-1.564000	0.00881	ATA	T|0.866;C|0.134	0.134	strong		0.502	OR2D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385986.1	NM_003700	
HUS1B	135458	hgsc.bcm.edu	37	6	656810	656810	+	Silent	SNP	A	A	G	rs61748571	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:656810A>G	ENST00000380907.2	-	1	153	c.135T>C	c.(133-135)ggT>ggC	p.G45G	EXOC2_ENST00000448181.3_Intron|EXOC2_ENST00000230449.4_Intron	NM_148959.3	NP_683762.2	Q8NHY5	HUS1B_HUMAN	HUS1 checkpoint homolog b (S. pombe)	45					DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)	checkpoint clamp complex (GO:0030896)|nucleolus (GO:0005730)				endometrium(3)|large_intestine(1)|lung(7)	11	Ovarian(93;0.0733)	Breast(5;0.00139)|all_lung(73;0.0691)|all_hematologic(90;0.0895)		OV - Ovarian serous cystadenocarcinoma(45;0.041)|BRCA - Breast invasive adenocarcinoma(62;0.0965)		GGCCGCCGGAACCCGCGGGGC	0.662													A|||	428	0.0854633	0.0166	0.0548	5008	,	,		15750	0.129		0.0477	False		,,,				2504	0.1943				p.G45G		Atlas-SNP	.											.	HUS1B	26	.	0			c.T135C						PASS	.	A	,	141,4241		2,137,2052	14.0	14.0	14.0		,135	-5.6	0.0	6	dbSNP_129	14	442,8128		15,412,3858	no	intron,coding-synonymous	EXOC2,HUS1B	NM_018303.4,NM_148959.3	,	17,549,5910	GG,GA,AA		5.1575,3.2177,4.5012	,	,45/279	656810	583,12369	2191	4285	6476	SO:0001819	synonymous_variant	135458	exon1			GCCGGAACCCGCG	AF508547	CCDS4470.1	6p25.3	2008-08-08	2001-11-28		ENSG00000188996	ENSG00000188996			16485	protein-coding gene	gene with protein product		609713	"""HUS1 (S. pombe) checkpoint homolog b"""			11944979	Standard	NM_148959		Approved		uc003mtg.3	Q8NHY5	OTTHUMG00000090059	ENST00000380907.2:c.135T>C	6.37:g.656810A>G		Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	37	22	0.594595	NM_148959	Q5T4Z2	Silent	SNP	ENST00000380907.2	37	CCDS4470.1																																																																																			A|0.942;G|0.058	0.058	strong		0.662	HUS1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000205617.2	NM_148959	
FCN1	2219	hgsc.bcm.edu	37	9	137809685	137809685	+	Silent	SNP	C	C	A	rs10858293	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:137809685C>A	ENST00000371806.3	-	1	124	c.33G>T	c.(31-33)ggG>ggT	p.G11G		NM_002003.3	NP_001994.2	O00602	FCN1_HUMAN	ficolin (collagen/fibrinogen domain containing) 1	11					cell surface pattern recognition receptor signaling pathway (GO:0002752)|complement activation (GO:0006956)|complement activation, lectin pathway (GO:0001867)|G-protein coupled receptor signaling pathway (GO:0007186)|innate immune response (GO:0045087)|opsonization (GO:0008228)|positive regulation of interleukin-8 secretion (GO:2000484)	collagen trimer (GO:0005581)|extracellular region (GO:0005576)|extrinsic component of external side of plasma membrane (GO:0031232)	antigen binding (GO:0003823)|calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|G-protein coupled receptor binding (GO:0001664)|signaling pattern recognition receptor activity (GO:0008329)			endometrium(3)|kidney(3)|large_intestine(8)|lung(13)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	37		Myeloproliferative disorder(178;0.0333)		OV - Ovarian serous cystadenocarcinoma(145;3.46e-08)|Epithelial(140;6.01e-08)|all cancers(34;3.69e-07)		GGACAGCGAGCCCCCGGGCCA	0.587													C|||	1230	0.245607	0.3313	0.2262	5008	,	,		17494	0.125		0.339	False		,,,				2504	0.1718				p.G11G		Atlas-SNP	.											.	FCN1	62	.	0			c.G33T						PASS	.	C		1404,3002	460.0+/-352.4	249,906,1048	86.0	83.0	84.0		33	-8.3	0.0	9	dbSNP_120	84	2894,5706	452.5+/-363.0	479,1936,1885	yes	coding-synonymous	FCN1	NM_002003.3		728,2842,2933	AA,AC,CC		33.6512,31.8656,33.0463		11/327	137809685	4298,8708	2203	4300	6503	SO:0001819	synonymous_variant	2219	exon1			AGCGAGCCCCCGG	D83920	CCDS6985.1	9q34	2013-02-06	2002-01-14		ENSG00000085265	ENSG00000085265		"""Fibrinogen C domain containing"""	3623	protein-coding gene	gene with protein product		601252	"""ficolin (collagen/fibrinogen domain-containing) 1"""			8573080, 8884275	Standard	NM_002003		Approved	FCNM	uc004cfi.3	O00602	OTTHUMG00000020895	ENST00000371806.3:c.33G>T	9.37:g.137809685C>A		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	65	60	0.923077	NM_002003	Q5VYV5|Q92596	Silent	SNP	ENST00000371806.3	37	CCDS6985.1																																																																																			C|0.693;A|0.307	0.307	strong		0.587	FCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054963.1	NM_002003	
EIF4G3	8672	hgsc.bcm.edu	37	1	21133836	21133836	+	Silent	SNP	T	T	C	rs146669269	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:21133836T>C	ENST00000264211.8	-	31	4928	c.4734A>G	c.(4732-4734)gcA>gcG	p.A1578A	EIF4G3_ENST00000374935.3_Silent_p.A1298A|EIF4G3_ENST00000400422.1_Silent_p.A1578A|EIF4G3_ENST00000602326.1_Silent_p.A1584A|EIF4G3_ENST00000374937.3_Silent_p.A1584A|EIF4G3_ENST00000537738.1_Silent_p.A1068A|EIF4G3_ENST00000536266.1_Silent_p.A1182A	NM_003760.4	NP_003751.2	O43432	IF4G3_HUMAN	eukaryotic translation initiation factor 4 gamma, 3	1578	EIF4A-binding. {ECO:0000250}.|Necessary but not sufficient for MKNK1- binding. {ECO:0000250}.|W2. {ECO:0000255|PROSITE- ProRule:PRU00695}.				cytokine-mediated signaling pathway (GO:0019221)|positive regulation of meiosis I (GO:0060903)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of translation (GO:0045727)|regulation of translational initiation (GO:0006446)|spermatogenesis (GO:0007283)|viral process (GO:0016032)	cytosol (GO:0005829)|eukaryotic translation initiation factor 4F complex (GO:0016281)	poly(A) RNA binding (GO:0044822)|RNA cap binding (GO:0000339)|translation factor activity, nucleic acid binding (GO:0008135)|translation initiation factor activity (GO:0003743)			endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(18)|lung(20)|ovary(1)|prostate(4)|skin(3)|stomach(1)|urinary_tract(3)	70		all_lung(284;2.61e-06)|Lung NSC(340;2.81e-06)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00149)|Ovarian(437;0.00338)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.023)|COAD - Colon adenocarcinoma(152;5.42e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000327)|GBM - Glioblastoma multiforme(114;0.000696)|Kidney(64;0.0018)|STAD - Stomach adenocarcinoma(196;0.00644)|KIRC - Kidney renal clear cell carcinoma(64;0.0185)|READ - Rectum adenocarcinoma(331;0.124)|Lung(427;0.191)		ACTCCTCTTCTGCTTCCCGCA	0.428													T|||	25	0.00499201	0.0038	0.0029	5008	,	,		17451	0.0		0.0119	False		,,,				2504	0.0061				p.A1614A		Atlas-SNP	.											.	EIF4G3	300	.	0			c.A4842G						PASS	.	T	,,	14,4392	21.2+/-45.6	0,14,2189	174.0	176.0	175.0		4842,4752,4734	-7.2	1.0	1	dbSNP_134	175	68,8532	40.8+/-97.7	2,64,4234	no	coding-synonymous,coding-synonymous,coding-synonymous	EIF4G3	NM_001198801.1,NM_001198802.1,NM_003760.4	,,	2,78,6423	CC,CT,TT		0.7907,0.3177,0.6305	,,	1614/1622,1584/1592,1578/1586	21133836	82,12924	2203	4300	6503	SO:0001819	synonymous_variant	8672	exon35			CTCTTCTGCTTCC	AF012072	CCDS214.1, CCDS55580.1, CCDS59192.1, CCDS72723.1	1p36.12	2008-02-05			ENSG00000075151	ENSG00000075151			3298	protein-coding gene	gene with protein product		603929				9418880	Standard	NM_001198801		Approved	eIF4GII	uc001bef.3	O43432	OTTHUMG00000002624	ENST00000264211.8:c.4734A>G	1.37:g.21133836T>C		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	138	60	0.434783	NM_001198801	B9EGQ7|Q15597|Q504Z1|Q5SWC3|Q8NEN1	Silent	SNP	ENST00000264211.8	37	CCDS214.1																																																																																			T|0.993;C|0.007	0.007	strong		0.428	EIF4G3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000007467.3	NM_003760	
CGNL1	84952	hgsc.bcm.edu	37	15	57731573	57731573	+	Missense_Mutation	SNP	C	C	T	rs7182648	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:57731573C>T	ENST00000281282.5	+	2	1454	c.1376C>T	c.(1375-1377)tCc>tTc	p.S459F		NM_001252335.1|NM_032866.4	NP_001239264.1|NP_116255.2	Q0VF96	CGNL1_HUMAN	cingulin-like 1	459	Head.		S -> F (in dbSNP:rs7182648). {ECO:0000269|PubMed:15489334}.			myosin complex (GO:0016459)|tight junction (GO:0005923)	motor activity (GO:0003774)			autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|endometrium(5)|kidney(4)|large_intestine(12)|lung(14)|ovary(4)|prostate(4)|skin(10)|stomach(2)|upper_aerodigestive_tract(1)	60				all cancers(107;0.121)|GBM - Glioblastoma multiforme(80;0.186)		TGTGCCCACTCCAGGCCTCCC	0.607													C|||	954	0.190495	0.1899	0.1599	5008	,	,		17593	0.1994		0.2107	False		,,,				2504	0.183				p.S459F		Atlas-SNP	.											.	CGNL1	125	.	0			c.C1376T						PASS	.	C	PHE/SER	904,3480	324.0+/-298.4	105,694,1393	36.0	36.0	36.0		1376	4.4	0.0	15	dbSNP_116	36	1867,6717	315.0+/-312.1	207,1453,2632	yes	missense	CGNL1	NM_032866.3	155	312,2147,4025	TT,TC,CC		21.7498,20.6204,21.368	benign	459/1303	57731573	2771,10197	2192	4292	6484	SO:0001583	missense	84952	exon2			CCCACTCCAGGCC	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.1376C>T	15.37:g.57731573C>T	ENSP00000281282:p.Ser459Phe	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	76	19	0.25	NM_032866	Q05BZ4|Q52LR0|Q695C7|Q7Z2L3|Q96JV2|Q96MN6|Q9C0B4	Missense_Mutation	SNP	ENST00000281282.5	37	CCDS10161.1	407	0.18635531135531136	84	0.17073170731707318	59	0.16298342541436464	105	0.18356643356643357	159	0.20976253298153033	C	9.131	1.011341	0.19277	0.206204	0.217498	ENSG00000128849	ENST00000281282	T	0.06768	3.26	5.34	4.4	0.53042	.	31.360300	0.00166	N	0.000002	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B	0.31485	0.325	B	0.30029	0.11	T	0.36648	-0.9739	9	0.37606	T	0.19	-9.6499	3.8164	0.08817	0.1844:0.5789:0.0:0.2368	rs7182648;rs60490041;rs7182648	459	Q0VF96	CGNL1_HUMAN	F	459	ENSP00000281282:S459F	ENSP00000281282:S459F	S	+	2	0	CGNL1	55518865	0.002000	0.14202	0.019000	0.16419	0.004000	0.04260	1.337000	0.33862	1.191000	0.43056	0.609000	0.83330	TCC	C|0.797;T|0.203	0.203	strong		0.607	CGNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255482.2	NM_032866	
PHIP	55023	hgsc.bcm.edu	37	6	79656562	79656562	+	Silent	SNP	A	A	T	rs2275291	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:79656562A>T	ENST00000275034.4	-	37	4403	c.4236T>A	c.(4234-4236)gcT>gcA	p.A1412A	PHIP_ENST00000479165.1_5'UTR	NM_017934.5	NP_060404	Q8WWQ0	PHIP_HUMAN	pleckstrin homology domain interacting protein	1412					cytoskeleton organization (GO:0007010)|insulin receptor signaling pathway (GO:0008286)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of mitosis (GO:0045840)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein import into nucleus (GO:0006606)|regulation of cell morphogenesis (GO:0022604)|regulation of growth (GO:0040008)|regulation of protein phosphorylation (GO:0001932)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	insulin receptor binding (GO:0005158)|lysine-acetylated histone binding (GO:0070577)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(10)|kidney(4)|large_intestine(20)|lung(20)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	68		all_cancers(76;0.00125)|Acute lymphoblastic leukemia(125;1.1e-05)|all_hematologic(105;0.00117)|all_epithelial(107;0.219)		BRCA - Breast invasive adenocarcinoma(397;0.231)		CTTCAAAGAAAGCAGACAGGC	0.333													A|||	1205	0.240615	0.2564	0.2853	5008	,	,		15350	0.1845		0.3211	False		,,,				2504	0.1626				p.A1412A		Atlas-SNP	.											.	PHIP	177	.	0			c.T4236A						PASS	.	A		1206,3200	399.2+/-331.1	160,886,1157	66.0	68.0	67.0		4236	4.4	1.0	6	dbSNP_100	67	2591,6009	415.3+/-351.7	410,1771,2119	no	coding-synonymous	PHIP	NM_017934.5		570,2657,3276	TT,TA,AA		30.1279,27.3718,29.1942		1412/1822	79656562	3797,9209	2203	4300	6503	SO:0001819	synonymous_variant	55023	exon37			AAAGAAAGCAGAC	AF310250	CCDS4987.1	6q14	2013-01-09			ENSG00000146247	ENSG00000146247		"""WD repeat domain containing"", ""DDB1 and CUL4 associated factors"""	15673	protein-coding gene	gene with protein product	"""DDB1 and CUL4 associated factor 14"""	612870		WDR11		11018022	Standard	NM_017934		Approved	ndrp, FLJ20705, DCAF14, BRWD2	uc003pir.3	Q8WWQ0	OTTHUMG00000015071	ENST00000275034.4:c.4236T>A	6.37:g.79656562A>T		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	62	61	0.983871	NM_017934	A7J992|B2RPK4|Q05CQ9|Q5VVH4|Q66I29|Q69YV1|Q8NBZ5|Q96H52|Q96ME2|Q9H261	Silent	SNP	ENST00000275034.4	37	CCDS4987.1																																																																																			A|0.719;T|0.281	0.281	strong		0.333	PHIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041297.2		
CFHR2	3080	hgsc.bcm.edu	37	1	196928188	196928188	+	Missense_Mutation	SNP	A	A	G	rs41310132	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:196928188A>G	ENST00000367415.5	+	5	891	c.791A>G	c.(790-792)tAt>tGt	p.Y264C	CFHR2_ENST00000476712.2_Missense_Mutation_p.Y248C|CFHR2_ENST00000496448.1_3'UTR|CFHR2_ENST00000367421.3_Missense_Mutation_p.Y264C	NM_005666.2	NP_005657.1	P36980	FHR2_HUMAN	complement factor H-related 2	264	Sushi 4. {ECO:0000255|PROSITE- ProRule:PRU00302}.					extracellular region (GO:0005576)				large_intestine(2)|ovary(1)|skin(3)	6						AAACTGGTATATCCCAGTTGT	0.303													A|||	61	0.0121805	0.0015	0.0101	5008	,	,		16690	0.001		0.0149	False		,,,				2504	0.0368				p.Y264C		Atlas-SNP	.											.	CFHR2	73	.	0			c.A791G						PASS	.	A	CYS/TYR	16,4390		0,16,2187	43.0	45.0	44.0		791	3.5	0.0	1	dbSNP_127	44	145,8447		2,141,4153	yes	missense	CFHR2	NM_005666.2	194	2,157,6340	GG,GA,AA		1.6876,0.3631,1.2387	probably-damaging	264/271	196928188	161,12837	2203	4296	6499	SO:0001583	missense	3080	exon5			TGGTATATCCCAG	X64877	CCDS30959.1	1q31.3	2008-02-05	2004-08-09	2006-02-28	ENSG00000080910	ENSG00000080910		"""Complement system"""	4890	protein-coding gene	gene with protein product		600889	"""H factor (complement)-like 3"""	HFL3, CFHL2		1533657, 7672821	Standard	NM_005666		Approved	FHR2	uc001gtq.1	P36980	OTTHUMG00000036518	ENST00000367415.5:c.791A>G	1.37:g.196928188A>G	ENSP00000356385:p.Tyr264Cys	Somatic	223	1	0.00448431		WXS	Illumina HiSeq	Phase_I	207	104	0.502415	NM_005666	Q14310|Q5T9T1	Missense_Mutation	SNP	ENST00000367415.5	37	CCDS30959.1	18	0.008241758241758242	2	0.0040650406504065045	3	0.008287292817679558	0	0.0	13	0.017150395778364115	.	13.05	2.121290	0.37436	0.003631	0.016876	ENSG00000080910	ENST00000367421;ENST00000367415	D;D	0.84800	-1.9;-1.9	3.52	3.52	0.40303	Complement control module (2);Sushi/SCR/CCP (2);	.	.	.	.	D	0.86577	0.5966	M	0.87097	2.86	0.09310	N	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.989;0.996	T	0.78568	-0.2154	9	0.59425	D	0.04	.	8.3591	0.32348	1.0:0.0:0.0:0.0	rs41310132	237;264	P36980-2;P36980	.;FHR2_HUMAN	C	264	ENSP00000356391:Y264C;ENSP00000356385:Y264C	ENSP00000356385:Y264C	Y	+	2	0	CFHR2	195194811	0.949000	0.32298	0.033000	0.17914	0.009000	0.06853	2.487000	0.45268	1.454000	0.47793	0.443000	0.29094	TAT	A|0.988;G|0.012	0.012	strong		0.303	CFHR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088815.2	NM_005666	
OSBPL7	114881	hgsc.bcm.edu	37	17	45890707	45890707	+	Silent	SNP	C	C	T	rs2301690	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:45890707C>T	ENST00000007414.3	-	16	1853	c.1662G>A	c.(1660-1662)aaG>aaA	p.K554K	OSBPL7_ENST00000392507.3_Silent_p.K554K	NM_145798.2	NP_665741.1	Q9BZF2	OSBL7_HUMAN	oxysterol binding protein-like 7	554					cellular response to cholesterol (GO:0071397)|lipid transport (GO:0006869)|positive regulation of proteasomal protein catabolic process (GO:1901800)	autophagic vacuole (GO:0005776)|cytosol (GO:0005829)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)	cholesterol binding (GO:0015485)			autonomic_ganglia(1)|endometrium(6)|kidney(2)|large_intestine(5)|liver(2)|lung(13)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	32						GGTTGAAGGGCTTGCAGCCGG	0.622													c|||	795	0.158746	0.0643	0.2233	5008	,	,		19047	0.0139		0.3569	False		,,,				2504	0.1861				p.K554K		Atlas-SNP	.											.	OSBPL7	65	.	0			c.G1662A						PASS	.			480,3926	224.6+/-240.7	22,436,1745	65.0	64.0	64.0		1662	1.4	1.0	17	dbSNP_100	64	3302,5298	494.0+/-373.7	653,1996,1651	no	coding-synonymous	OSBPL7	NM_145798.2		675,2432,3396	TT,TC,CC		38.3953,10.8942,29.0789		554/843	45890707	3782,9224	2203	4300	6503	SO:0001819	synonymous_variant	114881	exon16			GAAGGGCTTGCAG	AF392446	CCDS11515.1	17q21	2013-01-10				ENSG00000006025		"""Oxysterol binding proteins"", ""Pleckstrin homology (PH) domain containing"""	16387	protein-coding gene	gene with protein product		606735				14593528, 11735225	Standard	NM_145798		Approved	ORP7, MGC71150	uc002ilx.1	Q9BZF2		ENST00000007414.3:c.1662G>A	17.37:g.45890707C>T		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	74	44	0.594595	NM_145798	D3DTT6|Q6PIV6	Silent	SNP	ENST00000007414.3	37	CCDS11515.1																																																																																			C|0.759;T|0.241	0.241	strong		0.622	OSBPL7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441367.1	NM_017731	
PIEZO1	9780	hgsc.bcm.edu	37	16	88782676	88782676	+	Silent	SNP	A	A	G	rs2290902	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:88782676A>G	ENST00000301015.9	-	49	7305	c.7059T>C	c.(7057-7059)ccT>ccC	p.P2353P	MIR4722_ENST00000578292.1_RNA|PIEZO1_ENST00000327397.7_Silent_p.P221P|RP5-1142A6.9_ENST00000564984.1_RNA	NM_001142864.2	NP_001136336.2	Q92508	PIEZ1_HUMAN	piezo-type mechanosensitive ion channel component 1	2353					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						GGAAGAGATTAGGGATGACCC	0.662													G|||	4346	0.867812	0.8328	0.8458	5008	,	,		17189	0.9167		0.8946	False		,,,				2504	0.8528				p.P2353P		Atlas-SNP	.											.	PIEZO1	79	.	0			c.T7059C						PASS	.						42.0	43.0	43.0					16																	88782676		692	1590	2282	SO:0001819	synonymous_variant	9780	exon49			GAGATTAGGGATG	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.7059T>C	16.37:g.88782676A>G		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	79	79	1	NM_001142864	A6NHT9|A7E2B7|Q0KKZ9	Silent	SNP	ENST00000301015.9	37	CCDS54058.1	1914	0.8763736263736264	399	0.8109756097560976	315	0.8701657458563536	525	0.9178321678321678	675	0.8905013192612137	G	0.032	-1.328822	0.01298	.	.	ENSG00000103335	ENST00000451779	.	.	.	3.81	-0.413	0.12363	.	.	.	.	.	.	.	.	.	.	.	0.20563	P	0.999881344	.	.	.	.	.	.	.	.	.	.	.	.	.	-16.3644	1.8486	0.03164	0.3308:0.1893:0.367:0.1129	rs2290902;rs11547379;rs58469185;rs2290902	.	.	.	Q	2299	.	.	X	-	1	0	FAM38A	87310177	0.001000	0.12720	0.803000	0.32268	0.131000	0.20780	-0.273000	0.08548	-0.434000	0.07275	-4.544000	0.00004	TAA	A|0.131;G|0.869	0.869	strong		0.662	PIEZO1-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000345699.4	NM_014745	
IL2	3558	hgsc.bcm.edu	37	4	123377482	123377482	+	Silent	SNP	C	C	A	rs2069763	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	190	0	0		WXS	Illumina HiSeq	Phase_I	142	63	0.443662	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		
PCMTD1	115294	hgsc.bcm.edu	37	8	52733164	52733164	+	Missense_Mutation	SNP	G	G	C	rs149898988		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:52733164G>C	ENST00000360540.5	-	7	1227	c.821C>G	c.(820-822)cCc>cGc	p.P274R	PCMTD1_ENST00000519559.1_5'UTR|PCMTD1_ENST00000544451.1_Missense_Mutation_p.P198R|PCMTD1_ENST00000522514.1_Missense_Mutation_p.P274R	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	205	0	0		WXS	Illumina HiSeq	Phase_I	168	16	0.0952381	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	
WWC2	80014	hgsc.bcm.edu	37	4	184190233	184190233	+	Missense_Mutation	SNP	G	G	T	rs11941467	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:184190233G>T	ENST00000403733.3	+	15	2516	c.2317G>T	c.(2317-2319)Gcc>Tcc	p.A773S	WWC2_ENST00000504005.1_Missense_Mutation_p.A455S|WWC2_ENST00000506225.1_3'UTR|WWC2_ENST00000513834.1_Missense_Mutation_p.A724S|WWC2_ENST00000378925.3_Missense_Mutation_p.A675S|WWC2_ENST00000448232.2_Missense_Mutation_p.A773S	NM_024949.5	NP_079225.5	Q6AWC2	WWC2_HUMAN	WW and C2 domain containing 2	773	C2.		A -> S (in dbSNP:rs11941467). {ECO:0000269|PubMed:15489334}.		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)		GTTCAGAGTCGCCATTTCCCA	0.453													G|||	500	0.0998403	0.0166	0.072	5008	,	,		18521	0.0933		0.1143	False		,,,				2504	0.2239				p.A773S		Atlas-SNP	.											.	WWC2	78	.	0			c.G2317T						PASS	.	G	SER/ALA	164,4242	109.9+/-148.2	4,156,2043	148.0	146.0	146.0		2317	3.5	1.0	4	dbSNP_120	146	947,7653	208.3+/-249.8	60,827,3413	yes	missense	WWC2	NM_024949.5	99	64,983,5456	TT,TG,GG		11.0116,3.7222,8.5422	benign	773/1193	184190233	1111,11895	2203	4300	6503	SO:0001583	missense	80014	exon15			AGAGTCGCCATTT	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.2317G>T	4.37:g.184190233G>T	ENSP00000384222:p.Ala773Ser	Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	97	59	0.608247	NM_024949	Q32Q84|Q69YQ1|Q6AWB8|Q6ZSY9|Q6ZU09|Q7Z620|Q8TEB8|Q9H6P0	Missense_Mutation	SNP	ENST00000403733.3	37	CCDS34109.2	158	0.07234432234432235	3	0.006097560975609756	29	0.08011049723756906	46	0.08041958041958042	80	0.10554089709762533	G	6.837	0.523552	0.13066	0.037222	0.110116	ENSG00000151718	ENST00000403733;ENST00000378925;ENST00000513834;ENST00000448232;ENST00000504005	T;T;T;T;T	0.15017	2.46;2.46;2.46;2.46;2.46	5.35	3.5	0.40072	C2 calcium/lipid-binding domain, CaLB (1);	0.255724	0.33496	N	0.004843	T	0.00178	0.0005	N	0.12471	0.22	0.31698	N	0.641027	B;B;B	0.24186	0.044;0.01;0.099	B;B;B	0.22601	0.03;0.024;0.04	T	0.12915	-1.0529	10	0.14252	T	0.57	-6.6582	13.7162	0.62697	0.0:0.0:0.505:0.495	rs11941467;rs52814359;rs59395067;rs11941467	773;773;724	Q6AWC2-6;Q6AWC2;Q6AWC2-4	.;WWC2_HUMAN;.	S	773;675;724;773;455	ENSP00000384222:A773S;ENSP00000368205:A675S;ENSP00000425054:A724S;ENSP00000398577:A773S;ENSP00000427569:A455S	ENSP00000368205:A675S	A	+	1	0	WWC2	184427227	1.000000	0.71417	1.000000	0.80357	0.935000	0.57460	1.546000	0.36179	1.430000	0.47334	0.555000	0.69702	GCC	G|0.917;T|0.083	0.083	strong		0.453	WWC2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319608.1	NM_024949	
TET1	80312	hgsc.bcm.edu	37	10	70405237	70405237	+	Silent	SNP	G	G	A	rs12241767	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:70405237G>A	ENST00000373644.4	+	4	2960	c.2751G>A	c.(2749-2751)gaG>gaA	p.E917E		NM_030625.2	NP_085128.2	Q8NFU7	TET1_HUMAN	tet methylcytosine dioxygenase 1	917					chromatin modification (GO:0016568)|DNA demethylation (GO:0080111)|inner cell mass cell differentiation (GO:0001826)|negative regulation of methylation-dependent chromatin silencing (GO:0090310)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein O-linked glycosylation (GO:0006493)|regulation of DNA methylation (GO:0044030)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	iron ion binding (GO:0005506)|methylcytosine dioxygenase activity (GO:0070579)|structure-specific DNA binding (GO:0043566)|zinc ion binding (GO:0008270)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(2)|ovary(5)|prostate(1)|upper_aerodigestive_tract(2)	21						AGAAGGATGAGGAATCAGAGC	0.478													A|||	1066	0.212859	0.3918	0.1369	5008	,	,		18623	0.12		0.1342	False		,,,				2504	0.2014				p.E917E		Atlas-SNP	.											.	TET1	255	.	0			c.G2751A						PASS	.	A		1526,2880	662.5+/-401.1	265,996,942	77.0	80.0	79.0		2751	5.8	1.0	10	dbSNP_120	79	937,7663	771.8+/-407.7	55,827,3418	no	coding-synonymous	TET1	NM_030625.2		320,1823,4360	AA,AG,GG		10.8953,34.6346,18.9374		917/2137	70405237	2463,10543	2203	4300	6503	SO:0001819	synonymous_variant	80312	exon4			GGATGAGGAATCA	AF430147	CCDS7281.1	10q21	2014-02-18	2011-09-30	2008-03-12	ENSG00000138336	ENSG00000138336			29484	protein-coding gene	gene with protein product	"""leukemia-associated protein with a CXXC domain"", ""ten-eleven translocation-1"""	607790	"""CXXC zinc finger 6"", ""tet oncogene 1"""	CXXC6		12124344, 12646957	Standard	NM_030625		Approved	LCX, KIAA1676, bA119F7.1	uc001jok.4	Q8NFU7	OTTHUMG00000018359	ENST00000373644.4:c.2751G>A	10.37:g.70405237G>A		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	48	24	0.5	NM_030625	Q5VUP7|Q7Z6B6|Q8TCR1|Q9C0I7	Silent	SNP	ENST00000373644.4	37	CCDS7281.1																																																																																			G|0.807;A|0.193	0.193	strong		0.478	TET1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048354.1	NM_030625	
HDAC7	51564	hgsc.bcm.edu	37	12	48189061	48189061	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:48189061G>A	ENST00000427332.2	-	11	1229	c.1073C>T	c.(1072-1074)tCa>tTa	p.S358L	HDAC7_ENST00000354334.3_Missense_Mutation_p.S360L|HDAC7_ENST00000552960.1_Missense_Mutation_p.S380L|HDAC7_ENST00000080059.7_Missense_Mutation_p.S397L|HDAC7_ENST00000380610.4_Missense_Mutation_p.S414L			Q8WUI4	HDAC7_HUMAN	histone deacetylase 7	358	Transcription repression 2. {ECO:0000250}.				cell-cell junction assembly (GO:0007043)|negative regulation of interleukin-2 production (GO:0032703)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of cell migration involved in sprouting angiogenesis (GO:0090050)|transcription, DNA-templated (GO:0006351)|vasculogenesis (GO:0001570)	cytoplasm (GO:0005737)|histone deacetylase complex (GO:0000118)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	14-3-3 protein binding (GO:0071889)|activating transcription factor binding (GO:0033613)|chromatin binding (GO:0003682)|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 kinase binding (GO:0019901)|protein kinase C binding (GO:0005080)|repressing transcription factor binding (GO:0070491)|transcription corepressor activity (GO:0003714)			breast(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	25				GBM - Glioblastoma multiforme(48;0.137)		CAGGGGCTCTGAGCGAGTCCG	0.677																																					p.S397L		Atlas-SNP	.											HDAC7,NS,carcinoma,+1,1	HDAC7	71	1	0			c.C1190T						scavenged	.						28.0	33.0	31.0					12																	48189061		2195	4297	6492	SO:0001583	missense	51564	exon11			GGCTCTGAGCGAG	AF239243	CCDS8756.2, CCDS41776.1	12q13.1	2008-02-25	2008-02-25	2008-02-25	ENSG00000061273	ENSG00000061273			14067	protein-coding gene	gene with protein product		606542	"""histone deacetylase 7A"""	HDAC7A		10922406, 10640276	Standard	NM_015401		Approved	DKFZP586J0917	uc010slo.2	Q8WUI4	OTTHUMG00000152968	ENST00000427332.2:c.1073C>T	12.37:g.48189061G>A	ENSP00000404394:p.Ser358Leu	Somatic	42	1	0.0238095		WXS	Illumina HiSeq	Phase_I	46	16	0.347826	NM_015401	B3KY08|B4DWI0|B4E0Q5|Q6P1W9|Q6W9G7|Q7Z4K2|Q7Z5I1|Q96K01|Q9BR73|Q9H7L0|Q9NW41|Q9NWA9|Q9NYK9|Q9UFU7	Missense_Mutation	SNP	ENST00000427332.2	37		.	.	.	.	.	.	.	.	.	.	G	32	5.178706	0.94846	.	.	ENSG00000061273	ENST00000080059;ENST00000354334;ENST00000552960;ENST00000380610;ENST00000427332	T;T;T;T;T	0.74632	-0.66;-0.86;-0.63;-0.78;-0.57	4.37	4.37	0.52481	.	0.000000	0.64402	D	0.000001	D	0.84570	0.5501	M	0.69358	2.11	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.998;0.998;0.997	D	0.86580	0.1853	10	0.87932	D	0	.	16.0096	0.80391	0.0:0.0:1.0:0.0	.	397;380;360	Q8WUI4-5;Q8WUI4-6;Q8WUI4-7	.;.;.	L	397;360;380;414;358	ENSP00000080059:S397L;ENSP00000351326:S360L;ENSP00000448532:S380L;ENSP00000369984:S414L;ENSP00000404394:S358L	ENSP00000080059:S397L	S	-	2	0	HDAC7	46475328	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.065000	0.93941	2.418000	0.82041	0.561000	0.74099	TCA	.	.	none		0.677	HDAC7-013	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000328804.2		
KRTAP4-7	100132476	hgsc.bcm.edu	37	17	39240794	39240794	+	Silent	SNP	C	C	A	rs9894106|rs553572799	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:39240794C>A	ENST00000391417.4	+	1	336	c.336C>A	c.(334-336)ccC>ccA	p.P112P		NM_033061.3	NP_149050.3	Q9BYR0	KRA47_HUMAN	keratin associated protein 4-7	137	31 X 5 AA repeats of C-C-[GIKRQVHEML]- [SPTRV]-[STVQRCP].		Missing. {ECO:0000269|PubMed:15955084}.		aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)		p.R111_C115delRPSCC(1)|p.P112P(1)|p.?(1)		NS(1)|endometrium(3)|kidney(1)|lung(1)|prostate(2)|urinary_tract(1)	9						gctgccgccccagctgctgcc	0.667																																					p.P112P		Atlas-SNP	.											KRTAP4-7,NS,carcinoma,0,3	KRTAP4-7	49	3	3	Unknown(1)|Substitution - coding silent(1)|Deletion - In frame(1)	NS(2)|prostate(1)	c.C336A						scavenged	.						13.0	14.0	14.0					17																	39240794		691	1589	2280	SO:0001819	synonymous_variant	100132476	exon1			CCGCCCCAGCTGC	AJ406939	CCDS45673.1	17q21.2	2013-06-25			ENSG00000240871	ENSG00000240871		"""Keratin associated proteins"""	18898	protein-coding gene	gene with protein product						11279113	Standard	NM_033061		Approved	KAP4.7	uc010wfn.2	Q9BYR0	OTTHUMG00000133582	ENST00000391417.4:c.336C>A	17.37:g.39240794C>A		Somatic	21	0	0		WXS	Illumina HiSeq	Phase_I	37	6	0.162162	NM_033061	A0AVM6|A8MQ08|A8MTL4	Silent	SNP	ENST00000391417.4	37	CCDS45673.1																																																																																			.	.	weak		0.667	KRTAP4-7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257686.1		
FAM120B	84498	hgsc.bcm.edu	37	6	170627614	170627614	+	Missense_Mutation	SNP	T	T	C	rs6905356	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:170627614T>C	ENST00000476287.1	+	2	1244	c.1136T>C	c.(1135-1137)aTg>aCg	p.M379T	FAM120B_ENST00000537664.1_Missense_Mutation_p.M402T|FAM120B_ENST00000540480.1_Missense_Mutation_p.M391T|FAM120B_ENST00000252510.9_Intron	NM_032448.1	NP_115824.1	Q96EK7	F120B_HUMAN	family with sequence similarity 120B	379			M -> T (in dbSNP:rs6905356).		cell differentiation (GO:0030154)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(11)|liver(1)|lung(15)|ovary(1)|prostate(2)|skin(2)	44		Breast(66;0.000338)|Esophageal squamous(34;0.241)		OV - Ovarian serous cystadenocarcinoma(33;3.94e-22)|BRCA - Breast invasive adenocarcinoma(81;6.47e-06)|GBM - Glioblastoma multiforme(31;0.0899)		GAAGTTCCCATGTGTTCAGAC	0.527													T|||	800	0.159744	0.0756	0.2046	5008	,	,		19322	0.2817		0.1252	False		,,,				2504	0.1513				p.M379T		Atlas-SNP	.											.	FAM120B	108	.	0			c.T1136C						PASS	.	T	THR/MET	426,3980	205.5+/-227.4	21,384,1798	167.0	173.0	171.0		1136	2.2	0.0	6	dbSNP_116	171	1195,7405	242.1+/-272.2	75,1045,3180	no	missense	FAM120B	NM_032448.1	81	96,1429,4978	CC,CT,TT		13.8953,9.6686,12.4635	possibly-damaging	379/911	170627614	1621,11385	2203	4300	6503	SO:0001583	missense	84498	exon2			TTCCCATGTGTTC	AB058741	CCDS5314.1, CCDS75555.1	6q27	2011-04-13	2006-07-04	2006-07-04	ENSG00000112584	ENSG00000112584			21109	protein-coding gene	gene with protein product	"""PPARgamma constitutive coactivator 1"", ""constitutive coactivator of PPAR-gamma"""	612266	"""KIAA1838"""	KIAA1838		14585507	Standard	NM_032448		Approved	PGCC1, CCPG	uc003qxp.3	Q96EK7	OTTHUMG00000016080	ENST00000476287.1:c.1136T>C	6.37:g.170627614T>C	ENSP00000417970:p.Met379Thr	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	36	7	0.194444	NM_032448	B4DL34|Q86V68|Q96JI9	Missense_Mutation	SNP	ENST00000476287.1	37	CCDS5314.1	367	0.16804029304029305	48	0.0975609756097561	60	0.16574585635359115	161	0.28146853146853146	98	0.12928759894459102	T	13.15	2.150248	0.37923	0.096686	0.138953	ENSG00000112584	ENST00000540480;ENST00000537664;ENST00000476287	T;T;T	0.08370	3.1;3.1;3.11	3.41	2.24	0.28232	.	.	.	.	.	T	0.02688	0.0081	L	0.58101	1.795	0.50813	P	1.0100000000001774E-4	B;B	0.32467	0.005;0.372	B;B	0.33392	0.004;0.163	T	0.40776	-0.9545	8	0.13470	T	0.59	-1.2591	7.105	0.25358	0.0:0.1146:0.0:0.8854	rs6905356;rs52795961;rs6905356	379;379	Q96EK7;F2Z2E1	F120B_HUMAN;.	T	391;402;379	ENSP00000444125:M391T;ENSP00000440125:M402T;ENSP00000417970:M379T	ENSP00000436640:M379T	M	+	2	0	FAM120B	170469539	0.006000	0.16342	0.002000	0.10522	0.884000	0.51177	0.457000	0.21875	0.668000	0.31126	0.528000	0.53228	ATG	T|0.861;C|0.139	0.139	strong		0.527	FAM120B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000043259.2	NM_032448	
RP1L1	94137	hgsc.bcm.edu	37	8	10469340	10469340	+	Silent	SNP	G	G	A	rs57819090	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:10469340G>A	ENST00000382483.3	-	4	2491	c.2268C>T	c.(2266-2268)aaC>aaT	p.N756N		NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	756					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)		CAGAGGGAGCGTTGTGCGGGG	0.642													A|||	935	0.186701	0.0756	0.1643	5008	,	,		16943	0.2133		0.1352	False		,,,				2504	0.3783				p.N756N		Atlas-SNP	.											.	RP1L1	453	.	0			c.C2268T						PASS	.	A		324,3642		17,290,1676	47.0	54.0	52.0		2268	-9.6	0.0	8	dbSNP_129	52	1118,7194		84,950,3122	no	coding-synonymous	RP1L1	NM_178857.5		101,1240,4798	AA,AG,GG		13.4504,8.1694,11.7446		756/2401	10469340	1442,10836	1983	4156	6139	SO:0001819	synonymous_variant	94137	exon4			GGGAGCGTTGTGC	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.2268C>T	8.37:g.10469340G>A		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	85	21	0.247059	NM_178857	Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	Silent	SNP	ENST00000382483.3	37	CCDS43708.1																																																																																			G|0.852;A|0.148	0.148	strong		0.642	RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375673.1		
MB	4151	hgsc.bcm.edu	37	22	36007075	36007075	+	Silent	SNP	C	C	T	rs7293	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:36007075C>T	ENST00000397326.2	-	2	372	c.174G>A	c.(172-174)gcG>gcA	p.A58A	MB_ENST00000401702.1_Silent_p.A3A|MB_ENST00000406324.1_Silent_p.A58A|MB_ENST00000359787.1_Silent_p.A58A|MB_ENST00000397328.1_Silent_p.A58A	NM_005368.2	NP_005359.1	P02144	MYG_HUMAN	myoglobin	58					brown fat cell differentiation (GO:0050873)|enucleate erythrocyte differentiation (GO:0043353)|heart development (GO:0007507)|response to hormone (GO:0009725)|response to hydrogen peroxide (GO:0042542)|response to hypoxia (GO:0001666)|slow-twitch skeletal muscle fiber contraction (GO:0031444)	extracellular vesicular exosome (GO:0070062)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxygen binding (GO:0019825)|oxygen transporter activity (GO:0005344)			lung(1)	1						AGTCCTCAGACGCCTTCATCT	0.552													C|||	2659	0.53095	0.4501	0.4712	5008	,	,		21677	0.747		0.4483	False		,,,				2504	0.545				p.A58A	GBM(49;694 1113 16998 18419)|Esophageal Squamous(101;120 1973 10459 37086)	Atlas-SNP	.											MB_ENST00000447607,caecum,carcinoma,0,2	MB	7	2	0			c.G174A						PASS	.	C	,,	1974,2432	556.7+/-379.6	421,1132,650	139.0	110.0	120.0		174,174,174	-11.0	0.0	22	dbSNP_52	120	4016,4584	555.6+/-386.7	954,2108,1238	no	coding-synonymous,coding-synonymous,coding-synonymous	MB	NM_005368.2,NM_203377.1,NM_203378.1	,,	1375,3240,1888	TT,TC,CC		46.6977,44.8025,46.0557	,,	58/155,58/155,58/155	36007075	5990,7016	2203	4300	6503	SO:0001819	synonymous_variant	4151	exon3			CTCAGACGCCTTC		CCDS13917.1	22q13.1	2012-10-02			ENSG00000198125	ENSG00000198125			6915	protein-coding gene	gene with protein product		160000				10591208, 2989088	Standard	NM_005368		Approved	PVALB	uc003anz.3	P02144	OTTHUMG00000150606	ENST00000397326.2:c.174G>A	22.37:g.36007075C>T		Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	161	85	0.52795	NM_203377	Q52H51|Q5THY7	Silent	SNP	ENST00000397326.2	37	CCDS13917.1																																																																																			C|0.504;T|0.496	0.496	strong		0.552	MB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319057.2	NM_203377	
EQTN	54586	hgsc.bcm.edu	37	9	27296705	27296705	+	Silent	SNP	A	A	G	rs3824406	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:27296705A>G	ENST00000380032.3	-	2	191	c.108T>C	c.(106-108)gaT>gaC	p.D36D	EQTN_ENST00000537675.1_Silent_p.D36D|EQTN_ENST00000484994.1_5'UTR|EQTN_ENST00000380031.1_Silent_p.D36D	NM_020641.2	NP_065692.2	Q9NQ60	EQTN_HUMAN	equatorin, sperm acrosome associated	36					acrosomal vesicle exocytosis (GO:0060478)|endocytosis (GO:0006897)|fusion of sperm to egg plasma membrane (GO:0007342)	early endosome (GO:0005769)|inner acrosomal membrane (GO:0002079)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|outer acrosomal membrane (GO:0002081)|plasma membrane (GO:0005886)											GCTTATTAACATCTTCATTTA	0.294													A|||	611	0.122005	0.0129	0.0807	5008	,	,		17016	0.1994		0.1889	False		,,,				2504	0.1503				p.D36D		Atlas-SNP	.											.	.	.	.	0			c.T108C						PASS	.	A	,	164,4242	108.6+/-147.0	2,160,2041	86.0	83.0	84.0		108,108	1.3	0.0	9	dbSNP_107	84	1478,7102	279.5+/-294.0	122,1234,2934	no	coding-synonymous,coding-synonymous	C9orf11	NM_001161585.1,NM_020641.2	,	124,1394,4975	GG,GA,AA		17.2261,3.7222,12.6444	,	36/266,36/295	27296705	1642,11344	2203	4290	6493	SO:0001819	synonymous_variant	54586	exon2			ATTAACATCTTCA	AJ278482	CCDS35001.1, CCDS55300.1	9p21	2012-09-20	2012-09-20	2012-09-20	ENSG00000120160	ENSG00000120160			1359	protein-coding gene	gene with protein product	"""Acr formation associated factor"", ""Acrosome formation associated factor"", ""sperm acrosome associated 8"""		"""chromosome 9 open reading frame 11"", ""equatorin"""	C9orf11			Standard	NM_020641		Approved	AFAF, SPACA8, equatorin	uc003zql.3	Q9NQ60	OTTHUMG00000021033	ENST00000380032.3:c.108T>C	9.37:g.27296705A>G		Somatic	264	0	0		WXS	Illumina HiSeq	Phase_I	180	94	0.522222	NM_001161585	B2RPB3|B7ZMK1|Q5TCU1|Q96L22	Silent	SNP	ENST00000380032.3	37	CCDS35001.1																																																																																			A|0.873;G|0.127	0.127	strong		0.294	EQTN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055499.1	NM_020641	
ZNF469	84627	hgsc.bcm.edu	37	16	88501971	88501971	+	Missense_Mutation	SNP	T	T	A	rs3812956	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:88501971T>A	ENST00000437464.1	+	2	8009	c.8009T>A	c.(8008-8010)cTg>cAg	p.L2670Q	ZNF469_ENST00000565624.1_Missense_Mutation_p.L2698Q	NM_001127464.1	NP_001120936.1	Q96JG9	ZN469_HUMAN	zinc finger protein 469	2670			L -> Q (in dbSNP:rs3812956). {ECO:0000269|PubMed:11347906}.		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(4)|endometrium(6)|kidney(3)|large_intestine(1)|skin(6)	20						TTGGCCACTCTGGGACCTGGG	0.657													T|||	1474	0.294329	0.1815	0.3473	5008	,	,		15665	0.4028		0.3728	False		,,,				2504	0.2168				p.L2670Q		Atlas-SNP	.											.	ZNF469	121	.	0			c.T8009A						PASS	.	T	GLN/LEU	301,1083		33,235,424	18.0	21.0	20.0		8009	-6.5	0.0	16	dbSNP_107	20	1243,1937		247,749,594	yes	missense	ZNF469	NM_001127464.1	113	280,984,1018	AA,AT,TT		39.0881,21.7486,33.83	benign	2670/3926	88501971	1544,3020	692	1590	2282	SO:0001583	missense	84627	exon2			CCACTCTGGGACC	AB058761	CCDS45544.1	16q24	2010-08-04				ENSG00000225614		"""Zinc fingers, C2H2-type"""	23216	protein-coding gene	gene with protein product		612078				11347906	Standard	NM_001127464		Approved	KIAA1858	uc002fku.2	Q96JG9		ENST00000437464.1:c.8009T>A	16.37:g.88501971T>A	ENSP00000402343:p.Leu2670Gln	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	36	17	0.472222	NM_001127464		Missense_Mutation	SNP	ENST00000437464.1	37	CCDS45544.1	695	0.3182234432234432	92	0.18699186991869918	110	0.30386740331491713	209	0.36538461538461536	284	0.37467018469656993	T	4.345	0.063439	0.08388	0.217486	0.390881	ENSG00000225614	ENST00000437464	T	0.05382	3.45	3.23	-6.47	0.01902	.	.	.	.	.	T	0.00012	0.0000	N	0.03608	-0.345	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.48514	-0.9029	8	0.27785	T	0.31	.	0.6077	0.00755	0.1968:0.1814:0.3023:0.3196	rs3812956;rs60168268	2670	Q96JG9	ZN469_HUMAN	Q	2670	ENSP00000402343:L2670Q	ENSP00000402343:L2670Q	L	+	2	0	ZNF469	87029472	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.057000	0.03486	-2.507000	0.00506	-1.156000	0.01807	CTG	T|0.680;A|0.320	0.320	strong		0.657	ZNF469-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NG_012236	
MUC4	4585	hgsc.bcm.edu	37	3	195512212	195512212	+	Missense_Mutation	SNP	G	G	T	rs75588776	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195512212G>T	ENST00000463781.3	-	2	6698	c.6239C>A	c.(6238-6240)cCt>cAt	p.P2080H	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.P2080H	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0	EGF-like 2. {ECO:0000255|PROSITE- ProRule:PRU00076}.				cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.P2080H(2)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GACAAGAAGAGGGGTGGCGTG	0.567																																					p.P2080H		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,3	MUC4	1505	3	2	Substitution - Missense(2)	stomach(2)	c.C6239A						PASS	.						18.0	20.0	19.0					3																	195512212		684	1571	2255	SO:0001583	missense	4585	exon2			AGAAGAGGGGTGG	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.6239C>A	3.37:g.195512212G>T	ENSP00000417498:p.Pro2080His	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	87	19	0.218391	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	G	3.566	-0.088623	0.07097	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.32988	1.43;1.45	.	.	.	.	.	.	.	.	T	0.11495	0.0280	N	0.08118	0	0.09310	N	1	B	0.22909	0.077	B	0.06405	0.002	T	0.28744	-1.0034	7	.	.	.	.	2.8356	0.05513	3.0E-4:2.0E-4:0.5012:0.4983	.	2080	E7ESK3	.	H	2080	ENSP00000417498:P2080H;ENSP00000420243:P2080H	.	P	-	2	0	MUC4	196996607	0.000000	0.05858	0.053000	0.19242	0.070000	0.16714	0.024000	0.13555	0.064000	0.16427	0.064000	0.15345	CCT	G|0.816;T|0.185	0.185	strong		0.567	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
CDH9	1007	hgsc.bcm.edu	37	5	26902724	26902724	+	Missense_Mutation	SNP	T	T	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:26902724T>G	ENST00000231021.4	-	7	1286	c.1114A>C	c.(1114-1116)Ata>Cta	p.I372L		NM_016279.3	NP_057363.3	Q9ULB4	CADH9_HUMAN	cadherin 9, type 2 (T1-cadherin)	372	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)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(25)|lung(80)|ovary(5)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	137						TCCACAGATATTTTGACCACA	0.403																																					p.I372L	Melanoma(8;187 585 15745 40864 52829)	Atlas-SNP	.											.	CDH9	305	.	0			c.A1114C						PASS	.						124.0	121.0	122.0					5																	26902724		2203	4300	6503	SO:0001583	missense	1007	exon7			CAGATATTTTGAC	AB035302	CCDS3893.1	5p14	2010-01-26			ENSG00000113100	ENSG00000113100		"""Cadherins / Major cadherins"""	1768	protein-coding gene	gene with protein product		609974				2059658	Standard	NM_016279		Approved		uc003jgs.1	Q9ULB4	OTTHUMG00000090671	ENST00000231021.4:c.1114A>C	5.37:g.26902724T>G	ENSP00000231021:p.Ile372Leu	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	147	35	0.238095	NM_016279	Q3B7I5	Missense_Mutation	SNP	ENST00000231021.4	37	CCDS3893.1	.	.	.	.	.	.	.	.	.	.	T	16.37	3.102931	0.56183	.	.	ENSG00000113100	ENST00000231021	T	0.68181	-0.31	5.62	3.25	0.37280	Cadherin (3);Cadherin-like (1);	0.179874	0.51477	D	0.000089	T	0.70055	0.3180	M	0.83223	2.63	0.36617	D	0.875535	B	0.09022	0.002	B	0.36134	0.218	T	0.66244	-0.5972	9	.	.	.	.	7.5723	0.27915	0.0:0.2391:0.0:0.7609	.	372	Q9ULB4	CADH9_HUMAN	L	372	ENSP00000231021:I372L	.	I	-	1	0	CDH9	26938481	1.000000	0.71417	0.998000	0.56505	0.997000	0.91878	1.231000	0.32624	0.426000	0.26116	0.528000	0.53228	ATA	.	.	none		0.403	CDH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207352.1	NM_016279	
RNF213	57674	hgsc.bcm.edu	37	17	78262161	78262161	+	Splice_Site	SNP	T	T	C	rs17857135	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:78262161T>C	ENST00000582970.1	+	4	952	c.809T>C	c.(808-810)aTg>aCg	p.M270T	RNF213_ENST00000456466.1_Splice_Site_p.M270T|RNF213_ENST00000508628.2_Splice_Site_p.M319T|RNF213_ENST00000319921.4_Splice_Site_p.M270T	NM_001256071.1	NP_001243000.1	Q63HN8	RN213_HUMAN	ring finger protein 213	270				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)			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)			TCAGCCTCTATGGTGAGTCAT	0.657													C|||	1059	0.211462	0.4516	0.1153	5008	,	,		16204	0.0655		0.1402	False		,,,				2504	0.1789				p.M270T		Atlas-SNP	.											RNF213_ENST00000456466,NS,carcinoma,0,6	RNF213	766	6	0			c.T809C						PASS	.	C	THR/MET,THR/MET	1594,2772		309,976,898	25.0	30.0	28.0		956,809	-1.3	0.0	17	dbSNP_123	28	1293,7185		117,1059,3063	yes	missense-near-splice,missense-near-splice	RNF213	NM_020914.4,NM_020954.2	81,81	426,2035,3961	CC,CT,TT		15.2512,36.5094,22.4774	benign,benign	319/5257,270/1064	78262161	2887,9957	2183	4239	6422	SO:0001630	splice_region_variant	57674	exon4			CCTCTATGGTGAG	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.810+1T>C	17.37:g.78262161T>C		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	93	48	0.516129	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	407	0.18635531135531136	212	0.43089430894308944	42	0.11602209944751381	37	0.06468531468531469	116	0.15303430079155672	C	4.576	0.107008	0.08780	0.365094	0.152512	ENSG00000173821	ENST00000508628;ENST00000411702;ENST00000456466;ENST00000319921	T;T	0.40225	1.04;1.04	4.19	-1.33	0.09172	.	2.237800	0.02216	N	0.063634	T	0.00012	0.0000	N	0.08118	0	0.28504	P	0.9138847999999999	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.41124	-0.9526	9	0.15952	T	0.53	-2.9558	1.0092	0.01493	0.4316:0.1641:0.244:0.1603	rs17857135;rs17857217;rs56981151	270;270	Q9HCF4;Q9HCF4-2	ALO17_HUMAN;.	T	270;319;270;270	ENSP00000392123:M270T;ENSP00000324392:M270T	ENSP00000324392:M270T	M	+	2	0	RNF213	75876756	0.000000	0.05858	0.023000	0.16930	0.004000	0.04260	-0.744000	0.04839	-0.415000	0.07484	-0.762000	0.03455	ATG	T|0.785;C|0.215	0.215	strong		0.657	RNF213-020	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443298.1	NM_020914	Missense_Mutation
C10orf71	118461	hgsc.bcm.edu	37	10	50534862	50534862	+	Silent	SNP	T	T	C	rs12411843	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:50534862T>C	ENST00000374144.3	+	3	4560	c.4272T>C	c.(4270-4272)gaT>gaC	p.D1424D	C10orf71_ENST00000323868.4_Intron			Q711Q0	CJ071_HUMAN	chromosome 10 open reading frame 71	1424										endometrium(1)	1						TCTCCACTGATGACCTAGAGG	0.602													C|||	1521	0.303714	0.1316	0.3818	5008	,	,		14631	0.4127		0.333	False		,,,				2504	0.3384				p.D1424D		Atlas-SNP	.											.	C10orf71	179	.	0			c.T4272C						PASS	.	C	,	239,1145		19,201,472	29.0	33.0	32.0		4272,	-6.5	0.0	10	dbSNP_120	32	1018,2164		162,694,735	no	coding-synonymous,intron	C10orf71	NM_001135196.1,NM_199459.3	,	181,895,1207	CC,CT,TT		31.9925,17.2688,27.5296	,	1424/1436,	50534862	1257,3309	692	1591	2283	SO:0001819	synonymous_variant	118461	exon3			CACTGATGACCTA	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.4272T>C	10.37:g.50534862T>C		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	72	35	0.486111	NM_001135196	A0AVL8	Silent	SNP	ENST00000374144.3	37	CCDS44387.1																																																																																			T|0.690;C|0.310	0.310	strong		0.602	C10orf71-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047984.2	NM_199459	
MYBPC2	4606	hgsc.bcm.edu	37	19	50967640	50967640	+	Missense_Mutation	SNP	G	G	A	rs25667	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:50967640G>A	ENST00000357701.5	+	27	3317	c.3266G>A	c.(3265-3267)cGt>cAt	p.R1089H		NM_004533.3	NP_004524.3	Q14324	MYPC2_HUMAN	myosin binding protein C, fast type	1089	Ig-like C2-type 7.		R -> H (in dbSNP:rs25667).		cell adhesion (GO:0007155)|muscle filament sliding (GO:0030049)	cytosol (GO:0005829)|myosin filament (GO:0032982)	structural constituent of muscle (GO:0008307)			breast(1)	1		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.0079)|GBM - Glioblastoma multiforme(134;0.0144)		ATGGAAATCCGTGAAGATCCC	0.537													G|||	705	0.140775	0.0136	0.2522	5008	,	,		20485	0.126		0.2207	False		,,,				2504	0.1667				p.R1089H		Atlas-SNP	.											.	MYBPC2	103	.	0			c.G3266A						PASS	.	G	HIS/ARG	171,4039		2,167,1936	55.0	59.0	58.0		3266	-0.5	0.0	19	dbSNP_72	58	1622,6868		164,1294,2787	yes	missense	MYBPC2	NM_004533.3	29	166,1461,4723	AA,AG,GG		19.1048,4.0618,14.1181	benign	1089/1142	50967640	1793,10907	2105	4245	6350	SO:0001583	missense	4606	exon27			AAATCCGTGAAGA		CCDS46152.1	19q13.33	2013-02-11	2001-11-28		ENSG00000086967	ENSG00000086967		"""Myosin binding proteins"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	7550	protein-coding gene	gene with protein product	"""fast-type muscle myosin-binding-protein C"""	160793	"""myosin-binding protein C, fast-type"""			8375400	Standard	NM_004533		Approved	MYBPCF, MYBPC, MGC163408	uc002psf.2	Q14324		ENST00000357701.5:c.3266G>A	19.37:g.50967640G>A	ENSP00000350332:p.Arg1089His	Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	48	31	0.645833	NM_004533	A1L4G9	Missense_Mutation	SNP	ENST00000357701.5	37	CCDS46152.1	339	0.15521978021978022	9	0.018292682926829267	88	0.2430939226519337	80	0.13986013986013987	162	0.21372031662269128	g	2.377	-0.342929	0.05243	0.040618	0.191048	ENSG00000086967	ENST00000357701	T	0.68331	-0.32	3.99	-0.521	0.11931	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.234288	0.17079	N	0.187854	T	0.00012	0.0000	N	0.16862	0.45	0.80722	P	0.0	B	0.09022	0.002	B	0.13407	0.009	T	0.06679	-1.0813	9	0.45353	T	0.12	.	5.3863	0.16220	0.2583:0.1555:0.5862:0.0	rs25667;rs2230840;rs17403009;rs17718746;rs52798518;rs56519860;rs61720718;rs17403009	1089	Q14324	MYPC2_HUMAN	H	1089	ENSP00000350332:R1089H	ENSP00000350332:R1089H	R	+	2	0	MYBPC2	55659452	0.000000	0.05858	0.001000	0.08648	0.385000	0.30292	0.074000	0.14662	0.199000	0.20427	0.457000	0.33378	CGT	A|0.143;C|0.000;G|0.857	0.143	strong		0.537	MYBPC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464751.1	NM_004533	
KIF7	374654	hgsc.bcm.edu	37	15	90195948	90195948	+	Missense_Mutation	SNP	G	G	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:90195948G>C	ENST00000394412.3	-	2	290	c.214C>G	c.(214-216)Cag>Gag	p.Q72E		NM_198525.2	NP_940927.2	Q2M1P5	KIF7_HUMAN	kinesin family member 7	72	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				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)			ACGCAGGCCTGGTACACGGCC	0.637																																					p.Q72E		Atlas-SNP	.											.	KIF7	130	.	0			c.C214G						PASS	.						74.0	79.0	78.0					15																	90195948		689	1590	2279	SO:0001583	missense	374654	exon2			AGGCCTGGTACAC	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.214C>G	15.37:g.90195948G>C	ENSP00000377934:p.Gln72Glu	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	120	71	0.591667	NM_198525	Q3SXY0|Q6UXE9|Q8IW72	Missense_Mutation	SNP	ENST00000394412.3	37	CCDS32325.2	.	.	.	.	.	.	.	.	.	.	G	0.328	-0.957591	0.02267	.	.	ENSG00000166813	ENST00000394412	T	0.70869	-0.52	4.75	3.77	0.43336	Kinesin, motor domain (4);	.	.	.	.	T	0.36082	0.0954	N	0.00864	-1.135	0.24841	N	0.99247	B	0.09022	0.002	B	0.12156	0.007	T	0.24333	-1.0163	9	0.16420	T	0.52	.	7.1539	0.25626	0.0:0.2579:0.4681:0.274	.	72	Q2M1P5	KIF7_HUMAN	E	72	ENSP00000377934:Q72E	ENSP00000377934:Q72E	Q	-	1	0	KIF7	87996952	0.015000	0.18098	1.000000	0.80357	0.464000	0.32679	0.295000	0.19065	2.183000	0.69458	0.655000	0.94253	CAG	.	.	none		0.637	KIF7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347782.1	NM_198525	
SFI1	9814	hgsc.bcm.edu	37	22	32000872	32000872	+	Silent	SNP	G	G	A	rs8142346	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:32000872G>A	ENST00000400288.2	+	20	2100	c.1995G>A	c.(1993-1995)gtG>gtA	p.V665V	SFI1_ENST00000432498.1_Silent_p.V634V|SFI1_ENST00000414585.1_Silent_p.V512V|SFI1_ENST00000443011.1_Silent_p.V512V|SFI1_ENST00000540643.1_Silent_p.V610V|SFI1_ENST00000400289.1_Silent_p.V583V|SFI1_ENST00000443326.1_Silent_p.V583V	NM_001007467.2	NP_001007468.1	A8K8P3	SFI1_HUMAN	Sfi1 homolog, spindle assembly associated (yeast)	665					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|negative regulation of phosphatase activity (GO:0010923)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)	phosphatase binding (GO:0019902)			NS(2)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|large_intestine(7)|liver(1)|lung(11)|ovary(1)|prostate(3)|upper_aerodigestive_tract(3)	38						AGGGCAGGGTGCGAAGCATCC	0.637													G|||	53	0.0105831	0.0008	0.0072	5008	,	,		18231	0.0		0.0229	False		,,,				2504	0.0245				p.V665V		Atlas-SNP	.											.	SFI1	78	.	0			c.G1995A						PASS	.	G	,	31,3973		0,31,1971	26.0	29.0	28.0		1995,1902	-1.4	0.0	22	dbSNP_116	28	322,8042		7,308,3867	no	coding-synonymous,coding-synonymous	SFI1	NM_001007467.1,NM_014775.2	,	7,339,5838	AA,AG,GG		3.8498,0.7742,2.8541	,	665/1243,634/1212	32000872	353,12015	2002	4182	6184	SO:0001819	synonymous_variant	9814	exon20			CAGGGTGCGAAGC	AB011114	CCDS43004.1, CCDS43005.1, CCDS58803.1, CCDS58804.1	22q12.2	2014-06-13			ENSG00000198089	ENSG00000198089			29064	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 139"""	612765				14504268	Standard	NM_001007467		Approved	KIAA0542, PISD, PPP1R139	uc003ale.4	A8K8P3	OTTHUMG00000030249	ENST00000400288.2:c.1995G>A	22.37:g.32000872G>A		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	100	42	0.42	NM_001007467	A1L373|A1L387|A2A2L2|B1AKL9|B5MDB7|B7Z1V6|B7Z8G3|B7ZBE2|B7ZBE3|O60289|Q2TAN8|Q5W1B5|Q86TK0|Q8N4U8|Q8N8C1|Q8WU14	Silent	SNP	ENST00000400288.2	37	CCDS43004.1																																																																																			G|0.981;A|0.019	0.019	strong		0.637	SFI1-023	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337180.3	NM_014775	
TRPM8	79054	hgsc.bcm.edu	37	2	234854552	234854552	+	Missense_Mutation	SNP	A	A	G	rs17868387	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:234854552A>G	ENST00000324695.4	+	7	792	c.752A>G	c.(751-753)tAt>tGt	p.Y251C	TRPM8_ENST00000433712.2_5'UTR|AC005538.5_ENST00000455991.1_RNA	NM_024080.4	NP_076985.4	Q7Z2W7	TRPM8_HUMAN	transient receptor potential cation channel, subfamily M, member 8	251			Y -> C (in dbSNP:rs17868387).		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)	GATCCACTGTATATCCTGGAC	0.438													A|||	241	0.048123	0.0182	0.0836	5008	,	,		21869	0.0833		0.0368	False		,,,				2504	0.0389				p.Y251C		Atlas-SNP	.											.	TRPM8	146	.	0			c.A752G						PASS	.	A	CYS/TYR	108,4298	83.4+/-121.9	4,100,2099	140.0	126.0	131.0		752	5.7	1.0	2	dbSNP_123	131	441,8159	134.7+/-192.1	10,421,3869	yes	missense	TRPM8	NM_024080.4	194	14,521,5968	GG,GA,AA		5.1279,2.4512,4.2211	probably-damaging	251/1105	234854552	549,12457	2203	4300	6503	SO:0001583	missense	79054	exon7			CACTGTATATCCT	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.752A>G	2.37:g.234854552A>G	ENSP00000323926:p.Tyr251Cys	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	73	38	0.520548	NM_024080	A0AVG2|Q3YFM7|Q6QNH9|Q8TAC3|Q8TDX8|Q9BVK1	Missense_Mutation	SNP	ENST00000324695.4	37	CCDS33407.1	132	0.06043956043956044	10	0.02032520325203252	45	0.12430939226519337	45	0.07867132867132867	32	0.04221635883905013	A	17.06	3.293224	0.60086	0.024512	0.051279	ENSG00000144481	ENST00000324695	T	0.57752	0.38	5.72	5.72	0.89469	.	0.000000	0.64402	D	0.000006	T	0.01222	0.0040	L	0.32530	0.975	0.09310	P	1.0	D	0.63880	0.993	P	0.55667	0.781	T	0.16482	-1.0401	9	0.56958	D	0.05	-21.075	14.8445	0.70251	1.0:0.0:0.0:0.0	rs17868387;rs17868387	251	Q7Z2W7	TRPM8_HUMAN	C	251	ENSP00000323926:Y251C	ENSP00000323926:Y251C	Y	+	2	0	TRPM8	234519291	1.000000	0.71417	0.994000	0.49952	0.853000	0.48598	6.478000	0.73596	2.194000	0.70268	0.533000	0.62120	TAT	A|0.954;G|0.046	0.046	strong		0.438	TRPM8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131005.4	NM_024080	
RNF207	388591	hgsc.bcm.edu	37	1	6279370	6279370	+	Missense_Mutation	SNP	G	G	C	rs846111	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:6279370G>C	ENST00000377939.4	+	18	1935	c.1808G>C	c.(1807-1809)gGc>gCc	p.G603A	RNF207_ENST00000377948.2_3'UTR|ICMT_ENST00000495791.1_5'Flank|RNF207_ENST00000483336.1_3'UTR	NM_207396.2	NP_997279.2	Q6ZRF8	RN207_HUMAN	ring finger protein 207	603			G -> A (in dbSNP:rs846111). {ECO:0000269|PubMed:19305409}.			intracellular (GO:0005622)	zinc ion binding (GO:0008270)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(7)|ovary(2)	16	Ovarian(185;0.0634)	all_cancers(23;1.22e-38)|all_epithelial(116;4.25e-22)|all_lung(118;7.95e-08)|Lung NSC(185;1.6e-06)|all_neural(13;3.18e-06)|all_hematologic(16;8.99e-06)|Acute lymphoblastic leukemia(12;0.000365)|Breast(487;0.000496)|Renal(390;0.0007)|Colorectal(325;0.00104)|Glioma(11;0.00203)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0392)|Medulloblastoma(700;0.211)		Epithelial(90;4.84e-38)|GBM - Glioblastoma multiforme(13;5.77e-32)|OV - Ovarian serous cystadenocarcinoma(86;2.88e-19)|Colorectal(212;6.9e-08)|COAD - Colon adenocarcinoma(227;8.13e-06)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000896)|BRCA - Breast invasive adenocarcinoma(365;0.00108)|STAD - Stomach adenocarcinoma(132;0.00311)|READ - Rectum adenocarcinoma(331;0.0642)|Lung(427;0.182)		GCTCCGAACGGCCTCTCAGAA	0.498													G|||	864	0.172524	0.0227	0.1758	5008	,	,		16230	0.1756		0.2604	False		,,,				2504	0.2791				p.G603A		Atlas-SNP	.											RNF207,caecum,carcinoma,0,2	RNF207	45	2	0			c.G1808C						PASS	.	G	ALA/GLY	219,3517		9,201,1658	54.0	56.0	55.0	http://www.ncbi.nlm.nih.gov/pubmed?term	1808	1.0	0.0	1	dbSNP_86	55	2163,6045		285,1593,2226	yes	missense	RNF207	NM_207396.2	60	294,1794,3884	CC,CG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	26.3523,5.8619,19.9431	benign	603/635	6279370	2382,9562	1868	4104	5972	SO:0001583	missense	388591	exon18			CGAACGGCCTCTC	AK128246	CCDS59.2	1p36.31	2008-11-19			ENSG00000158286	ENSG00000158286		"""RING-type (C3HC4) zinc fingers"""	32947	protein-coding gene	gene with protein product	"""OTTHUMG00000001089"""		"""chromosome 1 open reading frame 188"""	C1orf188			Standard	NM_207396		Approved	FLJ46380, FLJ32096	uc001amg.3	Q6ZRF8	OTTHUMG00000001089	ENST00000377939.4:c.1808G>C	1.37:g.6279370G>C	ENSP00000367173:p.Gly603Ala	Somatic	221	0	0		WXS	Illumina HiSeq	Phase_I	224	128	0.571429	NM_207396	A2VCM8|B4DFR6|Q5TGS6|Q6ZS63|Q96MP2	Missense_Mutation	SNP	ENST00000377939.4	37	CCDS59.2	380	0.17399267399267399	13	0.026422764227642278	70	0.19337016574585636	101	0.17657342657342656	196	0.25857519788918204	G	7.864	0.726640	0.15439	0.058619	0.263523	ENSG00000158286	ENST00000377939	T	0.15952	2.38	5.33	1.01	0.19927	.	0.326684	0.20268	U	0.095722	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.10296	0.003	B	0.06405	0.002	T	0.45264	-0.9273	9	0.13470	T	0.59	-0.5354	1.7254	0.02921	0.1818:0.1635:0.4863:0.1684	rs846111;rs3765570;rs17437807;rs846111	603	Q6ZRF8	RN207_HUMAN	A	603	ENSP00000367173:G603A	ENSP00000367173:G603A	G	+	2	0	RNF207	6201957	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.127000	0.10547	0.314000	0.23086	-0.140000	0.14226	GGC	G|0.803;C|0.197	0.197	strong		0.498	RNF207-001	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000003669.2	NM_207396	
MTCL1	23255	hgsc.bcm.edu	37	18	8825192	8825192	+	Silent	SNP	A	A	G	rs581894	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:8825192A>G	ENST00000306329.11	+	13	4641	c.4641A>G	c.(4639-4641)ggA>ggG	p.G1547G	SOGA2_ENST00000400050.3_Silent_p.G1187G|SOGA2_ENST00000517570.1_Silent_p.G1187G|SOGA2_ENST00000359865.3_Silent_p.G1228G|SOGA2_ENST00000306285.7_Silent_p.G553G|SOGA2_ENST00000518815.1_Silent_p.G553G														p.G1229fs*52(1)									ACACCAAGGGAGGCCCTCCAG	0.687													G|||	2950	0.589058	0.7617	0.6441	5008	,	,		16650	0.4038		0.6342	False		,,,				2504	0.4611				p.G1228G		Atlas-SNP	.											CCDC165,NS,carcinoma,0,1	.	.	1	1	Deletion - Frameshift(1)	prostate(1)	c.A3684G						PASS	.	G		3180,1218		1179,822,198	18.0	21.0	20.0		3684	0.7	0.1	18	dbSNP_83	20	5108,3478		1604,1900,789	no	coding-synonymous	CCDC165	NM_015210.3		2783,2722,987	GG,GA,AA		40.5078,27.6944,36.1676		1228/1587	8825192	8288,4696	2199	4293	6492	SO:0001819	synonymous_variant	23255	exon15			CAAGGGAGGCCCT																												ENST00000306329.11:c.4641A>G	18.37:g.8825192A>G		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	111	55	0.495495	NM_015210		Silent	SNP	ENST00000306329.11	37																																																																																				A|0.389;G|0.611	0.611	strong		0.687	SOGA2-015	PUTATIVE	basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000444141.1		
MCF2L	23263	hgsc.bcm.edu	37	13	113741590	113741590	+	Silent	SNP	G	G	A	rs9604022	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:113741590G>A	ENST00000375608.3	+	23	2563	c.2505G>A	c.(2503-2505)tcG>tcA	p.S835S	MCF2L_ENST00000375604.2_Silent_p.S862S|MCF2L_ENST00000375597.4_Silent_p.S803S|MCF2L_ENST00000434480.2_Silent_p.S811S|MCF2L_ENST00000423482.2_Silent_p.S803S|MCF2L_ENST00000375601.3_Silent_p.S809S|MCF2L_ENST00000397030.1_Silent_p.S838S|MCF2L_ENST00000421756.1_Silent_p.S809S|MCF2L_ENST00000442652.2_Silent_p.S835S|MCF2L_ENST00000535094.2_Silent_p.S805S			O15068	MCF2L_HUMAN	MCF.2 cell line derived transforming sequence-like	835	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of 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)				TGCAGGGCTCGTTCAGCGTCT	0.637													g|||	812	0.162141	0.2466	0.1311	5008	,	,		19303	0.005		0.1571	False		,,,				2504	0.2372				p.S805S		Atlas-SNP	.											.	MCF2L	182	.	0			c.G2415A						PASS	.	G	,	950,3456	357.4+/-313.9	119,712,1372	68.0	59.0	62.0		2415,2409	-2.3	1.0	13	dbSNP_119	62	1427,7171	273.7+/-290.8	128,1171,3000	no	coding-synonymous,coding-synonymous	MCF2L	NM_001112732.2,NM_024979.4	,	247,1883,4372	AA,AG,GG		16.5969,21.5615,18.279	,	805/1126,803/1124	113741590	2377,10627	2203	4299	6502	SO:0001819	synonymous_variant	23263	exon22			GGGCTCGTTCAGC	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.2505G>A	13.37:g.113741590G>A		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	111	51	0.459459	NM_001112732	A2A2X1|A2A2X2|A2A3G6|A2A3G8|B4DHD6|B4DIL6|E9PDN8|Q5JU56|Q5VXT1|Q6ZWD4|Q765G8|Q765G9|Q8N679	Silent	SNP	ENST00000375608.3	37		284|284	0.13003663003663005|0.13003663003663005	123|123	0.25|0.25	53|53	0.1464088397790055|0.1464088397790055	5|5	0.008741258741258742|0.008741258741258742	103|103	0.1358839050131926|0.1358839050131926	G|G	2.941|2.941	-0.218814|-0.218814	0.06101|0.06101	0.215615|0.215615	0.165969|0.165969	ENSG00000126217|ENSG00000126217	ENST00000413354|ENST00000397017	.|.	.|.	.|.	4.34|4.34	-2.28|-2.28	0.06826|0.06826	.|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.09310|0.09310	P|P	1.0|1.0	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.34502|0.34502	-0.9826|-0.9826	3|3	.|.	.|.	.|.	.|.	1.8524|1.8524	0.03172|0.03172	0.3428:0.2912:0.2297:0.1363|0.3428:0.2912:0.2297:0.1363	rs9604022;rs9604022|rs9604022;rs9604022	.|.	.|.	.|.	H|I	35|466	.|.	.|.	R|V	+|+	2|1	0|0	MCF2L|MCF2L	112789591|112789591	0.006000|0.006000	0.16342|0.16342	0.956000|0.956000	0.39512|0.39512	0.324000|0.324000	0.28378|0.28378	-1.073000|-1.073000	0.03430|0.03430	-0.924000|-0.924000	0.03780|0.03780	-2.416000|-2.416000	0.00220|0.00220	CGT|GTT	G|0.832;A|0.168	0.168	strong		0.637	MCF2L-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000045849.4		
DPCR1	135656	hgsc.bcm.edu	37	6	30919391	30919391	+	Silent	SNP	G	G	A	rs3094086	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:30919391G>A	ENST00000462446.1	+	2	3178	c.3150G>A	c.(3148-3150)tcG>tcA	p.S1050S	DPCR1_ENST00000304311.2_5'UTR|HCG21_ENST00000419481.1_RNA			Q3MIW9	DPCR1_HUMAN	diffuse panbronchiolitis critical region 1	0						integral component of membrane (GO:0016021)				endometrium(1)|kidney(2)|large_intestine(3)|lung(3)|pancreas(1)	10						TGACCCCATCGGCCAATGAGA	0.488													a|||	193	0.0385383	0.0386	0.0288	5008	,	,		26019	0.0159		0.0964	False		,,,				2504	0.0092				p.S1050S		Atlas-SNP	.											.	DPCR1	99	.	0			c.G3150A						PASS	.	G		98,1286		2,94,596	194.0	172.0	179.0		3150	-6.0	0.0	6	dbSNP_103	179	431,2751		28,375,1188	no	coding-synonymous	DPCR1	NM_080870.3		30,469,1784	AA,AG,GG		13.5449,7.0809,11.5856		1050/1394	30919391	529,4037	692	1591	2283	SO:0001819	synonymous_variant	135656	exon2			CCCATCGGCCAAT	AB064272	CCDS4692.1, CCDS4692.2	6p21.32	2008-02-05			ENSG00000168631	ENSG00000168631			21666	protein-coding gene	gene with protein product		613928				12185533, 10677310	Standard	NM_080870		Approved	PBLT, bCX105N19.6	uc003nsg.2	Q3MIW9	OTTHUMG00000031104	ENST00000462446.1:c.3150G>A	6.37:g.30919391G>A		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	91	34	0.373626	NM_080870	C9IZC0|Q658M7|Q8WYN2	Silent	SNP	ENST00000462446.1	37	CCDS4692.2																																																																																			G|0.932;A|0.068	0.068	strong		0.488	DPCR1-001	NOVEL	not_organism_supported|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000076173.3	NM_080870	
MUC4	4585	hgsc.bcm.edu	37	3	195508490	195508490	+	Missense_Mutation	SNP	C	C	A	rs200820395	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195508490C>A	ENST00000463781.3	-	2	10420	c.9961G>T	c.(9961-9963)Gca>Tca	p.A3321S	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.A3321S	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.V3305_S3320delVSTGHATPLLVTDASS(1)|p.V3305_S3336delVSTGHATPLLVTDASSASTGHATPLHVTSPSS(1)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		CCTGTGGATGCTGAGGAAGCG	0.572													.|||	42	0.00838658	0.0015	0.0173	5008	,	,		10309	0.001		0.0268	False		,,,				2504	0.0				p.A3321S		Atlas-SNP	.											.	MUC4	1505	.	2	Deletion - In frame(2)	stomach(2)	c.G9961T						PASS	.						13.0	14.0	14.0					3																	195508490		671	1560	2231	SO:0001583	missense	4585	exon2			TGGATGCTGAGGA	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.9961G>T	3.37:g.195508490C>A	ENSP00000417498:p.Ala3321Ser	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	37	8	0.216216	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	7.260	0.605089	0.14002	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.36340	1.3;1.26	1.03	1.03	0.20045	.	.	.	.	.	T	0.14657	0.0354	N	0.14661	0.345	0.09310	N	1	P	0.38110	0.618	B	0.25884	0.064	T	0.11941	-1.0567	8	.	.	.	.	5.3938	0.16259	0.0:1.0:0.0:0.0	.	3193	E7ESK3	.	S	3321	ENSP00000417498:A3321S;ENSP00000420243:A3321S	.	A	-	1	0	MUC4	196993269	0.000000	0.05858	0.007000	0.13788	0.019000	0.09904	-3.950000	0.00327	0.494000	0.27859	0.089000	0.15464	GCA	.	.	weak		0.572	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
PRRG4	79056	hgsc.bcm.edu	37	11	32874926	32874926	+	Silent	SNP	G	G	A	rs11032025	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:32874926G>A	ENST00000257836.3	+	6	787	c.534G>A	c.(532-534)ccG>ccA	p.P178P		NM_024081.5	NP_076986.1	Q9BZD6	TMG4_HUMAN	proline rich Gla (G-carboxyglutamic acid) 4 (transmembrane)	178						extracellular region (GO:0005576)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)			large_intestine(2)|lung(2)|prostate(2)|urinary_tract(1)	7	Breast(20;0.206)					CTCCATTGCCGCCTTCTGTGG	0.522													G|||	2030	0.405351	0.3464	0.4841	5008	,	,		16145	0.4127		0.3986	False		,,,				2504	0.4284				p.P178P		Atlas-SNP	.											PRRG4,colon,carcinoma,0,1	PRRG4	15	1	0			c.G534A						scavenged	.	G		1643,2761	505.1+/-366.0	309,1025,868	109.0	101.0	104.0		534	0.2	0.0	11	dbSNP_120	104	3277,5321	490.4+/-372.8	621,2035,1643	yes	coding-synonymous	PRRG4	NM_024081.5		930,3060,2511	AA,AG,GG		38.1135,37.307,37.8403		178/227	32874926	4920,8082	2202	4299	6501	SO:0001819	synonymous_variant	79056	exon6			ATTGCCGCCTTCT	AF326351	CCDS7881.1	11p13	2008-02-05			ENSG00000135378	ENSG00000135378			30799	protein-coding gene	gene with protein product		611690				11171957	Standard	NM_024081		Approved	TMG4	uc001mtx.3	Q9BZD6	OTTHUMG00000166219	ENST00000257836.3:c.534G>A	11.37:g.32874926G>A		Somatic	66	1	0.0151515		WXS	Illumina HiSeq	Phase_I	62	45	0.725806	NM_024081		Silent	SNP	ENST00000257836.3	37	CCDS7881.1																																																																																			G|0.604;A|0.396	0.396	strong		0.522	PRRG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388446.1	NM_024081	
AP5B1	91056	hgsc.bcm.edu	37	11	65547455	65547455	+	Missense_Mutation	SNP	C	C	A	rs12362011	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:65547455C>A	ENST00000532090.2	-	2	719	c.509G>T	c.(508-510)gGg>gTg	p.G170V		NM_138368.4	NP_612377.4	Q2VPB7	AP5B1_HUMAN	adaptor-related protein complex 5, beta 1 subunit	170	Leu-rich.				endosomal transport (GO:0016197)|protein transport (GO:0015031)	AP-type membrane coat adaptor complex (GO:0030119)|lysosomal membrane (GO:0005765)				lung(1)	1						CCGCAGCAACCCCAGGGAGCC	0.692													C|||	702	0.140176	0.18	0.0922	5008	,	,		13977	0.2222		0.1362	False		,,,				2504	0.0399				p.G170V		Atlas-SNP	.											.	AP5B1	40	.	0			c.G509T						PASS	.	C	VAL/GLY	433,3095		25,383,1356	5.0	7.0	6.0		338	4.9	1.0	11	dbSNP_120	6	874,7096		43,788,3154	no	missense	DKFZp761E198	NM_138368.3	109	68,1171,4510	AA,AC,CC		10.9661,12.2732,11.3672	probably-damaging	113/822	65547455	1307,10191	1764	3985	5749	SO:0001583	missense	91056	exon2			AGCAACCCCAGGG	JQ313135	CCDS58146.1	11q13.1	2012-02-29			ENSG00000254470	ENSG00000254470			25104	protein-coding gene	gene with protein product		614367				22022230	Standard	NM_138368		Approved	PP1030, AP-5, DKFZp761E198	uc031qbm.1	Q2VPB7	OTTHUMG00000166593	ENST00000532090.2:c.509G>T	11.37:g.65547455C>A	ENSP00000454303:p.Gly170Val	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	73	46	0.630137	NM_138368	A1L0S6|H6WUK2|Q0D2Q2|Q8N3J7|Q8WYH6	Missense_Mutation	SNP	ENST00000532090.2	37	CCDS58146.1																																																																																			C|0.832;A|0.168	0.168	strong		0.692	AP5B1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390636.2	NM_138368	
ENOSF1	55556	hgsc.bcm.edu	37	18	674320	674320	+	Silent	SNP	A	A	G	rs3744962	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:674320A>G	ENST00000251101.7	-	16	1405	c.1317T>C	c.(1315-1317)ccT>ccC	p.P439P	ENOSF1_ENST00000319815.6_Silent_p.P209P|ENOSF1_ENST00000583973.1_5'UTR|ENOSF1_ENST00000383578.3_Silent_p.P357P|ENOSF1_ENST00000580982.1_Silent_p.P363P|ENOSF1_ENST00000340116.7_Silent_p.P446P	NM_017512.5	NP_059982.2	Q7L5Y1	ENOF1_HUMAN	enolase superfamily member 1	439					cellular amino acid catabolic process (GO:0009063)|cellular carbohydrate catabolic process (GO:0044275)	mitochondrion (GO:0005739)	isomerase activity (GO:0016853)|L-fuconate dehydratase activity (GO:0050023)|magnesium ion binding (GO:0000287)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(3)|ovary(1)|prostate(1)	10						TTTCTTGAGCAGGAAGGAGTT	0.368													A|||	551	0.110024	0.0204	0.2161	5008	,	,		16451	0.1855		0.0905	False		,,,				2504	0.0982				p.P446P		Atlas-SNP	.											.	ENOSF1	44	.	0			c.T1338C						PASS	.	A	,,	151,4255	102.1+/-140.7	6,139,2058	206.0	222.0	217.0		1071,1317,1338	1.6	0.7	18	dbSNP_107	217	763,7837	181.2+/-229.9	32,699,3569	no	coding-synonymous,coding-synonymous,coding-synonymous	ENOSF1	NM_001126123.3,NM_017512.5,NM_202758.3	,,	38,838,5627	GG,GA,AA		8.8721,3.4271,7.0275	,,	357/362,439/444,446/451	674320	914,12092	2203	4300	6503	SO:0001819	synonymous_variant	55556	exon15			TTGAGCAGGAAGG	X67098	CCDS11822.1, CCDS11823.1, CCDS45821.1	18p11.32	2005-01-26			ENSG00000132199	ENSG00000132199			30365	protein-coding gene	gene with protein product		607427				14508106	Standard	NM_001126123		Approved	HSRTSBETA, rTS, TYMSAS	uc002kku.4	Q7L5Y1	OTTHUMG00000131470	ENST00000251101.7:c.1317T>C	18.37:g.674320A>G		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	113	45	0.39823	NM_202758	A6NMP3|A8K9R5|B3KSL6|B3KXE4|D3DUH0|Q15407|Q15594|Q15595|Q6ZS08|Q9HAS5|Q9HAS6	Silent	SNP	ENST00000251101.7	37	CCDS11822.1																																																																																			A|0.917;G|0.083	0.083	strong		0.368	ENOSF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254312.2	NM_017512	
KIAA2026	158358	hgsc.bcm.edu	37	9	5969249	5969249	+	Silent	SNP	A	A	G	rs10739080	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:5969249A>G	ENST00000399933.3	-	3	981	c.982T>C	c.(982-984)Ttg>Ctg	p.L328L	KIAA2026_ENST00000381461.2_Silent_p.L328L	NM_001017969.2	NP_001017969.2	Q5HYC2	K2026_HUMAN	KIAA2026	328										breast(6)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(11)|lung(15)|ovary(2)|prostate(2)|skin(1)	46		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.00155)|Lung(218;0.124)		CAACGTTCCAATTCGTAAAAG	0.398													A|||	2552	0.509585	0.3238	0.5605	5008	,	,		19352	0.5427		0.6869	False		,,,				2504	0.5082				p.L328L		Atlas-SNP	.											.	KIAA2026	231	.	0			c.T982C						PASS	.	A		1465,2287		284,897,695	81.0	74.0	77.0		982	1.0	1.0	9	dbSNP_120	77	5897,2309		2103,1691,309	no	coding-synonymous	KIAA2026	NM_001017969.2		2387,2588,1004	GG,GA,AA		28.1379,39.0458,38.4345		328/2104	5969249	7362,4596	1876	4103	5979	SO:0001819	synonymous_variant	158358	exon3			GTTCCAATTCGTA	AB095946		9p24.1	2014-01-10			ENSG00000183354	ENSG00000183354			23378	protein-coding gene	gene with protein product							Standard	NM_001017969		Approved	FLJ20375	uc003zjq.4	Q5HYC2	OTTHUMG00000019507	ENST00000399933.3:c.982T>C	9.37:g.5969249A>G		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	118	63	0.533898	NM_001017969	A8MTP2|B9EGW7|Q4VXA2|Q8IVE5	Silent	SNP	ENST00000399933.3	37																																																																																				A|0.421;G|0.579	0.579	strong		0.398	KIAA2026-002	NOVEL	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051652.2	NM_001017969	
OR8J1	219477	hgsc.bcm.edu	37	11	56128031	56128031	+	Silent	SNP	G	G	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:56128031G>C	ENST00000303039.3	+	1	341	c.309G>C	c.(307-309)ggG>ggC	p.G103G		NM_001005205.2	NP_001005205.2	Q8NGP2	OR8J1_HUMAN	olfactory receptor, family 8, subfamily J, member 1	103						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(30)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	47	Esophageal squamous(21;0.00448)					AACTGGGAGGGTTCTTGTTCT	0.423																																					p.G103G		Atlas-SNP	.											.	OR8J1	87	.	0			c.G309C						PASS	.						150.0	140.0	143.0					11																	56128031		2201	4296	6497	SO:0001819	synonymous_variant	219477	exon1			GGGAGGGTTCTTG	AB065748	CCDS31529.1	11q11	2012-08-09			ENSG00000172487	ENSG00000172487		"""GPCR / Class A : Olfactory receptors"""	14855	protein-coding gene	gene with protein product							Standard	NM_001005205		Approved		uc010rjh.2	Q8NGP2	OTTHUMG00000166859	ENST00000303039.3:c.309G>C	11.37:g.56128031G>C		Somatic	216	0	0		WXS	Illumina HiSeq	Phase_I	187	49	0.262032	NM_001005205	B2RNQ6|B9EH63|Q6IFC2|Q96RC3	Silent	SNP	ENST00000303039.3	37	CCDS31529.1																																																																																			.	.	none		0.423	OR8J1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391606.2	NM_001005205	
ZNF180	7733	hgsc.bcm.edu	37	19	44981009	44981009	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:44981009G>T	ENST00000221327.4	-	5	1970	c.1689C>A	c.(1687-1689)caC>caA	p.H563Q	ZNF180_ENST00000592529.1_Missense_Mutation_p.H536Q|ZNF180_ENST00000585514.1_5'Flank|AC069278.4_ENST00000591684.1_lincRNA|ZNF180_ENST00000391956.4_Missense_Mutation_p.H538Q	NM_013256.3	NP_037388.2	Q9UJW8	ZN180_HUMAN	zinc finger protein 180	563					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(3)|kidney(5)|large_intestine(14)|lung(6)|ovary(2)|urinary_tract(1)	33		Prostate(69;0.0435)				GCATAACAAGGTGAGAACTGC	0.418																																					p.H563Q	Esophageal Squamous(180;1353 2003 32862 46574 49854)	Atlas-SNP	.											.	ZNF180	103	.	0			c.C1689A						PASS	.						103.0	104.0	104.0					19																	44981009		2203	4300	6503	SO:0001583	missense	7733	exon5			AACAAGGTGAGAA	AF192913	CCDS12639.1, CCDS62707.1, CCDS62708.1	19q13.2	2013-01-08	2006-08-22			ENSG00000167384		"""Zinc fingers, C2H2-type"", ""-"""	12970	protein-coding gene	gene with protein product		606740	"""zinc finger protein 180 (HHZ168)"""				Standard	NM_001288762		Approved	HHZ168	uc002ozf.4	Q9UJW8		ENST00000221327.4:c.1689C>A	19.37:g.44981009G>T	ENSP00000221327:p.His563Gln	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	81	15	0.185185	NM_013256	B2RCN6|B3KV56|K7EQX9|Q58F03|Q9P1U2	Missense_Mutation	SNP	ENST00000221327.4	37	CCDS12639.1	.	.	.	.	.	.	.	.	.	.	G	13.00	2.105656	0.37145	.	.	ENSG00000167384	ENST00000221327;ENST00000391956	T;T	0.07216	3.21;3.21	5.23	2.97	0.34412	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.44688	D	0.000440	T	0.04272	0.0118	N	0.12961	0.28	0.80722	D	1	P;P;P	0.47545	0.874;0.897;0.897	B;B;B	0.39068	0.191;0.289;0.289	T	0.37430	-0.9706	10	0.51188	T	0.08	-7.8305	6.5992	0.22691	0.1566:0.0:0.6887:0.1546	.	538;562;563	G5E9B8;Q58F03;Q9UJW8	.;.;ZN180_HUMAN	Q	563;538	ENSP00000221327:H563Q;ENSP00000375818:H538Q	ENSP00000221327:H563Q	H	-	3	2	ZNF180	49672849	0.000000	0.05858	1.000000	0.80357	0.872000	0.50106	-1.418000	0.02462	2.437000	0.82529	0.467000	0.42956	CAC	.	.	none		0.418	ZNF180-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451601.1	NM_013256	
DENND4C	55667	hgsc.bcm.edu	37	9	19290794	19290794	+	Missense_Mutation	SNP	A	A	C	rs41269019	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:19290794A>C	ENST00000380432.2	+	1	46	c.13A>C	c.(13-15)Att>Ctt	p.I5L	DENND4C_ENST00000434457.2_Missense_Mutation_p.I241L|RP11-146N23.4_ENST00000417577.2_RNA|DENND4C_ENST00000602925.1_Missense_Mutation_p.I241L			Q5VZ89	DEN4C_HUMAN	DENN/MADD domain containing 4C	5	UDENN.				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						GGGAGCTACTATTGAGTGCTG	0.378													A|||	58	0.0115815	0.0015	0.0274	5008	,	,		17056	0.0		0.0338	False		,,,				2504	0.0031				p.I241L		Atlas-SNP	.											.	DENND4C	120	.	0			c.A721C						PASS	.	A	LEU/ILE	26,3652		0,26,1813	145.0	132.0	136.0		13	5.4	1.0	9	dbSNP_127	136	241,7947		6,229,3859	yes	missense	DENND4C	NM_017925.4	5	6,255,5672	CC,CA,AA		2.9433,0.7069,2.2501	benign	5/1674	19290794	267,11599	1839	4094	5933	SO:0001583	missense	55667	exon5			GCTACTATTGAGT	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.13A>C	9.37:g.19290794A>C	ENSP00000369797:p.Ile5Leu	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	91	49	0.538462	NM_017925	A2A3R1|A2A3R2|A2A3R3|A2A3R9|Q6AI48|Q6ZUB3|Q8NCY7|Q9H6N4|Q9NUT1|Q9NWA5|Q9NWT3	Missense_Mutation	SNP	ENST00000380432.2	37		38	0.0173992673992674	0	0.0	13	0.03591160220994475	0	0.0	25	0.032981530343007916	A	26.2	4.716165	0.89205	0.007069	0.029433	ENSG00000137145	ENST00000380437	.	.	.	5.44	5.44	0.79542	uDENN (1);	0.170569	0.36555	U	0.002531	T	0.35537	0.0935	L	0.51914	1.62	0.80722	D	1	D	0.67145	0.996	D	0.63488	0.915	T	0.51442	-0.8705	9	0.21540	T	0.41	-17.1319	15.6559	0.77133	1.0:0.0:0.0:0.0	rs41269019	5	Q5VZ89	DEN4C_HUMAN	L	5	.	ENSP00000369802:I5L	I	+	1	0	DENND4C	19280794	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	6.109000	0.71528	2.287000	0.76781	0.482000	0.46254	ATT	A|0.979;C|0.021	0.021	strong		0.378	DENND4C-201	KNOWN	basic	protein_coding	protein_coding		NM_017925	
NUP188	23511	hgsc.bcm.edu	37	9	131752487	131752487	+	Silent	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:131752487G>A	ENST00000372577.2	+	25	2643	c.2622G>A	c.(2620-2622)ctG>ctA	p.L874L		NM_015354.1	NP_056169.1	Q5SRE5	NU188_HUMAN	nucleoporin 188kDa	874					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)	membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)				breast(2)|central_nervous_system(3)|endometrium(6)|kidney(4)|large_intestine(9)|lung(20)|ovary(6)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	60						CCATTCAGCTGCTGAAACGTC	0.473																																					p.L874L		Atlas-SNP	.											.	NUP188	140	.	0			c.G2622A						PASS	.						371.0	316.0	334.0					9																	131752487		2203	4300	6503	SO:0001819	synonymous_variant	23511	exon25			TCAGCTGCTGAAA	D79991	CCDS35156.1	9q34.13	2014-01-28	2004-03-19	2004-03-24	ENSG00000095319	ENSG00000095319			17859	protein-coding gene	gene with protein product		615587	"""KIAA0169"""	KIAA0169		11029043	Standard	NM_015354		Approved		uc004bws.2	Q5SRE5	OTTHUMG00000020768	ENST00000372577.2:c.2622G>A	9.37:g.131752487G>A		Somatic	202	0	0		WXS	Illumina HiSeq	Phase_I	187	38	0.203209	NM_015354	Q14675|Q2TA87|Q7Z3K8|Q8IWF1	Silent	SNP	ENST00000372577.2	37	CCDS35156.1																																																																																			.	.	none		0.473	NUP188-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054529.2		
OR5L2	26338	hgsc.bcm.edu	37	11	55594869	55594869	+	Missense_Mutation	SNP	G	G	A	rs56711116	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:55594869G>A	ENST00000378397.1	+	1	175	c.175G>A	c.(175-177)Gtg>Atg	p.V59M		NM_001004739.1	NP_001004739.1	Q8NGL0	OR5L2_HUMAN	olfactory receptor, family 5, subfamily L, member 2	59			V -> M (in dbSNP:rs56711116).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.V59M(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)				CCACACCCCCGTGTACTTTTT	0.468										HNSCC(27;0.073)			N|||	537	0.107228	0.1952	0.0461	5008	,	,		20056	0.0843		0.0924	False		,,,				2504	0.0706				p.V59M		Atlas-SNP	.											OR5L2,colon,carcinoma,0,2	OR5L2	135	2	1	Substitution - Missense(1)	stomach(1)	c.G175A						PASS	.	A	MET/VAL	658,3742		64,530,1606	244.0	226.0	232.0		175	5.3	1.0	11	dbSNP_129	232	702,7890		32,638,3626	no	missense	OR5L2	NM_001004739.1	21	96,1168,5232	AA,AG,GG		8.1704,14.9545,10.468	benign	59/312	55594869	1360,11632	2200	4296	6496	SO:0001583	missense	26338	exon1			ACCCCCGTGTACT	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.175G>A	11.37:g.55594869G>A	ENSP00000367650:p.Val59Met	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	152	114	0.75	NM_001004739	Q6IF66|Q96RB2	Missense_Mutation	SNP	ENST00000378397.1	37	CCDS31511.1	169	0.07738095238095238	62	0.12601626016260162	19	0.052486187845303865	35	0.06118881118881119	53	0.06992084432717678	.	1.359	-0.589350	0.03799	0.149545	0.081704	ENSG00000205030	ENST00000378397	T	0.01197	5.19	5.31	5.31	0.75309	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	N	0.000012	T	0.00012	0.0000	N	0.00005	-3.255	0.53005	P	3.6999999999953737E-5	B	0.02656	0.0	B	0.04013	0.001	T	0.25882	-1.0119	9	0.02654	T	1	-56.956	10.8374	0.46696	0.9241:0.0:0.0759:0.0	rs56711116;rs61739473	59	Q8NGL0	OR5L2_HUMAN	M	59	ENSP00000367650:V59M	ENSP00000367650:V59M	V	+	1	0	OR5L2	55351445	1.000000	0.71417	0.999000	0.59377	0.249000	0.25844	3.918000	0.56432	0.965000	0.38133	-0.377000	0.06932	GTG	G|0.901;A|0.099	0.099	strong		0.468	OR5L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391516.1	NM_001004739	
SLC17A3	10786	hgsc.bcm.edu	37	6	25862466	25862466	+	Missense_Mutation	SNP	C	C	T	rs1165165	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:25862466C>T	ENST00000360657.3	-	3	583	c.298G>A	c.(298-300)Gca>Aca	p.A100T	SLC17A3_ENST00000361703.6_Missense_Mutation_p.A100T|SLC17A3_ENST00000397060.4_Missense_Mutation_p.A100T			O00476	NPT4_HUMAN	solute carrier family 17 (organic anion transporter), member 3	100			A -> T (in dbSNP:rs1165165). {ECO:0000269|PubMed:15489334}.		drug transmembrane transport (GO:0006855)|drug transport (GO:0015893)|glucose-6-phosphate transport (GO:0015760)|ion transmembrane transport (GO:0034220)|organic acid transport (GO:0015849)|organic anion transport (GO:0015711)|phosphate ion transmembrane transport (GO:0035435)|phosphate ion transport (GO:0006817)|regulation of anion transport (GO:0044070)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|toxin transport (GO:1901998)|transmembrane transport (GO:0055085)|urate metabolic process (GO:0046415)|urate transport (GO:0015747)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	drug transmembrane transporter activity (GO:0015238)|efflux transmembrane transporter activity (GO:0015562)|organic anion transmembrane transporter activity (GO:0008514)|sodium:phosphate symporter activity (GO:0005436)|toxin transporter activity (GO:0019534)|urate transmembrane transporter activity (GO:0015143)|voltage-gated anion channel activity (GO:0008308)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(10)|prostate(1)	20						CTTACCTTTGCAGGAAGACTC	0.378													C|||	1084	0.216454	0.3275	0.1801	5008	,	,		19794	0.131		0.2276	False		,,,				2504	0.1687				p.A100T		Atlas-SNP	.											.	SLC17A3	95	.	0			c.G298A						PASS	.	C	THR/ALA,THR/ALA	1285,3121	434.9+/-344.1	196,893,1114	78.0	69.0	72.0		298,298	2.2	0.0	6	dbSNP_87	72	2014,6586	352.0+/-328.5	225,1564,2511	yes	missense,missense	SLC17A3	NM_001098486.1,NM_006632.3	58,58	421,2457,3625	TT,TC,CC		23.4186,29.1648,25.3652	benign,benign	100/499,100/421	25862466	3299,9707	2203	4300	6503	SO:0001583	missense	10786	exon3			CCTTTGCAGGAAG	U90545	CCDS4566.2, CCDS47385.1	6p22.2	2013-07-18	2013-07-18		ENSG00000124564	ENSG00000124564		"""Solute carriers"""	10931	protein-coding gene	gene with protein product		611034	"""solute carrier family 17 (sodium phosphate), member 3"""			9149941	Standard	NM_006632		Approved	NPT4	uc003nfk.4	O00476	OTTHUMG00000014412	ENST00000360657.3:c.298G>A	6.37:g.25862466C>T	ENSP00000353873:p.Ala100Thr	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	83	81	0.975904	NM_006632	B7WNJ5|B7Z511|Q8WWC7|Q9H533	Missense_Mutation	SNP	ENST00000360657.3	37	CCDS4566.2	499	0.22847985347985347	164	0.3333333333333333	74	0.20441988950276244	83	0.1451048951048951	178	0.23482849604221637	C	9.114	1.007252	0.19199	0.291648	0.234186	ENSG00000124564	ENST00000397060;ENST00000360657;ENST00000361703	T;T;T	0.64260	-0.09;-0.05;-0.05	3.57	2.17	0.27698	.	967.492000	0.00357	N	0.000023	T	0.22781	0.0550	N	0.22421	0.69	0.80722	P	0.0	B;B;B;B	0.31989	0.35;0.1;0.022;0.232	B;B;B;B	0.31547	0.132;0.06;0.06;0.064	T	0.13845	-1.0494	9	0.14656	T	0.56	.	4.9209	0.13869	0.0:0.7415:0.0:0.2585	rs1165165;rs1747544;rs17271037;rs17845568;rs17858467;rs59291168;rs1165165	100;81;100;100	B7Z531;B7Z3L7;B7Z511;O00476	.;.;.;NPT4_HUMAN	T	100	ENSP00000380250:A100T;ENSP00000353873:A100T;ENSP00000355307:A100T	ENSP00000353873:A100T	A	-	1	0	SLC17A3	25970445	0.002000	0.14202	0.008000	0.14137	0.061000	0.15899	0.224000	0.17738	0.612000	0.30071	0.544000	0.68410	GCA	C|0.755;T|0.245	0.245	strong		0.378	SLC17A3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000040070.2		
ZNF687	57592	hgsc.bcm.edu	37	1	151259043	151259043	+	Silent	SNP	C	C	T	rs2298265	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:151259043C>T	ENST00000368879.2	+	2	374	c.276C>T	c.(274-276)ccC>ccT	p.P92P		NM_020832.1	NP_065883.1	Q8N1G0	ZN687_HUMAN	zinc finger protein 687	92					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(3)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(11)|ovary(1)|upper_aerodigestive_tract(2)	32	Lung SC(34;0.00471)|Ovarian(49;0.0147)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.112)|LUSC - Lung squamous cell carcinoma(543;0.181)			CTGTGTGTCCCGAGCAGTCTG	0.607													c|||	510	0.101837	0.115	0.1412	5008	,	,		19268	0.0615		0.1282	False		,,,				2504	0.0706				p.P92P		Atlas-SNP	.											.	ZNF687	94	.	0			c.C276T						PASS	.	C		513,3893	235.5+/-248.0	28,457,1718	52.0	56.0	55.0		276	-8.6	0.9	1	dbSNP_100	55	1026,7574	218.1+/-256.6	55,916,3329	no	coding-synonymous	ZNF687	NM_020832.1		83,1373,5047	TT,TC,CC		11.9302,11.6432,11.833		92/1238	151259043	1539,11467	2203	4300	6503	SO:0001819	synonymous_variant	57592	exon2			GTGTCCCGAGCAG		CCDS992.1	1q21.2	2008-05-02			ENSG00000143373	ENSG00000143373			29277	protein-coding gene	gene with protein product		610568				10718198	Standard	NM_020832		Approved	KIAA1441	uc001exq.3	Q8N1G0	OTTHUMG00000012347	ENST00000368879.2:c.276C>T	1.37:g.151259043C>T		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	58	32	0.551724	NM_020832	D3DV17|Q68DQ8|Q9H937|Q9P2A7	Silent	SNP	ENST00000368879.2	37																																																																																				C|0.892;T|0.108	0.108	strong		0.607	ZNF687-201	KNOWN	basic	protein_coding	protein_coding		NM_020832	
MUC4	4585	hgsc.bcm.edu	37	3	195511142	195511142	+	Missense_Mutation	SNP	T	T	C	rs430037	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195511142T>C	ENST00000463781.3	-	2	7768	c.7309A>G	c.(7309-7311)Aac>Gac	p.N2437D	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.N2437D	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.N2437D(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)		GAGGAAACGTTGGTGACAGGA	0.597													.|||	2741	0.547324	0.4629	0.4841	5008	,	,		18811	0.75		0.5755	False		,,,				2504	0.4683				p.N2437D		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	1	Substitution - Missense(1)	prostate(1)	c.A7309G						scavenged	.						59.0	58.0	58.0					3																	195511142		645	1581	2226	SO:0001583	missense	4585	exon2			AAACGTTGGTGAC	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.7309A>G	3.37:g.195511142T>C	ENSP00000417498:p.Asn2437Asp	Somatic	239	1	0.0041841		WXS	Illumina HiSeq	Phase_I	211	44	0.208531	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	6.228	0.410269	0.11812	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.34667	1.36;1.35	.	.	.	.	.	.	.	.	T	0.14917	0.0360	N	0.08118	0	0.09310	N	1	B	0.15141	0.012	B	0.04013	0.001	T	0.26950	-1.0088	7	.	.	.	.	3.8346	0.08888	0.0:0.0:0.3913:0.6087	.	2437	E7ESK3	.	D	2437	ENSP00000417498:N2437D;ENSP00000420243:N2437D	.	N	-	1	0	MUC4	196995537	.	.	0.023000	0.16930	0.000000	0.00434	.	.	0.402000	0.25451	0.000000	0.15137	AAC	T|0.781;C|0.219	0.219	strong		0.597	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
HLA-A	3105	hgsc.bcm.edu	37	6	29910663	29910663	+	Missense_Mutation	SNP	G	G	A	rs707910	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:29910663G>A	ENST00000396634.1	+	4	544	c.203G>A	c.(202-204)aGg>aAg	p.R68K	HLA-A_ENST00000376802.2_Missense_Mutation_p.R68K|HLA-A_ENST00000376809.5_Missense_Mutation_p.R68K|HLA-A_ENST00000376806.5_Missense_Mutation_p.R68K			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	68	Alpha-1.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	beta-2-microglobulin binding (GO:0030881)|peptide antigen binding (GO:0042605)|TAP binding (GO:0046977)			central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	30						GCGAGCCAGAGGATGGAGCCG	0.687									Osteosarcoma, Familial Clustering of;Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of;Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of	Multiple Myeloma(9;0.094)			g|||	454	0.090655	0.0847	0.0476	5008	,	,		14754	0.0188		0.1262	False		,,,				2504	0.1667				p.R68K		Atlas-SNP	.											.	HLA-A	89	.	0			c.G203A						PASS	.	G	LYS/ARG	347,4057		17,313,1872	48.0	46.0	47.0		203	2.8	0.4	6	dbSNP_86	47	1395,7203		130,1135,3034	no	missense	HLA-A	NM_002116.7	26	147,1448,4906	AA,AG,GG		16.2247,7.8792,13.3979	benign	68/366	29910663	1742,11260	2202	4299	6501	SO:0001583	missense	3105	exon2	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	GCCAGAGGATGGA	D32129	CCDS34373.1	6p21.3	2013-01-11			ENSG00000206503	ENSG00000206503		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4931	protein-coding gene	gene with protein product		142800				8838351	Standard	NM_001242758		Approved		uc003nol.3	P01891	OTTHUMG00000130501	ENST00000396634.1:c.203G>A	6.37:g.29910663G>A	ENSP00000379873:p.Arg68Lys	Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	198	98	0.494949	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Missense_Mutation	SNP	ENST00000396634.1	37	CCDS34373.1	168	0.07692307692307693	39	0.07926829268292683	17	0.04696132596685083	10	0.017482517482517484	102	0.1345646437994723	.	13.11	2.139534	0.37728	0.078792	0.162247	ENSG00000206503	ENST00000396634;ENST00000376806;ENST00000376809;ENST00000355767;ENST00000376802	T;T;T;T	0.00816	5.66;5.66;5.66;5.66	3.72	2.85	0.33270	MHC class I, alpha chain, alpha1/alpha2 (3);MHC classes I/II-like antigen recognition protein (3);MHC class I-like antigen recognition (3);	0.236115	0.21148	U	0.079368	T	0.02047	0.0064	M	0.80508	2.5	0.58432	P	5.000000000032756E-6	P;B;B;B;B	0.51147	0.942;0.0;0.0;0.0;0.0	D;B;B;B;B	0.74348	0.983;0.001;0.002;0.001;0.004	T	0.23547	-1.0185	9	0.87932	D	0	.	7.302	0.26426	0.1248:0.0:0.8752:0.0	rs707910;rs2230979;rs3200124;rs9260131;rs16896268;rs41541315	68;68;68;68;68	P13746;Q5SRN7;P16188;Q5SRN5;P04439	1A11_HUMAN;.;1A30_HUMAN;.;1A03_HUMAN	K	68	ENSP00000379873:R68K;ENSP00000366002:R68K;ENSP00000366005:R68K;ENSP00000365998:R68K	ENSP00000348012:R68K	R	+	2	0	HLA-A	30018642	0.002000	0.14202	0.442000	0.26870	0.608000	0.37181	0.867000	0.27968	0.936000	0.37367	0.478000	0.44815	AGG	A|0.112;G|0.888	0.112	strong		0.687	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
HLA-DPA1	3113	hgsc.bcm.edu	37	6	33037640	33037640	+	Missense_Mutation	SNP	C	C	T	rs1126533|rs386699859	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:33037640C>T	ENST00000419277.1	-	3	253	c.124G>A	c.(124-126)Gcg>Acg	p.A42T	HLA-DPA1_ENST00000428995.1_Missense_Mutation_p.A42T|HLA-DPA1_ENST00000463066.1_5'UTR	NM_001242524.1|NM_001242525.1	NP_001229453.1|NP_001229454.1	P20036	DPA1_HUMAN	major histocompatibility complex, class II, DP alpha 1	42	Alpha-1.		A -> M (in allele DPA1*02:02, allele DPA1*02:04, allele DPA1*03:01, allele DPA1*03:02 and allele DPA1*03:03; requires 2 nucleotide substitutions).|A -> T (in dbSNP:rs1126533).|A -> V (in dbSNP:rs1126534).		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cellular response to interferon-gamma (GO:0071346)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell proliferation (GO:0042102)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			kidney(5)|large_intestine(1)|lung(6)|prostate(1)|skin(2)	15						TGTACAAACGCGGCATAAGTT	0.418													.|||	1189	0.23742	0.351	0.062	5008	,	,		20633	0.5496		0.0318	False		,,,				2504	0.0982				p.A42T		Atlas-SNP	.											HLA-DPA1,NS,carcinoma,+1,4	HLA-DPA1	20	4	0			c.G124A						scavenged	.	T	THR/ALA,THR/ALA,THR/ALA	590,2430		107,376,1027	53.0	76.0	68.0		124,124,124	-4.0	0.0	6	dbSNP_86	68	67,5349		2,63,2643	yes	missense,missense,missense	HLA-DPA1	NM_001242524.1,NM_001242525.1,NM_033554.3	58,58,58	109,439,3670	TT,TC,CC		1.2371,19.5364,7.7881	benign,benign,benign	42/261,42/261,42/261	33037640	657,7779	1510	2708	4218	SO:0001583	missense	3113	exon2			CAAACGCGGCATA	X00457	CCDS4764.1	6p21.3	2013-01-11			ENSG00000231389	ENSG00000231389		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4938	protein-coding gene	gene with protein product		142880		HLA-DP1A		6584734	Standard	NM_033554		Approved		uc003ocs.2	P20036	OTTHUMG00000031058	ENST00000419277.1:c.124G>A	6.37:g.33037640C>T	ENSP00000393566:p.Ala42Thr	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	75	22	0.293333	NM_033554	A9YWH7|B9UKH4|O19722|O46883|P01905|P79554|Q2Q060|Q2Q061|Q5EY03|Q5STP1|Q6DQK4|Q9BCQ1|Q9TPX3|Q9XS10	Missense_Mutation	SNP	ENST00000419277.1	37	CCDS4764.1	482	0.2206959706959707	170	0.34552845528455284	20	0.055248618784530384	272	0.4755244755244755	20	0.026385224274406333	T	1.487	-0.555778	0.03967	0.195364	0.012371	ENSG00000231389	ENST00000419277;ENST00000428995;ENST00000448544;ENST00000453337	T;T;T	0.00717	5.79;5.79;5.79	3.04	-3.99	0.04069	MHC class II, alpha/beta chain, N-terminal (1);MHC classes I/II-like antigen recognition protein (1);MHC class II, alpha chain, N-terminal (2);	1.357570	0.05045	N	0.477012	T	0.00144	0.0004	N	0.10685	0.025	0.80722	P	0.0	B	0.06786	0.001	B	0.10450	0.005	T	0.41680	-0.9495	9	0.09590	T	0.72	.	8.8761	0.35345	0.1425:0.7078:0.0:0.1497	rs1126533;rs2308903;rs3176948;rs3181625;rs17423937	42	P20036	DPA1_HUMAN	T	42	ENSP00000393566:A42T;ENSP00000402872:A42T;ENSP00000390929:A42T	ENSP00000393566:A42T	A	-	1	0	HLA-DPA1	33145618	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.217000	0.02979	-1.707000	0.01402	-1.254000	0.01491	GCG	T|0.125;C|0.875	0.125	strong		0.418	HLA-DPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076071.3	NM_033554	
NAGLU	4669	hgsc.bcm.edu	37	17	40696120	40696120	+	Missense_Mutation	SNP	A	A	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:40696120A>T	ENST00000225927.2	+	6	2197	c.2096A>T	c.(2095-2097)aAa>aTa	p.K699I	RP11-400F19.8_ENST00000585572.1_RNA	NM_000263.3	NP_000254.2	P54802	ANAG_HUMAN	N-acetylglucosaminidase, alpha	699					carbohydrate metabolic process (GO:0005975)|cerebellar Purkinje cell layer development (GO:0021680)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|inner ear receptor cell development (GO:0060119)|locomotor rhythm (GO:0045475)|lysosome organization (GO:0007040)|middle ear morphogenesis (GO:0042474)|nervous system development (GO:0007399)|retinal rod cell development (GO:0046548)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)	alpha-N-acetylglucosaminidase activity (GO:0004561)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(1)|ovary(2)|skin(1)	12		all_cancers(22;1.58e-05)|Breast(137;0.000153)|all_epithelial(22;0.000344)		BRCA - Breast invasive adenocarcinoma(366;0.13)	N-Acetyl-D-glucosamine(DB00141)	CAGTTTGACAAAAATGTCTTC	0.577																																					p.K699I		Atlas-SNP	.											.	NAGLU	36	.	0			c.A2096T						PASS	.						48.0	46.0	47.0					17																	40696120		2203	4300	6503	SO:0001583	missense	4669	exon6			TTGACAAAAATGT		CCDS11427.1	17q21.2	2010-07-27	2010-07-27		ENSG00000108784	ENSG00000108784	3.2.1.50		7632	protein-coding gene	gene with protein product	"""Sanfilippo disease IIIB"""	609701					Standard	XM_006721920		Approved	NAG	uc002hzv.3	P54802		ENST00000225927.2:c.2096A>T	17.37:g.40696120A>T	ENSP00000225927:p.Lys699Ile	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	53	17	0.320755	NM_000263		Missense_Mutation	SNP	ENST00000225927.2	37	CCDS11427.1	.	.	.	.	.	.	.	.	.	.	A	14.62	2.590453	0.46214	.	.	ENSG00000108784	ENST00000225927;ENST00000377405	D	0.98777	-5.13	5.03	2.8	0.32819	Alpha-N-acetylglucosaminidase, C-terminal (1);	0.606411	0.18227	N	0.147694	D	0.96059	0.8716	L	0.31526	0.94	0.09310	N	0.99999	P	0.38395	0.629	B	0.41619	0.361	D	0.92173	0.5745	10	0.46703	T	0.11	-5.9234	8.3135	0.32086	0.833:0.0:0.167:0.0	.	699	P54802	ANAG_HUMAN	I	699;375	ENSP00000225927:K699I	ENSP00000225927:K699I	K	+	2	0	NAGLU	37949646	0.903000	0.30736	0.023000	0.16930	0.900000	0.52787	2.106000	0.41835	0.879000	0.35944	0.454000	0.30748	AAA	.	.	none		0.577	NAGLU-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450385.1	NM_000263	
SHISA3	152573	hgsc.bcm.edu	37	4	42400112	42400112	+	Missense_Mutation	SNP	G	G	T	rs11733156	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:42400112G>T	ENST00000319234.4	+	1	257	c.39G>T	c.(37-39)tgG>tgT	p.W13C		NM_001080505.1	NP_001073974.1	A0PJX4	SHSA3_HUMAN	shisa family member 3	13			W -> C (in dbSNP:rs11733156). {ECO:0000269|PubMed:15489334}.		multicellular organismal development (GO:0007275)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(1)|lung(5)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	12						TCCTTGGCTGGCTGCGCTGGG	0.706													G|||	1027	0.205072	0.2231	0.281	5008	,	,		14398	0.1339		0.2306	False		,,,				2504	0.1738				p.W13C		Atlas-SNP	.											.	SHISA3	27	.	0			c.G39T						PASS	.	G	CYS/TRP	1029,3285		140,749,1268	8.0	9.0	9.0		39	4.4	1.0	4	dbSNP_120	9	2011,6359		280,1451,2454	no	missense	SHISA3	NM_001080505.1	215	420,2200,3722	TT,TG,GG		24.0263,23.8526,23.9672	benign	13/239	42400112	3040,9644	2157	4185	6342	SO:0001583	missense	152573	exon1			TGGCTGGCTGCGC	BC012029	CCDS33979.1	4p13	2013-07-31	2013-07-31		ENSG00000178343	ENSG00000178343		"""Shisa homologs"""	25159	protein-coding gene	gene with protein product			"""shisa homolog 3 (Xenopus laevis)"""				Standard	NM_001080505		Approved	hShisa3	uc003gwp.3	A0PJX4	OTTHUMG00000161043	ENST00000319234.4:c.39G>T	4.37:g.42400112G>T	ENSP00000326445:p.Trp13Cys	Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	39	39	1	NM_001080505	A0PJX3|Q96EQ5	Missense_Mutation	SNP	ENST00000319234.4	37	CCDS33979.1	430	0.19688644688644688	91	0.18495934959349594	95	0.26243093922651933	67	0.11713286713286714	177	0.23350923482849603	G	12.01	1.809960	0.31961	0.238526	0.240263	ENSG00000178343	ENST00000319234	T	0.42900	0.96	4.38	4.38	0.52667	.	0.492839	0.19949	N	0.102464	T	0.00012	0.0000	N	0.14661	0.345	0.25425	P	0.9882369	B	0.27732	0.187	B	0.26614	0.071	T	0.16660	-1.0395	9	0.51188	T	0.08	-2.9601	11.1392	0.48392	0.0:0.0:0.8152:0.1848	rs11733156;rs59183676	13	A0PJX4	SHSA3_HUMAN	C	13	ENSP00000326445:W13C	ENSP00000326445:W13C	W	+	3	0	SHISA3	42094869	1.000000	0.71417	0.996000	0.52242	0.684000	0.39900	1.787000	0.38704	2.247000	0.74100	0.467000	0.42956	TGG	G|0.801;T|0.199	0.199	strong		0.706	SHISA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363539.1	NM_001080505	
BDH2	56898	hgsc.bcm.edu	37	4	104013796	104013796	+	Missense_Mutation	SNP	T	T	C	rs1054707	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:104013796T>C	ENST00000296424.4	-	4	329	c.209A>G	c.(208-210)aAt>aGt	p.N70S		NM_020139.3	NP_064524.3	Q9BUT1	BDH2_HUMAN	3-hydroxybutyrate dehydrogenase, type 2	70			N -> S (in dbSNP:rs1054707). {ECO:0000269|PubMed:12975309, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.3}.		epithelial cell differentiation (GO:0030855)|fatty acid beta-oxidation (GO:0006635)|heme metabolic process (GO:0042168)|iron ion homeostasis (GO:0055072)|siderophore biosynthetic process (GO:0019290)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	3-hydroxybutyrate dehydrogenase activity (GO:0003858)|NAD binding (GO:0051287)|oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor (GO:0016628)			breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(4)|urinary_tract(1)	10		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;2.02e-08)		CTCAACTTCATTGGCAAACTG	0.323													T|||	793	0.158347	0.0492	0.1772	5008	,	,		22524	0.1548		0.1501	False		,,,				2504	0.3047				p.N70S		Atlas-SNP	.											.	BDH2	18	.	0			c.A209G						PASS	.	T	SER/ASN	292,4114	156.3+/-189.4	9,274,1920	88.0	89.0	89.0		209	-2.6	0.3	4	dbSNP_86	89	1360,7240	264.3+/-285.5	117,1126,3057	no	missense	BDH2	NM_020139.3	46	126,1400,4977	CC,CT,TT		15.814,6.6273,12.7018	benign	70/246	104013796	1652,11354	2203	4300	6503	SO:0001583	missense	56898	exon4			ACTTCATTGGCAA	AF164790	CCDS3663.1	4q24	2011-09-14			ENSG00000164039	ENSG00000164039	1.1.1.30	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"""	32389	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 15C, member 1"""		"""dehydrogenase/reductase (SDR family) member 6"""	DHRS6		16380372, 19027726	Standard	XM_005263140		Approved	UCPA-OR, FLJ13261, UNQ6308, PRO20933, SDR15C1	uc003hwz.3	Q9BUT1	OTTHUMG00000074039	ENST00000296424.4:c.209A>G	4.37:g.104013796T>C	ENSP00000296424:p.Asn70Ser	Somatic	330	0	0		WXS	Illumina HiSeq	Phase_I	275	149	0.541818	NM_020139	A8K295|B4DUF6|Q503A0|Q6IA46|Q6UWD3|Q9H8S8|Q9NRX8	Missense_Mutation	SNP	ENST00000296424.4	37	CCDS3663.1	278	0.12728937728937728	26	0.052845528455284556	61	0.1685082872928177	78	0.13636363636363635	113	0.14907651715039577	T	4.761	0.141483	0.09083	0.066273	0.15814	ENSG00000164039	ENST00000296424;ENST00000504285;ENST00000509245	T;T;D	0.87256	2.0;0.76;-2.23	4.83	-2.62	0.06152	NAD(P)-binding domain (1);	0.583303	0.19930	N	0.102891	T	0.00271	0.0008	N	0.01789	-0.72	0.45995	P	0.0011999999999999789	B	0.02656	0.0	B	0.01281	0.0	T	0.10730	-1.0617	9	0.13470	T	0.59	.	6.0507	0.19785	0.0:0.3221:0.1346:0.5433	rs1054707;rs3195228;rs11734617;rs17215638;rs17844934;rs17857667;rs1054707	70	Q9BUT1	BDH2_HUMAN	S	70	ENSP00000296424:N70S;ENSP00000427442:N70S;ENSP00000422891:N70S	ENSP00000296424:N70S	N	-	2	0	BDH2	104233245	0.972000	0.33761	0.280000	0.24747	0.327000	0.28475	0.038000	0.13862	-0.662000	0.05338	0.459000	0.35465	AAT	T|0.878;C|0.122	0.122	strong		0.323	BDH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157159.2	NM_020139	
STK10	6793	hgsc.bcm.edu	37	5	171523436	171523436	+	Silent	SNP	G	G	A	rs4868141	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:171523436G>A	ENST00000176763.5	-	8	1342	c.999C>T	c.(997-999)gcC>gcT	p.A333A	STK10_ENST00000517775.1_5'Flank	NM_005990.3	NP_005981.3	O94804	STK10_HUMAN	serine/threonine kinase 10	333					cell cycle (GO:0007049)|lymphocyte aggregation (GO:0071593)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of lymphocyte migration (GO:2000401)|signal transduction by phosphorylation (GO:0023014)	extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|polo kinase kinase activity (GO:0042801)|protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(15)|ovary(6)|pancreas(1)|prostate(1)|testis(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	47	Renal(175;0.000159)|Lung NSC(126;0.0056)|all_lung(126;0.0094)	Medulloblastoma(196;0.00868)|all_neural(177;0.026)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			TTACGGAGGCGGCATCCACGG	0.672													G|||	764	0.152556	0.0628	0.2291	5008	,	,		15635	0.1905		0.1889	False		,,,				2504	0.1431				p.A333A		Atlas-SNP	.											.	STK10	100	.	0			c.C999T						PASS	.	G		362,4044	187.1+/-213.8	17,328,1858	63.0	60.0	61.0		999	-6.7	0.0	5	dbSNP_111	61	1534,7066	288.4+/-298.7	149,1236,2915	no	coding-synonymous	STK10	NM_005990.3		166,1564,4773	AA,AG,GG		17.8372,8.2161,14.5779		333/969	171523436	1896,11110	2203	4300	6503	SO:0001819	synonymous_variant	6793	exon8			GGAGGCGGCATCC	AB015718	CCDS34290.1	5q35.1	2008-07-18			ENSG00000072786	ENSG00000072786			11388	protein-coding gene	gene with protein product		603919				10199912	Standard	NM_005990		Approved	LOK, PRO2729	uc003mbo.1	O94804	OTTHUMG00000163265	ENST00000176763.5:c.999C>T	5.37:g.171523436G>A		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	61	32	0.52459	NM_005990	A6ND35|B2R8F5|B3KMY1|Q6NSK0|Q9UIW4	Silent	SNP	ENST00000176763.5	37	CCDS34290.1																																																																																			G|0.856;A|0.144	0.144	strong		0.672	STK10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372374.2	NM_005990	
ACTL7B	10880	hgsc.bcm.edu	37	9	111617650	111617650	+	Silent	SNP	G	G	A	rs11543179	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:111617650G>A	ENST00000374667.3	-	1	1589	c.561C>T	c.(559-561)taC>taT	p.Y187Y		NM_006686.3	NP_006677.1	Q9Y614	ACL7B_HUMAN	actin-like 7B	187						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						TGCCGTAGGAGTAGATGGACA	0.652													G|||	1140	0.227636	0.2224	0.2378	5008	,	,		18645	0.2113		0.2097	False		,,,				2504	0.2628				p.Y187Y		Atlas-SNP	.											.	ACTL7B	57	.	0			c.C561T						PASS	.	G		962,3444	346.4+/-309.0	109,744,1350	44.0	43.0	43.0		561	2.8	1.0	9	dbSNP_120	43	1832,6762	306.5+/-307.9	195,1442,2660	no	coding-synonymous	ACTL7B	NM_006686.3		304,2186,4010	AA,AG,GG		21.3172,21.8339,21.4923		187/416	111617650	2794,10206	2203	4297	6500	SO:0001819	synonymous_variant	10880	exon1			GTAGGAGTAGATG	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.561C>T	9.37:g.111617650G>A		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	45	24	0.533333	NM_006686	B2R9Q2|Q5JSV1	Silent	SNP	ENST00000374667.3	37	CCDS6771.1																																																																																			G|0.782;A|0.218	0.218	strong		0.652	ACTL7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053571.1	NM_006686	
ITGA10	8515	hgsc.bcm.edu	37	1	145536082	145536082	+	Missense_Mutation	SNP	G	G	A	rs2274616	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:145536082G>A	ENST00000369304.3	+	17	2349	c.2174G>A	c.(2173-2175)cGg>cAg	p.R725Q	ITGA10_ENST00000538811.1_Missense_Mutation_p.R594Q|ITGA10_ENST00000539363.1_Missense_Mutation_p.R582Q	NM_003637.3	NP_003628.2	O75578	ITA10_HUMAN	integrin, alpha 10	725			R -> Q (in dbSNP:rs2274616).		axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)	integrin alpha10-beta1 complex (GO:0034680)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)	collagen binding (GO:0005518)|collagen binding involved in cell-matrix adhesion (GO:0098639)|metal ion binding (GO:0046872)			NS(1)|breast(2)|endometrium(3)|kidney(5)|large_intestine(12)|lung(25)|ovary(2)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	59	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					TTGTCCCCTCGGAGGCTCCGG	0.557													G|||	582	0.116214	0.0961	0.1383	5008	,	,		19331	0.0704		0.1441	False		,,,				2504	0.1462				p.R725Q		Atlas-SNP	.											ITGA10,NS,carcinoma,-1,1	ITGA10	131	1	0			c.G2174A						PASS	.	G	GLN/ARG	483,3923	226.9+/-242.2	22,439,1742	102.0	95.0	97.0		2174	2.4	0.6	1	dbSNP_100	97	1383,7217	267.8+/-287.5	107,1169,3024	yes	missense	ITGA10	NM_003637.3	43	129,1608,4766	AA,AG,GG		16.0814,10.9623,14.3472	benign	725/1168	145536082	1866,11140	2203	4300	6503	SO:0001583	missense	8515	exon17			CCCCTCGGAGGCT	AF074015	CCDS72869.1	1q21.1	2010-03-23			ENSG00000143127	ENSG00000143127		"""Integrins"""	6135	protein-coding gene	gene with protein product		604042				9685391, 10702680	Standard	NM_003637		Approved		uc001eoa.3	O75578	OTTHUMG00000013751	ENST00000369304.3:c.2174G>A	1.37:g.145536082G>A	ENSP00000358310:p.Arg725Gln	Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	144	72	0.5	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	
HJURP	55355	hgsc.bcm.edu	37	2	234749780	234749780	+	Missense_Mutation	SNP	G	G	C	rs3821238	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:234749780G>C	ENST00000411486.2	-	8	1711	c.1646C>G	c.(1645-1647)tCt>tGt	p.S549C	HJURP_ENST00000434039.1_5'Flank|HJURP_ENST00000441687.1_Missense_Mutation_p.S464C|HJURP_ENST00000432087.1_Missense_Mutation_p.S495C	NM_018410.3	NP_060880.3	Q8NCD3	HJURP_HUMAN	Holliday junction recognition protein	549			S -> C (in dbSNP:rs3821238). {ECO:0000269|PubMed:14702039}.		cell cycle (GO:0007049)|CENP-A containing nucleosome assembly (GO:0034080)|chromosome segregation (GO:0007059)|nucleosome assembly (GO:0006334)|regulation of DNA binding (GO:0051101)|regulation of protein complex assembly (GO:0043254)	chromosome, centromeric region (GO:0000775)|condensed chromosome kinetochore (GO:0000777)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone binding (GO:0042393)|identical protein binding (GO:0042802)	p.S549C(1)		NS(2)|breast(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(3)|lung(11)|ovary(2)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	38		Breast(86;0.00204)|all_lung(227;0.00433)|Renal(207;0.00685)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0719)|Lung SC(224;0.128)		Epithelial(121;2.01e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000186)|Lung(119;0.00521)|LUSC - Lung squamous cell carcinoma(224;0.00829)		AAATATTCCAGAACTATTTCC	0.468													G|||	832	0.166134	0.2375	0.1254	5008	,	,		19121	0.2827		0.0875	False		,,,				2504	0.0593				p.S549C		Atlas-SNP	.											HJURP,NS,carcinoma,0,1	HJURP	72	1	1	Substitution - Missense(1)	stomach(1)	c.C1646G						PASS	.	G	CYS/SER	864,3542	339.4+/-305.8	89,686,1428	117.0	121.0	119.0		1646	-1.1	0.0	2	dbSNP_107	119	825,7775	190.7+/-237.1	40,745,3515	yes	missense	HJURP	NM_018410.3	112	129,1431,4943	CC,CG,GG		9.593,19.6096,12.9863	probably-damaging	549/749	234749780	1689,11317	2203	4300	6503	SO:0001583	missense	55355	exon8			ATTCCAGAACTAT		CCDS33406.1, CCDS63166.1, CCDS63167.1	2q37.1	2007-12-06			ENSG00000123485	ENSG00000123485			25444	protein-coding gene	gene with protein product		612667				17823411	Standard	NM_001282962		Approved	DKFZp762E1312, URLC9, hFLEG1, FAKTS	uc002vvg.3	Q8NCD3	OTTHUMG00000059125	ENST00000411486.2:c.1646C>G	2.37:g.234749780G>C	ENSP00000414109:p.Ser549Cys	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	57	33	0.578947	NM_018410	A8IRH5|B4DWR0|B4DZV4|Q9BUT2|Q9NSL8	Missense_Mutation	SNP	ENST00000411486.2	37	CCDS33406.1	414	0.18956043956043955	116	0.23577235772357724	40	0.11049723756906077	186	0.32517482517482516	72	0.09498680738786279	G	14.36	2.510896	0.44660	0.196096	0.09593	ENSG00000123485	ENST00000411486;ENST00000432087;ENST00000441687;ENST00000414924	T;T;T;T	0.11604	3.06;3.07;3.07;2.76	4.29	-1.13	0.09775	.	1.608680	0.03391	N	0.201811	T	0.00012	0.0000	L	0.36672	1.1	0.80722	P	0.0	D;D;D	0.69078	0.997;0.997;0.994	P;P;P	0.57468	0.821;0.821;0.667	T	0.32134	-0.9918	9	0.45353	T	0.12	-0.9977	6.5815	0.22596	0.1926:0.1639:0.6434:0.0	rs3821238;rs56481334;rs59494558;rs3821238	464;495;549	Q8NCD3-3;Q8NCD3-2;Q8NCD3	.;.;HJURP_HUMAN	C	549;495;464;464	ENSP00000414109:S549C;ENSP00000407208:S495C;ENSP00000401944:S464C;ENSP00000393253:S464C	ENSP00000414109:S549C	S	-	2	0	HJURP	234414519	0.000000	0.05858	0.000000	0.03702	0.019000	0.09904	-0.637000	0.05459	-0.209000	0.10156	0.563000	0.77884	TCT	G|0.832;C|0.168	0.168	strong		0.468	HJURP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000130996.6	NM_018410	
CRIPAK	285464	hgsc.bcm.edu	37	4	1388553	1388553	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	116	2	0.0172414		WXS	Illumina HiSeq	Phase_I	102	10	0.0980392	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	
ITIH4	3700	hgsc.bcm.edu	37	3	52864635	52864635	+	Silent	SNP	A	A	G	rs2276818	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:52864635A>G	ENST00000266041.4	-	1	120	c.24T>C	c.(22-24)cgT>cgC	p.R8R	ITIH4_ENST00000406595.1_Silent_p.R8R|ITIH4_ENST00000485816.1_Silent_p.R8R|ITIH4_ENST00000346281.5_Silent_p.R8R|ITIH4_ENST00000434759.3_5'UTR|RP5-966M1.6_ENST00000513520.1_5'UTR|RP5-966M1.6_ENST00000468472.1_3'UTR	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	84	0	0		WXS	Illumina HiSeq	Phase_I	82	45	0.548781	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	
PROSER1	80209	hgsc.bcm.edu	37	13	39587677	39587677	+	Missense_Mutation	SNP	A	A	G	rs3751379	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:39587677A>G	ENST00000352251.3	-	11	2545	c.1712T>C	c.(1711-1713)gTg>gCg	p.V571A	PROSER1_ENST00000350125.3_Missense_Mutation_p.V549A|PROSER1_ENST00000484434.3_Intron	NM_025138.4	NP_079414.3	Q86XN7	PRSR1_HUMAN	proline and serine rich 1	571	Ser-rich.		V -> A (in dbSNP:rs3751379). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.														GCTAACTGGCACTGACGTGGA	0.562													G|||	1407	0.28095	0.4463	0.1801	5008	,	,		21158	0.2183		0.17	False		,,,				2504	0.3078				p.V571A		Atlas-SNP	.											.	.	.	.	0			c.T1712C						PASS	.	G	ALA/VAL,ALA/VAL	1902,2504	627.4+/-394.9	393,1116,694	88.0	92.0	90.0		1712,1646	-1.6	0.0	13	dbSNP_107	90	1282,7318	759.3+/-407.5	103,1076,3121	yes	missense,missense	PROSER1	NM_025138.3,NM_170719.2	64,64	496,2192,3815	GG,GA,AA		14.907,43.1684,24.481	benign,benign	571/945,549/923	39587677	3184,9822	2203	4300	6503	SO:0001583	missense	80209	exon11			ACTGGCACTGACG	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.1712T>C	13.37:g.39587677A>G	ENSP00000332034:p.Val571Ala	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	66	33	0.5	NM_025138	A6NJ97|Q6P2S2|Q7Z3X5|Q8N3D2|Q8N3P1|Q9H9M1	Missense_Mutation	SNP	ENST00000352251.3	37	CCDS9368.2	551	0.2522893772893773	222	0.45121951219512196	72	0.19889502762430938	127	0.22202797202797203	130	0.17150395778364116	G	2.517	-0.311523	0.05422	0.431684	0.14907	ENSG00000120685	ENST00000352251;ENST00000350125	T;T	0.32515	1.45;1.46	5.05	-1.6	0.08426	.	.	.	.	.	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.49153	-0.8969	7	.	.	.	0.7186	6.6741	0.23083	0.5677:0.2225:0.2098:0.0	rs3751379;rs17846511;rs17859582;rs60335909;rs3751379	549;571	A6NJ97;Q86XN7	.;PRSR1_HUMAN	A	571;549	ENSP00000332034:V571A;ENSP00000339123:V549A	.	V	-	2	0	PROSER1	38485677	0.000000	0.05858	0.000000	0.03702	0.067000	0.16453	0.098000	0.15189	-0.788000	0.04504	-1.163000	0.01768	GTG	G|0.254;N|0.000	0.254	strong		0.562	PROSER1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044607.5	NM_025138	
CPAMD8	27151	hgsc.bcm.edu	37	19	17088299	17088299	+	Missense_Mutation	SNP	T	T	C	rs1824152	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	40	0	0		WXS	Illumina HiSeq	Phase_I	31	31	1	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	
P2RX3	5024	hgsc.bcm.edu	37	11	57137424	57137424	+	Missense_Mutation	SNP	C	C	T	rs2276038	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	100	0	0		WXS	Illumina HiSeq	Phase_I	90	88	0.977778	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	
ARHGAP42	143872	hgsc.bcm.edu	37	11	100847069	100847069	+	Missense_Mutation	SNP	G	G	A	rs569336	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:100847069G>A	ENST00000298815.8	+	20	2140	c.2137G>A	c.(2137-2139)Gtt>Att	p.V713I	ARHGAP42_ENST00000524892.2_Missense_Mutation_p.V679I	NM_152432.2	NP_689645.2	A6NI28	RHG42_HUMAN	Rho GTPase activating protein 42	713	Ser-rich.			V -> I (in Ref. 3; BAB71456). {ECO:0000305}.	signal transduction (GO:0007165)	intracellular (GO:0005622)	GTPase activator activity (GO:0005096)			endometrium(3)|skin(2)	5						CCCAGGAGACGTTTCCCCACC	0.488													G|||	2485	0.496206	0.1505	0.5274	5008	,	,		21331	0.997		0.2883	False		,,,				2504	0.6391				p.V713I		Atlas-SNP	.											.	ARHGAP42	32	.	0			c.G2137A						PASS	.	G	ILE/VAL	307,1077		34,239,419	64.0	49.0	54.0		2137	2.4	0.0	11	dbSNP_83	54	987,2195		160,667,764	yes	missense	ARHGAP42	NM_152432.2	29	194,906,1183	AA,AG,GG		31.0182,22.1821,28.3399	benign	713/875	100847069	1294,3272	692	1591	2283	SO:0001583	missense	143872	exon20			GGAGACGTTTCCC			11q22.1	2012-04-19			ENSG00000165895	ENSG00000165895		"""Rho GTPase activating proteins"""	26545	protein-coding gene	gene with protein product		615936				18954304	Standard	NM_152432		Approved	FLJ32810, GRAF3	uc001pge.2	A6NI28	OTTHUMG00000167530	ENST00000298815.8:c.2137G>A	11.37:g.100847069G>A	ENSP00000298815:p.Val713Ile	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	96	23	0.239583	NM_152432	Q96M56	Missense_Mutation	SNP	ENST00000298815.8	37		1052	0.4816849816849817	87	0.17682926829268292	168	0.46408839779005523	572	1.0	225	0.29683377308707126	G	3.367	-0.129186	0.06753	0.221821	0.310182	ENSG00000165895	ENST00000524892;ENST00000298815	T;T	0.06849	3.25;3.34	5.7	2.36	0.29203	.	.	.	.	.	T	0.00012	0.0000	L	0.34521	1.04	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.37753	-0.9692	8	0.33141	T	0.24	.	12.4883	0.55885	0.2148:0.0:0.7852:0.0	rs569336;rs52827090;rs58116702;rs569336	713	A6NI28	RHG42_HUMAN	I	679;713	ENSP00000431776:V679I;ENSP00000298815:V713I	ENSP00000298815:V713I	V	+	1	0	ARHGAP42	100352279	0.011000	0.17503	0.008000	0.14137	0.397000	0.30659	1.390000	0.34464	0.760000	0.33108	0.655000	0.94253	GTT	G|0.552;A|0.448	0.448	strong		0.488	ARHGAP42-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_152432	
SPATA21	374955	hgsc.bcm.edu	37	1	16731510	16731510	+	Missense_Mutation	SNP	C	C	G	rs525409	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:16731510C>G	ENST00000335496.1	-	8	1245	c.763G>C	c.(763-765)Gtg>Ctg	p.V255L	SPATA21_ENST00000466212.1_5'UTR|SPATA21_ENST00000540400.1_Missense_Mutation_p.V232L	NM_198546.1	NP_940948.1	Q7Z572	SPT21_HUMAN	spermatogenesis associated 21	255	EF-hand. {ECO:0000255|PROSITE- ProRule:PRU00448}.		V -> L (in dbSNP:rs525409). {ECO:0000269|PubMed:15489334}.				calcium ion binding (GO:0005509)			breast(1)|endometrium(2)|lung(8)|ovary(2)|pancreas(3)|stomach(1)|urinary_tract(2)	19		Colorectal(325;0.000147)|Renal(390;0.00145)|Lung NSC(340;0.00215)|Breast(348;0.00224)|all_lung(284;0.00351)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|COAD - Colon adenocarcinoma(227;1.15e-05)|BRCA - Breast invasive adenocarcinoma(304;4.2e-05)|Kidney(64;0.000183)|KIRC - Kidney renal clear cell carcinoma(64;0.00269)|STAD - Stomach adenocarcinoma(313;0.0122)|READ - Rectum adenocarcinoma(331;0.0651)		GCCAGCGTCACAGAGAAGCCC	0.582													C|||	1403	0.280152	0.2027	0.402	5008	,	,		19702	0.1488		0.2416	False		,,,				2504	0.4734				p.V255L		Atlas-SNP	.											.	SPATA21	47	.	0			c.G763C						PASS	.	C	LEU/VAL	882,3524	343.1+/-307.5	93,696,1414	101.0	85.0	90.0		763	-0.3	1.0	1	dbSNP_83	90	2077,6523	359.8+/-331.7	251,1575,2474	yes	missense	SPATA21	NM_198546.1	32	344,2271,3888	GG,GC,CC		24.1512,20.0182,22.751	benign	255/470	16731510	2959,10047	2203	4300	6503	SO:0001583	missense	374955	exon8			GCGTCACAGAGAA		CCDS172.1	1p36.13	2013-01-10			ENSG00000187144	ENSG00000187144		"""EF-hand domain containing"""	28026	protein-coding gene	gene with protein product							Standard	NM_198546		Approved	spergen-2, spergen2	uc001ayn.3	Q7Z572	OTTHUMG00000002312	ENST00000335496.1:c.763G>C	1.37:g.16731510C>G	ENSP00000335612:p.Val255Leu	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	107	40	0.373832	NM_198546	B9EK40|F5GXP5	Missense_Mutation	SNP	ENST00000335496.1	37	CCDS172.1	472	0.21611721611721613	91	0.18495934959349594	122	0.3370165745856354	69	0.12062937062937062	190	0.25065963060686014	C	0.019	-1.448705	0.01080	0.200182	0.241512	ENSG00000187144	ENST00000335496;ENST00000540400	T;T	0.73789	-0.78;-0.78	4.53	-0.33	0.12683	EF-hand-like domain (1);	0.515634	0.16178	N	0.225994	T	0.00012	0.0000	N	0.00453	-1.485	0.52099	P	5.299999999996974E-5	B;B	0.06786	0.001;0.001	B;B	0.10450	0.003;0.005	T	0.21075	-1.0256	9	0.02654	T	1	-1.6805	0.875	0.01222	0.2244:0.2828:0.3244:0.1683	rs525409;rs52801517;rs56634096;rs525409	232;255	F5GXP5;Q7Z572	.;SPT21_HUMAN	L	255;232	ENSP00000335612:V255L;ENSP00000440046:V232L	ENSP00000335612:V255L	V	-	1	0	SPATA21	16604097	0.965000	0.33210	0.986000	0.45419	0.223000	0.24884	0.057000	0.14279	0.127000	0.18452	0.313000	0.20887	GTG	C|0.774;G|0.226	0.226	strong		0.582	SPATA21-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000006677.2	NM_198546	
FAM151A	338094	hgsc.bcm.edu	37	1	55075062	55075062	+	Missense_Mutation	SNP	C	C	T	rs2289015	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:55075062C>T	ENST00000302250.2	-	8	1797	c.1637G>A	c.(1636-1638)gGc>gAc	p.G546D	ACOT11_ENST00000371316.3_Intron|ACOT11_ENST00000481208.1_3'UTR|ACOT11_ENST00000343744.2_3'UTR|FAM151A_ENST00000371304.2_Missense_Mutation_p.G359D	NM_176782.2	NP_788954.2	Q8WW52	F151A_HUMAN	family with sequence similarity 151, member A	546			G -> D (in dbSNP:rs2289015).			extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(2)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	12						GGCATAGTCGCCCCCAGCTGG	0.642													C|||	402	0.0802716	0.034	0.1427	5008	,	,		16604	0.1687		0.0348	False		,,,				2504	0.0542				p.G546D		Atlas-SNP	.											.	FAM151A	58	.	0			c.G1637A						PASS	.	C	,,ASP/GLY	181,4225	116.7+/-154.6	3,175,2025	62.0	54.0	57.0		,,1637	2.4	0.0	1	dbSNP_100	57	230,8370	94.2+/-156.2	3,224,4073	yes	intron,utr-3,missense	ACOT11,FAM151A	NM_015547.3,NM_147161.3,NM_176782.2	,,94	6,399,6098	TT,TC,CC		2.6744,4.108,3.1601	,,possibly-damaging	,,546/586	55075062	411,12595	2203	4300	6503	SO:0001583	missense	338094	exon8			TAGTCGCCCCCAG	AK091901	CCDS594.1	1p32.3	2008-02-05	2007-12-18	2007-12-18	ENSG00000162391	ENSG00000162391			25032	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 179"""	C1orf179		17273976	Standard	NM_176782		Approved	MGC27169	uc001cxn.3	Q8WW52	OTTHUMG00000009888	ENST00000302250.2:c.1637G>A	1.37:g.55075062C>T	ENSP00000306888:p.Gly546Asp	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	80	41	0.5125	NM_176782	Q5VUG5|Q6DKH5|Q6UWV0|Q8NAX9|Q96KY5	Missense_Mutation	SNP	ENST00000302250.2	37	CCDS594.1	191	0.08745421245421245	15	0.03048780487804878	49	0.13535911602209943	98	0.17132867132867133	29	0.03825857519788918	C	3.386	-0.125295	0.06795	0.04108	0.026744	ENSG00000162391	ENST00000302250;ENST00000294370	T	0.10288	2.89	4.28	2.39	0.29439	.	0.447903	0.21792	N	0.069044	T	0.00039	0.0001	M	0.64997	1.995	0.58432	P	5.999999999950489E-6	B	0.17852	0.024	B	0.20767	0.031	T	0.10730	-1.0617	9	0.52906	T	0.07	-16.4261	7.9583	0.30055	0.0:0.7915:0.0:0.2085	rs2289015;rs2289015	546	Q8WW52	F151A_HUMAN	D	546;359	ENSP00000306888:G546D	ENSP00000294370:G359D	G	-	2	0	FAM151A	54847650	0.008000	0.16893	0.028000	0.17463	0.011000	0.07611	0.768000	0.26590	0.729000	0.32403	0.655000	0.94253	GGC	C|0.942;T|0.058	0.058	strong		0.642	FAM151A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027342.1	NM_176782	
C7orf31	136895	hgsc.bcm.edu	37	7	25194753	25194753	+	Missense_Mutation	SNP	C	C	T	rs12535348	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:25194753C>T	ENST00000409280.1	-	6	780	c.472G>A	c.(472-474)Gcc>Acc	p.A158T	C7orf31_ENST00000283905.3_Missense_Mutation_p.A158T			Q8N865	CG031_HUMAN	chromosome 7 open reading frame 31	158			A -> T (in dbSNP:rs12535348). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:17974005, ECO:0000269|Ref.3}.					p.A158T(1)		autonomic_ganglia(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(6)|skin(2)|stomach(1)	14						GGGAACATGGCGCCGCGACAG	0.502													C|||	1409	0.28135	0.0484	0.3919	5008	,	,		16730	0.1567		0.4891	False		,,,				2504	0.4325				p.A158T		Atlas-SNP	.											C7orf31,caecum,carcinoma,0,2	C7orf31	53	2	1	Substitution - Missense(1)	stomach(1)	c.G472A						PASS	.	C	THR/ALA	507,3899	234.6+/-247.4	33,441,1729	124.0	129.0	127.0		472	4.6	0.9	7	dbSNP_120	127	4293,4307	576.9+/-390.5	1042,2209,1049	yes	missense	C7orf31	NM_138811.3	58	1075,2650,2778	TT,TC,CC		49.9186,11.507,36.906	benign	158/591	25194753	4800,8206	2203	4300	6503	SO:0001583	missense	136895	exon6			ACATGGCGCCGCG	AK097248	CCDS5394.1	7p15.2	2011-11-24			ENSG00000153790	ENSG00000153790			21722	protein-coding gene	gene with protein product							Standard	NM_138811		Approved		uc003sxn.1	Q8N865	OTTHUMG00000128497	ENST00000409280.1:c.472G>A	7.37:g.25194753C>T	ENSP00000386604:p.Ala158Thr	Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	177	173	0.977401	NM_138811	A4D165|Q6MZV8|Q6P989|Q7LE28|Q86XK1|Q8N1H5|Q96BN4	Missense_Mutation	SNP	ENST00000409280.1	37	CCDS5394.1	615	0.2815934065934066	27	0.054878048780487805	150	0.4143646408839779	80	0.13986013986013987	358	0.47229551451187335	c	15.50	2.850917	0.51270	0.11507	0.499186	ENSG00000153790	ENST00000409280;ENST00000283905	T;T	0.09445	2.98;2.98	5.47	4.58	0.56647	.	0.102433	0.42964	D	0.000621	T	0.00012	0.0000	M	0.68952	2.095	0.31562	P	0.65745	D	0.63046	0.992	P	0.54431	0.752	T	0.49153	-0.8969	9	0.51188	T	0.08	-37.4962	11.8433	0.52368	0.1741:0.8259:0.0:0.0	rs12535348;rs17301740;rs52832524;rs59627706;rs12535348	158	Q8N865	CG031_HUMAN	T	158	ENSP00000386604:A158T;ENSP00000283905:A158T	ENSP00000283905:A158T	A	-	1	0	C7orf31	25161278	0.918000	0.31147	0.857000	0.33713	0.038000	0.13279	1.734000	0.38166	1.293000	0.44690	0.563000	0.77884	GCC	C|0.675;N|0.000	.	strong		0.502	C7orf31-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326929.1	NM_138811	
ENOSF1	55556	hgsc.bcm.edu	37	18	706558	706558	+	Silent	SNP	C	C	T	rs58085394	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:706558C>T	ENST00000251101.7	-	2	193	c.105G>A	c.(103-105)tcG>tcA	p.S35S	ENOSF1_ENST00000539164.1_Silent_p.S35S|RP11-806L2.6_ENST00000580007.1_RNA|ENOSF1_ENST00000383578.3_5'UTR|ENOSF1_ENST00000580982.1_Silent_p.S35S|ENOSF1_ENST00000340116.7_Silent_p.S56S	NM_017512.5	NP_059982.2	Q7L5Y1	ENOF1_HUMAN	enolase superfamily member 1	35					cellular amino acid catabolic process (GO:0009063)|cellular carbohydrate catabolic process (GO:0044275)	mitochondrion (GO:0005739)	isomerase activity (GO:0016853)|L-fuconate dehydratase activity (GO:0050023)|magnesium ion binding (GO:0000287)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(3)|ovary(1)|prostate(1)	10						CATAGGCAGCCGAGTAGTCAG	0.493													C|||	514	0.102636	0.0083	0.0778	5008	,	,		11807	0.2391		0.1581	False		,,,				2504	0.0501				p.S56S		Atlas-SNP	.											.	ENOSF1	44	.	0			c.G168A						PASS	.	C	,,	121,4285	92.5+/-131.2	1,119,2083	121.0	102.0	108.0		,105,168	-11.1	0.3	18	dbSNP_129	108	1188,7412	241.4+/-271.8	88,1012,3200	no	utr-5,coding-synonymous,coding-synonymous	ENOSF1	NM_001126123.3,NM_017512.5,NM_202758.3	,,	89,1131,5283	TT,TC,CC		13.814,2.7463,10.0646	,,	,35/444,56/451	706558	1309,11697	2203	4300	6503	SO:0001819	synonymous_variant	55556	exon2			GGCAGCCGAGTAG	X67098	CCDS11822.1, CCDS11823.1, CCDS45821.1	18p11.32	2005-01-26			ENSG00000132199	ENSG00000132199			30365	protein-coding gene	gene with protein product		607427				14508106	Standard	NM_001126123		Approved	HSRTSBETA, rTS, TYMSAS	uc002kku.4	Q7L5Y1	OTTHUMG00000131470	ENST00000251101.7:c.105G>A	18.37:g.706558C>T		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	83	35	0.421687	NM_202758	A6NMP3|A8K9R5|B3KSL6|B3KXE4|D3DUH0|Q15407|Q15594|Q15595|Q6ZS08|Q9HAS5|Q9HAS6	Silent	SNP	ENST00000251101.7	37	CCDS11822.1																																																																																			C|0.886;T|0.114	0.114	strong		0.493	ENOSF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254312.2	NM_017512	
OR5P2	120065	hgsc.bcm.edu	37	11	7817856	7817856	+	Missense_Mutation	SNP	C	C	T	rs78460198	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:7817856C>T	ENST00000329434.2	-	1	664	c.634G>A	c.(634-636)Gtc>Atc	p.V212I	RP11-35J10.5_ENST00000527565.1_lincRNA	NM_153444.1	NP_703145.1	Q8WZ92	OR5P2_HUMAN	olfactory receptor, family 5, subfamily P, member 2	212						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.V212I(1)		central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(4)	22				Epithelial(150;8.62e-08)|BRCA - Breast invasive adenocarcinoma(625;0.189)		ATGTAGCAGACGGCTATGACA	0.493													C|||	1185	0.236621	0.3472	0.2911	5008	,	,		18815	0.128		0.2763	False		,,,				2504	0.1196				p.V212I		Atlas-SNP	.											OR5P2,colon,carcinoma,0,2	OR5P2	68	2	1	Substitution - Missense(1)	large_intestine(1)	c.G634A						PASS	.	C	ILE/VAL	1371,2839		401,569,1135	99.0	104.0	102.0		634	-11.0	0.0	11	dbSNP_131	102	2425,6159		393,1639,2260	no	missense	OR5P2	NM_153444.1	29	794,2208,3395	TT,TC,CC		28.2502,32.5653,29.6702	benign	212/323	7817856	3796,8998	2105	4292	6397	SO:0001583	missense	120065	exon1			AGCAGACGGCTAT	AF173006	CCDS7782.1	11p15.4	2012-08-09			ENSG00000183303	ENSG00000183303		"""GPCR / Class A : Olfactory receptors"""	14783	protein-coding gene	gene with protein product							Standard	NM_153444		Approved	JCG3	uc001mfp.1	Q8WZ92	OTTHUMG00000165668	ENST00000329434.2:c.634G>A	11.37:g.7817856C>T	ENSP00000331823:p.Val212Ile	Somatic	196	0	0		WXS	Illumina HiSeq	Phase_I	183	149	0.814208	NM_153444	Q3MIS8	Missense_Mutation	SNP	ENST00000329434.2	37	CCDS7782.1	586	0.2683150183150183	180	0.36585365853658536	100	0.27624309392265195	84	0.14685314685314685	222	0.2928759894459103	C	0.005	-2.119520	0.00346	0.325653	0.282502	ENSG00000183303	ENST00000329434	T	0.37235	1.21	5.5	-11.0	0.00169	GPCR, rhodopsin-like superfamily (1);	0.814212	0.11083	N	0.601638	T	0.00012	0.0000	N	0.11000	0.08	0.80722	P	0.0	B	0.13594	0.008	B	0.18263	0.021	T	0.36578	-0.9742	9	0.02654	T	1	-5.754	20.7759	0.99721	0.0:0.328:0.0:0.672	.	212	Q8WZ92	OR5P2_HUMAN	I	212	ENSP00000331823:V212I	ENSP00000331823:V212I	V	-	1	0	OR5P2	7774432	0.000000	0.05858	0.000000	0.03702	0.379000	0.30106	-6.285000	0.00072	-3.387000	0.00174	-1.300000	0.01332	GTC	C|0.739;T|0.261	0.261	strong		0.493	OR5P2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385696.1	NM_153444	
MEFV	4210	hgsc.bcm.edu	37	16	3299749	3299749	+	Silent	SNP	G	G	A	rs224213	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:3299749G>A	ENST00000219596.1	-	3	981	c.942C>T	c.(940-942)cgC>cgT	p.R314R	MEFV_ENST00000339854.4_Silent_p.R134R|MEFV_ENST00000541159.1_Silent_p.R103R|MEFV_ENST00000536379.1_Silent_p.R103R	NM_000243.2	NP_000234.1	O15553	MEFV_HUMAN	Mediterranean fever	314					inflammatory response (GO:0006954)|innate immune response (GO:0045087)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-1 beta production (GO:0032691)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of macrophage inflammatory protein 1 alpha production (GO:0071641)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of cysteine-type endopeptidase activity (GO:2001056)	cell projection (GO:0042995)|cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|nucleus (GO:0005634)	actin binding (GO:0003779)|zinc ion binding (GO:0008270)			NS(2)|biliary_tract(1)|breast(5)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(6)|lung(19)|ovary(3)|prostate(1)|skin(6)	50						GGGCGTGGCAGCGGGGACTCG	0.607													A|||	3459	0.690695	0.7322	0.6412	5008	,	,		19762	0.7083		0.5606	False		,,,				2504	0.7853				p.R314R		Atlas-SNP	.											.	MEFV	170	.	0			c.C942T						PASS	.	A	,	3101,1293	431.4+/-342.9	1092,917,188	35.0	39.0	38.0		942,309	-5.9	0.0	16	dbSNP_79	38	4639,3961	544.1+/-384.5	1289,2061,950	no	coding-synonymous,coding-synonymous	MEFV	NM_000243.2,NM_001198536.1	,	2381,2978,1138	AA,AG,GG		46.0581,29.4265,40.434	,	314/782,103/446	3299749	7740,5254	2197	4300	6497	SO:0001819	synonymous_variant	4210	exon3			GTGGCAGCGGGGA	AF018080	CCDS10498.1, CCDS55981.1	16p13.3	2014-09-17			ENSG00000103313	ENSG00000103313		"""Tripartite motif containing / Tripartite motif containing"""	6998	protein-coding gene	gene with protein product	"""pyrin"""	608107		MEF		9288094	Standard	NM_000243		Approved	FMF, TRIM20	uc002cun.1	O15553	OTTHUMG00000129324	ENST00000219596.1:c.942C>T	16.37:g.3299749G>A		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	127	36	0.283465	NM_000243	D3DUC0|F5H0Q3|Q3MJ84|Q96PN4|Q96PN5	Silent	SNP	ENST00000219596.1	37	CCDS10498.1																																																																																			G|0.373;A|0.627	0.627	strong		0.607	MEFV-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251464.1	NM_000243	
CR1	1378	hgsc.bcm.edu	37	1	207790088	207790088	+	Missense_Mutation	SNP	C	C	G	rs3811381	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:207790088C>G	ENST00000367049.4	+	41	6830	c.6830C>G	c.(6829-6831)cCt>cGt	p.P2277R	CR1_ENST00000367053.1_Missense_Mutation_p.P1827R|CR1_ENST00000367052.1_Missense_Mutation_p.P1827R|CR1_ENST00000367051.1_Missense_Mutation_p.P1827R|CR1_ENST00000400960.2_Missense_Mutation_p.P1827R	NM_000651.4	NP_000642.3	P17927	CR1_HUMAN	complement component (3b/4b) receptor 1 (Knops blood group)	1827					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						ACAAGTGACCCTCAAGGGAAT	0.517													C|||	1316	0.26278	0.1172	0.2608	5008	,	,		19452	0.3224		0.1809	False		,,,				2504	0.4836				p.P2277R		Atlas-SNP	.											.	CR1	354	.	0			c.C6830G	GRCh37	CM025385	CR1	M	rs3811381	PASS	.	C	ARG/PRO,ARG/PRO	498,3414		34,430,1492	146.0	147.0	147.0		5480,6830	-5.6	0.0	1	dbSNP_107	147	1508,6762		125,1258,2752	no	missense,missense	CR1	NM_000573.3,NM_000651.4	103,103	159,1688,4244	GG,GC,CC		18.2346,12.7301,16.4669	benign,benign	1827/2040,2277/2490	207790088	2006,10176	1956	4135	6091	SO:0001583	missense	1378	exon41			GTGACCCTCAAGG	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.6830C>G	1.37:g.207790088C>G	ENSP00000356016:p.Pro2277Arg	Somatic	245	1	0.00408163		WXS	Illumina HiSeq	Phase_I	190	89	0.468421	NM_000651	Q16744|Q16745|Q5SR43|Q5SR45|Q9UQV2	Missense_Mutation	SNP	ENST00000367049.4	37	CCDS44308.1	429|429	0.19642857142857142|0.19642857142857142	64|64	0.13008130081300814|0.13008130081300814	102|102	0.281767955801105|0.281767955801105	131|131	0.229020979020979|0.229020979020979	132|132	0.1741424802110818|0.1741424802110818	C|C	0.010|0.010	-1.745772|-1.745772	0.00669|0.00669	0.127301|0.127301	0.182346|0.182346	ENSG00000203710|ENSG00000203710	ENST00000529814|ENST00000367052;ENST00000367051;ENST00000367053;ENST00000400960;ENST00000367049	.|T;T;T;T;T	.|0.21543	.|2.0;2.0;2.0;2.0;2.0	4.15|4.15	-5.58|-5.58	0.02512|0.02512	.|Complement control module (2);Sushi/SCR/CCP (3);	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.05078|0.05078	-0.115|-0.115	0.80722|0.80722	P|P	0.0|0.0	.|B;P	.|0.38711	.|0.005;0.643	.|B;B	.|0.32211	.|0.032;0.142	T|T	0.39643|0.39643	-0.9604|-0.9604	4|8	.|0.11794	.|T	.|0.64	.|.	3.1972|3.1972	0.06637|0.06637	0.5482:0.1261:0.1987:0.127|0.5482:0.1261:0.1987:0.127	rs3811381;rs56791502|rs3811381;rs56791502	.|1827;2277	.|P17927;E9PDY4	.|CR1_HUMAN;.	V|R	450|1827;1827;1827;1827;2277	.|ENSP00000356019:P1827R;ENSP00000356018:P1827R;ENSP00000356020:P1827R;ENSP00000383744:P1827R;ENSP00000356016:P2277R	.|ENSP00000356016:P2277R	L|P	+|+	1|2	0|0	CR1|CR1	205856711|205856711	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.021000|0.021000	0.10359|0.10359	-0.775000|-0.775000	0.04679|0.04679	-1.266000|-1.266000	0.02446|0.02446	-2.118000|-2.118000	0.00350|0.00350	CTC|CCT	C|0.800;G|0.200	0.200	strong		0.517	CR1-012	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382527.1	NM_000573	
PALLD	23022	hgsc.bcm.edu	37	4	169433326	169433326	+	Missense_Mutation	SNP	T	T	C	rs397718410|rs7655494|rs373066707	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:169433326T>C	ENST00000505667.1	+	2	844	c.671T>C	c.(670-672)aTg>aCg	p.M224T	PALLD_ENST00000261509.6_Missense_Mutation_p.M224T|PALLD_ENST00000335742.7_5'UTR|PALLD_ENST00000333488.4_Missense_Mutation_p.M101T			Q8WX93	PALLD_HUMAN	palladin, cytoskeletal associated protein	224			M -> I (in dbSNP:rs7671781).|M -> T (in dbSNP:rs7655494). {ECO:0000269|PubMed:14702039}.		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)		CAGAGCCCTATGGAAGACCAA	0.577									Pancreatic Cancer, Familial Clustering of				C|||	1200	0.239617	0.2368	0.1844	5008	,	,		17132	0.1935		0.33	False		,,,				2504	0.2372				p.M224T	Esophageal Squamous(109;1482 1532 18347 40239 51172)	Atlas-SNP	.											.	PALLD	179	.	0			c.T671C						PASS	.	C	THR/MET,THR/MET	1068,3338		151,766,1286	101.0	106.0	104.0		671,671	3.7	0.1	4	dbSNP_116	104	2621,5979		461,1699,2140	yes	missense,missense	PALLD	NM_001166108.1,NM_016081.3	81,81	612,2465,3426	CC,CT,TT		30.4767,24.2397,28.3638	benign,benign	224/1124,224/1107	169433326	3689,9317	2203	4300	6503	SO:0001583	missense	23022	exon2	Familial Cancer Database	incl.: Hereditary Pancreatic Adenocarcinoma, Insulin-Dependent Diabetes Mellitus - Exocrine Insufficiency - Familial Pancreatic Cancer, PNCA1	GCCCTATGGAAGA	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.671T>C	4.37:g.169433326T>C	ENSP00000425556:p.Met224Thr	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	56	56	1	NM_001166108	B3KTG2|B5MD56|B7ZMM5|Q7L3E0|Q7Z3W0|Q86WE8|Q8N1M2|Q9UGA0|Q9UQF5|Q9Y2J6|Q9Y3E9	Missense_Mutation	SNP	ENST00000505667.1	37	CCDS54818.1	447	0.20467032967032966	90	0.18292682926829268	68	0.1878453038674033	84	0.14685314685314685	205	0.2704485488126649	C	0.001	-2.912011	0.00056	0.242397	0.304767	ENSG00000129116	ENST00000261509;ENST00000505667;ENST00000508898;ENST00000333488	T;T;T;T	0.62364	0.14;0.41;0.03;0.11	5.41	3.67	0.42095	.	0.307711	0.17926	N	0.157333	T	0.00012	0.0000	N	0.01048	-1.04	0.52099	P	5.8000000000002494E-5	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.24905	-1.0147	9	0.06365	T	0.9	.	1.7516	0.02973	0.1746:0.4889:0.1151:0.2214	rs7655494;rs7655494	224;224	B7ZMM5;B2RTX2	.;.	T	224;224;203;101	ENSP00000261509:M224T;ENSP00000425556:M224T;ENSP00000423063:M203T;ENSP00000328945:M101T	ENSP00000261509:M224T	M	+	2	0	PALLD	169669901	0.008000	0.16893	0.120000	0.21714	0.007000	0.05969	0.369000	0.20416	0.273000	0.22049	-0.880000	0.02959	ATG	T|0.732;C|0.268	0.268	strong		0.577	PALLD-002	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000363762.1	NM_016081	
LRP3	4037	hgsc.bcm.edu	37	19	33693785	33693785	+	Silent	SNP	G	G	A	rs1056034	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:33693785G>A	ENST00000253193.7	+	3	355	c.153G>A	c.(151-153)acG>acA	p.T51T		NM_002333.3	NP_002324.2	O75074	LRP3_HUMAN	low density lipoprotein receptor-related protein 3	51	CUB 1. {ECO:0000255|PROSITE- ProRule:PRU00059}.				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)					AGCAGCACACGGAGCGGCGTG	0.652													G|||	262	0.0523163	0.0151	0.0793	5008	,	,		19186	0.121		0.0447	False		,,,				2504	0.0204				p.T51T		Atlas-SNP	.											LRP3,NS,carcinoma,+1,1	LRP3	46	1	0			c.G153A						PASS	.	G		140,4264		1,138,2063	37.0	30.0	32.0		153	-10.2	0.3	19	dbSNP_86	32	454,8146		14,426,3860	no	coding-synonymous	LRP3	NM_002333.3		15,564,5923	AA,AG,GG		5.2791,3.1789,4.5678		51/771	33693785	594,12410	2202	4300	6502	SO:0001819	synonymous_variant	4037	exon3			GCACACGGAGCGG	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.153G>A	19.37:g.33693785G>A		Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	128	58	0.453125	NM_002333	B3KQD6|B4DKF2	Silent	SNP	ENST00000253193.7	37	CCDS12430.1																																																																																			G|0.952;A|0.048	0.048	strong		0.652	LRP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450842.4		
GPR112	139378	hgsc.bcm.edu	37	X	135431358	135431358	+	Silent	SNP	C	C	T	rs5930933	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:135431358C>T	ENST00000394143.1	+	6	5784	c.5493C>T	c.(5491-5493)ccC>ccT	p.P1831P	GPR112_ENST00000412101.1_Silent_p.P1626P|GPR112_ENST00000370652.1_Silent_p.P1831P|GPR112_ENST00000287534.4_Silent_p.P1768P|GPR112_ENST00000394141.1_Silent_p.P1626P	NM_153834.3	NP_722576.3	Q8IZF6	GP112_HUMAN	G protein-coupled receptor 112	1831					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(13)|central_nervous_system(2)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(33)|lung(97)|ovary(5)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(2)	199	Acute lymphoblastic leukemia(192;0.000127)					CAACTCTACCCTCTTTGACAT	0.433													c|||	1787	0.473377	0.4236	0.3573	3775	,	,		16215	0.2778		0.3797	False		,,,				2504	0.3241				p.P1831P		Atlas-SNP	.											.	GPR112	459	.	0			c.C5493T						PASS	.			2112,1723		495,811,311,326,260	143.0	125.0	131.0		5493	0.4	0.0	X	dbSNP_114	131	3228,3500		567,1180,914,681,958	yes	coding-synonymous	GPR112	NM_153834.3		1062,1991,1225,1007,1218	TT,TC,T,CC,C		47.9786,44.9283,49.4462		1831/3081	135431358	5340,5223	2203	4300	6503	SO:0001819	synonymous_variant	139378	exon6			TCTACCCTCTTTG	AY140954	CCDS35409.1	Xq26.3	2014-08-08			ENSG00000156920	ENSG00000156920		"""-"", ""GPCR / Class B : Orphans"""	18992	protein-coding gene	gene with protein product						12435584	Standard	XM_005262367		Approved	RP1-299I16, PGR17	uc004ezu.1	Q8IZF6	OTTHUMG00000022508	ENST00000394143.1:c.5493C>T	X.37:g.135431358C>T		Somatic	185	1	0.00540541		WXS	Illumina HiSeq	Phase_I	102	101	0.990196	NM_153834	A2A2J1|A2A2J2|Q5EGP2|Q86SM6	Silent	SNP	ENST00000394143.1	37	CCDS35409.1																																																																																			C|0.507;0|0.003	.	strong		0.433	GPR112-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000286639.1		
NPHP4	261734	hgsc.bcm.edu	37	1	5940243	5940243	+	Missense_Mutation	SNP	G	G	A	rs17472401	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:5940243G>A	ENST00000378156.4	-	19	2807	c.2542C>T	c.(2542-2544)Cgg>Tgg	p.R848W	NPHP4_ENST00000478423.2_5'UTR	NM_015102.3	NP_055917.1	O75161	NPHP4_HUMAN	nephronophthisis 4	848			R -> W (does not affect interaction with RPGRIP1L; dbSNP:rs17472401). {ECO:0000269|PubMed:12205563, ECO:0000269|PubMed:15776426}.		actin cytoskeleton organization (GO:0030036)|hippo signaling (GO:0035329)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|retina development in camera-type eye (GO:0060041)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|visual behavior (GO:0007632)	cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytosol (GO:0005829)|membrane (GO:0016020)|nonmotile primary cilium (GO:0031513)|tight junction (GO:0005923)	structural molecule activity (GO:0005198)			NS(1)|breast(2)|cervix(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(15)|ovary(2)|pancreas(1)|prostate(4)	47	Ovarian(185;0.0634)	all_cancers(23;7.53e-41)|all_epithelial(116;3.96e-23)|all_lung(118;5.12e-09)|all_hematologic(16;5.45e-07)|Lung NSC(185;5.49e-07)|all_neural(13;3.21e-06)|Acute lymphoblastic leukemia(12;3.44e-05)|Breast(487;0.000601)|Renal(390;0.0007)|Colorectal(325;0.00113)|Hepatocellular(190;0.00213)|Glioma(11;0.00223)|Myeloproliferative disorder(586;0.0256)|Ovarian(437;0.04)|Lung SC(97;0.128)|Medulloblastoma(700;0.213)		Epithelial(90;1.69e-36)|GBM - Glioblastoma multiforme(13;5.07e-29)|OV - Ovarian serous cystadenocarcinoma(86;1.05e-19)|Colorectal(212;4.54e-07)|COAD - Colon adenocarcinoma(227;3.14e-05)|Kidney(185;0.00012)|BRCA - Breast invasive adenocarcinoma(365;0.00102)|KIRC - Kidney renal clear cell carcinoma(229;0.00179)|STAD - Stomach adenocarcinoma(132;0.00472)|READ - Rectum adenocarcinoma(331;0.0649)		GAGATGACCCGAGATCTGGAC	0.527													G|||	38	0.00758786	0.0015	0.0086	5008	,	,		21450	0.0		0.0278	False		,,,				2504	0.002				p.R848W		Atlas-SNP	.											.	NPHP4	119	.	0			c.C2542T	GRCh37	CM022976	NPHP4	M	rs17472401	PASS	.	G	TRP/ARG	15,4117		0,15,2051	82.0	89.0	87.0		2542	0.8	0.2	1	dbSNP_123	87	184,8206		2,180,4013	yes	missense	NPHP4	NM_015102.3	101	2,195,6064	AA,AG,GG		2.1931,0.363,1.5892	probably-damaging	848/1427	5940243	199,12323	2066	4195	6261	SO:0001583	missense	261734	exon19			TGACCCGAGATCT	AB014573	CCDS44052.1	1p36	2010-03-26			ENSG00000131697	ENSG00000131697			19104	protein-coding gene	gene with protein product	"""nephroretinin"", ""nephrocystin-4"", ""POC10 centriolar protein homolog (Chlamydomonas)"""	607215				11920287, 12205563	Standard	XR_244787		Approved	SLSN4, KIAA0673, POC10	uc001alq.2	O75161	OTTHUMG00000000701	ENST00000378156.4:c.2542C>T	1.37:g.5940243G>A	ENSP00000367398:p.Arg848Trp	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	72	26	0.361111	NM_015102	Q8IWC0	Missense_Mutation	SNP	ENST00000378156.4	37	CCDS44052.1	26	0.011904761904761904	1	0.0020325203252032522	4	0.011049723756906077	0	0.0	21	0.027704485488126648	G	12.26	1.883773	0.33255	0.00363	0.021931	ENSG00000131697	ENST00000378156	D	0.88124	-2.34	5.21	0.782	0.18567	.	0.153997	0.41500	D	0.000868	T	0.81059	0.4744	M	0.66939	2.045	0.23070	N	0.99835	D	0.89917	1.0	D	0.74674	0.984	T	0.79652	-0.1714	10	0.72032	D	0.01	.	12.097	0.53761	0.0:0.0:0.4162:0.5838	rs17472401;rs52814007;rs17472401	848	O75161	NPHP4_HUMAN	W	848	ENSP00000367398:R848W	ENSP00000367398:R848W	R	-	1	2	NPHP4	5862830	0.900000	0.30661	0.234000	0.24042	0.013000	0.08279	1.160000	0.31761	0.154000	0.19237	0.561000	0.74099	CGG	G|0.986;A|0.014	0.014	strong		0.527	NPHP4-001	KNOWN	non_canonical_polymorphism|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001715.2		
FBN3	84467	hgsc.bcm.edu	37	19	8139977	8139977	+	Silent	SNP	G	G	A	rs61729621	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:8139977G>A	ENST00000600128.1	-	61	8094	c.7680C>T	c.(7678-7680)caC>caT	p.H2560H	FBN3_ENST00000270509.2_Silent_p.H2560H|FBN3_ENST00000601739.1_Silent_p.H2560H			Q75N90	FBN3_HUMAN	fibrillin 3	2560	EGF-like 42; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.					proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(9)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(15)|lung(53)|ovary(7)|pancreas(2)|prostate(3)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	132						CCCACTGGGAGTGCTGGGTGA	0.617													G|||	112	0.0223642	0.0083	0.0346	5008	,	,		19034	0.0069		0.0417	False		,,,				2504	0.0286				p.H2560H		Atlas-SNP	.											.	FBN3	300	.	0			c.C7680T						PASS	.	G		49,4357		1,47,2155	44.0	49.0	47.0		7680	2.3	1.0	19	dbSNP_129	47	391,8209		7,377,3916	no	coding-synonymous	FBN3	NM_032447.3		8,424,6071	AA,AG,GG		4.5465,1.1121,3.3831		2560/2810	8139977	440,12566	2203	4300	6503	SO:0001819	synonymous_variant	84467	exon60			CTGGGAGTGCTGG		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.7680C>T	19.37:g.8139977G>A		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	56	31	0.553571	NM_032447	Q75N91|Q75N92|Q75N93|Q86SJ5|Q96JP8	Silent	SNP	ENST00000600128.1	37	CCDS12196.1																																																																																			G|0.969;A|0.031	0.031	strong		0.617	FBN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461428.2	NM_032447	
IFITM2	10581	hgsc.bcm.edu	37	11	309127	309127	+	Missense_Mutation	SNP	A	A	G	rs1059091	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:309127A>G	ENST00000399817.4	+	2	391	c.361A>G	c.(361-363)Atc>Gtc	p.I121V	RP11-326C3.7_ENST00000526612.1_RNA|IFITM2_ENST00000533141.1_Missense_Mutation_p.I101V|IFITM2_ENST00000602569.1_Missense_Mutation_p.I101V	NM_006435.2	NP_006426.2	Q01629	IFM2_HUMAN	interferon induced transmembrane protein 2	121			I -> V (in dbSNP:rs1059091). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:1906403}.		cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|immune response (GO:0006955)|negative regulation of viral entry into host cell (GO:0046597)|negative regulation of viral genome replication (GO:0045071)|response to interferon-alpha (GO:0035455)|response to interferon-beta (GO:0035456)|response to interferon-gamma (GO:0034341)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(1)|kidney(1)|large_intestine(1)|lung(1)	4		all_cancers(49;2e-09)|all_epithelial(84;3.36e-06)|Breast(177;0.000162)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.0538)|all_lung(207;0.0713)		all cancers(45;5.73e-28)|Epithelial(43;3.42e-27)|OV - Ovarian serous cystadenocarcinoma(40;1.14e-20)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0328)|LUSC - Lung squamous cell carcinoma(625;0.122)		CATTCTGCTCATCATCATCCC	0.577													N|||	2707	0.540535	0.5976	0.4553	5008	,	,		21628	0.6944		0.332	False		,,,				2504	0.5798				p.I121V		Atlas-SNP	.											.	IFITM2	21	.	0			c.A361G						PASS	.	G	VAL/ILE	2248,1872		615,1018,427	83.0	84.0	84.0		361	-3.8	0.0	11	dbSNP_86	84	2757,5609		453,1851,1879	yes	missense	IFITM2	NM_006435.2	29	1068,2869,2306	GG,GA,AA		32.9548,45.4369,40.0849	benign	121/133	309127	5005,7481	2060	4183	6243	SO:0001583	missense	10581	exon2			CTGCTCATCATCA	X57351	CCDS41583.1	11p15.5	2012-03-13	2012-03-13		ENSG00000185201	ENSG00000185201			5413	protein-coding gene	gene with protein product		605578	"""interferon induced transmembrane protein 2 (1-8D)"""			1906403	Standard	NM_006435		Approved	1-8D	uc001lox.4	Q01629		ENST00000399817.4:c.361A>G	11.37:g.309127A>G	ENSP00000382714:p.Ile121Val	Somatic	322	1	0.00310559		WXS	Illumina HiSeq	Phase_I	378	300	0.793651	NM_006435	Q6FH82|Q96DA8	Missense_Mutation	SNP	ENST00000399817.4	37	CCDS41583.1	1097|1097	0.5022893772893773|0.5022893772893773	287|287	0.5833333333333334|0.5833333333333334	160|160	0.4419889502762431|0.4419889502762431	396|396	0.6923076923076923|0.6923076923076923	254|254	0.33509234828496043|0.33509234828496043	G|G	8.381|8.381	0.837569|0.837569	0.16891|0.16891	0.545631|0.545631	0.329548|0.329548	ENSG00000185201|ENSG00000185201	ENST00000327366|ENST00000533141;ENST00000399817	.|D;D	.|0.86627	.|-2.15;-2.15	2.35|2.35	-3.77|-3.77	0.04346|0.04346	.|.	1.013090|.	0.07963|.	N|.	0.982712|.	T|T	0.00012|0.00012	0.0000|0.0000	M|M	0.69463|0.69463	2.115|2.115	0.80722|0.80722	P|P	0.0|0.0	.|B	.|0.02656	.|0.0	.|B	.|0.06405	.|0.002	T|T	0.42050|0.42050	-0.9474|-0.9474	6|8	0.87932|0.35671	D|T	0|0.21	-6.1667|-6.1667	4.3203|4.3203	0.11013|0.11013	0.3671:0.0:0.4565:0.1764|0.3671:0.0:0.4565:0.1764	rs1059091;rs3168356;rs3765194;rs17845234;rs17858050;rs1059091|rs1059091;rs3168356;rs3765194;rs17845234;rs17858050;rs1059091	.|121	.|Q01629	.|IFM2_HUMAN	R|V	117|101;121	.|ENSP00000434443:I101V;ENSP00000382714:I121V	ENSP00000327996:H117R|ENSP00000382714:I121V	H|I	+|+	2|1	0|0	IFITM2|IFITM2	299127|299127	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.004000|0.004000	0.04260|0.04260	-0.264000|-0.264000	0.08658|0.08658	-1.307000|-1.307000	0.02321|0.02321	-2.523000|-2.523000	0.00184|0.00184	CAT|ATC	A|0.607;C|0.000;G|0.393	0.393	strong		0.577	IFITM2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000383591.1	NM_006435	
CCDC110	256309	hgsc.bcm.edu	37	4	186382206	186382206	+	Silent	SNP	A	A	G	rs11132309	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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_ENST00000393540.3_Intron|CCDC110_ENST00000507501.1_5'UTR	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	137	0	0		WXS	Illumina HiSeq	Phase_I	98	38	0.387755	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	
POTEH	23784	hgsc.bcm.edu	37	22	16287673	16287673	+	Missense_Mutation	SNP	C	C	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:16287673C>G	ENST00000343518.6	-	1	264	c.213G>C	c.(211-213)tgG>tgC	p.W71C		NM_001136213.1	NP_001129685.1	Q6S545	POTEH_HUMAN	POTE ankyrin domain family, member H	71								p.W71C(1)		NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|lung(20)|ovary(1)|skin(7)|urinary_tract(2)	37						TCCCCCTGCACCAGGGGAAGC	0.582																																					p.W71C		Atlas-SNP	.											POTEH,NS,carcinoma,0,4	POTEH	114	4	1	Substitution - Missense(1)	NS(1)	c.G213C						scavenged	.						110.0	126.0	120.0					22																	16287673		2105	3940	6045	SO:0001583	missense	23784	exon1			CCTGCACCAGGGG	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.213G>C	22.37:g.16287673C>G	ENSP00000340610:p.Trp71Cys	Somatic	15	0	0		WXS	Illumina HiSeq	Phase_I	94	4	0.0425532	NM_001136213	A2CEK4|A6NCI1|A9Z1W0	Missense_Mutation	SNP	ENST00000343518.6	37	CCDS46658.1	.	.	.	.	.	.	.	.	.	.	.	0.001	-3.595853	0.00008	.	.	ENSG00000198062	ENST00000359587;ENST00000343518;ENST00000355872	T	0.25912	1.77	.	.	.	.	.	.	.	.	T	0.03608	0.0103	N	0.00321	-1.65	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.16012	-1.0417	7	0.02654	T	1	.	.	.	.	.	71	Q6S545	POTEH_HUMAN	C	71	ENSP00000340610:W71C	ENSP00000340610:W71C	W	-	3	0	POTEH	14667673	0.006000	0.16342	0.007000	0.13788	0.007000	0.05969	-0.619000	0.05572	-1.825000	0.01207	-1.799000	0.00621	TGG	.	.	none		0.582	POTEH-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000276918.4	NM_001136213	
NAV3	89795	hgsc.bcm.edu	37	12	78334179	78334179	+	Silent	SNP	A	A	G	rs17817265	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:78334179A>G	ENST00000397909.2	+	2	497	c.324A>G	c.(322-324)gcA>gcG	p.A108A	NAV3_ENST00000266692.7_Silent_p.A108A|NAV3_ENST00000228327.6_Silent_p.A108A|NAV3_ENST00000536525.2_Silent_p.A108A			Q8IVL0	NAV3_HUMAN	neuron navigator 3	108	CH. {ECO:0000255|PROSITE- ProRule:PRU00044}.					membrane (GO:0016020)|nuclear envelope (GO:0005635)				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						AAGACATTGCAGATGGAGTAC	0.453										HNSCC(70;0.22)			A|||	112	0.0223642	0.034	0.0216	5008	,	,		18214	0.0		0.0427	False		,,,				2504	0.0092				p.A108A		Atlas-SNP	.											.	NAV3	506	.	0			c.A324G						PASS	.	A		110,3722		3,104,1809	143.0	139.0	140.0		324	4.5	1.0	12	dbSNP_123	140	296,8008		6,284,3862	no	coding-synonymous	NAV3	NM_014903.4		9,388,5671	GG,GA,AA		3.5645,2.8706,3.3454		108/2364	78334179	406,11730	1916	4152	6068	SO:0001819	synonymous_variant	89795	exon2			CATTGCAGATGGA	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.324A>G	12.37:g.78334179A>G		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	139	71	0.510791	NM_014903	Q8NFW7|Q9Y2E7	Silent	SNP	ENST00000397909.2	37																																																																																				A|0.971;G|0.029	0.029	strong		0.453	NAV3-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000406812.1	NM_001024383	
PCNT	5116	hgsc.bcm.edu	37	21	47836653	47836653	+	Missense_Mutation	SNP	C	C	T	rs2070425	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:47836653C>T	ENST00000359568.5	+	30	6928	c.6821C>T	c.(6820-6822)cCg>cTg	p.P2274L	PCNT_ENST00000480896.1_3'UTR	NM_006031.5	NP_006022.3	O95613	PCNT_HUMAN	pericentrin	2274			P -> L (in dbSNP:rs2070425).		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)					ACCCAGGGGCCGGGGCTGCTT	0.692													C|||	1250	0.249601	0.1611	0.1686	5008	,	,		16607	0.3671		0.2942	False		,,,				2504	0.2597				p.P2274L		Atlas-SNP	.											.	PCNT	283	.	0			c.C6821T						PASS	.	C	LEU/PRO	653,3323		59,535,1394	19.0	23.0	22.0		6821	-0.6	0.0	21	dbSNP_96	22	2011,5839		262,1487,2176	yes	missense	PCNT	NM_006031.5	98	321,2022,3570	TT,TC,CC		25.6178,16.4235,22.5266	probably-damaging	2274/3337	47836653	2664,9162	1988	3925	5913	SO:0001583	missense	5116	exon30			AGGGGCCGGGGCT	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.6821C>T	21.37:g.47836653C>T	ENSP00000352572:p.Pro2274Leu	Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	75	26	0.346667	NM_006031	O43152|Q7Z7C9	Missense_Mutation	SNP	ENST00000359568.5	37	CCDS33592.1	594	0.27197802197802196	78	0.15853658536585366	73	0.20165745856353592	229	0.40034965034965037	214	0.28232189973614774	C	0.064	-1.217766	0.01542	0.164235	0.256178	ENSG00000160299	ENST00000359568	T	0.01422	4.91	4.57	-0.651	0.11454	.	0.870858	0.09368	N	0.811814	T	0.00012	0.0000	N	0.03115	-0.41	0.80722	P	0.0	B;B	0.15141	0.012;0.001	B;B	0.10450	0.005;0.001	T	0.20472	-1.0274	9	0.15066	T	0.55	.	4.5198	0.11954	0.0:0.4651:0.1559:0.379	rs2070425	2156;2274	O95613-2;O95613	.;PCNT_HUMAN	L	2274	ENSP00000352572:P2274L	ENSP00000352572:P2274L	P	+	2	0	PCNT	46661081	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.039000	0.13884	-0.235000	0.09767	-0.794000	0.03295	CCG	C|0.735;T|0.265	0.265	strong		0.692	PCNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207336.1	NM_006031	
NRP1	8829	hgsc.bcm.edu	37	10	33475282	33475282	+	Missense_Mutation	SNP	C	C	T	rs2228638	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:33475282C>T	ENST00000265371.4	-	15	2722	c.2197G>A	c.(2197-2199)Gtc>Atc	p.V733I	NRP1_ENST00000395995.1_Missense_Mutation_p.V733I|NRP1_ENST00000374867.2_Missense_Mutation_p.V733I|NRP1_ENST00000374875.1_Missense_Mutation_p.V545I			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						PASS	.	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	127	0	0		WXS	Illumina HiSeq	Phase_I	115	52	0.452174	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		
FAM102A	399665	hgsc.bcm.edu	37	9	130742413	130742413	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:130742413C>T	ENST00000373095.1	-	1	379	c.4G>A	c.(4-6)Gct>Act	p.A2T		NM_001035254.2	NP_001030331.1	Q5T9C2	F102A_HUMAN	family with sequence similarity 102, member A	2										breast(1)|cervix(1)|large_intestine(3)|lung(1)|ovary(4)	10						ATCAAGAAAGCCATGAGCGAG	0.517																																					p.A2T		Atlas-SNP	.											.	FAM102A	32	.	0			c.G4A						PASS	.						89.0	103.0	98.0					9																	130742413		2203	4300	6503	SO:0001583	missense	399665	exon1			AGAAAGCCATGAG		CCDS6888.1, CCDS35150.1	9q34.11	2012-11-05	2005-11-17	2005-11-17	ENSG00000167106	ENSG00000167106			31419	protein-coding gene	gene with protein product	"""sym-3 homolog A (C. elegans)"""	610891	"""chromosome 9 open reading frame 132"""	C9orf132			Standard	NM_001035254		Approved	Eeig1, bA203J24.7, SYM-3A	uc004bsx.2	Q5T9C2	OTTHUMG00000020720	ENST00000373095.1:c.4G>A	9.37:g.130742413C>T	ENSP00000362187:p.Ala2Thr	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	68	27	0.397059	NM_001035254	A2A329|Q8TEL4	Missense_Mutation	SNP	ENST00000373095.1	37	CCDS35150.1	.	.	.	.	.	.	.	.	.	.	C	16.50	3.141355	0.57044	.	.	ENSG00000167106	ENST00000373095	.	.	.	4.76	4.76	0.60689	.	0.117104	0.56097	D	0.000025	T	0.54013	0.1832	L	0.43152	1.355	0.80722	D	1	B	0.29162	0.235	B	0.17098	0.017	T	0.55023	-0.8205	9	0.42905	T	0.14	-9.6451	16.7632	0.85517	0.0:1.0:0.0:0.0	.	2	Q5T9C2	F102A_HUMAN	T	2	.	ENSP00000362187:A2T	A	-	1	0	FAM102A	129782234	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.711000	0.54868	2.185000	0.69588	0.462000	0.41574	GCT	.	.	none		0.517	FAM102A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054298.2		
ABCB8	11194	hgsc.bcm.edu	37	7	150730999	150730999	+	Missense_Mutation	SNP	G	G	A	rs4148844	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:150730999G>A	ENST00000297504.6	+	3	520	c.454G>A	c.(454-456)Gtc>Atc	p.V152I	ABCB8_ENST00000477092.1_Missense_Mutation_p.V135I|ABCB8_ENST00000542328.1_Intron|ABCB8_ENST00000498578.1_Missense_Mutation_p.V135I|ABCB8_ENST00000358849.4_Missense_Mutation_p.V135I|ABCB8_ENST00000356058.4_Missense_Mutation_p.V172I|ABCB8_ENST00000477719.1_Missense_Mutation_p.V135I|ABCB8_ENST00000493338.1_3'UTR			Q9NUT2	ABCB8_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 8	152	ABC transmembrane type-1. {ECO:0000255|PROSITE-ProRule:PRU00441}.		V -> I (in dbSNP:rs4148844). {ECO:0000269|PubMed:11829140}.		transmembrane transport (GO:0055085)|transport (GO:0006810)	ATP-binding cassette (ABC) transporter complex (GO:0043190)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial envelope (GO:0005740)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(8)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	26			OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)	Doxorubicin(DB00997)	GGGGGTAGCCGTCGTGGTGAG	0.632													G|||	299	0.0597045	0.0809	0.049	5008	,	,		18874	0.0615		0.0497	False		,,,				2504	0.047				p.V135I		Atlas-SNP	.											ABCB8,NS,carcinoma,-2,1	ABCB8	65	1	0			c.G403A						PASS	.	G	ILE/VAL	286,4120	158.5+/-191.2	4,278,1921	41.0	39.0	39.0		403	0.4	0.9	7	dbSNP_110	39	393,8207	126.2+/-184.7	9,375,3916	yes	missense	ABCB8	NM_007188.3	29	13,653,5837	AA,AG,GG		4.5698,6.4911,5.2207	benign	135/719	150730999	679,12327	2203	4300	6503	SO:0001583	missense	11194	exon2			GTAGCCGTCGTGG	AF047690	CCDS5913.1, CCDS64798.1, CCDS64799.1, CCDS64800.1	7q36.1	2012-05-16			ENSG00000197150	ENSG00000197150		"""ATP binding cassette transporters / subfamily B"""	49	protein-coding gene	gene with protein product	"""mitochondrial ABC protein"""	605464				8894702	Standard	NM_001282291		Approved	EST328128, M-ABC1, MABC1	uc003wik.4	Q9NUT2	OTTHUMG00000158686	ENST00000297504.6:c.454G>A	7.37:g.150730999G>A	ENSP00000297504:p.Val152Ile	Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	45	20	0.444444	NM_007188	A5D8W3|B2RBL8|B3KND2|B4DG02|G3XAP3|O95787|Q53GM0	Missense_Mutation	SNP	ENST00000297504.6	37		135	0.061813186813186816	36	0.07317073170731707	17	0.04696132596685083	43	0.07517482517482517	39	0.051451187335092345	G	0.743	-0.775803	0.02951	0.064911	0.045698	ENSG00000197150	ENST00000358849;ENST00000360651;ENST00000297504;ENST00000498578;ENST00000356058;ENST00000477719;ENST00000477092	D;D;D;D;D;D	0.87887	-2.31;-2.31;-2.31;-2.31;-2.31;-2.31	4.18	0.441	0.16577	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1);	0.237327	0.43110	N	0.000609	T	0.12518	0.0304	N	0.16903	0.455	0.30341	N	0.785671	B;B;B;B;B	0.12630	0.002;0.002;0.001;0.006;0.003	B;B;B;B;B	0.19946	0.016;0.016;0.01;0.027;0.007	T	0.29336	-1.0015	10	0.11794	T	0.64	-4.5688	6.3135	0.21178	0.6842:0.0:0.3158:0.0	rs4148844;rs11553420;rs59240019;rs4148844	135;152;135;135;172	A5D8W3;Q9NUT2;Q9NUT2-2;C9JTY4;E7ENE8	.;ABCB8_HUMAN;.;.;.	I	135;118;152;135;172;135;135	ENSP00000351717:V135I;ENSP00000297504:V152I;ENSP00000418271:V135I;ENSP00000348353:V172I;ENSP00000419891:V135I;ENSP00000419558:V135I	ENSP00000297504:V152I	V	+	1	0	ABCB8	150361932	0.955000	0.32602	0.918000	0.36340	0.729000	0.41735	-0.014000	0.12656	-0.008000	0.14320	-1.267000	0.01435	GTC	G|0.940;A|0.060	0.060	strong		0.632	ABCB8-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351733.2	NM_007188	
SERPINB8	5271	hgsc.bcm.edu	37	18	61654463	61654463	+	Missense_Mutation	SNP	A	A	G	rs3826616	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:61654463A>G	ENST00000397985.2	+	7	1332	c.1076A>G	c.(1075-1077)cAc>cGc	p.H359R	SERPINB8_ENST00000353706.2_Missense_Mutation_p.H359R|SERPINB8_ENST00000542677.1_Missense_Mutation_p.H177R|SERPINB8_ENST00000493661.1_Intron	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	98	0	0		WXS	Illumina HiSeq	Phase_I	121	75	0.619835	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	
USP8	9101	hgsc.bcm.edu	37	15	50785016	50785016	+	Missense_Mutation	SNP	A	A	G	rs148783236	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:50785016A>G	ENST00000396444.3	+	15	2691	c.2353A>G	c.(2353-2355)Act>Gct	p.T785A	USP8_ENST00000433963.1_Missense_Mutation_p.T785A|USP8_ENST00000307179.4_Missense_Mutation_p.T785A|USP8_ENST00000425032.3_Missense_Mutation_p.T679A|RP11-562A8.5_ENST00000560159.1_lincRNA	NM_001128610.1|NM_005154.3	NP_001122082.1|NP_005145.3	P40818	UBP8_HUMAN	ubiquitin specific peptidase 8	785	USP.				cell proliferation (GO:0008283)|endosome organization (GO:0007032)|mitotic cytokinesis (GO:0000281)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)|Ras protein signal transduction (GO:0007265)|ubiquitin-dependent protein catabolic process (GO:0006511)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|extrinsic component of plasma membrane (GO:0019897)|midbody (GO:0030496)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|ubiquitin-specific protease activity (GO:0004843)	p.T785A(2)		central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(5)|lung(16)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	35				all cancers(107;0.000225)|GBM - Glioblastoma multiforme(94;0.000771)		CTTAGGAAATACTTGTTATAT	0.398																																					p.T785A		Atlas-SNP	.											USP8,NS,carcinoma,0,3	USP8	90	3	2	Substitution - Missense(2)	prostate(2)	c.A2353G						PASS	.						118.0	105.0	110.0					15																	50785016		2196	4294	6490	SO:0001583	missense	9101	exon15			GGAAATACTTGTT	D29956	CCDS10137.1, CCDS61632.1	15q21.1	2014-03-03	2005-08-08		ENSG00000138592	ENSG00000138592		"""Ubiquitin-specific peptidases"""	12631	protein-coding gene	gene with protein product		603158	"""ubiquitin specific protease 8"""			12838346, 9582025, 24482476	Standard	NM_005154		Approved	HumORF8, KIAA0055, UBPY, SPG59	uc001zyl.4	P40818	OTTHUMG00000131645	ENST00000396444.3:c.2353A>G	15.37:g.50785016A>G	ENSP00000379721:p.Thr785Ala	Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	171	22	0.128655	NM_001128610	B4DKA8|Q2TB31|Q7Z3U2|Q86VA0|Q8IWI7	Missense_Mutation	SNP	ENST00000396444.3	37	CCDS10137.1	.	.	.	.	.	.	.	.	.	.	A	25.6	4.653902	0.88056	.	.	ENSG00000138592	ENST00000396444;ENST00000433963;ENST00000307179;ENST00000425032;ENST00000419830;ENST00000396440	T;T;T;T	0.46451	0.87;0.87;0.87;0.87	5.22	5.22	0.72569	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2, conserved site (1);Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.000000	0.85682	D	0.000000	T	0.74496	0.3724	H	0.95712	3.71	0.80722	D	1	D;D	0.89917	0.998;1.0	D;D	0.79108	0.964;0.992	T	0.83303	-0.0027	10	0.87932	D	0	-18.2981	15.3993	0.74827	1.0:0.0:0.0:0.0	.	679;785	B4DKA8;P40818	.;UBP8_HUMAN	A	785;785;785;679;10;10	ENSP00000379721:T785A;ENSP00000405537:T785A;ENSP00000302239:T785A;ENSP00000412682:T679A	ENSP00000302239:T785A	T	+	1	0	USP8	48572308	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	8.648000	0.91062	2.096000	0.63516	0.528000	0.53228	ACT	G|1.000;|0.000	1.000	weak		0.398	USP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254541.1	NM_005154	
F5	2153	hgsc.bcm.edu	37	1	169510475	169510475	+	Missense_Mutation	SNP	G	G	T	rs1046712	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:169510475G>T	ENST00000367797.3	-	13	4054	c.3853C>A	c.(3853-3855)Ctt>Att	p.L1285I	F5_ENST00000367796.3_Missense_Mutation_p.L1290I	NM_000130.4	NP_000121	P12259	FA5_HUMAN	coagulation factor V (proaccelerin, labile factor)	1285	35 X 9 AA approximate tandem repeats of [TNP]-L-S-P-D-L-S-Q-T.|B.		L -> I (in dbSNP:rs1046712). {ECO:0000269|PubMed:2827731, ECO:0000269|PubMed:8713778, ECO:0000269|Ref.3}.		blood circulation (GO:0008015)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)|vesicle (GO:0031982)	copper ion binding (GO:0005507)			NS(1)|breast(4)|central_nervous_system(4)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(24)|lung(55)|ovary(3)|prostate(4)|skin(5)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(1)	128	all_hematologic(923;0.208)				ART-123(DB05777)|Drotrecogin alfa(DB00055)	TCTAGAGAAAGGGTTGTATGG	0.522													G|||	825	0.164736	0.1611	0.1441	5008	,	,		20586	0.1131		0.1819	False		,,,				2504	0.2198				p.L1285I		Atlas-SNP	.											.	F5	301	.	0			c.C3853A						PASS	.	G	ILE/LEU	775,3631	313.8+/-293.3	79,617,1507	218.0	236.0	230.0		3853	-1.4	0.0	1	dbSNP_86	230	1502,7098	283.1+/-295.9	127,1248,2925	yes	missense	F5	NM_000130.4	5	206,1865,4432	TT,TG,GG		17.4651,17.5897,17.5073	benign	1285/2225	169510475	2277,10729	2203	4300	6503	SO:0001583	missense	2153	exon13			GAGAAAGGGTTGT	M14335	CCDS1281.1	1q23	2012-10-02			ENSG00000198734	ENSG00000198734			3542	protein-coding gene	gene with protein product		612309					Standard	NM_000130		Approved		uc001ggg.1	P12259	OTTHUMG00000034595	ENST00000367797.3:c.3853C>A	1.37:g.169510475G>T	ENSP00000356771:p.Leu1285Ile	Somatic	260	0	0		WXS	Illumina HiSeq	Phase_I	262	130	0.496183	NM_000130	A8K6E8|Q14285|Q2EHR5|Q5R346|Q5R347|Q6UPU6|Q8WWQ6	Missense_Mutation	SNP	ENST00000367797.3	37	CCDS1281.1	322	0.14743589743589744	63	0.12804878048780488	53	0.1464088397790055	68	0.11888111888111888	138	0.1820580474934037	G	2.831	-0.242704	0.05906	0.175897	0.174651	ENSG00000198734	ENST00000367797;ENST00000367796	T;T	0.37411	1.2;1.2	4.19	-1.42	0.08913	.	1.645520	0.02890	N	0.134092	T	0.07728	0.0194	L	0.35542	1.07	0.20307	N	0.999913	B	0.10296	0.003	B	0.06405	0.002	T	0.13072	-1.0523	9	0.21540	T	0.41	1.3999	0.7167	0.00933	0.1828:0.2731:0.2328:0.3113	rs1046712;rs9332606	1285	P12259	FA5_HUMAN	I	1285;1290	ENSP00000356771:L1285I;ENSP00000356770:L1290I	ENSP00000356770:L1290I	L	-	1	0	F5	167777099	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.152000	0.16302	-0.125000	0.11703	-1.513000	0.00942	CTT	G|0.827;T|0.173	0.173	strong		0.522	F5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083712.1	NM_000130	
GGTLC2	91227	hgsc.bcm.edu	37	22	22988864	22988864	+	Missense_Mutation	SNP	G	G	C	rs143048497	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:22988864G>C	ENST00000480559.1	+	1	49	c.49G>C	c.(49-51)Gac>Cac	p.D17H	GGTLC2_ENST00000448514.1_Missense_Mutation_p.D17H|POM121L1P_ENST00000402027.1_RNA	NM_199127.2	NP_954578.2	Q14390	GGTL2_HUMAN	gamma-glutamyltransferase light chain 2	17					glutathione metabolic process (GO:0006749)|leukotriene biosynthetic process (GO:0019370)	anchored component of external side of plasma membrane (GO:0031362)|extracellular vesicular exosome (GO:0070062)	gamma-glutamyltransferase activity (GO:0003840)	p.D17H(1)		endometrium(2)|large_intestine(1)|lung(1)|ovary(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)	11	all_hematologic(9;0.0135)|Acute lymphoblastic leukemia(84;0.17)	all_hematologic(6;1.3e-31)|Acute lymphoblastic leukemia(6;5.54e-23)		READ - Rectum adenocarcinoma(21;0.145)		GATCTCTGACGACACCACTCA	0.627													.|||	77	0.0153754	0.0068	0.0288	5008	,	,		6462	0.0129		0.0278	False		,,,				2504	0.0072				p.D17H		Atlas-SNP	.											GGTLC2,NS,carcinoma,0,1	GGTLC2	20	1	1	Substitution - Missense(1)	prostate(1)	c.G49C						scavenged	.	G	HIS/ASP	25,4335		0,25,2155	24.0	18.0	20.0		49		0.0	22	dbSNP_134	20	200,8106		5,190,3958	no	missense	GGTLC2	NM_199127.2	81	5,215,6113	CC,CG,GG		2.4079,0.5734,1.7764	benign	17/219	22988864	225,12441	2180	4153	6333	SO:0001583	missense	91227	exon1			TCTGACGACACCA	X98922	CCDS13802.2	22q11.21	2008-03-25	2008-03-10	2008-03-10	ENSG00000100121	ENSG00000100121		"""Gamma-glutamyltransferases"""	18596	protein-coding gene	gene with protein product		612339	"""gamma-glutamyltransferase-like 4"""	GGTL4		9074928, 18357469	Standard	NM_199127		Approved		uc010gtt.2	Q14390	OTTHUMG00000151177	ENST00000480559.1:c.49G>C	22.37:g.22988864G>C	ENSP00000419751:p.Asp17His	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	42	2	0.047619	NM_199127	A1A516|A2VCM9|Q5NV76|Q6ISH0	Missense_Mutation	SNP	ENST00000480559.1	37	CCDS13802.2	.	.	.	.	.	.	.	.	.	.	g	8.959	0.970048	0.18659	0.005734	0.024079	ENSG00000100121	ENST00000480559;ENST00000448514	T;T	0.07021	3.23;3.23	.	.	.	.	0.363223	0.30060	N	0.010509	T	0.05640	0.0148	M	0.76574	2.34	0.36339	D	0.859361	B;B	0.23185	0.034;0.081	B;B	0.34991	0.054;0.193	T	0.05699	-1.0869	9	0.42905	T	0.14	-4.1646	5.8178	0.18506	0.001:0.0:0.999:0.0	.	17;17	Q14390;B7WND7	GGTL2_HUMAN;.	H	17	ENSP00000419751:D17H;ENSP00000415676:D17H	ENSP00000415676:D17H	D	+	1	0	GGTLC2	21318864	1.000000	0.71417	0.000000	0.03702	0.000000	0.00434	1.021000	0.30040	-0.000000	0.14550	0.000000	0.15137	GAC	.	.	weak		0.627	GGTLC2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000321662.1	NM_199127	
LRIT1	26103	hgsc.bcm.edu	37	10	85992390	85992390	+	Missense_Mutation	SNP	G	G	T	rs12262099	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:85992390G>T	ENST00000372105.3	-	4	1186	c.1165C>A	c.(1165-1167)Ccc>Acc	p.P389T		NM_015613.2	NP_056428.1	Q9P2V4	LRIT1_HUMAN	leucine-rich repeat, immunoglobulin-like and transmembrane domains 1	389			P -> T (in dbSNP:rs12262099).			integral component of endoplasmic reticulum membrane (GO:0030176)				breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(13)|skin(1)	23						AGGACAGCGGGTTTGGGAATC	0.617													G|||	968	0.193291	0.5507	0.1081	5008	,	,		19158	0.0417		0.0378	False		,,,				2504	0.0869				p.P389T		Atlas-SNP	.											.	LRIT1	73	.	0			c.C1165A						PASS	.	G	THR/PRO	2073,2333	545.5+/-376.8	497,1079,627	59.0	48.0	51.0		1165	2.8	0.0	10	dbSNP_120	51	381,8219	122.4+/-181.4	4,373,3923	yes	missense	LRIT1	NM_015613.2	38	501,1452,4550	TT,TG,GG		4.4302,47.0495,18.8682	benign	389/624	85992390	2454,10552	2203	4300	6503	SO:0001583	missense	26103	exon4			CAGCGGGTTTGGG	AB031547	CCDS7373.1	10q23	2013-02-11	2007-06-19	2007-06-19	ENSG00000148602	ENSG00000148602		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	23404	protein-coding gene	gene with protein product	"""fibronectin type III, immunoglobulin and leucine rich repeat domains 9"""		"""leucine rich repeat containing 21"""	LRRC21		10777785	Standard	NM_015613		Approved	PAL, DKFZP434K091, FIGLER9	uc001kcz.1	Q9P2V4	OTTHUMG00000018632	ENST00000372105.3:c.1165C>A	10.37:g.85992390G>T	ENSP00000361177:p.Pro389Thr	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	91	48	0.527473	NM_015613	Q0QD41|Q9Y4N7	Missense_Mutation	SNP	ENST00000372105.3	37	CCDS7373.1	370	0.16941391941391942	260	0.5284552845528455	42	0.11602209944751381	26	0.045454545454545456	42	0.055408970976253295	G	0.586	-0.834861	0.02713	0.470495	0.044302	ENSG00000148602	ENST00000372105	T	0.35236	1.32	5.66	2.78	0.32641	.	0.653998	0.15885	N	0.239854	T	0.00012	0.0000	N	0.24115	0.695	0.80722	P	0.0	B	0.19445	0.036	B	0.06405	0.002	T	0.45116	-0.9283	9	0.05525	T	0.97	.	9.0016	0.36085	0.3071:0.0:0.6929:0.0	rs12262099;rs52819914;rs57593568;rs12262099	389	Q9P2V4	LRIT1_HUMAN	T	389	ENSP00000361177:P389T	ENSP00000361177:P389T	P	-	1	0	LRIT1	85982370	0.000000	0.05858	0.002000	0.10522	0.041000	0.13682	-0.135000	0.10420	0.317000	0.23160	0.655000	0.94253	CCC	G|0.815;T|0.185	0.185	strong		0.617	LRIT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049109.1	NM_015613	
FAM160B1	57700	hgsc.bcm.edu	37	10	116615045	116615045	+	Silent	SNP	T	T	C	rs3180654	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:116615045T>C	ENST00000369248.4	+	14	2228	c.1893T>C	c.(1891-1893)ttT>ttC	p.F631F	FAM160B1_ENST00000369250.3_Silent_p.F631F	NM_020940.3	NP_065991.3	Q5W0V3	F16B1_HUMAN	family with sequence similarity 160, member B1	631			F -> L (in dbSNP:rs3180654).							NS(1)|central_nervous_system(3)|endometrium(2)|kidney(1)|large_intestine(5)|lung(13)	25						CTGCTTTCTTTGAAGGTCATT	0.373													T|||	1275	0.254593	0.2322	0.2032	5008	,	,		17980	0.0357		0.3777	False		,,,				2504	0.4202				p.F631F		Atlas-SNP	.											.	FAM160B1	107	.	0			c.T1893C						PASS	.	T	,	1128,3278	402.8+/-332.5	138,852,1213	92.0	93.0	92.0		1893,1893	4.5	1.0	10	dbSNP_105	92	3324,5276	493.8+/-373.7	635,2054,1611	no	coding-synonymous,coding-synonymous	FAM160B1	NM_001135051.1,NM_020940.3	,	773,2906,2824	CC,CT,TT		38.6512,25.6015,34.2304	,	631/739,631/766	116615045	4452,8554	2203	4300	6503	SO:0001819	synonymous_variant	57700	exon14			TTTCTTTGAAGGT	AB046820	CCDS31290.1, CCDS44480.1	10q26.11	2008-06-05	2008-06-05	2008-06-05	ENSG00000151553	ENSG00000151553			29320	protein-coding gene	gene with protein product			"""KIAA1600"""	KIAA1600		10997877	Standard	NM_020940		Approved	bA106M7.3	uc001lcb.3	Q5W0V3	OTTHUMG00000019092	ENST00000369248.4:c.1893T>C	10.37:g.116615045T>C		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	91	45	0.494505	NM_020940	Q5H9P7|Q5W0V2|Q8IY76|Q9HCH2	Silent	SNP	ENST00000369248.4	37	CCDS31290.1																																																																																			C|0.312;T|0.688	0.312	strong		0.373	FAM160B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050499.1	XM_049351	
IGLL5	100423062	hgsc.bcm.edu	37	22	23230428	23230428	+	Missense_Mutation	SNP	C	C	G	rs151173231	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:23230428C>G	ENST00000526893.1	+	1	469	c.195C>G	c.(193-195)agC>agG	p.S65R	IGLL5_ENST00000531372.1_Missense_Mutation_p.S65R|IGLL5_ENST00000532223.2_Missense_Mutation_p.S65R|hsa-mir-5571_ENST00000577998.1_RNA	NM_001178126.1	NP_001171597.1	B9A064	IGLL5_HUMAN	immunoglobulin lambda-like polypeptide 5	65						extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|urinary_tract(1)	7						GCCTGCGGAGCCTGTGGGGCA	0.647																																					p.S65R		Atlas-SNP	.											IGLL5,caecum,carcinoma,+1,1	IGLL5	26	1	0			c.C195G						PASS	.																																			SO:0001583	missense	100423062	exon1			GCGGAGCCTGTGG	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.195C>G	22.37:g.23230428C>G	ENSP00000431254:p.Ser65Arg	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	86	22	0.255814	NM_001178126		Missense_Mutation	SNP	ENST00000526893.1	37	CCDS54506.1	.	.	.	.	.	.	.	.	.	.	C	14.52	2.558610	0.45590	.	.	ENSG00000254709	ENST00000532223;ENST00000526893;ENST00000531372	T;T	0.00576	6.45;6.54	3.92	1.8	0.24995	.	.	.	.	.	T	0.00468	0.0015	N	0.19112	0.55	0.09310	N	1	B	0.15930	0.015	B	0.12837	0.008	T	0.46775	-0.9167	9	0.56958	D	0.05	.	4.9248	0.13887	0.2081:0.6824:0.0:0.1095	.	65	B9A064	IGLL5_HUMAN	R	65	ENSP00000436353:S65R;ENSP00000431254:S65R	ENSP00000431254:S65R	S	+	3	2	IGLL5	21560428	0.000000	0.05858	0.001000	0.08648	0.004000	0.04260	-0.510000	0.06328	0.610000	0.30035	0.643000	0.83706	AGC	C|1.000;T|0.000	.	alt		0.647	IGLL5-002	KNOWN	basic|appris_candidate|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000385699.1	NM_001178126	
GIGYF2	26058	hgsc.bcm.edu	37	2	233697708	233697708	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:233697708C>T	ENST00000409547.1	+	24	2982	c.2671C>T	c.(2671-2673)Cgg>Tgg	p.R891W	GIGYF2_ENST00000373563.4_Missense_Mutation_p.R891W|GIGYF2_ENST00000409451.3_Missense_Mutation_p.R912W|GIGYF2_ENST00000373566.3_Missense_Mutation_p.R913W|GIGYF2_ENST00000409196.3_Missense_Mutation_p.R885W|GIGYF2_ENST00000409480.1_Missense_Mutation_p.R913W|GIGYF2_ENST00000452341.2_Missense_Mutation_p.R722W	NM_015575.3	NP_056390.2	Q6Y7W6	PERQ2_HUMAN	GRB10 interacting GYF protein 2	891	Gln-rich.				adult locomotory behavior (GO:0008344)|cell death (GO:0008219)|cellular protein metabolic process (GO:0044267)|feeding behavior (GO:0007631)|homeostasis of number of cells within a tissue (GO:0048873)|insulin-like growth factor receptor signaling pathway (GO:0048009)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|musculoskeletal movement (GO:0050881)|negative regulation of translation (GO:0017148)|neuromuscular process controlling balance (GO:0050885)|post-embryonic development (GO:0009791)|spinal cord motor neuron differentiation (GO:0021522)	membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(11)|kidney(2)|large_intestine(17)|lung(11)|ovary(5)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	63		Breast(86;0.00279)|all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0271)|Lung NSC(271;0.0839)		Epithelial(121;7.37e-16)|BRCA - Breast invasive adenocarcinoma(100;0.000472)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Lung(119;0.0118)|GBM - Glioblastoma multiforme(43;0.0145)		GGAGGTCCAGCGGCAGAAGGA	0.587																																					p.R912W		Atlas-SNP	.											.	GIGYF2	288	.	0			c.C2734T						PASS	.						21.0	21.0	21.0					2																	233697708		2188	4277	6465	SO:0001583	missense	26058	exon24			GTCCAGCGGCAGA	U80751	CCDS33401.1, CCDS46542.1, CCDS46543.1	2q37.1	2011-07-06	2008-02-11	2008-02-11	ENSG00000204120	ENSG00000204120		"""Trinucleotide (CAG) repeat containing"""	11960	protein-coding gene	gene with protein product	"""GYF domain containing 2"""	612003	"""PERQ amino acid rich, with GYF domain 2"", ""PERQ amino acid rich, with GYF domain 3"", ""trinucleotide repeat containing 15"", ""Parkinson disease (autosomal recessive, early onset) 11"""	PERQ2, PERQ3, TNRC15, PARK11		9225980, 9734811, 12771153, 18358451, 19279319	Standard	NM_015575		Approved	KIAA0642, GYF2	uc002vtk.4	Q6Y7W6	OTTHUMG00000153237	ENST00000409547.1:c.2671C>T	2.37:g.233697708C>T	ENSP00000386537:p.Arg891Trp	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	77	29	0.376623	NM_001103147	A6H8W4|B9EG55|E9PBB0|O75137|Q7Z2Z8|Q7Z3I2|Q96HU4|Q9NV82	Missense_Mutation	SNP	ENST00000409547.1	37	CCDS33401.1	.	.	.	.	.	.	.	.	.	.	C	15.37	2.812568	0.50527	.	.	ENSG00000204120	ENST00000373566;ENST00000373563;ENST00000409480;ENST00000409547;ENST00000409196;ENST00000409451;ENST00000452341	T;T;T;T;T;T;T	0.77098	-0.88;-0.88;-0.88;-0.88;-0.88;-0.88;-1.07	5.36	3.43	0.39272	.	0.054543	0.64402	D	0.000001	D	0.83589	0.5287	L	0.50333	1.59	0.46609	D	0.999126	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;P;P;P	0.76071	0.987;0.908;0.908;0.908	D	0.84996	0.0897	10	0.87932	D	0	-21.7548	12.8794	0.58008	0.4371:0.5629:0.0:0.0	.	722;912;891;885	E9PC50;A6H8W4;Q6Y7W6;E9PBB0	.;.;PERQ2_HUMAN;.	W	913;891;913;891;885;912;722	ENSP00000362667:R913W;ENSP00000362664:R891W;ENSP00000386765:R913W;ENSP00000386537:R891W;ENSP00000387070:R885W;ENSP00000387170:R912W;ENSP00000411505:R722W	ENSP00000362664:R891W	R	+	1	2	GIGYF2	233405952	0.993000	0.37304	1.000000	0.80357	0.815000	0.46073	1.280000	0.33202	1.188000	0.43014	0.655000	0.94253	CGG	.	.	none		0.587	GIGYF2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000330316.2	NM_001103146	
ANKMY1	51281	hgsc.bcm.edu	37	2	241463453	241463453	+	Missense_Mutation	SNP	C	C	A	rs3821348	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:241463453C>A	ENST00000272972.3	-	7	1628	c.1414G>T	c.(1414-1416)Gtg>Ttg	p.V472L	ANKMY1_ENST00000401804.1_Missense_Mutation_p.V561L|ANKMY1_ENST00000403283.1_Missense_Mutation_p.V410L|ANKMY1_ENST00000391987.1_Missense_Mutation_p.V472L|ANKMY1_ENST00000406958.1_Intron|ANKMY1_ENST00000405002.1_Missense_Mutation_p.V242L|ANKMY1_ENST00000462004.1_5'Flank|ANKMY1_ENST00000361678.4_Missense_Mutation_p.V331L|ANKMY1_ENST00000405523.3_Missense_Mutation_p.V331L|ANKMY1_ENST00000536462.1_Missense_Mutation_p.V284L|ANKMY1_ENST00000373318.2_Missense_Mutation_p.V331L|ANKMY1_ENST00000373320.4_Missense_Mutation_p.V242L	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	104	0	0		WXS	Illumina HiSeq	Phase_I	80	42	0.525	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	
STK31	56164	hgsc.bcm.edu	37	7	23794029	23794029	+	Missense_Mutation	SNP	G	G	A	rs4722266	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:23794029G>A	ENST00000355870.3	+	10	1348	c.1229G>A	c.(1228-1230)gGa>gAa	p.G410E	STK31_ENST00000405627.3_3'UTR|STK31_ENST00000354639.3_Missense_Mutation_p.G387E|STK31_ENST00000433467.2_Missense_Mutation_p.G410E|STK31_ENST00000428484.1_Missense_Mutation_p.G387E	NM_031414.4	NP_113602.2	Q9BXU1	STK31_HUMAN	serine/threonine kinase 31	410			G -> E (in dbSNP:rs4722266). {ECO:0000269|PubMed:17344846}.			acrosomal vesicle (GO:0001669)	ATP binding (GO:0005524)|hydrolase activity, acting on ester bonds (GO:0016788)|nucleic acid binding (GO:0003676)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(31)|ovary(2)|prostate(1)|skin(7)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	67						TCTTTGAATGGATTAGAGATA	0.388													G|||	1096	0.21885	0.1982	0.3112	5008	,	,		16388	0.2073		0.1342	False		,,,				2504	0.2802				p.G410E		Atlas-SNP	.											STK31,NS,carcinoma,+1,1	STK31	175	1	0			c.G1229A						PASS	.	G	GLU/GLY,GLU/GLY,GLU/GLY	879,3527	342.5+/-307.2	95,689,1419	169.0	170.0	170.0		1160,1229,1160	3.4	1.0	7	dbSNP_111	170	1218,7382	245.1+/-274.1	84,1050,3166	yes	missense,missense,missense	STK31	NM_001122833.1,NM_031414.3,NM_032944.2	98,98,98	179,1739,4585	AA,AG,GG		14.1628,19.9501,16.1233	benign,benign,benign	387/997,410/1020,387/997	23794029	2097,10909	2203	4300	6503	SO:0001583	missense	56164	exon10			TGAATGGATTAGA	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.1229G>A	7.37:g.23794029G>A	ENSP00000348132:p.Gly410Glu	Somatic	259	0	0		WXS	Illumina HiSeq	Phase_I	223	48	0.215247	NM_031414	B4DZ06|B7WPP5|C9J4F9|Q6PCD3|Q9BXH8	Missense_Mutation	SNP	ENST00000355870.3	37	CCDS5386.1	432	0.1978021978021978	106	0.21544715447154472	103	0.2845303867403315	125	0.21853146853146854	98	0.12928759894459102	G	1.635	-0.518037	0.04171	0.199501	0.141628	ENSG00000196335	ENST00000355870;ENST00000433467;ENST00000354639;ENST00000428484	T;T;T;T	0.12255	2.7;2.7;2.7;2.7	5.76	3.36	0.38483	.	0.639291	0.16334	N	0.218991	T	0.00012	0.0000	N	0.00677	-1.265	0.45108	P	0.0018799999999999928	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.45381	-0.9265	9	0.02654	T	1	-3.9124	6.2179	0.20665	0.754:0.1611:0.0849:0.0	rs4722266;rs17148339;rs52807853;rs58668439;rs4722266	410;410	B4DZ06;Q9BXU1	.;STK31_HUMAN	E	410;410;387;387	ENSP00000348132:G410E;ENSP00000411852:G410E;ENSP00000346660:G387E;ENSP00000406146:G387E	ENSP00000346660:G387E	G	+	2	0	STK31	23760554	0.993000	0.37304	1.000000	0.80357	0.776000	0.43924	2.818000	0.48041	0.435000	0.26365	-0.482000	0.04802	GGA	G|0.817;A|0.183	0.183	strong		0.388	STK31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214036.2	NM_031414	
TXNDC11	51061	hgsc.bcm.edu	37	16	11773662	11773662	+	Missense_Mutation	SNP	C	C	G	rs3190321	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:11773662C>G	ENST00000356957.3	-	13	2454	c.2347G>C	c.(2347-2349)Gtc>Ctc	p.V783L	TXNDC11_ENST00000570917.1_5'UTR|TXNDC11_ENST00000283033.5_Missense_Mutation_p.V756L			Q6PKC3	TXD11_HUMAN	thioredoxin domain containing 11	783	Thioredoxin 2. {ECO:0000255|PROSITE- ProRule:PRU00691}.		V -> L (in dbSNP:rs3190321). {ECO:0000269|PubMed:15489334}.		cell redox homeostasis (GO:0045454)|protein folding (GO:0006457)|response to endoplasmic reticulum stress (GO:0034976)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	protein disulfide isomerase activity (GO:0003756)			endometrium(3)|large_intestine(5)|lung(7)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	21						GTGATGGGGACGTCTTCGGGG	0.502													G|||	2263	0.451877	0.4342	0.3285	5008	,	,		19542	0.4345		0.5557	False		,,,				2504	0.4744				p.V756L		Atlas-SNP	.											.	TXNDC11	75	.	0			c.G2266C						PASS	.	G	LEU/VAL	1914,2480	621.4+/-393.7	423,1068,706	62.0	50.0	54.0		2266	3.6	1.0	16	dbSNP_105	54	4661,3939	539.3+/-383.6	1234,2193,873	yes	missense	TXNDC11	NM_015914.5	32	1657,3261,1579	GG,GC,CC		45.8023,43.5594,49.3997	benign	756/959	11773662	6575,6419	2197	4300	6497	SO:0001583	missense	51061	exon12			TGGGGACGTCTTC	BC013727	CCDS32387.1	16p13.13	2008-09-29				ENSG00000153066			28030	protein-coding gene	gene with protein product	"""EF-hand binding protein 1"""					8619474, 9110174	Standard	XM_005255346		Approved	EFP1	uc002dbg.1	Q6PKC3		ENST00000356957.3:c.2347G>C	16.37:g.11773662C>G	ENSP00000349439:p.Val783Leu	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	94	92	0.978723	NM_015914	O95887|Q6PJA6|Q8N2Q4|Q96K45|Q96K53	Missense_Mutation	SNP	ENST00000356957.3	37		1008	0.46153846153846156	201	0.40853658536585363	124	0.3425414364640884	256	0.44755244755244755	427	0.5633245382585752	G	1.789	-0.480073	0.04383	0.435594	0.541977	ENSG00000153066	ENST00000356957;ENST00000283033	T;T	0.11930	2.95;2.73	5.91	3.63	0.41609	Thioredoxin-like fold (2);	0.302325	0.32952	N	0.005449	T	0.00012	0.0000	N	0.01352	-0.895	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.39820	-0.9595	9	0.06891	T	0.86	-27.7888	9.1018	0.36673	0.0991:0.2825:0.6184:0.0	rs3190321;rs17416702;rs60110283;rs3190321	783;756	Q6PKC3;Q6PKC3-2	TXD11_HUMAN;.	L	783;756	ENSP00000349439:V783L;ENSP00000283033:V756L	ENSP00000283033:V756L	V	-	1	0	TXNDC11	11681163	1.000000	0.71417	1.000000	0.80357	0.687000	0.40016	1.521000	0.35910	0.850000	0.35239	-0.764000	0.03450	GTC	C|0.513;G|0.487	0.487	strong		0.502	TXNDC11-002	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000437057.1	NM_015914	
DEF8	54849	hgsc.bcm.edu	37	16	90028509	90028509	+	Silent	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:90028509C>T	ENST00000268676.7	+	9	1169	c.1080C>T	c.(1078-1080)taC>taT	p.Y360Y	DEF8_ENST00000567874.1_Silent_p.Y239Y|DEF8_ENST00000569453.1_Silent_p.Y299Y|DEF8_ENST00000563795.1_Silent_p.Y299Y|DEF8_ENST00000563594.1_Silent_p.Y299Y|DEF8_ENST00000563848.1_3'UTR|DEF8_ENST00000570182.1_Silent_p.Y289Y	NM_207514.2	NP_997397.1	Q6ZN54	DEFI8_HUMAN	differentially expressed in FDCP 8 homolog (mouse)	360					intracellular signal transduction (GO:0035556)		zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(1)|large_intestine(1)|lung(8)|upper_aerodigestive_tract(1)	12		all_cancers(9;7.59e-13)|Lung NSC(15;1.56e-06)|all_lung(18;2.18e-06)|all_neural(9;0.0019)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.0274)		TGTTCAGCTACGTGGAGGAGC	0.662																																					p.Y360Y		Atlas-SNP	.											.	DEF8	28	.	0			c.C1080T						PASS	.						44.0	36.0	39.0					16																	90028509		2198	4300	6498	SO:0001819	synonymous_variant	54849	exon9			CAGCTACGTGGAG	AK131370	CCDS10989.1, CCDS45555.1, CCDS58493.1, CCDS58494.1, CCDS58495.1, CCDS58496.1	16q24.3	2011-01-31			ENSG00000140995	ENSG00000140995			25969	protein-coding gene	gene with protein product						12477932	Standard	NM_207514		Approved	FLJ20186	uc002fpn.2	Q6ZN54	OTTHUMG00000138989	ENST00000268676.7:c.1080C>T	16.37:g.90028509C>T		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	107	74	0.691589	NM_207514	B3KT65|B4DK62|B4E0S9|B7Z3H6|H3BUG7|Q8N8N3|Q9NXL0	Silent	SNP	ENST00000268676.7	37	CCDS10989.1																																																																																			.	.	none		0.662	DEF8-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000272878.1	NM_207514	
PARVA	55742	hgsc.bcm.edu	37	11	12540037	12540037	+	Silent	SNP	T	T	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:12540037T>C	ENST00000550549.1	+	12	1064	c.1015T>C	c.(1015-1017)Ttg>Ctg	p.L339L	PARVA_ENST00000334956.8_Silent_p.L379L|PARVA_ENST00000539723.1_Silent_p.L339L			Q9NVD7	PARVA_HUMAN	parvin, alpha	339	CH 2. {ECO:0000255|PROSITE- ProRule:PRU00044}.				actin cytoskeleton reorganization (GO:0031532)|actin-mediated cell contraction (GO:0070252)|cell junction assembly (GO:0034329)|cilium morphogenesis (GO:0060271)|establishment or maintenance of cell polarity (GO:0007163)|heterotypic cell-cell adhesion (GO:0034113)|outflow tract septum morphogenesis (GO:0003148)|regulation of cell shape (GO:0008360)|smooth muscle cell chemotaxis (GO:0071670)|sprouting angiogenesis (GO:0002040)|substrate adhesion-dependent cell spreading (GO:0034446)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(4)	11				Epithelial(150;0.00624)		AGATGGAGGGTTGGAAAAGCC	0.512																																					p.L379L		Atlas-SNP	.											.	PARVA	27	.	0			c.T1135C						PASS	.						89.0	87.0	87.0					11																	12540037		1969	4145	6114	SO:0001819	synonymous_variant	55742	exon12			GGAGGGTTGGAAA	AF237771	CCDS44541.1, CCDS44541.2	11p15.3	2014-06-13	2005-05-26		ENSG00000197702	ENSG00000197702		"""Parvins"""	14652	protein-coding gene	gene with protein product		608120	"""matrix-remodelling associated 2"""	MXRA2		11171322	Standard	NM_018222		Approved	FLJ12254, FLJ10793	uc001mki.4	Q9NVD7	OTTHUMG00000165778	ENST00000550549.1:c.1015T>C	11.37:g.12540037T>C		Somatic	221	0	0		WXS	Illumina HiSeq	Phase_I	189	33	0.174603	NM_018222	Q96C85|Q9HA48	Silent	SNP	ENST00000550549.1	37																																																																																				.	.	none		0.512	PARVA-203	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_018222	
TDG	6996	hgsc.bcm.edu	37	12	104376608	104376608	+	Silent	SNP	G	G	A	rs61937629	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:104376608G>A	ENST00000392872.3	+	5	744	c.510G>A	c.(508-510)gaG>gaA	p.E170E	TDG_ENST00000544861.1_Silent_p.E27E|AC078819.1_ENST00000401157.1_RNA|TDG_ENST00000542036.1_5'UTR|TDG_ENST00000266775.9_Silent_p.E166E	NM_003211.4	NP_003202.3	Q13569	TDG_HUMAN	thymine-DNA glycosylase	170					base-excision repair (GO:0006284)|base-excision repair, AP site formation (GO:0006285)|chromatin modification (GO:0016568)|depyrimidination (GO:0045008)|DNA demethylation (GO:0080111)|DNA repair (GO:0006281)|embryo development (GO:0009790)|mismatch repair (GO:0006298)|negative regulation of chromatin binding (GO:0035562)|negative regulation of protein binding (GO:0032091)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of gene expression, epigenetic (GO:0040029)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|PML body (GO:0016605)	damaged DNA binding (GO:0003684)|DNA N-glycosylase activity (GO:0019104)|double-stranded DNA binding (GO:0003690)|mismatched DNA binding (GO:0030983)|protein homodimerization activity (GO:0042803)|pyrimidine-specific mismatch base pair DNA N-glycosylase activity (GO:0008263)|RNA polymerase II transcription cofactor activity (GO:0001104)|structure-specific DNA binding (GO:0043566)	p.E170E(1)		large_intestine(2)|lung(14)|ovary(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	24				BRCA - Breast invasive adenocarcinoma(302;0.00114)		GGCTCAGTGAGGTCCAGCTGA	0.443								Base excision repair (BER), DNA glycosylases																													p.E170E		Atlas-SNP	.											TDG,NS,carcinoma,0,1	TDG	43	1	1	Substitution - coding silent(1)	stomach(1)	c.G510A						scavenged	.						124.0	116.0	118.0					12																	104376608		2203	4300	6503	SO:0001819	synonymous_variant	6996	exon5			CAGTGAGGTCCAG	U51166	CCDS9095.1	12q24.1	2014-05-14			ENSG00000139372	ENSG00000139372	3.2.2.29		11700	protein-coding gene	gene with protein product	"""G/T mismatch-specific thymine DNA glycosylase"""	601423				8662714, 9299239	Standard	NM_003211		Approved		uc001tkg.3	Q13569	OTTHUMG00000168418	ENST00000392872.3:c.510G>A	12.37:g.104376608G>A		Somatic	335	2	0.00597015		WXS	Illumina HiSeq	Phase_I	343	20	0.058309	NM_003211	Q8IUZ6|Q8IZM3	Silent	SNP	ENST00000392872.3	37	CCDS9095.1																																																																																			G|0.924;A|0.076	0.076	strong		0.443	TDG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399673.2		
TMEM63B	55362	hgsc.bcm.edu	37	6	44117607	44117607	+	Silent	SNP	C	C	T	rs4714761	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:44117607C>T	ENST00000259746.9	+	16	1608	c.1425C>T	c.(1423-1425)atC>atT	p.I475I	TMEM63B_ENST00000323267.6_Silent_p.I475I			Q5T3F8	CSCL2_HUMAN	transmembrane protein 63B	475					ion transport (GO:0006811)	integral component of membrane (GO:0016021)	nucleotide binding (GO:0000166)	p.I475I(1)		breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(8)|ovary(1)|pancreas(2)|prostate(2)|stomach(4)	35	all_cancers(18;1.66e-06)|Lung NSC(15;0.00108)|all_lung(25;0.00278)|Hepatocellular(11;0.00309)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0215)			ACCCCATCATCACCCAGTTCT	0.622													C|||	483	0.0964457	0.0045	0.0821	5008	,	,		18853	0.2252		0.0755	False		,,,				2504	0.1196				p.I475I		Atlas-SNP	.											TMEM63B,NS,carcinoma,0,2	TMEM63B	77	2	1	Substitution - coding silent(1)	stomach(1)	c.C1425T						PASS	.	C		81,4325	70.3+/-108.2	2,77,2124	184.0	127.0	146.0		1425	4.5	1.0	6	dbSNP_111	146	663,7935	161.0+/-214.0	28,607,3664	no	coding-synonymous	TMEM63B	NM_018426.1		30,684,5788	TT,TC,CC		7.7111,1.8384,5.7213		475/833	44117607	744,12260	2203	4299	6502	SO:0001819	synonymous_variant	55362	exon16			CATCATCACCCAG	BC022095	CCDS34461.1	6p21.1	2008-02-05	2005-07-25	2005-07-25	ENSG00000137216	ENSG00000137216			17735	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 110"""	C6orf110			Standard	XM_005249211		Approved	DKFZp434P0531, dJ421H19.2	uc003owr.3	Q5T3F8	OTTHUMG00000014757	ENST00000259746.9:c.1425C>T	6.37:g.44117607C>T		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	110	49	0.445455	NM_018426	B9EGU3|Q5T3F9|Q6AHX4|Q6P5A0|Q8N219|Q8NDE1|Q9NSG5	Silent	SNP	ENST00000259746.9	37	CCDS34461.1	229	0.10485347985347986	1	0.0020325203252032522	31	0.0856353591160221	142	0.24825174825174826	55	0.07255936675461741	C	10.69	1.420175	0.25552	0.018384	0.077111	ENSG00000137216	ENST00000371893	.	.	.	4.49	4.49	0.54785	.	.	.	.	.	T	0.64483	0.2602	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.64504	-0.6392	3	.	.	.	.	16.6913	0.85322	0.0:1.0:0.0:0.0	rs4714761;rs61002242;rs4714761	.	.	.	L	404	.	.	S	+	2	0	TMEM63B	44225585	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.032000	0.49736	2.488000	0.83962	0.549000	0.68633	TCA	C|0.921;T|0.079	0.079	strong		0.622	TMEM63B-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040712.2	XM_166410	
KIAA1217	56243	hgsc.bcm.edu	37	10	24813454	24813454	+	Missense_Mutation	SNP	G	G	A	rs10828663	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:24813454G>A	ENST00000376454.3	+	13	2689	c.2659G>A	c.(2659-2661)Gcg>Acg	p.A887T	KIAA1217_ENST00000396446.1_Missense_Mutation_p.A570T|KIAA1217_ENST00000430453.2_Intron|KIAA1217_ENST00000376452.3_Missense_Mutation_p.A852T|KIAA1217_ENST00000396445.1_Missense_Mutation_p.A570T|KIAA1217_ENST00000376451.2_Missense_Mutation_p.A570T|KIAA1217_ENST00000307544.6_Missense_Mutation_p.A570T|KIAA1217_ENST00000458595.1_Missense_Mutation_p.A852T|KIAA1217_ENST00000376462.1_Missense_Mutation_p.A807T	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	74	0	0		WXS	Illumina HiSeq	Phase_I	77	40	0.519481	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	
PLIN4	729359	hgsc.bcm.edu	37	19	4512629	4512629	+	Missense_Mutation	SNP	C	C	T	rs146679364	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:4512629C>T	ENST00000301286.3	-	3	1300	c.1301G>A	c.(1300-1302)aGa>aAa	p.R434K		NM_001080400.1	NP_001073869.1	Q96Q06	PLIN4_HUMAN	perilipin 4	434	27 X 33 AA approximate tandem repeat.					cytoplasm (GO:0005737)|lipid particle (GO:0005811)|plasma membrane (GO:0005886)		p.R362T(1)		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						GATGGTTCCTCTGGCCAAATT	0.547																																					p.R434K		Atlas-SNP	.											PLIN4,NS,carcinoma,0,1	PLIN4	191	1	1	Substitution - Missense(1)	breast(1)	c.G1301A						PASS	.	C	LYS/ARG	454,3580		74,306,1637	130.0	149.0	143.0		1301	3.7	0.6	19	dbSNP_134	143	397,7961		38,321,3820	yes	missense	PLIN4	NM_001080400.1	26	112,627,5457	TT,TC,CC		4.7499,11.2543,6.8673	benign	434/1358	4512629	851,11541	2017	4179	6196	SO:0001583	missense	729359	exon3			GTTCCTCTGGCCA	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.1301G>A	19.37:g.4512629C>T	ENSP00000301286:p.Arg434Lys	Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	85	18	0.211765	NM_001080400	A6NEI2	Missense_Mutation	SNP	ENST00000301286.3	37	CCDS45927.1	80	0.03663003663003663	43	0.08739837398373984	9	0.024861878453038673	1	0.0017482517482517483	27	0.03562005277044855	c	0.010	-1.773753	0.00640	0.112543	0.047499	ENSG00000167676	ENST00000301286	T	0.03004	4.08	4.73	3.7	0.42460	.	0.111229	0.39544	N	0.001334	T	0.00012	0.0000	N	0.00015	-2.89	0.48135	P	4.089999999999927E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.31971	-0.9924	9	0.02654	T	1	-14.0488	8.4942	0.33119	0.0:0.0956:0.0:0.9044	.	434	Q96Q06	PLIN4_HUMAN	K	434	ENSP00000301286:R434K	ENSP00000301286:R434K	R	-	2	0	PLIN4	4463629	0.017000	0.18338	0.647000	0.29507	0.011000	0.07611	0.761000	0.26489	0.687000	0.31509	-0.856000	0.03024	AGA	C|0.949;T|0.051	0.051	strong		0.547	PLIN4-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395095.1	XM_170901	
GPRIN2	9721	hgsc.bcm.edu	37	10	47000217	47000217	+	Missense_Mutation	SNP	G	G	A	rs72780221	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:47000217G>A	ENST00000374317.1	+	3	1610	c.1337G>A	c.(1336-1338)cGc>cAc	p.R446H	GPRIN2_ENST00000374314.4_Missense_Mutation_p.R446H	NM_014696.3	NP_055511.2	O60269	GRIN2_HUMAN	G protein regulated inducer of neurite outgrowth 2	446								p.R446H(1)		breast(2)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(1)|lung(6)|prostate(1)	18						TCCCTGCGGCGCCCCAGCTGC	0.716																																					p.R446H		Atlas-SNP	.											GPRIN2,NS,carcinoma,0,2	GPRIN2	94	2	1	Substitution - Missense(1)	prostate(1)	c.G1337A						scavenged	.						8.0	9.0	9.0					10																	47000217		2121	4098	6219	SO:0001583	missense	9721	exon3			TGCGGCGCCCCAG	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.1337G>A	10.37:g.47000217G>A	ENSP00000363436:p.Arg446His	Somatic	11	0	0		WXS	Illumina HiSeq	Phase_I	7	3	0.428571	NM_014696	Q5SVF0	Missense_Mutation	SNP	ENST00000374317.1	37	CCDS31192.1	220	0.10073260073260074	86	0.17479674796747968	30	0.08287292817679558	25	0.043706293706293704	79	0.10422163588390501	G	13.52	2.261176	0.39995	.	.	ENSG00000204175	ENST00000374317;ENST00000374314	T;T	0.26223	1.75;1.75	5.11	3.2	0.36748	.	0.744361	0.10758	N	0.637492	T	0.00073	0.0002	L	0.49350	1.555	0.09310	N	1	B	0.24533	0.105	B	0.17433	0.018	T	0.22243	-1.0222	10	0.34782	T	0.22	-0.7153	5.5226	0.16941	0.1777:0.1655:0.6568:0.0	.	446	O60269	GRIN2_HUMAN	H	446	ENSP00000363436:R446H;ENSP00000363433:R446H	ENSP00000363433:R446H	R	+	2	0	GPRIN2	46420223	0.000000	0.05858	0.420000	0.26596	0.986000	0.74619	0.143000	0.16115	0.639000	0.30564	0.561000	0.74099	CGC	G|0.901;A|0.099	0.099	strong		0.716	GPRIN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047836.1	NM_014696	
TRIM51	84767	hgsc.bcm.edu	37	11	55652963	55652963	+	Missense_Mutation	SNP	A	A	G	rs2063276	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:55652963A>G	ENST00000449290.2	+	2	151	c.59A>G	c.(58-60)aAc>aGc	p.N20S	TRIM51_ENST00000244891.3_5'Flank	NM_032681.3	NP_116070.2	Q9BSJ1	TRI51_HUMAN	tripartite motif-containing 51	20						intracellular (GO:0005622)	zinc ion binding (GO:0008270)										ATCTGCATGAACTACTTCCTA	0.502													N|||	3414	0.681709	0.6452	0.683	5008	,	,		18043	0.7649		0.6153	False		,,,				2504	0.7127				p.N20S		Atlas-SNP	.											.	.	.	.	0			c.A59G						PASS	.	A	SER/ASN	897,487		308,281,103	21.0	18.0	19.0		59	0.8	0.0	11	dbSNP_94	19	1962,1198		615,732,233	no	missense	SPRYD5	NM_032681.3	46	923,1013,336	GG,GA,AA		37.9114,35.1879,37.0819	possibly-damaging	20/453	55652963	2859,1685	692	1580	2272	SO:0001583	missense	84767	exon2			GCATGAACTACTT	BC005014		11p11	2013-01-09	2012-05-18	2012-05-18	ENSG00000124900	ENSG00000124900		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	19023	protein-coding gene	gene with protein product			"""SPRY domain containing 5"""	SPRYD5			Standard	NM_032681		Approved	TRIM51A	uc010rip.2	Q9BSJ1	OTTHUMG00000156437	ENST00000449290.2:c.59A>G	11.37:g.55652963A>G	ENSP00000395086:p.Asn20Ser	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	133	28	0.210526	NM_032681	A6NMG2	Missense_Mutation	SNP	ENST00000449290.2	37		1411	0.6460622710622711	304	0.6178861788617886	235	0.649171270718232	421	0.736013986013986	451	0.5949868073878628	.	6.155	0.396776	0.11638	0.648121	0.620886	ENSG00000124900	ENST00000449290	D	0.83914	-1.78	0.803	0.803	0.18691	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (2);Zinc finger, C3HC4 RING-type (1);	.	.	.	.	T	0.00012	0.0000	N	0.16266	0.395	0.36627	P	0.12391600000000003	P	0.44429	0.835	P	0.49477	0.612	T	0.42155	-0.9468	8	0.59425	D	0.04	.	5.8508	0.18691	0.9999:0.0:1.0E-4:0.0	rs2063276	20	Q9BSJ1	SPRY5_HUMAN	S	20	ENSP00000395086:N20S	ENSP00000395086:N20S	N	+	2	0	SPRYD5	55409539	0.831000	0.29352	0.005000	0.12908	0.120000	0.20174	1.010000	0.29898	0.624000	0.30286	0.128000	0.15822	AAC	A|0.360;G|0.640	0.640	strong		0.502	TRIM51-004	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000391522.1	NM_032681	
B4GALNT3	283358	hgsc.bcm.edu	37	12	670595	670595	+	Missense_Mutation	SNP	G	G	A	rs36078145	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:670595G>A	ENST00000266383.5	+	20	2988	c.2975G>A	c.(2974-2976)cGt>cAt	p.R992H		NM_173593.3	NP_775864.3	Q6L9W6	B4GN3_HUMAN	beta-1,4-N-acetyl-galactosaminyl transferase 3	992			R -> H (in dbSNP:rs36078145).		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)			ATGTGGAGCCGTCGCCAGATG	0.622													G|||	135	0.0269569	0.0015	0.0461	5008	,	,		19895	0.001		0.0527	False		,,,				2504	0.0481				p.R992H		Atlas-SNP	.											.	B4GALNT3	64	.	0			c.G2975A						PASS	.	G	HIS/ARG	49,4357	49.6+/-84.7	0,49,2154	55.0	50.0	51.0		2975	4.7	1.0	12	dbSNP_126	51	531,8069	147.4+/-202.8	17,497,3786	yes	missense	B4GALNT3	NM_173593.3	29	17,546,5940	AA,AG,GG		6.1744,1.1121,4.4595	probably-damaging	992/999	670595	580,12426	2203	4300	6503	SO:0001583	missense	283358	exon20			GGAGCCGTCGCCA	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.2975G>A	12.37:g.670595G>A	ENSP00000266383:p.Arg992His	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	73	37	0.506849	NM_173593	Q6ZNC1|Q8N7T6	Missense_Mutation	SNP	ENST00000266383.5	37	CCDS8504.1	66	0.03021978021978022	1	0.0020325203252032522	24	0.06629834254143646	0	0.0	41	0.05408970976253298	G	11.84	1.757723	0.31137	0.011121	0.061744	ENSG00000139044	ENST00000266383	T	0.05513	3.43	4.72	4.72	0.59763	.	0.242135	0.40554	N	0.001070	T	0.00875	0.0029	M	0.72118	2.19	0.49582	D	0.999805	B	0.25390	0.125	B	0.30572	0.117	T	0.06463	-1.0825	10	0.54805	T	0.06	-19.2132	17.6819	0.88246	0.0:0.0:1.0:0.0	rs36078145	992	Q6L9W6	B4GN3_HUMAN	H	992	ENSP00000266383:R992H	ENSP00000266383:R992H	R	+	2	0	B4GALNT3	540856	1.000000	0.71417	0.998000	0.56505	0.112000	0.19704	3.892000	0.56235	2.164000	0.68074	0.313000	0.20887	CGT	G|0.958;A|0.042	0.042	strong		0.622	B4GALNT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251406.2	NM_173593	
MUC4	4585	hgsc.bcm.edu	37	3	195507494	195507494	+	Missense_Mutation	SNP	C	C	T	rs200217182		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195507494C>T	ENST00000463781.3	-	2	11416	c.10957G>A	c.(10957-10959)Gac>Aac	p.D3653N	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.D3653N	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)		GAGGAAGCGTCGGTGACAAGA	0.587																																					p.D3653N		Atlas-SNP	.											.	MUC4	1505	.	0			c.G10957A						PASS	.						20.0	15.0	17.0					3																	195507494		597	1485	2082	SO:0001583	missense	4585	exon2			AAGCGTCGGTGAC	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.10957G>A	3.37:g.195507494C>T	ENSP00000417498:p.Asp3653Asn	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	104	58	0.557692	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	8.021	0.759637	0.15846	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.52057	1.16;0.68	0.743	-1.49	0.08718	.	.	.	.	.	T	0.15349	0.0370	N	0.08118	0	0.80722	P	0.0	D	0.52996	0.957	B	0.31390	0.129	T	0.20140	-1.0284	7	.	.	.	.	2.142	0.03777	0.3241:0.3498:0.3261:0.0	.	3525	E7ESK3	.	N	3653	ENSP00000417498:D3653N;ENSP00000420243:D3653N	.	D	-	1	0	MUC4	196992273	0.000000	0.05858	0.018000	0.16275	0.018000	0.09664	-0.313000	0.08103	0.088000	0.17205	0.089000	0.15464	GAC	.	.	weak		0.587	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
WWP2	11060	hgsc.bcm.edu	37	16	69922079	69922079	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:69922079G>A	ENST00000359154.2	+	8	942	c.841G>A	c.(841-843)Gga>Aga	p.G281R	WWP2_ENST00000544162.1_3'UTR|WWP2_ENST00000448661.1_Missense_Mutation_p.G281R|WWP2_ENST00000356003.2_Missense_Mutation_p.G281R|WWP2_ENST00000569174.1_Missense_Mutation_p.G281R|WWP2_ENST00000542271.1_Missense_Mutation_p.G165R	NM_001270454.1|NM_007014.4	NP_001257383.1|NP_008945.2	O00308	WWP2_HUMAN	WW domain containing E3 ubiquitin protein ligase 2	281					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						ACCGGCTGAAGGAGAGGAACC	0.622																																					p.G281R		Atlas-SNP	.											.	WWP2	88	.	0			c.G841A						PASS	.						68.0	67.0	67.0					16																	69922079		2198	4300	6498	SO:0001583	missense	11060	exon8			GCTGAAGGAGAGG	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.841G>A	16.37:g.69922079G>A	ENSP00000352069:p.Gly281Arg	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	127	51	0.401575	NM_001270454	A6NEP1|B2R706|B4DTL5|F5H213|H3BRF3|I3RSG8|Q6ZTQ5|Q96CZ2|Q9BWN6	Missense_Mutation	SNP	ENST00000359154.2	37	CCDS10885.1	.	.	.	.	.	.	.	.	.	.	G	18.45	3.627292	0.66901	.	.	ENSG00000198373	ENST00000359154;ENST00000448661;ENST00000356003;ENST00000544162;ENST00000542271	T;T;T;T	0.32515	1.45;1.45;1.45;1.48	6.07	6.07	0.98685	.	3.592490	0.00447	N	0.000099	T	0.29556	0.0737	N	0.24115	0.695	0.47737	D	0.9995	P	0.34780	0.468	B	0.31191	0.125	T	0.17623	-1.0363	9	.	.	.	.	17.7999	0.88584	0.0:0.0:1.0:0.0	.	281	O00308	WWP2_HUMAN	R	281;281;281;168;165	ENSP00000352069:G281R;ENSP00000396871:G281R;ENSP00000348283:G281R;ENSP00000445616:G165R	.	G	+	1	0	WWP2	68479580	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.845000	0.55880	2.884000	0.98904	0.655000	0.94253	GGA	.	.	none		0.622	WWP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268954.1	NM_007014	
DCAF15	90379	hgsc.bcm.edu	37	19	14065341	14065341	+	Silent	SNP	T	T	C	rs10409785	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:14065341T>C	ENST00000254337.6	+	3	255	c.234T>C	c.(232-234)caT>caC	p.H78H	PODNL1_ENST00000588317.1_5'Flank|PODNL1_ENST00000538517.2_5'Flank|PODNL1_ENST00000538371.2_5'Flank	NM_138353.2	NP_612362.2	Q66K64	DCA15_HUMAN	DDB1 and CUL4 associated factor 15	78					protein ubiquitination (GO:0016567)					breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(5)|ovary(1)|pancreas(1)	11						CCCACAGACATATCTTCCTGG	0.622													t|||	870	0.173722	0.2587	0.1167	5008	,	,		17615	0.131		0.1581	False		,,,				2504	0.1595				p.H78H		Atlas-SNP	.											.	DCAF15	30	.	0			c.T234C						PASS	.			1089,3317	720.9+/-409.1	141,807,1255	60.0	56.0	57.0		234	0.3	1.0	19	dbSNP_119	57	1399,7201	753.5+/-407.4	111,1177,3012	no	coding-synonymous	DCAF15	NM_138353.2		252,1984,4267	CC,CT,TT		16.2674,24.7163,19.1296		78/601	14065341	2488,10518	2203	4300	6503	SO:0001819	synonymous_variant	90379	exon3			CAGACATATCTTC	BC002926	CCDS32926.1	19p13.12	2009-07-17	2009-07-17	2009-07-17	ENSG00000132017	ENSG00000132017		"""DDB1 and CUL4 associated factors"""	25095	protein-coding gene	gene with protein product			"""chromosome 19 open reading frame 72"""	C19orf72			Standard	NM_138353		Approved	MGC99481	uc002mxt.3	Q66K64		ENST00000254337.6:c.234T>C	19.37:g.14065341T>C		Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	137	68	0.49635	NM_138353	B3KS86|Q96DW0|Q9BU31	Silent	SNP	ENST00000254337.6	37	CCDS32926.1																																																																																			T|0.817;C|0.183	0.183	strong		0.622	DCAF15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458099.1	NM_138353	
LILRB1	10859	hgsc.bcm.edu	37	19	55144208	55144208	+	Missense_Mutation	SNP	G	G	A	rs201552016	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:55144208G>A	ENST00000396331.1	+	7	1312	c.955G>A	c.(955-957)Gca>Aca	p.A319T	LILRB1_ENST00000448689.1_Missense_Mutation_p.A319T|LILRB1_ENST00000396315.1_Missense_Mutation_p.A319T|LILRB1_ENST00000396321.2_Missense_Mutation_p.A319T|LILRB1_ENST00000324602.7_Missense_Mutation_p.A319T|LILRB1_ENST00000427581.2_Missense_Mutation_p.A355T|LILRB1_ENST00000396327.3_Missense_Mutation_p.A319T|LILRB1_ENST00000434867.2_Missense_Mutation_p.A319T|LILRB1_ENST00000396317.1_Missense_Mutation_p.A319T|LILRB1_ENST00000418536.2_Missense_Mutation_p.A319T|LILRB1_ENST00000396332.4_Missense_Mutation_p.A319T	NM_006669.3	NP_006660.3	Q8NHL6	LIRB1_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 1	319	Ig-like C2-type 4.				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)		CATCCTGATCGCAGGTGAGGA	0.682										HNSCC(37;0.09)																											p.A319T		Atlas-SNP	.											LILRB1,NS,carcinoma,0,1	LILRB1	140	1	0			c.G955A						scavenged	.						20.0	23.0	22.0					19																	55144208		2181	4241	6422	SO:0001583	missense	10859	exon6			CTGATCGCAGGTG	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.955G>A	19.37:g.55144208G>A	ENSP00000379622:p.Ala319Thr	Somatic	135	3	0.0222222		WXS	Illumina HiSeq	Phase_I	108	23	0.212963	NM_001081637	A2IXV4|A8MXT0|O75024|O75025|Q8NHJ9|Q8NHK0	Missense_Mutation	SNP	ENST00000396331.1	37	CCDS42617.1	.	.	.	.	.	.	.	.	.	.	g	0.007	-1.966601	0.00461	.	.	ENSG00000104972	ENST00000396321;ENST00000418536;ENST00000448689;ENST00000396331;ENST00000396327;ENST00000324602;ENST00000434867;ENST00000396332;ENST00000427581;ENST00000396317;ENST00000396315	T;T;T;T;T;T;T;T;T;T;T	0.00637	6.05;6.05;6.05;6.05;6.05;6.05;6.05;6.05;6.05;6.05;6.05	2.03	-4.06	0.03986	Immunoglobulin subtype (1);Immunoglobulin-like (1);	1.146900	0.06864	N	0.799690	T	0.00300	0.0009	N	0.02129	-0.67	0.09310	N	1	B;B;B;B;B	0.17667	0.023;0.011;0.023;0.011;0.006	B;B;B;B;B	0.16722	0.013;0.016;0.013;0.016;0.007	T	0.42949	-0.9421	10	0.15499	T	0.54	.	1.9292	0.03323	0.527:0.1368:0.1995:0.1367	.	319;319;319;319;319	A8MVE2;Q8NHL6-3;A2IXV4;Q8NHL6-2;Q8NHL6	.;.;.;.;LIRB1_HUMAN	T	319;319;319;319;319;319;319;319;355;319;319	ENSP00000379614:A319T;ENSP00000391514:A319T;ENSP00000409968:A319T;ENSP00000379622:A319T;ENSP00000379618:A319T;ENSP00000315997:A319T;ENSP00000405243:A319T;ENSP00000379623:A319T;ENSP00000395004:A355T;ENSP00000379610:A319T;ENSP00000379608:A319T	ENSP00000315997:A319T	A	+	1	0	LILRB1	59836020	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-5.559000	0.00113	-4.037000	0.00079	-2.903000	0.00092	GCA	G|0.936;A|0.064	0.064	strong		0.682	LILRB1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000140796.4		
KRT37	8688	hgsc.bcm.edu	37	17	39580310	39580310	+	Missense_Mutation	SNP	G	G	A	rs142829376		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:39580310G>A	ENST00000225550.3	-	1	465	c.466C>T	c.(466-468)Cgt>Tgt	p.R156C	AC003958.2_ENST00000432258.1_RNA	NM_003770.4	NP_003761.3	O76014	KRT37_HUMAN	keratin 37	156	Coil 1B.|Rod.					extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)	p.R156C(1)		NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(9)|lung(6)|skin(3)	25		Breast(137;0.000496)				TCGATTGTACGGAAGTAGGAC	0.597																																					p.R156C		Atlas-SNP	.											KRT37,hand,carcinoma,0,1	KRT37	61	1	1	Substitution - Missense(1)	skin(1)	c.C466T						scavenged	.	G	CYS/ARG	0,4406		0,0,2203	87.0	77.0	81.0		466	3.6	0.7	17	dbSNP_134	81	1,8599		0,1,4299	no	missense	KRT37	NM_003770.4	180	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign	156/450	39580310	1,13005	2203	4300	6503	SO:0001583	missense	8688	exon1			TTGTACGGAAGTA	Y16793	CCDS32653.1	17q21.2	2013-06-20	2006-07-17	2006-07-17	ENSG00000108417	ENSG00000108417		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6455	protein-coding gene	gene with protein product		604541	"""keratin, hair, acidic, 7"""	KRTHA7		9756910, 16831889	Standard	NM_003770		Approved		uc002hwp.1	O76014	OTTHUMG00000133606	ENST00000225550.3:c.466C>T	17.37:g.39580310G>A	ENSP00000225550:p.Arg156Cys	Somatic	91	1	0.010989		WXS	Illumina HiSeq	Phase_I	73	47	0.643836	NM_003770		Missense_Mutation	SNP	ENST00000225550.3	37	CCDS32653.1	.	.	.	.	.	.	.	.	.	.	.	12.99	2.103923	0.37145	0.0	1.16E-4	ENSG00000108417	ENST00000225550	D	0.89415	-2.51	4.69	3.62	0.41486	Filament (1);	0.297247	0.23563	N	0.046837	D	0.85885	0.5801	M	0.68593	2.085	0.09310	N	0.999993	B	0.18863	0.031	B	0.12156	0.007	T	0.76075	-0.3092	10	0.38643	T	0.18	.	10.3203	0.43762	0.0:0.1176:0.6892:0.1932	.	156	O76014	KRT37_HUMAN	C	156	ENSP00000225550:R156C	ENSP00000225550:R156C	R	-	1	0	KRT37	36833836	0.000000	0.05858	0.749000	0.31150	0.958000	0.62258	0.157000	0.16402	2.169000	0.68431	0.655000	0.94253	CGT	G|1.000;A|0.000	0.000	weak		0.597	KRT37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257714.2	NM_003770	
C16orf46	123775	hgsc.bcm.edu	37	16	81095099	81095099	+	Silent	SNP	C	C	G	rs2287995	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:81095099C>G	ENST00000299578.5	-	4	1090	c.855G>C	c.(853-855)gcG>gcC	p.A285A	C16orf46_ENST00000444657.3_5'Flank|RP11-303E16.8_ENST00000564536.1_RNA|C16orf46_ENST00000378611.4_Silent_p.A285A	NM_152337.2	NP_689550.2	Q6P387	CP046_HUMAN	chromosome 16 open reading frame 46	285						cytoplasm (GO:0005737)|nucleus (GO:0005634)				NS(1)|endometrium(2)|large_intestine(3)|lung(9)|prostate(1)|stomach(1)|urinary_tract(1)	18						ATATCTGGGCCGCTGGGGAAG	0.577													C|||	541	0.108027	0.0514	0.1066	5008	,	,		17352	0.1944		0.0934	False		,,,				2504	0.1115				p.A285A		Atlas-SNP	.											C16orf46_ENST00000378611,right_upper_lobe,carcinoma,-1,2	C16orf46	57	2	0			c.G855C						PASS	.	C	,	215,4189	122.9+/-160.3	7,201,1994	117.0	111.0	113.0		855,855	-0.8	0.0	16	dbSNP_100	113	662,7938	161.6+/-214.5	25,612,3663	no	coding-synonymous,coding-synonymous	C16orf46	NM_001100873.1,NM_152337.2	,	32,813,5657	GG,GC,CC		7.6977,4.8819,6.7441	,	285/389,285/396	81095099	877,12127	2202	4300	6502	SO:0001819	synonymous_variant	123775	exon3			CTGGGCCGCTGGG	BC064143	CCDS10932.1, CCDS42201.1	16q23.2	2012-10-09			ENSG00000166455	ENSG00000166455			26525	protein-coding gene	gene with protein product							Standard	NM_152337		Approved	FLJ32702	uc002fgc.4	Q6P387	OTTHUMG00000137629	ENST00000299578.5:c.855G>C	16.37:g.81095099C>G		Somatic	305	1	0.00327869		WXS	Illumina HiSeq	Phase_I	273	172	0.630037	NM_001100873	Q96MA7	Silent	SNP	ENST00000299578.5	37	CCDS10932.1																																																																																			C|0.916;G|0.084	0.084	strong		0.577	C16orf46-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000269054.2	NM_152337	
ADAMTSL3	57188	hgsc.bcm.edu	37	15	84651290	84651290	+	Silent	SNP	T	T	C	rs7176737	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:84651290T>C	ENST00000286744.5	+	21	3134	c.2910T>C	c.(2908-2910)caT>caC	p.H970H	ADAMTSL3_ENST00000567476.1_Silent_p.H970H	NM_207517.2	NP_997400.2	P82987	ATL3_HUMAN	ADAMTS-like 3	970	Ig-like C2-type 1.					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)			TAAAAATCCATGGTCTTGCTG	0.542													C|||	4353	0.869209	0.9735	0.8703	5008	,	,		18955	0.9544		0.7783	False		,,,				2504	0.7331				p.H970H		Atlas-SNP	.											.	ADAMTSL3	290	.	0			c.T2910C						PASS	.	C		4145,261	148.8+/-183.1	1951,243,9	84.0	84.0	84.0		2910	2.7	1.0	15	dbSNP_116	84	6702,1898	336.7+/-322.0	2603,1496,201	no	coding-synonymous	ADAMTSL3	NM_207517.2		4554,1739,210	CC,CT,TT		22.0698,5.9237,16.6		970/1692	84651290	10847,2159	2203	4300	6503	SO:0001819	synonymous_variant	57188	exon21			AATCCATGGTCTT	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.2910T>C	15.37:g.84651290T>C		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	85	85	1	NM_207517	A1A566|A1A567|Q9ULI7	Silent	SNP	ENST00000286744.5	37	CCDS10326.1																																																																																			T|0.141;C|0.859	0.859	strong		0.542	ADAMTSL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304007.2	NM_207517	
CIB1	10519	hgsc.bcm.edu	37	15	90771704	90771704	+	IGR	SNP	G	G	A	rs3751656	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:90771704G>A	ENST00000328649.6	-	0	1247				SEMA4B_ENST00000332496.6_Silent_p.P781P|SEMA4B_ENST00000411539.2_Silent_p.P781P|SEMA4B_ENST00000379122.3_Intron	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	50	0	0		WXS	Illumina HiSeq	Phase_I	60	37	0.616667	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		
LAMA5	3911	hgsc.bcm.edu	37	20	60898654	60898654	+	Silent	SNP	G	G	A	rs11696243	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:60898654G>A	ENST00000252999.3	-	45	5988	c.5922C>T	c.(5920-5922)aaC>aaT	p.N1974N		NM_005560.3	NP_005551.3	O15230	LAMA5_HUMAN	laminin, alpha 5	1974	Laminin EGF-like 19. {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)			TGGGGTCACCGTTGCCGCTGC	0.697													.|||	60	0.0119808	0.0015	0.0216	5008	,	,		13277	0.0		0.0388	False		,,,				2504	0.0041				p.N1974N		Atlas-SNP	.											.	LAMA5	268	.	0			c.C5922T						PASS	.	G		32,4354		0,32,2161	21.0	29.0	26.0		5922	-2.2	0.2	20	dbSNP_120	26	256,8322		4,248,4037	no	coding-synonymous	LAMA5	NM_005560.3		4,280,6198	AA,AG,GG		2.9844,0.7296,2.2215		1974/3696	60898654	288,12676	2193	4289	6482	SO:0001819	synonymous_variant	3911	exon45			GTCACCGTTGCCG	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.5922C>T	20.37:g.60898654G>A		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	97	47	0.484536	NM_005560	Q8TDF8|Q8WZA7|Q9H1P1	Silent	SNP	ENST00000252999.3	37	CCDS33502.1																																																																																			G|0.980;A|0.020	0.020	strong		0.697	LAMA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080014.2	NM_005560	
AP4B1	10717	hgsc.bcm.edu	37	1	114438951	114438951	+	Missense_Mutation	SNP	A	A	G	rs1217401	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:114438951A>G	ENST00000369569.1	-	8	1719	c.1439T>C	c.(1438-1440)tTg>tCg	p.L480S	AP4B1_ENST00000256658.4_Missense_Mutation_p.L480S|AP4B1-AS1_ENST00000419536.1_RNA|AP4B1_ENST00000462591.1_5'UTR|AP4B1_ENST00000369567.1_Missense_Mutation_p.L312S	NM_001253852.1	NP_001240781.1	Q9Y6B7	AP4B1_HUMAN	adaptor-related protein complex 4, beta 1 subunit	480			L -> S (in dbSNP:rs1217401). {ECO:0000269|PubMed:10066790, ECO:0000269|Ref.3}.		intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	clathrin adaptor complex (GO:0030131)|coated pit (GO:0005905)|trans-Golgi network (GO:0005802)	protein transporter activity (GO:0008565)|transporter activity (GO:0005215)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(9)|ovary(3)|prostate(3)	25	Lung SC(450;0.184)	all_cancers(81;4.5e-08)|all_epithelial(167;1.1e-07)|all_lung(203;1.53e-05)|Lung NSC(69;2.76e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		AAGGCGCAGCAAAGCAGTGAG	0.453													A|||	1888	0.376997	0.8003	0.2536	5008	,	,		20016	0.0794		0.2694	False		,,,				2504	0.3098				p.L480S		Atlas-SNP	.											.	AP4B1	72	.	0			c.T1439C						PASS	.	A	SER/LEU	3017,1389	689.6+/-405.1	1046,925,232	158.0	154.0	155.0		1439	6.0	0.9	1	dbSNP_87	155	2679,5921	430.6+/-356.6	424,1831,2045	yes	missense	AP4B1	NM_006594.2	145	1470,2756,2277	GG,GA,AA		31.1512,31.5252,43.7952	possibly-damaging	480/740	114438951	5696,7310	2203	4300	6503	SO:0001583	missense	10717	exon9			CGCAGCAAAGCAG	AF092094	CCDS865.1	1p13.2	2012-03-30			ENSG00000134262	ENSG00000134262			572	protein-coding gene	gene with protein product	"""beta 4 subunit of AP-4"""	607245	"""spastic paraplegia 47"""	SPG47		10066790	Standard	NM_006594		Approved	BETA-4	uc001eeb.3	Q9Y6B7	OTTHUMG00000011943	ENST00000369569.1:c.1439T>C	1.37:g.114438951A>G	ENSP00000358582:p.Leu480Ser	Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	123	123	1	NM_006594	B7Z4X3|Q59EJ4|Q96CL6	Missense_Mutation	SNP	ENST00000369569.1	37	CCDS865.1	756	0.34615384615384615	390	0.7926829268292683	103	0.2845303867403315	54	0.0944055944055944	209	0.2757255936675462	A	15.36	2.810246	0.50421	0.684748	0.311512	ENSG00000134262	ENST00000369567;ENST00000369569;ENST00000256658	T;T;T	0.24538	1.85;1.85;1.85	6.04	6.04	0.98038	Clathrin/coatomer adaptor, adaptin-like, N-terminal (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.389021	0.27996	N	0.017016	T	0.09598	0.0236	N	0.10809	0.05	0.09310	P	1.0	B;B;B;B	0.22541	0.071;0.008;0.033;0.001	B;B;B;B	0.30105	0.111;0.02;0.111;0.007	T	0.13442	-1.0509	9	0.52906	T	0.07	-2.4422	16.5885	0.84745	1.0:0.0:0.0:0.0	rs1217401;rs3170575;rs58628725;rs1217401	480;312;480;381	B2RBF6;B1ALD0;Q9Y6B7;B4DTG3	.;.;AP4B1_HUMAN;.	S	312;480;480	ENSP00000358580:L312S;ENSP00000358582:L480S;ENSP00000256658:L480S	ENSP00000256658:L480S	L	-	2	0	AP4B1	114240474	1.000000	0.71417	0.868000	0.34077	0.986000	0.74619	6.230000	0.72301	2.317000	0.78254	0.460000	0.39030	TTG	A|0.589;G|0.411	0.411	strong		0.453	AP4B1-009	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033037.1	NM_006594	
VPS16	64601	hgsc.bcm.edu	37	20	2840773	2840773	+	Silent	SNP	C	C	T	rs3818605	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:2840773C>T	ENST00000380445.3	+	3	288	c.216C>T	c.(214-216)tcC>tcT	p.S72S	VPS16_ENST00000380443.3_5'Flank|VPS16_ENST00000380469.3_Silent_p.S72S	NM_022575.2	NP_072097.2	Q9H269	VPS16_HUMAN	vacuolar protein sorting 16 homolog (S. cerevisiae)	72					intracellular protein transport (GO:0006886)|viral entry into host cell (GO:0046718)	actin filament (GO:0005884)|axon (GO:0030424)|early endosome (GO:0005769)|HOPS complex (GO:0030897)|late endosome (GO:0005770)|lysosomal membrane (GO:0005765)|neuronal cell body (GO:0043025)|recycling endosome (GO:0055037)		p.S72S(2)		NS(3)|breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(6)|lung(16)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|stomach(1)	37						ACTCTGCTTCCGGCATGCCTC	0.577													C|||	822	0.164137	0.0227	0.1009	5008	,	,		18545	0.25		0.165	False		,,,				2504	0.3108				p.S72S		Atlas-SNP	.											VPS16,NS,carcinoma,0,2	VPS16	76	2	2	Substitution - coding silent(2)	prostate(1)|stomach(1)	c.C216T						PASS	.	C	,	211,4195	129.8+/-166.5	6,199,1998	93.0	87.0	89.0		216,216	-7.5	0.4	20	dbSNP_107	89	1315,7285	258.7+/-282.2	100,1115,3085	no	coding-synonymous,coding-synonymous	VPS16	NM_022575.2,NM_080413.1	,	106,1314,5083	TT,TC,CC		15.2907,4.7889,11.733	,	72/840,72/696	2840773	1526,11480	2203	4300	6503	SO:0001819	synonymous_variant	64601	exon3			TGCTTCCGGCATG	AF308801	CCDS13036.1, CCDS13037.1	20p13	2009-07-07	2009-07-07	2009-07-07	ENSG00000215305	ENSG00000215305			14584	protein-coding gene	gene with protein product		608550					Standard	NM_022575		Approved		uc002whe.3	Q9H269	OTTHUMG00000031714	ENST00000380445.3:c.216C>T	20.37:g.2840773C>T		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	69	31	0.449275	NM_022575	Q5JUB1|Q8WU31|Q96EE7|Q96N92|Q9H1Q4|Q9H1Q5	Silent	SNP	ENST00000380445.3	37	CCDS13036.1																																																																																			C|0.867;T|0.133	0.133	strong		0.577	VPS16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077658.2	NM_022575	
C16orf46	123775	hgsc.bcm.edu	37	16	81094951	81094951	+	Missense_Mutation	SNP	A	A	G	rs10459872	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:81094951A>G	ENST00000299578.5	-	4	1238	c.1003T>C	c.(1003-1005)Tac>Cac	p.Y335H	C16orf46_ENST00000444657.3_5'Flank|RP11-303E16.8_ENST00000564536.1_RNA|C16orf46_ENST00000378611.4_Missense_Mutation_p.Y335H	NM_152337.2	NP_689550.2	Q6P387	CP046_HUMAN	chromosome 16 open reading frame 46	335			Y -> H (in dbSNP:rs10459872).			cytoplasm (GO:0005737)|nucleus (GO:0005634)				NS(1)|endometrium(2)|large_intestine(3)|lung(9)|prostate(1)|stomach(1)|urinary_tract(1)	18						TTGGATTTGTAGCTTTGCACT	0.537													A|||	524	0.104633	0.0393	0.1052	5008	,	,		18310	0.1944		0.0934	False		,,,				2504	0.1115				p.Y335H		Atlas-SNP	.											.	C16orf46	57	.	0			c.T1003C						PASS	.	A	HIS/TYR,HIS/TYR	181,4223	117.1+/-155.0	6,169,2027	135.0	130.0	132.0		1003,1003	0.3	0.4	16	dbSNP_119	132	670,7930	169.6+/-220.9	26,618,3656	yes	missense,missense	C16orf46	NM_001100873.1,NM_152337.2	83,83	32,787,5683	GG,GA,AA		7.7907,4.1099,6.5441	benign,benign	335/389,335/396	81094951	851,12153	2202	4300	6502	SO:0001583	missense	123775	exon3			ATTTGTAGCTTTG	BC064143	CCDS10932.1, CCDS42201.1	16q23.2	2012-10-09			ENSG00000166455	ENSG00000166455			26525	protein-coding gene	gene with protein product							Standard	NM_152337		Approved	FLJ32702	uc002fgc.4	Q6P387	OTTHUMG00000137629	ENST00000299578.5:c.1003T>C	16.37:g.81094951A>G	ENSP00000299578:p.Tyr335His	Somatic	262	0	0		WXS	Illumina HiSeq	Phase_I	263	153	0.581749	NM_001100873	Q96MA7	Missense_Mutation	SNP	ENST00000299578.5	37	CCDS10932.1	243	0.11126373626373626	20	0.04065040650406504	38	0.10497237569060773	111	0.19405594405594406	74	0.09762532981530343	A	0.219	-1.029958	0.02045	0.041099	0.077907	ENSG00000166455	ENST00000378611;ENST00000444657;ENST00000299578	T;T	0.17213	2.29;2.29	5.23	0.334	0.15948	.	0.903604	0.09492	N	0.794752	T	0.00012	0.0000	N	0.12746	0.255	0.80722	P	0.0	B;B	0.12013	0.005;0.005	B;B	0.14578	0.011;0.011	T	0.46062	-0.9218	9	0.15499	T	0.54	.	0.931	0.01335	0.4241:0.1573:0.267:0.1515	rs10459872;rs56607219;rs59323807;rs10459872	335;335	Q6P387-2;Q6P387	.;CP046_HUMAN	H	335;62;335	ENSP00000367874:Y335H;ENSP00000299578:Y335H	ENSP00000299578:Y335H	Y	-	1	0	C16orf46	79652452	0.013000	0.17824	0.415000	0.26534	0.010000	0.07245	0.090000	0.15025	0.393000	0.25203	-0.400000	0.06385	TAC	A|0.912;G|0.088	0.088	strong		0.537	C16orf46-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000269054.2	NM_152337	
OSBPL10	114884	hgsc.bcm.edu	37	3	31712393	31712393	+	Silent	SNP	C	C	T	rs3749405	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:31712393C>T	ENST00000396556.2	-	9	1931	c.1809G>A	c.(1807-1809)ccG>ccA	p.P603P	OSBPL10_ENST00000438237.2_Silent_p.P539P	NM_017784.4	NP_060254.2	Q9BXB5	OSB10_HUMAN	oxysterol binding protein-like 10	603					lipid transport (GO:0006869)		cholesterol binding (GO:0015485)			breast(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(15)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	34				STAD - Stomach adenocarcinoma(1;0.00406)		GCTCCACCCACGGGATGGTGA	0.567													T|||	2832	0.565495	0.854	0.4107	5008	,	,		20776	0.6756		0.3728	False		,,,				2504	0.3701				p.P603P		Atlas-SNP	.											OSBPL10_ENST00000396556,extremity,malignant_melanoma,-1,6	OSBPL10	160	6	0			c.G1809A						PASS	.	T	,	3339,1067	389.1+/-327.2	1266,807,130	134.0	118.0	123.0		1617,1809	-10.9	0.0	3	dbSNP_107	123	3086,5514	659.5+/-401.7	533,2020,1747	no	coding-synonymous,coding-synonymous	OSBPL10	NM_001174060.1,NM_017784.4	,	1799,2827,1877	TT,TC,CC		35.8837,24.217,49.4003	,	539/701,603/765	31712393	6425,6581	2203	4300	6503	SO:0001819	synonymous_variant	114884	exon9			CACCCACGGGATG	AF392451	CCDS2651.1, CCDS54559.1	3p23	2013-01-10			ENSG00000144645	ENSG00000144645		"""Oxysterol binding proteins"", ""Pleckstrin homology (PH) domain containing"""	16395	protein-coding gene	gene with protein product		606738					Standard	NM_001174060		Approved		uc021wuu.1	Q9BXB5	OTTHUMG00000130672	ENST00000396556.2:c.1809G>A	3.37:g.31712393C>T		Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	137	74	0.540146	NM_017784	B4E212|Q9BTU5	Silent	SNP	ENST00000396556.2	37	CCDS2651.1	1223	0.559981684981685	412	0.8373983739837398	150	0.4143646408839779	379	0.6625874125874126	282	0.3720316622691293	T	0.057	-1.232567	0.01505	0.75783	0.358837	ENSG00000144645	ENST00000429492	.	.	.	5.47	-10.9	0.00192	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999976	.	.	.	.	.	.	T	0.24440	-1.0160	3	.	.	.	-18.8515	1.9525	0.03370	0.1631:0.2346:0.2062:0.396	rs3749405;rs17383168;rs17849743;rs3749405	.	.	.	H	372	.	.	R	-	2	0	OSBPL10	31687397	0.000000	0.05858	0.005000	0.12908	0.008000	0.06430	-6.416000	0.00067	-6.038000	0.00007	-2.931000	0.00088	CGT	C|0.470;T|0.530	0.530	strong		0.567	OSBPL10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253165.2		
VILL	50853	hgsc.bcm.edu	37	3	38047680	38047680	+	Silent	SNP	G	G	A	rs11707277	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	113	0	0		WXS	Illumina HiSeq	Phase_I	103	55	0.533981	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	
IRGC	56269	hgsc.bcm.edu	37	19	44223145	44223145	+	Silent	SNP	C	C	T	rs34439296	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:44223145C>T	ENST00000244314.5	+	2	634	c.435C>T	c.(433-435)tgC>tgT	p.C145C		NM_019612.3	NP_062558.1	Q6NXR0	IIGP5_HUMAN	immunity-related GTPase family, cinema	145	IRG-type G.					membrane (GO:0016020)	GTP binding (GO:0005525)|hydrolase activity, acting on acid anhydrides (GO:0016817)			central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(16)|ovary(1)|prostate(1)|skin(2)	25		Prostate(69;0.0435)				CCCGCCGCTGCGGGGCCGTCG	0.652													C|||	258	0.0515176	0.0242	0.0548	5008	,	,		15818	0.001		0.1272	False		,,,				2504	0.0603				p.C145C	Colon(189;350 2037 11447 13433 38914)	Atlas-SNP	.											IRGC,NS,carcinoma,+1,1	IRGC	67	1	0			c.C435T						PASS	.	C		160,4046		4,152,1947	12.0	12.0	12.0		435	-0.3	0.0	19	dbSNP_126	12	901,7403		48,805,3299	no	coding-synonymous	IRGC	NM_019612.3		52,957,5246	TT,TC,CC		10.8502,3.8041,8.4812		145/464	44223145	1061,11449	2103	4152	6255	SO:0001819	synonymous_variant	56269	exon2			CCGCTGCGGGGCC	BC066939	CCDS12629.1	19q13.32	2008-02-05	2005-10-31	2005-10-31	ENSG00000124449	ENSG00000124449			28835	protein-coding gene	gene with protein product			"""immunity-related GTPase family, cinema 1"""	IRGC1		12477932	Standard	NM_019612		Approved	Iigp5, CINEMA	uc002oxh.3	Q6NXR0	OTTHUMG00000154587	ENST00000244314.5:c.435C>T	19.37:g.44223145C>T		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	61	40	0.655738	NM_019612	Q05BR8	Silent	SNP	ENST00000244314.5	37	CCDS12629.1																																																																																			C|0.927;T|0.073	0.073	strong		0.652	IRGC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336191.1	NM_019612	
PCDHB6	56130	hgsc.bcm.edu	37	5	140532165	140532165	+	Missense_Mutation	SNP	G	G	A	rs17844444	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	180	0	0		WXS	Illumina HiSeq	Phase_I	157	66	0.420382	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	
HSPA2	3306	hgsc.bcm.edu	37	14	65008004	65008004	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:65008004C>T	ENST00000394709.1	+	2	513	c.437C>T	c.(436-438)aCg>aTg	p.T146M	HSPA2_ENST00000554883.1_Intron|RP11-973N13.4_ENST00000554918.1_RNA|HSPA2_ENST00000247207.6_Missense_Mutation_p.T146M			P54652	HSP72_HUMAN	heat shock 70kDa protein 2	146					male meiosis (GO:0007140)|male meiosis I (GO:0007141)|negative regulation of inclusion body assembly (GO:0090084)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G2/M transition of mitotic cell cycle (GO:0031662)|protein refolding (GO:0042026)|response to unfolded protein (GO:0006986)|spermatid development (GO:0007286)|synaptonemal complex disassembly (GO:0070194)	blood microparticle (GO:0072562)|CatSper complex (GO:0036128)|cell surface (GO:0009986)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|male germ cell nucleus (GO:0001673)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|glycolipid binding (GO:0051861)|unfolded protein binding (GO:0051082)			breast(1)|endometrium(4)|large_intestine(3)|lung(7)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	22				all cancers(60;0.00515)|OV - Ovarian serous cystadenocarcinoma(108;0.00584)|BRCA - Breast invasive adenocarcinoma(234;0.045)		GCGGTCATAACGGTCCCGGCC	0.607																																					p.T146M	Pancreas(136;1211 1835 24894 31984 38227)	Atlas-SNP	.											HSPA2,NS,carcinoma,-1,1	HSPA2	83	1	0			c.C437T						scavenged	.						46.0	46.0	46.0					14																	65008004		2203	4300	6503	SO:0001583	missense	3306	exon1			TCATAACGGTCCC	L26336, BC001752	CCDS9766.1	14q23	2012-10-02	2002-08-29		ENSG00000126803	ENSG00000126803		"""Heat shock proteins / HSP70"""	5235	protein-coding gene	gene with protein product		140560	"""heat shock 70kD protein 2"""				Standard	NM_021979		Approved		uc001xhk.4	P54652	OTTHUMG00000141311	ENST00000394709.1:c.437C>T	14.37:g.65008004C>T	ENSP00000378199:p.Thr146Met	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	73	2	0.0273973	NM_021979	Q15508|Q53XM3|Q9UE78	Missense_Mutation	SNP	ENST00000394709.1	37	CCDS9766.1	.	.	.	.	.	.	.	.	.	.	C	18.65	3.669008	0.67814	.	.	ENSG00000126803	ENST00000394709;ENST00000247207	T;T	0.09350	2.99;2.99	5.38	5.38	0.77491	.	0.000000	0.56097	U	0.000031	T	0.63414	0.2509	H	0.99998	5.495	0.58432	D	0.999996	D	0.89917	1.0	D	0.71184	0.972	D	0.85382	0.1120	10	0.87932	D	0	-6.5366	19.1258	0.93384	0.0:1.0:0.0:0.0	.	146	P54652	HSP72_HUMAN	M	146	ENSP00000378199:T146M;ENSP00000247207:T146M	ENSP00000247207:T146M	T	+	2	0	HSPA2	64077757	1.000000	0.71417	0.994000	0.49952	0.916000	0.54674	7.818000	0.86416	2.514000	0.84764	0.563000	0.77884	ACG	.	.	none		0.607	HSPA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280651.1		
FAM71C	196472	hgsc.bcm.edu	37	12	100042040	100042040	+	Missense_Mutation	SNP	C	C	G	rs11109968	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:100042040C>G	ENST00000324341.1	+	1	510	c.88C>G	c.(88-90)Cgg>Ggg	p.R30G	ANKS1B_ENST00000547010.1_Intron|ANKS1B_ENST00000547776.2_Intron|ANKS1B_ENST00000329257.7_Intron	NM_153364.3	NP_699195.1	Q8NEG0	FA71C_HUMAN	family with sequence similarity 71, member C	30			R -> G (in dbSNP:rs11109968).							breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(8)|upper_aerodigestive_tract(1)|urinary_tract(1)	18				OV - Ovarian serous cystadenocarcinoma(2;0.00733)|Epithelial(2;0.0385)|all cancers(2;0.19)		GAAGCTGCAGCGGCAACTGTA	0.483													C|||	1096	0.21885	0.3094	0.1787	5008	,	,		20718	0.0992		0.2903	False		,,,				2504	0.1748				p.R30G		Atlas-SNP	.											.	FAM71C	48	.	0			c.C88G						PASS	.	C	,GLY/ARG	1341,3065	449.4+/-349.0	189,963,1051	100.0	97.0	98.0		,88	2.1	0.3	12	dbSNP_120	98	2549,6051	416.0+/-352.0	387,1775,2138	yes	intron,missense	ANKS1B,FAM71C	NM_152788.4,NM_153364.3	,125	576,2738,3189	GG,GC,CC		29.6395,30.4358,29.9093	,probably-damaging	,30/242	100042040	3890,9116	2203	4300	6503	SO:0001583	missense	196472	exon1			CTGCAGCGGCAAC		CCDS9072.1	12q23.1	2006-02-03				ENSG00000180219			28594	protein-coding gene	gene with protein product						12477932	Standard	NM_153364		Approved	MGC39520	uc001tgn.3	Q8NEG0		ENST00000324341.1:c.88C>G	12.37:g.100042040C>G	ENSP00000315247:p.Arg30Gly	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	122	67	0.54918	NM_153364	B2R6Y6	Missense_Mutation	SNP	ENST00000324341.1	37	CCDS9072.1	518	0.23717948717948717	154	0.3130081300813008	74	0.20441988950276244	56	0.0979020979020979	234	0.3087071240105541	C	9.922	1.212320	0.22289	0.304358	0.296395	ENSG00000180219	ENST00000324341	T	0.12879	2.64	3.94	2.13	0.27403	.	0.796330	0.10386	N	0.680965	T	0.00012	0.0000	L	0.43152	1.355	0.58432	P	4.000000000004E-6	D	0.55385	0.971	P	0.54544	0.755	T	0.46317	-0.9200	8	.	.	.	-0.5548	6.5232	0.22287	0.0:0.7798:0.0:0.2202	rs11109968;rs52790290;rs11109968	30	Q8NEG0	FA71C_HUMAN	G	30	ENSP00000315247:R30G	.	R	+	1	2	FAM71C	98566171	0.070000	0.21116	0.316000	0.25252	0.024000	0.10985	-0.007000	0.12810	0.643000	0.30638	-0.263000	0.10527	CGG	C|0.729;G|0.271	0.271	strong		0.483	FAM71C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408458.1	NM_153364	
MYH4	4622	hgsc.bcm.edu	37	17	10355763	10355763	+	Missense_Mutation	SNP	T	T	C	rs917361	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:10355763T>C	ENST00000255381.2	-	26	3428	c.3318A>G	c.(3316-3318)atA>atG	p.I1106M	CTC-297N7.11_ENST00000587182.2_RNA|RP11-799N11.1_ENST00000399342.2_RNA|RP11-799N11.1_ENST00000581304.1_RNA	NM_017533.2	NP_060003.2	Q9Y623	MYH4_HUMAN	myosin, heavy chain 4, skeletal muscle	1106			I -> M (in dbSNP:rs917361). {ECO:0000269|PubMed:10388558}.		actin filament-based movement (GO:0030048)|ATP catabolic process (GO:0006200)|membrane organization (GO:0061024)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|response to activity (GO:0014823)	muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin filament (GO:0032982)|sarcomere (GO:0030017)	ATP binding (GO:0005524)|double-stranded RNA binding (GO:0003725)|microfilament motor activity (GO:0000146)			NS(4)|breast(8)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(13)|lung(72)|ovary(10)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	149						TTTGTAGCTGTATTGCAAGGG	0.353													C|||	2674	0.533946	0.3442	0.5187	5008	,	,		18291	0.8631		0.3698	False		,,,				2504	0.6309				p.I1106M		Atlas-SNP	.											.	MYH4	349	.	0			c.A3318G						PASS	.	C	MET/ILE	1585,2821	666.0+/-401.6	281,1023,899	150.0	138.0	142.0		3318	4.6	1.0	17	dbSNP_86	142	3577,5023	628.0+/-398.0	760,2057,1483	yes	missense	MYH4	NM_017533.2	10	1041,3080,2382	CC,CT,TT		41.593,35.9737,39.6894	benign	1106/1940	10355763	5162,7844	2203	4300	6503	SO:0001583	missense	4622	exon26			TAGCTGTATTGCA		CCDS11154.1	17p13.1	2013-09-19	2006-09-29		ENSG00000264424	ENSG00000264424		"""Myosins / Myosin superfamily : Class II"""	7574	protein-coding gene	gene with protein product		160742	"""myosin, heavy polypeptide 4, skeletal muscle"""			8518795	Standard	NM_017533		Approved	MYH2B, MyHC-2B, MyHC-IIb	uc002gmn.3	Q9Y623	OTTHUMG00000130365	ENST00000255381.2:c.3318A>G	17.37:g.10355763T>C	ENSP00000255381:p.Ile1106Met	Somatic	233	1	0.00429185		WXS	Illumina HiSeq	Phase_I	201	109	0.542289	NM_017533		Missense_Mutation	SNP	ENST00000255381.2	37	CCDS11154.1	1125	0.5151098901098901	162	0.32926829268292684	181	0.5	498	0.8706293706293706	284	0.37467018469656993	C	7.093	0.572480	0.13623	0.359737	0.41593	ENSG00000141048	ENST00000255381	D	0.82984	-1.67	5.6	4.63	0.57726	Myosin tail (1);	0.000000	0.45361	N	0.000374	T	0.00012	0.0000	N	0.03050	-0.425	0.58432	P	9.000000000036756E-6	B	0.02656	0.0	B	0.08055	0.003	T	0.38950	-0.9637	9	0.34782	T	0.22	.	4.1163	0.10083	0.1302:0.6059:0.126:0.1378	rs917361;rs3744556;rs17811136;rs52820909;rs58019198;rs917361	1106	Q9Y623	MYH4_HUMAN	M	1106	ENSP00000255381:I1106M	ENSP00000255381:I1106M	I	-	3	3	MYH4	10296488	0.004000	0.15560	0.998000	0.56505	0.963000	0.63663	-0.314000	0.08092	0.854000	0.35336	-0.119000	0.15052	ATA	C|0.466;N|0.000	0.466	strong		0.353	MYH4-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252731.1	NM_017533	
GAR1	54433	hgsc.bcm.edu	37	4	110739212	110739212	+	Missense_Mutation	SNP	A	A	G	rs143266987		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:110739212A>G	ENST00000226796.6	+	3	599	c.335A>G	c.(334-336)aAa>aGa	p.K112R	RP11-602N24.3_ENST00000609440.1_lincRNA|GAR1_ENST00000394631.3_Missense_Mutation_p.K112R	NM_018983.3	NP_061856.1	Q9NY12	GAR1_HUMAN	GAR1 ribonucleoprotein	112					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|pseudouridine synthesis (GO:0001522)|rRNA processing (GO:0006364)	box H/ACA snoRNP complex (GO:0031429)|nucleolus (GO:0005730)|nucleus (GO:0005634)	cation channel activity (GO:0005261)|poly(A) RNA binding (GO:0044822)			kidney(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)	9						CAAATTGGAAAAGTGGATGAA	0.348													A|||	1	0.000199681	0.0	0.0014	5008	,	,		19750	0.0		0.0	False		,,,				2504	0.0				p.K112R		Atlas-SNP	.											.	GAR1	16	.	0			c.A335G						PASS	.	A	ARG/LYS,ARG/LYS	0,4406		0,0,2203	83.0	86.0	85.0		335,335	4.8	1.0	4	dbSNP_134	85	6,8594	3.0+/-9.4	0,6,4294	yes	missense,missense	GAR1	NM_018983.3,NM_032993.2	26,26	0,6,6497	GG,GA,AA		0.0698,0.0,0.0461	probably-damaging,probably-damaging	112/218,112/218	110739212	6,13000	2203	4300	6503	SO:0001583	missense	54433	exon3			TTGGAAAAGTGGA	AJ276003	CCDS34050.1	4q	2013-07-31	2013-07-31	2008-10-13	ENSG00000109534	ENSG00000109534			14264	protein-coding gene	gene with protein product		606468	"""nucleolar protein family A, member 1 (H/ACA small nucleolar RNPs)"", ""GAR1 ribonucleoprotein homolog (yeast)"""	NOLA1		10757788	Standard	XM_005263069		Approved		uc003hzu.3	Q9NY12	OTTHUMG00000161108	ENST00000226796.6:c.335A>G	4.37:g.110739212A>G	ENSP00000226796:p.Lys112Arg	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	60	30	0.5	NM_018983	Q5MJQ2	Missense_Mutation	SNP	ENST00000226796.6	37	CCDS34050.1	.	.	.	.	.	.	.	.	.	.	A	24.7	4.564745	0.86439	0.0	6.98E-4	ENSG00000109534	ENST00000394631;ENST00000226796	.	.	.	4.78	4.78	0.61160	Translation elongation/initiation factor/Ribosomal, beta-barrel (1);	0.000000	0.85682	D	0.000000	T	0.79587	0.4471	M	0.81341	2.54	0.58432	D	0.999997	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	T	0.82928	-0.0214	9	0.72032	D	0.01	.	14.6205	0.68582	1.0:0.0:0.0:0.0	.	112;112	Q9NY12-2;Q9NY12	.;GAR1_HUMAN	R	112	.	ENSP00000226796:K112R	K	+	2	0	GAR1	110958661	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.855000	0.92236	1.913000	0.55393	0.533000	0.62120	AAA	A|1.000;G|0.000	0.000	weak		0.348	GAR1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363810.2		
KIAA1755	85449	hgsc.bcm.edu	37	20	36859711	36859711	+	Silent	SNP	G	G	A	rs1205418	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:36859711G>A	ENST00000279024.4	-	5	2035	c.1764C>T	c.(1762-1764)gcC>gcT	p.A588A		NM_001029864.1	NP_001025035.1	Q5JYT7	K1755_HUMAN	KIAA1755	588										breast(2)|endometrium(3)|kidney(1)|large_intestine(5)|lung(31)|ovary(5)|pancreas(2)|skin(4)|stomach(1)	54		Myeloproliferative disorder(115;0.00874)				GGGGCCGCCCGGCCCTGTCCC	0.632													G|||	1303	0.260184	0.2458	0.2219	5008	,	,		18278	0.2778		0.2833	False		,,,				2504	0.2648				p.A588A		Atlas-SNP	.											.	KIAA1755	145	.	0			c.C1764T						PASS	.	G		1203,3203	396.7+/-330.2	161,881,1161	39.0	38.0	38.0		1764	-9.9	0.0	20	dbSNP_87	38	2617,5983	395.5+/-345.1	424,1769,2107	no	coding-synonymous	KIAA1755	NM_001029864.1		585,2650,3268	AA,AG,GG		30.4302,27.3037,29.3711		588/1201	36859711	3820,9186	2203	4300	6503	SO:0001819	synonymous_variant	85449	exon5			CCGCCCGGCCCTG	AB051542	CCDS33467.1	20q11.23	2007-12-07			ENSG00000149633	ENSG00000149633			29372	protein-coding gene	gene with protein product						11214970	Standard	NM_001029864		Approved	RP5-1054A22.3	uc002xhy.1	Q5JYT7	OTTHUMG00000032436	ENST00000279024.4:c.1764C>T	20.37:g.36859711G>A		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	36	14	0.388889	NM_001029864	Q9C0A8	Silent	SNP	ENST00000279024.4	37	CCDS33467.1																																																																																			G|0.703;A|0.297	0.297	strong		0.632	KIAA1755-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079144.3	NM_001029864	
TRIM38	10475	hgsc.bcm.edu	37	6	25983777	25983777	+	Silent	SNP	C	C	T	rs17528178	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:25983777C>T	ENST00000357085.3	+	8	1736	c.1260C>T	c.(1258-1260)gcC>gcT	p.A420A	U91328.21_ENST00000608931.1_RNA|TRIM38_ENST00000349458.3_Silent_p.A420A	NM_006355.3	NP_006346.1	O00635	TRI38_HUMAN	tripartite motif containing 38	420	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				negative regulation of defense response to virus (GO:0050687)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of viral entry into host cell (GO:0046598)|positive regulation of viral genome replication (GO:0045070)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein K48-linked ubiquitination (GO:0070936)|regulation of interferon-beta production (GO:0032648)|signal transduction (GO:0007165)	intracellular (GO:0005622)	signal transducer activity (GO:0004871)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(5)|lung(8)|upper_aerodigestive_tract(2)	23						ACTATGAGGCCGGAGTTGTAT	0.473													C|||	161	0.0321486	0.0514	0.0403	5008	,	,		18020	0.0		0.0646	False		,,,				2504	0.0				p.A420A		Atlas-SNP	.											.	TRIM38	50	.	0			c.C1260T						PASS	.	C		247,4159	144.2+/-179.2	6,235,1962	87.0	85.0	86.0		1260	-8.5	0.0	6	dbSNP_123	86	634,7966	163.3+/-215.9	22,590,3688	no	coding-synonymous	TRIM38	NM_006355.2		28,825,5650	TT,TC,CC		7.3721,5.606,6.7738		420/466	25983777	881,12125	2203	4300	6503	SO:0001819	synonymous_variant	10475	exon8			TGAGGCCGGAGTT	U90547	CCDS4568.1	6p21.3	2011-04-20	2011-01-25	2002-06-07	ENSG00000112343	ENSG00000112343		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	10059	protein-coding gene	gene with protein product			"""ring finger protein 15"", ""tripartite motif-containing 38"""	RNF15			Standard	XR_241880		Approved	RORET	uc003nfm.4	O00635	OTTHUMG00000014414	ENST00000357085.3:c.1260C>T	6.37:g.25983777C>T		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	108	51	0.472222	NM_006355	B2R862	Silent	SNP	ENST00000357085.3	37	CCDS4568.1																																																																																			C|0.942;G|0.000;T|0.058	0.058	strong		0.473	TRIM38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040076.2		
SEMA7A	8482	hgsc.bcm.edu	37	15	74703929	74703929	+	Silent	SNP	T	T	C	rs741761	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	71	0	0		WXS	Illumina HiSeq	Phase_I	68	47	0.691176	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	
DIDO1	11083	hgsc.bcm.edu	37	20	61542863	61542863	+	Silent	SNP	G	G	A	rs11907248	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:61542863G>A	ENST00000266070.4	-	3	427	c.102C>T	c.(100-102)atC>atT	p.I34I	DIDO1_ENST00000395335.2_Silent_p.I34I|DIDO1_ENST00000370371.4_Silent_p.I34I|DIDO1_ENST00000266071.5_Silent_p.I34I|DIDO1_ENST00000370368.1_Silent_p.I34I|DIDO1_ENST00000354665.4_Silent_p.I34I|DIDO1_ENST00000370366.1_Silent_p.I34I|DIDO1_ENST00000395340.1_Silent_p.I34I|DIDO1_ENST00000395343.1_Silent_p.I34I	NM_033081.2	NP_149072.2	Q9BTC0	DIDO1_HUMAN	death inducer-obliterator 1	34					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)					CTCGCTTGGCGATAGTGGTCC	0.637													G|||	330	0.0658946	0.1218	0.0447	5008	,	,		17396	0.0238		0.0497	False		,,,				2504	0.0654				p.I34I	Melanoma(25;381 482 3385 5362 7955 17159 17174 40604 47095)	Atlas-SNP	.											.	DIDO1	321	.	0			c.C102T						PASS	.	G	,,,,,	535,3869	232.6+/-246.1	32,471,1699	66.0	67.0	67.0		102,102,102,102,102,102	-10.8	0.0	20	dbSNP_120	67	481,8119	136.7+/-193.7	13,455,3832	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	DIDO1	NM_001193369.1,NM_001193370.1,NM_022105.4,NM_033081.2,NM_080796.3,NM_080797.3	,,,,,	45,926,5531	AA,AG,GG		5.593,12.148,7.813	,,,,,	34/2241,34/1190,34/563,34/2241,34/563,34/1190	61542863	1016,11988	2202	4300	6502	SO:0001819	synonymous_variant	11083	exon3			CTTGGCGATAGTG	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.102C>T	20.37:g.61542863G>A		Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	146	65	0.445205	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																																																																																			G|0.924;A|0.076	0.076	strong		0.637	DIDO1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080091.2	NM_080796	
ACAN	176	hgsc.bcm.edu	37	15	89398631	89398631	+	Missense_Mutation	SNP	T	T	A	rs938609	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:89398631T>A	ENST00000561243.1	+	11	2815	c.2815T>A	c.(2815-2817)Tct>Act	p.S939T	ACAN_ENST00000439576.2_Missense_Mutation_p.S939T|ACAN_ENST00000559004.1_Missense_Mutation_p.S939T|ACAN_ENST00000352105.7_Missense_Mutation_p.S939T			P16112	PGCA_HUMAN	aggrecan	938	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.S939T(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)			TGAACTGCCCTCTGGAGCTGA	0.562													T|||	1964	0.392173	0.3389	0.3804	5008	,	,		19067	0.2073		0.6521	False		,,,				2504	0.3957				p.S939T		Atlas-SNP	.											ACAN,NS,carcinoma,0,1	ACAN	220	1	1	Substitution - Missense(1)	stomach(1)	c.T2815A						PASS	.	T	THR/SER,THR/SER	1491,2313		281,929,692	54.0	59.0	57.0		2815,2815	1.2	0.2	15	dbSNP_86	57	5335,2901		1718,1899,501	yes	missense,missense	ACAN	NM_001135.3,NM_013227.3	58,58	1999,2828,1193	AA,AT,TT		35.2234,39.1956,43.3056	probably-damaging,probably-damaging	939/2432,939/2531	89398631	6826,5214	1902	4118	6020	SO:0001583	missense	176	exon12			CTGCCCTCTGGAG	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.2815T>A	15.37:g.89398631T>A	ENSP00000453342:p.Ser939Thr	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	90	89	0.988889	NM_001135	Q13650|Q9UCD3|Q9UCP4|Q9UCP5|Q9UDE0	Missense_Mutation	SNP	ENST00000561243.1	37	CCDS53970.1	929	0.42536630036630035	156	0.3170731707317073	166	0.4585635359116022	101	0.17657342657342656	506	0.6675461741424802	T	14.92	2.678067	0.47886	0.391956	0.647766	ENSG00000157766	ENST00000439576;ENST00000352105;ENST00000268134	D;D	0.97186	-4.28;-4.28	4.89	1.18	0.20946	.	.	.	.	.	T	0.00012	0.0000	M	0.63843	1.955	0.58432	P	5.000000000032756E-6	D;D	0.63046	0.992;0.992	P;P	0.55577	0.779;0.779	T	0.45056	-0.9287	8	0.18276	T	0.48	-0.2641	4.2498	0.10689	0.3539:0.0882:0.0:0.558	rs938609;rs17790663;rs938609	939;939	E7ENV9;E7EX88	.;.	T	939	ENSP00000387356:S939T;ENSP00000341615:S939T	ENSP00000268134:S939T	S	+	1	0	ACAN	87199635	0.000000	0.05858	0.188000	0.23233	0.595000	0.36748	-0.086000	0.11233	0.018000	0.15052	0.460000	0.39030	TCT	T|0.540;A|0.460	0.460	strong		0.562	ACAN-006	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416267.2	NM_001135	
EXOC6B	23233	hgsc.bcm.edu	37	2	72707874	72707874	+	Silent	SNP	A	A	G	rs653220	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:72707874A>G	ENST00000272427.6	-	17	1801	c.1671T>C	c.(1669-1671)gtT>gtC	p.V557V	EXOC6B_ENST00000410104.1_Silent_p.V557V	NM_015189.1	NP_056004.1	Q9Y2D4	EXC6B_HUMAN	exocyst complex component 6B	557					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						TAATAATCTGAACAAGCTAGA	0.363													G|||	1741	0.347644	0.9546	0.2118	5008	,	,		20736	0.0069		0.2346	False		,,,				2504	0.091				p.V557V		Atlas-SNP	.											.	EXOC6B	93	.	0			c.T1671C						PASS	.	G		2983,751		1207,569,91	54.0	54.0	54.0		1671	-0.5	1.0	2	dbSNP_83	54	1882,6312		214,1454,2429	yes	coding-synonymous	EXOC6B	NM_015189.1		1421,2023,2520	GG,GA,AA		22.968,20.1125,40.7864		557/812	72707874	4865,7063	1867	4097	5964	SO:0001819	synonymous_variant	23233	exon17			AATCTGAACAAGC	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.1671T>C	2.37:g.72707874A>G		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	53	40	0.754717	NM_015189	B8ZZY3	Silent	SNP	ENST00000272427.6	37	CCDS46333.1																																																																																			A|0.639;G|0.361	0.361	strong		0.363	EXOC6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327558.1	XM_039570	
CCDC183	84960	hgsc.bcm.edu	37	9	139700605	139700605	+	Missense_Mutation	SNP	T	T	C	rs2811795	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:139700605T>C	ENST00000338005.6	+	10	1059	c.1024T>C	c.(1024-1026)Tgg>Cgg	p.W342R	RP11-216L13.19_ENST00000415992.1_RNA|KIAA1984-AS1_ENST00000414656.1_RNA|RABL6_ENST00000371671.4_5'Flank|RABL6_ENST00000357466.2_5'Flank|RP11-216L13.18_ENST00000471502.1_RNA|RABL6_ENST00000311502.7_5'Flank|KIAA1984_ENST00000371682.3_3'UTR|RABL6_ENST00000371663.4_5'Flank	NM_001039374.4	NP_001034463.4	Q5T5S1	CC183_HUMAN		342			W -> R (in dbSNP:rs2811795). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15164053, ECO:0000269|PubMed:15489334}.							biliary_tract(1)|breast(1)|endometrium(1)|kidney(2)|lung(4)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(1)	13	all_cancers(76;0.0882)|all_epithelial(76;0.228)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;9.33e-06)|Epithelial(140;0.000124)		CTGTGAGGAGTGGCGGGTGCA	0.642													C|||	4274	0.853435	0.9826	0.719	5008	,	,		16974	0.8591		0.8042	False		,,,				2504	0.819				p.W342R		Atlas-SNP	.											.	KIAA1984	39	.	0			c.T1024C						PASS	.	C	ARG/TRP	3941,183		1881,179,2	25.0	37.0	33.0		1024	-9.6	0.0	9	dbSNP_100	33	6725,1659		2709,1307,176	yes	missense	KIAA1984	NM_001039374.4	101	4590,1486,178	CC,CT,TT		19.7877,4.4374,14.7266	benign	342/535	139700605	10666,1842	2062	4192	6254	SO:0001583	missense	84960	exon10			GAGGAGTGGCGGG																												ENST00000338005.6:c.1024T>C	9.37:g.139700605T>C	ENSP00000338013:p.Trp342Arg	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	77	35	0.454545	NM_001039374	B2RP89|C9JD38|Q6P2D9|Q8NAI4|Q8TF18	Missense_Mutation	SNP	ENST00000338005.6	37	CCDS43906.1	1849	0.8466117216117216	483	0.9817073170731707	267	0.7375690607734806	485	0.8479020979020979	614	0.8100263852242744	C	0.386	-0.925937	0.02377	0.955626	0.802123	ENSG00000213213	ENST00000423962;ENST00000338005	T	0.11604	2.76	5.07	-9.59	0.00556	.	0.173330	0.24856	N	0.035051	T	0.00012	0.0000	N	0.00210	-1.845	0.58432	P	4.000000000004E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.53422	-0.8441	9	0.18276	T	0.48	-16.5081	14.9117	0.70761	0.8083:0.1217:0.0:0.07	rs2811795;rs59993980;rs2811795	342	Q5T5S1	K1984_HUMAN	R	342	ENSP00000338013:W342R	ENSP00000338013:W342R	W	+	1	0	KIAA1984	138820426	0.001000	0.12720	0.001000	0.08648	0.660000	0.38997	-0.677000	0.05215	-1.882000	0.01122	-1.169000	0.01745	TGG	T|0.130;C|0.870	0.870	strong		0.642	KIAA1984-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354899.1		
ZNF845	91664	hgsc.bcm.edu	37	19	53856349	53856349	+	Missense_Mutation	SNP	A	A	T	rs55874600	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:53856349A>T	ENST00000595091.1	+	5	2640	c.2421A>T	c.(2419-2421)gaA>gaT	p.E807D	ZNF845_ENST00000458035.1_Missense_Mutation_p.E807D			Q96IR2	ZN845_HUMAN	zinc finger protein 845	807				E -> D (in Ref. 3; AAH07307). {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(10)|lung(7)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(2)	26						AGTGTAATGAATGTGGCAAGA	0.413													.|||	1021	0.203874	0.0431	0.2421	5008	,	,		22336	0.1052		0.3946	False		,,,				2504	0.2996				p.E807D		Atlas-SNP	.											.	ZNF845	101	.	0			c.A2421T						PASS	.	A	ASP/GLU	121,1263		6,109,577	54.0	49.0	51.0		2421	-4.2	0.0	19	dbSNP_129	51	1299,1883		268,763,560	no	missense	ZNF845	NM_138374.1	45	274,872,1137	TT,TA,AA		40.8234,8.7428,31.0994	possibly-damaging	807/971	53856349	1420,3146	692	1591	2283	SO:0001583	missense	91664	exon4			TAATGAATGTGGC	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.2421A>T	19.37:g.53856349A>T	ENSP00000470005:p.Glu807Asp	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	81	39	0.481481	NM_138374		Missense_Mutation	SNP	ENST00000595091.1	37	CCDS46170.1	473	0.21657509157509158	26	0.052845528455284556	91	0.2513812154696133	45	0.07867132867132867	311	0.4102902374670185	A	8.112	0.779021	0.16120	0.087428	0.408234	ENSG00000213799	ENST00000458035;ENST00000427984	T	0.41758	0.99	2.1	-4.2	0.03823	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	N	0.17631	0.505	0.80722	P	0.0	P	0.36647	0.563	B	0.43082	0.407	T	0.39583	-0.9607	8	0.38643	T	0.18	.	4.309	0.10962	0.4866:0.0:0.3554:0.1579	rs55874600;rs62115344	807	Q96IR2	ZN845_HUMAN	D	807;723	ENSP00000388311:E807D	ENSP00000412086:E723D	E	+	3	2	ZNF845	58548161	0.000000	0.05858	0.000000	0.03702	0.063000	0.16089	-6.159000	0.00078	-0.620000	0.05641	-0.650000	0.03912	GAA	A|0.782;T|0.218	0.218	strong		0.413	ZNF845-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464359.1	XM_039908	
RYR3	6263	hgsc.bcm.edu	37	15	33954552	33954552	+	Silent	SNP	T	T	C	rs200740143	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:33954552T>C	ENST00000389232.4	+	35	4891	c.4821T>C	c.(4819-4821)taT>taC	p.Y1607Y	RYR3_ENST00000415757.3_Silent_p.Y1607Y	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	1607	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)		CTGGTTTCTATGACCTGCTCA	0.567													T|||	2	0.000399361	0.0	0.0	5008	,	,		20622	0.0		0.002	False		,,,				2504	0.0				p.Y1607Y		Atlas-SNP	.											.	RYR3	760	.	0			c.T4821C						PASS	.	T		6,4026		0,6,2010	72.0	71.0	71.0		4821	3.7	1.0	15		71	36,8294		0,36,4129	no	coding-synonymous	RYR3	NM_001036.3		0,42,6139	CC,CT,TT		0.4322,0.1488,0.3398		1607/4871	33954552	42,12320	2016	4165	6181	SO:0001819	synonymous_variant	6263	exon35			TTTCTATGACCTG		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.4821T>C	15.37:g.33954552T>C		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	122	56	0.459016	NM_001243996	O15175|Q15412	Silent	SNP	ENST00000389232.4	37	CCDS45210.1																																																																																			T|0.999;C|0.001	0.001	strong		0.567	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1		
ALPK3	57538	hgsc.bcm.edu	37	15	85405995	85405995	+	Missense_Mutation	SNP	T	T	C	rs187316	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:85405995T>C	ENST00000258888.5	+	10	5032	c.4865T>C	c.(4864-4866)cTt>cCt	p.L1622P		NM_020778.4	NP_065829.3	Q96L96	ALPK3_HUMAN	alpha-kinase 3	1622	Alpha-type protein kinase. {ECO:0000255|PROSITE-ProRule:PRU00501}.		L -> P (in dbSNP:rs187316). {ECO:0000269|PubMed:17344846}.		heart development (GO:0007507)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(3)|breast(2)|central_nervous_system(2)|endometrium(12)|kidney(4)|large_intestine(9)|lung(27)|ovary(3)|prostate(5)|skin(8)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	81			BRCA - Breast invasive adenocarcinoma(143;0.0587)			GGGTGTGGCCTTCGGAAGGCC	0.612													T|||	753	0.150359	0.0129	0.2219	5008	,	,		18170	0.1438		0.2714	False		,,,				2504	0.1677				p.L1622P		Atlas-SNP	.											.	ALPK3	289	.	0			c.T4865C						PASS	.	T	PRO/LEU	242,4164	142.3+/-177.5	10,222,1971	79.0	76.0	77.0		4865	3.7	0.5	15	dbSNP_79	77	2353,6245	392.1+/-343.9	316,1721,2262	yes	missense	ALPK3	NM_020778.4	98	326,1943,4233	CC,CT,TT		27.3668,5.4925,19.9554	probably-damaging	1622/1908	85405995	2595,10409	2203	4299	6502	SO:0001583	missense	57538	exon10			GTGGCCTTCGGAA	AY044449	CCDS10333.1	15q25.2	2013-01-29			ENSG00000136383	ENSG00000136383		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	17574	protein-coding gene	gene with protein product	"""myocyte induction differentiation originator"", ""muscle alpha-kinase"""					10021370	Standard	NM_020778		Approved	MAK, KIAA1330, Midori	uc002ble.3	Q96L96	OTTHUMG00000148667	ENST00000258888.5:c.4865T>C	15.37:g.85405995T>C	ENSP00000258888:p.Leu1622Pro	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	148	93	0.628378	NM_020778	Q9P2L6	Missense_Mutation	SNP	ENST00000258888.5	37	CCDS10333.1	400	0.18315018315018314	9	0.018292682926829267	88	0.2430939226519337	88	0.15384615384615385	215	0.2836411609498681	T	15.74	2.923941	0.52653	0.054925	0.273668	ENSG00000136383	ENST00000258888	T	0.08193	3.12	4.86	3.7	0.42460	MHCK/EF2 kinase (3);Protein kinase-like domain (1);	0.418235	0.25050	N	0.033523	T	0.00012	0.0000	L	0.47716	1.5	0.29830	P	0.830098	D	0.62365	0.991	P	0.58172	0.834	T	0.40831	-0.9542	9	0.72032	D	0.01	-4.3524	9.7636	0.40548	0.0:0.0:0.1741:0.8259	rs187316;rs52801929;rs187316	1622	Q96L96	ALPK3_HUMAN	P	1622	ENSP00000258888:L1622P	ENSP00000258888:L1622P	L	+	2	0	ALPK3	83206999	0.094000	0.21725	0.465000	0.27155	0.906000	0.53458	1.711000	0.37930	0.838000	0.34948	0.533000	0.62120	CTT	T|0.815;C|0.185	0.185	strong		0.612	ALPK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000308997.1	NM_020778	
BTN3A2	11118	hgsc.bcm.edu	37	6	26370616	26370616	+	Missense_Mutation	SNP	G	G	C	rs9379861	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:26370616G>C	ENST00000356386.2	+	5	688	c.500G>C	c.(499-501)aGg>aCg	p.R167T	BTN3A2_ENST00000396948.1_Missense_Mutation_p.R167T|BTN3A2_ENST00000396934.3_Missense_Mutation_p.R144T|BTN3A2_ENST00000532994.1_3'UTR|BTN3A2_ENST00000527422.1_Missense_Mutation_p.R167T|BTN3A2_ENST00000508906.2_Missense_Mutation_p.R125T|BTN3A2_ENST00000377708.2_Missense_Mutation_p.R167T	NM_001197246.2|NM_001197247.1|NM_007047.3	NP_001184175.1|NP_001184176.1|NP_008978.2	P78410	BT3A2_HUMAN	butyrophilin, subfamily 3, member A2	167			R -> T (in dbSNP:rs9379861).		interferon-gamma secretion (GO:0072643)|T cell mediated immunity (GO:0002456)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(5)	10						CTGGAGTGCAGGTCCACCGGC	0.532													G|||	208	0.0415335	0.0015	0.0072	5008	,	,		18894	0.0863		0.0298	False		,,,				2504	0.0859				p.R167T		Atlas-SNP	.											.	BTN3A2	44	.	0			c.G500C						PASS	.	G	THR/ARG,THR/ARG,THR/ARG,THR/ARG,THR/ARG	16,4390	23.3+/-48.9	0,16,2187	120.0	106.0	111.0		500,500,431,374,500	-4.6	0.0	6	dbSNP_119	111	127,8473	64.6+/-126.8	1,125,4174	yes	missense,missense,missense,missense,missense	BTN3A2	NM_001197246.1,NM_001197247.1,NM_001197248.1,NM_001197249.1,NM_007047.3	71,71,71,71,71	1,141,6361	CC,CG,GG		1.4767,0.3631,1.0995	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	167/335,167/335,144/312,125/293,167/335	26370616	143,12863	2203	4300	6503	SO:0001583	missense	11118	exon3			AGTGCAGGTCCAC	U90546	CCDS4605.1, CCDS56399.1, CCDS56400.1	6p22.1	2014-01-14			ENSG00000186470	ENSG00000186470		"""Immunoglobulin superfamily / V-set domain containing"", ""Butyrophilins"""	1139	protein-coding gene	gene with protein product		613594				9149941	Standard	NM_007047		Approved	BTN3.2	uc010jqi.2	P78410	OTTHUMG00000014450	ENST00000356386.2:c.500G>C	6.37:g.26370616G>C	ENSP00000348751:p.Arg167Thr	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	97	46	0.474227	NM_001197246	B4DRT7|B4E103|F5H791|F8W6E0|O00477|O15338|O75658|Q76PA0|Q9BU81|Q9NR44	Missense_Mutation	SNP	ENST00000356386.2	37	CCDS4605.1	56	0.02564102564102564	2	0.0040650406504065045	3	0.008287292817679558	33	0.057692307692307696	18	0.023746701846965697	g	0.004	-2.298694	0.00243	0.003631	0.014767	ENSG00000186470	ENST00000532865;ENST00000535620;ENST00000527422;ENST00000356386;ENST00000396934;ENST00000377708;ENST00000396948;ENST00000508906	T;T;T;T;T;T;T	0.74737	-0.87;3.33;3.33;3.33;3.33;3.33;3.33	2.31	-4.62	0.03370	Immunoglobulin-like fold (1);	.	.	.	.	T	0.17959	0.0431	N	0.17901	0.54	0.09310	N	1	B;B	0.06786	0.001;0.0	B;B	0.06405	0.002;0.001	T	0.17899	-1.0354	9	0.02654	T	1	.	0.8132	0.01097	0.4343:0.2153:0.1762:0.1743	rs9379861;rs9379861	144;167	F8W6E0;P78410	.;BT3A2_HUMAN	T	125;167;167;167;144;167;167;125	ENSP00000435952:R125T;ENSP00000432138:R167T;ENSP00000348751:R167T;ENSP00000380140:R144T;ENSP00000366937:R167T;ENSP00000380152:R167T;ENSP00000442687:R125T	ENSP00000348751:R167T	R	+	2	0	BTN3A2	26478595	0.000000	0.05858	0.000000	0.03702	0.045000	0.14185	-0.242000	0.08928	-2.360000	0.00610	0.405000	0.27470	AGG	G|0.985;C|0.015	0.015	strong		0.532	BTN3A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040113.2		
SMARCC1	6599	hgsc.bcm.edu	37	3	47712202	47712202	+	Silent	SNP	T	T	C	rs1141601	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:47712202T>C	ENST00000254480.5	-	19	1964	c.1845A>G	c.(1843-1845)aaA>aaG	p.K615K	SMARCC1_ENST00000425518.1_5'UTR	NM_003074.3	NP_003065.3	Q92922	SMRC1_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 1	615					ATP-dependent chromatin remodeling (GO:0043044)|chromatin remodeling (GO:0006338)|insulin receptor signaling pathway (GO:0008286)|nervous system development (GO:0007399)|nucleosome disassembly (GO:0006337)|organ morphogenesis (GO:0009887)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)|XY body (GO:0001741)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|protein N-terminus binding (GO:0047485)|transcription coactivator activity (GO:0003713)			breast(1)|endometrium(5)|kidney(2)|large_intestine(3)|lung(15)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	33				BRCA - Breast invasive adenocarcinoma(193;7.47e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.00862)|Kidney(197;0.01)		CACTAGCACCTTTACTCTAAG	0.413													T|||	926	0.184904	0.0113	0.2795	5008	,	,		19467	0.251		0.3221	False		,,,				2504	0.1431				p.K615K		Atlas-SNP	.											.	SMARCC1	85	.	0			c.A1845G						PASS	.	T		257,4149	145.4+/-180.2	9,239,1955	119.0	103.0	108.0		1845	4.3	1.0	3	dbSNP_86	108	2428,6172	392.3+/-344.0	367,1694,2239	no	coding-synonymous	SMARCC1	NM_003074.3		376,1933,4194	CC,CT,TT		28.2326,5.833,20.6443		615/1106	47712202	2685,10321	2203	4300	6503	SO:0001819	synonymous_variant	6599	exon19			AGCACCTTTACTC	U66615	CCDS2758.1	3p21.31	2008-05-15			ENSG00000173473	ENSG00000173473			11104	protein-coding gene	gene with protein product		601732				8804307	Standard	NM_003074		Approved	BAF155, SRG3, Rsc8, CRACC1	uc003crq.2	Q92922	OTTHUMG00000133519	ENST00000254480.5:c.1845A>G	3.37:g.47712202T>C		Somatic	291	0	0		WXS	Illumina HiSeq	Phase_I	232	119	0.512931	NM_003074	Q17RS0|Q6P172|Q8IWH2	Silent	SNP	ENST00000254480.5	37	CCDS2758.1																																																																																			T|0.639;G|0.036	.	strong		0.413	SMARCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257491.1		
SSR3	6747	hgsc.bcm.edu	37	3	156266774	156266774	+	Silent	SNP	C	C	T	rs9296	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:156266774C>T	ENST00000265044.2	-	3	373	c.279G>A	c.(277-279)gaG>gaA	p.E93E	SSR3_ENST00000476217.1_Silent_p.E93E|SSR3_ENST00000496050.1_Silent_p.E41E|SSR3_ENST00000478842.1_5'UTR|SSR3_ENST00000467789.1_Silent_p.E93E|SSR3_ENST00000463503.1_Silent_p.E41E	NM_007107.3	NP_009038.1	Q9UNL2	SSRG_HUMAN	signal sequence receptor, gamma (translocon-associated protein gamma)	93					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)	integral component of endoplasmic reticulum membrane (GO:0030176)|Sec61 translocon complex (GO:0005784)				endometrium(1)|prostate(2)	3			LUSC - Lung squamous cell carcinoma(72;0.0461)|Lung(72;0.0465)			AAACAGCATCCTCCCTCTTCT	0.393													C|||	878	0.175319	0.1543	0.1542	5008	,	,		18154	0.2312		0.1481	False		,,,				2504	0.1892				p.E93E		Atlas-SNP	.											.	SSR3	17	.	0			c.G279A						PASS	.	C		601,3805	260.4+/-263.7	40,521,1642	95.0	93.0	93.0		279	3.6	1.0	3	dbSNP_52	93	1068,7532	223.3+/-260.1	68,932,3300	no	coding-synonymous	SSR3	NM_007107.3		108,1453,4942	TT,TC,CC		12.4186,13.6405,12.8325		93/186	156266774	1669,11337	2203	4300	6503	SO:0001819	synonymous_variant	6747	exon3			AGCATCCTCCCTC	BC017203	CCDS3176.1	3q25.31	2004-02-27			ENSG00000114850	ENSG00000114850			11325	protein-coding gene	gene with protein product		606213					Standard	NM_007107		Approved	TRAPG	uc003fau.3	Q9UNL2	OTTHUMG00000158632	ENST00000265044.2:c.279G>A	3.37:g.156266774C>T		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	65	31	0.476923	NM_007107	B2R7D0|B4E2P2|D3DNK5|Q549M4	Silent	SNP	ENST00000265044.2	37	CCDS3176.1																																																																																			C|0.865;T|0.135	0.135	strong		0.393	SSR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351521.1	NM_007107	
BPIFB4	149954	hgsc.bcm.edu	37	20	31671209	31671209	+	Missense_Mutation	SNP	G	G	C	rs13036385	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:31671209G>C	ENST00000375483.3	+	3	206	c.206G>C	c.(205-207)cGa>cCa	p.R69P		NM_182519.2	NP_872325.2	P59827	BPIB4_HUMAN	BPI fold containing family B, member 4	69						cytoplasm (GO:0005737)|extracellular region (GO:0005576)	lipid binding (GO:0008289)										TTCCATGTCCGAGGACCCCCC	0.498													g|||	1080	0.215655	0.1891	0.3069	5008	,	,		11957	0.1528		0.2316	False		,,,				2504	0.2352				p.R69P		Atlas-SNP	.											.	.	.	.	0			c.G206C						PASS	.		PRO/ARG	959,3447	359.4+/-314.8	119,721,1363	88.0	86.0	87.0		206	2.9	0.4	20	dbSNP_121	87	1995,6605	347.8+/-326.7	222,1551,2527	yes	missense	BPIFB4	NM_182519.2	103	341,2272,3890	CC,CG,GG		23.1977,21.7658,22.7126	probably-damaging	69/615	31671209	2954,10052	2203	4300	6503	SO:0001583	missense	149954	exon3			ATGTCCGAGGACC	AF549190	CCDS13213.2	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000186191	ENSG00000186191		"""BPI fold containing"""	16179	protein-coding gene	gene with protein product		615718	"""chromosome 20 open reading frame 186"""	C20orf186		11971875, 21787333	Standard	NM_182519		Approved	dJ726C3.5, LPLUNC4	uc010zue.2	P59827	OTTHUMG00000032235	ENST00000375483.3:c.206G>C	20.37:g.31671209G>C	ENSP00000364632:p.Arg69Pro	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	99	47	0.474747	NM_182519	Q5TDX6	Missense_Mutation	SNP	ENST00000375483.3	37	CCDS13213.2	464	0.21245421245421245	78	0.15853658536585366	113	0.31215469613259667	97	0.16958041958041958	176	0.23218997361477572	g	9.146	1.014987	0.19355	0.217658	0.231977	ENSG00000186191	ENST00000375483	T	0.01538	4.79	2.89	2.89	0.33648	.	0.000000	0.28414	U	0.015427	T	0.00012	0.0000	L	0.29908	0.895	0.58432	P	8.000000000008E-6	D	0.67145	0.996	D	0.70487	0.969	T	0.57952	-0.7722	9	0.49607	T	0.09	0.036	9.3529	0.38149	0.0:0.0:1.0:0.0	rs13036385;rs52795648;rs13036385	69	P59827	BPIB4_HUMAN	P	69	ENSP00000364632:R69P	ENSP00000364632:R69P	R	+	2	0	BPIFB4	31134870	0.998000	0.40836	0.432000	0.26747	0.013000	0.08279	2.545000	0.45769	1.607000	0.50170	0.306000	0.20318	CGA	G|0.777;C|0.223	0.223	strong		0.498	BPIFB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078655.5	NM_182519	
CLEC2D	29121	hgsc.bcm.edu	37	12	9822387	9822387	+	Missense_Mutation	SNP	C	C	G	rs16914640	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:9822387C>G	ENST00000290855.6	+	1	79	c.57C>G	c.(55-57)aaC>aaG	p.N19K	CLEC2D_ENST00000543300.1_Missense_Mutation_p.N19K|CLEC2D_ENST00000261339.6_Missense_Mutation_p.N19K|CLEC2D_ENST00000261340.7_Missense_Mutation_p.N19K|CLEC2D_ENST00000487752.1_Intron|CLEC2D_ENST00000545918.1_Missense_Mutation_p.N19K	NM_013269.5	NP_037401.1	Q9UHP7	CLC2D_HUMAN	C-type lectin domain family 2, member D	19			N -> K (in dbSNP:rs16914640). {ECO:0000269|PubMed:20843815}.		cell surface receptor signaling pathway (GO:0007166)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)|transmembrane signaling receptor activity (GO:0004888)	p.N19K(3)		endometrium(2)|kidney(1)|large_intestine(1)|lung(2)|prostate(2)|stomach(1)	9						TGCCTGCAAACCCAGGTAAGA	0.453													C|||	1003	0.20028	0.5204	0.147	5008	,	,		-128	0.0109		0.1392	False		,,,				2504	0.0634				p.N19K		Atlas-SNP	.											CLEC2D_ENST00000290855,NS,carcinoma,0,5	CLEC2D	54	5	3	Substitution - Missense(3)	prostate(2)|stomach(1)	c.C57G						PASS	.	C	LYS/ASN,LYS/ASN,LYS/ASN,LYS/ASN,LYS/ASN	2026,2380	564.7+/-381.5	462,1102,639	105.0	88.0	93.0		57,57,57,57,57	-3.0	0.0	12	dbSNP_123	93	1251,7349	248.7+/-276.3	86,1079,3135	yes	missense,missense,missense,missense,missense	CLEC2D	NM_001004419.3,NM_001197317.1,NM_001197318.1,NM_001197319.1,NM_013269.4	94,94,94,94,94	548,2181,3774	GG,GC,CC		14.5465,45.9828,25.1961	benign,benign,benign,benign,benign	19/195,19/155,19/133,19/96,19/192	9822387	3277,9729	2203	4300	6503	SO:0001583	missense	29121	exon1			TGCAAACCCAGGT	AF133299	CCDS8602.1, CCDS31741.1, CCDS55800.1, CCDS55801.1, CCDS55802.1	12p13.31	2011-05-24	2005-09-29		ENSG00000069493	ENSG00000069493		"""C-type lectin domain containing"""	14351	protein-coding gene	gene with protein product	"""C-type lectin related f"", ""lectin-like transcript 1"""	605659	"""C-type lectin superfamily 2, member D"""				Standard	NM_013269		Approved	LLT1, CLAX, OCIL	uc001qwf.3	Q9UHP7	OTTHUMG00000168369	ENST00000290855.6:c.57C>G	12.37:g.9822387C>G	ENSP00000290855:p.Asn19Lys	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	115	56	0.486957	NM_001197319	D6CI39|D6CI40|D6CI41|Q6YID5|Q8WUP7|Q9HD37|Q9HD38	Missense_Mutation	SNP	ENST00000290855.6	37	CCDS8602.1	435	0.19917582417582416	264	0.5365853658536586	63	0.17403314917127072	4	0.006993006993006993	104	0.13720316622691292	C	4.680	0.126409	0.08931	0.459828	0.145465	ENSG00000069493	ENST00000261340;ENST00000290855;ENST00000545918;ENST00000543300;ENST00000261339;ENST00000466035	T;T;T;T;T;T	0.10668	4.56;4.71;2.85;2.95;4.57;4.46	1.84	-3.04	0.05412	.	.	.	.	.	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B;P	0.40834	0.276;0.73	B;B	0.35550	0.057;0.205	T	0.40327	-0.9569	7	.	.	.	-2.8277	7.0382	0.25004	0.0:0.305:0.0:0.695	rs16914640;rs52794220;rs16914640	19;19	Q9UHP7;Q9UHP7-3	CLC2D_HUMAN;.	K	19;19;19;19;19;13	ENSP00000261340:N19K;ENSP00000290855:N19K;ENSP00000444818:N19K;ENSP00000443065:N19K;ENSP00000261339:N19K;ENSP00000446028:N13K	.	N	+	3	2	CLEC2D	9713654	0.000000	0.05858	0.000000	0.03702	0.015000	0.08874	-1.491000	0.02302	-0.999000	0.03442	-0.356000	0.07607	AAC	C|0.764;G|0.236	0.236	strong		0.453	CLEC2D-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000335424.2	NM_013269	
AQP11	282679	hgsc.bcm.edu	37	11	77301341	77301341	+	Missense_Mutation	SNP	G	G	A	rs2276415	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:77301341G>A	ENST00000313578.3	+	1	662	c.304G>A	c.(304-306)Ggc>Agc	p.G102S	AQP11_ENST00000528638.1_Intron	NM_173039.2	NP_766627.1	Q8NBQ7	AQP11_HUMAN	aquaporin 11	102			G -> S (in dbSNP:rs2276415).		endosomal lumen acidification (GO:0048388)|protein homooligomerization (GO:0051260)|proximal tubule development (GO:0072014)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cell surface (GO:0009986)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			kidney(2)|large_intestine(1)|lung(5)	8	all_cancers(14;1.75e-17)|all_epithelial(13;4.7e-20)|Ovarian(111;0.249)		Epithelial(5;4.73e-49)|BRCA - Breast invasive adenocarcinoma(5;1.4e-30)			CAACCCGTGCGGCGTGATGAT	0.637													G|||	731	0.145966	0.1377	0.1902	5008	,	,		19940	0.1825		0.0964	False		,,,				2504	0.1391				p.G102S		Atlas-SNP	.											.	AQP11	14	.	0			c.G304A						PASS	.	G	SER/GLY	594,3806	258.0+/-262.2	40,514,1646	72.0	62.0	66.0		304	3.7	1.0	11	dbSNP_100	66	801,7783	187.3+/-234.6	34,733,3525	yes	missense	AQP11	NM_173039.2	56	74,1247,5171	AA,AG,GG		9.3313,13.5,10.744	probably-damaging	102/272	77301341	1395,11589	2200	4292	6492	SO:0001583	missense	282679	exon1			CCGTGCGGCGTGA	AB028147	CCDS8251.1	11q13.5	2008-02-05			ENSG00000178301	ENSG00000178301		"""Ion channels / Aquaporins"""	19940	protein-coding gene	gene with protein product		609914				16107722	Standard	NM_173039		Approved		uc001oyj.3	Q8NBQ7	OTTHUMG00000165194	ENST00000313578.3:c.304G>A	11.37:g.77301341G>A	ENSP00000318770:p.Gly102Ser	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	103	79	0.76699	NM_173039		Missense_Mutation	SNP	ENST00000313578.3	37	CCDS8251.1	316	0.1446886446886447	74	0.15040650406504066	57	0.1574585635359116	113	0.19755244755244755	72	0.09498680738786279	G	17.49	3.402396	0.62288	0.135	0.093313	ENSG00000178301	ENST00000313578	D	0.84944	-1.92	5.54	3.68	0.42216	Aquaporin-like (2);	0.218216	0.47852	N	0.000215	T	0.00300	0.0009	M	0.63843	1.955	0.21762	P	0.99955712	P	0.52316	0.952	B	0.40602	0.334	T	0.07481	-1.0770	9	0.27082	T	0.32	-12.8909	9.8641	0.41131	0.2177:0.0:0.7823:0.0	rs2276415;rs52797374;rs59985599;rs2276415	102	Q8NBQ7	AQP11_HUMAN	S	102	ENSP00000318770:G102S	ENSP00000318770:G102S	G	+	1	0	AQP11	76978989	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	2.719000	0.47244	0.715000	0.32103	0.491000	0.48974	GGC	G|0.873;A|0.127	0.127	strong		0.637	AQP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382582.1	NM_173039	
NSFL1C	55968	hgsc.bcm.edu	37	20	1426393	1426393	+	Missense_Mutation	SNP	C	C	T	rs9575	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:1426393C>T	ENST00000216879.4	-	8	1735	c.868G>A	c.(868-870)Gac>Aac	p.D290N	NSFL1C_ENST00000353088.2_Missense_Mutation_p.D259N|NSFL1C_ENST00000461211.1_5'UTR|NSFL1C_ENST00000476071.1_Missense_Mutation_p.D292N|NSFL1C_ENST00000381658.4_Missense_Mutation_p.D179N|NSFL1C_ENST00000350991.4_Missense_Mutation_p.D292N	NM_016143.4	NP_057227.2	Q9UNZ2	NSF1C_HUMAN	NSFL1 (p97) cofactor (p47)	290			D -> N (in dbSNP:rs9575). {ECO:0000269|PubMed:11042152}.			chromosome (GO:0005694)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	lipid binding (GO:0008289)			breast(1)|large_intestine(5)|lung(6)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	16						TCTGATTCGTCGATTAAGATG	0.537													C|||	2336	0.466454	0.2534	0.5115	5008	,	,		19949	0.7887		0.4076	False		,,,				2504	0.4509				p.D290N		Atlas-SNP	.											NSFL1C,colon,carcinoma,+2,2	NSFL1C	38	2	0			c.G868A						PASS	.	C	ASN/ASP,ASN/ASP,ASN/ASP	1221,3185	423.4+/-340.1	169,883,1151	200.0	195.0	197.0		874,868,775	-1.4	0.1	20	dbSNP_52	197	3519,5081	514.1+/-378.3	735,2049,1516	yes	missense,missense,missense	NSFL1C	NM_001206736.1,NM_016143.4,NM_018839.4	23,23,23	904,2932,2667	TT,TC,CC		40.9186,27.7122,36.4447	benign,benign,benign	292/373,290/371,259/340	1426393	4740,8266	2203	4300	6503	SO:0001583	missense	55968	exon8			ATTCGTCGATTAA	AF112211	CCDS13015.1, CCDS13016.1, CCDS56175.1	20p13	2011-06-28			ENSG00000088833	ENSG00000088833		"""UBX domain containing"""	15912	protein-coding gene	gene with protein product	"""SHP1 homolog (S. cerevisiae)"", ""UBX domain protein 2C"""	606610				11042152	Standard	NM_016143		Approved	dJ776F14.1, p47, UBXD10, UBX1, UBXN2C	uc002wfc.3	Q9UNZ2	OTTHUMG00000031665	ENST00000216879.4:c.868G>A	20.37:g.1426393C>T	ENSP00000216879:p.Asp290Asn	Somatic	195	0	0		WXS	Illumina HiSeq	Phase_I	138	59	0.427536	NM_016143	A2A2L1|B2RD74|Q5JXA4|Q5JXA5|Q7Z533|Q9H102|Q9NVL9|Q9UI06	Missense_Mutation	SNP	ENST00000216879.4	37	CCDS13015.1	1054	0.4826007326007326	117	0.23780487804878048	172	0.47513812154696133	439	0.7674825174825175	326	0.43007915567282323	C	15.62	2.888671	0.52014	0.277122	0.409186	ENSG00000088833	ENST00000353088;ENST00000476071;ENST00000216879;ENST00000381658;ENST00000350991	T;T;T;T;T	0.44881	0.91;0.91;0.91;0.91;0.91	4.53	-1.35	0.09114	UBX (1);	0.224720	0.44688	N	0.000435	T	0.00012	0.0000	L	0.52759	1.655	0.20403	P	0.9999006895	B;B;B	0.20671	0.027;0.047;0.013	B;B;B	0.17433	0.007;0.017;0.018	T	0.27468	-1.0073	9	0.49607	T	0.09	-3.2202	9.1604	0.37019	0.0:0.65:0.0:0.35	rs9575;rs3171294;rs17719623;rs9575	259;179;290	Q9UNZ2-4;Q9UNZ2-6;Q9UNZ2	.;.;NSF1C_HUMAN	N	259;292;290;179;292	ENSP00000338643:D259N;ENSP00000418529:D292N;ENSP00000216879:D290N;ENSP00000371074:D179N;ENSP00000202584:D292N	ENSP00000216879:D290N	D	-	1	0	NSFL1C	1374393	0.977000	0.34250	0.137000	0.22149	0.916000	0.54674	1.085000	0.30840	-0.271000	0.09272	-0.367000	0.07326	GAC	C|0.589;T|0.411	0.411	strong		0.537	NSFL1C-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077525.2	NM_016143	
CCDC89	220388	hgsc.bcm.edu	37	11	85396746	85396746	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:85396746T>C	ENST00000316398.3	-	1	574	c.428A>G	c.(427-429)tAc>tGc	p.Y143C	CREBZF_ENST00000534224.1_5'Flank|CREBZF_ENST00000531515.1_5'Flank	NM_152723.1	NP_689936.1	Q8N998	CCD89_HUMAN	coiled-coil domain containing 89	143						cytoplasm (GO:0005737)|nucleus (GO:0005634)				NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(6)|skin(1)	15		Acute lymphoblastic leukemia(157;4.88e-06)|all_hematologic(158;0.00572)				CTCACTCTTGTATTCATCCTT	0.517																																					p.Y143C		Atlas-SNP	.											.	CCDC89	45	.	0			c.A428G						PASS	.						100.0	90.0	93.0					11																	85396746		2203	4299	6502	SO:0001583	missense	220388	exon1			CTCTTGTATTCAT	AK095478	CCDS8270.1	11q14.1	2006-03-16			ENSG00000179071	ENSG00000179071			26762	protein-coding gene	gene with protein product						12477932	Standard	NM_152723		Approved	FLJ38159	uc001pau.1	Q8N998	OTTHUMG00000166976	ENST00000316398.3:c.428A>G	11.37:g.85396746T>C	ENSP00000320649:p.Tyr143Cys	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	102	85	0.833333	NM_152723		Missense_Mutation	SNP	ENST00000316398.3	37	CCDS8270.1	.	.	.	.	.	.	.	.	.	.	t	13.79	2.340823	0.41498	.	.	ENSG00000179071	ENST00000316398	.	.	.	5.53	5.53	0.82687	.	0.343021	0.33110	N	0.005272	T	0.49779	0.1577	L	0.29908	0.895	0.37455	D	0.914985	D	0.54964	0.969	P	0.49528	0.614	T	0.54077	-0.8347	8	.	.	.	-8.5222	15.664	0.77213	0.0:0.0:0.0:1.0	.	143	Q8N998	CCD89_HUMAN	C	143	.	.	Y	-	2	0	CCDC89	85074394	1.000000	0.71417	0.950000	0.38849	0.578000	0.36192	5.298000	0.65710	2.104000	0.64026	0.529000	0.55759	TAC	.	.	none		0.517	CCDC89-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392182.1	NM_152723	
GALR1	2587	hgsc.bcm.edu	37	18	74980601	74980601	+	Missense_Mutation	SNP	A	A	T	rs77169818	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:74980601A>T	ENST00000299727.3	+	3	793	c.793A>T	c.(793-795)Atc>Ttc	p.I265F		NM_001480.3	NP_001471.2	P47211	GALR1_HUMAN	galanin receptor 1	265					adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|digestion (GO:0007586)|negative regulation of adenylate cyclase activity (GO:0007194)|neuropeptide signaling pathway (GO:0007218)|positive regulation of cortisol secretion (GO:0051464)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	galanin receptor activity (GO:0004966)|neuropeptide binding (GO:0042923)|peptide hormone binding (GO:0017046)			breast(2)|endometrium(1)|kidney(1)|large_intestine(3)|lung(13)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	24		Prostate(75;0.0865)|Esophageal squamous(42;0.129)|Melanoma(33;0.211)		OV - Ovarian serous cystadenocarcinoma(15;1.03e-06)|BRCA - Breast invasive adenocarcinoma(31;0.104)		GCCGCACCACATCATCCATCT	0.557													A|||	207	0.0413339	0.0015	0.0908	5008	,	,		14586	0.0565		0.0507	False		,,,				2504	0.0348				p.I265F		Atlas-SNP	.											.	GALR1	53	.	0			c.A793T						PASS	.	A	PHE/ILE	57,4349	55.5+/-91.7	2,53,2148	135.0	134.0	134.0		793	0.5	0.7	18	dbSNP_131	134	345,8255	118.8+/-178.2	5,335,3960	yes	missense	GALR1	NM_001480.3	21	7,388,6108	TT,TA,AA		4.0116,1.2937,3.0909	benign	265/350	74980601	402,12604	2203	4300	6503	SO:0001583	missense	2587	exon3			CACCACATCATCC	U90658	CCDS12012.1	18q23	2012-08-08			ENSG00000166573	ENSG00000166573		"""GPCR / Class A : Galanin receptors"""	4132	protein-coding gene	gene with protein product		600377		GALNR1, GALNR		7524088	Standard	NM_001480		Approved		uc002lms.4	P47211	OTTHUMG00000132875	ENST00000299727.3:c.793A>T	18.37:g.74980601A>T	ENSP00000299727:p.Ile265Phe	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	43	31	0.72093	NM_001480	Q4VBL7	Missense_Mutation	SNP	ENST00000299727.3	37	CCDS12012.1	117	0.05357142857142857	0	0.0	39	0.10773480662983426	35	0.06118881118881119	43	0.05672823218997362	A	13.23	2.174445	0.38413	0.012937	0.040116	ENSG00000166573	ENST00000299727	T	0.59638	0.25	4.74	0.465	0.16711	GPCR, rhodopsin-like superfamily (1);	0.195753	0.43260	D	0.000600	T	0.02649	0.0080	M	0.76574	2.34	0.37387	D	0.912277	B	0.30542	0.284	P	0.45610	0.487	T	0.42481	-0.9449	10	0.72032	D	0.01	.	9.0874	0.36590	0.4241:0.0:0.5759:0.0	.	265	P47211	GALR1_HUMAN	F	265	ENSP00000299727:I265F	ENSP00000299727:I265F	I	+	1	0	GALR1	73109589	0.940000	0.31905	0.727000	0.30756	0.147000	0.21601	1.474000	0.35398	-0.244000	0.09639	-0.376000	0.06991	ATC	A|0.965;T|0.035	0.035	strong		0.557	GALR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256362.1		
ZNF443	10224	hgsc.bcm.edu	37	19	12541547	12541547	+	Missense_Mutation	SNP	T	T	G	rs10402252|rs74181783	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:12541547T>G	ENST00000301547.5	-	4	1636	c.1439A>C	c.(1438-1440)aAa>aCa	p.K480T	CTD-3105H18.16_ENST00000595562.1_Intron	NM_005815.4	NP_005806	Q9Y2A4	ZN443_HUMAN	zinc finger protein 443	480				K -> T (in Ref. 1; BAA75543 and 3; AAH32753). {ECO:0000305}.	apoptotic process (GO:0006915)|regulation of transcription, DNA-templated (GO:0006355)|response to stress (GO:0006950)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(3)|endometrium(1)|kidney(1)|large_intestine(11)|lung(10)|pancreas(1)|prostate(1)	28						TTTCCCAAGTTTGCATTTATA	0.398													.|||	1308	0.261182	0.171	0.4207	5008	,	,		21103	0.1071		0.496	False		,,,				2504	0.1871				p.K480T		Atlas-SNP	.											.	ZNF443	63	.	0			c.A1439C						PASS	.	T	THR/LYS	949,3453	350.0+/-310.6	110,729,1362	68.0	72.0	71.0		1439	1.3	0.0	19	dbSNP_119	71	4323,4277	570.1+/-389.3	1098,2127,1075	no	missense	ZNF443	NM_005815.4	78	1208,2856,2437	GG,GT,TT		49.7326,21.5584,40.5476	possibly-damaging	480/672	12541547	5272,7730	2201	4300	6501	SO:0001583	missense	10224	exon4			CCAAGTTTGCATT	AB011414	CCDS32918.1	19p13.13	2013-01-08			ENSG00000180855	ENSG00000180855		"""Zinc fingers, C2H2-type"", ""-"""	20878	protein-coding gene	gene with protein product		606697				9731181	Standard	NM_005815		Approved	ZK1	uc002mtu.3	Q9Y2A4	OTTHUMG00000156404	ENST00000301547.5:c.1439A>C	19.37:g.12541547T>G	ENSP00000301547:p.Lys480Thr	Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	64	34	0.53125	NM_005815		Missense_Mutation	SNP	ENST00000301547.5	37	CCDS32918.1	711	0.32554945054945056	97	0.19715447154471544	161	0.4447513812154696	60	0.1048951048951049	393	0.5184696569920845	T	11.17	1.558917	0.27827	0.215584	0.502674	ENSG00000180855	ENST00000301547;ENST00000411622	T	0.19250	2.16	1.26	1.26	0.21427	Zinc finger, C2H2-like (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	N	0.12920	0.275	0.80722	P	0.0	D	0.60575	0.988	D	0.64877	0.93	T	0.44967	-0.9293	8	0.66056	D	0.02	.	4.2601	0.10737	0.0:0.1986:0.0:0.8014	rs10402252;rs17846014;rs17858998;rs60951533	480	Q9Y2A4	ZN443_HUMAN	T	480	ENSP00000301547:K480T	ENSP00000301547:K480T	K	-	2	0	ZNF443	12402547	0.000000	0.05858	0.004000	0.12327	0.031000	0.12232	-1.386000	0.02537	0.841000	0.35020	0.378000	0.23410	AAA	T|0.615;G|0.385	0.385	strong		0.398	ZNF443-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344084.1	NM_005815	
KIAA0368	23392	hgsc.bcm.edu	37	9	114146832	114146832	+	Silent	SNP	C	C	T	rs16916040	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:114146832C>T	ENST00000338205.5	-	33	3870	c.3651G>A	c.(3649-3651)gcG>gcA	p.A1217A	KIAA0368_ENST00000374378.3_5'UTR|KIAA0368_ENST00000259335.4_Silent_p.A1395A			Q5VYK3	ECM29_HUMAN	KIAA0368	1223					ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)	centrosome (GO:0005813)|cytoplasmic membrane-bounded vesicle (GO:0016023)|early endosome (GO:0005769)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle (GO:0030134)|late endosome (GO:0005770)|membrane (GO:0016020)|multivesicular body (GO:0005771)|nucleus (GO:0005634)|proteasome complex (GO:0000502)		p.A1395A(1)		NS(2)|breast(3)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(23)|prostate(3)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	65						CTAGTTCTGCCGCTTTTCGTA	0.403													T|||	481	0.0960463	0.1861	0.0187	5008	,	,		19176	0.1627		0.0119	False		,,,				2504	0.047				p.A1395A		Atlas-SNP	.											KIAA0368,NS,carcinoma,0,2	KIAA0368	144	2	1	Substitution - coding silent(1)	stomach(1)	c.G4185A						PASS	.	T		553,3193		43,467,1363	105.0	105.0	105.0		4185	-1.4	1.0	9	dbSNP_123	105	112,8080		0,112,3984	no	coding-synonymous	KIAA0368	NM_001080398.1		43,579,5347	TT,TC,CC		1.3672,14.7624,5.5704		1395/2018	114146832	665,11273	1873	4096	5969	SO:0001819	synonymous_variant	23392	exon35			TTCTGCCGCTTTT	AK025689	CCDS48006.1	9q32	2012-11-29	2006-11-23	2006-11-23	ENSG00000136813	ENSG00000136813			29020	protein-coding gene	gene with protein product	"""ECM29 homolog (S. cerevisiae)"""					9205841, 15496406, 20682791	Standard	NM_001080398		Approved	FLJ22036, ECM29	uc004bfe.1	Q5VYK3	OTTHUMG00000020489	ENST00000338205.5:c.3651G>A	9.37:g.114146832C>T		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	107	50	0.46729	NM_001080398	O15074|Q8WU82	Silent	SNP	ENST00000338205.5	37																																																																																				C|0.908;T|0.092	0.092	strong		0.403	KIAA0368-001	NOVEL	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000053637.2	NM_014686	
AKAP3	10566	hgsc.bcm.edu	37	12	4735969	4735969	+	Missense_Mutation	SNP	G	G	A	rs71441828|rs67512580|rs2041291	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:4735969G>A	ENST00000545990.2	-	5	2623	c.2099C>T	c.(2098-2100)tCt>tTt	p.S700F	AKAP3_ENST00000228850.1_Missense_Mutation_p.S700F|RP11-500M8.7_ENST00000536588.1_Intron	NM_001278309.1	NP_001265238.1	O75969	AKAP3_HUMAN	A kinase (PRKA) anchor protein 3	700			S -> F (in dbSNP:rs2041291).|S -> P (in dbSNP:rs2041290).	S -> L (in Ref. 2; AAC35854). {ECO:0000305}.	acrosome reaction (GO:0007340)|cellular component movement (GO:0006928)|protein localization (GO:0008104)|single fertilization (GO:0007338)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	acrosomal vesicle (GO:0001669)|nucleus (GO:0005634)|sperm fibrous sheath (GO:0035686)|sperm principal piece (GO:0097228)	protein kinase A binding (GO:0051018)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(13)|liver(1)|lung(17)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	51						GGCATCTCCAGACTTGTCATC	0.507													G|||	793	0.158347	0.1248	0.1225	5008	,	,		22362	0.1647		0.1143	False		,,,				2504	0.2679				p.S700F		Atlas-SNP	.											.	AKAP3	212	.	0			c.C2099T						PASS	.						78.0	67.0	71.0					12																	4735969		2203	4300	6503	SO:0001583	missense	10566	exon4			TCTCCAGACTTGT	U85715	CCDS8531.1	12p13.3	2009-03-12				ENSG00000111254		"""A-kinase anchor proteins"""	373	protein-coding gene	gene with protein product	"""Fibrous Sheath Protein of 95 kDa"", ""cancer/testis antigen 82"""	604689				10334916, 10319321	Standard	NM_001278309		Approved	FSP95, SOB1, AKAP110, CT82	uc001qnb.4	O75969		ENST00000545990.2:c.2099C>T	12.37:g.4735969G>A	ENSP00000440994:p.Ser700Phe	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	82	23	0.280488	NM_006422	O75945|Q86X01|Q9UM61	Missense_Mutation	SNP	ENST00000545990.2	37	CCDS8531.1	.	.	.	.	.	.	.	.	.	.	G	10.47	1.358997	0.24598	.	.	ENSG00000111254	ENST00000228850;ENST00000545990	T;T	0.09723	2.95;2.95	4.91	0.415	0.16411	A-kinase anchor 110kDa, C-terminal (1);	0.689588	0.13317	N	0.396989	T	0.25195	0.0612	M	0.65975	2.015	0.21105	N	0.999788	D	0.53462	0.96	P	0.54965	0.765	T	0.23833	-1.0177	10	0.54805	T	0.06	-2.5718	16.7329	0.85440	0.0:0.6383:0.3617:0.0	rs2041291;rs2041291	700	O75969	AKAP3_HUMAN	F	700	ENSP00000228850:S700F;ENSP00000440994:S700F	ENSP00000228850:S700F	S	-	2	0	AKAP3	4606230	0.985000	0.35326	0.805000	0.32314	0.119000	0.20118	0.055000	0.14229	-0.136000	0.11475	-0.211000	0.12701	TCT	G|0.936;A|0.064	0.064	strong		0.507	AKAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398911.2	NM_006422	
C10orf128	170371	hgsc.bcm.edu	37	10	50374930	50374930	+	Silent	SNP	C	C	T	rs45563932	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:50374930C>T	ENST00000474718.1	-	3	244	c.222G>A	c.(220-222)acG>acA	p.T74T	C10orf128_ENST00000470884.1_5'UTR|C10orf128_ENST00000374148.1_Silent_p.T74T|C10orf128_ENST00000374153.2_Silent_p.T74T|C10orf128_ENST00000374151.3_Silent_p.T74T	NM_001010863.1	NP_001010863.1	Q5T292	CJ128_HUMAN	chromosome 10 open reading frame 128	74						integral component of membrane (GO:0016021)				breast(1)|large_intestine(1)|lung(1)	3						GGCCCCCAGGCGTGCTTTTCA	0.607													C|||	398	0.0794728	0.0635	0.1455	5008	,	,		19879	0.001		0.1899	False		,,,				2504	0.0215				p.T74T		Atlas-SNP	.											.	C10orf128	20	.	0			c.G222A						PASS	.	C		318,3724		9,300,1712	72.0	76.0	75.0		222	-0.8	0.0	10	dbSNP_127	75	1780,6580		207,1366,2607	no	coding-synonymous	C10orf128	NM_001010863.1		216,1666,4319	TT,TC,CC		21.2919,7.8674,16.9166		74/106	50374930	2098,10304	2021	4180	6201	SO:0001819	synonymous_variant	170371	exon3			CCCAGGCGTGCTT	BC031641	CCDS41519.1, CCDS73128.1	10q11.23	2012-06-13			ENSG00000204161	ENSG00000204161			27274	protein-coding gene	gene with protein product						12477932	Standard	NM_001010863		Approved	Em:AC084727.5	uc001jhn.4	Q5T292	OTTHUMG00000018188	ENST00000474718.1:c.222G>A	10.37:g.50374930C>T		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	58	35	0.603448	NM_001010863	A6XND2|Q5T289|Q5T291	Silent	SNP	ENST00000474718.1	37	CCDS41519.1																																																																																			C|0.865;T|0.135	0.135	strong		0.607	C10orf128-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047978.1	NM_001010863	
MCMBP	79892	hgsc.bcm.edu	37	10	121586827	121586827	+	IGR	SNP	A	A	G	rs56055506	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:121586827A>G	ENST00000360003.3	-	0	4113				INPP5F_ENST00000361976.2_Silent_p.R978R|INPP5F_ENST00000369080.3_Silent_p.R368R	NM_001256378.1|NM_001256379.1|NM_024834.3	NP_001243307.1|NP_001243308.1|NP_079110.1	Q9BTE3	MCMBP_HUMAN	minichromosome maintenance complex binding protein						DNA-dependent DNA replication (GO:0006261)|mitotic nuclear division (GO:0007067)|sister chromatid cohesion (GO:0007062)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	chromatin binding (GO:0003682)	p.R978R(1)		breast(1)|endometrium(3)|large_intestine(4)|lung(9)|ovary(2)|skin(2)	21						CAGAGACCAGATCTGTGTCTC	0.433													G|||	1062	0.212061	0.1203	0.1254	5008	,	,		22364	0.1915		0.164	False		,,,				2504	0.4683				p.R978R		Atlas-SNP	.											INPP5F,NS,carcinoma,0,1	INPP5F	112	1	1	Substitution - coding silent(1)	stomach(1)	c.A2934G						PASS	.	G		571,3835	773.0+/-413.9	30,511,1662	74.0	70.0	71.0		2934	-5.6	0.0	10	dbSNP_129	71	1509,7091	748.2+/-407.3	142,1225,2933	no	coding-synonymous	INPP5F	NM_014937.3		172,1736,4595	GG,GA,AA		17.5465,12.9596,15.9926		978/1133	121586827	2080,10926	2203	4300	6503	SO:0001628	intergenic_variant	22876	exon20			GACCAGATCTGTG	BC007219	CCDS7617.1, CCDS58099.1	10q26.13	2013-10-11	2011-01-05	2011-01-05	ENSG00000197771	ENSG00000197771			25782	protein-coding gene	gene with protein product		610909	"""chromosome 10 open reading frame 119"""	C10orf119		17296731	Standard	NM_024834		Approved	FLJ13081, MCM-BP	uc001ler.3	Q9BTE3	OTTHUMG00000019159		10.37:g.121586827A>G		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	65	28	0.430769	NM_014937	B3KSP7|Q6IA56|Q9BVT9|Q9H916	Silent	SNP	ENST00000360003.3	37	CCDS7617.1																																																																																			A|0.835;G|0.165	0.165	strong		0.433	MCMBP-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000050684.1	NM_024834	
H2AFY	9555	hgsc.bcm.edu	37	5	134670756	134670756	+	Silent	SNP	G	G	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:134670756G>C	ENST00000511689.1	-	9	1622	c.1029C>G	c.(1027-1029)tcC>tcG	p.S343S	H2AFY_ENST00000312469.4_Silent_p.S340S|H2AFY_ENST00000423969.2_Silent_p.S171S|CTC-349C3.1_ENST00000432382.3_Intron|H2AFY_ENST00000512507.1_5'UTR|H2AFY_ENST00000304332.4_Silent_p.S342S|H2AFY_ENST00000510038.1_Silent_p.S343S	NM_001040158.1|NM_138610.2	NP_001035248.1|NP_613258.2	O75367	H2AY_HUMAN	H2A histone family, member Y	343	Macro. {ECO:0000255|PROSITE- ProRule:PRU00490}.				chromatin modification (GO:0016568)|dosage compensation (GO:0007549)|establishment of protein localization to chromatin (GO:0071169)|negative regulation of cell cycle G2/M phase transition (GO:1902750)|negative regulation of gene expression, epigenetic (GO:0045814)|negative regulation of histone phosphorylation (GO:0033128)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription of nuclear large rRNA transcript from RNA polymerase I promoter (GO:1901837)|nucleosome assembly (GO:0006334)	Barr body (GO:0001740)|condensed chromosome (GO:0000793)|extracellular vesicular exosome (GO:0070062)|nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleosome (GO:0000786)|nucleus (GO:0005634)|pericentric heterochromatin (GO:0005721)|sex chromatin (GO:0001739)	chromatin DNA binding (GO:0031490)|DNA binding (GO:0003677)|double-stranded methylated DNA binding (GO:0010385)|protein kinase binding (GO:0019901)|protein serine/threonine kinase inhibitor activity (GO:0030291)|rDNA binding (GO:0000182)|transcription regulatory region DNA binding (GO:0044212)			endometrium(3)|large_intestine(3)|lung(3)|ovary(1)|urinary_tract(1)	11			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			TGATGGAAGAGGACATTGTAG	0.478																																					p.S343S		Atlas-SNP	.											.	H2AFY	61	.	0			c.C1029G						PASS	.						142.0	129.0	133.0					5																	134670756		2203	4300	6503	SO:0001819	synonymous_variant	9555	exon9			GGAAGAGGACATT	AF054174	CCDS4183.1, CCDS4184.1, CCDS4185.1	5q31.1	2011-01-27			ENSG00000113648	ENSG00000113648		"""Histones / Replication-independent"""	4740	protein-coding gene	gene with protein product		610054				9653160, 9714746	Standard	NM_004893		Approved	macroH2A1.2	uc003lam.1	O75367	OTTHUMG00000129141	ENST00000511689.1:c.1029C>G	5.37:g.134670756G>C		Somatic	250	0	0		WXS	Illumina HiSeq	Phase_I	236	70	0.29661	NM_138610	O75377|Q503A8|Q7Z5E3|Q96D41|Q9H8P3|Q9UP96	Silent	SNP	ENST00000511689.1	37	CCDS4185.1																																																																																			.	.	none		0.478	H2AFY-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251196.3	NM_004893	
SPATA5L1	79029	hgsc.bcm.edu	37	15	45695695	45695695	+	Silent	SNP	G	G	A	rs1153849	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:45695695G>A	ENST00000305560.6	+	1	1167	c.1068G>A	c.(1066-1068)agG>agA	p.R356R	SPATA5L1_ENST00000559860.1_Silent_p.R356R|GATM_ENST00000458245.5_5'Flank	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	49	0	0		WXS	Illumina HiSeq	Phase_I	58	37	0.637931	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	
DUSP5	1847	hgsc.bcm.edu	37	10	112266771	112266771	+	Silent	SNP	C	C	T	rs1889567	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:112266771C>T	ENST00000369583.3	+	3	891	c.607C>T	c.(607-609)Ctg>Ttg	p.L203L	DUSP5_ENST00000468749.1_3'UTR	NM_004419.3	NP_004410.3	Q16690	DUS5_HUMAN	dual specificity phosphatase 5	203	Tyrosine-protein phosphatase.				endoderm formation (GO:0001706)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	nucleus (GO:0005634)	MAP kinase tyrosine/serine/threonine phosphatase activity (GO:0017017)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.L203L(1)		kidney(2)|large_intestine(3)|lung(5)|ovary(1)|upper_aerodigestive_tract(2)	13		Breast(234;0.0848)		Epithelial(162;0.000276)|all cancers(201;0.00465)|BRCA - Breast invasive adenocarcinoma(275;0.12)		CCTCGCCAACCTGCACATCAC	0.582													C|||	1420	0.283546	0.2753	0.2406	5008	,	,		19623	0.376		0.2853	False		,,,				2504	0.228				p.L203L		Atlas-SNP	.											DUSP5_ENST00000369583,NS,carcinoma,0,1	DUSP5	62	1	1	Substitution - coding silent(1)	stomach(1)	c.C607T						PASS	.	C		1321,3085	444.7+/-347.4	211,899,1093	214.0	208.0	210.0		607	3.4	1.0	10	dbSNP_92	210	2757,5843	439.7+/-359.3	457,1843,2000	no	coding-synonymous	DUSP5	NM_004419.3		668,2742,3093	TT,TC,CC		32.0581,29.9818,31.3548		203/385	112266771	4078,8928	2203	4300	6503	SO:0001819	synonymous_variant	1847	exon3			GCCAACCTGCACA	U16996	CCDS7566.1	10q25	2011-06-09			ENSG00000138166	ENSG00000138166		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : MAP kinase phosphatases"""	3071	protein-coding gene	gene with protein product		603069				7806236	Standard	NM_004419		Approved	HVH3	uc001kzd.3	Q16690	OTTHUMG00000019040	ENST00000369583.3:c.607C>T	10.37:g.112266771C>T		Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	141	67	0.475177	NM_004419	Q12997|Q5T603	Silent	SNP	ENST00000369583.3	37	CCDS7566.1																																																																																			C|0.692;T|0.308	0.308	strong		0.582	DUSP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050333.1	NM_004419	
FLVCR2	55640	hgsc.bcm.edu	37	14	76045691	76045691	+	Silent	SNP	C	C	T	rs8011292	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:76045691C>T	ENST00000238667.4	+	1	732	c.376C>T	c.(376-378)Ctg>Ttg	p.L126L	AC007182.6_ENST00000455232.1_RNA	NM_017791.2	NP_060261.2	Q9UPI3	FLVC2_HUMAN	feline leukemia virus subgroup C cellular receptor family, member 2	126					heme transport (GO:0015886)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	heme binding (GO:0020037)|heme transporter activity (GO:0015232)			endometrium(3)|kidney(2)|large_intestine(4)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	15				BRCA - Breast invasive adenocarcinoma(234;0.029)		CATTGACTGGCTGTCCATGTG	0.542													C|||	898	0.179313	0.2398	0.183	5008	,	,		22285	0.0764		0.161	False		,,,				2504	0.2198				p.L126L		Atlas-SNP	.											.	FLVCR2	39	.	0			c.C376T						PASS	.	C		898,3508	348.0+/-309.7	98,702,1403	193.0	159.0	170.0		376	3.8	1.0	14	dbSNP_116	170	1381,7219	269.3+/-288.3	112,1157,3031	no	coding-synonymous	FLVCR2	NM_017791.2		210,1859,4434	TT,TC,CC		16.0581,20.3813,17.5227		126/527	76045691	2279,10727	2203	4300	6503	SO:0001819	synonymous_variant	55640	exon1			GACTGGCTGTCCA	AK000378	CCDS9844.1, CCDS55933.1	14q24.3	2013-05-22	2007-05-01	2007-05-01	ENSG00000119686	ENSG00000119686		"""Solute carriers"""	20105	protein-coding gene	gene with protein product		610865	"""chromosome 14 open reading frame 58"", ""feline leukemia virus subgroup C cellular receptor 2"""	C14orf58		16439531, 20206334	Standard	NM_017791		Approved	FLJ20371, MFSD7C	uc001xrs.2	Q9UPI3	OTTHUMG00000171487	ENST00000238667.4:c.376C>T	14.37:g.76045691C>T		Somatic	198	0	0		WXS	Illumina HiSeq	Phase_I	144	82	0.569444	NM_017791	B7Z485|Q53ZT9|Q96JY3|Q9NX90	Silent	SNP	ENST00000238667.4	37	CCDS9844.1																																																																																			C|0.824;T|0.176	0.176	strong		0.542	FLVCR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413672.1	NM_017791	
CFAP44	55779	hgsc.bcm.edu	37	3	113146131	113146131	+	Silent	SNP	G	G	A	rs386664769|rs58474121	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:113146131G>A	ENST00000295868.2	-	3	318	c.156C>T	c.(154-156)acC>acT	p.T52T	WDR52-AS1_ENST00000498480.1_RNA|WDR52_ENST00000393845.2_Silent_p.T52T|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						CTTCCCCTTTGGTAAATGTTT	0.318													G|||	243	0.0485224	0.0106	0.0187	5008	,	,		18231	0.1062		0.0408	False		,,,				2504	0.0695				p.T52T		Atlas-SNP	.											.	WDR52	151	.	0			c.C156T						PASS	.	G	,	52,4354	51.6+/-87.1	0,52,2151	159.0	138.0	145.0		156,156	-6.3	0.0	3	dbSNP_129	145	303,8297	107.8+/-168.5	6,291,4003	no	coding-synonymous,coding-synonymous	WDR52	NM_001164496.1,NM_018338.3	,	6,343,6154	AA,AG,GG		3.5233,1.1802,2.7295	,	52/1855,52/983	113146131	355,12651	2203	4300	6503	SO:0001819	synonymous_variant	55779	exon3			CCCTTTGGTAAAT																												ENST00000295868.2:c.156C>T	3.37:g.113146131G>A		Somatic	245	0	0		WXS	Illumina HiSeq	Phase_I	221	117	0.529412	NM_001164496		Silent	SNP	ENST00000295868.2	37	CCDS2972.1																																																																																			G|0.969;A|0.031	0.031	strong		0.318	WDR52-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000354128.3		
MUC4	4585	hgsc.bcm.edu	37	3	195513493	195513493	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195513493C>A	ENST00000463781.3	-	2	5417	c.4958G>T	c.(4957-4959)aGc>aTc	p.S1653I	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.S1653I	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0	VWFD. {ECO:0000255|PROSITE- ProRule:PRU00580}.				cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.S1653I(3)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		TGAGGAAGGGCTGGTGACATG	0.592																																					p.S1653I		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,3	MUC4	1505	3	3	Substitution - Missense(3)	endometrium(2)|kidney(1)	c.G4958T						scavenged	.						27.0	30.0	29.0					3																	195513493		690	1576	2266	SO:0001583	missense	4585	exon2			GAAGGGCTGGTGA	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.4958G>T	3.37:g.195513493C>A	ENSP00000417498:p.Ser1653Ile	Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	243	16	0.0658436	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	-	0.027	-1.366531	0.01225	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.33216	1.42;1.43	0.595	-1.19	0.09585	.	.	.	.	.	T	0.08582	0.0213	N	0.08118	0	0.09310	N	1	P	0.42993	0.797	B	0.25884	0.064	T	0.26950	-1.0088	8	.	.	.	.	1.1981	0.01879	0.1873:0.2606:0.3737:0.1784	.	1653	E7ESK3	.	I	1653	ENSP00000417498:S1653I;ENSP00000420243:S1653I	.	S	-	2	0	MUC4	196997888	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.015000	0.03637	-4.523000	0.00044	-4.118000	0.00011	AGC	.	.	none		0.592	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
CTSC	1075	hgsc.bcm.edu	37	11	88027209	88027209	+	Missense_Mutation	SNP	T	T	C	rs3888798	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:88027209T>C	ENST00000227266.5	-	7	1471	c.1357A>G	c.(1357-1359)Ata>Gta	p.I453V		NM_001814.4	NP_001805	P53634	CATC_HUMAN	cathepsin C	453			I -> V (rare polymorphism; dbSNP:rs3888798). {ECO:0000269|PubMed:11180012}.		aging (GO:0007568)|immune response (GO:0006955)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of proteolysis involved in cellular protein catabolic process (GO:1903052)|proteolysis (GO:0006508)|response to organic substance (GO:0010033)|T cell mediated cytotoxicity (GO:0001913)	endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|lysosome (GO:0005764)|membrane (GO:0016020)	chaperone binding (GO:0051087)|chloride ion binding (GO:0031404)|cysteine-type peptidase activity (GO:0008234)|peptidase activator activity involved in apoptotic process (GO:0016505)|phosphatase binding (GO:0019902)|serine-type endopeptidase activity (GO:0004252)			large_intestine(7)|lung(8)|ovary(2)|prostate(3)|skin(2)	22		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)				GCCACTGCTATGCTCTCAATT	0.463													T|||	420	0.0838658	0.0802	0.1023	5008	,	,		16827	0.1151		0.0517	False		,,,				2504	0.0767				p.I453V		Atlas-SNP	.											.	CTSC	46	.	0			c.A1357G	GRCh37	CM086741	CTSC	M	rs3888798	PASS	.	T	VAL/ILE	302,4100	163.6+/-195.4	11,280,1910	87.0	82.0	84.0		1357	6.0	1.0	11	dbSNP_108	84	332,8266	115.7+/-175.5	6,320,3973	yes	missense	CTSC	NM_001814.4	29	17,600,5883	CC,CT,TT		3.8614,6.8605,4.8769	possibly-damaging	453/464	88027209	634,12366	2201	4299	6500	SO:0001583	missense	1075	exon7			CTGCTATGCTCTC	AK223038	CCDS8282.1, CCDS31654.1, CCDS44693.1	11q14.2	2014-09-17			ENSG00000109861	ENSG00000109861	3.4.14.1	"""Cathepsins"""	2528	protein-coding gene	gene with protein product	"""dipeptidyl peptidase 1"""	602365		PLS, PALS		7649281, 9092576	Standard	NM_148170		Approved	DPP1	uc001pck.4	P53634	OTTHUMG00000167290	ENST00000227266.5:c.1357A>G	11.37:g.88027209T>C	ENSP00000227266:p.Ile453Val	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	96	25	0.260417	NM_001814	A8K7V2|B5MDD5|Q2HIY8|Q53G93|Q71E75|Q71E76|Q7M4N9|Q7Z3G7|Q7Z5U7|Q8WY99|Q8WYA7|Q8WYA8	Missense_Mutation	SNP	ENST00000227266.5	37	CCDS8282.1	186	0.08516483516483517	35	0.07113821138211382	27	0.07458563535911603	75	0.13111888111888112	49	0.06464379947229551	T	24.7	4.556481	0.86231	0.068605	0.038614	ENSG00000109861	ENST00000393302;ENST00000227266	D	0.86627	-2.15	5.97	5.97	0.96955	Peptidase C1A, papain C-terminal (2);	0.000000	0.85682	D	0.000000	T	0.06280	0.0162	N	0.20574	0.59	0.80722	D	1	P;B	0.39759	0.687;0.444	P;B	0.52909	0.713;0.307	T	0.53585	-0.8418	9	.	.	.	.	16.4504	0.83984	0.0:0.0:0.0:1.0	rs3888798;rs4581448;rs56447948;rs3888798	436;453	B4DJQ8;P53634	.;CATC_HUMAN	V	436;453	ENSP00000227266:I453V	.	I	-	1	0	CTSC	87666857	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.156000	0.71840	2.288000	0.76882	0.533000	0.62120	ATA	T|0.939;C|0.061	0.061	strong		0.463	CTSC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394019.2	NM_001814	
PCM1	5108	hgsc.bcm.edu	37	8	17820714	17820714	+	Silent	SNP	A	A	T	rs6991775	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:17820714A>T	ENST00000519253.1	+	17	2819	c.2568A>T	c.(2566-2568)ctA>ctT	p.L856L	PCM1_ENST00000325083.8_Silent_p.L856L|PCM1_ENST00000524226.1_Silent_p.L857L			Q15154	PCM1_HUMAN	pericentriolar material 1	856					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)		GGCAAGGTCTAGCTGAAACTG	0.468			T	"""RET, JAK2"""	"""papillary thyroid, CML, MPD"""								G|||	1094	0.21845	0.2852	0.1427	5008	,	,		16808	0.37		0.1332	False		,,,				2504	0.1135				p.L856L		Atlas-SNP	.		Dom	yes		8	8p22-p21.3	5108	pericentriolar material 1  (PTC4)		"""E, L"""	.	PCM1	120	.	0			c.A2568T						PASS	.	G		1146,2872		152,842,1015	87.0	93.0	91.0		2568	-9.8	0.0	8	dbSNP_116	91	1240,7114		83,1074,3020	no	coding-synonymous	PCM1	NM_006197.3		235,1916,4035	TT,TA,AA		14.8432,28.5217,19.2855		856/2025	17820714	2386,9986	2009	4177	6186	SO:0001819	synonymous_variant	5108	exon17			AGGTCTAGCTGAA		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.2568A>T	8.37:g.17820714A>T		Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	154	33	0.214286	NM_006197	Q58F13|Q6P1K7|Q8NB85|Q9BWC1|Q9H4A2	Silent	SNP	ENST00000519253.1	37																																																																																				A|0.770;T|0.230	0.230	strong		0.468	PCM1-003	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000374800.1	NM_006197	
MUC4	4585	hgsc.bcm.edu	37	3	195507193	195507193	+	Missense_Mutation	SNP	G	G	A	rs201474621	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195507193G>A	ENST00000463781.3	-	2	11717	c.11258C>T	c.(11257-11259)gCa>gTa	p.A3753V	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.A3753V	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		ACCTGTGGATGCTGAGGAAGT	0.587																																					p.A3753V		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	0			c.C11258T						scavenged	.						31.0	26.0	27.0					3																	195507193		683	1583	2266	SO:0001583	missense	4585	exon2			GTGGATGCTGAGG	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.11258C>T	3.37:g.195507193G>A	ENSP00000417498:p.Ala3753Val	Somatic	59	2	0.0338983		WXS	Illumina HiSeq	Phase_I	69	24	0.347826	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	N	4.279	0.050873	0.08243	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.31510	1.49;1.5	0.885	-1.56	0.08532	.	0.000000	0.24912	U	0.034619	T	0.14184	0.0343	N	0.19112	0.55	0.09310	N	1	B	0.19200	0.034	B	0.14023	0.01	T	0.20706	-1.0267	9	.	.	.	.	5.5971	0.17333	0.2308:0.0:0.7692:0.0	rs9755674	3625	E7ESK3	.	V	3753	ENSP00000417498:A3753V;ENSP00000420243:A3753V	.	A	-	2	0	MUC4	196991972	0.009000	0.17119	0.041000	0.18516	0.025000	0.11179	0.313000	0.19415	-1.696000	0.01421	-2.092000	0.00371	GCA	G|0.993;T|0.007	.	strong		0.587	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
ZNF578	147660	hgsc.bcm.edu	37	19	53014787	53014787	+	Missense_Mutation	SNP	A	A	G	rs35356792	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:53014787A>G	ENST00000421239.2	+	6	1397	c.1153A>G	c.(1153-1155)Acc>Gcc	p.T385A	CTD-3099C6.5_ENST00000599143.1_RNA	NM_001099694.1	NP_001093164.1	Q96N58	ZN578_HUMAN	zinc finger protein 578	385					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)								GBM - Glioblastoma multiforme(134;0.00819)|OV - Ovarian serous cystadenocarcinoma(262;0.01)		TCAAAATTCAACCCTTGTAAT	0.378													a|||	301	0.0601038	0.1362	0.0591	5008	,	,		25349	0.001		0.0636	False		,,,				2504	0.0153				p.T385A		Atlas-SNP	.											.	.	.	.	0			c.A1153G						PASS	.	A	ALA/THR	508,3898		38,432,1733	96.0	101.0	99.0		1153	-3.0	0.0	19	dbSNP_126	99	570,8028		14,542,3743	no	missense	ZNF578	NM_001099694.1	58	52,974,5476	GG,GA,AA		6.6294,11.5297,8.2898	possibly-damaging	385/591	53014787	1078,11926	2203	4299	6502	SO:0001583	missense	147660	exon6			AATTCAACCCTTG	AK095562	CCDS54310.1	19q13.41	2013-09-20			ENSG00000258405	ENSG00000258405		"""Zinc fingers, C2H2-type"", ""-"""	26449	protein-coding gene	gene with protein product							Standard	NM_001099694		Approved	FLJ31384	uc002pzp.4	Q96N58	OTTHUMG00000156468	ENST00000421239.2:c.1153A>G	19.37:g.53014787A>G	ENSP00000459216:p.Thr385Ala	Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	42	22	0.52381	NM_001099694	B4DR51|I3L1Y6	Missense_Mutation	SNP	ENST00000421239.2	37	CCDS54310.1	130	0.05952380952380952	67	0.13617886178861788	18	0.049723756906077346	1	0.0017482517482517483	44	0.05804749340369393	-	0.314	-0.965816	0.02249	0.115297	0.066294	ENSG00000258405	ENST00000553364	.	.	.	1.48	-2.97	0.05530	.	.	.	.	.	T	0.00073	0.0002	N	0.02685	-0.53	0.80722	P	0.0	B	0.06786	0.001	B	0.09377	0.004	T	0.23013	-1.0200	6	.	.	.	.	0.5818	0.00713	0.4441:0.1578:0.131:0.2671	rs35356792;rs61746281	385	G3V4F6	.	A	385	.	.	T	+	1	0	ZNF578	57706599	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-13.157000	0.00001	-1.870000	0.01139	0.246000	0.17985	ACC	A|0.938;G|0.062	0.062	strong		0.378	ZNF578-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344298.3	NM_152472	
ESPN	83715	hgsc.bcm.edu	37	1	6500712	6500712	+	Silent	SNP	C	C	G	rs367944375		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:6500712C>G	ENST00000377828.1	+	4	870	c.702C>G	c.(700-702)tcC>tcG	p.S234S	RP1-202O8.2_ENST00000419034.1_RNA	NM_031475.2	NP_113663.2	B1AK53	ESPN_HUMAN	espin	234					locomotory behavior (GO:0007626)|negative regulation of cytoskeleton organization (GO:0051494)|parallel actin filament bundle assembly (GO:0030046)|positive regulation of filopodium assembly (GO:0051491)|sensory perception of sound (GO:0007605)	brush border (GO:0005903)|cytoplasm (GO:0005737)|filamentous actin (GO:0031941)|microvillus (GO:0005902)|stereocilium bundle tip (GO:0032426)	actin filament binding (GO:0051015)|SH3 domain binding (GO:0017124)			NS(1)|breast(2)|cervix(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|prostate(1)|skin(1)	17	Ovarian(185;0.0386)|all_lung(157;0.154)	all_cancers(23;3.6e-37)|all_epithelial(116;2.56e-22)|all_lung(118;7.57e-07)|Lung NSC(185;4.26e-06)|all_hematologic(16;6.92e-06)|Colorectal(325;4.47e-05)|Acute lymphoblastic leukemia(12;4.92e-05)|Breast(487;7.61e-05)|Renal(390;0.0007)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0392)		Epithelial(90;1.82e-35)|GBM - Glioblastoma multiforme(13;3e-28)|Kidney(185;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(229;5.63e-08)|Colorectal(212;7e-08)|COAD - Colon adenocarcinoma(227;1.41e-05)|BRCA - Breast invasive adenocarcinoma(365;0.000109)|STAD - Stomach adenocarcinoma(132;0.00167)|Lung(427;0.0108)|LUSC - Lung squamous cell carcinoma(448;0.0253)|READ - Rectum adenocarcinoma(331;0.0419)		TGAGCCTGTCCGAGCAGGACA	0.741																																					p.S234S		Atlas-SNP	.											.	ESPN	32	.	0			c.C702G						PASS	.						3.0	5.0	4.0					1																	6500712		1942	3924	5866	SO:0001819	synonymous_variant	83715	exon4			CCTGTCCGAGCAG	AF134401	CCDS70.1	1p36.31	2013-01-10			ENSG00000187017	ENSG00000187017		"""Ankyrin repeat domain containing"""	13281	protein-coding gene	gene with protein product		606351	"""deafness, autosomal recessive 36"""	DFNB36		10975527, 15286153	Standard	NM_031475		Approved		uc001amy.3	B1AK53	OTTHUMG00000000753	ENST00000377828.1:c.702C>G	1.37:g.6500712C>G		Somatic	9	0	0		WXS	Illumina HiSeq	Phase_I	12	10	0.833333	NM_031475	Q6XYB2|Q9H0A2|Q9Y329	Silent	SNP	ENST00000377828.1	37	CCDS70.1																																																																																			.	.	none		0.741	ESPN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001887.3	NM_031475	
HMCN1	83872	hgsc.bcm.edu	37	1	186121995	186121995	+	Missense_Mutation	SNP	A	A	T	rs114364265	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:186121995A>T	ENST00000271588.4	+	96	15239	c.15010A>T	c.(15010-15012)Act>Tct	p.T5004S	HMCN1_ENST00000367492.2_Missense_Mutation_p.T5004S	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	5004	Nidogen G2 beta-barrel. {ECO:0000255|PROSITE-ProRule:PRU00348}.				response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						TGCTGAAGTCACTGTAAAGGT	0.438													A|||	9	0.00179712	0.0	0.0	5008	,	,		18499	0.0		0.008	False		,,,				2504	0.001				p.T5004S		Atlas-SNP	.											.	HMCN1	797	.	0			c.A15010T						PASS	.	A	SER/THR	3,4403	4.2+/-10.8	0,3,2200	196.0	170.0	179.0		15010	0.8	0.1	1	dbSNP_133	179	28,8572	9.1+/-34.3	1,26,4273	yes	missense	HMCN1	NM_031935.2	58	1,29,6473	TT,TA,AA		0.3256,0.0681,0.2384	benign	5004/5636	186121995	31,12975	2203	4300	6503	SO:0001583	missense	83872	exon96			GAAGTCACTGTAA	AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"""Fibulins"", ""Immunoglobulin superfamily / I-set domain containing"""	19194	protein-coding gene	gene with protein product	"""fibulin 6"""	608548	"""age-related macular degeneration 1 (senile macular degeneration)"""	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.15010A>T	1.37:g.186121995A>T	ENSP00000271588:p.Thr5004Ser	Somatic	215	0	0		WXS	Illumina HiSeq	Phase_I	170	87	0.511765	NM_031935	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Missense_Mutation	SNP	ENST00000271588.4	37	CCDS30956.1	6	0.0027472527472527475	0	0.0	0	0.0	0	0.0	6	0.0079155672823219	A	2.871	-0.233991	0.05983	6.81E-4	0.003256	ENSG00000143341	ENST00000271588;ENST00000367492	T;T	0.32988	1.43;1.43	5.9	0.836	0.18891	G2 nidogen/fibulin G2F (2);Green fluorescent protein-like (1);	0.929918	0.09308	N	0.819936	T	0.08582	0.0213	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.32161	-0.9917	10	0.05833	T	0.94	.	6.2405	0.20787	0.6238:0.1195:0.2567:0.0	.	5004	Q96RW7	HMCN1_HUMAN	S	5004	ENSP00000271588:T5004S;ENSP00000356462:T5004S	ENSP00000271588:T5004S	T	+	1	0	HMCN1	184388618	0.001000	0.12720	0.065000	0.19835	0.779000	0.44077	0.806000	0.27126	-0.101000	0.12219	-0.263000	0.10527	ACT	A|0.996;T|0.004	0.004	strong		0.438	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935	
CCDC176	80127	hgsc.bcm.edu	37	14	74514674	74514674	+	Missense_Mutation	SNP	A	A	T	rs3784038	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:74514674A>T	ENST00000394009.3	+	7	812	c.689A>T	c.(688-690)gAt>gTt	p.D230V	AC005484.5_ENST00000492026.1_RNA|CCDC176_ENST00000489323.1_3'UTR|CCDC176_ENST00000553773.1_5'UTR	NM_025057.2	NP_079333.2	Q8ND07	BBOF1_HUMAN	coiled-coil domain containing 176	230			D -> V (in dbSNP:rs3784038). {ECO:0000269|PubMed:17974005}.		motile cilium assembly (GO:0044458)	ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)											AAAGAGAATGATTATCTTCAG	0.348													T|||	3164	0.631789	0.5454	0.5274	5008	,	,		17876	0.8829		0.4751	False		,,,				2504	0.7249				p.D230V		Atlas-SNP	.											.	.	.	.	0			c.A689T						PASS	.	T	VAL/ASP	1750,1386		483,784,301	80.0	71.0	74.0		689	5.8	1.0	14	dbSNP_107	74	3432,3732		818,1796,968	yes	missense	C14orf45	NM_025057.2	152	1301,2580,1269	TT,TA,AA		47.9062,44.1964,49.6893	benign	230/530	74514674	5182,5118	1568	3582	5150	SO:0001583	missense	80127	exon7			AGAATGATTATCT	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.689A>T	14.37:g.74514674A>T	ENSP00000377577:p.Asp230Val	Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	159	159	1	NM_025057	Q0P604|Q9H5P8	Missense_Mutation	SNP	ENST00000394009.3	37	CCDS32119.2	1311	0.6002747252747253	262	0.532520325203252	181	0.5	503	0.8793706293706294	365	0.4815303430079156	T	15.43	2.830233	0.50845	0.558036	0.479062	ENSG00000119636	ENST00000464394;ENST00000394009	T;T	0.32023	1.47;1.47	5.78	5.78	0.91487	.	0.403487	0.24776	N	0.035682	T	0.00012	0.0000	N	0.00069	-2.28	0.09310	P	0.9999999999999967	B	0.02656	0.0	B	0.01281	0.0	T	0.35968	-0.9767	9	0.26408	T	0.33	-1.8317	12.1639	0.54119	0.1283:0.0:0.0:0.8717	rs3784038;rs52825587;rs57060702;rs3784038	230	Q8ND07	CN045_HUMAN	V	90;230	ENSP00000451659:D90V;ENSP00000377577:D230V	ENSP00000377577:D230V	D	+	2	0	C14orf45	73584427	1.000000	0.71417	0.998000	0.56505	0.832000	0.47134	2.691000	0.47010	1.018000	0.39521	-0.265000	0.10407	GAT	A|0.410;T|0.590	0.590	strong		0.348	CCDC176-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327863.1	NM_025057	
OBSCN	84033	hgsc.bcm.edu	37	1	228476366	228476366	+	Missense_Mutation	SNP	G	G	T	rs3795789|rs386640016	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:228476366G>T	ENST00000422127.1	+	38	10160	c.10116G>T	c.(10114-10116)gaG>gaT	p.E3372D	OBSCN_ENST00000284548.11_Missense_Mutation_p.E3372D|OBSCN_ENST00000359599.6_Missense_Mutation_p.E2219D|OBSCN_ENST00000570156.2_Missense_Mutation_p.E3801D|OBSCN_ENST00000366709.4_Missense_Mutation_p.E491D|OBSCN_ENST00000366707.4_Missense_Mutation_p.E491D	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	3372	Ig-like 34.		E -> D (in dbSNP:rs3795789).		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)				GACACCAAGAGAGCATAGAAG	0.607													G|||	480	0.0958466	0.0514	0.0144	5008	,	,		21025	0.3165		0.0258	False		,,,				2504	0.0583				p.E3801D		Atlas-SNP	.											.	OBSCN	2142	.	0			c.G11403T						PASS	.	G	ASP/GLU,ASP/GLU	186,3926		8,170,1878	71.0	76.0	75.0		10116,10116	3.2	0.2	1	dbSNP_107	75	125,8281		0,125,4078	yes	missense,missense	OBSCN	NM_001098623.1,NM_052843.2	45,45	8,295,5956	TT,TG,GG		1.487,4.5233,2.4844	possibly-damaging,possibly-damaging	3372/7969,3372/6621	228476366	311,12207	2056	4203	6259	SO:0001583	missense	84033	exon43			CCAAGAGAGCATA	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.10116G>T	1.37:g.228476366G>T	ENSP00000409493:p.Glu3372Asp	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	56	29	0.517857	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	208	0.09523809523809523	17	0.034552845528455285	3	0.008287292817679558	167	0.291958041958042	21	0.027704485488126648	G	16.90	3.251180	0.59212	0.045233	0.01487	ENSG00000154358	ENST00000284548;ENST00000422127;ENST00000366707;ENST00000366709;ENST00000359599	T;T;T;T;T	0.69040	-0.37;-0.37;-0.37;-0.37;-0.37	5.07	3.15	0.36227	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.325170	0.22002	N	0.065982	T	0.00012	0.0000	M	0.87758	2.905	0.38410	P	0.054088000000000025	B;P	0.38863	0.139;0.65	P;P	0.51701	0.472;0.677	T	0.08785	-1.0705	9	0.32370	T	0.25	.	6.4245	0.21762	0.1648:0.0:0.6798:0.1554	rs3795789;rs3795789	3372;3372	Q5VST9;Q5VST9-3	OBSCN_HUMAN;.	D	3372;3372;491;491;2219	ENSP00000284548:E3372D;ENSP00000409493:E3372D;ENSP00000355668:E491D;ENSP00000355670:E491D;ENSP00000352613:E2219D	ENSP00000284548:E3372D	E	+	3	2	OBSCN	226542989	0.195000	0.23338	0.215000	0.23724	0.333000	0.28666	0.401000	0.20948	1.121000	0.41925	0.561000	0.74099	GAG	G|0.927;T|0.073	0.073	strong		0.607	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
KRTAP12-2	353323	hgsc.bcm.edu	37	21	46086407	46086407	+	Missense_Mutation	SNP	C	C	T	rs12481809	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:46086407C>T	ENST00000360770.3	-	1	437	c.397G>A	c.(397-399)Gtc>Atc	p.V133I	TSPEAR_ENST00000323084.4_Intron	NM_181684.2	NP_859012.1	P59991	KR122_HUMAN	keratin associated protein 12-2	133	23 X 5 AA approximate repeats.					keratin filament (GO:0045095)				central_nervous_system(1)|endometrium(1)|lung(3)	5						CTGCAGAGGACGCTGGTGCAG	0.622													C|||	731	0.145966	0.0946	0.1657	5008	,	,		19372	0.0923		0.2068	False		,,,				2504	0.1943				p.V133I		Atlas-SNP	.											.	KRTAP12-2	10	.	0			c.G397A						PASS	.	C	,ILE/VAL	403,3907		22,359,1774	54.0	60.0	58.0		,397	1.5	0.1	21	dbSNP_120	58	1732,6738		170,1392,2673	yes	intron,missense	TSPEAR,KRTAP12-2	NM_144991.2,NM_181684.2	,29	192,1751,4447	TT,TC,CC		20.4486,9.3503,16.7058	,benign	,133/147	46086407	2135,10645	2155	4235	6390	SO:0001583	missense	353323	exon1			AGAGGACGCTGGT	AJ566389	CCDS42965.1	21q22.3	2006-03-13			ENSG00000221864	ENSG00000221864		"""Keratin associated proteins"""	20530	protein-coding gene	gene with protein product							Standard	NM_181684		Approved	KRTAP12.2, KAP12.2	uc002zfu.3	P59991	OTTHUMG00000057636	ENST00000360770.3:c.397G>A	21.37:g.46086407C>T	ENSP00000354001:p.Val133Ile	Somatic	237	0	0		WXS	Illumina HiSeq	Phase_I	324	137	0.422839	NM_181684	A6NIS1|A6NMS9|Q0VAS4	Missense_Mutation	SNP	ENST00000360770.3	37	CCDS42965.1	321	0.14697802197802198	45	0.09146341463414634	61	0.1685082872928177	56	0.0979020979020979	159	0.20976253298153033	c	2.766	-0.256710	0.05829	0.093503	0.204486	ENSG00000221864	ENST00000360770;ENST00000539483	T	0.02656	4.21	3.62	1.54	0.23209	.	.	.	.	.	T	0.00012	0.0000	L	0.39898	1.24	0.80722	P	0.0	B	0.29936	0.262	B	0.23150	0.044	T	0.46762	-0.9168	8	0.24483	T	0.36	.	5.7725	0.18261	0.1361:0.2197:0.6442:0.0	rs12481809	133	P59991	KR122_HUMAN	I	133;83	ENSP00000354001:V133I	ENSP00000354001:V133I	V	-	1	0	KRTAP12-2	44910835	0.005000	0.15991	0.063000	0.19743	0.005000	0.04900	0.296000	0.19083	0.697000	0.31718	-0.502000	0.04539	GTC	C|0.844;T|0.156	0.156	strong		0.622	KRTAP12-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128039.1	NM_181684	
ATP10A	57194	hgsc.bcm.edu	37	15	25925094	25925094	+	Missense_Mutation	SNP	C	C	G	rs3816800	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:25925094C>G	ENST00000356865.6	-	21	4005	c.3894G>C	c.(3892-3894)agG>agC	p.R1298S		NM_024490.3	NP_077816.1	O60312	AT10A_HUMAN	ATPase, class V, type 10A	1298			R -> S (in dbSNP:rs3816800).		ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|regulation of cell shape (GO:0008360)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|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)			NS(1)|breast(2)|endometrium(8)|kidney(2)|large_intestine(33)|liver(1)|lung(41)|ovary(3)|pancreas(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	103		all_cancers(20;5.16e-25)|all_lung(180;1.51e-14)|Acute lymphoblastic leukemia(1;2.53e-05)|all_hematologic(1;0.000267)|Breast(32;0.00125)		all cancers(64;9.48e-07)|Epithelial(43;1.69e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0252)|Lung(196;0.244)		TGGGGAAAACCCTCCCCTGGA	0.498													G|||	2234	0.446086	0.4909	0.3948	5008	,	,		19918	0.3611		0.4841	False		,,,				2504	0.4703				p.R1298S		Atlas-SNP	.											.	ATP10A	270	.	0			c.G3894C						PASS	.	G	SER/ARG	2289,2117		600,1089,514	62.0	67.0	66.0		3894	0.7	0.4	15	dbSNP_107	66	4090,4510		977,2136,1187	yes	missense	ATP10A	NM_024490.3	110	1577,3225,1701	GG,GC,CC		47.5581,48.0481,49.0466	benign	1298/1500	25925094	6379,6627	2203	4300	6503	SO:0001583	missense	57194	exon21			GAAAACCCTCCCC	AB011138	CCDS32178.1	15q12	2010-04-20	2007-09-19		ENSG00000206190	ENSG00000206190		"""ATPases / P-type"""	13542	protein-coding gene	gene with protein product		605855	"""ATPase, Class V, type 10C"", ""ATPase, Class V, type 10A"""	ATP10C		11015572, 9628581	Standard	NM_024490		Approved	ATPVA, ATPVC, KIAA0566	uc010ayu.3	O60312		ENST00000356865.6:c.3894G>C	15.37:g.25925094C>G	ENSP00000349325:p.Arg1298Ser	Somatic	22	0	0		WXS	Illumina HiSeq	Phase_I	17	11	0.647059	NM_024490	Q4G0S9|Q969I4	Missense_Mutation	SNP	ENST00000356865.6	37	CCDS32178.1	965	0.44184981684981683	249	0.5060975609756098	150	0.4143646408839779	191	0.3339160839160839	375	0.4947229551451187	G	0.124	-1.122430	0.01785	0.519519	0.475581	ENSG00000206190	ENST00000356865	T	0.38887	1.11	5.41	0.738	0.18319	.	0.245365	0.39020	N	0.001499	T	0.00012	0.0000	N	0.00224	-1.81	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.40813	-0.9543	9	0.06236	T	0.91	-15.3662	2.3822	0.04357	0.3033:0.0923:0.4509:0.1535	rs3816800;rs52812289;rs60806869;rs3816800	1298	O60312	AT10A_HUMAN	S	1298	ENSP00000349325:R1298S	ENSP00000349325:R1298S	R	-	3	2	ATP10A	23476187	0.014000	0.17966	0.381000	0.26106	0.061000	0.15899	-1.403000	0.02497	0.006000	0.14734	-0.120000	0.15030	AGG	C|0.531;G|0.469	0.469	strong		0.498	ATP10A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414830.1	NM_024490	
MFSD4	148808	hgsc.bcm.edu	37	1	205554085	205554085	+	Missense_Mutation	SNP	G	G	C	rs7526132	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	123	0	0	2153	WXS	Illumina HiSeq	Phase_I	93	44	0.473118	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	
HERPUD1	9709	hgsc.bcm.edu	37	16	56969148	56969148	+	Splice_Site	SNP	G	G	A	rs2217332	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:56969148G>A	ENST00000439977.2	+	2	346	c.149G>A	c.(148-150)cGt>cAt	p.R50H	HERPUD1_ENST00000344114.4_Splice_Site_p.R50H|HERPUD1_ENST00000570273.1_3'UTR|HERPUD1_ENST00000379792.2_Splice_Site_p.R50H|HERPUD1_ENST00000300302.5_Splice_Site_p.R50H	NM_001010989.1|NM_014685.2	NP_001010989.1|NP_055500.1	Q15011	HERP1_HUMAN	homocysteine-inducible, endoplasmic reticulum stress-inducible, ubiquitin-like domain member 1	50	Ubiquitin-like. {ECO:0000255|PROSITE- ProRule:PRU00214}.		R -> H (in dbSNP:rs2217332).		activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular calcium ion homeostasis (GO:0006874)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|positive regulation of protein binding (GO:0032092)|regulation of protein ubiquitination (GO:0031396)|response to unfolded protein (GO:0006986)|ubiquitin-dependent protein catabolic process (GO:0006511)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)		p.R50H(1)		cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)|stomach(1)	11						CATGATCAGCGTCCAGAGGAC	0.393			T	ERG	prostate								G|||	745	0.148762	0.1172	0.1729	5008	,	,		20673	0.0823		0.1471	False		,,,				2504	0.2444				p.R50H		Atlas-SNP	.		Dom	yes		16	16q12.2-q13	9709	"""homocysteine-inducible, endoplasmic reticulum stress-inducible, ubiquitin-like domain member 1"""		E	HERPUD1,NS,carcinoma,0,1	HERPUD1	28	1	1	Substitution - Missense(1)	stomach(1)	c.G149A						scavenged	.	G	HIS/ARG,HIS/ARG,HIS/ARG	564,3832	253.0+/-259.1	42,480,1676	138.0	120.0	126.0	http://www.ncbi.nlm.nih.gov/pubmed?term	149,149,149	3.1	1.0	16	dbSNP_96	126	1340,7260	262.4+/-284.4	110,1120,3070	yes	missense-near-splice,missense-near-splice,missense-near-splice	HERPUD1	NM_001010989.1,NM_001010990.1,NM_014685.2	29,29,29	152,1600,4746	AA,AG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	15.5814,12.8298,14.6507	benign,benign,benign	50/391,50/367,50/392	56969148	1904,11092	2198	4300	6498	SO:0001630	splice_region_variant	9709	exon2			ATCAGCGTCCAGA	AB034989	CCDS10771.1, CCDS45492.1	16q13	2008-05-14			ENSG00000051108	ENSG00000051108			13744	protein-coding gene	gene with protein product		608070				10922362, 10708769	Standard	NM_001010989		Approved	KIAA0025, Mif1, HERP, SUP	uc002eke.2	Q15011	OTTHUMG00000133276	ENST00000439977.2:c.148-1G>A	16.37:g.56969148G>A		Somatic	140	2	0.0142857		WXS	Illumina HiSeq	Phase_I	169	105	0.621302	NM_014685	E9PGD1|O60644|Q6IAN8|Q96D92	Missense_Mutation	SNP	ENST00000439977.2	37	CCDS10771.1	256	0.11721611721611722	50	0.1016260162601626	60	0.16574585635359115	34	0.05944055944055944	112	0.14775725593667546	G	9.103	1.004518	0.19199	0.128298	0.155814	ENSG00000051108	ENST00000439977;ENST00000379792;ENST00000300302;ENST00000344114	T;T;T;T	0.73258	-0.73;-0.73;-0.73;-0.73	6.04	3.06	0.35304	Ubiquitin supergroup (1);Ubiquitin (2);	0.645525	0.16761	N	0.200620	T	0.00210	0.0006	N	0.24115	0.695	0.51482	P	7.599999999996498E-5	B;B;B;B;B;B	0.14012	0.009;0.002;0.003;0.0;0.001;0.001	B;B;B;B;B;B	0.15484	0.013;0.004;0.002;0.002;0.0;0.003	T	0.04053	-1.0981	9	0.45353	T	0.12	-23.2151	4.5891	0.12297	0.2351:0.0:0.6121:0.1528	rs2217332;rs11553779;rs52796206;rs60487936;rs2217332	50;50;50;50;50;50	B4E3N8;Q15011-3;A4UAE9;E9PGD1;Q15011-2;Q15011	.;.;.;.;.;HERP1_HUMAN	H	50	ENSP00000409555:R50H;ENSP00000369118:R50H;ENSP00000300302:R50H;ENSP00000340931:R50H	ENSP00000300302:R50H	R	+	2	0	HERPUD1	55526649	0.001000	0.12720	0.990000	0.47175	0.784000	0.44337	-0.041000	0.12084	0.901000	0.36495	-0.254000	0.11334	CGT	G|0.870;A|0.130	0.130	strong		0.393	HERPUD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257056.5		Missense_Mutation
PIGG	54872	hgsc.bcm.edu	37	4	517622	517622	+	Silent	SNP	C	C	T	rs13150531	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:517622C>T	ENST00000453061.2	+	9	2095	c.1989C>T	c.(1987-1989)gcC>gcT	p.A663A	PIGG_ENST00000383028.4_Silent_p.A530A|PIGG_ENST00000296306.7_3'UTR|PIGG_ENST00000504346.1_Silent_p.A574A|PIGG_ENST00000310340.5_Silent_p.A655A	NM_001127178.1	NP_001120650.1	Q5H8A4	PIGG_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class G	663					C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|GPI anchor biosynthetic process (GO:0006506)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	CP2 mannose-ethanolamine phosphotransferase activity (GO:0051267)|phosphotransferase activity, for other substituted phosphate groups (GO:0016780)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(5)|lung(16)|ovary(3)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	39						TAATACTGGCCTGCTGCCGGC	0.652													C|||	1123	0.224241	0.3964	0.0994	5008	,	,		16572	0.2202		0.1302	False		,,,				2504	0.181				p.A663A		Atlas-SNP	.											.	PIGG	86	.	0			c.C1989T						PASS	.	C	,	1447,2925		254,939,993	18.0	17.0	17.0		1989,1965	2.8	0.7	4	dbSNP_121	17	1018,7520		65,888,3316	no	coding-synonymous,coding-synonymous	PIGG	NM_001127178.1,NM_017733.3	,	319,1827,4309	TT,TC,CC		11.9232,33.097,19.0937	,	663/984,655/976	517622	2465,10445	2186	4269	6455	SO:0001819	synonymous_variant	54872	exon9			ACTGGCCTGCTGC		CCDS3336.1, CCDS46992.1, CCDS75080.1, CCDS75081.1, CCDS75082.1, CCDS75083.1	4p16.3	2013-02-26	2006-06-28		ENSG00000174227	ENSG00000174227		"""Phosphatidylinositol glycan anchor biosynthesis"""	25985	protein-coding gene	gene with protein product			"""phosphatidylinositol glycan, class G"""			15632136	Standard	XM_005272287		Approved	FLJ20265, GPI7, LAS21	uc003gak.4	Q5H8A4	OTTHUMG00000112457	ENST00000453061.2:c.1989C>T	4.37:g.517622C>T		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	101	59	0.584158	NM_001127178	B4DKC7|Q2TAK5|Q6UX31|Q7L5Y4|Q8N866|Q8NCC9|Q96SY9|Q9BVT7|Q9NXG5	Silent	SNP	ENST00000453061.2	37	CCDS46992.1																																																																																			C|0.779;T|0.221	0.221	strong		0.652	PIGG-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000357494.1	NM_017733	
CADM2	253559	hgsc.bcm.edu	37	3	85935455	85935455	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:85935455C>A	ENST00000407528.2	+	4	542	c.480C>A	c.(478-480)ttC>ttA	p.F160L	CADM2_ENST00000405615.2_Missense_Mutation_p.F162L|CADM2_ENST00000383699.3_Missense_Mutation_p.F169L	NM_001167674.1	NP_001161146.1	Q8N3J6	CADM2_HUMAN	cell adhesion molecule 2	160	Ig-like C2-type 1.				adherens junction organization (GO:0034332)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)	axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|neuronal cell body membrane (GO:0032809)|plasma membrane (GO:0005886)|synapse (GO:0045202)				endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(9)|lung(15)|ovary(1)|prostate(1)|skin(4)	38		Lung NSC(201;0.0148)		LUSC - Lung squamous cell carcinoma(29;0.000815)|Lung(72;0.00304)|BRCA - Breast invasive adenocarcinoma(55;0.156)|Epithelial(33;0.157)		TAAGATGGTTCAAAAATGACA	0.343																																					p.F169L		Atlas-SNP	.											.	CADM2	195	.	0			c.C507A						PASS	.						56.0	54.0	55.0					3																	85935455		2203	4300	6503	SO:0001583	missense	253559	exon5			ATGGTTCAAAAAT	AF538973	CCDS33792.1, CCDS54613.1, CCDS54614.1	3p12.2	2013-01-11	2007-02-07	2007-02-07	ENSG00000175161	ENSG00000175161		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"""	29849	protein-coding gene	gene with protein product	"""nectin-like 3"""	609938	"""immunoglobulin superfamily, member 4D"""	IGSF4D			Standard	NM_153184		Approved	NECL3, Necl-3, SynCAM2	uc003dqj.3	Q8N3J6	OTTHUMG00000158990	ENST00000407528.2:c.480C>A	3.37:g.85935455C>A	ENSP00000384575:p.Phe160Leu	Somatic	188	0	0		WXS	Illumina HiSeq	Phase_I	124	31	0.25	NM_001167675	G3XHN7|G3XHN8|Q3KQY9|Q658Q7|Q8IZP8	Missense_Mutation	SNP	ENST00000407528.2	37	CCDS54614.1	.	.	.	.	.	.	.	.	.	.	C	13.91	2.378550	0.42207	.	.	ENSG00000175161	ENST00000383699;ENST00000407528;ENST00000405615	T;T;T	0.73575	-0.76;-0.76;-0.76	5.3	3.04	0.35103	CD80-like, immunoglobulin C2-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.60196	0.2250	L	0.36672	1.1	0.58432	D	0.99999	B;B;B	0.25272	0.009;0.122;0.031	B;B;B	0.24848	0.02;0.056;0.047	T	0.51371	-0.8714	10	0.16896	T	0.51	.	9.3638	0.38212	0.0:0.7276:0.0:0.2724	.	162;169;160	Q8N3J6-3;G3XHN4;Q8N3J6	.;.;CADM2_HUMAN	L	169;160;162	ENSP00000373200:F169L;ENSP00000384575:F160L;ENSP00000384193:F162L	ENSP00000373200:F169L	F	+	3	2	CADM2	86018145	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	1.963000	0.40452	1.137000	0.42214	0.557000	0.71058	TTC	.	.	none		0.343	CADM2-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352822.1	NM_153184	
UBXN6	80700	hgsc.bcm.edu	37	19	4454083	4454083	+	Missense_Mutation	SNP	C	C	T	rs1127888	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:4454083C>T	ENST00000301281.6	-	2	215	c.91G>A	c.(91-93)Gcc>Acc	p.A31T	CTB-50L17.9_ENST00000592034.1_RNA|UBXN6_ENST00000394765.3_5'UTR	NM_025241.2	NP_079517.1	Q9BZV1	UBXN6_HUMAN	UBX domain protein 6	31			A -> T (in dbSNP:rs1127888).			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						TCTTTGTGGGCCTTTTCCCTG	0.662													C|||	836	0.166933	0.09	0.3213	5008	,	,		14937	0.0645		0.2624	False		,,,				2504	0.1687				p.A31T		Atlas-SNP	.											.	UBXN6	27	.	0			c.G91A						PASS	.	C	,THR/ALA	527,3879	242.1+/-252.3	30,467,1706	103.0	117.0	112.0		,91	2.0	1.0	19	dbSNP_86	112	2330,6270	388.9+/-342.7	319,1692,2289	yes	utr-5,missense	UBXN6	NM_001171091.1,NM_025241.2	,58	349,2159,3995	TT,TC,CC		27.093,11.961,21.9668	,benign	,31/442	4454083	2857,10149	2203	4300	6503	SO:0001583	missense	80700	exon2			TGTGGGCCTTTTC	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.91G>A	19.37:g.4454083C>T	ENSP00000301281:p.Ala31Thr	Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	38	14	0.368421	NM_025241	D6W626|Q96AH1|Q96IK9|Q9BZV0	Missense_Mutation	SNP	ENST00000301281.6	37	CCDS12129.1	381	0.17445054945054944	48	0.0975609756097561	104	0.287292817679558	37	0.06468531468531469	192	0.2532981530343008	C	8.633	0.894076	0.17613	0.11961	0.27093	ENSG00000167671	ENST00000301281	T	0.43294	0.95	4.13	1.96	0.26148	.	1.015050	0.07885	N	0.970198	T	0.00012	0.0000	L	0.50333	1.59	0.09310	P	1.0	B	0.06786	0.001	B	0.08055	0.003	T	0.33929	-0.9849	9	0.10902	T	0.67	-9.49	6.9264	0.24418	0.0:0.7783:0.0:0.2217	rs1127888;rs11558243	31	Q9BZV1	UBXN6_HUMAN	T	31	ENSP00000301281:A31T	ENSP00000301281:A31T	A	-	1	0	UBXN6	4405083	0.996000	0.38824	0.990000	0.47175	0.138000	0.21146	0.552000	0.23376	0.211000	0.20683	0.484000	0.47621	GCC	T|0.211;G|0.000;C|0.788	0.211	strong		0.662	UBXN6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458447.3	NM_025241	
NLRP8	126205	hgsc.bcm.edu	37	19	56467375	56467375	+	Missense_Mutation	SNP	C	C	T	rs41481648	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:56467375C>T	ENST00000291971.3	+	3	2022	c.1951C>T	c.(1951-1953)Cgg>Tgg	p.R651W	NLRP8_ENST00000590542.1_Missense_Mutation_p.R651W	NM_176811.2	NP_789781.2	Q86W28	NALP8_HUMAN	NLR family, pyrin domain containing 8	651			R -> W (in dbSNP:rs41481648).		neuron death (GO:0070997)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)			breast(4)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(14)|ovary(5)|skin(2)|stomach(3)|upper_aerodigestive_tract(2)	35		Colorectal(82;0.000147)|Ovarian(87;0.17)		GBM - Glioblastoma multiforme(193;0.0695)		TTGCCTGAAGCGGTGTCAATA	0.463													C|||	480	0.0958466	0.1309	0.0605	5008	,	,		19353	0.0685		0.0825	False		,,,				2504	0.1155				p.R651W		Atlas-SNP	.											.	NLRP8	225	.	0			c.C1951T						PASS	.	C	TRP/ARG	512,3894	235.2+/-247.8	29,454,1720	143.0	133.0	136.0		1951	-3.0	0.0	19	dbSNP_127	136	695,7905	172.0+/-222.8	21,653,3626	yes	missense	NLRP8	NM_176811.2	101	50,1107,5346	TT,TC,CC		8.0814,11.6205,9.2803	probably-damaging	651/1049	56467375	1207,11799	2203	4300	6503	SO:0001583	missense	126205	exon3			CTGAAGCGGTGTC	AY154463	CCDS12937.1	19q13.43	2008-02-05	2006-12-08	2006-12-08		ENSG00000179709		"""Nucleotide-binding domain and leucine rich repeat containing"""	22940	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 8"""	609659	"""NACHT, leucine rich repeat and PYD containing 8"""	NALP8		12563287	Standard	NM_176811		Approved	NOD16, PAN4, CLR19.2	uc002qmh.3	Q86W28		ENST00000291971.3:c.1951C>T	19.37:g.56467375C>T	ENSP00000291971:p.Arg651Trp	Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	156	72	0.461538	NM_176811	Q7RTR4	Missense_Mutation	SNP	ENST00000291971.3	37	CCDS12937.1	183	0.08379120879120878	62	0.12601626016260162	27	0.07458563535911603	39	0.06818181818181818	55	0.07255936675461741	C	10.88	1.474675	0.26511	0.116205	0.080814	ENSG00000179709	ENST00000291971	D	0.88277	-2.36	2.03	-3.03	0.05429	.	.	.	.	.	T	0.06826	0.0174	L	0.40543	1.245	0.80722	P	0.0	D;D	0.76494	0.997;0.999	P;P	0.56700	0.804;0.786	T	0.63594	-0.6602	8	0.72032	D	0.01	.	6.6284	0.22843	0.0:0.3271:0.0:0.6729	rs41481648;rs61730439;rs41481648	651;651	Q86W28-2;Q86W28	.;NALP8_HUMAN	W	651	ENSP00000291971:R651W	ENSP00000291971:R651W	R	+	1	2	NLRP8	61159187	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-1.670000	0.01956	-0.773000	0.04596	-0.362000	0.07510	CGG	C|0.909;T|0.091	0.091	strong		0.463	NLRP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457462.1	NM_176811	
SRFBP1	153443	hgsc.bcm.edu	37	5	121356189	121356189	+	Missense_Mutation	SNP	T	T	A	rs61734326	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:121356189T>A	ENST00000339397.4	+	6	831	c.759T>A	c.(757-759)ttT>ttA	p.F253L		NM_152546.2	NP_689759.2			serum response factor binding protein 1											central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(6)|skin(1)	15		all_cancers(142;0.0124)|Prostate(80;0.0322)	KIRC - Kidney renal clear cell carcinoma(527;0.206)	OV - Ovarian serous cystadenocarcinoma(64;0.000227)|Epithelial(69;0.000365)|all cancers(49;0.00517)		GAGAAGAATTTTGTGAAGAGG	0.403													A|||	364	0.0726837	0.1672	0.0476	5008	,	,		19053	0.0437		0.0318	False		,,,				2504	0.0348				p.F253L		Atlas-SNP	.											.	SRFBP1	47	.	0			c.T759A						PASS	.	A	LEU/PHE	659,3055		57,545,1255	128.0	115.0	119.0		759	-2.5	0.0	5	dbSNP_129	119	345,7847		4,337,3755	yes	missense	SRFBP1	NM_152546.2	22	61,882,5010	AA,AT,TT		4.2114,17.7437,8.4327	benign	253/430	121356189	1004,10902	1857	4096	5953	SO:0001583	missense	153443	exon6			AGAATTTTGTGAA	AK058015	CCDS43354.1	5q23.1	2006-12-21				ENSG00000151304			26333	protein-coding gene	gene with protein product	"""BUD22 homolog (S. cerevisiae)"""	610479				15492011	Standard	NM_152546		Approved	FLJ25286, p49, STRAP, BUD22, Rlb1	uc003kst.1	Q8NEF9		ENST00000339397.4:c.759T>A	5.37:g.121356189T>A	ENSP00000341324:p.Phe253Leu	Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	124	71	0.572581	NM_152546		Missense_Mutation	SNP	ENST00000339397.4	37	CCDS43354.1	150	0.06868131868131869	72	0.14634146341463414	22	0.06077348066298342	30	0.05244755244755245	26	0.03430079155672823	A	6.689	0.495677	0.12762	0.177437	0.042114	ENSG00000151304	ENST00000339397	.	.	.	4.99	-2.51	0.06365	.	1.301590	0.04885	N	0.448402	T	0.00012	0.0000	N	0.00197	-1.87	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.21999	-1.0229	8	0.10636	T	0.68	7.536	5.9321	0.19144	0.2771:0.0956:0.5321:0.0951	rs61734326	253	Q8NEF9	SRFB1_HUMAN	L	253	.	ENSP00000341324:F253L	F	+	3	2	SRFBP1	121384088	0.000000	0.05858	0.000000	0.03702	0.034000	0.12701	-0.410000	0.07151	-0.771000	0.04608	-0.522000	0.04353	TTT	T|0.938;A|0.062	0.062	strong		0.403	SRFBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371200.1	NM_152546	
PBRM1	55193	hgsc.bcm.edu	37	3	52610651	52610651	+	Silent	SNP	T	T	A	rs17264436	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:52610651T>A	ENST00000296302.7	-	22	3598	c.3597A>T	c.(3595-3597)ccA>ccT	p.P1199P	PBRM1_ENST00000409114.3_Silent_p.P1214P|SMIM4_ENST00000476842.1_Intron|PBRM1_ENST00000409767.1_Silent_p.P1214P|PBRM1_ENST00000356770.4_Silent_p.P1167P|PBRM1_ENST00000409057.1_Silent_p.P1199P|PBRM1_ENST00000337303.4_Silent_p.P1199P|PBRM1_ENST00000410007.1_Silent_p.P1174P|PBRM1_ENST00000394830.3_Silent_p.P1174P			Q86U86	PB1_HUMAN	polybromo 1	1199	BAH 2. {ECO:0000255|PROSITE- ProRule:PRU00370}.				chromatin remodeling (GO:0006338)|heart development (GO:0007507)|mitotic nuclear division (GO:0007067)|negative regulation of cell proliferation (GO:0008285)|placenta development (GO:0001890)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	kinetochore (GO:0000776)|nuclear chromosome (GO:0000228)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			breast(5)|endometrium(5)|kidney(301)|liver(1)|lung(22)|pancreas(1)	335				BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)		CTGTTTCTTCTGGGTGAATGA	0.373			"""Mis, N, F, S, D, O"""		"""clear cell renal carcinoma, breast"""								T|||	1583	0.316094	0.1483	0.4582	5008	,	,		16156	0.4276		0.4165	False		,,,				2504	0.2239				p.P1174P		Atlas-SNP	.		Rec	yes		3	3p21	55193	polybromo 1		E	.	PBRM1	1252	.	0			c.A3522T						PASS	.	T	,,	766,3640	312.7+/-292.7	63,640,1500	118.0	115.0	116.0		3501,3522,3597	2.5	1.0	3	dbSNP_123	116	3462,5138	507.6+/-376.9	720,2022,1558	no	coding-synonymous,coding-synonymous,coding-synonymous	PBRM1	NM_018165.4,NM_018313.4,NM_181042.3	,,	783,2662,3058	AA,AT,TT		40.2558,17.3854,32.5081	,,	1167/1603,1174/1583,1199/1583	52610651	4228,8778	2203	4300	6503	SO:0001819	synonymous_variant	55193	exon23			TTCTTCTGGGTGA	BC015323	CCDS43099.1	3p21	2007-03-29			ENSG00000163939	ENSG00000163939			30064	protein-coding gene	gene with protein product		606083				11078522, 11483580	Standard	NM_018313		Approved	BAF180, PB1	uc003der.2	Q86U86	OTTHUMG00000152663	ENST00000296302.7:c.3597A>T	3.37:g.52610651T>A		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	72	72	1	NM_018313	A1L381|A1L382|A4FUJ7|Q1RMD1|Q1RMD2|Q96MS2|Q9H2T3|Q9H2T4|Q9H2T5|Q9H301|Q9H314	Silent	SNP	ENST00000296302.7	37																																																																																				T|0.652;A|0.348	0.348	strong		0.373	PBRM1-008	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000327232.1	NM_018165	
SREBF2	6721	hgsc.bcm.edu	37	22	42290890	42290890	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:42290890T>C	ENST00000361204.4	+	13	2610	c.2444T>C	c.(2443-2445)tTg>tCg	p.L815S	SREBF2_ENST00000491541.1_3'UTR	NM_004599.2	NP_004590.2	Q12772	SRBP2_HUMAN	sterol regulatory element binding transcription factor 2	815					cellular lipid metabolic process (GO:0044255)|cellular response to laminar fluid shear stress (GO:0071499)|cholesterol metabolic process (GO:0008203)|lipid metabolic process (GO:0006629)|negative regulation of cholesterol efflux (GO:0090370)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cholesterol homeostasis (GO:2000188)|regulation of lipid transport by negative regulation of transcription from RNA polymerase II promoter (GO:0072368)|response to low-density lipoprotein particle (GO:0055098)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi membrane (GO:0000139)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SREBP-SCAP-Insig complex (GO:0032937)	E-box binding (GO:0070888)|protein C-terminus binding (GO:0008022)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(2)|breast(6)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(9)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	38						ATAGAGTCCTTGGTGAAACCT	0.572																																					p.L815S		Atlas-SNP	.											.	SREBF2	99	.	0			c.T2444C						PASS	.						82.0	83.0	83.0					22																	42290890		2203	4300	6503	SO:0001583	missense	6721	exon13			AGTCCTTGGTGAA	U02031	CCDS14023.1	22q13.2	2013-05-21			ENSG00000198911	ENSG00000198911		"""Basic helix-loop-helix proteins"""	11290	protein-coding gene	gene with protein product		600481				7903453	Standard	NM_004599		Approved	SREBP2, bHLHd2	uc003bbi.3	Q12772	OTTHUMG00000151261	ENST00000361204.4:c.2444T>C	22.37:g.42290890T>C	ENSP00000354476:p.Leu815Ser	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	73	21	0.287671	NM_004599	Q05BD5|Q6GTH7|Q86V36|Q9UH04	Missense_Mutation	SNP	ENST00000361204.4	37	CCDS14023.1	.	.	.	.	.	.	.	.	.	.	T	29.4	4.999699	0.93227	.	.	ENSG00000198911	ENST00000361204;ENST00000457567	T	0.27104	1.69	5.96	5.96	0.96718	.	0.063149	0.64402	D	0.000005	T	0.47655	0.1457	M	0.69358	2.11	0.80722	D	1	D	0.71674	0.998	P	0.61070	0.883	T	0.47812	-0.9088	10	0.87932	D	0	-12.0099	16.4484	0.83959	0.0:0.0:0.0:1.0	.	815	Q12772	SRBP2_HUMAN	S	815	ENSP00000354476:L815S	ENSP00000354476:L815S	L	+	2	0	SREBF2	40620836	1.000000	0.71417	0.996000	0.52242	0.994000	0.84299	7.049000	0.76613	2.285000	0.76669	0.533000	0.62120	TTG	.	.	none		0.572	SREBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321956.1	NM_004599	
LAMB2	3913	hgsc.bcm.edu	37	3	49161660	49161660	+	Silent	SNP	T	T	C	rs34290943	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:49161660T>C	ENST00000418109.1	-	24	3551	c.3387A>G	c.(3385-3387)caA>caG	p.Q1129Q	LAMB2_ENST00000464891.1_5'Flank|LAMB2_ENST00000305544.4_Silent_p.Q1129Q	NM_002292.3	NP_002283.3	P55268	LAMB2_HUMAN	laminin, beta 2 (laminin S)	1129	Laminin EGF-like 12. {ECO:0000255|PROSITE-ProRule:PRU00460}.				astrocyte development (GO:0014002)|axon extension involved in regeneration (GO:0048677)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|metanephric glomerular basement membrane development (GO:0072274)|metanephric glomerular visceral epithelial cell development (GO:0072249)|neuromuscular junction development (GO:0007528)|retina development in camera-type eye (GO:0060041)|Schwann cell development (GO:0014044)|visual perception (GO:0007601)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-11 complex (GO:0043260)|laminin-3 complex (GO:0005608)|synapse (GO:0045202)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|endometrium(15)|kidney(3)|large_intestine(6)|lung(21)|ovary(4)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	61				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00219)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)		AGTGGAGCTCTTGGCACTCAG	0.622													T|||	291	0.058107	0.0053	0.0418	5008	,	,		19896	0.002		0.1123	False		,,,				2504	0.1431				p.Q1129Q		Atlas-SNP	.											.	LAMB2	156	.	0			c.A3387G						PASS	.	T		89,4317	75.2+/-113.4	0,89,2114	56.0	57.0	56.0		3387	-1.0	1.0	3	dbSNP_126	56	1136,7464	233.0+/-266.5	74,988,3238	no	coding-synonymous	LAMB2	NM_002292.3		74,1077,5352	CC,CT,TT		13.2093,2.02,9.4187		1129/1799	49161660	1225,11781	2203	4300	6503	SO:0001819	synonymous_variant	3913	exon23			GAGCTCTTGGCAC		CCDS2789.1	3p21.3-p21.2	2013-03-01			ENSG00000172037	ENSG00000172037		"""Laminins"""	6487	protein-coding gene	gene with protein product	"""laminin S"""	150325		LAMS		2922051, 10393422	Standard	NM_002292		Approved		uc003cwe.3	P55268	OTTHUMG00000156807	ENST00000418109.1:c.3387A>G	3.37:g.49161660T>C		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	142	60	0.422535	NM_002292	Q16321	Silent	SNP	ENST00000418109.1	37	CCDS2789.1																																																																																			T|0.914;C|0.086	0.086	strong		0.622	LAMB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345939.1	NM_002292	
IRF8	3394	hgsc.bcm.edu	37	16	85942659	85942659	+	Missense_Mutation	SNP	A	A	G	rs397514711		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:85942659A>G	ENST00000268638.5	+	3	660	c.238A>G	c.(238-240)Acg>Gcg	p.T80A	IRF8_ENST00000563180.1_Missense_Mutation_p.T80A	NM_002163.2	NP_002154.1	Q02556	IRF8_HUMAN	interferon regulatory factor 8	80			T -> A (in IMD32A; impairs transcriptional activity by disrupting the interaction between IRF8 and DNA). {ECO:0000269|PubMed:21524210}.		cellular response to lipopolysaccharide (GO:0071222)|cytokine-mediated signaling pathway (GO:0019221)|defense response to bacterium (GO:0042742)|defense response to protozoan (GO:0042832)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|myeloid cell differentiation (GO:0030099)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|phagocytosis (GO:0006909)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|transcription from RNA polymerase II promoter (GO:0006366)|type I interferon signaling pathway (GO:0060337)	cytosol (GO:0005829)|nucleus (GO:0005634)	regulatory region DNA binding (GO:0000975)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)			breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|large_intestine(2)|lung(8)|ovary(2)|prostate(1)|urinary_tract(1)	24		Prostate(104;0.0771)				CACTTGGAAGACGAGGTTACG	0.458																																					p.T80A		Atlas-SNP	.											IRF8,NS,neuroblastoma,-1,1	IRF8	65	1	0			c.A238G						PASS	.						74.0	76.0	75.0					16																	85942659		2198	4300	6498	SO:0001583	missense	3394	exon3			TGGAAGACGAGGT	M91196	CCDS10956.1	16q24.1	2014-09-17	2004-11-12	2004-11-12	ENSG00000140968	ENSG00000140968			5358	protein-coding gene	gene with protein product		601565	"""interferon consensus sequence binding protein 1"""	ICSBP1		1460054, 11997525	Standard	NM_002163		Approved	IRF-8, ICSBP	uc002fjh.3	Q02556	OTTHUMG00000137648	ENST00000268638.5:c.238A>G	16.37:g.85942659A>G	ENSP00000268638:p.Thr80Ala	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	107	24	0.224299	NM_002163	A0AV82	Missense_Mutation	SNP	ENST00000268638.5	37	CCDS10956.1	.	.	.	.	.	.	.	.	.	.	A	19.11	3.763543	0.69878	.	.	ENSG00000140968	ENST00000268638	D	0.97688	-4.49	4.88	4.88	0.63580	Winged helix-turn-helix transcription repressor DNA-binding (1);Interferon regulatory factor DNA-binding domain (4);	0.046894	0.85682	D	0.000000	D	0.97791	0.9275	L	0.45470	1.425	0.80722	D	1	D;D	0.69078	0.997;0.997	D;D	0.91635	0.999;0.996	D	0.97383	0.9984	10	0.30854	T	0.27	-15.9347	14.7789	0.69751	1.0:0.0:0.0:0.0	.	80;80	B2R8V7;Q02556	.;IRF8_HUMAN	A	80	ENSP00000268638:T80A	ENSP00000268638:T80A	T	+	1	0	IRF8	84500160	1.000000	0.71417	0.999000	0.59377	0.997000	0.91878	8.780000	0.91799	1.973000	0.57446	0.397000	0.26171	ACG	.	.	none		0.458	IRF8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269100.2	NM_002163	
KCNAB2	8514	hgsc.bcm.edu	37	1	6142308	6142308	+	Silent	SNP	T	T	C	rs2227911	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:6142308T>C	ENST00000164247.1	+	6	819	c.255T>C	c.(253-255)gaT>gaC	p.D85D	KCNAB2_ENST00000378092.1_Silent_p.D71D|KCNAB2_ENST00000378083.3_Silent_p.D118D|KCNAB2_ENST00000378111.1_Silent_p.D85D|KCNAB2_ENST00000458166.2_Silent_p.D18D|KCNAB2_ENST00000602612.1_Silent_p.D85D|KCNAB2_ENST00000378087.3_Silent_p.D85D|KCNAB2_ENST00000352527.1_Silent_p.D71D|KCNAB2_ENST00000341524.1_Silent_p.D85D|KCNAB2_ENST00000378097.1_Silent_p.D85D	NM_001199860.1	NP_001186789.1	Q13303	KCAB2_HUMAN	potassium voltage-gated channel, shaker-related subfamily, beta member 2	85					hematopoietic progenitor cell differentiation (GO:0002244)|protein heterooligomerization (GO:0051291)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|juxtaparanode region of axon (GO:0044224)|plasma membrane (GO:0005886)	potassium channel regulator activity (GO:0015459)|voltage-gated potassium channel activity (GO:0005249)			large_intestine(1)|lung(4)|skin(3)	8	Ovarian(185;0.0634)	all_cancers(23;5.85e-39)|all_epithelial(116;4.88e-22)|all_lung(118;4.21e-08)|Lung NSC(185;9.77e-07)|all_hematologic(16;2.78e-06)|all_neural(13;3.18e-06)|Acute lymphoblastic leukemia(12;0.000272)|Breast(487;0.000496)|Renal(390;0.0007)|Colorectal(325;0.00106)|Glioma(11;0.00203)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0393)|Medulloblastoma(700;0.211)		Epithelial(90;6.9e-37)|GBM - Glioblastoma multiforme(13;8.8e-31)|OV - Ovarian serous cystadenocarcinoma(86;1.45e-19)|Colorectal(212;2.46e-07)|COAD - Colon adenocarcinoma(227;2.07e-05)|Kidney(185;7.88e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.00131)|BRCA - Breast invasive adenocarcinoma(365;0.00133)|STAD - Stomach adenocarcinoma(132;0.00391)|READ - Rectum adenocarcinoma(331;0.0649)		ACCTCTTCGATACAGCAGAAG	0.562													T|||	484	0.0966454	0.2171	0.0519	5008	,	,		20149	0.002		0.0924	False		,,,				2504	0.0675				p.D118D		Atlas-SNP	.											KCNAB2,colon,carcinoma,+2,2	KCNAB2	23	2	0			c.T354C						PASS	.	T	,,,,,	856,3550	336.5+/-304.4	78,700,1425	129.0	115.0	120.0		255,255,354,54,255,213	-4.5	0.2	1	dbSNP_120	120	867,7733	196.2+/-241.2	45,777,3478	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	KCNAB2	NM_001199860.1,NM_001199861.1,NM_001199862.1,NM_001199863.1,NM_003636.3,NM_172130.2	,,,,,	123,1477,4903	CC,CT,TT		10.0814,19.4281,13.2477	,,,,,	85/368,85/368,118/416,18/301,85/368,71/354	6142308	1723,11283	2203	4300	6503	SO:0001819	synonymous_variant	8514	exon5			CTTCGATACAGCA	U33429	CCDS55.1, CCDS56.1, CCDS55570.1, CCDS55571.1	1p36.3	2008-02-05			ENSG00000069424	ENSG00000069424		"""Potassium channels"", ""Aldo-keto reductases"""	6229	protein-coding gene	gene with protein product		601142				8838324	Standard	NM_003636		Approved	AKR6A5, KCNA2B, HKvbeta2.1, HKvbeta2.2	uc001aly.2	Q13303	OTTHUMG00000000795	ENST00000164247.1:c.255T>C	1.37:g.6142308T>C		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	69	24	0.347826	NM_001199862	A0AVM9|A8K1A4|B0AZR7|O43659|Q5TG82|Q5TG83|Q6ZNE4|Q99411	Silent	SNP	ENST00000164247.1	37	CCDS55.1																																																																																			T|0.887;C|0.113	0.113	strong		0.562	KCNAB2-006	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000002114.3	NM_172130	
SLC35F1	222553	hgsc.bcm.edu	37	6	118556737	118556737	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:118556737G>A	ENST00000360388.4	+	3	616	c.415G>A	c.(415-417)Gac>Aac	p.D139N		NM_001029858.3	NP_001025029.2	Q5T1Q4	S35F1_HUMAN	solute carrier family 35, member F1	139					transport (GO:0006810)	integral component of membrane (GO:0016021)		p.D139N(1)		breast(3)|kidney(1)|large_intestine(7)|lung(21)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	36				GBM - Glioblastoma multiforme(226;0.217)		GGGACTCATAGACCTGGAAGC	0.423																																					p.D139N		Atlas-SNP	.											SLC35F1,NS,carcinoma,0,1	SLC35F1	65	1	1	Substitution - Missense(1)	lung(1)	c.G415A						scavenged	.						160.0	144.0	149.0					6																	118556737		2203	4300	6503	SO:0001583	missense	222553	exon3			CTCATAGACCTGG	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.415G>A	6.37:g.118556737G>A	ENSP00000353557:p.Asp139Asn	Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	177	3	0.0169492	NM_001029858	E1P564|Q1RMG1|Q4G0U9|Q4G167|Q6N007	Missense_Mutation	SNP	ENST00000360388.4	37	CCDS34524.1	.	.	.	.	.	.	.	.	.	.	G	22.7	4.328185	0.81690	.	.	ENSG00000196376	ENST00000360388	T	0.68624	-0.34	5.76	5.76	0.90799	.	0.228598	0.42682	D	0.000678	D	0.83562	0.5281	M	0.88842	2.985	0.80722	D	1	D	0.60160	0.987	D	0.70487	0.969	D	0.84811	0.0790	10	0.66056	D	0.02	.	20.326	0.98701	0.0:0.0:1.0:0.0	.	139	Q5T1Q4	S35F1_HUMAN	N	139	ENSP00000353557:D139N	ENSP00000353557:D139N	D	+	1	0	SLC35F1	118663430	1.000000	0.71417	1.000000	0.80357	0.042000	0.13812	9.283000	0.95860	2.885000	0.99019	0.643000	0.83706	GAC	.	.	none		0.423	SLC35F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041991.2	XM_167044	
LRRC15	131578	hgsc.bcm.edu	37	3	194080174	194080174	+	Silent	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:194080174G>A	ENST00000347624.3	-	2	1684	c.1599C>T	c.(1597-1599)acC>acT	p.T533T	LRRC15_ENST00000439944.2_Silent_p.T539T|LRRC15_ENST00000428839.1_Silent_p.T539T	NM_130830.4	NP_570843.2	Q8TF66	LRC15_HUMAN	leucine rich repeat containing 15	533					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)		TCTGGGCCTGGGTCATGCCCC	0.587																																					p.T539T		Atlas-SNP	.											.	LRRC15	137	.	0			c.C1617T						PASS	.						89.0	88.0	88.0					3																	194080174		2203	4300	6503	SO:0001819	synonymous_variant	131578	exon3			GGCCTGGGTCATG	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.1599C>T	3.37:g.194080174G>A		Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	142	45	0.316901	NM_001135057	Q495Q6|Q7RTN7	Silent	SNP	ENST00000347624.3	37	CCDS3306.1																																																																																			.	.	none		0.587	LRRC15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342858.2		
OR10H2	26538	hgsc.bcm.edu	37	19	15839168	15839168	+	Silent	SNP	C	C	T	rs2003905	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:15839168C>T	ENST00000305899.3	+	1	335	c.315C>T	c.(313-315)ttC>ttT	p.F105F		NM_013939.2	NP_039227.1	O60403	O10H2_HUMAN	olfactory receptor, family 10, subfamily H, member 2	105						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(2)|skin(3)|stomach(1)	27	all_hematologic(1;0.0517)|Acute lymphoblastic leukemia(2;0.074)					TCTTCTCCTTCAGCTTCGGCT	0.627																																					p.F105F		Atlas-SNP	.											.	OR10H2	59	.	0			c.C315T						PASS	.						62.0	58.0	59.0					19																	15839168		2202	4277	6479	SO:0001819	synonymous_variant	26538	exon1			CTCCTTCAGCTTC	AC004597	CCDS12333.1	19p13.1	2012-08-09				ENSG00000171942		"""GPCR / Class A : Olfactory receptors"""	8173	protein-coding gene	gene with protein product							Standard	NM_013939		Approved		uc002nbm.2	O60403		ENST00000305899.3:c.315C>T	19.37:g.15839168C>T		Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	193	67	0.34715	NM_013939	Q6IFQ1|Q96R58	Silent	SNP	ENST00000305899.3	37	CCDS12333.1																																																																																			T|1.000;|0.000	1.000	weak		0.627	OR10H2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460917.1		
BPIFB1	92747	hgsc.bcm.edu	37	20	31876681	31876681	+	Missense_Mutation	SNP	A	A	G	rs1078761	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:31876681A>G	ENST00000253354.1	+	3	411	c.250A>G	c.(250-252)Atc>Gtc	p.I84V		NM_033197.2	NP_149974.2	Q8TDL5	BPIB1_HUMAN	BPI fold containing family B, member 1	84			I -> V (in dbSNP:rs1078761). {ECO:0000269|PubMed:15489334}.		innate immune response in mucosa (GO:0002227)|negative regulation of toll-like receptor 4 signaling pathway (GO:0034144)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	lipid binding (GO:0008289)										CCTGAAGCACATCATCTGGTG	0.617													A|||	1653	0.330072	0.4939	0.3934	5008	,	,		19393	0.245		0.3052	False		,,,				2504	0.1769				p.I84V		Atlas-SNP	.											C20orf114,NS,carcinoma,0,1	.	.	1	0			c.A250G						PASS	.	A	VAL/ILE	1964,2442	549.9+/-377.9	423,1118,662	65.0	48.0	54.0		250	1.8	0.0	20	dbSNP_86	54	2478,6122	403.5+/-347.8	359,1760,2181	yes	missense	BPIFB1	NM_033197.2	29	782,2878,2843	GG,GA,AA		28.814,44.5756,34.1535	benign	84/485	31876681	4442,8564	2203	4300	6503	SO:0001583	missense	92747	exon3			AAGCACATCATCT	BC008429	CCDS13218.1	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000125999	ENSG00000125999		"""BPI fold containing"""	16108	protein-coding gene	gene with protein product	"""von Ebner minor salivary gland protein"""		"""chromosome 20 open reading frame 114"""	C20orf114		11971875, 21787333	Standard	NM_033197		Approved	dJ1187J4.1, MGC14597, bA49G10.6, LPLUNC1, VEMSGP	uc002wyw.1	Q8TDL5	OTTHUMG00000032252	ENST00000253354.1:c.250A>G	20.37:g.31876681A>G	ENSP00000253354:p.Ile84Val	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	53	29	0.54717	NM_033197	A8K2H8|Q5QP43|Q6UWY1|Q6ZRU7|Q96HK6|Q9BQP8|Q9BWZ6|Q9H4V6	Missense_Mutation	SNP	ENST00000253354.1	37	CCDS13218.1	742	0.33974358974358976	230	0.46747967479674796	142	0.39226519337016574	148	0.25874125874125875	222	0.2928759894459103	A	9.223	1.033826	0.19590	0.445756	0.28814	ENSG00000125999	ENST00000423645;ENST00000253354	T;T	0.08008	3.14;3.47	5.34	1.84	0.25277	.	0.172979	0.40908	N	0.000997	T	0.00012	0.0000	L	0.55481	1.735	0.80722	P	0.0	B;B	0.16166	0.016;0.016	B;B	0.25506	0.061;0.061	T	0.44097	-0.9350	9	0.41790	T	0.15	-29.934	9.3438	0.38096	0.7648:0.0:0.2352:0.0	rs1078761;rs4637206;rs13036295;rs17124545;rs17845167;rs17857974;rs58754670;rs1078761	84;84	B2R7Z6;Q8TDL5	.;BPIB1_HUMAN	V	84	ENSP00000390471:I84V;ENSP00000253354:I84V	ENSP00000253354:I84V	I	+	1	0	BPIFB1	31340342	0.035000	0.19736	0.001000	0.08648	0.000000	0.00434	0.794000	0.26958	-0.045000	0.13468	-1.139000	0.01908	ATC	A|0.657;G|0.343	0.343	strong		0.617	BPIFB1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106499.2	NM_033197	
NPHP4	261734	hgsc.bcm.edu	37	1	5926507	5926507	+	Silent	SNP	T	T	C	rs555164	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:5926507T>C	ENST00000378156.4	-	26	3835	c.3570A>G	c.(3568-3570)gaA>gaG	p.E1190E	NPHP4_ENST00000478423.2_5'UTR	NM_015102.3	NP_055917.1	O75161	NPHP4_HUMAN	nephronophthisis 4	1190					actin cytoskeleton organization (GO:0030036)|hippo signaling (GO:0035329)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|retina development in camera-type eye (GO:0060041)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|visual behavior (GO:0007632)	cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytosol (GO:0005829)|membrane (GO:0016020)|nonmotile primary cilium (GO:0031513)|tight junction (GO:0005923)	structural molecule activity (GO:0005198)	p.E1190E(2)		NS(1)|breast(2)|cervix(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(15)|ovary(2)|pancreas(1)|prostate(4)	47	Ovarian(185;0.0634)	all_cancers(23;7.53e-41)|all_epithelial(116;3.96e-23)|all_lung(118;5.12e-09)|all_hematologic(16;5.45e-07)|Lung NSC(185;5.49e-07)|all_neural(13;3.21e-06)|Acute lymphoblastic leukemia(12;3.44e-05)|Breast(487;0.000601)|Renal(390;0.0007)|Colorectal(325;0.00113)|Hepatocellular(190;0.00213)|Glioma(11;0.00223)|Myeloproliferative disorder(586;0.0256)|Ovarian(437;0.04)|Lung SC(97;0.128)|Medulloblastoma(700;0.213)		Epithelial(90;1.69e-36)|GBM - Glioblastoma multiforme(13;5.07e-29)|OV - Ovarian serous cystadenocarcinoma(86;1.05e-19)|Colorectal(212;4.54e-07)|COAD - Colon adenocarcinoma(227;3.14e-05)|Kidney(185;0.00012)|BRCA - Breast invasive adenocarcinoma(365;0.00102)|KIRC - Kidney renal clear cell carcinoma(229;0.00179)|STAD - Stomach adenocarcinoma(132;0.00472)|READ - Rectum adenocarcinoma(331;0.0649)		TGTCCCGTGGTTCCCCGGGGC	0.562													C|||	1601	0.319688	0.1619	0.379	5008	,	,		17616	0.2837		0.4135	False		,,,				2504	0.4315				p.E1190E		Atlas-SNP	.											NPHP4,NS,carcinoma,0,1	NPHP4	119	1	2	Substitution - coding silent(2)	prostate(2)	c.A3570G						PASS	.	C		768,3102		79,610,1246	32.0	34.0	33.0		3570	3.2	1.0	1	dbSNP_83	33	3460,4784		760,1940,1422	no	coding-synonymous	NPHP4	NM_015102.3		839,2550,2668	CC,CT,TT		41.9699,19.845,34.9018		1190/1427	5926507	4228,7886	1935	4122	6057	SO:0001819	synonymous_variant	261734	exon26			CCGTGGTTCCCCG	AB014573	CCDS44052.1	1p36	2010-03-26			ENSG00000131697	ENSG00000131697			19104	protein-coding gene	gene with protein product	"""nephroretinin"", ""nephrocystin-4"", ""POC10 centriolar protein homolog (Chlamydomonas)"""	607215				11920287, 12205563	Standard	XR_244787		Approved	SLSN4, KIAA0673, POC10	uc001alq.2	O75161	OTTHUMG00000000701	ENST00000378156.4:c.3570A>G	1.37:g.5926507T>C		Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	107	21	0.196262	NM_015102	Q8IWC0	Silent	SNP	ENST00000378156.4	37	CCDS44052.1																																																																																			T|0.698;C|0.302	0.302	strong		0.562	NPHP4-001	KNOWN	non_canonical_polymorphism|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001715.2		
GJB7	375519	hgsc.bcm.edu	37	6	87994504	87994504	+	Missense_Mutation	SNP	C	C	T	rs35259282	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:87994504C>T	ENST00000525899.1	-	3	472	c.127G>A	c.(127-129)Gtg>Atg	p.V43M	GJB7_ENST00000296882.3_Missense_Mutation_p.V43M	NM_198568.2	NP_940970.1	Q6PEY0	CXB7_HUMAN	gap junction protein, beta 7, 25kDa	43				V -> M (in Ref. 1; CAC93845). {ECO:0000305}.	cell communication (GO:0007154)	connexon complex (GO:0005922)|integral component of membrane (GO:0016021)				endometrium(2)|large_intestine(3)	5		all_cancers(76;1.93e-06)|Acute lymphoblastic leukemia(125;3.55e-10)|Prostate(29;7.38e-10)|all_hematologic(105;3.29e-06)|all_epithelial(107;0.00323)		BRCA - Breast invasive adenocarcinoma(108;0.0167)		TCTTTCCACACGTGCTCTGCT	0.478													C|||	177	0.0353435	0.0061	0.0591	5008	,	,		19784	0.0188		0.0895	False		,,,				2504	0.0194				p.V43M		Atlas-SNP	.											.	GJB7	28	.	0			c.G127A						PASS	.	C	MET/VAL	80,4326	68.1+/-105.8	0,80,2123	117.0	105.0	109.0		127	4.1	0.3	6	dbSNP_126	109	779,7821	183.6+/-231.8	35,709,3556	yes	missense	GJB7	NM_198568.2	21	35,789,5679	TT,TC,CC		9.0581,1.8157,6.6046	probably-damaging	43/224	87994504	859,12147	2203	4300	6503	SO:0001583	missense	375519	exon3			TCCACACGTGCTC	AJ414563	CCDS5008.1	6q15	2008-02-05	2007-11-06			ENSG00000164411		"""Ion channels / Gap junction proteins (connexins)"""	16690	protein-coding gene	gene with protein product	"""connexin 25"""	611921	"""gap junction protein, beta 7"""				Standard	NM_198568		Approved	CX25, bA136M9.1	uc003plo.2	Q6PEY0		ENST00000525899.1:c.127G>A	6.37:g.87994504C>T	ENSP00000435355:p.Val43Met	Somatic	216	0	0		WXS	Illumina HiSeq	Phase_I	160	79	0.49375	NM_198568	B3KXL0|Q96KP0	Missense_Mutation	SNP	ENST00000525899.1	37	CCDS5008.1	110	0.05036630036630037	6	0.012195121951219513	23	0.06353591160220995	12	0.02097902097902098	69	0.09102902374670185	C	13.99	2.401570	0.42613	0.018157	0.090581	ENSG00000164411	ENST00000525899;ENST00000296882;ENST00000369576	D;D;D	0.99399	-5.83;-5.83;-5.83	4.99	4.13	0.48395	Connexin, N-terminal (2);	0.000000	0.64402	U	0.000006	D	0.99302	0.9756	M	0.83774	2.66	0.35760	D	0.820096	D	0.89917	1.0	D	0.80764	0.994	D	0.99901	1.1163	10	0.72032	D	0.01	.	9.7652	0.40557	0.0:0.8299:0.0:0.1701	rs35259282;rs62441378	43	Q6PEY0	CXB7_HUMAN	M	43	ENSP00000435355:V43M;ENSP00000296882:V43M;ENSP00000358589:V43M	ENSP00000296882:V43M	V	-	1	0	GJB7	88051223	0.998000	0.40836	0.343000	0.25615	0.250000	0.25880	3.751000	0.55165	1.105000	0.41606	-0.224000	0.12420	GTG	C|0.939;T|0.061	0.061	strong		0.478	GJB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394780.1		
PPM1A	5494	hgsc.bcm.edu	37	14	60749878	60749878	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:60749878A>G	ENST00000395076.4	+	2	887	c.457A>G	c.(457-459)Agg>Ggg	p.R153G	PPM1A_ENST00000529574.1_Missense_Mutation_p.R153G|PPM1A_ENST00000325642.3_Missense_Mutation_p.R226G|PPM1A_ENST00000325658.3_Missense_Mutation_p.R153G	NM_021003.4	NP_066283.1	P35813	PPM1A_HUMAN	protein phosphatase, Mg2+/Mn2+ dependent, 1A	153					cell cycle arrest (GO:0007050)|dephosphorylation (GO:0016311)|gene expression (GO:0010467)|insulin receptor signaling pathway (GO:0008286)|N-terminal protein myristoylation (GO:0006499)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|negative regulation of SMAD protein complex assembly (GO:0010991)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|peptidyl-threonine dephosphorylation (GO:0035970)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of Wnt signaling pathway (GO:0030177)|protein dephosphorylation (GO:0006470)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|membrane (GO:0016020)|neuron projection (GO:0043005)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|voltage-gated calcium channel complex (GO:0005891)	calmodulin-dependent protein phosphatase activity (GO:0033192)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|protein serine/threonine phosphatase activity (GO:0004722)|R-SMAD binding (GO:0070412)|signal transducer activity (GO:0004871)			cervix(1)|endometrium(1)|large_intestine(8)|lung(2)|skin(1)|upper_aerodigestive_tract(1)	14				OV - Ovarian serous cystadenocarcinoma(108;0.046)		TTTACTTTGTAGGAACAGGAA	0.413																																					p.R226G		Atlas-SNP	.											PPM1A_ENST00000325642,NS,carcinoma,0,2	PPM1A	72	2	0			c.A676G						scavenged	.						94.0	91.0	92.0					14																	60749878		2203	4300	6503	SO:0001583	missense	5494	exon2			CTTTGTAGGAACA	S87759	CCDS9744.1, CCDS9745.1, CCDS45120.1	14q23.1	2013-01-24	2010-03-05		ENSG00000100614	ENSG00000100614	3.1.3.16	"""Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent"""	9275	protein-coding gene	gene with protein product	"""phosphatase 2C alpha"", ""protein phosphatase 2C, alpha isoform"""	606108	"""protein phosphatase 1A (formerly 2C), magnesium-dependent, alpha isoform"""			1311954	Standard	NM_177952		Approved	MGC9201, PP2Calpha, PP2CA	uc001xew.4	P35813	OTTHUMG00000140333	ENST00000395076.4:c.457A>G	14.37:g.60749878A>G	ENSP00000378514:p.Arg153Gly	Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	199	2	0.0100503	NM_177952	B5BU11|J3KNM0|O75551	Missense_Mutation	SNP	ENST00000395076.4	37	CCDS9744.1	.	.	.	.	.	.	.	.	.	.	A	17.88	3.496633	0.64186	.	.	ENSG00000100614	ENST00000325642;ENST00000529574;ENST00000395076;ENST00000325658;ENST00000525399	T;T;T;T;T	0.13420	2.59;2.59;2.59;2.59;2.59	5.7	5.7	0.88788	Protein phosphatase 2C-like (5);	0.000000	0.64402	D	0.000017	T	0.37073	0.0990	M	0.85373	2.75	0.80722	D	1	D;P;D	0.57571	0.98;0.902;0.98	P;P;P	0.59825	0.864;0.563;0.864	T	0.26677	-1.0096	9	.	.	.	-5.4809	13.0143	0.58749	0.8659:0.1341:0.0:0.0	.	153;153;153	P35813;P35813-2;B2R8E4	PPM1A_HUMAN;.;.	G	226;153;153;153;153	ENSP00000327255:R226G;ENSP00000432966:R153G;ENSP00000378514:R153G;ENSP00000314850:R153G;ENSP00000435398:R153G	.	R	+	1	2	PPM1A	59819631	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.715000	0.54897	2.171000	0.68590	0.482000	0.46254	AGG	.	.	none		0.413	PPM1A-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000276949.2	NM_021003	
TLN2	83660	hgsc.bcm.edu	37	15	63047793	63047793	+	Silent	SNP	C	C	T	rs4775538	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:63047793C>T	ENST00000561311.1	+	36	4769	c.4539C>T	c.(4537-4539)atC>atT	p.I1513I	TLN2_ENST00000472902.1_5'Flank|TLN2_ENST00000306829.6_Silent_p.I1513I			Q9Y4G6	TLN2_HUMAN	talin 2	1513					cell adhesion (GO:0007155)|cell-cell junction assembly (GO:0007043)|cytoskeletal anchoring at plasma membrane (GO:0007016)	actin cytoskeleton (GO:0015629)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|synapse (GO:0045202)	actin binding (GO:0003779)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			NS(3)|breast(6)|central_nervous_system(3)|endometrium(8)|kidney(8)|large_intestine(20)|lung(34)|ovary(6)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)	99						CCTGCCGCATCGCCTCATCCA	0.577													C|||	1160	0.231629	0.2466	0.1297	5008	,	,		19253	0.3442		0.1988	False		,,,				2504	0.2014				p.I1513I		Atlas-SNP	.											.	TLN2	253	.	0			c.C4539T						PASS	.	C		889,3517	343.1+/-307.5	83,723,1397	97.0	73.0	81.0		4539	-6.1	0.7	15	dbSNP_111	81	1897,6703	337.4+/-322.3	211,1475,2614	no	coding-synonymous	TLN2	NM_015059.2		294,2198,4011	TT,TC,CC		22.0581,20.177,21.4209		1513/2543	63047793	2786,10220	2203	4300	6503	SO:0001819	synonymous_variant	83660	exon34			CCGCATCGCCTCA	AB002318	CCDS32261.1	15q15-q21	2008-07-03			ENSG00000171914	ENSG00000171914			15447	protein-coding gene	gene with protein product		607349				9205841, 11527381	Standard	NM_015059		Approved	KIAA0320, ILWEQ	uc002alb.4	Q9Y4G6	OTTHUMG00000133679	ENST00000561311.1:c.4539C>T	15.37:g.63047793C>T		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	101	65	0.643564	NM_015059	A6NLB8	Silent	SNP	ENST00000561311.1	37	CCDS32261.1																																																																																			C|0.774;T|0.226	0.226	strong		0.577	TLN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257878.2		
SLC25A39	51629	hgsc.bcm.edu	37	17	42398802	42398802	+	Splice_Site	SNP	G	G	A	rs34365655|rs11545313	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:42398802G>A	ENST00000377095.5	-	7	636	c.517C>T	c.(517-519)Ctg>Ttg	p.L173L	SLC25A39_ENST00000225308.8_Splice_Site_p.L165L|SLC25A39_ENST00000586016.1_Splice_Site_p.L41L|SLC25A39_ENST00000537904.2_Splice_Site_p.L150L|SLC25A39_ENST00000590194.1_Splice_Site_p.L165L	NM_001143780.1	NP_001137252.1	Q9BZJ4	S2539_HUMAN	solute carrier family 25, member 39	173					heme biosynthetic process (GO:0006783)|transport (GO:0006810)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)				endometrium(2)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	7		Prostate(33;0.0233)		BRCA - Breast invasive adenocarcinoma(366;0.189)		CTATGCTCACGGCGGGCCAGC	0.622													G|||	132	0.0263578	0.0091	0.0231	5008	,	,		17961	0.0		0.0855	False		,,,				2504	0.0184				p.L173L		Atlas-SNP	.											.	SLC25A39	24	.	0			c.C517T						PASS	.	G	,	80,4326	68.1+/-105.8	1,78,2124	44.0	54.0	51.0		517,493	-8.7	0.8	17	dbSNP_126	51	705,7895	172.2+/-222.9	34,637,3629	yes	coding-synonymous-near-splice,coding-synonymous-near-splice	SLC25A39	NM_001143780.1,NM_016016.2	,	35,715,5753	AA,AG,GG		8.1977,1.8157,6.0357	,	173/360,165/352	42398802	785,12221	2203	4300	6503	SO:0001630	splice_region_variant	51629	exon7			GCTCACGGCGGGC	BC096819	CCDS11482.1, CCDS45700.1	17q12	2013-05-22			ENSG00000013306	ENSG00000013306		"""Solute carriers"""	24279	protein-coding gene	gene with protein product		610820				16949250	Standard	NM_001143780		Approved	FLJ22407, CGI-69	uc002ign.2	Q9BZJ4	OTTHUMG00000132628	ENST00000377095.5:c.517+1C>T	17.37:g.42398802G>A		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	58	27	0.465517	NM_001143780	A8JZZ2|D3DX51|D3DX54|Q4V9M1|Q9P182|Q9UF66|Q9Y379	Silent	SNP	ENST00000377095.5	37	CCDS45700.1																																																																																			G|0.948;A|0.052	0.052	strong		0.622	SLC25A39-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457745.1	NM_016016	Silent
KRTAP12-2	353323	hgsc.bcm.edu	37	21	46086718	46086718	+	Missense_Mutation	SNP	G	G	C	rs7275281|rs368303093	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:46086718G>C	ENST00000360770.3	-	1	126	c.86C>G	c.(85-87)tCc>tGc	p.S29C	TSPEAR_ENST00000323084.4_Intron	NM_181684.2	NP_859012.1	P59991	KR122_HUMAN	keratin associated protein 12-2	29	23 X 5 AA approximate repeats.		S -> C (in dbSNP:rs7275281).|S -> P (in dbSNP:rs7276859).			keratin filament (GO:0045095)				central_nervous_system(1)|endometrium(1)|lung(3)	5						TGCCTGGCAGGAGCTGGGCAC	0.677													G|||	3070	0.613019	0.7262	0.5807	5008	,	,		16465	0.5675		0.5547	False		,,,				2504	0.59				p.S29C		Atlas-SNP	.											.	KRTAP12-2	10	.	0			c.C86G						PASS	.	G	CYS/SER,	1259,3073		510,239,1417	35.0	42.0	39.0		86,	-2.7	0.0	21	dbSNP_116	39	1526,6972		615,296,3338	no	missense,intron	TSPEAR,KRTAP12-2	NM_181684.2,NM_144991.2	112,	1125,535,4755	CC,CG,GG		17.9572,29.0628,21.7069	probably-damaging,	29/147,	46086718	2785,10045	2166	4249	6415	SO:0001583	missense	353323	exon1			TGGCAGGAGCTGG	AJ566389	CCDS42965.1	21q22.3	2006-03-13			ENSG00000221864	ENSG00000221864		"""Keratin associated proteins"""	20530	protein-coding gene	gene with protein product							Standard	NM_181684		Approved	KRTAP12.2, KAP12.2	uc002zfu.3	P59991	OTTHUMG00000057636	ENST00000360770.3:c.86C>G	21.37:g.46086718G>C	ENSP00000354001:p.Ser29Cys	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	106	60	0.566038	NM_181684	A6NIS1|A6NMS9|Q0VAS4	Missense_Mutation	SNP	ENST00000360770.3	37	CCDS42965.1	1165	0.5334249084249084	318	0.6463414634146342	199	0.5497237569060773	279	0.48776223776223776	369	0.4868073878627968	g	6.477	0.456248	0.12283	0.290628	0.179572	ENSG00000221864	ENST00000360770	T	0.03035	4.07	3.4	-2.73	0.05950	.	.	.	.	.	T	0.00012	0.0000	N	0.01761	-0.735	0.80722	P	0.0	D	0.58620	0.983	P	0.51297	0.665	T	0.36237	-0.9756	8	0.19147	T	0.46	.	3.0179	0.06066	0.0978:0.415:0.2069:0.2803	rs7275281	29	P59991	KR122_HUMAN	C	29	ENSP00000354001:S29C	ENSP00000354001:S29C	S	-	2	0	KRTAP12-2	44911146	0.004000	0.15560	0.000000	0.03702	0.019000	0.09904	-0.386000	0.07370	-1.078000	0.03117	0.462000	0.41574	TCC	.	.	alt		0.677	KRTAP12-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128039.1	NM_181684	
MAST4	375449	hgsc.bcm.edu	37	5	66462325	66462325	+	Missense_Mutation	SNP	T	T	A	rs3188121	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:66462325T>A	ENST00000403625.2	+	29	7613	c.7318T>A	c.(7318-7320)Tcc>Acc	p.S2440T	MAST4_ENST00000404260.3_Missense_Mutation_p.S2443T|MAST4_ENST00000403666.1_Missense_Mutation_p.S2251T|MAST4_ENST00000405643.1_Missense_Mutation_p.S2261T|MAST4_ENST00000261569.7_Missense_Mutation_p.S2246T	NM_001164664.1	NP_001158136.1	O15021	MAST4_HUMAN	microtubule associated serine/threonine kinase family member 4	2443						cytoplasm (GO:0005737)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(1)|kidney(2)|lung(6)|ovary(2)	13		Lung NSC(167;8.56e-06)|Prostate(74;0.00637)|Ovarian(174;0.0563)|Breast(144;0.0586)|Colorectal(97;0.245)		Lung(70;0.011)		CATGAAACGGTCCCCCTCAGC	0.647											OREG0016638	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	T|||	53	0.0105831	0.003	0.0202	5008	,	,		14681	0.0		0.0278	False		,,,				2504	0.0072				p.S2440T		Atlas-SNP	.											.	MAST4	218	.	0			c.T7318A						PASS	.	T	THR/SER,THR/SER	24,3922		0,24,1949	16.0	21.0	19.0		7318,6751	4.9	0.3	5	dbSNP_105	19	244,8072		3,238,3917	yes	missense,missense	MAST4	NM_001164664.1,NM_015183.2	58,58	3,262,5866	AA,AT,TT		2.9341,0.6082,2.1856	possibly-damaging,possibly-damaging	2440/2624,2251/2435	66462325	268,11994	1973	4158	6131	SO:0001583	missense	375449	exon29			AAACGGTCCCCCT	AY830839	CCDS47224.1, CCDS47225.1, CCDS54861.1, CCDS75254.1	5q12.3	2007-06-20			ENSG00000069020	ENSG00000069020			19037	protein-coding gene	gene with protein product						9205841	Standard	NM_198828		Approved	KIAA0303	uc021xzk.1	O15021	OTTHUMG00000152471	ENST00000403625.2:c.7318T>A	5.37:g.66462325T>A	ENSP00000385727:p.Ser2440Thr	Somatic	140	0	0	1092	WXS	Illumina HiSeq	Phase_I	196	55	0.280612	NM_001164664	A6NL49|B5ME48|Q05EE6|Q6ZN07|Q8N4X4|Q96LY3	Missense_Mutation	SNP	ENST00000403625.2	37	CCDS54861.1	35|35	0.016025641025641024|0.016025641025641024	1|1	0.0020325203252032522|0.0020325203252032522	6|6	0.016574585635359115|0.016574585635359115	0|0	0.0|0.0	28|28	0.036939313984168866|0.036939313984168866	T|T	8.148|8.148	0.786685|0.786685	0.16189|0.16189	0.006082|0.006082	0.029341|0.029341	ENSG00000069020|ENSG00000069020	ENST00000404260;ENST00000403625;ENST00000403666;ENST00000405643;ENST00000380908;ENST00000261569|ENST00000443808	T;T;T;T;T|.	0.72835|.	-0.68;-0.68;-0.69;-0.69;-0.66|.	4.94|4.94	4.94|4.94	0.65067|0.65067	.|.	0.000000|.	0.42420|.	D|.	0.000715|.	T|T	0.07638|0.07638	0.0192|0.0192	L|L	0.34521|0.34521	1.04|1.04	0.09310|0.09310	N|N	1|1	B;B|.	0.24258|.	0.06;0.1|.	B;B|.	0.18561|.	0.017;0.022|.	T|T	0.10474|0.10474	-1.0628|-1.0628	10|5	0.27785|.	T|.	0.31|.	-12.5679|-12.5679	5.4529|5.4529	0.16574|0.16574	0.1549:0.0836:0.0:0.7615|0.1549:0.0836:0.0:0.7615	rs3188121|rs3188121	2443;2251|.	O15021;O15021-3|.	MAST4_HUMAN;.|.	T|D	2443;2440;2251;2261;2261;2246|1496	ENSP00000385048:S2443T;ENSP00000385727:S2440T;ENSP00000384313:S2251T;ENSP00000384099:S2261T;ENSP00000261569:S2246T|.	ENSP00000261569:S2246T|.	S|V	+|+	1|2	0|0	MAST4|MAST4	66498081|66498081	0.811000|0.811000	0.29063|0.29063	0.256000|0.256000	0.24389|0.24389	0.026000|0.026000	0.11368|0.11368	1.310000|1.310000	0.33551|0.33551	2.069000|2.069000	0.61940|0.61940	0.379000|0.379000	0.24179|0.24179	TCC|GTC	T|0.983;A|0.017	0.017	strong		0.647	MAST4-001	NOVEL	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326324.2		
ETV1	2115	hgsc.bcm.edu	37	7	13978809	13978809	+	Missense_Mutation	SNP	T	T	C	rs9639168	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:13978809T>C	ENST00000430479.1	-	7	965	c.298A>G	c.(298-300)Agc>Ggc	p.S100G	ETV1_ENST00000405192.2_Missense_Mutation_p.S100G|ETV1_ENST00000420159.2_Missense_Mutation_p.S42G|ETV1_ENST00000403527.1_Missense_Mutation_p.S60G|ETV1_ENST00000242066.5_Missense_Mutation_p.S82G|ETV1_ENST00000405218.2_Missense_Mutation_p.S100G|ETV1_ENST00000343495.5_Missense_Mutation_p.S82G|ETV1_ENST00000403685.1_Missense_Mutation_p.S82G|ETV1_ENST00000476720.2_5'UTR|ETV1_ENST00000405358.4_Missense_Mutation_p.S114G|ETV1_ENST00000399357.3_Missense_Mutation_p.S60G	NM_004956.4	NP_004947.2	P50549	ETV1_HUMAN	ets variant 1	100			S -> G (in dbSNP:rs9639168). {ECO:0000269|PubMed:14702039, ECO:0000269|Ref.5}.		axon guidance (GO:0007411)|cell differentiation (GO:0030154)|mechanosensory behavior (GO:0007638)|muscle organ development (GO:0007517)|peripheral nervous system neuron development (GO:0048935)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)		TMPRSS2/ETV1(34)|ACSL3_ENST00000357430/ETV1(2)|EWSR1/ETV1(7)|KLK2/ETV1(3)|SLC45A3/ETV1(3)|HNRNPA2B1/ETV1(8)	breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(9)|lung(15)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	31						CAGGCAGAGCTGATTTCTGAA	0.403			T	"""EWSR1, TMPRSS2, SLC45A3, C15orf21, HNRNPA2B1. ACSL3"""	"""Ewing sarcoma, prostate"""								C|||	1599	0.319289	0.18	0.3458	5008	,	,		17089	0.4187		0.3439	False		,,,				2504	0.3609				p.S100G		Atlas-SNP	.		Dom	yes		7	7p22	2115	ets variant gene 1		"""M, E"""	ETV1_ENST00000403527,NS,meningioma,0,2	ETV1	138	2	0			c.A298G						PASS	.	C	GLY/SER,GLY/SER,GLY/SER,GLY/SER,GLY/SER,GLY/SER,GLY/SER	727,3007		85,557,1225	151.0	139.0	143.0		298,244,244,178,124,178,298	4.6	1.0	7	dbSNP_119	143	2766,5426		472,1822,1802	yes	missense,missense,missense,missense,missense,missense,missense	ETV1	NM_001163147.1,NM_001163148.1,NM_001163149.1,NM_001163150.1,NM_001163151.1,NM_001163152.1,NM_004956.4	56,56,56,56,56,56,56	557,2379,3027	CC,CT,TT		33.7646,19.4697,29.2889	benign,benign,benign,benign,benign,benign,benign	100/455,82/460,82/460,60/438,42/420,60/375,100/478	13978809	3493,8433	1867	4096	5963	SO:0001583	missense	2115	exon7			CAGAGCTGATTTC		CCDS55083.1, CCDS55084.1, CCDS55085.1, CCDS55086.1, CCDS55087.1, CCDS55088.1	7p22	2008-09-12	2008-09-12		ENSG00000006468	ENSG00000006468			3490	protein-coding gene	gene with protein product		600541	"""ets variant gene 1"""			1340465	Standard	NM_004956		Approved	ER81	uc003ssw.4	P50549	OTTHUMG00000152403	ENST00000430479.1:c.298A>G	7.37:g.13978809T>C	ENSP00000405327:p.Ser100Gly	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	73	73	1	NM_004956	A4D118|B2R768|B7Z2I4|B7Z618|B7Z9P2|C9JT37|E9PHB1|F5GXR2|O75849|Q4KMQ6|Q59GA7|Q6AI30|Q9UQ71|Q9Y636	Missense_Mutation	SNP	ENST00000430479.1	37	CCDS55088.1	696	0.31868131868131866	100	0.2032520325203252	140	0.3867403314917127	212	0.3706293706293706	244	0.32189973614775724	C	10.04	1.242238	0.22796	0.194697	0.337646	ENSG00000006468	ENST00000430479;ENST00000242066;ENST00000343495;ENST00000420159;ENST00000399357;ENST00000405192;ENST00000405358;ENST00000403527;ENST00000405218;ENST00000403685;ENST00000438956;ENST00000443608;ENST00000421381	T;T;T;T;T;T;T;T;T;T;T;T;T	0.22336	1.96;1.96;1.96;1.96;1.96;1.96;1.96;1.96;1.96;1.96;1.96;1.96;1.96	5.45	4.57	0.56435	PEA3-type ETS-domain transcription factor, N-terminal (1);	0.255451	0.47093	N	0.000255	T	0.00012	0.0000	N	0.17474	0.49	0.48341	P	3.649999999999487E-4	B;B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0;0.0	B;B;B;B;B;B	0.01281	0.0;0.0;0.0;0.0;0.0;0.0	T	0.48080	-0.9066	9	0.13108	T	0.6	.	8.696	0.34296	0.0:0.713:0.0:0.287	rs9639168;rs52830566;rs58087404;rs9639168	82;114;42;60;60;100	P50549-2;B5MCT2;F5GXR2;B7Z9P2;E9PHB1;P50549	.;.;.;.;.;ETV1_HUMAN	G	100;82;82;42;60;100;114;60;100;82;42;60;100	ENSP00000405327:S100G;ENSP00000242066:S82G;ENSP00000340853:S82G;ENSP00000411626:S42G;ENSP00000382293:S60G;ENSP00000385381:S100G;ENSP00000384085:S114G;ENSP00000384138:S60G;ENSP00000385551:S100G;ENSP00000385686:S82G;ENSP00000393078:S42G;ENSP00000394710:S60G;ENSP00000391043:S100G	ENSP00000242066:S82G	S	-	1	0	ETV1	13945334	0.980000	0.34600	0.998000	0.56505	0.987000	0.75469	0.877000	0.28106	0.791000	0.33826	-0.119000	0.15052	AGC	C|0.302;N|0.000	0.302	strong		0.403	ETV1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326111.1	NM_004956	
OBSCN	84033	hgsc.bcm.edu	37	1	228564884	228564884	+	Missense_Mutation	SNP	G	G	A	rs56174824	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:228564884G>A	ENST00000422127.1	+	101	23215	c.23171G>A	c.(23170-23172)cGc>cAc	p.R7724H	OBSCN_ENST00000570156.2_Missense_Mutation_p.R8681H|OBSCN_ENST00000366707.4_Missense_Mutation_p.R5358H	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	7724	Protein kinase 2. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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)				AAGGGCCTGCGCCACCCGCAC	0.692													G|||	705	0.140775	0.0983	0.0432	5008	,	,		16390	0.3085		0.0974	False		,,,				2504	0.1391				p.R8681H		Atlas-SNP	.											.	OBSCN	2142	.	0			c.G26042A						PASS	.	G	HIS/ARG	400,3686		14,372,1657	11.0	15.0	14.0		23171	-2.4	1.0	1	dbSNP_129	14	712,7690		31,650,3520	yes	missense	OBSCN	NM_001098623.1	29	45,1022,5177	AA,AG,GG		8.4742,9.7895,8.9045	benign	7724/7969	228564884	1112,11376	2043	4201	6244	SO:0001583	missense	84033	exon112			GCCTGCGCCACCC	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.23171G>A	1.37:g.228564884G>A	ENSP00000409493:p.Arg7724His	Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	31	17	0.548387	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	350	0.16025641025641027	64	0.13008130081300814	21	0.058011049723756904	190	0.3321678321678322	75	0.09894459102902374	G	16.84	3.232784	0.58777	0.097895	0.084742	ENSG00000154358	ENST00000422127;ENST00000366707	T;T	0.40476	1.03;1.03	4.82	-2.4	0.06583	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	91.976500	0.00166	N	0.000001	T	0.00012	0.0000	N	0.13098	0.295	0.09310	P	0.9999999999999908	B	0.02656	0.0	B	0.04013	0.001	T	0.28586	-1.0039	9	0.20519	T	0.43	.	11.4116	0.49929	0.7104:0.0:0.2896:0.0	rs56174824	7724	Q5VST9	OBSCN_HUMAN	H	7724;5358	ENSP00000409493:R7724H;ENSP00000355668:R5358H	ENSP00000355668:R5358H	R	+	2	0	OBSCN	226631507	0.595000	0.26857	0.990000	0.47175	0.541000	0.35023	1.120000	0.31271	-0.332000	0.08489	-0.671000	0.03813	CGC	G|0.852;A|0.148	0.148	strong		0.692	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
NMB	4828	hgsc.bcm.edu	37	15	85200520	85200520	+	Missense_Mutation	SNP	G	G	T	rs1051168	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:85200520G>T	ENST00000360476.3	-	2	612	c.217C>A	c.(217-219)Ccc>Acc	p.P73T	NMB_ENST00000394588.3_Missense_Mutation_p.P73T|WDR73_ENST00000434634.2_5'Flank|WDR73_ENST00000398528.3_5'Flank			P08949	NMB_HUMAN	neuromedin B	73			P -> T (in dbSNP:rs1051168). {ECO:0000269|PubMed:15489334}.	PLGTAPHTS -> HWGQLPTPP (in Ref. 1; AAA59934). {ECO:0000305}.	arachidonic acid secretion (GO:0050482)|cell-cell signaling (GO:0007267)|glucose homeostasis (GO:0042593)|negative regulation of hormone secretion (GO:0046888)|neuropeptide signaling pathway (GO:0007218)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of hormone secretion (GO:0046887)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|neuron projection (GO:0043005)	hormone activity (GO:0005179)			endometrium(1)	1				all cancers(203;3.5e-06)		GAGGTGTGGGGAGCTGTCCCC	0.607													G|||	693	0.138379	0.0136	0.1816	5008	,	,		18979	0.1359		0.2584	False		,,,				2504	0.1554				p.P73T		Atlas-SNP	.											.	NMB	14	.	0			c.C217A	GRCh37	CM045181	NMB	M	rs1051168	PASS	.	G	THR/PRO,THR/PRO	228,4176		8,212,1982	33.0	26.0	28.0		217,217	-1.4	0.0	15	dbSNP_86	28	2288,6310		281,1726,2292	yes	missense,missense	NMB	NM_021077.3,NM_205858.1	38,38	289,1938,4274	TT,TG,GG		26.6108,5.1771,19.3509	possibly-damaging,possibly-damaging	73/122,73/155	85200520	2516,10486	2202	4299	6501	SO:0001583	missense	4828	exon2			TGTGGGGAGCTGT		CCDS10332.1, CCDS42076.1	15q25.2-q25.3	2013-09-19			ENSG00000197696	ENSG00000197696			7842	protein-coding gene	gene with protein product		162340				2458345	Standard	NM_021077		Approved	MGC2277, MGC3936, MGC17211	uc002bla.3	P08949	OTTHUMG00000148666	ENST00000360476.3:c.217C>A	15.37:g.85200520G>T	ENSP00000353664:p.Pro73Thr	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	128	78	0.609375	NM_205858	Q96A06|Q96HH5	Missense_Mutation	SNP	ENST00000360476.3	37	CCDS10332.1	358	0.16391941391941392	5	0.01016260162601626	73	0.20165745856353592	81	0.14160839160839161	199	0.262532981530343	G	10.58	1.388808	0.25118	0.051771	0.266108	ENSG00000197696	ENST00000360476;ENST00000394588	T;T	0.47528	0.93;0.84	5.11	-1.37	0.09056	.	0.759821	0.12773	N	0.440331	T	0.00012	0.0000	N	0.17082	0.46	0.80722	P	0.0	B;B	0.22346	0.068;0.041	B;B	0.23419	0.046;0.021	T	0.23511	-1.0186	9	0.02654	T	1	-8.7065	4.2642	0.10756	0.4384:0.0:0.4065:0.1551	rs1051168;rs3191563;rs17850187;rs17850193;rs17857977;rs1051168	73;73	P08949-2;P08949	.;NMB_HUMAN	T	73	ENSP00000353664:P73T;ENSP00000378089:P73T	ENSP00000353664:P73T	P	-	1	0	NMB	83001524	0.077000	0.21312	0.001000	0.08648	0.943000	0.58893	0.191000	0.17076	0.065000	0.16485	-0.137000	0.14449	CCC	G|0.833;T|0.167	0.167	strong		0.607	NMB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000308995.1	NM_021077	
RNASEH1	246243	hgsc.bcm.edu	37	2	3597974	3597974	+	Silent	SNP	T	T	C	rs10186193	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:3597974T>C	ENST00000315212.3	-	4	853	c.498A>G	c.(496-498)ccA>ccG	p.P166P	RP13-512J5.1_ENST00000438485.1_5'Flank	NM_002936.3	NP_002927.2	O60930	RNH1_HUMAN	ribonuclease H1	166	RNase H. {ECO:0000255|PROSITE- ProRule:PRU00408}.				mitochondrial DNA replication (GO:0006264)|RNA catabolic process (GO:0006401)|RNA phosphodiester bond hydrolysis (GO:0090501)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	magnesium ion binding (GO:0000287)|nucleic acid binding (GO:0003676)|ribonuclease activity (GO:0004540)|RNA binding (GO:0003723)|RNA-DNA hybrid ribonuclease activity (GO:0004523)			endometrium(1)|kidney(1)|lung(7)|ovary(1)|prostate(2)|skin(1)	13	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.093)			OV - Ovarian serous cystadenocarcinoma(76;0.0713)|Epithelial(75;0.167)|all cancers(51;0.22)		AAGGATGGCCTGGCCCCCAGT	0.498													C|||	1881	0.375599	0.6233	0.2305	5008	,	,		17040	0.2371		0.3479	False		,,,				2504	0.3149				p.P166P		Atlas-SNP	.											.	RNASEH1	27	.	0			c.A498G						PASS	.	C		2631,1775	521.1+/-370.4	820,991,392	110.0	124.0	119.0		498	-10.9	0.1	2	dbSNP_119	119	3150,5450	652.1+/-400.9	596,1958,1746	yes	coding-synonymous	RNASEH1	NM_002936.3		1416,2949,2138	CC,CT,TT		36.6279,40.286,44.4487		166/287	3597974	5781,7225	2203	4300	6503	SO:0001819	synonymous_variant	246243	exon4			ATGGCCTGGCCCC	AF039652	CCDS1647.1	2p25	2008-03-11			ENSG00000171865	ENSG00000171865	3.1.26.-		18466	protein-coding gene	gene with protein product	"""RNase H1"""	604123				12036296, 17964265	Standard	XR_244873		Approved		uc002qxt.3	O60930	OTTHUMG00000090279	ENST00000315212.3:c.498A>G	2.37:g.3597974T>C		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	52	18	0.346154	NM_002936	B3KQU4|O60523|O60857|Q57Z93|Q5U0C1|Q6FHD4	Silent	SNP	ENST00000315212.3	37	CCDS1647.1																																																																																			T|0.579;C|0.421	0.421	strong		0.498	RNASEH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206605.2		
KRT84	3890	hgsc.bcm.edu	37	12	52777466	52777466	+	Silent	SNP	C	C	A	rs138204915	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:52777466C>A	ENST00000257951.3	-	2	729	c.663G>T	c.(661-663)ctG>ctT	p.L221L	RP3-416H24.4_ENST00000547174.1_RNA	NM_033045.3	NP_149034.2	Q9NSB2	KRT84_HUMAN	keratin 84	221	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)		ACTGCCTCCGCAGGTTGGTGA	0.542													C|||	7	0.00139776	0.0	0.0	5008	,	,		20929	0.0		0.006	False		,,,				2504	0.001				p.L221L		Atlas-SNP	.											.	KRT84	61	.	0			c.G663T						PASS	.	C		3,4403	6.2+/-15.9	0,3,2200	71.0	68.0	69.0		663	1.4	1.0	12	dbSNP_134	69	22,8578	16.0+/-53.3	0,22,4278	no	coding-synonymous	KRT84	NM_033045.3		0,25,6478	AA,AC,CC		0.2558,0.0681,0.1922		221/601	52777466	25,12981	2203	4300	6503	SO:0001819	synonymous_variant	3890	exon2			CCTCCGCAGGTTG	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.663G>T	12.37:g.52777466C>A		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	129	69	0.534884	NM_033045	B2RA43|Q6ISB0|Q701L6	Silent	SNP	ENST00000257951.3	37	CCDS8825.1																																																																																			C|0.998;A|0.002	0.002	strong		0.542	KRT84-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405187.1	NM_033045	
FER	2241	hgsc.bcm.edu	37	5	108294979	108294979	+	Silent	SNP	T	T	C	rs34869483	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:108294979T>C	ENST00000281092.4	+	13	1971	c.1587T>C	c.(1585-1587)gaT>gaC	p.D529D	FER_ENST00000536402.1_3'UTR|FER_ENST00000438717.2_Silent_p.D354D	NM_005246.2	NP_005237.2	P16591	FER_HUMAN	fer (fps/fes related) tyrosine kinase	529	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				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)		AACTTATAGATCATCACTATA	0.363													T|||	30	0.00599042	0.0015	0.0043	5008	,	,		15833	0.0		0.0119	False		,,,				2504	0.0133				p.D529D	Colon(146;1051 1799 9836 27344 47401)	Atlas-SNP	.											.	FER	100	.	0			c.T1587C						PASS	.	T		14,4390	21.2+/-45.6	0,14,2188	138.0	131.0	133.0		1587	-7.7	0.9	5	dbSNP_126	133	193,8405	84.8+/-147.2	4,185,4110	no	coding-synonymous	FER	NM_005246.2		4,199,6298	CC,CT,TT		2.2447,0.3179,1.5921		529/823	108294979	207,12795	2202	4299	6501	SO:0001819	synonymous_variant	2241	exon13			TATAGATCATCAC	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.1587T>C	5.37:g.108294979T>C		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	108	64	0.592593	NM_005246	B2RCR4|B4DSQ2|H2FLB8	Silent	SNP	ENST00000281092.4	37	CCDS4098.1																																																																																			T|0.988;C|0.012	0.012	strong		0.363	FER-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250664.1	NM_005246	
LYPD4	147719	hgsc.bcm.edu	37	19	42342319	42342319	+	Silent	SNP	A	A	G	rs2290695	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:42342319A>G	ENST00000330743.3	-	4	1439	c.228T>C	c.(226-228)gtT>gtC	p.V76V	AC020956.3_ENST00000593354.1_lincRNA|LYPD4_ENST00000343055.4_Silent_p.V41V|LYPD4_ENST00000601246.1_Silent_p.V41V	NM_173506.4	NP_775777.3	Q6UWN0	LYPD4_HUMAN	LY6/PLAUR domain containing 4	76						anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)				breast(1)|kidney(1)|large_intestine(4)|lung(3)|ovary(1)|skin(2)	12						TAAAGCCCACAACTCCCCTTG	0.577													-|||	3032	0.605431	0.91	0.5764	5008	,	,		17010	0.5208		0.4722	False		,,,				2504	0.4387				p.V76V		Atlas-SNP	.											.	LYPD4	30	.	0			c.T228C						PASS	.			3672,734	756.9+/-412.7	1543,586,74	56.0	55.0	55.0		228	-3.5	0.4	19	dbSNP_100	55	4144,4456	564.2+/-388.3	975,2194,1131	no	coding-synonymous	LYPD4	NM_173506.4		2518,2780,1205	GG,GA,AA		48.186,16.6591,39.9047		76/247	42342319	7816,5190	2203	4300	6503	SO:0001819	synonymous_variant	147719	exon4			GCCCACAACTCCC	AY358726	CCDS12587.1	19q13.2	2008-02-05				ENSG00000273111			28659	protein-coding gene	gene with protein product						12975309	Standard	XM_005278383		Approved	MGC42718	uc002orp.1	Q6UWN0		ENST00000330743.3:c.228T>C	19.37:g.42342319A>G		Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	29	29	1	NM_173506	Q8IYW0	Silent	SNP	ENST00000330743.3	37	CCDS12587.1																																																																																			A|0.389;G|0.611	0.611	strong		0.577	LYPD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463039.1	NM_173506	
TRIML1	339976	hgsc.bcm.edu	37	4	189061106	189061106	+	Missense_Mutation	SNP	G	G	A	rs13131525	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:189061106G>A	ENST00000332517.3	+	1	534	c.394G>A	c.(394-396)Gag>Aag	p.E132K	RP11-366H4.3_ENST00000501322.2_RNA	NM_178556.3	NP_848651.2	Q8N9V2	TRIML_HUMAN	tripartite motif family-like 1	132			E -> K (in dbSNP:rs13131525).		multicellular organismal development (GO:0007275)|protein ubiquitination (GO:0016567)		ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			NS(3)|breast(2)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(30)|ovary(2)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)	60		all_cancers(14;1.33e-43)|all_epithelial(14;7.86e-31)|all_lung(41;4.3e-13)|Lung NSC(41;9.69e-13)|Melanoma(20;7.86e-05)|Breast(6;0.000148)|Hepatocellular(41;0.0218)|Renal(120;0.0376)|Prostate(90;0.0513)|all_hematologic(60;0.062)		OV - Ovarian serous cystadenocarcinoma(60;1.52e-11)|BRCA - Breast invasive adenocarcinoma(30;4.19e-06)|GBM - Glioblastoma multiforme(59;0.000232)|STAD - Stomach adenocarcinoma(60;0.000279)|LUSC - Lung squamous cell carcinoma(40;0.00902)|READ - Rectum adenocarcinoma(43;0.156)		CAGCGAGGCTGAGGAGCATCA	0.582													G|||	1280	0.255591	0.1157	0.4942	5008	,	,		19109	0.0655		0.4672	False		,,,				2504	0.2536				p.E132K	Melanoma(31;213 1036 16579 23968 32372)	Atlas-SNP	.											.	TRIML1	126	.	0			c.G394A						PASS	.	G	LYS/GLU	785,3621	296.4+/-284.2	64,657,1482	45.0	42.0	43.0		394	4.8	1.0	4	dbSNP_121	43	4305,4295	549.9+/-385.6	1094,2117,1089	yes	missense	TRIML1	NM_178556.3	56	1158,2774,2571	AA,AG,GG		49.9419,17.8166,39.1358	benign	132/469	189061106	5090,7916	2203	4300	6503	SO:0001583	missense	339976	exon1			GAGGCTGAGGAGC	AK093499	CCDS3851.1	4q35.2	2013-01-09			ENSG00000184108	ENSG00000184108		"""RING-type (C3HC4) zinc fingers"""	26698	protein-coding gene	gene with protein product						12477932	Standard	NM_178556		Approved	FLJ36180, RNF209	uc003izm.1	Q8N9V2	OTTHUMG00000160237	ENST00000332517.3:c.394G>A	4.37:g.189061106G>A	ENSP00000327738:p.Glu132Lys	Somatic	263	0	0		WXS	Illumina HiSeq	Phase_I	294	159	0.540816	NM_178556	Q96BE5	Missense_Mutation	SNP	ENST00000332517.3	37	CCDS3851.1	635	0.2907509157509158	55	0.11178861788617886	176	0.4861878453038674	50	0.08741258741258741	354	0.46701846965699206	G	13.27	2.187911	0.38609	0.178166	0.500581	ENSG00000184108	ENST00000332517	T	0.61980	0.06	4.85	4.85	0.62838	.	0.325925	0.24472	N	0.038231	T	0.00012	0.0000	L	0.57536	1.79	0.26359	P	0.9770894999999999	D	0.61697	0.99	P	0.60068	0.868	T	0.49072	-0.8977	9	0.72032	D	0.01	-29.3586	14.1946	0.65662	0.0:0.0:1.0:0.0	rs13131525;rs60211754;rs13131525	132	Q8N9V2	TRIML_HUMAN	K	132	ENSP00000327738:E132K	ENSP00000327738:E132K	E	+	1	0	TRIML1	189298100	0.298000	0.24417	1.000000	0.80357	0.256000	0.26092	2.607000	0.46300	2.625000	0.88918	0.561000	0.74099	GAG	G|0.670;A|0.330	0.330	strong		0.582	TRIML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359813.1	NM_178556	
AKR1B15	441282	hgsc.bcm.edu	37	7	134264286	134264286	+	Silent	SNP	C	C	T	rs6467538	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:134264286C>T	ENST00000457545.2	+	12	1280	c.1020C>T	c.(1018-1020)ttC>ttT	p.F340F	AKR1B15_ENST00000423958.1_Silent_p.F312F	NM_001080538.2	NP_001074007.2	C9JRZ8	AK1BF_HUMAN	aldo-keto reductase family 1, member B15	340							oxidoreductase activity (GO:0016491)			endometrium(1)|kidney(3)|large_intestine(2)|lung(10)|ovary(1)|urinary_tract(1)	18						ACTTTCCCTTCGATGCAGAAT	0.408													C|||	1681	0.335663	0.559	0.3084	5008	,	,		20009	0.1438		0.339	False		,,,				2504	0.2474				p.F340F		Atlas-SNP	.											.	AKR1B15	105	.	0			c.C1020T						PASS	.	C		2235,2169	554.5+/-379.0	576,1083,543	87.0	88.0	87.0		1020	-1.6	0.0	7	dbSNP_116	87	2959,5641	449.5+/-362.1	520,1919,1861	no	coding-synonymous	AKR1B15	NM_001080538.2		1096,3002,2404	TT,TC,CC		34.407,49.2507,39.9416		340/345	134264286	5194,7810	2202	4300	6502	SO:0001819	synonymous_variant	441282	exon12			TCCCTTCGATGCA		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.1020C>T	7.37:g.134264286C>T		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	90	45	0.5	NM_001080538	C9J3V2	Silent	SNP	ENST00000457545.2	37	CCDS47715.2																																																																																			C|0.651;T|0.349	0.349	strong		0.408	AKR1B15-001	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000339726.2		
FUT10	84750	hgsc.bcm.edu	37	8	33246591	33246591	+	Missense_Mutation	SNP	G	G	C	rs17855838	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:33246591G>C	ENST00000327671.5	-	4	1733	c.1102C>G	c.(1102-1104)Ctc>Gtc	p.L368V	FUT10_ENST00000524021.1_Missense_Mutation_p.L340V|FUT10_ENST00000518076.1_5'UTR|FUT10_ENST00000335589.3_Missense_Mutation_p.L306V|FUT10_ENST00000518672.1_Missense_Mutation_p.L340V	NM_032664.3	NP_116053.3	Q6P4F1	FUT10_HUMAN	fucosyltransferase 10 (alpha (1,3) fucosyltransferase)	368			L -> V (in dbSNP:rs17855838). {ECO:0000269|PubMed:11698403, ECO:0000269|PubMed:15489334}.		embryo development (GO:0009790)|fertilization (GO:0009566)|fucosylation (GO:0036065)|hemopoiesis (GO:0030097)|L-fucose catabolic process (GO:0042355)|nervous system development (GO:0007399)|protein folding (GO:0006457)|protein glycosylation (GO:0006486)|protein targeting (GO:0006605)|wound healing (GO:0042060)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	alpha-(1->3)-fucosyltransferase activity (GO:0046920)	p.L368V(1)		cervix(1)|endometrium(1)|large_intestine(7)|liver(1)|lung(9)|ovary(1)|pancreas(1)|prostate(3)|stomach(3)|upper_aerodigestive_tract(2)	29				KIRC - Kidney renal clear cell carcinoma(67;0.129)|Kidney(114;0.154)		CGTTCCCTGAGAGCTGTCAGA	0.473													G|||	1367	0.272963	0.0855	0.1671	5008	,	,		21753	0.4683		0.1938	False		,,,				2504	0.4816				p.L368V		Atlas-SNP	.											FUT10,NS,carcinoma,0,1	FUT10	62	1	1	Substitution - Missense(1)	stomach(1)	c.C1102G						PASS	.	G	VAL/LEU	530,3876	238.0+/-249.6	22,486,1695	211.0	181.0	191.0		1102	4.1	1.0	8	dbSNP_123	191	1745,6855	316.6+/-312.8	176,1393,2731	yes	missense	FUT10	NM_032664.3	32	198,1879,4426	CC,CG,GG		20.2907,12.0291,17.4919	possibly-damaging	368/480	33246591	2275,10731	2203	4300	6503	SO:0001583	missense	84750	exon4			CCCTGAGAGCTGT	AJ512465	CCDS6088.1	8p12	2013-02-26			ENSG00000172728	ENSG00000172728		"""Fucosyltransferases"""	19234	protein-coding gene	gene with protein product							Standard	NM_032664		Approved		uc003xje.3	Q6P4F1	OTTHUMG00000163954	ENST00000327671.5:c.1102C>G	8.37:g.33246591G>C	ENSP00000332757:p.Leu368Val	Somatic	479	1	0.00208768		WXS	Illumina HiSeq	Phase_I	332	330	0.993976	NM_032664	A8KAC8|Q70GG3|Q8IVI6|Q8IVI7|Q8IVJ3|Q8TE43|Q9BSR3	Missense_Mutation	SNP	ENST00000327671.5	37	CCDS6088.1	473	0.21657509157509158	33	0.06707317073170732	56	0.15469613259668508	250	0.4370629370629371	134	0.17678100263852242	G	15.32	2.799234	0.50208	0.120291	0.202907	ENSG00000172728	ENST00000327671;ENST00000380081;ENST00000518672;ENST00000524021;ENST00000335589	T;T;T;T	0.44083	0.93;0.94;0.94;1.81	5.04	4.09	0.47781	.	0.262237	0.33110	N	0.005264	T	0.00012	0.0000	M	0.86343	2.81	0.21675	P	0.999592885	P;P;P;P;P;B	0.48998	0.861;0.498;0.918;0.638;0.684;0.443	P;B;P;B;B;B	0.48952	0.562;0.23;0.596;0.272;0.422;0.395	T	0.48559	-0.9025	9	0.51188	T	0.08	-19.205	10.2443	0.43332	0.0:0.0:0.6866:0.3134	rs17855838;rs17855838	418;368;340;306;368;410	B4E056;Q6P4F1-5;Q6P4F1-4;Q6P4F1-3;Q6P4F1;E7EU36	.;.;.;.;FUT10_HUMAN;.	V	368;410;340;340;306	ENSP00000332757:L368V;ENSP00000430428:L340V;ENSP00000429870:L340V;ENSP00000334997:L306V	ENSP00000332757:L368V	L	-	1	0	FUT10	33366133	0.981000	0.34729	0.996000	0.52242	0.989000	0.77384	1.797000	0.38804	2.493000	0.84123	0.557000	0.71058	CTC	G|0.815;C|0.185	0.185	strong		0.473	FUT10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376540.1	NM_032664	
PIEZO1	9780	hgsc.bcm.edu	37	16	88781125	88781125	+	IGR	SNP	T	T	C	rs8043637	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:88781125T>C	ENST00000301015.9	-	0	8072				MIR4722_ENST00000578292.1_RNA|CTU2_ENST00000312060.5_Silent_p.C444C|CTU2_ENST00000453996.2_Silent_p.C444C|CTU2_ENST00000378384.3_Silent_p.C357C|CTU2_ENST00000567949.1_Silent_p.C515C	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						CCCAGCGCTGTGGCCAGGGGG	0.701													C|||	4366	0.871805	0.8192	0.8689	5008	,	,		13484	0.9405		0.8926	False		,,,				2504	0.8528				p.C444C		Atlas-SNP	.											.	CTU2	66	.	0			c.T1332C						PASS	.	C	,	3638,688		1537,564,62	14.0	16.0	15.0		1332,1332	-0.1	0.0	16	dbSNP_116	15	7766,758		3544,678,40	no	coding-synonymous,coding-synonymous	CTU2	NM_001012759.1,NM_001012762.1	,	5081,1242,102	CC,CT,TT		8.8925,15.9038,11.2529	,	444/516,444/486	88781125	11404,1446	2163	4262	6425	SO:0001628	intergenic_variant	348180	exon12			GCGCTGTGGCCAG	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.88781125T>C		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	70	69	0.985714	NM_001012759	A6NHT9|A7E2B7|Q0KKZ9	Silent	SNP	ENST00000301015.9	37	CCDS54058.1																																																																																			T|0.117;C|0.883	0.883	strong		0.701	PIEZO1-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000345699.4	NM_014745	
ALPK2	115701	hgsc.bcm.edu	37	18	56202394	56202394	+	Silent	SNP	C	C	T	rs7240355	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:56202394C>T	ENST00000361673.3	-	5	5238	c.5025G>A	c.(5023-5025)aaG>aaA	p.K1675K	RP11-1151B14.4_ENST00000591360.1_RNA	NM_052947.3	NP_443179.3	Q86TB3	ALPK2_HUMAN	alpha-kinase 2	1675						nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(33)|ovary(7)|prostate(1)|skin(10)|upper_aerodigestive_tract(2)	84						CCAGGGTGCCCTTTTGACATG	0.547													C|||	361	0.0720847	0.0424	0.0706	5008	,	,		18119	0.0119		0.1272	False		,,,				2504	0.1186				p.K1675K		Atlas-SNP	.											.	ALPK2	487	.	0			c.G5025A						PASS	.	C		300,4106	156.6+/-189.7	16,268,1919	74.0	79.0	78.0		5025	2.9	0.9	18	dbSNP_116	78	1161,7439	220.5+/-258.2	78,1005,3217	no	coding-synonymous	ALPK2	NM_052947.3		94,1273,5136	TT,TC,CC		13.5,6.8089,11.2333		1675/2171	56202394	1461,11545	2203	4300	6503	SO:0001819	synonymous_variant	115701	exon5			GGTGCCCTTTTGA	AY044450	CCDS11966.2	18q21.31	2013-01-11			ENSG00000198796	ENSG00000198796		"""Immunoglobulin superfamily / I-set domain containing"""	20565	protein-coding gene	gene with protein product	"""heart alpha-kinase"""					10021370	Standard	NM_052947		Approved	HAK	uc002lhj.4	Q86TB3	OTTHUMG00000132755	ENST00000361673.3:c.5025G>A	18.37:g.56202394C>T		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	44	28	0.636364	NM_052947	Q6ZUX0|Q8NAT5|Q96L95	Silent	SNP	ENST00000361673.3	37	CCDS11966.2																																																																																			C|0.906;T|0.094	0.094	strong		0.547	ALPK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256126.1	NM_052947	
ZFP64	55734	hgsc.bcm.edu	37	20	50769183	50769183	+	Silent	SNP	G	G	A	rs3746415	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:50769183G>A	ENST00000216923.4	-	6	1897	c.1548C>T	c.(1546-1548)gcC>gcT	p.A516A	ZFP64_ENST00000346617.4_Silent_p.A462A|ZFP64_ENST00000371515.4_Silent_p.A514A|ZFP64_ENST00000477786.1_Intron|ZFP64_ENST00000361387.2_Intron|ZFP64_ENST00000371518.2_Intron	NM_018197.2|NM_199426.1	NP_060667.2|NP_955458.1	Q9NPA5	ZF64A_HUMAN	ZFP64 zinc finger protein	516					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(5)|large_intestine(8)|lung(11)|ovary(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	33						TCACTGCAGCGGCGGCAGCCT	0.637													G|||	780	0.155751	0.1029	0.2695	5008	,	,		17009	0.0843		0.2137	False		,,,				2504	0.1605				p.A516A		Atlas-SNP	.											.	ZFP64	240	.	0			c.C1548T						PASS	.	G	,,,	459,3947		25,409,1769	22.0	26.0	24.0		1548,1386,1542,	-11.1	0.0	20	dbSNP_107	24	1855,6745		192,1471,2637	no	coding-synonymous,coding-synonymous,coding-synonymous,intron	ZFP64	NM_018197.2,NM_022088.4,NM_199426.1,NM_199427.2	,,,	217,1880,4406	AA,AG,GG		21.5698,10.4176,17.7918	,,,	516/682,462/628,514/680,	50769183	2314,10692	2203	4300	6503	SO:0001819	synonymous_variant	55734	exon6			TGCAGCGGCGGCA	AK001596	CCDS13439.1, CCDS13440.1, CCDS13441.1, CCDS13442.1	20q13.11-q13.13	2013-01-08	2012-11-27		ENSG00000020256	ENSG00000020256		"""Zinc fingers, C2H2-type"""	15940	protein-coding gene	gene with protein product			"""zinc finger protein 338"", ""zinc finger protein 64 homolog (mouse)"", ""zinc finger protein 64"""	ZNF338		9034307	Standard	NM_199427		Approved	FLJ10734, dJ831D17.1, FLJ12628, dJ548G19.1	uc002xwl.3	Q9NPA5	OTTHUMG00000032756	ENST00000216923.4:c.1548C>T	20.37:g.50769183G>A		Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	20	13	0.65	NM_018197	Q9NTS7|Q9NVH4	Silent	SNP	ENST00000216923.4	37	CCDS13440.1																																																																																			G|0.839;A|0.161	0.161	strong		0.637	ZFP64-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000079744.1	NM_018197	
CYP4B1	1580	hgsc.bcm.edu	37	1	47280884	47280884	+	Missense_Mutation	SNP	C	C	T	rs4646491	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:47280884C>T	ENST00000271153.4	+	8	1054	c.1018C>T	c.(1018-1020)Cgt>Tgt	p.R340C	CYP4B1_ENST00000371919.4_Missense_Mutation_p.R326C|CYP4B1_ENST00000452782.2_Missense_Mutation_p.R178C|CYP4B1_ENST00000371923.4_Missense_Mutation_p.R341C			P13584	CP4B1_HUMAN	cytochrome P450, family 4, subfamily B, polypeptide 1	340			R -> C (in allele CYP4B1*2 and allele CYP4B1*7; dbSNP:rs4646491). {ECO:0000269|PubMed:12142726, ECO:0000269|Ref.5}.		biphenyl metabolic process (GO:0018879)|exogenous drug catabolic process (GO:0042738)|fluorene metabolic process (GO:0018917)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	aromatase activity (GO:0070330)|drug binding (GO:0008144)|fluorene oxygenase activity (GO:0018585)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxygen binding (GO:0019825)			NS(2)|breast(1)|endometrium(2)|kidney(1)|large_intestine(12)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	36	Acute lymphoblastic leukemia(166;0.155)				Midazolam(DB00683)|Phenobarbital(DB01174)|Thiamine(DB00152)	GCACCAGCATCGTTGTAGAGA	0.567													c|||	676	0.134984	0.0386	0.1816	5008	,	,		20496	0.255		0.1302	False		,,,				2504	0.1135				p.R341C		Atlas-SNP	.											.	CYP4B1	81	.	0			c.C1021T						PASS	.	C	CYS/ARG,CYS/ARG	251,4155	803.1+/-415.7	8,235,1960	114.0	93.0	100.0		1018,1021	3.0	0.0	1	dbSNP_111	100	1234,7366	761.7+/-407.6	92,1050,3158	yes	missense,missense	CYP4B1	NM_000779.3,NM_001099772.1	180,180	100,1285,5118	TT,TC,CC		14.3488,5.6968,11.4178	benign,benign	340/512,341/513	47280884	1485,11521	2203	4300	6503	SO:0001583	missense	1580	exon8			CAGCATCGTTGTA	BC017758	CCDS542.1, CCDS41328.1	1p33	2013-11-11	2003-01-14		ENSG00000142973	ENSG00000142973		"""Cytochrome P450s"""	2644	protein-coding gene	gene with protein product		124075	"""cytochrome P450, subfamily IVB, polypeptide 1"""				Standard	NM_000779		Approved		uc001cqn.4	P13584	OTTHUMG00000007984	ENST00000271153.4:c.1018C>T	1.37:g.47280884C>T	ENSP00000271153:p.Arg340Cys	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	121	56	0.46281	NM_001099772	Q1HBI2|Q8TD85|Q8WWF2|Q8WWU9|Q8WWV0	Missense_Mutation	SNP	ENST00000271153.4	37	CCDS542.1	381	0.17445054945054944	33	0.06707317073170732	58	0.16022099447513813	183	0.31993006993006995	107	0.14116094986807387	t	6.113	0.389115	0.11581	0.056968	0.143488	ENSG00000142973	ENST00000371923;ENST00000271153;ENST00000371919;ENST00000452782;ENST00000468637	D;D;T;D;D	0.81739	-1.53;-1.53;-0.57;-1.53;-1.53	5.85	2.98	0.34508	.	0.625227	0.17248	N	0.181285	T	0.00012	0.0000	M	0.85630	2.765	0.58432	P	1.0000000000287557E-6	B;P;P	0.35872	0.13;0.469;0.525	B;B;B	0.43783	0.08;0.305;0.431	T	0.02371	-1.1169	9	0.72032	D	0.01	.	6.2862	0.21035	0.3683:0.4999:0.0:0.1317	rs4646491;rs12725273;rs17102588;rs56426269;rs60773519;rs4646491	326;341;340	Q8IZB0;P13584-2;P13584	.;.;CP4B1_HUMAN	C	341;340;326;178;177	ENSP00000360991:R341C;ENSP00000271153:R340C;ENSP00000360987:R326C;ENSP00000400413:R178C;ENSP00000437670:R177C	ENSP00000271153:R340C	R	+	1	0	CYP4B1	47053471	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	0.635000	0.24629	0.396000	0.25283	-0.134000	0.14843	CGT	C|0.863;T|0.137	0.137	strong		0.567	CYP4B1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000021911.1	NM_000779	
MLX	6945	hgsc.bcm.edu	37	17	40722029	40722029	+	Missense_Mutation	SNP	A	A	G	rs665268	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:40722029A>G	ENST00000246912.4	+	7	721	c.668A>G	c.(667-669)cAg>cGg	p.Q223R	MLX_ENST00000346833.4_Missense_Mutation_p.Q139R|MLX_ENST00000435881.2_Missense_Mutation_p.Q169R	NM_170607.2	NP_733752.1	Q9UH92	MLX_HUMAN	MLX, MAX dimerization protein	223			Q -> R (in dbSNP:rs665268).		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)		AAGGCACACCAGGACAACCCC	0.547													A|||	1610	0.321486	0.1952	0.2075	5008	,	,		22617	0.4355		0.2654	False		,,,				2504	0.5133				p.Q223R	GBM(121;657 1601 4665 24731 34640)	Atlas-SNP	.											.	MLX	17	.	0			c.A668G						PASS	.	A	ARG/GLN,ARG/GLN,ARG/GLN	877,3529	341.8+/-306.9	88,701,1414	118.0	101.0	107.0		668,506,416	4.7	1.0	17	dbSNP_83	107	2350,6250	393.6+/-344.4	318,1714,2268	yes	missense,missense,missense	MLX	NM_170607.2,NM_198204.1,NM_198205.1	43,43,43	406,2415,3682	GG,GA,AA		27.3256,19.9047,24.8116	probably-damaging,probably-damaging,probably-damaging	223/299,169/245,139/215	40722029	3227,9779	2203	4300	6503	SO:0001583	missense	6945	exon7			CACACCAGGACAA	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.668A>G	17.37:g.40722029A>G	ENSP00000246912:p.Gln223Arg	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	108	54	0.5	NM_170607	A8K2J3|B2RAV8|B2RD73|Q53XM6|Q96FL2|Q9H2V0|Q9H2V1|Q9H2V2|Q9NXN3	Missense_Mutation	SNP	ENST00000246912.4	37	CCDS11430.1	634	0.2902930402930403	110	0.22357723577235772	71	0.19613259668508287	242	0.4230769230769231	211	0.2783641160949868	A	15.08	2.727690	0.48833	0.199047	0.273256	ENSG00000108788	ENST00000346833;ENST00000246912;ENST00000435881	T;T;T	0.80738	-1.08;-1.41;-1.12	5.72	4.65	0.58169	.	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	M	0.66939	2.045	0.09310	P	0.99999999486047	D;B;B	0.89917	1.0;0.005;0.011	D;B;B	0.74023	0.982;0.006;0.029	T	0.14531	-1.0469	9	0.25106	T	0.35	-16.5052	11.4367	0.50072	0.9298:0.0:0.0702:0.0	rs665268;rs665268	139;223;169	Q9UH92-2;Q9UH92;Q9UH92-3	.;MLX_HUMAN;.	R	139;223;169	ENSP00000320913:Q139R;ENSP00000246912:Q223R;ENSP00000416627:Q169R	ENSP00000246912:Q223R	Q	+	2	0	MLX	37975555	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.525000	0.81892	1.014000	0.39417	0.459000	0.35465	CAG	A|0.732;G|0.268	0.268	strong		0.547	MLX-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000450415.1	NM_170607	
DSPP	1834	hgsc.bcm.edu	37	4	88537258	88537258	+	Silent	SNP	T	T	C	rs199966097		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:88537258T>C	ENST00000282478.7	+	4	3477	c.3444T>C	c.(3442-3444)agT>agC	p.S1148S	RP11-742B18.1_ENST00000506480.1_RNA|DSPP_ENST00000399271.1_Silent_p.S1148S			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	1148	Asp/Ser-rich.				biomineral tissue development (GO:0031214)|cellular response to cell-matrix adhesion (GO:0071460)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)	p.S1148S(1)		breast(2)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|skin(3)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Hepatocellular(203;0.114)|all_hematologic(202;0.236)		OV - Ovarian serous cystadenocarcinoma(123;0.000508)		gtgacagcagtgaaagcagcg	0.562																																					p.S1148S		Atlas-SNP	.											DSPP,NS,carcinoma,0,2	DSPP	174	2	1	Substitution - coding silent(1)	kidney(1)	c.T3444C						PASS	.						47.0	63.0	57.0					4																	88537258		1566	2841	4407	SO:0001819	synonymous_variant	1834	exon5			CAGCAGTGAAAGC	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.3444T>C	4.37:g.88537258T>C		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	91	30	0.32967	NM_014208	A8MUI0|O95815	Silent	SNP	ENST00000282478.7	37	CCDS43248.1																																																																																			.	.	none		0.562	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208	
CMYA5	202333	hgsc.bcm.edu	37	5	79027030	79027030	+	Missense_Mutation	SNP	A	A	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:79027030A>T	ENST00000446378.2	+	2	2473	c.2442A>T	c.(2440-2442)aaA>aaT	p.K814N		NM_153610.3	NP_705838.3	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	814					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)		CTCAAAAGAAAATAATCAATG	0.443																																					p.K814N		Atlas-SNP	.											.	CMYA5	643	.	0			c.A2442T						PASS	.						85.0	81.0	83.0					5																	79027030		1922	4130	6052	SO:0001583	missense	202333	exon2			AAAGAAAATAATC	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.2442A>T	5.37:g.79027030A>T	ENSP00000394770:p.Lys814Asn	Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	100	20	0.2	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	.	.	.	.	.	.	.	.	.	.	A	12.71	2.018125	0.35606	.	.	ENSG00000164309	ENST00000446378	T	0.39229	1.09	5.41	-3.18	0.05186	.	0.937011	0.08936	N	0.872269	T	0.24431	0.0592	L	0.41236	1.265	0.09310	N	1	B	0.25441	0.126	B	0.22753	0.041	T	0.27331	-1.0077	10	0.29301	T	0.29	.	0.3705	0.00378	0.2947:0.1275:0.2331:0.3446	.	814	Q8N3K9	CMYA5_HUMAN	N	814	ENSP00000394770:K814N	ENSP00000394770:K814N	K	+	3	2	CMYA5	79062786	0.001000	0.12720	0.000000	0.03702	0.009000	0.06853	0.107000	0.15375	-0.130000	0.11599	0.528000	0.53228	AAA	.	.	none		0.443	CMYA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369497.1	NM_153610	
SAMD8	142891	hgsc.bcm.edu	37	10	76910705	76910705	+	Missense_Mutation	SNP	A	A	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:76910705A>T	ENST00000542569.1	+	2	522	c.419A>T	c.(418-420)cAt>cTt	p.H140L	SAMD8_ENST00000372690.3_Missense_Mutation_p.H203L|SAMD8_ENST00000372687.4_Missense_Mutation_p.H140L	NM_001174156.1|NM_144660.2	NP_001167627.1|NP_653261.1	Q96LT4	SAMD8_HUMAN	sterile alpha motif domain containing 8	140					ceramide biosynthetic process (GO:0046513)|regulation of ceramide biosynthetic process (GO:2000303)|sphingomyelin biosynthetic process (GO:0006686)	integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)	transferase activity (GO:0016740)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|prostate(1)	12	all_cancers(46;0.0207)|all_epithelial(25;0.00126)|Prostate(51;0.0112)|Ovarian(15;0.0348)					AAAAACAAACATTCTGTTCGA	0.373																																					p.H140L		Atlas-SNP	.											.	SAMD8	57	.	0			c.A419T						PASS	.						73.0	68.0	69.0					10																	76910705		2203	4300	6503	SO:0001583	missense	142891	exon2			ACAAACATTCTGT	AK057811	CCDS7347.1, CCDS53543.1	10q22.3	2013-01-10			ENSG00000156671	ENSG00000156671		"""Sterile alpha motif (SAM) domain containing"""	26320	protein-coding gene	gene with protein product		611575					Standard	NM_144660		Approved	FLJ25082	uc001jwx.2	Q96LT4	OTTHUMG00000018515	ENST00000542569.1:c.419A>T	10.37:g.76910705A>T	ENSP00000438042:p.His140Leu	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	88	20	0.227273	NM_144660	Q5JSC5|Q5JSC8|Q66K52	Missense_Mutation	SNP	ENST00000542569.1	37	CCDS53543.1	.	.	.	.	.	.	.	.	.	.	A	12.25	1.881147	0.33255	.	.	ENSG00000156671	ENST00000447533;ENST00000372690;ENST00000542569;ENST00000372687	.	.	.	5.7	5.7	0.88788	.	0.046754	0.85682	D	0.000000	T	0.45276	0.1334	L	0.29908	0.895	0.43141	D	0.994895	P;B	0.36535	0.557;0.007	B;B	0.33620	0.167;0.009	T	0.40117	-0.9580	9	0.23302	T	0.38	-17.3105	15.9627	0.79941	1.0:0.0:0.0:0.0	.	140;140	Q96LT4-2;Q96LT4	.;SAMD8_HUMAN	L	140;203;140;140	.	ENSP00000361772:H140L	H	+	2	0	SAMD8	76580711	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	6.750000	0.74888	2.179000	0.69175	0.402000	0.26972	CAT	.	.	none		0.373	SAMD8-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_144660	
TGFBR3	7049	hgsc.bcm.edu	37	1	92177938	92177938	+	Silent	SNP	A	A	G	rs1805113	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:92177938A>G	ENST00000525962.1	-	12	2089	c.2028T>C	c.(2026-2028)ttT>ttC	p.F676F	TGFBR3_ENST00000370399.2_Silent_p.F675F|TGFBR3_ENST00000212355.4_Silent_p.F676F			Q03167	TGBR3_HUMAN	transforming growth factor, beta receptor III	676	ZP. {ECO:0000255|PROSITE- ProRule:PRU00375}.				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)		GCGGGATAGGAAAGTGCACTC	0.428													A|||	1401	0.279752	0.3101	0.2882	5008	,	,		20898	0.0863		0.4304	False		,,,				2504	0.2771				p.F676F		Atlas-SNP	.											.	TGFBR3	103	.	0			c.T2028C						PASS	.	A	,,	1515,2891	481.0+/-359.0	255,1005,943	156.0	150.0	152.0		2025,2025,2028	-0.4	1.0	1	dbSNP_89	152	3750,4850	533.3+/-382.4	822,2106,1372	no	coding-synonymous,coding-synonymous,coding-synonymous	TGFBR3	NM_001195683.1,NM_001195684.1,NM_003243.4	,,	1077,3111,2315	GG,GA,AA		43.6047,34.3849,40.4813	,,	675/851,675/851,676/852	92177938	5265,7741	2203	4300	6503	SO:0001819	synonymous_variant	7049	exon13			GATAGGAAAGTGC	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.2028T>C	1.37:g.92177938A>G		Somatic	150	1	0.00666667		WXS	Illumina HiSeq	Phase_I	105	105	1	NM_003243	A0AUW8|A8K5N0|B9EG88|Q5T2T4|Q5U731|Q9UGI2	Silent	SNP	ENST00000525962.1	37	CCDS30770.1																																																																																			A|0.655;G|0.345	0.345	strong		0.428	TGFBR3-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382308.1	NM_003243	
HIST1H4H	8365	hgsc.bcm.edu	37	6	26285503	26285503	+	Silent	SNP	C	C	T	rs41266829	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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						scavenged	.	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	143	1	0.00699301		WXS	Illumina HiSeq	Phase_I	95	41	0.431579	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	
LRRC16B	90668	hgsc.bcm.edu	37	14	24529209	24529209	+	Silent	SNP	C	C	T	rs61564890	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:24529209C>T	ENST00000342740.5	+	23	2053	c.1899C>T	c.(1897-1899)ccC>ccT	p.P633P	LRRC16B_ENST00000334420.7_5'UTR	NM_138360.3	NP_612369.3	Q8ND23	LR16B_HUMAN	leucine rich repeat containing 16B	633						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)		TGTCCTTCCCCGTGAGCGACA	0.642													C|||	959	0.191494	0.0416	0.2104	5008	,	,		20833	0.4643		0.0616	False		,,,				2504	0.2331				p.P633P		Atlas-SNP	.											.	LRRC16B	120	.	0			c.C1899T						PASS	.	C		199,4207	122.1+/-159.5	6,187,2010	154.0	131.0	139.0		1899	-9.1	0.2	14	dbSNP_129	139	474,8126	139.5+/-196.2	11,452,3837	no	coding-synonymous	LRRC16B	NM_138360.3		17,639,5847	TT,TC,CC		5.5116,4.5166,5.1745		633/1373	24529209	673,12333	2203	4300	6503	SO:0001819	synonymous_variant	90668	exon23			CTTCCCCGTGAGC	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.1899C>T	14.37:g.24529209C>T		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	80	79	0.9875	NM_138360	Q8TEF7|Q96HS9	Silent	SNP	ENST00000342740.5	37	CCDS32054.1																																																																																			C|0.908;T|0.092	0.092	strong		0.642	LRRC16B-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416527.1	NM_138360	
TRIML2	205860	hgsc.bcm.edu	37	4	189020293	189020293	+	Silent	SNP	G	G	A	rs11736108	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:189020293G>A	ENST00000512729.1	-	4	741	c.367C>T	c.(367-369)Ctg>Ttg	p.L123L	TRIML2_ENST00000536972.1_Silent_p.L173L|TRIML2_ENST00000326754.3_Silent_p.L123L	NM_173553.1	NP_775824.1	Q8N7C3	TRIMM_HUMAN	tripartite motif family-like 2	123					protein ubiquitination (GO:0016567)|response to retinoic acid (GO:0032526)		ligase activity (GO:0016874)			central_nervous_system(2)|kidney(1)|large_intestine(7)|lung(25)|prostate(3)|urinary_tract(1)	39		all_cancers(14;3.11e-44)|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)|all_hematologic(60;0.0202)|Hepatocellular(41;0.0218)|Renal(120;0.0376)|Prostate(90;0.0513)		OV - Ovarian serous cystadenocarcinoma(60;1.79e-11)|BRCA - Breast invasive adenocarcinoma(30;4.52e-06)|GBM - Glioblastoma multiforme(59;1.62e-05)|STAD - Stomach adenocarcinoma(60;0.000279)|LUSC - Lung squamous cell carcinoma(40;0.0091)|READ - Rectum adenocarcinoma(43;0.163)		CTCTCCTTCAGTTTCTCCATG	0.502													G|||	68	0.0135783	0.003	0.0187	5008	,	,		16412	0.0		0.0457	False		,,,				2504	0.0051				p.L123L		Atlas-SNP	.											.	TRIML2	80	.	0			c.C367T						PASS	.	G		55,4351	52.9+/-88.7	3,49,2151	132.0	130.0	130.0		367	3.9	1.0	4	dbSNP_120	130	457,8143	137.0+/-194.0	15,427,3858	no	coding-synonymous	TRIML2	NM_173553.1		18,476,6009	AA,AG,GG		5.314,1.2483,3.9366		123/388	189020293	512,12494	2203	4300	6503	SO:0001819	synonymous_variant	205860	exon4			CCTTCAGTTTCTC	AK098667	CCDS3850.1	4q35.2	2014-02-12	2007-12-14		ENSG00000179046	ENSG00000179046			26378	protein-coding gene	gene with protein product	"""SPRY domain containing 6"""						Standard	NM_173553		Approved	FLJ25801, SPRYD6	uc003izl.2	Q8N7C3	OTTHUMG00000160225	ENST00000512729.1:c.367C>T	4.37:g.189020293G>A		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	101	50	0.49505	NM_173553	B7Z6J6	Silent	SNP	ENST00000512729.1	37	CCDS3850.1																																																																																			G|0.966;A|0.034	0.034	strong		0.502	TRIML2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000359733.1	NM_173553	
OR6S1	341799	hgsc.bcm.edu	37	14	21109385	21109385	+	Missense_Mutation	SNP	C	C	T	rs11622969	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:21109385C>T	ENST00000320704.3	-	1	465	c.466G>A	c.(466-468)Gtc>Atc	p.V156I		NM_001001968.1	NP_001001968.1	Q8NH40	OR6S1_HUMAN	olfactory receptor, family 6, subfamily S, member 1	156			V -> I (in dbSNP:rs11622969).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			kidney(1)|large_intestine(3)|lung(13)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	23	all_cancers(95;0.00304)		Epithelial(56;1.23e-06)|all cancers(55;1.01e-05)	GBM - Glioblastoma multiforme(265;0.0135)		AGCACAGGGACGAGTCCCCCC	0.612													C|||	2246	0.448482	0.4887	0.5375	5008	,	,		20938	0.252		0.5219	False		,,,				2504	0.4581				p.V156I		Atlas-SNP	.											.	OR6S1	49	.	0			c.G466A						PASS	.	C	ILE/VAL	2247,2159	591.6+/-387.6	552,1143,508	81.0	66.0	71.0		466	-0.8	0.7	14	dbSNP_120	71	4680,3920	602.9+/-394.6	1273,2134,893	yes	missense	OR6S1	NM_001001968.1	29	1825,3277,1401	TT,TC,CC		45.5814,49.0014,46.74	benign	156/332	21109385	6927,6079	2203	4300	6503	SO:0001583	missense	341799	exon1			CAGGGACGAGTCC	AL163636	CCDS32038.1	14q11.2	2013-09-24			ENSG00000181803	ENSG00000181803		"""GPCR / Class A : Olfactory receptors"""	15363	protein-coding gene	gene with protein product							Standard	NM_001001968		Approved	OR6S1Q	uc001vxv.1	Q8NH40	OTTHUMG00000171010	ENST00000320704.3:c.466G>A	14.37:g.21109385C>T	ENSP00000313110:p.Val156Ile	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	75	38	0.506667	NM_001001968	Q6IFJ9	Missense_Mutation	SNP	ENST00000320704.3	37	CCDS32038.1	997	0.4565018315018315	229	0.4654471544715447	212	0.585635359116022	158	0.2762237762237762	398	0.525065963060686	C	4.909	0.168995	0.09339	0.509986	0.544186	ENSG00000181803	ENST00000320704	T	0.37584	1.19	5.76	-0.768	0.11013	GPCR, rhodopsin-like superfamily (1);	0.502259	0.16827	N	0.197918	T	0.00012	0.0000	N	0.10629	0.01	0.80722	P	0.0	B	0.23854	0.092	B	0.20184	0.028	T	0.40572	-0.9556	9	0.54805	T	0.06	-4.6747	2.6503	0.04996	0.1442:0.4007:0.2291:0.226	rs11622969;rs52800855;rs60154084;rs11622969	156	Q8NH40	OR6S1_HUMAN	I	156	ENSP00000313110:V156I	ENSP00000313110:V156I	V	-	1	0	OR6S1	20179225	0.000000	0.05858	0.698000	0.30274	0.050000	0.14768	-1.513000	0.02256	-0.153000	0.11137	-1.114000	0.02060	GTC	C|0.498;T|0.502	0.502	strong		0.612	OR6S1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411227.1		
CCDC88C	440193	hgsc.bcm.edu	37	14	91792320	91792320	+	Silent	SNP	G	G	A	rs17127245	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:91792320G>A	ENST00000389857.6	-	11	1217	c.1131C>T	c.(1129-1131)ggC>ggT	p.G377G		NM_001080414.3	NP_001073883.2	Q9P219	DAPLE_HUMAN	coiled-coil domain containing 88C	377					protein destabilization (GO:0031648)|protein homooligomerization (GO:0051260)|regulation of protein phosphorylation (GO:0001932)|Wnt signaling pathway (GO:0016055)		PDZ domain binding (GO:0030165)|protein self-association (GO:0043621)			central_nervous_system(3)|endometrium(2)|kidney(3)|large_intestine(2)|lung(6)|ovary(6)|pancreas(1)|urinary_tract(1)	24		all_cancers(154;0.0468)				GGACTTTATCGCCCCGGGCCC	0.468													G|||	437	0.0872604	0.0809	0.0346	5008	,	,		18227	0.1438		0.0497	False		,,,				2504	0.1135				p.G377G		Atlas-SNP	.											.	CCDC88C	192	.	0			c.C1131T						PASS	.	G		282,3648		11,260,1694	52.0	51.0	51.0		1131	-10.4	0.0	14	dbSNP_123	51	351,7971		12,327,3822	no	coding-synonymous	CCDC88C	NM_001080414.3		23,587,5516	AA,AG,GG		4.2177,7.1756,5.1665		377/2029	91792320	633,11619	1965	4161	6126	SO:0001819	synonymous_variant	440193	exon11			TTTATCGCCCCGG		CCDS45151.1	14q32.12	2014-07-30	2007-05-31	2007-05-31		ENSG00000015133			19967	protein-coding gene	gene with protein product	"""Dvl-associating protein with a high frequency of leucine residues"", ""spinocerebellar ataxia 40"""	611204	"""KIAA1509"""	KIAA1509		17185515, 25062847	Standard	NM_001080414		Approved	DAPLE, HkRP2, SCA40	uc010aty.3	Q9P219		ENST00000389857.6:c.1131C>T	14.37:g.91792320G>A		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	97	46	0.474227	NM_001080414	Q69YK1|Q7L1M2|Q86SX7|Q8IYG8	Silent	SNP	ENST00000389857.6	37	CCDS45151.1																																																																																			G|0.922;A|0.078	0.078	strong		0.468	CCDC88C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411650.1	XM_029353	
SETD7	80854	hgsc.bcm.edu	37	4	140450204	140450204	+	Silent	SNP	G	G	A	rs35062373	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:140450204G>A	ENST00000274031.3	-	4	1179	c.543C>T	c.(541-543)caC>caT	p.H181H	SETD7_ENST00000506866.2_Silent_p.H181H	NM_030648.2	NP_085151.1	Q8WTS6	SETD7_HUMAN	SET domain containing (lysine methyltransferase) 7	181					chromatin modification (GO:0016568)|peptidyl-lysine dimethylation (GO:0018027)|peptidyl-lysine monomethylation (GO:0018026)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)|p53 binding (GO:0002039)|protein-lysine N-methyltransferase activity (GO:0016279)			central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(1)|ovary(1)|upper_aerodigestive_tract(1)	8	all_hematologic(180;0.156)					TCAGTTCAAAGTGAGGCCTCC	0.448													G|||	106	0.0211661	0.0053	0.0216	5008	,	,		19102	0.0169		0.0288	False		,,,				2504	0.0389				p.H181H		Atlas-SNP	.											.	SETD7	35	.	0			c.C543T						PASS	.	G		42,4364	45.3+/-79.5	0,42,2161	126.0	120.0	122.0		543	4.0	1.0	4	dbSNP_126	122	306,8294	109.8+/-170.3	6,294,4000	no	coding-synonymous	SETD7	NM_030648.2		6,336,6161	AA,AG,GG		3.5581,0.9532,2.6757		181/367	140450204	348,12658	2203	4300	6503	SO:0001819	synonymous_variant	80854	exon4			TTCAAAGTGAGGC	AB051504	CCDS3748.1	4q31.1	2011-07-01			ENSG00000145391	ENSG00000145391		"""Chromatin-modifying enzymes / K-methyltransferases"""	30412	protein-coding gene	gene with protein product		606594				11850410, 11779497	Standard	NM_030648		Approved	KIAA1717, SET7, SET7/9, Set9, KMT7	uc003ihw.3	Q8WTS6	OTTHUMG00000133385	ENST00000274031.3:c.543C>T	4.37:g.140450204G>A		Somatic	207	0	0		WXS	Illumina HiSeq	Phase_I	164	77	0.469512	NM_030648	B5WWL3|Q0VAH3|Q4W5A9|Q9C0E6	Silent	SNP	ENST00000274031.3	37	CCDS3748.1																																																																																			G|0.974;A|0.026	0.026	strong		0.448	SETD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257236.1	NM_030648	
ANKLE1	126549	hgsc.bcm.edu	37	19	17397244	17397244	+	Silent	SNP	C	C	T	rs10425939	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:17397244C>T	ENST00000394458.3	+	9	2007	c.1731C>T	c.(1729-1731)ggC>ggT	p.G577G	ANKLE1_ENST00000404085.1_Silent_p.G573G|ANKLE1_ENST00000598347.1_Missense_Mutation_p.A505V|ANKLE1_ENST00000594072.1_Silent_p.G540G|ANKLE1_ENST00000433424.2_3'UTR	NM_152363.4	NP_689576	Q8NAG6	ANKL1_HUMAN	ankyrin repeat and LEM domain containing 1	577										large_intestine(1)|lung(3)|prostate(1)|skin(1)|urinary_tract(1)	7						TGGTGGCAGGCTGGCCACCTG	0.637													C|||	494	0.0986422	0.1354	0.0908	5008	,	,		15259	0.001		0.163	False		,,,				2504	0.089				p.G577G		Atlas-SNP	.											.	ANKLE1	27	.	0			c.C1731T						PASS	.	C		639,3765	258.6+/-262.5	48,543,1611	37.0	33.0	35.0		1731	2.0	0.5	19	dbSNP_119	35	1581,7013	278.7+/-293.6	156,1269,2872	no	coding-synonymous	ANKLE1	NM_152363.4		204,1812,4483	TT,TC,CC		18.3966,14.5095,17.0796		577/616	17397244	2220,10778	2202	4297	6499	SO:0001819	synonymous_variant	126549	exon9			GGCAGGCTGGCCA	AK096688	CCDS12354.2, CCDS12354.3	19p13.11	2013-01-10	2008-03-25	2008-03-25	ENSG00000160117	ENSG00000160117		"""Ankyrin repeat domain containing"""	26812	protein-coding gene	gene with protein product	"""LEM domain containing 6"""		"""ankyrin repeat domain 41"""	ANKRD41			Standard	NM_152363		Approved	FLJ39369, LEMD6	uc002nga.2	Q8NAG6	OTTHUMG00000150839	ENST00000394458.3:c.1731C>T	19.37:g.17397244C>T		Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	111	52	0.468468	NM_152363	A8VU82|Q8N8J8	Silent	SNP	ENST00000394458.3	37	CCDS12354.2	221	0.10119047619047619	60	0.12195121951219512	35	0.09668508287292818	1	0.0017482517482517483	125	0.16490765171503957	C	10.12	1.261737	0.23051	0.145095	0.183966	ENSG00000160117	ENST00000438921	.	.	.	5.42	2.04	0.26737	.	.	.	.	.	T	0.00073	0.0002	.	.	.	0.09310	P	0.9999999999999992	B	0.27823	0.19	B	0.22386	0.039	T	0.07404	-1.0774	6	0.62326	D	0.03	.	4.6632	0.12652	0.0:0.5771:0.1644:0.2584	rs10425939	505	E7ETZ9	.	V	505	.	ENSP00000415429:A505V	A	+	2	0	ANKLE1	17258244	0.040000	0.19996	0.452000	0.26994	0.978000	0.69477	0.390000	0.20768	0.227000	0.20999	0.491000	0.48974	GCT	C|0.850;T|0.150	0.150	strong		0.637	ANKLE1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000325392.2	NM_152363	
RXFP2	122042	hgsc.bcm.edu	37	13	32360547	32360547	+	Silent	SNP	A	A	G	rs7325513	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:32360547A>G	ENST00000298386.2	+	12	1028	c.957A>G	c.(955-957)gaA>gaG	p.E319E	RXFP2_ENST00000380314.1_Silent_p.E295E	NM_130806.3	NP_570718.1	Q8WXD0	RXFP2_HUMAN	relaxin/insulin-like family peptide receptor 2	319					adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|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)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	peptide hormone binding (GO:0017046)|protein-hormone receptor activity (GO:0016500)			cervix(1)|endometrium(2)|large_intestine(15)|lung(13)|prostate(1)|stomach(1)	33		Lung SC(185;0.0262)		all cancers(112;0.000559)|Epithelial(112;0.0017)|OV - Ovarian serous cystadenocarcinoma(117;0.0145)|BRCA - Breast invasive adenocarcinoma(63;0.0535)		CGATAACGGAACTATCACCTC	0.353													G|||	3174	0.633786	0.6044	0.5072	5008	,	,		18811	0.7758		0.5676	False		,,,				2504	0.6851				p.E319E		Atlas-SNP	.											.	RXFP2	95	.	0			c.A957G						PASS	.	G	,	2721,1685	510.9+/-367.7	843,1035,325	115.0	105.0	109.0		885,957	2.9	1.0	13	dbSNP_116	109	5153,3447	505.3+/-376.3	1548,2057,695	no	coding-synonymous,coding-synonymous	RXFP2	NM_001166058.1,NM_130806.3	,	2391,3092,1020	GG,GA,AA		40.0814,38.2433,39.4587	,	295/731,319/755	32360547	7874,5132	2203	4300	6503	SO:0001819	synonymous_variant	122042	exon12			AACGGAACTATCA	AF403384	CCDS9342.1, CCDS53862.1	13q12.3	2012-08-08	2006-05-09	2006-05-09	ENSG00000133105	ENSG00000133105		"""GPCR / Class A : Relaxin family peptide receptors"""	17318	protein-coding gene	gene with protein product		606655	"""leucine-rich repeat-containing G protein-coupled receptor 8"""	LGR8		12217959, 12970298, 15956688, 16507880	Standard	NM_130806		Approved	GREAT, GPR106, INSL3R, RXFPR2	uc001utt.3	Q8WXD0	OTTHUMG00000016690	ENST00000298386.2:c.957A>G	13.37:g.32360547A>G		Somatic	190	0	0		WXS	Illumina HiSeq	Phase_I	147	69	0.469388	NM_130806	B1ALE9|Q3KU23	Silent	SNP	ENST00000298386.2	37	CCDS9342.1																																																																																			A|0.387;G|0.613	0.613	strong		0.353	RXFP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000044399.1	NM_130806	
TUT1	64852	hgsc.bcm.edu	37	11	62343141	62343141	+	Missense_Mutation	SNP	C	C	T	rs369889181		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:62343141C>T	ENST00000476907.1	-	9	2741	c.2050G>A	c.(2050-2052)Ggt>Agt	p.G684S	EEF1G_ENST00000329251.4_5'Flank|EEF1G_ENST00000532986.1_5'Flank|EEF1G_ENST00000378019.3_5'Flank|MIR3654_ENST00000496634.2_Intron|TUT1_ENST00000308436.7_Missense_Mutation_p.G722S			Q9H6E5	STPAP_HUMAN	terminal uridylyl transferase 1, U6 snRNA-specific	684					mRNA cleavage (GO:0006379)|mRNA polyadenylation (GO:0006378)|snRNA processing (GO:0016180)	intercellular bridge (GO:0045171)|nuclear speck (GO:0016607)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|metal ion binding (GO:0046872)|mRNA 3'-UTR binding (GO:0003730)|polynucleotide adenylyltransferase activity (GO:0004652)|RNA binding (GO:0003723)|RNA uridylyltransferase activity (GO:0050265)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(3)|lung(15)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	29						TCTTCCCCACCGTCCCCTGCA	0.577																																					p.G722S		Atlas-SNP	.											.	TUT1	122	.	0			c.G2164A						PASS	.						455.0	441.0	446.0					11																	62343141		2202	4299	6501	SO:0001583	missense	64852	exon9			CCCCACCGTCCCC	BC005013	CCDS8021.1, CCDS8021.2	11q12.2	2014-03-05	2006-10-06	2006-10-06	ENSG00000149016	ENSG00000149016	2.7.7.52	"""RNA binding motif (RRM) containing"""	26184	protein-coding gene	gene with protein product	"""RNA uridylyltransferase"", ""U6 TUTase"", ""TUTase 6"""	610641	"""RNA binding motif protein 21"""	RBM21		16790842	Standard	NM_022830		Approved	FLJ22347, FLJ22267, FLJ21850, PAPD2, TUTase	uc001nto.2	Q9H6E5	OTTHUMG00000158564	ENST00000476907.1:c.2050G>A	11.37:g.62343141C>T	ENSP00000419607:p.Gly684Ser	Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	133	111	0.834586	NM_022830	A1A527|A8K995|Q2NL65|Q7L583|Q9H6H7	Missense_Mutation	SNP	ENST00000476907.1	37		.	.	.	.	.	.	.	.	.	.	C	2.734	-0.263855	0.05754	.	.	ENSG00000149016	ENST00000308436;ENST00000476907	T;T	0.34859	1.34;1.35	5.63	2.54	0.30619	.	1.415740	0.03776	N	0.260632	T	0.24314	0.0589	N	0.14661	0.345	0.09310	N	1	B;B	0.12013	0.005;0.005	B;B	0.06405	0.001;0.002	T	0.18745	-1.0327	10	0.17369	T	0.5	-2.5756	10.007	0.41964	0.0:0.2926:0.5678:0.1396	.	684;722	Q9H6E5;F5H0R1	STPAP_HUMAN;.	S	722;684	ENSP00000308000:G722S;ENSP00000419607:G684S	ENSP00000308000:G722S	G	-	1	0	TUT1	62099717	0.003000	0.15002	0.003000	0.11579	0.011000	0.07611	1.233000	0.32648	0.723000	0.32274	-0.165000	0.13383	GGT	.	.	none		0.577	TUT1-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000351319.2	NM_022830	
ANPEP	290	hgsc.bcm.edu	37	15	90349558	90349558	+	Missense_Mutation	SNP	C	C	T	rs25653	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:90349558C>T	ENST00000300060.6	-	2	570	c.257G>A	c.(256-258)cGg>cAg	p.R86Q		NM_001150.2	NP_001141.2	P15144	AMPN_HUMAN	alanyl (membrane) aminopeptidase	86	Metalloprotease.		R -> Q (in dbSNP:rs25653). {ECO:0000269|PubMed:2564851, ECO:0000269|PubMed:2901990, ECO:0000269|Ref.6}.		angiogenesis (GO:0001525)|angiotensin maturation (GO:0002003)|cell differentiation (GO:0030154)|cellular protein metabolic process (GO:0044267)|viral process (GO:0016032)	endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|receptor activity (GO:0004872)|virus receptor activity (GO:0001618)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|liver(1)|lung(20)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(3)	57	Lung NSC(78;0.0221)|all_lung(78;0.0448)		BRCA - Breast invasive adenocarcinoma(143;0.0146)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.169)		Ezetimibe(DB00973)|Icatibant(DB06196)	CAGCGTCACCCGGTAGGAATC	0.607													T|||	2900	0.579073	0.8986	0.3948	5008	,	,		19374	0.4861		0.5169	False		,,,				2504	0.4376				p.R86Q	NSCLC(30;827 977 2459 19669 26125)	Atlas-SNP	.											.	ANPEP	124	.	0			c.G257A						PASS	.	T	GLN/ARG	3726,674	284.0+/-277.4	1578,570,52	121.0	97.0	105.0		257	-5.4	0.0	15	dbSNP_72	105	4515,4083	560.3+/-387.6	1189,2137,973	yes	missense	ANPEP	NM_001150.2	43	2767,2707,1025	TT,TC,CC		47.4878,15.3182,36.5979	benign	86/968	90349558	8241,4757	2200	4299	6499	SO:0001583	missense	290	exon2			GTCACCCGGTAGG	M22324	CCDS10356.1	15q25-q26	2008-07-31	2008-07-31		ENSG00000166825	ENSG00000166825	3.4.11.2	"""CD molecules"""	500	protein-coding gene	gene with protein product	"""aminopeptidase N"", ""aminopeptidase M"", ""microsomal aminopeptidase"""	151530		CD13, PEPN		2428842, 1977688	Standard	NM_001150		Approved	LAP1, gp150, p150	uc002bop.4	P15144	OTTHUMG00000149814	ENST00000300060.6:c.257G>A	15.37:g.90349558C>T	ENSP00000300060:p.Arg86Gln	Somatic	225	0	0		WXS	Illumina HiSeq	Phase_I	201	127	0.631841	NM_001150	Q16728|Q6GT90|Q8IUK3|Q8IVH3|Q9UCE0	Missense_Mutation	SNP	ENST00000300060.6	37	CCDS10356.1	1294	0.5924908424908425	446	0.9065040650406504	162	0.44751381215469616	281	0.49125874125874125	405	0.5343007915567283	T	7.027	0.559778	0.13436	0.846818	0.525122	ENSG00000166825	ENST00000300060	T	0.04234	3.67	4.74	-5.37	0.02681	Peptidase M1, membrane alanine aminopeptidase, N-terminal (1);	1.230460	0.05459	N	0.550827	T	0.00012	0.0000	N	0.10760	0.04	0.80722	P	0.0	B	0.02656	0.0	B	0.09377	0.004	T	0.14035	-1.0487	9	0.33141	T	0.24	.	7.5308	0.27681	0.0:0.4116:0.1755:0.4129	rs25653;rs59164325;rs25653	86	P15144	AMPN_HUMAN	Q	86	ENSP00000300060:R86Q	ENSP00000300060:R86Q	R	-	2	0	ANPEP	88150562	0.000000	0.05858	0.006000	0.13384	0.261000	0.26267	-0.405000	0.07196	-0.826000	0.04284	-0.516000	0.04426	CGG	C|0.373;T|0.627	0.627	strong		0.607	ANPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313425.1		
TTC28	23331	hgsc.bcm.edu	37	22	28504183	28504183	+	Silent	SNP	G	G	A	rs9625408	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:28504183G>A	ENST00000397906.2	-	7	1791	c.1650C>T	c.(1648-1650)cgC>cgT	p.R550R		NM_001145418.1	NP_001138890.1	Q96AY4	TTC28_HUMAN	tetratricopeptide repeat domain 28	550					mitotic nuclear division (GO:0007067)|regulation of mitotic cell cycle (GO:0007346)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|midbody (GO:0030496)				endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)	12						CCTGTGAGGCGCGGTCATTCA	0.582													G|||	276	0.0551118	0.0439	0.0677	5008	,	,		16746	0.003		0.0746	False		,,,				2504	0.0951				p.R550R		Atlas-SNP	.											.	TTC28	84	.	0			c.C1650T						PASS	.	G		73,1311		0,73,619	84.0	80.0	81.0		1650	-11.8	0.4	22	dbSNP_119	81	264,2918		15,234,1342	no	coding-synonymous	TTC28	NM_001145418.1		15,307,1961	AA,AG,GG		8.2967,5.2746,7.3806		550/2482	28504183	337,4229	692	1591	2283	SO:0001819	synonymous_variant	23331	exon7			TGAGGCGCGGTCA	AB028966	CCDS46678.1	22q12.1	2013-01-10			ENSG00000100154	ENSG00000100154		"""Tetratricopeptide (TTC) repeat domain containing"""	29179	protein-coding gene	gene with protein product		615098				10470851	Standard	NM_001145418		Approved	KIAA1043	uc003adp.4	Q96AY4	OTTHUMG00000151006	ENST00000397906.2:c.1650C>T	22.37:g.28504183G>A		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	117	57	0.487179	NM_001145418	K7ZRV2|O95928|O95929|Q5W189|Q9NTE4|Q9UG31|Q9UGG5|Q9UPV8|Q9Y3S5	Silent	SNP	ENST00000397906.2	37	CCDS46678.1																																																																																			G|0.949;A|0.051	0.051	strong		0.582	TTC28-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000320930.2	XM_929318	
KRTAP10-2	386679	hgsc.bcm.edu	37	21	45971152	45971152	+	Missense_Mutation	SNP	G	G	A	rs199607801	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:45971152G>A	ENST00000391621.1	-	1	236	c.190C>T	c.(190-192)Ccc>Tcc	p.P64S	TSPEAR_ENST00000397916.1_Intron|TSPEAR_ENST00000323084.4_Intron|KRTAP10-2_ENST00000498210.1_Intron	NM_198693.2	NP_941966.1	P60368	KR102_HUMAN	keratin associated protein 10-2	64	22 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				large_intestine(1)|lung(4)|skin(1)	6						CAGGCGCTGGGCTCACAGGCC	0.706																																					p.P64S		Atlas-SNP	.											KRTAP10-2,colon,carcinoma,0,1	KRTAP10-2	21	1	0			c.C190T						scavenged	.						33.0	39.0	37.0					21																	45971152		2198	4287	6485	SO:0001583	missense	386679	exon1			CGCTGGGCTCACA	AJ566381	CCDS42955.1	21q22.3	2007-10-05			ENSG00000205445	ENSG00000205445		"""Keratin associated proteins"""	22967	protein-coding gene	gene with protein product				KRTAP18-2			Standard	NM_198693		Approved	KAP10.2, KAP18.2	uc002zfi.1	P60368	OTTHUMG00000057625	ENST00000391621.1:c.190C>T	21.37:g.45971152G>A	ENSP00000375479:p.Pro64Ser	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	142	41	0.288732	NM_198693	Q70LJ5	Missense_Mutation	SNP	ENST00000391621.1	37	CCDS42955.1	.	.	.	.	.	.	.	.	.	.	g	0.927	-0.713936	0.03206	.	.	ENSG00000205445	ENST00000391621	T	0.00672	5.89	2.06	-0.231	0.13086	.	.	.	.	.	T	0.00552	0.0018	N	0.13140	0.3	0.09310	N	1	B	0.20164	0.042	B	0.10450	0.005	T	0.44982	-0.9292	9	0.33940	T	0.23	.	5.0625	0.14564	0.3226:0.0:0.6774:0.0	.	64	P60368	KR102_HUMAN	S	64	ENSP00000375479:P64S	ENSP00000375479:P64S	P	-	1	0	KRTAP10-2	44795580	0.000000	0.05858	0.165000	0.22776	0.031000	0.12232	-0.338000	0.07842	-0.390000	0.07774	0.306000	0.20318	CCC	G|0.978;A|0.022	0.022	strong		0.706	KRTAP10-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128027.1		
ANKRD30A	91074	hgsc.bcm.edu	37	10	37442545	37442545	+	Missense_Mutation	SNP	G	G	T	rs200557667		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:37442545G>T	ENST00000602533.1	+	13	1684	c.1585G>T	c.(1585-1587)Gct>Tct	p.A529S	ANKRD30A_ENST00000361713.1_Missense_Mutation_p.A529S|ANKRD30A_ENST00000374660.1_Missense_Mutation_p.A529S			Q9BXX3	AN30A_HUMAN	ankyrin repeat domain 30A	585					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						TTTACCCAAGGCTACACATCA	0.294																																					p.A529S		Atlas-SNP	.											ANKRD30A,NS,carcinoma,0,1	ANKRD30A	448	1	0			c.G1585T						scavenged	.	G	SER/ALA	2,3602		0,2,1800	149.0	148.0	149.0		1585	1.5	0.0	10		149	7,8129		0,7,4061	no	missense	ANKRD30A	NM_052997.2	99	0,9,5861	TT,TG,GG		0.086,0.0555,0.0767	possibly-damaging	529/1342	37442545	9,11731	1802	4068	5870	SO:0001583	missense	91074	exon13			CCCAAGGCTACAC	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.1585G>T	10.37:g.37442545G>T	ENSP00000473551:p.Ala529Ser	Somatic	779	0	0		WXS	Illumina HiSeq	Phase_I	714	132	0.184874	NM_052997	Q5W025	Missense_Mutation	SNP	ENST00000602533.1	37		.	.	.	.	.	.	.	.	.	.	.	10.35	1.325943	0.24080	5.55E-4	8.6E-4	ENSG00000148513	ENST00000361713;ENST00000374660	T;T	0.08458	3.09;3.09	1.47	1.47	0.22746	.	.	.	.	.	T	0.13841	0.0335	L	0.34521	1.04	0.09310	N	1	D	0.58970	0.984	D	0.65443	0.935	T	0.18429	-1.0337	9	0.39692	T	0.17	.	6.4351	0.21819	0.0:0.0:1.0:0.0	.	585	Q9BXX3	AN30A_HUMAN	S	529	ENSP00000354432:A529S;ENSP00000363792:A529S	ENSP00000354432:A529S	A	+	1	0	ANKRD30A	37482551	0.001000	0.12720	0.015000	0.15790	0.022000	0.10575	0.229000	0.17833	1.140000	0.42260	0.384000	0.25694	GCT	G|0.999;T|0.001	0.001	weak		0.294	ANKRD30A-001	KNOWN	NMD_exception|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000047588.2	NM_052997	
TEKT5	146279	hgsc.bcm.edu	37	16	10788624	10788624	+	Missense_Mutation	SNP	T	T	C	rs145995713	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:10788624T>C	ENST00000283025.2	-	1	178	c.107A>G	c.(106-108)tAt>tGt	p.Y36C	RP11-109M19.1_ENST00000576710.1_RNA	NM_144674.1	NP_653275.1	Q96M29	TEKT5_HUMAN	tektin 5	36						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						GTAGGGCTGATAGCATTCCTG	0.562													T|||	19	0.00379393	0.0	0.0043	5008	,	,		17761	0.0		0.0119	False		,,,				2504	0.0041				p.Y36C		Atlas-SNP	.											.	TEKT5	66	.	0			c.A107G						PASS	.	T	CYS/TYR	3,4391		0,3,2194	79.0	74.0	75.0		107	5.3	1.0	16	dbSNP_134	75	73,8527		0,73,4227	yes	missense	TEKT5	NM_144674.1	194	0,76,6421	CC,CT,TT		0.8488,0.0683,0.5849	probably-damaging	36/486	10788624	76,12918	2197	4300	6497	SO:0001583	missense	146279	exon1			GGCTGATAGCATT		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.107A>G	16.37:g.10788624T>C	ENSP00000283025:p.Tyr36Cys	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	69	56	0.811594	NM_144674	A1L3Z3	Missense_Mutation	SNP	ENST00000283025.2	37	CCDS10542.1	13	0.005952380952380952	0	0.0	2	0.0055248618784530384	0	0.0	11	0.014511873350923483	.	11.16	1.557014	0.27827	6.83E-4	0.008488	ENSG00000153060	ENST00000283025	T	0.03212	4.01	5.29	5.29	0.74685	.	0.000000	0.56097	D	0.000032	T	0.08846	0.0219	M	0.72894	2.215	0.49483	D	0.999795	D	0.69078	0.997	D	0.63192	0.912	T	0.01356	-1.1376	10	0.39692	T	0.17	-39.6857	8.7187	0.34428	0.0:0.0854:0.0:0.9146	.	36	Q96M29	TEKT5_HUMAN	C	36	ENSP00000283025:Y36C	ENSP00000283025:Y36C	Y	-	2	0	TEKT5	10696125	1.000000	0.71417	1.000000	0.80357	0.389000	0.30415	1.922000	0.40045	1.992000	0.58205	0.533000	0.62120	TAT	T|0.994;C|0.006	0.006	strong		0.562	TEKT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251963.1	NM_144674	
CCP110	9738	hgsc.bcm.edu	37	16	19548116	19548116	+	Missense_Mutation	SNP	G	G	A	rs7190666	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:19548116G>A	ENST00000381396.5	+	4	1372	c.1125G>A	c.(1123-1125)atG>atA	p.M375I	CCP110_ENST00000396208.2_Missense_Mutation_p.M375I|CCP110_ENST00000396212.2_Missense_Mutation_p.M375I	NM_001199022.1	NP_001185951	O43303	CP110_HUMAN	centriolar coiled coil protein 110kDa	375	Interaction with CEP76.		M -> I (in dbSNP:rs7190666).		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						GTCCTAAAATGCACCGAAGAC	0.378													G|||	780	0.155751	0.1725	0.1844	5008	,	,		21808	0.1587		0.1581	False		,,,				2504	0.1074				p.M375I		Atlas-SNP	.											.	CCP110	57	.	0			c.G1125A						PASS	.	G	ILE/MET,ILE/MET	696,3696	276.6+/-273.2	49,598,1549	56.0	56.0	56.0		1125,1125	4.0	1.0	16	dbSNP_116	56	1341,7259	254.8+/-279.9	101,1139,3060	yes	missense,missense	CCP110	NM_001199022.1,NM_014711.4	10,10	150,1737,4609	AA,AG,GG		15.593,15.847,15.6789	probably-damaging,probably-damaging	375/1013,375/992	19548116	2037,10955	2196	4300	6496	SO:0001583	missense	9738	exon4			TAAAATGCACCGA	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.1125G>A	16.37:g.19548116G>A	ENSP00000370803:p.Met375Ile	Somatic	284	0	0		WXS	Illumina HiSeq	Phase_I	306	121	0.395425	NM_001199022	B7WP23|O43335|Q68DV9|Q8NE13	Missense_Mutation	SNP	ENST00000381396.5	37	CCDS55992.1	378	0.17307692307692307	80	0.16260162601626016	74	0.20441988950276244	110	0.19230769230769232	114	0.1503957783641161	G	18.86	3.714216	0.68730	0.15847	0.15593	ENSG00000103540	ENST00000396212;ENST00000381396;ENST00000396208	T;T;T	0.19806	2.12;2.12;2.12	6.07	4.02	0.46733	.	0.049908	0.85682	N	0.000000	T	0.00039	0.0001	L	0.59436	1.845	0.23585	P	0.99735991	D;D	0.71674	0.998;0.998	D;D	0.78314	0.991;0.991	T	0.01993	-1.1233	9	0.72032	D	0.01	-7.9835	15.5763	0.76392	0.0:0.0:0.7493:0.2507	rs7190666;rs57463792;rs7190666	375;375	O43303;O43303-2	CP110_HUMAN;.	I	375	ENSP00000379515:M375I;ENSP00000370803:M375I;ENSP00000379511:M375I	ENSP00000370803:M375I	M	+	3	0	CCP110	19455617	1.000000	0.71417	1.000000	0.80357	0.949000	0.60115	4.303000	0.59098	1.526000	0.49068	0.655000	0.94253	ATG	G|0.843;A|0.157	0.157	strong		0.378	CCP110-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254284.2	NM_014711	
SERPINA5	5104	hgsc.bcm.edu	37	14	95053849	95053849	+	Silent	SNP	T	T	C	rs6113	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:95053849T>C	ENST00000554866.1	+	2	264	c.150T>C	c.(148-150)ttT>ttC	p.F50F	SERPINA5_ENST00000554276.1_Silent_p.F50F|SERPINA5_ENST00000553780.1_Silent_p.F50F|SERPINA5_ENST00000329597.7_Silent_p.F50F			P05154	IPSP_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 5	50					fusion of sperm to egg plasma membrane (GO:0007342)|lipid transport (GO:0006869)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of proteolysis (GO:0045861)|regulation of proteolysis (GO:0030162)|spermatogenesis (GO:0007283)	acrosomal membrane (GO:0002080)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|platelet alpha granule (GO:0031091)|platelet dense tubular network (GO:0031094)|protein C inhibitor-coagulation factor V complex (GO:0097181)|protein C inhibitor-coagulation factor Xa complex (GO:0097182)|protein C inhibitor-coagulation factor XI complex (GO:0097183)|protein C inhibitor-KLK3 complex (GO:0036029)|protein C inhibitor-plasma kallikrein complex (GO:0036030)|protein C inhibitor-PLAT complex (GO:0036026)|protein C inhibitor-PLAU complex (GO:0036027)|protein C inhibitor-thrombin complex (GO:0036028)|protein C inhibitor-TMPRSS11E complex (GO:0036025)|protein C inhibitor-TMPRSS7 complex (GO:0036024)|protein complex (GO:0043234)	acrosin binding (GO:0032190)|glycosaminoglycan binding (GO:0005539)|heparin binding (GO:0008201)|phosphatidylcholine binding (GO:0031210)|protease binding (GO:0002020)|retinoic acid binding (GO:0001972)|serine-type endopeptidase inhibitor activity (GO:0004867)			endometrium(3)|large_intestine(5)|lung(18)|ovary(2)|skin(5)|upper_aerodigestive_tract(3)	36				COAD - Colon adenocarcinoma(157;0.21)	Drotrecogin alfa(DB00055)|Urokinase(DB00013)	ACTTTACCTTTGACCTCTACA	0.627													C|||	1378	0.27516	0.6157	0.1182	5008	,	,		18499	0.2798		0.0905	False		,,,				2504	0.1115				p.F50F		Atlas-SNP	.											.	SERPINA5	69	.	0			c.T150C						PASS	.	C		2249,2157	580.2+/-385.1	575,1099,529	47.0	44.0	45.0		150	-8.1	0.0	14	dbSNP_52	45	817,7783	780.7+/-407.7	41,735,3524	no	coding-synonymous	SERPINA5	NM_000624.4		616,1834,4053	CC,CT,TT		9.5,48.956,23.5737		50/407	95053849	3066,9940	2203	4300	6503	SO:0001819	synonymous_variant	5104	exon3			TACCTTTGACCTC	M68516	CCDS9928.1	14q32.1	2014-02-18	2005-08-18		ENSG00000188488	ENSG00000188488		"""Serine (or cysteine) peptidase inhibitors"""	8723	protein-coding gene	gene with protein product		601841	"""serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 5"""	PLANH3, PCI		1714450, 8381582, 24172014	Standard	NM_000624		Approved	PAI3, PROCI	uc001ydm.3	P05154	OTTHUMG00000170860	ENST00000554866.1:c.150T>C	14.37:g.95053849T>C		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	50	21	0.42	NM_000624	Q07616|Q9UG30	Silent	SNP	ENST00000554866.1	37	CCDS9928.1																																																																																			C|0.249;N|0.000	0.249	strong		0.627	SERPINA5-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410726.1	NM_000624	
KIF27	55582	hgsc.bcm.edu	37	9	86504005	86504005	+	Missense_Mutation	SNP	C	C	T	rs13289566	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:86504005C>T	ENST00000297814.2	-	7	2116	c.1973G>A	c.(1972-1974)gGa>gAa	p.G658E	KIF27_ENST00000413982.1_Missense_Mutation_p.G658E|KIF27_ENST00000376347.1_Missense_Mutation_p.G49E|KIF27_ENST00000334204.2_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	114	0	0		WXS	Illumina HiSeq	Phase_I	117	42	0.358974	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	
MFHAS1	9258	hgsc.bcm.edu	37	8	8748686	8748686	+	Missense_Mutation	SNP	C	C	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:8748686C>G	ENST00000276282.6	-	1	2469	c.1883G>C	c.(1882-1884)aGc>aCc	p.S628T		NM_004225.2	NP_004216.2	Q9Y4C4	MFHA1_HUMAN	malignant fibrous histiocytoma amplified sequence 1	628	Roc. {ECO:0000255|PROSITE- ProRule:PRU00758}.									endometrium(1)|kidney(3)|large_intestine(7)|lung(6)|ovary(1)|prostate(2)|stomach(1)	21		Hepatocellular(245;0.217)		COAD - Colon adenocarcinoma(149;0.124)		GTCCCTGCAGCTAACAGGCAA	0.567																																					p.S628T	Melanoma(103;1201 2045 17515 28966)	Atlas-SNP	.											.	MFHAS1	58	.	0			c.G1883C						PASS	.						75.0	63.0	67.0					8																	8748686		2203	4300	6503	SO:0001583	missense	9258	exon1			CTGCAGCTAACAG	AB016816	CCDS34844.1	8p23.1	2014-03-07			ENSG00000147324	ENSG00000147324			16982	protein-coding gene	gene with protein product	"""leucine rich repeat containing 65"", ""malignant fibrous histiocytoma-amplified sequences with leucine-rich tandem repeats 1"""	605352				9973190	Standard	NM_004225		Approved	MASL1, LRRC65	uc003wsj.1	Q9Y4C4	OTTHUMG00000163676	ENST00000276282.6:c.1883G>C	8.37:g.8748686C>G	ENSP00000276282:p.Ser628Thr	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	39	15	0.384615	NM_004225	Q96CI0	Missense_Mutation	SNP	ENST00000276282.6	37	CCDS34844.1	.	.	.	.	.	.	.	.	.	.	C	15.29	2.789423	0.49997	.	.	ENSG00000147324	ENST00000276282	D	0.91295	-2.82	5.28	5.28	0.74379	ROC GTPase (1);	0.051489	0.85682	N	0.000000	D	0.90728	0.7090	M	0.71036	2.16	0.58432	D	0.999998	B	0.27791	0.189	B	0.30179	0.112	D	0.89321	0.3640	10	0.66056	D	0.02	.	18.0901	0.89472	0.0:1.0:0.0:0.0	.	628	Q9Y4C4	MFHA1_HUMAN	T	628	ENSP00000276282:S628T	ENSP00000276282:S628T	S	-	2	0	MFHAS1	8786096	1.000000	0.71417	0.992000	0.48379	0.715000	0.41141	7.591000	0.82666	2.736000	0.93811	0.655000	0.94253	AGC	.	.	none		0.567	MFHAS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374724.2	NM_004225	
TTN	7273	hgsc.bcm.edu	37	2	179432185	179432185	+	Missense_Mutation	SNP	A	A	G	rs12463674	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:179432185A>G	ENST00000591111.1	-	276	73975	c.73751T>C	c.(73750-73752)aTt>aCt	p.I24584T	TTN-AS1_ENST00000438095.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.I17285T|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.I23657T|TTN-AS1_ENST00000586452.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.I17160T|TTN-AS1_ENST00000591332.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.I26225T|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.I17352T|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590932.1_RNA			Q8WZ42	TITIN_HUMAN	titin	24584	Ig-like 122.		I -> T. {ECO:0000269|PubMed:17344846}.		adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TAACCACTCAATGGTAGGTAG	0.368													A|||	651	0.129992	0.0053	0.1124	5008	,	,		22267	0.0427		0.3091	False		,,,				2504	0.2168				p.I26225T		Atlas-SNP	.											.	TTN	18412	.	0			c.T78674C						PASS	.	A	THR/ILE,THR/ILE,THR/ILE,THR/ILE	200,3480		5,190,1645	102.0	98.0	99.0		51479,70970,51854,52055	5.7	1.0	2	dbSNP_120	99	2480,5706		365,1750,1978	yes	missense,missense,missense,missense	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	89,89,89,89	370,1940,3623	GG,GA,AA		30.2956,5.4348,22.5855	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	17160/26927,23657/33424,17285/27052,17352/27119	179432185	2680,9186	1840	4093	5933	SO:0001583	missense	7273	exon326			CACTCAATGGTAG	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.73751T>C	2.37:g.179432185A>G	ENSP00000465570:p.Ile24584Thr	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	84	39	0.464286	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	
ZFPM1	161882	hgsc.bcm.edu	37	16	88599659	88599659	+	Missense_Mutation	SNP	G	G	T	rs71395304	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:88599659G>T	ENST00000319555.3	+	10	1615	c.1293G>T	c.(1291-1293)aaG>aaT	p.K431N	RP11-21B21.4_ENST00000563243.1_RNA	NM_153813.2	NP_722520.2	Q8IX07	FOG1_HUMAN	zinc finger protein, FOG family member 1	431					atrial septum morphogenesis (GO:0060413)|atrioventricular valve morphogenesis (GO:0003181)|blood coagulation (GO:0007596)|cardiac muscle tissue morphogenesis (GO:0055008)|definitive erythrocyte differentiation (GO:0060318)|embryonic hemopoiesis (GO:0035162)|erythrocyte differentiation (GO:0030218)|granulocyte differentiation (GO:0030851)|megakaryocyte development (GO:0035855)|megakaryocyte differentiation (GO:0030219)|mitral valve formation (GO:0003192)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of interleukin-4 biosynthetic process (GO:0045403)|negative regulation of mast cell differentiation (GO:0060377)|negative regulation of protein binding (GO:0032091)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|outflow tract morphogenesis (GO:0003151)|platelet formation (GO:0030220)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|primitive erythrocyte differentiation (GO:0060319)|regulation of chemokine production (GO:0032642)|regulation of definitive erythrocyte differentiation (GO:0010724)|T-helper cell lineage commitment (GO:0002295)|transcriptional activation by promoter-enhancer looping (GO:0071733)|tricuspid valve formation (GO:0003195)|ventricular septum morphogenesis (GO:0060412)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|transcription factor complex (GO:0005667)|transcriptional repressor complex (GO:0017053)	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)|RNA polymerase II transcription factor binding (GO:0001085)|transcription factor binding (GO:0008134)			central_nervous_system(1)|ovary(2)|urinary_tract(1)	4				BRCA - Breast invasive adenocarcinoma(80;0.0478)		TGGACAGAAAGGCCCTGGCCG	0.721													G|||	612	0.122204	0.0091	0.1398	5008	,	,		9175	0.3294		0.0915	False		,,,				2504	0.0808				p.K431N	Pancreas(49;850 1106 29641 32847 38344)	Atlas-SNP	.											.	ZFPM1	32	.	0			c.G1293T						PASS	.	G	ASN/LYS	61,3871		0,61,1905	4.0	5.0	4.0		1293	-1.2	0.1	16	dbSNP_130	4	544,7434		10,524,3455	yes	missense	ZFPM1	NM_153813.2	94	10,585,5360	TT,TG,GG		6.8188,1.5514,5.0798	probably-damaging	431/1007	88599659	605,11305	1966	3989	5955	SO:0001583	missense	161882	exon10			CAGAAAGGCCCTG	AF488691	CCDS32502.1	16q24.2	2013-01-10	2012-11-27		ENSG00000179588	ENSG00000179588		"""Zinc fingers, C2H2-type"", ""Zinc fingers, C2HC-type containing"""	19762	protein-coding gene	gene with protein product		601950	"""zinc finger protein, multitype 1"""				Standard	NM_153813		Approved	FOG1, FOG, ZNF89A, ZC2HC11A	uc002fkv.3	Q8IX07	OTTHUMG00000173152	ENST00000319555.3:c.1293G>T	16.37:g.88599659G>T	ENSP00000326630:p.Lys431Asn	Somatic	6	0	0		WXS	Illumina HiSeq	Phase_I	20	20	1	NM_153813		Missense_Mutation	SNP	ENST00000319555.3	37	CCDS32502.1	308	0.14102564102564102	9	0.018292682926829267	49	0.13535911602209943	192	0.3356643356643357	58	0.07651715039577836	G	10.12	1.262467	0.23051	0.015514	0.068188	ENSG00000179588	ENST00000319555	T	0.08008	3.14	3.39	-1.17	0.09648	.	1.163550	0.06454	U	0.728227	T	0.00012	0.0000	L	0.60455	1.87	0.40357	P	0.02080599999999999	D	0.69078	0.997	P	0.57911	0.829	T	0.41161	-0.9524	9	0.42905	T	0.14	-7.9024	6.4423	0.21856	0.5249:0.0:0.4751:0.0	.	431	Q8IX07	FOG1_HUMAN	N	431	ENSP00000326630:K431N	ENSP00000326630:K431N	K	+	3	2	ZFPM1	87127160	0.522000	0.26266	0.089000	0.20774	0.599000	0.36880	0.335000	0.19806	-0.105000	0.12132	0.289000	0.19496	AAG	G|0.858;T|0.142	0.142	strong		0.721	ZFPM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422270.2		
FARSA	2193	hgsc.bcm.edu	37	19	13035006	13035006	+	Silent	SNP	G	G	A	rs1045913	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	51	0	0		WXS	Illumina HiSeq	Phase_I	33	20	0.606061	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	
NUP62	23636	hgsc.bcm.edu	37	19	50412516	50412516	+	Silent	SNP	C	C	T	rs1984656	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:50412516C>T	ENST00000596217.1	-	2	2436	c.549G>A	c.(547-549)acG>acA	p.T183T	NUP62_ENST00000600583.1_5'Flank|NUP62_ENST00000422090.2_Silent_p.T183T|NUP62_ENST00000413454.1_Silent_p.T183T|IL4I1_ENST00000341114.3_Intron|NUP62_ENST00000597723.1_Silent_p.T183T|NUP62_ENST00000352066.3_Silent_p.T183T|IL4I1_ENST00000595948.1_Intron|NUP62_ENST00000597029.1_Silent_p.T183T			P37198	NUP62_HUMAN	nucleoporin 62kDa	183	15 X 9 AA approximate repeats.|Ala-rich.|Thr-rich.				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)		TGGCAGGTGCCGTGGGCTGGG	0.627													C|||	109	0.0217652	0.0613	0.0245	5008	,	,		14325	0.0		0.0099	False		,,,				2504	0.001				p.T183T		Atlas-SNP	.											.	NUP62	50	.	0			c.G549A						PASS	.	C	,,,,,	196,4210	122.5+/-159.9	13,170,2020	67.0	69.0	68.0		549,549,549,549,549,	-10.1	0.0	19	dbSNP_92	68	90,8510	51.5+/-111.7	2,86,4212	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,intron	NUP62,IL4I1	NM_001193357.1,NM_012346.4,NM_016553.4,NM_153718.3,NM_153719.3,NM_172374.1	,,,,,	15,256,6232	TT,TC,CC		1.0465,4.4485,2.199	,,,,,	183/523,183/523,183/523,183/523,183/523,	50412516	286,12720	2203	4300	6503	SO:0001819	synonymous_variant	23636	exon3			AGGTGCCGTGGGC	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.549G>A	19.37:g.50412516C>T		Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	143	76	0.531469	NM_153719	B3KWU5|Q503A4|Q6GTM2|Q96C43|Q9NSL1	Silent	SNP	ENST00000596217.1	37	CCDS12788.1																																																																																			C|0.978;T|0.022	0.022	strong		0.627	NUP62-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464991.1	NM_153719	
MUC4	4585	hgsc.bcm.edu	37	3	195507372	195507372	+	Missense_Mutation	SNP	C	C	G	rs147904363	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195507372C>G	ENST00000463781.3	-	2	11538	c.11079G>C	c.(11077-11079)caG>caC	p.Q3693H	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.Q3693H	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)		GAGGGGTGGCCTGACCTGTGG	0.577													.|||	193	0.0385383	0.0613	0.0231	5008	,	,		9332	0.0317		0.0219	False		,,,				2504	0.0429				p.Q3693H		Atlas-SNP	.											.	MUC4	1505	.	0			c.G11079C						PASS	.						26.0	25.0	25.0					3																	195507372		643	1587	2230	SO:0001583	missense	4585	exon2			GGTGGCCTGACCT	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.11079G>C	3.37:g.195507372C>G	ENSP00000417498:p.Gln3693His	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	52	37	0.711538	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	1010	0.4624542124542125	219	0.4451219512195122	152	0.4198895027624309	284	0.4965034965034965	355	0.4683377308707124	N	0.301	-0.973799	0.02215	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.33438	1.44;1.41	.	.	.	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	.	.	.	.	.	.	T	0.44787	-0.9305	4	.	.	.	.	2.144	0.03782	0.0:0.329:0.3427:0.3283	.	3565	E7ESK3	.	H	3693	ENSP00000417498:Q3693H;ENSP00000420243:Q3693H	.	Q	-	3	2	MUC4	196992151	0.000000	0.05858	0.003000	0.11579	0.003000	0.03518	-2.713000	0.00816	-2.387000	0.00589	-2.332000	0.00249	CAG	C|0.539;G|0.461	0.461	strong		0.577	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
SCLY	51540	hgsc.bcm.edu	37	2	238990388	238990388	+	Missense_Mutation	SNP	G	G	A	rs3210400	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:238990388G>A	ENST00000555827.1	+	5	587	c.523G>A	c.(523-525)Gca>Aca	p.A175T	SCLY_ENST00000409736.2_Missense_Mutation_p.A175T|SCLY_ENST00000422984.2_Missense_Mutation_p.A81T|SCLY_ENST00000373332.3_Missense_Mutation_p.A93T|SCLY_ENST00000429612.2_Intron|SCLY_ENST00000254663.6_Missense_Mutation_p.A183T			Q96I15	SCLY_HUMAN	selenocysteine lyase	175			A -> T (in dbSNP:rs3210400). {ECO:0000269|PubMed:15489334}.		cellular amino acid metabolic process (GO:0006520)	cytosol (GO:0005829)	pyridoxal phosphate binding (GO:0030170)|selenocysteine lyase activity (GO:0009000)|transferase activity (GO:0016740)			endometrium(1)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(6)|lung(5)|ovary(2)|prostate(2)|stomach(1)|urinary_tract(1)	22		Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0481)|all_hematologic(139;0.158)|all_lung(227;0.198)|Melanoma(123;0.203)|Hepatocellular(293;0.244)		Epithelial(121;1.37e-23)|OV - Ovarian serous cystadenocarcinoma(60;4.6e-12)|Kidney(56;3.21e-09)|KIRC - Kidney renal clear cell carcinoma(57;8.25e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000128)|Lung(119;0.0118)|LUSC - Lung squamous cell carcinoma(224;0.0285)		GAGCGGGCAGGCAGAGGTGGA	0.572													G|||	1272	0.253994	0.0393	0.438	5008	,	,		18735	0.2321		0.4563	False		,,,				2504	0.228				p.A183T	Melanoma(24;424 891 11947 32582 36034)|Ovarian(46;648 1065 26199 32764 45893)	Atlas-SNP	.											.	SCLY	51	.	0			c.G547A						PASS	.	G	THR/ALA	415,3991	203.1+/-225.7	18,379,1806	109.0	95.0	99.0		547	5.0	0.0	2	dbSNP_105	99	3642,4958	523.6+/-380.4	794,2054,1452	yes	missense	SCLY	NM_016510.5	58	812,2433,3258	AA,AG,GG		42.3488,9.419,31.1933	benign	183/454	238990388	4057,8949	2203	4300	6503	SO:0001583	missense	51540	exon5			GGGCAGGCAGAGG	AF175767	CCDS2524.1, CCDS2524.2	2q37.3	2008-02-05			ENSG00000132330	ENSG00000132330			18161	protein-coding gene	gene with protein product	"""putative selenocysteine lyase"""	611056				10692412	Standard	NM_016510		Approved	SCL	uc010fyv.4	Q96I15	OTTHUMG00000133336	ENST00000555827.1:c.523G>A	2.37:g.238990388G>A	ENSP00000450613:p.Ala175Thr	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	86	86	1	NM_016510	B9A068|J3KN06|Q53SN1|Q53SN8|Q7L670|Q9NVT7|Q9NZR7	Missense_Mutation	SNP	ENST00000555827.1	37		647|647	0.29624542124542125|0.29624542124542125	21|21	0.042682926829268296|0.042682926829268296	156|156	0.430939226519337|0.430939226519337	122|122	0.21328671328671328|0.21328671328671328	348|348	0.45910290237467016|0.45910290237467016	G|G	13.64|13.64	2.296062|2.296062	0.40594|0.40594	0.09419|0.09419	0.423488|0.423488	ENSG00000132330|ENSG00000132330	ENST00000254663;ENST00000555827;ENST00000373332;ENST00000413463;ENST00000409736;ENST00000422984;ENST00000450965|ENST00000437134	T;T;T;D;T;T;T|.	0.86627|.	1.98;1.98;1.56;-2.15;1.56;1.98;1.56|.	5.84|5.84	4.96|4.96	0.65561|0.65561	Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);Aminotransferase, class V/Cysteine desulfurase (1);|.	0.522273|.	0.21381|.	N|.	0.075472|.	T|T	0.00012|0.00012	0.0000|0.0000	L|L	0.43152|0.43152	1.355|1.355	0.24182|0.24182	P|P	0.9955825700000001|0.9955825700000001	P;B;P|.	0.42296|.	0.775;0.452;0.696|.	P;B;B|.	0.48873|.	0.593;0.314;0.281|.	T|T	0.50923|0.50923	-0.8770|-0.8770	9|4	0.87932|.	D|.	0|.	-21.4942|-21.4942	10.0151|10.0151	0.42010|0.42010	0.1556:0.0:0.8444:0.0|0.1556:0.0:0.8444:0.0	rs3210400;rs3739052;rs52837213;rs60128375;rs3210400|rs3210400;rs3739052;rs52837213;rs60128375;rs3210400	81;175;175|.	E7ESG3;Q96I15;Q96I15-2|.	.;SCLY_HUMAN;.|.	T|D	183;175;93;89;175;81;5|18	ENSP00000254663:A183T;ENSP00000450613:A175T;ENSP00000362429:A93T;ENSP00000414165:A89T;ENSP00000387162:A175T;ENSP00000416865:A81T;ENSP00000414053:A5T|.	ENSP00000254663:A175T|.	A|G	+|+	1|2	0|0	SCLY|SCLY	238655127|238655127	1.000000|1.000000	0.71417|0.71417	0.008000|0.008000	0.14137|0.14137	0.123000|0.123000	0.20343|0.20343	4.874000|4.874000	0.63064|0.63064	1.464000|1.464000	0.47987|0.47987	0.655000|0.655000	0.94253|0.94253	GCA|GGC	G|0.715;A|0.285	0.285	strong		0.572	SCLY-204	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_016510	
TMEM8A	58986	hgsc.bcm.edu	37	16	427479	427479	+	Missense_Mutation	SNP	T	T	C	rs11248931	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:427479T>C	ENST00000431232.2	-	3	566	c.406A>G	c.(406-408)Aca>Gca	p.T136A	TMEM8A_ENST00000476735.1_5'UTR|TMEM8A_ENST00000250930.3_5'UTR	NM_021259.2	NP_067082.2	Q9HCN3	TMM8A_HUMAN	transmembrane protein 8A	136			T -> A (in dbSNP:rs11248931). {ECO:0000269|PubMed:11006113, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.3}.		cell adhesion (GO:0007155)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)				central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|pancreas(1)|prostate(1)	14						CTTCTCGGTGTGGTGCTCAGC	0.682											OREG0003703	type=REGULATORY REGION|Gene=TMEM8|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	C|||	2677	0.534545	0.6188	0.4755	5008	,	,		15166	0.3006		0.5408	False		,,,				2504	0.6973				p.T136A		Atlas-SNP	.											TMEM8A,colon,carcinoma,0,1	TMEM8A	49	1	0			c.A406G						PASS	.	C	ALA/THR	2729,1649		847,1035,307	22.0	22.0	22.0		406	1.0	0.0	16	dbSNP_120	22	4876,3718		1417,2042,838	yes	missense	TMEM8A	NM_021259.2	58	2264,3077,1145	CC,CT,TT		43.2627,37.6656,41.3737	benign	136/772	427479	7605,5367	2189	4297	6486	SO:0001583	missense	58986	exon3			TCGGTGTGGTGCT	AB045292	CCDS10407.1	16p13.3	2009-06-12	2009-06-12	2009-06-12	ENSG00000129925	ENSG00000129925			17205	protein-coding gene	gene with protein product			"""transmembrane protein 6"", ""transmembrane protein 8 (five membrane-spanning domains)"""	TMEM6, TMEM8		11006113	Standard	NM_021259		Approved	M83	uc002cgu.4	Q9HCN3	OTTHUMG00000047996	ENST00000431232.2:c.406A>G	16.37:g.427479T>C	ENSP00000401338:p.Thr136Ala	Somatic	156	0	0	588	WXS	Illumina HiSeq	Phase_I	85	85	1	NM_021259	D3DU49|Q4TT35|Q8WU24|Q96S25|Q9BR03|Q9BT97|Q9H7B9	Missense_Mutation	SNP	ENST00000431232.2	37	CCDS10407.1	1089	0.49862637362637363	335	0.6808943089430894	181	0.5	163	0.28496503496503495	410	0.5408970976253298	C	0.003	-2.441316	0.00180	0.623344	0.567373	ENSG00000129925	ENST00000431232	T	0.23147	1.92	3.34	0.981	0.19756	.	3.558320	0.02310	N	0.072046	T	0.00012	0.0000	N	0.01352	-0.895	0.58432	P	2.9999999999752447E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.40590	-0.9555	9	0.06099	T	0.92	-8.0545	4.5877	0.12291	0.15:0.2114:0.0:0.6386	rs11248931;rs17845652;rs17858586;rs57237473;rs11248931	136	Q9HCN3	TMM8A_HUMAN	A	136	ENSP00000401338:T136A	ENSP00000401338:T136A	T	-	1	0	TMEM8A	367480	0.000000	0.05858	0.001000	0.08648	0.000000	0.00434	-1.411000	0.02478	-0.100000	0.12241	-1.309000	0.01313	ACA	T|0.463;C|0.537	0.537	strong		0.682	TMEM8A-001	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000109257.2	NM_021259	
KIF6	221458	hgsc.bcm.edu	37	6	39507889	39507889	+	Missense_Mutation	SNP	C	C	T	rs2273063	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:39507889C>T	ENST00000287152.7	-	13	1629	c.1535G>A	c.(1534-1536)cGc>cAc	p.R512H	KIF6_ENST00000538893.1_Intron|KIF6_ENST00000373215.3_Missense_Mutation_p.R512H|KIF6_ENST00000373216.3_Missense_Mutation_p.R512H|KIF6_ENST00000373213.4_Missense_Mutation_p.R351H	NM_145027.4	NP_659464.3	Q6ZMV9	KIF6_HUMAN	kinesin family member 6	512			R -> H (in dbSNP:rs2273063).		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)			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						GTTTCCTAGGCGGAAGGGTGG	0.498													C|||	409	0.0816693	0.0348	0.0216	5008	,	,		17622	0.2262		0.0268	False		,,,				2504	0.0951				p.R512H		Atlas-SNP	.											KIF6_ENST00000287152,NS,carcinoma,-1,2	KIF6	233	2	0			c.G1535A						PASS	.	C	HIS/ARG	181,4225	118.0+/-155.7	3,175,2025	192.0	194.0	194.0		1535	-0.7	0.0	6	dbSNP_100	194	256,8344	101.0+/-162.3	4,248,4048	yes	missense	KIF6	NM_145027.4	29	7,423,6073	TT,TC,CC		2.9767,4.108,3.36	benign	512/815	39507889	437,12569	2203	4300	6503	SO:0001583	missense	221458	exon13			CCTAGGCGGAAGG	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.1535G>A	6.37:g.39507889C>T	ENSP00000287152:p.Arg512His	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	127	58	0.456693	NM_145027	Q2MDE3|Q2MDE4|Q5T8J6|Q6ZWE3|Q86T87|Q8WTV4	Missense_Mutation	SNP	ENST00000287152.7	37	CCDS4844.1	185|185	0.08470695970695971|0.08470695970695971	14|14	0.028455284552845527|0.028455284552845527	7|7	0.019337016574585635|0.019337016574585635	142|142	0.24825174825174826|0.24825174825174826	22|22	0.029023746701846966|0.029023746701846966	C|C	12.20|12.20	1.866153|1.866153	0.32977|0.32977	0.04108|0.04108	0.029767|0.029767	ENSG00000164627|ENSG00000164627	ENST00000458470|ENST00000287152;ENST00000373216;ENST00000373213;ENST00000373215	.|T;T;T;T	.|0.71698	.|-0.58;-0.59;-0.42;-0.59	6.04|6.04	-0.657|-0.657	0.11432|0.11432	.|.	.|.	.|.	.|.	.|.	T|T	0.22898|0.22898	0.0553|0.0553	N|N	0.19112|0.19112	0.55|0.55	0.80722|0.80722	P|P	0.0|0.0	.|B;P;B	.|0.44090	.|0.34;0.826;0.23	.|B;B;B	.|0.32289	.|0.091;0.143;0.042	T|T	0.07809|0.07809	-1.0753|-1.0753	4|8	.|0.45353	.|T	.|0.12	.|.	2.1231|2.1231	0.03731|0.03731	0.3193:0.1259:0.4275:0.1274|0.3193:0.1259:0.4275:0.1274	rs2273063;rs52808020;rs2273063|rs2273063;rs52808020;rs2273063	.|512;512;512	.|E7EUN7;Q6ZMV9-3;Q6ZMV9	.|.;.;KIF6_HUMAN	T|H	404|512;512;351;512	.|ENSP00000287152:R512H;ENSP00000362312:R512H;ENSP00000362309:R351H;ENSP00000362311:R512H	.|ENSP00000287152:R512H	A|R	-|-	1|2	0|0	KIF6|KIF6	39615867|39615867	0.019000|0.019000	0.18553|0.18553	0.001000|0.001000	0.08648|0.08648	0.044000|0.044000	0.14063|0.14063	0.516000|0.516000	0.22817|0.22817	-0.061000|-0.061000	0.13110|0.13110	-0.226000|-0.226000	0.12346|0.12346	GCC|CGC	C|0.941;T|0.059	0.059	strong		0.498	KIF6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040455.2	NM_145027	
CCT8	10694	hgsc.bcm.edu	37	21	30433615	30433615	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:30433615C>T	ENST00000286788.4	-	13	1614	c.1408G>A	c.(1408-1410)Gta>Ata	p.V470I	CCT8_ENST00000542732.1_Missense_Mutation_p.V451I|CCT8_ENST00000540844.1_Missense_Mutation_p.V397I|AF129075.5_ENST00000457162.2_RNA|CCT8_ENST00000470450.1_5'UTR	NM_006585.2	NP_006576.2	P50990	TCPQ_HUMAN	chaperonin containing TCP1, subunit 8 (theta)	470					'de novo' posttranslational protein folding (GO:0051084)|ATP catabolic process (GO:0006200)|binding of sperm to zona pellucida (GO:0007339)|cellular protein metabolic process (GO:0044267)|protein folding (GO:0006457)	aggresome (GO:0016235)|cell body (GO:0044297)|centrosome (GO:0005813)|chaperonin-containing T-complex (GO:0005832)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intermediate filament cytoskeleton (GO:0045111)|microtubule (GO:0005874)|zona pellucida receptor complex (GO:0002199)	ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)			breast(3)|endometrium(1)|kidney(1)|large_intestine(4)|liver(1)|lung(1)|prostate(3)	14						TCTTGATGTACTGCATAAAGT	0.358																																					p.V470I		Atlas-SNP	.											CCT8,NS,carcinoma,+1,1	CCT8	38	1	0			c.G1408A						scavenged	.						101.0	104.0	103.0					21																	30433615		2203	4300	6503	SO:0001583	missense	10694	exon13			GATGTACTGCATA	Z37163	CCDS33528.1, CCDS68180.1	21q21.3	2011-09-02			ENSG00000156261	ENSG00000156261		"""Heat Shock Proteins / Chaperonins"""	1623	protein-coding gene	gene with protein product			"""chromosome 21 open reading frame 112"""	C21orf112		7890169	Standard	NM_006585		Approved	Cctq, PRED71	uc002ynb.3	P50990	OTTHUMG00000044595	ENST00000286788.4:c.1408G>A	21.37:g.30433615C>T	ENSP00000286788:p.Val470Ile	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	178	3	0.0168539	NM_006585	A6NN54|B4DEM7|B4DQH4|Q4VBP8	Missense_Mutation	SNP	ENST00000286788.4	37	CCDS33528.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	15.51|15.51	2.853961|2.853961	0.51270|0.51270	.|.	.|.	ENSG00000156261|ENSG00000156261	ENST00000432178|ENST00000389159;ENST00000286788;ENST00000542732;ENST00000540844	.|T;T;T	.|0.78481	.|-1.18;-1.18;-1.18	5.19|5.19	5.19|5.19	0.71726|0.71726	.|.	.|0.242216	.|0.42821	.|D	.|0.000651	T|T	0.66086|0.66086	0.2754|0.2754	N|N	0.17082|0.17082	0.46|0.46	0.30781|0.30781	N|N	0.741942|0.741942	.|B;B;B;B;B	.|0.17038	.|0.02;0.001;0.008;0.006;0.016	.|B;B;B;B;B	.|0.31390	.|0.129;0.021;0.129;0.079;0.077	T|T	0.65990|0.65990	-0.6034|-0.6034	5|10	.|0.59425	.|D	.|0.04	-22.7218|-22.7218	10.7936|10.7936	0.46447|0.46447	0.0:0.8543:0.0:0.1457|0.0:0.8543:0.0:0.1457	.|.	.|397;451;470;469;470	.|B4DQH4;B4DEM7;Q53HU0;G5E9B2;P50990	.|.;.;.;.;TCPQ_HUMAN	N|I	28|469;470;451;397	.|ENSP00000286788:V470I;ENSP00000444984:V451I;ENSP00000442730:V397I	.|ENSP00000286788:V470I	S|V	-|-	2|1	0|0	CCT8|CCT8	29355486|29355486	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	2.267000|2.267000	0.43329|0.43329	2.857000|2.857000	0.98124|0.98124	0.650000|0.650000	0.86243|0.86243	AGT|GTA	.	.	none		0.358	CCT8-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171822.1		
GPR126	57211	hgsc.bcm.edu	37	6	142688827	142688827	+	Silent	SNP	C	C	T	rs35699755	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:142688827C>T	ENST00000230173.6	+	3	701	c.225C>T	c.(223-225)acC>acT	p.T75T	GPR126_ENST00000296932.8_Silent_p.T75T|GPR126_ENST00000367608.2_Silent_p.T75T|GPR126_ENST00000367609.3_Silent_p.T75T|GPR126_ENST00000545477.1_3'UTR	NM_020455.5	NP_065188	Q86SQ4	GP126_HUMAN	G protein-coupled receptor 126	75	CUB. {ECO:0000255|PROSITE- ProRule:PRU00059}.				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)			cervix(1)|endometrium(1)|kidney(3)|large_intestine(12)|lung(10)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	36	Breast(32;0.176)			OV - Ovarian serous cystadenocarcinoma(155;9.33e-06)|GBM - Glioblastoma multiforme(68;0.00121)		GAGCCCCCACCGGTTATATCA	0.463													C|||	177	0.0353435	0.0832	0.0101	5008	,	,		17884	0.0526		0.001	False		,,,				2504	0.0061				p.T75T		Atlas-SNP	.											.	GPR126	192	.	0			c.C225T						PASS	.	C	,,,	290,3510		10,270,1620	78.0	80.0	79.0		225,225,225,225	-10.3	0.0	6	dbSNP_126	79	10,8230		0,10,4110	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	GPR126	NM_001032394.2,NM_001032395.2,NM_020455.5,NM_198569.2	,,,	10,280,5730	TT,TC,CC		0.1214,7.6316,2.4917	,,,	75/1194,75/1223,75/1222,75/1251	142688827	300,11740	1900	4120	6020	SO:0001819	synonymous_variant	57211	exon3			CCCCACCGGTTAT	AK027843	CCDS47489.1, CCDS47490.1, CCDS47491.1, CCDS55064.1	6q23.1-q24.3	2014-08-08			ENSG00000112414	ENSG00000112414		"""-"", ""GPCR / Class B : Orphans"""	13841	protein-coding gene	gene with protein product		612243				12565841	Standard	NM_001032395		Approved	FLJ14937	uc010khe.3	Q86SQ4	OTTHUMG00000015709	ENST00000230173.6:c.225C>T	6.37:g.142688827C>T		Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	117	31	0.264957	NM_198569	Q5TGN7|Q6DHZ4|Q6F3F5|Q6F3F6|Q6F3F7|Q6F3F8|Q6MZU7|Q8IXA4|Q8NC14|Q96JW0	Silent	SNP	ENST00000230173.6	37	CCDS47490.1																																																																																			C|0.964;T|0.036	0.036	strong		0.463	GPR126-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000042487.2		
PRSS41	360226	hgsc.bcm.edu	37	16	2854507	2854507	+	RNA	SNP	T	T	G	rs61747737	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:2854507T>G	ENST00000399677.1	+	0	698							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)										GATTCCATGTTTTGTGCTGGT	0.522													T|||	100	0.0199681	0.0008	0.0288	5008	,	,		20028	0.0		0.0696	False		,,,				2504	0.0092				p.F233C		Atlas-SNP	.											.	.	.	.	0			c.T698G						PASS	.	T	CYS/PHE	16,1368		0,16,676	197.0	171.0	178.0		698	4.2	0.2	16	dbSNP_129	178	248,2934		6,236,1349	yes	missense	PRSS41	NM_001135086.1	205	6,252,2025	GG,GT,TT		7.7938,1.1561,5.7819	possibly-damaging	233/319	2854507	264,4302	692	1591	2283			360226	exon4			CCATGTTTTGTGC			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.2854507T>G		Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	148	107	0.722973	NM_001135086		Missense_Mutation	SNP	ENST00000399677.1	37																																																																																				T|0.963;G|0.037	0.037	strong		0.522	PRSS41-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000436450.1	NM_183379	
MCPH1	79648	hgsc.bcm.edu	37	8	6303025	6303025	+	Silent	SNP	G	G	A	rs2584	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:6303025G>A	ENST00000344683.5	+	8	1858	c.1782G>A	c.(1780-1782)acG>acA	p.T594T	MCPH1_ENST00000519480.1_Silent_p.T594T|MCPH1_ENST00000522905.1_Silent_p.T546T	NM_024596.3	NP_078872	Q8NEM0	MCPH1_HUMAN	microcephalin 1	594					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)		ACATGGAGACGTCTACAGAAG	0.423													G|||	662	0.132188	0.0174	0.245	5008	,	,		20565	0.0268		0.338	False		,,,				2504	0.1043				p.T594T	Colon(95;1448 1467 8277 34473 35819)	Atlas-SNP	.											MCPH1,caecum,carcinoma,+1,1	MCPH1	65	1	0			c.G1782A						PASS	.	G	,,	248,3494		9,230,1632	61.0	55.0	57.0		1782,1638,1782	-9.1	0.0	8	dbSNP_36	57	2706,5502		452,1802,1850	no	coding-synonymous,coding-synonymous,coding-synonymous	MCPH1	NM_001172574.1,NM_001172575.1,NM_024596.3	,,	461,2032,3482	AA,AG,GG		32.9678,6.6275,24.7197	,,	594/611,546/563,594/836	6303025	2954,8996	1871	4104	5975	SO:0001819	synonymous_variant	79648	exon8			GGAGACGTCTACA	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.1782G>A	8.37:g.6303025G>A		Somatic	209	0	0		WXS	Illumina HiSeq	Phase_I	169	127	0.751479	NM_001172574	B4DWW2|E9PGU5|E9PH63|Q66GU1|Q9H9C7	Silent	SNP	ENST00000344683.5	37	CCDS43689.1																																																																																			G|0.814;A|0.186	0.186	strong		0.423	MCPH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374532.2	NM_024596	
ENGASE	64772	hgsc.bcm.edu	37	17	77073776	77073776	+	Silent	SNP	A	A	T	rs62063818	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:77073776A>T	ENST00000579016.1	+	3	246	c.246A>T	c.(244-246)ccA>ccT	p.P82P	ENGASE_ENST00000539857.2_5'UTR	NM_001042573.2	NP_001036038.1	Q8NFI3	ENASE_HUMAN	endo-beta-N-acetylglucosaminidase	82						cytoplasm (GO:0005737)	mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase activity (GO:0033925)			breast(2)|endometrium(4)|large_intestine(1)|lung(15)|prostate(2)|skin(1)	25						CCACCAAACCAATCAGCTTTT	0.473													T|||	205	0.0409345	0.0371	0.0677	5008	,	,		16491	0.001		0.0865	False		,,,				2504	0.0215				p.P82P		Atlas-SNP	.											.	ENGASE	55	.	0			c.A246T						PASS	.	T		137,3741		0,137,1802	122.0	124.0	123.0		246	-0.6	0.1	17	dbSNP_129	123	652,7610		24,604,3503	no	coding-synonymous	ENGASE	NM_001042573.1		24,741,5305	TT,TA,AA		7.8916,3.5327,6.4992		82/744	77073776	789,11351	1939	4131	6070	SO:0001819	synonymous_variant	64772	exon3			CAAACCAATCAGC	AF512564	CCDS42394.1	17q25.3	2009-03-03			ENSG00000167280	ENSG00000167280	3.2.1.96		24622	protein-coding gene	gene with protein product	"""Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase"", ""Di-N-acetylchitobiosyl beta-N-acetylglucosaminidase"""	611898				12114544, 18586680	Standard	NM_001042573		Approved	FLJ21865	uc002jwv.4	Q8NFI3	OTTHUMG00000167714	ENST00000579016.1:c.246A>T	17.37:g.77073776A>T		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	56	27	0.482143	NM_001042573	Q659F0|Q8TB86|Q9H6U4	Silent	SNP	ENST00000579016.1	37	CCDS42394.1																																																																																			A|0.929;T|0.071	0.071	strong		0.473	ENGASE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395807.1	NM_022759	
ALPK2	115701	hgsc.bcm.edu	37	18	56202470	56202470	+	Missense_Mutation	SNP	G	G	A	rs55656447	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:56202470G>A	ENST00000361673.3	-	5	5162	c.4949C>T	c.(4948-4950)gCg>gTg	p.A1650V	RP11-1151B14.4_ENST00000591360.1_RNA	NM_052947.3	NP_443179.3	Q86TB3	ALPK2_HUMAN	alpha-kinase 2	1650						nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(33)|ovary(7)|prostate(1)|skin(10)|upper_aerodigestive_tract(2)	84						CAAGGTCTTCGCTGAGGAGCT	0.453													G|||	26	0.00519169	0.0015	0.0187	5008	,	,		20727	0.0		0.0089	False		,,,				2504	0.002				p.A1650V		Atlas-SNP	.											.	ALPK2	487	.	0			c.C4949T						PASS	.	G	VAL/ALA	19,4387	25.3+/-52.1	0,19,2184	75.0	79.0	77.0		4949	-1.1	0.0	18	dbSNP_129	77	112,8488	57.9+/-119.4	1,110,4189	yes	missense	ALPK2	NM_052947.3	64	1,129,6373	AA,AG,GG		1.3023,0.4312,1.0072	benign	1650/2171	56202470	131,12875	2203	4300	6503	SO:0001583	missense	115701	exon5			GTCTTCGCTGAGG	AY044450	CCDS11966.2	18q21.31	2013-01-11			ENSG00000198796	ENSG00000198796		"""Immunoglobulin superfamily / I-set domain containing"""	20565	protein-coding gene	gene with protein product	"""heart alpha-kinase"""					10021370	Standard	NM_052947		Approved	HAK	uc002lhj.4	Q86TB3	OTTHUMG00000132755	ENST00000361673.3:c.4949C>T	18.37:g.56202470G>A	ENSP00000354991:p.Ala1650Val	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	40	21	0.525	NM_052947	Q6ZUX0|Q8NAT5|Q96L95	Missense_Mutation	SNP	ENST00000361673.3	37	CCDS11966.2	16	0.007326007326007326	2	0.0040650406504065045	6	0.016574585635359115	0	0.0	8	0.010554089709762533	G	16.95	3.264457	0.59431	0.004312	0.013023	ENSG00000198796	ENST00000361673	T	0.43688	0.94	5.74	-1.14	0.09741	.	2.962290	0.00633	N	0.000494	T	0.11623	0.0283	L	0.48642	1.525	0.09310	N	1	P;P	0.46952	0.887;0.482	B;B	0.32211	0.142;0.04	T	0.28586	-1.0039	10	0.02654	T	1	-0.4975	0.6684	0.00854	0.2374:0.1259:0.2499:0.3868	rs55656447	1645;1650	Q86TB3-2;Q86TB3	.;ALPK2_HUMAN	V	1650	ENSP00000354991:A1650V	ENSP00000354991:A1650V	A	-	2	0	ALPK2	54353450	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	0.250000	0.18235	0.060000	0.16281	0.655000	0.94253	GCG	G|0.987;A|0.013	0.013	strong		0.453	ALPK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256126.1	NM_052947	
TLR1	7096	hgsc.bcm.edu	37	4	38800214	38800214	+	Missense_Mutation	SNP	C	C	G	rs5743611	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:38800214C>G	ENST00000502213.2	-	3	468	c.239G>C	c.(238-240)aGa>aCa	p.R80T	TLR1_ENST00000308979.2_Missense_Mutation_p.R80T			Q15399	TLR1_HUMAN	toll-like receptor 1	80			R -> T (in dbSNP:rs5743611). {ECO:0000269|PubMed:19924287, ECO:0000269|PubMed:21618349, ECO:0000269|PubMed:7584026}.		cellular response to triacyl bacterial lipopeptide (GO:0071727)|detection of triacyl bacterial lipopeptide (GO:0042495)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|macrophage activation (GO:0042116)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of interleukin-6 biosynthetic process (GO:0045410)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|regulation of cytokine secretion (GO:0050707)|signal transduction (GO:0007165)|toll-like receptor 1 signaling pathway (GO:0034130)	cytoplasmic vesicle (GO:0031410)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|Toll-like receptor 1-Toll-like receptor 2 protein complex (GO:0035354)	protein heterodimerization activity (GO:0046982)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|skin(4)|stomach(2)	28						ATACTGGATTCTATTATGAGA	0.333													C|||	113	0.0225639	0.0061	0.013	5008	,	,		19839	0.0		0.0934	False		,,,				2504	0.002				p.R80T	GBM(5;216 373 40795 46382)	Atlas-SNP	.											.	TLR1	70	.	0			c.G239C	GRCh37	CM065490	TLR1	M	rs5743611	PASS	.	C	THR/ARG	62,4344	58.7+/-95.3	0,62,2141	96.0	106.0	103.0		239	3.2	1.0	4	dbSNP_114	103	781,7819	183.0+/-231.3	42,697,3561	yes	missense	TLR1	NM_003263.3	71	42,759,5702	GG,GC,CC		9.0814,1.4072,6.4816	benign	80/787	38800214	843,12163	2203	4300	6503	SO:0001583	missense	7096	exon4			TGGATTCTATTAT	U88540	CCDS33973.1	4p14	2008-02-05				ENSG00000174125		"""CD molecules"""	11847	protein-coding gene	gene with protein product		601194				9435236, 7584026	Standard	NM_003263		Approved	rsc786, KIAA0012, CD281	uc003gtl.3	Q15399		ENST00000502213.2:c.239G>C	4.37:g.38800214C>G	ENSP00000421259:p.Arg80Thr	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	70	36	0.514286	NM_003263	D1CS39|D1CS41|O15452|Q32MK3|Q32MK4|Q9UG90	Missense_Mutation	SNP	ENST00000502213.2	37	CCDS33973.1	85	0.03891941391941392	3	0.006097560975609756	3	0.008287292817679558	0	0.0	79	0.10422163588390501	C	8.080	0.772095	0.16051	0.014072	0.090814	ENSG00000174125	ENST00000308979;ENST00000502213;ENST00000505940;ENST00000515861	T;T;T;D	0.83837	0.22;0.22;0.22;-1.77	4.93	3.22	0.36961	.	0.470993	0.21177	N	0.078888	T	0.10981	0.0268	M	0.75777	2.31	0.80722	P	0.0	B	0.25719	0.132	B	0.32211	0.142	T	0.63184	-0.6694	9	0.56958	D	0.05	.	3.8395	0.08908	0.2657:0.4846:0.0:0.2497	rs5743611;rs52835785;rs5743611	80	Q15399	TLR1_HUMAN	T	80	ENSP00000354932:R80T;ENSP00000421259:R80T;ENSP00000421856:R80T;ENSP00000423017:R80T	ENSP00000354932:R80T	R	-	2	0	TLR1	38476609	0.842000	0.29525	0.980000	0.43619	0.162000	0.22319	0.057000	0.14279	0.794000	0.33899	0.655000	0.94253	AGA	C|0.950;G|0.050	0.050	strong		0.333	TLR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360510.3		
CENPM	79019	hgsc.bcm.edu	37	22	42341308	42341308	+	Splice_Site	SNP	A	A	G	rs7293091	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:42341308A>G	ENST00000215980.5	-	4	318	c.231T>C	c.(229-231)agT>agC	p.S77S	CENPM_ENST00000402338.1_Splice_Site_p.S43S|CENPM_ENST00000402420.1_Missense_Mutation_p.S72P|CENPM_ENST00000407253.3_Splice_Site_p.S77S|CENPM_ENST00000404067.1_Splice_Site_p.S43S	NM_024053.3	NP_076958.1	Q9NSP4	CENPM_HUMAN	centromere protein M	77					mitotic cell cycle (GO:0000278)	cytosol (GO:0005829)|kinetochore (GO:0000776)|nucleus (GO:0005634)				kidney(1)|large_intestine(1)|prostate(1)	3						TGTTCTGGAGACTGGGGTGGC	0.532													G|||	1482	0.295927	0.3971	0.4496	5008	,	,		15295	0.123		0.2008	False		,,,				2504	0.3262				p.S77S		Atlas-SNP	.											.	CENPM	8	.	0			c.T231C						PASS	.	G	,	1735,2671	646.9+/-398.4	348,1039,816	71.0	59.0	63.0		231,231	1.2	1.0	22	dbSNP_116	63	1712,6888	736.8+/-407.0	182,1348,2770	yes	coding-synonymous-near-splice,coding-synonymous-near-splice	CENPM	NM_001002876.1,NM_024053.3	,	530,2387,3586	GG,GA,AA		19.907,39.3781,26.5032	,	77/108,77/181	42341308	3447,9559	2203	4300	6503	SO:0001630	splice_region_variant	79019	exon4			CTGGAGACTGGGG	BC000705	CCDS14025.1, CCDS46719.1, CCDS46720.1	22q13.2	2013-11-05	2006-06-15	2006-06-15	ENSG00000100162	ENSG00000100162			18352	protein-coding gene	gene with protein product		610152	"""chromosome 22 open reading frame 18"""	C22orf18		16622420, 16622419	Standard	NM_001110215		Approved	Pane1, CENP-M, MGC861	uc003bbn.3	Q9NSP4	OTTHUMG00000151277	ENST00000215980.5:c.231-1T>C	22.37:g.42341308A>G		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	94	93	0.989362	NM_024053	A7LM22|B1AHQ9|Q6I9W3	Silent	SNP	ENST00000215980.5	37	CCDS14025.1	575	0.2632783882783883	197	0.40040650406504064	153	0.42265193370165743	77	0.1346153846153846	148	0.19525065963060687	G	15.04	2.714778	0.48622	0.393781	0.19907	ENSG00000100162	ENST00000402420	.	.	.	5.71	1.19	0.21007	.	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	.	.	.	0.46396	P	9.799999999999809E-4	.	.	.	.	.	.	T	0.40850	-0.9541	5	0.72032	D	0.01	.	9.8874	0.41270	0.3615:0.0:0.6385:0.0	rs7293091;rs11538411;rs58896815;rs7293091	.	.	.	P	72	.	ENSP00000384132:S72P	S	-	1	0	CENPM	40671254	1.000000	0.71417	0.974000	0.42286	0.565000	0.35776	0.950000	0.29122	0.148000	0.19059	-0.119000	0.15052	TCT	A|0.729;G|0.271	0.271	strong		0.532	CENPM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322058.1	NM_024053	Silent
MFSD3	113655	hgsc.bcm.edu	37	8	145735120	145735120	+	Missense_Mutation	SNP	G	G	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:145735120G>C	ENST00000301327.4	+	1	664	c.404G>C	c.(403-405)gGc>gCc	p.G135A	RECQL4_ENST00000532237.1_5'Flank|CTD-2517M22.17_ENST00000580385.1_RNA	NM_138431.1	NP_612440.1	Q96ES6	MFSD3_HUMAN	major facilitator superfamily domain containing 3	135	Leu-rich.				transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)				central_nervous_system(2)|endometrium(1)|kidney(1)|lung(4)	8	all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055)			CTGGGGCCGGGCAATACCGTG	0.692											OREG0019059	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.G135A		Atlas-SNP	.											.	MFSD3	17	.	0			c.G404C						PASS	.						8.0	8.0	8.0					8																	145735120		2127	4210	6337	SO:0001583	missense	113655	exon1			GGCCGGGCAATAC		CCDS6431.1	8q24.3	2005-11-17			ENSG00000167700	ENSG00000167700			25157	protein-coding gene	gene with protein product							Standard	NM_138431		Approved		uc003zdi.1	Q96ES6	OTTHUMG00000165177	ENST00000301327.4:c.404G>C	8.37:g.145735120G>C	ENSP00000301327:p.Gly135Ala	Somatic	29	0	0	1696	WXS	Illumina HiSeq	Phase_I	32	18	0.5625	NM_138431		Missense_Mutation	SNP	ENST00000301327.4	37	CCDS6431.1	.	.	.	.	.	.	.	.	.	.	G	20.8	4.053076	0.75960	.	.	ENSG00000167700	ENST00000301327	T	0.47869	0.83	5.02	5.02	0.67125	Major facilitator superfamily domain, general substrate transporter (1);	0.000000	0.85682	D	0.000000	T	0.67002	0.2847	M	0.66506	2.035	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.68322	-0.5439	10	0.52906	T	0.07	-7.8332	16.1659	0.81754	0.0:0.0:1.0:0.0	.	135	Q96ES6	MFSD3_HUMAN	A	135	ENSP00000301327:G135A	ENSP00000301327:G135A	G	+	2	0	MFSD3	145705928	1.000000	0.71417	0.980000	0.43619	0.068000	0.16541	4.514000	0.60482	2.484000	0.83849	0.561000	0.74099	GGC	.	.	none		0.692	MFSD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382478.2	NM_138431	
PPIG	9360	hgsc.bcm.edu	37	2	170493103	170493103	+	Missense_Mutation	SNP	T	T	A	rs1050354	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:170493103T>A	ENST00000260970.3	+	14	1555	c.1335T>A	c.(1333-1335)gaT>gaA	p.D445E	PPIG_ENST00000482772.1_3'UTR|PPIG_ENST00000448752.2_Missense_Mutation_p.D445E|PPIG_ENST00000409714.3_Missense_Mutation_p.D430E	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	126	0	0		WXS	Illumina HiSeq	Phase_I	139	71	0.510791	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		
SWAP70	23075	hgsc.bcm.edu	37	11	9685781	9685781	+	Missense_Mutation	SNP	C	C	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:9685781C>G	ENST00000318950.6	+	1	158	c.55C>G	c.(55-57)Ctc>Gtc	p.L19V	SWAP70_ENST00000447399.2_Missense_Mutation_p.L19V	NM_015055.2	NP_055870.2	Q9UH65	SWP70_HUMAN	SWAP switching B-cell complex 70kDa subunit	19					isotype switching (GO:0045190)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|DNA binding (GO:0003677)			NS(1)|breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(2)|ovary(2)|pancreas(1)	11				all cancers(16;1.21e-10)|Epithelial(150;2.81e-09)|BRCA - Breast invasive adenocarcinoma(625;0.00649)		CTTCACCGCACTCGACCAGGA	0.701																																					p.L19V		Atlas-SNP	.											.	SWAP70	40	.	0			c.C55G						PASS	.						32.0	26.0	28.0					11																	9685781		2187	4288	6475	SO:0001583	missense	23075	exon1			ACCGCACTCGACC	AB014540	CCDS31426.1, CCDS73257.1	11p15	2013-01-10			ENSG00000133789	ENSG00000133789		"""Pleckstrin homology (PH) domain containing"", ""EF-hand domain containing"""	17070	protein-coding gene	gene with protein product		604762				9734811, 10681448	Standard	XM_005252829		Approved	KIAA0640, SWAP-70	uc001mhw.3	Q9UH65	OTTHUMG00000165865	ENST00000318950.6:c.55C>G	11.37:g.9685781C>G	ENSP00000315630:p.Leu19Val	Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	251	57	0.227092	NM_015055	D3DQV1|O75135|Q7LCY6|Q9P061|Q9P0Z8	Missense_Mutation	SNP	ENST00000318950.6	37	CCDS31426.1	.	.	.	.	.	.	.	.	.	.	C	20.2	3.950471	0.73787	.	.	ENSG00000133789	ENST00000447399;ENST00000318950	D;T	0.86956	-2.19;2.8	5.5	5.5	0.81552	EF-hand-like domain (1);	0.000000	0.85682	D	0.000000	D	0.93874	0.8040	M	0.81497	2.545	0.53005	D	0.999966	D;P;D	0.69078	0.993;0.748;0.997	D;B;D	0.78314	0.987;0.351;0.991	D	0.94329	0.7560	10	0.87932	D	0	-7.6476	19.0354	0.92974	0.0:1.0:0.0:0.0	.	19;19;19	E7EMB1;Q9UH65;B3KUB9	.;SWP70_HUMAN;.	V	19	ENSP00000399056:L19V;ENSP00000315630:L19V	ENSP00000315630:L19V	L	+	1	0	SWAP70	9642357	1.000000	0.71417	1.000000	0.80357	0.609000	0.37215	3.715000	0.54897	2.584000	0.87258	0.563000	0.77884	CTC	.	.	none		0.701	SWAP70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386766.2	NM_015055	
KIAA1551	55196	hgsc.bcm.edu	37	12	32138410	32138410	+	Silent	SNP	A	A	G	rs12827942	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:32138410A>G	ENST00000312561.4	+	4	4935	c.4521A>G	c.(4519-4521)gaA>gaG	p.E1507E	KIAA1551_ENST00000535596.1_Intron	NM_018169.3	NP_060639	Q9HCM1	K1551_HUMAN	KIAA1551	1507																	CCTCTAAAGAATCATTAAATG	0.393													A|||	259	0.0517173	0.0371	0.0879	5008	,	,		17744	0.0149		0.0984	False		,,,				2504	0.0358				p.E1507E		Atlas-SNP	.											.	.	.	.	0			c.A4521G						PASS	.	A		224,4180	130.2+/-166.9	5,214,1983	48.0	50.0	49.0		4521	0.1	0.0	12	dbSNP_121	49	1021,7579	213.4+/-253.3	56,909,3335	no	coding-synonymous	C12orf35	NM_018169.3		61,1123,5318	GG,GA,AA		11.8721,5.0863,9.574		1507/1748	32138410	1245,11759	2202	4300	6502	SO:0001819	synonymous_variant	55196	exon4			TAAAGAATCATTA	AK001514	CCDS8725.2	12p11.21	2012-08-14	2012-08-14	2012-08-14	ENSG00000174718	ENSG00000174718			25559	protein-coding gene	gene with protein product			"""chromosome 12 open reading frame 35"""	C12orf35		10997877	Standard	NM_018169		Approved	FLJ20696, FLJ10652	uc001rks.3	Q9HCM1	OTTHUMG00000128501	ENST00000312561.4:c.4521A>G	12.37:g.32138410A>G		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	54	26	0.481481	NM_018169	B2RTU5|Q4KN17|Q9NVL6|Q9NWP9	Silent	SNP	ENST00000312561.4	37	CCDS8725.2																																																																																			A|0.921;G|0.079	0.079	strong		0.393	KIAA1551-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250307.2	NM_018169	
CEP170B	283638	hgsc.bcm.edu	37	14	105344823	105344823	+	Silent	SNP	G	G	A	rs41314519	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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_ENST00000418279.1_Silent_p.P36P|CEP170B_ENST00000556508.1_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						PASS	.	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	63	0	0		WXS	Illumina HiSeq	Phase_I	74	28	0.378378	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	
PCSK1	5122	hgsc.bcm.edu	37	5	95728898	95728898	+	Missense_Mutation	SNP	C	C	G	rs6235	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:95728898C>G	ENST00000311106.3	-	14	2306	c.2069G>C	c.(2068-2070)aGt>aCt	p.S690T	PCSK1_ENST00000513085.1_5'UTR|CTD-2337A12.1_ENST00000502645.2_RNA|PCSK1_ENST00000508626.1_Missense_Mutation_p.S643T	NM_000439.4|NM_001177876.1	NP_000430.3|NP_001171347.1	P29120	NEC1_HUMAN	proprotein convertase subtilisin/kexin type 1	690			S -> T (in dbSNP:rs6235). {ECO:0000269|PubMed:10391209, ECO:0000269|PubMed:17595246}.		cell-cell signaling (GO:0007267)|cellular protein metabolic process (GO:0044267)|metabolic process (GO:0008152)|peptide biosynthetic process (GO:0043043)|peptide hormone processing (GO:0016486)|proteolysis (GO:0006508)|regulation of insulin secretion (GO:0050796)	extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|secretory granule lumen (GO:0034774)	serine-type endopeptidase activity (GO:0004252)			NS(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(14)|ovary(2)|prostate(3)|skin(3)|urinary_tract(2)	36		all_cancers(142;2.67e-06)|all_epithelial(76;6.92e-09)|all_lung(232;0.00307)|Lung NSC(167;0.00452)|Ovarian(225;0.0112)|Colorectal(57;0.0341)|Breast(839;0.244)		all cancers(79;3.44e-16)	"""""""Insulin(DB00071)|Insulin Regular(DB00030)"""	GAGCTTTGCACTTGGGGACTT	0.483													C|||	1221	0.24381	0.1263	0.2305	5008	,	,		19208	0.3591		0.2594	False		,,,				2504	0.2771				p.S690T		Atlas-SNP	.											.	PCSK1	93	.	0			c.G2069C						PASS	.	C	THR/SER,THR/SER,THR/SER	702,3704	291.5+/-281.6	53,596,1554	115.0	121.0	119.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	2069,1928,1139	4.0	1.0	5	dbSNP_52	119	2389,6211	397.4+/-345.7	301,1787,2212	yes	missense,missense,missense	PCSK1	NM_000439.4,NM_001177875.1,NM_001177876.1	58,58,58	354,2383,3766	GG,GC,CC	http://www.ncbi.nlm.nih.gov/pubmed?term	27.7791,15.9328,23.766	benign,benign,benign	690/754,643/707,380/444	95728898	3091,9915	2203	4300	6503	SO:0001583	missense	5122	exon14			TTTGCACTTGGGG		CCDS4081.1, CCDS54881.1	5q15-q21	2008-07-18			ENSG00000175426	ENSG00000175426			8743	protein-coding gene	gene with protein product	"""prohormone convertase 3"", ""prohormone convertase 1"", ""neuroendocrine convertase 1"", ""proprotein convertase 1"""	162150		NEC1		1765368	Standard	NM_000439		Approved	PC1, PC3, SPC3	uc003kls.2	P29120	OTTHUMG00000122089	ENST00000311106.3:c.2069G>C	5.37:g.95728898C>G	ENSP00000308024:p.Ser690Thr	Somatic	381	0	0		WXS	Illumina HiSeq	Phase_I	381	191	0.501312	NM_000439	B7Z8T7|E9PHA1|P78478|Q92532	Missense_Mutation	SNP	ENST00000311106.3	37	CCDS4081.1	538	0.24633699633699635	51	0.10365853658536585	83	0.2292817679558011	196	0.34265734265734266	208	0.27440633245382584	C	8.948	0.967513	0.18659	0.159328	0.277791	ENSG00000175426	ENST00000311106;ENST00000508626	T;T	0.66280	-0.05;-0.2	5.76	3.95	0.45737	.	0.280490	0.40554	N	0.001078	T	0.00012	0.0000	L	0.50333	1.59	0.48696	P	3.0399999999997096E-4	B;B	0.10296	0.003;0.001	B;B	0.09377	0.004;0.002	T	0.13308	-1.0514	9	0.14656	T	0.56	-7.0802	9.5219	0.39140	0.0:0.8156:0.0:0.1844	rs6235;rs52800779;rs6235	643;690	E9PHA1;P29120	.;NEC1_HUMAN	T	690;643	ENSP00000308024:S690T;ENSP00000421600:S643T	ENSP00000308024:S690T	S	-	2	0	PCSK1	95754654	0.131000	0.22433	0.983000	0.44433	0.308000	0.27856	0.893000	0.28336	2.713000	0.92767	0.655000	0.94253	AGT	C|0.756;G|0.244	0.244	strong		0.483	PCSK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000242851.1	NM_000439	
ZNRF4	148066	hgsc.bcm.edu	37	19	5455990	5455990	+	Missense_Mutation	SNP	G	G	A	rs17304380	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:5455990G>A	ENST00000222033.4	+	1	565	c.488G>A	c.(487-489)cGc>cAc	p.R163H		NM_181710.3	NP_859061.3	Q8WWF5	ZNRF4_HUMAN	zinc and ring finger 4	163	PA.		R -> C (in dbSNP:rs8104246).|R -> H (in dbSNP:rs17304380). {ECO:0000269|PubMed:15489334}.			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)		CTGATCCGCCGCTACGACTGC	0.672													G|||	935	0.186701	0.0227	0.1916	5008	,	,		17231	0.3671		0.1948	False		,,,				2504	0.2106				p.R163H		Atlas-SNP	.											.	ZNRF4	59	.	0			c.G488A						PASS	.	G	HIS/ARG	215,4077		6,203,1937	34.0	36.0	35.0		488	3.6	0.0	19	dbSNP_123	35	1418,7076		126,1166,2955	yes	missense	ZNRF4	NM_181710.3	29	132,1369,4892	AA,AG,GG		16.6941,5.0093,12.7718	probably-damaging	163/430	5455990	1633,11153	2146	4247	6393	SO:0001583	missense	148066	exon1			TCCGCCGCTACGA	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.488G>A	19.37:g.5455990G>A	ENSP00000222033:p.Arg163His	Somatic	16	0	0		WXS	Illumina HiSeq	Phase_I	23	17	0.73913	NM_181710	A8K886|O75866	Missense_Mutation	SNP	ENST00000222033.4	37	CCDS42475.1	450	0.20604395604395603	15	0.03048780487804878	77	0.212707182320442	208	0.36363636363636365	150	0.19788918205804748	G	14.97	2.694842	0.48202	0.050093	0.166941	ENSG00000105428	ENST00000222033	T	0.12147	2.71	4.65	3.57	0.40892	Protease-associated domain, PA (1);	0.067634	0.56097	U	0.000021	T	0.00012	0.0000	H	0.98866	4.355	0.80722	P	0.0	D	0.89917	1.0	D	0.74674	0.984	T	0.27365	-1.0076	9	0.62326	D	0.03	-12.9553	11.4607	0.50208	0.0:0.1911:0.8089:0.0	rs17304380;rs17851546;rs17304380	163	Q8WWF5	ZNRF4_HUMAN	H	163	ENSP00000222033:R163H	ENSP00000222033:R163H	R	+	2	0	ZNRF4	5406990	0.052000	0.20516	0.004000	0.12327	0.173000	0.22820	2.500000	0.45381	0.907000	0.36646	0.491000	0.48974	CGC	G|0.813;A|0.187	0.187	strong		0.672	ZNRF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450924.1	NM_181710	
DCLK3	85443	hgsc.bcm.edu	37	3	36759599	36759599	+	Missense_Mutation	SNP	G	G	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:36759599G>C	ENST00000416516.2	-	4	2145	c.1655C>G	c.(1654-1656)cCa>cGa	p.P552R	DCLK3_ENST00000498047.1_5'UTR	NM_033403.1	NP_208382.1	Q9C098	DCLK3_HUMAN	doublecortin-like kinase 3	552	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.					cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(3)|endometrium(3)|kidney(2)|large_intestine(11)|lung(20)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	48						GCTGCGGAATGGGGGAAAGCC	0.552																																					p.P552R		Atlas-SNP	.											.	DCLK3	95	.	0			c.C1655G						PASS	.						157.0	171.0	167.0					3																	36759599		2085	4248	6333	SO:0001583	missense	85443	exon4			CGGAATGGGGGAA	AB051552	CCDS43064.1	3p22.3	2007-04-02	2007-04-02	2007-04-02	ENSG00000163673	ENSG00000163673			19005	protein-coding gene	gene with protein product		613167	"""doublecortin and CaM kinase-like 3"""	DCAMKL3		11214970, 16869982	Standard	NM_033403		Approved	KIAA1765, DCDC3C	uc003cgi.2	Q9C098	OTTHUMG00000155805	ENST00000416516.2:c.1655C>G	3.37:g.36759599G>C	ENSP00000394484:p.Pro552Arg	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	89	28	0.314607	NM_033403		Missense_Mutation	SNP	ENST00000416516.2	37	CCDS43064.1	.	.	.	.	.	.	.	.	.	.	G	19.91	3.913710	0.72983	.	.	ENSG00000163673	ENST00000416516	T	0.58652	0.32	5.51	5.51	0.81932	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.32518	N	0.005993	D	0.86464	0.5939	H	0.98446	4.235	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.91296	0.5063	10	0.87932	D	0	.	19.7913	0.96458	0.0:0.0:1.0:0.0	.	552	Q9C098	DCLK3_HUMAN	R	552	ENSP00000394484:P552R	ENSP00000394484:P552R	P	-	2	0	DCLK3	36734603	1.000000	0.71417	0.754000	0.31244	0.213000	0.24496	9.869000	0.99810	2.765000	0.95021	0.555000	0.69702	CCA	.	.	none		0.552	DCLK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341727.1	XM_047355	
SNX5	27131	hgsc.bcm.edu	37	20	17932210	17932210	+	Silent	SNP	C	C	T	rs2273448	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:17932210C>T	ENST00000377768.3	-	7	855	c.543G>A	c.(541-543)gaG>gaA	p.E181E	SNX5_ENST00000377759.4_Silent_p.E181E|SNX5_ENST00000483485.1_5'UTR	NM_152227.1	NP_689413.1	Q9Y5X3	SNX5_HUMAN	sorting nexin 5	181					intracellular protein transport (GO:0006886)|pinocytosis (GO:0006907)	cytoplasmic vesicle (GO:0031410)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|extrinsic component of endosome membrane (GO:0031313)|macropinocytic cup (GO:0070685)	phosphatidylinositol binding (GO:0035091)			endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|prostate(1)	11						CACCAAACATCTCTTTAGTAT	0.343													C|||	1488	0.297125	0.115	0.232	5008	,	,		18237	0.4375		0.2634	False		,,,				2504	0.4796				p.E181E		Atlas-SNP	.											.	SNX5	38	.	0			c.G543A						PASS	.	C	,	710,3696	291.8+/-281.7	64,582,1557	111.0	106.0	108.0		543,543	4.3	1.0	20	dbSNP_100	108	2500,6100	407.9+/-349.3	353,1794,2153	no	coding-synonymous,coding-synonymous	SNX5	NM_014426.2,NM_152227.1	,	417,2376,3710	TT,TC,CC		29.0698,16.1144,24.6809	,	181/405,181/405	17932210	3210,9796	2203	4300	6503	SO:0001819	synonymous_variant	27131	exon6			AAACATCTCTTTA	AF121855	CCDS13130.1	20p11	2008-05-22			ENSG00000089006	ENSG00000089006		"""Sorting nexins"""	14969	protein-coding gene	gene with protein product		605937				10600472, 17148574	Standard	NM_152227		Approved		uc002wqc.3	Q9Y5X3	OTTHUMG00000031953	ENST00000377768.3:c.543G>A	20.37:g.17932210C>T		Somatic	351	0	0		WXS	Illumina HiSeq	Phase_I	321	158	0.492212	NM_014426	B7ZKN3|D3DW26|Q52LC4|Q7KZN0|Q9BWP0	Silent	SNP	ENST00000377768.3	37	CCDS13130.1																																																																																			C|0.749;T|0.251	0.251	strong		0.343	SNX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078137.4		
SYNE1	23345	hgsc.bcm.edu	37	6	152466674	152466674	+	Intron	SNP	T	T	C	rs2747662	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:152466674T>C	ENST00000367255.5	-	138	25578				SYNE1_ENST00000265368.4_Intron|SYNE1_ENST00000448038.1_Silent_p.E8260E|SYNE1_ENST00000539504.1_Intron|SYNE1_ENST00000423061.1_Silent_p.E8260E|SYNE1_ENST00000356820.4_Intron|SYNE1_ENST00000354674.4_Silent_p.E486E|SYNE1_ENST00000341594.5_Intron|SYNE1_ENST00000347037.5_5'UTR	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1						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)		CCTCAGGGCTTTCGGGGATCA	0.473										HNSCC(10;0.0054)			T|||	1834	0.366214	0.3389	0.5058	5008	,	,		17781	0.2976		0.331	False		,,,				2504	0.411				p.E8260E		Atlas-SNP	.											.	SYNE1	3227	.	0			c.A24780G						PASS	.	T	,	1530,2876	483.5+/-359.7	264,1002,937	110.0	106.0	107.0		24780,	-1.4	0.1	6	dbSNP_100	107	2839,5761	447.0+/-361.4	462,1915,1923	no	coding-synonymous,intron	SYNE1	NM_033071.3,NM_182961.3	,	726,2917,2860	CC,CT,TT		33.0116,34.7254,33.5922	,	8260/8750,	152466674	4369,8637	2203	4300	6503	SO:0001627	intron_variant	23345	exon137			AGGGCTTTCGGGG	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.24977-1774A>G	6.37:g.152466674T>C		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	58	36	0.62069	NM_033071	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Silent	SNP	ENST00000367255.5	37	CCDS5236.2																																																																																			T|0.660;C|0.340	0.340	strong		0.473	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961	
CRIPAK	285464	hgsc.bcm.edu	37	4	1389046	1389046	+	Silent	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:1389046C>T	ENST00000324803.4	+	1	3707	c.747C>T	c.(745-747)gcC>gcT	p.A249A		NM_175918.3	NP_787114.2	Q8N1N5	CRPAK_HUMAN	cysteine-rich PAK1 inhibitor	249					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)			TGTGGAGTGCCCGCCTGCTCA	0.692																																					p.A249A		Atlas-SNP	.											CRIPAK,colon,carcinoma,0,1	CRIPAK	185	1	0			c.C747T						PASS	.						148.0	130.0	136.0					4																	1389046		2202	4299	6501	SO:0001819	synonymous_variant	285464	exon1			GAGTGCCCGCCTG	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.747C>T	4.37:g.1389046C>T		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	59	9	0.152542	NM_175918	Q8NB03	Silent	SNP	ENST00000324803.4	37	CCDS3349.1																																																																																			.	.	none		0.692	CRIPAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241607.2	NM_175918	
EPHB3	2049	hgsc.bcm.edu	37	3	184299068	184299068	+	Silent	SNP	G	G	A	rs9881589	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:184299068G>A	ENST00000330394.2	+	15	3212	c.2760G>A	c.(2758-2760)acG>acA	p.T920T	EIF2B5_ENST00000444495.1_Intron	NM_004443.3	NP_004434.2	P54753	EPHB3_HUMAN	EPH receptor B3	920					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)			TGGACCGCACGGTCCCAGATT	0.567													G|||	788	0.157348	0.1377	0.1095	5008	,	,		19897	0.1597		0.1899	False		,,,				2504	0.182				p.T920T		Atlas-SNP	.											.	EPHB3	114	.	0			c.G2760A						PASS	.	G		645,3761	274.9+/-272.2	47,551,1605	117.0	109.0	112.0		2760	-6.0	0.8	3	dbSNP_119	112	1517,7083	287.1+/-298.1	150,1217,2933	no	coding-synonymous	EPHB3	NM_004443.3		197,1768,4538	AA,AG,GG		17.6395,14.6391,16.6231		920/999	184299068	2162,10844	2203	4300	6503	SO:0001819	synonymous_variant	2049	exon15			CCGCACGGTCCCA	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.2760G>A	3.37:g.184299068G>A		Somatic	210	0	0		WXS	Illumina HiSeq	Phase_I	210	104	0.495238	NM_004443	Q7Z740	Silent	SNP	ENST00000330394.2	37	CCDS3268.1																																																																																			G|0.834;A|0.166	0.166	strong		0.567	EPHB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345413.1	NM_004443	
FGF6	2251	hgsc.bcm.edu	37	12	4554413	4554413	+	Silent	SNP	C	C	T	rs11611403	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:4554413C>T	ENST00000228837.2	-	1	367	c.324G>A	c.(322-324)ggG>ggA	p.G108G		NM_020996.1	NP_066276.2	P10767	FGF6_HUMAN	fibroblast growth factor 6	108					angiogenesis (GO:0001525)|cartilage condensation (GO:0001502)|cell proliferation (GO:0008283)|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)|myoblast differentiation (GO:0045445)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|sarcolemma (GO:0042383)	growth factor activity (GO:0008083)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	20			Colorectal(7;0.00165)|COAD - Colon adenocarcinoma(12;0.0229)			CCTCGTGGGTCCCGCTGATCC	0.632													C|||	777	0.155152	0.3018	0.1196	5008	,	,		16677	0.0129		0.1451	False		,,,				2504	0.1391				p.G108G		Atlas-SNP	.											.	FGF6	40	.	0			c.G324A						PASS	.	C		1169,3237		163,843,1197	27.0	27.0	27.0		324	-2.6	0.8	12	dbSNP_120	27	1380,7220		129,1122,3049	no	coding-synonymous	FGF6	NM_020996.1		292,1965,4246	TT,TC,CC		16.0465,26.532,19.5986		108/209	4554413	2549,10457	2203	4300	6503	SO:0001819	synonymous_variant	2251	exon1			GTGGGTCCCGCTG	X63454	CCDS8527.1	12p13	2014-01-30				ENSG00000111241		"""Endogenous ligands"""	3684	protein-coding gene	gene with protein product		134921				16597617	Standard	NM_020996		Approved		uc001qmr.1	P10767		ENST00000228837.2:c.324G>A	12.37:g.4554413C>T		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	50	29	0.58	NM_020996	Q0VAE1	Silent	SNP	ENST00000228837.2	37	CCDS8527.1																																																																																			C|0.833;T|0.167	0.167	strong		0.632	FGF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398939.1	NM_020996	
SLC36A2	153201	hgsc.bcm.edu	37	5	150723127	150723127	+	Silent	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:150723127G>A	ENST00000335244.4	-	3	417	c.288C>T	c.(286-288)ttC>ttT	p.F96F	SLC36A2_ENST00000521967.1_Silent_p.F96F	NM_181776.2	NP_861441.2	Q495M3	S36A2_HUMAN	solute carrier family 36 (proton/amino acid symporter), member 2	96					amino acid transport (GO:0006865)|ion transport (GO:0006811)|proline transmembrane transport (GO:0035524)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	glycine transmembrane transporter activity (GO:0015187)|hydrogen:amino acid symporter activity (GO:0005280)|L-alanine transmembrane transporter activity (GO:0015180)|L-proline transmembrane transporter activity (GO:0015193)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(14)|large_intestine(3)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	33		Medulloblastoma(196;0.109)|all_hematologic(541;0.243)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		Cycloserine(DB00260)	GGCAGGCAATGAAGCCCATCA	0.527																																					p.F96F		Atlas-SNP	.											SLC36A2,NS,malignant_melanoma,0,2	SLC36A2	71	2	0			c.C288T						scavenged	.						102.0	100.0	100.0					5																	150723127		2203	4300	6503	SO:0001819	synonymous_variant	153201	exon3			GGCAATGAAGCCC	AY162214	CCDS4315.1	5q33.1	2013-05-22			ENSG00000186335	ENSG00000186335		"""Solute carriers"""	18762	protein-coding gene	gene with protein product		608331				11959859	Standard	NM_181776		Approved	PAT2, tramdorin, TRAMD1	uc003lty.3	Q495M3	OTTHUMG00000130129	ENST00000335244.4:c.288C>T	5.37:g.150723127G>A		Somatic	193	2	0.0103627		WXS	Illumina HiSeq	Phase_I	193	6	0.0310881	NM_181776	Q495M4|Q495M6|Q6ZWK5|Q7Z6B5	Silent	SNP	ENST00000335244.4	37	CCDS4315.1																																																																																			.	.	none		0.527	SLC36A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252437.1		
ZNF554	115196	hgsc.bcm.edu	37	19	2833864	2833864	+	Missense_Mutation	SNP	G	G	A	rs867169	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:2833864G>A	ENST00000317243.5	+	5	829	c.631G>A	c.(631-633)Gtt>Att	p.V211I	ZNF554_ENST00000591265.1_3'UTR	NM_001102651.1	NP_001096121.1	Q86TJ5	ZN554_HUMAN	zinc finger protein 554	211			V -> I (in dbSNP:rs867169).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|liver(3)|lung(10)|ovary(1)|upper_aerodigestive_tract(1)	23		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CGTAGTGGCCGTTCCTCAGGA	0.507													G|||	1278	0.255192	0.1165	0.4193	5008	,	,		19289	0.4415		0.2127	False		,,,				2504	0.1779				p.V211I		Atlas-SNP	.											.	ZNF554	47	.	0			c.G631A						PASS	.	G	ILE/VAL	428,3364		19,390,1487	99.0	101.0	100.0		631	-2.9	0.0	19	dbSNP_86	100	1456,6776		120,1216,2780	yes	missense	ZNF554	NM_001102651.1	29	139,1606,4267	AA,AG,GG		17.6871,11.2869,15.6687	benign	211/539	2833864	1884,10140	1896	4116	6012	SO:0001583	missense	115196	exon5			GTGGCCGTTCCTC	AK027860	CCDS42462.1	19p13.3	2013-09-20			ENSG00000172006	ENSG00000172006		"""Zinc fingers, C2H2-type"", ""-"""	26629	protein-coding gene	gene with protein product						12477932	Standard	NM_001102651		Approved	FLJ34817	uc002lwm.2	Q86TJ5	OTTHUMG00000180493	ENST00000317243.5:c.631G>A	19.37:g.2833864G>A	ENSP00000321132:p.Val211Ile	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	77	40	0.519481	NM_001102651	Q8NAT3|Q9BWN3	Missense_Mutation	SNP	ENST00000317243.5	37	CCDS42462.1	631	0.2889194139194139	71	0.1443089430894309	141	0.38950276243093923	249	0.4353146853146853	170	0.22427440633245382	G	0.551	-0.849394	0.02651	0.112869	0.176871	ENSG00000172006	ENST00000317243	T	0.06608	3.28	2.71	-2.92	0.05615	.	.	.	.	.	T	0.00012	0.0000	N	0.14661	0.345	0.58432	P	4.000000000004E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.44952	-0.9294	8	0.22706	T	0.39	.	3.0196	0.06071	0.1963:0.1042:0.5028:0.1968	rs867169;rs17685329;rs52800819;rs57600764;rs867169	211	Q86TJ5	ZN554_HUMAN	I	211	ENSP00000321132:V211I	ENSP00000321132:V211I	V	+	1	0	ZNF554	2784864	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.752000	0.04797	-1.490000	0.01842	-2.913000	0.00091	GTT	G|0.741;A|0.259	0.259	strong		0.507	ZNF554-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451598.3	NM_152303	
ACTR3C	653857	hgsc.bcm.edu	37	7	149983566	149983566	+	Nonsense_Mutation	SNP	G	G	A	rs181975624	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:149983566G>A	ENST00000539352.1	-	5	612	c.361C>T	c.(361-363)Cag>Tag	p.Q121*	ACTR3C_ENST00000252071.4_Nonsense_Mutation_p.Q121*	NM_001164458.1	NP_001157930.1	Q9C0K3	ARP3C_HUMAN	ARP3 actin-related protein 3 homolog C (yeast)	121						extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)										ATCCACTTCTGGGGATCCACA	0.413													G|||	164	0.0327476	0.0106	0.0187	5008	,	,		18474	0.006		0.0427	False		,,,				2504	0.09				p.Q121X		Atlas-SNP	.											Q9C0K3_HUMAN,NS,carcinoma,+1,1	.	.	1	0			c.C361T						scavenged	.						174.0	207.0	197.0					7																	149983566		692	1591	2283	SO:0001587	stop_gained	653857	exon5			ACTTCTGGGGATC		CCDS47744.1	7q36.1	2009-09-23			ENSG00000106526	ENSG00000106526			37282	protein-coding gene	gene with protein product						11162478, 14651955	Standard	NM_001164458		Approved	ARP11	uc022aps.1	Q9C0K3	OTTHUMG00000158323	ENST00000539352.1:c.361C>T	7.37:g.149983566G>A	ENSP00000440990:p.Gln121*	Somatic	201	0	0		WXS	Illumina HiSeq	Phase_I	122	33	0.270492	NM_001164459	Q5CZI4	Nonsense_Mutation	SNP	ENST00000539352.1	37	CCDS47744.1	26	0.011904761904761904	2	0.0040650406504065045	4	0.011049723756906077	3	0.005244755244755245	17	0.022427440633245383	G	1.579	-0.532207	0.04112	.	.	ENSG00000106526	ENST00000478393;ENST00000252071;ENST00000539352;ENST00000477871	.	.	.	2.42	1.48	0.22813	.	0.175232	0.37761	N	0.001946	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-0.2029	8.2737	0.31860	0.0:0.4893:0.5107:0.0	.	.	.	.	X	119;121;121;220	.	.	Q	-	1	0	ACTR3C	149614499	0.000000	0.05858	0.720000	0.30636	0.180000	0.23129	0.325000	0.19628	0.544000	0.28883	0.184000	0.17185	CAG	G|0.500;A|0.500	0.500	weak		0.413	ACTR3C-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350676.2		
WDR66	144406	hgsc.bcm.edu	37	12	122413481	122413481	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:122413481C>T	ENST00000288912.4	+	19	3750	c.2896C>T	c.(2896-2898)Cgc>Tgc	p.R966C		NM_144668.5	NP_653269.3	Q8TBY9	WDR66_HUMAN	WD repeat domain 66	966							calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(11)|liver(2)|lung(13)|ovary(2)|prostate(2)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	43	all_neural(191;0.0496)|Medulloblastoma(191;0.0922)			OV - Ovarian serous cystadenocarcinoma(86;0.000155)|Epithelial(86;0.000634)|BRCA - Breast invasive adenocarcinoma(302;0.248)		TTCTCAGCTCCGCAGTCAAGG	0.438																																					p.R966C	Esophageal Squamous(85;849 1794 49757 52143)	Atlas-SNP	.											.	WDR66	143	.	0			c.C2896T						PASS	.						107.0	97.0	101.0					12																	122413481		1935	4131	6066	SO:0001583	missense	144406	exon19			CAGCTCCGCAGTC	AL833930	CCDS41853.1, CCDS53840.1	12q24.31	2014-07-31			ENSG00000158023	ENSG00000158023		"""WD repeat domain containing"""	28506	protein-coding gene	gene with protein product						17967944	Standard	NM_001178003		Approved	MGC33630, CaM-IP4	uc009zxk.3	Q8TBY9	OTTHUMG00000168948	ENST00000288912.4:c.2896C>T	12.37:g.122413481C>T	ENSP00000288912:p.Arg966Cys	Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	132	59	0.44697	NM_144668	C9J1W2|Q8IYA3|Q8N898|Q8NDE7	Missense_Mutation	SNP	ENST00000288912.4	37	CCDS41853.1	.	.	.	.	.	.	.	.	.	.	C	14.04	2.417308	0.42918	.	.	ENSG00000158023	ENST00000288912	T	0.08546	3.08	5.26	5.26	0.73747	.	0.400698	0.27096	N	0.020942	T	0.12092	0.0294	M	0.84326	2.69	0.80722	D	1	P	0.44429	0.835	B	0.35278	0.199	T	0.01702	-1.1292	10	0.54805	T	0.06	.	9.8744	0.41194	0.1397:0.7858:0.0:0.0745	.	966	Q8TBY9	WDR66_HUMAN	C	966	ENSP00000288912:R966C	ENSP00000288912:R966C	R	+	1	0	WDR66	120897864	1.000000	0.71417	1.000000	0.80357	0.763000	0.43281	1.700000	0.37815	2.452000	0.82932	0.561000	0.74099	CGC	.	.	none		0.438	WDR66-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401700.1	NM_144668	
LCE1E	353135	hgsc.bcm.edu	37	1	152760096	152760096	+	Silent	SNP	A	A	T	rs115864544	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:152760096A>T	ENST00000368770.3	+	2	374	c.321A>T	c.(319-321)ggA>ggT	p.G107G	LCE1E_ENST00000368771.1_Silent_p.G107G	NM_178353.1	NP_848130.1	Q5T753	LCE1E_HUMAN	late cornified envelope 1E	107	Cys-rich.				keratinization (GO:0031424)					lung(5)|stomach(1)	6	Lung NSC(65;3.97e-29)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)			GCTGCTGTGGAGGGGGCAGCG	0.622													A|||	882	0.176118	0.239	0.1383	5008	,	,		14571	0.2639		0.0616	False		,,,				2504	0.1452				p.G107G		Atlas-SNP	.											LCE1E,NS,carcinoma,0,1	LCE1E	26	1	0			c.A321T						scavenged	.	A		397,3855		43,311,1772	39.0	58.0	52.0		321	1.2	1.0	1	dbSNP_132	52	221,8299		15,191,4054	no	coding-synonymous	LCE1E	NM_178353.1		58,502,5826	TT,TA,AA		2.5939,9.3368,4.8387		107/119	152760096	618,12154	2126	4260	6386	SO:0001819	synonymous_variant	353135	exon2			CTGTGGAGGGGGC	BC038391	CCDS1024.1	1q21.3	2008-02-05			ENSG00000186226	ENSG00000186226		"""Late cornified envelopes"""	29466	protein-coding gene	gene with protein product		612607				11698679	Standard	NM_178353		Approved	LEP5	uc001fan.3	Q5T753	OTTHUMG00000012405	ENST00000368770.3:c.321A>T	1.37:g.152760096A>T		Somatic	514	1	0.00194553		WXS	Illumina HiSeq	Phase_I	287	43	0.149826	NM_178353	D3DV30	Silent	SNP	ENST00000368770.3	37	CCDS1024.1																																																																																			A|0.901;T|0.099	0.099	strong		0.622	LCE1E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034525.1	NM_178353	
CNTNAP4	85445	hgsc.bcm.edu	37	16	76461474	76461474	+	Silent	SNP	C	C	T	rs76327478	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:76461474C>T	ENST00000476707.1	+	3	664	c.525C>T	c.(523-525)atC>atT	p.I175I	CNTNAP4_ENST00000377504.4_Silent_p.I171I|CNTNAP4_ENST00000478060.1_Silent_p.I147I|CNTNAP4_ENST00000307431.8_Silent_p.I171I|CNTNAP4_ENST00000469589.1_3'UTR			Q9C0A0	CNTP4_HUMAN	contactin associated protein-like 4	172	F5/8 type C. {ECO:0000255|PROSITE- ProRule:PRU00081}.				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						GAATGCGAATCGAAGTGTTCG	0.403													C|||	73	0.0145767	0.0	0.0	5008	,	,		19317	0.0694		0.001	False		,,,				2504	0.002				p.I147I		Atlas-SNP	.											.	CNTNAP4	600	.	0			c.C441T						PASS	.	C	,	1,4395	2.1+/-5.4	0,1,2197	109.0	102.0	104.0		515,441	-3.2	0.8	16	dbSNP_132	104	3,8597	3.0+/-9.4	0,3,4297	yes	coding-synonymous,coding-synonymous	CNTNAP4	NM_033401.3,NM_138994.3	,	0,4,6494	TT,TC,CC		0.0349,0.0227,0.0308	,	172/1309,147/1236	76461474	4,12992	2198	4300	6498	SO:0001819	synonymous_variant	85445	exon4			GCGAATCGAAGTG	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.525C>T	16.37:g.76461474C>T		Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	196	76	0.387755	NM_138994	E9PFZ6|Q86YZ7	Silent	SNP	ENST00000476707.1	37																																																																																				C|0.993;T|0.007	0.007	strong		0.403	CNTNAP4-005	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000348216.1	NM_033401	
DFNA5	1687	hgsc.bcm.edu	37	7	24758795	24758795	+	Silent	SNP	T	T	C	rs78941420|rs876305	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:24758795T>C	ENST00000342947.3	-	4	872	c.447A>G	c.(445-447)gaA>gaG	p.E149E	DFNA5_ENST00000409775.3_Silent_p.E149E|DFNA5_ENST00000559637.1_5'UTR|DFNA5_ENST00000419307.1_5'UTR|DFNA5_ENST00000545231.1_5'UTR|DFNA5_ENST00000409970.1_5'UTR	NM_004403.2	NP_004394.1	O60443	DFNA5_HUMAN	deafness, autosomal dominant 5	149					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						CATTCCTTCCTTCCAGCACCT	0.493													C|||	3694	0.73762	0.8275	0.6643	5008	,	,		23268	0.9841		0.4135	False		,,,				2504	0.7474				p.E149E	GBM(78;184 1250 20134 20900 23600)	Atlas-SNP	.											.	DFNA5	51	.	0			c.A447G						PASS	.	C	,,	3370,1036	379.0+/-323.1	1295,780,128	161.0	143.0	149.0		447,,447	3.3	0.9	7	dbSNP_86	149	3619,4981	624.4+/-397.6	755,2109,1436	no	coding-synonymous,utr-5,coding-synonymous	DFNA5	NM_001127453.1,NM_001127454.1,NM_004403.2	,,	2050,2889,1564	CC,CT,TT		42.0814,23.5134,46.2633	,,	149/497,,149/497	24758795	6989,6017	2203	4300	6503	SO:0001819	synonymous_variant	1687	exon4			CCTTCCTTCCAGC	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.447A>G	7.37:g.24758795T>C		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	60	8	0.133333	NM_001127453	A4D156|B2RAX9|B3KT05|O14590|Q08AQ8|Q9UBV3	Silent	SNP	ENST00000342947.3	37	CCDS5389.1																																																																																			T|0.394;C|0.606	0.606	strong		0.493	DFNA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214060.2	NM_004403	
UTRN	7402	hgsc.bcm.edu	37	6	144869785	144869785	+	Missense_Mutation	SNP	A	A	G	rs1534443	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:144869785A>G	ENST00000367545.3	+	46	6605	c.6605A>G	c.(6604-6606)aAt>aGt	p.N2202S		NM_007124.2	NP_009055.2	P46939	UTRO_HUMAN	utrophin	2202			N -> S (in dbSNP:rs1534443).		aging (GO:0007568)|muscle cell differentiation (GO:0042692)|muscle contraction (GO:0006936)|muscle organ development (GO:0007517)|neuron projection morphogenesis (GO:0048812)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of sodium ion transmembrane transporter activity (GO:2000649)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dystrophin-associated glycoprotein complex (GO:0016010)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane (GO:0016020)|membrane raft (GO:0045121)|myofibril (GO:0030016)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|protein kinase binding (GO:0019901)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(1)|cervix(2)|endometrium(21)|kidney(10)|large_intestine(29)|lung(56)|ovary(5)|pancreas(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	148		Ovarian(120;0.218)		OV - Ovarian serous cystadenocarcinoma(155;5.72e-07)|GBM - Glioblastoma multiforme(68;4.9e-05)|Colorectal(48;0.213)		GCTCATCCTAATGTCCAAAAG	0.353													G|||	1868	0.373003	0.3328	0.2147	5008	,	,		18651	0.5952		0.2515	False		,,,				2504	0.4356				p.N2202S		Atlas-SNP	.											.	UTRN	327	.	0			c.A6605G						PASS	.	G	SER/ASN	1311,3095	696.2+/-406.1	194,923,1086	76.0	72.0	73.0		6605	-6.3	0.0	6	dbSNP_88	73	2016,6584	719.8+/-406.3	249,1518,2533	yes	missense	UTRN	NM_007124.2	46	443,2441,3619	GG,GA,AA		23.4419,29.7549,25.5805	benign	2202/3434	144869785	3327,9679	2203	4300	6503	SO:0001583	missense	7402	exon46			ATCCTAATGTCCA	AK023675	CCDS34547.1	6q24	2008-02-05	2006-12-13		ENSG00000152818	ENSG00000152818			12635	protein-coding gene	gene with protein product		128240	"""utrophin (homologous to dystrophin)"""	DMDL		1426262	Standard	NM_007124		Approved	DRP, DRP1	uc003qkt.3	P46939	OTTHUMG00000015746	ENST00000367545.3:c.6605A>G	6.37:g.144869785A>G	ENSP00000356515:p.Asn2202Ser	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	79	78	0.987342	NM_007124	Q5SYY1|Q5SZ57|Q9UJ40	Missense_Mutation	SNP	ENST00000367545.3	37	CCDS34547.1	781	0.3576007326007326	161	0.32723577235772355	86	0.23756906077348067	352	0.6153846153846154	182	0.24010554089709762	G	2.009	-0.427481	0.04701	0.297549	0.234419	ENSG00000152818	ENST00000367545	T	0.58358	0.34	5.38	-6.34	0.01982	.	1.235210	0.05557	N	0.568514	T	0.05181	0.0138	N	0.04508	-0.205	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.05194	-1.0900	9	0.05525	T	0.97	.	2.0573	0.03584	0.3677:0.3206:0.0947:0.217	rs1534443;rs52835913;rs58543842;rs1534443	2202	P46939	UTRO_HUMAN	S	2202	ENSP00000356515:N2202S	ENSP00000356515:N2202S	N	+	2	0	UTRN	144911478	0.000000	0.05858	0.000000	0.03702	0.883000	0.51084	-0.108000	0.10857	-1.221000	0.02591	-0.954000	0.02651	AAT	A|0.684;G|0.316	0.316	strong		0.353	UTRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042551.1		
MRGPRX3	117195	hgsc.bcm.edu	37	11	18158993	18158993	+	Missense_Mutation	SNP	T	T	C	rs12291017	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:18158993T>C	ENST00000396275.2	+	3	605	c.244T>C	c.(244-246)Tgt>Cgt	p.C82R		NM_054031.3	NP_473372.3	Q96LB0	MRGX3_HUMAN	MAS-related GPR, member X3	82			C -> R (in dbSNP:rs12291017). {ECO:0000269|PubMed:15489334}.			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(5)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	27						CCACATTATATGTTCGCCGTT	0.552													N|||	1160	0.231629	0.5628	0.1398	5008	,	,		21475	0.0208		0.1789	False		,,,				2504	0.1207				p.C82R		Atlas-SNP	.											.	MRGPRX3	59	.	0			c.T244C						PASS	.	C	ARG/CYS	2101,2299	600.2+/-389.4	502,1097,601	94.0	91.0	92.0		244	-2.9	0.0	11	dbSNP_120	92	1516,7070	746.9+/-407.3	160,1196,2937	yes	missense	MRGPRX3	NM_054031.3	180	662,2293,3538	CC,CT,TT		17.6567,47.75,27.8531	benign	82/323	18158993	3617,9369	2200	4293	6493	SO:0001583	missense	117195	exon3			ATTATATGTTCGC		CCDS7830.1	11p15.1	2013-10-10			ENSG00000179826	ENSG00000179826		"""GPCR / Class A : Orphans"""	17980	protein-coding gene	gene with protein product		607229				11551509	Standard	NM_054031		Approved	MRGX3	uc001mnu.3	Q96LB0	OTTHUMG00000166435	ENST00000396275.2:c.244T>C	11.37:g.18158993T>C	ENSP00000379571:p.Cys82Arg	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	84	67	0.797619	NM_054031	B0M0L1|Q8TDE0|Q8TDE1	Missense_Mutation	SNP	ENST00000396275.2	37	CCDS7830.1	460	0.21062271062271062	256	0.5203252032520326	56	0.15469613259668508	15	0.026223776223776224	133	0.17546174142480211	C	0.810	-0.752365	0.03041	0.4775	0.176567	ENSG00000179826	ENST00000396275;ENST00000531264	T;T	0.09255	3.0;3.0	1.46	-2.93	0.05598	GPCR, rhodopsin-like superfamily (1);	4.188610	0.00465	N	0.000101	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	0.48269	-0.9050	9	0.25751	T	0.34	.	0.6705	0.00858	0.2106:0.1538:0.3389:0.2968	rs12291017;rs16935000;rs56427318;rs12291017	82	Q96LB0	MRGX3_HUMAN	R	82	ENSP00000379571:C82R;ENSP00000436242:C82R	ENSP00000379571:C82R	C	+	1	0	MRGPRX3	18115569	.	.	0.000000	0.03702	0.000000	0.00434	.	.	-2.910000	0.00308	-1.946000	0.00489	TGT	T|0.747;C|0.253	0.253	strong		0.552	MRGPRX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389767.1	NM_054031	
PTBP1	5725	hgsc.bcm.edu	37	19	808586	808586	+	Silent	SNP	C	C	G	rs13169	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:808586C>G	ENST00000349038.4	+	12	1282	c.1209C>G	c.(1207-1209)ccC>ccG	p.P403P	PTBP1_ENST00000350092.4_Silent_p.P69P|PTBP1_ENST00000356948.6_Silent_p.P429P|PTBP1_ENST00000394601.4_Silent_p.P422P	NM_031991.3	NP_114368.1	P26599	PTBP1_HUMAN	polypyrimidine tract binding protein 1	403	RRM 3. {ECO:0000255|PROSITE- ProRule:PRU00176}.				alternative mRNA splicing, via spliceosome (GO:0000380)|gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|negative regulation of muscle cell differentiation (GO:0051148)|negative regulation of RNA splicing (GO:0033119)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing (GO:0008380)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|poly-pyrimidine tract binding (GO:0008187)|pre-mRNA binding (GO:0036002)|RNA binding (GO:0003723)	p.P429P(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|skin(2)|upper_aerodigestive_tract(4)	19		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;6.59e-06)|all_lung(49;9.97e-06)|Breast(49;0.000172)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		ACGGGAAGCCCATCCGCATCA	0.697													C|||	805	0.160743	0.1339	0.2666	5008	,	,		9699	0.0218		0.1451	False		,,,				2504	0.2812				p.P429P		Atlas-SNP	.											PTBP1,NS,lymphoid_neoplasm,0,1	PTBP1	43	1	1	Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(1)	c.C1287G						PASS	.	C	,,,	558,3840		44,470,1685	37.0	29.0	31.0		1287,1266,1209,207	-10.3	0.3	19	dbSNP_52	31	1250,7346		87,1076,3135	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PTBP1	NM_002819.4,NM_031990.3,NM_031991.3,NM_175847.2	,,,	131,1546,4820	GG,GC,CC		14.5416,12.6876,13.9141	,,,	429/558,422/551,403/532,69/198	808586	1808,11186	2199	4298	6497	SO:0001819	synonymous_variant	5725	exon13			GAAGCCCATCCGC	X60648	CCDS32859.1, CCDS42456.1, CCDS45892.1	19p13.3	2013-07-16	2002-01-25	2002-01-25	ENSG00000011304	ENSG00000011304		"""RNA binding motif (RRM) containing"""	9583	protein-coding gene	gene with protein product	"""heterogeneous nuclear ribonucleoprotein I"""	600693	"""polypyrimidine tract binding protein (heterogeneous nuclear ribonucleoprotein I)"""	PTB		1906036, 11024286	Standard	NM_002819		Approved	HNRPI, HNRNP-I, PTB2, PTB3, PTB-1, PTB4, pPTB	uc002lpp.2	P26599		ENST00000349038.4:c.1209C>G	19.37:g.808586C>G		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	69	69	1	NM_002819	Q9BUQ0	Silent	SNP	ENST00000349038.4	37	CCDS32859.1																																																																																			C|0.867;G|0.133	0.133	strong		0.697	PTBP1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457605.1		
SYNE1	23345	hgsc.bcm.edu	37	6	152763258	152763258	+	Silent	SNP	T	T	C	rs138705766	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:152763258T>C	ENST00000367255.5	-	31	4561	c.3960A>G	c.(3958-3960)acA>acG	p.T1320T	SYNE1_ENST00000367253.4_Silent_p.T1320T|SYNE1_ENST00000367248.3_Silent_p.T1310T|SYNE1_ENST00000265368.4_Silent_p.T1320T|SYNE1_ENST00000413186.2_Silent_p.T1320T|SYNE1_ENST00000448038.1_Silent_p.T1327T|SYNE1_ENST00000423061.1_Silent_p.T1327T|SYNE1_ENST00000341594.5_Silent_p.T1386T	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	1320					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)		GGCCATCCAGTGTGCTCTCCA	0.632										HNSCC(10;0.0054)			G|||	64	0.0127796	0.0106	0.0159	5008	,	,		16360	0.001		0.0209	False		,,,				2504	0.0174				p.T1327T		Atlas-SNP	.											.	SYNE1	3227	.	0			c.A3981G						PASS	.	G	,	51,4355		0,51,2152	72.0	70.0	71.0		3981,3960	-1.4	0.7	6	dbSNP_134	71	158,8442		2,154,4144	no	coding-synonymous,coding-synonymous	SYNE1	NM_033071.3,NM_182961.3	,	2,205,6296	CC,CT,TT		1.8372,1.1575,1.607	,	1327/8750,1320/8798	152763258	209,12797	2203	4300	6503	SO:0001819	synonymous_variant	23345	exon31			ATCCAGTGTGCTC	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.3960A>G	6.37:g.152763258T>C		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	43	33	0.767442	NM_033071	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Silent	SNP	ENST00000367255.5	37	CCDS5236.2																																																																																			T|0.983;C|0.017	0.017	strong		0.632	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961	
OPLAH	26873	hgsc.bcm.edu	37	8	145114643	145114643	+	Silent	SNP	G	G	A	rs6558292	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:145114643G>A	ENST00000426825.1	-	3	303	c.222C>T	c.(220-222)atC>atT	p.I74I	OPLAH_ENST00000534424.1_5'UTR	NM_017570.3	NP_060040.1	O14841	OPLA_HUMAN	5-oxoprolinase (ATP-hydrolysing)	74					glutathione biosynthetic process (GO:0006750)|glutathione derivative biosynthetic process (GO:1901687)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	5-oxoprolinase (ATP-hydrolyzing) activity (GO:0017168)|ATP binding (GO:0005524)			breast(1)|central_nervous_system(1)|endometrium(1)|lung(13)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	20	all_cancers(97;1.06e-10)|all_epithelial(106;1.5e-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;6.79e-41)|Epithelial(56;1.02e-39)|all cancers(56;2.24e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			GGATGCTGGCGATATGACTGG	0.692													G|||	335	0.066893	0.1399	0.0548	5008	,	,		15951	0.001		0.0815	False		,,,				2504	0.0297				p.I74I		Atlas-SNP	.											.	OPLAH	78	.	0			c.C222T						PASS	.	G		541,3803		33,475,1664	25.0	32.0	30.0		222	-10.5	0.1	8	dbSNP_116	30	568,7942		13,542,3700	no	coding-synonymous	OPLAH	NM_017570.3		46,1017,5364	AA,AG,GG		6.6745,12.454,8.6277		74/1289	145114643	1109,11745	2172	4255	6427	SO:0001819	synonymous_variant	26873	exon3			GCTGGCGATATGA	AF024672, AB122018	CCDS75802.1	8q24.3	2010-11-23			ENSG00000178814	ENSG00000178814	3.5.2.9		8149	protein-coding gene	gene with protein product		614243				14993790	Standard	NM_017570		Approved	OPLA, 5-Opase	uc003zar.3	O14841		ENST00000426825.1:c.222C>T	8.37:g.145114643G>A		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	56	55	0.982143	NM_017570	A5PKY8|Q75W65|Q9Y4Q0	Silent	SNP	ENST00000426825.1	37																																																																																				G|0.920;A|0.080	0.080	strong		0.692	OPLAH-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_017570	
CTAGE5	4253	hgsc.bcm.edu	37	14	39818028	39818028	+	Missense_Mutation	SNP	A	A	G	rs1140952	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:39818028A>G	ENST00000280083.3	+	23	2409	c.2095A>G	c.(2095-2097)Atc>Gtc	p.I699V	CTAGE5_ENST00000557038.1_Missense_Mutation_p.I619V|CTAGE5_ENST00000341502.5_Missense_Mutation_p.I699V|CTAGE5_ENST00000553352.1_Missense_Mutation_p.I670V|CTAGE5_ENST00000348007.3_Missense_Mutation_p.I656V|CTAGE5_ENST00000553383.1_3'UTR|RP11-407N17.3_ENST00000553728.1_Missense_Mutation_p.I1234V|CTAGE5_ENST00000341749.3_Missense_Mutation_p.I687V|CTAGE5_ENST00000556148.1_Missense_Mutation_p.I624V|RP11-407N17.3_ENST00000603904.1_Missense_Mutation_p.I670V|CTAGE5_ENST00000396158.2_Missense_Mutation_p.I704V|CTAGE5_ENST00000396165.4_Missense_Mutation_p.I670V			O15320	CTGE5_HUMAN	CTAGE family, member 5	699	Pro-rich.		I -> V (in dbSNP:rs1140952). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9356211}.		positive regulation of catalytic activity (GO:0043085)	membrane (GO:0016020)	enzyme activator activity (GO:0008047)		CTAGE5/SIP1(2)	breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(11)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	28	Hepatocellular(127;0.213)		LUAD - Lung adenocarcinoma(48;0.000565)|Lung(238;0.000711)	GBM - Glioblastoma multiforme(112;0.0475)		TCTTGCTCCAATCAGAGGTCC	0.493													A|||	1926	0.384585	0.2519	0.3415	5008	,	,		16436	0.5923		0.4115	False		,,,				2504	0.3528				p.I704V		Atlas-SNP	.											CTAGE5,rectum,carcinoma,0,1	CTAGE5	75	1	0			c.A2110G						PASS	.	A	VAL/ILE,VAL/ILE,VAL/ILE,VAL/ILE	1173,3233	412.2+/-336.0	151,871,1181	191.0	199.0	196.0		2095,2059,1966,2008	-2.0	0.0	14	dbSNP_86	196	3395,5205	500.7+/-375.3	671,2053,1576	yes	missense,missense,missense,missense	CTAGE5	NM_005930.3,NM_203354.2,NM_203355.2,NM_203356.2	29,29,29,29	822,2924,2757	GG,GA,AA		39.4767,26.6228,35.1223	benign,benign,benign,benign	699/805,687/793,656/762,670/776	39818028	4568,8438	2203	4300	6503	SO:0001583	missense	4253	exon23			GCTCCAATCAGAG	U94780	CCDS9673.1, CCDS9674.1, CCDS9675.1, CCDS9676.1, CCDS58316.1, CCDS58317.1	14q21.1	2009-09-11	2004-08-24	2004-08-26	ENSG00000150527	ENSG00000150527			7057	protein-coding gene	gene with protein product		602132	"""meningioma expressed antigen 6 (coiled-coil proline-rich)"""	MGEA, MGEA6		9356211, 11149944	Standard	NM_203355		Approved	MEA6, cTAGE-5A, cTAGE-5B, cTAGE-5C, cTAGE-5D, MGEA11	uc001wvi.4	O15320	OTTHUMG00000140258	ENST00000280083.3:c.2095A>G	14.37:g.39818028A>G	ENSP00000280083:p.Ile699Val	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	105	62	0.590476	NM_001247989	B3KRA6|B4DQS6|D3DSA6|G3XAC5|O00169|Q6MZN2|Q6P2R8|Q86TF6|Q8IX92|Q8IX93	Missense_Mutation	SNP	ENST00000280083.3	37	CCDS9674.1	937	0.429029304029304	131	0.266260162601626	136	0.3756906077348066	359	0.6276223776223776	311	0.4102902374670185	A	0.004	-2.297832	0.00243	0.266228	0.394767	ENSG00000258941;ENSG00000150527;ENSG00000150527;ENSG00000150527;ENSG00000150527;ENSG00000150527;ENSG00000150527;ENSG00000150527;ENSG00000150527;ENSG00000150527	ENST00000553728;ENST00000341749;ENST00000557038;ENST00000396165;ENST00000341502;ENST00000396158;ENST00000280083;ENST00000556148;ENST00000348007;ENST00000553352	T;T;T;T;T;T;T;T;T;T	0.06528	3.49;3.33;3.33;3.29;3.55;3.58;3.58;3.33;3.83;3.29	5.41	-2.01	0.07410	.	1.206650	0.06423	N	0.722732	T	0.00012	0.0000	N	0.13043	0.29	0.80722	P	0.0	B;B;B;B;B	0.06786	0.0;0.001;0.0;0.001;0.0	B;B;B;B;B	0.09377	0.002;0.004;0.002;0.004;0.002	T	0.32241	-0.9914	8	.	.	.	.	8.1094	0.30905	0.1281:0.1851:0.6868:0.0	rs1140952;rs3204972;rs17846661;rs17859758;rs1140952	704;656;699;627;687	O15320-5;O15320-2;O15320;O15320-7;G3XAC5	.;.;CTGE5_HUMAN;.;.	V	1234;687;619;670;699;704;699;624;656;670	ENSP00000452252:I1234V;ENSP00000343897:I687V;ENSP00000450869:I619V;ENSP00000379468:I670V;ENSP00000339286:I699V;ENSP00000379462:I704V;ENSP00000280083:I699V;ENSP00000452562:I624V;ENSP00000343912:I656V;ENSP00000450449:I670V	.	I	+	1	0	CTAGE5;RP11-407N17.3	38887779	0.000000	0.05858	0.000000	0.03702	0.124000	0.20399	-1.436000	0.02421	-0.792000	0.04480	-0.316000	0.08728	ATC	A|0.632;G|0.368	0.368	strong		0.493	CTAGE5-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000276771.2	NM_005930	
USP42	84132	hgsc.bcm.edu	37	7	6189780	6189780	+	Silent	SNP	T	T	C	rs3764814	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:6189780T>C	ENST00000306177.5	+	13	2111	c.1953T>C	c.(1951-1953)ctT>ctC	p.L651L		NM_032172.2	NP_115548.1	Q9H9J4	UBP42_HUMAN	ubiquitin specific peptidase 42	651					cell differentiation (GO:0030154)|protein deubiquitination (GO:0016579)|spermatogenesis (GO:0007283)|ubiquitin-dependent protein catabolic process (GO:0006511)		ubiquitin-specific protease activity (GO:0004843)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(2)|lung(14)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	35		Ovarian(82;0.0423)		UCEC - Uterine corpus endometrioid carcinoma (126;0.108)|OV - Ovarian serous cystadenocarcinoma(56;5.77e-14)		CGCACGAGCTTCAAGAACCCA	0.577													C|||	1416	0.282748	0.4349	0.1844	5008	,	,		19683	0.4276		0.0885	False		,,,				2504	0.1973				p.L651L		Atlas-SNP	.											.	USP42	138	.	0			c.T1953C						PASS	.	C		1484,2590		263,958,816	34.0	40.0	38.0		1953	-6.2	0.0	7	dbSNP_107	38	596,7796		34,528,3634	no	coding-synonymous	USP42	NM_032172.2		297,1486,4450	CC,CT,TT		7.102,36.4261,16.6854		651/1317	6189780	2080,10386	2037	4196	6233	SO:0001819	synonymous_variant	84132	exon13			CGAGCTTCAAGAA	AK022759	CCDS47535.1	7p22.2	2005-08-08	2005-08-08		ENSG00000106346	ENSG00000106346		"""Ubiquitin-specific peptidases"""	20068	protein-coding gene	gene with protein product			"""ubiquitin specific protease 42"""			12838346	Standard	NM_032172		Approved	FLJ12697	uc011jwp.2	Q9H9J4	OTTHUMG00000151888	ENST00000306177.5:c.1953T>C	7.37:g.6189780T>C		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	37	27	0.72973	NM_032172	A2RUE3|B5MDA5|Q0VIN8|Q3C166|Q6P9B4	Silent	SNP	ENST00000306177.5	37	CCDS47535.1																																																																																			T|0.728;C|0.272	0.272	strong		0.577	USP42-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324262.3	XM_166526	
SCML4	256380	hgsc.bcm.edu	37	6	108029180	108029180	+	Missense_Mutation	SNP	G	G	A	rs56215636	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:108029180G>A	ENST00000369020.3	-	7	1254	c.1009C>T	c.(1009-1011)Cgg>Tgg	p.R337W	SCML4_ENST00000369022.2_Missense_Mutation_p.R279W|SCML4_ENST00000369025.2_Missense_Mutation_p.R95W	NM_198081.3	NP_932347.2	Q8N228	SCML4_HUMAN	sex comb on midleg-like 4 (Drosophila)	337	SAM.				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)		CTCCGTGGCCGCCTGGCATCC	0.647													G|||	48	0.00958466	0.003	0.0159	5008	,	,		18606	0.0		0.0278	False		,,,				2504	0.0051				p.R337W		Atlas-SNP	.											.	SCML4	65	.	0			c.C1009T						PASS	.	G	TRP/ARG	10,1374		0,10,682	42.0	52.0	49.0		1009	2.7	1.0	6	dbSNP_129	49	97,3085		2,93,1496	yes	missense	SCML4	NM_198081.3	101	2,103,2178	AA,AG,GG		3.0484,0.7225,2.3434	probably-damaging	337/415	108029180	107,4459	692	1591	2283	SO:0001583	missense	256380	exon7			GTGGCCGCCTGGC		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.1009C>T	6.37:g.108029180G>A	ENSP00000358016:p.Arg337Trp	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	87	49	0.563218	NM_198081	B0QZ10|B0QZ11|B7ZBX3|Q5JXD0|Q5T0T6|Q8IYY6	Missense_Mutation	SNP	ENST00000369020.3	37	CCDS5060.2	31	0.014194139194139194	1	0.0020325203252032522	5	0.013812154696132596	0	0.0	25	0.032981530343007916	G	19.26	3.793207	0.70452	0.007225	0.030484	ENSG00000146285	ENST00000369022;ENST00000369025;ENST00000369020	T;T	0.50001	0.77;0.76	5.65	2.66	0.31614	Sterile alpha motif/pointed domain (2);	0.721431	0.13042	N	0.418430	T	0.54822	0.1882	M	0.71036	2.16	0.58432	D	0.999999	D	0.71674	0.998	D	0.72625	0.978	T	0.57201	-0.7852	10	0.72032	D	0.01	.	10.3722	0.44060	0.0:0.1226:0.5074:0.3699	rs56215636;rs61740236	337	Q8N228	SCML4_HUMAN	W	279;95;337	ENSP00000358018:R279W;ENSP00000358016:R337W	ENSP00000358016:R337W	R	-	1	2	SCML4	108135873	0.935000	0.31712	1.000000	0.80357	0.929000	0.56500	1.733000	0.38156	0.688000	0.31529	0.650000	0.86243	CGG	G|0.984;A|0.016	0.016	strong		0.647	SCML4-005	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000041700.3	XM_171128	
ZNF831	128611	hgsc.bcm.edu	37	20	57769140	57769140	+	Missense_Mutation	SNP	G	G	C	rs55786258	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	44	0	0		WXS	Illumina HiSeq	Phase_I	34	16	0.470588	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	
TOR1AIP1	26092	hgsc.bcm.edu	37	1	179858444	179858444	+	Intron	SNP	G	G	A	rs2245425	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:179858444G>A	ENST00000606911.2	+	3	744				TOR1AIP1_ENST00000474875.1_Intron|TOR1AIP1_ENST00000435319.4_Intron|TOR1AIP1_ENST00000528443.2_Splice_Site|TOR1AIP1_ENST00000271583.3_Splice_Site			Q5JTV8	TOIP1_HUMAN	torsin A interacting protein 1						positive regulation of ATPase activity (GO:0032781)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)	ATPase activator activity (GO:0001671)|ATPase binding (GO:0051117)|cytoskeletal protein binding (GO:0008092)			breast(4)|central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(4)|ovary(2)|skin(1)|urinary_tract(1)	18						TCCTATATTAGCAGTGAGTGA	0.323													G|||	3182	0.635383	0.4644	0.6916	5008	,	,		16866	0.7778		0.6064	False		,,,				2504	0.7096				.		Atlas-SNP	.											.	TOR1AIP1	58	.	0			c.554-1G>A						PASS	.	G		2219,2187	590.7+/-387.4	553,1113,537	102.0	102.0	102.0			5.3	0.1	1	dbSNP_100	102	5362,3234	649.3+/-400.6	1674,2014,610	no	intron	TOR1AIP1	NM_015602.2		2227,3127,1147	AA,AG,GG		37.6221,49.6369,41.6936			179858444	7581,5421	2203	4298	6501	SO:0001627	intron_variant	26092	exon3			ATATTAGCAGTGA		CCDS1335.1, CCDS65737.1	1q24.2	2008-02-05			ENSG00000143337	ENSG00000143337			29456	protein-coding gene	gene with protein product	"""lamina associated polypeptide 1B"""	614512				12061773, 15767459	Standard	NM_015602		Approved	LAP1B, FLJ13142	uc001gnp.2	Q5JTV8	OTTHUMG00000035257	ENST00000606911.2:c.554-4G>A	1.37:g.179858444G>A		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	60	26	0.433333	NM_001267578	A8K630|B0QZ57|Q5JTV6|Q8IZ65|Q9H8Y6|Q9HAJ1|Q9NV52|Q9Y3X5	Splice_Site	SNP	ENST00000606911.2	37	CCDS1335.1	1369	0.6268315018315018	218	0.44308943089430897	241	0.6657458563535912	451	0.7884615384615384	459	0.6055408970976254	G	11.86	1.764619	0.31228	0.503631	0.623779	ENSG00000143337	ENST00000528443;ENST00000271583	.	.	.	5.26	5.26	0.73747	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	0.9999999999999999	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.7301	0.69374	0.0:0.0:1.0:0.0	rs2245425;rs16854913;rs59592554;rs2245425	.	.	.	.	-1	.	.	.	+	.	.	TOR1AIP1	178125067	0.993000	0.37304	0.123000	0.21794	0.006000	0.05464	4.200000	0.58433	2.598000	0.87819	0.557000	0.71058	.	G|0.377;A|0.623	0.623	strong		0.323	TOR1AIP1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000100313.4	NM_015602	
SNAPC4	6621	hgsc.bcm.edu	37	9	139276448	139276448	+	Silent	SNP	A	A	G	rs150900916	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:139276448A>G	ENST00000298532.2	-	17	2513	c.2145T>C	c.(2143-2145)caT>caC	p.H715H		NM_003086.2	NP_003077.2			small nuclear RNA activating complex, polypeptide 4, 190kDa											biliary_tract(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(13)|ovary(1)|prostate(3)|skin(2)|urinary_tract(1)	33		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;5.31e-06)|Epithelial(140;7.13e-06)		GCCACTGCACATGGGATCGGG	0.657													A|||	2	0.000399361	0.0	0.0	5008	,	,		17692	0.0		0.002	False		,,,				2504	0.0				p.H715H		Atlas-SNP	.											.	SNAPC4	82	.	0			c.T2145C						PASS	.	A		2,4396		0,2,2197	19.0	20.0	20.0		2145	-8.2	0.0	9	dbSNP_134	20	11,8579		0,11,4284	no	coding-synonymous	SNAPC4	NM_003086.2		0,13,6481	GG,GA,AA		0.1281,0.0455,0.1001		715/1470	139276448	13,12975	2199	4295	6494	SO:0001819	synonymous_variant	6621	exon17			CTGCACATGGGAT	AF032387	CCDS6998.1	9q34.3	2008-07-21	2002-08-29		ENSG00000165684	ENSG00000165684			11137	protein-coding gene	gene with protein product		602777	"""small nuclear RNA activating complex, polypeptide 4, 190kD"""			9418884	Standard	XM_005266096		Approved	SNAP190, PTFalpha, FLJ13451	uc004chh.3	Q5SXM2	OTTHUMG00000020929	ENST00000298532.2:c.2145T>C	9.37:g.139276448A>G		Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	112	62	0.553571	NM_003086		Silent	SNP	ENST00000298532.2	37	CCDS6998.1																																																																																			A|0.999;G|0.001	0.001	strong		0.657	SNAPC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055071.1	NM_003086	
PCDHGA2	56113	hgsc.bcm.edu	37	5	140719090	140719090	+	Silent	SNP	G	G	A	rs6861047	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:140719090G>A	ENST00000394576.2	+	1	552	c.552G>A	c.(550-552)agG>agA	p.R184R	PCDHGA1_ENST00000517417.1_Intron	NM_018915.2	NP_061738.1	Q9Y5H1	PCDG2_HUMAN	protocadherin gamma subfamily A, 2	184	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(20)|lung(32)|ovary(1)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	77			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ACGTGCGAAGGGGAGCTGATG	0.562													N|||	533	0.10643	0.0809	0.1124	5008	,	,		19274	0.0605		0.174	False		,,,				2504	0.1145				p.R184R		Atlas-SNP	.											.	PCDHGA2	205	.	0			c.G552A						PASS	.	C	,,	416,3990		18,380,1805	92.0	89.0	90.0		,552,552	-0.5	0.0	5	dbSNP_116	90	1365,7235		97,1171,3032	no	intron,coding-synonymous,coding-synonymous	PCDHGA2,PCDHGA1	NM_018912.2,NM_018915.2,NM_032009.1	,,	115,1551,4837	AA,AG,GG		15.8721,9.4417,13.6937	,,	,184/933,184/824	140719090	1781,11225	2203	4300	6503	SO:0001819	synonymous_variant	56113	exon1			GCGAAGGGGAGCT	AF152508	CCDS47289.1	5q31	2011-03-28			ENSG00000081853	ENSG00000081853		"""Cadherins / Protocadherins : Clustered"""	8700	other	protocadherin		606289				10380929	Standard	NM_018915		Approved	PCDH-GAMMA-A2		Q9Y5H1	OTTHUMG00000163679	ENST00000394576.2:c.552G>A	5.37:g.140719090G>A		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	68	33	0.485294	NM_018915	Q52LL6|Q9Y5D5	Silent	SNP	ENST00000394576.2	37	CCDS47289.1																																																																																			G|0.884;A|0.116	0.116	strong		0.562	PCDHGA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374738.1	NM_018915	
SPAG17	200162	hgsc.bcm.edu	37	1	118693217	118693217	+	Silent	SNP	T	T	C	rs1935992	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:118693217T>C	ENST00000336338.5	-	3	329	c.264A>G	c.(262-264)tcA>tcG	p.S88S		NM_206996.2	NP_996879.1	Q6Q759	SPG17_HUMAN	sperm associated antigen 17	88						cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)|sperm flagellum (GO:0036126)				NS(1)|biliary_tract(1)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(30)|liver(2)|lung(56)|ovary(3)|prostate(5)|skin(5)|upper_aerodigestive_tract(6)|urinary_tract(1)	123	Esophageal squamous(2;0.0106)	all_cancers(81;0.0204)|all_lung(203;9.46e-05)|Lung NSC(69;0.000675)|all_epithelial(167;0.01)		Lung(183;0.0858)		CCTTTTTAGATGAAGCAGATC	0.259													T|||	1137	0.227037	0.0129	0.3458	5008	,	,		15639	0.4048		0.2356	False		,,,				2504	0.2403				p.S88S		Atlas-SNP	.											SPAG17,NS,carcinoma,0,1	SPAG17	263	1	0			c.A264G						PASS	.	T		213,4183	122.5+/-159.9	7,199,1992	69.0	71.0	70.0		264	0.9	0.0	1	dbSNP_92	70	1868,6702	326.4+/-317.4	206,1456,2623	no	coding-synonymous	SPAG17	NM_206996.2		213,1655,4615	CC,CT,TT		21.797,4.8453,16.0497		88/2224	118693217	2081,10885	2198	4285	6483	SO:0001819	synonymous_variant	200162	exon3			TTTAGATGAAGCA		CCDS899.1	1p12	2014-01-21			ENSG00000155761	ENSG00000155761			26620	protein-coding gene	gene with protein product							Standard	NM_206996		Approved	FLJ34497, PF6, RP4-776P7.2, CT143	uc001ehk.2	Q6Q759	OTTHUMG00000012198	ENST00000336338.5:c.264A>G	1.37:g.118693217T>C		Somatic	226	0	0		WXS	Illumina HiSeq	Phase_I	222	107	0.481982	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	
IGFN1	91156	hgsc.bcm.edu	37	1	201163306	201163306	+	Missense_Mutation	SNP	C	C	G	rs41313898	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:201163306C>G	ENST00000335211.4	+	3	162	c.32C>G	c.(31-33)cCt>cGt	p.P11R	IGFN1_ENST00000451870.2_Missense_Mutation_p.P11R|IGFN1_ENST00000295591.8_5'UTR	NM_001164586.1	NP_001158058.1	Q86VF2	IGFN1_HUMAN	immunoglobulin-like and fibronectin type III domain containing 1	11						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						TCCCACATCCCTGGAGTGAGC	0.607													C|||	7	0.00139776	0.0015	0.0014	5008	,	,		18751	0.0		0.004	False		,,,				2504	0.0				p.P11R		Atlas-SNP	.											.	IGFN1	220	.	0			c.C32G						PASS	.						30.0	36.0	34.0					1																	201163306		692	1591	2283	SO:0001583	missense	91156	exon3			ACATCCCTGGAGT	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.32C>G	1.37:g.201163306C>G	ENSP00000334714:p.Pro11Arg	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	116	116	1	NM_001164586	F8WAI1|Q9NT72	Missense_Mutation	SNP	ENST00000335211.4	37	CCDS53455.1	2	9.157509157509158E-4	1	0.0020325203252032522	0	0.0	0	0.0	1	0.0013192612137203166	C	11.13	1.547817	0.27652	.	.	ENSG00000163395	ENST00000335211;ENST00000451870	T;T	0.62788	0.24;0.0	4.55	3.61	0.41365	.	.	.	.	.	T	0.66723	0.2818	L	0.55481	1.735	0.80722	D	1	.	.	.	.	.	.	T	0.68146	-0.5486	7	0.87932	D	0	.	10.9911	0.47549	0.1992:0.8008:0.0:0.0	rs41313898	.	.	.	R	11	ENSP00000334714:P11R;ENSP00000398386:P11R	ENSP00000334714:P11R	P	+	2	0	IGFN1	199429929	0.281000	0.24258	0.781000	0.31783	0.577000	0.36160	2.171000	0.42453	0.840000	0.34995	0.637000	0.83480	CCT	C|0.999;G|0.001	0.001	strong		0.607	IGFN1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_178275	
PON3	5446	hgsc.bcm.edu	37	7	95001555	95001555	+	Silent	SNP	C	C	T	rs1053275	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:95001555C>T	ENST00000265627.5	-	4	307	c.297G>A	c.(295-297)gcG>gcA	p.A99A	PON1_ENST00000542556.1_Intron|PON3_ENST00000427422.1_Silent_p.A99A|PON3_ENST00000451904.1_Silent_p.A99A	NM_000940.2	NP_000931.1	Q15166	PON3_HUMAN	paraoxonase 3	99					aromatic compound catabolic process (GO:0019439)|carboxylic acid catabolic process (GO:0046395)|coumarin catabolic process (GO:0046226)|phenylacetate catabolic process (GO:0010124)|response to external stimulus (GO:0009605)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)	3,4-dihydrocoumarin hydrolase activity (GO:0018733)|aryldialkylphosphatase activity (GO:0004063)|arylesterase activity (GO:0004064)|dihydrocoumarin hydrolase activity (GO:0047856)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)			breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)|pancreas(1)|prostate(2)|skin(2)	24	all_cancers(62;1.04e-10)|all_epithelial(64;3.67e-09)|Lung NSC(181;0.239)		STAD - Stomach adenocarcinoma(171;0.0151)		Edetic Acid(DB00974)|Lovastatin(DB00227)	TGATTTCTAGCGCTTGTGCCC	0.398													T|||	3308	0.660543	0.6422	0.6772	5008	,	,		17161	0.7788		0.501	False		,,,				2504	0.7157				p.A99A		Atlas-SNP	.											.	PON3	59	.	0			c.G297A						PASS	.	T		2501,1905	544.8+/-376.6	708,1085,410	156.0	147.0	150.0		297	-0.6	0.0	7	dbSNP_86	150	3933,4667	604.0+/-394.7	906,2121,1273	no	coding-synonymous	PON3	NM_000940.2		1614,3206,1683	TT,TC,CC		45.7326,43.2365,49.4695		99/355	95001555	6434,6572	2203	4300	6503	SO:0001819	synonymous_variant	5446	exon4			TTCTAGCGCTTGT	L48516, AF320003	CCDS5639.1	7q21.3	2014-03-14			ENSG00000105852	ENSG00000105852	3.1.1.2	"""Paraoxonases"""	9206	protein-coding gene	gene with protein product	"""arylesterase 3"""	602720				8661009	Standard	NM_000940		Approved			Q15166	OTTHUMG00000153917	ENST00000265627.5:c.297G>A	7.37:g.95001555C>T		Somatic	237	0	0		WXS	Illumina HiSeq	Phase_I	218	97	0.444954	NM_000940	A4D1H8|O75855|O76060|Q6IRU9|Q8IX97|Q9BZH9	Silent	SNP	ENST00000265627.5	37	CCDS5639.1																																																																																			C|0.417;T|0.583	0.583	strong		0.398	PON3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333007.1	NM_000940	
OR2T34	127068	hgsc.bcm.edu	37	1	248737329	248737329	+	Missense_Mutation	SNP	C	C	T	rs75095367	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:248737329C>T	ENST00000328782.2	-	1	751	c.730G>A	c.(730-732)Gcc>Acc	p.A244T		NM_001001821.1	NP_001001821.1	Q8NGX1	O2T34_HUMAN	olfactory receptor, family 2, subfamily T, member 34	244						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(1)|large_intestine(6)|lung(28)|ovary(2)|skin(2)|stomach(3)	43	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			GAGCAGGTGGCCAAGGCCTTC	0.562																																					p.A244T		Atlas-SNP	.											.	OR2T34	72	.	0			c.G730A						PASS	.	C	THR/ALA	894,3456		168,558,1449	101.0	114.0	110.0		730	0.0	0.4	1	dbSNP_131	110	734,7866		28,678,3594	no	missense	OR2T34	NM_001001821.1	58	196,1236,5043	TT,TC,CC		8.5349,20.5517,12.5714	benign	244/319	248737329	1628,11322	2175	4300	6475	SO:0001583	missense	127068	exon1			AGGTGGCCAAGGC	BK004477	CCDS31120.1	1q44	2012-08-09			ENSG00000183310	ENSG00000183310		"""GPCR / Class A : Olfactory receptors"""	31256	protein-coding gene	gene with protein product							Standard	NM_001001821		Approved		uc001iep.1	Q8NGX1	OTTHUMG00000040387	ENST00000328782.2:c.730G>A	1.37:g.248737329C>T	ENSP00000330904:p.Ala244Thr	Somatic	302	0	0		WXS	Illumina HiSeq	Phase_I	227	114	0.502203	NM_001001821	B2RNJ8|Q6IEY5|Q96R31	Missense_Mutation	SNP	ENST00000328782.2	37	CCDS31120.1	526	0.24084249084249085	133	0.2703252032520325	54	0.14917127071823205	259	0.4527972027972028	80	0.10554089709762533	.	2.736	-0.263225	0.05754	0.205517	0.085349	ENSG00000183310	ENST00000328782	T	0.00063	8.78	2.37	0.0258	0.14147	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00012	0.0000	N	0.21583	0.68	0.80722	P	0.0	B	0.26672	0.156	B	0.30943	0.122	T	0.00171	-1.1960	8	0.27082	T	0.32	.	4.2667	0.10766	0.453:0.4117:0.0:0.1352	.	244	Q8NGX1	O2T34_HUMAN	T	244	ENSP00000330904:A244T	ENSP00000330904:A244T	A	-	1	0	OR2T34	246803952	0.008000	0.16893	0.422000	0.26621	0.327000	0.28475	0.078000	0.14761	0.208000	0.20626	0.123000	0.15791	GCC	C|0.816;T|0.184	0.184	strong		0.562	OR2T34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097138.1	NM_001001821	
ATP2A3	489	hgsc.bcm.edu	37	17	3840928	3840928	+	Silent	SNP	A	A	G	rs3179783	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:3840928A>G	ENST00000352011.3	-	15	2157	c.2103T>C	c.(2101-2103)acT>acC	p.T701T	ATP2A3_ENST00000397043.3_Silent_p.T701T|ATP2A3_ENST00000359983.3_Silent_p.T701T|ATP2A3_ENST00000397041.3_Silent_p.T701T|ATP2A3_ENST00000397035.3_Silent_p.T701T|ATP2A3_ENST00000309890.7_Silent_p.T701T|ATP2A3_ENST00000397039.1_5'UTR			Q93084	AT2A3_HUMAN	ATPase, Ca++ transporting, ubiquitous	701					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)		CTCCATCGCCAGTCTGTGGGC	0.612													A|||	1039	0.207468	0.3578	0.17	5008	,	,		20549	0.0655		0.1918	False		,,,				2504	0.1933				p.T701T	GBM(32;29 774 15719 37967)	Atlas-SNP	.											.	ATP2A3	148	.	0			c.T2103C						PASS	.	A	,,,,,,	1436,2970	455.5+/-351.0	245,946,1012	42.0	38.0	40.0		2103,2103,2103,2103,2103,2103,2103	-1.1	1.0	17	dbSNP_105	40	1710,6890	307.6+/-308.5	157,1396,2747	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ATP2A3	NM_005173.3,NM_174953.2,NM_174954.2,NM_174955.2,NM_174956.2,NM_174957.2,NM_174958.2	,,,,,,	402,2342,3759	GG,GA,AA		19.8837,32.5919,24.1888	,,,,,,	701/1000,701/1053,701/1045,701/1044,701/1030,701/999,701/1030	3840928	3146,9860	2203	4300	6503	SO:0001819	synonymous_variant	489	exon15			ATCGCCAGTCTGT		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.2103T>C	17.37:g.3840928A>G		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	56	29	0.517857	NM_174956	A8MZG0|D3DTJ8|O60900|O60901|O75501|O75502|Q16115|Q6JHX1|Q8TEX5|Q8TEX6	Silent	SNP	ENST00000352011.3	37	CCDS11041.1																																																																																			A|0.782;G|0.218	0.218	strong		0.612	ATP2A3-015	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000438401.1	NM_174953	
TGFBR2	7048	hgsc.bcm.edu	37	3	30713842	30713842	+	Silent	SNP	C	C	T	rs2228048	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:30713842C>T	ENST00000295754.5	+	4	1549	c.1167C>T	c.(1165-1167)aaC>aaT	p.N389N	TGFBR2_ENST00000359013.4_Silent_p.N414N	NM_003242.5	NP_003233.4	P37173	TGFR2_HUMAN	transforming growth factor, beta receptor II (70/80kDa)	389	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of protein kinase activity (GO:0032147)|aging (GO:0007568)|apoptotic process (GO:0006915)|blood vessel development (GO:0001568)|brain development (GO:0007420)|bronchus morphogenesis (GO:0060434)|cartilage development (GO:0051216)|common-partner SMAD protein phosphorylation (GO:0007182)|digestive tract development (GO:0048565)|embryo implantation (GO:0007566)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic hemopoiesis (GO:0035162)|gastrulation (GO:0007369)|heart development (GO:0007507)|in utero embryonic development (GO:0001701)|lens development in camera-type eye (GO:0002088)|lens fiber cell apoptotic process (GO:1990086)|lung lobe morphogenesis (GO:0060463)|mammary gland morphogenesis (GO:0060443)|myeloid dendritic cell differentiation (GO:0043011)|negative regulation of cardiac muscle cell proliferation (GO:0060044)|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)|patterning of blood vessels (GO:0001569)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of angiogenesis (GO:0045766)|positive regulation of B cell tolerance induction (GO:0002663)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of NK T cell differentiation (GO:0051138)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of skeletal muscle tissue regeneration (GO:0043415)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of T cell tolerance induction (GO:0002666)|positive regulation of tolerance induction to self antigen (GO:0002651)|protein phosphorylation (GO:0006468)|receptor-mediated endocytosis (GO:0006898)|regulation of cell proliferation (GO:0042127)|response to cholesterol (GO:0070723)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|response to glucose (GO:0009749)|response to mechanical stimulus (GO:0009612)|response to nutrient (GO:0007584)|smoothened signaling pathway (GO:0007224)|trachea formation (GO:0060440)|transforming growth factor beta receptor signaling pathway (GO:0007179)|vasculogenesis (GO:0001570)|wound healing (GO:0042060)	caveola (GO:0005901)|cytosol (GO:0005829)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|transforming growth factor beta receptor homodimeric complex (GO:0070022)	ATP binding (GO:0005524)|glycosaminoglycan binding (GO:0005539)|metal ion binding (GO:0046872)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|SMAD binding (GO:0046332)|transforming growth factor beta binding (GO:0050431)|transforming growth factor beta receptor activity, type II (GO:0005026)|transforming growth factor beta-activated receptor activity (GO:0005024)|transmembrane receptor protein serine/threonine kinase activity (GO:0004675)|type I transforming growth factor beta receptor binding (GO:0034713)|type III transforming growth factor beta receptor binding (GO:0034714)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(15)|lung(10)|ovary(3)|pancreas(12)|skin(1)|stomach(5)|upper_aerodigestive_tract(2)	53						TCGTGAAGAACGACCTAACCT	0.557													C|||	518	0.103435	0.0431	0.0101	5008	,	,		21448	0.2986		0.0129	False		,,,				2504	0.1431				p.N414N		Atlas-SNP	.											.	TGFBR2	139	.	0			c.C1242T						PASS	.	C	,	143,4263	101.6+/-140.2	1,141,2061	305.0	268.0	281.0		1242,1167	-4.6	0.8	3	dbSNP_98	281	95,8505	52.7+/-113.3	0,95,4205	no	coding-synonymous,coding-synonymous	TGFBR2	NM_001024847.2,NM_003242.5	,	1,236,6266	TT,TC,CC		1.1047,3.2456,1.8299	,	414/593,389/568	30713842	238,12768	2203	4300	6503	SO:0001819	synonymous_variant	7048	exon5			GAAGAACGACCTA		CCDS2648.1, CCDS33727.1	3p22	2014-09-17	2002-08-29		ENSG00000163513	ENSG00000163513			11773	protein-coding gene	gene with protein product		190182	"""transforming growth factor, beta receptor II (70-80kD)"""	MFS2		1319842, 15235604	Standard	NM_001024847		Approved		uc003cen.3	P37173	OTTHUMG00000130569	ENST00000295754.5:c.1167C>T	3.37:g.30713842C>T		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	149	60	0.402685	NM_001024847	B4DTV5|Q15580|Q6DKT6|Q99474	Silent	SNP	ENST00000295754.5	37	CCDS2648.1																																																																																			C|0.947;T|0.053	0.053	strong		0.557	TGFBR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252994.2		
APMAP	57136	hgsc.bcm.edu	37	20	24964558	24964558	+	Missense_Mutation	SNP	T	T	C	rs12242	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:24964558T>C	ENST00000217456.2	-	2	483	c.193A>G	c.(193-195)Ata>Gta	p.I65V	APMAP_ENST00000447138.1_Missense_Mutation_p.I65V	NM_020531.2	NP_065392.1	Q9HDC9	APMAP_HUMAN	adipocyte plasma membrane associated protein	65			I -> V (in dbSNP:rs17298715).		biosynthetic process (GO:0009058)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	arylesterase activity (GO:0004064)|strictosidine synthase activity (GO:0016844)										TGTGGATCTATAGGAGATTCC	0.517													T|||	84	0.0167732	0.0038	0.0245	5008	,	,		17985	0.0		0.0567	False		,,,				2504	0.0051				p.I65V		Atlas-SNP	.											.	APMAP	3	.	0			c.A193G						PASS	.	T	VAL/ILE	38,4368	42.3+/-75.8	0,38,2165	87.0	91.0	90.0		193	5.9	1.0	20	dbSNP_123	90	490,8110	141.9+/-198.1	11,468,3821	yes	missense	C20orf3	NM_020531.2	29	11,506,5986	CC,CT,TT		5.6977,0.8625,4.0597	benign	65/417	24964558	528,12478	2203	4300	6503	SO:0001583	missense	57136	exon2			GATCTATAGGAGA	AB033767	CCDS13166.1	20p11.2	2012-07-20	2012-07-20	2012-07-20	ENSG00000101474	ENSG00000101474			13238	protein-coding gene	gene with protein product		615884	"""chromosome 20 open reading frame 3"""	C20orf3		10945474, 11583587, 20552250	Standard	NM_020531		Approved	BSCv	uc002wty.3	Q9HDC9	OTTHUMG00000032107	ENST00000217456.2:c.193A>G	20.37:g.24964558T>C	ENSP00000217456:p.Ile65Val	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	43	23	0.534884	NM_020531	A8K514|B4DXG1|Q6UVZ8|Q9GZS8|Q9NUB2	Missense_Mutation	SNP	ENST00000217456.2	37	CCDS13166.1	55	0.025183150183150184	3	0.006097560975609756	8	0.022099447513812154	0	0.0	44	0.05804749340369393	T	18.64	3.667973	0.67814	0.008625	0.056977	ENSG00000101474	ENST00000217456;ENST00000447138	T;T	0.32272	1.87;1.46	5.93	5.93	0.95920	Six-bladed beta-propeller, TolB-like (1);	0.000000	0.85682	D	0.000000	T	0.04182	0.0116	L	0.56280	1.765	0.53688	D	0.999973	P;P;D	0.54397	0.947;0.615;0.966	P;B;P	0.45794	0.481;0.1;0.493	T	0.00926	-1.1512	10	0.23891	T	0.37	-29.4431	12.7716	0.57423	0.0:0.0:0.0:1.0	rs17298715	65;49;65	Q9HDC9-2;A2A2F9;Q9HDC9	.;.;APMAP_HUMAN	V	65	ENSP00000217456:I65V;ENSP00000415373:I65V	ENSP00000217456:I65V	I	-	1	0	C20orf3	24912558	1.000000	0.71417	0.998000	0.56505	0.991000	0.79684	5.378000	0.66190	2.271000	0.75665	0.533000	0.62120	ATA	T|0.964;C|0.036	0.036	strong		0.517	APMAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078380.2	NM_020531	
ATP2A3	489	hgsc.bcm.edu	37	17	3839685	3839685	+	Silent	SNP	G	G	A	rs1062683	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:3839685G>A	ENST00000352011.3	-	16	2454	c.2400C>T	c.(2398-2400)gaC>gaT	p.D800D	ATP2A3_ENST00000397043.3_Silent_p.D800D|ATP2A3_ENST00000359983.3_Silent_p.D800D|ATP2A3_ENST00000397041.3_Silent_p.D800D|ATP2A3_ENST00000397035.3_Silent_p.D800D|ATP2A3_ENST00000309890.7_Silent_p.D800D|ATP2A3_ENST00000397039.1_De_novo_Start_OutOfFrame			Q93084	AT2A3_HUMAN	ATPase, Ca++ transporting, ubiquitous	800					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)		CAGGTAGGCCGTCTGTCACCA	0.622													G|||	849	0.169529	0.2194	0.1585	5008	,	,		17621	0.0655		0.1918	False		,,,				2504	0.1943				p.D800D	GBM(32;29 774 15719 37967)	Atlas-SNP	.											.	ATP2A3	148	.	0			c.C2400T						PASS	.	G	,,,,,,	946,3460	360.9+/-315.4	98,750,1355	78.0	80.0	79.0		2400,2400,2400,2400,2400,2400,2400	0.7	1.0	17	dbSNP_86	79	1710,6890	312.5+/-310.9	156,1398,2746	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ATP2A3	NM_005173.3,NM_174953.2,NM_174954.2,NM_174955.2,NM_174956.2,NM_174957.2,NM_174958.2	,,,,,,	254,2148,4101	AA,AG,GG		19.8837,21.4707,20.4213	,,,,,,	800/1000,800/1053,800/1045,800/1044,800/1030,800/999,800/1030	3839685	2656,10350	2203	4300	6503	SO:0001819	synonymous_variant	489	exon16			TAGGCCGTCTGTC		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.2400C>T	17.37:g.3839685G>A		Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	168	86	0.511905	NM_174956	A8MZG0|D3DTJ8|O60900|O60901|O75501|O75502|Q16115|Q6JHX1|Q8TEX5|Q8TEX6	Silent	SNP	ENST00000352011.3	37	CCDS11041.1																																																																																			T|0.000;G|0.815;C|0.000;A|0.184	0.184	strong		0.622	ATP2A3-015	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000438401.1	NM_174953	
PCNXL3	399909	hgsc.bcm.edu	37	11	65386029	65386029	+	Missense_Mutation	SNP	G	G	A	rs538665832		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:65386029G>A	ENST00000355703.3	+	6	1735	c.1196G>A	c.(1195-1197)cGa>cAa	p.R399Q		NM_032223.2	NP_115599.2	Q9H6A9	PCX3_HUMAN	pecanex-like 3 (Drosophila)	399						integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(6)|prostate(1)	13						CCACCCCTGCGAAGACACTCT	0.657													G|||	1	0.000199681	0.0008	0.0	5008	,	,		14826	0.0		0.0	False		,,,				2504	0.0				p.R399Q		Atlas-SNP	.											.	PCNXL3	140	.	0			c.G1196A						PASS	.						17.0	19.0	18.0					11																	65386029		1990	4164	6154	SO:0001583	missense	399909	exon6			CCCTGCGAAGACA	BX640978	CCDS44650.1	11q12.1	2008-07-21			ENSG00000197136	ENSG00000197136			18760	protein-coding gene	gene with protein product						15146197	Standard	NM_032223		Approved	FLJ22427	uc001oey.2	Q9H6A9	OTTHUMG00000166539	ENST00000355703.3:c.1196G>A	11.37:g.65386029G>A	ENSP00000347931:p.Arg399Gln	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	53	16	0.301887	NM_032223	Q6MZN8	Missense_Mutation	SNP	ENST00000355703.3	37	CCDS44650.1	.	.	.	.	.	.	.	.	.	.	G	11.99	1.802379	0.31869	.	.	ENSG00000197136	ENST00000355703	T	0.01051	5.4	4.47	3.55	0.40652	.	0.000000	0.31381	N	0.007758	T	0.00967	0.0032	L	0.27053	0.805	0.30274	N	0.791956	B	0.13594	0.008	B	0.04013	0.001	T	0.32851	-0.9891	10	0.15499	T	0.54	.	8.6129	0.33813	0.1056:0.0:0.8944:0.0	.	399	Q9H6A9	PCX3_HUMAN	Q	399	ENSP00000347931:R399Q	ENSP00000347931:R399Q	R	+	2	0	PCNXL3	65142605	0.853000	0.29707	0.917000	0.36280	0.882000	0.50991	2.024000	0.41049	1.098000	0.41479	0.462000	0.41574	CGA	.	.	none		0.657	PCNXL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390321.1	NM_032223	
OR10H2	26538	hgsc.bcm.edu	37	19	15838967	15838967	+	Silent	SNP	G	G	A	rs2285955	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:15838967G>A	ENST00000305899.3	+	1	134	c.114G>A	c.(112-114)acG>acA	p.T38T		NM_013939.2	NP_039227.1	O60403	O10H2_HUMAN	olfactory receptor, family 10, subfamily H, member 2	38						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(2)|skin(3)|stomach(1)	27	all_hematologic(1;0.0517)|Acute lymphoblastic leukemia(2;0.074)					ACCTGTTCACGCTGCTGGGCA	0.587													G|||	1755	0.350439	0.233	0.3112	5008	,	,		22410	0.3135		0.4394	False		,,,				2504	0.4836				p.T38T		Atlas-SNP	.											OR10H2,NS,carcinoma,+1,1	OR10H2	59	1	0			c.G114A						PASS	.	G		1225,3181		174,877,1152	237.0	198.0	211.0		114	-5.8	1.0	19	dbSNP_100	211	3845,4751		870,2105,1323	no	coding-synonymous	OR10H2	NM_013939.2		1044,2982,2475	AA,AG,GG		44.7301,27.803,38.994		38/316	15838967	5070,7932	2203	4298	6501	SO:0001819	synonymous_variant	26538	exon1			GTTCACGCTGCTG	AC004597	CCDS12333.1	19p13.1	2012-08-09				ENSG00000171942		"""GPCR / Class A : Olfactory receptors"""	8173	protein-coding gene	gene with protein product							Standard	NM_013939		Approved		uc002nbm.2	O60403		ENST00000305899.3:c.114G>A	19.37:g.15838967G>A		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	191	65	0.340314	NM_013939	Q6IFQ1|Q96R58	Silent	SNP	ENST00000305899.3	37	CCDS12333.1																																																																																			G|0.611;A|0.389	0.389	strong		0.587	OR10H2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460917.1		
UGT1A7	54577	hgsc.bcm.edu	37	2	234590975	234590975	+	Missense_Mutation	SNP	G	G	A	rs17868324|rs397726009|rs66534818|rs386656364|rs71405712	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:234590975G>A	ENST00000373426.3	+	1	392	c.392G>A	c.(391-393)cGa>cAa	p.R131Q	UGT1A1_ENST00000373450.4_Intron|UGT1A10_ENST00000373445.1_Intron|UGT1A9_ENST00000354728.4_Intron|UGT1A10_ENST00000344644.5_Intron|UGT1A1_ENST00000609637.1_Intron	NM_019077.2	NP_061950.2	Q9HAW7	UD17_HUMAN	UDP glucuronosyltransferase 1 family, polypeptide A7	131			R -> K (in allele UGT1A7*2 and allele UGT1A7*3). {ECO:0000269|PubMed:11037804, ECO:0000269|PubMed:11434514, ECO:0000269|PubMed:19204906, ECO:0000269|Ref.3}.|R -> Q (in dbSNP:rs17868324).		cellular glucuronidation (GO:0052695)|coumarin metabolic process (GO:0009804)|drug metabolic process (GO:0017144)|excretion (GO:0007588)|flavone metabolic process (GO:0051552)|flavonoid glucuronidation (GO:0052696)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cellular glucuronidation (GO:2001030)|negative regulation of fatty acid metabolic process (GO:0045922)|retinoic acid metabolic process (GO:0042573)|xenobiotic glucuronidation (GO:0052697)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	drug binding (GO:0008144)|enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)|glucuronosyltransferase activity (GO:0015020)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase C binding (GO:0005080)|retinoic acid binding (GO:0001972)			NS(1)|endometrium(6)|kidney(5)|large_intestine(5)|liver(1)|lung(12)|ovary(1)|prostate(1)|skin(1)	33		Breast(86;0.000765)|all_lung(227;0.00267)|Renal(207;0.00339)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0328)|Lung NSC(271;0.0457)|Lung SC(224;0.128)		Epithelial(121;8.93e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000412)|Lung(119;0.00333)|LUSC - Lung squamous cell carcinoma(224;0.00746)	Mycophenolate mofetil(DB00688)|Mycophenolic acid(DB01024)	TTTAATGACCGAAAATTAGTA	0.368													A|||	2886	0.576278	0.6097	0.5072	5008	,	,		19096	0.4385		0.6034	False		,,,				2504	0.6943				p.R131Q		Atlas-SNP	.											.	UGT1A7	74	.	0			c.G392A						PASS	.						69.0	76.0	74.0					2																	234590975		2201	4296	6497	SO:0001583	missense	54577	exon1			ATGACCGAAAATT	U39570	CCDS2506.1	2q37	2010-03-05	2005-07-20		ENSG00000244122	ENSG00000244122		"""UDP glucuronosyltransferases"""	12539	other	complex locus constituent		606432	"""UDP glycosyltransferase 1 family, polypeptide A6"""			9295054, 11434514	Standard	NM_019077		Approved	UGT1G		Q9HAW7	OTTHUMG00000059004	ENST00000373426.3:c.392G>A	2.37:g.234590975G>A	ENSP00000362525:p.Arg131Gln	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	73	22	0.30137	NM_019077	B8K293|O00473	Missense_Mutation	SNP	ENST00000373426.3	37	CCDS2506.1	992	0.4542124542124542	234	0.47560975609756095	176	0.4861878453038674	207	0.3618881118881119	375	0.4947229551451187	A	6.902	0.535926	0.13188	.	.	ENSG00000244122	ENST00000373426	T	0.59906	0.23	4.51	-9.01	0.00744	.	.	.	.	.	T	0.00012	0.0000	N	0.11870	0.19	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.30090	-0.9990	8	0.27082	T	0.32	.	5.8774	0.18836	0.6524:0.0972:0.1839:0.0666	rs17868324	131;131	Q5DSZ7;Q9HAW7	.;UD17_HUMAN	Q	131	ENSP00000362525:R131Q	ENSP00000362525:R131Q	R	+	2	0	UGT1A7	234255714	0.000000	0.05858	0.000000	0.03702	0.031000	0.12232	-0.670000	0.05256	-2.128000	0.00818	-1.305000	0.01319	CGA	.	.	weak		0.368	UGT1A7-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000130614.1	NM_019077	
PCDHB7	56129	hgsc.bcm.edu	37	5	140553664	140553664	+	Silent	SNP	G	G	A	rs3733695|rs386692905	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	141	0	0		WXS	Illumina HiSeq	Phase_I	161	87	0.540373	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	
ZZEF1	23140	hgsc.bcm.edu	37	17	3926110	3926110	+	Missense_Mutation	SNP	C	C	G	rs711177	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:3926110C>G	ENST00000381638.2	-	44	7229	c.7105G>C	c.(7105-7107)Gag>Cag	p.E2369Q		NM_015113.3	NP_055928.3	O43149	ZZEF1_HUMAN	zinc finger, ZZ-type with EF-hand domain 1	2369			E -> Q (in dbSNP:rs711177). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9455477}.				calcium ion binding (GO:0005509)|zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(17)|lung(19)|ovary(3)|pancreas(1)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(3)	84						CGGATCTCCTCAAAACCGTGA	0.478													C|||	718	0.143371	0.2504	0.1311	5008	,	,		21530	0.0724		0.0706	False		,,,				2504	0.1554				p.E2369Q		Atlas-SNP	.											.	ZZEF1	195	.	0			c.G7105C						PASS	.	C	GLN/GLU	1179,3227	413.3+/-336.4	161,857,1185	80.0	72.0	75.0		7105	5.0	1.0	17	dbSNP_86	75	497,8103	143.0+/-199.1	15,467,3818	yes	missense	ZZEF1	NM_015113.3	29	176,1324,5003	GG,GC,CC		5.7791,26.759,12.8864	benign	2369/2962	3926110	1676,11330	2203	4300	6503	SO:0001583	missense	23140	exon44			TCTCCTCAAAACC	BC035319	CCDS11043.1	17p13.3	2013-01-10	2004-11-03		ENSG00000074755	ENSG00000074755		"""Zinc fingers, ZZ-type"", ""EF-hand domain containing"""	29027	protein-coding gene	gene with protein product			"""zinc finger, ZZ-type with EF hand domain 1"""			9455477	Standard	XM_005256560		Approved	KIAA0399, ZZZ4, FLJ10821	uc002fxe.3	O43149	OTTHUMG00000090741	ENST00000381638.2:c.7105G>C	17.37:g.3926110C>G	ENSP00000371051:p.Glu2369Gln	Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	46	23	0.5	NM_015113	A7MBM5|Q6NXG0|Q6ZRA1|Q6ZSF4|Q9NVB9	Missense_Mutation	SNP	ENST00000381638.2	37	CCDS11043.1	264	0.12087912087912088	121	0.2459349593495935	45	0.12430939226519337	38	0.06643356643356643	60	0.079155672823219	C	19.67	3.871784	0.72180	0.26759	0.057791	ENSG00000074755	ENST00000381638	T	0.26810	1.71	5.96	4.97	0.65823	.	0.163737	0.52532	N	0.000067	T	0.00012	0.0000	N	0.19112	0.55	0.21499	P	0.999669417	B	0.27498	0.18	B	0.23150	0.044	T	0.37842	-0.9688	9	0.42905	T	0.14	-13.283	11.0647	0.47968	0.0:0.6898:0.2439:0.0664	rs711177;rs3816483;rs17763614;rs711177	2369	O43149	ZZEF1_HUMAN	Q	2369	ENSP00000371051:E2369Q	ENSP00000371051:E2369Q	E	-	1	0	ZZEF1	3872859	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	3.495000	0.53280	1.472000	0.48140	0.655000	0.94253	GAG	C|0.870;G|0.130	0.130	strong		0.478	ZZEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207480.1	NM_015113	
ZNF345	25850	hgsc.bcm.edu	37	19	37368492	37368492	+	Missense_Mutation	SNP	G	G	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:37368492G>C	ENST00000529555.1	+	2	1548	c.760G>C	c.(760-762)Ggt>Cgt	p.G254R	ZNF345_ENST00000432005.2_Intron|ZNF345_ENST00000589046.1_Missense_Mutation_p.G254R|ZNF345_ENST00000420450.1_Missense_Mutation_p.G254R|ZNF345_ENST00000526123.1_Intron			Q14585	ZN345_HUMAN	zinc finger protein 345	254					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)			AATTCATACCGGTGAGAAACC	0.423																																					p.G254R		Atlas-SNP	.											.	ZNF345	68	.	0			c.G760C						PASS	.						73.0	74.0	74.0					19																	37368492		2203	4300	6503	SO:0001583	missense	25850	exon4			CATACCGGTGAGA	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.760G>C	19.37:g.37368492G>C	ENSP00000431202:p.Gly254Arg	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	41	13	0.317073	NM_001242476		Missense_Mutation	SNP	ENST00000529555.1	37	CCDS12497.1	.	.	.	.	.	.	.	.	.	.	G	17.36	3.369349	0.61624	.	.	ENSG00000251247	ENST00000420450;ENST00000529555;ENST00000344705	T;T	0.01629	4.72;4.72	3.96	3.96	0.45880	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.07007	0.0178	L	0.55743	1.74	0.32084	N	0.592773	D	0.76494	0.999	D	0.63877	0.919	T	0.02156	-1.1204	9	0.87932	D	0	.	13.8686	0.63603	0.0:0.0:1.0:0.0	.	254	Q14585	ZN345_HUMAN	R	254;254;18	ENSP00000431216:G254R;ENSP00000431202:G254R	ENSP00000442320:G18R	G	+	1	0	ZNF345	42060332	0.974000	0.33945	0.999000	0.59377	0.975000	0.68041	3.047000	0.49854	2.176000	0.68965	0.561000	0.74099	GGT	.	.	none		0.423	ZNF345-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388258.1		
SPAG9	9043	hgsc.bcm.edu	37	17	49067870	49067870	+	Missense_Mutation	SNP	G	G	A	rs534277665		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:49067870G>A	ENST00000262013.7	-	20	2766	c.2558C>T	c.(2557-2559)aCg>aTg	p.T853M	SPAG9_ENST00000510283.1_Missense_Mutation_p.T696M|SPAG9_ENST00000505279.1_Missense_Mutation_p.T843M|SPAG9_ENST00000357122.4_Missense_Mutation_p.T839M	NM_001130528.2	NP_001124000.1	O60271	JIP4_HUMAN	sperm associated antigen 9	853					activation of JUN kinase activity (GO:0007257)|muscle cell differentiation (GO:0042692)|negative regulation of protein homodimerization activity (GO:0090074)|positive regulation of cell migration (GO:0030335)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuron differentiation (GO:0045666)|protein homooligomerization (GO:0051260)|retrograde transport, endosome to Golgi (GO:0042147)|spermatogenesis (GO:0007283)|striated muscle cell differentiation (GO:0051146)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)				NS(1)|breast(3)|endometrium(3)|kidney(4)|large_intestine(8)|lung(14)|ovary(1)|prostate(1)|skin(1)|stomach(1)	37			BRCA - Breast invasive adenocarcinoma(22;4.24e-07)			GGCAGCTCCCGTCACACCTTC	0.468																																					p.T853M		Atlas-SNP	.											.	SPAG9	151	.	0			c.C2558T						PASS	.						112.0	84.0	93.0					17																	49067870		2203	4300	6503	SO:0001583	missense	9043	exon20			GCTCCCGTCACAC	AB011088	CCDS11577.1, CCDS45740.1, CCDS58577.1, CCDS58578.1	17q21.33	2013-09-23			ENSG00000008294	ENSG00000008294			14524	protein-coding gene	gene with protein product	"""sperm surface protein"", ""JNK/SAPK-associated protein"", ""JNK interacting protein"", ""sperm specific protein"", ""c-Jun NH2-terminal kinase-associated leucine zipper protein"", ""Max-binding protein"", ""JNK-associated leucine-zipper protein"", ""HLC-4 protein"", ""lung cancer oncogene 4"", ""proliferation-inducing gene 6"", ""cancer/testis antigen 89"""	605430				9480848, 11106729	Standard	NM_003971		Approved	HSS, SYD1, KIAA0516, MGC14967, MGC74461, MGC117291, JLP, PHET, HLC4, PIG6, FLJ13450, FLJ14006, FLJ26141, FLJ34602, CT89	uc002itc.3	O60271	OTTHUMG00000162316	ENST00000262013.7:c.2558C>T	17.37:g.49067870G>A	ENSP00000262013:p.Thr853Met	Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	146	75	0.513699	NM_001130528	A6H8U5|A8MSX0|B4DHH2|O60905|Q3KQU8|Q3MKM7|Q86WC7|Q86WC8|Q8IZX7|Q96II0|Q9H811	Missense_Mutation	SNP	ENST00000262013.7	37	CCDS45740.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	14.61|14.61	2.587305|2.587305	0.46110|0.46110	.|.	.|.	ENSG00000008294|ENSG00000008294	ENST00000513906|ENST00000262013;ENST00000376407;ENST00000357804;ENST00000357791;ENST00000510283;ENST00000505279;ENST00000357122;ENST00000535445	.|T;T;T;T	.|0.24723	.|1.84;1.85;1.84;1.84	5.9|5.9	3.59|3.59	0.41128|0.41128	.|WD40 repeat-like-containing domain (1);	.|0.377306	.|0.31648	.|N	.|0.007293	T|T	0.23410|0.23410	0.0566|0.0566	L|L	0.34521|0.34521	1.04|1.04	0.09310|0.09310	N|N	1|1	.|P;P;P;P;P;P	.|0.44659	.|0.84;0.72;0.597;0.646;0.592;0.742	.|B;P;B;B;B;B	.|0.44732	.|0.438;0.459;0.336;0.12;0.277;0.191	T|T	0.07158|0.07158	-1.0787|-1.0787	5|10	.|0.51188	.|T	.|0.08	-3.8257|-3.8257	11.9883|11.9883	0.53161|0.53161	0.1577:0.0:0.8423:0.0|0.1577:0.0:0.8423:0.0	.|.	.|839;853;843;853;839;696	.|O60271-5;O60271-3;O60271-2;O60271;O60271-4;E7ENU2	.|.;.;.;JIP4_HUMAN;.;.	W|M	112|853;610;600;390;696;843;839;451	.|ENSP00000262013:T853M;ENSP00000423165:T696M;ENSP00000426900:T843M;ENSP00000349636:T839M	.|ENSP00000262013:T853M	R|T	-|-	1|2	2|0	SPAG9|SPAG9	46422869|46422869	0.997000|0.997000	0.39634|0.39634	0.969000|0.969000	0.41365|0.41365	0.983000|0.983000	0.72400|0.72400	4.424000|4.424000	0.59868|0.59868	1.512000|1.512000	0.48834|0.48834	0.650000|0.650000	0.86243|0.86243	CGG|ACG	.	.	none		0.468	SPAG9-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000368543.2	NM_003971	
ATP13A2	23400	hgsc.bcm.edu	37	1	17326767	17326767	+	Missense_Mutation	SNP	C	C	T	rs56367069	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:17326767C>T	ENST00000326735.8	-	10	914	c.881G>A	c.(880-882)cGg>cAg	p.R294Q	ATP13A2_ENST00000452699.1_Missense_Mutation_p.R289Q|RP1-37C10.3_ENST00000446261.1_RNA|ATP13A2_ENST00000502860.1_5'UTR|ATP13A2_ENST00000341676.5_Missense_Mutation_p.R289Q			Q9NQ11	AT132_HUMAN	ATPase type 13A2	294			R -> Q (in dbSNP:rs56367069). {ECO:0000269|PubMed:19085912}.		cell death (GO:0008219)|cellular response to manganese ion (GO:0071287)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(11)|ovary(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	32		Colorectal(325;0.000147)|Breast(348;0.00104)|Renal(390;0.00145)|Lung NSC(340;0.00566)|all_lung(284;0.00797)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00462)|COAD - Colon adenocarcinoma(227;1.11e-05)|BRCA - Breast invasive adenocarcinoma(304;1.99e-05)|Kidney(64;0.000171)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00645)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.182)		CACGCACACCCGCATGGACAA	0.706													C|||	31	0.0061901	0.0	0.0159	5008	,	,		9523	0.0		0.0179	False		,,,				2504	0.002				p.R294Q		Atlas-SNP	.											.	ATP13A2	85	.	0			c.G881A						PASS	.	C	GLN/ARG,GLN/ARG,GLN/ARG	10,4370		0,10,2180	20.0	18.0	19.0		866,866,881	-0.7	0.0	1	dbSNP_129	19	145,8437		0,145,4146	yes	missense,missense,missense	ATP13A2	NM_001141973.1,NM_001141974.1,NM_022089.2	43,43,43	0,155,6326	TT,TC,CC		1.6896,0.2283,1.1958	benign,benign,benign	289/1176,289/1159,294/1181	17326767	155,12807	2190	4291	6481	SO:0001583	missense	23400	exon10			CACACCCGCATGG	AL354615	CCDS175.1, CCDS44072.1, CCDS44073.1	1p36	2014-09-17			ENSG00000159363	ENSG00000159363		"""ATPases / P-type"", ""Parkinson disease"""	30213	protein-coding gene	gene with protein product		610513	"""Parkinson disease (autosomal recessive) 9 (Kufor-Rakeb syndrome)"""	PARK9		15381061, 16964263	Standard	XM_005245809		Approved	HSA9947, CLN12	uc001baa.2	Q9NQ11	OTTHUMG00000002293	ENST00000326735.8:c.881G>A	1.37:g.17326767C>T	ENSP00000327214:p.Arg294Gln	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	106	62	0.584906	NM_022089	O75700|Q5JXY1|Q5JXY2|Q6S9Z9	Missense_Mutation	SNP	ENST00000326735.8	37	CCDS175.1	19	0.0086996336996337	0	0.0	5	0.013812154696132596	0	0.0	14	0.018469656992084433	C	11.45	1.641391	0.29157	0.002283	0.016896	ENSG00000159363	ENST00000326735;ENST00000341676;ENST00000452699;ENST00000506174;ENST00000511957	D;D;D;D;T	0.90788	-2.68;-2.68;-2.68;-2.73;-0.11	4.82	-0.711	0.11230	ATPase, P-type, ATPase-associated domain (1);ATPase,  P-type, cytoplasmic transduction domain A (1);	0.388711	0.29273	N	0.012630	T	0.64000	0.2559	N	0.13352	0.335	0.09310	N	1	B;B;B;B;B	0.25850	0.0;0.136;0.127;0.102;0.08	B;B;B;B;B	0.23150	0.002;0.038;0.044;0.007;0.023	T	0.58951	-0.7545	10	0.13853	T	0.58	-12.0197	8.8023	0.34916	0.0:0.5583:0.0:0.4417	rs56367069	7;7;289;289;294	Q52PK6;Q6ZP48;Q5JXY1;Q6S9Z9;Q9NQ11	.;.;.;.;AT132_HUMAN	Q	294;289;289;14;189	ENSP00000327214:R294Q;ENSP00000341115:R289Q;ENSP00000413307:R289Q;ENSP00000424393:R14Q;ENSP00000427241:R189Q	ENSP00000327214:R294Q	R	-	2	0	ATP13A2	17199354	0.000000	0.05858	0.003000	0.11579	0.727000	0.41649	-0.265000	0.08644	-0.357000	0.08175	-0.224000	0.12420	CGG	C|0.989;T|0.011	0.011	strong		0.706	ATP13A2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000006617.1	NM_022089	
PKD1	5310	hgsc.bcm.edu	37	16	2156021	2156021	+	Silent	SNP	A	A	G	rs28575767	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:2156021A>G	ENST00000262304.4	-	20	7916	c.7708T>C	c.(7708-7710)Ttg>Ctg	p.L2570L	PKD1_ENST00000561991.1_5'UTR|PKD1_ENST00000423118.1_Silent_p.L2570L	NM_001009944.2	NP_001009944	P98161	PKD1_HUMAN	polycystic kidney disease 1 (autosomal dominant)	2570	REJ. {ECO:0000255|PROSITE- ProRule:PRU00511}.				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						GTGATGGCCAAAGACCTACGA	0.701													g|||	890	0.177716	0.5212	0.1383	5008	,	,		15830	0.0		0.0905	False		,,,				2504	0.0143				p.L2570L		Atlas-SNP	.											PKD1,right_upper_lobe,carcinoma,+2,1	PKD1	184	1	0			c.T7708C						scavenged	.						23.0	36.0	31.0					16																	2156021		1407	2607	4014	SO:0001819	synonymous_variant	5310	exon20			TGGCCAAAGACCT	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.7708T>C	16.37:g.2156021A>G		Somatic	10	1	0.1		WXS	Illumina HiSeq	Phase_I	15	9	0.6	NM_000296	Q15140|Q15141	Silent	SNP	ENST00000262304.4	37	CCDS32369.1																																																																																			A|0.873;G|0.127	0.127	strong		0.701	PKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341688.1		
RHBG	57127	hgsc.bcm.edu	37	1	156347131	156347131	+	Missense_Mutation	SNP	G	G	A	rs2245623	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:156347131G>A	ENST00000368249.1	+	2	265	c.227G>A	c.(226-228)gGc>gAc	p.G76D	RHBG_ENST00000255013.3_Missense_Mutation_p.G7D|RHBG_ENST00000537040.1_Intron|RHBG_ENST00000451864.2_Missense_Mutation_p.G7D|RHBG_ENST00000400992.2_Missense_Mutation_p.G7D|RHBG_ENST00000368246.2_Missense_Mutation_p.G76D	NM_001256396.1|NM_020407.4	NP_001243325.1|NP_065140.3	Q9H310	RHBG_HUMAN	Rh family, B glycoprotein (gene/pseudogene)	76			G -> D (in dbSNP:rs2245623). {ECO:0000269|PubMed:14702039, ECO:0000269|Ref.5}.		ammonium transmembrane transport (GO:0072488)|ammonium transport (GO:0015696)|transepithelial ammonium transport (GO:0070634)|transmembrane transport (GO:0055085)	anchored component of plasma membrane (GO:0046658)|basolateral plasma membrane (GO:0016323)|cytoplasmic vesicle (GO:0031410)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|spectrin-associated cytoskeleton (GO:0014731)	ammonium transmembrane transporter activity (GO:0008519)|ankyrin binding (GO:0030506)			endometrium(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(3)|skin(2)|stomach(1)|urinary_tract(1)	22	Hepatocellular(266;0.158)					GTGGGCTTTGGCTTCCTCATG	0.637													G|||	1355	0.270567	0.1936	0.2781	5008	,	,		21225	0.1012		0.4563	False		,,,				2504	0.3528				p.G76D		Atlas-SNP	.											.	RHBG	133	.	0			c.G227A						PASS	.	G	ASP/GLY	993,3413	365.9+/-317.6	106,781,1316	142.0	144.0	143.0		227	4.9	1.0	1	dbSNP_100	143	3847,4753	537.9+/-383.3	886,2075,1339	yes	missense	RHBG	NM_020407.3	94	992,2856,2655	AA,AG,GG		44.7326,22.5374,37.2136	probably-damaging	76/459	156347131	4840,8166	2203	4300	6503	SO:0001583	missense	57127	exon2			GCTTTGGCTTCCT	AF193807		1q22	2013-05-22	2009-01-22		ENSG00000132677	ENSG00000132677		"""Solute carriers"""	14572	protein-coding gene	gene with protein product		607079	"""Rhesus blood group, B glycoprotein"""			10852913	Standard	NM_020407		Approved	SLC42A2	uc010pho.3	Q9H310	OTTHUMG00000024057	ENST00000368249.1:c.227G>A	1.37:g.156347131G>A	ENSP00000357232:p.Gly76Asp	Somatic	252	0	0		WXS	Illumina HiSeq	Phase_I	192	189	0.984375	NM_020407	A8K475|Q5SZW4|Q5SZW6|Q5SZW7|Q6P193|Q6YJI2|Q6YJI3	Missense_Mutation	SNP	ENST00000368249.1	37		608	0.2783882783882784	95	0.19308943089430894	109	0.3011049723756906	58	0.10139860139860139	346	0.45646437994722955	G	34	5.389342	0.95988	0.225374	0.447326	ENSG00000132677	ENST00000368249;ENST00000368246;ENST00000400992;ENST00000255013;ENST00000451864	D;D;D;D;D	0.81579	-1.51;-1.51;-1.51;-1.51;-1.51	4.86	4.86	0.63082	Ammonium transporter AmtB-like (3);	0.000000	0.85682	D	0.000000	D	0.91744	0.7389	H	0.94582	3.555	0.09310	P	0.9999999999972279	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.93736	0.7046	9	0.87932	D	0	-6.6399	16.7188	0.85405	0.0:0.0:1.0:0.0	rs2245623;rs17387461;rs2245623	76;7;113	Q9H310;Q9H310-3;Q5SZW5	RHBG_HUMAN;.;.	D	76;76;7;7;7	ENSP00000357232:G76D;ENSP00000357229:G76D;ENSP00000383777:G7D;ENSP00000255013:G7D;ENSP00000389836:G7D	ENSP00000255013:G7D	G	+	2	0	RHBG	154613755	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	9.395000	0.97266	2.512000	0.84698	0.561000	0.74099	GGC	G|0.713;A|0.287	0.287	strong		0.637	RHBG-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000060589.2	NM_001256395	
LDLR	3949	hgsc.bcm.edu	37	19	11224265	11224265	+	Silent	SNP	A	A	G	rs5930	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:11224265A>G	ENST00000558518.1	+	10	1600	c.1413A>G	c.(1411-1413)agA>agG	p.R471R	LDLR_ENST00000557933.1_Silent_p.R471R|LDLR_ENST00000455727.2_Silent_p.R303R|LDLR_ENST00000558013.1_Silent_p.R471R|LDLR_ENST00000545707.1_Silent_p.R344R|LDLR_ENST00000535915.1_Silent_p.R430R	NM_000527.4|NM_001195798.1	NP_000518.1|NP_001182727.1	P01130	LDLR_HUMAN	low density lipoprotein receptor	471			R -> G (found in a patient with hypercholesterolemia). {ECO:0000269|PubMed:21418584}.		cholesterol homeostasis (GO:0042632)|cholesterol import (GO:0070508)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|endocytosis (GO:0006897)|intestinal cholesterol absorption (GO:0030299)|lipid metabolic process (GO:0006629)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|low-density lipoprotein particle clearance (GO:0034383)|phospholipid transport (GO:0015914)|phototransduction, visible light (GO:0007603)|positive regulation of triglyceride biosynthetic process (GO:0010867)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol homeostasis (GO:2000188)|regulation of phosphatidylcholine catabolic process (GO:0010899)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|coated pit (GO:0005905)|early endosome (GO:0005769)|endosome membrane (GO:0010008)|external side of plasma membrane (GO:0009897)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|low-density lipoprotein particle (GO:0034362)|lysosome (GO:0005764)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|glycoprotein binding (GO:0001948)|low-density lipoprotein particle binding (GO:0030169)|low-density lipoprotein receptor activity (GO:0005041)|very-low-density lipoprotein particle receptor activity (GO:0030229)	p.?(1)		breast(2)|endometrium(2)|large_intestine(5)|lung(8)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	26		Lung NSC(9;0.000245)|Renal(1328;0.0007)|Hepatocellular(1079;0.0524)		GBM - Glioblastoma multiforme(1328;1.36e-05)|STAD - Stomach adenocarcinoma(1328;0.000766)|Lung(535;0.197)	Porfimer(DB00707)	TCATCAGCAGAGACATCCAGG	0.607													G|||	3280	0.654952	0.7504	0.7147	5008	,	,		18170	0.5952		0.5785	False		,,,				2504	0.6237				p.R471R	GBM(18;201 575 7820 21545)	Atlas-SNP	.											LDLR,NS,carcinoma,0,1	LDLR	72	1	1	Unknown(1)	lung(1)	c.A1413G						PASS	.	G	,,,,,	3241,1165	409.1+/-334.9	1190,861,152	48.0	46.0	47.0		1413,1413,1290,909,1050,1032	-2.2	0.0	19	dbSNP_52	47	5299,3301	491.0+/-373.0	1628,2043,629	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	LDLR	NM_000527.4,NM_001195798.1,NM_001195799.1,NM_001195800.1,NM_001195802.1,NM_001195803.1	,,,,,	2818,2904,781	GG,GA,AA		38.3837,26.4412,34.338	,,,,,	471/861,471/859,430/820,303/693,350/740,344/683	11224265	8540,4466	2203	4300	6503	SO:0001819	synonymous_variant	3949	exon10			CAGCAGAGACATC	AY114155	CCDS12254.1, CCDS56083.1, CCDS56084.1, CCDS56085.1, CCDS58651.1	19p13.2	2014-09-17	2008-08-01		ENSG00000130164	ENSG00000130164		"""Low density lipoprotein receptors"""	6547	protein-coding gene	gene with protein product	"""familial hypercholesterolemia"""	606945					Standard	NM_000527		Approved	LDLCQ2	uc002mqk.4	P01130		ENST00000558518.1:c.1413A>G	19.37:g.11224265A>G		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	68	67	0.985294	NM_001195798	B4DII3|B4DJZ8|B4DR00|B4DTQ3|C0JYY8|H0YLU8|H0YNT7|Q53ZD9|Q59FQ1|Q9UDH7	Silent	SNP	ENST00000558518.1	37	CCDS12254.1																																																																																			A|0.345;G|0.655	0.655	strong		0.607	LDLR-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000415973.2		
PCM1	5108	hgsc.bcm.edu	37	8	17817553	17817553	+	Missense_Mutation	SNP	G	G	T	rs17635381	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	112	0	0		WXS	Illumina HiSeq	Phase_I	116	35	0.301724	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	
TEK	7010	hgsc.bcm.edu	37	9	27203002	27203002	+	Silent	SNP	G	G	A	rs45563539	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:27203002G>A	ENST00000380036.4	+	13	2536	c.2094G>A	c.(2092-2094)caG>caA	p.Q698Q	TEK_ENST00000406359.4_Silent_p.Q655Q|TEK_ENST00000519097.1_Silent_p.Q551Q	NM_000459.3	NP_000450	Q02763	TIE2_HUMAN	TEK tyrosine kinase, endothelial	698	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				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)	CTCAGTATCAGCTCAAGGGCC	0.443													G|||	170	0.0339457	0.0038	0.0303	5008	,	,		20576	0.0456		0.0487	False		,,,				2504	0.0501				p.Q698Q		Atlas-SNP	.											.	TEK	250	.	0			c.G2094A						PASS	.	G		48,4358	48.9+/-83.8	0,48,2155	141.0	120.0	127.0		2094	-2.2	1.0	9	dbSNP_127	127	418,8182	130.3+/-188.3	10,398,3892	no	coding-synonymous	TEK	NM_000459.3		10,446,6047	AA,AG,GG		4.8605,1.0894,3.583		698/1125	27203002	466,12540	2203	4300	6503	SO:0001819	synonymous_variant	7010	exon13			GTATCAGCTCAAG	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.2094G>A	9.37:g.27203002G>A		Somatic	190	0	0		WXS	Illumina HiSeq	Phase_I	170	84	0.494118	NM_000459	A8K6W0|B4DH20|B4DHD3|D3DRK5|E7EWI2|Q5TCU2|Q8IV34	Silent	SNP	ENST00000380036.4	37	CCDS6519.1																																																																																			G|0.961;A|0.039	0.039	strong		0.443	TEK-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051965.3		
ZNF366	167465	hgsc.bcm.edu	37	5	71739602	71739602	+	Missense_Mutation	SNP	G	G	C	rs13188519	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:71739602G>C	ENST00000318442.5	-	5	2706	c.2216C>G	c.(2215-2217)gCa>gGa	p.A739G	RP11-389C8.2_ENST00000564956.1_RNA	NM_152625.1	NP_689838.1	Q8N895	ZN366_HUMAN	zinc finger protein 366	739	Interaction with CTBP1.|Interaction with NRIP1.		A -> G (in dbSNP:rs13188519).		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)		TAAAAGCACTGCTTGTTTTTC	0.388													G|||	363	0.072484	0.0605	0.0389	5008	,	,		18997	0.0714		0.0964	False		,,,				2504	0.089				p.A739G		Atlas-SNP	.											.	ZNF366	108	.	0			c.C2216G						PASS	.	G	GLY/ALA	259,4117		4,251,1933	46.0	52.0	50.0		2216	5.9	1.0	5	dbSNP_121	50	927,7669		45,837,3416	yes	missense	ZNF366	NM_152625.1	60	49,1088,5349	CC,CG,GG		10.7841,5.9186,9.1428	benign	739/745	71739602	1186,11786	2188	4298	6486	SO:0001583	missense	167465	exon5			AGCACTGCTTGTT	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.2216C>G	5.37:g.71739602G>C	ENSP00000313158:p.Ala739Gly	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	116	43	0.37069	NM_152625	Q5HYI9|Q7RTV4	Missense_Mutation	SNP	ENST00000318442.5	37	CCDS4015.1	140	0.0641025641025641	30	0.06097560975609756	13	0.03591160220994475	20	0.03496503496503497	77	0.10158311345646438	G	16.77	3.215688	0.58452	0.059186	0.107841	ENSG00000178175	ENST00000318442	T	0.10288	2.89	5.87	5.87	0.94306	.	0.171581	0.41605	D	0.000860	T	0.00210	0.0006	L	0.29908	0.895	0.33098	D	0.538779	P	0.36282	0.546	B	0.32149	0.141	T	0.05386	-1.0888	10	0.59425	D	0.04	-6.1181	16.1124	0.81273	0.0:0.0:0.8657:0.1343	rs13188519;rs52832178;rs13188519	739	Q8N895	ZN366_HUMAN	G	739	ENSP00000313158:A739G	ENSP00000313158:A739G	A	-	2	0	ZNF366	71775358	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.660000	0.61511	2.941000	0.99782	0.655000	0.94253	GCA	G|0.916;C|0.084	0.084	strong		0.388	ZNF366-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218574.3		
LAMC2	3918	hgsc.bcm.edu	37	1	183184616	183184616	+	Silent	SNP	C	C	T	rs2274980	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:183184616C>T	ENST00000264144.4	+	3	362	c.297C>T	c.(295-297)tcC>tcT	p.S99S	LAMC2_ENST00000493293.1_Silent_p.S99S	NM_005562.2	NP_005553.2	Q13753	LAMC2_HUMAN	laminin, gamma 2	99	Laminin EGF-like 2. {ECO:0000255|PROSITE- ProRule:PRU00460}.				cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	cell cortex (GO:0005938)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|laminin-2 complex (GO:0005607)|laminin-5 complex (GO:0005610)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)	heparin binding (GO:0008201)			breast(2)|endometrium(6)|kidney(8)|large_intestine(11)|lung(18)|ovary(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	55						GTGACAACTCCGGACGGTGCA	0.517													C|||	1571	0.313698	0.4024	0.317	5008	,	,		20715	0.3333		0.1571	False		,,,				2504	0.3323				p.S99S		Atlas-SNP	.											LAMC2,NS,carcinoma,+1,1	LAMC2	113	1	0			c.C297T						scavenged	.	C	,	1682,2724	509.4+/-367.2	348,986,869	105.0	93.0	97.0		297,297	-1.6	0.6	1	dbSNP_100	97	1519,7081	286.9+/-297.9	130,1259,2911	no	coding-synonymous,coding-synonymous	LAMC2	NM_005562.2,NM_018891.2	,	478,2245,3780	TT,TC,CC		17.6628,38.1752,24.6117	,	99/1194,99/1112	183184616	3201,9805	2203	4300	6503	SO:0001819	synonymous_variant	3918	exon3			CAACTCCGGACGG	Z15008	CCDS1352.1, CCDS44285.1	1q25-q31	2013-03-01	2002-08-29		ENSG00000058085	ENSG00000058085		"""Laminins"""	6493	protein-coding gene	gene with protein product		150292	"""laminin, gamma 2 (nicein (100kD), kalinin (105kD), BM600 (100kD), Herlitz junctional epidermolysis bullosa))"""	EBR2, LAMB2T, LAMNB2, EBR2A		1383240	Standard	NM_005562		Approved	nicein-100kDa, kalinin-105kDa, BM600-100kDa	uc001gqa.2	Q13753	OTTHUMG00000035520	ENST00000264144.4:c.297C>T	1.37:g.183184616C>T		Somatic	129	1	0.00775194		WXS	Illumina HiSeq	Phase_I	145	80	0.551724	NM_005562	Q02536|Q02537|Q13752|Q14941|Q14DF7|Q2M1N2|Q5VYE8	Silent	SNP	ENST00000264144.4	37	CCDS1352.1																																																																																			C|0.732;T|0.268	0.268	strong		0.517	LAMC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086258.1	NM_005562	
DAPP1	27071	hgsc.bcm.edu	37	4	100784980	100784980	+	Silent	SNP	C	C	T	rs3737484	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:100784980C>T	ENST00000512369.1	+	7	722	c.654C>T	c.(652-654)ttC>ttT	p.F218F	DAPP1_ENST00000296414.7_Silent_p.F218F	NM_014395.2	NP_055210.2	Q9UN19	DAPP1_HUMAN	dual adaptor of phosphotyrosine and 3-phosphoinositides	218	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.			VQFDYSQERVNCFC -> MICNILCSFFCPIS (in Ref. 6). {ECO:0000305}.	protein dephosphorylation (GO:0006470)|signal transduction (GO:0007165)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|phospholipid binding (GO:0005543)			endometrium(1)|kidney(1)|lung(4)	6				OV - Ovarian serous cystadenocarcinoma(123;7.04e-09)		CTGTACAATTCGATTATTCAC	0.308													C|||	1337	0.266973	0.4713	0.2363	5008	,	,		20193	0.1528		0.2565	False		,,,				2504	0.1411				p.F218F		Atlas-SNP	.											.	DAPP1	47	.	0			c.C654T						PASS	.	C		1438,2188		295,848,670	82.0	83.0	83.0		654	-0.8	1.0	4	dbSNP_107	83	1955,6193		228,1499,2347	no	coding-synonymous	DAPP1	NM_014395.2		523,2347,3017	TT,TC,CC		23.9936,39.658,28.8177		218/281	100784980	3393,8381	1813	4074	5887	SO:0001819	synonymous_variant	27071	exon7			ACAATTCGATTAT	AF186022	CCDS47112.1	4q25-q27	2013-02-14			ENSG00000070190	ENSG00000070190		"""Pleckstrin homology (PH) domain containing"", ""SH2 domain containing"""	16500	protein-coding gene	gene with protein product		605768				10432293	Standard	NM_014395		Approved	BAM32	uc003hvf.4	Q9UN19	OTTHUMG00000160974	ENST00000512369.1:c.654C>T	4.37:g.100784980C>T		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	58	23	0.396552	NM_014395	Q8TCK5|Q9UHF2	Silent	SNP	ENST00000512369.1	37	CCDS47112.1																																																																																			C|0.705;T|0.295	0.295	strong		0.308	DAPP1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000363215.1		
ZNF417	147687	hgsc.bcm.edu	37	19	58420152	58420152	+	Silent	SNP	C	C	A	rs17845779	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:58420152C>A	ENST00000312026.5	-	3	1658	c.1494G>T	c.(1492-1494)ggG>ggT	p.G498G	ZNF417_ENST00000536263.1_Silent_p.G299G|ZNF417_ENST00000595559.1_Silent_p.G497G|CTD-2583A14.9_ENST00000602124.1_Intron	NM_152475.2	NP_689688.2	Q8TAU3	ZN417_HUMAN	zinc finger protein 417	498					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.G498G(1)		central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|stomach(3)|upper_aerodigestive_tract(1)	18		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0151)		GAAATGATTTCCCACATTCAT	0.398													A|||	1399	0.279353	0.2761	0.2248	5008	,	,		21369	0.2847		0.2992	False		,,,				2504	0.2965				p.G498G		Atlas-SNP	.											ZNF417,NS,carcinoma,0,1	ZNF417	44	1	1	Substitution - coding silent(1)	stomach(1)	c.G1494T						PASS	.						104.0	85.0	91.0					19																	58420152		2203	4296	6499	SO:0001819	synonymous_variant	147687	exon3			TGATTTCCCACAT	BC025783	CCDS12965.1, CCDS74469.1	19q13.43	2013-01-08				ENSG00000173480		"""Zinc fingers, C2H2-type"", ""-"""	20646	protein-coding gene	gene with protein product							Standard	NM_152475		Approved	MGC34079	uc002qqq.3	Q8TAU3		ENST00000312026.5:c.1494G>T	19.37:g.58420152C>A		Somatic	248	1	0.00403226		WXS	Illumina HiSeq	Phase_I	217	96	0.442396	NM_152475	B4DEU1	Silent	SNP	ENST00000312026.5	37	CCDS12965.1																																																																																			C|0.765;A|0.235	0.235	strong		0.398	ZNF417-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466860.1	NM_152475	
SPICE1	152185	hgsc.bcm.edu	37	3	113222036	113222036	+	Silent	SNP	G	G	A	rs11537650	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:113222036G>A	ENST00000295872.4	-	3	397	c.138C>T	c.(136-138)ccC>ccT	p.P46P		NM_144718.3	NP_653319.1	Q8N0Z3	SPICE_HUMAN	spindle and centriole associated protein 1	46					metaphase plate congression (GO:0051310)|regulation of centriole replication (GO:0046599)|spindle assembly involved in mitosis (GO:0090307)	centriole (GO:0005814)|centrosome (GO:0005813)|spindle (GO:0005819)				NS(1)|autonomic_ganglia(1)|breast(4)|endometrium(3)|large_intestine(9)|lung(10)|ovary(2)|skin(2)|urinary_tract(1)	33						CCAGATCTTCGGGAGTTGCCC	0.313													A|||	1223	0.244209	0.3684	0.1427	5008	,	,		14743	0.2212		0.2286	False		,,,				2504	0.1881				p.P46P		Atlas-SNP	.											.	SPICE1	130	.	0			c.C138T						PASS	.	A		1548,2858	666.6+/-401.7	277,994,932	52.0	55.0	54.0		138	5.6	1.0	3	dbSNP_120	54	1972,6626	721.7+/-406.4	228,1516,2555	no	coding-synonymous	SPICE1	NM_144718.3		505,2510,3487	AA,AG,GG		22.9356,35.1339,27.0686		46/856	113222036	3520,9484	2203	4299	6502	SO:0001819	synonymous_variant	152185	exon3			ATCTTCGGGAGTT	AY099107	CCDS2973.1	3q13.2	2010-09-01	2010-09-01	2010-09-01	ENSG00000163611	ENSG00000163611			25083	protein-coding gene	gene with protein product	"""spindle and centriole protein"""	613447	"""coiled-coil domain containing 52"""	CCDC52		20736305	Standard	NM_144718		Approved	SPICE	uc003eag.4	Q8N0Z3	OTTHUMG00000159261	ENST00000295872.4:c.138C>T	3.37:g.113222036G>A		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	98	45	0.459184	NM_144718	D3DN72|Q8WUX6	Silent	SNP	ENST00000295872.4	37	CCDS2973.1																																																																																			T|0.051;G|0.602;C|0.139;A|0.208	0.208	strong		0.313	SPICE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354177.2	NM_144718	
SPG20	23111	hgsc.bcm.edu	37	13	36886469	36886469	+	Silent	SNP	T	T	C	rs2274293	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:36886469T>C	ENST00000451493.1	-	7	1846	c.1629A>G	c.(1627-1629)gcA>gcG	p.A543A	SPG20_ENST00000438666.2_Silent_p.A543A|SPG20_ENST00000494062.2_Silent_p.A543A|SPG20_ENST00000355182.4_Silent_p.A543A	NM_001142295.1	NP_001135767.1	Q8N0X7	SPG20_HUMAN	spastic paraplegia 20 (Troyer syndrome)	543					abscission (GO:0009838)|adipose tissue development (GO:0060612)|cell death (GO:0008219)|cell division (GO:0051301)|lipid particle organization (GO:0034389)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of collateral sprouting in absence of injury (GO:0048698)|neuromuscular process (GO:0050905)|regulation of mitochondrial membrane potential (GO:0051881)	cytoplasm (GO:0005737)|lipid particle (GO:0005811)|midbody (GO:0030496)|mitochondrial outer membrane (GO:0005741)|plasma membrane (GO:0005886)|synapse (GO:0045202)	ubiquitin protein ligase binding (GO:0031625)			breast(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(10)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	27		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;2.42e-08)|Epithelial(112;1.58e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.00128)|BRCA - Breast invasive adenocarcinoma(63;0.0125)|GBM - Glioblastoma multiforme(144;0.026)		GAACACTACTTGCTGCTACAA	0.378													C|||	1448	0.289137	0.1384	0.3516	5008	,	,		16360	0.5139		0.2455	False		,,,				2504	0.2618				p.A543A		Atlas-SNP	.											.	SPG20	87	.	0			c.A1629G						PASS	.	C	,,,	712,3694	759.3+/-412.9	51,610,1542	136.0	135.0	135.0		1629,1629,1629,1629	0.3	1.0	13	dbSNP_100	135	2215,6385	710.3+/-405.8	306,1603,2391	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SPG20	NM_001142294.1,NM_001142295.1,NM_001142296.1,NM_015087.4	,,,	357,2213,3933	CC,CT,TT		25.7558,16.1598,22.505	,,,	543/667,543/667,543/667,543/667	36886469	2927,10079	2203	4300	6503	SO:0001819	synonymous_variant	23111	exon7			ACTACTTGCTGCT	AB011182	CCDS9356.1	13q13.1	2008-07-04	2007-04-23		ENSG00000133104	ENSG00000133104			18514	protein-coding gene	gene with protein product	"""spartin"""	607111				6022528, 12134148	Standard	NM_001142294		Approved	KIAA0610, TAHCCP1	uc001uvm.3	Q8N0X7	OTTHUMG00000016730	ENST00000451493.1:c.1629A>G	13.37:g.36886469T>C		Somatic	289	0	0		WXS	Illumina HiSeq	Phase_I	211	96	0.454976	NM_015087	O60349|Q86Y67|Q9H1T2|Q9H1T3	Silent	SNP	ENST00000451493.1	37	CCDS9356.1																																																																																			T|0.736;C|0.264	0.264	strong		0.378	SPG20-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044494.2		
TRIM31	11074	hgsc.bcm.edu	37	6	30080274	30080274	+	Silent	SNP	G	G	A	rs2517598	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:30080274G>A	ENST00000376734.3	-	2	434	c.309C>T	c.(307-309)caC>caT	p.H103H	TRIM31_ENST00000540829.1_Silent_p.H103H|TRIM31-AS1_ENST00000440874.1_RNA|TRIM31_ENST00000485864.1_5'Flank	NM_007028.3	NP_008959.3	Q9BZY9	TRI31_HUMAN	tripartite motif containing 31	103					innate immune response (GO:0045087)|negative regulation of viral entry into host cell (GO:0046597)|negative regulation of viral transcription (GO:0032897)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein ubiquitination (GO:0016567)|regulation of viral release from host cell (GO:1902186)	mitochondrion (GO:0005739)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(5)|ovary(2)|prostate(2)|skin(2)	15						CGCAGAAATAGTGGAACATCT	0.493													A|||	606	0.121006	0.093	0.1297	5008	,	,		21287	0.0873		0.1252	False		,,,				2504	0.183				p.H103H		Atlas-SNP	.											.	TRIM31	40	.	0			c.C309T						PASS	.	A		306,2716		16,274,1221	138.0	122.0	127.0		309	-3.8	0.0	6	dbSNP_100	127	785,4633		51,683,1975	no	coding-synonymous	TRIM31	NM_007028.3		67,957,3196	AA,AG,GG		14.4887,10.1257,12.9265		103/426	30080274	1091,7349	1511	2709	4220	SO:0001819	synonymous_variant	11074	exon2			GAAATAGTGGAAC	AF230386	CCDS34374.1	6p21.3	2013-01-09	2011-01-25		ENSG00000204616	ENSG00000204616		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	16289	protein-coding gene	gene with protein product		609316	"""tripartite motif-containing 31"""			11331580	Standard	XM_006714977		Approved	RNF, HCGI, C6orf13, HCG1	uc003npg.1	Q9BZY9	OTTHUMG00000031064	ENST00000376734.3:c.309C>T	6.37:g.30080274G>A		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	123	45	0.365854	NM_007028	A6NLX6|A9R9Q4|Q53H52|Q5RI37|Q5SRJ7|Q5SRJ8|Q5SS28|Q96AK4|Q96AP8|Q99579|Q9BZY8	Silent	SNP	ENST00000376734.3	37	CCDS34374.1																																																																																			G|0.878;A|0.122	0.122	strong		0.493	TRIM31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076081.2		
GRK4	2868	hgsc.bcm.edu	37	4	2993980	2993980	+	Silent	SNP	T	T	C	rs2515941	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:2993980T>C	ENST00000398052.4	+	4	643	c.300T>C	c.(298-300)gaT>gaC	p.D100D	GRK4_ENST00000345167.6_Silent_p.D68D|GRK4_ENST00000504933.1_Silent_p.D100D|GRK4_ENST00000398051.4_Silent_p.D68D	NM_182982.2	NP_892027.2	P32298	GRK4_HUMAN	G protein-coupled receptor kinase 4	100	N-terminal.|RGS. {ECO:0000255|PROSITE- ProRule:PRU00171}.				G-protein coupled receptor internalization (GO:0002031)|receptor internalization (GO:0031623)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|signal transduction (GO:0007165)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytosol (GO:0005829)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)	ATP binding (GO:0005524)|G-protein coupled receptor kinase activity (GO:0004703)|rhodopsin kinase activity (GO:0050254)			lung(1)|upper_aerodigestive_tract(1)	2				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)		ACCGAAGTGATTGTGGACTGT	0.368													T|||	1465	0.292532	0.4644	0.3256	5008	,	,		19673	0.0942		0.3767	False		,,,				2504	0.1544				p.D100D		Atlas-SNP	.											.	GRK4	72	.	0			c.T300C						PASS	.	T	,,	1905,2501	545.2+/-376.7	388,1129,686	151.0	148.0	149.0		204,300,300	-10.7	0.0	4	dbSNP_100	149	3090,5510	473.0+/-368.5	581,1928,1791	no	coding-synonymous,coding-synonymous,coding-synonymous	GRK4	NM_001004056.1,NM_001004057.1,NM_182982.2	,,	969,3057,2477	CC,CT,TT		35.9302,43.2365,38.4054	,,	68/547,100/533,100/579	2993980	4995,8011	2203	4300	6503	SO:0001819	synonymous_variant	2868	exon4			AAGTGATTGTGGA		CCDS33946.1, CCDS33947.1, CCDS47002.1, CCDS68656.1	4p16.3	2008-02-05	2004-02-04	2004-02-06	ENSG00000125388	ENSG00000125388			4543	protein-coding gene	gene with protein product		137026	"""G protein-coupled receptor kinase 2-like (Drosophila)"""	GPRK2L		1338872	Standard	NM_182982		Approved	GPRK4	uc003ggn.1	P32298	OTTHUMG00000159914	ENST00000398052.4:c.300T>C	4.37:g.2993980T>C		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	118	116	0.983051	NM_182982	O00641|O00642|Q13293|Q13294|Q13295|Q14453|Q14725|Q15313|Q15314|Q15315|Q15316|Q17RH6|Q53EQ8	Silent	SNP	ENST00000398052.4	37	CCDS33946.1																																																																																			T|0.639;C|0.361	0.361	strong		0.368	GRK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358176.2	NM_005307	
UMODL1	89766	hgsc.bcm.edu	37	21	43504228	43504228	+	Silent	SNP	T	T	C	rs7278485	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:43504228T>C	ENST00000408910.2	+	3	354	c.354T>C	c.(352-354)ccT>ccC	p.P118P	UMODL1_ENST00000400427.1_Silent_p.P46P|UMODL1_ENST00000400424.2_Silent_p.P46P|UMODL1_ENST00000408989.2_Silent_p.P118P	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						scavenged	.	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	137	2	0.0145985		WXS	Illumina HiSeq	Phase_I	149	148	0.993289	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		
CDRT1	374286	hgsc.bcm.edu	37	17	15510888	15510888	+	Splice_Site	SNP	G	G	A	rs62070401	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:15510888G>A	ENST00000395906.3	-	6	1231	c.1232C>T	c.(1231-1233)aCg>aTg	p.T411M	RP11-385D13.1_ENST00000455584.2_Splice_Site_p.T721M	NM_006382.3	NP_006373.2	O95170	CDRT1_HUMAN	CMT1A duplicated region transcript 1	411										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)		CAGTACCTACGTGTCAGAGAG	0.493													G|||	1466	0.292732	0.264	0.2767	5008	,	,		18548	0.4514		0.1511	False		,,,				2504	0.3252				p.T411M		Atlas-SNP	.											.	CDRT1	83	.	0			c.C1232T						PASS	.	G	MET/THR	1085,3321	390.3+/-327.6	143,799,1261	68.0	65.0	66.0		1232	-4.1	0.8	17	dbSNP_129	66	1459,7141	275.3+/-291.7	127,1205,2968	no	missense-near-splice	CDRT1	NM_006382.3	81	270,2004,4229	AA,AG,GG		16.9651,24.6255,19.5602	possibly-damaging	411/753	15510888	2544,10462	2203	4300	6503	SO:0001630	splice_region_variant	374286	exon6			ACCTACGTGTCAG	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.1232+1C>T	17.37:g.15510888G>A		Somatic	223	0	0		WXS	Illumina HiSeq	Phase_I	206	206	1	NM_006382	O43848|O95611	Missense_Mutation	SNP	ENST00000395906.3	37	CCDS45619.1	570|570	0.260989010989011|0.260989010989011	100|100	0.2032520325203252|0.2032520325203252	86|86	0.23756906077348067|0.23756906077348067	256|256	0.44755244755244755|0.44755244755244755	128|128	0.16886543535620052|0.16886543535620052	G|G	9.414|9.414	1.081185|1.081185	0.20309|0.20309	0.246255|0.246255	0.169651|0.169651	ENSG00000251537|ENSG00000251537	ENST00000455584|ENST00000261644;ENST00000395906	.|T	.|0.58940	.|0.3	4.99|4.99	-4.14|-4.14	0.03892|0.03892	.|WD40 repeat-like-containing domain (1);	.|0.395907	.|0.18373	.|U	.|0.143193	T|T	0.00012|0.00012	0.0000|0.0000	L|L	0.51422|0.51422	1.61|1.61	0.09310|0.09310	P|P	0.99999999077601|0.99999999077601	.|D;B	.|0.56521	.|0.976;0.203	.|B;B	.|0.42959	.|0.403;0.029	T|T	0.32955|0.32955	-0.9887|-0.9887	4|8	.|.	.|.	.|.	.|.	6.6345|6.6345	0.22875|0.22875	0.5699:0.138:0.2921:0.0|0.5699:0.138:0.2921:0.0	rs62070401|rs62070401	.|411;735	.|O95170;Q59EB2	.|CDRT1_HUMAN;.	C|M	736|441;411	.|ENSP00000379242:T411M	.|.	R|T	-|-	1|2	0|0	RP11-385D13.1|RP11-385D13.1	15451613|15451613	0.231000|0.231000	0.23751|0.23751	0.832000|0.832000	0.32986|0.32986	0.010000|0.010000	0.07245|0.07245	-0.782000|-0.782000	0.04643|0.04643	-0.694000|-0.694000	0.05113|0.05113	-1.259000|-1.259000	0.01468|0.01468	CGT|ACG	G|0.754;A|0.246	0.246	strong		0.493	CDRT1-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448127.1	NM_006382	Missense_Mutation
C19orf45	374877	hgsc.bcm.edu	37	19	7569245	7569245	+	Missense_Mutation	SNP	A	A	G	rs145077335		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:7569245A>G	ENST00000361664.2	+	4	871	c.730A>G	c.(730-732)Acg>Gcg	p.T244A	CTD-2207O23.12_ENST00000599312.1_5'Flank	NM_198534.2	NP_940936.2	Q8NA69	CS045_HUMAN	chromosome 19 open reading frame 45	244										endometrium(1)|kidney(1)|liver(1)|lung(2)|ovary(2)|stomach(1)	8						CTATGGATCAACGTGTTCGGA	0.592													a|||	1	0.000199681	0.0	0.0	5008	,	,		16125	0.0		0.001	False		,,,				2504	0.0				p.T244A		Atlas-SNP	.											.	C19orf45	36	.	0			c.A730G						PASS	.	A	ALA/THR	2,4404	6.2+/-15.9	0,2,2201	63.0	65.0	64.0		730	-6.4	0.0	19	dbSNP_134	64	10,8590	7.1+/-27.0	0,10,4290	yes	missense	C19orf45	NM_198534.2	58	0,12,6491	GG,GA,AA		0.1163,0.0454,0.0923	benign	244/506	7569245	12,12994	2203	4300	6503	SO:0001583	missense	374877	exon4			GGATCAACGTGTT	BC029824	CCDS12179.2	19p13.2	2008-02-05			ENSG00000198723	ENSG00000198723			24745	protein-coding gene	gene with protein product						12477932	Standard	NM_198534		Approved	FLJ35784	uc002mgm.2	Q8NA69	OTTHUMG00000157183	ENST00000361664.2:c.730A>G	19.37:g.7569245A>G	ENSP00000355241:p.Thr244Ala	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	116	70	0.603448	NM_198534	Q8N115	Missense_Mutation	SNP	ENST00000361664.2	37	CCDS12179.2	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	a	5.651	0.304727	0.10678	4.54E-4	0.001163	ENSG00000198723	ENST00000361664	T	0.13420	2.59	4.37	-6.39	0.01951	.	2.395820	0.01247	N	0.008772	T	0.07593	0.0191	N	0.22421	0.69	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.21759	-1.0236	10	0.27785	T	0.31	-0.997	2.6616	0.05028	0.2167:0.4136:0.2533:0.1164	.	244	Q8NA69	CS045_HUMAN	A	244	ENSP00000355241:T244A	ENSP00000355241:T244A	T	+	1	0	C19orf45	7475245	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-1.028000	0.03589	-1.595000	0.01613	-0.549000	0.04216	ACG	A|0.999;G|0.001	0.001	strong		0.592	C19orf45-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347808.1	NM_198534	
ZNF783	100289678	hgsc.bcm.edu	37	7	148963652	148963652	+	Missense_Mutation	SNP	C	C	T	rs61729506	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:148963652C>T	ENST00000434415.1	+	2	414	c.251C>T	c.(250-252)aCa>aTa	p.T84I		NM_001195220.1	NP_001182149.1	Q6ZMS7	ZN783_HUMAN	zinc finger family member 783	84					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(10)|prostate(1)	22	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.0014)			TGCGAGAAGACAGCTGTGGAG	0.642													C|||	275	0.0549121	0.1241	0.0706	5008	,	,		17096	0.0		0.0557	False		,,,				2504	0.0061				p.T84I		Atlas-SNP	.											.	ZNF783	28	.	0			c.C251T						PASS	.	C	ILE/THR	470,3936	221.7+/-238.7	25,420,1758	63.0	64.0	64.0		251	3.6	1.0	7	dbSNP_129	64	600,8000	158.3+/-211.8	17,566,3717	no	missense	ZNF783	NM_001195220.1	89	42,986,5475	TT,TC,CC		6.9767,10.6673,8.227		84/547	148963652	1070,11936	2203	4300	6503	SO:0001583	missense	0	exon2			AGAAGACAGCTGT	AK131504	CCDS56519.1	7q36.1	2013-01-08	2008-05-28		ENSG00000204946	ENSG00000204946		"""Zinc fingers, C2H2-type"", ""-"""	27222	protein-coding gene	gene with protein product						8619474, 9110174	Standard	NM_001195220		Approved	DKFZp667J212	uc011kuo.2	Q6ZMS7	OTTHUMG00000158969	ENST00000434415.1:c.251C>T	7.37:g.148963652C>T	ENSP00000410890:p.Thr84Ile	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	50	17	0.34	NM_001195220	C9J9J2	Missense_Mutation	SNP	ENST00000434415.1	37	CCDS56519.1	129	0.059065934065934064	54	0.10975609756097561	33	0.09116022099447514	0	0.0	42	0.055408970976253295	C	14.15	2.448779	0.43531	0.106673	0.069767	ENSG00000204946	ENST00000434415	T	0.25085	1.82	4.73	3.62	0.41486	.	0.000000	0.33980	N	0.004363	T	0.00936	0.0031	M	0.80847	2.515	0.18873	P	0.9999855317	.	.	.	.	.	.	T	0.18429	-1.0337	7	0.87932	D	0	-16.7672	8.7454	0.34583	0.0:0.8755:0.0:0.1245	rs61729506	.	.	.	I	84	ENSP00000410890:T84I	ENSP00000367291:T84I	T	+	2	0	ZNF783	148594585	0.673000	0.27539	0.976000	0.42696	0.362000	0.29581	0.985000	0.29578	2.190000	0.69967	0.561000	0.74099	ACA	C|0.942;T|0.058	0.058	strong		0.642	ZNF783-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352715.1	NM_001195220	
TMCO4	255104	hgsc.bcm.edu	37	1	20072082	20072082	+	Missense_Mutation	SNP	C	C	T	rs35760408	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:20072082C>T	ENST00000294543.6	-	10	1061	c.820G>A	c.(820-822)Ggc>Agc	p.G274S	TMCO4_ENST00000375122.2_Intron|TMCO4_ENST00000375127.1_Missense_Mutation_p.G274S	NM_181719.4	NP_859070.3	Q5TGY1	TMCO4_HUMAN	transmembrane and coiled-coil domains 4	274						integral component of membrane (GO:0016021)				biliary_tract(1)|breast(2)|endometrium(2)|kidney(1)|lung(11)|skin(1)|upper_aerodigestive_tract(1)	19		Colorectal(325;0.000147)|Renal(390;0.000469)|all_lung(284;0.00519)|Breast(348;0.00526)|Lung NSC(340;0.00544)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0439)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00708)|COAD - Colon adenocarcinoma(152;2.28e-05)|BRCA - Breast invasive adenocarcinoma(304;5.8e-05)|Kidney(64;0.000367)|GBM - Glioblastoma multiforme(114;0.000377)|KIRC - Kidney renal clear cell carcinoma(64;0.00459)|STAD - Stomach adenocarcinoma(196;0.0072)|READ - Rectum adenocarcinoma(331;0.0862)|Lung(427;0.223)		AGCTGCCTGCCCTCCGTCAGA	0.572													C|||	157	0.0313498	0.0	0.0677	5008	,	,		14564	0.0605		0.0159	False		,,,				2504	0.0337				p.G274S		Atlas-SNP	.											.	TMCO4	46	.	0			c.G820A						PASS	.	C	SER/GLY	16,4390	24.3+/-50.5	0,16,2187	124.0	122.0	123.0		820	5.0	1.0	1	dbSNP_126	123	152,8448	73.8+/-136.5	1,150,4149	yes	missense	TMCO4	NM_181719.4	56	1,166,6336	TT,TC,CC		1.7674,0.3631,1.2917	possibly-damaging	274/635	20072082	168,12838	2203	4300	6503	SO:0001583	missense	255104	exon10			GCCTGCCCTCCGT		CCDS198.1	1p36.13	2008-02-05			ENSG00000162542	ENSG00000162542			27393	protein-coding gene	gene with protein product							Standard	NM_181719		Approved	DKFZp686C23231	uc001bcn.3	Q5TGY1	OTTHUMG00000002697	ENST00000294543.6:c.820G>A	1.37:g.20072082C>T	ENSP00000294543:p.Gly274Ser	Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	130	54	0.415385	NM_181719	Q5TGY2|Q6MZN5|Q7Z6K6|Q9UQP4|Q9Y3K1	Missense_Mutation	SNP	ENST00000294543.6	37	CCDS198.1	59	0.027014652014652016	0	0.0	14	0.03867403314917127	34	0.05944055944055944	11	0.014511873350923483	C	33	5.193426	0.94960	0.003631	0.017674	ENSG00000162542	ENST00000294543;ENST00000375127	T;T	0.39997	1.05;1.05	5.02	5.02	0.67125	.	0.000000	0.85682	D	0.000000	T	0.11067	0.0270	L	0.39467	1.215	0.80722	D	1	D	0.54397	0.966	P	0.62885	0.908	T	0.03863	-1.0997	10	0.41790	T	0.15	-17.103	16.2009	0.82078	0.0:1.0:0.0:0.0	rs35760408	274	Q5TGY1	TMCO4_HUMAN	S	274	ENSP00000294543:G274S;ENSP00000364269:G274S	ENSP00000294543:G274S	G	-	1	0	TMCO4	19944669	1.000000	0.71417	0.988000	0.46212	0.950000	0.60333	7.072000	0.76777	2.492000	0.84095	0.455000	0.32223	GGC	C|0.981;T|0.019	0.019	strong		0.572	TMCO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007658.1	NM_181719	
C5	727	hgsc.bcm.edu	37	9	123725926	123725926	+	Missense_Mutation	SNP	T	T	G	rs17612	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:123725926T>G	ENST00000223642.1	-	34	4340	c.4311A>C	c.(4309-4311)gaA>gaC	p.E1437D		NM_001735.2	NP_001726.2	P01031	CO5_HUMAN	complement component 5	1437			E -> D (in dbSNP:rs17612). {ECO:0000269|Ref.2}.		activation of MAPK activity (GO:0000187)|cell chemotaxis (GO:0060326)|cell surface receptor signaling pathway (GO:0007166)|cellular calcium ion homeostasis (GO:0006874)|chemotaxis (GO:0006935)|complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|complement activation, classical pathway (GO:0006958)|cytolysis (GO:0019835)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|in utero embryonic development (GO:0001701)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|leukocyte migration involved in inflammatory response (GO:0002523)|negative regulation of dopamine secretion (GO:0033602)|negative regulation of macrophage chemotaxis (GO:0010760)|negative regulation of norepinephrine secretion (GO:0010700)|positive regulation of angiogenesis (GO:0045766)|positive regulation of chemokine secretion (GO:0090197)|positive regulation of chemotaxis (GO:0050921)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of complement activation (GO:0030449)|response to stress (GO:0006950)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane attack complex (GO:0005579)	chemokine activity (GO:0008009)|endopeptidase inhibitor activity (GO:0004866)|receptor binding (GO:0005102)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(14)|lung(5)|ovary(2)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	46				OV - Ovarian serous cystadenocarcinoma(323;4.98e-53)|GBM - Glioblastoma multiforme(294;0.0242)	Eculizumab(DB01257)|Intravenous Immunoglobulin(DB00028)	CTTTTAAGTCTTCTTCATTTG	0.353													T|||	177	0.0353435	0.0083	0.0375	5008	,	,		16581	0.002		0.0596	False		,,,				2504	0.0798				p.E1437D		Atlas-SNP	.											.	C5	124	.	0			c.A4311C						PASS	.	T	ASP/GLU	101,4305	80.4+/-118.8	0,101,2102	72.0	67.0	68.0		4311	-2.9	0.8	9	dbSNP_63	68	600,8000	159.5+/-212.8	32,536,3732	yes	missense	C5	NM_001735.2	45	32,637,5834	GG,GT,TT		6.9767,2.2923,5.3898	benign	1437/1677	123725926	701,12305	2203	4300	6503	SO:0001583	missense	727	exon34			TAAGTCTTCTTCA	M57729	CCDS6826.1	9q33-q34	2014-09-17			ENSG00000106804	ENSG00000106804		"""Complement system"", ""Endogenous ligands"""	1331	protein-coding gene	gene with protein product	"""prepro-C5"", ""C5a anaphylatoxin"""	120900					Standard	NM_001735		Approved	CPAMD4, C5a, C5b	uc004bkv.3	P01031	OTTHUMG00000020579	ENST00000223642.1:c.4311A>C	9.37:g.123725926T>G	ENSP00000223642:p.Glu1437Asp	Somatic	294	0	0		WXS	Illumina HiSeq	Phase_I	251	120	0.478088	NM_001735	Q14CJ0|Q27I61	Missense_Mutation	SNP	ENST00000223642.1	37	CCDS6826.1	64	0.029304029304029304	6	0.012195121951219513	14	0.03867403314917127	0	0.0	44	0.05804749340369393	T	12.35	1.911353	0.33721	0.022923	0.069767	ENSG00000106804	ENST00000223642	T	0.28895	1.59	5.33	-2.86	0.05717	Alpha-macroglobulin, receptor-binding (3);	0.217109	0.46758	N	0.000271	T	0.01061	0.0035	L	0.28694	0.88	0.35098	D	0.764931	B	0.09022	0.002	B	0.17098	0.017	T	0.23619	-1.0183	10	0.19147	T	0.46	.	5.7421	0.18100	0.4801:0.0817:0.0:0.4381	rs17612;rs16910239;rs17612	1437	P01031	CO5_HUMAN	D	1437	ENSP00000223642:E1437D	ENSP00000223642:E1437D	E	-	3	2	C5	122765747	0.951000	0.32395	0.775000	0.31657	0.886000	0.51366	-0.254000	0.08781	-0.719000	0.04942	-0.302000	0.09304	GAA	T|0.954;G|0.046	0.046	strong		0.353	C5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053844.1	NM_001735	
RGS12	6002	hgsc.bcm.edu	37	4	3429856	3429856	+	Missense_Mutation	SNP	A	A	G	rs2269497	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:3429856A>G	ENST00000344733.5	+	15	4275	c.3371A>G	c.(3370-3372)aAc>aGc	p.N1124S	RGS12_ENST00000306648.7_Missense_Mutation_p.N522S|RGS12_ENST00000338806.4_Missense_Mutation_p.N476S|RGS12_ENST00000382788.3_Missense_Mutation_p.N1124S|RGS12_ENST00000538395.1_Missense_Mutation_p.N466S|RGS12_ENST00000508158.1_3'UTR|RGS12_ENST00000336727.3_Missense_Mutation_p.N1124S	NM_198229.2	NP_937872.1	O14924	RGS12_HUMAN	regulator of G-protein signaling 12	1124			N -> S (in dbSNP:rs2269497).		positive regulation of GTPase activity (GO:0043547)|regulation of catalytic activity (GO:0050790)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|transcription, DNA-templated (GO:0006351)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)|GTPase regulator activity (GO:0030695)|receptor signaling protein activity (GO:0005057)			autonomic_ganglia(1)|breast(4)|endometrium(3)|kidney(2)|large_intestine(9)|lung(16)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	43				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)		GTGAAACAGAACACAGCTGTA	0.517													A|||	206	0.0411342	0.0219	0.0764	5008	,	,		17724	0.0526		0.0358	False		,,,				2504	0.0358				p.N1124S		Atlas-SNP	.											.	RGS12	128	.	0			c.A3371G						PASS	.	A	SER/ASN,SER/ASN,SER/ASN	91,4315	75.7+/-113.9	0,91,2112	155.0	159.0	157.0		3371,1427,3371	-10.0	0.0	4	dbSNP_100	157	276,8324	104.0+/-165.0	6,264,4030	yes	missense,missense,missense	RGS12	NM_002926.3,NM_198227.1,NM_198229.2	46,46,46	6,355,6142	GG,GA,AA		3.2093,2.0654,2.8218	benign,benign,benign	1124/1377,476/800,1124/1448	3429856	367,12639	2203	4300	6503	SO:0001583	missense	6002	exon15			AACAGAACACAGC	AF035152	CCDS3366.1, CCDS3367.1, CCDS3368.1	4p16.3	2008-02-05	2007-08-14		ENSG00000159788	ENSG00000159788		"""Regulators of G-protein signaling"""	9994	protein-coding gene	gene with protein product		602512	"""regulator of G-protein signalling 12"""			9651375	Standard	NM_198229		Approved		uc003ggw.3	O14924	OTTHUMG00000090277	ENST00000344733.5:c.3371A>G	4.37:g.3429856A>G	ENSP00000339381:p.Asn1124Ser	Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	153	68	0.444444	NM_002926	B1AQ30|B1AQ31|B1AQ32|B7Z764|E7EMN9|O14922|O14923|O43510|O75338|Q147X0|Q8WX95	Missense_Mutation	SNP	ENST00000344733.5	37	CCDS3366.1	118	0.05402930402930403	17	0.034552845528455285	30	0.08287292817679558	44	0.07692307692307693	27	0.03562005277044855	A	0.363	-0.938043	0.02340	0.020654	0.032093	ENSG00000159788	ENST00000344733;ENST00000336727;ENST00000382788;ENST00000306648;ENST00000338806;ENST00000538395	T;T;T;T;T;T	0.32023	1.77;1.79;1.79;1.47;1.48;1.49	5.01	-10.0	0.00425	.	0.907276	0.09627	N	0.776740	T	0.00580	0.0019	N	0.16066	0.365	0.09310	N	0.999999	B;B;B;B;B;B;B;B	0.11235	0.0;0.004;0.004;0.004;0.004;0.001;0.001;0.001	B;B;B;B;B;B;B;B	0.14023	0.001;0.004;0.004;0.01;0.009;0.001;0.002;0.005	T	0.34403	-0.9830	10	0.02654	T	1	-7.6303	13.5795	0.61893	0.1834:0.192:0.6247:0.0	rs2269497;rs52812809;rs56723557;rs2269497	466;323;323;466;476;522;1124;1124	B7Z764;B3KVS7;A8K440;O14924-2;O14924-3;Q8WX95;O14924;O14924-4	.;.;.;.;.;.;RGS12_HUMAN;.	S	1124;1124;1124;522;476;466	ENSP00000339381:N1124S;ENSP00000338509:N1124S;ENSP00000372238:N1124S;ENSP00000304459:N522S;ENSP00000342133:N476S;ENSP00000438888:N466S	ENSP00000304459:N522S	N	+	2	0	RGS12	3399654	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.551000	0.06027	-2.256000	0.00695	-0.982000	0.02568	AAC	A|0.964;G|0.036	0.036	strong		0.517	RGS12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206602.1	NM_002926	
SLC9C1	285335	hgsc.bcm.edu	37	3	111962851	111962851	+	Missense_Mutation	SNP	T	T	C	rs6768523	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:111962851T>C	ENST00000305815.5	-	11	1522	c.1270A>G	c.(1270-1272)Act>Gct	p.T424A	SLC9C1_ENST00000487372.1_Missense_Mutation_p.T376A	NM_183061.1	NP_898884.1	Q4G0N8	SL9C1_HUMAN	solute carrier family 9, subfamily C (Na+-transporting carboxylic acid decarboxylase), member 1	424			T -> A (in dbSNP:rs6768523). {ECO:0000269|PubMed:14702039}.		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)										CCTAGTATAGTAACTGCCACT	0.313													T|||	1627	0.32488	0.3427	0.3963	5008	,	,		17034	0.3304		0.2376	False		,,,				2504	0.3344				p.T424A		Atlas-SNP	.											.	.	.	.	0			c.A1270G						PASS	.	T	ALA/THR	1465,2941	465.1+/-354.1	249,967,987	69.0	74.0	72.0		1270	4.0	0.9	3	dbSNP_116	72	2328,6272	387.2+/-342.1	320,1688,2292	yes	missense	SLC9A10	NM_183061.1	58	569,2655,3279	CC,CT,TT		27.0698,33.2501,29.1635	benign	424/1178	111962851	3793,9213	2203	4300	6503	SO:0001583	missense	285335	exon11			GTATAGTAACTGC	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.1270A>G	3.37:g.111962851T>C	ENSP00000306627:p.Thr424Ala	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	135	133	0.985185	NM_183061	Q6ZRP4|Q7RTP2	Missense_Mutation	SNP	ENST00000305815.5	37	CCDS33817.1	669	0.30631868131868134	167	0.3394308943089431	134	0.3701657458563536	183	0.31993006993006995	185	0.24406332453825857	T	2.635	-0.285462	0.05605	0.332501	0.270698	ENSG00000172139	ENST00000305815;ENST00000487372	T;T	0.76709	-1.04;-1.04	5.11	3.96	0.45880	.	1.027890	0.07726	N	0.944446	T	0.00012	0.0000	L	0.40543	1.245	0.38456	P	0.052908999999999984	B;P	0.34462	0.202;0.454	B;B	0.38755	0.281;0.192	T	0.09250	-1.0683	9	0.30078	T	0.28	-7.0031	7.6407	0.28292	0.0:0.0978:0.0:0.9022	rs6768523;rs52800559;rs56653457;rs6768523	376;424	Q4G0N8-2;Q4G0N8	.;S9A10_HUMAN	A	424;376	ENSP00000306627:T424A;ENSP00000420688:T376A	ENSP00000306627:T424A	T	-	1	0	SLC9A10	113445541	0.185000	0.23213	0.936000	0.37596	0.290000	0.27261	0.071000	0.14594	0.896000	0.36366	0.352000	0.21897	ACT	T|0.708;C|0.292	0.292	strong		0.313	SLC9C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354066.1	NM_183061	
PCNX	22990	hgsc.bcm.edu	37	14	71502824	71502824	+	Missense_Mutation	SNP	G	G	T	rs117405927	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:71502824G>T	ENST00000304743.2	+	19	4263	c.3817G>T	c.(3817-3819)Ggt>Tgt	p.G1273C	PCNX_ENST00000238570.5_Missense_Mutation_p.G1273C|PCNX_ENST00000439984.3_Missense_Mutation_p.G1162C	NM_014982.2	NP_055797.2	Q96RV3	PCX1_HUMAN	pecanex homolog (Drosophila)	1273						integral component of membrane (GO:0016021)				NS(2)|biliary_tract(1)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(14)|liver(2)|lung(40)|ovary(1)|prostate(7)|skin(2)|urinary_tract(1)	87			KIRC - Kidney renal clear cell carcinoma(12;0.206)	all cancers(60;0.00835)|BRCA - Breast invasive adenocarcinoma(234;0.00951)|OV - Ovarian serous cystadenocarcinoma(108;0.0417)		CATTGTAATTGGTGTGCTGTA	0.328													G|||	2	0.000399361	0.0	0.0	5008	,	,		18875	0.0		0.002	False		,,,				2504	0.0				p.G1273C		Atlas-SNP	.											.	PCNX	198	.	0			c.G3817T						PASS	.	G	CYS/GLY	3,4403	6.2+/-15.9	0,3,2200	280.0	246.0	257.0		3817	5.5	1.0	14	dbSNP_133	257	9,8591	6.4+/-24.3	0,9,4291	yes	missense	PCNX	NM_014982.2	159	0,12,6491	TT,TG,GG		0.1047,0.0681,0.0923	probably-damaging	1273/2342	71502824	12,12994	2203	4300	6503	SO:0001583	missense	22990	exon19			GTAATTGGTGTGC	AF233450, AB018348	CCDS9806.1	14q24.2	2014-07-03							19740	protein-coding gene	gene with protein product			"""pecanex-like 1 (Drosophila)"""	PCNXL1		9244429, 15777640	Standard	NM_014982		Approved	KIAA0995, KIAA0805, pecanex	uc001xmo.2	Q96RV3		ENST00000304743.2:c.3817G>T	14.37:g.71502824G>T	ENSP00000304192:p.Gly1273Cys	Somatic	242	0	0		WXS	Illumina HiSeq	Phase_I	191	98	0.513089	NM_014982	B2RTR6|O94897|Q96AI7|Q9Y2J9	Missense_Mutation	SNP	ENST00000304743.2	37	CCDS9806.1	1|1	4.578754578754579E-4|4.578754578754579E-4	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	1|1	0.0013192612137203166|0.0013192612137203166	G|G	17.74|17.74	3.464833|3.464833	0.63513|0.63513	6.81E-4|6.81E-4	0.001047|0.001047	ENSG00000100731|ENSG00000100731	ENST00000304743;ENST00000238570;ENST00000439984|ENST00000554691	T;T;T|.	0.09911|.	3.37;3.37;2.93|.	5.47|5.47	5.47|5.47	0.80525|0.80525	.|.	0.101356|.	0.64402|.	D|.	0.000003|.	T|T	0.60025|0.60025	0.2237|0.2237	L|L	0.31926|0.31926	0.97|0.97	0.58432|0.58432	D|D	0.999997|0.999997	D;D;D|.	0.64830|.	0.975;0.994;0.983|.	P;D;P|.	0.65987|.	0.742;0.94;0.754|.	T|T	0.54050|0.54050	-0.8351|-0.8351	10|5	0.62326|.	D|.	0.03|.	.|.	19.329|19.329	0.94278|0.94278	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	1273;1162;1273|.	Q96RV3-3;B2RTR6;Q96RV3|.	.;.;PCX1_HUMAN|.	C|F	1273;1273;1162|331	ENSP00000304192:G1273C;ENSP00000238570:G1273C;ENSP00000396617:G1162C|.	ENSP00000238570:G1273C|.	G|L	+|+	1|3	0|2	PCNX|PCNX	70572577|70572577	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.991000|0.991000	0.79684|0.79684	9.289000|9.289000	0.96061|0.96061	2.565000|2.565000	0.86533|0.86533	0.467000|0.467000	0.42956|0.42956	GGT|TTG	G|0.999;T|0.001	0.001	strong		0.328	PCNX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412479.1	NM_014982	
GPR146	115330	hgsc.bcm.edu	37	7	1097952	1097952	+	Silent	SNP	C	C	T	rs6953080	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:1097952C>T	ENST00000397095.1	+	2	1024	c.801C>T	c.(799-801)gaC>gaT	p.D267D	GPR146_ENST00000297468.3_Silent_p.D267D|RP11-449P15.1_ENST00000549241.1_RNA|C7orf50_ENST00000488073.1_Intron|C7orf50_ENST00000397100.2_Intron|C7orf50_ENST00000357429.6_Intron|C7orf50_ENST00000397098.3_Intron			Q96CH1	GP146_HUMAN	G protein-coupled receptor 146	267						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)		AGCCCGTGGACGCACACTACC	0.577													C|||	352	0.0702875	0.0998	0.134	5008	,	,		19172	0.0238		0.0626	False		,,,				2504	0.0409				p.D267D		Atlas-SNP	.											.	GPR146	20	.	0			c.C801T						PASS	.		,,,	366,4040	187.4+/-214.1	19,328,1856	106.0	92.0	96.0		,,,801	-10.0	0.0	7	dbSNP_116	96	529,8071	148.5+/-203.7	21,487,3792	no	intron,intron,intron,coding-synonymous	C7orf50,GPR146	NM_001134395.1,NM_001134396.1,NM_032350.5,NM_138445.2	,,,	40,815,5648	TT,TC,CC		6.1512,8.3069,6.8814	,,,	,,,267/334	1097952	895,12111	2203	4300	6503	SO:0001819	synonymous_variant	115330	exon1			CGTGGACGCACAC	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.801C>T	7.37:g.1097952C>T		Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	33	23	0.69697	NM_138445	Q86SP5	Silent	SNP	ENST00000397095.1	37	CCDS5321.1																																																																																			C|0.925;T|0.075	0.075	strong		0.577	GPR146-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206855.1	NM_138445	
BTN2A1	11120	hgsc.bcm.edu	37	6	26463660	26463660	+	Missense_Mutation	SNP	G	G	A	rs13195509	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:26463660G>A	ENST00000312541.5	+	4	867	c.619G>A	c.(619-621)Gtg>Atg	p.V207M	BTN2A1_ENST00000469185.1_Missense_Mutation_p.V207M|BTN2A1_ENST00000541522.1_Missense_Mutation_p.V146M|BTN2A1_ENST00000429381.1_Missense_Mutation_p.V207M	NM_007049.3|NM_078476.2	NP_008980.1|NP_510961.1	Q7KYR7	BT2A1_HUMAN	butyrophilin, subfamily 2, member A1	207			V -> M (in dbSNP:rs13195509).		lipid metabolic process (GO:0006629)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)				breast(3)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(2)|lung(9)|ovary(2)|prostate(1)|skin(3)|urinary_tract(3)	27						CACCACGGCTGTGATCATCAG	0.537													G|||	187	0.0373403	0.034	0.0346	5008	,	,		20403	0.0089		0.0825	False		,,,				2504	0.0266				p.V207M		Atlas-SNP	.											.	BTN2A1	118	.	0			c.G619A						PASS	.	G	MET/VAL,MET/VAL,MET/VAL,MET/VAL	188,4218	118.8+/-156.5	4,180,2019	142.0	128.0	132.0		436,619,619,619	2.0	0.5	6	dbSNP_121	132	795,7805	185.9+/-233.5	39,717,3544	yes	missense,missense,missense,missense	BTN2A1	NM_001197233.1,NM_001197234.1,NM_007049.3,NM_078476.2	21,21,21,21	43,897,5563	AA,AG,GG		9.2442,4.2669,7.5581	benign,benign,benign,benign	146/467,207/331,207/528,207/335	26463660	983,12023	2203	4300	6503	SO:0001583	missense	11120	exon4			ACGGCTGTGATCA	U90543	CCDS4613.1, CCDS47390.1, CCDS56404.1, CCDS56405.1	6p22.1	2014-01-14			ENSG00000112763	ENSG00000112763		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Butyrophilins"""	1136	protein-coding gene	gene with protein product		613590				9382921, 9149941	Standard	NM_007049		Approved	BT2.1, BTF1, BTN2.1	uc003nib.2	Q7KYR7	OTTHUMG00000014457	ENST00000312541.5:c.619G>A	6.37:g.26463660G>A	ENSP00000312158:p.Val207Met	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	84	43	0.511905	NM_001197234	B4DLP9|E9PGR4|O00475|P78408|Q59EN4|Q7KYQ7|Q7Z386|Q96AV7|Q9NU62	Missense_Mutation	SNP	ENST00000312541.5	37	CCDS4613.1	101	0.04624542124542125	18	0.036585365853658534	11	0.03038674033149171	7	0.012237762237762238	65	0.08575197889182058	G	14.35	2.508995	0.44660	0.042669	0.092442	ENSG00000112763	ENST00000312541;ENST00000541522;ENST00000429381;ENST00000265424;ENST00000469185	T;T;T;T	0.75589	-0.95;-0.95;-0.95;-0.95	2.88	2.0	0.26442	CD80-like, immunoglobulin C2-set (1);	0.341466	0.22162	N	0.063768	T	0.75451	0.3851	M	0.79475	2.455	0.46564	P	8.909999999999751E-4	D;D	0.71674	0.998;0.996	D;D	0.76071	0.987;0.97	T	0.72782	-0.4189	9	0.52906	T	0.07	.	4.7866	0.13227	0.2899:0.0:0.7101:0.0	rs13195509;rs52819217;rs57892055;rs13195509	207;207	Q96AV7;Q7KYR7	.;BT2A1_HUMAN	M	207;146;207;207;207	ENSP00000312158:V207M;ENSP00000443909:V146M;ENSP00000416945:V207M;ENSP00000419043:V207M	ENSP00000265424:V207M	V	+	1	0	BTN2A1	26571639	0.012000	0.17670	0.513000	0.27749	0.926000	0.56050	0.225000	0.17757	0.756000	0.33013	0.561000	0.74099	GTG	G|0.939;A|0.061	0.061	strong		0.537	BTN2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040122.2	NM_007049	
KHDC3L	154288	hgsc.bcm.edu	37	6	74072937	74072937	+	Missense_Mutation	SNP	G	G	C	rs564533	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:74072937G>C	ENST00000370367.3	+	2	342	c.289G>C	c.(289-291)Gag>Cag	p.E97Q		NM_001017361.2	NP_001017361.1	Q587J8	KHD3L_HUMAN	KH domain containing 3-like, subcortical maternal complex member	97	KH; atypical.		E -> Q (in dbSNP:rs564533).				RNA binding (GO:0003723)										TTCTTACCAGGAGGACACAAT	0.547													G|||	306	0.0611022	0.0068	0.0562	5008	,	,		18661	0.0288		0.1421	False		,,,				2504	0.0879				p.E97Q		Atlas-SNP	.											.	.	.	.	0			c.G289C						PASS	.	G	GLN/GLU	113,4293	85.8+/-124.5	0,113,2090	128.0	114.0	119.0		289	-6.8	0.0	6	dbSNP_83	119	1047,7553	223.3+/-260.1	63,921,3316	yes	missense	C6orf221	NM_001017361.2	29	63,1034,5406	CC,CG,GG		12.1744,2.5647,8.919	benign	97/218	74072937	1160,11846	2203	4300	6503	SO:0001583	missense	154288	exon2			TACCAGGAGGACA	AB211062	CCDS34484.1	6q13	2012-06-25	2012-06-25	2012-06-25	ENSG00000203908	ENSG00000203908			33699	protein-coding gene	gene with protein product	"""ES cell associated transcript 1"""	611687	"""chromosome 6 open reading frame 221"""	C6orf221		21885028	Standard	NM_001017361		Approved	ECAT1	uc003pgt.4	Q587J8	OTTHUMG00000015024	ENST00000370367.3:c.289G>C	6.37:g.74072937G>C	ENSP00000359392:p.Glu97Gln	Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	122	65	0.532787	NM_001017361	B2RNW7	Missense_Mutation	SNP	ENST00000370367.3	37	CCDS34484.1	156	0.07142857142857142	5	0.01016260162601626	20	0.055248618784530384	13	0.022727272727272728	118	0.15567282321899736	G	6.113	0.389129	0.11581	0.025647	0.121744	ENSG00000203908	ENST00000370367	T	0.11169	2.8	3.38	-6.76	0.01732	.	0.867683	0.09784	N	0.756230	T	0.01387	0.0045	N	0.22421	0.69	0.80722	P	0.0	B	0.15930	0.015	B	0.14023	0.01	T	0.45026	-0.9289	9	0.10636	T	0.68	-5.5569	10.0216	0.42046	0.1432:0.5796:0.2772:0.0	rs564533;rs17812444;rs52813757;rs564533	97	Q587J8	ECAT1_HUMAN	Q	97	ENSP00000359392:E97Q	ENSP00000359392:E97Q	E	+	1	0	C6orf221	74129658	0.086000	0.21541	0.001000	0.08648	0.229000	0.25112	-0.786000	0.04623	-2.576000	0.00465	-0.367000	0.07326	GAG	G|0.916;C|0.084	0.084	strong		0.547	KHDC3L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041202.3	NM_001017361	
ASB17	127247	hgsc.bcm.edu	37	1	76397871	76397871	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:76397871C>T	ENST00000284142.6	-	1	245	c.106G>A	c.(106-108)Ggt>Agt	p.G36S		NM_080868.2	NP_543144.1	Q8WXJ9	ASB17_HUMAN	ankyrin repeat and SOCS box containing 17	36					intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)					breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(11)|ovary(2)|urinary_tract(1)	21						CCCCACTGACCCAAAAACTGT	0.388																																					p.G36S		Atlas-SNP	.											.	ASB17	53	.	0			c.G106A						PASS	.						106.0	106.0	106.0					1																	76397871		2203	4300	6503	SO:0001583	missense	127247	exon1			ACTGACCCAAAAA	AF403035	CCDS671.1	1p22.3	2013-01-11	2011-01-25		ENSG00000154007	ENSG00000154007		"""Ankyrin repeat domain containing"""	19769	protein-coding gene	gene with protein product			"""ankyrin repeat and SOCS box-containing 17"""			12076535	Standard	NM_080868		Approved		uc001dhe.2	Q8WXJ9	OTTHUMG00000009787	ENST00000284142.6:c.106G>A	1.37:g.76397871C>T	ENSP00000284142:p.Gly36Ser	Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	147	42	0.285714	NM_080868	B1APB8|Q8N0X5	Missense_Mutation	SNP	ENST00000284142.6	37	CCDS671.1	.	.	.	.	.	.	.	.	.	.	C	19.99	3.929346	0.73327	.	.	ENSG00000154007	ENST00000284142	T	0.36340	1.26	6.08	3.06	0.35304	.	0.328218	0.26525	N	0.023882	T	0.09512	0.0234	N	0.19112	0.55	0.32637	N	0.521267	B	0.13594	0.008	B	0.08055	0.003	T	0.08617	-1.0713	10	0.52906	T	0.07	.	7.9022	0.29742	0.0:0.6092:0.3092:0.0817	.	36	Q8WXJ9	ASB17_HUMAN	S	36	ENSP00000284142:G36S	ENSP00000284142:G36S	G	-	1	0	ASB17	76170459	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	1.786000	0.38694	0.901000	0.36495	-0.136000	0.14681	GGT	.	.	none		0.388	ASB17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026982.1	NM_080868	
MIER3	166968	hgsc.bcm.edu	37	5	56242774	56242774	+	Silent	SNP	T	T	C	rs2034244	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:56242774T>C	ENST00000381199.3	-	3	169	c.159A>G	c.(157-159)tcA>tcG	p.S53S	MIER3_ENST00000381213.3_Silent_p.S53S|AC016644.1_ENST00000438553.1_RNA|MIER3_ENST00000546593.1_5'Flank|MIER3_ENST00000381226.3_Silent_p.S58S			Q7Z3K6	MIER3_HUMAN	mesoderm induction early response 1, family member 3	53					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|liver(1)|lung(2)|urinary_tract(1)	19		Lung NSC(810;4.65e-05)|Prostate(74;0.0253)|Breast(144;0.0503)|Ovarian(174;0.223)		OV - Ovarian serous cystadenocarcinoma(10;1.24e-37)		CTTCAATTTCTGAACTGAAGT	0.303													C|||	2053	0.409944	0.4607	0.4135	5008	,	,		14510	0.5327		0.2674	False		,,,				2504	0.3589				p.S53S		Atlas-SNP	.											.	MIER3	33	.	0			c.A159G						PASS	.	C		1897,2507	615.1+/-392.5	418,1061,723	54.0	55.0	54.0		159	0.3	1.0	5	dbSNP_94	54	2148,6452	709.2+/-405.7	264,1620,2416	no	coding-synonymous	MIER3	NM_152622.3		682,2681,3139	CC,CT,TT		24.9767,43.0745,31.1058		53/550	56242774	4045,8959	2202	4300	6502	SO:0001819	synonymous_variant	166968	exon3			AATTTCTGAACTG	BX537798	CCDS3973.2, CCDS75248.1	5q11.2	2009-03-19			ENSG00000155545	ENSG00000155545			26678	protein-coding gene	gene with protein product						12477932	Standard	XM_005248448		Approved	FLJ35954, DKFZp686L09111, DKFZp781I1119	uc003jra.1	Q7Z3K6	OTTHUMG00000059589	ENST00000381199.3:c.159A>G	5.37:g.56242774T>C		Somatic	312	1	0.00320513		WXS	Illumina HiSeq	Phase_I	283	279	0.985866	NM_152622	B4DRI9|B8ZZQ0|Q5CZI0|Q68CS3|Q6MZS7|Q86YG8|Q8NA13	Silent	SNP	ENST00000381199.3	37																																																																																				T|0.666;C|0.334	0.334	strong		0.303	MIER3-004	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000132523.2	NM_152622	
SEMA3A	10371	hgsc.bcm.edu	37	7	83764113	83764113	+	Silent	SNP	T	T	C	rs74349534	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:83764113T>C	ENST00000265362.4	-	2	581	c.267A>G	c.(265-267)caA>caG	p.Q89Q	SEMA3A_ENST00000436949.1_Silent_p.Q89Q	NM_006080.2	NP_006071.1	Q14563	SEM3A_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3A	89	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				apoptotic process (GO:0006915)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|axonogenesis involved in innervation (GO:0060385)|branchiomotor neuron axon guidance (GO:0021785)|dendrite morphogenesis (GO:0048813)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|facial nerve structural organization (GO:0021612)|gonadotrophin-releasing hormone neuronal migration to the hypothalamus (GO:0021828)|negative regulation of axon extension involved in axon guidance (GO:0048843)|negative regulation of epithelial cell migration (GO:0010633)|nerve development (GO:0021675)|neural crest cell migration involved in autonomic nervous system development (GO:1901166)|neural crest cell migration involved in sympathetic nervous system development (GO:1903045)|neuron migration (GO:0001764)|olfactory bulb development (GO:0021772)|positive regulation of male gonad development (GO:2000020)|positive regulation of neuron migration (GO:2001224)|regulation of axon extension involved in axon guidance (GO:0048841)|regulation of heart rate (GO:0002027)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|semaphorin-plexin signaling pathway involved in neuron projection guidance (GO:1902285)|sensory system development (GO:0048880)|sympathetic ganglion development (GO:0061549)|sympathetic nervous system development (GO:0048485)|sympathetic neuron projection extension (GO:0097490)|sympathetic neuron projection guidance (GO:0097491)|trigeminal nerve structural organization (GO:0021637)	axon (GO:0030424)|dendrite (GO:0030425)|extracellular region (GO:0005576)|membrane (GO:0016020)	chemorepellent activity (GO:0045499)|neuropilin binding (GO:0038191)|receptor activity (GO:0004872)			breast(3)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|liver(1)|lung(22)|ovary(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	53						CTGATACCTTTTGAAAATCCT	0.328													t|||	14	0.00279553	0.0008	0.0043	5008	,	,		18311	0.0		0.0099	False		,,,				2504	0.0				p.Q89Q		Atlas-SNP	.											.	SEMA3A	121	.	0			c.A267G						PASS	.	T		12,4394	17.9+/-39.9	0,12,2191	73.0	73.0	73.0		267	3.6	1.0	7	dbSNP_132	73	101,8499	54.8+/-115.7	1,99,4200	no	coding-synonymous	SEMA3A	NM_006080.2		1,111,6391	CC,CT,TT		1.1744,0.2724,0.8688		89/772	83764113	113,12893	2203	4300	6503	SO:0001819	synonymous_variant	10371	exon2			TACCTTTTGAAAA	L26081	CCDS5599.1	7p12.1	2013-01-11			ENSG00000075213	ENSG00000075213		"""Semaphorins"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	10723	protein-coding gene	gene with protein product	"""sema III"""	603961		SEMAD		8269517, 7748561	Standard	NM_006080		Approved	SEMA1, SemD, coll-1, Hsema-I	uc003uhz.3	Q14563	OTTHUMG00000023443	ENST00000265362.4:c.267A>G	7.37:g.83764113T>C		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	72	38	0.527778	NM_006080		Silent	SNP	ENST00000265362.4	37	CCDS5599.1																																																																																			T|0.993;C|0.007	0.007	strong		0.328	SEMA3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253355.2	NM_006080	
LMF2	91289	hgsc.bcm.edu	37	22	50944128	50944128	+	Silent	SNP	G	G	A	rs743615	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:50944128G>A	ENST00000474879.2	-	6	906	c.891C>T	c.(889-891)caC>caT	p.H297H	LMF2_ENST00000216080.5_Silent_p.H272H|NCAPH2_ENST00000420993.2_5'Flank|NCAPH2_ENST00000299821.11_5'Flank|LMF2_ENST00000505981.1_5'UTR|LMF2_ENST00000380796.3_Silent_p.H297H|NCAPH2_ENST00000395698.3_5'Flank|NCAPH2_ENST00000395701.3_5'Flank	NM_033200.2	NP_149977.2	Q9BU23	LMF2_HUMAN	lipase maturation factor 2	297						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				breast(1)|cervix(1)|kidney(1)|lung(4)|prostate(1)|skin(2)	10		all_cancers(38;1.31e-09)|all_epithelial(38;1.81e-08)|all_lung(38;0.000817)|Breast(42;0.00387)|Lung NSC(38;0.0124)|Ovarian(80;0.104)|Lung SC(80;0.162)|Hepatocellular(38;0.178)		BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)		TGCGGCTGCCGTGGCCAGGCT	0.612													g|||	1732	0.345847	0.2859	0.3357	5008	,	,		16978	0.3909		0.2604	False		,,,				2504	0.4755				p.H297H		Atlas-SNP	.											.	LMF2	40	.	0			c.C891T						PASS	.	G		1334,3068	425.9+/-341.0	213,908,1080	40.0	43.0	42.0		891	-5.8	0.0	22	dbSNP_86	42	2492,6108	395.4+/-345.0	368,1756,2176	no	coding-synonymous	LMF2	NM_033200.2		581,2664,3256	AA,AG,GG		28.9767,30.3044,29.4262		297/708	50944128	3826,9176	2201	4300	6501	SO:0001819	synonymous_variant	91289	exon6			GCTGCCGTGGCCA	BC002942	CCDS14093.1, CCDS14093.2	22q13.33	2008-02-04	2007-11-29	2007-11-29	ENSG00000100258	ENSG00000100258			25096	protein-coding gene	gene with protein product			"""transmembrane protein 153"", ""transmembrane protein 112B"""	TMEM153, TMEM112B		12477932	Standard	NM_033200		Approved		uc003blp.2	Q9BU23	OTTHUMG00000150206	ENST00000474879.2:c.891C>T	22.37:g.50944128G>A		Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	159	80	0.503145	NM_033200	A6NEZ0|Q13392|Q6ZNR2|Q8WU74|Q96C62	Silent	SNP	ENST00000474879.2	37	CCDS14093.2	642	0.29395604395604397	126	0.25609756097560976	108	0.2983425414364641	216	0.3776223776223776	192	0.2532981530343008	G	0.026	-1.368851	0.01225	0.303044	0.289767	ENSG00000100258	ENST00000487499	.	.	.	4.64	-5.84	0.02318	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.39251	-0.9623	3	.	.	.	-2.9625	7.5986	0.28063	0.2623:0.3932:0.3445:0.0	rs743615;rs11549570;rs17851223;rs17851866	.	.	.	W	304	.	.	R	-	1	2	LMF2	49290994	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.487000	0.06505	-0.874000	0.04027	-1.851000	0.00568	CGG	G|0.706;A|0.294	0.294	strong		0.612	LMF2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316833.2	NM_033200	
PANK4	55229	hgsc.bcm.edu	37	1	2449631	2449631	+	Missense_Mutation	SNP	C	C	G	rs144881953		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:2449631C>G	ENST00000378466.3	-	9	1202	c.1190G>C	c.(1189-1191)gGc>gCc	p.G397A	PANK4_ENST00000435556.3_Missense_Mutation_p.G358A	NM_018216.1	NP_060686.1	Q9NVE7	PANK4_HUMAN	pantothenate kinase 4	397					coenzyme A biosynthetic process (GO:0015937)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|pantothenate kinase activity (GO:0004594)			breast(2)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(4)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(4)	23	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;1.54e-37)|OV - Ovarian serous cystadenocarcinoma(86;6.95e-23)|GBM - Glioblastoma multiforme(42;2.81e-08)|Colorectal(212;4.25e-05)|COAD - Colon adenocarcinoma(227;0.000196)|Kidney(185;0.000342)|BRCA - Breast invasive adenocarcinoma(365;0.00445)|KIRC - Kidney renal clear cell carcinoma(229;0.00549)|STAD - Stomach adenocarcinoma(132;0.00644)|Lung(427;0.201)		CTGCGCCGGGCCGAGCTCGGG	0.657																																					p.G397A		Atlas-SNP	.											.	PANK4	64	.	0			c.G1190C						PASS	.						34.0	37.0	36.0					1																	2449631		2198	4297	6495	SO:0001583	missense	55229	exon9			GCCGGGCCGAGCT	AK001644	CCDS42.1	1p36.32	2008-02-05			ENSG00000157881	ENSG00000157881			19366	protein-coding gene	gene with protein product		606162				11479594	Standard	XR_241034		Approved	FLJ10782	uc001ajm.1	Q9NVE7	OTTHUMG00000000791	ENST00000378466.3:c.1190G>C	1.37:g.2449631C>G	ENSP00000367727:p.Gly397Ala	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	26	8	0.307692	NM_018216	B9DI84|Q53EU3|Q5TA84|Q7RTX3|Q9H3X5	Missense_Mutation	SNP	ENST00000378466.3	37	CCDS42.1	.	.	.	.	.	.	.	.	.	.	C	1.513	-0.548845	0.04024	.	.	ENSG00000157881	ENST00000378466;ENST00000435556	D;D	0.96491	-4.03;-3.75	4.81	2.37	0.29283	.	0.356706	0.32106	N	0.006574	D	0.85296	0.5664	N	0.11560	0.145	0.23023	N	0.99841	B;B	0.13145	0.007;0.0	B;B	0.14023	0.01;0.001	T	0.72354	-0.4319	10	0.02654	T	1	-16.9416	1.8614	0.03189	0.2961:0.4266:0.0:0.2773	.	358;397	E9PHT6;Q9NVE7	.;PANK4_HUMAN	A	397;358	ENSP00000367727:G397A;ENSP00000421433:G358A	ENSP00000367727:G397A	G	-	2	0	PANK4	2439491	1.000000	0.71417	0.974000	0.42286	0.034000	0.12701	2.218000	0.42889	2.226000	0.72624	0.561000	0.74099	GGC	C|1.000;T|0.000	.	alt		0.657	PANK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002082.1		
ZNF429	353088	hgsc.bcm.edu	37	19	21719401	21719401	+	Silent	SNP	T	T	C	rs35782355	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:21719401T>C	ENST00000358491.4	+	4	754	c.546T>C	c.(544-546)ttT>ttC	p.F182F	ZNF429_ENST00000597078.1_Intron	NM_001001415.2	NP_001001415.2	Q86V71	ZN429_HUMAN	zinc finger protein 429	182					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|kidney(2)|large_intestine(13)|lung(10)|ovary(2)|pancreas(1)|prostate(1)|soft_tissue(1)|upper_aerodigestive_tract(2)	34						GCAAATCATTTTGCATGCTTT	0.328													t|||	2793	0.557708	0.4781	0.5288	5008	,	,		20186	0.6389		0.5388	False		,,,				2504	0.6217				p.F182F		Atlas-SNP	.											.	ZNF429	338	.	0			c.T546C						PASS	.	T		2049,2339		493,1063,638	49.0	52.0	51.0		546	0.2	0.2	19	dbSNP_126	51	4797,3801		1380,2037,882	no	coding-synonymous	ZNF429	NM_001001415.2		1873,3100,1520	CC,CT,TT		44.208,46.6955,47.2817		182/675	21719401	6846,6140	2194	4299	6493	SO:0001819	synonymous_variant	353088	exon4			ATCATTTTGCATG	AY269786	CCDS42537.1	19p12	2014-02-14			ENSG00000197013	ENSG00000197013		"""Zinc fingers, C2H2-type"", ""-"""	20817	protein-coding gene	gene with protein product							Standard	NM_001001415		Approved		uc002nqd.1	Q86V71	OTTHUMG00000182848	ENST00000358491.4:c.546T>C	19.37:g.21719401T>C		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	32	14	0.4375	NM_001001415	A6NLV7|Q9BZE6	Silent	SNP	ENST00000358491.4	37	CCDS42537.1																																																																																			T|0.444;C|0.556	0.556	strong		0.328	ZNF429-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463981.1	NM_001001415	
KIAA2026	158358	hgsc.bcm.edu	37	9	6007500	6007500	+	Silent	SNP	G	G	A	rs1061767	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:6007500G>A	ENST00000399933.3	-	1	287	c.288C>T	c.(286-288)ggC>ggT	p.G96G	MIR4665_ENST00000581132.1_RNA|KIAA2026_ENST00000381461.2_Silent_p.G96G	NM_001017969.2	NP_001017969.2	Q5HYC2	K2026_HUMAN	KIAA2026	96										breast(6)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(11)|lung(15)|ovary(2)|prostate(2)|skin(1)	46		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.00155)|Lung(218;0.124)		GGGCGGTGAGGCCCCGGTGCT	0.711													G|||	855	0.170727	0.0998	0.1744	5008	,	,		14281	0.3194		0.1849	False		,,,				2504	0.0961				p.G96G		Atlas-SNP	.											.	KIAA2026	231	.	0			c.C288T						PASS	.	G		449,3521		27,395,1563	19.0	24.0	22.0		288	3.2	1.0	9	dbSNP_86	22	1636,6640		161,1314,2663	no	coding-synonymous	KIAA2026	NM_001017969.2		188,1709,4226	AA,AG,GG		19.768,11.3098,17.026		96/2104	6007500	2085,10161	1985	4138	6123	SO:0001819	synonymous_variant	158358	exon1			GGTGAGGCCCCGG	AB095946		9p24.1	2014-01-10			ENSG00000183354	ENSG00000183354			23378	protein-coding gene	gene with protein product							Standard	NM_001017969		Approved	FLJ20375	uc003zjq.4	Q5HYC2	OTTHUMG00000019507	ENST00000399933.3:c.288C>T	9.37:g.6007500G>A		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	67	33	0.492537	NM_001017969	A8MTP2|B9EGW7|Q4VXA2|Q8IVE5	Silent	SNP	ENST00000399933.3	37																																																																																				G|0.786;A|0.214	0.214	strong		0.711	KIAA2026-002	NOVEL	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051652.2	NM_001017969	
RUFY1	80230	hgsc.bcm.edu	37	5	179020622	179020622	+	Silent	SNP	T	T	C	rs4701135	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:179020622T>C	ENST00000319449.4	+	11	1401	c.1389T>C	c.(1387-1389)aaT>aaC	p.N463N	RUFY1_ENST00000393438.2_Silent_p.N355N|RP11-1379J22.2_ENST00000500262.1_RNA|RUFY1_ENST00000377001.2_3'UTR|RUFY1_ENST00000437570.2_Silent_p.N355N	NM_025158.4	NP_079434.3	Q96T51	RUFY1_HUMAN	RUN and FYVE domain containing 1	463					endocytosis (GO:0006897)|regulation of endocytosis (GO:0030100)	cytoplasm (GO:0005737)|endosome (GO:0005768)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)	lipid binding (GO:0008289)|protein transporter activity (GO:0008565)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(11)|ovary(4)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	26	all_cancers(89;0.00018)|all_epithelial(37;8.37e-05)|Renal(175;0.000159)|Lung NSC(126;0.00108)|all_lung(126;0.00195)	all_cancers(40;0.0322)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			AAGCGATTAATTTACAGATGT	0.468										HNSCC(44;0.11)			T|||	369	0.0736821	0.0431	0.0793	5008	,	,		19915	0.0853		0.1054	False		,,,				2504	0.0665				p.N463N		Atlas-SNP	.											.	RUFY1	101	.	0			c.T1389C						PASS	.	T	,,	222,4184	133.7+/-170.0	7,208,1988	95.0	100.0	98.0		1065,1065,1389	-2.8	0.2	5	dbSNP_111	98	958,7642	208.3+/-249.8	60,838,3402	no	coding-synonymous,coding-synonymous,coding-synonymous	RUFY1	NM_001040451.1,NM_001040452.1,NM_025158.3	,,	67,1046,5390	CC,CT,TT		11.1395,5.0386,9.0727	,,	355/601,355/601,463/709	179020622	1180,11826	2203	4300	6503	SO:0001819	synonymous_variant	80230	exon11			GATTAATTTACAG	AF361055	CCDS4445.2, CCDS34312.1	5q35.3	2008-02-05			ENSG00000176783	ENSG00000176783		"""Zinc fingers, FYVE domain containing"""	19760	protein-coding gene	gene with protein product		610327				11877430	Standard	NM_001040451		Approved	FLJ22251, ZFYVE12, RABIP4	uc003mka.2	Q96T51	OTTHUMG00000130913	ENST00000319449.4:c.1389T>C	5.37:g.179020622T>C		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	132	83	0.628788	NM_025158	Q59FF3|Q71S93|Q9H6I3	Silent	SNP	ENST00000319449.4	37	CCDS4445.2	176|176	0.08058608058608059|0.08058608058608059	24|24	0.04878048780487805|0.04878048780487805	30|30	0.08287292817679558|0.08287292817679558	47|47	0.08216783216783216|0.08216783216783216	75|75	0.09894459102902374|0.09894459102902374	T|T	0.692|0.692	-0.794213|-0.794213	0.02862|0.02862	0.050386|0.050386	0.111395|0.111395	ENSG00000176783|ENSG00000176783	ENST00000502434|ENST00000508609	.|.	.|.	.|.	5.1|5.1	-2.79|-2.79	0.05841|0.05841	.|.	.|.	.|.	.|.	.|.	T|T	0.01387|0.01387	0.0045|0.0045	.|.	.|.	.|.	0.09310|0.09310	P|P	0.9999999999357027|0.9999999999357027	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.41787|0.41787	-0.9489|-0.9489	3|3	.|.	.|.	.|.	-12.0535|-12.0535	13.6985|13.6985	0.62593|0.62593	0.0:0.6314:0.0:0.3686|0.0:0.6314:0.0:0.3686	rs4701135;rs4701135|rs4701135;rs4701135	.|.	.|.	.|.	L|T	141|252	.|.	.|.	F|I	+|+	1|2	0|0	RUFY1|RUFY1	178953228|178953228	0.004000|0.004000	0.15560|0.15560	0.243000|0.243000	0.24186|0.24186	0.022000|0.022000	0.10575|0.10575	-0.566000|-0.566000	0.05922|0.05922	-0.427000|-0.427000	0.07350|0.07350	0.459000|0.459000	0.35465|0.35465	TTT|ATT	T|0.912;C|0.088	0.088	strong		0.468	RUFY1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000253505.2	NM_001040451	
VEZT	55591	hgsc.bcm.edu	37	12	95694111	95694111	+	Missense_Mutation	SNP	T	T	G	rs17855934	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:95694111T>G	ENST00000436874.1	+	12	2107	c.2002T>G	c.(2002-2004)Tct>Gct	p.S668A	VEZT_ENST00000261219.6_Missense_Mutation_p.S620A|VEZT_ENST00000356859.4_3'UTR	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	153	0	0		WXS	Illumina HiSeq	Phase_I	87	39	0.448276	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	
AHNAK2	113146	hgsc.bcm.edu	37	14	105417765	105417765	+	Silent	SNP	A	A	C	rs2894636	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:105417765A>C	ENST00000333244.5	-	7	4142	c.4023T>G	c.(4021-4023)tcT>tcG	p.S1341S	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	1341						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)			TGCCTGGGGCAGACACCCCGA	0.607																																					p.S1341S		Atlas-SNP	.											.	AHNAK2	719	.	0			c.T4023G						PASS	.	A		167,3493		42,83,1705	128.0	119.0	122.0		4023	-8.6	0.0	14	dbSNP_101	122	39,6505		8,23,3241	no	coding-synonymous	AHNAK2	NM_138420.2		50,106,4946	CC,CA,AA		0.596,4.5628,2.0188		1341/5796	105417765	206,9998	1830	3272	5102	SO:0001819	synonymous_variant	113146	exon7			TGGGGCAGACACC	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.4023T>G	14.37:g.105417765A>C		Somatic	0	0	.		WXS	Illumina HiSeq	Phase_I	64	62	0.96875	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Silent	SNP	ENST00000333244.5	37	CCDS45177.1																																																																																			A|0.831;C|0.169	0.169	strong		0.607	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
GIMAP5	55340	hgsc.bcm.edu	37	7	150439500	150439500	+	Silent	SNP	C	C	T	rs759011	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:150439500C>T	ENST00000358647.3	+	3	640	c.273C>T	c.(271-273)gcC>gcT	p.A91A	GIMAP5_ENST00000479556.1_3'UTR	NM_018384.4	NP_060854.2	Q96F15	GIMA5_HUMAN	GTPase, IMAP family member 5	91	AIG1-type G.				myeloid dendritic cell differentiation (GO:0043011)|negative regulation of apoptotic process (GO:0043066)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of lipid catabolic process (GO:0050995)|negative regulation of nitric oxide biosynthetic process (GO:0045019)|negative regulation of T cell activation (GO:0050868)|positive regulation of calcium ion transport into cytosol (GO:0010524)|positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation (GO:0032831)|positive regulation of gamma-delta T cell differentiation (GO:0045588)|positive regulation of humoral immune response mediated by circulating immunoglobulin (GO:0002925)|positive regulation of membrane potential (GO:0045838)|positive regulation of natural killer cell cytokine production (GO:0002729)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|regulation of mitochondrial membrane permeability (GO:0046902)|T cell differentiation (GO:0030217)|T cell homeostasis (GO:0043029)|temperature homeostasis (GO:0001659)	integral component of membrane (GO:0016021)|lysosome (GO:0005764)|mitochondrial outer membrane (GO:0005741)	GTP binding (GO:0005525)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|urinary_tract(2)	19			OV - Ovarian serous cystadenocarcinoma(82;0.0145)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		AGTCACAGGCCGATACCCAAG	0.597													T|||	1953	0.389976	0.5696	0.2651	5008	,	,		18052	0.3006		0.3082	False		,,,				2504	0.4121				p.A295A		Atlas-SNP	.											GIMAP5,NS,carcinoma,0,1	.	.	1	0			c.C885T						PASS	.	T	,	2405,2001	560.3+/-380.4	672,1061,470	111.0	99.0	103.0		885,273	1.4	0.0	7	dbSNP_86	103	2642,5958	686.6+/-404.1	390,1862,2048	no	coding-synonymous,coding-synonymous	GIMAP5,GIMAP1-GIMAP5	NM_001199577.1,NM_018384.4	,	1062,2923,2518	TT,TC,CC		30.7209,45.4153,38.8052	,	295/512,91/308	150439500	5047,7959	2203	4300	6503	SO:0001819	synonymous_variant	0	exon6			ACAGGCCGATACC	AK002158	CCDS5907.1	7q36.1	2014-04-04	2004-10-29	2004-10-30	ENSG00000196329	ENSG00000196329		"""GTPases, IMAP"""	18005	protein-coding gene	gene with protein product	"""immune-associated nucleotide-binding protein 5"""	608086	"""immune associated nucleotide 4 like 1 (mouse)"""	IAN4L1			Standard	NM_018384		Approved	HIMAP3, IAN5		Q96F15	OTTHUMG00000157542	ENST00000358647.3:c.273C>T	7.37:g.150439500C>T		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	63	63	1	NM_001199577	D3DWZ5|Q6IA75|Q96NE4|Q9NUK9	Silent	SNP	ENST00000358647.3	37	CCDS5907.1																																																																																			T|0.385;G|0.004	0.385	strong		0.597	GIMAP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349108.2	NM_018384	
SLC15A2	6565	hgsc.bcm.edu	37	3	121648168	121648168	+	Missense_Mutation	SNP	G	G	A	rs1143672	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:121648168G>A	ENST00000489711.1	+	17	1914	c.1526G>A	c.(1525-1527)aGa>aAa	p.R509K	SLC15A2_ENST00000295605.2_Missense_Mutation_p.R478K|SLC15A2_ENST00000465060.1_3'UTR	NM_021082.3	NP_066568.3	Q16348	S15A2_HUMAN	solute carrier family 15 (oligopeptide transporter), member 2	509			R -> K (in dbSNP:rs1143672).		drug transport (GO:0015893)|ion transport (GO:0006811)|protein transport (GO:0015031)|proton transport (GO:0015992)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	antibiotic transporter activity (GO:0042895)|dipeptide transporter activity (GO:0042936)|high-affinity oligopeptide transporter activity (GO:0015334)|peptide:proton symporter activity (GO:0015333)			NS(1)|endometrium(1)|kidney(4)|large_intestine(5)|lung(17)|skin(6)|upper_aerodigestive_tract(2)	36				GBM - Glioblastoma multiforme(114;0.0967)	Aminolevulinic acid(DB00855)|Amoxicillin(DB01060)|Ampicillin(DB00415)|Azidocillin(DB08795)|Benazepril(DB00542)|Benzylpenicillin(DB01053)|Cefaclor(DB00833)|Cefadroxil(DB01140)|Cefalotin(DB00456)|Cefdinir(DB00535)|Cefepime(DB01413)|Cefixime(DB00671)|Cefmetazole(DB00274)|Cefotaxime(DB00493)|Cefradine(DB01333)|Ceftazidime(DB00438)|Ceftibuten(DB01415)|Ceftriaxone(DB01212)|Cefuroxime(DB01112)|Cephalexin(DB00567)|Chlorpropamide(DB00672)|Cilazapril(DB01340)|Cloxacillin(DB01147)|Cyclacillin(DB01000)|Dicloxacillin(DB00485)|Fosinopril(DB00492)|Glyburide(DB01016)|Moexipril(DB00691)|Nateglinide(DB00731)|Oxacillin(DB00713)|Perindopril(DB00790)|Quinapril(DB00881)|Ramipril(DB00178)|Spirapril(DB01348)|Tolbutamide(DB01124)|Trandolapril(DB00519)|Tranexamic Acid(DB00302)|Valaciclovir(DB00577)|Valganciclovir(DB01610)	ACAGAAAGCAGAACAACCAAT	0.403													A|||	2263	0.451877	0.4834	0.2939	5008	,	,		22274	0.6984		0.4235	False		,,,				2504	0.2965				p.R509K		Atlas-SNP	.											.	SLC15A2	92	.	0			c.G1526A						PASS	.	A	LYS/ARG,LYS/ARG	2150,2256	595.1+/-388.4	532,1086,585	170.0	159.0	163.0		1433,1526	-2.8	0.0	3	dbSNP_86	163	3904,4696	605.9+/-395.0	879,2146,1275	yes	missense,missense	SLC15A2	NM_001145998.1,NM_021082.3	26,26	1411,3232,1860	AA,AG,GG		45.3953,48.7971,46.5477	benign,benign	478/699,509/730	121648168	6054,6952	2203	4300	6503	SO:0001583	missense	6565	exon17			AAAGCAGAACAAC	BC044572	CCDS3007.1, CCDS54631.1	3q21.1	2013-07-18	2013-07-18		ENSG00000163406	ENSG00000163406		"""Solute carriers"""	10921	protein-coding gene	gene with protein product		602339	"""solute carrier family 15 (H+/peptide transporter), member 2"""			7756356	Standard	NM_021082		Approved	PEPT2	uc003eep.2	Q16348	OTTHUMG00000159423	ENST00000489711.1:c.1526G>A	3.37:g.121648168G>A	ENSP00000417085:p.Arg509Lys	Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	109	45	0.412844	NM_021082	A8K1A5|B4E2A7	Missense_Mutation	SNP	ENST00000489711.1	37	CCDS3007.1	1071	0.49038461538461536	227	0.4613821138211382	100	0.27624309392265195	427	0.7465034965034965	317	0.4182058047493404	A	0.124	-1.121929	0.01785	0.487971	0.453953	ENSG00000163406	ENST00000489711;ENST00000542599;ENST00000295605	T;T	0.28666	1.6;1.6	4.95	-2.82	0.05787	.	0.588424	0.18577	N	0.137154	T	0.00012	0.0000	N	0.00037	-2.53	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.34354	-0.9832	9	0.02654	T	1	1.4543	1.7513	0.02973	0.2761:0.4017:0.1701:0.1522	rs1143672;rs1920316;rs2293609;rs17366654;rs57961332;rs1143672	478;509	B4E2A7;Q16348	.;S15A2_HUMAN	K	509;471;478	ENSP00000417085:R509K;ENSP00000295605:R478K	ENSP00000295605:R478K	R	+	2	0	SLC15A2	123130858	0.271000	0.24162	0.006000	0.13384	0.559000	0.35586	0.069000	0.14552	-0.474000	0.06862	-0.254000	0.11334	AGA	G|0.523;A|0.477	0.477	strong		0.403	SLC15A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355239.1	NM_021082	
PRDM16	63976	hgsc.bcm.edu	37	1	3301721	3301721	+	Silent	SNP	C	C	T	rs2282198	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:3301721C>T	ENST00000270722.5	+	4	493	c.444C>T	c.(442-444)tcC>tcT	p.S148S	PRDM16_ENST00000512462.1_3'UTR|PRDM16_ENST00000378391.2_Silent_p.S148S|PRDM16_ENST00000442529.2_Silent_p.S148S|PRDM16_ENST00000441472.2_Silent_p.S148S|PRDM16_ENST00000514189.1_Silent_p.S149S|PRDM16_ENST00000511072.1_Silent_p.S149S|PRDM16_ENST00000378398.3_Silent_p.S148S			Q9HAZ2	PRD16_HUMAN	PR domain containing 16	148	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				brown fat cell differentiation (GO:0050873)|negative regulation of granulocyte differentiation (GO:0030853)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neurogenesis (GO:0022008)|palate development (GO:0060021)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cellular respiration (GO:0043457)|somatic stem cell maintenance (GO:0035019)|tongue development (GO:0043586)|transcription, DNA-templated (GO:0006351)|white fat cell differentiation (GO:0050872)	nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|transcription coactivator activity (GO:0003713)			breast(4)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(7)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(3)	59	all_cancers(77;0.00208)|all_epithelial(69;0.000732)|Ovarian(185;0.0634)|Lung NSC(156;0.109)|all_lung(157;0.111)	all_epithelial(116;2.03e-21)|all_lung(118;7.55e-09)|Lung NSC(185;1.28e-06)|Breast(487;0.000792)|Renal(390;0.00137)|Hepatocellular(190;0.00515)|Myeloproliferative disorder(586;0.0267)|Ovarian(437;0.0365)|Lung SC(97;0.114)|Medulloblastoma(700;0.134)		Epithelial(90;5.59e-35)|OV - Ovarian serous cystadenocarcinoma(86;1.99e-20)|GBM - Glioblastoma multiforme(42;3.72e-11)|Colorectal(212;0.000425)|BRCA - Breast invasive adenocarcinoma(365;0.000946)|COAD - Colon adenocarcinoma(227;0.000968)|Kidney(185;0.00155)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0175)|Lung(427;0.137)		AGCAGATCTCCGAAGACCTGG	0.607			T	EVI1	"""MDS, AML"""								C|||	1705	0.340455	0.0386	0.3285	5008	,	,		18269	0.622		0.2684	False		,,,				2504	0.5409				p.S148S		Atlas-SNP	.		Dom	yes		1	1p36.23-p33	63976	PR domain containing 16		L	.	PRDM16	147	.	0			c.C444T						PASS	.	C	,	351,3947		22,307,1820	75.0	85.0	82.0		444,444	-9.1	0.5	1	dbSNP_100	82	2281,6267		290,1701,2283	no	coding-synonymous,coding-synonymous	PRDM16	NM_022114.3,NM_199454.2	,	312,2008,4103	TT,TC,CC		26.6846,8.1666,20.4889	,	148/1277,148/1258	3301721	2632,10214	2149	4274	6423	SO:0001819	synonymous_variant	63976	exon4			GATCTCCGAAGAC	AF294278	CCDS41236.1, CCDS44048.1, CCDS41236.2, CCDS44048.2	1p36.23-p33	2013-01-08			ENSG00000142611	ENSG00000142611		"""Zinc fingers, C2H2-type"""	14000	protein-coding gene	gene with protein product	"""MDS1/EVI1-like"", ""PR-domain zinc finger protein 16"", ""transcription factor MEL1"""	605557				11050005	Standard	NM_199454		Approved	MEL1, PFM13, KIAA1675, MGC166915	uc001akf.3	Q9HAZ2	OTTHUMG00000000581	ENST00000270722.5:c.444C>T	1.37:g.3301721C>T		Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	85	31	0.364706	NM_022114	A6NHQ8|B1AJP7|B1AJP8|B1AJP9|B1WB48|Q8WYJ9|Q9C0I8	Silent	SNP	ENST00000270722.5	37	CCDS41236.2																																																																																			C|0.713;T|0.287	0.287	strong		0.607	PRDM16-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000001382.3	NM_022114	
SLFN14	342618	hgsc.bcm.edu	37	17	33881718	33881718	+	Missense_Mutation	SNP	G	G	A	rs321613	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:33881718G>A	ENST00000415846.3	-	2	1101	c.1066C>T	c.(1066-1068)Ccc>Tcc	p.P356S	RP11-1094M14.12_ENST00000588445.1_RNA	NM_001129820.1	NP_001123292.1	P0C7P3	SLN14_HUMAN	schlafen family member 14	356				P -> S (in Ref. 2; AAI40848/AAI57878/ AAI57880). {ECO:0000305}.			ATP binding (GO:0005524)			breast(3)|central_nervous_system(1)|endometrium(2)|kidney(3)	9						ACCAAACTGGGAGGAGCTAGA	0.368													A|||	3142	0.627396	0.7163	0.6556	5008	,	,		10864	0.6895		0.5805	False		,,,				2504	0.4714				p.P356S		Atlas-SNP	.											.	SLFN14	43	.	0			c.C1066T						PASS	.	A	SER/PRO	956,428		326,304,62	95.0	80.0	84.0		1066	1.4	0.0	17	dbSNP_79	84	1919,1263		577,765,249	yes	missense	SLFN14	NM_001129820.1	74	903,1069,311	AA,AG,GG		39.692,30.9249,37.0346	benign	356/913	33881718	2875,1691	692	1591	2283	SO:0001583	missense	342618	exon2			AACTGGGAGGAGC		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.1066C>T	17.37:g.33881718G>A	ENSP00000391101:p.Pro356Ser	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	62	29	0.467742	NM_001129820	B2RTW9	Missense_Mutation	SNP	ENST00000415846.3	37	CCDS45650.1	1406	0.6437728937728938	338	0.6869918699186992	245	0.6767955801104972	391	0.6835664335664335	432	0.5699208443271768	A	1.933	-0.445528	0.04604	0.690751	0.60308	ENSG00000236320	ENST00000415846	T	0.58358	0.34	4.75	1.39	0.22231	.	.	.	.	.	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	0.44375	-0.9332	8	0.02654	T	1	.	7.0888	0.25272	0.5987:0.0:0.4013:0.0	rs321613;rs772400;rs1280801;rs56783690;rs321613	356	P0C7P3	SLN14_HUMAN	S	356	ENSP00000391101:P356S	ENSP00000391101:P356S	P	-	1	0	SLFN14	30905831	0.009000	0.17119	0.001000	0.08648	0.176000	0.22953	0.427000	0.21379	0.098000	0.17522	-0.361000	0.07541	CCC	G|0.352;A|0.648	0.648	strong		0.368	SLFN14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448928.1	NM_001129820	
TBC1D1	23216	hgsc.bcm.edu	37	4	38138856	38138856	+	Missense_Mutation	SNP	G	G	A	rs13110318	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:38138856G>A	ENST00000261439.4	+	20	3762	c.3407G>A	c.(3406-3408)cGg>cAg	p.R1136Q	TBC1D1_ENST00000508802.1_Missense_Mutation_p.R1127Q|TBC1D1_ENST00000407365.1_3'UTR	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	1136			R -> Q (in dbSNP:rs13110318).		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						GAACTGGAGCGGTCGGCCCTG	0.642													G|||	458	0.0914537	0.0514	0.1772	5008	,	,		15563	0.123		0.0944	False		,,,				2504	0.0491				p.R1136Q		Atlas-SNP	.											.	TBC1D1	94	.	0			c.G3407A						PASS	.	G	GLN/ARG	236,4170	136.1+/-172.1	7,222,1974	41.0	45.0	43.0		3407	4.3	0.1	4	dbSNP_121	43	790,7810	179.2+/-228.4	39,712,3549	yes	missense	TBC1D1	NM_015173.2	43	46,934,5523	AA,AG,GG		9.186,5.3563,7.8887	benign	1136/1169	38138856	1026,11980	2203	4300	6503	SO:0001583	missense	23216	exon20			TGGAGCGGTCGGC	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.3407G>A	4.37:g.38138856G>A	ENSP00000261439:p.Arg1136Gln	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	77	44	0.571429	NM_015173	B7Z3D9|E9PGH8|Q96K82|Q9UPP4	Missense_Mutation	SNP	ENST00000261439.4	37	CCDS33972.1	229	0.10485347985347986	30	0.06097560975609756	61	0.1685082872928177	64	0.11188811188811189	74	0.09762532981530343	G	13.62	2.292186	0.40594	0.053563	0.09186	ENSG00000065882	ENST00000508802;ENST00000261439;ENST00000454732	T;T	0.04502	3.61;3.99	5.16	4.32	0.51571	.	0.000000	0.64402	D	0.000015	T	0.00039	0.0001	L	0.50333	1.59	0.09310	P	0.99999203063	D;D;P	0.76494	0.999;0.999;0.454	P;P;B	0.58391	0.838;0.789;0.044	T	0.51498	-0.8698	9	0.20046	T	0.44	-24.773	13.5429	0.61686	0.0741:0.0:0.9259:0.0	rs13110318;rs17607771;rs52827591;rs58048766;rs13110318	1127;868;1136	E9PGH8;Q6PJJ8;Q86TI0	.;.;TBCD1_HUMAN	Q	1127;1136;400	ENSP00000423651:R1127Q;ENSP00000261439:R1136Q	ENSP00000261439:R1136Q	R	+	2	0	TBC1D1	37815251	1.000000	0.71417	0.075000	0.20258	0.025000	0.11179	4.627000	0.61276	1.406000	0.46857	0.650000	0.86243	CGG	G|0.914;A|0.086	0.086	strong		0.642	TBC1D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317443.2	NM_015173	
DSPP	1834	hgsc.bcm.edu	37	4	88536451	88536451	+	Silent	SNP	C	C	T	rs111205176|rs149201255		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:88536451C>T	ENST00000282478.7	+	4	2670	c.2637C>T	c.(2635-2637)agC>agT	p.S879S	RP11-742B18.1_ENST00000506480.1_RNA|DSPP_ENST00000399271.1_Silent_p.S879S			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	879	Asp/Ser-rich.				biomineral tissue development (GO:0031214)|cellular response to cell-matrix adhesion (GO:0071460)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|skin(3)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Hepatocellular(203;0.114)|all_hematologic(202;0.236)		OV - Ovarian serous cystadenocarcinoma(123;0.000508)		gcagtgacagcagtgatagca	0.493																																					p.S879S		Atlas-SNP	.											DSPP,colon,carcinoma,0,1	DSPP	174	1	0			c.C2637T						PASS	.						71.0	84.0	80.0					4																	88536451		1629	2928	4557	SO:0001819	synonymous_variant	1834	exon5			TGACAGCAGTGAT	AF163151	CCDS43248.1	4q21.3	2008-02-05			ENSG00000152591	ENSG00000152591			3054	protein-coding gene	gene with protein product		125485		DFNA39, DGI1		8995371, 9533027	Standard	NM_014208		Approved	DMP3	uc003hqu.3	Q9NZW4	OTTHUMG00000161061	ENST00000282478.7:c.2637C>T	4.37:g.88536451C>T		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	71	12	0.169014	NM_014208	A8MUI0|O95815	Silent	SNP	ENST00000282478.7	37	CCDS43248.1																																																																																			.	.	weak		0.493	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208	
HIST1H1C	3006	hgsc.bcm.edu	37	6	26056484	26056484	+	Missense_Mutation	SNP	G	G	A	rs550065694		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:26056484G>A	ENST00000343677.2	-	1	215	c.173C>T	c.(172-174)tCt>tTt	p.S58F		NM_005319.3	NP_005310.1	P16403	H12_HUMAN	histone cluster 1, H1c	58	H15. {ECO:0000255|PROSITE- ProRule:PRU00837}.				nucleosome assembly (GO:0006334)|nucleosome positioning (GO:0016584)	nuclear euchromatin (GO:0005719)|nucleosome (GO:0000786)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(6)|kidney(1)|large_intestine(1)|lung(8)|ovary(4)|prostate(3)|skin(3)|upper_aerodigestive_tract(3)	34						AGCAGCCAGAGAAACTCCGCT	0.572																																					p.S58F		Atlas-SNP	.											HIST1H1C,colon,carcinoma,0,1	HIST1H1C	80	1	0			c.C173T						scavenged	.						75.0	84.0	81.0					6																	26056484		2203	4300	6503	SO:0001583	missense	3006	exon1			GCCAGAGAAACTC	X57129	CCDS4577.1	6p21.3	2012-10-02	2006-10-11	2003-02-21	ENSG00000187837	ENSG00000187837		"""Histones / Replication-dependent"""	4716	protein-coding gene	gene with protein product		142710	"""H1 histone family, member 2"", ""histone 1, H1c"""	H1F2		2759094, 12408966	Standard	NM_005319		Approved	H1.2, H1s-1, H1c	uc003nfw.3	P16403	OTTHUMG00000016140	ENST00000343677.2:c.173C>T	6.37:g.26056484G>A	ENSP00000339566:p.Ser58Phe	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	96	3	0.03125	NM_005319	A8K4I2	Missense_Mutation	SNP	ENST00000343677.2	37	CCDS4577.1	.	.	.	.	.	.	.	.	.	.	G	17.64	3.439574	0.63067	.	.	ENSG00000187837	ENST00000343677	T	0.53640	0.61	5.73	5.73	0.89815	Histone H1/H5 (3);Winged helix-turn-helix transcription repressor DNA-binding (1);	0.000000	0.85682	D	0.000000	T	0.80481	0.4631	H	0.98559	4.265	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.87256	0.2276	10	0.87932	D	0	-27.9918	19.2479	0.93909	0.0:0.0:1.0:0.0	.	58	P16403	H12_HUMAN	F	58	ENSP00000339566:S58F	ENSP00000339566:S58F	S	-	2	0	HIST1H1C	26164463	1.000000	0.71417	0.911000	0.35937	0.004000	0.04260	7.736000	0.84948	2.861000	0.98227	0.655000	0.94253	TCT	.	.	none		0.572	HIST1H1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043372.1	NM_005319	
RBFOX1	54715	hgsc.bcm.edu	37	16	7629841	7629841	+	Silent	SNP	A	A	G	rs140174146	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:7629841A>G	ENST00000550418.1	+	6	1321	c.333A>G	c.(331-333)gaA>gaG	p.E111E	RBFOX1_ENST00000535565.2_Intron|RBFOX1_ENST00000311745.5_Silent_p.E131E|RBFOX1_ENST00000436368.2_Silent_p.E131E|RBFOX1_ENST00000340209.4_Silent_p.E116E|RBFOX1_ENST00000355637.4_Silent_p.E131E|RBFOX1_ENST00000553186.1_Silent_p.E111E|RBFOX1_ENST00000547338.1_Silent_p.E111E|RBFOX1_ENST00000552089.1_Silent_p.E146E|RBFOX1_ENST00000422070.4_Silent_p.E154E|RBFOX1_ENST00000547372.1_Silent_p.E154E	NM_018723.3	NP_061193.2	Q9NWB1	RFOX1_HUMAN	RNA binding protein, fox-1 homolog (C. elegans) 1	111					mRNA processing (GO:0006397)|neuromuscular process controlling balance (GO:0050885)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)|RNA transport (GO:0050658)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|trans-Golgi network (GO:0005802)	nucleotide binding (GO:0000166)|protein C-terminus binding (GO:0008022)|RNA binding (GO:0003723)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(11)|lung(17)|ovary(1)|pancreas(1)|prostate(5)|skin(5)|upper_aerodigestive_tract(2)	55						AAAACACGGAAAACAAGTCTC	0.507													A|||	26	0.00519169	0.0008	0.0	5008	,	,		17993	0.0		0.0109	False		,,,				2504	0.0143				p.E131E	Ovarian(157;934 2567 15163 39509)	Atlas-SNP	.											.	RBFOX1	341	.	0			c.A393G						PASS	.	A	,,,,,	10,4384	16.8+/-37.8	0,10,2187	147.0	134.0	139.0		333,333,333,393,393,393	3.2	1.0	16	dbSNP_134	139	116,8484	61.7+/-123.6	0,116,4184	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	RBFOX1	NM_001142333.1,NM_001142334.1,NM_018723.3,NM_145891.2,NM_145892.2,NM_145893.2	,,,,,	0,126,6371	GG,GA,AA		1.3488,0.2276,0.9697	,,,,,	111/371,111/398,111/398,131/419,131/393,131/396	7629841	126,12868	2197	4300	6497	SO:0001819	synonymous_variant	54715	exon3			CACGGAAAACAAG	AF107203	CCDS10531.1, CCDS10532.1, CCDS45405.1, CCDS55983.1, CCDS55984.1	16p13.3	2013-02-12			ENSG00000078328	ENSG00000078328		"""RNA binding motif (RRM) containing"""	18222	protein-coding gene	gene with protein product	"""ataxin 2-binding protein 1"", ""hexaribonucleotide binding protein 1"""	605104				10814712, 16260614	Standard	NM_018723		Approved	A2BP1, FOX-1, HRNBP1	uc002cyy.2	Q9NWB1	OTTHUMG00000129551	ENST00000550418.1:c.333A>G	16.37:g.7629841A>G		Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	132	103	0.780303	NM_145891	Q7Z7I7|Q8TAE3|Q8TAF2|Q8WYB2|Q9NS20	Silent	SNP	ENST00000550418.1	37	CCDS55983.1																																																																																			A|0.991;G|0.009	0.009	strong		0.507	RBFOX1-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000409492.2	NM_145891	
AHNAK2	113146	hgsc.bcm.edu	37	14	105418234	105418234	+	Missense_Mutation	SNP	G	G	A	rs76024300	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:105418234G>A	ENST00000333244.5	-	7	3673	c.3554C>T	c.(3553-3555)tCg>tTg	p.S1185L	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	1185						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)			CACATCCACCGAGGCCTCGAT	0.597													.|||	404	0.0806709	0.1324	0.0331	5008	,	,		19091	0.1161		0.0169	False		,,,				2504	0.0736				p.S1185L		Atlas-SNP	.											.	AHNAK2	719	.	0			c.C3554T						PASS	.						166.0	162.0	163.0					14																	105418234		1947	4121	6068	SO:0001583	missense	113146	exon7			TCCACCGAGGCCT	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.3554C>T	14.37:g.105418234G>A	ENSP00000353114:p.Ser1185Leu	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	173	17	0.0982659	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	.	.	.	.	.	.	.	.	.	.	g	16.54	3.151098	0.57151	.	.	ENSG00000185567	ENST00000333244	T	0.00745	5.75	4.4	4.4	0.53042	.	.	.	.	.	T	0.01523	0.0049	M	0.72894	2.215	0.09310	N	1	P	0.52463	0.953	B	0.43916	0.436	T	0.52275	-0.8597	9	0.33940	T	0.23	.	10.1024	0.42513	0.0:0.0:0.7407:0.2593	.	1185	Q8IVF2	AHNK2_HUMAN	L	1185	ENSP00000353114:S1185L	ENSP00000353114:S1185L	S	-	2	0	AHNAK2	104489279	0.038000	0.19896	0.013000	0.15412	0.054000	0.15201	2.474000	0.45154	1.998000	0.58463	0.491000	0.48974	TCG	.	.	weak		0.597	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
CTDP1	9150	hgsc.bcm.edu	37	18	77473086	77473086	+	Silent	SNP	G	G	A	rs599554	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:77473086G>A	ENST00000299543.7	+	7	1125	c.978G>A	c.(976-978)acG>acA	p.T326T	CTDP1_ENST00000075430.7_Silent_p.T326T	NM_001202504.1|NM_004715.4	NP_001189433.1|NP_004706.3	Q9Y5B0	CTDP1_HUMAN	CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) phosphatase, subunit 1	326	FCP1 homology. {ECO:0000255|PROSITE- ProRule:PRU00336}.				exit from mitosis (GO:0010458)|gene expression (GO:0010467)|positive regulation of viral transcription (GO:0050434)|protein dephosphorylation (GO:0006470)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	actin cytoskeleton (GO:0015629)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|midbody (GO:0030496)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)|spindle midzone (GO:0051233)|spindle pole (GO:0000922)	CTD phosphatase activity (GO:0008420)|DNA-directed RNA polymerase activity (GO:0003899)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(14)|ovary(2)|prostate(2)|urinary_tract(1)	35		Esophageal squamous(42;0.0157)|Melanoma(33;0.144)		OV - Ovarian serous cystadenocarcinoma(15;5.2e-06)|BRCA - Breast invasive adenocarcinoma(31;0.0277)		TCCAGGGCACGGGTGATATGA	0.448													G|||	1046	0.208866	0.3147	0.2205	5008	,	,		15472	0.1389		0.175	False		,,,				2504	0.1646				p.T326T		Atlas-SNP	.											.	CTDP1	67	.	0			c.G978A						PASS	.	G	,,	1272,3134	435.3+/-344.3	200,872,1131	77.0	74.0	75.0		621,978,978	-9.6	0.0	18	dbSNP_83	75	1463,7135	278.0+/-293.2	134,1195,2970	no	coding-synonymous,coding-synonymous,coding-synonymous	CTDP1	NM_001202504.1,NM_004715.4,NM_048368.3	,,	334,2067,4101	AA,AG,GG		17.0156,28.8697,21.032	,,	207/843,326/962,326/868	77473086	2735,10269	2203	4299	6502	SO:0001819	synonymous_variant	9150	exon7			GGGCACGGGTGAT	AF081287	CCDS12017.1, CCDS12018.1, CCDS74239.1	18q23	2014-09-17			ENSG00000060069	ENSG00000060069		"""Serine/threonine phosphatases / CTD aspartate-based phosphatases"""	2498	protein-coding gene	gene with protein product		604927				9405607, 9765293	Standard	NM_004715		Approved	FCP1	uc002lnh.2	Q9Y5B0	OTTHUMG00000132920	ENST00000299543.7:c.978G>A	18.37:g.77473086G>A		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	73	22	0.30137	NM_004715	A8MY97|Q7Z644|Q96BZ1|Q9Y6F5	Silent	SNP	ENST00000299543.7	37	CCDS12017.1																																																																																			A|0.215;C|0.003	0.215	strong		0.448	CTDP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256432.1	NM_004715	
LILRA6	79168	hgsc.bcm.edu	37	19	54744711	54744711	+	Missense_Mutation	SNP	C	C	G	rs1132599	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:54744711C>G	ENST00000396365.2	-	5	990	c.951G>C	c.(949-951)atG>atC	p.M317I	LILRA6_ENST00000245621.5_Missense_Mutation_p.M317I|LILRA6_ENST00000440558.2_Missense_Mutation_p.M317I|LILRA6_ENST00000270464.5_Intron|LILRB3_ENST00000407860.2_Intron|LILRA6_ENST00000419410.2_Missense_Mutation_p.M317I|LILRA6_ENST00000391735.3_3'UTR	NM_024318.2	NP_077294	Q6PI73	LIRA6_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 6	317					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)		CCTCACCTGCCATCAGGATGT	0.692													.|||	119	0.023762	0.0424	0.0202	5008	,	,		19749	0.001		0.0129	False		,,,				2504	0.0358				p.M317I		Atlas-SNP	.											.	LILRA6	75	.	0			c.G951C						PASS	.						17.0	26.0	23.0					19																	54744711		2084	4143	6227	SO:0001583	missense	79168	exon5			ACCTGCCATCAGG	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.951G>C	19.37:g.54744711C>G	ENSP00000379651:p.Met317Ile	Somatic	202	0	0		WXS	Illumina HiSeq	Phase_I	147	16	0.108844	NM_024318		Missense_Mutation	SNP	ENST00000396365.2	37	CCDS42610.1	.	.	.	.	.	.	.	.	.	.	G	0.001	-3.376427	0.00015	.	.	ENSG00000244482	ENST00000440558;ENST00000419410;ENST00000421123;ENST00000396365;ENST00000245621	T;T;T;T	0.00648	5.99;5.99;5.99;5.99	2.16	-4.31	0.03698	.	0.839827	0.09740	N	0.762011	T	0.00144	0.0004	N	0.00029	-2.625	0.09310	N	0.999999	B;B;B;B	0.17852	0.001;0.024;0.0;0.0	B;B;B;B	0.09377	0.0;0.004;0.0;0.0	T	0.37174	-0.9717	10	0.02654	T	1	.	7.4079	0.27001	0.3138:0.5245:0.1617:0.0	.	317;317;317;317	C9JFH3;Q6PI73;F8WCY4;D3YTC4	.;LIRA6_HUMAN;.;.	I	317	ENSP00000390120:M317I;ENSP00000411227:M317I;ENSP00000379651:M317I;ENSP00000245621:M317I	ENSP00000245621:M317I	M	-	3	0	LILRA6	59436523	0.010000	0.17322	0.000000	0.03702	0.010000	0.07245	-0.018000	0.12568	-2.030000	0.00929	-1.042000	0.02369	ATG	C|0.976;G|0.024	0.024	strong		0.692	LILRA6-003	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000313725.1	NM_024318	
BTC	685	hgsc.bcm.edu	37	4	75719517	75719517	+	Missense_Mutation	SNP	A	A	C	rs28549760	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:75719517A>C	ENST00000395743.3	-	1	379	c.19T>G	c.(19-21)Tgc>Ggc	p.C7G		NM_001729.2	NP_001720.1	P35070	BTC_HUMAN	betacellulin	7			C -> G (in dbSNP:rs28549760).		epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|negative regulation of apoptotic process (GO:0043066)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of mitosis (GO:0045840)|positive regulation of urine volume (GO:0035810)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	epidermal growth factor receptor binding (GO:0005154)|growth factor activity (GO:0008083)			central_nervous_system(1)|cervix(1)|kidney(1)|large_intestine(3)|lung(2)|skin(1)|upper_aerodigestive_tract(1)	10			Lung(101;0.219)			GCGCCGCTGCACCGGGCGGCC	0.711													C|||	1256	0.250799	0.528	0.1931	5008	,	,		11677	0.0526		0.1252	False		,,,				2504	0.2505				p.C7G		Atlas-SNP	.											BTC,NS,carcinoma,0,1	BTC	23	1	0			c.T19G	GRCh37	CM051015	BTC	M	rs28549760	PASS	.	C	GLY/CYS	1222,2206		223,776,715	3.0	4.0	4.0		19	2.0	0.2	4	dbSNP_125	4	707,5837		52,603,2617	no	missense	BTC	NM_001729.2	159	275,1379,3332	CC,CA,AA		10.8038,35.6476,19.3442	possibly-damaging	7/179	75719517	1929,8043	1714	3272	4986	SO:0001583	missense	685	exon1			CGCTGCACCGGGC	S55606	CCDS3566.1	4q13.3	2012-09-20			ENSG00000174808	ENSG00000174808			1121	protein-coding gene	gene with protein product		600345				8439318, 11522793	Standard	NM_001729		Approved		uc003hig.2	P35070	OTTHUMG00000130107	ENST00000395743.3:c.19T>G	4.37:g.75719517A>C	ENSP00000379092:p.Cys7Gly	Somatic	15	0	0		WXS	Illumina HiSeq	Phase_I	9	5	0.555556	NM_001729	Q96F48	Missense_Mutation	SNP	ENST00000395743.3	37	CCDS3566.1	423	0.1936813186813187	234	0.47560975609756095	68	0.1878453038674033	27	0.0472027972027972	94	0.12401055408970976	C	0.003	-2.407671	0.00193	0.356476	0.108038	ENSG00000174808	ENST00000395743	T	0.08546	3.08	2.87	2.0	0.26442	.	1.854280	0.02912	N	0.136898	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	0.46148	-0.9212	9	0.02654	T	1	-10.1459	5.4134	0.16360	0.2346:0.5378:0.2276:0.0	rs28549760	7	P35070	BTC_HUMAN	G	7	ENSP00000379092:C7G	ENSP00000379092:C7G	C	-	1	0	BTC	75938541	0.143000	0.22626	0.175000	0.22980	0.197000	0.23852	0.419000	0.21247	0.244000	0.21351	-0.358000	0.07595	TGC	A|0.802;C|0.198	0.198	strong		0.711	BTC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252413.1		
ANKEF1	63926	hgsc.bcm.edu	37	20	10030452	10030452	+	Missense_Mutation	SNP	G	G	A	rs524625	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:10030452G>A	ENST00000378380.3	+	6	1564	c.1235G>A	c.(1234-1236)gGa>gAa	p.G412E	SNAP25-AS1_ENST00000421143.2_RNA|SNAP25-AS1_ENST00000603542.1_RNA|ANKEF1_ENST00000378392.1_Missense_Mutation_p.G412E|ANKEF1_ENST00000488991.1_3'UTR	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	35	0	0		WXS	Illumina HiSeq	Phase_I	39	21	0.538462	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	
LINGO1	84894	hgsc.bcm.edu	37	15	77907784	77907784	+	Silent	SNP	G	G	A	rs2271398	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:77907784G>A	ENST00000355300.6	-	2	639	c.465C>T	c.(463-465)atC>atT	p.I155I	LINGO1_ENST00000561030.1_Silent_p.I149I	NM_032808.5	NP_116197.4	Q96FE5	LIGO1_HUMAN	leucine rich repeat and Ig domain containing 1	155					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						GTAGGATAACGATCTTGTTCT	0.562													G|||	3584	0.715655	0.6831	0.6527	5008	,	,		22015	0.7937		0.6461	False		,,,				2504	0.7955				p.I155I		Atlas-SNP	.											.	LINGO1	76	.	0			c.C465T						PASS	.	G		2922,1350		1008,906,222	123.0	128.0	127.0		465	1.7	1.0	15	dbSNP_100	127	5385,3093		1694,1997,548	no	coding-synonymous	LINGO1	NM_032808.5		2702,2903,770	AA,AG,GG		36.4827,31.6011,34.8471		155/621	77907784	8307,4443	2136	4239	6375	SO:0001819	synonymous_variant	84894	exon2			GATAACGATCTTG	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.465C>T	15.37:g.77907784G>A		Somatic	194	0	0		WXS	Illumina HiSeq	Phase_I	188	188	1	NM_032808	D3DW80|Q6NUK3|Q6UXM3|Q6VVG0|Q6VVG1|Q6VVG2|Q8N3K5|Q96K52	Silent	SNP	ENST00000355300.6	37	CCDS45313.1																																																																																			G|0.300;A|0.700	0.700	strong		0.562	LINGO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419546.1	NM_032808	
SPATA31C2	645961	hgsc.bcm.edu	37	9	90746159	90746159	+	IGR	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:90746159C>T								U6 (132909 upstream) : U3 (243024 downstream)																							AAGCCAGGATCGACGCACACT	0.527																																					p.R598Q		Atlas-SNP	.											.	.	.	.	0			c.G1793A						PASS	.						45.0	38.0	40.0					9																	90746159		692	1591	2283	SO:0001628	intergenic_variant	645961	exon4			CAGGATCGACGCA																													9.37:g.90746159C>T		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	78	20	0.25641	NM_001166137		Missense_Mutation	SNP		37																																																																																				.	.	none	0	0.527								
GALC	2581	hgsc.bcm.edu	37	14	88414211	88414211	+	Silent	SNP	G	G	A	rs398076	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:88414211G>A	ENST00000261304.2	-	13	1456	c.1350C>T	c.(1348-1350)agC>agT	p.S450S	GALC_ENST00000393569.2_Silent_p.S424S|GALC_ENST00000544807.2_Silent_p.S394S|GALC_ENST00000393568.4_Silent_p.S427S	NM_000153.3|NM_001201401.1	NP_000144.2|NP_001188330.1	P54803	GALC_HUMAN	galactosylceramidase	450					carbohydrate metabolic process (GO:0005975)|galactosylceramide catabolic process (GO:0006683)|glycosphingolipid metabolic process (GO:0006687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)	galactosylceramidase activity (GO:0004336)			endometrium(2)|kidney(2)|large_intestine(1)|lung(10)|ovary(1)|prostate(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	21						AACTGCCATCGCTGTCAAGGA	0.458													G|||	1836	0.366613	0.4387	0.33	5008	,	,		17166	0.2302		0.4105	False		,,,				2504	0.3906				p.S450S		Atlas-SNP	.											.	GALC	48	.	0			c.C1350T						PASS	.	G	,,	1755,2369		398,959,705	73.0	75.0	74.0		1350,1281,1272	-2.8	0.0	14	dbSNP_80	74	3357,5039		672,2013,1513	no	coding-synonymous,coding-synonymous,coding-synonymous	GALC	NM_000153.3,NM_001201401.1,NM_001201402.1	,,	1070,2972,2218	AA,AG,GG		39.9833,42.5558,40.8307	,,	450/686,427/663,424/660	88414211	5112,7408	2062	4198	6260	SO:0001819	synonymous_variant	2581	exon13			GCCATCGCTGTCA	L23116	CCDS9878.2, CCDS55936.1, CCDS55937.1	14q31	2009-01-06	2005-11-29		ENSG00000054983	ENSG00000054983	3.2.1.46		4115	protein-coding gene	gene with protein product	"""Krabbe disease"""	606890	"""galactosylceramidase (Krabbe disease)"""				Standard	NM_000153		Approved		uc001xvt.3	P54803	OTTHUMG00000028646	ENST00000261304.2:c.1350C>T	14.37:g.88414211G>A		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	92	44	0.478261	NM_000153	B4DKE8|B4DYN1|B4DZJ8|B7Z7Z2|J3KN25|J3KPP8|Q8J030	Silent	SNP	ENST00000261304.2	37	CCDS9878.2																																																																																			G|0.650;A|0.350	0.350	strong		0.458	GALC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071559.2		
MCPH1	79648	hgsc.bcm.edu	37	8	6479042	6479042	+	Missense_Mutation	SNP	C	C	T	rs1057090	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:6479042C>T	ENST00000344683.5	+	13	2358	c.2282C>T	c.(2281-2283)gCg>gTg	p.A761V	MCPH1_ENST00000521175.1_3'UTR|CTD-2541M15.1_ENST00000522897.1_RNA|CTD-2541M15.1_ENST00000515608.1_RNA	NM_024596.3	NP_078872	Q8NEM0	MCPH1_HUMAN	microcephalin 1	761	BRCT 3. {ECO:0000255|PROSITE- ProRule:PRU00033}.		V -> A (may be associated with cranial volume variation in males in a Chinese population; dbSNP:rs1057090). {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)		GACCAGCCAGCGATGTTTGTC	0.637													T|||	2414	0.482029	0.4539	0.3646	5008	,	,		16153	0.6716		0.4076	False		,,,				2504	0.4847				p.A761V	Colon(95;1448 1467 8277 34473 35819)	Atlas-SNP	.											.	MCPH1	65	.	0			c.C2282T	GRCh37	CM081694	MCPH1	M	rs1057090	PASS	.	T	VAL/ALA	1888,2360		443,1002,679	45.0	54.0	51.0		2282	-8.3	0.0	8	dbSNP_86	51	3316,5134		631,2054,1540	yes	missense	MCPH1	NM_024596.3	64	1074,3056,2219	TT,TC,CC		39.2426,44.4444,40.9828	benign	761/836	6479042	5204,7494	2124	4225	6349	SO:0001583	missense	79648	exon13			AGCCAGCGATGTT	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.2282C>T	8.37:g.6479042C>T	ENSP00000342924:p.Ala761Val	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	28	27	0.964286	NM_024596	B4DWW2|E9PGU5|E9PH63|Q66GU1|Q9H9C7	Missense_Mutation	SNP	ENST00000344683.5	37	CCDS43689.1	1078	0.4935897435897436	248	0.5040650406504065	143	0.39502762430939226	370	0.6468531468531469	317	0.4182058047493404	T	1.080	-0.667396	0.03428	0.444444	0.392426	ENSG00000147316	ENST00000344683	D	0.88124	-2.34	5.38	-8.27	0.01017	.	2.695450	0.01484	N	0.016817	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.28744	-1.0034	6	0.02654	T	1	0.8077	8.9087	0.35539	0.102:0.6286:0.0989:0.1705	rs1057090;rs3197702;rs17556803;rs52816102;rs1057090	.	.	.	V	761	ENSP00000342924:A761V	ENSP00000342924:A761V	A	+	2	0	MCPH1	6466450	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-0.677000	0.05215	-1.782000	0.01275	-0.360000	0.07572	GCG	C|0.519;A|0.008	.	strong		0.637	MCPH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374532.2	NM_024596	
ADCY9	115	hgsc.bcm.edu	37	16	4033436	4033436	+	Missense_Mutation	SNP	T	T	C	rs2230739	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:4033436T>C	ENST00000294016.3	-	7	2854	c.2316A>G	c.(2314-2316)atA>atG	p.I772M		NM_001116.3	NP_001107.2	O60503	ADCY9_HUMAN	adenylate cyclase 9	772			I -> M (in 37.5% of the Asian population, in 30% of the Caucasian population and in 16.3% of the African-American population; reduced adenylyl cyclase activity in response to stimulation of the beta- adregnergic receptor by the agonists Mn(2+), isoproteronol and NaF; increased albuterol-stimulated adenylyl cyclase activity in the presence of corticosteroid; dbSNP:rs2230739). {ECO:0000269|PubMed:12972952, ECO:0000269|PubMed:15879435}.		activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	axon (GO:0030424)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)			breast(4)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(3)|large_intestine(11)|lung(9)|ovary(5)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	47						GGGAGTTCTTTATGACCTGTG	0.572													T|||	1304	0.260383	0.1172	0.2334	5008	,	,		19237	0.3819		0.341	False		,,,				2504	0.2648				p.I772M		Atlas-SNP	.											ADCY9,NS,carcinoma,0,1	ADCY9	151	1	0			c.A2316G	GRCh37	CM034003	ADCY9	M	rs2230739	PASS	.	T	MET/ILE	649,3745		40,569,1588	71.0	60.0	64.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	2316	-7.9	0.0	16	dbSNP_98	64	2688,5912		445,1798,2057	yes	missense	ADCY9	NM_001116.3	10	485,2367,3645	CC,CT,TT		31.2558,14.7701,25.6811	benign	772/1354	4033436	3337,9657	2197	4300	6497	SO:0001583	missense	115	exon7			GTTCTTTATGACC	AF036927	CCDS32382.1	16p13.3	2013-02-04				ENSG00000162104	4.6.1.1	"""Adenylate cyclases"""	240	protein-coding gene	gene with protein product		603302				9628827	Standard	NM_001116		Approved	AC9	uc002cvx.3	O60503		ENST00000294016.3:c.2316A>G	16.37:g.4033436T>C	ENSP00000294016:p.Ile772Met	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	77	59	0.766234	NM_001116	A7E2V5|A7E2X2|D3DUD1|O60273|Q4ZHT9|Q4ZIR5|Q9BWT4|Q9UGP2	Missense_Mutation	SNP	ENST00000294016.3	37	CCDS32382.1	610	0.2793040293040293	50	0.1016260162601626	91	0.2513812154696133	228	0.3986013986013986	241	0.3179419525065963	T	6.786	0.513906	0.12944	0.147701	0.312558	ENSG00000162104	ENST00000294016	D	0.82433	-1.61	5.94	-7.94	0.01152	.	0.557796	0.20751	N	0.086357	T	0.00012	0.0000	N	0.12182	0.205	0.80722	P	0.0	B	0.06786	0.001	B	0.04013	0.001	T	0.11717	-1.0576	9	0.19590	T	0.45	.	11.3789	0.49746	0.0:0.3363:0.4723:0.1914	rs2230739;rs2531981;rs17184038;rs60378382;rs2230739	772	O60503	ADCY9_HUMAN	M	772	ENSP00000294016:I772M	ENSP00000294016:I772M	I	-	3	3	ADCY9	3973437	0.000000	0.05858	0.005000	0.12908	0.081000	0.17604	-1.685000	0.01930	-1.914000	0.01078	-0.429000	0.05907	ATA	T|0.736;C|0.264	0.264	strong		0.572	ADCY9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438076.1		
GPR162	27239	hgsc.bcm.edu	37	12	6933787	6933787	+	Silent	SNP	A	A	G	rs1051409	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:6933787A>G	ENST00000311268.3	+	2	1510	c.723A>G	c.(721-723)gtA>gtG	p.V241V	GPR162_ENST00000428545.2_Intron|GPR162_ENST00000382315.3_Intron	NM_019858.1	NP_062832.1	Q16538	GP162_HUMAN	G protein-coupled receptor 162	241						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						CTTTTGAGGTACCAGCCATTG	0.692													G|||	2451	0.489417	0.5734	0.5144	5008	,	,		-128	0.5675		0.4563	False		,,,				2504	0.3119				p.V241V		Atlas-SNP	.											.	GPR162	55	.	0			c.A723G						PASS	.	G	,	2427,1979	556.5+/-379.5	679,1069,455	49.0	51.0	50.0		,723	2.5	1.0	12	dbSNP_86	50	3933,4667	602.4+/-394.5	912,2109,1279	no	intron,coding-synonymous	GPR162	NM_014449.1,NM_019858.1	,	1591,3178,1734	GG,GA,AA		45.7326,44.916,48.9005	,	,241/589	6933787	6360,6646	2203	4300	6503	SO:0001819	synonymous_variant	27239	exon2			TGAGGTACCAGCC	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.723A>G	12.37:g.6933787A>G		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	63	31	0.492063	NM_019858	Q16664|Q59EH5|Q66K56	Silent	SNP	ENST00000311268.3	37	CCDS8563.1																																																																																			A|0.507;G|0.493	0.493	strong		0.692	GPR162-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399478.1	NM_019858	
ZNF701	55762	hgsc.bcm.edu	37	19	53077411	53077411	+	Missense_Mutation	SNP	T	T	C	rs162832	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:53077411T>C	ENST00000540331.1	+	3	434	c.209T>C	c.(208-210)cTt>cCt	p.L70P	ZNF701_ENST00000391785.3_Missense_Mutation_p.L4P|CTD-3099C6.7_ENST00000599222.1_RNA|ZNF701_ENST00000301093.2_Missense_Mutation_p.L70P	NM_001172655.1	NP_001166126.1	Q9NV72	ZN701_HUMAN	zinc finger protein 701	70			L -> P (in dbSNP:rs162832). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(5)|kidney(1)|large_intestine(2)|lung(6)	14				OV - Ovarian serous cystadenocarcinoma(262;0.0105)|GBM - Glioblastoma multiforme(134;0.0402)		ATGGCTCTTCTTCAGGTGAGA	0.443													C|||	3578	0.714457	0.9433	0.6758	5008	,	,		21053	0.4276		0.7227	False		,,,				2504	0.7198				p.L70P	NSCLC(89;451 1475 9611 20673 52284)	Atlas-SNP	.											.	ZNF701	44	.	0			c.T209C						PASS	.	C	PRO/LEU,PRO/LEU	3990,416		1812,366,25	180.0	136.0	151.0		209,11	-2.4	0.0	19	dbSNP_79	151	6262,2336		2306,1650,343	no	missense,missense	ZNF701	NM_001172655.1,NM_018260.2	98,98	4118,2016,368	CC,CT,TT		27.1691,9.4417,21.1627	benign,benign	70/532,4/466	53077411	10252,2752	2203	4299	6502	SO:0001583	missense	55762	exon3			CTCTTCTTCAGGT	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.209T>C	19.37:g.53077411T>C	ENSP00000444339:p.Leu70Pro	Somatic	20	0	0		WXS	Illumina HiSeq	Phase_I	24	24	1	NM_001172655	A2RRM8|B9EGF2|F5GZM6|Q66K42	Missense_Mutation	SNP	ENST00000540331.1	37	CCDS54311.1	1365	0.625	398	0.8089430894308943	236	0.6519337016574586	232	0.40559440559440557	499	0.658311345646438	N	4.288	0.052590	0.08291	0.905583	0.728309	ENSG00000167562	ENST00000391785;ENST00000301093;ENST00000540331	T;T;T	0.00824	5.65;5.65;5.65	1.53	-2.36	0.06663	Krueppel-associated box (1);	.	.	.	.	T	0.00012	0.0000	N	0.03608	-0.345	0.54753	P	1.4999999999987246E-5	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.07177	-1.0786	7	.	.	.	.	3.4633	0.07540	0.0:0.281:0.2183:0.5006	rs162832;rs637554;rs1300322;rs57532628;rs162832	70;4	F5GZM6;Q9NV72	.;ZN701_HUMAN	P	4;70;70	ENSP00000375662:L4P;ENSP00000301093:L70P;ENSP00000444339:L70P	.	L	+	2	0	ZNF701	57769223	0.025000	0.19082	0.001000	0.08648	0.440000	0.31957	-0.042000	0.12063	-1.123000	0.02940	-0.665000	0.03846	CTT	T|0.261;C|0.739	0.739	strong		0.443	ZNF701-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000463467.1	NM_018260	
PIGQ	9091	hgsc.bcm.edu	37	16	624101	624101	+	Silent	SNP	G	G	A	rs61753370	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:624101G>A	ENST00000026218.5	+	2	115	c.27G>A	c.(25-27)acG>acA	p.T9T	PIGQ_ENST00000409527.2_Silent_p.T9T|PIGQ_ENST00000321878.5_Silent_p.T9T|PIGQ_ENST00000470411.2_Silent_p.T9T	NM_148920.2	NP_683721.1	Q9BRB3	PIGQ_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class Q	9					C-terminal protein lipidation (GO:0006501)|carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)	endoplasmic reticulum membrane (GO:0005789)|glycosylphosphatidylinositol-N-acetylglucosaminyltransferase (GPI-GnT) complex (GO:0000506)|integral component of membrane (GO:0016021)	phosphatidylinositol N-acetylglucosaminyltransferase activity (GO:0017176)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(1)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)	13		Hepatocellular(780;0.00335)				TCTTCCCCACGTGCTGCGTCT	0.682													G|||	45	0.00898562	0.003	0.0173	5008	,	,		17267	0.0		0.0239	False		,,,				2504	0.0051				p.T9T		Atlas-SNP	.											PIGQ,NS,carcinoma,0,1	PIGQ	43	1	0			c.G27A						PASS	.	G	,	23,4379	29.9+/-59.1	0,23,2178	54.0	48.0	50.0		27,27	-7.0	1.0	16	dbSNP_129	50	304,8296	110.0+/-170.5	2,300,3998	no	coding-synonymous,coding-synonymous	PIGQ	NM_004204.3,NM_148920.1	,	2,323,6176	AA,AG,GG		3.5349,0.5225,2.515	,	9/582,9/761	624101	327,12675	2201	4300	6501	SO:0001819	synonymous_variant	9091	exon2			CCCCACGTGCTGC	AB003723	CCDS10411.1, CCDS10412.1	16p13.3	2013-03-28	2006-06-28		ENSG00000007541	ENSG00000007541		"""Phosphatidylinositol glycan anchor biosynthesis"""	14135	protein-coding gene	gene with protein product		605754	"""phosphatidylinositol glycan, class Q"""			9463366, 9729469	Standard	NM_004204		Approved	hGPI1, GPI1	uc002cho.3	Q9BRB3	OTTHUMG00000168047	ENST00000026218.5:c.27G>A	16.37:g.624101G>A		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	64	50	0.78125	NM_148920	A2IDE1|D3DU52|O14927|Q96G00|Q96S22|Q9UJH4	Silent	SNP	ENST00000026218.5	37	CCDS10411.1																																																																																			G|0.978;A|0.022	0.022	strong		0.682	PIGQ-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000239270.2	NM_004204	
FMO1	2326	hgsc.bcm.edu	37	1	171250044	171250044	+	Silent	SNP	C	C	T	rs742350	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:171250044C>T	ENST00000354841.4	+	5	878	c.747C>T	c.(745-747)acC>acT	p.T249T	FMO1_ENST00000402921.2_Silent_p.T186T|FMO1_ENST00000367750.3_Silent_p.T249T|FMO1_ENST00000469112.1_3'UTR	NM_001282692.1	NP_001269621.1	Q01740	FMO1_HUMAN	flavin containing monooxygenase 1	249					NADPH oxidation (GO:0070995)|organic acid metabolic process (GO:0006082)|small molecule metabolic process (GO:0044281)|toxin metabolic process (GO:0009404)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum lumen (GO:0005788)|integral component of membrane (GO:0016021)	flavin adenine dinucleotide binding (GO:0050660)|monooxygenase activity (GO:0004497)|N,N-dimethylaniline monooxygenase activity (GO:0004499)|NADP binding (GO:0050661)			NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(13)|prostate(2)|skin(2)	27	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)				Cevimeline(DB00185)|Cimetidine(DB00501)|Lorcaserin(DB04871)|Tamoxifen(DB00675)|Vandetanib(DB05294)|Voriconazole(DB00582)	CCCTCCCAACCCCAATTGTGA	0.463													T|||	1120	0.223642	0.5083	0.1124	5008	,	,		20629	0.0218		0.1392	False		,,,				2504	0.2127				p.T249T		Atlas-SNP	.											.	FMO1	79	.	0			c.C747T						PASS	.	T		1979,2427	619.0+/-393.3	429,1121,653	105.0	98.0	100.0		747	2.5	1.0	1	dbSNP_86	100	1153,7447	766.0+/-407.6	76,1001,3223	no	coding-synonymous	FMO1	NM_002021.1		505,2122,3876	TT,TC,CC		13.407,44.916,24.0812		249/533	171250044	3132,9874	2203	4300	6503	SO:0001819	synonymous_variant	2326	exon6			CCCAACCCCAATT	M64082	CCDS1294.1, CCDS60351.1	1q24.3	2011-08-04			ENSG00000010932	ENSG00000010932	1.14.13.8		3769	protein-coding gene	gene with protein product		136130					Standard	XM_005245037		Approved		uc001ghl.3	Q01740	OTTHUMG00000035502	ENST00000354841.4:c.747C>T	1.37:g.171250044C>T		Somatic	248	0	0		WXS	Illumina HiSeq	Phase_I	162	68	0.419753	NM_002021	A8K248|B7Z3P4|Q5QPT2|Q9UJC2	Silent	SNP	ENST00000354841.4	37	CCDS1294.1																																																																																			C|0.784;T|0.216	0.216	strong		0.463	FMO1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086212.1	NM_002021	
PCSK5	5125	hgsc.bcm.edu	37	9	78938186	78938186	+	Missense_Mutation	SNP	G	G	C	rs2803429	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:78938186G>C	ENST00000545128.1	+	31	4778	c.4240G>C	c.(4240-4242)Gag>Cag	p.E1414Q		NM_001190482.1	NP_001177411.1	Q92824	PCSK5_HUMAN	proprotein convertase subtilisin/kexin type 5	1414	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						TTATGAAAAGGAGACTAAGGA	0.532													G|||	1611	0.321685	0.4667	0.2392	5008	,	,		15651	0.1369		0.3529	False		,,,				2504	0.3425				p.E1414Q		Atlas-SNP	.											.	PCSK5	329	.	0			c.G4240C						PASS	.	G	GLN/GLU	791,961		189,413,274	57.0	55.0	56.0		4240	-5.4	0.0	9	dbSNP_100	56	1344,2638		235,874,882	yes	missense	PCSK5	NM_001190482.1	29	424,1287,1156	CC,CG,GG		33.7519,45.1484,37.234	benign	1414/1861	78938186	2135,3599	876	1991	2867	SO:0001583	missense	5125	exon31			GAAAAGGAGACTA		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.4240G>C	9.37:g.78938186G>C	ENSP00000446280:p.Glu1414Gln	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	120	56	0.466667	NM_001190482	F5H2G7|Q13527|Q96EP4	Missense_Mutation	SNP	ENST00000545128.1	37	CCDS55320.1	686	0.3141025641025641	239	0.48577235772357724	99	0.27348066298342544	76	0.13286713286713286	272	0.35883905013192613	G	4.588	0.109191	0.08780	0.451484	0.337519	ENSG00000099139	ENST00000545128;ENST00000376754;ENST00000424854	T;T	0.28666	1.6;1.67	5.35	-5.44	0.02624	.	1.452020	0.03812	N	0.266049	T	0.00012	0.0000	L	0.31804	0.96	0.80722	P	0.0	.	.	.	.	.	.	T	0.43750	-0.9372	7	0.14656	T	0.56	0.7389	2.3399	0.04257	0.3703:0.298:0.2304:0.1014	rs2803429;rs17777849;rs61513592;rs2803429	.	.	.	Q	1414;1144;1114	ENSP00000446280:E1414Q;ENSP00000411654:E1114Q	ENSP00000365945:E1144Q	E	+	1	0	PCSK5	78128006	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.431000	0.21444	-1.152000	0.02832	-0.859000	0.03014	GAG	G|0.675;C|0.325	0.325	strong		0.532	PCSK5-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
DIRAS3	9077	hgsc.bcm.edu	37	1	68512893	68512893	+	Missense_Mutation	SNP	T	T	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:68512893T>G	ENST00000370981.1	-	4	724	c.88A>C	c.(88-90)Aag>Cag	p.K30Q	GNG12-AS1_ENST00000420587.1_RNA|DIRAS3_ENST00000395201.1_Missense_Mutation_p.K30Q|GNG12-AS1_ENST00000413628.1_RNA			O95661	DIRA3_HUMAN	DIRAS family, GTP-binding RAS-like 3	30					regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of gene expression by genetic imprinting (GO:0006349)|small GTPase mediated signal transduction (GO:0007264)	plasma membrane (GO:0005886)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			NS(1)|cervix(1)|endometrium(2)|large_intestine(1)|lung(6)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	14						CTGTGGGGCTTGAAGGCGCGG	0.607																																					p.K30Q		Atlas-SNP	.											DIRAS3,NS,carcinoma,+2,1	DIRAS3	31	1	0			c.A88C						scavenged	.						45.0	50.0	49.0					1																	68512893		2203	4300	6503	SO:0001583	missense	9077	exon2			GGGGCTTGAAGGC	U96750	CCDS641.1	1p31	2014-05-09		2005-01-27	ENSG00000162595	ENSG00000162595			687	protein-coding gene	gene with protein product		605193	"""ras homolog gene family, member I"""	ARHI		9874798	Standard	XM_006711027		Approved	NOEY2	uc001ded.3	O95661	OTTHUMG00000009544	ENST00000370981.1:c.88A>C	1.37:g.68512893T>G	ENSP00000360020:p.Lys30Gln	Somatic	100	2	0.02		WXS	Illumina HiSeq	Phase_I	86	23	0.267442	NM_004675	B3KMP3	Missense_Mutation	SNP	ENST00000370981.1	37	CCDS641.1	.	.	.	.	.	.	.	.	.	.	T	9.916	1.210778	0.22289	.	.	ENSG00000162595	ENST00000370981;ENST00000395201	T;T	0.73258	-0.73;-0.73	3.98	-5.83	0.02325	.	.	.	.	.	T	0.21103	0.0508	N	0.19112	0.55	0.09310	N	1	B	0.26775	0.159	B	0.18263	0.021	T	0.06552	-1.0820	9	0.27082	T	0.32	.	2.268	0.04084	0.1192:0.3611:0.1562:0.3635	.	30	O95661	DIRA3_HUMAN	Q	30	ENSP00000360020:K30Q;ENSP00000378627:K30Q	ENSP00000360020:K30Q	K	-	1	0	DIRAS3	68285481	0.001000	0.12720	0.000000	0.03702	0.001000	0.01503	-0.537000	0.06128	-1.117000	0.02965	-0.468000	0.05107	AAG	.	.	none		0.607	DIRAS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026354.2	NM_004675	
USH2A	7399	hgsc.bcm.edu	37	1	215848587	215848587	+	Silent	SNP	T	T	C	rs2797234	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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						scavenged	.	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	184	1	0.00543478		WXS	Illumina HiSeq	Phase_I	156	72	0.461538	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	
ENPP2	5168	hgsc.bcm.edu	37	8	120594802	120594802	+	Silent	SNP	A	A	G	rs4871364	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:120594802A>G	ENST00000075322.6	-	18	1642	c.1584T>C	c.(1582-1584)caT>caC	p.H528H	ENPP2_ENST00000427067.2_Silent_p.H524H|ENPP2_ENST00000522167.1_Silent_p.H167H|ENPP2_ENST00000259486.6_Silent_p.H580H|ENPP2_ENST00000522826.1_Silent_p.H528H	NM_001040092.2	NP_001035181.1	Q13822	ENPP2_HUMAN	ectonucleotide pyrophosphatase/phosphodiesterase 2	528					cellular component movement (GO:0006928)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|phosphate-containing compound metabolic process (GO:0006796)|phosphatidylcholine catabolic process (GO:0034638)|phospholipid catabolic process (GO:0009395)|regulation of cell migration (GO:0030334)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	alkylglycerophosphoethanolamine phosphodiesterase activity (GO:0047391)|calcium ion binding (GO:0005509)|hydrolase activity (GO:0016787)|lysophospholipase activity (GO:0004622)|nucleic acid binding (GO:0003676)|nucleotide diphosphatase activity (GO:0004551)|phosphodiesterase I activity (GO:0004528)|polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(15)|lung(30)|ovary(2)|prostate(2)|skin(4)|upper_aerodigestive_tract(4)	69	Lung NSC(37;5.03e-06)|Ovarian(258;0.0249)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00185)			TCAAACTTCCATGGGTCCCAT	0.423													A|||	1329	0.265375	0.5227	0.1499	5008	,	,		18881	0.1389		0.174	False		,,,				2504	0.2239				p.H580H	Melanoma(20;305 879 2501 4818 31020)	Atlas-SNP	.											.	ENPP2	254	.	0			c.T1740C						PASS	.	A	,,	2179,2227	585.1+/-386.2	529,1121,553	159.0	163.0	161.0		1584,1584,1740	1.2	1.0	8	dbSNP_111	161	1559,7041	293.6+/-301.5	122,1315,2863	no	coding-synonymous,coding-synonymous,coding-synonymous	ENPP2	NM_001040092.1,NM_001130863.1,NM_006209.3	,,	651,2436,3416	GG,GA,AA		18.1279,49.4553,28.7406	,,	528/864,528/889,580/916	120594802	3738,9268	2203	4300	6503	SO:0001819	synonymous_variant	5168	exon19			ACTTCCATGGGTC	D45421	CCDS6329.1, CCDS34936.1, CCDS47914.1	8q24.12	2014-04-09	2008-08-01		ENSG00000136960	ENSG00000136960	3.1.4.1, 3.6.1.9		3357	protein-coding gene	gene with protein product	"""autotaxin"""	601060		PDNP2		8586446	Standard	NM_001040092		Approved	ATX, PD-IALPHA	uc003yos.2	Q13822	OTTHUMG00000164995	ENST00000075322.6:c.1584T>C	8.37:g.120594802A>G		Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	140	30	0.214286	NM_006209	A8UHA1|E9PHP7|Q13827|Q14555|Q15117|Q9UCQ8|Q9UCR0|Q9UCR1|Q9UCR2|Q9UCR3|Q9UCR4	Silent	SNP	ENST00000075322.6	37	CCDS34936.1																																																																																			A|0.735;G|0.265	0.265	strong		0.423	ENPP2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000381390.1		
MPP3	4356	hgsc.bcm.edu	37	17	41891437	41891437	+	Silent	SNP	G	G	A	rs17742929	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:41891437G>A	ENST00000398389.4	-	16	1362	c.1197C>T	c.(1195-1197)caC>caT	p.H399H	MPP3_ENST00000475450.1_5'UTR|MPP3_ENST00000398393.1_Silent_p.H424H	NM_001932.4	NP_001923.2	Q13368	MPP3_HUMAN	membrane protein, palmitoylated 3 (MAGUK p55 subfamily member 3)	399	Guanylate kinase-like. {ECO:0000255|PROSITE-ProRule:PRU00100}.				nucleotide phosphorylation (GO:0046939)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)	guanylate kinase activity (GO:0004385)			endometrium(2)|kidney(2)|large_intestine(5)|lung(11)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	26		Breast(137;0.00394)		BRCA - Breast invasive adenocarcinoma(366;0.119)		GCTTCAGCTCGTGCAGTCGGG	0.592													G|||	533	0.10643	0.025	0.1239	5008	,	,		18892	0.001		0.2505	False		,,,				2504	0.1646				p.H399H		Atlas-SNP	.											.	MPP3	42	.	0			c.C1197T						PASS	.	G		173,3755		4,165,1795	89.0	93.0	91.0		1197	-8.4	0.7	17	dbSNP_123	91	1791,6515		197,1397,2559	no	coding-synonymous	MPP3	NM_001932.4		201,1562,4354	AA,AG,GG		21.5627,4.4043,16.0536		399/586	41891437	1964,10270	1964	4153	6117	SO:0001819	synonymous_variant	4356	exon16			CAGCTCGTGCAGT		CCDS42344.1	17q12-q21	2008-07-18			ENSG00000161647	ENSG00000161647			7221	protein-coding gene	gene with protein product	"""MAGUK p55 subfamily member 3"", ""discs, large (Drosophila) homolog 3"", ""membrane protein palmitoylated 3"""	601114		DLG3		8824795	Standard	NR_003562		Approved		uc002iei.4	Q13368	OTTHUMG00000133838	ENST00000398389.4:c.1197C>T	17.37:g.41891437G>A		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	76	35	0.460526	NM_001932	B2R7N0|D3DX47|Q4GX05|Q6PGR3|Q86SV1	Silent	SNP	ENST00000398389.4	37	CCDS42344.1																																																																																			G|0.872;A|0.128	0.128	strong		0.592	MPP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258371.1	NM_001932	
RAET1L	154064	hgsc.bcm.edu	37	6	150342232	150342232	+	Missense_Mutation	SNP	G	G	A	rs61730071	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:150342232G>A	ENST00000367341.1	-	3	439	c.440C>T	c.(439-441)aCc>aTc	p.T147I	RAET1L_ENST00000286380.2_Missense_Mutation_p.T147I			Q5VY80	RET1L_HUMAN	retinoic acid early transcript 1L	147	MHC class I alpha-2 like. {ECO:0000250}.				antigen processing and presentation (GO:0019882)|immune response (GO:0006955)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)				endometrium(1)|large_intestine(1)|lung(1)|ovary(1)|skin(1)	5		Ovarian(120;0.028)	BRCA - Breast invasive adenocarcinoma(37;0.193)	OV - Ovarian serous cystadenocarcinoma(155;2.4e-12)		GAGTAGGAAGGTCTGTCCATC	0.502													A|||	1648	0.329073	0.3033	0.2925	5008	,	,		19640	0.2401		0.4394	False		,,,				2504	0.3681				p.T147I		Atlas-SNP	.											.	RAET1L	21	.	0			c.C440T						PASS	.	A	ILE/THR	1375,3031		217,941,1045	284.0	245.0	258.0		440	-0.8	0.0	6	dbSNP_129	258	3839,4761		854,2131,1315	yes	missense	RAET1L	NM_130900.2	89	1071,3072,2360	AA,AG,GG		44.6395,31.2074,40.0892	benign	147/247	150342232	5214,7792	2203	4300	6503	SO:0001583	missense	154064	exon3			AGGAAGGTCTGTC	AY039682	CCDS5224.1	6q24.1-25.1	2008-02-05			ENSG00000155918	ENSG00000155918			16798	protein-coding gene	gene with protein product		611047				11827464	Standard	NM_130900		Approved		uc011eei.2	Q5VY80	OTTHUMG00000015809	ENST00000367341.1:c.440C>T	6.37:g.150342232G>A	ENSP00000356310:p.Thr147Ile	Somatic	313	0	0		WXS	Illumina HiSeq	Phase_I	253	176	0.695652	NM_130900	A3KME4|Q8TE74	Missense_Mutation	SNP	ENST00000367341.1	37	CCDS5224.1	739	0.3383699633699634	153	0.31097560975609756	122	0.3370165745856354	125	0.21853146853146854	339	0.4472295514511873	N	0.003	-2.509455	0.00153	0.312074	0.446395	ENSG00000155918	ENST00000367341;ENST00000286380	T;T	0.00717	5.79;5.79	1.91	-0.819	0.10829	MHC class I, alpha chain, alpha1/alpha2 (1);MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);	.	.	.	.	T	0.00144	0.0004	N	0.04203	-0.255	0.80722	P	0.0	B	0.06786	0.001	B	0.06405	0.002	T	0.17806	-1.0357	8	0.27082	T	0.32	.	2.1695	0.03846	0.4177:0.0:0.3358:0.2465	.	147	Q5VY80	RET1L_HUMAN	I	147	ENSP00000356310:T147I;ENSP00000286380:T147I	ENSP00000286380:T147I	T	-	2	0	RAET1L	150383925	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.278000	0.02809	-0.646000	0.05452	-1.305000	0.01319	ACC	G|0.611;A|0.389	0.389	strong		0.502	RAET1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042676.1	NM_130900	
VWF	7450	hgsc.bcm.edu	37	12	6174423	6174423	+	Silent	SNP	T	T	A	rs1800375	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:6174423T>A	ENST00000261405.5	-	11	1427	c.1173A>T	c.(1171-1173)acA>acT	p.T391T		NM_000552.3	NP_000543	P04275	VWF_HUMAN	von Willebrand factor	391	VWFD 2. {ECO:0000255|PROSITE- ProRule:PRU00580}.				blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|cell adhesion (GO:0007155)|cell-substrate adhesion (GO:0031589)|extracellular matrix organization (GO:0030198)|hemostasis (GO:0007599)|liver development (GO:0001889)|placenta development (GO:0001890)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|protein homooligomerization (GO:0051260)|response to wounding (GO:0009611)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|proteinaceous extracellular matrix (GO:0005578)|Weibel-Palade body (GO:0033093)	chaperone binding (GO:0051087)|collagen binding (GO:0005518)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|immunoglobulin binding (GO:0019865)|integrin binding (GO:0005178)|protease binding (GO:0002020)|protein homodimerization activity (GO:0042803)|protein N-terminus binding (GO:0047485)	p.T391T(1)		NS(1)|breast(6)|central_nervous_system(5)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(25)|lung(41)|ovary(7)|pancreas(2)|prostate(6)|skin(15)|stomach(1)|upper_aerodigestive_tract(5)	129					Antihemophilic Factor(DB00025)	GTGATTGACCTGTGACAAGGC	0.552													T|||	1357	0.270966	0.5076	0.1297	5008	,	,		21004	0.247		0.1213	False		,,,				2504	0.2301				p.T391T		Atlas-SNP	.											VWF,NS,carcinoma,0,1	VWF	338	1	1	Substitution - coding silent(1)	stomach(1)	c.A1173T						PASS	.	T		2055,2351	564.0+/-381.3	506,1043,654	83.0	78.0	80.0		1173	-5.9	0.6	12	dbSNP_89	80	1092,7508	227.8+/-263.0	76,940,3284	no	coding-synonymous	VWF	NM_000552.3		582,1983,3938	AA,AT,TT		12.6977,46.6409,24.1965		391/2814	6174423	3147,9859	2203	4300	6503	SO:0001819	synonymous_variant	7450	exon11			TTGACCTGTGACA		CCDS8539.1	12p13.3	2014-09-17			ENSG00000110799	ENSG00000110799		"""Endogenous ligands"""	12726	protein-coding gene	gene with protein product		613160		F8VWF		2251280	Standard	NM_000552		Approved		uc001qnn.1	P04275	OTTHUMG00000168265	ENST00000261405.5:c.1173A>T	12.37:g.6174423T>A		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	48	48	1	NM_000552	Q8TCE8|Q99806	Silent	SNP	ENST00000261405.5	37	CCDS8539.1																																																																																			T|0.770;A|0.230	0.230	strong		0.552	VWF-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399020.1	NM_000552	
BMP3	651	hgsc.bcm.edu	37	4	81967150	81967150	+	Missense_Mutation	SNP	G	G	A	rs3733549	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:81967150G>A	ENST00000282701.2	+	2	895	c.575G>A	c.(574-576)cGa>cAa	p.R192Q		NM_001201.2	NP_001192.2	P12645	BMP3_HUMAN	bone morphogenetic protein 3	192			R -> Q (in dbSNP:rs3733549).		cartilage development (GO:0051216)|cell differentiation (GO:0030154)|cell-cell signaling (GO:0007267)|growth (GO:0040007)|ossification (GO:0001503)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|skeletal system development (GO:0001501)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	BMP receptor binding (GO:0070700)|receptor binding (GO:0005102)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(8)|ovary(4)|pancreas(1)|prostate(1)|stomach(1)|urinary_tract(1)	29						AAATCTCATCGAGATATTATG	0.413													G|||	641	0.127995	0.0681	0.1167	5008	,	,		20082	0.127		0.0716	False		,,,				2504	0.2761				p.R192Q		Atlas-SNP	.											.	BMP3	59	.	0			c.G575A						PASS	.	G	GLN/ARG	304,4102	163.6+/-195.4	13,278,1912	139.0	147.0	144.0		575	3.1	0.9	4	dbSNP_107	144	592,8008	157.2+/-210.9	18,556,3726	yes	missense	BMP3	NM_001201.2	43	31,834,5638	AA,AG,GG		6.8837,6.8997,6.8891	possibly-damaging	192/473	81967150	896,12110	2203	4300	6503	SO:0001583	missense	651	exon2			CTCATCGAGATAT	M22491	CCDS3588.1	4q21	2013-02-06	2008-05-22		ENSG00000152785	ENSG00000152785		"""Bone morphogenetic proteins"""	1070	protein-coding gene	gene with protein product	"""osteogenin"""	112263	"""bone morphogenetic protein 3 (osteogenic)"""				Standard	NM_001201		Approved		uc003hmg.4	P12645	OTTHUMG00000130292	ENST00000282701.2:c.575G>A	4.37:g.81967150G>A	ENSP00000282701:p.Arg192Gln	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	60	31	0.516667	NM_001201	Q4VAS5	Missense_Mutation	SNP	ENST00000282701.2	37	CCDS3588.1	201	0.09203296703296704	35	0.07113821138211382	43	0.11878453038674033	76	0.13286713286713286	47	0.06200527704485488	G	9.044	0.990414	0.18966	0.068997	0.068837	ENSG00000152785	ENST00000282701	T	0.73897	-0.79	4.84	3.12	0.35913	Transforming growth factor-beta, N-terminal (1);	0.278401	0.39341	N	0.001382	T	0.01320	0.0043	L	0.55834	1.745	0.25119	P	0.9906585	B	0.19817	0.039	B	0.15484	0.013	T	0.33163	-0.9879	9	0.23302	T	0.38	.	10.7924	0.46440	0.155:0.0:0.845:0.0	rs3733549;rs17005032;rs3733549	192	P12645	BMP3_HUMAN	Q	192	ENSP00000282701:R192Q	ENSP00000282701:R192Q	R	+	2	0	BMP3	82186174	0.999000	0.42202	0.857000	0.33713	0.003000	0.03518	2.498000	0.45363	0.777000	0.33496	-0.136000	0.14681	CGA	G|0.923;A|0.077	0.077	strong		0.413	BMP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252634.1		
CRYBB2	1415	hgsc.bcm.edu	37	22	25627604	25627604	+	Silent	SNP	G	G	A	rs8140949	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:25627604G>A	ENST00000398215.2	+	6	654	c.483G>A	c.(481-483)ggG>ggA	p.G161G		NM_000496.2	NP_000487.1	P43320	CRBB2_HUMAN	crystallin, beta B2	161	Beta/gamma crystallin 'Greek key' 4. {ECO:0000255|PROSITE-ProRule:PRU00028}.				camera-type eye development (GO:0043010)|response to stimulus (GO:0050896)|visual perception (GO:0007601)		identical protein binding (GO:0042802)|structural constituent of eye lens (GO:0005212)|structural molecule activity (GO:0005198)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(5)|skin(1)	10						GCTACCGTGGGCTGCAGTACC	0.632													G|||	1654	0.330272	0.2784	0.2839	5008	,	,		17136	0.4325		0.2058	False		,,,				2504	0.456				p.G161G		Atlas-SNP	.											.	CRYBB2	18	.	0			c.G483A						PASS	.	G		1214,3192	421.5+/-339.4	180,854,1169	98.0	91.0	94.0		483	0.6	1.0	22	dbSNP_116	94	1820,6780	326.6+/-317.4	202,1416,2682	no	coding-synonymous	CRYBB2	NM_000496.2		382,2270,3851	AA,AG,GG		21.1628,27.5533,23.3277		161/206	25627604	3034,9972	2203	4300	6503	SO:0001819	synonymous_variant	1415	exon6			CCGTGGGCTGCAG		CCDS13831.1	22q11.23	2008-06-10			ENSG00000244752	ENSG00000244752			2398	protein-coding gene	gene with protein product		123620		CCA2, CRYB2A, CRYB2		9158139, 8224918	Standard	XM_006724141		Approved		uc003abp.1	P43320	OTTHUMG00000150905	ENST00000398215.2:c.483G>A	22.37:g.25627604G>A		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	133	133	1	NM_000496	Q9UCM8	Silent	SNP	ENST00000398215.2	37	CCDS13831.1																																																																																			G|0.756;A|0.244	0.244	strong		0.632	CRYBB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320350.1	NM_000496	
GALNT7	51809	hgsc.bcm.edu	37	4	174090004	174090004	+	Silent	SNP	G	G	A	rs3733477	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:174090004G>A	ENST00000265000.4	+	1	101	c.18G>A	c.(16-18)ggG>ggA	p.G6G	GALNT7_ENST00000512285.1_Silent_p.G6G|RP11-10K16.1_ENST00000500914.2_RNA|RP11-10K16.1_ENST00000510523.1_RNA|RP11-10K16.1_ENST00000499322.2_RNA	NM_017423.2	NP_059119.2	Q86SF2	GALT7_HUMAN	polypeptide N-acetylgalactosaminyltransferase 7	6					carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein O-linked glycosylation (GO:0006493)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			central_nervous_system(1)|kidney(3)|large_intestine(5)|liver(1)|lung(9)	19		Prostate(90;0.0132)|Renal(120;0.0183)|Melanoma(52;0.0749)|all_hematologic(60;0.107)|all_neural(102;0.122)		all cancers(43;1.87e-18)|Epithelial(43;3.44e-17)|OV - Ovarian serous cystadenocarcinoma(60;2.48e-09)|STAD - Stomach adenocarcinoma(60;0.0019)|GBM - Glioblastoma multiforme(59;0.0119)|LUSC - Lung squamous cell carcinoma(193;0.0199)		TGAAGATTGGGTTCATCTTAC	0.667													G|||	3213	0.641573	0.5825	0.5231	5008	,	,		7096	0.7183		0.7018	False		,,,				2504	0.6646				p.G6G		Atlas-SNP	.											.	GALNT7	61	.	0			c.G18A						PASS	.	G		2679,1727	646.0+/-398.3	831,1017,355	150.0	132.0	138.0		18	2.2	1.0	4	dbSNP_107	138	5837,2763	677.0+/-403.3	1997,1843,460	no	coding-synonymous	GALNT7	NM_017423.2		2828,2860,815	AA,AG,GG		32.1279,39.1966,34.5225		6/658	174090004	8516,4490	2203	4300	6503	SO:0001819	synonymous_variant	51809	exon1			GATTGGGTTCATC	AJ002744	CCDS3815.1	4q31.1	2014-03-13	2014-03-13		ENSG00000109586	ENSG00000109586		"""Glycosyltransferase family 2 domain containing"""	4129	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase 7"""	605005	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 7 (GalNAc-T7)"""			10544240	Standard	NM_017423		Approved	GALNAC-T7	uc003isz.4	Q86SF2	OTTHUMG00000160817	ENST00000265000.4:c.18G>A	4.37:g.174090004G>A		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	72	72	1	NM_017423	B3KQU3|Q7Z5W7|Q9UJ28	Silent	SNP	ENST00000265000.4	37	CCDS3815.1																																																																																			T|0.000;G|0.353;A|0.647	0.647	strong		0.667	GALNT7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362456.2	NM_017423	
GPR88	54112	hgsc.bcm.edu	37	1	101005554	101005554	+	Silent	SNP	C	C	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:101005554C>A	ENST00000315033.4	+	2	1471	c.1032C>A	c.(1030-1032)cgC>cgA	p.R344R		NM_022049.2	NP_071332.2	Q9GZN0	GPR88_HUMAN	G protein-coupled receptor 88	344					G-protein coupled receptor signaling pathway (GO:0007186)|locomotory behavior (GO:0007626)|neuromuscular process controlling balance (GO:0050885)|neuronal action potential (GO:0019228)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			large_intestine(2)|skin(1)	3		all_epithelial(167;1.19e-05)|all_lung(203;0.00159)|Lung NSC(277;0.00171)		Epithelial(280;0.0372)|all cancers(265;0.0558)|COAD - Colon adenocarcinoma(174;0.141)|Colorectal(144;0.156)|Lung(183;0.189)		AGGAGTTCCGCCGCTCCGTGC	0.736																																					p.R344R		Atlas-SNP	.											.	GPR88	17	.	0			c.C1032A						PASS	.						5.0	6.0	6.0					1																	101005554		2049	4046	6095	SO:0001819	synonymous_variant	54112	exon2			GTTCCGCCGCTCC	AB042411	CCDS772.1	1p21.3	2012-08-21	2006-02-15		ENSG00000181656	ENSG00000181656		"""GPCR / Class A : Orphans"""	4539	protein-coding gene	gene with protein product		607468	"""G-protein coupled receptor 88"", ""G protein coupled receptor 88"""				Standard	NM_022049		Approved		uc001dth.3	Q9GZN0	OTTHUMG00000010981	ENST00000315033.4:c.1032C>A	1.37:g.101005554C>A		Somatic	5	0	0		WXS	Illumina HiSeq	Phase_I	16	5	0.3125	NM_022049	Q29S24|Q6VN48	Silent	SNP	ENST00000315033.4	37	CCDS772.1																																																																																			.	.	none		0.736	GPR88-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030212.1	NM_022049	
SCUBE2	57758	hgsc.bcm.edu	37	11	9051475	9051475	+	Missense_Mutation	SNP	G	G	C	rs3751057	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:9051475G>C	ENST00000309263.3	-	18	2444	c.2372C>G	c.(2371-2373)aCt>aGt	p.T791S	SCUBE2_ENST00000520467.1_Missense_Mutation_p.T763S|SCUBE2_ENST00000450649.2_Missense_Mutation_p.T665S|SCUBE2_ENST00000457346.2_Missense_Mutation_p.T820S|RP11-467K18.2_ENST00000531592.1_RNA			Q9NQ36	SCUB2_HUMAN	signal peptide, CUB domain, EGF-like 2	791			T -> S (in dbSNP:rs3751057).			extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			breast(1)|endometrium(5)|kidney(3)|large_intestine(15)|liver(1)|lung(10)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	42				all cancers(16;8.57e-09)|Epithelial(150;4.42e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0116)		GTCAGTCGTAGTATTTCCTGG	0.433													G|||	475	0.0948482	0.1097	0.0519	5008	,	,		20560	0.121		0.0676	False		,,,				2504	0.1063				p.T763S		Atlas-SNP	.											.	SCUBE2	102	.	0			c.C2288G						PASS	.	G	SER/THR,SER/THR	476,3926	226.2+/-241.8	20,436,1745	208.0	202.0	204.0		1994,2288	5.2	1.0	11	dbSNP_107	204	703,7889	173.2+/-223.7	27,649,3620	yes	missense,missense	SCUBE2	NM_001170690.1,NM_020974.2	58,58	47,1085,5365	CC,CG,GG		8.182,10.8133,9.0734	probably-damaging,probably-damaging	665/808,763/972	9051475	1179,11815	2201	4296	6497	SO:0001583	missense	57758	exon18			GTCGTAGTATTTC	AK131552	CCDS7797.1, CCDS7797.2, CCDS53599.1	11p15.4	2014-09-04			ENSG00000175356	ENSG00000175356			30425	protein-coding gene	gene with protein product		611747				12270931, 11528127	Standard	NM_020974		Approved	Cegf1, Cegb1, FLJ16792	uc001mhi.2	Q9NQ36	OTTHUMG00000163880	ENST00000309263.3:c.2372C>G	11.37:g.9051475G>C	ENSP00000310658:p.Thr791Ser	Somatic	309	0	0		WXS	Illumina HiSeq	Phase_I	350	60	0.171429	NM_020974	Q2NKQ8|Q6ZWI1	Missense_Mutation	SNP	ENST00000309263.3	37		176	0.08058608058608059	57	0.11585365853658537	17	0.04696132596685083	53	0.09265734265734266	49	0.06464379947229551	G	26.1	4.705731	0.89018	0.108133	0.08182	ENSG00000175356	ENST00000457346;ENST00000309263;ENST00000450649;ENST00000520467	T;T;T;T	0.63096	-0.02;-0.02;-0.02;-0.02	5.19	5.19	0.71726	Tyrosine-protein kinase ephrin type A/B receptor-like (1);Growth factor, receptor (1);	0.000000	0.85682	D	0.000000	T	0.06050	0.0157	M	0.84585	2.705	0.09310	P	0.9999999293489	D;D;D	0.89917	0.998;1.0;1.0	D;D;D	0.91635	0.994;0.999;0.999	T	0.55127	-0.8189	9	0.62326	D	0.03	.	18.7036	0.91630	0.0:0.0:1.0:0.0	rs3751057;rs52803158;rs56444362;rs3751057	665;763;791	Q9NQ36-3;Q9NQ36-2;Q9NQ36	.;.;SCUB2_HUMAN	S	820;791;665;763	ENSP00000390481:T820S;ENSP00000310658:T791S;ENSP00000415187:T665S;ENSP00000429969:T763S	ENSP00000310658:T791S	T	-	2	0	SCUBE2	9008051	1.000000	0.71417	0.964000	0.40570	0.981000	0.71138	7.879000	0.87236	2.415000	0.81967	0.491000	0.48974	ACT	G|0.908;C|0.092	0.092	strong		0.433	SCUBE2-005	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000385812.2	NM_020974	
CCDC37	348807	hgsc.bcm.edu	37	3	126137558	126137558	+	Silent	SNP	C	C	T	rs4679242|rs386665601	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:126137558C>T	ENST00000352312.1	+	7	690	c.591C>T	c.(589-591)gcC>gcT	p.A197A	CCDC37_ENST00000393425.1_Silent_p.A198A|CCDC37_ENST00000505024.1_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	86	0	0		WXS	Illumina HiSeq	Phase_I	67	28	0.41791	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	
PJA2	9867	hgsc.bcm.edu	37	5	108672946	108672946	+	Missense_Mutation	SNP	C	C	T	rs246105	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:108672946C>T	ENST00000361189.2	-	10	2352	c.2113G>A	c.(2113-2115)Gca>Aca	p.A705T	PJA2_ENST00000361557.3_Missense_Mutation_p.A705T	NM_014819.4	NP_055634.3	O43164	PJA2_HUMAN	praja ring finger 2, E3 ubiquitin protein ligase	705	Interaction with PRKAR1A, PRKAR2A and PRKAR2B.		A -> T (in dbSNP:rs246105).		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)		GGTGCTTCTGCAATACTGTCA	0.423													C|||	1497	0.298922	0.1172	0.2781	5008	,	,		14077	0.5565		0.2475	False		,,,				2504	0.3466				p.A705T		Atlas-SNP	.											.	PJA2	53	.	0			c.G2113A						PASS	.	C	THR/ALA	713,3691	293.8+/-282.8	67,579,1556	100.0	97.0	98.0		2113	0.4	0.0	5	dbSNP_79	98	2016,6584	352.2+/-328.6	242,1532,2526	yes	missense	PJA2	NM_014819.4	58	309,2111,4082	TT,TC,CC		23.4419,16.1898,20.9859	benign	705/709	108672946	2729,10275	2202	4300	6502	SO:0001583	missense	9867	exon10			CTTCTGCAATACT	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.2113G>A	5.37:g.108672946C>T	ENSP00000354775:p.Ala705Thr	Somatic	188	0	0		WXS	Illumina HiSeq	Phase_I	189	86	0.455026	NM_014819	A8K6U4|D3DSZ5|Q68D49|Q8N1G5	Missense_Mutation	SNP	ENST00000361189.2	37	CCDS4099.1	687	0.31456043956043955	64	0.13008130081300814	96	0.26519337016574585	338	0.5909090909090909	189	0.24934036939313983	C	12.36	1.913297	0.33815	0.161898	0.234419	ENSG00000198961	ENST00000361189;ENST00000361557	T;T	0.11169	2.8;2.8	5.9	0.451	0.16629	.	0.691756	0.13453	N	0.386738	T	0.00012	0.0000	N	0.08118	0	0.51482	P	7.299999999998974E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.30475	-0.9977	9	0.48119	T	0.1	-5.7798	3.7465	0.08549	0.2706:0.3504:0.0:0.379	rs246105;rs17292734;rs17745933;rs58995813;rs246105	705	O43164	PJA2_HUMAN	T	705	ENSP00000354775:A705T;ENSP00000355284:A705T	ENSP00000354775:A705T	A	-	1	0	PJA2	108700845	0.225000	0.23685	0.026000	0.17262	0.307000	0.27823	0.041000	0.13927	0.125000	0.18397	0.650000	0.86243	GCA	C|0.735;T|0.265	0.265	strong		0.423	PJA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250663.1	NM_014819	
ADRM1	11047	hgsc.bcm.edu	37	20	60883192	60883192	+	Silent	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:60883192G>A	ENST00000253003.2	+	8	1018	c.972G>A	c.(970-972)gcG>gcA	p.A324A	RP11-157P1.4_ENST00000414042.1_RNA|LAMA5_ENST00000492698.1_5'UTR	NM_007002.2|NM_175573.1	NP_008933.2|NP_783163.1	Q16186	ADRM1_HUMAN	adhesion regulating molecule 1	324					positive regulation of endopeptidase activity (GO:0010950)|proteasome assembly (GO:0043248)|transcription elongation from RNA polymerase II promoter (GO:0006368)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|proteasome complex (GO:0000502)	endopeptidase activator activity (GO:0061133)|protease binding (GO:0002020)|proteasome binding (GO:0070628)			central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|urinary_tract(1)	5	Breast(26;7.76e-09)		BRCA - Breast invasive adenocarcinoma(19;2.51e-06)			CGCAGACCGCGGATGAGATCC	0.652																																					p.A324A		Atlas-SNP	.											.	ADRM1	28	.	0			c.G972A						PASS	.						39.0	39.0	39.0					20																	60883192		2199	4295	6494	SO:0001819	synonymous_variant	11047	exon8			GACCGCGGATGAG	D64154	CCDS13496.1, CCDS74747.1	20q13.33	2008-05-22			ENSG00000130706	ENSG00000130706			15759	protein-coding gene	gene with protein product		610650				8033103	Standard	NM_007002		Approved	GP110, Rpn13, ARM1	uc002yco.3	Q16186	OTTHUMG00000032904	ENST00000253003.2:c.972G>A	20.37:g.60883192G>A		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	48	12	0.25	NM_175573	A0PKB1|Q96FJ7|Q9H1P2	Silent	SNP	ENST00000253003.2	37	CCDS13496.1																																																																																			.	.	none		0.652	ADRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080007.1		
GSTA2	2939	hgsc.bcm.edu	37	6	52617738	52617738	+	Missense_Mutation	SNP	G	G	A	rs2234951	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	172	0	0		WXS	Illumina HiSeq	Phase_I	158	88	0.556962	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	
ABCB5	340273	hgsc.bcm.edu	37	7	20767981	20767981	+	Missense_Mutation	SNP	T	T	C	rs117749018	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:20767981T>C	ENST00000404938.2	+	23	3422	c.2770T>C	c.(2770-2772)Ttc>Ctc	p.F924L	ABCB5_ENST00000258738.6_Missense_Mutation_p.F479L	NM_001163941.1	NP_001157413.1	Q2M3G0	ABCB5_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 5	924	ABC transmembrane type-1 2. {ECO:0000255|PROSITE-ProRule:PRU00441}.				antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent (GO:0002485)|antigen processing and presentation of endogenous peptide antigen via MHC class Ib via ER pathway, TAP-dependent (GO:0002489)|antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent (GO:0002481)|cell differentiation (GO:0030154)|compound eye corneal lens development (GO:0048058)|positive regulation of antigen processing and presentation of peptide antigen via MHC class I (GO:0002591)|regulation of membrane potential (GO:0042391)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|efflux transmembrane transporter activity (GO:0015562)			breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(11)|liver(1)|lung(37)|ovary(1)|pancreas(1)|prostate(1)|skin(10)|upper_aerodigestive_tract(1)	77						CTGTTATGCATTCAGCCATGC	0.393													T|||	23	0.00459265	0.0	0.0072	5008	,	,		18255	0.0		0.0109	False		,,,				2504	0.0072				p.F924L		Atlas-SNP	.											.	ABCB5	357	.	0			c.T2770C						PASS	.	T	LEU/PHE,LEU/PHE	13,4393	20.2+/-43.8	0,13,2190	150.0	154.0	153.0		2770,1435	2.7	1.0	7	dbSNP_132	153	103,8497	56.8+/-118.0	0,103,4197	yes	missense,missense	ABCB5	NM_001163941.1,NM_178559.5	22,22	0,116,6387	CC,CT,TT		1.1977,0.2951,0.8919	benign,benign	924/1258,479/813	20767981	116,12890	2203	4300	6503	SO:0001583	missense	340273	exon23			TATGCATTCAGCC	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.2770T>C	7.37:g.20767981T>C	ENSP00000384881:p.Phe924Leu	Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	134	31	0.231343	NM_001163941	A4D131|A7BKA4|B5MD19|B7WPL1|F8QQP8|F8QQP9|J3KQ04|Q2M3I5|Q5I5Q7|Q5I5Q8|Q6KG50|Q6XFQ5|Q8IXA1	Missense_Mutation	SNP	ENST00000404938.2	37	CCDS55090.1	10	0.004578754578754579	0	0.0	1	0.0027624309392265192	0	0.0	9	0.011873350923482849	T	11.75	1.732023	0.30684	0.002951	0.011977	ENSG00000004846	ENST00000404938;ENST00000258738	D;D	0.90133	-2.62;-2.62	3.91	2.73	0.32206	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1);	0.220353	0.30464	N	0.009574	T	0.73345	0.3575	N	0.17474	0.49	0.29103	N	0.881356	B;B;B	0.16802	0.019;0.0;0.004	B;B;B	0.23150	0.044;0.005;0.02	T	0.64141	-0.6477	10	0.25751	T	0.34	.	4.4745	0.11729	0.1917:0.0:0.2168:0.5914	.	924;102;479	A7BKA4;A0ASV4;Q2M3G0	.;.;ABCB5_HUMAN	L	924;479	ENSP00000384881:F924L;ENSP00000258738:F479L	ENSP00000258738:F479L	F	+	1	0	ABCB5	20734506	0.810000	0.29049	0.998000	0.56505	0.990000	0.78478	1.014000	0.29950	0.827000	0.34685	0.533000	0.62120	TTC	T|0.992;C|0.008	0.008	strong		0.393	ABCB5-004	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000326736.2	NM_178559	
ARHGEF11	9826	hgsc.bcm.edu	37	1	156907081	156907081	+	Missense_Mutation	SNP	T	T	C	rs945508	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:156907081T>C	ENST00000361409.2	-	38	5022	c.4280A>G	c.(4279-4281)cAt>cGt	p.H1427R	ARHGEF11_ENST00000487682.1_5'UTR|ARHGEF11_ENST00000315174.8_Missense_Mutation_p.H843R|ARHGEF11_ENST00000368194.3_Missense_Mutation_p.H1467R|MIR765_ENST00000390226.1_RNA	NM_014784.3	NP_055599.1	O15085	ARHGB_HUMAN	Rho guanine nucleotide exchange factor (GEF) 11	1427			H -> R (in dbSNP:rs945508). {ECO:0000269|Ref.3}.		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)					CTCAATGGTATGGAAGATCAT	0.597													C|||	3818	0.76238	0.888	0.7233	5008	,	,		19155	0.8512		0.5517	False		,,,				2504	0.7454				p.H1467R		Atlas-SNP	.											.	ARHGEF11	168	.	0			c.A4400G	GRCh37	CM074015	ARHGEF11	M	rs945508	PASS	.	C	ARG/HIS,ARG/HIS	3701,705	293.0+/-282.3	1557,587,59	88.0	83.0	85.0		4280,4400	-1.6	0.0	1	dbSNP_86	85	4757,3843	539.8+/-383.7	1320,2117,863	yes	missense,missense	ARHGEF11	NM_014784.2,NM_198236.1	29,29	2877,2704,922	CC,CT,TT		44.686,16.0009,34.9685	benign,benign	1427/1523,1467/1563	156907081	8458,4548	2203	4300	6503	SO:0001583	missense	9826	exon39			ATGGTATGGAAGA	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.4280A>G	1.37:g.156907081T>C	ENSP00000354644:p.His1427Arg	Somatic	282	0	0		WXS	Illumina HiSeq	Phase_I	211	210	0.995261	NM_198236	D3DVD0|Q5VY40|Q6PFW2	Missense_Mutation	SNP	ENST00000361409.2	37	CCDS1162.1	1587	0.7266483516483516	440	0.8943089430894309	244	0.6740331491712708	486	0.8496503496503497	417	0.5501319261213721	C	0.894	-0.724522	0.03158	0.839991	0.55314	ENSG00000132694	ENST00000368194;ENST00000361409;ENST00000315174	T;T;T	0.64618	-0.11;-0.1;-0.04	5.33	-1.64	0.08318	.	0.989663	0.08214	N	0.980184	T	0.13670	0.0331	N	0.08118	0	0.58432	P	1.0000000000287557E-6	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.0;0.001	T	0.19451	-1.0305	9	0.02654	T	1	-0.8299	11.2722	0.49147	0.0:0.4578:0.0:0.5422	rs945508;rs57261442;rs945508	843;1427;1467	F8W8P9;O15085;O15085-2	.;ARHGB_HUMAN;.	R	1467;1427;843	ENSP00000357177:H1467R;ENSP00000354644:H1427R;ENSP00000313470:H843R	ENSP00000313470:H843R	H	-	2	0	ARHGEF11	155173705	0.000000	0.05858	0.007000	0.13788	0.905000	0.53344	-0.502000	0.06390	-0.682000	0.05197	-0.215000	0.12644	CAT	T|0.310;C|0.690	0.690	strong		0.597	ARHGEF11-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000098931.1	NM_198236	
ABCC5	10057	hgsc.bcm.edu	37	3	183699516	183699516	+	Splice_Site	SNP	T	T	C	rs7636910	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:183699516T>C	ENST00000334444.6	-	8	1386	c.1146A>G	c.(1144-1146)caA>caG	p.Q382Q	ABCC5_ENST00000492216.1_5'UTR|ABCC5_ENST00000265586.6_Splice_Site_p.Q382Q	NM_005688.2	NP_005679.2	O15440	MRP5_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 5	382	ABC transmembrane type-1 1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan biosynthetic process (GO:0030213)|hyaluronan metabolic process (GO:0030212)|organic anion transport (GO:0015711)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|organic anion transmembrane transporter activity (GO:0008514)	p.Q382Q(1)		NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(32)|ovary(3)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	62	all_cancers(143;1.85e-10)|Ovarian(172;0.0303)		Epithelial(37;1.74e-35)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)		Adefovir Dipivoxil(DB00718)|Alprostadil(DB00770)|Atorvastatin(DB01076)|Cisplatin(DB00515)|Dinoprostone(DB00917)|Dipyridamole(DB00975)|Fluorouracil(DB00544)|Glutathione(DB00143)|Mercaptopurine(DB01033)|Probenecid(DB01032)|Rifampicin(DB01045)|Sildenafil(DB00203)|Sulfinpyrazone(DB01138)|Zidovudine(DB00495)	TAAACTCACTTTGAACACTCT	0.378													T|||	1674	0.334265	0.2224	0.2925	5008	,	,		20737	0.4167		0.3867	False		,,,				2504	0.3763				p.Q382Q		Atlas-SNP	.											ABCC5,NS,carcinoma,0,1	ABCC5	142	1	1	Substitution - coding silent(1)	stomach(1)	c.A1146G						PASS	.	T		1026,2724		144,738,993	96.0	94.0	94.0		1146	4.6	1.0	3	dbSNP_116	94	3065,5149		562,1941,1604	yes	coding-synonymous-near-splice	ABCC5	NM_005688.2		706,2679,2597	CC,CT,TT		37.3143,27.36,34.1942		382/1438	183699516	4091,7873	1875	4107	5982	SO:0001630	splice_region_variant	10057	exon8			CTCACTTTGAACA	AF104942	CCDS33898.1, CCDS43176.1	3q27	2012-03-14			ENSG00000114770	ENSG00000114770		"""ATP binding cassette transporters / subfamily C"""	56	protein-coding gene	gene with protein product		605251				8894702, 9827529	Standard	XM_005247058		Approved	MRP5, SMRP, EST277145, MOAT-C	uc003fmg.3	O15440	OTTHUMG00000156871	ENST00000334444.6:c.1147+1A>G	3.37:g.183699516T>C		Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	114	60	0.526316	NM_005688	B9EIQ2|O14517|Q29ZA9|Q29ZB1|Q86UX3|Q86W30|Q9UN85|Q9UNP5|Q9UQC3	Silent	SNP	ENST00000334444.6	37	CCDS43176.1																																																																																			T|0.657;C|0.343	0.343	strong		0.378	ABCC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346350.1	NM_005688	Silent
TMEM86B	255043	hgsc.bcm.edu	37	19	55739605	55739605	+	Silent	SNP	C	C	T	rs4606850	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:55739605C>T	ENST00000327042.4	-	2	774	c.252G>A	c.(250-252)tcG>tcA	p.S84S	AC010327.2_ENST00000598855.1_3'UTR	NM_173804.4	NP_776165.3	Q8N661	TM86B_HUMAN	transmembrane protein 86B	84					ether lipid metabolic process (GO:0046485)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	alkenylglycerophosphocholine hydrolase activity (GO:0047408)|alkenylglycerophosphoethanolamine hydrolase activity (GO:0047409)			skin(2)	2			BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0443)		CCCCCACAGCCGAGCACACAA	0.657													C|||	842	0.168131	0.1989	0.2205	5008	,	,		16486	0.0754		0.1968	False		,,,				2504	0.1554				p.S84S		Atlas-SNP	.											.	TMEM86B	12	.	0			c.G252A						PASS	.	C		816,3588		68,680,1454	29.0	30.0	30.0		252	-10.8	0.0	19	dbSNP_111	30	1723,6877		180,1363,2757	no	coding-synonymous	TMEM86B	NM_173804.4		248,2043,4211	TT,TC,CC		20.0349,18.5286,19.5248		84/227	55739605	2539,10465	2202	4300	6502	SO:0001819	synonymous_variant	255043	exon2			CACAGCCGAGCAC	BC023000	CCDS12920.1	19q13.42	2011-07-12					3.3.2.2, 3.3.2.5		28448	protein-coding gene	gene with protein product						21515882	Standard	NM_173804		Approved	MGC30208	uc002qju.3	Q8N661		ENST00000327042.4:c.252G>A	19.37:g.55739605C>T		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	67	26	0.38806	NM_173804		Silent	SNP	ENST00000327042.4	37	CCDS12920.1																																																																																			C|0.829;T|0.171	0.171	strong		0.657	TMEM86B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452659.1	NM_173804	
TTC3	7267	hgsc.bcm.edu	37	21	38563639	38563639	+	Missense_Mutation	SNP	C	C	T	rs61740519	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:38563639C>T	ENST00000399017.2	+	40	7776	c.5029C>T	c.(5029-5031)Cct>Tct	p.P1677S	TTC3_ENST00000479930.1_3'UTR|TTC3-AS1_ENST00000424733.1_RNA|TTC3_ENST00000354749.2_Missense_Mutation_p.P1677S|TTC3_ENST00000355666.1_Missense_Mutation_p.P1677S	NM_003316.3	NP_003307.3	P53804	TTC3_HUMAN	tetratricopeptide repeat domain 3	1677					negative regulation of cell morphogenesis involved in differentiation (GO:0010771)|negative regulation of neuron differentiation (GO:0045665)|protein K48-linked ubiquitination (GO:0070936)|ubiquitin-dependent protein catabolic process (GO:0006511)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|vacuole (GO:0005773)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(5)|endometrium(7)|kidney(5)|large_intestine(17)|liver(1)|lung(18)|ovary(4)|prostate(2)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(5)	75		Myeloproliferative disorder(46;0.0412)				TTTCAGTGATCCTGCAGCATA	0.299													C|||	86	0.0171725	0.025	0.0274	5008	,	,		13496	0.0		0.0288	False		,,,				2504	0.0051				p.P1677S	Ovarian(38;194 1649 35661)	Atlas-SNP	.											.	TTC3	182	.	0			c.C5029T						PASS	.	C	SER/PRO,SER/PRO	133,4271	95.3+/-134.0	1,131,2070	40.0	38.0	39.0		5029,5029	1.0	0.5	21	dbSNP_129	39	235,8345	93.5+/-155.5	3,229,4058	no	missense,missense	TTC3	NM_001001894.1,NM_003316.3	74,74	4,360,6128	TT,TC,CC		2.7389,3.02,2.8343	benign,benign	1677/2026,1677/2026	38563639	368,12616	2202	4290	6492	SO:0001583	missense	7267	exon40			AGTGATCCTGCAG	D84296	CCDS13651.1	21q22.2	2013-01-11			ENSG00000182670	ENSG00000182670		"""RING-type (C3HC4) zinc fingers"", ""Tetratricopeptide (TTC) repeat domain containing"""	12393	protein-coding gene	gene with protein product		602259				8947847	Standard	NM_003316		Approved	TPRD, TPRDI, DCRR1, TPRDII, TPRDIII, RNF105	uc002yvz.3	P53804	OTTHUMG00000086654	ENST00000399017.2:c.5029C>T	21.37:g.38563639C>T	ENSP00000381981:p.Pro1677Ser	Somatic	226	0	0		WXS	Illumina HiSeq	Phase_I	246	139	0.565041	NM_001001894	A8K7H7|B2RPA7|D3DSG9|D3DSH2|D3DSH3|O60767|P78476|P78477|Q569I2|Q6P578|Q9UEK4	Missense_Mutation	SNP	ENST00000399017.2	37	CCDS13651.1	46|46	0.021062271062271064|0.021062271062271064	13|13	0.026422764227642278|0.026422764227642278	10|10	0.027624309392265192|0.027624309392265192	0|0	0.0|0.0	23|23	0.030343007915567283|0.030343007915567283	C|C	1.347|1.347	-0.592473|-0.592473	0.03799|0.03799	0.0302|0.0302	0.027389|0.027389	ENSG00000182670|ENSG00000182670	ENST00000355666;ENST00000399017;ENST00000354749|ENST00000428693	T;T;T|.	0.07567|.	3.18;3.18;3.18|.	5.31|5.31	0.969|0.969	0.19686|0.19686	.|.	0.399010|.	0.21452|.	N|.	0.074308|.	T|T	0.01976|0.01976	0.0062|0.0062	N|N	0.00263|0.00263	-1.745|-1.745	0.28063|0.28063	N|N	0.932901|0.932901	B|.	0.02656|.	0.0|.	B|.	0.01281|.	0.0|.	T|T	0.36768|0.36768	-0.9734|-0.9734	10|5	0.02654|.	T|.	1|.	-0.7894|-0.7894	7.386|7.386	0.26882|0.26882	0.0:0.2956:0.0:0.7044|0.0:0.2956:0.0:0.7044	rs61740519|rs61740519	1677|.	P53804|.	TTC3_HUMAN|.	S|F	1677|2	ENSP00000347889:P1677S;ENSP00000381981:P1677S;ENSP00000346791:P1677S|.	ENSP00000346791:P1677S|.	P|S	+|+	1|2	0|0	TTC3|TTC3	37485509|37485509	0.147000|0.147000	0.22687|0.22687	0.465000|0.465000	0.27155|0.27155	0.973000|0.973000	0.67179|0.67179	0.746000|0.746000	0.26275|0.26275	0.025000|0.025000	0.15241|0.15241	-0.300000|-0.300000	0.09419|0.09419	CCT|TCC	C|0.974;T|0.026	0.026	strong		0.299	TTC3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194776.1		
ZNF283	284349	hgsc.bcm.edu	37	19	44352639	44352639	+	Missense_Mutation	SNP	G	G	A	rs1061768	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:44352639G>A	ENST00000324461.7	+	7	2183	c.1886G>A	c.(1885-1887)cGt>cAt	p.R629H	ZNF283_ENST00000588797.1_Missense_Mutation_p.R490H	NM_181845.1	NP_862828.1	Q8N7M2	ZN283_HUMAN	zinc finger protein 283	629			R -> H (in dbSNP:rs1061768).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|large_intestine(3)|lung(4)	8		Prostate(69;0.0352)				CTTTATCAACGTAAGGAATTC	0.398													G|||	750	0.14976	0.1316	0.1787	5008	,	,		20278	0.0744		0.2227	False		,,,				2504	0.1564				p.R629H		Atlas-SNP	.											.	ZNF283	83	.	0			c.G1886A						PASS	.	G	HIS/ARG	565,3571		23,519,1526	102.0	110.0	107.0		1886	2.6	0.2	19	dbSNP_86	107	1754,6704		175,1404,2650	yes	missense	ZNF283	NM_181845.1	29	198,1923,4176	AA,AG,GG		20.7378,13.6605,18.4135	benign	629/680	44352639	2319,10275	2068	4229	6297	SO:0001583	missense	284349	exon7			ATCAACGTAAGGA	AK098175	CCDS46097.1, CCDS74387.1	19q13.31	2013-01-08			ENSG00000167637	ENSG00000167637		"""Zinc fingers, C2H2-type"", ""-"""	13077	protein-coding gene	gene with protein product						12743021	Standard	NM_181845		Approved		uc002oxr.4	Q8N7M2		ENST00000324461.7:c.1886G>A	19.37:g.44352639G>A	ENSP00000327314:p.Arg629His	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	57	21	0.368421	NM_181845	B4DGZ5|B7WP04|Q6RFR9|Q86WM6	Missense_Mutation	SNP	ENST00000324461.7	37	CCDS46097.1	357	0.16346153846153846	83	0.16869918699186992	53	0.1464088397790055	45	0.07867132867132867	176	0.23218997361477572	G	12.00	1.805208	0.31961	0.136605	0.207378	ENSG00000167637	ENST00000324461	T	0.14766	2.48	2.61	2.61	0.31194	Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	N	0.11201	0.11	0.09310	P	1.0	P	0.36660	0.564	B	0.31337	0.128	T	0.42716	-0.9435	8	0.87932	D	0	.	12.3634	0.55215	0.0:0.0:1.0:0.0	rs1061768;rs3170394;rs56865400;rs1061768	629	Q8N7M2	ZN283_HUMAN	H	629	ENSP00000327314:R629H	ENSP00000327314:R629H	R	+	2	0	ZNF283	49044479	0.986000	0.35501	0.234000	0.24042	0.459000	0.32528	3.677000	0.54619	1.440000	0.47531	0.563000	0.77884	CGT	G|0.832;A|0.168	0.168	strong		0.398	ZNF283-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459909.1	NM_181845	
PLA2G3	50487	hgsc.bcm.edu	37	22	31532960	31532960	+	Missense_Mutation	SNP	C	C	T	rs2232183	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:31532960C>T	ENST00000215885.3	-	5	1385	c.1133G>A	c.(1132-1134)cGg>cAg	p.R378Q		NM_015715.3	NP_056530.2	Q9NZ20	PA2G3_HUMAN	phospholipase A2, group III	378			R -> Q (in dbSNP:rs2232183).		acrosome assembly (GO:0001675)|cilium morphogenesis (GO:0060271)|glycerophospholipid biosynthetic process (GO:0046474)|lipid catabolic process (GO:0016042)|lipoxygenase pathway (GO:0019372)|mast cell degranulation (GO:0043303)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|sperm axoneme assembly (GO:0007288)	centriole (GO:0005814)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|mast cell granule (GO:0042629)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|calcium-dependent phospholipase A2 activity (GO:0047498)			large_intestine(1)|lung(10)|ovary(1)|prostate(2)|skin(3)|urinary_tract(1)	18						CTCGATTTCCCGGGGCCCAAT	0.662													T|||	670	0.133786	0.0772	0.1657	5008	,	,		17246	0.0238		0.2505	False		,,,				2504	0.181				p.R378Q		Atlas-SNP	.											.	PLA2G3	85	.	0			c.G1133A						PASS	.	T	GLN/ARG	460,3934		30,400,1767	36.0	36.0	36.0		1133	2.3	1.0	22	dbSNP_98	36	2196,6386		287,1622,2382	yes	missense	PLA2G3	NM_015715.3	43	317,2022,4149	TT,TC,CC		25.5884,10.4688,20.4686	benign	378/510	31532960	2656,10320	2197	4291	6488	SO:0001583	missense	50487	exon5			ATTTCCCGGGGCC	AF220490	CCDS13889.1	22q12.2	2008-09-19			ENSG00000100078	ENSG00000100078	3.1.1.4		17934	protein-coding gene	gene with protein product		611651				10713052	Standard	NM_015715		Approved	GIII-SPLA2	uc003aka.3	Q9NZ20	OTTHUMG00000151255	ENST00000215885.3:c.1133G>A	22.37:g.31532960C>T	ENSP00000215885:p.Arg378Gln	Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	165	73	0.442424	NM_015715	O95768	Missense_Mutation	SNP	ENST00000215885.3	37	CCDS13889.1	321	0.14697802197802198	42	0.08536585365853659	72	0.19889502762430938	17	0.02972027972027972	190	0.25065963060686014	T	2.164	-0.391533	0.04932	0.104688	0.255884	ENSG00000100078	ENST00000215885	T	0.28255	1.62	5.62	2.33	0.28932	Phospholipase A2 (2);	0.413631	0.24370	N	0.039117	T	0.00012	0.0000	N	0.00358	-1.6	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.42481	-0.9449	9	0.02654	T	1	-0.8315	8.7555	0.34643	0.0:0.2921:0.0:0.7079	rs2232183;rs17760495;rs52823364;rs57463724;rs2232183	378	Q9NZ20	PA2G3_HUMAN	Q	378	ENSP00000215885:R378Q	ENSP00000215885:R378Q	R	-	2	0	PLA2G3	29862960	0.072000	0.21174	0.993000	0.49108	0.312000	0.27988	0.110000	0.15437	0.111000	0.17947	-1.062000	0.02293	CGG	C|0.845;T|0.155	0.155	strong		0.662	PLA2G3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321938.1	NM_015715	
MAP7D2	256714	hgsc.bcm.edu	37	X	20071046	20071046	+	Missense_Mutation	SNP	T	T	C	rs34519770	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:20071046T>C	ENST00000379651.3	-	5	563	c.545A>G	c.(544-546)aAt>aGt	p.N182S	MAP7D2_ENST00000452324.3_Missense_Mutation_p.N138S|MAP7D2_ENST00000443379.3_Intron|MAP7D2_ENST00000543767.1_Missense_Mutation_p.N75S|MAP7D2_ENST00000379643.5_Missense_Mutation_p.N182S	NM_152780.3	NP_689993.2	Q96T17	MA7D2_HUMAN	MAP7 domain containing 2	182			N -> S (in dbSNP:rs34519770). {ECO:0000269|PubMed:15489334}.		microtubule cytoskeleton organization (GO:0000226)	microtubule (GO:0005874)				NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(9)|lung(13)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	37						CAGGCGTTTATTCATGGGAGG	0.438													C|||	1357	0.35947	0.7005	0.196	3775	,	,		17451	0.0248		0.1899	False		,,,				2504	0.0808				p.N182S		Atlas-SNP	.											.	MAP7D2	165	.	0			c.A545G						PASS	.	C	,SER/ASN,SER/ASN,SER/ASN	3197,638		1131,453,482,48,89	244.0	193.0	210.0		,545,413,545	2.9	1.0	X	dbSNP_126	210	1806,4922		164,948,530,1316,1342	yes	intron,missense,missense,missense	MAP7D2	NM_001168466.1,NM_152780.3,NM_001168467.1,NM_001168465.1	,46,46,46	1295,1401,1012,1364,1431	CC,CT,C,TT,T		26.843,16.6362,47.3634	,benign,benign,benign	,182/733,138/681,182/774	20071046	5003,5560	2203	4300	6503	SO:0001583	missense	256714	exon5			CGTTTATTCATGG	BC089400	CCDS14195.1, CCDS55384.1, CCDS55385.1, CCDS55386.1	Xp22.12	2008-02-05			ENSG00000184368	ENSG00000184368			25899	protein-coding gene	gene with protein product						12477932	Standard	NM_152780		Approved	FLJ14503	uc010nfo.2	Q96T17	OTTHUMG00000021228	ENST00000379651.3:c.545A>G	X.37:g.20071046T>C	ENSP00000368972:p.Asn182Ser	Somatic	263	0	0		WXS	Illumina HiSeq	Phase_I	201	201	1	NM_152780	B7Z2J8|B7Z3S7|B9EGC7|C9JMA4|C9JYW0|Q5EBN1|Q5JPS7|Q6PIC7|Q8N792	Missense_Mutation	SNP	ENST00000379651.3	37	CCDS14195.1	580	0.34960819770946355	238	0.8380281690140845	60	0.18404907975460122	7	0.012455516014234875	100	0.1510574018126888	C	4.736	0.136847	0.09032	0.833638	0.26843	ENSG00000184368	ENST00000379651;ENST00000379643;ENST00000543767;ENST00000452324;ENST00000330274	T;T;T;T	0.03496	4.06;4.06;3.91;4.06	5.64	2.93	0.34026	.	0.061993	0.64402	N	0.000003	T	0.00012	0.0000	N	0.01761	-0.735	0.58432	P	4.000000000004E-6	B;B;B;B;B	0.06786	0.0;0.0;0.001;0.0;0.0	B;B;B;B;B	0.12156	0.001;0.001;0.007;0.0;0.001	T	0.28004	-1.0057	9	0.02654	T	1	-4.5167	9.4993	0.39008	0.0:0.6418:0.0:0.3582	rs34519770;rs61426853;rs34519770	138;182;215;182;75	C9JYW0;Q96T17-2;B5ME62;Q96T17;F5GYC2	.;.;.;MA7D2_HUMAN;.	S	182;182;75;138;215	ENSP00000368972:N182S;ENSP00000368964:N182S;ENSP00000440691:N75S;ENSP00000413301:N138S	ENSP00000332677:N215S	N	-	2	0	MAP7D2	19980967	1.000000	0.71417	0.998000	0.56505	0.994000	0.84299	0.953000	0.29162	-0.033000	0.13736	-0.170000	0.13304	AAT	T|0.544;C|0.456	0.456	strong		0.438	MAP7D2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000056001.1	NM_152780	
OR51F1	256892	hgsc.bcm.edu	37	11	4790948	4790948	+	Missense_Mutation	SNP	C	C	A	rs11033800	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:4790948C>A	ENST00000380383.1	-	1	220	c.221G>T	c.(220-222)aGg>aTg	p.R74M	OR51F1_ENST00000343430.3_Missense_Mutation_p.R67M|MMP26_ENST00000477339.1_Intron|MMP26_ENST00000380390.1_Intron			A6NGY5	O51F1_HUMAN	olfactory receptor, family 51, subfamily F, member 1	74			R -> M (in dbSNP:rs11033800).			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)		GGCTGATAGCCTGAAGAGGAA	0.438													A|||	1080	0.215655	0.4569	0.2017	5008	,	,		21734	0.0		0.2704	False		,,,				2504	0.0654				p.R67M		Atlas-SNP	.											.	OR51F1	60	.	0			c.G200T						PASS	.	A	MET/ARG	1967,2435	618.8+/-393.2	444,1079,678	69.0	65.0	66.0		200	3.7	0.7	11	dbSNP_120	66	2179,6417	711.6+/-405.8	291,1597,2410	yes	missense	OR51F1	NM_001004752.1	91	735,2676,3088	AA,AC,CC		25.349,44.6842,31.8972	benign	67/313	4790948	4146,8852	2201	4298	6499	SO:0001583	missense	256892	exon1			GATAGCCTGAAGA	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.221G>T	11.37:g.4790948C>A	ENSP00000369744:p.Arg74Met	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	88	15	0.170455	NM_001004752		Missense_Mutation	SNP	ENST00000380383.1	37		494	0.2261904761904762	225	0.4573170731707317	82	0.2265193370165746	0	0.0	187	0.24670184696569922	A	0.008	-1.904301	0.00512	0.446842	0.25349	ENSG00000188069	ENST00000343430;ENST00000380383	T;T	0.03035	4.07;4.07	4.81	3.66	0.41972	GPCR, rhodopsin-like superfamily (1);	0.189083	0.36628	N	0.002497	T	0.00012	0.0000	N	0.00000	-3.89	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.41305	-0.9516	9	0.02654	T	1	.	6.5145	0.22240	0.5426:0.3089:0.0:0.1485	rs11033800;rs52809349;rs60993028;rs11033800	74	A6NGY5	O51F1_HUMAN	M	67;74	ENSP00000345163:R67M;ENSP00000369744:R74M	ENSP00000345163:R67M	R	-	2	0	OR51F1	4747524	0.947000	0.32204	0.679000	0.29978	0.608000	0.37181	2.960000	0.49161	0.324000	0.23333	-0.346000	0.07831	AGG	C|0.707;A|0.293	0.293	strong		0.438	OR51F1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001004752	
COL4A1	1282	hgsc.bcm.edu	37	13	110833702	110833702	+	Silent	SNP	C	C	T	rs16975492	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:110833702C>T	ENST00000375820.4	-	29	2251	c.2130G>A	c.(2128-2130)ccG>ccA	p.P710P		NM_001845.4	NP_001836.2	P02462	CO4A1_HUMAN	collagen, type IV, alpha 1	710	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)			CTGGAGTCCCCGGTGGCCCCA	0.522													C|||	1538	0.307109	0.2088	0.3516	5008	,	,		16288	0.2768		0.3628	False		,,,				2504	0.3824				p.P710P		Atlas-SNP	.											.	COL4A1	372	.	0			c.G2130A						PASS	.	C		1092,3314	391.9+/-328.3	143,806,1254	46.0	45.0	46.0		2130	-9.7	0.0	13	dbSNP_123	46	3091,5509	464.9+/-366.4	568,1955,1777	no	coding-synonymous	COL4A1	NM_001845.4		711,2761,3031	TT,TC,CC		35.9419,24.7844,32.1621		710/1670	110833702	4183,8823	2203	4300	6503	SO:0001819	synonymous_variant	1282	exon29			AGTCCCCGGTGGC	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.2130G>A	13.37:g.110833702C>T		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	104	52	0.5	NM_001845	A7E2W4|B1AM70|Q1P9S9|Q5VWF6|Q86X41|Q8NF88|Q9NYC5	Silent	SNP	ENST00000375820.4	37	CCDS9511.1																																																																																			C|0.691;T|0.309	0.309	strong		0.522	COL4A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045759.3		
TGM2	7052	hgsc.bcm.edu	37	20	36770588	36770588	+	Silent	SNP	C	C	T	rs2076390	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:36770588C>T	ENST00000361475.2	-	7	1046	c.873G>A	c.(871-873)ctG>ctA	p.L291L	TGM2_ENST00000536701.1_Silent_p.L210L|TGM2_ENST00000536724.1_Silent_p.L231L	NM_004613.2|NM_198951.1	NP_004604.2|NP_945189.1	P21980	TGM2_HUMAN	transglutaminase 2	291					apoptotic cell clearance (GO:0043277)|blood vessel remodeling (GO:0001974)|branching involved in salivary gland morphogenesis (GO:0060445)|isopeptide cross-linking via N6-(L-isoglutamyl)-L-lysine (GO:0018153)|negative regulation of endoplasmic reticulum calcium ion concentration (GO:0032471)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of inflammatory response (GO:0050729)|positive regulation of mitochondrial calcium ion concentration (GO:0051561)|positive regulation of smooth muscle cell proliferation (GO:0048661)|protein homooligomerization (GO:0051260)|salivary gland cavitation (GO:0060662)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|metal ion binding (GO:0046872)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)			endometrium(2)|large_intestine(11)|liver(1)|lung(7)|ovary(2)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32		Myeloproliferative disorder(115;0.00878)			L-Glutamine(DB00130)	TAGGGATGCCCAGGCACCTCA	0.597													C|||	1012	0.202077	0.2141	0.1196	5008	,	,		18709	0.2718		0.1392	False		,,,				2504	0.2372				p.L291L		Atlas-SNP	.											.	TGM2	88	.	0			c.G873A						PASS	.	C	,	833,3573	329.6+/-301.1	85,663,1455	175.0	141.0	152.0		873,873	-10.3	0.5	20	dbSNP_96	152	1208,7392	244.7+/-273.8	77,1054,3169	no	coding-synonymous,coding-synonymous	TGM2	NM_004613.2,NM_198951.1	,	162,1717,4624	TT,TC,CC		14.0465,18.906,15.6928	,	291/688,291/549	36770588	2041,10965	2203	4300	6503	SO:0001819	synonymous_variant	7052	exon7			GATGCCCAGGCAC	M98478	CCDS13302.1	20q12	2013-05-02	2013-05-02		ENSG00000198959	ENSG00000198959	2.3.2.13	"""Transglutaminases"""	11778	protein-coding gene	gene with protein product	"""C polypeptide, protein-glutamine-gamma-glutamyltransferase"""	190196	"""transglutaminase 2 (C polypeptide, protein-glutamine-gamma-glutamyltransferase)"""			7912692, 11390390	Standard	NM_004613		Approved	TGC	uc002xhr.3	P21980	OTTHUMG00000032437	ENST00000361475.2:c.873G>A	20.37:g.36770588C>T		Somatic	191	0	0		WXS	Illumina HiSeq	Phase_I	179	79	0.441341	NM_198951	E1P5V9|Q16436|Q6B838|Q9BTN7|Q9UH35	Silent	SNP	ENST00000361475.2	37	CCDS13302.1																																																																																			C|0.831;T|0.169	0.169	strong		0.597	TGM2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079151.2	NM_198951	
ANXA9	8416	hgsc.bcm.edu	37	1	150955582	150955582	+	Start_Codon_SNP	SNP	A	A	G	rs267731	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:150955582A>G	ENST00000368947.4	+	3	477	c.1A>G	c.(1-3)Atg>Gtg	p.M1V	ANXA9_ENST00000474997.1_Intron	NM_003568.2	NP_003559.2	O76027	ANXA9_HUMAN	annexin A9	1					single organismal cell-cell adhesion (GO:0016337)|synaptic transmission (GO:0007268)	cell surface (GO:0009986)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	acetylcholine receptor activity (GO:0015464)|calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|phosphatidylserine binding (GO:0001786)|phospholipid binding (GO:0005543)|protein homodimerization activity (GO:0042803)			endometrium(1)|large_intestine(1)|lung(4)|skin(2)	8	all_lung(15;1.09e-34)|Lung NSC(24;1.1e-30)|Lung SC(34;0.00202)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.211)			CAGTAGCACCATGTCTGTGAC	0.602													A|||	35	0.00698882	0.0015	0.0159	5008	,	,		18217	0.0		0.0199	False		,,,				2504	0.002				p.M1V		Atlas-SNP	.											.	ANXA9	28	.	0			c.A1G						PASS	.	A	VAL/MET	31,4375	36.8+/-68.6	0,31,2172	58.0	57.0	57.0		1	3.9	1.0	1	dbSNP_79	57	328,8272	115.0+/-174.9	8,312,3980	yes	missense	ANXA9	NM_003568.2	21	8,343,6152	GG,GA,AA		3.814,0.7036,2.7603	possibly-damaging	1/346	150955582	359,12647	2203	4300	6503	SO:0001582	initiator_codon_variant	8416	exon3			AGCACCATGTCTG	AJ009985	CCDS975.2	1q21.2	2008-02-05			ENSG00000143412	ENSG00000143412		"""Annexins"""	547	protein-coding gene	gene with protein product		603319		ANX31		9742942, 9931420	Standard	NM_003568		Approved		uc001ewa.2	O76027	OTTHUMG00000035063	ENST00000368947.4:c.1A>G	1.37:g.150955582A>G	ENSP00000357943:p.Met1Val	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	45	20	0.444444	NM_003568	Q5SZF1|Q6FI55|Q9BS00|Q9HBJ6	Missense_Mutation	SNP	ENST00000368947.4	37	CCDS975.2	21	0.009615384615384616	1	0.0020325203252032522	5	0.013812154696132596	0	0.0	15	0.01978891820580475	A	13.04	2.118348	0.37339	0.007036	0.03814	ENSG00000143412	ENST00000368947	T	0.01725	4.67	5.06	3.94	0.45596	.	0.288673	0.35013	N	0.003511	T	0.00754	0.0025	.	.	.	0.36325	D	0.858502	B	0.06786	0.001	B	0.06405	0.002	T	0.47018	-0.9149	9	0.87932	D	0	.	7.2848	0.26333	0.9023:0.0:0.0977:0.0	rs267731;rs559201;rs267731	1	O76027	ANXA9_HUMAN	V	1	ENSP00000357943:M1V	ENSP00000357943:M1V	M	+	1	0	ANXA9	149222206	0.999000	0.42202	0.987000	0.45799	0.028000	0.11728	2.835000	0.48175	0.971000	0.38288	0.460000	0.39030	ATG	A|0.983;G|0.017	0.017	strong		0.602	ANXA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084895.2	NM_003568	Missense_Mutation
SLC26A3	1811	hgsc.bcm.edu	37	7	107423254	107423254	+	Silent	SNP	C	C	T	rs3735605	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:107423254C>T	ENST00000340010.5	-	11	1483	c.1299G>A	c.(1297-1299)gcG>gcA	p.A433A	SLC26A3_ENST00000422236.2_Silent_p.A398A	NM_000111.2	NP_000102.1	P40879	S26A3_HUMAN	solute carrier family 26 (anion exchanger), member 3	433					anion transport (GO:0006820)|cellular response to cAMP (GO:0071320)|excretion (GO:0007588)|intracellular pH elevation (GO:0051454)|ion transport (GO:0006811)|membrane hyperpolarization (GO:0060081)|regulation of RNA biosynthetic process (GO:2001141)|regulation of transcription, DNA-templated (GO:0006355)|sperm capacitation (GO:0048240)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|sperm midpiece (GO:0097225)	anion:anion antiporter activity (GO:0015301)|bicarbonate transmembrane transporter activity (GO:0015106)|chloride transmembrane transporter activity (GO:0015108)|secondary active sulfate transmembrane transporter activity (GO:0008271)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription cofactor activity (GO:0003712)|transporter activity (GO:0005215)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(18)|ovary(4)|prostate(1)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	46						TTTGTAGAGGCGCCAGGAGAA	0.413													C|||	756	0.150958	0.0552	0.1369	5008	,	,		18734	0.2758		0.175	False		,,,				2504	0.137				p.A433A		Atlas-SNP	.											SLC26A3,caecum,carcinoma,0,1	SLC26A3	120	1	0			c.G1299A						PASS	.	C		328,4078	174.4+/-204.0	16,296,1891	86.0	85.0	85.0		1299	-0.1	0.1	7	dbSNP_107	85	1523,7077	287.5+/-298.3	148,1227,2925	no	coding-synonymous	SLC26A3	NM_000111.2		164,1523,4816	TT,TC,CC		17.7093,7.4444,14.2319		433/765	107423254	1851,11155	2203	4300	6503	SO:0001819	synonymous_variant	1811	exon11			TAGAGGCGCCAGG	L02785	CCDS5748.1	7q31	2014-09-17	2013-07-18		ENSG00000091138	ENSG00000091138		"""Solute carriers"""	3018	protein-coding gene	gene with protein product		126650	"""congenital chloride diarrhea"", ""solute carrier family 26, member 3"""	DRA, CLD		8020951, 11087667	Standard	NM_000111		Approved		uc003ver.2	P40879	OTTHUMG00000154812	ENST00000340010.5:c.1299G>A	7.37:g.107423254C>T		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	88	44	0.5	NM_000111		Silent	SNP	ENST00000340010.5	37	CCDS5748.1																																																																																			C|0.847;T|0.153	0.153	strong		0.413	SLC26A3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337190.1	NM_000111	
SLC4A4	8671	hgsc.bcm.edu	37	4	72363294	72363294	+	Missense_Mutation	SNP	A	A	T	rs35891845	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:72363294A>T	ENST00000264485.5	+	16	2168	c.2051A>T	c.(2050-2052)aAc>aTc	p.N684I	SLC4A4_ENST00000351898.6_Missense_Mutation_p.N684I|SLC4A4_ENST00000425175.1_Missense_Mutation_p.N684I|SLC4A4_ENST00000340595.3_Missense_Mutation_p.N640I	NM_001098484.2	NP_001091954.1	Q9Y6R1	S4A4_HUMAN	solute carrier family 4 (sodium bicarbonate cotransporter), member 4	684					bicarbonate transport (GO:0015701)|ion transport (GO:0006811)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)|transport (GO:0006810)	basolateral plasma membrane (GO:0016323)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)|sodium:bicarbonate symporter activity (GO:0008510)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(9)|liver(1)|lung(21)|ovary(3)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	58			Lung(101;0.0739)|LUSC - Lung squamous cell carcinoma(112;0.225)		Sodium bicarbonate(DB01390)	CTCGTCGGGAACAACTGTAAT	0.378													A|||	2	0.000399361	0.0	0.0	5008	,	,		18419	0.0		0.002	False		,,,				2504	0.0				p.N684I		Atlas-SNP	.											.	SLC4A4	269	.	0			c.A2051T						PASS	.	A	ILE/ASN,ILE/ASN,ILE/ASN	1,4405	2.1+/-5.4	0,1,2202	115.0	117.0	116.0		2051,2051,1919	3.0	1.0	4	dbSNP_126	116	24,8576	17.9+/-57.8	0,24,4276	yes	missense,missense,missense	SLC4A4	NM_001098484.2,NM_001134742.1,NM_003759.3	149,149,149	0,25,6478	TT,TA,AA		0.2791,0.0227,0.1922	benign,benign,benign	684/1080,684/1095,640/1036	72363294	25,12981	2203	4300	6503	SO:0001583	missense	8671	exon16			TCGGGAACAACTG	AF007216	CCDS3549.1, CCDS43236.1, CCDS47071.1	4q13.3	2013-07-19	2013-07-19		ENSG00000080493	ENSG00000080493		"""Solute carriers"""	11030	protein-coding gene	gene with protein product		603345	"""solute carrier family 4, sodium bicarbonate cotransporter, member 4"""	SLC4A5		9235899, 9651366	Standard	NM_001098484		Approved	NBC1, HNBC1, NBC2, pNBC, hhNMC	uc010iic.3	Q9Y6R1	OTTHUMG00000129907	ENST00000264485.5:c.2051A>T	4.37:g.72363294A>T	ENSP00000264485:p.Asn684Ile	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	140	66	0.471429	NM_001098484	C4B714|O15153|Q8NEJ2|Q9H262|Q9NRZ1|Q9UIC0|Q9UIC1|Q9UP50	Missense_Mutation	SNP	ENST00000264485.5	37	CCDS43236.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	A	12.64	1.999658	0.35320	2.27E-4	0.002791	ENSG00000080493	ENST00000264485;ENST00000425175;ENST00000351898;ENST00000340595	T;T;T;T	0.78707	-1.2;-1.2;-1.2;-1.2	5.44	3.02	0.34903	Bicarbonate transporter, C-terminal (1);	0.219123	0.53938	D	0.000044	T	0.73544	0.3600	N	0.14661	0.345	0.48087	D	0.999585	P;D;B;B	0.69078	0.592;0.997;0.313;0.136	P;D;B;B	0.64042	0.477;0.921;0.346;0.353	T	0.72364	-0.4316	10	0.41790	T	0.15	.	9.4956	0.38986	0.8562:0.0:0.1438:0.0	rs35891845	684;684;640;684	A5JJ20;Q9Y6R1-4;Q9Y6R1-2;Q9Y6R1	.;.;.;S4A4_HUMAN	I	684;684;684;640	ENSP00000264485:N684I;ENSP00000393557:N684I;ENSP00000307349:N684I;ENSP00000344272:N640I	ENSP00000264485:N684I	N	+	2	0	SLC4A4	72582158	1.000000	0.71417	1.000000	0.80357	0.241000	0.25554	3.803000	0.55560	1.002000	0.39104	0.533000	0.62120	AAC	A|0.998;T|0.002	0.002	strong		0.378	SLC4A4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362090.1	NM_003759	
IFT140	9742	hgsc.bcm.edu	37	16	1652418	1652418	+	Missense_Mutation	SNP	C	C	T	rs146128830	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:1652418C>T	ENST00000426508.2	-	4	685	c.322G>A	c.(322-324)Gtg>Atg	p.V108M	LA16c-395F10.2_ENST00000563162.1_RNA|IFT140_ENST00000439987.2_5'UTR	NM_014714.3	NP_055529.2	Q96RY7	IF140_HUMAN	intraflagellar transport 140	108					cilium assembly (GO:0042384)|intraciliary retrograde transport (GO:0035721)|protein localization to cilium (GO:0061512)|regulation of cilium assembly (GO:1902017)|renal system development (GO:0072001)|retina development in camera-type eye (GO:0060041)|skeletal system morphogenesis (GO:0048705)	axoneme (GO:0005930)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|intraciliary transport particle A (GO:0030991)|photoreceptor connecting cilium (GO:0032391)				breast(1)|central_nervous_system(2)|endometrium(7)|kidney(4)|large_intestine(12)|lung(10)|ovary(5)|pancreas(1)|prostate(4)|skin(4)|stomach(2)|urinary_tract(1)	53		Hepatocellular(780;0.219)				CAACGGAGCACGGTGATGTCG	0.582													C|||	14	0.00279553	0.0023	0.0029	5008	,	,		17970	0.0		0.007	False		,,,				2504	0.002				p.V108M		Atlas-SNP	.											IFT140,NS,carcinoma,0,1	IFT140	128	1	0			c.G322A						PASS	.	C	MET/VAL	12,4386	19.1+/-41.9	0,12,2187	110.0	80.0	90.0		322	-1.2	0.0	16	dbSNP_134	90	81,8519	47.6+/-106.9	0,81,4219	yes	missense	IFT140	NM_014714.3	21	0,93,6406	TT,TC,CC		0.9419,0.2729,0.7155	possibly-damaging	108/1463	1652418	93,12905	2199	4300	6499	SO:0001583	missense	9742	exon4			GGAGCACGGTGAT	AB011162	CCDS10439.1	16p13.3	2014-07-03	2014-07-03	2005-11-02	ENSG00000187535	ENSG00000187535		"""Intraflagellar transport homologs"", ""WD repeat domain containing"""	29077	protein-coding gene	gene with protein product		614620	"""WD and tetratricopeptide repeats 2"", ""intraflagellar transport 140 homolog (Chlamydomonas)"""	WDTC2		9628581	Standard	NM_014714		Approved	gs114, KIAA0590	uc002cmb.3	Q96RY7	OTTHUMG00000128585	ENST00000426508.2:c.322G>A	16.37:g.1652418C>T	ENSP00000406012:p.Val108Met	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	85	15	0.176471	NM_014714	A2A2A8|D3DU75|O60332|Q9UG52	Missense_Mutation	SNP	ENST00000426508.2	37	CCDS10439.1	8	0.003663003663003663	0	0.0	1	0.0027624309392265192	0	0.0	7	0.009234828496042216	C	11.51	1.660137	0.29515	0.002729	0.009419	ENSG00000187535	ENST00000397417;ENST00000426508;ENST00000439987	T;T	0.60299	0.7;0.2	4.83	-1.19	0.09585	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.456706	0.22233	N	0.062786	T	0.56790	0.2009	M	0.78801	2.425	0.24640	N	0.993577	D	0.59357	0.985	P	0.56042	0.79	T	0.58126	-0.7691	10	0.32370	T	0.25	.	9.8005	0.40761	0.0:0.4051:0.0:0.5949	.	108	Q96RY7	IF140_HUMAN	M	108	ENSP00000380562:V108M;ENSP00000406012:V108M	ENSP00000380562:V108M	V	-	1	0	IFT140	1592419	0.004000	0.15560	0.008000	0.14137	0.004000	0.04260	-0.032000	0.12266	-0.555000	0.06142	0.561000	0.74099	GTG	C|0.993;T|0.007	0.007	strong		0.582	IFT140-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250438.2	NM_014714	
SIRPG	55423	hgsc.bcm.edu	37	20	1616137	1616137	+	Missense_Mutation	SNP	G	G	A	rs6034239	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:1616137G>A	ENST00000303415.3	-	4	921	c.857C>T	c.(856-858)tCg>tTg	p.S286L	SIRPG_ENST00000344103.4_Intron|SIRPG_ENST00000381583.2_Intron|RP11-77C3.3_ENST00000437384.1_RNA|SIRPG_ENST00000381580.1_Missense_Mutation_p.S253L|SIRPG_ENST00000216927.4_Intron|RP11-77C3.3_ENST00000456177.1_RNA	NM_018556.3	NP_061026.2	Q9P1W8	SIRPG_HUMAN	signal-regulatory protein gamma	286	Ig-like C1-type 2.		S -> L (in dbSNP:rs6034239). {ECO:0000269|PubMed:11185750}.		blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|intracellular signal transduction (GO:0035556)|leukocyte migration (GO:0050900)|negative regulation of cell proliferation (GO:0008285)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of T cell activation (GO:0050870)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(14)|ovary(1)|prostate(2)|stomach(1)	27						TCCATTCTCCGACCAGGTCAG	0.532													a|||	2983	0.595647	0.7625	0.4236	5008	,	,		21388	0.6369		0.4254	False		,,,				2504	0.6247				p.S286L		Atlas-SNP	.											.	SIRPG	61	.	0			c.C857T						PASS	.	A	,LEU/SER,	3201,1205		1155,891,157	176.0	149.0	158.0		,857,	1.6	1.0	20	dbSNP_114	158	3540,5060		754,2032,1514	yes	intron,missense,intron	SIRPG	NM_001039508.1,NM_018556.3,NM_080816.2	,145,	1909,2923,1671	AA,AG,GG		41.1628,27.3491,48.1701	,benign,	,286/388,	1616137	6741,6265	2203	4300	6503	SO:0001583	missense	55423	exon4			TTCTCCGACCAGG	AB042624	CCDS13020.2, CCDS13021.2, CCDS33434.1	20p13	2013-01-11	2006-02-03	2006-02-03	ENSG00000089012	ENSG00000089012		"""Signal-regulatory proteins"", ""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C1-set domain containing"""	15757	protein-coding gene	gene with protein product		605466	"""signal-regulatory protein beta 2"""	SIRPB2		11185750, 16339511	Standard	XM_005260749		Approved	bA77C3.1, SIRP-B2, SIRPgamma, CD172g	uc002wfm.1	Q9P1W8	OTTHUMG00000031680	ENST00000303415.3:c.857C>T	20.37:g.1616137G>A	ENSP00000305529:p.Ser286Leu	Somatic	243	0	0		WXS	Illumina HiSeq	Phase_I	258	132	0.511628	NM_018556	B1AKP6|Q5D051|Q5JV25|Q5MKL4|Q8WWA5|Q9NQK8	Missense_Mutation	SNP	ENST00000303415.3	37	CCDS13020.2	1209	0.5535714285714286	377	0.766260162601626	164	0.4530386740331492	345	0.6031468531468531	323	0.4261213720316623	.	0.051	-1.249973	0.01469	0.726509	0.411628	ENSG00000089012	ENST00000381580;ENST00000303415	T;T	0.00574	6.47;6.47	1.6	1.6	0.23607	Immunoglobulin-like (1);Immunoglobulin C1-set (2);Immunoglobulin-like fold (1);	0.300419	0.23369	N	0.048925	T	0.00012	0.0000	N	0.00010	-3.025	0.09310	P	0.99999962275	B	0.02656	0.0	B	0.01281	0.0	T	0.16482	-1.0401	9	0.02654	T	1	.	3.5698	0.07913	0.7797:0.0:0.2203:0.0	rs6034239;rs6514586;rs6034239	286	Q9P1W8	SIRPG_HUMAN	L	253;286	ENSP00000370992:S253L;ENSP00000305529:S286L	ENSP00000305529:S286L	S	-	2	0	SIRPG	1564137	0.938000	0.31826	0.970000	0.41538	0.023000	0.10783	1.384000	0.34396	0.090000	0.17273	-1.298000	0.01336	TCG	G|0.459;A|0.541	0.541	strong		0.532	SIRPG-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077566.2	NM_018556	
OR5K3	403277	hgsc.bcm.edu	37	3	98109640	98109640	+	Missense_Mutation	SNP	G	G	A	rs13068323	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	339	0	0		WXS	Illumina HiSeq	Phase_I	295	155	0.525424	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		
IGLL5	100423062	hgsc.bcm.edu	37	22	23230394	23230394	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:23230394C>T	ENST00000526893.1	+	1	435	c.161C>T	c.(160-162)gCc>gTc	p.A54V	IGLL5_ENST00000531372.1_Missense_Mutation_p.A54V|IGLL5_ENST00000532223.2_Missense_Mutation_p.A54V|hsa-mir-5571_ENST00000577998.1_RNA	NM_001178126.1	NP_001171597.1	B9A064	IGLL5_HUMAN	immunoglobulin lambda-like polypeptide 5	54						extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|urinary_tract(1)	7						GACCCTGGAGCCTCAGTTGGA	0.667																																					p.A54V		Atlas-SNP	.											.	IGLL5	26	.	0			c.C161T						PASS	.																																			SO:0001583	missense	100423062	exon1			CTGGAGCCTCAGT	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.161C>T	22.37:g.23230394C>T	ENSP00000431254:p.Ala54Val	Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	114	24	0.210526	NM_001178126		Missense_Mutation	SNP	ENST00000526893.1	37	CCDS54506.1	.	.	.	.	.	.	.	.	.	.	C	15.92	2.975826	0.53720	.	.	ENSG00000254709	ENST00000532223;ENST00000526893;ENST00000531372	T;T	0.00617	6.19;6.19	3.92	-1.07	0.09968	.	.	.	.	.	T	0.00552	0.0018	L	0.29908	0.895	0.09310	N	1	B	0.21821	0.061	B	0.11329	0.006	T	0.47071	-0.9145	9	0.87932	D	0	.	2.5676	0.04787	0.1918:0.3543:0.3485:0.1053	.	54	B9A064	IGLL5_HUMAN	V	54	ENSP00000436353:A54V;ENSP00000431254:A54V	ENSP00000431254:A54V	A	+	2	0	IGLL5	21560394	0.001000	0.12720	0.000000	0.03702	0.003000	0.03518	0.197000	0.17197	-0.079000	0.12707	-0.152000	0.13540	GCC	.	.	none		0.667	IGLL5-002	KNOWN	basic|appris_candidate|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000385699.1	NM_001178126	
GJA9	81025	hgsc.bcm.edu	37	1	39340875	39340875	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:39340875C>T	ENST00000360786.3	-	1	1148	c.896G>A	c.(895-897)aGt>aAt	p.S299N	MYCBP_ENST00000489803.1_5'UTR|RP5-864K19.4_ENST00000443161.1_RNA|GJA9_ENST00000454994.2_Missense_Mutation_p.S299N|MYCBP_ENST00000397572.2_5'Flank|GJA9_ENST00000357771.3_Missense_Mutation_p.S299N|RP5-864K19.4_ENST00000433671.2_RNA|RP5-864K19.4_ENST00000456813.1_RNA			P57773	CXA9_HUMAN	gap junction protein, alpha 9, 59kDa	299					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)			TGAATTTAAACTAGGGTACAC	0.388																																					p.S299N		Atlas-SNP	.											GJA9,rectum,carcinoma,-1,1	GJA9	55	1	0			c.G896A						scavenged	.						102.0	101.0	101.0					1																	39340875		2203	4300	6503	SO:0001583	missense	81025	exon2			TTTAAACTAGGGT	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.896G>A	1.37:g.39340875C>T	ENSP00000354020:p.Ser299Asn	Somatic	305	0	0		WXS	Illumina HiSeq	Phase_I	275	3	0.0109091	NM_030772	B2R722|B3KVQ2|Q5TA63|Q96KG0	Missense_Mutation	SNP	ENST00000360786.3	37	CCDS432.1	.	.	.	.	.	.	.	.	.	.	C	1.629	-0.519561	0.04171	.	.	ENSG00000131233	ENST00000454994;ENST00000357771;ENST00000360786	D;D;D	0.97620	-4.46;-4.39;-4.39	4.72	0.394	0.16299	.	2.234430	0.02228	U	0.064609	D	0.91955	0.7452	N	0.19112	0.55	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	D	0.84469	0.0598	10	0.15066	T	0.55	.	3.9412	0.09328	0.3609:0.3837:0.0:0.2554	.	299	P57773	CXA9_HUMAN	N	299	ENSP00000406846:S299N;ENSP00000350415:S299N;ENSP00000354020:S299N	ENSP00000350415:S299N	S	-	2	0	GJA9	39113462	0.816000	0.29132	0.068000	0.19968	0.202000	0.24057	1.637000	0.37155	-0.022000	0.13986	-0.794000	0.03295	AGT	.	.	none		0.388	GJA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001205.1	NM_030772	
POLE4	56655	hgsc.bcm.edu	37	2	75185856	75185856	+	Missense_Mutation	SNP	G	G	T	rs12366	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:75185856G>T	ENST00000483063.1	+	1	238	c.50G>T	c.(49-51)gGa>gTa	p.G17V	POLE4_ENST00000459636.1_3'UTR	NM_019896.2	NP_063949.2	Q9NR33	DPOE4_HUMAN	polymerase (DNA-directed), epsilon 4, accessory subunit	17			G -> V (in dbSNP:rs12366). {ECO:0000269|PubMed:10801849, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17525332}.		DNA-dependent DNA replication (GO:0006261)|histone H3 acetylation (GO:0043966)	Ada2/Gcn5/Ada3 transcription activator complex (GO:0005671)|epsilon DNA polymerase complex (GO:0008622)|nucleus (GO:0005634)	DNA-directed DNA polymerase activity (GO:0003887)|sequence-specific DNA binding (GO:0043565)			lung(1)	1					Cladribine(DB00242)	GAGGAGGAGGGACCTGCTGGG	0.751													G|||	1711	0.341653	0.2965	0.3545	5008	,	,		9775	0.4206		0.3917	False		,,,				2504	0.2607				p.G17V		Atlas-SNP	.											.	POLE4	2	.	0			c.G50T						PASS	.	G	VAL/GLY	1078,2746		168,742,1002	6.0	8.0	7.0		50	3.6	0.8	2	dbSNP_52	7	2577,4845		504,1569,1638	no	missense	POLE4	NM_019896.2	109	672,2311,2640	TT,TG,GG		34.7211,28.1904,32.5004	possibly-damaging	17/118	75185856	3655,7591	1912	3711	5623	SO:0001583	missense	56655	exon1			AGGAGGGACCTGC	AF261688	CCDS1957.1	2p12	2012-05-18	2012-05-18		ENSG00000115350	ENSG00000115350		"""DNA polymerases"""	18755	protein-coding gene	gene with protein product		607269	"""polymerase (DNA-directed), epsilon 4 (p12 subunit)"""			10801849	Standard	NM_019896		Approved	p12	uc002snf.3	Q9NR33	OTTHUMG00000129971	ENST00000483063.1:c.50G>T	2.37:g.75185856G>T	ENSP00000420176:p.Gly17Val	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	53	52	0.981132	NM_019896	Q53TR2	Missense_Mutation	SNP	ENST00000483063.1	37	CCDS1957.1	827	0.37866300366300365	124	0.25203252032520324	145	0.4005524861878453	253	0.4423076923076923	305	0.4023746701846966	G	11.83	1.756056	0.31137	0.281904	0.347211	ENSG00000115350	ENST00000483063	T	0.30981	1.51	5.41	3.58	0.41010	Histone-fold (1);	0.159172	0.56097	D	0.000033	T	0.00012	0.0000	N	0.12182	0.205	0.18873	P	0.9999885704	P	0.34780	0.468	B	0.39503	0.301	T	0.46414	-0.9193	9	0.49607	T	0.09	-6.284	7.1936	0.25839	0.0936:0.18:0.7264:0.0	rs12366;rs3171885;rs17296293;rs17845953;rs17858934	17	Q9NR33	DPOE4_HUMAN	V	17	ENSP00000420176:G17V	ENSP00000420176:G17V	G	+	2	0	POLE4	75039364	0.978000	0.34361	0.787000	0.31911	0.697000	0.40408	2.026000	0.41069	0.631000	0.30412	0.591000	0.81541	GGA	G|0.638;T|0.362	0.362	strong		0.751	POLE4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252237.2	NM_019896	
OR51G1	79324	hgsc.bcm.edu	37	11	4944892	4944892	+	Silent	SNP	G	G	C	rs34583466	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:4944892G>C	ENST00000321961.2	-	1	745	c.678C>G	c.(676-678)acC>acG	p.T226T	MMP26_ENST00000477339.1_Intron|MMP26_ENST00000380390.1_Intron	NM_001005237.1	NP_001005237.1	Q8NGK1	O51G1_HUMAN	olfactory receptor, family 51, subfamily G, member 1	226						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)|large_intestine(2)|lung(11)|ovary(2)|prostate(3)|skin(4)|soft_tissue(1)	25		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;2.58e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0284)|LUSC - Lung squamous cell carcinoma(625;0.19)		TGCTGAGCACGGTGCGAAGGA	0.542													G|||	244	0.048722	0.0136	0.0937	5008	,	,		20944	0.0		0.1441	False		,,,				2504	0.0164				p.T226T		Atlas-SNP	.											.	OR51G1	74	.	0			c.C678G						PASS	.	G		162,4240	108.6+/-147.0	3,156,2042	125.0	100.0	108.0		678	-5.5	0.0	11	dbSNP_126	108	1140,7456	235.3+/-267.9	97,946,3255	no	coding-synonymous	OR51G1	NM_001005237.1		100,1102,5297	CC,CG,GG		13.262,3.6801,10.0169		226/322	4944892	1302,11696	2201	4298	6499	SO:0001819	synonymous_variant	79324	exon1			GAGCACGGTGCGA	AB065793	CCDS31366.1	11p15.4	2012-08-09			ENSG00000176879	ENSG00000176879		"""GPCR / Class A : Olfactory receptors"""	14738	protein-coding gene	gene with protein product				OR51G3P			Standard	NM_001005237		Approved		uc010qyr.2	Q8NGK1	OTTHUMG00000066532	ENST00000321961.2:c.678C>G	11.37:g.4944892G>C		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	99	20	0.20202	NM_001005237	B9EGW8|Q6IFH6	Silent	SNP	ENST00000321961.2	37	CCDS31366.1																																																																																			G|0.903;C|0.097	0.097	strong		0.542	OR51G1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142345.1	NM_001005237	
BRD2	6046	hgsc.bcm.edu	37	6	32942302	32942302	+	Silent	SNP	G	G	A	rs516535	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:32942302G>A	ENST00000374825.4	+	3	1794	c.93G>A	c.(91-93)aaG>aaA	p.K31K	BRD2_ENST00000395287.1_Silent_p.K31K|BRD2_ENST00000395289.2_Silent_p.K31K|BRD2_ENST00000449085.2_5'UTR|BRD2_ENST00000443797.2_5'UTR|XXbac-BPG181M17.6_ENST00000580587.1_RNA|BRD2_ENST00000374831.4_Silent_p.K31K	NM_005104.3	NP_005095.1	P25440	BRD2_HUMAN	bromodomain containing 2	31					chromatin modification (GO:0016568)|nucleosome assembly (GO:0006334)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|lysine-acetylated histone binding (GO:0070577)			central_nervous_system(3)|stomach(2)	5						CACCAGGGAAGAGGATTCGAA	0.572													A|||	3051	0.609225	0.7927	0.5389	5008	,	,		18019	0.504		0.5954	False		,,,				2504	0.5337				p.K31K		Atlas-SNP	.											.	BRD2	70	.	0			c.G93A						PASS	.	A	,,,	3427,979	365.4+/-317.4	1338,751,114	94.0	96.0	95.0		93,93,,93	2.9	1.0	6	dbSNP_83	95	5125,3475	508.7+/-377.1	1544,2037,719	yes	coding-synonymous,coding-synonymous,utr-5,coding-synonymous	BRD2	NM_001113182.2,NM_001199455.1,NM_001199456.1,NM_005104.3	,,,	2882,2788,833	AA,AG,GG		40.407,22.2197,34.2457	,,,	31/802,31/837,,31/802	32942302	8552,4454	2203	4300	6503	SO:0001819	synonymous_variant	6046	exon3			AGGGAAGAGGATT	X96670	CCDS4762.1, CCDS56420.1, CCDS56421.1	6p21.3	2010-12-23	2002-01-14		ENSG00000204256	ENSG00000204256			1103	protein-coding gene	gene with protein product		601540	"""bromodomain-containing 2"""			1352711, 8781126	Standard	NM_005104		Approved	KIAA9001, RING3, D6S113E, NAT, FSRG1	uc021ywf.1	P25440	OTTHUMG00000031241	ENST00000374825.4:c.93G>A	6.37:g.32942302G>A		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	123	44	0.357724	NM_005104	A2AAU0|B0S7P0|B1AZT1|O00699|O00700|Q15310|Q5STC9|Q63HQ9|Q658Y7|Q6P3U2|Q969U4	Silent	SNP	ENST00000374825.4	37	CCDS4762.1	1336	0.6117216117216118	404	0.8211382113821138	193	0.5331491712707183	280	0.48951048951048953	459	0.6055408970976254	A	8.816	0.936314	0.18206	0.777803	0.59593	ENSG00000204256	ENST00000456339;ENST00000449025	.	.	.	5.26	2.9	0.33743	.	.	.	.	.	T	0.25901	0.0631	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.08086	-1.0739	3	.	.	.	-16.5361	7.4925	0.27471	0.7191:0.0:0.2809:0.0	rs516535;rs3189384;rs3752527;rs17584137;rs58877819;rs516535	.	.	.	K	33;37	.	.	R	+	2	0	BRD2	33050280	0.991000	0.36638	1.000000	0.80357	0.804000	0.45430	0.394000	0.20834	0.474000	0.27392	-0.268000	0.10319	AGA	G|0.363;A|0.637	0.637	strong		0.572	BRD2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076503.2		
C6orf222	389384	hgsc.bcm.edu	37	6	36287312	36287312	+	Missense_Mutation	SNP	G	G	C	rs743852	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:36287312G>C	ENST00000437635.2	-	11	1921	c.1744C>G	c.(1744-1746)Ctg>Gtg	p.L582V		NM_001010903.4	NP_001010903.3	P0C671	CF222_HUMAN	chromosome 6 open reading frame 222	582			L -> V (in dbSNP:rs743852).							breast(4)|kidney(1)|large_intestine(3)|lung(8)|ovary(2)|skin(4)|urinary_tract(4)	26						TGGCTGCGCAGGGTGGCTACC	0.532													G|||	1945	0.388379	0.3737	0.3689	5008	,	,		20115	0.2183		0.5596	False		,,,				2504	0.4213				p.L582V		Atlas-SNP	.											.	C6orf222	72	.	0			c.C1744G						PASS	.	G	VAL/LEU	1750,2656	521.5+/-370.6	363,1024,816	73.0	72.0	72.0		1744	3.6	0.7	6	dbSNP_86	72	4783,3817	613.1+/-396.1	1368,2047,885	yes	missense	C6orf222	NM_001010903.4	32	1731,3071,1701	CC,CG,GG		44.3837,39.7186,49.7693	probably-damaging	582/653	36287312	6533,6473	2203	4300	6503	SO:0001583	missense	389384	exon11			TGCGCAGGGTGGC		CCDS34439.1	6p21.31	2012-02-22			ENSG00000189325	ENSG00000189325			33769	protein-coding gene	gene with protein product							Standard	NM_001010903		Approved	DKFZp779B1540	uc003oly.3	P0C671	OTTHUMG00000014591	ENST00000437635.2:c.1744C>G	6.37:g.36287312G>C	ENSP00000418983:p.Leu582Val	Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	69	38	0.550725	NM_001010903	B2RTY8	Missense_Mutation	SNP	ENST00000437635.2	37	CCDS34439.1	851	0.38965201465201466	191	0.3882113821138211	136	0.3756906077348066	108	0.1888111888111888	416	0.5488126649076517	G	18.82	3.704316	0.68615	0.397186	0.556163	ENSG00000189325	ENST00000437635	T	0.62498	0.02	5.43	3.6	0.41247	.	0.000000	0.37178	N	0.002217	T	0.67449	0.2894	M	0.78637	2.42	0.42422	P	0.007353999999999972	D	0.89917	1.0	D	0.79784	0.993	T	0.71606	-0.4542	9	0.66056	D	0.02	-36.1032	7.0432	0.25031	0.2052:0.0:0.7948:0.0	rs743852;rs743852	582	P0C671	CF222_HUMAN	V	582	ENSP00000418983:L582V	ENSP00000418983:L582V	L	-	1	2	C6orf222	36395290	0.600000	0.26899	0.704000	0.30370	0.973000	0.67179	0.853000	0.27777	1.398000	0.46701	0.563000	0.77884	CTG	G|0.540;C|0.460	0.460	strong		0.532	C6orf222-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040338.2	NM_001010903	
MUC20	200958	hgsc.bcm.edu	37	3	195453014	195453014	+	Missense_Mutation	SNP	G	G	A	rs3828410	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195453014G>A	ENST00000447234.2	+	2	1666	c.1540G>A	c.(1540-1542)Ggg>Agg	p.G514R	MUC20_ENST00000436408.1_Missense_Mutation_p.G514R|MUC20_ENST00000445522.2_Missense_Mutation_p.G479R|MUC20_ENST00000320736.6_Missense_Mutation_p.G343R	NM_001282506.1	NP_001269435.1	Q8N307	MUC20_HUMAN	mucin 20, cell surface associated	514	Involved in oligomerization.		G -> R (in dbSNP:rs3828410).|Missing. {ECO:0000269|PubMed:14702039}.		activation of MAPK activity (GO:0000187)|cellular protein metabolic process (GO:0044267)|hepatocyte growth factor receptor signaling pathway (GO:0048012)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein homooligomerization (GO:0051260)	basal plasma membrane (GO:0009925)|cell projection (GO:0042995)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)				NS(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(4)|skin(4)|stomach(3)|upper_aerodigestive_tract(1)	23	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)	Lung NSC(153;0.191)	Epithelial(36;1e-21)|all cancers(36;9.02e-20)|OV - Ovarian serous cystadenocarcinoma(49;1.6e-18)|Lung(62;0.000104)|LUSC - Lung squamous cell carcinoma(58;0.000128)	GBM - Glioblastoma multiforme(46;1.66e-05)		GACAGCACCCGGGGCCACGAC	0.582																																					p.G343R		Atlas-SNP	.											.	MUC20	84	.	0			c.G1027A						PASS	.						56.0	52.0	53.0					3																	195453014		2138	4219	6357	SO:0001583	missense	200958	exon3			GCACCCGGGGCCA	AB037780	CCDS63877.1	3q29	2008-08-07	2006-03-14		ENSG00000176945	ENSG00000176945		"""Mucins"""	23282	protein-coding gene	gene with protein product		610360				14565953	Standard	NM_001282506		Approved	FLJ14408, KIAA1359	uc010hzo.3	Q8N307	OTTHUMG00000155823	ENST00000447234.2:c.1540G>A	3.37:g.195453014G>A	ENSP00000414350:p.Gly514Arg	Somatic	400	1	0.0025		WXS	Illumina HiSeq	Phase_I	367	123	0.33515	NM_152673	Q6UX97|Q76I83|Q76I85|Q86ST8|Q8NBY6|Q96KA1|Q9P2I8	Missense_Mutation	SNP	ENST00000447234.2	37		568	0.2600732600732601	178	0.3617886178861789	85	0.23480662983425415	231	0.40384615384615385	74	0.09762532981530343	A	2.041	-0.420045	0.04734	.	.	ENSG00000176945	ENST00000447234;ENST00000320736;ENST00000436408;ENST00000445522	T;T;T;T	0.15139	2.88;2.91;3.04;2.45	3.41	-3.4	0.04853	.	1.360490	0.04987	N	0.466686	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	0.45498	-0.9257	9	0.09084	T	0.74	0.7227	6.8673	0.24100	0.2228:0.346:0.4312:0.0	rs3828410;rs3828410	343	E9PH32	.	R	514;343;514;479	ENSP00000414350:G514R;ENSP00000325431:G343R;ENSP00000396774:G514R;ENSP00000405629:G479R	ENSP00000325431:G343R	G	+	1	0	MUC20	196938685	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-0.677000	0.05215	-1.154000	0.02825	-0.439000	0.05793	GGG	G|0.800;A|0.200	0.200	strong		0.582	MUC20-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000341835.1	NM_152673	
CDH11	1009	hgsc.bcm.edu	37	16	65022114	65022114	+	Silent	SNP	C	C	T	rs28216	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:65022114C>T	ENST00000268603.4	-	7	1560	c.945G>A	c.(943-945)tcG>tcA	p.S315S	CDH11_ENST00000394156.3_Silent_p.S315S|CDH11_ENST00000566827.1_Silent_p.S189S	NM_001797.2	NP_001788.2	P55287	CAD11_HUMAN	cadherin 11, type 2, OB-cadherin (osteoblast)	315	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)|corticospinal tract morphogenesis (GO:0021957)|homophilic cell adhesion (GO:0007156)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(19)|lung(40)|ovary(3)|prostate(3)|skin(2)|urinary_tract(2)	88		Ovarian(137;0.0973)		OV - Ovarian serous cystadenocarcinoma(108;0.205)		TGATTTCAAACGATTCCATAC	0.443			T	USP6	aneurysmal bone cysts					TSP Lung(24;0.17)			C|||	1120	0.223642	0.0734	0.255	5008	,	,		19686	0.2054		0.4066	False		,,,				2504	0.2352				p.S315S		Atlas-SNP	.		Dom	yes		16	16q22.1	1009	"""cadherin 11, type 2, OB-cadherin (osteoblast)"""		M	CDH11_ENST00000394156,NS,carcinoma,-1,2	CDH11	260	2	0			c.G945A						PASS	.	C		530,3876	241.2+/-251.7	31,468,1704	368.0	309.0	329.0		945	5.7	1.0	16	dbSNP_76	329	3660,4940	527.1+/-381.1	774,2112,1414	no	coding-synonymous	CDH11	NM_001797.2		805,2580,3118	TT,TC,CC		42.5581,12.0291,32.2159		315/797	65022114	4190,8816	2203	4300	6503	SO:0001819	synonymous_variant	1009	exon7			TTCAAACGATTCC	D21255	CCDS10803.1	16q21	2010-01-26			ENSG00000140937	ENSG00000140937		"""Cadherins / Major cadherins"""	1750	protein-coding gene	gene with protein product	"""OB-Cadherin"""	600023				9615235	Standard	NM_001797		Approved	OB, CAD11	uc002eoi.3	P55287	OTTHUMG00000137494	ENST00000268603.4:c.945G>A	16.37:g.65022114C>T		Somatic	276	0	0		WXS	Illumina HiSeq	Phase_I	329	329	1	NM_001797	A8K5D6|A8MZC8|B7WP28|Q15065|Q15066|Q9UQ93|Q9UQ94	Silent	SNP	ENST00000268603.4	37	CCDS10803.1																																																																																			C|0.715;T|0.285	0.285	strong		0.443	CDH11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268755.1	NM_033664	
NUAK1	9891	hgsc.bcm.edu	37	12	106460938	106460938	+	Missense_Mutation	SNP	G	G	C	rs3741883	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:106460938G>C	ENST00000261402.2	-	7	3007	c.1628C>G	c.(1627-1629)cCt>cGt	p.P543R		NM_014840.2	NP_055655.1	O60285	NUAK1_HUMAN	NUAK family, SNF1-like kinase, 1	543			P -> R (in dbSNP:rs3741883). {ECO:0000269|PubMed:17344846}.		cell adhesion (GO:0007155)|cellular response to DNA damage stimulus (GO:0006974)|regulation of cell adhesion (GO:0030155)|regulation of cell proliferation (GO:0042127)|regulation of cellular senescence (GO:2000772)|regulation of myosin-light-chain-phosphatase activity (GO:0035507)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|p53 binding (GO:0002039)|protein serine/threonine kinase activity (GO:0004674)	p.P543R(2)		NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(8)|lung(13)|ovary(1)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	37						GGGCATTTCAGGGCTGACCAG	0.622													G|||	1109	0.221446	0.0408	0.2133	5008	,	,		15631	0.4177		0.2207	False		,,,				2504	0.2699				p.P543R		Atlas-SNP	.											NUAK1_ENST00000261402,NS,carcinoma,0,2	NUAK1	196	2	2	Substitution - Missense(2)	stomach(2)	c.C1628G						PASS	.	G	ARG/PRO	306,4100	162.2+/-194.2	11,284,1908	60.0	67.0	65.0		1628	5.5	1.0	12	dbSNP_107	65	1961,6639	342.1+/-324.3	237,1487,2576	yes	missense	NUAK1	NM_014840.2	103	248,1771,4484	CC,CG,GG		22.8023,6.9451,17.4304	possibly-damaging	543/662	106460938	2267,10739	2203	4300	6503	SO:0001583	missense	9891	exon7			ATTTCAGGGCTGA	AB011109	CCDS31892.1	12q23.3	2005-08-09				ENSG00000074590			14311	protein-coding gene	gene with protein product	"""AMP-activated protein kinase family member 5"""	608130				12409306, 13679856	Standard	NM_014840		Approved	ARK5, KIAA0537, NuaK1	uc001tlj.1	O60285	OTTHUMG00000169763	ENST00000261402.2:c.1628C>G	12.37:g.106460938G>C	ENSP00000261402:p.Pro543Arg	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	87	87	1	NM_014840	A7MD39|Q96KA8	Missense_Mutation	SNP	ENST00000261402.2	37	CCDS31892.1	504	0.23076923076923078	21	0.042682926829268296	76	0.20994475138121546	243	0.42482517482517484	164	0.21635883905013192	G	9.640	1.138832	0.21123	0.069451	0.228023	ENSG00000074590	ENST00000261402	T	0.73575	-0.76	5.53	5.53	0.82687	.	0.000000	0.64402	D	0.000012	T	0.00012	0.0000	N	0.08118	0	0.26688	P	0.9714141	P	0.49961	0.93	B	0.42319	0.383	T	0.30937	-0.9961	9	0.27082	T	0.32	.	12.7544	0.57325	0.0749:0.0:0.9251:0.0	rs3741883;rs3741883	543	O60285	NUAK1_HUMAN	R	543	ENSP00000261402:P543R	ENSP00000261402:P543R	P	-	2	0	NUAK1	104985068	1.000000	0.71417	0.994000	0.49952	0.204000	0.24138	3.525000	0.53502	2.596000	0.87737	0.462000	0.41574	CCT	G|0.796;C|0.204	0.204	strong		0.622	NUAK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405767.2	NM_014840	
COL15A1	1306	hgsc.bcm.edu	37	9	101804329	101804329	+	Silent	SNP	T	T	C	rs7854112	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:101804329T>C	ENST00000375001.3	+	24	2937	c.2514T>C	c.(2512-2514)ggT>ggC	p.G838G		NM_001855.3	NP_001846.3	P39059	COFA1_HUMAN	collagen, type XV, alpha 1	838	Collagen-like 3.|Triple-helical region 4 (COL4).				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)				CCTTCCAGGGTCCTAGAGGAC	0.413													C|||	753	0.150359	0.0817	0.1441	5008	,	,		18387	0.1736		0.1481	False		,,,				2504	0.226				p.G838G		Atlas-SNP	.											.	COL15A1	211	.	0			c.T2514C						PASS	.	C		385,4021	788.3+/-414.9	23,339,1841	96.0	104.0	101.0		2514	0.4	1.0	9	dbSNP_116	101	1159,7441	765.1+/-407.6	84,991,3225	no	coding-synonymous	COL15A1	NM_001855.3		107,1330,5066	CC,CT,TT		13.4767,8.7381,11.8714		838/1389	101804329	1544,11462	2203	4300	6503	SO:0001819	synonymous_variant	1306	exon24			CCAGGGTCCTAGA	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.2514T>C	9.37:g.101804329T>C		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	33	14	0.424242	NM_001855	Q5T6J4|Q9UDC5|Q9Y4W4	Silent	SNP	ENST00000375001.3	37	CCDS35081.1																																																																																			T|0.871;C|0.129	0.129	strong		0.413	COL15A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053386.3	NM_001855	
SLC37A1	54020	hgsc.bcm.edu	37	21	43979127	43979127	+	Silent	SNP	C	C	T	rs118032072	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:43979127C>T	ENST00000352133.2	+	11	1891	c.909C>T	c.(907-909)caC>caT	p.H303H	AP001625.6_ENST00000442605.1_RNA|SLC37A1_ENST00000398341.3_Silent_p.H303H			P57057	GLPT_HUMAN	solute carrier family 37 (glucose-6-phosphate transporter), member 1	303				H -> Q (in Ref. 2; AAG29853). {ECO:0000305}.	carbohydrate transport (GO:0008643)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	transporter activity (GO:0005215)			breast(1)|endometrium(6)|kidney(1)|large_intestine(2)|liver(2)|lung(3)	15						ACCCGAACCACGTCGTCATTC	0.567													C|||	92	0.0183706	0.0068	0.0274	5008	,	,		16341	0.0		0.0616	False		,,,				2504	0.002				p.H303H		Atlas-SNP	.											.	SLC37A1	48	.	0			c.C909T						PASS	.	C		44,4362	46.0+/-80.4	0,44,2159	63.0	52.0	56.0		909	1.3	0.2	21	dbSNP_132	56	493,8107	141.9+/-198.1	13,467,3820	no	coding-synonymous	SLC37A1	NM_018964.3		13,511,5979	TT,TC,CC		5.7326,0.9986,4.1289		303/534	43979127	537,12469	2203	4300	6503	SO:0001819	synonymous_variant	54020	exon12			GAACCACGTCGTC	AJ269529	CCDS13689.1	21q22.3	2013-07-17	2013-07-17		ENSG00000160190	ENSG00000160190		"""Solute carriers"""	11024	protein-coding gene	gene with protein product		608094	"""solute carrier family 37 (glycerol-3-phosphate transporter), member 1"""			11112347	Standard	NM_018964		Approved		uc002zbi.3	P57057	OTTHUMG00000086803	ENST00000352133.2:c.909C>T	21.37:g.43979127C>T		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	101	59	0.584158	NM_018964	D3DSJ7|Q9HAQ1	Silent	SNP	ENST00000352133.2	37	CCDS13689.1																																																																																			C|0.961;T|0.039	0.039	strong		0.567	SLC37A1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195377.1		
KIAA0226	9711	hgsc.bcm.edu	37	3	197432036	197432036	+	Missense_Mutation	SNP	C	C	T	rs61743568	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:197432036C>T	ENST00000296343.5	-	3	229	c.230G>A	c.(229-231)cGc>cAc	p.R77H	KIAA0226_ENST00000449205.1_Missense_Mutation_p.R77H|KIAA0226_ENST00000273582.5_Missense_Mutation_p.R17H|KIAA0226_ENST00000389665.5_Missense_Mutation_p.R77H|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	52	29	0.557692	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	
ALMS1	7840	hgsc.bcm.edu	37	2	73679956	73679956	+	Missense_Mutation	SNP	C	C	T	rs28730854	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:73679956C>T	ENST00000264448.6	+	8	6410	c.6299C>T	c.(6298-6300)tCg>tTg	p.S2100L	ALMS1_ENST00000377715.1_Missense_Mutation_p.S2100L|ALMS1_ENST00000409009.1_Missense_Mutation_p.S2058L	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	2100	34 X 47 AA approximate tandem repeat.				endosomal transport (GO:0016197)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of stress fiber assembly (GO:0051492)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)				breast(4)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(31)|lung(68)|ovary(4)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	147						AGAGAGAAATCGAATATTTTC	0.388													C|||	74	0.0147764	0.0023	0.0231	5008	,	,		20291	0.0		0.0497	False		,,,				2504	0.0051				p.S2100L		Atlas-SNP	.											.	ALMS1	384	.	0			c.C6299T						PASS	.	C	LEU/SER	25,3661		0,25,1818	29.0	29.0	29.0		6299	3.4	0.0	2	dbSNP_125	29	266,7900		7,252,3824	yes	missense	ALMS1	NM_015120.4	145	7,277,5642	TT,TC,CC		3.2574,0.6782,2.4553	possibly-damaging	2100/4168	73679956	291,11561	1843	4083	5926	SO:0001583	missense	7840	exon8			AGAAATCGAATAT	AB002326	CCDS42697.1	2p13.1	2014-09-17			ENSG00000116127	ENSG00000116127			428	protein-coding gene	gene with protein product		606844				9063741	Standard	NM_015120		Approved	KIAA0328	uc002sje.1	Q8TCU4	OTTHUMG00000152812	ENST00000264448.6:c.6299C>T	2.37:g.73679956C>T	ENSP00000264448:p.Ser2100Leu	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	89	32	0.359551	NM_015120	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Missense_Mutation	SNP	ENST00000264448.6	37	CCDS42697.1	42	0.019230769230769232	3	0.006097560975609756	9	0.024861878453038673	0	0.0	30	0.0395778364116095	C	11.24	1.578934	0.28180	0.006782	0.032574	ENSG00000116127	ENST00000409009;ENST00000264448;ENST00000377715	T;T;T	0.22539	2.86;2.86;1.95	4.26	3.36	0.38483	.	1.002150	0.08050	N	0.996567	T	0.09818	0.0241	L	0.46157	1.445	0.09310	N	1	D;D;D	0.69078	0.997;0.997;0.993	P;P;P	0.57620	0.824;0.824;0.768	T	0.08186	-1.0734	10	0.62326	D	0.03	.	10.0841	0.42408	0.0:0.7961:0.2038:0.0	rs28730854	2100;2058;2100	Q8TCU4-3;B8ZZJ3;Q8TCU4	.;.;ALMS1_HUMAN	L	2058;2100;2100	ENSP00000386627:S2058L;ENSP00000264448:S2100L;ENSP00000366944:S2100L	ENSP00000264448:S2100L	S	+	2	0	ALMS1	73533464	0.170000	0.23016	0.012000	0.15200	0.077000	0.17291	0.281000	0.18810	1.336000	0.45506	0.650000	0.86243	TCG	C|0.972;T|0.028	0.028	strong		0.388	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120	
TCP11L1	55346	hgsc.bcm.edu	37	11	33090362	33090362	+	Silent	SNP	C	C	T	rs34745218	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:33090362C>T	ENST00000334274.4	+	9	1684	c.1284C>T	c.(1282-1284)atC>atT	p.I428I	TCP11L1_ENST00000324357.9_Silent_p.I207I|TCP11L1_ENST00000531632.2_Silent_p.I428I|TCP11L1_ENST00000432887.1_Silent_p.I428I	NM_018393.3	NP_060863.3	Q9NUJ3	T11L1_HUMAN	t-complex 11, testis-specific-like 1	428						microtubule (GO:0005874)				kidney(1)|liver(2)|lung(2)|skin(1)	6						AGGGCCAGATCCAGGCCGTGG	0.642													C|||	47	0.00938498	0.0015	0.0144	5008	,	,		20263	0.0		0.0308	False		,,,				2504	0.0041				p.I428I		Atlas-SNP	.											.	TCP11L1	40	.	0			c.C1284T						PASS	.	C	,	28,4376	33.5+/-64.1	0,28,2174	88.0	68.0	75.0		1284,1284	4.5	1.0	11	dbSNP_126	75	265,8331	102.1+/-163.3	3,259,4036	no	coding-synonymous,coding-synonymous	TCP11L1	NM_001145541.1,NM_018393.3	,	3,287,6210	TT,TC,CC		3.0828,0.6358,2.2538	,	428/510,428/510	33090362	293,12707	2202	4298	6500	SO:0001819	synonymous_variant	55346	exon9			CCAGATCCAGGCC	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.1284C>T	11.37:g.33090362C>T		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	70	8	0.114286	NM_001145541	D3DR01|Q8IVX4	Silent	SNP	ENST00000334274.4	37	CCDS7882.1	39	0.017857142857142856	1	0.0020325203252032522	10	0.027624309392265192	0	0.0	28	0.036939313984168866	C	9.683	1.149909	0.21371	0.006358	0.030828	ENSG00000176148	ENST00000528962	.	.	.	5.67	4.46	0.54185	.	.	.	.	.	T	0.26412	0.0645	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.35549	-0.9784	4	.	.	.	-31.4284	8.1608	0.31198	0.0:0.7197:0.0:0.2803	rs34745218	.	.	.	S	44	.	.	P	+	1	0	TCP11L1	33046938	0.991000	0.36638	1.000000	0.80357	0.843000	0.47879	0.317000	0.19487	1.020000	0.39573	0.462000	0.41574	CCA	C|0.980;T|0.020	0.020	strong		0.642	TCP11L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383377.4	NM_018393	
BUD13	84811	hgsc.bcm.edu	37	11	116633862	116633862	+	Missense_Mutation	SNP	G	G	A	rs11820589	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:116633862G>A	ENST00000260210.4	-	4	466	c.443C>T	c.(442-444)cCg>cTg	p.P148L	BUD13_ENST00000375445.3_Missense_Mutation_p.P148L	NM_032725.3	NP_116114.1	Q9BRD0	BUD13_HUMAN	BUD13 homolog (S. cerevisiae)	148	Arg-rich.		P -> L (in dbSNP:rs11820589).		mRNA export from nucleus (GO:0006406)|mRNA splicing, via spliceosome (GO:0000398)	nucleus (GO:0005634)|RES complex (GO:0070274)	poly(A) RNA binding (GO:0044822)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(11)|pancreas(2)|skin(1)|urinary_tract(1)	22	all_hematologic(175;0.0487)	all_cancers(61;1.72e-06)|all_epithelial(67;0.000735)|Melanoma(852;0.022)|Acute lymphoblastic leukemia(157;0.0255)|Medulloblastoma(222;0.0523)|Breast(348;0.056)|all_hematologic(158;0.0588)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|Epithelial(105;5.81e-06)|all cancers(92;0.000144)|OV - Ovarian serous cystadenocarcinoma(223;0.154)		AGATGGATCCGGGGTGTCATG	0.572													G|||	445	0.0888578	0.1808	0.134	5008	,	,		16456	0.0		0.0696	False		,,,				2504	0.044				p.P148L		Atlas-SNP	.											.	BUD13	41	.	0			c.C443T						PASS	.	G	LEU/PRO,LEU/PRO	725,3677	295.0+/-283.4	66,593,1542	99.0	106.0	104.0	http://www.ncbi.nlm.nih.gov/pubmed?term	443,443	4.1	0.4	11	dbSNP_120	104	586,8004	154.2+/-208.4	16,554,3725	yes	missense,missense	BUD13	NM_001159736.1,NM_032725.3	98,98	82,1147,5267	AA,AG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	6.8219,16.4698,10.0908	benign,benign	148/486,148/620	116633862	1311,11681	2201	4295	6496	SO:0001583	missense	84811	exon4			GGATCCGGGGTGT	BC006350	CCDS8374.1, CCDS53712.1	11q23.3	2012-06-07	2007-01-12		ENSG00000137656	ENSG00000137656			28199	protein-coding gene	gene with protein product	"""functional spliceosome-associated protein 71"""		"""BUD13 homolog (yeast)"""			12477932	Standard	NM_032725		Approved	MGC13125, fSAP71, Cwc26	uc001ppn.3	Q9BRD0	OTTHUMG00000045136	ENST00000260210.4:c.443C>T	11.37:g.116633862G>A	ENSP00000260210:p.Pro148Leu	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	77	17	0.220779	NM_001159736	A8K0S0|Q96LS7	Missense_Mutation	SNP	ENST00000260210.4	37	CCDS8374.1	170	0.07783882783882784	88	0.17886178861788618	36	0.09944751381215469	0	0.0	46	0.06068601583113457	G	10.42	1.346601	0.24426	0.164698	0.068219	ENSG00000137656	ENST00000375445;ENST00000260210	T;T	0.20069	2.15;2.1	5.01	4.08	0.47627	.	0.318031	0.37669	N	0.001982	T	0.00039	0.0001	M	0.75777	2.31	0.09310	P	0.99999896671	B;P;B	0.40931	0.084;0.733;0.047	B;B;B	0.36608	0.016;0.229;0.011	T	0.10870	-1.0611	9	0.87932	D	0	-0.6497	12.9589	0.58447	0.0794:0.0:0.9206:0.0	rs11820589;rs52824190;rs11820589	148;148;148	A8K4Z6;Q9BRD0-2;Q9BRD0	.;.;BUD13_HUMAN	L	148	ENSP00000364594:P148L;ENSP00000260210:P148L	ENSP00000260210:P148L	P	-	2	0	BUD13	116139072	1.000000	0.71417	0.358000	0.25811	0.036000	0.12997	4.403000	0.59729	2.597000	0.87782	0.609000	0.83330	CCG	G|0.905;A|0.095	0.095	strong		0.572	BUD13-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000104864.1	NM_032725	
OBSCN	84033	hgsc.bcm.edu	37	1	228464303	228464303	+	Missense_Mutation	SNP	G	G	T	rs75280352	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:228464303G>T	ENST00000422127.1	+	22	6417	c.6373G>T	c.(6373-6375)Gct>Tct	p.A2125S	OBSCN_ENST00000284548.11_Missense_Mutation_p.A2125S|OBSCN_ENST00000359599.6_Missense_Mutation_p.A972S|OBSCN_ENST00000570156.2_Missense_Mutation_p.A2500S|OBSCN_ENST00000366709.4_5'UTR|RP5-1139B12.3_ENST00000602947.1_RNA|RP5-1139B12.2_ENST00000602517.1_RNA|RP5-1139B12.3_ENST00000602529.1_RNA|OBSCN_ENST00000366707.4_5'UTR	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	2125	Ig-like 21.				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)				GTGCCACCTGGCTGTGCGGGG	0.672													G|||	23	0.00459265	0.0008	0.0101	5008	,	,		15176	0.0		0.0139	False		,,,				2504	0.001				p.A2500S		Atlas-SNP	.											.	OBSCN	2142	.	0			c.G7498T						PASS	.	G	SER/ALA,SER/ALA	19,4145		0,19,2063	16.0	21.0	20.0		6373,6373	1.9	0.1	1	dbSNP_131	20	234,8182		4,226,3978	yes	missense,missense	OBSCN	NM_001098623.1,NM_052843.2	99,99	4,245,6041	TT,TG,GG		2.7804,0.4563,2.0111	benign,benign	2125/7969,2125/6621	228464303	253,12327	2082	4208	6290	SO:0001583	missense	84033	exon26			CACCTGGCTGTGC	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.6373G>T	1.37:g.228464303G>T	ENSP00000409493:p.Ala2125Ser	Somatic	234	0	0		WXS	Illumina HiSeq	Phase_I	232	134	0.577586	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	15	0.006868131868131868	1	0.0020325203252032522	5	0.013812154696132596	0	0.0	9	0.011873350923482849	G	10.48	1.363003	0.24684	0.004563	0.027804	ENSG00000154358	ENST00000284548;ENST00000422127;ENST00000359599	T;T;T	0.04234	3.67;3.67;3.67	5.23	1.86	0.25419	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	0.356983	0.26203	N	0.025723	T	0.00724	0.0024	N	0.13168	0.305	0.20403	N	0.999906	P;P	0.44816	0.844;0.499	B;B	0.39152	0.292;0.069	T	0.39901	-0.9591	10	0.08599	T	0.76	.	4.5827	0.12266	0.298:0.0:0.5441:0.1578	.	2125;2125	Q5VST9;Q5VST9-3	OBSCN_HUMAN;.	S	2125;2125;972	ENSP00000284548:A2125S;ENSP00000409493:A2125S;ENSP00000352613:A972S	ENSP00000284548:A2125S	A	+	1	0	OBSCN	226530926	0.038000	0.19896	0.075000	0.20258	0.026000	0.11368	1.268000	0.33062	1.193000	0.43086	0.549000	0.68633	GCT	G|0.993;T|0.007	0.007	strong		0.672	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
DNAJC1	64215	hgsc.bcm.edu	37	10	22048330	22048330	+	Silent	SNP	C	C	T	rs9045	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	120	0	0		WXS	Illumina HiSeq	Phase_I	131	69	0.526718	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	
SMARCA2	6595	hgsc.bcm.edu	37	9	2039793	2039793	+	Missense_Mutation	SNP	A	A	C	rs62534884	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:2039793A>C	ENST00000382203.1	+	4	892	c.683A>C	c.(682-684)cAg>cCg	p.Q228P	RP11-264I13.2_ENST00000426860.1_RNA|SMARCA2_ENST00000357248.2_Missense_Mutation_p.Q228P|SMARCA2_ENST00000382194.1_Missense_Mutation_p.Q228P|SMARCA2_ENST00000349721.2_Missense_Mutation_p.Q228P|SMARCA2_ENST00000491574.1_3'UTR			P51531	SMCA2_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2	228	Poly-Gln.				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)		cagcagcagcagcagcagcag	0.622													a|||	146	0.0291534	0.0303	0.0259	5008	,	,		11307	0.002		0.0755	False		,,,				2504	0.0102				p.Q228P		Atlas-SNP	.											SMARCA2_ENST00000349721,caecum,carcinoma,0,2	SMARCA2	313	2	0			c.A683C						PASS	.						9.0	11.0	11.0					9																	2039793		1895	3790	5685	SO:0001583	missense	6595	exon4			AGCAGCAGCAGCA	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.683A>C	9.37:g.2039793A>C	ENSP00000371638:p.Gln228Pro	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	74	33	0.445946	NM_139045	B1ALG3|B1ALG4|D3DRH4|D3DRH5	Missense_Mutation	SNP	ENST00000382203.1	37	CCDS34977.1	63	0.028846153846153848	8	0.016260162601626018	7	0.019337016574585635	0	0.0	48	0.0633245382585752	a	2.004	-0.428824	0.04701	.	.	ENSG00000080503	ENST00000349721;ENST00000357248;ENST00000450198;ENST00000382203;ENST00000382194	T;T;T;T;T	0.30981	1.51;1.51;1.51;1.51;1.51	2.48	-0.297	0.12820	.	0.424911	0.23457	N	0.047973	T	0.01287	0.0042	N	0.19112	0.55	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.31668	-0.9935	10	0.02654	T	1	.	7.7965	0.29150	0.5942:0.4058:0.0:0.0	rs62534884	228;228	P51531-2;P51531	.;SMCA2_HUMAN	P	228	ENSP00000265773:Q228P;ENSP00000349788:Q228P;ENSP00000392081:Q228P;ENSP00000371638:Q228P;ENSP00000371629:Q228P	ENSP00000265773:Q228P	Q	+	2	0	SMARCA2	2029793	0.951000	0.32395	0.169000	0.22859	0.260000	0.26232	0.791000	0.26915	-0.059000	0.13154	0.373000	0.22412	CAG	A|0.970;C|0.030	0.030	strong		0.622	SMARCA2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000051505.1	NM_003070	
ESYT2	57488	hgsc.bcm.edu	37	7	158528233	158528233	+	Silent	SNP	A	A	G	rs3816462	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	88	0	0		WXS	Illumina HiSeq	Phase_I	66	26	0.393939	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	
NOTCH2NL	388677	hgsc.bcm.edu	37	1	145281656	145281656	+	Missense_Mutation	SNP	A	A	T	rs4649852	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:145281656A>T	ENST00000369340.3	+	5	1030	c.586A>T	c.(586-588)Acc>Tcc	p.T196S	RP11-458D21.5_ENST00000468030.1_Missense_Mutation_p.T196S|NOTCH2NL_ENST00000362074.6_Missense_Mutation_p.T196S|NOTCH2NL_ENST00000344859.3_Missense_Mutation_p.T196S			Q7Z3S9	NT2NL_HUMAN	notch 2 N-terminal like	196	EGF-like 6. {ECO:0000255|PROSITE- ProRule:PRU00076}.		T -> S (in dbSNP:rs4649852).		cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|Notch signaling pathway (GO:0007219)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(10)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	27						CAATGGAGGCACCTGTCGGCA	0.572																																					p.T196S		Atlas-SNP	.											NOTCH2NL_ENST00000362074,NS,carcinoma,-2,6	NOTCH2NL	100	6	0			c.A586T						scavenged	.						145.0	146.0	146.0					1																	145281656		2203	4300	6503	SO:0001583	missense	388677	exon4			GGAGGCACCTGTC		CCDS72880.1	1q21.2	2010-06-24	2010-06-24		ENSG00000213240	ENSG00000213240			31862	protein-coding gene	gene with protein product			"""Notch homolog 2 (Drosophila) N-terminal like"""			14673143	Standard	NM_203458		Approved	N2N	uc001emn.4	Q7Z3S9	OTTHUMG00000013754	ENST00000369340.3:c.586A>T	1.37:g.145281656A>T	ENSP00000358346:p.Thr196Ser	Somatic	955	3	0.00314136		WXS	Illumina HiSeq	Phase_I	840	127	0.15119	NM_203458	Q5BKT8|Q5VTG9|Q5XG84|Q6P192|Q8NC23|Q8WUQ9|Q96FY1	Missense_Mutation	SNP	ENST00000369340.3	37	CCDS909.1	.	.	.	.	.	.	.	.	.	.	A	18.20	3.571953	0.65765	.	.	ENSG00000213240	ENST00000362074;ENST00000344859;ENST00000369340	T;D;T	0.91631	-0.19;-2.88;-0.19	2.87	2.87	0.33458	Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	.	.	.	.	D	0.91737	0.7387	L	0.59912	1.85	0.25729	N	0.985286	D;D	0.76494	0.998;0.999	D;D	0.76071	0.987;0.955	D	0.83497	0.0073	9	0.49607	T	0.09	.	9.1743	0.37102	1.0:0.0:0.0:0.0	rs4649852	196;196	Q7Z3S9-2;Q7Z3S9	.;NT2NL_HUMAN	S	196	ENSP00000354929:T196S;ENSP00000344557:T196S;ENSP00000358346:T196S	ENSP00000344557:T196S	T	+	1	0	NOTCH2NL	143993013	1.000000	0.71417	0.999000	0.59377	0.784000	0.44337	9.063000	0.93927	1.309000	0.44985	0.329000	0.21502	ACC	A|0.863;T|0.137	0.137	strong		0.572	NOTCH2NL-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000038546.1	NM_203458	
MUC4	4585	hgsc.bcm.edu	37	3	195506483	195506483	+	Missense_Mutation	SNP	T	T	G	rs201375109	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195506483T>G	ENST00000463781.3	-	2	12427	c.11968A>C	c.(11968-11970)Act>Cct	p.T3990P	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.T3990P	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.T3990P(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)		ACTGAGGAAGTGTCGGTGACA	0.592													.|||	303	0.0605032	0.0772	0.062	5008	,	,		8297	0.0169		0.0795	False		,,,				2504	0.0624				p.T3990P		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	1	Substitution - Missense(1)	endometrium(1)	c.A11968C						scavenged	.						10.0	7.0	8.0					3																	195506483		622	1355	1977	SO:0001583	missense	4585	exon2			AGGAAGTGTCGGT	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.11968A>C	3.37:g.195506483T>G	ENSP00000417498:p.Thr3990Pro	Somatic	56	3	0.0535714		WXS	Illumina HiSeq	Phase_I	49	14	0.285714	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	N	1.493	-0.554047	0.03996	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.34859	1.34;1.42	0.481	-0.864	0.10666	.	0.562686	0.09843	U	0.748557	T	0.32071	0.0817	N	0.08118	0	0.09310	N	1	D	0.57257	0.979	D	0.68192	0.956	T	0.29212	-1.0019	9	.	.	.	.	5.8902	0.18909	0.0:0.618:0.0:0.382	.	3862	E7ESK3	.	P	3990	ENSP00000417498:T3990P;ENSP00000420243:T3990P	.	T	-	1	0	MUC4	196991262	0.000000	0.05858	0.001000	0.08648	0.052000	0.14988	-2.288000	0.01150	-2.052000	0.00902	-2.075000	0.00382	ACT	C|0.002;G|0.002;T|0.996	0.002	weak		0.592	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
TMCC3	57458	hgsc.bcm.edu	37	12	95044161	95044161	+	Missense_Mutation	SNP	A	A	C	rs1274523	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:95044161A>C	ENST00000261226.4	-	1	177	c.46T>G	c.(46-48)Tac>Gac	p.Y16D		NM_020698.2	NP_065749	Q9ULS5	TMCC3_HUMAN	transmembrane and coiled-coil domain family 3	16			Y -> D (in dbSNP:rs1274523). {ECO:0000269|PubMed:15489334}.	DRTYSYPGRHHRCKSR -> ASCRSCSAPGFAVWPL (in Ref. 3; BAA86459). {ECO:0000305}.		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						CGGCCGGGGTACGAGTAGGTC	0.796													C|||	4985	0.995407	0.9992	0.9957	5008	,	,		5677	0.999		0.9901	False		,,,				2504	0.9918				p.Y16D		Atlas-SNP	.											.	TMCC3	63	.	0			c.T46G						PASS	.						2.0	3.0	3.0					12																	95044161		1370	2776	4146	SO:0001583	missense	57458	exon1			CGGGGTACGAGTA	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.46T>G	12.37:g.95044161A>C	ENSP00000261226:p.Tyr16Asp	Somatic	0	0	.		WXS	Illumina HiSeq	Phase_I	7	7	1	NM_020698	Q8IWB2	Missense_Mutation	SNP	ENST00000261226.4	37	CCDS31877.1	2109	0.9656593406593407	464	0.943089430894309	346	0.9558011049723757	560	0.9790209790209791	739	0.974934036939314	C	11.59	1.684496	0.29872	.	.	ENSG00000057704	ENST00000261226	T	0.27890	1.64	4.95	4.07	0.47477	.	0.790881	0.11840	N	0.524376	T	0.00012	0.0000	N	0.03608	-0.345	0.09310	P	0.9999999999999301	B	0.02656	0.0	B	0.01281	0.0	T	0.28744	-1.0034	9	0.33940	T	0.23	-19.2869	7.3281	0.26567	0.1669:0.7462:0.0:0.0869	rs1274523;rs59024685	16	Q9ULS5	TMCC3_HUMAN	D	16	ENSP00000261226:Y16D	ENSP00000261226:Y16D	Y	-	1	0	TMCC3	93568292	0.998000	0.40836	0.975000	0.42487	0.434000	0.31775	1.836000	0.39191	0.527000	0.28560	-0.333000	0.08304	TAC	A|0.034;C|0.966	0.966	strong		0.796	TMCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408113.1	NM_020698	
ZAK	51776	hgsc.bcm.edu	37	2	174055646	174055646	+	Silent	SNP	T	T	C	rs35853276	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:174055646T>C	ENST00000375213.3	+	6	517	c.439T>C	c.(439-441)Ttg>Ctg	p.L147L	MLTK_ENST00000409176.2_Silent_p.L147L|MLTK_ENST00000539448.1_Silent_p.L147L|MLK7-AS1_ENST00000422703.1_RNA|MLK7-AS1_ENST00000419609.1_RNA|MLTK_ENST00000338983.3_Silent_p.L147L|MLTK_ENST00000480606.1_3'UTR|MLTK_ENST00000431503.2_Silent_p.L46L	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	114	0	0		WXS	Illumina HiSeq	Phase_I	63	35	0.555556	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		
IFT140	9742	hgsc.bcm.edu	37	16	1608082	1608082	+	Silent	SNP	A	A	G	rs2076436	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:1608082A>G	ENST00000426508.2	-	19	2616	c.2253T>C	c.(2251-2253)ccT>ccC	p.P751P	IFT140_ENST00000439987.2_5'UTR	NM_014714.3	NP_055529.2	Q96RY7	IF140_HUMAN	intraflagellar transport 140	751					cilium assembly (GO:0042384)|intraciliary retrograde transport (GO:0035721)|protein localization to cilium (GO:0061512)|regulation of cilium assembly (GO:1902017)|renal system development (GO:0072001)|retina development in camera-type eye (GO:0060041)|skeletal system morphogenesis (GO:0048705)	axoneme (GO:0005930)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|intraciliary transport particle A (GO:0030991)|photoreceptor connecting cilium (GO:0032391)		p.P751P(1)		breast(1)|central_nervous_system(2)|endometrium(7)|kidney(4)|large_intestine(12)|lung(10)|ovary(5)|pancreas(1)|prostate(4)|skin(4)|stomach(2)|urinary_tract(1)	53		Hepatocellular(780;0.219)				ACACCATCTGAGGGATGTGGT	0.547													A|||	1740	0.347444	0.5507	0.1844	5008	,	,		18218	0.3433		0.2087	False		,,,				2504	0.3354				p.P751P		Atlas-SNP	.											IFT140,NS,carcinoma,0,1	IFT140	128	1	1	Substitution - coding silent(1)	stomach(1)	c.T2253C						PASS	.	A		2135,2263	579.6+/-385.0	518,1099,582	146.0	144.0	145.0		2253	0.7	0.3	16	dbSNP_96	145	1861,6739	333.7+/-320.7	197,1467,2636	no	coding-synonymous	IFT140	NM_014714.3		715,2566,3218	GG,GA,AA		21.6395,48.5448,30.7432		751/1463	1608082	3996,9002	2199	4300	6499	SO:0001819	synonymous_variant	9742	exon19			CATCTGAGGGATG	AB011162	CCDS10439.1	16p13.3	2014-07-03	2014-07-03	2005-11-02	ENSG00000187535	ENSG00000187535		"""Intraflagellar transport homologs"", ""WD repeat domain containing"""	29077	protein-coding gene	gene with protein product		614620	"""WD and tetratricopeptide repeats 2"", ""intraflagellar transport 140 homolog (Chlamydomonas)"""	WDTC2		9628581	Standard	NM_014714		Approved	gs114, KIAA0590	uc002cmb.3	Q96RY7	OTTHUMG00000128585	ENST00000426508.2:c.2253T>C	16.37:g.1608082A>G		Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	149	29	0.194631	NM_014714	A2A2A8|D3DU75|O60332|Q9UG52	Silent	SNP	ENST00000426508.2	37	CCDS10439.1																																																																																			A|0.687;G|0.313	0.313	strong		0.547	IFT140-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250438.2	NM_014714	
DSC1	1823	hgsc.bcm.edu	37	18	28734749	28734749	+	Silent	SNP	A	A	G	rs2249810	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:28734749A>G	ENST00000257198.5	-	5	876	c.615T>C	c.(613-615)taT>taC	p.Y205Y	DSC1_ENST00000257197.3_Silent_p.Y205Y|RP11-408H20.2_ENST00000581836.1_RNA	NM_024421.2	NP_077739.1	Q08554	DSC1_HUMAN	desmocollin 1	205	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|gap junction (GO:0005921)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(20)|ovary(3)|skin(10)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	53			OV - Ovarian serous cystadenocarcinoma(10;0.00778)			CAAACTGTTCATATTTCTCAC	0.328													A|||	2397	0.478634	0.2057	0.5749	5008	,	,		15175	0.6657		0.6183	False		,,,				2504	0.4427				p.Y205Y		Atlas-SNP	.											.	DSC1	240	.	0			c.T615C						PASS	.	A	,	1212,3194	419.3+/-338.6	165,882,1156	59.0	57.0	58.0		615,615	2.8	0.3	18	dbSNP_100	58	4955,3645	621.0+/-397.1	1412,2131,757	yes	coding-synonymous,coding-synonymous	DSC1	NM_004948.3,NM_024421.2	,	1577,3013,1913	GG,GA,AA		42.3837,27.5079,47.4166	,	205/841,205/895	28734749	6167,6839	2203	4300	6503	SO:0001819	synonymous_variant	1823	exon5			CTGTTCATATTTC	AF293358	CCDS11894.1, CCDS11895.1	18q12.1	2010-01-26			ENSG00000134765	ENSG00000134765		"""Cadherins / Major cadherins"""	3035	protein-coding gene	gene with protein product		125643				8486729	Standard	NM_024421		Approved	CDHF1	uc002kwn.3	Q08554	OTTHUMG00000131982	ENST00000257198.5:c.615T>C	18.37:g.28734749A>G		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	41	41	1	NM_004948	Q9HB01	Silent	SNP	ENST00000257198.5	37	CCDS11894.1																																																																																			G|0.484;N|0.000	0.484	strong		0.328	DSC1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254946.1	NM_004948, NM_024421	
LRIG1	26018	hgsc.bcm.edu	37	3	66433676	66433676	+	Silent	SNP	A	A	G	rs900171	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:66433676A>G	ENST00000273261.3	-	15	2745	c.2221T>C	c.(2221-2223)Ttg>Ctg	p.L741L	SLC25A26_ENST00000536651.1_Intron|LRIG1_ENST00000496559.2_5'UTR|LRIG1_ENST00000383703.3_Silent_p.L718L	NM_015541.2	NP_056356.2	Q96JA1	LRIG1_HUMAN	leucine-rich repeats and immunoglobulin-like domains 1	741	Ig-like C2-type 3.				innervation (GO:0060384)|otolith morphogenesis (GO:0032474)|sensory perception of sound (GO:0007605)	integral component of membrane (GO:0016021)				NS(2)|breast(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(12)|ovary(3)|prostate(1)|skin(4)|stomach(4)|urinary_tract(1)	42		Lung NSC(201;0.0101)		BRCA - Breast invasive adenocarcinoma(55;0.00047)		TCAGGGGTCAAGTGGTGCCGC	0.632													A|||	3478	0.694489	0.7247	0.6441	5008	,	,		19173	0.8036		0.5974	False		,,,				2504	0.6769				p.L741L		Atlas-SNP	.											.	LRIG1	138	.	0			c.T2221C						PASS	.	A		3087,1319	696.1+/-406.0	1077,933,193	69.0	66.0	67.0		2221	5.7	1.0	3	dbSNP_86	67	4828,3772	614.9+/-396.3	1375,2078,847	no	coding-synonymous	LRIG1	NM_015541.2		2452,3011,1040	GG,GA,AA		43.8605,29.9365,39.1435		741/1094	66433676	7915,5091	2203	4300	6503	SO:0001819	synonymous_variant	26018	exon15			GGGTCAAGTGGTG	AB050468	CCDS33783.1	3p14	2013-01-14			ENSG00000144749	ENSG00000144749		"""Immunoglobulin superfamily / I-set domain containing"""	17360	protein-coding gene	gene with protein product	"""ortholog of mouse integral membrane glycoprotein LIG-1"", ""leucine-rich repeat protein LRIG1"""	608868				11414704, 12234026	Standard	NM_015541		Approved	LIG-1, DKFZP586O1624, LIG1	uc003dmx.3	Q96JA1	OTTHUMG00000158727	ENST00000273261.3:c.2221T>C	3.37:g.66433676A>G		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	118	60	0.508475	NM_015541	Q6IQ51|Q96CF9|Q9BYB8|Q9UFI4	Silent	SNP	ENST00000273261.3	37	CCDS33783.1																																																																																			A|0.361;G|0.639	0.639	strong		0.632	LRIG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351930.1	NM_015541	
TRIM17	51127	hgsc.bcm.edu	37	1	228602660	228602660	+	Silent	SNP	G	G	C	rs503203	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:228602660G>C	ENST00000366697.2	-	1	1070	c.114C>G	c.(112-114)gcC>gcG	p.A38A	TRIM17_ENST00000456946.2_Silent_p.A38A|TRIM17_ENST00000366698.2_Silent_p.A38A|TRIM17_ENST00000295033.3_Silent_p.A38A			Q9Y577	TRI17_HUMAN	tripartite motif containing 17	38					protein autoubiquitination (GO:0051865)	intracellular (GO:0005622)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|ovary(1)	10		Prostate(94;0.0724)				GCTGGATGCAGGCTCGGCAGA	0.597													C|||	1482	0.295927	0.6513	0.098	5008	,	,		18452	0.3095		0.1014	False		,,,				2504	0.1421				p.A38A		Atlas-SNP	.											.	TRIM17	66	.	0			c.C114G						PASS	.	C	,,	2358,2048	556.5+/-379.5	615,1128,460	35.0	31.0	33.0		114,114,114	1.4	0.5	1	dbSNP_83	33	824,7776	767.5+/-407.6	41,742,3517	no	coding-synonymous,coding-synonymous,coding-synonymous	TRIM17	NM_001024940.2,NM_001134855.1,NM_016102.3	,,	656,1870,3977	CC,CG,GG		9.5814,46.4821,24.4656	,,	38/478,38/344,38/478	228602660	3182,9824	2203	4300	6503	SO:0001819	synonymous_variant	51127	exon2			GATGCAGGCTCGG	AF156271	CCDS1571.1, CCDS44327.1	1q42	2013-01-09	2011-01-25	2001-11-30	ENSG00000162931	ENSG00000162931		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	13430	protein-coding gene	gene with protein product	"""ring finger protein 16"", ""RING finger protein terf"", ""testis RING finger protein"""	606123	"""tripartite motif-containing 17"""	RNF16		9792805, 10894938	Standard	NM_016102		Approved	terf, RBCC	uc001hsv.3	Q9Y577	OTTHUMG00000039974	ENST00000366697.2:c.114C>G	1.37:g.228602660G>C		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	116	63	0.543103	NM_001024940	B4DVJ2|Q5VST8	Silent	SNP	ENST00000366697.2	37	CCDS1571.1																																																																																			G|0.745;C|0.255	0.255	strong		0.597	TRIM17-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096439.2	NM_016102	
XPO5	57510	hgsc.bcm.edu	37	6	43492578	43492578	+	Silent	SNP	G	G	A	rs2257082	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:43492578G>A	ENST00000265351.7	-	30	3513	c.3303C>T	c.(3301-3303)taC>taT	p.Y1101Y	POLR1C_ENST00000304004.3_Intron	NM_020750.2	NP_065801.1	Q9HAV4	XPO5_HUMAN	exportin 5	1101					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)			CCAGTGCCTCGTATATCTGGA	0.557													G|||	1627	0.32488	0.1611	0.2983	5008	,	,		21459	0.62		0.2853	False		,,,				2504	0.3016				p.Y1101Y		Atlas-SNP	.											.	XPO5	79	.	0			c.C3303T						PASS	.	G		720,3440		72,576,1432	57.0	61.0	60.0		3303	-6.1	0.9	6	dbSNP_100	60	2173,6235		274,1625,2305	no	coding-synonymous	XPO5	NM_020750.2		346,2201,3737	AA,AG,GG		25.8444,17.3077,23.0188		1101/1205	43492578	2893,9675	2080	4204	6284	SO:0001819	synonymous_variant	57510	exon30			TGCCTCGTATATC	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.3303C>T	6.37:g.43492578G>A		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	71	71	1	NM_020750	Q5JTE6|Q96G48|Q96HN3|Q9BWM6|Q9BZV5|Q9H9M4|Q9NT89|Q9NW39|Q9ULC9	Silent	SNP	ENST00000265351.7	37	CCDS47430.1	766	0.3507326007326007	90	0.18292682926829268	105	0.2900552486187845	351	0.6136363636363636	220	0.29023746701846964	G	3.527	-0.096513	0.07010	0.173077	0.258444	ENSG00000124571	ENST00000455285	.	.	.	6.08	-6.07	0.02158	.	.	.	.	.	T	0.47544	0.1451	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.57353	-0.7826	3	.	.	.	-16.2365	19.3651	0.94459	0.255:0.0:0.745:0.0	rs2257082;rs3198268;rs11544381;rs13212498;rs17287943;rs17846608;rs17859692;rs61216486;rs2257082	.	.	.	M	216	.	.	T	-	2	0	XPO5	43600556	0.233000	0.23772	0.921000	0.36526	0.496000	0.33645	-0.282000	0.08445	-0.948000	0.03668	-0.948000	0.02665	ACG	G|0.652;N|0.002	.	strong		0.557	XPO5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040657.2	NM_020750	
ALOX12	239	hgsc.bcm.edu	37	17	6904934	6904934	+	Missense_Mutation	SNP	A	A	G	rs434473	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:6904934A>G	ENST00000251535.6	+	8	1018	c.965A>G	c.(964-966)aAc>aGc	p.N322S	AC027763.2_ENST00000575727.1_Intron|AC027763.2_ENST00000399541.2_Intron|RP11-589P10.7_ENST00000572547.1_RNA|AC027763.2_ENST00000574377.1_Intron|AC027763.2_ENST00000399540.2_3'UTR	NM_000697.2	NP_000688.2	P18054	LOX12_HUMAN	arachidonate 12-lipoxygenase	322	Lipoxygenase. {ECO:0000255|PROSITE- ProRule:PRU00726}.		N -> S (in dbSNP:rs434473). {ECO:0000269|PubMed:2244907, ECO:0000269|PubMed:2377602, ECO:0000269|Ref.4}.		aging (GO:0007568)|arachidonic acid metabolic process (GO:0019369)|cellular component movement (GO:0006928)|cellular response to lipid (GO:0071396)|establishment of skin barrier (GO:0061436)|fatty acid oxidation (GO:0019395)|hepoxilin biosynthetic process (GO:0051122)|hepoxilin metabolic process (GO:0051121)|leukotriene A4 metabolic process (GO:1901751)|linoleic acid metabolic process (GO:0043651)|lipoxin A4 biosynthetic process (GO:2001303)|lipoxin B4 biosynthetic process (GO:2001306)|lipoxin metabolic process (GO:2001300)|lipoxygenase pathway (GO:0019372)|negative regulation of apoptotic process (GO:0043066)|negative regulation of muscle cell apoptotic process (GO:0010656)|negative regulation of platelet aggregation (GO:0090331)|positive regulation of angiogenesis (GO:0045766)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of gene expression (GO:0010628)|positive regulation of mitochondrial depolarization (GO:0051901)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of vasodilation (GO:0045909)|reactive oxygen species metabolic process (GO:0072593)|small molecule metabolic process (GO:0044281)|superoxide anion generation (GO:0042554)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|sarcolemma (GO:0042383)	arachidonate 12-lipoxygenase activity (GO:0004052)|hepoxilin A3 synthase activity (GO:0051120)|hepoxilin-epoxide hydrolase activity (GO:0047977)|iron ion binding (GO:0005506)|linoleate 13S-lipoxygenase activity (GO:0016165)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen (GO:0016702)			breast(2)|central_nervous_system(1)|endometrium(3)|large_intestine(4)|lung(4)|ovary(1)|prostate(3)|urinary_tract(1)	19						CAGCCTCCCAACCCCAGCTCT	0.493													A|||	1709	0.341254	0.1528	0.268	5008	,	,		18924	0.4712		0.4016	False		,,,				2504	0.4519				p.N322S		Atlas-SNP	.											.	ALOX12	49	.	0			c.A965G						PASS	.	A	SER/ASN	862,3544	340.2+/-306.1	80,702,1421	158.0	158.0	158.0		965	-4.4	0.8	17	dbSNP_80	158	3626,4974	523.0+/-380.2	767,2092,1441	yes	missense	ALOX12	NM_000697.2	46	847,2794,2862	GG,GA,AA		42.1628,19.5642,34.5072	benign	322/664	6904934	4488,8518	2203	4300	6503	SO:0001583	missense	239	exon8			CTCCCAACCCCAG	M35418	CCDS11084.1	17p13.1	2010-01-14			ENSG00000108839	ENSG00000108839	1.13.11.31	"""Arachidonate lipoxygenases"""	429	protein-coding gene	gene with protein product	"""platelet 12-LOX"""	152391				1570320	Standard	NM_000697		Approved	12S-LOX	uc002gdx.4	P18054	OTTHUMG00000102088	ENST00000251535.6:c.965A>G	17.37:g.6904934A>G	ENSP00000251535:p.Asn322Ser	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	71	32	0.450704	NM_000697	O95569|Q6ISF8|Q9UQM4	Missense_Mutation	SNP	ENST00000251535.6	37	CCDS11084.1	749	0.34294871794871795	78	0.15853658536585366	107	0.2955801104972376	262	0.458041958041958	302	0.39841688654353563	A	0.780	-0.762597	0.02996	0.195642	0.421628	ENSG00000108839	ENST00000251535	T	0.76186	-1.0	4.78	-4.4	0.03600	Lipoxygenase, C-terminal (3);	0.561606	0.20079	N	0.099691	T	0.00012	0.0000	N	0.05383	-0.06	0.46586	P	8.820000000000494E-4	B	0.02656	0.0	B	0.09377	0.004	T	0.23440	-1.0188	9	0.07813	T	0.8	-10.9398	8.2298	0.31590	0.3783:0.1187:0.503:0.0	rs434473;rs1126668;rs57549908;rs434473	322	P18054	LOX12_HUMAN	S	322	ENSP00000251535:N322S	ENSP00000251535:N322S	N	+	2	0	ALOX12	6845658	0.000000	0.05858	0.829000	0.32907	0.091000	0.18340	-0.487000	0.06505	-0.672000	0.05266	-0.380000	0.06706	AAC	A|0.648;G|0.352	0.352	strong		0.493	ALOX12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219922.2		
HIST1H2BE	8344	hgsc.bcm.edu	37	6	26184041	26184041	+	Silent	SNP	A	A	G	rs16891375	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:26184041A>G	ENST00000356530.3	+	1	84	c.18A>G	c.(16-18)aaA>aaG	p.K6K		NM_003523.2	NP_003514.2	P62807	H2B1C_HUMAN	histone cluster 1, H2be	6					antibacterial humoral response (GO:0019731)|chromatin organization (GO:0006325)|defense response to Gram-positive bacterium (GO:0050830)|innate immune response in mucosa (GO:0002227)|nucleosome assembly (GO:0006334)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(1)|large_intestine(2)|lung(1)	4						AGCCAGCGAAATCCGCTCCCG	0.522													A|||	332	0.0662939	0.0061	0.0403	5008	,	,		19039	0.0526		0.1133	False		,,,				2504	0.1319				p.K6K		Atlas-SNP	.											.	HIST1H2BE	10	.	0			c.A18G						PASS	.	A		82,4324		1,80,2122	79.0	77.0	77.0		18	0.2	0.5	6	dbSNP_123	77	772,7828		20,732,3548	no	coding-synonymous	HIST1H2BE	NM_003523.2		21,812,5670	GG,GA,AA		8.9767,1.8611,6.5662		6/127	26184041	854,12152	2203	4300	6503	SO:0001819	synonymous_variant	8344	exon1			AGCGAAATCCGCT	Z80780	CCDS4588.1	6p22.1	2011-01-27	2006-10-11	2003-02-14	ENSG00000197697	ENSG00000274290		"""Histones / Replication-dependent"""	4753	protein-coding gene	gene with protein product		602805	"""H2B histone family, member H"", ""histone 1, H2be"""	H2BFH		9119399, 12408966	Standard	NM_003523		Approved	H2B/h, H2B.h	uc003ngt.3	P62807	OTTHUMG00000014427	ENST00000356530.3:c.18A>G	6.37:g.26184041A>G		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	85	32	0.376471	NM_003523	P02278|Q3B872|Q4VB69|Q93078|Q93080	Silent	SNP	ENST00000356530.3	37	CCDS4588.1																																																																																			A|0.936;G|0.064	0.064	strong		0.522	HIST1H2BE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040090.1	NM_003523	
HLA-A	3105	hgsc.bcm.edu	37	6	29912280	29912280	+	Missense_Mutation	SNP	T	T	C	rs35946537|rs1136903	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:29912280T>C	ENST00000396634.1	+	7	1240	c.899T>C	c.(898-900)cTg>cCg	p.L300P	HLA-A_ENST00000376802.2_Intron|HLA-A_ENST00000376809.5_Missense_Mutation_p.L300P|HLA-A_ENST00000376806.5_Missense_Mutation_p.L300P			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	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)	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						TTCCCAGAGCTGTCTTCCCAG	0.597									Osteosarcoma, Familial Clustering of;Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of;Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of	Multiple Myeloma(9;0.094)			N|||	3437	0.686302	0.7307	0.7738	5008	,	,		19138	0.6885		0.6342	False		,,,				2504	0.6155				p.L300P		Atlas-SNP	.											.	HLA-A	89	.	0			c.T899C						PASS	.	C	PRO/LEU	2105,917		702,701,108	79.0	74.0	76.0		899	2.5	0.1	6	dbSNP_86	76	3266,2152		982,1302,425	no	missense	HLA-A	NM_002116.7	98	1684,2003,533	CC,CT,TT		39.7195,30.3441,36.3626	benign	300/366	29912280	5371,3069	1511	2709	4220	SO:0001583	missense	3105	exon5	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	CAGAGCTGTCTTC	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.899T>C	6.37:g.29912280T>C	ENSP00000379873:p.Leu300Pro	Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	115	43	0.373913	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Missense_Mutation	SNP	ENST00000396634.1	37	CCDS34373.1	1474	0.674908424908425	352	0.7154471544715447	262	0.7237569060773481	403	0.7045454545454546	457	0.6029023746701847	.	4.576	0.107015	0.08780	0.696559	0.602805	ENSG00000206503	ENST00000396634;ENST00000376806;ENST00000376809	T;T;T	0.00644	6.02;6.01;6.02	3.34	2.46	0.29980	Immunoglobulin-like fold (3);	0.174722	0.26991	N	0.021463	T	0.00241	0.0007	.	.	.	0.40565	P	0.018757000000000024	B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0	B;B;B;B;B	0.04013	0.001;0.0;0.0;0.0;0.0	T	0.48163	-0.9059	8	0.87932	D	0	.	5.789	0.18349	0.0:0.7416:0.0:0.2584	rs1136903;rs2231101;rs3179249;rs3200555;rs16868062;rs17845172;rs17857980;rs41541812;rs52814613	179;300;300;300;300	B4DVB9;P16188;Q5SRN5;P30455;P04439	.;1A30_HUMAN;.;1A36_HUMAN;1A03_HUMAN	P	300	ENSP00000379873:L300P;ENSP00000366002:L300P;ENSP00000366005:L300P	ENSP00000366002:L300P	L	+	2	0	HLA-A	30020259	0.000000	0.05858	0.127000	0.21898	0.087000	0.18053	-0.580000	0.05827	0.264000	0.21851	-0.665000	0.03846	CTG	.	.	alt		0.597	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
ACAN	176	hgsc.bcm.edu	37	15	89391160	89391160	+	Silent	SNP	C	C	A	rs2272023	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:89391160C>A	ENST00000561243.1	+	8	1623	c.1623C>A	c.(1621-1623)ccC>ccA	p.P541P	ACAN_ENST00000439576.2_Silent_p.P541P|ACAN_ENST00000559004.1_Silent_p.P541P|ACAN_ENST00000352105.7_Silent_p.P541P|ACAN_ENST00000558207.1_Silent_p.P541P			P16112	PGCA_HUMAN	aggrecan	541	G2-B.|Link 3. {ECO:0000255|PROSITE- ProRule:PRU00323}.				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.P541P(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)			TTGTGAGCCCCCGGACCCCAT	0.602													A|||	3477	0.694289	0.8918	0.6138	5008	,	,		11204	0.4802		0.7406	False		,,,				2504	0.6575				p.P541P		Atlas-SNP	.											ACAN,NS,carcinoma,0,1	ACAN	220	1	1	Substitution - coding silent(1)	stomach(1)	c.C1623A						PASS	.	A	,	3447,451		1522,403,24	72.0	75.0	74.0		1623,1623	-10.7	0.3	15	dbSNP_100	74	6260,2032		2367,1526,253	no	coding-synonymous,coding-synonymous	ACAN	NM_001135.3,NM_013227.3	,	3889,1929,277	AA,AC,CC		24.5055,11.57,20.3692	,	541/2432,541/2531	89391160	9707,2483	1949	4146	6095	SO:0001819	synonymous_variant	176	exon9			GAGCCCCCGGACC	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.1623C>A	15.37:g.89391160C>A		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	98	94	0.959184	NM_001135	Q13650|Q9UCD3|Q9UCP4|Q9UCP5|Q9UDE0	Silent	SNP	ENST00000561243.1	37	CCDS53970.1																																																																																			C|0.305;A|0.695	0.695	strong		0.602	ACAN-006	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416267.2	NM_001135	
ENTPD2	954	hgsc.bcm.edu	37	9	139945971	139945971	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:139945971C>T	ENST00000355097.2	-	3	424	c.377G>A	c.(376-378)cGc>cAc	p.R126H	ENTPD2_ENST00000460614.1_5'Flank|RP11-229P13.15_ENST00000439076.1_RNA|ENTPD2_ENST00000312665.5_Missense_Mutation_p.R126H	NM_001246.3|NM_203468.2	NP_001237.1|NP_982293.1	Q9Y5L3	ENTP2_HUMAN	ectonucleoside triphosphate diphosphohydrolase 2	126					G-protein coupled receptor signaling pathway (GO:0007186)|platelet activation (GO:0030168)|purine ribonucleoside diphosphate catabolic process (GO:0009181)	basal lamina (GO:0005605)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|nucleoside-diphosphatase activity (GO:0017110)|nucleoside-triphosphatase activity (GO:0017111)			endometrium(1)|lung(5)|prostate(1)|skin(2)|urinary_tract(3)	12	all_cancers(76;0.0926)	Myeloproliferative disorder(178;0.0511)	STAD - Stomach adenocarcinoma(284;0.123)	OV - Ovarian serous cystadenocarcinoma(145;2.94e-05)|Epithelial(140;0.00048)		CTTGAGCAGGCGCATACCCGC	0.632																																					p.R126H		Atlas-SNP	.											ENTPD2,NS,carcinoma,-1,1	ENTPD2	30	1	0			c.G377A						scavenged	.						66.0	64.0	65.0					9																	139945971		2203	4300	6503	SO:0001583	missense	954	exon3			AGCAGGCGCATAC	U91510	CCDS7025.1, CCDS7026.1	9q34	2008-07-21			ENSG00000054179	ENSG00000054179			3364	protein-coding gene	gene with protein product	"""CD39-like-1"", ""ecto-ATPase"""	602012		CD39L1		9271669	Standard	NM_203468		Approved	NTPDase-2	uc004ckw.2	Q9Y5L3	OTTHUMG00000020953	ENST00000355097.2:c.377G>A	9.37:g.139945971C>T	ENSP00000347213:p.Arg126His	Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	153	3	0.0196078	NM_203468	O15464|Q5SPY6|Q5SPY7	Missense_Mutation	SNP	ENST00000355097.2	37	CCDS7026.1	.	.	.	.	.	.	.	.	.	.	C	29.5	5.008471	0.93346	.	.	ENSG00000054179	ENST00000355097;ENST00000312665	T;T	0.41065	1.01;1.01	4.78	3.86	0.44501	.	0.000000	0.85682	D	0.000000	T	0.75496	0.3857	H	0.97635	4.045	0.51233	D	0.999917	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.83659	0.0160	10	0.87932	D	0	-33.8039	13.2282	0.59927	0.1605:0.8395:0.0:0.0	.	126;126	Q9Y5L3-2;Q9Y5L3	.;ENTP2_HUMAN	H	126	ENSP00000347213:R126H;ENSP00000312494:R126H	ENSP00000312494:R126H	R	-	2	0	ENTPD2	139065792	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.611000	0.61162	0.968000	0.38212	0.561000	0.74099	CGC	.	.	none		0.632	ENTPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055169.1	NM_203468	
UBXN11	91544	hgsc.bcm.edu	37	1	26608873	26608873	+	Missense_Mutation	SNP	T	T	A	rs1134583	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:26608873T>A	ENST00000374222.1	-	16	1944	c.1480A>T	c.(1480-1482)Agt>Tgt	p.S494C	UBXN11_ENST00000314675.7_Missense_Mutation_p.S374C|UBXN11_ENST00000374221.3_Missense_Mutation_p.S494C|UBXN11_ENST00000374217.2_Missense_Mutation_p.S461C|UBXN11_ENST00000357089.4_Missense_Mutation_p.S461C|UBXN11_ENST00000374223.1_Missense_Mutation_p.S251C			Q5T124	UBX11_HUMAN	UBX domain protein 11	494	3 X 8 AA tandem repeats of P-G-P-G-P-G-P- S.|Pro-rich.		Missing.|Missing. {ECO:0000269|PubMed:14702039, ECO:0000269|Ref.2}.			cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)		p.G490_P515delGPGPSPGPGPGPSPGPGPGPSPCPGP(1)		endometrium(3)|kidney(2)|large_intestine(4)|lung(6)|ovary(2)|prostate(3)|upper_aerodigestive_tract(3)	23						ggaccgggactggggccggga	0.711																																					p.S494C		Atlas-SNP	.											UBXN11,NS,carcinoma,0,1	UBXN11	54	1	1	Deletion - In frame(1)	ovary(1)	c.A1480T						scavenged	.						28.0	33.0	32.0					1																	26608873		1776	4034	5810	SO:0001583	missense	91544	exon16			CGGGACTGGGGCC	AF521017	CCDS41286.1, CCDS41287.1, CCDS41288.1	1p36.11	2008-07-25	2008-07-25	2008-07-25	ENSG00000158062	ENSG00000158062		"""UBX domain containing"""	30600	protein-coding gene	gene with protein product	"""socius"""	609151	"""UBX domain containing 5"""	UBXD5		11940653	Standard	NM_183008		Approved	SOC, SOCI	uc001blw.3	Q5T124	OTTHUMG00000003382	ENST00000374222.1:c.1480A>T	1.37:g.26608873T>A	ENSP00000363339:p.Ser494Cys	Somatic	19	1	0.0526316		WXS	Illumina HiSeq	Phase_I	27	12	0.444444	NM_183008	D3DPK6|Q5T117|Q5T120|Q5T125|Q5T126|Q5T129|Q5T131|Q5T133|Q63HM6|Q71RB3|Q8IY27|Q8N1L6|Q8N9M4|Q8NA18|Q8NFE3|Q8NFE4|Q8NFE6	Missense_Mutation	SNP	ENST00000374222.1	37	CCDS41288.1	.	.	.	.	.	.	.	.	.	.	T	10.17	1.275650	0.23307	.	.	ENSG00000158062	ENST00000314675;ENST00000374223;ENST00000357089;ENST00000374221;ENST00000374222;ENST00000374217	T;T;T;T;T;T	0.19250	2.16;2.17;2.43;2.41;2.41;2.43	1.27	-0.135	0.13477	.	.	.	.	.	T	0.08268	0.0206	N	0.08118	0	0.09310	N	0.999997	P;P;P;P	0.50819	0.939;0.893;0.939;0.9	B;B;B;B	0.37601	0.187;0.187;0.254;0.129	T	0.21895	-1.0232	9	0.66056	D	0.02	.	5.0204	0.14358	0.0:0.3611:0.0:0.6389	rs1134583;rs17838089	461;456;374;494	Q5T124-2;Q5T124-4;Q5T124-3;Q5T124	.;.;.;UBX11_HUMAN	C	374;251;461;494;494;461	ENSP00000324721:S374C;ENSP00000363340:S251C;ENSP00000349601:S461C;ENSP00000363338:S494C;ENSP00000363339:S494C;ENSP00000363334:S461C	ENSP00000324721:S374C	S	-	1	0	UBXN11	26481460	0.000000	0.05858	0.011000	0.14972	0.011000	0.07611	-1.315000	0.02713	-0.170000	0.10816	-0.582000	0.04134	AGT	T|0.870;A|0.130	0.130	strong		0.711	UBXN11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000009500.1	NM_145345	
PDXDC1	23042	hgsc.bcm.edu	37	16	15098047	15098047	+	Missense_Mutation	SNP	C	C	G	rs11549900	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:15098047C>G	ENST00000396410.4	+	5	343	c.246C>G	c.(244-246)atC>atG	p.I82M	PDXDC1_ENST00000450288.2_Missense_Mutation_p.I54M|PDXDC1_ENST00000447912.2_Intron|PDXDC1_ENST00000325823.7_Missense_Mutation_p.I67M|PDXDC1_ENST00000563679.1_Missense_Mutation_p.I100M|PDXDC1_ENST00000535621.2_Missense_Mutation_p.I82M|PDXDC1_ENST00000455313.2_Missense_Mutation_p.I82M|PDXDC1_ENST00000569715.1_Missense_Mutation_p.I55M	NM_015027.2	NP_055842.2	Q6P996	PDXD1_HUMAN	pyridoxal-dependent decarboxylase domain containing 1	82				I -> M (in Ref. 2; BAG61167 and 5; AAZ14099). {ECO:0000305}.	carboxylic acid metabolic process (GO:0019752)	Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)	carboxy-lyase activity (GO:0016831)|pyridoxal phosphate binding (GO:0030170)			central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(2)|liver(1)|lung(10)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						TTAACAGAATCCAAAATATTG	0.348																																					p.I82M		Atlas-SNP	.											.	PDXDC1	59	.	0			c.C246G						PASS	.						107.0	119.0	115.0					16																	15098047		2197	4300	6497	SO:0001583	missense	23042	exon5			CAGAATCCAAAAT	AK025504, BX647809	CCDS32393.1, CCDS66954.1, CCDS66957.1, CCDS73830.1, CCDS73831.1	16p13.11	2008-02-05							28995	protein-coding gene	gene with protein product		614244					Standard	XM_005255173		Approved	KIAA0251	uc002dda.4	Q6P996	OTTHUMG00000166304	ENST00000396410.4:c.246C>G	16.37:g.15098047C>G	ENSP00000379691:p.Ile82Met	Somatic	318	0	0		WXS	Illumina HiSeq	Phase_I	264	99	0.375	NM_015027	B4DR55|B4DSL3|E7EMH5|E7EPL4|H3BNZ1|O00236|Q4F6X7|Q6PID7|Q86YF1|Q8N4Q9|Q8TBS5	Missense_Mutation	SNP	ENST00000396410.4	37	CCDS32393.1	653	0.298992673992674	66	0.13414634146341464	138	0.3812154696132597	251	0.4388111888111888	198	0.2612137203166227	C	6.258	0.415784	0.11870	.	.	ENSG00000179889	ENST00000325823;ENST00000535621;ENST00000396410;ENST00000450288;ENST00000455313	T;T;T;T;T	0.37915	1.17;1.17;1.17;2.07;1.17	5.72	2.76	0.32466	Pyridoxal phosphate-dependent transferase, major domain (1);	0.318283	0.36555	N	0.002527	T	0.00012	0.0000	N	0.08118	0	0.09310	P	1.0	B;B;B;B	0.20780	0.048;0.005;0.048;0.005	B;B;B;B	0.19391	0.02;0.005;0.012;0.025	T	0.47142	-0.9140	9	0.40728	T	0.16	.	9.1032	0.36681	0.0:0.6898:0.0:0.3102	rs11549900	54;82;82;82	E7EPL4;Q86XE2;Q6P996;Q6P996-2	.;.;PDXD1_HUMAN;.	M	67;82;82;54;82	ENSP00000322807:I67M;ENSP00000437835:I82M;ENSP00000379691:I82M;ENSP00000391147:I54M;ENSP00000406703:I82M	ENSP00000322807:I67M	I	+	3	3	PDXDC1	15005548	1.000000	0.71417	1.000000	0.80357	0.351000	0.29236	1.821000	0.39041	0.455000	0.26910	-0.142000	0.14014	ATC	C|0.742;G|0.258	0.258	strong		0.348	PDXDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389065.2	NM_015027	
MTIF3	219402	hgsc.bcm.edu	37	13	28009851	28009851	+	Silent	SNP	G	G	A	rs7669	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:28009851G>A	ENST00000381116.1	-	7	1032	c.798C>T	c.(796-798)gaC>gaT	p.D266D	MTIF3_ENST00000381120.3_Silent_p.D266D|MTIF3_ENST00000405591.2_Silent_p.D266D|MTIF3_ENST00000461838.1_5'UTR|MTIF3_ENST00000431572.2_Silent_p.D266D			Q9H2K0	IF3M_HUMAN	mitochondrial translational initiation factor 3	266					formation of translation initiation complex (GO:0001732)|regulation of translational initiation (GO:0006446)|ribosome disassembly (GO:0032790)	mitochondrion (GO:0005739)	ribosomal small subunit binding (GO:0043024)|translation factor activity, nucleic acid binding (GO:0008135)|translation initiation factor activity (GO:0003743)			endometrium(1)|large_intestine(1)|lung(2)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	7		Lung SC(185;0.0161)	Colorectal(13;0.00042)|READ - Rectum adenocarcinoma(15;0.105)	all cancers(112;0.108)|OV - Ovarian serous cystadenocarcinoma(117;0.157)		CATTTCCATGGTCTTTGTTCA	0.378													G|||	585	0.116813	0.0635	0.0922	5008	,	,		21270	0.1488		0.1938	False		,,,				2504	0.0941				p.D266D		Atlas-SNP	.											.	MTIF3	21	.	0			c.C798T						PASS	.	G	,,,	389,4017	193.0+/-218.2	17,355,1831	208.0	207.0	207.0		798,798,798,798	-1.9	0.0	13	dbSNP_52	207	1555,7045	290.9+/-300.1	148,1259,2893	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	MTIF3	NM_001166261.1,NM_001166262.1,NM_001166263.1,NM_152912.4	,,,	165,1614,4724	AA,AG,GG		18.0814,8.8289,14.9469	,,,	266/279,266/279,266/279,266/279	28009851	1944,11062	2203	4300	6503	SO:0001819	synonymous_variant	219402	exon6			TCCATGGTCTTTG	BC046166	CCDS9322.1	13q12.2	2007-05-03			ENSG00000122033	ENSG00000122033			29788	protein-coding gene	gene with protein product						12095986	Standard	NM_152912		Approved	IF-3mt, IF3(mt)	uc001uri.3	Q9H2K0	OTTHUMG00000016633	ENST00000381116.1:c.798C>T	13.37:g.28009851G>A		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	101	54	0.534653	NM_001166263	Q05BL8|Q5W0V0|Q86X68	Silent	SNP	ENST00000381116.1	37	CCDS9322.1																																																																																			A|0.137;C|0.000;G|0.863	0.137	strong		0.378	MTIF3-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044300.1	NM_152912	
MUC4	4585	hgsc.bcm.edu	37	3	195513779	195513779	+	Missense_Mutation	SNP	C	C	T	rs3103959		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195513779C>T	ENST00000463781.3	-	2	5131	c.4672G>A	c.(4672-4674)Gct>Act	p.A1558T	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.A1558T	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0	VWFD. {ECO:0000255|PROSITE- ProRule:PRU00580}.				cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		ACTGAGGAAGCGTCGGTGACA	0.577																																					p.A1558T		Atlas-SNP	.											.	MUC4	1505	.	0			c.G4672A						PASS	.						13.0	10.0	11.0					3																	195513779		683	1561	2244	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.4672G>A	3.37:g.195513779C>T	ENSP00000417498:p.Ala1558Thr	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	36	12	0.333333	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	-	7.475	0.647427	0.14516	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.32272	1.46;1.46	0.844	0.844	0.18943	.	.	.	.	.	T	0.12561	0.0305	N	0.19112	0.55	0.09310	N	1	P	0.52463	0.953	B	0.32149	0.141	T	0.16424	-1.0403	8	.	.	.	.	5.0592	0.14548	0.0:0.6209:0.379:0.0	.	1558	E7ESK3	.	T	1558	ENSP00000417498:A1558T;ENSP00000420243:A1558T	.	A	-	1	0	MUC4	196998174	0.000000	0.05858	0.011000	0.14972	0.011000	0.07611	-5.191000	0.00143	0.088000	0.17205	0.089000	0.15464	GCT	.	.	weak		0.577	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
PYGB	5834	hgsc.bcm.edu	37	20	25276297	25276297	+	Silent	SNP	G	G	A	rs1130694	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:25276297G>A	ENST00000216962.4	+	19	2480	c.2370G>A	c.(2368-2370)caG>caA	p.Q790Q	PYGB_ENST00000471359.1_3'UTR|ABHD12_ENST00000376542.3_Intron	NM_002862.3	NP_002853.2	P11216	PYGB_HUMAN	phosphorylase, glycogen; brain	790					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						AGGTGGACCAGCTGTACCGGG	0.582													G|||	2562	0.511581	0.3729	0.3314	5008	,	,		19374	0.9107		0.4264	False		,,,				2504	0.5031				p.Q790Q		Atlas-SNP	.											.	PYGB	84	.	0			c.G2370A						PASS	.	G	,	1602,2804	494.6+/-363.0	289,1024,890	74.0	72.0	73.0		2370,	1.5	1.0	20	dbSNP_86	73	3660,4940	524.8+/-380.6	763,2134,1403	no	coding-synonymous,intron	PYGB,ABHD12	NM_002862.3,NM_015600.4	,	1052,3158,2293	AA,AG,GG		42.5581,36.3595,40.4583	,	790/844,	25276297	5262,7744	2203	4300	6503	SO:0001819	synonymous_variant	5834	exon19			GGACCAGCTGTAC		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.2370G>A	20.37:g.25276297G>A		Somatic	196	0	0		WXS	Illumina HiSeq	Phase_I	187	99	0.529412	NM_002862	Q96AK1|Q9NPX8	Silent	SNP	ENST00000216962.4	37	CCDS13171.1	1160	0.5311355311355311	181	0.3678861788617886	123	0.3397790055248619	530	0.9265734265734266	326	0.43007915567282323	G	9.855	1.194604	0.22037	0.363595	0.425581	ENSG00000100994	ENST00000428458	.	.	.	4.64	1.51	0.23008	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999393846	.	.	.	.	.	.	T	0.16512	-1.0400	3	.	.	.	-24.2095	5.1835	0.15173	0.2442:0.0:0.6053:0.1505	rs1130694;rs1802895;rs2227893;rs2258727;rs3177790;rs3189839;rs11549035;rs1130694	.	.	.	N	209	.	.	S	+	2	0	PYGB	25224297	0.491000	0.26019	0.998000	0.56505	0.988000	0.76386	0.237000	0.17985	0.251000	0.21505	0.561000	0.74099	AGC	G|0.542;A|0.458	0.458	strong		0.582	PYGB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078415.2	NM_002862	
ADCY9	115	hgsc.bcm.edu	37	16	4016943	4016943	+	Silent	SNP	A	A	G	rs2230741	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:4016943A>G	ENST00000294016.3	-	11	3433	c.2895T>C	c.(2893-2895)agT>agC	p.S965S		NM_001116.3	NP_001107.2	O60503	ADCY9_HUMAN	adenylate cyclase 9	965					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	axon (GO:0030424)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)			breast(4)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(3)|large_intestine(11)|lung(9)|ovary(5)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	47						GCGGCACCGAACTATTGCACG	0.607													G|||	849	0.169529	0.3835	0.0504	5008	,	,		17025	0.2371		0.0268	False		,,,				2504	0.0419				p.S965S		Atlas-SNP	.											.	ADCY9	151	.	0			c.T2895C						PASS	.	G		1328,3050		205,918,1066	39.0	45.0	43.0		2895	3.2	0.8	16	dbSNP_107	43	248,8330		8,232,4049	no	coding-synonymous	ADCY9	NM_001116.3		213,1150,5115	GG,GA,AA		2.8911,30.3335,12.1642		965/1354	4016943	1576,11380	2189	4289	6478	SO:0001819	synonymous_variant	115	exon11			CACCGAACTATTG	AF036927	CCDS32382.1	16p13.3	2013-02-04				ENSG00000162104	4.6.1.1	"""Adenylate cyclases"""	240	protein-coding gene	gene with protein product		603302				9628827	Standard	NM_001116		Approved	AC9	uc002cvx.3	O60503		ENST00000294016.3:c.2895T>C	16.37:g.4016943A>G		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	73	11	0.150685	NM_001116	A7E2V5|A7E2X2|D3DUD1|O60273|Q4ZHT9|Q4ZIR5|Q9BWT4|Q9UGP2	Silent	SNP	ENST00000294016.3	37	CCDS32382.1																																																																																			A|0.856;G|0.144	0.144	strong		0.607	ADCY9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438076.1		
DNAH1	25981	hgsc.bcm.edu	37	3	52407041	52407041	+	Silent	SNP	C	C	T	rs1546737	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:52407041C>T	ENST00000420323.2	+	44	7218	c.6957C>T	c.(6955-6957)caC>caT	p.H2319H		NM_015512.4	NP_056327	Q9P2D7	DYH1_HUMAN	dynein, axonemal, heavy chain 1	2319	AAA 3. {ECO:0000250}.				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)		GGATGGACCACGGCGGCTGGT	0.622													C|||	1004	0.200479	0.0129	0.2651	5008	,	,		13907	0.1776		0.3459	False		,,,				2504	0.2822				p.H2319H		Atlas-SNP	.											.	DNAH1	534	.	0			c.C6957T						PASS	.	C		257,3885		14,229,1828	46.0	51.0	50.0		6957	-3.1	0.6	3	dbSNP_88	50	2780,5618		476,1828,1895	no	coding-synonymous	DNAH1	NM_015512.4		490,2057,3723	TT,TC,CC		33.1031,6.2047,24.2185		2319/4266	52407041	3037,9503	2071	4199	6270	SO:0001819	synonymous_variant	25981	exon44			GGACCACGGCGGC	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.6957C>T	3.37:g.52407041C>T		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	58	27	0.465517	NM_015512	B0I1R6|O00436|O15435|O95491|Q6ZU48|Q86YK7|Q8TEJ4|Q92863|Q9H8E6|Q9UFW6|Q9Y4Z7	Silent	SNP	ENST00000420323.2	37	CCDS46842.1																																																																																			C|0.781;T|0.219	0.219	strong		0.622	DNAH1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350816.1	NM_015512	
SLC2A2	6514	hgsc.bcm.edu	37	3	170715830	170715830	+	Silent	SNP	G	G	A	rs5398	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:170715830G>A	ENST00000314251.3	-	11	1516	c.1437C>T	c.(1435-1437)ttC>ttT	p.F479F	SLC2A2_ENST00000382808.4_Silent_p.F360F	NM_000340.1	NP_000331.1	P11168	GTR2_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 2	479					carbohydrate metabolic process (GO:0005975)|endocrine pancreas development (GO:0031018)|energy reserve metabolic process (GO:0006112)|glucose transport (GO:0015758)|hexose transmembrane transport (GO:0035428)|hexose transport (GO:0008645)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	brush border (GO:0005903)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	D-glucose transmembrane transporter activity (GO:0055056)|dehydroascorbic acid transporter activity (GO:0033300)|glucose transmembrane transporter activity (GO:0005355)|hexose transmembrane transporter activity (GO:0015149)			central_nervous_system(1)|endometrium(2)|large_intestine(9)|lung(9)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24	all_cancers(22;1.41e-19)|all_lung(20;1.59e-15)|Lung NSC(18;7.08e-15)|Ovarian(172;0.00197)|Breast(254;0.122)		LUSC - Lung squamous cell carcinoma(14;1.1e-14)|Lung(28;2.99e-14)		Streptozocin(DB00428)	TAAAAAATGTGAACAGGGTAA	0.438													A|||	1866	0.372604	0.6354	0.3084	5008	,	,		17963	0.2411		0.2903	False		,,,				2504	0.2832				p.F479F		Atlas-SNP	.											.	SLC2A2	71	.	0			c.C1437T						PASS	.	A		2589,1817	496.7+/-363.6	767,1055,381	43.0	47.0	46.0		1437	-3.7	0.1	3	dbSNP_52	46	2567,6033	674.3+/-403.1	354,1859,2087	no	coding-synonymous	SLC2A2	NM_000340.1		1121,2914,2468	AA,AG,GG		29.8488,41.2392,39.6432		479/525	170715830	5156,7850	2203	4300	6503	SO:0001819	synonymous_variant	6514	exon11			AAATGTGAACAGG	J03810	CCDS3215.1	3q26.2-q27	2013-05-22			ENSG00000163581	ENSG00000163581		"""Solute carriers"""	11006	protein-coding gene	gene with protein product		138160		GLUT2		1852621	Standard	NM_000340		Approved		uc003fhe.1	P11168	OTTHUMG00000158997	ENST00000314251.3:c.1437C>T	3.37:g.170715830G>A		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	87	87	1	NM_000340	A8K481|B2R936|B7Z547|F8W8V8|Q9UCW9	Silent	SNP	ENST00000314251.3	37	CCDS3215.1																																																																																			G|0.622;A|0.378	0.378	strong		0.438	SLC2A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352834.1	NM_000340	
MUC4	4585	hgsc.bcm.edu	37	3	195507251	195507251	+	Missense_Mutation	SNP	G	G	T	rs201456607|rs74187968		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195507251G>T	ENST00000463781.3	-	2	11659	c.11200C>A	c.(11200-11202)Cct>Act	p.P3734T	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_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						PASS	.						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	78	0	0		WXS	Illumina HiSeq	Phase_I	91	19	0.208791	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	
ZC2HC1A	51101	hgsc.bcm.edu	37	8	79610710	79610710	+	Silent	SNP	A	A	G	rs1054283	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:79610710A>G	ENST00000263849.4	+	7	768	c.666A>G	c.(664-666)ttA>ttG	p.L222L		NM_016010.2	NP_057094.2	Q96GY0	ZC21A_HUMAN	zinc finger, C2HC-type containing 1A	222							metal ion binding (GO:0046872)										TTCAGACCTTATCTCCCTCTC	0.343													A|||	3592	0.717252	0.4985	0.7968	5008	,	,		16940	0.8978		0.7157	False		,,,				2504	0.772				p.L222L		Atlas-SNP	.											FAM164A,rectum,carcinoma,0,1	.	.	1	0			c.A666G						PASS	.	A		2401,2005	615.4+/-392.6	668,1065,470	117.0	113.0	114.0		666	2.0	1.0	8	dbSNP_86	114	6317,2283	706.5+/-405.5	2325,1667,308	no	coding-synonymous	FAM164A	NM_016010.2		2993,2732,778	GG,GA,AA		26.5465,45.5061,32.9694		222/326	79610710	8718,4288	2203	4300	6503	SO:0001819	synonymous_variant	51101	exon7			GACCTTATCTCCC		CCDS6223.1	8q21.11	2013-01-10	2012-02-03	2012-02-03	ENSG00000104427	ENSG00000104427		"""Zinc fingers, C2HC-type containing"""	24277	protein-coding gene	gene with protein product			"""chromosome 8 open reading frame 70"", ""family with sequence similarity 164, member A"""	C8orf70, FAM164A		10810093	Standard	NM_016010		Approved	CGI-62	uc003ybd.3	Q96GY0	OTTHUMG00000164619	ENST00000263849.4:c.666A>G	8.37:g.79610710A>G		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	72	51	0.708333	NM_016010	Q9Y372	Silent	SNP	ENST00000263849.4	37	CCDS6223.1	1586	0.7261904761904762	244	0.4959349593495935	291	0.8038674033149171	508	0.8881118881118881	543	0.716358839050132	A	6.349	0.432414	0.12045	0.544939	0.734535	ENSG00000104427	ENST00000519307	.	.	.	5.85	2.0	0.26442	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999973996	.	.	.	.	.	.	T	0.15122	-1.0448	3	.	.	.	-4.1446	5.4563	0.16592	0.641:0.1342:0.2248:0.0	rs1054283;rs3194797;rs13258774;rs17418488;rs17845203;rs17858015;rs1054283	.	.	.	V	55	.	.	I	+	1	0	FAM164A	79773265	0.992000	0.36948	0.996000	0.52242	0.666000	0.39218	0.371000	0.20450	0.096000	0.17463	-0.379000	0.06801	ATC	A|0.323;G|0.677	0.677	strong		0.343	ZC2HC1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379423.2	NM_016010	
SCML4	256380	hgsc.bcm.edu	37	6	108068003	108068003	+	Missense_Mutation	SNP	C	C	T	rs6934505	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:108068003C>T	ENST00000369020.3	-	4	622	c.377G>A	c.(376-378)cGg>cAg	p.R126Q	SCML4_ENST00000369021.3_Missense_Mutation_p.R97Q|SCML4_ENST00000479803.1_5'Flank|SCML4_ENST00000369022.2_Missense_Mutation_p.R68Q	NM_198081.3	NP_932347.2	Q8N228	SCML4_HUMAN	sex comb on midleg-like 4 (Drosophila)	126			R -> Q (in dbSNP:rs6934505). {ECO:0000269|PubMed:14702039}.		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(2)|large_intestine(7)|lung(11)|ovary(3)|prostate(1)|skin(1)	25		all_cancers(87;3.26e-06)|Acute lymphoblastic leukemia(125;3.08e-08)|all_hematologic(75;1.15e-06)|all_epithelial(87;0.00142)|Colorectal(196;0.0316)		BRCA - Breast invasive adenocarcinoma(108;0.01)|Epithelial(106;0.0509)|all cancers(137;0.0586)|OV - Ovarian serous cystadenocarcinoma(136;0.0758)		CGCCGATGGCCGCTCGGGCCC	0.632													C|||	586	0.117013	0.0212	0.1427	5008	,	,		16476	0.0972		0.1938	False		,,,				2504	0.1697				p.R126Q		Atlas-SNP	.											.	SCML4	65	.	0			c.G377A						PASS	.	C	GLN/ARG	200,4206	122.5+/-159.9	3,194,2006	55.0	55.0	55.0		377	2.1	0.8	6	dbSNP_116	55	1524,7076	282.8+/-295.8	145,1234,2921	yes	missense	SCML4	NM_198081.3	43	148,1428,4927	TT,TC,CC		17.7209,4.5393,13.2554	probably-damaging	126/415	108068003	1724,11282	2203	4300	6503	SO:0001583	missense	256380	exon4			GATGGCCGCTCGG		CCDS5060.2, CCDS69163.1, CCDS75500.1	6q21	2013-01-10			ENSG00000146285	ENSG00000146285		"""Sterile alpha motif (SAM) domain containing"""	21397	protein-coding gene	gene with protein product							Standard	NM_001286409		Approved	dJ47M23.1	uc010kdf.3	Q8N228	OTTHUMG00000015313	ENST00000369020.3:c.377G>A	6.37:g.108068003C>T	ENSP00000358016:p.Arg126Gln	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	106	106	1	NM_198081	B0QZ10|B0QZ11|B7ZBX3|Q5JXD0|Q5T0T6|Q8IYY6	Missense_Mutation	SNP	ENST00000369020.3	37	CCDS5060.2	245	0.11217948717948718	10	0.02032520325203252	53	0.1464088397790055	41	0.07167832167832168	141	0.18601583113456466	C	12.90	2.075751	0.36662	0.045393	0.177209	ENSG00000146285	ENST00000369022;ENST00000369020;ENST00000369021;ENST00000440927	T;T;T;T	0.43294	0.95;0.95;0.95;0.95	4.88	2.14	0.27477	.	0.316704	0.36234	N	0.002711	T	0.19644	0.0472	M	0.77103	2.36	0.21652	P	0.999606207	B;B	0.34372	0.234;0.451	B;B	0.29524	0.087;0.103	T	0.11155	-1.0599	9	0.15952	T	0.53	.	10.2202	0.43192	0.0:0.7909:0.0:0.2091	rs6934505;rs60016463;rs6934505	126;97	Q8N228;Q8N228-3	SCML4_HUMAN;.	Q	68;126;97;97	ENSP00000358018:R68Q;ENSP00000358016:R126Q;ENSP00000358017:R97Q;ENSP00000404688:R97Q	ENSP00000358016:R126Q	R	-	2	0	SCML4	108174696	0.985000	0.35326	0.762000	0.31397	0.286000	0.27126	3.207000	0.51106	0.265000	0.21872	0.563000	0.77884	CGG	C|0.875;T|0.125	0.125	strong		0.632	SCML4-005	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000041700.3	XM_171128	
GGCX	2677	hgsc.bcm.edu	37	2	85788528	85788528	+	Silent	SNP	C	C	T	rs371622780		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:85788528C>T	ENST00000233838.4	-	1	104	c.24G>A	c.(22-24)gcG>gcA	p.A8A	GGCX_ENST00000430215.3_Silent_p.A8A|VAMP8_ENST00000432071.1_5'Flank	NM_000821.5	NP_000812.2	P38435	VKGC_HUMAN	gamma-glutamyl carboxylase	8					blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|cellular protein modification process (GO:0006464)|peptidyl-glutamic acid carboxylation (GO:0017187)|post-translational protein modification (GO:0043687)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	gamma-glutamyl carboxylase activity (GO:0008488)			endometrium(3)|large_intestine(5)|lung(3)|ovary(1)|stomach(1)|urinary_tract(2)	15					Anisindione(DB01125)|Coagulation Factor IX(DB00100)|Coagulation factor VIIa(DB00036)|Drotrecogin alfa(DB00055)|Menadione(DB00170)|Phylloquinone(DB01022)	GCGAGGTCCGCGCGGACCCGG	0.697																																					p.A8A		Atlas-SNP	.											.	GGCX	44	.	0			c.G24A						PASS	.	C	,	0,4272		0,0,2136	6.0	8.0	8.0		24,24	1.2	0.1	2		8	5,8413		0,5,4204	no	coding-synonymous,coding-synonymous	GGCX	NM_000821.5,NM_001142269.2	,	0,5,6340	TT,TC,CC		0.0594,0.0,0.0394	,	8/759,8/702	85788528	5,12685	2136	4209	6345	SO:0001819	synonymous_variant	2677	exon1			GGTCCGCGCGGAC		CCDS1978.1, CCDS46353.1	2p12	2008-05-21			ENSG00000115486	ENSG00000115486			4247	protein-coding gene	gene with protein product	"""vitamin K-dependent gamma-carboxylase"""	137167				1749935	Standard	NM_000821		Approved	VKCFD1	uc002sps.3	P38435	OTTHUMG00000130173	ENST00000233838.4:c.24G>A	2.37:g.85788528C>T		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	137	67	0.489051	NM_000821	B4DMC5|E9PEE1|Q14415|Q6GU45	Silent	SNP	ENST00000233838.4	37	CCDS1978.1																																																																																			.	.	weak		0.697	GGCX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252490.3	NM_000821	
CD8A	925	hgsc.bcm.edu	37	2	87017662	87017662	+	Silent	SNP	G	G	T	rs2229239	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:87017662G>T	ENST00000409511.2	-	5	1222	c.192C>A	c.(190-192)gcC>gcA	p.A64A	CD8A_ENST00000538832.1_Silent_p.A105A|CD8A_ENST00000409781.1_Silent_p.A64A|CD8A_ENST00000283635.3_Silent_p.A64A|CD8A_ENST00000456996.2_Silent_p.A64A|CD8A_ENST00000352580.3_Silent_p.A64A	NM_001145873.1	NP_001139345.1	P01732	CD8A_HUMAN	CD8a molecule	64	Ig-like V-type.				antigen processing and presentation (GO:0019882)|cytotoxic T cell differentiation (GO:0045065)|defense response to virus (GO:0051607)|immune response (GO:0006955)|positive regulation of calcium-mediated signaling (GO:0050850)|regulation of immune response (GO:0050776)|T cell activation (GO:0042110)|T cell mediated immunity (GO:0002456)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|T cell receptor complex (GO:0042101)	coreceptor activity (GO:0015026)|MHC class I protein binding (GO:0042288)			lung(4)|ovary(1)|prostate(2)|urinary_tract(1)	8						TGGGACTGGCGGCGGCGCCGC	0.672													G|||	183	0.0365415	0.0696	0.0288	5008	,	,		10342	0.0		0.0626	False		,,,				2504	0.0082				p.A64A		Atlas-SNP	.											.	CD8A	28	.	0			c.C192A						PASS	.	G	,,	346,4056		17,312,1872	38.0	47.0	44.0		192,192,192	1.7	0.0	2	dbSNP_98	44	647,7947		25,597,3675	no	coding-synonymous,coding-synonymous,coding-synonymous	CD8A	NM_001145873.1,NM_001768.6,NM_171827.3	,,	42,909,5547	TT,TG,GG		7.5285,7.8601,7.6408	,,	64/236,64/236,64/199	87017662	993,12003	2201	4297	6498	SO:0001819	synonymous_variant	925	exon5			ACTGGCGGCGGCG		CCDS1992.1, CCDS1993.1	2p12	2014-09-17	2006-03-28		ENSG00000153563	ENSG00000153563		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"""	1706	protein-coding gene	gene with protein product		186910	"""CD8 antigen, alpha polypeptide (p32)"", ""T-cell surface glycoprotein CD8 alpha chain"""	CD8		1541829	Standard	NM_171827		Approved		uc002sru.3	P01732	OTTHUMG00000130265	ENST00000409511.2:c.192C>A	2.37:g.87017662G>T		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	42	19	0.452381	NM_001145873	B4DT80|D6W5M8|Q13970|Q4ZG17	Silent	SNP	ENST00000409511.2	37	CCDS1992.1																																																																																			G|0.932;T|0.068	0.068	strong		0.672	CD8A-006	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000330784.3	NM_001768	
FAM53A	152877	hgsc.bcm.edu	37	4	1656801	1656801	+	Silent	SNP	A	A	C	rs62287700	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:1656801A>C	ENST00000308132.6	-	4	978	c.786T>G	c.(784-786)ccT>ccG	p.P262P	FAM53A_ENST00000472884.2_Silent_p.P262P|FAM53A_ENST00000461064.1_Silent_p.P262P|FAM53A_ENST00000489363.1_Silent_p.P262P	NM_001174070.1	NP_001167541.1	Q6NSI3	FA53A_HUMAN	family with sequence similarity 53, member A	262						nucleus (GO:0005634)				breast(2)|central_nervous_system(2)|large_intestine(1)|lung(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	10		all_epithelial(65;0.206)|Breast(71;0.212)	OV - Ovarian serous cystadenocarcinoma(23;0.0145)			TGAGCACGCAAGGCTGTGAGC	0.701													C|||	1165	0.232628	0.1271	0.2305	5008	,	,		12141	0.0615		0.3698	False		,,,				2504	0.4121				p.P262P		Atlas-SNP	.											FAM53A,NS,carcinoma,0,1	FAM53A	25	1	0			c.T786G						scavenged	.	C	,	668,3736		60,548,1594	23.0	20.0	21.0		786,786	-9.0	0.0	4	dbSNP_129	21	2920,5672		503,1914,1879	no	coding-synonymous,coding-synonymous	FAM53A	NM_001013622.3,NM_001174070.1	,	563,2462,3473	CC,CA,AA		33.9851,15.168,27.6085	,	262/399,262/399	1656801	3588,9408	2202	4296	6498	SO:0001819	synonymous_variant	152877	exon4			CACGCAAGGCTGT	BC070112	CCDS33939.1, CCDS75091.1	4p16.3	2005-08-09			ENSG00000174137	ENSG00000174137			31860	protein-coding gene	gene with protein product							Standard	NM_001013622		Approved	DNTNP	uc021xkl.1	Q6NSI3	OTTHUMG00000159855	ENST00000308132.6:c.786T>G	4.37:g.1656801A>C		Somatic	46	1	0.0217391		WXS	Illumina HiSeq	Phase_I	38	14	0.368421	NM_001013622	Q6ZUL5	Silent	SNP	ENST00000308132.6	37	CCDS33939.1	481	0.22023809523809523	67	0.13617886178861788	102	0.281767955801105	30	0.05244755244755245	282	0.3720316622691293	C	0.053	-1.245306	0.01481	0.15168	0.339851	ENSG00000174137	ENST00000489029	.	.	.	4.51	-9.02	0.00741	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999996236	.	.	.	.	.	.	T	0.07443	-1.0772	3	.	.	.	3.862	1.6068	0.02685	0.2264:0.1615:0.3607:0.2513	rs62287700	.	.	.	R	112	.	.	L	-	2	0	FAM53A	1626598	0.000000	0.05858	0.002000	0.10522	0.007000	0.05969	-3.903000	0.00338	-6.035000	0.00007	-6.070000	0.00000	CTT	A|0.738;C|0.262	0.262	strong		0.701	FAM53A-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359224.1	NM_001013622	
ZKSCAN4	387032	hgsc.bcm.edu	37	6	28213527	28213527	+	Silent	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:28213527C>T	ENST00000377294.2	-	5	1248	c.1005G>A	c.(1003-1005)ctG>ctA	p.L335L	ZKSCAN4_ENST00000423974.2_Silent_p.L180L	NM_019110.3	NP_061983.2	Q969J2	ZKSC4_HUMAN	zinc finger with KRAB and SCAN domains 4	335					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|large_intestine(2)|lung(10)|ovary(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	18						TGTGTTTAGTCAGGCCTGAAC	0.453																																					p.L335L		Atlas-SNP	.											.	ZKSCAN4	42	.	0			c.G1005A						PASS	.						130.0	114.0	119.0					6																	28213527		2203	4300	6503	SO:0001819	synonymous_variant	387032	exon5			TTTAGTCAGGCCT	AK056698	CCDS4647.1	6p21	2013-01-09	2007-02-20	2007-02-20	ENSG00000187626	ENSG00000187626		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	13854	protein-coding gene	gene with protein product		611643	"""zinc finger protein 307"", ""zinc finger protein 427"""	ZNF307, ZNF427		12477932	Standard	NM_019110		Approved	p373c6.1, P1P373C6, FLJ32136, ZSCAN36	uc003nks.1	Q969J2	OTTHUMG00000014511	ENST00000377294.2:c.1005G>A	6.37:g.28213527C>T		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	138	54	0.391304	NM_019110	B2RE32|Q5U7L4	Silent	SNP	ENST00000377294.2	37	CCDS4647.1																																																																																			.	.	none		0.453	ZKSCAN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040179.1	NM_019110	
LRIG1	26018	hgsc.bcm.edu	37	3	66430870	66430870	+	Silent	SNP	G	G	A	rs61754218	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:66430870G>A	ENST00000273261.3	-	19	3623	c.3099C>T	c.(3097-3099)tcC>tcT	p.S1033S	SLC25A26_ENST00000536651.1_3'UTR|LRIG1_ENST00000496559.2_5'UTR|LRIG1_ENST00000383703.3_Silent_p.S1010S	NM_015541.2	NP_056356.2	Q96JA1	LRIG1_HUMAN	leucine-rich repeats and immunoglobulin-like domains 1	1033					innervation (GO:0060384)|otolith morphogenesis (GO:0032474)|sensory perception of sound (GO:0007605)	integral component of membrane (GO:0016021)				NS(2)|breast(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(12)|ovary(3)|prostate(1)|skin(4)|stomach(4)|urinary_tract(1)	42		Lung NSC(201;0.0101)		BRCA - Breast invasive adenocarcinoma(55;0.00047)		GTAGCTCTGTGGAGTCCGGGT	0.527													G|||	223	0.0445288	0.003	0.0533	5008	,	,		19006	0.0179		0.0885	False		,,,				2504	0.0767				p.S1033S		Atlas-SNP	.											.	LRIG1	138	.	0			c.C3099T						PASS	.	G		72,4334	65.8+/-103.3	1,70,2132	109.0	113.0	112.0		3099	-0.2	0.0	3	dbSNP_129	112	611,7989	160.4+/-213.5	20,571,3709	no	coding-synonymous	LRIG1	NM_015541.2		21,641,5841	AA,AG,GG		7.1047,1.6341,5.2514		1033/1094	66430870	683,12323	2203	4300	6503	SO:0001819	synonymous_variant	26018	exon19			CTCTGTGGAGTCC	AB050468	CCDS33783.1	3p14	2013-01-14			ENSG00000144749	ENSG00000144749		"""Immunoglobulin superfamily / I-set domain containing"""	17360	protein-coding gene	gene with protein product	"""ortholog of mouse integral membrane glycoprotein LIG-1"", ""leucine-rich repeat protein LRIG1"""	608868				11414704, 12234026	Standard	NM_015541		Approved	LIG-1, DKFZP586O1624, LIG1	uc003dmx.3	Q96JA1	OTTHUMG00000158727	ENST00000273261.3:c.3099C>T	3.37:g.66430870G>A		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	85	41	0.482353	NM_015541	Q6IQ51|Q96CF9|Q9BYB8|Q9UFI4	Silent	SNP	ENST00000273261.3	37	CCDS33783.1																																																																																			A|0.049;C|0.000;G|0.950	0.049	strong		0.527	LRIG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351930.1	NM_015541	
ARHGEF11	9826	hgsc.bcm.edu	37	1	156907115	156907115	+	Missense_Mutation	SNP	T	T	C	rs868188	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:156907115T>C	ENST00000361409.2	-	38	4988	c.4246A>G	c.(4246-4248)Agc>Ggc	p.S1416G	ARHGEF11_ENST00000487682.1_5'UTR|ARHGEF11_ENST00000315174.8_Missense_Mutation_p.S832G|ARHGEF11_ENST00000368194.3_Missense_Mutation_p.S1456G|MIR765_ENST00000390226.1_RNA	NM_014784.3	NP_055599.1	O15085	ARHGB_HUMAN	Rho guanine nucleotide exchange factor (GEF) 11	1416			S -> G (in dbSNP:rs868188).		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)					AGGGCCAGGCTTGGAGGAGAG	0.627													T|||	2036	0.40655	0.2284	0.5014	5008	,	,		18795	0.5169		0.3569	False		,,,				2504	0.5174				p.S1456G		Atlas-SNP	.											.	ARHGEF11	168	.	0			c.A4366G	GRCh37	CM061640	ARHGEF11	M	rs868188	PASS	.	T	GLY/SER,GLY/SER	987,3419	366.4+/-317.8	106,775,1322	64.0	62.0	63.0		4246,4366	0.5	0.1	1	dbSNP_86	63	3067,5533	465.4+/-366.5	557,1953,1790	yes	missense,missense	ARHGEF11	NM_014784.2,NM_198236.1	56,56	663,2728,3112	CC,CT,TT		35.6628,22.4013,31.1702	probably-damaging,probably-damaging	1416/1523,1456/1563	156907115	4054,8952	2203	4300	6503	SO:0001583	missense	9826	exon39			CCAGGCTTGGAGG	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.4246A>G	1.37:g.156907115T>C	ENSP00000354644:p.Ser1416Gly	Somatic	296	0	0		WXS	Illumina HiSeq	Phase_I	226	224	0.99115	NM_198236	D3DVD0|Q5VY40|Q6PFW2	Missense_Mutation	SNP	ENST00000361409.2	37	CCDS1162.1	805	0.3685897435897436	109	0.22154471544715448	149	0.4116022099447514	272	0.4755244755244755	275	0.3627968337730871	T	6.223	0.409363	0.11812	0.224013	0.356628	ENSG00000132694	ENST00000368194;ENST00000361409;ENST00000315174	T;T;T	0.68624	-0.34;-0.33;-0.23	4.15	0.503	0.16940	.	0.558310	0.17430	N	0.174513	T	0.31136	0.0787	L	0.29908	0.895	0.37737	P	0.07450400000000001	B;B;B	0.10296	0.003;0.0;0.003	B;B;B	0.13407	0.009;0.001;0.008	T	0.05007	-1.0912	9	0.59425	D	0.04	-4.126	7.6539	0.28365	0.0:0.2703:0.0:0.7297	rs868188	832;1416;1456	F8W8P9;O15085;O15085-2	.;ARHGB_HUMAN;.	G	1456;1416;832	ENSP00000357177:S1456G;ENSP00000354644:S1416G;ENSP00000313470:S832G	ENSP00000313470:S832G	S	-	1	0	ARHGEF11	155173739	0.657000	0.27393	0.107000	0.21349	0.140000	0.21249	1.112000	0.31172	-0.078000	0.12730	-0.379000	0.06801	AGC	.	.	none		0.627	ARHGEF11-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000098931.1	NM_198236	
NOMO2	283820	hgsc.bcm.edu	37	16	18532182	18532182	+	Missense_Mutation	SNP	A	A	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:18532182A>T	ENST00000381474.3	-	19	2243	c.2178T>A	c.(2176-2178)aaT>aaA	p.N726K	NOMO2_ENST00000543392.1_Missense_Mutation_p.N559K|NOMO2_ENST00000330537.6_Missense_Mutation_p.N726K	NM_001004060.1	NP_001004060.1	Q5JPE7	NOMO2_HUMAN	NODAL modulator 2	726			N -> K (in dbSNP:rs370986).			endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			endometrium(4)|kidney(1)|large_intestine(2)|liver(3)|lung(5)|ovary(3)|prostate(1)|skin(1)	20						CACCTTCCTCATTGCCGTTTT	0.562																																					p.N726K		Atlas-SNP	.											NOMO2,NS,carcinoma,0,1	NOMO2	36	1	0			c.T2178A						scavenged	.						224.0	232.0	229.0					16																	18532182		2196	4297	6493	SO:0001583	missense	283820	exon19			TTCCTCATTGCCG	AL512687	CCDS10570.1, CCDS32394.1	16p12.3	2008-02-05			ENSG00000185164	ENSG00000185164			22652	protein-coding gene	gene with protein product		609158				15257293	Standard	NM_001004060		Approved	NOMO, PM5	uc002dfe.3	Q5JPE7	OTTHUMG00000131366	ENST00000381474.3:c.2178T>A	16.37:g.18532182A>T	ENSP00000370883:p.Asn726Lys	Somatic	1013	1	0.000987167		WXS	Illumina HiSeq	Phase_I	769	52	0.0676203	NM_173614	Q4G177	Missense_Mutation	SNP	ENST00000381474.3	37	CCDS32394.1	.	.	.	.	.	.	.	.	.	.	.	0.004	-2.260122	0.00262	.	.	ENSG00000185164	ENST00000330537;ENST00000381474;ENST00000543392	T;T;T	0.03663	3.87;3.86;3.85	3.37	-2.16	0.07080	.	0.796012	0.12016	N	0.507432	T	0.01523	0.0049	N	0.14661	0.345	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.46190	-0.9209	10	0.05351	T	0.99	1.8419	2.0563	0.03582	0.1237:0.3142:0.1267:0.4354	.	559;726	Q4G177;Q5JPE7	.;NOMO2_HUMAN	K	726;726;559	ENSP00000331851:N726K;ENSP00000370883:N726K;ENSP00000439970:N559K	ENSP00000331851:N726K	N	-	3	2	NOMO2	18439683	0.000000	0.05858	0.000000	0.03702	0.180000	0.23129	-1.326000	0.02685	-1.117000	0.02965	-0.545000	0.04230	AAT	.	.	weak		0.562	NOMO2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000435858.1	NM_001004060	
SGCG	6445	hgsc.bcm.edu	37	13	23898509	23898509	+	Silent	SNP	T	T	C	rs1800353	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:23898509T>C	ENST00000218867.3	+	8	829	c.705T>C	c.(703-705)ctT>ctC	p.L235L	SGCG_ENST00000545013.1_Silent_p.L235L|SGCG_ENST00000537476.1_Silent_p.L235L	NM_000231.2	NP_000222	Q13326	SGCG_HUMAN	sarcoglycan, gamma (35kDa dystrophin-associated glycoprotein)	235					muscle organ development (GO:0007517)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sarcoglycan complex (GO:0016012)|sarcolemma (GO:0042383)				NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	22		all_cancers(29;4.34e-23)|all_epithelial(30;4.4e-19)|all_lung(29;2.45e-18)|Lung SC(185;0.0228)|Breast(139;0.188)		all cancers(112;0.00255)|Epithelial(112;0.0129)|OV - Ovarian serous cystadenocarcinoma(117;0.0365)|Lung(94;0.205)		CCAACCAGCTTGTGCTTGATG	0.522													T|||	3154	0.629792	0.3253	0.7493	5008	,	,		20308	0.748		0.6918	False		,,,				2504	0.771				p.L235L		Atlas-SNP	.											.	SGCG	64	.	0			c.T705C						PASS	.	T		1772,2634	526.2+/-371.8	354,1064,785	91.0	73.0	79.0		705	-4.4	0.9	13	dbSNP_89	79	5722,2878	672.5+/-402.9	1892,1938,470	no	coding-synonymous	SGCG	NM_000231.2		2246,3002,1255	CC,CT,TT		33.4651,40.2179,42.3804		235/292	23898509	7494,5512	2203	4300	6503	SO:0001819	synonymous_variant	6445	exon8			CCAGCTTGTGCTT	U34976	CCDS9299.1	13q12-q13	2014-09-17	2002-08-29		ENSG00000102683	ENSG00000102683			10809	protein-coding gene	gene with protein product	"""Maghrebian myopathy (autosomal recessive)"", ""35kD dystrophin-associated glycoprotein"", ""limb girdle muscular dystrophy 2C (Duchenne-like muscular dystrophy, autosomal recessive)"", ""gamma sarcoglycan"""	608896	"""sarcoglycan, gamma (35kD dystrophin-associated glycoprotein)"""	DMDA1, MAM, LGMD2C		8968757	Standard	NM_000231		Approved	SCARMD2, DAGA4, SCG3, DMDA, TYPE, A4, MGC130048	uc001uom.2	Q13326	OTTHUMG00000016563	ENST00000218867.3:c.705T>C	13.37:g.23898509T>C		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	72	34	0.472222	NM_000231	Q32M32|Q5T9J6	Silent	SNP	ENST00000218867.3	37	CCDS9299.1																																																																																			T|0.406;C|0.594	0.594	strong		0.522	SGCG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044151.1	NM_000231	
TDRD5	163589	hgsc.bcm.edu	37	1	179562740	179562740	+	Missense_Mutation	SNP	G	G	C	rs61310274	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:179562740G>C	ENST00000367614.1	+	3	737	c.378G>C	c.(376-378)agG>agC	p.R126S	RP11-545A16.4_ENST00000567150.1_RNA|TDRD5_ENST00000444136.1_Missense_Mutation_p.R126S|TDRD5_ENST00000294848.8_Missense_Mutation_p.R126S	NM_001199091.1	NP_001186020.1	Q8NAT2	TDRD5_HUMAN	tudor domain containing 5	126				R -> S (in Ref. 3; AAI30533/AAI44059). {ECO:0000305}.	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						ACCGAGGAAGGGTTGCCCCTA	0.453													G|||	1541	0.307708	0.0877	0.4092	5008	,	,		20589	0.371		0.3897	False		,,,				2504	0.3834				p.R126S		Atlas-SNP	.											TDRD5,NS,neuroblastoma,+1,1	TDRD5	149	1	0			c.G378C						PASS	.	G	SER/ARG,SER/ARG,SER/ARG,SER/ARG	658,3748	279.6+/-274.9	54,550,1599	167.0	155.0	159.0		378,378,378,378	2.6	1.0	1	dbSNP_129	159	3124,5476	477.0+/-369.5	555,2014,1731	yes	missense,missense,missense,missense	TDRD5	NM_001199085.1,NM_001199089.1,NM_001199091.1,NM_173533.3	110,110,110,110	609,2564,3330	CC,CG,GG		36.3256,14.9342,29.0789	probably-damaging,probably-damaging,probably-damaging,probably-damaging	126/1036,126/1036,126/982,126/982	179562740	3782,9224	2203	4300	6503	SO:0001583	missense	163589	exon3			AGGAAGGGTTGCC	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.378G>C	1.37:g.179562740G>C	ENSP00000356586:p.Arg126Ser	Somatic	295	0	0		WXS	Illumina HiSeq	Phase_I	267	129	0.483146	NM_173533	A1L4G5|B7ZLV0|Q5EBN4|Q5VTV0|Q6ZSK2	Missense_Mutation	SNP	ENST00000367614.1	37	CCDS1332.1	725	0.33195970695970695	46	0.09349593495934959	153	0.42265193370165743	236	0.4125874125874126	290	0.38258575197889183	G	18.60	3.658717	0.67586	0.149342	0.363256	ENSG00000162782	ENST00000367614;ENST00000294848;ENST00000444136	T;T;T	0.12879	2.64;2.64;2.78	5.59	2.58	0.30949	.	0.200944	0.41194	D	0.000923	T	0.00012	0.0000	L	0.27053	0.805	0.31208	P	0.6990000000000001	D;D	0.89917	1.0;1.0	D;D	0.80764	0.994;0.986	T	0.46162	-0.9211	9	0.30854	T	0.27	-0.0298	7.1341	0.25519	0.3841:0.0:0.6159:0.0	rs61310274	126;126	Q8NAT2-1;Q8NAT2	.;TDRD5_HUMAN	S	126	ENSP00000356586:R126S;ENSP00000294848:R126S;ENSP00000406052:R126S	ENSP00000294848:R126S	R	+	3	2	TDRD5	177829363	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	0.835000	0.27531	0.625000	0.30304	0.655000	0.94253	AGG	G|0.693;C|0.307	0.307	strong		0.453	TDRD5-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000085295.1	NM_173533	
TEF	7008	hgsc.bcm.edu	37	22	41783659	41783659	+	Silent	SNP	C	C	T	rs11546403	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:41783659C>T	ENST00000266304.4	+	2	578	c.462C>T	c.(460-462)acC>acT	p.T154T	TEF_ENST00000406644.3_Silent_p.T124T	NM_003216.3	NP_003207.1	Q10587	TEF_HUMAN	thyrotrophic embryonic factor	154					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|rhythmic process (GO:0048511)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			kidney(1)|large_intestine(2)|lung(2)|ovary(1)	6						CCTCTGAAACCGTGTCCAGCA	0.582													C|||	999	0.199481	0.0227	0.4409	5008	,	,		20290	0.0565		0.2376	False		,,,				2504	0.3753				p.T154T		Atlas-SNP	.											.	TEF	21	.	0			c.C462T						PASS	.	C	,	235,4171	137.7+/-173.5	11,213,1979	59.0	39.0	45.0		372,462	-3.9	1.0	22	dbSNP_120	45	2003,6597	344.5+/-325.3	255,1493,2552	yes	coding-synonymous,coding-synonymous	TEF	NM_001145398.1,NM_003216.2	,	266,1706,4531	TT,TC,CC		23.2907,5.3336,17.2074	,	124/274,154/304	41783659	2238,10768	2203	4300	6503	SO:0001819	synonymous_variant	7008	exon2			TGAAACCGTGTCC		CCDS14014.1, CCDS46716.1	22q13.2	2013-01-10			ENSG00000167074	ENSG00000167074		"""basic leucine zipper proteins"""	11722	protein-coding gene	gene with protein product		188595				7835883, 15665112	Standard	NM_001145398		Approved	KIAA1655	uc003azy.4	Q10587	OTTHUMG00000150968	ENST00000266304.4:c.462C>T	22.37:g.41783659C>T		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	53	26	0.490566	NM_003216	B0QYS8|B2RC22|Q15729|Q7Z3J7|Q8IU94|Q96TG4	Silent	SNP	ENST00000266304.4	37	CCDS14014.1	397	0.18177655677655677	15	0.03048780487804878	170	0.4696132596685083	35	0.06118881118881119	177	0.23350923482849603	C	9.161	1.018676	0.19355	0.053336	0.232907	ENSG00000167074	ENST00000413942	.	.	.	5.34	-3.92	0.04155	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999829783	.	.	.	.	.	.	T	0.48736	-0.9009	3	.	.	.	-26.1812	1.7282	0.02926	0.1914:0.3023:0.0972:0.4091	rs12484449;rs17437924;rs17853902;rs17854207;rs12484449	.	.	.	L	120	.	.	P	+	2	0	TEF	40113605	0.502000	0.26107	0.994000	0.49952	0.984000	0.73092	-0.492000	0.06467	-0.207000	0.10187	-0.253000	0.11424	CCG	C|0.825;T|0.175	0.175	strong		0.582	TEF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320692.1	NM_003216	
CLDND2	125875	hgsc.bcm.edu	37	19	51871194	51871194	+	Missense_Mutation	SNP	C	C	T	rs61736500	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:51871194C>T	ENST00000291715.1	-	2	681	c.256G>A	c.(256-258)Gac>Aac	p.D86N	ETFB_ENST00000309244.4_5'Flank|CLDND2_ENST00000601435.1_Missense_Mutation_p.D86N|CTD-2616J11.10_ENST00000595500.1_RNA|CTD-2616J11.11_ENST00000600067.1_Missense_Mutation_p.D21N	NM_152353.2	NP_689566.1	Q8NHS1	CLDN2_HUMAN	claudin domain containing 2	86						integral component of membrane (GO:0016021)				endometrium(1)|kidney(1)|large_intestine(2)	4		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000211)|OV - Ovarian serous cystadenocarcinoma(262;0.00979)		TCGCCCTCGTCGCACCGAATC	0.726													C|||	17	0.00339457	0.0008	0.0072	5008	,	,		11998	0.0		0.0089	False		,,,				2504	0.002				p.D86N		Atlas-SNP	.											.	CLDND2	11	.	0			c.G256A						PASS	.	C	ASN/ASP	2,4398		0,2,2198	29.0	29.0	29.0		256	-0.3	0.0	19	dbSNP_129	29	54,8540		0,54,4243	yes	missense	CLDND2	NM_152353.2	23	0,56,6441	TT,TC,CC		0.6283,0.0455,0.431	benign	86/168	51871194	56,12938	2200	4297	6497	SO:0001583	missense	125875	exon2			CCTCGTCGCACCG	BC029518	CCDS12829.1	19q13.41	2008-02-05				ENSG00000160318			28511	protein-coding gene	gene with protein product						12477932	Standard	NM_152353		Approved	MGC33839	uc002pwi.1	Q8NHS1		ENST00000291715.1:c.256G>A	19.37:g.51871194C>T	ENSP00000291715:p.Asp86Asn	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	118	68	0.576271	NM_152353		Missense_Mutation	SNP	ENST00000291715.1	37	CCDS12829.1	12	0.005494505494505495	0	0.0	5	0.013812154696132596	0	0.0	7	0.009234828496042216	C	7.665	0.685760	0.14973	4.55E-4	0.006283	ENSG00000160318	ENST00000291715	D	0.88509	-2.39	4.69	-0.277	0.12898	.	1.778600	0.02886	N	0.133517	T	0.67859	0.2938	N	0.08118	0	0.09310	N	1	B	0.12013	0.005	B	0.04013	0.001	T	0.62388	-0.6865	10	0.12766	T	0.61	-0.1713	3.1085	0.06350	0.097:0.3345:0.3983:0.1702	.	86	Q8NHS1	CLDN2_HUMAN	N	86	ENSP00000291715:D86N	ENSP00000291715:D86N	D	-	1	0	CLDND2	56563006	0.000000	0.05858	0.010000	0.14722	0.379000	0.30106	0.451000	0.21779	0.081000	0.16988	-0.228000	0.12330	GAC	C|0.995;T|0.005	0.005	strong		0.726	CLDND2-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464268.1	NM_152353	
ARHGEF10	9639	hgsc.bcm.edu	37	8	1817367	1817367	+	Silent	SNP	G	G	A	rs7003969	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:1817367G>A	ENST00000398564.1	+	7	705	c.705G>A	c.(703-705)gaG>gaA	p.E235E	ARHGEF10_ENST00000398560.1_Silent_p.E235E|ARHGEF10_ENST00000518288.1_Silent_p.E235E|ARHGEF10_ENST00000349830.3_Silent_p.E210E|ARHGEF10_ENST00000520359.1_Silent_p.E211E|ARHGEF10_ENST00000262112.6_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	263	1	0.00380228		WXS	Illumina HiSeq	Phase_I	198	153	0.772727	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			
CNTN3	5067	hgsc.bcm.edu	37	3	74334560	74334560	+	Missense_Mutation	SNP	C	C	T	rs143021649	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:74334560C>T	ENST00000263665.6	-	19	2627	c.2600G>A	c.(2599-2601)cGg>cAg	p.R867Q		NM_020872.1	NP_065923.1	Q9P232	CNTN3_HUMAN	contactin 3 (plasmacytoma associated)	867	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|nervous system development (GO:0007399)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)				NS(2)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(39)|ovary(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	83		Lung NSC(201;0.138)|Lung SC(41;0.21)		Epithelial(33;0.00212)|BRCA - Breast invasive adenocarcinoma(55;0.00258)|LUSC - Lung squamous cell carcinoma(21;0.00461)|Lung(16;0.01)		CTTCAGGCCCCGTAGTCTGGC	0.547													C|||	115	0.0229633	0.0008	0.0202	5008	,	,		13600	0.001		0.0388	False		,,,				2504	0.0613				p.R867Q		Atlas-SNP	.											CNTN3,caecum,carcinoma,+1,1	CNTN3	174	1	0			c.G2600A						PASS	.	C	GLN/ARG	33,4373	38.4+/-70.7	2,29,2172	170.0	150.0	156.0		2600	-6.2	0.0	3	dbSNP_134	156	304,8296	108.8+/-169.4	4,296,4000	yes	missense	CNTN3	NM_020872.1	43	6,325,6172	TT,TC,CC		3.5349,0.749,2.5911	benign	867/1029	74334560	337,12669	2203	4300	6503	SO:0001583	missense	5067	exon19			AGGCCCCGTAGTC	AB040929	CCDS33790.1	3p12.3	2013-02-11			ENSG00000113805	ENSG00000113805		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	2173	protein-coding gene	gene with protein product		601325		PANG		8661054, 8586965	Standard	XM_005264757		Approved	BIG-1	uc003dpm.1	Q9P232	OTTHUMG00000158813	ENST00000263665.6:c.2600G>A	3.37:g.74334560C>T	ENSP00000263665:p.Arg867Gln	Somatic	202	0	0		WXS	Illumina HiSeq	Phase_I	175	80	0.457143	NM_020872	B9EK50|Q9H039	Missense_Mutation	SNP	ENST00000263665.6	37	CCDS33790.1	47	0.02152014652014652	1	0.0020325203252032522	12	0.03314917127071823	0	0.0	34	0.044854881266490766	C	9.922	1.212320	0.22289	0.00749	0.035349	ENSG00000113805	ENST00000263665	T	0.56776	0.44	5.28	-6.19	0.02078	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.626858	0.15628	N	0.252515	T	0.07503	0.0189	L	0.27944	0.81	0.09310	N	1	B	0.16603	0.018	B	0.16289	0.015	T	0.04333	-1.0959	10	0.29301	T	0.29	.	5.9098	0.19020	0.0758:0.3308:0.0959:0.4975	.	867	Q9P232	CNTN3_HUMAN	Q	867	ENSP00000263665:R867Q	ENSP00000263665:R867Q	R	-	2	0	CNTN3	74417250	0.000000	0.05858	0.000000	0.03702	0.243000	0.25628	0.023000	0.13533	-1.455000	0.01923	-1.740000	0.00687	CGG	C|0.976;T|0.024	0.024	strong		0.547	CNTN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352306.1	NM_020872	
MTRR	4552	hgsc.bcm.edu	37	5	7900056	7900056	+	Missense_Mutation	SNP	A	A	G	rs148909799	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:7900056A>G	ENST00000264668.2	+	15	2093	c.2063A>G	c.(2062-2064)cAt>cGt	p.H688R	MTRR_ENST00000440940.2_Missense_Mutation_p.H661R	NM_002454.2|NM_024010.2	NP_002445.2|NP_076915.2	Q9UBK8	MTRR_HUMAN	5-methyltetrahydrofolate-homocysteine methyltransferase reductase	688					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)	AAGGATGTACATGATGCCCTT	0.358													A|||	3	0.000599042	0.0	0.0	5008	,	,		17957	0.0		0.002	False		,,,				2504	0.001				p.H688R		Atlas-SNP	.											.	MTRR	74	.	0			c.A2063G						PASS	.	A	ARG/HIS,ARG/HIS	3,4403	4.2+/-10.8	0,3,2200	100.0	105.0	103.0		1982,2063	3.3	0.0	5	dbSNP_134	103	24,8576	17.3+/-56.4	1,22,4277	yes	missense,missense	MTRR	NM_002454.2,NM_024010.2	29,29	1,25,6477	GG,GA,AA		0.2791,0.0681,0.2076	benign,benign	661/699,688/726	7900056	27,12979	2203	4300	6503	SO:0001583	missense	4552	exon15			ATGTACATGATGC	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.2063A>G	5.37:g.7900056A>G	ENSP00000264668:p.His688Arg	Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	129	67	0.51938	NM_024010	O60471|Q32MA9|Q7Z4M8	Missense_Mutation	SNP	ENST00000264668.2	37	CCDS3874.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	A	9.273	1.046111	0.19748	6.81E-4	0.002791	ENSG00000124275	ENST00000264668;ENST00000440940	D;D	0.85629	-2.01;-2.01	5.71	3.29	0.37713	Oxidoreductase FAD/NAD(P)-binding (1);	0.266108	0.46758	D	0.000276	T	0.72399	0.3455	N	0.16862	0.45	0.44316	D	0.997191	B	0.21821	0.061	B	0.24974	0.057	T	0.64228	-0.6457	10	0.27785	T	0.31	-16.3277	9.6534	0.39910	0.7885:0.0:0.2115:0.0	.	688	Q9UBK8	MTRR_HUMAN	R	688;661	ENSP00000264668:H688R;ENSP00000402510:H661R	ENSP00000264668:H688R	H	+	2	0	MTRR	7953056	1.000000	0.71417	0.013000	0.15412	0.988000	0.76386	2.540000	0.45727	0.999000	0.39023	0.533000	0.62120	CAT	A|0.998;G|0.002	0.002	strong		0.358	MTRR-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000206931.1		
XYLB	9942	hgsc.bcm.edu	37	3	38404472	38404472	+	Missense_Mutation	SNP	C	C	A	rs17118	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:38404472C>A	ENST00000207870.3	+	4	345	c.255C>A	c.(253-255)gaC>gaA	p.D85E	XYLB_ENST00000542835.1_Intron	NM_005108.3	NP_005099.2	O75191	XYLB_HUMAN	xylulokinase homolog (H. influenzae)	85			D -> E (in dbSNP:rs17118). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:9763671, ECO:0000269|Ref.3}.		carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|D-xylose metabolic process (GO:0042732)|generation of precursor metabolites and energy (GO:0006091)|xylulose catabolic process (GO:0005998)|xylulose metabolic process (GO:0005997)	extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|xylulokinase activity (GO:0004856)			endometrium(3)|kidney(3)|large_intestine(3)|liver(1)|lung(12)|ovary(1)|prostate(1)	24				KIRC - Kidney renal clear cell carcinoma(284;0.00372)|Kidney(284;0.00405)		CGGGCTTCGACTTCTCTCAAG	0.532													C|||	1177	0.235024	0.1051	0.304	5008	,	,		16920	0.2857		0.3469	False		,,,				2504	0.1943				p.D85E		Atlas-SNP	.											XYLB,caecum,carcinoma,+2,1	XYLB	50	1	0			c.C255A						scavenged	.	C	GLU/ASP	626,3780	270.4+/-269.6	53,520,1630	121.0	121.0	121.0		255	0.7	1.0	3	dbSNP_60	121	3031,5569	466.4+/-366.8	547,1937,1816	yes	missense	XYLB	NM_005108.3	45	600,2457,3446	AA,AC,CC		35.2442,14.2079,28.1178	possibly-damaging	85/537	38404472	3657,9349	2203	4300	6503	SO:0001583	missense	9942	exon4			CTTCGACTTCTCT	AB015046	CCDS2678.1	3p22-p21.3	2006-12-18	2001-12-04		ENSG00000093217	ENSG00000093217			12839	protein-coding gene	gene with protein product		604049	"""xylulokinase (H. influenzae) homolog"""			9763671	Standard	NM_005108		Approved	FLJ10343, FLJ12539	uc003cic.2	O75191	OTTHUMG00000131294	ENST00000207870.3:c.255C>A	3.37:g.38404472C>A	ENSP00000207870:p.Asp85Glu	Somatic	73	1	0.0136986		WXS	Illumina HiSeq	Phase_I	54	22	0.407407	NM_005108	B2RAW4|B4DDT2|B9EH64	Missense_Mutation	SNP	ENST00000207870.3	37	CCDS2678.1	572	0.2619047619047619	70	0.14227642276422764	105	0.2900552486187845	144	0.2517482517482518	253	0.3337730870712401	C	18.21	3.573801	0.65765	0.142079	0.352442	ENSG00000093217	ENST00000207870	T	0.46819	0.86	4.93	0.69	0.18039	Carbohydrate kinase, FGGY, N-terminal (1);	0.700768	0.14941	N	0.289492	T	0.00012	0.0000	M	0.67953	2.075	0.09310	P	0.999999999768008	B	0.31318	0.319	P	0.46339	0.513	T	0.37103	-0.9720	9	0.48119	T	0.1	.	4.3919	0.11344	0.0:0.4086:0.3182:0.2732	rs17118;rs151612;rs574507;rs17037616;rs17854790;rs56462081;rs57457746;rs17118	85	O75191	XYLB_HUMAN	E	85	ENSP00000207870:D85E	ENSP00000207870:D85E	D	+	3	2	XYLB	38379476	0.986000	0.35501	0.984000	0.44739	0.933000	0.57130	0.155000	0.16362	0.198000	0.20407	0.455000	0.32223	GAC	C|0.731;A|0.269	0.269	strong		0.532	XYLB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254062.2	NM_005108	
TAAR8	83551	hgsc.bcm.edu	37	6	132874814	132874814	+	Missense_Mutation	SNP	A	A	C	rs8192627	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:132874814A>C	ENST00000275200.1	+	1	983	c.983A>C	c.(982-984)gAt>gCt	p.D328A		NM_053278.1	NP_444508.1	Q969N4	TAAR8_HUMAN	trace amine associated receptor 8	328			D -> A (in dbSNP:rs8192627).		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)|trace-amine receptor activity (GO:0001594)			endometrium(3)|large_intestine(2)|lung(14)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	22	Breast(56;0.112)			OV - Ovarian serous cystadenocarcinoma(155;0.00412)|GBM - Glioblastoma multiforme(226;0.00792)		TTAAGTGGAGATGTTTTAAAG	0.269													A|||	211	0.0421326	0.0318	0.036	5008	,	,		15502	0.0159		0.0686	False		,,,				2504	0.0603				p.D328A		Atlas-SNP	.											.	TAAR8	38	.	0			c.A983C						PASS	.	A	ALA/ASP	120,4284	86.8+/-125.4	2,116,2084	53.0	56.0	55.0		983	0.6	0.0	6	dbSNP_117	55	618,7982	156.7+/-210.5	22,574,3704	yes	missense	TAAR8	NM_053278.1	126	24,690,5788	CC,CA,AA		7.186,2.7248,5.6752	benign	328/343	132874814	738,12266	2202	4300	6502	SO:0001583	missense	83551	exon1			GTGGAGATGTTTT	AF380193	CCDS5154.1	6q23.2	2014-05-14	2005-02-23	2005-02-24	ENSG00000146385	ENSG00000146385		"""GPCR / Class A : Trace amine associated receptors"""	14964	protein-coding gene	gene with protein product		606927	"""trace amine receptor 5"""	GPR102, TRAR5		11574155, 15718104	Standard	NM_053278		Approved	TA5, TAR5	uc011ecj.2	Q969N4	OTTHUMG00000015586	ENST00000275200.1:c.983A>C	6.37:g.132874814A>C	ENSP00000275200:p.Asp328Ala	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	44	26	0.590909	NM_053278	Q5VUQ0	Missense_Mutation	SNP	ENST00000275200.1	37	CCDS5154.1	106	0.048534798534798536	25	0.0508130081300813	14	0.03867403314917127	12	0.02097902097902098	55	0.07255936675461741	A	4.585	0.108597	0.08780	0.027248	0.07186	ENSG00000146385	ENST00000275200	T	0.68903	-0.36	4.58	0.633	0.17712	.	0.968910	0.08470	N	0.941206	T	0.21718	0.0523	N	0.03608	-0.345	0.09310	N	1	B	0.09022	0.002	B	0.17722	0.019	T	0.30416	-0.9979	10	0.59425	D	0.04	2.0129	8.4676	0.32966	0.7545:0.0:0.2455:0.0	rs8192627;rs52804672;rs57702951;rs8192627	328	Q969N4	TAAR8_HUMAN	A	328	ENSP00000275200:D328A	ENSP00000275200:D328A	D	+	2	0	TAAR8	132916507	0.002000	0.14202	0.000000	0.03702	0.088000	0.18126	1.733000	0.38156	0.019000	0.15079	0.459000	0.35465	GAT	A|0.949;C|0.051	0.051	strong		0.269	TAAR8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042262.1	NM_053278	
VEZT	55591	hgsc.bcm.edu	37	12	95660182	95660182	+	Missense_Mutation	SNP	A	A	G	rs17855933	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	231	1	0.004329		WXS	Illumina HiSeq	Phase_I	210	107	0.509524	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	
WDR93	56964	hgsc.bcm.edu	37	15	90245253	90245253	+	Silent	SNP	C	C	T	rs4316730	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:90245253C>T	ENST00000268130.7	+	2	377	c.276C>T	c.(274-276)acC>acT	p.T92T	WDR93_ENST00000560294.1_Silent_p.T92T|RP11-300G22.2_ENST00000557964.1_RNA|WDR93_ENST00000558000.1_Silent_p.T92T	NM_020212.1	NP_064597.1	Q6P2C0	WDR93_HUMAN	WD repeat domain 93	92					electron transport chain (GO:0022900)		oxidoreductase activity, acting on NAD(P)H (GO:0016651)			NS(1)|breast(3)|endometrium(2)|kidney(4)|large_intestine(5)|liver(2)|lung(8)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	33	Lung NSC(78;0.0237)|all_lung(78;0.0478)		KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|BRCA - Breast invasive adenocarcinoma(143;0.128)			TCCAGCCCACCGTCTACCCTC	0.483													C|||	1986	0.396565	0.5234	0.3631	5008	,	,		19440	0.2063		0.4026	False		,,,				2504	0.4387				p.T92T		Atlas-SNP	.											.	WDR93	63	.	0			c.C276T						PASS	.	C		2200,2200	588.5+/-386.9	559,1082,559	51.0	55.0	53.0		276	-3.0	0.0	15	dbSNP_111	53	3847,4751	540.1+/-383.7	846,2155,1298	yes	coding-synonymous	WDR93	NM_020212.1		1405,3237,1857	TT,TC,CC		44.743,50.0,46.5225		92/687	90245253	6047,6951	2200	4299	6499	SO:0001819	synonymous_variant	56964	exon2			GCCCACCGTCTAC		CCDS32326.1, CCDS66862.1, CCDS73779.1	15q26.1	2012-11-02						"""WD repeat domain containing"""	26924	protein-coding gene	gene with protein product							Standard	NM_020212		Approved		uc002boj.3	Q6P2C0		ENST00000268130.7:c.276C>T	15.37:g.90245253C>T		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	98	32	0.326531	NM_020212	Q8N7Y8|Q9NP89	Silent	SNP	ENST00000268130.7	37	CCDS32326.1																																																																																			C|0.564;T|0.436	0.436	strong		0.483	WDR93-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000416369.1	NM_020212	
FYCO1	79443	hgsc.bcm.edu	37	3	46009487	46009487	+	Missense_Mutation	SNP	G	G	A	rs33910087	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:46009487G>A	ENST00000296137.2	-	8	1544	c.1339C>T	c.(1339-1341)Cgc>Tgc	p.R447C	FYCO1_ENST00000535325.1_Missense_Mutation_p.R447C	NM_024513.3	NP_078789.2	Q9BQS8	FYCO1_HUMAN	FYVE and coiled-coil domain containing 1	447			R -> C (in dbSNP:rs33910087).		plus-end-directed vesicle transport along microtubule (GO:0072383)	autophagic vacuole (GO:0005776)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)	metal ion binding (GO:0046872)			NS(4)|breast(3)|central_nervous_system(1)|endometrium(11)|kidney(2)|large_intestine(9)|lung(17)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	54				BRCA - Breast invasive adenocarcinoma(193;0.00147)|KIRC - Kidney renal clear cell carcinoma(197;0.0272)|Kidney(197;0.0323)		TTCACCAGGCGCTCCAGGCTG	0.622													G|||	542	0.108227	0.0166	0.0591	5008	,	,		17259	0.005		0.1223	False		,,,				2504	0.3589				p.R447C		Atlas-SNP	.											.	FYCO1	115	.	0			c.C1339T						PASS	.	G	CYS/ARG	136,4270	97.6+/-136.3	1,134,2068	133.0	146.0	142.0		1339	-5.4	0.0	3	dbSNP_126	142	948,7652	208.7+/-250.1	49,850,3401	yes	missense	FYCO1	NM_024513.2	180	50,984,5469	AA,AG,GG		11.0233,3.0867,8.3346	possibly-damaging	447/1479	46009487	1084,11922	2203	4300	6503	SO:0001583	missense	79443	exon8			CCAGGCGCTCCAG	AJ292348	CCDS2734.1	3p21.3	2008-02-05			ENSG00000163820	ENSG00000163820		"""Zinc fingers, FYVE domain containing"""	14673	protein-coding gene	gene with protein product		607182				11896456	Standard	NM_024513		Approved	FLJ13335, ZFYVE7	uc003cpb.5	Q9BQS8	OTTHUMG00000133447	ENST00000296137.2:c.1339C>T	3.37:g.46009487G>A	ENSP00000296137:p.Arg447Cys	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	110	58	0.527273	NM_024513	B7ZKT7|Q3MJE6|Q86T41|Q86TB1|Q8TEF9|Q96IV5|Q9H8P9	Missense_Mutation	SNP	ENST00000296137.2	37	CCDS2734.1	135	0.061813186813186816	9	0.018292682926829267	19	0.052486187845303865	0	0.0	107	0.14116094986807387	G	7.220	0.597222	0.13875	0.030867	0.110233	ENSG00000163820	ENST00000296137;ENST00000535325	T;T	0.21543	2.0;2.03	5.14	-5.38	0.02673	.	1.186910	0.05604	N	0.576849	T	0.00109	0.0003	L	0.44542	1.39	0.80722	P	0.0	P;P	0.52463	0.712;0.953	B;B	0.38712	0.216;0.28	T	0.14980	-1.0453	9	0.66056	D	0.02	0.1586	0.9601	0.01393	0.2509:0.3417:0.1553:0.2521	rs33910087	447;447	B7ZKT7;Q9BQS8	.;FYCO1_HUMAN	C	447	ENSP00000296137:R447C;ENSP00000441178:R447C	ENSP00000296137:R447C	R	-	1	0	FYCO1	45984491	0.000000	0.05858	0.001000	0.08648	0.201000	0.24016	-0.006000	0.12833	-0.676000	0.05238	-0.345000	0.07892	CGC	G|0.916;A|0.084	0.084	strong		0.622	FYCO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257320.2	NM_024513	
ITPRIPL1	150771	hgsc.bcm.edu	37	2	96993884	96993884	+	Silent	SNP	A	A	G	rs1048675	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:96993884A>G	ENST00000439118.2	+	3	1766	c.1515A>G	c.(1513-1515)ccA>ccG	p.P505P	ITPRIPL1_ENST00000542887.1_Silent_p.P497P|ITPRIPL1_ENST00000536814.1_Silent_p.P497P|ITPRIPL1_ENST00000361124.4_Silent_p.P513P	NM_001008949.2	NP_001008949.1	Q6GPH6	IPIL1_HUMAN	inositol 1,4,5-trisphosphate receptor interacting protein-like 1	505						integral component of membrane (GO:0016021)|membrane (GO:0016020)		p.P513P(1)		breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(7)|ovary(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27						TGACCATCCCAATCCCTAAGA	0.522													G|||	1903	0.379992	0.2784	0.317	5008	,	,		19077	0.2778		0.3191	False		,,,				2504	0.7301				p.P513P		Atlas-SNP	.											ITPRIPL1,NS,carcinoma,0,1	ITPRIPL1	58	1	1	Substitution - coding silent(1)	stomach(1)	c.A1539G						PASS	.	G	,,,	1245,3161	705.2+/-407.2	178,889,1136	69.0	67.0	68.0		1515,1491,1491,1539	-11.3	0.1	2	dbSNP_86	68	2885,5715	672.5+/-402.9	508,1869,1923	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ITPRIPL1	NM_001008949.2,NM_001163523.1,NM_001163524.1,NM_178495.5	,,,	686,2758,3059	GG,GA,AA		33.5465,28.2569,31.7546	,,,	505/556,497/548,497/548,513/564	96993884	4130,8876	2203	4300	6503	SO:0001819	synonymous_variant	150771	exon1			CATCCCAATCCCT		CCDS33250.1, CCDS46360.1, CCDS54378.1	2q11.2	2011-04-28	2011-04-28	2008-08-11	ENSG00000198885	ENSG00000198885			29371	protein-coding gene	gene with protein product			"""KIAA1754-like"", ""inositol 1,4,5-triphosphate receptor interacting protein-like 1"""	KIAA1754L		12477932	Standard	NM_178495		Approved		uc010yul.2	Q6GPH6	OTTHUMG00000155230	ENST00000439118.2:c.1515A>G	2.37:g.96993884A>G		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	106	50	0.471698	NM_178495	F5H1L8|Q8NE61	Silent	SNP	ENST00000439118.2	37	CCDS46360.1	629	0.288003663003663	128	0.2601626016260163	113	0.31215469613259667	146	0.25524475524475526	242	0.31926121372031663	G	3.885	-0.025099	0.07589	0.282569	0.335465	ENSG00000198885	ENST00000420728	.	.	.	5.65	-11.3	0.00108	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.31482	P	0.667034	.	.	.	.	.	.	T	0.07809	-1.0753	3	.	.	.	-15.6452	7.7271	0.28765	0.3095:0.4735:0.1489:0.0681	rs1048675;rs3171926;rs58857385;rs1048675	.	.	.	R	537	.	.	Q	+	2	0	ITPRIPL1	96357611	0.012000	0.17670	0.061000	0.19648	0.970000	0.65996	-1.787000	0.01764	-2.991000	0.00279	-0.808000	0.03180	CAA	A|0.691;C|0.000;G|0.309	0.309	strong		0.522	ITPRIPL1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000338896.1	NM_178495	
SCAF11	9169	hgsc.bcm.edu	37	12	46322449	46322449	+	Silent	SNP	C	C	T	rs10880868	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:46322449C>T	ENST00000369367.3	-	11	1268	c.1035G>A	c.(1033-1035)ggG>ggA	p.G345G	SCAF11_ENST00000419565.2_Silent_p.G345G|SCAF11_ENST00000465950.1_Silent_p.G30G|SCAF11_ENST00000549162.1_Silent_p.G153G	NM_004719.2	NP_004710.2	Q99590	SCAFB_HUMAN	SR-related CTD-associated factor 11	345					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)|spliceosomal complex assembly (GO:0000245)	nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.G345G(1)		breast(2)|central_nervous_system(1)|endometrium(2)|kidney(8)|large_intestine(17)|lung(25)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	69						GGGCATCACACCCAGAATTGT	0.453													C|||	557	0.111222	0.0068	0.0994	5008	,	,		15358	0.1319		0.2038	False		,,,				2504	0.1442				p.G345G		Atlas-SNP	.											SCAF11,NS,carcinoma,0,1	SCAF11	145	1	1	Substitution - coding silent(1)	stomach(1)	c.G1035A						PASS	.	C		172,4234	114.2+/-152.2	3,166,2034	193.0	189.0	190.0		1035	0.7	1.0	12	dbSNP_120	190	1815,6785	326.8+/-317.6	179,1457,2664	no	coding-synonymous	SCAF11	NM_004719.2		182,1623,4698	TT,TC,CC		21.1047,3.9038,15.2776		345/1464	46322449	1987,11019	2203	4300	6503	SO:0001819	synonymous_variant	9169	exon11			ATCACACCCAGAA	Y11251	CCDS8748.2	12q13.11	2013-01-09	2011-01-10	2011-01-10	ENSG00000139218	ENSG00000139218		"""RING-type (C3HC4) zinc fingers"""	10784	protein-coding gene	gene with protein product		603668	"""splicing factor, arginine/serine-rich 2, interacting protein"", ""serine/arginine-rich splicing factor 2, interacting protein"""	SFRS2IP, SRSF2IP		9224939, 9447963	Standard	NM_004719		Approved	SIP1, SRRP129, CASP11	uc001rox.3	Q99590	OTTHUMG00000149930	ENST00000369367.3:c.1035G>A	12.37:g.46322449C>T		Somatic	201	0	0		WXS	Illumina HiSeq	Phase_I	181	80	0.441989	NM_004719	A6NEU9|A6NLW5|Q8IW59	Silent	SNP	ENST00000369367.3	37	CCDS8748.2																																																																																			C|0.857;T|0.143	0.143	strong		0.453	SCAF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313992.2	NM_004719	
FRY	10129	hgsc.bcm.edu	37	13	32776616	32776616	+	Missense_Mutation	SNP	T	T	A	rs61750791	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:32776616T>A	ENST00000380250.3	+	31	4466	c.3970T>A	c.(3970-3972)Tgt>Agt	p.C1324S		NM_023037.2	NP_075463.2	Q5TBA9	FRY_HUMAN	furry homolog (Drosophila)	1324						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)		CCTCTTGTCATGTGAGCTGGC	0.493													T|||	495	0.0988419	0.003	0.0389	5008	,	,		15378	0.2649		0.0358	False		,,,				2504	0.1646				p.C1324S		Atlas-SNP	.											.	FRY	312	.	0			c.T3970A						PASS	.	T	SER/CYS	36,3976		0,36,1970	81.0	81.0	81.0		3970	2.8	0.0	13	dbSNP_129	81	360,7966		10,340,3813	yes	missense	FRY	NM_023037.2	112	10,376,5783	AA,AT,TT		4.3238,0.8973,3.2096	benign	1324/3014	32776616	396,11942	2006	4163	6169	SO:0001583	missense	10129	exon31			TTGTCATGTGAGC	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.3970T>A	13.37:g.32776616T>A	ENSP00000369600:p.Cys1324Ser	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	98	47	0.479592	NM_023037	Q9Y3N6	Missense_Mutation	SNP	ENST00000380250.3	37	CCDS41875.1	213	0.09752747252747253	1	0.0020325203252032522	16	0.04419889502762431	172	0.3006993006993007	24	0.0316622691292876	T	0.309	-0.969295	0.02232	0.008973	0.043238	ENSG00000073910	ENST00000380250;ENST00000380257	T	0.20200	2.09	5.39	2.81	0.32909	.	0.428442	0.28521	N	0.015051	T	0.00012	0.0000	N	0.11560	0.145	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.46789	-0.9166	9	0.10111	T	0.7	.	4.345	0.11129	0.2479:0.1404:0.0:0.6117	rs61750791	1324	Q5TBA9	FRY_HUMAN	S	1324;163	ENSP00000369600:C1324S	ENSP00000369600:C1324S	C	+	1	0	FRY	31674616	0.637000	0.27216	0.030000	0.17652	0.107000	0.19398	2.088000	0.41663	0.307000	0.22880	0.374000	0.22700	TGT	T|0.916;A|0.084	0.084	strong		0.493	FRY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044405.1	NM_023037	
GLYATL2	219970	hgsc.bcm.edu	37	11	58602309	58602309	+	Splice_Site	SNP	C	C	T	rs11229651	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:58602309C>T	ENST00000287275.1	-	6	868	c.478G>A	c.(478-480)Gaa>Aaa	p.E160K	GLYATL2_ENST00000532258.1_Splice_Site_p.E160K|GLYATL2_ENST00000533636.1_5'UTR	NM_145016.3	NP_659453.3	Q8WU03	GLYL2_HUMAN	glycine-N-acyltransferase-like 2	160			E -> K (in dbSNP:rs11229651). {ECO:0000269|Ref.1}.			endoplasmic reticulum (GO:0005783)|mitochondrion (GO:0005739)	glycine N-acyltransferase activity (GO:0047961)	p.E160K(1)		breast(1)|kidney(1)|large_intestine(3)|lung(12)|ovary(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	23		Breast(21;0.0044)|all_epithelial(135;0.0216)			Glycine(DB00145)	AAGTTTCCTTCCCTGTGAAGA	0.343													C|||	1670	0.333466	0.2852	0.3242	5008	,	,		20670	0.4841		0.2018	False		,,,				2504	0.3855				p.E160K		Atlas-SNP	.											GLYATL2,NS,carcinoma,0,1	GLYATL2	40	1	1	Substitution - Missense(1)	stomach(1)	c.G478A						PASS	.	C	LYS/GLU	994,2856		152,690,1083	35.0	33.0	34.0		478	-1.4	0.0	11	dbSNP_120	34	1556,6738		141,1274,2732	yes	missense-near-splice	GLYATL2	NM_145016.3	56	293,1964,3815	TT,TC,CC		18.7605,25.8182,20.998	benign	160/295	58602309	2550,9594	1925	4147	6072	SO:0001630	splice_region_variant	219970	exon6			TTCCTTCCCTGTG	AF426250	CCDS41649.1	11q12.1	2008-02-05				ENSG00000156689			24178	protein-coding gene	gene with protein product		614762				12477932	Standard	NM_145016		Approved	BXMAS2-10, MGC24009	uc001nnd.4	Q8WU03		ENST00000287275.1:c.477-1G>A	11.37:g.58602309C>T		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	97	29	0.298969	NM_145016	A5LGC7|Q86WC3|Q96AT2	Missense_Mutation	SNP	ENST00000287275.1	37	CCDS41649.1	663	0.30357142857142855	132	0.2682926829268293	97	0.26795580110497236	261	0.4562937062937063	173	0.22823218997361477	C	0.061	-1.225198	0.01530	0.258182	0.187605	ENSG00000156689	ENST00000287275;ENST00000532258	T;T	0.14022	2.54;2.54	2.79	-1.35	0.09114	Acyl-CoA N-acyltransferase (1);Glycine N-acyltransferase, N-terminal (1);	1.319930	0.05354	N	0.532409	T	0.00012	0.0000	N	0.01705	-0.755	0.09310	P	0.99999999507813	B	0.02656	0.0	B	0.01281	0.0	T	0.44877	-0.9299	9	0.02654	T	1	.	5.6535	0.17631	0.0:0.4619:0.0:0.5381	rs11229651;rs17845505;rs17858392;rs52831818;rs58248646;rs11229651	160	Q8WU03	GLYL2_HUMAN	K	160	ENSP00000287275:E160K;ENSP00000434277:E160K	ENSP00000287275:E160K	E	-	1	0	GLYATL2	58358885	0.007000	0.16637	0.007000	0.13788	0.012000	0.07955	0.205000	0.17356	0.057000	0.16193	-0.405000	0.06341	GAA	C|0.732;T|0.268	0.268	strong		0.343	GLYATL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394599.1	NM_145016	Missense_Mutation
PBK	55872	hgsc.bcm.edu	37	8	27667969	27667969	+	Silent	SNP	C	C	G	rs2294092	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	142	0	0		WXS	Illumina HiSeq	Phase_I	127	126	0.992126	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	
ZFHX4	79776	hgsc.bcm.edu	37	8	77745635	77745635	+	Silent	SNP	G	G	A	rs2733733	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:77745635G>A	ENST00000521891.2	+	5	3835	c.3387G>A	c.(3385-3387)tcG>tcA	p.S1129S	ZFHX4_ENST00000050961.6_Intron|ZFHX4_ENST00000455469.2_Intron|ZFHX4_ENST00000518282.1_Silent_p.S1103S	NM_024721.4	NP_078997.4	Q86UP3	ZFHX4_HUMAN	zinc finger homeobox 4	1100					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)			AGTTGAGATCGACCTCAGGTA	0.413										HNSCC(33;0.089)			A|||	3045	0.608027	0.8343	0.5	5008	,	,		19872	0.6478		0.4493	False		,,,				2504	0.501				p.S1129S		Atlas-SNP	.											.	ZFHX4	878	.	0			c.G3387A						PASS	.	A		2974,902		1140,694,104	102.0	94.0	96.0		3387	-0.9	0.1	8	dbSNP_100	96	3808,4500		880,2048,1226	no	coding-synonymous	ZFHX4	NM_024721.4		2020,2742,1330	AA,AG,GG		45.8353,23.2714,44.3368		1129/3617	77745635	6782,5402	1938	4154	6092	SO:0001819	synonymous_variant	79776	exon5			GAGATCGACCTCA		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.3387G>A	8.37:g.77745635G>A		Somatic	155	1	0.00645161		WXS	Illumina HiSeq	Phase_I	124	124	1	NM_024721	G3V138|Q18PS0|Q6ZN20	Silent	SNP	ENST00000521891.2	37	CCDS47878.2																																																																																			G|0.387;A|0.613	0.613	strong		0.413	ZFHX4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379197.2	NM_024721	
ATP10B	23120	hgsc.bcm.edu	37	5	160115007	160115007	+	Silent	SNP	C	C	T	rs201071012		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:160115007C>T	ENST00000327245.5	-	5	921	c.75G>A	c.(73-75)tcG>tcA	p.S25S	ATP10B_ENST00000518411.1_5'UTR|CTC-529G1.1_ENST00000524198.1_RNA	NM_025153.2	NP_079429.2	O94823	AT10B_HUMAN	ATPase, class V, type 10B	25					phospholipid translocation (GO:0045332)	cytoplasmic vesicle (GO:0031410)|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)			NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|liver(2)|lung(37)|ovary(4)|pancreas(1)|prostate(5)|skin(3)|stomach(1)	75	Renal(175;0.00196)	Medulloblastoma(196;0.0377)|all_neural(177;0.121)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			GTGTGGTTTCCGATGGACAAT	0.537													T|||	1	0.000199681	0.0	0.0	5008	,	,		18673	0.0		0.001	False		,,,				2504	0.0				p.S25S		Atlas-SNP	.											.	ATP10B	201	.	0			c.G75A						PASS	.	T		3,4129		0,3,2063	96.0	98.0	97.0		75	1.4	0.9	5		97	20,8428		0,20,4204	no	coding-synonymous	ATP10B	NM_025153.2		0,23,6267	TT,TC,CC		0.2367,0.0726,0.1828		25/1462	160115007	23,12557	2066	4224	6290	SO:0001819	synonymous_variant	23120	exon5			GGTTTCCGATGGA	AB018258	CCDS43394.1	5q34	2010-04-20	2007-09-19		ENSG00000118322	ENSG00000118322		"""ATPases / P-type"""	13543	protein-coding gene	gene with protein product			"""ATPase, Class V, type 10B"""			9872452, 11015572	Standard	NM_025153		Approved	ATPVB, KIAA0715, FLJ21477	uc003lym.1	O94823	OTTHUMG00000163551	ENST00000327245.5:c.75G>A	5.37:g.160115007C>T		Somatic	177	1	0.00564972		WXS	Illumina HiSeq	Phase_I	146	86	0.589041	NM_025153	Q9H725	Silent	SNP	ENST00000327245.5	37	CCDS43394.1																																																																																			C|0.996;T|0.005	0.005	strong		0.537	ATP10B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374127.1	NM_025153	
BPIFB4	149954	hgsc.bcm.edu	37	20	31671663	31671663	+	Silent	SNP	T	T	C	rs2424945	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:31671663T>C	ENST00000375483.3	+	3	660	c.660T>C	c.(658-660)acT>acC	p.T220T		NM_182519.2	NP_872325.2	P59827	BPIB4_HUMAN	BPI fold containing family B, member 4	220	Gly-rich.					cytoplasm (GO:0005737)|extracellular region (GO:0005576)	lipid binding (GO:0008289)										TCCTCAGCACTGTGCAAGGCA	0.637													C|||	1899	0.379193	0.6074	0.4035	5008	,	,		17966	0.1984		0.333	False		,,,				2504	0.2873				p.T220T		Atlas-SNP	.											.	.	.	.	0			c.T660C						PASS	.	C		2492,1892		751,990,451	33.0	38.0	36.0		660	-1.4	1.0	20	dbSNP_100	36	2915,5623		517,1881,1871	no	coding-synonymous	BPIFB4	NM_182519.2		1268,2871,2322	CC,CT,TT		34.1415,43.1569,41.8434		220/615	31671663	5407,7515	2192	4269	6461	SO:0001819	synonymous_variant	149954	exon3			CAGCACTGTGCAA	AF549190	CCDS13213.2	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000186191	ENSG00000186191		"""BPI fold containing"""	16179	protein-coding gene	gene with protein product		615718	"""chromosome 20 open reading frame 186"""	C20orf186		11971875, 21787333	Standard	NM_182519		Approved	dJ726C3.5, LPLUNC4	uc010zue.2	P59827	OTTHUMG00000032235	ENST00000375483.3:c.660T>C	20.37:g.31671663T>C		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	32	19	0.59375	NM_182519	Q5TDX6	Silent	SNP	ENST00000375483.3	37	CCDS13213.2																																																																																			T|0.623;C|0.377	0.377	strong		0.637	BPIFB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078655.5	NM_182519	
GRIN3A	116443	hgsc.bcm.edu	37	9	104335682	104335682	+	Missense_Mutation	SNP	C	C	T	rs3739722	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	186	0	0		WXS	Illumina HiSeq	Phase_I	189	96	0.507937	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		
PMPCA	23203	hgsc.bcm.edu	37	9	139305140	139305140	+	Missense_Mutation	SNP	C	C	A	rs149055087	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:139305140C>A	ENST00000371717.3	+	1	29	c.20C>A	c.(19-21)gCg>gAg	p.A7E	PMPCA_ENST00000371720.1_Missense_Mutation_p.A7E|SDCCAG3_ENST00000357365.3_5'Flank|PMPCA_ENST00000399219.3_5'UTR|SDCCAG3_ENST00000371725.3_5'Flank|SDCCAG3_ENST00000298537.7_5'Flank	NM_001282946.1|NM_015160.1	NP_001269875.1|NP_055975.1	Q10713	MPPA_HUMAN	peptidase (mitochondrial processing) alpha	7					cellular protein metabolic process (GO:0044267)|protein targeting to mitochondrion (GO:0006626)|proteolysis (GO:0006508)	extracellular space (GO:0005615)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			endometrium(3)|kidney(1)|large_intestine(1)|lung(6)|ovary(2)|urinary_tract(1)	14		Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;9.3e-06)|Epithelial(140;1.15e-05)		GTGGTGCTGGCGGCGACGCGG	0.721													C|||	20	0.00399361	0.0	0.0086	5008	,	,		9105	0.0		0.0129	False		,,,				2504	0.001				p.A7E		Atlas-SNP	.											.	PMPCA	29	.	0			c.C20A						PASS	.	C	GLU/ALA	15,4375		0,15,2180	29.0	31.0	31.0		20	0.6	0.0	9	dbSNP_134	31	128,8456		1,126,4165	yes	missense	PMPCA	NM_015160.1	107	1,141,6345	AA,AC,CC		1.4911,0.3417,1.1022	benign	7/526	139305140	143,12831	2195	4292	6487	SO:0001583	missense	23203	exon1			TGCTGGCGGCGAC	D21064	CCDS35180.1, CCDS65192.1	9q34.3	2008-02-05	2003-06-13	2003-06-20	ENSG00000165688	ENSG00000165688			18667	protein-coding gene	gene with protein product		613036	"""inositol polyphosphate-5-phosphatase, 72 kD"""	INPP5E		8590280, 7788527	Standard	NM_015160		Approved	KIAA0123, Alpha-MPP	uc004chl.3	Q10713	OTTHUMG00000020926	ENST00000371717.3:c.20C>A	9.37:g.139305140C>A	ENSP00000360782:p.Ala7Glu	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	150	88	0.586667	NM_015160	B4DKL3|E7ET61|Q16639|Q5SXM9|Q8N513	Missense_Mutation	SNP	ENST00000371717.3	37	CCDS35180.1	17	0.007783882783882784	0	0.0	5	0.013812154696132596	0	0.0	12	0.0158311345646438	C	7.160	0.585420	0.13749	0.003417	0.014911	ENSG00000165688	ENST00000371720;ENST00000371717	T	0.12361	2.69	3.64	0.628	0.17681	.	0.689178	0.13331	N	0.395900	T	0.03564	0.0102	N	0.22421	0.69	0.21147	N	0.999776	B;B	0.34290	0.447;0.074	B;B	0.25987	0.065;0.062	T	0.20505	-1.0273	10	0.72032	D	0.01	.	8.3735	0.32430	0.0:0.6814:0.0:0.3186	.	7;7	B4DRK5;Q10713	.;MPPA_HUMAN	E	7	ENSP00000360782:A7E	ENSP00000360782:A7E	A	+	2	0	PMPCA	138424961	0.000000	0.05858	0.002000	0.10522	0.001000	0.01503	-0.552000	0.06020	-0.414000	0.07495	-1.814000	0.00607	GCG	C|0.991;A|0.009	0.009	strong		0.721	PMPCA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055054.1	NM_015160	
GPRC5D	55507	hgsc.bcm.edu	37	12	13102605	13102605	+	Silent	SNP	G	G	A	rs4630382	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:13102605G>A	ENST00000228887.1	-	1	713	c.714C>T	c.(712-714)gaC>gaT	p.D238D	RP11-392P7.6_ENST00000538231.1_RNA|RP11-392P7.6_ENST00000545914.1_RNA|RP11-392P7.6_ENST00000542078.1_RNA|RP11-392P7.6_ENST00000540198.1_RNA|RP11-392P7.6_ENST00000394742.3_RNA|RP11-392P7.6_ENST00000536029.1_RNA|RP11-392P7.6_ENST00000543515.2_RNA|GPRC5D_ENST00000396333.3_Silent_p.D238D	NM_018654.1	NP_061124.1	Q9NZD1	GPC5D_HUMAN	G protein-coupled receptor, class C, group 5, member D	238						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			kidney(2)|large_intestine(2)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	9		Prostate(47;0.183)		BRCA - Breast invasive adenocarcinoma(232;0.15)		CGACCGGGTCGTCCCACTGGG	0.552													g|||	1035	0.206669	0.0204	0.2046	5008	,	,		20154	0.1865		0.3817	False		,,,				2504	0.3006				p.D238D		Atlas-SNP	.											.	GPRC5D	23	.	0			c.C714T						PASS	.	A		350,4056	180.8+/-209.0	12,326,1865	97.0	99.0	98.0		714	-3.6	0.9	12	dbSNP_111	98	3395,5205	502.3+/-375.6	674,2047,1579	no	coding-synonymous	GPRC5D	NM_018654.1		686,2373,3444	AA,AG,GG		39.4767,7.9437,28.7944		238/346	13102605	3745,9261	2203	4300	6503	SO:0001819	synonymous_variant	55507	exon1			CGGGTCGTCCCAC	AF209923	CCDS8658.1	12p13.3	2014-01-30	2014-01-30		ENSG00000111291	ENSG00000111291		"""GPCR / Class C : Orphans"""	13310	protein-coding gene	gene with protein product		607437	"""G protein-coupled receptor, family C, group 5, member D"""				Standard	XM_005253421		Approved		uc010shp.2	Q9NZD1	OTTHUMG00000168711	ENST00000228887.1:c.714C>T	12.37:g.13102605G>A		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	112	57	0.508929	NM_018654	Q3KNV3|Q7Z5J9|Q8TDS6	Silent	SNP	ENST00000228887.1	37	CCDS8658.1																																																																																			G|0.739;A|0.261	0.261	strong		0.552	GPRC5D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400687.1		
RIT2	6014	hgsc.bcm.edu	37	18	40323497	40323497	+	Silent	SNP	G	G	T	rs1804730	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:40323497G>T	ENST00000326695.5	-	5	786	c.615C>A	c.(613-615)ctC>ctA	p.L205L	RIT2_ENST00000589109.1_3'UTR|RIT2_ENST00000590910.1_3'UTR	NM_002930.2	NP_002921.1	Q99578	RIT2_HUMAN	Ras-like without CAAX 2	205					neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|synaptic transmission (GO:0007268)	nucleus (GO:0005634)|plasma membrane (GO:0005886)	calmodulin binding (GO:0005516)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)			endometrium(1)|large_intestine(2)|lung(11)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						AAGAACCTTTGAGCTTCTTCC	0.388													T|||	2954	0.589856	0.8215	0.6023	5008	,	,		17979	0.6984		0.3519	False		,,,				2504	0.4008				p.L205L		Atlas-SNP	.											.	RIT2	56	.	0			c.C615A						PASS	.	T		3291,1115	399.2+/-331.1	1246,799,158	139.0	145.0	143.0		615	1.5	1.0	18	dbSNP_89	143	3106,5494	657.9+/-401.5	577,1952,1771	no	coding-synonymous	RIT2	NM_002930.2		1823,2751,1929	TT,TG,GG		36.1163,25.3064,49.185		205/218	40323497	6397,6609	2203	4300	6503	SO:0001819	synonymous_variant	6014	exon5			ACCTTTGAGCTTC	BC018060	CCDS11921.1, CCDS62431.1	18q12.3	2014-05-09	2002-09-11	2002-09-13	ENSG00000152214	ENSG00000152214			10017	protein-coding gene	gene with protein product		609592	"""Ric (Drosophila)-like, expressed in neurons"""	RIN		8824319, 8918462	Standard	NM_002930		Approved	RIBA	uc002lav.4	Q99578	OTTHUMG00000132611	ENST00000326695.5:c.615C>A	18.37:g.40323497G>T		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	77	43	0.558442	NM_002930	B2R9L1|O15295|Q8TD69|Q8WVF6|Q92964	Silent	SNP	ENST00000326695.5	37	CCDS11921.1																																																																																			G|0.455;T|0.545	0.545	strong		0.388	RIT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255852.1	NM_002930	
SLFN13	146857	hgsc.bcm.edu	37	17	33769034	33769034	+	Silent	SNP	G	G	A	rs62078110	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:33769034G>A	ENST00000285013.6	-	5	1745	c.1470C>T	c.(1468-1470)acC>acT	p.T490T	SLFN13_ENST00000526861.1_Silent_p.T490T|SLFN13_ENST00000533791.1_Silent_p.T490T|SLFN13_ENST00000534689.1_Silent_p.T172T|SLFN13_ENST00000360502.2_Silent_p.T172T|SLFN13_ENST00000542635.1_Silent_p.T490T	NM_144682.5	NP_653283.3	Q68D06	SLN13_HUMAN	schlafen family member 13	490						intracellular (GO:0005622)	ATP binding (GO:0005524)	p.T490T(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)		AAGTAAAGGCGGTGCGAGTGC	0.567													G|||	2284	0.45607	0.4569	0.4337	5008	,	,		25283	0.4921		0.4165	False		,,,				2504	0.4744				p.T490T		Atlas-SNP	.											SLFN13,rectum,carcinoma,0,1	SLFN13	79	1	1	Substitution - coding silent(1)	large_intestine(1)	c.C1470T						scavenged	.						101.0	87.0	92.0					17																	33769034		2203	4300	6503	SO:0001819	synonymous_variant	146857	exon5			AAAGGCGGTGCGA	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.1470C>T	17.37:g.33769034G>A		Somatic	764	6	0.0078534		WXS	Illumina HiSeq	Phase_I	686	310	0.451895	NM_144682	E1P645|Q658M1|Q6ZS51|Q96A81	Silent	SNP	ENST00000285013.6	37	CCDS32620.1																																																																																			.	.	weak		0.567	SLFN13-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381883.1	NM_144682	
CHDH	55349	hgsc.bcm.edu	37	3	53855738	53855738	+	Silent	SNP	G	G	C	rs35064726	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:53855738G>C	ENST00000315251.6	-	5	1358	c.921C>G	c.(919-921)ctC>ctG	p.L307L		NM_018397.4	NP_060867.2	Q8NE62	CHDH_HUMAN	choline dehydrogenase	307					glycine betaine biosynthetic process from choline (GO:0019285)	mitochondrial inner membrane (GO:0005743)	choline dehydrogenase activity (GO:0008812)|flavin adenine dinucleotide binding (GO:0050660)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(2)|prostate(1)	17		Hepatocellular(537;0.152)		BRCA - Breast invasive adenocarcinoma(193;0.000158)|KIRC - Kidney renal clear cell carcinoma(284;0.00588)|Kidney(284;0.00673)|OV - Ovarian serous cystadenocarcinoma(275;0.118)	Choline(DB00122)	CGATGCCAGAGAGCATGAGCA	0.562													G|||	123	0.0245607	0.0023	0.0216	5008	,	,		19271	0.0		0.0527	False		,,,				2504	0.0532				p.L307L		Atlas-SNP	.											.	CHDH	34	.	0			c.C921G						PASS	.	G		50,4356	50.9+/-86.3	0,50,2153	142.0	126.0	131.0		921	-2.7	0.6	3	dbSNP_126	131	472,8128	138.7+/-195.5	17,438,3845	no	coding-synonymous	CHDH	NM_018397.4		17,488,5998	CC,CG,GG		5.4884,1.1348,4.0135		307/595	53855738	522,12484	2203	4300	6503	SO:0001819	synonymous_variant	55349	exon5			GCCAGAGAGCATG	AJ272267	CCDS2873.1	3p21	2004-11-24			ENSG00000016391	ENSG00000016391	1.1.99.1		24288	protein-coding gene	gene with protein product							Standard	NM_018397		Approved		uc003dgz.3	Q8NE62	OTTHUMG00000158281	ENST00000315251.6:c.921C>G	3.37:g.53855738G>C		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	71	38	0.535211	NM_018397	Q9NY17	Silent	SNP	ENST00000315251.6	37	CCDS2873.1																																																																																			G|0.958;C|0.042	0.042	strong		0.562	CHDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350567.2	NM_018397	
NES	10763	hgsc.bcm.edu	37	1	156640156	156640156	+	Missense_Mutation	SNP	G	G	A	rs3748570	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:156640156G>A	ENST00000368223.3	-	4	3956	c.3824C>T	c.(3823-3825)cCc>cTc	p.P1275L		NM_006617.1	NP_006608.1	P48681	NEST_HUMAN	nestin	1275	Tail.		P -> L (in dbSNP:rs3748570). {ECO:0000269|PubMed:1478958, ECO:0000269|PubMed:18669648, ECO:0000269|PubMed:21406692}.		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)					TTCCTCCTGGGGGCCCTCGGG	0.652													A|||	3628	0.724441	0.711	0.7104	5008	,	,		18440	0.87		0.6551	False		,,,				2504	0.6738				p.P1275L		Atlas-SNP	.											.	NES	196	.	0			c.C3824T						PASS	.	A	LEU/PRO	3055,1351	450.2+/-349.3	1044,967,192	74.0	87.0	83.0		3824	4.9	1.0	1	dbSNP_107	83	5527,3073	469.3+/-367.5	1817,1893,590	yes	missense	NES	NM_006617.1	98	2861,2860,782	AA,AG,GG		35.7326,30.6627,34.0151	benign	1275/1622	156640156	8582,4424	2203	4300	6503	SO:0001583	missense	10763	exon4			TCCTGGGGGCCCT	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.3824C>T	1.37:g.156640156G>A	ENSP00000357206:p.Pro1275Leu	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	60	25	0.416667	NM_006617	O00552|Q3LIF5|Q5SYZ6	Missense_Mutation	SNP	ENST00000368223.3	37	CCDS1151.1	1594	0.7298534798534798	349	0.709349593495935	256	0.7071823204419889	495	0.8653846153846154	494	0.6517150395778364	A	0.026	-1.373560	0.01214	0.693373	0.642674	ENSG00000132688	ENST00000368223	D	0.83250	-1.7	4.95	4.95	0.65309	.	0.000000	0.29348	N	0.012416	T	0.18130	0.0435	N	0.00142	-2.005	0.49051	P	2.60000000000038E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.20405	-1.0276	9	0.02654	T	1	.	4.6302	0.12498	0.7404:0.0:0.0923:0.1673	rs3748570;rs58877600;rs3748570	1275	P48681	NEST_HUMAN	L	1275	ENSP00000357206:P1275L	ENSP00000357206:P1275L	P	-	2	0	NES	154906780	0.964000	0.33143	0.999000	0.59377	0.334000	0.28698	0.911000	0.28584	0.732000	0.32470	-0.381000	0.06696	CCC	G|0.310;A|0.690	0.690	strong		0.652	NES-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000082844.2	NM_006617	
TRIM31	11074	hgsc.bcm.edu	37	6	30075843	30075843	+	Silent	SNP	T	T	C	rs3132679	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:30075843T>C	ENST00000376734.3	-	6	995	c.870A>G	c.(868-870)ctA>ctG	p.L290L	TRIM31_ENST00000540829.1_Silent_p.L290L|TRIM31-AS1_ENST00000440874.1_RNA|TRIM31_ENST00000485864.1_5'UTR	NM_007028.3	NP_008959.3	Q9BZY9	TRI31_HUMAN	tripartite motif containing 31	290					innate immune response (GO:0045087)|negative regulation of viral entry into host cell (GO:0046597)|negative regulation of viral transcription (GO:0032897)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein ubiquitination (GO:0016567)|regulation of viral release from host cell (GO:1902186)	mitochondrion (GO:0005739)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(5)|ovary(2)|prostate(2)|skin(2)	15						TGAATTTTTTTAGGCTCCCTG	0.433													C|||	4192	0.837061	0.6876	0.853	5008	,	,		19781	0.9196		0.8638	False		,,,				2504	0.9151				p.L290L		Atlas-SNP	.											.	TRIM31	40	.	0			c.A870G						PASS	.	C		2183,839		790,603,118	62.0	59.0	60.0		870	2.5	0.0	6	dbSNP_103	60	4584,834		1938,708,63	yes	coding-synonymous	TRIM31	NM_007028.3		2728,1311,181	CC,CT,TT		15.3931,27.7631,19.8223		290/426	30075843	6767,1673	1511	2709	4220	SO:0001819	synonymous_variant	11074	exon6			TTTTTTTAGGCTC	AF230386	CCDS34374.1	6p21.3	2013-01-09	2011-01-25		ENSG00000204616	ENSG00000204616		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	16289	protein-coding gene	gene with protein product		609316	"""tripartite motif-containing 31"""			11331580	Standard	XM_006714977		Approved	RNF, HCGI, C6orf13, HCG1	uc003npg.1	Q9BZY9	OTTHUMG00000031064	ENST00000376734.3:c.870A>G	6.37:g.30075843T>C		Somatic	207	0	0		WXS	Illumina HiSeq	Phase_I	124	123	0.991935	NM_007028	A6NLX6|A9R9Q4|Q53H52|Q5RI37|Q5SRJ7|Q5SRJ8|Q5SS28|Q96AK4|Q96AP8|Q99579|Q9BZY8	Silent	SNP	ENST00000376734.3	37	CCDS34374.1																																																																																			T|0.196;C|0.804	0.804	strong		0.433	TRIM31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076081.2		
HAS1	3036	hgsc.bcm.edu	37	19	52217174	52217174	+	Missense_Mutation	SNP	C	C	T	rs45625331	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:52217174C>T	ENST00000222115.1	-	5	1277	c.1243G>A	c.(1243-1245)Gtg>Atg	p.V415M	HAS1_ENST00000594621.1_3'UTR|HAS1_ENST00000601714.1_Missense_Mutation_p.V422M|HAS1_ENST00000540069.2_Missense_Mutation_p.V414M	NM_001523.2	NP_001514.2	Q92839	HYAS1_HUMAN	hyaluronan synthase 1	415					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)		GTGGCCGCCACGAAGAAGGGG	0.672													c|||	5	0.000998403	0.0	0.0029	5008	,	,		16422	0.0		0.002	False		,,,				2504	0.001				p.V415M	NSCLC(132;636 2450 45807 47979)	Atlas-SNP	.											.	HAS1	61	.	0			c.G1243A						PASS	.		MET/VAL	5,4393	8.1+/-20.4	0,5,2194	48.0	42.0	44.0		1243	3.2	1.0	19	dbSNP_127	44	58,8542	32.8+/-85.7	0,58,4242	yes	missense	HAS1	NM_001523.2	21	0,63,6436	TT,TC,CC		0.6744,0.1137,0.4847	probably-damaging	415/579	52217174	63,12935	2199	4300	6499	SO:0001583	missense	3036	exon5			CCGCCACGAAGAA	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.1243G>A	19.37:g.52217174C>T	ENSP00000222115:p.Val415Met	Somatic	21	0	0		WXS	Illumina HiSeq	Phase_I	17	8	0.470588	NM_001523	Q14470|Q9NS49	Missense_Mutation	SNP	ENST00000222115.1	37	CCDS12838.1	3	0.0013736263736263737	0	0.0	2	0.0055248618784530384	0	0.0	1	0.0013192612137203166	c	16.44	3.122752	0.56613	0.001137	0.006744	ENSG00000105509	ENST00000540069;ENST00000222115	T;T	0.59638	0.25;0.25	3.19	3.19	0.36642	.	0.000000	0.64402	U	0.000002	T	0.56093	0.1962	L	0.49778	1.585	0.58432	D	0.999992	D;D;D	0.67145	0.992;0.996;0.996	P;P;P	0.58013	0.63;0.831;0.831	T	0.65919	-0.6051	10	0.72032	D	0.01	-12.5318	12.2755	0.54733	0.0:1.0:0.0:0.0	rs45625331	414;415;414	G3V1S7;Q92839;Q8IYH3	.;HAS1_HUMAN;.	M	414;415	ENSP00000445021:V414M;ENSP00000222115:V415M	ENSP00000222115:V415M	V	-	1	0	HAS1	56908986	1.000000	0.71417	1.000000	0.80357	0.304000	0.27724	3.956000	0.56722	1.812000	0.52913	0.165000	0.16767	GTG	C|0.997;T|0.003	0.003	strong		0.672	HAS1-005	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466953.1	NM_001523	
PLEKHH2	130271	hgsc.bcm.edu	37	2	43931176	43931176	+	Silent	SNP	T	T	C	rs4953002	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:43931176T>C	ENST00000282406.4	+	9	1817	c.1707T>C	c.(1705-1707)aaT>aaC	p.N569N		NM_172069.3	NP_742066.2	Q8IVE3	PKHH2_HUMAN	pleckstrin homology domain containing, family H (with MyTH4 domain) member 2	569					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)				AGGCCTTCAATATGGAGAGTG	0.378													T|||	2243	0.447883	0.6029	0.4337	5008	,	,		17505	0.1319		0.5408	False		,,,				2504	0.4785				p.N569N		Atlas-SNP	.											PLEKHH2,NS,carcinoma,0,1	PLEKHH2	156	1	0			c.T1707C						PASS	.	T		2563,1843	635.0+/-396.3	745,1073,385	105.0	101.0	102.0		1707	-1.9	0.2	2	dbSNP_111	102	4567,4033	596.3+/-393.6	1220,2127,953	no	coding-synonymous	PLEKHH2	NM_172069.3		1965,3200,1338	CC,CT,TT		46.8953,41.8293,45.1791		569/1494	43931176	7130,5876	2203	4300	6503	SO:0001819	synonymous_variant	130271	exon9			CTTCAATATGGAG	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.1707T>C	2.37:g.43931176T>C		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	68	68	1	NM_172069	Q5JPJ6|Q6P4Q1|Q8N3Q3	Silent	SNP	ENST00000282406.4	37	CCDS1812.1																																																																																			T|0.587;C|0.413	0.413	strong		0.378	PLEKHH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250537.1	NM_172069	
TTLL9	164395	hgsc.bcm.edu	37	20	30527065	30527065	+	Silent	SNP	T	T	C	rs6061043	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:30527065T>C	ENST00000375938.4	+	14	1492	c.1239T>C	c.(1237-1239)caT>caC	p.H413H	TTLL9_ENST00000375934.4_3'UTR|TTLL9_ENST00000535842.1_Silent_p.H413H|TTLL9_ENST00000375922.4_Intron|TTLL9_ENST00000375921.2_3'UTR			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	58	0	0		WXS	Illumina HiSeq	Phase_I	39	16	0.410256	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	
RBM44	375316	hgsc.bcm.edu	37	2	238733016	238733016	+	Silent	SNP	G	G	A	rs4663795	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:238733016G>A	ENST00000409864.1	+	10	2660	c.2406G>A	c.(2404-2406)caG>caA	p.Q802Q	RBM44_ENST00000316997.4_Silent_p.Q802Q			Q6ZP01	RBM44_HUMAN	RNA binding motif protein 44	801						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)		CAGGGACACAGGGAAATCAAG	0.428													A|||	1319	0.263379	0.3033	0.183	5008	,	,		18610	0.3859		0.1352	False		,,,				2504	0.272				p.Q802Q		Atlas-SNP	.											.	RBM44	167	.	0			c.G2406A						PASS	.	A		1163,2721		186,791,965	117.0	120.0	119.0		2406	-0.2	0.0	2	dbSNP_111	119	1166,7144		85,996,3074	no	coding-synonymous	RBM44	NM_001080504.2		271,1787,4039	AA,AG,GG		14.0313,29.9434,19.0996		802/1053	238733016	2329,9865	1942	4155	6097	SO:0001819	synonymous_variant	375316	exon10			GACACAGGGAAAT	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.2406G>A	2.37:g.238733016G>A		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	102	46	0.45098	NM_001080504	A0AUW3	Silent	SNP	ENST00000409864.1	37	CCDS46554.1																																																																																			G|0.738;A|0.262	0.262	strong		0.428	RBM44-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328733.2	NM_001080504	
WBSCR28	135886	hgsc.bcm.edu	37	7	73275565	73275565	+	Missense_Mutation	SNP	T	T	A	rs11770052	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:73275565T>A	ENST00000320531.2	+	1	77	c.41T>A	c.(40-42)aTc>aAc	p.I14N		NM_182504.3	NP_872310.2	Q6UE05	WBS28_HUMAN	Williams-Beuren syndrome chromosome region 28	14			I -> N (in dbSNP:rs11770052). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:18398435}.			integral component of membrane (GO:0016021)				breast(2)|kidney(2)|lung(6)|skin(1)	11		Lung NSC(55;0.159)				CTTTTGGGGATCCTGTTGCAG	0.622													T|||	2728	0.544728	0.2852	0.6037	5008	,	,		13720	0.63		0.7256	False		,,,				2504	0.5798				p.I14N		Atlas-SNP	.											.	WBSCR28	24	.	0			c.T41A						PASS	.	T	ASN/ILE	1476,2316		291,894,711	55.0	52.0	53.0		41	3.1	0.0	7	dbSNP_120	53	6148,2076		2304,1540,268	yes	missense	WBSCR28	NM_182504.3	149	2595,2434,979	AA,AT,TT		25.2432,38.9241,36.5513	benign	14/266	73275565	7624,4392	1896	4112	6008	SO:0001583	missense	135886	exon1			TGGGGATCCTGTT	BC030643	CCDS43597.1	7q11.23	2006-07-04			ENSG00000175877	ENSG00000175877			23018	protein-coding gene	gene with protein product		612547				8812460	Standard	NM_182504		Approved	MGC26719	uc003tzk.2	Q6UE05	OTTHUMG00000157243	ENST00000320531.2:c.41T>A	7.37:g.73275565T>A	ENSP00000316775:p.Ile14Asn	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	43	42	0.976744	NM_182504	Q6UE04|Q8NHP4	Missense_Mutation	SNP	ENST00000320531.2	37	CCDS43597.1	1264	0.5787545787545788	145	0.29471544715447157	213	0.5883977900552486	352	0.6153846153846154	554	0.7308707124010554	T	0.735	-0.778461	0.02929	0.389241	0.747568	ENSG00000175877	ENST00000320531	T	0.22134	1.97	4.21	3.07	0.35406	.	0.468250	0.16327	N	0.219284	T	0.00012	0.0000	L	0.27053	0.805	0.80722	P	0.0	P	0.44429	0.835	P	0.48400	0.576	T	0.04153	-1.0973	9	0.54805	T	0.06	-1.7877	5.6334	0.17524	0.0:0.1295:0.0:0.8705	rs11770052;rs17845923;rs17858902;rs11770052	14	Q6UE05	WBS28_HUMAN	N	14	ENSP00000316775:I14N	ENSP00000316775:I14N	I	+	2	0	WBSCR28	72913501	0.030000	0.19436	0.002000	0.10522	0.019000	0.09904	2.013000	0.40942	0.805000	0.34159	0.529000	0.55759	ATC	T|0.385;A|0.615	0.615	strong		0.622	WBSCR28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348130.1	NM_182504	
METTL11B	149281	hgsc.bcm.edu	37	1	170135765	170135765	+	Silent	SNP	T	T	C	rs6669514	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:170135765T>C	ENST00000439373.2	+	3	560	c.453T>C	c.(451-453)ttT>ttC	p.F151F	METTL11B_ENST00000367764.3_3'UTR	NM_001136107.1	NP_001129579.1	Q5VVY1	NTM1B_HUMAN	methyltransferase like 11B	151						nucleus (GO:0005634)	methyltransferase activity (GO:0008168)			NS(1)|breast(2)|endometrium(3)|prostate(2)	8						TGGAATCCTTTCTCCTTGAAG	0.512													T|||	1330	0.265575	0.4758	0.2219	5008	,	,		18181	0.1349		0.2207	False		,,,				2504	0.1933				p.F151F		Atlas-SNP	.											.	METTL11B	18	.	0			c.T453C						PASS	.	T		599,785		131,337,224	111.0	101.0	104.0		453	2.3	1.0	1	dbSNP_116	104	752,2430		97,558,936	no	coding-synonymous	METTL11B	NM_001136107.1		228,895,1160	CC,CT,TT		23.6329,43.2803,29.5883		151/284	170135765	1351,3215	692	1591	2283	SO:0001819	synonymous_variant	149281	exon3			ATCCTTTCTCCTT	AL445203, CAH72139	CCDS44275.1	1q24.2	2012-11-05	2008-06-11	2008-06-11	ENSG00000203740	ENSG00000203740			31932	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 184"""	C1orf184			Standard	NM_001136107		Approved	HOMT1B	uc009wvv.1	Q5VVY1	OTTHUMG00000035959	ENST00000439373.2:c.453T>C	1.37:g.170135765T>C		Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	131	73	0.557252	NM_001136107	B2RXI0	Silent	SNP	ENST00000439373.2	37	CCDS44275.1																																																																																			T|0.746;C|0.254	0.254	strong		0.512	METTL11B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087586.2	NM_001136107	
ELP2	55250	hgsc.bcm.edu	37	18	33718326	33718326	+	Missense_Mutation	SNP	A	A	C	rs1785934	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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_ENST00000423854.2_Missense_Mutation_p.T128P|ELP2_ENST00000350494.6_Missense_Mutation_p.T128P|ELP2_ENST00000442325.2_Missense_Mutation_p.T128P|ELP2_ENST00000542824.1_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	85	0	0		WXS	Illumina HiSeq	Phase_I	89	47	0.52809	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	
OR5L2	26338	hgsc.bcm.edu	37	11	55595017	55595017	+	Missense_Mutation	SNP	G	G	T	rs117277709|rs34954823|rs386753700	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:55595017G>T	ENST00000378397.1	+	1	323	c.323G>T	c.(322-324)gGa>gTa	p.G108V		NM_001004739.1	NP_001004739.1	Q8NGL0	OR5L2_HUMAN	olfactory receptor, family 5, subfamily L, member 2	108						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.G108V(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)				TGCACATGTGGAGTCACTGAG	0.483										HNSCC(27;0.073)			N|||	342	0.0682907	0.0938	0.036	5008	,	,		22494	0.0704		0.0736	False		,,,				2504	0.0491				p.G108V		Atlas-SNP	.											OR5L2,NS,carcinoma,-1,2	OR5L2	135	2	1	Substitution - Missense(1)	stomach(1)	c.G323T						PASS	.						184.0	173.0	177.0					11																	55595017		2190	4290	6480	SO:0001583	missense	26338	exon1			CATGTGGAGTCAC	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.323G>T	11.37:g.55595017G>T	ENSP00000367650:p.Gly108Val	Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	70	36	0.514286	NM_001004739	Q6IF66|Q96RB2	Missense_Mutation	SNP	ENST00000378397.1	37	CCDS31511.1	.	.	.	.	.	.	.	.	.	.	.	0	-2.868356	0.00063	.	.	ENSG00000205030	ENST00000378397	T	0.01359	4.98	5.18	-5.23	0.02798	GPCR, rhodopsin-like superfamily (1);	0.868328	0.09720	N	0.764589	T	0.00815	0.0027	N	0.13272	0.32	0.09310	N	0.999996	B	0.02656	0.0	B	0.04013	0.001	T	0.48019	-0.9071	10	0.02654	T	1	3.6392	9.8956	0.41316	0.0:0.2622:0.5569:0.1809	.	108	Q8NGL0	OR5L2_HUMAN	V	108	ENSP00000367650:G108V	ENSP00000367650:G108V	G	+	2	0	OR5L2	55351593	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-6.226000	0.00075	-0.884000	0.03976	-1.313000	0.01306	GGA	.	.	weak		0.483	OR5L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391516.1	NM_001004739	
CHD5	26038	hgsc.bcm.edu	37	1	6211183	6211183	+	Silent	SNP	G	G	A	rs9434711	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:6211183G>A	ENST00000262450.3	-	7	1002	c.903C>T	c.(901-903)ttC>ttT	p.F301F	CHD5_ENST00000378021.1_5'UTR	NM_015557.2	NP_056372.1	O00258	WRB_HUMAN	chromodomain helicase DNA binding protein 5	0					tail-anchored membrane protein insertion into ER membrane (GO:0071816)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)				breast(3)|central_nervous_system(3)|liver(1)|lung(1)|ovary(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)	16	Ovarian(185;0.0634)	all_cancers(23;5.36e-32)|all_epithelial(116;2.32e-17)|all_neural(13;3.68e-06)|all_lung(118;3.94e-06)|all_hematologic(16;2.39e-05)|Lung NSC(185;5.33e-05)|Acute lymphoblastic leukemia(12;0.000372)|Glioma(11;0.00127)|Renal(390;0.00188)|Colorectal(325;0.00342)|Breast(487;0.00373)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.15)		Epithelial(90;3.08e-37)|GBM - Glioblastoma multiforme(13;1.36e-31)|OV - Ovarian serous cystadenocarcinoma(86;7.7e-19)|Colorectal(212;9.97e-08)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(185;6.16e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.00109)|BRCA - Breast invasive adenocarcinoma(365;0.0012)|STAD - Stomach adenocarcinoma(132;0.00346)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.193)		TGGCGCTGTCGAAGTCCGACT	0.602													G|||	2535	0.50619	0.6906	0.2089	5008	,	,		19415	0.6528		0.3002	False		,,,				2504	0.5286				p.F301F		Atlas-SNP	.											.	CHD5	267	.	0			c.C903T						PASS	.			2701,1705	652.2+/-399.4	834,1033,336	98.0	84.0	88.0		903	-6.9	0.9	1	dbSNP_119	88	2423,6177	401.7+/-347.2	348,1727,2225	no	coding-synonymous	CHD5	NM_015557.2		1182,2760,2561	AA,AG,GG		28.1744,38.6972,39.3972		301/1955	6211183	5124,7882	2203	4300	6503	SO:0001819	synonymous_variant	26038	exon7			GCTGTCGAAGTCC	AF425231	CCDS57.1	1p36.3	2013-01-28			ENSG00000116254	ENSG00000116254		"""Zinc fingers, PHD-type"""	16816	protein-coding gene	gene with protein product		610771				11889561, 12592387	Standard	NM_015557		Approved		uc001amb.2	Q8TDI0	OTTHUMG00000000952	ENST00000262450.3:c.903C>T	1.37:g.6211183G>A		Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	121	47	0.38843	NM_015557	A8KAP8|A8MQ44|D3DSH9|O60740	Silent	SNP	ENST00000262450.3	37	CCDS57.1																																																																																			G|0.588;A|0.412	0.412	strong		0.602	CHD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002823.2	NM_015557	
KRTAP4-11	653240	hgsc.bcm.edu	37	17	39274266	39274266	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:39274266C>T	ENST00000391413.2	-	1	340	c.302G>A	c.(301-303)cGc>cAc	p.R101H		NM_033059.3	NP_149048.2	Q9BYQ6	KR411_HUMAN	keratin associated protein 4-11	101	27 X 5 AA repeats of C-C-[GIKRQVHEL]- [SPTR]-[STVQRMC].					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)			gcatctggggcggcagcaAGT	0.647																																					p.R101H		Atlas-SNP	.											.	KRTAP4-11	94	.	0			c.G302A						PASS	.						5.0	9.0	8.0					17																	39274266		655	1560	2215	SO:0001583	missense	653240	exon1			CTGGGGCGGCAGC	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.302G>A	17.37:g.39274266C>T	ENSP00000375232:p.Arg101His	Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	32	8	0.25	NM_033059	A0AUY2	Missense_Mutation	SNP	ENST00000391413.2	37	CCDS45675.1	.	.	.	.	.	.	.	.	.	.	.	10.07	1.249110	0.22880	.	.	ENSG00000212721	ENST00000391413	T	0.00638	6.04	3.99	1.96	0.26148	.	1.399950	0.05646	U	0.584357	T	0.01189	0.0039	M	0.78456	2.415	0.09310	N	1	B	0.15473	0.013	B	0.08055	0.003	T	0.50550	-0.8815	10	0.42905	T	0.14	.	3.6707	0.08273	0.1929:0.5877:0.0:0.2193	.	101	Q9BYQ6	KR411_HUMAN	H	101	ENSP00000375232:R101H	ENSP00000375232:R101H	R	-	2	0	KRTAP4-11	36527792	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-0.701000	0.05075	0.180000	0.19960	-0.192000	0.12808	CGC	.	.	none		0.647	KRTAP4-11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257690.1		
GPRIN1	114787	hgsc.bcm.edu	37	5	176026122	176026122	+	Silent	SNP	C	C	T	rs142779818|rs550332435|rs3797464|rs371149640|rs386695335	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:176026122C>T	ENST00000303991.4	-	2	891	c.714G>A	c.(712-714)ttG>ttA	p.L238L		NM_052899.2	NP_443131.2	Q7Z2K8	GRIN1_HUMAN	G protein regulated inducer of neurite outgrowth 1	238				Missing (in Ref. 4; CAD38868). {ECO:0000305}.	neuron projection development (GO:0031175)	cell projection (GO:0042995)|plasma membrane (GO:0005886)				NS(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(3)|liver(1)|lung(15)|ovary(2)|prostate(5)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	35	all_cancers(89;0.00263)|Renal(175;0.000269)|Lung NSC(126;0.00902)|all_lung(126;0.0142)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CCACCTTTCTCAAAGACCCAG	0.488																																					p.L238L		Atlas-SNP	.											GPRIN1,rectum,carcinoma,-1,2	GPRIN1	77	2	0			c.G714A						PASS	.						90.0	94.0	93.0					5																	176026122		2171	4246	6417	SO:0001819	synonymous_variant	114787	exon2			CTTTCTCAAAGAC	AB067480	CCDS4405.1	5q35.2	2008-02-05			ENSG00000169258	ENSG00000169258			24835	protein-coding gene	gene with protein product		611239				11572484	Standard	NM_052899		Approved	GRIN1, KIAA1893	uc003meo.1	Q7Z2K8	OTTHUMG00000130659	ENST00000303991.4:c.714G>A	5.37:g.176026122C>T		Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	125	29	0.232	NM_052899	C9JM70|Q8ND74|Q96PZ4	Silent	SNP	ENST00000303991.4	37	CCDS4405.1																																																																																			.	.	weak		0.488	GPRIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253149.1	NM_052899	
RNF111	54778	hgsc.bcm.edu	37	15	59347929	59347929	+	Silent	SNP	C	C	A	rs1446239	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:59347929C>A	ENST00000557998.1	+	4	1343	c.1056C>A	c.(1054-1056)tcC>tcA	p.S352S	RNF111_ENST00000561186.1_Silent_p.S352S|RNF111_ENST00000434298.1_Silent_p.S352S|RNF111_ENST00000559209.1_Silent_p.S352S|RNF111_ENST00000348370.4_Silent_p.S352S	NM_001270530.1	NP_001257459.1	Q6ZNA4	RN111_HUMAN	ring finger protein 111	352	Interaction with AXIN1.|Ser-rich.				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)		GCCAGGGTTCCAGTTCTCATG	0.433													A|||	2212	0.441693	0.6611	0.4986	5008	,	,		16383	0.4405		0.3161	False		,,,				2504	0.2352				p.S352S	NSCLC(72;983 1365 10746 34387 47081)	Atlas-SNP	.											RNF111_ENST00000434298,rectum,carcinoma,0,4	RNF111	179	4	0			c.C1056A						scavenged	.	A		2723,1661	505.6+/-366.2	863,997,332	56.0	48.0	51.0		1056	-0.0	1.0	15	dbSNP_88	51	3016,5566	661.7+/-401.9	560,1896,1835	yes	coding-synonymous	RNF111	NM_017610.6		1423,2893,2167	AA,AC,CC		35.1433,37.8878,44.2619		352/987	59347929	5739,7227	2192	4291	6483	SO:0001819	synonymous_variant	54778	exon4			GGGTTCCAGTTCT	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.1056C>A	15.37:g.59347929C>A		Somatic	126	1	0.00793651		WXS	Illumina HiSeq	Phase_I	154	100	0.649351	NM_017610	C9JUS4|H0YN55|Q6P9A4|Q6ZMU2|Q7L428|Q7Z346|Q8N1P9|Q8WUA3|Q9NSR1	Silent	SNP	ENST00000557998.1	37	CCDS58366.1																																																																																			C|0.554;A|0.446	0.446	strong		0.433	RNF111-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000416012.1	NM_017610	
DPH3	285381	hgsc.bcm.edu	37	3	16305674	16305674	+	Silent	SNP	C	C	G	rs14080	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:16305674C>G	ENST00000488423.1	-	2	266	c.171G>C	c.(169-171)gtG>gtC	p.V57V	OXNAD1_ENST00000606098.1_5'Flank|OXNAD1_ENST00000605932.1_5'Flank|DPH3_ENST00000285082.4_5'UTR|OXNAD1_ENST00000435829.2_5'Flank|DPH3_ENST00000383775.4_Intron|OXNAD1_ENST00000285083.5_5'Flank	NM_206831.2	NP_996662.1	Q96FX2	DPH3_HUMAN	diphthamide biosynthesis 3	57					negative regulation of protein secretion (GO:0050709)|peptidyl-diphthamide biosynthetic process from peptidyl-histidine (GO:0017183)|positive regulation of binding (GO:0051099)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)			large_intestine(2)	2						TGTCATAAATCACTTTTATAA	0.418													C|||	2172	0.433706	0.3079	0.4712	5008	,	,		17298	0.4762		0.4324	False		,,,				2504	0.5348				p.V57V		Atlas-SNP	.											DPH3,NS,adenoma,0,1	DPH3	7	1	0			c.G171C						PASS	.	C	,	1546,2860	483.5+/-359.7	274,998,931	107.0	99.0	102.0		,171	3.8	1.0	3	dbSNP_52	102	3648,4952	520.9+/-379.8	782,2084,1434	no	intron,coding-synonymous	DPH3	NM_001047434.2,NM_206831.2	,	1056,3082,2365	GG,GC,CC		42.4186,35.0885,39.9354	,	,57/83	16305674	5194,7812	2203	4300	6503	SO:0001819	synonymous_variant	285381	exon2			ATAAATCACTTTT	BC010181	CCDS2629.1, CCDS43058.1	3p25.1	2013-06-19	2013-06-19	2006-10-25	ENSG00000154813	ENSG00000154813			27717	protein-coding gene	gene with protein product	"""DPH3A, KTI11 homolog A (S. cerevisiae)"""	608959	"""zinc finger, CSL-type containing 2"", ""DPH3 homolog (KTI11, S. cerevisiae)"", ""DPH3, KTI11 homolog (S. cerevisiae)"""	ZCSL2		14527407, 14980502, 15485916, 16648478	Standard	NM_001047434		Approved	DESR1, DELGIP1, MGC20197, KTI11, DELGIP, DPH3A	uc003cau.3	Q96FX2	OTTHUMG00000129866	ENST00000488423.1:c.171G>C	3.37:g.16305674C>G		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	117	114	0.974359	NM_206831		Silent	SNP	ENST00000488423.1	37	CCDS2629.1																																																																																			C|0.590;G|0.410	0.410	strong		0.418	DPH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252108.2	NM_206831	
KIF13A	63971	hgsc.bcm.edu	37	6	17794494	17794494	+	Silent	SNP	G	G	A	rs3734234	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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_ENST00000378843.2_Silent_p.L1070L|KIF13A_ENST00000378826.2_Silent_p.L1070L|KIF13A_ENST00000378814.5_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	96	0	0		WXS	Illumina HiSeq	Phase_I	91	90	0.989011	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		
HIST1H3C	8352	hgsc.bcm.edu	37	6	26045905	26045905	+	Silent	SNP	G	G	C	rs3752417	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:26045905G>C	ENST00000540144.1	+	1	267	c.267G>C	c.(265-267)gcG>gcC	p.A89A	HIST1H2BB_ENST00000357905.2_5'Flank	NM_003531.2	NP_003522.1	P68431	H31_HUMAN	histone cluster 1, H3c	89					blood coagulation (GO:0007596)|chromatin organization (GO:0006325)|DNA replication-dependent nucleosome assembly (GO:0006335)|regulation of gene silencing (GO:0060968)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear chromosome (GO:0000228)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|ovary(1)|skin(1)	8						AGAGCTCTGCGGTGATGGCGC	0.587													G|||	334	0.0666933	0.1203	0.0634	5008	,	,		19784	0.0149		0.0835	False		,,,				2504	0.0327				p.A89A		Atlas-SNP	.											.	HIST1H3C	34	.	0			c.G267C						PASS	.	G		487,3919	224.6+/-240.7	32,423,1748	59.0	57.0	58.0		267	-4.6	0.7	6	dbSNP_107	58	840,7760	190.8+/-237.2	39,762,3499	no	coding-synonymous	HIST1H3C	NM_003531.2		71,1185,5247	CC,CG,GG		9.7674,11.0531,10.203		89/137	26045905	1327,11679	2203	4300	6503	SO:0001819	synonymous_variant	8352	exon1			CTCTGCGGTGATG	X57128	CCDS4576.1	6p22.1	2011-01-27	2006-10-11	2003-02-14	ENSG00000196532	ENSG00000278272		"""Histones / Replication-dependent"""	4768	protein-coding gene	gene with protein product		602812	"""H3 histone family, member C"", ""histone 1, H3c"""	H3FC		8227173, 9119399, 12408966	Standard	NM_003531		Approved	H3/c, H3.1	uc003nfv.3	P68431	OTTHUMG00000014416	ENST00000540144.1:c.267G>C	6.37:g.26045905G>C		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	88	41	0.465909	NM_003531	A0PJT7|A5PLR1|P02295|P02296|P16106|Q6ISV8|Q6NWP8|Q6NWP9|Q6NXU4|Q71DJ3|Q93081	Silent	SNP	ENST00000540144.1	37	CCDS4576.1																																																																																			G|0.908;C|0.092	0.092	strong		0.587	HIST1H3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040078.1	NM_003531	
DAPK1	1612	hgsc.bcm.edu	37	9	90252966	90252966	+	Silent	SNP	C	C	T	rs55800264	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:90252966C>T	ENST00000408954.3	+	4	728	c.393C>T	c.(391-393)caC>caT	p.H131H	DAPK1_ENST00000469640.2_Silent_p.H131H|DAPK1_ENST00000358077.5_Silent_p.H131H|DAPK1_ENST00000491893.1_Silent_p.H131H|DAPK1_ENST00000472284.1_Silent_p.H131H	NM_004938.2	NP_004929.2	P53355	DAPK1_HUMAN	death-associated protein kinase 1	131	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cellular response to interferon-gamma (GO:0071346)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|intracellular signal transduction (GO:0035556)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of translation (GO:0017148)|positive regulation of apoptotic process (GO:0043065)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of apoptotic process (GO:0042981)|regulation of autophagy (GO:0010506)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)	ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|calmodulin-dependent protein kinase activity (GO:0004683)|identical protein binding (GO:0042802)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(27)|liver(2)|lung(17)|ovary(1)|prostate(2)|skin(3)|stomach(1)	72						ACTACCTGCACTCCCTTCAAA	0.408									Chronic Lymphocytic Leukemia, Familial Clustering of				C|||	19	0.00379393	0.0	0.0101	5008	,	,		20103	0.0		0.0089	False		,,,				2504	0.0031				p.H131H		Atlas-SNP	.											.	DAPK1	329	.	0			c.C393T						PASS	.	C		13,3843		0,13,1915	101.0	94.0	96.0		393	0.3	1.0	9	dbSNP_129	96	140,8146		1,138,4004	no	coding-synonymous	DAPK1	NM_004938.2		1,151,5919	TT,TC,CC		1.6896,0.3371,1.2601		131/1431	90252966	153,11989	1928	4143	6071	SO:0001819	synonymous_variant	1612	exon4	Familial Cancer Database	Familial CLL	CCTGCACTCCCTT	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.393C>T	9.37:g.90252966C>T		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	75	32	0.426667	NM_004938	B7ZLD2|B7ZLE7|Q14CQ7|Q1W5W0|Q68CP8|Q6ZRZ3|Q9BTL8	Silent	SNP	ENST00000408954.3	37	CCDS43842.1																																																																																			C|0.991;T|0.009	0.009	strong		0.408	DAPK1-010	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356843.1	NM_004938	
PMEL	6490	hgsc.bcm.edu	37	12	56351346	56351346	+	Silent	SNP	G	G	A	rs1052165	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:56351346G>A	ENST00000548747.1	-	6	1403	c.741C>T	c.(739-741)ccC>ccT	p.P247P	PMEL_ENST00000360714.4_Silent_p.P247P|PMEL_ENST00000449260.2_Silent_p.P247P|PMEL_ENST00000552882.1_Silent_p.P247P|PMEL_ENST00000550447.1_Intron|PMEL_ENST00000550464.1_Silent_p.P161P|PMEL_ENST00000539511.1_Silent_p.P161P|PMEL_ENST00000536427.1_Silent_p.P247P|PMEL_ENST00000548689.1_5'Flank|PMEL_ENST00000548493.1_Silent_p.P247P			P40967	PMEL_HUMAN	premelanosome protein	247					melanin biosynthetic process (GO:0042438)|melanosome organization (GO:0032438)	endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|melanosome (GO:0042470)|multivesicular body membrane (GO:0032585)|plasma membrane (GO:0005886)				NS(1)|breast(2)|endometrium(2)|large_intestine(4)|lung(4)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	21						GATAGCCACTGGGGTCATGGA	0.557													G|||	1067	0.213059	0.0204	0.1686	5008	,	,		21344	0.2391		0.2734	False		,,,				2504	0.4162				p.P247P		Atlas-SNP	.											.	PMEL	60	.	0			c.C741T						PASS	.	G	,,	267,4139	149.5+/-183.7	12,243,1948	113.0	117.0	116.0		483,741,741	3.8	1.0	12	dbSNP_86	116	2405,6195	397.5+/-345.8	349,1707,2244	no	coding-synonymous,coding-synonymous,coding-synonymous	PMEL	NM_001200053.1,NM_001200054.1,NM_006928.4	,,	361,1950,4192	AA,AG,GG		27.9651,6.0599,20.5444	,,	161/576,247/669,247/662	56351346	2672,10334	2203	4300	6503	SO:0001819	synonymous_variant	6490	exon6			GCCACTGGGGTCA	AK092881	CCDS8897.1, CCDS55833.1, CCDS55834.1	12q13-q14	2010-12-17	2010-12-17	2010-12-17	ENSG00000185664	ENSG00000185664			10880	protein-coding gene	gene with protein product		155550	"""silver (mouse homolog) like"", ""silver homolog (mouse)"""	SIL, SILV		8739560	Standard	NM_001200053		Approved	D12S53E, SI, Pmel17, gp100	uc001siq.3	P40967		ENST00000548747.1:c.741C>T	12.37:g.56351346G>A		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	84	47	0.559524	NM_001200054	B3KS57|B7Z6D7|Q12763|Q14448|Q14817|Q16565	Silent	SNP	ENST00000548747.1	37	CCDS8897.1	411	0.18818681318681318	18	0.036585365853658534	63	0.17403314917127072	125	0.21853146853146854	205	0.2704485488126649	G	9.900	1.206517	0.22205	0.060599	0.279651	ENSG00000185664	ENST00000549404	.	.	.	5.6	3.75	0.43078	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	.	.	.	.	.	.	.	-4.0299	12.1891	0.54257	0.1507:0.0:0.8493:0.0	rs1052165;rs3192587;rs17849477;rs58583770;rs1052165	.	.	.	X	135	.	.	Q	-	1	0	PMEL	54637613	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.096000	0.50243	1.509000	0.48786	0.655000	0.94253	CAG	G|0.799;N|0.000	.	strong		0.557	PMEL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409626.1	NM_006928	
RCAN3	11123	hgsc.bcm.edu	37	1	24859665	24859665	+	Silent	SNP	G	G	A	rs196430	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:24859665G>A	ENST00000374395.4	+	4	775	c.462G>A	c.(460-462)ccG>ccA	p.P154P	RCAN3_ENST00000538532.1_Silent_p.P96P|RCAN3_ENST00000374393.2_Intron|RCAN3_ENST00000412742.2_Intron|RCAN3_ENST00000436717.2_Silent_p.P144P	NM_001251978.1|NM_001251979.1|NM_001251984.1	NP_001238907.1|NP_001238908.1|NP_001238913.1	Q9UKA8	RCAN3_HUMAN	RCAN family member 3	154					anatomical structure morphogenesis (GO:0009653)|calcium-mediated signaling (GO:0019722)		RNA binding (GO:0003723)|troponin I binding (GO:0031013)			central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(2)	7		Colorectal(325;3.46e-05)|Renal(390;0.0007)|Lung NSC(340;0.000946)|all_lung(284;0.00125)|Ovarian(437;0.00473)|Breast(348;0.0148)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.19)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0427)|OV - Ovarian serous cystadenocarcinoma(117;1.13e-24)|Colorectal(126;6.09e-08)|COAD - Colon adenocarcinoma(152;3.33e-06)|GBM - Glioblastoma multiforme(114;0.000923)|BRCA - Breast invasive adenocarcinoma(304;0.0018)|KIRC - Kidney renal clear cell carcinoma(1967;0.00359)|STAD - Stomach adenocarcinoma(196;0.00493)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.14)		CCTCTCCCCCGGTGGGGTGGA	0.532													G|||	1921	0.383586	0.2458	0.3314	5008	,	,		14137	0.6776		0.3221	False		,,,				2504	0.3671				p.P154P		Atlas-SNP	.											.	RCAN3	22	.	0			c.G462A						PASS	.	G		1176,3230	414.4+/-336.8	146,884,1173	70.0	68.0	69.0		462	-10.9	0.0	1	dbSNP_79	69	2749,5851	437.9+/-358.8	434,1881,1985	no	coding-synonymous	RCAN3	NM_013441.2		580,2765,3158	AA,AG,GG		31.9651,26.6909,30.1784		154/242	24859665	3925,9081	2203	4300	6503	SO:0001819	synonymous_variant	11123	exon4			TCCCCCGGTGGGG		CCDS254.1, CCDS57980.1, CCDS57981.1, CCDS57982.1, CCDS72730.1	1p35.3-p33	2008-02-05	2007-06-26	2007-06-26	ENSG00000117602	ENSG00000117602			3042	protein-coding gene	gene with protein product		605860	"""Down syndrome critical region gene 1-like 2"""	DSCR1L2		10756093	Standard	NM_001251984		Approved		uc001bjj.3	Q9UKA8	OTTHUMG00000003298	ENST00000374395.4:c.462G>A	1.37:g.24859665G>A		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	67	28	0.41791	NM_001251979	A4GU14|A4LA69|E3VWE2|E5L4P0|E5L4P7|E7ENV1|E7EWD8|G1FI66|G1FLF0|Q5ECL3|Q5TGC6|Q9NUC8|Q9UKA7	Silent	SNP	ENST00000374395.4	37	CCDS254.1																																																																																			A|0.338;C|0.003	0.338	strong		0.532	RCAN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009176.2		
SUCO	51430	hgsc.bcm.edu	37	1	172547465	172547465	+	Silent	SNP	A	A	G	rs2285664	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:172547465A>G	ENST00000263688.3	+	14	1587	c.1368A>G	c.(1366-1368)gaA>gaG	p.E456E	SUCO_ENST00000610051.1_Silent_p.E419E|SUCO_ENST00000608151.1_Silent_p.E608E|SUCO_ENST00000367723.4_Silent_p.E607E	NM_014283.3	NP_055098.1	Q9UBS9	SUCO_HUMAN	SUN domain containing ossification factor	456					multicellular organismal development (GO:0007275)|ossification (GO:0001503)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of osteoblast differentiation (GO:0045669)|regulation of bone remodeling (GO:0046850)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|rough endoplasmic reticulum (GO:0005791)											TGGTGGAAGAATATGAAGAAA	0.358													A|||	1273	0.254193	0.2368	0.2089	5008	,	,		17330	0.2024		0.2296	False		,,,				2504	0.3885				p.E456E		Atlas-SNP	.											.	.	.	.	0			c.A1368G						PASS	.	A	,	1025,3381	378.3+/-322.8	111,803,1289	132.0	124.0	127.0		1368,1236	5.4	1.0	1	dbSNP_100	127	2069,6531	359.0+/-331.4	229,1611,2460	no	coding-synonymous,coding-synonymous	C1orf9	NM_014283.3,NM_016227.2	,	340,2414,3749	GG,GA,AA		24.0581,23.2637,23.789	,	456/1255,412/1211	172547465	3094,9912	2203	4300	6503	SO:0001819	synonymous_variant	51430	exon14			GGAAGAATATGAA	AF097535	CCDS1303.1, CCDS65726.1, CCDS65727.1, CCDS72984.1	1q24	2012-07-10	2012-07-10	2012-07-10	ENSG00000094975	ENSG00000094975			1240	protein-coding gene	gene with protein product	"""SUN-like protein 1"", ""osteopotentia"""		"""chromosome 1 open reading frame 9"""	C1orf9		10673381, 20440000	Standard	NM_001282750		Approved	CH1, SLP1, OPT	uc001giq.4	Q9UBS9	OTTHUMG00000034839	ENST00000263688.3:c.1368A>G	1.37:g.172547465A>G		Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	175	90	0.514286	NM_014283	B2RNU4|Q9BQB9|Q9BXQ2|Q9UL04	Silent	SNP	ENST00000263688.3	37	CCDS1303.1																																																																																			A|0.770;G|0.230	0.230	strong		0.358	SUCO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084273.1	NM_016227	
PKHD1L1	93035	hgsc.bcm.edu	37	8	110460488	110460488	+	Missense_Mutation	SNP	G	G	T	rs1673407	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:110460488G>T	ENST00000378402.5	+	39	5997	c.5893G>T	c.(5893-5895)Gtg>Ttg	p.V1965L		NM_177531.4	NP_803875.2	Q86WI1	PKHL1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1	1965	IPT/TIG 12.		V -> L (in dbSNP:rs1673407). {ECO:0000269|PubMed:12620974}.		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)			TGATAGTGTGGTGCAGTGCAT	0.433										HNSCC(38;0.096)			T|||	3077	0.614417	0.7474	0.6671	5008	,	,		13927	0.4048		0.5119	False		,,,				2504	0.7188				p.V1965L		Atlas-SNP	.											PKHD1L1,colon,carcinoma,0,1	PKHD1L1	522	1	0			c.G5893T						PASS	.	T	LEU/VAL	2958,1114		1086,786,164	95.0	97.0	96.0		5893	-3.2	0.0	8	dbSNP_89	96	4512,3902		1234,2044,929	yes	missense	PKHD1L1	NM_177531.4	32	2320,2830,1093	TT,TG,GG		46.3751,27.3576,40.173	benign	1965/4244	110460488	7470,5016	2036	4207	6243	SO:0001583	missense	93035	exon39			AGTGTGGTGCAGT	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.5893G>T	8.37:g.110460488G>T	ENSP00000367655:p.Val1965Leu	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	90	68	0.755556	NM_177531	Q567P2|Q9UF27	Missense_Mutation	SNP	ENST00000378402.5	37	CCDS47911.1	1220	0.5586080586080586	356	0.7235772357723578	235	0.649171270718232	245	0.42832167832167833	384	0.5065963060686016	T	0.432	-0.902887	0.02453	0.726424	0.536249	ENSG00000205038	ENST00000378402	D	0.81499	-1.5	5.49	-3.17	0.05202	Cell surface receptor IPT/TIG (2);Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.224078	0.28933	N	0.013661	T	0.00012	0.0000	N	0.00707	-1.245	0.80722	P	0.0	B	0.02656	0.0	B	0.11329	0.006	T	0.29458	-1.0011	9	0.07813	T	0.8	.	2.4839	0.04594	0.1127:0.3488:0.2314:0.3071	rs1673407;rs13264278;rs16879586;rs52798906;rs61398933;rs1673407	1965	Q86WI1	PKHL1_HUMAN	L	1965	ENSP00000367655:V1965L	ENSP00000367655:V1965L	V	+	1	0	PKHD1L1	110529664	0.000000	0.05858	0.001000	0.08648	0.617000	0.37484	-1.884000	0.01622	-1.308000	0.02318	-0.346000	0.07831	GTG	G|0.427;T|0.573	0.573	strong		0.433	PKHD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381017.1	NM_177531	
OR13C3	138803	hgsc.bcm.edu	37	9	107298270	107298270	+	Silent	SNP	C	C	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:107298270C>A	ENST00000374781.2	-	1	867	c.825G>T	c.(823-825)ctG>ctT	p.L275L		NM_001001961.1	NP_001001961.1	Q8NGS6	O13C3_HUMAN	olfactory receptor, family 13, subfamily C, member 3	275						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|large_intestine(7)|lung(7)|pancreas(1)|prostate(1)|skin(1)	19						TCACCACAGTCAGGTGAGCTG	0.423																																					p.L275L	GBM(86;1248 1274 14222 15028 46219)	Atlas-SNP	.											.	OR13C3	45	.	0			c.G825T						PASS	.						134.0	126.0	129.0					9																	107298270		2203	4300	6503	SO:0001819	synonymous_variant	138803	exon1			CACAGTCAGGTGA		CCDS35089.1	9q31.1	2013-09-24			ENSG00000204246	ENSG00000204246		"""GPCR / Class A : Olfactory receptors"""	14704	protein-coding gene	gene with protein product							Standard	NM_001001961		Approved		uc004bcb.1	Q8NGS6	OTTHUMG00000020406	ENST00000374781.2:c.825G>T	9.37:g.107298270C>A		Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	108	22	0.203704	NM_001001961	Q5VVG1|Q6IF52	Silent	SNP	ENST00000374781.2	37	CCDS35089.1																																																																																			.	.	none		0.423	OR13C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053477.2		
PKD1L1	168507	hgsc.bcm.edu	37	7	47840387	47840387	+	Missense_Mutation	SNP	C	C	T	rs13231277	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:47840387C>T	ENST00000289672.2	-	54	8103	c.8053G>A	c.(8053-8055)Gcc>Acc	p.A2685T	C7orf69_ENST00000258776.4_Intron|C7orf69_ENST00000418326.2_Intron	NM_138295.3	NP_612152.1	Q8TDX9	PK1L1_HUMAN	polycystic kidney disease 1 like 1	2685			A -> T (in dbSNP:rs13231277).		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						CCGGGGAAGGCGTCTGTGAAG	0.572													C|||	583	0.116414	0.2239	0.0922	5008	,	,		16675	0.0357		0.1153	False		,,,				2504	0.0726				p.A2685T		Atlas-SNP	.											.	PKD1L1	328	.	0			c.G8053A						PASS	.	C	,THR/ALA	1025,3381	379.7+/-323.4	116,793,1294	85.0	87.0	86.0		,8053	-9.6	0.0	7	dbSNP_121	86	977,7623	212.1+/-252.5	54,869,3377	yes	intron,missense	C7orf69,PKD1L1	NM_025031.2,NM_138295.3	,58	170,1662,4671	TT,TC,CC		11.3605,23.2637,15.3929	,possibly-damaging	,2685/2850	47840387	2002,11004	2203	4300	6503	SO:0001583	missense	168507	exon54			GGAAGGCGTCTGT	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.8053G>A	7.37:g.47840387C>T	ENSP00000289672:p.Ala2685Thr	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	60	42	0.7	NM_138295	Q6UWK1	Missense_Mutation	SNP	ENST00000289672.2	37	CCDS34633.1	249	0.11401098901098901	107	0.21747967479674796	39	0.10773480662983426	16	0.027972027972027972	87	0.11477572559366754	C	5.355	0.250713	0.10130	0.232637	0.113605	ENSG00000158683	ENST00000289672	T	0.19669	2.13	4.79	-9.59	0.00556	.	0.913079	0.08831	N	0.887252	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B	0.25955	0.138	B	0.14023	0.01	T	0.34104	-0.9842	9	0.27785	T	0.31	-1.5221	8.4698	0.32977	0.1741:0.6512:0.0759:0.0988	rs13231277;rs17131818;rs52838274;rs60072826;rs13231277	2685	Q8TDX9	PK1L1_HUMAN	T	2685	ENSP00000289672:A2685T	ENSP00000289672:A2685T	A	-	1	0	PKD1L1	47806912	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.536000	0.02208	-2.079000	0.00871	-0.311000	0.09066	GCC	C|0.858;T|0.142	0.142	strong		0.572	PKD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340974.1	NM_138295	
KRTAP4-6	81871	hgsc.bcm.edu	37	17	39296361	39296361	+	Missense_Mutation	SNP	A	A	G	rs146882220		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:39296361A>G	ENST00000345847.4	-	1	378	c.379T>C	c.(379-381)Tcc>Ccc	p.S127P		NM_030976.1	NP_112238.1	Q9BYQ5	KRA46_HUMAN	keratin associated protein 4-6	127	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						CAGCACTGGGACCTGCAGCAC	0.652																																					p.S127P		Atlas-SNP	.											KRTAP4-6,NS,carcinoma,0,3	KRTAP4-6	46	3	0			c.T379C						scavenged	.																																			SO:0001583	missense	81871	exon1			ACTGGGACCTGCA	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.379T>C	17.37:g.39296361A>G	ENSP00000328270:p.Ser127Pro	Somatic	72	3	0.0416667		WXS	Illumina HiSeq	Phase_I	92	26	0.282609	NM_030976	Q9BYR1	Missense_Mutation	SNP	ENST00000345847.4	37	CCDS54125.1	.	.	.	.	.	.	.	.	.	.	.	3.733	-0.055148	0.07362	.	.	ENSG00000198090	ENST00000345847	T	0.00578	6.44	3.53	1.53	0.23141	.	.	.	.	.	T	0.00241	0.0007	N	0.00750	-1.22	0.80722	P	0.0	.	.	.	.	.	.	T	0.30001	-0.9993	6	0.02654	T	1	.	6.9259	0.24414	0.3255:0.0:0.6745:0.0	.	.	.	.	P	127	ENSP00000328270:S127P	ENSP00000328270:S127P	S	-	1	0	KRTAP4-6	36549887	0.016000	0.18221	0.000000	0.03702	0.559000	0.35586	0.236000	0.17967	-0.043000	0.13513	-0.124000	0.14976	TCC	.	.	weak		0.652	KRTAP4-6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257779.1		
DOK7	285489	hgsc.bcm.edu	37	4	3494956	3494956	+	Missense_Mutation	SNP	C	C	T	rs16844464	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:3494956C>T	ENST00000340083.5	+	7	1308	c.1243C>T	c.(1243-1245)Cct>Tct	p.P415S	DOK7_ENST00000389653.2_Missense_Mutation_p.P415S|DOK7_ENST00000512714.1_3'UTR|DOK7_ENST00000507039.1_3'UTR	NM_173660.4	NP_775931.3	Q18PE1	DOK7_HUMAN	docking protein 7	415			P -> S (in dbSNP:rs16844464). {ECO:0000269|PubMed:22661499}.		neuromuscular junction development (GO:0007528)|positive regulation of protein tyrosine kinase activity (GO:0061098)|receptor clustering (GO:0043113)	cell junction (GO:0030054)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)	phosphatidylinositol binding (GO:0035091)|protein kinase binding (GO:0019901)			kidney(1)|large_intestine(1)|skin(2)|upper_aerodigestive_tract(1)	5				UCEC - Uterine corpus endometrioid carcinoma (64;0.163)		TTGCCTGGCTCCTAGAGACCA	0.706													.|||	407	0.08127	0.1566	0.0807	5008	,	,		14763	0.0397		0.0348	False		,,,				2504	0.0706				p.P415S		Atlas-SNP	.											DOK7,NS,carcinoma,0,1	DOK7	44	1	0			c.C1243T						PASS	.	C	,SER/PRO	533,3845		36,461,1692	14.0	15.0	15.0		,1243	1.0	0.0	4	dbSNP_123	15	288,8290		7,274,4008	yes	utr-3,missense	DOK7	NM_001164673.1,NM_173660.4	,74	43,735,5700	TT,TC,CC		3.3574,12.1745,6.3368	,probably-damaging	,415/505	3494956	821,12135	2189	4289	6478	SO:0001583	missense	285489	exon7			CTGGCTCCTAGAG	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.1243C>T	4.37:g.3494956C>T	ENSP00000344432:p.Pro415Ser	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	78	34	0.435897	NM_173660	A2A499|A2RRD4|E9PB56|Q6P6A6|Q86XG5|Q8N2J3|Q8NBC1	Missense_Mutation	SNP	ENST00000340083.5	37	CCDS3370.2	130	0.05952380952380952	58	0.11788617886178862	27	0.07458563535911603	21	0.03671328671328671	24	0.0316622691292876	C	4.330	0.060659	0.08339	0.121745	0.033574	ENSG00000175920	ENST00000389653;ENST00000340083	T;T	0.63580	-0.05;0.03	3.77	1.02	0.19986	.	0.483231	0.18723	N	0.132972	T	0.02571	0.0078	M	0.70595	2.14	0.09310	N	1	P;D;B	0.89917	0.454;1.0;0.007	B;D;B	0.87578	0.032;0.998;0.007	T	0.04140	-1.0974	10	0.33940	T	0.23	-7.2048	4.6184	0.12438	0.142:0.4983:0.2764:0.0833	rs16844464;rs60265678;rs16844464	415;277;415	Q18PE1-3;Q18PE1-2;Q18PE1	.;.;DOK7_HUMAN	S	415	ENSP00000374304:P415S;ENSP00000344432:P415S	ENSP00000344432:P415S	P	+	1	0	DOK7	3464754	0.065000	0.20965	0.002000	0.10522	0.046000	0.14306	0.199000	0.17237	-0.006000	0.14370	0.555000	0.69702	CCT	C|0.935;T|0.065	0.065	strong		0.706	DOK7-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000313538.1	NM_173660	
FAM218A	152756	hgsc.bcm.edu	37	4	165878335	165878335	+	Missense_Mutation	SNP	A	A	G	rs3733418	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	231	0	0		WXS	Illumina HiSeq	Phase_I	164	87	0.530488	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	
LPCAT1	79888	hgsc.bcm.edu	37	5	1466919	1466919	+	Silent	SNP	G	G	A	rs2277006	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:1466919G>A	ENST00000283415.3	-	13	1497	c.1365C>T	c.(1363-1365)acC>acT	p.T455T	LPCAT1_ENST00000503252.1_5'UTR	NM_024830.3	NP_079106.3	Q8NF37	PCAT1_HUMAN	lysophosphatidylcholine acyltransferase 1	455	EF-hand 2. {ECO:0000255|PROSITE- ProRule:PRU00448}.				cellular lipid metabolic process (GO:0044255)|glycerophospholipid biosynthetic process (GO:0046474)|negative regulation of phosphatidylcholine biosynthetic process (GO:2001246)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|phospholipid biosynthetic process (GO:0008654)|phospholipid metabolic process (GO:0006644)|positive regulation of protein catabolic process (GO:0045732)|retina development in camera-type eye (GO:0060041)|small molecule metabolic process (GO:0044281)|surfactant homeostasis (GO:0043129)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lipid particle (GO:0005811)|membrane (GO:0016020)	1-acylglycerophosphocholine O-acyltransferase activity (GO:0047184)|1-alkenylglycerophosphocholine O-acyltransferase activity (GO:0047159)|1-alkylglycerophosphocholine O-acetyltransferase activity (GO:0047192)|1-alkylglycerophosphocholine O-acyltransferase activity (GO:0047191)|calcium ion binding (GO:0005509)	p.T455T(1)		breast(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(12)|ovary(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30			OV - Ovarian serous cystadenocarcinoma(19;0.0274)|all cancers(22;0.0534)	GBM - Glioblastoma multiforme(108;0.156)		GGTCGGTCACGGTGAGCTCTG	0.632																																					p.T455T		Atlas-SNP	.											LPCAT1,NS,carcinoma,0,1	LPCAT1	70	1	1	Substitution - coding silent(1)	prostate(1)	c.C1365T						PASS	.	G		1812,2594	532.3+/-373.4	381,1050,772	127.0	109.0	115.0		1365	-8.5	0.0	5	dbSNP_100	115	1722,6878	315.1+/-312.1	173,1376,2751	no	coding-synonymous	LPCAT1	NM_024830.3		554,2426,3523	AA,AG,GG		20.0233,41.1257,27.1721		455/535	1466919	3534,9472	2203	4300	6503	SO:0001819	synonymous_variant	79888	exon13			GGTCACGGTGAGC	BC020166	CCDS3864.1	5p15.33	2013-01-10	2007-12-17	2007-12-17	ENSG00000153395	ENSG00000153395		"""EF-hand domain containing"""	25718	protein-coding gene	gene with protein product		610472	"""acyltransferase like 2"""	AYTL2		8619474, 16704971	Standard	NM_024830		Approved	FLJ12443	uc003jcm.3	Q8NF37	OTTHUMG00000131017	ENST00000283415.3:c.1365C>T	5.37:g.1466919G>A		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	111	66	0.594595	NM_024830	Q1HAQ1|Q7Z4G6|Q8N3U7|Q8WUL8|Q9GZW6	Silent	SNP	ENST00000283415.3	37	CCDS3864.1																																																																																			G|0.696;A|0.304	0.304	strong		0.632	LPCAT1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304032.1	NM_024830	
C9orf43	257169	hgsc.bcm.edu	37	9	116187302	116187302	+	Missense_Mutation	SNP	C	C	G	rs111748634	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:116187302C>G	ENST00000288462.4	+	9	1257	c.811C>G	c.(811-813)Cca>Gca	p.P271A	C9orf43_ENST00000374165.1_Missense_Mutation_p.P271A	NM_152786.1	NP_689999.1	Q8TAL5	CI043_HUMAN	chromosome 9 open reading frame 43	271										breast(2)|large_intestine(6)|lung(2)|ovary(1)|pancreas(1)|prostate(3)	15						TCTCCAGAGACCAGCACTGCG	0.408													C|||	201	0.0401358	0.0098	0.0231	5008	,	,		20238	0.0139		0.0517	False		,,,				2504	0.1084				p.P271A		Atlas-SNP	.											.	C9orf43	49	.	0			c.C811G						PASS	.	C	ALA/PRO	60,4346	57.4+/-93.9	0,60,2143	99.0	91.0	94.0		811	4.1	0.6	9	dbSNP_132	94	488,8112	140.6+/-197.1	10,468,3822	yes	missense	C9orf43	NM_152786.1	27	10,528,5965	GG,GC,CC		5.6744,1.3618,4.2134	probably-damaging	271/462	116187302	548,12458	2203	4300	6503	SO:0001583	missense	257169	exon9			CAGAGACCAGCAC	BC026884	CCDS6796.1	9q33.1	2012-03-15			ENSG00000157653	ENSG00000157653			23570	protein-coding gene	gene with protein product						12477932	Standard	NM_152786		Approved	MGC17358	uc004bhp.3	Q8TAL5	OTTHUMG00000020526	ENST00000288462.4:c.811C>G	9.37:g.116187302C>G	ENSP00000288462:p.Pro271Ala	Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	31	17	0.548387	NM_152786		Missense_Mutation	SNP	ENST00000288462.4	37	CCDS6796.1	59	0.027014652014652016	3	0.006097560975609756	9	0.024861878453038673	6	0.01048951048951049	41	0.05408970976253298	C	17.18	3.324360	0.60634	0.013618	0.056744	ENSG00000157653	ENST00000374165;ENST00000288462	T;T	0.70516	-0.49;-0.49	4.11	4.11	0.48088	.	0.000000	0.42053	D	0.000763	T	0.28400	0.0702	L	0.34521	1.04	0.25982	N	0.982359	D	0.89917	1.0	D	0.72338	0.977	T	0.47471	-0.9115	10	0.54805	T	0.06	-6.7323	12.1743	0.54176	0.0:1.0:0.0:0.0	.	271	Q8TAL5	CI043_HUMAN	A	271	ENSP00000363280:P271A;ENSP00000288462:P271A	ENSP00000288462:P271A	P	+	1	0	C9orf43	115227123	0.956000	0.32656	0.562000	0.28370	0.306000	0.27790	3.121000	0.50438	2.579000	0.87056	0.557000	0.71058	CCA	C|0.957;G|0.043	0.043	strong		0.408	C9orf43-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053739.1	NM_152786	
ANO2	57101	hgsc.bcm.edu	37	12	6030437	6030437	+	Silent	SNP	A	A	G	rs3741904	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:6030437A>G	ENST00000356134.5	-	3	362	c.291T>C	c.(289-291)taT>taC	p.Y97Y	ANO2_ENST00000546188.1_Silent_p.Y97Y|ANO2_ENST00000327087.8_Silent_p.Y97Y	NM_001278596.1	NP_001265525.1	Q9NQ90	ANO2_HUMAN	anoctamin 2, calcium activated chloride channel	101					chloride transmembrane transport (GO:1902476)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	chloride channel complex (GO:0034707)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	intracellular calcium activated chloride channel activity (GO:0005229)			central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(11)|lung(23)|ovary(4)|pancreas(1)|prostate(1)|skin(5)|stomach(3)|upper_aerodigestive_tract(1)	58						AGGCAAGTACATAGTCGACCT	0.582													A|||	474	0.0946486	0.0129	0.0648	5008	,	,		19939	0.1855		0.0616	False		,,,				2504	0.1667				p.Y97Y		Atlas-SNP	.											.	ANO2	309	.	0			c.T291C						PASS	.	A		87,4075		1,85,1995	73.0	73.0	73.0		291	-7.5	0.8	12	dbSNP_107	73	515,7899		18,479,3710	no	coding-synonymous	ANO2	NM_020373.2		19,564,5705	GG,GA,AA		6.1208,2.0903,4.7869		97/999	6030437	602,11974	2081	4207	6288	SO:0001819	synonymous_variant	57101	exon3			AAGTACATAGTCG	AJ272204	CCDS44807.1, CCDS44807.2	12p13.3	2014-04-09	2014-04-09	2008-08-28		ENSG00000047617		"""Ion channels / Chloride channels : Calcium activated : Anoctamins"""	1183	protein-coding gene	gene with protein product	"""transmembrane protein 16B (eight membrane-spanning domains)"""	610109	"""chromosome 12 open reading frame 3"", ""transmembrane protein 16B"", ""anoctamin 2"""	C12orf3, TMEM16B		12739008, 15067359, 24692353	Standard	NM_001278596		Approved		uc001qnm.2	Q9NQ90		ENST00000356134.5:c.291T>C	12.37:g.6030437A>G		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	95	44	0.463158	NM_020373	C4N787|Q9H847	Silent	SNP	ENST00000356134.5	37																																																																																				A|0.917;G|0.083	0.083	strong		0.582	ANO2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000399019.4	NM_020373	
UTS2	10911	hgsc.bcm.edu	37	1	7909737	7909737	+	Missense_Mutation	SNP	C	C	T	rs2890565	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:7909737C>T	ENST00000361696.5	-	3	252	c.221G>A	c.(220-222)aGt>aAt	p.S74N	UTS2_ENST00000054668.5_Missense_Mutation_p.S89N|UTS2_ENST00000377516.2_Missense_Mutation_p.S74N	NM_006786.3	NP_006777.1	O95399	UTS2_HUMAN	urotensin 2	74			S -> N (in dbSNP:rs2890565).		muscle contraction (GO:0006936)|negative regulation of blood pressure (GO:0045776)|negative regulation of glomerular filtration (GO:0003105)|negative regulation of heart rate (GO:0010459)|negative regulation of insulin secretion (GO:0046676)|negative regulation of renal sodium excretion (GO:0035814)|negative regulation of urine volume (GO:0035811)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood pressure (GO:0045777)|positive regulation of cell differentiation (GO:0045597)|positive regulation of circadian sleep/wake cycle, REM sleep (GO:0046005)|positive regulation of circadian sleep/wake cycle, wakefulness (GO:0010841)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of heart rate (GO:0010460)|positive regulation of synaptic transmission, cholinergic (GO:0032224)|positive regulation of vasodilation (GO:0045909)|regulation of blood pressure (GO:0008217)|response to drug (GO:0042493)|response to hypoxia (GO:0001666)|response to testosterone (GO:0033574)|synaptic transmission (GO:0007268)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	hormone activity (GO:0005179)|receptor binding (GO:0005102)			kidney(1)|lung(4)|urinary_tract(1)	6	Ovarian(185;0.0634)|all_lung(157;0.178)	all_epithelial(116;1.38e-20)|all_lung(118;1.29e-06)|Lung NSC(185;7.5e-06)|Renal(390;0.000147)|Breast(348;0.00086)|Colorectal(325;0.000959)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|all cancers(8;9.26e-71)|GBM - Glioblastoma multiforme(8;5.15e-36)|Colorectal(212;1.27e-07)|COAD - Colon adenocarcinoma(227;1.33e-05)|Kidney(185;4.89e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000386)|KIRC - Kidney renal clear cell carcinoma(229;0.000894)|STAD - Stomach adenocarcinoma(132;0.000951)|READ - Rectum adenocarcinoma(331;0.0642)		AATGTTGGTACTTGAGTCTGA	0.303													C|||	565	0.112819	0.0552	0.2075	5008	,	,		17873	0.2808		0.0179	False		,,,				2504	0.0481				p.S89N		Atlas-SNP	.											.	UTS2	18	.	0			c.G266A	GRCh37	CM032391	UTS2	M	rs2890565	PASS	.	C	ASN/SER,ASN/SER	226,4178	132.9+/-169.3	4,218,1980	72.0	74.0	73.0		221,266	-0.9	0.0	1	dbSNP_101	73	252,8346	99.5+/-161.0	3,246,4050	yes	missense,missense	UTS2	NM_006786.3,NM_021995.2	46,46	7,464,6030	TT,TC,CC		2.9309,5.1317,3.6764	benign,benign	74/125,89/140	7909737	478,12524	2202	4299	6501	SO:0001583	missense	10911	exon4			TTGGTACTTGAGT	AF104118	CCDS90.1, CCDS91.1	1p36	2013-02-28			ENSG00000049247	ENSG00000049247		"""Endogenous ligands"""	12636	protein-coding gene	gene with protein product	"""prepro U-II"""	604097				9861051, 10499587	Standard	NM_021995		Approved	UII, U-II, UCN2, PRO1068	uc001aos.3	O95399	OTTHUMG00000001218	ENST00000361696.5:c.221G>A	1.37:g.7909737C>T	ENSP00000355163:p.Ser74Asn	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	98	49	0.5	NM_021995	Q5H8X7|Q6UXF6|Q9UKP7	Missense_Mutation	SNP	ENST00000361696.5	37	CCDS91.1	260	0.11904761904761904	27	0.054878048780487805	62	0.1712707182320442	155	0.270979020979021	16	0.021108179419525065	C	9.865	1.197327	0.22037	0.051317	0.029309	ENSG00000049247	ENST00000377516;ENST00000400910;ENST00000361696;ENST00000054668	T;T;T	0.38560	1.13;1.23;1.17	4.9	-0.916	0.10489	.	0.598725	0.18186	N	0.148988	T	0.00012	0.0000	L	0.34521	1.04	0.80722	P	0.0	B;B;P	0.36535	0.403;0.18;0.557	B;B;B	0.35971	0.157;0.056;0.215	T	0.29058	-1.0024	9	0.30854	T	0.27	-0.7879	3.8096	0.08791	0.1083:0.4016:0.3378:0.1523	rs2890565;rs2890565	89;74;74	O95399-2;O95399;Q5H8X8	.;UTS2_HUMAN;.	N	74;74;74;89	ENSP00000366738:S74N;ENSP00000355163:S74N;ENSP00000054668:S89N	ENSP00000054668:S89N	S	-	2	0	UTS2	7832324	0.000000	0.05858	0.000000	0.03702	0.016000	0.09150	-0.501000	0.06398	-0.348000	0.08286	0.650000	0.86243	AGT	C|0.928;T|0.072	0.072	strong		0.303	UTS2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000003612.1	NM_006786	
MIS12	79003	hgsc.bcm.edu	37	17	5392791	5392791	+	Silent	SNP	A	A	G	rs74577983	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:5392791A>G	ENST00000381165.3	+	3	1162	c.609A>G	c.(607-609)aaA>aaG	p.K203K	DERL2_ENST00000571968.1_5'Flank|MIS12_ENST00000573759.1_Silent_p.K203K	NM_001258217.1|NM_001258219.1|NM_001258220.1|NM_024039.2	NP_001245146.1|NP_001245148.1|NP_001245149.1|NP_076944.1			MIS12 kinetochore complex component											central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|prostate(1)|skin(2)	12						AACGACTGAAAATATCTTAAT	0.383													A|||	189	0.0377396	0.0023	0.0245	5008	,	,		20132	0.0982		0.0189	False		,,,				2504	0.0521				p.K203K		Atlas-SNP	.											.	MIS12	19	.	0			c.A609G						PASS	.	A		22,4380		0,22,2179	53.0	54.0	54.0		609	2.6	0.3	17	dbSNP_132	54	227,8369		1,225,4072	no	coding-synonymous	MIS12	NM_024039.1		1,247,6251	GG,GA,AA		2.6408,0.4998,1.9157		203/206	5392791	249,12749	2201	4298	6499	SO:0001819	synonymous_variant	79003	exon2			ACTGAAAATATCT	AL136906	CCDS11074.1	17p13.3	2013-07-03	2013-07-03		ENSG00000167842	ENSG00000167842			24967	protein-coding gene	gene with protein product		609178	"""MIS12, MIND kinetochore complex component, homolog (yeast)"", ""MIS12, MIND kinetochore complex component, homolog (S. pombe)"""			11230166, 12515822	Standard	NM_001258217		Approved	MGC2488, hMIS12, KNTC2AP, MTW1	uc031qyj.1	Q9H081	OTTHUMG00000102042	ENST00000381165.3:c.609A>G	17.37:g.5392791A>G		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	71	23	0.323944	NM_001258220		Silent	SNP	ENST00000381165.3	37	CCDS11074.1																																																																																			A|0.972;G|0.028	0.028	strong		0.383	MIS12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219827.1	NM_024039	
SP140L	93349	hgsc.bcm.edu	37	2	231256812	231256812	+	Silent	SNP	A	A	G	rs7559665|rs386656123	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:231256812A>G	ENST00000415673.2	+	12	1061	c.975A>G	c.(973-975)gcA>gcG	p.A325A	SP140L_ENST00000243810.6_Silent_p.A325A|SP140L_ENST00000444636.1_Silent_p.A325A|SP140L_ENST00000396563.4_Silent_p.A290A	NM_138402.4	NP_612411.4	Q9H930	SP14L_HUMAN	SP140 nuclear body protein-like	325	SAND. {ECO:0000255|PROSITE- ProRule:PRU00185}.					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						GAACCTTGGCAAAGTGTATAC	0.502													G|||	1026	0.204872	0.1997	0.2248	5008	,	,		19277	0.0685		0.3221	False		,,,				2504	0.2178				p.A325A		Atlas-SNP	.											.	SP140L	68	.	0			c.A975G						PASS	.	G		848,3146		90,668,1239	105.0	111.0	109.0		975	1.6	0.0	2	dbSNP_116	109	2560,5820		384,1792,2014	no	coding-synonymous	SP140L	NM_138402.4		474,2460,3253	GG,GA,AA		30.5489,21.2318,27.5416		325/581	231256812	3408,8966	1997	4190	6187	SO:0001819	synonymous_variant	93349	exon12			CTTGGCAAAGTGT	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.975A>G	2.37:g.231256812A>G		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	113	113	1	NM_138402	Q2M375|Q4ZG65|Q9BSP3	Silent	SNP	ENST00000415673.2	37	CCDS46538.1																																																																																			A|0.801;G|0.199	0.199	strong		0.502	SP140L-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374538.1	NM_138402	
PKHD1L1	93035	hgsc.bcm.edu	37	8	110465060	110465060	+	Silent	SNP	G	G	C	rs1673404	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:110465060G>C	ENST00000378402.5	+	43	6725	c.6621G>C	c.(6619-6621)ctG>ctC	p.L2207L		NM_177531.4	NP_803875.2	Q86WI1	PKHL1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1	2207	G8 1. {ECO:0000255|PROSITE- ProRule:PRU00817}.				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)			AGACCATTCTGCTGGATCAAA	0.393										HNSCC(38;0.096)			G|||	2507	0.500599	0.3858	0.6196	5008	,	,		11314	0.4028		0.503	False		,,,				2504	0.6697				p.L2207L		Atlas-SNP	.											PKHD1L1,NS,carcinoma,+2,1	PKHD1L1	522	1	0			c.G6621C						PASS	.	G		1554,2088		330,894,597	60.0	56.0	57.0		6621	0.6	0.9	8	dbSNP_89	57	4233,3913		1125,1983,965	no	coding-synonymous	PKHD1L1	NM_177531.4		1455,2877,1562	CC,CG,GG		48.0358,42.6689,49.0923		2207/4244	110465060	5787,6001	1821	4073	5894	SO:0001819	synonymous_variant	93035	exon43			CATTCTGCTGGAT	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.6621G>C	8.37:g.110465060G>C		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	53	38	0.716981	NM_177531	Q567P2|Q9UF27	Silent	SNP	ENST00000378402.5	37	CCDS47911.1																																																																																			G|0.517;C|0.483	0.483	strong		0.393	PKHD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381017.1	NM_177531	
CCDC110	256309	hgsc.bcm.edu	37	4	186380243	186380243	+	Missense_Mutation	SNP	A	A	C	rs59319722	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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_ENST00000393540.3_Missense_Mutation_p.Y463D|CCDC110_ENST00000507501.1_5'Flank	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	85	0	0		WXS	Illumina HiSeq	Phase_I	43	22	0.511628	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	
CCDC168	643677	hgsc.bcm.edu	37	13	103392127	103392127	+	5'Flank	SNP	T	T	A	rs74435572	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:103392127T>A	ENST00000322527.2	-	0	0					NM_001146197.1	NP_001139669.1	Q8NDH2	CC168_HUMAN	coiled-coil domain containing 168																		CAATTGTTTCTTTATTCAATT	0.308													T|||	338	0.067492	0.0166	0.0648	5008	,	,		21643	0.0129		0.1252	False		,,,				2504	0.135				p.K3640N		Atlas-SNP	.											.	.	.	.	0			c.A10920T						PASS	.	T	ASN/LYS	27,1357		1,25,666	221.0	169.0	185.0		10920	0.7	0.0	13	dbSNP_132	185	376,2806		22,332,1237	yes	missense	CCDC168	NM_001146197.1	94	23,357,1903	AA,AT,TT		11.8165,1.9509,8.8261		3640/7082	103392127	403,4163	692	1591	2283	SO:0001631	upstream_gene_variant	643677	exon4			TGTTTCTTTATTC		CCDS73596.1	13q33.1	2014-06-17	2011-08-09	2011-08-09	ENSG00000175820	ENSG00000175820			26851	protein-coding gene	gene with protein product			"""chromosome 13 open reading frame 40"""	C13orf40			Standard	NM_001146197		Approved	FLJ40176	uc001vpm.3	Q8NDH2	OTTHUMG00000187287		13.37:g.103392127T>A	Exception_encountered	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	78	33	0.423077	NM_001146197	Q8N800	Missense_Mutation	SNP	ENST00000322527.2	37																																																																																				T|0.933;A|0.067	0.067	strong		0.308	CCDC168-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001146197	
ADRA2B	151	hgsc.bcm.edu	37	2	96780716	96780716	+	Silent	SNP	T	T	G	rs2229169	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:96780716T>G	ENST00000409345.3	-	1	1268	c.1173A>C	c.(1171-1173)ggA>ggC	p.G391G		NM_000682.5	NP_000673	P18089	ADA2B_HUMAN	adrenoceptor alpha 2B	391					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)	GGCAGATGGCTCCCAGGCTGT	0.567													G|||	3532	0.705272	0.7685	0.6571	5008	,	,		17100	0.5962		0.6819	False		,,,				2504	0.7904				p.G391G		Atlas-SNP	.											.	ADRA2B	115	.	0			c.A1173C						PASS	.	G		3265,1099		1211,843,128	50.0	56.0	54.0		1173	-4.9	1.0	2	dbSNP_98	54	5858,2724		1987,1884,420	no	coding-synonymous	ADRA2B	NM_000682.5		3198,2727,548	GG,GT,TT		31.7409,25.1833,29.5304		391/448	96780716	9123,3823	2182	4291	6473	SO:0001819	synonymous_variant	151	exon1			GATGGCTCCCAGG	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.1173A>C	2.37:g.96780716T>G		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	89	89	1	NM_000682	Q4TUH9|Q53RF2|Q9BZK0	Silent	SNP	ENST00000409345.3	37	CCDS56129.1																																																																																			T|0.317;G|0.683	0.683	strong		0.567	ADRA2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334990.1		
RFX6	222546	hgsc.bcm.edu	37	6	117243260	117243260	+	Silent	SNP	T	T	C	rs7764347	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:117243260T>C	ENST00000332958.2	+	13	1399	c.1383T>C	c.(1381-1383)acT>acC	p.T461T		NM_173560.3	NP_775831.2	Q8HWS3	RFX6_HUMAN	regulatory factor X, 6	461					endocrine pancreas development (GO:0031018)|glucose homeostasis (GO:0042593)|pancreatic A cell differentiation (GO:0003310)|pancreatic D cell differentiation (GO:0003311)|pancreatic epsilon cell differentiation (GO:0090104)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of insulin secretion (GO:0050796)|transcription, DNA-templated (GO:0006351)|type B pancreatic cell differentiation (GO:0003309)	nucleus (GO:0005634)	transcription regulatory region DNA binding (GO:0044212)			cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(29)|ovary(1)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	59						AGAATGCCACTGTGGAGGCTT	0.338													C|||	1699	0.339257	0.2935	0.2939	5008	,	,		16993	0.4226		0.2217	False		,,,				2504	0.4683				p.T461T		Atlas-SNP	.											.	RFX6	141	.	0			c.T1383C						PASS	.	C		1237,3169	705.8+/-407.3	187,863,1153	102.0	106.0	105.0		1383	-6.9	0.9	6	dbSNP_116	105	1530,7070	746.7+/-407.3	144,1242,2914	no	coding-synonymous	RFX6	NM_173560.3		331,2105,4067	CC,CT,TT		17.7907,28.0754,21.2748		461/929	117243260	2767,10239	2203	4300	6503	SO:0001819	synonymous_variant	222546	exon13			TGCCACTGTGGAG	BC039248	CCDS5113.1	6q22.31	2008-08-04	2008-08-04	2008-08-04	ENSG00000185002	ENSG00000185002			21478	protein-coding gene	gene with protein product		612659	"""regulatory factor X domain containing 1"""	RFXDC1			Standard	NM_173560		Approved	MGC33442, dJ955L16.1	uc003pxm.3	Q8HWS3	OTTHUMG00000015449	ENST00000332958.2:c.1383T>C	6.37:g.117243260T>C		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	45	22	0.488889	NM_173560	Q5T6B3	Silent	SNP	ENST00000332958.2	37	CCDS5113.1																																																																																			T|0.750;C|0.250	0.250	strong		0.338	RFX6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041970.2	NM_173560	
CFH	3075	hgsc.bcm.edu	37	1	196695742	196695742	+	Silent	SNP	A	A	G	rs3753396	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:196695742A>G	ENST00000367429.4	+	13	2256	c.2016A>G	c.(2014-2016)caA>caG	p.Q672Q		NM_000186.3	NP_000177.2	P08603	CFAH_HUMAN	complement factor H	672	Sushi 11. {ECO:0000255|PROSITE- ProRule:PRU00302}.				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)	heparan sulfate proteoglycan binding (GO:0043395)|heparin binding (GO:0008201)			NS(3)|breast(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(24)|lung(33)|ovary(1)|prostate(5)|skin(9)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	101						ATAAAATTCAATGTGTTGATG	0.299													A|||	1016	0.202875	0.0378	0.1916	5008	,	,		15851	0.5099		0.1759	False		,,,				2504	0.1452				p.Q672Q		Atlas-SNP	.											CFH,NS,carcinoma,+2,3	CFH	251	3	0			c.A2016G	GRCh37	CM033783	CFH	M	rs3753396	PASS	.	A		293,4113	159.2+/-191.8	10,273,1920	95.0	98.0	97.0		2016	-2.2	0.9	1	dbSNP_107	97	1488,7112	281.7+/-295.2	140,1208,2952	no	coding-synonymous	CFH	NM_000186.3		150,1481,4872	GG,GA,AA		17.3023,6.65,13.6937		672/1232	196695742	1781,11225	2203	4300	6503	SO:0001819	synonymous_variant	3075	exon13			AATTCAATGTGTT	Y00716	CCDS1385.1	1q32	2014-09-17	2004-08-09	2004-08-12	ENSG00000000971	ENSG00000000971		"""Complement system"""	4883	protein-coding gene	gene with protein product	"""beta-1H"", ""H factor 2 (complement)"", ""age-related maculopathy susceptibility 1"""	134370	"""H factor 1 (complement)"""	HF, HF1, HF2		2889480, 2963625	Standard	NM_000186		Approved	HUS, FHL1, ARMS1, ARMD4	uc001gtj.4	P08603	OTTHUMG00000035607	ENST00000367429.4:c.2016A>G	1.37:g.196695742A>G		Somatic	215	1	0.00465116		WXS	Illumina HiSeq	Phase_I	148	70	0.472973	NM_000186	A5PL14|P78435|Q14570|Q2TAZ5|Q38G77|Q5TFM3|Q8N708|Q9NU86	Silent	SNP	ENST00000367429.4	37	CCDS1385.1																																																																																			A|0.777;G|0.223	0.223	strong		0.299	CFH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086412.2	NM_000186	
PTPRA	5786	hgsc.bcm.edu	37	20	2996497	2996497	+	Silent	SNP	C	C	T	rs1178016	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:2996497C>T	ENST00000216877.6	+	11	1282	c.882C>T	c.(880-882)ggC>ggT	p.G294G	PTPRA_ENST00000358719.4_Silent_p.G159G|PTPRA_ENST00000356147.3_Silent_p.G294G|PTPRA_ENST00000380393.3_Silent_p.G303G|PTPRA_ENST00000425918.2_Silent_p.G314G|PTPRA_ENST00000399903.2_Silent_p.G303G|PTPRA_ENST00000318266.5_Silent_p.G294G	NM_080840.2	NP_543030.1	P18433	PTPRA_HUMAN	protein tyrosine phosphatase, receptor type, A	303	Tyrosine-protein phosphatase 1. {ECO:0000255|PROSITE-ProRule:PRU00160}.				axon guidance (GO:0007411)|insulin receptor signaling pathway (GO:0008286)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein phosphorylation (GO:0006468)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(1)|endometrium(3)|large_intestine(3)|lung(5)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17						CACCCCAGGGCTACCAAGAAA	0.353													C|||	3072	0.613419	0.5575	0.5288	5008	,	,		17432	0.8234		0.498	False		,,,				2504	0.6513				p.G303G		Atlas-SNP	.											.	PTPRA	75	.	0			c.C909T						PASS	.	C	,,	2359,2047	609.0+/-391.3	640,1079,484	97.0	99.0	98.0		909,882,882	3.1	1.0	20	dbSNP_87	98	4166,4434	566.7+/-388.7	1013,2140,1147	no	coding-synonymous,coding-synonymous,coding-synonymous	PTPRA	NM_002836.3,NM_080840.2,NM_080841.2	,,	1653,3219,1631	TT,TC,CC		48.4419,46.4594,49.8308	,,	303/803,294/794,294/794	2996497	6525,6481	2203	4300	6503	SO:0001819	synonymous_variant	5786	exon16			CCAGGGCTACCAA		CCDS13038.1, CCDS13039.1	20p13	2011-06-09			ENSG00000132670	ENSG00000132670		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"""	9664	protein-coding gene	gene with protein product		176884		PTPRL2, PTPA		2172030, 2169617	Standard	NM_080840		Approved	LRP, HLPR, HPTPA, RPTPA	uc002whn.3	P18433	OTTHUMG00000031718	ENST00000216877.6:c.882C>T	20.37:g.2996497C>T		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	56	27	0.482143	NM_002836	A8K2G8|D3DVX5|Q14513|Q7Z2I2|Q96TD9	Silent	SNP	ENST00000216877.6	37	CCDS13039.1																																																																																			C|0.453;T|0.547	0.547	strong		0.353	PTPRA-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077682.3		
PTHLH	5744	hgsc.bcm.edu	37	12	28116465	28116465	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:28116465A>G	ENST00000545234.1	-	5	880	c.340T>C	c.(340-342)Tac>Cac	p.Y114H	PTHLH_ENST00000395868.3_Missense_Mutation_p.Y114H|PTHLH_ENST00000538310.1_Missense_Mutation_p.Y114H|PTHLH_ENST00000535992.1_Missense_Mutation_p.Y114H|RP11-993B23.3_ENST00000538113.1_RNA|PTHLH_ENST00000395872.1_Missense_Mutation_p.Y114H|PTHLH_ENST00000354417.3_Missense_Mutation_p.Y114H|PTHLH_ENST00000201015.4_Missense_Mutation_p.Y114H|PTHLH_ENST00000539239.1_Missense_Mutation_p.Y114H			P12272	PTHR_HUMAN	parathyroid hormone-like hormone	114					adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|cAMP metabolic process (GO:0046058)|cell-cell signaling (GO:0007267)|endochondral ossification (GO:0001958)|endoderm development (GO:0007492)|epidermis development (GO:0008544)|epithelial cell differentiation (GO:0030855)|female pregnancy (GO:0007565)|lung alveolus development (GO:0048286)|mammary gland bud elongation (GO:0060649)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|nipple sheath formation (GO:0060659)|osteoblast development (GO:0002076)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cell proliferation (GO:0008284)|protein processing (GO:0016485)|regulation of gene expression (GO:0010468)|skeletal system development (GO:0001501)|surfactant homeostasis (GO:0043129)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	hormone activity (GO:0005179)|peptide hormone receptor binding (GO:0051428)			breast(1)|endometrium(1)|large_intestine(2)|lung(4)|skin(1)|stomach(1)	10	Lung SC(9;0.184)					TGCTCTTTGTACGTCTCCACC	0.517																																					p.Y114H		Atlas-SNP	.											.	PTHLH	36	.	0			c.T340C						PASS	.						160.0	151.0	154.0					12																	28116465		2203	4300	6503	SO:0001583	missense	5744	exon3			CTTTGTACGTCTC		CCDS8715.1, CCDS44853.1	12p12.1-p11.2	2014-01-07			ENSG00000087494	ENSG00000087494		"""Endogenous ligands"""	9607	protein-coding gene	gene with protein product	"""osteostatin"", ""parathyroid hormone-like hormone preproprotein"", ""parathyroid hormone-related protein preproprotein"""	168470				2708388	Standard	NM_002820		Approved	PTHRP, HHM, PLP, PTHR	uc001ril.3	P12272	OTTHUMG00000169221	ENST00000545234.1:c.340T>C	12.37:g.28116465A>G	ENSP00000441765:p.Tyr114His	Somatic	214	0	0		WXS	Illumina HiSeq	Phase_I	169	38	0.224852	NM_198964	Q15251|Q6FH74	Missense_Mutation	SNP	ENST00000545234.1	37	CCDS44853.1	.	.	.	.	.	.	.	.	.	.	A	22.1	4.241957	0.79912	.	.	ENSG00000087494	ENST00000395872;ENST00000539239;ENST00000545234;ENST00000538310;ENST00000354417;ENST00000201015;ENST00000535992;ENST00000395868;ENST00000542963	D;D;D;D;D;D;D;D;D	0.84730	-1.89;-1.89;-1.89;-1.89;-1.89;-1.89;-1.89;-1.89;-1.89	5.56	5.56	0.83823	.	0.054525	0.85682	D	0.000000	D	0.88808	0.6537	L	0.39245	1.2	0.58432	D	0.999998	D	0.89917	1.0	D	0.91635	0.999	D	0.88398	0.3013	10	0.41790	T	0.15	-16.5447	14.8854	0.70564	1.0:0.0:0.0:0.0	.	114	P12272	PTHR_HUMAN	H	114	ENSP00000379213:Y114H;ENSP00000441571:Y114H;ENSP00000441765:Y114H;ENSP00000441890:Y114H;ENSP00000346398:Y114H;ENSP00000201015:Y114H;ENSP00000440613:Y114H;ENSP00000379209:Y114H;ENSP00000444519:Y114H	ENSP00000201015:Y114H	Y	-	1	0	PTHLH	28007732	1.000000	0.71417	0.891000	0.34965	0.917000	0.54804	7.859000	0.86982	2.111000	0.64477	0.477000	0.44152	TAC	.	.	none		0.517	PTHLH-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000402913.1	NM_198965	
CPED1	79974	hgsc.bcm.edu	37	7	120906785	120906785	+	Silent	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:120906785C>T	ENST00000310396.5	+	20	3023	c.2556C>T	c.(2554-2556)ggC>ggT	p.G852G		NM_024913.4	NP_079189.4	A4D0V7	CPED1_HUMAN	cadherin-like and PC-esterase domain containing 1	852						endoplasmic reticulum (GO:0005783)											AGAATACTGGCCAGACTGTAT	0.388																																					p.G852G		Atlas-SNP	.											C7orf58,NS,carcinoma,+2,1	.	.	1	0			c.C2556T						scavenged	.						166.0	144.0	151.0					7																	120906785		2203	4300	6503	SO:0001819	synonymous_variant	79974	exon20			TACTGGCCAGACT		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.2556C>T	7.37:g.120906785C>T		Somatic	392	0	0		WXS	Illumina HiSeq	Phase_I	354	5	0.0141243	NM_024913	A8K1R3|Q6UXT1|Q86T76|Q86T84|Q8N2T5|Q96NC9	Silent	SNP	ENST00000310396.5	37	CCDS34739.1																																																																																			.	.	none		0.388	CPED1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346959.1	NM_024913	
UBN1	29855	hgsc.bcm.edu	37	16	4925291	4925291	+	Silent	SNP	T	T	G	rs17137364	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:4925291T>G	ENST00000396658.4	+	14	3583	c.2880T>G	c.(2878-2880)gtT>gtG	p.V960V	UBN1_ENST00000590769.1_Silent_p.V960V|UBN1_ENST00000545171.1_Silent_p.V960V|UBN1_ENST00000262376.6_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	73	0	0		WXS	Illumina HiSeq	Phase_I	60	48	0.8	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	
PSD3	23362	hgsc.bcm.edu	37	8	18729459	18729459	+	Silent	SNP	T	T	C	rs13273954	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:18729459T>C	ENST00000327040.8	-	3	1017	c.915A>G	c.(913-915)gaA>gaG	p.E305E	PSD3_ENST00000523619.1_Silent_p.E240E|PSD3_ENST00000440756.2_Silent_p.E305E	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	238	0	0		WXS	Illumina HiSeq	Phase_I	250	175	0.7	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	
SPATA31E1	286234	hgsc.bcm.edu	37	9	90502458	90502458	+	Missense_Mutation	SNP	T	T	A	rs10868670	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:90502458T>A	ENST00000325643.5	+	4	3122	c.3056T>A	c.(3055-3057)gTg>gAg	p.V1019E		NM_178828.4	NP_849150.3	Q6ZUB1	S31E1_HUMAN	SPATA31 subfamily E, member 1	1019			V -> E (in dbSNP:rs10868670). {ECO:0000269|PubMed:14702039}.		cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											GCCCTGCAAGTGCTCAGCATA	0.587													.|||	3815	0.761781	0.9501	0.7205	5008	,	,		18207	0.88		0.5666	False		,,,				2504	0.6155				p.V1019E		Atlas-SNP	.											.	.	.	.	0			c.T3056A						PASS	.	A	GLU/VAL	3882,524		1717,448,38	38.0	42.0	41.0		3056	2.2	0.0	9	dbSNP_120	41	4640,3960		1278,2084,938	yes	missense	C9orf79	NM_178828.4	121	2995,2532,976	AA,AT,TT		46.0465,11.8929,34.4764	benign	1019/1446	90502458	8522,4484	2203	4300	6503	SO:0001583	missense	286234	exon4			TGCAAGTGCTCAG	AK093185	CCDS6676.1	9q22.1-q22.2	2012-10-12	2012-10-12	2012-10-12	ENSG00000177992	ENSG00000177992			26672	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 79"", ""family with sequence similarity 75, member E1"""	C9orf79, FAM75E1			Standard	NM_178828		Approved	FLJ35866	uc004app.4	Q6ZUB1	OTTHUMG00000020157	ENST00000325643.5:c.3056T>A	9.37:g.90502458T>A	ENSP00000322640:p.Val1019Glu	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	102	49	0.480392	NM_178828	B2RPB1|Q5SQC9|Q8NA41|Q8ND27	Missense_Mutation	SNP	ENST00000325643.5	37	CCDS6676.1	1644	0.7527472527472527	462	0.9390243902439024	256	0.7071823204419889	499	0.8723776223776224	427	0.5633245382585752	N	0.018	-1.486716	0.01018	0.881071	0.539535	ENSG00000177992	ENST00000325643	T	0.03035	4.07	3.3	2.16	0.27623	.	.	.	.	.	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	0.22730	-1.0208	8	0.02654	T	1	.	2.7404	0.05252	0.6514:0.0:0.1255:0.2231	rs10868670;rs10868670	1019	Q6ZUB1	CI079_HUMAN	E	1019	ENSP00000322640:V1019E	ENSP00000322640:V1019E	V	+	2	0	C9orf79	89692278	0.001000	0.12720	0.000000	0.03702	0.035000	0.12851	-0.014000	0.12656	0.189000	0.20188	-0.375000	0.07067	GTG	T|0.313;A|0.687	0.687	strong		0.587	SPATA31E1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052954.2	NM_178828	
ITGA3	3675	hgsc.bcm.edu	37	17	48149386	48149386	+	Silent	SNP	C	C	T	rs2269772	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:48149386C>T	ENST00000320031.8	+	7	1326	c.996C>T	c.(994-996)ttC>ttT	p.F332F	ITGA3_ENST00000007722.7_Silent_p.F332F|ITGA3_ENST00000544892.1_Silent_p.F107F	NM_002204.2|NM_005501.2	NP_002195.1|NP_005492.1	P26006	ITA3_HUMAN	integrin, alpha 3 (antigen CD49C, alpha 3 subunit of VLA-3 receptor)	332					blood coagulation (GO:0007596)|cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|lung development (GO:0030324)|maternal process involved in female pregnancy (GO:0060135)|memory (GO:0007613)|mesodermal cell differentiation (GO:0048333)|negative regulation of cell projection organization (GO:0031345)|nephron development (GO:0072006)|neuron migration (GO:0001764)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of gene expression (GO:0010628)|positive regulation of neuron projection development (GO:0010976)|regulation of BMP signaling pathway (GO:0030510)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|regulation of Wnt signaling pathway (GO:0030111)|renal filtration (GO:0097205)|response to drug (GO:0042493)|response to gonadotropin (GO:0034698)|skin development (GO:0043588)	basolateral plasma membrane (GO:0016323)|cell periphery (GO:0071944)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|integrin alpha3-beta1 complex (GO:0034667)|integrin complex (GO:0008305)|invadopodium membrane (GO:0071438)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|synapse (GO:0045202)	glycoprotein binding (GO:0001948)|metal ion binding (GO:0046872)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)			endometrium(3)|kidney(2)|large_intestine(7)|lung(11)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(2)	31						CCTACTACTTCGAGAGGAAAG	0.567													T|||	1235	0.246605	0.3411	0.2421	5008	,	,		17513	0.2778		0.0726	False		,,,				2504	0.2689				p.F332F		Atlas-SNP	.											.	ITGA3	128	.	0			c.C996T						PASS	.	T	,	1456,2950	681.0+/-403.9	205,1046,952	65.0	54.0	58.0		996,996	-0.7	1.0	17	dbSNP_100	58	779,7821	783.5+/-407.6	29,721,3550	no	coding-synonymous,coding-synonymous	ITGA3	NM_002204.2,NM_005501.2	,	234,1767,4502	TT,TC,CC		9.0581,33.0458,17.1844	,	332/1052,332/1067	48149386	2235,10771	2203	4300	6503	SO:0001819	synonymous_variant	3675	exon7			CTACTTCGAGAGG	M59911	CCDS11557.1, CCDS11558.1	17q21.33	2010-03-23	2003-10-13		ENSG00000005884	ENSG00000005884		"""CD molecules"", ""Integrins"""	6139	protein-coding gene	gene with protein product		605025	"""antigen identified by monoclonal antibody J143"""	MSK18		1655803, 9704023	Standard	NM_005501		Approved	CD49c, VLA3a, VCA-2, GAP-B3	uc010dbm.3	P26006	OTTHUMG00000161890	ENST00000320031.8:c.996C>T	17.37:g.48149386C>T		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	72	27	0.375	NM_005501	A7E246|B7ZM80|B9EGQ1|D3DTX4|D3DTX5	Silent	SNP	ENST00000320031.8	37	CCDS11558.1																																																																																			C|0.807;T|0.193	0.193	strong		0.567	ITGA3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000366298.1	NM_005501	
C1orf110	339512	hgsc.bcm.edu	37	1	162824960	162824960	+	Silent	SNP	G	G	A	rs190249067	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:162824960G>A	ENST00000367910.1	-	4	624	c.504C>T	c.(502-504)gaC>gaT	p.D168D	C1orf110_ENST00000524691.1_Intron|C1orf110_ENST00000367911.2_Silent_p.D163D|C1orf110_ENST00000367912.2_Silent_p.D167D	NM_178550.4	NP_848645.3	Q86UF4	CA110_HUMAN	chromosome 1 open reading frame 110	168										endometrium(2)|kidney(1)|lung(6)|prostate(1)|skin(2)	12						TGGGGTCTACGTCCTTAGATG	0.463													G|||	3	0.000599042	0.0	0.0	5008	,	,		20117	0.002		0.001	False		,,,				2504	0.0				p.D168D		Atlas-SNP	.											.	C1orf110	22	.	0			c.C504T						PASS	.	G		2,3840		0,2,1919	274.0	261.0	265.0		504	-0.1	0.0	1		265	33,8235		0,33,4101	no	coding-synonymous	C1orf110	NM_178550.4		0,35,6020	AA,AG,GG		0.3991,0.0521,0.289		168/303	162824960	35,12075	1921	4134	6055	SO:0001819	synonymous_variant	339512	exon4			GTCTACGTCCTTA	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.504C>T	1.37:g.162824960G>A		Somatic	242	0	0		WXS	Illumina HiSeq	Phase_I	215	103	0.47907	NM_178550	Q5JSG1|Q6ZW57	Silent	SNP	ENST00000367910.1	37	CCDS44269.1																																																																																			G|0.999;A|0.001	0.001	strong		0.463	C1orf110-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083211.2	NM_178550	
STK11IP	114790	hgsc.bcm.edu	37	2	220473355	220473355	+	Missense_Mutation	SNP	G	G	A	rs673951	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:220473355G>A	ENST00000456909.1	+	15	1744	c.1654G>A	c.(1654-1656)Gta>Ata	p.V552I	STK11IP_ENST00000295641.10_Missense_Mutation_p.V563I			Q8N1F8	S11IP_HUMAN	serine/threonine kinase 11 interacting protein	563	Glu-rich.				protein localization (GO:0008104)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal membrane (GO:0005765)	protein kinase binding (GO:0019901)			breast(2)|endometrium(5)|kidney(1)|large_intestine(2)|lung(10)|ovary(1)|prostate(1)|urinary_tract(1)	23		Renal(207;0.0183)		Epithelial(149;2.69e-07)|all cancers(144;5.91e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		GCCTGAGGGCGTACGGGGCAG	0.602													G|||	1755	0.350439	0.0272	0.3919	5008	,	,		17351	0.6825		0.3598	False		,,,				2504	0.4059				p.V563I		Atlas-SNP	.											.	STK11IP	152	.	0			c.G1687A						PASS	.	G	ILE/VAL	292,3702		11,270,1716	52.0	57.0	55.0		1687	0.5	0.0	2	dbSNP_83	55	2801,5485		461,1879,1803	yes	missense	STK11IP	NM_052902.2	29	472,2149,3519	AA,AG,GG		33.804,7.311,25.1873	benign	563/1100	220473355	3093,9187	1997	4143	6140	SO:0001583	missense	114790	exon15			GAGGGCGTACGGG	AF450267	CCDS46521.1	2q35	2008-06-03			ENSG00000144589	ENSG00000144589			19184	protein-coding gene	gene with protein product	"""LKB1 interacting protein"""	607172				11741830	Standard	NM_052902		Approved	LIP1, KIAA1898, LKB1IP, STK11IP1	uc002vml.3	Q8N1F8	OTTHUMG00000059239	ENST00000456909.1:c.1654G>A	2.37:g.220473355G>A	ENSP00000389383:p.Val552Ile	Somatic	241	0	0		WXS	Illumina HiSeq	Phase_I	228	109	0.47807	NM_052902	Q8NAW9|Q8WXE4|Q96CN3|Q96PY9	Missense_Mutation	SNP	ENST00000456909.1	37		840	0.38461538461538464	18	0.036585365853658534	136	0.3756906077348066	407	0.7115384615384616	279	0.36807387862796836	G	2.879	-0.232288	0.05983	0.07311	0.33804	ENSG00000144589	ENST00000456909;ENST00000426736;ENST00000295641	T;T	0.05081	3.5;3.5	4.5	0.456	0.16655	.	0.943966	0.08791	N	0.893239	T	0.00012	0.0000	L	0.60455	1.87	0.80722	P	0.0	B;B	0.33022	0.035;0.394	B;B	0.28465	0.009;0.09	T	0.19582	-1.0301	9	0.20519	T	0.43	-1.1691	4.1782	0.10362	0.0846:0.2921:0.4728:0.1505	rs673951;rs734848;rs17853278;rs60175423;rs673951	563;563	Q8N1F8-2;Q8N1F8	.;S11IP_HUMAN	I	552;531;563	ENSP00000389383:V552I;ENSP00000295641:V563I	ENSP00000295641:V563I	V	+	1	0	STK11IP	220181599	0.000000	0.05858	0.001000	0.08648	0.029000	0.11900	-0.183000	0.09712	-0.102000	0.12197	-0.219000	0.12488	GTA	G|0.643;A|0.357	0.357	strong		0.602	STK11IP-001	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000131432.1	NM_052902	
ZNF80	7634	hgsc.bcm.edu	37	3	113955820	113955820	+	Silent	SNP	G	G	C	rs3732780	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:113955820G>C	ENST00000482457.2	-	1	605	c.102C>G	c.(100-102)tcC>tcG	p.S34S	RP11-553L6.2_ENST00000493033.1_RNA|RP11-553L6.2_ENST00000481773.1_RNA	NM_007136.3	NP_009067.2	P51504	ZNF80_HUMAN	zinc finger protein 80	34					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)				TTGGTCCCTGGGAGTCACATT	0.502													G|||	1560	0.311502	0.3593	0.2594	5008	,	,		22578	0.375		0.2734	False		,,,				2504	0.2577				p.S34S	GBM(23;986 1114 21716)	Atlas-SNP	.											.	ZNF80	75	.	0			c.C102G						PASS	.	G		1512,2894	480.8+/-358.9	252,1008,943	119.0	112.0	114.0		102	-1.5	0.0	3	dbSNP_107	114	2217,6383	375.8+/-337.9	291,1635,2374	no	coding-synonymous	ZNF80	NM_007136.3		543,2643,3317	CC,CG,GG		25.7791,34.3168,28.6714		34/274	113955820	3729,9277	2203	4300	6503	SO:0001819	synonymous_variant	7634	exon1			TCCCTGGGAGTCA	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.102C>G	3.37:g.113955820G>C		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	123	48	0.390244	NM_007136	Q6NSW4|Q6NT14	Silent	SNP	ENST00000482457.2	37	CCDS2979.1																																																																																			G|0.703;C|0.297	0.297	strong		0.502	ZNF80-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354696.2	NM_007136	
MUC4	4585	hgsc.bcm.edu	37	3	195512742	195512742	+	Silent	SNP	G	G	A	rs113755990	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195512742G>A	ENST00000463781.3	-	2	6168	c.5709C>T	c.(5707-5709)acC>acT	p.T1903T	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_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	55	0	0		WXS	Illumina HiSeq	Phase_I	115	30	0.26087	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	
PHPT1	29085	hgsc.bcm.edu	37	9	139744578	139744578	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:139744578G>A	ENST00000247665.10	+	2	611	c.274G>A	c.(274-276)Ggc>Agc	p.G92S	PHPT1_ENST00000492540.1_3'UTR|PHPT1_ENST00000545326.1_Missense_Mutation_p.G92S|MAMDC4_ENST00000445819.1_5'Flank|MAMDC4_ENST00000317446.2_5'Flank|PHPT1_ENST00000371661.1_Missense_Mutation_p.G92S	NM_014172.4	NP_054891.2	Q9NRX4	PHP14_HUMAN	phosphohistidine phosphatase 1	92					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)		TCACGTGTACGGCTATTCCAT	0.657																																					p.G92S		Atlas-SNP	.											.	PHPT1	14	.	0			c.G274A						PASS	.						97.0	90.0	92.0					9																	139744578		2202	4300	6502	SO:0001583	missense	29085	exon2			GTGTACGGCTATT	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.274G>A	9.37:g.139744578G>A	ENSP00000247665:p.Gly92Ser	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	146	39	0.267123	NM_001135861	B1AMX0|B1AMX1|Q9H0Y3	Missense_Mutation	SNP	ENST00000247665.10	37	CCDS7009.1	.	.	.	.	.	.	.	.	.	.	.	35	5.458139	0.96240	.	.	ENSG00000054148	ENST00000371661;ENST00000545326;ENST00000247665	.	.	.	4.61	4.61	0.57282	.	.	.	.	.	D	0.85270	0.5658	M	0.91768	3.24	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.88984	0.3410	8	0.66056	D	0.02	-0.5277	16.4133	0.83726	0.0:0.0:1.0:0.0	.	92;92	Q9NRX4-2;Q9NRX4	.;PHP14_HUMAN	S	92	.	ENSP00000247665:G92S	G	+	1	0	PHPT1	138864399	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	4.076000	0.57591	2.098000	0.63641	0.455000	0.32223	GGC	.	.	none		0.657	PHPT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055150.1	NM_014172	
PSME4	23198	hgsc.bcm.edu	37	2	54127041	54127041	+	Silent	SNP	C	C	T	rs805423	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	297	1	0.003367		WXS	Illumina HiSeq	Phase_I	503	376	0.747515	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	
TUBG2	27175	hgsc.bcm.edu	37	17	40818699	40818699	+	Missense_Mutation	SNP	A	A	G	rs1046097	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:40818699A>G	ENST00000251412.7	+	11	1436	c.1237A>G	c.(1237-1239)Atg>Gtg	p.M413V	PLEKHH3_ENST00000456950.2_5'Flank	NM_016437.2	NP_057521.1	Q9NRH3	TBG2_HUMAN	tubulin, gamma 2	413			M -> V (in dbSNP:rs1046097).		cytoplasmic microtubule organization (GO:0031122)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule nucleation (GO:0007020)|mitotic cell cycle (GO:0000278)	cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|gamma-tubulin complex (GO:0000930)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|pericentriolar material (GO:0000242)|spindle microtubule (GO:0005876)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)	15		Breast(137;0.00116)		BRCA - Breast invasive adenocarcinoma(366;0.141)		TAAGGAGGACATGTTCAAGGA	0.502													A|||	2393	0.477835	0.3147	0.4697	5008	,	,		20591	0.4643		0.5258	False		,,,				2504	0.6687				p.M413V		Atlas-SNP	.											.	TUBG2	43	.	0			c.A1237G						PASS	.	A	VAL/MET	1500,2906	479.5+/-358.5	261,978,964	121.0	108.0	112.0		1237	5.1	1.0	17	dbSNP_86	112	4683,3917	605.5+/-395.0	1298,2087,915	yes	missense	TUBG2	NM_016437.2	21	1559,3065,1879	GG,GA,AA		45.5465,34.0445,47.5396	benign	413/452	40818699	6183,6823	2203	4300	6503	SO:0001583	missense	27175	exon11			GAGGACATGTTCA	AF225971	CCDS32658.1	17q21.2	2014-09-04			ENSG00000037042	ENSG00000037042		"""Tubulins"""	12419	protein-coding gene	gene with protein product		605785					Standard	NM_016437		Approved		uc010wgr.2	Q9NRH3	OTTHUMG00000180640	ENST00000251412.7:c.1237A>G	17.37:g.40818699A>G	ENSP00000251412:p.Met413Val	Somatic	241	0	0		WXS	Illumina HiSeq	Phase_I	177	93	0.525424	NM_016437	A6NDI4|Q32NB2	Missense_Mutation	SNP	ENST00000251412.7	37	CCDS32658.1	996	0.45604395604395603	178	0.3617886178861789	156	0.430939226519337	262	0.458041958041958	400	0.5277044854881267	A	10.96	1.498948	0.26861	0.340445	0.544535	ENSG00000037042	ENST00000251412	D	0.85013	-1.93	5.07	5.07	0.68467	Tubulin, C-terminal (1);Tubulin/FtsZ, C-terminal (1);	0.219619	0.45361	D	0.000374	T	0.00012	0.0000	L	0.41236	1.265	0.29642	P	0.8446549999999999	B	0.02656	0.0	B	0.01281	0.0	T	0.33752	-0.9856	9	0.11182	T	0.66	-17.4115	14.9891	0.71371	1.0:0.0:0.0:0.0	rs1046097;rs3186067;rs17355568;rs1046097	413	Q9NRH3	TBG2_HUMAN	V	413	ENSP00000251412:M413V	ENSP00000251412:M413V	M	+	1	0	TUBG2	38072225	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.164000	0.77533	2.132000	0.65825	0.459000	0.35465	ATG	A|0.531;G|0.469	0.469	strong		0.502	TUBG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452326.1	NM_016437	
MYH7B	57644	hgsc.bcm.edu	37	20	33581955	33581955	+	Silent	SNP	G	G	A	rs2425012	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:33581955G>A	ENST00000262873.7	+	25	2669	c.2577G>A	c.(2575-2577)gcG>gcA	p.A859A		NM_020884.3	NP_065935.2	A7E2Y1	MYH7B_HUMAN	myosin, heavy chain 7B, cardiac muscle, beta	817						membrane (GO:0016020)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(2)|breast(5)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(19)|ovary(5)|prostate(3)|upper_aerodigestive_tract(2)|urinary_tract(3)	54			BRCA - Breast invasive adenocarcinoma(18;0.00691)			CTAGGGATGCGCTGTTCACCA	0.557													G|||	1987	0.396765	0.171	0.621	5008	,	,		20265	0.5546		0.4861	False		,,,				2504	0.2883				p.A859A		Atlas-SNP	.											.	MYH7B	145	.	0			c.G2577A						PASS	.	G		922,3332		107,708,1312	91.0	97.0	95.0		2577	0.1	1.0	20	dbSNP_100	95	3623,4885		760,2103,1391	no	coding-synonymous	MYH7B	NM_020884.3		867,2811,2703	AA,AG,GG		42.5835,21.6737,35.6135		859/1984	33581955	4545,8217	2127	4254	6381	SO:0001819	synonymous_variant	57644	exon27			GGATGCGCTGTTC	AB040945	CCDS42869.1	20q11	2011-09-27	2006-09-29		ENSG00000078814	ENSG00000078814		"""Myosins / Myosin superfamily : Class II"""	15906	protein-coding gene	gene with protein product		609928	"""myosin, heavy polypeptide 7B, cardiac muscle, beta"""			11919279, 15014174	Standard	XM_006723839		Approved	KIAA1512, dJ756N5.1, MYH14, MHC14	uc002xbi.2	A7E2Y1	OTTHUMG00000032320	ENST00000262873.7:c.2577G>A	20.37:g.33581955G>A		Somatic	224	0	0		WXS	Illumina HiSeq	Phase_I	223	106	0.475336	NM_020884	Q5JVW7|Q6NT44|Q6NT57|Q6WG75|Q96I57|Q9NWE2|Q9P216	Silent	SNP	ENST00000262873.7	37	CCDS42869.1																																																																																			G|0.585;A|0.415	0.415	strong		0.557	MYH7B-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000078833.2	NM_020884	
GBP3	2635	hgsc.bcm.edu	37	1	89475135	89475135	+	Missense_Mutation	SNP	C	C	T	rs10493821	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:89475135C>T	ENST00000370481.4	-	9	1625	c.1405G>A	c.(1405-1407)Gtg>Atg	p.V469M		NM_018284.2	NP_060754.2	Q8WXF7	ATLA1_HUMAN	guanylate binding protein 3	0	Sufficient for membrane association.				axonogenesis (GO:0007409)|cell death (GO:0008219)|endoplasmic reticulum organization (GO:0007029)|GTP catabolic process (GO:0006184)|protein homooligomerization (GO:0051260)	cell projection (GO:0042995)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|Golgi cis cisterna (GO:0000137)|integral component of membrane (GO:0016021)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)			breast(3)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|stomach(1)	26		Lung NSC(277;0.123)		all cancers(265;0.0103)|Epithelial(280;0.0293)		GCATCGGTCACAGACTCCTTG	0.433													C|||	995	0.198682	0.0439	0.2421	5008	,	,		17404	0.2034		0.3201	False		,,,				2504	0.2474				p.V469M		Atlas-SNP	.											.	GBP3	53	.	0			c.G1405A						PASS	.	C	MET/VAL	370,4036	190.2+/-216.2	14,342,1847	147.0	134.0	138.0		1405	-1.0	0.0	1	dbSNP_119	138	2716,5884	434.1+/-357.6	398,1920,1982	yes	missense	GBP3	NM_018284.2	21	412,2262,3829	TT,TC,CC		31.5814,8.3976,23.7275	benign	469/596	89475135	3086,9920	2203	4300	6503	SO:0001583	missense	2635	exon9			CGGTCACAGACTC	BC063819	CCDS717.2	1p22.2	2008-02-05			ENSG00000117226	ENSG00000117226			4184	protein-coding gene	gene with protein product		600413				7518790	Standard	NM_018284		Approved	FLJ10961	uc001dmt.3	Q9H0R5	OTTHUMG00000010616	ENST00000370481.4:c.1405G>A	1.37:g.89475135C>T	ENSP00000359512:p.Val469Met	Somatic	272	0	0		WXS	Illumina HiSeq	Phase_I	254	142	0.559055	NM_018284	A6NND5|A8K2C0|G5E9T1|O95890|Q69YH7|Q96FK0	Missense_Mutation	SNP	ENST00000370481.4	37	CCDS717.2	491	0.22481684981684982	34	0.06910569105691057	102	0.281767955801105	116	0.20279720279720279	239	0.3153034300791557	C	8.154	0.788131	0.16258	0.083976	0.315814	ENSG00000117226	ENST00000370482;ENST00000370481;ENST00000445969	T;T	0.02552	4.25;4.25	3.98	-1.05	0.10036	Guanylate-binding protein, C-terminal (3);	1.106200	0.06789	N	0.786735	T	0.00998	0.0033	L	0.31926	0.97	0.80722	P	0.0	B;B	0.24920	0.073;0.114	B;B	0.31101	0.119;0.124	T	0.46569	-0.9182	9	0.33940	T	0.23	.	8.276	0.31873	0.0:0.5593:0.0:0.4407	rs10493821;rs17433801;rs10493821	335;469	F6X827;Q9H0R5	.;GBP3_HUMAN	M	437;469;49	ENSP00000359512:V469M;ENSP00000415087:V49M	ENSP00000359512:V469M	V	-	1	0	GBP3	89247723	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-0.665000	0.05286	-0.311000	0.08754	-0.192000	0.12808	GTG	C|0.773;T|0.227	0.227	strong		0.433	GBP3-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313541.3	NM_018284	
PPP1R26	9858	hgsc.bcm.edu	37	9	138377853	138377853	+	Silent	SNP	A	A	G	rs2004074	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:138377853A>G	ENST00000356818.2	+	4	2046	c.1497A>G	c.(1495-1497)gtA>gtG	p.V499V	PPP1R26_ENST00000604351.1_Silent_p.V499V|PPP1R26_ENST00000401470.3_Silent_p.V499V|PPP1R26_ENST00000602993.1_Intron|PPP1R26_ENST00000605660.1_Silent_p.V499V|PPP1R26_ENST00000605286.1_Silent_p.V499V	NM_014811.3	NP_055626.3	Q5T8A7	PPR26_HUMAN	protein phosphatase 1, regulatory subunit 26	499					negative regulation of phosphatase activity (GO:0010923)	nucleus (GO:0005634)	phosphatase binding (GO:0019902)|protein phosphatase inhibitor activity (GO:0004864)										CGGCCCCTGTAGAGGGCAGTG	0.612													G|||	2141	0.427516	0.3275	0.4971	5008	,	,		18876	0.6577		0.2107	False		,,,				2504	0.499				p.V499V		Atlas-SNP	.											KIAA0649,colon,carcinoma,0,1	.	.	1	0			c.A1497G						PASS	.	G		1266,3140	686.0+/-404.6	174,918,1111	48.0	48.0	48.0		1497	2.8	0.0	9	dbSNP_92	48	1799,6801	719.5+/-406.3	193,1413,2694	no	coding-synonymous	KIAA0649	NM_014811.3		367,2331,3805	GG,GA,AA		20.9186,28.7335,23.566		499/1210	138377853	3065,9941	2203	4300	6503	SO:0001819	synonymous_variant	9858	exon4			CCCTGTAGAGGGC	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.1497A>G	9.37:g.138377853A>G		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	56	25	0.446429	NM_014811	Q86WU0|Q8WVV0|Q9Y4D3	Silent	SNP	ENST00000356818.2	37	CCDS6988.1																																																																																			A|0.691;G|0.309	0.309	strong		0.612	PPP1R26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054987.1	NM_014811	
CACNA1H	8912	hgsc.bcm.edu	37	16	1252369	1252369	+	Missense_Mutation	SNP	C	C	T	rs61734410	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:1252369C>T	ENST00000348261.5	+	9	2167	c.1919C>T	c.(1918-1920)cCg>cTg	p.P640L	CACNA1H_ENST00000565831.1_Missense_Mutation_p.P640L|CACNA1H_ENST00000358590.4_Missense_Mutation_p.P640L	NM_021098.2	NP_066921.2	O95180	CAC1H_HUMAN	calcium channel, voltage-dependent, T type, alpha 1H subunit	640			P -> L (in dbSNP:rs61734410). {ECO:0000269|PubMed:12891677, ECO:0000269|Ref.7}.		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)	GCCGGTGGACCGCCAGGCACC	0.687													C|||	2203	0.439896	0.2368	0.4683	5008	,	,		14593	0.8383		0.3002	False		,,,				2504	0.4274				p.P640L		Atlas-SNP	.											CACNA1H_ENST00000358590,bladder,carcinoma,-1,2	CACNA1H	317	2	0			c.C1919T						PASS	.	C	LEU/PRO,LEU/PRO	747,3103		83,581,1261	5.0	7.0	7.0		1919,1919	2.6	0.0	16	dbSNP_129	7	1905,6109		242,1421,2344	yes	missense,missense	CACNA1H	NM_001005407.1,NM_021098.2	98,98	325,2002,3605	TT,TC,CC		23.7709,19.4026,22.3533	benign,benign	640/2348,640/2354	1252369	2652,9212	1925	4007	5932	SO:0001583	missense	8912	exon9			GTGGACCGCCAGG	AL031703	CCDS45375.1, CCDS45376.1	16p13.3	2012-03-07	2007-02-16					"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1395	protein-coding gene	gene with protein product		607904				9670923, 16382099	Standard	NM_021098		Approved	Cav3.2	uc002cks.3	O95180		ENST00000348261.5:c.1919C>T	16.37:g.1252369C>T	ENSP00000334198:p.Pro640Leu	Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	73	54	0.739726	NM_021098	B5ME00|F8WFD1|O95802|Q8WWI6|Q96QI6|Q96RZ9|Q9NYY4|Q9NYY5	Missense_Mutation	SNP	ENST00000348261.5	37	CCDS45375.1	977	0.44734432234432236	106	0.21544715447154472	149	0.4116022099447514	487	0.8513986013986014	235	0.3100263852242744	C	10.68	1.417079	0.25552	0.194026	0.237709	ENSG00000196557	ENST00000348261;ENST00000358590	D;D	0.96265	-3.96;-3.9	3.55	2.56	0.30785	.	2509.280000	0.00166	N	0.000000	T	0.00012	0.0000	L	0.43152	1.355	0.80722	P	0.0	P;B	0.36378	0.55;0.216	B;B	0.25614	0.062;0.019	T	0.49303	-0.8954	9	0.37606	T	0.19	.	9.4648	0.38806	0.3835:0.6165:0.0:0.0	rs61734410	640;640	O95180-2;O95180	.;CAC1H_HUMAN	L	640	ENSP00000334198:P640L;ENSP00000351401:P640L	ENSP00000334198:P640L	P	+	2	0	CACNA1H	1192370	0.001000	0.12720	0.001000	0.08648	0.002000	0.02628	1.293000	0.33353	0.650000	0.30769	0.563000	0.77884	CCG	C|0.556;T|0.444	0.444	strong		0.687	CACNA1H-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000421601.1	NM_001005407	
GLYATL3	389396	hgsc.bcm.edu	37	6	49479775	49479775	+	Silent	SNP	A	A	T	rs1480615	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:49479775A>T	ENST00000371197.4	+	2	185	c.72A>T	c.(70-72)tcA>tcT	p.S24S		NM_001010904.1	NP_001010904.1	Q5SZD4	GLYL3_HUMAN	glycine-N-acyltransferase-like 3	24						mitochondrion (GO:0005739)	glycine N-acyltransferase activity (GO:0047961)			NS(1)|endometrium(1)|kidney(3)|lung(1)|skin(3)|stomach(2)	11						TTCCTGAATCACTCAAGGTAC	0.313													A|||	2271	0.453474	0.3608	0.3631	5008	,	,		14524	0.378		0.6362	False		,,,				2504	0.5327				p.S24S		Atlas-SNP	.											GLYATL3,trunk,malignant_melanoma,+1,1	GLYATL3	19	1	0			c.A72T						PASS	.	A		562,822		112,338,242	165.0	139.0	147.0		72	1.7	1.0	6	dbSNP_88	147	2062,1120		673,716,202	no	coding-synonymous	GLYATL3	NM_001010904.1		785,1054,444	TT,TA,AA		35.198,40.6069,42.5318		24/289	49479775	2624,1942	692	1591	2283	SO:0001819	synonymous_variant	389396	exon2			TGAATCACTCAAG		CCDS47440.1	6p12.3	2009-12-14	2009-12-14	2009-12-14	ENSG00000203972	ENSG00000203972			21349	protein-coding gene	gene with protein product		614763	"""chromosome 6 open reading frame 140"""	C6orf140			Standard	NM_001010904		Approved	bA28H17.2	uc003ozi.3	Q5SZD4	OTTHUMG00000014818	ENST00000371197.4:c.72A>T	6.37:g.49479775A>T		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	35	14	0.4	NM_001010904		Silent	SNP	ENST00000371197.4	37	CCDS47440.1																																																																																			T|0.431;N|0.000	0.431	strong		0.313	GLYATL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040866.3	NM_001010904	
FAM135B	51059	hgsc.bcm.edu	37	8	139165068	139165068	+	Silent	SNP	C	C	T	rs3763590	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:139165068C>T	ENST00000395297.1	-	13	1820	c.1650G>A	c.(1648-1650)gtG>gtA	p.V550V		NM_015912.3	NP_056996.2	Q49AJ0	F135B_HUMAN	family with sequence similarity 135, member B	550										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)			TGTAGGTCAGCACTGGGGCCT	0.502										HNSCC(54;0.14)			C|||	1825	0.364417	0.1566	0.4135	5008	,	,		17906	0.5298		0.3757	False		,,,				2504	0.4284				p.V550V		Atlas-SNP	.											.	FAM135B	423	.	0			c.G1650A						PASS	.	C		741,3163		75,591,1286	83.0	82.0	82.0		1650	-9.9	0.0	8	dbSNP_107	82	2847,5445		498,1851,1797	no	coding-synonymous	FAM135B	NM_015912.3		573,2442,3083	TT,TC,CC		34.3343,18.9805,29.4195		550/1407	139165068	3588,8608	1952	4146	6098	SO:0001819	synonymous_variant	51059	exon13			GGTCAGCACTGGG	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.1650G>A	8.37:g.139165068C>T		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	94	94	1	NM_015912	B5MDB3|O95879|Q2WGJ7|Q3KP46	Silent	SNP	ENST00000395297.1	37	CCDS6375.2																																																																																			C|0.632;T|0.368	0.368	strong		0.502	FAM135B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313590.3	NM_015912	
AKAP6	9472	hgsc.bcm.edu	37	14	33014869	33014869	+	Missense_Mutation	SNP	C	C	T	rs3742926	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:33014869C>T	ENST00000280979.4	+	4	1180	c.1010C>T	c.(1009-1011)gCt>gTt	p.A337V	AKAP6_ENST00000557272.1_Missense_Mutation_p.A337V|AKAP6_ENST00000557354.1_Missense_Mutation_p.A337V	NM_004274.4	NP_004265.3	Q13023	AKAP6_HUMAN	A kinase (PRKA) anchor protein 6	337			A -> V (in dbSNP:rs3742926).		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)		ACAAATGCTGCTCAACCCTCC	0.493													T|||	881	0.175919	0.233	0.1859	5008	,	,		20444	0.1815		0.1004	False		,,,				2504	0.1636				p.A337V	Melanoma(49;821 1200 7288 13647 42351)	Atlas-SNP	.											.	AKAP6	308	.	0			c.C1010T						PASS	.	T	VAL/ALA	887,3519	741.1+/-411.2	78,731,1394	73.0	64.0	67.0		1010	-5.0	0.0	14	dbSNP_107	67	804,7796	781.9+/-407.6	37,730,3533	yes	missense	AKAP6	NM_004274.4	64	115,1461,4927	TT,TC,CC		9.3488,20.1316,13.0017	benign	337/2320	33014869	1691,11315	2203	4300	6503	SO:0001583	missense	9472	exon4			ATGCTGCTCAACC	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.1010C>T	14.37:g.33014869C>T	ENSP00000280979:p.Ala337Val	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	78	78	1	NM_004274	A7E242|A7E2D4|O15028	Missense_Mutation	SNP	ENST00000280979.4	37	CCDS9644.1	367	0.16804029304029305	121	0.2459349593495935	62	0.1712707182320442	97	0.16958041958041958	87	0.11477572559366754	T	0.013	-1.629818	0.00813	0.201316	0.093488	ENSG00000151320	ENST00000280979;ENST00000557354;ENST00000557272;ENST00000553547	T;T;T;T	0.32753	1.44;1.44;1.44;1.44	5.61	-4.96	0.03038	.	1.589520	0.03277	N	0.185626	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	0.29458	-1.0011	9	0.16420	T	0.52	1.892	0.6198	0.00776	0.2906:0.2271:0.3018:0.1805	rs3742926;rs52801792;rs61666772;rs3742926	337;337	A7E242;Q13023	.;AKAP6_HUMAN	V	337;337;337;95	ENSP00000280979:A337V;ENSP00000450531:A337V;ENSP00000451247:A337V;ENSP00000451239:A95V	ENSP00000280979:A337V	A	+	2	0	AKAP6	32084620	0.000000	0.05858	0.000000	0.03702	0.021000	0.10359	-0.734000	0.04893	-0.707000	0.05022	-0.254000	0.11334	GCT	C|0.859;T|0.141	0.141	strong		0.493	AKAP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276617.2	NM_004274	
MMP3	4314	hgsc.bcm.edu	37	11	102713465	102713465	+	Silent	SNP	A	A	G	rs602128	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:102713465A>G	ENST00000299855.5	-	2	544	c.288T>C	c.(286-288)gaT>gaC	p.D96D		NM_002422.3	NP_002413.1	P08254	MMP3_HUMAN	matrix metallopeptidase 3 (stromelysin 1, progelatinase)	96					cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of hydrogen peroxide metabolic process (GO:0010727)|positive regulation of oxidative stress-induced cell death (GO:1903209)|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)|endopeptidase activity (GO:0004175)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(3)|large_intestine(3)|liver(1)|lung(7)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	22		all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)		BRCA - Breast invasive adenocarcinoma(274;0.0142)	Marimastat(DB00786)	AGTGACCAACATCAGGAACTC	0.498													G|||	3098	0.61861	0.5499	0.6643	5008	,	,		16797	0.6667		0.5278	False		,,,				2504	0.7229				p.D96D		Atlas-SNP	.											MMP3,NS,carcinoma,0,1	MMP3	60	1	0			c.T288C						PASS	.	G		2375,2031	563.8+/-381.3	636,1103,464	73.0	66.0	68.0		288	-12.1	0.0	11	dbSNP_83	68	4301,4297	577.9+/-390.6	1066,2169,1064	no	coding-synonymous	MMP3	NM_002422.3		1702,3272,1528	GG,GA,AA		49.9767,46.0962,48.662		96/478	102713465	6676,6328	2203	4299	6502	SO:0001819	synonymous_variant	4314	exon2			ACCAACATCAGGA	X05232	CCDS8323.1	11q22.3	2012-10-02	2005-08-08		ENSG00000149968	ENSG00000149968	3.4.24.17		7173	protein-coding gene	gene with protein product		185250	"""matrix metalloproteinase 3 (stromelysin 1, progelatinase)"""	STMY1, STMY			Standard	NM_002422		Approved		uc001phj.1	P08254	OTTHUMG00000048254	ENST00000299855.5:c.288T>C	11.37:g.102713465A>G		Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	127	126	0.992126	NM_002422	B2R8B8|Q3B7S0|Q6GRF8	Silent	SNP	ENST00000299855.5	37	CCDS8323.1																																																																																			A|0.461;G|0.539	0.539	strong		0.498	MMP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109758.2	NM_002422	
KRTAP4-6	81871	hgsc.bcm.edu	37	17	39296422	39296422	+	Silent	SNP	A	A	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:39296422A>G	ENST00000345847.4	-	1	317	c.318T>C	c.(316-318)cgT>cgC	p.R106R		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						TGCAGCTGGGACGGCAGCAAG	0.652																																					p.R106R		Atlas-SNP	.											KRTAP4-6,NS,carcinoma,-1,2	KRTAP4-6	46	2	0			c.T318C						scavenged	.																																			SO:0001819	synonymous_variant	81871	exon1			GCTGGGACGGCAG	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.318T>C	17.37:g.39296422A>G		Somatic	65	2	0.0307692		WXS	Illumina HiSeq	Phase_I	50	6	0.12	NM_030976	Q9BYR1	Silent	SNP	ENST00000345847.4	37	CCDS54125.1																																																																																			.	.	none		0.652	KRTAP4-6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257779.1		
LDLR	3949	hgsc.bcm.edu	37	19	11222300	11222300	+	Missense_Mutation	SNP	G	G	A	rs11669576	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:11222300G>A	ENST00000558518.1	+	8	1358	c.1171G>A	c.(1171-1173)Gcc>Acc	p.A391T	LDLR_ENST00000557933.1_Missense_Mutation_p.A391T|LDLR_ENST00000455727.2_Missense_Mutation_p.A223T|LDLR_ENST00000558013.1_Missense_Mutation_p.A391T|LDLR_ENST00000545707.1_Missense_Mutation_p.A264T|LDLR_ENST00000535915.1_Missense_Mutation_p.A350T	NM_000527.4|NM_001195798.1	NP_000518.1|NP_001182727.1	P01130	LDLR_HUMAN	low density lipoprotein receptor	391	EGF-like 2; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.		A -> T (in dbSNP:rs11669576).		cholesterol homeostasis (GO:0042632)|cholesterol import (GO:0070508)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|endocytosis (GO:0006897)|intestinal cholesterol absorption (GO:0030299)|lipid metabolic process (GO:0006629)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|low-density lipoprotein particle clearance (GO:0034383)|phospholipid transport (GO:0015914)|phototransduction, visible light (GO:0007603)|positive regulation of triglyceride biosynthetic process (GO:0010867)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol homeostasis (GO:2000188)|regulation of phosphatidylcholine catabolic process (GO:0010899)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|coated pit (GO:0005905)|early endosome (GO:0005769)|endosome membrane (GO:0010008)|external side of plasma membrane (GO:0009897)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|low-density lipoprotein particle (GO:0034362)|lysosome (GO:0005764)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|glycoprotein binding (GO:0001948)|low-density lipoprotein particle binding (GO:0030169)|low-density lipoprotein receptor activity (GO:0005041)|very-low-density lipoprotein particle receptor activity (GO:0030229)	p.?(1)		breast(2)|endometrium(2)|large_intestine(5)|lung(8)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	26		Lung NSC(9;0.000245)|Renal(1328;0.0007)|Hepatocellular(1079;0.0524)		GBM - Glioblastoma multiforme(1328;1.36e-05)|STAD - Stomach adenocarcinoma(1328;0.000766)|Lung(535;0.197)	Porfimer(DB00707)	CCACACGAAGGCCTGCAAGGC	0.642													G|||	339	0.0676917	0.202	0.0375	5008	,	,		16827	0.0		0.0437	False		,,,				2504	0.002				p.A391T	GBM(18;201 575 7820 21545)	Atlas-SNP	.											.	LDLR	72	.	1	Unknown(1)	lung(1)	c.G1171A	GRCh37	CM014366	LDLR	M	rs11669576	PASS	.	G	THR/ALA,THR/ALA,THR/ALA,THR/ALA,THR/ALA,THR/ALA	762,3644	304.6+/-288.6	78,606,1519	41.0	40.0	40.0		1171,1171,1048,667,808,790	-0.8	0.1	19	dbSNP_120	40	416,8184	127.8+/-186.1	15,386,3899	yes	missense,missense,missense,missense,missense,missense	LDLR	NM_000527.4,NM_001195798.1,NM_001195799.1,NM_001195800.1,NM_001195802.1,NM_001195803.1	58,58,58,58,58,58	93,992,5418	AA,AG,GG		4.8372,17.2946,9.0574	benign,benign,benign,benign,benign,benign	391/861,391/859,350/820,223/693,270/740,264/683	11222300	1178,11828	2203	4300	6503	SO:0001583	missense	3949	exon8			ACGAAGGCCTGCA	AY114155	CCDS12254.1, CCDS56083.1, CCDS56084.1, CCDS56085.1, CCDS58651.1	19p13.2	2014-09-17	2008-08-01		ENSG00000130164	ENSG00000130164		"""Low density lipoprotein receptors"""	6547	protein-coding gene	gene with protein product	"""familial hypercholesterolemia"""	606945					Standard	NM_000527		Approved	LDLCQ2	uc002mqk.4	P01130		ENST00000558518.1:c.1171G>A	19.37:g.11222300G>A	ENSP00000454071:p.Ala391Thr	Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	24	13	0.541667	NM_001195798	B4DII3|B4DJZ8|B4DR00|B4DTQ3|C0JYY8|H0YLU8|H0YNT7|Q53ZD9|Q59FQ1|Q9UDH7	Missense_Mutation	SNP	ENST00000558518.1	37	CCDS12254.1	165	0.07554945054945054	116	0.23577235772357724	15	0.04143646408839779	0	0.0	34	0.044854881266490766	G	0.031	-1.331617	0.01298	0.172946	0.048372	ENSG00000130164	ENST00000252444;ENST00000545707;ENST00000535915;ENST00000455727	D;D;D	0.91894	-2.93;-2.93;-2.93	5.56	-0.825	0.10809	Growth factor, receptor (1);EGF-like region, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	0.361880	0.23079	N	0.052177	T	0.00039	0.0001	N	0.00045	-2.45	0.48452	P	3.4599999999995745E-4	B;B;B;B;B;B	0.12013	0.005;0.002;0.005;0.003;0.005;0.005	B;B;B;B;B;B	0.21360	0.009;0.023;0.034;0.023;0.034;0.034	T	0.48305	-0.9047	9	0.05620	T	0.96	.	3.2134	0.06690	0.4419:0.0:0.2395:0.3186	rs11669576;rs11669576	223;264;270;350;403;391	B4DR00;B4DJZ8;B4DII3;B4DTQ3;Q59FQ1;P01130	.;.;.;.;.;LDLR_HUMAN	T	391;264;350;223	ENSP00000437639:A264T;ENSP00000440520:A350T;ENSP00000397829:A223T	ENSP00000252444:A391T	A	+	1	0	LDLR	11083300	0.000000	0.05858	0.134000	0.22075	0.182000	0.23217	-0.187000	0.09656	0.036000	0.15547	0.591000	0.81541	GCC	G|0.916;A|0.084	0.084	strong		0.642	LDLR-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000415973.2		
ARHGAP19	84986	hgsc.bcm.edu	37	10	99006083	99006083	+	Silent	SNP	G	G	A	rs13439	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:99006083G>A	ENST00000358531.4	-	7	967	c.939C>T	c.(937-939)taC>taT	p.Y313Y	ARHGAP19-SLIT1_ENST00000316676.8_Silent_p.Y313Y|ARHGAP19_ENST00000355366.5_Silent_p.Y304Y|ARHGAP19-SLIT1_ENST00000358308.3_Silent_p.Y284Y|ARHGAP19-SLIT1_ENST00000453547.2_Silent_p.Y313Y|ARHGAP19_ENST00000487035.1_5'UTR|ARHGAP19_ENST00000371027.1_Silent_p.Y304Y	NM_001204300.1|NM_032900.5	NP_001191229.1|NP_116289.4	Q14CB8	RHG19_HUMAN	Rho GTPase activating protein 19	313					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|nucleus (GO:0005634)	GTPase activator activity (GO:0005096)	p.Y313Y(1)		NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|prostate(1)|stomach(2)|urinary_tract(1)	13		Colorectal(252;0.0854)		Epithelial(162;7.65e-09)|all cancers(201;4.49e-07)		ACTCCCGAATGTAAGCAGGAG	0.433													G|||	1263	0.252196	0.3321	0.2651	5008	,	,		17612	0.0992		0.2674	False		,,,				2504	0.2771				p.Y313Y		Atlas-SNP	.											ARHGAP19_ENST00000358531,caecum,carcinoma,-2,3	ARHGAP19	72	3	1	Substitution - coding silent(1)	stomach(1)	c.C939T						PASS	.	G	,	1426,2980	462.8+/-353.4	233,960,1010	66.0	65.0	65.0		852,939	-10.1	0.6	10	dbSNP_52	65	2719,5881	434.0+/-357.6	422,1875,2003	no	coding-synonymous,coding-synonymous	ARHGAP19	NM_001204300.1,NM_032900.5	,	655,2835,3013	AA,AG,GG		31.6163,32.365,31.8699	,	284/466,313/495	99006083	4145,8861	2203	4300	6503	SO:0001819	synonymous_variant	84986	exon7			CCGAATGTAAGCA	AK074122	CCDS7454.2, CCDS58092.1, CCDS73175.1	10q24.2	2011-06-29			ENSG00000213390	ENSG00000213390		"""Rho GTPase activating proteins"""	23724	protein-coding gene	gene with protein product		611587					Standard	NM_032900		Approved	FLJ00194, MGC14258	uc001knb.3	Q14CB8	OTTHUMG00000018845	ENST00000358531.4:c.939C>T	10.37:g.99006083G>A		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	52	27	0.519231	NM_032900	A1XCP1|B4DZR1|Q14CF2|Q5J8M2|Q5T460|Q5T462|Q68DG6|Q8N9X1|Q8NF34|Q8TEK1	Silent	SNP	ENST00000358531.4	37	CCDS7454.2																																																																																			G|0.724;A|0.276	0.276	strong		0.433	ARHGAP19-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049647.2	NM_032900	
GCLC	2729	hgsc.bcm.edu	37	6	53387242	53387242	+	Silent	SNP	C	C	A	rs2066508	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:53387242C>A	ENST00000229416.6	-	2	717	c.234G>T	c.(232-234)ctG>ctT	p.L78L	GCLC_ENST00000514004.1_Silent_p.L78L	NM_001197115.1|NM_001498.3	NP_001184044.1|NP_001489.1	P48506	GSH1_HUMAN	glutamate-cysteine ligase, catalytic subunit	78					apoptotic mitochondrial changes (GO:0008637)|cell redox homeostasis (GO:0045454)|cellular nitrogen compound metabolic process (GO:0034641)|cysteine metabolic process (GO:0006534)|glutamate metabolic process (GO:0006536)|glutathione biosynthetic process (GO:0006750)|glutathione derivative biosynthetic process (GO:1901687)|L-ascorbic acid metabolic process (GO:0019852)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|regulation of blood vessel size (GO:0050880)|regulation of mitochondrial depolarization (GO:0051900)|response to arsenic-containing substance (GO:0046685)|response to heat (GO:0009408)|response to hormone (GO:0009725)|response to nitrosative stress (GO:0051409)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|glutamate-cysteine ligase complex (GO:0017109)	ADP binding (GO:0043531)|ATP binding (GO:0005524)|coenzyme binding (GO:0050662)|glutamate binding (GO:0016595)|glutamate-cysteine ligase activity (GO:0004357)|magnesium ion binding (GO:0000287)			breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(4)|liver(1)|lung(11)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	22	Lung NSC(77;0.0137)				L-Cysteine(DB00151)|Vitamin E(DB00163)	CCTTCTCTTGCAGAGTTTCAA	0.368													C|||	67	0.0133786	0.0023	0.0231	5008	,	,		19298	0.0		0.0388	False		,,,				2504	0.0092				p.L78L		Atlas-SNP	.											.	GCLC	58	.	0			c.G234T						PASS	.	C	,	36,4370	39.2+/-71.8	0,36,2167	110.0	108.0	109.0		234,234	-9.0	0.9	6	dbSNP_94	109	347,8253	118.1+/-177.6	7,333,3960	no	coding-synonymous,coding-synonymous	GCLC	NM_001197115.1,NM_001498.3	,	7,369,6127	AA,AC,CC		4.0349,0.8171,2.9448	,	78/600,78/638	53387242	383,12623	2203	4300	6503	SO:0001819	synonymous_variant	2729	exon2			CTCTTGCAGAGTT	M90656	CCDS4952.1, CCDS75471.1	6p12	2008-02-05				ENSG00000001084	6.3.2.2		4311	protein-coding gene	gene with protein product		606857		GLCLC, GLCL		1350904	Standard	NM_001498		Approved	GCS	uc003pbw.2	P48506		ENST00000229416.6:c.234G>T	6.37:g.53387242C>A		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	66	28	0.424242	NM_001197115	Q14399	Silent	SNP	ENST00000229416.6	37	CCDS4952.1	41	0.018772893772893772	1	0.0020325203252032522	8	0.022099447513812154	0	0.0	32	0.04221635883905013	C	9.304	1.053958	0.19907	0.008171	0.040349	ENSG00000001084	ENST00000513939	.	.	.	5.67	-8.97	0.00758	.	.	.	.	.	T	0.51109	0.1655	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.69030	-0.5253	4	.	.	.	.	18.1162	0.89556	0.0:0.7717:0.1025:0.1258	rs2066508;rs17882831	.	.	.	F	66	.	.	C	-	2	0	GCLC	53495201	0.160000	0.22878	0.862000	0.33874	0.961000	0.63080	-0.608000	0.05641	-1.418000	0.02014	-1.155000	0.01812	TGC	C|0.975;A|0.025	0.025	strong		0.368	GCLC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359710.2		
TMEM82	388595	hgsc.bcm.edu	37	1	16069644	16069644	+	Silent	SNP	C	C	T	rs11584945	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:16069644C>T	ENST00000375782.1	+	3	429	c.291C>T	c.(289-291)ctC>ctT	p.L97L	RP11-169K16.4_ENST00000418525.1_RNA|TMEM82_ENST00000465575.1_3'UTR	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	83	0	0		WXS	Illumina HiSeq	Phase_I	88	49	0.556818	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	
RADIL	55698	hgsc.bcm.edu	37	7	4841614	4841614	+	Missense_Mutation	SNP	C	C	T	rs117943885	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:4841614C>T	ENST00000399583.3	-	12	2699	c.2512G>A	c.(2512-2514)Gtg>Atg	p.V838M	RADIL_ENST00000538469.1_Missense_Mutation_p.V598M|RADIL_ENST00000536091.1_3'UTR	NM_018059.4	NP_060529.4	Q96JH8	RADIL_HUMAN	Ras association and DIL domains	838					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)		TCAAGGACCACGTGGTGCATA	0.677													C|||	64	0.0127796	0.0015	0.0187	5008	,	,		13575	0.0		0.0249	False		,,,				2504	0.0245				p.V838M		Atlas-SNP	.											.	RADIL	110	.	0			c.G2512A						PASS	.	C	MET/VAL	10,3304		0,10,1647	5.0	6.0	6.0		2512	-3.5	0.0	7	dbSNP_132	6	139,6811		3,133,3339	yes	missense	RADIL	NM_018059.4	21	3,143,4986	TT,TC,CC		2.0,0.3018,1.4517	benign	838/1076	4841614	149,10115	1657	3475	5132	SO:0001583	missense	55698	exon12			GGACCACGTGGTG	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.2512G>A	7.37:g.4841614C>T	ENSP00000382492:p.Val838Met	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	119	22	0.184874	NM_018059	A4D1Z5|A5YM49|B7ZL20|Q0VFZ9|Q75LH3|Q9BSP5|Q9H0M6|Q9NW43|Q9NWC4	Missense_Mutation	SNP	ENST00000399583.3	37	CCDS43544.1	34	0.015567765567765568	2	0.0040650406504065045	13	0.03591160220994475	0	0.0	19	0.025065963060686015	C	8.995	0.978733	0.18812	0.003018	0.02	ENSG00000157927	ENST00000399583;ENST00000316919;ENST00000544486;ENST00000538469	T;T	0.07114	3.29;3.22	4.15	-3.5	0.04710	.	0.941613	0.08946	N	0.870830	T	0.00815	0.0027	N	0.08118	0	0.09310	N	1	B;B	0.16396	0.017;0.004	B;B	0.06405	0.002;0.0	T	0.41645	-0.9497	10	0.51188	T	0.08	-1.412	5.9949	0.19489	0.0:0.1746:0.2538:0.5716	.	838;146	Q96JH8;Q75LH2	RADIL_HUMAN;.	M	838;809;572;598	ENSP00000382492:V838M;ENSP00000442966:V598M	ENSP00000320946:V809M	V	-	1	0	RADIL	4808140	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.693000	0.05121	-1.147000	0.02851	-1.340000	0.01251	GTG	C|0.984;T|0.016	0.016	strong		0.677	RADIL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323769.2	NM_018059	
PPP2R3A	5523	hgsc.bcm.edu	37	3	135721208	135721208	+	Missense_Mutation	SNP	A	A	G	rs146596318	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:135721208A>G	ENST00000264977.3	+	2	1485	c.868A>G	c.(868-870)Aaa>Gaa	p.K290E	PPP2R3A_ENST00000490467.1_Intron	NM_001190447.1|NM_002718.4	NP_001177376.1|NP_002709.2	Q06190	P2R3A_HUMAN	protein phosphatase 2, regulatory subunit B'', alpha	290					eye photoreceptor cell differentiation (GO:0001754)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of protein catabolic process (GO:0045732)|protein dephosphorylation (GO:0006470)|regulation of catalytic activity (GO:0050790)|regulation of cell motility involved in somitogenic axis elongation (GO:0090249)|somatic muscle development (GO:0007525)|somite development (GO:0061053)|Wnt signaling pathway involved in somitogenesis (GO:0090244)	protein phosphatase type 2A complex (GO:0000159)	calcium ion binding (GO:0005509)|protein phosphatase type 2A regulator activity (GO:0008601)			breast(2)|cervix(1)|endometrium(2)|large_intestine(7)|lung(10)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31						ATCCTATCTGAAAAAGTTACC	0.378																																					p.K290E		Atlas-SNP	.											.	PPP2R3A	114	.	0			c.A868G						PASS	.	A	,GLU/LYS	0,4406		0,0,2203	93.0	91.0	91.0		,868	5.3	1.0	3	dbSNP_134	91	4,8596	3.7+/-12.6	0,4,4296	yes	intron,missense	PPP2R3A	NM_001190447.1,NM_002718.4	,56	0,4,6499	GG,GA,AA		0.0465,0.0,0.0308	,possibly-damaging	,290/1151	135721208	4,13002	2203	4300	6503	SO:0001583	missense	5523	exon2			TATCTGAAAAAGT	L12146	CCDS3087.1, CCDS3088.1, CCDS54642.1	3q22.2-q22.3	2013-01-10	2010-06-18	2002-04-26	ENSG00000073711	ENSG00000073711	3.1.3.16	"""Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"", ""EF-hand domain containing"""	9307	protein-coding gene	gene with protein product		604944	"""protein phosphatase 2 (formerly 2A), regulatory subunit B'' (PR 72), alpha isoform and (PR 130), beta isoform"", ""protein phosphatase 2 (formerly 2A), regulatory subunit B'', alpha"""	PPP2R3		8392071	Standard	NM_002718		Approved		uc003eqv.2	Q06190	OTTHUMG00000159766	ENST00000264977.3:c.868A>G	3.37:g.135721208A>G	ENSP00000264977:p.Lys290Glu	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	44	22	0.5	NM_002718	A8KAE7|B4DNU1|B7ZAE3|Q06189|Q9NPQ5	Missense_Mutation	SNP	ENST00000264977.3	37	CCDS3087.1	.	.	.	.	.	.	.	.	.	.	A	17.74	3.463519	0.63513	0.0	4.65E-4	ENSG00000073711	ENST00000264977	T	0.16897	2.31	5.34	5.34	0.76211	.	0.102401	0.64402	D	0.000004	T	0.23611	0.0571	L	0.58101	1.795	0.80722	D	1	P	0.45348	0.856	B	0.43754	0.43	T	0.01894	-1.1252	10	0.87932	D	0	.	14.5059	0.67752	1.0:0.0:0.0:0.0	.	290	Q06190	P2R3A_HUMAN	E	290	ENSP00000264977:K290E	ENSP00000264977:K290E	K	+	1	0	PPP2R3A	137203898	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.957000	0.93082	2.010000	0.58986	0.533000	0.62120	AAA	A|1.000;G|0.000	0.000	strong		0.378	PPP2R3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357232.1	NM_002718	
RC3H2	54542	hgsc.bcm.edu	37	9	125639808	125639808	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:125639808C>T	ENST00000373670.1	-	8	1867	c.1267G>A	c.(1267-1269)Ggg>Agg	p.G423R	RC3H2_ENST00000357244.2_Missense_Mutation_p.G423R|RC3H2_ENST00000335387.5_Missense_Mutation_p.G423R|RC3H2_ENST00000373665.2_Missense_Mutation_p.G423R|SNORD90_ENST00000391145.1_RNA|RC3H2_ENST00000423239.2_Missense_Mutation_p.G423R			Q9HBD1	RC3H2_HUMAN	ring finger and CCCH-type domains 2	423					B cell homeostasis (GO:0001782)|limb development (GO:0060173)|lung alveolus development (GO:0048286)|lymph node development (GO:0048535)|multicellular organism growth (GO:0035264)|positive regulation of NIK/NF-kappaB signaling (GO:1901224)|post-embryonic development (GO:0009791)|posttranscriptional regulation of gene expression (GO:0010608)|protein polyubiquitination (GO:0000209)|spleen development (GO:0048536)|T cell homeostasis (GO:0043029)|T cell proliferation (GO:0042098)|T follicular helper cell differentiation (GO:0061470)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|endometrium(6)|large_intestine(4)|liver(1)|lung(11)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	33						GGACAACCCCCTTGCTGTCGC	0.418																																					p.G423R		Atlas-SNP	.											.	RC3H2	150	.	0			c.G1267A						PASS	.						276.0	270.0	272.0					9																	125639808		1898	4121	6019	SO:0001583	missense	54542	exon9			AACCCCCTTGCTG	AK000308	CCDS43874.1, CCDS48014.1	9q34	2013-01-18	2010-09-15	2007-02-06	ENSG00000056586	ENSG00000056586		"""RING-type (C3HC4) zinc fingers"", ""Zinc fingers, CCCH-type domain containing"""	21461	protein-coding gene	gene with protein product		615231	"""membrane associated DNA binding protein"", ""ring finger and CCCH-type zinc finger domains 2"""	MNAB		10938276	Standard	NM_001100588		Approved	FLJ20301, FLJ20713, RNF164	uc010mwc.1	Q9HBD1	OTTHUMG00000020632	ENST00000373670.1:c.1267G>A	9.37:g.125639808C>T	ENSP00000362774:p.Gly423Arg	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	60	37	0.616667	NM_018835	Q4VXB1|Q5JPD7|Q86ST6|Q8N3D6|Q96F27|Q9H5J2|Q9HBD2|Q9NWN9|Q9NXE1	Missense_Mutation	SNP	ENST00000373670.1	37	CCDS43874.1	.	.	.	.	.	.	.	.	.	.	C	27.2	4.810872	0.90707	.	.	ENSG00000056586	ENST00000373670;ENST00000357244;ENST00000373663;ENST00000423239;ENST00000373665;ENST00000335387	T;T;T;T;T	0.75821	-0.97;-0.97;-0.97;-0.97;-0.97	5.54	5.54	0.83059	Zinc finger, CCCH-type (3);	0.109140	0.64402	N	0.000006	D	0.84660	0.5521	M	0.69463	2.115	0.54753	D	0.999985	B;D;D;D	0.76494	0.329;0.988;0.999;0.998	B;D;D;D	0.70487	0.327;0.954;0.969;0.948	T	0.82774	-0.0291	10	0.35671	T	0.21	-10.2029	18.4783	0.90800	0.0:1.0:0.0:0.0	.	423;294;423;423	A6NHN2;Q4VXB0;Q9HBD1;Q9HBD1-4	.;.;RC3H2_HUMAN;.	R	423;423;294;423;423;423	ENSP00000362774:G423R;ENSP00000349783:G423R;ENSP00000411767:G423R;ENSP00000362769:G423R;ENSP00000335150:G423R	ENSP00000335150:G423R	G	-	1	0	RC3H2	124679629	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	6.043000	0.71004	2.627000	0.88993	0.637000	0.83480	GGG	.	.	none		0.418	RC3H2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053966.1	NM_018835	
C10orf71	118461	hgsc.bcm.edu	37	10	50533237	50533237	+	Missense_Mutation	SNP	G	G	A	rs12217617	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:50533237G>A	ENST00000374144.3	+	3	2935	c.2647G>A	c.(2647-2649)Gac>Aac	p.D883N	C10orf71_ENST00000323868.4_Intron			Q711Q0	CJ071_HUMAN	chromosome 10 open reading frame 71	883			D -> N (in dbSNP:rs12217617). {ECO:0000269|PubMed:17974005}.							endometrium(1)	1						GTCCTTGGAGGACTCCCTCAG	0.517													G|||	864	0.172524	0.0893	0.2594	5008	,	,		20741	0.3085		0.1481	False		,,,				2504	0.1084				p.D883N		Atlas-SNP	.											.	C10orf71	179	.	0			c.G2647A						PASS	.	G	ASN/ASP,	153,1231		8,137,547	91.0	85.0	87.0		2647,	2.9	0.4	10	dbSNP_120	87	492,2690		32,428,1131	yes	missense,intron	C10orf71	NM_001135196.1,NM_199459.3	23,	40,565,1678	AA,AG,GG		15.462,11.0549,14.1261	,	883/1436,	50533237	645,3921	692	1591	2283	SO:0001583	missense	118461	exon3			TTGGAGGACTCCC	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.2647G>A	10.37:g.50533237G>A	ENSP00000363259:p.Asp883Asn	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	58	26	0.448276	NM_001135196	A0AVL8	Missense_Mutation	SNP	ENST00000374144.3	37	CCDS44387.1	469	0.21474358974358973	62	0.12601626016260162	90	0.24861878453038674	200	0.34965034965034963	117	0.15435356200527706	G	13.72	2.321098	0.41096	0.110549	0.15462	ENSG00000177354	ENST00000374144	T	0.04706	3.57	5.17	2.91	0.33838	.	0.782162	0.10403	U	0.678855	T	0.00012	0.0000	L	0.27053	0.805	0.58432	P	1.0000000000287557E-6	.	.	.	.	.	.	T	0.51996	-0.8634	7	0.35671	T	0.21	.	9.1161	0.36758	0.0876:0.0:0.7585:0.1539	rs12217617;rs52791677;rs12217617	.	.	.	N	883	ENSP00000363259:D883N	ENSP00000363259:D883N	D	+	1	0	C10orf71	50203243	0.994000	0.37717	0.431000	0.26735	0.347000	0.29111	3.362000	0.52314	1.149000	0.42402	0.491000	0.48974	GAC	G|0.803;A|0.197	0.197	strong		0.517	C10orf71-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047984.2	NM_199459	
KDM2B	84678	hgsc.bcm.edu	37	12	122018761	122018761	+	Missense_Mutation	SNP	T	T	C	rs191586330	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:122018761T>C	ENST00000377071.4	-	1	128	c.56A>G	c.(55-57)cAt>cGt	p.H19R	RP13-941N14.1_ENST00000541574.1_lincRNA|KDM2B_ENST00000377069.4_5'Flank|KDM2B_ENST00000538046.2_Missense_Mutation_p.H19R|KDM2B_ENST00000536437.1_5'UTR	NM_032590.4	NP_115979.3	Q8NHM5	KDM2B_HUMAN	lysine (K)-specific demethylase 2B	19					embryonic camera-type eye morphogenesis (GO:0048596)|forebrain development (GO:0030900)|fourth ventricle development (GO:0021592)|hindbrain development (GO:0030902)|histone demethylation (GO:0016577)|histone H2A monoubiquitination (GO:0035518)|initiation of neural tube closure (GO:0021993)|lateral ventricle development (GO:0021670)|midbrain development (GO:0030901)|midbrain-hindbrain boundary morphogenesis (GO:0021555)|negative regulation of neural precursor cell proliferation (GO:2000178)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|spermatogenesis (GO:0007283)|third ventricle development (GO:0021678)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone demethylase activity (GO:0032452)|histone demethylase activity (H3-K36 specific) (GO:0051864)|rRNA binding (GO:0019843)|zinc ion binding (GO:0008270)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	19						TTCTGCTGCATGTCTTTTTCG	0.483													T|||	11	0.00219649	0.0015	0.0043	5008	,	,		15136	0.0		0.005	False		,,,				2504	0.001				p.H19R		Atlas-SNP	.											.	KDM2B	218	.	0			c.A56G						PASS	.	T	ARG/HIS	7,3715		0,7,1854	146.0	146.0	146.0		56	-1.0	0.8	12		146	55,8117		0,55,4031	yes	missense	KDM2B	NM_032590.4	29	0,62,5885	CC,CT,TT		0.673,0.1881,0.5213	benign	19/1337	122018761	62,11832	1861	4086	5947	SO:0001583	missense	84678	exon1			GCTGCATGTCTTT	AJ459424	CCDS41849.1, CCDS41850.1	12q24.31	2014-02-18	2009-04-06	2009-04-06	ENSG00000089094	ENSG00000089094		"""F-boxes / Leucine-rich repeats"", ""Chromatin-modifying enzymes / K-demethylases"""	13610	protein-coding gene	gene with protein product	"""jumonji C domain-containing histone demethylase 1B"""	609078	"""F-box and leucine-rich repeat protein 10"""	FBXL10		10799292	Standard	NM_032590		Approved	PCCX2, CXXC2, Fbl10, JHDM1B	uc001uat.3	Q8NHM5	OTTHUMG00000169071	ENST00000377071.4:c.56A>G	12.37:g.122018761T>C	ENSP00000366271:p.His19Arg	Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	172	78	0.453488	NM_032590	A8MRS1|Q8NCI2|Q96HC7|Q96SL0|Q96T03|Q9NS96|Q9UF75	Missense_Mutation	SNP	ENST00000377071.4	37	CCDS41850.1	5	0.0022893772893772895	0	0.0	0	0.0	0	0.0	5	0.006596306068601583	T	9.028	0.986489	0.18889	0.001881	0.00673	ENSG00000089094	ENST00000397480;ENST00000377071;ENST00000397478;ENST00000261824	T	0.21191	2.02	4.22	-0.984	0.10259	.	6.934330	0.00166	N	0.000000	T	0.07818	0.0196	N	0.08118	0	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.27905	-1.0060	10	0.87932	D	0	2.4562	3.1302	0.06420	0.1837:0.3182:0.0:0.4981	.	19;19	E7EML5;Q8NHM5	.;KDM2B_HUMAN	R	19	ENSP00000366271:H19R	ENSP00000261824:H19R	H	-	2	0	KDM2B	120503144	0.009000	0.17119	0.815000	0.32552	0.236000	0.25371	-0.146000	0.10250	-0.042000	0.13535	0.379000	0.24179	CAT	T|0.997;C|0.003	0.003	strong		0.483	KDM2B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000402132.2	NM_032590	
PTK2B	2185	hgsc.bcm.edu	37	8	27293865	27293865	+	Splice_Site	SNP	C	C	T	rs7005936	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:27293865C>T	ENST00000397501.1	+	20	2149	c.1341C>T	c.(1339-1341)caC>caT	p.H447H	PTK2B_ENST00000517339.1_Splice_Site_p.H447H|PTK2B_ENST00000346049.5_Splice_Site_p.H447H|PTK2B_ENST00000544172.1_Splice_Site_p.H447H|PTK2B_ENST00000420218.2_Splice_Site_p.H447H|PTK2B_ENST00000338238.4_Splice_Site_p.H447H|PTK2B_ENST00000397497.4_Splice_Site_p.H193H	NM_173174.2	NP_775266.1	Q14289	FAK2_HUMAN	protein tyrosine kinase 2 beta	447	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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)	ACACAAATCACGTGAGTTCTA	0.498													C|||	1854	0.370208	0.4607	0.3804	5008	,	,		21147	0.1954		0.3867	False		,,,				2504	0.4039				p.H447H		Atlas-SNP	.											PTK2B_ENST00000544172,brain,glioma,0,6	PTK2B	304	6	0			c.C1341T						PASS	.	C	,,,	1959,2447	554.2+/-379.0	444,1071,688	250.0	227.0	235.0		1341,1341,1341,1341	-0.6	1.0	8	dbSNP_116	235	3396,5204	502.2+/-375.6	689,2018,1593	yes	coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice	PTK2B	NM_004103.4,NM_173174.2,NM_173175.2,NM_173176.2	,,,	1133,3089,2281	TT,TC,CC		39.4884,44.4621,41.1733	,,,	447/1010,447/1010,447/968,447/1010	27293865	5355,7651	2203	4300	6503	SO:0001630	splice_region_variant	2185	exon20			AAATCACGTGAGT	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.1341+1C>T	8.37:g.27293865C>T		Somatic	342	0	0		WXS	Illumina HiSeq	Phase_I	275	45	0.163636	NM_173174	D3DST0|Q13475|Q14290|Q16709|Q6PID4	Silent	SNP	ENST00000397501.1	37	CCDS6057.1																																																																																			C|0.638;T|0.362	0.362	strong		0.498	PTK2B-009	PUTATIVE	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219916.1	NM_004103	Silent
KRTAP10-2	386679	hgsc.bcm.edu	37	21	45971162	45971162	+	Silent	SNP	C	C	T	rs199922020	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:45971162C>T	ENST00000391621.1	-	1	226	c.180G>A	c.(178-180)gcG>gcA	p.A60A	TSPEAR_ENST00000397916.1_Intron|TSPEAR_ENST00000323084.4_Intron|KRTAP10-2_ENST00000498210.1_Intron	NM_198693.2	NP_941966.1	P60368	KR102_HUMAN	keratin associated protein 10-2	60	22 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				large_intestine(1)|lung(4)|skin(1)	6						GCTCACAGGCCGCCTGGCAGC	0.706																																					p.A60A		Atlas-SNP	.											KRTAP10-2,colon,carcinoma,0,1	KRTAP10-2	21	1	0			c.G180A						scavenged	.																																			SO:0001819	synonymous_variant	386679	exon1			ACAGGCCGCCTGG	AJ566381	CCDS42955.1	21q22.3	2007-10-05			ENSG00000205445	ENSG00000205445		"""Keratin associated proteins"""	22967	protein-coding gene	gene with protein product				KRTAP18-2			Standard	NM_198693		Approved	KAP10.2, KAP18.2	uc002zfi.1	P60368	OTTHUMG00000057625	ENST00000391621.1:c.180G>A	21.37:g.45971162C>T		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	131	37	0.282443	NM_198693	Q70LJ5	Silent	SNP	ENST00000391621.1	37	CCDS42955.1																																																																																			.	.	weak		0.706	KRTAP10-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128027.1		
KRTAP3-3	85293	hgsc.bcm.edu	37	17	39150284	39150284	+	Silent	SNP	A	A	G	rs2010201	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	161	0	0		WXS	Illumina HiSeq	Phase_I	133	66	0.496241	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		
ABCF3	55324	hgsc.bcm.edu	37	3	183904049	183904049	+	Silent	SNP	A	A	G	rs11539876	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:183904049A>G	ENST00000429586.2	+	1	239	c.54A>G	c.(52-54)caA>caG	p.Q18Q	ABCF3_ENST00000292808.5_Silent_p.Q18Q|EIF2B5_ENST00000444495.1_Intron	NM_018358.2	NP_060828.2	Q9NUQ8	ABCF3_HUMAN	ATP-binding cassette, sub-family F (GCN20), member 3	18					defense response to virus (GO:0051607)	membrane (GO:0016020)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(2)|cervix(1)|endometrium(2)|large_intestine(5)|lung(20)|ovary(3)|prostate(5)|upper_aerodigestive_tract(1)	39	all_cancers(143;1.12e-10)|Ovarian(172;0.0339)		Epithelial(37;2.35e-34)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			TTGACGGACAAGTCTTCGACT	0.627													A|||	864	0.172524	0.0242	0.3343	5008	,	,		14981	0.3075		0.1918	False		,,,				2504	0.0992				p.Q18Q		Atlas-SNP	.											.	ABCF3	72	.	0			c.A54G						PASS	.	A		235,4171	138.0+/-173.8	7,221,1975	68.0	65.0	66.0		54	3.5	1.0	3	dbSNP_120	66	1618,6982	300.6+/-305.0	158,1302,2840	no	coding-synonymous	ABCF3	NM_018358.2		165,1523,4815	GG,GA,AA		18.814,5.3336,14.2473		18/710	183904049	1853,11153	2203	4300	6503	SO:0001819	synonymous_variant	55324	exon1			CGGACAAGTCTTC	U66685	CCDS3254.1	3q27.1	2012-05-16			ENSG00000161204	ENSG00000161204		"""ATP binding cassette transporters / subfamily F"""	72	protein-coding gene	gene with protein product						8894702	Standard	NM_018358		Approved	EST201864	uc003fmz.2	Q9NUQ8	OTTHUMG00000156824	ENST00000429586.2:c.54A>G	3.37:g.183904049A>G		Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	138	61	0.442029	NM_018358	A8K241|Q86UA2|Q8NAN1|Q96GS8|Q9H7A8	Silent	SNP	ENST00000429586.2	37	CCDS3254.1																																																																																			A|0.835;G|0.165	0.165	strong		0.627	ABCF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346047.1	NM_018358	
IGSF3	3321	hgsc.bcm.edu	37	1	117122130	117122130	+	Missense_Mutation	SNP	T	T	C	rs6703791	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:117122130T>C	ENST00000369486.3	-	10	3983	c.3218A>G	c.(3217-3219)cAa>cGa	p.Q1073R	IGSF3_ENST00000369483.1_Missense_Mutation_p.Q1093R|IGSF3_ENST00000318837.6_Missense_Mutation_p.Q1093R	NM_001007237.1	NP_001007238.1	O75054	IGSF3_HUMAN	immunoglobulin superfamily, member 3	1073	Ig-like C2-type 8.		Q -> R (in dbSNP:rs6703791).		lacrimal gland development (GO:0032808)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)				NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(31)|ovary(4)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	62	Lung SC(450;0.225)	all_cancers(81;1.24e-06)|all_epithelial(167;4.85e-07)|all_lung(203;1.66e-06)|Lung NSC(69;1.11e-05)		Lung(183;0.0142)|Colorectal(144;0.0929)|LUSC - Lung squamous cell carcinoma(189;0.108)|COAD - Colon adenocarcinoma(174;0.139)|all cancers(265;0.159)|Epithelial(280;0.166)		GCCTGTATCTTGGGGGCTTGC	0.632													C|||	1724	0.344249	0.3472	0.304	5008	,	,		19301	0.5169		0.167	False		,,,				2504	0.3732				p.Q1093R		Atlas-SNP	.											.	IGSF3	294	.	0			c.A3278G						PASS	.	C	ARG/GLN,ARG/GLN	1555,2851	667.5+/-401.9	285,985,933	47.0	50.0	49.0		3218,3278	-4.5	0.0	1	dbSNP_116	49	1560,7040	743.0+/-407.2	137,1286,2877	yes	missense,missense	IGSF3	NM_001007237.1,NM_001542.2	43,43	422,2271,3810	CC,CT,TT		18.1395,35.2928,23.9505	benign,benign	1073/1195,1093/1215	117122130	3115,9891	2203	4300	6503	SO:0001583	missense	3321	exon11			GTATCTTGGGGGC	AF031174	CCDS30813.1, CCDS30814.1	1p13	2013-01-29			ENSG00000143061	ENSG00000143061		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5950	protein-coding gene	gene with protein product		603491				9790749	Standard	NM_001007237		Approved	V8, EWI-3, MGC117164	uc031pnr.1	O75054	OTTHUMG00000022751	ENST00000369486.3:c.3218A>G	1.37:g.117122130T>C	ENSP00000358498:p.Gln1073Arg	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	70	23	0.328571	NM_001542	A6NJZ6|A6NMC7	Missense_Mutation	SNP	ENST00000369486.3	37	CCDS30813.1	720	0.32967032967032966	175	0.3556910569105691	106	0.292817679558011	316	0.5524475524475524	123	0.16226912928759896	C	0.016	-1.511898	0.00984	0.352928	0.181395	ENSG00000143061	ENST00000369486;ENST00000369483;ENST00000318837	T;T;T	0.21191	2.02;2.02;2.02	4.67	-4.48	0.03515	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	1.403970	0.04240	N	0.336820	T	0.03827	0.0108	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	0.31364	-0.9946	9	0.16420	T	0.52	-7.9962	15.5741	0.76362	0.0:0.1649:0.0:0.8351	rs6703791;rs56967300;rs6703791	1073;1093	O75054;A6NJZ6	IGSF3_HUMAN;.	R	1073;1093;1093	ENSP00000358498:Q1073R;ENSP00000358495:Q1093R;ENSP00000321184:Q1093R	ENSP00000321184:Q1093R	Q	-	2	0	IGSF3	116923653	0.000000	0.05858	0.001000	0.08648	0.063000	0.16089	-0.212000	0.09319	-1.780000	0.01279	-1.403000	0.01137	CAA	T|0.725;C|0.275	0.275	strong		0.632	IGSF3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000059040.1	NM_001542	
ZNF334	55713	hgsc.bcm.edu	37	20	45131665	45131665	+	Missense_Mutation	SNP	T	T	C	rs111517766	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:45131665T>C	ENST00000347606.4	-	5	495	c.313A>G	c.(313-315)Aac>Gac	p.N105D	ZNF334_ENST00000457685.2_Missense_Mutation_p.N67D|ZNF334_ENST00000593880.1_Missense_Mutation_p.N128D	NM_018102.4	NP_060572.3	Q9HCZ1	ZN334_HUMAN	zinc finger protein 334	105					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	32		Myeloproliferative disorder(115;0.0122)				AGTGTTTTGTTGCTGAAGAAT	0.343													T|||	44	0.00878594	0.0174	0.0058	5008	,	,		20363	0.0		0.0109	False		,,,				2504	0.0061				p.N105D		Atlas-SNP	.											ZNF334,NS,carcinoma,+1,1	ZNF334	101	1	0			c.A313G						PASS	.	T	ASP/ASN,ASP/ASN	56,4350	54.2+/-90.2	1,54,2148	103.0	86.0	92.0		313,199	0.6	0.0	20	dbSNP_132	92	115,8485	60.6+/-122.4	1,113,4186	yes	missense,missense	ZNF334	NM_018102.3,NM_199441.1	23,23	2,167,6334	CC,CT,TT		1.3372,1.271,1.3148	possibly-damaging,possibly-damaging	105/681,67/643	45131665	171,12835	2203	4300	6503	SO:0001583	missense	55713	exon5			TTTTGTTGCTGAA	AK001331	CCDS33480.1, CCDS74736.1	20q13.12	2013-09-20			ENSG00000198185	ENSG00000198185		"""Zinc fingers, C2H2-type"", ""-"""	15806	protein-coding gene	gene with protein product							Standard	NM_018102		Approved	bA179N14.1	uc002xsc.4	Q9HCZ1	OTTHUMG00000032654	ENST00000347606.4:c.313A>G	20.37:g.45131665T>C	ENSP00000255129:p.Asn105Asp	Somatic	331	0	0		WXS	Illumina HiSeq	Phase_I	301	137	0.45515	NM_018102	Q5T6U2|Q9NVW4	Missense_Mutation	SNP	ENST00000347606.4	37	CCDS33480.1	21	0.009615384615384616	9	0.018292682926829267	3	0.008287292817679558	0	0.0	9	0.011873350923482849	T	13.62	2.290638	0.40494	0.01271	0.013372	ENSG00000198185	ENST00000457685;ENST00000347606	T;T	0.08458	3.33;3.09	3.26	0.606	0.17559	.	.	.	.	.	T	0.02083	0.0065	L	0.31664	0.95	0.09310	N	1	B;B;B	0.29432	0.148;0.148;0.244	B;B;B	0.22386	0.027;0.027;0.039	T	0.44298	-0.9337	9	0.14656	T	0.56	.	4.6764	0.12713	0.186:0.0:0.1904:0.6236	.	67;105;128	B3KQ93;Q9HCZ1;Q8N3P8	.;ZN334_HUMAN;.	D	67;105	ENSP00000402582:N67D;ENSP00000255129:N105D	ENSP00000255129:N105D	N	-	1	0	ZNF334	44565072	0.000000	0.05858	0.043000	0.18650	0.633000	0.38033	0.325000	0.19628	0.424000	0.26061	0.482000	0.46254	AAC	T|0.986;C|0.014	0.014	strong		0.343	ZNF334-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079575.1		
OPN1SW	611	hgsc.bcm.edu	37	7	128415195	128415195	+	Silent	SNP	T	T	G	rs1799922	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:128415195T>G	ENST00000249389.2	-	2	365	c.366A>C	c.(364-366)ggA>ggC	p.G122G		NM_001708.2	NP_001699.1	P03999	OPSB_HUMAN	opsin 1 (cone pigments), short-wave-sensitive	122					phototransduction (GO:0007602)|phototransduction, visible light (GO:0007603)|protein-chromophore linkage (GO:0018298)|retinoid metabolic process (GO:0001523)|signal transduction (GO:0007165)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|photoreceptor outer segment membrane (GO:0042622)	G-protein coupled receptor activity (GO:0004930)|photoreceptor activity (GO:0009881)|receptor activity (GO:0004872)	p.G122G(1)		NS(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(10)|stomach(1)	19						CCAGTGACCATCCTGTAACCA	0.567													G|||	937	0.187101	0.112	0.2291	5008	,	,		21414	0.0675		0.4095	False		,,,				2504	0.1534				p.G122G		Atlas-SNP	.											OPN1SW,NS,carcinoma,0,1	OPN1SW	52	1	1	Substitution - coding silent(1)	stomach(1)	c.A366C						PASS	.	G		651,3755	765.7+/-413.4	47,557,1599	65.0	52.0	56.0		366	0.8	1.0	7	dbSNP_89	56	3471,5129	634.5+/-398.9	706,2059,1535	no	coding-synonymous	OPN1SW	NM_001708.2		753,2616,3134	GG,GT,TT		40.3605,14.7753,31.6931		122/349	128415195	4122,8884	2203	4300	6503	SO:0001819	synonymous_variant	611	exon2			TGACCATCCTGTA	U53874	CCDS5806.1	7q31.3-q32	2013-01-08	2008-04-16		ENSG00000128617	ENSG00000128617		"""GPCR / Class A : Opsin receptors"""	1012	protein-coding gene	gene with protein product	"""color blindness, tritan"", ""blue-sensitive opsin"""	613522	"""blue cone photoreceptor pigment"""	BCP		2937147, 8270261	Standard	NM_001708		Approved	BOP, CBT	uc003vnt.4	P03999	OTTHUMG00000158311	ENST00000249389.2:c.366A>C	7.37:g.128415195T>G		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	49	22	0.44898	NM_001708	Q13877	Silent	SNP	ENST00000249389.2	37	CCDS5806.1																																																																																			T|0.710;G|0.290	0.290	strong		0.567	OPN1SW-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350655.1	NM_001708	
PNPLA6	10908	hgsc.bcm.edu	37	19	7606908	7606908	+	Missense_Mutation	SNP	G	G	C	rs17854645	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:7606908G>C	ENST00000221249.6	+	13	1521	c.1090G>C	c.(1090-1092)Gcc>Ccc	p.A364P	PNPLA6_ENST00000545201.2_Missense_Mutation_p.A364P|PNPLA6_ENST00000600737.1_Missense_Mutation_p.A403P|PNPLA6_ENST00000450331.3_Missense_Mutation_p.A364P|PNPLA6_ENST00000414982.3_Missense_Mutation_p.A412P	NM_006702.4	NP_006693.3	Q8IY17	PLPL6_HUMAN	patatin-like phospholipase domain containing 6	403					angiogenesis (GO:0001525)|cell death (GO:0008219)|lipid catabolic process (GO:0016042)|organ morphogenesis (GO:0009887)|phosphatidylcholine metabolic process (GO:0046470)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	lysophospholipase activity (GO:0004622)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(6)|lung(14)|ovary(3)|stomach(1)|upper_aerodigestive_tract(1)	35						AACCCCCTCGGCCCCTCTGCT	0.627													G|||	593	0.118411	0.1036	0.1268	5008	,	,		14735	0.002		0.2087	False		,,,				2504	0.1595				p.A412P		Atlas-SNP	.											.	PNPLA6	163	.	0			c.G1234C						PASS	.	G	PRO/ALA,PRO/ALA,PRO/ALA,PRO/ALA,PRO/ALA	454,3952	211.8+/-231.9	27,400,1776	53.0	53.0	53.0		1234,1090,1090,1207,1090	4.6	1.0	19	dbSNP_123	53	1863,6737	321.2+/-315.0	188,1487,2625	yes	missense,missense,missense,missense,missense	PNPLA6	NM_001166111.1,NM_001166112.1,NM_001166113.1,NM_001166114.1,NM_006702.4	27,27,27,27,27	215,1887,4401	CC,CG,GG		21.6628,10.3041,17.8149	benign,benign,benign,benign,benign	412/1376,364/1301,364/1328,403/1366,364/1328	7606908	2317,10689	2203	4300	6503	SO:0001583	missense	10908	exon12			CCCTCGGCCCCTC	AJ004832	CCDS32891.1, CCDS54206.1, CCDS54207.1, CCDS59343.1	19p13.2	2013-09-11						"""Patatin-like phospholipase domain containing"""	16268	protein-coding gene	gene with protein product	"""neuropathy target esterase"""	603197				9576844, 16799181, 19029121	Standard	NM_006702		Approved	NTE, sws, iPLA2delta, SPG39	uc010xjq.2	Q8IY17		ENST00000221249.6:c.1090G>C	19.37:g.7606908G>C	ENSP00000221249:p.Ala364Pro	Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	24	8	0.333333	NM_001166111	A6NGQ0|B4DFB9|B7Z7T2|F5H5K9|J3KQS3|O60859|Q86W58|Q9UG58	Missense_Mutation	SNP	ENST00000221249.6	37	CCDS32891.1	267	0.12225274725274725	54	0.10975609756097561	55	0.15193370165745856	0	0.0	158	0.20844327176781002	G	13.94	2.387933	0.42308	0.103041	0.216628	ENSG00000032444	ENST00000221249;ENST00000545201;ENST00000414982;ENST00000544207;ENST00000450331	T;T;T;T	0.04194	3.7;3.7;3.68;3.7	5.63	4.57	0.56435	.	0.331114	0.32548	N	0.005947	T	0.00012	0.0000	N	0.16478	0.41	0.27854	P	0.9406483	B;B;B;B	0.11235	0.003;0.004;0.002;0.004	B;B;B;B	0.15052	0.001;0.012;0.007;0.003	T	0.51236	-0.8731	9	0.26408	T	0.33	.	12.376	0.55281	0.0:0.1695:0.8305:0.0	rs17854645	403;364;403;364	Q8IY17;F5H5K9;Q8IY17-3;Q8IY17-2	PLPL6_HUMAN;.;.;.	P	364;364;412;301;364	ENSP00000221249:A364P;ENSP00000443323:A364P;ENSP00000407509:A412P;ENSP00000394348:A364P	ENSP00000221249:A364P	A	+	1	0	PNPLA6	7512908	0.246000	0.23909	0.960000	0.40013	0.961000	0.63080	2.817000	0.48034	1.343000	0.45638	0.655000	0.94253	GCC	G|0.837;C|0.163	0.163	strong		0.627	PNPLA6-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459275.1	NM_006702	
MUC4	4585	hgsc.bcm.edu	37	3	195511204	195511204	+	Missense_Mutation	SNP	T	T	G	rs423290	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195511204T>G	ENST00000463781.3	-	2	7706	c.7247A>C	c.(7246-7248)cAt>cCt	p.H2416P	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.H2416P	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.H2416P(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)		GACAGGAAGATGGGTGGCGTG	0.592													.|||	175	0.0349441	0.0537	0.0288	5008	,	,		22673	0.002		0.0557	False		,,,				2504	0.0266				p.H2416P		Atlas-SNP	.											MUC4_ENST00000463781,extremity,malignant_melanoma,0,2	MUC4	1505	2	2	Substitution - Missense(2)	skin(2)	c.A7247C						scavenged	.						48.0	46.0	46.0					3																	195511204		653	1587	2240	SO:0001583	missense	4585	exon2			GGAAGATGGGTGG	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.7247A>C	3.37:g.195511204T>G	ENSP00000417498:p.His2416Pro	Somatic	211	6	0.028436		WXS	Illumina HiSeq	Phase_I	167	13	0.0778443	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	3.537	-0.094518	0.07053	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.30714	1.52;1.52	.	.	.	.	.	.	.	.	T	0.08670	0.0215	N	0.02539	-0.55	0.09310	N	1	B	0.15141	0.012	B	0.01281	0.0	T	0.27434	-1.0074	7	.	.	.	.	1.4229	0.02316	0.3314:0.0:0.3284:0.3402	.	2416	E7ESK3	.	P	2416	ENSP00000417498:H2416P;ENSP00000420243:H2416P	.	H	-	2	0	MUC4	196995599	0.004000	0.15560	0.001000	0.08648	0.000000	0.00434	-4.701000	0.00196	-0.912000	0.03837	0.000000	0.15137	CAT	T|0.987;G|0.013	0.013	strong		0.592	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
PIPOX	51268	hgsc.bcm.edu	37	17	27371919	27371919	+	Missense_Mutation	SNP	C	C	T	rs543013733		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:27371919C>T	ENST00000323372.4	+	2	483	c.157C>T	c.(157-159)Cgg>Tgg	p.R53W	PIPOX_ENST00000583215.1_3'UTR	NM_016518.2	NP_057602.2	Q9P0Z9	SOX_HUMAN	pipecolic acid oxidase	53					L-lysine catabolic process to acetyl-CoA via L-pipecolate (GO:0033514)|oxidation-reduction process (GO:0055114)|tetrahydrofolate metabolic process (GO:0046653)	peroxisome (GO:0005777)	L-pipecolate oxidase activity (GO:0050031)|receptor binding (GO:0005102)|sarcosine oxidase activity (GO:0008115)			endometrium(2)|large_intestine(4)|lung(1)|prostate(1)|skin(1)|urinary_tract(1)	10	Lung NSC(42;0.015)		Epithelial(11;9.87e-06)|BRCA - Breast invasive adenocarcinoma(11;3.92e-05)|all cancers(11;5.59e-05)|Colorectal(6;0.0102)|COAD - Colon adenocarcinoma(6;0.031)		Glycine(DB00145)	TGGACAAAGCCGGATAATCCG	0.517																																					p.R53W		Atlas-SNP	.											PIPOX,NS,carcinoma,-1,1	PIPOX	42	1	0			c.C157T						PASS	.						123.0	108.0	113.0					17																	27371919		2203	4300	6503	SO:0001583	missense	51268	exon2			CAAAGCCGGATAA	AF134593	CCDS11248.1	17p13.2	2008-07-18			ENSG00000179761	ENSG00000179761			17804	protein-coding gene	gene with protein product	"""L-pipecolic acid oxidase"""					10772957, 10642506	Standard	NM_016518		Approved	LPIPOX	uc002hdr.1	Q9P0Z9	OTTHUMG00000132679	ENST00000323372.4:c.157C>T	17.37:g.27371919C>T	ENSP00000317721:p.Arg53Trp	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	108	18	0.166667	NM_016518	B3KNH0|Q96H28|Q9C070	Missense_Mutation	SNP	ENST00000323372.4	37	CCDS11248.1	.	.	.	.	.	.	.	.	.	.	C	24.0	4.484929	0.84854	.	.	ENSG00000179761	ENST00000323372	D	0.81908	-1.55	5.8	4.82	0.62117	FAD dependent oxidoreductase (1);	0.167524	0.51477	D	0.000093	D	0.90556	0.7040	M	0.90542	3.125	0.80722	D	1	D	0.67145	0.996	P	0.58520	0.84	D	0.91764	0.5422	10	0.66056	D	0.02	-12.3601	13.0057	0.58703	0.0:0.9201:0.0:0.0798	.	53	Q9P0Z9	SOX_HUMAN	W	53	ENSP00000317721:R53W	ENSP00000317721:R53W	R	+	1	2	PIPOX	24396045	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.408000	0.44574	2.740000	0.93945	0.650000	0.86243	CGG	.	.	none		0.517	PIPOX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255954.1	NM_016518	
MED13L	23389	hgsc.bcm.edu	37	12	116457158	116457158	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:116457158C>T	ENST00000281928.3	-	7	1086	c.880G>A	c.(880-882)Gtt>Att	p.V294I		NM_015335.4	NP_056150.1	Q71F56	MD13L_HUMAN	mediator complex subunit 13-like	294						mediator complex (GO:0016592)	RNA polymerase II transcription cofactor activity (GO:0001104)			NS(2)|breast(1)|endometrium(9)|kidney(3)|large_intestine(18)|lung(34)|ovary(4)|prostate(4)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	85	all_neural(191;0.117)|Medulloblastoma(191;0.163)			BRCA - Breast invasive adenocarcinoma(302;0.0407)		CTCTGAGGAACCGGGATGTCA	0.498																																					p.V294I		Atlas-SNP	.											MED13L,NS,carcinoma,0,1	MED13L	193	1	0			c.G880A						scavenged	.						129.0	116.0	121.0					12																	116457158		2203	4300	6503	SO:0001583	missense	23389	exon7			GAGGAACCGGGAT	AB028948	CCDS9177.1	12q24.22	2010-07-29	2007-07-30	2007-07-30	ENSG00000123066	ENSG00000123066			22962	protein-coding gene	gene with protein product		608771	"""thyroid hormone receptor associated protein 2"""	THRAP2			Standard	NM_015335		Approved	KIAA1025, TRAP240L	uc001tvw.3	Q71F56	OTTHUMG00000169404	ENST00000281928.3:c.880G>A	12.37:g.116457158C>T	ENSP00000281928:p.Val294Ile	Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	132	3	0.0227273	NM_015335	A1L469|Q68DN4|Q9H8C0|Q9NSY9|Q9UFD8|Q9UPX5	Missense_Mutation	SNP	ENST00000281928.3	37	CCDS9177.1	.	.	.	.	.	.	.	.	.	.	C	13.75	2.329077	0.41197	.	.	ENSG00000123066	ENST00000281928	T	0.77098	-1.07	5.32	5.32	0.75619	Mediator complex, subunit Med13, N-terminal, metazoa/fungi (1);	0.158124	0.43579	D	0.000542	T	0.64638	0.2616	L	0.38175	1.15	0.23180	N	0.998161	B	0.06786	0.001	B	0.12156	0.007	T	0.45220	-0.9276	10	0.19590	T	0.45	.	7.7413	0.28843	0.0:0.7272:0.1515:0.1213	.	294	Q71F56	MD13L_HUMAN	I	294	ENSP00000281928:V294I	ENSP00000281928:V294I	V	-	1	0	MED13L	114941541	0.082000	0.21442	0.999000	0.59377	0.991000	0.79684	0.483000	0.22292	2.773000	0.95371	0.585000	0.79938	GTT	.	.	none		0.498	MED13L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403879.3		
SLC35G5	83650	hgsc.bcm.edu	37	8	11189591	11189591	+	Missense_Mutation	SNP	C	C	T	rs62488717		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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						PASS	.						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	76	0	0		WXS	Illumina HiSeq	Phase_I	106	40	0.377358	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	
KIAA0825	285600	hgsc.bcm.edu	37	5	93812885	93812885	+	Silent	SNP	C	C	T	rs10057902	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:93812885C>T	ENST00000513200.3	-	6	1230	c.1158G>A	c.(1156-1158)gaG>gaA	p.E386E	KIAA0825_ENST00000312498.7_Silent_p.E386E|KIAA0825_ENST00000427991.2_Silent_p.E386E	NM_001145678.1	NP_001139150.1	Q8IV33	K0825_HUMAN	KIAA0825	386										breast(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(1)|pancreas(1)|prostate(1)|skin(1)	13						CCATTACAACCTCTCTATCGG	0.313													T|||	684	0.136581	0.326	0.0764	5008	,	,		17817	0.0843		0.0239	False		,,,				2504	0.093				p.E386E		Atlas-SNP	.											.	KIAA0825	172	.	0			c.G1158A						PASS	.	T		391,993		57,277,358	236.0	184.0	200.0		1158	3.3	0.0	5	dbSNP_119	200	81,3097		0,81,1508	no	coding-synonymous	KIAA0825	NM_001145678.1		57,358,1866	TT,TC,CC		2.5488,28.2514,10.3463		386/1276	93812885	472,4090	692	1589	2281	SO:0001819	synonymous_variant	285600	exon7			TACAACCTCTCTA	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.1158G>A	5.37:g.93812885C>T		Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	145	65	0.448276	NM_001145678	O94914|Q6ZNN2	Silent	SNP	ENST00000513200.3	37																																																																																				C|0.879;T|0.121	0.121	strong		0.313	KIAA0825-001	KNOWN	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000254102.5	NM_173665	
EPS15	2060	hgsc.bcm.edu	37	1	51873951	51873951	+	Silent	SNP	G	G	A	rs1065754	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:51873951G>A	ENST00000371733.3	-	15	1425	c.1329C>T	c.(1327-1329)taC>taT	p.Y443Y	EPS15_ENST00000493793.1_5'UTR|EPS15_ENST00000371730.2_Intron|EPS15_ENST00000396122.4_Silent_p.Y120Y	NM_001981.2	NP_001972.1	P42566	EPS15_HUMAN	epidermal growth factor receptor pathway substrate 15	443					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						ATTCTTCTTCGTAAGTGGAGA	0.423			T	MLL	ALL								A|||	4120	0.822684	0.8941	0.7622	5008	,	,		17874	0.9921		0.6223	False		,,,				2504	0.8006				p.Y443Y		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.C1329T						PASS	.	A	,	3854,552	250.0+/-257.2	1681,492,30	144.0	139.0	141.0		387,1329	-1.7	1.0	1	dbSNP_86	141	5631,2969	460.6+/-365.2	1838,1955,507	no	coding-synonymous,coding-synonymous	EPS15	NM_001159969.1,NM_001981.2	,	3519,2447,537	AA,AG,GG		34.5233,12.5284,27.0721	,	129/583,443/897	51873951	9485,3521	2203	4300	6503	SO:0001819	synonymous_variant	2060	exon15			TTCTTCGTAAGTG	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.1329C>T	1.37:g.51873951G>A		Somatic	340	0	0		WXS	Illumina HiSeq	Phase_I	266	263	0.988722	NM_001981	B2R8J7|D3DPJ2|Q5SRH4	Silent	SNP	ENST00000371733.3	37	CCDS557.1																																																																																			G|0.242;A|0.758	0.758	strong		0.423	EPS15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022422.1	NM_001981	
ATMIN	23300	hgsc.bcm.edu	37	16	81077204	81077204	+	Silent	SNP	T	T	A	rs16954513	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:81077204T>A	ENST00000299575.4	+	4	1125	c.1101T>A	c.(1099-1101)ccT>ccA	p.P367P	ATMIN_ENST00000539819.1_3'UTR|ATMIN_ENST00000564241.1_Silent_p.P211P|ATMIN_ENST00000566488.1_Silent_p.P211P	NM_015251.2	NP_056066.2	O43313	ATMIN_HUMAN	ATM interactor	367	Required for formation of RAD51 foci.				cellular response to DNA damage stimulus (GO:0006974)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	dynein binding (GO:0045502)|metal ion binding (GO:0046872)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(9)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	20						AGAGCCTACCTCTTTTCAAAA	0.463													T|||	274	0.0547125	0.1097	0.0447	5008	,	,		20369	0.001		0.0815	False		,,,				2504	0.0153				p.P367P		Atlas-SNP	.											.	ATMIN	50	.	0			c.T1101A						PASS	.	T		420,3984	197.7+/-221.8	19,382,1801	54.0	53.0	54.0		1101	2.2	0.9	16	dbSNP_123	54	574,8026	151.5+/-206.2	17,540,3743	no	coding-synonymous	ATMIN	NM_015251.2		36,922,5544	AA,AT,TT		6.6744,9.5368,7.6438		367/824	81077204	994,12010	2202	4300	6502	SO:0001819	synonymous_variant	23300	exon4			CCTACCTCTTTTC	BC002701	CCDS32494.1, CCDS73917.1	16q23.2	2013-01-07			ENSG00000166454	ENSG00000166454		"""Zinc fingers, C2H2-type"""	29034	protein-coding gene	gene with protein product	"""ATM/ATR-Substrate Chk2-Interacting Zn++-finger protein"", ""ATM INteracting protein"""	614693				15933716, 17525732, 19001856	Standard	XM_005255866		Approved	ASCIZ, KIAA0431, ZNF822	uc002ffz.1	O43313	OTTHUMG00000176469	ENST00000299575.4:c.1101T>A	16.37:g.81077204T>A		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	145	83	0.572414	NM_015251	A8K4H8|Q68DC9	Silent	SNP	ENST00000299575.4	37	CCDS32494.1																																																																																			T|0.929;A|0.071	0.071	strong		0.463	ATMIN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000432140.1	NM_015251	
AAMDC	28971	hgsc.bcm.edu	37	11	77553638	77553638	+	Silent	SNP	T	T	C	rs585721	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:77553638T>C	ENST00000526415.1	+	3	269	c.96T>C	c.(94-96)ggT>ggC	p.G32G	AAMDC_ENST00000527134.1_Silent_p.G32G|AAMDC_ENST00000304716.8_Silent_p.G32G|AAMDC_ENST00000533193.1_Silent_p.G32G|RP11-91P24.7_ENST00000525594.1_RNA|AAMDC_ENST00000525409.1_Silent_p.G32G|AAMDC_ENST00000393427.2_Silent_p.G32G|AAMDC_ENST00000525034.1_Silent_p.G51G|AAMDC_ENST00000532481.1_Silent_p.G32G			Q9H7C9	AAMDC_HUMAN	adipogenesis associated, Mth938 domain containing	32	MTH138-like domain. {ECO:0000250}.				negative regulation of apoptotic process (GO:0043066)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	cytoplasm (GO:0005737)		p.G32G(1)									GGCCAGGGGGTAGTCGGACTT	0.433													C|||	1957	0.390775	0.5265	0.3948	5008	,	,		17605	0.2688		0.3688	False		,,,				2504	0.3528				p.G32G		Atlas-SNP	.											C11orf67,NS,carcinoma,0,1	.	.	1	1	Substitution - coding silent(1)	stomach(1)	c.T96C						scavenged	.	C		2296,2104	575.6+/-384.0	583,1130,487	69.0	67.0	68.0		96	-1.8	1.0	11	dbSNP_83	68	3162,5422	653.5+/-401.1	586,1990,1716	no	coding-synonymous	C11orf67	NM_024684.2		1169,3120,2203	CC,CT,TT		36.836,47.8182,42.0364		32/123	77553638	5458,7526	2200	4292	6492	SO:0001819	synonymous_variant	28971	exon2			AGGGGGTAGTCGG	BC016854	CCDS8254.1	11q14.1	2012-10-08	2012-10-08	2012-10-08	ENSG00000087884	ENSG00000087884			30205	protein-coding gene	gene with protein product			"""chromosome 11 open reading frame 67"""	C11orf67		12477932	Standard	NM_024684		Approved	PTD015, FLJ21035, CK067	uc001oyq.3	Q9H7C9	OTTHUMG00000166651	ENST00000526415.1:c.96T>C	11.37:g.77553638T>C		Somatic	72	1	0.0138889		WXS	Illumina HiSeq	Phase_I	52	34	0.653846	NM_024684	Q96AQ4|Q9Y6B1	Silent	SNP	ENST00000526415.1	37	CCDS8254.1																																																																																			T|0.588;C|0.412	0.412	strong		0.433	AAMDC-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390976.1	NM_024684	
STYXL1	51657	hgsc.bcm.edu	37	7	75659815	75659815	+	Silent	SNP	T	T	C	rs1044483	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:75659815T>C	ENST00000248600.1	-	2	369	c.27A>G	c.(25-27)ccA>ccG	p.P9P	STYXL1_ENST00000359697.3_Silent_p.P9P|STYXL1_ENST00000460184.2_5'UTR|STYXL1_ENST00000340062.5_Silent_p.P9P|STYXL1_ENST00000431581.1_Silent_p.P9P|STYXL1_ENST00000451157.1_Silent_p.P9P|STYXL1_ENST00000360591.3_Silent_p.P9P	NM_016086.2	NP_057170.1	Q9Y6J8	STYL1_HUMAN	serine/threonine/tyrosine interacting-like 1	9					intracellular signal transduction (GO:0035556)|protein dephosphorylation (GO:0006470)		protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			endometrium(1)|large_intestine(2)|lung(4)|ovary(1)|prostate(1)|skin(1)	10						AAAGCTCTGTTGGTTCACATA	0.388													N|||	2329	0.465056	0.2337	0.5836	5008	,	,		16745	0.3929		0.673	False		,,,				2504	0.5542				p.P9P		Atlas-SNP	.											.	STYXL1	35	.	0			c.A27G						PASS	.	C		1420,2986	684.8+/-404.5	238,944,1021	113.0	97.0	103.0		27	0.6	0.9	7	dbSNP_86	103	6003,2597	418.9+/-352.9	2082,1839,379	no	coding-synonymous	STYXL1	NM_016086.2		2320,2783,1400	CC,CT,TT		30.1977,32.2288,42.9263		9/314	75659815	7423,5583	2203	4300	6503	SO:0001819	synonymous_variant	51657	exon2			CTCTGTTGGTTCA	AF069762	CCDS5580.1	7q11.23	2011-06-09	2005-09-22	2005-09-22	ENSG00000127952	ENSG00000127952		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : MAP kinase phosphatases"""	18165	protein-coding gene	gene with protein product			"""dual specificity phosphatase 24 (putative)"""	DUSP24		9757831	Standard	NM_016086		Approved	MK-STYX	uc003uel.3	Q9Y6J8	OTTHUMG00000130459	ENST00000248600.1:c.27A>G	7.37:g.75659815T>C		Somatic	216	0	0		WXS	Illumina HiSeq	Phase_I	181	94	0.519337	NM_016086	Q9UBP1|Q9UK06|Q9UK07|Q9UKG2|Q9UKG3	Silent	SNP	ENST00000248600.1	37	CCDS5580.1																																																																																			T|0.452;C|0.548;A|0.000	0.548	strong		0.388	STYXL1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344825.1	NM_016086	
ALDH18A1	5832	hgsc.bcm.edu	37	10	97388162	97388162	+	Missense_Mutation	SNP	G	G	A	rs2275272	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:97388162G>A	ENST00000371224.2	-	8	1033	c.896C>T	c.(895-897)aCc>aTc	p.T299I	ALDH18A1_ENST00000371221.3_Missense_Mutation_p.T297I	NM_002860.3	NP_002851.2	P54886	P5CS_HUMAN	aldehyde dehydrogenase 18 family, member A1	299	Glutamate 5-kinase.		T -> I (in dbSNP:rs2275272). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.	T -> P (in Ref. 1; CAA64224). {ECO:0000305}.	cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|citrulline biosynthetic process (GO:0019240)|glutamate metabolic process (GO:0006536)|L-proline biosynthetic process (GO:0055129)|ornithine biosynthetic process (GO:0006592)|proline biosynthetic process (GO:0006561)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|glutamate 5-kinase activity (GO:0004349)|glutamate-5-semialdehyde dehydrogenase activity (GO:0004350)|poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(9)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	28		Colorectal(252;0.0402)		Epithelial(162;9.1e-07)|all cancers(201;2.55e-05)		TCTAGACTTGGTTCCAAATGT	0.413													G|||	359	0.0716853	0.0439	0.0922	5008	,	,		18912	0.0377		0.1421	False		,,,				2504	0.0573				p.T299I		Atlas-SNP	.											.	ALDH18A1	63	.	0			c.C896T						PASS	.	G	ILE/THR,ILE/THR	232,4174	138.4+/-174.2	6,220,1977	140.0	137.0	138.0		890,896	6.0	1.0	10	dbSNP_100	138	1084,7516	226.9+/-262.5	74,936,3290	yes	missense,missense	ALDH18A1	NM_001017423.1,NM_002860.3	89,89	80,1156,5267	AA,AG,GG		12.6047,5.2655,10.1184	benign,benign	297/794,299/796	97388162	1316,11690	2203	4300	6503	SO:0001583	missense	5832	exon8			GACTTGGTTCCAA	X94453	CCDS7443.1, CCDS31257.1	10q24.3-q24.6	2004-08-12	2004-08-12	2004-08-12	ENSG00000059573	ENSG00000059573		"""Aldehyde dehydrogenases"""	9722	protein-coding gene	gene with protein product		138250	"""pyrroline-5-carboxylate synthetase (glutamate gamma-semialdehyde synthetase)"""	GSAS, PYCS		8921385	Standard	XM_006717933		Approved	P5CS	uc001kkz.3	P54886	OTTHUMG00000018815	ENST00000371224.2:c.896C>T	10.37:g.97388162G>A	ENSP00000360268:p.Thr299Ile	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	64	18	0.28125	NM_002860	B2R5Q4|B7Z350|B7Z5X8|B7ZLP1|D3DR44|O95952|Q3KQU2|Q5T566|Q5T567|Q9UM72	Missense_Mutation	SNP	ENST00000371224.2	37	CCDS7443.1	185	0.08470695970695971	24	0.04878048780487805	37	0.10220994475138122	20	0.03496503496503497	104	0.13720316622691292	G	17.42	3.385973	0.61956	0.052655	0.126047	ENSG00000059573	ENST00000371224;ENST00000371221	T;T	0.77620	-1.11;-1.11	5.97	5.97	0.96955	Aspartate/glutamate/uridylate kinase (3);	0.047339	0.85682	D	0.000000	T	0.01627	0.0052	L	0.39397	1.21	0.09310	P	0.9999997726	B;B	0.21071	0.051;0.041	B;B	0.32583	0.148;0.091	T	0.39292	-0.9621	9	0.56958	D	0.05	-24.3606	17.9326	0.89002	0.0:0.0:1.0:0.0	rs2275272;rs17539447;rs52791494;rs60885636;rs2275272	299;297	P54886;P54886-2	P5CS_HUMAN;.	I	299;297	ENSP00000360268:T299I;ENSP00000360265:T297I	ENSP00000360265:T297I	T	-	2	0	ALDH18A1	97378152	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	6.152000	0.71812	2.836000	0.97738	0.655000	0.94253	ACC	G|0.912;A|0.088	0.088	strong		0.413	ALDH18A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049552.1	NM_002860	
DUOX1	53905	hgsc.bcm.edu	37	15	45444133	45444133	+	Missense_Mutation	SNP	T	T	C	rs16939752	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:45444133T>C	ENST00000321429.4	+	25	3483	c.3076T>C	c.(3076-3078)Tgt>Cgt	p.C1026R	DUOX1_ENST00000561166.1_Missense_Mutation_p.C672R|DUOX1_ENST00000389037.3_Missense_Mutation_p.C1026R|CTD-2651B20.1_ENST00000558039.1_lincRNA	NM_017434.3	NP_059130.2	Q9NRD9	DUOX1_HUMAN	dual oxidase 1	1026	Interaction with TXNDC11. {ECO:0000250}.		C -> R (in dbSNP:rs16939752). {ECO:0000269|PubMed:14702039}.		cuticle development (GO:0042335)|cytokine-mediated signaling pathway (GO:0019221)|hormone biosynthetic process (GO:0042446)|hydrogen peroxide biosynthetic process (GO:0050665)|hydrogen peroxide catabolic process (GO:0042744)|oxidation-reduction process (GO:0055114)|response to cAMP (GO:0051591)|superoxide anion generation (GO:0042554)|thyroid hormone generation (GO:0006590)	apical plasma membrane (GO:0016324)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|heme binding (GO:0020037)|NAD(P)H oxidase activity (GO:0016174)|NADP binding (GO:0050661)|peroxidase activity (GO:0004601)	p.C1026R(1)		breast(2)|central_nervous_system(1)|endometrium(5)|kidney(5)|large_intestine(13)|lung(16)|ovary(6)|prostate(1)|skin(3)|stomach(4)|upper_aerodigestive_tract(1)	57		all_cancers(109;5.7e-11)|all_epithelial(112;4.65e-09)|Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;5.77e-18)|GBM - Glioblastoma multiforme(94;5.11e-07)|COAD - Colon adenocarcinoma(120;0.071)|Colorectal(133;0.0717)		CCAACGCAGCTGTCTCCACCA	0.587													C|||	1517	0.302915	0.3245	0.1945	5008	,	,		19840	0.4167		0.1292	False		,,,				2504	0.4121				p.C1026R		Atlas-SNP	.											DUOX1,NS,carcinoma,0,1	DUOX1	125	1	1	Substitution - Missense(1)	stomach(1)	c.T3076C						PASS	.	C	ARG/CYS,ARG/CYS	1175,3221	710.9+/-407.9	154,867,1177	75.0	72.0	73.0		3076,3076	3.2	1.0	15	dbSNP_123	73	996,7600	773.0+/-407.7	56,884,3358	yes	missense,missense	DUOX1	NM_017434.3,NM_175940.1	180,180	210,1751,4535	CC,CT,TT		11.5868,26.7288,16.7103	benign,benign	1026/1552,1026/1552	45444133	2171,10821	2198	4298	6496	SO:0001583	missense	53905	exon25			CGCAGCTGTCTCC	AF213465	CCDS32221.1	15q21	2013-01-10				ENSG00000137857		"""EF-hand domain containing"""	3062	protein-coding gene	gene with protein product	"""NADPH thyroid oxidase 1"", ""flavoprotein NADPH oxidase"", ""nicotinamide adenine dinucleotide phosphate oxidase"""	606758				10806195	Standard	XM_005254463		Approved	NOXEF1, THOX1, LNOX1	uc001zut.1	Q9NRD9		ENST00000321429.4:c.3076T>C	15.37:g.45444133T>C	ENSP00000317997:p.Cys1026Arg	Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	198	119	0.60101	NM_017434	A6NH28|Q14C94|Q6ZMB3|Q6ZR09|Q9NZC1	Missense_Mutation	SNP	ENST00000321429.4	37	CCDS32221.1	597	0.2733516483516483	176	0.35772357723577236	77	0.212707182320442	251	0.4388111888111888	93	0.12269129287598944	C	10.54	1.378582	0.24944	0.267288	0.115868	ENSG00000137857	ENST00000431588;ENST00000321429;ENST00000389037	D;D	0.84660	-1.88;-1.88	4.17	3.25	0.37280	.	0.264295	0.37304	N	0.002148	T	0.00012	0.0000	N	0.00583	-1.355	0.36558	P	0.127749	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.39078	-0.9631	9	0.23891	T	0.37	-4.8419	3.8893	0.09111	0.1884:0.6075:0.0:0.2041	rs16939752;rs52810022;rs57005737;rs16939752	159;1026	Q9NT13;Q9NRD9	.;DUOX1_HUMAN	R	1026	ENSP00000317997:C1026R;ENSP00000373689:C1026R	ENSP00000317997:C1026R	C	+	1	0	DUOX1	43231425	0.998000	0.40836	0.956000	0.39512	0.973000	0.67179	2.047000	0.41269	0.519000	0.28406	-0.119000	0.15052	TGT	C|0.231;N|0.000	0.231	strong		0.587	DUOX1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416251.1	NM_017434	
MUC4	4585	hgsc.bcm.edu	37	3	195506676	195506676	+	Silent	SNP	G	G	A	rs147667126	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195506676G>A	ENST00000463781.3	-	2	12234	c.11775C>T	c.(11773-11775)gaC>gaT	p.D3925D	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Silent_p.D3925D	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)		CCGAGGAAACGTCGGTGACAG	0.587													.|||	605	0.120807	0.3185	0.0994	5008	,	,		11176	0.0208		0.0885	False		,,,				2504	0.0051				p.D3925D		Atlas-SNP	.											.	MUC4	1505	.	0			c.C11775T						PASS	.						24.0	25.0	24.0					3																	195506676		539	1108	1647	SO:0001819	synonymous_variant	4585	exon2			GGAAACGTCGGTG	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.11775C>T	3.37:g.195506676G>A		Somatic	205	0	0		WXS	Illumina HiSeq	Phase_I	117	112	0.957265	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|0.740;A|0.260	0.260	strong		0.587	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
FCGBP	8857	hgsc.bcm.edu	37	19	40399508	40399508	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:40399508C>T	ENST00000221347.6	-	13	6194	c.6187G>A	c.(6187-6189)Ggc>Agc	p.G2063S		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	2063						extracellular vesicular exosome (GO:0070062)				NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(5)|endometrium(13)|kidney(9)|large_intestine(27)|lung(49)|ovary(8)|pancreas(3)|prostate(13)|skin(9)|stomach(9)|upper_aerodigestive_tract(6)|urinary_tract(3)	165	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			GGCTGGCAGCCGTGCTGGCCG	0.657																																					p.G2063S		Atlas-SNP	.											FCGBP,NS,carcinoma,0,1	FCGBP	416	1	0			c.G6187A						scavenged	.						1.0	1.0	1.0					19																	40399508		183	426	609	SO:0001583	missense	8857	exon13			GGCAGCCGTGCTG	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.6187G>A	19.37:g.40399508C>T	ENSP00000221347:p.Gly2063Ser	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	126	22	0.174603	NM_003890	O95784	Missense_Mutation	SNP	ENST00000221347.6	37	CCDS12546.1	.	.	.	.	.	.	.	.	.	.	C	14.27	2.485186	0.44147	.	.	ENSG00000090920	ENST00000221347	T	0.05025	3.51	3.01	3.01	0.34805	von Willebrand factor, type D domain (1);	.	.	.	.	T	0.20170	0.0485	M	0.77103	2.36	0.31064	N	0.713759	D	0.76494	0.999	D	0.66196	0.942	T	0.07868	-1.0750	9	0.14656	T	0.56	.	12.9123	0.58187	0.0:1.0:0.0:0.0	.	2063	Q9Y6R7	FCGBP_HUMAN	S	2063	ENSP00000221347:G2063S	ENSP00000221347:G2063S	G	-	1	0	FCGBP	45091348	0.935000	0.31712	0.871000	0.34182	0.831000	0.47069	-0.229000	0.09098	1.536000	0.49237	0.298000	0.19748	GGC	.	.	weak		0.657	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890	
DSCAML1	57453	hgsc.bcm.edu	37	11	117309989	117309989	+	Silent	SNP	C	C	T	rs11216386	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:117309989C>T	ENST00000321322.6	-	23	4318	c.4317G>A	c.(4315-4317)ctG>ctA	p.L1439L	DSCAML1_ENST00000527706.1_Silent_p.L1169L	NM_020693.2	NP_065744.2	Q8TD84	DSCL1_HUMAN	Down syndrome cell adhesion molecule like 1	1379	Fibronectin type-III 5. {ECO:0000255|PROSITE-ProRule:PRU00316}.				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)			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)		CACCTTGCACCAGAAGGTTGA	0.572													C|||	1263	0.252196	0.1997	0.1758	5008	,	,		20500	0.5565		0.1064	False		,,,				2504	0.2137				p.L1439L		Atlas-SNP	.											.	DSCAML1	286	.	0			c.G4317A						PASS	.	C		824,3578	328.8+/-300.7	66,692,1443	105.0	97.0	100.0		4317	0.8	1.0	11	dbSNP_120	100	836,7756	192.1+/-238.2	40,756,3500	no	coding-synonymous	DSCAML1	NM_020693.2		106,1448,4943	TT,TC,CC		9.73,18.7188,12.7751		1439/2114	117309989	1660,11334	2201	4296	6497	SO:0001819	synonymous_variant	57453	exon23			TTGCACCAGAAGG		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.4317G>A	11.37:g.117309989C>T		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	97	21	0.216495	NM_020693	Q76MU9|Q8IZY3|Q8IZY4|Q8WXU7|Q9ULT7	Silent	SNP	ENST00000321322.6	37	CCDS8384.1																																																																																			C|0.805;T|0.195	0.195	strong		0.572	DSCAML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392907.2	NM_020693	
C1QTNF6	114904	hgsc.bcm.edu	37	22	37581422	37581422	+	Missense_Mutation	SNP	G	G	C	rs229526	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:37581422G>C	ENST00000337843.2	-	2	200	c.125C>G	c.(124-126)cCt>cGt	p.P42R	C1QTNF6_ENST00000470655.1_5'UTR|C1QTNF6_ENST00000255836.6_5'Flank|RP1-151B14.6_ENST00000419128.1_RNA|C1QTNF6_ENST00000397110.2_Missense_Mutation_p.P42R	NM_031910.3	NP_114116.3	Q9BXI9	C1QT6_HUMAN	C1q and tumor necrosis factor related protein 6	23					protein heterotrimerization (GO:0070208)	collagen trimer (GO:0005581)|extracellular space (GO:0005615)				breast(1)|large_intestine(2)|lung(6)|stomach(1)|upper_aerodigestive_tract(1)	11						CTCCACCATAGGGATCTCACA	0.612													G|||	947	0.189097	0.2769	0.1369	5008	,	,		18321	0.1071		0.2068	False		,,,				2504	0.1738				p.P42R		Atlas-SNP	.											.	C1QTNF6	32	.	0			c.C125G						PASS	.	G	ARG/PRO,ARG/PRO	1169,3237	404.6+/-333.2	155,859,1189	40.0	40.0	40.0	http://www.ncbi.nlm.nih.gov/pubmed?term	125,125	4.5	0.2	22	dbSNP_79	40	1919,6681	338.1+/-322.6	217,1485,2598	yes	missense,missense	C1QTNF6	NM_031910.3,NM_182486.1	103,103	372,2344,3787	CC,CG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	22.314,26.532,23.7429	probably-damaging,probably-damaging	42/279,42/279	37581422	3088,9918	2203	4300	6503	SO:0001583	missense	114904	exon2			ACCATAGGGATCT	AF329842	CCDS13943.1	22q13.1	2014-02-21			ENSG00000133466	ENSG00000133466			14343	protein-coding gene	gene with protein product		614910				12975309	Standard	NM_031910		Approved	CTRP6, ZACRP6	uc003aqy.1	Q9BXI9	OTTHUMG00000150538	ENST00000337843.2:c.125C>G	22.37:g.37581422G>C	ENSP00000338812:p.Pro42Arg	Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	60	30	0.5	NM_182486	Q5H9G8|Q6ZRM7	Missense_Mutation	SNP	ENST00000337843.2	37	CCDS13943.1	394	0.1804029304029304	136	0.2764227642276423	58	0.16022099447513813	55	0.09615384615384616	145	0.19129287598944592	G	11.16	1.557493	0.27827	0.26532	0.22314	ENSG00000133466	ENST00000397110;ENST00000337843	T;T	0.39406	1.08;1.08	4.49	4.49	0.54785	.	0.162471	0.41097	D	0.000960	T	0.00012	0.0000	M	0.73598	2.24	0.09310	P	0.9999999999995662	P;P	0.49090	0.919;0.718	P;B	0.45506	0.483;0.387	T	0.12243	-1.0555	9	0.44086	T	0.13	.	15.3686	0.74545	0.0:0.0:1.0:0.0	rs229526;rs17812735;rs52834593;rs59914011;rs229526	42;23	Q9BXI9-2;Q9BXI9	.;C1QT6_HUMAN	R	42	ENSP00000380299:P42R;ENSP00000338812:P42R	ENSP00000338812:P42R	P	-	2	0	C1QTNF6	35911368	1.000000	0.71417	0.229000	0.23960	0.004000	0.04260	3.883000	0.56168	2.039000	0.60335	0.491000	0.48974	CCT	G|0.791;C|0.208	0.208	strong		0.612	C1QTNF6-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318807.1	NM_182486	
KIF13A	63971	hgsc.bcm.edu	37	6	17764896	17764896	+	Missense_Mutation	SNP	G	G	C	rs41267712	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:17764896G>C	ENST00000259711.6	-	39	4968	c.4863C>G	c.(4861-4863)gaC>gaG	p.D1621E	KIF13A_ENST00000378816.5_Missense_Mutation_p.D1586E|KIF13A_ENST00000378843.2_Missense_Mutation_p.D1573E|KIF13A_ENST00000378826.2_Missense_Mutation_p.D1586E|KIF13A_ENST00000378814.5_Missense_Mutation_p.D1573E	NM_022113.5	NP_071396.4	Q9H1H9	KI13A_HUMAN	kinesin family member 13A	1621					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)			TGGCCAGCTGGTCTGAGCTGT	0.537													G|||	17	0.00339457	0.0008	0.0029	5008	,	,		18971	0.0		0.0119	False		,,,				2504	0.002				p.D1621E		Atlas-SNP	.											.	KIF13A	276	.	0			c.C4863G						PASS	.	G	GLU/ASP,GLU/ASP,GLU/ASP,GLU/ASP	7,4099		0,7,2046	76.0	76.0	76.0		4758,4719,4719,4863	-10.1	0.3	6	dbSNP_127	76	89,8313		0,89,4112	yes	missense,missense,missense,missense	KIF13A	NM_001105566.2,NM_001105567.2,NM_001105568.2,NM_022113.5	45,45,45,45	0,96,6158	CC,CG,GG		1.0593,0.1705,0.7675	probably-damaging,probably-damaging,probably-damaging,probably-damaging	1586/1771,1573/1758,1573/1750,1621/1806	17764896	96,12412	2053	4201	6254	SO:0001583	missense	63971	exon39			CAGCTGGTCTGAG	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.4863C>G	6.37:g.17764896G>C	ENSP00000259711:p.Asp1621Glu	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	67	37	0.552239	NM_022113	A0JP21|A0JP22|F2Z382|Q5THQ2|Q5THQ3|Q9H193|Q9H194|Q9H1H8	Missense_Mutation	SNP	ENST00000259711.6	37	CCDS47381.1	10	0.004578754578754579	0	0.0	2	0.0055248618784530384	0	0.0	8	0.010554089709762533	G	22.2	4.253429	0.80135	0.001705	0.010593	ENSG00000137177	ENST00000378814;ENST00000502297;ENST00000259711;ENST00000378826;ENST00000378843;ENST00000378816	T;T;T;T;T;T	0.67345	-0.26;-0.26;-0.26;-0.26;-0.26;-0.26	6.08	-10.1	0.00402	.	0.000000	0.85682	D	0.000000	T	0.49677	0.1571	L	0.34521	1.04	0.33165	D	0.54753	D;D;D;D	0.67145	0.996;0.996;0.988;0.996	D;D;P;D	0.77557	0.99;0.99;0.675;0.99	T	0.76876	-0.2797	10	0.05721	T	0.95	.	21.8125	0.99961	0.3087:0.0:0.6913:0.0	rs41267712	1573;1586;1621;1573	Q9H1H9-4;Q9H1H9-2;Q9H1H9;Q9H1H9-3	.;.;KI13A_HUMAN;.	E	1573;625;1621;1586;1573;1586	ENSP00000368091:D1573E;ENSP00000425616:D625E;ENSP00000259711:D1621E;ENSP00000368103:D1586E;ENSP00000368120:D1573E;ENSP00000368093:D1586E	ENSP00000259711:D1621E	D	-	3	2	KIF13A	17872875	0.992000	0.36948	0.342000	0.25602	0.975000	0.68041	0.249000	0.18216	-1.853000	0.01165	-0.423000	0.05987	GAC	G|0.995;C|0.005	0.005	strong		0.537	KIF13A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000039954.4		
ZNF469	84627	hgsc.bcm.edu	37	16	88504850	88504850	+	Missense_Mutation	SNP	G	G	C	rs1105066	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	74	0	0		WXS	Illumina HiSeq	Phase_I	51	51	1	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	
PDE3A	5139	hgsc.bcm.edu	37	12	20522252	20522252	+	Missense_Mutation	SNP	G	G	A	rs12305038	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:20522252G>A	ENST00000359062.3	+	1	74	c.34G>A	c.(34-36)Gac>Aac	p.D12N	RP11-284H19.1_ENST00000535755.1_RNA	NM_000921.4|NM_001244683.1	NP_000912.3|NP_001231612.1	Q14432	PDE3A_HUMAN	phosphodiesterase 3A, cGMP-inhibited	12			D -> N (in dbSNP:rs12305038). {ECO:0000269|PubMed:8695850}.		blood coagulation (GO:0007596)|cAMP catabolic process (GO:0006198)|cAMP-mediated signaling (GO:0019933)|cellular response to cGMP (GO:0071321)|cellular response to transforming growth factor beta stimulus (GO:0071560)|cGMP-mediated signaling (GO:0019934)|diterpenoid metabolic process (GO:0016101)|lipid metabolic process (GO:0006629)|negative regulation of apoptotic process (GO:0043066)|negative regulation of vascular permeability (GO:0043116)|oocyte maturation (GO:0001556)|positive regulation of oocyte development (GO:0060282)|positive regulation of vascular permeability (GO:0043117)|regulation of meiosis (GO:0040020)|response to cAMP (GO:0051591)|response to drug (GO:0042493)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|cAMP binding (GO:0030552)|cGMP-inhibited cyclic-nucleotide phosphodiesterase activity (GO:0004119)|metal ion binding (GO:0046872)			NS(1)|breast(3)|endometrium(4)|kidney(3)|large_intestine(7)|lung(29)|ovary(4)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	58	Esophageal squamous(101;0.125)	Breast(259;0.134)			Aminophylline(DB01223)|Amrinone(DB01427)|Anagrelide(DB00261)|Caffeine(DB00201)|Cilostazol(DB01166)|Enoximone(DB04880)|Ibudilast(DB05266)|Levosimendan(DB00922)|Milrinone(DB00235)|Oxtriphylline(DB01303)|Theophylline(DB00277)|Tofisopam(DB08811)	ACGAGTCAGGGACAAGCCCGT	0.726													G|||	1671	0.333666	0.5061	0.219	5008	,	,		10216	0.3056		0.3091	False		,,,				2504	0.2362				p.D12N		Atlas-SNP	.											PDE3A,NS,carcinoma,0,1	PDE3A	184	1	0			c.G34A						scavenged	.	G	ASN/ASP	1554,2186		396,762,712	4.0	7.0	6.0		34	3.9	0.0	12	dbSNP_120	6	1943,5269		352,1239,2015	yes	missense	PDE3A	NM_000921.4	23	748,2001,2727	AA,AG,GG		26.9412,41.5508,31.9302	possibly-damaging	12/1142	20522252	3497,7455	1870	3606	5476	SO:0001583	missense	5139	exon1			GTCAGGGACAAGC		CCDS31754.1	12p12.2	2011-04-15			ENSG00000172572	ENSG00000172572	3.1.4.17	"""Phosphodiesterases"""	8778	protein-coding gene	gene with protein product		123805				1315035, 10679291	Standard	NM_000921		Approved	CGI-PDE	uc001reh.2	Q14432	OTTHUMG00000168962	ENST00000359062.3:c.34G>A	12.37:g.20522252G>A	ENSP00000351957:p.Asp12Asn	Somatic	19	1	0.0526316		WXS	Illumina HiSeq	Phase_I	14	6	0.428571	NM_000921	O60865|Q13348|Q17RD1	Missense_Mutation	SNP	ENST00000359062.3	37	CCDS31754.1	726	0.3324175824175824	269	0.5467479674796748	81	0.22375690607734808	140	0.24475524475524477	236	0.3113456464379947	G	9.693	1.152350	0.21371	0.415508	0.269412	ENSG00000172572	ENST00000359062	T	0.62232	0.04	3.9	3.9	0.45041	.	4.361550	0.00166	N	0.000016	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.23058	0.079	B	0.20955	0.032	T	0.33059	-0.9883	9	0.33940	T	0.23	.	11.4979	0.50419	0.0:0.1835:0.8165:0.0	rs12305038;rs12305038	12	Q14432	PDE3A_HUMAN	N	12	ENSP00000351957:D12N	ENSP00000351957:D12N	D	+	1	0	PDE3A	20413519	0.164000	0.22935	0.032000	0.17829	0.460000	0.32559	3.310000	0.51911	1.999000	0.58509	0.484000	0.47621	GAC	G|0.663;A|0.337	0.337	strong		0.726	PDE3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401756.2		
PPP1R32	220004	hgsc.bcm.edu	37	11	61252200	61252200	+	Missense_Mutation	SNP	A	A	G	rs146231065	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:61252200A>G	ENST00000338608.2	+	5	547	c.422A>G	c.(421-423)cAg>cGg	p.Q141R	PPP1R32_ENST00000432063.2_Missense_Mutation_p.Q141R|RP11-286N22.8_ENST00000544880.1_3'UTR	NM_145017.2	NP_659454.2	Q7Z5V6	PPR32_HUMAN	protein phosphatase 1, regulatory subunit 32	141							phosphatase binding (GO:0019902)										CACGGGCCTCAGGCCATCACG	0.642													A|||	25	0.00499201	0.0	0.0	5008	,	,		17677	0.001		0.0089	False		,,,				2504	0.0153				p.Q141R		Atlas-SNP	.											.	.	.	.	0			c.A422G						PASS	.	A	ARG/GLN,ARG/GLN	11,4393	19.1+/-41.9	1,9,2192	32.0	29.0	30.0		422,422	5.3	0.5	11	dbSNP_134	30	63,8535	37.4+/-92.8	0,63,4236	yes	missense,missense	C11orf66	NM_001170753.1,NM_145017.2	43,43	1,72,6428	GG,GA,AA		0.7327,0.2498,0.5691	possibly-damaging,possibly-damaging	141/406,141/426	61252200	74,12928	2202	4299	6501	SO:0001583	missense	220004	exon5			GGCCTCAGGCCAT	AK057333	CCDS8008.1, CCDS53641.1	11q12.2	2012-04-17	2011-10-11	2011-10-11	ENSG00000162148	ENSG00000162148		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	28869	protein-coding gene	gene with protein product			"""chromosome 11 open reading frame 66"""	C11orf66		12477932	Standard	NM_145017		Approved	IIIG9, FLJ32771	uc001nru.2	Q7Z5V6	OTTHUMG00000168176	ENST00000338608.2:c.422A>G	11.37:g.61252200A>G	ENSP00000344140:p.Gln141Arg	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	84	48	0.571429	NM_001170753	Q4G0P4|Q96M77	Missense_Mutation	SNP	ENST00000338608.2	37	CCDS8008.1	9	0.004120879120879121	0	0.0	0	0.0	0	0.0	9	0.011873350923482849	A	13.34	2.208254	0.39003	0.002498	0.007327	ENSG00000162148	ENST00000432063;ENST00000338608	T;T	0.45276	0.9;1.49	5.33	5.33	0.75918	.	0.548000	0.17786	N	0.162044	T	0.29491	0.0735	M	0.63428	1.95	0.29499	N	0.855042	B;B	0.32829	0.386;0.386	B;B	0.31101	0.124;0.124	T	0.35251	-0.9796	9	.	.	.	-12.7669	7.9832	0.30196	0.9082:0.0:0.0918:0.0	.	141;141	Q7Z5V6-2;Q7Z5V6	.;PPR32_HUMAN	R	141	ENSP00000391560:Q141R;ENSP00000344140:Q141R	.	Q	+	2	0	C11orf66	61008776	0.092000	0.21681	0.540000	0.28089	0.816000	0.46133	1.745000	0.38278	2.028000	0.59812	0.379000	0.24179	CAG	A|0.995;G|0.005	0.005	strong		0.642	PPP1R32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398621.1	NM_145017	
PSAPL1	768239	hgsc.bcm.edu	37	4	7435901	7435901	+	Missense_Mutation	SNP	C	C	T	rs56269914	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:7435901C>T	ENST00000319098.4	-	1	799	c.706G>A	c.(706-708)Gac>Aac	p.D236N	SORCS2_ENST00000511199.1_Intron|SORCS2_ENST00000507866.2_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	76	0	0		WXS	Illumina HiSeq	Phase_I	55	29	0.527273	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		
TRIM63	84676	hgsc.bcm.edu	37	1	26384973	26384973	+	Nonsense_Mutation	SNP	G	G	A	rs148395034		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:26384973G>A	ENST00000374272.3	-	5	877	c.739C>T	c.(739-741)Cag>Tag	p.Q247*	TRIM63_ENST00000483052.1_5'Flank	NM_032588.3	NP_115977.2	Q969Q1	TRI63_HUMAN	tripartite motif containing 63, E3 ubiquitin protein ligase	247					cellular response to dexamethasone stimulus (GO:0071549)|muscle contraction (GO:0006936)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|regulation of gene expression (GO:0010468)|response to electrical stimulus involved in regulation of muscle adaptation (GO:0014878)|response to interleukin-1 (GO:0070555)|signal transduction (GO:0007165)|skeletal muscle atrophy (GO:0014732)	contractile fiber (GO:0043292)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)	ligase activity (GO:0016874)|signal transducer activity (GO:0004871)|titin binding (GO:0031432)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			kidney(1)|large_intestine(1)|ovary(1)|skin(1)|stomach(1)	5		Colorectal(325;3.46e-05)|Lung NSC(340;0.000154)|all_lung(284;0.00021)|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;9.15e-26)|Colorectal(126;3.16e-08)|COAD - Colon adenocarcinoma(152;1.72e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.000767)|BRCA - Breast invasive adenocarcinoma(304;0.00101)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.00655)|READ - Rectum adenocarcinoma(331;0.0649)		TGGTACTGCTGGATGAGGGCC	0.557													G|||	1	0.000199681	0.0	0.0014	5008	,	,		19266	0.0		0.0	False		,,,				2504	0.0				p.Q247X		Atlas-SNP	.											.	TRIM63	33	.	0			c.C739T						PASS	.	G	stop/GLN	0,4406		0,0,2203	142.0	129.0	133.0		739	5.5	1.0	1	dbSNP_134	133	6,8594	5.0+/-18.6	0,6,4294	yes	stop-gained	TRIM63	NM_032588.2		0,6,6497	AA,AG,GG		0.0698,0.0,0.0461		247/354	26384973	6,13000	2203	4300	6503	SO:0001587	stop_gained	84676	exon5			ACTGCTGGATGAG	AF353673	CCDS273.1	1p34-p33	2014-09-17	2012-02-23	2004-11-17	ENSG00000158022	ENSG00000158022		"""RING-type (C3HC4) zinc fingers"", ""Tripartite motif containing / Tripartite motif containing"""	16007	protein-coding gene	gene with protein product	"""muscle-specific RING finger protein 1"", ""iris ring finger protein"", ""striated muscle RING zinc finger protein"""	606131	"""ring finger protein 28"", ""tripartite motif-containing 63"", ""tripartite motif containing 63"""	RNF28		11243782, 11283016	Standard	NM_032588		Approved	MURF-1, IRF, SMRZ	uc001bli.2	Q969Q1	OTTHUMG00000007510	ENST00000374272.3:c.739C>T	1.37:g.26384973G>A	ENSP00000363390:p.Gln247*	Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	160	73	0.45625	NM_032588	B4DN95|Q5T2I1|Q96BD3|Q96KD9|Q9BYV4	Nonsense_Mutation	SNP	ENST00000374272.3	37	CCDS273.1	.	.	.	.	.	.	.	.	.	.	G	36	5.623049	0.96660	0.0	6.98E-4	ENSG00000158022	ENST00000374272	.	.	.	5.5	5.5	0.81552	.	0.425067	0.28436	N	0.015350	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.05620	T	0.96	.	9.3577	0.38177	0.0778:0.1466:0.7756:0.0	.	.	.	.	X	247	.	ENSP00000363390:Q247X	Q	-	1	0	TRIM63	26257560	0.561000	0.26578	1.000000	0.80357	0.968000	0.65278	0.572000	0.23684	2.581000	0.87130	0.561000	0.74099	CAG	G|0.999;A|0.001	0.001	strong		0.557	TRIM63-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019750.1	NM_032588	
MUC17	140453	hgsc.bcm.edu	37	7	100683796	100683796	+	Silent	SNP	T	T	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:100683796T>C	ENST00000306151.4	+	3	9163	c.9099T>C	c.(9097-9099)ggT>ggC	p.G3033G		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	3033	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)					CTGCTGAAGGTACCGGCATAC	0.512																																					p.G3033G		Atlas-SNP	.											MUC17,caecum,carcinoma,+2,2	MUC17	804	2	0			c.T9099C						scavenged	.						265.0	278.0	274.0					7																	100683796		2203	4300	6503	SO:0001819	synonymous_variant	140453	exon3			TGAAGGTACCGGC	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.9099T>C	7.37:g.100683796T>C		Somatic	24	0	0		WXS	Illumina HiSeq	Phase_I	35	2	0.0571429	NM_001040105	O14761|Q685J2|Q8TDH7	Silent	SNP	ENST00000306151.4	37	CCDS34711.1																																																																																			.	.	none		0.512	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
KRTAP1-4	728255	hgsc.bcm.edu	37	17	39186031	39186031	+	Silent	SNP	C	C	T	rs8074117	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:39186031C>T	ENST00000377747.4	-	1	325	c.300G>A	c.(298-300)ccG>ccA	p.P100P	KRTAP1-5_ENST00000361883.5_5'Flank	NM_001257305.1	NP_001244234.1	P0C5Y4	KRA14_HUMAN	keratin associated protein 1-4	100						keratin filament (GO:0045095)				lung(1)	1						CACAGTAGGACGGGCGGCAGC	0.652													c|||	1710	0.341454	0.3578	0.3602	5008	,	,		19153	0.3085		0.2644	False		,,,				2504	0.4192				p.P100P		Atlas-SNP	.											.	KRTAP1-4	4	.	0			c.G300A						PASS	.																																			SO:0001819	synonymous_variant	728255	exon1			GTAGGACGGGCGG	AC007455	CCDS58548.1	17q21.2	2010-06-22			ENSG00000204887	ENSG00000204887		"""Keratin associated proteins"""	18904	protein-coding gene	gene with protein product		608821					Standard	NM_001257305		Approved	KAP1.4	uc031raf.1	P0C5Y4	OTTHUMG00000133631	ENST00000377747.4:c.300G>A	17.37:g.39186031C>T		Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	112	53	0.473214	NM_001257305	A6NJ92	Silent	SNP	ENST00000377747.4	37	CCDS58548.1																																																																																			C|0.701;T|0.299	0.299	strong		0.652	KRTAP1-4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257776.3		
FAM120B	84498	hgsc.bcm.edu	37	6	170628009	170628009	+	Missense_Mutation	SNP	T	T	G	rs9348266	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:170628009T>G	ENST00000476287.1	+	2	1639	c.1531T>G	c.(1531-1533)Tgt>Ggt	p.C511G	FAM120B_ENST00000537664.1_Missense_Mutation_p.C534G|FAM120B_ENST00000540480.1_Missense_Mutation_p.C523G|FAM120B_ENST00000252510.9_Intron	NM_032448.1	NP_115824.1	Q96EK7	F120B_HUMAN	family with sequence similarity 120B	511			C -> G (in dbSNP:rs9348266).		cell differentiation (GO:0030154)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(11)|liver(1)|lung(15)|ovary(1)|prostate(2)|skin(2)	44		Breast(66;0.000338)|Esophageal squamous(34;0.241)		OV - Ovarian serous cystadenocarcinoma(33;3.94e-22)|BRCA - Breast invasive adenocarcinoma(81;6.47e-06)|GBM - Glioblastoma multiforme(31;0.0899)		AGTTCCCATATGTACAGATCC	0.403													T|||	799	0.159545	0.0749	0.2046	5008	,	,		22148	0.2817		0.1252	False		,,,				2504	0.1513				p.C511G		Atlas-SNP	.											.	FAM120B	108	.	0			c.T1531G						PASS	.		GLY/CYS	422,3984	207.2+/-228.6	23,376,1804	81.0	83.0	82.0		1531	-2.0	0.0	6	dbSNP_119	82	1215,7385	246.4+/-274.8	95,1025,3180	yes	missense	FAM120B	NM_032448.1	159	118,1401,4984	GG,GT,TT		14.1279,9.5778,12.5865	benign	511/911	170628009	1637,11369	2203	4300	6503	SO:0001583	missense	84498	exon2			CCCATATGTACAG	AB058741	CCDS5314.1, CCDS75555.1	6q27	2011-04-13	2006-07-04	2006-07-04	ENSG00000112584	ENSG00000112584			21109	protein-coding gene	gene with protein product	"""PPARgamma constitutive coactivator 1"", ""constitutive coactivator of PPAR-gamma"""	612266	"""KIAA1838"""	KIAA1838		14585507	Standard	NM_032448		Approved	PGCC1, CCPG	uc003qxp.3	Q96EK7	OTTHUMG00000016080	ENST00000476287.1:c.1531T>G	6.37:g.170628009T>G	ENSP00000417970:p.Cys511Gly	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	62	23	0.370968	NM_032448	B4DL34|Q86V68|Q96JI9	Missense_Mutation	SNP	ENST00000476287.1	37	CCDS5314.1	367	0.16804029304029305	48	0.0975609756097561	60	0.16574585635359115	161	0.28146853146853146	98	0.12928759894459102	T	2.916	-0.224297	0.06061	0.095778	0.141279	ENSG00000112584	ENST00000540480;ENST00000537664;ENST00000476287	T;T;T	0.10763	2.86;2.84;2.87	2.48	-1.96	0.07525	.	.	.	.	.	T	0.01695	0.0054	L	0.34521	1.04	0.80722	P	0.0	P;B	0.36249	0.545;0.056	B;B	0.35114	0.196;0.01	T	0.43015	-0.9417	8	0.23302	T	0.38	.	1.1069	0.01696	0.1903:0.132:0.3864:0.2914	rs9348266;rs56865004;rs9348266	511;511	Q96EK7;F2Z2E1	F120B_HUMAN;.	G	523;534;511	ENSP00000444125:C523G;ENSP00000440125:C534G;ENSP00000417970:C511G	ENSP00000436640:C511G	C	+	1	0	FAM120B	170469934	0.000000	0.05858	0.000000	0.03702	0.015000	0.08874	-1.014000	0.03641	-0.415000	0.07484	0.459000	0.35465	TGT	T|0.851;G|0.149	0.149	strong		0.403	FAM120B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000043259.2	NM_032448	
OR10Q1	219960	hgsc.bcm.edu	37	11	57996084	57996084	+	Silent	SNP	G	G	A	rs61902844	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:57996084G>A	ENST00000316770.2	-	1	306	c.264C>T	c.(262-264)aaC>aaT	p.N88N		NM_001004471.2	NP_001004471.1	Q8NGQ4	O10Q1_HUMAN	olfactory receptor, family 10, subfamily Q, member 1	88						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			autonomic_ganglia(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(26)|ovary(2)	35		Breast(21;0.0589)				CCCCCAAAATGTTGGAAAGCA	0.542													g|||	1276	0.254792	0.1369	0.2882	5008	,	,		20320	0.1438		0.4404	False		,,,				2504	0.3139				p.N88N		Atlas-SNP	.											OR10Q1,NS,carcinoma,-2,1	OR10Q1	79	1	0			c.C264T						PASS	.	G		730,3672	300.7+/-286.5	72,586,1543	75.0	69.0	71.0		264	1.7	0.8	11	dbSNP_129	71	3741,4849	533.1+/-382.3	798,2145,1352	no	coding-synonymous	OR10Q1	NM_001004471.2		870,2731,2895	AA,AG,GG		43.5506,16.5834,34.4135		88/320	57996084	4471,8521	2201	4295	6496	SO:0001819	synonymous_variant	219960	exon1			CAAAATGTTGGAA	AB065735	CCDS31547.1	11q12.1	2012-08-09			ENSG00000180475	ENSG00000180475		"""GPCR / Class A : Olfactory receptors"""	15134	protein-coding gene	gene with protein product							Standard	NM_001004471		Approved		uc010rkd.2	Q8NGQ4	OTTHUMG00000167542	ENST00000316770.2:c.264C>T	11.37:g.57996084G>A		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	55	50	0.909091	NM_001004471	Q6IFG4	Silent	SNP	ENST00000316770.2	37	CCDS31547.1																																																																																			G|0.667;A|0.333	0.333	strong		0.542	OR10Q1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394706.1	NM_001004471	
CHSY1	22856	hgsc.bcm.edu	37	15	101718097	101718097	+	Silent	SNP	C	C	G	rs28364839	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:101718097C>G	ENST00000254190.3	-	3	2380	c.1905G>C	c.(1903-1905)gtG>gtC	p.V635V	CHSY1_ENST00000543813.1_5'UTR	NM_014918.4	NP_055733.2	Q86X52	CHSS1_HUMAN	chondroitin sulfate synthase 1	635					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)			CTGTAGTAAACACGAGGTCGA	0.448													C|||	1206	0.240815	0.4644	0.1527	5008	,	,		20757	0.0347		0.2256	False		,,,				2504	0.229				p.V635V		Atlas-SNP	.											.	CHSY1	60	.	0			c.G1905C						PASS	.	C		1824,2582	534.4+/-373.9	388,1048,767	69.0	67.0	68.0		1905	2.8	1.0	15	dbSNP_125	68	2053,6547	352.9+/-328.9	235,1583,2482	no	coding-synonymous	CHSY1	NM_014918.4		623,2631,3249	GG,GC,CC		23.8721,41.3981,29.8093		635/803	101718097	3877,9129	2203	4300	6503	SO:0001819	synonymous_variant	22856	exon3			AGTAAACACGAGG	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.1905G>C	15.37:g.101718097C>G		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	108	57	0.527778	NM_014918	Q6UX38|Q7LFU5|Q9Y2J5	Silent	SNP	ENST00000254190.3	37	CCDS10390.1																																																																																			C|0.724;G|0.276	0.276	strong		0.448	CHSY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313624.1	NM_014918	
ARHGAP29	9411	hgsc.bcm.edu	37	1	94643531	94643531	+	Silent	SNP	T	T	C	rs1048854	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	115	0	0		WXS	Illumina HiSeq	Phase_I	85	34	0.4	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	
ATP9B	374868	hgsc.bcm.edu	37	18	77067000	77067000	+	Silent	SNP	T	T	G	rs3760541	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:77067000T>G	ENST00000426216.2	+	15	1556	c.1539T>G	c.(1537-1539)gcT>gcG	p.A513A	ATP9B_ENST00000307671.7_Silent_p.A513A	NM_198531.3	NP_940933.3	O43861	ATP9B_HUMAN	ATPase, class II, type 9B	513					establishment of protein localization to Golgi (GO:0072600)|phospholipid translocation (GO:0045332)	integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|trans-Golgi network (GO:0005802)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(15)|ovary(3)|prostate(1)|skin(2)|stomach(1)	38		Esophageal squamous(42;0.018)|Melanoma(33;0.0964)|Prostate(75;0.171)		OV - Ovarian serous cystadenocarcinoma(15;1.44e-07)|BRCA - Breast invasive adenocarcinoma(31;0.0405)		AGTCTCAAGCTGGTGGAAACA	0.358													T|||	2020	0.403355	0.3623	0.4481	5008	,	,		20069	0.38		0.4483	False		,,,				2504	0.4049				p.A513A		Atlas-SNP	.											.	ATP9B	96	.	0			c.T1539G						PASS	.	T		1699,2707	509.4+/-367.2	338,1023,842	69.0	65.0	66.0		1539	-1.6	0.0	18	dbSNP_107	66	3792,4808	536.0+/-382.9	855,2082,1363	no	coding-synonymous	ATP9B	NM_198531.3		1193,3105,2205	GG,GT,TT		44.093,38.5611,42.219		513/1148	77067000	5491,7515	2203	4300	6503	SO:0001819	synonymous_variant	374868	exon15			TCAAGCTGGTGGA	R51412	CCDS12014.1	18q23	2010-04-20	2007-09-19		ENSG00000166377	ENSG00000166377		"""ATPases / P-type"""	13541	protein-coding gene	gene with protein product		614446	"""ATPase, Class II, type 9B"""			9548971, 11015572	Standard	NM_198531		Approved	ATPIIB	uc002lmx.3	O43861	OTTHUMG00000132898	ENST00000426216.2:c.1539T>G	18.37:g.77067000T>G		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	47	29	0.617021	NM_198531	O60872|Q08AD8|Q08AD9	Silent	SNP	ENST00000426216.2	37	CCDS12014.1																																																																																			T|0.570;G|0.430	0.430	strong		0.358	ATP9B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256402.3	NM_198531	
AHNAK2	113146	hgsc.bcm.edu	37	14	105417837	105417837	+	Silent	SNP	A	A	G	rs76231332	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:105417837A>G	ENST00000333244.5	-	7	4070	c.3951T>C	c.(3949-3951)gcT>gcC	p.A1317A	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	1317						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)			CGTCCTTGTCAGCCAGGGACA	0.612													.|||	1322	0.263978	0.3026	0.1398	5008	,	,		14856	0.3006		0.1511	False		,,,				2504	0.3783				p.A1317A		Atlas-SNP	.											.	AHNAK2	719	.	0			c.T3951C						PASS	.	A		1055,2763		260,535,1114	131.0	117.0	122.0		3951	-8.2	0.0	14	dbSNP_131	122	550,6068		180,190,2939	no	coding-synonymous	AHNAK2	NM_138420.2		440,725,4053	GG,GA,AA		8.3107,27.6323,15.3795		1317/5796	105417837	1605,8831	1909	3309	5218	SO:0001819	synonymous_variant	113146	exon7			CTTGTCAGCCAGG	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.3951T>C	14.37:g.105417837A>G		Somatic	0	0	.		WXS	Illumina HiSeq	Phase_I	70	70	1	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Silent	SNP	ENST00000333244.5	37	CCDS45177.1																																																																																			A|0.777;G|0.223	0.223	strong		0.612	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
SCAPER	49855	hgsc.bcm.edu	37	15	77025687	77025687	+	Silent	SNP	C	C	T	rs144694379	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:77025687C>T	ENST00000563290.1	-	16	2000	c.1905G>A	c.(1903-1905)caG>caA	p.Q635Q	SCAPER_ENST00000538941.2_Silent_p.Q389Q|SCAPER_ENST00000324767.7_Silent_p.Q635Q			Q9BY12	SCAPE_HUMAN	S-phase cyclin A-associated protein in the ER	635	Glu-rich.					endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)	metal ion binding (GO:0046872)			NS(1)|breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(16)|ovary(2)|prostate(2)|skin(1)|urinary_tract(2)	39						GACGTTTATTCTGGGCTTCAA	0.348													C|||	38	0.00758786	0.0015	0.0187	5008	,	,		19249	0.0		0.0129	False		,,,				2504	0.0102				p.Q635Q		Atlas-SNP	.											SCAPER_ENST00000538941,NS,carcinoma,-2,2	SCAPER	160	2	0			c.G1905A						PASS	.	C	,	22,3630		0,22,1804	106.0	93.0	97.0		1167,1905	4.6	1.0	15	dbSNP_134	97	207,7951		2,203,3874	no	coding-synonymous,coding-synonymous	SCAPER	NM_001145923.1,NM_020843.2	,	2,225,5678	TT,TC,CC		2.5374,0.6024,1.939	,	389/1155,635/1401	77025687	229,11581	1826	4079	5905	SO:0001819	synonymous_variant	49855	exon15			TTTATTCTGGGCT	AB040887, AF242528	CCDS53961.1, CCDS53962.1	15q24.3	2012-10-05	2009-03-11	2007-08-20	ENSG00000140386	ENSG00000140386		"""Zinc fingers, C2H2-type"""	13081	protein-coding gene	gene with protein product		611611	"""zinc finger protein 291"""	ZNF291		17698606	Standard	NM_020843		Approved	Zfp291	uc002bby.3	Q9BY12	OTTHUMG00000172655	ENST00000563290.1:c.1905G>A	15.37:g.77025687C>T		Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	189	103	0.544974	NM_020843	F5H7X8|H3BNR7|Q3B7X7|Q96BS9|Q9H3D8|Q9NT03|Q9P274	Silent	SNP	ENST00000563290.1	37	CCDS53962.1																																																																																			C|0.988;T|0.012	0.012	strong		0.348	SCAPER-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419698.1	NM_020843	
FAR2	55711	hgsc.bcm.edu	37	12	29423460	29423460	+	Silent	SNP	G	G	A	rs2216854	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:29423460G>A	ENST00000536681.3	+	2	324	c.78G>A	c.(76-78)ctG>ctA	p.L26L	FAR2_ENST00000547116.1_Intron|FAR2_ENST00000182377.4_Silent_p.L26L	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	139	0	0		WXS	Illumina HiSeq	Phase_I	121	120	0.991736	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	
RASSF7	8045	hgsc.bcm.edu	37	11	562437	562437	+	Silent	SNP	G	G	A	rs11246189	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:562437G>A	ENST00000397583.3	+	3	916	c.483G>A	c.(481-483)agG>agA	p.R161R	RP11-496I9.1_ENST00000527620.1_RNA|RASSF7_ENST00000344375.4_Silent_p.R161R|RASSF7_ENST00000454668.2_Silent_p.R161R|RASSF7_ENST00000431809.1_Silent_p.R161R|C11orf35_ENST00000329451.3_5'Flank|RASSF7_ENST00000524468.1_3'UTR|RP11-496I9.1_ENST00000527113.1_RNA|RASSF7_ENST00000397582.3_Silent_p.R161R	NM_003475.3	NP_003466.1	Q02833	RASF7_HUMAN	Ras association (RalGDS/AF-6) domain family (N-terminal) member 7	161					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)		TGGAGCTCAGGGTGCAGAGGA	0.711													G|||	784	0.15655	0.239	0.2478	5008	,	,		16375	0.0188		0.1948	False		,,,				2504	0.0828				p.R161R	Pancreas(184;1170 3913 7268)	Atlas-SNP	.											.	RASSF7	22	.	0			c.G483A						PASS	.	G	,,	938,3214		123,692,1261	14.0	13.0	13.0		483,483,483	0.5	0.5	11	dbSNP_120	13	1641,6559		163,1315,2622	no	coding-synonymous,coding-synonymous,coding-synonymous	RASSF7	NM_001143993.1,NM_001143994.1,NM_003475.3	,,	286,2007,3883	AA,AG,GG		20.0122,22.5915,20.8792	,,	161/338,161/321,161/374	562437	2579,9773	2076	4100	6176	SO:0001819	synonymous_variant	8045	exon3			GCTCAGGGTGCAG	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.483G>A	11.37:g.562437G>A		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	143	114	0.797203	NM_001143994	G5E9N9|Q3KP41|Q3KP42	Silent	SNP	ENST00000397583.3	37	CCDS7702.1																																																																																			G|0.827;A|0.173	0.173	strong		0.711	RASSF7-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254972.2	NM_003475	
SETX	23064	hgsc.bcm.edu	37	9	135203838	135203838	+	Silent	SNP	G	G	A	rs3739921	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	122	0	0		WXS	Illumina HiSeq	Phase_I	97	39	0.402062	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	
CMAS	55907	hgsc.bcm.edu	37	12	22213786	22213786	+	Silent	SNP	C	C	T	rs10841930	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:22213786C>T	ENST00000229329.2	+	5	844	c.714C>T	c.(712-714)taC>taT	p.Y238Y		NM_018686.4	NP_061156.1	Q8NFW8	NEUA_HUMAN	cytidine monophosphate N-acetylneuraminic acid synthetase	238					lipopolysaccharide biosynthetic process (GO:0009103)|N-acetylneuraminate metabolic process (GO:0006054)	membrane (GO:0016020)|nucleus (GO:0005634)	N-acylneuraminate cytidylyltransferase activity (GO:0008781)			autonomic_ganglia(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(6)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	24						TGGCATACTACGAAATGCGAG	0.303													C|||	1268	0.253195	0.1452	0.1902	5008	,	,		15496	0.4524		0.0885	False		,,,				2504	0.408				p.Y238Y		Atlas-SNP	.											.	CMAS	45	.	0			c.C714T						PASS	.	C		681,3725	287.2+/-279.2	46,589,1568	118.0	123.0	121.0		714	-11.1	0.4	12	dbSNP_120	121	865,7731	197.5+/-242.1	39,787,3472	no	coding-synonymous	CMAS	NM_018686.3		85,1376,5040	TT,TC,CC		10.0628,15.4562,11.8905		238/435	22213786	1546,11456	2203	4298	6501	SO:0001819	synonymous_variant	55907	exon5			ATACTACGAAATG	AF271388	CCDS8696.1	12p12.1	2008-08-04			ENSG00000111726	ENSG00000111726			18290	protein-coding gene	gene with protein product	"""CMP-Neu5Ac synthetase"""	603316				8889549, 7566098	Standard	NM_018686		Approved		uc001rfm.4	Q8NFW8	OTTHUMG00000169097	ENST00000229329.2:c.714C>T	12.37:g.22213786C>T		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	30	16	0.533333	NM_018686	Q96AX5|Q9NQZ0	Silent	SNP	ENST00000229329.2	37	CCDS8696.1																																																																																			C|0.831;G|0.000;T|0.169	0.169	strong		0.303	CMAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402235.1	NM_018686	
TRIM66	9866	hgsc.bcm.edu	37	11	8662649	8662649	+	Missense_Mutation	SNP	A	A	G	rs61743935	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:8662649A>G	ENST00000299550.6	-	9	1032	c.838T>C	c.(838-840)Tat>Cat	p.Y280H	TRIM66_ENST00000402157.2_Missense_Mutation_p.Y278H	NM_014818.1	NP_055633.1	O15016	TRI66_HUMAN	tripartite motif containing 66	280						aggresome (GO:0016235)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(4)|kidney(1)|lung(1)|skin(2)	9						AAGCCTCCATAAGCAGGAGCA	0.483													A|||	163	0.0325479	0.003	0.0533	5008	,	,		20953	0.0		0.0596	False		,,,				2504	0.0634				p.Y280H		Atlas-SNP	.											.	TRIM66	45	.	0			c.T838C						PASS	.	A	HIS/TYR	14,1370		0,14,678	30.0	30.0	30.0		838	5.1	1.0	11	dbSNP_129	30	227,2955		7,213,1371	yes	missense	TRIM66	NM_014818.1	83	7,227,2049	GG,GA,AA		7.1339,1.0116,5.2781	probably-damaging	280/1217	8662649	241,4325	692	1591	2283	SO:0001583	missense	9866	exon9			CTCCATAAGCAGG	AB002296		11p15.4	2013-01-28	2011-01-25		ENSG00000166436	ENSG00000166436		"""Tripartite motif containing / Tripartite motif containing"", ""Zinc fingers, PHD-type"""	29005	protein-coding gene	gene with protein product		612000	"""chromosome 11 open reading frame 29"", ""tripartite motif-containing 66"""	C11orf29		9205841	Standard	NM_014818		Approved	KIAA0298, TIF1D	uc010rbo.2	O15016	OTTHUMG00000150481	ENST00000299550.6:c.838T>C	11.37:g.8662649A>G	ENSP00000299550:p.Tyr280His	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	128	114	0.890625	NM_014818	Q9BQQ4	Missense_Mutation	SNP	ENST00000299550.6	37		64	0.029304029304029304	1	0.0020325203252032522	13	0.03591160220994475	0	0.0	50	0.06596306068601583	A	19.67	3.871213	0.72065	0.010116	0.071339	ENSG00000166436	ENST00000299550;ENST00000402157	T;T	0.19669	2.13;2.13	5.1	5.1	0.69264	.	0.000000	0.45867	D	0.000332	T	0.04770	0.0129	M	0.69823	2.125	0.28258	N	0.924964	D	0.89917	1.0	D	0.76575	0.988	T	0.03051	-1.1078	10	0.23891	T	0.37	-12.5638	14.8856	0.70567	1.0:0.0:0.0:0.0	rs61743935	280	O15016	TRI66_HUMAN	H	280;278	ENSP00000299550:Y280H;ENSP00000384876:Y278H	ENSP00000299550:Y280H	Y	-	1	0	TRIM66	8619225	1.000000	0.71417	1.000000	0.80357	0.933000	0.57130	6.391000	0.73208	1.922000	0.55676	0.397000	0.26171	TAT	A|0.964;G|0.036	0.036	strong		0.483	TRIM66-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		XM_084529	
CDK17	5128	hgsc.bcm.edu	37	12	96676330	96676330	+	Silent	SNP	C	C	A	rs35751611	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:96676330C>A	ENST00000261211.3	-	15	2016	c.1413G>T	c.(1411-1413)gtG>gtT	p.V471V	CDK17_ENST00000542666.1_Silent_p.V418V|CDK17_ENST00000543119.2_Silent_p.V471V	NM_001170464.2|NM_002595.4	NP_001163935.1|NP_002586.2	Q00537	CDK17_HUMAN	cyclin-dependent kinase 17	471	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				protein phosphorylation (GO:0006468)		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(8)|kidney(3)|large_intestine(6)|lung(11)|ovary(4)|prostate(2)|skin(1)	37						TTCGAAAGTACACATGTTTCA	0.363													C|||	504	0.100639	0.0121	0.0389	5008	,	,		19830	0.1339		0.1064	False		,,,				2504	0.2239				p.V471V		Atlas-SNP	.											.	CDK17	71	.	0			c.G1413T						PASS	.	C	,	129,4277	94.8+/-133.5	6,117,2080	134.0	126.0	129.0		1413,1413	-4.0	1.0	12	dbSNP_126	129	815,7785	189.6+/-236.3	49,717,3534	yes	coding-synonymous,coding-synonymous	CDK17	NM_001170464.2,NM_002595.4	,	55,834,5614	AA,AC,CC		9.4767,2.9278,7.2582	,	471/524,471/524	96676330	944,12062	2203	4300	6503	SO:0001819	synonymous_variant	5128	exon15			AAAGTACACATGT		CCDS9061.1, CCDS53819.1	12q23.1	2011-11-08	2009-12-16	2009-12-16		ENSG00000059758		"""Cyclin-dependent kinases"""	8750	protein-coding gene	gene with protein product		603440	"""PCTAIRE protein kinase 2"""	PCTK2		9370357, 19884882	Standard	NM_001170464		Approved	PCTAIRE2	uc009ztk.3	Q00537		ENST00000261211.3:c.1413G>T	12.37:g.96676330C>A		Somatic	188	0	0		WXS	Illumina HiSeq	Phase_I	160	85	0.53125	NM_001170464	A8K1U6|B2RCQ2|Q8NEB8	Silent	SNP	ENST00000261211.3	37	CCDS9061.1																																																																																			C|0.924;A|0.076	0.076	strong		0.363	CDK17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408751.1	NM_002595	
MKRN1	23608	hgsc.bcm.edu	37	7	140159721	140159721	+	Silent	SNP	T	T	C	rs10243155	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:140159721T>C	ENST00000255977.2	-	3	554	c.330A>G	c.(328-330)aaA>aaG	p.K110K	MKRN1_ENST00000437223.2_Intron|MKRN1_ENST00000481705.1_5'Flank|MKRN1_ENST00000474576.1_Silent_p.K46K|MKRN1_ENST00000480552.1_Intron|MKRN1_ENST00000443720.2_Silent_p.K110K	NM_013446.3	NP_038474.2	Q9UHC7	MKRN1_HUMAN	makorin ring finger protein 1	110					protein polyubiquitination (GO:0000209)		chromatin binding (GO:0003682)|ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(3)|lung(9)|ovary(1)|skin(1)	16	Melanoma(164;0.00956)					GTTTCAATGGTTTGCTATGTT	0.443													N|||	1505	0.300519	0.7345	0.1326	5008	,	,		18806	0.1796		0.1123	False		,,,				2504	0.1513				p.K110K		Atlas-SNP	.											.	MKRN1	35	.	0			c.A330G						PASS	.	C	,	2708,1698		879,950,374	110.0	115.0	114.0		330,330	0.1	1.0	7	dbSNP_119	114	1011,7589		60,891,3349	no	coding-synonymous,coding-synonymous	MKRN1	NM_001145125.1,NM_013446.3	,	939,1841,3723	CC,CT,TT		11.7558,38.5384,28.5945	,	110/330,110/483	140159721	3719,9287	2203	4300	6503	SO:0001819	synonymous_variant	23608	exon3			CAATGGTTTGCTA	AF192784	CCDS5860.1, CCDS47725.1	7q34	2013-01-09	2008-08-13		ENSG00000133606	ENSG00000133606		"""RING-type (C3HC4) zinc fingers"""	7112	protein-coding gene	gene with protein product		607754				10843807	Standard	NM_013446		Approved	RNF61	uc003vvt.2	Q9UHC7	OTTHUMG00000157412	ENST00000255977.2:c.330A>G	7.37:g.140159721T>C		Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	90	39	0.433333	NM_013446	A4D1T7|B3KXB4|Q256Y7|Q59G11|Q6GSF1|Q9H0G0|Q9UEZ7|Q9UHW2	Silent	SNP	ENST00000255977.2	37	CCDS5860.1																																																																																			T|0.721;C|0.279	0.279	strong		0.443	MKRN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348752.1	NM_013446	
PTPRH	5794	hgsc.bcm.edu	37	19	55708573	55708573	+	Silent	SNP	G	G	A	rs2288520	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:55708573G>A	ENST00000376350.3	-	9	1924	c.1902C>T	c.(1900-1902)gcC>gcT	p.A634A	PTPRH_ENST00000588559.1_5'UTR|PTPRH_ENST00000263434.5_Silent_p.A456A	NM_002842.3	NP_002833.3	Q9HD43	PTPRH_HUMAN	protein tyrosine phosphatase, receptor type, H	634	Fibronectin type-III 7. {ECO:0000255|PROSITE-ProRule:PRU00316}.				apoptotic process (GO:0006915)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(2)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(8)|lung(27)|ovary(2)|prostate(5)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(2)	67		Renal(1328;0.245)	BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0479)		CGGGTTCCAGGGCCTCCACTT	0.587													G|||	346	0.0690895	0.0151	0.0706	5008	,	,		18796	0.0536		0.1262	False		,,,				2504	0.0982				p.A634A		Atlas-SNP	.											.	PTPRH	139	.	0			c.C1902T						PASS	.	G	,	121,4285	91.6+/-130.3	2,117,2084	122.0	104.0	110.0		1368,1902	0.5	0.0	19	dbSNP_100	110	980,7620	212.5+/-252.8	53,874,3373	no	coding-synonymous,coding-synonymous	PTPRH	NM_001161440.1,NM_002842.3	,	55,991,5457	AA,AG,GG		11.3953,2.7463,8.4653	,	456/938,634/1116	55708573	1101,11905	2203	4300	6503	SO:0001819	synonymous_variant	5794	exon9			TTCCAGGGCCTCC		CCDS33110.1, CCDS54321.1	19q13.4	2013-02-11				ENSG00000080031		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9672	protein-coding gene	gene with protein product		602510				8294459	Standard	XM_006723312		Approved	SAP-1	uc002qjq.3	Q9HD43		ENST00000376350.3:c.1902C>T	19.37:g.55708573G>A		Somatic	270	1	0.0037037		WXS	Illumina HiSeq	Phase_I	252	118	0.468254	NM_002842	C9JCH2|Q15426|Q2NKN9|Q2NKP0	Silent	SNP	ENST00000376350.3	37	CCDS33110.1																																																																																			G|0.925;A|0.075	0.075	strong		0.587	PTPRH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452649.1		
XRN1	54464	hgsc.bcm.edu	37	3	142078759	142078759	+	Missense_Mutation	SNP	C	C	T	rs73238159	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:142078759C>T	ENST00000264951.4	-	30	3526	c.3409G>A	c.(3409-3411)Gat>Aat	p.D1137N	XRN1_ENST00000392981.2_Missense_Mutation_p.D1137N	NM_019001.3	NP_061874.3	Q8IZH2	XRN1_HUMAN	5'-3' exoribonuclease 1	1137					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|histone mRNA catabolic process (GO:0071044)|mRNA metabolic process (GO:0016071)|nuclear mRNA surveillance (GO:0071028)|nuclear-transcribed mRNA catabolic process (GO:0000956)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|RNA metabolic process (GO:0016070)|rRNA catabolic process (GO:0016075)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|membrane (GO:0016020)	5'-3' exonuclease activity (GO:0008409)|DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(3)|endometrium(6)|kidney(12)|large_intestine(11)|liver(1)|lung(17)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	61						AATAGTACATCGGCTTCTCTA	0.318													C|||	417	0.0832668	0.0303	0.0821	5008	,	,		16090	0.0952		0.1451	False		,,,				2504	0.0798				p.D1137N		Atlas-SNP	.											.	XRN1	138	.	0			c.G3409A						PASS	.	C	ASN/ASP,ASN/ASP	206,4200	126.6+/-163.6	4,198,2001	69.0	71.0	70.0		3409,3409	5.5	1.0	3	dbSNP_130	70	1151,7447	233.7+/-266.9	75,1001,3223	yes	missense,missense	XRN1	NM_001042604.1,NM_019001.3	23,23	79,1199,5224	TT,TC,CC		13.3868,4.6754,10.4353	benign,benign	1137/1694,1137/1707	142078759	1357,11647	2203	4299	6502	SO:0001583	missense	54464	exon30			GTACATCGGCTTC	AY137776	CCDS3123.1, CCDS63801.1, CCDS75028.1	3q23	2008-02-05			ENSG00000114127	ENSG00000114127			30654	protein-coding gene	gene with protein product		607994				12515382	Standard	XM_005247544		Approved	SEP1	uc003eus.3	Q8IZH2	OTTHUMG00000159251	ENST00000264951.4:c.3409G>A	3.37:g.142078759C>T	ENSP00000264951:p.Asp1137Asn	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	34	8	0.235294	NM_001042604	Q4G0S3|Q68D88|Q6AI24|Q6MZS8|Q86WS7|Q8N8U4|Q9UF39	Missense_Mutation	SNP	ENST00000264951.4	37	CCDS3123.1	219	0.10027472527472528	14	0.028455284552845527	30	0.08287292817679558	64	0.11188811188811189	111	0.14643799472295516	C	28.2	4.902564	0.92035	0.046754	0.133868	ENSG00000114127	ENST00000264951;ENST00000392981	T;T	0.33216	1.42;1.42	5.51	5.51	0.81932	.	0.056674	0.64402	D	0.000001	T	0.00271	0.0008	L	0.61036	1.89	0.09310	P	1.0	P;P	0.52170	0.951;0.919	P;B	0.46940	0.532;0.332	T	0.00185	-1.1943	9	0.42905	T	0.14	-17.9298	19.427	0.94746	0.0:1.0:0.0:0.0	.	1137;1137	Q8IZH2-2;Q8IZH2	.;XRN1_HUMAN	N	1137	ENSP00000264951:D1137N;ENSP00000376707:D1137N	ENSP00000264951:D1137N	D	-	1	0	XRN1	143561449	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	6.656000	0.74396	2.573000	0.86826	0.655000	0.94253	GAT	C|0.901;T|0.099	0.099	strong		0.318	XRN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000354087.2	NM_019001	
TMEM44	93109	hgsc.bcm.edu	37	3	194346704	194346704	+	Missense_Mutation	SNP	A	A	G	rs140271606	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:194346704A>G	ENST00000392432.2	-	3	485	c.280T>C	c.(280-282)Tac>Cac	p.Y94H	TMEM44_ENST00000473092.1_Missense_Mutation_p.Y94H|TMEM44_ENST00000381975.3_Missense_Mutation_p.Y94H|TMEM44_ENST00000273580.7_Missense_Mutation_p.Y94H|TMEM44_ENST00000347147.4_Missense_Mutation_p.Y94H|TMEM44_ENST00000330115.3_5'UTR	NM_001166305.1	NP_001159777.1	Q2T9K0	TMM44_HUMAN	transmembrane protein 44	94						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)		GCTGCTAGGTAGGCACCAGTG	0.468													A|||	6	0.00119808	0.0	0.0014	5008	,	,		20623	0.0		0.003	False		,,,				2504	0.002				p.Y94H		Atlas-SNP	.											.	TMEM44	42	.	0			c.T280C						PASS	.	A	HIS/TYR,HIS/TYR,HIS/TYR,HIS/TYR	1,4405		0,1,2202	149.0	129.0	135.0		280,280,280,280	4.9	1.0	3	dbSNP_134	135	17,8583	12.6+/-44.7	0,17,4283	yes	missense,missense,missense,missense	TMEM44	NM_001011655.2,NM_001166305.1,NM_001166306.1,NM_138399.4	83,83,83,83	0,18,6485	GG,GA,AA		0.1977,0.0227,0.1384	probably-damaging,probably-damaging,probably-damaging,probably-damaging	94/429,94/476,94/397,94/439	194346704	18,12988	2203	4300	6503	SO:0001583	missense	93109	exon3			CTAGGTAGGCACC	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.280T>C	3.37:g.194346704A>G	ENSP00000376227:p.Tyr94His	Somatic	218	0	0		WXS	Illumina HiSeq	Phase_I	195	90	0.461538	NM_138399	A1L3V7|B7ZLZ5|B7ZLZ6|C9JJ62|E9PGA9|Q0P6F7|Q6ZT47|Q8IXR1|Q8N4G3	Missense_Mutation	SNP	ENST00000392432.2	37	CCDS54699.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	A	14.86	2.662149	0.47572	2.27E-4	0.001977	ENSG00000145014	ENST00000392432;ENST00000273580;ENST00000347147;ENST00000381975;ENST00000473092	T;T;T;T;T	0.35973	1.28;1.28;1.28;1.28;1.28	4.94	4.94	0.65067	.	0.104825	0.38837	N	0.001559	T	0.54191	0.1843	L	0.60455	1.87	0.42318	D	0.992247	D;D;D;D;D	0.89917	0.999;1.0;1.0;0.999;1.0	D;D;D;D;D	0.87578	0.997;0.998;0.998;0.996;0.998	T	0.58081	-0.7699	10	0.87932	D	0	-18.408	11.2784	0.49180	1.0:0.0:0.0:0.0	.	94;94;94;94;94	E9PGA9;Q2T9K0;Q2T9K0-4;Q2T9K0-2;Q2T9K0-6	.;TMM44_HUMAN;.;.;.	H	94	ENSP00000376227:Y94H;ENSP00000273580:Y94H;ENSP00000333355:Y94H;ENSP00000371402:Y94H;ENSP00000418674:Y94H	ENSP00000273580:Y94H	Y	-	1	0	TMEM44	195827993	1.000000	0.71417	1.000000	0.80357	0.339000	0.28857	4.194000	0.58393	1.980000	0.57719	0.459000	0.35465	TAC	A|0.998;G|0.002	0.002	strong		0.468	TMEM44-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000342750.1	NM_138399	
ROS1	6098	hgsc.bcm.edu	37	6	117683821	117683821	+	Missense_Mutation	SNP	G	G	A	rs2229079	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:117683821G>A	ENST00000368508.3	-	21	3524	c.3326C>T	c.(3325-3327)tCa>tTa	p.S1109L	ROS1_ENST00000368507.3_Missense_Mutation_p.S1104L|GOPC_ENST00000467125.1_Intron	NM_002944.2	NP_002935.2	P08922	ROS1_HUMAN	ROS proto-oncogene 1 , receptor tyrosine kinase	1109	Fibronectin type-III 5. {ECO:0000255|PROSITE-ProRule:PRU00316}.		S -> L (in dbSNP:rs2229079). {ECO:0000269|PubMed:17344846}.		cell differentiation (GO:0030154)|cell growth (GO:0016049)|cell proliferation (GO:0008283)|columnar/cuboidal epithelial cell development (GO:0002066)|negative regulation of gene expression (GO:0010629)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein phosphorylation (GO:0006468)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of phosphate transport (GO:0010966)|regulation of TOR signaling (GO:0032006)|spermatogenesis (GO:0007283)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)		TPM3_ENST00000368530/ROS1(4)|LRIG3/ROS1(2)|CD74_ENST00000009530/ROS1(32)|SLC34A2/ROS1(14)|EZR/ROS1(4)|GOPC/ROS1(14)|SDC4/ROS1(7)	NS(2)|breast(7)|central_nervous_system(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(28)|lung(56)|ovary(8)|prostate(5)|skin(19)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	162		all_cancers(87;0.00846)|all_epithelial(87;0.0242)		GBM - Glioblastoma multiforme(226;0.0387)|OV - Ovarian serous cystadenocarcinoma(136;0.0954)|all cancers(137;0.137)		AGACATCACTGAGGGAGTGAC	0.368			T	"""GOPC, SDC4, SLC34A2, EZR, LRIG3"""	"""glioblastoma, NSCLC"""								G|||	249	0.0497204	0.025	0.0403	5008	,	,		17334	0.003		0.0924	False		,,,				2504	0.0941				p.S1109L		Atlas-SNP	.		Dom	yes		6	6q22	6098	v-ros UR2 sarcoma virus oncogene homolog 1 (avian)		"""O, E"""	.	ROS1	728	.	0			c.C3326T						PASS	.	G	LEU/SER	229,4177	135.7+/-171.8	6,217,1980	129.0	121.0	124.0		3326	4.1	0.6	6	dbSNP_98	124	764,7836	181.9+/-230.5	44,676,3580	yes	missense	ROS1	NM_002944.2	145	50,893,5560	AA,AG,GG		8.8837,5.1975,7.6349	possibly-damaging	1109/2348	117683821	993,12013	2203	4300	6503	SO:0001583	missense	6098	exon21			ATCACTGAGGGAG	M13599	CCDS5116.1	6q21-q22	2014-06-26	2014-06-26		ENSG00000047936	ENSG00000047936		"""Fibronectin type III domain containing"""	10261	protein-coding gene	gene with protein product		165020	"""v-ros avian UR2 sarcoma virus oncogene homolog 1"", ""v-ros UR2 sarcoma virus oncogene homolog 1 (avian)"", ""c-ros oncogene 1 , receptor tyrosine kinase"""			1611909	Standard	NM_002944		Approved	MCF3, ROS, c-ros-1	uc003pxp.1	P08922	OTTHUMG00000016188	ENST00000368508.3:c.3326C>T	6.37:g.117683821G>A	ENSP00000357494:p.Ser1109Leu	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	110	47	0.427273	NM_002944	Q15368|Q5TDB5	Missense_Mutation	SNP	ENST00000368508.3	37	CCDS5116.1	114	0.0521978021978022	15	0.03048780487804878	18	0.049723756906077346	2	0.0034965034965034965	79	0.10422163588390501	G	12.28	1.889490	0.33348	0.051975	0.088837	ENSG00000047936	ENST00000368508;ENST00000368507	T;T	0.59224	0.28;0.28	5.03	4.14	0.48551	.	0.350015	0.24803	N	0.035467	T	0.35008	0.0917	M	0.62723	1.935	0.22940	N	0.998533	B	0.15719	0.014	B	0.19666	0.026	T	0.35549	-0.9784	10	0.52906	T	0.07	.	8.8243	0.35045	0.0804:0.1527:0.7669:0.0	rs2229079;rs59204588;rs2229079	1109	P08922	ROS1_HUMAN	L	1109;1104	ENSP00000357494:S1109L;ENSP00000357493:S1104L	ENSP00000357493:S1104L	S	-	2	0	ROS1	117790514	0.227000	0.23707	0.636000	0.29352	0.741000	0.42261	2.689000	0.46993	1.404000	0.46819	0.655000	0.94253	TCA	G|0.939;A|0.061	0.061	strong		0.368	ROS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043464.1		
NPC1L1	29881	hgsc.bcm.edu	37	7	44555406	44555406	+	Silent	SNP	G	G	A	rs10264715	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:44555406G>A	ENST00000289547.4	-	19	3928	c.3873C>T	c.(3871-3873)taC>taT	p.Y1291Y	NPC1L1_ENST00000546276.1_Silent_p.Y1218Y|NPC1L1_ENST00000381160.3_Silent_p.Y1264Y	NM_013389.2	NP_037521.2	Q9UHC9	NPCL1_HUMAN	NPC1-like 1	1291					cholesterol biosynthetic process (GO:0006695)|cholesterol transport (GO:0030301)|intestinal cholesterol absorption (GO:0030299)|lipoprotein metabolic process (GO:0042157)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)|sterol transport (GO:0015918)	brush border membrane (GO:0031526)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	drug binding (GO:0008144)|hedgehog receptor activity (GO:0008158)|myosin V binding (GO:0031489)|Rab GTPase binding (GO:0017137)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(4)|large_intestine(7)|lung(27)|ovary(6)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	57					Ezetimibe(DB00973)	ACTCACCCACGTAGCTGAGGA	0.542													G|||	404	0.0806709	0.0265	0.1009	5008	,	,		21742	0.005		0.2087	False		,,,				2504	0.0859				p.Y1291Y		Atlas-SNP	.											.	NPC1L1	141	.	0			c.C3873T						PASS	.	G	,	245,4161	141.5+/-176.9	11,223,1969	78.0	76.0	77.0		3792,3873	-0.1	0.9	7	dbSNP_119	77	1951,6649	343.7+/-325.0	231,1489,2580	no	coding-synonymous,coding-synonymous	NPC1L1	NM_001101648.1,NM_013389.2	,	242,1712,4549	AA,AG,GG		22.686,5.5606,16.8845	,	1264/1333,1291/1360	44555406	2196,10810	2203	4300	6503	SO:0001819	synonymous_variant	29881	exon19			ACCCACGTAGCTG		CCDS5491.1, CCDS43575.1, CCDS75587.1	7p13	2012-11-15	2012-11-15		ENSG00000015520	ENSG00000015520			7898	protein-coding gene	gene with protein product		608010	"""NPC1 (Niemann-Pick disease, type C1, gene)-like 1"""			10783261	Standard	NM_013389		Approved		uc003tlb.3	Q9UHC9	OTTHUMG00000023691	ENST00000289547.4:c.3873C>T	7.37:g.44555406G>A		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	43	38	0.883721	NM_013389	A4D2J7|B7ZLE6|D3DVK9|Q17RV5|Q6R3Q4|Q9UHC8	Silent	SNP	ENST00000289547.4	37	CCDS5491.1																																																																																			G|0.866;A|0.134	0.134	strong		0.542	NPC1L1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251256.1	NM_013389	
HSPA6	3310	hgsc.bcm.edu	37	1	161495344	161495344	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:161495344T>C	ENST00000309758.4	+	1	1309	c.896T>C	c.(895-897)aTc>aCc	p.I299T	RP11-25K21.6_ENST00000537821.2_RNA	NM_002155.3	NP_002146.2	P17066	HSP76_HUMAN	heat shock 70kDa protein 6 (HSP70B')	299					ATP catabolic process (GO:0006200)|cellular response to heat (GO:0034605)|protein refolding (GO:0042026)|response to unfolded protein (GO:0006986)	blood microparticle (GO:0072562)|centriole (GO:0005814)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)|enzyme binding (GO:0019899)|heat shock protein binding (GO:0031072)|unfolded protein binding (GO:0051082)			endometrium(3)|large_intestine(5)|lung(9)|prostate(2)|skin(2)	21	all_cancers(52;4.89e-16)|all_hematologic(112;0.0207)		BRCA - Breast invasive adenocarcinoma(70;0.00376)			TACACGTCCATCACTCGTGCC	0.647																																					p.I299T		Atlas-SNP	.											.	HSPA6	53	.	0			c.T896C						PASS	.						29.0	32.0	31.0					1																	161495344		2203	4300	6503	SO:0001583	missense	3310	exon1			CGTCCATCACTCG		CCDS1231.1	1q23.3	2011-09-02	2002-08-29		ENSG00000173110	ENSG00000173110		"""Heat shock proteins / HSP70"""	5239	protein-coding gene	gene with protein product		140555	"""heat shock 70kD protein 6 (HSP70B')"""			1346391	Standard	NM_002155		Approved		uc001gaq.3	P17066	OTTHUMG00000034461	ENST00000309758.4:c.896T>C	1.37:g.161495344T>C	ENSP00000310219:p.Ile299Thr	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	75	17	0.226667	NM_002155	Q1HBA8|Q8IYK7|Q9BT95	Missense_Mutation	SNP	ENST00000309758.4	37	CCDS1231.1	.	.	.	.	.	.	.	.	.	.	.	15.17	2.755454	0.49362	.	.	ENSG00000173110	ENST00000309758;ENST00000545155	T	0.01165	5.24	3.12	3.12	0.35913	.	0.000000	0.39475	U	0.001354	T	0.09774	0.0240	H	0.99806	4.795	0.43953	D	0.996624	P	0.43885	0.82	D	0.74023	0.982	T	0.00206	-1.1920	10	0.87932	D	0	.	9.3095	0.37895	0.0:0.0:0.0:1.0	.	299	P17066	HSP76_HUMAN	T	299;275	ENSP00000310219:I299T	ENSP00000310219:I299T	I	+	2	0	HSPA6	159761968	1.000000	0.71417	0.972000	0.41901	0.619000	0.37552	5.244000	0.65400	1.264000	0.44198	0.443000	0.29094	ATC	.	.	none		0.647	HSPA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083308.1	NM_002155	
IRAK4	51135	hgsc.bcm.edu	37	12	44177511	44177511	+	Missense_Mutation	SNP	G	G	A	rs55944915	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:44177511G>A	ENST00000448290.2	+	10	1243	c.1172G>A	c.(1171-1173)cGt>cAt	p.R391H	IRAK4_ENST00000440781.2_Missense_Mutation_p.R267H|IRAK4_ENST00000431837.1_Missense_Mutation_p.R267H|IRAK4_ENST00000551736.1_Missense_Mutation_p.R391H	NM_016123.3	NP_057207.2	Q9NWZ3	IRAK4_HUMAN	interleukin-1 receptor-associated kinase 4	391	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		R -> H (in dbSNP:rs55944915). {ECO:0000269|PubMed:17344846}.		cytokine production (GO:0001816)|cytokine-mediated signaling pathway (GO:0019221)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)	cytosol (GO:0005829)|endosome membrane (GO:0010008)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)					all_cancers(12;0.00149)	Lung NSC(34;0.0804)|all_lung(34;0.181)		GBM - Glioblastoma multiforme(48;0.04)		GATGAACACCGTGAACCTCAG	0.308													G|||	35	0.00698882	0.0008	0.0072	5008	,	,		17222	0.0		0.0159	False		,,,				2504	0.0133				p.R391H		Atlas-SNP	.											.	IRAK4	77	.	0			c.G1172A						PASS	.	G	HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG	16,4390	23.3+/-48.9	0,16,2187	98.0	99.0	99.0		1172,800,800,800,1172	5.7	1.0	12	dbSNP_129	99	130,8470	65.6+/-127.9	2,126,4172	yes	missense,missense,missense,missense,missense	IRAK4	NM_001114182.2,NM_001145256.1,NM_001145257.1,NM_001145258.1,NM_016123.3	29,29,29,29,29	2,142,6359	AA,AG,GG		1.5116,0.3631,1.1226	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	391/461,267/337,267/337,267/337,391/461	44177511	146,12860	2203	4300	6503	SO:0001583	missense	51135	exon10			AACACCGTGAACC	AF155118	CCDS8744.1, CCDS44862.1	12q12	2014-09-17				ENSG00000198001			17967	protein-coding gene	gene with protein product		606883				3772297, 10508479	Standard	NM_001114182		Approved	NY-REN-64	uc001rnt.3	Q9NWZ3		ENST00000448290.2:c.1172G>A	12.37:g.44177511G>A	ENSP00000390651:p.Arg391His	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	64	30	0.46875	NM_016123	Q69FE1|Q8TDF7|Q9Y589	Missense_Mutation	SNP	ENST00000448290.2	37	CCDS8744.1	14	0.00641025641025641	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	12	0.0158311345646438	G	23.9	4.466425	0.84425	0.003631	0.015116	ENSG00000198001	ENST00000440781;ENST00000431837;ENST00000448290;ENST00000551736	D;D;D;D	0.93426	-3.22;-3.22;-3.22;-3.22	5.68	5.68	0.88126	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.113219	0.64402	D	0.000012	D	0.93344	0.7878	M	0.71296	2.17	0.58432	D	0.999993	D	0.76494	0.999	D	0.65684	0.937	D	0.92969	0.6396	10	0.87932	D	0	-14.5611	19.8002	0.96504	0.0:0.0:1.0:0.0	rs55944915	391	Q9NWZ3	IRAK4_HUMAN	H	267;267;391;391	ENSP00000408734:R267H;ENSP00000390327:R267H;ENSP00000390651:R391H;ENSP00000446490:R391H	ENSP00000390327:R267H	R	+	2	0	IRAK4	42463778	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	5.622000	0.67750	2.674000	0.91012	0.655000	0.94253	CGT	G|0.989;A|0.011	0.011	strong		0.308	IRAK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403947.1		
ELP2	55250	hgsc.bcm.edu	37	18	33725931	33725931	+	Missense_Mutation	SNP	G	G	A	rs1785928	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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_ENST00000423854.2_Missense_Mutation_p.V235M|ELP2_ENST00000350494.6_Missense_Mutation_p.V344M|ELP2_ENST00000442325.2_Missense_Mutation_p.V370M|ELP2_ENST00000542824.1_Missense_Mutation_p.V279M	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	215	0	0		WXS	Illumina HiSeq	Phase_I	174	76	0.436782	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	
PPP1R26	9858	hgsc.bcm.edu	37	9	138377433	138377433	+	Silent	SNP	G	G	A	rs3827827	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:138377433G>A	ENST00000356818.2	+	4	1626	c.1077G>A	c.(1075-1077)gcG>gcA	p.A359A	PPP1R26_ENST00000604351.1_Silent_p.A359A|PPP1R26_ENST00000401470.3_Silent_p.A359A|PPP1R26_ENST00000602993.1_Intron|PPP1R26_ENST00000605660.1_Silent_p.A359A|PPP1R26_ENST00000605286.1_Silent_p.A359A	NM_014811.3	NP_055626.3	Q5T8A7	PPR26_HUMAN	protein phosphatase 1, regulatory subunit 26	359					negative regulation of phosphatase activity (GO:0010923)	nucleus (GO:0005634)	phosphatase binding (GO:0019902)|protein phosphatase inhibitor activity (GO:0004864)										CGTCCGAGGCGTCCGACTCCA	0.622													G|||	1001	0.19988	0.1717	0.2839	5008	,	,		18482	0.1141		0.175	False		,,,				2504	0.2924				p.A359A		Atlas-SNP	.											KIAA0649,NS,carcinoma,0,1	.	.	1	0			c.G1077A						PASS	.	G		660,3746	267.4+/-267.8	44,572,1587	51.0	59.0	57.0		1077	-10.7	0.0	9	dbSNP_107	57	1507,7093	274.3+/-291.2	141,1225,2934	no	coding-synonymous	KIAA0649	NM_014811.3		185,1797,4521	AA,AG,GG		17.5233,14.9796,16.6615		359/1210	138377433	2167,10839	2203	4300	6503	SO:0001819	synonymous_variant	9858	exon4			CGAGGCGTCCGAC	AB014549	CCDS6988.1	9q34.3	2012-04-17	2011-10-11	2011-10-11	ENSG00000196422	ENSG00000196422		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	29089	protein-coding gene	gene with protein product	"""DRIM/UTP20 interacting protein"", ""1A6/DRIM (down-regulated in metastasis) interacting protein"""	614056	"""KIAA0649"""	KIAA0649		9734811, 16053918	Standard	NM_014811		Approved		uc004cfr.1	Q5T8A7	OTTHUMG00000020904	ENST00000356818.2:c.1077G>A	9.37:g.138377433G>A		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	105	47	0.447619	NM_014811	Q86WU0|Q8WVV0|Q9Y4D3	Silent	SNP	ENST00000356818.2	37	CCDS6988.1																																																																																			G|0.824;A|0.176	0.176	strong		0.622	PPP1R26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054987.1	NM_014811	
PPIG	9360	hgsc.bcm.edu	37	2	170441001	170441001	+	Splice_Site	SNP	G	G	A	rs2276611	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:170441001G>A	ENST00000260970.3	+	1	151		c.e1+1		PPIG_ENST00000448752.2_5'UTR|PPIG_ENST00000462903.1_5'UTR|PPIG_ENST00000409714.3_Splice_Site	NM_004792.2	NP_004783.2	Q13427	PPIG_HUMAN	peptidylprolyl isomerase G (cyclophilin G)						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)	ACCGGTGCAGGTAAGTGGTAT	0.607													G|||	970	0.19369	0.1762	0.1686	5008	,	,		17429	0.2212		0.1193	False		,,,				2504	0.2832				.		Atlas-SNP	.											.	PPIG	100	.	0			.						PASS	.																																			SO:0001630	splice_region_variant	9360	.			GTGCAGGTAAGTG	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.-70+1G>A	2.37:g.170441001G>A		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	67	33	0.492537	.	D3DPC5|D3DPC6|O00706|Q53R40|Q53SN4|Q96DG9	Splice_Site	SNP	ENST00000260970.3	37	CCDS2235.1	371	0.16987179487179488	81	0.16463414634146342	62	0.1712707182320442	134	0.23426573426573427	94	0.12401055408970976	G	34	5.373470	0.95923	.	.	ENSG00000138398	ENST00000433207	.	.	.	5.43	5.43	0.79202	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.6144	0.68539	0.0:0.0:1.0:0.0	rs2276611;rs2276611	.	.	.	.	-1	.	.	.	+	.	.	PPIG	170149247	1.000000	0.71417	0.992000	0.48379	0.954000	0.61252	4.235000	0.58666	2.826000	0.97356	0.655000	0.94253	.	G|0.830;A|0.170	0.170	strong		0.607	PPIG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255264.2		Intron
ADAP1	11033	hgsc.bcm.edu	37	7	943868	943868	+	Silent	SNP	G	G	A	rs61730955	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:943868G>A	ENST00000265846.5	-	6	762	c.543C>T	c.(541-543)aaC>aaT	p.N181N	ADAP1_ENST00000539900.1_Silent_p.N192N|ADAP1_ENST00000449296.2_Silent_p.N109N|ADAP1_ENST00000463358.1_5'UTR	NM_001284308.1|NM_001284309.1|NM_001284311.1|NM_006869.2	NP_001271237.1|NP_001271238.1|NP_001271240.1|NP_006860	O75689	ADAP1_HUMAN	ArfGAP with dual PH domains 1	181	PH 1. {ECO:0000255|PROSITE- ProRule:PRU00145}.				cell surface receptor signaling pathway (GO:0007166)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF GTPase activity (GO:0032312)|regulation of GTPase activity (GO:0043087)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ARF GTPase activator activity (GO:0008060)|inositol 1,3,4,5 tetrakisphosphate binding (GO:0043533)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|lung(3)|upper_aerodigestive_tract(1)	6						GGAAGGTGGCGTTCAGGTGCT	0.612													G|||	211	0.0421326	0.0507	0.0548	5008	,	,		17370	0.0188		0.0577	False		,,,				2504	0.0297				p.N181N		Atlas-SNP	.											.	ADAP1	23	.	0			c.C543T						PASS	.	G		163,4241	107.8+/-146.2	2,159,2041	149.0	122.0	131.0		543	-5.7	0.8	7	dbSNP_129	131	545,8049	149.5+/-204.6	11,523,3763	no	coding-synonymous	ADAP1	NM_006869.2		13,682,5804	AA,AG,GG		6.3416,3.7012,5.447		181/375	943868	708,12290	2202	4297	6499	SO:0001819	synonymous_variant	11033	exon6			GGTGGCGTTCAGG	AJ006422	CCDS5318.1, CCDS64576.1, CCDS64577.1, CCDS75558.1	7p22.3	2013-01-10	2008-09-22	2008-09-22	ENSG00000105963	ENSG00000105963		"""ADP-ribosylation factor GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"""	16486	protein-coding gene	gene with protein product		608114	"""centaurin, alpha 1"""	CENTA1		10333475	Standard	NM_006869		Approved	GCS1L	uc003sjo.4	O75689	OTTHUMG00000023380	ENST00000265846.5:c.543C>T	7.37:g.943868G>A		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	118	26	0.220339	NM_006869	A4D2Q2|B3KRZ4|B4DVA6|F6XZ68|H7C2Q4	Silent	SNP	ENST00000265846.5	37	CCDS5318.1	110|110	0.05036630036630037|0.05036630036630037	28|28	0.056910569105691054|0.056910569105691054	22|22	0.06077348066298342|0.06077348066298342	14|14	0.024475524475524476|0.024475524475524476	46|46	0.06068601583113457|0.06068601583113457	g|g	1.019|1.019	-0.685321|-0.685321	0.03328|0.03328	0.037012|0.037012	0.063416|0.063416	ENSG00000105963|ENSG00000105963	ENST00000454383|ENST00000446141;ENST00000437486;ENST00000453823	.|.	.|.	.|.	4.29|4.29	-5.72|-5.72	0.02406|0.02406	.|.	.|.	.|.	.|.	.|.	T|T	0.11410|0.11410	0.0278|0.0278	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.51228|0.51228	-0.8732|-0.8732	4|4	.|.	.|.	.|.	-38.1015|-38.1015	11.5039|11.5039	0.50454|0.50454	0.578:0.0:0.422:0.0|0.578:0.0:0.422:0.0	.|.	.|.	.|.	.|.	C|M	122|164;115;124	.|.	.|.	R|T	-|-	1|2	0|0	ADAP1|ADAP1	910394|910394	0.959000|0.959000	0.32827|0.32827	0.789000|0.789000	0.31954|0.31954	0.059000|0.059000	0.15707|0.15707	0.211000|0.211000	0.17474|0.17474	-0.723000|-0.723000	0.04915|0.04915	-0.471000|-0.471000	0.05019|0.05019	CGC|ACG	G|0.946;A|0.054	0.054	strong		0.612	ADAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059701.2	NM_006869	
COL5A3	50509	hgsc.bcm.edu	37	19	10078589	10078589	+	Silent	SNP	T	T	C	rs3815748	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:10078589T>C	ENST00000264828.3	-	61	4480	c.4395A>G	c.(4393-4395)aaA>aaG	p.K1465K		NM_015719.3	NP_056534.2	P25940	CO5A3_HUMAN	collagen, type V, alpha 3	1465	Collagen-like 6.|Triple-helical 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)			CCGGAGACCCTTTTGAGCCTT	0.572													C|||	1210	0.241613	0.093	0.2363	5008	,	,		15764	0.3105		0.1759	False		,,,				2504	0.4427				p.K1465K		Atlas-SNP	.											.	COL5A3	243	.	0			c.A4395G						PASS	.	C		449,3957	782.1+/-414.5	23,403,1777	116.0	113.0	114.0		4395	0.9	1.0	19	dbSNP_107	114	1420,7180	747.2+/-407.3	132,1156,3012	no	coding-synonymous	COL5A3	NM_015719.3		155,1559,4789	CC,CT,TT		16.5116,10.1906,14.3703		1465/1746	10078589	1869,11137	2203	4300	6503	SO:0001819	synonymous_variant	50509	exon61			AGACCCTTTTGAG	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.4395A>G	19.37:g.10078589T>C		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	83	40	0.481928	NM_015719	Q9NZQ6	Silent	SNP	ENST00000264828.3	37	CCDS12222.1																																																																																			T|0.837;C|0.163	0.163	strong		0.572	COL5A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315788.1	NM_015719	
CLDN6	9074	hgsc.bcm.edu	37	16	3065596	3065596	+	Missense_Mutation	SNP	T	T	C	rs2257295	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:3065596T>C	ENST00000396925.1	-	3	855	c.427A>G	c.(427-429)Atc>Gtc	p.I143V	TNFRSF12A_ENST00000573001.1_5'Flank|CLDN6_ENST00000328796.4_Missense_Mutation_p.I143V|CLDN6_ENST00000572154.1_Intron			P56747	CLD6_HUMAN	claudin 6	143			I -> V (in dbSNP:rs2257295). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:16303743, ECO:0000269|Ref.1, ECO:0000269|Ref.2}.		calcium-independent cell-cell adhesion (GO:0016338)|cell-cell junction organization (GO:0045216)|viral process (GO:0016032)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	identical protein binding (GO:0042802)|structural molecule activity (GO:0005198)			kidney(1)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	10						TCCCGGATGATGGCATGCGCC	0.617													T|||	1497	0.298922	0.3548	0.3343	5008	,	,		18815	0.1925		0.3708	False		,,,				2504	0.2342				p.I143V		Atlas-SNP	.											CLDN6,rectum,carcinoma,0,3	CLDN6	31	3	0			c.A427G						PASS	.	T	VAL/ILE	1631,2761		311,1009,876	23.0	25.0	25.0		427	2.5	0.9	16	dbSNP_100	25	3379,5217		688,2003,1607	no	missense	CLDN6	NM_021195.4	29	999,3012,2483	CC,CT,TT		39.309,37.1357,38.5741	benign	143/221	3065596	5010,7978	2196	4298	6494	SO:0001583	missense	9074	exon2			GGATGATGGCATG	AJ249735	CCDS10488.1	16p13.3	2008-08-01			ENSG00000184697	ENSG00000184697		"""Claudins"""	2048	protein-coding gene	gene with protein product		615798				9892664, 18234789	Standard	NM_021195		Approved		uc002csu.4	P56747	OTTHUMG00000128999	ENST00000396925.1:c.427A>G	16.37:g.3065596T>C	ENSP00000380131:p.Ile143Val	Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	92	65	0.706522	NM_021195	B3KQP9|D3DUA5	Missense_Mutation	SNP	ENST00000396925.1	37	CCDS10488.1	695	0.3182234432234432	179	0.3638211382113821	122	0.3370165745856354	124	0.21678321678321677	270	0.3562005277044855	T	6.973	0.549571	0.13374	0.371357	0.39309	ENSG00000184697	ENST00000396925;ENST00000328796	D;D	0.89270	-2.49;-2.49	4.76	2.51	0.30379	.	0.125321	0.52532	N	0.000076	T	0.00012	0.0000	L	0.33245	0.995	0.32491	P	0.540211	B	0.22276	0.067	B	0.27500	0.08	T	0.10776	-1.0615	9	0.23302	T	0.38	.	7.5467	0.27770	0.0:0.1806:0.0:0.8194	rs2257295;rs17850428;rs61137178;rs2257295	143	P56747	CLD6_HUMAN	V	143	ENSP00000380131:I143V;ENSP00000328674:I143V	ENSP00000328674:I143V	I	-	1	0	CLDN6	3005597	1.000000	0.71417	0.941000	0.38009	0.114000	0.19823	1.726000	0.38085	0.423000	0.26033	0.533000	0.62120	ATC	T|0.645;C|0.355	0.355	strong		0.617	CLDN6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250988.1	NM_021195	
CDH18	1016	hgsc.bcm.edu	37	5	19591174	19591174	+	Silent	SNP	A	A	G	rs17285716	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:19591174A>G	ENST00000507958.1	-	9	1981	c.991T>C	c.(991-993)Tta>Cta	p.L331L	CDH18_ENST00000502796.1_Silent_p.L331L|CDH18_ENST00000506372.1_Silent_p.L331L|CDH18_ENST00000382275.1_Silent_p.L331L|CDH18_ENST00000274170.4_Silent_p.L331L|CDH18_ENST00000511273.1_Silent_p.L331L			Q13634	CAD18_HUMAN	cadherin 18, type 2	331	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(24)|lung(76)|ovary(5)|prostate(4)|skin(6)|upper_aerodigestive_tract(1)	138	Lung NSC(1;0.00734)|all_lung(1;0.0197)					ACCTTCTTTAAAGAAAGGATT	0.403													A|||	480	0.0958466	0.0151	0.1945	5008	,	,		16900	0.004		0.1799	False		,,,				2504	0.1431				p.L331L		Atlas-SNP	.											CDH18_ENST00000507958,NS,adenoma,0,4	CDH18	561	4	0			c.T991C						PASS	.	A	,	208,4198	127.8+/-164.7	7,194,2002	88.0	77.0	81.0		991,991	4.1	1.0	5	dbSNP_123	81	1595,7005	295.4+/-302.4	131,1333,2836	no	coding-synonymous,coding-synonymous	CDH18	NM_001167667.1,NM_004934.3	,	138,1527,4838	GG,GA,AA		18.5465,4.7208,13.8628	,	331/575,331/791	19591174	1803,11203	2203	4300	6503	SO:0001819	synonymous_variant	1016	exon7			TCTTTAAAGAAAG	U59325	CCDS3889.1, CCDS54835.1, CCDS75229.1	5p14.3	2010-01-26			ENSG00000145526	ENSG00000145526		"""Cadherins / Major cadherins"""	1757	protein-coding gene	gene with protein product		603019				9030594, 10191097	Standard	NM_004934		Approved	CDH14, EY-CADHERIN	uc003jgd.3	Q13634	OTTHUMG00000090578	ENST00000507958.1:c.991T>C	5.37:g.19591174A>G		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	105	51	0.485714	NM_001167667	A8K0I2|B4DHG6|Q8N5Z2	Silent	SNP	ENST00000507958.1	37	CCDS3889.1																																																																																			A|0.879;G|0.121	0.121	strong		0.403	CDH18-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366747.1	NM_004934	
SLIT2	9353	hgsc.bcm.edu	37	4	20487867	20487867	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:20487867T>C	ENST00000504154.1	+	7	836	c.584T>C	c.(583-585)tTc>tCc	p.F195S	SLIT2_ENST00000503837.1_Missense_Mutation_p.F195S|SLIT2_ENST00000273739.5_Missense_Mutation_p.F195S|SLIT2_ENST00000503823.1_Missense_Mutation_p.F195S	NM_004787.1	NP_004778.1	O94813	SLIT2_HUMAN	slit homolog 2 (Drosophila)	195					apoptotic process involved in luteolysis (GO:0061364)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|branching morphogenesis of an epithelial tube (GO:0048754)|cell migration involved in sprouting angiogenesis (GO:0002042)|cellular response to heparin (GO:0071504)|cellular response to hormone stimulus (GO:0032870)|chemorepulsion involved in postnatal olfactory bulb interneuron migration (GO:0021836)|corticospinal neuron axon guidance through spinal cord (GO:0021972)|dorsal/ventral axon guidance (GO:0033563)|in utero embryonic development (GO:0001701)|induction of negative chemotaxis (GO:0050929)|mammary duct terminal end bud growth (GO:0060763)|metanephros development (GO:0001656)|motor neuron axon guidance (GO:0008045)|negative chemotaxis (GO:0050919)|negative regulation of actin filament polymerization (GO:0030837)|negative regulation of axon extension (GO:0030517)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cellular response to growth factor stimulus (GO:0090288)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of gene expression (GO:0010629)|negative regulation of lamellipodium assembly (GO:0010593)|negative regulation of leukocyte chemotaxis (GO:0002689)|negative regulation of monocyte chemotaxis (GO:0090027)|negative regulation of mononuclear cell migration (GO:0071676)|negative regulation of neutrophil chemotaxis (GO:0090024)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of retinal ganglion cell axon guidance (GO:0090260)|negative regulation of small GTPase mediated signal transduction (GO:0051058)|negative regulation of smooth muscle cell chemotaxis (GO:0071672)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of vascular permeability (GO:0043116)|positive regulation of apoptotic process (GO:0043065)|positive regulation of axonogenesis (GO:0050772)|response to cortisol (GO:0051414)|retinal ganglion cell axon guidance (GO:0031290)|Roundabout signaling pathway (GO:0035385)|single organismal cell-cell adhesion (GO:0016337)|ureteric bud development (GO:0001657)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|chemorepellent activity (GO:0045499)|GTPase inhibitor activity (GO:0005095)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|laminin-1 binding (GO:0043237)|protein homodimerization activity (GO:0042803)|proteoglycan binding (GO:0043394)|Roundabout binding (GO:0048495)			NS(1)|breast(4)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(7)|large_intestine(17)|lung(60)|ovary(3)|pancreas(1)|prostate(2)|skin(10)|upper_aerodigestive_tract(1)	116						GTGGCAAGTTTCAACCATATG	0.289																																					p.F195S		Atlas-SNP	.											.	SLIT2	290	.	0			c.T584C						PASS	.						76.0	77.0	77.0					4																	20487867		2202	4299	6501	SO:0001583	missense	9353	exon7			CAAGTTTCAACCA	AF055585	CCDS3426.1, CCDS75110.1, CCDS75111.1	4p15.2	2008-08-01	2001-11-28		ENSG00000145147	ENSG00000145147			11086	protein-coding gene	gene with protein product		603746	"""slit (Drosophila) homolog 2"""	SLIL3		9813312, 18269211	Standard	XM_005248211		Approved	Slit-2	uc003gpr.1	O94813	OTTHUMG00000128551	ENST00000504154.1:c.584T>C	4.37:g.20487867T>C	ENSP00000422591:p.Phe195Ser	Somatic	269	0	0		WXS	Illumina HiSeq	Phase_I	163	45	0.276074	NM_004787	B7ZLR5|O95710|Q17RU3|Q9Y5Q7	Missense_Mutation	SNP	ENST00000504154.1	37	CCDS3426.1	.	.	.	.	.	.	.	.	.	.	T	27.8	4.867172	0.91511	.	.	ENSG00000145147	ENST00000503823;ENST00000504154;ENST00000273739;ENST00000382173;ENST00000503837	T;T;T;T	0.70749	-0.51;-0.51;-0.51;-0.51	5.3	5.3	0.74995	.	0.090982	0.85682	D	0.000000	D	0.88175	0.6366	H	0.94620	3.56	0.80722	D	1	D;D	0.76494	0.999;0.997	D;D	0.75484	0.986;0.978	D	0.91139	0.4944	10	0.59425	D	0.04	.	15.5307	0.75960	0.0:0.0:0.0:1.0	.	195;195	O94813-3;O94813	.;SLIT2_HUMAN	S	195	ENSP00000427548:F195S;ENSP00000422591:F195S;ENSP00000273739:F195S;ENSP00000422261:F195S	ENSP00000273739:F195S	F	+	2	0	SLIT2	20096965	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.997000	0.88414	2.120000	0.65058	0.459000	0.35465	TTC	.	.	none		0.289	SLIT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250396.2		
ITIH1	3697	hgsc.bcm.edu	37	3	52825585	52825585	+	Silent	SNP	T	T	C	rs9324	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:52825585T>C	ENST00000273283.2	+	21	2571	c.2547T>C	c.(2545-2547)tcT>tcC	p.S849S	ITIH1_ENST00000542827.1_3'UTR|ITIH1_ENST00000540715.1_Silent_p.S707S|ITIH1_ENST00000405128.3_Silent_p.S215S|ITIH1_ENST00000537050.1_Silent_p.S561S	NM_002215.3	NP_002206.2	P19827	ITIH1_HUMAN	inter-alpha-trypsin inhibitor heavy chain 1	849	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)		ACCCAGGCTCTGACCCCACAA	0.597													C|||	2063	0.411941	0.5825	0.4669	5008	,	,		19605	0.373		0.3926	False		,,,				2504	0.2025				p.S849S		Atlas-SNP	.											.	ITIH1	108	.	0			c.T2547C						PASS	.	C	,,,	2279,2127	577.5+/-384.5	573,1133,497	88.0	85.0	86.0		2121,1683,1683,2547	-7.7	0.4	3	dbSNP_52	86	3140,5460	657.0+/-401.4	594,1952,1754	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ITIH1	NM_001166434.1,NM_001166435.1,NM_001166436.1,NM_002215.2	,,,	1167,3085,2251	CC,CT,TT		36.5116,48.2751,41.6654	,,,	707/770,561/624,561/624,849/912	52825585	5419,7587	2203	4300	6503	SO:0001819	synonymous_variant	3697	exon21			AGGCTCTGACCCC		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.2547T>C	3.37:g.52825585T>C		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	49	47	0.959184	NM_002215	A8K9N5|B2RAH9|B7Z558|B7Z8C0|F5H165|F5H7Y8|P78455|Q01746|Q562G1	Silent	SNP	ENST00000273283.2	37	CCDS2864.1																																																																																			T|0.568;C|0.432	0.432	strong		0.597	ITIH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317522.1	NM_002215	
MYO9B	4650	hgsc.bcm.edu	37	19	17273893	17273893	+	Silent	SNP	G	G	T	rs7256689	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:17273893G>T	ENST00000594824.1	+	10	1779	c.1632G>T	c.(1630-1632)ctG>ctT	p.L544L	MYO9B_ENST00000595618.1_Silent_p.L544L|MYO9B_ENST00000397274.2_Silent_p.L544L|CTD-3032J10.2_ENST00000597216.1_RNA|CTD-3032J10.2_ENST00000599360.1_RNA			Q13459	MYO9B_HUMAN	myosin IXB	544	Myosin motor.				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						ATGAGCAGCTGCAGTATTACT	0.468													A|||	3747	0.748203	0.9629	0.7406	5008	,	,		20340	0.7312		0.6501	False		,,,				2504	0.5818				p.L544L		Atlas-SNP	.											.	MYO9B	264	.	0			c.G1632T						PASS	.	A	,	3671,333		1689,293,20	62.0	57.0	59.0		1632,1632	-10.1	0.2	19	dbSNP_116	59	5548,2876		1808,1932,472	no	coding-synonymous,coding-synonymous	MYO9B	NM_001130065.1,NM_004145.3	,	3497,2225,492	TT,TG,GG		34.1406,8.3167,25.8207	,	544/2023,544/2158	17273893	9219,3209	2002	4212	6214	SO:0001819	synonymous_variant	4650	exon10			GCAGCTGCAGTAT		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.1632G>T	19.37:g.17273893G>T		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	106	52	0.490566	NM_001130065	O75314|Q9NUJ2|Q9UHN0	Silent	SNP	ENST00000594824.1	37																																																																																				G|0.238;T|0.762	0.762	strong		0.468	MYO9B-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000463236.1		
HIST1H1A	3024	hgsc.bcm.edu	37	6	26017542	26017542	+	Missense_Mutation	SNP	T	T	C	rs16891235	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:26017542T>C	ENST00000244573.3	-	1	498	c.419A>G	c.(418-420)aAa>aGa	p.K140R		NM_005325.3	NP_005316.1	Q02539	H11_HUMAN	histone cluster 1, H1a	140			K -> R (in dbSNP:rs16891235).		nucleosome assembly (GO:0006334)|spermatogenesis (GO:0007283)	nuclear chromatin (GO:0000790)|nuclear euchromatin (GO:0005719)|nucleosome (GO:0000786)	chromatin DNA binding (GO:0031490)			cervix(1)|endometrium(4)|kidney(1)|large_intestine(3)|ovary(3)|prostate(1)	13						CGTGGCCTTTTTGAGCTTTTT	0.493													T|||	369	0.0736821	0.1324	0.0706	5008	,	,		16862	0.0149		0.0944	False		,,,				2504	0.0358				p.K140R		Atlas-SNP	.											.	HIST1H1A	25	.	0			c.A419G						PASS	.	T	ARG/LYS	519,3887		36,447,1720	120.0	128.0	125.0		419	-1.0	0.0	6	dbSNP_123	125	888,7712		45,798,3457	yes	missense	HIST1H1A	NM_005325.3	26	81,1245,5177	CC,CT,TT		10.3256,11.7794,10.8181	benign	140/216	26017542	1407,11599	2203	4300	6503	SO:0001583	missense	3024	exon1			GCCTTTTTGAGCT	AF531299	CCDS4569.1	6p22.1	2012-11-16	2006-10-11	2003-02-21	ENSG00000124610	ENSG00000124610		"""Histones / Replication-dependent"""	4715	protein-coding gene	gene with protein product		142709	"""H1 histone family, member 1"", ""histone 1, H1a"""	H1F1		2759094, 12408966	Standard	NM_005325		Approved	H1.1, H1a	uc003nfo.3	Q02539	OTTHUMG00000016413	ENST00000244573.3:c.419A>G	6.37:g.26017542T>C	ENSP00000244573:p.Lys140Arg	Somatic	210	0	0		WXS	Illumina HiSeq	Phase_I	177	94	0.531073	NM_005325	Q3MJ34	Missense_Mutation	SNP	ENST00000244573.3	37	CCDS4569.1	166	0.076007326007326	52	0.10569105691056911	27	0.07458563535911603	10	0.017482517482517484	77	0.10158311345646438	N	4.085	0.013674	0.07959	0.117794	0.103256	ENSG00000124610	ENST00000244573	T	0.21932	1.98	4.31	-1.02	0.10135	.	0.774546	0.11638	N	0.544065	T	0.02929	0.0087	N	0.08118	0	0.33361	P	0.427677	B	0.13145	0.007	B	0.10450	0.005	T	0.45906	-0.9229	9	0.28530	T	0.3	-21.4092	8.7383	0.34541	0.0:0.3184:0.0:0.6816	rs16891235;rs52798641;rs58813645;rs16891235	140	Q02539	H11_HUMAN	R	140	ENSP00000244573:K140R	ENSP00000244573:K140R	K	-	2	0	HIST1H1A	26125521	0.933000	0.31639	0.003000	0.11579	0.033000	0.12548	1.692000	0.37731	-0.266000	0.09339	-0.315000	0.08773	AAA	T|0.908;C|0.092	0.092	strong		0.493	HIST1H1A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043884.1	NM_005325	
OBSCN	84033	hgsc.bcm.edu	37	1	228492220	228492220	+	Intron	SNP	C	C	T	rs41270183	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:228492220C>T	ENST00000422127.1	+	44	11703				OBSCN_ENST00000284548.11_Intron|RP5-1139B12.4_ENST00000602778.1_RNA|OBSCN_ENST00000570156.2_Missense_Mutation_p.S4740L|OBSCN_ENST00000366709.4_Intron|OBSCN_ENST00000366707.4_Missense_Mutation_p.S1430L	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)				GGGGAGTACTCGTGCGTGTGT	0.577													C|||	27	0.00539137	0.0	0.0072	5008	,	,		20854	0.0		0.0199	False		,,,				2504	0.002				p.S4740L		Atlas-SNP	.											.	OBSCN	2142	.	0			c.C14219T						PASS	.	C	,	3,1749		0,3,873	155.0	130.0	137.0		,	-3.3	0.0	1	dbSNP_127	137	63,3919		0,63,1928	no	intron,intron	OBSCN	NM_001098623.1,NM_052843.2	,	0,66,2801	TT,TC,CC		1.5821,0.1712,1.151	,	,	228492220	66,5668	876	1991	2867	SO:0001627	intron_variant	84033	exon53			AGTACTCGTGCGT	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.11660-1853C>T	1.37:g.228492220C>T		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	95	61	0.642105	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	23	0.010531135531135532	0	0.0	5	0.013812154696132596	0	0.0	18	0.023746701846965697	C	15.44	2.834112	0.50951	0.001712	0.015821	ENSG00000154358	ENST00000366707	T	0.04862	3.54	5.15	-3.29	0.05017	.	.	.	.	.	T	0.02267	0.0070	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.46428	-0.9192	5	.	.	.	.	8.8639	0.35274	0.0:0.3538:0.3799:0.2663	rs41270183;rs61825287	.	.	.	L	1430	ENSP00000355668:S1430L	.	S	+	2	0	OBSCN	226558843	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-0.811000	0.04500	-0.202000	0.10268	0.561000	0.74099	TCG	C|0.988;T|0.012	0.012	strong		0.577	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
ZNF804A	91752	hgsc.bcm.edu	37	2	185801917	185801917	+	Silent	SNP	A	A	G	rs728534	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	76	0	0		WXS	Illumina HiSeq	Phase_I	75	74	0.986667	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	
ZNF215	7762	hgsc.bcm.edu	37	11	6953858	6953858	+	Missense_Mutation	SNP	A	A	G	rs11041108	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:6953858A>G	ENST00000278319.5	+	3	943	c.355A>G	c.(355-357)Atg>Gtg	p.M119V	ZNF215_ENST00000529903.1_Missense_Mutation_p.M119V|ZNF215_ENST00000414517.2_Missense_Mutation_p.M119V|ZNF215_ENST00000527171.1_3'UTR	NM_013250.2	NP_037382.2	Q9UL58	ZN215_HUMAN	zinc finger protein 215	119	SCAN box. {ECO:0000255|PROSITE- ProRule:PRU00187}.		M -> V (in dbSNP:rs11041108).		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)		CAGTAAAGATATGGTGACCCT	0.378													A|||	1301	0.259784	0.0393	0.3026	5008	,	,		20131	0.37		0.3658	False		,,,				2504	0.3047				p.M119V		Atlas-SNP	.											.	ZNF215	72	.	0			c.A355G						PASS	.	A	VAL/MET	401,4001	192.3+/-217.7	27,347,1827	58.0	61.0	60.0		355	2.2	0.9	11	dbSNP_120	60	3115,5477	473.0+/-368.5	559,1997,1740	yes	missense	ZNF215	NM_013250.2	21	586,2344,3567	GG,GA,AA		36.2547,9.1095,27.0586	benign	119/518	6953858	3516,9478	2201	4296	6497	SO:0001583	missense	7762	exon3			AAAGATATGGTGA	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.355A>G	11.37:g.6953858A>G	ENSP00000278319:p.Met119Val	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	94	11	0.117021	NM_013250	Q96C84	Missense_Mutation	SNP	ENST00000278319.5	37	CCDS7775.1	599	0.2742673992673993	23	0.046747967479674794	103	0.2845303867403315	203	0.3548951048951049	270	0.3562005277044855	A	0	-2.754117	0.00085	0.091095	0.362547	ENSG00000149054	ENST00000278319;ENST00000414517;ENST00000529903	T;T;T	0.04502	3.61;3.61;3.61	4.14	2.17	0.27698	Retrovirus capsid, C-terminal (1);Transcription regulator SCAN (3);	0.516931	0.14835	N	0.295605	T	0.00012	0.0000	N	0.00017	-2.845	0.45762	P	0.0013450000000000406	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.0;0.0	T	0.42949	-0.9421	9	0.02654	T	1	-3.9644	6.3178	0.21200	0.2259:0.0:0.7741:0.0	rs11041108;rs52821111;rs58656969;rs11041108	119;119;119	B4DYW9;Q96C84;Q9UL58	.;.;ZN215_HUMAN	V	119	ENSP00000278319:M119V;ENSP00000393202:M119V;ENSP00000432306:M119V	ENSP00000278319:M119V	M	+	1	0	ZNF215	6910434	0.981000	0.34729	0.871000	0.34182	0.052000	0.14988	1.693000	0.37742	0.678000	0.31325	-0.177000	0.13119	ATG	A|0.721;G|0.279	0.279	strong		0.378	ZNF215-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384550.1		
SEMA4D	10507	hgsc.bcm.edu	37	9	92003679	92003679	+	Missense_Mutation	SNP	C	C	T	rs11526468	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:92003679C>T	ENST00000450295.1	-	11	1755	c.979G>A	c.(979-981)Gcc>Acc	p.A327T	SEMA4D_ENST00000339861.4_Missense_Mutation_p.A327T|SEMA4D_ENST00000420987.1_Missense_Mutation_p.A327T|SEMA4D_ENST00000438547.2_Missense_Mutation_p.A327T|SEMA4D_ENST00000455551.2_Missense_Mutation_p.A327T|SEMA4D_ENST00000356444.2_Missense_Mutation_p.A327T|SEMA4D_ENST00000422704.2_Missense_Mutation_p.A327T|SEMA4D_ENST00000343780.4_Missense_Mutation_p.A327T			Q92854	SEM4D_HUMAN	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4D	327	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.		A -> T (in dbSNP:rs11526468).		axon guidance (GO:0007411)|cell adhesion (GO:0007155)|immune response (GO:0006955)|leukocyte aggregation (GO:0070486)|negative regulation of alkaline phosphatase activity (GO:0010693)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell adhesion (GO:0007162)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of peptidyl-tyrosine phosphorylation (GO:0050732)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|ossification involved in bone maturation (GO:0043931)|positive regulation of cell migration (GO:0030335)|positive regulation of collateral sprouting (GO:0048672)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell projection organization (GO:0031344)|regulation of cell shape (GO:0008360)|regulation of dendrite morphogenesis (GO:0048814)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in bone trabecula morphogenesis (GO:1900220)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)|receptor binding (GO:0005102)|semaphorin receptor binding (GO:0030215)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(8)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	34						AGGTTGTAGGCGCACACTGCC	0.627													C|||	1128	0.22524	0.0174	0.2723	5008	,	,		19441	0.3294		0.3072	False		,,,				2504	0.2812				p.A327T		Atlas-SNP	.											.	SEMA4D	81	.	0			c.G979A						PASS	.	C	THR/ALA,THR/ALA	278,4128	153.7+/-187.2	11,256,1936	76.0	61.0	66.0		979,979	4.0	1.0	9	dbSNP_120	66	2486,6114	407.8+/-349.3	349,1788,2163	yes	missense,missense	SEMA4D	NM_001142287.1,NM_006378.3	58,58	360,2044,4099	TT,TC,CC		28.907,6.3096,21.2517	probably-damaging,probably-damaging	327/739,327/863	92003679	2764,10242	2203	4300	6503	SO:0001583	missense	10507	exon13			TGTAGGCGCACAC	U60800	CCDS6685.1, CCDS47991.1	9q22-q31	2013-01-11			ENSG00000187764	ENSG00000187764		"""Semaphorins"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	10732	protein-coding gene	gene with protein product	"""M-sema G"""	601866	"""chromosome 9 open reading frame 164"""	SEMAJ, C9orf164		8876214, 8969198	Standard	NM_006378		Approved	CD100, coll-4, FLJ39737	uc004aqo.1	Q92854	OTTHUMG00000020185	ENST00000450295.1:c.979G>A	9.37:g.92003679C>T	ENSP00000416523:p.Ala327Thr	Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	31	14	0.451613	NM_006378	B2RPM6|Q7Z5S4|Q8N8B0	Missense_Mutation	SNP	ENST00000450295.1	37	CCDS6685.1	573	0.2623626373626374	13	0.026422764227642278	107	0.2955801104972376	218	0.3811188811188811	235	0.3100263852242744	C	25.8	4.678510	0.88542	0.063096	0.28907	ENSG00000187764	ENST00000339861;ENST00000420987;ENST00000455551;ENST00000343780;ENST00000450295;ENST00000438547;ENST00000356444;ENST00000422704	T;T;T;T;T;T;T;T	0.14266	2.52;2.52;2.52;2.52;2.52;2.52;2.52;2.52	4.96	4.03	0.46877	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.092834	0.85682	D	0.000000	T	0.00012	0.0000	H	0.94886	3.595	0.09310	P	0.999991156	D;D	0.89917	0.997;1.0	P;D	0.73380	0.871;0.98	T	0.33854	-0.9852	9	0.41790	T	0.15	.	14.4731	0.67529	0.1481:0.8519:0.0:0.0	rs11526468	327;327	Q92854-2;Q92854	.;SEM4D_HUMAN	T	327	ENSP00000344923:A327T;ENSP00000391733:A327T;ENSP00000411981:A327T;ENSP00000343418:A327T;ENSP00000416523:A327T;ENSP00000405102:A327T;ENSP00000348822:A327T;ENSP00000388768:A327T	ENSP00000344923:A327T	A	-	1	0	SEMA4D	91193499	1.000000	0.71417	0.985000	0.45067	0.882000	0.50991	5.521000	0.67086	1.250000	0.43966	0.561000	0.74099	GCC	C|0.774;T|0.226	0.226	strong		0.627	SEMA4D-018	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342411.1	NM_006378	
IRF8	3394	hgsc.bcm.edu	37	16	85945231	85945231	+	Silent	SNP	C	C	T	rs8052064	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:85945231C>T	ENST00000268638.5	+	4	836	c.414C>T	c.(412-414)tgC>tgT	p.C138C	IRF8_ENST00000562492.1_5'Flank	NM_002163.2	NP_002154.1	Q02556	IRF8_HUMAN	interferon regulatory factor 8	138					cellular response to lipopolysaccharide (GO:0071222)|cytokine-mediated signaling pathway (GO:0019221)|defense response to bacterium (GO:0042742)|defense response to protozoan (GO:0042832)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|myeloid cell differentiation (GO:0030099)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|phagocytosis (GO:0006909)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|transcription from RNA polymerase II promoter (GO:0006366)|type I interferon signaling pathway (GO:0060337)	cytosol (GO:0005829)|nucleus (GO:0005634)	regulatory region DNA binding (GO:0000975)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)			breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|large_intestine(2)|lung(8)|ovary(2)|prostate(1)|urinary_tract(1)	24		Prostate(104;0.0771)				AGATGGAGTGCGGTCGCTCTG	0.547													C|||	438	0.0874601	0.1203	0.1052	5008	,	,		21585	0.001		0.1302	False		,,,				2504	0.0757				p.C138C		Atlas-SNP	.											.	IRF8	65	.	0			c.C414T						PASS	.	C		573,3823	256.4+/-261.2	31,511,1656	139.0	117.0	125.0		414	-9.9	0.0	16	dbSNP_116	125	1208,7392	245.1+/-274.1	82,1044,3174	no	coding-synonymous	IRF8	NM_002163.2		113,1555,4830	TT,TC,CC		14.0465,13.0346,13.7042		138/427	85945231	1781,11215	2198	4300	6498	SO:0001819	synonymous_variant	3394	exon4			GGAGTGCGGTCGC	M91196	CCDS10956.1	16q24.1	2014-09-17	2004-11-12	2004-11-12	ENSG00000140968	ENSG00000140968			5358	protein-coding gene	gene with protein product		601565	"""interferon consensus sequence binding protein 1"""	ICSBP1		1460054, 11997525	Standard	NM_002163		Approved	IRF-8, ICSBP	uc002fjh.3	Q02556	OTTHUMG00000137648	ENST00000268638.5:c.414C>T	16.37:g.85945231C>T		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	53	39	0.735849	NM_002163	A0AV82	Silent	SNP	ENST00000268638.5	37	CCDS10956.1																																																																																			C|0.882;T|0.118	0.118	strong		0.547	IRF8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269100.2	NM_002163	
JPH3	57338	hgsc.bcm.edu	37	16	87678441	87678441	+	Silent	SNP	C	C	T	rs8051448	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:87678441C>T	ENST00000284262.2	+	2	1202	c.960C>T	c.(958-960)cgC>cgT	p.R320R		NM_020655.2	NP_065706.2	Q8WXH2	JPH3_HUMAN	junctophilin 3	320					calcium ion transport into cytosol (GO:0060402)|exploration behavior (GO:0035640)|learning (GO:0007612)|locomotion (GO:0040011)|memory (GO:0007613)|neuromuscular process controlling balance (GO:0050885)|regulation of neuronal synaptic plasticity (GO:0048168)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)	calcium-release channel activity (GO:0015278)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(3)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	30				BRCA - Breast invasive adenocarcinoma(80;0.0287)		GCAACCGGCGCCATGGCTACG	0.652													C|||	563	0.11242	0.1452	0.1023	5008	,	,		14511	0.0119		0.1252	False		,,,				2504	0.1656				p.R320R		Atlas-SNP	.											.	JPH3	95	.	0			c.C960T						PASS	.	C		641,3755	272.2+/-270.6	59,523,1616	57.0	65.0	62.0		960	-1.6	1.0	16	dbSNP_116	62	1150,7450	233.5+/-266.7	74,1002,3224	no	coding-synonymous	JPH3	NM_020655.2		133,1525,4840	TT,TC,CC		13.3721,14.5814,13.7812		320/749	87678441	1791,11205	2198	4300	6498	SO:0001819	synonymous_variant	57338	exon2			CCGGCGCCATGGC	AB042636	CCDS10962.1	16q24.3	2008-02-05	2002-11-13		ENSG00000154118	ENSG00000154118			14203	protein-coding gene	gene with protein product		605268	"""trinucleotide repeat containing 22"""	TNRC22		10949023, 10891348	Standard	NM_020655		Approved	JP-3, CAGL237, HDL2, JP3	uc002fkd.4	Q8WXH2	OTTHUMG00000137656	ENST00000284262.2:c.960C>T	16.37:g.87678441C>T		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	85	56	0.658824	NM_020655	D3DUN2|Q8N471|Q9HDC3|Q9HDC4	Silent	SNP	ENST00000284262.2	37	CCDS10962.1																																																																																			C|0.876;G|0.000;T|0.124	0.124	strong		0.652	JPH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269108.2		
COL5A3	50509	hgsc.bcm.edu	37	19	10077419	10077419	+	Missense_Mutation	SNP	C	C	G	rs3745584	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:10077419C>G	ENST00000264828.3	-	63	4547	c.4462G>C	c.(4462-4464)Gcc>Ccc	p.A1488P		NM_015719.3	NP_056534.2	P25940	CO5A3_HUMAN	collagen, type V, alpha 3	1488	Collagen-like 6.|Triple-helical region.		A -> P (in dbSNP:rs3745584).		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)			TCGGCAGGGGCACCCTGGGCG	0.672													G|||	1834	0.366214	0.1392	0.3329	5008	,	,		12299	0.5337		0.3509	False		,,,				2504	0.5399				p.A1488P		Atlas-SNP	.											.	COL5A3	243	.	0			c.G4462C						PASS	.	G	PRO/ALA	480,3178		43,394,1392	3.0	3.0	3.0		4462	2.0	0.4	19	dbSNP_107	3	2011,5393		291,1429,1982	yes	missense	COL5A3	NM_015719.3	27	334,1823,3374	GG,GC,CC		27.161,13.1219,22.5185	benign	1488/1746	10077419	2491,8571	1829	3702	5531	SO:0001583	missense	50509	exon63			CAGGGGCACCCTG	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.4462G>C	19.37:g.10077419C>G	ENSP00000264828:p.Ala1488Pro	Somatic	14	0	0		WXS	Illumina HiSeq	Phase_I	9	7	0.777778	NM_015719	Q9NZQ6	Missense_Mutation	SNP	ENST00000264828.3	37	CCDS12222.1	769	0.35210622710622713	68	0.13821138211382114	124	0.3425414364640884	313	0.5472027972027972	264	0.3482849604221636	G	0.046	-1.264850	0.01433	0.131219	0.27161	ENSG00000080573	ENST00000264828	D	0.88046	-2.33	4.18	2.01	0.26516	.	0.342020	0.26627	N	0.023334	T	0.00012	0.0000	N	0.02403	-0.565	0.45676	P	0.0014079999999999648	B	0.02656	0.0	B	0.01281	0.0	T	0.37454	-0.9705	9	0.02654	T	1	.	4.0727	0.09889	0.2249:0.1938:0.5813:0.0	rs3745584;rs61076096;rs3745584	1488	P25940	CO5A3_HUMAN	P	1488	ENSP00000264828:A1488P	ENSP00000264828:A1488P	A	-	1	0	COL5A3	9938419	0.322000	0.24634	0.402000	0.26371	0.167000	0.22549	0.127000	0.15790	0.080000	0.16959	-0.368000	0.07277	GCC	C|0.641;G|0.359	0.359	strong		0.672	COL5A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315788.1	NM_015719	
LCE2B	26239	hgsc.bcm.edu	37	1	152659471	152659471	+	Missense_Mutation	SNP	T	T	G	rs3737859	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:152659471T>G	ENST00000368780.3	+	2	206	c.152T>G	c.(151-153)aTc>aGc	p.I51S	LCE2B_ENST00000417924.2_Missense_Mutation_p.I51S	NM_014357.4	NP_055172.1	O14633	LCE2B_HUMAN	late cornified envelope 2B	51	Cys-rich.		I -> S (in dbSNP:rs3737859).		epidermis development (GO:0008544)|keratinization (GO:0031424)			p.I51S(1)		endometrium(1)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	11	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)			TGTGGTCCCATCTCTGGGGGC	0.637													G|||	1033	0.20627	0.3071	0.1556	5008	,	,		14305	0.2946		0.0875	False		,,,				2504	0.137				p.I51S		Atlas-SNP	.											LCE2B,NS,carcinoma,0,1	LCE2B	40	1	1	Substitution - Missense(1)	stomach(1)	c.T152G						scavenged	.	G	SER/ILE	1263,3143	701.8+/-406.8	184,895,1124	126.0	139.0	135.0		152	2.4	1.0	1	dbSNP_107	135	700,7900	787.6+/-407.6	35,630,3635	no	missense	LCE2B	NM_014357.4	142	219,1525,4759	GG,GT,TT		8.1395,28.6655,15.093	benign	51/111	152659471	1963,11043	2203	4300	6503	SO:0001583	missense	26239	exon2			GTCCCATCTCTGG	BI670514	CCDS1020.1	1q21	2008-02-05	2004-10-11	2004-10-15	ENSG00000159455	ENSG00000159455		"""Late cornified envelopes"""	16610	protein-coding gene	gene with protein product		612610	"""small proline rich-like (epidermal differentiation complex) 1B"""	SPRL1B		11698679, 9344646	Standard	NM_014357		Approved	LEP10, XP5	uc001fai.3	O14633	OTTHUMG00000012404	ENST00000368780.3:c.152T>G	1.37:g.152659471T>G	ENSP00000357769:p.Ile51Ser	Somatic	141	1	0.0070922		WXS	Illumina HiSeq	Phase_I	121	56	0.46281	NM_014357	Q5TA80	Missense_Mutation	SNP	ENST00000368780.3	37	CCDS1020.1	424	0.19413919413919414	142	0.2886178861788618	42	0.11602209944751381	170	0.2972027972027972	70	0.09234828496042216	G	1.573	-0.533501	0.04082	0.286655	0.081395	ENSG00000159455	ENST00000417924;ENST00000368780	T;T	0.03152	4.03;4.03	2.37	2.37	0.29283	.	.	.	.	.	T	0.00241	0.0007	N	0.00170	-1.935	0.58432	P	4.000000000004E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.34004	-0.9846	8	0.07325	T	0.83	.	6.1109	0.20100	0.0:0.0:0.6964:0.3036	rs3737859;rs52809414;rs3737859	51	O14633	LCE2B_HUMAN	S	51	ENSP00000414043:I51S;ENSP00000357769:I51S	ENSP00000357769:I51S	I	+	2	0	LCE2B	150926095	0.359000	0.24955	0.981000	0.43875	0.019000	0.09904	0.875000	0.28079	0.211000	0.20683	-0.648000	0.03929	ATC	T|0.841;G|0.159	0.159	strong		0.637	LCE2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034524.1	NM_014357	
WDR48	57599	hgsc.bcm.edu	37	3	39111140	39111140	+	Silent	SNP	C	C	A	rs2293312	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	91	0	0		WXS	Illumina HiSeq	Phase_I	64	40	0.625	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	
MUC4	4585	hgsc.bcm.edu	37	3	195508133	195508133	+	Missense_Mutation	SNP	G	G	A	rs202065387		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195508133G>A	ENST00000463781.3	-	2	10777	c.10318C>T	c.(10318-10320)Cct>Tct	p.P3440S	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.P3440S	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.P3440S(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)		ACAGGAACAGGGGTGGCGTGA	0.592																																					p.P3440S		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,4	MUC4	1505	4	2	Substitution - Missense(2)	endometrium(2)	c.C10318T						scavenged	.						30.0	24.0	26.0					3																	195508133		685	1583	2268	SO:0001583	missense	4585	exon2			GAACAGGGGTGGC	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.10318C>T	3.37:g.195508133G>A	ENSP00000417498:p.Pro3440Ser	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	90	5	0.0555556	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	3.286	-0.146045	0.06627	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.29917	1.58;1.55	.	.	.	.	.	.	.	.	T	0.22003	0.0530	N	0.14661	0.345	0.09310	N	1	P	0.48350	0.909	P	0.50440	0.641	T	0.15809	-1.0424	6	.	.	.	.	.	.	.	.	3312	E7ESK3	.	S	3440	ENSP00000417498:P3440S;ENSP00000420243:P3440S	.	P	-	1	0	MUC4	196992912	0.016000	0.18221	0.006000	0.13384	0.005000	0.04900	-0.684000	0.05173	0.088000	0.17205	0.089000	0.15464	CCT	.	.	weak		0.592	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
PER3	8863	hgsc.bcm.edu	37	1	7887605	7887605	+	Silent	SNP	G	G	A	rs17031614	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:7887605G>A	ENST00000361923.2	+	17	2767	c.2592G>A	c.(2590-2592)tcG>tcA	p.S864S	RP3-467L1.4_ENST00000451646.1_RNA|PER3_ENST00000377532.3_Silent_p.S872S	NM_016831.1	NP_058515.1	P56645	PER3_HUMAN	period circadian clock 3	864	Pro-rich.				circadian regulation of gene expression (GO:0032922)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of circadian sleep/wake cycle, sleep (GO:0045187)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	signal transducer activity (GO:0004871)			breast(4)|central_nervous_system(3)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(9)|lung(8)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	39	Ovarian(185;0.0634)|all_lung(157;0.178)	all_epithelial(116;9.35e-21)|all_lung(118;7.57e-07)|Lung NSC(185;4.52e-06)|Renal(390;0.000147)|Breast(487;0.00086)|Colorectal(325;0.000959)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0234)|all cancers(8;8.58e-70)|GBM - Glioblastoma multiforme(8;1.81e-35)|Colorectal(212;2.06e-07)|COAD - Colon adenocarcinoma(227;1.92e-05)|Kidney(185;7.18e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000472)|STAD - Stomach adenocarcinoma(132;0.00118)|KIRC - Kidney renal clear cell carcinoma(229;0.00122)|READ - Rectum adenocarcinoma(331;0.0649)		TGTCGCCATCGTTTTTGCCAT	0.532													G|||	483	0.0964457	0.0076	0.2046	5008	,	,		20455	0.2728		0.0189	False		,,,				2504	0.0378				p.S864S		Atlas-SNP	.											.	PER3	95	.	0			c.G2592A						PASS	.	G		63,4343	60.5+/-97.4	1,61,2141	186.0	181.0	182.0		2592	-8.4	0.0	1	dbSNP_123	182	252,8348	99.9+/-161.4	3,246,4051	no	coding-synonymous	PER3	NM_016831.1		4,307,6192	AA,AG,GG		2.9302,1.4299,2.422		864/1202	7887605	315,12691	2203	4300	6503	SO:0001819	synonymous_variant	8863	exon17			GCCATCGTTTTTG	BC026102	CCDS89.1, CCDS72695.1	1p36.23	2012-12-13	2012-12-13		ENSG00000049246	ENSG00000049246			8847	protein-coding gene	gene with protein product		603427	"""period (Drosophila) homolog 3"", ""period homolog 3 (Drosophila)"""			9427249	Standard	XM_005263520		Approved		uc001aoo.3	P56645	OTTHUMG00000001216	ENST00000361923.2:c.2592G>A	1.37:g.7887605G>A		Somatic	211	0	0		WXS	Illumina HiSeq	Phase_I	174	74	0.425287	NM_016831	Q5H8X4|Q5H8X5|Q969K6|Q96S77|Q96S78|Q9C0J3|Q9NSP9|Q9UGU8	Silent	SNP	ENST00000361923.2	37	CCDS89.1																																																																																			G|0.940;A|0.060	0.060	strong		0.532	PER3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000003607.1	NM_016831	
FCGR3A	2214	hgsc.bcm.edu	37	1	161514542	161514542	+	Missense_Mutation	SNP	A	A	C	rs396991	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:161514542A>C	ENST00000436743.1	-	5	680	c.526T>G	c.(526-528)Ttt>Gtt	p.F176V	RP11-25K21.6_ENST00000537821.2_RNA|FCGR3A_ENST00000443193.1_Missense_Mutation_p.F211V|FCGR3A_ENST00000540048.1_Missense_Mutation_p.F176V|FCGR3A_ENST00000367969.3_Missense_Mutation_p.F212V|FCGR3A_ENST00000476031.1_5'Flank	NM_001127593.1|NM_001127595.1|NM_001127596.1	NP_001121065.1|NP_001121067.1|NP_001121068.1	P08637	FCG3A_HUMAN	Fc fragment of IgG, low affinity IIIa, receptor (CD16a)	176	Ig-like C2-type 2.		F -> V (shows a higher binding capacity of IgG1, IgG3 and IgG4; dbSNP:rs396991). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:7700021, ECO:0000269|PubMed:9242542, ECO:0000269|PubMed:9276722, ECO:0000269|Ref.3}.		Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|immune response (GO:0006955)|innate immune response (GO:0045087)|regulation of immune response (GO:0050776)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(14)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	24	all_cancers(52;4.89e-16)|all_hematologic(112;0.0207)		BRCA - Breast invasive adenocarcinoma(70;0.00376)		Abciximab(DB00054)|Adalimumab(DB00051)|Alefacept(DB00092)|Alemtuzumab(DB00087)|Basiliximab(DB00074)|Bevacizumab(DB00112)|Cetuximab(DB00002)|Daclizumab(DB00111)|Efalizumab(DB00095)|Etanercept(DB00005)|Gemtuzumab ozogamicin(DB00056)|Ibritumomab(DB00078)|Intravenous Immunoglobulin(DB00028)|Muromonab(DB00075)|Natalizumab(DB00108)|Palivizumab(DB00110)|Rituximab(DB00073)|Tositumomab(DB00081)|Trastuzumab(DB00072)	TTACTCCCAAAAAGCCCCCTG	0.478																																					p.F212V		Atlas-SNP	.											.	FCGR3A	38	.	0			c.T634G	GRCh37	CM992625	FCGR3A	M	rs396991	PASS	.	C	VAL/PHE,VAL/PHE,VAL/PHE,VAL/PHE,VAL/PHE	1150,3256		243,664,1296	74.0	75.0	75.0		523,526,526,631,634	-0.1	0.0	1	dbSNP_80	75	2412,6188		505,1402,2393	no	missense,missense,missense,missense,missense	FCGR3A	NM_001127596.1,NM_001127595.1,NM_001127593.1,NM_001127592.1,NM_000569.6	50,50,50,50,50	748,2066,3689	CC,CA,AA		28.0465,26.1008,27.3874	benign,benign,benign,benign,benign	175/254,176/255,176/255,211/290,212/291	161514542	3562,9444	2203	4300	6503	SO:0001583	missense	2214	exon4			TCCCAAAAAGCCC	BC036723	CCDS1232.1, CCDS44266.1	1q23	2014-09-17	2005-02-02		ENSG00000203747	ENSG00000203747		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	3619	protein-coding gene	gene with protein product		146740	"""Fc fragment of IgG, low affinity IIIa, receptor for (CD16)"""	FCGR3, FCG3		2139735	Standard	NM_001127592		Approved	CD16, CD16a	uc001gar.3	P08637	OTTHUMG00000034466	ENST00000436743.1:c.526T>G	1.37:g.161514542A>C	ENSP00000416607:p.Phe176Val	Somatic	271	0	0		WXS	Illumina HiSeq	Phase_I	235	108	0.459574	NM_000569	A2N6W9|Q53FJ0|Q53FL6|Q5EBR4|Q65ZM6|Q6PIJ0	Missense_Mutation	SNP	ENST00000436743.1	37	CCDS44266.1	535|535	0.24496336996336995|0.24496336996336995	106|106	0.21544715447154472|0.21544715447154472	71|71	0.19613259668508287|0.19613259668508287	154|154	0.2692307692307692|0.2692307692307692	204|204	0.2691292875989446|0.2691292875989446	N|N	8.451|8.451	0.853189|0.853189	0.17106|0.17106	0.261008|0.261008	0.280465|0.280465	ENSG00000203747|ENSG00000203747	ENST00000426740|ENST00000367969;ENST00000443193;ENST00000436743;ENST00000367967;ENST00000540048	.|T;T;T;T;T	.|0.11604	.|2.76;2.76;2.76;2.76;2.76	5.03|5.03	-0.103|-0.103	0.13609|0.13609	.|Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.285436|0.285436	0.25027|0.25027	N|N	0.033707|0.033707	T|T	0.00998|0.00998	0.0033|0.0033	N|N	0.04355|0.04355	-0.22|-0.22	0.80722|0.80722	P|P	0.0|0.0	.|B;B	.|0.02656	.|0.0;0.0	.|B;B	.|0.01281	.|0.0;0.0	T|T	0.46925|0.46925	-0.9156|-0.9156	5|9	.|0.44086	.|T	.|0.13	.|.	0.3561|0.3561	0.00357|0.00357	0.2836:0.1629:0.1472:0.4063|0.2836:0.1629:0.1472:0.4063	rs396991;rs2229097;rs3171040;rs4151086;rs17857127;rs61228128|rs396991;rs2229097;rs3171040;rs4151086;rs17857127;rs61228128	.|176;211	.|P08637;E9PG94	.|FCG3A_HUMAN;.	L|V	192|212;211;176;176;176	.|ENSP00000356946:F212V;ENSP00000392047:F211V;ENSP00000416607:F176V;ENSP00000356944:F176V;ENSP00000444971:F176V	.|ENSP00000356944:F176V	F|F	-|-	3|1	2|0	FCGR3A|FCGR3A	159781166|159781166	0.000000|0.000000	0.05858|0.05858	0.001000|0.001000	0.08648|0.08648	0.003000|0.003000	0.03518|0.03518	-0.208000|-0.208000	0.09371|0.09371	-0.464000|-0.464000	0.06963|0.06963	-5.115000|-5.115000	0.00001|0.00001	TTT|TTT	A|0.681;C|0.319	0.319	strong		0.478	FCGR3A-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102169.2	NM_000569	
NCOR2	9612	hgsc.bcm.edu	37	12	124821416	124821416	+	Missense_Mutation	SNP	C	C	T	rs2227277	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:124821416C>T	ENST00000405201.1	-	38	5998	c.5998G>A	c.(5998-6000)Gca>Aca	p.A2000T	NCOR2_ENST00000356219.3_Missense_Mutation_p.A2007T|NCOR2_ENST00000429285.2_Missense_Mutation_p.A1990T|NCOR2_ENST00000404621.1_Missense_Mutation_p.A1990T|NCOR2_ENST00000404121.2_Missense_Mutation_p.A1561T|NCOR2_ENST00000397355.1_Missense_Mutation_p.A1991T			Q9Y618	NCOR2_HUMAN	nuclear receptor corepressor 2	2011					cellular lipid metabolic process (GO:0044255)|gene expression (GO:0010467)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|regulation of cellular ketone metabolic process by negative regulation of transcription from RNA polymerase II promoter (GO:0072365)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	membrane (GO:0016020)|nuclear body (GO:0016604)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone deacetylase binding (GO:0042826)|Notch binding (GO:0005112)|protein N-terminus binding (GO:0047485)|transcription corepressor activity (GO:0003714)			breast(5)|central_nervous_system(2)|endometrium(7)|kidney(5)|large_intestine(7)|lung(28)|ovary(3)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	69	all_neural(191;0.0804)|Medulloblastoma(191;0.163)			Epithelial(86;3.99e-05)|OV - Ovarian serous cystadenocarcinoma(86;9.14e-05)|all cancers(50;0.000402)|BRCA - Breast invasive adenocarcinoma(302;0.0764)		TGGTGAGGTGCGAGGTTCTTC	0.692													c|||	287	0.0573083	0.0348	0.0288	5008	,	,		10689	0.0298		0.0447	False		,,,				2504	0.1493				p.A2000T		Atlas-SNP	.											.	NCOR2	475	.	0			c.G5998A						PASS	.		THR/ALA,THR/ALA,THR/ALA	180,3784		6,168,1808	24.0	29.0	27.0		5968,5968,5998	-0.4	0.3	12	dbSNP_98	27	281,8005		10,261,3872	yes	missense,missense,missense	NCOR2	NM_001077261.3,NM_001206654.1,NM_006312.5	58,58,58	16,429,5680	TT,TC,CC		3.3913,4.5409,3.7633	possibly-damaging,possibly-damaging,possibly-damaging	1990/2459,1990/2505,2000/2515	124821416	461,11789	1982	4143	6125	SO:0001583	missense	9612	exon40			GAGGTGCGAGGTT	U37146	CCDS41857.1, CCDS41858.1, CCDS41857.2, CCDS41858.2, CCDS55892.1	12q24	2010-06-10	2010-06-10		ENSG00000196498	ENSG00000196498			7673	protein-coding gene	gene with protein product		600848	"""nuclear receptor co-repressor 2"""			7566127, 8813722	Standard	NM_001077261		Approved	SMRT, SMRTE, TRAC-1, CTG26, TNRC14	uc010tbb.2	Q9Y618	OTTHUMG00000150455	ENST00000405201.1:c.5998G>A	12.37:g.124821416C>T	ENSP00000384018:p.Ala2000Thr	Somatic	12	0	0		WXS	Illumina HiSeq	Phase_I	35	27	0.771429	NM_006312	O00613|O15416|O15421|Q13354|Q56D06|Q59GM0|Q9Y5U0	Missense_Mutation	SNP	ENST00000405201.1	37	CCDS41858.2	83	0.038003663003663	27	0.054878048780487805	9	0.024861878453038673	20	0.03496503496503497	27	0.03562005277044855	c	12.06	1.825670	0.32237	0.045409	0.033913	ENSG00000196498	ENST00000405201;ENST00000404621;ENST00000356219;ENST00000397355;ENST00000447011;ENST00000404121;ENST00000447675;ENST00000429285	T;T;T;T;T;T	0.18016	2.24;2.5;2.24;2.5;2.24;2.5	4.78	-0.36	0.12568	.	0.689868	0.14427	N	0.320273	T	0.02119	0.0066	N	0.14661	0.345	0.09310	N	1	D;D;P	0.76494	0.999;0.999;0.703	P;P;B	0.61132	0.769;0.884;0.06	T	0.19679	-1.0298	10	0.16420	T	0.52	-3.3309	6.2623	0.20907	0.0:0.3473:0.1688:0.4839	rs2227277;rs3741510	1991;2000;2011	C9J239;C9JFD3;Q9Y618	.;.;NCOR2_HUMAN	T	2000;1990;2007;1991;1999;1561;92;1990	ENSP00000384018:A2000T;ENSP00000384202:A1990T;ENSP00000348551:A2007T;ENSP00000380513:A1991T;ENSP00000385618:A1561T;ENSP00000400281:A1990T	ENSP00000348551:A2007T	A	-	1	0	NCOR2	123387369	0.191000	0.23288	0.307000	0.25127	0.424000	0.31475	-0.093000	0.11111	0.098000	0.17522	-0.265000	0.10407	GCA	C|0.959;T|0.041	0.041	strong		0.692	NCOR2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318173.2	NM_006312	
AHNAK2	113146	hgsc.bcm.edu	37	14	105417683	105417683	+	Missense_Mutation	SNP	C	C	T	rs367930189		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:105417683C>T	ENST00000333244.5	-	7	4224	c.4105G>A	c.(4105-4107)Ggg>Agg	p.G1369R	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	1369						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)			TTGAGGTCCCCCTGCATGGAG	0.647																																					p.G1369R		Atlas-SNP	.											AHNAK2_ENST00000333244,NS,carcinoma,+2,1	AHNAK2	719	1	0			c.G4105A						PASS	.	C	ARG/GLY	0,3684		0,0,1842	99.0	74.0	83.0		4105	2.3	0.0	14		83	2,6232		1,0,3116	no	missense	AHNAK2	NM_138420.2	125	1,0,4958	TT,TC,CC		0.0321,0.0,0.0202	probably-damaging	1369/5796	105417683	2,9916	1842	3117	4959	SO:0001583	missense	113146	exon7			GGTCCCCCTGCAT	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.4105G>A	14.37:g.105417683C>T	ENSP00000353114:p.Gly1369Arg	Somatic	0	0	.		WXS	Illumina HiSeq	Phase_I	88	4	0.0454545	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	.	.	.	.	.	.	.	.	.	.	-	15.55	2.867501	0.51588	0.0	3.21E-4	ENSG00000185567	ENST00000333244	T	0.01584	4.75	4.18	2.29	0.28610	.	.	.	.	.	T	0.06188	0.0160	M	0.75264	2.295	0.09310	N	1	D	0.62365	0.991	P	0.61592	0.891	T	0.32745	-0.9895	9	0.25106	T	0.35	.	6.5072	0.22202	0.1794:0.7206:0.0:0.1001	.	1369	Q8IVF2	AHNK2_HUMAN	R	1369	ENSP00000353114:G1369R	ENSP00000353114:G1369R	G	-	1	0	AHNAK2	104488728	0.006000	0.16342	0.000000	0.03702	0.087000	0.18053	1.114000	0.31196	0.237000	0.21200	0.485000	0.47835	GGG	.	.	weak		0.647	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
FKBP15	23307	hgsc.bcm.edu	37	9	115968797	115968797	+	Missense_Mutation	SNP	C	C	T	rs1133618	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:115968797C>T	ENST00000238256.3	-	4	433	c.316G>A	c.(316-318)Gcc>Acc	p.A106T	FKBP15_ENST00000493847.1_5'UTR	NM_015258.1	NP_056073.1	Q5T1M5	FKB15_HUMAN	FK506 binding protein 15, 133kDa	106	Important for function in growth cone organization. {ECO:0000250}.		A -> T (in dbSNP:rs1133618).		endocytosis (GO:0006897)|negative regulation of phosphatase activity (GO:0010923)|protein folding (GO:0006457)	actin filament (GO:0005884)|axon (GO:0030424)|endosome (GO:0005768)|growth cone (GO:0030426)|membrane (GO:0016020)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(3)|lung(9)|ovary(3)|urinary_tract(1)	26						ACCTCTCTGGCTGTGTGGTTC	0.423													C|||	952	0.190096	0.3298	0.2161	5008	,	,		17470	0.0228		0.2078	False		,,,				2504	0.137				p.A106T		Atlas-SNP	.											.	FKBP15	128	.	0			c.G316A						PASS	.	C	THR/ALA	1052,2738		152,748,995	116.0	112.0	113.0		316	2.8	1.0	9	dbSNP_86	113	1576,6668		170,1236,2716	yes	missense	FKBP15	NM_015258.1	58	322,1984,3711	TT,TC,CC		19.1169,27.7573,21.8381	benign	106/1220	115968797	2628,9406	1895	4122	6017	SO:0001583	missense	23307	exon4			CTCTGGCTGTGTG	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.316G>A	9.37:g.115968797C>T	ENSP00000238256:p.Ala106Thr	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	86	44	0.511628	NM_015258	Q05DK8|Q5T1M2|Q6DD85|Q9Y4D0	Missense_Mutation	SNP	ENST00000238256.3	37	CCDS48007.1	403	0.18452380952380953	150	0.3048780487804878	76	0.20994475138121546	13	0.022727272727272728	164	0.21635883905013192	C	5.870	0.344614	0.11126	0.277573	0.191169	ENSG00000119321	ENST00000446284;ENST00000238256;ENST00000414250	T;T;T	0.42513	0.97;0.97;0.97	5.71	2.84	0.33178	.	.	.	.	.	T	0.00012	0.0000	N	0.11789	0.175	0.41464	P	0.011938000000000004	B;B;B	0.12630	0.006;0.002;0.004	B;B;B	0.16289	0.015;0.003;0.007	T	0.40232	-0.9574	8	0.10377	T	0.69	-1.6684	6.3222	0.21225	0.1488:0.6889:0.0:0.1623	rs1133618;rs3195502;rs11558693;rs52819213;rs56950186;rs1133618	106;106;106	Q5T1M5-2;Q5T1M5-3;Q5T1M5	.;.;FKB15_HUMAN	T	131;106;131	ENSP00000416158:A131T;ENSP00000238256:A106T;ENSP00000415733:A131T	ENSP00000238256:A106T	A	-	1	0	FKBP15	115008618	0.899000	0.30636	0.999000	0.59377	0.993000	0.82548	1.143000	0.31553	0.329000	0.23460	0.563000	0.77884	GCC	C|0.805;T|0.195	0.195	strong		0.423	FKBP15-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_015258	
LGALS14	56891	hgsc.bcm.edu	37	19	40196548	40196548	+	Intron	SNP	A	A	G	rs140242272	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:40196548A>G	ENST00000392052.3	+	2	238				LGALS14_ENST00000360675.3_Start_Codon_SNP_p.M1V	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)			CCCTCCAGTTATGTCCCTGAC	0.478													a|||	2	0.000399361	0.0	0.0014	5008	,	,		21476	0.0		0.001	False		,,,				2504	0.0				p.M1V		Atlas-SNP	.											.	LGALS14	38	.	0			c.A1G						PASS	.	A	,VAL/MET	0,4406		0,0,2203	184.0	141.0	156.0		,1	-0.4	0.0	19	dbSNP_134	156	7,8593		0,7,4293	no	intron,missense	LGALS14	NM_020129.2,NM_203471.1	,21	0,7,6496	GG,GA,AA		0.0814,0.0,0.0538	,	,1/169	40196548	7,12999	2203	4300	6503	SO:0001627	intron_variant	56891	exon2			CCAGTTATGTCCC	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.16-689A>G	19.37:g.40196548A>G		Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	156	72	0.461538	NM_203471	A8MPV8|B2R530|C5HZ19|Q7Z4X8|Q96KD4|Q96KD5|Q96KD6|Q9NR03	Missense_Mutation	SNP	ENST00000392052.3	37	CCDS46073.1	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	.	6.163	0.398345	0.11696	0.0	8.14E-4	ENSG00000006659	ENST00000360675	T	0.06933	3.24	0.906	-0.363	0.12556	.	.	.	.	.	T	0.06462	0.0166	.	.	.	0.80722	D	1	B	0.26041	0.14	B	0.26202	0.067	T	0.29119	-1.0022	8	0.62326	D	0.03	.	3.5978	0.08013	0.5843:0.4157:0.0:0.0	.	1	A8MPV8	.	V	1	ENSP00000353893:M1V	ENSP00000353893:M1V	M	+	1	0	LGALS14	44888388	0.000000	0.05858	0.000000	0.03702	0.221000	0.24807	-0.385000	0.07379	-0.203000	0.10251	0.260000	0.18958	ATG	A|0.999;G|0.001	0.001	strong		0.478	LGALS14-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000465222.1	NM_020129	
GATA5	140628	hgsc.bcm.edu	37	20	61039958	61039958	+	Silent	SNP	T	T	C	rs6061550	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:61039958T>C	ENST00000252997.2	-	7	1189	c.1128A>G	c.(1126-1128)ccA>ccG	p.P376P		NM_080473.4	NP_536721.1	Q9BWX5	GATA5_HUMAN	GATA binding protein 5	376					blood coagulation (GO:0007596)|cellular response to BMP stimulus (GO:0071773)|intestinal epithelial cell differentiation (GO:0060575)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	enhancer sequence-specific DNA binding (GO:0001158)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			kidney(1)|lung(3)|ovary(1)|stomach(1)	6	Breast(26;2.05e-08)		BRCA - Breast invasive adenocarcinoma(19;3.08e-06)			CCTGGGGGCTTGGGGCCGTGG	0.672													C|||	3151	0.629193	0.8442	0.451	5008	,	,		12990	0.5238		0.4791	False		,,,				2504	0.728				p.P376P		Atlas-SNP	.											.	GATA5	22	.	0			c.A1128G						PASS	.	C		3430,976		1348,734,121	25.0	29.0	28.0		1128	4.3	1.0	20	dbSNP_114	28	4379,4217		1121,2137,1040	no	coding-synonymous	GATA5	NM_080473.4		2469,2871,1161	CC,CT,TT		49.0577,22.1516,39.94		376/398	61039958	7809,5193	2203	4298	6501	SO:0001819	synonymous_variant	140628	exon7			GGGGCTTGGGGCC	BC047790, BC117356	CCDS13499.1	20q13.33	2013-07-17	2001-11-28		ENSG00000130700	ENSG00000130700		"""GATA zinc finger domain containing"""	15802	protein-coding gene	gene with protein product		611496	"""GATA-binding protein 5"""			9566909	Standard	NM_080473		Approved	bB379O24.1, GATAS	uc002ycx.1	Q9BWX5	OTTHUMG00000032919	ENST00000252997.2:c.1128A>G	20.37:g.61039958T>C		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	61	32	0.52459	NM_080473	D9ZGF7|Q17RE2|Q86VU4	Silent	SNP	ENST00000252997.2	37	CCDS13499.1																																																																																			T|0.412;C|0.588	0.588	strong		0.672	GATA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080038.2	NM_080473	
HEATR5A	25938	hgsc.bcm.edu	37	14	31790886	31790886	+	Splice_Site	SNP	T	T	G	rs28396248	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:31790886T>G	ENST00000389961.3	-	24	3769	c.3770A>C	c.(3769-3771)aAt>aCt	p.N1257T	HEATR5A_ENST00000543095.2_Splice_Site_p.N1263T|HEATR5A_ENST00000439727.1_Splice_Site_p.N970T|HEATR5A_ENST00000439348.1_Splice_Site_p.N1257T			Q86XA9	HTR5A_HUMAN	HEAT repeat containing 5A	1257				N -> T (in Ref. 3; AAH63867). {ECO:0000305}.				p.N1257T(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(5)|lung(13)|ovary(1)	26	Hepatocellular(127;0.0877)|Breast(36;0.137)		LUAD - Lung adenocarcinoma(48;0.00292)|Lung(238;0.0164)|BRCA - Breast invasive adenocarcinoma(188;0.0797)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.0059)		CAAAAAGTCATCTATAAGATT	0.358													T|||	455	0.0908546	0.1188	0.085	5008	,	,		17929	0.1488		0.0467	False		,,,				2504	0.0429				p.N1263T		Atlas-SNP	.											HEATR5A_ENST00000389961,NS,carcinoma,0,1	HEATR5A	181	1	1	Substitution - Missense(1)	stomach(1)	c.A3788C						PASS	.	T	THR/ASN	449,3245		27,395,1425	23.0	22.0	22.0		3788	2.8	1.0	14	dbSNP_125	22	550,7624		16,518,3553	yes	missense-near-splice	HEATR5A	NM_015473.3	65	43,913,4978	GG,GT,TT		6.7287,12.1548,8.4176	benign	1263/2047	31790886	999,10869	1847	4087	5934	SO:0001630	splice_region_variant	25938	exon25			AAGTCATCTATAA	AB037737		14q12	2012-04-19	2007-01-02	2007-01-02	ENSG00000129493	ENSG00000129493			20276	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 125"""	C14orf125			Standard	NM_015473		Approved	DKFZP434I1735	uc001wrf.4	Q86XA9	OTTHUMG00000169043	ENST00000389961.3:c.3770-1A>C	14.37:g.31790886T>G		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	69	35	0.507246	NM_015473	Q68DD8|Q6P3S5|Q6P5R9|Q9H8D7|Q9NXB7|Q9P2N0|Q9UFQ3	Missense_Mutation	SNP	ENST00000389961.3	37		203|203	0.09294871794871795|0.09294871794871795	47|47	0.09552845528455285|0.09552845528455285	37|37	0.10220994475138122|0.10220994475138122	78|78	0.13636363636363635|0.13636363636363635	41|41	0.05408970976253298|0.05408970976253298	T|T	1.616|1.616	-0.522746|-0.522746	0.04141|0.04141	0.121548|0.121548	0.067287|0.067287	ENSG00000129493|ENSG00000129493	ENST00000538864|ENST00000389961;ENST00000439348;ENST00000439727;ENST00000543095	.|T;T;T;T	.|0.47177	.|0.85;0.85;0.85;0.85	5.16|5.16	2.8|2.8	0.32819|0.32819	.|.	.|0.455902	.|0.24891	.|N	.|0.034771	T|T	0.00241|0.00241	0.0007|0.0007	N|N	0.21097|0.21097	0.63|0.63	0.09310|0.09310	P|P	1.0|1.0	.|B	.|0.19583	.|0.037	.|B	.|0.28232	.|0.087	T|T	0.14062|0.14062	-1.0486|-1.0486	4|9	.|0.16420	.|T	.|0.52	.|.	6.6849|6.6849	0.23140|0.23140	0.0:0.2775:0.0:0.7225|0.0:0.2775:0.0:0.7225	rs28396248|rs28396248	.|1257	.|Q86XA9-2	.|.	L|T	891|1257;1257;970;1263	.|ENSP00000374611:N1257T;ENSP00000405407:N1257T;ENSP00000408681:N970T;ENSP00000437968:N1263T	.|ENSP00000374611:N1257T	M|N	-|-	1|2	0|0	HEATR5A|HEATR5A	30860637|30860637	1.000000|1.000000	0.71417|0.71417	0.997000|0.997000	0.53966|0.53966	0.133000|0.133000	0.20885|0.20885	0.862000|0.862000	0.27899|0.27899	0.308000|0.308000	0.22923|0.22923	0.164000|0.164000	0.16699|0.16699	ATG|AAT	T|0.909;G|0.091	0.091	strong		0.358	HEATR5A-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_015473	Missense_Mutation
FSCB	84075	hgsc.bcm.edu	37	14	44975606	44975606	+	Missense_Mutation	SNP	G	G	T	rs3809429	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:44975606G>T	ENST00000340446.4	-	1	876	c.585C>A	c.(583-585)caC>caA	p.H195Q	RP11-163M18.1_ENST00000557465.1_RNA|RP11-163M18.1_ENST00000555433.1_RNA|RP11-163M18.1_ENST00000556228.1_RNA	NM_032135.3	NP_115511.3	Q5H9T9	FSCB_HUMAN	fibrous sheath CABYR binding protein	195			H -> Q (in dbSNP:rs3809429). {ECO:0000269|PubMed:15489334}.			sperm fibrous sheath (GO:0035686)|sperm principal piece (GO:0097228)	calcium ion binding (GO:0005509)	p.H195Q(1)		breast(4)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(10)|lung(47)|ovary(2)|pancreas(1)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(1)	89				GBM - Glioblastoma multiforme(112;0.128)		GAAATTCAGGGTGTTCACTAG	0.403													G|||	1360	0.271565	0.2859	0.3055	5008	,	,		19485	0.3968		0.1193	False		,,,				2504	0.2556				p.H195Q		Atlas-SNP	.											FSCB,NS,carcinoma,0,1	FSCB	173	1	1	Substitution - Missense(1)	stomach(1)	c.C585A						scavenged	.	G	GLN/HIS	1185,3221	414.8+/-337.0	157,871,1175	134.0	140.0	138.0		585	-2.3	0.3	14	dbSNP_107	138	947,7653	206.5+/-248.5	50,847,3403	yes	missense	FSCB	NM_032135.3	24	207,1718,4578	TT,TG,GG		11.0116,26.8951,16.3924	probably-damaging	195/826	44975606	2132,10874	2203	4300	6503	SO:0001583	missense	84075	exon1			TTCAGGGTGTTCA	AK124110	CCDS9679.1	14q21.3	2007-11-22	2007-11-22	2007-11-22	ENSG00000189139	ENSG00000189139			20494	protein-coding gene	gene with protein product		611779	"""chromosome 14 open reading frame 155"""	C14orf155		17855365	Standard	NM_032135		Approved	DKFZP434F1017	uc001wvn.3	Q5H9T9	OTTHUMG00000140262	ENST00000340446.4:c.585C>A	14.37:g.44975606G>T	ENSP00000344579:p.His195Gln	Somatic	119	1	0.00840336		WXS	Illumina HiSeq	Phase_I	112	56	0.5	NM_032135	Q5H9U7|Q86YI2|Q9H0J3	Missense_Mutation	SNP	ENST00000340446.4	37	CCDS9679.1	542	0.24816849816849818	138	0.2804878048780488	97	0.26795580110497236	223	0.38986013986013984	84	0.11081794195250659	G	9.402	1.078233	0.20227	0.268951	0.110116	ENSG00000189139	ENST00000340446;ENST00000537803	T	0.24350	1.86	4.2	-2.28	0.06826	.	.	.	.	.	T	0.00012	0.0000	L	0.53249	1.67	0.58432	P	1.0000000000287557E-6	P	0.37573	0.6	B	0.38500	0.275	T	0.43798	-0.9369	8	0.19590	T	0.45	-3.8899	4.8286	0.13428	0.5279:0.1605:0.3116:0.0	rs3809429;rs17846266;rs17859288;rs52805697;rs61689159;rs3809429	195	Q5H9T9	FSCB_HUMAN	Q	195	ENSP00000344579:H195Q	ENSP00000344579:H195Q	H	-	3	2	FSCB	44045356	0.026000	0.19158	0.284000	0.24805	0.229000	0.25112	-0.134000	0.10436	-0.303000	0.08856	-2.303000	0.00259	CAC	G|0.789;T|0.211	0.211	strong		0.403	FSCB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276788.1	NM_032135	
KIF19	124602	hgsc.bcm.edu	37	17	72350362	72350362	+	Silent	SNP	G	G	A	rs72852235	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:72350362G>A	ENST00000389916.4	+	18	2508	c.2370G>A	c.(2368-2370)tcG>tcA	p.S790S	AC103809.2_ENST00000599136.1_5'Flank	NM_153209.3	NP_694941.2	Q2TAC6	KIF19_HUMAN	kinesin family member 19	790					ATP catabolic process (GO:0006200)|axonemal microtubule depolymerization (GO:0060404)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|plus-end specific microtubule depolymerization (GO:0070462)	cilium (GO:0005929)|cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|plus-end-directed microtubule motor activity (GO:0008574)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(6)|large_intestine(3)|lung(16)|ovary(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	41						GGCGGCGCTCGCGGGCCCTGG	0.682													G|||	1277	0.254992	0.1051	0.3012	5008	,	,		14395	0.3452		0.2803	False		,,,				2504	0.3057				p.S790S		Atlas-SNP	.											KIF19,NS,carcinoma,0,1	KIF19	102	1	0			c.G2370A						PASS	.	G		461,3551		32,397,1577	35.0	46.0	42.0		2370	-10.1	0.3	17	dbSNP_130	42	2350,5960		329,1692,2134	no	coding-synonymous	KIF19	NM_153209.3		361,2089,3711	AA,AG,GG		28.2792,11.4905,22.8129		790/999	72350362	2811,9511	2006	4155	6161	SO:0001819	synonymous_variant	124602	exon18			GCGCTCGCGGGCC	AK094619	CCDS32718.2	17q25	2007-02-13			ENSG00000196169	ENSG00000196169		"""Kinesins"""	26735	protein-coding gene	gene with protein product						11416179	Standard	NM_153209		Approved	FLJ37300, KIF19A	uc031rei.1	Q2TAC6	OTTHUMG00000150694	ENST00000389916.4:c.2370G>A	17.37:g.72350362G>A		Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	35	35	1	NM_153209	A6NLG2|B7ZKR1|Q52M87|Q8N1X8|Q8TAB6	Silent	SNP	ENST00000389916.4	37	CCDS32718.2																																																																																			G|0.736;A|0.264	0.264	strong		0.682	KIF19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319644.2	NM_153209	
UNC93A	54346	hgsc.bcm.edu	37	6	167728775	167728775	+	Missense_Mutation	SNP	G	G	A	rs71545154|rs9459921	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:167728775G>A	ENST00000230256.3	+	8	1384	c.1209G>A	c.(1207-1209)atG>atA	p.M403I	UNC93A_ENST00000366829.2_Missense_Mutation_p.M361I	NM_018974.3	NP_061847.2	Q86WB7	UN93A_HUMAN	unc-93 homolog A (C. elegans)	403			M -> I (in dbSNP:rs9459921).|M -> T (in dbSNP:rs663606). {ECO:0000269|PubMed:12381271}.			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(7)|lung(20)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	40		Breast(66;7.62e-05)|Ovarian(120;0.105)		OV - Ovarian serous cystadenocarcinoma(33;2.22e-20)|BRCA - Breast invasive adenocarcinoma(81;6.17e-07)|GBM - Glioblastoma multiforme(31;0.00492)		GGTACAGCATGTTTTTGTGCG	0.572													A|||	1343	0.268171	0.2519	0.2089	5008	,	,		15967	0.2847		0.2356	False		,,,				2504	0.3487				p.M403I		Atlas-SNP	.											.	UNC93A	66	.	0			c.G1209A						PASS	.						87.0	140.0	122.0					6																	167728775		2203	4293	6496	SO:0001583	missense	54346	exon8			CAGCATGTTTTTG	AJ508812	CCDS5300.1, CCDS47515.1	6q27	2014-05-16	2001-11-28		ENSG00000112494	ENSG00000112494			12570	protein-coding gene	gene with protein product		607995	"""unc93 (C.elegans) homolog A"""			12381271	Standard	NM_001143947		Approved	dJ366N23.2, dJ366N23.1	uc003qvq.3	Q86WB7	OTTHUMG00000016021	ENST00000230256.3:c.1209G>A	6.37:g.167728775G>A	ENSP00000230256:p.Met403Ile	Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	57	41	0.719298	NM_018974	B3KRP5|Q4QQJ4|Q5JZD6	Missense_Mutation	SNP	ENST00000230256.3	37	CCDS5300.1	450	0.20604395604395603	96	0.1951219512195122	63	0.17403314917127072	150	0.26223776223776224	141	0.18601583113456466	A	5.760	0.324549	0.10900	.	.	ENSG00000112494	ENST00000230256;ENST00000366829	T;T	0.80480	-1.38;-1.38	3.86	-7.71	0.01254	Major facilitator superfamily domain, general substrate transporter (1);	0.177325	0.48286	D	0.000189	T	0.32406	0.0828	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	0.04153	-1.0973	9	0.35671	T	0.21	-2.8542	9.3036	0.37861	0.4757:0.3393:0.1849:0.0	rs9459921;rs13192122	361;403	Q4QQJ4;Q86WB7	.;UN93A_HUMAN	I	403;361	ENSP00000230256:M403I;ENSP00000355794:M361I	ENSP00000230256:M403I	M	+	3	0	UNC93A	167648765	0.162000	0.22906	0.001000	0.08648	0.004000	0.04260	-0.283000	0.08433	-2.386000	0.00590	-1.711000	0.00714	ATG	G|0.806;A|0.194	0.194	strong		0.572	UNC93A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043125.2	NM_018974	
HPS4	89781	hgsc.bcm.edu	37	22	26866723	26866723	+	Silent	SNP	C	C	T	rs13054747	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:26866723C>T	ENST00000398145.2	-	7	1174	c.558G>A	c.(556-558)tcG>tcA	p.S186S	HPS4_ENST00000402105.3_Silent_p.S181S|HPS4_ENST00000398141.1_Silent_p.S181S|HPS4_ENST00000336873.5_Silent_p.S186S	NM_022081.5	NP_071364.4	Q9NQG7	HPS4_HUMAN	Hermansky-Pudlak syndrome 4	186					blood coagulation (GO:0007596)|hemostasis (GO:0007599)|lysosome organization (GO:0007040)|melanocyte differentiation (GO:0030318)|positive regulation of eye pigmentation (GO:0048075)|protein stabilization (GO:0050821)|protein targeting (GO:0006605)	BLOC-3 complex (GO:0031085)|cytoplasm (GO:0005737)|lysosome (GO:0005764)|melanosome (GO:0042470)|membrane (GO:0016020)|platelet dense granule (GO:0042827)	protein dimerization activity (GO:0046983)|protein homodimerization activity (GO:0042803)			breast(2)|endometrium(3)|kidney(5)|large_intestine(4)|lung(12)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	32						GAATGTGAGGCGAGCGCTGGC	0.577									Hermansky-Pudlak syndrome				C|||	108	0.0215655	0.0265	0.0317	5008	,	,		18732	0.003		0.0298	False		,,,				2504	0.0184				p.S186S		Atlas-SNP	.											HPS4_ENST00000398141,colon,carcinoma,0,2	HPS4	123	2	0			c.G558A						scavenged	.	C	,	118,4288	87.8+/-126.4	0,118,2085	54.0	51.0	52.0		558,543	-9.7	0.0	22	dbSNP_121	52	367,8233	120.4+/-179.7	11,345,3944	no	coding-synonymous,coding-synonymous	HPS4	NM_022081.4,NM_152841.1	,	11,463,6029	TT,TC,CC		4.2674,2.6782,3.729	,	186/709,181/704	26866723	485,12521	2203	4300	6503	SO:0001819	synonymous_variant	89781	exon7	Familial Cancer Database	HPS, HPS1-8	GTGAGGCGAGCGC		CCDS13835.1, CCDS46677.1	22q12.1	2014-09-17			ENSG00000100099	ENSG00000100099			15844	protein-coding gene	gene with protein product		606682				11836498, 12663659	Standard	NM_022081		Approved	KIAA1667, LE	uc003aci.4	Q9NQG7	OTTHUMG00000030459	ENST00000398145.2:c.558G>A	22.37:g.26866723C>T		Somatic	182	1	0.00549451		WXS	Illumina HiSeq	Phase_I	163	88	0.539877	NM_022081	B1AHQ4|Q5H8V6|Q96LX6|Q9BY93|Q9UH37|Q9UH38	Silent	SNP	ENST00000398145.2	37	CCDS13835.1																																																																																			C|0.968;T|0.032	0.032	strong		0.577	HPS4-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320778.1	NM_022081	
ARHGEF5	7984	hgsc.bcm.edu	37	7	144060802	144060802	+	Missense_Mutation	SNP	C	C	T	rs3823677		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:144060802C>T	ENST00000056217.5	+	2	1214	c.1040C>T	c.(1039-1041)aCc>aTc	p.T347I	ARHGEF5_ENST00000471847.2_5'Flank	NM_005435.3	NP_005426.2	Q12774	ARHG5_HUMAN	Rho guanine nucleotide exchange factor (GEF) 5	347					actin cytoskeleton organization (GO:0030036)|intracellular signal transduction (GO:0035556)|myeloid dendritic cell chemotaxis (GO:0002408)|positive regulation of podosome assembly (GO:0071803)|regulation of Rho GTPase activity (GO:0032319)		GTP binding (GO:0005525)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|endometrium(6)|kidney(8)|large_intestine(9)|liver(1)|lung(8)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	40	Melanoma(164;0.14)					AAGAGTCAAACCTTTTTGGGA	0.527																																					p.T347I		Atlas-SNP	.											ARHGEF5,colon,carcinoma,+1,1	ARHGEF5	73	1	0			c.C1040T						scavenged	.						62.0	56.0	58.0					7																	144060802		2079	3981	6060	SO:0001583	missense	7984	exon2			GTCAAACCTTTTT	U02082	CCDS34771.1	7q35	2012-09-20			ENSG00000050327	ENSG00000050327		"""Rho guanine nucleotide exchange factors"""	13209	protein-coding gene	gene with protein product	"""transforming immortalized mammary oncogene"", ""guanine nucleotide regulatory protein TIM"""	600888				8134109, 7656213	Standard	NM_005435		Approved	TIM, TIM1, GEF5, P60	uc003wel.3	Q12774	OTTHUMG00000158004	ENST00000056217.5:c.1040C>T	7.37:g.144060802C>T	ENSP00000056217:p.Thr347Ile	Somatic	402	0	0		WXS	Illumina HiSeq	Phase_I	943	212	0.224814	NM_005435	A6NNJ2|Q6ZML7	Missense_Mutation	SNP	ENST00000056217.5	37	CCDS34771.1	764	0.3498168498168498	142	0.2886178861788618	126	0.34806629834254144	284	0.4965034965034965	212	0.2796833773087071	c	8.471	0.857559	0.17106	.	.	ENSG00000050327	ENST00000056217	T	0.73047	-0.71	3.54	-2.18	0.07037	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.06786	0.001	B	0.08055	0.003	T	0.44802	-0.9304	7	.	.	.	-0.3178	0.5401	0.00644	0.2016:0.2872:0.2203:0.2909	.	347	Q12774	ARHG5_HUMAN	I	347	ENSP00000056217:T347I	.	T	+	2	0	ARHGEF5	143691735	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.478000	0.06575	-0.083000	0.12618	-0.235000	0.12190	ACC	.	.	weak		0.527	ARHGEF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349981.1	NM_005435	
KRT32	3882	hgsc.bcm.edu	37	17	39619193	39619193	+	Missense_Mutation	SNP	C	C	T	rs11078993	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:39619193C>T	ENST00000225899.3	-	6	1209	c.1106G>A	c.(1105-1107)cGg>cAg	p.R369Q		NM_002278.3	NP_002269.3	Q14532	K1H2_HUMAN	keratin 32	369	Coil 2.|Rod.				epidermis development (GO:0008544)	extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)	p.R369Q(1)		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)				CAGGTCAGCCCGGATCTCAGC	0.642													C|||	597	0.119209	0.053	0.1931	5008	,	,		17508	0.2073		0.0467	False		,,,				2504	0.1401				p.R369Q		Atlas-SNP	.											KRT32,NS,carcinoma,0,1	KRT32	57	1	1	Substitution - Missense(1)	stomach(1)	c.G1106A						PASS	.	C	GLN/ARG	272,4134	153.3+/-186.9	9,254,1940	76.0	74.0	75.0		1106	4.0	0.8	17	dbSNP_120	75	416,8184	130.3+/-188.3	20,376,3904	no	missense	KRT32	NM_002278.3	43	29,630,5844	TT,TC,CC		4.8372,6.1734,5.2899	probably-damaging	369/449	39619193	688,12318	2203	4300	6503	SO:0001583	missense	3882	exon6			TCAGCCCGGATCT	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.1106G>A	17.37:g.39619193C>T	ENSP00000225899:p.Arg369Gln	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	92	40	0.434783	NM_002278		Missense_Mutation	SNP	ENST00000225899.3	37	CCDS11393.1	227	0.10393772893772894	21	0.042682926829268296	66	0.18232044198895028	105	0.18356643356643357	35	0.04617414248021108	C	18.59	3.656817	0.67586	0.061734	0.048372	ENSG00000108759	ENST00000225899	D	0.91124	-2.79	4.98	4.0	0.46444	Filament (1);	0.000000	0.38436	N	0.001695	T	0.04452	0.0122	M	0.88031	2.925	0.25924	P	0.9830841	D	0.89917	1.0	D	0.97110	1.0	T	0.11916	-1.0568	9	0.87932	D	0	.	13.099	0.59210	0.0:0.9211:0.0:0.0789	rs11078993;rs59123042	369	Q14532	K1H2_HUMAN	Q	369	ENSP00000225899:R369Q	ENSP00000225899:R369Q	R	-	2	0	KRT32	36872719	0.997000	0.39634	0.771000	0.31576	0.291000	0.27294	4.973000	0.63763	1.197000	0.43143	0.491000	0.48974	CGG	C|0.935;T|0.065	0.065	strong		0.642	KRT32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257293.1	NM_002278	
AIM1	202	hgsc.bcm.edu	37	6	106967778	106967778	+	Missense_Mutation	SNP	T	T	C	rs3747787	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:106967778T>C	ENST00000369066.3	+	2	1958	c.1471T>C	c.(1471-1473)Tgc>Cgc	p.C491R		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)		CAGTTTCCCATGCACTGATCT	0.458													T|||	872	0.174121	0.1808	0.1354	5008	,	,		22330	0.1161		0.2515	False		,,,				2504	0.1728				p.C491R		Atlas-SNP	.											.	AIM1	161	.	0			c.T1471C						PASS	.	T	ARG/CYS	733,3673	297.8+/-285.0	58,617,1528	83.0	89.0	87.0		1471	-5.8	0.0	6	dbSNP_107	87	2104,6496	356.3+/-330.2	259,1586,2455	yes	missense	AIM1	NM_001624.2	180	317,2203,3983	CC,CT,TT		24.4651,16.6364,21.813	benign	491/1724	106967778	2837,10169	2203	4300	6503	SO:0001583	missense	202	exon2			TTCCCATGCACTG	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.1471T>C	6.37:g.106967778T>C	ENSP00000358062:p.Cys491Arg	Somatic	199	0	0		WXS	Illumina HiSeq	Phase_I	178	94	0.52809	NM_001624	Q6P2P0|Q9BTM3	Missense_Mutation	SNP	ENST00000369066.3	37	CCDS34506.1	390	0.17857142857142858	92	0.18699186991869918	57	0.1574585635359116	56	0.0979020979020979	185	0.24406332453825857	T	10.37	1.330824	0.24167	0.166364	0.244651	ENSG00000112297	ENST00000285105;ENST00000369066	T	0.71341	-0.56	6.17	-5.75	0.02384	.	1.231230	0.05863	N	0.623317	T	0.23210	0.0561	N	0.20685	0.6	0.53005	P	3.500000000000725E-5	B	0.06786	0.001	B	0.06405	0.002	T	0.05131	-1.0904	9	0.23891	T	0.37	.	2.4107	0.04423	0.2004:0.1489:0.4535:0.1972	rs3747787;rs17495394;rs52819883;rs58298313;rs3747787	491	Q9Y4K1	AIM1_HUMAN	R	899;491	ENSP00000358062:C491R	ENSP00000285105:C899R	C	+	1	0	AIM1	107074471	0.000000	0.05858	0.000000	0.03702	0.014000	0.08584	-0.826000	0.04429	-0.749000	0.04747	0.533000	0.62120	TGC	T|0.805;C|0.195	0.195	strong		0.458	AIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041669.1		
LAMA1	284217	hgsc.bcm.edu	37	18	6986259	6986259	+	Silent	SNP	G	G	A	rs62081531	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:6986259G>A	ENST00000389658.3	-	37	5349	c.5256C>T	c.(5254-5256)caC>caT	p.H1752H		NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	1752	Domain II and I.				axon guidance (GO:0007411)|branching involved in salivary gland morphogenesis (GO:0060445)|cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|establishment of epithelial cell apical/basal polarity (GO:0045198)|extracellular matrix organization (GO:0030198)|morphogenesis of an epithelial sheet (GO:0002011)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)|retinal blood vessel morphogenesis (GO:0061304)	basement membrane (GO:0005604)|cell-cell junction (GO:0005911)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|laminin-1 complex (GO:0005606)|laminin-3 complex (GO:0005608)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)	p.H1752H(1)		NS(4)|breast(7)|central_nervous_system(3)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(49)|liver(1)|lung(71)|ovary(9)|pancreas(3)|prostate(5)|skin(11)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(3)	205		Colorectal(10;0.172)				TTGAAAGGACGTGGCTTGCTG	0.468													g|||	690	0.13778	0.0068	0.147	5008	,	,		17245	0.1915		0.2326	False		,,,				2504	0.1554				p.H1752H		Atlas-SNP	.											LAMA1,colon,carcinoma,0,2	LAMA1	458	2	1	Substitution - coding silent(1)	stomach(1)	c.C5256T						PASS	.	G		233,4173	138.4+/-174.2	7,219,1977	154.0	133.0	140.0		5256	3.2	0.8	18	dbSNP_129	140	2248,6352	381.0+/-339.9	295,1658,2347	no	coding-synonymous	LAMA1	NM_005559.3		302,1877,4324	AA,AG,GG		26.1395,5.2882,19.0758		1752/3076	6986259	2481,10525	2203	4300	6503	SO:0001819	synonymous_variant	284217	exon37			AAGGACGTGGCTT	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.5256C>T	18.37:g.6986259G>A		Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	163	91	0.558282	NM_005559		Silent	SNP	ENST00000389658.3	37	CCDS32787.1																																																																																			G|0.810;A|0.190	0.190	strong		0.468	LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1	NM_005559	
ENGASE	64772	hgsc.bcm.edu	37	17	77082174	77082174	+	Missense_Mutation	SNP	C	C	T	rs117014247	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:77082174C>T	ENST00000579016.1	+	14	1975	c.1975C>T	c.(1975-1977)Cgt>Tgt	p.R659C		NM_001042573.2	NP_001036038.1	Q8NFI3	ENASE_HUMAN	endo-beta-N-acetylglucosaminidase	659						cytoplasm (GO:0005737)	mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase activity (GO:0033925)			breast(2)|endometrium(4)|large_intestine(1)|lung(15)|prostate(2)|skin(1)	25						CTCACAAGTCCGTTGCTTCCG	0.637													C|||	34	0.00678914	0.0015	0.013	5008	,	,		17023	0.0		0.0199	False		,,,				2504	0.0031				p.R659C		Atlas-SNP	.											.	ENGASE	55	.	0			c.C1975T						PASS	.	C	CYS/ARG	17,4281		0,17,2132	58.0	68.0	64.0		1975	2.0	0.1	17	dbSNP_132	64	185,8325		1,183,4071	yes	missense	ENGASE	NM_001042573.1	180	1,200,6203	TT,TC,CC		2.1739,0.3955,1.5771	benign	659/744	77082174	202,12606	2149	4255	6404	SO:0001583	missense	64772	exon14			CAAGTCCGTTGCT	AF512564	CCDS42394.1	17q25.3	2009-03-03			ENSG00000167280	ENSG00000167280	3.2.1.96		24622	protein-coding gene	gene with protein product	"""Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase"", ""Di-N-acetylchitobiosyl beta-N-acetylglucosaminidase"""	611898				12114544, 18586680	Standard	NM_001042573		Approved	FLJ21865	uc002jwv.4	Q8NFI3	OTTHUMG00000167714	ENST00000579016.1:c.1975C>T	17.37:g.77082174C>T	ENSP00000462333:p.Arg659Cys	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	63	42	0.666667	NM_001042573	Q659F0|Q8TB86|Q9H6U4	Missense_Mutation	SNP	ENST00000579016.1	37	CCDS42394.1	22	0.010073260073260074	2	0.0040650406504065045	5	0.013812154696132596	0	0.0	15	0.01978891820580475	C	6.060	0.379407	0.11466	0.003955	0.021739	ENSG00000167280	ENST00000545583	.	.	.	4.26	2.01	0.26516	.	0.333614	0.31797	N	0.007049	T	0.16642	0.0400	L	0.56769	1.78	0.09310	N	0.999999	B	0.27594	0.182	B	0.17979	0.02	T	0.20107	-1.0285	9	0.54805	T	0.06	-3.595	2.1577	0.03816	0.4416:0.2981:0.1551:0.1052	.	659	Q8NFI3	ENASE_HUMAN	C	659	.	ENSP00000438577:R659C	R	+	1	0	ENGASE	74593769	0.000000	0.05858	0.093000	0.20910	0.199000	0.23934	-0.105000	0.10907	0.939000	0.37446	0.467000	0.42956	CGT	C|0.982;T|0.018	0.018	strong		0.637	ENGASE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395807.1	NM_022759	
CLDN14	23562	hgsc.bcm.edu	37	21	37833931	37833931	+	Silent	SNP	C	C	T	rs117560775	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:37833931C>T	ENST00000399137.1	-	3	929	c.63G>A	c.(61-63)acG>acA	p.T21T	AP000695.6_ENST00000429588.1_RNA|CLDN14_ENST00000399139.1_Silent_p.T21T|AP000695.4_ENST00000454980.1_RNA|CLDN14_ENST00000342108.2_Silent_p.T21T|CLDN14_ENST00000399136.1_Silent_p.T21T|AP000695.4_ENST00000428667.1_RNA|CLDN14_ENST00000399135.1_Silent_p.T21T	NM_144492.2	NP_652763.1	O95500	CLD14_HUMAN	claudin 14	21					calcium-independent cell-cell adhesion (GO:0016338)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|protein complex assembly (GO:0006461)|tight junction assembly (GO:0070830)	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)			endometrium(1)|lung(5)|skin(1)	7						TGGTGATCAACGTGCCCACCA	0.662													C|||	112	0.0223642	0.0038	0.0836	5008	,	,		17333	0.001		0.0308	False		,,,				2504	0.0174				p.T21T		Atlas-SNP	.											.	CLDN14	25	.	0			c.G63A						PASS	.	C	,,,,	23,4377		0,23,2177	22.0	18.0	19.0		63,63,63,63,63	-2.1	0.8	21	dbSNP_132	19	261,8339		2,257,4041	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CLDN14	NM_001146077.1,NM_001146078.1,NM_001146079.1,NM_012130.2,NM_144492.2	,,,,	2,280,6218	TT,TC,CC		3.0349,0.5227,2.1846	,,,,	21/240,21/240,21/240,21/240,21/240	37833931	284,12716	2200	4300	6500	SO:0001819	synonymous_variant	23562	exon3			GATCAACGTGCCC	AJ132445	CCDS13645.1	21q22.3	2008-07-31			ENSG00000159261	ENSG00000159261		"""Claudins"""	2035	protein-coding gene	gene with protein product		605608		DFNB29		11163249	Standard	NM_144492		Approved		uc002yvk.2	O95500	OTTHUMG00000086638	ENST00000399137.1:c.63G>A	21.37:g.37833931C>T		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	66	40	0.606061	NM_144492		Silent	SNP	ENST00000399137.1	37	CCDS13645.1																																																																																			C|0.978;T|0.022	0.022	strong		0.662	CLDN14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194697.1	NM_144492	
ADAMTS7	11173	hgsc.bcm.edu	37	15	79058951	79058951	+	Missense_Mutation	SNP	T	T	C	rs28699256	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:79058951T>C	ENST00000388820.4	-	19	3512	c.3302A>G	c.(3301-3303)cAt>cGt	p.H1101R	ADAMTS7_ENST00000566303.1_5'Flank	NM_014272.3	NP_055087.2	Q9UKP4	ATS7_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 7	1101				H -> R (in Ref. 2; AAQ94616). {ECO:0000305}.	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						CGCAGCAGGATGGCTGTGTGG	0.652													t|||	1361	0.271765	0.2065	0.3256	5008	,	,		11467	0.1042		0.4483	False		,,,				2504	0.3129				p.H1101R		Atlas-SNP	.											.	ADAMTS7	142	.	0			c.A3302G						PASS	.	C	ARG/HIS	1012,3308		157,698,1305	13.0	20.0	17.0		3302	-2.7	0.0	15	dbSNP_125	17	3722,4824		858,2006,1409	no	missense	ADAMTS7	NM_014272.3	29	1015,2704,2714	CC,CT,TT		43.5525,23.4259,36.7947	benign	1101/1687	79058951	4734,8132	2160	4273	6433	SO:0001583	missense	11173	exon19			GCAGGATGGCTGT	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.3302A>G	15.37:g.79058951T>C	ENSP00000373472:p.His1101Arg	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	105	55	0.52381	NM_014272	Q14F51|Q6P7J9	Missense_Mutation	SNP	ENST00000388820.4	37	CCDS32303.1	577	0.2641941391941392	99	0.20121951219512196	127	0.35082872928176795	42	0.07342657342657342	309	0.4076517150395778	t	0.008	-1.919274	0.00498	0.234259	0.435525	ENSG00000136378	ENST00000388820	T	0.40476	1.03	2.22	-2.73	0.05950	.	2.129250	0.01689	N	0.026553	T	0.00012	0.0000	N	0.01576	-0.805	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.36359	-0.9751	9	0.13470	T	0.59	.	4.1049	0.10032	0.0:0.46:0.1752:0.3648	rs28699256;rs60983041	1101	Q9UKP4	ATS7_HUMAN	R	1101	ENSP00000373472:H1101R	ENSP00000373472:H1101R	H	-	2	0	ADAMTS7	76846006	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.791000	0.00767	-0.686000	0.05170	-1.569000	0.00873	CAT	T|0.695;C|0.305	0.305	strong		0.652	ADAMTS7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421331.1	NM_014272	
PLEKHG5	57449	hgsc.bcm.edu	37	1	6528589	6528589	+	Silent	SNP	C	C	T	rs3138150	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:6528589C>T	ENST00000400915.3	-	21	2541	c.2475G>A	c.(2473-2475)acG>acA	p.T825T	PLEKHG5_ENST00000377728.3_Silent_p.T769T|PLEKHG5_ENST00000535355.1_Silent_p.T838T|TNFRSF25_ENST00000356876.3_5'Flank|PLEKHG5_ENST00000544978.1_Silent_p.T769T|TNFRSF25_ENST00000351959.5_5'Flank|PLEKHG5_ENST00000400913.1_Silent_p.T769T|TNFRSF25_ENST00000348333.3_5'Flank|TNFRSF25_ENST00000461703.2_5'Flank|TNFRSF25_ENST00000377782.3_5'Flank|PLEKHG5_ENST00000537245.1_Silent_p.T848T|PLEKHG5_ENST00000377725.1_Silent_p.T769T|TNFRSF25_ENST00000351748.3_5'Flank|PLEKHG5_ENST00000340850.5_Silent_p.T769T|PLEKHG5_ENST00000377740.3_Intron|PLEKHG5_ENST00000377732.1_Silent_p.T806T|PLEKHG5_ENST00000377748.1_Silent_p.T846T|PLEKHG5_ENST00000377737.2_Silent_p.T769T	NM_001042663.1	NP_001036128.1	O94827	PKHG5_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 5	825					apoptotic signaling pathway (GO:0097190)|endothelial cell chemotaxis (GO:0035767)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)|signal transducer activity (GO:0004871)			liver(1)	1	Ovarian(185;0.02)|all_lung(157;0.154)	all_cancers(23;1.7e-35)|all_epithelial(116;2.78e-22)|all_lung(118;7.57e-07)|Lung NSC(185;4.26e-06)|Colorectal(325;4.47e-05)|all_hematologic(16;0.00014)|Breast(487;0.000688)|Renal(390;0.0007)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0448)		Epithelial(90;5.51e-35)|GBM - Glioblastoma multiforme(13;3.57e-27)|Colorectal(212;6.23e-08)|COAD - Colon adenocarcinoma(227;1.33e-05)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000894)|BRCA - Breast invasive adenocarcinoma(365;0.00107)|STAD - Stomach adenocarcinoma(132;0.00159)|READ - Rectum adenocarcinoma(331;0.0419)		GGGAGGACAGCGTGTCCCCAG	0.627													c|||	279	0.0557109	0.0787	0.0519	5008	,	,		18051	0.0		0.0557	False		,,,				2504	0.0849				p.T848T		Atlas-SNP	.											.	PLEKHG5	66	.	0			c.G2544A						PASS	.	C	,,,,	321,4077		7,307,1885	34.0	36.0	35.0		2475,2307,2307,2307,2538	-6.5	0.0	1	dbSNP_104	35	492,8096		13,466,3815	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PLEKHG5	NM_001042663.1,NM_001042664.1,NM_001042665.1,NM_020631.3,NM_198681.2	,,,,	20,773,5700	TT,TC,CC		5.7289,7.2988,6.2606	,,,,	825/1063,769/1007,769/1007,769/1007,846/1084	6528589	813,12173	2199	4294	6493	SO:0001819	synonymous_variant	57449	exon21			GGACAGCGTGTCC	AK024676	CCDS79.1, CCDS41240.1, CCDS41241.1, CCDS57967.1, CCDS57968.1, CCDS57969.1	1p36.31	2014-09-17		2005-08-09	ENSG00000171680	ENSG00000171680		"""Pleckstrin homology (PH) domain containing"""	29105	protein-coding gene	gene with protein product	"""synectin-binding guanine exchange factor"""	611101				17564964	Standard	NM_001042663		Approved	KIAA0720, Syx, GEF720, Tech	uc010nzr.1	O94827	OTTHUMG00000000905	ENST00000400915.3:c.2475G>A	1.37:g.6528589C>T		Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	147	73	0.496599	NM_001265592	B3KU07|B7Z2M3|B7Z5X2|F5GZ21|F5H1I0|Q5SY17|Q5T8W5|Q5T8W9|Q6ZNM0|Q7Z436|Q86YD8|Q96BS1	Silent	SNP	ENST00000400915.3	37	CCDS41241.1																																																																																			C|0.939;T|0.061	0.061	strong		0.627	PLEKHG5-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000002631.1	NM_020631	
UTP20	27340	hgsc.bcm.edu	37	12	101685852	101685852	+	Silent	SNP	G	G	A	rs11110737	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	117	0	0		WXS	Illumina HiSeq	Phase_I	90	36	0.4	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	
ABCA7	10347	hgsc.bcm.edu	37	19	1062192	1062192	+	Silent	SNP	T	T	C	rs4147921	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:1062192T>C	ENST00000263094.6	+	42	5823	c.5592T>C	c.(5590-5592)gcT>gcC	p.A1864A	ABCA7_ENST00000435683.2_Silent_p.A1726A|ABCA7_ENST00000433129.1_Silent_p.A1864A	NM_019112.3	NP_061985.2	Q8IZY2	ABCA7_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 7	1864	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				apolipoprotein A-I-mediated signaling pathway (GO:0038027)|ATP catabolic process (GO:0006200)|cholesterol efflux (GO:0033344)|high-density lipoprotein particle assembly (GO:0034380)|memory (GO:0007613)|negative regulation of amyloid precursor protein biosynthetic process (GO:0042985)|negative regulation of ATPase activity (GO:0032780)|negative regulation of beta-amyloid formation (GO:1902430)|peptide cross-linking (GO:0018149)|phagocytosis (GO:0006909)|phospholipid efflux (GO:0033700)|phospholipid scrambling (GO:0017121)|positive regulation of ATPase activity (GO:0032781)|positive regulation of beta-amyloid clearance (GO:1900223)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of engulfment of apoptotic cell (GO:1901076)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of phagocytosis (GO:0050766)|positive regulation of phospholipid efflux (GO:1902995)|protein localization to nucleus (GO:0034504)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|ATP-binding cassette (ABC) transporter complex (GO:0043190)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|phagocytic cup (GO:0001891)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	apolipoprotein A-I receptor activity (GO:0034188)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|phospholipid transporter activity (GO:0005548)|transporter activity (GO:0005215)			NS(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(7)|lung(22)|ovary(1)|pancreas(7)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	65		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		AACCCAGTGCTGCGCACCTCA	0.672													T|||	283	0.0565096	0.0023	0.0115	5008	,	,		16831	0.1736		0.0398	False		,,,				2504	0.0583				p.A1864A		Atlas-SNP	.											.	ABCA7	174	.	0			c.T5592C						PASS	.	T		38,4368	40.0+/-72.8	0,38,2165	88.0	97.0	94.0		5592	-7.3	0.0	19	dbSNP_110	94	349,8251	115.2+/-175.0	4,341,3955	no	coding-synonymous	ABCA7	NM_019112.3		4,379,6120	CC,CT,TT		4.0581,0.8625,2.9755		1864/2147	1062192	387,12619	2203	4300	6503	SO:0001819	synonymous_variant	10347	exon42			CAGTGCTGCGCAC	AF328787	CCDS12055.1	19p13.3	2012-03-14			ENSG00000064687	ENSG00000064687		"""ATP binding cassette transporters / subfamily A"""	37	protein-coding gene	gene with protein product		605414					Standard	NM_019112		Approved	ABCX	uc002lqw.4	Q8IZY2	OTTHUMG00000167547	ENST00000263094.6:c.5592T>C	19.37:g.1062192T>C		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	153	59	0.385621	NM_019112	Q96S58|Q9BZC4|Q9NR73|Q9UKP8	Silent	SNP	ENST00000263094.6	37	CCDS12055.1																																																																																			T|0.960;C|0.040	0.040	strong		0.672	ABCA7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000394993.1	NM_019112	
SH3RF1	57630	hgsc.bcm.edu	37	4	170038894	170038894	+	Silent	SNP	A	A	G	rs74798922	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:170038894A>G	ENST00000284637.9	-	9	1898	c.1557T>C	c.(1555-1557)tcT>tcC	p.S519S	SH3RF1_ENST00000508685.1_5'UTR	NM_020870.3	NP_065921.2	Q7Z6J0	SH3R1_HUMAN	SH3 domain containing ring finger 1	519	Interaction with AKT2. {ECO:0000250}.				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)		GGCCAGCTGTAGACATAGGGA	0.547													A|||	192	0.0383387	0.0023	0.0086	5008	,	,		16053	0.125		0.0109	False		,,,				2504	0.047				p.S519S		Atlas-SNP	.											.	SH3RF1	60	.	0			c.T1557C						PASS	.	A		12,4394	17.9+/-39.9	0,12,2191	46.0	44.0	45.0		1557	-3.6	0.8	4	dbSNP_131	45	105,8495	56.4+/-117.6	1,103,4196	no	coding-synonymous	SH3RF1	NM_020870.3		1,115,6387	GG,GA,AA		1.2209,0.2724,0.8996		519/889	170038894	117,12889	2203	4300	6503	SO:0001819	synonymous_variant	57630	exon9			AGCTGTAGACATA	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.1557T>C	4.37:g.170038894A>G		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	82	40	0.487805	NM_020870	Q05BT2|Q8IW46|Q9HAM2|Q9P234	Silent	SNP	ENST00000284637.9	37	CCDS34099.1																																																																																			A|0.982;G|0.018	0.018	strong		0.547	SH3RF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363382.3	NM_020870	
VCAN	1462	hgsc.bcm.edu	37	5	82815170	82815170	+	Missense_Mutation	SNP	A	A	G	rs61749613	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:82815170A>G	ENST00000265077.3	+	7	1610	c.1045A>G	c.(1045-1047)Aaa>Gaa	p.K349E	VCAN_ENST00000502527.2_Intron|VCAN_ENST00000512590.2_Missense_Mutation_p.K301E|VCAN_ENST00000343200.5_Intron|VCAN_ENST00000342785.4_Missense_Mutation_p.K349E	NM_004385.4	NP_004376.2	P13611	CSPG2_HUMAN	versican	349	GAG-alpha (glucosaminoglycan attachment domain).				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)	TTTTCTAGCTAAAGAGGCTAC	0.368													A|||	100	0.0199681	0.0008	0.0317	5008	,	,		19029	0.001		0.0487	False		,,,				2504	0.0276				p.K349E		Atlas-SNP	.											.	VCAN	498	.	0			c.A1045G						PASS	.	A	,,GLU/LYS,GLU/LYS	40,4364	41.6+/-74.8	1,38,2163	66.0	69.0	68.0		,,1045,1045	5.6	1.0	5	dbSNP_129	68	358,8238	115.5+/-175.4	8,342,3948	yes	intron,intron,missense,missense	VCAN	NM_001126336.2,NM_001164097.1,NM_001164098.1,NM_004385.4	,,56,56	9,380,6111	GG,GA,AA		4.1647,0.9083,3.0615	,,probably-damaging,probably-damaging	,,349/1643,349/3397	82815170	398,12602	2202	4298	6500	SO:0001583	missense	1462	exon7			CTAGCTAAAGAGG	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.1045A>G	5.37:g.82815170A>G	ENSP00000265077:p.Lys349Glu	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	81	37	0.45679	NM_004385	P20754|Q13010|Q13189|Q15123|Q9UCL9|Q9UNW5	Missense_Mutation	SNP	ENST00000265077.3	37	CCDS4060.1	53	0.024267399267399268	0	0.0	12	0.03314917127071823	1	0.0017482517482517483	40	0.052770448548812667	A	16.74	3.207760	0.58343	0.009083	0.041647	ENSG00000038427	ENST00000265077;ENST00000342785;ENST00000512590	T;T;T	0.09350	2.99;2.99;2.99	5.64	5.64	0.86602	C-type lectin fold (1);C-type lectin-like (1);	0.000000	0.64402	D	0.000006	T	0.03651	0.0104	M	0.61703	1.905	0.44454	D	0.997384	P;P	0.42692	0.694;0.787	P;P	0.55545	0.778;0.512	T	0.04693	-1.0933	10	0.11794	T	0.64	.	13.3803	0.60762	1.0:0.0:0.0:0.0	rs61749613	349;349	P13611-3;P13611	.;CSPG2_HUMAN	E	349;349;301	ENSP00000265077:K349E;ENSP00000342768:K349E;ENSP00000425959:K301E	ENSP00000265077:K349E	K	+	1	0	VCAN	82850926	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	2.860000	0.48372	2.151000	0.67156	0.533000	0.62120	AAA	A|0.973;G|0.027	0.027	strong		0.368	VCAN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254092.3	NM_004385	
TPRX1	284355	hgsc.bcm.edu	37	19	48305654	48305654	+	Missense_Mutation	SNP	C	C	T	rs73036913	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:48305654C>T	ENST00000322175.3	-	2	769	c.614G>A	c.(613-615)gGc>gAc	p.G205D	TPRX1_ENST00000535759.1_Missense_Mutation_p.G302D|TPRX1_ENST00000543508.1_Missense_Mutation_p.G195D	NM_198479.2	NP_940881.2	Q8N7U7	TPRX1_HUMAN	tetra-peptide repeat homeobox 1	205	Gly-rich.					nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(5)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|prostate(2)|skin(1)	18		all_cancers(25;3.02e-09)|all_epithelial(76;7e-07)|all_lung(116;2.48e-06)|Lung NSC(112;5.15e-06)|Ovarian(192;0.0139)|all_neural(266;0.0146)|Breast(70;0.133)		OV - Ovarian serous cystadenocarcinoma(262;0.000241)|all cancers(93;0.00036)|Epithelial(262;0.0127)|GBM - Glioblastoma multiforme(486;0.048)		tgggatcgggcctgggatcgg	0.677													G|||	184	0.0367412	0.0045	0.0432	5008	,	,		16236	0.0		0.1103	False		,,,				2504	0.0378				p.G205D	Esophageal Squamous(123;175 2281 3051 32395)	Atlas-SNP	.											TPRX1,colon,carcinoma,0,1	TPRX1	46	1	0			c.G614A						PASS	.	C	ASP/GLY	63,3517		0,63,1727	13.0	10.0	11.0		614	-0.8	0.0	19	dbSNP_130	11	632,6154		20,592,2781	no	missense	TPRX1	NM_198479.2	94	20,655,4508	TT,TC,CC		9.3133,1.7598,6.7046	possibly-damaging	205/412	48305654	695,9671	1790	3393	5183	SO:0001583	missense	284355	exon2			ATCGGGCCTGGGA		CCDS33066.1	19q13.33	2011-07-08			ENSG00000178928	ENSG00000178928		"""Homeoboxes / PRD class"""	32174	protein-coding gene	gene with protein product		611166					Standard	XM_005258788		Approved	FLJ40321	uc002php.2	Q8N7U7		ENST00000322175.3:c.614G>A	19.37:g.48305654C>T	ENSP00000323455:p.Gly205Asp	Somatic	19	0	0		WXS	Illumina HiSeq	Phase_I	27	9	0.333333	NM_198479	A5D8Y3|B2RPL5	Missense_Mutation	SNP	ENST00000322175.3	37	CCDS33066.1	104	0.047619047619047616	2	0.0040650406504065045	14	0.03867403314917127	0	0.0	88	0.11609498680738786	-	9.378	1.072204	0.20147	0.017598	0.093133	ENSG00000178928	ENST00000322175;ENST00000535759;ENST00000543508	T;T;T	0.40476	1.03;1.03;1.03	0.401	-0.802	0.10889	.	.	.	.	.	T	0.00241	0.0007	N	0.08118	0	0.09310	N	1	P	0.49185	0.92	B	0.39805	0.31	T	0.04870	-1.0921	8	0.13108	T	0.6	.	.	.	.	.	205	Q8N7U7	TPRX1_HUMAN	D	205;302;195	ENSP00000323455:G205D;ENSP00000438832:G302D;ENSP00000438712:G195D	ENSP00000323455:G205D	G	-	2	0	TPRX1	52997466	0.001000	0.12720	0.004000	0.12327	0.004000	0.04260	-0.104000	0.10923	-0.484000	0.06763	-0.486000	0.04755	GGC	C|0.949;T|0.051	0.051	strong		0.677	TPRX1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000409868.1	NM_198479	
UTRN	7402	hgsc.bcm.edu	37	6	144774982	144774982	+	Missense_Mutation	SNP	T	T	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:144774982T>G	ENST00000367545.3	+	18	2261	c.2261T>G	c.(2260-2262)aTc>aGc	p.I754S		NM_007124.2	NP_009055.2	P46939	UTRO_HUMAN	utrophin	754	Interaction with SYNM.				aging (GO:0007568)|muscle cell differentiation (GO:0042692)|muscle contraction (GO:0006936)|muscle organ development (GO:0007517)|neuron projection morphogenesis (GO:0048812)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of sodium ion transmembrane transporter activity (GO:2000649)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dystrophin-associated glycoprotein complex (GO:0016010)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane (GO:0016020)|membrane raft (GO:0045121)|myofibril (GO:0030016)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|protein kinase binding (GO:0019901)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(1)|cervix(2)|endometrium(21)|kidney(10)|large_intestine(29)|lung(56)|ovary(5)|pancreas(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	148		Ovarian(120;0.218)		OV - Ovarian serous cystadenocarcinoma(155;5.72e-07)|GBM - Glioblastoma multiforme(68;4.9e-05)|Colorectal(48;0.213)		ACTGGACAAATCCTTGTGGAG	0.358																																					p.I754S		Atlas-SNP	.											.	UTRN	327	.	0			c.T2261G						PASS	.						90.0	95.0	93.0					6																	144774982		2203	4300	6503	SO:0001583	missense	7402	exon18			GACAAATCCTTGT	AK023675	CCDS34547.1	6q24	2008-02-05	2006-12-13		ENSG00000152818	ENSG00000152818			12635	protein-coding gene	gene with protein product		128240	"""utrophin (homologous to dystrophin)"""	DMDL		1426262	Standard	NM_007124		Approved	DRP, DRP1	uc003qkt.3	P46939	OTTHUMG00000015746	ENST00000367545.3:c.2261T>G	6.37:g.144774982T>G	ENSP00000356515:p.Ile754Ser	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	58	30	0.517241	NM_007124	Q5SYY1|Q5SZ57|Q9UJ40	Missense_Mutation	SNP	ENST00000367545.3	37	CCDS34547.1	.	.	.	.	.	.	.	.	.	.	T	0.223	-1.027393	0.02045	.	.	ENSG00000152818	ENST00000367529;ENST00000367545	T	0.32988	1.43	5.87	-1.66	0.08265	.	0.697165	0.12797	N	0.438319	T	0.04588	0.0125	N	0.24115	0.695	0.32854	D	0.507058	B	0.21309	0.054	B	0.15484	0.013	T	0.39014	-0.9634	10	0.09084	T	0.74	.	5.6165	0.17434	0.1604:0.2957:0.0:0.5439	.	754	P46939	UTRO_HUMAN	S	754	ENSP00000356515:I754S	ENSP00000356499:I754S	I	+	2	0	UTRN	144816675	0.915000	0.31059	0.238000	0.24106	0.304000	0.27724	0.951000	0.29135	-0.106000	0.12110	-0.290000	0.09829	ATC	.	.	none		0.358	UTRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042551.1		
CEP112	201134	hgsc.bcm.edu	37	17	63898348	63898348	+	Silent	SNP	T	T	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:63898348T>C	ENST00000392769.2	-	20	2303	c.2085A>G	c.(2083-2085)gaA>gaG	p.E695E	CEP112_ENST00000537949.1_Silent_p.E653E|CEP112_ENST00000535342.2_Silent_p.E695E|CEP112_ENST00000541355.1_Silent_p.E330E	NM_145036.3	NP_659473.2	Q8N8E3	CE112_HUMAN	centrosomal protein 112kDa	695					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						TTTCCAGGTTTTCAATTTCCC	0.433																																					p.E695E		Atlas-SNP	.											CEP112,NS,carcinoma,-2,1	CEP112	192	1	0			c.A2085G						scavenged	.						188.0	157.0	167.0					17																	63898348		2203	4300	6503	SO:0001819	synonymous_variant	201134	exon20			CAGGTTTTCAATT	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.2085A>G	17.37:g.63898348T>C		Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	149	3	0.0201342	NM_001199165	Q6PIB5|Q8NCR4|Q8NFR4	Silent	SNP	ENST00000392769.2	37	CCDS32710.1																																																																																			.	.	none		0.433	CEP112-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446582.1	NM_145036	
T	6862	hgsc.bcm.edu	37	6	166579270	166579270	+	Missense_Mutation	SNP	C	C	T	rs2305089	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:166579270C>T	ENST00000296946.2	-	4	998	c.530G>A	c.(529-531)gGt>gAt	p.G177D	T_ENST00000366871.3_Missense_Mutation_p.G177D	NM_003181.3	NP_003172.1	O15178	BRAC_HUMAN	T, brachyury homolog (mouse)	177			G -> D (in dbSNP:rs2305089). {ECO:0000269|PubMed:15489334}.		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)		GCGCTGTGGACCCCCAACTCT	0.537									Chordoma, Familial Clustering of				C|||	1962	0.391773	0.2042	0.5288	5008	,	,		18633	0.3423		0.495	False		,,,				2504	0.4928				p.G177D		Atlas-SNP	.											.	T	77	.	0			c.G530A						PASS	.	C	ASP/GLY	1164,3242	409.5+/-335.0	160,844,1199	325.0	283.0	297.0		530	4.1	0.1	6	dbSNP_100	297	4407,4193	585.9+/-391.9	1136,2135,1029	yes	missense	T	NM_003181.2	94	1296,2979,2228	TT,TC,CC		48.7558,26.4185,42.8341	benign	177/436	166579270	5571,7435	2203	4300	6503	SO:0001583	missense	6862	exon4	Familial Cancer Database		TGTGGACCCCCAA	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.530G>A	6.37:g.166579270C>T	ENSP00000296946:p.Gly177Asp	Somatic	195	0	0		WXS	Illumina HiSeq	Phase_I	128	36	0.28125	NM_003181	E7ERD6|Q4KMP4	Missense_Mutation	SNP	ENST00000296946.2	37	CCDS5290.1	853	0.39056776556776557	117	0.23780487804878048	193	0.5331491712707183	184	0.32167832167832167	359	0.4736147757255937	C	9.764	1.170949	0.21621	0.264185	0.512442	ENSG00000164458	ENST00000366876;ENST00000296946;ENST00000366871	T;T;T	0.79845	-1.31;-1.31;-1.31	4.94	4.06	0.47325	p53-like transcription factor, DNA-binding (1);	0.110544	0.64402	D	0.000012	T	0.58061	0.2096	L	0.37897	1.145	0.09310	P	0.99999999595714	B;B	0.27117	0.168;0.006	B;B	0.35353	0.201;0.035	T	0.54768	-0.8244	9	0.07813	T	0.8	.	14.4316	0.67254	0.0:0.8518:0.1482:0.0	rs2305089;rs52793205;rs61421018;rs2305089	177;177	E7ERD6;O15178	.;BRAC_HUMAN	D	177	ENSP00000355841:G177D;ENSP00000296946:G177D;ENSP00000355836:G177D	ENSP00000296946:G177D	G	-	2	0	T	166499260	1.000000	0.71417	0.142000	0.22268	0.065000	0.16274	5.496000	0.66918	1.059000	0.40554	-0.304000	0.09214	GGT	C|0.583;T|0.417	0.417	strong		0.537	T-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043037.2	NM_003181	
UNC45B	146862	hgsc.bcm.edu	37	17	33476001	33476001	+	Missense_Mutation	SNP	G	G	A	rs16970659	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:33476001G>A	ENST00000268876.5	+	3	275	c.178G>A	c.(178-180)Gtc>Atc	p.V60I	UNC45B_ENST00000591048.1_Missense_Mutation_p.V60I|UNC45B_ENST00000378449.1_Missense_Mutation_p.V60I|UNC45B_ENST00000433649.1_Missense_Mutation_p.V60I|UNC45B_ENST00000394570.2_Missense_Mutation_p.V60I	NM_173167.2	NP_775259.1	Q8IWX7	UN45B_HUMAN	unc-45 homolog B (C. elegans)	60			V -> I (in dbSNP:rs16970659). {ECO:0000269|PubMed:15489334}.		cell differentiation (GO:0030154)|chaperone-mediated protein folding (GO:0061077)|muscle organ development (GO:0007517)	cytoplasm (GO:0005737)|cytosol (GO:0005829)		p.V60I(1)		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)				GGAGAGCTACGTCCAGGCAGC	0.567													G|||	284	0.0567093	0.0038	0.1441	5008	,	,		20079	0.0377		0.0398	False		,,,				2504	0.1033				p.V60I		Atlas-SNP	.											UNC45B,NS,carcinoma,0,1	UNC45B	133	1	1	Substitution - Missense(1)	stomach(1)	c.G178A						PASS	.	G	ILE/VAL,ILE/VAL	52,4354	51.6+/-87.1	0,52,2151	149.0	125.0	133.0		178,178	1.5	0.4	17	dbSNP_123	133	328,8272	114.6+/-174.5	6,316,3978	yes	missense,missense	UNC45B	NM_001033576.1,NM_173167.2	29,29	6,368,6129	AA,AG,GG		3.814,1.1802,2.9217	benign,benign	60/930,60/932	33476001	380,12626	2203	4300	6503	SO:0001583	missense	146862	exon3			AGCTACGTCCAGG	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.178G>A	17.37:g.33476001G>A	ENSP00000268876:p.Val60Ile	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	120	61	0.508333	NM_001267052	Q495Q8|Q495Q9	Missense_Mutation	SNP	ENST00000268876.5	37	CCDS11292.1	94	0.04304029304029304	4	0.008130081300813009	36	0.09944751381215469	20	0.03496503496503497	34	0.044854881266490766	G	8.432	0.848945	0.17034	0.011802	0.03814	ENSG00000141161	ENST00000394570;ENST00000268876;ENST00000433649;ENST00000378449	T;T;T;T	0.60299	0.2;0.2;0.2;0.2	4.59	1.47	0.22746	Elongated TPR repeat-containing domain (1);Tetratricopeptide repeat-containing (1);	1.403240	0.03993	N	0.295111	T	0.01523	0.0049	N	0.20445	0.575	0.09310	N	1	B;B;B	0.25521	0.128;0.0;0.0	B;B;B	0.26864	0.074;0.001;0.002	T	0.09885	-1.0654	10	0.41790	T	0.15	-3.4617	9.1054	0.36694	0.2437:0.0:0.7563:0.0	rs16970659;rs16970659	60;60;60	Q8IWX7-2;Q8IWX7-3;Q8IWX7	.;.;UN45B_HUMAN	I	60	ENSP00000378071:V60I;ENSP00000268876:V60I;ENSP00000412840:V60I;ENSP00000367710:V60I	ENSP00000268876:V60I	V	+	1	0	UNC45B	30500114	0.012000	0.17670	0.418000	0.26571	0.545000	0.35147	1.843000	0.39259	0.564000	0.29238	0.561000	0.74099	GTC	G|0.963;A|0.037	0.037	strong		0.567	UNC45B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256458.2	NM_173167	
MECOM	2122	hgsc.bcm.edu	37	3	169098992	169098992	+	Missense_Mutation	SNP	G	G	A	rs7622799	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:169098992G>A	ENST00000494292.1	-	2	455	c.358C>T	c.(358-360)Ccc>Tcc	p.P120S	MECOM_ENST00000485957.1_5'UTR	NM_004991.3	NP_004982.2	Q13465	MDS1_HUMAN	MDS1 and EVI1 complex locus	120			P -> S (in dbSNP:rs7622799).		regulation of transcription, DNA-templated (GO:0006355)		sequence-specific DNA binding transcription factor activity (GO:0003700)	p.P114S(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(13)|liver(1)|lung(28)|ovary(2)|pancreas(1)|prostate(2)|skin(12)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(4)	85						CCATAACTGGGGTCTTTCAGG	0.408													G|||	766	0.152955	0.1362	0.3329	5008	,	,		20490	0.1558		0.1233	False		,,,				2504	0.0757				p.P120S		Atlas-SNP	.											MDS1,NS,carcinoma,0,1	MECOM	216	1	1	Substitution - Missense(1)	stomach(1)	c.C358T						PASS	.	G	,SER/PRO	483,3245		32,419,1413	90.0	87.0	88.0		,358	4.5	1.0	3	dbSNP_116	88	932,7278		53,826,3226	yes	intron,missense	MECOM	NM_001205194.1,NM_004991.3	,74	85,1245,4639	AA,AG,GG		11.352,12.956,11.8529	,possibly-damaging	,120/1240	169098992	1415,10523	1864	4105	5969	SO:0001583	missense	2122	exon2			AACTGGGGTCTTT	S82592, AF164154	CCDS3205.1, CCDS54669.1, CCDS54670.1	3q26.2	2013-01-08	2009-08-07	2009-08-07	ENSG00000085276	ENSG00000085276		"""Zinc fingers, C2H2-type"""	3498	protein-coding gene	gene with protein product		165215	"""myelodysplasia syndrome 1"", ""ecotropic viral integration site 1"""	MDS1, EVI1		2115646, 8171026, 8643684	Standard	NM_001105077		Approved	MDS1-EVI1, PRDM3	uc011bpj.1	Q03112	OTTHUMG00000158596	ENST00000494292.1:c.358C>T	3.37:g.169098992G>A	ENSP00000417899:p.Pro120Ser	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	132	56	0.424242	NM_004991	Q13466|Q6FH90	Missense_Mutation	SNP	ENST00000494292.1	37		344	0.1575091575091575	59	0.11991869918699187	89	0.24585635359116023	94	0.16433566433566432	102	0.1345646437994723	G	1.493	-0.554124	0.03996	0.12956	0.11352	ENSG00000085276	ENST00000494292	T	0.71698	-0.59	5.4	4.52	0.55395	.	0.105398	0.42964	N	0.000640	T	0.00012	0.0000	N	0.12746	0.255	0.09310	P	1.0	B;B	0.30281	0.275;0.0	B;B	0.28916	0.096;0.002	T	0.06734	-1.0810	9	0.46703	T	0.11	.	13.2366	0.59972	0.0775:0.0:0.9225:0.0	rs7622799;rs52817261;rs59561788;rs7622799	120;120	Q13465;Q03112-3	MDS1_HUMAN;.	S	120	ENSP00000417899:P120S	ENSP00000417899:P120S	P	-	1	0	MECOM	170581686	1.000000	0.71417	0.974000	0.42286	0.381000	0.30169	2.496000	0.45346	1.252000	0.44001	0.650000	0.86243	CCC	G|0.861;A|0.139	0.139	strong		0.408	MECOM-004	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000351517.3	NM_005241, NM_004991	
LILRA3	11026	hgsc.bcm.edu	37	19	54802548	54802548	+	Missense_Mutation	SNP	G	G	T	rs575974414	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:54802548G>T	ENST00000251390.3	-	5	984	c.893C>A	c.(892-894)tCc>tAc	p.S298Y	LILRA3_ENST00000391744.3_Missense_Mutation_p.S234Y|LILRA3_ENST00000391745.1_Missense_Mutation_p.S315Y	NM_006865.3	NP_006856.3	Q8N6C8	LIRA3_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (without TM domain), member 3	298	Ig-like C2-type 3.				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)	p.S298Y(1)		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)		GTATGCACCGGAGCATGTGTA	0.682													.|||	90	0.0179712	0.0068	0.0173	5008	,	,		9760	0.0179		0.0318	False		,,,				2504	0.0194				p.S298Y		Atlas-SNP	.											LILRA3,NS,malignant_melanoma,0,1	LILRA3	65	1	1	Substitution - Missense(1)	NS(1)	c.C893A						scavenged	.						40.0	41.0	41.0					19																	54802548		2194	4172	6366	SO:0001583	missense	11026	exon5			GCACCGGAGCATG	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.893C>A	19.37:g.54802548G>T	ENSP00000251390:p.Ser298Tyr	Somatic	181	5	0.0276243		WXS	Illumina HiSeq	Phase_I	193	13	0.0673575	NM_006865	J3KPM2|O15469|O15470|O75016|Q8N151|Q8N154|Q8NHJ1|Q8NHJ2|Q8NHJ3|Q8NHJ4	Missense_Mutation	SNP	ENST00000251390.3	37	CCDS12887.1	.	.	.	.	.	.	.	.	.	.	G	0.003	-2.464423	0.00171	.	.	ENSG00000170866	ENST00000251390;ENST00000391744;ENST00000391745	T;T;T	0.12672	2.66;2.66;2.66	2.03	-0.337	0.12654	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.527930	0.14277	N	0.329764	T	0.01730	0.0055	N	0.00064	-2.315	0.09310	N	1	B;B	0.06786	0.001;0.0	B;B	0.12837	0.008;0.004	T	0.44298	-0.9337	10	0.02654	T	1	.	6.5221	0.22281	0.0:0.0:0.5604:0.4396	.	298;298	E7EU74;Q8N6C8	.;LIRA3_HUMAN	Y	298;234;315	ENSP00000251390:S298Y;ENSP00000375624:S234Y;ENSP00000375625:S315Y	ENSP00000251390:S298Y	S	-	2	0	LILRA3	59494360	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.183000	0.09712	-0.119000	0.11830	-0.485000	0.04761	TCC	.	.	none		0.682	LILRA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140236.1		
IGLL5	100423062	hgsc.bcm.edu	37	22	23230312	23230312	+	Silent	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:23230312C>T	ENST00000526893.1	+	1	353	c.79C>T	c.(79-81)Ctg>Ttg	p.L27L	IGLL5_ENST00000531372.1_Silent_p.L27L|IGLL5_ENST00000532223.2_Silent_p.L27L|hsa-mir-5571_ENST00000577998.1_RNA	NM_001178126.1	NP_001171597.1	B9A064	IGLL5_HUMAN	immunoglobulin lambda-like polypeptide 5	27						extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|urinary_tract(1)	7						CTGGCCCCTGCTGCTGCTGGG	0.667																																					p.L27L		Atlas-SNP	.											IGLL5,NS,lymphoid_neoplasm,-2,1	IGLL5	26	1	0			c.C79T						PASS	.																																			SO:0001819	synonymous_variant	100423062	exon1			CCCCTGCTGCTGC	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.79C>T	22.37:g.23230312C>T		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	159	41	0.257862	NM_001178126		Silent	SNP	ENST00000526893.1	37	CCDS54506.1																																																																																			.	.	none		0.667	IGLL5-002	KNOWN	basic|appris_candidate|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000385699.1	NM_001178126	
VPS33B	26276	hgsc.bcm.edu	37	15	91543761	91543761	+	Missense_Mutation	SNP	C	C	T	rs11073964	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:91543761C>T	ENST00000333371.3	-	20	1893	c.1540G>A	c.(1540-1542)Ggt>Agt	p.G514S	VPS33B_ENST00000535843.1_Missense_Mutation_p.G423S|VPS33B_ENST00000535906.1_Missense_Mutation_p.G487S	NM_018668.3	NP_061138.3	Q9H267	VP33B_HUMAN	vacuolar protein sorting 33 homolog B (yeast)	514			G -> S (in dbSNP:rs11073964). {ECO:0000269|PubMed:10894945, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		lysosome localization (GO:0032418)|melanosome localization (GO:0032400)|membrane fusion (GO:0061025)|platelet alpha granule organization (GO:0070889)|protein transport (GO:0015031)|vesicle docking involved in exocytosis (GO:0006904)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|platelet alpha granule (GO:0031091)				central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(5)|ovary(2)|prostate(2)|stomach(2)	16	Lung NSC(78;0.0987)|all_lung(78;0.175)					TAAGCACCACCGAAGACGTAA	0.493													T|||	3845	0.767772	0.9607	0.6686	5008	,	,		20263	0.996		0.3986	False		,,,				2504	0.7219				p.G514S		Atlas-SNP	.											.	VPS33B	42	.	0			c.G1540A						PASS	.	T	SER/GLY	3870,526	240.6+/-251.3	1709,452,37	118.0	96.0	104.0		1540	5.8	1.0	15	dbSNP_120	104	3422,5174	637.6+/-399.2	670,2082,1546	yes	missense	VPS33B	NM_018668.3	56	2379,2534,1583	TT,TC,CC		39.8092,11.9654,43.8732	benign	514/618	91543761	7292,5700	2198	4298	6496	SO:0001583	missense	26276	exon20			CACCACCGAAGAC	AF201694	CCDS10369.1, CCDS73783.1	15q26.1	2006-12-19	2006-12-19		ENSG00000184056	ENSG00000184056			12712	protein-coding gene	gene with protein product		608552	"""vacuolar protein sorting 33B (yeast homolog)"""			8996080	Standard	XM_005254887		Approved	FLJ14848	uc002bqp.1	Q9H267	OTTHUMG00000149835	ENST00000333371.3:c.1540G>A	15.37:g.91543761C>T	ENSP00000327650:p.Gly514Ser	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	70	70	1	NM_018668	B3KQF6|Q96K14|Q9NRP6|Q9NSF3	Missense_Mutation	SNP	ENST00000333371.3	37	CCDS10369.1	1573	0.7202380952380952	469	0.9532520325203252	218	0.6022099447513812	571	0.9982517482517482	315	0.4155672823218997	T	10.36	1.328511	0.24167	0.880346	0.398092	ENSG00000184056	ENST00000333371;ENST00000535906;ENST00000535843;ENST00000537510	T;T;T	0.74737	-0.87;-0.87;-0.87	5.83	5.83	0.93111	.	0.000000	0.85682	N	0.000000	T	0.00012	0.0000	N	0.00303	-1.675	0.39820	P	0.027178999999999953	B;B	0.12630	0.006;0.002	B;B	0.08055	0.002;0.003	T	0.44559	-0.9320	9	0.02654	T	1	-15.2107	11.7519	0.51853	0.0:0.0695:0.0:0.9305	rs11073964;rs17515382;rs17845495;rs17858380;rs57245246;rs11073964	487;514	F5H008;Q9H267	.;VP33B_HUMAN	S	514;487;423;469	ENSP00000327650:G514S;ENSP00000444053:G487S;ENSP00000446267:G423S	ENSP00000327650:G514S	G	-	1	0	VPS33B	89344765	1.000000	0.71417	1.000000	0.80357	0.829000	0.46940	4.267000	0.58877	1.028000	0.39785	-0.269000	0.10298	GGT	C|0.359;T|0.641	0.641	strong		0.493	VPS33B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313496.1	NM_018668	
OR5L2	26338	hgsc.bcm.edu	37	11	55595114	55595114	+	Silent	SNP	G	G	T	rs34929168|rs386753701	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:55595114G>T	ENST00000378397.1	+	1	420	c.420G>T	c.(418-420)ctG>ctT	p.L140L		NM_001004739.1	NP_001004739.1	Q8NGL0	OR5L2_HUMAN	olfactory receptor, family 5, subfamily L, member 2	140						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)|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)				CTCAGAAGCTGCGTGTGGAGC	0.522										HNSCC(27;0.073)			N|||	449	0.0896565	0.1309	0.0403	5008	,	,		21339	0.0853		0.0924	False		,,,				2504	0.0706				p.L140L		Atlas-SNP	.											.	OR5L2	135	.	0			c.G420T						PASS	.						211.0	182.0	192.0					11																	55595114		2200	4296	6496	SO:0001819	synonymous_variant	26338	exon1			GAAGCTGCGTGTG	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.420G>T	11.37:g.55595114G>T		Somatic	249	0	0		WXS	Illumina HiSeq	Phase_I	205	143	0.697561	NM_001004739	Q6IF66|Q96RB2	Silent	SNP	ENST00000378397.1	37	CCDS31511.1																																																																																			G|0.913;T|0.087	0.087	strong		0.522	OR5L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391516.1	NM_001004739	
CHD2	1106	hgsc.bcm.edu	37	15	93536197	93536197	+	Silent	SNP	C	C	T	rs2272457	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:93536197C>T	ENST00000394196.4	+	28	4632	c.3564C>T	c.(3562-3564)taC>taT	p.Y1188Y	CHD2_ENST00000557381.1_Silent_p.Y1188Y	NM_001271.3	NP_001262.3	O14647	CHD2_HUMAN	chromodomain helicase DNA binding protein 2	1188					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)			TGCAGGAATACGAAGAGCAGC	0.507													C|||	969	0.19349	0.1702	0.2046	5008	,	,		21322	0.1319		0.2604	False		,,,				2504	0.2117				p.Y1188Y		Atlas-SNP	.											.	CHD2	280	.	0			c.C3564T						PASS	.	C		873,3521	340.5+/-306.2	85,703,1409	110.0	93.0	99.0		3564	-1.7	0.9	15	dbSNP_100	99	2355,6241	392.9+/-344.2	340,1675,2283	no	coding-synonymous	CHD2	NM_001271.3		425,2378,3692	TT,TC,CC		27.3965,19.868,24.8499		1188/1829	93536197	3228,9762	2197	4298	6495	SO:0001819	synonymous_variant	1106	exon28			GGAATACGAAGAG	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.3564C>T	15.37:g.93536197C>T		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	79	30	0.379747	NM_001271	C6G482|Q96IP5	Silent	SNP	ENST00000394196.4	37	CCDS10374.2																																																																																			C|0.770;T|0.230	0.230	strong		0.507	CHD2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000313528.3	NM_001271	
SEMA5B	54437	hgsc.bcm.edu	37	3	122642590	122642590	+	Silent	SNP	G	G	A	rs2276778	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:122642590G>A	ENST00000357599.3	-	10	1532	c.1146C>T	c.(1144-1146)atC>atT	p.I382I	SEMA5B_ENST00000195173.4_Silent_p.I382I|SEMA5B_ENST00000451055.2_Silent_p.I436I	NM_001031702.3|NM_001256348.1	NP_001026872.2|NP_001243277.1	Q9P283	SEM5B_HUMAN	sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5B	382	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				cell differentiation (GO:0030154)|nervous system development (GO:0007399)	integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(13)|lung(26)|ovary(2)|pancreas(3)|skin(2)|upper_aerodigestive_tract(3)	55				GBM - Glioblastoma multiforme(114;0.0367)		CAGAAGCCGCGATGCTGTTTC	0.582													G|||	2085	0.416334	0.1861	0.4366	5008	,	,		19040	0.3006		0.6511	False		,,,				2504	0.591				p.I436I		Atlas-SNP	.											.	SEMA5B	303	.	0			c.C1308T						PASS	.	G		1172,3234	408.4+/-334.6	172,828,1203	97.0	94.0	95.0		1146	-10.8	0.0	3	dbSNP_100	95	5751,2849	674.6+/-403.1	1930,1891,479	no	coding-synonymous	SEMA5B	NM_001031702.2		2102,2719,1682	AA,AG,GG		33.1279,26.6001,46.7707		382/1152	122642590	6923,6083	2203	4300	6503	SO:0001819	synonymous_variant	54437	exon10			AGCCGCGATGCTG	AB040878	CCDS35491.1, CCDS58848.1, CCDS74995.1	3q21.1	2008-07-18			ENSG00000082684	ENSG00000082684		"""Semaphorins"""	10737	protein-coding gene	gene with protein product		609298		SEMAG		8817451	Standard	NM_001256346		Approved	SemG, KIAA1445, FLJ10372	uc031sbm.1	Q9P283	OTTHUMG00000140392	ENST00000357599.3:c.1146C>T	3.37:g.122642590G>A		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	93	89	0.956989	NM_001256347	A8K5U2|B7Z393|F8W9U8|Q6DD89|Q6UY12|Q9NW17	Silent	SNP	ENST00000357599.3	37	CCDS35491.1																																																																																			G|0.514;A|0.486	0.486	strong		0.582	SEMA5B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000277165.1	NM_001031702	
C7orf31	136895	hgsc.bcm.edu	37	7	25182405	25182405	+	Missense_Mutation	SNP	G	G	T	rs11984293	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:25182405G>T	ENST00000409280.1	-	8	1021	c.713C>A	c.(712-714)cCa>cAa	p.P238Q	C7orf31_ENST00000283905.3_Missense_Mutation_p.P238Q			Q8N865	CG031_HUMAN	chromosome 7 open reading frame 31	238			P -> Q (in dbSNP:rs11984293). {ECO:0000269|PubMed:15489334}.							autonomic_ganglia(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(6)|skin(2)|stomach(1)	14						GTAGAATACTGGCTTATTTTT	0.368													G|||	1043	0.208267	0.416	0.1167	5008	,	,		17166	0.1587		0.167	False		,,,				2504	0.0859				p.P238Q		Atlas-SNP	.											.	C7orf31	53	.	0			c.C713A						PASS	.	G	GLN/PRO	1721,2685	514.7+/-368.7	366,989,848	84.0	90.0	88.0		713	4.6	1.0	7	dbSNP_120	88	1219,7381	243.9+/-273.3	71,1077,3152	yes	missense	C7orf31	NM_138811.3	76	437,2066,4000	TT,TG,GG		14.1744,39.0604,22.605	benign	238/591	25182405	2940,10066	2203	4300	6503	SO:0001583	missense	136895	exon8			AATACTGGCTTAT	AK097248	CCDS5394.1	7p15.2	2011-11-24			ENSG00000153790	ENSG00000153790			21722	protein-coding gene	gene with protein product							Standard	NM_138811		Approved		uc003sxn.1	Q8N865	OTTHUMG00000128497	ENST00000409280.1:c.713C>A	7.37:g.25182405G>T	ENSP00000386604:p.Pro238Gln	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	112	12	0.107143	NM_138811	A4D165|Q6MZV8|Q6P989|Q7LE28|Q86XK1|Q8N1H5|Q96BN4	Missense_Mutation	SNP	ENST00000409280.1	37	CCDS5394.1	467	0.21382783882783882	199	0.40447154471544716	46	0.1270718232044199	93	0.16258741258741258	129	0.17018469656992086	G	8.678	0.904534	0.17760	0.390604	0.141744	ENSG00000153790	ENST00000409280;ENST00000283905	T;T	0.06068	3.35;3.35	5.51	4.55	0.56014	.	0.233450	0.33895	N	0.004443	T	0.00012	0.0000	N	0.20986	0.625	0.35616	P	0.19092600000000004	P	0.35745	0.518	B	0.32533	0.147	T	0.30475	-0.9977	9	0.06365	T	0.9	-43.9912	7.4526	0.27248	0.0:0.1327:0.5487:0.3186	rs11984293;rs52799441;rs58679665;rs11984293	238	Q8N865	CG031_HUMAN	Q	238	ENSP00000386604:P238Q;ENSP00000283905:P238Q	ENSP00000283905:P238Q	P	-	2	0	C7orf31	25148930	1.000000	0.71417	0.999000	0.59377	0.974000	0.67602	3.457000	0.53007	2.594000	0.87642	0.484000	0.47621	CCA	G|0.777;T|0.223	0.223	strong		0.368	C7orf31-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326929.1	NM_138811	
KRTAP10-2	386679	hgsc.bcm.edu	37	21	45970993	45970993	+	Missense_Mutation	SNP	C	C	G	rs233239	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:45970993C>G	ENST00000391621.1	-	1	395	c.349G>C	c.(349-351)Gct>Cct	p.A117P	TSPEAR_ENST00000397916.1_Intron|TSPEAR_ENST00000323084.4_Intron|KRTAP10-2_ENST00000498210.1_Intron	NM_198693.2	NP_941966.1	P60368	KR102_HUMAN	keratin associated protein 10-2	117	22 X 5 AA repeats of C-C-X(3).		A -> P (in dbSNP:rs233239). {ECO:0000269|PubMed:15028290}.			keratin filament (GO:0045095)				large_intestine(1)|lung(4)|skin(1)	6						CATGAAGAAGCCCCACAGCAG	0.647													c|||	1141	0.227835	0.2209	0.1585	5008	,	,		21182	0.3651		0.2048	False		,,,				2504	0.1687				p.A117P		Atlas-SNP	.											.	KRTAP10-2	21	.	0			c.G349C						PASS	.	G	PRO/ALA,	1007,3399	361.1+/-315.5	113,781,1309	113.0	118.0	116.0		349,	0.1	0.0	21	dbSNP_79	116	1685,6915	305.2+/-307.3	158,1369,2773	no	missense,intron	TSPEAR,KRTAP10-2	NM_198693.2,NM_144991.2	27,	271,2150,4082	GG,GC,CC		19.593,22.8552,20.6981	possibly-damaging,	117/256,	45970993	2692,10314	2203	4300	6503	SO:0001583	missense	386679	exon1			AAGAAGCCCCACA	AJ566381	CCDS42955.1	21q22.3	2007-10-05			ENSG00000205445	ENSG00000205445		"""Keratin associated proteins"""	22967	protein-coding gene	gene with protein product				KRTAP18-2			Standard	NM_198693		Approved	KAP10.2, KAP18.2	uc002zfi.1	P60368	OTTHUMG00000057625	ENST00000391621.1:c.349G>C	21.37:g.45970993C>G	ENSP00000375479:p.Ala117Pro	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	166	70	0.421687	NM_198693	Q70LJ5	Missense_Mutation	SNP	ENST00000391621.1	37	CCDS42955.1	560	0.2564102564102564	111	0.22560975609756098	63	0.17403314917127072	215	0.3758741258741259	171	0.22559366754617413	c	2.552	-0.303826	0.05495	0.228552	0.19593	ENSG00000205445	ENST00000391621	T	0.00686	5.85	3.22	0.117	0.14652	.	.	.	.	.	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	P	0.47106	0.89	B	0.39185	0.293	T	0.03017	-1.1082	8	0.02654	T	1	.	6.221	0.20681	0.0:0.3402:0.5229:0.1369	rs233239;rs478904;rs905517	117	P60368	KR102_HUMAN	P	117	ENSP00000375479:A117P	ENSP00000375479:A117P	A	-	1	0	KRTAP10-2	44795421	0.009000	0.17119	0.000000	0.03702	0.007000	0.05969	0.105000	0.15333	0.092000	0.17331	-0.394000	0.06481	GCT	C|0.702;G|0.298	0.298	strong		0.647	KRTAP10-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128027.1		
CLUAP1	23059	hgsc.bcm.edu	37	16	3558389	3558389	+	Missense_Mutation	SNP	C	C	T	rs79133712	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:3558389C>T	ENST00000576634.1	+	4	464	c.320C>T	c.(319-321)gCt>gTt	p.A107V	CLUAP1_ENST00000572600.1_5'Flank|CLUAP1_ENST00000341633.5_Missense_Mutation_p.A107V|LA16c-306E5.3_ENST00000574423.2_RNA|CLUAP1_ENST00000417763.2_5'UTR|CLUAP1_ENST00000571025.1_Missense_Mutation_p.A107V	NM_015041.2	NP_055856.1	Q96AJ1	CLUA1_HUMAN	clusterin associated protein 1	107					cilium assembly (GO:0042384)	centrosome (GO:0005813)|cilium (GO:0005929)|intracellular membrane-bounded organelle (GO:0043231)|intraciliary transport particle B (GO:0030992)|nucleus (GO:0005634)				breast(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(1)|ovary(1)|pancreas(1)|urinary_tract(2)	16						CTTTATAATGCTATGAAGACC	0.423													C|||	275	0.0549121	0.028	0.049	5008	,	,		20249	0.1468		0.008	False		,,,				2504	0.0491				p.A107V		Atlas-SNP	.											.	CLUAP1	32	.	0			c.C320T						PASS	.	C	VAL/ALA	87,4307	73.6+/-111.7	1,85,2111	138.0	122.0	127.0		320	4.9	1.0	16	dbSNP_131	127	36,8564	24.6+/-71.5	0,36,4264	yes	missense	CLUAP1	NM_015041.1	64	1,121,6375	TT,TC,CC		0.4186,1.98,0.9466	probably-damaging	107/414	3558389	123,12871	2197	4300	6497	SO:0001583	missense	23059	exon4			ATAATGCTATGAA	BC017070	CCDS32381.1, CCDS45398.1	16p13.3	2014-07-18				ENSG00000103351		"""Intraflagellar transport homologs"""	19009	protein-coding gene	gene with protein product	"""flagellar associated protein 22, qilin-like protein, homolog (Chlamydomonas)"", ""cilia and flagella associated protein 22"""					15480429, 9734811, 19253336	Standard	NM_015041		Approved	FLJ13297, KIAA0643, FAP22, CFAP22	uc002cvk.2	Q96AJ1		ENST00000576634.1:c.320C>T	16.37:g.3558389C>T	ENSP00000460850:p.Ala107Val	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	80	64	0.8	NM_015041	O75138|Q65ZA3|Q9H8R4|Q9H8T1	Missense_Mutation	SNP	ENST00000576634.1	37	CCDS32381.1	141	0.06456043956043957	9	0.018292682926829267	19	0.052486187845303865	107	0.18706293706293706	6	0.0079155672823219	C	27.8	4.861494	0.91433	0.0198	0.004186	ENSG00000103351	ENST00000341633	T	0.51071	0.72	4.89	4.89	0.63831	.	0.000000	0.85682	D	0.000000	T	0.00300	0.0009	M	0.91249	3.19	0.09310	P	1.0	D	0.89917	1.0	D	0.87578	0.998	T	0.15093	-1.0449	9	0.72032	D	0.01	-19.4994	15.5415	0.76052	0.0:1.0:0.0:0.0	.	107	Q96AJ1	CLUA1_HUMAN	V	107	ENSP00000344392:A107V	ENSP00000344392:A107V	A	+	2	0	CLUAP1	3498390	1.000000	0.71417	0.993000	0.49108	0.969000	0.65631	7.669000	0.83911	2.268000	0.75426	0.467000	0.42956	GCT	C|0.975;T|0.025	0.025	strong		0.423	CLUAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437883.2	NM_024793	
GOSR2	9570	hgsc.bcm.edu	37	17	45000565	45000565	+	Missense_Mutation	SNP	C	C	A	rs12944167	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:45000565C>A	ENST00000393456.2	+	1	64	c.7C>A	c.(7-9)Ccc>Acc	p.P3T	RNU6ATAC3P_ENST00000387974.1_RNA|GOSR2_ENST00000575949.1_Missense_Mutation_p.P3T|RP11-156P1.2_ENST00000571841.1_Missense_Mutation_p.P3T|GOSR2_ENST00000225567.4_Missense_Mutation_p.P3T|GOSR2_ENST00000415811.2_Missense_Mutation_p.P3T|GOSR2_ENST00000439730.2_Missense_Mutation_p.P3T|GOSR2_ENST00000576910.2_Missense_Mutation_p.P3T|RP11-63A1.1_ENST00000572349.1_lincRNA	NM_004287.3	NP_004278.2	O14653	GOSR2_HUMAN	golgi SNAP receptor complex member 2	3					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 to Golgi vesicle-mediated transport (GO:0006888)|membrane fusion (GO:0061025)|protein transport (GO:0015031)	Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	transporter activity (GO:0005215)			kidney(1)|large_intestine(2)|liver(1)|lung(1)|ovary(1)|skin(1)	7			BRCA - Breast invasive adenocarcinoma(9;0.102)			CGACATGGATCCCCTGTTCCA	0.701													C|||	55	0.0109824	0.0015	0.0187	5008	,	,		15563	0.0		0.0229	False		,,,				2504	0.0174				p.P3T		Atlas-SNP	.											.	GOSR2	38	.	0			c.C7A						PASS	.	C	THR/PRO,THR/PRO,THR/PRO	12,3466		0,12,1727	14.0	16.0	16.0		7,7,7	4.0	1.0	17	dbSNP_121	16	116,6356		1,114,3121	no	missense,missense,missense	GOSR2	NM_001012511.1,NM_004287.3,NM_054022.2	38,38,38	1,126,4848	AA,AC,CC		1.7923,0.345,1.2864	benign,benign,benign	3/196,3/213,3/214	45000565	128,9822	1739	3236	4975	SO:0001583	missense	9570	exon1			ATGGATCCCCTGT	AF007548	CCDS11507.1, CCDS42355.1, CCDS45719.1	17q21	2006-02-10				ENSG00000108433			4431	protein-coding gene	gene with protein product		604027				9349823, 10198168	Standard	XM_005257843		Approved	GS27, Bos1	uc002ikz.3	O14653		ENST00000393456.2:c.7C>A	17.37:g.45000565C>A	ENSP00000377101:p.Pro3Thr	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	122	47	0.385246	NM_001012511	D3DXJ5|D3DXJ6|Q8N4B8|Q96DA5|Q9BZZ4	Missense_Mutation	SNP	ENST00000393456.2	37	CCDS42355.1	29	0.013278388278388278	1	0.0020325203252032522	9	0.024861878453038673	0	0.0	19	0.025065963060686015	C	2.338	-0.351686	0.05173	0.00345	0.017923	ENSG00000108433	ENST00000225567;ENST00000393456;ENST00000415811;ENST00000439730	T;T;T;T	0.61980	0.06;0.08;0.07;0.08	4.98	4.01	0.46588	.	0.157511	0.64402	D	0.000019	T	0.08935	0.0221	N	0.00661	-1.28	0.34360	D	0.690846	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.08055	0.001;0.0;0.001;0.003	T	0.30851	-0.9964	10	0.02654	T	1	-15.5814	10.9955	0.47573	0.186:0.814:0.0:0.0	rs12944167;rs12944167	3;3;3;3	E7EQ34;O14653;O14653-2;Q8N4B8	.;GOSR2_HUMAN;.;.	T	3	ENSP00000225567:P3T;ENSP00000377101:P3T;ENSP00000394559:P3T;ENSP00000390577:P3T	ENSP00000225567:P3T	P	+	1	0	GOSR2	42355564	1.000000	0.71417	1.000000	0.80357	0.179000	0.23085	1.463000	0.35277	1.456000	0.47831	-0.152000	0.13540	CCC	C|0.984;A|0.016	0.016	strong		0.701	GOSR2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440438.1		
WNK1	65125	hgsc.bcm.edu	37	12	939268	939268	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:939268C>A	ENST00000315939.6	+	4	1896	c.1253C>A	c.(1252-1254)tCt>tAt	p.S418Y	WNK1_ENST00000530271.2_Missense_Mutation_p.S418Y|WNK1_ENST00000540360.1_3'UTR|WNK1_ENST00000537687.1_Missense_Mutation_p.S418Y|WNK1_ENST00000535572.1_Missense_Mutation_p.S418Y	NM_018979.3	NP_061852.3	Q9H4A3	WNK1_HUMAN	WNK lysine deficient protein kinase 1	418	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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)			ATGGCTACATCTGAATATCCT	0.468																																					p.S418Y	Colon(19;451 567 6672 12618 28860)	Atlas-SNP	.											.	WNK1	403	.	0			c.C1253A						PASS	.						241.0	202.0	215.0					12																	939268		2203	4300	6503	SO:0001583	missense	65125	exon4			CTACATCTGAATA	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.1253C>A	12.37:g.939268C>A	ENSP00000313059:p.Ser418Tyr	Somatic	280	0	0		WXS	Illumina HiSeq	Phase_I	293	72	0.245734	NM_001184985	A1L4B0|C5HTZ5|C5HTZ6|C5HTZ7|H6WZW3|O15052|P54963|Q4VBX9|Q6IFS5|Q86WL5|Q8N673|Q96CZ6|Q9P1S9	Missense_Mutation	SNP	ENST00000315939.6	37	CCDS8506.1	.	.	.	.	.	.	.	.	.	.	C	29.8	5.037262	0.93630	.	.	ENSG00000060237	ENST00000535572;ENST00000315939;ENST00000537687;ENST00000530271	T;T;T;T	0.24723	1.84;1.84;1.84;1.84	5.49	5.49	0.81192	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.64402	D	0.000006	T	0.43700	0.1259	L	0.32530	0.975	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.87578	0.998;0.998	T	0.36890	-0.9729	10	0.87932	D	0	-15.3704	19.3708	0.94484	0.0:1.0:0.0:0.0	.	418;418	F5GWT4;Q9H4A3	.;WNK1_HUMAN	Y	418	ENSP00000441972:S418Y;ENSP00000313059:S418Y;ENSP00000444465:S418Y;ENSP00000433548:S418Y	ENSP00000313059:S418Y	S	+	2	0	WNK1	809529	1.000000	0.71417	0.998000	0.56505	0.994000	0.84299	7.818000	0.86416	2.571000	0.86741	0.467000	0.42956	TCT	.	.	none		0.468	WNK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206683.1	NM_018979	
SRD5A1	6715	hgsc.bcm.edu	37	5	6652009	6652009	+	Silent	SNP	G	G	A	rs8192186	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:6652009G>A	ENST00000274192.5	+	2	582	c.348G>A	c.(346-348)gcG>gcA	p.A116A	SRD5A1_ENST00000504286.1_3'UTR|SRD5A1_ENST00000537411.1_3'UTR|SRD5A1_ENST00000538824.1_Intron	NM_001047.2	NP_001038.1	P18405	S5A1_HUMAN	steroid-5-alpha-reductase, alpha polypeptide 1 (3-oxo-5 alpha-steroid delta 4-dehydrogenase alpha 1)	116					androgen biosynthetic process (GO:0006702)|cell differentiation (GO:0030154)|sex determination (GO:0007530)|sex differentiation (GO:0007548)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	3-oxo-5-alpha-steroid 4-dehydrogenase activity (GO:0003865)|cholestenone 5-alpha-reductase activity (GO:0047751)|electron carrier activity (GO:0009055)	p.A116A(1)		endometrium(3)|kidney(1)|large_intestine(1)|lung(8)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	19					Dutasteride(DB01126)|Finasteride(DB01216)|Levonorgestrel(DB00367)|Spironolactone(DB00421)	CACTGTTGGCGTGTACAATGG	0.413													G|||	1463	0.292133	0.3328	0.3919	5008	,	,		18667	0.1587		0.3897	False		,,,				2504	0.2035				p.A116A		Atlas-SNP	.											SRD5A1,NS,carcinoma,0,1	SRD5A1	31	1	1	Substitution - coding silent(1)	stomach(1)	c.G348A						PASS	.	G		1441,2965	467.7+/-354.9	242,957,1004	178.0	154.0	162.0		348	-11.4	0.0	5	dbSNP_117	162	3219,5381	486.1+/-371.8	610,1999,1691	no	coding-synonymous	SRD5A1	NM_001047.2		852,2956,2695	AA,AG,GG		37.4302,32.7054,35.8296		116/260	6652009	4660,8346	2203	4300	6503	SO:0001819	synonymous_variant	6715	exon2			GTTGGCGTGTACA	M32313	CCDS3870.1	5p15.31	2008-02-05			ENSG00000145545	ENSG00000145545	1.3.99.5		11284	protein-coding gene	gene with protein product		184753				1686016	Standard	XR_427663		Approved		uc003jdw.3	P18405	OTTHUMG00000090456	ENST00000274192.5:c.348G>A	5.37:g.6652009G>A		Somatic	211	0	0		WXS	Illumina HiSeq	Phase_I	179	79	0.441341	NM_001047	B2R7Q1|Q9UHY4|Q9UP36|Q9UP37	Silent	SNP	ENST00000274192.5	37	CCDS3870.1																																																																																			G|0.652;A|0.348	0.348	strong		0.413	SRD5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206903.1	NM_001047	
HCN4	10021	hgsc.bcm.edu	37	15	73615097	73615097	+	Missense_Mutation	SNP	T	T	C	rs142735148	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:73615097T>C	ENST00000261917.3	-	8	4330	c.3337A>G	c.(3337-3339)Atg>Gtg	p.M1113V		NM_005477.2	NP_005468.1	Q9Y3Q4	HCN4_HUMAN	hyperpolarization activated cyclic nucleotide-gated potassium channel 4	1113					blood circulation (GO:0008015)|cation transport (GO:0006812)|cellular response to cAMP (GO:0071320)|cellular response to cGMP (GO:0071321)|in utero embryonic development (GO:0001701)|muscle contraction (GO:0006936)|potassium ion transmembrane transport (GO:0071805)|regulation of heart rate (GO:0002027)|regulation of membrane potential (GO:0042391)|sodium ion transmembrane transport (GO:0035725)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|intrinsic component of plasma membrane (GO:0031226)|plasma membrane (GO:0005886)|terminal bouton (GO:0043195)	cAMP binding (GO:0030552)|cation channel activity (GO:0005261)|identical protein binding (GO:0042802)|intracellular cAMP activated cation channel activity (GO:0005222)|voltage-gated potassium channel activity (GO:0005249)|voltage-gated sodium channel activity (GO:0005248)			NS(2)|biliary_tract(1)|breast(1)|endometrium(4)|kidney(1)|large_intestine(13)|liver(1)|lung(18)|ovary(6)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	55				COAD - Colon adenocarcinoma(1;0.142)		AAGGCAGCCATGGACTCCCCT	0.716													T|||	41	0.0081869	0.0068	0.0086	5008	,	,		11518	0.0		0.0129	False		,,,				2504	0.0133				p.M1113V		Atlas-SNP	.											.	HCN4	150	.	0			c.A3337G						PASS	.	T	VAL/MET	29,4303		0,29,2137	8.0	10.0	9.0		3337	-5.1	0.3	15	dbSNP_134	9	107,8365		2,103,4131	no	missense	HCN4	NM_005477.2	21	2,132,6268	CC,CT,TT		1.263,0.6694,1.0622	benign	1113/1204	73615097	136,12668	2166	4236	6402	SO:0001583	missense	10021	exon8			CAGCCATGGACTC	AJ132429	CCDS10248.1	15q24.1	2011-07-05			ENSG00000138622	ENSG00000138622		"""Voltage-gated ion channels / Cyclic nucleotide-regulated channels"""	16882	protein-coding gene	gene with protein product		605206				10228147, 10430953, 16382102	Standard	NM_005477		Approved		uc002avp.3	Q9Y3Q4	OTTHUMG00000137563	ENST00000261917.3:c.3337A>G	15.37:g.73615097T>C	ENSP00000261917:p.Met1113Val	Somatic	24	0	0		WXS	Illumina HiSeq	Phase_I	33	19	0.575758	NM_005477	Q9UMQ7	Missense_Mutation	SNP	ENST00000261917.3	37	CCDS10248.1	18	0.008241758241758242	2	0.0040650406504065045	5	0.013812154696132596	0	0.0	11	0.014511873350923483	T	0.004	-2.366028	0.00212	0.006694	0.01263	ENSG00000138622	ENST00000261917	D	0.96651	-4.08	3.32	-5.11	0.02901	.	.	.	.	.	T	0.77698	0.4169	N	0.00926	-1.1	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.76063	-0.3096	9	0.02654	T	1	.	10.5547	0.45110	0.0:0.421:0.0:0.579	.	1113	Q9Y3Q4	HCN4_HUMAN	V	1113	ENSP00000261917:M1113V	ENSP00000261917:M1113V	M	-	1	0	HCN4	71402150	0.000000	0.05858	0.260000	0.24451	0.142000	0.21351	-1.800000	0.01744	-1.006000	0.03412	-0.659000	0.03860	ATG	T|0.992;C|0.008	0.008	strong		0.716	HCN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268900.2	NM_005477	
CNST	163882	hgsc.bcm.edu	37	1	246829147	246829147	+	Missense_Mutation	SNP	C	C	G	rs138848173		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:246829147C>G	ENST00000366513.4	+	11	2387	c.2118C>G	c.(2116-2118)ttC>ttG	p.F706L		NM_152609.2	NP_689822.2	Q6PJW8	CNST_HUMAN	consortin, connexin sorting protein	706					negative regulation of phosphatase activity (GO:0010923)|positive regulation of Golgi to plasma membrane protein transport (GO:0042998)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|trans-Golgi network (GO:0005802)|transport vesicle (GO:0030133)	connexin binding (GO:0071253)|phosphatase binding (GO:0019902)			breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(12)|prostate(1)|urinary_tract(2)	28						ACATGGACTTCTATTACACTA	0.463																																					p.F706L		Atlas-SNP	.											.	CNST	73	.	0			c.C2118G						PASS	.						143.0	126.0	132.0					1																	246829147		2203	4300	6503	SO:0001583	missense	163882	exon11			GGACTTCTATTAC	AK056563	CCDS1628.1, CCDS44343.1	1q44	2012-04-17	2009-11-03	2009-11-03	ENSG00000162852	ENSG00000162852		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	26486	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 64"""	613439	"""chromosome 1 open reading frame 71"""	C1orf71		19864490	Standard	NM_152609		Approved	FLJ32001, PPP1R64	uc001ibp.3	Q6PJW8	OTTHUMG00000040090	ENST00000366513.4:c.2118C>G	1.37:g.246829147C>G	ENSP00000355470:p.Phe706Leu	Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	128	54	0.421875	NM_152609	Q5VSY9|Q5VTM7|Q8IYA9|Q8N3L5|Q8NB09|Q8TEI2|Q96MR5	Missense_Mutation	SNP	ENST00000366513.4	37	CCDS1628.1	.	.	.	.	.	.	.	.	.	.	C	18.29	3.592013	0.66219	.	.	ENSG00000162852	ENST00000366513	T	0.28255	1.62	5.61	3.73	0.42828	.	0.000000	0.85682	D	0.000000	T	0.49508	0.1561	M	0.77103	2.36	0.80722	D	1	D	0.76494	0.999	D	0.73380	0.98	T	0.51084	-0.8750	10	0.66056	D	0.02	-20.4305	5.088	0.14693	0.1498:0.5976:0.0:0.2526	.	706	Q6PJW8	CNST_HUMAN	L	706	ENSP00000355470:F706L	ENSP00000355470:F706L	F	+	3	2	CNST	244895770	0.999000	0.42202	1.000000	0.80357	0.998000	0.95712	0.581000	0.23819	1.366000	0.46076	0.655000	0.94253	TTC	C|1.000;T|0.000	.	alt		0.463	CNST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096780.1	NM_152609	
SVIL	6840	hgsc.bcm.edu	37	10	29754609	29754609	+	Silent	SNP	T	T	C	rs1057952	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:29754609T>C	ENST00000355867.4	-	34	6800	c.6048A>G	c.(6046-6048)acA>acG	p.T2016T	SVIL_ENST00000375400.3_Silent_p.T1590T|PTCHD3P1_ENST00000446807.1_RNA|SVIL_ENST00000535393.1_Silent_p.T930T|PTCHD3P1_ENST00000423223.1_RNA|SVIL_ENST00000375398.2_Silent_p.T2016T|PTCHD3P1_ENST00000455774.1_RNA|PTCHD3P1_ENST00000445521.1_RNA|PTCHD3P1_ENST00000413405.1_RNA|PTCHD3P1_ENST00000414457.1_RNA	NM_021738.2	NP_068506.2	O95425	SVIL_HUMAN	supervillin	2016					cytoskeleton organization (GO:0007010)|skeletal muscle tissue development (GO:0007519)	actin cytoskeleton (GO:0015629)|cell projection (GO:0042995)|costamere (GO:0043034)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)	p.T2016T(1)		breast(1)|central_nervous_system(3)|cervix(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(24)|lung(35)|ovary(8)|prostate(2)|skin(4)|stomach(7)|upper_aerodigestive_tract(2)|urinary_tract(2)	112		Breast(68;0.103)				ACACAAACTCTGTGGCTGCAA	0.557													C|||	2119	0.423123	0.3638	0.4323	5008	,	,		16072	0.5625		0.3817	False		,,,				2504	0.3957				p.T2016T		Atlas-SNP	.											SVIL,NS,carcinoma,0,1	SVIL	226	1	1	Substitution - coding silent(1)	stomach(1)	c.A6048G						PASS	.	C	,	1667,2739	647.6+/-398.6	316,1035,852	36.0	41.0	39.0		4770,6048	-9.4	0.0	10	dbSNP_86	39	2973,5627	656.6+/-401.4	531,1911,1858	no	coding-synonymous,coding-synonymous	SVIL	NM_003174.3,NM_021738.2	,	847,2946,2710	CC,CT,TT		34.5698,37.8348,35.6758	,	1590/1789,2016/2215	29754609	4640,8366	2203	4300	6503	SO:0001819	synonymous_variant	6840	exon34			AAACTCTGTGGCT	AF051851	CCDS7163.1, CCDS7164.1	10p11.2	2008-07-29			ENSG00000197321	ENSG00000197321			11480	protein-coding gene	gene with protein product	"""archvillin"""	604126				9382871	Standard	NM_003174		Approved		uc001iut.1	O95425	OTTHUMG00000017882	ENST00000355867.4:c.6048A>G	10.37:g.29754609T>C		Somatic	296	1	0.00337838		WXS	Illumina HiSeq	Phase_I	273	130	0.47619	NM_021738	D3DRW9|M1J557|O60611|O60612|Q5VZK5|Q5VZK6|Q9H1R7	Silent	SNP	ENST00000355867.4	37	CCDS7164.1																																																																																			T|0.629;C|0.371	0.371	strong		0.557	SVIL-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047395.1		
PYGB	5834	hgsc.bcm.edu	37	20	25264814	25264814	+	Silent	SNP	T	T	C	rs2227892	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:25264814T>C	ENST00000216962.4	+	14	1805	c.1695T>C	c.(1693-1695)gaT>gaC	p.D565D		NM_002862.3	NP_002853.2	P11216	PYGB_HUMAN	phosphorylase, glycogen; brain	565					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						CCATGTTCGATGTGCATGTGA	0.552													C|||	2689	0.536941	0.4516	0.3473	5008	,	,		20398	0.9107		0.4334	False		,,,				2504	0.5082				p.D565D		Atlas-SNP	.											.	PYGB	84	.	0			c.T1695C						PASS	.	C		1903,2503	629.0+/-395.2	401,1101,701	228.0	159.0	183.0		1695	-4.5	0.9	20	dbSNP_98	183	3754,4846	616.5+/-396.5	813,2128,1359	no	coding-synonymous	PYGB	NM_002862.3		1214,3229,2060	CC,CT,TT		43.6512,43.1911,43.4953		565/844	25264814	5657,7349	2203	4300	6503	SO:0001819	synonymous_variant	5834	exon14			GTTCGATGTGCAT		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.1695T>C	20.37:g.25264814T>C		Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	113	50	0.442478	NM_002862	Q96AK1|Q9NPX8	Silent	SNP	ENST00000216962.4	37	CCDS13171.1																																																																																			T|0.523;C|0.477	0.477	strong		0.552	PYGB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078415.2	NM_002862	
MAP4K4	9448	hgsc.bcm.edu	37	2	102314984	102314984	+	Missense_Mutation	SNP	A	A	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:102314984A>T	ENST00000347699.4	+	2	107	c.107A>T	c.(106-108)tAt>tTt	p.Y36F	MAP4K4_ENST00000302217.5_Missense_Mutation_p.Y36F|MAP4K4_ENST00000413150.2_Missense_Mutation_p.Y36F|MAP4K4_ENST00000350198.4_Missense_Mutation_p.Y36F|MAP4K4_ENST00000456652.1_Missense_Mutation_p.Y36F|MAP4K4_ENST00000425019.1_Missense_Mutation_p.Y36F|MAP4K4_ENST00000324219.4_Missense_Mutation_p.Y36F	NM_001242559.1|NM_145687.3	NP_001229488.1|NP_663720.1	O95819	M4K4_HUMAN	mitogen-activated protein kinase kinase kinase kinase 4	36	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				intracellular signal transduction (GO:0035556)|protein phosphorylation (GO:0006468)|regulation of JNK cascade (GO:0046328)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)			breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(15)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	41						AATGGCACCTATGGACAAGTC	0.488																																					p.Y36F		Atlas-SNP	.											.	MAP4K4	111	.	0			c.A107T						PASS	.						247.0	242.0	244.0					2																	102314984		1880	4108	5988	SO:0001583	missense	9448	exon2			GCACCTATGGACA	AF096300	CCDS56130.1, CCDS74546.1	2q11.2-q12	2011-06-09			ENSG00000071054	ENSG00000071054		"""Mitogen-activated protein kinase cascade / Kinase kinase kinase kinases"""	6866	protein-coding gene	gene with protein product	"""HPK/GCK-like kinase"", ""hepatocyte progenitor kinase-like/germinal center kinase-like kinase"""	604666				9890973, 9734811, 9135144	Standard	NM_004834		Approved	HGK, NIK, FLH21957	uc002tbf.3	O95819	OTTHUMG00000155394	ENST00000347699.4:c.107A>T	2.37:g.102314984A>T	ENSP00000314363:p.Tyr36Phe	Somatic	402	1	0.00248756		WXS	Illumina HiSeq	Phase_I	312	90	0.288462	NM_004834	O75172|Q9NST7	Missense_Mutation	SNP	ENST00000347699.4	37	CCDS56130.1	.	.	.	.	.	.	.	.	.	.	A	18.54	3.645786	0.67358	.	.	ENSG00000071054	ENST00000427603;ENST00000425019;ENST00000324219;ENST00000350198;ENST00000302217;ENST00000413150;ENST00000456652;ENST00000347699	T;T;T;T;T;T;T;T	0.17691	3.68;2.26;2.26;2.26;2.26;2.26;2.26;2.26	4.26	4.26	0.50523	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.49305	U	0.000157	T	0.17023	0.0409	N	0.02345	-0.59	0.80722	D	1	D;P;P;P;P;P;P;P	0.64830	0.994;0.939;0.809;0.939;0.939;0.475;0.925;0.925	D;D;P;D;D;P;D;D	0.67548	0.942;0.952;0.739;0.952;0.952;0.634;0.92;0.92	T	0.43360	-0.9396	10	0.72032	D	0.01	.	13.0603	0.59003	1.0:0.0:0.0:0.0	.	36;36;36;36;36;36;36;36	B7Z3V5;C9J840;O95819-4;O95819;E7EN19;G3XAA2;O95819-2;G5E948	.;.;.;M4K4_HUMAN;.;.;.;.	F	36	ENSP00000403016:Y36F;ENSP00000392830:Y36F;ENSP00000313644:Y36F;ENSP00000281111:Y36F;ENSP00000303600:Y36F;ENSP00000389752:Y36F;ENSP00000387370:Y36F;ENSP00000314363:Y36F	ENSP00000303600:Y36F	Y	+	2	0	MAP4K4	101681416	1.000000	0.71417	0.996000	0.52242	0.998000	0.95712	8.623000	0.90957	1.544000	0.49359	0.482000	0.46254	TAT	.	.	none		0.488	MAP4K4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000339839.1	NM_004834	
DPCR1	135656	hgsc.bcm.edu	37	6	30920124	30920124	+	Missense_Mutation	SNP	G	G	A	rs3132580	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:30920124G>A	ENST00000462446.1	+	2	3911	c.3883G>A	c.(3883-3885)Gag>Aag	p.E1295K	DPCR1_ENST00000304311.2_Missense_Mutation_p.E137K|HCG21_ENST00000419481.1_RNA			Q3MIW9	DPCR1_HUMAN	diffuse panbronchiolitis critical region 1	419						integral component of membrane (GO:0016021)				endometrium(1)|kidney(2)|large_intestine(3)|lung(3)|pancreas(1)	10						CACAGGAAACGAGAGCCATCC	0.443													G|||	192	0.0383387	0.0378	0.0288	5008	,	,		20858	0.0159		0.0964	False		,,,				2504	0.0092				p.E1295K		Atlas-SNP	.											.	DPCR1	99	.	0			c.G3883A						PASS	.	G	LYS/GLU	308,4098	166.2+/-197.5	7,294,1902	95.0	90.0	92.0		3883	-7.2	0.0	6	dbSNP_103	92	1135,7465	234.0+/-267.1	72,991,3237	yes	missense	DPCR1	NM_080870.3	56	79,1285,5139	AA,AG,GG		13.1977,6.9905,11.0949	benign	1295/1394	30920124	1443,11563	2203	4300	6503	SO:0001583	missense	135656	exon2			GGAAACGAGAGCC	AB064272	CCDS4692.1, CCDS4692.2	6p21.32	2008-02-05			ENSG00000168631	ENSG00000168631			21666	protein-coding gene	gene with protein product		613928				12185533, 10677310	Standard	NM_080870		Approved	PBLT, bCX105N19.6	uc003nsg.2	Q3MIW9	OTTHUMG00000031104	ENST00000462446.1:c.3883G>A	6.37:g.30920124G>A	ENSP00000417182:p.Glu1295Lys	Somatic	214	1	0.0046729		WXS	Illumina HiSeq	Phase_I	191	97	0.507853	NM_080870	C9IZC0|Q658M7|Q8WYN2	Missense_Mutation	SNP	ENST00000462446.1	37	CCDS4692.2	134	0.06135531135531135	30	0.06097560975609756	11	0.03038674033149171	14	0.024475524475524476	79	0.10422163588390501	G	7.300	0.612780	0.14066	0.069905	0.131977	ENSG00000168631	ENST00000462446;ENST00000450344;ENST00000304311	T;T	0.24350	1.86;1.97	3.61	-7.22	0.01485	.	.	.	.	.	T	0.01661	0.0053	N	0.04508	-0.205	0.80722	P	0.0	B	0.18968	0.032	B	0.13407	0.009	T	0.36553	-0.9743	8	0.10111	T	0.7	0.1331	3.183	0.06590	0.193:0.4849:0.1963:0.1259	rs3132580;rs52797861;rs59423268;rs3132580	1295	E9PEI6	.	K	1295;419;137	ENSP00000417182:E1295K;ENSP00000305948:E137K	ENSP00000305948:E137K	E	+	1	0	DPCR1	31028103	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.956000	0.03865	-2.176000	0.00770	-0.499000	0.04595	GAG	G|0.913;A|0.087	0.087	strong		0.443	DPCR1-001	NOVEL	not_organism_supported|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000076173.3	NM_080870	
GRIN2B	2904	hgsc.bcm.edu	37	12	13720043	13720043	+	Silent	SNP	G	G	A	rs3026160	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:13720043G>A	ENST00000609686.1	-	12	2723	c.2514C>T	c.(2512-2514)tgC>tgT	p.C838C		NM_000834.3	NP_000825.2	Q13224	NMDE2_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2B	838					behavioral fear response (GO:0001662)|behavioral response to pain (GO:0048266)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|glutamate receptor signaling pathway (GO:0007215)|in utero embryonic development (GO:0001701)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|learning (GO:0007612)|learning or memory (GO:0007611)|memory (GO:0007613)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of synaptic plasticity (GO:0048167)|response to ethanol (GO:0045471)|sensory organ development (GO:0007423)|startle response (GO:0001964)|suckling behavior (GO:0001967)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuron projection (GO:0043005)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|synaptic vesicle (GO:0008021)	calcium channel activity (GO:0005262)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glycine binding (GO:0016594)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|central_nervous_system(5)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(12)|liver(1)|lung(70)|ovary(4)|prostate(6)|skin(10)|upper_aerodigestive_tract(5)|urinary_tract(1)	143					Acamprosate(DB00659)|Acetylcysteine(DB06151)|Atomoxetine(DB00289)|Felbamate(DB00949)|Gabapentin(DB00996)|Haloperidol(DB00502)|Ketobemidone(DB06738)|Memantine(DB01043)|Milnacipran(DB04896)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	AAAGGTGTTCGCAGATGAAGG	0.502													G|||	208	0.0415335	0.0045	0.0403	5008	,	,		20273	0.001		0.1074	False		,,,				2504	0.0665				p.C838C		Atlas-SNP	.											.	GRIN2B	303	.	0			c.C2514T						PASS	.	G		107,4299	82.4+/-120.9	2,103,2098	133.0	112.0	119.0		2514	-7.1	0.7	12	dbSNP_102	119	1117,7483	231.7+/-265.6	71,975,3254	no	coding-synonymous	GRIN2B	NM_000834.3		73,1078,5352	AA,AG,GG		12.9884,2.4285,9.411		838/1485	13720043	1224,11782	2203	4300	6503	SO:0001819	synonymous_variant	2904	exon12			GTGTTCGCAGATG		CCDS8662.1	12p13.1	2014-07-16			ENSG00000273079			"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4586	protein-coding gene	gene with protein product		138252		NMDAR2B		1350383	Standard	NM_000834		Approved	GluN2B	uc001rbt.2	Q13224	OTTHUMG00000137373	ENST00000609686.1:c.2514C>T	12.37:g.13720043G>A		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	106	48	0.45283	NM_000834	Q12919|Q13220|Q13225|Q14CU4|Q9UM56	Silent	SNP	ENST00000609686.1	37	CCDS8662.1																																																																																			G|0.922;A|0.078	0.078	strong		0.502	GRIN2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268014.2		
TF	7018	hgsc.bcm.edu	37	3	133474328	133474328	+	Silent	SNP	G	G	A	rs12769	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:133474328G>A	ENST00000402696.3	+	5	1109	c.624G>A	c.(622-624)tcG>tcA	p.S208S	TF_ENST00000264998.3_Silent_p.S81S|TFP1_ENST00000460564.1_RNA	NM_001063.3	NP_001054	P02787	TRFE_HUMAN	transferrin	208	Transferrin-like 1. {ECO:0000255|PROSITE- ProRule:PRU00741}.				blood coagulation (GO:0007596)|cellular iron ion homeostasis (GO:0006879)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|retina homeostasis (GO:0001895)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|basal part of cell (GO:0045178)|basal plasma membrane (GO:0009925)|blood microparticle (GO:0072562)|cell surface (GO:0009986)|coated pit (GO:0005905)|cytoplasmic membrane-bounded vesicle (GO:0016023)|early endosome (GO:0005769)|endocytic vesicle (GO:0030139)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|late endosome (GO:0005770)|perinuclear region of cytoplasm (GO:0048471)|recycling endosome (GO:0055037)|secretory granule lumen (GO:0034774)|vesicle (GO:0031982)	ferric iron binding (GO:0008199)			NS(1)|autonomic_ganglia(1)|breast(3)|endometrium(7)|large_intestine(13)|liver(2)|lung(16)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	49					Aluminium(DB01370)|Bismuth Subsalicylate(DB01294)|Gallium nitrate(DB05260)|Iron Dextran(DB00893)	TCGGCTACTCGGGAGCCTTCA	0.582													G|||	1559	0.311302	0.087	0.3775	5008	,	,		19938	0.4454		0.3211	False		,,,				2504	0.4192				p.S208S		Atlas-SNP	.											.	TF	116	.	0			c.G624A						PASS	.	G		592,3814	260.4+/-263.7	34,524,1645	77.0	66.0	70.0		624	-10.2	0.0	3	dbSNP_52	70	2787,5813	442.2+/-360.0	473,1841,1986	no	coding-synonymous	TF	NM_001063.3		507,2365,3631	AA,AG,GG		32.407,13.4362,25.9803		208/699	133474328	3379,9627	2203	4300	6503	SO:0001819	synonymous_variant	7018	exon5			CTACTCGGGAGCC		CCDS3080.1	3q21	2012-10-02			ENSG00000091513	ENSG00000091513			11740	protein-coding gene	gene with protein product		190000				6585826	Standard	NM_001063		Approved	PRO1557, PRO2086	uc003epv.2	P02787	OTTHUMG00000150356	ENST00000402696.3:c.624G>A	3.37:g.133474328G>A		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	67	32	0.477612	NM_001063	O43890|Q1HBA5|Q9NQB8|Q9UHV0	Silent	SNP	ENST00000402696.3	37	CCDS3080.1																																																																																			G|0.727;A|0.273	0.273	strong		0.582	TF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317775.1	NM_001063	
KRTAP4-8	728224	hgsc.bcm.edu	37	17	39254054	39254054	+	Missense_Mutation	SNP	A	A	T	rs76270529		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:39254054A>T	ENST00000333822.4	-	1	339	c.283T>A	c.(283-285)Tgc>Agc	p.C95S		NM_031960.2	NP_114166.1	Q9BYQ9	KRA48_HUMAN	keratin associated protein 4-8	95	25 X 5 AA repeats of C-C-[IKRQVHEC]- [SPRT]-[STCVQPR].				aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)		p.C95S(4)		endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(1)|prostate(1)	11						ctggagatgcagcagcTAGGG	0.677																																					p.C95S		Atlas-SNP	.											KRTAP4-8,rectum,carcinoma,0,8	KRTAP4-8	57	8	4	Substitution - Missense(4)	endometrium(3)|kidney(1)	c.T283A						PASS	.						7.0	11.0	10.0					17																	39254054		685	1582	2267	SO:0001583	missense	728224	exon1			AGATGCAGCAGCT	AJ406940	CCDS45674.1	17q21.2	2013-06-25			ENSG00000204880	ENSG00000204880		"""Keratin associated proteins"""	17230	protein-coding gene	gene with protein product						11279113	Standard	NM_031960		Approved	KAP4.8	uc010wfo.2	Q9BYQ9	OTTHUMG00000133580	ENST00000333822.4:c.283T>A	17.37:g.39254054A>T	ENSP00000328444:p.Cys95Ser	Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	41	4	0.097561	NM_031960	A8MSH3	Missense_Mutation	SNP	ENST00000333822.4	37	CCDS45674.1	.	.	.	.	.	.	.	.	.	.	.	15.18	2.755714	0.49362	.	.	ENSG00000204880	ENST00000333822;ENST00000332991	T	0.02280	4.36	3.11	2.01	0.26516	.	0.000000	0.52532	U	0.000067	T	0.04497	0.0123	M	0.83223	2.63	0.25182	N	0.99019	B	0.21606	0.058	B	0.27887	0.084	T	0.21793	-1.0235	10	0.54805	T	0.06	.	6.3859	0.21559	0.8715:0.0:0.1285:0.0	.	95	Q9BYQ9	KRA48_HUMAN	S	95;80	ENSP00000328444:C95S	ENSP00000414561:C80S	C	-	1	0	KRTAP4-8	36507580	0.999000	0.42202	0.393000	0.26258	0.649000	0.38597	3.122000	0.50446	0.404000	0.25506	0.374000	0.22700	TGC	A|0.500;T|0.500	0.500	weak		0.677	KRTAP4-8-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257684.1	NM_031960	
HIVEP3	59269	hgsc.bcm.edu	37	1	42050366	42050366	+	Missense_Mutation	SNP	C	C	T	rs2146315	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:42050366C>T	ENST00000372583.1	-	4	988	c.103G>A	c.(103-105)Gtc>Atc	p.V35I	HIVEP3_ENST00000372584.1_Missense_Mutation_p.V35I|HIVEP3_ENST00000247584.5_Missense_Mutation_p.V35I|HIVEP3_ENST00000429157.2_Missense_Mutation_p.V35I	NM_024503.4	NP_078779.2	Q5T1R4	ZEP3_HUMAN	human immunodeficiency virus type I enhancer binding protein 3	35			V -> I (in dbSNP:rs2146315).		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)				GGGTATGGGACGCTGGAAGAA	0.612													C|||	1549	0.309305	0.3215	0.1945	5008	,	,		16176	0.4345		0.2326	False		,,,				2504	0.3241				p.V35I		Atlas-SNP	.											HIVEP3,colon,carcinoma,0,1	HIVEP3	235	1	0			c.G103A						PASS	.	C	ILE/VAL,ILE/VAL	1310,3096	432.8+/-343.4	208,894,1101	111.0	126.0	121.0		103,103	-2.9	0.0	1	dbSNP_96	121	2006,6594	349.8+/-327.6	244,1518,2538	yes	missense,missense	HIVEP3	NM_001127714.2,NM_024503.4	29,29	452,2412,3639	TT,TC,CC		23.3256,29.7322,25.4959	benign,benign	35/2406,35/2407	42050366	3316,9690	2203	4300	6503	SO:0001583	missense	59269	exon4			ATGGGACGCTGGA	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.103G>A	1.37:g.42050366C>T	ENSP00000361664:p.Val35Ile	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	109	109	1	NM_024503	A7YY91|Q5T1R5|Q9BZS0|Q9HCL7	Missense_Mutation	SNP	ENST00000372583.1	37	CCDS463.1	637	0.2916666666666667	148	0.3008130081300813	79	0.21823204419889503	237	0.4143356643356643	173	0.22823218997361477	C	0.410	-0.913671	0.02415	0.297322	0.233256	ENSG00000127124	ENST00000372584;ENST00000372583;ENST00000247584;ENST00000429157	T;T;T;T	0.05649	3.42;3.41;3.41;3.42	4.55	-2.92	0.05615	.	1.488660	0.04134	N	0.318452	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	0.47824	-0.9087	9	0.21014	T	0.42	-3.7482	10.9259	0.47191	0.0:0.4412:0.0:0.5588	rs2146315;rs58344483;rs2146315	35;35	Q5T1R4-2;Q5T1R4	.;ZEP3_HUMAN	I	35	ENSP00000361665:V35I;ENSP00000361664:V35I;ENSP00000247584:V35I;ENSP00000410828:V35I	ENSP00000247584:V35I	V	-	1	0	HIVEP3	41822953	0.000000	0.05858	0.000000	0.03702	0.303000	0.27691	-0.973000	0.03798	-0.735000	0.04837	-0.244000	0.11960	GTC	C|0.726;T|0.274	0.274	strong		0.612	HIVEP3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000016978.1	NM_024503	
ITLN1	55600	hgsc.bcm.edu	37	1	160851826	160851826	+	Missense_Mutation	SNP	A	A	T	rs2274907	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:160851826A>T	ENST00000326245.3	-	4	441	c.326T>A	c.(325-327)gTc>gAc	p.V109D	ITLN1_ENST00000487531.1_5'Flank	NM_017625.2	NP_060095.2	Q8WWA0	ITLN1_HUMAN	intelectin 1 (galactofuranose binding)	109	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.		V -> D (in dbSNP:rs2274907). {ECO:0000269|PubMed:11313366}.		positive regulation of glucose import (GO:0046326)|positive regulation of protein phosphorylation (GO:0001934)|response to nematode (GO:0009624)	anchored component of membrane (GO:0031225)|brush border membrane (GO:0031526)|extracellular vesicular exosome (GO:0070062)|membrane raft (GO:0045121)|receptor complex (GO:0043235)	carbohydrate binding (GO:0030246)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(1)|lung(6)|ovary(2)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)	21	all_cancers(52;2.99e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00737)			CTCTGGGTAGACTGCTTTGCT	0.617													T|||	2911	0.58127	0.3275	0.696	5008	,	,		17183	0.6935		0.6779	False		,,,				2504	0.6278				p.V109D		Atlas-SNP	.											.	ITLN1	45	.	0			c.T326A						PASS	.	T	ASP/VAL	1660,2746	658.0+/-400.3	308,1044,851	160.0	136.0	144.0		326	4.2	0.7	1	dbSNP_100	144	5864,2736	437.0+/-358.5	2024,1816,460	no	missense	ITLN1	NM_017625.2	152	2332,2860,1311	TT,TA,AA		31.814,37.6759,42.1498	benign	109/314	160851826	7524,5482	2203	4300	6503	SO:0001583	missense	55600	exon4			GGGTAGACTGCTT	AB036706	CCDS1211.1	1q21.3	2008-02-05			ENSG00000179914	ENSG00000179914			18259	protein-coding gene	gene with protein product		609873				11313366, 11181563	Standard	NM_017625		Approved	ITLN, FLJ20022, LFR, HL-1, hIntL	uc001fxc.3	Q8WWA0	OTTHUMG00000028604	ENST00000326245.3:c.326T>A	1.37:g.160851826A>T	ENSP00000323587:p.Val109Asp	Somatic	210	0	0		WXS	Illumina HiSeq	Phase_I	156	80	0.512821	NM_017625	Q5IWS4|Q5VYI4|Q6YDJ3|Q9NP67	Missense_Mutation	SNP	ENST00000326245.3	37	CCDS1211.1	1331	0.6094322344322345	168	0.34146341463414637	240	0.6629834254143646	411	0.7185314685314685	512	0.6754617414248021	T	2.672	-0.277429	0.05679	0.376759	0.68186	ENSG00000179914	ENST00000326245	T	0.10573	2.86	4.17	4.17	0.49024	Fibrinogen, alpha/beta/gamma chain, C-terminal globular (2);Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 (1);	0.262450	0.30483	N	0.009522	T	0.00412	0.0013	N	0.00027	-2.655	0.40004	P	0.024792999999999954	B	0.02656	0.0	B	0.01281	0.0	T	0.41680	-0.9495	9	0.06757	T	0.87	-13.7648	8.262	0.31790	0.1778:0.0:0.0:0.8222	rs2274907;rs52805845;rs59910824;rs2274907	109	Q8WWA0	ITLN1_HUMAN	D	109	ENSP00000323587:V109D	ENSP00000323587:V109D	V	-	2	0	ITLN1	159118450	0.805000	0.28982	0.685000	0.30070	0.979000	0.70002	1.547000	0.36190	0.638000	0.30545	-0.257000	0.10917	GTC	A|0.411;N|0.001	.	strong		0.617	ITLN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071462.1	NM_017625	
KEAP1	9817	hgsc.bcm.edu	37	19	10600442	10600442	+	Silent	SNP	G	G	C	rs1048290	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:10600442G>C	ENST00000171111.5	-	4	1960	c.1413C>G	c.(1411-1413)ctC>ctG	p.L471L	KEAP1_ENST00000588024.1_5'Flank|KEAP1_ENST00000393623.2_Silent_p.L471L|CTC-429L19.3_ENST00000592671.1_RNA	NM_203500.1	NP_987096.1	Q14145	KEAP1_HUMAN	kelch-like ECH-associated protein 1	471					cellular response to interleukin-4 (GO:0071353)|in utero embryonic development (GO:0001701)|proteasomal ubiquitin-independent protein catabolic process (GO:0010499)|protein ubiquitination (GO:0016567)|regulation of epidermal cell differentiation (GO:0045604)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|nucleus (GO:0005634)		p.L471L(1)		breast(3)|endometrium(2)|kidney(4)|large_intestine(4)|liver(2)|lung(69)|ovary(2)|pancreas(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	92			OV - Ovarian serous cystadenocarcinoma(20;2.71e-09)|Epithelial(33;2.32e-06)|all cancers(31;1.42e-05)		Dimethyl fumarate(DB08908)	CGGCATAAAGGAGACGATTGA	0.562													C|||	2545	0.508187	0.7534	0.2983	5008	,	,		14922	0.5337		0.3549	False		,,,				2504	0.4571				p.L471L		Atlas-SNP	.											KEAP1,NS,carcinoma,0,1	KEAP1	182	1	1	Substitution - coding silent(1)	stomach(1)	c.C1413G						PASS	.	C	,	3017,1389	455.9+/-351.1	1037,943,223	77.0	63.0	68.0		1413,1413	0.6	1.0	19	dbSNP_86	68	3200,5400	653.2+/-401.0	612,1976,1712	no	coding-synonymous,coding-synonymous	KEAP1	NM_012289.3,NM_203500.1	,	1649,2919,1935	CC,CG,GG		37.2093,31.5252,47.801	,	471/625,471/625	10600442	6217,6789	2203	4300	6503	SO:0001819	synonymous_variant	9817	exon4			ATAAAGGAGACGA	AF361886	CCDS12239.1	19p13.2	2013-01-30				ENSG00000079999		"""Kelch-like"", ""BTB/POZ domain containing"""	23177	protein-coding gene	gene with protein product	"""kelch-like family member 19"""	606016					Standard	NM_012289		Approved	KIAA0132, MGC10630, MGC1114, MGC20887, MGC4407, MGC9454, INrf2, KLHL19	uc002mor.1	Q14145		ENST00000171111.5:c.1413C>G	19.37:g.10600442G>C		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	114	114	1	NM_012289	B3KPD5|Q6LEP0|Q8WTX1|Q9BPY9	Silent	SNP	ENST00000171111.5	37	CCDS12239.1																																																																																			G|0.511;C|0.489	0.489	strong		0.562	KEAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452000.1	NM_012289	
SH2D4B	387694	hgsc.bcm.edu	37	10	82363404	82363404	+	Missense_Mutation	SNP	A	A	G	rs7075840	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	70	0	0		WXS	Illumina HiSeq	Phase_I	76	31	0.407895	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	
TEAD4	7004	hgsc.bcm.edu	37	12	3120180	3120180	+	De_novo_Start_InFrame	SNP	G	G	A	rs147476820		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:3120180G>A	ENST00000397122.2	+	0	135				TEAD4_ENST00000359864.2_Silent_p.E79E|TEAD4_ENST00000358409.2_Silent_p.E79E	NM_201443.2	NP_958851.1	Q15561	TEAD4_HUMAN	TEA domain family member 4						gene expression (GO:0010467)|hippo signaling (GO:0035329)|muscle organ development (GO:0007517)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|skeletal system development (GO:0001501)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|large_intestine(3)|lung(4)|upper_aerodigestive_tract(1)	10	Ovarian(42;0.211)		OV - Ovarian serous cystadenocarcinoma(31;0.000563)|COAD - Colon adenocarcinoma(12;0.0831)			GTCGGAACGAGCTGATTGCCC	0.642													G|||	1	0.000199681	0.0	0.0	5008	,	,		16156	0.0		0.001	False		,,,				2504	0.0				p.E79E		Atlas-SNP	.											.	TEAD4	45	.	0			c.G237A						PASS	.	G	,,	1,4405	2.1+/-5.4	0,1,2202	74.0	71.0	72.0		237,237,	3.3	1.0	12	dbSNP_134	72	5,8595	4.3+/-15.6	0,5,4295	no	coding-synonymous,coding-synonymous,utr-5	TEAD4	NM_003213.3,NM_201441.2,NM_201443.2	,,	0,6,6497	AA,AG,GG		0.0581,0.0227,0.0461	,,	79/435,79/392,	3120180	6,13000	2203	4300	6503			7004	exon4			GAACGAGCTGATT	X94438	CCDS31729.1, CCDS31730.1, CCDS41737.1	12p13.3-p13.2	2008-05-14				ENSG00000197905			11717	protein-coding gene	gene with protein product		601714		TCF13L1		9889009, 8921372	Standard	NM_003213		Approved	TEF-3, TEFR-1, EFTR-2, RTEF-1	uc010sej.2	Q15561			12.37:g.3120180G>A		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	139	78	0.561151	NM_003213	H0Y308|Q6MZR9|Q8NEV5|Q92883|Q96BK2	Silent	SNP	ENST00000397122.2	37	CCDS41737.1																																																																																			G|0.999;A|0.001	0.001	strong		0.642	TEAD4-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398477.1	NM_003213	
OR2M3	127062	hgsc.bcm.edu	37	1	248366632	248366632	+	Missense_Mutation	SNP	G	G	T	rs139107079	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:248366632G>T	ENST00000456743.1	+	1	301	c.263G>T	c.(262-264)gGc>gTc	p.G88V		NM_001004689.1	NP_001004689.1	Q8NG83	OR2M3_HUMAN	olfactory receptor, family 2, subfamily M, member 3	88						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(6)|large_intestine(4)|lung(33)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	50	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0245)			TACCTGTCTGGCAGCAAGTCC	0.502													G|||	2	0.000399361	0.0	0.0	5008	,	,		20388	0.0		0.002	False		,,,				2504	0.0				p.G88V		Atlas-SNP	.											.	OR2M3	116	.	0			c.G263T						PASS	.	G	VAL/GLY	2,4404	4.2+/-10.8	0,2,2201	267.0	265.0	265.0		263	0.3	0.0	1	dbSNP_134	265	2,8598	3.0+/-9.4	0,2,4298	no	missense	OR2M3	NM_001004689.1	109	0,4,6499	TT,TG,GG		0.0233,0.0454,0.0308	probably-damaging	88/313	248366632	4,13002	2203	4300	6503	SO:0001583	missense	127062	exon1			TGTCTGGCAGCAA		CCDS31107.1	1q44	2012-08-09		2004-03-10	ENSG00000228198	ENSG00000228198		"""GPCR / Class A : Olfactory receptors"""	8269	protein-coding gene	gene with protein product				OR2M6, OR2M3P			Standard	NM_001004689		Approved	OST003	uc010pzg.2	Q8NG83	OTTHUMG00000040459	ENST00000456743.1:c.263G>T	1.37:g.248366632G>T	ENSP00000389625:p.Gly88Val	Somatic	207	0	0		WXS	Illumina HiSeq	Phase_I	142	68	0.478873	NM_001004689	B9EH06|Q6IEY0	Missense_Mutation	SNP	ENST00000456743.1	37	CCDS31107.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	G	8.552	0.875710	0.17395	4.54E-4	2.33E-4	ENSG00000228198	ENST00000456743	T	0.02656	4.21	2.44	0.325	0.15903	GPCR, rhodopsin-like superfamily (1);	0.000000	0.32640	U	0.005825	T	0.05777	0.0151	M	0.81239	2.535	0.09310	N	1	P	0.49783	0.928	P	0.47705	0.555	T	0.21415	-1.0246	10	0.87932	D	0	.	2.9467	0.05848	0.2618:0.0:0.4954:0.2428	.	88	Q8NG83	OR2M3_HUMAN	V	88	ENSP00000389625:G88V	ENSP00000389625:G88V	G	+	2	0	OR2M3	246433255	0.000000	0.05858	0.006000	0.13384	0.038000	0.13279	-0.139000	0.10358	0.312000	0.23038	0.405000	0.27470	GGC	G|0.999;T|0.001	0.001	strong		0.502	OR2M3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097355.1	NM_001004689	
GLT6D1	360203	hgsc.bcm.edu	37	9	138516119	138516119	+	Missense_Mutation	SNP	G	G	A	rs17040344	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:138516119G>A	ENST00000371763.1	-	5	908	c.655C>T	c.(655-657)Ccg>Tcg	p.P219S		NM_182974.2	NP_892019.2	Q7Z4J2	GL6D1_HUMAN	glycosyltransferase 6 domain containing 1	219			P -> S (in dbSNP:rs17040344). {ECO:0000269|PubMed:19218399}.		carbohydrate metabolic process (GO:0005975)	integral component of membrane (GO:0016021)	transferase activity, transferring hexosyl groups (GO:0016758)			endometrium(2)|large_intestine(5)|lung(3)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(1)	15		Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;4.3e-07)|Epithelial(140;1.58e-06)|all cancers(34;5.36e-05)		TGTCCAAACGGGATGCAAGCT	0.493													G|||	175	0.0349441	0.0166	0.0389	5008	,	,		19867	0.0		0.0656	False		,,,				2504	0.0613				p.P219S		Atlas-SNP	.											GLT6D1,NS,carcinoma,+2,1	GLT6D1	56	1	0			c.C655T						PASS	.	G	SER/PRO	100,3740		1,98,1821	102.0	102.0	102.0		655	2.6	0.3	9	dbSNP_123	102	619,7637		29,561,3538	yes	missense	GLT6D1	NM_182974.2	74	30,659,5359	AA,AG,GG		7.4976,2.6042,5.9441	probably-damaging	219/277	138516119	719,11377	1920	4128	6048	SO:0001583	missense	360203	exon5			CAAACGGGATGCA	AY336054	CCDS43900.1	9q34.3	2013-02-22	2004-09-16	2004-09-17	ENSG00000204007	ENSG00000204007		"""Glycosyltransferase family 6 domain containing"""	23671	protein-coding gene	gene with protein product		613699	"""galactosyltransferase family 6 domain containing 1"""	GLTDC1			Standard	NM_182974		Approved		uc010nbd.1	Q7Z4J2	OTTHUMG00000020911	ENST00000371763.1:c.655C>T	9.37:g.138516119G>A	ENSP00000360829:p.Pro219Ser	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	51	21	0.411765	NM_182974		Missense_Mutation	SNP	ENST00000371763.1	37	CCDS43900.1	68	0.031135531135531136	10	0.02032520325203252	14	0.03867403314917127	0	0.0	44	0.05804749340369393	G	12.75	2.030604	0.35797	0.026042	0.074976	ENSG00000204007	ENST00000371763	T	0.01438	4.89	3.49	2.6	0.31112	.	0.237735	0.30235	N	0.010091	T	0.00440	0.0014	M	0.78049	2.395	0.23602	N	0.997312	D	0.69078	0.997	P	0.60682	0.878	T	0.16600	-1.0397	10	0.48119	T	0.1	-24.6388	9.3947	0.38394	0.1085:0.0:0.8915:0.0	rs17040344;rs52810151;rs17040344	219	Q7Z4J2	GL6D1_HUMAN	S	219	ENSP00000360829:P219S	ENSP00000360829:P219S	P	-	1	0	GLT6D1	137655940	0.997000	0.39634	0.265000	0.24526	0.002000	0.02628	2.316000	0.43761	1.072000	0.40860	-0.126000	0.14955	CCG	G|0.955;A|0.045	0.045	strong		0.493	GLT6D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055005.2	NM_182974	
FYCO1	79443	hgsc.bcm.edu	37	3	46007823	46007823	+	Missense_Mutation	SNP	G	G	T	rs13079478|rs71622515|rs199842602	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:46007823G>T	ENST00000296137.2	-	8	3208	c.3003C>A	c.(3001-3003)aaC>aaA	p.N1001K	FYCO1_ENST00000535325.1_Missense_Mutation_p.N1001K	NM_024513.3	NP_078789.2	Q9BQS8	FYCO1_HUMAN	FYVE and coiled-coil domain containing 1	1001			N -> D (in dbSNP:rs13059238).		plus-end-directed vesicle transport along microtubule (GO:0072383)	autophagic vacuole (GO:0005776)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)	metal ion binding (GO:0046872)			NS(4)|breast(3)|central_nervous_system(1)|endometrium(11)|kidney(2)|large_intestine(9)|lung(17)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	54				BRCA - Breast invasive adenocarcinoma(193;0.00147)|KIRC - Kidney renal clear cell carcinoma(197;0.0272)|Kidney(197;0.0323)		ACTTGAGGGTGTTGAGCTCCT	0.612													G|||	527	0.105232	0.0053	0.0591	5008	,	,		19406	0.004		0.1223	False		,,,				2504	0.3599				p.N1001K		Atlas-SNP	.											.	FYCO1	115	.	0			c.C3003A						PASS	.	G	LYS/ASN	0,4406		0,0,2203	97.0	84.0	89.0		3003	1.4	0.3	3	dbSNP_121	89	12,8588		1,10,4289	yes	missense	FYCO1	NM_024513.2	94	1,10,6492	TT,TG,GG		0.1395,0.0,0.0923	benign	1001/1479	46007823	12,12994	2203	4300	6503	SO:0001583	missense	79443	exon8			GAGGGTGTTGAGC	AJ292348	CCDS2734.1	3p21.3	2008-02-05			ENSG00000163820	ENSG00000163820		"""Zinc fingers, FYVE domain containing"""	14673	protein-coding gene	gene with protein product		607182				11896456	Standard	NM_024513		Approved	FLJ13335, ZFYVE7	uc003cpb.5	Q9BQS8	OTTHUMG00000133447	ENST00000296137.2:c.3003C>A	3.37:g.46007823G>T	ENSP00000296137:p.Asn1001Lys	Somatic	187	0	0		WXS	Illumina HiSeq	Phase_I	181	72	0.39779	NM_024513	B7ZKT7|Q3MJE6|Q86T41|Q86TB1|Q8TEF9|Q96IV5|Q9H8P9	Missense_Mutation	SNP	ENST00000296137.2	37	CCDS2734.1	129	0.059065934065934064	3	0.006097560975609756	19	0.052486187845303865	0	0.0	107	0.14116094986807387	G	9.521	1.108394	0.20714	0.0	0.001395	ENSG00000163820	ENST00000296137;ENST00000535325	T;T	0.79940	-1.32;-1.32	5.49	1.44	0.22558	.	0.437095	0.25572	N	0.029755	T	0.00580	0.0019	N	0.14661	0.345	0.80722	P	0.0	B;B	0.15719	0.014;0.008	B;B	0.15484	0.013;0.008	T	0.03534	-1.1027	9	0.06891	T	0.86	-17.5834	3.5326	0.07782	0.4252:0.0:0.4016:0.1732	rs13079478	1001;1001	B7ZKT7;Q9BQS8	.;FYCO1_HUMAN	K	1001	ENSP00000296137:N1001K;ENSP00000441178:N1001K	ENSP00000296137:N1001K	N	-	3	2	FYCO1	45982827	0.033000	0.19621	0.300000	0.25030	0.997000	0.91878	0.297000	0.19101	0.281000	0.22233	0.655000	0.94253	AAC	GTT|0.500;TTC|0.500	.	alt		0.612	FYCO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257320.2	NM_024513	
MINA	84864	hgsc.bcm.edu	37	3	97686159	97686159	+	Silent	SNP	C	C	T	rs34097037	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:97686159C>T	ENST00000333396.7	-	2	861	c.279G>A	c.(277-279)ggG>ggA	p.G93G	MINA_ENST00000394198.2_Silent_p.G93G|MINA_ENST00000330299.2_Silent_p.G93G|MINA_ENST00000360258.4_Silent_p.G93G	NM_001042533.2|NM_032778.5	NP_001035998.1|NP_116167.3			MYC induced nuclear antigen											breast(2)|endometrium(1)|large_intestine(1)|lung(8)|ovary(1)	13						CATAGTACATCCCCCGGCTGC	0.473													C|||	10	0.00199681	0.0	0.0043	5008	,	,		18523	0.0		0.007	False		,,,				2504	0.0				p.G93G		Atlas-SNP	.											.	MINA	39	.	0			c.G279A						PASS	.	C	,,	6,4400	11.4+/-27.6	0,6,2197	215.0	231.0	226.0		279,279,279	-6.5	0.0	3	dbSNP_126	226	52,8548	33.3+/-86.6	0,52,4248	no	coding-synonymous,coding-synonymous,coding-synonymous	MINA	NM_001042533.1,NM_032778.4,NM_153182.2	,,	0,58,6445	TT,TC,CC		0.6047,0.1362,0.4459	,,	93/466,93/465,93/466	97686159	58,12948	2203	4300	6503	SO:0001819	synonymous_variant	84864	exon2			GTACATCCCCCGG	AB083189	CCDS2929.1, CCDS43114.1	3q22.1	2005-07-22			ENSG00000170854	ENSG00000170854			19441	protein-coding gene	gene with protein product		612049				12091391	Standard	NM_001042533		Approved	MINA53, FLJ14393, mdig	uc003dsb.1	Q8IUF8	OTTHUMG00000160107	ENST00000333396.7:c.279G>A	3.37:g.97686159C>T		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	107	51	0.476636	NM_001261829		Silent	SNP	ENST00000333396.7	37	CCDS43114.1																																																																																			C|0.996;T|0.004	0.004	strong		0.473	MINA-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000359244.3	NM_032778	
KRTAP10-3	386682	hgsc.bcm.edu	37	21	45978488	45978488	+	Silent	SNP	G	G	A	rs12483390|rs386819171	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:45978488G>A	ENST00000391620.1	-	1	155	c.111C>T	c.(109-111)tgC>tgT	p.C37C	TSPEAR_ENST00000397916.1_Intron|TSPEAR_ENST00000323084.4_Intron	NM_198696.2	NP_941969.2	P60369	KR103_HUMAN	keratin associated protein 10-3	37	18 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				kidney(1)|lung(4)|prostate(1)|skin(1)	7						GGGCCGGGGCGCAGCAGCTGG	0.697													G|||	1267	0.252995	0.0893	0.2363	5008	,	,		14190	0.128		0.4642	False		,,,				2504	0.3978				p.C37C		Atlas-SNP	.											.	KRTAP10-3	17	.	0			c.C111T						PASS	.	G	,	539,3761		45,449,1656	25.0	26.0	26.0		,111	-1.9	0.7	21	dbSNP_120	26	3914,4552		928,2058,1247	no	intron,coding-synonymous	TSPEAR,KRTAP10-3	NM_144991.2,NM_198696.2	,	973,2507,2903	AA,AG,GG		46.232,12.5349,34.8817	,	,37/222	45978488	4453,8313	2150	4233	6383	SO:0001819	synonymous_variant	386682	exon1			CGGGGCGCAGCAG	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.111C>T	21.37:g.45978488G>A		Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	68	38	0.558824	NM_198696	A3KN67|Q70LJ4	Silent	SNP	ENST00000391620.1	37	CCDS42956.1																																																																																			G|0.755;A|0.245	0.245	strong		0.697	KRTAP10-3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128031.1		
LAMA3	3909	hgsc.bcm.edu	37	18	21453038	21453038	+	Intron	SNP	C	C	T	rs145044428	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:21453038C>T	ENST00000313654.9	+	38	5239				LAMA3_ENST00000269217.6_Silent_p.C10C|LAMA3_ENST00000399516.3_Intron|LAMA3_ENST00000587184.1_Silent_p.C10C	NM_198129.1	NP_937762.1	Q16787	LAMA3_HUMAN	laminin, alpha 3						cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-5 complex (GO:0005610)	structural molecule activity (GO:0005198)			NS(2)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(24)|lung(54)|ovary(8)|prostate(6)|skin(7)|urinary_tract(4)	128	all_cancers(21;7.81e-05)|all_epithelial(16;4.45e-07)|Lung NSC(20;0.00156)|all_lung(20;0.00508)|Colorectal(14;0.0202)|Ovarian(20;0.17)					GGTCAGCCTGCAGCATGGGAT	0.612													C|||	5	0.000998403	0.0	0.0014	5008	,	,		19022	0.0		0.003	False		,,,				2504	0.001				p.C10C		Atlas-SNP	.											.	LAMA3	397	.	0			c.C30T						PASS	.	C	,,,	0,4406		0,0,2203	84.0	81.0	82.0		30,,30,	0.3	0.0	18	dbSNP_134	82	9,8591	7.7+/-29.5	0,9,4291	no	coding-synonymous,intron,coding-synonymous,intron	LAMA3	NM_000227.3,NM_001127717.1,NM_001127718.1,NM_198129.1	,,,	0,9,6494	TT,TC,CC		0.1047,0.0,0.0692	,,,	10/1725,,10/1669,	21453038	9,12997	2203	4300	6503	SO:0001627	intron_variant	3909	exon1			AGCCTGCAGCATG	L34155	CCDS11880.1, CCDS42419.1, CCDS45838.1, CCDS59307.1	18q11.2	2013-03-01	2002-08-29		ENSG00000053747	ENSG00000053747		"""Laminins"""	6483	protein-coding gene	gene with protein product		600805	"""laminin, alpha 3 (nicein (150kD), kalinin (165kD), BM600 (150kD), epilegrin)"""	LAMNA		8077230	Standard	NM_000227		Approved	nicein-150kDa, kalinin-165kDa, BM600-150kDa, epiligrin	uc002kuq.3	Q16787	OTTHUMG00000131874	ENST00000313654.9:c.4998+1413C>T	18.37:g.21453038C>T		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	86	41	0.476744	NM_001127718	B0YJ33|Q13679|Q13680|Q6VU67|Q6VU68|Q6VU69|Q76E14|Q96TG0	Silent	SNP	ENST00000313654.9	37	CCDS42419.1																																																																																			C|0.999;T|0.001	0.001	strong		0.612	LAMA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254824.3	NM_000227, NM_198129	
TENC1	23371	hgsc.bcm.edu	37	12	53453456	53453456	+	Silent	SNP	C	C	T	rs34044566	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:53453456C>T	ENST00000314250.6	+	18	2321	c.2031C>T	c.(2029-2031)gtC>gtT	p.V677V	TENC1_ENST00000546602.1_Silent_p.V677V|TENC1_ENST00000552570.1_Silent_p.V677V|TENC1_ENST00000451358.1_Silent_p.V677V|TENC1_ENST00000379902.3_Silent_p.V553V|TENC1_ENST00000549700.1_Silent_p.V677V|TENC1_ENST00000314276.3_Silent_p.V687V	NM_170754.2	NP_736610.2	Q63HR2	TENC1_HUMAN	tensin like C1 domain containing phosphatase (tensin 2)	677					cellular homeostasis (GO:0019725)|collagen metabolic process (GO:0032963)|intracellular signal transduction (GO:0035556)|kidney development (GO:0001822)|multicellular organism growth (GO:0035264)|multicellular organismal homeostasis (GO:0048871)|negative regulation of cell proliferation (GO:0008285)|response to muscle activity (GO:0014850)	focal adhesion (GO:0005925)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|phosphoprotein phosphatase activity (GO:0004721)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(2)|lung(19)|ovary(1)|pancreas(1)|stomach(3)	34						GGGAGGTGGTCATCCTGGAGG	0.647													C|||	317	0.0632987	0.0045	0.0476	5008	,	,		18405	0.1954		0.0606	False		,,,				2504	0.0204				p.V687V		Atlas-SNP	.											TENC1_ENST00000314276,NS,carcinoma,0,2	TENC1	148	2	0			c.C2061T						PASS	.	C	,,	48,4358	47.5+/-82.1	0,48,2155	47.0	48.0	48.0		2061,2031,1659	1.4	1.0	12	dbSNP_126	48	512,8088	141.9+/-198.1	13,486,3801	no	coding-synonymous,coding-synonymous,coding-synonymous	TENC1	NM_015319.2,NM_170754.2,NM_198316.1	,,	13,534,5956	TT,TC,CC		5.9535,1.0894,4.3057	,,	687/1420,677/1410,553/1286	53453456	560,12446	2203	4300	6503	SO:0001819	synonymous_variant	23371	exon18			GGTGGTCATCCTG	AF518729	CCDS8842.1, CCDS8843.1, CCDS8844.1	12q13.13	2013-02-14	2004-03-05			ENSG00000111077		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"", ""SH2 domain containing"""	19737	protein-coding gene	gene with protein product	"""tensin 2"""	607717	"""tensin like C1 domain-containing phosphatase"""				Standard	NM_015319		Approved	KIAA1075, C1-TEN, TNS2	uc001sbp.3	Q63HR2	OTTHUMG00000169730	ENST00000314250.6:c.2031C>T	12.37:g.53453456C>T		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	77	41	0.532468	NM_015319	A2VDF2|A2VDF3|A2VDI8|A5PKY4|Q2NL80|Q76MW6|Q7Z5T9|Q8NFF9|Q8NFG0|Q96P25|Q9NT29|Q9UPS7	Silent	SNP	ENST00000314250.6	37	CCDS8843.1																																																																																			C|0.947;T|0.053	0.053	strong		0.647	TENC1-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405779.1	NM_170754	
PSORS1C1	170679	hgsc.bcm.edu	37	6	31088145	31088145	+	Intron	SNP	T	T	A	rs546626089	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:31088145T>A	ENST00000259881.9	+	2	61				CDSN_ENST00000376288.2_Missense_Mutation_p.M18L	NM_014068.2	NP_054787.2	Q9UIG5	PS1C1_HUMAN	psoriasis susceptibility 1 candidate 1											kidney(1)|ovary(2)|prostate(1)|skin(1)	5						AGCAGTGCCATCATCCCGTGC	0.687													T|||	510	0.101837	0.1172	0.0778	5008	,	,		15043	0.0625		0.1819	False		,,,				2504	0.0562				p.M18L		Atlas-SNP	.											CDSN,NS,carcinoma,0,1	CDSN	48	1	0			c.A52T						scavenged	.	T	LEU/MET,	615,3769		33,549,1610	36.0	30.0	32.0		52,	0.5	0.0	6	dbSNP_103	32	1831,6765		210,1411,2677	yes	missense,intron	CDSN,PSORS1C1	NM_001264.4,NM_014068.2	15,	243,1960,4287	AA,AT,TT		21.3006,14.0283,18.8444	benign,	18/530,	31088145	2446,10534	2192	4298	6490	SO:0001627	intron_variant	1041	exon1			GTGCCATCATCCC	AB031479	CCDS34390.1	6p21.3	2014-01-28	2003-06-12		ENSG00000204540	ENSG00000204540			17202	protein-coding gene	gene with protein product		613525	"""chromosome 6 open reading frame 16"""	C6orf16			Standard	NM_014068		Approved	SEEK1	uc003nsl.2	Q9UIG5	OTTHUMG00000031077	ENST00000259881.9:c.-228-5308T>A	6.37:g.31088145T>A		Somatic	204	1	0.00490196		WXS	Illumina HiSeq	Phase_I	186	79	0.424731	NM_001264	B0V083|Q5ST21|Q86WJ8|Q86WJ9|Q96QC3	Missense_Mutation	SNP	ENST00000259881.9	37	CCDS34390.1	256	0.11721611721611722	55	0.11178861788617886	29	0.08011049723756906	29	0.050699300699300696	143	0.18865435356200527	T	4.791	0.147084	0.09134	0.140283	0.213006	ENSG00000204539	ENST00000376288	T	0.05855	3.38	4.35	0.505	0.16953	.	0.370723	0.19751	N	0.106888	T	0.00695	0.0023	N	0.25201	0.72	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.45920	-0.9228	9	0.02654	T	1	0.1892	0.8311	0.01130	0.1927:0.1215:0.1999:0.4859	rs3095318;rs9263680;rs17855560	18	Q15517	CDSN_HUMAN	L	18	ENSP00000365465:M18L	ENSP00000365465:M18L	M	-	1	0	CDSN	31196124	0.005000	0.15991	0.002000	0.10522	0.557000	0.35523	-0.033000	0.12246	-0.059000	0.13154	0.519000	0.50382	ATG	T|0.831;A|0.169	0.169	strong		0.687	PSORS1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076110.3	NM_014068	
OR13D1	286365	hgsc.bcm.edu	37	9	107456763	107456763	+	Missense_Mutation	SNP	T	T	C	rs10991359	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	144	0	0		WXS	Illumina HiSeq	Phase_I	91	50	0.549451	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		
DDX52	11056	hgsc.bcm.edu	37	17	35988672	35988672	+	Silent	SNP	C	C	T	rs7224513	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:35988672C>T	ENST00000349699.2	-	6	835	c.792G>A	c.(790-792)agG>agA	p.R264R	DDX52_ENST00000394367.3_Silent_p.R156R	NM_007010.3	NP_008941.2	Q9Y2R4	DDX52_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 52	264	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.					membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)			biliary_tract(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(5)|ovary(1)|skin(3)	17		Breast(25;0.00637)|Ovarian(249;0.15)				TCATGTGTATCCTGAATCCTG	0.343													C|||	2844	0.567891	0.3986	0.7133	5008	,	,		15639	0.5526		0.7535	False		,,,				2504	0.5184				p.R264R		Atlas-SNP	.											.	DDX52	40	.	0			c.G792A						PASS	.	C		2118,2288	576.4+/-384.2	522,1074,607	134.0	125.0	128.0		792	-1.6	1.0	17	dbSNP_116	128	6828,1772	734.1+/-406.9	2714,1400,186	no	coding-synonymous	DDX52	NM_007010.3		3236,2474,793	TT,TC,CC		20.6047,48.0708,31.2164		264/600	35988672	8946,4060	2203	4300	6503	SO:0001819	synonymous_variant	11056	exon6			GTGTATCCTGAAT	AF077033	CCDS11323.1	17q21.1	2014-05-06			ENSG00000141141	ENSG00000278053		"""DEAD-boxes"""	20038	protein-coding gene	gene with protein product		612500				11124703	Standard	XM_006721650		Approved	ROK1	uc002hoi.2	Q9Y2R4	OTTHUMG00000188475	ENST00000349699.2:c.792G>A	17.37:g.35988672C>T		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	95	48	0.505263	NM_007010	Q86YG1|Q8N213|Q9NVE0|Q9Y482	Silent	SNP	ENST00000349699.2	37	CCDS11323.1																																																																																			C|0.357;T|0.643	0.643	strong		0.343	DDX52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256795.1	NM_152300	
TRIOBP	11078	hgsc.bcm.edu	37	22	38129332	38129332	+	Silent	SNP	G	G	A	rs7284476	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:38129332G>A	ENST00000406386.3	+	8	4230	c.3975G>A	c.(3973-3975)caG>caA	p.Q1325Q		NM_001039141.2	NP_001034230.1	Q9H2D6	TARA_HUMAN	TRIO and F-actin binding protein	1325					actin modification (GO:0030047)|barbed-end actin filament capping (GO:0051016)|mitotic nuclear division (GO:0007067)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	actin filament binding (GO:0051015)|GTP-Rho binding (GO:0017049)|myosin II binding (GO:0045159)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	12	Melanoma(58;0.0574)					GGGCCTTCCAGGCCCAGGACG	0.662													G|||	1689	0.33726	0.1573	0.2867	5008	,	,		14945	0.5843		0.3877	False		,,,				2504	0.3098				p.Q1325Q		Atlas-SNP	.											.	TRIOBP	262	.	0			c.G3975A						PASS	.	G		735,3103		119,497,1303	10.0	16.0	14.0		3975	5.8	1.0	22	dbSNP_116	14	3389,4547		832,1725,1411	no	coding-synonymous	TRIOBP	NM_001039141.2		951,2222,2714	AA,AG,GG		42.7041,19.1506,35.0263		1325/2366	38129332	4124,7650	1919	3968	5887	SO:0001819	synonymous_variant	11078	exon8			CTTCCAGGCCCAG	AB051449	CCDS33644.1, CCDS43015.1, CCDS43016.1	22q13.1	2014-06-03			ENSG00000100106	ENSG00000100106		"""Pleckstrin homology (PH) domain containing"""	17009	protein-coding gene	gene with protein product		609761		DFNB28		11148140, 16385457, 16385458	Standard	NM_001039141		Approved	HRIHFB2122, KIAA1662, Tara, TAP68	uc003atr.3	Q9H2D6	OTTHUMG00000150657	ENST00000406386.3:c.3975G>A	22.37:g.38129332G>A		Somatic	199	0	0		WXS	Illumina HiSeq	Phase_I	176	77	0.4375	NM_001039141	B1AHD4|B1AHD7|F2Z2W0|F8W6V6|O94797|Q2PZW8|Q2Q3Z9|Q2Q400|Q5R3M6|Q96DW1|Q9BT77|Q9BTL7|Q9BY98|Q9Y3L4	Silent	SNP	ENST00000406386.3	37	CCDS43015.1																																																																																			G|0.639;A|0.361	0.361	strong		0.662	TRIOBP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319439.2		
MCM10	55388	hgsc.bcm.edu	37	10	13230915	13230915	+	Missense_Mutation	SNP	C	C	T	rs35114749	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:13230915C>T	ENST00000484800.2	+	10	1356	c.1253C>T	c.(1252-1254)gCt>gTt	p.A418V	MCM10_ENST00000378714.3_Missense_Mutation_p.A417V|MCM10_ENST00000378694.1_Missense_Mutation_p.A417V			Q7L590	MCM10_HUMAN	minichromosome maintenance complex component 10	418			A -> V (in dbSNP:rs35114749).		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)			central_nervous_system(1)|large_intestine(4)|ovary(2)|skin(1)|stomach(1)	9						CATGTCCAGGCTCAGTACAAG	0.547													C|||	49	0.00978435	0.0	0.0086	5008	,	,		18533	0.001		0.0179	False		,,,				2504	0.0245				p.A418V		Atlas-SNP	.											.	MCM10	76	.	0			c.C1253T						PASS	.	C	VAL/ALA,VAL/ALA	8,4398	12.9+/-30.5	0,8,2195	142.0	131.0	134.0		1250,1253	5.9	1.0	10	dbSNP_126	134	110,8490	58.3+/-119.8	0,110,4190	yes	missense,missense	MCM10	NM_018518.4,NM_182751.2	64,64	0,118,6385	TT,TC,CC		1.2791,0.1816,0.9073	possibly-damaging,possibly-damaging	417/875,418/876	13230915	118,12888	2203	4300	6503	SO:0001583	missense	55388	exon10			TCCAGGCTCAGTA	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.1253C>T	10.37:g.13230915C>T	ENSP00000418268:p.Ala418Val	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	88	38	0.431818	NM_182751	A8K9I6|B7ZKZ8|Q3MIR3|Q7LD55|Q96GX4|Q96NB6|Q9H0D7|Q9H3P9|Q9P177	Missense_Mutation	SNP	ENST00000484800.2	37	CCDS7096.1	13	0.005952380952380952	0	0.0	0	0.0	1	0.0017482517482517483	12	0.0158311345646438	C	33	5.250184	0.95305	0.001816	0.012791	ENSG00000065328	ENST00000378714;ENST00000361282;ENST00000484800;ENST00000378694	T;T;T	0.45668	0.89;0.89;0.89	5.87	5.87	0.94306	Zinc finger, Mcm10/DnaG-type (1);	0.191044	0.56097	D	0.000036	T	0.30008	0.0751	L	0.54323	1.7	0.80722	D	1	D;P;P	0.55385	0.971;0.827;0.857	P;B;B	0.44696	0.458;0.26;0.378	T	0.09271	-1.0682	10	0.31617	T	0.26	-15.6206	20.5827	0.99408	0.0:1.0:0.0:0.0	rs35114749	417;417;418	Q5T670;Q7L590-2;Q7L590	.;.;MCM10_HUMAN	V	417;418;418;417	ENSP00000367986:A417V;ENSP00000418268:A418V;ENSP00000367966:A417V	ENSP00000354945:A418V	A	+	2	0	MCM10	13270921	1.000000	0.71417	0.990000	0.47175	0.646000	0.38490	6.030000	0.70903	2.941000	0.99782	0.655000	0.94253	GCT	C|0.991;T|0.009	0.009	strong		0.547	MCM10-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356853.1	NM_182751	
ACSBG2	81616	hgsc.bcm.edu	37	19	6156483	6156483	+	Missense_Mutation	SNP	T	T	C	rs4807840	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:6156483T>C	ENST00000586696.1	+	5	704	c.428T>C	c.(427-429)gTt>gCt	p.V143A	ACSBG2_ENST00000588304.1_Missense_Mutation_p.V93A|ACSBG2_ENST00000591403.1_Missense_Mutation_p.V143A|ACSBG2_ENST00000252669.5_Missense_Mutation_p.V143A|ACSBG2_ENST00000588485.1_Intron			Q5FVE4	ACBG2_HUMAN	acyl-CoA synthetase bubblegum family member 2	143			V -> A (in dbSNP:rs4807840). {ECO:0000269|PubMed:11230166, ECO:0000269|PubMed:12975309, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:15685348, ECO:0000269|PubMed:16762313}.		cell differentiation (GO:0030154)|fatty acid metabolic process (GO:0006631)|long-chain fatty acid metabolic process (GO:0001676)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)	acyl-CoA hydrolase activity (GO:0047617)|ATP binding (GO:0005524)|long-chain fatty acid-CoA ligase activity (GO:0004467)			breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(12)|lung(3)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						TCTGCCGAGGTTTGTCAATAT	0.443													C|||	3566	0.712061	0.7337	0.7478	5008	,	,		20184	0.7153		0.7127	False		,,,				2504	0.6534				p.V143A		Atlas-SNP	.											ACSBG2,NS,carcinoma,+1,1	ACSBG2	83	1	0			c.T428C						PASS	.	C	ALA/VAL	3187,1219	423.2+/-340.0	1162,863,178	168.0	159.0	162.0		428	5.9	0.1	19	dbSNP_111	162	5918,2682	431.3+/-356.8	2005,1908,387	yes	missense	ACSBG2	NM_030924.3	64	3167,2771,565	CC,CT,TT		31.186,27.6668,29.9938	benign	143/667	6156483	9105,3901	2203	4300	6503	SO:0001583	missense	81616	exon5			CCGAGGTTTGTCA		CCDS12159.1, CCDS74269.1	19p13.3	2012-10-02			ENSG00000130377	ENSG00000130377		"""Acyl-CoA synthetase family"""	24174	protein-coding gene	gene with protein product	"""bubblegum related protein"""	614363				11230166	Standard	XM_005259653		Approved	BGR, PRTD-NY3, DKFZp434K1635	uc002meh.1	Q5FVE4	OTTHUMG00000180754	ENST00000586696.1:c.428T>C	19.37:g.6156483T>C	ENSP00000465589:p.Val143Ala	Somatic	246	1	0.00406504		WXS	Illumina HiSeq	Phase_I	213	117	0.549296	NM_030924	B3KSF2|Q6UWJ3|Q7Z5A0|Q8WW03|Q96M36|Q9BYZ3|Q9H0C4	Missense_Mutation	SNP	ENST00000586696.1	37	CCDS12159.1	1605	0.7348901098901099	369	0.75	271	0.7486187845303868	420	0.7342657342657343	545	0.7189973614775725	C	4.063	0.009457	0.07912	0.723332	0.68814	ENSG00000130377	ENST00000252669	T	0.37584	1.19	5.9	5.9	0.94986	AMP-dependent synthetase/ligase (1);	0.000000	0.39146	N	0.001445	T	0.00012	0.0000	N	0.00002	-3.505	0.45806	P	0.001318999999999959	B	0.02656	0.0	B	0.01281	0.0	T	0.45190	-0.9278	9	0.02654	T	1	-29.499	13.1437	0.59448	0.0:0.9233:0.0:0.0767	rs4807840;rs17845670;rs17858608;rs52832814;rs56448071;rs59539360;rs4807840	143	Q5FVE4	ACBG2_HUMAN	A	143	ENSP00000252669:V143A	ENSP00000252669:V143A	V	+	2	0	ACSBG2	6107483	1.000000	0.71417	0.107000	0.21349	0.250000	0.25880	5.346000	0.65992	1.511000	0.48818	-0.128000	0.14901	GTT	T|0.289;C|0.711	0.711	strong		0.443	ACSBG2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452898.1	NM_030924	
ANKRD27	84079	hgsc.bcm.edu	37	19	33096816	33096816	+	Silent	SNP	C	C	T	rs7248273	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:33096816C>T	ENST00000306065.4	-	24	2576	c.2418G>A	c.(2416-2418)aaG>aaA	p.K806K	SNORA68_ENST00000364518.1_RNA	NM_032139.2	NP_115515.2	Q96NW4	ANR27_HUMAN	ankyrin repeat domain 27 (VPS9 domain)	806					early endosome to late endosome transport (GO:0045022)|positive regulation of GTPase activity (GO:0043547)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|lysosome (GO:0005764)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)	p.K806K(1)		breast(3)|endometrium(7)|kidney(2)|large_intestine(6)|lung(15)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(2)	42	Esophageal squamous(110;0.137)					CACTGAGGTCCTTCTTATTGG	0.507													C|||	909	0.18151	0.2572	0.1297	5008	,	,		12726	0.2262		0.1113	False		,,,				2504	0.1421				p.K806K		Atlas-SNP	.											ANKRD27,NS,NS,0,1	ANKRD27	86	1	1	Substitution - coding silent(1)	pancreas(1)	c.G2418A						PASS	.	C		980,3426	359.9+/-315.0	113,754,1336	161.0	152.0	155.0		2418	5.8	1.0	19	dbSNP_116	155	1026,7574	215.0+/-254.5	62,902,3336	no	coding-synonymous	ANKRD27	NM_032139.2		175,1656,4672	TT,TC,CC		11.9302,22.2424,15.4237		806/1051	33096816	2006,11000	2203	4300	6503	SO:0001819	synonymous_variant	84079	exon24			GAGGTCCTTCTTA	AK054561	CCDS32986.1	19q13.12	2013-01-10				ENSG00000105186		"""Ankyrin repeat domain containing"""	25310	protein-coding gene	gene with protein product	"""Vps9 domain and ankyrin-repeat-containing protein"""					11230166, 16525121	Standard	NM_032139		Approved	FLJ00040, DKFZp434L0718, VARP	uc002ntn.1	Q96NW4		ENST00000306065.4:c.2418G>A	19.37:g.33096816C>T		Somatic	200	0	0		WXS	Illumina HiSeq	Phase_I	115	45	0.391304	NM_032139	Q71MF5|Q86UC3|Q8ND80|Q9H0I4	Silent	SNP	ENST00000306065.4	37	CCDS32986.1																																																																																			C|0.838;N|0.000	.	strong		0.507	ANKRD27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450329.1	NM_032139	
CMKLR1	1240	hgsc.bcm.edu	37	12	108686572	108686572	+	Silent	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:108686572C>T	ENST00000312143.7	-	3	531	c.168G>A	c.(166-168)ctG>ctA	p.L56L	CMKLR1_ENST00000412676.1_Silent_p.L56L|CMKLR1_ENST00000552995.1_Silent_p.L54L|CMKLR1_ENST00000397688.2_Silent_p.L54L|CMKLR1_ENST00000550402.1_Silent_p.L56L	NM_001142344.1|NM_004072.2	NP_001135816.1|NP_004063.1	Q99788	CML1_HUMAN	chemokine-like receptor 1	56					chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of macrophage chemotaxis (GO:0010759)|regulation of calcium-mediated signaling (GO:0050848)|skeletal system development (GO:0001501)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	chemokine receptor activity (GO:0004950)|G-protein coupled receptor activity (GO:0004930)|receptor activity (GO:0004872)			endometrium(5)|large_intestine(3)|lung(20)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)	37						GACCATTGCCCAGAATCCCGA	0.517																																					p.L56L		Atlas-SNP	.											CMKLR1,NS,carcinoma,-2,1	CMKLR1	67	1	0			c.G168A						PASS	.						101.0	100.0	100.0					12																	108686572		2010	4173	6183	SO:0001819	synonymous_variant	1240	exon3			ATTGCCCAGAATC	U79526	CCDS41829.1, CCDS44965.1	12q23.3	2013-07-29			ENSG00000174600	ENSG00000174600		"""GPCR / Class A : Resolvin receptors"""	2121	protein-coding gene	gene with protein product	"""resolvin E1 receptor"", ""chemerin receptor"""	602351					Standard	NM_004072		Approved	RVER1	uc009zuw.3	Q99788	OTTHUMG00000169576	ENST00000312143.7:c.168G>A	12.37:g.108686572C>T		Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	117	28	0.239316	NM_001142344	A8K6Y5|O75748|Q3KP37|Q5U0H0|Q99789	Silent	SNP	ENST00000312143.7	37	CCDS44965.1																																																																																			.	.	none		0.517	CMKLR1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000404867.1		
SUSD5	26032	hgsc.bcm.edu	37	3	33194990	33194990	+	Missense_Mutation	SNP	C	C	A	rs6810039	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:33194990C>A	ENST00000309558.3	-	5	1551	c.1134G>T	c.(1132-1134)gaG>gaT	p.E378D		NM_015551.1	NP_056366.1	O60279	SUSD5_HUMAN	sushi domain containing 5	378			E -> D (in dbSNP:rs6810039). {ECO:0000269|PubMed:9628581}.		cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)	hyaluronic acid binding (GO:0005540)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(4)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	24						TCCAAGCCCCCTCTGTCACAG	0.557													A|||	3305	0.659944	0.7307	0.6441	5008	,	,		21284	0.8542		0.3936	False		,,,				2504	0.6493				p.E378D		Atlas-SNP	.											.	SUSD5	53	.	0			c.G1134T						PASS	.	A	ASP/GLU	2899,1285		1014,871,207	99.0	107.0	105.0		1134	-9.8	0.0	3	dbSNP_116	105	3273,5189		644,1985,1602	yes	missense	SUSD5	NM_015551.1	45	1658,2856,1809	AA,AC,CC		38.6788,30.7122,48.8059	benign	378/630	33194990	6172,6474	2092	4231	6323	SO:0001583	missense	26032	exon5			AGCCCCCTCTGTC	AB011099	CCDS46787.1	3p23	2014-02-12	2006-01-13		ENSG00000173705	ENSG00000173705			29061	protein-coding gene	gene with protein product							Standard	NM_015551		Approved	KIAA0527	uc003cfo.1	O60279	OTTHUMG00000155829	ENST00000309558.3:c.1134G>T	3.37:g.33194990C>A	ENSP00000308727:p.Glu378Asp	Somatic	233	0	0		WXS	Illumina HiSeq	Phase_I	173	85	0.491329	NM_015551		Missense_Mutation	SNP	ENST00000309558.3	37	CCDS46787.1	1384	0.6336996336996337	362	0.7357723577235772	205	0.5662983425414365	510	0.8916083916083916	307	0.4050131926121372	A	2.099	-0.406519	0.04832	0.692878	0.386788	ENSG00000173705	ENST00000309558	T	0.05996	3.36	5.84	-9.81	0.00487	.	0.218834	0.37955	N	0.001879	T	0.00012	0.0000	N	0.00138	-2.015	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.41270	-0.9518	9	0.08381	T	0.77	-19.8019	8.3556	0.32329	0.1666:0.1655:0.5626:0.1052	rs6810039;rs52836781;rs56655667;rs6810039	378	O60279	SUSD5_HUMAN	D	378	ENSP00000308727:E378D	ENSP00000308727:E378D	E	-	3	2	SUSD5	33169994	0.057000	0.20700	0.005000	0.12908	0.820000	0.46376	-0.950000	0.03889	-2.418000	0.00566	-0.996000	0.02517	GAG	C|0.374;A|0.626	0.626	strong		0.557	SUSD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341902.1	XM_171054	
KLHL13	90293	hgsc.bcm.edu	37	X	117035896	117035896	+	Silent	SNP	A	A	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:117035896A>G	ENST00000262820.3	-	6	2289	c.1380T>C	c.(1378-1380)tgT>tgC	p.C460C	KLHL13_ENST00000539496.1_Silent_p.C463C|KLHL13_ENST00000545703.1_Silent_p.C418C|KLHL13_ENST00000540167.1_Silent_p.C444C|KLHL13_ENST00000469946.1_Silent_p.C409C|KLHL13_ENST00000371882.1_Silent_p.C409C|KLHL13_ENST00000371876.1_Silent_p.C409C|KLHL13_ENST00000541812.1_Silent_p.C444C|KLHL13_ENST00000371878.1_Silent_p.C409C	NM_033495.3	NP_277030.2	Q9P2N7	KLH13_HUMAN	kelch-like family member 13	460					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						TTGGATTGTAACATTCTACTG	0.318																																					p.C463C		Atlas-SNP	.											.	KLHL13	87	.	0			c.T1389C						PASS	.						133.0	112.0	119.0					X																	117035896		2203	4300	6503	SO:0001819	synonymous_variant	90293	exon7			ATTGTAACATTCT	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.1380T>C	X.37:g.117035896A>G		Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	112	34	0.303571	NM_001168299	B3KV78|B3KWM7|B7Z3S9|B7Z5P2|B7Z802|D3DWH6|Q6P2E3|Q96QI7|Q9UDN9	Silent	SNP	ENST00000262820.3	37	CCDS14571.1																																																																																			.	.	none		0.318	KLHL13-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_033495	
B9D1	27077	hgsc.bcm.edu	37	17	19247075	19247075	+	Intron	SNP	G	G	A	rs4924987	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:19247075G>A	ENST00000261499.4	-	6	616				B9D1_ENST00000395616.3_Intron|B9D1_ENST00000461069.2_Intron|B9D1_ENST00000575403.1_Intron|B9D1_ENST00000395615.1_Intron|B9D1_ENST00000477478.2_Missense_Mutation_p.H143Y|MIR1180_ENST00000408613.1_RNA	NM_015681.3	NP_056496.1	Q9UPM9	B9D1_HUMAN	B9 protein domain 1						camera-type eye development (GO:0043010)|cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|embryonic digit morphogenesis (GO:0042733)|in utero embryonic development (GO:0001701)|neuroepithelial cell differentiation (GO:0060563)|regulation of protein localization (GO:0032880)|smoothened signaling pathway (GO:0007224)|vasculature development (GO:0001944)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|ciliary transition zone (GO:0035869)|cytoplasm (GO:0005737)|membrane (GO:0016020)|TCTN-B9D complex (GO:0036038)	hedgehog receptor activity (GO:0008158)			large_intestine(3)|urinary_tract(1)	4	all_cancers(12;2.04e-05)|all_epithelial(12;0.000806)|Hepatocellular(7;0.00345)|Breast(13;0.143)					TATGGGGGATGGGGGTAAGAG	0.642													G|||	1555	0.310503	0.0726	0.5173	5008	,	,		16653	0.004		0.8121	False		,,,				2504	0.2853				p.H187Y		Atlas-SNP	.											.	B9D1	8	.	0			c.C559T						PASS	.	G		860,3546	329.9+/-301.2	90,680,1433	38.0	44.0	42.0			-0.6	0.0	17	dbSNP_111	42	6938,1662	729.9+/-406.7	2794,1350,156	no	intron	B9D1	NM_015681.3		2884,2030,1589	AA,AG,GG		19.3256,19.5188,40.0431			19247075	7798,5208	2203	4300	6503	SO:0001627	intron_variant	27077	exon6			GGGGATGGGGGTA	BC002944	CCDS11205.1, CCDS58528.1	17p11.2	2014-09-17			ENSG00000108641	ENSG00000108641			24123	protein-coding gene	gene with protein product	"""endothelial precursor protein B9"""	614144				21493627	Standard	NM_015681		Approved	B9, EPPB9, MKS9	uc010vyr.2	Q9UPM9	OTTHUMG00000059586	ENST00000261499.4:c.472+27C>T	17.37:g.19247075G>A		Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	30	18	0.6	NM_001243473	Q9BU22	Missense_Mutation	SNP	ENST00000261499.4	37	CCDS11205.1																																																																																			G|0.579;A|0.421	0.421	strong		0.642	B9D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132494.1	NM_015681	
STOX2	56977	hgsc.bcm.edu	37	4	184930961	184930961	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:184930961G>A	ENST00000308497.4	+	3	2405	c.970G>A	c.(970-972)Gtg>Atg	p.V324M	STOX2_ENST00000438269.1_Missense_Mutation_p.V324M	NM_020225.1	NP_064610.1	Q9P2F5	STOX2_HUMAN	storkhead box 2	324					embryo development (GO:0009790)|maternal placenta development (GO:0001893)					breast(1)|endometrium(7)|lung(6)	14		all_lung(41;1.89e-12)|Lung NSC(41;3.48e-12)|Colorectal(36;0.00435)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|all_hematologic(60;0.027)|Prostate(90;0.0283)		all cancers(43;2.85e-26)|Epithelial(43;2.27e-22)|OV - Ovarian serous cystadenocarcinoma(60;3.4e-10)|Colorectal(24;8.23e-06)|GBM - Glioblastoma multiforme(59;1.64e-05)|STAD - Stomach adenocarcinoma(60;3.6e-05)|COAD - Colon adenocarcinoma(29;4.37e-05)|LUSC - Lung squamous cell carcinoma(40;0.008)|READ - Rectum adenocarcinoma(43;0.227)		AGACCTGACCGTGGAAAATGT	0.562																																					p.V324M		Atlas-SNP	.											.	STOX2	142	.	0			c.G970A						PASS	.						24.0	24.0	24.0					4																	184930961		1943	4139	6082	SO:0001583	missense	56977	exon3			CTGACCGTGGAAA	AB037813	CCDS47167.1	4q35.1	2014-09-11			ENSG00000173320	ENSG00000173320			25450	protein-coding gene	gene with protein product							Standard	XM_005263142		Approved	DKFZp762K222	uc003ivz.1	Q9P2F5	OTTHUMG00000160618	ENST00000308497.4:c.970G>A	4.37:g.184930961G>A	ENSP00000311257:p.Val324Met	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	51	11	0.215686	NM_020225	A6H8U4|Q9NPS8	Missense_Mutation	SNP	ENST00000308497.4	37	CCDS47167.1	.	.	.	.	.	.	.	.	.	.	G	18.39	3.612462	0.66672	.	.	ENSG00000173320	ENST00000308497;ENST00000438269	T;D	0.88741	-1.49;-2.42	6.08	6.08	0.98989	.	0.000000	0.85682	D	0.000000	D	0.94922	0.8358	M	0.79123	2.44	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.91635	0.999;0.987	D	0.94499	0.7708	10	0.87932	D	0	-21.6529	20.6634	0.99662	0.0:0.0:1.0:0.0	.	324;324	Q9P2F5-2;Q9P2F5	.;STOX2_HUMAN	M	324	ENSP00000311257:V324M;ENSP00000390127:V324M	ENSP00000311257:V324M	V	+	1	0	STOX2	185167955	1.000000	0.71417	0.988000	0.46212	0.374000	0.29953	9.869000	0.99810	2.894000	0.99253	0.655000	0.94253	GTG	.	.	none		0.562	STOX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361433.3	NM_020225	
CLEC18B	497190	hgsc.bcm.edu	37	16	74451970	74451970	+	Missense_Mutation	SNP	G	G	C	rs201240581	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:74451970G>C	ENST00000339953.5	-	3	564	c.443C>G	c.(442-444)aCc>aGc	p.T148S		NM_001011880.2	NP_001011880.2	Q6UXF7	CL18B_HUMAN	C-type lectin domain family 18, member B	148	SCP.					extracellular region (GO:0005576)	carbohydrate binding (GO:0030246)	p.T148S(1)		endometrium(3)|kidney(9)|large_intestine(3)|lung(7)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	27						CGTGTAGTGGGTGCAGGTGGC	0.612																																					p.T148S		Atlas-SNP	.											CLEC18B,mouth,carcinoma,0,1	CLEC18B	45	1	1	Substitution - Missense(1)	upper_aerodigestive_tract(1)	c.C443G						scavenged	.						10.0	11.0	11.0					16																	74451970		1710	3535	5245	SO:0001583	missense	497190	exon3			TAGTGGGTGCAGG	AY358373	CCDS32484.1	16q22.3	2010-04-27	2009-03-10	2009-03-10		ENSG00000140839		"""C-type lectin domain containing"""	33849	protein-coding gene	gene with protein product							Standard	NM_001011880		Approved		uc002fct.3	Q6UXF7		ENST00000339953.5:c.443C>G	16.37:g.74451970G>C	ENSP00000341051:p.Thr148Ser	Somatic	266	0	0		WXS	Illumina HiSeq	Phase_I	638	44	0.0689655	NM_001011880	B4DF90	Missense_Mutation	SNP	ENST00000339953.5	37	CCDS32484.1	.	.	.	.	.	.	.	.	.	.	g	3.129	-0.178796	0.06380	.	.	ENSG00000140839	ENST00000429489;ENST00000339953;ENST00000268492	T	0.07688	3.17	3.57	3.57	0.40892	CAP domain (3);	0.557277	0.19650	N	0.109248	T	0.05135	0.0137	N	0.25286	0.73	0.22342	N	0.999188	B;B	0.14012	0.005;0.009	B;B	0.13407	0.007;0.009	T	0.39702	-0.9601	10	0.07030	T	0.85	.	10.55	0.45083	0.0:0.0:1.0:0.0	.	148;148	C9JSV1;Q6UXF7	.;CL18B_HUMAN	S	148	ENSP00000341051:T148S	ENSP00000268492:T148S	T	-	2	0	CLEC18B	73009471	0.995000	0.38212	0.998000	0.56505	0.761000	0.43186	1.684000	0.37649	1.821000	0.53095	0.531000	0.56144	ACC	.	.	weak		0.612	CLEC18B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434697.1	NM_001011880	
DNAJC30	84277	hgsc.bcm.edu	37	7	73097238	73097238	+	Silent	SNP	G	G	A	rs1569062	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:73097238G>A	ENST00000395176.2	-	1	545	c.516C>T	c.(514-516)taC>taT	p.Y172Y	WBSCR22_ENST00000423497.1_5'Flank|WBSCR22_ENST00000423166.2_5'Flank|WBSCR22_ENST00000265758.2_5'Flank	NM_032317.2	NP_115693.2	Q96LL9	DJC30_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 30	172						mitochondrion (GO:0005739)				kidney(1)|large_intestine(2)|lung(1)	4						GTTGTTCCCCGTAGTGGGCCT	0.672													G|||	1163	0.232228	0.0325	0.3473	5008	,	,		12916	0.1746		0.337	False		,,,				2504	0.3722				p.Y172Y		Atlas-SNP	.											.	DNAJC30	12	.	0			c.C516T						PASS	.	G		361,4045	174.4+/-204.0	19,323,1861	32.0	33.0	33.0		516	2.1	1.0	7	dbSNP_88	33	2907,5693	430.2+/-356.4	509,1889,1902	no	coding-synonymous	DNAJC30	NM_032317.2		528,2212,3763	AA,AG,GG		33.8023,8.1934,25.1269		172/227	73097238	3268,9738	2203	4300	6503	SO:0001819	synonymous_variant	84277	exon1			TTCCCCGTAGTGG	AF412025	CCDS5556.1	7q11.23	2011-09-02	2008-06-17	2008-06-17	ENSG00000176410	ENSG00000176410		"""Heat shock proteins / DNAJ (HSP40)"""	16410	protein-coding gene	gene with protein product			"""Williams Beuren syndrome chromosome region 18"""	WBSCR18		12073013	Standard	NM_032317		Approved		uc003tys.1	Q96LL9	OTTHUMG00000023290	ENST00000395176.2:c.516C>T	7.37:g.73097238G>A		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	64	37	0.578125	NM_032317	Q9BSG8	Silent	SNP	ENST00000395176.2	37	CCDS5556.1																																																																																			G|0.763;A|0.237	0.237	strong		0.672	DNAJC30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252304.2		
KIF13A	63971	hgsc.bcm.edu	37	6	17764530	17764530	+	Silent	SNP	C	C	T	rs9371018	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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_ENST00000378843.2_Silent_p.E1695E|KIF13A_ENST00000378826.2_Silent_p.E1708E|KIF13A_ENST00000378814.5_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	172	0	0		WXS	Illumina HiSeq	Phase_I	109	53	0.486239	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		
TRPV3	162514	hgsc.bcm.edu	37	17	3447914	3447914	+	Silent	SNP	C	C	T	rs1039519	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:3447914C>T	ENST00000576742.1	-	4	591	c.270G>A	c.(268-270)caG>caA	p.Q90Q	TRPV3_ENST00000301365.4_Silent_p.Q90Q|TRPV3_ENST00000572519.1_Silent_p.Q90Q	NM_001258205.1|NM_145068.3	NP_001245134.1|NP_659505.1	Q8NET8	TRPV3_HUMAN	transient receptor potential cation channel, subfamily V, member 3	90					calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|negative regulation of hair cycle (GO:0042636)|positive regulation of calcium ion import (GO:0090280)|response to heat (GO:0009408)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium channel activity (GO:0005262)			breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(12)|ovary(5)|prostate(1)|skin(2)|stomach(1)|urinary_tract(2)	35					Menthol(DB00825)	TCACATCATCCTGAGGAGACT	0.582													c|||	3318	0.66254	0.5461	0.7781	5008	,	,		16033	0.7937		0.5885	False		,,,				2504	0.6789				p.Q90Q		Atlas-SNP	.											.	TRPV3	85	.	0			c.G270A						PASS	.			2464,1942	620.9+/-393.6	680,1104,419	40.0	39.0	39.0		270	3.2	1.0	17	dbSNP_86	39	5160,3440	634.3+/-398.8	1527,2106,667	no	coding-synonymous	TRPV3	NM_145068.2		2207,3210,1086	TT,TC,CC		40.0,44.0763,41.3809		90/791	3447914	7624,5382	2203	4300	6503	SO:0001819	synonymous_variant	162514	exon4			ATCATCCTGAGGA	AF514998	CCDS11029.1, CCDS58500.1	17p13.3	2013-01-10			ENSG00000167723	ENSG00000167723		"""Voltage-gated ion channels / Transient receptor potential cation channels"", ""Ankyrin repeat domain containing"""	18084	protein-coding gene	gene with protein product		607066				12016205, 12077606, 16382100	Standard	NM_001258205		Approved	VRL3	uc002fvr.3	Q8NET8	OTTHUMG00000090695	ENST00000576742.1:c.270G>A	17.37:g.3447914C>T		Somatic	21	0	0		WXS	Illumina HiSeq	Phase_I	17	6	0.352941	NM_001258205	Q8NDW7|Q8NET9|Q8NFH2	Silent	SNP	ENST00000576742.1	37	CCDS11029.1																																																																																			C|0.383;T|0.617	0.617	strong		0.582	TRPV3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000207379.2	NM_145068	
POFUT1	23509	hgsc.bcm.edu	37	20	30795819	30795819	+	Silent	SNP	T	T	C	rs1923095	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:30795819T>C	ENST00000375749.3	+	1	137	c.75T>C	c.(73-75)ccT>ccC	p.P25P	POFUT1_ENST00000539210.1_5'UTR|PLAGL2_ENST00000246229.4_5'Flank|POFUT1_ENST00000375730.3_Silent_p.P25P|POFUT1_ENST00000486717.1_3'UTR	NM_015352.1	NP_056167.1	Q9H488	OFUT1_HUMAN	protein O-fucosyltransferase 1	25					angiogenesis (GO:0001525)|embryo development (GO:0009790)|fucose metabolic process (GO:0006004)|heart development (GO:0007507)|nervous system development (GO:0007399)|Notch signaling pathway (GO:0007219)|O-glycan processing (GO:0016266)|protein O-linked fucosylation (GO:0036066)|protein O-linked glycosylation (GO:0006493)|regulation of transcription, DNA-templated (GO:0006355)|somitogenesis (GO:0001756)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)	fucosyltransferase activity (GO:0008417)|peptide-O-fucosyltransferase activity (GO:0046922)			breast(1)|endometrium(1)|large_intestine(1)|lung(2)|urinary_tract(1)	6			UCEC - Uterine corpus endometrioid carcinoma (5;0.0241)			CGGGGATGCCTGCGGGCTCCT	0.701													C|||	3829	0.764577	0.9652	0.7262	5008	,	,		10635	0.994		0.5398	False		,,,				2504	0.5153				p.P25P		Atlas-SNP	.											POFUT1_ENST00000375730,NS,carcinoma,0,2	POFUT1	52	2	0			c.T75C						PASS	.	C	,	3794,518		1697,400,59	6.0	9.0	8.0		75,75	-2.8	0.0	20	dbSNP_92	8	4732,3702		1408,1916,893	no	coding-synonymous,coding-synonymous	POFUT1	NM_015352.1,NM_172236.1	,	3105,2316,952	CC,CT,TT		43.8938,12.013,33.1084	,	25/389,25/195	30795819	8526,4220	2156	4217	6373	SO:0001819	synonymous_variant	23509	exon1			GATGCCTGCGGGC	AF375884	CCDS13198.1, CCDS13199.1	20q11	2013-03-06			ENSG00000101346	ENSG00000101346	2.4.1.221	"""Fucosyltransferases"""	14988	protein-coding gene	gene with protein product	"""peptide-O-fucosyltransferase"", ""GDP-fucose protein O-fucosyltransferase 1"""	607491				9023546, 9525914	Standard	NM_015352		Approved	O-FUT, O-Fuc-T, KIAA0180, FUT12	uc002wxp.3	Q9H488	OTTHUMG00000133268	ENST00000375749.3:c.75T>C	20.37:g.30795819T>C		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	34	33	0.970588	NM_172236	A8K4R8|E1P5M4|Q14685|Q5W185|Q9BW76	Silent	SNP	ENST00000375749.3	37	CCDS13198.1																																																																																			T|0.236;C|0.764	0.764	strong		0.701	POFUT1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078613.1	NM_015352	
BTBD6	90135	hgsc.bcm.edu	37	14	105716854	105716854	+	Missense_Mutation	SNP	G	G	A	rs146426875	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:105716854G>A	ENST00000392554.3	+	4	1600	c.1303G>A	c.(1303-1305)Gtc>Atc	p.V435I	BRF1_ENST00000440513.3_Intron|BRF1_ENST00000379937.2_Intron|BRF1_ENST00000546474.1_Intron|BRF1_ENST00000392557.4_5'Flank|BTBD6_ENST00000327471.3_Missense_Mutation_p.V360I|BRF1_ENST00000446501.2_5'Flank|BRF1_ENST00000327359.3_Intron|BTBD6_ENST00000463376.2_Missense_Mutation_p.V360I|BTBD6_ENST00000536364.1_Missense_Mutation_p.V435I			Q96KE9	BTBD6_HUMAN	BTB (POZ) domain containing 6	435						cytoplasm (GO:0005737)				endometrium(1)|lung(3)	4		Melanoma(154;0.226)	OV - Ovarian serous cystadenocarcinoma(23;0.0163)|Epithelial(46;0.0391)	Epithelial(152;0.18)		GGCCAGTGCCGTCCTGGACGG	0.572													G|||	8	0.00159744	0.0	0.0	5008	,	,		19762	0.0		0.002	False		,,,				2504	0.0061				p.V435I		Atlas-SNP	.											.	BTBD6	24	.	0			c.G1303A						PASS	.	G	,,,,ILE/VAL	3,4403	6.2+/-15.9	0,3,2200	95.0	83.0	87.0		,,,,1303	3.1	0.6	14	dbSNP_134	87	25,8575	17.9+/-57.8	0,25,4275	yes	intron,intron,intron,intron,missense	BRF1,BTBD6	NM_001242786.1,NM_001242787.1,NM_001242788.1,NM_001519.3,NM_033271.2	,,,,29	0,28,6475	AA,AG,GG		0.2907,0.0681,0.2153	,,,,benign	,,,,435/486	105716854	28,12978	2203	4300	6503	SO:0001583	missense	90135	exon5			AGTGCCGTCCTGG	AF353674	CCDS10002.1, CCDS10002.2	14q32.33	2013-01-08			ENSG00000184887	ENSG00000184887		"""BTB/POZ domain containing"""	19897	protein-coding gene	gene with protein product							Standard	NM_033271		Approved	BDPL	uc010tyq.2	Q96KE9	OTTHUMG00000029887	ENST00000392554.3:c.1303G>A	14.37:g.105716854G>A	ENSP00000376337:p.Val435Ile	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	56	29	0.517857	NM_033271	Q8IVQ7|Q9BR94	Missense_Mutation	SNP	ENST00000392554.3	37	CCDS10002.2	.	.	.	.	.	.	.	.	.	.	G	2.830	-0.242885	0.05906	6.81E-4	0.002907	ENSG00000184887	ENST00000536364;ENST00000392554;ENST00000327471	T;T;T	0.73789	-0.78;-0.78;-0.69	5.16	3.06	0.35304	PHR (1);	0.122234	0.53938	D	0.000047	T	0.43188	0.1236	N	0.02802	-0.49	0.80722	D	1	B	0.16603	0.018	B	0.17979	0.02	T	0.16571	-1.0398	9	.	.	.	-41.9028	4.7344	0.12981	0.3872:0.0:0.6128:0.0	.	435	Q96KE9	BTBD6_HUMAN	I	435;435;360	ENSP00000443091:V435I;ENSP00000376337:V435I;ENSP00000329361:V360I	.	V	+	1	0	BTBD6	104787899	1.000000	0.71417	0.641000	0.29422	0.440000	0.31957	4.545000	0.60698	1.161000	0.42604	0.655000	0.94253	GTC	G|0.997;A|0.003	0.003	strong		0.572	BTBD6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000074556.4		
FAT1	2195	hgsc.bcm.edu	37	4	187542755	187542755	+	Missense_Mutation	SNP	T	T	C	rs28489116	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:187542755T>C	ENST00000441802.2	-	10	5194	c.4985A>G	c.(4984-4986)aAc>aGc	p.N1662S		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	1662	Cadherin 14. {ECO:0000255|PROSITE- ProRule:PRU00043}.				actin filament organization (GO:0007015)|anatomical structure morphogenesis (GO:0009653)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.N1662S(2)|p.N1665S(1)		NS(1)|breast(3)|central_nervous_system(3)|endometrium(38)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(33)|lung(88)|ovary(13)|pancreas(2)|prostate(16)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	228						CGGAGAGGCGTTGTCAGCAAT	0.408										HNSCC(5;0.00058)			T|||	1004	0.200479	0.2141	0.1988	5008	,	,		19433	0.3849		0.1113	False		,,,				2504	0.0849				p.N1662S	Colon(197;1040 2055 4143 4984 49344)	Atlas-SNP	.											FAT1,NS,carcinoma,0,2	FAT1	500	2	3	Substitution - Missense(3)	prostate(3)	c.A4985G						PASS	.	T	SER/ASN	605,3161		61,483,1339	94.0	91.0	92.0		4985	5.2	1.0	4	dbSNP_125	92	971,7257		69,833,3212	yes	missense	FAT1	NM_005245.3	46	130,1316,4551	CC,CT,TT		11.8012,16.0648,13.1399	benign	1662/4589	187542755	1576,10418	1883	4114	5997	SO:0001583	missense	2195	exon10			GAGGCGTTGTCAG	X87241	CCDS47177.1	4q35.2	2013-05-31	2013-05-31	2008-10-30	ENSG00000083857	ENSG00000083857		"""Cadherins / Cadherin-related"""	3595	protein-coding gene	gene with protein product	"""cadherin-related family member 8"""	600976	"""FAT tumor suppressor (Drosophila) homolog"", ""FAT tumor suppressor homolog 1 (Drosophila)"""	FAT		8586420	Standard	XM_005262834		Approved	CDHF7, CDHR8	uc003izf.3	Q14517	OTTHUMG00000160320	ENST00000441802.2:c.4985A>G	4.37:g.187542755T>C	ENSP00000406229:p.Asn1662Ser	Somatic	250	0	0		WXS	Illumina HiSeq	Phase_I	181	81	0.447514	NM_005245		Missense_Mutation	SNP	ENST00000441802.2	37	CCDS47177.1	495	0.22664835164835165	103	0.20934959349593496	75	0.20718232044198895	229	0.40034965034965037	88	0.11609498680738786	T	16.23	3.063325	0.55432	0.160648	0.118012	ENSG00000083857	ENST00000441802;ENST00000260147	T	0.60672	0.17	5.19	5.19	0.71726	Cadherin (3);Cadherin-like (1);	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	M	0.77616	2.38	0.09310	P	0.99999999775895	D	0.71674	0.998	D	0.79784	0.993	T	0.17379	-1.0371	9	0.37606	T	0.19	.	15.5098	0.75772	0.0:0.0:0.0:1.0	rs28489116;rs58264946	1662	Q14517	FAT1_HUMAN	S	1662;1664	ENSP00000406229:N1662S	ENSP00000260147:N1664S	N	-	2	0	FAT1	187779749	1.000000	0.71417	0.999000	0.59377	0.794000	0.44872	7.825000	0.86693	2.304000	0.77564	0.528000	0.53228	AAC	T|0.794;C|0.206	0.206	strong		0.408	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245	
DMBT1	1755	hgsc.bcm.edu	37	10	124351954	124351954	+	Silent	SNP	G	G	A	rs4752722	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:124351954G>A	ENST00000338354.3	+	20	2449	c.2343G>A	c.(2341-2343)tcG>tcA	p.S781S	DMBT1_ENST00000368909.3_Silent_p.S781S|DMBT1_ENST00000359586.6_Intron|DMBT1_ENST00000344338.3_Silent_p.S771S|DMBT1_ENST00000368955.3_Silent_p.S771S|DMBT1_ENST00000330163.4_Intron|DMBT1_ENST00000368956.2_Intron			Q9UGM3	DMBT1_HUMAN	deleted in malignant brain tumors 1	781	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)				GGGCCACGTCGGCCCCAGGAA	0.617													g|||	1864	0.372204	0.5469	0.2435	5008	,	,		17432	0.4395		0.1511	False		,,,				2504	0.3855				p.S781S	Ovarian(182;93 2026 18125 22222 38972)	Atlas-SNP	.											.	DMBT1	677	.	0			c.G2343A						PASS	.	A	,,	1880,2108		461,958,575	179.0	145.0	156.0		,2343,2313	-7.7	0.0	10	dbSNP_111	156	1157,7105		170,817,3144	no	intron,coding-synonymous,coding-synonymous	DMBT1	NM_004406.2,NM_007329.2,NM_017579.2	,,	631,1775,3719	AA,AG,GG		14.0039,47.1414,24.7918	,,	,781/2414,771/2404	124351954	3037,9213	1994	4131	6125	SO:0001819	synonymous_variant	1755	exon20			CACGTCGGCCCCA		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.2343G>A	10.37:g.124351954G>A		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	42	30	0.714286	NM_007329	A6NDG4|A6NDJ5|A8E4R5|B1ARE7|B1ARE8|B1ARE9|B1ARF0|B7Z8Y2|F8WEF7|Q59EX0|Q5JR26|Q6MZN4|Q96DU4|Q9UGM2|Q9UJ57|Q9UKJ4|Q9Y211|Q9Y4V9	Silent	SNP	ENST00000338354.3	37																																																																																				G|0.732;A|0.268	0.268	strong		0.617	DMBT1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050792.2	NM_004406	
CRIPAK	285464	hgsc.bcm.edu	37	4	1388378	1388378	+	Missense_Mutation	SNP	T	T	C	rs55884223	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	127	2	0.015748		WXS	Illumina HiSeq	Phase_I	90	23	0.255556	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	
ZNF585A	199704	hgsc.bcm.edu	37	19	37644051	37644051	+	Silent	SNP	T	T	C	rs57916401	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:37644051T>C	ENST00000356958.4	-	5	1008	c.750A>G	c.(748-750)gcA>gcG	p.A250A	ZNF585A_ENST00000588723.1_Intron|ZNF585A_ENST00000292841.5_Silent_p.A195A|ZNF585A_ENST00000355533.2_Silent_p.A195A|ZNF585A_ENST00000392157.2_Silent_p.A195A			Q6P3V2	Z585A_HUMAN	zinc finger protein 585A	250					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)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(4)|central_nervous_system(1)|endometrium(2)|large_intestine(17)|lung(11)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	42			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			TTTGTGTGAATGCTTTGCCAC	0.448													C|||	1702	0.339856	0.5431	0.4078	5008	,	,		19448	0.0933		0.3628	False		,,,				2504	0.2474				p.A195A		Atlas-SNP	.											.	ZNF585A	117	.	0			c.A585G						PASS	.	C	,	2336,2070	570.9+/-383.0	584,1168,451	151.0	150.0	150.0		585,585	-5.4	0.2	19	dbSNP_129	150	3066,5528	660.0+/-401.7	544,1978,1775	no	coding-synonymous,coding-synonymous	ZNF585A	NM_152655.2,NM_199126.1	,	1128,3146,2226	CC,CT,TT		35.6761,46.9814,41.5538	,	195/715,195/715	37644051	5402,7598	2203	4297	6500	SO:0001819	synonymous_variant	199704	exon6			TGTGAATGCTTTG	AK074345	CCDS12499.1, CCDS74353.1	19q13.13	2013-01-08				ENSG00000196967		"""Zinc fingers, C2H2-type"", ""-"""	26305	protein-coding gene	gene with protein product						12477932	Standard	NM_199126		Approved	FLJ23765	uc002ofn.1	Q6P3V2		ENST00000356958.4:c.750A>G	19.37:g.37644051T>C		Somatic	236	0	0		WXS	Illumina HiSeq	Phase_I	156	97	0.621795	NM_199126	Q8TE95|Q96MV3	Silent	SNP	ENST00000356958.4	37																																																																																				T|0.630;C|0.370	0.370	strong		0.448	ZNF585A-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000457980.2	NM_152655	
CC2D2B	387707	hgsc.bcm.edu	37	10	97772358	97772358	+	Missense_Mutation	SNP	A	A	G	rs17383738	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:97772358A>G	ENST00000344386.3	+	4	354	c.190A>G	c.(190-192)Aac>Gac	p.N64D	ENTPD1-AS1_ENST00000451364.1_RNA|CC2D2B_ENST00000410012.2_Missense_Mutation_p.N64D|ENTPD1-AS1_ENST00000454638.1_RNA|ENTPD1-AS1_ENST00000452728.1_RNA|CC2D2B_ENST00000371198.2_Intron|RP11-690P14.4_ENST00000475252.2_Intron|ENTPD1-AS1_ENST00000416301.1_RNA	NM_001001732.3	NP_001001732.2	Q6DHV5	C2D2B_HUMAN	coiled-coil and C2 domain containing 2B	64			N -> D (in dbSNP:rs17383738).							large_intestine(1)|lung(7)|ovary(1)|urinary_tract(1)	10		Colorectal(252;0.158)		Epithelial(162;7.08e-08)|all cancers(201;2.71e-06)		AATGTTTCCCAACCGAAGAAT	0.333													A|||	482	0.096246	0.1694	0.085	5008	,	,		18533	0.005		0.1571	False		,,,				2504	0.0368				p.N64D		Atlas-SNP	.											.	CC2D2B	46	.	0			c.A190G						PASS	.	A	ASP/ASN,ASP/ASN	602,3062		51,500,1281	106.0	101.0	103.0		190,190	2.7	1.0	10	dbSNP_123	103	1089,7071		72,945,3063	yes	missense,missense	CC2D2B	NM_001001732.3,NM_001159747.1	23,23	123,1445,4344	GG,GA,AA		13.3456,16.4301,14.3014	benign,benign	64/323,64/402	97772358	1691,10133	1832	4080	5912	SO:0001583	missense	387707	exon4			TTTCCCAACCGAA	BC075861	CCDS41555.1, CCDS53560.1	10q23.33	2008-11-06	2007-10-19	2007-10-19	ENSG00000188649	ENSG00000188649			31666	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 130"""	C10orf130			Standard	NM_001001732		Approved	bA248J23.4	uc010qop.2	Q6DHV5	OTTHUMG00000018820	ENST00000344386.3:c.190A>G	10.37:g.97772358A>G	ENSP00000343747:p.Asn64Asp	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	112	64	0.571429	NM_001001732	A2A3E9|B4DYD4|E9PCC3|Q5VUS0	Missense_Mutation	SNP	ENST00000344386.3	37	CCDS41555.1	219	0.10027472527472528	66	0.13414634146341464	29	0.08011049723756906	1	0.0017482517482517483	123	0.16226912928759896	A	12.87	2.066477	0.36470	0.164301	0.133456	ENSG00000188649	ENST00000424464;ENST00000451649;ENST00000410012;ENST00000344386	T;D;T	0.81579	-1.29;-1.51;-0.85	5.19	2.74	0.32292	.	.	.	.	.	T	0.00468	0.0015	L	0.40543	1.245	0.50171	P	1.4300000000000423E-4	P;B	0.35272	0.493;0.009	B;B	0.31101	0.124;0.008	T	0.08472	-1.0720	8	0.13108	T	0.6	.	5.2716	0.15628	0.7586:0.0:0.0858:0.1556	rs17383738;rs52789998;rs17383738	64;64	E9PCC3;Q6DHV5	.;C2D2B_HUMAN	D	125;64;64;64	ENSP00000391834:N125D;ENSP00000386988:N64D;ENSP00000343747:N64D	ENSP00000343747:N64D	N	+	1	0	CC2D2B	97762348	0.983000	0.35010	0.980000	0.43619	0.959000	0.62525	1.965000	0.40471	0.268000	0.21939	0.477000	0.44152	AAC	A|0.889;G|0.111	0.111	strong		0.333	CC2D2B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000049573.3	NM_001001732	
BIN3	55909	hgsc.bcm.edu	37	8	22481449	22481449	+	Silent	SNP	A	A	G	rs1871900	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:22481449A>G	ENST00000276416.6	-	8	662	c.594T>C	c.(592-594)ttT>ttC	p.F198F	BIN3_ENST00000519513.1_Silent_p.F144F|BIN3_ENST00000519335.1_5'UTR|BIN3_ENST00000399977.4_Silent_p.F150F	NM_018688.4	NP_061158.1	Q9NQY0	BIN3_HUMAN	bridging integrator 3	198	BAR. {ECO:0000255|PROSITE- ProRule:PRU00361}.				actin filament organization (GO:0007015)|barrier septum assembly (GO:0000917)|cytokinesis (GO:0000910)|myoblast migration involved in skeletal muscle regeneration (GO:0014839)|protein localization (GO:0008104)|regulation of lamellipodium assembly (GO:0010591)|skeletal muscle fiber development (GO:0048741)|unidimensional cell growth (GO:0009826)	actin filament (GO:0005884)|cytoplasm (GO:0005737)	cytoskeletal adaptor activity (GO:0008093)			kidney(1)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)|urinary_tract(1)	9		Prostate(55;0.0424)|Breast(100;0.102)|all_epithelial(46;0.143)		BRCA - Breast invasive adenocarcinoma(99;0.00664)|Colorectal(74;0.0189)|COAD - Colon adenocarcinoma(73;0.0727)		TGAGGGACTCAAAGCTGGGCT	0.622													a|||	2490	0.497204	0.6067	0.3977	5008	,	,		15483	0.3978		0.4394	False		,,,				2504	0.5818				p.F198F		Atlas-SNP	.											.	BIN3	16	.	0			c.T594C						PASS	.	G		2138,1810		583,972,419	21.0	27.0	25.0		594	-11.0	0.2	8	dbSNP_92	25	3451,4843		723,2005,1419	no	coding-synonymous	BIN3	NM_018688.4		1306,2977,1838	GG,GA,AA		41.6084,45.846,45.6543		198/254	22481449	5589,6653	1974	4147	6121	SO:0001819	synonymous_variant	55909	exon8			GGACTCAAAGCTG		CCDS47825.1	8p21.2	2008-07-04			ENSG00000147439	ENSG00000147439			1054	protein-coding gene	gene with protein product		606396				16524918	Standard	NM_018688		Approved		uc003xcl.3	Q9NQY0	OTTHUMG00000163844	ENST00000276416.6:c.594T>C	8.37:g.22481449A>G		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	64	48	0.75	NM_018688	Q9BVG2|Q9NVY9	Silent	SNP	ENST00000276416.6	37	CCDS47825.1																																																																																			G|0.475;C|0.000;A|0.525	0.475	strong		0.622	BIN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375895.1		
LRIG3	121227	hgsc.bcm.edu	37	12	59282702	59282702	+	Silent	SNP	T	T	C	rs17533647	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:59282702T>C	ENST00000320743.3	-	6	988	c.702A>G	c.(700-702)acA>acG	p.T234T	LRIG3_ENST00000379141.4_Silent_p.T174T	NM_153377.4	NP_700356.2	Q6UXM1	LRIG3_HUMAN	leucine-rich repeats and immunoglobulin-like domains 3	234					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)			GGCCTTGGAATGTCAGTCCAT	0.378			T	ROS1	NSCLC								T|||	306	0.0611022	0.0129	0.0461	5008	,	,		19089	0.0397		0.1163	False		,,,				2504	0.1022				p.T234T		Atlas-SNP	.		Dom	yes		12	12q14.1	121227	leucine-rich repeats and immunoglobulin-like domains 3		E	LRIG3,NS,carcinoma,-2,1	LRIG3	120	1	0			c.A702G						PASS	.	T	,	148,4258	101.2+/-139.8	4,140,2059	198.0	185.0	189.0		522,702	-11.0	0.8	12	dbSNP_123	189	995,7605	214.6+/-254.2	51,893,3356	no	coding-synonymous,coding-synonymous	LRIG3	NM_001136051.1,NM_153377.3	,	55,1033,5415	CC,CT,TT		11.5698,3.3591,8.7883	,	174/1060,234/1120	59282702	1143,11863	2203	4300	6503	SO:0001819	synonymous_variant	121227	exon6			TTGGAATGTCAGT	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.702A>G	12.37:g.59282702T>C		Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	171	73	0.426901	NM_153377	Q6UXL7|Q8NC72	Silent	SNP	ENST00000320743.3	37	CCDS8960.1																																																																																			T|0.928;C|0.072	0.072	strong		0.378	LRIG3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406623.1	NM_153377	
CTR9	9646	hgsc.bcm.edu	37	11	10786175	10786175	+	Silent	SNP	C	C	T	rs7118399	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:10786175C>T	ENST00000361367.2	+	12	1920	c.1494C>T	c.(1492-1494)acC>acT	p.T498T		NM_014633.3	NP_055448.1	Q6PD62	CTR9_HUMAN	CTR9, Paf1/RNA polymerase II complex component	498					cellular response to lipopolysaccharide (GO:0071222)|endodermal cell fate commitment (GO:0001711)|histone H2B ubiquitination (GO:0033523)|histone H3-K4 trimethylation (GO:0080182)|histone monoubiquitination (GO:0010390)|interleukin-6-mediated signaling pathway (GO:0070102)|JAK-STAT cascade (GO:0007259)|negative regulation of myeloid cell differentiation (GO:0045638)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of histone H3-K79 methylation (GO:2001162)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	Cdc73/Paf1 complex (GO:0016593)|transcriptionally active chromatin (GO:0035327)		p.T498T(1)		breast(4)|central_nervous_system(2)|cervix(1)|endometrium(7)|kidney(3)|large_intestine(7)|lung(12)|ovary(2)|pancreas(1)|stomach(1)	40				all cancers(16;1.64e-07)|Epithelial(150;2.47e-07)|BRCA - Breast invasive adenocarcinoma(625;0.111)		TTTCCGTTACCACGTCATATA	0.393													C|||	997	0.199081	0.1112	0.1542	5008	,	,		17362	0.2133		0.3052	False		,,,				2504	0.226				p.T498T		Atlas-SNP	.											CTR9,NS,carcinoma,0,1	CTR9	94	1	1	Substitution - coding silent(1)	stomach(1)	c.C1494T						PASS	.	C		613,3789	267.1+/-267.6	47,519,1635	92.0	81.0	85.0		1494	-4.3	0.8	11	dbSNP_116	85	2626,5962	424.0+/-354.5	404,1818,2072	no	coding-synonymous	CTR9	NM_014633.3		451,2337,3707	TT,TC,CC		30.5776,13.9255,24.9346		498/1174	10786175	3239,9751	2201	4294	6495	SO:0001819	synonymous_variant	9646	exon12			CGTTACCACGTCA	D63875	CCDS7805.1	11p15.3	2013-07-03	2013-07-03	2006-05-22	ENSG00000198730	ENSG00000198730		"""Tetratricopeptide (TTC) repeat domain containing"""	16850	protein-coding gene	gene with protein product		609366	"""SH2 domain binding protein 1 (tetratricopeptide repeat containing)"", ""Ctr9, Paf1/RNA polymerase II complex component, homolog (S. cerevisiae)"""	SH2BP1		8590280, 8636124	Standard	NM_014633		Approved	KIAA0155, TSBP, p150TSP	uc001mja.3	Q6PD62	OTTHUMG00000165789	ENST00000361367.2:c.1494C>T	11.37:g.10786175C>T		Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	188	25	0.132979	NM_014633	D3DQV8|Q15015	Silent	SNP	ENST00000361367.2	37	CCDS7805.1																																																																																			C|0.772;T|0.228	0.228	strong		0.393	CTR9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386215.1	NM_014633	
WDR78	79819	hgsc.bcm.edu	37	1	67390468	67390468	+	Missense_Mutation	SNP	C	C	G	rs1886686	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:67390468C>G	ENST00000371026.3	-	1	102	c.47G>C	c.(46-48)gGa>gCa	p.G16A	MIER1_ENST00000401041.1_5'Flank|MIER1_ENST00000371018.3_5'Flank|WDR78_ENST00000431318.1_5'UTR|MIER1_ENST00000371014.1_5'Flank|WDR78_ENST00000371023.3_Missense_Mutation_p.G16A|MIER1_ENST00000371012.2_5'Flank|WDR78_ENST00000371022.3_Missense_Mutation_p.G16A|MIER1_ENST00000371016.1_5'Flank|MIER1_ENST00000357692.2_5'Flank|MIER1_ENST00000355977.6_5'Flank	NM_024763.4	NP_079039.4	Q5VTH9	WDR78_HUMAN	WD repeat domain 78	16			G -> A (in dbSNP:rs1886686). {ECO:0000269|PubMed:15489334}.		hematopoietic progenitor cell differentiation (GO:0002244)					NS(1)|endometrium(3)|kidney(6)|large_intestine(6)|lung(10)|ovary(3)|skin(3)	32						CCAAGCTCCTCCGTTAGCGGC	0.677													G|||	4220	0.842652	0.8608	0.8372	5008	,	,		13846	0.8829		0.7336	False		,,,				2504	0.8926				p.G16A		Atlas-SNP	.											.	WDR78	102	.	0			c.G47C						PASS	.	G	ALA/GLY,ALA/GLY	3751,655	280.5+/-275.4	1609,533,61	82.0	88.0	86.0		47,47	2.2	0.1	1	dbSNP_92	86	6295,2305	386.5+/-341.9	2322,1651,327	yes	missense,missense	WDR78	NM_024763.4,NM_207014.2	60,60	3931,2184,388	GG,GC,CC		26.8023,14.8661,22.7587	benign,benign	16/849,16/546	67390468	10046,2960	2203	4300	6503	SO:0001583	missense	79819	exon1			GCTCCTCCGTTAG	BX648840	CCDS635.1, CCDS44157.1	1p31.2	2014-02-21	2013-02-19	2013-02-19	ENSG00000152763	ENSG00000152763		"""WD repeat domain containing"""	26252	protein-coding gene	gene with protein product						21953912	Standard	NM_207014		Approved	DIC4, FLJ23129	uc001dcx.3	Q5VTH9	OTTHUMG00000009165	ENST00000371026.3:c.47G>C	1.37:g.67390468C>G	ENSP00000360065:p.Gly16Ala	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	42	41	0.97619	NM_207014	A8K9W5|B5MDT3|H7BY80|Q5VTI0|Q8N5G5|Q9H5R9|Q9UF44	Missense_Mutation	SNP	ENST00000371026.3	37	CCDS635.1	1790	0.8195970695970696	421	0.8556910569105691	313	0.8646408839779005	510	0.8916083916083916	546	0.7203166226912929	G	7.558	0.664105	0.14710	0.851339	0.731977	ENSG00000152763	ENST00000371026;ENST00000371023;ENST00000371022	T;T;T	0.59502	0.26;1.87;1.05	3.12	2.2	0.27929	.	0.802694	0.10227	N	0.700180	T	0.07143	0.0181	N	0.02011	-0.69	0.47341	P	6.089999999999707E-4	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.31696	-0.9934	9	0.02654	T	1	1.9447	4.4058	0.11409	0.1312:0.2349:0.6339:0.0	rs1886686;rs1886686	16;16	Q5TAD8;Q5VTH9	.;WDR78_HUMAN	A	16	ENSP00000360065:G16A;ENSP00000360062:G16A;ENSP00000360061:G16A	ENSP00000360061:G16A	G	-	2	0	WDR78	67163056	0.393000	0.25237	0.083000	0.20561	0.004000	0.04260	0.927000	0.28818	0.377000	0.24735	-0.216000	0.12614	GGA	C|0.209;G|0.791	0.791	strong		0.677	WDR78-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025404.1	NM_024763	
CHGB	1114	hgsc.bcm.edu	37	20	5903894	5903894	+	Silent	SNP	A	A	G	rs236153	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:5903894A>G	ENST00000378961.4	+	4	1308	c.1104A>G	c.(1102-1104)gaA>gaG	p.E368E		NM_001819.2	NP_001810.2	P05060	SCG1_HUMAN	chromogranin B (secretogranin 1)	368						extracellular region (GO:0005576)|secretory granule (GO:0030141)	hormone activity (GO:0005179)			breast(7)|kidney(2)|large_intestine(8)|lung(19)|ovary(1)|pancreas(2)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)	47						GAGGAAGTGAAGAATACAGGG	0.512													G|||	2580	0.515176	0.6573	0.5231	5008	,	,		20454	0.5288		0.3499	False		,,,				2504	0.4734				p.E368E		Atlas-SNP	.											.	CHGB	112	.	0			c.A1104G						PASS	.	G		2743,1663	505.2+/-366.1	871,1001,331	103.0	103.0	103.0		1104	-4.0	0.1	20	dbSNP_79	103	3092,5508	657.7+/-401.5	551,1990,1759	no	coding-synonymous	CHGB	NM_001819.2		1422,2991,2090	GG,GA,AA		35.9535,37.744,44.8639		368/678	5903894	5835,7171	2203	4300	6503	SO:0001819	synonymous_variant	1114	exon4			AAGTGAAGAATAC		CCDS13092.1	20p12.3	2013-09-19			ENSG00000089199	ENSG00000089199			1930	protein-coding gene	gene with protein product	"""secretogranin B"""	118920		SCG1		3608978	Standard	NM_001819		Approved		uc002wmg.3	P05060	OTTHUMG00000031821	ENST00000378961.4:c.1104A>G	20.37:g.5903894A>G		Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	27	13	0.481481	NM_001819	A8K021|Q59EU9|Q6IBS6|Q9BQV6|Q9UC25|Q9UJA6	Silent	SNP	ENST00000378961.4	37	CCDS13092.1																																																																																			A|0.533;G|0.467	0.467	strong		0.512	CHGB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077897.2	NM_001819	
ERMAP	114625	hgsc.bcm.edu	37	1	43296173	43296173	+	Silent	SNP	C	C	T	rs33950227	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:43296173C>T	ENST00000372517.2	+	3	298	c.54C>T	c.(52-54)ctC>ctT	p.L18L	ERMAP_ENST00000372514.3_Silent_p.L18L|ERMAP_ENST00000328249.3_5'UTR|ERMAP_ENST00000487556.1_Intron	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	112	0	0		WXS	Illumina HiSeq	Phase_I	102	102	1	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	
PLIN4	729359	hgsc.bcm.edu	37	19	4512613	4512613	+	Silent	SNP	T	T	G	rs74327986	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:4512613T>G	ENST00000301286.3	-	3	1316	c.1317A>C	c.(1315-1317)acA>acC	p.T439T		NM_001080400.1	NP_001073869.1	Q96Q06	PLIN4_HUMAN	perilipin 4	439	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						TGTCCACGCCTGTCTGGATGG	0.572													t|||	544	0.108626	0.261	0.0865	5008	,	,		21727	0.001		0.1004	False		,,,				2504	0.0378				p.T439T		Atlas-SNP	.											.	PLIN4	191	.	0			c.A1317C						PASS	.	T		689,3363		76,537,1413	143.0	154.0	150.0		1317	-9.5	0.0	19	dbSNP_132	150	638,7726		41,556,3585	no	coding-synonymous	PLIN4	NM_001080400.1		117,1093,4998	GG,GT,TT		7.6279,17.0039,10.6878		439/1358	4512613	1327,11089	2026	4182	6208	SO:0001819	synonymous_variant	729359	exon3			CACGCCTGTCTGG	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.1317A>C	19.37:g.4512613T>G		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	99	30	0.30303	NM_001080400	A6NEI2	Silent	SNP	ENST00000301286.3	37	CCDS45927.1																																																																																			T|0.916;G|0.084	0.084	strong		0.572	PLIN4-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395095.1	XM_170901	
DPT	1805	hgsc.bcm.edu	37	1	168683476	168683476	+	Silent	SNP	C	C	T	rs35449613	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:168683476C>T	ENST00000367817.3	-	2	503	c.414G>A	c.(412-414)agG>agA	p.R138R		NM_001937.4	NP_001928.2	Q07507	DERM_HUMAN	dermatopontin	138	2 X 53-55 AA tandem repeats.|3 X 6 AA repeats of D-R-[EQ]-W-[NQK]- [FY].				cell adhesion (GO:0007155)|collagen fibril organization (GO:0030199)|negative regulation of cell proliferation (GO:0008285)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)				kidney(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(2)	12	all_hematologic(923;0.208)					AATATGGGCACCTCTTGCTGT	0.567													C|||	149	0.0297524	0.0023	0.0245	5008	,	,		16666	0.001		0.0596	False		,,,				2504	0.0695				p.R138R		Atlas-SNP	.											.	DPT	29	.	0			c.G414A						PASS	.	C		53,4353	53.6+/-89.4	1,51,2151	83.0	74.0	77.0		414	-1.8	1.0	1	dbSNP_126	77	536,8064	148.3+/-203.6	18,500,3782	no	coding-synonymous	DPT	NM_001937.4		19,551,5933	TT,TC,CC		6.2326,1.2029,4.5287		138/202	168683476	589,12417	2203	4300	6503	SO:0001819	synonymous_variant	1805	exon2			TGGGCACCTCTTG	BC033736	CCDS1275.1	1q12-q23	2008-02-05			ENSG00000143196	ENSG00000143196			3011	protein-coding gene	gene with protein product		125597				8104875	Standard	NM_001937		Approved		uc001gfp.3	Q07507	OTTHUMG00000034554	ENST00000367817.3:c.414G>A	1.37:g.168683476C>T		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	66	33	0.5	NM_001937	A8K981|Q8N4R2|Q9UIX8	Silent	SNP	ENST00000367817.3	37	CCDS1275.1																																																																																			C|0.957;G|0.000;T|0.043	0.043	strong		0.567	DPT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083618.1	NM_001937	
SP110	3431	hgsc.bcm.edu	37	2	231042276	231042276	+	Missense_Mutation	SNP	A	A	G	rs1135791	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:231042276A>G	ENST00000358662.4	-	14	1646	c.1568T>C	c.(1567-1569)aTg>aCg	p.M523T	SP110_ENST00000540870.1_Missense_Mutation_p.M529T|SP110_ENST00000258381.6_Missense_Mutation_p.M523T|SP110_ENST00000338556.3_Missense_Mutation_p.M225T|SP110_ENST00000258382.5_Missense_Mutation_p.M523T|SP110_ENST00000392048.3_Missense_Mutation_p.M521T	NM_004509.3	NP_004500	Q9HB58	SP110_HUMAN	SP110 nuclear body protein	523	SAND. {ECO:0000255|PROSITE- ProRule:PRU00185}.		M -> T (in dbSNP:rs1135791). {ECO:0000269|PubMed:10913195, ECO:0000269|PubMed:16803959}.		regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|signal transducer activity (GO:0004871)|zinc ion binding (GO:0008270)			breast(4)|endometrium(3)|large_intestine(5)|lung(8)|ovary(2)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	29		Renal(207;0.0112)|all_lung(227;0.0223)|Lung NSC(271;0.0983)|all_hematologic(139;0.104)|Acute lymphoblastic leukemia(138;0.169)		Epithelial(121;2.61e-12)|all cancers(144;6.39e-10)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.0097)		TCCTAGGGTCATTCCTTCACA	0.423													G|||	1627	0.32488	0.208	0.3545	5008	,	,		20126	0.1677		0.496	False		,,,				2504	0.4479				p.M529T		Atlas-SNP	.											.	SP110	105	.	0			c.T1586C						PASS	.	G	THR/MET,THR/MET,THR/MET,THR/MET	1124,3282	717.8+/-408.8	128,868,1207	370.0	347.0	355.0		1586,1568,1568,1568	-0.8	0.0	2	dbSNP_86	355	4306,4294	577.4+/-390.5	1110,2086,1104	yes	missense,missense,missense,missense	SP110	NM_001185015.1,NM_004509.3,NM_004510.3,NM_080424.2	81,81,81,81	1238,2954,2311	GG,GA,AA		49.9302,25.5107,41.75	benign,benign,benign,benign	529/556,523/690,523/550,523/714	231042276	5430,7576	2203	4300	6503	SO:0001583	missense	3431	exon15			AGGGTCATTCCTT	L22343	CCDS2474.1, CCDS2475.1, CCDS2476.1, CCDS54435.1	2q37.1	2014-09-17	2001-12-19	2001-12-20	ENSG00000135899	ENSG00000135899			5401	protein-coding gene	gene with protein product		604457	"""interferon-induced protein 41, 30kD"""	IFI41, IFI75		7693701, 10388521	Standard	NM_080424		Approved		uc002vqg.3	Q9HB58	OTTHUMG00000133204	ENST00000358662.4:c.1568T>C	2.37:g.231042276A>G	ENSP00000351488:p.Met523Thr	Somatic	336	0	0		WXS	Illumina HiSeq	Phase_I	291	168	0.57732	NM_001185015	B4DVI4|F5H1M1|Q14976|Q14977|Q53TG2|Q8WUZ6|Q9HCT8	Missense_Mutation	SNP	ENST00000358662.4	37	CCDS2474.1	738	0.33791208791208793	120	0.24390243902439024	146	0.40331491712707185	97	0.16958041958041958	375	0.4947229551451187	G	3.063	-0.192867	0.06259	0.255107	0.500698	ENSG00000135899	ENST00000258381;ENST00000358662;ENST00000392048;ENST00000258382;ENST00000540870;ENST00000338556	T;T;T;T;T;T	0.70164	-0.46;-0.46;-0.46;-0.46;-0.46;-0.46	4.61	-0.782	0.10961	SAND domain-like (2);SAND domain (3);	0.977573	0.08310	N	0.965581	T	0.00012	0.0000	N	0.02247	-0.625	0.80722	P	0.0	B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0	B;B;B;B;B	0.01281	0.0;0.0;0.0;0.0;0.0	T	0.41928	-0.9481	9	0.21014	T	0.42	.	0.2939	0.00262	0.2799:0.1726:0.15:0.3975	rs1135791;rs1804027;rs3198703;rs11556889;rs17327944;rs59171471;rs1135791	521;225;529;523;523	G5E9C0;E7ER70;F5H1M1;Q9HB58;Q9HB58-6	.;.;.;SP110_HUMAN;.	T	523;523;521;523;529;225	ENSP00000258381:M523T;ENSP00000351488:M523T;ENSP00000375902:M521T;ENSP00000258382:M523T;ENSP00000439558:M529T;ENSP00000344049:M225T	ENSP00000258381:M523T	M	-	2	0	SP110	230750520	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.527000	0.06200	-0.498000	0.06632	-1.974000	0.00461	ATG	A|0.640;G|0.360	0.360	strong		0.423	SP110-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000332414.1	NM_080424	
HTT	3064	hgsc.bcm.edu	37	4	3189547	3189547	+	Missense_Mutation	SNP	C	C	A	rs363125	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:3189547C>A	ENST00000355072.5	+	39	5304	c.5159C>A	c.(5158-5160)aCt>aAt	p.T1720N		NM_002111.6	NP_002102	P42858	HD_HUMAN	huntingtin	1720			T -> N (in dbSNP:rs363125).		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)		GGGGACAGTACTTCAACGCTA	0.373													A|||	947	0.189097	0.4834	0.1225	5008	,	,		20071	0.0089		0.1083	False		,,,				2504	0.1074				p.T1720N		Atlas-SNP	.											.	HTT	221	.	0			c.C5159A						PASS	.	A	ASN/THR	1484,2210		308,868,671	119.0	111.0	113.0		5159	-11.3	0.0	4	dbSNP_79	113	960,7248		44,872,3188	yes	missense	HTT	NM_002111.6	65	352,1740,3859	AA,AC,CC		11.6959,40.1733,20.5344	benign	1720/3143	3189547	2444,9458	1847	4104	5951	SO:0001583	missense	3064	exon39			ACAGTACTTCAAC	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.5159C>A	4.37:g.3189547C>A	ENSP00000347184:p.Thr1720Asn	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	74	38	0.513514	NM_002111	Q9UQB7	Missense_Mutation	SNP	ENST00000355072.5	37	CCDS43206.1	362	0.16575091575091574	234	0.47560975609756095	42	0.11602209944751381	2	0.0034965034965034965	84	0.11081794195250659	A	1.789	-0.479891	0.04383	0.401733	0.116959	ENSG00000197386	ENST00000355072	T	0.04706	3.57	5.66	-11.3	0.00108	.	0.988029	0.08277	N	0.970573	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	0.48234	-0.9053	9	0.17369	T	0.5	.	8.4339	0.32775	0.177:0.4818:0.2725:0.0687	rs363125;rs363125	1720	P42858	HD_HUMAN	N	1720	ENSP00000347184:T1720N	ENSP00000347184:T1720N	T	+	2	0	HTT	3159345	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-1.105000	0.03323	-2.325000	0.00638	-0.256000	0.11100	ACT	C|0.812;A|0.188	0.188	strong		0.373	HTT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358234.2	NM_002111	
ZFAT	57623	hgsc.bcm.edu	37	8	135622851	135622851	+	Missense_Mutation	SNP	G	G	A	rs75596750	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:135622851G>A	ENST00000377838.3	-	4	670	c.496C>T	c.(496-498)Cgg>Tgg	p.R166W	ZFAT_ENST00000520214.1_Missense_Mutation_p.R154W|ZFAT_ENST00000523399.1_Intron|ZFAT_ENST00000520356.1_Missense_Mutation_p.R154W|ZFAT_ENST00000520727.1_Missense_Mutation_p.R154W|ZFAT_ENST00000429442.2_Missense_Mutation_p.R154W	NM_001174157.1|NM_020863.3	NP_001167628.1|NP_065914.2	Q9P243	ZFAT_HUMAN	zinc finger and AT hook domain containing	166					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)			GCTTTTTCCCGATCATCTTCC	0.448													G|||	2	0.000399361	0.0	0.0	5008	,	,		23535	0.0		0.002	False		,,,				2504	0.0				p.R166W		Atlas-SNP	.											.	ZFAT	265	.	0			c.C496T						PASS	.	G	TRP/ARG,TRP/ARG,,TRP/ARG,TRP/ARG	1,3813		0,1,1906	179.0	166.0	170.0		460,460,,460,496	4.4	1.0	8	dbSNP_132	170	7,8231		0,7,4112	yes	missense,missense,intron,missense,missense	ZFAT	NM_001029939.3,NM_001167583.2,NM_001174157.1,NM_001174158.1,NM_020863.3	101,101,,101,101	0,8,6018	AA,AG,GG		0.085,0.0262,0.0664	probably-damaging,probably-damaging,,probably-damaging,probably-damaging	154/1232,154/1232,,154/1146,166/1244	135622851	8,12044	1907	4119	6026	SO:0001583	missense	57623	exon4			TTTCCCGATCATC	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.496C>T	8.37:g.135622851G>A	ENSP00000367069:p.Arg166Trp	Somatic	309	0	0		WXS	Illumina HiSeq	Phase_I	286	62	0.216783	NM_020863	B7ZL15|E9PER3|Q3MIM5|Q6PJ01|Q75PJ6|Q75PJ7|Q75PJ9|Q86X64	Missense_Mutation	SNP	ENST00000377838.3	37	CCDS47924.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	20.3	3.967099	0.74131	2.62E-4	8.5E-4	ENSG00000066827	ENST00000520356;ENST00000520727;ENST00000429442;ENST00000377838;ENST00000520214;ENST00000318135;ENST00000398946;ENST00000522257	T;T;T;T;T;T	0.54279	2.82;2.75;2.76;2.74;2.75;0.58	5.36	4.43	0.53597	.	0.087086	0.48286	D	0.000185	T	0.60392	0.2265	L	0.34521	1.04	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.965;0.999;0.998	T	0.62478	-0.6846	10	0.66056	D	0.02	-7.6436	12.0426	0.53462	0.0:0.0:0.7035:0.2965	.	154;154;166	E9PBN4;Q9P243-3;Q9P243	.;.;ZFAT_HUMAN	W	154;154;154;166;154;154;154;104	ENSP00000427879:R154W;ENSP00000427831:R154W;ENSP00000394501:R154W;ENSP00000367069:R166W;ENSP00000428483:R154W;ENSP00000429983:R104W	ENSP00000326997:R154W	R	-	1	2	ZFAT	135692033	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	3.592000	0.53993	2.498000	0.84270	0.655000	0.94253	CGG	G|0.999;A|0.001	0.001	strong		0.448	ZFAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378272.1	NM_001029939	
KIAA1217	56243	hgsc.bcm.edu	37	10	24669877	24669877	+	Missense_Mutation	SNP	C	C	G	rs17506606	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:24669877C>G	ENST00000376454.3	+	3	464	c.434C>G	c.(433-435)gCt>gGt	p.A145G	KIAA1217_ENST00000430453.2_Missense_Mutation_p.A66G|KIAA1217_ENST00000376452.3_Missense_Mutation_p.A145G|KIAA1217_ENST00000458595.1_Missense_Mutation_p.A145G|KIAA1217_ENST00000376462.1_Missense_Mutation_p.A65G	NM_019590.3	NP_062536.2	Q5T5P2	SKT_HUMAN	KIAA1217	145			A -> G (in dbSNP:rs17506606).		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						GAGACGTCCGCTGATTCTTTG	0.547													C|||	519	0.103634	0.0113	0.1196	5008	,	,		14086	0.002		0.2614	False		,,,				2504	0.1595				p.A145G		Atlas-SNP	.											KIAA1217,caecum,carcinoma,+1,1	KIAA1217	235	1	0			c.C434G						PASS	.	C	GLY/ALA,GLY/ALA,GLY/ALA	231,4175	136.9+/-172.8	5,221,1977	67.0	70.0	69.0		194,434,434	-0.2	0.0	10	dbSNP_123	69	2237,6363	380.1+/-339.5	297,1643,2360	yes	missense,missense,missense	KIAA1217	NM_001098500.1,NM_001098501.1,NM_019590.3	60,60,60	302,1864,4337	GG,GC,CC		26.0116,5.2429,18.9759	benign,benign,benign	65/1265,145/1310,145/1944	24669877	2468,10538	2203	4300	6503	SO:0001583	missense	56243	exon3			CGTCCGCTGATTC	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.434C>G	10.37:g.24669877C>G	ENSP00000365637:p.Ala145Gly	Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	60	23	0.383333	NM_019590	A5LHW9|A6NLF3|A6PVQ5|A6PVQ6|A6PVQ7|B9EGK4|Q4KMG4|Q5T5P3|Q5T7H3|Q6MZZ6|Q6ZUI4|Q8WV45|Q9NSR2|Q9ULK3	Missense_Mutation	SNP	ENST00000376454.3	37	CCDS31165.1	271	0.12408424908424909	10	0.02032520325203252	55	0.15193370165745856	1	0.0017482517482517483	205	0.2704485488126649	C	10.81	1.455385	0.26161	0.052429	0.260116	ENSG00000120549	ENST00000376462;ENST00000376456;ENST00000458595;ENST00000376454;ENST00000376452;ENST00000430453	T;D;T;T;T;T	0.94793	-0.21;-3.52;-0.21;-0.21;-0.21;-0.21	5.54	-0.211	0.13172	.	0.377421	0.29932	N	0.010838	T	0.00073	0.0002	N	0.21282	0.65	0.38500	P	0.05179999999999996	B;B;B;B	0.10296	0.003;0.002;0.001;0.0	B;B;B;B	0.11329	0.002;0.006;0.002;0.0	T	0.16482	-1.0401	9	0.20046	T	0.44	.	15.5179	0.75840	0.0:0.735:0.1778:0.0872	rs17506606;rs56583113;rs17506606	145;145;145;145	Q5T5P2-7;A6NLF3;Q5T5P2;Q5T5P2-2	.;.;SKT_HUMAN;.	G	65;145;145;145;145;66	ENSP00000365645:A65G;ENSP00000365639:A145G;ENSP00000392625:A145G;ENSP00000365637:A145G;ENSP00000365635:A145G;ENSP00000389680:A66G	ENSP00000365635:A145G	A	+	2	0	KIAA1217	24709883	0.640000	0.27243	0.008000	0.14137	0.498000	0.33706	1.095000	0.30964	-0.005000	0.14395	-0.282000	0.10007	GCT	C|0.845;G|0.155	0.155	strong		0.547	KIAA1217-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047223.2	NM_019590	
TPM1	7168	hgsc.bcm.edu	37	15	63351840	63351840	+	Silent	SNP	C	C	A	rs1071646	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:63351840C>A	ENST00000403994.3	+	4	533	c.453C>A	c.(451-453)gcC>gcA	p.A151A	TPM1_ENST00000559397.1_Silent_p.A151A|TPM1_ENST00000267996.7_Silent_p.A151A|TPM1_ENST00000317516.7_Silent_p.A115A|TPM1_ENST00000559281.1_Silent_p.A115A|TPM1_ENST00000357980.4_Silent_p.A193A|TPM1_ENST00000288398.6_Silent_p.A151A|TPM1_ENST00000404484.4_Silent_p.A115A|TPM1_ENST00000358278.3_Silent_p.A151A|TPM1_ENST00000334895.5_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	68	0	0		WXS	Illumina HiSeq	Phase_I	53	53	1	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	
UNC13A	23025	hgsc.bcm.edu	37	19	17749893	17749893	+	Splice_Site	SNP	G	G	A	rs200328448	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:17749893G>A	ENST00000519716.2	-	25	3079	c.3080C>T	c.(3079-3081)cCg>cTg	p.P1027L	UNC13A_ENST00000550896.1_Splice_Site_p.P1025L|UNC13A_ENST00000552293.1_Splice_Site_p.P1027L|UNC13A_ENST00000252773.7_Splice_Site_p.P1027L|UNC13A_ENST00000551649.1_Splice_Site_p.P1027L|UNC13A_ENST00000428389.2_Splice_Site_p.P1115L	NM_001080421.2	NP_001073890.2	Q9UPW8	UN13A_HUMAN	unc-13 homolog A (C. elegans)	1027					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						GAGTCTCACCGGGTCTGTCTG	0.517													G|||	3	0.000599042	0.0	0.0029	5008	,	,		16830	0.0		0.001	False		,,,				2504	0.0				p.P1027L		Atlas-SNP	.											UNC13A_ENST00000519716,NS,carcinoma,0,2	UNC13A	299	2	0			c.C3080T						PASS	.	G	LEU/PRO	7,3979		0,7,1986	27.0	28.0	28.0		3080	1.0	0.0	19		28	54,8314		0,54,4130	yes	missense-near-splice	UNC13A	NM_001080421.2	98	0,61,6116	AA,AG,GG		0.6453,0.1756,0.4938	possibly-damaging	1027/1704	17749893	61,12293	1993	4184	6177	SO:0001630	splice_region_variant	23025	exon24			CTCACCGGGTCTG	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.3081+1C>T	19.37:g.17749893G>A		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	67	39	0.58209	NM_001080421	E5RHY9	Missense_Mutation	SNP	ENST00000519716.2	37	CCDS46013.2	.	.	.	.	.	.	.	.	.	.	G	11.97	1.796712	0.31777	0.001756	0.006453	ENSG00000130477	ENST00000519716;ENST00000428389;ENST00000252773;ENST00000551649;ENST00000552293;ENST00000550896	T;T;T;T;T;T	0.81247	-1.45;-1.47;-1.45;-1.32;-1.33;-1.46	3.39	1.0	0.19881	Calcium-dependent secretion activator (1);	0.182504	0.35262	U	0.003331	T	0.57873	0.2083	L	0.34521	1.04	0.58432	D	0.999999	P	0.48089	0.905	B	0.36808	0.233	T	0.60525	-0.7246	10	0.66056	D	0.02	.	9.4402	0.38664	0.0:0.0:0.6171:0.3828	.	1027	Q9UPW8	UN13A_HUMAN	L	1027;1115;1027;1027;1027;1025	ENSP00000429562:P1027L;ENSP00000400409:P1115L;ENSP00000252773:P1027L;ENSP00000447236:P1027L;ENSP00000447572:P1027L;ENSP00000446831:P1025L	ENSP00000252773:P1027L	P	-	2	0	UNC13A	17610893	1.000000	0.71417	0.020000	0.16555	0.803000	0.45373	7.588000	0.82629	0.066000	0.16515	0.478000	0.44815	CCG	G|0.996;A|0.004	0.004	strong		0.517	UNC13A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000376169.2	XM_038604	Missense_Mutation
C4orf36	132989	hgsc.bcm.edu	37	4	87809025	87809025	+	Missense_Mutation	SNP	T	T	C	rs28664715	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:87809025T>C	ENST00000473559.1	-	7	905	c.242A>G	c.(241-243)tAt>tGt	p.Y81C	C4orf36_ENST00000295898.3_Missense_Mutation_p.Y81C|C4orf36_ENST00000503001.1_5'Flank			Q96KX1	CD036_HUMAN	chromosome 4 open reading frame 36	81										breast(1)|kidney(1)|lung(1)|prostate(1)	4		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.00141)		CTTCACTTCATACTCCCTTTC	0.373													T|||	188	0.0375399	0.0083	0.0519	5008	,	,		22453	0.0		0.1004	False		,,,				2504	0.0409				p.Y81C		Atlas-SNP	.											.	C4orf36	10	.	0			c.A242G						PASS	.	T	CYS/TYR	80,4326	69.2+/-107.0	1,78,2124	79.0	74.0	76.0		242	1.1	1.0	4	dbSNP_125	76	775,7825	183.3+/-231.6	36,703,3561	yes	missense	C4orf36	NM_144645.3	194	37,781,5685	CC,CT,TT		9.0116,1.8157,6.5739	possibly-damaging	81/118	87809025	855,12151	2203	4300	6503	SO:0001583	missense	132989	exon4			ACTTCATACTCCC	BC016746	CCDS3615.1	4q21.3	2008-02-05			ENSG00000163633	ENSG00000163633			28386	protein-coding gene	gene with protein product						12477932	Standard	NM_144645		Approved	MGC26744	uc003hqe.4	Q96KX1	OTTHUMG00000130597	ENST00000473559.1:c.242A>G	4.37:g.87809025T>C	ENSP00000420949:p.Tyr81Cys	Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	94	94	1	NM_144645		Missense_Mutation	SNP	ENST00000473559.1	37	CCDS3615.1	105	0.04807692307692308	6	0.012195121951219513	20	0.055248618784530384	0	0.0	79	0.10422163588390501	T	14.49	2.549723	0.45383	0.018157	0.090116	ENSG00000163633	ENST00000295898;ENST00000473559;ENST00000506308;ENST00000504008	T;T;T;T	0.44083	0.93;0.93;0.93;0.93	5.23	1.14	0.20703	.	0.707713	0.12912	N	0.428898	T	0.00695	0.0023	L	0.29908	0.895	0.32622	P	0.5232479999999999	B	0.20261	0.043	B	0.23018	0.043	T	0.10132	-1.0643	9	0.87932	D	0	-2.0824	4.1319	0.10152	0.3133:0.0873:0.0:0.5994	rs28664715	81	Q96KX1	CD036_HUMAN	C	81	ENSP00000295898:Y81C;ENSP00000420949:Y81C;ENSP00000421141:Y81C;ENSP00000422720:Y81C	ENSP00000295898:Y81C	Y	-	2	0	C4orf36	88028049	0.533000	0.26354	0.997000	0.53966	0.473000	0.32948	0.163000	0.16520	0.424000	0.26061	-0.441000	0.05720	TAT	T|0.938;C|0.062	0.062	strong		0.373	C4orf36-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253045.2	NM_144645	
NACC2	138151	hgsc.bcm.edu	37	9	138905136	138905136	+	Silent	SNP	C	C	T	rs2280486	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:138905136C>T	ENST00000371753.1	-	4	1222	c.1164G>A	c.(1162-1164)acG>acA	p.T388T	NACC2_ENST00000277554.2_Silent_p.T388T|NACC2_ENST00000467669.1_5'Flank			Q96BF6	NACC2_HUMAN	NACC family member 2, BEN and BTB (POZ) domain containing	388	BEN. {ECO:0000255|PROSITE- ProRule:PRU00784}.				cellular protein complex localization (GO:0034629)|histone deacetylation (GO:0016575)|negative regulation of cell proliferation (GO:0008285)|negative regulation of G1/S transition of mitotic cell cycle by negative regulation of transcription from RNA polymerase II promoter (GO:1900477)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902231)|posttranscriptional regulation of gene expression (GO:0010608)|protein homooligomerization (GO:0051260)|transcription from RNA polymerase II promoter (GO:0006366)	nuclear body (GO:0016604)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	histone deacetylase activity (GO:0004407)|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 negative regulation of transcription (GO:0001078)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)			endometrium(2)|kidney(1)|lung(1)|urinary_tract(1)	5						TGTTGGCCAGCGTGTTCCTGG	0.672													C|||	2325	0.464257	0.5469	0.4741	5008	,	,		11939	0.4494		0.4284	False		,,,				2504	0.3978				p.T388T		Atlas-SNP	.											.	NACC2	16	.	0			c.G1164A						PASS	.	C		2254,2150	576.4+/-384.2	586,1082,534	43.0	47.0	46.0		1164	-9.9	0.6	9	dbSNP_100	46	3615,4977	512.0+/-377.8	765,2085,1446	no	coding-synonymous	NACC2	NM_144653.4		1351,3167,1980	TT,TC,CC		42.074,48.8193,45.16		388/588	138905136	5869,7127	2202	4296	6498	SO:0001819	synonymous_variant	138151	exon5			GGCCAGCGTGTTC	BC015649	CCDS6993.1	9q34.3	2013-01-09	2008-10-03	2008-10-03	ENSG00000148411	ENSG00000148411		"""BEN domain containing"", ""BTB/POZ domain containing"""	23846	protein-coding gene	gene with protein product	"""BEN domain containing 9"""	615786	"""BTB (POZ) domain containing 14A"""	BTBD14A		12477932	Standard	NM_144653		Approved	MGC23427, BEND9, BTBD31	uc004cgv.4	Q96BF6	OTTHUMG00000020921	ENST00000371753.1:c.1164G>A	9.37:g.138905136C>T		Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	149	76	0.510067	NM_144653		Silent	SNP	ENST00000371753.1	37	CCDS6993.1																																																																																			C|0.543;T|0.457	0.457	strong		0.672	NACC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055040.1	NM_144653	
DDR1	780	hgsc.bcm.edu	37	6	30862423	30862423	+	Silent	SNP	C	C	T	rs1264319	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:30862423C>T	ENST00000324771.8	+	13	2036	c.1488C>T	c.(1486-1488)tcC>tcT	p.S496S	DDR1_ENST00000418800.2_Silent_p.S496S|DDR1_ENST00000376568.3_Silent_p.S496S|DDR1_ENST00000376570.4_Silent_p.S496S|DDR1_ENST00000376569.3_Silent_p.S496S|DDR1_ENST00000452441.1_Silent_p.S496S|DDR1_ENST00000513240.1_Silent_p.S496S|DDR1_ENST00000361741.4_Missense_Mutation_p.P200L|DDR1_ENST00000376567.2_Silent_p.S496S|DDR1_ENST00000376575.3_Silent_p.S496S|DDR1_ENST00000454612.2_Silent_p.S496S|DDR1_ENST00000446312.1_3'UTR|DDR1_ENST00000508312.1_Silent_p.S514S			Q08345	DDR1_HUMAN	discoidin domain receptor tyrosine kinase 1	496	Gly/Pro-rich.		S -> A (in a lung squamous cell carcinoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		branching involved in mammary gland duct morphogenesis (GO:0060444)|cell adhesion (GO:0007155)|collagen-activated tyrosine kinase receptor signaling pathway (GO:0038063)|ear development (GO:0043583)|embryo implantation (GO:0007566)|extracellular matrix organization (GO:0030198)|lactation (GO:0007595)|mammary gland alveolus development (GO:0060749)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine autophosphorylation (GO:0038083)|protein autophosphorylation (GO:0046777)|regulation of cell growth (GO:0001558)|regulation of cell-matrix adhesion (GO:0001952)|regulation of extracellular matrix disassembly (GO:0010715)|smooth muscle cell migration (GO:0014909)|smooth muscle cell-matrix adhesion (GO:0061302)|wound healing, spreading of cells (GO:0044319)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|collagen binding (GO:0005518)|metal ion binding (GO:0046872)|protein tyrosine kinase collagen receptor activity (GO:0038062)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			central_nervous_system(3)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(14)|ovary(1)|prostate(1)|skin(1)	29					Imatinib(DB00619)	CGCCCCACTCCGCTCCCTGTG	0.582													C|||	642	0.128195	0.177	0.0951	5008	,	,		19738	0.0585		0.162	False		,,,				2504	0.1227				p.P469L		Atlas-SNP	.											.	DDR1	213	.	0			c.C1406T						PASS	.	C	,LEU/PRO,,,,	858,3548	335.7+/-304.0	90,678,1435	75.0	75.0	75.0		1488,1406,1542,1488,1488,1488	2.7	1.0	6	dbSNP_87	75	1699,6901	311.0+/-310.2	162,1375,2763	yes	coding-synonymous,missense,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	DDR1	NM_001202521.1,NM_001202522.1,NM_001202523.1,NM_001954.4,NM_013993.2,NM_013994.2	,98,,,,	252,2053,4198	TT,TC,CC		19.7558,19.4734,19.6602	,,,,,	496/509,469/768,514/895,496/877,496/914,496/920	30862423	2557,10449	2203	4300	6503	SO:0001819	synonymous_variant	780	exon10			CCACTCCGCTCCC	X99031	CCDS4690.1, CCDS34385.1, CCDS47396.1, CCDS56411.1, CCDS75419.1	6p21.33	2010-02-17	2008-01-23		ENSG00000204580	ENSG00000204580	2.7.10.1	"""CD molecules"""	2730	protein-coding gene	gene with protein product		600408	"""discoidin domain receptor family, member 1"""	NTRK4, PTK3A, NEP, CAK, EDDR1		7789998	Standard	NM_001954		Approved	RTK6, CD167	uc003nrv.3	Q08345	OTTHUMG00000031236	ENST00000324771.8:c.1488C>T	6.37:g.30862423C>T		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	60	26	0.433333	NM_001202522	B5A975|B5A976|B7Z2K0|Q14196|Q16562|Q2L6H3|Q4LE50|Q5ST11|Q5ST12|Q6NSK4|Q9UD35|Q9UD36|Q9UD37|Q9UD86|Q9UDL2	Missense_Mutation	SNP	ENST00000324771.8	37	CCDS34385.1	341|341	0.15613553113553114|0.15613553113553114	127|127	0.258130081300813|0.258130081300813	44|44	0.12154696132596685|0.12154696132596685	39|39	0.06818181818181818|0.06818181818181818	131|131	0.17282321899736147|0.17282321899736147	C|C	7.986|7.986	0.752226|0.752226	0.15778|0.15778	0.194734|0.194734	0.197558|0.197558	ENSG00000204580|ENSG00000204580	ENST00000417521;ENST00000361741;ENST00000451954|ENST00000514434	T;T|.	0.79454|.	-1.19;-1.27|.	5.24|5.24	2.73|2.73	0.32206|0.32206	.|.	.|.	.|.	.|.	.|.	T|T	0.26268|0.26268	0.0641|0.0641	.|.	.|.	.|.	0.26362|0.26362	P|P	0.9770315|0.9770315	B|.	0.02656|.	0.0|.	B|.	0.01281|.	0.0|.	T|T	0.08207|0.08207	-1.0733|-1.0733	7|3	0.20519|.	T|.	0.43|.	.|.	7.4808|7.4808	0.27404|0.27404	0.0:0.1817:0.0:0.8183|0.0:0.1817:0.0:0.8183	rs1264319;rs1264319|rs1264319;rs1264319	265|.	A2ABM8|.	.|.	L|C	265;200;152|25	ENSP00000398682:P265L;ENSP00000354844:P200L|.	ENSP00000354844:P200L|.	P|R	+|+	2|1	0|0	DDR1|DDR1	30970402|30970402	0.976000|0.976000	0.34144|0.34144	1.000000|1.000000	0.80357|0.80357	0.986000|0.986000	0.74619|0.74619	0.405000|0.405000	0.21015|0.21015	0.837000|0.837000	0.34925|0.34925	-0.455000|-0.455000	0.05494|0.05494	CCG|CGC	C|0.820;T|0.180	0.180	strong		0.582	DDR1-005	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076494.3	NM_013994	
ANO7	50636	hgsc.bcm.edu	37	2	242157228	242157228	+	Silent	SNP	G	G	T	rs78605785	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	90	0	0		WXS	Illumina HiSeq	Phase_I	91	53	0.582418	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	
OR10H1	26539	hgsc.bcm.edu	37	19	15918380	15918380	+	Silent	SNP	C	C	T	rs28426969	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:15918380C>T	ENST00000334920.2	-	1	556	c.468G>A	c.(466-468)ggG>ggA	p.G156G		NM_013940.2	NP_039228.1	Q9Y4A9	O10H1_HUMAN	olfactory receptor, family 10, subfamily H, member 1	156						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.G156G(1)		cervix(1)|endometrium(3)|kidney(4)|large_intestine(6)|lung(8)|ovary(4)|skin(2)|urinary_tract(1)	29						TCACCACCATCCCCATGACCA	0.622													.|||	1585	0.316494	0.5257	0.3386	5008	,	,		20451	0.0635		0.3857	False		,,,				2504	0.2076				p.G156G		Atlas-SNP	.											OR10H1,NS,carcinoma,0,1	OR10H1	59	1	1	Substitution - coding silent(1)	ovary(1)	c.G468A						PASS	.	C		2184,2222		553,1078,572	95.0	77.0	83.0		468	2.4	0.1	19	dbSNP_125	83	2991,5609		495,2001,1804	no	coding-synonymous	OR10H1	NM_013940.2		1048,3079,2376	TT,TC,CC		34.7791,49.5688,39.7893		156/319	15918380	5175,7831	2203	4300	6503	SO:0001819	synonymous_variant	26539	exon1			CACCATCCCCATG	AC004510	CCDS12335.1	19p13.1	2012-08-09				ENSG00000186723		"""GPCR / Class A : Olfactory receptors"""	8172	protein-coding gene	gene with protein product							Standard	NM_013940		Approved		uc002nbq.2	Q9Y4A9		ENST00000334920.2:c.468G>A	19.37:g.15918380C>T		Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	153	86	0.562092	NM_013940	Q6IFQ2|Q96R59	Silent	SNP	ENST00000334920.2	37	CCDS12335.1																																																																																			C|0.618;T|0.382	0.382	strong		0.622	OR10H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460364.1		
SH3BP4	23677	hgsc.bcm.edu	37	2	235951183	235951183	+	Silent	SNP	G	G	A	rs140262787	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:235951183G>A	ENST00000409212.1	+	4	2277	c.1770G>A	c.(1768-1770)cgG>cgA	p.R590R	SH3BP4_ENST00000344528.4_Silent_p.R590R|SH3BP4_ENST00000392011.2_Silent_p.R590R			Q9P0V3	SH3B4_HUMAN	SH3-domain binding protein 4	590					cellular response to amino acid stimulus (GO:0071230)|endocytosis (GO:0006897)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of GTPase activity (GO:0034260)|negative regulation of TOR signaling (GO:0032007)|positive regulation of autophagy (GO:0010508)|protein localization to lysosome (GO:0061462)|regulation of catalytic activity (GO:0050790)	coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	GDP-dissociation inhibitor activity (GO:0005092)|identical protein binding (GO:0042802)|Ras GTPase binding (GO:0017016)			central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(6)|lung(13)|ovary(4)|prostate(2)|skin(6)|stomach(3)|urinary_tract(2)	44		Breast(86;0.000332)|Renal(207;0.00339)|all_lung(227;0.00458)|all_hematologic(139;0.0296)|Lung NSC(271;0.0419)		Epithelial(121;7.66e-20)|BRCA - Breast invasive adenocarcinoma(100;0.000402)|Lung(119;0.00299)|LUSC - Lung squamous cell carcinoma(224;0.00645)|GBM - Glioblastoma multiforme(43;0.237)		TCACGCTGCGGGTTCAGGTGA	0.587													G|||	39	0.00778754	0.0	0.0029	5008	,	,		16535	0.0		0.0149	False		,,,				2504	0.0225				p.R590R		Atlas-SNP	.											SH3BP4,NS,carcinoma,+2,1	SH3BP4	109	1	0			c.G1770A						PASS	.	G		8,4398	14.3+/-33.2	0,8,2195	60.0	64.0	63.0		1770	5.1	1.0	2	dbSNP_134	63	92,8508	51.5+/-111.7	1,90,4209	no	coding-synonymous	SH3BP4	NM_014521.2		1,98,6404	AA,AG,GG		1.0698,0.1816,0.7689		590/964	235951183	100,12906	2203	4300	6503	SO:0001819	synonymous_variant	23677	exon4			GCTGCGGGTTCAG	AF147747	CCDS2513.1	2q37.1-q37.2	2008-05-15			ENSG00000130147	ENSG00000130147			10826	protein-coding gene	gene with protein product		605611				10644451	Standard	NM_014521		Approved		uc002vvp.3	Q9P0V3	OTTHUMG00000133292	ENST00000409212.1:c.1770G>A	2.37:g.235951183G>A		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	73	38	0.520548	NM_014521	O95082|Q309A3|Q53QD0|Q53TD1	Silent	SNP	ENST00000409212.1	37	CCDS2513.1																																																																																			G|0.992;A|0.008	0.008	strong		0.587	SH3BP4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329763.1		
KIAA1143	57456	hgsc.bcm.edu	37	3	44794881	44794881	+	Missense_Mutation	SNP	A	A	C	rs112645395	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:44794881A>C	ENST00000296121.4	-	3	476	c.417T>G	c.(415-417)atT>atG	p.I139M	KIAA1143_ENST00000484437.1_5'UTR	NM_020696.3	NP_065747.1	Q96AT1	K1143_HUMAN	KIAA1143	139			I -> M (in dbSNP:rs3853404). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.							NS(1)|breast(1)|central_nervous_system(1)|large_intestine(1)|stomach(1)	5				BRCA - Breast invasive adenocarcinoma(193;0.00847)|KIRC - Kidney renal clear cell carcinoma(197;0.0465)|Kidney(197;0.0582)		TACTATTTTTAATTTGTTTTT	0.299													A|||	190	0.0379393	0.0083	0.0764	5008	,	,		15712	0.0446		0.0467	False		,,,				2504	0.0348				p.I139M		Atlas-SNP	.											.	KIAA1143	10	.	0			c.T417G						PASS	.	A	MET/ILE	68,4336		0,68,2134	69.0	77.0	74.0		417	-10.3	0.4	3	dbSNP_132	74	335,8259		5,325,3967	no	missense	KIAA1143	NM_020696.3	10	5,393,6101	CC,CA,AA		3.8981,1.5441,3.1005	benign	139/155	44794881	403,12595	2202	4297	6499	SO:0001583	missense	57456	exon3			ATTTTTAATTTGT	AB032969	CCDS2721.1	3p21.31	2005-08-15			ENSG00000163807	ENSG00000163807			29198	protein-coding gene	gene with protein product						10574461	Standard	NM_020696		Approved		uc011bac.2	Q96AT1	OTTHUMG00000133088	ENST00000296121.4:c.417T>G	3.37:g.44794881A>C	ENSP00000296121:p.Ile139Met	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	112	50	0.446429	NM_020696	A8K0I4|Q96HJ8|Q9ULS7	Missense_Mutation	SNP	ENST00000296121.4	37	CCDS2721.1	87	0.03983516483516483	4	0.008130081300813009	23	0.06353591160220995	22	0.038461538461538464	38	0.05013192612137203	A	14.05	2.420633	0.42918	0.015441	0.038981	ENSG00000163807	ENST00000296121	T	0.42900	0.96	5.17	-10.3	0.00346	.	0.373750	0.30483	N	0.009523	T	0.05318	0.0141	L	0.53249	1.67	0.24096	N	0.995892	P	0.35908	0.527	P	0.44518	0.452	T	0.44143	-0.9347	10	0.56958	D	0.05	-2.9024	14.2241	0.65848	0.1135:0.0:0.1644:0.7221	.	139	Q96AT1	K1143_HUMAN	M	139	ENSP00000296121:I139M	ENSP00000296121:I139M	I	-	3	3	KIAA1143	44769885	0.000000	0.05858	0.395000	0.26283	0.780000	0.44128	-3.926000	0.00333	-2.050000	0.00905	-0.917000	0.02746	ATT	A|1.000;|0.000	.	weak		0.299	KIAA1143-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256746.1	NM_020696	
NCKAP1	10787	hgsc.bcm.edu	37	2	183848053	183848053	+	Silent	SNP	A	A	G	rs35142583	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:183848053A>G	ENST00000361354.4	-	11	1434	c.1062T>C	c.(1060-1062)gcT>gcC	p.A354A	NCKAP1_ENST00000360982.2_Silent_p.A360A	NM_013436.3	NP_038464.1	Q9Y2A7	NCKP1_HUMAN	NCK-associated protein 1	354					apical protein localization (GO:0045176)|apoptotic process (GO:0006915)|basal protein localization (GO:0045175)|central nervous system development (GO:0007417)|embryonic body morphogenesis (GO:0010172)|embryonic foregut morphogenesis (GO:0048617)|embryonic heart tube development (GO:0035050)|endoderm development (GO:0007492)|establishment or maintenance of actin cytoskeleton polarity (GO:0030950)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|lamellipodium assembly (GO:0030032)|mesodermal cell migration (GO:0008078)|neural tube closure (GO:0001843)|notochord morphogenesis (GO:0048570)|paraxial mesoderm morphogenesis (GO:0048340)|positive regulation of Arp2/3 complex-mediated actin nucleation (GO:2000601)|positive regulation of lamellipodium assembly (GO:0010592)|protein stabilization (GO:0050821)|Rac protein signal transduction (GO:0016601)|regulation of protein localization (GO:0032880)|somitogenesis (GO:0001756)|zygotic determination of anterior/posterior axis, embryo (GO:0007354)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|SCAR complex (GO:0031209)	protein complex binding (GO:0032403)			breast(3)|cervix(2)|endometrium(3)|kidney(4)|large_intestine(11)|lung(16)|ovary(2)|prostate(2)|upper_aerodigestive_tract(2)	45			OV - Ovarian serous cystadenocarcinoma(117;0.0942)|Epithelial(96;0.209)			AGAGGACAGTAGCCAATTCCT	0.343													A|||	140	0.0279553	0.0416	0.0403	5008	,	,		17473	0.0		0.0437	False		,,,				2504	0.0133				p.A360A		Atlas-SNP	.											.	NCKAP1	105	.	0			c.T1080C						PASS	.	A	,	186,4220	118.8+/-156.5	1,184,2018	116.0	112.0	113.0		1062,1080	-0.1	1.0	2	dbSNP_126	113	345,8255	117.4+/-177.0	3,339,3958	no	coding-synonymous,coding-synonymous	NCKAP1	NM_013436.3,NM_205842.1	,	4,523,5976	GG,GA,AA		4.0116,4.2215,4.0827	,	354/1129,360/1135	183848053	531,12475	2203	4300	6503	SO:0001819	synonymous_variant	10787	exon12			GACAGTAGCCAAT	AB014509	CCDS2287.1, CCDS2288.1	2q32	2009-08-14			ENSG00000061676	ENSG00000061676			7666	protein-coding gene	gene with protein product		604891				10673335, 12181570, 9344857	Standard	NM_013436		Approved	Nap1, HEM2, NAP125	uc002upb.4	Q9Y2A7	OTTHUMG00000132623	ENST00000361354.4:c.1062T>C	2.37:g.183848053A>G		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	126	54	0.428571	NM_205842	O60329|Q53QN5|Q53S94|Q53Y35	Silent	SNP	ENST00000361354.4	37	CCDS2287.1																																																																																			A|0.961;G|0.039	0.039	strong		0.343	NCKAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255867.2	NM_205842	
COG5	10466	hgsc.bcm.edu	37	7	107002806	107002806	+	Missense_Mutation	SNP	A	A	G	rs2269970	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:107002806A>G	ENST00000347053.3	-	9	1038	c.988T>C	c.(988-990)Ttc>Ctc	p.F330L	COG5_ENST00000297135.3_Missense_Mutation_p.F330L|COG5_ENST00000393603.2_Missense_Mutation_p.F330L	NM_181733.2	NP_859422.2	Q9UP83	COG5_HUMAN	component of oligomeric golgi complex 5	330			F -> L (in dbSNP:rs2269970). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9792665}.		intra-Golgi vesicle-mediated transport (GO:0006891)|protein transport (GO:0015031)	Golgi apparatus (GO:0005794)|Golgi transport complex (GO:0017119)|membrane (GO:0016020)		p.F330L(1)		breast(3)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(17)|ovary(2)|skin(4)|stomach(1)	40						TTGGTCCAGAATGAGGCACGC	0.393													G|||	3247	0.648363	0.9803	0.5058	5008	,	,		16792	0.6429		0.5417	False		,,,				2504	0.4162				p.F330L		Atlas-SNP	.											COG5,NS,carcinoma,0,1	COG5	78	1	1	Substitution - Missense(1)	stomach(1)	c.T988C						PASS	.	G	LEU/PHE,LEU/PHE,LEU/PHE	3973,433	211.8+/-231.9	1784,405,14	83.0	82.0	82.0		988,988,988	4.8	0.7	7	dbSNP_100	82	4542,4058	559.6+/-387.4	1211,2120,969	yes	missense,missense,missense	COG5	NM_001161520.1,NM_006348.3,NM_181733.2	22,22,22	2995,2525,983	GG,GA,AA		47.186,9.8275,34.5302	benign,benign,benign	330/824,330/861,330/840	107002806	8515,4491	2203	4300	6503	SO:0001583	missense	10466	exon9			TCCAGAATGAGGC	AF058718	CCDS5742.1, CCDS5743.1, CCDS55152.1	7q31	2010-06-24	2001-12-07	2002-05-10	ENSG00000164597	ENSG00000164597		"""Components of oligomeric golgi complex"""	14857	protein-coding gene	gene with protein product		606821	"""golgi transport complex 1 (90 kDa subunit)"""	GOLTC1		9792665, 11980916	Standard	NM_006348		Approved	GTC90	uc003vec.2	Q9UP83	OTTHUMG00000023895	ENST00000347053.3:c.988T>C	7.37:g.107002806A>G	ENSP00000334703:p.Phe330Leu	Somatic	231	0	0		WXS	Illumina HiSeq	Phase_I	205	92	0.44878	NM_006348	A4D0R6|A4D0R7|O14555|O95008|Q6NUL5	Missense_Mutation	SNP	ENST00000347053.3	37	CCDS5743.1	1465	0.6707875457875457	478	0.9715447154471545	195	0.5386740331491713	370	0.6468531468531469	422	0.5567282321899736	G	7.813	0.716216	0.15306	0.901725	0.52814	ENSG00000164597	ENST00000347053;ENST00000297135;ENST00000393603	T;T;T	0.27402	1.67;1.67;1.67	5.69	4.8	0.61643	.	0.000000	0.85682	N	0.000000	T	0.00012	0.0000	N	0.00013	-2.945	0.43471	P	0.0043159999999999865	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.40869	-0.9540	9	0.02654	T	1	-5.2259	13.0763	0.59089	0.1317:0.0:0.8683:0.0	rs2269970;rs10377771;rs17351107;rs52812313;rs59416115;rs2269970	330;330	Q9UP83;Q9UP83-2	COG5_HUMAN;.	L	330	ENSP00000334703:F330L;ENSP00000297135:F330L;ENSP00000377228:F330L	ENSP00000297135:F330L	F	-	1	0	COG5	106790042	1.000000	0.71417	0.729000	0.30791	0.445000	0.32107	6.030000	0.70903	0.865000	0.35603	-0.119000	0.15052	TTC	A|0.339;G|0.661	0.661	strong		0.393	COG5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000060216.4		
MKI67	4288	hgsc.bcm.edu	37	10	129901501	129901501	+	Missense_Mutation	SNP	G	G	C	rs2071496	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:129901501G>C	ENST00000368654.3	-	13	8978	c.8603C>G	c.(8602-8604)aCc>aGc	p.T2868S	MKI67_ENST00000368653.3_Missense_Mutation_p.T2508S	NM_002417.4	NP_002408.3	P46013	KI67_HUMAN	marker of proliferation Ki-67	2868	16 X 122 AA approximate repeats.		T -> S (in dbSNP:rs2071496).		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.T2868S(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)				GGTGTGCGTGGTCTCCCCTGA	0.542													G|||	903	0.180312	0.0787	0.3112	5008	,	,		19291	0.119		0.2714	False		,,,				2504	0.1943				p.T2868S		Atlas-SNP	.											MKI67,NS,carcinoma,0,1	MKI67	363	1	1	Substitution - Missense(1)	stomach(1)	c.C8603G						PASS	.	G	SER/THR,SER/THR	415,3991	202.1+/-225.0	16,383,1804	180.0	159.0	166.0		7523,8603	-2.3	0.0	10	dbSNP_96	166	2130,6470	366.3+/-334.3	271,1588,2441	yes	missense,missense	MKI67	NM_001145966.1,NM_002417.4	58,58	287,1971,4245	CC,CG,GG		24.7674,9.419,19.5679	probably-damaging,probably-damaging	2508/2897,2868/3257	129901501	2545,10461	2203	4300	6503	SO:0001583	missense	4288	exon13			TGCGTGGTCTCCC	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.8603C>G	10.37:g.129901501G>C	ENSP00000357643:p.Thr2868Ser	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	100	55	0.55	NM_002417	Q5VWH2	Missense_Mutation	SNP	ENST00000368654.3	37	CCDS7659.1	433	0.19826007326007325	29	0.05894308943089431	118	0.3259668508287293	83	0.1451048951048951	203	0.2678100263852243	G	11.81	1.750579	0.31046	0.09419	0.247674	ENSG00000148773	ENST00000368654;ENST00000368653;ENST00000537609	T;T	0.02345	4.33;4.33	4.68	-2.31	0.06765	.	.	.	.	.	T	0.00012	0.0000	L	0.33485	1.01	0.80722	P	0.0	D;D;P	0.61697	0.99;0.984;0.906	P;P;P	0.56434	0.789;0.798;0.73	T	0.23547	-1.0185	8	0.08381	T	0.77	.	2.8949	0.05688	0.1654:0.3928:0.3079:0.1339	rs2071496;rs17731347;rs52835871;rs2071496	2867;2508;2868	F5H4V4;P46013-2;P46013	.;.;KI67_HUMAN	S	2868;2508;2867	ENSP00000357643:T2868S;ENSP00000357642:T2508S	ENSP00000357642:T2508S	T	-	2	0	MKI67	129791491	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.652000	0.05366	-0.761000	0.04670	-0.140000	0.14226	ACC	G|0.798;C|0.202	0.202	strong		0.542	MKI67-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050999.1	NM_002417	
OR10G2	26534	hgsc.bcm.edu	37	14	22102439	22102439	+	Missense_Mutation	SNP	C	C	G	rs35963889	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	394	2	0.00507614		WXS	Illumina HiSeq	Phase_I	236	46	0.194915	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		
SLC12A5	57468	hgsc.bcm.edu	37	20	44680412	44680412	+	Silent	SNP	C	C	T	rs3746522	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	77	0	0		WXS	Illumina HiSeq	Phase_I	74	43	0.581081	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		
HIVEP2	3097	hgsc.bcm.edu	37	6	143091769	143091769	+	Silent	SNP	G	G	A	rs34947356	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:143091769G>A	ENST00000367604.1	-	4	4746	c.4107C>T	c.(4105-4107)gtC>gtT	p.V1369V	HIVEP2_ENST00000012134.2_Silent_p.V1369V|HIVEP2_ENST00000367603.2_Silent_p.V1369V			P31629	ZEP2_HUMAN	human immunodeficiency virus type I enhancer binding protein 2	1369					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|breast(4)|central_nervous_system(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(19)|lung(35)|ovary(4)|prostate(6)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	100				OV - Ovarian serous cystadenocarcinoma(155;1.61e-05)|GBM - Glioblastoma multiforme(68;0.0102)		TATTCTCATCGACTTTGCATA	0.507													G|||	703	0.140375	0.0991	0.1124	5008	,	,		22982	0.0794		0.1948	False		,,,				2504	0.2229				p.V1369V	Esophageal Squamous(107;843 1510 13293 16805 42198)	Atlas-SNP	.											.	HIVEP2	225	.	0			c.C4107T						PASS	.	G		405,3687		26,353,1667	88.0	87.0	87.0		4107	-10.2	0.0	6	dbSNP_126	87	1554,6874		141,1272,2801	no	coding-synonymous	HIVEP2	NM_006734.3		167,1625,4468	AA,AG,GG		18.4385,9.8974,15.647		1369/2447	143091769	1959,10561	2046	4214	6260	SO:0001819	synonymous_variant	3097	exon5			CTCATCGACTTTG	M60119	CCDS43510.1	6q23-q24	2013-01-08	2001-11-28		ENSG00000010818	ENSG00000010818		"""Zinc fingers, C2H2-type"""	4921	protein-coding gene	gene with protein product	"""c-myc intron binding protein 1"""	143054	"""human immunodeficiency virus type I enhancer-binding protein 2"""			1733857, 2022670	Standard	NM_006734		Approved	MBP-2, HIV-EP2, MIBP1, ZAS2, Schnurri-2, ZNF40B	uc003qjd.3	P31629	OTTHUMG00000015713	ENST00000367604.1:c.4107C>T	6.37:g.143091769G>A		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	56	44	0.785714	NM_006734	Q02646|Q5THT5|Q9NS05	Silent	SNP	ENST00000367604.1	37	CCDS43510.1																																																																																			G|0.859;A|0.141	0.141	strong		0.507	HIVEP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042495.1		
C3orf30	152405	hgsc.bcm.edu	37	3	118865332	118865332	+	Missense_Mutation	SNP	A	A	G	rs11550908	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:118865332A>G	ENST00000295622.1	+	1	336	c.296A>G	c.(295-297)gAc>gGc	p.D99G	IGSF11_ENST00000354673.2_5'Flank|IGSF11_ENST00000441144.2_5'Flank|RP11-484M3.5_ENST00000490594.1_5'Flank|IGSF11_ENST00000425327.2_5'Flank	NM_152539.2	NP_689752.2	Q96M34	CC030_HUMAN	chromosome 3 open reading frame 30	99			D -> G (in dbSNP:rs11550908).							NS(1)|breast(1)|cervix(1)|endometrium(1)|large_intestine(6)|lung(20)|ovary(2)|prostate(1)|urinary_tract(1)	34				GBM - Glioblastoma multiforme(114;0.222)		GATGTTTCTGACCTTAGAGCA	0.468													A|||	720	0.14377	0.1339	0.0663	5008	,	,		24050	0.2371		0.1531	False		,,,				2504	0.1063				p.D99G		Atlas-SNP	.											.	C3orf30	64	.	0			c.A296G						PASS	.	A	GLY/ASP	518,3888	235.5+/-248.0	28,462,1713	47.0	45.0	46.0		296	-0.1	0.0	3	dbSNP_120	46	1186,7414	233.5+/-266.7	74,1038,3188	yes	missense	C3orf30	NM_152539.2	94	102,1500,4901	GG,GA,AA		13.7907,11.7567,13.1016	possibly-damaging	99/537	118865332	1704,11302	2203	4300	6503	SO:0001583	missense	152405	exon1			TTTCTGACCTTAG	AK057421	CCDS2984.1	3q13.32	2011-08-09			ENSG00000163424	ENSG00000163424			26553	protein-coding gene	gene with protein product							Standard	NM_152539		Approved	FLJ32859	uc003ecb.1	Q96M34	OTTHUMG00000159349	ENST00000295622.1:c.296A>G	3.37:g.118865332A>G	ENSP00000295622:p.Asp99Gly	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	107	48	0.448598	NM_152539	A1L4B7	Missense_Mutation	SNP	ENST00000295622.1	37	CCDS2984.1	360|360	0.16483516483516483|0.16483516483516483	79|79	0.16056910569105692|0.16056910569105692	22|22	0.06077348066298342|0.06077348066298342	132|132	0.23076923076923078|0.23076923076923078	127|127	0.16754617414248021|0.16754617414248021	A|A	13.70|13.70	2.316641|2.316641	0.40996|0.40996	0.117567|0.117567	0.137907|0.137907	ENSG00000163424|ENSG00000163424	ENST00000295622;ENST00000470341|ENST00000460150	T|.	0.24908|.	1.83|.	2.39|2.39	-0.0946|-0.0946	0.13644|0.13644	.|.	.|.	.|.	.|.	.|.	T|.	0.00012|.	0.0000|.	N|N	0.24115|0.24115	0.695|0.695	0.80722|0.80722	P|P	0.0|0.0	P;P|.	0.50819|.	0.939;0.75|.	P;B|.	0.47044|.	0.535;0.373|.	T|.	0.31364|.	-0.9946|.	8|.	0.23302|.	T|.	0.38|.	.|.	4.06|4.06	0.09834|0.09834	0.5932:0.2719:0.135:0.0|0.5932:0.2719:0.135:0.0	rs11550908;rs52805947;rs57514040;rs11550908|rs11550908;rs52805947;rs57514040;rs11550908	99;99|.	E9PFE5;Q96M34|.	.;CC030_HUMAN|.	G|W	99|62	ENSP00000295622:D99G|.	ENSP00000295622:D99G|.	D|X	+|+	2|3	0|0	C3orf30|C3orf30	120348022|120348022	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.160000|0.160000	0.22226|0.22226	0.028000|0.028000	0.13644|0.13644	-0.038000|-0.038000	0.13624|0.13624	0.460000|0.460000	0.39030|0.39030	GAC|TGA	A|0.855;G|0.145	0.145	strong		0.468	C3orf30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354838.1	NM_152539	
FKBP9	11328	hgsc.bcm.edu	37	7	33035785	33035785	+	Silent	SNP	C	C	T	rs141599926	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:33035785C>T	ENST00000242209.4	+	7	1219	c.1050C>T	c.(1048-1050)ccC>ccT	p.P350P	AVL9_ENST00000404479.1_Intron|FKBP9_ENST00000538336.1_Silent_p.P403P|FKBP9_ENST00000538443.1_Silent_p.P212P|FKBP9_ENST00000490776.2_Silent_p.P118P	NM_001284343.1|NM_007270.3	NP_001271272.1|NP_009201.2	O95302	FKBP9_HUMAN	FK506 binding protein 9, 63 kDa	350	PPIase FKBP-type 3. {ECO:0000255|PROSITE- ProRule:PRU00277}.				chaperone-mediated protein folding (GO:0061077)|protein folding (GO:0006457)|protein peptidyl-prolyl isomerization (GO:0000413)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)	calcium ion binding (GO:0005509)|FK506 binding (GO:0005528)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			central_nervous_system(13)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(6)|lung(9)|ovary(2)|upper_aerodigestive_tract(1)	39			GBM - Glioblastoma multiforme(11;0.0156)			GGAATATCCCCGGCTCGGCTG	0.562													C|||	51	0.0101837	0.0008	0.0086	5008	,	,		18989	0.0		0.0169	False		,,,				2504	0.0276				p.P350P		Atlas-SNP	.											.	FKBP9	335	.	0			c.C1050T						PASS	.	C		14,4392	21.2+/-45.6	0,14,2189	123.0	109.0	114.0		1050	-8.1	0.9	7	dbSNP_134	114	151,8449	73.2+/-135.9	1,149,4150	no	coding-synonymous	FKBP9	NM_007270.3		1,163,6339	TT,TC,CC		1.7558,0.3177,1.2686		350/571	33035785	165,12841	2203	4300	6503	SO:0001819	synonymous_variant	11328	exon7			TATCCCCGGCTCG	AF089745	CCDS5439.1, CCDS64622.1, CCDS64623.1	7p11.1	2013-01-10	2002-08-29		ENSG00000122642	ENSG00000122642		"""EF-hand domain containing"""	3725	protein-coding gene	gene with protein product			"""FK506-binding protein 9 (63 kD)"""			12036304	Standard	NM_007270		Approved	FKBP60, FKBP63	uc003tdh.3	O95302	OTTHUMG00000097847	ENST00000242209.4:c.1050C>T	7.37:g.33035785C>T		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	119	90	0.756303	NM_007270	B3KY35|B7Z1G9|B7Z6H3|Q2M2A1|Q3MIR7|Q6IN76|Q6P2N1|Q96EX5|Q96IJ9	Silent	SNP	ENST00000242209.4	37	CCDS5439.1																																																																																			C|0.988;T|0.012	0.012	strong		0.562	FKBP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215137.1	NM_007270	
PCDH15	65217	hgsc.bcm.edu	37	10	55955610	55955610	+	Missense_Mutation	SNP	C	C	T	rs10825269	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:55955610C>T	ENST00000320301.6	-	11	1532	c.1138G>A	c.(1138-1140)Ggt>Agt	p.G380S	PCDH15_ENST00000409834.1_5'UTR|PCDH15_ENST00000395432.2_Missense_Mutation_p.G343S|PCDH15_ENST00000395433.1_Missense_Mutation_p.G358S|PCDH15_ENST00000395445.1_Missense_Mutation_p.G380S|PCDH15_ENST00000373957.3_Missense_Mutation_p.G358S|PCDH15_ENST00000395442.1_Intron|PCDH15_ENST00000395438.1_Missense_Mutation_p.G380S|PCDH15_ENST00000373965.2_Missense_Mutation_p.G380S|PCDH15_ENST00000395430.1_Missense_Mutation_p.G380S|PCDH15_ENST00000395440.1_Missense_Mutation_p.G380S|PCDH15_ENST00000395446.1_Missense_Mutation_p.G380S|PCDH15_ENST00000373955.1_Missense_Mutation_p.G380S|PCDH15_ENST00000414778.1_Missense_Mutation_p.G385S|PCDH15_ENST00000437009.1_Missense_Mutation_p.G380S|PCDH15_ENST00000361849.3_Missense_Mutation_p.G380S	NM_033056.3	NP_149045.3	Q96QU1	PCD15_HUMAN	protocadherin-related 15	380	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.		G -> S (in dbSNP:rs10825269). {ECO:0000269|PubMed:22815625}.		equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|synapse (GO:0045202)	calcium ion binding (GO:0005509)			NS(3)|breast(6)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(39)|lung(108)|ovary(5)|pancreas(6)|prostate(6)|skin(12)|upper_aerodigestive_tract(12)|urinary_tract(1)	237		Melanoma(3;0.117)|Lung SC(717;0.238)				ATGTGTAGACCGGCAAAGGCA	0.383										HNSCC(58;0.16)			T|||	1218	0.243211	0.4871	0.2104	5008	,	,		16076	0.0863		0.1382	False		,,,				2504	0.2065				p.G385S		Atlas-SNP	.											.	PCDH15	1715	.	0			c.G1153A						PASS	.	T	SER/GLY,SER/GLY,SER/GLY,SER/GLY,SER/GLY,SER/GLY,SER/GLY,SER/GLY,SER/GLY,SER/GLY,SER/GLY,SER/GLY	1947,2459	622.6+/-394.0	442,1063,698	127.0	122.0	124.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1153,1138,1138,1138,1027,1072,1153,1138,1153,1138,1072,1138	5.2	1.0	10	dbSNP_120	124	1101,7499	768.8+/-407.6	65,971,3264	yes	missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense	PCDH15	NM_001142763.1,NM_001142764.1,NM_001142765.1,NM_001142766.1,NM_001142767.1,NM_001142768.1,NM_001142769.1,NM_001142770.1,NM_001142771.1,NM_001142772.1,NM_001142773.1,NM_033056.3	56,56,56,56,56,56,56,56,56,56,56,56	507,2034,3962	TT,TC,CC		12.8023,44.1897,23.4353	benign,benign,benign,benign,benign,benign,benign,benign,benign,benign,benign,benign	385/1963,380/1958,380/1887,380/1953,343/1916,358/1936,385/1791,380/1540,385/1683,380/1678,358/1933,380/1956	55955610	3048,9958	2203	4300	6503	SO:0001583	missense	65217	exon12			GTAGACCGGCAAA	AY029205	CCDS7248.1, CCDS44400.1, CCDS44401.1, CCDS44403.1, CCDS44404.1, CCDS73134.1, CCDS73135.1, CCDS73136.1, CCDS73137.1, CCDS73138.1	10q21.1	2013-01-08	2010-01-25		ENSG00000150275	ENSG00000150275		"""Cadherins / Cadherin-related"""	14674	protein-coding gene	gene with protein product	"""cadherin-related family member 15"""	605514	"""deafness, autosomal recessive 23"", ""protocadherin 15"""	USH1F, DFNB23		11398101, 14570705	Standard	NM_033056		Approved	CDHR15	uc010qhy.1	Q96QU1	OTTHUMG00000018259	ENST00000320301.6:c.1138G>A	10.37:g.55955610C>T	ENSP00000322604:p.Gly380Ser	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	76	41	0.539474	NM_001142763	A6NL19|C6ZEF5|C6ZEF6|C6ZEF7|Q5VY38|Q5VY39|Q6TRH8|Q8NDB9|Q96QT8	Missense_Mutation	SNP	ENST00000320301.6	37	CCDS7248.1	454	0.2078754578754579	235	0.47764227642276424	68	0.1878453038674033	49	0.08566433566433566	102	0.1345646437994723	T	5.780	0.328284	0.10956	0.441897	0.128023	ENSG00000150275	ENST00000373965;ENST00000414778;ENST00000455746;ENST00000395438;ENST00000395445;ENST00000395446;ENST00000395440;ENST00000395432;ENST00000361849;ENST00000395433;ENST00000373957;ENST00000320301;ENST00000395430;ENST00000417177;ENST00000437009;ENST00000373955	T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.36520	1.25;1.25;1.25;1.25;1.25;1.25;2.53;1.25;1.25;1.25;1.25;1.25;1.25;1.25	5.17	5.17	0.71159	Cadherin (3);Cadherin-like (1);	.	.	.	.	T	0.00012	0.0000	N	0.11201	0.11	0.51767	P	7.00000000000145E-5	B;B;B;B;B;B;B;B;B;B;B;B;B;B;B	0.16396	0.017;0.004;0.004;0.007;0.004;0.007;0.017;0.0;0.014;0.014;0.0;0.0;0.0;0.001;0.007	B;B;B;B;B;B;B;B;B;B;B;B;B;B;B	0.09377	0.004;0.002;0.002;0.003;0.003;0.002;0.004;0.0;0.003;0.003;0.0;0.0;0.001;0.001;0.002	T	0.41448	-0.9508	8	0.05959	T	0.93	.	10.7228	0.46050	0.0:0.0763:0.0:0.9237	rs10825269;rs52818022;rs59807776;rs10825269	358;380;380;385;380;343;380;380;380;380;380;385;380;358;380	A2A3E8;E7EMG4;A2A3E7;C9JIG1;E7EM53;E7EMG0;A2A3E6;A2A3E3;C6ZEF5;A2A3E2;C6ZEF7;C9J4F3;Q96QU1-3;A2A3D8;Q96QU1	.;.;.;.;.;.;.;.;.;.;.;.;.;.;PCD15_HUMAN	S	380;385;380;380;380;380;380;343;380;358;358;380;380;385;380;380	ENSP00000363076:G380S;ENSP00000410304:G385S;ENSP00000378826:G380S;ENSP00000378832:G380S;ENSP00000378833:G380S;ENSP00000378827:G380S;ENSP00000378820:G343S;ENSP00000354950:G380S;ENSP00000378821:G358S;ENSP00000363068:G358S;ENSP00000322604:G380S;ENSP00000378818:G380S;ENSP00000412628:G380S;ENSP00000363066:G380S	ENSP00000322604:G380S	G	-	1	0	PCDH15	55625616	1.000000	0.71417	1.000000	0.80357	0.919000	0.55068	2.210000	0.42816	0.823000	0.34589	-0.332000	0.08345	GGT	C|0.772;T|0.228	0.228	strong		0.383	PCDH15-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000048121.2	NM_033056	
HTT	3064	hgsc.bcm.edu	37	4	3234980	3234980	+	Missense_Mutation	SNP	G	G	A	rs362272	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:3234980G>A	ENST00000355072.5	+	61	8501	c.8356G>A	c.(8356-8358)Gtc>Atc	p.V2786I	HTT_ENST00000513806.1_Intron	NM_002111.6	NP_002102	P42858	HD_HUMAN	huntingtin	2786			V -> I (in dbSNP:rs362272). {ECO:0000269|PubMed:7903579}.		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)		CCTGCACGGCGTCCTCTATGT	0.642													G|||	1053	0.210264	0.0106	0.2867	5008	,	,		19312	0.3185		0.3091	False		,,,				2504	0.2127				p.V2786I		Atlas-SNP	.											HTT,NS,carcinoma,0,1	HTT	221	1	0			c.G8356A						PASS	.	G	ILE/VAL	285,3955		18,249,1853	94.0	107.0	103.0		8356	-4.2	0.0	4	dbSNP_79	103	2508,5958		359,1790,2084	yes	missense	HTT	NM_002111.6	29	377,2039,3937	AA,AG,GG		29.6244,6.7217,21.9817	benign	2786/3143	3234980	2793,9913	2120	4233	6353	SO:0001583	missense	3064	exon61			CACGGCGTCCTCT	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.8356G>A	4.37:g.3234980G>A	ENSP00000347184:p.Val2786Ile	Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	139	62	0.446043	NM_002111	Q9UQB7	Missense_Mutation	SNP	ENST00000355072.5	37	CCDS43206.1	539	0.2467948717948718	6	0.012195121951219513	110	0.30386740331491713	179	0.3129370629370629	244	0.32189973614775724	G	5.633	0.301421	0.10678	0.067217	0.296244	ENSG00000197386	ENST00000355072	T	0.65549	-0.16	5.08	-4.25	0.03766	.	0.893841	0.09733	N	0.762867	T	0.00012	0.0000	N	0.10874	0.06	0.80722	P	0.0	B	0.09022	0.002	B	0.06405	0.002	T	0.26815	-1.0092	9	0.06365	T	0.9	.	12.9961	0.58648	0.6315:0.0:0.3685:0.0	rs362272;rs2229986;rs59711124;rs362272	2786	P42858	HD_HUMAN	I	2786	ENSP00000347184:V2786I	ENSP00000347184:V2786I	V	+	1	0	HTT	3204778	0.646000	0.27295	0.006000	0.13384	0.820000	0.46376	1.389000	0.34453	-0.795000	0.04462	-0.487000	0.04747	GTC	G|0.759;T|0.008	.	strong		0.642	HTT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358234.2	NM_002111	
PALLD	23022	hgsc.bcm.edu	37	4	169433327	169433327	+	Missense_Mutation	SNP	G	G	A	rs397718410|rs373066707|rs7671781	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:169433327G>A	ENST00000505667.1	+	2	845	c.672G>A	c.(670-672)atG>atA	p.M224I	PALLD_ENST00000261509.6_Missense_Mutation_p.M224I|PALLD_ENST00000335742.7_5'UTR|PALLD_ENST00000333488.4_Missense_Mutation_p.M101I			Q8WX93	PALLD_HUMAN	palladin, cytoskeletal associated protein	224			M -> I (in dbSNP:rs7671781).|M -> T (in dbSNP:rs7655494). {ECO:0000269|PubMed:14702039}.		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)		AGAGCCCTATGGAAGACCAAG	0.582									Pancreatic Cancer, Familial Clustering of				G|||	1200	0.239617	0.2368	0.1844	5008	,	,		17181	0.1935		0.33	False		,,,				2504	0.2372				p.M224I	Esophageal Squamous(109;1482 1532 18347 40239 51172)	Atlas-SNP	.											.	PALLD	179	.	0			c.G672A						PASS	.	G	ILE/MET,ILE/MET	1065,3341		151,763,1289	101.0	105.0	104.0		672,672	-10.8	0.0	4	dbSNP_116	104	2624,5976		460,1704,2136	yes	missense,missense	PALLD	NM_001166108.1,NM_016081.3	10,10	611,2467,3425	AA,AG,GG		30.5116,24.1716,28.3638	benign,benign	224/1124,224/1107	169433327	3689,9317	2203	4300	6503	SO:0001583	missense	23022	exon2	Familial Cancer Database	incl.: Hereditary Pancreatic Adenocarcinoma, Insulin-Dependent Diabetes Mellitus - Exocrine Insufficiency - Familial Pancreatic Cancer, PNCA1	CCCTATGGAAGAC	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.672G>A	4.37:g.169433327G>A	ENSP00000425556:p.Met224Ile	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	58	57	0.982759	NM_001166108	B3KTG2|B5MD56|B7ZMM5|Q7L3E0|Q7Z3W0|Q86WE8|Q8N1M2|Q9UGA0|Q9UQF5|Q9Y2J6|Q9Y3E9	Missense_Mutation	SNP	ENST00000505667.1	37	CCDS54818.1	447	0.20467032967032966	89	0.18089430894308944	68	0.1878453038674033	84	0.14685314685314685	206	0.2717678100263852	G	10.73	1.433994	0.25813	0.241716	0.305116	ENSG00000129116	ENST00000261509;ENST00000505667;ENST00000508898;ENST00000333488	T;T;T;T	0.61742	0.18;0.46;0.08;0.18	5.41	-10.8	0.00216	.	0.307711	0.17926	N	0.157333	T	0.00012	0.0000	N	0.08118	0	0.53688	P	2.6999999999999247E-5	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.08576	-1.0715	9	0.13853	T	0.58	.	2.9803	0.05951	0.2733:0.4205:0.1616:0.1446	rs7671781	224;224	B7ZMM5;B2RTX2	.;.	I	224;224;203;101	ENSP00000261509:M224I;ENSP00000425556:M224I;ENSP00000423063:M203I;ENSP00000328945:M101I	ENSP00000261509:M224I	M	+	3	0	PALLD	169669902	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-4.466000	0.00229	-4.316000	0.00057	-0.918000	0.02743	ATG	G|0.733;A|0.267	0.267	strong		0.582	PALLD-002	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000363762.1	NM_016081	
TMEM176A	55365	hgsc.bcm.edu	37	7	150500729	150500729	+	Missense_Mutation	SNP	A	A	G	rs741064	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:150500729A>G	ENST00000484928.1	+	5	945	c.364A>G	c.(364-366)Acg>Gcg	p.T122A	TMEM176A_ENST00000461345.1_Missense_Mutation_p.T63A|TMEM176A_ENST00000004103.3_Missense_Mutation_p.T122A|TMEM176B_ENST00000447204.2_5'Flank			Q96HP8	T176A_HUMAN	transmembrane protein 176A	122			T -> A (in dbSNP:rs741064). {ECO:0000269|PubMed:12097419}.		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)		GACTCTGCTAACGCTGGCAGC	0.532													G|||	4508	0.90016	0.9856	0.879	5008	,	,		19834	0.9365		0.8002	False		,,,				2504	0.865				p.T122A		Atlas-SNP	.											TMEM176A,NS,carcinoma,0,1	TMEM176A	35	1	0			c.A364G						PASS	.	G	ALA/THR	4223,183	116.7+/-154.6	2023,177,3	66.0	71.0	69.0		364	-3.8	0.0	7	dbSNP_86	69	6830,1770	320.0+/-314.4	2711,1408,181	yes	missense	TMEM176A	NM_018487.2	58	4734,1585,184	GG,GA,AA		20.5814,4.1534,15.0161	benign	122/236	150500729	11053,1953	2203	4300	6503	SO:0001583	missense	55365	exon5			CTGCTAACGCTGG	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.364A>G	7.37:g.150500729A>G	ENSP00000417626:p.Thr122Ala	Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	38	37	0.973684	NM_018487	D3DX00|Q9NYC7	Missense_Mutation	SNP	ENST00000484928.1	37	CCDS5909.1	1939	0.8878205128205128	481	0.9776422764227642	315	0.8701657458563536	540	0.9440559440559441	603	0.7955145118733509	G	2.854	-0.237626	0.05944	0.958466	0.794186	ENSG00000002933	ENST00000484928;ENST00000004103;ENST00000461345;ENST00000475536;ENST00000468689	T;T;T;T;T	0.02236	4.38;4.38;4.38;4.38;4.38	3.56	-3.79	0.04320	.	1.273530	0.05221	N	0.508493	T	0.00012	0.0000	N	0.04880	-0.145	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.06463	-1.0825	9	0.15952	T	0.53	-7.1138	3.6593	0.08233	0.3903:0.0:0.2134:0.3963	rs741064;rs11537894;rs52824110;rs741064	122	Q96HP8	T176A_HUMAN	A	122;122;63;74;63	ENSP00000417626:T122A;ENSP00000004103:T122A;ENSP00000420818:T63A;ENSP00000417834:T74A;ENSP00000420081:T63A	ENSP00000004103:T122A	T	+	1	0	TMEM176A	150131662	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.289000	0.02780	-1.335000	0.02241	-0.227000	0.12334	ACG	A|0.127;G|0.873	0.873	strong		0.532	TMEM176A-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350222.1	NM_018487	
NEDD9	4739	hgsc.bcm.edu	37	6	11193860	11193860	+	Silent	SNP	G	G	A	rs16871074	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:11193860G>A	ENST00000379446.5	-	3	691	c.525C>T	c.(523-525)gaC>gaT	p.D175D	RP3-510L9.1_ENST00000500636.2_RNA|NEDD9_ENST00000504387.1_Silent_p.D175D	NM_001271033.1|NM_006403.3	NP_001257962.1|NP_006394.1	Q14511	CASL_HUMAN	neural precursor cell expressed, developmentally down-regulated 9	175	Interacts strongly with spindle- regulatory protein D1M1.				actin filament bundle assembly (GO:0051017)|cell adhesion (GO:0007155)|cytoskeleton organization (GO:0007010)|integrin-mediated signaling pathway (GO:0007229)|mitotic nuclear division (GO:0007067)|regulation of growth (GO:0040008)|signal transduction (GO:0007165)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|spindle (GO:0005819)|spindle pole (GO:0000922)		p.D175D(1)		endometrium(3)|kidney(2)|large_intestine(8)|liver(1)|lung(9)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	26	Breast(50;0.0768)|Ovarian(93;0.152)	all_hematologic(90;0.135)	Epithelial(50;0.0647)|all cancers(50;0.179)			TATCATAGACGTCCTTTTGGT	0.512													g|||	987	0.197085	0.1498	0.2104	5008	,	,		17740	0.256		0.1879	False		,,,				2504	0.2004				p.D175D		Atlas-SNP	.											NEDD9_ENST00000379446,NS,carcinoma,0,1	NEDD9	191	1	1	Substitution - coding silent(1)	stomach(1)	c.C525T						scavenged	.		,	617,3789	270.7+/-269.8	37,543,1623	186.0	151.0	163.0		525,525	2.6	1.0	6	dbSNP_123	163	1675,6925	308.4+/-308.9	165,1345,2790	no	coding-synonymous,coding-synonymous	NEDD9	NM_001142393.1,NM_006403.3	,	202,1888,4413	AA,AG,GG		19.4767,14.0036,17.6226	,	175/835,175/835	11193860	2292,10714	2203	4300	6503	SO:0001819	synonymous_variant	4739	exon4			ATAGACGTCCTTT	L43821	CCDS4520.1, CCDS34340.1, CCDS47373.1, CCDS75400.1	6p25-p24	2011-04-13			ENSG00000111859	ENSG00000111859		"""Cas scaffolding proteins"""	7733	protein-coding gene	gene with protein product	"""Cas scaffolding protein family member 2"", ""Cas-like"""	602265					Standard	NM_182966		Approved	HEF1, CAS-L, CASS2	uc003mzv.2	Q14511	OTTHUMG00000014255	ENST00000379446.5:c.525C>T	6.37:g.11193860G>A		Somatic	150	2	0.0133333		WXS	Illumina HiSeq	Phase_I	156	58	0.371795	NM_001142393	A8K9G7|A8MSJ9|G5E9Y9|Q5T9R4|Q5XKI0	Silent	SNP	ENST00000379446.5	37	CCDS4520.1																																																																																			G|0.813;A|0.187	0.187	strong		0.512	NEDD9-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000039853.2	NM_006403	
CRIP3	401262	hgsc.bcm.edu	37	6	43273604	43273604	+	3'UTR	SNP	A	A	G	rs2242416	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:43273604A>G	ENST00000274990.4	-	0	758				CRIP3_ENST00000372569.3_Missense_Mutation_p.I188T|ZNF318_ENST00000607252.1_5'Flank			Q6Q6R5	CRIP3_HUMAN	cysteine-rich protein 3						T cell proliferation (GO:0042098)	cytoplasm (GO:0005737)	zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	10			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.00998)|OV - Ovarian serous cystadenocarcinoma(102;0.0305)			CACATCGCCAATGTTCACACC	0.542													A|||	2088	0.416933	0.0719	0.4035	5008	,	,		20332	0.621		0.5765	False		,,,				2504	0.5184				p.I188T		Atlas-SNP	.											.	CRIP3	30	.	0			c.T563C						PASS	.	A	THR/ILE	705,3685		55,595,1545	76.0	80.0	79.0		563	5.8	1.0	6	dbSNP_98	79	5031,3559		1445,2141,709	yes	missense	CRIP3	NM_206922.2	89	1500,2736,2254	GG,GA,AA		41.4319,16.0592,44.1911	benign	188/205	43273604	5736,7244	2195	4295	6490	SO:0001624	3_prime_UTR_variant	401262	exon8			TCGCCAATGTTCA	AY555741	CCDS4894.2	6p21	2008-02-05			ENSG00000146215	ENSG00000146215			17751	protein-coding gene	gene with protein product						15380775	Standard	NM_206922		Approved	TLP-A, bA480N24.2, TLP	uc003ouu.1	Q6Q6R5	OTTHUMG00000014727	ENST00000274990.4:c.*100T>C	6.37:g.43273604A>G		Somatic	115	1	0.00869565		WXS	Illumina HiSeq	Phase_I	95	95	1	NM_206922	A2A436|Q5T043|Q6Q6R4|Q6Q6R6|Q6Q6R7	Missense_Mutation	SNP	ENST00000274990.4	37		1000	0.45787545787545786	30	0.06097560975609756	157	0.43370165745856354	371	0.6486013986013986	442	0.58311345646438	A	10.18	1.279807	0.23392	0.160592	0.585681	ENSG00000146215	ENST00000372569	D	0.92397	-3.03	5.77	5.77	0.91146	.	.	.	.	.	T	0.78400	0.4277	.	.	.	0.09310	P	1.0	B	0.23891	0.093	B	0.23574	0.047	T	0.72997	-0.4121	7	0.12766	T	0.61	.	14.039	0.64663	1.0:0.0:0.0:0.0	rs2242416;rs17287893;rs56983690;rs2242416	188	Q6Q6R5-3	.	T	188	ENSP00000361650:I188T	ENSP00000361650:I188T	I	-	2	0	CRIP3	43381582	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.562000	0.60816	2.200000	0.70718	0.533000	0.62120	ATT	G|0.469;N|0.000	0.469	strong		0.542	CRIP3-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000313968.1		
KMT2C	58508	hgsc.bcm.edu	37	7	151970858	151970858	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:151970858C>T	ENST00000262189.6	-	7	1162	c.944G>A	c.(943-945)gGc>gAc	p.G315D	KMT2C_ENST00000355193.2_Missense_Mutation_p.G315D	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	315					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)										CTGAAAGGTGCCGGCTCCTGC	0.428																																					p.G315D		Atlas-SNP	.											MLL3_ENST00000355193,NS,carcinoma,-1,14	MLL3	1564	14	0			c.G944A						scavenged	.						269.0	250.0	256.0					7																	151970858		2203	4300	6503	SO:0001583	missense	58508	exon7			AAGGTGCCGGCTC	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.944G>A	7.37:g.151970858C>T	ENSP00000262189:p.Gly315Asp	Somatic	332	2	0.0060241		WXS	Illumina HiSeq	Phase_I	339	6	0.0176991	NM_170606	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Missense_Mutation	SNP	ENST00000262189.6	37	CCDS5931.1	.	.	.	.	.	.	.	.	.	.	C	19.56	3.850147	0.71719	.	.	ENSG00000055609	ENST00000262189;ENST00000355193	T;T	0.72615	-0.67;-0.67	4.87	4.87	0.63330	Zinc finger, PHD-type (1);	0.000000	0.45606	D	0.000359	D	0.83714	0.5314	M	0.71206	2.165	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.85380	0.1119	10	0.62326	D	0.03	.	18.3752	0.90433	0.0:1.0:0.0:0.0	.	315	Q8NEZ4	MLL3_HUMAN	D	315	ENSP00000262189:G315D;ENSP00000347325:G315D	ENSP00000262189:G315D	G	-	2	0	MLL3	151601791	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	7.752000	0.85141	2.423000	0.82170	0.650000	0.86243	GGC	C|0.600;T|0.400	0.400	strong		0.428	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3		
OR5L1	219437	hgsc.bcm.edu	37	11	55579419	55579419	+	Silent	SNP	T	T	C	rs34948392	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:55579419T>C	ENST00000333973.2	+	1	566	c.477T>C	c.(475-477)caT>caC	p.H159H		NM_001004738.1	NP_001004738.1	Q8NGL2	OR5L1_HUMAN	olfactory receptor, family 5, subfamily L, member 1	159						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.H159H(1)		NS(1)|breast(2)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(4)|liver(4)|lung(36)|ovary(2)|pancreas(1)|prostate(5)|skin(9)|stomach(4)|upper_aerodigestive_tract(3)	78		all_epithelial(135;0.208)				CTCTGATTCATTTGTGCTTAG	0.443													N|||	525	0.104832	0.1884	0.0461	5008	,	,		22589	0.0813		0.0924	False		,,,				2504	0.0706				p.H159H		Atlas-SNP	.											OR5L1,NS,carcinoma,+2,3	OR5L1	145	3	1	Substitution - coding silent(1)	stomach(1)	c.T477C						PASS	.	C		670,3730		63,544,1593	217.0	191.0	200.0		477	-4.7	0.0	11	dbSNP_126	200	725,7867		32,661,3603	no	coding-synonymous	OR5L1	NM_001004738.1		95,1205,5196	CC,CT,TT		8.4381,15.2273,10.7374		159/312	55579419	1395,11597	2200	4296	6496	SO:0001819	synonymous_variant	219437	exon1			GATTCATTTGTGC	AB065780	CCDS31509.1	11q11	2012-08-09			ENSG00000186117	ENSG00000186117		"""GPCR / Class A : Olfactory receptors"""	8350	protein-coding gene	gene with protein product							Standard	NM_001004738		Approved	OST262	uc001nhw.1	Q8NGL2	OTTHUMG00000166810	ENST00000333973.2:c.477T>C	11.37:g.55579419T>C		Somatic	358	0	0		WXS	Illumina HiSeq	Phase_I	302	234	0.774834	NM_001004738	B2RNK6|Q6IFD0	Silent	SNP	ENST00000333973.2	37	CCDS31509.1																																																																																			T|0.896;C|0.104	0.104	strong		0.443	OR5L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391514.1	NM_001004738	
MS4A14	84689	hgsc.bcm.edu	37	11	60184191	60184191	+	Missense_Mutation	SNP	G	G	A	rs3825020	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:60184191G>A	ENST00000300187.6	+	5	2027	c.1750G>A	c.(1750-1752)Gga>Aga	p.G584R	MS4A14_ENST00000395005.2_Missense_Mutation_p.G567R|MS4A14_ENST00000531783.1_Missense_Mutation_p.G617R|MS4A14_ENST00000531787.1_Missense_Mutation_p.G472R	NM_032597.4	NP_115986.3	Q96JA4	M4A14_HUMAN	membrane-spanning 4-domains, subfamily A, member 14	584	Gln-rich.		G -> R (in dbSNP:rs3825020). {ECO:0000269|PubMed:17974005, ECO:0000269|Ref.1, ECO:0000269|Ref.2}.			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						ATCTAAAGATGGACAAGTTAA	0.458													G|||	2495	0.498203	0.5182	0.6513	5008	,	,		21541	0.3433		0.6262	False		,,,				2504	0.3906				p.G617R		Atlas-SNP	.											.	MS4A14	120	.	0			c.G1849A						PASS	.	G	ARG/GLY,ARG/GLY	2155,2251	581.2+/-385.3	521,1113,569	72.0	62.0	65.0		1699,1750	-1.4	0.0	11	dbSNP_107	65	5324,3276	645.7+/-400.2	1639,2046,615	yes	missense,missense	MS4A14	NM_001079692.1,NM_032597.3	125,125	2160,3159,1184	AA,AG,GG		38.093,48.9106,42.4958	benign,benign	567/663,584/680	60184191	7479,5527	2203	4300	6503	SO:0001583	missense	84689	exon6			AAAGATGGACAAG	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.1750G>A	11.37:g.60184191G>A	ENSP00000300187:p.Gly584Arg	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	67	16	0.238806	NM_001261828	E9PJE3|Q2TVT5|Q3B7W3|Q86XH8|Q9NTC2	Missense_Mutation	SNP	ENST00000300187.6	37	CCDS31569.1	1179	0.5398351648351648	254	0.516260162601626	226	0.6243093922651933	228	0.3986013986013986	471	0.6213720316622692	G	5.096	0.203398	0.09704	0.489106	0.61907	ENSG00000166928	ENST00000531787;ENST00000300187;ENST00000395005;ENST00000531783	T;T;T;T	0.30981	1.51;2.73;1.52;3.1	4.31	-1.43	0.08884	.	4.009310	0.00541	N	0.000226	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	B;B	0.13145	0.007;0.004	B;B	0.08055	0.003;0.001	T	0.45948	-0.9226	9	0.15499	T	0.54	4.9183	3.2257	0.06731	0.3862:0.0:0.3485:0.2652	rs3825020;rs52806143;rs60869380;rs3825020	567;584	Q96JA4-2;Q96JA4	.;M4A14_HUMAN	R	472;584;567;617	ENSP00000437222:G472R;ENSP00000300187:G584R;ENSP00000378453:G567R;ENSP00000433761:G617R	ENSP00000300187:G584R	G	+	1	0	MS4A14	59940767	0.000000	0.05858	0.000000	0.03702	0.055000	0.15305	-0.859000	0.04277	-0.031000	0.13781	0.655000	0.94253	GGA	G|0.445;A|0.555	0.555	strong		0.458	MS4A14-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000395383.2		
PIGS	94005	hgsc.bcm.edu	37	17	26881923	26881923	+	Silent	SNP	C	C	T	rs146249165	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:26881923C>T	ENST00000308360.7	-	11	1713	c.1338G>A	c.(1336-1338)gcG>gcA	p.A446A	UNC119_ENST00000335765.4_5'Flank|UNC119_ENST00000301032.4_5'Flank|PIGS_ENST00000543734.1_Silent_p.A385A|PIGS_ENST00000395346.2_Silent_p.A438A	NM_033198.3	NP_149975.1	Q96S52	PIGS_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class S	446					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)	endoplasmic reticulum membrane (GO:0005789)|GPI-anchor transamidase complex (GO:0042765)|membrane (GO:0016020)	GPI-anchor transamidase activity (GO:0003923)			breast(3)|endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	16	Lung NSC(42;0.00431)					CCAGAAGCTGCGCCAGGGAGG	0.587																																					p.A446A		Atlas-SNP	.											.	PIGS	42	.	0			c.G1338A						PASS	.	C		0,4406		0,0,2203	123.0	101.0	109.0		1338	-2.2	1.0	17	dbSNP_134	109	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	PIGS	NM_033198.3		0,3,6500	TT,TC,CC		0.0349,0.0,0.0231		446/556	26881923	3,13003	2203	4300	6503	SO:0001819	synonymous_variant	94005	exon11			AAGCTGCGCCAGG		CCDS11235.1	17p13.2	2013-02-26	2006-06-28		ENSG00000087111	ENSG00000087111		"""Phosphatidylinositol glycan anchor biosynthesis"""	14937	protein-coding gene	gene with protein product	"""GPI transamidase subunit"""	610271	"""phosphatidylinositol glycan, class S"""				Standard	NM_033198		Approved		uc002hbo.2	Q96S52	OTTHUMG00000132604	ENST00000308360.7:c.1338G>A	17.37:g.26881923C>T		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	111	53	0.477477	NM_033198	Q6UVX6	Silent	SNP	ENST00000308360.7	37	CCDS11235.1																																																																																			C|1.000;T|0.000	0.000	strong		0.587	PIGS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255833.3	NM_033198	
ATAD5	79915	hgsc.bcm.edu	37	17	29167653	29167653	+	Missense_Mutation	SNP	A	A	C	rs3764421	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:29167653A>C	ENST00000321990.4	+	4	2473	c.2095A>C	c.(2095-2097)Aac>Cac	p.N699H	CTD-2349P21.11_ENST00000580873.1_RNA	NM_024857.3	NP_079133.3	Q96QE3	ATAD5_HUMAN	ATPase family, AAA domain containing 5	699			N -> H (in dbSNP:rs3764421).		cellular response to DNA damage stimulus (GO:0006974)	nucleus (GO:0005634)	ATP binding (GO:0005524)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(3)|large_intestine(18)|lung(13)|ovary(3)|pancreas(1)	51		all_hematologic(16;0.0202)|Acute lymphoblastic leukemia(14;0.0238)|Myeloproliferative disorder(56;0.0393)				TACTTCAAAAAACATATCAAA	0.284													A|||	722	0.144169	0.0711	0.1859	5008	,	,		15768	0.1359		0.1074	False		,,,				2504	0.2597				p.N699H		Atlas-SNP	.											ATAD5,NS,carcinoma,0,1	ATAD5	150	1	0			c.A2095C						PASS	.	A	HIS/ASN	320,4086	147.6+/-182.1	15,290,1898	79.0	85.0	83.0		2095	5.9	1.0	17	dbSNP_107	83	890,7710	175.5+/-225.5	37,816,3447	yes	missense	ATAD5	NM_024857.3	68	52,1106,5345	CC,CA,AA		10.3488,7.2628,9.3034	possibly-damaging	699/1845	29167653	1210,11796	2203	4300	6503	SO:0001583	missense	79915	exon4			TCAAAAAACATAT		CCDS11260.1	17q11.2	2010-04-21	2007-02-08	2007-02-08	ENSG00000176208	ENSG00000176208		"""ATPases / AAA-type"""	25752	protein-coding gene	gene with protein product	"""enhanced level of genomic instability 1 homolog (S. cerevisiae)"""	609534	"""chromosome 17 open reading frame 41"""	C17orf41		15983387, 11468690, 19755857	Standard	NM_024857		Approved	FLJ12735, FRAG1, ELG1	uc002hfs.1	Q96QE3	OTTHUMG00000132794	ENST00000321990.4:c.2095A>C	17.37:g.29167653A>C	ENSP00000313171:p.Asn699His	Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	97	38	0.391753	NM_024857	Q05DH0|Q69YR6|Q9H9I1	Missense_Mutation	SNP	ENST00000321990.4	37	CCDS11260.1	274	0.12545787545787546	45	0.09146341463414634	65	0.17955801104972377	92	0.16083916083916083	72	0.09498680738786279	A	12.78	2.039141	0.35989	0.072628	0.103488	ENSG00000176208	ENST00000321990	T	0.09817	2.94	5.9	5.9	0.94986	.	0.925252	0.09360	N	0.812877	T	0.00073	0.0002	M	0.61703	1.905	0.28364	P	0.9203312	D;D	0.71674	0.996;0.998	D;D	0.65874	0.939;0.915	T	0.01795	-1.1272	9	0.72032	D	0.01	.	16.3155	0.82918	1.0:0.0:0.0:0.0	rs3764421;rs52792999;rs59938755;rs3764421	699;699	Q96QE3-2;Q96QE3	.;ATAD5_HUMAN	H	699	ENSP00000313171:N699H	ENSP00000313171:N699H	N	+	1	0	ATAD5	26191779	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	4.491000	0.60326	2.260000	0.74910	0.528000	0.53228	AAC	A|0.885;C|0.115	0.115	strong		0.284	ATAD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256206.2	NM_024857	
MUC4	4585	hgsc.bcm.edu	37	3	195513420	195513420	+	Silent	SNP	G	G	A	rs71321842	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195513420G>A	ENST00000463781.3	-	2	5490	c.5031C>T	c.(5029-5031)caC>caT	p.H1677H	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Silent_p.H1677H	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)		GAGGGGTGGCGTGACCGGTGG	0.612																																					p.H1677H		Atlas-SNP	.											.	MUC4	1505	.	0			c.C5031T						PASS	.						36.0	34.0	34.0					3																	195513420		690	1583	2273	SO:0001819	synonymous_variant	4585	exon2			GGTGGCGTGACCG	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.5031C>T	3.37:g.195513420G>A		Somatic	205	0	0		WXS	Illumina HiSeq	Phase_I	171	44	0.25731	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Silent	SNP	ENST00000463781.3	37	CCDS54700.1																																																																																			G|0.500;A|0.500	0.500	strong		0.612	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
RPS6KA1	6195	hgsc.bcm.edu	37	1	26883511	26883511	+	Missense_Mutation	SNP	A	A	C	rs2229712	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:26883511A>C	ENST00000374168.2	+	13	1158	c.1004A>C	c.(1003-1005)aAg>aCg	p.K335T	MIR1976_ENST00000459548.1_RNA|RPS6KA1_ENST00000488985.1_3'UTR|RPS6KA1_ENST00000526792.1_Missense_Mutation_p.K243T|RPS6KA1_ENST00000530003.1_Missense_Mutation_p.K319T|RPS6KA1_ENST00000531382.1_Missense_Mutation_p.K344T|RPS6KA1_ENST00000374166.4_Missense_Mutation_p.K324T|RPS6KA1_ENST00000374162.2_Missense_Mutation_p.K243T	NM_002953.3	NP_002944.2	Q15418	KS6A1_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide 1	335	AGC-kinase C-terminal.		K -> T (in dbSNP:rs2229712). {ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:8141249}.		axon guidance (GO:0007411)|cell cycle (GO:0007049)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell growth (GO:0030307)|positive regulation of hepatic stellate cell activation (GO:2000491)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of DNA-templated transcription in response to stress (GO:0043620)|regulation of translation in response to stress (GO:0043555)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|synaptic transmission (GO:0007268)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	ATP binding (GO:0005524)|cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)			lung(1)	1		all_cancers(24;2.49e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.00571)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Epithelial(14;1.12e-50)|OV - Ovarian serous cystadenocarcinoma(117;2.89e-29)|Colorectal(126;1.4e-08)|COAD - Colon adenocarcinoma(152;9.31e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000537)|KIRC - Kidney renal clear cell carcinoma(1967;0.000759)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.0361)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.161)|LUSC - Lung squamous cell carcinoma(448;0.234)		CGTGAGATCAAGCCACCCTTC	0.577													A|||	806	0.160942	0.0083	0.2651	5008	,	,		19808	0.1855		0.1938	False		,,,				2504	0.2342				p.K344T		Atlas-SNP	.											.	RPS6KA1	65	.	0			c.A1031C						PASS	.	A	THR/LYS,THR/LYS	209,4197	126.1+/-163.2	5,199,1999	229.0	162.0	185.0		1031,1004	5.5	1.0	1	dbSNP_98	185	2051,6549	357.5+/-330.8	257,1537,2506	yes	missense,missense	RPS6KA1	NM_001006665.1,NM_002953.3	78,78	262,1736,4505	CC,CA,AA		23.8488,4.7435,17.3766	benign,benign	344/745,335/736	26883511	2260,10746	2203	4300	6503	SO:0001583	missense	6195	exon12			AGATCAAGCCACC	BC014966	CCDS284.1, CCDS30649.1	1p	2011-04-05	2002-08-29		ENSG00000117676	ENSG00000117676			10430	protein-coding gene	gene with protein product		601684	"""ribosomal protein S6 kinase, 90kD, polypeptide 1"""			8141249	Standard	NM_001006665		Approved	RSK, RSK1, HU-1	uc001bms.1	Q15418	OTTHUMG00000004003	ENST00000374168.2:c.1004A>C	1.37:g.26883511A>C	ENSP00000363283:p.Lys335Thr	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	125	45	0.36	NM_001006665	A6NGG4|A8K9K7|B2RDY8|B7Z5J0|Q5SVM5|Q5SVM8|Q5SVM9|Q96C05|Q9BQK2	Missense_Mutation	SNP	ENST00000374168.2	37	CCDS284.1	364	0.16666666666666666	7	0.014227642276422764	96	0.26519337016574585	112	0.1958041958041958	149	0.19656992084432717	A	15.44	2.834313	0.50951	0.047435	0.238488	ENSG00000117676	ENST00000374168;ENST00000374166;ENST00000526792;ENST00000374162;ENST00000530003;ENST00000374164;ENST00000531382	T;T;T;T;T;T	0.53206	0.63;0.63;0.63;0.63;0.63;0.63	5.49	5.49	0.81192	AGC-kinase, C-terminal (2);Protein kinase-like domain (1);	0.090341	0.85682	D	0.000000	T	0.00012	0.0000	L	0.37897	1.145	0.09310	P	0.999999877667	B;B;B	0.30793	0.088;0.031;0.295	B;B;B	0.29598	0.104;0.012;0.055	T	0.19353	-1.0308	9	0.49607	T	0.09	.	10.011	0.41986	0.9244:0.0:0.0756:0.0	rs2229712;rs3816540;rs11546002;rs58836104;rs3816540	319;344;335	B7Z2K7;Q15418-2;Q15418	.;.;KS6A1_HUMAN	T	335;324;243;243;319;55;344	ENSP00000363283:K335T;ENSP00000363281:K324T;ENSP00000431651:K243T;ENSP00000363277:K243T;ENSP00000432281:K319T;ENSP00000435412:K344T	ENSP00000363277:K243T	K	+	2	0	RPS6KA1	26756098	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.218000	0.77991	2.093000	0.63338	0.533000	0.62120	AAG	A|0.833;C|0.167	0.167	strong		0.577	RPS6KA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011431.1	NM_002953	
SF3B1	23451	hgsc.bcm.edu	37	2	198257075	198257075	+	Silent	SNP	G	G	A	rs78516934	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:198257075G>A	ENST00000335508.6	-	25	3958	c.3867C>T	c.(3865-3867)aaC>aaT	p.N1289N		NM_012433.2	NP_036565.2	O75533	SF3B1_HUMAN	splicing factor 3b, subunit 1, 155kDa	1289					anterior/posterior pattern specification (GO:0009952)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U12-type spliceosomal complex (GO:0005689)	chromatin binding (GO:0003682)|poly(A) RNA binding (GO:0044822)			NS(35)|breast(10)|central_nervous_system(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(524)|kidney(4)|large_intestine(10)|lung(19)|ovary(1)|pancreas(4)|prostate(6)|salivary_gland(1)|skin(4)|testis(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	633			OV - Ovarian serous cystadenocarcinoma(117;0.246)			TCTTATCATCGTTGTAGATTC	0.358			Mis		myelodysplastic syndrome								G|||	16	0.00319489	0.0008	0.0014	5008	,	,		17476	0.0		0.0139	False		,,,				2504	0.0				p.N1289N		Atlas-SNP	.		Dom	yes		2	2q33.1	23451	"""splicing factor 3b, subunit 1, 155kDa"""		L	.	SF3B1	1038	.	0			c.C3867T						PASS	.	G		5,4401	9.9+/-24.2	0,5,2198	122.0	121.0	121.0		3867	0.9	1.0	2	dbSNP_132	121	86,8514	49.8+/-109.6	0,86,4214	no	coding-synonymous	SF3B1	NM_012433.2		0,91,6412	AA,AG,GG		1.0,0.1135,0.6997		1289/1305	198257075	91,12915	2203	4300	6503	SO:0001819	synonymous_variant	23451	exon25			ATCATCGTTGTAG	AF054284	CCDS33356.1, CCDS46479.1	2q33.1	2014-09-17	2002-08-29		ENSG00000115524	ENSG00000115524			10768	protein-coding gene	gene with protein product		605590	"""splicing factor 3b, subunit 1, 155kD"""			9585501	Standard	XM_005246428		Approved	SAP155, SF3b155, PRPF10, Prp10, Hsh155	uc002uue.3	O75533	OTTHUMG00000154447	ENST00000335508.6:c.3867C>T	2.37:g.198257075G>A		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	106	40	0.377358	NM_012433	E9PCH3	Silent	SNP	ENST00000335508.6	37	CCDS33356.1																																																																																			G|0.993;A|0.007	0.007	strong		0.358	SF3B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335245.2		
MCEMP1	199675	hgsc.bcm.edu	37	19	7743821	7743821	+	Missense_Mutation	SNP	A	A	G	rs72996468	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:7743821A>G	ENST00000333598.3	+	6	953	c.499A>G	c.(499-501)Att>Gtt	p.I167V	CTD-3214H19.16_ENST00000597959.1_Missense_Mutation_p.H39R|TRAPPC5_ENST00000426877.2_5'Flank|TRAPPC5_ENST00000317378.5_5'Flank|TRAPPC5_ENST00000596148.1_5'Flank|C19orf59_ENST00000597445.1_Missense_Mutation_p.I124V	NM_174918.2	NP_777578.2	Q8IX19	MCEM1_HUMAN		167			I -> V (in dbSNP:rs72996468). {ECO:0000269|PubMed:15953541}.			integral component of membrane (GO:0016021)				endometrium(1)|lung(2)|skin(1)|stomach(1)	5						CATAAAAAACATTGACACAAA	0.557											OREG0025208	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	A|||	463	0.0924521	0.0832	0.0821	5008	,	,		12957	0.1052		0.1431	False		,,,				2504	0.047				p.I167V		Atlas-SNP	.											.	C19orf59	15	.	0			c.A499G						PASS	.	A	VAL/ILE	398,4006		23,352,1827	22.0	24.0	23.0		499	-0.2	0.0	19	dbSNP_130	23	1207,7391		92,1023,3184	yes	missense	C19orf59	NM_174918.2	29	115,1375,5011	GG,GA,AA		14.0381,9.0372,12.3443	benign	167/188	7743821	1605,11397	2202	4299	6501	SO:0001583	missense	199675	exon6			AAAAACATTGACA																												ENST00000333598.3:c.499A>G	19.37:g.7743821A>G	ENSP00000329920:p.Ile167Val	Somatic	165	0	0	644	WXS	Illumina HiSeq	Phase_I	184	91	0.494565	NM_174918	Q8IX20	Missense_Mutation	SNP	ENST00000333598.3	37	CCDS12183.1	234	0.10714285714285714	35	0.07113821138211382	33	0.09116022099447514	50	0.08741258741258741	116	0.15303430079155672	A	4.490	0.090819	0.08632	0.090372	0.140381	ENSG00000183019	ENST00000333598	T	0.20881	2.04	3.23	-0.146	0.13432	.	0.504904	0.15100	N	0.280569	T	0.00073	0.0002	N	0.19112	0.55	0.80722	P	0.0	B	0.13594	0.008	B	0.12156	0.007	T	0.31806	-0.9930	9	0.32370	T	0.25	-8.7911	6.0971	0.20027	0.6369:0.0:0.3631:0.0	.	167	Q8IX19	MCEM1_HUMAN	V	167	ENSP00000329920:I167V	ENSP00000329920:I167V	I	+	1	0	C19orf59	7649821	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.106000	0.10890	-0.129000	0.11620	-0.537000	0.04273	ATT	A|0.897;G|0.103	0.103	strong		0.557	C19orf59-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461248.1		
OSBPL6	114880	hgsc.bcm.edu	37	2	179201048	179201048	+	Silent	SNP	G	G	T	rs16866263	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:179201048G>T	ENST00000190611.4	+	9	1054	c.678G>T	c.(676-678)ccG>ccT	p.P226P	OSBPL6_ENST00000359685.3_Silent_p.P226P|OSBPL6_ENST00000392505.2_Silent_p.P226P|OSBPL6_ENST00000409631.1_Silent_p.P226P|OSBPL6_ENST00000357080.4_Silent_p.P226P|OSBPL6_ENST00000315022.2_Silent_p.P205P|OSBPL6_ENST00000409045.3_Silent_p.P226P	NM_032523.3	NP_115912.1	Q9BZF3	OSBL6_HUMAN	oxysterol binding protein-like 6	226					lipid transport (GO:0006869)	cytosol (GO:0005829)|nuclear membrane (GO:0031965)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)	lipid binding (GO:0008289)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(13)|lung(18)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	46			OV - Ovarian serous cystadenocarcinoma(117;0.00578)|Epithelial(96;0.00847)|all cancers(119;0.0335)			ACAGCTTTCCGTGGCAGTCCC	0.443													G|||	350	0.0698882	0.0499	0.0548	5008	,	,		21802	0.0278		0.0567	False		,,,				2504	0.1646				p.P226P		Atlas-SNP	.											OSBPL6_ENST00000392505,mucosal,malignant_melanoma,+2,2	OSBPL6	178	2	0			c.G678T						PASS	.	G	,,,,	218,4188	132.5+/-169.0	6,206,1991	217.0	215.0	216.0		678,678,678,678,615	-11.1	0.2	2	dbSNP_123	216	368,8232	121.8+/-180.9	7,354,3939	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	OSBPL6	NM_001201480.1,NM_001201481.1,NM_001201482.1,NM_032523.3,NM_145739.2	,,,,	13,560,5930	TT,TG,GG		4.2791,4.9478,4.5056	,,,,	226/960,226/904,226/899,226/935,205/939	179201048	586,12420	2203	4300	6503	SO:0001819	synonymous_variant	114880	exon9			CTTTCCGTGGCAG	AF392448	CCDS2277.1, CCDS2278.1, CCDS56150.1, CCDS56151.1, CCDS56152.1	2q32.1	2008-05-27			ENSG00000079156	ENSG00000079156		"""Oxysterol binding proteins"""	16388	protein-coding gene	gene with protein product	"""OSBP-related protein 6"""	606734				11483621	Standard	NM_001201480		Approved	ORP6	uc002uly.3	Q9BZF3	OTTHUMG00000132579	ENST00000190611.4:c.678G>T	2.37:g.179201048G>T		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	51	30	0.588235	NM_001201482	B4DTW1|C4AMC0|C4AME4|D3DPF6|D3DPF7|Q4ZG68|Q53T68|Q59H61|Q7Z4Q1|Q86V84|Q8N9T0|Q96SR1	Silent	SNP	ENST00000190611.4	37	CCDS2277.1																																																																																			G|0.955;T|0.045	0.045	strong		0.443	OSBPL6-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000334393.2	NM_032523	
PITRM1	10531	hgsc.bcm.edu	37	10	3214942	3214942	+	Missense_Mutation	SNP	T	T	C	rs11818724	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:3214942T>C	ENST00000224949.4	-	1	57	c.23A>G	c.(22-24)cAg>cGg	p.Q8R	PITRM1_ENST00000380989.2_Missense_Mutation_p.Q8R|PITRM1_ENST00000451104.2_Silent_p.A10A			Q5JRX3	PREP_HUMAN	pitrilysin metallopeptidase 1	8			Q -> R (in dbSNP:rs11818724). {ECO:0000269|PubMed:15489334}.		positive regulation of catalytic activity (GO:0043085)|proteolysis (GO:0006508)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	enzyme activator activity (GO:0008047)|metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			breast(2)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(5)|liver(1)|lung(5)|ovary(1)|pancreas(1)|prostate(4)|skin(1)|stomach(2)|urinary_tract(3)	33						ACACAGGCCCTGCCGCCCGCC	0.746													T|||	247	0.0493211	0.0416	0.0793	5008	,	,		8780	0.0		0.1004	False		,,,				2504	0.0368				p.Q8R		Atlas-SNP	.											.	PITRM1	109	.	0			c.A23G						PASS	.	T	ARG/GLN,,ARG/GLN	69,3643		2,65,1789	4.0	7.0	6.0		23,30,23	-5.3	0.0	10	dbSNP_120	6	355,7157		7,341,3408	no	missense,coding-synonymous,missense	PITRM1	NM_001242307.1,NM_001242309.1,NM_014889.3	43,,43	9,406,5197	CC,CT,TT		4.7258,1.8588,3.7776	benign,,benign	8/1039,10/940,8/1038	3214942	424,10800	1856	3756	5612	SO:0001583	missense	10531	exon1			AGGCCCTGCCGCC	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.23A>G	10.37:g.3214942T>C	ENSP00000224949:p.Gln8Arg	Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	45	19	0.422222	NM_014889	B3KMJ6|B4E0J8|C9JSL2|E7ES23|O95204|Q2M2G6|Q4VBR1|Q5JRW7|Q7L5Z7|Q9BSI6|Q9BVJ5|Q9UPP8	Missense_Mutation	SNP	ENST00000224949.4	37	CCDS59208.1	133	0.060897435897435896	13	0.026422764227642278	36	0.09944751381215469	6	0.01048951048951049	78	0.10290237467018469	T	2.957	-0.215562	0.06101	0.018588	0.047258	ENSG00000107959	ENST00000224949;ENST00000380989	T;T	0.03635	3.86;3.86	2.65	-5.29	0.02747	.	1.236170	0.05795	N	0.611110	T	0.00073	0.0002	.	.	.	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.48514	-0.9029	8	0.11485	T	0.65	.	5.5752	0.17218	0.0:0.5019:0.2589:0.2392	rs11818724;rs17356065	8;8	Q5JRX3-2;Q5JRX3	.;PREP_HUMAN	R	8	ENSP00000224949:Q8R;ENSP00000370377:Q8R	ENSP00000224949:Q8R	Q	-	2	0	PITRM1	3204942	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.684000	0.05173	-1.341000	0.02225	-2.324000	0.00251	CAG	T|0.938;C|0.062	0.062	strong		0.746	PITRM1-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000046469.2		
NOM1	64434	hgsc.bcm.edu	37	7	156761818	156761818	+	Missense_Mutation	SNP	G	G	A	rs2302445	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:156761818G>A	ENST00000275820.3	+	10	2351	c.2336G>A	c.(2335-2337)cGt>cAt	p.R779H		NM_138400.1	NP_612409.1	Q5C9Z4	NOM1_HUMAN	nucleolar protein with MIF4G domain 1	779			R -> H (in dbSNP:rs2302445).			nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(5)|kidney(4)|large_intestine(9)|lung(7)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	31	Ovarian(565;0.218)	all_hematologic(28;0.0749)	OV - Ovarian serous cystadenocarcinoma(82;0.00301)	UCEC - Uterine corpus endometrioid carcinoma (81;0.169)		CCCAGAGTCCGTTTTTTACGA	0.368													A|||	2240	0.447284	0.4334	0.5231	5008	,	,		15269	0.2778		0.5706	False		,,,				2504	0.4601				p.R779H		Atlas-SNP	.											.	NOM1	73	.	0			c.G2336A						PASS	.	A	HIS/ARG	1930,2476	621.6+/-393.8	435,1060,708	77.0	79.0	78.0		2336	2.7	1.0	7	dbSNP_100	78	4903,3697	529.1+/-381.5	1387,2129,784	yes	missense	NOM1	NM_138400.1	29	1822,3189,1492	AA,AG,GG		42.9884,43.8039,47.4627	benign	779/861	156761818	6833,6173	2203	4300	6503	SO:0001583	missense	64434	exon10			GAGTCCGTTTTTT	AF107455	CCDS34787.1	7q36.3	2014-06-13	2005-03-30	2005-03-30	ENSG00000146909	ENSG00000146909			13244	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 113"""	611269	"""chromosome 7 open reading frame 3"""	C7orf3		10329000	Standard	XM_005249560		Approved	SGD1, PPP1R113	uc003wmy.3	Q5C9Z4	OTTHUMG00000152639	ENST00000275820.3:c.2336G>A	7.37:g.156761818G>A	ENSP00000275820:p.Arg779His	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	74	74	1	NM_138400	Q96I08	Missense_Mutation	SNP	ENST00000275820.3	37	CCDS34787.1	1002	0.45879120879120877	230	0.46747967479674796	198	0.5469613259668509	154	0.2692307692307692	420	0.554089709762533	A	5.608	0.296935	0.10622	0.438039	0.570116	ENSG00000146909	ENST00000275820	T	0.12774	2.65	5.14	2.73	0.32206	.	0.453294	0.25944	N	0.027293	T	0.00012	0.0000	N	0.11789	0.175	0.44871	P	0.0021170000000000355	B	0.18461	0.028	B	0.14023	0.01	T	0.44406	-0.9330	9	0.06365	T	0.9	-13.4943	1.4392	0.02350	0.4974:0.1363:0.2347:0.1316	rs2302445;rs12698008;rs52802201;rs56649293;rs58095136;rs2302445	779	Q5C9Z4	NOM1_HUMAN	H	779	ENSP00000275820:R779H	ENSP00000275820:R779H	R	+	2	0	NOM1	156454579	0.429000	0.25530	0.960000	0.40013	0.912000	0.54170	1.128000	0.31369	0.002000	0.14630	-0.332000	0.08345	CGT	G|0.508;A|0.492	0.492	strong		0.368	NOM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327098.1	NM_138400	
MANSC1	54682	hgsc.bcm.edu	37	12	12496086	12496086	+	Missense_Mutation	SNP	C	C	T	rs3741798	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:12496086C>T	ENST00000535902.1	-	2	726	c.163G>A	c.(163-165)Gta>Ata	p.V55I	MANSC1_ENST00000396349.3_Missense_Mutation_p.V21I			Q9H8J5	MANS1_HUMAN	MANSC domain containing 1	55	MANSC. {ECO:0000255|PROSITE- ProRule:PRU00341}.		V -> I (in dbSNP:rs3741798). {ECO:0000269|PubMed:15489334}.			integral component of membrane (GO:0016021)				breast(2)|endometrium(1)|kidney(2)|large_intestine(4)|lung(9)|skin(1)|stomach(4)	23		Prostate(47;0.0865)		BRCA - Breast invasive adenocarcinoma(232;0.185)		GAAGTATATACGGGCTCATTG	0.388													C|||	401	0.0800719	0.0772	0.0879	5008	,	,		21408	0.0764		0.1163	False		,,,				2504	0.045				p.V55I		Atlas-SNP	.											.	MANSC1	38	.	0			c.G163A						PASS	.	C	ILE/VAL	415,3991	203.5+/-225.9	23,369,1811	170.0	168.0	168.0		163	-2.2	0.0	12	dbSNP_107	168	993,7607	215.0+/-254.5	51,891,3358	yes	missense	MANSC1	NM_018050.2	29	74,1260,5169	TT,TC,CC		11.5465,9.419,10.8258	benign	55/432	12496086	1408,11598	2203	4300	6503	SO:0001583	missense	54682	exon2			TATATACGGGCTC	AK001160	CCDS8648.1	12p13.2	2006-04-12				ENSG00000111261			25505	protein-coding gene	gene with protein product						12975309	Standard	NM_018050		Approved	FLJ10298, LOH12CR3	uc001rai.1	Q9H8J5		ENST00000535902.1:c.163G>A	12.37:g.12496086C>T	ENSP00000438205:p.Val55Ile	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	124	60	0.483871	NM_018050	Q8NEC1|Q9NW60	Missense_Mutation	SNP	ENST00000535902.1	37	CCDS8648.1	213	0.09752747252747253	44	0.08943089430894309	35	0.09668508287292818	56	0.0979020979020979	78	0.10290237467018469	C	0.032	-1.326428	0.01309	0.09419	0.115465	ENSG00000111261	ENST00000535902;ENST00000396349;ENST00000543314	T;T;T	0.36157	1.99;1.99;1.27	5.66	-2.16	0.07080	Seven cysteines (1);Seven cysteines, N-terminal (2);	1.386070	0.05028	N	0.474172	T	0.00144	0.0004	N	0.00677	-1.265	0.58432	P	5.000000000032756E-6	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.32613	-0.9900	9	0.02654	T	1	-5.2156	10.6695	0.45749	0.0:0.4575:0.0:0.5425	rs3741798;rs17846030;rs17859014;rs52831774;rs60985477;rs3741798	21;55	Q9NW60;Q9H8J5	.;MANS1_HUMAN	I	55;21;55	ENSP00000438205:V55I;ENSP00000379638:V21I;ENSP00000437624:V55I	ENSP00000379638:V21I	V	-	1	0	MANSC1	12387353	0.016000	0.18221	0.037000	0.18230	0.332000	0.28634	-0.418000	0.07080	-0.402000	0.07633	-1.063000	0.02288	GTA	C|0.898;T|0.102	0.102	strong		0.388	MANSC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400144.1	NM_018050	
DFNA5	1687	hgsc.bcm.edu	37	7	24758818	24758818	+	Missense_Mutation	SNP	G	G	T	rs754554	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:24758818G>T	ENST00000342947.3	-	4	849	c.424C>A	c.(424-426)Cct>Act	p.P142T	DFNA5_ENST00000409775.3_Missense_Mutation_p.P142T|DFNA5_ENST00000559637.1_5'UTR|DFNA5_ENST00000419307.1_5'UTR|DFNA5_ENST00000545231.1_5'UTR|DFNA5_ENST00000409970.1_5'UTR	NM_004403.2	NP_004394.1	O60443	DFNA5_HUMAN	deafness, autosomal dominant 5	142			P -> T (in dbSNP:rs754554). {ECO:0000269|PubMed:12690205}.		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						TGGAGCACAGGGTTTCTCAGA	0.483													G|||	1298	0.259185	0.1982	0.1383	5008	,	,		22470	0.4444		0.1501	False		,,,				2504	0.3487				p.P142T	GBM(78;184 1250 20134 20900 23600)	Atlas-SNP	.											DFNA5,colon,carcinoma,+1,1	DFNA5	51	1	0			c.C424A						PASS	.	G	THR/PRO,,THR/PRO	925,3481	355.1+/-312.9	106,713,1384	110.0	106.0	107.0		424,,424	0.2	0.0	7	dbSNP_86	107	1230,7370	246.8+/-275.1	79,1072,3149	yes	missense,utr-5,missense	DFNA5	NM_001127453.1,NM_001127454.1,NM_004403.2	38,,38	185,1785,4533	TT,TG,GG		14.3023,20.9941,16.5693	possibly-damaging,,possibly-damaging	142/497,,142/497	24758818	2155,10851	2203	4300	6503	SO:0001583	missense	1687	exon4			GCACAGGGTTTCT	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.424C>A	7.37:g.24758818G>T	ENSP00000339587:p.Pro142Thr	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	47	5	0.106383	NM_001127453	A4D156|B2RAX9|B3KT05|O14590|Q08AQ8|Q9UBV3	Missense_Mutation	SNP	ENST00000342947.3	37	CCDS5389.1	527	0.2413003663003663	90	0.18292682926829268	47	0.1298342541436464	276	0.4825174825174825	114	0.1503957783641161	G	4.384	0.070890	0.08436	0.209941	0.143023	ENSG00000105928	ENST00000342947;ENST00000409775	T;T	0.20881	2.04;2.04	5.17	0.252	0.15545	.	0.885835	0.10104	N	0.715585	T	0.00012	0.0000	M	0.65975	2.015	0.47905	P	4.6000000000001595E-4	B;B	0.30068	0.267;0.267	B;B	0.32805	0.153;0.153	T	0.45264	-0.9273	9	0.16420	T	0.52	-2.0218	8.6313	0.33922	0.4149:0.0:0.5851:0.0	rs754554;rs16873696;rs52826337;rs754554	142;142	A4FTY0;O60443	.;DFNA5_HUMAN	T	142	ENSP00000339587:P142T;ENSP00000386670:P142T	ENSP00000339587:P142T	P	-	1	0	DFNA5	24725343	0.035000	0.19736	0.000000	0.03702	0.002000	0.02628	0.711000	0.25764	-0.022000	0.13986	-0.150000	0.13652	CCT	G|0.798;T|0.202	0.202	strong		0.483	DFNA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214060.2	NM_004403	
AKAP9	10142	hgsc.bcm.edu	37	7	91708898	91708898	+	Missense_Mutation	SNP	A	A	G	rs35759833	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:91708898A>G	ENST00000359028.2	+	32	7712	c.7487A>G	c.(7486-7488)aAa>aGa	p.K2496R	AKAP9_ENST00000358100.2_Missense_Mutation_p.K2496R|AKAP9_ENST00000356239.3_Missense_Mutation_p.K2484R			Q99996	AKAP9_HUMAN	A kinase (PRKA) anchor protein 9	2496	Glu-rich.		K -> R (in dbSNP:rs35759833).		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)			ACATACTTCAAATCTTTTGAA	0.378			T	BRAF	papillary thyroid								A|||	328	0.0654952	0.0136	0.0605	5008	,	,		19752	0.0327		0.1252	False		,,,				2504	0.1115				p.K2484R		Atlas-SNP	.		Dom	yes		7	7q21-q22	10142	A kinase (PRKA) anchor protein (yotiao) 9		E	AKAP9_ENST00000356239,colon,carcinoma,0,2	AKAP9	788	2	0			c.A7451G						PASS	.	A	ARG/LYS,ARG/LYS	134,4272	93.4+/-132.2	2,130,2071	54.0	56.0	55.0		7451,7427	-8.7	0.0	7	dbSNP_126	55	1095,7505	225.7+/-261.6	72,951,3277	yes	missense,missense	AKAP9	NM_005751.4,NM_147185.2	26,26	74,1081,5348	GG,GA,AA		12.7326,3.0413,9.4495	benign,benign	2484/3908,2476/3900	91708898	1229,11777	2203	4300	6503	SO:0001583	missense	10142	exon31			ACTTCAAATCTTT	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.7487A>G	7.37:g.91708898A>G	ENSP00000351922:p.Lys2496Arg	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	52	19	0.365385	NM_005751	A4D1F0|A4D1F2|A4D1F4|O14869|O43355|O94895|Q75N20|Q9UQH3|Q9UQQ4|Q9Y6B8|Q9Y6Y2	Missense_Mutation	SNP	ENST00000359028.2	37		146	0.06684981684981685	10	0.02032520325203252	24	0.06629834254143646	9	0.015734265734265736	103	0.1358839050131926	A	2.366	-0.345577	0.05208	0.030413	0.127326	ENSG00000127914	ENST00000356239;ENST00000359028;ENST00000358100;ENST00000413120;ENST00000394534	T;T;T;T	0.03386	4.04;4.04;4.05;3.95	4.37	-8.74	0.00838	.	1.680560	0.03658	N	0.242093	T	0.00012	0.0000	N	0.12182	0.205	0.80722	P	0.0	B;B;B;B	0.06786	0.0;0.0;0.001;0.0	B;B;B;B	0.04013	0.0;0.0;0.001;0.0	T	0.45293	-0.9271	9	0.11794	T	0.64	.	5.2652	0.15595	0.1954:0.2911:0.423:0.0905	rs35759833;rs61749903	2488;2496;2484;2476	Q99996-6;Q99996;Q99996-2;Q99996-3	.;AKAP9_HUMAN;.;.	R	2484;2496;2496;2488;330	ENSP00000348573:K2484R;ENSP00000351922:K2496R;ENSP00000350813:K2496R;ENSP00000378042:K330R	ENSP00000348573:K2484R	K	+	2	0	AKAP9	91546834	0.000000	0.05858	0.000000	0.03702	0.172000	0.22775	-0.864000	0.04254	-1.991000	0.00976	-0.334000	0.08254	AAA	A|0.911;G|0.089	0.089	strong		0.378	AKAP9-202	KNOWN	basic	protein_coding	protein_coding		NM_005751	
BRD8	10902	hgsc.bcm.edu	37	5	137475787	137475787	+	Silent	SNP	C	C	T	rs423258	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:137475787C>T	ENST00000254900.5	-	27	4055	c.3684G>A	c.(3682-3684)gtG>gtA	p.V1228V	NME5_ENST00000265191.2_5'Flank	NM_139199.1	NP_631938	Q9H0E9	BRD8_HUMAN	bromodomain containing 8	1228					cell surface receptor signaling pathway (GO:0007166)|chromatin organization (GO:0006325)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|intracellular receptor signaling pathway (GO:0030522)|regulation of growth (GO:0040008)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)	mitochondrion (GO:0005739)|NuA4 histone acetyltransferase complex (GO:0035267)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Swr1 complex (GO:0000812)	sequence-specific DNA binding transcription factor activity (GO:0003700)|thyroid hormone receptor activity (GO:0004887)	p.V1228V(1)		breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(9)|ovary(1)|prostate(1)|skin(1)|stomach(3)|urinary_tract(1)	35			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)			TTCCATCATCCACTGGGTTAG	0.433													C|||	1486	0.296725	0.0862	0.4035	5008	,	,		17057	0.3839		0.3091	False		,,,				2504	0.4029				p.V1228V		Atlas-SNP	.											BRD8,NS,carcinoma,0,1	BRD8	192	1	1	Substitution - coding silent(1)	stomach(1)	c.G3684A						PASS	.	C		653,3753	281.1+/-275.7	51,551,1601	157.0	149.0	152.0		3684	4.2	0.8	5	dbSNP_80	152	3061,5539	471.7+/-368.2	535,1991,1774	no	coding-synonymous	BRD8	NM_139199.1		586,2542,3375	TT,TC,CC		35.593,14.8207,28.5561		1228/1236	137475787	3714,9292	2203	4300	6503	SO:0001819	synonymous_variant	10902	exon27			ATCATCCACTGGG	AF016270	CCDS4198.1, CCDS34241.1, CCDS54907.1	5q31	2008-02-05			ENSG00000112983	ENSG00000112983			19874	protein-coding gene	gene with protein product		602848				8611617, 9368056	Standard	NM_001164326		Approved	SMAP, p120	uc003lcf.1	Q9H0E9	OTTHUMG00000129204	ENST00000254900.5:c.3684G>A	5.37:g.137475787C>T		Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	141	140	0.992908	NM_139199	O43178|Q15355|Q58AB0|Q59GN0|Q969M9	Silent	SNP	ENST00000254900.5	37	CCDS4198.1																																																																																			C|0.714;T|0.286	0.286	strong		0.433	BRD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251282.3	NM_006696	
PGLS	25796	hgsc.bcm.edu	37	19	17628587	17628587	+	Silent	SNP	A	A	G	rs6743	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:17628587A>G	ENST00000252603.2	+	4	611	c.567A>G	c.(565-567)acA>acG	p.T189T	CTD-3131K8.3_ENST00000596192.1_RNA	NM_012088.2	NP_036220.1	O95336	6PGL_HUMAN	6-phosphogluconolactonase	189					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						TGACCCTCACACTACCTGTCC	0.572													A|||	3010	0.601038	0.8169	0.6398	5008	,	,		18822	0.4573		0.5596	False		,,,				2504	0.4724				p.T189T		Atlas-SNP	.											.	PGLS	12	.	0			c.A567G						PASS	.	A		3431,975	733.1+/-410.4	1356,719,128	116.0	93.0	101.0		567	-11.9	0.0	19	dbSNP_52	101	4624,3976	601.0+/-394.3	1250,2124,926	no	coding-synonymous	PGLS	NM_012088.2		2606,2843,1054	GG,GA,AA		46.2326,22.1289,38.067		189/259	17628587	8055,4951	2203	4300	6503	SO:0001819	synonymous_variant	25796	exon4			CCTCACACTACCT	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.567A>G	19.37:g.17628587A>G		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	70	70	1	NM_012088		Silent	SNP	ENST00000252603.2	37	CCDS12361.1																																																																																			A|0.390;G|0.610	0.610	strong		0.572	PGLS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464154.1		
SULT4A1	25830	hgsc.bcm.edu	37	22	44234792	44234792	+	Nonsense_Mutation	SNP	G	G	A	rs199511302		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:44234792G>A	ENST00000330884.4	-	4	583	c.463C>T	c.(463-465)Cga>Tga	p.R155*	SULT4A1_ENST00000540422.1_Intron|SULT4A1_ENST00000249130.5_Nonsense_Mutation_p.R155*	NM_014351.3	NP_055166.1	Q9BR01	ST4A1_HUMAN	sulfotransferase family 4A, member 1	155					3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	sulfotransferase activity (GO:0008146)			kidney(1)|large_intestine(3)|lung(4)|ovary(1)	9		Ovarian(80;0.024)|all_neural(38;0.0416)		Colorectal(1;0.00242)|READ - Rectum adenocarcinoma(1;0.0419)		AAGGTGCCTCGGTAGCTCATG	0.537																																					p.R155X		Atlas-SNP	.											SULT4A1,NS,carcinoma,+1,1	SULT4A1	26	1	0			c.C463T						scavenged	.						98.0	82.0	87.0					22																	44234792		2203	4300	6503	SO:0001587	stop_gained	25830	exon4			TGCCTCGGTAGCT	AF188698	CCDS14051.1	22q13.2	2012-11-05			ENSG00000130540	ENSG00000130540		"""Sulfotransferases, cytosolic"""	14903	protein-coding gene	gene with protein product		608359				10698717	Standard	NM_014351		Approved	SULTX3, hBR-STL-1	uc003bee.1	Q9BR01	OTTHUMG00000141314	ENST00000330884.4:c.463C>T	22.37:g.44234792G>A	ENSP00000332565:p.Arg155*	Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	124	2	0.016129	NM_014351	B2R7N3|O43728	Nonsense_Mutation	SNP	ENST00000330884.4	37	CCDS14051.1	.	.	.	.	.	.	.	.	.	.	G	39	7.655218	0.98415	.	.	ENSG00000130540	ENST00000330884;ENST00000249130	.	.	.	4.82	3.75	0.43078	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.15952	T	0.53	.	12.4765	0.55817	0.0:0.0:0.7167:0.2833	.	.	.	.	X	155	.	ENSP00000249130:R155X	R	-	1	2	SULT4A1	42566125	1.000000	0.71417	0.996000	0.52242	0.992000	0.81027	3.768000	0.55295	2.230000	0.72887	0.561000	0.74099	CGA	G|0.999;T|0.001	.	alt		0.537	SULT4A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280660.2	NM_014351	
USP24	23358	hgsc.bcm.edu	37	1	55620442	55620442	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:55620442A>G	ENST00000294383.6	-	13	1455	c.1456T>C	c.(1456-1458)Tca>Cca	p.S486P	USP24_ENST00000407756.1_Missense_Mutation_p.S374P	NM_015306.2	NP_056121.2	Q9UPU5	UBP24_HUMAN	ubiquitin specific peptidase 24	486					ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type peptidase activity (GO:0008234)|ubiquitinyl hydrolase activity (GO:0036459)			breast(4)|cervix(1)|endometrium(8)|kidney(13)|large_intestine(7)|lung(16)|ovary(6)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	60						ACAGTAGATGATTGTCCTGAC	0.378																																					p.S486P		Atlas-SNP	.											USP24_ENST00000294383,NS,carcinoma,+2,2	USP24	323	2	0			c.T1456C						scavenged	.						70.0	65.0	66.0					1																	55620442		1830	4091	5921	SO:0001583	missense	23358	exon13			TAGATGATTGTCC	AB028980	CCDS44154.1, CCDS44154.2	1p32.3	2008-04-11	2005-08-08		ENSG00000162402	ENSG00000162402		"""Ubiquitin-specific peptidases"""	12623	protein-coding gene	gene with protein product		610569	"""ubiquitin specific protease 24"""			12838346	Standard	NM_015306		Approved	KIAA1057	uc021onw.1	Q9UPU5	OTTHUMG00000008135	ENST00000294383.6:c.1456T>C	1.37:g.55620442A>G	ENSP00000294383:p.Ser486Pro	Somatic	204	0	0		WXS	Illumina HiSeq	Phase_I	178	3	0.0168539	NM_015306	Q6ZSY2|Q8N2Y4|Q9NXD1	Missense_Mutation	SNP	ENST00000294383.6	37	CCDS44154.2	.	.	.	.	.	.	.	.	.	.	A	13.15	2.152531	0.38021	.	.	ENSG00000162402	ENST00000294383;ENST00000407756	T;T	0.78924	-0.27;-1.22	5.75	5.75	0.90469	.	0.000000	0.64402	D	0.000002	T	0.63165	0.2488	N	0.16478	0.41	0.44643	D	0.997622	B	0.02656	0.0	B	0.01281	0.0	T	0.59878	-0.7371	10	0.44086	T	0.13	.	11.1506	0.48455	0.9288:0.0:0.0712:0.0	.	374	B7WPF4	.	P	486;374	ENSP00000294383:S486P;ENSP00000385700:S374P	ENSP00000294383:S486P	S	-	1	0	USP24	55393030	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	5.976000	0.70484	2.188000	0.69820	0.528000	0.53228	TCA	.	.	none		0.378	USP24-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022275.2		
CAV1	857	hgsc.bcm.edu	37	7	116165140	116165140	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:116165140C>A	ENST00000341049.2	+	1	302	c.24C>A	c.(22-24)gaC>gaA	p.D8E	CAV1_ENST00000393467.1_5'Flank|CAV1_ENST00000393470.1_Missense_Mutation_p.D8E|CAV1_ENST00000393468.1_5'Flank|CAV1_ENST00000405348.1_5'Flank	NM_001753.4	NP_001744.2	Q03135	CAV1_HUMAN	caveolin 1, caveolae protein, 22kDa	8					angiogenesis (GO:0001525)|apoptotic signaling pathway (GO:0097190)|blood coagulation (GO:0007596)|calcium ion homeostasis (GO:0055074)|calcium ion transport (GO:0006816)|caveola assembly (GO:0070836)|caveolin-mediated endocytosis (GO:0072584)|cellular calcium ion homeostasis (GO:0006874)|cellular response to hyperoxia (GO:0071455)|cellular response to starvation (GO:0009267)|cholesterol homeostasis (GO:0042632)|cholesterol transport (GO:0030301)|cytosolic calcium ion homeostasis (GO:0051480)|inactivation of MAPK activity (GO:0000188)|lactation (GO:0007595)|leukocyte migration (GO:0050900)|lipid storage (GO:0019915)|maintenance of protein location in cell (GO:0032507)|mammary gland development (GO:0030879)|mammary gland involution (GO:0060056)|MAPK cascade (GO:0000165)|membrane depolarization (GO:0051899)|negative regulation of anoikis (GO:2000811)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cytokine-mediated signaling pathway (GO:0001960)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of epithelial cell differentiation (GO:0030857)|negative regulation of JAK-STAT cascade (GO:0046426)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of nitric oxide biosynthetic process (GO:0045019)|negative regulation of nitric-oxide synthase activity (GO:0051001)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|negative regulation of pinocytosis (GO:0048550)|negative regulation of protein binding (GO:0032091)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of tyrosine phosphorylation of Stat5 protein (GO:0042524)|nitric oxide homeostasis (GO:0033484)|nitric oxide metabolic process (GO:0046209)|positive regulation of calcium ion transport into cytosol (GO:0010524)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of metalloenzyme activity (GO:0048554)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of vasoconstriction (GO:0045907)|protein homooligomerization (GO:0051260)|protein localization (GO:0008104)|receptor internalization involved in canonical Wnt signaling pathway (GO:2000286)|regulation of blood coagulation (GO:0030193)|regulation of fatty acid metabolic process (GO:0019217)|regulation of nitric-oxide synthase activity (GO:0050999)|regulation of peptidase activity (GO:0052547)|regulation of smooth muscle contraction (GO:0006940)|regulation of the force of heart contraction by chemical signal (GO:0003057)|response to calcium ion (GO:0051592)|response to estrogen (GO:0043627)|response to hypoxia (GO:0001666)|response to ischemia (GO:0002931)|response to progesterone (GO:0032570)|skeletal muscle tissue development (GO:0007519)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|triglyceride metabolic process (GO:0006641)|vasculogenesis (GO:0001570)|vasoconstriction (GO:0042310)|vesicle organization (GO:0016050)|viral process (GO:0016032)	acrosomal membrane (GO:0002080)|apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|caveola (GO:0005901)|cell cortex (GO:0005938)|cilium (GO:0005929)|cytoplasmic vesicle (GO:0031410)|endocytic vesicle membrane (GO:0030666)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|focal adhesion (GO:0005925)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|lipid particle (GO:0005811)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	cholesterol binding (GO:0015485)|enzyme binding (GO:0019899)|nitric-oxide synthase binding (GO:0050998)|patched binding (GO:0005113)|peptidase activator activity (GO:0016504)|protein complex scaffold (GO:0032947)|receptor binding (GO:0005102)|structural molecule activity (GO:0005198)			endometrium(1)|large_intestine(1)|lung(1)|urinary_tract(1)	4	all_epithelial(6;1.42e-06)|Lung NSC(10;0.0056)|all_lung(10;0.00609)		STAD - Stomach adenocarcinoma(10;0.00878)			AATACGTAGACTCGGAGGTAG	0.612																																					p.D8E		Atlas-SNP	.											.	CAV1	13	.	0			c.C24A						PASS	.						87.0	100.0	96.0					7																	116165140		2203	4300	6503	SO:0001583	missense	857	exon1			CGTAGACTCGGAG	AF125348	CCDS5767.1, CCDS55156.1	7q31	2006-02-09	2002-08-29		ENSG00000105974	ENSG00000105974			1527	protein-coding gene	gene with protein product		601047	"""caveolin 1, caveolae protein, 22kD"""	CAV		10087206	Standard	NM_001753		Approved		uc003vif.2	Q03135	OTTHUMG00000023413	ENST00000341049.2:c.24C>A	7.37:g.116165140C>A	ENSP00000339191:p.Asp8Glu	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	92	37	0.402174	NM_001753	Q9UGP1|Q9UNG1|Q9UQH6	Missense_Mutation	SNP	ENST00000341049.2	37	CCDS5767.1	.	.	.	.	.	.	.	.	.	.	C	16.66	3.184175	0.57800	.	.	ENSG00000105974	ENST00000341049;ENST00000393470	D;D	0.93189	-3.18;-3.06	4.71	2.91	0.33838	.	0.683428	0.14907	N	0.291489	D	0.90307	0.6968	L	0.56769	1.78	0.80722	D	1	B	0.09022	0.002	B	0.09377	0.004	D	0.86138	0.1579	10	0.66056	D	0.02	-15.711	8.0118	0.30357	0.0:0.7413:0.0:0.2587	.	8	Q03135	CAV1_HUMAN	E	8	ENSP00000339191:D8E;ENSP00000377113:D8E	ENSP00000339191:D8E	D	+	3	2	CAV1	115952376	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	0.667000	0.25112	0.696000	0.31696	0.650000	0.86243	GAC	.	.	none		0.612	CAV1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000059734.4	NM_001753	
RAVER1	125950	hgsc.bcm.edu	37	19	10439501	10439501	+	Silent	SNP	C	C	T	rs3745263	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:10439501C>T	ENST00000293677.6	-	3	705	c.624G>A	c.(622-624)tcG>tcA	p.S208S		NM_133452.2	NP_597709.2	Q8IY67	RAVR1_HUMAN	ribonucleoprotein, PTB-binding 1	191	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.					cytoplasm (GO:0005737)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(3)|large_intestine(1)|lung(8)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)	18			OV - Ovarian serous cystadenocarcinoma(20;1.81e-09)|Epithelial(33;3.65e-06)|all cancers(31;8.35e-06)			CCAGCAGGTCCGACTTGGCAC	0.632													C|||	108	0.0215655	0.0015	0.0058	5008	,	,		13773	0.0407		0.0338	False		,,,				2504	0.0276				p.S208S		Atlas-SNP	.											.	RAVER1	67	.	0			c.G624A						PASS	.	C		40,4254		0,40,2107	24.0	30.0	28.0		624	-6.7	0.9	19	dbSNP_107	28	275,8223		6,263,3980	no	coding-synonymous	RAVER1	NM_133452.2		6,303,6087	TT,TC,CC		3.2361,0.9315,2.4625		208/757	10439501	315,12477	2147	4249	6396	SO:0001819	synonymous_variant	125950	exon3			CAGGTCCGACTTG		CCDS45960.1	19p13.2	2013-02-12				ENSG00000161847		"""RNA binding motif (RRM) containing"""	30296	protein-coding gene	gene with protein product		609950				11853319, 11724819	Standard	NM_133452		Approved	KIAA1978	uc002moa.3	Q8IY67		ENST00000293677.6:c.624G>A	19.37:g.10439501C>T		Somatic	249	0	0		WXS	Illumina HiSeq	Phase_I	187	86	0.459893	NM_133452	A6NMU4|Q8IY60|Q8TF24	Silent	SNP	ENST00000293677.6	37	CCDS45960.1																																																																																			C|0.971;T|0.029	0.029	strong		0.632	RAVER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451227.1	NM_133452	
C17orf97	400566	hgsc.bcm.edu	37	17	263645	263645	+	Silent	SNP	C	C	T	rs71369083|rs71145728		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:263645C>T	ENST00000360127.6	+	2	1027	c.1011C>T	c.(1009-1011)ccC>ccT	p.P337P	AC108004.3_ENST00000466740.2_RNA|C17orf97_ENST00000571106.1_Intron	NM_001013672.4	NP_001013694.4	Q6ZQX7	CQ097_HUMAN	chromosome 17 open reading frame 97	367	20 X 10 AA approximative tandem repeat of A-L-K-G-F-H-P-D-P-E.									breast(1)|kidney(2)|large_intestine(4)|lung(4)|ovary(1)|prostate(1)|skin(1)	14						GCTTCCACCCCGACCCCGAGG	0.692																																					p.P337P		Atlas-SNP	.											C17orf97_ENST00000360127,NS,carcinoma,+2,2	C17orf97	76	2	0			c.C1011T						scavenged	.																																			SO:0001819	synonymous_variant	400566	exon2			CCACCCCGACCCC	AK128660, BC057385	CCDS32519.2	17p13.3	2008-08-15			ENSG00000187624	ENSG00000187624			33800	protein-coding gene	gene with protein product						12477932	Standard	NM_001013672		Approved	LOC400566	uc021tna.1	Q6ZQX7	OTTHUMG00000132479	ENST00000360127.6:c.1011C>T	17.37:g.263645C>T		Somatic	210	6	0.0285714		WXS	Illumina HiSeq	Phase_I	115	6	0.0521739	NM_001013672	A5D8T6|Q6NSI2|Q6PFW9	Silent	SNP	ENST00000360127.6	37	CCDS32519.2																																																																																			C|0.981;T|0.019	0.019	strong		0.692	C17orf97-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255648.4	NM_001013672	
C14orf37	145407	hgsc.bcm.edu	37	14	58563694	58563694	+	Missense_Mutation	SNP	G	G	C	rs2273442	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:58563694G>C	ENST00000267485.7	-	5	2031	c.1837C>G	c.(1837-1839)Caa>Gaa	p.Q613E		NM_001001872.2	NP_001001872.2	Q86TY3	CN037_HUMAN	chromosome 14 open reading frame 37	613	Glu-rich.		Q -> E (in dbSNP:rs2273442).			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						tcatcttcttGTCCCTCTAGG	0.378													C|||	2448	0.488818	0.615	0.487	5008	,	,		22445	0.3502		0.502	False		,,,				2504	0.4489				p.Q613E		Atlas-SNP	.											.	C14orf37	87	.	0			c.C1837G						PASS	.	C	GLU/GLN	2625,1781	526.5+/-371.9	784,1057,362	157.0	121.0	133.0		1837	4.1	1.0	14	dbSNP_100	133	4457,4143	564.7+/-388.4	1159,2139,1002	yes	missense	C14orf37	NM_001001872.2	29	1943,3196,1364	CC,CG,GG		48.1744,40.4222,45.5482	benign	613/775	58563694	7082,5924	2203	4300	6503	SO:0001583	missense	145407	exon5			CTTCTTGTCCCTC		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.1837C>G	14.37:g.58563694G>C	ENSP00000267485:p.Gln613Glu	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	91	91	1	NM_001001872	A8K8Z8|Q6P5Q1|Q86TY1	Missense_Mutation	SNP	ENST00000267485.7	37	CCDS32089.1	1053	0.48214285714285715	297	0.6036585365853658	171	0.4723756906077348	207	0.3618881118881119	378	0.49868073878627966	C	0.552	-0.849121	0.02651	0.595778	0.518256	ENSG00000139971	ENST00000267485;ENST00000438670	T	0.05081	3.5	4.14	4.14	0.48551	Armadillo-like helical (1);	0.400018	0.23910	N	0.043358	T	0.00012	0.0000	N	0.00246	-1.78	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.38845	-0.9642	9	0.02654	T	1	-2.3617	11.3564	0.49617	0.0:0.8154:0.1846:0.0	rs2273442;rs17832831;rs56475407;rs2273442	651;613;613	B4DMS4;A8K990;Q86TY3	.;.;CN037_HUMAN	E	613;651	ENSP00000267485:Q613E	ENSP00000267485:Q613E	Q	-	1	0	C14orf37	57633447	1.000000	0.71417	1.000000	0.80357	0.748000	0.42578	3.297000	0.51810	0.883000	0.36040	-0.216000	0.12614	CAA	G|0.481;C|0.519	0.519	strong		0.378	C14orf37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412059.1	NM_001001872	
ACSM5	54988	hgsc.bcm.edu	37	16	20441077	20441077	+	Missense_Mutation	SNP	A	A	G	rs12931877	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:20441077A>G	ENST00000331849.4	+	8	1226	c.1079A>G	c.(1078-1080)cAc>cGc	p.H360R		NM_017888.2	NP_060358.2	Q6NUN0	ACSM5_HUMAN	acyl-CoA synthetase medium-chain family member 5	360			H -> R (in dbSNP:rs12931877). {ECO:0000269|PubMed:12654705}.		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						AAGTGGAAACACCAGACTGGT	0.587													G|||	455	0.0908546	0.0522	0.0865	5008	,	,		16674	0.1667		0.0378	False		,,,				2504	0.1227				p.H360R		Atlas-SNP	.											.	ACSM5	101	.	0			c.A1079G						PASS	.	G	ARG/HIS	14,4392	821.2+/-416.4	2,10,2191	88.0	90.0	90.0		1079	-3.6	0.4	16	dbSNP_121	90	25,8575	815.3+/-407.0	1,23,4276	no	missense	ACSM5	NM_017888.2	29	3,33,6467	GG,GA,AA		0.2907,0.3177,0.2999	benign	360/580	20441077	39,12967	2203	4300	6503	SO:0001583	missense	54988	exon8			GGAAACACCAGAC		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.1079A>G	16.37:g.20441077A>G	ENSP00000327916:p.His360Arg	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	40	12	0.3	NM_017888	Q96AV1|Q96CX8|Q9NWV3	Missense_Mutation	SNP	ENST00000331849.4	37	CCDS10585.1	199	0.09111721611721611	23	0.046747967479674794	30	0.08287292817679558	108	0.1888111888111888	38	0.05013192612137203	G	0.236	-1.017660	0.02078	0.003177	0.002907	ENSG00000183549	ENST00000331849	T	0.45276	0.9	4.44	-3.59	0.04583	AMP-dependent synthetase/ligase (1);	1.074500	0.07217	N	0.860124	T	0.00012	0.0000	N	0.01109	-1.01	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.19647	-1.0299	9	0.16420	T	0.52	2.3997	3.4546	0.07511	0.5429:0.1197:0.2157:0.1216	rs12931877	360	Q6NUN0	ACSM5_HUMAN	R	360	ENSP00000327916:H360R	ENSP00000327916:H360R	H	+	2	0	ACSM5	20348578	0.000000	0.05858	0.351000	0.25721	0.088000	0.18126	-2.326000	0.01114	-0.856000	0.04120	-0.996000	0.02517	CAC	A|0.969;G|0.031	0.031	strong		0.587	ACSM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254413.1	NM_017888	
TMPRSS11E	28983	hgsc.bcm.edu	37	4	69337325	69337325	+	Missense_Mutation	SNP	C	C	G	rs2603188	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	412	0	0		WXS	Illumina HiSeq	Phase_I	325	324	0.996923	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	
CBX3	11335	hgsc.bcm.edu	37	7	26245986	26245986	+	Splice_Site	SNP	A	A	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:26245986A>T	ENST00000337620.4	+	3	452		c.e3-1		CBX3_ENST00000409747.1_Splice_Site|CBX3_ENST00000396386.2_Splice_Site|CBX3_ENST00000497498.1_Splice_Site	NM_007276.4	NP_009207.2	Q13185	CBX3_HUMAN	chromobox homolog 3						chromatin remodeling (GO:0006338)|negative regulation of transcription, DNA-templated (GO:0045892)|rhythmic process (GO:0048511)|transcription, DNA-templated (GO:0006351)	chromatin (GO:0000785)|condensed chromosome, centromeric region (GO:0000779)|nuclear envelope (GO:0005635)|nuclear euchromatin (GO:0005719)|nuclear heterochromatin (GO:0005720)|nuclear inner membrane (GO:0005637)|nuclear pericentric heterochromatin (GO:0031618)|nucleus (GO:0005634)|spindle (GO:0005819)	enzyme binding (GO:0019899)|histone methyltransferase binding (GO:1990226)|identical protein binding (GO:0042802)|protein domain specific binding (GO:0019904)			endometrium(4)|large_intestine(2)|lung(2)|ovary(1)	9						GTTTTATTTTAGCAAAAAATG	0.308																																					.		Atlas-SNP	.											CBX3,colon,adenoma,0,1	CBX3	25	1	0			c.25-2A>T						scavenged	.						32.0	33.0	32.0					7																	26245986		2200	4300	6500	SO:0001630	splice_region_variant	11335	exon3			TATTTTAGCAAAA	U26312	CCDS5398.1	7p15.2	2010-07-06	2010-06-24		ENSG00000122565	ENSG00000122565			1553	protein-coding gene	gene with protein product	"""HP1 gamma homolog (Drosophila)"""	604477	"""chromobox homolog 3 (Drosophila HP1 gamma)"""			8663349	Standard	NM_016587		Approved	HP1Hs-gamma	uc003sxu.3	Q13185	OTTHUMG00000022911	ENST00000337620.4:c.25-1A>T	7.37:g.26245986A>T		Somatic	37	1	0.027027		WXS	Illumina HiSeq	Phase_I	26	6	0.230769	NM_007276	Q96CD7|Q99409|Q9BVS3|Q9P0Z6	Splice_Site	SNP	ENST00000337620.4	37	CCDS5398.1	.	.	.	.	.	.	.	.	.	.	A	16.00	2.999549	0.54147	.	.	ENSG00000122565	ENST00000337620;ENST00000396386;ENST00000456948;ENST00000409747	.	.	.	5.75	5.75	0.90469	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.2344	0.54508	0.8582:0.1418:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	CBX3	26212511	1.000000	0.71417	1.000000	0.80357	0.892000	0.51952	3.092000	0.50207	2.323000	0.78572	0.533000	0.62120	.	.	.	none		0.308	CBX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214117.1	NM_007276	Intron
DHDH	27294	hgsc.bcm.edu	37	19	49447713	49447713	+	Missense_Mutation	SNP	G	G	A	rs3765148	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:49447713G>A	ENST00000221403.2	+	6	884	c.844G>A	c.(844-846)Ggg>Agg	p.G282R	DHDH_ENST00000522614.1_Intron|DHDH_ENST00000523250.1_Missense_Mutation_p.G143R	NM_014475.3	NP_055290.1	Q9UQ10	DHDH_HUMAN	dihydrodiol dehydrogenase (dimeric)	282			G -> R (in dbSNP:rs3765148).		carbohydrate metabolic process (GO:0005975)|D-xylose catabolic process (GO:0042843)		D-xylose 1-dehydrogenase (NADP+) activity (GO:0047837)|electron carrier activity (GO:0009055)|NAD(P)+ transhydrogenase activity (GO:0008746)|trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity (GO:0047115)			central_nervous_system(1)|large_intestine(3)|lung(3)|ovary(1)|soft_tissue(1)	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;0.000158)|all cancers(93;0.000258)|Epithelial(262;0.0173)|GBM - Glioblastoma multiforme(486;0.0179)		TTTTGACAACGGGGCAGGCAT	0.617													g|||	371	0.0740815	0.1248	0.0663	5008	,	,		20067	0.0506		0.0636	False		,,,				2504	0.046				p.G282R		Atlas-SNP	.											.	DHDH	35	.	0			c.G844A						PASS	.	A	ARG/GLY	456,3950	218.1+/-236.3	30,396,1777	68.0	66.0	66.0		844	0.1	0.0	19	dbSNP_107	66	520,8080	146.2+/-201.8	14,492,3794	yes	missense	DHDH	NM_014475.3	125	44,888,5571	AA,AG,GG		6.0465,10.3495,7.5042	probably-damaging	282/335	49447713	976,12030	2203	4300	6503	SO:0001583	missense	27294	exon6			GACAACGGGGCAG	AB021933	CCDS12741.1	19q13.3	2008-02-05			ENSG00000104808	ENSG00000104808	1.3.1.20		17887	protein-coding gene	gene with protein product		606377				10477285	Standard	NM_014475		Approved	HUM2DD	uc002ple.1	Q9UQ10	OTTHUMG00000165029	ENST00000221403.2:c.844G>A	19.37:g.49447713G>A	ENSP00000221403:p.Gly282Arg	Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	145	75	0.517241	NM_014475		Missense_Mutation	SNP	ENST00000221403.2	37	CCDS12741.1	164	0.07509157509157509	56	0.11382113821138211	24	0.06629834254143646	35	0.06118881118881119	49	0.06464379947229551	g	14.99	2.699163	0.48307	0.103495	0.060465	ENSG00000104808	ENST00000221403;ENST00000523250	T;T	0.22539	1.95;1.95	5.03	0.0863	0.14445	.	0.379543	0.31519	N	0.007503	T	0.00524	0.0017	L	0.58583	1.82	0.80722	P	0.0	D	0.89917	1.0	P	0.60236	0.871	T	0.03157	-1.1066	9	0.45353	T	0.12	-8.112	2.9488	0.05855	0.0883:0.157:0.4313:0.3234	rs3765148;rs52813110;rs59994821;rs3765148	282	Q9UQ10	DHDH_HUMAN	R	282;143	ENSP00000221403:G282R;ENSP00000428935:G143R	ENSP00000221403:G282R	G	+	1	0	DHDH	54139525	0.021000	0.18746	0.000000	0.03702	0.020000	0.10135	0.960000	0.29253	0.380000	0.24823	-0.320000	0.08662	GGG	G|0.920;A|0.080	0.080	strong		0.617	DHDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381477.1	NM_014475	
FAM46C	54855	hgsc.bcm.edu	37	1	118165691	118165691	+	Missense_Mutation	SNP	C	C	G	rs1630312	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:118165691C>G	ENST00000369448.3	+	2	448	c.201C>G	c.(199-201)caC>caG	p.H67Q		NM_017709.3	NP_060179.2	Q5VWP2	FA46C_HUMAN	family with sequence similarity 46, member C	67			H -> Q (in dbSNP:rs1630312).							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)		TCAAAGTGCACGACGTCCGGC	0.557			"""Mis, F, O"""		MM					Multiple Myeloma(3;1.13e-06)			G|||	635	0.126797	0.2617	0.085	5008	,	,		22050	0.122		0.0626	False		,,,				2504	0.045				p.H67Q		Atlas-SNP	.		Rec	yes		1	1p12	54855	"""family with sequence similarity 46, member C"""		L	.	FAM46C	25	.	0			c.C201G						PASS	.						87.0	84.0	85.0					1																	118165691		2203	4300	6503	SO:0001583	missense	54855	exon2			AGTGCACGACGTC	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.201C>G	1.37:g.118165691C>G	ENSP00000358458:p.His67Gln	Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	157	70	0.44586	NM_017709	A3KMG2|Q8NE25|Q9NXK0	Missense_Mutation	SNP	ENST00000369448.3	37	CCDS896.1	.	.	.	.	.	.	.	.	.	.	G	10.56	1.383795	0.25031	.	.	ENSG00000183508	ENST00000369448	T	0.20598	2.06	5.75	5.75	0.90469	Domain of unknown function DUF1693 (1);	0.361437	0.26331	N	0.024995	T	0.05135	0.0137	N	0.17082	0.46	0.22989	N	0.998469	B	0.02656	0.0	B	0.04013	0.001	T	0.23332	-1.0191	10	0.41790	T	0.15	-3.2272	10.9521	0.47336	0.0:0.3738:0.4948:0.1313	rs1630312;rs3738417;rs17853647	67	Q5VWP2	FA46C_HUMAN	Q	67	ENSP00000358458:H67Q	ENSP00000358458:H67Q	H	+	3	2	FAM46C	117967214	0.998000	0.40836	1.000000	0.80357	0.976000	0.68499	0.413000	0.21148	1.446000	0.47643	-0.120000	0.15030	CAC	T|0.288;G|0.015;C|0.697	0.015	strong		0.557	FAM46C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038424.1	NM_017709	
PCNXL4	64430	hgsc.bcm.edu	37	14	60592491	60592491	+	Missense_Mutation	SNP	A	A	G	rs145320435	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:60592491A>G	ENST00000406854.1	+	10	3771	c.3217A>G	c.(3217-3219)Att>Gtt	p.I1073V	PCNXL4_ENST00000535349.1_Missense_Mutation_p.I280V|PCNXL4_ENST00000317623.4_Missense_Mutation_p.I839V|PCNXL4_ENST00000406949.1_Missense_Mutation_p.I839V|PCNXL4_ENST00000404681.2_Missense_Mutation_p.I1073V			Q63HM2	PCX4_HUMAN	pecanex-like 4 (Drosophila)	1073						integral component of membrane (GO:0016021)											GAAGGAAGCAATTTTACAAGA	0.323													A|||	10	0.00199681	0.0	0.0029	5008	,	,		17125	0.0		0.005	False		,,,				2504	0.0031				p.I839V		Atlas-SNP	.											.	.	.	.	0			c.A2515G						PASS	.	A	VAL/ILE	2,4404	4.2+/-10.8	0,2,2201	67.0	70.0	69.0		2515	-1.6	0.9	14	dbSNP_134	69	38,8562	24.0+/-70.4	0,38,4262	yes	missense	C14orf135	NM_022495.5	29	0,40,6463	GG,GA,AA		0.4419,0.0454,0.3076	benign	839/939	60592491	40,12966	2203	4300	6503	SO:0001583	missense	64430	exon9			GAAGCAATTTTAC	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.3217A>G	14.37:g.60592491A>G	ENSP00000384801:p.Ile1073Val	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	101	48	0.475248	NM_022495	A8MXM2|Q9BQG8|Q9H9F2	Missense_Mutation	SNP	ENST00000406854.1	37		4	0.0018315018315018315	0	0.0	1	0.0027624309392265192	0	0.0	3	0.00395778364116095	A	2.385	-0.341295	0.05243	4.54E-4	0.004419	ENSG00000126773	ENST00000317623;ENST00000406854;ENST00000406949;ENST00000404681;ENST00000535349	T;T;T;T;T	0.37411	1.2;1.2;1.2;1.2;1.2	5.26	-1.63	0.08345	.	0.323849	0.32120	N	0.006555	T	0.11537	0.0281	N	0.02266	-0.62	0.32445	N	0.546244	B;B	0.06786	0.001;0.0	B;B	0.06405	0.001;0.002	T	0.43261	-0.9402	10	0.02654	T	1	.	13.3605	0.60652	0.2688:0.0:0.7312:0.0	.	1073;839	Q63HM2;B5MC47	CN135_HUMAN;.	V	839;1073;839;1073;280	ENSP00000317396:I839V;ENSP00000384801:I1073V;ENSP00000385201:I839V;ENSP00000385713:I1073V;ENSP00000445644:I280V	ENSP00000317396:I839V	I	+	1	0	C14orf135	59662244	0.998000	0.40836	0.917000	0.36280	0.928000	0.56348	1.437000	0.34991	-0.407000	0.07576	-0.410000	0.06199	ATT	A|0.998;G|0.002	0.002	strong		0.323	PCNXL4-005	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000317847.1	NM_022495	
ZNF681	148213	hgsc.bcm.edu	37	19	23926916	23926916	+	Missense_Mutation	SNP	T	T	C	rs1852432	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:23926916T>C	ENST00000402377.3	-	4	1577	c.1436A>G	c.(1435-1437)aAa>aGa	p.K479R	ZNF681_ENST00000395385.3_Missense_Mutation_p.K410R	NM_138286.2	NP_612143.2	Q96N22	ZN681_HUMAN	zinc finger protein 681	479					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)|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)				TTCTTCACATTTGTAGGGTTT	0.373													T|||	617	0.123203	0.1127	0.0504	5008	,	,		21172	0.2123		0.1034	False		,,,				2504	0.1176				p.K479R		Atlas-SNP	.											.	ZNF681	76	.	0			c.A1436G						PASS	.	T	ARG/LYS	461,3945		20,421,1762	53.0	58.0	56.0		1436	1.5	0.4	19	dbSNP_92	56	676,7912		24,628,3642	no	missense	ZNF681	NM_138286.2	26	44,1049,5404	CC,CT,TT		7.8714,10.463,8.7502	possibly-damaging	479/646	23926916	1137,11857	2203	4294	6497	SO:0001583	missense	148213	exon4			TCACATTTGTAGG	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.1436A>G	19.37:g.23926916T>C	ENSP00000384000:p.Lys479Arg	Somatic	19	0	0		WXS	Illumina HiSeq	Phase_I	19	9	0.473684	NM_138286	B3KVF7	Missense_Mutation	SNP	ENST00000402377.3	37	CCDS12414.2	277	0.12683150183150182	55	0.11178861788617886	25	0.06906077348066299	119	0.20804195804195805	78	0.10290237467018469	.	1.481	-0.557255	0.03967	0.10463	0.078714	ENSG00000196172	ENST00000402377;ENST00000395385	T;T	0.35973	1.28;1.28	1.51	1.51	0.23008	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	N	0.17723	0.515	0.80722	P	0.0	P	0.41188	0.741	P	0.45232	0.474	T	0.16335	-1.0406	8	0.66056	D	0.02	.	4.3299	0.11059	0.0:0.0:0.3553:0.6447	rs1852432	479	Q96N22	ZN681_HUMAN	R	479;410	ENSP00000384000:K479R;ENSP00000378783:K410R	ENSP00000378783:K410R	K	-	2	0	ZNF681	23718756	0.000000	0.05858	0.371000	0.25978	0.233000	0.25261	-1.076000	0.03420	0.663000	0.31027	0.260000	0.18958	AAA	T|0.898;C|0.102	0.102	strong		0.373	ZNF681-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320248.2	NM_138286	
TDRD10	126668	hgsc.bcm.edu	37	1	154516578	154516578	+	Missense_Mutation	SNP	G	G	A	rs3811448	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:154516578G>A	ENST00000368480.3	+	9	728	c.643G>A	c.(643-645)Gtc>Atc	p.V215I	TDRD10_ENST00000479937.1_3'UTR|TDRD10_ENST00000368482.4_Missense_Mutation_p.V215I			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	106	0	0		WXS	Illumina HiSeq	Phase_I	99	47	0.474747	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	
CDC42BPA	8476	hgsc.bcm.edu	37	1	227504794	227504794	+	Silent	SNP	T	T	C	rs11804613	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:227504794T>C	ENST00000366769.3	-	1	1381	c.90A>G	c.(88-90)acA>acG	p.T30T	CDC42BPA_ENST00000334218.5_Silent_p.T30T|CDC42BPA_ENST00000366766.2_Silent_p.T30T|CDC42BPA_ENST00000366767.3_Silent_p.T30T|CDC42BPA_ENST00000535525.1_Silent_p.T30T|CDC42BPA_ENST00000366765.3_Silent_p.T30T|CDC42BPA_ENST00000366764.2_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	213	0	0		WXS	Illumina HiSeq	Phase_I	155	86	0.554839	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	
VIT	5212	hgsc.bcm.edu	37	2	37041480	37041480	+	Silent	SNP	G	G	A	rs17441812	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:37041480G>A	ENST00000389975.3	+	15	2315	c.2013G>A	c.(2011-2013)gaG>gaA	p.E671E	VIT_ENST00000401530.1_Silent_p.E650E|VIT_ENST00000404084.1_Silent_p.E623E|VIT_ENST00000497382.1_Silent_p.E340E|VIT_ENST00000379241.3_Silent_p.E649E|VIT_ENST00000379242.3_Silent_p.E686E	NM_001177969.1|NM_001177970.1	NP_001171440.1|NP_001171441.1	Q6UXI7	VITRN_HUMAN	vitrin	671					extracellular matrix organization (GO:0030198)|positive regulation of cell-substrate adhesion (GO:0010811)	interstitial matrix (GO:0005614)	glycosaminoglycan binding (GO:0005539)			autonomic_ganglia(1)|breast(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	57		all_hematologic(82;0.248)				TTTGTACAGAGTTCAACTCAC	0.522													G|||	103	0.0205671	0.0015	0.0288	5008	,	,		20102	0.0		0.0696	False		,,,				2504	0.0112				p.E686E		Atlas-SNP	.											.	VIT	138	.	0			c.G2058A						PASS	.	G	,,,	60,4346	56.8+/-93.2	0,60,2143	102.0	91.0	94.0		2013,1950,1947,2058	4.5	1.0	2	dbSNP_123	94	551,8049	150.4+/-205.3	19,513,3768	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	VIT	NM_001177969.1,NM_001177970.1,NM_001177971.1,NM_053276.3	,,,	19,573,5911	AA,AG,GG		6.407,1.3618,4.6978	,,,	671/679,650/658,649/657,686/694	37041480	611,12395	2203	4300	6503	SO:0001819	synonymous_variant	5212	exon16			TACAGAGTTCAAC	AF063833	CCDS33180.1, CCDS54347.1, CCDS54348.1, CCDS54349.1, CCDS54350.1	2p22.2	2008-05-15			ENSG00000205221	ENSG00000205221			12697	protein-coding gene	gene with protein product							Standard	NM_001177969		Approved		uc002rpl.3	Q6UXI7	OTTHUMG00000152149	ENST00000389975.3:c.2013G>A	2.37:g.37041480G>A		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	70	37	0.528571	NM_053276	A1A526|A6NKI9|A8K7Y4|E9PF47|Q6P7T3|Q96DM8|Q96DT1|Q9UDN0	Silent	SNP	ENST00000389975.3	37	CCDS54347.1																																																																																			G|0.956;A|0.044	0.044	strong		0.522	VIT-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding			
CAPZA1	829	hgsc.bcm.edu	37	1	113197203	113197203	+	Silent	SNP	A	A	G	rs3790599	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:113197203A>G	ENST00000263168.3	+	5	1008	c.336A>G	c.(334-336)gaA>gaG	p.E112E	snoU13_ENST00000459345.1_RNA|CAPZA1_ENST00000476936.1_Intron	NM_006135.2	NP_006126.1	P52907	CAZA1_HUMAN	capping protein (actin filament) muscle Z-line, alpha 1	112					actin cytoskeleton organization (GO:0030036)|actin filament capping (GO:0051693)|blood coagulation (GO:0007596)|cellular component movement (GO:0006928)|innate immune response (GO:0045087)|protein complex assembly (GO:0006461)	actin cytoskeleton (GO:0015629)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|F-actin capping protein complex (GO:0008290)|WASH complex (GO:0071203)	actin binding (GO:0003779)			breast(1)|kidney(2)|large_intestine(2)|lung(3)|prostate(1)	9	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)		AGCCAGAAGAAGCAGATGGAG	0.423													A|||	349	0.0696885	0.053	0.196	5008	,	,		15573	0.0655		0.0537	False		,,,				2504	0.0235				p.E112E		Atlas-SNP	.											.	CAPZA1	16	.	0			c.A336G						PASS	.	A		249,4157	132.9+/-169.3	4,241,1958	150.0	162.0	158.0		336	-9.1	0.1	1	dbSNP_107	158	497,8103	140.9+/-197.4	15,467,3818	no	coding-synonymous	CAPZA1	NM_006135.2		19,708,5776	GG,GA,AA		5.7791,5.6514,5.7358		112/287	113197203	746,12260	2203	4300	6503	SO:0001819	synonymous_variant	829	exon5			AGAAGAAGCAGAT	U56637	CCDS30805.1	1p13.2	2014-05-09			ENSG00000116489	ENSG00000116489			1488	protein-coding gene	gene with protein product		601580				7665558, 9119363	Standard	NM_006135		Approved		uc001ecj.1	P52907	OTTHUMG00000011769	ENST00000263168.3:c.336A>G	1.37:g.113197203A>G		Somatic	233	0	0		WXS	Illumina HiSeq	Phase_I	216	105	0.486111	NM_006135	Q53FQ6|Q6FHD5	Silent	SNP	ENST00000263168.3	37	CCDS30805.1																																																																																			A|0.935;G|0.065	0.065	strong		0.423	CAPZA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032567.2	NM_006135	
ELFN2	114794	hgsc.bcm.edu	37	22	37770357	37770357	+	Silent	SNP	A	A	G	rs7292751	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:37770357A>G	ENST00000402918.2	-	3	2003	c.1218T>C	c.(1216-1218)ttT>ttC	p.F406F	RP1-63G5.5_ENST00000430883.1_RNA|ELFN2_ENST00000435824.1_5'Flank|RP1-63G5.8_ENST00000609322.1_RNA	NM_052906.3	NP_443138.2	Q5R3F8	PPR29_HUMAN	extracellular leucine-rich repeat and fibronectin type III domain containing 2	406					negative regulation of phosphatase activity (GO:0010923)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	phosphatase binding (GO:0019902)|protein phosphatase inhibitor activity (GO:0004864)			NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(13)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	35	Melanoma(58;0.0574)					TAACCATGCCAAAGAGGCAGC	0.617													G|||	2234	0.446086	0.6135	0.6225	5008	,	,		20561	0.3492		0.3698	False		,,,				2504	0.273				p.F406F		Atlas-SNP	.											.	ELFN2	89	.	0			c.T1218C						PASS	.	G		2713,1693	511.4+/-367.8	834,1045,324	99.0	92.0	95.0		1218	-0.1	1.0	22	dbSNP_116	95	3273,5327	647.7+/-400.4	629,2015,1656	no	coding-synonymous	ELFN2	NM_052906.3		1463,3060,1980	GG,GA,AA		38.0581,38.4249,46.0249		406/821	37770357	5986,7020	2203	4300	6503	SO:0001819	synonymous_variant	114794	exon3			CATGCCAAAGAGG	BC041596	CCDS33642.1	22q13.1	2013-02-11	2011-10-27	2011-10-27	ENSG00000166897	ENSG00000166897		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Fibronectin type III domain containing"""	29396	protein-coding gene	gene with protein product			"""leucine rich repeat containing 62"", ""extracellular leucine-rich repeat and fibronectin type III containing 2"", ""extracellular leucine-rich repeat and fibronectin type III domain containing 2"", ""protein phosphatase 1, regulatory subunit 29"""	LRRC62, PPP1R29		17868438	Standard	XR_244427		Approved	dJ63G5.3, KIAA1904	uc003asq.4	Q5R3F8	OTTHUMG00000150558	ENST00000402918.2:c.1218T>C	22.37:g.37770357A>G		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	80	38	0.475	NM_052906	Q96PY3	Silent	SNP	ENST00000402918.2	37	CCDS33642.1																																																																																			A|0.542;G|0.458	0.458	strong		0.617	ELFN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318900.2	NM_052906	
AP1M1	8907	hgsc.bcm.edu	37	19	16339715	16339715	+	Silent	SNP	C	C	T	rs3752797	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:16339715C>T	ENST00000291439.3	+	9	1472	c.1023C>T	c.(1021-1023)atC>atT	p.I341I	AP1M1_ENST00000541844.1_Silent_p.I269I|AP1M1_ENST00000444449.2_Silent_p.I353I|AP1M1_ENST00000429941.2_Intron|AP1M1_ENST00000590756.1_Silent_p.I269I	NM_032493.3	NP_115882.1	Q9BXS5	AP1M1_HUMAN	adaptor-related protein complex 1, mu 1 subunit	341	MHD. {ECO:0000255|PROSITE- ProRule:PRU00404}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|endosome to melanosome transport (GO:0035646)|intracellular protein transport (GO:0006886)|melanosome organization (GO:0032438)|membrane organization (GO:0061024)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of defense response to virus by virus (GO:0050690)|viral process (GO:0016032)	clathrin adaptor complex (GO:0030131)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|trans-Golgi network membrane (GO:0032588)				breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(7)|ovary(3)|prostate(2)	21						ACAGCGAGATCGTGTGGTCCA	0.612													C|||	2264	0.452077	0.177	0.585	5008	,	,		19833	0.3641		0.7008	False		,,,				2504	0.5644				p.I353I		Atlas-SNP	.											.	AP1M1	48	.	0			c.C1059T						PASS	.	C	,	1123,3283	401.7+/-332.1	156,811,1236	235.0	137.0	171.0		1059,1023	-3.5	1.0	19	dbSNP_107	171	6136,2464	696.5+/-404.9	2200,1736,364	no	coding-synonymous,coding-synonymous	AP1M1	NM_001130524.1,NM_032493.3	,	2356,2547,1600	TT,TC,CC		28.6512,25.488,44.1873	,	353/436,341/424	16339715	7259,5747	2203	4300	6503	SO:0001819	synonymous_variant	8907	exon10			CGAGATCGTGTGG		CCDS12342.1, CCDS46008.1	19p13.12	2008-05-23							13667	protein-coding gene	gene with protein product		603535				9653655, 17988225	Standard	NM_032493		Approved	AP47, CLAPM2	uc002ndv.2	Q9BXS5		ENST00000291439.3:c.1023C>T	19.37:g.16339715C>T		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	96	96	1	NM_001130524	Q4TTY5	Silent	SNP	ENST00000291439.3	37	CCDS12342.1																																																																																			C|0.486;T|0.514	0.514	strong		0.612	AP1M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460492.1	NM_032493	
HSD17B3	3293	hgsc.bcm.edu	37	9	99064378	99064378	+	Silent	SNP	G	G	A	rs139582148	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:99064378G>A	ENST00000375263.3	-	1	56	c.9C>T	c.(7-9)gaC>gaT	p.D3D	HSD17B3_ENST00000375262.2_Silent_p.D3D	NM_000197.1	NP_000188.1	P37058	DHB3_HUMAN	hydroxysteroid (17-beta) dehydrogenase 3	3					androgen biosynthetic process (GO:0006702)|male genitalia development (GO:0030539)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|testosterone biosynthetic process (GO:0061370)	endoplasmic reticulum membrane (GO:0005789)|intracellular membrane-bounded organelle (GO:0043231)	testosterone 17-beta-dehydrogenase (NADP+) activity (GO:0047045)			breast(1)|endometrium(3)|large_intestine(2)|lung(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	13		Acute lymphoblastic leukemia(62;0.0171)|all_hematologic(171;0.214)				GTTCCAGGACGTCCCCCATGG	0.567													G|||	8	0.00159744	0.0038	0.0014	5008	,	,		17045	0.0		0.002	False		,,,				2504	0.0				p.D3D		Atlas-SNP	.											.	HSD17B3	32	.	0			c.C9T						PASS	.	G		6,4400	11.4+/-27.6	0,6,2197	82.0	72.0	75.0		9	-6.7	0.0	9	dbSNP_134	75	6,8594	5.0+/-18.6	0,6,4294	no	coding-synonymous	HSD17B3	NM_000197.1		0,12,6491	AA,AG,GG		0.0698,0.1362,0.0923		3/311	99064378	12,12994	2203	4300	6503	SO:0001819	synonymous_variant	3293	exon1			CAGGACGTCCCCC		CCDS6716.1	9q22	2011-09-20			ENSG00000130948	ENSG00000130948	1.1.1.62	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 3"""	5212	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 12C, member 2"""	605573				8075637, 19027726	Standard	NM_000197		Approved	SDR12C2	uc004awa.1	P37058	OTTHUMG00000020292	ENST00000375263.3:c.9C>T	9.37:g.99064378G>A		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	109	56	0.513761	NM_000197	Q5U0Q6	Silent	SNP	ENST00000375263.3	37	CCDS6716.1																																																																																			G|0.999;A|0.001	0.001	strong		0.567	HSD17B3-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053259.1	NM_000197	
HEG1	57493	hgsc.bcm.edu	37	3	124748226	124748226	+	Silent	SNP	G	G	A	rs2860440	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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						scavenged	.	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	51	0	0		WXS	Illumina HiSeq	Phase_I	61	25	0.409836	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	
FSTL4	23105	hgsc.bcm.edu	37	5	132535046	132535046	+	Missense_Mutation	SNP	G	G	A	rs3749817	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:132535046G>A	ENST00000265342.7	-	16	2519	c.2270C>T	c.(2269-2271)aCg>aTg	p.T757M	CTB-49A3.2_ENST00000509051.1_RNA	NM_015082.1	NP_055897.1	Q6MZW2	FSTL4_HUMAN	follistatin-like 4	757			T -> M (in dbSNP:rs3749817). {ECO:0000269|PubMed:17974005}.			extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(8)|skin(2)|upper_aerodigestive_tract(1)	23		all_cancers(142;0.244)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			GTCCGGCTCCGTGTGCAGAGC	0.582													G|||	1329	0.265375	0.062	0.4049	5008	,	,		19463	0.3948		0.2316	False		,,,				2504	0.3425				p.T757M		Atlas-SNP	.											.	FSTL4	74	.	0			c.C2270T						PASS	.	G	MET/THR	384,4022	193.0+/-218.2	12,360,1831	64.0	63.0	64.0		2270	-6.3	0.0	5	dbSNP_107	64	1863,6737	331.5+/-319.7	186,1491,2623	yes	missense	FSTL4	NM_015082.1	81	198,1851,4454	AA,AG,GG		21.6628,8.7154,17.2766	benign	757/843	132535046	2247,10759	2203	4300	6503	SO:0001583	missense	23105	exon16			GGCTCCGTGTGCA	AB028984	CCDS34238.1	5q31.1	2013-01-29			ENSG00000053108	ENSG00000053108		"""EF-hand domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	21389	protein-coding gene	gene with protein product						10470851, 15527507	Standard	NM_015082		Approved	KIAA1061	uc003kyn.1	Q6MZW2	OTTHUMG00000162729	ENST00000265342.7:c.2270C>T	5.37:g.132535046G>A	ENSP00000265342:p.Thr757Met	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	85	85	1	NM_015082	Q8TBU0|Q9UPU1	Missense_Mutation	SNP	ENST00000265342.7	37	CCDS34238.1	574	0.26282051282051283	30	0.06097560975609756	126	0.34806629834254144	246	0.43006993006993005	172	0.22691292875989447	G	2.282	-0.364594	0.05103	0.087154	0.216628	ENSG00000053108	ENST00000265342;ENST00000360575	T	0.21734	1.99	4.76	-6.31	0.02001	WD40/YVTN repeat-like-containing domain (1);	1.045250	0.07416	N	0.893264	T	0.00012	0.0000	N	0.24115	0.695	0.80722	P	0.0	B;B	0.30584	0.014;0.286	B;B	0.18561	0.006;0.022	T	0.44802	-0.9304	9	0.45353	T	0.12	2.3158	2.6468	0.04986	0.4779:0.1994:0.2182:0.1044	rs3749817;rs60534030;rs3749817	757;406	Q6MZW2;B3KPF3	FSTL4_HUMAN;.	M	757;588	ENSP00000265342:T757M	ENSP00000265342:T757M	T	-	2	0	FSTL4	132562945	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.316000	0.19469	-1.355000	0.02186	-2.109000	0.00356	ACG	G|0.785;N|0.000	.	strong		0.582	FSTL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370212.1	XM_048786	
SYNGR2	9144	hgsc.bcm.edu	37	17	76167047	76167047	+	Silent	SNP	C	C	T	rs1062668	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:76167047C>T	ENST00000225777.3	+	2	308	c.249C>T	c.(247-249)gcC>gcT	p.A83A	SYNGR2_ENST00000590201.1_Silent_p.A27A|SYNGR2_ENST00000588282.1_Silent_p.A83A|SYNGR2_ENST00000585591.1_Silent_p.A83A|SYNGR2_ENST00000589711.1_Intron|SYNGR2_ENST00000592456.1_3'UTR			O43760	SNG2_HUMAN	synaptogyrin 2	83	MARVEL. {ECO:0000255|PROSITE- ProRule:PRU00581}.				protein targeting (GO:0006605)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|synaptic vesicle (GO:0008021)				endometrium(2)|large_intestine(1)|liver(1)|lung(1)|skin(1)|urinary_tract(1)	7			BRCA - Breast invasive adenocarcinoma(99;0.00269)|Lung(188;0.0973)|OV - Ovarian serous cystadenocarcinoma(97;0.0994)			TGGCCTCGGCCTTCTTCTTGG	0.582													C|||	383	0.0764776	0.0386	0.1153	5008	,	,		19484	0.002		0.1203	False		,,,				2504	0.1319				p.A83A		Atlas-SNP	.											SYNGR2,NS,carcinoma,+2,1	SYNGR2	17	1	0			c.C249T						PASS	.	C		252,4154	146.5+/-181.1	7,238,1958	121.0	98.0	106.0		249	3.9	1.0	17	dbSNP_86	106	1254,7346	250.7+/-277.5	87,1080,3133	no	coding-synonymous	SYNGR2	NM_004710.3		94,1318,5091	TT,TC,CC		14.5814,5.7195,11.5793		83/225	76167047	1506,11500	2203	4300	6503	SO:0001819	synonymous_variant	9144	exon2			CTCGGCCTTCTTC	AJ002308	CCDS11753.1	17q25.3	2014-09-11			ENSG00000108639	ENSG00000108639			11499	protein-coding gene	gene with protein product	"""cellugyrin"""	603926				9760194	Standard	NM_004710		Approved		uc002juu.1	O43760	OTTHUMG00000177457	ENST00000225777.3:c.249C>T	17.37:g.76167047C>T		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	98	38	0.387755	NM_004710	O43762|Q3KQZ2|Q658S7	Silent	SNP	ENST00000225777.3	37	CCDS11753.1																																																																																			C|0.889;T|0.111	0.111	strong		0.582	SYNGR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437009.2		
IQCB1	9657	hgsc.bcm.edu	37	3	121500699	121500699	+	Missense_Mutation	SNP	C	C	T	rs17849995	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:121500699C>T	ENST00000310864.6	-	13	1515	c.1301G>A	c.(1300-1302)tGc>tAc	p.C434Y	IQCB1_ENST00000349820.6_Missense_Mutation_p.C301Y	NM_001023570.2	NP_001018864.2	Q15051	IQCB1_HUMAN	IQ motif containing B1	434	IQ 4. {ECO:0000255|PROSITE- ProRule:PRU00116}.		C -> Y (in dbSNP:rs17849995). {ECO:0000269|PubMed:15489334}.		cilium assembly (GO:0042384)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)|photoreceptor connecting cilium (GO:0032391)|photoreceptor outer segment (GO:0001750)	calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)			NS(1)|biliary_tract(1)|breast(3)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(11)|prostate(1)|skin(1)	30				GBM - Glioblastoma multiforme(114;0.0983)		TTTCTTACGGCACTTCGCTAG	0.403													C|||	1516	0.302716	0.2413	0.5043	5008	,	,		19245	0.1647		0.2495	False		,,,				2504	0.4397				p.C434Y		Atlas-SNP	.											.	IQCB1	50	.	0			c.G1301A						PASS	.	C	TYR/CYS,TYR/CYS	1026,3380	380.2+/-323.6	119,788,1296	113.0	109.0	110.0		1301,902	3.7	1.0	3	dbSNP_123	110	2057,6543	356.9+/-330.5	235,1587,2478	yes	missense,missense	IQCB1	NM_001023570.2,NM_001023571.2	194,194	354,2375,3774	TT,TC,CC		23.9186,23.2864,23.7044	possibly-damaging,possibly-damaging	434/599,301/466	121500699	3083,9923	2203	4300	6503	SO:0001583	missense	9657	exon13			TTACGGCACTTCG	D25278	CCDS33836.1, CCDS33837.1	3q21.1	2014-01-28	2004-09-02		ENSG00000173226	ENSG00000173226			28949	protein-coding gene	gene with protein product	"""nephrocystin-5"""	609237	"""IQ calmodulin-binding motif containing 1"""			15723066	Standard	NM_001023571		Approved	KIAA0036, NPHP5, SLSN5	uc010hre.1	Q15051	OTTHUMG00000128677	ENST00000310864.6:c.1301G>A	3.37:g.121500699C>T	ENSP00000311505:p.Cys434Tyr	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	71	37	0.521127	NM_001023570	Q3KS08|Q3KS09|Q5DKQ7|Q8NI79|Q9BS08	Missense_Mutation	SNP	ENST00000310864.6	37	CCDS33837.1	571	0.26144688644688646	130	0.26422764227642276	169	0.46685082872928174	77	0.1346153846153846	195	0.25725593667546176	C	5.418	0.262198	0.10239	0.232864	0.239186	ENSG00000173226	ENST00000310864;ENST00000349820	T;T	0.71461	-0.57;-0.57	4.61	3.74	0.42951	.	0.105267	0.64402	D	0.000003	T	0.00012	0.0000	L	0.36672	1.1	0.33126	P	0.45759000000000005	P;D	0.64830	0.826;0.994	B;P	0.59703	0.191;0.862	T	0.40136	-0.9579	9	0.02654	T	1	0.2067	8.7599	0.34667	0.0:0.8971:0.0:0.1029	rs17849995	434;301	Q15051;Q15051-2	IQCB1_HUMAN;.	Y	434;301	ENSP00000311505:C434Y;ENSP00000323756:C301Y	ENSP00000311505:C434Y	C	-	2	0	IQCB1	122983389	0.946000	0.32159	0.998000	0.56505	0.043000	0.13939	2.801000	0.47908	1.298000	0.44778	0.591000	0.81541	TGC	C|0.759;T|0.241	0.241	strong		0.403	IQCB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250573.1	NM_014642	
SSPO	23145	hgsc.bcm.edu	37	7	149520553	149520553	+	RNA	SNP	G	G	A	rs141884347	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:149520553G>A	ENST00000378016.2	+	0	13371							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)			CCTGCCAGCCGGGCTGCTACT	0.627													G|||	48	0.00958466	0.0008	0.013	5008	,	,		17506	0.002		0.0129	False		,,,				2504	0.0235				p.P4457P		Atlas-SNP	.											.	.	.	.	0			c.G13371A						PASS	.	G		5,4069		0,5,2032	34.0	41.0	39.0		13385	-9.9	0.6	7	dbSNP_134	39	118,8248		1,116,4066	yes	coding-notMod3	SSPO	NM_198455.2		1,121,6098	AA,AG,GG		1.4105,0.1227,0.9887			149520553	123,12317	2037	4183	6220			23145	exon92			CCAGCCGGGCTGC	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.149520553G>A		Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	45	18	0.4	NM_198455	Q76B61	Silent	SNP	ENST00000378016.2	37																																																																																				G|0.990;A|0.010	0.010	strong		0.627	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript			
PPP6R2	9701	hgsc.bcm.edu	37	22	50878196	50878196	+	Missense_Mutation	SNP	G	G	A	rs13057311	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:50878196G>A	ENST00000216061.5	+	21	2565	c.2195G>A	c.(2194-2196)aGg>aAg	p.R732K	PPP6R2_ENST00000395744.3_Missense_Mutation_p.R705K|PPP6R2_ENST00000395741.3_Missense_Mutation_p.R706K|PPP6R2_ENST00000359139.3_Missense_Mutation_p.R706K			O75170	PP6R2_HUMAN	protein phosphatase 6, regulatory subunit 2	732			R -> K (in dbSNP:rs13057311).			cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)				NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(2)|liver(1)|lung(6)|ovary(2)|skin(1)|urinary_tract(1)	22						GGAGTGGTGAGGGACGTGGGT	0.602													G|||	970	0.19369	0.1059	0.2565	5008	,	,		20218	0.1419		0.2962	False		,,,				2504	0.2157				p.R732K		Atlas-SNP	.											.	PPP6R2	71	.	0			c.G2195A						PASS	.	G	LYS/ARG,LYS/ARG,LYS/ARG,LYS/ARG	567,3839	245.9+/-254.7	39,489,1675	69.0	58.0	62.0		2195,2117,2117,2114	1.5	0.0	22	dbSNP_121	62	2430,6170	398.7+/-346.2	358,1714,2228	no	missense,missense,missense,missense	PPP6R2	NM_001242898.1,NM_001242899.1,NM_001242900.1,NM_014678.4	26,26,26,26	397,2203,3903	AA,AG,GG		28.2558,12.8688,23.0432	benign,benign,benign,benign	732/960,706/934,706/928,705/933	50878196	2997,10009	2203	4300	6503	SO:0001583	missense	9701	exon20			TGGTGAGGGACGT	AB014585	CCDS33681.1, CCDS56235.1, CCDS56236.1, CCDS74881.1	22q13.33	2012-04-17	2010-06-28	2010-06-28	ENSG00000100239	ENSG00000100239		"""Serine/threonine phosphatases / Protein phosphatase 6, regulatory subunits"""	19253	protein-coding gene	gene with protein product		610877	"""KIAA0685"", ""SAPS domain family, member 2"""	KIAA0685, SAPS2		16769727	Standard	NM_014678		Approved	dJ579N16.1, SAP190	uc003blc.3	O75170	OTTHUMG00000150199	ENST00000216061.5:c.2195G>A	22.37:g.50878196G>A	ENSP00000216061:p.Arg732Lys	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	145	66	0.455172	NM_001242898	A6PVG3|B7Z7T3|Q5U5P3|Q7Z2L2|Q7Z5G5|Q7Z731|Q9UGB9	Missense_Mutation	SNP	ENST00000216061.5	37		463	0.211996336996337	62	0.12601626016260162	96	0.26519337016574585	82	0.14335664335664336	223	0.2941952506596306	G	0.039	-1.293713	0.01375	0.128688	0.282558	ENSG00000100239	ENST00000359139;ENST00000395741;ENST00000395744;ENST00000216061	T;T;T;T	0.40476	1.03;1.03;1.03;1.03	4.83	1.46	0.22682	.	0.800541	0.12348	N	0.476819	T	0.00012	0.0000	N	0.22421	0.69	0.51482	P	7.500000000004725E-5	P;B;B;B;B;B	0.35174	0.488;0.113;0.069;0.113;0.113;0.191	B;B;B;B;B;B	0.26416	0.05;0.048;0.021;0.048;0.048;0.069	T	0.28396	-1.0045	9	0.05959	T	0.93	-2.4742	7.137	0.25533	0.1152:0.0:0.4072:0.4776	rs13057311;rs17183769;rs13057311	265;732;732;706;705;706	F2Z3M7;O75170-5;O75170;O75170-3;O75170-4;O75170-2	.;.;PP6R2_HUMAN;.;.;.	K	706;706;705;732	ENSP00000352051:R706K;ENSP00000379090:R706K;ENSP00000379093:R705K;ENSP00000216061:R732K	ENSP00000216061:R732K	R	+	2	0	PPP6R2	49225062	.	.	0.023000	0.16930	0.201000	0.24016	.	.	0.071000	0.16664	-0.291000	0.09656	AGG	G|0.783;A|0.217	0.217	strong		0.602	PPP6R2-004	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000316809.1	NM_014678	
HIST1H2AC	8334	hgsc.bcm.edu	37	6	26124563	26124563	+	Missense_Mutation	SNP	C	C	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:26124563C>G	ENST00000602637.1	+	1	133	c.103C>G	c.(103-105)Ctc>Gtc	p.L35V	HIST1H2BC_ENST00000396984.1_5'Flank|HIST1H2BC_ENST00000314332.5_5'Flank|HIST1H2AC_ENST00000377791.2_Missense_Mutation_p.L35V			Q93077	H2A1C_HUMAN	histone cluster 1, H2ac	35						extracellular vesicular exosome (GO:0070062)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(4)|lung(5)	12						GCACCGCCTGCTCCGTAAAGG	0.657																																					p.L35V		Atlas-SNP	.											.	HIST1H2AC	29	.	0			c.C103G						PASS	.						42.0	44.0	44.0					6																	26124563		2203	4300	6503	SO:0001583	missense	8334	exon1			CGCCTGCTCCGTA	Z80778	CCDS4585.1	6p22.1	2011-01-27	2006-10-11	2003-02-21	ENSG00000180573	ENSG00000180573		"""Histones / Replication-dependent"""	4733	protein-coding gene	gene with protein product		602794	"""H2A histone family, member L"", ""histone 1, H2ac"""	H2AFL		9119399, 12408966	Standard	NM_003512		Approved		uc003ngm.3	Q93077	OTTHUMG00000014428	ENST00000602637.1:c.103C>G	6.37:g.26124563C>G	ENSP00000473534:p.Leu35Val	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	100	32	0.32	NM_003512	B2R4F7|O00775|O00776|O00777|O00778|Q540R1	Missense_Mutation	SNP	ENST00000602637.1	37	CCDS4585.1	.	.	.	.	.	.	.	.	.	.	.	14.39	2.522457	0.44866	.	.	ENSG00000180573	ENST00000377791;ENST00000314088	T;T	0.59224	0.28;0.28	5.6	5.6	0.85130	Histone-fold (2);Histone core (1);Histone H2A (2);	0.000000	0.38897	N	0.001536	T	0.80199	0.4579	H	0.97564	4.03	0.40025	D	0.975457	D	0.64830	0.994	D	0.66351	0.943	D	0.85943	0.1459	10	0.87932	D	0	.	12.3103	0.54925	0.0:0.9229:0.0:0.0771	.	35	Q93077	H2A1C_HUMAN	V	35	ENSP00000367022:L35V;ENSP00000321389:L35V	ENSP00000321389:L35V	L	+	1	0	HIST1H2AC	26232542	1.000000	0.71417	0.810000	0.32431	0.125000	0.20455	3.848000	0.55903	2.793000	0.96121	0.591000	0.81541	CTC	.	.	none		0.657	HIST1H2AC-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000468023.1	NM_003512	
MTMR10	54893	hgsc.bcm.edu	37	15	31267147	31267147	+	Silent	SNP	C	C	T	rs1133642	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:31267147C>T	ENST00000435680.1	-	4	415	c.318G>A	c.(316-318)gaG>gaA	p.E106E	MTMR10_ENST00000314404.8_5'Flank|MTMR10_ENST00000425768.1_Silent_p.E106E|MTMR10_ENST00000563714.1_Silent_p.E24E	NM_017762.2	NP_060232.2	Q9NXD2	MTMRA_HUMAN	myotubularin related protein 10	106							phosphatase activity (GO:0016791)			autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|ovary(1)|upper_aerodigestive_tract(1)	9		all_lung(180;2.81e-11)		all cancers(64;7.26e-15)|Epithelial(43;7.2e-11)|GBM - Glioblastoma multiforme(186;0.000158)|BRCA - Breast invasive adenocarcinoma(123;0.00426)|Lung(196;0.174)		TGACAATTTGCTCAATACATG	0.323													C|||	2404	0.480032	0.1884	0.4741	5008	,	,		17120	0.8313		0.4453	False		,,,				2504	0.5521				p.E106E		Atlas-SNP	.											.	MTMR10	74	.	0			c.G318A						PASS	.	C		834,2826		112,610,1108	61.0	56.0	58.0		318	0.8	1.0	15	dbSNP_86	58	3577,4575		780,2017,1279	no	coding-synonymous	MTMR10	NM_017762.2		892,2627,2387	TT,TC,CC		43.8788,22.7869,37.3434		106/778	31267147	4411,7401	1830	4076	5906	SO:0001819	synonymous_variant	54893	exon4			AATTTGCTCAATA	AK000320	CCDS45204.1	15q13.3	2011-06-09				ENSG00000166912		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"""	25999	protein-coding gene	gene with protein product						12495846	Standard	NM_017762		Approved	FLJ20313	uc001zfh.1	Q9NXD2		ENST00000435680.1:c.318G>A	15.37:g.31267147C>T		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	73	73	1	NM_017762	Q6P4Q6	Silent	SNP	ENST00000435680.1	37	CCDS45204.1																																																																																			A|0.000;C|0.421;T|0.579	0.579	strong		0.323	MTMR10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430747.1	NM_017762	
FBLN2	2199	hgsc.bcm.edu	37	3	13612020	13612020	+	Silent	SNP	T	T	C	rs3732667	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:13612020T>C	ENST00000295760.7	+	2	234	c.165T>C	c.(163-165)tgT>tgC	p.C55C	FBLN2_ENST00000535798.1_Silent_p.C81C|FBLN2_ENST00000404922.3_Silent_p.C55C|FBLN2_ENST00000492059.1_Silent_p.C55C	NM_001998.2	NP_001989.2	P98095	FBLN2_HUMAN	fibulin 2	55	N.|Subdomain NA (Cys-rich).				extracellular matrix organization (GO:0030198)|positive regulation of cell-substrate adhesion (GO:0010811)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	calcium ion binding (GO:0005509)|extracellular matrix binding (GO:0050840)|extracellular matrix structural constituent (GO:0005201)			haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(10)|ovary(3)|prostate(3)|urinary_tract(1)	24			UCEC - Uterine corpus endometrioid carcinoma (1;0.00416)			GTGCCTGCTGTGCCACGTGTG	0.706													C|||	1416	0.282748	0.4493	0.0922	5008	,	,		17137	0.3879		0.0755	False		,,,				2504	0.2975				p.C55C		Atlas-SNP	.											.	FBLN2	137	.	0			c.T165C						PASS	.	C	,,	1426,2714		243,940,887	8.0	12.0	10.0		165,165,165	-1.4	0.4	3	dbSNP_107	10	565,7793		17,531,3631	no	coding-synonymous,coding-synonymous,coding-synonymous	FBLN2	NM_001004019.1,NM_001165035.1,NM_001998.2	,,	260,1471,4518	CC,CT,TT		6.76,34.4444,15.9305	,,	55/1232,55/1232,55/1185	13612020	1991,10507	2070	4179	6249	SO:0001819	synonymous_variant	2199	exon2			CTGCTGTGCCACG	X82494	CCDS46761.1, CCDS46762.1	3p25-p24	2010-06-15			ENSG00000163520	ENSG00000163520		"""Fibulins"""	3601	protein-coding gene	gene with protein product		135821				7806230	Standard	NM_001165035		Approved		uc011ava.2	P98095	OTTHUMG00000155437	ENST00000295760.7:c.165T>C	3.37:g.13612020T>C		Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	162	60	0.37037	NM_001998	B7Z9C5|Q8IUI0|Q8IUI1	Silent	SNP	ENST00000295760.7	37	CCDS46762.1																																																																																			T|0.745;G|0.000;C|0.255	0.255	strong		0.706	FBLN2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000340083.3	NM_001004019	
LIMD1	8994	hgsc.bcm.edu	37	3	45637253	45637253	+	Silent	SNP	C	C	T	rs267237	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:45637253C>T	ENST00000273317.4	+	1	903	c.882C>T	c.(880-882)acC>acT	p.T294T	LIMD1_ENST00000465039.1_Intron|LIMD1_ENST00000440097.1_Silent_p.T294T	NM_014240.2	NP_055055.1	Q9UGP4	LIMD1_HUMAN	LIM domains containing 1	294					cell migration (GO:0016477)|cytoplasmic mRNA processing body assembly (GO:0033962)|cytoskeleton organization (GO:0007010)|gene silencing by miRNA (GO:0035195)|multicellular organismal development (GO:0007275)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of hippo signaling (GO:0035331)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of transcription, DNA-templated (GO:0045892)|osteoblast development (GO:0002076)|phosphorylation (GO:0016310)|positive regulation of gene silencing by miRNA (GO:2000637)|regulation of cell shape (GO:0008360)|regulation of transcription, DNA-templated (GO:0006355)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	adherens junction (GO:0005912)|cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|RISC complex (GO:0016442)	transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|skin(1)	10				BRCA - Breast invasive adenocarcinoma(193;0.011)|KIRC - Kidney renal clear cell carcinoma(197;0.0264)|Kidney(197;0.0315)		AGCCCAGGACCCCTTCTGTGT	0.632													C|||	3431	0.685104	0.5915	0.6542	5008	,	,		18786	0.9345		0.5497	False		,,,				2504	0.7157				p.T294T		Atlas-SNP	.											LIMD1,NS,carcinoma,0,1	LIMD1	34	1	0			c.C882T						PASS	.	C		2630,1776	636.1+/-396.5	788,1054,361	46.0	49.0	48.0		882	1.3	0.0	3	dbSNP_79	48	4934,3666	611.0+/-395.8	1430,2074,796	no	coding-synonymous	LIMD1	NM_014240.2		2218,3128,1157	TT,TC,CC		42.6279,40.3087,41.8422		294/677	45637253	7564,5442	2203	4300	6503	SO:0001819	synonymous_variant	8994	exon1			CAGGACCCCTTCT	AJ132408	CCDS2729.1	3p21.31	2008-02-01			ENSG00000144791	ENSG00000144791			6612	protein-coding gene	gene with protein product		604543				10647888	Standard	NM_014240		Approved		uc003coq.3	Q9UGP4	OTTHUMG00000133453	ENST00000273317.4:c.882C>T	3.37:g.45637253C>T		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	81	36	0.444444	NM_014240	Q17RQ1|Q9BQQ9|Q9NQ47	Silent	SNP	ENST00000273317.4	37	CCDS2729.1																																																																																			C|0.394;T|0.606	0.606	strong		0.632	LIMD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257327.1	NM_014240	
CEP70	80321	hgsc.bcm.edu	37	3	138244400	138244400	+	Silent	SNP	C	C	T	rs9878436	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:138244400C>T	ENST00000264982.3	-	11	1142	c.876G>A	c.(874-876)acG>acA	p.T292T	CEP70_ENST00000484888.1_Silent_p.T292T|CEP70_ENST00000489254.1_Silent_p.T140T|CEP70_ENST00000481834.1_Silent_p.T292T|CEP70_ENST00000542237.1_Silent_p.T272T	NM_024491.2	NP_077817.2	Q8NHQ1	CEP70_HUMAN	centrosomal protein 70kDa	292					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)				breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(6)|skin(3)	24						ATTCATGCTGCGTAGGCCTGT	0.289													T|||	1542	0.307907	0.416	0.2911	5008	,	,		10639	0.0585		0.4483	False		,,,				2504	0.2863				p.T292T		Atlas-SNP	.											.	CEP70	51	.	0			c.G876A						PASS	.	T		1840,2558	604.9+/-390.4	384,1072,743	55.0	61.0	59.0		876	3.9	1.0	3	dbSNP_119	59	3739,4839	606.3+/-395.1	841,2057,1391	no	coding-synonymous	CEP70	NM_024491.2		1225,3129,2134	TT,TC,CC		43.5882,41.8372,42.9948		292/598	138244400	5579,7397	2199	4289	6488	SO:0001819	synonymous_variant	80321	exon11			ATGCTGCGTAGGC	AF202146	CCDS3102.1, CCDS75022.1, CCDS75023.1, CCDS75024.1	3q22.3	2014-02-20			ENSG00000114107	ENSG00000114107			29972	protein-coding gene	gene with protein product		614310				14654843	Standard	XM_005247802		Approved	BITE, FLJ13036	uc003esl.3	Q8NHQ1	OTTHUMG00000159891	ENST00000264982.3:c.876G>A	3.37:g.138244400C>T		Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	16	15	0.9375	NM_024491	B7Z5I8|B7Z7E8|D3DNE9|F5GZX8|Q96B31|Q9H2C3|Q9H2Z1|Q9H940	Silent	SNP	ENST00000264982.3	37	CCDS3102.1																																																																																			C|0.619;T|0.381	0.381	strong		0.289	CEP70-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000358001.1	NM_024491	
PSPH	5723	hgsc.bcm.edu	37	7	56084977	56084977	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:56084977T>C	ENST00000395471.3	-	6	1176	c.371A>G	c.(370-372)aAt>aGt	p.N124S	PSPH_ENST00000275605.3_Missense_Mutation_p.N124S|PSPH_ENST00000459834.1_Intron			P78330	SERB_HUMAN	phosphoserine phosphatase	124					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)			TGCTGGGATATTGAGCTTTGA	0.413																																					p.N124S		Atlas-SNP	.											.	PSPH	23	.	0			c.A371G						PASS	.						95.0	79.0	84.0					7																	56084977		2203	4300	6503	SO:0001583	missense	5723	exon6			GGGATATTGAGCT	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.371A>G	7.37:g.56084977T>C	ENSP00000378854:p.Asn124Ser	Somatic	548	1	0.00182482		WXS	Illumina HiSeq	Phase_I	508	130	0.255906	NM_004577	B2RCR5|Q7Z3S5	Missense_Mutation	SNP	ENST00000395471.3	37	CCDS5522.1	.	.	.	.	.	.	.	.	.	.	T	12.28	1.891711	0.33442	.	.	ENSG00000146733	ENST00000275605;ENST00000395471;ENST00000421626	D;D;D	0.84442	-1.85;-1.85;-1.85	4.85	2.45	0.29901	Haloacid dehalogenase-like hydrolase (1);HAD-like domain (2);	0.459751	0.25414	N	0.030855	T	0.74928	0.3781	L	0.33668	1.02	0.23700	N	0.997076	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.002	T	0.64106	-0.6485	10	0.46703	T	0.11	-8.4835	7.6611	0.28404	0.0:0.1848:0.0:0.8152	.	124;124	Q53EY1;P78330	.;SERB_HUMAN	S	124	ENSP00000275605:N124S;ENSP00000378854:N124S;ENSP00000398653:N124S	ENSP00000275605:N124S	N	-	2	0	PSPH	56052471	0.897000	0.30589	0.689000	0.30133	0.972000	0.66771	1.222000	0.32515	0.742000	0.32697	0.472000	0.43445	AAT	.	.	none		0.413	PSPH-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343304.1	NM_004577	
HNRNPCL1	343069	hgsc.bcm.edu	37	1	12907385	12907385	+	Missense_Mutation	SNP	G	G	A	rs150590256		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:12907385G>A	ENST00000317869.6	-	2	983	c.758C>T	c.(757-759)cCa>cTa	p.P253L		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	253						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						ATCATCCAGTGGGTCCCCCTC	0.507																																					p.P253L		Atlas-SNP	.											HNRNPCL1,NS,carcinoma,0,1	HNRNPCL1	68	1	0			c.C758T						scavenged	.						104.0	106.0	105.0					1																	12907385		2202	4295	6497	SO:0001583	missense	343069	exon2			TCCAGTGGGTCCC	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.758C>T	1.37:g.12907385G>A	ENSP00000365370:p.Pro253Leu	Somatic	163	15	0.0920245		WXS	Illumina HiSeq	Phase_I	156	14	0.0897436	NM_001013631	B2RP44	Missense_Mutation	SNP	ENST00000317869.6	37	CCDS30591.1	.	.	.	.	.	.	.	.	.	.	.	0.006	-2.105909	0.00356	.	.	ENSG00000179172	ENST00000317869	T	0.08008	3.14	0.848	-1.58	0.08479	.	0.359505	0.22097	N	0.064662	T	0.01287	0.0042	N	0.00074	-2.255	0.23930	N	0.996434	B	0.02656	0.0	B	0.01281	0.0	T	0.47032	-0.9148	10	0.45353	T	0.12	.	4.3013	0.10925	0.7598:0.0:0.2402:0.0	.	253	O60812	HNRCL_HUMAN	L	253	ENSP00000365370:P253L	ENSP00000365370:P253L	P	-	2	0	HNRNPCL1	12829972	1.000000	0.71417	0.049000	0.19019	0.006000	0.05464	1.770000	0.38532	-0.163000	0.10946	-0.755000	0.03482	CCA	.	.	weak		0.507	HNRNPCL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005462.1	NM_001013631	
PROSER1	80209	hgsc.bcm.edu	37	13	39587889	39587889	+	Silent	SNP	T	T	C	rs3751377	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:39587889T>C	ENST00000352251.3	-	11	2333	c.1500A>G	c.(1498-1500)ctA>ctG	p.L500L	PROSER1_ENST00000350125.3_Silent_p.L478L|PROSER1_ENST00000484434.3_Intron	NM_025138.4	NP_079414.3	Q86XN7	PRSR1_HUMAN	proline and serine rich 1	500	Ser-rich.																TAAGAGAAGATAGTGAAGCCA	0.473													T|||	1117	0.223043	0.2458	0.1599	5008	,	,		21247	0.2183		0.162	False		,,,				2504	0.3047				p.L500L		Atlas-SNP	.											.	.	.	.	0			c.A1500G						PASS	.	T	,	1076,3330	390.5+/-327.7	117,842,1244	86.0	83.0	84.0		1500,1434	-10.5	0.0	13	dbSNP_107	84	1205,7395	244.4+/-273.7	90,1025,3185	no	coding-synonymous,coding-synonymous	PROSER1	NM_025138.3,NM_170719.2	,	207,1867,4429	CC,CT,TT		14.0116,24.4212,17.5381	,	500/945,478/923	39587889	2281,10725	2203	4300	6503	SO:0001819	synonymous_variant	80209	exon11			AGAAGATAGTGAA	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.1500A>G	13.37:g.39587889T>C		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	75	35	0.466667	NM_025138	A6NJ97|Q6P2S2|Q7Z3X5|Q8N3D2|Q8N3P1|Q9H9M1	Silent	SNP	ENST00000352251.3	37	CCDS9368.2																																																																																			T|0.809;C|0.191	0.191	strong		0.473	PROSER1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044607.5	NM_025138	
MUC6	4588	hgsc.bcm.edu	37	11	1017068	1017068	+	Silent	SNP	C	C	T	rs78992004		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	396	40	0.10101		WXS	Illumina HiSeq	Phase_I	509	62	0.121807	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	
ARHGAP42	143872	hgsc.bcm.edu	37	11	100847050	100847050	+	Silent	SNP	A	A	G	rs569270	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:100847050A>G	ENST00000298815.8	+	20	2121	c.2118A>G	c.(2116-2118)tcA>tcG	p.S706S	ARHGAP42_ENST00000524892.2_Silent_p.S672S	NM_152432.2	NP_689645.2	A6NI28	RHG42_HUMAN	Rho GTPase activating protein 42	706	Ser-rich.				signal transduction (GO:0007165)	intracellular (GO:0005622)	GTPase activator activity (GO:0005096)			endometrium(3)|skin(2)	5						GTGTTGCTTCAGTCACTAGCC	0.478													G|||	2805	0.560104	0.2027	0.6009	5008	,	,		21556	0.997		0.4344	False		,,,				2504	0.6933				p.S706S		Atlas-SNP	.											.	ARHGAP42	32	.	0			c.A2118G						PASS	.	G		423,961		64,295,333	73.0	55.0	61.0		2118	-11.4	0.0	11	dbSNP_83	61	1402,1780		313,776,502	no	coding-synonymous	ARHGAP42	NM_152432.2		377,1071,835	GG,GA,AA		44.0603,30.5636,39.9693		706/875	100847050	1825,2741	692	1591	2283	SO:0001819	synonymous_variant	143872	exon20			TGCTTCAGTCACT			11q22.1	2012-04-19			ENSG00000165895	ENSG00000165895		"""Rho GTPase activating proteins"""	26545	protein-coding gene	gene with protein product		615936				18954304	Standard	NM_152432		Approved	FLJ32810, GRAF3	uc001pge.2	A6NI28	OTTHUMG00000167530	ENST00000298815.8:c.2118A>G	11.37:g.100847050A>G		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	101	21	0.207921	NM_152432	Q96M56	Silent	SNP	ENST00000298815.8	37																																																																																				A|0.479;G|0.521	0.521	strong		0.478	ARHGAP42-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_152432	
AVPR1B	553	hgsc.bcm.edu	37	1	206230958	206230958	+	Missense_Mutation	SNP	G	G	A	rs28632197	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:206230958G>A	ENST00000367126.4	+	2	1556	c.1091G>A	c.(1090-1092)cGc>cAc	p.R364H		NM_000707.3	NP_000698.1	P47901	V1BR_HUMAN	arginine vasopressin receptor 1B	364			R -> H (in dbSNP:rs28632197). {ECO:0000269|PubMed:17909131, ECO:0000269|Ref.7}.		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)	CCCAGGATGCGCCGGCGGCTC	0.692													G|||	594	0.11861	0.087	0.0793	5008	,	,		12706	0.0883		0.1183	False		,,,				2504	0.2209				p.R364H		Atlas-SNP	.											.	AVPR1B	47	.	0			c.G1091A	GRCh37	CM086326	AVPR1B	M	rs28632197	PASS	.	G	HIS/ARG	417,3989		19,379,1805	20.0	19.0	19.0		1091	1.0	0.7	1	dbSNP_125	19	948,7652		51,846,3403	no	missense	AVPR1B	NM_000707.3	29	70,1225,5208	AA,AG,GG		11.0233,9.4644,10.4952	benign	364/425	206230958	1365,11641	2203	4300	6503	SO:0001583	missense	553	exon2			GGATGCGCCGGCG	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.1091G>A	1.37:g.206230958G>A	ENSP00000356094:p.Arg364His	Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	32	18	0.5625	NM_000707	B0M0J6|Q5TZ00	Missense_Mutation	SNP	ENST00000367126.4	37	CCDS30994.1	219	0.10027472527472528	46	0.09349593495934959	23	0.06353591160220995	66	0.11538461538461539	84	0.11081794195250659	G	9.389	1.075016	0.20227	0.094644	0.110233	ENSG00000198049	ENST00000367126	T	0.37915	1.17	5.69	1.05	0.20165	.	2.682860	0.00979	N	0.003342	T	0.00356	0.0011	L	0.29908	0.895	0.53005	P	3.799999999998249E-5	B	0.09022	0.002	B	0.04013	0.001	T	0.08973	-1.0696	9	0.37606	T	0.19	-0.8523	2.8989	0.05699	0.4746:0.0:0.3239:0.2016	rs28632197	364	P47901	V1BR_HUMAN	H	364	ENSP00000356094:R364H	ENSP00000356094:R364H	R	+	2	0	AVPR1B	204397581	0.002000	0.14202	0.710000	0.30468	0.073000	0.16967	0.330000	0.19715	0.300000	0.22699	0.563000	0.77884	CGC	G|0.894;A|0.106	0.106	strong		0.692	AVPR1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087996.1	NM_000707	
VWA8	23078	hgsc.bcm.edu	37	13	42385446	42385446	+	Missense_Mutation	SNP	T	T	C	rs9562353	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	89	0	0		WXS	Illumina HiSeq	Phase_I	88	47	0.534091	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	
BTN2A1	11120	hgsc.bcm.edu	37	6	26468545	26468545	+	Missense_Mutation	SNP	G	G	C	rs3734543	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:26468545G>C	ENST00000312541.5	+	8	1600	c.1352G>C	c.(1351-1353)gGc>gCc	p.G451A	BTN2A1_ENST00000469185.1_Intron|BTN2A1_ENST00000541522.1_Missense_Mutation_p.G390A|BTN2A1_ENST00000429381.1_3'UTR	NM_007049.3|NM_078476.2	NP_008980.1|NP_510961.1	Q7KYR7	BT2A1_HUMAN	butyrophilin, subfamily 2, member A1	451	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.		G -> A (in dbSNP:rs3734543).		lipid metabolic process (GO:0006629)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)				breast(3)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(2)|lung(9)|ovary(2)|prostate(1)|skin(3)|urinary_tract(3)	27						TGCCGGGTGGGCGTCTTCCTG	0.542													G|||	190	0.0379393	0.0333	0.0346	5008	,	,		20708	0.0099		0.0825	False		,,,				2504	0.0297				p.G451A		Atlas-SNP	.											BTN2A1_ENST00000265424,NS,carcinoma,-1,2	BTN2A1	118	2	0			c.G1352C						PASS	.	G	ALA/GLY,,ALA/GLY,	189,4217	119.2+/-156.9	4,181,2018	128.0	114.0	119.0		1169,,1352,	0.7	0.1	6	dbSNP_107	119	795,7805	185.7+/-233.4	39,717,3544	no	missense,intron,missense,utr-3	BTN2A1	NM_001197233.1,NM_001197234.1,NM_007049.3,NM_078476.2	60,,60,	43,898,5562	CC,CG,GG		9.2442,4.2896,7.5657	possibly-damaging,,possibly-damaging,	390/467,,451/528,	26468545	984,12022	2203	4300	6503	SO:0001583	missense	11120	exon8			GGGTGGGCGTCTT	U90543	CCDS4613.1, CCDS47390.1, CCDS56404.1, CCDS56405.1	6p22.1	2014-01-14			ENSG00000112763	ENSG00000112763		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Butyrophilins"""	1136	protein-coding gene	gene with protein product		613590				9382921, 9149941	Standard	NM_007049		Approved	BT2.1, BTF1, BTN2.1	uc003nib.2	Q7KYR7	OTTHUMG00000014457	ENST00000312541.5:c.1352G>C	6.37:g.26468545G>C	ENSP00000312158:p.Gly451Ala	Somatic	279	0	0		WXS	Illumina HiSeq	Phase_I	256	112	0.4375	NM_007049	B4DLP9|E9PGR4|O00475|P78408|Q59EN4|Q7KYQ7|Q7Z386|Q96AV7|Q9NU62	Missense_Mutation	SNP	ENST00000312541.5	37	CCDS4613.1	100	0.045787545787545784	16	0.032520325203252036	11	0.03038674033149171	8	0.013986013986013986	65	0.08575197889182058	G	11.33	1.605979	0.28623	0.042896	0.092442	ENSG00000112763	ENST00000312541;ENST00000541522;ENST00000265424	D;D	0.82711	-1.64;-1.64	2.6	0.669	0.17918	Concanavalin A-like lectin/glucanase (1);SPla/RYanodine receptor subgroup (1);Butyrophylin-like (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	0.558553	0.16195	N	0.225196	T	0.74854	0.3771	M	0.85859	2.78	0.80722	P	0.0	P;B	0.39903	0.694;0.189	B;B	0.42361	0.385;0.132	T	0.68534	-0.5383	9	0.56958	D	0.05	.	5.8105	0.18463	0.1453:0.582:0.2726:0.0	rs3734543	390;451	B4DLP9;Q7KYR7	.;BT2A1_HUMAN	A	451;390;437	ENSP00000312158:G451A;ENSP00000443909:G390A	ENSP00000265424:G437A	G	+	2	0	BTN2A1	26576524	0.872000	0.30054	0.075000	0.20258	0.335000	0.28730	3.331000	0.52075	0.127000	0.18452	0.491000	0.48974	GGC	.	.	weak		0.542	BTN2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040122.2	NM_007049	
C5orf55	116349	hgsc.bcm.edu	37	5	442790	442790	+	Missense_Mutation	SNP	G	G	A	rs10035653	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:442790G>A	ENST00000408966.2	-	1	468	c.148C>T	c.(148-150)Cct>Tct	p.P50S	EXOC3_ENST00000512944.1_5'Flank	NM_138464.2	NP_612473.1	Q8N2X6	CE055_HUMAN	chromosome 5 open reading frame 55	50			P -> S (in dbSNP:rs10035653).			extracellular region (GO:0005576)				large_intestine(1)|lung(2)	3						CTGGTGGCAGGTATGACAGAC	0.592													G|||	417	0.0832668	0.0257	0.147	5008	,	,		17805	0.1329		0.0726	False		,,,				2504	0.0757				p.P50S		Atlas-SNP	.											.	C5orf55	11	.	0			c.C148T						PASS	.	G	SER/PRO	132,3846		2,128,1859	148.0	167.0	161.0		148	-1.4	0.0	5	dbSNP_119	161	741,7589		38,665,3462	yes	missense	C5orf55	NM_138464.2	74	40,793,5321	AA,AG,GG		8.8956,3.3183,7.0929	possibly-damaging	50/120	442790	873,11435	1989	4165	6154	SO:0001583	missense	116349	exon1			TGGCAGGTATGAC	BC014011	CCDS43298.1	5p15.33	2012-02-24			ENSG00000221990	ENSG00000221990			25175	protein-coding gene	gene with protein product						12477932	Standard	NM_138464		Approved		uc010ita.3	Q8N2X6	OTTHUMG00000162235	ENST00000408966.2:c.148C>T	5.37:g.442790G>A	ENSP00000386139:p.Pro50Ser	Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	124	61	0.491935	NM_138464	Q96CR9	Missense_Mutation	SNP	ENST00000408966.2	37	CCDS43298.1	182	0.08333333333333333	17	0.034552845528455285	47	0.1298342541436464	54	0.0944055944055944	64	0.08443271767810026	G	4.564	0.104746	0.08731	0.033183	0.088956	ENSG00000221990	ENST00000408966	T	0.41065	1.01	0.677	-1.35	0.09114	.	.	.	.	.	T	0.00178	0.0005	N	0.08118	0	0.80722	P	0.0	P	0.35481	0.504	B	0.29440	0.102	T	0.09552	-1.0669	7	0.87932	D	0	.	.	.	.	rs10035653;rs10035653	50	Q8N2X6	CE055_HUMAN	S	50	ENSP00000386139:P50S	ENSP00000386139:P50S	P	-	1	0	C5orf55	495790	0.000000	0.05858	0.010000	0.14722	0.040000	0.13550	-0.037000	0.12164	-0.457000	0.07033	0.205000	0.17691	CCT	G|0.917;A|0.083	0.083	strong		0.592	C5orf55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368033.1	NM_138464	
BOD1	91272	hgsc.bcm.edu	37	5	173036394	173036394	+	Missense_Mutation	SNP	C	C	T	rs72822197	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:173036394C>T	ENST00000311086.4	-	3	629	c.406G>A	c.(406-408)Gtg>Atg	p.V136M	BOD1_ENST00000285908.5_Intron|BOD1_ENST00000480951.1_Intron|BOD1_ENST00000471339.1_5'Flank	NM_138369.2	NP_612378.1	Q96IK1	BOD1_HUMAN	biorientation of chromosomes in cell division 1	136					mitotic nuclear division (GO:0007067)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|kinetochore (GO:0000776)				endometrium(1)|large_intestine(2)|lung(2)|ovary(2)	7						GGATCCACCACCTGAGAAATA	0.468																																					p.V136M		Atlas-SNP	.											.	BOD1	15	.	0			c.G406A						PASS	.						150.0	136.0	141.0					5																	173036394		2203	4300	6503	SO:0001583	missense	91272	exon3			CCACCACCTGAGA	AY303777	CCDS4389.1, CCDS54951.1	5q35.2	2013-10-11	2009-03-04	2009-03-04	ENSG00000145919	ENSG00000145919			25114	protein-coding gene	gene with protein product	"""biorientation defective 1"""		"""family with sequence similarity 44, member B"""	FAM44B		17938248	Standard	NM_138369		Approved		uc003mcq.2	Q96IK1	OTTHUMG00000130540	ENST00000311086.4:c.406G>A	5.37:g.173036394C>T	ENSP00000309644:p.Val136Met	Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	286	34	0.118881	NM_138369	B4DXH8|Q9BTW1	Missense_Mutation	SNP	ENST00000311086.4	37	CCDS4389.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	27.1|27.1	4.803392|4.803392	0.90623|0.90623	.|.	.|.	ENSG00000145919|ENSG00000145919	ENST00000477985|ENST00000311086;ENST00000462674	.|.	.|.	.|.	5.65|5.65	5.65|5.65	0.86999|0.86999	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.71367|0.71367	0.3331|0.3331	M|M	0.73962|0.73962	2.25|2.25	0.80722|0.80722	D|D	1|1	.|P	.|0.46987	.|0.888	.|P	.|0.46825	.|0.528	T|T	0.75470|0.75470	-0.3306|-0.3306	5|9	.|0.72032	.|D	.|0.01	-25.5605|-25.5605	19.7198|19.7198	0.96137|0.96137	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|136	.|Q96IK1	.|BOD1_HUMAN	D|M	68|136;31	.|.	.|ENSP00000309644:V136M	G|V	-|-	2|1	0|0	BOD1|BOD1	172969000|172969000	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	7.474000|7.474000	0.81024|0.81024	2.668000|2.668000	0.90789|0.90789	0.655000|0.655000	0.94253|0.94253	GGT|GTG	C|0.946;T|0.054	0.054	strong		0.468	BOD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252963.1	NM_138369	
MKS1	54903	hgsc.bcm.edu	37	17	56294075	56294075	+	Missense_Mutation	SNP	G	G	C	rs142813109	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:56294075G>C	ENST00000393119.2	-	3	287	c.213C>G	c.(211-213)gaC>gaG	p.D71E	MKS1_ENST00000537529.2_Missense_Mutation_p.D61E|MKS1_ENST00000337050.7_Missense_Mutation_p.D71E|LPO_ENST00000582328.1_5'Flank|MKS1_ENST00000313863.6_Missense_Mutation_p.D71E|MKS1_ENST00000546108.1_5'UTR	NM_017777.3	NP_060247.2	Q9NXB0	MKS1_HUMAN	Meckel syndrome, type 1	71					branching morphogenesis of an epithelial tube (GO:0048754)|cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|membrane (GO:0016020)|TCTN-B9D complex (GO:0036038)		p.D71V(1)		endometrium(5)|kidney(3)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	26						CCTCCTCTTCGTCTTCCTCTG	0.483													G|||	8	0.00159744	0.0	0.0029	5008	,	,		18460	0.0		0.006	False		,,,				2504	0.0				p.D71E		Atlas-SNP	.											MKS1_ENST00000337050,NS,carcinoma,0,2	MKS1	100	2	1	Substitution - Missense(1)	upper_aerodigestive_tract(1)	c.C213G						PASS	.	G	GLU/ASP,GLU/ASP	8,3946		0,8,1969	135.0	140.0	138.0		183,213	-3.3	1.0	17	dbSNP_134	138	48,8250		0,48,4101	yes	missense,missense	MKS1	NM_001165927.1,NM_017777.3	45,45	0,56,6070	CC,CG,GG		0.5785,0.2023,0.4571	benign,benign	61/550,71/560	56294075	56,12196	1977	4149	6126	SO:0001583	missense	54903	exon3			CTCTTCGTCTTCC	DQ185029	CCDS11603.2, CCDS54148.1	17q21-q24	2014-09-17			ENSG00000011143	ENSG00000011143			7121	protein-coding gene	gene with protein product	"""POC12 centriolar protein homolog (Chlamydomonas)"""	609883		MKS		7550354, 16415886, 18327255	Standard	NM_017777		Approved	FLJ20345, POC12, BBS13	uc002ivr.2	Q9NXB0	OTTHUMG00000133714	ENST00000393119.2:c.213C>G	17.37:g.56294075G>C	ENSP00000376827:p.Asp71Glu	Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	151	71	0.470199	NM_017777	B7WNX4|F5H885|Q284T0|Q96G13	Missense_Mutation	SNP	ENST00000393119.2	37	CCDS11603.2	5|5	0.0022893772893772895|0.0022893772893772895	0|0	0.0|0.0	2|2	0.0055248618784530384|0.0055248618784530384	0|0	0.0|0.0	3|3	0.00395778364116095|0.00395778364116095	G|G	11.11|11.11	1.542037|1.542037	0.27563|0.27563	0.002023|0.002023	0.005785|0.005785	ENSG00000011143|ENSG00000011143	ENST00000537529;ENST00000393120;ENST00000393119;ENST00000337050|ENST00000313863	T;T;T;T|.	0.68331|.	-0.32;1.5;-0.27;-0.04|.	5.41|5.41	-3.29|-3.29	0.05017|0.05017	.|.	0.246500|.	0.23866|.	N|.	0.043797|.	T|T	0.10294|0.10294	0.0252|0.0252	N|N	0.02539|0.02539	-0.55|-0.55	0.80722|0.80722	D|D	1|1	B;B|.	0.02656|.	0.0;0.0|.	B;B|.	0.06405|.	0.002;0.001|.	T|T	0.19877|0.19877	-1.0292|-1.0292	10|5	0.06891|.	T|.	0.86|.	-13.0566|-13.0566	1.4484|1.4484	0.02369|0.02369	0.2305:0.3965:0.1768:0.1963|0.2305:0.3965:0.1768:0.1963	.|.	71;71|.	A8MPP8;Q9NXB0|.	.;MKS1_HUMAN|.	E|R	61;71;71;71|72	ENSP00000442096:D61E;ENSP00000376828:D71E;ENSP00000376827:D71E;ENSP00000338407:D71E|.	ENSP00000338407:D71E|.	D|T	-|-	3|2	2|0	MKS1|MKS1	53649074|53649074	0.123000|0.123000	0.22298|0.22298	0.997000|0.997000	0.53966|0.53966	0.988000|0.988000	0.76386|0.76386	-0.681000|-0.681000	0.05191|0.05191	-0.194000|-0.194000	0.10399|0.10399	-0.323000|-0.323000	0.08544|0.08544	GAC|ACG	G|0.996;C|0.004	0.004	strong		0.483	MKS1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258015.2	NM_017777	
FAM135B	51059	hgsc.bcm.edu	37	8	139164192	139164192	+	Silent	SNP	G	G	A	rs3750306	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:139164192G>A	ENST00000395297.1	-	13	2696	c.2526C>T	c.(2524-2526)ccC>ccT	p.P842P		NM_015912.3	NP_056996.2	Q49AJ0	F135B_HUMAN	family with sequence similarity 135, member B	842										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)			CTATGTATCCGGGGCCCTGCT	0.512										HNSCC(54;0.14)			G|||	1862	0.371805	0.1815	0.4207	5008	,	,		19302	0.5298		0.3757	False		,,,				2504	0.4274				p.P842P		Atlas-SNP	.											.	FAM135B	423	.	0			c.C2526T						PASS	.	G		973,3433	365.6+/-317.5	115,743,1345	92.0	81.0	85.0		2526	-10.9	0.0	8	dbSNP_107	85	3009,5591	465.1+/-366.4	542,1925,1833	no	coding-synonymous	FAM135B	NM_015912.3		657,2668,3178	AA,AG,GG		34.9884,22.0835,30.6166		842/1407	139164192	3982,9024	2203	4300	6503	SO:0001819	synonymous_variant	51059	exon13			GTATCCGGGGCCC	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.2526C>T	8.37:g.139164192G>A		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	60	59	0.983333	NM_015912	B5MDB3|O95879|Q2WGJ7|Q3KP46	Silent	SNP	ENST00000395297.1	37	CCDS6375.2																																																																																			G|0.665;A|0.335	0.335	strong		0.512	FAM135B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313590.3	NM_015912	
UBE2D1	7321	hgsc.bcm.edu	37	10	60127732	60127732	+	Silent	SNP	C	C	G	rs61749178	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:60127732C>G	ENST00000373910.4	+	6	581	c.354C>G	c.(352-354)ccC>ccG	p.P118P		NM_001204880.1|NM_003338.4	NP_001191809.1|NP_003329.1	P51668	UB2D1_HUMAN	ubiquitin-conjugating enzyme E2D 1	118					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|BMP signaling pathway (GO:0030509)|cellular response to hypoxia (GO:0071456)|gene expression (GO:0010467)|innate immune response (GO:0045087)|mitotic cell cycle (GO:0000278)|mitotic spindle assembly checkpoint (GO:0007094)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K48-linked ubiquitination (GO:0070936)|protein polyubiquitination (GO:0000209)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|protein complex (GO:0043234)|ubiquitin ligase complex (GO:0000151)	acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)|ubiquitin-protein transferase activity (GO:0004842)			central_nervous_system(1)|kidney(3)|large_intestine(1)|lung(2)|prostate(1)|skin(2)	10						CAGATGACCCCTTAGTACCAG	0.313													C|||	35	0.00698882	0.0015	0.0043	5008	,	,		14748	0.001		0.0189	False		,,,				2504	0.0102				p.P118P		Atlas-SNP	.											.	UBE2D1	16	.	0			c.C354G						PASS	.	C	,	24,4382	31.7+/-61.6	0,24,2179	203.0	181.0	188.0		240,354	-2.3	1.0	10	dbSNP_129	188	237,8359	95.2+/-157.0	4,229,4065	no	coding-synonymous,coding-synonymous	UBE2D1	NM_001204880.1,NM_003338.4	,	4,253,6244	GG,GC,CC		2.7571,0.5447,2.0074	,	80/110,118/148	60127732	261,12741	2203	4298	6501	SO:0001819	synonymous_variant	7321	exon6			TGACCCCTTAGTA	BC015997	CCDS7252.1, CCDS73139.1	10q21.1	2011-05-19	2011-05-19		ENSG00000072401	ENSG00000072401		"""Ubiquitin-conjugating enzymes E2"""	12474	protein-coding gene	gene with protein product		602961	"""stimulator of Fe transport"", ""ubiquitin-conjugating enzyme E2D 1 (UBC4/5 homolog, yeast)"""	SFT		10072594, 8530467	Standard	NM_003338		Approved	UbcH5A, UBCH5, UBC4/5, E2(17)KB1	uc001jke.2	P51668	OTTHUMG00000018269	ENST00000373910.4:c.354C>G	10.37:g.60127732C>G		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	73	40	0.547945	NM_003338	A6NLF6|A8K786	Silent	SNP	ENST00000373910.4	37	CCDS7252.1																																																																																			C|0.984;G|0.016	0.016	strong		0.313	UBE2D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048143.2	NM_003338	
SH2D4B	387694	hgsc.bcm.edu	37	10	82363340	82363340	+	Silent	SNP	C	C	A	rs7069048	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	74	0	0		WXS	Illumina HiSeq	Phase_I	46	22	0.478261	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	
GLI3	2737	hgsc.bcm.edu	37	7	42005678	42005678	+	Missense_Mutation	SNP	G	G	A	rs929387	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:42005678G>A	ENST00000395925.3	-	15	3077	c.2993C>T	c.(2992-2994)cCg>cTg	p.P998L	GLI3_ENST00000479210.1_5'UTR	NM_000168.5	NP_000159.3	P10071	GLI3_HUMAN	GLI family zinc finger 3	998			P -> L (in dbSNP:rs929387). {ECO:0000269|PubMed:10441342, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:2118997}.		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						GCCGTGGCCCGGCGCATCGTG	0.746									Pallister-Hall syndrome;Greig Cephalopolysyndactyly				G|||	2111	0.421526	0.1619	0.4424	5008	,	,		11700	0.7688		0.3161	False		,,,				2504	0.5082				p.P998L		Atlas-SNP	.											GLI3,NS,adenocarcinoma,+1,1	GLI3	312	1	0			c.C2993T						scavenged	.	G	LEU/PRO	654,2960		69,516,1222	4.0	5.0	5.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	2993	3.8	0.2	7	dbSNP_86	5	2170,5232		331,1508,1862	no	missense	GLI3	NM_000168.5	98	400,2024,3084	AA,AG,GG		29.3164,18.0963,25.6354	benign	998/1581	42005678	2824,8192	1807	3701	5508	SO:0001583	missense	2737	exon15	Familial Cancer Database	;	TGGCCCGGCGCAT		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.2993C>T	7.37:g.42005678G>A	ENSP00000379258:p.Pro998Leu	Somatic	0	0	.		WXS	Illumina HiSeq	Phase_I	2	2	1	NM_000168	A4D1W1|O75219|Q17RW4|Q75MT0|Q75MU9|Q9UDT5|Q9UJ39	Missense_Mutation	SNP	ENST00000395925.3	37	CCDS5465.1	917	0.4198717948717949	75	0.1524390243902439	153	0.42265193370165743	451	0.7884615384615384	238	0.31398416886543534	G	1.729	-0.494582	0.04322	0.180963	0.293164	ENSG00000106571	ENST00000395925	T	0.15256	2.44	4.98	3.83	0.44106	.	0.327528	0.33217	N	0.005158	T	0.00012	0.0000	N	0.05554	-0.025	0.09310	P	0.9999999999224007	B	0.06786	0.001	B	0.04013	0.001	T	0.16247	-1.0409	9	0.17369	T	0.5	.	5.4162	0.16376	0.7624:0.0:0.0842:0.1533	rs929387;rs929387	998	P10071	GLI3_HUMAN	L	998	ENSP00000379258:P998L	ENSP00000379258:P998L	P	-	2	0	GLI3	41972203	1.000000	0.71417	0.171000	0.22900	0.021000	0.10359	4.758000	0.62220	0.733000	0.32492	-0.471000	0.05019	CCG	G|0.565;A|0.435	0.435	strong		0.746	GLI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250806.3	NM_000168	
MYO9B	4650	hgsc.bcm.edu	37	19	17316782	17316782	+	Missense_Mutation	SNP	T	T	C	rs7248508	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:17316782T>C	ENST00000594824.1	+	32	5225	c.5078T>C	c.(5077-5079)gTt>gCt	p.V1693A	MYO9B_ENST00000595618.1_Missense_Mutation_p.V1693A|MYO9B_ENST00000397274.2_Missense_Mutation_p.V1693A|CTD-3032J10.3_ENST00000601929.1_RNA			Q13459	MYO9B_HUMAN	myosin IXB	1693	Tail.			V -> A (in Ref. 1; AAC50402). {ECO:0000305}.	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						GAGCCAGGCGTTGAGCCTGGC	0.667													C|||	3163	0.631589	0.708	0.6772	5008	,	,		12871	0.746		0.3917	False		,,,				2504	0.6247				p.V1693A		Atlas-SNP	.											MYO9B_ENST00000319396,NS,carcinoma,0,2	MYO9B	264	2	0			c.T5078C						PASS	.	C	ALA/VAL,ALA/VAL	2660,1460		885,890,285	21.0	27.0	25.0		5078,5078	4.7	0.0	19	dbSNP_116	25	3346,5022		710,1926,1548	yes	missense,missense	MYO9B	NM_001130065.1,NM_004145.3	64,64	1595,2816,1833	CC,CT,TT		39.9857,35.4369,48.0942	benign,benign	1693/2023,1693/2158	17316782	6006,6482	2060	4184	6244	SO:0001583	missense	4650	exon32			CAGGCGTTGAGCC		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.5078T>C	19.37:g.17316782T>C	ENSP00000471367:p.Val1693Ala	Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	31	10	0.322581	NM_001130065	O75314|Q9NUJ2|Q9UHN0	Missense_Mutation	SNP	ENST00000594824.1	37		1311	0.6002747252747253	331	0.6727642276422764	232	0.6408839779005525	445	0.777972027972028	303	0.3997361477572559	C	2.673	-0.277158	0.05679	0.645631	0.399857	ENSG00000099331	ENST00000397274;ENST00000319396	D	0.84442	-1.85	4.74	4.74	0.60224	.	0.234317	0.29676	N	0.011484	T	0.00012	0.0000	N	0.00436	-1.5	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	0.41142	-0.9525	9	0.05959	T	0.93	.	10.8777	0.46921	0.0:0.9112:0.0:0.0888	rs7248508;rs11545735;rs7248508	1693;1693;1699	Q13459;B0I1T6;Q4LE74	MYO9B_HUMAN;.;.	A	1693;38	ENSP00000380444:V1693A	ENSP00000314032:V38A	V	+	2	0	MYO9B	17177782	0.001000	0.12720	0.039000	0.18376	0.005000	0.04900	1.204000	0.32296	1.136000	0.42199	-0.215000	0.12644	GTT	T|0.406;C|0.594	0.594	strong		0.667	MYO9B-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000463236.1		
SPATA31E1	286234	hgsc.bcm.edu	37	9	90502819	90502819	+	Silent	SNP	T	T	C	rs10868671	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:90502819T>C	ENST00000325643.5	+	4	3483	c.3417T>C	c.(3415-3417)acT>acC	p.T1139T		NM_178828.4	NP_849150.3	Q6ZUB1	S31E1_HUMAN	SPATA31 subfamily E, member 1	1139					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											ACATGCTCACTGCCGCAGACA	0.647													.|||	2884	0.575879	0.6611	0.5533	5008	,	,		16964	0.5556		0.5328	False		,,,				2504	0.5419				p.T1139T		Atlas-SNP	.											.	.	.	.	0			c.T3417C						PASS	.	C		2716,1690		840,1036,327	42.0	48.0	46.0		3417	-5.3	0.0	9	dbSNP_120	46	4317,4283		1122,2073,1105	no	coding-synonymous	C9orf79	NM_178828.4		1962,3109,1432	CC,CT,TT		49.8023,38.3568,45.925		1139/1446	90502819	7033,5973	2203	4300	6503	SO:0001819	synonymous_variant	286234	exon4			GCTCACTGCCGCA	AK093185	CCDS6676.1	9q22.1-q22.2	2012-10-12	2012-10-12	2012-10-12	ENSG00000177992	ENSG00000177992			26672	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 79"", ""family with sequence similarity 75, member E1"""	C9orf79, FAM75E1			Standard	NM_178828		Approved	FLJ35866	uc004app.4	Q6ZUB1	OTTHUMG00000020157	ENST00000325643.5:c.3417T>C	9.37:g.90502819T>C		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	70	45	0.642857	NM_178828	B2RPB1|Q5SQC9|Q8NA41|Q8ND27	Silent	SNP	ENST00000325643.5	37	CCDS6676.1																																																																																			T|0.461;C|0.539	0.539	strong		0.647	SPATA31E1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052954.2	NM_178828	
KIF17	57576	hgsc.bcm.edu	37	1	21031042	21031042	+	Missense_Mutation	SNP	T	T	C	rs2296225	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:21031042T>C	ENST00000247986.2	-	5	1331	c.1021A>G	c.(1021-1023)Atc>Gtc	p.I341V	KIF17_ENST00000400463.3_Missense_Mutation_p.I341V|KIF17_ENST00000375044.1_Missense_Mutation_p.I241V			Q9P2E2	KIF17_HUMAN	kinesin family member 17	341			I -> V (in dbSNP:rs2296225).		ATP catabolic process (GO:0006200)|cell projection organization (GO:0030030)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|neurogenesis (GO:0022008)|protein complex localization (GO:0031503)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|intraciliary transport particle B (GO:0030992)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|plus-end-directed microtubule motor activity (GO:0008574)			NS(2)|endometrium(3)|kidney(3)|large_intestine(9)|liver(1)|lung(23)|ovary(4)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	50		all_lung(284;2.99e-05)|Lung NSC(340;3.26e-05)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00179)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|COAD - Colon adenocarcinoma(152;1.43e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000168)|Kidney(64;0.000221)|GBM - Glioblastoma multiforme(114;0.000651)|KIRC - Kidney renal clear cell carcinoma(64;0.0031)|STAD - Stomach adenocarcinoma(196;0.00336)|READ - Rectum adenocarcinoma(331;0.0686)|Lung(427;0.209)		TCCTCATTGATGCGCGGCTTG	0.597													T|||	820	0.163738	0.1021	0.062	5008	,	,		17209	0.2927		0.0915	False		,,,				2504	0.2607				p.I341V		Atlas-SNP	.											.	KIF17	130	.	0			c.A1021G						PASS	.	T	VAL/ILE,VAL/ILE	428,3978	207.5+/-228.8	17,394,1792	158.0	119.0	132.0		1021,1021	5.3	1.0	1	dbSNP_100	132	720,7880	176.2+/-226.1	33,654,3613	yes	missense,missense	KIF17	NM_001122819.1,NM_020816.2	29,29	50,1048,5405	CC,CT,TT		8.3721,9.714,8.8267	benign,benign	341/1029,341/1030	21031042	1148,11858	2203	4300	6503	SO:0001583	missense	57576	exon5			CATTGATGCGCGG	AB037826	CCDS213.1, CCDS44079.1, CCDS72722.1	1p36.13	2012-08-01			ENSG00000117245	ENSG00000117245		"""Kinesins"""	19167	protein-coding gene	gene with protein product	"""kinesin-like protein KIF17"", ""KIF3-related motor protein"", ""KIF17 variant protein"""	605037				10846156	Standard	XR_241202		Approved	KIAA1405, KIF3X, KIF17B, OSM-3, KLP-2	uc001bdr.4	Q9P2E2	OTTHUMG00000002863	ENST00000247986.2:c.1021A>G	1.37:g.21031042T>C	ENSP00000247986:p.Ile341Val	Somatic	237	0	0		WXS	Illumina HiSeq	Phase_I	250	138	0.552	NM_001122819	A2A3Q7|A2A3Q8|O95077|Q53YS6|Q5VWA9|Q6GSA8|Q8N411	Missense_Mutation	SNP	ENST00000247986.2	37	CCDS213.1	306	0.1401098901098901	56	0.11382113821138211	28	0.07734806629834254	155	0.270979020979021	67	0.08839050131926121	T	12.43	1.936368	0.34189	0.09714	0.083721	ENSG00000117245	ENST00000375044;ENST00000400463;ENST00000247986	T;T;T	0.71579	-0.58;-0.58;-0.58	5.26	5.26	0.73747	Kinesin, motor domain (2);	0.000000	0.33057	U	0.005340	T	0.00012	0.0000	N	0.13168	0.305	0.23221	P	0.99809292	B;B	0.23377	0.084;0.05	B;B	0.28784	0.094;0.039	T	0.05852	-1.0860	9	0.56958	D	0.05	.	9.2176	0.37358	0.0:0.0811:0.0:0.9189	rs2296225;rs52834908;rs2296225	341;341	Q9P2E2-3;Q9P2E2	.;KIF17_HUMAN	V	241;341;341	ENSP00000364184:I241V;ENSP00000383311:I341V;ENSP00000247986:I341V	ENSP00000247986:I341V	I	-	1	0	KIF17	20903629	1.000000	0.71417	1.000000	0.80357	0.883000	0.51084	1.483000	0.35497	2.127000	0.65507	0.379000	0.24179	ATC	T|0.885;C|0.115	0.115	strong		0.597	KIF17-009	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276995.1	NM_020816	
ZFAT	57623	hgsc.bcm.edu	37	8	135524797	135524797	+	Silent	SNP	G	G	T	rs3739429	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:135524797G>T	ENST00000377838.3	-	14	3456	c.3282C>A	c.(3280-3282)atC>atA	p.I1094I	ZFAT_ENST00000520214.1_Silent_p.I1082I|ZFAT_ENST00000517307.1_5'Flank|ZFAT_ENST00000523399.1_Silent_p.I1032I|ZFAT_ENST00000520356.1_Intron|ZFAT_ENST00000520727.1_Silent_p.I1082I|ZFAT_ENST00000429442.2_Silent_p.I1082I	NM_001174157.1|NM_020863.3	NP_001167628.1|NP_065914.2	Q9P243	ZFAT_HUMAN	zinc finger and AT hook domain containing	1094					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)			CGGCCTCTGTGATGTGGAGAT	0.527													G|||	970	0.19369	0.388	0.1009	5008	,	,		17745	0.2599		0.0626	False		,,,				2504	0.0634				p.I1094I		Atlas-SNP	.											.	ZFAT	265	.	0			c.C3282A						PASS	.	G	,,,,	1279,2667		208,863,902	150.0	157.0	155.0		3246,3246,3096,,3282	3.9	1.0	8	dbSNP_107	155	613,7681		23,567,3557	no	coding-synonymous,coding-synonymous,coding-synonymous,intron,coding-synonymous	ZFAT	NM_001029939.3,NM_001167583.2,NM_001174157.1,NM_001174158.1,NM_020863.3	,,,,	231,1430,4459	TT,TG,GG		7.3909,32.4126,15.4575	,,,,	1082/1232,1082/1232,1032/1182,,1094/1244	135524797	1892,10348	1973	4147	6120	SO:0001819	synonymous_variant	57623	exon14			CTCTGTGATGTGG	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.3282C>A	8.37:g.135524797G>T		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	109	81	0.743119	NM_020863	B7ZL15|E9PER3|Q3MIM5|Q6PJ01|Q75PJ6|Q75PJ7|Q75PJ9|Q86X64	Silent	SNP	ENST00000377838.3	37	CCDS47924.1																																																																																			G|0.797;T|0.203	0.203	strong		0.527	ZFAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378272.1	NM_001029939	
PRCC	5546	hgsc.bcm.edu	37	1	156756948	156756948	+	Silent	SNP	C	C	T	rs201827573		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:156756948C>T	ENST00000271526.4	+	3	1337	c.1065C>T	c.(1063-1065)gcC>gcT	p.A355A	PRCC_ENST00000491853.1_3'UTR|PRCC_ENST00000353233.3_Silent_p.A355A	NM_005973.4	NP_005964.3	Q92733	PRCC_HUMAN	papillary renal cell carcinoma (translocation-associated)	355					mitotic cell cycle checkpoint (GO:0007093)	intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)			PRCC/TFE3(25)	breast(1)|central_nervous_system(3)|endometrium(1)|kidney(2)|large_intestine(1)|liver(1)|lung(5)|upper_aerodigestive_tract(1)	15	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)					ATGCCAATGCCGCTGGTGCTT	0.532			T	TFE3	papillary renal								C|||	1	0.000199681	0.0	0.0	5008	,	,		14844	0.0		0.001	False		,,,				2504	0.0				p.A355A		Atlas-SNP	.		Dom	yes		1	1q21.1	5546	papillary renal cell carcinoma (translocation-associated)		E	.	PRCC	39	.	0			c.C1065T						PASS	.	C		0,4406		0,0,2203	116.0	121.0	119.0		1065	-2.6	1.0	1		119	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	PRCC	NM_005973.4		0,2,6501	TT,TC,CC		0.0233,0.0,0.0154		355/492	156756948	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	5546	exon3			CAATGCCGCTGGT	X99720	CCDS1157.1	1q21.1	2008-02-05			ENSG00000143294	ENSG00000143294			9343	protein-coding gene	gene with protein product		179755				8872474	Standard	NM_005973		Approved	RCCP1	uc001fqa.3	Q92733	OTTHUMG00000041294	ENST00000271526.4:c.1065C>T	1.37:g.156756948C>T		Somatic	405	0	0		WXS	Illumina HiSeq	Phase_I	327	157	0.480122	NM_005973	A8K1F7|O00665|O00724|Q5SZ06	Silent	SNP	ENST00000271526.4	37	CCDS1157.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	7.757	0.704598	0.15172	0.0	2.33E-4	ENSG00000143294	ENST00000454659	.	.	.	5.15	-2.57	0.06248	.	.	.	.	.	T	0.30665	0.0772	.	.	.	0.52501	D	0.999954	.	.	.	.	.	.	T	0.32455	-0.9906	4	.	.	.	-9.8382	4.9292	0.13909	0.0964:0.5476:0.0971:0.2588	.	.	.	.	L	89	.	.	P	+	2	0	PRCC	155023572	0.271000	0.24162	0.973000	0.42090	0.986000	0.74619	-0.613000	0.05610	-0.687000	0.05162	-1.094000	0.02160	CCG	C|0.999;T|0.001	0.001	strong		0.532	PRCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098941.2	NM_005973	
NCOA2	10499	hgsc.bcm.edu	37	8	71126255	71126255	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:71126255C>T	ENST00000452400.2	-	4	323	c.142G>A	c.(142-144)Gaa>Aaa	p.E48K		NM_006540.2	NP_006531.1	Q15596	NCOA2_HUMAN	nuclear receptor coactivator 2	48	bHLH. {ECO:0000255|PROSITE- ProRule:PRU00981}.				cellular lipid metabolic process (GO:0044255)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of glucose metabolic process (GO:0010906)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	chromatin binding (GO:0003682)|histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)|signal transducer activity (GO:0004871)|thyroid hormone receptor coactivator activity (GO:0030375)|transcription coactivator activity (GO:0003713)		PAX3/NCOA2(4)|HEY1/NCOA2(10)	NS(1)|breast(4)|endometrium(7)|kidney(4)|large_intestine(10)|lung(25)|ovary(1)|pancreas(2)|prostate(2)|skin(4)	60	Breast(64;0.201)		Epithelial(68;0.0147)|OV - Ovarian serous cystadenocarcinoma(28;0.0455)|all cancers(69;0.0606)			TCTGCAAGTTCTTCTATATAT	0.299			T	"""RUNXBP2, HEY1"""	"""AML, Chondrosarcoma"""																																p.E48K		Atlas-SNP	.		Dom	yes		8	8q13.1	10499	nuclear receptor coactivator 2 (TIF2)		L	NCOA2,NS,carcinoma,0,1	NCOA2	147	1	0			c.G142A						PASS	.						111.0	101.0	104.0					8																	71126255		1783	4058	5841	SO:0001583	missense	10499	exon4			CAAGTTCTTCTAT	X97674	CCDS47872.1	8q13.3	2011-07-01			ENSG00000140396	ENSG00000140396		"""Chromatin-modifying enzymes / K-acetyltransferases"", ""Basic helix-loop-helix proteins"""	7669	protein-coding gene	gene with protein product		601993				9111344, 8670870	Standard	XM_005251128		Approved	TIF2, GRIP1, NCoA-2, KAT13C, bHLHe75	uc003xyn.1	Q15596	OTTHUMG00000164671	ENST00000452400.2:c.142G>A	8.37:g.71126255C>T	ENSP00000399968:p.Glu48Lys	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	77	4	0.0519481	NM_006540	Q14CD2	Missense_Mutation	SNP	ENST00000452400.2	37	CCDS47872.1	.	.	.	.	.	.	.	.	.	.	C	34	5.304743	0.95601	.	.	ENSG00000140396	ENST00000452400	T	0.02446	4.29	5.53	5.53	0.82687	Helix-loop-helix DNA-binding (4);	0.000000	0.85682	D	0.000000	T	0.19046	0.0457	M	0.82630	2.6	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.00191	-1.1936	10	0.87932	D	0	.	19.466	0.94939	0.0:1.0:0.0:0.0	.	48	Q15596	NCOA2_HUMAN	K	48	ENSP00000399968:E48K	ENSP00000399968:E48K	E	-	1	0	NCOA2	71288809	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.818000	0.86416	2.607000	0.88179	0.655000	0.94253	GAA	.	.	none		0.299	NCOA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379696.1		
C12orf65	91574	hgsc.bcm.edu	37	12	123738494	123738494	+	Silent	SNP	C	C	T	rs2280424	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:123738494C>T	ENST00000253233.1	+	2	917	c.273C>T	c.(271-273)atC>atT	p.I91I	C12orf65_ENST00000366329.2_Silent_p.I91I|RP11-282O18.3_ENST00000543217.2_RNA|RP11-282O18.3_ENST00000541002.3_RNA|C12orf65_ENST00000429587.2_Silent_p.I91I	NM_152269.4	NP_689482.1	Q9H3J6	CL065_HUMAN	chromosome 12 open reading frame 65	91	GGQ domain. {ECO:0000250}.				cell death (GO:0008219)	mitochondrion (GO:0005739)	translation release factor activity (GO:0003747)			endometrium(1)|large_intestine(1)|lung(1)|prostate(1)	4	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000595)|Epithelial(86;0.00199)		CCTCAGGCATCGTTGTAAAGG	0.567													C|||	455	0.0908546	0.0424	0.0605	5008	,	,		19339	0.2569		0.0507	False		,,,				2504	0.0481				p.I91I		Atlas-SNP	.											.	C12orf65	15	.	0			c.C273T						PASS	.	C	,,	191,4215	115.0+/-153.0	0,191,2012	50.0	55.0	54.0		273,273,273	-0.1	1.0	12	dbSNP_100	54	332,8268	113.3+/-173.4	10,312,3978	no	coding-synonymous,coding-synonymous,coding-synonymous	C12orf65	NM_001143905.2,NM_001194995.1,NM_152269.4	,,	10,503,5990	TT,TC,CC		3.8605,4.335,4.0212	,,	91/167,91/167,91/167	123738494	523,12483	2203	4300	6503	SO:0001819	synonymous_variant	91574	exon2			AGGCATCGTTGTA	AK095982	CCDS9244.1	12q24.31	2013-01-07			ENSG00000130921	ENSG00000130921			26784	protein-coding gene	gene with protein product		613541				20598281, 22688947, 23188110	Standard	NM_152269		Approved	FLJ38663, SPG55	uc001uen.3	Q9H3J6	OTTHUMG00000168852	ENST00000253233.1:c.273C>T	12.37:g.123738494C>T		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	64	29	0.453125	NM_001194995	Q8WUC6	Silent	SNP	ENST00000253233.1	37	CCDS9244.1																																																																																			C|0.929;T|0.071	0.071	strong		0.567	C12orf65-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401375.1	NM_152269	
KCNAB1	7881	hgsc.bcm.edu	37	3	156249214	156249214	+	Silent	SNP	T	T	C	rs2280031	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:156249214T>C	ENST00000490337.1	+	13	1162	c.1098T>C	c.(1096-1098)aaT>aaC	p.N366N	KCNAB1_ENST00000497291.1_3'UTR|KCNAB1_ENST00000389636.5_Silent_p.N337N|KCNAB1_ENST00000389634.5_Silent_p.N319N|KCNAB1_ENST00000302490.8_Silent_p.N348N|KCNAB1_ENST00000471742.1_Silent_p.N355N	NM_172160.2	NP_751892.1	Q14722	KCAB1_HUMAN	potassium voltage-gated channel, shaker-related subfamily, beta member 1	366					learning or memory (GO:0007611)|potassium ion transport (GO:0006813)|regulation of potassium ion transmembrane transporter activity (GO:1901016)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	potassium channel regulator activity (GO:0015459)|voltage-gated potassium channel activity (GO:0005249)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(8)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	28			LUSC - Lung squamous cell carcinoma(72;0.0461)|Lung(72;0.0465)			GCCTGAGAAATGAAGGTGTGA	0.478													t|||	1300	0.259585	0.2171	0.268	5008	,	,		22188	0.3175		0.2435	False		,,,				2504	0.2679				p.N366N		Atlas-SNP	.											.	KCNAB1	176	.	0			c.T1098C						PASS	.		,,	963,3443	364.1+/-316.8	102,759,1342	247.0	214.0	225.0		1065,1044,1098	-4.5	0.9	3	dbSNP_100	225	2027,6573	354.0+/-329.3	244,1539,2517	no	coding-synonymous,coding-synonymous,coding-synonymous	KCNAB1	NM_003471.3,NM_172159.3,NM_172160.2	,,	346,2298,3859	CC,CT,TT		23.5698,21.8566,22.9894	,,	355/409,348/402,366/420	156249214	2990,10016	2203	4300	6503	SO:0001819	synonymous_variant	7881	exon13			GAGAAATGAAGGT	U33428	CCDS3174.1, CCDS3175.1, CCDS33882.1	3q26.1	2006-11-29			ENSG00000169282	ENSG00000169282		"""Potassium channels"", ""Aldo-keto reductases"""	6228	protein-coding gene	gene with protein product		601141				8838324, 7499366	Standard	NM_172160		Approved	AKR6A3, KCNA1B, hKvBeta3, Kvb1.3, hKvb3	uc003far.2	Q14722	OTTHUMG00000158552	ENST00000490337.1:c.1098T>C	3.37:g.156249214T>C		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	119	59	0.495798	NM_172160	A8K9H8|A8KAD4|B3KPZ4|Q13031|Q13302|Q16547|Q6PI60|Q99869	Silent	SNP	ENST00000490337.1	37	CCDS3174.1																																																																																			T|0.756;C|0.244	0.244	strong		0.478	KCNAB1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000351411.1	NM_003471	
L3HYPDH	112849	hgsc.bcm.edu	37	14	59950690	59950690	+	Silent	SNP	A	A	C	rs2296842	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:59950690A>C	ENST00000247194.4	-	1	458	c.345T>G	c.(343-345)gcT>gcG	p.A115A	L3HYPDH_ENST00000487285.1_5'Flank|JKAMP_ENST00000356057.5_5'Flank|JKAMP_ENST00000554271.1_5'Flank|RP11-701B16.2_ENST00000554253.1_RNA|JKAMP_ENST00000425728.2_5'Flank|JKAMP_ENST00000261247.9_5'Flank|JKAMP_ENST00000556985.1_5'Flank	NM_144581.1	NP_653182.1	Q96EM0	T3HPD_HUMAN	L-3-hydroxyproline dehydratase (trans-)	115					metabolic process (GO:0008152)		hydro-lyase activity (GO:0016836)|trans-L-3-hydroxyproline dehydratase activity (GO:0050346)									L-Proline(DB00172)	CGAAGTCCAAAGCGAAGCGGC	0.706											OREG0022712	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	A|||	1328	0.265176	0.1861	0.3833	5008	,	,		16051	0.1825		0.2376	False		,,,				2504	0.4018				p.A115A		Atlas-SNP	.											C14orf149,NS,carcinoma,0,1	.	.	1	0			c.T345G						PASS	.	A		853,3413		111,631,1391	10.0	10.0	10.0		345	-9.7	0.0	14	dbSNP_100	10	1857,6475		235,1387,2544	no	coding-synonymous	C14orf149	NM_144581.1		346,2018,3935	CC,CA,AA		22.2876,19.9953,21.5114		115/355	59950690	2710,9888	2133	4166	6299	SO:0001819	synonymous_variant	112849	exon1			GTCCAAAGCGAAG	AI762327	CCDS9739.1	14q23.1	2012-08-15	2012-08-15	2012-08-15	ENSG00000126790	ENSG00000126790	4.2.1.77		20488	protein-coding gene	gene with protein product	"""trans-L-3-hydroxyproline dehydratase"""	614811	"""chromosome 14 open reading frame 149"""	C14orf149		22528483	Standard	NM_144581		Approved	FLJ25436	uc001xee.1	Q96EM0	OTTHUMG00000028941	ENST00000247194.4:c.345T>G	14.37:g.59950690A>C		Somatic	7	0	0	1042	WXS	Illumina HiSeq	Phase_I	13	6	0.461538	NM_144581	Q96LJ5	Silent	SNP	ENST00000247194.4	37	CCDS9739.1																																																																																			A|0.786;C|0.214	0.214	strong		0.706	L3HYPDH-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000072254.5	NM_144581	
OR9G1	390174	hgsc.bcm.edu	37	11	56468155	56468155	+	Missense_Mutation	SNP	T	T	G	rs11228732	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:56468155T>G	ENST00000312153.1	+	1	292	c.292T>G	c.(292-294)Tgt>Ggt	p.C98G		NM_001005213.1	NP_001005213.1	Q8NH87	OR9G1_HUMAN	olfactory receptor, family 9, subfamily G, member 1	98			C -> G (in dbSNP:rs11228732).			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						TGGCTGCCTGTGTCAGTTCTT	0.522													T|||	1812	0.361821	0.6778	0.2507	5008	,	,		18842	0.2292		0.3091	False		,,,				2504	0.2045				p.C98G		Atlas-SNP	.											.	.	.	.	0			c.T292G						PASS	.						119.0	116.0	117.0					11																	56468155		2201	4296	6497	SO:0001583	missense	504191	exon1			TGCCTGTGTCAGT	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.292T>G	11.37:g.56468155T>G	ENSP00000309012:p.Cys98Gly	Somatic	193	0	0		WXS	Illumina HiSeq	Phase_I	178	69	0.38764	NM_001013358	Q6IEU9|Q8NGQ0	Missense_Mutation	SNP	ENST00000312153.1	37	CCDS31536.1	616	0.28205128205128205	225	0.4573170731707317	74	0.20441988950276244	110	0.19230769230769232	207	0.27308707124010556	T	5.319	0.244291	0.10077	.	.	ENSG00000174914	ENST00000312153	T	0.01335	5.0	4.54	-1.49	0.08718	GPCR, rhodopsin-like superfamily (1);	1.255020	0.05595	N	0.575322	T	0.00012	0.0000	N	0.11560	0.145	0.09310	N	1	B	0.14805	0.011	B	0.17722	0.019	T	0.34576	-0.9823	10	0.59425	D	0.04	-0.3613	5.7266	0.18017	0.0704:0.0978:0.3717:0.46	rs11228732	98	Q8NH87	OR9G1_HUMAN	G	98	ENSP00000309012:C98G	ENSP00000309012:C98G	C	+	1	0	OR9G1	56224731	0.000000	0.05858	0.000000	0.03702	0.400000	0.30750	-2.671000	0.00843	-0.374000	0.07967	-0.356000	0.07607	TGT	T|0.749;G|0.251	0.251	strong		0.522	OR9G1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393253.1	NM_001005213	
LILRA1	11024	hgsc.bcm.edu	37	19	55106239	55106239	+	Silent	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:55106239G>A	ENST00000251372.3	+	4	362	c.180G>A	c.(178-180)ctG>ctA	p.L60L	LILRB1_ENST00000448689.1_Intron|LILRB1_ENST00000396321.2_Intron|LILRA1_ENST00000473156.1_3'UTR|LILRB1_ENST00000418536.2_Intron|LILRA1_ENST00000453777.1_Silent_p.L60L	NM_006863.2	NP_006854.1	O75019	LIRA1_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 1	60	Ig-like C2-type 1.				cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)|immune system process (GO:0002376)|regulation of immune response (GO:0050776)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	antigen binding (GO:0003823)|transmembrane signaling receptor activity (GO:0004888)	p.L60L(3)		breast(2)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(5)|liver(1)|lung(23)|ovary(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)	47				GBM - Glioblastoma multiforme(193;0.0348)		AGTACCGTCTGTATAGAGAAA	0.572																																					p.L60L		Atlas-SNP	.											LILRA1,NS,carcinoma,0,3	LILRA1	105	3	3	Substitution - coding silent(3)	kidney(3)	c.G180A						scavenged	.						124.0	119.0	121.0					19																	55106239		2203	4300	6503	SO:0001819	synonymous_variant	11024	exon4			CCGTCTGTATAGA	AF025530	CCDS12901.1, CCDS62802.1	19q13.4	2013-01-11			ENSG00000104974	ENSG00000104974		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6602	protein-coding gene	gene with protein product		604810				9548455	Standard	NM_006863		Approved	LIR-6, CD85i, LIR6	uc002qgh.2	O75019	OTTHUMG00000065701	ENST00000251372.3:c.180G>A	19.37:g.55106239G>A		Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	122	4	0.0327869	NM_006863	O75018|Q3MJA6	Silent	SNP	ENST00000251372.3	37	CCDS12901.1																																																																																			.	.	none		0.572	LILRA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140807.2	NM_006863	
GGT1	2678	hgsc.bcm.edu	37	22	25023881	25023881	+	Missense_Mutation	SNP	T	T	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:25023881T>G	ENST00000400382.1	+	13	2026	c.1271T>G	c.(1270-1272)tTc>tGc	p.F424C	GGT1_ENST00000466310.1_3'UTR|GGT1_ENST00000404223.1_Missense_Mutation_p.F80C|GGT1_ENST00000406383.2_Missense_Mutation_p.F424C|GGT1_ENST00000400383.1_Missense_Mutation_p.F424C|GGT1_ENST00000403838.1_Missense_Mutation_p.F80C|GGT1_ENST00000248923.4_Missense_Mutation_p.F424C|GGT1_ENST00000404532.1_Missense_Mutation_p.F80C|GGT1_ENST00000400380.1_Missense_Mutation_p.F424C|GGT1_ENST00000404920.1_Missense_Mutation_p.F80C|GGT1_ENST00000401885.1_Missense_Mutation_p.F80C			P19440	GGT1_HUMAN	gamma-glutamyltransferase 1	424					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)			breast(1)|endometrium(2)|kidney(14)|large_intestine(2)|lung(6)|pancreas(1)|prostate(6)|skin(7)|upper_aerodigestive_tract(1)	40					Glutathione(DB00143)	ATGGACGACTTCAGCTCTCCC	0.617																																					p.F424C		Atlas-SNP	.											.	GGT1	68	.	0			c.T1271G						PASS	.						75.0	82.0	79.0					22																	25023881		2203	4300	6503	SO:0001583	missense	2678	exon13			ACGACTTCAGCTC	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.1271T>G	22.37:g.25023881T>G	ENSP00000383232:p.Phe424Cys	Somatic	538	0	0		WXS	Illumina HiSeq	Phase_I	431	104	0.241299	NM_013430	Q08247|Q14404|Q8TBS1|Q9UMK1	Missense_Mutation	SNP	ENST00000400382.1	37	CCDS42992.1	.	.	.	.	.	.	.	.	.	.	.	13.74	2.326429	0.41197	.	.	ENSG00000100031	ENST00000248923;ENST00000412658;ENST00000400382;ENST00000400383;ENST00000400380;ENST00000406383;ENST00000401885;ENST00000404532;ENST00000403838;ENST00000404223;ENST00000404920	T;T;T;T;T;T;T;T;T;T;T	0.12569	2.67;2.67;2.67;2.67;2.67;2.67;2.67;2.67;2.67;2.67;2.67	3.49	3.49	0.39957	.	0.000000	0.85682	D	0.000000	T	0.53834	0.1821	H	0.99357	4.53	0.48511	D	0.999661	D	0.89917	1.0	D	0.81914	0.995	T	0.72001	-0.4422	10	0.87932	D	0	-41.2004	11.6793	0.51448	0.0:0.0:0.0:1.0	.	424	P19440	GGT1_HUMAN	C	424;424;424;424;424;424;80;80;80;80;80	ENSP00000248923:F424C;ENSP00000393537:F424C;ENSP00000383232:F424C;ENSP00000383233:F424C;ENSP00000383231:F424C;ENSP00000385975:F424C;ENSP00000384381:F80C;ENSP00000385445:F80C;ENSP00000384820:F80C;ENSP00000385016:F80C;ENSP00000385001:F80C	ENSP00000248923:F424C	F	+	2	0	GGT1	23353881	1.000000	0.71417	1.000000	0.80357	0.006000	0.05464	3.722000	0.54948	1.593000	0.50029	0.373000	0.22412	TTC	.	.	none		0.617	GGT1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250797.1	NM_013430	
STOX1	219736	hgsc.bcm.edu	37	10	70645697	70645697	+	Silent	SNP	C	C	T	rs10509306	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:70645697C>T	ENST00000298596.6	+	3	2228	c.2145C>T	c.(2143-2145)aaC>aaT	p.N715N	STOX1_ENST00000421961.2_Silent_p.N605N|STOX1_ENST00000399169.4_Silent_p.N715N|STOX1_ENST00000399162.2_Intron|STOX1_ENST00000399165.4_Intron	NM_152709.4	NP_689922.3	Q6ZVD7	STOX1_HUMAN	storkhead box 1	715						cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(5)|endometrium(2)|kidney(2)|large_intestine(5)|liver(2)|lung(8)|prostate(1)|skin(3)	28						AGCTTTCTAACGATGACCAGG	0.408													c|||	441	0.0880591	0.0098	0.1527	5008	,	,		23379	0.0556		0.1461	False		,,,				2504	0.1217				p.N715N		Atlas-SNP	.											.	STOX1	75	.	0			c.C2145T						PASS	.	T	,,,,	94,3782		2,90,1846	110.0	100.0	103.0		,,2145,1815,2145	-6.0	0.0	10	dbSNP_119	103	1006,7270		62,882,3194	no	intron,intron,coding-synonymous,coding-synonymous,coding-synonymous	STOX1	NM_001130159.2,NM_001130160.2,NM_001130161.2,NM_001130162.2,NM_152709.4	,,,,	64,972,5040	TT,TC,CC		12.1556,2.4252,9.052	,,,,	,,715/990,605/880,715/990	70645697	1100,11052	1938	4138	6076	SO:0001819	synonymous_variant	219736	exon3			TTCTAACGATGAC	AK057891	CCDS41535.1, CCDS44416.1, CCDS44417.1	10q22.1	2005-11-29	2005-04-04	2005-04-04	ENSG00000165730	ENSG00000165730			23508	protein-coding gene	gene with protein product		609397	"""chromosome 10 open reading frame 24"""	C10orf24			Standard	NM_152709		Approved	FLJ25162	uc001joq.3	Q6ZVD7	OTTHUMG00000018367	ENST00000298596.6:c.2145C>T	10.37:g.70645697C>T		Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	158	80	0.506329	NM_152709	A2A3Q9|A5D6Y7|B0QZA4|B0QZA5|B0QZA6|Q4F8Q6|Q5I946|Q5I947|Q5I948|Q5VX38|Q5VX39|Q6ZRY3|Q96LR3|Q96LS0	Silent	SNP	ENST00000298596.6	37	CCDS41535.1																																																																																			C|0.912;T|0.088	0.088	strong		0.408	STOX1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276849.3	NM_152709	
OR5M1	390168	hgsc.bcm.edu	37	11	56380134	56380134	+	Missense_Mutation	SNP	C	C	G	rs4939078	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:56380134C>G	ENST00000526538.1	-	1	844	c.845G>C	c.(844-846)aGc>aCc	p.S282T		NM_001004740.1	NP_001004740.1	Q8NGP8	OR5M1_HUMAN	olfactory receptor, family 5, subfamily M, member 1	282			S -> T (in dbSNP:rs4939078).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(7)|upper_aerodigestive_tract(1)	12						CAGCATTGGGCTCAAAAAAGT	0.398													C|||	2095	0.418331	0.1815	0.5605	5008	,	,		17293	0.622		0.3141	False		,,,				2504	0.5348				p.S282T		Atlas-SNP	.											.	OR5M1	92	.	0			c.G845C						PASS	.	C	THR/SER	726,2938		76,574,1182	181.0	175.0	177.0		845	2.8	0.9	11	dbSNP_111	177	2452,5744		372,1708,2018	no	missense	OR5M1	NM_001004740.1	58	448,2282,3200	GG,GC,CC		29.917,19.8144,26.796	probably-damaging	282/316	56380134	3178,8682	1832	4098	5930	SO:0001583	missense	390168	exon1			ATTGGGCTCAAAA	AB065742	CCDS53631.1	11q11	2012-08-09				ENSG00000255012		"""GPCR / Class A : Olfactory receptors"""	8352	protein-coding gene	gene with protein product							Standard	NM_001004740		Approved	OST050	uc001nja.1	Q8NGP8		ENST00000526538.1:c.845G>C	11.37:g.56380134C>G	ENSP00000435416:p.Ser282Thr	Somatic	401	0	0		WXS	Illumina HiSeq	Phase_I	359	94	0.261838	NM_001004740	Q6IF60|Q96RB6	Missense_Mutation	SNP	ENST00000526538.1	37	CCDS53631.1	867	0.39697802197802196	77	0.1565040650406504	198	0.5469613259668509	354	0.6188811188811189	238	0.31398416886543534	C	12.26	1.884258	0.33255	0.198144	0.29917	ENSG00000255012	ENST00000526538	T	0.38240	1.15	3.71	2.77	0.32553	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00012	0.0000	N	0.00205	-1.85	0.41029	P	0.014854000000000034	D	0.67145	0.996	D	0.68039	0.955	T	0.15065	-1.0450	8	0.72032	D	0.01	.	6.8855	0.24197	0.1801:0.4941:0.3259:0.0	rs4939078	282	Q8NGP8	OR5M1_HUMAN	T	282	ENSP00000435416:S282T	ENSP00000435416:S282T	S	-	2	0	OR5M1	56136710	0.001000	0.12720	0.879000	0.34478	0.505000	0.33919	0.674000	0.25218	0.775000	0.33450	0.280000	0.19369	AGC	C|0.621;G|0.379	0.379	strong		0.398	OR5M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391610.1	NM_001004740	
FGF6	2251	hgsc.bcm.edu	37	12	4553332	4553332	+	Silent	SNP	A	A	G	rs2241280	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:4553332A>G	ENST00000228837.2	-	2	460	c.417T>C	c.(415-417)gtT>gtC	p.V139V		NM_020996.1	NP_066276.2	P10767	FGF6_HUMAN	fibroblast growth factor 6	139					angiogenesis (GO:0001525)|cartilage condensation (GO:0001502)|cell proliferation (GO:0008283)|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)|myoblast differentiation (GO:0045445)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|sarcolemma (GO:0042383)	growth factor activity (GO:0008083)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	20			Colorectal(7;0.00165)|COAD - Colon adenocarcinoma(12;0.0229)			TGTTCATGGCAACGAAGAGGG	0.507													A|||	2365	0.472244	0.5749	0.3487	5008	,	,		21392	0.4177		0.3857	False		,,,				2504	0.5665				p.V139V		Atlas-SNP	.											FGF6,NS,carcinoma,-2,1	FGF6	40	1	0			c.T417C						PASS	.	A		2464,1942	622.5+/-394.0	693,1078,432	106.0	81.0	90.0		417	-7.1	0.1	12	dbSNP_98	90	3432,5168	503.5+/-375.9	667,2098,1535	no	coding-synonymous	FGF6	NM_020996.1		1360,3176,1967	GG,GA,AA		39.907,44.0763,45.3329		139/209	4553332	5896,7110	2203	4300	6503	SO:0001819	synonymous_variant	2251	exon2			CATGGCAACGAAG	X63454	CCDS8527.1	12p13	2014-01-30				ENSG00000111241		"""Endogenous ligands"""	3684	protein-coding gene	gene with protein product		134921				16597617	Standard	NM_020996		Approved		uc001qmr.1	P10767		ENST00000228837.2:c.417T>C	12.37:g.4553332A>G		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	144	62	0.430556	NM_020996	Q0VAE1	Silent	SNP	ENST00000228837.2	37	CCDS8527.1																																																																																			A|0.554;G|0.446	0.446	strong		0.507	FGF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398939.1	NM_020996	
ERICH6	131831	hgsc.bcm.edu	37	3	150384657	150384657	+	Missense_Mutation	SNP	G	G	A	rs114572143	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:150384657G>A	ENST00000295910.6	-	13	1697	c.1645C>T	c.(1645-1647)Cgc>Tgc	p.R549C	FAM194A_ENST00000491361.1_Missense_Mutation_p.R403C	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						TCTAAGATGCGGACTCCAATA	0.388													G|||	39	0.00778754	0.0015	0.0101	5008	,	,		19368	0.0		0.0268	False		,,,				2504	0.0031				p.R549C		Atlas-SNP	.											.	FAM194A	91	.	0			c.C1645T						PASS	.	G	CYS/ARG	21,4385	27.2+/-55.0	0,21,2182	123.0	118.0	120.0		1645	5.4	1.0	3	dbSNP_132	120	198,8402	85.8+/-148.2	1,196,4103	yes	missense	FAM194A	NM_152394.3	180	1,217,6285	AA,AG,GG		2.3023,0.4766,1.6838	probably-damaging	549/664	150384657	219,12787	2203	4300	6503	SO:0001583	missense	131831	exon13			AGATGCGGACTCC																												ENST00000295910.6:c.1645C>T	3.37:g.150384657G>A	ENSP00000295910:p.Arg549Cys	Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	134	61	0.455224	NM_152394		Missense_Mutation	SNP	ENST00000295910.6	37	CCDS3151.2	25	0.011446886446886446	2	0.0040650406504065045	3	0.008287292817679558	0	0.0	20	0.026385224274406333	G	18.67	3.673185	0.67928	0.004766	0.023023	ENSG00000163645	ENST00000295910;ENST00000491361;ENST00000313811	T;T	0.17054	2.3;2.3	5.41	5.41	0.78517	.	0.000000	0.64402	D	0.000009	T	0.17492	0.0420	M	0.69823	2.125	0.51233	D	0.999917	D	0.89917	1.0	D	0.97110	1.0	T	0.02167	-1.1202	10	0.87932	D	0	-15.9343	11.6494	0.51279	0.0:0.0:0.7149:0.2851	.	549	Q7L0X2	F194A_HUMAN	C	549;403;507	ENSP00000295910:R549C;ENSP00000419366:R403C	ENSP00000295910:R549C	R	-	1	0	FAM194A	151867347	1.000000	0.71417	0.993000	0.49108	0.990000	0.78478	3.319000	0.51983	2.544000	0.85801	0.655000	0.94253	CGC	G|0.986;A|0.014	0.014	strong		0.388	FAM194A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257666.1		
CARD9	64170	hgsc.bcm.edu	37	9	139270901	139270901	+	5'Flank	SNP	G	G	A	rs61745672	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:139270901G>A	ENST00000371732.5	-	0	0				CARD9_ENST00000315908.7_5'Flank|SNAPC4_ENST00000298532.2_Silent_p.S1439S|CARD9_ENST00000371734.3_5'Flank	NM_052813.4	NP_434700.2	Q9H257	CARD9_HUMAN	caspase recruitment domain family, member 9						defense response to Gram-positive bacterium (GO:0050830)|defense response to virus (GO:0051607)|innate immune response (GO:0045087)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of JNK cascade (GO:0046330)|positive regulation of stress-activated MAPK cascade (GO:0032874)|positive regulation of tumor necrosis factor production (GO:0032760)|regulation of apoptotic process (GO:0042981)|regulation of interleukin-2 biosynthetic process (GO:0045076)|regulation of interleukin-6 biosynthetic process (GO:0045408)|regulation of tumor necrosis factor biosynthetic process (GO:0042534)|response to drug (GO:0042493)|response to exogenous dsRNA (GO:0043330)|response to fungus (GO:0009620)|response to muramyl dipeptide (GO:0032495)|response to peptidoglycan (GO:0032494)	cytoplasm (GO:0005737)	CARD domain binding (GO:0050700)|protein homodimerization activity (GO:0042803)			endometrium(2)|kidney(2)|large_intestine(3)|lung(3)|pancreas(1)|prostate(3)|skin(1)	15		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;4.58e-06)|Epithelial(140;5.65e-06)		CCAGGCAGGAGGAAGCAGAGC	0.607													G|||	171	0.0341454	0.0091	0.0461	5008	,	,		20815	0.002		0.1064	False		,,,				2504	0.0184				p.S1439S		Atlas-SNP	.											.	SNAPC4	82	.	0			c.C4317T						PASS	.	G		117,4289	87.3+/-125.9	3,111,2089	140.0	136.0	137.0		4317	0.3	0.0	9	dbSNP_129	137	823,7777	190.1+/-236.7	36,751,3513	no	coding-synonymous	SNAPC4	NM_003086.2		39,862,5602	AA,AG,GG		9.5698,2.6555,7.2274		1439/1470	139270901	940,12066	2203	4300	6503	SO:0001631	upstream_gene_variant	6621	exon22			GCAGGAGGAAGCA	AF311287	CCDS6997.1, CCDS48057.1	9q34	2014-09-17			ENSG00000187796	ENSG00000187796			16391	protein-coding gene	gene with protein product		607212				11053425	Standard	NM_052813		Approved		uc004chg.3	Q9H257	OTTHUMG00000020925		9.37:g.139270901G>A	Exception_encountered	Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	122	44	0.360656	NM_003086	Q5SXM5|Q5SXM6|Q9H854	Silent	SNP	ENST00000371732.5	37	CCDS6997.1																																																																																			G|0.934;A|0.066	0.066	strong		0.607	CARD9-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055053.1	NM_052813	
TMEM132C	92293	hgsc.bcm.edu	37	12	129153986	129153986	+	Missense_Mutation	SNP	G	G	A	rs4272850	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:129153986G>A	ENST00000435159.2	+	5	1330	c.1330G>A	c.(1330-1332)Gta>Ata	p.V444I	AC107020.1_ENST00000408822.1_RNA|TMEM132C_ENST00000315208.8_Missense_Mutation_p.V60I	NM_001136103.2	NP_001129575.2	Q8N3T6	T132C_HUMAN	transmembrane protein 132C	444			V -> I (in dbSNP:rs4272850).			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						GAACACCGCCGTACTCACAGG	0.498													A|||	1712	0.341853	0.4523	0.3199	5008	,	,		21362	0.248		0.2783	False		,,,				2504	0.3701				p.V444I		Atlas-SNP	.											.	TMEM132C	142	.	0			c.G1330A						PASS	.	A	ILE/VAL	589,795		126,337,229	110.0	99.0	103.0		1330	1.3	0.5	12	dbSNP_111	103	802,2380		108,586,897	yes	missense	TMEM132C	NM_001136103.2	29	234,923,1126	AA,AG,GG		25.2043,42.5578,30.4643	benign	444/1109	129153986	1391,3175	692	1591	2283	SO:0001583	missense	92293	exon5			ACCGCCGTACTCA	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.1330G>A	12.37:g.129153986G>A	ENSP00000410852:p.Val444Ile	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	148	72	0.486486	NM_001136103	Q69YX8	Missense_Mutation	SNP	ENST00000435159.2	37		671	0.30723443223443225	216	0.43902439024390244	120	0.3314917127071823	130	0.22727272727272727	205	0.2704485488126649	A	0.020	-1.446847	0.01089	0.425578	0.252043	ENSG00000181234	ENST00000435159;ENST00000315208	T;T	0.11495	2.77;2.77	5.01	1.33	0.21861	.	0.000000	0.56097	N	0.000030	T	0.00012	0.0000	N	0.00538	-1.39	0.47949	P	4.450000000000287E-4	B	0.06786	0.001	B	0.08055	0.003	T	0.47235	-0.9133	9	0.02654	T	1	.	9.0375	0.36296	0.7069:0.0:0.2931:0.0	rs4272850;rs52821868;rs60998550;rs4272850	444	Q8N3T6	T132C_HUMAN	I	444;60	ENSP00000410852:V444I;ENSP00000324458:V60I	ENSP00000324458:V60I	V	+	1	0	TMEM132C	127719939	0.576000	0.26700	0.479000	0.27329	0.106000	0.19336	1.199000	0.32235	-0.273000	0.09246	-1.062000	0.02293	GTA	G|0.692;A|0.308	0.308	strong		0.498	TMEM132C-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		XM_044062	
IGLL5	100423062	hgsc.bcm.edu	37	22	23230419	23230419	+	Silent	SNP	C	C	T	rs554734650	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:23230419C>T	ENST00000526893.1	+	1	460	c.186C>T	c.(184-186)agC>agT	p.S62S	IGLL5_ENST00000531372.1_Silent_p.S62S|IGLL5_ENST00000532223.2_Silent_p.S62S|hsa-mir-5571_ENST00000577998.1_RNA	NM_001178126.1	NP_001171597.1	B9A064	IGLL5_HUMAN	immunoglobulin lambda-like polypeptide 5	62						extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|urinary_tract(1)	7						GCCGATCCAGCCTGCGGAGCC	0.647													C|||	3	0.000599042	0.0008	0.0	5008	,	,		11441	0.001		0.001	False		,,,				2504	0.0				p.A27V		Atlas-SNP	.											.	IGLL5	26	.	0			c.C80T						PASS	.																																			SO:0001819	synonymous_variant	100423062	exon1			ATCCAGCCTGCGG	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.186C>T	22.37:g.23230419C>T		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	97	25	0.257732	NM_001256296		Missense_Mutation	SNP	ENST00000526893.1	37	CCDS54506.1																																																																																			.	.	none		0.647	IGLL5-002	KNOWN	basic|appris_candidate|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000385699.1	NM_001178126	
POT1	25913	hgsc.bcm.edu	37	7	124481185	124481185	+	Missense_Mutation	SNP	C	C	A	rs35536751	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:124481185C>A	ENST00000357628.3	-	14	1809	c.1211G>T	c.(1210-1212)gGt>gTt	p.G404V	POT1_ENST00000393329.1_Missense_Mutation_p.G273V	NM_015450.2	NP_056265.2	Q9NUX5	POTE1_HUMAN	protection of telomeres 1	404					DNA duplex unwinding (GO:0032508)|negative regulation of telomerase activity (GO:0051974)|negative regulation of telomere maintenance via telomerase (GO:0032211)|positive regulation of DNA strand elongation (GO:0060383)|positive regulation of helicase activity (GO:0051096)|positive regulation of telomerase activity (GO:0051973)|positive regulation of telomere maintenance via telomerase (GO:0032212)|telomere capping (GO:0016233)|telomere formation via telomerase (GO:0032203)|telomere maintenance (GO:0000723)|telomere maintenance via telomerase (GO:0007004)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|nuclear telomere cap complex (GO:0000783)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DEAD/H-box RNA helicase binding (GO:0017151)|single-stranded telomeric DNA binding (GO:0043047)|telomerase inhibitor activity (GO:0010521)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(4)|liver(1)|lung(23)|ovary(1)|prostate(1)|skin(3)|stomach(1)|urinary_tract(1)	47						TTTAGTTGCACCATCCTGAAA	0.348													C|||	26	0.00519169	0.0	0.0058	5008	,	,		14561	0.0		0.0109	False		,,,				2504	0.0112				p.G404V	Esophageal Squamous(149;1032 1141 16047 36610 40540 42429 44687 51642)	Atlas-SNP	.											.	POT1	186	.	0			c.G1211T						PASS	.	C	VAL/GLY,VAL/GLY	12,4394	19.1+/-41.9	0,12,2191	140.0	139.0	139.0		818,1211	-1.5	0.0	7	dbSNP_126	139	140,8460	70.7+/-133.2	3,134,4163	yes	missense,missense	POT1	NM_001042594.1,NM_015450.2	109,109	3,146,6354	AA,AC,CC		1.6279,0.2724,1.1687	benign,benign	273/504,404/635	124481185	152,12854	2203	4300	6503	SO:0001583	missense	25913	exon14			GTTGCACCATCCT	AK022580	CCDS5793.1	7q31.33	2013-01-21	2013-01-21		ENSG00000128513	ENSG00000128513			17284	protein-coding gene	gene with protein product		606478	"""protection of telomeres 1 homolog (S. pombe)"""			11349150, 12391173	Standard	NR_003102		Approved	hPot1, DKFZp586D211	uc003vlm.3	Q9NUX5	OTTHUMG00000157194	ENST00000357628.3:c.1211G>T	7.37:g.124481185C>A	ENSP00000350249:p.Gly404Val	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	106	47	0.443396	NM_015450	O95018|Q5MJ36|Q9H662|Q9NW19|Q9UG95	Missense_Mutation	SNP	ENST00000357628.3	37	CCDS5793.1	7	0.003205128205128205	0	0.0	1	0.0027624309392265192	0	0.0	6	0.0079155672823219	C	8.360	0.832782	0.16820	0.002724	0.016279	ENSG00000128513	ENST00000357628;ENST00000393329;ENST00000451720;ENST00000440969;ENST00000265391	T;T	0.41065	1.01;1.01	5.55	-1.51	0.08664	.	0.894418	0.10102	N	0.715890	T	0.16514	0.0397	L	0.44542	1.39	0.09310	N	1	B	0.09022	0.002	B	0.06405	0.002	T	0.23154	-1.0196	10	0.49607	T	0.09	-2.4198	5.4362	0.16482	0.096:0.5063:0.264:0.1338	rs35536751;rs61756406	404	Q9NUX5	POTE1_HUMAN	V	404;273;404;404;403	ENSP00000350249:G404V;ENSP00000377002:G273V	ENSP00000265391:G403V	G	-	2	0	POT1	124268421	0.004000	0.15560	0.007000	0.13788	0.714000	0.41099	-0.021000	0.12504	-0.162000	0.10964	0.655000	0.94253	GGT	C|0.990;A|0.010	0.010	strong		0.348	POT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347861.1		
SSPN	8082	hgsc.bcm.edu	37	12	26383959	26383959	+	Missense_Mutation	SNP	G	G	A	rs12313736	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:26383959G>A	ENST00000242729.2	+	3	859	c.682G>A	c.(682-684)Gtc>Atc	p.V228I	RP11-283G6.5_ENST00000541940.1_RNA|SSPN_ENST00000422622.2_Missense_Mutation_p.V125I|SSPN_ENST00000535504.1_Intron|RP11-283G6.5_ENST00000537525.1_RNA|SSPN_ENST00000540266.1_Missense_Mutation_p.V125I|RP11-283G6.5_ENST00000540625.1_RNA|RP11-283G6.4_ENST00000540392.1_RNA	NM_005086.4	NP_005077.2	Q14714	SSPN_HUMAN	sarcospan	228			V -> I (in dbSNP:rs12313736).		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)				kidney(1)|large_intestine(2)|lung(5)|skin(1)|stomach(1)	10	Colorectal(261;0.0847)					CTATGTGGGTGTCAGGATATG	0.483													G|||	457	0.091254	0.2821	0.0605	5008	,	,		17485	0.0		0.0258	False		,,,				2504	0.0164				p.V228I		Atlas-SNP	.											.	SSPN	19	.	0			c.G682A						PASS	.	G	ILE/VAL,ILE/VAL	993,3413	370.5+/-319.6	128,737,1338	107.0	103.0	104.0		373,682	3.9	0.9	12	dbSNP_120	104	302,8298	109.8+/-170.3	6,290,4004	yes	missense,missense	SSPN	NM_001135823.1,NM_005086.4	29,29	134,1027,5342	AA,AG,GG		3.5116,22.5374,9.9569	benign,benign	125/141,228/244	26383959	1295,11711	2203	4300	6503	SO:0001583	missense	8082	exon3			GTGGGTGTCAGGA	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.682G>A	12.37:g.26383959G>A	ENSP00000242729:p.Val228Ile	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	57	28	0.491228	NM_005086	B3KS67	Missense_Mutation	SNP	ENST00000242729.2	37	CCDS8707.1	141	0.06456043956043957	104	0.21138211382113822	17	0.04696132596685083	0	0.0	20	0.026385224274406333	G	14.98	2.697051	0.48202	0.225374	0.035116	ENSG00000123096	ENST00000540266;ENST00000422622;ENST00000242729;ENST00000441067	T;T;T	0.33865	1.47;1.47;1.39	4.81	3.9	0.45041	.	0.202595	0.42821	D	0.000653	T	0.00012	0.0000	L	0.57536	1.79	0.22050	P	0.999396981	B	0.11235	0.004	B	0.06405	0.002	T	0.08764	-1.0706	8	.	.	.	-8.9216	7.5114	0.27575	0.1437:0.148:0.7083:0.0	rs12313736;rs52831951;rs12313736	228	Q14714	SSPN_HUMAN	I	125;125;228;202	ENSP00000442893:V125I;ENSP00000396087:V125I;ENSP00000242729:V228I	.	V	+	1	0	SSPN	26275226	0.003000	0.15002	0.919000	0.36401	0.943000	0.58893	1.274000	0.33132	2.396000	0.81511	0.563000	0.77884	GTC	G|0.913;A|0.087	0.087	strong		0.483	SSPN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402654.2	NM_005086	
MST1L	11223	hgsc.bcm.edu	37	1	17085452	17085452	+	RNA	SNP	A	A	G	rs3981980		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:17085452A>G	ENST00000455405.2	-	0	0							Q2TV78	MST1L_HUMAN	macrophage stimulating 1-like							extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)										GAGCGGGAGCAAAATCGTGGC	0.617																																					p.F413F		Atlas-SNP	.											Q13209_HUMAN,NS,carcinoma,0,1	.	.	1	0			c.T1239C						scavenged	.																																					11223	exon10			GGGAGCAAAATCG	U28055, AF083416		1p36.33	2013-03-27	2012-11-09	2012-11-09	ENSG00000186715	ENSG00000186715			7390	other	unknown			"""macrophage stimulating, pseudogene 7"", ""macrophage stimulating, pseudogene 9"", ""macrophage stimulating 1 (hepatocyte growth factor-like) pseudogene 9"""	MSTP7, MSTP9, MST1P9		10728827	Standard	NM_001271733		Approved	D1F15S1A, MSPL7, MSPL-7	uc010ock.3	Q2TV78	OTTHUMG00000002578		1.37:g.17085452A>G		Somatic	197	3	0.0152284		WXS	Illumina HiSeq	Phase_I	211	41	0.194313	NM_001271733	B7WPB1|Q13209	Silent	SNP	ENST00000455405.2	37																																																																																				A|1.000;|0.000	.	weak		0.617	MST1L-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000400328.1	NM_001271733	
DARS2	55157	hgsc.bcm.edu	37	1	173822936	173822936	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:173822936C>T	ENST00000361951.4	+	15	2294	c.1567C>T	c.(1567-1569)Cgt>Tgt	p.R523C	DARS2_ENST00000239457.5_Intron|DARS2_ENST00000471476.1_Intron	NM_018122.4	NP_060592.2	Q6PI48	SYDM_HUMAN	aspartyl-tRNA synthetase 2, mitochondrial	523					gene expression (GO:0010467)|mitochondrial asparaginyl-tRNA aminoacylation (GO:0070145)|tRNA aminoacylation (GO:0043039)|tRNA aminoacylation for protein translation (GO:0006418)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	aspartate-tRNA ligase activity (GO:0004815)|aspartate-tRNA(Asn) ligase activity (GO:0050560)|ATP binding (GO:0005524)|protein homodimerization activity (GO:0042803)|tRNA binding (GO:0000049)	p.R523S(1)		breast(4)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(4)|lung(10)|ovary(1)|pancreas(1)|urinary_tract(1)	30					L-Aspartic Acid(DB00128)	CTTCTAGGCCCGTAGCCAACA	0.388																																					p.R523C		Atlas-SNP	.											.	DARS2	61	.	1	Substitution - Missense(1)	lung(1)	c.C1567T						PASS	.						101.0	105.0	103.0					1																	173822936		2203	4300	6503	SO:0001583	missense	55157	exon15			TAGGCCCGTAGCC	AK022754	CCDS1311.1	1q25.1	2011-07-01	2007-02-23		ENSG00000117593	ENSG00000117593	6.1.1.12	"""Aminoacyl tRNA synthetases / Class II"""	25538	protein-coding gene	gene with protein product	"""aspartate tRNA ligase 2, mitochondrial"""	610956				15779907	Standard	NM_018122		Approved	FLJ10514	uc001gjh.2	Q6PI48	OTTHUMG00000034803	ENST00000361951.4:c.1567C>T	1.37:g.173822936C>T	ENSP00000355086:p.Arg523Cys	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	63	15	0.238095	NM_018122		Missense_Mutation	SNP	ENST00000361951.4	37	CCDS1311.1	.	.	.	.	.	.	.	.	.	.	C	23.2	4.384482	0.82792	.	.	ENSG00000117593	ENST00000361951	T	0.80123	-1.34	4.65	4.65	0.58169	Aminoacyl-tRNA synthetase, class II (1);Aminoacyl-tRNA synthetase, class II (D/K/N) (1);	0.055932	0.64402	D	0.000001	D	0.92492	0.7616	H	0.96777	3.88	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.94831	0.7996	10	0.72032	D	0.01	-15.4489	16.6683	0.85259	0.0:1.0:0.0:0.0	.	523	Q6PI48	SYDM_HUMAN	C	523	ENSP00000355086:R523C	ENSP00000355086:R523C	R	+	1	0	DARS2	172089559	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	5.614000	0.67695	2.304000	0.77564	0.591000	0.81541	CGT	.	.	none		0.388	DARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084220.1	NM_018122	
SIPA1L2	57568	hgsc.bcm.edu	37	1	232650867	232650867	+	Silent	SNP	C	C	T	rs4649383	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:232650867C>T	ENST00000366630.1	-	2	577	c.219G>A	c.(217-219)aaG>aaA	p.K73K	SIPA1L2_ENST00000262861.4_Silent_p.K73K			Q9P2F8	SI1L2_HUMAN	signal-induced proliferation-associated 1 like 2	73					regulation of small GTPase mediated signal transduction (GO:0051056)		GTPase activator activity (GO:0005096)			NS(1)|breast(5)|central_nervous_system(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(13)|lung(49)|ovary(2)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	103		all_cancers(173;0.00605)|Prostate(94;0.128)|all_epithelial(177;0.186)				TCACACCCATCTTGGGCACAG	0.522													C|||	2782	0.555511	0.4569	0.6369	5008	,	,		19169	0.3333		0.7952	False		,,,				2504	0.6135				p.K73K		Atlas-SNP	.											.	SIPA1L2	218	.	0			c.G219A						PASS	.	C		1948,1900		515,918,491	114.0	111.0	112.0		219	-1.6	1.0	1	dbSNP_111	112	6614,1660		2637,1340,160	no	coding-synonymous	SIPA1L2	NM_020808.3		3152,2258,651	TT,TC,CC		20.0628,49.3763,29.3681		73/1723	232650867	8562,3560	1924	4137	6061	SO:0001819	synonymous_variant	57568	exon1			ACCCATCTTGGGC	AB037810	CCDS41474.1	1q42.2	2008-02-05			ENSG00000116991	ENSG00000116991			23800	protein-coding gene	gene with protein product		611609					Standard	NM_020808		Approved	KIAA1389	uc001hvg.3	Q9P2F8	OTTHUMG00000037820	ENST00000366630.1:c.219G>A	1.37:g.232650867C>T		Somatic	198	1	0.00505051		WXS	Illumina HiSeq	Phase_I	150	150	1	NM_020808	Q2TV88|Q5VXR7|Q5VXR8|Q641Q4|Q8NA38|Q96DZ3|Q9H9F6	Silent	SNP	ENST00000366630.1	37	CCDS41474.1																																																																																			C|0.410;T|0.590	0.590	strong		0.522	SIPA1L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092318.1	XM_045839	
LAMA1	284217	hgsc.bcm.edu	37	18	6985270	6985270	+	Missense_Mutation	SNP	C	C	T	rs11664063	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:6985270C>T	ENST00000389658.3	-	39	5719	c.5626G>A	c.(5626-5628)Gct>Act	p.A1876T		NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	1876	Domain II and I.		A -> T (in dbSNP:rs11664063). {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)	p.A1876T(1)		NS(4)|breast(7)|central_nervous_system(3)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(49)|liver(1)|lung(71)|ovary(9)|pancreas(3)|prostate(5)|skin(11)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(3)	205		Colorectal(10;0.172)				TGGAACTCAGCGGCATGGTCC	0.493													C|||	679	0.135583	0.0068	0.1383	5008	,	,		17821	0.1915		0.2276	False		,,,				2504	0.1554				p.A1876T		Atlas-SNP	.											LAMA1,NS,carcinoma,0,1	LAMA1	458	1	1	Substitution - Missense(1)	stomach(1)	c.G5626A						PASS	.	C	THR/ALA	225,4181	135.3+/-171.4	7,211,1985	200.0	163.0	176.0		5626	-0.6	0.0	18	dbSNP_120	176	2201,6399	375.3+/-337.7	281,1639,2380	yes	missense	LAMA1	NM_005559.3	58	288,1850,4365	TT,TC,CC		25.593,5.1067,18.6529	benign	1876/3076	6985270	2426,10580	2203	4300	6503	SO:0001583	missense	284217	exon39			ACTCAGCGGCATG	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.5626G>A	18.37:g.6985270C>T	ENSP00000374309:p.Ala1876Thr	Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	165	70	0.424242	NM_005559		Missense_Mutation	SNP	ENST00000389658.3	37	CCDS32787.1	347	0.15888278388278387	6	0.012195121951219513	63	0.17403314917127072	96	0.16783216783216784	182	0.24010554089709762	C	8.183	0.794177	0.16327	0.051067	0.25593	ENSG00000101680	ENST00000389658	T	0.17854	2.25	5.58	-0.587	0.11690	.	0.452259	0.22669	N	0.057082	T	0.00012	0.0000	M	0.68593	2.085	0.53688	P	2.199999999996649E-5	B	0.26547	0.152	B	0.15484	0.013	T	0.44112	-0.9349	9	0.15952	T	0.53	.	6.1433	0.20271	0.1159:0.4954:0.0:0.3887	rs11664063;rs52811359;rs58155506;rs11664063	1876	P25391	LAMA1_HUMAN	T	1876	ENSP00000374309:A1876T	ENSP00000374309:A1876T	A	-	1	0	LAMA1	6975270	0.009000	0.17119	0.016000	0.15963	0.006000	0.05464	0.065000	0.14466	-0.449000	0.07117	-0.123000	0.14984	GCT	C|0.823;T|0.177	0.177	strong		0.493	LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1	NM_005559	
TRAPPC10	7109	hgsc.bcm.edu	37	21	45506819	45506819	+	Silent	SNP	T	T	C	rs1131999	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:45506819T>C	ENST00000291574.4	+	16	2692	c.2517T>C	c.(2515-2517)gcT>gcC	p.A839A		NM_003274.4	NP_003265.3	P48553	TPC10_HUMAN	trafficking protein particle complex 10	839					sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|vesicle-mediated transport (GO:0016192)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	sodium ion transmembrane transporter activity (GO:0015081)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(8)|ovary(1)|prostate(2)|skin(2)|urinary_tract(4)	41						AGAGCAGGGCTGTGGTCTACT	0.602													C|||	2107	0.420727	0.7466	0.3184	5008	,	,		19871	0.2986		0.164	False		,,,				2504	0.4427				p.A839A		Atlas-SNP	.											.	TRAPPC10	109	.	0			c.T2517C						PASS	.	C		2970,1436	465.3+/-354.1	1008,954,241	72.0	65.0	67.0		2517	-11.5	0.0	21	dbSNP_86	67	1525,7075	746.8+/-407.3	160,1205,2935	yes	coding-synonymous	TRAPPC10	NM_003274.4		1168,2159,3176	CC,CT,TT		17.7326,32.5919,34.561		839/1260	45506819	4495,8511	2203	4300	6503	SO:0001819	synonymous_variant	7109	exon16			CAGGGCTGTGGTC	U19252	CCDS13704.1	21q22.3	2008-05-07	2008-05-07	2008-05-07	ENSG00000160218	ENSG00000160218		"""Trafficking protein particle complex"""	11868	protein-coding gene	gene with protein product	"""trafficking protein particle complex subunit 130"", ""TRAPP 130 kDa subunit"""	602103	"""transmembrane protein 1"""	TMEM1		7633421	Standard	NM_003274		Approved	EHOC-1, TRS130	uc002zea.3	P48553	OTTHUMG00000086894	ENST00000291574.4:c.2517T>C	21.37:g.45506819T>C		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	132	131	0.992424	NM_003274	Q3MIR2|Q86SI7|Q9UMD4|Q9Y4L3	Silent	SNP	ENST00000291574.4	37	CCDS13704.1																																																																																			T|0.658;C|0.342	0.342	strong		0.602	TRAPPC10-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000195737.1	NM_003274	
MARCH10	162333	hgsc.bcm.edu	37	17	60814273	60814273	+	Missense_Mutation	SNP	A	A	G	rs9891498	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:60814273A>G	ENST00000311269.5	-	6	1230	c.956T>C	c.(955-957)tTt>tCt	p.F319S	RP11-156L14.1_ENST00000582564.1_RNA|RP11-156L14.1_ENST00000584597.1_RNA|MARCH10_ENST00000583600.1_Missense_Mutation_p.F357S|RP11-156L14.1_ENST00000577270.1_RNA|MARCH10_ENST00000456609.2_Missense_Mutation_p.F319S|MARCH10_ENST00000544856.2_Missense_Mutation_p.F318S|RP11-156L14.1_ENST00000579201.1_RNA	NM_152598.2	NP_689811.2	Q8NA82	MARHA_HUMAN	membrane-associated ring finger (C3HC4) 10, E3 ubiquitin protein ligase	319			F -> S (in dbSNP:rs9891498). {ECO:0000269|PubMed:14702039}.		protein ubiquitination (GO:0016567)		ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(11)|liver(1)|lung(15)	38						TGTCCCCCCAAATCTACTTCT	0.458													A|||	1362	0.271965	0.1324	0.3876	5008	,	,		19391	0.2083		0.4215	False		,,,				2504	0.2904				p.F319S		Atlas-SNP	.											.	MARCH10	102	.	0			c.T956C						PASS	.	A	SER/PHE,SER/PHE	820,3586	318.8+/-295.8	86,648,1469	192.0	194.0	193.0		956,956	2.8	0.0	17	dbSNP_119	193	3386,5214	487.7+/-372.2	717,1952,1631	yes	missense,missense	MARCH10	NM_001100875.1,NM_152598.2	155,155	803,2600,3100	GG,GA,AA		39.3721,18.611,32.3389	probably-damaging,probably-damaging	319/809,319/809	60814273	4206,8800	2203	4300	6503	SO:0001583	missense	162333	exon6			CCCCCAAATCTAC	AK093076	CCDS11635.1, CCDS74122.1, CCDS74123.1	17q23.3	2013-01-09	2012-02-23	2007-08-20		ENSG00000173838		"""RING-type (C3HC4) zinc fingers"", ""MARCH membrane-associated ring fingers"""	26655	protein-coding gene	gene with protein product		613337	"""ring finger protein 190"", ""membrane-associated ring finger (C3HC4) 10"""	RNF190		17604280	Standard	XM_005257103		Approved	FLJ35757, MARCH-X	uc002jag.4	Q8NA82		ENST00000311269.5:c.956T>C	17.37:g.60814273A>G	ENSP00000311496:p.Phe319Ser	Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	139	139	1	NM_001100875	D3DU09|Q8IYS7|Q8N7Z7	Missense_Mutation	SNP	ENST00000311269.5	37	CCDS11635.1	651	0.2980769230769231	64	0.13008130081300814	149	0.4116022099447514	116	0.20279720279720279	322	0.42480211081794195	A	8.846	0.943485	0.18281	0.18611	0.393721	ENSG00000173838	ENST00000456609;ENST00000311269;ENST00000544856	T;T;T	0.59083	0.29;0.29;0.29	5.17	2.75	0.32379	.	0.378995	0.22924	N	0.053999	T	0.00012	0.0000	M	0.72118	2.19	0.80722	P	0.0	D;D;D	0.63880	0.988;0.993;0.988	P;P;P	0.55391	0.601;0.775;0.601	T	0.33369	-0.9871	9	0.66056	D	0.02	-8.2489	8.95	0.35783	0.6338:0.3662:0.0:0.0	rs9891498;rs52833447;rs9891498	318;318;319	B3KVK0;G3V1Q5;Q8NA82	.;.;MARHA_HUMAN	S	319;319;318	ENSP00000416177:F319S;ENSP00000311496:F319S;ENSP00000443746:F318S	ENSP00000311496:F319S	F	-	2	0	MARCH10	58168005	0.002000	0.14202	0.011000	0.14972	0.021000	0.10359	1.449000	0.35123	0.775000	0.33450	0.459000	0.35465	TTT	A|0.682;G|0.318	0.318	strong		0.458	MARCH10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000445252.1	NM_152598	
GH1	2688	hgsc.bcm.edu	37	17	61995189	61995189	+	Silent	SNP	G	G	A	rs370785603		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:61995189G>A	ENST00000323322.5	-	4	429	c.387C>T	c.(385-387)taC>taT	p.Y129Y	GH1_ENST00000458650.2_Silent_p.Y114Y|GH1_ENST00000351388.4_Silent_p.Y89Y|CSHL1_ENST00000392824.4_Intron|GH1_ENST00000342364.4_Intron	NM_000515.3	NP_000506.2	P01241	SOMA_HUMAN	growth hormone 1	129					bone maturation (GO:0070977)|glucose transport (GO:0015758)|growth hormone receptor signaling pathway (GO:0060396)|JAK-STAT cascade (GO:0007259)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|positive regulation of activation of JAK2 kinase activity (GO:0010535)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|response to estradiol (GO:0032355)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	growth factor activity (GO:0008083)|growth hormone receptor binding (GO:0005131)|metal ion binding (GO:0046872)|prolactin receptor binding (GO:0005148)			breast(3)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(10)	19						CAGAGGCGCCGTACACCAGGC	0.607																																					p.Y129Y		Atlas-SNP	.											GH1,caecum,carcinoma,0,1	GH1	39	1	0			c.C387T						scavenged	.	A	,,,,	1,4405	826.1+/-416.6	0,1,2202	67.0	66.0	66.0		387,342,267,,	-4.1	0.6	17		66	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous,intron,intron	GH1	NM_000515.3,NM_022559.2,NM_022560.2,NM_022561.2,NM_022562.2	,,,,	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	,,,,	129/218,114/203,89/178,,	61995189	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	2688	exon4			GGCGCCGTACACC	M13438	CCDS11653.1, CCDS11654.1, CCDS45760.1	17q22-q24	2014-01-30				ENSG00000259384		"""Endogenous ligands"""	4261	protein-coding gene	gene with protein product	"""pituitary growth hormone"", ""somatotropin"""	139250				6306568	Standard	XM_005257218		Approved	GH-N, GHN, GH, hGH-N	uc002jdj.3	P01241		ENST00000323322.5:c.387C>T	17.37:g.61995189G>A		Somatic	131	1	0.00763359		WXS	Illumina HiSeq	Phase_I	101	30	0.29703	NM_000515	A6NEF6|Q14405|Q16631|Q5EB53|Q9HBZ1|Q9UMJ7|Q9UNL5	Silent	SNP	ENST00000323322.5	37	CCDS11653.1																																																																																			.	.	weak		0.607	GH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417708.1	NM_000515	
HTR3D	200909	hgsc.bcm.edu	37	3	183755822	183755822	+	Missense_Mutation	SNP	G	G	A	rs1000952	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:183755822G>A	ENST00000382489.3	+	6	674	c.674G>A	c.(673-675)cGc>cAc	p.R225H	HTR3D_ENST00000334128.2_Missense_Mutation_p.R52H|HTR3D_ENST00000453435.1_Missense_Mutation_p.R6H|HTR3D_ENST00000428798.2_Missense_Mutation_p.R177H	NM_001163646.1	NP_001157118.1	Q70Z44	5HT3D_HUMAN	5-hydroxytryptamine (serotonin) receptor 3D, ionotropic	225			R -> H (in dbSNP:rs1000952). {ECO:0000269|PubMed:15489334}.		ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	extracellular ligand-gated ion channel activity (GO:0005230)			large_intestine(3)|lung(3)|prostate(1)|skin(1)|stomach(2)	10	all_cancers(143;2.33e-10)|Ovarian(172;0.0303)		Epithelial(37;6.23e-36)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)		Ergoloid mesylate(DB01049)	GCCATCAGGCGCAGGTGCAGG	0.572													G|||	3826	0.763978	0.8623	0.7061	5008	,	,		18146	0.9167		0.6531	False		,,,				2504	0.6288				p.R225H		Atlas-SNP	.											.	HTR3D	65	.	0			c.G674A						PASS	.	G	HIS/ARG,HIS/ARG,HIS/ARG	3626,780	752.0+/-412.2	1489,648,66	49.0	42.0	44.0		530,674,155	0.2	1.0	3	dbSNP_86	44	5462,3138	655.2+/-401.2	1734,1994,572	yes	missense,missense,missense	HTR3D	NM_001145143.1,NM_001163646.1,NM_182537.2	29,29,29	3223,2642,638	AA,AG,GG		36.4884,17.7031,30.1246	possibly-damaging,possibly-damaging,possibly-damaging	177/405,225/455,52/280	183755822	9088,3918	2203	4300	6503	SO:0001583	missense	200909	exon6			TCAGGCGCAGGTG	AY159812	CCDS3249.1, CCDS46966.1, CCDS54685.1	3q27	2012-05-22	2012-02-03		ENSG00000186090	ENSG00000186090		"""5-HT (serotonin) receptors"", ""Ligand-gated ion channels / 5-HT (serotonin) receptors, ionotropic"""	24004	protein-coding gene	gene with protein product		610122	"""5-hydroxytryptamine (serotonin) receptor 3 family member D"""			12801637	Standard	NM_001145143		Approved		uc011bqv.2	Q70Z44	OTTHUMG00000156858	ENST00000382489.3:c.674G>A	3.37:g.183755822G>A	ENSP00000371929:p.Arg225His	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	80	41	0.5125	NM_001163646	C9J2I6|J3QT78|Q495N5|Q495N6|Q7Z6B3	Missense_Mutation	SNP	ENST00000382489.3	37	CCDS54685.1	1660	0.76007326007326	407	0.8272357723577236	243	0.6712707182320442	527	0.9213286713286714	483	0.637203166226913	G	3.556	-0.090615	0.07053	0.822969	0.635116	ENSG00000186090	ENST00000334128;ENST00000428798;ENST00000382489;ENST00000453435	T;D;D;T	0.93133	-1.05;-2.0;-3.17;-0.94	0.149	0.149	0.14863	Neurotransmitter-gated ion-channel ligand-binding (1);	0.145914	0.46145	N	0.000310	T	0.00012	0.0000	L	0.55213	1.73	0.51767	P	6.799999999995698E-5	D;B;B;B	0.71674	0.998;0.228;0.114;0.45	P;B;B;B	0.54460	0.753;0.171;0.071;0.249	T	0.42699	-0.9436	8	0.66056	D	0.02	-7.3849	.	.	.	rs1000952;rs17671237;rs1000952	225;52;6;52	Q70Z44;Q70Z44-2;Q70Z44-3;F6WC43	5HT3D_HUMAN;.;.;.	H	52;177;225;6	ENSP00000334315:R52H;ENSP00000405409:R177H;ENSP00000371929:R225H;ENSP00000389268:R6H	ENSP00000334315:R52H	R	+	2	0	HTR3D	185238516	0.602000	0.26916	0.962000	0.40283	0.012000	0.07955	0.251000	0.18257	0.192000	0.20272	0.195000	0.17529	CGC	G|0.272;A|0.728	0.728	strong		0.572	HTR3D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000346289.1	NM_182537	
HSPG2	3339	hgsc.bcm.edu	37	1	22154845	22154845	+	Silent	SNP	A	A	G	rs2228347	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:22154845A>G	ENST00000374695.3	-	89	12391	c.12312T>C	c.(12310-12312)gaT>gaC	p.D4104D	HSPG2_ENST00000486901.1_5'UTR	NM_005529.5	NP_005520.4	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2	4104	EGF-like 3. {ECO:0000255|PROSITE- ProRule:PRU00076}.				angiogenesis (GO:0001525)|brain development (GO:0007420)|carbohydrate metabolic process (GO:0005975)|cardiac muscle tissue development (GO:0048738)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|chondrocyte differentiation (GO:0002062)|chondroitin sulfate metabolic process (GO:0030204)|embryonic skeletal system morphogenesis (GO:0048704)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|lipoprotein metabolic process (GO:0042157)|phototransduction, visible light (GO:0007603)|protein localization (GO:0008104)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	basal lamina (GO:0005605)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)			breast(6)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(15)|liver(1)|lung(44)|ovary(10)|pancreas(1)|prostate(10)|skin(9)|upper_aerodigestive_tract(3)|urinary_tract(3)	127		Colorectal(325;3.46e-05)|all_lung(284;7.93e-05)|Lung NSC(340;8.71e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0498)|OV - Ovarian serous cystadenocarcinoma(117;1.14e-26)|Colorectal(126;4.18e-07)|COAD - Colon adenocarcinoma(152;1.82e-05)|GBM - Glioblastoma multiforme(114;3.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000756)|STAD - Stomach adenocarcinoma(196;0.00656)|KIRC - Kidney renal clear cell carcinoma(1967;0.00942)|READ - Rectum adenocarcinoma(331;0.0721)|Lung(427;0.223)	Palifermin(DB00039)	ATGGGGAGCTATCATAGCATT	0.587													G|||	1288	0.257188	0.1172	0.2161	5008	,	,		18078	0.1577		0.3241	False		,,,				2504	0.5092				p.D4104D		Atlas-SNP	.											.	HSPG2	311	.	0			c.T12312C						PASS	.	G		648,3758	764.0+/-413.3	57,534,1612	99.0	85.0	90.0		12312	3.5	1.0	1	dbSNP_98	90	2634,5966	686.8+/-404.2	403,1828,2069	no	coding-synonymous	HSPG2	NM_005529.5		460,2362,3681	GG,GA,AA		30.6279,14.7072,25.2345		4104/4392	22154845	3282,9724	2203	4300	6503	SO:0001819	synonymous_variant	3339	exon89			GGAGCTATCATAG	M85289	CCDS30625.1	1p36.1-p35	2013-01-29	2007-02-16	2007-02-16	ENSG00000142798	ENSG00000142798		"""Proteoglycans / Extracellular Matrix : Other"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5273	protein-coding gene	gene with protein product	"""perlecan proteoglycan"""	142461	"""Schwartz-Jampel syndrome 1 (chondrodystrophic myotonia)"""	SJS1		1685141, 11941538	Standard	XM_005245863		Approved	perlecan, PRCAN	uc001bfj.3	P98160	OTTHUMG00000002674	ENST00000374695.3:c.12312T>C	1.37:g.22154845A>G		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	57	26	0.45614	NM_005529	Q16287|Q5SZI3|Q9H3V5	Silent	SNP	ENST00000374695.3	37	CCDS30625.1																																																																																			T|0.000;G|0.250;A|0.750	0.250	strong		0.587	HSPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007598.1	NM_005529	
HTR3A	3359	hgsc.bcm.edu	37	11	113857365	113857365	+	Silent	SNP	G	G	A	rs56232120	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:113857365G>A	ENST00000504030.2	+	7	1276	c.831G>A	c.(829-831)aaG>aaA	p.K277K	HTR3A_ENST00000506841.2_Silent_p.K277K|HTR3A_ENST00000535865.1_Silent_p.K21K|HTR3A_ENST00000299961.5_Silent_p.K262K|HTR3A_ENST00000375498.2_Silent_p.K283K|HTR3A_ENST00000355556.2_Silent_p.K283K			P46098	5HT3A_HUMAN	5-hydroxytryptamine (serotonin) receptor 3A, ionotropic	277					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|cellular response to growth factor stimulus (GO:0071363)|digestion (GO:0007586)|ion transmembrane transport (GO:0034220)|response to cocaine (GO:0042220)|response to ethanol (GO:0045471)|serotonin receptor signaling pathway (GO:0007210)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	receptor activity (GO:0004872)|serotonin binding (GO:0051378)|serotonin receptor activity (GO:0004993)|serotonin-activated cation-selective channel activity (GO:0005232)|voltage-gated potassium channel activity (GO:0005249)			central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(14)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	36		all_cancers(61;2.31e-17)|all_epithelial(67;2.1e-10)|all_hematologic(158;4.64e-05)|Melanoma(852;0.000312)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|all_neural(223;0.0281)|Prostate(24;0.0294)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;2.71e-06)|Epithelial(105;2.58e-05)|all cancers(92;0.000238)|OV - Ovarian serous cystadenocarcinoma(223;0.191)	Alosetron(DB00969)|Amoxapine(DB00543)|Aripiprazole(DB01238)|Chloroprocaine(DB01161)|Cisapride(DB00604)|Clozapine(DB00363)|Dolasetron(DB00757)|Ergoloid mesylate(DB01049)|Granisetron(DB00889)|Loxapine(DB00408)|Memantine(DB01043)|Methadone(DB00333)|Metoclopramide(DB01233)|Mirtazapine(DB00370)|Olanzapine(DB00334)|Ondansetron(DB00904)|Palonosetron(DB00377)|Procaine(DB00721)|Quetiapine(DB01224)|Rocuronium(DB00728)|Tapentadol(DB06204)|Trimipramine(DB00726)|Tubocurarine(DB01199)|Ziprasidone(DB00246)	TCTCTTTCAAGATTACACTCC	0.572													G|||	55	0.0109824	0.0	0.0202	5008	,	,		17531	0.0		0.0288	False		,,,				2504	0.0123				p.K283K		Atlas-SNP	.											.	HTR3A	93	.	0			c.G849A						PASS	.	G	,,	16,4386	23.3+/-48.9	0,16,2185	96.0	77.0	84.0		849,786,849	3.0	1.0	11	dbSNP_129	84	174,8418	78.9+/-141.6	1,172,4123	no	coding-synonymous,coding-synonymous,coding-synonymous	HTR3A	NM_000869.5,NM_001161772.2,NM_213621.3	,,	1,188,6308	AA,AG,GG		2.0251,0.3635,1.4622	,,	283/485,262/464,283/517	113857365	190,12804	2201	4296	6497	SO:0001819	synonymous_variant	3359	exon7			TTTCAAGATTACA	D49394	CCDS8365.1, CCDS8366.1, CCDS8365.2, CCDS8366.2, CCDS53710.1	11q23.1-q23.2	2012-05-22	2012-02-03					"""5-HT (serotonin) receptors"", ""Ligand-gated ion channels / 5-HT (serotonin) receptors, ionotropic"""	5297	protein-coding gene	gene with protein product		182139	"""5-hydroxytryptamine (serotonin) receptor 3A"""	HTR3		8530095, 12867984	Standard	NM_000869		Approved	5-HT3R, 5-HT3A	uc010rxb.2	P46098		ENST00000504030.2:c.831G>A	11.37:g.113857365G>A		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	72	56	0.777778	NM_000869	B4DSY6|G5E986|O60854|Q7KZM7|Q99918|Q9BSZ9	Silent	SNP	ENST00000504030.2	37																																																																																				G|0.986;A|0.014	0.014	strong		0.572	HTR3A-001	KNOWN	upstream_ATG|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000360822.2	NM_000869	
SLBP	7884	hgsc.bcm.edu	37	4	1701317	1701317	+	Silent	SNP	G	G	A	rs2247341	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:1701317G>A	ENST00000489418.1	-	5	819	c.453C>T	c.(451-453)taC>taT	p.Y151Y	SLBP_ENST00000318386.4_Silent_p.Y158Y|SLBP_ENST00000429429.2_Silent_p.Y112Y|SLBP_ENST00000488267.1_Silent_p.Y116Y	NM_006527.2	NP_006518.1	Q14493	SLBP_HUMAN	stem-loop binding protein	151	RNA-binding.				gene expression (GO:0010467)|histone mRNA 3'-end processing (GO:0006398)|histone mRNA metabolic process (GO:0008334)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA transport (GO:0051028)|nuclear cell cycle DNA replication (GO:0033260)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|histone pre-mRNA 3'end processing complex (GO:0071204)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	histone pre-mRNA DCP binding (GO:0071208)|histone pre-mRNA stem-loop binding (GO:0071207)|mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)			endometrium(1)|large_intestine(2)|lung(2)	5		Breast(71;0.212)|all_epithelial(65;0.241)	OV - Ovarian serous cystadenocarcinoma(23;0.0055)			TATAACGATCGTAGGCAATTG	0.433													G|||	1951	0.389577	0.1263	0.366	5008	,	,		19279	0.6935		0.332	False		,,,				2504	0.5082				p.Y151Y		Atlas-SNP	.											.	SLBP	12	.	0			c.C453T						PASS	.	G		795,3611	321.3+/-297.0	89,617,1497	170.0	157.0	161.0		453	-6.9	1.0	4	dbSNP_100	161	2953,5647	459.5+/-364.9	512,1929,1859	yes	coding-synonymous	SLBP	NM_006527.2		601,2546,3356	AA,AG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	34.3372,18.0436,28.8175		151/271	1701317	3748,9258	2203	4300	6503	SO:0001819	synonymous_variant	7884	exon5			ACGATCGTAGGCA	Z71188	CCDS3350.1	4p16.3	2008-02-11	2008-02-11		ENSG00000163950	ENSG00000163950			10904	protein-coding gene	gene with protein product	"""histone binding protein"""	602422	"""stem-loop (histone) binding protein"""			9049306, 1338771	Standard	NM_006527		Approved	HBP	uc003gdi.1	Q14493	OTTHUMG00000089349	ENST00000489418.1:c.453C>T	4.37:g.1701317G>A		Somatic	273	0	0		WXS	Illumina HiSeq	Phase_I	217	91	0.419355	NM_006527	B3KRJ5	Silent	SNP	ENST00000489418.1	37	CCDS3350.1	850|850	0.3891941391941392|0.3891941391941392	63|63	0.12804878048780488|0.12804878048780488	132|132	0.36464088397790057|0.36464088397790057	392|392	0.6853146853146853|0.6853146853146853	263|263	0.3469656992084433|0.3469656992084433	G|G	10.10|10.10	1.257050|1.257050	0.22965|0.22965	0.180436|0.180436	0.343372|0.343372	ENSG00000163950|ENSG00000163950	ENST00000480936|ENST00000483348	.|.	.|.	.|.	5.19|5.19	-6.91|-6.91	0.01649|0.01649	.|.	.|.	.|.	.|.	.|.	.|T	.|0.00012	.|0.0000	.|.	.|.	.|.	0.09310|0.09310	P|P	1.0|1.0	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.10019	.|-1.0648	.|3	.|.	.|.	.|.	-11.6628|-11.6628	15.2628|15.2628	0.73637|0.73637	0.9153:0.0:0.0847:0.0|0.9153:0.0:0.0847:0.0	rs2247341;rs56570242;rs60784822;rs2247341|rs2247341;rs56570242;rs60784822;rs2247341	.|.	.|.	.|.	X|M	159|106	.|.	.|.	R|T	-|-	1|2	2|0	SLBP|SLBP	1671115|1671115	0.401000|0.401000	0.25303|0.25303	0.964000|0.964000	0.40570|0.40570	0.992000|0.992000	0.81027|0.81027	-0.109000|-0.109000	0.10840|0.10840	-0.982000|-0.982000	0.03515|0.03515	-0.322000|-0.322000	0.08575|0.08575	CGA|ACG	G|0.647;T|0.001	.	strong		0.433	SLBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000203176.1	NM_006527	
GPR37	2861	hgsc.bcm.edu	37	7	124387092	124387092	+	Silent	SNP	C	C	G	rs3735270	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:124387092C>G	ENST00000303921.2	-	2	1979	c.1329G>C	c.(1327-1329)ctG>ctC	p.L443L		NM_005302.3	NP_005293.1	O15354	GPR37_HUMAN	G protein-coupled receptor 37 (endothelin receptor type B-like)	443					dopamine biosynthetic process (GO:0042416)|G-protein coupled receptor signaling pathway (GO:0007186)|locomotion involved in locomotory behavior (GO:0031987)|positive regulation of dopamine metabolic process (GO:0045964)	endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|ubiquitin ligase complex (GO:0000151)	G-protein coupled receptor activity (GO:0004930)|heat shock protein binding (GO:0031072)|Hsp70 protein binding (GO:0030544)|ubiquitin protein ligase binding (GO:0031625)	p.L443L(1)		breast(2)|central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(8)|lung(11)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	36						AATACCACCACAGTCTCGCAC	0.483													G|||	1987	0.396765	0.18	0.4409	5008	,	,		20395	0.5367		0.4632	False		,,,				2504	0.4458				p.L443L		Atlas-SNP	.											GPR37,NS,carcinoma,0,1	GPR37	89	1	1	Substitution - coding silent(1)	prostate(1)	c.G1329C						scavenged	.	G		1053,3353	725.2+/-409.6	129,795,1279	160.0	135.0	143.0		1329	2.9	1.0	7	dbSNP_107	143	4165,4435	585.9+/-392.0	974,2217,1109	no	coding-synonymous	GPR37	NM_005302.2		1103,3012,2388	GG,GC,CC		48.4302,23.8992,40.1199		443/614	124387092	5218,7788	2203	4300	6503	SO:0001819	synonymous_variant	2861	exon2			CCACCACAGTCTC		CCDS5792.1	7q31	2012-08-21			ENSG00000170775	ENSG00000170775		"""GPCR / Class A : Orphans"""	4494	protein-coding gene	gene with protein product		602583				9339362	Standard	NM_005302		Approved	EDNRBL, hET(B)R-LP, PAELR	uc003vli.4	O15354	OTTHUMG00000157197	ENST00000303921.2:c.1329G>C	7.37:g.124387092C>G		Somatic	63	1	0.015873		WXS	Illumina HiSeq	Phase_I	71	71	1	NM_005302	A4D0Y6|O00348|O14768|Q8TD39	Silent	SNP	ENST00000303921.2	37	CCDS5792.1																																																																																			C|0.590;G|0.410	0.410	strong		0.483	GPR37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347873.1	NM_005302	
PARL	55486	hgsc.bcm.edu	37	3	183558402	183558402	+	Missense_Mutation	SNP	C	C	G	rs3732581	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:183558402C>G	ENST00000317096.4	-	7	844	c.784G>C	c.(784-786)Gtg>Ctg	p.V262L	PARL_ENST00000435888.1_Missense_Mutation_p.V212L|PARL_ENST00000311101.5_Missense_Mutation_p.V212L	NM_018622.5	NP_061092.3	Q9H300	PARL_HUMAN	presenilin associated, rhomboid-like	262			V -> L (in dbSNP:rs3732581). {ECO:0000269|PubMed:12214059, ECO:0000269|Ref.3}.		membrane protein proteolysis (GO:0033619)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|negative regulation of release of cytochrome c from mitochondria (GO:0090201)|proteolysis (GO:0006508)|regulation of protein targeting to mitochondrion (GO:1903214)|regulation of reactive oxygen species metabolic process (GO:2000377)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	endopeptidase activity (GO:0004175)|serine-type endopeptidase activity (GO:0004252)	p.V262L(1)		endometrium(2)|large_intestine(3)|liver(1)|lung(6)|prostate(1)|skin(1)|stomach(2)|urinary_tract(1)	17	all_cancers(143;6.55e-10)|Ovarian(172;0.0303)		all cancers(12;2.21e-41)|Epithelial(37;1.34e-36)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)			ACTTTACCCACGTAACTGACA	0.259													C|||	2281	0.455471	0.4947	0.4971	5008	,	,		14534	0.4087		0.4781	False		,,,				2504	0.3978				p.V262L		Atlas-SNP	.											PARL,NS,carcinoma,0,1	PARL	32	1	1	Substitution - Missense(1)	stomach(1)	c.G784C						PASS	.	C	LEU/VAL,LEU/VAL	2166,2240	572.9+/-383.4	534,1098,571	49.0	48.0	49.0		634,784	2.3	0.9	3	dbSNP_107	49	4161,4437	561.4+/-387.8	1009,2143,1147	yes	missense,missense	PARL	NM_001037639.1,NM_018622.5	32,32	1543,3241,1718	GG,GC,CC		48.395,49.1602,48.6543	possibly-damaging,possibly-damaging	212/330,262/380	183558402	6327,6677	2203	4299	6502	SO:0001583	missense	55486	exon7			TACCCACGTAACT	AF116692	CCDS3248.1, CCDS33897.1	3q27.3	2008-02-05		2006-02-28	ENSG00000175193	ENSG00000175193			18253	protein-coding gene	gene with protein product	"""rhomboid 7 homolog 1 (Drosophila)"""	607858		PSARL			Standard	XM_005247587		Approved	PRO2207, PSARL1, RHBDS1	uc003fmd.3	Q9H300	OTTHUMG00000156890	ENST00000317096.4:c.784G>C	3.37:g.183558402C>G	ENSP00000325421:p.Val262Leu	Somatic	327	0	0		WXS	Illumina HiSeq	Phase_I	224	106	0.473214	NM_018622	Q96CQ4|Q9BTJ6|Q9P1E3	Missense_Mutation	SNP	ENST00000317096.4	37	CCDS3248.1	1039|1039	0.4757326007326007|0.4757326007326007	232|232	0.4715447154471545|0.4715447154471545	192|192	0.5303867403314917|0.5303867403314917	258|258	0.45104895104895104|0.45104895104895104	357|357	0.470976253298153|0.470976253298153	C|C	11.77|11.77	1.738030|1.738030	0.30774|0.30774	0.491602|0.491602	0.48395|0.48395	ENSG00000175193|ENSG00000175193	ENST00000417784;ENST00000449306|ENST00000317096;ENST00000311101;ENST00000450375;ENST00000435888	.|T;T;T;T	.|0.11063	.|2.81;3.12;2.81;3.12	5.08|5.08	2.32|2.32	0.28847|0.28847	.|Peptidase S54, rhomboid domain (1);	.|0.372080	.|0.27544	.|N	.|0.018894	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.12611|0.12611	0.24|0.24	0.21064|0.21064	P|P	0.999791612|0.999791612	.|B;B	.|0.27732	.|0.187;0.002	.|B;B	.|0.31614	.|0.133;0.011	T|T	0.31194|0.31194	-0.9952|-0.9952	4|9	.|0.11485	.|T	.|0.65	-16.5729|-16.5729	10.5808|10.5808	0.45255|0.45255	0.0:0.7885:0.0:0.2115|0.0:0.7885:0.0:0.2115	rs3732581;rs17670811;rs52807469;rs3732581|rs3732581;rs17670811;rs52807469;rs3732581	.|212;262	.|Q9H300-2;Q9H300	.|.;PARL_HUMAN	P|L	53;125|262;212;42;212	.|ENSP00000325421:V262L;ENSP00000310676:V212L;ENSP00000402689:V42L;ENSP00000402137:V212L	.|ENSP00000310676:V212L	R|V	-|-	2|1	0|0	PARL|PARL	185041096|185041096	0.775000|0.775000	0.28604|0.28604	0.908000|0.908000	0.35775|0.35775	0.925000|0.925000	0.55904|0.55904	1.740000|1.740000	0.38228|0.38228	0.272000|0.272000	0.22027|0.22027	-0.253000|-0.253000	0.11424|0.11424	CGT|GTG	C|0.516;G|0.484	0.484	strong		0.259	PARL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346465.1	NM_018622	
TLN2	83660	hgsc.bcm.edu	37	15	62994208	62994208	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:62994208G>A	ENST00000561311.1	+	17	1944	c.1714G>A	c.(1714-1716)Gac>Aac	p.D572N	TLN2_ENST00000306829.6_Missense_Mutation_p.D572N			Q9Y4G6	TLN2_HUMAN	talin 2	572					cell adhesion (GO:0007155)|cell-cell junction assembly (GO:0007043)|cytoskeletal anchoring at plasma membrane (GO:0007016)	actin cytoskeleton (GO:0015629)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|synapse (GO:0045202)	actin binding (GO:0003779)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			NS(3)|breast(6)|central_nervous_system(3)|endometrium(8)|kidney(8)|large_intestine(20)|lung(34)|ovary(6)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)	99						TGCAGACACTGACTACACAGC	0.517																																					p.D572N		Atlas-SNP	.											.	TLN2	253	.	0			c.G1714A						PASS	.						97.0	77.0	83.0					15																	62994208		2203	4300	6503	SO:0001583	missense	83660	exon15			GACACTGACTACA	AB002318	CCDS32261.1	15q15-q21	2008-07-03			ENSG00000171914	ENSG00000171914			15447	protein-coding gene	gene with protein product		607349				9205841, 11527381	Standard	NM_015059		Approved	KIAA0320, ILWEQ	uc002alb.4	Q9Y4G6	OTTHUMG00000133679	ENST00000561311.1:c.1714G>A	15.37:g.62994208G>A	ENSP00000453508:p.Asp572Asn	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	129	65	0.503876	NM_015059	A6NLB8	Missense_Mutation	SNP	ENST00000561311.1	37	CCDS32261.1	.	.	.	.	.	.	.	.	.	.	G	19.41	3.822336	0.71028	.	.	ENSG00000171914	ENST00000306829	T	0.70282	-0.47	5.1	5.1	0.69264	Talin, central (3);	0.000000	0.85682	D	0.000000	T	0.70141	0.3190	L	0.61387	1.9	0.80722	D	1	B	0.21905	0.062	B	0.23419	0.046	T	0.66006	-0.6030	10	0.30854	T	0.27	-28.968	18.8833	0.92365	0.0:0.0:1.0:0.0	.	572	Q9Y4G6	TLN2_HUMAN	N	572	ENSP00000303476:D572N	ENSP00000303476:D572N	D	+	1	0	TLN2	60781500	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	9.813000	0.99286	2.532000	0.85374	0.561000	0.74099	GAC	.	.	none		0.517	TLN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257878.2		
TMF1	7110	hgsc.bcm.edu	37	3	69073223	69073223	+	Missense_Mutation	SNP	G	G	A	rs185749329	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:69073223G>A	ENST00000398559.2	-	16	3337	c.3121C>T	c.(3121-3123)Ctt>Ttt	p.L1041F	CTD-2013N24.2_ENST00000597950.1_RNA|CTD-2013N24.2_ENST00000597366.1_RNA|CTD-2013N24.2_ENST00000599467.1_RNA|TMF1_ENST00000543976.1_Missense_Mutation_p.L1044F|CTD-2013N24.2_ENST00000598783.1_RNA|CTD-2013N24.2_ENST00000596523.1_RNA|TMF1_ENST00000489370.1_5'Flank|CTD-2013N24.2_ENST00000596732.1_RNA|CTD-2013N24.2_ENST00000482368.2_RNA|CTD-2013N24.2_ENST00000595925.1_RNA|CTD-2013N24.2_ENST00000601511.1_RNA|CTD-2013N24.2_ENST00000601735.1_RNA			P82094	TMF1_HUMAN	TATA element modulatory factor 1	1041					acrosome assembly (GO:0001675)|cellular response to organic cyclic compound (GO:0071407)|defense response to bacterium (GO:0042742)|Leydig cell differentiation (GO:0033327)|luteinizing hormone secretion (GO:0032275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of gene expression (GO:0010629)|positive regulation of cytokine production (GO:0001819)|positive regulation of testosterone secretion (GO:2000845)|regulation of proteasomal protein catabolic process (GO:0061136)|regulation of transcription, DNA-templated (GO:0006355)|sperm motility (GO:0030317)|spermatid nucleus differentiation (GO:0007289)|transcription from RNA polymerase II promoter (GO:0006366)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|transcription cofactor activity (GO:0003712)			cervix(1)|kidney(1)|large_intestine(4)|lung(13)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	22		Lung NSC(201;0.0193)|Prostate(884;0.174)		BRCA - Breast invasive adenocarcinoma(55;4.48e-05)|Epithelial(33;0.000274)|LUSC - Lung squamous cell carcinoma(21;0.0123)|KIRC - Kidney renal clear cell carcinoma(39;0.211)|Kidney(39;0.247)		TGAGTTCTAAGTTTGGGTATC	0.303													G|||	4	0.000798722	0.0	0.0043	5008	,	,		15654	0.0		0.001	False		,,,				2504	0.0				p.L1041F		Atlas-SNP	.											.	TMF1	77	.	0			c.C3121T						PASS	.	G	PHE/LEU	2,3652		0,2,1825	158.0	144.0	149.0		3121	5.6	1.0	3		149	12,8158		0,12,4073	yes	missense	TMF1	NM_007114.2	22	0,14,5898	AA,AG,GG		0.1469,0.0547,0.1184	probably-damaging	1041/1094	69073223	14,11810	1827	4085	5912	SO:0001583	missense	7110	exon16			TTCTAAGTTTGGG		CCDS43105.1	3p21-p12	2009-02-11			ENSG00000144747	ENSG00000144747			11870	protein-coding gene	gene with protein product		601126				1409643	Standard	NM_007114		Approved	ARA160, TMF	uc003dnn.3	P82094	OTTHUMG00000158771	ENST00000398559.2:c.3121C>T	3.37:g.69073223G>A	ENSP00000381567:p.Leu1041Phe	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	138	70	0.507246	NM_007114	B7ZLJ2|Q17R87|Q59GK0	Missense_Mutation	SNP	ENST00000398559.2	37	CCDS43105.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	G	18.43	3.621363	0.66787	5.47E-4	0.001469	ENSG00000144747	ENST00000398559;ENST00000543976;ENST00000356248	D;D	0.83591	-1.74;-1.74	5.59	5.59	0.84812	.	0.000000	0.64402	D	0.000001	D	0.91771	0.7397	M	0.88512	2.96	0.58432	D	0.999993	D;D	0.89917	1.0;0.981	D;D	0.91635	0.999;0.91	D	0.92645	0.6128	10	0.72032	D	0.01	-10.3062	12.4791	0.55831	0.1197:0.0:0.8803:0.0	.	1044;1041	P82094-2;P82094	.;TMF1_HUMAN	F	1041;1044;957	ENSP00000381567:L1041F;ENSP00000438706:L1044F	ENSP00000348582:L957F	L	-	1	0	TMF1	69155913	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.905000	0.56333	2.620000	0.88729	0.557000	0.71058	CTT	G|0.999;A|0.001	0.001	strong		0.303	TMF1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000352106.1	NM_007114	
ALX4	60529	hgsc.bcm.edu	37	11	44289071	44289071	+	Silent	SNP	G	G	A	rs12419361	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:44289071G>A	ENST00000329255.3	-	3	982	c.879C>T	c.(877-879)ctC>ctT	p.L293L		NM_021926.3	NP_068745.2	Q9H161	ALX4_HUMAN	ALX homeobox 4	293					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						CTCGGGTGAGGAGGGGCAGCT	0.617													G|||	519	0.103634	0.0477	0.0922	5008	,	,		17040	0.1359		0.1183	False		,,,				2504	0.1391				p.L293L		Atlas-SNP	.											.	ALX4	58	.	0			c.C879T						PASS	.	G		252,4154	145.4+/-180.2	11,230,1962	159.0	126.0	137.0		879	-2.1	0.9	11	dbSNP_120	137	900,7698	201.8+/-245.2	36,828,3435	no	coding-synonymous	ALX4	NM_021926.3		47,1058,5397	AA,AG,GG		10.4676,5.7195,8.8588		293/412	44289071	1152,11852	2203	4299	6502	SO:0001819	synonymous_variant	60529	exon3			GGTGAGGAGGGGC	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.879C>T	11.37:g.44289071G>A		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	66	16	0.242424	NM_021926	Q96JN7|Q9H198|Q9HAY9	Silent	SNP	ENST00000329255.3	37	CCDS31468.1																																																																																			G|0.905;A|0.095	0.095	strong		0.617	ALX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390399.1		
DSPP	1834	hgsc.bcm.edu	37	4	88535869	88535869	+	Silent	SNP	C	C	T	rs200233307		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:88535869C>T	ENST00000282478.7	+	4	2088	c.2055C>T	c.(2053-2055)aaC>aaT	p.N685N	RP11-742B18.1_ENST00000506480.1_RNA|DSPP_ENST00000399271.1_Silent_p.N685N			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	685	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)		acagcagcaacagcagtgata	0.478																																					p.N685N		Atlas-SNP	.											DSPP,NS,carcinoma,0,2	DSPP	174	2	0			c.C2055T						scavenged	.						116.0	132.0	126.0					4																	88535869		1685	3089	4774	SO:0001819	synonymous_variant	1834	exon5			CAGCAACAGCAGT	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.2055C>T	4.37:g.88535869C>T		Somatic	132	1	0.00757576		WXS	Illumina HiSeq	Phase_I	93	12	0.129032	NM_014208	A8MUI0|O95815	Silent	SNP	ENST00000282478.7	37	CCDS43248.1																																																																																			.	.	weak		0.478	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208	
MET	4233	hgsc.bcm.edu	37	7	116339282	116339282	+	Silent	SNP	G	G	A	rs11762213	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:116339282G>A	ENST00000318493.6	+	2	331	c.144G>A	c.(142-144)gcG>gcA	p.A48A	MET_ENST00000397752.3_Silent_p.A48A|MET_ENST00000436117.2_Silent_p.A48A			Q9NWH9	SLTM_HUMAN	MET proto-oncogene, receptor tyrosine kinase	0	SAP. {ECO:0000255|PROSITE- ProRule:PRU00186}.				apoptotic process (GO:0006915)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(10)|breast(4)|central_nervous_system(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(5)|kidney(25)|large_intestine(8)|liver(3)|lung(70)|ovary(10)|pleura(2)|prostate(4)|skin(5)|stomach(6)|testis(1)|thyroid(4)|upper_aerodigestive_tract(64)|urinary_tract(3)	233	all_cancers(3;1.25e-07)|all_epithelial(6;4.07e-08)|Lung NSC(10;0.00108)|all_lung(10;0.00125)	Ovarian(593;0.133)	GBM - Glioblastoma multiforme(2;2.31e-07)|all cancers(2;0.000419)|STAD - Stomach adenocarcinoma(10;0.000512)			ACTTCACCGCGGAAACACCCA	0.433			Mis		"""papillary renal, head-neck squamous cell """	papillary renal			Hereditary Papillary Renal Carcinoma (type 1)				G|||	77	0.0153754	0.0023	0.0346	5008	,	,		21839	0.0		0.0398	False		,,,				2504	0.0102				p.A48A		Atlas-SNP	.		Dom	yes	Familial Papillary Renal Cancer	7	7q31	4233	met proto-oncogene (hepatocyte growth factor receptor)		E	MET,NS,adenocarcinoma,+1,2	MET	412	2	0			c.G144A						PASS	.	G	,	42,3886		0,42,1922	100.0	99.0	99.0		144,144	-11.8	0.0	7	dbSNP_120	99	391,7915		6,379,3768	no	coding-synonymous,coding-synonymous	MET	NM_000245.2,NM_001127500.1	,	6,421,5690	AA,AG,GG		4.7074,1.0692,3.5393	,	48/1391,48/1409	116339282	433,11801	1964	4153	6117	SO:0001819	synonymous_variant	4233	exon2	Familial Cancer Database	HPRC, Hereditary Papillary Renal Cell Cancer	CACCGCGGAAACA	M35073	CCDS43636.1, CCDS47689.1	7q31	2014-09-17	2014-06-26		ENSG00000105976	ENSG00000105976	2.7.10.1		7029	protein-coding gene	gene with protein product	"""hepatocyte growth factor receptor"""	164860	"""met proto-oncogene"""			1846706, 1611909	Standard	NM_001127500		Approved	HGFR, RCCP2	uc010lkh.3	P08581	OTTHUMG00000023299	ENST00000318493.6:c.144G>A	7.37:g.116339282G>A		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	136	69	0.507353	NM_000245	A8K5V8|B2RTX3|Q2VPK7|Q52MB3|Q658J7|Q6ZNF2|Q86TK6|Q9H7C3|Q9H8U9	Silent	SNP	ENST00000318493.6	37	CCDS47689.1																																																																																			G|0.974;A|0.026	0.026	strong		0.433	MET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059620.3		
KIF15	56992	hgsc.bcm.edu	37	3	44881909	44881909	+	Silent	SNP	A	A	G	rs76526953	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:44881909A>G	ENST00000326047.4	+	28	3530	c.3381A>G	c.(3379-3381)caA>caG	p.Q1127Q	KIF15_ENST00000425755.1_Silent_p.Q762Q	NM_020242.2	NP_064627.1	Q9NS87	KIF15_HUMAN	kinesin family member 15	1127					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|cell proliferation (GO:0008283)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic nuclear division (GO:0007067)	centrosome (GO:0005813)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)|plus-end kinesin complex (GO:0005873)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(7)|liver(2)|lung(9)|ovary(1)|prostate(4)|urinary_tract(5)	36				BRCA - Breast invasive adenocarcinoma(193;0.0099)|KIRC - Kidney renal clear cell carcinoma(197;0.0564)|Kidney(197;0.0707)		AAATGAGGCAACTAGAACATG	0.338													A|||	295	0.0589058	0.0696	0.098	5008	,	,		17908	0.0437		0.0567	False		,,,				2504	0.0348				p.Q1127Q		Atlas-SNP	.											.	KIF15	103	.	0			c.A3381G						PASS	.	A		300,4106	164.0+/-195.7	5,290,1908	118.0	113.0	115.0		3381	-11.5	0.2	3	dbSNP_132	115	429,8171	132.6+/-190.3	8,413,3879	no	coding-synonymous	KIF15	NM_020242.2		13,703,5787	GG,GA,AA		4.9884,6.8089,5.6051		1127/1389	44881909	729,12277	2203	4300	6503	SO:0001819	synonymous_variant	56992	exon28			GAGGCAACTAGAA	AB035898	CCDS33744.1	3p21.31	2008-03-03	2005-03-15	2005-03-17	ENSG00000163808	ENSG00000163808		"""Kinesins"""	17273	protein-coding gene	gene with protein product			"""kinesin-like 7"""	KNSL7		10878014	Standard	NM_020242		Approved	HKLP2, NY-BR-62	uc003cnx.4	Q9NS87	OTTHUMG00000156307	ENST00000326047.4:c.3381A>G	3.37:g.44881909A>G		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	86	31	0.360465	NM_020242	Q17RV9|Q69YL6|Q96JX7|Q9H280	Silent	SNP	ENST00000326047.4	37	CCDS33744.1																																																																																			A|0.943;G|0.057	0.057	strong		0.338	KIF15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343831.2		
MORC3	23515	hgsc.bcm.edu	37	21	37741352	37741352	+	Silent	SNP	G	G	A	rs61739936	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:37741352G>A	ENST00000400485.1	+	15	1762	c.1686G>A	c.(1684-1686)caG>caA	p.Q562Q	MORC3_ENST00000487909.1_3'UTR	NM_015358.2	NP_056173.1	Q14149	MORC3_HUMAN	MORC family CW-type zinc finger 3	562					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						TGAGTAGTCAGTTTGAAAATT	0.328													G|||	312	0.0623003	0.0121	0.0749	5008	,	,		19872	0.0298		0.0905	False		,,,				2504	0.1258				p.Q562Q		Atlas-SNP	.											MORC3,NS,carcinoma,+2,1	MORC3	78	1	0			c.G1686A						PASS	.	G		69,3671		1,67,1802	77.0	69.0	71.0		1686	-4.4	0.1	21	dbSNP_129	71	823,7403		46,731,3336	no	coding-synonymous	MORC3	NM_015358.2		47,798,5138	AA,AG,GG		10.0049,1.8449,7.4545		562/940	37741352	892,11074	1870	4113	5983	SO:0001819	synonymous_variant	23515	exon15			TAGTCAGTTTGAA	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.1686G>A	21.37:g.37741352G>A		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	185	62	0.335135	NM_015358	A8KA92|Q9UEZ2	Silent	SNP	ENST00000400485.1	37	CCDS42924.1																																																																																			G|0.919;A|0.081	0.081	strong		0.328	MORC3-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000194640.1	NM_015358	
PLAUR	5329	hgsc.bcm.edu	37	19	44156472	44156472	+	Missense_Mutation	SNP	T	T	C	rs2302524	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:44156472T>C	ENST00000340093.3	-	6	888	c.659A>G	c.(658-660)aAg>aGg	p.K220R	PLAUR_ENST00000601723.1_Intron|PLAUR_ENST00000339082.3_Missense_Mutation_p.K220R|PLAUR_ENST00000221264.4_Missense_Mutation_p.K175R	NM_002659.3	NP_002650.1	Q03405	UPAR_HUMAN	plasminogen activator, urokinase receptor	220	UPAR/Ly6 3.		K -> R (in dbSNP:rs2302524). {ECO:0000269|Ref.8}.		attachment of GPI anchor to protein (GO:0016255)|blood coagulation (GO:0007596)|C-terminal protein lipidation (GO:0006501)|cellular component movement (GO:0006928)|cellular protein metabolic process (GO:0044267)|chemotaxis (GO:0006935)|fibrinolysis (GO:0042730)|post-translational protein modification (GO:0043687)|regulation of proteolysis (GO:0030162)|signal transduction (GO:0007165)|urokinase plasminogen activator signaling pathway (GO:0038195)	anchored component of membrane (GO:0031225)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|receptor activity (GO:0004872)|urokinase plasminogen activator receptor activity (GO:0030377)	p.K220R(1)		endometrium(1)|kidney(4)|large_intestine(5)|lung(5)|ovary(1)|stomach(1)|urinary_tract(3)	20		Prostate(69;0.0153)			Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)|Urokinase(DB00013)	GCTGTTCCCCTTGCAGCTGTA	0.527											OREG0025532	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	T|||	827	0.165136	0.208	0.2666	5008	,	,		18524	0.0833		0.1412	False		,,,				2504	0.1442				p.K220R		Atlas-SNP	.											PLAUR,NS,carcinoma,0,1	PLAUR	71	1	1	Substitution - Missense(1)	stomach(1)	c.A659G						PASS	.	T	ARG/LYS,ARG/LYS,ARG/LYS	870,3536	340.5+/-306.2	87,696,1420	93.0	87.0	89.0		659,524,659	4.5	1.0	19	dbSNP_100	89	1432,7168	273.1+/-290.5	109,1214,2977	yes	missense,missense,missense	PLAUR	NM_001005376.2,NM_001005377.2,NM_002659.3	26,26,26	196,1910,4397	CC,CT,TT		16.6512,19.7458,17.6995	benign,benign,benign	220/282,175/291,220/336	44156472	2302,10704	2203	4300	6503	SO:0001583	missense	5329	exon6			TTCCCCTTGCAGC		CCDS12628.1, CCDS33041.1, CCDS33042.1, CCDS74386.1	19q13	2012-03-15			ENSG00000011422	ENSG00000011422		"""CD molecules"""	9053	protein-coding gene	gene with protein product	"""urokinase-type plasminogen activator (uPA) receptor"", ""urokinase plasminogen activator surface receptor"""	173391					Standard	NM_002659		Approved	URKR, UPAR, CD87	uc002oxf.2	Q03405		ENST00000340093.3:c.659A>G	19.37:g.44156472T>C	ENSP00000339328:p.Lys220Arg	Somatic	152	0	0	921	WXS	Illumina HiSeq	Phase_I	119	44	0.369748	NM_001005376	A8K409|Q12876|Q15845|Q16887|Q6IB52|Q9BWT0|Q9NYC8|Q9UD69|Q9UEA6|Q9UM92|Q9UMV0	Missense_Mutation	SNP	ENST00000340093.3	37	CCDS12628.1	363	0.1662087912087912	122	0.24796747967479674	87	0.24033149171270718	45	0.07867132867132867	109	0.1437994722955145	T	15.77	2.930532	0.52866	0.197458	0.166512	ENSG00000011422	ENST00000339082;ENST00000340093;ENST00000221264	T;T;T	0.69806	-0.43;-0.43;-0.43	4.49	4.49	0.54785	Ly-6 antigen / uPA receptor -like (1);CD59 antigen, conserved site (1);CD59 antigen (1);	0.911534	0.09086	N	0.850673	T	0.00012	0.0000	N	0.19112	0.55	0.33460	P	0.41516299999999995	B;B;B;B	0.26744	0.103;0.067;0.067;0.158	B;B;B;B	0.25614	0.037;0.033;0.033;0.062	T	0.03364	-1.1044	9	0.54805	T	0.06	-13.6979	10.3442	0.43897	0.0:0.0:0.0:1.0	rs2302524;rs59102150;rs2302524	175;220;220;220	Q03405-3;Q03405;Q9UPI5;Q03405-2	.;UPAR_HUMAN;.;.	R	220;220;175	ENSP00000342049:K220R;ENSP00000339328:K220R;ENSP00000221264:K175R	ENSP00000221264:K175R	K	-	2	0	PLAUR	48848312	1.000000	0.71417	1.000000	0.80357	0.689000	0.40095	3.565000	0.53798	2.014000	0.59158	0.459000	0.35465	AAG	T|0.832;C|0.168	0.168	strong		0.527	PLAUR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463571.1	NM_002659	
MUC4	4585	hgsc.bcm.edu	37	3	195512567	195512567	+	Missense_Mutation	SNP	G	G	A	rs150659095|rs71254296		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195512567G>A	ENST00000463781.3	-	2	6343	c.5884C>T	c.(5884-5886)Ccc>Tcc	p.P1962S	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.P1962S	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.P1952_T1967delPLPVTDASSVPTGHAT(4)|p.P1962S(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)		TGACCTGTGGGTACTGAGGAA	0.602																																					p.P1962S		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	5	Deletion - In frame(4)|Substitution - Missense(1)	stomach(4)|endometrium(1)	c.C5884T						scavenged	.						55.0	43.0	46.0					3																	195512567		692	1591	2283	SO:0001583	missense	4585	exon2			CTGTGGGTACTGA	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.5884C>T	3.37:g.195512567G>A	ENSP00000417498:p.Pro1962Ser	Somatic	54	1	0.0185185		WXS	Illumina HiSeq	Phase_I	118	33	0.279661	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	A	8.651	0.898205	0.17686	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.27256	1.72;1.68	1.12	-1.6	0.08426	.	.	.	.	.	T	0.06005	0.0156	N	0.02539	-0.55	0.09310	N	1	P	0.47604	0.898	B	0.28638	0.092	T	0.36841	-0.9731	8	.	.	.	.	6.4409	0.21849	0.2158:0.0:0.7842:0.0	.	1962	E7ESK3	.	S	1962	ENSP00000417498:P1962S;ENSP00000420243:P1962S	.	P	-	1	0	MUC4	196996962	0.000000	0.05858	0.002000	0.10522	0.013000	0.08279	-1.724000	0.01865	-1.752000	0.01325	-2.092000	0.00371	CCC	.	.	weak		0.602	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
BTN1A1	696	hgsc.bcm.edu	37	6	26509382	26509382	+	Missense_Mutation	SNP	C	C	T	rs35555795	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:26509382C>T	ENST00000244513.6	+	7	1627	c.1561C>T	c.(1561-1563)Ccc>Tcc	p.P521S		NM_001732.2	NP_001723.2	Q13410	BT1A1_HUMAN	butyrophilin, subfamily 1, member A1	521			P -> S (in dbSNP:rs35555795).			extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)	receptor activity (GO:0004872)			endometrium(1)|kidney(1)|large_intestine(5)|lung(15)|ovary(1)|skin(1)|soft_tissue(1)|urinary_tract(1)	26						CCCTACCCAACCCAGCCAAGG	0.527													C|||	191	0.038139	0.0348	0.0346	5008	,	,		14149	0.0089		0.0815	False		,,,				2504	0.0307				p.P521S		Atlas-SNP	.											.	BTN1A1	68	.	0			c.C1561T						PASS	.	C	SER/PRO	184,4220		4,176,2022	87.0	93.0	91.0		1561	-2.1	0.0	6	dbSNP_126	91	790,7806		38,714,3546	yes	missense	BTN1A1	NM_001732.2	74	42,890,5568	TT,TC,CC		9.1903,4.178,7.4923	possibly-damaging	521/527	26509382	974,12026	2202	4298	6500	SO:0001583	missense	696	exon7			ACCCAACCCAGCC	U39576	CCDS4614.1	6p22.1	2014-01-14			ENSG00000124557	ENSG00000124557		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Butyrophilins"""	1135	protein-coding gene	gene with protein product		601610		BTN		8114113, 9382921	Standard	NM_001732		Approved	BT, BTN1	uc003nif.4	Q13410	OTTHUMG00000016358	ENST00000244513.6:c.1561C>T	6.37:g.26509382C>T	ENSP00000244513:p.Pro521Ser	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	67	29	0.432836	NM_001732	Q4VAN3|Q4VAN4|Q9H458	Missense_Mutation	SNP	ENST00000244513.6	37	CCDS4614.1	100	0.045787545787545784	18	0.036585365853658534	11	0.03038674033149171	7	0.012237762237762238	64	0.08443271767810026	C	8.290	0.817509	0.16607	0.04178	0.091903	ENSG00000124557	ENST00000244513;ENST00000377586	T	0.36699	1.24	5.41	-2.07	0.07276	.	0.653000	0.14428	N	0.320212	T	0.07503	0.0189	L	0.32530	0.975	0.80722	P	0.0	P	0.35745	0.518	B	0.32149	0.141	T	0.14282	-1.0478	9	0.72032	D	0.01	.	1.5958	0.02663	0.1187:0.3669:0.2316:0.2829	rs35555795;rs61747505	521	Q13410	BT1A1_HUMAN	S	521;489	ENSP00000244513:P521S	ENSP00000244513:P521S	P	+	1	0	BTN1A1	26617361	0.000000	0.05858	0.001000	0.08648	0.155000	0.21991	-1.703000	0.01900	-0.673000	0.05259	-0.768000	0.03414	CCC	C|0.934;T|0.066	0.066	strong		0.527	BTN1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043776.1	NM_001732	
TRIM66	9866	hgsc.bcm.edu	37	11	8646763	8646763	+	Missense_Mutation	SNP	G	G	C	rs7935453	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:8646763G>C	ENST00000299550.6	-	11	2082	c.1888C>G	c.(1888-1890)Ctg>Gtg	p.L630V	TRIM66_ENST00000402157.2_Missense_Mutation_p.L628V	NM_014818.1	NP_055633.1	O15016	TRI66_HUMAN	tripartite motif containing 66	630						aggresome (GO:0016235)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(4)|kidney(1)|lung(1)|skin(2)	9						ATGATGCTCAGCGAGGTGGAG	0.572													C|||	1552	0.309904	0.2746	0.2608	5008	,	,		21059	0.3621		0.2505	False		,,,				2504	0.3998				p.L630V		Atlas-SNP	.											.	TRIM66	45	.	0			c.C1888G						PASS	.						9.0	9.0	9.0					11																	8646763		692	1590	2282	SO:0001583	missense	9866	exon11			TGCTCAGCGAGGT	AB002296		11p15.4	2013-01-28	2011-01-25		ENSG00000166436	ENSG00000166436		"""Tripartite motif containing / Tripartite motif containing"", ""Zinc fingers, PHD-type"""	29005	protein-coding gene	gene with protein product		612000	"""chromosome 11 open reading frame 29"", ""tripartite motif-containing 66"""	C11orf29		9205841	Standard	NM_014818		Approved	KIAA0298, TIF1D	uc010rbo.2	O15016	OTTHUMG00000150481	ENST00000299550.6:c.1888C>G	11.37:g.8646763G>C	ENSP00000299550:p.Leu630Val	Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	61	56	0.918033	NM_014818	Q9BQQ4	Missense_Mutation	SNP	ENST00000299550.6	37		613	0.2806776556776557	124	0.25203252032520324	104	0.287292817679558	192	0.3356643356643357	193	0.2546174142480211	C	0.011	-1.692612	0.00731	.	.	ENSG00000166436	ENST00000299550;ENST00000402157	T;T	0.63417	-0.04;-0.02	5.72	2.82	0.32997	.	0.126710	0.36002	N	0.002849	T	0.00012	0.0000	N	0.00707	-1.245	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.33007	-0.9885	9	0.10902	T	0.67	-4.491	3.4232	0.07401	0.1293:0.4771:0.251:0.1426	rs7935453;rs52800221;rs7935453	630	O15016	TRI66_HUMAN	V	630;628	ENSP00000299550:L630V;ENSP00000384876:L628V	ENSP00000299550:L630V	L	-	1	2	TRIM66	8603339	0.198000	0.23374	0.384000	0.26145	0.519000	0.34347	0.427000	0.21379	0.356000	0.24157	-0.120000	0.15030	CTG	G|0.719;C|0.281	0.281	strong		0.572	TRIM66-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		XM_084529	
OR5B3	441608	hgsc.bcm.edu	37	11	58170025	58170025	+	Silent	SNP	C	C	G	rs12271646	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:58170025C>G	ENST00000309403.2	-	1	857	c.858G>C	c.(856-858)ctG>ctC	p.L286L		NM_001005469.1	NP_001005469.1	Q8NH48	OR5B3_HUMAN	olfactory receptor, family 5, subfamily B, member 3	286						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L286L(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(17)|ovary(1)|prostate(1)|skin(2)|stomach(6)|upper_aerodigestive_tract(1)	34	Esophageal squamous(5;0.0027)	Breast(21;0.0778)				GACTATAGACCAGAGGGTTCA	0.438													C|||	1453	0.290136	0.3533	0.2695	5008	,	,		20773	0.1448		0.3628	False		,,,				2504	0.2945				p.L286L		Atlas-SNP	.											OR5B3,NS,carcinoma,0,1	OR5B3	65	1	1	Substitution - coding silent(1)	stomach(1)	c.G858C						PASS	.	C		1442,2960	468.3+/-355.1	229,984,988	140.0	121.0	127.0		858	-0.6	0.2	11	dbSNP_120	127	3093,5497	473.2+/-368.5	550,1993,1752	no	coding-synonymous	OR5B3	NM_001005469.1		779,2977,2740	GG,GC,CC		36.007,32.7578,34.9061		286/315	58170025	4535,8457	2201	4295	6496	SO:0001819	synonymous_variant	441608	exon1			ATAGACCAGAGGG	AB065545	CCDS31549.1	11q12.1	2012-08-09			ENSG00000172769	ENSG00000172769		"""GPCR / Class A : Olfactory receptors"""	8324	protein-coding gene	gene with protein product				OR5B13			Standard	NM_001005469		Approved	OST129	uc010rkf.2	Q8NH48	OTTHUMG00000167516	ENST00000309403.2:c.858G>C	11.37:g.58170025C>G		Somatic	200	0	0		WXS	Illumina HiSeq	Phase_I	169	109	0.64497	NM_001005469	Q6IEV6	Silent	SNP	ENST00000309403.2	37	CCDS31549.1																																																																																			C|0.665;G|0.335	0.335	strong		0.438	OR5B3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394886.1	NM_001005469	
L3MBTL2	83746	hgsc.bcm.edu	37	22	41613188	41613188	+	Silent	SNP	C	C	T	rs9611519	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:41613188C>T	ENST00000216237.5	+	5	740	c.582C>T	c.(580-582)ccC>ccT	p.P194P	RP4-756G23.5_ENST00000451176.1_RNA|RP4-756G23.5_ENST00000441316.1_RNA	NM_031488.4	NP_113676.2	Q969R5	LMBL2_HUMAN	l(3)mbt-like 2 (Drosophila)	194					chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	histone binding (GO:0042393)|methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)	p.P194P(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(4)|ovary(4)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24						AGGCTGCTCCCGTCAGCTGTT	0.632													C|||	1205	0.240615	0.1112	0.4625	5008	,	,		17448	0.0526		0.3072	False		,,,				2504	0.3834				p.P194P		Atlas-SNP	.											L3MBTL2,NS,carcinoma,0,1	L3MBTL2	61	1	1	Substitution - coding silent(1)	stomach(1)	c.C582T						PASS	.	C		562,3844	250.9+/-257.8	39,484,1680	75.0	65.0	69.0		582	0.3	1.0	22	dbSNP_119	69	2398,6202	398.5+/-346.1	338,1722,2240	no	coding-synonymous	L3MBTL2	NM_031488.4		377,2206,3920	TT,TC,CC		27.8837,12.7553,22.7587		194/706	41613188	2960,10046	2203	4300	6503	SO:0001819	synonymous_variant	83746	exon5			TGCTCCCGTCAGC	AJ305226	CCDS14011.1	22q13.31-q13.33	2008-06-11			ENSG00000100395	ENSG00000100395			18594	protein-coding gene	gene with protein product		611865				11682070	Standard	NM_031488		Approved	H-l(3)mbt-l, DKFZP761I141, dJ756G23.3	uc003azo.3	Q969R5	OTTHUMG00000150942	ENST00000216237.5:c.582C>T	22.37:g.41613188C>T		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	34	14	0.411765	NM_031488	Q8TEN1|Q96SC4|Q9BQI2|Q9UGS4	Silent	SNP	ENST00000216237.5	37	CCDS14011.1	492	0.22527472527472528	53	0.10772357723577236	172	0.47513812154696133	32	0.055944055944055944	235	0.3100263852242744	C	13.71	2.319041	0.41096	0.127553	0.278837	ENSG00000100395	ENST00000449635	.	.	.	5.15	0.282	0.15692	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.47661	-0.9100	3	.	.	.	.	3.7648	0.08619	0.1031:0.1411:0.106:0.6499	rs9611519;rs9611519	.	.	.	C	142	.	.	R	+	1	0	L3MBTL2	39943134	0.007000	0.16637	1.000000	0.80357	0.977000	0.68977	-1.167000	0.03126	0.149000	0.19098	-1.044000	0.02363	CGT	C|0.775;T|0.225	0.225	strong		0.632	L3MBTL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320613.1	NM_031488	
FSIP1	161835	hgsc.bcm.edu	37	15	39910404	39910404	+	Missense_Mutation	SNP	G	G	A	rs12908846	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:39910404G>A	ENST00000350221.3	-	11	1440	c.1231C>T	c.(1231-1233)Ctt>Ttt	p.L411F		NM_152597.4	NP_689810.3	Q8NA03	FSIP1_HUMAN	fibrous sheath interacting protein 1	411			L -> F (in dbSNP:rs12908846).							NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(4)|ovary(2)|skin(4)|stomach(2)|urinary_tract(1)	23		all_cancers(109;2.66e-19)|all_epithelial(112;2.66e-16)|Lung NSC(122;1.5e-11)|all_lung(180;4.03e-10)|Melanoma(134;0.0575)|Ovarian(310;0.0827)|Colorectal(260;0.119)		GBM - Glioblastoma multiforme(113;8.22e-06)|BRCA - Breast invasive adenocarcinoma(123;0.142)		TCATCCAGAAGACACTTTAAC	0.353													G|||	788	0.157348	0.0333	0.1196	5008	,	,		19671	0.2907		0.1471	False		,,,				2504	0.2249				p.L411F		Atlas-SNP	.											.	FSIP1	53	.	0			c.C1231T						PASS	.	G	PHE/LEU	230,4164		3,224,1970	51.0	54.0	53.0		1231	5.1	1.0	15	dbSNP_121	53	1107,7475		65,977,3249	yes	missense	FSIP1	NM_152597.4	22	68,1201,5219	AA,AG,GG		12.8991,5.2344,10.3036	probably-damaging	411/582	39910404	1337,11639	2197	4291	6488	SO:0001583	missense	161835	exon11			CCAGAAGACACTT	BC045191	CCDS10050.1	15q14	2012-11-19			ENSG00000150667	ENSG00000150667			21674	protein-coding gene	gene with protein product		615795				14702039	Standard	NM_152597		Approved	FLJ35989	uc001zki.3	Q8NA03	OTTHUMG00000172456	ENST00000350221.3:c.1231C>T	15.37:g.39910404G>A	ENSP00000280236:p.Leu411Phe	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	135	68	0.503704	NM_152597	Q6X2C8|Q86Y89	Missense_Mutation	SNP	ENST00000350221.3	37	CCDS10050.1	349	0.15979853479853479	16	0.032520325203252036	48	0.13259668508287292	178	0.3111888111888112	107	0.14116094986807387	G	20.4	3.987146	0.74589	0.052344	0.128991	ENSG00000150667	ENST00000350221	T	0.35789	1.29	5.06	5.06	0.68205	.	0.104654	0.38217	N	0.001773	T	0.00012	0.0000	L	0.29908	0.895	0.27465	P	0.9530472	D	0.89917	1.0	D	0.91635	0.999	T	0.18808	-1.0325	8	.	.	.	-7.7703	17.1261	0.86714	0.0:0.0:1.0:0.0	rs12908846;rs59692160;rs12908846	411	Q8NA03	FSIP1_HUMAN	F	411	ENSP00000280236:L411F	.	L	-	1	0	FSIP1	37697696	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.542000	0.67218	2.785000	0.95823	0.655000	0.94253	CTT	G|0.862;A|0.138	0.138	strong		0.353	FSIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252118.2	NM_152597	
KANK3	256949	hgsc.bcm.edu	37	19	8389405	8389405	+	Silent	SNP	G	G	A	rs12981073	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	148	0	0		WXS	Illumina HiSeq	Phase_I	130	64	0.492308	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	
PSORS1C1	170679	hgsc.bcm.edu	37	6	31084639	31084639	+	Intron	SNP	C	C	T	rs4713436	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:31084639C>T	ENST00000259881.9	+	1	61				PSORS1C1_ENST00000467107.1_3'UTR|CDSN_ENST00000376288.2_Silent_p.R251R	NM_014068.2	NP_054787.2	Q9UIG5	PS1C1_HUMAN	psoriasis susceptibility 1 candidate 1											kidney(1)|ovary(2)|prostate(1)|skin(1)	5						CCACCACAGGCCTCTGACCCC	0.652													C|||	981	0.195887	0.0893	0.2104	5008	,	,		16280	0.2054		0.1968	False		,,,				2504	0.319				p.R251R		Atlas-SNP	.											.	CDSN	48	.	0			c.G753A						PASS	.	C	,	509,3895		22,465,1715	24.0	26.0	25.0		753,	2.8	0.8	6	dbSNP_111	25	1548,7046		144,1260,2893	no	coding-synonymous,intron	CDSN,PSORS1C1	NM_001264.4,NM_014068.2	,	166,1725,4608	TT,TC,CC		18.0126,11.5577,15.8255	,	251/530,	31084639	2057,10941	2202	4297	6499	SO:0001627	intron_variant	1041	exon2			CACAGGCCTCTGA	AB031479	CCDS34390.1	6p21.3	2014-01-28	2003-06-12		ENSG00000204540	ENSG00000204540			17202	protein-coding gene	gene with protein product		613525	"""chromosome 6 open reading frame 16"""	C6orf16			Standard	NM_014068		Approved	SEEK1	uc003nsl.2	Q9UIG5	OTTHUMG00000031077	ENST00000259881.9:c.-229+1971C>T	6.37:g.31084639C>T		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	45	18	0.4	NM_001264	B0V083|Q5ST21|Q86WJ8|Q86WJ9|Q96QC3	Silent	SNP	ENST00000259881.9	37	CCDS34390.1																																																																																			C|0.838;T|0.162	0.162	strong		0.652	PSORS1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076110.3	NM_014068	
FAT3	120114	hgsc.bcm.edu	37	11	92088177	92088177	+	Silent	SNP	C	C	T	rs7479732	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:92088177C>T	ENST00000298047.6	+	1	2916	c.2899C>T	c.(2899-2901)Ctg>Ttg	p.L967L	FAT3_ENST00000525166.1_Silent_p.L817L|FAT3_ENST00000409404.2_Silent_p.L967L|FAT3_ENST00000541502.1_Silent_p.L967L			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	967	Cadherin 9. {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)				AGATCTTGGACTGGGGGGTCA	0.458										TCGA Ovarian(4;0.039)			T|||	1758	0.351038	0.8079	0.1801	5008	,	,		19090	0.1746		0.2038	False		,,,				2504	0.1881				p.L967L		Atlas-SNP	.											FAT3_ENST00000409404,colon,carcinoma,0,2	FAT3	1822	2	0			c.C2899T						PASS	.	T		2521,1247		857,807,220	71.0	70.0	70.0		2899	2.5	1.0	11	dbSNP_116	70	1774,6460		199,1376,2542	no	coding-synonymous	FAT3	NM_001008781.2		1056,2183,2762	TT,TC,CC		21.5448,33.0945,35.7857		967/4558	92088177	4295,7707	1884	4117	6001	SO:0001819	synonymous_variant	120114	exon1			CTTGGACTGGGGG	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.2899C>T	11.37:g.92088177C>T		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	87	24	0.275862	NM_001008781	B5MDB0|Q96AU6	Silent	SNP	ENST00000298047.6	37																																																																																				C|0.697;T|0.303	0.303	strong		0.458	FAT3-201	KNOWN	basic	protein_coding	protein_coding		NM_001008781	
PRDM9	56979	hgsc.bcm.edu	37	5	23527469	23527469	+	Missense_Mutation	SNP	C	C	A	rs112501567	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:23527469C>A	ENST00000296682.3	+	11	2454	c.2272C>A	c.(2272-2274)Cgc>Agc	p.R758S		NM_020227.2	NP_064612.2	Q9NQV7	PRDM9_HUMAN	PR domain containing 9	758					meiotic gene conversion (GO:0006311)|positive regulation of meiosis I (GO:0060903)|positive regulation of reciprocal meiotic recombination (GO:0010845)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)	histone methyltransferase activity (H3-K4 specific) (GO:0042800)|metal ion binding (GO:0046872)|recombination hotspot binding (GO:0010844)|sequence-specific DNA binding (GO:0043565)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(15)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(27)|lung(87)|ovary(6)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(11)	172						GCGGGGCTTTCGCGATAAGTC	0.572										HNSCC(3;0.000094)			A|||	79	0.0157748	0.0514	0.0014	5008	,	,		9432	0.002		0.002	False		,,,				2504	0.0061				p.R758S		Atlas-SNP	.											PRDM9,NS,carcinoma,-1,2	PRDM9	344	2	0			c.C2272A						scavenged	.						61.0	85.0	77.0					5																	23527469		2096	4292	6388	SO:0001583	missense	56979	exon11			GGCTTTCGCGATA	AF275816	CCDS43307.1	5p14.2	2014-06-03			ENSG00000164256	ENSG00000164256		"""-"", ""Zinc fingers, C2H2-type"""	13994	protein-coding gene	gene with protein product	"""PR-domain containing protein 9"""	609760	"""minisatellite binding protein 3, 115kDa"", ""minisatellite binding protein 3 (115kD)"""	MSBP3		10668202, 2062643, 24634223	Standard	NM_020227		Approved	PFM6, ZNF899	uc003jgo.3	Q9NQV7	OTTHUMG00000161918	ENST00000296682.3:c.2272C>A	5.37:g.23527469C>A	ENSP00000296682:p.Arg758Ser	Somatic	87	2	0.0229885		WXS	Illumina HiSeq	Phase_I	66	15	0.227273	NM_020227	B4DX22|Q27Q50	Missense_Mutation	SNP	ENST00000296682.3	37	CCDS43307.1	70	0.03205128205128205	47	0.09552845528455285	10	0.027624309392265192	7	0.012237762237762238	6	0.0079155672823219	A	0.001	-3.244943	0.00022	.	.	ENSG00000164256	ENST00000296682	T	0.35605	1.3	2.65	2.65	0.31530	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00412	0.0013	N	0.20574	0.59	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.24048	-1.0171	8	0.05620	T	0.96	.	3.4855	0.07618	0.534:0.2366:0.0:0.2294	.	758	Q9NQV7	PRDM9_HUMAN	S	758	ENSP00000296682:R758S	ENSP00000296682:R758S	R	+	1	0	PRDM9	23563226	0.000000	0.05858	0.052000	0.19188	0.010000	0.07245	-0.386000	0.07370	0.423000	0.26033	-0.512000	0.04463	CGC	C|0.978;A|0.022	0.022	strong		0.572	PRDM9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366375.1	NM_020227	
KIAA1841	84542	hgsc.bcm.edu	37	2	61304271	61304271	+	Silent	SNP	A	A	G	rs1729659	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:61304271A>G	ENST00000402291.1	+	6	889	c.648A>G	c.(646-648)aaA>aaG	p.K216K	KIAA1841_ENST00000356719.2_Silent_p.K216K|KIAA1841_ENST00000295031.5_Silent_p.K216K|KIAA1841_ENST00000482513.1_3'UTR|KIAA1841_ENST00000453873.1_Silent_p.K216K	NM_001129993.1	NP_001123465.1	Q6NSI8	K1841_HUMAN	KIAA1841	216								p.K216K(1)		breast(3)|kidney(1)|large_intestine(4)|lung(12)|ovary(1)|skin(2)|stomach(1)|urinary_tract(1)	25			Epithelial(17;0.193)			AGGAGAATAAAGATTGTGAGA	0.383													A|||	1732	0.345847	0.3911	0.4294	5008	,	,		18960	0.4167		0.3191	False		,,,				2504	0.18				p.K216K		Atlas-SNP	.											KIAA1841,NS,carcinoma,0,1	KIAA1841	95	1	1	Substitution - coding silent(1)	stomach(1)	c.A648G						PASS	.	A	,	1673,2733	500.0+/-364.6	326,1021,856	77.0	83.0	81.0		648,648	1.9	1.0	2	dbSNP_89	81	2868,5732	446.7+/-361.3	501,1866,1933	no	coding-synonymous,coding-synonymous	KIAA1841	NM_001129993.1,NM_032506.2	,	827,2887,2789	GG,GA,AA		33.3488,37.9709,34.9147	,	216/719,216/708	61304271	4541,8465	2203	4300	6503	SO:0001819	synonymous_variant	84542	exon6			GAATAAAGATTGT	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	ENST00000402291.1:c.648A>G	2.37:g.61304271A>G		Somatic	149	1	0.00671141		WXS	Illumina HiSeq	Phase_I	236	187	0.792373	NM_032506	Q49AF0|Q6ZND0|Q96JI6	Silent	SNP	ENST00000402291.1	37	CCDS46296.1																																																																																			A|0.639;G|0.361	0.361	strong		0.383	KIAA1841-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325477.1	NM_032506	
GPR123	84435	hgsc.bcm.edu	37	10	134942832	134942832	+	Silent	SNP	G	G	A	rs45586231	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:134942832G>A	ENST00000392607.3	+	7	1936	c.1500G>A	c.(1498-1500)ccG>ccA	p.P500P	GPR123_ENST00000392606.2_Silent_p.P403P|GPR123_ENST00000607359.1_Silent_p.P1219P	NM_001083909.1	NP_001077378.1	Q86SQ6	GP123_HUMAN	G protein-coupled receptor 123	500					G-protein coupled receptor signaling pathway (GO:0007186)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			endometrium(2)|kidney(2)|large_intestine(1)|lung(6)|prostate(3)	14		all_cancers(35;1.8e-10)|all_epithelial(44;8.95e-09)|Lung NSC(174;0.000845)|all_lung(145;0.00144)|all_neural(114;0.0299)|Colorectal(31;0.0585)|Melanoma(40;0.123)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;9.16e-06)|Epithelial(32;1.21e-05)|all cancers(32;1.63e-05)		CCACGCAGCCGGGCAGGGAGG	0.706													G|||	1275	0.254593	0.2648	0.2421	5008	,	,		13293	0.4454		0.0905	False		,,,				2504	0.2219				p.P500P		Atlas-SNP	.											.	GPR123	118	.	0			c.G1500A						PASS	.	G		899,3391		95,709,1341	8.0	8.0	8.0		1500	-7.4	0.0	10	dbSNP_127	8	622,7836		33,556,3640	no	coding-synonymous	GPR123	NM_001083909.1		128,1265,4981	AA,AG,GG		7.354,20.9557,11.9313		500/561	134942832	1521,11227	2145	4229	6374	SO:0001819	synonymous_variant	84435	exon7			GCAGCCGGGCAGG	AB058731	CCDS41580.1	10q26	2014-08-08			ENSG00000197177	ENSG00000197177		"""-"", ""GPCR / Class B : Orphans"""	13838	protein-coding gene	gene with protein product		612302				12565841	Standard	XM_005252695		Approved	KIAA1828	uc001llw.3	Q86SQ6	OTTHUMG00000019304	ENST00000392607.3:c.1500G>A	10.37:g.134942832G>A		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	45	24	0.533333	NM_001083909	A5HL16|A6NG50|Q5T234|Q86SN7|Q96JJ9	Silent	SNP	ENST00000392607.3	37	CCDS41580.1																																																																																			G|0.756;A|0.244	0.244	strong		0.706	GPR123-003	NOVEL	basic|appris_candidate|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000051113.2		
PDILT	204474	hgsc.bcm.edu	37	16	20370816	20370816	+	Missense_Mutation	SNP	C	C	T	rs9652589	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:20370816C>T	ENST00000302451.4	-	12	1828	c.1580G>A	c.(1579-1581)aGg>aAg	p.R527K		NM_174924.1	NP_777584.1	Q8N807	PDILT_HUMAN	protein disulfide isomerase-like, testis expressed	527			R -> K (in dbSNP:rs9652589). {ECO:0000269|PubMed:14702039}.		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						TAACCCTTTCCTCATCATAGG	0.478													t|||	1785	0.35643	0.4153	0.3473	5008	,	,		18474	0.1538		0.4732	False		,,,				2504	0.3722				p.R527K		Atlas-SNP	.											.	PDILT	120	.	0			c.G1580A						PASS	.	T	LYS/ARG	1864,2542	633.8+/-396.1	395,1074,734	202.0	171.0	182.0		1580	2.6	0.0	16	dbSNP_119	182	4313,4287	575.7+/-390.3	1107,2099,1094	yes	missense	PDILT	NM_174924.1	26	1502,3173,1828	TT,TC,CC		49.8488,42.3059,47.4935	benign	527/585	20370816	6177,6829	2203	4300	6503	SO:0001583	missense	204474	exon12			CCTTTCCTCATCA		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.1580G>A	16.37:g.20370816C>T	ENSP00000305465:p.Arg527Lys	Somatic	233	0	0		WXS	Illumina HiSeq	Phase_I	271	94	0.346863	NM_174924	Q8IVQ5	Missense_Mutation	SNP	ENST00000302451.4	37	CCDS10584.1	778	0.35622710622710624	198	0.4024390243902439	128	0.35359116022099446	87	0.1520979020979021	365	0.4815303430079156	T	0.073	-1.198838	0.01581	0.423059	0.501512	ENSG00000169340	ENST00000302451	T	0.02916	4.11	3.72	2.63	0.31362	.	1.361560	0.05274	N	0.518087	T	0.00012	0.0000	N	0.01576	-0.805	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.40001	-0.9586	9	0.02654	T	1	.	5.7063	0.17911	0.0:0.2236:0.0:0.7764	rs9652589;rs52814673;rs56730734;rs9652589	527	Q8N807	PDILT_HUMAN	K	527	ENSP00000305465:R527K	ENSP00000305465:R527K	R	-	2	0	PDILT	20278317	0.002000	0.14202	0.000000	0.03702	0.000000	0.00434	1.003000	0.29809	0.269000	0.21961	-1.551000	0.00897	AGG	C|0.584;T|0.416	0.416	strong		0.478	PDILT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254332.1	NM_174924	
UGT2B7	7364	hgsc.bcm.edu	37	4	69964271	69964271	+	Silent	SNP	A	A	G	rs28365062	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:69964271A>G	ENST00000508661.1	+	2	762	c.735A>G	c.(733-735)acA>acG	p.T245T	UGT2B7_ENST00000305231.7_Silent_p.T245T|UGT2B7_ENST00000509763.1_3'UTR			P16662	UD2B7_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide B7	245					androgen metabolic process (GO:0008209)|cellular glucuronidation (GO:0052695)|lipid metabolic process (GO:0006629)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	glucuronosyltransferase activity (GO:0015020)			autonomic_ganglia(1)|endometrium(3)|kidney(4)|large_intestine(6)|lung(16)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	38					Atorvastatin(DB01076)|Carbamazepine(DB00564)|Chenodeoxycholic acid(DB06777)|Codeine(DB00318)|Dabigatran etexilate(DB06695)|Dapagliflozin(DB06292)|Diclofenac(DB00586)|Epirubicin(DB00445)|Etodolac(DB00749)|Ezetimibe(DB00973)|Flunitrazepam(DB01544)|Flurbiprofen(DB00712)|Fluvastatin(DB01095)|Ibuprofen(DB01050)|Indomethacin(DB00328)|Losartan(DB00678)|Lovastatin(DB00227)|Mitiglinide(DB01252)|Morphine(DB00295)|Mycophenolate mofetil(DB00688)|Mycophenolic acid(DB01024)|Naproxen(DB00788)|Oxazepam(DB00842)|Pitavastatin(DB08860)|Silodosin(DB06207)|Simvastatin(DB00641)|Suprofen(DB00870)|Tapentadol(DB06204)|Valproic Acid(DB00313)|Zidovudine(DB00495)	GACCCACTACATTATCTGAGA	0.368													A|||	744	0.148562	0.1543	0.3228	5008	,	,		14253	0.0437		0.1551	False		,,,				2504	0.1186				p.T245T		Atlas-SNP	.											.	UGT2B7	79	.	0			c.A735G	GRCh37	CS086286	UGT2B7	S	rs28365062	PASS	.	A		639,3767	271.3+/-270.1	42,555,1606	107.0	109.0	109.0		735	-5.4	0.0	4	dbSNP_126	109	1183,7417	238.3+/-269.8	86,1011,3203	no	coding-synonymous	UGT2B7	NM_001074.2		128,1566,4809	GG,GA,AA		13.7558,14.503,14.0089		245/530	69964271	1822,11184	2203	4300	6503	SO:0001819	synonymous_variant	7364	exon2			CACTACATTATCT	BC030974	CCDS3526.1	4q13	2008-02-05	2005-07-20		ENSG00000171234	ENSG00000171234		"""UDP glucuronosyltransferases"""	12554	protein-coding gene	gene with protein product		600068	"""UDP glycosyltransferase 2 family, polypeptide B7"""			2159463, 7835904	Standard	NM_001074		Approved	UGT2B9	uc003heg.4	P16662	OTTHUMG00000129404	ENST00000508661.1:c.735A>G	4.37:g.69964271A>G		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	78	45	0.576923	NM_001074	B2R810|Q6GTW0	Silent	SNP	ENST00000508661.1	37																																																																																				A|0.854;G|0.146	0.146	strong		0.368	UGT2B7-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000362103.1	NM_001074	
WBSCR27	155368	hgsc.bcm.edu	37	7	73249299	73249299	+	Missense_Mutation	SNP	G	G	C	rs13232463	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:73249299G>C	ENST00000297873.4	-	6	561	c.512C>G	c.(511-513)tCg>tGg	p.S171W		NM_152559.2	NP_689772.2	Q8N6F8	WBS27_HUMAN	Williams Beuren syndrome chromosome region 27	171			S -> W (in dbSNP:rs13232463). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:18398435, ECO:0000269|Ref.1}.							NS(1)|central_nervous_system(1)|lung(2)|prostate(1)	5		Lung NSC(55;0.159)				AAGGTTGGACGAGTTGGTCCT	0.662													G|||	2910	0.58107	0.4629	0.6124	5008	,	,		12835	0.5813		0.7256	False		,,,				2504	0.5695				p.S171W		Atlas-SNP	.											.	WBSCR27	21	.	0			c.C512G						PASS	.	G	TRP/SER	2289,2117	591.9+/-387.7	593,1103,507	37.0	36.0	36.0		512	5.1	0.9	7	dbSNP_121	36	6383,2217	707.0+/-405.6	2369,1645,286	yes	missense	WBSCR27	NM_152559.2	177	2962,2748,793	CC,CG,GG		25.7791,48.0481,33.3231	possibly-damaging	171/246	73249299	8672,4334	2203	4300	6503	SO:0001583	missense	155368	exon6			TTGGACGAGTTGG	AF534110	CCDS5561.1	7q11.23	2004-07-05			ENSG00000165171	ENSG00000165171			19068	protein-coding gene	gene with protein product		612546					Standard	NM_152559		Approved		uc003tzj.2	Q8N6F8	OTTHUMG00000130033	ENST00000297873.4:c.512C>G	7.37:g.73249299G>C	ENSP00000297873:p.Ser171Trp	Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	59	59	1	NM_152559		Missense_Mutation	SNP	ENST00000297873.4	37	CCDS5561.1	1327	0.6076007326007326	227	0.4613821138211382	218	0.6022099447513812	328	0.5734265734265734	554	0.7308707124010554	G	14.67	2.604998	0.46423	0.519519	0.742209	ENSG00000165171	ENST00000297873	T	0.34472	1.36	5.09	5.09	0.68999	.	0.868358	0.10152	N	0.709478	T	0.00012	0.0000	L	0.34521	1.04	0.24901	P	0.99210339	D	0.63880	0.993	P	0.56700	0.804	T	0.16217	-1.0410	9	0.38643	T	0.18	-11.3487	14.1593	0.65436	0.0:0.0:1.0:0.0	rs13232463;rs17855551;rs13232463	171	Q8N6F8	WBS27_HUMAN	W	171	ENSP00000297873:S171W	ENSP00000297873:S171W	S	-	2	0	WBSCR27	72887235	0.966000	0.33281	0.950000	0.38849	0.277000	0.26821	1.649000	0.37281	2.413000	0.81919	0.549000	0.68633	TCG	G|0.360;C|0.640	0.640	strong		0.662	WBSCR27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252312.1	NM_152559	
LRRN1	57633	hgsc.bcm.edu	37	3	3887093	3887093	+	Silent	SNP	A	A	G	rs9844909	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:3887093A>G	ENST00000319331.3	+	2	1529	c.768A>G	c.(766-768)caA>caG	p.Q256Q	SUMF1_ENST00000534863.1_Intron	NM_020873.5	NP_065924.3	Q6UXK5	LRRN1_HUMAN	leucine rich repeat neuronal 1	256						integral component of membrane (GO:0016021)				NS(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(9)|prostate(1)|skin(1)|urinary_tract(2)	26				Epithelial(13;0.000886)|all cancers(10;0.0032)|OV - Ovarian serous cystadenocarcinoma(96;0.00608)|STAD - Stomach adenocarcinoma(44;0.0617)		AAGTCCCTCAACTTGCCCTGC	0.393													A|||	1262	0.251997	0.1422	0.2032	5008	,	,		17992	0.3224		0.2525	False		,,,				2504	0.362				p.Q256Q		Atlas-SNP	.											.	LRRN1	82	.	0			c.A768G						PASS	.	A		602,3802	237.4+/-249.2	42,518,1642	77.0	85.0	82.0		768	-1.2	1.0	3	dbSNP_119	82	2011,6589	346.7+/-326.3	237,1537,2526	no	coding-synonymous	LRRN1	NM_020873.5		279,2055,4168	GG,GA,AA		23.3837,13.6694,20.0938		256/717	3887093	2613,10391	2202	4300	6502	SO:0001819	synonymous_variant	57633	exon2			CCCTCAACTTGCC	AB040930	CCDS33685.1	3p26.2	2013-01-11			ENSG00000175928	ENSG00000175928		"""Immunoglobulin superfamily / I-set domain containing"""	20980	protein-coding gene	gene with protein product	"""fibronectin type III, immunoglobulin and leucine rich repeat domains 3"""					10819331	Standard	NM_020873		Approved	FIGLER3	uc003bpt.4	Q6UXK5	OTTHUMG00000154934	ENST00000319331.3:c.768A>G	3.37:g.3887093A>G		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	72	37	0.513889	NM_020873	Q3LID5|Q8IYV5|Q9H8V1|Q9P231	Silent	SNP	ENST00000319331.3	37	CCDS33685.1																																																																																			A|0.775;G|0.225	0.225	strong		0.393	LRRN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337704.2	NM_020873	
MUC4	4585	hgsc.bcm.edu	37	3	195513680	195513680	+	Missense_Mutation	SNP	A	A	T	rs7372250		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195513680A>T	ENST00000463781.3	-	2	5230	c.4771T>A	c.(4771-4773)Tcc>Acc	p.S1591T	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.S1591T	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0	VWFD. {ECO:0000255|PROSITE- ProRule:PRU00580}.				cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GATGCTGAGGAAGTGTCGGTG	0.577																																					p.S1591T		Atlas-SNP	.											.	MUC4	1505	.	0			c.T4771A						PASS	.						29.0	23.0	25.0					3																	195513680		672	1580	2252	SO:0001583	missense	4585	exon2			CTGAGGAAGTGTC	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.4771T>A	3.37:g.195513680A>T	ENSP00000417498:p.Ser1591Thr	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	67	22	0.328358	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	-	0.021	-1.419052	0.01136	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.31769	1.48;1.48	0.312	-0.624	0.11552	.	.	.	.	.	T	0.15869	0.0382	N	0.19112	0.55	0.09310	N	1	P	0.42584	0.784	B	0.39419	0.299	T	0.12400	-1.0549	8	.	.	.	.	4.0022	0.09585	0.7133:0.0:0.2867:0.0	.	1591	E7ESK3	.	T	1591	ENSP00000417498:S1591T;ENSP00000420243:S1591T	.	S	-	1	0	MUC4	196998075	0.676000	0.27567	0.005000	0.12908	0.002000	0.02628	1.188000	0.32102	-1.513000	0.01789	-2.001000	0.00444	TCC	A|1.000;|0.000	.	weak		0.577	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
CHGB	1114	hgsc.bcm.edu	37	20	5903067	5903067	+	Missense_Mutation	SNP	T	T	A	rs6085324	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:5903067T>A	ENST00000378961.4	+	4	481	c.277T>A	c.(277-279)Tcg>Acg	p.S93T		NM_001819.2	NP_001810.2	P05060	SCG1_HUMAN	chromogranin B (secretogranin 1)	93			S -> T (in dbSNP:rs6085324). {ECO:0000269|PubMed:14702039, ECO:0000269|Ref.4}.			extracellular region (GO:0005576)|secretory granule (GO:0030141)	hormone activity (GO:0005179)	p.S93T(1)		breast(7)|kidney(2)|large_intestine(8)|lung(19)|ovary(1)|pancreas(2)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)	47						AGCTGATGCCTCGGAAGCCCA	0.493													T|||	1165	0.232628	0.0749	0.2392	5008	,	,		18246	0.379		0.2594	False		,,,				2504	0.2628				p.S93T		Atlas-SNP	.											CHGB,colon,carcinoma,0,2	CHGB	112	2	1	Substitution - Missense(1)	stomach(1)	c.T277A						PASS	.	T	THR/SER	530,3876	240.6+/-251.3	39,452,1712	52.0	53.0	53.0		277	0.7	0.0	20	dbSNP_114	53	2285,6315	378.2+/-338.8	307,1671,2322	yes	missense	CHGB	NM_001819.2	58	346,2123,4034	AA,AT,TT		26.5698,12.0291,21.6439	possibly-damaging	93/678	5903067	2815,10191	2203	4300	6503	SO:0001583	missense	1114	exon4			GATGCCTCGGAAG		CCDS13092.1	20p12.3	2013-09-19			ENSG00000089199	ENSG00000089199			1930	protein-coding gene	gene with protein product	"""secretogranin B"""	118920		SCG1		3608978	Standard	NM_001819		Approved		uc002wmg.3	P05060	OTTHUMG00000031821	ENST00000378961.4:c.277T>A	20.37:g.5903067T>A	ENSP00000368244:p.Ser93Thr	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	91	41	0.450549	NM_001819	A8K021|Q59EU9|Q6IBS6|Q9BQV6|Q9UC25|Q9UJA6	Missense_Mutation	SNP	ENST00000378961.4	37	CCDS13092.1	529	0.24221611721611722	48	0.0975609756097561	78	0.2154696132596685	206	0.36013986013986016	197	0.2598944591029024	T	9.771	1.172828	0.21704	0.120291	0.265698	ENSG00000089199	ENST00000378961;ENST00000455042	T;T	0.02067	4.47;4.47	4.26	0.681	0.17986	.	0.988393	0.08223	N	0.978839	T	0.00012	0.0000	M	0.62723	1.935	0.80722	P	0.0	B	0.17268	0.021	B	0.19666	0.026	T	0.41179	-0.9523	9	0.25106	T	0.35	-4.0E-4	3.7604	0.08602	0.1617:0.1884:0.0:0.6498	rs6085324	93	P05060	SCG1_HUMAN	T	93;73	ENSP00000368244:S93T;ENSP00000416643:S73T	ENSP00000368244:S93T	S	+	1	0	CHGB	5851067	0.003000	0.15002	0.000000	0.03702	0.007000	0.05969	0.677000	0.25262	0.081000	0.16988	0.460000	0.39030	TCG	T|0.776;A|0.224	0.224	strong		0.493	CHGB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077897.2	NM_001819	
CPAMD8	27151	hgsc.bcm.edu	37	19	17108135	17108135	+	Missense_Mutation	SNP	C	C	T	rs3745340	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:17108135C>T	ENST00000443236.1	-	11	1053	c.1022G>A	c.(1021-1023)cGg>cAg	p.R341Q	CPAMD8_ENST00000388925.4_Missense_Mutation_p.R294Q	NM_015692.2	NP_056507.2	Q8IZJ3	CPMD8_HUMAN	C3 and PZP-like, alpha-2-macroglobulin domain containing 8	294						extracellular space (GO:0005615)|plasma membrane (GO:0005886)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(11)|central_nervous_system(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(17)|lung(14)|ovary(7)|pancreas(2)|prostate(4)|skin(5)	82						GTCGAAGTCCCGGGAGCCGAG	0.607													c|||	1649	0.329273	0.1649	0.353	5008	,	,		19240	0.5		0.3976	False		,,,				2504	0.2883				p.R341Q		Atlas-SNP	.											.	CPAMD8	192	.	0			c.G1022A						PASS	.	C	GLN/ARG	795,3235		79,637,1299	13.0	15.0	14.0		1022	-3.8	0.8	19	dbSNP_107	14	3138,5204		619,1900,1652	no	missense	CPAMD8	NM_015692.2	43	698,2537,2951	TT,TC,CC		37.6169,19.727,31.7895	possibly-damaging	341/1933	17108135	3933,8439	2015	4171	6186	SO:0001583	missense	27151	exon11			AAGTCCCGGGAGC	AY101765	CCDS42519.1	19p13.12	2008-02-05			ENSG00000160111	ENSG00000160111			23228	protein-coding gene	gene with protein product		608841				10574462	Standard	NM_015692		Approved	KIAA1283, VIP, K-CAP	uc002nfb.3	Q8IZJ3	OTTHUMG00000133549	ENST00000443236.1:c.1022G>A	19.37:g.17108135C>T	ENSP00000402505:p.Arg341Gln	Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	146	137	0.938356	NM_015692	Q8NC09|Q9ULD7	Missense_Mutation	SNP	ENST00000443236.1	37	CCDS42519.1	815|815	0.3731684981684982|0.3731684981684982	87|87	0.17682926829268292|0.17682926829268292	147|147	0.40607734806629836|0.40607734806629836	276|276	0.4825174825174825|0.4825174825174825	305|305	0.4023746701846966|0.4023746701846966	c|c	9.619|9.619	1.133286|1.133286	0.21041|0.21041	0.19727|0.19727	0.376169|0.376169	ENSG00000160111|ENSG00000160111	ENST00000443236|ENST00000291440;ENST00000388925	.|T;T	.|0.51325	.|0.71;0.72	3.0|3.0	-3.79|-3.79	0.04320|0.04320	.|.	.|0.186387	.|0.32488	.|N	.|0.006027	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.00707|0.00707	-1.245|-1.245	0.51767|0.51767	P|P	6.799999999995698E-5|6.799999999995698E-5	.|B	.|0.06786	.|0.001	.|B	.|0.01281	.|0.0	T|T	0.47315|0.47315	-0.9127|-0.9127	4|9	.|0.25751	.|T	.|0.34	.|.	6.6288|6.6288	0.22845|0.22845	0.0:0.38:0.371:0.2489|0.0:0.38:0.371:0.2489	rs3745340;rs57931423;rs3745340|rs3745340;rs57931423;rs3745340	.|294	.|Q8IZJ3	.|CPMD8_HUMAN	R|Q	352|341;294	.|ENSP00000291440:R341Q;ENSP00000373577:R294Q	.|ENSP00000291440:R341Q	G|R	-|-	1|2	0|0	CPAMD8|CPAMD8	16969135|16969135	0.997000|0.997000	0.39634|0.39634	0.786000|0.786000	0.31890|0.31890	0.743000|0.743000	0.42351|0.42351	2.354000|2.354000	0.44098|0.44098	-0.514000|-0.514000	0.06488|0.06488	-0.417000|-0.417000	0.06048|0.06048	GGG|CGG	C|0.647;T|0.353	0.353	strong		0.607	CPAMD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257531.2	NM_015692	
MCCC1	56922	hgsc.bcm.edu	37	3	182755209	182755209	+	Missense_Mutation	SNP	T	T	G	rs2270968	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:182755209T>G	ENST00000265594.4	-	13	1537	c.1391A>C	c.(1390-1392)cAc>cCc	p.H464P	MCCC1_ENST00000489909.1_5'Flank|MCCC1_ENST00000539926.1_Missense_Mutation_p.H329P|MCCC1_ENST00000492597.1_Missense_Mutation_p.H355P	NM_020166.3	NP_064551.3	Q96RQ3	MCCA_HUMAN	methylcrotonoyl-CoA carboxylase 1 (alpha)	464	Biotin carboxylation.		H -> P (in dbSNP:rs2270968). {ECO:0000269|PubMed:11181649, ECO:0000269|PubMed:11406611, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.6}.		biotin metabolic process (GO:0006768)|branched-chain amino acid catabolic process (GO:0009083)|cellular nitrogen compound metabolic process (GO:0034641)|leucine catabolic process (GO:0006552)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|biotin binding (GO:0009374)|biotin carboxylase activity (GO:0004075)|metal ion binding (GO:0046872)|methylcrotonoyl-CoA carboxylase activity (GO:0004485)			central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(9)|liver(1)|lung(17)|ovary(1)|pancreas(2)|prostate(1)|skin(2)	40	all_cancers(143;1.84e-14)|Ovarian(172;0.0355)		all cancers(12;1.8e-44)|Epithelial(37;3.23e-38)|LUSC - Lung squamous cell carcinoma(7;5.04e-25)|Lung(8;5.03e-23)|OV - Ovarian serous cystadenocarcinoma(80;5.07e-21)		Biotin(DB00121)	AATGTTGGTGTGCAGTCCAAC	0.433													T|||	2328	0.464856	0.1929	0.6297	5008	,	,		20070	0.3323		0.7346	False		,,,				2504	0.5746				p.H464P		Atlas-SNP	.											.	MCCC1	87	.	0			c.A1391C						PASS	.	T	PRO/HIS	1267,3139	433.7+/-343.7	204,859,1140	91.0	81.0	84.0		1391	3.5	1.0	3	dbSNP_100	84	6339,2261	707.6+/-405.6	2336,1667,297	yes	missense	MCCC1	NM_020166.3	77	2540,2526,1437	GG,GT,TT		26.2907,28.7562,41.5193	benign	464/726	182755209	7606,5400	2203	4300	6503	SO:0001583	missense	56922	exon13			TTGGTGTGCAGTC	AF310972	CCDS3241.1	3q27.1	2010-04-30	2010-04-30		ENSG00000078070	ENSG00000078070	6.4.1.4		6936	protein-coding gene	gene with protein product		609010	"""methylcrotonoyl-Coenzyme A carboxylase 1 (alpha)"""			11170888	Standard	XR_241502		Approved	MCCA	uc003fle.3	Q96RQ3	OTTHUMG00000158355	ENST00000265594.4:c.1391A>C	3.37:g.182755209T>G	ENSP00000265594:p.His464Pro	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	133	133	1	NM_020166	Q59ES4|Q9H959|Q9NS97	Missense_Mutation	SNP	ENST00000265594.4	37	CCDS3241.1	1043	0.4775641025641026	109	0.22154471544715448	209	0.5773480662983426	182	0.3181818181818182	543	0.716358839050132	T	9.294	1.051243	0.19827	0.287562	0.737093	ENSG00000078070	ENST00000265594;ENST00000492597;ENST00000392616;ENST00000539926;ENST00000476176;ENST00000448585	T;T;T;T	0.80909	-1.43;-1.43;-1.43;-1.43	5.93	3.51	0.40186	Rudiment single hybrid motif (1);ATP-grasp fold, subdomain 2 (1);Biotin carboxylation domain (1);Biotin carboxylase, C-terminal (2);	0.212673	0.64402	D	0.000020	T	0.00012	0.0000	N	0.00175	-1.925	0.36830	P	0.11313200000000001	B;B;B	0.06786	0.001;0.0;0.0	B;B;B	0.09377	0.003;0.001;0.004	T	0.46582	-0.9181	9	0.28530	T	0.3	.	8.3092	0.32060	0.0:0.3158:0.0:0.6842	rs2270968;rs3207461;rs11540929;rs17408941;rs17845000;rs17857761;rs17857766;rs52791788;rs2270968	417;355;464	E9PG35;E9PHF7;Q96RQ3	.;.;MCCA_HUMAN	P	464;355;314;329;417;417	ENSP00000265594:H464P;ENSP00000419898:H355P;ENSP00000441253:H329P;ENSP00000420433:H417P	ENSP00000265594:H464P	H	-	2	0	MCCC1	184237903	1.000000	0.71417	0.990000	0.47175	0.990000	0.78478	1.118000	0.31246	0.474000	0.27392	0.459000	0.35465	CAC	T|0.479;G|0.521	0.521	strong		0.433	MCCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350775.1	NM_020166	
ZNF862	643641	hgsc.bcm.edu	37	7	149559177	149559177	+	Silent	SNP	C	C	T	rs370165112		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:149559177C>T	ENST00000223210.4	+	7	3173	c.2928C>T	c.(2926-2928)ttC>ttT	p.F976F	RP4-751H13.7_ENST00000608963.1_RNA	NM_001099220.1	NP_001092690.1	O60290	ZN862_HUMAN	zinc finger protein 862	976					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						CCAGGTATTTCGAGTGCTCCC	0.537																																					p.F976F		Atlas-SNP	.											ZNF862,NS,carcinoma,0,2	ZNF862	97	2	0			c.C2928T						scavenged	.	C		0,4026		0,0,2013	80.0	85.0	83.0		2928	-2.7	0.0	7		83	1,8383		0,1,4191	no	coding-synonymous	ZNF862	NM_001099220.1		0,1,6204	TT,TC,CC		0.0119,0.0,0.0081		976/1170	149559177	1,12409	2013	4192	6205	SO:0001819	synonymous_variant	643641	exon7			GTATTTCGAGTGC	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.2928C>T	7.37:g.149559177C>T		Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	145	3	0.0206897	NM_001099220	A0AUL8	Silent	SNP	ENST00000223210.4	37	CCDS47741.1																																																																																			.	.	weak		0.537	ZNF862-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350165.1	NM_001099220	
NXNL1	115861	hgsc.bcm.edu	37	19	17566634	17566634	+	Missense_Mutation	SNP	T	T	A	rs56248314	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:17566634T>A	ENST00000301944.2	-	2	545	c.461A>T	c.(460-462)gAg>gTg	p.E154V	CTD-2521M24.10_ENST00000594663.1_Missense_Mutation_p.E61V|CTD-2521M24.11_ENST00000598950.1_lincRNA|AC010319.1_ENST00000410873.1_RNA	NM_138454.1	NP_612463.1	Q96CM4	NXNL1_HUMAN	nucleoredoxin-like 1	154	Thioredoxin. {ECO:0000255|PROSITE- ProRule:PRU00691}.				photoreceptor cell maintenance (GO:0045494)	membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)				central_nervous_system(1)|cervix(1)|large_intestine(1)|lung(1)|prostate(1)|upper_aerodigestive_tract(1)	6						CTCGGCCGCCTCCTGCCAGTT	0.711													t|||	355	0.0708866	0.0068	0.0749	5008	,	,		9724	0.0734		0.1302	False		,,,				2504	0.091				p.E154V		Atlas-SNP	.											.	NXNL1	13	.	0			c.A461T						PASS	.		VAL/GLU	114,4066		2,110,1978	11.0	9.0	10.0		461	3.6	1.0	19	dbSNP_129	10	1071,7205		65,941,3132	yes	missense	NXNL1	NM_138454.1	121	67,1051,5110	AA,AT,TT		12.941,2.7273,9.5135	probably-damaging	154/213	17566634	1185,11271	2090	4138	6228	SO:0001583	missense	115861	exon2			GCCGCCTCCTGCC	BC014127	CCDS12360.1	19p13.11	2014-05-21	2007-08-16	2007-08-16	ENSG00000171773	ENSG00000171773			25179	protein-coding gene	gene with protein product		608791	"""thioredoxin-like 6"""	TXNL6		12477932	Standard	NM_138454		Approved	RDCVF	uc002ngs.3	Q96CM4	OTTHUMG00000182798	ENST00000301944.2:c.461A>T	19.37:g.17566634T>A	ENSP00000305631:p.Glu154Val	Somatic	24	0	0		WXS	Illumina HiSeq	Phase_I	19	5	0.263158	NM_138454	Q0QD37	Missense_Mutation	SNP	ENST00000301944.2	37	CCDS12360.1	179	0.08195970695970696	5	0.01016260162601626	30	0.08287292817679558	47	0.08216783216783216	97	0.1279683377308707	t	19.56	3.850035	0.71603	0.027273	0.12941	ENSG00000171773	ENST00000301944	D	0.86297	-2.1	3.6	3.6	0.41247	Thioredoxin-like fold (1);	0.000000	0.85682	U	0.000000	T	0.12646	0.0307	M	0.76574	2.34	0.80722	D	1	D	0.89917	1.0	D	0.71414	0.973	T	0.55573	-0.8120	10	0.54805	T	0.06	.	10.221	0.43196	0.0:0.0:0.0:1.0	rs56248314	154	Q96CM4	NXNL1_HUMAN	V	154	ENSP00000305631:E154V	ENSP00000305631:E154V	E	-	2	0	NXNL1	17427634	1.000000	0.71417	0.981000	0.43875	0.555000	0.35460	7.395000	0.79876	1.519000	0.48950	0.235000	0.17854	GAG	T|0.913;A|0.087	0.087	strong		0.711	NXNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463803.1	NM_138454	
PARP4	143	hgsc.bcm.edu	37	13	25000617	25000617	+	Missense_Mutation	SNP	C	C	T	rs7571	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:25000617C>T	ENST00000381989.3	-	33	5071	c.4966G>A	c.(4966-4968)Gct>Act	p.A1656T		NM_006437.3	NP_006428.2	Q9UKK3	PARP4_HUMAN	poly (ADP-ribose) polymerase family, member 4	1656	Interaction with the major vault protein.			A -> P (in Ref. 1; AAD47250, 2; AAC62491 and 3; BAA11494). {ECO:0000305}.	cell death (GO:0008219)|cellular protein modification process (GO:0006464)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|inflammatory response (GO:0006954)|protein ADP-ribosylation (GO:0006471)|response to drug (GO:0042493)|transport (GO:0006810)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|spindle microtubule (GO:0005876)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|NAD+ ADP-ribosyltransferase activity (GO:0003950)	p.A1656P(1)		autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(14)|lung(18)|ovary(3)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	63		all_epithelial(30;7.67e-16)|Lung SC(185;0.0225)|Breast(139;0.052)		all cancers(112;0.000127)|Epithelial(112;0.000778)|Kidney(163;0.039)|OV - Ovarian serous cystadenocarcinoma(117;0.0578)|KIRC - Kidney renal clear cell carcinoma(186;0.135)|Lung(94;0.195)		GAAATAGAAGCGTCATCCATT	0.343																																					p.A1656T		Atlas-SNP	.											PARP4,NS,carcinoma,0,1	PARP4	142	1	1	Substitution - Missense(1)	stomach(1)	c.G4966A						scavenged	.						79.0	80.0	79.0					13																	25000617		2203	4300	6503	SO:0001583	missense	143	exon33			TAGAAGCGTCATC	AF057160	CCDS9307.1	13q11	2010-09-29	2004-08-20	2004-08-26	ENSG00000102699	ENSG00000102699		"""Poly (ADP-ribose) polymerases"""	271	protein-coding gene	gene with protein product	"""von Willebrand factor A domain containing 5C"""	607519	"""ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase)-like 1"""	ADPRTL1		10644454	Standard	NM_006437		Approved	VAULT3, p193, VPARP, VWA5C	uc001upl.3	Q9UKK3	OTTHUMG00000016582	ENST00000381989.3:c.4966G>A	13.37:g.25000617C>T	ENSP00000371419:p.Ala1656Thr	Somatic	334	0	0		WXS	Illumina HiSeq	Phase_I	263	3	0.0114068	NM_006437	O75903|Q14682|Q5QNZ9|Q9H1M6	Missense_Mutation	SNP	ENST00000381989.3	37	CCDS9307.1	.	.	.	.	.	.	.	.	.	.	g	9.594	1.126907	0.20959	.	.	ENSG00000102699	ENST00000381989	D	0.88046	-2.33	4.09	-4.32	0.03688	.	0.441750	0.17430	U	0.174485	T	0.74199	0.3685	L	0.44542	1.39	0.80722	P	0.0	B	0.25955	0.138	B	0.12156	0.007	T	0.59526	-0.7438	9	0.36615	T	0.2	.	3.8199	0.08832	0.1321:0.2003:0.5103:0.1573	.	1656	Q9UKK3	PARP4_HUMAN	T	1656	ENSP00000371419:A1656T	ENSP00000371419:A1656T	A	-	1	0	PARP4	23898617	0.000000	0.05858	0.000000	0.03702	0.133000	0.20885	-2.291000	0.01147	-0.515000	0.06479	-0.371000	0.07208	GCT	C|0.568;G|0.432	.	alt		0.343	PARP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044189.1	NM_006437	
LRRC72	100506049	hgsc.bcm.edu	37	7	16566645	16566645	+	Missense_Mutation	SNP	C	C	G	rs2301968	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:16566645C>G	ENST00000401542.2	+	1	125	c.68C>G	c.(67-69)aCt>aGt	p.T23S	SOSTDC1_ENST00000396652.1_Intron|LRRC72_ENST00000482711.1_3'UTR	NM_001195280.1	NP_001182209.1	A6NJI9	LRC72_HUMAN	leucine rich repeat containing 72	23																	GCATCCGAAACTGCCCTACAG	0.672													C|||	386	0.0770767	0.0386	0.0533	5008	,	,		14684	0.1528		0.1183	False		,,,				2504	0.0256				p.T23S		Atlas-SNP	.											.	.	.	.	0			c.C68G						PASS	.																																			SO:0001583	missense	100506049	exon1			CCGAAACTGCCCT		CCDS56464.1	7p21.1	2011-10-07			ENSG00000205858	ENSG00000205858			42972	protein-coding gene	gene with protein product							Standard	NM_001195280		Approved		uc022aaf.1	A6NJI9	OTTHUMG00000152446	ENST00000401542.2:c.68C>G	7.37:g.16566645C>G	ENSP00000384971:p.Thr23Ser	Somatic	18	0	0		WXS	Illumina HiSeq	Phase_I	21	7	0.333333	NM_001195280		Missense_Mutation	SNP	ENST00000401542.2	37	CCDS56464.1	205	0.09386446886446886	16	0.032520325203252036	28	0.07734806629834254	70	0.12237762237762238	91	0.12005277044854881	C	2.190	-0.385487	0.04966	.	.	ENSG00000205858	ENST00000401542	T	0.23147	1.92	4.43	-0.694	0.11294	.	.	.	.	.	T	0.00144	0.0004	N	0.12182	0.205	0.80722	P	0.0	.	.	.	.	.	.	T	0.32693	-0.9897	6	0.21540	T	0.41	.	0.6047	0.00750	0.1807:0.3562:0.1635:0.2995	rs2301968;rs17465070;rs52837496;rs2301968	.	.	.	S	23	ENSP00000384971:T23S	ENSP00000371558:T23S	T	+	2	0	AC005014.4	16533170	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.248000	0.08854	-0.132000	0.11557	0.655000	0.94253	ACT	C|0.908;G|0.092	0.092	strong		0.672	LRRC72-001	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326249.2		
CAMK2B	816	hgsc.bcm.edu	37	7	44282928	44282928	+	Silent	SNP	G	G	A	rs17172630	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:44282928G>A	ENST00000395749.2	-	8	598	c.522C>T	c.(520-522)ttC>ttT	p.F174F	CAMK2B_ENST00000347193.4_Silent_p.F174F|CAMK2B_ENST00000258682.6_Silent_p.F174F|CAMK2B_ENST00000440254.2_Silent_p.F174F|CAMK2B_ENST00000457475.1_Silent_p.F174F|CAMK2B_ENST00000358707.3_Silent_p.F174F|CAMK2B_ENST00000346990.4_Silent_p.F174F|CAMK2B_ENST00000502837.2_Silent_p.F45F|CAMK2B_ENST00000395747.2_Silent_p.F174F|CAMK2B_ENST00000350811.3_Silent_p.F174F|CAMK2B_ENST00000353625.4_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	108	0	0		WXS	Illumina HiSeq	Phase_I	103	76	0.737864	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	
ESYT2	57488	hgsc.bcm.edu	37	7	158536267	158536267	+	Missense_Mutation	SNP	T	T	C	rs2305473	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	143	0	0		WXS	Illumina HiSeq	Phase_I	127	56	0.440945	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	
TGM7	116179	hgsc.bcm.edu	37	15	43579566	43579566	+	Silent	SNP	A	A	G	rs513970	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:43579566A>G	ENST00000452443.2	-	6	781	c.777T>C	c.(775-777)agT>agC	p.S259S		NM_052955.2	NP_443187.1	Q96PF1	TGM7_HUMAN	transglutaminase 7	259					peptide cross-linking (GO:0018149)		metal ion binding (GO:0046872)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(8)|lung(16)|ovary(2)|prostate(4)|skin(1)	39		all_cancers(109;2.12e-14)|all_epithelial(112;1.99e-12)|Lung NSC(122;2.46e-08)|all_lung(180;2.75e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;9.14e-07)	L-Glutamine(DB00130)	GGATGGCCACACTGCCCTTCC	0.597													G|||	2679	0.534944	0.9682	0.3429	5008	,	,		18061	0.4077		0.34	False		,,,				2504	0.4172				p.S259S		Atlas-SNP	.											.	TGM7	86	.	0			c.T777C						PASS	.	G		3742,662	281.6+/-276.1	1593,556,53	71.0	58.0	62.0		777	-10.3	0.2	15	dbSNP_83	62	2819,5779	673.6+/-403.0	477,1865,1957	no	coding-synonymous	TGM7	NM_052955.2		2070,2421,2010	GG,GA,AA		32.7867,15.0318,49.5385		259/711	43579566	6561,6441	2202	4299	6501	SO:0001819	synonymous_variant	116179	exon6			GGCCACACTGCCC	AF363393	CCDS32213.1	15q15.2	2004-07-01				ENSG00000159495		"""Transglutaminases"""	30790	protein-coding gene	gene with protein product	"""transglutaminase Z"""	606776				11390390	Standard	NM_052955		Approved	TGMZ	uc001zrf.1	Q96PF1		ENST00000452443.2:c.777T>C	15.37:g.43579566A>G		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	121	53	0.438017	NM_052955		Silent	SNP	ENST00000452443.2	37	CCDS32213.1																																																																																			A|0.492;G|0.508	0.508	strong		0.597	TGM7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432489.1	NM_052955	
P2RX7	5027	hgsc.bcm.edu	37	12	121605355	121605355	+	Missense_Mutation	SNP	G	G	A	rs7958311	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:121605355G>A	ENST00000546057.1	+	8	952	c.809G>A	c.(808-810)cGt>cAt	p.R270H	P2RX7_ENST00000328963.5_Missense_Mutation_p.R100H|P2RX7_ENST00000541446.1_Intron|P2RX7_ENST00000535250.1_Missense_Mutation_p.R180H|P2RX7_ENST00000377162.2_Intron|P2RX7_ENST00000443520.3_3'UTR	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	126	0	0		WXS	Illumina HiSeq	Phase_I	124	41	0.330645	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	
MUC17	140453	hgsc.bcm.edu	37	7	100681751	100681751	+	Missense_Mutation	SNP	A	A	G	rs73712044	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:100681751A>G	ENST00000306151.4	+	3	7118	c.7054A>G	c.(7054-7056)Agt>Ggt	p.S2352G		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	2352	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)					AATGGTGGCCAGTTTTGAAAC	0.488													A|||	150	0.0299521	0.0734	0.0072	5008	,	,		26842	0.0278		0.0159	False		,,,				2504	0.0041				p.S2352G		Atlas-SNP	.											.	MUC17	804	.	0			c.A7054G						PASS	.	A	GLY/SER	344,4062	177.6+/-206.5	10,324,1869	237.0	235.0	236.0		7054	-1.4	0.0	7	dbSNP_130	236	93,8507	52.3+/-112.8	0,93,4207	yes	missense	MUC17	NM_001040105.1	56	10,417,6076	GG,GA,AA		1.0814,7.8075,3.36	benign	2352/4494	100681751	437,12569	2203	4300	6503	SO:0001583	missense	140453	exon3			GTGGCCAGTTTTG	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.7054A>G	7.37:g.100681751A>G	ENSP00000302716:p.Ser2352Gly	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	49	22	0.44898	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	85	0.03891941391941392	48	0.0975609756097561	4	0.011049723756906077	22	0.038461538461538464	11	0.014511873350923483	A	0.649	-0.810163	0.02798	0.078075	0.010814	ENSG00000169876	ENST00000306151	T	0.02552	4.25	0.679	-1.36	0.09085	.	.	.	.	.	T	0.00073	0.0002	N	0.19112	0.55	0.09310	N	1	B	0.14805	0.011	B	0.04013	0.001	T	0.47824	-0.9087	9	0.33141	T	0.24	.	1.4255	0.02322	0.4123:0.0:0.2653:0.3223	.	2352	Q685J3	MUC17_HUMAN	G	2352	ENSP00000302716:S2352G	ENSP00000302716:S2352G	S	+	1	0	MUC17	100468471	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.115000	0.15540	-0.685000	0.05177	0.113000	0.15668	AGT	A|0.965;G|0.035	0.035	strong		0.488	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
PPAT	5471	hgsc.bcm.edu	37	4	57268328	57268328	+	Silent	SNP	T	T	C	rs2271924	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:57268328T>C	ENST00000264220.2	-	6	818	c.681A>G	c.(679-681)acA>acG	p.T227T	PPAT_ENST00000507648.1_5'UTR	NM_002703.4	NP_002694.3	Q06203	PUR1_HUMAN	phosphoribosyl pyrophosphate amidotransferase	227	Glutamine amidotransferase type-2. {ECO:0000255|PROSITE-ProRule:PRU00609}.				'de novo' IMP biosynthetic process (GO:0006189)|cellular response to drug (GO:0035690)|cellular response to insulin stimulus (GO:0032869)|G1/S transition of mitotic cell cycle (GO:0000082)|glutamine catabolic process (GO:0006543)|kidney development (GO:0001822)|lactation (GO:0007595)|maternal process involved in female pregnancy (GO:0060135)|nucleobase-containing small molecule metabolic process (GO:0055086)|nucleoside metabolic process (GO:0009116)|organ regeneration (GO:0031100)|protein homotetramerization (GO:0051289)|purine nucleobase biosynthetic process (GO:0009113)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide biosynthetic process (GO:0006164)|purine ribonucleoside monophosphate biosynthetic process (GO:0009168)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	4 iron, 4 sulfur cluster binding (GO:0051539)|amidophosphoribosyltransferase activity (GO:0004044)|metal ion binding (GO:0046872)			cervix(1)|endometrium(2)|large_intestine(6)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)	20	Glioma(25;0.08)|all_neural(26;0.101)				Fluorouracil(DB00544)|L-Glutamine(DB00130)|Mercaptopurine(DB01033)	CCCATCCTTCTGTTTCTGATG	0.318													T|||	629	0.125599	0.1067	0.0634	5008	,	,		15735	0.2381		0.0974	False		,,,				2504	0.1084				p.T227T		Atlas-SNP	.											.	PPAT	41	.	0			c.A681G						PASS	.	T		406,4000	201.1+/-224.2	21,364,1818	101.0	103.0	102.0		681	-10.7	0.4	4	dbSNP_100	102	633,7961	163.0+/-215.7	28,577,3692	no	coding-synonymous	PPAT	NM_002703.4		49,941,5510	CC,CT,TT		7.3656,9.2147,7.9923		227/518	57268328	1039,11961	2203	4297	6500	SO:0001819	synonymous_variant	5471	exon6			TCCTTCTGTTTCT		CCDS3505.1	4q12	2012-10-02			ENSG00000128059	ENSG00000128059	2.4.2.14		9238	protein-coding gene	gene with protein product		172450					Standard	NM_002703		Approved	GPAT, PRAT	uc003hbr.3	Q06203	OTTHUMG00000128842	ENST00000264220.2:c.681A>G	4.37:g.57268328T>C		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	70	32	0.457143	NM_002703		Silent	SNP	ENST00000264220.2	37	CCDS3505.1																																																																																			T|0.907;C|0.093	0.093	strong		0.318	PPAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250781.2	NM_002703	
UGCG	7357	hgsc.bcm.edu	37	9	114694486	114694486	+	Silent	SNP	A	A	G	rs7850023	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:114694486A>G	ENST00000374279.3	+	8	1311	c.861A>G	c.(859-861)acA>acG	p.T287T	MIR4668_ENST00000582284.1_RNA	NM_003358.1	NP_003349.1	Q16739	CEGT_HUMAN	UDP-glucose ceramide glucosyltransferase	287					epidermis development (GO:0008544)|glucosylceramide biosynthetic process (GO:0006679)|glycosphingolipid biosynthetic process (GO:0006688)|glycosphingolipid metabolic process (GO:0006687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	ceramide glucosyltransferase activity (GO:0008120)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(1)|ovary(1)|urinary_tract(1)	12				OV - Ovarian serous cystadenocarcinoma(323;0.0433)	Miglustat(DB00419)	TTCCTGCTACAATAATTTGTG	0.353													A|||	1660	0.33147	0.3759	0.4251	5008	,	,		19974	0.2986		0.2813	False		,,,				2504	0.2904				p.T287T		Atlas-SNP	.											.	UGCG	32	.	0			c.A861G						PASS	.	A		1539,2867	485.7+/-360.4	261,1017,925	144.0	140.0	141.0		861	2.3	1.0	9	dbSNP_116	141	2224,6376	378.0+/-338.7	293,1638,2369	no	coding-synonymous	UGCG	NM_003358.1		554,2655,3294	GG,GA,AA		25.8605,34.9296,28.9328		287/395	114694486	3763,9243	2203	4300	6503	SO:0001819	synonymous_variant	7357	exon8			TGCTACAATAATT	D50840	CCDS6782.1	9q31	2014-03-13			ENSG00000148154	ENSG00000148154	2.4.1.80	"""Glycosyltransferase family 2 domain containing"""	12524	protein-coding gene	gene with protein product	"""glucosylceramide synthase"", ""ceramide glucosyltransferase"""	602874				8643456, 9605861	Standard	NM_003358		Approved	GCS	uc004bft.3	Q16739	OTTHUMG00000020498	ENST00000374279.3:c.861A>G	9.37:g.114694486A>G		Somatic	206	0	0		WXS	Illumina HiSeq	Phase_I	221	129	0.58371	NM_003358	Q5T258	Silent	SNP	ENST00000374279.3	37	CCDS6782.1																																																																																			A|0.701;G|0.299	0.299	strong		0.353	UGCG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053661.1	NM_003358	
PRDM12	59335	hgsc.bcm.edu	37	9	133553993	133553993	+	Silent	SNP	C	C	T	rs7021384	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:133553993C>T	ENST00000253008.2	+	4	708	c.648C>T	c.(646-648)ccC>ccT	p.P216P		NM_021619.2	NP_067632.2	Q9H4Q4	PRD12_HUMAN	PR domain containing 12	216					neurogenesis (GO:0022008)|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)			kidney(2)|large_intestine(3)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	11		all_hematologic(13;0.0433)|Acute lymphoblastic leukemia(5;0.0534)		OV - Ovarian serous cystadenocarcinoma(145;0.000344)		CAGGTGTGCCCGGGCTAGAGG	0.592													C|||	1893	0.377995	0.3336	0.451	5008	,	,		18722	0.4722		0.3211	False		,,,				2504	0.3476				p.P216P		Atlas-SNP	.											.	PRDM12	24	.	0			c.C648T						PASS	.	C		1542,2864	486.4+/-360.6	264,1014,925	89.0	85.0	86.0		648	-11.5	0.0	9	dbSNP_116	86	2733,5867	436.9+/-358.5	436,1861,2003	no	coding-synonymous	PRDM12	NM_021619.2		700,2875,2928	TT,TC,CC		31.7791,34.9977,32.8694		216/368	133553993	4275,8731	2203	4300	6503	SO:0001819	synonymous_variant	59335	exon4			TGTGCCCGGGCTA	AY004252	CCDS6934.1	9q33-q34	2013-01-08			ENSG00000130711	ENSG00000130711		"""Zinc fingers, C2H2-type"""	13997	protein-coding gene	gene with protein product	"""PR-domain containing protein 12"", ""PR-domain zinc finger protein 12"""					14523459	Standard	NM_021619		Approved		uc004bzt.1	Q9H4Q4	OTTHUMG00000020808	ENST00000253008.2:c.648C>T	9.37:g.133553993C>T		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	93	38	0.408602	NM_021619	A3KFK9	Silent	SNP	ENST00000253008.2	37	CCDS6934.1																																																																																			C|0.650;T|0.350	0.350	strong		0.592	PRDM12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054664.1	NM_021619	
ALKBH3	221120	hgsc.bcm.edu	37	11	43940602	43940602	+	Missense_Mutation	SNP	C	C	G	rs1130290	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:43940602C>G	ENST00000302708.4	+	9	1095	c.684C>G	c.(682-684)gaC>gaG	p.D228E	RP11-613D13.4_ENST00000526408.1_RNA|ALKBH3-AS1_ENST00000499194.1_RNA|ALKBH3_ENST00000532410.1_3'UTR|ALKBH3-AS1_ENST00000534287.1_RNA|ALKBH3-AS1_ENST00000527960.1_RNA|ALKBH3-AS1_ENST00000528285.1_RNA	NM_139178.3	NP_631917.1	Q96Q83	ALKB3_HUMAN	alkB, alkylation repair homolog 3 (E. coli)	228	Fe2OG dioxygenase. {ECO:0000255|PROSITE- ProRule:PRU00805}.		D -> E (in dbSNP:rs2434470). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.2}.		cell proliferation (GO:0008283)|DNA dealkylation involved in DNA repair (GO:0006307)|DNA repair (GO:0006281)|oxidative single-stranded DNA demethylation (GO:0035552)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	DNA-N1-methyladenine dioxygenase activity (GO:0043734)|ferrous iron binding (GO:0008198)|L-ascorbic acid binding (GO:0031418)	p.D228E(1)		endometrium(2)|kidney(1)|lung(4)|prostate(1)	8					Vitamin C(DB00126)	AGAATGGAGACTACACATATG	0.413								Direct reversal of damage					C|||	696	0.138978	0.0802	0.1398	5008	,	,		24051	0.0933		0.2575	False		,,,				2504	0.1431				p.D228E		Atlas-SNP	.											ALKBH3,NS,carcinoma,0,1	ALKBH3	33	1	1	Substitution - Missense(1)	prostate(1)	c.C684G						PASS	.	C	GLU/ASP	431,3975	209.8+/-230.5	22,387,1794	179.0	152.0	161.0		684	5.9	1.0	11	dbSNP_100	161	2245,6355	379.7+/-339.4	291,1663,2346	yes	missense	ALKBH3	NM_139178.3	45	313,2050,4140	GG,GC,CC		26.1047,9.7821,20.5751	probably-damaging	228/287	43940602	2676,10330	2203	4300	6503	SO:0001583	missense	221120	exon9			TGGAGACTACACA	AB042029	CCDS7906.1	11p11.2	2013-10-11			ENSG00000166199	ENSG00000166199		"""Alkylation repair homologs"""	30141	protein-coding gene	gene with protein product		610603				22055184	Standard	NM_139178		Approved	DEPC-1	uc001mxs.2	Q96Q83	OTTHUMG00000166417	ENST00000302708.4:c.684C>G	11.37:g.43940602C>G	ENSP00000302232:p.Asp228Glu	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	49	49	1	NM_139178	A6NDJ1|Q3SYI0|Q6NX57|Q96BU8	Missense_Mutation	SNP	ENST00000302708.4	37	CCDS7906.1	350|350	0.16025641025641027|0.16025641025641027	48|48	0.0975609756097561|0.0975609756097561	56|56	0.15469613259668508|0.15469613259668508	48|48	0.08391608391608392|0.08391608391608392	198|198	0.2612137203166227|0.2612137203166227	C|C	25.6|25.6	4.658695|4.658695	0.88154|0.88154	0.097821|0.097821	0.261047|0.261047	ENSG00000166199|ENSG00000166199	ENST00000302708|ENST00000532129	T|.	0.13538|.	2.58|.	5.91|5.91	5.91|5.91	0.95273|0.95273	Oxoglutarate/iron-dependent oxygenase (2);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.00039|0.00039	0.0001|0.0001	M|M	0.68593|0.68593	2.085|2.085	0.09310|0.09310	P|P	1.0|1.0	P|.	0.47604|.	0.898|.	P|.	0.55577|.	0.779|.	T|T	0.00085|0.00085	-1.2098|-1.2098	9|4	0.72032|.	D|.	0.01|.	-24.4655|-24.4655	15.7986|15.7986	0.78433|0.78433	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	rs2434470;rs3740986;rs17565250;rs52822276;rs56569355;rs2434470|rs2434470;rs3740986;rs17565250;rs52822276;rs56569355;rs2434470	228|.	Q96Q83|.	ALKB3_HUMAN|.	E|V	228|98	ENSP00000302232:D228E|.	ENSP00000302232:D228E|.	D|L	+|+	3|1	2|2	ALKBH3|ALKBH3	43897178|43897178	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.971000|0.971000	0.66376|0.66376	2.591000|2.591000	0.46163|0.46163	2.793000|2.793000	0.96121|0.96121	0.655000|0.655000	0.94253|0.94253	GAC|CTA	C|0.827;G|0.173	0.173	strong		0.413	ALKBH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389693.1	NM_139178	
PHTF2	57157	hgsc.bcm.edu	37	7	77567051	77567051	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:77567051T>C	ENST00000248550.7	+	12	1439	c.1363T>C	c.(1363-1365)Tcc>Ccc	p.S455P	PHTF2_ENST00000307305.8_Missense_Mutation_p.S417P|PHTF2_ENST00000454592.1_3'UTR|PHTF2_ENST00000416283.2_Missense_Mutation_p.S421P|PHTF2_ENST00000275575.7_Missense_Mutation_p.S417P|PHTF2_ENST00000422959.2_Missense_Mutation_p.S421P|PHTF2_ENST00000424760.1_Missense_Mutation_p.S417P			Q8N3S3	PHTF2_HUMAN	putative homeodomain transcription factor 2	455					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						GCTCCATAGTTCCCACCCAGG	0.289																																					p.S421P		Atlas-SNP	.											.	PHTF2	104	.	0			c.T1261C						PASS	.						53.0	47.0	49.0					7																	77567051		1795	4059	5854	SO:0001583	missense	57157	exon11			CATAGTTCCCACC	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.1363T>C	7.37:g.77567051T>C	ENSP00000248550:p.Ser455Pro	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	83	5	0.060241	NM_001127357	A0JP04|A0JP05|A4D1C2|E9PEE3|G5E9H7|Q6NW35|Q8TBW4|Q9H099	Missense_Mutation	SNP	ENST00000248550.7	37		.	.	.	.	.	.	.	.	.	.	T	15.62	2.887106	0.52014	.	.	ENSG00000006576	ENST00000427986;ENST00000422959;ENST00000307305;ENST00000424760;ENST00000275575;ENST00000416283;ENST00000248550	.	.	.	5.19	2.81	0.32909	.	0.292942	0.33553	N	0.004795	T	0.38241	0.1033	L	0.38175	1.15	0.39118	D	0.961615	P;P;B;P;P;P	0.50156	0.731;0.918;0.437;0.736;0.49;0.932	B;P;B;B;B;P	0.48571	0.347;0.556;0.244;0.232;0.315;0.582	T	0.18967	-1.0320	9	0.27082	T	0.32	-0.7834	4.84	0.13485	0.1369:0.1486:0.0:0.7145	.	417;280;421;455;417;417	Q8N3S3-4;Q8N5I6;Q8N3S3-2;Q8N3S3;Q8N3S3-3;B3KQZ2	.;.;.;PHTF2_HUMAN;.;.	P	421;421;417;417;417;421;455	.	ENSP00000248550:S455P	S	+	1	0	PHTF2	77404987	1.000000	0.71417	0.979000	0.43373	0.994000	0.84299	1.931000	0.40134	0.391000	0.25143	0.482000	0.46254	TCC	.	.	none		0.289	PHTF2-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000340638.2	NM_020432	
INSL3	3640	hgsc.bcm.edu	37	19	17932289	17932289	+	Silent	SNP	C	C	T	rs2286663	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:17932289C>T	ENST00000317306.7	-	1	43	c.27G>A	c.(25-27)gcG>gcA	p.A9A	INSL3_ENST00000379695.5_Silent_p.A9A	NM_005543.3	NP_005534.2	P51460	INSL3_HUMAN	insulin-like 3 (Leydig cell)	9					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						GCAGCACCAGCGCCCAGGCGG	0.726													C|||	615	0.122804	0.112	0.1513	5008	,	,		13113	0.2024		0.0547	False		,,,				2504	0.1053				p.A9A		Atlas-SNP	.											.	INSL3	8	.	0			c.G27A						PASS	.	C		234,3118		10,214,1452	4.0	7.0	6.0		27	-4.7	0.1	19	dbSNP_100	6	233,6007		3,227,2890	no	coding-synonymous	INSL3	NM_005543.2		13,441,4342	TT,TC,CC		3.734,6.9809,4.8686		9/132	17932289	467,9125	1676	3120	4796	SO:0001819	synonymous_variant	3640	exon1			CACCAGCGCCCAG		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.27G>A	19.37:g.17932289C>T		Somatic	7	0	0		WXS	Illumina HiSeq	Phase_I	16	9	0.5625	NM_005543	B4DZ72|G3XAG0|Q3KPI5|Q3KPI6|Q6YNB5|Q9UEA2|Q9UPH6	Silent	SNP	ENST00000317306.7	37	CCDS12365.1																																																																																			C|0.875;T|0.125	0.125	strong		0.726	INSL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466836.1	NM_005543	
ATP2A1	487	hgsc.bcm.edu	37	16	28898778	28898778	+	Silent	SNP	C	C	G	rs113803159	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:28898778C>G	ENST00000357084.3	+	8	930	c.663C>G	c.(661-663)ggC>ggG	p.G221G	ATP2A1_ENST00000536376.1_Silent_p.G96G|ATP2A1_ENST00000395503.4_Silent_p.G221G	NM_173201.3	NP_775293.1	O14983	AT2A1_HUMAN	ATPase, Ca++ transporting, cardiac muscle, fast twitch 1	221					apoptotic mitochondrial changes (GO:0008637)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|ion transmembrane transport (GO:0034220)|maintenance of mitochondrion location (GO:0051659)|negative regulation of endoplasmic reticulum calcium ion concentration (GO:0032471)|negative regulation of striated muscle contraction (GO:0045988)|positive regulation of endoplasmic reticulum calcium ion concentration (GO:0032470)|positive regulation of fast-twitch skeletal muscle fiber contraction (GO:0031448)|positive regulation of mitochondrial calcium ion concentration (GO:0051561)|regulation of striated muscle contraction (GO:0006942)|relaxation of skeletal muscle (GO:0090076)|response to endoplasmic reticulum stress (GO:0034976)|transmembrane transport (GO:0055085)	calcium channel complex (GO:0034704)|endoplasmic reticulum membrane (GO:0005789)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|H zone (GO:0031673)|I band (GO:0031674)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|platelet dense tubular network membrane (GO:0031095)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calcium-transporting ATPase activity (GO:0005388)|protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(10)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|urinary_tract(2)	38						AGGCCTTGGGCATCGTGGCCA	0.607													C|||	9	0.00179712	0.0	0.0014	5008	,	,		18988	0.0		0.008	False		,,,				2504	0.0				p.G221G		Atlas-SNP	.											.	ATP2A1	116	.	0			c.C663G						PASS	.	C	,	7,4387	12.9+/-30.5	0,7,2190	85.0	82.0	83.0		663,663	3.4	1.0	16	dbSNP_132	83	72,8528	43.6+/-101.6	1,70,4229	no	coding-synonymous,coding-synonymous	ATP2A1	NM_004320.4,NM_173201.3	,	1,77,6419	GG,GC,CC		0.8372,0.1593,0.608	,	221/995,221/1002	28898778	79,12915	2197	4300	6497	SO:0001819	synonymous_variant	487	exon8			CTTGGGCATCGTG		CCDS10643.1, CCDS42139.1, CCDS66997.1	16p12.1	2012-10-22			ENSG00000196296	ENSG00000196296	3.6.3.8	"""ATPases / P-type"""	811	protein-coding gene	gene with protein product	"""sarcoplasmic/endoplasmic reticulum calcium ATPase 1"", ""calcium pump 1"""	108730		ATP2A			Standard	NM_004320		Approved	SERCA1	uc002dro.1	O14983	OTTHUMG00000131760	ENST00000357084.3:c.663C>G	16.37:g.28898778C>G		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	74	43	0.581081	NM_004320	A8K5J9|B3KY17|O14984	Silent	SNP	ENST00000357084.3	37	CCDS10643.1																																																																																			C|0.995;G|0.005	0.005	strong		0.607	ATP2A1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254686.2	NM_004320	
ACACB	32	hgsc.bcm.edu	37	12	109577735	109577735	+	Silent	SNP	C	C	T	rs2878960	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:109577735C>T	ENST00000338432.7	+	2	644	c.525C>T	c.(523-525)tcC>tcT	p.S175S	ACACB_ENST00000377854.5_Silent_p.S175S|ACACB_ENST00000377848.3_Silent_p.S175S			O00763	ACACB_HUMAN	acetyl-CoA carboxylase beta	175					acetyl-CoA metabolic process (GO:0006084)|biotin metabolic process (GO:0006768)|carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|malonyl-CoA biosynthetic process (GO:2001295)|positive regulation of cellular metabolic process (GO:0031325)|protein homotetramerization (GO:0051289)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	acetyl-CoA carboxylase activity (GO:0003989)|ATP binding (GO:0005524)|biotin binding (GO:0009374)|biotin carboxylase activity (GO:0004075)|metal ion binding (GO:0046872)			NS(1)|breast(2)|endometrium(9)|kidney(5)|large_intestine(20)|lung(40)|ovary(6)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95					Adenine(DB00173)|Biotin(DB00121)	ACTACTCCTCCGACGAGGACT	0.577													C|||	1992	0.397764	0.2564	0.3977	5008	,	,		16869	0.2589		0.6879	False		,,,				2504	0.4335				p.S175S		Atlas-SNP	.											.	ACACB	330	.	0			c.C525T						PASS	.	C		1326,3080	441.6+/-346.4	195,936,1072	81.0	83.0	82.0		525	-4.1	0.1	12	dbSNP_101	82	5769,2831	668.1+/-402.5	1928,1913,459	no	coding-synonymous	ACACB	NM_001093.3		2123,2849,1531	TT,TC,CC		32.9186,30.0953,45.4483		175/2459	109577735	7095,5911	2203	4300	6503	SO:0001819	synonymous_variant	32	exon1			CTCCTCCGACGAG	U89344	CCDS31898.1	12q24.1	2010-05-07	2010-04-30		ENSG00000076555	ENSG00000076555	6.4.1.2		85	protein-coding gene	gene with protein product	"""acetyl-CoA carboxylase 2"""	601557	"""acetyl-Coenzyme A carboxylase beta"""			8670171	Standard	NM_001093		Approved	HACC275, ACC2, ACCB	uc001toc.3	O00763	OTTHUMG00000169250	ENST00000338432.7:c.525C>T	12.37:g.109577735C>T		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	103	55	0.533981	NM_001093	A6NK36|Q16852|Q1HEC1|Q6KE87|Q6KE89|Q6TY48	Silent	SNP	ENST00000338432.7	37	CCDS31898.1																																																																																			C|0.511;T|0.489	0.489	strong		0.577	ACACB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403077.1	NM_001093	
SLC19A3	80704	hgsc.bcm.edu	37	2	228563835	228563835	+	Missense_Mutation	SNP	A	A	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:228563835A>C	ENST00000258403.3	-	3	667	c.596T>G	c.(595-597)tTt>tGt	p.F199C	SLC19A3_ENST00000541617.1_Missense_Mutation_p.F195C|SLC19A3_ENST00000409287.1_Intron	NM_025243.3	NP_079519.1	Q9BZV2	S19A3_HUMAN	solute carrier family 19 (thiamine transporter), member 3	199					small molecule metabolic process (GO:0044281)|thiamine transmembrane transport (GO:0071934)|thiamine-containing compound metabolic process (GO:0042723)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	thiamine uptake transmembrane transporter activity (GO:0015403)			breast(1)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(5)|lung(8)|ovary(2)|skin(3)	30		Renal(207;0.0112)|all_lung(227;0.0335)|Lung NSC(271;0.142)|all_hematologic(139;0.21)|Esophageal squamous(248;0.236)		Epithelial(121;1.58e-10)|all cancers(144;8.55e-08)|Lung(261;0.00948)|LUSC - Lung squamous cell carcinoma(224;0.0125)	L-Cysteine(DB00151)	TTTTGCATGAAAAAACATGCT	0.433																																					p.F199C		Atlas-SNP	.											.	SLC19A3	62	.	0			c.T596G						PASS	.						91.0	83.0	86.0					2																	228563835		2203	4300	6503	SO:0001583	missense	80704	exon3			GCATGAAAAAACA	AF271633	CCDS2468.1	2q37	2013-07-18	2013-07-18		ENSG00000135917	ENSG00000135917		"""Solute carriers"""	16266	protein-coding gene	gene with protein product	"""thiamine transporter 2"""	606152	"""solute carrier family 19, member 3"""			11136550, 15871139	Standard	XM_005246871		Approved	THTR2	uc002vpi.3	Q9BZV2	OTTHUMG00000133185	ENST00000258403.3:c.596T>G	2.37:g.228563835A>C	ENSP00000258403:p.Phe199Cys	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	90	23	0.255556	NM_025243		Missense_Mutation	SNP	ENST00000258403.3	37	CCDS2468.1	.	.	.	.	.	.	.	.	.	.	A	22.6	4.308304	0.81247	.	.	ENSG00000135917	ENST00000258403;ENST00000541617	D;D	0.91295	-2.82;-2.82	5.77	5.77	0.91146	Major facilitator superfamily domain, general substrate transporter (1);	0.044924	0.85682	D	0.000000	D	0.95996	0.8696	M	0.88979	2.995	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.994;0.998	D	0.96405	0.9300	10	0.59425	D	0.04	-19.6375	16.0872	0.81065	1.0:0.0:0.0:0.0	.	195;199	F5H2M8;Q9BZV2	.;S19A3_HUMAN	C	199;195	ENSP00000258403:F199C;ENSP00000445519:F195C	ENSP00000258403:F199C	F	-	2	0	SLC19A3	228272079	1.000000	0.71417	1.000000	0.80357	0.892000	0.51952	7.160000	0.77495	2.202000	0.70862	0.533000	0.62120	TTT	.	.	none		0.433	SLC19A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256894.1		
LGR6	59352	hgsc.bcm.edu	37	1	202287813	202287813	+	Silent	SNP	T	T	C	rs788793	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	135	0	0		WXS	Illumina HiSeq	Phase_I	140	65	0.464286	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	
VCAN	1462	hgsc.bcm.edu	37	5	82815408	82815408	+	Missense_Mutation	SNP	G	G	A	rs2287926	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:82815408G>A	ENST00000265077.3	+	7	1848	c.1283G>A	c.(1282-1284)gGc>gAc	p.G428D	VCAN_ENST00000502527.2_Intron|VCAN_ENST00000512590.2_Missense_Mutation_p.G380D|VCAN_ENST00000343200.5_Intron|VCAN_ENST00000342785.4_Missense_Mutation_p.G428D	NM_004385.4	NP_004376.2	P13611	CSPG2_HUMAN	versican	428	GAG-alpha (glucosaminoglycan attachment domain).		G -> D (in dbSNP:rs2287926).		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)	ACACCTACTGGCAGTACCAAG	0.463													G|||	1066	0.212859	0.3275	0.1412	5008	,	,		20371	0.1796		0.1173	False		,,,				2504	0.2413				p.G428D		Atlas-SNP	.											.	VCAN	498	.	0			c.G1283A						PASS	.	G	,,ASP/GLY,ASP/GLY	1229,3177	414.4+/-336.8	175,879,1149	82.0	84.0	83.0		,,1283,1283	0.9	0.0	5	dbSNP_100	83	984,7616	211.3+/-251.9	55,874,3371	yes	intron,intron,missense,missense	VCAN	NM_001126336.2,NM_001164097.1,NM_001164098.1,NM_004385.4	,,94,94	230,1753,4520	AA,AG,GG		11.4419,27.8938,17.0152	,,probably-damaging,probably-damaging	,,428/1643,428/3397	82815408	2213,10793	2203	4300	6503	SO:0001583	missense	1462	exon7			CTACTGGCAGTAC	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.1283G>A	5.37:g.82815408G>A	ENSP00000265077:p.Gly428Asp	Somatic	218	0	0		WXS	Illumina HiSeq	Phase_I	158	78	0.493671	NM_004385	P20754|Q13010|Q13189|Q15123|Q9UCL9|Q9UNW5	Missense_Mutation	SNP	ENST00000265077.3	37	CCDS4060.1	407	0.18635531135531136	163	0.3313008130081301	51	0.1408839779005525	103	0.18006993006993008	90	0.11873350923482849	G	6.902	0.535981	0.13188	0.278938	0.114419	ENSG00000038427	ENST00000265077;ENST00000342785;ENST00000512590	D;D;D	0.85702	-1.91;-1.99;-2.02	5.92	0.918	0.19386	.	0.421595	0.22627	N	0.057628	T	0.00012	0.0000	M	0.64997	1.995	0.80722	P	0.0	P;D	0.61697	0.939;0.99	P;P	0.54889	0.66;0.763	T	0.09530	-1.0670	9	0.35671	T	0.21	.	1.2917	0.02061	0.2548:0.2651:0.3444:0.1357	rs2287926;rs52819906;rs57562090;rs2287926	428;428	P13611-3;P13611	.;CSPG2_HUMAN	D	428;428;380	ENSP00000265077:G428D;ENSP00000342768:G428D;ENSP00000425959:G380D	ENSP00000265077:G428D	G	+	2	0	VCAN	82851164	0.049000	0.20398	0.000000	0.03702	0.025000	0.11179	0.632000	0.24583	-0.114000	0.11936	-0.175000	0.13238	GGC	G|0.819;A|0.181	0.181	strong		0.463	VCAN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254092.3	NM_004385	
TARBP1	6894	hgsc.bcm.edu	37	1	234546245	234546245	+	Silent	SNP	C	C	T	rs1141264	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:234546245C>T	ENST00000040877.1	-	23	3737	c.3738G>A	c.(3736-3738)acG>acA	p.T1246T	TARBP1_ENST00000483404.1_5'Flank	NM_005646.3	NP_005637.3	Q13395	TARB1_HUMAN	TAR (HIV-1) RNA binding protein 1	1246					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)			CTGCTAAAAACGTACAAATGC	0.284													T|||	1688	0.337061	0.211	0.3847	5008	,	,		18371	0.3958		0.3907	False		,,,				2504	0.3579				p.T1246T		Atlas-SNP	.											.	TARBP1	111	.	0			c.G3738A						PASS	.	T		1057,3343	692.5+/-405.5	132,793,1275	53.0	57.0	55.0		3738	-0.3	1.0	1	dbSNP_86	55	3311,5281	633.0+/-398.7	618,2075,1603	no	coding-synonymous	TARBP1	NM_005646.3		750,2868,2878	TT,TC,CC		38.5358,24.0227,33.6207		1246/1622	234546245	4368,8624	2200	4296	6496	SO:0001819	synonymous_variant	6894	exon23			TAAAAACGTACAA		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.3738G>A	1.37:g.234546245C>T		Somatic	251	0	0		WXS	Illumina HiSeq	Phase_I	196	85	0.433673	NM_005646	Q9H581	Silent	SNP	ENST00000040877.1	37	CCDS1601.1																																																																																			C|0.658;T|0.342	0.342	strong		0.284	TARBP1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092616.1	NM_005646	
PRKD1	5587	hgsc.bcm.edu	37	14	30066914	30066914	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:30066914G>T	ENST00000331968.5	-	16	2446	c.2217C>A	c.(2215-2217)ttC>ttA	p.F739L	PRKD1_ENST00000415220.2_Missense_Mutation_p.F747L	NM_002742.2	NP_002733.2	Q15139	KPCD1_HUMAN	protein kinase D1	739	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)		CTGACCTCCGGAAAGACTTCT	0.488																																					p.F739L		Atlas-SNP	.											.	PRKD1	316	.	0			c.C2217A						PASS	.						68.0	70.0	70.0					14																	30066914		2203	4300	6503	SO:0001583	missense	5587	exon16			CCTCCGGAAAGAC		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.2217C>A	14.37:g.30066914G>T	ENSP00000333568:p.Phe739Leu	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	38	9	0.236842	NM_002742	A6NL64|B2RAF6	Missense_Mutation	SNP	ENST00000331968.5	37	CCDS9637.1	.	.	.	.	.	.	.	.	.	.	G	18.33	3.600019	0.66332	.	.	ENSG00000184304	ENST00000331968;ENST00000415220	T;T	0.64438	-0.1;-0.1	5.72	4.82	0.62117	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.34483	0.0899	N	0.01668	-0.77	0.80722	D	1	P	0.37207	0.587	B	0.37091	0.241	T	0.46498	-0.9187	10	0.56958	D	0.05	-19.8775	10.6337	0.45551	0.2039:0.0:0.7961:0.0	.	739	Q15139	KPCD1_HUMAN	L	739;747	ENSP00000333568:F739L;ENSP00000390535:F747L	ENSP00000333568:F739L	F	-	3	2	PRKD1	29136665	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.672000	0.46850	1.517000	0.48917	0.650000	0.86243	TTC	.	.	none		0.488	PRKD1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000276611.2	NM_002742	
ANKRD30A	91074	hgsc.bcm.edu	37	10	37508450	37508450	+	Silent	SNP	A	A	C	rs1148259	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:37508450A>C	ENST00000602533.1	+	34	3741	c.3642A>C	c.(3640-3642)gcA>gcC	p.A1214A	ANKRD30A_ENST00000361713.1_Silent_p.A1214A|ANKRD30A_ENST00000374660.1_Silent_p.A1333A			Q9BXX3	AN30A_HUMAN	ankyrin repeat domain 30A	1270					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						TCAATTATGCAGGAGATGCTC	0.368													A|||	2672	0.533546	0.382	0.5	5008	,	,		19799	0.6746		0.4125	False		,,,				2504	0.7413				p.A1214A		Atlas-SNP	.											.	ANKRD30A	448	.	0			c.A3642C						PASS	.	A		1406,2328		267,872,728	60.0	52.0	54.0	http://www.ncbi.nlm.nih.gov/pubmed?term	3642	-1.5	0.0	10	dbSNP_87	54	3465,4723		725,2015,1354	yes	coding-synonymous	ANKRD30A	NM_052997.2		992,2887,2082	CC,CA,AA	http://www.ncbi.nlm.nih.gov/pubmed?term	42.318,37.654,40.8572		1214/1342	37508450	4871,7051	1867	4094	5961	SO:0001819	synonymous_variant	91074	exon34			TTATGCAGGAGAT	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.3642A>C	10.37:g.37508450A>C		Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	125	123	0.984	NM_052997	Q5W025	Silent	SNP	ENST00000602533.1	37																																																																																				A|0.458;C|0.542	0.542	strong		0.368	ANKRD30A-001	KNOWN	NMD_exception|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000047588.2	NM_052997	
SIGLEC10	89790	hgsc.bcm.edu	37	19	51919949	51919949	+	Missense_Mutation	SNP	G	G	A	rs9304711	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:51919949G>A	ENST00000339313.5	-	3	793	c.677C>T	c.(676-678)gCa>gTa	p.A226V	SIGLEC10_ENST00000525998.1_Missense_Mutation_p.A226V|CTD-2616J11.2_ENST00000526996.1_RNA|SIGLEC10_ENST00000441969.3_Missense_Mutation_p.A168V|CTD-2616J11.2_ENST00000532688.1_RNA|SIGLEC10_ENST00000442846.3_Missense_Mutation_p.A168V|SIGLEC10_ENST00000432469.2_Intron|SIGLEC10_ENST00000436984.2_Missense_Mutation_p.A178V|SIGLEC10_ENST00000353836.5_Missense_Mutation_p.A226V|SIGLEC10_ENST00000439889.2_Missense_Mutation_p.A168V|SIGLEC10_ENST00000356298.5_Missense_Mutation_p.A226V|CTD-2616J11.3_ENST00000532473.1_RNA			Q96LC7	SIG10_HUMAN	sialic acid binding Ig-like lectin 10	226	Ig-like C2-type 1.		A -> V (in dbSNP:rs9304711). {ECO:0000269|PubMed:11284738, ECO:0000269|PubMed:11358961, ECO:0000269|PubMed:12163025, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		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)		GGTCCTCTGTGCGCTCACACC	0.652													g|||	1357	0.270966	0.4841	0.2233	5008	,	,		16594	0.006		0.3012	False		,,,				2504	0.2587				p.A226V		Atlas-SNP	.											.	SIGLEC10	112	.	0			c.C677T						PASS	.	G	VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA,,VAL/ALA,VAL/ALA	1956,2450		441,1074,688	116.0	93.0	101.0		503,677,533,503,,503,677	3.7	0.0	19	dbSNP_119	101	2484,6110		365,1754,2178	no	missense,missense,missense,missense,intron,missense,missense	SIGLEC10	NM_001171156.1,NM_001171157.1,NM_001171158.1,NM_001171159.1,NM_001171160.1,NM_001171161.1,NM_033130.4	64,64,64,64,,64,64	806,2828,2866	AA,AG,GG		28.9039,44.394,34.1538	benign,benign,benign,benign,,benign,benign	168/640,226/603,178/555,168/545,,168/455,226/698	51919949	4440,8560	2203	4297	6500	SO:0001583	missense	89790	exon3			CTCTGTGCGCTCA	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.677C>T	19.37:g.51919949G>A	ENSP00000345243:p.Ala226Val	Somatic	232	0	0		WXS	Illumina HiSeq	Phase_I	174	94	0.54023	NM_001171157	A8K1I5|A8K3C7|C9JJ33|C9JM10|F8W917|Q3MIR5|Q6UXI8|Q96G54|Q96LC8	Missense_Mutation	SNP	ENST00000339313.5	37	CCDS12832.1	569	0.26053113553113555	252	0.5121951219512195	93	0.2569060773480663	3	0.005244755244755245	221	0.29155672823219	.	14.46	2.541723	0.45280	0.44394	0.289039	ENSG00000142512	ENST00000353836;ENST00000442846;ENST00000356298;ENST00000441969;ENST00000525998;ENST00000439889;ENST00000436984;ENST00000339313;ENST00000529627	T;D;T;D;T;D;D;T;D	0.85955	4.05;-2.05;4.05;-2.05;4.05;-2.05;-2.05;4.05;-2.05	4.69	3.65	0.41850	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.354249	0.24474	N	0.038202	T	0.00012	0.0000	L	0.28400	0.85	0.80722	P	0.0	B;B;B;B;B;B;B	0.31893	0.087;0.345;0.329;0.005;0.165;0.095;0.112	B;B;B;B;B;B;B	0.33392	0.097;0.163;0.127;0.007;0.075;0.061;0.091	T	0.41161	-0.9524	9	0.14252	T	0.57	.	8.6839	0.34225	0.1084:0.0:0.8916:0.0	rs9304711;rs60900575	178;226;168;226;168;168;226	C9JM10;E9PL79;C9JJ33;Q96LC7-2;Q96LC7-6;Q96LC7-3;Q96LC7	.;.;.;.;.;.;SIG10_HUMAN	V	226;168;226;168;226;168;178;226;40	ENSP00000342389:A226V;ENSP00000395475:A168V;ENSP00000348646:A226V;ENSP00000408387:A168V;ENSP00000431444:A226V;ENSP00000389132:A168V;ENSP00000414324:A178V;ENSP00000345243:A226V;ENSP00000435281:A40V	ENSP00000345243:A226V	A	-	2	0	SIGLEC10	56611761	0.000000	0.05858	0.002000	0.10522	0.153000	0.21895	0.645000	0.24782	0.961000	0.38030	0.313000	0.20887	GCA	G|0.682;A|0.318	0.318	strong		0.652	SIGLEC10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384620.2	NM_033130	
C3orf67	200844	hgsc.bcm.edu	37	3	58870321	58870321	+	Missense_Mutation	SNP	C	C	T	rs116534917	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:58870321C>T	ENST00000482387.1	-	3	386	c.290G>A	c.(289-291)cGc>cAc	p.R97H	RP11-147N17.1_ENST00000493123.1_RNA|RP11-147N17.1_ENST00000482372.1_RNA|C3orf67_ENST00000295966.7_Missense_Mutation_p.R97H|RP11-147N17.1_ENST00000492031.1_RNA|RP11-147N17.1_ENST00000463703.1_RNA|C3orf67_ENST00000472469.1_Missense_Mutation_p.R17H			Q6ZVT6	CC067_HUMAN	chromosome 3 open reading frame 67	97										endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(3)|prostate(2)|skin(1)	19		all_cancers(2;0.000156)|all_epithelial(2;0.000493)|Breast(2;0.00446)|all_lung(2;0.074)|Lung NSC(2;0.248)		BRCA - Breast invasive adenocarcinoma(55;5.93e-06)|Kidney(10;0.00155)|KIRC - Kidney renal clear cell carcinoma(10;0.00172)|OV - Ovarian serous cystadenocarcinoma(275;0.23)		TTCAGTTTGGCGAAGTTTAGT	0.413													C|||	10	0.00199681	0.0	0.0043	5008	,	,		18406	0.0		0.005	False		,,,				2504	0.002				p.R97H		Atlas-SNP	.											C3orf67,NS,carcinoma,-1,1	C3orf67	45	1	0			c.G290A						PASS	.	C	HIS/ARG	10,4396	16.8+/-37.8	0,10,2193	204.0	196.0	199.0		290	1.8	1.0	3	dbSNP_132	199	93,8507	52.7+/-113.3	1,91,4208	yes	missense	C3orf67	NM_198463.2	29	1,101,6401	TT,TC,CC		1.0814,0.227,0.7919	benign	97/564	58870321	103,12903	2203	4300	6503	SO:0001583	missense	200844	exon7			GTTTGGCGAAGTT	AK124920	CCDS33776.1	3p14.2	2011-01-25			ENSG00000163689	ENSG00000163689			24763	protein-coding gene	gene with protein product							Standard	NM_198463		Approved	FLJ42117, FLJ42930	uc003dkt.1	Q6ZVT6	OTTHUMG00000159151	ENST00000482387.1:c.290G>A	3.37:g.58870321C>T	ENSP00000417122:p.Arg97His	Somatic	188	0	0		WXS	Illumina HiSeq	Phase_I	170	78	0.458824	NM_198463	B9EKV6|Q6ZV69	Missense_Mutation	SNP	ENST00000482387.1	37		7	0.003205128205128205	0	0.0	2	0.0055248618784530384	0	0.0	5	0.006596306068601583	C	14.64	2.594771	0.46318	0.00227	0.010814	ENSG00000163689	ENST00000295966;ENST00000482387;ENST00000472469	T;T;T	0.50277	0.75;0.75;0.75	5.61	1.83	0.25207	.	0.410282	0.27906	N	0.017375	T	0.23886	0.0578	L	0.41824	1.3	0.80722	D	1	B;B	0.22983	0.078;0.045	B;B	0.20384	0.029;0.019	T	0.04607	-1.0939	9	.	.	.	-1.7255	4.7606	0.13106	0.1522:0.6058:0.0:0.242	.	17;97	C9J3M8;Q6ZVT6-2	.;.	H	97;97;17	ENSP00000295966:R97H;ENSP00000417122:R97H;ENSP00000417271:R17H	.	R	-	2	0	C3orf67	58845361	0.994000	0.37717	0.992000	0.48379	0.517000	0.34286	0.505000	0.22642	0.318000	0.23185	-0.140000	0.14226	CGC	C|0.994;T|0.006	0.006	strong		0.413	C3orf67-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000353803.1	NM_198463	
SAFB2	9667	hgsc.bcm.edu	37	19	5622579	5622579	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:5622579C>T	ENST00000252542.4	-	1	412	c.148G>A	c.(148-150)Ggc>Agc	p.G50S	SAFB_ENST00000592224.1_5'Flank|SAFB_ENST00000588852.1_5'Flank|SAFB_ENST00000292123.5_5'Flank|SAFB_ENST00000538656.1_5'Flank|SAFB_ENST00000454510.1_5'Flank|SAFB_ENST00000433404.1_5'Flank	NM_014649.2	NP_055464.1	Q14151	SAFB2_HUMAN	scaffold attachment factor B2	50	SAP. {ECO:0000255|PROSITE- ProRule:PRU00186}.				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)|identical protein binding (GO:0042802)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			endometrium(3)|kidney(4)|large_intestine(7)|lung(8)|ovary(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29				UCEC - Uterine corpus endometrioid carcinoma (162;0.000228)		TTGTTGCCGCCCGTGTCCAGG	0.716																																					p.G50S	Ovarian(127;888 1728 23957 44128 52668)	Atlas-SNP	.											.	SAFB2	90	.	0			c.G148A						PASS	.						26.0	25.0	25.0					19																	5622579		2203	4300	6503	SO:0001583	missense	9667	exon1			TGCCGCCCGTGTC	D50928	CCDS32879.1	19p13.3	2013-02-12				ENSG00000130254		"""RNA binding motif (RRM) containing"""	21605	protein-coding gene	gene with protein product		608066				12660241	Standard	NM_014649		Approved	KIAA0138	uc002mcd.3	Q14151		ENST00000252542.4:c.148G>A	19.37:g.5622579C>T	ENSP00000252542:p.Gly50Ser	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	105	37	0.352381	NM_014649	B4DKG3|Q8TB13	Missense_Mutation	SNP	ENST00000252542.4	37	CCDS32879.1	.	.	.	.	.	.	.	.	.	.	C	12.42	1.932295	0.34096	.	.	ENSG00000130254	ENST00000434962;ENST00000415313;ENST00000394625;ENST00000252542;ENST00000536849	T	0.06528	3.29	3.87	1.73	0.24493	DNA-binding SAP (4);	0.285141	0.24671	N	0.036545	T	0.03520	0.0101	N	0.00621	-1.32	0.41073	D	0.985466	P;D	0.89917	0.529;1.0	P;D	0.87578	0.536;0.998	T	0.50767	-0.8789	10	0.05436	T	0.98	-16.0604	6.3775	0.21515	0.0:0.6753:0.151:0.1737	.	50;50	A0PJ47;Q14151	.;SAFB2_HUMAN	S	50;50;50;50;29	ENSP00000252542:G50S	ENSP00000252542:G50S	G	-	1	0	SAFB2	5573579	0.881000	0.30235	0.979000	0.43373	0.956000	0.61745	0.882000	0.28186	0.420000	0.25954	0.561000	0.74099	GGC	.	.	none		0.716	SAFB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451016.1	NM_014649	
LRRTM1	347730	hgsc.bcm.edu	37	2	80529595	80529595	+	Nonsense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:80529595C>T	ENST00000295057.3	-	2	2006	c.1350G>A	c.(1348-1350)tgG>tgA	p.W450*	CTNNA2_ENST00000541047.1_Intron|CTNNA2_ENST00000402739.4_Intron|CTNNA2_ENST00000540488.1_Intron|CTNNA2_ENST00000466387.1_Intron|CTNNA2_ENST00000361291.4_Intron|CTNNA2_ENST00000496558.1_Intron|LRRTM1_ENST00000409148.1_Nonsense_Mutation_p.W450*	NM_178839.4	NP_849161.2	Q86UE6	LRRT1_HUMAN	leucine rich repeat transmembrane neuronal 1	450					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						GGAAACACTTCCAGGACACGT	0.577										HNSCC(69;0.2)																											p.W450X		Atlas-SNP	.											.	LRRTM1	251	.	0			c.G1350A						PASS	.						100.0	89.0	93.0					2																	80529595		2203	4300	6503	SO:0001587	stop_gained	347730	exon2			ACACTTCCAGGAC	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.1350G>A	2.37:g.80529595C>T	ENSP00000295057:p.Trp450*	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	91	22	0.241758	NM_178839	A8K397|D6W5K1|Q96DN1	Nonsense_Mutation	SNP	ENST00000295057.3	37	CCDS1966.1	.	.	.	.	.	.	.	.	.	.	C	38	7.112766	0.98070	.	.	ENSG00000162951	ENST00000295057;ENST00000409148	.	.	.	5.18	5.18	0.71444	.	0.077796	0.56097	U	0.000031	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.6948	0.91596	0.0:1.0:0.0:0.0	.	.	.	.	X	450	.	.	W	-	3	0	LRRTM1	80383106	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.803000	0.62546	2.383000	0.81215	0.561000	0.74099	TGG	.	.	none		0.577	LRRTM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313614.1	NM_178839	
BCL2L2	599	hgsc.bcm.edu	37	14	23777099	23777099	+	Silent	SNP	G	G	A	rs2231301	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:23777099G>A	ENST00000250405.5	+	3	352	c.123G>A	c.(121-123)ccG>ccA	p.P41P	BCL2L2-PABPN1_ENST00000553781.1_Silent_p.P41P|BCL2L2-PABPN1_ENST00000557008.1_Silent_p.P41P	NM_001199839.1|NM_004050.4	NP_001186768.1|NP_004041	Q92843	B2CL2_HUMAN	BCL2-like 2	41					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)|Sertoli cell proliferation (GO:0060011)|spermatogenesis (GO:0007283)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrial outer membrane (GO:0005741)	protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|lung(4)|prostate(1)	6	all_cancers(95;5.54e-06)			GBM - Glioblastoma multiforme(265;0.00654)		CAGCTGACCCGCTGCACCAAG	0.627													G|||	1247	0.249002	0.0454	0.3069	5008	,	,		16556	0.4752		0.2336	False		,,,				2504	0.2658				p.P41P		Atlas-SNP	.											.	.	.	.	0			c.G123A						PASS	.	G	,,	348,4058	172.7+/-202.6	11,326,1866	35.0	38.0	37.0		123,123,123	-3.6	0.9	14	dbSNP_98	37	1976,6622	327.2+/-317.7	239,1498,2562	no	coding-synonymous,coding-synonymous,coding-synonymous	BCL2L2,BCL2L2-PABPN1	NM_001199839.1,NM_001199864.1,NM_004050.4	,,	250,1824,4428	AA,AG,GG		22.9821,7.8983,17.8714	,,	41/194,41/334,41/194	23777099	2324,10680	2203	4299	6502	SO:0001819	synonymous_variant	100529063	exon3			TGACCCGCTGCAC	D87461	CCDS9591.1	14q11.2-q12	2014-03-07			ENSG00000129473	ENSG00000129473		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	995	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 51"""	601931				8761287	Standard	NM_001199839		Approved	KIAA0271, BCL-W, PPP1R51		Q92843	OTTHUMG00000028738	ENST00000250405.5:c.123G>A	14.37:g.23777099G>A		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	98	52	0.530612	NM_001199864	A8K0F4|Q2M3U0|Q5U0H4	Silent	SNP	ENST00000250405.5	37	CCDS9591.1																																																																																			G|0.792;A|0.208	0.208	strong		0.627	BCL2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071763.3	NM_004050	
THBS2	7058	hgsc.bcm.edu	37	6	169641971	169641971	+	Silent	SNP	C	C	T	rs61730651	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:169641971C>T	ENST00000366787.3	-	6	1026	c.777G>A	c.(775-777)tcG>tcA	p.S259S	XXyac-YX65C7_A.2_ENST00000444188.1_RNA	NM_003247.2	NP_003238.2	P35442	TSP2_HUMAN	thrombospondin 2	259					cell adhesion (GO:0007155)|negative regulation of angiogenesis (GO:0016525)|positive regulation of synapse assembly (GO:0051965)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|platelet alpha granule (GO:0031091)	calcium ion binding (GO:0005509)|heparin binding (GO:0008201)			NS(3)|biliary_tract(1)|endometrium(8)|kidney(3)|large_intestine(23)|liver(1)|lung(56)|ovary(6)|prostate(1)|skin(3)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	111		Breast(66;1.78e-05)|Ovarian(120;0.0728)|Esophageal squamous(34;0.247)		OV - Ovarian serous cystadenocarcinoma(33;1.85e-21)|BRCA - Breast invasive adenocarcinoma(81;1.43e-06)|GBM - Glioblastoma multiforme(31;0.000379)		GCCTCCTCTCCGAGCTGGGGC	0.632													C|||	465	0.0928514	0.034	0.0951	5008	,	,		18000	0.0079		0.1889	False		,,,				2504	0.1595				p.S259S	Esophageal Squamous(91;219 1934 18562 44706)	Atlas-SNP	.											.	THBS2	230	.	0			c.G777A						PASS	.	C		266,4140	148.8+/-183.1	9,248,1946	57.0	54.0	55.0		777	-1.5	0.0	6	dbSNP_129	55	1597,6999	293.0+/-301.1	152,1293,2853	no	coding-synonymous	THBS2	NM_003247.2		161,1541,4799	TT,TC,CC		18.5784,6.0372,14.3286		259/1173	169641971	1863,11139	2203	4298	6501	SO:0001819	synonymous_variant	7058	exon6			CCTCTCCGAGCTG		CCDS34574.1	6q27	2008-07-28			ENSG00000186340	ENSG00000186340			11786	protein-coding gene	gene with protein product		188061				18455130	Standard	NM_003247		Approved	TSP2	uc003qwt.3	P35442	OTTHUMG00000045408	ENST00000366787.3:c.777G>A	6.37:g.169641971C>T		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	44	10	0.227273	NM_003247	A6H8N1|A7E232|Q5RI52	Silent	SNP	ENST00000366787.3	37	CCDS34574.1																																																																																			C|0.871;T|0.129	0.129	strong		0.632	THBS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000105439.1	NM_003247	
ATR	545	hgsc.bcm.edu	37	3	142178144	142178144	+	Missense_Mutation	SNP	C	C	T	rs2229032	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:142178144C>T	ENST00000350721.4	-	43	7395	c.7274G>A	c.(7273-7275)cGa>cAa	p.R2425Q	ATR_ENST00000383101.3_Missense_Mutation_p.R2361Q	NM_001184.3	NP_001175.2	Q13535	ATR_HUMAN	ATR serine/threonine kinase	2425	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.		R -> Q (in dbSNP:rs2229032). {ECO:0000269|PubMed:17344846}.		cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|cellular response to UV (GO:0034644)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|multicellular organismal development (GO:0007275)|negative regulation of DNA replication (GO:0008156)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|protein autophosphorylation (GO:0046777)|regulation of protein binding (GO:0043393)|replicative senescence (GO:0090399)|response to drug (GO:0042493)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)|PML body (GO:0016605)|XY body (GO:0001741)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|MutLalpha complex binding (GO:0032405)|MutSalpha complex binding (GO:0032407)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.R2425Q(1)		NS(1)|breast(10)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(20)|liver(2)|lung(45)|ovary(3)|skin(10)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(4)	122						GAGAAATTCTCGGAATACTTT	0.403								Other conserved DNA damage response genes					C|||	512	0.102236	0.0658	0.1037	5008	,	,		17089	0.1012		0.172	False		,,,				2504	0.0798				p.R2425Q		Atlas-SNP	.											ATR,NS,carcinoma,0,1	ATR	285	1	1	Substitution - Missense(1)	stomach(1)	c.G7274A						PASS	.	C	GLN/ARG	388,4018	193.6+/-218.7	17,354,1832	67.0	66.0	67.0		7274	-9.1	0.4	3	dbSNP_98	67	1357,7243	264.2+/-285.4	118,1121,3061	yes	missense	ATR	NM_001184.3	43	135,1475,4893	TT,TC,CC		15.7791,8.8062,13.4169	benign	2425/2645	142178144	1745,11261	2203	4300	6503	SO:0001583	missense	545	exon43			AATTCTCGGAATA	U76308	CCDS3124.1	3q23	2014-06-17	2014-06-17		ENSG00000175054	ENSG00000175054			882	protein-coding gene	gene with protein product	"""MEC1, mitosis entry checkpoint 1, homolog (S. cerevisiae)"""	601215	"""ataxia telangiectasia and Rad3 related"""			8978690, 8610130	Standard	NM_001184		Approved	FRP1, SCKL, SCKL1, MEC1	uc003eux.4	Q13535	OTTHUMG00000159234	ENST00000350721.4:c.7274G>A	3.37:g.142178144C>T	ENSP00000343741:p.Arg2425Gln	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	114	68	0.596491	NM_001184	Q59HB2|Q7KYL3|Q93051|Q9BXK4	Missense_Mutation	SNP	ENST00000350721.4	37	CCDS3124.1	262	0.11996336996336997	27	0.054878048780487805	39	0.10773480662983426	64	0.11188811188811189	132	0.1741424802110818	C	11.32	1.602569	0.28534	0.088062	0.157791	ENSG00000175054	ENST00000350721;ENST00000383101	T;T	0.76186	-1.0;-1.0	4.58	-9.12	0.00707	Protein kinase-like domain (1);Phosphatidylinositol 3-/4-kinase, catalytic (3);	0.601425	0.15707	N	0.248596	T	0.00210	0.0006	N	0.16233	0.39	0.44995	P	0.0019900000000000473	B	0.02656	0.0	B	0.04013	0.001	T	0.03278	-1.1053	9	0.16420	T	0.52	0.6971	19.1019	0.93277	0.0:0.161:0.0:0.839	rs2229032;rs17698526;rs57742124;rs2229032	2425	Q13535	ATR_HUMAN	Q	2425;2361	ENSP00000343741:R2425Q;ENSP00000372581:R2361Q	ENSP00000343741:R2425Q	R	-	2	0	ATR	143660834	0.963000	0.33076	0.437000	0.26809	0.948000	0.59901	0.044000	0.13992	-2.531000	0.00491	-1.406000	0.01132	CGA	C|0.883;T|0.117	0.117	strong		0.403	ATR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353995.2	NM_001184	
CATSPER1	117144	hgsc.bcm.edu	37	11	65793454	65793454	+	Missense_Mutation	SNP	C	C	T	rs1203998	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:65793454C>T	ENST00000312106.5	-	1	534	c.397G>A	c.(397-399)Ggt>Agt	p.G133S		NM_053054.3	NP_444282.3	Q8NEC5	CTSR1_HUMAN	cation channel, sperm associated 1	133	His-rich.		G -> S (in dbSNP:rs1203998).		calcium ion import (GO:0070509)|cell differentiation (GO:0030154)|fusion of sperm to egg plasma membrane (GO:0007342)|membrane depolarization during action potential (GO:0086010)|multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|regulation of calcium ion transport (GO:0051924)|regulation of cilium beat frequency involved in ciliary motility (GO:0060296)|single fertilization (GO:0007338)|sperm motility (GO:0030317)|sperm-egg recognition (GO:0035036)|spermatogenesis (GO:0007283)	CatSper complex (GO:0036128)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|voltage-gated calcium channel activity (GO:0005245)			breast(3)|central_nervous_system(1)|endometrium(9)|kidney(3)|large_intestine(6)|liver(3)|lung(12)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	44						TGGAACCCACCGTATTGGGAC	0.557													T|||	1685	0.336462	0.4546	0.4625	5008	,	,		23104	0.3859		0.2763	False		,,,				2504	0.0982				p.G133S		Atlas-SNP	.											.	CATSPER1	101	.	0			c.G397A						PASS	.	T	SER/GLY	1941,2461	622.4+/-393.9	429,1083,689	76.0	65.0	69.0		397	-3.4	0.0	11	dbSNP_87	69	2390,6202	700.4+/-405.1	323,1744,2229	yes	missense	CATSPER1	NM_053054.3	56	752,2827,2918	TT,TC,CC		27.8166,44.0936,33.3308	benign	133/781	65793454	4331,8663	2201	4296	6497	SO:0001583	missense	117144	exon1			ACCCACCGTATTG	AF407333	CCDS8127.1	11q12.1	2011-07-05			ENSG00000175294	ENSG00000175294		"""Voltage-gated ion channels / Cation channels, sperm associated"""	17116	protein-coding gene	gene with protein product		606389				11675491, 11595941, 16382101	Standard	NM_053054		Approved	CATSPER	uc001ogt.3	Q8NEC5	OTTHUMG00000166668	ENST00000312106.5:c.397G>A	11.37:g.65793454C>T	ENSP00000309052:p.Gly133Ser	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	73	56	0.767123	NM_053054	Q96P76	Missense_Mutation	SNP	ENST00000312106.5	37	CCDS8127.1	809	0.37042124542124544	236	0.4796747967479675	143	0.39502762430939226	220	0.38461538461538464	210	0.2770448548812665	T	3.768	-0.048212	0.07407	0.440936	0.278166	ENSG00000175294	ENST00000312106	D	0.96587	-4.06	3.61	-3.4	0.04853	.	1.234910	0.06153	N	0.674630	T	0.00012	0.0000	N	0.00801	-1.175	0.80722	P	0.0	B	0.06786	0.001	B	0.01281	0.0	T	0.15694	-1.0428	9	0.02654	T	1	.	6.871	0.24121	0.0:0.3272:0.1272:0.5455	rs1203998;rs52832806;rs60332406;rs1203998	133	Q8NEC5	CTSR1_HUMAN	S	133	ENSP00000309052:G133S	ENSP00000309052:G133S	G	-	1	0	CATSPER1	65550030	0.000000	0.05858	0.000000	0.03702	0.075000	0.17131	-2.144000	0.01296	-1.063000	0.03177	-0.817000	0.03123	GGT	C|0.656;T|0.344	0.344	strong		0.557	CATSPER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391055.1	NM_053054	
PHACTR3	116154	hgsc.bcm.edu	37	20	58342349	58342349	+	Missense_Mutation	SNP	C	C	T	rs73598372	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:58342349C>T	ENST00000371015.1	+	5	1117	c.650C>T	c.(649-651)cCt>cTt	p.P217L	PHACTR3_ENST00000361300.4_Intron|PHACTR3_ENST00000541461.1_Missense_Mutation_p.P176L|PHACTR3_ENST00000395636.2_Missense_Mutation_p.P176L|PHACTR3_ENST00000355648.4_Missense_Mutation_p.P176L|PHACTR3_ENST00000359926.3_Missense_Mutation_p.P214L|PHACTR3_ENST00000395639.4_Intron	NM_001281507.1|NM_080672.3	NP_001268436.1|NP_542403.1	Q96KR7	PHAR3_HUMAN	phosphatase and actin regulator 3	217	Pro-rich.					nucleus (GO:0005634)	protein phosphatase inhibitor activity (GO:0004864)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|liver(2)|lung(32)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	59	all_lung(29;0.00344)		BRCA - Breast invasive adenocarcinoma(7;2.76e-09)			CTGGACAGTCCTCCCAGACCT	0.612													C|||	102	0.0203674	0.0	0.0043	5008	,	,		16709	0.0377		0.0129	False		,,,				2504	0.0491				p.P217L		Atlas-SNP	.											.	PHACTR3	104	.	0			c.C650T						PASS	.	C	LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO,	12,4394	19.1+/-41.9	0,12,2191	42.0	41.0	41.0		641,527,650,527,	3.7	1.0	20	dbSNP_130	41	104,8496	55.6+/-116.7	0,104,4196	yes	missense,missense,missense,missense,intron	PHACTR3	NM_001199505.1,NM_001199506.1,NM_080672.3,NM_183244.1,NM_183246.1	98,98,98,98,	0,116,6387	TT,TC,CC		1.2093,0.2724,0.8919	benign,benign,benign,benign,	214/557,176/519,217/560,176/519,	58342349	116,12890	2203	4300	6503	SO:0001583	missense	116154	exon5			ACAGTCCTCCCAG	AJ311122	CCDS13480.1, CCDS13481.1, CCDS42895.1, CCDS56202.1	20q13.32-q13.33	2014-06-13	2004-05-20	2004-05-20	ENSG00000087495	ENSG00000087495		"""Phosphatase and actin regulators"""	15833	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 123"""	608725	"""chromosome 20 open reading frame 101"""	C20orf101		15107502	Standard	NM_001199505		Approved	PPP1R123	uc002yau.3	Q96KR7	OTTHUMG00000032869	ENST00000371015.1:c.650C>T	20.37:g.58342349C>T	ENSP00000360054:p.Pro217Leu	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	109	58	0.53211	NM_080672	B1AKX0|B1AN68|B1AN69|B2RB46|Q32P33|Q707P6|Q9H4T4	Missense_Mutation	SNP	ENST00000371015.1	37	CCDS13480.1	34	0.015567765567765568	0	0.0	2	0.0055248618784530384	23	0.04020979020979021	9	0.011873350923482849	C	15.45	2.838151	0.50951	0.002724	0.012093	ENSG00000087495	ENST00000359926;ENST00000371015;ENST00000541461;ENST00000355648;ENST00000395636	T;T;T;T;T	0.26518	1.73;1.77;1.79;1.79;1.79	4.7	3.74	0.42951	.	0.297029	0.25714	N	0.028791	T	0.04634	0.0126	L	0.33485	1.01	0.80722	D	1	B;B	0.18461	0.028;0.006	B;B	0.13407	0.009;0.004	T	0.03651	-1.1016	10	0.52906	T	0.07	-9.1105	12.1901	0.54266	0.0:0.9151:0.0:0.0849	.	217;214	Q96KR7;B1AKX0	PHAR3_HUMAN;.	L	214;217;176;176;176	ENSP00000353002:P214L;ENSP00000360054:P217L;ENSP00000442483:P176L;ENSP00000347866:P176L;ENSP00000378998:P176L	ENSP00000347866:P176L	P	+	2	0	PHACTR3	57775744	0.991000	0.36638	1.000000	0.80357	0.991000	0.79684	3.791000	0.55469	2.166000	0.68216	0.460000	0.39030	CCT	C|0.989;T|0.011	0.011	strong		0.612	PHACTR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079923.3	NM_080672	
BCL7A	605	hgsc.bcm.edu	37	12	122460048	122460048	+	Missense_Mutation	SNP	T	T	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:122460048T>G	ENST00000261822.4	+	1	257	c.51T>G	c.(49-51)gaT>gaG	p.D17E	BCL7A_ENST00000538010.1_Missense_Mutation_p.D17E|RP11-87C12.5_ENST00000538710.1_lincRNA	NM_001024808.1	NP_001019979.1	Q4VC05	BCL7A_HUMAN	B-cell CLL/lymphoma 7A	17					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)		CCAAAGATGATATCAAGAGGG	0.716			T	MYC	BNHL																																p.D17E	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.T51G						PASS	.						23.0	23.0	23.0					12																	122460048		2201	4297	6498	SO:0001583	missense	605	exon1			AGATGATATCAAG	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.51T>G	12.37:g.122460048T>G	ENSP00000261822:p.Asp17Glu	Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	47	8	0.170213	NM_020993	B4DJN6|B7ZB21|Q13843|Q14CT7	Missense_Mutation	SNP	ENST00000261822.4	37	CCDS53841.1	.	.	.	.	.	.	.	.	.	.	t	12.37	1.916812	0.33815	.	.	ENSG00000110987	ENST00000538010;ENST00000261822	T;T	0.62788	0.0;0.06	4.22	0.427	0.16489	.	0.000000	0.85682	U	0.000000	T	0.63248	0.2495	L	0.42245	1.32	0.46078	D	0.998856	D;P	0.63046	0.992;0.537	D;B	0.76071	0.987;0.391	T	0.58261	-0.7667	10	0.35671	T	0.21	.	3.1649	0.06533	0.1787:0.3071:0.0:0.5142	.	17;17	Q4VC05;Q4VC05-2	BCL7A_HUMAN;.	E	17	ENSP00000445868:D17E;ENSP00000261822:D17E	ENSP00000261822:D17E	D	+	3	2	BCL7A	120944431	1.000000	0.71417	0.996000	0.52242	0.059000	0.15707	1.804000	0.38873	-0.181000	0.10619	-0.570000	0.04155	GAT	.	.	none		0.716	BCL7A-002	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000401712.1		
FAM188B	84182	hgsc.bcm.edu	37	7	30818128	30818128	+	Silent	SNP	A	A	G	rs200053449	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:30818128A>G	ENST00000265299.6	+	2	221	c.144A>G	c.(142-144)cgA>cgG	p.R48R	INMT-FAM188B_ENST00000458257.1_3'UTR	NM_032222.2	NP_115598.2	Q4G0A6	F188B_HUMAN	family with sequence similarity 188, member B	48										endometrium(1)|large_intestine(5)|lung(19)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						ATGATCTTCGAAAGGTTTTGC	0.453													A|||	5	0.000998403	0.0	0.0014	5008	,	,		21808	0.0		0.004	False		,,,				2504	0.0				p.R48R		Atlas-SNP	.											FAM188B,colon,carcinoma,+2,4	FAM188B	62	4	0			c.A144G						PASS	.	A		4,3884		0,4,1940	123.0	120.0	121.0		144	-3.1	1.0	7		121	62,8220		0,62,4079	no	coding-synonymous	FAM188B	NM_032222.2		0,66,6019	GG,GA,AA		0.7486,0.1029,0.5423		48/758	30818128	66,12104	1944	4141	6085	SO:0001819	synonymous_variant	84182	exon2			TCTTCGAAAGGTT	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.144A>G	7.37:g.30818128A>G		Somatic	224	0	0		WXS	Illumina HiSeq	Phase_I	205	47	0.229268	NM_032222	Q71AZ7|Q9H6D2	Silent	SNP	ENST00000265299.6	37	CCDS43565.1																																																																																			A|0.998;G|0.002	0.002	strong		0.453	FAM188B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327962.1	NM_032222	
CES1	1066	hgsc.bcm.edu	37	16	55862712	55862712	+	Missense_Mutation	SNP	C	C	T	rs2307240	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:55862712C>T	ENST00000361503.4	-	2	354	c.224G>A	c.(223-225)aGc>aAc	p.S75N	CES1_ENST00000360526.3_Missense_Mutation_p.S76N|CES1_ENST00000422046.2_Missense_Mutation_p.S75N|CES1_ENST00000566555.1_5'Flank			P23141	EST1_HUMAN	carboxylesterase 1	75			S -> N (in dbSNP:rs2307240).	S -> A (in Ref. 14; AA sequence). {ECO:0000305}.	epithelial cell differentiation (GO:0030855)|metabolic process (GO:0008152)|response to toxic substance (GO:0009636)	endoplasmic reticulum (GO:0005783)	carboxylic ester hydrolase activity (GO:0052689)|methylumbelliferyl-acetate deacetylase activity (GO:0047374)								all cancers(182;0.13)|Epithelial(162;0.137)	Benzocaine(DB01086)|Capecitabine(DB01101)|Ciclesonide(DB01410)|Clopidogrel(DB00758)|Cyclandelate(DB04838)|Dabigatran etexilate(DB06695)|Indomethacin(DB00328)|Irinotecan(DB00762)|L-Carnitine(DB00583)|Mycophenolate mofetil(DB00688)|Oseltamivir(DB00198)|Probucol(DB01599)|Rufinamide(DB06201)|Tamoxifen(DB00675)|Trandolapril(DB00519)	CTTCACAAAGCTCCATGGTTC	0.542													.|||	252	0.0503195	0.0356	0.0231	5008	,	,		31596	0.0437		0.0606	False		,,,				2504	0.0859				p.S76N	NSCLC(162;1801 2756 42904 52896)	Atlas-SNP	.											.	CES1	78	.	0			c.G227A						PASS	.	C	ASN/SER,ASN/SER,ASN/SER	199,4197		0,199,1999	111.0	110.0	110.0		224,227,224	-9.0	0.1	16	dbSNP_100	110	454,8146		0,454,3846	yes	missense,missense,missense	CES1	NM_001025194.1,NM_001025195.1,NM_001266.4	46,46,46	0,653,5845	TT,TC,CC		5.2791,4.5268,5.0246	benign,benign,benign	75/568,76/569,75/567	55862712	653,12343	2198	4300	6498	SO:0001583	missense	1066	exon2			ACAAAGCTCCATG	BC012418	CCDS32450.1, CCDS45488.1, CCDS45489.1	16q22.2	2010-10-12	2010-10-12		ENSG00000198848	ENSG00000198848	3.1.1.1	"""Carboxylesterases"""	1863	protein-coding gene	gene with protein product	"""human monocyte/macrophage serine esterase 1"""	114835	"""carboxylesterase 1 (monocyte/macrophage serine esterase 1)"""			2070086, 20931200	Standard	XM_005255774		Approved	HMSE, CES2, HMSE1, SES1, CEH, CES1A1, CES1A2	uc002eil.3	P23141		ENST00000361503.4:c.224G>A	16.37:g.55862712C>T	ENSP00000355193:p.Ser75Asn	Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	109	32	0.293578	NM_001025195	A6NIM1|A8K3K8|A8K844|E9PAU8|P82127|Q00015|Q13657|Q14062|Q16737|Q16788|Q549X7|Q549X8|Q86UK2|Q96EE8|Q9UC52|Q9UDG8|Q9UK77|Q9ULY2	Missense_Mutation	SNP	ENST00000361503.4	37	CCDS45488.1	98	0.04487179487179487	18	0.036585365853658534	10	0.027624309392265192	25	0.043706293706293704	45	0.059366754617414245	.	5.134	0.210398	0.09757	0.045268	0.052791	ENSG00000198848	ENST00000360526;ENST00000361503;ENST00000422046	T;T;T	0.09723	3.13;3.13;2.95	4.48	-8.96	0.00761	Carboxylesterase, type B (1);	1.157410	0.06501	N	0.736348	T	0.00695	0.0023	L	0.34521	1.04	0.09310	N	1	B;B;B	0.11235	0.002;0.004;0.001	B;B;B	0.12837	0.008;0.008;0.005	T	0.31024	-0.9958	10	0.35671	T	0.21	.	8.6444	0.33996	0.0:0.2843:0.149:0.5667	rs2307240;rs52810343;rs2307240	75;75;76	E9PAU8;P23141;P23141-2	.;EST1_HUMAN;.	N	76;75;75	ENSP00000353720:S76N;ENSP00000355193:S75N;ENSP00000390492:S75N	ENSP00000353720:S76N	S	-	2	0	CES1	54420213	0.000000	0.05858	0.103000	0.21229	0.008000	0.06430	-0.082000	0.11304	-2.439000	0.00551	-0.515000	0.04445	AGC	C|0.956;T|0.044	0.044	strong		0.542	CES1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000433285.1	NM_001266	
MUC4	4585	hgsc.bcm.edu	37	3	195509171	195509171	+	Missense_Mutation	SNP	G	G	A	rs71634716		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195509171G>A	ENST00000463781.3	-	2	9739	c.9280C>T	c.(9280-9282)Ctt>Ttt	p.L3094F	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.L3094F	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.L3094F(1)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		ACTGAGGAAAGGCTGGTGACA	0.602																																					p.L3094F		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	1	Substitution - Missense(1)	kidney(1)	c.C9280T						scavenged	.						13.0	10.0	11.0					3																	195509171		666	1549	2215	SO:0001583	missense	4585	exon2			AGGAAAGGCTGGT	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.9280C>T	3.37:g.195509171G>A	ENSP00000417498:p.Leu3094Phe	Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	125	12	0.096	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	N	13.68	2.309979	0.40895	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.36520	1.4;1.25	.	.	.	.	.	.	.	.	T	0.17280	0.0415	N	0.14661	0.345	0.09310	N	0.999996	P	0.47604	0.898	B	0.40165	0.321	T	0.07462	-1.0771	7	.	.	.	.	3.4791	0.07595	1.0E-4:1.0E-4:0.5545:0.4454	.	2966	E7ESK3	.	F	3094	ENSP00000417498:L3094F;ENSP00000420243:L3094F	.	L	-	1	0	MUC4	196993950	.	.	0.015000	0.15790	0.000000	0.00434	.	.	0.497000	0.27926	0.000000	0.15137	CTT	.	.	none		0.602	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
LMF1	64788	hgsc.bcm.edu	37	16	961054	961054	+	Silent	SNP	C	C	T	rs2277892	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:961054C>T	ENST00000262301.11	-	4	558	c.540G>A	c.(538-540)acG>acA	p.T180T	LMF1_ENST00000568897.1_5'UTR|LMF1_ENST00000539379.1_3'UTR|LMF1_ENST00000399843.2_Silent_p.T180T|LMF1_ENST00000543238.1_Intron	NM_022773.2	NP_073610.2	Q96S06	LMF1_HUMAN	lipase maturation factor 1	180					chylomicron remnant clearance (GO:0034382)|ER to Golgi vesicle-mediated transport (GO:0006888)|positive regulation of lipoprotein lipase activity (GO:0051006)|protein glycosylation in Golgi (GO:0033578)|protein maturation (GO:0051604)|protein secretion (GO:0009306)|regulation of cholesterol metabolic process (GO:0090181)|regulation of triglyceride metabolic process (GO:0090207)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)		p.T180T(1)		central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|prostate(1)|stomach(2)|urinary_tract(1)	18		Hepatocellular(780;0.00308)				CCAGGAACCCCGTCTCCAGAA	0.532													C|||	1255	0.250599	0.4107	0.2421	5008	,	,		16912	0.244		0.0924	False		,,,				2504	0.2096				p.T180T		Atlas-SNP	.											LMF1,NS,carcinoma,0,1	LMF1	42	1	1	Substitution - coding silent(1)	stomach(1)	c.G540A						PASS	.	C		1382,2584		228,926,829	44.0	51.0	49.0		540	-9.1	0.2	16	dbSNP_100	49	894,7386		51,792,3297	no	coding-synonymous	LMF1	NM_022773.2		279,1718,4126	TT,TC,CC		10.7971,34.8462,18.5857		180/568	961054	2276,9970	1983	4140	6123	SO:0001819	synonymous_variant	64788	exon4			GAACCCCGTCTCC	AK022743	CCDS45373.1	16p13.3	2008-02-05	2007-11-29	2007-11-29	ENSG00000103227	ENSG00000103227			14154	protein-coding gene	gene with protein product		611761	"""chromosome 16 open reading frame 26"", ""transmembrane protein 112"""	C16orf26, TMEM112		11157797, 17994020	Standard	NM_022773		Approved	FLJ12681, JFP11, FLJ22302, TMEM112A	uc021tae.1	Q96S06	OTTHUMG00000047848	ENST00000262301.11:c.540G>A	16.37:g.961054C>T		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	65	19	0.292308	NM_022773	Q68CJ3|Q96FJ4|Q9H6G4|Q9H9K7	Silent	SNP	ENST00000262301.11	37	CCDS45373.1																																																																																			C|0.774;T|0.226	0.226	strong		0.532	LMF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000109071.3	NM_022773	
LRPPRC	10128	hgsc.bcm.edu	37	2	44201317	44201317	+	Missense_Mutation	SNP	A	A	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:44201317A>C	ENST00000260665.7	-	9	1184	c.1127T>G	c.(1126-1128)tTt>tGt	p.F376C	LRPPRC_ENST00000409659.1_Missense_Mutation_p.F376C|LRPPRC_ENST00000409946.1_Missense_Mutation_p.F376C	NM_133259.3	NP_573566.2	P42704	LPPRC_HUMAN	leucine-rich pentatricopeptide repeat containing	376					mitochondrion transport along microtubule (GO:0047497)|mRNA transport (GO:0051028)|negative regulation of mitochondrial RNA catabolic process (GO:0000961)|regulation of mitochondrial translation (GO:0070129)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	condensed nuclear chromosome (GO:0000794)|cytoskeleton (GO:0005856)|membrane (GO:0016020)|microtubule (GO:0005874)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|ribonucleoprotein complex (GO:0030529)	beta-tubulin binding (GO:0048487)|microtubule binding (GO:0008017)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)			breast(3)|endometrium(3)|kidney(5)|large_intestine(9)|lung(15)|ovary(2)|prostate(2)|skin(2)	41		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)				GTGTTGTAAAAAGAAACTGCC	0.358																																					p.F376C		Atlas-SNP	.											.	LRPPRC	105	.	0			c.T1127G						PASS	.						98.0	97.0	97.0					2																	44201317		2203	4300	6503	SO:0001583	missense	10128	exon9			TGTAAAAAGAAAC	M92439	CCDS33189.1	2p21	2012-02-24	2012-02-24		ENSG00000138095	ENSG00000138095			15714	protein-coding gene	gene with protein product		607544	"""Leigh syndrome, French-Canadian type (cytochrome oxidase deficiency)"""	LSFC		8012652, 8619474, 22045337	Standard	NM_133259		Approved	GP130, LRP130	uc002rtr.2	P42704	OTTHUMG00000152782	ENST00000260665.7:c.1127T>G	2.37:g.44201317A>C	ENSP00000260665:p.Phe376Cys	Somatic	347	0	0		WXS	Illumina HiSeq	Phase_I	555	64	0.115315	NM_133259	A0PJE3|A8K1V1|Q53PC0|Q53QN7|Q6ZUD8|Q7Z7A6|Q96D84	Missense_Mutation	SNP	ENST00000260665.7	37	CCDS33189.1	.	.	.	.	.	.	.	.	.	.	A	23.3	4.396960	0.83120	.	.	ENSG00000138095	ENST00000465633;ENST00000260665;ENST00000409946;ENST00000409659;ENST00000447246	T;T;T;T	0.70516	0.2;0.21;0.22;-0.49	6.08	6.08	0.98989	.	0.000000	0.85682	D	0.000000	D	0.83704	0.5312	M	0.82630	2.6	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.987;0.998	D	0.84275	0.0491	10	0.42905	T	0.14	-11.3834	11.417	0.49958	0.8652:0.0:0.0:0.1348	.	276;350;376	F5H4J6;C9JCA9;P42704	.;.;LPPRC_HUMAN	C	276;376;376;376;350	ENSP00000260665:F376C;ENSP00000386234:F376C;ENSP00000386562:F376C;ENSP00000403637:F350C	ENSP00000260665:F376C	F	-	2	0	LRPPRC	44054821	1.000000	0.71417	0.969000	0.41365	0.952000	0.60782	7.100000	0.76989	2.333000	0.79357	0.482000	0.46254	TTT	.	.	none		0.358	LRPPRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327823.1	NM_133259	
DUSP27	92235	hgsc.bcm.edu	37	1	167096931	167096931	+	Missense_Mutation	SNP	A	A	C	rs267746	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	88	0	0		WXS	Illumina HiSeq	Phase_I	65	33	0.507692	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	
ARHGAP42	143872	hgsc.bcm.edu	37	11	100846936	100846936	+	Silent	SNP	A	A	G	rs654593	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:100846936A>G	ENST00000298815.8	+	20	2007	c.2004A>G	c.(2002-2004)ccA>ccG	p.P668P	ARHGAP42_ENST00000524892.2_Silent_p.P634P	NM_152432.2	NP_689645.2	A6NI28	RHG42_HUMAN	Rho GTPase activating protein 42	668	Ser-rich.				signal transduction (GO:0007165)	intracellular (GO:0005622)	GTPase activator activity (GO:0005096)			endometrium(3)|skin(2)	5						TTGCAACCCCATCATCTTCCA	0.473													G|||	2874	0.573882	0.2511	0.6081	5008	,	,		20996	0.997		0.4344	False		,,,				2504	0.6933				p.P668P		Atlas-SNP	.											.	ARHGAP42	32	.	0			c.A2004G						PASS	.	G		471,913		83,305,304	54.0	43.0	46.0		2004	-7.1	0.1	11	dbSNP_83	46	1401,1781		313,775,503	no	coding-synonymous	ARHGAP42	NM_152432.2		396,1080,807	GG,GA,AA		44.0289,34.0318,40.9987		668/875	100846936	1872,2694	692	1591	2283	SO:0001819	synonymous_variant	143872	exon20			AACCCCATCATCT			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.2004A>G	11.37:g.100846936A>G		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	56	17	0.303571	NM_152432	Q96M56	Silent	SNP	ENST00000298815.8	37																																																																																				A|0.462;G|0.538	0.538	strong		0.473	ARHGAP42-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_152432	
BPIFA2	140683	hgsc.bcm.edu	37	20	31768363	31768363	+	Silent	SNP	C	C	T	rs34968847	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:31768363C>T	ENST00000253362.2	+	8	893	c.747C>T	c.(745-747)atC>atT	p.I249I	BPIFA2_ENST00000354932.5_Silent_p.I249I			Q96DR5	BPIA2_HUMAN	BPI fold containing family A, member 2	249						extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	lipopolysaccharide binding (GO:0001530)										AAACCCTCATCTGAAGAGGAC	0.498													C|||	350	0.0698882	0.1831	0.0418	5008	,	,		21402	0.0238		0.0427	False		,,,				2504	0.0123				p.I249I		Atlas-SNP	.											.	.	.	.	0			c.C747T						PASS	.	C		571,3835	255.2+/-260.5	42,487,1674	80.0	77.0	78.0		747	2.3	0.3	20	dbSNP_126	78	273,8327	103.6+/-164.7	5,263,4032	no	coding-synonymous	BPIFA2	NM_080574.2		47,750,5706	TT,TC,CC		3.1744,12.9596,6.4893		249/250	31768363	844,12162	2203	4300	6503	SO:0001819	synonymous_variant	140683	exon8			CCTCATCTGAAGA	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.747C>T	20.37:g.31768363C>T		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	122	64	0.52459	NM_080574	Q9BQQ0	Silent	SNP	ENST00000253362.2	37	CCDS13214.1																																																																																			C|0.940;T|0.060	0.060	strong		0.498	BPIFA2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257117.1	NM_080574	
USP38	84640	hgsc.bcm.edu	37	4	144130750	144130750	+	Silent	SNP	T	T	C	rs7670426	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:144130750T>C	ENST00000307017.4	+	7	1943	c.1437T>C	c.(1435-1437)aaT>aaC	p.N479N	USP38_ENST00000510377.1_Silent_p.N479N	NM_032557.5	NP_115946.2	Q8NB14	UBP38_HUMAN	ubiquitin specific peptidase 38	479	USP.				protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)		ubiquitin-specific protease activity (GO:0004843)			breast(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(9)|lung(12)|ovary(1)|pancreas(1)|prostate(2)|urinary_tract(3)	33	all_hematologic(180;0.158)					TAAATCTAAATGGGTGCAATT	0.303													T|||	413	0.0824681	0.1717	0.0605	5008	,	,		16958	0.0079		0.0765	False		,,,				2504	0.0603				p.N479N		Atlas-SNP	.											.	USP38	92	.	0			c.T1437C						PASS	.	T		690,3714	285.7+/-278.4	67,556,1579	64.0	69.0	68.0		1437	1.8	1.0	4	dbSNP_116	68	667,7933	167.5+/-219.3	38,591,3671	no	coding-synonymous	USP38	NM_032557.5		105,1147,5250	CC,CT,TT		7.7558,15.6676,10.4353		479/1043	144130750	1357,11647	2202	4300	6502	SO:0001819	synonymous_variant	84640	exon7			TCTAAATGGGTGC	AF211481	CCDS3758.1	4q31.1	2008-02-05	2005-08-08		ENSG00000170185	ENSG00000170185		"""Ubiquitin-specific peptidases"""	20067	protein-coding gene	gene with protein product			"""ubiquitin specific protease 38"""			12838346	Standard	NM_032557		Approved	KIAA1891, HP43.8KD	uc003ijb.3	Q8NB14	OTTHUMG00000161420	ENST00000307017.4:c.1437T>C	4.37:g.144130750T>C		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	55	21	0.381818	NM_032557	B3KX93|Q3ZCV1|Q8NDF5|Q96DK6|Q96PZ6|Q9BY55	Silent	SNP	ENST00000307017.4	37	CCDS3758.1																																																																																			T|0.908;C|0.092	0.092	strong		0.303	USP38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364869.1	NM_032557	
PLEKHG1	57480	hgsc.bcm.edu	37	6	151161018	151161018	+	Silent	SNP	A	A	G	rs17348890	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:151161018A>G	ENST00000358517.2	+	16	3355	c.3144A>G	c.(3142-3144)agA>agG	p.R1048R	PLEKHG1_ENST00000367328.1_Silent_p.R1048R			Q9ULL1	PKHG1_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 1	1048							Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(10)|lung(19)|ovary(5)|prostate(4)|stomach(1)|urinary_tract(3)	53			BRCA - Breast invasive adenocarcinoma(37;0.0923)	OV - Ovarian serous cystadenocarcinoma(155;6.69e-13)		TTGTATTCAGAGAGTCTCCCT	0.478													A|||	638	0.127396	0.0348	0.2133	5008	,	,		18591	0.1071		0.1461	False		,,,				2504	0.1933				p.R1048R		Atlas-SNP	.											.	PLEKHG1	97	.	0			c.A3144G						PASS	.	A		256,4150	146.1+/-180.8	2,252,1949	78.0	81.0	80.0		3144	2.2	1.0	6	dbSNP_123	80	1406,7194	271.7+/-289.7	138,1130,3032	yes	coding-synonymous	PLEKHG1	NM_001029884.1		140,1382,4981	GG,GA,AA		16.3488,5.8103,12.7787		1048/1386	151161018	1662,11344	2203	4300	6503	SO:0001819	synonymous_variant	57480	exon17			ATTCAGAGAGTCT	AB033035	CCDS34552.1	6q25.1	2013-01-11			ENSG00000120278	ENSG00000120278		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	20884	protein-coding gene	gene with protein product						10574462	Standard	XM_005267064		Approved	KIAA1209, ARHGEF41	uc003qny.1	Q9ULL1	OTTHUMG00000015824	ENST00000358517.2:c.3144A>G	6.37:g.151161018A>G		Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	92	62	0.673913	NM_001029884	Q5T1F2	Silent	SNP	ENST00000358517.2	37	CCDS34552.1																																																																																			A|0.883;G|0.117	0.117	strong		0.478	PLEKHG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042691.1		
EXOC3L2	90332	hgsc.bcm.edu	37	19	45728059	45728059	+	Missense_Mutation	SNP	T	T	C	rs10411314	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:45728059T>C	ENST00000252482.3	-	5	544	c.517A>G	c.(517-519)Aac>Gac	p.N173D	EXOC3L2_ENST00000413988.1_Missense_Mutation_p.N173D			Q2M3D2	EX3L2_HUMAN	exocyst complex component 3-like 2	173			N -> D (in dbSNP:rs10411314).		exocytosis (GO:0006887)	exocyst (GO:0000145)				endometrium(1)|large_intestine(5)|lung(3)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	12		all_neural(266;0.224)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.00883)		AACAGCAGGTTGGCCACGACA	0.687													C|||	501	0.10004	0.1732	0.036	5008	,	,		14516	0.123		0.0447	False		,,,				2504	0.0798				p.N173D		Atlas-SNP	.											.	EXOC3L2	30	.	0			c.A517G						PASS	.	C	ASP/ASN	654,3684		46,562,1561	29.0	24.0	26.0		517	4.6	0.8	19	dbSNP_119	26	351,8125		6,339,3893	yes	missense	EXOC3L2	NM_138568.3	23	52,901,5454	CC,CT,TT		4.1411,15.0761,7.843	benign	173/410	45728059	1005,11809	2169	4238	6407	SO:0001583	missense	90332	exon6			GCAGGTTGGCCAC	AK093466	CCDS12657.1	19q13.32	2011-07-07			ENSG00000130201	ENSG00000130201			30162	protein-coding gene	gene with protein product						21566143	Standard	NM_138568		Approved	FLJ36147, XTP7	uc002pay.1	Q2M3D2	OTTHUMG00000155018	ENST00000252482.3:c.517A>G	19.37:g.45728059T>C	ENSP00000252482:p.Asn173Asp	Somatic	390	0	0		WXS	Illumina HiSeq	Phase_I	373	168	0.450402	NM_138568	Q8N9W2|Q96GV2	Missense_Mutation	SNP	ENST00000252482.3	37	CCDS12657.1	215	0.09844322344322344	92	0.18699186991869918	11	0.03038674033149171	77	0.1346153846153846	35	0.04617414248021108	C	0.906	-0.720681	0.03182	0.150761	0.041411	ENSG00000130201	ENST00000252482;ENST00000413988	T;T	0.05382	3.45;3.45	4.55	4.55	0.56014	.	0.716298	0.13491	N	0.383977	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	0.36915	-0.9728	9	0.02654	T	1	.	9.1301	0.36839	0.0:0.8951:0.0:0.1049	rs10411314;rs59172754;rs10411314	173	Q2M3D2	EX3L2_HUMAN	D	173	ENSP00000252482:N173D;ENSP00000400713:N173D	ENSP00000252482:N173D	N	-	1	0	EXOC3L2	50419899	0.862000	0.29867	0.791000	0.31998	0.256000	0.26092	1.641000	0.37197	1.061000	0.40601	-0.215000	0.12644	AAC	T|0.896;C|0.104	0.104	strong		0.687	EXOC3L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338073.1	NM_138568	
ANKEF1	63926	hgsc.bcm.edu	37	20	10030188	10030188	+	Missense_Mutation	SNP	T	T	A	rs652633	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:10030188T>A	ENST00000378380.3	+	6	1300	c.971T>A	c.(970-972)cTg>cAg	p.L324Q	SNAP25-AS1_ENST00000421143.2_RNA|SNAP25-AS1_ENST00000603542.1_RNA|ANKEF1_ENST00000378392.1_Missense_Mutation_p.L324Q|ANKEF1_ENST00000488991.1_3'UTR	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	108	0	0		WXS	Illumina HiSeq	Phase_I	83	50	0.60241	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	
ATL1	51062	hgsc.bcm.edu	37	14	51054598	51054598	+	Silent	SNP	A	A	G	rs35014209	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:51054598A>G	ENST00000358385.6	+	2	325	c.84A>G	c.(82-84)ccA>ccG	p.P28P	ATL1_ENST00000441560.2_Silent_p.P28P|ATL1_ENST00000556478.2_3'UTR|ATL1_ENST00000354525.4_Silent_p.P28P|ATL1_ENST00000357032.3_Silent_p.P28P	NM_015915.4	NP_056999.2	Q8WXF7	ATLA1_HUMAN	atlastin GTPase 1	28					axonogenesis (GO:0007409)|cell death (GO:0008219)|endoplasmic reticulum organization (GO:0007029)|GTP catabolic process (GO:0006184)|protein homooligomerization (GO:0051260)	cell projection (GO:0042995)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|Golgi cis cisterna (GO:0000137)|integral component of membrane (GO:0016021)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)			central_nervous_system(1)|cervix(2)|large_intestine(4)|liver(1)|lung(6)|ovary(1)|skin(3)	18						AGGAGGAGCCAGTGAAAAAGG	0.453													A|||	822	0.164137	0.3623	0.1225	5008	,	,		20809	0.0655		0.1282	False		,,,				2504	0.0644				p.P28P		Atlas-SNP	.											.	ATL1	46	.	0			c.A84G						PASS	.	A	,,	1384,3022	456.1+/-351.2	209,966,1028	109.0	105.0	107.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	84,84,84	-1.2	1.0	14	dbSNP_126	107	1236,7364	247.4+/-275.4	96,1044,3160	no	coding-synonymous,coding-synonymous,coding-synonymous	ATL1	NM_001127713.1,NM_015915.4,NM_181598.3	,,	305,2010,4188	GG,GA,AA		14.3721,31.4117,20.1445	,,	28/554,28/559,28/554	51054598	2620,10386	2203	4300	6503	SO:0001819	synonymous_variant	51062	exon2			GGAGCCAGTGAAA	AF131801	CCDS9700.1, CCDS32077.1	14q21.3	2014-09-17	2008-09-17	2008-09-17	ENSG00000198513	ENSG00000198513			11231	protein-coding gene	gene with protein product	"""atlastin"""	606439	"""spastic paraplegia 3A (autosomal dominant)"""	SPG3, SPG3A		8252041, 7825576	Standard	NM_015915		Approved	FSP1, AD-FSP	uc001wyd.4	Q8WXF7	OTTHUMG00000140297	ENST00000358385.6:c.84A>G	14.37:g.51054598A>G		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	70	30	0.428571	NM_015915	A6NND5|A8K2C0|G5E9T1|O95890|Q69YH7|Q96FK0	Silent	SNP	ENST00000358385.6	37	CCDS9700.1																																																																																			A|0.807;G|0.193	0.193	strong		0.453	ATL1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000276884.2		
KLC1	3831	hgsc.bcm.edu	37	14	104166994	104166994	+	Silent	SNP	C	C	T	rs3212102	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:104166994C>T	ENST00000348520.6	+	14	1972	c.1653C>T	c.(1651-1653)ggC>ggT	p.G551G	XRCC3_ENST00000555832.1_5'Flank|XRCC3_ENST00000352127.7_Intron|KLC1_ENST00000554280.1_Missense_Mutation_p.A586V|KLC1_ENST00000555836.1_Silent_p.G608G|XRCC3_ENST00000445556.1_Intron|XRCC3_ENST00000554913.1_Intron|KLC1_ENST00000334553.6_Silent_p.G617G|XRCC3_ENST00000553264.1_Intron|KLC1_ENST00000452929.2_Missense_Mutation_p.A595V|XRCC3_ENST00000555055.1_Intron|XRCC3_ENST00000554974.1_Intron|KLC1_ENST00000557450.1_Silent_p.G542G	NM_182923.3	NP_891553.2	Q07866	KLC1_HUMAN	kinesin light chain 1	551					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)				ATCTCCAGGGCGTCTCTGGCC	0.637													C|||	48	0.00958466	0.0008	0.0216	5008	,	,		18081	0.0		0.0258	False		,,,				2504	0.0061				p.A595V		Atlas-SNP	.											.	KLC1	54	.	0			c.C1784T						PASS	.	C	,,,,VAL/ALA	21,3961		1,19,1971	47.0	53.0	51.0		,,,1653,1784	-1.9	0.0	14	dbSNP_105	51	195,8115		3,189,3963	yes	intron,intron,intron,coding-synonymous,missense	KLC1,XRCC3	NM_001100118.1,NM_001100119.1,NM_005432.3,NM_182923.3,NM_001130107.1	,,,,64	4,208,5934	TT,TC,CC		2.3466,0.5274,1.7572	,,,,benign	,,,551/574,595/619	104166994	216,12076	1991	4155	6146	SO:0001819	synonymous_variant	3831	exon15			CCAGGGCGTCTCT	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.1653C>T	14.37:g.104166994C>T		Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	53	38	0.716981	NM_001130107	A6NF62|F8VTM4|Q7RTM2|Q7RTM3|Q7RTM5|Q7RTP9|Q7RTQ3|Q7RTQ5|Q7RTQ6|Q86SF5|Q86TF5|Q86V74|Q86V75|Q86V76|Q86V77|Q86V78|Q86V79|Q96H62	Missense_Mutation	SNP	ENST00000348520.6	37	CCDS41996.1	28	0.01282051282051282	0	0.0	12	0.03314917127071823	0	0.0	16	0.021108179419525065	C	8.352	0.831228	0.16820	0.005274	0.023466	ENSG00000126214	ENST00000554280;ENST00000452929	T;T	0.75938	-0.98;-0.98	4.36	-1.91	0.07641	.	.	.	.	.	T	0.35537	0.0935	.	.	.	0.32378	N	0.554939	B	0.18610	0.029	B	0.09377	0.004	T	0.49437	-0.8940	8	0.56958	D	0.05	.	8.0117	0.30357	0.0:0.5295:0.0:0.4705	rs3212102;rs60044973;rs3212102	595	F8VTM4	.	V	586;595	ENSP00000451242:A586V;ENSP00000414982:A595V	ENSP00000414982:A595V	A	+	2	0	KLC1	103236747	0.002000	0.14202	0.029000	0.17559	0.073000	0.16967	-0.533000	0.06157	-0.275000	0.09219	0.561000	0.74099	GCG	C|0.982;T|0.018	0.018	strong		0.637	KLC1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000402947.2	NM_005552	
ALLC	55821	hgsc.bcm.edu	37	2	3729254	3729254	+	Missense_Mutation	SNP	C	C	T	rs13426642	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:3729254C>T	ENST00000252505.3	+	6	491	c.329C>T	c.(328-330)aCc>aTc	p.T110I		NM_018436.3	NP_060906.3	Q8N6M5	ALLC_HUMAN	allantoicase	129					allantoin catabolic process (GO:0000256)		allantoicase activity (GO:0004037)			breast(4)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(12)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	30	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.088)	all_cancers(51;0.24)		OV - Ovarian serous cystadenocarcinoma(76;0.088)|all cancers(51;0.151)|Epithelial(75;0.206)		GAAAGAGGAACCAGGACAGGA	0.443										HNSCC(21;0.051)			T|||	958	0.191294	0.3487	0.1326	5008	,	,		18597	0.13		0.174	False		,,,				2504	0.1012				p.T110I		Atlas-SNP	.											.	ALLC	61	.	0			c.C329T						PASS	.	T	ILE/THR	1109,2681		150,809,936	53.0	56.0	55.0		329	-1.7	0.0	2	dbSNP_121	55	1577,6649		159,1259,2695	yes	missense	ALLC	NM_018436.3	89	309,2068,3631	TT,TC,CC		19.1709,29.2612,22.3535	benign	110/392	3729254	2686,9330	1895	4113	6008	SO:0001583	missense	55821	exon6			GAGGAACCAGGAC	AF215924	CCDS46223.1	2p25.3	2008-02-05			ENSG00000151360	ENSG00000151360			17377	protein-coding gene	gene with protein product		612396				11054555	Standard	NM_018436		Approved	ALC	uc010ewt.3	Q8N6M5	OTTHUMG00000151485	ENST00000252505.3:c.329C>T	2.37:g.3729254C>T	ENSP00000252505:p.Thr110Ile	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	118	72	0.610169	NM_018436	Q53T95|Q5RL81|Q96RE6|Q9NZA7	Missense_Mutation	SNP	ENST00000252505.3	37	CCDS46223.1	428	0.19597069597069597	175	0.3556910569105691	53	0.1464088397790055	69	0.12062937062937062	131	0.17282321899736147	T	2.425	-0.332270	0.05314	0.292612	0.191709	ENSG00000151360	ENST00000252505	.	.	.	4.98	-1.69	0.08186	Allantoicase domain (1);Galactose-binding domain-like (1);	1.431930	0.04091	N	0.311285	T	0.00012	0.0000	N	0.00289	-1.7	0.80722	P	0.0	B	0.02656	0.0	B	0.06405	0.002	T	0.40403	-0.9565	8	0.36615	T	0.2	-6.0446	1.6428	0.02756	0.148:0.3466:0.153:0.3524	rs13426642;rs17856846;rs59065366;rs13426642	129	Q8N6M5	ALLC_HUMAN	I	110	.	ENSP00000252505:T110I	T	+	2	0	ALLC	3707129	0.000000	0.05858	0.005000	0.12908	0.006000	0.05464	-0.729000	0.04920	-0.411000	0.07530	-0.269000	0.10298	ACC	C|0.801;T|0.199	0.199	strong		0.443	ALLC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322855.1		
SLC16A3	9123	hgsc.bcm.edu	37	17	80195163	80195163	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:80195163C>T	ENST00000581287.1	+	3	2839	c.517C>T	c.(517-519)Cgc>Tgc	p.R173C	SLC16A3_ENST00000582743.1_Missense_Mutation_p.R173C|SLC16A3_ENST00000392339.1_Missense_Mutation_p.R173C|SLC16A3_ENST00000392341.1_Missense_Mutation_p.R173C	NM_001206951.1|NM_001206952.1	NP_001193880.1|NP_001193881.1	O15427	MOT4_HUMAN	solute carrier family 16 (monocarboxylate transporter), member 3	173					blood coagulation (GO:0007596)|cellular metabolic process (GO:0044237)|leukocyte migration (GO:0050900)|monocarboxylic acid transport (GO:0015718)|pyruvate metabolic process (GO:0006090)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	actin cytoskeleton (GO:0015629)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nuclear membrane (GO:0031965)|plasma membrane (GO:0005886)	monocarboxylic acid transmembrane transporter activity (GO:0008028)|poly(A) RNA binding (GO:0044822)|secondary active monocarboxylate transmembrane transporter activity (GO:0015355)|symporter activity (GO:0015293)			endometrium(2)|kidney(1)|lung(3)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	9	Breast(20;0.00285)|all_neural(118;0.0804)|Lung NSC(278;0.128)|all_lung(278;0.145)|Ovarian(332;0.227)		OV - Ovarian serous cystadenocarcinoma(97;0.00463)|BRCA - Breast invasive adenocarcinoma(99;0.0149)		Gamma Hydroxybutyric Acid(DB01440)|Niacin(DB00627)|Pyruvic acid(DB00119)	GCTGCAGGACCGCTACGGCTG	0.701																																					p.R173C	Pancreas(52;652 1135 19190 37282 52456)	Atlas-SNP	.											.	SLC16A3	19	.	0			c.C517T						PASS	.						6.0	6.0	6.0					17																	80195163		2142	4199	6341	SO:0001583	missense	9123	exon4			CAGGACCGCTACG	U81800	CCDS11804.1	17q25.3	2013-07-18	2013-07-18		ENSG00000141526	ENSG00000141526		"""Solute carriers"""	10924	protein-coding gene	gene with protein product		603877	"""solute carrier family 16 (monocarboxylic acid transporters), member 3"", ""solute carrier family 16, member 3 (monocarboxylic acid transporter 4)"""			9425115	Standard	NM_004207		Approved	MCT3, MCT4	uc021ufm.1	O15427	OTTHUMG00000178832	ENST00000581287.1:c.517C>T	17.37:g.80195163C>T	ENSP00000463978:p.Arg173Cys	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	108	34	0.314815	NM_001206950	B3KXG8|Q2M1P8	Missense_Mutation	SNP	ENST00000581287.1	37	CCDS11804.1	.	.	.	.	.	.	.	.	.	.	C	11.76	1.735148	0.30774	.	.	ENSG00000141526	ENST00000392341;ENST00000392339	T;T	0.37584	1.19;1.19	5.69	4.71	0.59529	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.834666	0.11530	N	0.554741	T	0.41419	0.1158	L	0.40543	1.245	0.33977	D	0.647467	P;D	0.53462	0.919;0.96	P;P	0.53062	0.717;0.657	T	0.49293	-0.8955	10	0.56958	D	0.05	.	9.2009	0.37258	0.0:0.6825:0.2372:0.0802	.	173;173	Q53G91;O15427	.;MOT4_HUMAN	C	173	ENSP00000376152:R173C;ENSP00000376150:R173C	ENSP00000376150:R173C	R	+	1	0	SLC16A3	77788452	0.010000	0.17322	0.980000	0.43619	0.812000	0.45895	0.633000	0.24598	2.696000	0.92011	0.655000	0.94253	CGC	.	.	none		0.701	SLC16A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443498.1	NM_004207	
OSBP2	23762	hgsc.bcm.edu	37	22	31091139	31091139	+	Silent	SNP	A	A	G	rs13053290	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:31091139A>G	ENST00000332585.6	+	1	347	c.243A>G	c.(241-243)gaA>gaG	p.E81E	OSBP2_ENST00000382310.3_Silent_p.E81E|OSBP2_ENST00000407373.1_Intron|OSBP2_ENST00000446658.2_Silent_p.E81E|OSBP2_ENST00000403222.3_Intron	NM_001282739.1|NM_001282740.1|NM_001282741.1|NM_001282742.1|NM_030758.3	NP_001269668.1|NP_001269669.1|NP_001269670.1|NP_001269671.1|NP_110385.1	Q969R2	OSBP2_HUMAN	oxysterol binding protein 2	81					lipid transport (GO:0006869)	membrane (GO:0016020)	cholesterol binding (GO:0015485)			breast(3)|central_nervous_system(1)|endometrium(2)|kidney(2)|lung(6)|ovary(1)|skin(3)|urinary_tract(1)	19						CAAGATCGGAACCTGTGTCCG	0.682													g|||	1261	0.251797	0.525	0.2104	5008	,	,		11206	0.004		0.2972	False		,,,				2504	0.1207				p.E81E		Atlas-SNP	.											OSBP2,NS,carcinoma,0,1	OSBP2	52	1	0			c.A243G						scavenged	.	T		1980,2314		487,1006,654	30.0	40.0	37.0		243	-0.1	0.0	22	dbSNP_121	37	2443,6075		333,1777,2149	no	coding-synonymous	OSBP2	NM_030758.3		820,2783,2803	GG,GA,AA		28.6804,46.1109,34.5223		81/917	31091139	4423,8389	2147	4259	6406	SO:0001819	synonymous_variant	23762	exon1			ATCGGAACCTGTG		CCDS43002.1, CCDS63448.1, CCDS63449.1, CCDS63450.1, CCDS63451.1	22q12.2	2013-01-10			ENSG00000184792	ENSG00000184792		"""Oxysterol binding proteins"", ""Pleckstrin homology (PH) domain containing"""	8504	protein-coding gene	gene with protein product		606729		OSBPL1		10591208, 11278871, 11802775	Standard	NM_001282738		Approved	KIAA1664, ORP-4, ORP4	uc003aiy.1	Q969R2	OTTHUMG00000151153	ENST00000332585.6:c.243A>G	22.37:g.31091139A>G		Somatic	170	2	0.0117647		WXS	Illumina HiSeq	Phase_I	118	118	1	NM_030758	B0QYG1|B4DK24|B4DKE4|B4DTR3|F5H2A3|O60396|Q0VF99|Q8NA37|Q9BY96|Q9BZF0	Silent	SNP	ENST00000332585.6	37	CCDS43002.1																																																																																			A|0.726;G|0.274	0.274	strong		0.682	OSBP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000321547.2	NM_030758	
PRRC2C	23215	hgsc.bcm.edu	37	1	171486912	171486912	+	Missense_Mutation	SNP	G	G	A	rs10913157	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:171486912G>A	ENST00000338920.4	+	6	940	c.703G>A	c.(703-705)Gct>Act	p.A235T	PRRC2C_ENST00000367742.3_Missense_Mutation_p.A237T|RNU6-773P_ENST00000364256.1_RNA|PRRC2C_ENST00000476522.1_3'UTR|PRRC2C_ENST00000426496.2_Missense_Mutation_p.A235T|PRRC2C_ENST00000392078.3_Missense_Mutation_p.A237T	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	122	0	0		WXS	Illumina HiSeq	Phase_I	75	42	0.56	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	
DHRS2	10202	hgsc.bcm.edu	37	14	24114437	24114437	+	Missense_Mutation	SNP	T	T	A	rs146187363	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:24114437T>A	ENST00000250383.6	+	9	1294	c.818T>A	c.(817-819)gTg>gAg	p.V273E	DHRS2_ENST00000344777.7_Missense_Mutation_p.W277R	NM_005794.3	NP_005785.1	Q13268	DHRS2_HUMAN	dehydrogenase/reductase (SDR family) member 2	273					C21-steroid hormone metabolic process (GO:0008207)|cellular response to oxidative stress (GO:0034599)|myeloid dendritic cell differentiation (GO:0043011)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|oxidation-reduction process (GO:0055114)|response to toxic substance (GO:0009636)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)	carbonyl reductase (NADPH) activity (GO:0004090)			endometrium(1)|large_intestine(5)|lung(5)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	14				GBM - Glioblastoma multiforme(265;0.00659)		AACATTGCGGTGGCAGGCTAC	0.597													t|||	14	0.00279553	0.0	0.0	5008	,	,		18947	0.0		0.0	False		,,,				2504	0.0143				p.W277R		Atlas-SNP	.											.	DHRS2	78	.	0			c.T829A						PASS	.		GLU/VAL,ARG/TRP	0,4406		0,0,2203	109.0	93.0	99.0		818,829	4.4	0.7	14	dbSNP_134	99	2,8598	2.2+/-6.3	0,2,4298	yes	missense,missense	DHRS2	NM_005794.3,NM_182908.4	121,101	0,2,6501	AA,AT,TT		0.0233,0.0,0.0154	probably-damaging,probably-damaging	273/281,277/301	24114437	2,13004	2203	4300	6503	SO:0001583	missense	10202	exon9			TTGCGGTGGCAGG		CCDS9604.1, CCDS41927.1	14q11.2	2011-09-14			ENSG00000100867	ENSG00000100867		"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"""	18349	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 25C, member 1"""	615194				7556196, 11944995, 16685466, 19027726	Standard	NM_182908		Approved	HEP27, SDR25C1	uc001wkt.4	Q13268	OTTHUMG00000028771	ENST00000250383.6:c.818T>A	14.37:g.24114437T>A	ENSP00000250383:p.Val273Glu	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	84	38	0.452381	NM_182908	D3DS54|Q53GS4|Q7Z789|Q9H2R2	Missense_Mutation	SNP	ENST00000250383.6	37	CCDS9604.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	15.18|15.18	2.758232|2.758232	0.49468|0.49468	0.0|0.0	2.33E-4|2.33E-4	ENSG00000100867|ENSG00000100867	ENST00000250383|ENST00000344777	T|D	0.39056|0.82526	1.1|-1.62	4.42|4.42	4.42|4.42	0.53409|0.53409	.|.	.|0.473111	.|0.23616	.|N	.|0.046297	D|D	0.88919|0.88919	0.6568|0.6568	.|.	.|.	.|.	0.30039|0.30039	N|N	0.812755|0.812755	D|D	0.89917|0.89917	1.0|1.0	D|D	0.91635|0.69479	0.999|0.964	D|D	0.85869|0.85869	0.1415|0.1415	8|9	0.87932|0.56958	D|D	0|0.05	.|.	11.9261|11.9261	0.52820|0.52820	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	273|255	D3DS54|Q13268-2	.|.	E|R	273|277	ENSP00000250383:V273E|ENSP00000344674:W277R	ENSP00000250383:V273E|ENSP00000344674:W277R	V|W	+|+	2|1	0|0	DHRS2|DHRS2	23184277|23184277	1.000000|1.000000	0.71417|0.71417	0.707000|0.707000	0.30419|0.30419	0.018000|0.018000	0.09664|0.09664	6.595000|6.595000	0.74109|0.74109	1.981000|1.981000	0.57761|0.57761	0.455000|0.455000	0.32223|0.32223	GTG|TGG	T|1.000;A|0.000	0.000	weak		0.597	DHRS2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000071842.2	NM_182908	
YLPM1	56252	hgsc.bcm.edu	37	14	75248652	75248652	+	Missense_Mutation	SNP	C	C	G	rs45617140	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:75248652C>G	ENST00000552421.1	+	4	2030	c.1906C>G	c.(1906-1908)Cct>Gct	p.P636A	YLPM1_ENST00000325680.7_Missense_Mutation_p.P636A|YLPM1_ENST00000238571.3_Missense_Mutation_p.P441A			P49750	YLPM1_HUMAN	YLP motif containing 1	0					regulation of telomere maintenance (GO:0032204)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)			breast(4)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(12)|lung(24)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	62			KIRC - Kidney renal clear cell carcinoma(43;0.238)	BRCA - Breast invasive adenocarcinoma(234;0.00162)		AATACCTCCCCCTGGAGTTCC	0.557													C|||	217	0.0433307	0.0045	0.0418	5008	,	,		18860	0.001		0.0994	False		,,,				2504	0.0828				p.P636A		Atlas-SNP	.											.	YLPM1	298	.	0			c.C1906G						PASS	.	C	ALA/PRO	67,3957		1,65,1946	87.0	91.0	89.0		1906	6.1	1.0	14	dbSNP_127	89	799,7543		35,729,3407	yes	missense	YLPM1	NM_019589.2	27	36,794,5353	GG,GC,CC		9.578,1.665,7.0031	possibly-damaging	636/2147	75248652	866,11500	2012	4171	6183	SO:0001583	missense	56252	exon4			CCTCCCCCTGGAG	AK090435	CCDS45135.1	14q24.3	2014-06-13	2004-07-15	2004-07-15	ENSG00000119596	ENSG00000119596			17798	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 169"""		"""chromosome 14 open reading frame 170"""	C14orf170		7596406	Standard	NM_019589		Approved	ZAP, PPP1R169	uc001xqj.4	P49750	OTTHUMG00000172503	ENST00000552421.1:c.1906C>G	14.37:g.75248652C>G	ENSP00000447921:p.Pro636Ala	Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	144	70	0.486111	NM_019589	P49752|Q96I64|Q9P1V7	Missense_Mutation	SNP	ENST00000552421.1	37		111	0.050824175824175824	5	0.01016260162601626	19	0.052486187845303865	1	0.0017482517482517483	86	0.11345646437994723	C	12.49	1.954788	0.34471	0.01665	0.09578	ENSG00000119596	ENST00000552421;ENST00000325680;ENST00000238571;ENST00000423680	.	.	.	6.08	6.08	0.98989	.	0.000000	0.64402	D	0.000002	T	0.00875	0.0029	L	0.43152	1.355	0.31358	P	0.6816800000000001	P	0.47191	0.891	P	0.45610	0.487	T	0.07083	-1.0791	8	0.07175	T	0.84	-9.5661	11.8778	0.52558	0.0:0.8913:0.0:0.1087	rs45617140	636	P49750-4	.	A	636;636;441;349	.	ENSP00000238571:P441A	P	+	1	0	YLPM1	74318405	0.621000	0.27077	1.000000	0.80357	0.843000	0.47879	1.279000	0.33191	2.894000	0.99253	0.591000	0.81541	CCT	C|0.936;G|0.064	0.064	strong		0.557	YLPM1-008	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000404450.1	NM_019589	
PRDM9	56979	hgsc.bcm.edu	37	5	23527492	23527492	+	Missense_Mutation	SNP	A	A	T	rs112815500	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:23527492A>T	ENST00000296682.3	+	11	2477	c.2295A>T	c.(2293-2295)agA>agT	p.R765S		NM_020227.2	NP_064612.2	Q9NQV7	PRDM9_HUMAN	PR domain containing 9	765					meiotic gene conversion (GO:0006311)|positive regulation of meiosis I (GO:0060903)|positive regulation of reciprocal meiotic recombination (GO:0010845)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)	histone methyltransferase activity (H3-K4 specific) (GO:0042800)|metal ion binding (GO:0046872)|recombination hotspot binding (GO:0010844)|sequence-specific DNA binding (GO:0043565)	p.R765S(2)		NS(1)|breast(1)|central_nervous_system(3)|endometrium(15)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(27)|lung(87)|ovary(6)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(11)	172						ACCTCCTCAGACACCAGAGGA	0.572										HNSCC(3;0.000094)																											p.R765S		Atlas-SNP	.											PRDM9,NS,haematopoietic_neoplasm,0,2	PRDM9	344	2	2	Substitution - Missense(2)	haematopoietic_and_lymphoid_tissue(1)|lung(1)	c.A2295T						PASS	.						59.0	79.0	72.0					5																	23527492		2156	4296	6452	SO:0001583	missense	56979	exon11			CCTCAGACACCAG	AF275816	CCDS43307.1	5p14.2	2014-06-03			ENSG00000164256	ENSG00000164256		"""-"", ""Zinc fingers, C2H2-type"""	13994	protein-coding gene	gene with protein product	"""PR-domain containing protein 9"""	609760	"""minisatellite binding protein 3, 115kDa"", ""minisatellite binding protein 3 (115kD)"""	MSBP3		10668202, 2062643, 24634223	Standard	NM_020227		Approved	PFM6, ZNF899	uc003jgo.3	Q9NQV7	OTTHUMG00000161918	ENST00000296682.3:c.2295A>T	5.37:g.23527492A>T	ENSP00000296682:p.Arg765Ser	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	83	13	0.156627	NM_020227	B4DX22|Q27Q50	Missense_Mutation	SNP	ENST00000296682.3	37	CCDS43307.1	.	.	.	.	.	.	.	.	.	.	T	0.004	-2.270564	0.00257	.	.	ENSG00000164256	ENST00000296682	T	0.25749	1.78	2.95	-5.91	0.02269	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.13372	0.0324	L	0.38838	1.175	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.38845	-0.9642	9	0.08179	T	0.78	.	6.3167	0.21194	0.6783:0.0:0.1377:0.184	.	765	Q9NQV7	PRDM9_HUMAN	S	765	ENSP00000296682:R765S	ENSP00000296682:R765S	R	+	3	2	PRDM9	23563249	0.000000	0.05858	0.002000	0.10522	0.003000	0.03518	-9.315000	0.00012	-2.336000	0.00628	-2.032000	0.00423	AGA	A|0.998;T|0.002	0.002	strong		0.572	PRDM9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366375.1	NM_020227	
TOP2A	7153	hgsc.bcm.edu	37	17	38545824	38545824	+	Missense_Mutation	SNP	C	C	A	rs11540720	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:38545824C>A	ENST00000423485.1	-	35	4701	c.4543G>T	c.(4543-4545)Gca>Tca	p.A1515S	Y_RNA_ENST00000410949.1_RNA	NM_001067.3	NP_001058.2	P11388	TOP2A_HUMAN	topoisomerase (DNA) II alpha 170kDa	1515			A -> S (in dbSNP:rs11540720).		apoptotic chromosome condensation (GO:0030263)|ATP catabolic process (GO:0006200)|cellular response to DNA damage stimulus (GO:0006974)|chromosome segregation (GO:0007059)|DNA ligation (GO:0006266)|DNA topological change (GO:0006265)|DNA unwinding involved in DNA replication (GO:0006268)|embryonic cleavage (GO:0040016)|hematopoietic progenitor cell differentiation (GO:0002244)|mitotic cell cycle (GO:0000278)|mitotic DNA integrity checkpoint (GO:0044774)|mitotic recombination (GO:0006312)|positive regulation of apoptotic process (GO:0043065)|positive regulation of single stranded viral RNA replication via double stranded DNA intermediate (GO:0045870)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of viral genome replication (GO:0045070)|resolution of meiotic recombination intermediates (GO:0000712)|sister chromatid segregation (GO:0000819)	condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|DNA topoisomerase complex (ATP-hydrolyzing) (GO:0009330)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA binding, bending (GO:0008301)|DNA topoisomerase type II (ATP-hydrolyzing) activity (GO:0003918)|DNA-dependent ATPase activity (GO:0008094)|drug binding (GO:0008144)|enzyme binding (GO:0019899)|histone deacetylase binding (GO:0042826)|magnesium ion binding (GO:0000287)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase C binding (GO:0005080)|ubiquitin binding (GO:0043130)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(9)|ovary(5)|pancreas(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)	39		Breast(137;0.00328)	STAD - Stomach adenocarcinoma(5;0.00183)		Amsacrine(DB00276)|Ciprofloxacin(DB00537)|Dactinomycin(DB00970)|Daunorubicin(DB00694)|Dexrazoxane(DB00380)|Doxorubicin(DB00997)|Enoxacin(DB00467)|Epirubicin(DB00445)|Etoposide(DB00773)|Fleroxacin(DB04576)|Idarubicin(DB01177)|Levofloxacin(DB01137)|Lomefloxacin(DB00978)|Lucanthone(DB04967)|Mitoxantrone(DB01204)|Moxifloxacin(DB00218)|Norfloxacin(DB01059)|Ofloxacin(DB01165)|Pefloxacin(DB00487)|Podofilox(DB01179)|Sparfloxacin(DB01208)|Teniposide(DB00444)|Trovafloxacin(DB00685)|Valrubicin(DB00385)	GGTTTCTTTGCCCGTACAGAT	0.413													C|||	171	0.0341454	0.0998	0.0173	5008	,	,		17081	0.0		0.0209	False		,,,				2504	0.0061				p.A1515S		Atlas-SNP	.											.	TOP2A	124	.	0			c.G4543T						PASS	.	C	SER/ALA	296,3402		10,276,1563	54.0	51.0	52.0		4543	2.2	0.0	17	dbSNP_120	52	181,7997		4,173,3912	yes	missense	TOP2A	NM_001067.3	99	14,449,5475	AA,AC,CC		2.2133,8.0043,4.0165	possibly-damaging	1515/1532	38545824	477,11399	1849	4089	5938	SO:0001583	missense	7153	exon35			TCTTTGCCCGTAC		CCDS45672.1	17q21-q22	2008-08-06	2002-08-29		ENSG00000131747	ENSG00000131747	5.99.1.2		11989	protein-coding gene	gene with protein product		126430	"""topoisomerase (DNA) II alpha (170kD)"""	TOP2			Standard	NM_001067		Approved		uc002huq.3	P11388	OTTHUMG00000155008	ENST00000423485.1:c.4543G>T	17.37:g.38545824C>A	ENSP00000411532:p.Ala1515Ser	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	112	60	0.535714	NM_001067	B2RTS1|Q71UN1|Q71UQ5|Q9HB24|Q9HB25|Q9HB26|Q9UP44|Q9UQP9	Missense_Mutation	SNP	ENST00000423485.1	37	CCDS45672.1	82	0.037545787545787544	60	0.12195121951219512	9	0.024861878453038673	0	0.0	13	0.017150395778364115	C	10.07	1.250112	0.22880	0.080043	0.022133	ENSG00000131747	ENST00000423485;ENST00000269577;ENST00000348049;ENST00000357601	T	0.53423	0.62	5.35	2.21	0.28008	DTHCT (1);	0.378221	0.30185	N	0.010201	T	0.00524	0.0017	L	0.53249	1.67	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.10450	0.005	T	0.06862	-1.0803	9	0.48119	T	0.1	.	2.2969	0.04153	0.2593:0.461:0.1266:0.1532	rs11540720;rs11540720	1515	P11388	TOP2A_HUMAN	S	1515;1595;1538;1552	ENSP00000411532:A1515S	ENSP00000269577:A1595S	A	-	1	0	TOP2A	35799350	0.031000	0.19500	0.044000	0.18714	0.511000	0.34104	0.139000	0.16036	0.439000	0.26476	0.655000	0.94253	GCA	C|0.957;A|0.043	0.043	strong		0.413	TOP2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338035.1		
RSF1	51773	hgsc.bcm.edu	37	11	77378505	77378505	+	Silent	SNP	A	A	G	rs28930682	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:77378505A>G	ENST00000308488.6	-	16	4085	c.3783T>C	c.(3781-3783)gaT>gaC	p.D1261D	RSF1_ENST00000360355.2_Silent_p.D1230D|RSF1_ENST00000480887.1_Silent_p.D1009D			Q96T23	RSF1_HUMAN	remodeling and spacing factor 1	1261					CENP-A containing nucleosome assembly (GO:0034080)|chromatin remodeling (GO:0006338)|DNA-templated transcription, initiation (GO:0006352)|negative regulation of DNA binding (GO:0043392)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome assembly (GO:0006334)|nucleosome positioning (GO:0016584)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of viral transcription (GO:0050434)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|RSF complex (GO:0031213)	histone binding (GO:0042393)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(2)|endometrium(3)|kidney(4)|large_intestine(9)|lung(14)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	43	all_cancers(14;1.54e-17)|all_epithelial(13;4.06e-20)|Ovarian(111;0.152)		Epithelial(5;3e-50)|all cancers(3;6.37e-47)|BRCA - Breast invasive adenocarcinoma(5;9.82e-31)			TAGCTAGCTCATCATCTTCAG	0.443													G|||	983	0.196286	0.329	0.2147	5008	,	,		19989	0.1736		0.0984	False		,,,				2504	0.1278				p.D1261D		Atlas-SNP	.											.	RSF1	105	.	0			c.T3783C						PASS	.	G		1327,3073		199,929,1072	57.0	59.0	58.0		3783	2.6	1.0	11	dbSNP_125	58	823,7761		36,751,3505	no	coding-synonymous	RSF1	NM_016578.3		235,1680,4577	GG,GA,AA		9.5876,30.1591,16.5588		1261/1442	77378505	2150,10834	2200	4292	6492	SO:0001819	synonymous_variant	51773	exon16			TAGCTCATCATCT	AF380176, AF227948	CCDS8253.1	11q14.1	2013-01-28	2006-05-25	2006-05-25	ENSG00000048649	ENSG00000048649		"""Zinc fingers, PHD-type"""	18118	protein-coding gene	gene with protein product		608522	"""hepatitis B virus x associated protein"""	HBXAP		11788598, 12972596	Standard	NM_016578		Approved	XAP8, RSF-1, p325	uc001oyn.3	Q96T23	OTTHUMG00000150433	ENST00000308488.6:c.3783T>C	11.37:g.77378505A>G		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	34	31	0.911765	NM_016578	Q86X86|Q9H3L8|Q9NVZ8|Q9NYU0	Silent	SNP	ENST00000308488.6	37	CCDS8253.1																																																																																			A|0.816;G|0.184	0.184	strong		0.443	RSF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318075.2	NM_016578	
CCDC27	148870	hgsc.bcm.edu	37	1	3677933	3677933	+	Missense_Mutation	SNP	T	T	C	rs1181883	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:3677933T>C	ENST00000294600.2	+	5	884	c.800T>C	c.(799-801)aTg>aCg	p.M267T		NM_152492.2	NP_689705.2	Q2M243	CCD27_HUMAN	coiled-coil domain containing 27	267			M -> T (in dbSNP:rs1181883). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.							breast(1)|endometrium(2)|kidney(1)|large_intestine(8)|liver(2)|lung(17)|prostate(1)|skin(2)|urinary_tract(2)	36	all_cancers(77;0.0385)|Ovarian(185;0.0634)|Lung NSC(156;0.21)|all_lung(157;0.218)	all_epithelial(116;5.52e-17)|all_lung(118;1.04e-06)|Lung NSC(185;0.000214)|Renal(390;0.00357)|Breast(487;0.00446)|Hepatocellular(190;0.0218)|Lung SC(97;0.0367)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.127)		Epithelial(90;1.11e-38)|OV - Ovarian serous cystadenocarcinoma(86;1.35e-22)|GBM - Glioblastoma multiforme(42;3.46e-16)|Colorectal(212;1.17e-05)|COAD - Colon adenocarcinoma(227;5.76e-05)|Kidney(185;0.00036)|BRCA - Breast invasive adenocarcinoma(365;0.000696)|KIRC - Kidney renal clear cell carcinoma(229;0.00558)|STAD - Stomach adenocarcinoma(132;0.00645)|Lung(427;0.203)		GCCCTGAAGATGCAGCTGAAA	0.577													C|||	2384	0.476038	0.6944	0.4683	5008	,	,		18850	0.2788		0.4354	False		,,,				2504	0.4315				p.M267T		Atlas-SNP	.											.	CCDC27	79	.	0			c.T800C						PASS	.	C	THR/MET	2721,1685	508.9+/-367.1	851,1019,333	80.0	77.0	78.0		800	-1.3	0.3	1	dbSNP_87	78	3371,5229	641.1+/-399.7	666,2039,1595	yes	missense	CCDC27	NM_152492.2	81	1517,3058,1928	CC,CT,TT		39.1977,38.2433,46.8399	benign	267/657	3677933	6092,6914	2203	4300	6503	SO:0001583	missense	148870	exon5			TGAAGATGCAGCT		CCDS50.1	1p36.32	2008-02-05			ENSG00000162592	ENSG00000162592			26546	protein-coding gene	gene with protein product							Standard	NM_152492		Approved	FLJ32825	uc001akv.2	Q2M243	OTTHUMG00000003504	ENST00000294600.2:c.800T>C	1.37:g.3677933T>C	ENSP00000294600:p.Met267Thr	Somatic	231	1	0.004329		WXS	Illumina HiSeq	Phase_I	140	96	0.685714	NM_152492	Q5TBV3|Q96M50	Missense_Mutation	SNP	ENST00000294600.2	37	CCDS50.1	994	0.4551282051282051	356	0.7235772357723578	164	0.4530386740331492	148	0.25874125874125875	326	0.43007915567282323	C	0.025	-1.378822	0.01204	0.617567	0.391977	ENSG00000162592	ENST00000294600	T	0.16897	2.31	3.75	-1.31	0.09230	.	0.477568	0.17824	N	0.160777	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	0.24870	-1.0148	9	0.17832	T	0.49	-30.5079	0.0397	0.00008	0.2978:0.1762:0.2037:0.3224	rs1181883;rs17371673;rs52791836;rs58427864;rs1181883	267	Q2M243	CCD27_HUMAN	T	267	ENSP00000294600:M267T	ENSP00000294600:M267T	M	+	2	0	CCDC27	3667793	0.039000	0.19947	0.345000	0.25642	0.018000	0.09664	-0.489000	0.06490	-0.433000	0.07286	-3.293000	0.00046	ATG	T|0.530;C|0.470	0.470	strong		0.577	CCDC27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009740.1	NM_152492	
TAGLN3	29114	hgsc.bcm.edu	37	3	111719786	111719786	+	Silent	SNP	A	A	T	rs2292583	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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_ENST00000273368.4_Silent_p.L116L|TAGLN3_ENST00000486460.1_Silent_p.L32L|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	50	20	0.4	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	
GIT1	28964	hgsc.bcm.edu	37	17	27903998	27903998	+	Silent	SNP	A	A	C	rs144787773		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:27903998A>C	ENST00000225394.3	-	12	1358	c.1110T>G	c.(1108-1110)tcT>tcG	p.S370S	GIT1_ENST00000394869.3_Silent_p.S379S|RP11-68I3.2_ENST00000581474.1_RNA|GIT1_ENST00000581348.1_Silent_p.S379S|GIT1_ENST00000579937.1_Silent_p.S370S	NM_014030.3	NP_054749.2	Q9Y2X7	GIT1_HUMAN	G protein-coupled receptor kinase interacting ArfGAP 1	370	PTK2/FAK1-binding. {ECO:0000250}.				regulation of ARF GTPase activity (GO:0032312)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|membrane (GO:0016020)	ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)			large_intestine(2)|lung(3)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	9				READ - Rectum adenocarcinoma(3;0.0419)|Colorectal(3;0.069)		GGCTCCGCAGAGACAGCTCGA	0.627																																					p.S379S	Colon(81;41 1719 20078 35068)	Atlas-SNP	.											.	GIT1	84	.	0			c.T1137G						PASS	.						48.0	49.0	49.0					17																	27903998		2203	4300	6503	SO:0001819	synonymous_variant	28964	exon13			CCGCAGAGACAGC	AF124490	CCDS11250.1, CCDS42290.1	17p11.2	2013-01-10	2008-09-05		ENSG00000108262	ENSG00000108262		"""ADP-ribosylation factor GTPase activating proteins"", ""Ankyrin repeat domain containing"""	4272	protein-coding gene	gene with protein product		608434	"""G protein-coupled receptor kinase interactor 1"""			9826657, 10896954	Standard	NM_014030		Approved		uc002heg.2	Q9Y2X7	OTTHUMG00000132730	ENST00000225394.3:c.1110T>G	17.37:g.27903998A>C		Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	31	19	0.612903	NM_001085454	B4DGU9|B4DSV3|Q86SS0|Q9BRJ4	Silent	SNP	ENST00000225394.3	37	CCDS11250.1																																																																																			A|0.998;C|0.002	0.002	weak		0.627	GIT1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256073.1	NM_014030	
CHRD	8646	hgsc.bcm.edu	37	3	184099050	184099050	+	Missense_Mutation	SNP	C	C	T	rs34095724	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:184099050C>T	ENST00000204604.1	+	3	526	c.280C>T	c.(280-282)Cct>Tct	p.P94S	CHRD_ENST00000348986.3_Missense_Mutation_p.P94S|EIF2B5_ENST00000444495.1_Intron|CHRD_ENST00000482805.1_3'UTR|CHRD_ENST00000450923.1_Missense_Mutation_p.P94S|CHRD_ENST00000545352.1_5'Flank	NM_003741.2	NP_003732.2	Q9H2X0	CHRD_HUMAN	chordin	94	VWFC 1. {ECO:0000255|PROSITE- ProRule:PRU00220}.		P -> S (in dbSNP:rs34095724).		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)			TACCAGGGGCCCTGGCAGGGT	0.657													C|||	195	0.0389377	0.093	0.0173	5008	,	,		14626	0.002		0.0378	False		,,,				2504	0.0204				p.P94S		Atlas-SNP	.											.	CHRD	149	.	0			c.C280T						PASS	.	C	SER/PRO	410,3994		18,374,1810	21.0	26.0	24.0		280	4.3	1.0	3	dbSNP_126	24	292,8302		2,288,4007	yes	missense	CHRD	NM_003741.2	74	20,662,5817	TT,TC,CC		3.3977,9.3097,5.4008	benign	94/956	184099050	702,12296	2202	4297	6499	SO:0001583	missense	8646	exon3			AGGGGCCCTGGCA	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.280C>T	3.37:g.184099050C>T	ENSP00000204604:p.Pro94Ser	Somatic	267	0	0		WXS	Illumina HiSeq	Phase_I	250	144	0.576	NM_003741	O95254|Q2M1I8|Q6UW83|Q9H2D3|Q9H2W8|Q9H2W9|Q9P0Z2|Q9P0Z3|Q9P0Z4|Q9P0Z5	Missense_Mutation	SNP	ENST00000204604.1	37	CCDS3266.1	92	0.04212454212454213	53	0.10772357723577236	9	0.024861878453038673	1	0.0017482517482517483	29	0.03825857519788918	C	3.315	-0.140029	0.06669	0.093097	0.033977	ENSG00000090539	ENST00000204604;ENST00000450923;ENST00000348986	T;T;T	0.13307	2.83;2.6;2.61	5.18	4.3	0.51218	von Willebrand factor, type C (3);	0.242099	0.43110	D	0.000610	T	0.00144	0.0004	N	0.12182	0.205	0.80722	D	1	B;B	0.11235	0.0;0.004	B;B	0.15870	0.007;0.014	T	0.49960	-0.8883	10	0.20519	T	0.43	-8.4545	7.7367	0.28819	0.0:0.5773:0.3366:0.0861	rs34095724	94;94	E7ESX1;Q9H2X0	.;CHRD_HUMAN	S	94	ENSP00000204604:P94S;ENSP00000408972:P94S;ENSP00000334036:P94S	ENSP00000204604:P94S	P	+	1	0	CHRD	185581744	0.001000	0.12720	1.000000	0.80357	0.678000	0.39670	0.462000	0.21956	1.169000	0.42739	0.561000	0.74099	CCT	C|0.949;T|0.051	0.051	strong		0.657	CHRD-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000280432.1	NM_003741	
TMEM132A	54972	hgsc.bcm.edu	37	11	60704213	60704213	+	Missense_Mutation	SNP	C	C	T	rs2469887	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:60704213C>T	ENST00000453848.2	+	11	3064	c.2906C>T	c.(2905-2907)gCg>gTg	p.A969V	TMEM132A_ENST00000005286.4_Missense_Mutation_p.A970V			Q24JP5	T132A_HUMAN	transmembrane protein 132A	969	Confers cellular localization similar to full-length form. {ECO:0000250}.		A -> V (in dbSNP:rs2469887). {ECO:0000269|PubMed:14702039}.			endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				breast(1)|cervix(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(14)|ovary(3)|prostate(1)|skin(3)	32						GTGACATTTGCGCCAGCCCCT	0.672													C|||	2113	0.421925	0.4735	0.4467	5008	,	,		16318	0.3165		0.4225	False		,,,				2504	0.4427				p.A970V		Atlas-SNP	.											.	TMEM132A	135	.	0			c.C2909T						PASS	.	C	VAL/ALA,VAL/ALA	2057,2349	530.1+/-372.8	469,1119,615	23.0	28.0	27.0		2909,2906	3.7	0.2	11	dbSNP_100	27	3702,4896	503.5+/-375.9	801,2100,1398	yes	missense,missense	TMEM132A	NM_017870.3,NM_178031.2	64,64	1270,3219,2013	TT,TC,CC		43.0565,46.6863,44.2864	probably-damaging,probably-damaging	970/1025,969/1024	60704213	5759,7245	2203	4299	6502	SO:0001583	missense	54972	exon11			CATTTGCGCCAGC	AK000546	CCDS7997.1, CCDS44618.1	11q12.2	2006-03-02	2006-03-02	2006-03-02	ENSG00000006118	ENSG00000006118			31092	protein-coding gene	gene with protein product			"""heat shock 70kDa protein 5 (glucose-regulated protein, 78kDa) binding protein 1"""	HSPA5BP1		12514190, 10997877	Standard	NM_017870		Approved	GBP, FLJ20539	uc001nqi.3	Q24JP5	OTTHUMG00000167803	ENST00000453848.2:c.2906C>T	11.37:g.60704213C>T	ENSP00000405823:p.Ala969Val	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	69	67	0.971014	NM_017870	Q69YU7|Q86VZ8|Q86W97|Q9H8K3|Q9HCI9|Q9NWY0	Missense_Mutation	SNP	ENST00000453848.2	37	CCDS44618.1	901	0.4125457875457875	232	0.4715447154471545	164	0.4530386740331492	185	0.32342657342657344	320	0.42216358839050133	C	13.07	2.127516	0.37533	0.466863	0.430565	ENSG00000006118	ENST00000444690;ENST00000453848;ENST00000005286	T;T	0.06608	3.28;3.28	4.61	3.7	0.42460	.	0.312828	0.26149	N	0.026050	T	0.00012	0.0000	L	0.59436	1.845	0.36902	P	0.10954900000000001	B;B	0.24132	0.098;0.098	B;B	0.12837	0.008;0.008	T	0.45775	-0.9238	9	0.87932	D	0	-17.4679	5.1482	0.14996	0.1462:0.6297:0.1422:0.0819	rs2469887;rs56748518;rs2469887	969;970	Q24JP5;Q24JP5-2	T132A_HUMAN;.	V	720;969;970	ENSP00000405823:A969V;ENSP00000005286:A970V	ENSP00000005286:A970V	A	+	2	0	TMEM132A	60460789	0.939000	0.31865	0.222000	0.23844	0.691000	0.40173	4.120000	0.57897	1.312000	0.45043	0.655000	0.94253	GCG	C|0.570;T|0.430	0.430	strong		0.672	TMEM132A-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000396352.1	NM_017870	
CCDC170	80129	hgsc.bcm.edu	37	6	151936677	151936677	+	Missense_Mutation	SNP	G	G	A	rs6929137	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:151936677G>A	ENST00000239374.7	+	10	1909	c.1810G>A	c.(1810-1812)Gtc>Atc	p.V604I	CCDC170_ENST00000367290.5_Missense_Mutation_p.V611I|RNU6-813P_ENST00000384691.1_RNA	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	162	0	0		WXS	Illumina HiSeq	Phase_I	93	93	1	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	
SPATA5L1	79029	hgsc.bcm.edu	37	15	45695445	45695445	+	Missense_Mutation	SNP	C	C	G	rs143453038	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:45695445C>G	ENST00000305560.6	+	1	917	c.818C>G	c.(817-819)tCc>tGc	p.S273C	SPATA5L1_ENST00000559860.1_Missense_Mutation_p.S273C|GATM_ENST00000458245.5_5'Flank	NM_024063.2	NP_076968.2	Q9BVQ7	SPA5L_HUMAN	spermatogenesis associated 5-like 1	273						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)		CTGCAGGGTTCCCGGCCTGGG	0.761													C|||	50	0.00998403	0.0023	0.0202	5008	,	,		12129	0.0		0.0298	False		,,,				2504	0.0031				p.S273C		Atlas-SNP	.											.	SPATA5L1	40	.	0			c.C818G						PASS	.	C	CYS/SER	17,3375		0,17,1679	3.0	4.0	4.0		818	4.9	0.3	15	dbSNP_134	4	149,7059		1,147,3456	no	missense	SPATA5L1	NM_024063.2	112	1,164,5135	GG,GC,CC		2.0671,0.5012,1.566	possibly-damaging	273/754	45695445	166,10434	1696	3604	5300	SO:0001583	missense	79029	exon1			AGGGTTCCCGGCC	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.818C>G	15.37:g.45695445C>G	ENSP00000305494:p.Ser273Cys	Somatic	5	0	0		WXS	Illumina HiSeq	Phase_I	22	6	0.272727	NM_024063	C9JHR5|Q9H8W7|Q9HA41	Missense_Mutation	SNP	ENST00000305560.6	37	CCDS10123.1	40	0.018315018315018316	8	0.016260162601626018	9	0.024861878453038673	0	0.0	23	0.030343007915567283	C	20.5	3.999282	0.74818	0.005012	0.020671	ENSG00000171763	ENST00000305560	D	0.93426	-3.22	4.9	4.9	0.64082	ATPase, AAA-type, core (1);ATPase, AAA+ type, core (1);	0.367137	0.28560	N	0.014910	D	0.89111	0.6622	M	0.68728	2.09	0.20307	N	0.999919	D	0.56035	0.974	P	0.57057	0.812	D	0.85330	0.1089	10	0.87932	D	0	-22.4119	16.8259	0.85931	0.0:1.0:0.0:0.0	.	273	Q9BVQ7	SPA5L_HUMAN	C	273	ENSP00000305494:S273C	ENSP00000305494:S273C	S	+	2	0	SPATA5L1	43482737	0.758000	0.28405	0.314000	0.25224	0.281000	0.26958	7.247000	0.78257	2.536000	0.85505	0.585000	0.79938	TCC	C|0.982;G|0.018	0.018	strong		0.761	SPATA5L1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000254218.1	NM_024063	
PCDHB10	56126	hgsc.bcm.edu	37	5	140572668	140572668	+	Silent	SNP	C	C	T	rs597064	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:140572668C>T	ENST00000239446.4	+	1	727	c.543C>T	c.(541-543)aaC>aaT	p.N181N		NM_018930.3	NP_061753.1	Q9UN67	PCDBA_HUMAN	protocadherin beta 10	181	Cadherin 2. {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)			TCCATATTAACATTAGTGGCG	0.478													t|||	2440	0.48722	0.5083	0.5432	5008	,	,		18344	0.5685		0.4076	False		,,,				2504	0.4172				p.N181N		Atlas-SNP	.											.	PCDHB10	177	.	0			c.C543T						PASS	.	A		2071,2335	578.4+/-384.7	491,1089,623	129.0	151.0	144.0		543	-2.5	0.0	5	dbSNP_83	144	3527,5073	626.0+/-397.8	760,2007,1533	no	coding-synonymous	PCDHB10	NM_018930.3		1251,3096,2156	TT,TC,CC		41.0116,47.0041,43.0417		181/801	140572668	5598,7408	2203	4300	6503	SO:0001819	synonymous_variant	56126	exon1			TATTAACATTAGT	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.543C>T	5.37:g.140572668C>T		Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	152	72	0.473684	NM_018930	Q96T99	Silent	SNP	ENST00000239446.4	37	CCDS4252.1																																																																																			C|0.561;T|0.439	0.439	strong		0.478	PCDHB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251821.1	NM_018930	
LAMA5	3911	hgsc.bcm.edu	37	20	60887028	60887028	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:60887028C>T	ENST00000252999.3	-	70	9649	c.9583G>A	c.(9583-9585)Ggc>Agc	p.G3195S	LAMA5_ENST00000492698.1_5'Flank	NM_005560.3	NP_005551.3	O15230	LAMA5_HUMAN	laminin, alpha 5	3195	Laminin G-like 3. {ECO:0000255|PROSITE- ProRule:PRU00122}.				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)			TCGGCGAAGCCCGCTTGAGTT	0.647																																					p.G3195S		Atlas-SNP	.											.	LAMA5	268	.	0			c.G9583A						PASS	.						64.0	69.0	67.0					20																	60887028		2203	4298	6501	SO:0001583	missense	3911	exon70			CGAAGCCCGCTTG	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.9583G>A	20.37:g.60887028C>T	ENSP00000252999:p.Gly3195Ser	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	51	5	0.0980392	NM_005560	Q8TDF8|Q8WZA7|Q9H1P1	Missense_Mutation	SNP	ENST00000252999.3	37	CCDS33502.1	.	.	.	.	.	.	.	.	.	.	c	4.219	0.039521	0.08148	.	.	ENSG00000130702	ENST00000252999	T	0.76709	-1.04	4.62	1.51	0.23008	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	0.886282	0.09702	N	0.766863	T	0.45538	0.1347	N	0.01352	-0.895	0.09310	N	1	B	0.10296	0.003	B	0.17098	0.017	T	0.35574	-0.9783	10	0.06757	T	0.87	.	7.2199	0.25981	0.0:0.4457:0.3986:0.1557	.	3195	O15230	LAMA5_HUMAN	S	3195	ENSP00000252999:G3195S	ENSP00000252999:G3195S	G	-	1	0	LAMA5	60320423	0.000000	0.05858	0.001000	0.08648	0.008000	0.06430	-0.515000	0.06290	0.049000	0.15920	0.556000	0.70494	GGC	.	.	none		0.647	LAMA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080014.2	NM_005560	
ZDHHC11	79844	hgsc.bcm.edu	37	5	837553	837553	+	Missense_Mutation	SNP	C	C	G	rs528116435	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:837553C>G	ENST00000283441.8	-	6	1210	c.827G>C	c.(826-828)cGc>cCc	p.R276P	ZDHHC11_ENST00000503758.2_5'UTR|ZDHHC11_ENST00000424784.2_Missense_Mutation_p.R276P	NM_024786.2	NP_079062.1	Q9H8X9	ZDH11_HUMAN	zinc finger, DHHC-type containing 11	276						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)			CTCTTCTTTGCGGTTATTAAT	0.483													C|||	6	0.00119808	0.0	0.0029	5008	,	,		29960	0.0		0.002	False		,,,				2504	0.002				p.R276P		Atlas-SNP	.											ZDHHC11_ENST00000424784,NS,carcinoma,-1,2	ZDHHC11	97	2	0			c.G827C						scavenged	.						198.0	225.0	216.0					5																	837553		2203	4300	6503	SO:0001583	missense	79844	exon6			TCTTTGCGGTTAT	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.827G>C	5.37:g.837553C>G	ENSP00000283441:p.Arg276Pro	Somatic	322	0	0		WXS	Illumina HiSeq	Phase_I	372	39	0.104839	NM_024786	Q6UWR9	Missense_Mutation	SNP	ENST00000283441.8	37	CCDS3857.1	.	.	.	.	.	.	.	.	.	.	c	11.45	1.641159	0.29157	.	.	ENSG00000188818	ENST00000424784;ENST00000283441;ENST00000511193	T;T;T	0.72615	1.41;1.41;-0.67	1.51	-0.417	0.12347	.	571.534000	0.01140	U	0.006193	T	0.67961	0.2949	N	0.08118	0	0.09310	N	1	D	0.89917	1.0	D	0.78314	0.991	T	0.57283	-0.7838	10	0.66056	D	0.02	-3.877	3.9923	0.09543	0.0:0.5616:0.0:0.4384	.	276	Q9H8X9	ZDH11_HUMAN	P	276;276;51	ENSP00000397719:R276P;ENSP00000283441:R276P;ENSP00000426873:R51P	ENSP00000283441:R276P	R	-	2	0	ZDHHC11	890553	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-1.333000	0.02667	-0.128000	0.11641	0.383000	0.25322	CGC	.	.	none		0.483	ZDHHC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206681.3	NM_024786	
ITPR3	3710	hgsc.bcm.edu	37	6	33651129	33651129	+	Silent	SNP	C	C	T	rs942636	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:33651129C>T	ENST00000374316.5	+	36	5803	c.4743C>T	c.(4741-4743)ccC>ccT	p.P1581P	ITPR3_ENST00000605930.1_Silent_p.P1581P			Q14573	ITPR3_HUMAN	inositol 1,4,5-trisphosphate receptor, type 3	1581					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|calcium ion transport into cytosol (GO:0060402)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|long-term synaptic potentiation (GO:0060291)|memory (GO:0007613)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|regulation of insulin secretion (GO:0050796)|response to calcium ion (GO:0051592)|sensory perception of bitter taste (GO:0050913)|sensory perception of sweet taste (GO:0050916)|sensory perception of umami taste (GO:0050917)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	apical part of cell (GO:0045177)|brush border (GO:0005903)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|myelin sheath (GO:0043209)|neuronal cell body (GO:0043025)|nuclear outer membrane (GO:0005640)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|platelet dense tubular network membrane (GO:0031095)|receptor complex (GO:0043235)	inositol 1,3,4,5 tetrakisphosphate binding (GO:0043533)|inositol 1,4,5 trisphosphate binding (GO:0070679)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|inositol hexakisphosphate binding (GO:0000822)|intracellular ligand-gated calcium channel activity (GO:0005218)|phosphatidylinositol binding (GO:0035091)			NS(1)|breast(6)|central_nervous_system(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|liver(1)|lung(24)|ovary(8)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	85					Caffeine(DB00201)	GCGTCACCCCCACCGCCAACC	0.642													C|||	945	0.188698	0.1664	0.3357	5008	,	,		17048	0.1012		0.2008	False		,,,				2504	0.1922				p.P1581P		Atlas-SNP	.											.	ITPR3	409	.	0			c.C4743T						PASS	.	C		777,3615		74,629,1493	20.0	17.0	18.0		4743	2.7	1.0	6	dbSNP_86	18	1398,7194		115,1168,3013	no	coding-synonymous	ITPR3	NM_002224.3		189,1797,4506	TT,TC,CC		16.2709,17.6913,16.7514		1581/2672	33651129	2175,10809	2196	4296	6492	SO:0001819	synonymous_variant	3710	exon35			CACCCCCACCGCC	D26351	CCDS4783.1	6p21.31	2011-11-24	2011-04-28		ENSG00000096433	ENSG00000096433		"""Ion channels / Inositol triphosphate receptors"""	6182	protein-coding gene	gene with protein product		147267	"""inositol 1,4,5-triphosphate receptor, type 3"""			8081734, 8288584	Standard	NM_002224		Approved	IP3R3	uc021ywr.1	Q14573	OTTHUMG00000014532	ENST00000374316.5:c.4743C>T	6.37:g.33651129C>T		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	91	52	0.571429	NM_002224	Q14649|Q5TAQ2	Silent	SNP	ENST00000374316.5	37	CCDS4783.1																																																																																			C|0.835;T|0.165	0.165	strong		0.642	ITPR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040204.2	NM_002224	
ACER3	55331	hgsc.bcm.edu	37	11	76701606	76701606	+	Silent	SNP	G	G	A	rs3740767	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:76701606G>A	ENST00000532485.1	+	6	530	c.426G>A	c.(424-426)ccG>ccA	p.P142P	ACER3_ENST00000530182.1_3'UTR|ACER3_ENST00000526597.1_Silent_p.P47P|ACER3_ENST00000538157.1_Silent_p.P100P|ACER3_ENST00000533873.1_Silent_p.P105P	NM_018367.5	NP_060837.3	Q9NUN7	ACER3_HUMAN	alkaline ceramidase 3	142					ceramide metabolic process (GO:0006672)|phytosphingosine biosynthetic process (GO:0071602)|positive regulation of cell proliferation (GO:0008284)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|sphingosine biosynthetic process (GO:0046512)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of Golgi membrane (GO:0030173)	phytoceramidase activity (GO:0070774)			endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|prostate(1)	9						TAAAAGAGCCGATATTCCATC	0.333													G|||	2669	0.532947	0.1906	0.5072	5008	,	,		20718	0.6349		0.7366	False		,,,				2504	0.6994				p.P142P		Atlas-SNP	.											.	ACER3	19	.	0			c.G426A						PASS	.	G		1259,3141	428.9+/-342.0	201,857,1142	195.0	187.0	190.0		426	-0.8	0.6	11	dbSNP_107	190	6522,2062	717.8+/-406.2	2488,1546,258	yes	coding-synonymous	ACER3	NM_018367.5		2689,2403,1400	AA,AG,GG		24.0214,28.6136,40.0724		142/268	76701606	7781,5203	2200	4292	6492	SO:0001819	synonymous_variant	55331	exon6			AGAGCCGATATTC	AF214454	CCDS8247.1, CCDS73352.1	11q13.5	2013-01-25	2008-12-19	2008-12-19	ENSG00000078124	ENSG00000078124	3.5.1.23	"""Alkaline ceramidase"""	16066	protein-coding gene	gene with protein product	"""alkaline phytoceramidase"""		"""phytoceramidase, alkaline"""	PHCA		11356846, 18619555	Standard	XM_005274090		Approved	FLJ11238, APHC	uc009yum.1	Q9NUN7	OTTHUMG00000165225	ENST00000532485.1:c.426G>A	11.37:g.76701606G>A		Somatic	199	0	0		WXS	Illumina HiSeq	Phase_I	148	31	0.209459	NM_018367	B2RC99	Silent	SNP	ENST00000532485.1	37	CCDS8247.1																																																																																			G|0.409;A|0.591	0.591	strong		0.333	ACER3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382770.2	NM_018367	
PLA2R1	22925	hgsc.bcm.edu	37	2	160901517	160901517	+	Silent	SNP	A	A	G	rs4665143	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:160901517A>G	ENST00000283243.7	-	2	467	c.261T>C	c.(259-261)agT>agC	p.S87S	PLA2R1_ENST00000392771.1_Silent_p.S87S	NM_001195641.1|NM_007366.4	NP_001182570.1|NP_031392.3	Q13018	PLA2R_HUMAN	phospholipase A2 receptor 1, 180kDa	87	Ricin B-type lectin. {ECO:0000255|PROSITE-ProRule:PRU00174}.				cytokine production (GO:0001816)|negative regulation of arachidonic acid secretion (GO:1900139)|negative regulation of phospholipase A2 activity (GO:1900138)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of arachidonic acid secretion (GO:0090238)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|reactive oxygen species metabolic process (GO:0072593)|receptor-mediated endocytosis (GO:0006898)|replicative senescence (GO:0090399)	cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	carbohydrate binding (GO:0030246)|phospholipase binding (GO:0043274)|receptor activity (GO:0004872)		PLA2R1/RBMS1(2)	central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(17)|lung(20)|ovary(1)|pancreas(1)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)	60						CCAGGCAACCACTGCCTCCTA	0.502													G|||	2290	0.457268	0.1278	0.6614	5008	,	,		17561	0.5992		0.6292	False		,,,				2504	0.4346				p.S87S		Atlas-SNP	.											.	PLA2R1	153	.	0			c.T261C						PASS	.	G	,,	965,3441	734.6+/-410.6	102,761,1340	70.0	64.0	66.0		261,261,261	-6.6	0.5	2	dbSNP_111	66	5455,3145	478.0+/-369.8	1742,1971,587	no	coding-synonymous,coding-synonymous,coding-synonymous	PLA2R1	NM_001007267.2,NM_001195641.1,NM_007366.4	,,	1844,2732,1927	GG,GA,AA		36.5698,21.902,49.3618	,,	87/1325,87/1462,87/1464	160901517	6420,6586	2203	4300	6503	SO:0001819	synonymous_variant	22925	exon2			GCAACCACTGCCT	U17033	CCDS33309.1, CCDS42767.1	2q23-q24	2011-08-30	2002-08-29		ENSG00000153246	ENSG00000153246		"""C-type lectin domain containing"""	9042	protein-coding gene	gene with protein product		604939	"""phospholipase A2 receptor 1, 180kD"""			7721806, 7925459	Standard	NM_007366		Approved	PLA2G1R, PLA2IR, PLA2-R, CLEC13C	uc002ube.2	Q13018	OTTHUMG00000154087	ENST00000283243.7:c.261T>C	2.37:g.160901517A>G		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	108	53	0.490741	NM_001195641	B2RTU9|D3DPB1|Q13019|Q15095|Q53R45|Q53RR7	Silent	SNP	ENST00000283243.7	37	CCDS33309.1																																																																																			A|0.497;G|0.503	0.503	strong		0.502	PLA2R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333820.1		
PPRC1	23082	hgsc.bcm.edu	37	10	103900729	103900729	+	Missense_Mutation	SNP	G	G	A	rs61731871	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:103900729G>A	ENST00000278070.2	+	5	2503	c.2464G>A	c.(2464-2466)Gta>Ata	p.V822I	PPRC1_ENST00000370012.1_5'Flank|PPRC1_ENST00000413464.2_Missense_Mutation_p.V822I	NM_015062.3	NP_055877.3	Q5VV67	PPRC1_HUMAN	peroxisome proliferator-activated receptor gamma, coactivator-related 1	822	Pro-rich.				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)		CCTTGTGCCTGTAGGTCCCAG	0.572													g|||	386	0.0770767	0.1989	0.062	5008	,	,		19839	0.0		0.0656	False		,,,				2504	0.0143				p.V822I		Atlas-SNP	.											PPRC1,NS,carcinoma,0,1	PPRC1	151	1	0			c.G2464A						PASS	.	A	ILE/VAL	738,3668	304.4+/-288.4	58,622,1523	107.0	100.0	103.0		2464	-5.6	0.3	10	dbSNP_129	103	518,8082	145.9+/-201.5	16,486,3798	yes	missense	PPRC1	NM_015062.3	29	74,1108,5321	AA,AG,GG		6.0233,16.7499,9.6571	benign	822/1665	103900729	1256,11750	2203	4300	6503	SO:0001583	missense	23082	exon5			GTGCCTGTAGGTC	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.2464G>A	10.37:g.103900729G>A	ENSP00000278070:p.Val822Ile	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	57	29	0.508772	NM_015062	Q5VV66|Q6P3U5|Q6P3W1|Q76N31|Q9BUJ3|Q9BZE5|Q9Y4E0	Missense_Mutation	SNP	ENST00000278070.2	37	CCDS7529.1	178	0.0815018315018315	90	0.18292682926829268	29	0.08011049723756906	0	0.0	59	0.07783641160949868	G	5.765	0.325524	0.10900	0.167499	0.060233	ENSG00000148840	ENST00000278070;ENST00000413464	T;T	0.25912	1.83;1.77	5.41	-5.61	0.02489	.	9.604230	0.00166	N	0.000002	T	0.00039	0.0001	L	0.29908	0.895	0.80722	P	0.0	B;B;B	0.23249	0.049;0.082;0.049	B;B;B	0.24269	0.023;0.052;0.01	T	0.21109	-1.0255	9	0.42905	T	0.14	.	1.9402	0.03345	0.4003:0.0952:0.3113:0.1932	rs61731871	822;702;822	E7EVG6;Q5VV67-2;Q5VV67	.;.;PPRC1_HUMAN	I	822	ENSP00000278070:V822I;ENSP00000399743:V822I	ENSP00000278070:V822I	V	+	1	0	PPRC1	103890719	0.001000	0.12720	0.274000	0.24659	0.027000	0.11550	-0.864000	0.04254	-0.651000	0.05415	-0.974000	0.02594	GTA	G|0.912;A|0.088	0.088	strong		0.572	PPRC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050021.1	NM_015062	
MUC4	4585	hgsc.bcm.edu	37	3	195513102	195513102	+	Silent	SNP	A	A	G	rs3103958	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195513102A>G	ENST00000463781.3	-	2	5808	c.5349T>C	c.(5347-5349)tcT>tcC	p.S1783S	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Silent_p.S1783S	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.S1783S(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)		TGGAAGCTGAAGAAAGGCCGG	0.592																																					p.S1783S		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	1	Substitution - coding silent(1)	endometrium(1)	c.T5349C						scavenged	.						77.0	79.0	78.0					3																	195513102		692	1591	2283	SO:0001819	synonymous_variant	4585	exon2			AGCTGAAGAAAGG	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.5349T>C	3.37:g.195513102A>G		Somatic	185	4	0.0216216		WXS	Illumina HiSeq	Phase_I	337	93	0.275964	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Silent	SNP	ENST00000463781.3	37	CCDS54700.1																																																																																			A|0.500;G|0.500	0.500	strong		0.592	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
CECR5	27440	hgsc.bcm.edu	37	22	17630486	17630486	+	Silent	SNP	C	C	A	rs1034859	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:17630486C>A	ENST00000336737.4	-	2	301	c.276G>T	c.(274-276)ggG>ggT	p.G92G	CECR5_ENST00000399852.3_Intron|CECR5_ENST00000155674.5_Silent_p.G62G|CECR5_ENST00000480451.1_5'UTR	NM_033070.2	NP_149061.1	Q9BXW7	CECR5_HUMAN	cat eye syndrome chromosome region, candidate 5	92						mitochondrion (GO:0005739)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|liver(1)|lung(10)|pancreas(1)|prostate(1)	21		all_epithelial(15;0.0181)|Lung NSC(13;0.109)|all_lung(157;0.132)				GTAAGATGTTCCCAGCATTTG	0.592													C|||	2676	0.534345	0.3759	0.6744	5008	,	,		17538	0.6796		0.5447	False		,,,				2504	0.4888				p.G92G		Atlas-SNP	.											.	CECR5	46	.	0			c.G276T						PASS	.	C	,	1707,2699	514.7+/-368.7	324,1059,820	100.0	100.0	100.0		186,276	1.5	1.0	22	dbSNP_86	100	4584,4016	596.6+/-393.6	1224,2136,940	no	coding-synonymous,coding-synonymous	CECR5	NM_017829.5,NM_033070.2	,	1548,3195,1760	AA,AC,CC		46.6977,38.7426,48.37	,	62/394,92/424	17630486	6291,6715	2203	4300	6503	SO:0001819	synonymous_variant	27440	exon2			GATGTTCCCAGCA	AF273270	CCDS13741.1, CCDS33595.1	22q11.2	2008-06-12			ENSG00000069998	ENSG00000069998			1843	protein-coding gene	gene with protein product						11381032	Standard	NM_017829		Approved		uc002zmf.3	Q9BXW7	OTTHUMG00000150071	ENST00000336737.4:c.276G>T	22.37:g.17630486C>A		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	45	14	0.311111	NM_033070	B2RCK5|Q9BXW8|Q9NWA8|Q9NX41	Silent	SNP	ENST00000336737.4	37	CCDS33595.1																																																																																			C|0.487;A|0.513	0.513	strong		0.592	CECR5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316100.1	NM_017829	
SPTBN2	6712	hgsc.bcm.edu	37	11	66476403	66476403	+	Silent	SNP	G	G	A	rs74909073	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:66476403G>A	ENST00000533211.1	-	11	1492	c.1161C>T	c.(1159-1161)cgC>cgT	p.R387R	SPTBN2_ENST00000309996.2_Silent_p.R387R|SPTBN2_ENST00000529997.1_Silent_p.R387R			O15020	SPTN2_HUMAN	spectrin, beta, non-erythrocytic 2	387					actin filament capping (GO:0051693)|adult behavior (GO:0030534)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|axon guidance (GO:0007411)|cell death (GO:0008219)|cerebellar Purkinje cell layer morphogenesis (GO:0021692)|multicellular organism growth (GO:0035264)|synapse assembly (GO:0007416)|vesicle-mediated transport (GO:0016192)	apical plasma membrane (GO:0016324)|cytosol (GO:0005829)|extracellular space (GO:0005615)|neuronal cell body (GO:0043025)|spectrin (GO:0008091)	actin binding (GO:0003779)|phospholipid binding (GO:0005543)|structural constituent of cytoskeleton (GO:0005200)			autonomic_ganglia(1)|breast(1)|central_nervous_system(4)|cervix(1)|endometrium(10)|kidney(5)|large_intestine(15)|liver(1)|lung(22)|ovary(2)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	74						GCCGGCCCTCGCGGGGCGTGT	0.622													G|||	6	0.00119808	0.0	0.0	5008	,	,		15517	0.0		0.006	False		,,,				2504	0.0				p.R387R		Atlas-SNP	.											SPTBN2,colon,carcinoma,-2,3	SPTBN2	188	3	0			c.C1161T						PASS	.	G		3,4397	6.2+/-15.9	0,3,2197	66.0	66.0	66.0		1161	-10.3	0.6	11	dbSNP_134	66	36,8554	25.1+/-72.6	1,34,4260	no	coding-synonymous	SPTBN2	NM_006946.2		1,37,6457	AA,AG,GG		0.4191,0.0682,0.3002		387/2391	66476403	39,12951	2200	4295	6495	SO:0001819	synonymous_variant	6712	exon10			GCCCTCGCGGGGC	AB008567, AF026487, AF026488, AF079569	CCDS8150.1	11q13.2	2013-01-10			ENSG00000173898	ENSG00000173898		"""Pleckstrin homology (PH) domain containing"""	11276	protein-coding gene	gene with protein product		604985	"""spinocerebellar ataxia 5"""	SCA5		9826670, 16429157	Standard	NM_006946		Approved		uc001ojd.3	O15020	OTTHUMG00000167262	ENST00000533211.1:c.1161C>T	11.37:g.66476403G>A		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	95	28	0.294737	NM_006946	O14872|O14873	Silent	SNP	ENST00000533211.1	37	CCDS8150.1																																																																																			G|0.996;A|0.004	0.004	strong		0.622	SPTBN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393892.2	NM_006946	
KRT82	3888	hgsc.bcm.edu	37	12	52788814	52788814	+	Missense_Mutation	SNP	C	C	T	rs61730587	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:52788814C>T	ENST00000257974.2	-	9	1564	c.1487G>A	c.(1486-1488)cGg>cAg	p.R496Q	RP3-416H24.4_ENST00000547174.1_RNA	NM_033033.3	NP_149022.3	Q9NSB4	KRT82_HUMAN	keratin 82	496	Tail.					keratin filament (GO:0045095)	structural constituent of epidermis (GO:0030280)			endometrium(1)|kidney(2)|large_intestine(6)|liver(2)|lung(13)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	29				BRCA - Breast invasive adenocarcinoma(357;0.193)		GCTGGATTTCCGCCCGCTCCC	0.642													c|||	21	0.00419329	0.0023	0.0072	5008	,	,		16513	0.0		0.0089	False		,,,				2504	0.0041				p.R496Q		Atlas-SNP	.											KRT82,NS,carcinoma,-1,1	KRT82	45	1	0			c.G1487A						PASS	.	T	GLN/ARG	14,4392	21.2+/-45.6	0,14,2189	48.0	48.0	48.0		1487	-0.4	0.0	12	dbSNP_129	48	113,8487	58.7+/-120.3	1,111,4188	yes	missense	KRT82	NM_033033.3	43	1,125,6377	TT,TC,CC		1.314,0.3177,0.9765	benign	496/514	52788814	127,12879	2203	4300	6503	SO:0001583	missense	3888	exon9			GATTTCCGCCCGC	Y19207	CCDS8826.1	12q13	2013-01-16	2006-07-17	2006-07-17		ENSG00000161850		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6459	protein-coding gene	gene with protein product	"""hard keratin type II 2"""	601078	"""keratin, hair, basic, 2"""	KRTHB2		2431943, 16831889	Standard	NM_033033		Approved	Hb-2	uc001sai.1	Q9NSB4	OTTHUMG00000169636	ENST00000257974.2:c.1487G>A	12.37:g.52788814C>T	ENSP00000257974:p.Arg496Gln	Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	114	56	0.491228	NM_033033		Missense_Mutation	SNP	ENST00000257974.2	37	CCDS8826.1	11	0.005036630036630037	0	0.0	4	0.011049723756906077	0	0.0	7	0.009234828496042216	c	11.54	1.670563	0.29693	0.003177	0.01314	ENSG00000161850	ENST00000257974	D	0.82255	-1.59	4.59	-0.424	0.12321	.	0.753921	0.10873	N	0.624709	T	0.52933	0.1765	N	0.08118	0	0.09310	N	1	B	0.14438	0.01	B	0.04013	0.001	T	0.39800	-0.9596	10	0.25106	T	0.35	.	4.4613	0.11668	0.1481:0.4148:0.0:0.4371	rs61730587	496	Q9NSB4	KRT82_HUMAN	Q	496	ENSP00000257974:R496Q	ENSP00000257974:R496Q	R	-	2	0	KRT82	51075081	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.155000	0.16362	-0.326000	0.08564	-0.215000	0.12644	CGG	C|0.991;T|0.009	0.009	strong		0.642	KRT82-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405189.1	NM_033033	
MANBA	4126	hgsc.bcm.edu	37	4	103611845	103611845	+	Missense_Mutation	SNP	C	C	T	rs227368	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:103611845C>T	ENST00000226578.4	-	6	856	c.757G>A	c.(757-759)Gta>Ata	p.V253I	MANBA_ENST00000505239.1_Missense_Mutation_p.V196I	NM_005908.3	NP_005899.3	O00462	MANBA_HUMAN	mannosidase, beta A, lysosomal	253			V -> I (in dbSNP:rs227368). {ECO:0000269|PubMed:9384606}.|V -> L (in dbSNP:rs227368).		cellular protein modification process (GO:0006464)|glycoprotein catabolic process (GO:0006516)|mannan catabolic process (GO:0046355)	intracellular membrane-bounded organelle (GO:0043231)|lysosome (GO:0005764)	beta-mannosidase activity (GO:0004567)|mannose binding (GO:0005537)			cervix(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(12)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	42		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;4.44e-08)		GGGATGGCTACGATCACTTGA	0.393													C|||	1886	0.376597	0.1195	0.3545	5008	,	,		12527	0.4732		0.497	False		,,,				2504	0.5164				p.V253I		Atlas-SNP	.											.	MANBA	78	.	0			c.G757A						PASS	.	C	ILE/VAL	929,3477	354.1+/-312.5	107,715,1381	271.0	229.0	243.0		757	1.3	0.0	4	dbSNP_79	243	4081,4519	560.9+/-387.7	967,2147,1186	yes	missense	MANBA	NM_005908.3	29	1074,2862,2567	TT,TC,CC		47.4535,21.0849,38.5207	benign	253/880	103611845	5010,7996	2203	4300	6503	SO:0001583	missense	4126	exon6			TGGCTACGATCAC		CCDS3658.1	4q24	2013-09-20			ENSG00000109323	ENSG00000109323	3.2.1.25		6831	protein-coding gene	gene with protein product		609489				7876128	Standard	NM_005908		Approved		uc003hwg.3	O00462	OTTHUMG00000131123	ENST00000226578.4:c.757G>A	4.37:g.103611845C>T	ENSP00000226578:p.Val253Ile	Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	160	83	0.51875	NM_005908	Q96BC3|Q9NYX9	Missense_Mutation	SNP	ENST00000226578.4	37	CCDS3658.1	865	0.39606227106227104	58	0.11788617886178862	137	0.3784530386740331	288	0.5034965034965035	382	0.503957783641161	C	7.365	0.625609	0.14257	0.210849	0.474535	ENSG00000109323	ENST00000226578;ENST00000505239	T;T	0.55760	0.5;0.5	4.93	1.29	0.21616	.	0.358272	0.29342	N	0.012434	T	0.00012	0.0000	L	0.37800	1.135	0.48830	P	2.8799999999995496E-4	B;B	0.19583	0.037;0.016	B;B	0.08055	0.003;0.003	T	0.48536	-0.9027	9	0.25751	T	0.34	-10.9971	8.9216	0.35615	0.0:0.702:0.0:0.298	rs227368;rs3912789;rs52818263;rs58634559;rs227368	196;253	E9PFW2;O00462	.;MANBA_HUMAN	I	253;196	ENSP00000226578:V253I;ENSP00000427322:V196I	ENSP00000226578:V253I	V	-	1	0	MANBA	103830893	0.000000	0.05858	0.007000	0.13788	0.915000	0.54546	-0.243000	0.08915	0.016000	0.14998	-0.143000	0.13931	GTA	T|0.377;G|0.002;C|0.617;A|0.004	0.377	strong		0.393	MANBA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253803.2		
SRGN	5552	hgsc.bcm.edu	37	10	70856963	70856963	+	Missense_Mutation	SNP	C	C	G	rs67852477	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:70856963C>G	ENST00000242465.3	+	2	243	c.203C>G	c.(202-204)cCc>cGc	p.P68R	SRGN_ENST00000462445.1_Intron	NM_002727.2	NP_002718.2	P10124	SRGN_HUMAN	serglycin	68					biomineral tissue development (GO:0031214)|blood coagulation (GO:0007596)|granzyme-mediated apoptotic signaling pathway (GO:0008626)|maintenance of granzyme B location in T cell secretory granule (GO:0033382)|maintenance of protease location in mast cell secretory granule (GO:0033373)|mast cell secretory granule organization (GO:0033364)|negative regulation of bone mineralization (GO:0030502)|negative regulation of cytokine secretion (GO:0050710)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|protein processing (GO:0016485)|T cell secretory granule organization (GO:0033371)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|mast cell granule (GO:0042629)|platelet alpha granule lumen (GO:0031093)|zymogen granule (GO:0042588)				large_intestine(1)|lung(1)|skin(2)|upper_aerodigestive_tract(3)	7						AACAAGATCCCCCGTCTGAGG	0.413													C|||	22	0.00439297	0.0008	0.0029	5008	,	,		16334	0.001		0.0149	False		,,,				2504	0.0031				p.P68R		Atlas-SNP	.											SRGN,NS,carcinoid-endocrine_tumour,0,1	SRGN	15	1	0			c.C203G						PASS	.	C	ARG/PRO	12,4394	19.1+/-41.9	0,12,2191	96.0	87.0	90.0		203	0.2	0.0	10	dbSNP_130	90	107,8493	57.2+/-118.5	1,105,4194	yes	missense	SRGN	NM_002727.2	103	1,117,6385	GG,GC,CC		1.2442,0.2724,0.915	possibly-damaging	68/159	70856963	119,12887	2203	4300	6503	SO:0001583	missense	5552	exon2			AGATCCCCCGTCT	BC015516	CCDS7285.1	10q22.1	2007-02-16	2007-02-15	2007-02-15	ENSG00000122862	ENSG00000122862		"""Proteoglycans / Extracellular Matrix : Other"""	9361	protein-coding gene	gene with protein product	"""serglycin proteoglycan"""	177040	"""proteoglycan 1, secretory granule"""	PRG, PRG1			Standard	NR_036430		Approved	PPG	uc001joz.3	P10124	OTTHUMG00000018369	ENST00000242465.3:c.203C>G	10.37:g.70856963C>G	ENSP00000242465:p.Pro68Arg	Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	122	62	0.508197	NM_002727	B2R4L7|Q5VW06	Missense_Mutation	SNP	ENST00000242465.3	37	CCDS7285.1	15	0.006868131868131868	0	0.0	2	0.0055248618784530384	1	0.0017482517482517483	12	0.0158311345646438	C	4.802	0.149123	0.09185	0.002724	0.012442	ENSG00000122862	ENST00000242465	T	0.50548	0.74	5.26	0.242	0.15498	.	1.444430	0.04231	N	0.335288	T	0.22704	0.0548	L	0.29908	0.895	0.09310	N	1	B	0.25955	0.138	B	0.32677	0.15	T	0.33292	-0.9874	10	0.59425	D	0.04	-14.8937	4.3284	0.11051	0.0:0.2911:0.1779:0.531	.	68	P10124	SRGN_HUMAN	R	68	ENSP00000242465:P68R	ENSP00000242465:P68R	P	+	2	0	SRGN	70526969	0.002000	0.14202	0.000000	0.03702	0.006000	0.05464	0.360000	0.20250	-0.129000	0.11620	-0.367000	0.07326	CCC	C|0.991;G|0.009	0.009	strong		0.413	SRGN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048379.1	NM_002727	
DPP3	10072	hgsc.bcm.edu	37	11	66254085	66254085	+	Missense_Mutation	SNP	G	G	T	rs11550299	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:66254085G>T	ENST00000360510.2	+	4	500	c.435G>T	c.(433-435)caG>caT	p.Q145H	DPP3_ENST00000531863.1_Missense_Mutation_p.Q165H|DPP3_ENST00000532677.1_Missense_Mutation_p.Q164H|DPP3_ENST00000453114.1_Missense_Mutation_p.Q145H|DPP3_ENST00000541961.1_Missense_Mutation_p.Q145H|DPP3_ENST00000530165.1_Missense_Mutation_p.Q115H			Q9NY33	DPP3_HUMAN	dipeptidyl-peptidase 3	145			Q -> H (in dbSNP:rs11550299). {ECO:0000269|Ref.1}.		proteolysis (GO:0006508)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	dipeptidyl-peptidase activity (GO:0008239)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.Q145H(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|skin(2)|stomach(1)	23						GCCTCTGGCAGACCTGCGGGG	0.627													G|||	1083	0.216254	0.1884	0.1599	5008	,	,		18833	0.2887		0.2416	False		,,,				2504	0.1933				p.Q145H		Atlas-SNP	.											DPP3,colon,carcinoma,0,2	DPP3	61	2	1	Substitution - Missense(1)	stomach(1)	c.G435T						PASS	.	G	HIS/GLN,HIS/GLN	742,3658	306.3+/-289.4	57,628,1515	86.0	87.0	86.0		435,435	4.0	1.0	11	dbSNP_120	86	2007,6583	351.3+/-328.2	227,1553,2515	yes	missense,missense	DPP3	NM_005700.3,NM_130443.2	24,24	284,2181,4030	TT,TG,GG		23.3644,16.8636,21.1624	benign,benign	145/738,145/738	66254085	2749,10241	2200	4295	6495	SO:0001583	missense	10072	exon4			CTGGCAGACCTGC	AB017970	CCDS8141.1, CCDS58147.1	11q12-q13.1	2008-02-05	2006-01-12		ENSG00000254986	ENSG00000254986	3.4.14.4		3008	protein-coding gene	gene with protein product		606818	"""dipeptidylpeptidase III"", ""dipeptidylpeptidase 3"""			10773679	Standard	NM_005700		Approved		uc001oif.2	Q9NY33	OTTHUMG00000167143	ENST00000360510.2:c.435G>T	11.37:g.66254085G>T	ENSP00000353701:p.Gln145His	Somatic	215	0	0		WXS	Illumina HiSeq	Phase_I	213	149	0.699531	NM_130443	B2RDB5|B4DLX4|F5H8L6|O95748|Q969H2|Q9BV67|Q9HAL6	Missense_Mutation	SNP	ENST00000360510.2	37	CCDS8141.1	519	0.23763736263736263	85	0.17276422764227642	71	0.19613259668508287	167	0.291958041958042	196	0.25857519788918204	G	10.43	1.346721	0.24426	0.168636	0.233644	ENSG00000254986	ENST00000531863;ENST00000532677;ENST00000360510;ENST00000453114;ENST00000541961;ENST00000532019;ENST00000526515;ENST00000530165;ENST00000533725;ENST00000543807;ENST00000347422;ENST00000531354	T;T;T;T;T;T;T;T;T;T	0.22945	1.93;1.93;1.93;1.93;1.93;1.93;1.93;1.93;1.93;1.93	5.02	4.04	0.47022	.	0.388366	0.26844	N	0.022209	T	0.00012	0.0000	N	0.20986	0.625	0.36036	P	0.16023600000000005	B;B	0.06786	0.001;0.001	B;B	0.14578	0.011;0.006	T	0.29882	-0.9997	9	0.42905	T	0.14	.	6.2999	0.21107	0.0985:0.1891:0.7125:0.0	rs11550299;rs58287157;rs11550299	164;145	G3V1D3;Q9NY33	.;DPP3_HUMAN	H	165;164;145;145;145;43;115;115;43;43;145;145	ENSP00000432782:Q165H;ENSP00000435284:Q164H;ENSP00000353701:Q145H;ENSP00000389943:Q145H;ENSP00000440502:Q145H;ENSP00000437101:Q43H;ENSP00000431606:Q115H;ENSP00000436941:Q115H;ENSP00000434518:Q43H;ENSP00000432618:Q145H	ENSP00000309957:Q145H	Q	+	3	2	DPP3	66010661	0.923000	0.31300	1.000000	0.80357	0.358000	0.29455	0.497000	0.22514	2.323000	0.78572	0.561000	0.74099	CAG	G|0.781;T|0.219	0.219	strong		0.627	DPP3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393424.2		
MYCBP2	23077	hgsc.bcm.edu	37	13	77672767	77672767	+	Missense_Mutation	SNP	C	C	T	rs142807127	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:77672767C>T	ENST00000544440.2	-	56	8425	c.8408G>A	c.(8407-8409)cGc>cAc	p.R2803H	MYCBP2-AS1_ENST00000593933.1_RNA|MYCBP2_ENST00000357337.6_Missense_Mutation_p.R2803H|MYCBP2_ENST00000360084.5_Missense_Mutation_p.R326H|MYCBP2_ENST00000482517.1_5'UTR|MYCBP2_ENST00000407578.2_Missense_Mutation_p.R2841H					MYC binding protein 2, E3 ubiquitin protein ligase											NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|lung(51)|ovary(5)|pancreas(2)|prostate(5)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	118		Breast(118;0.212)|Acute lymphoblastic leukemia(28;0.22)		GBM - Glioblastoma multiforme(99;0.109)		TGAGGAGGAGCGTGGAGAACT	0.488													C|||	7	0.00139776	0.0	0.0029	5008	,	,		21001	0.001		0.004	False		,,,				2504	0.0				p.R2841H		Atlas-SNP	.											MYCBP2_ENST00000407578,colon,carcinoma,-1,4	MYCBP2	1029	4	0			c.G8522A						scavenged	.	C	HIS/ARG	0,4406		0,0,2203	151.0	150.0	150.0		8522	5.4	1.0	13	dbSNP_134	150	13,8587	9.8+/-36.6	0,13,4287	yes	missense	MYCBP2	NM_015057.4	29	0,13,6490	TT,TC,CC		0.1512,0.0,0.1	possibly-damaging	2841/4679	77672767	13,12993	2203	4300	6503	SO:0001583	missense	23077	exon56			GAGGAGCGTGGAG	AB020723		13q22	2012-02-23	2012-02-23		ENSG00000005810	ENSG00000005810			23386	protein-coding gene	gene with protein product		610392	"""MYC binding protein 2"""			9689053, 15057823	Standard	NM_015057		Approved	PAM, KIAA0916, FLJ10106	uc021rks.1	O75592	OTTHUMG00000017105	ENST00000544440.2:c.8408G>A	13.37:g.77672767C>T	ENSP00000444596:p.Arg2803His	Somatic	224	0	0		WXS	Illumina HiSeq	Phase_I	196	2	0.0102041	NM_015057		Missense_Mutation	SNP	ENST00000544440.2	37		5	0.0022893772893772895	0	0.0	2	0.0055248618784530384	1	0.0017482517482517483	2	0.002638522427440633	C	14.61	2.586329	0.46110	0.0	0.001512	ENSG00000005810	ENST00000357337;ENST00000407578;ENST00000544440;ENST00000360084	T;T;T;T	0.51574	1.42;1.41;1.42;0.7	5.45	5.45	0.79879	.	0.107596	0.64402	D	0.000004	T	0.30198	0.0757	L	0.27053	0.805	0.45097	D	0.998113	B;B;B	0.27192	0.171;0.005;0.004	B;B;B	0.16722	0.016;0.002;0.001	T	0.09729	-1.0661	10	0.42905	T	0.14	.	19.2929	0.94110	0.0:1.0:0.0:0.0	.	189;2803;2803	Q9UG08;O75592-2;O75592	.;.;MYCB2_HUMAN	H	2803;2841;2803;326	ENSP00000349892:R2803H;ENSP00000384288:R2841H;ENSP00000444596:R2803H;ENSP00000353197:R326H	ENSP00000349892:R2803H	R	-	2	0	MYCBP2	76570768	1.000000	0.71417	0.999000	0.59377	0.994000	0.84299	5.617000	0.67716	2.579000	0.87056	0.591000	0.81541	CGC	C|0.998;T|0.002	0.002	strong		0.488	MYCBP2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000045326.1	NM_015057	
CACNA1C	775	hgsc.bcm.edu	37	12	2788879	2788879	+	Silent	SNP	G	G	A	rs1051375	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:2788879G>A	ENST00000347598.4	+	44	5505	c.5505G>A	c.(5503-5505)acG>acA	p.T1835T	CACNA1C_ENST00000335762.5_Silent_p.T1812T|CACNA1C_ENST00000399621.1_Silent_p.T1806T|CACNA1C_ENST00000399617.1_Silent_p.T1787T|CACNA1C_ENST00000399644.1_Silent_p.T1787T|CACNA1C_ENST00000399634.1_Silent_p.T1787T|CACNA1C_ENST00000399603.1_Silent_p.T1787T|CACNA1C_ENST00000399649.1_Silent_p.T1793T|CACNA1C_ENST00000327702.7_Silent_p.T1787T|CACNA1C_ENST00000399655.1_Silent_p.T1787T|CACNA1C_ENST00000406454.3_Silent_p.T1787T|CACNA1C_ENST00000399637.1_Silent_p.T1806T|CACNA1C_ENST00000399591.1_Silent_p.T1795T|CACNA1C_ENST00000399641.1_Silent_p.T1787T|CACNA1C_ENST00000399606.1_Silent_p.T1807T|CACNA1C-AS1_ENST00000501371.1_RNA|CACNA1C_ENST00000399601.1_Silent_p.T1787T|CACNA1C_ENST00000399629.1_Silent_p.T1804T|CACNA1C_ENST00000402845.3_Silent_p.T1806T|CACNA1C_ENST00000344100.3_Silent_p.T1828T|CACNA1C_ENST00000399638.1_Silent_p.T1815T|CACNA1C_ENST00000399595.1_Silent_p.T1795T|CACNA1C_ENST00000399597.1_Silent_p.T1787T	NM_001129827.1|NM_199460.2	NP_001123299.1|NP_955630.2	Q13936	CAC1C_HUMAN	calcium channel, voltage-dependent, L type, alpha 1C subunit	1835					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)	ACCCCAGCACGGTCAGCACTG	0.687													G|||	2636	0.526358	0.1717	0.6542	5008	,	,		17117	0.6062		0.7038	False		,,,				2504	0.6503				p.T1835T		Atlas-SNP	.											.	CACNA1C	1023	.	0			c.G5505A						PASS	.	G	,,,,,,,,,,,,,,,,,,,,,,	1118,2944		170,778,1083	39.0	45.0	43.0		5361,5505,5484,5361,5445,5421,5418,5418,5418,5412,5385,5385,5379,5361,5361,5361,5361,5352,5328,5361,5361,5328,5505	-10.1	0.0	12	dbSNP_86	43	6110,2266		2243,1624,321	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	,,,,,,,,,,,,,,,,,,,,,,	2413,2402,1404	AA,AG,GG		27.0535,27.5234,41.8878	,,,,,,,,,,,,,,,,,,,,,,	1787/2139,1835/2187,1828/2180,1787/2174,1815/2167,1807/2159,1806/2158,1806/2158,1806/2158,1804/2156,1795/2147,1795/2147,1793/2145,1787/2139,1787/2139,1787/2139,1787/2139,1784/2136,1776/2128,1787/2139,1787/2174,1776/2199,1835/2222	2788879	7228,5210	2031	4188	6219	SO:0001819	synonymous_variant	775	exon44			CAGCACGGTCAGC	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.5505G>A	12.37:g.2788879G>A		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	85	84	0.988235	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																																																																																			G|0.374;A|0.626	0.626	strong		0.687	CACNA1C-017	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317035.1	NM_000719	
FBXL5	26234	hgsc.bcm.edu	37	4	15640168	15640168	+	Silent	SNP	C	C	T	rs3182730	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:15640168C>T	ENST00000341285.3	-	4	670	c.546G>A	c.(544-546)aaG>aaA	p.K182K	FBXL5_ENST00000382358.4_Silent_p.K56K|FBXL5_ENST00000412094.2_Silent_p.K165K	NM_001193534.1|NM_001193535.1|NM_012161.3	NP_001180463.1|NP_001180464.1|NP_036293.1	Q9UKA1	FBXL5_HUMAN	F-box and leucine-rich repeat protein 5	182					iron ion homeostasis (GO:0055072)|protein ubiquitination (GO:0016567)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)	perinuclear region of cytoplasm (GO:0048471)|SCF ubiquitin ligase complex (GO:0019005)|ubiquitin ligase complex (GO:0000151)	iron ion binding (GO:0005506)|ubiquitin-protein transferase activity (GO:0004842)			endometrium(2)|large_intestine(3)|lung(5)|ovary(1)|pancreas(1)|prostate(1)	13						ATTTAAAAAACTTCTGTCGCT	0.338													C|||	481	0.0960463	0.0696	0.0807	5008	,	,		17245	0.0337		0.1581	False		,,,				2504	0.1431				p.K182K		Atlas-SNP	.											.	FBXL5	52	.	0			c.G546A						PASS	.	C	,,	325,4079	169.8+/-200.3	11,303,1888	71.0	66.0	68.0		546,495,546	1.8	1.0	4	dbSNP_105	68	1251,7349	250.0+/-277.0	99,1053,3148	no	coding-synonymous,coding-synonymous,coding-synonymous	FBXL5	NM_001193534.1,NM_001193535.1,NM_012161.3	,,	110,1356,5036	TT,TC,CC		14.5465,7.3797,12.1193	,,	182/691,165/675,182/692	15640168	1576,11428	2202	4300	6502	SO:0001819	synonymous_variant	26234	exon4			AAAAAACTTCTGT	AF174591	CCDS3415.1, CCDS54745.1	4p15.33	2011-06-09			ENSG00000118564	ENSG00000118564		"""F-boxes / Leucine-rich repeats"""	13602	protein-coding gene	gene with protein product		605655				10531035	Standard	NM_012161		Approved	FBL4, FBL5, FLR1	uc003goc.2	Q9UKA1	OTTHUMG00000097097	ENST00000341285.3:c.546G>A	4.37:g.15640168C>T		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	84	42	0.5	NM_001193534	A8MSK4|B4DIB5|Q4W5A8|Q8NHP3|Q9NXN2|Q9P0I0|Q9P0X5|Q9UJT7|Q9UKC8	Silent	SNP	ENST00000341285.3	37	CCDS3415.1	212	0.09706959706959707	50	0.1016260162601626	35	0.09668508287292818	18	0.03146853146853147	109	0.1437994722955145	C	7.981	0.751222	0.15778	0.073797	0.145465	ENSG00000118564	ENST00000513163	.	.	.	5.49	1.79	0.24919	.	.	.	.	.	T	0.00356	0.0011	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.09574	-1.0668	3	.	.	.	-22.075	10.3944	0.44192	0.0:0.6401:0.0:0.3599	rs3182730;rs17418670	.	.	.	I	103	.	.	V	-	1	0	FBXL5	15249266	0.999000	0.42202	0.996000	0.52242	0.856000	0.48823	0.528000	0.23002	0.080000	0.16959	-0.961000	0.02630	GTT	T|0.112;G|0.000;C|0.888	0.112	strong		0.338	FBXL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214235.2		
TIAM2	26230	hgsc.bcm.edu	37	6	155500242	155500242	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:155500242T>C	ENST00000461783.3	+	13	3866	c.2593T>C	c.(2593-2595)Tgc>Cgc	p.C865R	TIAM2_ENST00000318981.5_Missense_Mutation_p.C865R|TIAM2_ENST00000360366.4_Missense_Mutation_p.C889R|TIAM2_ENST00000528391.2_Missense_Mutation_p.C201R|TIAM2_ENST00000529824.2_Missense_Mutation_p.C865R|TIAM2_ENST00000456144.1_Missense_Mutation_p.C865R|TIAM2_ENST00000456877.2_Missense_Mutation_p.C177R|TIAM2_ENST00000367174.2_Missense_Mutation_p.C241R			Q8IVF5	TIAM2_HUMAN	T-cell lymphoma invasion and metastasis 2	865	RBD. {ECO:0000255|PROSITE- ProRule:PRU00262}.				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)		TGTTGAGTATTGCATCCCTGC	0.383																																					p.C865R		Atlas-SNP	.											.	TIAM2	161	.	0			c.T2593C						PASS	.						118.0	107.0	111.0					6																	155500242		2203	4300	6503	SO:0001583	missense	26230	exon10			GAGTATTGCATCC		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.2593T>C	6.37:g.155500242T>C	ENSP00000437188:p.Cys865Arg	Somatic	210	0	0		WXS	Illumina HiSeq	Phase_I	146	46	0.315068	NM_012454	B2RP56|C9JZV2|Q6NXN9|Q6ZUP9|Q9UFG6|Q9UKV9|Q9UKW0	Missense_Mutation	SNP	ENST00000461783.3	37	CCDS34558.1	.	.	.	.	.	.	.	.	.	.	T	6.692	0.496320	0.12762	.	.	ENSG00000146426	ENST00000461783;ENST00000528928;ENST00000528535;ENST00000456144;ENST00000318981;ENST00000367174;ENST00000360366;ENST00000529824;ENST00000456877;ENST00000528391	T;T;T;T;T;T;T;T;T	0.37411	1.2;1.2;1.2;1.2;1.2;1.2;1.2;1.2;1.2	5.18	1.17	0.20885	Raf-like Ras-binding (2);PDZ/DHR/GLGF (1);	0.495104	0.22584	N	0.058171	T	0.09730	0.0239	L	0.44542	1.39	0.09310	N	0.999997	B;B;B;B	0.09022	0.001;0.002;0.002;0.001	B;B;B;B	0.09377	0.001;0.003;0.004;0.001	T	0.27773	-1.0064	10	0.28530	T	0.3	.	5.0741	0.14622	0.2795:0.0759:0.0:0.6446	.	201;865;889;865	E9PKT1;Q8IVF5-2;Q8IVF5-5;Q8IVF5	.;.;.;TIAM2_HUMAN	R	865;1111;865;865;865;241;889;865;177;201	ENSP00000437188:C865R;ENSP00000434901:C865R;ENSP00000407746:C865R;ENSP00000327315:C865R;ENSP00000356142:C241R;ENSP00000353528:C889R;ENSP00000433348:C865R;ENSP00000407183:C177R;ENSP00000435335:C201R	ENSP00000327315:C865R	C	+	1	0	TIAM2	155541934	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.639000	0.24690	0.379000	0.24794	0.533000	0.62120	TGC	.	.	none		0.383	TIAM2-005	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000387980.2	NM_012454	
PCDH15	65217	hgsc.bcm.edu	37	10	55892642	55892642	+	Missense_Mutation	SNP	T	T	C	rs61731389	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:55892642T>C	ENST00000320301.6	-	15	2304	c.1910A>G	c.(1909-1911)aAt>aGt	p.N637S	PCDH15_ENST00000409834.1_Missense_Mutation_p.N248S|PCDH15_ENST00000395432.2_Missense_Mutation_p.N600S|PCDH15_ENST00000395433.1_Missense_Mutation_p.N615S|PCDH15_ENST00000395445.1_Missense_Mutation_p.N644S|PCDH15_ENST00000373957.3_Missense_Mutation_p.N615S|PCDH15_ENST00000395442.1_Intron|PCDH15_ENST00000395438.1_Missense_Mutation_p.N637S|PCDH15_ENST00000373965.2_Missense_Mutation_p.N644S|PCDH15_ENST00000395430.1_Missense_Mutation_p.N637S|PCDH15_ENST00000395440.1_Intron|PCDH15_ENST00000395446.1_Missense_Mutation_p.N637S|PCDH15_ENST00000373955.1_Missense_Mutation_p.N637S|PCDH15_ENST00000414778.1_Missense_Mutation_p.N642S|PCDH15_ENST00000437009.1_Intron|PCDH15_ENST00000361849.3_Missense_Mutation_p.N637S	NM_033056.3	NP_149045.3	Q96QU1	PCD15_HUMAN	protocadherin-related 15	637	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|synapse (GO:0045202)	calcium ion binding (GO:0005509)			NS(3)|breast(6)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(39)|lung(108)|ovary(5)|pancreas(6)|prostate(6)|skin(12)|upper_aerodigestive_tract(12)|urinary_tract(1)	237		Melanoma(3;0.117)|Lung SC(717;0.238)				TACCTGTAGATTTAATAAAAC	0.408										HNSCC(58;0.16)			T|||	158	0.0315495	0.0461	0.0144	5008	,	,		17098	0.001		0.0338	False		,,,				2504	0.0532				p.N642S		Atlas-SNP	.											.	PCDH15	1715	.	0			c.A1925G						PASS	.	T	SER/ASN,SER/ASN,,SER/ASN,SER/ASN,SER/ASN,SER/ASN,SER/ASN,SER/ASN,SER/ASN,SER/ASN,SER/ASN	161,4245	108.2+/-146.6	3,155,2045	100.0	81.0	87.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1925,1910,,1910,1799,1844,1946,1910,1925,1910,1844,1910	3.2	1.0	10	dbSNP_129	87	242,8358	95.4+/-157.2	6,230,4064	yes	missense,missense,intron,missense,missense,missense,missense,missense,missense,missense,missense,missense	PCDH15	NM_001142763.1,NM_001142764.1,NM_001142765.1,NM_001142766.1,NM_001142767.1,NM_001142768.1,NM_001142769.1,NM_001142770.1,NM_001142771.1,NM_001142772.1,NM_001142773.1,NM_033056.3	46,46,,46,46,46,46,46,46,46,46,46	9,385,6109	CC,CT,TT		2.814,3.6541,3.0986	possibly-damaging,possibly-damaging,,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	642/1963,637/1958,,637/1953,600/1916,615/1936,649/1791,637/1540,642/1683,637/1678,615/1933,637/1956	55892642	403,12603	2203	4300	6503	SO:0001583	missense	65217	exon16			TGTAGATTTAATA	AY029205	CCDS7248.1, CCDS44400.1, CCDS44401.1, CCDS44403.1, CCDS44404.1, CCDS73134.1, CCDS73135.1, CCDS73136.1, CCDS73137.1, CCDS73138.1	10q21.1	2013-01-08	2010-01-25		ENSG00000150275	ENSG00000150275		"""Cadherins / Cadherin-related"""	14674	protein-coding gene	gene with protein product	"""cadherin-related family member 15"""	605514	"""deafness, autosomal recessive 23"", ""protocadherin 15"""	USH1F, DFNB23		11398101, 14570705	Standard	NM_033056		Approved	CDHR15	uc010qhy.1	Q96QU1	OTTHUMG00000018259	ENST00000320301.6:c.1910A>G	10.37:g.55892642T>C	ENSP00000322604:p.Asn637Ser	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	82	35	0.426829	NM_001142763	A6NL19|C6ZEF5|C6ZEF6|C6ZEF7|Q5VY38|Q5VY39|Q6TRH8|Q8NDB9|Q96QT8	Missense_Mutation	SNP	ENST00000320301.6	37	CCDS7248.1	55	0.025183150183150184	26	0.052845528455284556	3	0.008287292817679558	0	0.0	26	0.03430079155672823	T	16.74	3.206373	0.58343	0.036541	0.02814	ENSG00000150275	ENST00000373965;ENST00000414778;ENST00000455746;ENST00000395438;ENST00000409834;ENST00000395445;ENST00000395446;ENST00000395432;ENST00000361849;ENST00000395433;ENST00000373957;ENST00000320301;ENST00000395430;ENST00000417177;ENST00000373955	T;T;T;T;T;T;T;T;T;T;T;T;T	0.50813	0.73;0.73;0.73;0.73;0.73;0.73;0.73;0.73;0.73;0.73;0.73;0.73;0.73	5.67	3.23	0.37069	Cadherin (3);Cadherin-like (1);	.	.	.	.	T	0.13286	0.0322	N	0.25286	0.73	0.80722	D	1	D;P;D;P;P;D;P;D;P;P;D;P;D;P	0.76494	0.999;0.87;0.969;0.723;0.935;0.999;0.955;0.988;0.939;0.939;0.988;0.859;0.975;0.743	D;P;P;P;P;D;P;P;P;P;P;P;P;P	0.85130	0.997;0.661;0.81;0.636;0.772;0.997;0.78;0.9;0.867;0.867;0.9;0.597;0.829;0.661	T	0.04229	-1.0967	9	0.37606	T	0.19	.	8.3448	0.32266	0.1315:0.0:0.1378:0.7307	.	615;637;637;642;600;637;637;644;644;637;642;637;615;637	A2A3E8;E7EMG4;A2A3E7;C9JIG1;E7EMG0;A2A3E6;A2A3E3;C6ZEF5;A2A3E2;C6ZEF7;C9J4F3;Q96QU1-3;A2A3D8;Q96QU1	.;.;.;.;.;.;.;.;.;.;.;.;.;PCD15_HUMAN	S	644;642;637;637;248;644;637;600;637;615;615;637;637;642;637	ENSP00000363076:N644S;ENSP00000410304:N642S;ENSP00000378826:N637S;ENSP00000386693:N248S;ENSP00000378832:N644S;ENSP00000378833:N637S;ENSP00000378820:N600S;ENSP00000354950:N637S;ENSP00000378821:N615S;ENSP00000363068:N615S;ENSP00000322604:N637S;ENSP00000378818:N637S;ENSP00000363066:N637S	ENSP00000322604:N637S	N	-	2	0	PCDH15	55562648	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	5.968000	0.70413	0.446000	0.26666	0.482000	0.46254	AAT	T|0.969;C|0.031	0.031	strong		0.408	PCDH15-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000048121.2	NM_033056	
HRNR	388697	hgsc.bcm.edu	37	1	152192549	152192549	+	Missense_Mutation	SNP	T	T	G	rs12145941	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:152192549T>G	ENST00000368801.2	-	3	1631	c.1556A>C	c.(1555-1557)cAg>cCg	p.Q519P	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_001009931.1	NP_001009931.1	Q86YZ3	HORN_HUMAN	hornerin	519					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)			AGACCCATGCTGACCATAGCT	0.582													T|||	173	0.0345447	0.003	0.0735	5008	,	,		22960	0.0		0.0835	False		,,,				2504	0.0348				p.Q519P		Atlas-SNP	.											.	HRNR	403	.	0			c.A1556C						PASS	.	T	PRO/GLN	65,4341	61.1+/-98.1	0,65,2138	250.0	240.0	244.0		1556	0.6	0.0	1	dbSNP_120	244	737,7863	178.2+/-227.6	26,685,3589	yes	missense	HRNR	NM_001009931.1	76	26,750,5727	GG,GT,TT		8.5698,1.4753,6.1664	possibly-damaging	519/2851	152192549	802,12204	2203	4300	6503	SO:0001583	missense	388697	exon3			CCATGCTGACCAT	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.1556A>C	1.37:g.152192549T>G	ENSP00000357791:p.Gln519Pro	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	76	39	0.513158	NM_001009931	Q5DT20|Q5U1F4	Missense_Mutation	SNP	ENST00000368801.2	37	CCDS30859.1	96	0.04395604395604396	2	0.0040650406504065045	30	0.08287292817679558	0	0.0	64	0.08443271767810026	T	3.533	-0.095353	0.07010	0.014753	0.085698	ENSG00000197915	ENST00000368801	T	0.01767	4.65	3.15	0.586	0.17434	.	.	.	.	.	T	0.00356	0.0011	N	0.14661	0.345	0.09310	N	1	P	0.50943	0.94	B	0.38378	0.272	T	0.42599	-0.9442	9	0.30078	T	0.28	.	2.9033	0.05713	0.1847:0.2313:0.0:0.584	rs12145941	519	Q86YZ3	HORN_HUMAN	P	519	ENSP00000357791:Q519P	ENSP00000357791:Q519P	Q	-	2	0	HRNR	150459173	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.108000	0.15396	-0.038000	0.13624	-0.451000	0.05528	CAG	T|0.939;G|0.061	0.061	strong		0.582	HRNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034016.1	XM_373868	
CLEC18A	348174	hgsc.bcm.edu	37	16	69996928	69996928	+	Missense_Mutation	SNP	G	G	A	rs201545424	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:69996928G>A	ENST00000288040.6	+	11	1448	c.1261G>A	c.(1261-1263)Gac>Aac	p.D421N	CLEC18A_ENST00000393701.2_Missense_Mutation_p.D421N|CLEC18A_ENST00000449317.2_Missense_Mutation_p.D430N|CLEC18A_ENST00000568461.1_Missense_Mutation_p.D421N	NM_001136214.2	NP_001129686.1	A5D8T8	CL18A_HUMAN	C-type lectin domain family 18, member A	421	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.			D -> N (in Ref. 4; AAH78143). {ECO:0000305}.		extracellular region (GO:0005576)	carbohydrate binding (GO:0030246)			NS(1)|endometrium(2)|lung(1)|skin(1)	5						CAACTGGAACGACCAGCGCTG	0.597																																					p.D421N		Atlas-SNP	.											CLEC18A,NS,carcinoma,0,1	CLEC18A	9	1	0			c.G1261A						scavenged	.						50.0	33.0	39.0					16																	69996928		2178	3959	6137	SO:0001583	missense	348174	exon12			TGGAACGACCAGC	AF428259	CCDS10886.1	16q22.1	2010-04-27	2009-03-10	2009-03-10		ENSG00000157322		"""C-type lectin domain containing"""	30388	protein-coding gene	gene with protein product	"""mannose receptor-like"""					12975309	Standard	NM_001136214		Approved	MRCL	uc010vlo.3	A5D8T8		ENST00000288040.6:c.1261G>A	16.37:g.69996928G>A	ENSP00000288040:p.Asp421Asn	Somatic	339	1	0.00294985		WXS	Illumina HiSeq	Phase_I	429	64	0.149184	NM_001271197	A8K1G9|Q6DCB3|Q7Z5K9|Q96HH2	Missense_Mutation	SNP	ENST00000288040.6	37	CCDS10886.1	.	.	.	.	.	.	.	.	.	.	.	15.17	2.752501	0.49362	.	.	ENSG00000157322	ENST00000393701;ENST00000449317;ENST00000288040	T;T;T	0.59906	0.23;0.23;0.23	1.77	1.77	0.24775	C-type lectin fold (1);C-type lectin, conserved site (1);C-type lectin-like (1);C-type lectin (3);	0.063063	0.64402	D	0.000011	T	0.64249	0.2581	L	0.52364	1.645	0.33125	D	0.542299	D	0.76494	0.999	D	0.83275	0.996	T	0.68454	-0.5404	9	.	.	.	.	7.0966	0.25313	0.0:0.0:1.0:0.0	.	421	A5D8T8	CL18A_HUMAN	N	421;430;421	ENSP00000377304:D421N;ENSP00000413990:D430N;ENSP00000288040:D421N	.	D	+	1	0	CLEC18A	68554429	1.000000	0.71417	1.000000	0.80357	0.665000	0.39181	3.563000	0.53784	1.309000	0.44985	0.175000	0.17021	GAC	G|0.500;A|0.500	0.500	weak		0.597	CLEC18A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000268955.2	NM_182619	
UNC5CL	222643	hgsc.bcm.edu	37	6	40996173	40996173	+	Missense_Mutation	SNP	G	G	C	rs742491	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:40996173G>C	ENST00000373164.1	-	8	1556	c.1496C>G	c.(1495-1497)cCa>cGa	p.P499R	UNC5CL_ENST00000470102.1_5'UTR|UNC5CL_ENST00000244565.3_Missense_Mutation_p.P499R			Q8IV45	UN5CL_HUMAN	unc-5 homolog C (C. elegans)-like	499					positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of JNK cascade (GO:0046330)|proteolysis (GO:0006508)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	peptidase activity (GO:0008233)			endometrium(1)|kidney(3)|large_intestine(3)|lung(3)|ovary(2)|upper_aerodigestive_tract(1)	13	Ovarian(28;0.0418)|Colorectal(47;0.196)					CTCGGGGCCTGGGCTGCCGCC	0.701											OREG0017423	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	39	0.00778754	0.0	0.0317	5008	,	,		14141	0.0		0.0119	False		,,,				2504	0.0051				p.P499R		Atlas-SNP	.											UNC5CL,NS,carcinoma,-1,1	UNC5CL	52	1	0			c.C1496G						scavenged	.	G	ARG/PRO	6,4344		0,6,2169	15.0	16.0	16.0		1496	4.3	0.9	6	dbSNP_86	16	94,8406		0,94,4156	yes	missense	UNC5CL	NM_173561.2	103	0,100,6325	CC,CG,GG		1.1059,0.1379,0.7782	probably-damaging	499/519	40996173	100,12750	2175	4250	6425	SO:0001583	missense	222643	exon9			GGGCCTGGGCTGC	BC035284	CCDS4847.1	6p21.1	2013-10-15			ENSG00000124602	ENSG00000124602			21203	protein-coding gene	gene with protein product	"""ZU5 and death domain containing"""					14769797	Standard	NM_173561		Approved	MGC34763, ZUD	uc003opi.3	Q8IV45	OTTHUMG00000014665	ENST00000373164.1:c.1496C>G	6.37:g.40996173G>C	ENSP00000362258:p.Pro499Arg	Somatic	93	1	0.0107527	897	WXS	Illumina HiSeq	Phase_I	119	63	0.529412	NM_173561	Q5TGU1	Missense_Mutation	SNP	ENST00000373164.1	37	CCDS4847.1	19	0.0086996336996337	2	0.0040650406504065045	8	0.022099447513812154	0	0.0	9	0.011873350923482849	G	14.69	2.611437	0.46631	0.001379	0.011059	ENSG00000124602	ENST00000244565;ENST00000373164	T;T	0.14893	2.47;2.47	4.32	4.32	0.51571	.	0.000000	0.42294	D	0.000740	T	0.06234	0.0161	L	0.34521	1.04	0.27905	N	0.938813	B	0.14805	0.011	B	0.11329	0.006	T	0.17961	-1.0352	10	0.87932	D	0	-9.0643	12.31	0.54924	0.0:0.0:1.0:0.0	rs742491	499	Q8IV45	UN5CL_HUMAN	R	499	ENSP00000244565:P499R;ENSP00000362258:P499R	ENSP00000244565:P499R	P	-	2	0	UNC5CL	41104151	0.997000	0.39634	0.857000	0.33713	0.038000	0.13279	3.183000	0.50918	1.956000	0.56807	0.563000	0.77884	CCA	G|0.992;C|0.008	0.008	strong		0.701	UNC5CL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040491.1	NM_173561	
CDH6	1004	hgsc.bcm.edu	37	5	31302288	31302288	+	Silent	SNP	C	C	T	rs2287582	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:31302288C>T	ENST00000265071.2	+	6	1147	c.882C>T	c.(880-882)gaC>gaT	p.D294D	CDH6_ENST00000514738.1_Silent_p.D239D	NM_004932.3	NP_004923.1	P55285	CADH6_HUMAN	cadherin 6, type 2, K-cadherin (fetal kidney)	294	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(3)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(42)|ovary(4)|prostate(6)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(1)	77						AAGCCAGCGACGCTGATGTGG	0.463													C|||	2029	0.405152	0.062	0.4986	5008	,	,		17768	0.5238		0.5547	False		,,,				2504	0.5266				p.D294D		Atlas-SNP	.											.	CDH6	175	.	0			c.C882T						PASS	.	C		664,3742	281.1+/-275.7	56,552,1595	127.0	119.0	122.0		882	-5.9	0.3	5	dbSNP_100	122	4545,4055	595.4+/-393.5	1238,2069,993	no	coding-synonymous	CDH6	NM_004932.3		1294,2621,2588	TT,TC,CC		47.1512,15.0704,40.0507		294/791	31302288	5209,7797	2203	4300	6503	SO:0001819	synonymous_variant	1004	exon6			CAGCGACGCTGAT	D31784	CCDS3894.1	5p13.3	2010-01-26			ENSG00000113361	ENSG00000113361		"""Cadherins / Major cadherins"""	1765	protein-coding gene	gene with protein product	"""K-Cadherin"""	603007				7743525, 10191097	Standard	NM_004932		Approved		uc003jhe.2	P55285	OTTHUMG00000090673	ENST00000265071.2:c.882C>T	5.37:g.31302288C>T		Somatic	234	0	0		WXS	Illumina HiSeq	Phase_I	265	264	0.996226	NM_004932	A8K5H5|Q9BWS0	Silent	SNP	ENST00000265071.2	37	CCDS3894.1																																																																																			C|0.591;T|0.409	0.409	strong		0.463	CDH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207355.2	NM_004932	
PBRM1	55193	hgsc.bcm.edu	37	3	52584787	52584787	+	Silent	SNP	T	T	C	rs2251219	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:52584787T>C	ENST00000296302.7	-	28	4657	c.4656A>G	c.(4654-4656)ccA>ccG	p.P1552P	PBRM1_ENST00000409114.3_Silent_p.P1515P|RNU6-856P_ENST00000516959.1_RNA|SMIM4_ENST00000476842.1_Intron|PBRM1_ENST00000409767.1_Silent_p.P1460P|PBRM1_ENST00000356770.4_Silent_p.P1465P|PBRM1_ENST00000409057.1_Silent_p.P1497P|PBRM1_ENST00000337303.4_Silent_p.P1445P|PBRM1_ENST00000410007.1_Silent_p.P1472P|PBRM1_ENST00000394830.3_Silent_p.P1445P			Q86U86	PB1_HUMAN	polybromo 1	1552	Pro-rich.				chromatin remodeling (GO:0006338)|heart development (GO:0007507)|mitotic nuclear division (GO:0007067)|negative regulation of cell proliferation (GO:0008285)|placenta development (GO:0001890)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	kinetochore (GO:0000776)|nuclear chromosome (GO:0000228)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			breast(5)|endometrium(5)|kidney(301)|liver(1)|lung(22)|pancreas(1)	335				BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)		GACTTCCACCTGGTGCTGGAG	0.468			"""Mis, N, F, S, D, O"""		"""clear cell renal carcinoma, breast"""								T|||	1618	0.323083	0.1452	0.4654	5008	,	,		20114	0.4296		0.4195	False		,,,				2504	0.2536				p.P1445P		Atlas-SNP	.		Rec	yes		3	3p21	55193	polybromo 1		E	.	PBRM1	1252	.	0			c.A4335G						PASS	.	T	,,	766,3640	313.0+/-292.9	65,636,1502	80.0	74.0	76.0	http://www.ncbi.nlm.nih.gov/pubmed?term	4395,4335,4335	3.5	1.0	3	dbSNP_100	76	3517,5083	512.3+/-377.9	740,2037,1523	yes	coding-synonymous,coding-synonymous,coding-synonymous	PBRM1	NM_018165.4,NM_018313.4,NM_181042.3	,,	805,2673,3025	CC,CT,TT	http://www.ncbi.nlm.nih.gov/pubmed?term	40.8953,17.3854,32.931	,,	1465/1603,1445/1583,1445/1583	52584787	4283,8723	2203	4300	6503	SO:0001819	synonymous_variant	55193	exon28			TCCACCTGGTGCT	BC015323	CCDS43099.1	3p21	2007-03-29			ENSG00000163939	ENSG00000163939			30064	protein-coding gene	gene with protein product		606083				11078522, 11483580	Standard	NM_018313		Approved	BAF180, PB1	uc003der.2	Q86U86	OTTHUMG00000152663	ENST00000296302.7:c.4656A>G	3.37:g.52584787T>C		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	125	124	0.992	NM_018313	A1L381|A1L382|A4FUJ7|Q1RMD1|Q1RMD2|Q96MS2|Q9H2T3|Q9H2T4|Q9H2T5|Q9H301|Q9H314	Silent	SNP	ENST00000296302.7	37																																																																																				T|0.654;C|0.346	0.346	strong		0.468	PBRM1-008	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000327232.1	NM_018165	
WNK1	65125	hgsc.bcm.edu	37	12	994030	994030	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:994030G>A	ENST00000315939.6	+	19	4703	c.4060G>A	c.(4060-4062)Gca>Aca	p.A1354T	WNK1_ENST00000530271.2_Missense_Mutation_p.A1852T|WNK1_ENST00000537687.1_Missense_Mutation_p.A1614T|WNK1_ENST00000535572.1_Missense_Mutation_p.A1107T|WNK1_ENST00000340908.4_Missense_Mutation_p.A947T	NM_018979.3	NP_061852.3	Q9H4A3	WNK1_HUMAN	WNK lysine deficient protein kinase 1	1354					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)			AGCAGCCACAGCACCAGTCCC	0.498																																					p.A1614T	Colon(19;451 567 6672 12618 28860)	Atlas-SNP	.											.	WNK1	403	.	0			c.G4840A						PASS	.						92.0	88.0	89.0					12																	994030		2203	4300	6503	SO:0001583	missense	65125	exon19			GCCACAGCACCAG	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.4060G>A	12.37:g.994030G>A	ENSP00000313059:p.Ala1354Thr	Somatic	190	0	0		WXS	Illumina HiSeq	Phase_I	180	62	0.344444	NM_001184985	A1L4B0|C5HTZ5|C5HTZ6|C5HTZ7|H6WZW3|O15052|P54963|Q4VBX9|Q6IFS5|Q86WL5|Q8N673|Q96CZ6|Q9P1S9	Missense_Mutation	SNP	ENST00000315939.6	37	CCDS8506.1	.	.	.	.	.	.	.	.	.	.	G	7.571	0.666826	0.14710	.	.	ENSG00000060237	ENST00000535572;ENST00000315939;ENST00000537687;ENST00000252477;ENST00000530271;ENST00000340908	T;T;T;T;T	0.44083	0.93;0.93;0.93;0.93;0.93	5.63	2.65	0.31530	.	0.499734	0.20150	N	0.098164	T	0.22704	0.0548	N	0.14661	0.345	0.18873	N	0.999989	B;B;B	0.19200	0.01;0.034;0.02	B;B;B	0.21708	0.022;0.036;0.016	T	0.14227	-1.0480	10	0.29301	T	0.29	-1.4729	6.408	0.21676	0.2705:0.1226:0.6068:0.0	.	1107;1107;1354	Q9H4A3-2;F5GWT4;Q9H4A3	.;.;WNK1_HUMAN	T	1107;1354;1614;527;1852;947	ENSP00000441972:A1107T;ENSP00000313059:A1354T;ENSP00000444465:A1614T;ENSP00000433548:A1852T;ENSP00000341292:A947T	ENSP00000252477:A527T	A	+	1	0	WNK1	864291	0.191000	0.23288	0.918000	0.36340	0.051000	0.14879	0.566000	0.23593	0.850000	0.35239	0.655000	0.94253	GCA	.	.	none		0.498	WNK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206683.1	NM_018979	
VSIG10	54621	hgsc.bcm.edu	37	12	118509191	118509191	+	Missense_Mutation	SNP	G	G	A	rs7307331	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	106	0	0		WXS	Illumina HiSeq	Phase_I	106	56	0.528302	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	
TIAM1	7074	hgsc.bcm.edu	37	21	32638550	32638550	+	Missense_Mutation	SNP	C	C	T	rs2070418|rs386817934	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:32638550C>T	ENST00000286827.3	-	5	1210	c.739G>A	c.(739-741)Ggg>Agg	p.G247R	TIAM1_ENST00000469412.1_Intron|TIAM1_ENST00000541036.1_Missense_Mutation_p.G247R	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	105	0	0		WXS	Illumina HiSeq	Phase_I	96	60	0.625	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	
BDP1	55814	hgsc.bcm.edu	37	5	70818150	70818150	+	Missense_Mutation	SNP	C	C	G	rs12187098	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:70818150C>G	ENST00000358731.4	+	23	5289	c.5026C>G	c.(5026-5028)Caa>Gaa	p.Q1676E	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	1676			Q -> E (in dbSNP:rs12187098).		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)		TAGTTCAGCACAAATGACAAG	0.348													C|||	101	0.0201677	0.0454	0.013	5008	,	,		17087	0.0		0.0298	False		,,,				2504	0.002				p.Q1676E		Atlas-SNP	.											.	BDP1	204	.	0			c.C5026G						PASS	.	C	GLU/GLN	182,3514		3,176,1669	130.0	127.0	128.0		5026	4.5	0.1	5	dbSNP_120	128	196,7988		6,184,3902	yes	missense	BDP1	NM_018429.2	29	9,360,5571	GG,GC,CC		2.3949,4.9242,3.1818	possibly-damaging	1676/2625	70818150	378,11502	1848	4092	5940	SO:0001583	missense	55814	exon23			TCAGCACAAATGA	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.5026C>G	5.37:g.70818150C>G	ENSP00000351575:p.Gln1676Glu	Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	197	67	0.340102	NM_018429	Q68DS6|Q68DY5|Q6MZL9|Q6PIM7|Q86W98|Q96LR8|Q9C0H4|Q9H197|Q9H1A1|Q9HAW1|Q9HAW2|Q9HCY0|Q9ULH9	Missense_Mutation	SNP	ENST00000358731.4	37	CCDS43328.1	41	0.018772893772893772	19	0.03861788617886179	5	0.013812154696132596	0	0.0	17	0.022427440633245383	C	8.668	0.902198	0.17760	0.049242	0.023949	ENSG00000145734	ENST00000358731;ENST00000451951	T	0.10477	2.87	5.35	4.48	0.54585	.	1.312210	0.05133	N	0.493011	T	0.01489	0.0048	L	0.47716	1.5	0.49687	D	0.999812	P;P	0.42871	0.557;0.792	B;B	0.37601	0.116;0.254	T	0.48514	-0.9029	10	0.02654	T	1	.	11.1063	0.48205	0.0:0.9126:0.0:0.0874	rs12187098;rs13169583;rs52833258;rs56647603;rs12187098	1676;1676	A6H8Y1;A6H8Y1-2	BDP1_HUMAN;.	E	1676;1256	ENSP00000351575:Q1676E	ENSP00000351575:Q1676E	Q	+	1	0	BDP1	70853906	0.019000	0.18553	0.098000	0.21074	0.052000	0.14988	2.086000	0.41643	1.251000	0.43983	0.555000	0.69702	CAA	C|0.971;G|0.029	0.029	strong		0.348	BDP1-016	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000374681.2	NM_018429	
C19orf40	91442	hgsc.bcm.edu	37	19	33467357	33467357	+	Silent	SNP	G	G	A	rs2304102	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:33467357G>A	ENST00000588258.1	+	5	527	c.417G>A	c.(415-417)gaG>gaA	p.E139E	C19orf40_ENST00000589646.1_Silent_p.E44E|C19orf40_ENST00000590281.1_Silent_p.E139E|C19orf40_ENST00000590179.1_Silent_p.E44E	NM_152266.3	NP_689479.1	Q9BTP7	FAP24_HUMAN	chromosome 19 open reading frame 40	139					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)					AAACCAAAGAGCCCAGTAAGA	0.498								Direct reversal of damage			OREG0025408	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	g|||	2123	0.423922	0.4024	0.6023	5008	,	,		17719	0.4365		0.3757	False		,,,				2504	0.363				p.E139E		Atlas-SNP	.											.	C19orf40	21	.	0			c.G417A						PASS	.	G		1757,2649	521.7+/-370.6	350,1057,796	66.0	68.0	67.0		417	2.0	1.0	19	dbSNP_100	67	3162,5438	478.7+/-369.9	536,2090,1674	no	coding-synonymous	C19orf40	NM_152266.3		886,3147,2470	AA,AG,GG		36.7674,39.8774,37.821		139/216	33467357	4919,8087	2203	4300	6503	SO:0001819	synonymous_variant	91442	exon5			CAAAGAGCCCAGT	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.417G>A	19.37:g.33467357G>A		Somatic	117	0	0	840	WXS	Illumina HiSeq	Phase_I	94	47	0.5	NM_152266	B3KY46|Q8WUJ7|Q96FX6	Silent	SNP	ENST00000588258.1	37	CCDS12426.1																																																																																			G|0.605;A|0.395	0.395	strong		0.498	C19orf40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450823.2	NM_152266	
UGT2A1	10941	hgsc.bcm.edu	37	4	70460328	70460328	+	Missense_Mutation	SNP	C	C	T	rs4148304	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:70460328C>T	ENST00000503640.1	-	5	1226	c.1171G>A	c.(1171-1173)Gtt>Att	p.V391I	UGT2A2_ENST00000457664.2_Missense_Mutation_p.V400I|UGT2A1_ENST00000286604.4_Missense_Mutation_p.V391I|UGT2A1_ENST00000514019.1_Missense_Mutation_p.V557I|UGT2A1_ENST00000512704.1_Missense_Mutation_p.V347I|UGT2A1_ENST00000502343.1_5'UTR	NM_006798.3	NP_006789.2	Q9Y4X1	UD2A1_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide A1, complex locus	391			V -> I (in dbSNP:rs4148304). {ECO:0000269|PubMed:14702039}.		cellular glucuronidation (GO:0052695)|detection of chemical stimulus (GO:0009593)|metabolic process (GO:0008152)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)	glucuronosyltransferase activity (GO:0015020)	p.V391I(1)|p.V400I(1)		NS(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(8)|lung(11)|ovary(2)|prostate(1)|skin(2)	30						AACATGGGAACTCCCACCATA	0.448													c|||	593	0.118411	0.1256	0.1513	5008	,	,		17734	0.0288		0.17	False		,,,				2504	0.1247				p.V557I		Atlas-SNP	.											UGT2A1_ENST00000457664,NS,carcinoma,0,2	UGT2A1	131	2	2	Substitution - Missense(2)	prostate(2)	c.G1669A						scavenged	.	T	ILE/VAL,ILE/VAL	453,3953	214.1+/-233.5	20,413,1770	115.0	98.0	104.0		1198,1171	-2.7	0.0	4	dbSNP_110	104	1506,7094	286.1+/-297.5	143,1220,2937	yes	missense,missense	UGT2A1,UGT2A2	NM_001105677.2,NM_006798.2	29,29	163,1633,4707	TT,TC,CC		17.5116,10.2814,15.0623	benign,benign	400/537,391/528	70460328	1959,11047	2203	4300	6503	SO:0001583	missense	10941	exon6			TGGGAACTCCCAC	AJ006054	CCDS3529.1, CCDS58901.1, CCDS58902.1	4q13	2013-03-28	2010-12-02					"""UDP glucuronosyltransferases"""	12542	protein-coding gene	gene with protein product		604716	"""UDP glycosyltransferase 2 family, polypeptide A1"", ""UDP glucuronosyltransferase 2 family, polypeptide A1"""			10359671	Standard	NM_001252274		Approved		uc011caq.2	Q9Y4X1	OTTHUMG00000184942	ENST00000503640.1:c.1171G>A	4.37:g.70460328C>T	ENSP00000424478:p.Val391Ile	Somatic	192	1	0.00520833		WXS	Illumina HiSeq	Phase_I	150	77	0.513333	NM_001252274	B4E2F4|D3GER1|D3GER2|E9PDM7|J3KNA3	Missense_Mutation	SNP	ENST00000503640.1	37	CCDS3529.1	231	0.10576923076923077	44	0.08943089430894309	52	0.143646408839779	8	0.013986013986013986	127	0.16754617414248021	c	0.337	-0.952667	0.02285	0.102814	0.175116	ENSG00000173610	ENST00000457664;ENST00000503640;ENST00000512704;ENST00000514019;ENST00000286604	T;T;T;T;T	0.61510	0.1;0.1;0.1;0.1;0.33	4.53	-2.67	0.06059	.	0.590343	0.17077	N	0.187942	T	0.00039	0.0001	N	0.00510	-1.415	.	.	.	B;B;B;B	0.17268	0.021;0.003;0.006;0.014	B;B;B;B	0.16722	0.014;0.015;0.005;0.016	T	0.10753	-1.0616	9	0.02654	T	1	.	7.051	0.25073	0.0:0.3199:0.1282:0.5519	rs4148304;rs4148304	557;347;400;391	E9PDM7;D6RFW5;Q9Y4X1-2;Q9Y4X1	.;.;.;UD2A1_HUMAN	I	400;391;347;557;391	ENSP00000387888:V400I;ENSP00000424478:V391I;ENSP00000421432:V347I;ENSP00000425497:V557I;ENSP00000286604:V391I	ENSP00000286604:V391I	V	-	1	0	UGT2A1	70494917	0.051000	0.20477	0.001000	0.08648	0.944000	0.59088	0.340000	0.19892	-0.819000	0.04323	-0.133000	0.14855	GTT	C|0.876;T|0.124	0.124	strong		0.448	UGT2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251554.3	NM_006798	
TANC1	85461	hgsc.bcm.edu	37	2	160084473	160084473	+	Silent	SNP	A	A	C	rs2288110	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:160084473A>C	ENST00000263635.6	+	25	4284	c.4047A>C	c.(4045-4047)acA>acC	p.T1349T	TANC1_ENST00000454300.1_Silent_p.T1243T	NM_001145909.1|NM_033394.2	NP_001139381.1|NP_203752.2	Q9C0D5	TANC1_HUMAN	tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 1	1349					dendritic spine maintenance (GO:0097062)|myoblast fusion (GO:0007520)|visual learning (GO:0008542)	axon terminus (GO:0043679)|cell junction (GO:0030054)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)|postsynaptic membrane (GO:0045211)				breast(3)|central_nervous_system(4)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(9)|lung(25)|ovary(7)|pancreas(1)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(2)	77						GAAGAAAAACAAATGTAAGCT	0.493													A|||	2398	0.478834	0.351	0.6009	5008	,	,		21388	0.6151		0.3718	False		,,,				2504	0.5348				p.T1349T		Atlas-SNP	.											.	TANC1	157	.	0			c.A4047C						PASS	.	A	,	1371,2477		252,867,805	89.0	89.0	89.0		4023,4047	-0.8	0.9	2	dbSNP_100	89	2888,5378		515,1858,1760	no	coding-synonymous,coding-synonymous	TANC1	NM_001145909.1,NM_033394.2	,	767,2725,2565	CC,CA,AA		34.9383,35.6289,35.1577	,	1341/1391,1349/1862	160084473	4259,7855	1924	4133	6057	SO:0001819	synonymous_variant	85461	exon25			AAAAACAAATGTA	AB051515	CCDS42766.1	2q24.2	2013-01-11			ENSG00000115183	ENSG00000115183		"""Ankyrin repeat domain containing"", ""Tetratricopeptide (TTC) repeat domain containing"""	29364	protein-coding gene	gene with protein product	"""rolling pebbles homolog B (Drosophila)"""	611397				15673434	Standard	NM_033394		Approved	KIAA1728, ROLSB	uc002uag.3	Q9C0D5	OTTHUMG00000153945	ENST00000263635.6:c.4047A>C	2.37:g.160084473A>C		Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	26	11	0.423077	NM_033394	C9JD88|Q49AI8	Silent	SNP	ENST00000263635.6	37	CCDS42766.1																																																																																			A|0.566;C|0.434	0.434	strong		0.493	TANC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333135.1		
FOXO3	2309	hgsc.bcm.edu	37	6	108882570	108882570	+	Silent	SNP	C	C	T	rs11757217	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:108882570C>T	ENST00000343882.6	+	2	463	c.159C>T	c.(157-159)gcC>gcT	p.A53A	FOXO3_ENST00000406360.1_Silent_p.A53A	NM_201559.2	NP_963853.1	O43524	FOXO3_HUMAN	forkhead box O3	53					antral ovarian follicle growth (GO:0001547)|cellular response to oxidative stress (GO:0034599)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|epidermal growth factor receptor signaling pathway (GO:0007173)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose homeostasis (GO:0042593)|initiation of primordial ovarian follicle growth (GO:0001544)|innate immune response (GO:0045087)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neurotrophin TRK receptor signaling pathway (GO:0048011)|oocyte maturation (GO:0001556)|ovulation from ovarian follicle (GO:0001542)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of translation (GO:0006417)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|protein kinase binding (GO:0019901)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(5)|endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(2)|prostate(4)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	26		all_cancers(87;1.78e-07)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;3.88e-05)|Colorectal(196;0.0294)|all_lung(197;0.0487)|Lung SC(18;0.152)		Epithelial(106;0.000759)|all cancers(137;0.00121)|BRCA - Breast invasive adenocarcinoma(108;0.00163)|OV - Ovarian serous cystadenocarcinoma(136;0.00718)		AGACGGCCGCCGACTCCATGA	0.731													C|||	923	0.184305	0.3147	0.2133	5008	,	,		10040	0.0526		0.1829	False		,,,				2504	0.1247				p.A53A		Atlas-SNP	.											FOXO3,brain,glioma,0,4	FOXO3	67	4	0			c.C159T						scavenged	.						3.0	3.0	3.0					6																	108882570		1560	3279	4839	SO:0001819	synonymous_variant	2309	exon1			GGCCGCCGACTCC	AF032886	CCDS5068.1	6q21	2008-09-08	2007-05-02	2007-05-02	ENSG00000118689	ENSG00000118689		"""Forkhead boxes"""	3821	protein-coding gene	gene with protein product		602681		FKHRL1, FOXO3A		9479491	Standard	NM_001455		Approved	AF6q21, FOXO2	uc003psm.2	O43524	OTTHUMG00000015327	ENST00000343882.6:c.159C>T	6.37:g.108882570C>T		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	43	18	0.418605	NM_001455	B4DVZ6|E1P5E6|O15171|Q5T2I7|Q9BZ04	Silent	SNP	ENST00000343882.6	37	CCDS5068.1																																																																																			.	.	weak		0.731	FOXO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041722.2		
PPP1R16A	84988	hgsc.bcm.edu	37	8	145722726	145722726	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:145722726C>A	ENST00000292539.4	+	2	1066	c.149C>A	c.(148-150)cCt>cAt	p.P50H	PPP1R16A_ENST00000529009.1_3'UTR|CTD-2517M22.14_ENST00000532766.1_RNA|PPP1R16A_ENST00000435887.1_Missense_Mutation_p.P50H|CTD-2517M14.5_ENST00000569326.1_RNA			Q96I34	PP16A_HUMAN	protein phosphatase 1, regulatory subunit 16A	50				Missing (in Ref. 1; BAC03452). {ECO:0000305}.		plasma membrane (GO:0005886)				NS(1)|endometrium(1)|kidney(2)|lung(3)|prostate(1)	8	all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055)			AAGAAGGGTCCTGGGGAGCGT	0.652																																					p.P50H		Atlas-SNP	.											.	PPP1R16A	25	.	0			c.C149A						PASS	.						48.0	43.0	45.0					8																	145722726		2203	4299	6502	SO:0001583	missense	84988	exon1			AGGGTCCTGGGGA		CCDS6429.1	8q24.3	2013-01-10	2011-10-04		ENSG00000160972	ENSG00000160972		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Ankyrin repeat domain containing"""	14941	protein-coding gene	gene with protein product		609172	"""protein phosphatase 1, regulatory (inhibitor) subunit 16A"""			11948623	Standard	NM_032902		Approved	MGC14333, MYPT3	uc003zdf.3	Q96I34	OTTHUMG00000165173	ENST00000292539.4:c.149C>A	8.37:g.145722726C>A	ENSP00000292539:p.Pro50His	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	145	80	0.551724	NM_032902	D3DWM5	Missense_Mutation	SNP	ENST00000292539.4	37	CCDS6429.1	.	.	.	.	.	.	.	.	.	.	C	10.05	1.245088	0.22796	.	.	ENSG00000160972	ENST00000292539;ENST00000435887	T;T	0.70986	-0.53;-0.53	4.49	-8.98	0.00754	.	0.960193	0.08687	N	0.908585	T	0.34106	0.0886	N	0.00926	-1.1	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.41698	-0.9494	10	0.42905	T	0.14	.	10.2052	0.43109	0.1214:0.5237:0.3549:0.0	.	50	Q96I34	PP16A_HUMAN	H	50	ENSP00000292539:P50H;ENSP00000391126:P50H	ENSP00000292539:P50H	P	+	2	0	PPP1R16A	145693534	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-1.717000	0.01876	-1.769000	0.01297	-0.521000	0.04368	CCT	.	.	none		0.652	PPP1R16A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382459.1	NM_032902	
NEFH	4744	hgsc.bcm.edu	37	22	29881828	29881828	+	Silent	SNP	C	C	T	rs165734	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:29881828C>T	ENST00000310624.6	+	3	1233	c.1200C>T	c.(1198-1200)gcC>gcT	p.A400A		NM_021076.3	NP_066554.2	P12036	NFH_HUMAN	neurofilament, heavy polypeptide	400	Coil 2B.|Rod.				axon development (GO:0061564)|axonogenesis (GO:0007409)|cell death (GO:0008219)|cell projection assembly (GO:0030031)|microtubule cytoskeleton organization (GO:0000226)|neurofilament bundle assembly (GO:0033693)|peripheral nervous system neuron axonogenesis (GO:0048936)|regulation of organelle transport along microtubule (GO:1902513)	axon (GO:0030424)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|neurofibrillary tangle (GO:0097418)|neurofilament (GO:0005883)	dynein binding (GO:0045502)|kinesin binding (GO:0019894)|microtubule binding (GO:0008017)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(12)|ovary(2)|skin(3)	30						TAGAGATAGCCGCTTACAGGT	0.552													C|||	498	0.0994409	0.0401	0.121	5008	,	,		17468	0.0526		0.1431	False		,,,				2504	0.1677				p.A400A		Atlas-SNP	.											.	NEFH	178	.	0			c.C1200T						PASS	.	C		256,4150	146.5+/-181.1	10,236,1957	79.0	70.0	73.0		1200	-4.4	1.0	22	dbSNP_79	73	1316,7284	259.7+/-282.8	86,1144,3070	no	coding-synonymous	NEFH	NM_021076.3		96,1380,5027	TT,TC,CC		15.3023,5.8103,12.0867		400/1021	29881828	1572,11434	2203	4300	6503	SO:0001819	synonymous_variant	4744	exon3			GATAGCCGCTTAC		CCDS13858.1	22q12.2	2013-01-16	2008-09-19		ENSG00000100285	ENSG00000100285		"""Intermediate filaments type IV"""	7737	protein-coding gene	gene with protein product		162230	"""neurofilament, heavy polypeptide 200kDa"""				Standard	NM_021076		Approved		uc003afo.3	P12036	OTTHUMG00000151155	ENST00000310624.6:c.1200C>T	22.37:g.29881828C>T		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	66	33	0.5	NM_021076	B4DYY4|Q96HF8|Q9UJS7|Q9UQ14	Silent	SNP	ENST00000310624.6	37	CCDS13858.1																																																																																			C|0.890;T|0.110	0.110	strong		0.552	NEFH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321553.2	NM_021076	
DST	667	hgsc.bcm.edu	37	6	56480500	56480500	+	Missense_Mutation	SNP	T	T	C	rs150191284	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:56480500T>C	ENST00000370765.6	-	24	7872	c.7765A>G	c.(7765-7767)Att>Gtt	p.I2589V	DST_ENST00000370769.4_Intron|DST_ENST00000361203.3_Intron|DST_ENST00000244364.6_Intron|DST_ENST00000312431.6_Intron|DST_ENST00000446842.2_Intron|DST_ENST00000370754.5_Intron|DST_ENST00000370788.2_Intron|DST_ENST00000421834.2_Intron	NM_001723.5	NP_001714.1	Q03001	DYST_HUMAN	dystonin	1885					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)			TTTGTGGCAATGAGGACATCT	0.373													T|||	51	0.0101837	0.0015	0.0101	5008	,	,		18703	0.0		0.0258	False		,,,				2504	0.0164				p.I2589V		Atlas-SNP	.											.	DST	1427	.	0			c.A7765G						PASS	.	T	VAL/ILE,	35,4371	39.2+/-71.8	0,35,2168	142.0	141.0	141.0		7765,	4.4	1.0	6	dbSNP_134	141	367,8233	121.7+/-180.7	10,347,3943	yes	missense,intron	DST	NM_001723.5,NM_015548.4	29,	10,382,6111	CC,CT,TT		4.2674,0.7944,3.0909	,	2589/2650,	56480500	402,12604	2203	4300	6503	SO:0001583	missense	667	exon24			TGGCAATGAGGAC	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.7765A>G	6.37:g.56480500T>C	ENSP00000359801:p.Ile2589Val	Somatic	179	0	0		WXS	Illumina HiSeq	Phase_I	147	67	0.455782	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	25	0.011446886446886446	2	0.0040650406504065045	6	0.016574585635359115	0	0.0	17	0.022427440633245383	T	11.28	1.591540	0.28357	0.007944	0.042674	ENSG00000151914	ENST00000370765	T	0.73363	-0.74	5.61	4.45	0.53987	.	.	.	.	.	T	0.53367	0.1792	.	.	.	0.09310	N	1.0	B	0.15930	0.015	B	0.18871	0.023	T	0.54682	-0.8257	7	0.72032	D	0.01	.	12.6638	0.56830	0.0:0.0:0.1522:0.8477	.	2589	Q03001-3	.	V	2589	ENSP00000359801:I2589V	ENSP00000359801:I2589V	I	-	1	0	DST	56588459	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	5.175000	0.65021	0.944000	0.37579	0.455000	0.32223	ATT	T|0.974;C|0.026	0.026	strong		0.373	DST-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000041027.2	NM_001723	
MYH15	22989	hgsc.bcm.edu	37	3	108179165	108179165	+	Silent	SNP	C	C	T	rs61739469	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:108179165C>T	ENST00000273353.3	-	18	2030	c.1974G>A	c.(1972-1974)acG>acA	p.T658T	MYH15_ENST00000495753.2_5'UTR	NM_014981.1	NP_055796.1	Q9Y2K3	MYH15_HUMAN	myosin, heavy chain 15	658	Myosin motor.					cytoplasm (GO:0005737)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(1)|breast(3)|central_nervous_system(2)|cervix(4)|endometrium(10)|kidney(4)|large_intestine(14)|lung(47)|ovary(5)|pancreas(2)|prostate(6)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	105						GAGATGCAACCGTTTGGAATG	0.303													C|||	26	0.00519169	0.0015	0.0159	5008	,	,		18629	0.0		0.0129	False		,,,				2504	0.0				p.T658T		Atlas-SNP	.											.	MYH15	223	.	0			c.G1974A						PASS	.	C		12,3632		0,12,1810	67.0	65.0	66.0		1974	-2.0	0.0	3	dbSNP_129	66	197,7937		3,191,3873	no	coding-synonymous	MYH15	NM_014981.1		3,203,5683	TT,TC,CC		2.4219,0.3293,1.7745		658/1947	108179165	209,11569	1822	4067	5889	SO:0001819	synonymous_variant	22989	exon18			TGCAACCGTTTGG	AB023217	CCDS43127.1	3q13	2011-09-27	2006-09-29		ENSG00000144821	ENSG00000144821		"""Myosins / Myosin superfamily : Class II"""	31073	protein-coding gene	gene with protein product		609929	"""myosin, heavy polypeptide 15"""			15014174, 15042088	Standard	NM_014981		Approved	KIAA1000	uc003dxa.1	Q9Y2K3	OTTHUMG00000159226	ENST00000273353.3:c.1974G>A	3.37:g.108179165C>T		Somatic	231	0	0		WXS	Illumina HiSeq	Phase_I	179	81	0.452514	NM_014981		Silent	SNP	ENST00000273353.3	37	CCDS43127.1																																																																																			C|0.987;T|0.013	0.013	strong		0.303	MYH15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353935.1	XM_036988	
ITSN2	50618	hgsc.bcm.edu	37	2	24431184	24431184	+	Missense_Mutation	SNP	C	C	T	rs2303291	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:24431184C>T	ENST00000355123.4	-	37	5043	c.4600G>A	c.(4600-4602)Gcc>Acc	p.A1534T	ITSN2_ENST00000361999.3_Missense_Mutation_p.A1507T	NM_006277.2	NP_006268.2	Q9NZM3	ITSN2_HUMAN	intersectin 2	1534	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.		A -> T (in dbSNP:rs2303291).		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)					TGCACCCAGGCGGTCCTACGG	0.592													C|||	696	0.138978	0.0204	0.134	5008	,	,		18660	0.123		0.2594	False		,,,				2504	0.1953				p.A1534T		Atlas-SNP	.											.	ITSN2	224	.	0			c.G4600A						PASS	.	C	THR/ALA,THR/ALA	261,4145	146.9+/-181.5	8,245,1950	96.0	90.0	92.0		4600,4519	4.9	1.0	2	dbSNP_100	92	2084,6516	361.3+/-332.3	254,1576,2470	yes	missense,missense	ITSN2	NM_006277.2,NM_019595.3	58,58	262,1821,4420	TT,TC,CC		24.2326,5.9237,18.0301	probably-damaging,probably-damaging	1534/1698,1507/1671	24431184	2345,10661	2203	4300	6503	SO:0001583	missense	50618	exon37			CCCAGGCGGTCCT	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.4600G>A	2.37:g.24431184C>T	ENSP00000347244:p.Ala1534Thr	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	104	44	0.423077	NM_006277	O95062|Q15812|Q9HAK4|Q9NXE6|Q9NYG0|Q9NZM2|Q9ULG4	Missense_Mutation	SNP	ENST00000355123.4	37	CCDS1710.2	347	0.15888278388278387	20	0.04065040650406504	54	0.14917127071823205	71	0.12412587412587413	202	0.26649076517150394	C	14.81	2.646229	0.47258	0.059237	0.242326	ENSG00000198399	ENST00000361999;ENST00000355123;ENST00000380868	T;T;T	0.44083	0.93;0.93;0.93	4.86	4.86	0.63082	Pleckstrin homology-type (1);Pleckstrin homology domain (2);C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.36628	U	0.002485	T	0.00012	0.0000	N	0.24115	0.695	0.09310	P	0.999999852117	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.992	T	0.09487	-1.0672	9	0.35671	T	0.21	.	18.3604	0.90372	0.0:1.0:0.0:0.0	rs2303291;rs52805758;rs56718449;rs2303291	1507;1534	Q9NZM3-2;Q9NZM3	.;ITSN2_HUMAN	T	1507;1534;1507	ENSP00000354561:A1507T;ENSP00000347244:A1534T;ENSP00000370250:A1507T	ENSP00000347244:A1534T	A	-	1	0	ITSN2	24284688	1.000000	0.71417	0.978000	0.43139	0.526000	0.34562	7.308000	0.78929	2.397000	0.81536	0.542000	0.68232	GCC	C|0.829;T|0.171	0.171	strong		0.592	ITSN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207620.2	NM_006277	
SLC35G5	83650	hgsc.bcm.edu	37	8	11188743	11188743	+	Missense_Mutation	SNP	C	C	T	rs13260331	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:11188743C>T	ENST00000382435.4	+	1	347	c.128C>T	c.(127-129)gCc>gTc	p.A43V		NM_001282300.1|NM_054028.1	NP_001269229.1|NP_473369.1	Q96KT7	S35G5_HUMAN	solute carrier family 35, member G5	43						integral component of membrane (GO:0016021)											CTGCTGGTGGCCCTGCTGGGT	0.682													C|||	1588	0.317093	0.0197	0.3401	5008	,	,		16598	0.5833		0.3588	False		,,,				2504	0.3855				p.A43V		Atlas-SNP	.											.	.	.	.	0			c.C128T						PASS	.	C	VAL/ALA	384,4022	190.2+/-216.2	20,344,1839	50.0	56.0	54.0		128	0.3	0.8	8	dbSNP_121	54	3350,5250	496.3+/-374.2	674,2002,1624	no	missense	SLC35G5	NM_054028.1	64	694,2346,3463	TT,TC,CC		38.9535,8.7154,28.7098	possibly-damaging	43/339	11188743	3734,9272	2203	4300	6503	SO:0001583	missense	83650	exon1			TGGTGGCCCTGCT	AJ291677	CCDS5980.1	8p23.1	2013-05-22	2011-08-03	2011-08-03	ENSG00000177710	ENSG00000177710		"""Solute carriers"""	15546	protein-coding gene	gene with protein product		615199	"""acyl-malonyl condensing enzyme 1-like 2"""	AMAC, AMAC1L2			Standard	NM_054028		Approved		uc003wtp.1	Q96KT7	OTTHUMG00000090653	ENST00000382435.4:c.128C>T	8.37:g.11188743C>T	ENSP00000371872:p.Ala43Val	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	82	16	0.195122	NM_054028	A2RRL6	Missense_Mutation	SNP	ENST00000382435.4	37	CCDS5980.1	730	0.3342490842490842	15	0.03048780487804878	118	0.3259668508287293	332	0.5804195804195804	265	0.3496042216358839	C	11.44	1.638949	0.29157	0.087154	0.389535	ENSG00000177710	ENST00000382435	T	0.31510	1.49	0.34	0.34	0.15985	.	0.000000	0.44688	D	0.000436	T	0.00012	0.0000	L	0.29908	0.895	0.33612	P	0.39624499999999996	D	0.69078	0.997	D	0.75020	0.985	T	0.43686	-0.9376	9	0.18710	T	0.47	-8.3892	2.848	0.05549	0.0:0.5979:0.0:0.4021	rs13260331;rs59076275	43	Q96KT7	S35G5_HUMAN	V	43	ENSP00000371872:A43V	ENSP00000371872:A43V	A	+	2	0	SLC35G5	11226153	0.799000	0.28903	0.849000	0.33467	0.193000	0.23685	0.269000	0.18589	0.426000	0.26116	0.089000	0.15464	GCC	C|0.705;T|0.295	0.295	strong		0.682	SLC35G5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207313.2	NM_054028	
HSD17B7	51478	hgsc.bcm.edu	37	1	162782145	162782145	+	Missense_Mutation	SNP	A	A	G	rs2684875	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:162782145A>G	ENST00000254521.3	+	9	1016	c.961A>G	c.(961-963)Aag>Gag	p.K321E	HSD17B7_ENST00000485405.1_3'UTR|HSD17B7_ENST00000367917.3_Missense_Mutation_p.K286E	NM_016371.2	NP_057455.1	P56937	DHB7_HUMAN	hydroxysteroid (17-beta) dehydrogenase 7	321					cholesterol biosynthetic process (GO:0006695)|estrogen biosynthetic process (GO:0006703)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	3-keto sterol reductase activity (GO:0000253)|estradiol 17-beta-dehydrogenase activity (GO:0004303)			endometrium(3)|kidney(2)|large_intestine(1)|lung(1)|ovary(1)|skin(1)	9	all_hematologic(112;0.115)					GGAACTGGAAAAGCACATTAG	0.393													A|||	392	0.0782748	0.1021	0.0259	5008	,	,		16749	0.0744		0.0427	False		,,,				2504	0.1237				p.K321E		Atlas-SNP	.											.	HSD17B7	25	.	0			c.A961G						PASS	.	A	GLU/LYS	300,4066		18,264,1901	22.0	22.0	22.0		961	3.9	0.8	1	dbSNP_100	22	304,8252		3,298,3977	no	missense	HSD17B7	NM_016371.2	56	21,562,5878	GG,GA,AA		3.5531,6.8713,4.6742	benign	321/342	162782145	604,12318	2183	4278	6461	SO:0001583	missense	51478	exon9			CTGGAAAAGCACA	AF098786	CCDS1242.1	1q23	2011-09-14			ENSG00000132196	ENSG00000132196	1.1.1.270	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2"""	5215	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 37C, member 1"""	606756				10544267, 10419022, 19027726	Standard	NM_016371		Approved	PRAP, SDR37C1	uc001gci.3	P56937	OTTHUMG00000034420	ENST00000254521.3:c.961A>G	1.37:g.162782145A>G	ENSP00000254521:p.Lys321Glu	Somatic	350	0	0		WXS	Illumina HiSeq	Phase_I	289	119	0.411765	NM_016371	Q5T246|Q7Z4V9|Q8WWS2|Q9UF00	Missense_Mutation	SNP	ENST00000254521.3	37	CCDS1242.1	133	0.060897435897435896	50	0.1016260162601626	7	0.019337016574585635	45	0.07867132867132867	31	0.040897097625329816	A	12.52	1.961643	0.34659	0.068713	0.035531	ENSG00000132196	ENST00000367917;ENST00000254521	D;T	0.86230	-2.09;-1.04	3.89	3.89	0.44902	.	0.979280	0.08409	N	0.950271	T	0.75722	0.3888	M	0.67953	2.075	0.22521	N	0.999023	B	0.28713	0.22	B	0.22386	0.039	T	0.71447	-0.4590	9	0.66056	D	0.02	-37.9864	6.0419	0.19738	0.8842:0.0:0.1158:0.0	rs2684875	321	P56937	DHB7_HUMAN	E	286;321	ENSP00000356894:K286E;ENSP00000254521:K321E	ENSP00000254521:K321E	K	+	1	0	HSD17B7	161048769	0.994000	0.37717	0.845000	0.33349	0.938000	0.57974	3.539000	0.53604	1.751000	0.51876	0.477000	0.44152	AAG	.	.	weak		0.393	HSD17B7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083207.1	NM_016371	
FAM129C	199786	hgsc.bcm.edu	37	19	17660300	17660300	+	Missense_Mutation	SNP	G	G	A	rs11666267	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:17660300G>A	ENST00000335393.4	+	15	1945	c.1807G>A	c.(1807-1809)Ggc>Agc	p.G603S	FAM129C_ENST00000599124.1_Missense_Mutation_p.G536S|FAM129C_ENST00000601861.1_Missense_Mutation_p.G572S|FAM129C_ENST00000600871.1_Intron|FAM129C_ENST00000599164.1_Missense_Mutation_p.G572S|FAM129C_ENST00000449408.2_Missense_Mutation_p.G329S|FAM129C_ENST00000352727.3_Missense_Mutation_p.G567S|FAM129C_ENST00000332386.5_Missense_Mutation_p.G603S|FAM129C_ENST00000595684.1_Missense_Mutation_p.G603S	NM_173544.4	NP_775815	Q86XR2	NIBL2_HUMAN	family with sequence similarity 129, member C	603			G -> S (in dbSNP:rs11666267).					p.G603S(1)		autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(8)|liver(2)|lung(14)|ovary(1)|skin(3)|stomach(1)	33						CACTCTGGACGGCTGCTTGGA	0.562													G|||	2018	0.402955	0.3427	0.3818	5008	,	,		19109	0.3651		0.5537	False		,,,				2504	0.3834				p.G603S		Atlas-SNP	.											FAM129C,NS,carcinoma,0,1	FAM129C	110	1	1	Substitution - Missense(1)	stomach(1)	c.G1807A						PASS	.	G	SER/GLY,SER/GLY	1659,2747	504.9+/-366.0	311,1037,855	119.0	116.0	117.0		1807,1807	1.7	0.0	19	dbSNP_120	117	4833,3767	615.5+/-396.4	1375,2083,842	yes	missense,missense	FAM129C	NM_001098524.1,NM_173544.4	56,56	1686,3120,1697	AA,AG,GG		43.8023,37.6532,49.9154	possibly-damaging,possibly-damaging	603/652,603/698	17660300	6492,6514	2203	4300	6503	SO:0001583	missense	199786	exon15			CTGGACGGCTGCT	AY254198	CCDS12362.1, CCDS42521.1	19p13.11	2008-02-05				ENSG00000167483			24130	protein-coding gene	gene with protein product	B cell novel protein 1	609967				12886250	Standard	NM_173544		Approved	FLJ39802, BCNP1	uc021uqj.1	Q86XR2		ENST00000335393.4:c.1807G>A	19.37:g.17660300G>A	ENSP00000335040:p.Gly603Ser	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	60	31	0.516667	NM_001098524	B4DNU3|B4DVN7|Q7Z6H6|Q86XR3|Q86XR4|Q8TEQ3	Missense_Mutation	SNP	ENST00000335393.4	37	CCDS12362.1	906	0.41483516483516486	167	0.3394308943089431	149	0.4116022099447514	178	0.3111888111888112	412	0.5435356200527705	G	7.374	0.627412	0.14257	0.376532	0.561977	ENSG00000167483	ENST00000335393;ENST00000332386;ENST00000352727;ENST00000449408	T;T;T;T	0.24350	2.21;2.3;1.96;1.86	2.73	1.68	0.24146	.	0.676700	0.12241	N	0.486478	T	0.00012	0.0000	L	0.47716	1.5	0.80722	P	0.0	P;P;P;P	0.40230	0.708;0.708;0.708;0.708	B;B;B;B	0.31946	0.138;0.087;0.087;0.087	T	0.40924	-0.9537	9	0.06494	T	0.89	-11.9487	5.6065	0.17383	0.154:0.0:0.846:0.0	rs11666267;rs17710528;rs52789437;rs57563079;rs11666267	603;603;567;603	Q86XR2;Q86XR2-3;Q86XR2-4;Q86XR2-2	NIBL2_HUMAN;.;.;.	S	603;603;567;329	ENSP00000335040:G603S;ENSP00000333447:G603S;ENSP00000341067:G567S;ENSP00000394929:G329S	ENSP00000333447:G603S	G	+	1	0	FAM129C	17521300	0.007000	0.16637	0.002000	0.10522	0.003000	0.03518	1.228000	0.32588	0.729000	0.32403	0.557000	0.71058	GGC	G|0.543;A|0.456	0.456	strong		0.562	FAM129C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464206.1	NM_173544	
KIR3DL1	3811	hgsc.bcm.edu	37	19	55285072	55285072	+	Intron	SNP	A	A	G	rs138345877	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:55285072A>G	ENST00000538269.1	+	2	61				KIR2DL3_ENST00000434419.2_Intron|KIR2DL1_ENST00000291633.7_Missense_Mutation_p.I120V|KIR2DL1_ENST00000336077.6_Missense_Mutation_p.I120V|KIR3DL1_ENST00000402254.2_Intron|KIR3DL1_ENST00000541392.1_Intron|KIR2DL4_ENST00000396284.2_Intron|CTB-61M7.1_ENST00000400864.3_RNA			P43629	KI3L1_HUMAN	killer cell immunoglobulin-like receptor, three domains, long cytoplasmic tail, 1						immune response (GO:0006955)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	HLA-B specific inhibitory MHC class I receptor activity (GO:0030109)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	11				GBM - Glioblastoma multiforme(193;0.0192)		CCCTCTGGACATCGTGATCAT	0.517													.|||	86	0.0171725	0.0424	0.0216	5008	,	,		17371	0.0		0.0129	False		,,,				2504	0.002				p.I120V		Atlas-SNP	.											.	KIR2DL1	46	.	0			c.A358G						PASS	.	A	VAL/ILE	257,4091		34,189,1951	211.0	190.0	197.0		358	-2.5	0.0	19	dbSNP_134	197	108,8310		21,66,4122	no	missense	KIR2DL1	NM_014218.2	29	55,255,6073	GG,GA,AA		1.283,5.9108,2.8592		120/349	55285072	365,12401	2174	4209	6383	SO:0001627	intron_variant	3802	exon3			CTGGACATCGTGA	L41269	CCDS42621.1	19q13.4	2014-05-22			ENSG00000167633	ENSG00000167633		"""Killer cell immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6338	protein-coding gene	gene with protein product		604946		KIR		7716543, 7749980	Standard	NM_013289		Approved	cl-2, NKB1, cl-11, nkat3, NKB1B, AMB11, CD158e1/2, CD158E1, CD158e2		P43629	OTTHUMG00000065933	ENST00000538269.1:c.35-43917A>G	19.37:g.55285072A>G		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	62	26	0.419355	NM_014218	O43473|Q14946|Q16541	Missense_Mutation	SNP	ENST00000538269.1	37		31	0.014194139194139194	17	0.034552845528455285	5	0.013812154696132596	0	0.0	9	0.011873350923482849	A	1.706	-0.500217	0.04291	0.059108	0.01283	ENSG00000125498	ENST00000336077;ENST00000291633	T;T	0.00840	5.63;5.63	1.24	-2.48	0.06423	.	.	.	.	.	T	0.00210	0.0006	M	0.84585	2.705	0.09310	N	1	B;P	0.35481	0.0;0.504	B;B	0.33750	0.004;0.169	T	0.15954	-1.0419	9	0.72032	D	0.01	.	3.0195	0.06071	0.34:0.4343:0.0:0.2257	.	120;120	Q6IST4;Q6H2H3	.;.	V	120	ENSP00000336769:I120V;ENSP00000291633:I120V	ENSP00000291633:I120V	I	+	1	0	KIR2DL1	59976884	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	0.048000	0.14078	-1.981000	0.00989	-0.933000	0.02702	ATC	A|0.983;G|0.017	0.017	strong		0.517	KIR3DL1-202	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_013289	
GABRA5	2558	hgsc.bcm.edu	37	15	27182422	27182422	+	Missense_Mutation	SNP	A	A	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:27182422A>T	ENST00000335625.5	+	8	1559	c.671A>T	c.(670-672)cAg>cTg	p.Q224L	GABRA5_ENST00000355395.5_Missense_Mutation_p.Q224L|GABRA5_ENST00000400081.3_Missense_Mutation_p.Q224L|GABRB3_ENST00000541819.2_Intron	NM_000810.3	NP_000801.1	P31644	GBRA5_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha 5	224					associative learning (GO:0008306)|behavioral fear response (GO:0001662)|brain development (GO:0007420)|cochlea development (GO:0090102)|gamma-aminobutyric acid signaling pathway (GO:0007214)|inner ear receptor cell development (GO:0060119)|innervation (GO:0060384)|ion transmembrane transport (GO:0034220)|negative regulation of neuron apoptotic process (GO:0043524)|sensory perception of sound (GO:0007605)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|neuronal cell body membrane (GO:0032809)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|receptor complex (GO:0043235)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)|receptor activity (GO:0004872)|transporter activity (GO:0005215)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(26)|ovary(1)|upper_aerodigestive_tract(1)	49		all_lung(180;4.59e-13)|Breast(32;0.000563)|Colorectal(260;0.227)		all cancers(64;1.45e-08)|Epithelial(43;4.96e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0232)|Lung(196;0.182)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amobarbital(DB01351)|Amoxapine(DB00543)|Aprobarbital(DB01352)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Secobarbital(DB00418)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Thiopental(DB00599)|Topiramate(DB00273)|Triazolam(DB00897)|Zopiclone(DB01198)	AGACTGAACCAGTACCACCTG	0.597																																					p.Q224L		Atlas-SNP	.											GABRA5,colon,carcinoma,-1,1	GABRA5	127	1	0			c.A671T						PASS	.						80.0	84.0	83.0					15																	27182422		2112	4220	6332	SO:0001583	missense	2558	exon8			TGAACCAGTACCA		CCDS45194.1	15q12	2012-06-22			ENSG00000186297	ENSG00000186297		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	4079	protein-coding gene	gene with protein product	"""GABA(A) receptor, alpha 5"""	137142				1321750	Standard	NM_000810		Approved		uc021sgi.1	P31644	OTTHUMG00000171824	ENST00000335625.5:c.671A>T	15.37:g.27182422A>T	ENSP00000335592:p.Gln224Leu	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	77	32	0.415584	NM_001165037	A8K338|Q14DC2|Q53XL6|Q9NYT3|Q9NYT4|Q9NYT5	Missense_Mutation	SNP	ENST00000335625.5	37	CCDS45194.1	.	.	.	.	.	.	.	.	.	.	A	32	5.143883	0.94603	.	.	ENSG00000186297	ENST00000335625;ENST00000355395;ENST00000400081	T;T;T	0.79141	-1.24;-1.24;-1.24	5.28	5.28	0.74379	Neurotransmitter-gated ion-channel ligand-binding (3);	0.000000	0.85682	D	0.000000	D	0.88966	0.6581	M	0.88704	2.975	0.80722	D	1	D	0.63046	0.992	D	0.66351	0.943	D	0.91133	0.4939	10	0.87932	D	0	.	14.6925	0.69096	1.0:0.0:0.0:0.0	.	224	P31644	GBRA5_HUMAN	L	224	ENSP00000335592:Q224L;ENSP00000347557:Q224L;ENSP00000382953:Q224L	ENSP00000335592:Q224L	Q	+	2	0	GABRA5	24765168	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.084000	0.94076	2.114000	0.64651	0.379000	0.24179	CAG	.	.	none		0.597	GABRA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415234.1		
AHNAK2	113146	hgsc.bcm.edu	37	14	105417285	105417285	+	Silent	SNP	C	C	T	rs76453246	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:105417285C>T	ENST00000333244.5	-	7	4622	c.4503G>A	c.(4501-4503)ccG>ccA	p.P1501P	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	1501						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)			CCCCGAACGACGGCATCTTGA	0.607													.|||	331	0.0660942	0.0333	0.0836	5008	,	,		14865	0.003		0.162	False		,,,				2504	0.0644				p.P1501P		Atlas-SNP	.											AHNAK2_ENST00000333244,colon,carcinoma,-1,1	AHNAK2	719	1	0			c.G4503A						scavenged	.	G		179,3707		37,105,1801	193.0	134.0	153.0		4503	-8.1	0.1	14	dbSNP_131	153	1343,6733		343,657,3038	no	coding-synonymous	AHNAK2	NM_138420.2		380,762,4839	TT,TC,CC		16.6295,4.6063,12.7236		1501/5796	105417285	1522,10440	1943	4038	5981	SO:0001819	synonymous_variant	113146	exon7			GAACGACGGCATC	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.4503G>A	14.37:g.105417285C>T		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	116	20	0.172414	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Silent	SNP	ENST00000333244.5	37	CCDS45177.1																																																																																			C|0.948;T|0.052	0.052	strong		0.607	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
C2orf16	84226	hgsc.bcm.edu	37	2	27799712	27799712	+	Silent	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:27799712G>A	ENST00000408964.2	+	1	324	c.273G>A	c.(271-273)gtG>gtA	p.V91V		NM_032266.3	NP_115642.3	Q68DN1	CB016_HUMAN	chromosome 2 open reading frame 16	91						extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(33)|urinary_tract(1)	47	Acute lymphoblastic leukemia(172;0.155)					TAAAATCTGTGGAATTAGCAC	0.393																																					p.V91V		Atlas-SNP	.											.	C2orf16	357	.	0			c.G273A						PASS	.						65.0	60.0	61.0					2																	27799712		1873	4107	5980	SO:0001819	synonymous_variant	84226	exon1			ATCTGTGGAATTA	AL136898	CCDS42666.1	2p23.3	2013-09-20			ENSG00000221843	ENSG00000221843			25275	protein-coding gene	gene with protein product	"""P-S-E-R-S-H-H-S repeats containing"""						Standard	NM_032266		Approved	DKFZp434G118	uc002rkz.4	Q68DN1	OTTHUMG00000159099	ENST00000408964.2:c.273G>A	2.37:g.27799712G>A		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	185	89	0.481081	NM_032266	B9EIQ4|Q53S01|Q8ND64|Q9H088	Silent	SNP	ENST00000408964.2	37	CCDS42666.1																																																																																			.	.	none		0.393	C2orf16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353292.1	NM_032266	
DUSP2	1844	hgsc.bcm.edu	37	2	96810085	96810085	+	Missense_Mutation	SNP	G	G	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:96810085G>C	ENST00000288943.4	-	3	623	c.538C>G	c.(538-540)Ctg>Gtg	p.L180V	AC012307.2_ENST00000449242.1_lincRNA	NM_004418.3	NP_004409.1	Q05923	DUS2_HUMAN	dual specificity phosphatase 2	180					endoderm formation (GO:0001706)|inactivation of MAPK activity (GO:0000188)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	nucleus (GO:0005634)	MAP kinase tyrosine/serine/threonine phosphatase activity (GO:0017017)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)|protein tyrosine/threonine phosphatase activity (GO:0008330)			NS(1)|breast(1)|lung(2)|skin(1)	5		Ovarian(717;0.0228)				CCCAGGAACAGGTAGGGCAAG	0.662																																					p.L180V		Atlas-SNP	.											.	DUSP2	20	.	0			c.C538G						PASS	.						39.0	42.0	41.0					2																	96810085		2203	4300	6503	SO:0001583	missense	1844	exon3			GGAACAGGTAGGG	L11329	CCDS2016.1	2q11	2011-06-09			ENSG00000158050	ENSG00000158050		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : MAP kinase phosphatases"""	3068	protein-coding gene	gene with protein product		603068				7806236, 7590752, 12673251	Standard	NM_004418		Approved	PAC-1	uc002svk.4	Q05923	OTTHUMG00000130456	ENST00000288943.4:c.538C>G	2.37:g.96810085G>C	ENSP00000288943:p.Leu180Val	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	61	10	0.163934	NM_004418	Q53T45	Missense_Mutation	SNP	ENST00000288943.4	37	CCDS2016.1	.	.	.	.	.	.	.	.	.	.	g	18.49	3.636287	0.67130	.	.	ENSG00000158050	ENST00000288943	D	0.86627	-2.15	4.56	1.77	0.24775	Dual specificity phosphatase, catalytic domain (1);Dual specificity phosphatase, subgroup, catalytic domain (2);	0.000000	0.64402	D	0.000013	D	0.91998	0.7465	M	0.83953	2.67	0.49687	D	0.999815	D	0.56035	0.974	D	0.80764	0.994	D	0.90547	0.4506	10	0.66056	D	0.02	.	7.8982	0.29719	0.2871:0.0:0.7129:0.0	.	180	Q05923	DUS2_HUMAN	V	180	ENSP00000288943:L180V	ENSP00000288943:L180V	L	-	1	2	DUSP2	96173812	1.000000	0.71417	0.980000	0.43619	0.696000	0.40369	2.783000	0.47766	0.680000	0.31366	0.550000	0.68814	CTG	.	.	none		0.662	DUSP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252847.1	NM_004418	
CRYBB2	1415	hgsc.bcm.edu	37	22	25623839	25623839	+	Missense_Mutation	SNP	G	G	T	rs16986560	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:25623839G>T	ENST00000398215.2	+	4	364	c.193G>T	c.(193-195)Gcc>Tcc	p.A65S		NM_000496.2	NP_000487.1	P43320	CRBB2_HUMAN	crystallin, beta B2	65	Beta/gamma crystallin 'Greek key' 2. {ECO:0000255|PROSITE-ProRule:PRU00028}.		A -> S (in dbSNP:rs16986560).		camera-type eye development (GO:0043010)|response to stimulus (GO:0050896)|visual perception (GO:0007601)		identical protein binding (GO:0042802)|structural constituent of eye lens (GO:0005212)|structural molecule activity (GO:0005198)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(5)|skin(1)	10						CTATGAACAGGCCAACTGCAA	0.577													G|||	104	0.0207668	0.025	0.0029	5008	,	,		18572	0.0109		0.007	False		,,,				2504	0.0521				p.A65S		Atlas-SNP	.											.	CRYBB2	18	.	0			c.G193T						PASS	.	G	SER/ALA	136,4270		1,134,2068	80.0	80.0	80.0		193	4.1	1.0	22	dbSNP_123	80	79,8521		0,79,4221	no	missense	CRYBB2	NM_000496.2	99	1,213,6289	TT,TG,GG		0.9186,3.0867,1.6531	benign	65/206	25623839	215,12791	2203	4300	6503	SO:0001583	missense	1415	exon4			GAACAGGCCAACT		CCDS13831.1	22q11.23	2008-06-10			ENSG00000244752	ENSG00000244752			2398	protein-coding gene	gene with protein product		123620		CCA2, CRYB2A, CRYB2		9158139, 8224918	Standard	XM_006724141		Approved		uc003abp.1	P43320	OTTHUMG00000150905	ENST00000398215.2:c.193G>T	22.37:g.25623839G>T	ENSP00000381273:p.Ala65Ser	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	66	25	0.378788	NM_000496	Q9UCM8	Missense_Mutation	SNP	ENST00000398215.2	37	CCDS13831.1	27	0.012362637362637362	14	0.028455284552845527	1	0.0027624309392265192	6	0.01048951048951049	6	0.0079155672823219	.	5.032	0.191549	0.09547	0.030867	0.009186	ENSG00000244752	ENST00000398215	T	0.76186	-1.0	5.08	4.06	0.47325	Beta/gamma crystallin (5);Gamma-crystallin-related (1);	0.372895	0.29616	N	0.011656	T	0.32615	0.0835	N	0.24115	0.695	0.32936	D	0.517772	B	0.02656	0.0	B	0.11329	0.006	T	0.54063	-0.8349	10	0.34782	T	0.22	.	7.7139	0.28694	0.0889:0.1669:0.7442:0.0	rs16986560;rs16986560	65	P43320	CRBB2_HUMAN	S	65	ENSP00000381273:A65S	ENSP00000381273:A65S	A	+	1	0	CRYBB2	23953839	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	1.300000	0.33436	2.366000	0.80165	0.650000	0.86243	GCC	G|0.985;T|0.015	0.015	strong		0.577	CRYBB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320350.1	NM_000496	
NUTM2F	54754	hgsc.bcm.edu	37	9	97082699	97082699	+	Missense_Mutation	SNP	G	G	A	rs10993163	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:97082699G>A	ENST00000253262.4	-	5	1179	c.1159C>T	c.(1159-1161)Cct>Tct	p.P387S	NUTM2F_ENST00000335456.7_Missense_Mutation_p.P372S|NUTM2F_ENST00000341207.4_Missense_Mutation_p.P372S	NM_017561.1	NP_060031.1	A1L443	NTM2F_HUMAN	NUT family member 2F	387	Pro-rich.																ATCTCCTCAGGGACCTTGGTC	0.672													.|||	919	0.183506	0.115	0.2637	5008	,	,		15860	0.3571		0.0586	False		,,,				2504	0.1687				p.P387S		Atlas-SNP	.											.	FAM22F	72	.	0			c.C1159T						PASS	.	G	SER/PRO	403,3523		24,355,1584	49.0	59.0	56.0		1159	1.2	0.0	9	dbSNP_120	56	394,7870		9,376,3747	no	missense	FAM22F	NM_017561.1	74	33,731,5331	AA,AG,GG		4.7677,10.2649,6.5381	probably-damaging	387/757	97082699	797,11393	1963	4132	6095	SO:0001583	missense	54754	exon5			CCTCAGGGACCTT		CCDS47994.1	9q22.32	2013-05-02	2013-03-14	2013-05-02	ENSG00000130950	ENSG00000130950			23450	protein-coding gene	gene with protein product			"""family with sequence similarity 22, member F"""	FAM22F			Standard	NM_017561		Approved	DKFZp434I1117		A1L443	OTTHUMG00000020260	ENST00000253262.4:c.1159C>T	9.37:g.97082699G>A	ENSP00000253262:p.Pro387Ser	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	71	24	0.338028	NM_017561	B6ZDF0|Q5SR58|Q5SR59|Q9UFB1	Missense_Mutation	SNP	ENST00000253262.4	37	CCDS47994.1	377	0.17261904761904762	53	0.10772357723577236	83	0.2292817679558011	191	0.3339160839160839	50	0.06596306068601583	.	12.41	1.930455	0.34096	0.102649	0.047677	ENSG00000130950	ENST00000335456;ENST00000253262;ENST00000341207	T;T;T	0.34472	1.36;2.07;2.07	1.2	1.2	0.21068	Nuclear Testis protein, C-terminal (1);	0.125438	0.36972	N	0.002302	T	0.00012	0.0000	M	0.76170	2.325	0.58432	P	8.000000000008E-6	D	0.89917	1.0	D	0.97110	1.0	T	0.15321	-1.0441	9	0.87932	D	0	.	8.3567	0.32335	0.0:0.0:1.0:0.0	rs10993163	387	A1L443	FA22F_HUMAN	S	372;387;372	ENSP00000335067:P372S;ENSP00000253262:P387S;ENSP00000343865:P372S	ENSP00000253262:P387S	P	-	1	0	FAM22F	96122520	0.060000	0.20803	0.018000	0.16275	0.013000	0.08279	1.765000	0.38481	0.992000	0.38840	0.456000	0.33151	CCT	G|0.856;A|0.144	0.144	strong		0.672	NUTM2F-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053173.2	NM_017561	
LAMB3	3914	hgsc.bcm.edu	37	1	209823354	209823354	+	Silent	SNP	G	G	A	rs2228339	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:209823354G>A	ENST00000356082.4	-	3	272	c.138C>T	c.(136-138)acC>acT	p.T46T	LAMB3_ENST00000391911.1_Silent_p.T46T|LAMB3_ENST00000367030.3_Silent_p.T46T	NM_000228.2	NP_000219.2	Q13751	LAMB3_HUMAN	laminin, beta 3	46	Laminin N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00466}.				brown fat cell differentiation (GO:0050873)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	extracellular region (GO:0005576)|laminin-5 complex (GO:0005610)	structural molecule activity (GO:0005198)	p.T46T(1)		NS(1)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(11)|lung(13)|ovary(1)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	45				OV - Ovarian serous cystadenocarcinoma(81;0.0519)		TCAGTCCACAGGTAGATGAAG	0.617													G|||	1492	0.297923	0.2088	0.4078	5008	,	,		17612	0.3393		0.2674	False		,,,				2504	0.3292				p.T46T		Atlas-SNP	.											LAMB3,NS,carcinoma,0,1	LAMB3	136	1	1	Substitution - coding silent(1)	stomach(1)	c.C138T						PASS	.	G	,,	1002,3404	373.7+/-320.9	106,790,1307	90.0	77.0	82.0		138,138,138	5.4	1.0	1	dbSNP_107	82	2150,6450	370.0+/-335.7	277,1596,2427	no	coding-synonymous,coding-synonymous,coding-synonymous	LAMB3	NM_000228.2,NM_001017402.1,NM_001127641.1	,,	383,2386,3734	AA,AG,GG		25.0,22.7417,24.235	,,	46/1173,46/1173,46/1173	209823354	3152,9854	2203	4300	6503	SO:0001819	synonymous_variant	3914	exon3			TCCACAGGTAGAT	D37766	CCDS1487.1	1q32	2013-03-01	2002-08-29		ENSG00000196878	ENSG00000196878		"""Laminins"""	6490	protein-coding gene	gene with protein product		150310	"""laminin, beta 3 (nicein (125kD), kalinin (140kD), BM600 (125kD))"""	LAMNB1		8088808, 7774918	Standard	NM_001127641		Approved	nicein-125kDa, kalinin-140kDa, BM600-125kDa	uc001hhh.3	Q13751	OTTHUMG00000036360	ENST00000356082.4:c.138C>T	1.37:g.209823354G>A		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	63	38	0.603175	NM_000228	D3DT88|O14947|Q14733|Q9UJK4|Q9UJL1	Silent	SNP	ENST00000356082.4	37	CCDS1487.1																																																																																			G|0.739;A|0.261	0.261	strong		0.617	LAMB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088525.2	NM_000228	
TAF1L	138474	hgsc.bcm.edu	37	9	32631369	32631369	+	Silent	SNP	C	C	T	rs10971047	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:32631369C>T	ENST00000242310.4	-	1	4298	c.4209G>A	c.(4207-4209)acG>acA	p.T1403T	RP11-555J4.4_ENST00000430787.1_RNA	NM_153809.2	NP_722516.1	Q8IZX4	TAF1L_HUMAN	TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 210kDa-like	1403					DNA-templated transcription, initiation (GO:0006352)|histone acetylation (GO:0016573)|male meiosis (GO:0007140)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	transcription factor TFIID complex (GO:0005669)	DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|lysine-acetylated histone binding (GO:0070577)|protein serine/threonine kinase activity (GO:0004674)|TBP-class protein binding (GO:0017025)			breast(6)|central_nervous_system(4)|endometrium(14)|kidney(11)|large_intestine(32)|liver(2)|lung(68)|ovary(2)|pancreas(2)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(1)	159			LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.00301)		TGGATGACAGCGTCACCATAG	0.458													C|||	809	0.161542	0.1097	0.1182	5008	,	,		21985	0.3095		0.1034	False		,,,				2504	0.1697				p.T1403T		Atlas-SNP	.											TAF1L,NS,carcinoma,-1,1	TAF1L	382	1	0			c.G4209A						PASS	.	C		374,4032	188.5+/-214.9	13,348,1842	297.0	272.0	280.0		4209	-0.9	0.9	9	dbSNP_120	280	893,7707	201.1+/-244.7	44,805,3451	no	coding-synonymous	TAF1L	NM_153809.2		57,1153,5293	TT,TC,CC		10.3837,8.4884,9.7417		1403/1827	32631369	1267,11739	2203	4300	6503	SO:0001819	synonymous_variant	138474	exon1			TGACAGCGTCACC	AF390562	CCDS35003.1	9p12	2007-07-27	2007-07-27		ENSG00000122728	ENSG00000122728			18056	protein-coding gene	gene with protein product		607798	"""TAF1-like RNA polymerase II, TATA box binding protein (TBP)-associated factor, 210kDa"""			12217962	Standard	NM_153809		Approved		uc003zrg.1	Q8IZX4	OTTHUMG00000019747	ENST00000242310.4:c.4209G>A	9.37:g.32631369C>T		Somatic	382	0	0		WXS	Illumina HiSeq	Phase_I	317	134	0.422713	NM_153809	Q0VG57	Silent	SNP	ENST00000242310.4	37	CCDS35003.1																																																																																			C|0.873;T|0.127	0.127	strong		0.458	TAF1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052012.2		
RELN	5649	hgsc.bcm.edu	37	7	103155705	103155705	+	Silent	SNP	A	A	G	rs2229864	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:103155705A>G	ENST00000428762.1	-	50	8205	c.8046T>C	c.(8044-8046)caT>caC	p.H2682H	RELN_ENST00000424685.2_Silent_p.H2682H|RELN_ENST00000343529.5_Silent_p.H2682H|CTB-107G13.1_ENST00000422488.1_RNA	NM_005045.3	NP_005036.2	P78509	RELN_HUMAN	reelin	2682					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)		GGGAGCGCTCATGCTGGGGTA	0.522													G|||	3247	0.648363	0.829	0.4496	5008	,	,		17128	0.8353		0.3459	False		,,,				2504	0.6636				p.H2682H	NSCLC(146;835 1944 15585 22231 52158)	Atlas-SNP	.											.	RELN	593	.	0			c.T8046C						PASS	.	G	,	3341,1065	388.2+/-326.8	1259,823,121	48.0	46.0	47.0		8046,8046	-4.0	0.8	7	dbSNP_98	47	3103,5497	658.3+/-401.6	566,1971,1763	no	coding-synonymous,coding-synonymous	RELN	NM_005045.3,NM_173054.2	,	1825,2794,1884	GG,GA,AA		36.0814,24.1716,49.5464	,	2682/3461,2682/3459	103155705	6444,6562	2203	4300	6503	SO:0001819	synonymous_variant	5649	exon50			GCGCTCATGCTGG		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.8046T>C	7.37:g.103155705A>G		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	101	43	0.425743	NM_173054	A4D0P9|A4D0Q0|Q86UJ0|Q86UJ8|Q8NDV0|Q9UDQ2	Silent	SNP	ENST00000428762.1	37	CCDS47680.1																																																																																			A|0.467;G|0.533	0.533	strong		0.522	RELN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348148.1	NM_005045	
AHNAK2	113146	hgsc.bcm.edu	37	14	105415608	105415608	+	Missense_Mutation	SNP	G	G	C	rs11850848	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:105415608G>C	ENST00000333244.5	-	7	6299	c.6180C>G	c.(6178-6180)caC>caG	p.H2060Q	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	2060						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)			CCTCGGGCACGTGGCCCTCCG	0.627													.|||	1818	0.363019	0.562	0.3329	5008	,	,		11574	0.3333		0.1163	False		,,,				2504	0.3998				p.H2060Q		Atlas-SNP	.											.	AHNAK2	719	.	0			c.C6180G						PASS	.	G	GLN/HIS	1936,1626		688,560,533	90.0	72.0	79.0		6180	-2.5	0.0	14	dbSNP_120	79	629,5089		217,195,2447	no	missense	AHNAK2	NM_138420.2	24	905,755,2980	CC,CG,GG		11.0003,45.6485,27.6401	benign	2060/5796	105415608	2565,6715	1781	2859	4640	SO:0001583	missense	113146	exon7			GGGCACGTGGCCC	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.6180C>G	14.37:g.105415608G>C	ENSP00000353114:p.His2060Gln	Somatic	0	0	.		WXS	Illumina HiSeq	Phase_I	55	46	0.836364	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	747	0.34203296703296704	269	0.5467479674796748	152	0.4198895027624309	184	0.32167832167832167	142	0.18733509234828497	-	7.258	0.604635	0.14002	0.543515	0.110003	ENSG00000185567	ENST00000333244	T	0.00882	5.58	4.25	-2.47	0.06442	.	.	.	.	.	T	0.00012	0.0000	L	0.55017	1.72	0.80722	P	0.0	B	0.17465	0.022	B	0.20384	0.029	T	0.08289	-1.0729	8	0.12766	T	0.61	.	8.9245	0.35632	0.0:0.1777:0.6214:0.2009	rs11850848;rs60903782	2060	Q8IVF2	AHNK2_HUMAN	Q	2060	ENSP00000353114:H2060Q	ENSP00000353114:H2060Q	H	-	3	2	AHNAK2	104486653	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-5.080000	0.00153	-0.084000	0.12595	-0.494000	0.04653	CAC	G|0.698;C|0.302	0.302	strong		0.627	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
TTC13	79573	hgsc.bcm.edu	37	1	231057247	231057247	+	Silent	SNP	A	A	T	rs2275333	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:231057247A>T	ENST00000366661.4	-	16	1825	c.1818T>A	c.(1816-1818)ggT>ggA	p.G606G	TTC13_ENST00000414259.1_Silent_p.G553G|TTC13_ENST00000366662.4_Silent_p.G553G	NM_024525.4	NP_078801.3	Q8NBP0	TTC13_HUMAN	tetratricopeptide repeat domain 13	606										central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(9)|lung(16)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	39	Breast(184;0.0871)|Ovarian(103;0.183)	Prostate(94;0.167)		COAD - Colon adenocarcinoma(196;0.243)		TGATCACCTGACCCCTATAAG	0.259													A|||	1074	0.214457	0.1354	0.1167	5008	,	,		14479	0.3879		0.17	False		,,,				2504	0.2577				p.G606G		Atlas-SNP	.											.	TTC13	74	.	0			c.T1818A						PASS	.	A	,	657,3687		41,575,1556	30.0	32.0	31.0		1659,1818	1.9	1.0	1	dbSNP_100	31	1515,7005		135,1245,2880	no	coding-synonymous,coding-synonymous	TTC13	NM_001122835.2,NM_024525.4	,	176,1820,4436	TT,TA,AA		17.7817,15.1243,16.8843	,	553/807,606/861	231057247	2172,10692	2172	4260	6432	SO:0001819	synonymous_variant	79573	exon16			CACCTGACCCCTA		CCDS1588.1, CCDS44332.1, CCDS44332.2	1q42.2	2013-01-10			ENSG00000143643	ENSG00000143643		"""Tetratricopeptide (TTC) repeat domain containing"""	26204	protein-coding gene	gene with protein product							Standard	NM_024525		Approved	FLJ22584	uc001huf.4	Q8NBP0	OTTHUMG00000037788	ENST00000366661.4:c.1818T>A	1.37:g.231057247A>T		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	56	23	0.410714	NM_024525	B1AQI1|B1AQI2|Q8IVP8|Q8NBI0|Q8ND20	Silent	SNP	ENST00000366661.4	37	CCDS1588.1																																																																																			A|0.818;T|0.182	0.182	strong		0.259	TTC13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092229.2	NM_024525	
DUSP22	56940	hgsc.bcm.edu	37	6	350829	350829	+	Silent	SNP	G	G	A	rs1129085	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	323	1	0.00309598		WXS	Illumina HiSeq	Phase_I	218	79	0.362385	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	
GRM4	2914	hgsc.bcm.edu	37	6	34003928	34003928	+	Silent	SNP	C	C	T	rs34858760	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:34003928C>T	ENST00000538487.2	-	9	2402	c.1959G>A	c.(1957-1959)tcG>tcA	p.S653S	GRM4_ENST00000374177.3_Silent_p.S537S|GRM4_ENST00000374181.4_Silent_p.S653S|GRM4_ENST00000455714.2_Silent_p.S513S|GRM4_ENST00000609222.1_Silent_p.S520S|GRM4_ENST00000545715.1_5'UTR|GRM4_ENST00000535756.1_Silent_p.S520S|GRM4_ENST00000544773.2_Silent_p.S484S	NM_000841.2|NM_001256811.1	NP_000832.1|NP_001243740.1	Q14833	GRM4_HUMAN	glutamate receptor, metabotropic 4	653					activation of MAPK activity (GO:0000187)|adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|learning (GO:0007612)|neurotransmitter secretion (GO:0007269)|positive regulation of MAPK cascade (GO:0043410)|regulation of neuron apoptotic process (GO:0043523)|regulation of synaptic transmission, glutamatergic (GO:0051966)|synaptic transmission (GO:0007268)	cytoplasmic vesicle (GO:0031410)|dendritic shaft (GO:0043198)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|presynaptic active zone membrane (GO:0048787)|presynaptic membrane (GO:0042734)|terminal bouton (GO:0043195)	G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)|group III metabotropic glutamate receptor activity (GO:0001642)			NS(1)|breast(1)|endometrium(4)|kidney(4)|large_intestine(9)|liver(1)|lung(19)|ovary(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	48						TTCGGCGCAGCGAGCAGGTGC	0.607													C|||	136	0.0271565	0.0961	0.0072	5008	,	,		22264	0.0		0.004	False		,,,				2504	0.0				p.S653S		Atlas-SNP	.											.	GRM4	317	.	0			c.G1959A						PASS	.	C		292,4114	159.6+/-192.1	13,266,1924	100.0	92.0	94.0		1959	-7.7	0.7	6	dbSNP_126	94	37,8563	25.1+/-72.6	0,37,4263	no	coding-synonymous	GRM4	NM_000841.1		13,303,6187	TT,TC,CC		0.4302,6.6273,2.5296		653/913	34003928	329,12677	2203	4300	6503	SO:0001819	synonymous_variant	2914	exon9			GCGCAGCGAGCAG	U92457	CCDS4787.1, CCDS59010.1, CCDS59011.1, CCDS59012.1, CCDS75432.1	6p21.3	2012-08-29			ENSG00000124493	ENSG00000124493		"""GPCR / Class C : Glutamate receptors, metabotropic"", ""Glutamate receptors"""	4596	protein-coding gene	gene with protein product		604100				8738157, 9473604	Standard	NM_000841		Approved	GPRC1D, mGlu4, MGLUR4	uc010jvh.4	Q14833	OTTHUMG00000014538	ENST00000538487.2:c.1959G>A	6.37:g.34003928C>T		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	104	44	0.423077	NM_000841	B3KVL9|B7Z1T9|B7Z1U6|F5GXM5|Q5SZ84|Q6ZMQ2	Silent	SNP	ENST00000538487.2	37	CCDS4787.1																																																																																			C|0.975;T|0.025	0.025	strong		0.607	GRM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040213.2		
MYCBP2	23077	hgsc.bcm.edu	37	13	77740577	77740577	+	Missense_Mutation	SNP	T	T	C	rs111642157	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:77740577T>C	ENST00000544440.2	-	41	6130	c.6113A>G	c.(6112-6114)aAt>aGt	p.N2038S	MYCBP2_ENST00000357337.6_Missense_Mutation_p.N2038S|MYCBP2_ENST00000360084.5_5'UTR|MYCBP2_ENST00000407578.2_Missense_Mutation_p.N2076S					MYC binding protein 2, E3 ubiquitin protein ligase											NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|lung(51)|ovary(5)|pancreas(2)|prostate(5)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	118		Breast(118;0.212)|Acute lymphoblastic leukemia(28;0.22)		GBM - Glioblastoma multiforme(99;0.109)		ATATCCTGAATTCTGAACAGT	0.398													T|||	16	0.00319489	0.0068	0.0072	5008	,	,		17955	0.0		0.002	False		,,,				2504	0.0				p.N2076S		Atlas-SNP	.											.	MYCBP2	1029	.	0			c.A6227G						PASS	.	T	SER/ASN	24,4382	30.8+/-60.4	0,24,2179	109.0	107.0	108.0		6227	3.3	1.0	13	dbSNP_132	108	9,8591	7.1+/-27.0	0,9,4291	yes	missense	MYCBP2	NM_015057.4	46	0,33,6470	CC,CT,TT		0.1047,0.5447,0.2537	benign	2076/4679	77740577	33,12973	2203	4300	6503	SO:0001583	missense	23077	exon41			CCTGAATTCTGAA	AB020723		13q22	2012-02-23	2012-02-23		ENSG00000005810	ENSG00000005810			23386	protein-coding gene	gene with protein product		610392	"""MYC binding protein 2"""			9689053, 15057823	Standard	NM_015057		Approved	PAM, KIAA0916, FLJ10106	uc021rks.1	O75592	OTTHUMG00000017105	ENST00000544440.2:c.6113A>G	13.37:g.77740577T>C	ENSP00000444596:p.Asn2038Ser	Somatic	193	0	0		WXS	Illumina HiSeq	Phase_I	131	73	0.557252	NM_015057		Missense_Mutation	SNP	ENST00000544440.2	37		7	0.003205128205128205	3	0.006097560975609756	4	0.011049723756906077	0	0.0	0	0.0	T	8.715	0.913023	0.17907	0.005447	0.001047	ENSG00000005810	ENST00000357337;ENST00000407578;ENST00000544440	T;T;T	0.28069	1.63;1.63;1.63	5.79	3.27	0.37495	.	0.264107	0.38326	N	0.001731	T	0.05868	0.0153	N	0.01874	-0.695	0.23030	N	0.998406	B	0.02656	0.0	B	0.01281	0.0	T	0.30822	-0.9965	10	0.08599	T	0.76	.	3.9352	0.09302	0.3857:0.1334:0.0:0.4809	.	2038	O75592	MYCB2_HUMAN	S	2038;2076;2038	ENSP00000349892:N2038S;ENSP00000384288:N2076S;ENSP00000444596:N2038S	ENSP00000349892:N2038S	N	-	2	0	MYCBP2	76638578	1.000000	0.71417	0.993000	0.49108	0.943000	0.58893	1.627000	0.37050	0.978000	0.38470	0.528000	0.53228	AAT	T|0.997;C|0.003	0.003	strong		0.398	MYCBP2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000045326.1	NM_015057	
NEK4	6787	hgsc.bcm.edu	37	3	52797634	52797634	+	Missense_Mutation	SNP	G	G	C	rs1029871	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:52797634G>C	ENST00000233027.5	-	5	875	c.673C>G	c.(673-675)Cca>Gca	p.P225A	NEK4_ENST00000383721.4_Missense_Mutation_p.P225A|NEK4_ENST00000535191.1_Missense_Mutation_p.P136A	NM_001193533.1|NM_003157.4	NP_001180462.1|NP_003148.2	P51957	NEK4_HUMAN	NIMA-related kinase 4	225	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		P -> A (in dbSNP:rs1029871). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:8208544, ECO:0000269|Ref.2}.		mitotic nuclear division (GO:0007067)|protein phosphorylation (GO:0006468)	nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(9)|lung(10)	26				BRCA - Breast invasive adenocarcinoma(193;7.44e-05)|Kidney(197;0.000711)|KIRC - Kidney renal clear cell carcinoma(197;0.00086)|OV - Ovarian serous cystadenocarcinoma(275;0.0513)		CTTGGCATTGGTGGCAGCTAC	0.398													G|||	1534	0.30631	0.1278	0.4553	5008	,	,		17414	0.4246		0.4175	False		,,,				2504	0.2055				p.P225A		Atlas-SNP	.											.	NEK4	51	.	0			c.C673G						PASS	.	G	ALA/PRO,ALA/PRO	668,3738	278.7+/-274.4	57,554,1592	108.0	107.0	107.0		406,673	5.9	1.0	3	dbSNP_86	107	3469,5131	502.6+/-375.7	723,2023,1554	yes	missense,missense	NEK4	NM_001193533.1,NM_003157.4	27,27	780,2577,3146	CC,CG,GG		40.3372,15.1611,31.8084	possibly-damaging,possibly-damaging	136/753,225/842	52797634	4137,8869	2203	4300	6503	SO:0001583	missense	6787	exon5			GCATTGGTGGCAG	L20321	CCDS2863.1, CCDS54593.1	3p21.1	2012-11-15	2012-11-15	2002-05-10	ENSG00000114904	ENSG00000114904	2.7.11.1		11399	protein-coding gene	gene with protein product	"""serine/threonine protein kinase-2"""	601959	"""serine/threonine kinase 2"", ""NIMA (never in mitosis gene a)-related kinase 4"""	STK2		8208544	Standard	NM_001193533		Approved	NRK2, pp12301	uc003dfq.4	P51957	OTTHUMG00000158836	ENST00000233027.5:c.673C>G	3.37:g.52797634G>C	ENSP00000233027:p.Pro225Ala	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	39	39	1	NM_003157	A5YM70|B2R633|B7Z200|Q6P576	Missense_Mutation	SNP	ENST00000233027.5	37	CCDS2863.1	841	0.3850732600732601	69	0.1402439024390244	171	0.4723756906077348	280	0.48951048951048953	321	0.4234828496042216	G	29.2	4.983685	0.93044	0.151611	0.403372	ENSG00000114904	ENST00000233027;ENST00000535191;ENST00000383721;ENST00000461689	T;T;T;T	0.25579	1.79;1.79;1.79;1.79	5.93	5.93	0.95920	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.224369	0.39759	N	0.001264	T	0.00012	0.0000	L	0.46670	1.46	0.09310	P	0.99999871006	P;P;P	0.52692	0.955;0.855;0.88	P;P;P	0.58660	0.843;0.64;0.755	T	0.48502	-0.9030	9	0.56958	D	0.05	.	20.3422	0.98769	0.0:0.0:1.0:0.0	rs1029871;rs2230536;rs17418589;rs17855779;rs1029871	136;225;225	B7Z200;P51957-2;P51957	.;.;NEK4_HUMAN	A	225;136;225;136	ENSP00000233027:P225A;ENSP00000437703:P136A;ENSP00000373227:P225A;ENSP00000419666:P136A	ENSP00000233027:P225A	P	-	1	0	NEK4	52772674	1.000000	0.71417	0.998000	0.56505	0.995000	0.86356	7.529000	0.81952	2.810000	0.96702	0.655000	0.94253	CCA	G|0.654;C|0.346	0.346	strong		0.398	NEK4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000352386.2	NM_003157	
KCNK10	54207	hgsc.bcm.edu	37	14	88651962	88651962	+	Missense_Mutation	SNP	C	C	T	rs17762463	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:88651962C>T	ENST00000340700.5	-	7	1985	c.1534G>A	c.(1534-1536)Gct>Act	p.A512T	KCNK10_ENST00000319231.5_Missense_Mutation_p.A517T|KCNK10_ENST00000312350.5_Missense_Mutation_p.A517T	NM_021161.4	NP_066984.1	P57789	KCNKA_HUMAN	potassium channel, subfamily K, member 10	512			A -> T (in dbSNP:rs17762463). {ECO:0000269|PubMed:14702039}.		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						TCCAACTCAGCGTGCTGCTGG	0.498													C|||	512	0.102236	0.0151	0.1412	5008	,	,		19750	0.0089		0.2942	False		,,,				2504	0.091				p.A517T		Atlas-SNP	.											.	KCNK10	273	.	0			c.G1549A						PASS	.	C	THR/ALA,THR/ALA,THR/ALA	285,4121	158.1+/-190.9	14,257,1932	164.0	155.0	158.0		1534,1549,1549	3.5	0.0	14	dbSNP_123	158	2382,6218	396.7+/-345.5	334,1714,2252	yes	missense,missense,missense	KCNK10	NM_021161.4,NM_138317.2,NM_138318.2	58,58,58	348,1971,4184	TT,TC,CC		27.6977,6.4685,20.5059	benign,benign,benign	512/539,517/544,517/544	88651962	2667,10339	2203	4300	6503	SO:0001583	missense	54207	exon7			ACTCAGCGTGCTG	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.1534G>A	14.37:g.88651962C>T	ENSP00000343104:p.Ala512Thr	Somatic	283	0	0		WXS	Illumina HiSeq	Phase_I	199	82	0.41206	NM_138318	B2R8T4|B2RCT3|B5TJL4|Q6B014|Q8TDK7|Q8TDK8|Q9HB59	Missense_Mutation	SNP	ENST00000340700.5	37	CCDS9880.1	310	0.14194139194139194	10	0.02032520325203252	60	0.16574585635359115	9	0.015734265734265736	231	0.30474934036939316	C	6.980	0.550869	0.13374	0.064685	0.276977	ENSG00000100433	ENST00000340700;ENST00000312350;ENST00000319231	D;D;D	0.90955	-2.76;-2.76;-2.75	5.5	3.49	0.39957	.	1.607370	0.03015	N	0.149895	T	0.00039	0.0001	N	0.22421	0.69	0.80722	P	0.0	B;B;B	0.20261	0.043;0.043;0.012	B;B;B	0.14023	0.01;0.005;0.01	T	0.15954	-1.0419	9	0.62326	D	0.03	.	12.4173	0.55500	0.4059:0.5941:0.0:0.0	rs17762463;rs52818966;rs17762463	512;517;517	P57789;B2R8T4;Q6B014	KCNKA_HUMAN;.;.	T	512;517;517	ENSP00000343104:A512T;ENSP00000310568:A517T;ENSP00000312811:A517T	ENSP00000310568:A517T	A	-	1	0	KCNK10	87721715	0.178000	0.23122	0.016000	0.15963	0.150000	0.21749	2.380000	0.44327	0.657000	0.30906	0.655000	0.94253	GCT	C|0.833;T|0.167	0.167	strong		0.498	KCNK10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410167.1	NM_021161	
WDR33	55339	hgsc.bcm.edu	37	2	128522383	128522383	+	Intron	SNP	T	T	C	rs11557685	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:128522383T>C	ENST00000322313.4	-	6	785				WDR33_ENST00000393006.1_Intron|WDR33_ENST00000409658.3_Silent_p.P215P	NM_018383.4	NP_060853.3	Q9C0J8	WDR33_HUMAN	WD repeat domain 33						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)		CTACAGAAAATGGTATATTGT	0.423													T|||	285	0.0569089	0.0575	0.049	5008	,	,		19874	0.0427		0.0716	False		,,,				2504	0.0613				p.P215P		Atlas-SNP	.											WDR33_ENST00000409658,NS,carcinoma,-2,1	WDR33	136	1	0			c.A645G						PASS	.	T	,,	297,4109	164.4+/-196.0	11,275,1917	138.0	119.0	126.0		645,,	5.7	1.0	2	dbSNP_120	126	777,7823	183.6+/-231.8	32,713,3555	no	coding-synonymous,intron,intron	WDR33	NM_001006622.2,NM_001006623.2,NM_018383.4	,,	43,988,5472	CC,CT,TT		9.0349,6.7408,8.2577	,,	215/327,,	128522383	1074,11932	2203	4300	6503	SO:0001627	intron_variant	55339	exon6			AGAAAATGGTATA		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.626+18A>G	2.37:g.128522383T>C		Somatic	191	0	0		WXS	Illumina HiSeq	Phase_I	146	67	0.458904	NM_001006622	Q05DP8|Q53FG9|Q587J1|Q69YF7|Q6NUQ0|Q9NUL1	Silent	SNP	ENST00000322313.4	37	CCDS2150.1																																																																																			T|0.938;C|0.062	0.062	strong		0.423	WDR33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331141.2	NM_018383	
KCNJ3	3760	hgsc.bcm.edu	37	2	155711357	155711357	+	Silent	SNP	T	T	C	rs17642086	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:155711357T>C	ENST00000295101.2	+	3	1515	c.1038T>C	c.(1036-1038)caT>caC	p.H346H	KCNJ3_ENST00000544049.1_3'UTR|KCNJ3_ENST00000493505.1_3'UTR	NM_001260509.1|NM_002239.3	NP_001247438.1|NP_002230.1	P48549	KCNJ3_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 3	346					potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|response to electrical stimulus (GO:0051602)|synaptic transmission (GO:0007268)	external side of plasma membrane (GO:0009897)|plasma membrane (GO:0005886)|T-tubule (GO:0030315)|voltage-gated potassium channel complex (GO:0008076)	G-protein activated inward rectifier potassium channel activity (GO:0015467)			breast(2)|endometrium(2)|kidney(3)|large_intestine(9)|lung(30)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	54					Halothane(DB01159)	CCCAGTTCCATGCAACATTTG	0.418													T|||	836	0.166933	0.1293	0.2147	5008	,	,		16666	0.0367		0.3549	False		,,,				2504	0.1247				p.H346H		Atlas-SNP	.											.	KCNJ3	126	.	0			c.T1038C						PASS	.	T		692,3714	289.8+/-280.6	54,584,1565	114.0	115.0	114.0		1038	2.0	1.0	2	dbSNP_123	114	2954,5646	459.1+/-364.8	498,1958,1844	no	coding-synonymous	KCNJ3	NM_002239.2		552,2542,3409	CC,CT,TT		34.3488,15.7059,28.0332		346/502	155711357	3646,9360	2203	4300	6503	SO:0001819	synonymous_variant	3760	exon3			GTTCCATGCAACA	U50964	CCDS2200.1, CCDS58733.1	2q24.1	2011-07-05			ENSG00000162989	ENSG00000162989		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Inwardly rectifying"""	6264	protein-coding gene	gene with protein product		601534				8088798, 16382105	Standard	NM_002239		Approved	Kir3.1, GIRK1, KGA	uc002tyv.2	P48549	OTTHUMG00000131937	ENST00000295101.2:c.1038T>C	2.37:g.155711357T>C		Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	130	129	0.992308	NM_002239	B4DEW7|Q8TBI0	Silent	SNP	ENST00000295101.2	37	CCDS2200.1																																																																																			T|0.753;C|0.247	0.247	strong		0.418	KCNJ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254890.2	NM_002239	
BTN2A1	11120	hgsc.bcm.edu	37	6	26468660	26468660	+	Silent	SNP	G	G	A	rs3734544	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:26468660G>A	ENST00000312541.5	+	8	1715	c.1467G>A	c.(1465-1467)agG>agA	p.R489R	BTN2A1_ENST00000469185.1_Intron|BTN2A1_ENST00000541522.1_Silent_p.R428R|BTN2A1_ENST00000429381.1_3'UTR	NM_007049.3|NM_078476.2	NP_008980.1|NP_510961.1	Q7KYR7	BT2A1_HUMAN	butyrophilin, subfamily 2, member A1	489	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				lipid metabolic process (GO:0006629)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)				breast(3)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(2)|lung(9)|ovary(2)|prostate(1)|skin(3)|urinary_tract(3)	27						CCTTCTTCAGGTTGGGGTGTG	0.562													G|||	813	0.16234	0.2103	0.1081	5008	,	,		20145	0.1161		0.1759	False		,,,				2504	0.1697				p.R489R		Atlas-SNP	.											.	BTN2A1	118	.	0			c.G1467A						PASS	.	G	,,,	861,3545	335.7+/-304.0	88,685,1430	153.0	121.0	132.0		1284,,1467,	-0.3	0.7	6	dbSNP_107	132	1481,7119	282.3+/-295.5	126,1229,2945	no	coding-synonymous,intron,coding-synonymous,utr-3	BTN2A1	NM_001197233.1,NM_001197234.1,NM_007049.3,NM_078476.2	,,,	214,1914,4375	AA,AG,GG		17.2209,19.5415,18.0071	,,,	428/467,,489/528,	26468660	2342,10664	2203	4300	6503	SO:0001819	synonymous_variant	11120	exon8			CTTCAGGTTGGGG	U90543	CCDS4613.1, CCDS47390.1, CCDS56404.1, CCDS56405.1	6p22.1	2014-01-14			ENSG00000112763	ENSG00000112763		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Butyrophilins"""	1136	protein-coding gene	gene with protein product		613590				9382921, 9149941	Standard	NM_007049		Approved	BT2.1, BTF1, BTN2.1	uc003nib.2	Q7KYR7	OTTHUMG00000014457	ENST00000312541.5:c.1467G>A	6.37:g.26468660G>A		Somatic	246	0	0		WXS	Illumina HiSeq	Phase_I	172	77	0.447674	NM_007049	B4DLP9|E9PGR4|O00475|P78408|Q59EN4|Q7KYQ7|Q7Z386|Q96AV7|Q9NU62	Silent	SNP	ENST00000312541.5	37	CCDS4613.1																																																																																			G|0.824;A|0.176	0.176	strong		0.562	BTN2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040122.2	NM_007049	
CCDC154	645811	hgsc.bcm.edu	37	16	1488141	1488141	+	Silent	SNP	C	C	T	rs12925639	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:1488141C>T	ENST00000389176.3	-	10	1255	c.1089G>A	c.(1087-1089)ggG>ggA	p.G363G	CCDC154_ENST00000409671.1_Silent_p.G209G	NM_001143980.1	NP_001137452.1	A6NI56	CC154_HUMAN	coiled-coil domain containing 154	363						endosome (GO:0005768)				NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)	5						CGGCCAGCTCCCCAGCCCGGC	0.682													C|||	1214	0.242412	0.3646	0.232	5008	,	,		15426	0.1141		0.1998	False		,,,				2504	0.2607				p.G354G		Atlas-SNP	.											.	CCDC154	27	.	0			c.G1062A						PASS	.	C		480,904		85,310,297	30.0	32.0	31.0		1062	2.7	0.5	16	dbSNP_121	31	594,2584		51,492,1046	no	coding-synonymous	CCDC154	NM_001143980.1		136,802,1343	TT,TC,CC		18.691,34.6821,23.5423		354/668	1488141	1074,3488	692	1589	2281	SO:0001819	synonymous_variant	645811	exon10			CAGCTCCCCAGCC			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.1089G>A	16.37:g.1488141C>T		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	73	15	0.205479	NM_001143980	G9JV18	Silent	SNP	ENST00000389176.3	37																																																																																				C|0.791;T|0.209	0.209	strong		0.682	CCDC154-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_001143980	
SH3BP2	6452	hgsc.bcm.edu	37	4	2826912	2826912	+	Silent	SNP	C	C	G	rs16843413	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:2826912C>G	ENST00000356331.5	+	5	678	c.417C>G	c.(415-417)ccC>ccG	p.P139P	SH3BP2_ENST00000515183.1_3'UTR|SH3BP2_ENST00000435136.2_Silent_p.P139P|SH3BP2_ENST00000442312.2_Silent_p.P167P|SH3BP2_ENST00000452765.2_Silent_p.P139P|SH3BP2_ENST00000511747.1_Silent_p.P139P|SH3BP2_ENST00000503393.2_Silent_p.P196P	NM_003023.4	NP_003014.3	P78314	3BP2_HUMAN	SH3-domain binding protein 2	139					positive regulation of signal transduction (GO:0009967)|signal transduction (GO:0007165)		SH3/SH2 adaptor activity (GO:0005070)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)	20				UCEC - Uterine corpus endometrioid carcinoma (64;0.164)		AAGACCTGCCCTTGGACACCA	0.697									Cherubism				c|||	735	0.146765	0.292	0.1499	5008	,	,		17726	0.0645		0.0616	False		,,,				2504	0.1207				p.P196P		Atlas-SNP	.											.	SH3BP2	43	.	0			c.C588G						PASS	.	C	,,,	1025,3359		137,751,1304	44.0	41.0	42.0		417,501,588,417	-3.1	0.1	4	dbSNP_123	42	516,8064		23,470,3797	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SH3BP2	NM_001122681.1,NM_001145855.1,NM_001145856.1,NM_003023.4	,,,	160,1221,5101	GG,GC,CC		6.014,23.3805,11.8868	,,,	139/562,167/590,196/619,139/562	2826912	1541,11423	2192	4290	6482	SO:0001819	synonymous_variant	6452	exon5	Familial Cancer Database	Familial Benign Giant-cell Tumor of the Jaw, Familial Multilocular Cystic Disease	CCTGCCCTTGGAC	BC022996	CCDS33944.1, CCDS54715.1, CCDS54716.1	4p16.3	2013-02-14				ENSG00000087266		"""Pleckstrin homology (PH) domain containing"", ""SH2 domain containing"""	10825	protein-coding gene	gene with protein product		602104	"""Cherubism"""			9299232, 11381256	Standard	NM_003023		Approved	RES4-23, CRBM	uc003gfj.4	P78314		ENST00000356331.5:c.417C>G	4.37:g.2826912C>G		Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	153	75	0.490196	NM_001145856	A6NNC2|B2R5R6|B4DT04|D3DVR0|D6R919|O00500|O15373|P78315	Silent	SNP	ENST00000356331.5	37	CCDS33944.1																																																																																			C|0.875;G|0.125	0.125	strong		0.697	SH3BP2-007	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000362406.2	NM_003023	
NFE2L3	9603	hgsc.bcm.edu	37	7	26224313	26224313	+	Missense_Mutation	SNP	C	C	T	rs147199325		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:26224313C>T	ENST00000056233.3	+	4	1254	c.995C>T	c.(994-996)aCa>aTa	p.T332I		NM_004289.6	NP_004280.5	Q9Y4A8	NF2L3_HUMAN	nuclear factor, erythroid 2-like 3	332					transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			breast(2)|endometrium(1)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|prostate(2)|skin(5)|urinary_tract(7)	29						AGAGATCCAACAGCAAGGACT	0.408																																					p.T332I		Atlas-SNP	.											.	NFE2L3	77	.	0			c.C995T						PASS	.						108.0	96.0	100.0					7																	26224313		2203	4300	6503	SO:0001583	missense	9603	exon4			ATCCAACAGCAAG	AB010812	CCDS5396.1	7p15.2	2013-08-23	2013-08-23		ENSG00000050344	ENSG00000050344		"""basic leucine zipper proteins"""	7783	protein-coding gene	gene with protein product		604135	"""nuclear factor (erythroid-derived 2)-like 3"""			10037736	Standard	NM_004289		Approved	Nrf3	uc003sxq.3	Q9Y4A8	OTTHUMG00000023882	ENST00000056233.3:c.995C>T	7.37:g.26224313C>T	ENSP00000056233:p.Thr332Ile	Somatic	381	0	0		WXS	Illumina HiSeq	Phase_I	459	67	0.145969	NM_004289	Q6NUS0|Q7Z498|Q86UJ4|Q86VR5|Q9UQA4	Missense_Mutation	SNP	ENST00000056233.3	37	CCDS5396.1	.	.	.	.	.	.	.	.	.	.	c	0.830	-0.745584	0.03065	.	.	ENSG00000050344	ENST00000056233;ENST00000398175	T	0.31247	1.5	4.63	-5.14	0.02875	.	1.593220	0.03300	N	0.188821	T	0.13927	0.0337	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.20107	-1.0285	10	0.38643	T	0.18	1.2662	4.7543	0.13075	0.1048:0.4831:0.2352:0.177	.	332	Q9Y4A8	NF2L3_HUMAN	I	332;38	ENSP00000056233:T332I	ENSP00000056233:T332I	T	+	2	0	NFE2L3	26190838	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-0.396000	0.07278	-0.575000	0.05982	-1.912000	0.00520	ACA	.	.	weak		0.408	NFE2L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214088.1		
PARP16	54956	hgsc.bcm.edu	37	15	65553246	65553246	+	Silent	SNP	C	C	T	rs2304896	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:65553246C>T	ENST00000444347.2	-	3	881	c.465G>A	c.(463-465)gtG>gtA	p.V155V	PARP16_ENST00000261888.6_Silent_p.V270V			Q8N5Y8	PAR16_HUMAN	poly (ADP-ribose) polymerase family, member 16	270	PARP catalytic. {ECO:0000255|PROSITE- ProRule:PRU00397}.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of cell death (GO:0060548)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|protein ADP-ribosylation (GO:0006471)|protein auto-ADP-ribosylation (GO:0070213)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum tubular network (GO:0071782)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear envelope (GO:0005635)	kinase binding (GO:0019900)|NAD(P)+-protein-arginine ADP-ribosyltransferase activity (GO:0003956)|NAD+ ADP-ribosyltransferase activity (GO:0003950)|protein serine/threonine kinase activator activity (GO:0043539)			kidney(1)|large_intestine(1)|lung(5)|prostate(1)|skin(1)	9						TCTGTGAATACACCAGGAGGT	0.498													C|||	1155	0.230631	0.2572	0.4049	5008	,	,		19655	0.125		0.2714	False		,,,				2504	0.138				p.V270V	NSCLC(50;885 1163 13509 21242 41978)	Atlas-SNP	.											.	PARP16	23	.	0			c.G810A						PASS	.	C		1145,3257	406.9+/-334.0	150,845,1206	181.0	162.0	169.0		810	1.9	1.0	15	dbSNP_100	169	2567,6031	417.6+/-352.5	374,1819,2106	yes	coding-synonymous	PARP16	NM_017851.4		524,2664,3312	TT,TC,CC		29.8558,26.0109,28.5538		270/324	65553246	3712,9288	2201	4299	6500	SO:0001819	synonymous_variant	54956	exon5			TGAATACACCAGG	AK000516	CCDS10204.1	15q22.2	2010-02-16	2004-08-25	2004-08-25	ENSG00000138617	ENSG00000138617		"""Poly (ADP-ribose) polymerases"""	26040	protein-coding gene	gene with protein product			"""chromosome 15 open reading frame 30"""	C15orf30		15273990	Standard	NM_017851		Approved	FLJ20509, FLJ25281, pART15	uc002aoq.3	Q8N5Y8	OTTHUMG00000133138	ENST00000444347.2:c.465G>A	15.37:g.65553246C>T		Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	206	86	0.417476	NM_017851	Q6PK64|Q9NX03	Silent	SNP	ENST00000444347.2	37																																																																																				C|0.729;T|0.271	0.271	strong		0.498	PARP16-002	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000418174.1	NM_017851	
PKD1L2	114780	hgsc.bcm.edu	37	16	81253759	81253759	+	RNA	SNP	A	A	G	rs9924371	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:81253759A>G	ENST00000525539.1	-	0	216				PKD1L2_ENST00000337114.4_RNA	NM_052892.3	NP_443124.3	Q7Z442	PK1L2_HUMAN	polycystic kidney disease 1-like 2						ion transport (GO:0006811)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(20)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44						TGCAGAAACCACTGGGTGCCT	0.572													G|||	2677	0.534545	0.5983	0.562	5008	,	,		22265	0.4405		0.6511	False		,,,				2504	0.4059				p.W73R		Atlas-SNP	.											.	PKD1L2	361	.	0			c.T217C						PASS	.	G	ARG/TRP,ARG/TRP	2615,1463		849,917,273	103.0	101.0	101.0		217,217	-0.1	0.0	16	dbSNP_119	101	5314,3088		1668,1978,555	yes	missense,missense	PKD1L2	NM_001076780.1,NM_052892.3	101,101	2517,2895,828	GG,GA,AA		36.7532,35.8754,36.4663	benign,benign	73/992,73/2460	81253759	7929,4551	2039	4201	6240			114780	exon1			GAAACCACTGGGT	AY164483	CCDS61998.1, CCDS61999.1	16q23.2	2014-09-11			ENSG00000166473	ENSG00000166473			21715	protein-coding gene	gene with protein product		607894				12782129	Standard	NM_052892		Approved	KIAA1879	uc002fgf.1	Q7Z442	OTTHUMG00000166126		16.37:g.81253759A>G		Somatic	134	1	0.00746269		WXS	Illumina HiSeq	Phase_I	144	144	1	NM_001076780	Q6UEE1|Q6ZN46|Q6ZSP2|Q8N1H9|Q96CL2|Q96Q08	Missense_Mutation	SNP	ENST00000525539.1	37		1248	0.5714285714285714	298	0.6056910569105691	225	0.6215469613259669	233	0.40734265734265734	492	0.6490765171503958	G	0.003	-2.430925	0.00184	0.641246	0.632468	ENSG00000166473	ENST00000337114	T	0.16597	2.33	4.17	-0.109	0.13584	C-type lectin fold (1);C-type lectin (3);	0.543965	0.16764	N	0.200499	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.34329	-0.9833	8	0.15499	T	0.54	0.6019	0.212	0.00157	0.2358:0.2029:0.2363:0.3249	rs9924371;rs58449243;rs9924371	73;73	Q7Z442-3;Q7Z442	.;PK1L2_HUMAN	R	73	ENSP00000337397:W73R	ENSP00000337397:W73R	W	-	1	0	PKD1L2	79811260	0.984000	0.35163	0.022000	0.16811	0.214000	0.24535	0.397000	0.20883	-0.436000	0.07254	-0.930000	0.02707	TGG	A|0.425;G|0.575	0.575	strong		0.572	PKD1L2-001	KNOWN	non_canonical_polymorphism|basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000387972.2		
CDAN1	146059	hgsc.bcm.edu	37	15	43028592	43028592	+	Silent	SNP	G	G	A	rs7167392	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:43028592G>A	ENST00000356231.3	-	2	500	c.477C>T	c.(475-477)ccC>ccT	p.P159P		NM_138477.2	NP_612486.2	Q8IWY9	CDAN1_HUMAN	codanin 1	159					chromatin assembly (GO:0031497)|chromatin organization (GO:0006325)|negative regulation of DNA replication (GO:0008156)|protein localization (GO:0008104)	cytoplasm (GO:0005737)|endomembrane system (GO:0012505)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				endometrium(2)|kidney(4)|large_intestine(3)|lung(6)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(3)	24		all_cancers(109;5.4e-16)|all_epithelial(112;2.97e-14)|Lung NSC(122;1.75e-08)|all_lung(180;5.99e-08)|Melanoma(134;0.0179)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;2.49e-07)		TGGGGCGGCTGGGGCTGCCAG	0.736													G|||	1305	0.260583	0.4365	0.1427	5008	,	,		10276	0.0546		0.2227	False		,,,				2504	0.3579				p.P159P		Atlas-SNP	.											.	CDAN1	70	.	0			c.C477T						PASS	.	G		1658,2690		315,1028,831	16.0	19.0	18.0		477	-2.9	0.3	15	dbSNP_116	18	1804,6730		201,1402,2664	no	coding-synonymous	CDAN1	NM_138477.2		516,2430,3495	AA,AG,GG		21.139,38.1325,26.8747		159/1228	43028592	3462,9420	2174	4267	6441	SO:0001819	synonymous_variant	146059	exon2			GCGGCTGGGGCTG	AF525398	CCDS32209.1	15q15.2	2012-04-25	2012-04-25			ENSG00000140326			1713	protein-coding gene	gene with protein product		607465	"""congenital dyserythropoietic anemia, type I"""			8634422, 12434312	Standard	XM_005254177		Approved	CDA-I, CDAI	uc001zql.3	Q8IWY9		ENST00000356231.3:c.477C>T	15.37:g.43028592G>A		Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	53	32	0.603774	NM_138477	Q6NYD0|Q7Z7L5|Q969N3	Silent	SNP	ENST00000356231.3	37	CCDS32209.1																																																																																			G|0.766;A|0.234	0.234	strong		0.736	CDAN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000431103.1	XM_085300	
ASCL1	429	hgsc.bcm.edu	37	12	103352649	103352649	+	Silent	SNP	C	C	G	rs731682	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:103352649C>G	ENST00000266744.3	+	1	1186	c.627C>G	c.(625-627)gtC>gtG	p.V209V		NM_004316.3	NP_004307.2	P50553	ASCL1_HUMAN	achaete-scute family bHLH transcription factor 1	209					adrenal chromaffin cell differentiation (GO:0061104)|carotid body glomus cell differentiation (GO:0061103)|cell maturation (GO:0048469)|cellular response to magnetism (GO:0071259)|central nervous system neuron development (GO:0021954)|cerebral cortex development (GO:0021987)|cerebral cortex GABAergic interneuron differentiation (GO:0021892)|commitment of neuronal cell to specific neuron type in forebrain (GO:0021902)|lung epithelial cell differentiation (GO:0060487)|lung neuroendocrine cell differentiation (GO:0061100)|musculoskeletal movement, spinal reflex action (GO:0050883)|negative regulation of apoptotic process (GO:0043066)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of transcription, DNA-templated (GO:0045892)|neuroblast fate determination (GO:0007400)|neuroblast proliferation (GO:0007405)|neurogenesis (GO:0022008)|neuron fate specification (GO:0048665)|neuron migration (GO:0001764)|noradrenergic neuron development (GO:0003358)|noradrenergic neuron fate commitment (GO:0003359)|Notch signaling pathway (GO:0007219)|olfactory pit development (GO:0060166)|oligodendrocyte development (GO:0014003)|positive regulation of cell cycle (GO:0045787)|positive regulation of neural precursor cell proliferation (GO:2000179)|positive regulation of neurogenesis (GO:0050769)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of epithelial cell differentiation (GO:0030856)|regulation of gene expression (GO:0010468)|regulation of mitotic cell cycle (GO:0007346)|regulation of timing of subpallium neuron differentiation (GO:0060165)|response to epidermal growth factor (GO:0070849)|response to folic acid (GO:0051593)|response to lithium ion (GO:0010226)|response to retinoic acid (GO:0032526)|spinal cord association neuron differentiation (GO:0021527)|spinal cord oligodendrocyte cell fate specification (GO:0021530)|stomach neuroendocrine cell differentiation (GO:0061102)|subpallium neuron fate commitment (GO:0060163)|sympathetic ganglion development (GO:0061549)|sympathetic nervous system development (GO:0048485)|transcription, DNA-templated (GO:0006351)|ventral spinal cord interneuron fate commitment (GO:0060579)|vestibular nucleus development (GO:0021750)	neuronal cell body (GO:0043025)|nucleus (GO:0005634)	bHLH transcription factor binding (GO:0043425)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|E-box binding (GO:0070888)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding transcription factor activity (GO:0000989)			NS(3)|large_intestine(1)|lung(1)	5						GCTCGCCGGTCTCATCCTACT	0.647													C|||	357	0.0712859	0.205	0.0317	5008	,	,		15749	0.0		0.0457	False		,,,				2504	0.0184				p.V209V		Atlas-SNP	.											.	ASCL1	16	.	0			c.C627G						PASS	.	C		887,3515		96,695,1410	28.0	31.0	30.0		627	1.9	1.0	12	dbSNP_86	30	463,8125		15,433,3846	no	coding-synonymous	ASCL1	NM_004316.3		111,1128,5256	GG,GC,CC		5.3912,20.1499,10.3926		209/237	103352649	1350,11640	2201	4294	6495	SO:0001819	synonymous_variant	429	exon1			GCCGGTCTCATCC	L08424	CCDS31886.1	12q22-q23	2013-10-17	2013-10-17			ENSG00000139352		"""Basic helix-loop-helix proteins"""	738	protein-coding gene	gene with protein product		100790	"""achaete-scute complex (Drosophila) homolog-like 1"", ""achaete-scute complex-like 1 (Drosophila)"", ""achaete-scute complex homolog 1 (Drosophila)"""			8390674	Standard	NM_004316		Approved	ASH1, HASH1, bHLHa46	uc001tjr.4	P50553		ENST00000266744.3:c.627C>G	12.37:g.103352649C>G		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	120	60	0.5	NM_004316	A8K3C4|Q9BQ30	Silent	SNP	ENST00000266744.3	37	CCDS31886.1																																																																																			C|0.917;G|0.083	0.083	strong		0.647	ASCL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406707.1		
PROSER1	80209	hgsc.bcm.edu	37	13	39587865	39587865	+	Silent	SNP	A	A	C	rs3751378	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:39587865A>C	ENST00000352251.3	-	11	2357	c.1524T>G	c.(1522-1524)tcT>tcG	p.S508S	PROSER1_ENST00000350125.3_Silent_p.S486S|PROSER1_ENST00000484434.3_Intron	NM_025138.4	NP_079414.3	Q86XN7	PRSR1_HUMAN	proline and serine rich 1	508	Ser-rich.																CAGAAGAGTCAGAGTTCTGAA	0.512													A|||	1117	0.223043	0.2458	0.1599	5008	,	,		20185	0.2183		0.162	False		,,,				2504	0.3047				p.S508S		Atlas-SNP	.											C13orf23,NS,carcinoma,-1,1	.	.	1	0			c.T1524G						PASS	.	A	,	1073,3333	389.8+/-327.4	114,845,1244	79.0	77.0	78.0		1524,1458	-10.2	0.0	13	dbSNP_107	78	1209,7391	244.9+/-273.9	91,1027,3182	no	coding-synonymous,coding-synonymous	PROSER1	NM_025138.3,NM_170719.2	,	205,1872,4426	CC,CA,AA		14.0581,24.3532,17.5457	,	508/945,486/923	39587865	2282,10724	2203	4300	6503	SO:0001819	synonymous_variant	80209	exon11			AGAGTCAGAGTTC	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.1524T>G	13.37:g.39587865A>C		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	76	33	0.434211	NM_025138	A6NJ97|Q6P2S2|Q7Z3X5|Q8N3D2|Q8N3P1|Q9H9M1	Silent	SNP	ENST00000352251.3	37	CCDS9368.2																																																																																			A|0.810;C|0.190	0.190	strong		0.512	PROSER1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044607.5	NM_025138	
ZNF879	345462	hgsc.bcm.edu	37	5	178459283	178459283	+	Missense_Mutation	SNP	A	A	G	rs17078988	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	95	0	0		WXS	Illumina HiSeq	Phase_I	114	57	0.5	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	
KRT37	8688	hgsc.bcm.edu	37	17	39580559	39580559	+	Missense_Mutation	SNP	T	T	A	rs9916475	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:39580559T>A	ENST00000225550.3	-	1	216	c.217A>T	c.(217-219)Agt>Tgt	p.S73C	AC003958.2_ENST00000432258.1_RNA	NM_003770.4	NP_003761.3	O76014	KRT37_HUMAN	keratin 37	73	Head.		S -> C (in dbSNP:rs9916475).			extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(9)|lung(6)|skin(3)	25		Breast(137;0.000496)				GCAGTGTGACTGGTTGGGGGC	0.617													A|||	1960	0.391374	0.1846	0.3415	5008	,	,		21312	0.4067		0.4592	False		,,,				2504	0.6207				p.S73C		Atlas-SNP	.											.	KRT37	61	.	0			c.A217T						PASS	.	A	CYS/SER	985,3421		111,763,1329	49.0	46.0	47.0		217	4.7	0.7	17	dbSNP_119	47	4177,4423		1020,2137,1143	yes	missense	KRT37	NM_003770.4	112	1131,2900,2472	AA,AT,TT		48.5698,22.3559,39.6894	benign	73/450	39580559	5162,7844	2203	4300	6503	SO:0001583	missense	8688	exon1			TGTGACTGGTTGG	Y16793	CCDS32653.1	17q21.2	2013-06-20	2006-07-17	2006-07-17	ENSG00000108417	ENSG00000108417		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6455	protein-coding gene	gene with protein product		604541	"""keratin, hair, acidic, 7"""	KRTHA7		9756910, 16831889	Standard	NM_003770		Approved		uc002hwp.1	O76014	OTTHUMG00000133606	ENST00000225550.3:c.217A>T	17.37:g.39580559T>A	ENSP00000225550:p.Ser73Cys	Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	115	52	0.452174	NM_003770		Missense_Mutation	SNP	ENST00000225550.3	37	CCDS32653.1	812	0.3717948717948718	101	0.20528455284552846	145	0.4005524861878453	227	0.3968531468531469	339	0.4472295514511873	.	5.406	0.260139	0.10239	0.223559	0.485698	ENSG00000108417	ENST00000225550	T	0.81415	-1.49	4.69	4.69	0.59074	.	0.000000	0.53938	N	0.000046	T	0.00012	0.0000	N	0.00065	-2.305	0.53688	P	2.6999999999999247E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.45323	-0.9269	9	0.02654	T	1	.	2.6648	0.05041	0.6159:0.1533:0.0832:0.1475	rs9916475;rs52814129;rs59236563;rs9916475	73	O76014	KRT37_HUMAN	C	73	ENSP00000225550:S73C	ENSP00000225550:S73C	S	-	1	0	KRT37	36834085	0.952000	0.32445	0.665000	0.29768	0.002000	0.02628	1.043000	0.30316	0.661000	0.30985	-0.257000	0.10917	AGT	T|0.606;A|0.394	0.394	strong		0.617	KRT37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257714.2	NM_003770	
OPLAH	26873	hgsc.bcm.edu	37	8	145111529	145111529	+	Silent	SNP	A	A	G	rs11993554	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:145111529A>G	ENST00000426825.1	-	13	1917	c.1836T>C	c.(1834-1836)ttT>ttC	p.F612F	OPLAH_ENST00000534424.1_5'UTR	NM_017570.3	NP_060040.1	O14841	OPLA_HUMAN	5-oxoprolinase (ATP-hydrolysing)	612					glutathione biosynthetic process (GO:0006750)|glutathione derivative biosynthetic process (GO:1901687)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	5-oxoprolinase (ATP-hydrolyzing) activity (GO:0017168)|ATP binding (GO:0005524)			breast(1)|central_nervous_system(1)|endometrium(1)|lung(13)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	20	all_cancers(97;1.06e-10)|all_epithelial(106;1.5e-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;6.79e-41)|Epithelial(56;1.02e-39)|all cancers(56;2.24e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			ACCGCTCCACAAAGGCTGCCC	0.692													G|||	707	0.141174	0.3835	0.0735	5008	,	,		14960	0.001		0.0944	False		,,,				2504	0.0542				p.F612F		Atlas-SNP	.											.	OPLAH	78	.	0			c.T1836C						PASS	.	G		1378,2896		223,932,982	29.0	36.0	33.0		1836	-4.3	0.3	8	dbSNP_120	33	634,7876		18,598,3639	yes	coding-synonymous	OPLAH	NM_017570.3		241,1530,4621	GG,GA,AA		7.4501,32.2415,15.7384		612/1289	145111529	2012,10772	2137	4255	6392	SO:0001819	synonymous_variant	26873	exon13			CTCCACAAAGGCT	AF024672, AB122018	CCDS75802.1	8q24.3	2010-11-23			ENSG00000178814	ENSG00000178814	3.5.2.9		8149	protein-coding gene	gene with protein product		614243				14993790	Standard	NM_017570		Approved	OPLA, 5-Opase	uc003zar.3	O14841		ENST00000426825.1:c.1836T>C	8.37:g.145111529A>G		Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	102	100	0.980392	NM_017570	A5PKY8|Q75W65|Q9Y4Q0	Silent	SNP	ENST00000426825.1	37																																																																																				A|0.879;G|0.121	0.121	strong		0.692	OPLAH-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_017570	
GIPC1	10755	hgsc.bcm.edu	37	19	14589378	14589378	+	Splice_Site	SNP	C	C	T	rs1127307	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:14589378C>T	ENST00000393033.4	-	9	1121	c.852G>A	c.(850-852)gcG>gcA	p.A284A	GIPC1_ENST00000393029.3_Splice_Site_p.A187A|GIPC1_ENST00000586027.1_Splice_Site_p.A284A|GIPC1_ENST00000345425.2_Splice_Site_p.A284A|GIPC1_ENST00000591349.1_Splice_Site_p.A187A|GIPC1_ENST00000393028.1_Splice_Site_p.A187A	NM_005716.3	NP_005707.1	O14908	GIPC1_HUMAN	GIPC PDZ domain containing family, member 1	284					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						CCATGGTGGCCGCTATTGGGG	0.637													C|||	1243	0.248203	0.27	0.2651	5008	,	,		16097	0.3036		0.2217	False		,,,				2504	0.1769				p.A284A	Pancreas(33;78 923 2910 41023 52850)	Atlas-SNP	.											.	GIPC1	21	.	0			c.G852A						PASS	.		,,,,,	1186,3220	409.7+/-335.1	158,870,1175	45.0	49.0	47.0		852,561,852,561,852,561	-0.7	1.0	19	dbSNP_86	47	1786,6814	316.8+/-312.9	196,1394,2710	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	GIPC1	NM_005716.2,NM_202467.1,NM_202468.1,NM_202469.1,NM_202470.1,NM_202494.1	,,,,,	354,2264,3885	TT,TC,CC		20.7674,26.9178,22.851	,,,,,	284/334,187/237,284/334,187/237,284/334,187/237	14589378	2972,10034	2203	4300	6503	SO:0001630	splice_region_variant	10755	exon8			GGTGGCCGCTATT	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.851-1G>A	19.37:g.14589378C>T		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	116	61	0.525862	NM_202468	A8K4I3|A8MZG3|Q9BTC9	Silent	SNP	ENST00000393033.4	37	CCDS12310.1																																																																																			T|0.235;G|0.000;C|0.765	0.235	strong		0.637	GIPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460239.2		Silent
WWC3	55841	hgsc.bcm.edu	37	X	10085582	10085582	+	Missense_Mutation	SNP	G	G	A	rs5934750	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:10085582G>A	ENST00000380861.4	+	11	1874	c.1483G>A	c.(1483-1485)Gcc>Acc	p.A495T	WWC3_ENST00000454666.1_Missense_Mutation_p.A495T	NM_015691.3	NP_056506.2	Q9ULE0	WWC3_HUMAN	WWC family member 3	495			A -> T (in dbSNP:rs5934750).		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(3)|endometrium(10)|kidney(1)|large_intestine(11)|lung(17)|ovary(5)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	52						AGGCCTGGGCGCCCTAGACAG	0.716													G|||	103	0.0272848	0.0015	0.1153	3775	,	,		11338	0.0		0.0179	False		,,,				2504	0.0031				p.A495T		Atlas-SNP	.											.	WWC3	142	.	0			c.G1483A						PASS	.	G	THR/ALA	17,3724		0,15,2,1590,529	6.0	7.0	7.0		1483	-1.5	0.0	X	dbSNP_114	7	117,6434		1,87,28,2309,1729	yes	missense	WWC3	NM_015691.3	58	1,102,30,3899,2258	AA,AG,A,GG,G		1.786,0.4544,1.302	benign	495/1093	10085582	134,10158	2136	4154	6290	SO:0001583	missense	55841	exon11			CTGGGCGCCCTAG	AK091936	CCDS14136.1	Xp22.32	2008-02-05			ENSG00000047644	ENSG00000047644		"""WW, C2 and coiled-coil domain containing"""	29237	protein-coding gene	gene with protein product						10574462	Standard	NM_015691		Approved	KIAA1280, BM042	uc004csx.4	Q9ULE0	OTTHUMG00000021123	ENST00000380861.4:c.1483G>A	X.37:g.10085582G>A	ENSP00000370242:p.Ala495Thr	Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	61	60	0.983607	NM_015691	A8KA96|Q659C1|Q9BTQ1	Missense_Mutation	SNP	ENST00000380861.4	37	CCDS14136.1	43	0.02591922845087402	2	0.0040650406504065045	20	0.057803468208092484	0	0.0	10	0.013333333333333334	G	6.680	0.494023	0.12702	0.004544	0.01786	ENSG00000047644	ENST00000380861;ENST00000454666;ENST00000543293;ENST00000398613	T;T	0.04970	3.52;3.52	5.43	-1.5	0.08691	.	0.930558	0.09241	N	0.829226	T	0.00328	0.0010	N	0.08118	0	0.80722	P	0.0	B	0.11235	0.004	B	0.04013	0.001	T	0.48525	-0.9028	9	0.13108	T	0.6	-0.0979	4.8631	0.13594	0.3152:0.0:0.4536:0.2312	rs5934750	495	Q9ULE0	WWC3_HUMAN	T	495;495;159;495	ENSP00000370242:A495T;ENSP00000399584:A495T	ENSP00000370242:A495T	A	+	1	0	WWC3	10045582	0.000000	0.05858	0.000000	0.03702	0.567000	0.35839	0.043000	0.13971	-0.495000	0.06659	-0.382000	0.06688	GCC	G|0.973;A|0.027	0.027	strong		0.716	WWC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055725.1	NM_015691	
UBA6	55236	hgsc.bcm.edu	37	4	68562365	68562365	+	Silent	SNP	A	A	G	rs17572160	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:68562365A>G	ENST00000322244.5	-	2	191	c.132T>C	c.(130-132)taT>taC	p.Y44Y	UBA6_ENST00000420827.2_Silent_p.Y44Y	NM_018227.5	NP_060697.4	A0AVT1	UBA6_HUMAN	ubiquitin-like modifier activating enzyme 6	44					protein ubiquitination (GO:0016567)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	ATP binding (GO:0005524)|FAT10 activating enzyme activity (GO:0019780)|ligase activity (GO:0016874)			central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(6)|liver(1)|lung(23)|skin(2)|upper_aerodigestive_tract(2)	44						ATTCTTACCTATACAATGCAT	0.303													G|||	925	0.184704	0.1906	0.2277	5008	,	,		15105	0.1746		0.2575	False		,,,				2504	0.0818				p.Y44Y		Atlas-SNP	.											.	UBA6	98	.	0			c.T132C						PASS	.	G		863,3541	743.2+/-411.4	86,691,1425	88.0	85.0	86.0		132	1.1	1.0	4	dbSNP_123	86	2212,6378	707.8+/-405.6	291,1630,2374	no	coding-synonymous	UBA6	NM_018227.5		377,2321,3799	GG,GA,AA		25.7509,19.5958,23.6648		44/1053	68562365	3075,9919	2202	4295	6497	SO:0001819	synonymous_variant	55236	exon2			TTACCTATACAAT	AK094164	CCDS3516.1	4q13.2	2008-02-05	2007-11-30	2007-11-30	ENSG00000033178	ENSG00000033178		"""Ubiquitin-like modifier activating enzymes"""	25581	protein-coding gene	gene with protein product	"""UBA6, ubiquitin-activating enzyme E1"""	611361	"""ubiquitin-activating enzyme E1-like 2"""	UBE1L2		17580310	Standard	NM_018227		Approved	FLJ10808	uc003hdg.4	A0AVT1	OTTHUMG00000129299	ENST00000322244.5:c.132T>C	4.37:g.68562365A>G		Somatic	400	0	0		WXS	Illumina HiSeq	Phase_I	311	144	0.463023	NM_018227	A6N8M7|B2RAV3|Q4W5K0|Q6UV21|Q86T78|Q86TC7|Q8N5T3|Q8N9E4|Q9H3T7|Q9NVC9	Silent	SNP	ENST00000322244.5	37	CCDS3516.1																																																																																			A|0.778;G|0.222	0.222	strong		0.303	UBA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251429.2	NM_018227	
KIF4A	24137	hgsc.bcm.edu	37	X	69561780	69561780	+	Splice_Site	SNP	T	T	G	rs1199457	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:69561780T>G	ENST00000374403.3	+	11	1347	c.1265T>G	c.(1264-1266)tTg>tGg	p.L422W	KIF4A_ENST00000374388.3_Splice_Site_p.L422W	NM_012310.4	NP_036442.3	O95239	KIF4A_HUMAN	kinesin family member 4A	422			L -> W (in dbSNP:rs1199457). {ECO:0000269|PubMed:10978527, ECO:0000269|PubMed:15489334}.		anterograde axon cargo transport (GO:0008089)|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)|organelle organization (GO:0006996)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|membrane (GO:0016020)|midbody (GO:0030496)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)			breast(6)|endometrium(9)|kidney(3)|large_intestine(8)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	51						AGGATCATTTTGGTAAGCCCC	0.403													T|||	451	0.11947	0.2799	0.0375	3775	,	,		12134	0.0		0.0398	False		,,,				2504	0.0153				p.L422W		Atlas-SNP	.											.	KIF4A	118	.	0			c.T1265G						PASS	.	T	TRP/LEU	1333,2502		212,708,201,712,370	95.0	95.0	95.0		1265	4.8	1.0	X	dbSNP_87	95	323,6405		3,227,90,2198,1782	yes	missense-near-splice	KIF4A	NM_012310.4	61	215,935,291,2910,2152	GG,GT,G,TT,T		4.8008,34.7588,15.6774	possibly-damaging	422/1233	69561780	1656,8907	2203	4300	6503	SO:0001630	splice_region_variant	24137	exon11			TCATTTTGGTAAG	AF179308	CCDS14401.1	Xq13.1	2008-08-11			ENSG00000090889	ENSG00000090889		"""Kinesins"""	13339	protein-coding gene	gene with protein product	"""chromokinesin"""	300521				10773663	Standard	NM_012310		Approved	KIF4-G1, KIF4, HSA271784, FLJ12530, FLJ12655, FLJ14204, FLJ20631	uc004dyg.3	O95239	OTTHUMG00000021775	ENST00000374403.3:c.1266+1T>G	X.37:g.69561780T>G		Somatic	313	1	0.00319489		WXS	Illumina HiSeq	Phase_I	229	228	0.995633	NM_012310	B2R7V5|D3DVU4|Q86TN3|Q86XX7|Q9NNY6|Q9NY24|Q9UMW3	Missense_Mutation	SNP	ENST00000374403.3	37	CCDS14401.1	160	0.09644364074743822	73	0.17464114832535885	13	0.03672316384180791	0	0.0	20	0.0273224043715847	T	18.31	3.595877	0.66332	0.347588	0.048008	ENSG00000090889	ENST00000374388;ENST00000374403	T;T	0.52983	0.64;0.64	4.77	4.77	0.60923	.	0.151044	0.31167	N	0.008127	T	0.00012	0.0000	L	0.27053	0.805	0.20307	P	0.9999110836	D;D	0.67145	0.995;0.996	P;D	0.63703	0.844;0.917	T	0.31861	-0.9928	9	0.72032	D	0.01	.	12.2319	0.54492	0.0:0.0:0.0:1.0	rs1199457;rs52827837;rs1199457	422;422	O95239;O95239-2	KIF4A_HUMAN;.	W	422	ENSP00000363509:L422W;ENSP00000363524:L422W	ENSP00000363509:L422W	L	+	2	0	KIF4A	69478505	1.000000	0.71417	1.000000	0.80357	0.715000	0.41141	3.976000	0.56867	1.765000	0.52091	0.345000	0.21793	TTG	T|0.841;0|0.015	.	strong		0.403	KIF4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057068.1	NM_012310	Missense_Mutation
KIF19	124602	hgsc.bcm.edu	37	17	72351406	72351406	+	Silent	SNP	C	C	T	rs2271536	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:72351406C>T	ENST00000389916.4	+	20	3090	c.2952C>T	c.(2950-2952)caC>caT	p.H984H		NM_153209.3	NP_694941.2	Q2TAC6	KIF19_HUMAN	kinesin family member 19	984					ATP catabolic process (GO:0006200)|axonemal microtubule depolymerization (GO:0060404)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|plus-end specific microtubule depolymerization (GO:0070462)	cilium (GO:0005929)|cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|plus-end-directed microtubule motor activity (GO:0008574)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(6)|large_intestine(3)|lung(16)|ovary(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	41						GCCTGCCCCACGGCACAAGCA	0.652													C|||	1757	0.350839	0.2163	0.3804	5008	,	,		18224	0.4077		0.3598	False		,,,				2504	0.4438				p.H984H		Atlas-SNP	.											.	KIF19	102	.	0			c.C2952T						PASS	.	C		979,2863		131,717,1073	31.0	34.0	33.0		2952	-6.1	0.0	17	dbSNP_100	33	3026,5216		571,1884,1666	yes	coding-synonymous	KIF19	NM_153209.3		702,2601,2739	TT,TC,CC		36.7144,25.4815,33.143		984/999	72351406	4005,8079	1921	4121	6042	SO:0001819	synonymous_variant	124602	exon20			GCCCCACGGCACA	AK094619	CCDS32718.2	17q25	2007-02-13			ENSG00000196169	ENSG00000196169		"""Kinesins"""	26735	protein-coding gene	gene with protein product						11416179	Standard	NM_153209		Approved	FLJ37300, KIF19A	uc031rei.1	Q2TAC6	OTTHUMG00000150694	ENST00000389916.4:c.2952C>T	17.37:g.72351406C>T		Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	38	38	1	NM_153209	A6NLG2|B7ZKR1|Q52M87|Q8N1X8|Q8TAB6	Silent	SNP	ENST00000389916.4	37	CCDS32718.2																																																																																			C|0.650;T|0.350	0.350	strong		0.652	KIF19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319644.2	NM_153209	
KRTAP10-3	386682	hgsc.bcm.edu	37	21	45978587	45978587	+	Silent	SNP	A	A	G	rs448908|rs67272426	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:45978587A>G	ENST00000391620.1	-	1	56	c.12T>C	c.(10-12)tcT>tcC	p.S4S	TSPEAR_ENST00000397916.1_Intron|TSPEAR_ENST00000323084.4_Intron	NM_198696.2	NP_941969.2	P60369	KR103_HUMAN	keratin associated protein 10-3	4						keratin filament (GO:0045095)				kidney(1)|lung(4)|prostate(1)|skin(1)	7						CGGACATGGTAGACGTGGCCA	0.652													.|||	1049	0.209465	0.1399	0.2579	5008	,	,		17625	0.1964		0.33	False		,,,				2504	0.1585				p.S4S		Atlas-SNP	.											.	KRTAP10-3	17	.	0			c.T12C						PASS	.	A	,	689,3717	737.0+/-410.8	58,573,1572	63.0	63.0	63.0		,12	-2.2	0.1	21	dbSNP_80	63	2788,5812	664.1+/-402.1	463,1862,1975	no	intron,coding-synonymous	TSPEAR,KRTAP10-3	NM_144991.2,NM_198696.2	,	521,2435,3547	GG,GA,AA		32.4186,15.6378,26.7338	,	,4/222	45978587	3477,9529	2203	4300	6503	SO:0001819	synonymous_variant	386682	exon1			CATGGTAGACGTG	AJ566383	CCDS42956.1	21q22.3	2007-10-05			ENSG00000212935	ENSG00000212935		"""Keratin associated proteins"""	22968	protein-coding gene	gene with protein product				KRTAP18-3			Standard	NM_198696		Approved	KAP10.3, KAP18.3	uc002zfj.1	P60369	OTTHUMG00000057628	ENST00000391620.1:c.12T>C	21.37:g.45978587A>G		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	119	50	0.420168	NM_198696	A3KN67|Q70LJ4	Silent	SNP	ENST00000391620.1	37	CCDS42956.1																																																																																			AGACAT|0.500;GGACGC|0.500	.	alt		0.652	KRTAP10-3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128031.1		
ZDHHC11	79844	hgsc.bcm.edu	37	5	843815	843815	+	Silent	SNP	C	C	T	rs71591190	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:843815C>T	ENST00000283441.8	-	4	911	c.528G>A	c.(526-528)tcG>tcA	p.S176S	ZDHHC11_ENST00000503758.2_5'Flank|ZDHHC11_ENST00000424784.2_Silent_p.S176S|ZDHHC11_ENST00000511539.1_5'UTR	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	271	0	0		WXS	Illumina HiSeq	Phase_I	375	115	0.306667	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	
HIST1H2BL	8340	hgsc.bcm.edu	37	6	27775674	27775674	+	Missense_Mutation	SNP	A	A	G	rs200484	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:27775674A>G	ENST00000377401.2	-	1	35	c.11T>C	c.(10-12)cTg>cCg	p.L4P	HIST1H3H_ENST00000369163.2_5'Flank|HIST1H2AI_ENST00000358739.3_5'Flank	NM_003519.3	NP_003510.1	Q99880	H2B1L_HUMAN	histone cluster 1, H2bl	4			L -> P (in dbSNP:rs200484).		chromatin organization (GO:0006325)|nucleosome assembly (GO:0006334)	extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			cervix(1)|endometrium(1)|large_intestine(2)|lung(7)|urinary_tract(1)	12						AGACTTGGCCAGCTCGGGCAT	0.532													G|||	604	0.120607	0.2103	0.1412	5008	,	,		15542	0.0655		0.0865	False		,,,				2504	0.0767				p.L4P		Atlas-SNP	.											.	HIST1H2BL	48	.	0			c.T11C						PASS	.	G	PRO/LEU	831,3575		84,663,1456	62.0	67.0	66.0		11	4.3	0.5	6	dbSNP_79	66	955,7645		52,851,3397	yes	missense	HIST1H2BL	NM_003519.3	98	136,1514,4853	GG,GA,AA		11.1047,18.8606,13.7321	benign	4/127	27775674	1786,11220	2203	4300	6503	SO:0001583	missense	8340	exon1			TTGGCCAGCTCGG	Z83740	CCDS4625.1	6p22.1	2011-01-27	2006-10-11	2003-02-28	ENSG00000185130	ENSG00000185130		"""Histones / Replication-dependent"""	4748	protein-coding gene	gene with protein product		602800	"""H2B histone family, member C"", ""histone 1, H2bl"""	H2BFC		9439656, 12408966	Standard	NM_003519		Approved	H2B/c, dJ97D16.4	uc003njl.3	Q99880	OTTHUMG00000014485	ENST00000377401.2:c.11T>C	6.37:g.27775674A>G	ENSP00000366618:p.Leu4Pro	Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	105	56	0.533333	NM_003519	B2R5A3|Q52LW9	Missense_Mutation	SNP	ENST00000377401.2	37	CCDS4625.1	267	0.12225274725274725	99	0.20121951219512196	49	0.13535911602209943	50	0.08741258741258741	69	0.09102902374670185	.	0.044	-1.273737	0.01421	0.188606	0.111047	ENSG00000185130	ENST00000377401	T	0.17054	2.3	4.35	4.35	0.52113	.	.	.	.	.	T	0.01124	0.0037	N	0.00422	-1.515	0.26306	P	0.9778921	B	0.02656	0.0	B	0.01281	0.0	T	0.43909	-0.9362	8	0.02654	T	1	.	12.3065	0.54906	0.0843:0.0:0.9157:0.0	rs200484;rs684759;rs13205042;rs16868046;rs52805182;rs56710826;rs200484	4	Q99880	H2B1L_HUMAN	P	4	ENSP00000366618:L4P	ENSP00000366618:L4P	L	-	2	0	HIST1H2BL	27883653	0.997000	0.39634	0.497000	0.27552	0.012000	0.07955	2.724000	0.47285	1.126000	0.42016	-0.128000	0.14901	CTG	A|0.876;G|0.124	0.124	strong		0.532	HIST1H2BL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040153.1	NM_003519	
DHTKD1	55526	hgsc.bcm.edu	37	10	12131081	12131081	+	Missense_Mutation	SNP	T	T	G	rs3740015	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:12131081T>G	ENST00000263035.4	+	5	876	c.814T>G	c.(814-816)Tac>Gac	p.Y272D	DHTKD1_ENST00000465617.1_Intron	NM_018706.5	NP_061176	Q96HY7	DHTK1_HUMAN	dehydrogenase E1 and transketolase domain containing 1	272			Y -> D (in dbSNP:rs3740015). {ECO:0000269|PubMed:10997877, ECO:0000269|PubMed:15489334}.		cell death (GO:0008219)|generation of precursor metabolites and energy (GO:0006091)|glycolytic process (GO:0006096)|hematopoietic progenitor cell differentiation (GO:0002244)|tricarboxylic acid cycle (GO:0006099)	mitochondrion (GO:0005739)	oxoglutarate dehydrogenase (succinyl-transferring) activity (GO:0004591)|thiamine pyrophosphate binding (GO:0030976)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(11)|liver(2)|lung(14)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|soft_tissue(1)|stomach(3)|upper_aerodigestive_tract(1)	44		Renal(717;0.228)	BRCA - Breast invasive adenocarcinoma(52;0.188)			TGTGGACCTGTACTTTGGGGC	0.562													G|||	2426	0.484425	0.2073	0.4669	5008	,	,		18050	0.4812		0.5915	False		,,,				2504	0.7648				p.Y272D		Atlas-SNP	.											.	DHTKD1	104	.	0			c.T814G						PASS	.	G	ASP/TYR	1180,3226	712.0+/-408.1	144,892,1167	136.0	113.0	121.0		814	4.2	1.0	10	dbSNP_107	121	5064,3536	515.9+/-378.7	1474,2116,710	yes	missense	DHTKD1	NM_018706.5	160	1618,3008,1877	GG,GT,TT		41.1163,26.7817,48.0086	benign	272/920	12131081	6244,6762	2203	4300	6503	SO:0001583	missense	55526	exon5			GACCTGTACTTTG	BC002477	CCDS7087.1	10p14	2003-11-24			ENSG00000181192	ENSG00000181192			23537	protein-coding gene	gene with protein product		614984				10997877	Standard	NM_018706		Approved	KIAA1630, MGC3090, DKFZP762M115	uc001ild.5	Q96HY7	OTTHUMG00000017677	ENST00000263035.4:c.814T>G	10.37:g.12131081T>G	ENSP00000263035:p.Tyr272Asp	Somatic	107	1	0.00934579		WXS	Illumina HiSeq	Phase_I	94	93	0.989362	NM_018706	Q68CU5|Q9BUM8|Q9HCE2	Missense_Mutation	SNP	ENST00000263035.4	37	CCDS7087.1	1020	0.46703296703296704	119	0.241869918699187	181	0.5	274	0.479020979020979	446	0.5883905013192612	G	2.179	-0.388009	0.04932	0.267817	0.588837	ENSG00000181192	ENST00000263035;ENST00000437298	D;T	0.95853	-3.83;2.35	5.1	4.19	0.49359	Dehydrogenase, E1 component (1);	0.043855	0.85682	N	0.000000	T	0.00012	0.0000	N	0.00265	-1.74	0.29948	P	0.8204819999999999	B	0.02656	0.0	B	0.01281	0.0	T	0.47761	-0.9092	9	0.21014	T	0.42	-5.2831	12.1561	0.54077	0.0:0.1304:0.7337:0.1359	rs3740015;rs17819995;rs17844945;rs17857684;rs52831881;rs61557928;rs3740015	272	Q96HY7	DHTK1_HUMAN	D	272;207	ENSP00000263035:Y272D;ENSP00000388163:Y207D	ENSP00000263035:Y272D	Y	+	1	0	DHTKD1	12171087	1.000000	0.71417	0.999000	0.59377	0.483000	0.33249	6.649000	0.74364	0.554000	0.29061	-0.215000	0.12644	TAC	T|0.518;G|0.482	0.482	strong		0.562	DHTKD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046777.1	NM_018706	
PCDHA11	56138	hgsc.bcm.edu	37	5	140249884	140249884	+	Missense_Mutation	SNP	C	C	T	rs62622798	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:140249884C>T	ENST00000398640.2	+	1	1196	c.1196C>T	c.(1195-1197)aCc>aTc	p.T399I	PCDHA4_ENST00000512229.2_Intron|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|PCDHA5_ENST00000529619.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA1_ENST00000504120.2_Intron	NM_018902.3	NP_061725.1	Q9Y5I1	PCDAB_HUMAN	protocadherin alpha 11	399	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)			breast(1)|lung(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTGGTGTCCACCTTCAAGAAT	0.602													.|||	62	0.0123802	0.0008	0.0461	5008	,	,		21105	0.0		0.0149	False		,,,				2504	0.0143				p.T399I		Atlas-SNP	.											.	PCDHA11	209	.	0			c.C1196T						PASS	.	C	,,ILE/THR,,,,,,,,,,,,ILE/THR	34,4372	40.0+/-72.8	0,34,2169	146.0	134.0	138.0		,,1196,,,,,,,,,,,,1196	4.8	1.0	5	dbSNP_129	138	234,8366	95.6+/-157.4	1,232,4067	no	intron,intron,missense,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,missense	PCDHA9,PCDHA11,PCDHA10,PCDHA8,PCDHA7,PCDHA6,PCDHA5,PCDHA4,PCDHA3,PCDHA2,PCDHA1	NM_018900.2,NM_018901.2,NM_018902.3,NM_018905.2,NM_018906.2,NM_018907.2,NM_018908.2,NM_018909.2,NM_018910.2,NM_018911.2,NM_031411.1,NM_031849.1,NM_031857.1,NM_031860.1,NM_031861.1	,,89,,,,,,,,,,,,89	1,266,6236	TT,TC,CC		2.7209,0.7717,2.0606	,,,,,,,,,,,,,,	,,399/950,,,,,,,,,,,,399/811	140249884	268,12738	2203	4300	6503	SO:0001583	missense	56138	exon1			TGTCCACCTTCAA	AF152476	CCDS47284.1, CCDS75326.1	5q31	2010-11-26			ENSG00000249158	ENSG00000249158		"""Cadherins / Protocadherins : Clustered"""	8665	other	complex locus constituent	"""KIAA0345-like 3"", ""ortholog of mouse CNR7"""	606317		CNRS7		10380929, 10662547	Standard	NM_018902		Approved	CNR7, CRNR7, CNRN7, PCDH-ALPHA11		Q9Y5I1	OTTHUMG00000163369	ENST00000398640.2:c.1196C>T	5.37:g.140249884C>T	ENSP00000381636:p.Thr399Ile	Somatic	239	0	0		WXS	Illumina HiSeq	Phase_I	178	80	0.449438	NM_018902	B2RN58|O75279	Missense_Mutation	SNP	ENST00000398640.2	37	CCDS47284.1	26	0.011904761904761904	0	0.0	13	0.03591160220994475	0	0.0	13	0.017150395778364115	C	13.18	2.161051	0.38119	0.007717	0.027209	ENSG00000249158	ENST00000398640	T	0.29142	1.58	5.7	4.81	0.61882	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.15522	0.0374	L	0.29908	0.895	0.24765	N	0.992905	D;D	0.76494	0.998;0.999	D;D	0.76575	0.986;0.988	T	0.17410	-1.0370	9	0.87932	D	0	.	15.4515	0.75277	0.14:0.86:0.0:0.0	rs62622798	399;399	Q9Y5I1-2;Q9Y5I1	.;PCDAB_HUMAN	I	399	ENSP00000381636:T399I	ENSP00000381636:T399I	T	+	2	0	PCDHA11	140230068	0.030000	0.19436	0.997000	0.53966	0.560000	0.35617	3.034000	0.49751	1.338000	0.45544	0.563000	0.77884	ACC	C|0.989;T|0.011	0.011	strong		0.602	PCDHA11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372885.2	NM_018902	
CCDC67	159989	hgsc.bcm.edu	37	11	93129484	93129484	+	Missense_Mutation	SNP	A	A	G	rs12282288|rs386756254	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	152	0	0		WXS	Illumina HiSeq	Phase_I	115	114	0.991304	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	
CCDC110	256309	hgsc.bcm.edu	37	4	186379899	186379899	+	Missense_Mutation	SNP	G	G	C	rs35596415	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:186379899G>C	ENST00000307588.3	-	6	1917	c.1842C>G	c.(1840-1842)atC>atG	p.I614M	CCDC110_ENST00000510617.1_Missense_Mutation_p.I614M|CCDC110_ENST00000393540.3_Missense_Mutation_p.I577M|CCDC110_ENST00000507501.1_5'Flank	NM_152775.3	NP_689988.1	Q8TBZ0	CC110_HUMAN	coiled-coil domain containing 110	614			I -> M (in dbSNP:rs35596415).			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)		CTTTTAGCTGGATTATCTCTA	0.318													C|||	1925	0.384385	0.2784	0.3631	5008	,	,		16990	0.2837		0.5378	False		,,,				2504	0.4888				p.I614M		Atlas-SNP	.											.	CCDC110	78	.	0			c.C1842G						PASS	.	C	MET/ILE,MET/ILE	1453,2947	646.9+/-398.4	232,989,979	73.0	77.0	75.0		1731,1842	0.8	0.0	4	dbSNP_126	75	4853,3737	513.6+/-378.2	1374,2105,816	yes	missense,missense	CCDC110	NM_001145411.1,NM_152775.3	10,10	1606,3094,1795	CC,CG,GG		43.5041,33.0227,48.545	benign,benign	577/797,614/834	186379899	6306,6684	2200	4295	6495	SO:0001583	missense	256309	exon6			TAGCTGGATTATC	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.1842C>G	4.37:g.186379899G>C	ENSP00000306776:p.Ile614Met	Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	164	77	0.469512	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	C	0.015	-1.544608	0.00934	0.330227	0.564959	ENSG00000168491	ENST00000393540;ENST00000307588;ENST00000510617	T;T;T	0.32272	1.46;1.46;1.46	5.55	0.793	0.18632	.	1.074150	0.07154	N	0.849608	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	0.43228	-0.9404	9	0.37606	T	0.19	0.2996	7.0835	0.25244	0.0:0.4836:0.114:0.4024	rs35596415;rs61706177;rs62345629	614;577;614	B4DZA2;Q8TBZ0-2;Q8TBZ0	.;.;CC110_HUMAN	M	577;614;614	ENSP00000377172:I577M;ENSP00000306776:I614M;ENSP00000427246:I614M	ENSP00000306776:I614M	I	-	3	3	CCDC110	186616893	0.002000	0.14202	0.048000	0.18961	0.424000	0.31475	-0.419000	0.07071	-0.084000	0.12595	-0.769000	0.03391	ATC	G|0.545;C|0.455	0.455	strong		0.318	CCDC110-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000360519.2	NM_152775	
VSX2	338917	hgsc.bcm.edu	37	14	74707911	74707911	+	Nonsense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:74707911C>T	ENST00000261980.2	+	2	487	c.397C>T	c.(397-399)Cga>Tga	p.R133*		NM_182894.2	NP_878314.1	P58304	VSX2_HUMAN	visual system homeobox 2	133	Ser/Thr-rich.				cell fate commitment (GO:0045165)|negative regulation of cell proliferation (GO:0008285)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to stimulus (GO:0050896)|retinal bipolar neuron differentiation (GO:0060040)|transcription, DNA-templated (GO:0006351)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			endometrium(1)|large_intestine(1)|lung(1)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	7				BRCA - Breast invasive adenocarcinoma(234;0.00154)		CTCCAGCGATCGAAAAATGTC	0.597																																					p.R133X		Atlas-SNP	.											VSX2,right_upper_lobe,carcinoma,-1,1	VSX2	32	1	0			c.C397T						PASS	.						83.0	85.0	84.0					14																	74707911		2203	4300	6503	SO:0001587	stop_gained	338917	exon2			AGCGATCGAAAAA	AC005519	CCDS9827.1	14q24.3	2011-06-20	2007-08-21	2007-08-21		ENSG00000119614		"""Homeoboxes / PRD class"""	1975	protein-coding gene	gene with protein product		142993	"""C elegans ceh-10 homeo domain-containing homolog"", ""ceh-10 homeo domain containing homolog (C. elegans)"", ""ceh-10 homeodomain containing homolog (C. elegans)"""	HOX10, CHX10		1973146	Standard	NM_182894		Approved	RET1	uc001xpq.3	P58304		ENST00000261980.2:c.397C>T	14.37:g.74707911C>T	ENSP00000261980:p.Arg133*	Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	49	10	0.204082	NM_182894	A1A4X6	Nonsense_Mutation	SNP	ENST00000261980.2	37	CCDS9827.1	.	.	.	.	.	.	.	.	.	.	C	37	6.112200	0.97296	.	.	ENSG00000119614	ENST00000261980	.	.	.	4.56	2.52	0.30459	.	0.000000	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	13.2645	0.60125	0.3715:0.6285:0.0:0.0	.	.	.	.	X	133	.	ENSP00000261980:R133X	R	+	1	2	VSX2	73777664	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	2.035000	0.41155	1.126000	0.42016	0.462000	0.41574	CGA	.	.	none		0.597	VSX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412323.1	NM_182894	
KDELC1	79070	hgsc.bcm.edu	37	13	103449202	103449202	+	Missense_Mutation	SNP	T	T	C	rs1047740	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:103449202T>C	ENST00000376004.4	-	2	676	c.340A>G	c.(340-342)Att>Gtt	p.I114V	BIVM_ENST00000448849.2_5'Flank|KDELC1_ENST00000460338.1_5'UTR|BIVM_ENST00000257336.1_5'Flank|BIVM_ENST00000419638.1_5'Flank	NM_024089.2	NP_076994.2	Q6UW63	KDEL1_HUMAN	KDEL (Lys-Asp-Glu-Leu) containing 1	114			I -> V (in dbSNP:rs1047740). {ECO:0000269|PubMed:15489334}.			endoplasmic reticulum lumen (GO:0005788)				central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(9)|ovary(1)|prostate(1)|skin(1)	19	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.211)					TGGAATTTAATTTCCACCTTC	0.328													C|||	2091	0.417532	0.7269	0.2752	5008	,	,		14031	0.4821		0.2316	False		,,,				2504	0.2249				p.I114V		Atlas-SNP	.											.	KDELC1	66	.	0			c.A340G						PASS	.	C	VAL/ILE	2875,1531	483.3+/-359.7	923,1029,251	130.0	124.0	126.0		340	4.8	1.0	13	dbSNP_86	126	1892,6708	727.2+/-406.6	198,1496,2606	yes	missense	KDELC1	NM_024089.2	29	1121,2525,2857	CC,CT,TT		22.0,34.7481,36.6523	benign	114/503	103449202	4767,8239	2203	4300	6503	SO:0001583	missense	79070	exon2			ATTTAATTTCCAC	BC001297	CCDS9504.1	13q33	2010-11-18			ENSG00000134901	ENSG00000134901			19350	protein-coding gene	gene with protein product		611613					Standard	NM_024089		Approved	MGC5302, EP58	uc001vpq.4	Q6UW63	OTTHUMG00000017307	ENST00000376004.4:c.340A>G	13.37:g.103449202T>C	ENSP00000365172:p.Ile114Val	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	116	54	0.465517	NM_024089	Q53HL3|Q9BVD2	Missense_Mutation	SNP	ENST00000376004.4	37	CCDS9504.1	939	0.42994505494505497	356	0.7235772357723578	101	0.27900552486187846	303	0.5297202797202797	179	0.23614775725593667	C	3.165	-0.171246	0.06421	0.652519	0.22	ENSG00000134901	ENST00000376004	D	0.81739	-1.53	5.69	4.85	0.62838	Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.123413	0.56097	N	0.000036	T	0.00012	0.0000	N	0.00707	-1.245	0.43489	P	0.004274	B	0.02656	0.0	B	0.04013	0.001	T	0.43845	-0.9366	9	0.02654	T	1	.	10.0883	0.42432	0.0:0.7953:0.0:0.2047	rs1047740;rs3187754;rs17856043;rs52798404;rs58208195;rs1047740	114	Q6UW63	KDEL1_HUMAN	V	114	ENSP00000365172:I114V	ENSP00000365172:I114V	I	-	1	0	KDELC1	102247203	0.996000	0.38824	0.997000	0.53966	0.971000	0.66376	0.957000	0.29215	0.884000	0.36064	-0.119000	0.15052	ATT	T|0.602;C|0.398	0.398	strong		0.328	KDELC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045699.1		
PCDHGC3	5098	hgsc.bcm.edu	37	5	140856265	140856265	+	Silent	SNP	G	G	C	rs2075661	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:140856265G>C	ENST00000308177.3	+	1	686	c.582G>C	c.(580-582)gcG>gcC	p.A194A	PCDHGA3_ENST00000253812.6_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGB1_ENST00000523390.1_Intron|RN7SL68P_ENST00000488078.2_RNA|PCDHGB2_ENST00000522605.1_Intron|PCDHGA10_ENST00000398610.2_Intron|PCDHGA11_ENST00000518882.1_Intron|PCDHGB7_ENST00000398594.2_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA11_ENST00000398587.2_Intron|PCDHGA12_ENST00000252085.3_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA8_ENST00000398604.2_Intron	NM_002588.2|NM_032402.1	NP_002579.2|NP_115778.1	Q9UN70	PCDGK_HUMAN	protocadherin gamma subfamily C, 3	194	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|skin(2)|urinary_tract(1)	29			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CCAAGTACGCGGAGCTGGTGT	0.602													G|||	1007	0.201078	0.1921	0.3444	5008	,	,		20259	0.1508		0.2087	False		,,,				2504	0.1554				p.A194A		Atlas-SNP	.											.	PCDHGC3	173	.	0			c.G582C						PASS	.	G	,,,,,,,,,,,,,,,,,,,,,,	870,3536	336.5+/-304.4	84,702,1417	39.0	35.0	36.0		582,,,,,,,,,,,,,,,,,,,,,582,	-2.8	1.0	5	dbSNP_96	36	1642,6958	298.6+/-304.0	148,1346,2806	no	coding-synonymous,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,coding-synonymous,intron	PCDHGC3,PCDHGB4,PCDHGA8,PCDHGA12,PCDHGB7,PCDHGB6,PCDHGB5,PCDHGB3,PCDHGB2,PCDHGB1,PCDHGA11,PCDHGA10,PCDHGA9,PCDHGA7,PCDHGA6,PCDHGA5,PCDHGA4,PCDHGA3,PCDHGA2,PCDHGA1	NM_002588.2,NM_003735.2,NM_003736.2,NM_018912.2,NM_018913.2,NM_018914.2,NM_018915.2,NM_018916.3,NM_018917.2,NM_018918.2,NM_018919.2,NM_018920.2,NM_018921.2,NM_018922.2,NM_018923.2,NM_018924.2,NM_018925.2,NM_018926.2,NM_018927.3,NM_032088.1,NM_032092.1,NM_032402.1,NM_032403.1	,,,,,,,,,,,,,,,,,,,,,,	232,2048,4223	CC,CG,GG		19.093,19.7458,19.3142	,,,,,,,,,,,,,,,,,,,,,,	194/935,,,,,,,,,,,,,,,,,,,,,194/864,	140856265	2512,10494	2203	4300	6503	SO:0001819	synonymous_variant	5098	exon1			GTACGCGGAGCTG	AF152337	CCDS4261.1, CCDS75347.1, CCDS75348.1	5q31	2010-01-26			ENSG00000240184	ENSG00000240184		"""Cadherins / Protocadherins : Clustered"""	8716	other	protocadherin	"""cadherin-like 2"", ""protocadherin 2"", ""protocadherin 43"""	603627		PCDH2		9360932, 8508762	Standard	NM_032402		Approved	PC-43, PC43, PCDH-GAMMA-C3		Q9UN70	OTTHUMG00000129613	ENST00000308177.3:c.582G>C	5.37:g.140856265G>C		Somatic	104	1	0.00961538		WXS	Illumina HiSeq	Phase_I	110	110	1	NM_032402	O60622|Q08192|Q9Y5C4	Silent	SNP	ENST00000308177.3	37	CCDS4261.1																																																																																			G|0.809;C|0.191	0.191	strong		0.602	PCDHGC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251808.2	NM_002588	
SLC37A2	219855	hgsc.bcm.edu	37	11	124951767	124951767	+	Missense_Mutation	SNP	G	G	A	rs143239155	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:124951767G>A	ENST00000403796.2	+	9	1151	c.850G>A	c.(850-852)Gct>Act	p.A284T	SLC37A2_ENST00000298280.5_Missense_Mutation_p.A284T|SLC37A2_ENST00000308074.4_Missense_Mutation_p.A284T|SLC37A2_ENST00000407458.1_Missense_Mutation_p.A284T	NM_001145290.1	NP_001138762.1	Q8TED4	SPX2_HUMAN	solute carrier family 37 (glucose-6-phosphate transporter), member 2	284					carbohydrate transport (GO:0008643)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	transporter activity (GO:0005215)			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)		CGAAGAGCCTGCTGCCATCAG	0.557													G|||	2	0.000399361	0.0	0.0	5008	,	,		18767	0.0		0.002	False		,,,				2504	0.0				p.A284T	Melanoma(11;373 620 21213 26083 47768)	Atlas-SNP	.											.	SLC37A2	105	.	0			c.G850A						PASS	.	G	THR/ALA,THR/ALA	0,4402		0,0,2201	54.0	54.0	54.0		850,850	1.5	0.3	11	dbSNP_134	54	19,8579	14.0+/-48.4	0,19,4280	yes	missense,missense	SLC37A2	NM_001145290.1,NM_198277.2	58,58	0,19,6481	AA,AG,GG		0.221,0.0,0.1462	benign,benign	284/502,284/506	124951767	19,12981	2201	4299	6500	SO:0001583	missense	219855	exon9			GAGCCTGCTGCCA	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.850G>A	11.37:g.124951767G>A	ENSP00000384407:p.Ala284Thr	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	68	53	0.779412	NM_001145290	A8K2P9|Q6P599|Q7Z7P8|Q8TEM2	Missense_Mutation	SNP	ENST00000403796.2	37	CCDS44757.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	G	2.657	-0.280533	0.05642	0.0	0.00221	ENSG00000134955	ENST00000403796;ENST00000407458;ENST00000298280;ENST00000308074	T;T;T;T	0.58797	0.31;0.31;0.31;0.31	4.54	1.53	0.23141	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.642521	0.15596	N	0.254169	T	0.42653	0.1212	L	0.35341	1.055	0.09310	N	1	B;B	0.12013	0.005;0.003	B;B	0.16722	0.016;0.016	T	0.33548	-0.9864	10	0.51188	T	0.08	0.1127	6.8982	0.24267	0.0824:0.0:0.6082:0.3094	.	284;284	Q8TED4-2;Q8TED4	.;SPX2_HUMAN	T	284	ENSP00000384407:A284T;ENSP00000385126:A284T;ENSP00000298280:A284T;ENSP00000311833:A284T	ENSP00000298280:A284T	A	+	1	0	SLC37A2	124456977	0.002000	0.14202	0.349000	0.25694	0.102000	0.19082	1.264000	0.33015	0.236000	0.21180	-0.182000	0.12963	GCT	G|0.999;A|0.001	0.001	strong		0.557	SLC37A2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000386837.1	XM_166184	
Unknown	0	hgsc.bcm.edu	37	Y	21154426	21154426	+	IGR	SNP	G	G	A	rs52812045		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrY:21154426G>A								TTTY14 (114312 upstream) : RNU6-255P (26442 downstream)																							ACCACCAGCCGCCTTGGTGGT	0.493																																					p.A57V		Atlas-SNP	.											.	.	.	.	0			c.C170T						PASS	.						41.0	51.0	48.0					Y																	21154426		692	1591	2283	SO:0001628	intergenic_variant	100133941	exon1			CCAGCCGCCTTGG																													Y.37:g.21154426G>A		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	91	36	0.395604	NM_013230		Missense_Mutation	SNP		37																																																																																				G|0.500;A|0.500	0.500	weak	0	0.493								
MUC4	4585	hgsc.bcm.edu	37	3	195513519	195513519	+	Silent	SNP	A	A	T	rs201585392	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195513519A>T	ENST00000463781.3	-	2	5391	c.4932T>A	c.(4930-4932)ggT>ggA	p.G1644G	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Silent_p.G1644G	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0	VWFD. {ECO:0000255|PROSITE- ProRule:PRU00580}.				cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.N1637_T1652delNASSLSTGHATPLHVT(2)|p.G1644G(1)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GGGTGGCGTGACCTGTGGATA	0.587																																					p.G1644G		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	3	Deletion - In frame(2)|Substitution - coding silent(1)	stomach(2)|endometrium(1)	c.T4932A						PASS	.						30.0	37.0	35.0					3																	195513519		690	1580	2270	SO:0001819	synonymous_variant	4585	exon2			GGCGTGACCTGTG	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.4932T>A	3.37:g.195513519A>T		Somatic	196	0	0		WXS	Illumina HiSeq	Phase_I	256	45	0.175781	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Silent	SNP	ENST00000463781.3	37	CCDS54700.1																																																																																			A|0.964;T|0.036	0.036	strong		0.587	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
CD44	960	hgsc.bcm.edu	37	11	35226155	35226155	+	Missense_Mutation	SNP	A	A	G	rs9666607	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:35226155A>G	ENST00000428726.2	+	10	1373	c.1250A>G	c.(1249-1251)aAa>aGa	p.K417R	CD44_ENST00000526669.2_Intron|CD44_ENST00000352818.4_Intron|CD44_ENST00000360158.4_Intron|CD44_ENST00000437706.2_Missense_Mutation_p.K417R|CD44_ENST00000278386.6_Intron|CD44_ENST00000449691.2_Intron|CD44_ENST00000433892.2_Intron|CD44_ENST00000415148.2_Missense_Mutation_p.K374R|CD44_ENST00000434472.2_Intron|CD44_ENST00000433354.2_Missense_Mutation_p.K418R|CD44_ENST00000263398.6_Intron	NM_000610.3	NP_000601.3	P16070	CD44_HUMAN	CD44 molecule (Indian blood group)	417	Stem.		K -> R (in dbSNP:rs9666607). {ECO:0000269|PubMed:1465456, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:1717145, ECO:0000269|PubMed:7508842}.		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)	CAAACACCCAAAGAAGACTCC	0.458													G|||	4158	0.830272	0.9221	0.6859	5008	,	,		21334	0.9306		0.6839	False		,,,				2504	0.8558				p.K417R		Atlas-SNP	.											.	CD44	48	.	0			c.A1250G						PASS	.	G	ARG/LYS,ARG/LYS,,,,,,	3820,584	258.3+/-262.4	1661,498,43	152.0	130.0	137.0		1250,1121,,,,,,	1.9	0.7	11	dbSNP_119	137	5961,2635	425.3+/-354.9	2060,1841,397	yes	missense,missense,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	26,26,,,,,,	3721,2339,440	GG,GA,AA		30.6538,13.2607,24.7615	benign,benign,,,,,,	417/743,374/700,,,,,,	35226155	9781,3219	2202	4298	6500	SO:0001583	missense	960	exon10			CACCCAAAGAAGA	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.1250A>G	11.37:g.35226155A>G	ENSP00000398632:p.Lys417Arg	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	77	75	0.974026	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	Missense_Mutation	SNP	ENST00000428726.2	37	CCDS7897.1	1774	0.8122710622710623	455	0.9247967479674797	248	0.6850828729281768	532	0.9300699300699301	539	0.7110817941952506	G	1.428	-0.571126	0.03882	0.867393	0.693462	ENSG00000026508	ENST00000415148;ENST00000433354;ENST00000437706;ENST00000428726;ENST00000531110;ENST00000528672	T;T;T;T;T;T	0.17054	2.3;2.3;2.3;2.3;2.3;2.3	5.15	1.86	0.25419	.	0.824072	0.10878	N	0.624063	T	0.00012	0.0000	L	0.36672	1.1	0.20403	P	0.9999084273	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.001	T	0.26503	-1.0101	9	0.14252	T	0.57	-22.3568	7.2875	0.26348	0.6587:0.0:0.3413:0.0	rs9666607;rs17447510;rs17856113;rs58715480;rs9666607	374;417	P16070-4;P16070	.;CD44_HUMAN	R	374;418;417;417;129;69	ENSP00000389830:K374R;ENSP00000414567:K418R;ENSP00000403990:K417R;ENSP00000398632:K417R;ENSP00000436549:K129R;ENSP00000431860:K69R	ENSP00000389830:K374R	K	+	2	0	CD44	35182731	0.125000	0.22332	0.701000	0.30321	0.005000	0.04900	0.453000	0.21811	0.019000	0.15079	-0.733000	0.03571	AAA	A|0.218;G|0.782	0.782	strong		0.458	CD44-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000388927.1	NM_000610	
NEK3	4752	hgsc.bcm.edu	37	13	52726772	52726772	+	Missense_Mutation	SNP	C	C	T	rs56190615	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:52726772C>T	ENST00000400357.2	-	4	1658	c.365G>A	c.(364-366)cGt>cAt	p.R122H	NEK3_ENST00000378101.2_Missense_Mutation_p.R122H|NEK3_ENST00000452082.2_Missense_Mutation_p.R143H|NEK3_ENST00000339406.3_Missense_Mutation_p.R122H			P51956	NEK3_HUMAN	NIMA-related kinase 3	122	Interaction with VAV2.|Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		R -> H (in dbSNP:rs56190615). {ECO:0000269|PubMed:17344846}.		mitotic nuclear division (GO:0007067)|protein phosphorylation (GO:0006468)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(3)|ovary(1)|prostate(1)|stomach(2)	18		Breast(56;0.000207)|Lung NSC(96;0.00145)|Prostate(109;0.034)|Hepatocellular(98;0.065)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;2.81e-08)		GTGTAGCACACGTTTCTTGTG	0.353													C|||	16	0.00319489	0.0	0.0043	5008	,	,		18153	0.0		0.0089	False		,,,				2504	0.0041				p.R122H		Atlas-SNP	.											.	NEK3	41	.	0			c.G365A						PASS	.	C	HIS/ARG,HIS/ARG	3,3687		0,3,1842	165.0	150.0	154.0		365,365	4.1	1.0	13	dbSNP_129	154	55,8141		1,53,4044	yes	missense,missense	NEK3	NM_001146099.1,NM_152720.2	29,29	1,56,5886	TT,TC,CC		0.6711,0.0813,0.488	probably-damaging,probably-damaging	122/490,122/507	52726772	58,11828	1845	4098	5943	SO:0001583	missense	4752	exon5			AGCACACGTTTCT	AK290259, BC019916	CCDS73576.1	13q14.2-q21.1	2014-07-17	2012-11-15		ENSG00000136098	ENSG00000136098	2.7.11.1		7746	protein-coding gene	gene with protein product	"""serine/threonine-protein kinase NEK3"", ""phosphorylase B kinase kinase"", ""glycogen synthase A kinase"", ""hydroxyalkyl-protein kinase"""	604044	"""NIMA (never in mitosis gene a)-related kinase 3"""			8274451, 7522034	Standard	NM_002498		Approved	HSPK36, MGC29949	uc010tgy.2	P51956	OTTHUMG00000016958	ENST00000400357.2:c.365G>A	13.37:g.52726772C>T	ENSP00000383210:p.Arg122His	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	105	51	0.485714	NM_002498	A8K2J4|Q5TAP2|Q8J023|Q8WUN5	Missense_Mutation	SNP	ENST00000400357.2	37	CCDS53871.1	10	0.004578754578754579	0	0.0	3	0.008287292817679558	0	0.0	7	0.009234828496042216	C	15.21	2.765809	0.49574	8.13E-4	0.006711	ENSG00000136098	ENST00000339406;ENST00000378101;ENST00000400357;ENST00000452082;ENST00000547422	T;T;T;T;T	0.50277	1.82;1.82;1.82;1.82;0.75	5.92	4.1	0.47936	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.106321	0.64402	N	0.000020	T	0.27098	0.0664	.	.	.	0.41280	D	0.986903	B;P;P	0.45348	0.174;0.856;0.727	B;B;B	0.39562	0.12;0.303;0.201	T	0.03268	-1.1054	9	0.19590	T	0.45	.	11.7317	0.51741	0.0:0.849:0.0:0.151	rs56190615	122;143;116	P51956;Q6ZN64;F8VS47	NEK3_HUMAN;.;.	H	122;122;122;143;116	ENSP00000339429:R122H;ENSP00000367341:R122H;ENSP00000383210:R122H;ENSP00000404197:R143H;ENSP00000448716:R116H	ENSP00000448782:R122H	R	-	2	0	NEK3	51624773	1.000000	0.71417	1.000000	0.80357	0.577000	0.36160	2.816000	0.48026	0.741000	0.32674	-0.136000	0.14681	CGT	C|0.995;T|0.005	0.005	strong		0.353	NEK3-002	KNOWN	upstream_ATG|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000045047.3		
SERPINI1	5274	hgsc.bcm.edu	37	3	167506937	167506937	+	Missense_Mutation	SNP	C	C	G	rs33917740	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:167506937C>G	ENST00000295777.5	+	2	452	c.21C>G	c.(19-21)ttC>ttG	p.F7L	SERPINI1_ENST00000446050.2_Missense_Mutation_p.F7L	NM_005025.4	NP_005016.1	Q99574	NEUS_HUMAN	serpin peptidase inhibitor, clade I (neuroserpin), member 1	7					cell death (GO:0008219)|central nervous system development (GO:0007417)|negative regulation of endopeptidase activity (GO:0010951)|peripheral nervous system development (GO:0007422)|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(3)|large_intestine(4)|lung(7)|skin(2)	20						TTGGACTCTTCTCTTTGCTGG	0.383													C|||	572	0.114217	0.2057	0.1542	5008	,	,		18775	0.0516		0.1004	False		,,,				2504	0.0409				p.F7L		Atlas-SNP	.											.	SERPINI1	52	.	0			c.C21G						PASS	.	C	LEU/PHE,LEU/PHE	875,3531	341.5+/-306.7	79,717,1407	78.0	80.0	79.0		21,21	1.8	1.0	3	dbSNP_126	79	758,7842	181.3+/-230.0	27,704,3569	yes	missense,missense	SERPINI1	NM_001122752.1,NM_005025.4	22,22	106,1421,4976	GG,GC,CC		8.814,19.8593,12.5557	benign,benign	7/411,7/411	167506937	1633,11373	2203	4300	6503	SO:0001583	missense	5274	exon2			ACTCTTCTCTTTG	Z81326	CCDS3203.1	3q26.1	2014-02-18	2005-08-18		ENSG00000163536	ENSG00000163536		"""Serine (or cysteine) peptidase inhibitors"""	8943	protein-coding gene	gene with protein product		602445	"""serine (or cysteine) proteinase inhibitor, clade I (neuroserpin), member 1"""	PI12		24172014	Standard	NM_005025		Approved	neuroserpin	uc003ffa.4	Q99574	OTTHUMG00000158450	ENST00000295777.5:c.21C>G	3.37:g.167506937C>G	ENSP00000295777:p.Phe7Leu	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	53	24	0.45283	NM_005025	A8K217|D3DNP1|Q6AHZ4	Missense_Mutation	SNP	ENST00000295777.5	37	CCDS3203.1	248	0.11355311355311355	98	0.1991869918699187	42	0.11602209944751381	35	0.06118881118881119	73	0.09630606860158311	C	0.675	-0.800592	0.02841	0.198593	0.08814	ENSG00000163536	ENST00000472941;ENST00000446050;ENST00000295777;ENST00000472747	T;D;D;T	0.83250	-0.98;-1.7;-1.7;-1.48	5.03	1.81	0.25067	Serpin domain (1);	0.181335	0.45867	N	0.000338	T	0.00073	0.0002	N	0.01109	-1.01	0.09310	P	0.9999999999997295	B	0.02656	0.0	B	0.01281	0.0	T	0.11060	-1.0603	9	0.02654	T	1	.	10.4901	0.44746	0.0:0.5473:0.3679:0.0848	rs33917740	7	Q99574	NEUS_HUMAN	L	7	ENSP00000420133:F7L;ENSP00000397373:F7L;ENSP00000295777:F7L;ENSP00000420561:F7L	ENSP00000295777:F7L	F	+	3	2	SERPINI1	168989631	1.000000	0.71417	1.000000	0.80357	0.159000	0.22180	1.117000	0.31234	0.572000	0.29383	0.655000	0.94253	TTC	C|0.879;G|0.121	0.121	strong		0.383	SERPINI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351056.1		
CCDC122	160857	hgsc.bcm.edu	37	13	44411421	44411421	+	Missense_Mutation	SNP	C	C	T	rs79782223	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:44411421C>T	ENST00000444614.3	-	7	1075	c.817G>A	c.(817-819)Gag>Aag	p.E273K		NM_144974.3	NP_659411.2	Q5T0U0	CC122_HUMAN	coiled-coil domain containing 122	273										endometrium(1)|large_intestine(2)|lung(5)|stomach(1)	9		Lung NSC(96;7.5e-06)|Breast(139;0.00765)|Hepatocellular(98;0.00826)|Prostate(109;0.0143)|Lung SC(185;0.0262)		GBM - Glioblastoma multiforme(144;0.000767)|BRCA - Breast invasive adenocarcinoma(63;0.128)		CAATGTTACTCTTGCATTCCA	0.373													C|||	91	0.0181709	0.0023	0.0187	5008	,	,		19462	0.001		0.0676	False		,,,				2504	0.0061				p.E273K		Atlas-SNP	.											.	CCDC122	21	.	0			c.G817A						PASS	.	C	LYS/GLU	46,3678		0,46,1816	147.0	131.0	136.0		817	4.2	0.5	13	dbSNP_131	136	476,7700		19,438,3631	yes	missense	CCDC122	NM_144974.3	56	19,484,5447	TT,TC,CC		5.8219,1.2352,4.3866	benign	273/274	44411421	522,11378	1862	4088	5950	SO:0001583	missense	160857	exon7			GTTACTCTTGCAT	AK056408	CCDS9390.2	13q14.11	2008-10-30			ENSG00000151773	ENSG00000151773			26478	protein-coding gene	gene with protein product		613408					Standard	NM_144974		Approved	FLJ31846	uc010acf.3	Q5T0U0	OTTHUMG00000017413	ENST00000444614.3:c.817G>A	13.37:g.44411421C>T	ENSP00000407763:p.Glu273Lys	Somatic	203	0	0		WXS	Illumina HiSeq	Phase_I	126	125	0.992063	NM_144974	B2RP70|B7ZMI9|Q96MV0	Missense_Mutation	SNP	ENST00000444614.3	37	CCDS9390.2	60	0.027472527472527472	2	0.0040650406504065045	10	0.027624309392265192	1	0.0017482517482517483	47	0.06200527704485488	C	16.17	3.045981	0.55110	0.012352	0.058219	ENSG00000151773	ENST00000444614	T	0.52526	0.66	5.09	4.24	0.50183	.	.	.	.	.	T	0.04048	0.0113	N	0.24115	0.695	0.58432	D	0.999999	B	0.34290	0.447	B	0.30646	0.118	T	0.02505	-1.1149	9	0.62326	D	0.03	.	10.7217	0.46044	0.0:0.91:0.0:0.09	.	273	Q5T0U0	CC122_HUMAN	K	273	ENSP00000407763:E273K	ENSP00000407763:E273K	E	-	1	0	CCDC122	43309421	0.043000	0.20138	0.460000	0.27093	0.164000	0.22412	0.570000	0.23653	1.256000	0.44068	0.585000	0.79938	GAG	C|0.963;T|0.037	0.037	strong		0.373	CCDC122-004	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276172.4	NM_144974	
DSPP	1834	hgsc.bcm.edu	37	4	88536917	88536917	+	Missense_Mutation	SNP	G	G	A	rs199901845		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:88536917G>A	ENST00000282478.7	+	4	3136	c.3103G>A	c.(3103-3105)Gat>Aat	p.D1035N	RP11-742B18.1_ENST00000506480.1_RNA|DSPP_ENST00000399271.1_Missense_Mutation_p.D1035N			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	1035	Asp/Ser-rich.				biomineral tissue development (GO:0031214)|cellular response to cell-matrix adhesion (GO:0071460)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)	p.D1035N(1)		breast(2)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|skin(3)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Hepatocellular(203;0.114)|all_hematologic(202;0.236)		OV - Ovarian serous cystadenocarcinoma(123;0.000508)		tgacagcagcgatagcagtga	0.522																																					p.D1035N		Atlas-SNP	.											DSPP,NS,carcinoma,-2,3	DSPP	174	3	1	Substitution - Missense(1)	kidney(1)	c.G3103A						PASS	.						62.0	68.0	66.0					4																	88536917		1560	2750	4310	SO:0001583	missense	1834	exon5			AGCAGCGATAGCA	AF163151	CCDS43248.1	4q21.3	2008-02-05			ENSG00000152591	ENSG00000152591			3054	protein-coding gene	gene with protein product		125485		DFNA39, DGI1		8995371, 9533027	Standard	NM_014208		Approved	DMP3	uc003hqu.3	Q9NZW4	OTTHUMG00000161061	ENST00000282478.7:c.3103G>A	4.37:g.88536917G>A	ENSP00000282478:p.Asp1035Asn	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	65	6	0.0923077	NM_014208	A8MUI0|O95815	Missense_Mutation	SNP	ENST00000282478.7	37	CCDS43248.1	.	.	.	.	.	.	.	.	.	.	g	5.819	0.335399	0.11013	.	.	ENSG00000152591	ENST00000399271;ENST00000282478	D;D	0.88664	-2.41;-2.41	1.43	0.544	0.17185	.	.	.	.	.	T	0.73999	0.3659	L	0.29908	0.895	0.18873	N	0.999989	B	0.30542	0.284	B	0.13407	0.009	T	0.59783	-0.7389	9	0.06494	T	0.89	-6.585	4.0989	0.10004	0.2347:0.0:0.7653:0.0	.	1035	Q9NZW4	DSPP_HUMAN	N	1035	ENSP00000382213:D1035N;ENSP00000282478:D1035N	ENSP00000282478:D1035N	D	+	1	0	DSPP	88755941	0.238000	0.23825	0.544000	0.28141	0.014000	0.08584	1.337000	0.33862	0.180000	0.19960	-0.791000	0.03333	GAT	.	.	weak		0.522	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208	
LGR6	59352	hgsc.bcm.edu	37	1	202276494	202276494	+	Silent	SNP	C	C	T	rs896551	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	180	0	0		WXS	Illumina HiSeq	Phase_I	161	68	0.42236	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	
FBXL7	23194	hgsc.bcm.edu	37	5	15937010	15937010	+	Silent	SNP	C	C	T	rs61748187	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:15937010C>T	ENST00000504595.1	+	4	1672	c.1191C>T	c.(1189-1191)ctC>ctT	p.L397L	MIR887_ENST00000401258.1_RNA|FBXL7_ENST00000510662.1_Silent_p.L350L|FBXL7_ENST00000329673.7_Silent_p.L385L	NM_001278317.1|NM_012304.3	NP_001265246.1|NP_036436.1	Q9UJT9	FBXL7_HUMAN	F-box and leucine-rich repeat protein 7	397					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)			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						TGGAGTACCTCGCCAAGAACT	0.602													C|||	51	0.0101837	0.0015	0.013	5008	,	,		20130	0.0		0.0318	False		,,,				2504	0.0082				p.L397L		Atlas-SNP	.											FBXL7,NS,carcinoma,+2,1	FBXL7	138	1	0			c.C1191T						PASS	.	C		27,4305		0,27,2139	97.0	104.0	102.0		1191	-7.5	0.9	5	dbSNP_129	102	274,8230		6,262,3984	no	coding-synonymous	FBXL7	NM_012304.3		6,289,6123	TT,TC,CC		3.222,0.6233,2.345		397/492	15937010	301,12535	2166	4252	6418	SO:0001819	synonymous_variant	23194	exon4			GTACCTCGCCAAG	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.1191C>T	5.37:g.15937010C>T		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	145	87	0.6	NM_012304	B9EGF1|D6RDY7|O94926	Silent	SNP	ENST00000504595.1	37	CCDS54833.1																																																																																			C|0.982;T|0.018	0.018	strong		0.602	FBXL7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366117.1	NM_012304	
SMYD1	150572	hgsc.bcm.edu	37	2	88407959	88407959	+	Silent	SNP	T	T	C	rs2970918	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:88407959T>C	ENST00000419482.2	+	9	1300	c.1215T>C	c.(1213-1215)caT>caC	p.H405H	SMYD1_ENST00000438570.1_Intron|SMYD1_ENST00000444564.2_Silent_p.H392H	NM_198274.3	NP_938015.1	Q8NB12	SMYD1_HUMAN	SET and MYND domain containing 1	405					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						CCAACTGGCATGCTGGTAACA	0.552													t|||	1995	0.398363	0.525	0.1441	5008	,	,		18792	0.5278		0.1819	False		,,,				2504	0.4969				p.H405H		Atlas-SNP	.											.	SMYD1	95	.	0			c.T1215C						PASS	.			2016,2390	563.2+/-381.1	455,1106,642	144.0	108.0	120.0		1215	-7.4	0.8	2	dbSNP_101	120	1593,7007	295.8+/-302.6	148,1297,2855	no	coding-synonymous	SMYD1	NM_198274.3		603,2403,3497	CC,CT,TT		18.5233,45.7558,27.7487		405/491	88407959	3609,9397	2203	4300	6503	SO:0001819	synonymous_variant	150572	exon9			CTGGCATGCTGGT	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.1215T>C	2.37:g.88407959T>C		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	98	51	0.520408	NM_198274	A0AV30|A6NE13	Silent	SNP	ENST00000419482.2	37	CCDS33240.1																																																																																			T|0.711;G|0.000;C|0.288;A|0.000	0.288	strong		0.552	SMYD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338229.2	XM_097915	
ZNF286B	729288	hgsc.bcm.edu	37	17	18565423	18565423	+	Missense_Mutation	SNP	G	G	A	rs9912852	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:18565423G>A	ENST00000545289.1	-	5	1646	c.1396C>T	c.(1396-1398)Ccg>Tcg	p.P466S	ZNF286B_ENST00000285274.5_3'UTR	NM_001145045.1	NP_001138517.1	P0CG31	Z286B_HUMAN	zinc finger protein 286B	466					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|lung(1)	2						CATTTGTACGGTTTCTTTCCA	0.393													.|||	1375	0.274561	0.2027	0.4496	5008	,	,		22033	0.1935		0.4066	False		,,,				2504	0.1953				p.P466S		Atlas-SNP	.											ZNF286B_ENST00000545289,colon,carcinoma,+2,2	ZNF286B	75	2	0			c.C1396T						PASS	.	G	SER/PRO	333,1051		41,251,400	137.0	131.0	133.0		1396	2.6	1.0	17	dbSNP_119	133	1243,1939		237,769,585	no	missense	ZNF286B	NM_001145045.1	74	278,1020,985	AA,AG,GG		39.0635,24.0607,34.516	probably-damaging	466/523	18565423	1576,2990	692	1591	2283	SO:0001583	missense	729288	exon5			TGTACGGTTTCTT		CCDS58523.1	17p11.2	2013-01-08			ENSG00000249459	ENSG00000249459		"""Zinc fingers, C2H2-type"""	33241	protein-coding gene	gene with protein product	"""zinc finger protein 590"""		"""zinc finger protein 286-like"", ""zinc finger 286C pseudogene"""	ZNF286L, ZNF286C			Standard	NM_001145045		Approved	ZNF590	uc010vyd.1	P0CG31	OTTHUMG00000178136	ENST00000545289.1:c.1396C>T	17.37:g.18565423G>A	ENSP00000461413:p.Pro466Ser	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	145	129	0.889655	NM_001145045		Missense_Mutation	SNP	ENST00000545289.1	37	CCDS58523.1																																																																																			G|0.698;A|0.302	0.302	strong		0.393	ZNF286B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		XM_001723047	
PHLPP2	23035	hgsc.bcm.edu	37	16	71682796	71682796	+	Silent	SNP	T	T	C	rs61733125	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:71682796T>C	ENST00000568954.1	-	19	4347	c.3969A>G	c.(3967-3969)ctA>ctG	p.L1323L	PHLPP2_ENST00000393524.2_Silent_p.L1256L|PHLPP2_ENST00000540628.1_Intron|PHLPP2_ENST00000356272.3_Silent_p.L1323L|PHLPP2_ENST00000567016.1_Silent_p.L1358L|PHLPP2_ENST00000360429.3_Intron			Q6ZVD8	PHLP2_HUMAN	PH domain and leucine rich repeat protein phosphatase 2	1323					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)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment membrane (GO:0042622)	metal ion binding (GO:0046872)|protein serine/threonine phosphatase activity (GO:0004722)			central_nervous_system(1)|endometrium(5)|kidney(5)|large_intestine(7)|lung(15)|ovary(1)|prostate(1)|skin(1)|stomach(1)	37						GGGGCAGTCATAGTGCTGTGT	0.562													T|||	1199	0.239417	0.118	0.2003	5008	,	,		17968	0.1895		0.2197	False		,,,				2504	0.5031				p.L1323L		Atlas-SNP	.											.	PHLPP2	96	.	0			c.A3969G						PASS	.	T		577,3819	248.1+/-256.1	41,495,1662	52.0	52.0	52.0		3969	-0.3	0.9	16	dbSNP_129	52	1743,6857	306.0+/-307.7	190,1363,2747	no	coding-synonymous	PHLPP2	NM_015020.2		231,1858,4409	CC,CT,TT		20.2674,13.1256,17.8516		1323/1324	71682796	2320,10676	2198	4300	6498	SO:0001819	synonymous_variant	23035	exon18			CAGTCATAGTGCT	BX647823	CCDS32479.1, CCDS73910.1	16q22.2	2013-01-11	2009-05-26	2009-05-26	ENSG00000040199	ENSG00000040199		"""Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent"", ""Pleckstrin homology (PH) domain containing"""	29149	protein-coding gene	gene with protein product		611066	"""PH domain and leucine rich repeat protein phosphatase-like"""	PHLPPL		17386267	Standard	NM_001289003		Approved	KIAA0931	uc002fax.3	Q6ZVD8		ENST00000568954.1:c.3969A>G	16.37:g.71682796T>C		Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	136	82	0.602941	NM_015020	A1L374|Q9NV17|Q9Y2E3	Silent	SNP	ENST00000568954.1	37	CCDS32479.1																																																																																			T|0.817;C|0.183	0.183	strong		0.562	PHLPP2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000434139.1	NM_015020	
CD22	933	hgsc.bcm.edu	37	19	35835739	35835739	+	Silent	SNP	G	G	A	rs7259477	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:35835739G>A	ENST00000085219.5	+	10	2109	c.2043G>A	c.(2041-2043)ccG>ccA	p.P681P	CD22_ENST00000544992.2_Silent_p.P681P|CD22_ENST00000419549.2_Silent_p.P509P|CD22_ENST00000341773.6_Silent_p.P504P|CD22_ENST00000270311.6_Silent_p.P561P|MIR5196_ENST00000578146.1_RNA|CD22_ENST00000536635.2_Silent_p.P593P|CD22_ENST00000594250.1_Silent_p.P504P	NM_001771.3	NP_001762.2	P20273	CD22_HUMAN	CD22 molecule	681					cell adhesion (GO:0007155)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	carbohydrate binding (GO:0030246)			breast(2)|endometrium(2)|kidney(3)|large_intestine(14)|lung(21)|ovary(5)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	54	all_lung(56;9.78e-09)|Lung NSC(56;1.46e-08)|Esophageal squamous(110;0.162)		Epithelial(14;5.83e-19)|OV - Ovarian serous cystadenocarcinoma(14;3.19e-18)|all cancers(14;3.41e-16)|LUSC - Lung squamous cell carcinoma(66;0.0417)			CAGATAGCCCGGAGACCATCG	0.617													G|||	14	0.00279553	0.0	0.0072	5008	,	,		18790	0.0		0.0089	False		,,,				2504	0.0				p.P681P	Ovarian(42;1009 1133 23674 26041)	Atlas-SNP	.											.	CD22	129	.	0			c.G2043A						PASS	.	G	,,,	10,4396	16.8+/-37.8	0,10,2193	116.0	121.0	120.0		1779,2043,1512,2043	-9.6	0.0	19	dbSNP_116	120	81,8519	46.7+/-105.8	0,81,4219	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CD22	NM_001185099.1,NM_001185100.1,NM_001185101.1,NM_001771.3	,,,	0,91,6412	AA,AG,GG		0.9419,0.227,0.6997	,,,	593/760,681/752,504/671,681/848	35835739	91,12915	2203	4300	6503	SO:0001819	synonymous_variant	933	exon10			TAGCCCGGAGACC	X52785	CCDS12457.1, CCDS54247.1, CCDS54248.1, CCDS54249.1, CCDS62634.1	19q13.1	2013-01-29	2006-03-28		ENSG00000012124	ENSG00000012124		"""CD molecules"", ""Sialic acid binding Ig-like lectins"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	1643	protein-coding gene	gene with protein product	"""sialic acid binding Ig-like lectin 2"""	107266	"""CD22 antigen"""			8496602, 1691828	Standard	NM_001185099		Approved	SIGLEC-2, SIGLEC2	uc010edt.3	P20273		ENST00000085219.5:c.2043G>A	19.37:g.35835739G>A		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	62	35	0.564516	NM_001185100	F5GYU4|F5H7U3|O95699|O95701|O95702|O95703|Q01665|Q32M46|Q92872|Q92873|Q9UQA6|Q9UQA7|Q9UQA8|Q9UQA9|Q9UQB0|Q9Y2A6	Silent	SNP	ENST00000085219.5	37	CCDS12457.1																																																																																			G|0.996;A|0.004	0.004	strong		0.617	CD22-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466099.1	NM_001771	
CCDC40	55036	hgsc.bcm.edu	37	17	78059889	78059889	+	Missense_Mutation	SNP	G	G	A	rs60684213	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:78059889G>A	ENST00000397545.4	+	14	2350	c.2323G>A	c.(2323-2325)Gtg>Atg	p.V775M	CCDC40_ENST00000374877.3_Missense_Mutation_p.V775M	NM_017950.3	NP_060420.2	Q4G0X9	CCD40_HUMAN	coiled-coil domain containing 40	775					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)			CCAGGCCCAGGTGACCTGGCT	0.602													G|||	530	0.105831	0.2368	0.0605	5008	,	,		16937	0.0		0.0944	False		,,,				2504	0.0818				p.V775M		Atlas-SNP	.											.	CCDC40	198	.	0			c.G2323A						PASS	.	G	MET/VAL	775,3419		75,625,1397	42.0	49.0	46.0		2323	2.7	0.9	17	dbSNP_129	46	711,7691		46,619,3536	yes	missense	CCDC40	NM_017950.3	21	121,1244,4933	AA,AG,GG		8.4623,18.4788,11.7974	benign	775/1143	78059889	1486,11110	2097	4201	6298	SO:0001583	missense	55036	exon14			GCCCAGGTGACCT	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.2323G>A	17.37:g.78059889G>A	ENSP00000380679:p.Val775Met	Somatic	182	0	0		WXS	Illumina HiSeq	Phase_I	186	90	0.483871	NM_017950	A8MTD2|C9JTI9|C9JTJ0|C9JXW1|Q6PE47|Q9HCD2|Q9NWL5	Missense_Mutation	SNP	ENST00000397545.4	37	CCDS42395.1	200	0.09157509157509157	100	0.2032520325203252	24	0.06629834254143646	0	0.0	76	0.10026385224274406	G	12.61	1.989989	0.35131	0.184788	0.084623	ENSG00000141519	ENST00000374877;ENST00000397545	T;T	0.45668	0.89;0.91	4.94	2.68	0.31781	.	.	.	.	.	T	0.00039	0.0001	N	0.25647	0.755	0.48975	P	2.649999999999597E-4	B;B	0.27882	0.192;0.066	B;B	0.26310	0.068;0.027	T	0.15752	-1.0426	8	0.40728	T	0.16	-26.9755	2.5819	0.04820	0.3972:0.263:0.3399:0.0	rs60684213;rs61749055	775;558	Q4G0X9;Q4G0X9-3	CCD40_HUMAN;.	M	775	ENSP00000364011:V775M;ENSP00000380679:V775M	ENSP00000364011:V775M	V	+	1	0	CCDC40	75674484	0.995000	0.38212	0.942000	0.38095	0.884000	0.51177	1.869000	0.39519	1.052000	0.40392	0.514000	0.50259	GTG	G|0.904;A|0.096	0.096	strong		0.602	CCDC40-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256005.2	XM_371082	
TNNT2	7139	hgsc.bcm.edu	37	1	201334382	201334382	+	Silent	SNP	G	G	A	rs3729547	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:201334382G>A	ENST00000509001.1	-	9	604	c.318C>T	c.(316-318)atC>atT	p.I106I	TNNT2_ENST00000460780.1_5'Flank|TNNT2_ENST00000458432.2_Silent_p.I118I|TNNT2_ENST00000367322.1_Silent_p.I106I|TNNT2_ENST00000367320.2_Intron|TNNT2_ENST00000236918.7_Silent_p.I111I|TNNT2_ENST00000360372.4_Silent_p.I101I|TNNT2_ENST00000367315.2_Silent_p.I106I|TNNT2_ENST00000421663.2_Silent_p.I108I|TNNT2_ENST00000367317.4_Silent_p.I106I|TNNT2_ENST00000367318.5_Silent_p.I106I	NM_001276347.1	NP_001263276.1	P45379	TNNT2_HUMAN	troponin T type 2 (cardiac)	116					ATP catabolic process (GO:0006200)|atrial cardiac muscle tissue morphogenesis (GO:0055009)|muscle filament sliding (GO:0030049)|negative regulation of ATPase activity (GO:0032780)|positive regulation of ATPase activity (GO:0032781)|regulation of heart contraction (GO:0008016)|regulation of muscle contraction (GO:0006937)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	cytosol (GO:0005829)|sarcomere (GO:0030017)|striated muscle thin filament (GO:0005865)|troponin complex (GO:0005861)	actin binding (GO:0003779)|structural constituent of cytoskeleton (GO:0005200)|tropomyosin binding (GO:0005523)|troponin C binding (GO:0030172)|troponin I binding (GO:0031013)			breast(2)|cervix(1)|endometrium(3)|large_intestine(4)|liver(1)|lung(9)	20						AGTGAGCCTCGATCAGCGCCT	0.557													G|||	3481	0.695088	0.6293	0.7997	5008	,	,		20398	0.5268		0.7416	False		,,,				2504	0.8354				p.I116I		Atlas-SNP	.											TNNT2,colon,carcinoma,0,1	TNNT2	43	1	0			c.C348T						PASS	.	G	,,,	2702,1704	651.8+/-399.3	827,1048,328	198.0	176.0	183.0		348,318,318,303	3.1	1.0	1	dbSNP_107	183	6178,2422	698.3+/-405.0	2224,1730,346	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TNNT2	NM_000364.2,NM_001001430.1,NM_001001431.1,NM_001001432.1	,,,	3051,2778,674	AA,AG,GG		28.1628,38.6745,31.7238	,,,	116/296,106/289,106/286,101/283	201334382	8880,4126	2203	4300	6503	SO:0001819	synonymous_variant	7139	exon10			AGCCTCGATCAGC	X74819	CCDS30968.1, CCDS30969.1, CCDS60390.1, CCDS73002.1, CCDS73003.1	1q32	2014-09-17	2005-09-12		ENSG00000118194	ENSG00000118194			11949	protein-coding gene	gene with protein product		191045	"""troponin T2, cardiac"", ""cardiomyopathy, hypertrophic 2"", ""cardiomyopathy, dilated 1D (autosomal dominant)"""	CMH2, CMD1D		8088824, 8205619, 9482583	Standard	NM_001001430		Approved	CMPD2	uc001gwf.4	P45379	OTTHUMG00000035733	ENST00000509001.1:c.318C>T	1.37:g.201334382G>A		Somatic	141	1	0.0070922		WXS	Illumina HiSeq	Phase_I	126	126	1	NM_001276345	A2TDB9|A8K3K6|O60214|Q99596|Q99597|Q9BUF6|Q9UM96	Silent	SNP	ENST00000509001.1	37	CCDS30969.1																																																																																			G|0.318;A|0.682	0.682	strong		0.557	TNNT2-008	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000360358.1	NM_000364	
SLIRP	81892	hgsc.bcm.edu	37	14	78174473	78174473	+	Silent	SNP	A	A	C	rs11159286	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:78174473A>C	ENST00000557342.1	+	1	60	c.19A>C	c.(19-21)Aga>Cga	p.R7R	SLIRP_ENST00000238688.5_Silent_p.R7R|SLIRP_ENST00000557431.1_Silent_p.R7R|SLIRP_ENST00000557623.1_Silent_p.R7R|ALKBH1_ENST00000216489.3_5'Flank	NM_001267864.1|NM_031210.5	NP_001254793.1|NP_112487.1	Q9GZT3	SLIRP_HUMAN	SRA stem-loop interacting RNA binding protein	7					mitochondrion morphogenesis (GO:0070584)|negative regulation of mitochondrial RNA catabolic process (GO:0000961)|regulation of transcription, DNA-templated (GO:0006355)|single fertilization (GO:0007338)|sperm motility (GO:0030317)|spermatid development (GO:0007286)|transcription, DNA-templated (GO:0006351)	acrosomal vesicle (GO:0001669)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|ribonucleoprotein complex (GO:0030529)|sperm flagellum (GO:0036126)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			kidney(1)|prostate(1)	2						CTCAGCAGCGAGAGGTGCTGC	0.562													C|||	4357	0.870008	0.826	0.938	5008	,	,		16764	0.8363		0.9642	False		,,,				2504	0.819				p.R7R		Atlas-SNP	.											SLIRP,NS,carcinoma,-1,1	SLIRP	6	1	0			c.A19C						PASS	.	C		3728,678	287.5+/-279.3	1578,572,53	61.0	62.0	62.0		19	-4.4	0.0	14	dbSNP_120	62	8288,312	111.0+/-171.3	3994,300,6	no	coding-synonymous	SLIRP	NM_031210.4		5572,872,59	CC,CA,AA		3.6279,15.3881,7.6119		7/110	78174473	12016,990	2203	4300	6503	SO:0001819	synonymous_variant	81892	exon1			GCAGCGAGAGGTG	AF253980	CCDS9866.1, CCDS58331.1, CCDS73668.1	14q24.3	2013-02-12	2011-06-17	2011-06-17	ENSG00000119705	ENSG00000119705		"""RNA binding motif (RRM) containing"""	20495	protein-coding gene	gene with protein product		610211	"""chromosome 14 open reading frame 156"""	C14orf156		16762838	Standard	NM_031210		Approved	DC50	uc001xue.5	Q9GZT3		ENST00000557342.1:c.19A>C	14.37:g.78174473A>C		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	87	86	0.988506	NM_001267864	J3KMY7	Silent	SNP	ENST00000557342.1	37	CCDS9866.1																																																																																			A|0.093;C|0.907	0.907	strong		0.562	SLIRP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000413901.1	NM_031210	
ACVR1	90	hgsc.bcm.edu	37	2	158634674	158634674	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:158634674A>G	ENST00000263640.3	-	5	941	c.512T>C	c.(511-513)aTc>aCc	p.I171T	ACVR1_ENST00000487456.1_5'UTR|ACVR1_ENST00000410057.2_Missense_Mutation_p.I171T|ACVR1_ENST00000434821.1_Missense_Mutation_p.I171T|ACVR1_ENST00000409283.2_Missense_Mutation_p.I171T	NM_001105.4	NP_001096.1	Q04771	ACVR1_HUMAN	activin A receptor, type I	171					activin receptor signaling pathway (GO:0032924)|acute inflammatory response (GO:0002526)|atrial septum primum morphogenesis (GO:0003289)|BMP signaling pathway (GO:0030509)|cardiac muscle cell fate commitment (GO:0060923)|cellular response to glucocorticoid stimulus (GO:0071385)|determination of left/right symmetry (GO:0007368)|embryonic heart tube morphogenesis (GO:0003143)|endocardial cushion cell fate commitment (GO:0061445)|G1/S transition of mitotic cell cycle (GO:0000082)|gastrulation with mouth forming second (GO:0001702)|germ cell development (GO:0007281)|in utero embryonic development (GO:0001701)|mesoderm formation (GO:0001707)|mitral valve morphogenesis (GO:0003183)|negative regulation of activin receptor signaling pathway (GO:0032926)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of signal transduction (GO:0009968)|neural crest cell migration (GO:0001755)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|patterning of blood vessels (GO:0001569)|peptidyl-threonine phosphorylation (GO:0018107)|pharyngeal system development (GO:0060037)|positive regulation of bone mineralization (GO:0030501)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|regulation of ossification (GO:0030278)|regulation of skeletal muscle tissue development (GO:0048641)|smooth muscle cell differentiation (GO:0051145)|transforming growth factor beta receptor signaling pathway (GO:0007179)|urogenital system development (GO:0001655)	activin receptor complex (GO:0048179)|apical part of cell (GO:0045177)|integral component of plasma membrane (GO:0005887)	activin binding (GO:0048185)|activin receptor activity, type I (GO:0016361)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|peptide hormone binding (GO:0017046)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|SMAD binding (GO:0046332)|transforming growth factor beta binding (GO:0050431)|transforming growth factor beta receptor activity, type I (GO:0005025)|transmembrane receptor protein serine/threonine kinase activity (GO:0004675)			endometrium(4)|kidney(1)|large_intestine(4)|lung(6)|ovary(2)|skin(2)	19				BRCA - Breast invasive adenocarcinoma(221;0.104)	Adenosine triphosphate(DB00171)	ATTGGTGGTGATGAGCCCTTC	0.502																																					p.I171T		Atlas-SNP	.											ACVR1,NS,carcinoma,-1,1	ACVR1	52	1	0			c.T512C						scavenged	.						149.0	128.0	135.0					2																	158634674		2203	4300	6503	SO:0001583	missense	90	exon5			GTGGTGATGAGCC		CCDS2206.1	2q23-q24	2008-06-13			ENSG00000115170	ENSG00000115170			171	protein-coding gene	gene with protein product		102576		ACVRLK2		8397373	Standard	NM_001105		Approved	SKR1, ALK2, ACVR1A	uc010fog.2	Q04771	OTTHUMG00000131967	ENST00000263640.3:c.512T>C	2.37:g.158634674A>G	ENSP00000263640:p.Ile171Thr	Somatic	253	0	0		WXS	Illumina HiSeq	Phase_I	275	3	0.0109091	NM_001105		Missense_Mutation	SNP	ENST00000263640.3	37	CCDS2206.1	.	.	.	.	.	.	.	.	.	.	A	15.19	2.759191	0.49468	.	.	ENSG00000115170	ENST00000263640;ENST00000409283;ENST00000434821;ENST00000410057	D;D;D;D	0.85171	-1.95;-1.95;-1.95;-1.95	5.95	5.95	0.96441	.	0.000000	0.85682	D	0.000000	T	0.77870	0.4195	L	0.27053	0.805	0.80722	D	1	B	0.15141	0.012	B	0.17098	0.017	T	0.71859	-0.4465	10	0.22706	T	0.39	.	16.0893	0.81082	1.0:0.0:0.0:0.0	.	171	Q04771	ACVR1_HUMAN	T	171	ENSP00000263640:I171T;ENSP00000387273:I171T;ENSP00000405004:I171T;ENSP00000387127:I171T	ENSP00000263640:I171T	I	-	2	0	ACVR1	158342920	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	9.307000	0.96226	2.279000	0.76181	0.533000	0.62120	ATC	.	.	none		0.502	ACVR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254927.1	NM_001105	
USHBP1	83878	hgsc.bcm.edu	37	19	17367435	17367435	+	Missense_Mutation	SNP	T	T	C	rs9676419	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	76	0	0		WXS	Illumina HiSeq	Phase_I	95	43	0.452632	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	
SGK1	6446	hgsc.bcm.edu	37	6	134493397	134493397	+	Silent	SNP	G	G	A	rs1057293	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:134493397G>A	ENST00000237305.7	-	8	808	c.720C>T	c.(718-720)gaC>gaT	p.D240D	SGK1_ENST00000475719.2_Silent_p.D196D|SGK1_ENST00000489458.2_5'UTR|SGK1_ENST00000528577.1_Silent_p.D268D|SGK1_ENST00000367858.5_Silent_p.D335D|SGK1_ENST00000367857.5_Silent_p.D230D|SGK1_ENST00000413996.3_Silent_p.D254D	NM_005627.3	NP_005618.2	O00141	SGK1_HUMAN	serum/glucocorticoid regulated kinase 1	240	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|cellular response to DNA damage stimulus (GO:0006974)|ion transmembrane transport (GO:0034220)|long-term memory (GO:0007616)|positive regulation of transporter activity (GO:0032411)|protein phosphorylation (GO:0006468)|regulation of apoptotic process (GO:0042981)|regulation of blood pressure (GO:0008217)|regulation of catalytic activity (GO:0050790)|regulation of cell growth (GO:0001558)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of gastric acid secretion (GO:0060453)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|renal sodium ion absorption (GO:0070294)|response to stress (GO:0006950)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium channel regulator activity (GO:0005246)|chloride channel regulator activity (GO:0017081)|potassium channel regulator activity (GO:0015459)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|sodium channel regulator activity (GO:0017080)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(21)|kidney(3)|large_intestine(3)|lung(10)|ovary(1)|skin(4)|stomach(1)	46	Colorectal(23;0.221)			OV - Ovarian serous cystadenocarcinoma(155;0.00317)|GBM - Glioblastoma multiforme(68;0.00847)		AGAGTCCGAAGTCAGTAAGGA	0.438													G|||	573	0.114417	0.0726	0.1326	5008	,	,		20195	0.2232		0.0765	False		,,,				2504	0.0849				p.D335D		Atlas-SNP	.											.	SGK1	387	.	0			c.C1005T						PASS	.	G	,,,	427,3979	209.2+/-230.0	18,391,1794	245.0	218.0	227.0		1005,804,762,720	5.2	1.0	6	dbSNP_86	227	841,7759	193.2+/-239.0	47,747,3506	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SGK1	NM_001143676.1,NM_001143677.1,NM_001143678.1,NM_005627.3	,,,	65,1138,5300	AA,AG,GG		9.7791,9.6913,9.7493	,,,	335/527,268/460,254/446,240/432	134493397	1268,11738	2203	4300	6503	SO:0001819	synonymous_variant	6446	exon10			TCCGAAGTCAGTA	AJ000512	CCDS5170.1, CCDS47476.1, CCDS47477.1, CCDS47478.1	6q23	2008-02-05	2007-12-05	2007-12-05	ENSG00000118515	ENSG00000118515			10810	protein-coding gene	gene with protein product		602958	"""serum/glucocorticoid regulated kinase"""	SGK		9114008, 9722955	Standard	NM_005627		Approved		uc003qeo.4	O00141	OTTHUMG00000015613	ENST00000237305.7:c.720C>T	6.37:g.134493397G>A		Somatic	187	0	0		WXS	Illumina HiSeq	Phase_I	97	23	0.237113	NM_001143676	B7UUP7|B7UUP8|B7UUP9|B7Z5B2|E1P583|Q5TCN2|Q5TCN3|Q5TCN4|Q5VY65|Q9UN56	Silent	SNP	ENST00000237305.7	37	CCDS5170.1																																																																																			G|0.894;A|0.106	0.106	strong		0.438	SGK1-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042312.2		
PDE4DIP	9659	hgsc.bcm.edu	37	1	144859816	144859816	+	Missense_Mutation	SNP	T	T	C	rs587702923	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:144859816T>C	ENST00000369354.3	-	38	6457	c.6268A>G	c.(6268-6270)Att>Gtt	p.I2090V	PDE4DIP_ENST00000369359.4_Missense_Mutation_p.I2226V|PDE4DIP_ENST00000313382.9_Missense_Mutation_p.I1984V|PDE4DIP_ENST00000369356.4_Missense_Mutation_p.I2090V|RP4-791M13.4_ENST00000532137.1_RNA|PDE4DIP_ENST00000530740.1_Missense_Mutation_p.I2175V|PDE4DIP_ENST00000524974.1_5'UTR			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	2090					cellular protein complex assembly (GO:0043623)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|myofibril (GO:0030016)|nucleus (GO:0005634)	enzyme binding (GO:0019899)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(12)|lung(106)|ovary(8)|prostate(7)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	176				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		TTCTGGTTAATGGAGGAGGGG	0.577			T	PDGFRB	MPD																																p.I2090V		Atlas-SNP	.		Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	.	PDE4DIP	817	.	0			c.A6268G						PASS	.						65.0	63.0	63.0					1																	144859816		2203	4300	6503	SO:0001583	missense	9659	exon38			GGTTAATGGAGGA	AB007923, AB007946	CCDS72887.1, CCDS72888.1, CCDS72889.1, CCDS72890.1, CCDS72891.1, CCDS72892.1, CCDS72893.1, CCDS72894.1	1q21.1	2008-07-31	2008-07-31		ENSG00000178104	ENSG00000178104			15580	protein-coding gene	gene with protein product	"""myomegalin"""	608117	"""cardiomyopathy associated 2"""	CMYA2		9455484, 11134006	Standard	NM_022359		Approved	KIAA0477, KIAA0454, MMGL	uc021ouh.1	Q5VU43	OTTHUMG00000013846	ENST00000369354.3:c.6268A>G	1.37:g.144859816T>C	ENSP00000358360:p.Ile2090Val	Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	153	11	0.0718954	NM_014644	A2RU15|O75042|O75065|Q2YDC1|Q5VU42|Q5VU44|Q5VU45|Q5VU46|Q5VU47|Q5VU48|Q5VU49|Q68DU2|Q6AZ93|Q6PK88|Q86T40|Q86TB2|Q8N3W0|Q8TAY9|Q9HCP2|Q9HCP3|Q9HCP4|Q9HCP5	Missense_Mutation	SNP	ENST00000369354.3	37	CCDS30824.1	.	.	.	.	.	.	.	.	.	.	T	0.010	-1.760839	0.00657	.	.	ENSG00000178104	ENST00000313382;ENST00000369354;ENST00000369356;ENST00000530740;ENST00000369359	T;T;T;T;T	0.01685	4.69;4.78;4.78;4.8;4.79	4.63	-9.26	0.00662	.	.	.	.	.	T	0.00178	0.0005	N	0.03608	-0.345	0.09310	N	0.999999	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.47058	-0.9146	9	0.02654	T	1	.	5.9795	0.19399	0.0819:0.4615:0.1653:0.2913	.	1984;2090	Q5VU43-3;Q5VU43	.;MYOME_HUMAN	V	1984;2090;2090;2175;2226	ENSP00000327209:I1984V;ENSP00000358360:I2090V;ENSP00000358363:I2090V;ENSP00000435654:I2175V;ENSP00000358366:I2226V	ENSP00000327209:I1984V	I	-	1	0	PDE4DIP	143571173	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-4.249000	0.00266	-3.114000	0.00240	-1.162000	0.01777	ATT	.	.	none		0.577	PDE4DIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000038858.2	NM_022359	
TDRKH	11022	hgsc.bcm.edu	37	1	151747970	151747970	+	Silent	SNP	A	A	G	rs11204885	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:151747970A>G	ENST00000368822.1	-	10	1965	c.1332T>C	c.(1330-1332)caT>caC	p.H444H	TDRKH_ENST00000368827.6_Silent_p.H444H|TDRKH_ENST00000440583.2_Silent_p.H220H|TDRKH_ENST00000368825.3_Silent_p.H399H|TDRKH_ENST00000368823.1_Silent_p.H440H|TDRKH_ENST00000368824.3_Silent_p.H444H|TDRKH_ENST00000458431.2_Silent_p.H444H			Q9Y2W6	TDRKH_HUMAN	tudor and KH domain containing	444					cell differentiation (GO:0030154)|DNA methylation involved in gamete generation (GO:0043046)|fertilization (GO:0009566)|gene silencing by RNA (GO:0031047)|male meiosis (GO:0007140)|piRNA metabolic process (GO:0034587)|spermatogenesis (GO:0007283)	mitochondrion (GO:0005739)|pi-body (GO:0071546)|piP-body (GO:0071547)	RNA binding (GO:0003723)			breast(5)|cervix(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	26	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.14)		LUSC - Lung squamous cell carcinoma(543;0.181)			AGTCAGCACAATGAGTGAGTC	0.473																																					p.H444H		Atlas-SNP	.											.	TDRKH	45	.	0			c.T1332C						PASS	.	A	,,,	409,3479		19,371,1554	128.0	120.0	122.0		1332,1197,1332,1332	3.7	1.0	1	dbSNP_120	122	1816,6470		194,1428,2521	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TDRKH	NM_001083963.1,NM_001083964.1,NM_001083965.1,NM_006862.3	,,,	213,1799,4075	GG,GA,AA		21.9165,10.5195,18.2767	,,,	444/562,399/517,444/562,444/562	151747970	2225,9949	1944	4143	6087	SO:0001819	synonymous_variant	11022	exon10			AGCACAATGAGTG	AF227192	CCDS41394.1, CCDS41395.1	1q21	2013-01-23	2003-11-07		ENSG00000182134	ENSG00000182134		"""Tudor domain containing"""	11713	protein-coding gene	gene with protein product		609501	"""tudor and KH domain containing"""			10767542	Standard	NM_001083964		Approved	TDRD2	uc001eza.4	Q9Y2W6	OTTHUMG00000013062	ENST00000368822.1:c.1332T>C	1.37:g.151747970A>G		Somatic	188	0	0		WXS	Illumina HiSeq	Phase_I	172	83	0.482558	NM_001083965	D3DV24|Q5SZR3|Q5SZR5|Q8N582|Q9NYV5	Silent	SNP	ENST00000368822.1	37	CCDS41394.1																																																																																			A|0.773;G|0.227	0.227	strong		0.473	TDRKH-005	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000036648.2	NM_006862	
FAM179A	165186	hgsc.bcm.edu	37	2	29222070	29222070	+	Missense_Mutation	SNP	G	G	A	rs13009279	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:29222070G>A	ENST00000379558.4	+	4	514	c.163G>A	c.(163-165)Gcc>Acc	p.A55T	FAM179A_ENST00000403861.2_Missense_Mutation_p.A55T	NM_199280.2	NP_954974.2	Q6ZUX3	F179A_HUMAN	family with sequence similarity 179, member A	55			A -> T (in dbSNP:rs13009279).							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						TGAGCCAAGAGCCCTGCTGAA	0.617													G|||	1645	0.328474	0.2337	0.281	5008	,	,		19748	0.627		0.2813	False		,,,				2504	0.2311				p.A55T		Atlas-SNP	.											.	FAM179A	106	.	0			c.G163A						PASS	.	G	THR/ALA	981,3273		112,757,1258	37.0	41.0	40.0		163	-0.1	0.0	2	dbSNP_121	40	2284,6178		318,1648,2265	yes	missense	FAM179A	NM_199280.2	58	430,2405,3523	AA,AG,GG		26.9913,23.0606,25.6763	benign	55/1020	29222070	3265,9451	2127	4231	6358	SO:0001583	missense	165186	exon4			CCAAGAGCCCTGC	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.163G>A	2.37:g.29222070G>A	ENSP00000368876:p.Ala55Thr	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	70	39	0.557143	NM_199280	Q6ZUF5	Missense_Mutation	SNP	ENST00000379558.4	37	CCDS1769.2	752	0.3443223443223443	107	0.21747967479674796	95	0.26243093922651933	334	0.583916083916084	216	0.2849604221635884	G	7.400	0.632493	0.14322	0.230606	0.269913	ENSG00000189350	ENST00000420297;ENST00000379558;ENST00000403861	T;T;T	0.44881	0.91;3.16;3.01	5.31	-0.0693	0.13752	.	.	.	.	.	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	0.45381	-0.9265	8	0.41790	T	0.15	.	9.9487	0.41626	0.3511:0.0:0.6489:0.0	rs13009279;rs13009279	55;55	F8W8E4;Q6ZUX3	.;F179A_HUMAN	T	55	ENSP00000402415:A55T;ENSP00000368876:A55T;ENSP00000384699:A55T	ENSP00000368876:A55T	A	+	1	0	FAM179A	29075574	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.377000	0.07456	-0.323000	0.08602	-1.303000	0.01326	GCC	G|0.655;A|0.345	0.345	strong		0.617	FAM179A-003	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317848.4	NM_199280	
HOXB7	3217	hgsc.bcm.edu	37	17	46688135	46688135	+	Missense_Mutation	SNP	G	G	A	rs79247310	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:46688135G>A	ENST00000239165.7	-	1	244	c.146C>T	c.(145-147)gCt>gTt	p.A49V	HOXB7_ENST00000567101.2_Intron	NM_004502.3	NP_004493.3	P09629	HXB7_HUMAN	homeobox B7	49				A -> V (in Ref. 2; BAF83342 and 3; BAD96969). {ECO:0000305}.	anterior/posterior pattern specification (GO:0009952)|embryonic skeletal system morphogenesis (GO:0048704)|multicellular organismal development (GO:0007275)|myeloid cell differentiation (GO:0030099)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|large_intestine(2)|lung(4)|upper_aerodigestive_tract(1)	8						GGCGAAGGAAGCGCCCGAACC	0.687													G|||	429	0.0856629	0.0469	0.0216	5008	,	,		12239	0.2341		0.0497	False		,,,				2504	0.0675				p.A49V		Atlas-SNP	.											.	HOXB7	15	.	0			c.C146T						PASS	.	G	VAL/ALA	175,4173		1,173,2000	12.0	15.0	14.0		146	4.3	0.9	17	dbSNP_132	14	241,8277		3,235,4021	no	missense	HOXB7	NM_004502.3	64	4,408,6021	AA,AG,GG		2.8293,4.0248,3.2333	possibly-damaging	49/218	46688135	416,12450	2174	4259	6433	SO:0001583	missense	3217	exon1			AAGGAAGCGCCCG		CCDS11532.1	17q21.32	2013-05-22	2005-12-22					"""Homeoboxes / ANTP class : HOXL subclass"""	5118	protein-coding gene	gene with protein product		142962	"""homeo box B7"""	HOX2, HOX2C		1973146, 1358459	Standard	NM_004502		Approved		uc002inv.3	P09629	OTTHUMG00000170231	ENST00000239165.7:c.146C>T	17.37:g.46688135G>A	ENSP00000239165:p.Ala49Val	Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	40	24	0.6	NM_004502	A8K3N8|Q15957|Q53FN3|Q96BQ6	Missense_Mutation	SNP	ENST00000239165.7	37	CCDS11532.1	218	0.09981684981684982	22	0.044715447154471545	8	0.022099447513812154	148	0.25874125874125875	40	0.052770448548812667	G	16.68	3.190187	0.58017	0.040248	0.028293	ENSG00000120087	ENST00000239165	T	0.34275	1.37	4.26	4.26	0.50523	.	0.286515	0.33401	N	0.004954	T	0.00012	0.0000	M	0.81239	2.535	0.32650	P	0.5194840000000001	B	0.22003	0.063	B	0.19666	0.026	T	0.12344	-1.0551	9	0.62326	D	0.03	.	14.6281	0.68638	0.0:0.0:1.0:0.0	.	49	P09629	HXB7_HUMAN	V	49	ENSP00000239165:A49V	ENSP00000239165:A49V	A	-	2	0	HOXB7	44043134	0.001000	0.12720	0.922000	0.36590	0.967000	0.64934	1.156000	0.31712	2.207000	0.71202	0.555000	0.69702	GCT	G|0.917;A|0.083	0.083	strong		0.687	HOXB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358097.3		
CAND2	23066	hgsc.bcm.edu	37	3	12858244	12858244	+	Missense_Mutation	SNP	C	C	T	rs367818782		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:12858244C>T	ENST00000456430.2	+	10	1854	c.1813C>T	c.(1813-1815)Cgg>Tgg	p.R605W	CAND2_ENST00000295989.5_Missense_Mutation_p.R512W	NM_001162499.1	NP_001155971.1	O75155	CAND2_HUMAN	cullin-associated and neddylation-dissociated 2 (putative)	605					positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	intracellular (GO:0005622)|nucleus (GO:0005634)				breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(8)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	37						CCTGGGTGACCGGCTTGGGGA	0.652																																					p.R605W	GBM(43;676 868 1633 6395 37496)	Atlas-SNP	.											CAND2_ENST00000456430,NS,carcinoma,-1,2	CAND2	138	2	0			c.C1813T						scavenged	.						75.0	86.0	82.0					3																	12858244		2115	4219	6334	SO:0001583	missense	23066	exon10			GGTGACCGGCTTG		CCDS43053.1, CCDS54554.1	3p25.2	2008-02-05			ENSG00000144712	ENSG00000144712			30689	protein-coding gene	gene with protein product	"""TBP interacting protein"""	610403				9734811, 10441524	Standard	NM_012298		Approved	TIP120B, KIAA0667, Tp120b	uc003bxk.2	O75155	OTTHUMG00000155397	ENST00000456430.2:c.1813C>T	3.37:g.12858244C>T	ENSP00000387641:p.Arg605Trp	Somatic	171	1	0.00584795		WXS	Illumina HiSeq	Phase_I	136	24	0.176471	NM_001162499	B9EGM9|E9KL24	Missense_Mutation	SNP	ENST00000456430.2	37	CCDS54554.1	.	.	.	.	.	.	.	.	.	.	C	9.667	1.145683	0.21288	.	.	ENSG00000144712	ENST00000295989;ENST00000456430	T;T	0.45276	0.9;0.9	5.12	1.9	0.25705	Armadillo-like helical (1);Armadillo-type fold (1);	0.415040	0.22498	N	0.059262	T	0.26521	0.0648	N	0.21448	0.665	0.80722	D	1	B;B	0.06786	0.0;0.001	B;B	0.01281	0.0;0.0	T	0.05599	-1.0875	10	0.38643	T	0.18	-24.9762	9.6179	0.39704	0.0:0.7203:0.0:0.2797	.	605;512	O75155;O75155-2	CAND2_HUMAN;.	W	512;605	ENSP00000295989:R512W;ENSP00000387641:R605W	ENSP00000295989:R512W	R	+	1	2	CAND2	12833244	0.773000	0.28580	0.905000	0.35620	0.800000	0.45204	1.268000	0.33062	0.577000	0.29470	-0.254000	0.11334	CGG	.	.	weak		0.652	CAND2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339856.4	XM_371617	
LINC00283	100874057	hgsc.bcm.edu	37	13	103397890	103397890	+	RNA	SNP	G	G	A	rs75285783	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:103397890G>A	ENST00000430111.1	+	0	3894									long intergenic non-protein coding RNA 283																		TATTGAGCATGTATGAAATTG	0.388													G|||	375	0.0748802	0.0454	0.0648	5008	,	,		21767	0.0129		0.1243	False		,,,				2504	0.135				p.Y1719Y		Atlas-SNP	.											.	.	.	.	0			c.C5157T						PASS	.	G		57,1327		3,51,638	139.0	114.0	122.0		5157	1.2	0.0	13	dbSNP_132	122	376,2806		22,332,1237	no	coding-synonymous	CCDC168	NM_001146197.1		25,383,1875	AA,AG,GG		11.8165,4.1185,9.4831		1719/7082	103397890	433,4133	692	1591	2283			643677	exon4			GAGCATGTATGAA			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.103397890G>A		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	99	47	0.474747	NM_001146197		Silent	SNP	ENST00000430111.1	37																																																																																				G|0.930;A|0.070	0.070	strong		0.388	LINC00283-001	KNOWN	not_organism_supported|basic	antisense	antisense	OTTHUMT00000045714.1		
TACC2	10579	hgsc.bcm.edu	37	10	123810060	123810060	+	Silent	SNP	G	G	A	rs11200367	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:123810060G>A	ENST00000369005.1	+	3	481	c.141G>A	c.(139-141)gcG>gcA	p.A47A	TACC2_ENST00000358010.1_Silent_p.A47A|TACC2_ENST00000334433.3_Silent_p.A47A|TACC2_ENST00000515603.1_Silent_p.A47A|TACC2_ENST00000453444.2_Silent_p.A47A|TACC2_ENST00000513429.1_Silent_p.A47A|TACC2_ENST00000515273.1_Silent_p.A47A	NM_206862.2	NP_996744.2	O95359	TACC2_HUMAN	transforming, acidic coiled-coil containing protein 2	47					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)				ACAGAGACGCGTCCAGGTAGG	0.577													G|||	759	0.151558	0.1997	0.2565	5008	,	,		17204	0.1329		0.0785	False		,,,				2504	0.1063				p.A47A		Atlas-SNP	.											.	TACC2	271	.	0			c.G141A						PASS	.	G	,	708,3698	291.5+/-281.6	58,592,1553	40.0	42.0	41.0		141,141	-6.1	0.0	10	dbSNP_120	41	640,7960	163.9+/-216.4	21,598,3681	no	coding-synonymous,coding-synonymous	TACC2	NM_206861.1,NM_206862.2	,	79,1190,5234	AA,AG,GG		7.4419,16.069,10.3644	,	47/1095,47/2949	123810060	1348,11658	2203	4300	6503	SO:0001819	synonymous_variant	10579	exon3			AGACGCGTCCAGG	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.141G>A	10.37:g.123810060G>A		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	119	59	0.495798	NM_206861	Q4VXL0|Q4VXL3|Q4VXL6|Q4VXL7|Q5U5T7|Q86WG6|Q86WG7|Q8TCK9|Q9BVQ1|Q9NZ41|Q9NZR5	Silent	SNP	ENST00000369005.1	37	CCDS7626.1	302	0.1382783882783883	87	0.17682926829268292	77	0.212707182320442	75	0.13111888111888112	63	0.08311345646437995	G	5.307	0.242046	0.10077	0.16069	0.074419	ENSG00000138162	ENST00000491540	.	.	.	4.0	-6.14	0.02111	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.29088	-1.0023	3	.	.	.	7.7494	2.5773	0.04809	0.4326:0.1168:0.3325:0.1181	rs11200367;rs11200367	.	.	.	I	64	.	.	V	+	1	0	TACC2	123800050	0.000000	0.05858	0.000000	0.03702	0.042000	0.13812	-1.091000	0.03369	-1.183000	0.02723	-0.940000	0.02684	GTC	G|0.885;A|0.115	0.115	strong		0.577	TACC2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090004.1		
CWF19L2	143884	hgsc.bcm.edu	37	11	107197640	107197640	+	Missense_Mutation	SNP	T	T	C	rs3758911	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:107197640T>C	ENST00000282251.5	-	18	2708	c.2681A>G	c.(2680-2682)tAt>tGt	p.Y894C		NM_152434.2	NP_689647.2	Q2TBE0	C19L2_HUMAN	CWF19-like 2, cell cycle control (S. pombe)	894			Y -> C (in dbSNP:rs3758911). {ECO:0000269|PubMed:15489334}.				catalytic activity (GO:0003824)			endometrium(4)|kidney(2)|large_intestine(13)|lung(21)	40		Melanoma(852;1.75e-05)|all_epithelial(67;6.27e-05)|Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Breast(348;0.0258)		Epithelial(105;7.18e-06)|BRCA - Breast invasive adenocarcinoma(274;1.65e-05)|all cancers(92;1.76e-05)		TACACCTCAATAGTTTTTACT	0.413													C|||	1283	0.25619	0.2095	0.2003	5008	,	,		18994	0.2927		0.3121	False		,,,				2504	0.2638				p.Y894C		Atlas-SNP	.											.	CWF19L2	135	.	0			c.A2681G						PASS	.	C	CYS/TYR	959,3443	733.1+/-410.4	108,743,1350	92.0	96.0	94.0		2681	2.0	0.0	11	dbSNP_107	94	2871,5725	672.2+/-402.9	491,1889,1918	yes	missense	CWF19L2	NM_152434.2	194	599,2632,3268	CC,CT,TT		33.3993,21.7856,29.4661	benign	894/895	107197640	3830,9168	2201	4298	6499	SO:0001583	missense	143884	exon18			CCTCAATAGTTTT	AK056905	CCDS8336.2	11q23.1	2005-09-22			ENSG00000152404	ENSG00000152404			26508	protein-coding gene	gene with protein product						14702039	Standard	NM_152434		Approved	FLJ32343	uc010rvp.2	Q2TBE0	OTTHUMG00000152975	ENST00000282251.5:c.2681A>G	11.37:g.107197640T>C	ENSP00000282251:p.Tyr894Cys	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	58	15	0.258621	NM_152434	A4FU66|A4FU67|A4FU68|Q6PHW1|Q96MI1	Missense_Mutation	SNP	ENST00000282251.5	37	CCDS8336.2	583	0.26694139194139194	105	0.21341463414634146	85	0.23480662983425415	153	0.2674825174825175	240	0.316622691292876	C	13.95	2.390991	0.42410	0.217856	0.333993	ENSG00000152404	ENST00000282251	T	0.10960	2.82	4.94	2.01	0.26516	.	1.226040	0.05686	N	0.591429	T	0.00012	0.0000	N	0.00926	-1.1	0.47441	P	5.730000000000457E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.45760	-0.9239	9	0.62326	D	0.03	.	0.9374	0.01347	0.1549:0.3768:0.1508:0.3174	rs3758911;rs52805989;rs58247370;rs3758911	894	Q2TBE0	C19L2_HUMAN	C	894	ENSP00000282251:Y894C	ENSP00000282251:Y894C	Y	-	2	0	CWF19L2	106702850	0.999000	0.42202	0.004000	0.12327	0.046000	0.14306	1.008000	0.29872	0.026000	0.15269	-0.128000	0.14901	TAT	T|0.725;C|0.275	0.275	strong		0.413	CWF19L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328825.2	NM_152434	
WNK1	65125	hgsc.bcm.edu	37	12	988894	988894	+	Silent	SNP	G	G	A	rs9804992	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:988894G>A	ENST00000315939.6	+	11	3172	c.2529G>A	c.(2527-2529)caG>caA	p.Q843Q	WNK1_ENST00000530271.2_Silent_p.Q1341Q|WNK1_ENST00000537687.1_Intron|WNK1_ENST00000535572.1_Intron|WNK1_ENST00000340908.4_Silent_p.Q436Q	NM_018979.3	NP_061852.3	Q9H4A3	WNK1_HUMAN	WNK lysine deficient protein kinase 1	843					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)	p.Q843Q(1)		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)			CTGTCTCTCAGATTCCCATAT	0.547													A|||	730	0.145767	0.1203	0.2003	5008	,	,		19266	0.1091		0.1382	False		,,,				2504	0.1871				p.Q843Q	Colon(19;451 567 6672 12618 28860)	Atlas-SNP	.											WNK1,NS,carcinoma,0,2	WNK1	403	2	1	Substitution - coding silent(1)	stomach(1)	c.G2529A						PASS	.	A	,,,	573,3833	773.5+/-414.0	34,505,1664	204.0	176.0	185.0		,,2529,	-4.9	0.8	12	dbSNP_119	185	1349,7251	756.1+/-407.5	103,1143,3054	no	intron,intron,coding-synonymous,intron	WNK1	NM_001184985.1,NM_014823.2,NM_018979.3,NM_213655.4	,,,	137,1648,4718	AA,AG,GG		15.686,13.005,14.7778	,,,	,,843/2383,	988894	1922,11084	2203	4300	6503	SO:0001819	synonymous_variant	65125	exon11			CTCTCAGATTCCC	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.2529G>A	12.37:g.988894G>A		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	97	47	0.484536	NM_018979	A1L4B0|C5HTZ5|C5HTZ6|C5HTZ7|H6WZW3|O15052|P54963|Q4VBX9|Q6IFS5|Q86WL5|Q8N673|Q96CZ6|Q9P1S9	Silent	SNP	ENST00000315939.6	37	CCDS8506.1																																																																																			G|0.860;A|0.140	0.140	strong		0.547	WNK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206683.1	NM_018979	
ASB8	140461	hgsc.bcm.edu	37	12	48543584	48543584	+	Silent	SNP	G	G	C	rs3936179	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:48543584G>C	ENST00000317697.3	-	4	601	c.432C>G	c.(430-432)gtC>gtG	p.V144V	ASB8_ENST00000537754.1_5'UTR|ASB8_ENST00000536953.1_3'UTR|ASB8_ENST00000539528.1_3'UTR|ASB8_ENST00000536549.1_Silent_p.V144V|ASB8_ENST00000535055.1_3'UTR	NM_024095.3	NP_077000.1	Q9H765	ASB8_HUMAN	ankyrin repeat and SOCS box containing 8	144					intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)				breast(1)|kidney(2)|large_intestine(2)|lung(5)|soft_tissue(1)	11						CCAGGGCATTGACAGAGGCCC	0.527													G|||	135	0.0269569	0.0136	0.0346	5008	,	,		19708	0.0		0.0835	False		,,,				2504	0.0092				p.V144V		Atlas-SNP	.											.	ASB8	25	.	0			c.C432G						PASS	.	G		116,4290	88.2+/-126.9	0,116,2087	78.0	73.0	74.0		432	4.2	1.0	12	dbSNP_108	74	726,7874	176.6+/-226.4	31,664,3605	no	coding-synonymous	ASB8	NM_024095.3		31,780,5692	CC,CG,GG		8.4419,2.6328,6.4739		144/289	48543584	842,12164	2203	4300	6503	SO:0001819	synonymous_variant	140461	exon4			GGCATTGACAGAG	AK024908	CCDS8761.1	12q13.12	2013-01-10	2011-01-25			ENSG00000177981		"""Ankyrin repeat domain containing"""	17183	protein-coding gene	gene with protein product		615053	"""ankyrin repeat and SOCS box-containing 8"""			12076535	Standard	NM_024095		Approved	MGC5540, FLJ21255	uc001rrh.3	Q9H765		ENST00000317697.3:c.432C>G	12.37:g.48543584G>C		Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	156	67	0.429487	NM_024095	A8K1P2|Q547Q2	Silent	SNP	ENST00000317697.3	37	CCDS8761.1																																																																																			G|0.946;C|0.054	0.054	strong		0.527	ASB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396497.1		
FAM135B	51059	hgsc.bcm.edu	37	8	139165273	139165273	+	Missense_Mutation	SNP	G	G	A	rs71505459|rs13280444	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:139165273G>A	ENST00000395297.1	-	13	1615	c.1445C>T	c.(1444-1446)cCa>cTa	p.P482L		NM_015912.3	NP_056996.2	Q49AJ0	F135B_HUMAN	family with sequence similarity 135, member B	482										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)			ATTCTCACCTGGCTCTGGACA	0.388										HNSCC(54;0.14)			G|||	1804	0.360224	0.1399	0.415	5008	,	,		18502	0.5298		0.3757	False		,,,				2504	0.4284				p.P482L		Atlas-SNP	.											.	FAM135B	423	.	0			c.C1445T						PASS	.	G	LEU/PRO	683,3153		63,557,1298	117.0	111.0	113.0		1445	0.8	0.0	8	dbSNP_121	113	2831,5447		499,1833,1807	yes	missense	FAM135B	NM_015912.3	98	562,2390,3105	AA,AG,GG		34.1991,17.805,29.0078	benign	482/1407	139165273	3514,8600	1918	4139	6057	SO:0001583	missense	51059	exon13			TCACCTGGCTCTG	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.1445C>T	8.37:g.139165273G>A	ENSP00000378710:p.Pro482Leu	Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	150	148	0.986667	NM_015912	B5MDB3|O95879|Q2WGJ7|Q3KP46	Missense_Mutation	SNP	ENST00000395297.1	37	CCDS6375.2	701	0.320970695970696	87	0.17682926829268292	108	0.2983425414364641	269	0.47027972027972026	237	0.31266490765171506	G	4.611	0.113469	0.08831	0.17805	0.341991	ENSG00000147724	ENST00000395297	T	0.14022	2.54	5.75	0.762	0.18454	.	1.828030	0.02172	N	0.059783	T	0.00012	0.0000	L	0.60455	1.87	0.80722	P	0.0	B;B;B	0.06786	0.001;0.001;0.0	B;B;B	0.08055	0.003;0.002;0.0	T	0.47535	-0.9110	9	0.08599	T	0.76	0.0139	3.4649	0.07547	0.2837:0.1058:0.5027:0.1079	rs13280444	482;482;482	Q49AJ0-3;Q49AJ0-4;Q49AJ0	.;.;F135B_HUMAN	L	482	ENSP00000378710:P482L	ENSP00000276737:P482L	P	-	2	0	FAM135B	139234455	0.001000	0.12720	0.000000	0.03702	0.000000	0.00434	0.461000	0.21940	0.073000	0.16731	-0.940000	0.02684	CCA	G|0.670;A|0.330	0.330	strong		0.388	FAM135B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313590.3	NM_015912	
HEPH	9843	hgsc.bcm.edu	37	X	65390579	65390579	+	Splice_Site	SNP	T	T	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:65390579T>C	ENST00000343002.2	+	1	831	c.167T>C	c.(166-168)aTa>aCa	p.I56T	HEPH_ENST00000374727.3_Splice_Site_p.I59T|HEPH_ENST00000419594.1_Splice_Site_p.I59T|HEPH_ENST00000519389.1_Splice_Site_p.I110T|HEPH_ENST00000336279.5_Intron|HEPH_ENST00000441993.2_Splice_Site_p.I59T			Q9BQS7	HEPH_HUMAN	hephaestin	56	Plastocyanin-like 1.			DI -> QR (in Ref. 7; BAA31673). {ECO:0000305}.	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						GACAGTGACATGTAGGTTTAA	0.522																																					p.I110T		Atlas-SNP	.											.	HEPH	224	.	0			c.T329C						PASS	.						83.0	52.0	63.0					X																	65390579		2203	4300	6503	SO:0001630	splice_region_variant	9843	exon2			GTGACATGTAGGT	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.167+1T>C	X.37:g.65390579T>C		Somatic	200	0	0		WXS	Illumina HiSeq	Phase_I	158	54	0.341772	NM_138737	B1AJX8|D3DVT7|E9PHN8|O75180|Q6UW45|Q9C058	Missense_Mutation	SNP	ENST00000343002.2	37		.	.	.	.	.	.	.	.	.	.	T	2.827	-0.243436	0.05906	.	.	ENSG00000089472	ENST00000519389;ENST00000374727;ENST00000458621;ENST00000441993;ENST00000419594;ENST00000343002;ENST00000425114	D;D;D;D;D;D;D	0.98807	-5.15;-5.15;-5.15;-5.15;-5.15;-5.15;-5.15	5.01	-4.52	0.03472	Cupredoxin (2);	1.081160	0.07043	N	0.830517	D	0.91123	0.7205	N	0.04508	-0.205	0.28301	N	0.923116	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	D	0.88495	0.3078	10	0.09590	T	0.72	.	0.9233	0.01319	0.3612:0.1545:0.1092:0.3751	.	110;59;56	E9PHN8;E7ES21;Q9BQS7	.;.;HEPH_HUMAN	T	110;59;56;59;59;56;56	ENSP00000430620:I110T;ENSP00000363859:I59T;ENSP00000396907:I56T;ENSP00000411687:I59T;ENSP00000413211:I59T;ENSP00000343939:I56T;ENSP00000398078:I56T	ENSP00000343939:I56T	I	+	2	0	HEPH	65307304	0.002000	0.14202	0.871000	0.34182	0.557000	0.35523	-2.384000	0.01063	-0.859000	0.04105	-0.438000	0.05819	ATA	.	.	none		0.522	HEPH-002	KNOWN	alternative_5_UTR|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000056995.1	NM_138737	Missense_Mutation
NES	10763	hgsc.bcm.edu	37	1	156640678	156640678	+	Missense_Mutation	SNP	G	G	A	rs2886443	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:156640678G>A	ENST00000368223.3	-	4	3434	c.3302C>T	c.(3301-3303)cCg>cTg	p.P1101L		NM_006617.1	NP_006608.1	P48681	NEST_HUMAN	nestin	1101	Tail.		P -> L (in dbSNP:rs2886443). {ECO:0000269|PubMed:1478958}.		brain development (GO:0007420)|cell projection morphogenesis (GO:0048858)|central nervous system development (GO:0007417)|embryonic camera-type eye development (GO:0031076)|G2/M transition of mitotic cell cycle (GO:0000086)|negative regulation of catalytic activity (GO:0043086)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of protein binding (GO:0032091)|positive regulation of intermediate filament depolymerization (GO:0030844)|positive regulation of neural precursor cell proliferation (GO:2000179)|stem cell proliferation (GO:0072089)	cytoplasm (GO:0005737)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)	intermediate filament binding (GO:0019215)|structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(30)|ovary(6)|prostate(1)|skin(3)|stomach(1)|urinary_tract(4)	64	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					CCCCTGCCCCGGGCCTGGCTC	0.647													G|||	3116	0.622204	0.3858	0.67	5008	,	,		11968	0.8621		0.6481	False		,,,				2504	0.6339				p.P1101L		Atlas-SNP	.											NES,NS,carcinoma,0,1	NES	196	1	0			c.C3302T						PASS	.	G	LEU/PRO	1788,2592		377,1034,779	18.0	22.0	21.0		3302	-4.2	0.0	1	dbSNP_101	21	5445,3117		1815,1815,651	yes	missense	NES	NM_006617.1	98	2192,2849,1430	AA,AG,GG		36.405,40.8219,44.1122	probably-damaging	1101/1622	156640678	7233,5709	2190	4281	6471	SO:0001583	missense	10763	exon4			TGCCCCGGGCCTG	X65964	CCDS1151.1	1q23	2013-01-16			ENSG00000132688	ENSG00000132688		"""Intermediate filaments type IV"""	7756	protein-coding gene	gene with protein product		600915				1478958, 9104587	Standard	NM_006617		Approved	FLJ21841	uc001fpq.3	P48681	OTTHUMG00000034299	ENST00000368223.3:c.3302C>T	1.37:g.156640678G>A	ENSP00000357206:p.Pro1101Leu	Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	133	49	0.368421	NM_006617	O00552|Q3LIF5|Q5SYZ6	Missense_Mutation	SNP	ENST00000368223.3	37	CCDS1151.1	1421	0.6506410256410257	199	0.40447154471544716	242	0.6685082872928176	489	0.8548951048951049	491	0.6477572559366754	G	6.686	0.495244	0.12762	0.408219	0.63595	ENSG00000132688	ENST00000368223	D	0.84873	-1.91	4.16	-4.17	0.03857	.	1.304050	0.05885	N	0.627213	T	0.55305	0.1912	L	0.56769	1.78	0.80722	P	0.0	B	0.06786	0.001	B	0.01281	0.0	T	0.32903	-0.9889	9	0.07030	T	0.85	.	4.0525	0.09801	0.2772:0.0:0.3442:0.3786	rs2886443;rs3748572;rs57956552;rs2886443	1101	P48681	NEST_HUMAN	L	1101	ENSP00000357206:P1101L	ENSP00000357206:P1101L	P	-	2	0	NES	154907302	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.984000	0.00320	-0.966000	0.03587	-1.141000	0.01876	CCG	G|0.356;A|0.644	0.644	strong		0.647	NES-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000082844.2	NM_006617	
SP1	6667	hgsc.bcm.edu	37	12	53777171	53777171	+	Silent	SNP	A	A	G	rs3741651	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:53777171A>G	ENST00000327443.4	+	3	1538	c.1440A>G	c.(1438-1440)caA>caG	p.Q480Q	SP1_ENST00000426431.2_Silent_p.Q473Q	NM_001251825.1|NM_138473.2	NP_001238754.1|NP_612482.2	P08047	SP1_HUMAN	Sp1 transcription factor	480	Transactivation domain B (Gln-rich).				cellular lipid metabolic process (GO:0044255)|definitive hemopoiesis (GO:0060216)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic placenta development (GO:0001892)|embryonic process involved in female pregnancy (GO:0060136)|embryonic skeletal system development (GO:0048706)|enucleate erythrocyte differentiation (GO:0043353)|gene expression (GO:0010467)|liver development (GO:0001889)|lung development (GO:0030324)|megakaryocyte differentiation (GO:0030219)|ossification (GO:0001503)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|rhythmic process (GO:0048511)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|trophectodermal cell differentiation (GO:0001829)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein-DNA complex (GO:0032993)	bHLH transcription factor binding (GO:0043425)|core promoter sequence-specific DNA binding (GO:0001046)|DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|enhancer binding (GO:0035326)|histone deacetylase binding (GO:0042826)|HMG box domain binding (GO:0071837)|metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)|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 core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II repressing transcription factor binding (GO:0001103)|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)			breast(1)|large_intestine(1)|ovary(1)|skin(1)|stomach(1)	5				BRCA - Breast invasive adenocarcinoma(357;0.00527)		CACAAGCCCAAACAATCACCT	0.557													G|||	941	0.187899	0.2216	0.2147	5008	,	,		21711	0.1796		0.162	False		,,,				2504	0.1585				p.Q480Q		Atlas-SNP	.											.	SP1	57	.	0			c.A1440G						PASS	.	G	,	884,3522	742.6+/-411.4	95,694,1414	169.0	162.0	164.0		1419,1440	4.7	1.0	12	dbSNP_107	164	1506,7094	748.0+/-407.3	126,1254,2920	no	coding-synonymous,coding-synonymous	SP1	NM_003109.1,NM_138473.2	,	221,1948,4334	GG,GA,AA		17.5116,20.0635,18.3761	,	473/779,480/786	53777171	2390,10616	2203	4300	6503	SO:0001819	synonymous_variant	6667	exon3			AGCCCAAACAATC	J03133	CCDS8857.1, CCDS44898.1	12q13.1	2013-01-08						"""Specificity protein transcription factors"", ""Zinc fingers, C2H2-type"""	11205	protein-coding gene	gene with protein product	"""specificity protein 1"""	189906				1662663	Standard	NM_003109		Approved		uc001scw.3	P08047	OTTHUMG00000170047	ENST00000327443.4:c.1440A>G	12.37:g.53777171A>G		Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	151	68	0.450331	NM_138473	E4Z9M7|G5E9M8|Q86TN8|Q9H3Q5|Q9NR51|Q9NY21|Q9NYE7	Silent	SNP	ENST00000327443.4	37	CCDS8857.1																																																																																			A|0.814;G|0.186	0.186	strong		0.557	SP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407044.1		
LRP5	4041	hgsc.bcm.edu	37	11	68193582	68193582	+	Silent	SNP	G	G	A	rs117289001	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:68193582G>A	ENST00000294304.7	+	16	3670	c.3564G>A	c.(3562-3564)cgG>cgA	p.R1188R		NM_002335.2	NP_002326.2	O75197	LRP5_HUMAN	low density lipoprotein receptor-related protein 5	1188	Beta-propeller 4.				adipose tissue development (GO:0060612)|anatomical structure regression (GO:0060033)|anterior/posterior pattern specification (GO:0009952)|apoptotic process involved in patterning of blood vessels (GO:1902262)|bone marrow development (GO:0048539)|bone morphogenesis (GO:0060349)|bone remodeling (GO:0046849)|branching involved in mammary gland duct morphogenesis (GO:0060444)|canonical Wnt signaling pathway (GO:0060070)|cell migration involved in gastrulation (GO:0042074)|cell-cell signaling involved in mammary gland development (GO:0060764)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic digit morphogenesis (GO:0042733)|embryonic limb morphogenesis (GO:0030326)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|endocytosis (GO:0006897)|extracellular matrix-cell signaling (GO:0035426)|gastrulation with mouth forming second (GO:0001702)|glucose catabolic process (GO:0006007)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|osteoblast development (GO:0002076)|positive regulation of cell proliferation (GO:0008284)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of mitosis (GO:0045840)|positive regulation of osteoblast proliferation (GO:0033690)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of apoptotic process (GO:0042981)|regulation of blood pressure (GO:0008217)|regulation of bone remodeling (GO:0046850)|regulation of canonical Wnt signaling pathway (GO:0060828)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|response to peptide hormone (GO:0043434)|retina morphogenesis in camera-type eye (GO:0060042)|retinal blood vessel morphogenesis (GO:0061304)|somatic stem cell maintenance (GO:0035019)|Wnt signaling pathway (GO:0016055)|Wnt signaling pathway involved in dorsal/ventral axis specification (GO:0044332)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	coreceptor activity (GO:0015026)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			autonomic_ganglia(1)|breast(3)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(24)|ovary(5)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						GGGACAAGCGGACTCGCATCC	0.632													G|||	19	0.00379393	0.0	0.0086	5008	,	,		17781	0.0		0.0129	False		,,,				2504	0.0				p.R1188R		Atlas-SNP	.											.	LRP5	136	.	0			c.G3564A						PASS	.	G		11,4389	19.1+/-41.9	0,11,2189	99.0	86.0	90.0		3564	-1.0	0.8	11	dbSNP_132	90	110,8478	57.9+/-119.4	3,104,4187	no	coding-synonymous	LRP5	NM_002335.2		3,115,6376	AA,AG,GG		1.2809,0.25,0.9316		1188/1616	68193582	121,12867	2200	4294	6494	SO:0001819	synonymous_variant	4041	exon16			CAAGCGGACTCGC	AF064548	CCDS8181.1	11q13.4	2014-01-28	2003-03-12		ENSG00000162337	ENSG00000162337		"""Low density lipoprotein receptors"""	6697	protein-coding gene	gene with protein product		603506	"""osteoporosis pseudoglioma syndrome"", ""exudative vitreoretinopathy 1"""	LRP7, OPPG, EVR1		9714764, 10049586	Standard	XM_005273994		Approved	LR3, BMND1, HBM, OPS, OPTA1, VBCH2, EVR4	uc001ont.3	O75197	OTTHUMG00000167570	ENST00000294304.7:c.3564G>A	11.37:g.68193582G>A		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	52	38	0.730769	NM_002335	Q96TD6|Q9UES7|Q9UP66	Silent	SNP	ENST00000294304.7	37	CCDS8181.1																																																																																			G|0.992;A|0.008	0.008	strong		0.632	LRP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395088.1	NM_002335	
TNIK	23043	hgsc.bcm.edu	37	3	170825920	170825920	+	Silent	SNP	G	G	A	rs2291900	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:170825920G>A	ENST00000436636.2	-	20	2660	c.2316C>T	c.(2314-2316)ctC>ctT	p.L772L	TNIK_ENST00000357327.5_Silent_p.L743L|TNIK_ENST00000538048.1_Silent_p.L717L|TNIK_ENST00000369326.5_Silent_p.L743L|TNIK_ENST00000470834.1_Silent_p.L743L|TNIK_ENST00000460047.1_Silent_p.L717L|TNIK_ENST00000488470.1_Silent_p.L717L|TNIK_ENST00000284483.8_Silent_p.L772L|MIR569_ENST00000385228.1_RNA|TNIK_ENST00000341852.6_Silent_p.L688L|TNIK_ENST00000475336.1_Silent_p.L688L	NM_015028.2	NP_055843.1	Q9UKE5	TNIK_HUMAN	TRAF2 and NCK interacting kinase	772	Mediates interaction with NEDD4.				actin cytoskeleton reorganization (GO:0031532)|activation of JNKK activity (GO:0007256)|cytoskeleton organization (GO:0007010)|intracellular signal transduction (GO:0035556)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of dendrite morphogenesis (GO:0048814)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)	p.L772L(1)		cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(14)|lung(22)|ovary(5)|pancreas(1)|prostate(4)|upper_aerodigestive_tract(2)	62	all_cancers(22;2.55e-19)|all_lung(20;2.22e-14)|Ovarian(172;0.00197)|Breast(254;0.122)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)			GCTCATGGGGGAGCACAGGTG	0.488													G|||	987	0.197085	0.0787	0.2421	5008	,	,		18113	0.1885		0.2883	False		,,,				2504	0.2403				p.L772L		Atlas-SNP	.											TNIK_ENST00000436636,NS,carcinoma,0,3	TNIK	313	3	1	Substitution - coding silent(1)	stomach(1)	c.C2316T						PASS	.	G	,,,,,,,	391,3407		21,349,1529	51.0	54.0	53.0		2316,2229,2229,2151,2151,2064,2064,2316	4.7	1.0	3	dbSNP_100	53	2204,6048		314,1576,2236	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TNIK	NM_001161560.1,NM_001161561.1,NM_001161562.1,NM_001161563.1,NM_001161564.1,NM_001161565.1,NM_001161566.1,NM_015028.2	,,,,,,,	335,1925,3765	AA,AG,GG		26.7087,10.2949,21.5353	,,,,,,,	772/1353,743/1332,743/1324,717/1306,717/1298,688/1277,688/1269,772/1361	170825920	2595,9455	1899	4126	6025	SO:0001819	synonymous_variant	23043	exon20			ATGGGGGAGCACA	AF172264	CCDS46956.1, CCDS54673.1, CCDS54674.1, CCDS54675.1, CCDS54676.1, CCDS54677.1, CCDS54678.1, CCDS54679.1	3q26.31	2008-01-23			ENSG00000154310	ENSG00000154310			30765	protein-coding gene	gene with protein product		610005				9628581, 10521462	Standard	NR_027767		Approved	KIAA0551	uc003fhh.2	Q9UKE5	OTTHUMG00000159036	ENST00000436636.2:c.2316C>T	3.37:g.170825920G>A		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	45	30	0.666667	NM_015028	A7E2A3|A8K4U1|D3DNQ6|O60298|Q8WUY7|Q9UKD8|Q9UKD9|Q9UKE0|Q9UKE1|Q9UKE2|Q9UKE3|Q9UKE4	Silent	SNP	ENST00000436636.2	37	CCDS46956.1																																																																																			G|0.792;A|0.208	0.208	strong		0.488	TNIK-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000352973.2	XM_039796	
CR1	1378	hgsc.bcm.edu	37	1	207669708	207669708	+	Silent	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:207669708G>A	ENST00000367049.4	+	1	96	c.96G>A	c.(94-96)gtG>gtA	p.V32V	CR1_ENST00000367053.1_Silent_p.V32V|CR1_ENST00000367052.1_Silent_p.V32V|CR1_ENST00000367051.1_Silent_p.V32V|CR1_ENST00000367050.4_3'UTR|CR1_ENST00000400960.2_Silent_p.V32V	NM_000651.4	NP_000642.3	P17927	CR1_HUMAN	complement component (3b/4b) receptor 1 (Knops blood group)	32					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						CGGTTGTGGTGCTGCTTGCGC	0.741																																					p.V32V		Atlas-SNP	.											.	CR1	354	.	0			c.G96A						PASS	.						10.0	13.0	12.0					1																	207669708		1820	4065	5885	SO:0001819	synonymous_variant	1378	exon1			TGTGGTGCTGCTT	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.96G>A	1.37:g.207669708G>A		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	44	15	0.340909	NM_000573	Q16744|Q16745|Q5SR43|Q5SR45|Q9UQV2	Silent	SNP	ENST00000367049.4	37	CCDS44308.1	.	.	.	.	.	.	.	.	.	.	G	11.17	1.559458	0.27827	.	.	ENSG00000203710	ENST00000529814	.	.	.	3.59	2.67	0.31697	.	.	.	.	.	T	0.55433	0.1920	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.50338	-0.8840	4	.	.	.	.	7.0064	0.24838	0.1239:0.0:0.8761:0.0	.	.	.	.	Y	8	.	.	C	+	2	0	CR1	205736331	0.998000	0.40836	0.834000	0.33040	0.918000	0.54935	3.349000	0.52217	1.078000	0.41014	0.591000	0.81541	TGC	.	.	none		0.741	CR1-012	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382527.1	NM_000573	
PSME4	23198	hgsc.bcm.edu	37	2	54133744	54133744	+	Silent	SNP	T	T	C	rs805316	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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						PASS	.	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	164	0	0		WXS	Illumina HiSeq	Phase_I	340	275	0.808824	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	
CCR8	1237	hgsc.bcm.edu	37	3	39373902	39373902	+	Missense_Mutation	SNP	C	C	G	rs2853699	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:39373902C>G	ENST00000326306.4	+	2	218	c.80C>G	c.(79-81)gCg>gGg	p.A27G	CCR8_ENST00000545843.1_Missense_Mutation_p.R2G|CCR8_ENST00000414803.1_Missense_Mutation_p.A27G	NM_005201.3	NP_005192.1	P51685	CCR8_HUMAN	chemokine (C-C motif) receptor 8	27			A -> G (in dbSNP:rs2853699). {ECO:0000269|PubMed:12551893}.		cell adhesion (GO:0007155)|chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|positive regulation of cytosolic calcium ion concentration (GO:0007204)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	C-C chemokine receptor activity (GO:0016493)|chemokine receptor activity (GO:0004950)|coreceptor activity (GO:0015026)			NS(3)|breast(1)|endometrium(3)|large_intestine(5)|lung(7)|ovary(1)|skin(1)	21				KIRC - Kidney renal clear cell carcinoma(284;0.0504)|Kidney(284;0.0635)		CCCTGTGATGCGGAACTTATT	0.478													C|||	649	0.129593	0.1014	0.1628	5008	,	,		19549	0.002		0.2982	False		,,,				2504	0.1022				p.A27G		Atlas-SNP	.											.	CCR8	34	.	0			c.C80G						PASS	.	C	GLY/ALA	635,3771	273.4+/-271.3	57,521,1625	195.0	173.0	181.0		80	-3.2	0.0	3	dbSNP_100	181	2611,5989	422.9+/-354.2	402,1807,2091	yes	missense	CCR8	NM_005201.3	60	459,2328,3716	GG,GC,CC		30.3605,14.4122,24.9577	benign	27/356	39373902	3246,9760	2203	4300	6503	SO:0001583	missense	1237	exon2			GTGATGCGGAACT	D49919	CCDS2684.1	3p22	2012-08-08			ENSG00000179934	ENSG00000179934		"""GPCR / Class A : Chemokine receptors : C-C motif"", ""CD molecules"""	1609	protein-coding gene	gene with protein product		601834		CMKBRL2, CMKBR8		8816377, 8886020	Standard	NM_005201		Approved	CY6, TER1, CKR-L1, GPR-CY6, CDw198	uc010hhr.2	P51685	OTTHUMG00000131290	ENST00000326306.4:c.80C>G	3.37:g.39373902C>G	ENSP00000326432:p.Ala27Gly	Somatic	288	0	0		WXS	Illumina HiSeq	Phase_I	283	133	0.469965	NM_005201	B2RC64|Q3KNQ8|Q3KNR3|Q9BYX5	Missense_Mutation	SNP	ENST00000326306.4	37	CCDS2684.1	347|347	0.15888278388278387|0.15888278388278387	57|57	0.11585365853658537|0.11585365853658537	73|73	0.20165745856353592|0.20165745856353592	0|0	0.0|0.0	217|217	0.2862796833773087|0.2862796833773087	C|C	9.150|9.150	1.016035|1.016035	0.19355|0.19355	0.144122|0.144122	0.303605|0.303605	ENSG00000179934|ENSG00000179934	ENST00000326306;ENST00000414803|ENST00000545843	T;T|T	0.20200|0.67345	2.09;2.09|-0.26	4.84|4.84	-3.17|-3.17	0.05202|0.05202	.|.	1.810430|.	0.02947|.	N|.	0.141190|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.08118|0.08118	0|0	0.80722|0.80722	P|P	0.0|0.0	B|B	0.02656|0.02656	0.0|0.0	B|B	0.04013|0.08055	0.001|0.003	T|T	0.18429|0.18429	-1.0337|-1.0337	9|7	0.36615|.	T|.	0.2|.	.|.	2.32|2.32	0.04208|0.04208	0.3225:0.3806:0.1841:0.1127|0.3225:0.3806:0.1841:0.1127	rs2853699;rs52818746;rs61481415;rs2853699|rs2853699;rs52818746;rs61481415;rs2853699	27|2	P51685|Q3KNR3	CCR8_HUMAN|.	G|G	27|2	ENSP00000326432:A27G;ENSP00000390104:A27G|ENSP00000440474:R2G	ENSP00000326432:A27G|.	A|R	+|+	2|1	0|2	CCR8|CCR8	39348906|39348906	0.000000|0.000000	0.05858|0.05858	0.001000|0.001000	0.08648|0.08648	0.012000|0.012000	0.07955|0.07955	-1.350000|-1.350000	0.02624|0.02624	-0.487000|-0.487000	0.06735|0.06735	-1.325000|-1.325000	0.01285|0.01285	GCG|CGG	C|0.791;G|0.209	0.209	strong		0.478	CCR8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254058.2	NM_005201	
TNFRSF6B	8771	hgsc.bcm.edu	37	20	62328267	62328267	+	Silent	SNP	C	C	T	rs2257440	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:62328267C>T	ENST00000369996.1	+	1	247	c.147C>T	c.(145-147)tgC>tgT	p.C49C	ARFRP1_ENST00000485858.1_5'Flank|RTEL1_ENST00000318100.4_Missense_Mutation_p.R1352C|RTEL1-TNFRSF6B_ENST00000482936.1_Missense_Mutation_p.R1352C	NM_003823.3	NP_003814.1	O95407	TNF6B_HUMAN	tumor necrosis factor receptor superfamily, member 6b, decoy	49					apoptotic process (GO:0006915)|negative regulation of apoptotic process (GO:0043066)	extracellular space (GO:0005615)	receptor activity (GO:0004872)			central_nervous_system(1)|lung(2)|skin(1)	4	all_cancers(38;4.66e-12)|all_epithelial(29;2.56e-13)|Lung NSC(23;1.06e-08)|all_lung(23;3.34e-08)		Epithelial(9;1.78e-08)|all cancers(9;7.89e-08)|OV - Ovarian serous cystadenocarcinoma(5;0.00504)			GGCTGGTGTGCGCCCAGTGCC	0.711													C|||	1321	0.263778	0.0242	0.2637	5008	,	,		10794	0.6478		0.2038	False		,,,				2504	0.2536				p.C49C		Atlas-SNP	.											.	TNFRSF6B	22	.	0			c.C147T						PASS	.	C		298,4042		14,270,1886	15.0	18.0	17.0		147	-8.1	0.0	20	dbSNP_100	17	1903,6643		226,1451,2596	no	coding-synonymous	TNFRSF6B	NM_003823.3		240,1721,4482	TT,TC,CC		22.2677,6.8664,17.0806		49/301	62328267	2201,10685	2170	4273	6443	SO:0001819	synonymous_variant	8771	exon1			GGTGTGCGCCCAG	AF104419	CCDS13532.1	20q13.33	2012-06-27						"""Tumor necrosis factor receptor superfamily"""	11921	protein-coding gene	gene with protein product		603361				9872321, 10318773	Standard	NM_003823		Approved	DcR3, DCR3, TR6, M68	uc002yfz.3	O95407	OTTHUMG00000143724	ENST00000369996.1:c.147C>T	20.37:g.62328267C>T		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	43	24	0.55814	NM_003823		Silent	SNP	ENST00000369996.1	37	CCDS13532.1	623	0.28525641025641024	14	0.028455284552845527	71	0.19613259668508287	371	0.6486013986013986	167	0.22031662269129287	C	9.458	1.092457	0.20471	0.068664	0.222677	ENSG00000258366	ENST00000318100	D	0.83335	-1.71	4.06	-8.12	0.01078	.	4.628610	0.00921	N	0.002584	T	0.00012	0.0000	.	.	.	0.33623	P	0.39491299999999996	.	.	.	.	.	.	T	0.49072	-0.8977	6	0.72032	D	0.01	-21.338	18.8802	0.92353	0.0:0.8572:0.0:0.1428	rs2257440;rs3787087	.	.	.	C	1352	ENSP00000322287:R1352C	ENSP00000322287:R1352C	R	+	1	0	AL353715.1	61798711	0.000000	0.05858	0.000000	0.03702	0.152000	0.21847	-1.308000	0.02730	-1.993000	0.00974	-1.327000	0.01280	CGC	C|0.779;T|0.221	0.221	strong		0.711	TNFRSF6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080182.1		
PLRG1	5356	hgsc.bcm.edu	37	4	155459194	155459194	+	Silent	SNP	A	A	T	rs7668818	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:155459194A>T	ENST00000499023.2	-	13	1344	c.1218T>A	c.(1216-1218)atT>atA	p.I406I	PLRG1_ENST00000302078.5_Silent_p.I397I|PLRG1_ENST00000393905.2_Silent_p.I406I	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	257	1	0.00389105		WXS	Illumina HiSeq	Phase_I	188	188	1	NM_002669	B3KMK4|Q3KQY5|Q8WUD8	Silent	SNP	ENST00000499023.2	37	CCDS34083.1																																																																																			A|0.748;T|0.252	0.252	strong		0.303	PLRG1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364824.1	NM_002669	
FMO2	2327	hgsc.bcm.edu	37	1	171168584	171168584	+	Missense_Mutation	SNP	C	C	T	rs386636736|rs2020862	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:171168584C>T	ENST00000209929.7	+	5	742	c.584C>T	c.(583-585)tCa>tTa	p.S195L	RP1-127D3.4_ENST00000445290.1_RNA|FMO2_ENST00000441535.1_Missense_Mutation_p.S195L|FMO2_ENST00000529935.1_Intron|RP1-127D3.4_ENST00000445909.1_RNA|RP1-127D3.4_ENST00000422841.1_RNA			P31512	FMO4_HUMAN	flavin containing monooxygenase 2 (non-functional)	195					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)	p.S195L(1)		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)					ATGGGAAACTCAGGCTCAGAT	0.488													C|||	2368	0.472843	0.5265	0.4827	5008	,	,		19421	0.5456		0.2962	False		,,,				2504	0.5				p.S195L		Atlas-SNP	.											FMO2,NS,carcinoma,-1,2	FMO2	66	2	1	Substitution - Missense(1)	stomach(1)	c.C584T	GRCh37	CM033900	FMO2	M	rs2020862	PASS	.	C	LEU/SER	2174,2232	585.1+/-386.2	561,1052,590	134.0	140.0	138.0		584	6.2	1.0	1	dbSNP_98	138	2753,5847	439.1+/-359.1	448,1857,1995	yes	missense	FMO2	NM_001460.2	145	1009,2909,2585	TT,TC,CC		32.0116,49.3418,37.8825	probably-damaging	195/472	171168584	4927,8079	2203	4300	6503	SO:0001583	missense	2327	exon5			GAAACTCAGGCTC	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.584C>T	1.37:g.171168584C>T	ENSP00000209929:p.Ser195Leu	Somatic	198	0	0		WXS	Illumina HiSeq	Phase_I	166	86	0.518072	NM_001460	Q53XR0	Missense_Mutation	SNP	ENST00000209929.7	37	CCDS1293.1	788	0.3608058608058608	190	0.3861788617886179	136	0.3756906077348066	272	0.4755244755244755	190	0.25065963060686014	C	22.4	4.283324	0.80803	0.493418	0.320116	ENSG00000094963	ENST00000209929;ENST00000441535	T;T	0.60548	0.18;0.18	6.17	6.17	0.99709	.	0.056199	0.85682	D	0.000000	T	0.80824	0.4697	H	0.99689	4.705	0.09310	P	0.9999999445746	B	0.29232	0.238	B	0.41764	0.366	T	0.82810	-0.0273	9	0.87932	D	0	-3.8921	19.6509	0.95805	0.0:1.0:0.0:0.0	rs2020862;rs2266706;rs58871762;rs2020862	195	Q99518	FMO2_HUMAN	L	195	ENSP00000209929:S195L;ENSP00000405905:S195L	ENSP00000209929:S195L	S	+	2	0	FMO2	169435208	1.000000	0.71417	0.969000	0.41365	0.124000	0.20399	5.980000	0.70516	2.941000	0.99782	0.655000	0.94253	TCA	C|0.606;T|0.394	0.394	strong		0.488	FMO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086216.2	NM_001460	
C6orf15	29113	hgsc.bcm.edu	37	6	31080016	31080016	+	Missense_Mutation	SNP	C	C	G	rs2233974	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:31080016C>G	ENST00000259870.3	-	2	123	c.120G>C	c.(118-120)ttG>ttC	p.L40F	PSORS1C1_ENST00000259881.9_5'Flank	NM_014070.2	NP_054789.2	Q6UXA7	CF015_HUMAN	chromosome 6 open reading frame 15	40			L -> F (in dbSNP:rs2233974). {ECO:0000269|PubMed:12975309, ECO:0000269|PubMed:14574404}.		extracellular matrix organization (GO:0030198)	interstitial matrix (GO:0005614)	heparin binding (GO:0008201)|hyaluronic acid binding (GO:0005540)			endometrium(3)|large_intestine(2)|lung(9)|prostate(1)|skin(1)|stomach(1)	17						AGTTGGTCCCCAAGTTTTGGG	0.557													C|||	527	0.105232	0.1218	0.1066	5008	,	,		19205	0.0466		0.1461	False		,,,				2504	0.1002				p.L40F		Atlas-SNP	.											.	C6orf15	29	.	0			c.G120C						PASS	.	C	PHE/LEU	569,3753		41,487,1633	127.0	149.0	142.0		120	2.7	0.0	6	dbSNP_98	142	1529,6989		138,1253,2868	yes	missense	C6orf15	NM_014070.2	22	179,1740,4501	GG,GC,CC		17.9502,13.1652,16.3396	possibly-damaging	40/326	31080016	2098,10742	2161	4259	6420	SO:0001583	missense	29113	exon2			GGTCCCCAAGTTT	AB031481	CCDS4693.1	6p21	2011-12-12			ENSG00000204542	ENSG00000204542			13927	protein-coding gene	gene with protein product		611401					Standard	NM_014070		Approved	STG	uc003nsk.1	Q6UXA7	OTTHUMG00000031111	ENST00000259870.3:c.120G>C	6.37:g.31080016C>G	ENSP00000259870:p.Leu40Phe	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	68	68	1	NM_014070	B0S7V8|Q0EFA6|Q2L6G7|Q5SQ81|Q86Z05|Q9UIG3	Missense_Mutation	SNP	ENST00000259870.3	37	CCDS4693.1	246	0.11263736263736264	71	0.1443089430894309	45	0.12430939226519337	19	0.033216783216783216	111	0.14643799472295516	C	13.84	2.357554	0.41801	0.131652	0.179502	ENSG00000204542	ENST00000259870	T	0.07114	3.22	4.44	2.65	0.31530	.	1.477720	0.05072	N	0.481790	T	0.08626	0.0214	L	0.51422	1.61	0.80722	P	0.0	D	0.61697	0.99	P	0.59487	0.858	T	0.14671	-1.0464	9	0.44086	T	0.13	.	6.7339	0.23399	0.0:0.7832:0.0:0.2168	rs2233974;rs52811515;rs2233974	40	Q6UXA7	CF015_HUMAN	F	40	ENSP00000259870:L40F	ENSP00000259870:L40F	L	-	3	2	C6orf15	31187995	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.062000	0.11674	0.492000	0.27815	-0.275000	0.10095	TTG	C|0.832;G|0.168	0.168	strong		0.557	C6orf15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076184.2	NM_014070	
KIAA1755	85449	hgsc.bcm.edu	37	20	36870122	36870122	+	Silent	SNP	T	T	G	rs1205435	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:36870122T>G	ENST00000279024.4	-	3	682	c.411A>C	c.(409-411)ccA>ccC	p.P137P		NM_001029864.1	NP_001025035.1	Q5JYT7	K1755_HUMAN	KIAA1755	137										breast(2)|endometrium(3)|kidney(1)|large_intestine(5)|lung(31)|ovary(5)|pancreas(2)|skin(4)|stomach(1)	54		Myeloproliferative disorder(115;0.00874)				AGGCTGGCTCTGGAACAGGCT	0.517													G|||	1326	0.264776	0.2027	0.2262	5008	,	,		19761	0.2728		0.3191	False		,,,				2504	0.3119				p.P137P		Atlas-SNP	.											.	KIAA1755	145	.	0			c.A411C						PASS	.	G		910,3496	645.6+/-398.2	148,614,1441	102.0	101.0	102.0		411	-11.7	0.0	20	dbSNP_87	102	2807,5793	656.2+/-401.3	517,1773,2010	no	coding-synonymous	KIAA1755	NM_001029864.1		665,2387,3451	GG,GT,TT		32.6395,20.6537,28.5791		137/1201	36870122	3717,9289	2203	4300	6503	SO:0001819	synonymous_variant	85449	exon3			TGGCTCTGGAACA	AB051542	CCDS33467.1	20q11.23	2007-12-07			ENSG00000149633	ENSG00000149633			29372	protein-coding gene	gene with protein product						11214970	Standard	NM_001029864		Approved	RP5-1054A22.3	uc002xhy.1	Q5JYT7	OTTHUMG00000032436	ENST00000279024.4:c.411A>C	20.37:g.36870122T>G		Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	135	66	0.488889	NM_001029864	Q9C0A8	Silent	SNP	ENST00000279024.4	37	CCDS33467.1																																																																																			T|0.674;G|0.319;A|0.007	0.319	strong		0.517	KIAA1755-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079144.3	NM_001029864	
COG5	10466	hgsc.bcm.edu	37	7	106897237	106897237	+	Intron	SNP	A	A	C	rs17349904	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:106897237A>C	ENST00000347053.3	-	15	1830				COG5_ENST00000297135.3_Silent_p.V594V|COG5_ENST00000393603.2_Silent_p.V594V	NM_181733.2	NP_859422.2	Q9UP83	COG5_HUMAN	component of oligomeric golgi complex 5						intra-Golgi vesicle-mediated transport (GO:0006891)|protein transport (GO:0015031)	Golgi apparatus (GO:0005794)|Golgi transport complex (GO:0017119)|membrane (GO:0016020)				breast(3)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(17)|ovary(2)|skin(4)|stomach(1)	40						GACTGGAAACAACCTAGAACA	0.338													A|||	650	0.129792	0.0136	0.121	5008	,	,		16049	0.1587		0.2028	False		,,,				2504	0.1881				p.V594V		Atlas-SNP	.											.	COG5	78	.	0			c.T1782G						PASS	.	A	,,	220,4186	131.0+/-167.6	6,208,1989	78.0	78.0	78.0		1782,1782,	-3.4	1.0	7	dbSNP_123	78	1847,6753	326.9+/-317.6	207,1433,2660	no	coding-synonymous,coding-synonymous,intron	COG5	NM_001161520.1,NM_006348.3,NM_181733.2	,,	213,1641,4649	CC,CA,AA		21.4767,4.9932,15.8927	,,	594/824,594/861,	106897237	2067,10939	2203	4300	6503	SO:0001627	intron_variant	10466	exon16			GGAAACAACCTAG	AF058718	CCDS5742.1, CCDS5743.1, CCDS55152.1	7q31	2010-06-24	2001-12-07	2002-05-10	ENSG00000164597	ENSG00000164597		"""Components of oligomeric golgi complex"""	14857	protein-coding gene	gene with protein product		606821	"""golgi transport complex 1 (90 kDa subunit)"""	GOLTC1		9792665, 11980916	Standard	NM_006348		Approved	GTC90	uc003vec.2	Q9UP83	OTTHUMG00000023895	ENST00000347053.3:c.1779+1480T>G	7.37:g.106897237A>C		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	46	23	0.5	NM_006348	A4D0R6|A4D0R7|O14555|O95008|Q6NUL5	Silent	SNP	ENST00000347053.3	37	CCDS5743.1																																																																																			A|0.851;C|0.149	0.149	strong		0.338	COG5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000060216.4		
ABCA7	10347	hgsc.bcm.edu	37	19	1043748	1043748	+	Missense_Mutation	SNP	A	A	G	rs3752232	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:1043748A>G	ENST00000263094.6	+	10	1186	c.955A>G	c.(955-957)Acc>Gcc	p.T319A	ABCA7_ENST00000435683.2_Missense_Mutation_p.T181A|ABCA7_ENST00000433129.1_Missense_Mutation_p.T319A	NM_019112.3	NP_061985.2	Q8IZY2	ABCA7_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 7	319			T -> A (in dbSNP:rs3752232). {ECO:0000269|PubMed:12111378}.		apolipoprotein A-I-mediated signaling pathway (GO:0038027)|ATP catabolic process (GO:0006200)|cholesterol efflux (GO:0033344)|high-density lipoprotein particle assembly (GO:0034380)|memory (GO:0007613)|negative regulation of amyloid precursor protein biosynthetic process (GO:0042985)|negative regulation of ATPase activity (GO:0032780)|negative regulation of beta-amyloid formation (GO:1902430)|peptide cross-linking (GO:0018149)|phagocytosis (GO:0006909)|phospholipid efflux (GO:0033700)|phospholipid scrambling (GO:0017121)|positive regulation of ATPase activity (GO:0032781)|positive regulation of beta-amyloid clearance (GO:1900223)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of engulfment of apoptotic cell (GO:1901076)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of phagocytosis (GO:0050766)|positive regulation of phospholipid efflux (GO:1902995)|protein localization to nucleus (GO:0034504)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|ATP-binding cassette (ABC) transporter complex (GO:0043190)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|phagocytic cup (GO:0001891)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	apolipoprotein A-I receptor activity (GO:0034188)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|phospholipid transporter activity (GO:0005548)|transporter activity (GO:0005215)			NS(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(7)|lung(22)|ovary(1)|pancreas(7)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	65		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CGAGGAGCTCACCCTGCTGAG	0.637													G|||	565	0.112819	0.2708	0.0288	5008	,	,		10969	0.0923		0.0358	False		,,,				2504	0.0593				p.T319A		Atlas-SNP	.											.	ABCA7	174	.	0			c.A955G						PASS	.	G	ALA/THR	1119,3287	716.8+/-408.6	139,841,1223	137.0	133.0	135.0		955	3.4	1.0	19	dbSNP_107	135	351,8249	803.1+/-407.3	4,343,3953	yes	missense	ABCA7	NM_019112.3	58	143,1184,5176	GG,GA,AA		4.0814,25.3972,11.3025	benign	319/2147	1043748	1470,11536	2203	4300	6503	SO:0001583	missense	10347	exon10			GAGCTCACCCTGC	AF328787	CCDS12055.1	19p13.3	2012-03-14			ENSG00000064687	ENSG00000064687		"""ATP binding cassette transporters / subfamily A"""	37	protein-coding gene	gene with protein product		605414					Standard	NM_019112		Approved	ABCX	uc002lqw.4	Q8IZY2	OTTHUMG00000167547	ENST00000263094.6:c.955A>G	19.37:g.1043748A>G	ENSP00000263094:p.Thr319Ala	Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	25	16	0.64	NM_019112	Q96S58|Q9BZC4|Q9NR73|Q9UKP8	Missense_Mutation	SNP	ENST00000263094.6	37	CCDS12055.1	221	0.10119047619047619	136	0.2764227642276423	11	0.03038674033149171	47	0.08216783216783216	27	0.03562005277044855	G	0.174	-1.068483	0.01934	0.253972	0.040814	ENSG00000064687	ENST00000263094;ENST00000433129	D;D	0.85013	-1.93;-1.93	4.47	3.42	0.39159	.	.	.	.	.	T	0.00012	0.0000	N	0.00368	-1.59	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.13629	-1.0502	8	0.02654	T	1	.	7.098	0.25321	0.2969:0.0:0.7031:0.0	rs3752232;rs57150329;rs3752232	181;319	Q8IZY2-2;Q8IZY2	.;ABCA7_HUMAN	A	319	ENSP00000263094:T319A;ENSP00000414062:T319A	ENSP00000263094:T319A	T	+	1	0	ABCA7	994748	0.911000	0.30947	0.990000	0.47175	0.084000	0.17831	1.483000	0.35497	0.887000	0.36136	-0.374000	0.07098	ACC	A|0.884;G|0.116	0.116	strong		0.637	ABCA7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000394993.1	NM_019112	
ZNF713	349075	hgsc.bcm.edu	37	7	56007576	56007576	+	Silent	SNP	C	C	T	rs34016595	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:56007576C>T	ENST00000429591.2	+	4	1208	c.1170C>T	c.(1168-1170)tgC>tgT	p.C390C	MRPS17_ENST00000426595.1_Intron	NM_182633.1	NP_872439.1	Q8N859	ZN713_HUMAN	zinc finger protein 713	390					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(10)|ovary(2)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	25	Breast(14;0.214)		Lung(13;0.00024)|LUSC - Lung squamous cell carcinoma(13;0.00099)			GTAATGAATGCGGGAAAGCCT	0.413													C|||	1723	0.34405	0.4009	0.3256	5008	,	,		16521	0.2976		0.2753	False		,,,				2504	0.3988				p.C390C		Atlas-SNP	.											.	ZNF713	47	.	0			c.C1170T						PASS	.	C		1687,2719	504.6+/-365.9	316,1055,832	50.0	52.0	51.0		1170	2.3	1.0	7	dbSNP_126	51	2232,6368	378.3+/-338.9	279,1674,2347	no	coding-synonymous	ZNF713	NM_182633.1		595,2729,3179	TT,TC,CC		25.9535,38.2887,30.1322		390/431	56007576	3919,9087	2203	4300	6503	SO:0001819	synonymous_variant	349075	exon4			TGAATGCGGGAAA	AK097282	CCDS34639.1	7p11.2	2013-01-08			ENSG00000178665	ENSG00000178665		"""Zinc fingers, C2H2-type"", ""-"""	22043	protein-coding gene	gene with protein product							Standard	NM_182633		Approved	FLJ39963	uc003trc.1	Q8N859	OTTHUMG00000156175	ENST00000429591.2:c.1170C>T	7.37:g.56007576C>T		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	47	24	0.510638	NM_182633		Silent	SNP	ENST00000429591.2	37	CCDS34639.1																																																																																			C|0.694;T|0.306	0.306	strong		0.413	ZNF713-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343297.1	NM_182633	
F13B	2165	hgsc.bcm.edu	37	1	197009798	197009798	+	Silent	SNP	A	A	G	rs5998	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:197009798A>G	ENST00000367412.1	-	11	1849	c.1806T>C	c.(1804-1806)aaT>aaC	p.N602N	F13B_ENST00000490002.1_5'UTR	NM_001994.2	NP_001985.2	P05160	F13B_HUMAN	coagulation factor XIII, B polypeptide	602	Sushi 10. {ECO:0000255|PROSITE- ProRule:PRU00302}.				blood coagulation (GO:0007596)	extracellular region (GO:0005576)				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(5)|liver(1)|lung(40)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)	66						TGTGTGGTCTATTGTCAAAAT	0.294													A|||	2629	0.52496	0.1921	0.6455	5008	,	,		16714	0.8194		0.501	False		,,,				2504	0.6104				p.N602N		Atlas-SNP	.											.	F13B	137	.	0			c.T1806C						PASS	.	A		1010,3390	369.3+/-319.0	137,736,1327	59.0	56.0	57.0		1806	-4.4	0.9	1	dbSNP_52	57	4038,4552	551.5+/-385.9	967,2104,1224	no	coding-synonymous	F13B	NM_001994.2		1104,2840,2551	GG,GA,AA		47.0081,22.9545,38.8607		602/662	197009798	5048,7942	2200	4295	6495	SO:0001819	synonymous_variant	2165	exon11			TGGTCTATTGTCA	M14057	CCDS1388.1	1q31-q32.1	2012-10-02			ENSG00000143278	ENSG00000143278			3534	protein-coding gene	gene with protein product		134580				2339067, 2271707	Standard	NM_001994		Approved	FXIIIB	uc001gtt.1	P05160	OTTHUMG00000036519	ENST00000367412.1:c.1806T>C	1.37:g.197009798A>G		Somatic	296	1	0.00337838		WXS	Illumina HiSeq	Phase_I	243	240	0.987654	NM_001994	A8K3E5|Q5VYL5	Silent	SNP	ENST00000367412.1	37	CCDS1388.1																																																																																			A|0.547;G|0.453	0.453	strong		0.294	F13B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088821.2	NM_001994	
GAS2L1	10634	hgsc.bcm.edu	37	22	29704125	29704125	+	Silent	SNP	C	C	T	rs11090564	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:29704125C>T	ENST00000406549.3	+	2	180	c.30C>T	c.(28-30)ggC>ggT	p.G10G	GAS2L1_ENST00000407647.2_Silent_p.G10G|GAS2L1_ENST00000360113.2_Silent_p.G10G|GAS2L1_ENST00000403764.1_Silent_p.G10G|GAS2L1_ENST00000341313.6_Silent_p.G10G|GAS2L1_ENST00000471961.1_Silent_p.G10G|GAS2L1_ENST00000407854.1_Silent_p.G10G	NM_001278730.1	NP_001265659.1	Q99501	GA2L1_HUMAN	growth arrest-specific 2 like 1	10					cell cycle arrest (GO:0007050)|cellular response to starvation (GO:0009267)|cellular response to thyroid hormone stimulus (GO:0097067)|microtubule bundle formation (GO:0001578)|negative regulation of cell growth (GO:0030308)|negative regulation of erythrocyte differentiation (GO:0045647)|negative regulation of gene expression (GO:0010629)|negative regulation of microtubule depolymerization (GO:0007026)|regulation of cell cycle (GO:0051726)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	cytoskeletal adaptor activity (GO:0008093)|microtubule binding (GO:0008017)|thyroid hormone receptor binding (GO:0046966)			endometrium(2)|lung(2)|prostate(1)	5						GCATCGCGGGCTCGGCGGCCA	0.662													C|||	1639	0.327276	0.1808	0.5159	5008	,	,		12397	0.2847		0.3588	False		,,,				2504	0.4029				p.G10G		Atlas-SNP	.											GAS2L1_ENST00000333679,NS,carcinoma,0,4	GAS2L1	54	4	0			c.C30T						PASS	.	C	,,	892,3496		106,680,1408	17.0	17.0	17.0		30,30,30	3.3	1.0	22	dbSNP_120	17	3271,5303		656,1959,1672	no	coding-synonymous,coding-synonymous,coding-synonymous	GAS2L1	NM_006478.3,NM_152236.1,NM_152237.1	,,	762,2639,3080	TT,TC,CC		38.1502,20.3282,32.117	,,	10/682,10/682,10/338	29704125	4163,8799	2194	4287	6481	SO:0001819	synonymous_variant	10634	exon2			CGCGGGCTCGGCG	BC001782	CCDS63438.1, CCDS74840.1	22q12.2	2008-06-11			ENSG00000185340	ENSG00000185340			16955	protein-coding gene	gene with protein product		602128				8975699, 12584248, 1607387	Standard	NM_001278730		Approved	GAR22	uc003afc.1	Q99501	OTTHUMG00000151108	ENST00000406549.3:c.30C>T	22.37:g.29704125C>T		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	45	18	0.4	NM_152237	B5MCR7|Q53EN7|Q92640|Q9BUY9	Silent	SNP	ENST00000406549.3	37																																																																																				C|0.704;T|0.296	0.296	strong		0.662	GAS2L1-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000321365.1	NM_006478	
AHNAK2	113146	hgsc.bcm.edu	37	14	105417768	105417768	+	Silent	SNP	C	C	A	rs2396458	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:105417768C>A	ENST00000333244.5	-	7	4139	c.4020G>T	c.(4018-4020)gtG>gtT	p.V1340V	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	1340						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)			CTGGGGCAGACACCCCGAACG	0.612													.|||	80	0.0159744	0.0605	0.0	5008	,	,		13723	0.0		0.0	False		,,,				2504	0.0				p.V1340V		Atlas-SNP	.											.	AHNAK2	719	.	0			c.G4020T						PASS	.	C		912,2740		433,46,1347	129.0	120.0	124.0		4020	-8.3	0.0	14	dbSNP_100	124	227,6321		100,27,3147	no	coding-synonymous	AHNAK2	NM_138420.2		533,73,4494	AA,AC,CC		3.4667,24.9726,11.1667		1340/5796	105417768	1139,9061	1826	3274	5100	SO:0001819	synonymous_variant	113146	exon7			GGCAGACACCCCG	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.4020G>T	14.37:g.105417768C>A		Somatic	0	0	.		WXS	Illumina HiSeq	Phase_I	63	62	0.984127	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Silent	SNP	ENST00000333244.5	37	CCDS45177.1																																																																																			C|0.809;A|0.191	0.191	strong		0.612	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
DLG4	1742	hgsc.bcm.edu	37	17	7099811	7099811	+	Silent	SNP	G	G	A	rs17203281	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	135	0	0		WXS	Illumina HiSeq	Phase_I	94	46	0.489362	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	
GIPC2	54810	hgsc.bcm.edu	37	1	78585086	78585086	+	Missense_Mutation	SNP	T	T	C	rs540742	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:78585086T>C	ENST00000370759.3	+	4	810	c.617T>C	c.(616-618)cTg>cCg	p.L206P		NM_017655.4	NP_060125.4	Q8TF65	GIPC2_HUMAN	GIPC PDZ domain containing family, member 2	206			L -> P (in dbSNP:rs540742). {ECO:0000269|PubMed:15489334}.			cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)				endometrium(3)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|skin(2)	20						GAAATAGAGCTGAGGTCAAAG	0.413													C|||	1538	0.307109	0.2186	0.1758	5008	,	,		18381	0.6637		0.2266	False		,,,				2504	0.2352				p.L206P		Atlas-SNP	.											.	GIPC2	37	.	0			c.T617C						PASS	.	C	PRO/LEU	990,3416	731.6+/-410.3	129,732,1342	90.0	89.0	90.0		617	4.7	0.0	1	dbSNP_83	90	1878,6722	726.7+/-406.6	197,1484,2619	yes	missense	GIPC2	NM_017655.4	98	326,2216,3961	CC,CT,TT		21.8372,22.4694,22.0514	benign	206/316	78585086	2868,10138	2203	4300	6503	SO:0001583	missense	54810	exon4			TAGAGCTGAGGTC	AB073737	CCDS685.1	1p31.1	2010-05-28			ENSG00000137960	ENSG00000137960			18177	protein-coding gene	gene with protein product	"""semaphorin cytoplasmic domain associated protein 2"""					11836570	Standard	NM_017655		Approved	FLJ20075, SEMCAP-2	uc001dik.3	Q8TF65	OTTHUMG00000041145	ENST00000370759.3:c.617T>C	1.37:g.78585086T>C	ENSP00000359795:p.Leu206Pro	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	73	72	0.986301	NM_017655	Q8IYD3|Q9NXS7	Missense_Mutation	SNP	ENST00000370759.3	37	CCDS685.1	737	0.3374542124542125	127	0.258130081300813	67	0.1850828729281768	373	0.6520979020979021	170	0.22427440633245382	C	0.003	-2.457311	0.00173	0.224694	0.218372	ENSG00000137960	ENST00000370759	T	0.80566	-1.39	5.59	4.68	0.58851	PDZ/DHR/GLGF (1);	0.098868	0.64402	N	0.000001	T	0.13114	0.0318	N	0.00024	-2.69	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.17077	-1.0381	9	0.02654	T	1	-17.525	9.1027	0.36678	0.0:0.8313:0.0:0.1687	rs540742;rs3748650;rs17846165;rs17859175;rs52792767;rs57550733;rs540742	206	Q8TF65	GIPC2_HUMAN	P	206	ENSP00000359795:L206P	ENSP00000359795:L206P	L	+	2	0	GIPC2	78357674	0.535000	0.26370	0.007000	0.13788	0.001000	0.01503	2.060000	0.41394	0.867000	0.35654	-0.733000	0.03571	CTG	A|0.004;C|0.271	0.271	strong		0.413	GIPC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098629.1	NM_017655	
SNX13	23161	hgsc.bcm.edu	37	7	17879553	17879553	+	Silent	SNP	G	G	A	rs12720473	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:17879553G>A	ENST00000409389.1	-	13	1408	c.1236C>T	c.(1234-1236)acC>acT	p.T412T	SNX13_ENST00000428135.3_Silent_p.T412T			Q9Y5W8	SNX13_HUMAN	sorting nexin 13	412	RGS. {ECO:0000255|PROSITE- ProRule:PRU00171}.				intracellular protein transport (GO:0006886)|positive regulation of GTPase activity (GO:0043547)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	early endosome (GO:0005769)|membrane (GO:0016020)	phosphatidylinositol binding (GO:0035091)			breast(1)|central_nervous_system(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(10)|lung(13)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	38	Lung NSC(10;0.0261)|all_lung(11;0.0521)					GCTGTTGGGCGGTAACCCGGT	0.398													G|||	107	0.0213658	0.0038	0.0403	5008	,	,		16659	0.0		0.0686	False		,,,				2504	0.0051				p.T412T		Atlas-SNP	.											.	SNX13	113	.	0			c.C1236T						PASS	.	G		68,3700		2,64,1818	123.0	114.0	117.0		1236	4.1	1.0	7	dbSNP_126	117	626,7590		29,568,3511	no	coding-synonymous	SNX13	NM_015132.4		31,632,5329	AA,AG,GG		7.6193,1.8047,5.7911		412/958	17879553	694,11290	1884	4108	5992	SO:0001819	synonymous_variant	23161	exon13			TTGGGCGGTAACC	AF420470	CCDS47551.1	7p21.1	2008-03-11			ENSG00000071189	ENSG00000071189		"""Sorting nexins"""	21335	protein-coding gene	gene with protein product		606589				11485546, 11729322	Standard	NM_015132		Approved	RGS-PX1, KIAA0713	uc003stv.3	Q9Y5W8	OTTHUMG00000152730	ENST00000409389.1:c.1236C>T	7.37:g.17879553G>A		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	92	15	0.163043	NM_015132	B2RCI9|O94821|Q8WVZ2|Q8WXH8	Silent	SNP	ENST00000409389.1	37																																																																																				G|0.957;A|0.043	0.043	strong		0.398	SNX13-002	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000327608.1	NM_015132	
TBCK	93627	hgsc.bcm.edu	37	4	107133919	107133919	+	Silent	SNP	A	A	G	rs17036613	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:107133919A>G	ENST00000273980.5	-	21	2295	c.1848T>C	c.(1846-1848)ggT>ggC	p.G616G	TBCK_ENST00000394706.3_Silent_p.G577G|TBCK_ENST00000394708.2_Silent_p.G616G|TBCK_ENST00000514689.1_5'UTR|TBCK_ENST00000432496.2_Silent_p.G616G|TBCK_ENST00000361687.4_Silent_p.G553G					TBC1 domain containing kinase											NS(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(9)|ovary(1)|pancreas(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(1)	25						CTGGAATGAAACCAATCTCAT	0.323													G|||	1067	0.213059	0.2829	0.134	5008	,	,		17461	0.1468		0.1799	False		,,,				2504	0.2771				p.G616G		Atlas-SNP	.											TBCK,NS,carcinoma,0,2	TBCK	89	2	0			c.T1848C						PASS	.	G	,,,	1198,3208	708.8+/-407.7	164,870,1169	147.0	151.0	150.0		1848,1848,1731,1659	2.2	1.0	4	dbSNP_123	150	1492,7104	747.9+/-407.3	141,1210,2947	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TBCK	NM_001163435.1,NM_001163436.1,NM_001163437.1,NM_033115.3	,,,	305,2080,4116	GG,GA,AA		17.3569,27.1902,20.6891	,,,	616/894,616/894,577/855,553/831	107133919	2690,10312	2203	4298	6501	SO:0001819	synonymous_variant	93627	exon20			AATGAAACCAATC		CCDS3673.1, CCDS54788.1, CCDS54789.1	4q24	2014-09-17			ENSG00000145348	ENSG00000145348			28261	protein-coding gene	gene with protein product						12471243	Standard	XR_427553		Approved	MGC16169, HSPC302	uc010ilv.2	Q8TEA7	OTTHUMG00000131214	ENST00000273980.5:c.1848T>C	4.37:g.107133919A>G		Somatic	412	0	0		WXS	Illumina HiSeq	Phase_I	293	138	0.47099	NM_001163436		Silent	SNP	ENST00000273980.5	37	CCDS54788.1																																																																																			A|0.802;G|0.198	0.198	strong		0.323	TBCK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253953.4	NM_033115	
ENDOG	2021	hgsc.bcm.edu	37	9	131584732	131584732	+	Missense_Mutation	SNP	C	C	T	rs61737987	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:131584732C>T	ENST00000372642.4	+	3	948	c.737C>T	c.(736-738)aCc>aTc	p.T246I	C9orf114_ENST00000361256.5_3'UTR	NM_004435.2	NP_004426.2	Q14249	NUCG_HUMAN	endonuclease G	246					apoptotic DNA fragmentation (GO:0006309)|DNA recombination (GO:0006310)|in utero embryonic development (GO:0001701)|positive regulation of apoptotic process (GO:0043065)|response to antibiotic (GO:0046677)|response to tumor necrosis factor (GO:0034612)	mitochondrion (GO:0005739)	endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)|nuclease activity (GO:0004518)|nucleic acid binding (GO:0003676)										GAGCTCCGCACCTACGTGATG	0.592													C|||	5	0.000998403	0.0	0.0014	5008	,	,		21151	0.0		0.001	False		,,,				2504	0.0031				p.T246I		Atlas-SNP	.											.	ENDOG	8	.	0			c.C737T						PASS	.	C	ILE/THR,	3,4401		0,3,2199	72.0	63.0	66.0		737,	5.6	1.0	9	dbSNP_129	66	19,8581		0,19,4281	yes	missense,utr-3	ENDOG,C9orf114	NM_004435.2,NM_016390.2	89,	0,22,6480	TT,TC,CC		0.2209,0.0681,0.1692	benign,	246/298,	131584732	22,12982	2202	4300	6502	SO:0001583	missense	2021	exon3			TCCGCACCTACGT	X79444	CCDS6912.1	9q34.1	2008-06-04			ENSG00000167136	ENSG00000167136			3346	protein-coding gene	gene with protein product		600440				7789991	Standard	NM_004435		Approved		uc004bwc.3	Q14249	OTTHUMG00000020763	ENST00000372642.4:c.737C>T	9.37:g.131584732C>T	ENSP00000361725:p.Thr246Ile	Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	139	71	0.510791	NM_004435	Q5T281|Q9BSP2	Missense_Mutation	SNP	ENST00000372642.4	37	CCDS6912.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	C	17.73	3.462148	0.63513	6.81E-4	0.002209	ENSG00000167136	ENST00000372642	T	0.29397	1.57	5.63	5.63	0.86233	DNA/RNA non-specific endonuclease (2);Extracellular Endonuclease, subunit A (2);	0.063535	0.64402	D	0.000004	T	0.25344	0.0616	N	0.08118	0	0.80722	D	1	B	0.26002	0.139	B	0.36030	0.216	T	0.22382	-1.0218	10	0.87932	D	0	-0.0021	18.6823	0.91551	0.0:1.0:0.0:0.0	rs61737987	246	Q14249	NUCG_HUMAN	I	246	ENSP00000361725:T246I	ENSP00000361725:T246I	T	+	2	0	ENDOG	130624553	1.000000	0.71417	1.000000	0.80357	0.343000	0.28985	7.227000	0.78070	2.651000	0.90000	0.455000	0.32223	ACC	C|0.998;T|0.002	0.002	strong		0.592	ENDOG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054505.1	NM_004435	
CENPU	79682	hgsc.bcm.edu	37	4	185637699	185637699	+	Missense_Mutation	SNP	A	A	G	rs6552804	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:185637699A>G	ENST00000281453.5	-	6	540	c.470T>C	c.(469-471)aTa>aCa	p.I157T	MLF1IP_ENST00000541971.1_Missense_Mutation_p.I157T|MLF1IP_ENST00000506535.1_5'Flank	NM_024629.3	NP_078905.2														endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|stomach(1)	13		all_lung(41;7.57e-14)|Lung NSC(41;1.81e-13)|Hepatocellular(41;0.000519)|Colorectal(36;0.00172)|Renal(120;0.00988)|Prostate(90;0.0235)|all_neural(102;0.0299)|all_hematologic(60;0.0592)|Medulloblastoma(177;0.146)		all cancers(43;7.83e-28)|Epithelial(43;2.56e-24)|OV - Ovarian serous cystadenocarcinoma(60;4.5e-11)|Colorectal(24;3.27e-06)|STAD - Stomach adenocarcinoma(60;2.66e-05)|GBM - Glioblastoma multiforme(59;3.16e-05)|BRCA - Breast invasive adenocarcinoma(30;0.000252)|COAD - Colon adenocarcinoma(29;0.000512)|LUSC - Lung squamous cell carcinoma(40;0.01)|READ - Rectum adenocarcinoma(43;0.0419)		TTGTGTACTTATTTTCTCTGC	0.418													A|||	724	0.144569	0.295	0.1354	5008	,	,		16847	0.001		0.1481	False		,,,				2504	0.092				p.I157T		Atlas-SNP	.											.	MLF1IP	33	.	0			c.T470C						PASS	.	A	THR/ILE	1188,3218	416.1+/-337.4	159,870,1174	146.0	130.0	136.0		470	-7.8	0.0	4	dbSNP_116	136	1407,7193	271.1+/-289.3	117,1173,3010	yes	missense	MLF1IP	NM_024629.3	89	276,2043,4184	GG,GA,AA		16.3605,26.9632,19.9523	benign	157/419	185637699	2595,10411	2203	4300	6503	SO:0001583	missense	79682	exon6			GTACTTATTTTCT																												ENST00000281453.5:c.470T>C	4.37:g.185637699A>G	ENSP00000281453:p.Ile157Thr	Somatic	302	0	0		WXS	Illumina HiSeq	Phase_I	235	116	0.493617	NM_024629		Missense_Mutation	SNP	ENST00000281453.5	37	CCDS3838.1	307	0.14056776556776557	145	0.29471544715447157	56	0.15469613259668508	0	0.0	106	0.13984168865435356	A	1.405	-0.577006	0.03854	0.269632	0.163605	ENSG00000151725	ENST00000281453;ENST00000541665;ENST00000541971;ENST00000514781	T;T;T	0.22743	1.94;1.94;1.94	3.9	-7.79	0.01218	.	1.516070	0.04345	N	0.354643	T	0.00012	0.0000	N	0.17674	0.51	0.80722	P	0.0	B;B	0.14012	0.0;0.009	B;B	0.15052	0.001;0.012	T	0.37056	-0.9722	9	0.13470	T	0.59	-31.0236	1.544	0.02561	0.3069:0.1148:0.3517:0.2266	rs6552804;rs52802357;rs59579517;rs6552804	157;157	Q09GN1;Q71F23	.;CENPU_HUMAN	T	157;157;157;128	ENSP00000281453:I157T;ENSP00000445862:I157T;ENSP00000423167:I128T	ENSP00000281453:I157T	I	-	2	0	MLF1IP	185874693	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.801000	0.04550	-2.532000	0.00491	-1.773000	0.00660	ATA	A|0.825;G|0.175	0.175	strong		0.418	MLF1IP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000360841.2		
SLC41A1	254428	hgsc.bcm.edu	37	1	205767885	205767885	+	Silent	SNP	G	G	A	rs708727	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:205767885G>A	ENST00000367137.3	-	6	1770	c.756C>T	c.(754-756)aaC>aaT	p.N252N	SLC41A1_ENST00000468057.1_5'UTR	NM_173854.4	NP_776253.3	Q8IVJ1	S41A1_HUMAN	solute carrier family 41 (magnesium transporter), member 1	252					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cation transmembrane transporter activity (GO:0008324)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(4)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	17	Breast(84;0.0799)		BRCA - Breast invasive adenocarcinoma(75;0.0252)			GTGTGGCCACGTTGTCTGGGT	0.577													G|||	708	0.141374	0.0227	0.2291	5008	,	,		18060	0.003		0.3966	False		,,,				2504	0.1196				p.N252N		Atlas-SNP	.											SLC41A1,colon,carcinoma,0,1	SLC41A1	46	1	0			c.C756T						scavenged	.	G		368,4038	187.4+/-214.1	24,320,1859	103.0	96.0	99.0		756	-2.1	1.0	1	dbSNP_86	99	3492,5108	511.3+/-377.7	710,2072,1518	no	coding-synonymous	SLC41A1	NM_173854.4		734,2392,3377	AA,AG,GG		40.6047,8.3522,29.6786		252/514	205767885	3860,9146	2203	4300	6503	SO:0001819	synonymous_variant	254428	exon6			GGCCACGTTGTCT	AJ514402	CCDS30988.1	1q32.1	2013-07-17	2013-07-17		ENSG00000133065	ENSG00000133065		"""Solute carriers"""	19429	protein-coding gene	gene with protein product		610801				12810078, 18367447	Standard	NM_173854		Approved	MgtE	uc001hdh.1	Q8IVJ1	OTTHUMG00000036000	ENST00000367137.3:c.756C>T	1.37:g.205767885G>A		Somatic	291	2	0.00687285		WXS	Illumina HiSeq	Phase_I	260	135	0.519231	NM_173854	Q63HJ4|Q658Z5|Q659A4|Q6MZK2	Silent	SNP	ENST00000367137.3	37	CCDS30988.1																																																																																			G|0.751;A|0.249	0.249	strong		0.577	SLC41A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087731.1		
ADAM21	8747	hgsc.bcm.edu	37	14	70924693	70924693	+	Silent	SNP	T	T	C	rs45480894	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:70924693T>C	ENST00000603540.1	+	2	735	c.477T>C	c.(475-477)taT>taC	p.Y159Y	RP11-486O13.4_ENST00000556646.1_lincRNA|ADAM21_ENST00000267499.3_Silent_p.Y159Y	NM_003813.3	NP_003804.2	Q9UKJ8	ADA21_HUMAN	ADAM metallopeptidase domain 21	159					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.Y159Y(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)		ACCTGGTTTATAAGATAAACA	0.423													T|||	1281	0.255791	0.3094	0.1326	5008	,	,		18949	0.505		0.1203	False		,,,				2504	0.1534				p.Y159Y		Atlas-SNP	.											ADAM21_ENST00000267499,NS,carcinoma,0,1	ADAM21	181	1	1	Substitution - coding silent(1)	stomach(1)	c.T477C						scavenged	.	T		72,4182		15,42,2070	39.0	48.0	45.0		477	2.6	0.1	14	dbSNP_127	45	13,8573		1,11,4281	no	coding-synonymous	ADAM21	NM_003813.3		16,53,6351	CC,CT,TT		0.1514,1.6925,0.662		159/723	70924693	85,12755	2127	4293	6420	SO:0001819	synonymous_variant	8747	exon2			GGTTTATAAGATA	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.477T>C	14.37:g.70924693T>C		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	60	12	0.2	NM_003813	O43507|Q2VPC6|Q32MR0	Silent	SNP	ENST00000603540.1	37	CCDS9804.1																																																																																			T|0.945;C|0.055	0.055	strong		0.423	ADAM21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413008.3		
PLIN4	729359	hgsc.bcm.edu	37	19	4512409	4512409	+	Silent	SNP	T	T	C	rs10410197	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:4512409T>C	ENST00000301286.3	-	3	1520	c.1521A>G	c.(1519-1521)gtA>gtG	p.V507V		NM_001080400.1	NP_001073869.1	Q96Q06	PLIN4_HUMAN	perilipin 4	507	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						TGGTGGTGTCTACGCCGGTCT	0.612													C|||	475	0.0948482	0.1982	0.0879	5008	,	,		21686	0.002		0.1103	False		,,,				2504	0.0399				p.V507V		Atlas-SNP	.											.	PLIN4	191	.	0			c.A1521G						PASS	.	C		661,3407		69,523,1442	106.0	112.0	110.0		1521	4.4	1.0	19	dbSNP_119	110	897,7463		50,797,3333	no	coding-synonymous	PLIN4	NM_001080400.1		119,1320,4775	CC,CT,TT		10.7297,16.2488,12.5362		507/1358	4512409	1558,10870	2034	4180	6214	SO:0001819	synonymous_variant	729359	exon3			GGTGTCTACGCCG	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.1521A>G	19.37:g.4512409T>C		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	131	66	0.503817	NM_001080400	A6NEI2	Silent	SNP	ENST00000301286.3	37	CCDS45927.1																																																																																			T|0.896;C|0.104	0.104	strong		0.612	PLIN4-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395095.1	XM_170901	
MDN1	23195	hgsc.bcm.edu	37	6	90372574	90372574	+	Missense_Mutation	SNP	A	A	C	rs36040566	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	250	1	0.004		WXS	Illumina HiSeq	Phase_I	213	104	0.488263	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		
ZNF775	285971	hgsc.bcm.edu	37	7	150094853	150094853	+	Silent	SNP	G	G	A	rs7780011	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:150094853G>A	ENST00000329630.5	+	3	1391	c.1284G>A	c.(1282-1284)acG>acA	p.T428T		NM_173680.3	NP_775951.2	Q96BV0	ZN775_HUMAN	zinc finger protein 775	428			T -> A (in dbSNP:rs13225910).		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)|haematopoietic_and_lymphoid_tissue(1)|liver(1)|lung(7)|skin(1)	11	Ovarian(565;0.183)|Melanoma(164;0.226)		OV - Ovarian serous cystadenocarcinoma(82;0.0173)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		CCCGGGACACGCTGTGGGGCC	0.751													G|||	2293	0.457867	0.5514	0.5677	5008	,	,		7268	0.3115		0.4563	False		,,,				2504	0.4059				p.T428T		Atlas-SNP	.											ZNF775,NS,carcinoma,0,1	ZNF775	34	1	0			c.G1284A						PASS	.	G		1766,1896		496,774,561	4.0	5.0	5.0		1284	-3.5	0.0	7	dbSNP_116	5	3387,4247		854,1679,1284	no	coding-synonymous	ZNF775	NM_173680.3		1350,2453,1845	AA,AG,GG		44.3673,48.225,45.6179		428/538	150094853	5153,6143	1831	3817	5648	SO:0001819	synonymous_variant	285971	exon3			GGACACGCTGTGG	BC038111	CCDS43678.1	7q36.1	2013-01-08			ENSG00000196456	ENSG00000196456		"""Zinc fingers, C2H2-type"""	28501	protein-coding gene	gene with protein product						12477932	Standard	NM_173680		Approved	MGC33584	uc003whf.1	Q96BV0	OTTHUMG00000158324	ENST00000329630.5:c.1284G>A	7.37:g.150094853G>A		Somatic	2	0	0		WXS	Illumina HiSeq	Phase_I	10	10	1	NM_173680	Q8IY24	Silent	SNP	ENST00000329630.5	37	CCDS43678.1																																																																																			G|0.551;A|0.449	0.449	strong		0.751	ZNF775-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350679.1	NM_173680	
SLCO4C1	353189	hgsc.bcm.edu	37	5	101592919	101592919	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:101592919C>T	ENST00000310954.6	-	8	1655	c.1369G>A	c.(1369-1371)Gca>Aca	p.A457T		NM_180991.4	NP_851322.3			solute carrier organic anion transporter family, member 4C1											breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(16)|ovary(1)|pancreas(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(5)	50		all_cancers(142;1.86e-08)|all_epithelial(76;5.24e-12)|Prostate(80;0.00124)|Colorectal(57;0.00332)|Ovarian(225;0.024)|Lung NSC(167;0.0402)|all_lung(232;0.0486)		Epithelial(69;4.07e-14)|COAD - Colon adenocarcinoma(37;0.00986)		GTGAACAGTGCAAACTTCATT	0.378																																					p.A457T		Atlas-SNP	.											.	SLCO4C1	113	.	0			c.G1369A						PASS	.						109.0	108.0	108.0					5																	101592919		2203	4300	6503	SO:0001583	missense	353189	exon8			ACAGTGCAAACTT	AY273896	CCDS34205.1	5q21	2013-05-22	2003-11-25		ENSG00000173930	ENSG00000173930		"""Solute carriers"""	23612	protein-coding gene	gene with protein product		609013					Standard	NM_180991		Approved	SLC21A20, OATP4C1, OATPX, OATP-H	uc003knm.3	Q6ZQN7	OTTHUMG00000162757	ENST00000310954.6:c.1369G>A	5.37:g.101592919C>T	ENSP00000309741:p.Ala457Thr	Somatic	410	0	0		WXS	Illumina HiSeq	Phase_I	355	93	0.261972	NM_180991		Missense_Mutation	SNP	ENST00000310954.6	37	CCDS34205.1	.	.	.	.	.	.	.	.	.	.	C	13.99	2.402413	0.42613	.	.	ENSG00000173930	ENST00000310954	T	0.80393	-1.37	5.78	3.75	0.43078	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.276470	0.30959	N	0.008529	T	0.68375	0.2994	L	0.39566	1.225	0.31887	N	0.617758	B	0.11235	0.004	B	0.18871	0.023	T	0.62520	-0.6837	10	0.19147	T	0.46	.	6.7535	0.23499	0.4703:0.4272:0.0:0.1024	.	457	Q6ZQN7	SO4C1_HUMAN	T	457	ENSP00000309741:A457T	ENSP00000309741:A457T	A	-	1	0	SLCO4C1	101620818	0.994000	0.37717	0.995000	0.50966	0.725000	0.41563	0.657000	0.24963	1.381000	0.46364	0.585000	0.79938	GCA	.	.	none		0.378	SLCO4C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370332.1	NM_180991	
UGT1A7	54577	hgsc.bcm.edu	37	2	234591339	234591339	+	Silent	SNP	G	G	A	rs17864686	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:234591339G>A	ENST00000373426.3	+	1	756	c.756G>A	c.(754-756)ttG>ttA	p.L252L	UGT1A1_ENST00000373450.4_Intron|UGT1A10_ENST00000373445.1_Intron|UGT1A9_ENST00000354728.4_Intron|UGT1A10_ENST00000344644.5_Intron|UGT1A1_ENST00000609637.1_Intron	NM_019077.2	NP_061950.2	Q9HAW7	UD17_HUMAN	UDP glucuronosyltransferase 1 family, polypeptide A7	252					cellular glucuronidation (GO:0052695)|coumarin metabolic process (GO:0009804)|drug metabolic process (GO:0017144)|excretion (GO:0007588)|flavone metabolic process (GO:0051552)|flavonoid glucuronidation (GO:0052696)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cellular glucuronidation (GO:2001030)|negative regulation of fatty acid metabolic process (GO:0045922)|retinoic acid metabolic process (GO:0042573)|xenobiotic glucuronidation (GO:0052697)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	drug binding (GO:0008144)|enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)|glucuronosyltransferase activity (GO:0015020)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase C binding (GO:0005080)|retinoic acid binding (GO:0001972)			NS(1)|endometrium(6)|kidney(5)|large_intestine(5)|liver(1)|lung(12)|ovary(1)|prostate(1)|skin(1)	33		Breast(86;0.000765)|all_lung(227;0.00267)|Renal(207;0.00339)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0328)|Lung NSC(271;0.0457)|Lung SC(224;0.128)		Epithelial(121;8.93e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000412)|Lung(119;0.00333)|LUSC - Lung squamous cell carcinoma(224;0.00746)	Mycophenolate mofetil(DB00688)|Mycophenolic acid(DB01024)	CAATTTGGTTGTTGCGAACTG	0.428													G|||	866	0.172923	0.0825	0.1542	5008	,	,		19257	0.2143		0.2197	False		,,,				2504	0.2178				p.L252L		Atlas-SNP	.											.	UGT1A7	74	.	0			c.G756A						PASS	.	G	,,,	500,3906	234.2+/-247.1	27,446,1730	195.0	198.0	197.0		,,756,	2.7	0.9	2	dbSNP_123	197	1868,6732	328.5+/-318.3	211,1446,2643	no	intron,intron,coding-synonymous,intron	UGT1A10,UGT1A8,UGT1A7,UGT1A9	NM_019075.2,NM_019076.4,NM_019077.2,NM_021027.2	,,,	238,1892,4373	AA,AG,GG		21.7209,11.3482,18.207	,,,	,,252/531,	234591339	2368,10638	2203	4300	6503	SO:0001819	synonymous_variant	54577	exon1			TTGGTTGTTGCGA	U39570	CCDS2506.1	2q37	2010-03-05	2005-07-20		ENSG00000244122	ENSG00000244122		"""UDP glucuronosyltransferases"""	12539	other	complex locus constituent		606432	"""UDP glycosyltransferase 1 family, polypeptide A6"""			9295054, 11434514	Standard	NM_019077		Approved	UGT1G		Q9HAW7	OTTHUMG00000059004	ENST00000373426.3:c.756G>A	2.37:g.234591339G>A		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	104	56	0.538462	NM_019077	B8K293|O00473	Silent	SNP	ENST00000373426.3	37	CCDS2506.1	385	0.1762820512820513	50	0.1016260162601626	59	0.16298342541436464	103	0.18006993006993008	173	0.22823218997361477	G	1.014	-0.687085	0.03328	0.113482	0.217209	ENSG00000244122	ENST00000485022	.	.	.	3.59	2.71	0.32032	.	.	.	.	.	T	0.00039	0.0001	.	.	.	0.09310	P	0.999999999957562	.	.	.	.	.	.	T	0.12941	-1.0528	3	.	.	.	.	8.102	0.30863	0.0981:0.3248:0.5771:0.0	rs17864686;rs17864686	.	.	.	Y	109	.	.	C	+	2	0	UGT1A7	234256078	0.000000	0.05858	0.938000	0.37757	0.251000	0.25915	-0.373000	0.07494	0.737000	0.32582	0.485000	0.47835	TGT	G|0.822;A|0.178	0.178	strong		0.428	UGT1A7-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000130614.1	NM_019077	
ZNF813	126017	hgsc.bcm.edu	37	19	53993923	53993923	+	Missense_Mutation	SNP	C	C	T	rs35712939	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:53993923C>T	ENST00000396403.4	+	4	565	c.437C>T	c.(436-438)tCg>tTg	p.S146L	ZNF813_ENST00000396421.4_Intron	NM_001004301.3	NP_001004301.2	Q6ZN06	ZN813_HUMAN	zinc finger protein 813	146					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			large_intestine(1)	1				GBM - Glioblastoma multiforme(134;0.00619)		AGCTTTCATTCGCATCTGCCT	0.413													c|||	1002	0.20008	0.2133	0.2003	5008	,	,		20208	0.0615		0.2565	False		,,,				2504	0.2669				p.S146L		Atlas-SNP	.											.	ZNF813	81	.	0			c.C437T						PASS	.	C	LEU/SER	934,3472	349.3+/-310.3	98,738,1367	161.0	164.0	163.0		437	1.0	0.0	19	dbSNP_126	163	2201,6393	365.7+/-334.0	282,1637,2378	no	missense	ZNF813	NM_001004301.3	145	380,2375,3745	TT,TC,CC		25.6109,21.1984,24.1154	benign	146/618	53993923	3135,9865	2203	4297	6500	SO:0001583	missense	126017	exon4			TTCATTCGCATCT	AK091460	CCDS46172.1	19q13.41	2013-01-08			ENSG00000198346	ENSG00000198346		"""Zinc fingers, C2H2-type"", ""-"""	33257	protein-coding gene	gene with protein product							Standard	NM_001004301		Approved	FLJ16542	uc002qbu.2	Q6ZN06	OTTHUMG00000158309	ENST00000396403.4:c.437C>T	19.37:g.53993923C>T	ENSP00000379684:p.Ser146Leu	Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	113	52	0.460177	NM_001004301		Missense_Mutation	SNP	ENST00000396403.4	37	CCDS46172.1	423	0.1936813186813187	114	0.23170731707317074	80	0.22099447513812154	31	0.05419580419580419	198	0.2612137203166227	C	7.752	0.703554	0.15172	0.211984	0.256109	ENSG00000198346	ENST00000468450;ENST00000396403	T;T	0.05996	3.76;3.36	0.961	0.961	0.19638	.	.	.	.	.	T	0.00012	0.0000	M	0.62088	1.915	0.32253	P	0.57116	B	0.32101	0.356	B	0.23852	0.049	T	0.42582	-0.9443	8	0.52906	T	0.07	.	5.2224	0.15375	0.0:1.0:0.0:0.0	rs35712939;rs58445793	146	Q6ZN06	ZN813_HUMAN	L	93;146	ENSP00000419821:S93L;ENSP00000379684:S146L	ENSP00000379684:S146L	S	+	2	0	ZNF813	58685735	0.000000	0.05858	0.002000	0.10522	0.055000	0.15305	-1.331000	0.02672	0.820000	0.34516	0.205000	0.17691	TCG	C|0.986;T|0.014	0.014	weak		0.413	ZNF813-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350638.1	NM_001004301	
SLC6A6	6533	hgsc.bcm.edu	37	3	14489107	14489107	+	Missense_Mutation	SNP	G	G	A	rs62233560	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:14489107G>A	ENST00000454876.2	+	5	711	c.382G>A	c.(382-384)Gtt>Att	p.V128I	SLC6A6_ENST00000416216.2_Missense_Mutation_p.V128I|SLC6A6_ENST00000360861.3_Missense_Mutation_p.V128I|SLC6A6_ENST00000484191.1_3'UTR			P31641	SC6A6_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 6	128					amino acid transport (GO:0006865)|cellular amino acid metabolic process (GO:0006520)|ion transport (GO:0006811)|taurine transport (GO:0015734)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	neurotransmitter:sodium symporter activity (GO:0005328)|taurine binding (GO:0030977)|taurine:sodium symporter activity (GO:0005369)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(11)|ovary(1)|prostate(1)|skin(2)	28						CTATGCCTCCGTTGTAATTGT	0.547													A|||	27	0.00539137	0.0	0.0101	5008	,	,		21505	0.001		0.0129	False		,,,				2504	0.0061				p.V128I		Atlas-SNP	.											.	SLC6A6	58	.	0			c.G382A						PASS	.	A	ILE/VAL,ILE/VAL,ILE/VAL	12,4394	825.1+/-416.5	0,12,2191	410.0	392.0	398.0		382,382,382	5.1	1.0	3	dbSNP_129	398	72,8528	816.0+/-406.9	2,68,4230	yes	missense,missense,missense	SLC6A6	NM_001134367.1,NM_001134368.1,NM_003043.3	29,29,29	2,80,6421	AA,AG,GG		0.8372,0.2724,0.6459	benign,benign,benign	128/621,128/201,128/621	14489107	84,12922	2203	4300	6503	SO:0001583	missense	6533	exon5			GCCTCCGTTGTAA		CCDS33705.1, CCDS46765.1	3p25.1	2013-07-19	2013-07-19		ENSG00000131389	ENSG00000131389		"""Solute carriers"""	11052	protein-coding gene	gene with protein product	"""taurine transporter"""	186854	"""solute carrier family 6 (neurotransmitter transporter, taurine), member 6"""			8010975, 8382624	Standard	XM_006713307		Approved	TAUT	uc010heg.4	P31641	OTTHUMG00000155525	ENST00000454876.2:c.382G>A	3.37:g.14489107G>A	ENSP00000398063:p.Val128Ile	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	118	57	0.483051	NM_003043	B2RNU7|Q9BRI2|Q9BXB0	Missense_Mutation	SNP	ENST00000454876.2	37	CCDS33705.1	15	0.006868131868131868	0	0.0	4	0.011049723756906077	1	0.0017482517482517483	10	0.013192612137203167	A	5.409	0.260708	0.10239	0.002724	0.008372	ENSG00000131389	ENST00000454876;ENST00000360861;ENST00000416216	T;T;T	0.75938	-0.98;-0.98;-0.98	5.05	5.05	0.67936	.	0.106550	0.64402	N	0.000007	T	0.44414	0.1292	N	0.05608	-0.01	0.09310	N	0.999997	B	0.02656	0.0	B	0.04013	0.001	T	0.26018	-1.0115	10	0.17832	T	0.49	.	10.8576	0.46808	0.9255:0.0:0.0745:0.0	rs62233560	128	P31641	SC6A6_HUMAN	I	128	ENSP00000398063:V128I;ENSP00000354107:V128I;ENSP00000401167:V128I	ENSP00000354107:V128I	V	+	1	0	SLC6A6	14464111	1.000000	0.71417	0.999000	0.59377	0.076000	0.17211	2.449000	0.44935	0.778000	0.33520	-0.434000	0.05882	GTT	G|0.992;A|0.008	0.008	strong		0.547	SLC6A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340507.1	NM_003043	
CENPU	79682	hgsc.bcm.edu	37	4	185655171	185655171	+	Splice_Site	SNP	C	C	T	rs902174	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:185655171C>T	ENST00000281453.5	-	1	116	c.46G>A	c.(46-48)Ggc>Agc	p.G16S	MLF1IP_ENST00000541971.1_Splice_Site_p.G16S	NM_024629.3	NP_078905.2														endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|stomach(1)	13		all_lung(41;7.57e-14)|Lung NSC(41;1.81e-13)|Hepatocellular(41;0.000519)|Colorectal(36;0.00172)|Renal(120;0.00988)|Prostate(90;0.0235)|all_neural(102;0.0299)|all_hematologic(60;0.0592)|Medulloblastoma(177;0.146)		all cancers(43;7.83e-28)|Epithelial(43;2.56e-24)|OV - Ovarian serous cystadenocarcinoma(60;4.5e-11)|Colorectal(24;3.27e-06)|STAD - Stomach adenocarcinoma(60;2.66e-05)|GBM - Glioblastoma multiforme(59;3.16e-05)|BRCA - Breast invasive adenocarcinoma(30;0.000252)|COAD - Colon adenocarcinoma(29;0.000512)|LUSC - Lung squamous cell carcinoma(40;0.01)|READ - Rectum adenocarcinoma(43;0.0419)		AGTACTTACCCCTCAGACCTG	0.726													C|||	1689	0.33726	0.1044	0.389	5008	,	,		12283	0.7321		0.2306	False		,,,				2504	0.318				p.G16S		Atlas-SNP	.											.	MLF1IP	33	.	0			c.G46A						PASS	.	C	SER/GLY	509,3827		38,433,1697	10.0	11.0	11.0		46	-0.2	0.1	4	dbSNP_86	11	1949,6555		232,1485,2535	yes	missense-near-splice	MLF1IP	NM_024629.3	56	270,1918,4232	TT,TC,CC		22.9186,11.7389,19.1433	possibly-damaging	16/419	185655171	2458,10382	2168	4252	6420	SO:0001630	splice_region_variant	79682	exon1			CTTACCCCTCAGA																												ENST00000281453.5:c.47+1G>A	4.37:g.185655171C>T		Somatic	17	0	0		WXS	Illumina HiSeq	Phase_I	16	13	0.8125	NM_024629		Missense_Mutation	SNP	ENST00000281453.5	37	CCDS3838.1	746|746	0.3415750915750916|0.3415750915750916	53|53	0.10772357723577236|0.10772357723577236	128|128	0.35359116022099446|0.35359116022099446	387|387	0.6765734265734266|0.6765734265734266	178|178	0.23482849604221637|0.23482849604221637	C|C	9.719|9.719	1.159177|1.159177	0.21454|0.21454	0.117389|0.117389	0.229186|0.229186	ENSG00000151725|ENSG00000151725	ENST00000541665|ENST00000281453;ENST00000541971	.|T;T	.|0.19669	.|2.19;2.13	3.66|3.66	-0.251|-0.251	0.13003|0.13003	.|.	.|0.854162	.|0.10010	.|N	.|0.727321	.|T	.|0.00012	.|0.0000	N|N	0.24115|0.24115	0.695|0.695	0.51233|0.51233	P|P	8.20000000000265E-5|8.20000000000265E-5	.|P;P	.|0.43857	.|0.819;0.608	.|B;B	.|0.35114	.|0.196;0.151	.|T	.|0.30765	.|-0.9967	.|9	.|0.48119	.|T	.|0.1	.|-7.3742	7.1902|7.1902	0.25821|0.25821	0.0:0.3724:0.5225:0.1051|0.0:0.3724:0.5225:0.1051	rs902174;rs1137716;rs3201524;rs11542157;rs17625279;rs60983112;rs902174|rs902174;rs1137716;rs3201524;rs11542157;rs17625279;rs60983112;rs902174	.|16;16	.|Q09GN1;Q71F23	.|.;CENPU_HUMAN	.|S	-1|16	.|ENSP00000281453:G16S;ENSP00000445862:G16S	.|ENSP00000281453:G16S	.|G	-|-	.|1	.|0	MLF1IP|MLF1IP	185892165|185892165	0.024000|0.024000	0.19004|0.19004	0.062000|0.062000	0.19696|0.19696	0.005000|0.005000	0.04900|0.04900	-0.164000|-0.164000	0.09983|0.09983	-0.082000|-0.082000	0.12640|0.12640	0.655000|0.655000	0.94253|0.94253	.|GGC	C|0.641;T|0.359	0.359	strong		0.726	MLF1IP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000360841.2		Missense_Mutation
CDK10	8558	hgsc.bcm.edu	37	16	89758285	89758285	+	Missense_Mutation	SNP	C	C	T	rs143430910	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:89758285C>T	ENST00000353379.7	+	5	450	c.407C>T	c.(406-408)tCg>tTg	p.S136L	CDK10_ENST00000505473.1_Missense_Mutation_p.S65L|CDK10_ENST00000331006.8_Missense_Mutation_p.S89L	NM_001098533.2|NM_001160367.1|NM_052988.4	NP_001092003.2|NP_001153839.1|NP_443714.3	Q15131	CDK10_HUMAN	cyclin-dependent kinase 10	136	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				negative regulation of cell proliferation (GO:0008285)|traversing start control point of mitotic cell cycle (GO:0007089)		ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)			ovary(1)	1		Lung NSC(15;2.19e-05)|all_lung(18;3.07e-05)|all_hematologic(23;0.0256)		BRCA - Breast invasive adenocarcinoma(80;0.0276)		ACACCCTTCTCGGAGGCTCAG	0.572																																					p.S136L		Atlas-SNP	.											CDK10_ENST00000353379,NS,carcinoma,0,1	CDK10	26	1	0			c.C407T						scavenged	.	C	LEU/SER,LEU/SER,LEU/SER,LEU/SER	0,4396		0,0,2198	59.0	54.0	56.0		194,194,194,407	4.1	1.0	16	dbSNP_134	56	2,8598	2.2+/-6.3	0,2,4298	yes	missense,missense,missense,missense	CDK10	NM_001098533.2,NM_001160367.1,NM_052987.3,NM_052988.4	145,145,145,145	0,2,6496	TT,TC,CC		0.0233,0.0,0.0154	benign,benign,benign,benign	65/284,65/290,65/273,136/361	89758285	2,12994	2198	4300	6498	SO:0001583	missense	8558	exon5			CCTTCTCGGAGGC	L33264	CCDS10984.2, CCDS32514.1, CCDS32514.2	16q24.3	2011-11-08	2007-11-21		ENSG00000185324	ENSG00000185324		"""Cyclin-dependent kinases"""	1770	protein-coding gene	gene with protein product		603464	"""cyclin-dependent kinase (CDC2-like) 10"""			8208557, 8084611	Standard	NM_052988		Approved	PISSLRE	uc010cio.3	Q15131	OTTHUMG00000138049	ENST00000353379.7:c.407C>T	16.37:g.89758285C>T	ENSP00000338673:p.Ser136Leu	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	106	3	0.0283019	NM_052988	A8K370|A8K8I6|A8MXU6|B3KQJ3|B7Z420|D3DX82|D3DX83|Q0VGZ7|Q15130|Q6PJC0	Missense_Mutation	SNP	ENST00000353379.7	37	CCDS10984.2	.	.	.	.	.	.	.	.	.	.	C	12.58	1.979987	0.34942	0.0	2.33E-4	ENSG00000185324	ENST00000331006;ENST00000393082;ENST00000505473;ENST00000353379	T;T;T	0.50277	0.75;0.75;0.75	5.03	4.06	0.47325	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.43964	0.1271	M	0.70903	2.155	0.80722	D	1	B;B;B;B;B;P;B	0.36483	0.429;0.059;0.376;0.205;0.101;0.555;0.426	B;B;B;B;B;B;B	0.35240	0.198;0.052;0.168;0.105;0.034;0.108;0.09	T	0.35943	-0.9768	10	0.09590	T	0.72	-20.4565	13.6798	0.62476	0.1557:0.8443:0.0:0.0	.	130;65;136;65;65;94;130	B7Z319;A8K370;Q15131;Q15131-3;Q15131-4;Q59EI2;B3KQJ3	.;.;CDK10_HUMAN;.;.;.;.	L	89;107;65;136	ENSP00000329957:S89L;ENSP00000424415:S65L;ENSP00000338673:S136L	ENSP00000329957:S89L	S	+	2	0	CDK10	88285786	1.000000	0.71417	0.962000	0.40283	0.745000	0.42441	7.317000	0.79018	1.068000	0.40764	0.491000	0.48974	TCG	C|1.000;T|0.000	0.000	strong		0.572	CDK10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269925.2		
UHRF1BP1L	23074	hgsc.bcm.edu	37	12	100444984	100444984	+	Missense_Mutation	SNP	G	G	A	rs7296162	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:100444984G>A	ENST00000279907.7	-	16	3652	c.3440C>T	c.(3439-3441)tCa>tTa	p.S1147L	UHRF1BP1L_ENST00000545232.2_Missense_Mutation_p.S797L	NM_015054.1	NP_055869.1	A0JNW5	UH1BL_HUMAN	UHRF1 binding protein 1-like	1147			S -> L (in dbSNP:rs7296162). {ECO:0000269|PubMed:15489334}.							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						ATTTGTAGTTGAGTTCTTTTT	0.333													G|||	303	0.0605032	0.0605	0.0519	5008	,	,		16085	0.0179		0.0696	False		,,,				2504	0.1012				p.S1147L		Atlas-SNP	.											.	UHRF1BP1L	144	.	0			c.C3440T						PASS	.	G	LEU/SER	292,4114	161.4+/-193.6	9,274,1920	79.0	75.0	76.0		3440	2.2	0.0	12	dbSNP_116	76	653,7947	165.5+/-217.6	22,609,3669	yes	missense	UHRF1BP1L	NM_015054.1	145	31,883,5589	AA,AG,GG		7.593,6.6273,7.2659	benign	1147/1465	100444984	945,12061	2203	4300	6503	SO:0001583	missense	23074	exon16			GTAGTTGAGTTCT		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.3440C>T	12.37:g.100444984G>A	ENSP00000279907:p.Ser1147Leu	Somatic	197	0	0		WXS	Illumina HiSeq	Phase_I	131	61	0.465649	NM_015054	A0PJE5|O75183|Q8NDL1|Q96C30|Q9BTS5|Q9H0F1	Missense_Mutation	SNP	ENST00000279907.7	37	CCDS31882.1	110	0.05036630036630037	30	0.06097560975609756	25	0.06906077348066299	4	0.006993006993006993	51	0.06728232189973615	G	8.982	0.975462	0.18736	0.066273	0.07593	ENSG00000111647	ENST00000279907;ENST00000545232	T;T	0.10860	2.83;2.83	5.03	2.21	0.28008	.	0.773311	0.12068	N	0.502521	T	0.00637	0.0021	L	0.56769	1.78	0.21105	N	0.99979	B	0.26400	0.148	B	0.26310	0.068	T	0.18713	-1.0328	10	0.56958	D	0.05	0.0529	9.3245	0.37984	0.2347:0.0:0.7653:0.0	rs7296162;rs52825756;rs57057163;rs7296162	1147	A0JNW5	UH1BL_HUMAN	L	1147;797	ENSP00000279907:S1147L;ENSP00000444824:S797L	ENSP00000279907:S1147L	S	-	2	0	UHRF1BP1L	98969115	0.962000	0.33011	0.030000	0.17652	0.286000	0.27126	1.599000	0.36751	0.174000	0.19809	-0.142000	0.14014	TCA	G|0.939;A|0.061	0.061	strong		0.333	UHRF1BP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407875.1	NM_001006947	
RYR3	6263	hgsc.bcm.edu	37	15	34137200	34137200	+	Silent	SNP	T	T	G	rs41279228	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:34137200T>G	ENST00000389232.4	+	93	13504	c.13434T>G	c.(13432-13434)cgT>cgG	p.R4478R	RYR3_ENST00000415757.3_Silent_p.R4473R	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	4478					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)		CAACCCTGCGTGCCCTGGCCA	0.498													G|||	551	0.110024	0.1097	0.1412	5008	,	,		19803	0.0069		0.2078	False		,,,				2504	0.0941				p.R4478R		Atlas-SNP	.											RYR3,brain,glioma,0,1	RYR3	760	1	0			c.T13434G						PASS	.	G		467,3611		28,411,1600	141.0	139.0	140.0		13434	2.3	1.0	15	dbSNP_127	140	1788,6612		176,1436,2588	no	coding-synonymous	RYR3	NM_001036.3		204,1847,4188	GG,GT,TT		21.2857,11.4517,18.0718		4478/4871	34137200	2255,10223	2039	4200	6239	SO:0001819	synonymous_variant	6263	exon93			CCTGCGTGCCCTG		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.13434T>G	15.37:g.34137200T>G		Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	112	112	1	NM_001036	O15175|Q15412	Silent	SNP	ENST00000389232.4	37	CCDS45210.1																																																																																			T|0.854;G|0.146	0.146	strong		0.498	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1		
STXBP2	6813	hgsc.bcm.edu	37	19	7711221	7711221	+	Silent	SNP	T	T	C	rs10001	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:7711221T>C	ENST00000221283.5	+	16	1474	c.1443T>C	c.(1441-1443)gaT>gaC	p.D481D	STXBP2_ENST00000602355.1_Silent_p.D16D|STXBP2_ENST00000414284.2_Silent_p.D478D|STXBP2_ENST00000441779.2_Silent_p.D492D	NM_006949.2	NP_008880.2	Q15833	STXB2_HUMAN	syntaxin binding protein 2	481					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						TCATCAAGGATGTAATGGAGG	0.667													C|||	2525	0.504193	0.5356	0.4669	5008	,	,		17100	0.7034		0.4036	False		,,,				2504	0.3865				p.D492D		Atlas-SNP	.											STXBP2,NS,adenoma,0,1	STXBP2	63	1	0			c.T1476C						PASS	.	C	,	2187,2217		534,1119,549	35.0	29.0	31.0		1434,1443	-3.7	0.9	19	dbSNP_52	31	3217,5383		585,2047,1668	no	coding-synonymous,coding-synonymous	STXBP2	NM_001127396.1,NM_006949.2	,	1119,3166,2217	CC,CT,TT		37.407,49.6594,41.5564	,	478/591,481/594	7711221	5404,7600	2202	4300	6502	SO:0001819	synonymous_variant	6813	exon16			CAAGGATGTAATG	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.1443T>C	19.37:g.7711221T>C		Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	138	69	0.5	NM_001272034	B4E175|E7EQD5|Q9BU65	Silent	SNP	ENST00000221283.5	37	CCDS12181.1																																																																																			T|0.548;C|0.452	0.452	strong		0.667	STXBP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460963.1	NM_006949	
PTPRN2	5799	hgsc.bcm.edu	37	7	157959895	157959895	+	Missense_Mutation	SNP	C	C	T	rs1130496	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:157959895C>T	ENST00000389418.4	-	6	647	c.638G>A	c.(637-639)cGc>cAc	p.R213H	PTPRN2_ENST00000409483.1_Missense_Mutation_p.R175H|PTPRN2_ENST00000389416.4_Missense_Mutation_p.R196H|PTPRN2_ENST00000389413.3_Missense_Mutation_p.R213H|PTPRN2_ENST00000404321.2_Missense_Mutation_p.R236H	NM_002847.3	NP_002838.2	Q92932	PTPR2_HUMAN	protein tyrosine phosphatase, receptor type, N polypeptide 2	213			R -> H (in dbSNP:rs1130496). {ECO:0000269|PubMed:9205841}.		negative regulation of GTPase activity (GO:0034260)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	endoplasmic reticulum lumen (GO:0005788)|integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)|secretory granule (GO:0030141)|terminal bouton (GO:0043195)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|liver(1)|lung(42)|ovary(4)|pleura(1)|prostate(2)|skin(10)|upper_aerodigestive_tract(1)	86	all_neural(206;0.181)	all_cancers(7;8.99e-13)|all_epithelial(9;2.4e-06)|all_hematologic(28;0.0155)|Breast(660;0.132)	OV - Ovarian serous cystadenocarcinoma(82;0.00463)	STAD - Stomach adenocarcinoma(7;0.0875)		GAGGTCCTCGCGGAGCTGGGT	0.652													C|||	1697	0.338858	0.1399	0.4179	5008	,	,		15810	0.4087		0.4543	False		,,,				2504	0.3609				p.R213H		Atlas-SNP	.											.	PTPRN2	243	.	0			c.G638A						PASS	.		HIS/ARG,HIS/ARG,HIS/ARG	746,3658	296.7+/-284.4	74,598,1530	40.0	42.0	41.0		638,587,638	3.7	0.0	7	dbSNP_86	41	3733,4867	519.5+/-379.5	792,2149,1359	no	missense,missense,missense	PTPRN2	NM_002847.3,NM_130842.2,NM_130843.2	29,29,29	866,2747,2889	TT,TC,CC		43.407,16.9391,34.4432	possibly-damaging,possibly-damaging,possibly-damaging	213/1016,196/999,213/987	157959895	4479,8525	2202	4300	6502	SO:0001583	missense	5799	exon6			TCCTCGCGGAGCT	AB002385	CCDS5947.1, CCDS5948.1, CCDS5949.1	7q36	2011-06-09			ENSG00000155093	ENSG00000155093		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"""	9677	protein-coding gene	gene with protein product	"""IAR PTPRP"""	601698				8954911, 9220540	Standard	NM_130842		Approved	KIAA0387, phogrin, ICAAR, IA-2beta	uc003wno.3	Q92932	OTTHUMG00000152646	ENST00000389418.4:c.638G>A	7.37:g.157959895C>T	ENSP00000374069:p.Arg213His	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	60	59	0.983333	NM_130843	E9PC57|Q8N4I5|Q92662|Q9Y4F8|Q9Y4I6	Missense_Mutation	SNP	ENST00000389418.4	37	CCDS5947.1	771	0.35302197802197804	72	0.14634146341463414	160	0.4419889502762431	202	0.3531468531468531	337	0.4445910290237467	C	6.763	0.509606	0.12883	0.169391	0.43407	ENSG00000155093	ENST00000409483;ENST00000389413;ENST00000389416;ENST00000389418;ENST00000404321	T;T;T;T;T	0.03004	4.1;4.08;4.09;4.1;4.09	4.59	3.71	0.42584	.	0.568731	0.13381	N	0.392177	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	P;P;P;P;P	0.49358	0.923;0.733;0.825;0.733;0.733	B;B;B;B;B	0.34722	0.188;0.092;0.188;0.092;0.092	T	0.30650	-0.9971	9	0.33141	T	0.24	.	10.7818	0.46382	0.0:0.1952:0.8048:0.0	rs1130496;rs3189412;rs10385220;rs17847411;rs56726755;rs1130496	236;175;213;196;213	Q92932-3;E7EM83;Q92932-2;E9PC57;Q92932	.;.;.;.;PTPR2_HUMAN	H	175;213;196;213;236	ENSP00000387114:R175H;ENSP00000374064:R213H;ENSP00000374067:R196H;ENSP00000374069:R213H;ENSP00000385464:R236H	ENSP00000374064:R213H	R	-	2	0	PTPRN2	157652656	0.601000	0.26907	0.012000	0.15200	0.055000	0.15305	2.538000	0.45710	0.936000	0.37367	-0.244000	0.11960	CGC	C|0.653;T|0.347	0.347	strong		0.652	PTPRN2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000353214.1		
GOLGA6C	653641	hgsc.bcm.edu	37	15	75562493	75562493	+	Missense_Mutation	SNP	C	C	A	rs201864661		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:75562493C>A	ENST00000300576.5	+	18	2035	c.2035C>A	c.(2035-2037)Ccg>Acg	p.P679T	RN7SL489P_ENST00000486185.2_RNA	NM_001164404.1	NP_001157876.1	A6NDK9	GOG6C_HUMAN	golgin A6 family, member C	679						Golgi apparatus (GO:0005794)				ovary(1)	1						TGACAACCCCCCGGTACAGCA	0.602																																					p.P679T		Atlas-SNP	.											GOLGA6C_ENST00000300576,bladder,carcinoma,-2,3	GOLGA6C	12	3	0			c.C2035A						scavenged	.																																			SO:0001583	missense	653641	exon18			AACCCCCCGGTAC		CCDS58388.1	15q24.2	2014-02-12	2010-02-12		ENSG00000167195	ENSG00000167195			32206	protein-coding gene	gene with protein product			"""golgi autoantigen, golgin subfamily a, 6C"""				Standard	NM_001164404		Approved		uc002azs.2	A6NDK9	OTTHUMG00000172671	ENST00000300576.5:c.2035C>A	15.37:g.75562493C>A	ENSP00000300576:p.Pro679Thr	Somatic	79	5	0.0632911		WXS	Illumina HiSeq	Phase_I	73	10	0.136986	NM_001164404		Missense_Mutation	SNP	ENST00000300576.5	37	CCDS58388.1	.	.	.	.	.	.	.	.	.	.	-	0.005	-2.235243	0.00277	.	.	ENSG00000167195	ENST00000300576	T	0.12465	2.68	.	.	.	.	.	.	.	.	T	0.01254	0.0041	N	0.00012	-2.95	0.09310	N	0.999997	B	0.02656	0.0	B	0.01281	0.0	T	0.34179	-0.9839	8	0.02654	T	1	.	4.0506	0.09793	0.6453:0.3546:1.0E-4:0.0	.	679	A6NDK9	GOG6C_HUMAN	T	679	ENSP00000300576:P679T	ENSP00000300576:P679T	P	+	1	0	GOLGA6C	73349546	1.000000	0.71417	0.004000	0.12327	0.004000	0.04260	3.804000	0.55568	-1.404000	0.02050	-1.477000	0.00996	CCG	.	.	weak		0.602	GOLGA6C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419797.1	NM_001164404	
GPR116	221395	hgsc.bcm.edu	37	6	46827239	46827239	+	Missense_Mutation	SNP	C	C	T	rs9395218	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:46827239C>T	ENST00000283296.7	-	17	2689	c.2401G>A	c.(2401-2403)Gtc>Atc	p.V801I	GPR116_ENST00000362015.4_Missense_Mutation_p.V801I|GPR116_ENST00000456426.2_Missense_Mutation_p.V659I|GPR116_ENST00000265417.7_Missense_Mutation_p.V801I|GPR116_ENST00000545669.1_Missense_Mutation_p.V230I	NM_001098518.1	NP_001091988.1	Q8IZF2	GP116_HUMAN	G protein-coupled receptor 116	801			V -> I (in dbSNP:rs9395218). {ECO:0000269|PubMed:17974005}.		energy reserve metabolic process (GO:0006112)|fat cell differentiation (GO:0045444)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|neuropeptide signaling pathway (GO:0007218)|regulation of lipid metabolic process (GO:0019216)|surfactant homeostasis (GO:0043129)	cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(2)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|lung(21)|ovary(1)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	59			Lung(136;0.192)			CCAAGGATGACATTAACCGTA	0.398													C|||	1437	0.286941	0.2738	0.2738	5008	,	,		19972	0.3571		0.1968	False		,,,				2504	0.3344				p.V801I	NSCLC(59;410 1274 8751 36715 50546)	Atlas-SNP	.											.	GPR116	133	.	0			c.G2401A						PASS	.	C	ILE/VAL,ILE/VAL	1111,3295	357.4+/-313.9	129,853,1221	37.0	37.0	37.0		2401,2401	-3.8	0.0	6	dbSNP_119	37	1721,6879	289.0+/-299.1	170,1381,2749	no	missense,missense	GPR116	NM_001098518.1,NM_015234.4	29,29	299,2234,3970	TT,TC,CC		20.0116,25.2156,21.7746	benign,benign	801/1347,801/1347	46827239	2832,10174	2203	4300	6503	SO:0001583	missense	221395	exon17			GGATGACATTAAC	AB018301	CCDS4919.1	6p12.3	2014-08-08			ENSG00000069122	ENSG00000069122		"""-"", ""GPCR / Class B : Orphans"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	19030	protein-coding gene	gene with protein product						12435584	Standard	NM_001098518		Approved	DKFZp564O1923, KIAA0758	uc003oyo.3	Q8IZF2	OTTHUMG00000014793	ENST00000283296.7:c.2401G>A	6.37:g.46827239C>T	ENSP00000283296:p.Val801Ile	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	82	37	0.451219	NM_015234	O94858|Q5TF06|Q6RGN2|Q86SP0|Q9Y3Z2	Missense_Mutation	SNP	ENST00000283296.7	37	CCDS4919.1	637	0.2916666666666667	156	0.3170731707317073	99	0.27348066298342544	223	0.38986013986013984	159	0.20976253298153033	C	0.095	-1.161749	0.01673	0.252156	0.200116	ENSG00000069122	ENST00000452370;ENST00000283296;ENST00000362015;ENST00000456426;ENST00000545557;ENST00000265417;ENST00000545669	T;T;T;T;T	0.26810	1.72;2.1;1.74;1.72;1.71	5.58	-3.83	0.04269	.	0.768838	0.11639	N	0.543978	T	0.04861	0.0131	N	0.21097	0.63	0.58432	P	1.0000000000287557E-6	B;B;B;B;B	0.19935	0.014;0.002;0.016;0.04;0.016	B;B;B;B;B	0.24155	0.023;0.005;0.005;0.051;0.005	T	0.44726	-0.9309	9	0.15952	T	0.53	-6.8349	11.0734	0.48016	0.0976:0.2321:0.0:0.6703	rs9395218;rs57548061;rs9395218	230;356;801;659;801	F5GWK9;B4DTV3;E9PBS6;Q8IZF2-3;Q8IZF2	.;.;.;.;GP116_HUMAN	I	801;801;801;659;172;801;230	ENSP00000283296:V801I;ENSP00000354563:V801I;ENSP00000412866:V659I;ENSP00000265417:V801I;ENSP00000441581:V230I	ENSP00000265417:V801I	V	-	1	0	GPR116	46935198	0.000000	0.05858	0.002000	0.10522	0.028000	0.11728	-0.596000	0.05720	-0.881000	0.03992	-0.378000	0.06908	GTC	C|0.761;T|0.239	0.239	strong		0.398	GPR116-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040806.2	NM_015234	
ITGAE	3682	hgsc.bcm.edu	37	17	3632836	3632836	+	Missense_Mutation	SNP	G	G	A	rs1716	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:3632836G>A	ENST00000263087.4	-	24	2946	c.2848C>T	c.(2848-2850)Cgg>Tgg	p.R950W	CTD-3195I5.4_ENST00000575043.1_RNA|ITGAE_ENST00000571185.1_Intron	NM_002208.4	NP_002199.3	P38570	ITAE_HUMAN	integrin, alpha E (antigen CD103, human mucosal lymphocyte antigen 1; alpha polypeptide)	950			R -> W (in dbSNP:rs1716). {ECO:0000269|PubMed:10673275}.		cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)	external side of plasma membrane (GO:0009897)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)			NS(1)|breast(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|lung(14)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	41				UCEC - Uterine corpus endometrioid carcinoma (3;0.0813)		GCCAAAGACCGTCTTTCATTG	0.498													G|||	1329	0.265375	0.0537	0.1599	5008	,	,		21959	0.2956		0.3221	False		,,,				2504	0.5368				p.R950W	NSCLC(182;635 2928 8995 38788)	Atlas-SNP	.											.	ITGAE	96	.	0			c.C2848T	GRCh37	CM065287	ITGAE	M	rs1716	PASS	.	G	TRP/ARG	417,3989	204.5+/-226.7	25,367,1811	217.0	173.0	188.0		2848	-0.3	0.0	17	dbSNP_36	188	2871,5729	451.3+/-362.6	473,1925,1902	yes	missense	ITGAE	NM_002208.4	101	498,2292,3713	AA,AG,GG		33.3837,9.4644,25.2806	probably-damaging	950/1180	3632836	3288,9718	2203	4300	6503	SO:0001583	missense	3682	exon24			AAGACCGTCTTTC	L25851	CCDS32531.1	17p13	2010-03-23				ENSG00000083457		"""CD molecules"", ""Integrins"""	6147	protein-coding gene	gene with protein product		604682				8119947	Standard	NM_002208		Approved	CD103, HUMINAE	uc002fwo.4	P38570		ENST00000263087.4:c.2848C>T	17.37:g.3632836G>A	ENSP00000263087:p.Arg950Trp	Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	153	74	0.48366	NM_002208	Q17RS6|Q9NZU9	Missense_Mutation	SNP	ENST00000263087.4	37	CCDS32531.1	511	0.23397435897435898	25	0.0508130081300813	65	0.17955801104972377	174	0.3041958041958042	247	0.3258575197889182	G	15.97	2.990592	0.54041	0.094644	0.333837	ENSG00000083457	ENST00000263087	T	0.47177	0.85	4.6	-0.312	0.12758	Integrin alpha-2 (1);	.	.	.	.	T	0.00012	0.0000	L	0.47716	1.5	0.80722	P	0.0	D	0.76494	0.999	P	0.57679	0.825	T	0.15263	-1.0443	8	0.66056	D	0.02	.	1.8277	0.03124	0.1589:0.0972:0.3601:0.3838	rs1716;rs52790797;rs56955069;rs1716	950	P38570	ITAE_HUMAN	W	950	ENSP00000263087:R950W	ENSP00000263087:R950W	R	-	1	2	ITGAE	3579585	0.000000	0.05858	0.000000	0.03702	0.246000	0.25737	-0.208000	0.09371	0.007000	0.14760	-0.262000	0.10625	CGG	G|0.755;A|0.245	0.245	strong		0.498	ITGAE-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438169.1	NM_002208	
KLF14	136259	hgsc.bcm.edu	37	7	130418525	130418525	+	Silent	SNP	G	G	A	rs76603546	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:130418525G>A	ENST00000310992.4	-	1	363	c.336C>T	c.(334-336)tcC>tcT	p.S112S		NM_138693.2	NP_619638.2	Q8TD94	KLF14_HUMAN	Kruppel-like factor 14	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)			large_intestine(3)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	6	Melanoma(18;0.0435)					CGGAGAAGCCGGACGAGGCGC	0.746													G|||	1930	0.385383	0.1067	0.4697	5008	,	,		9011	0.5397		0.498	False		,,,				2504	0.4274				p.S112S		Atlas-SNP	.											.	KLF14	15	.	0			c.C336T						PASS	.	G		729,3497		105,519,1489	6.0	10.0	8.0		336	-6.1	0.0	7	dbSNP_131	8	3856,4508		998,1860,1324	no	coding-synonymous	KLF14	NM_138693.2		1103,2379,2813	AA,AG,GG		46.1023,17.2504,36.4178		112/324	130418525	4585,8005	2113	4182	6295	SO:0001819	synonymous_variant	136259	exon1			GAAGCCGGACGAG	AF490374	CCDS5825.1	7q32.3	2014-05-06			ENSG00000174595	ENSG00000266265		"""Kruppel-like transcription factors"", ""Zinc fingers, C2H2-type"""	23025	protein-coding gene	gene with protein product		609393				17480121	Standard	NM_138693		Approved	BTEB5	uc003vqk.2	Q8TD94	OTTHUMG00000188298	ENST00000310992.4:c.336C>T	7.37:g.130418525G>A		Somatic	5	0	0		WXS	Illumina HiSeq	Phase_I	16	11	0.6875	NM_138693	Q19A42|Q19A43	Silent	SNP	ENST00000310992.4	37	CCDS5825.1																																																																																			G|0.582;A|0.418	0.418	strong		0.746	KLF14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338013.1	NM_138693	
MCPH1	79648	hgsc.bcm.edu	37	8	6479178	6479178	+	Silent	SNP	C	C	A	rs2912016	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:6479178C>A	ENST00000344683.5	+	13	2494	c.2418C>A	c.(2416-2418)gcC>gcA	p.A806A	MCPH1_ENST00000521175.1_3'UTR|CTD-2541M15.1_ENST00000522897.1_RNA|CTD-2541M15.1_ENST00000515608.1_RNA	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	71	0	0		WXS	Illumina HiSeq	Phase_I	64	63	0.984375	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	
MARCH7	64844	hgsc.bcm.edu	37	2	160604936	160604936	+	Missense_Mutation	SNP	G	G	A	rs13024801	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:160604936G>A	ENST00000259050.4	+	5	1257	c.1135G>A	c.(1135-1137)Ggt>Agt	p.G379S	MARCH7_ENST00000409175.1_Missense_Mutation_p.G379S|MARCH7_ENST00000409591.1_Missense_Mutation_p.G341S|MARCH7_ENST00000539065.1_Missense_Mutation_p.G323S	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	379	Ser-rich.		G -> S (in dbSNP:rs13024801). {ECO:0000269|Ref.2}.		protein ubiquitination (GO:0016567)		ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|kidney(3)|large_intestine(5)|lung(3)|prostate(1)|skin(1)|stomach(2)	18						AGAATCTGAAGGTAGAAATAC	0.408													G|||	225	0.0449281	0.0318	0.0461	5008	,	,		20450	0.004		0.0676	False		,,,				2504	0.0808				p.G379S		Atlas-SNP	.											.	MARCH7	48	.	0			c.G1135A						PASS	.	G	SER/GLY	186,4220	102.5+/-141.1	4,178,2021	73.0	77.0	76.0		1135	1.5	1.0	2	dbSNP_121	76	647,7953	160.7+/-213.8	31,585,3684	yes	missense	MARCH7	NM_022826.2	56	35,763,5705	AA,AG,GG		7.5233,4.2215,6.4047	benign	379/705	160604936	833,12173	2203	4300	6503	SO:0001583	missense	64844	exon5			TCTGAAGGTAGAA	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.1135G>A	2.37:g.160604936G>A	ENSP00000259050:p.Gly379Ser	Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	152	67	0.440789	NM_022826	A8K9X1|B7Z7P5|D3DPB0|Q53GQ1|Q9BTR9	Missense_Mutation	SNP	ENST00000259050.4	37	CCDS2210.1	93	0.042582417582417584	17	0.034552845528455285	24	0.06629834254143646	1	0.0017482517482517483	51	0.06728232189973615	G	6.565	0.472641	0.12461	0.042215	0.075233	ENSG00000136536	ENST00000409175;ENST00000539065;ENST00000259050;ENST00000409591	T;T;T;T	0.27557	1.66;1.66;1.66;1.66	5.79	1.48	0.22813	.	0.662545	0.16116	N	0.228847	T	0.00524	0.0017	N	0.04880	-0.145	0.40864	P	0.016145999999999994	B;B;B	0.12013	0.005;0.003;0.0	B;B;B	0.13407	0.009;0.002;0.002	T	0.32981	-0.9886	9	0.02654	T	1	-1.9462	6.7138	0.23292	0.6109:0.0:0.3891:0.0	rs13024801;rs52796907;rs13024801	323;341;379	F5H6W4;B7Z7P5;Q9H992	.;.;MARH7_HUMAN	S	379;323;379;341	ENSP00000386830:G379S;ENSP00000442992:G323S;ENSP00000259050:G379S;ENSP00000387238:G341S	ENSP00000259050:G379S	G	+	1	0	MARCH7	160313182	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	2.377000	0.44300	0.367000	0.24454	-0.126000	0.14955	GGT	G|0.944;A|0.056	0.056	strong		0.408	MARCH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255040.3	NM_022826	
OR2C1	4993	hgsc.bcm.edu	37	16	3406626	3406626	+	Missense_Mutation	SNP	G	G	A	rs11648783	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	79	0	0		WXS	Illumina HiSeq	Phase_I	92	73	0.793478	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		
ESPNL	339768	hgsc.bcm.edu	37	2	239039057	239039057	+	Missense_Mutation	SNP	A	A	G	rs13033248	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:239039057A>G	ENST00000343063.3	+	9	1965	c.1702A>G	c.(1702-1704)Atc>Gtc	p.I568V	ESPNL_ENST00000477241.1_3'UTR|ESPNL_ENST00000409506.1_Missense_Mutation_p.I200V|ESPNL_ENST00000409169.1_Missense_Mutation_p.I524V	NM_194312.2	NP_919288.2	Q6ZVH7	ESPNL_HUMAN	espin-like	568			I -> V (in dbSNP:rs13033248). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.							endometrium(1)|lung(8)|pancreas(2)|skin(2)	13		Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0481)|all_hematologic(139;0.158)|all_lung(227;0.198)|Melanoma(123;0.203)|Hepatocellular(293;0.244)		Epithelial(121;4.71e-24)|OV - Ovarian serous cystadenocarcinoma(60;3.02e-12)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;5.63e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000109)|Lung(119;0.0108)|LUSC - Lung squamous cell carcinoma(224;0.0253)		GGAGGCCTCAATCCCAGCGGC	0.711													A|||	1976	0.394569	0.3411	0.3876	5008	,	,		14221	0.4444		0.3847	False		,,,				2504	0.4305				p.I568V		Atlas-SNP	.											.	ESPNL	63	.	0			c.A1702G						PASS	.	A	VAL/ILE	1561,2787		305,951,918	9.0	12.0	11.0		1702	-2.8	0.0	2	dbSNP_121	11	3366,5156		703,1960,1598	no	missense	ESPNL	NM_194312.2	29	1008,2911,2516	GG,GA,AA		39.4978,35.9016,38.2828	benign	568/1006	239039057	4927,7943	2174	4261	6435	SO:0001583	missense	339768	exon9			GCCTCAATCCCAG	AK124559	CCDS2525.1	2q37.3	2013-01-10			ENSG00000144488	ENSG00000144488		"""Ankyrin repeat domain containing"""	27937	protein-coding gene	gene with protein product						12975309	Standard	NM_194312		Approved	FLJ42568	uc002vxq.4	Q6ZVH7	OTTHUMG00000133335	ENST00000343063.3:c.1702A>G	2.37:g.239039057A>G	ENSP00000339115:p.Ile568Val	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	50	24	0.48	NM_194312	Q66K27|Q6ZVG1|Q8IVU2	Missense_Mutation	SNP	ENST00000343063.3	37	CCDS2525.1	856	0.39194139194139194	179	0.3638211382113821	150	0.4143646408839779	240	0.4195804195804196	287	0.3786279683377309	A	0	-2.766231	0.00082	0.359016	0.394978	ENSG00000144488	ENST00000343063;ENST00000409169;ENST00000409506	T;T;T	0.61274	0.12;1.23;0.81	3.37	-2.79	0.05841	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.36286	-0.9754	8	0.02654	T	1	0.231	0.1428	0.00085	0.2568:0.1676:0.237:0.3387	rs13033248	524;568	Q6ZVH7-2;Q6ZVH7	.;ESPNL_HUMAN	V	568;524;200	ENSP00000339115:I568V;ENSP00000386577:I524V;ENSP00000386579:I200V	ENSP00000339115:I568V	I	+	1	0	ESPNL	238703796	0.000000	0.05858	0.000000	0.03702	0.014000	0.08584	-0.058000	0.11750	-0.164000	0.10927	-0.548000	0.04221	ATC	A|0.615;G|0.385	0.385	strong		0.711	ESPNL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257164.2	NM_194312	
MUC4	4585	hgsc.bcm.edu	37	3	195508108	195508108	+	Missense_Mutation	SNP	G	G	A	rs374140595		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195508108G>A	ENST00000463781.3	-	2	10802	c.10343C>T	c.(10342-10344)tCa>tTa	p.S3448L	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.S3448L	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		TGTAGATGCTGAGGAAGTGCT	0.597																																					p.S3448L		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	0			c.C10343T						PASS	.						24.0	21.0	22.0					3																	195508108		680	1577	2257	SO:0001583	missense	4585	exon2			GATGCTGAGGAAG	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.10343C>T	3.37:g.195508108G>A	ENSP00000417498:p.Ser3448Leu	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	80	17	0.2125	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	g	6.150	0.395913	0.11638	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.35421	1.31;1.42	0.743	-1.49	0.08718	.	.	.	.	.	T	0.33089	0.0851	N	0.19112	0.55	0.09310	N	1	P	0.52170	0.951	D	0.65443	0.935	T	0.20240	-1.0281	8	.	.	.	.	2.1531	0.03805	0.0:0.3256:0.3506:0.3237	.	3320	E7ESK3	.	L	3448	ENSP00000417498:S3448L;ENSP00000420243:S3448L	.	S	-	2	0	MUC4	196992887	0.051000	0.20477	0.010000	0.14722	0.010000	0.07245	0.898000	0.28404	0.088000	0.17205	0.089000	0.15464	TCA	.	.	weak		0.597	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
ZNF585B	92285	hgsc.bcm.edu	37	19	37677748	37677748	+	Missense_Mutation	SNP	T	T	A	rs45626541	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:37677748T>A	ENST00000532828.2	-	5	942	c.691A>T	c.(691-693)Ata>Tta	p.I231L	CTC-454I21.3_ENST00000585860.2_Intron|ZNF585B_ENST00000527838.1_3'UTR|ZNF585B_ENST00000531805.1_Missense_Mutation_p.I176L|ZNF585B_ENST00000312908.5_5'UTR	NM_152279.3	NP_689492.3	Q52M93	Z585B_HUMAN	zinc finger protein 585B	231					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)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(3)|endometrium(1)|large_intestine(9)|lung(13)|ovary(1)|prostate(1)	29			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			TTCTCATGTATACTGAGATCT	0.393													T|||	1388	0.277157	0.3268	0.3876	5008	,	,		19250	0.0883		0.3579	False		,,,				2504	0.2434				p.I231L	Melanoma(93;882 1454 18863 28917 48427)	Atlas-SNP	.											.	ZNF585B	91	.	0			c.A691T						PASS	.	T	LEU/ILE	1570,2836	484.8+/-360.1	265,1040,898	122.0	119.0	120.0		691	0.2	0.0	19	dbSNP_127	120	3054,5546	463.1+/-365.9	519,2016,1765	yes	missense	ZNF585B	NM_152279.3	5	784,3056,2663	AA,AT,TT		35.5116,35.6332,35.5528	benign	231/770	37677748	4624,8382	2203	4300	6503	SO:0001583	missense	92285	exon5			CATGTATACTGAG	AK027834	CCDS12500.1	19q13.13	2013-01-08				ENSG00000245680		"""Zinc fingers, C2H2-type"", ""-"""	30948	protein-coding gene	gene with protein product						12477932	Standard	NM_152279		Approved	FLJ14928, SZFP41	uc002ofq.3	Q52M93		ENST00000532828.2:c.691A>T	19.37:g.37677748T>A	ENSP00000433773:p.Ile231Leu	Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	142	65	0.457746	NM_152279	Q8IZD3|Q96JW6	Missense_Mutation	SNP	ENST00000532828.2	37	CCDS12500.1	609	0.27884615384615385	149	0.30284552845528456	128	0.35359116022099446	46	0.08041958041958042	286	0.37730870712401055	T	6.677	0.493463	0.12702	0.356332	0.355116	ENSG00000245680	ENST00000531805;ENST00000532828	T;T	0.17854	2.25;2.25	2.78	0.175	0.15045	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.194135	0.25058	N	0.033472	T	0.00012	0.0000	N	0.08118	0	0.58432	P	2.9999999999752447E-6	B;B	0.21688	0.033;0.059	B;B	0.22753	0.018;0.041	T	0.49818	-0.8899	9	0.27082	T	0.32	.	8.6099	0.33795	0.0:0.0:0.3604:0.6396	rs45626541	176;231	E9PQH3;Q52M93	.;Z585B_HUMAN	L	176;231	ENSP00000436774:I176L;ENSP00000433773:I231L	ENSP00000436774:I176L	I	-	1	0	ZNF585B	42369588	0.000000	0.05858	0.037000	0.18230	0.926000	0.56050	-2.382000	0.01064	0.265000	0.21872	0.374000	0.22700	ATA	T|0.676;A|0.324	0.324	strong		0.393	ZNF585B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388272.2	NM_152279	
LAMB3	3914	hgsc.bcm.edu	37	1	209795909	209795909	+	Silent	SNP	T	T	C	rs3179860	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:209795909T>C	ENST00000356082.4	-	18	2807	c.2673A>G	c.(2671-2673)ctA>ctG	p.L891L	MIR4260_ENST00000583107.1_RNA|LAMB3_ENST00000391911.1_Silent_p.L891L|LAMB3_ENST00000367030.3_Silent_p.L891L	NM_000228.2	NP_000219.2	Q13751	LAMB3_HUMAN	laminin, beta 3	891	Domain I.				brown fat cell differentiation (GO:0050873)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	extracellular region (GO:0005576)|laminin-5 complex (GO:0005610)	structural molecule activity (GO:0005198)			NS(1)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(11)|lung(13)|ovary(1)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	45				OV - Ovarian serous cystadenocarcinoma(81;0.0519)		CCTGCTGGATTAGGAGCCGTG	0.597													T|||	515	0.102835	0.0446	0.0865	5008	,	,		18362	0.001		0.16	False		,,,				2504	0.2393				p.L891L		Atlas-SNP	.											.	LAMB3	136	.	0			c.A2673G						PASS	.	T	,,	241,4165	141.1+/-176.5	5,231,1967	178.0	163.0	168.0		2673,2673,2673	3.5	1.0	1	dbSNP_105	168	1331,7269	261.4+/-283.8	105,1121,3074	no	coding-synonymous,coding-synonymous,coding-synonymous	LAMB3	NM_000228.2,NM_001017402.1,NM_001127641.1	,,	110,1352,5041	CC,CT,TT		15.4767,5.4698,12.0867	,,	891/1173,891/1173,891/1173	209795909	1572,11434	2203	4300	6503	SO:0001819	synonymous_variant	3914	exon18			CTGGATTAGGAGC	D37766	CCDS1487.1	1q32	2013-03-01	2002-08-29		ENSG00000196878	ENSG00000196878		"""Laminins"""	6490	protein-coding gene	gene with protein product		150310	"""laminin, beta 3 (nicein (125kD), kalinin (140kD), BM600 (125kD))"""	LAMNB1		8088808, 7774918	Standard	NM_001127641		Approved	nicein-125kDa, kalinin-140kDa, BM600-125kDa	uc001hhh.3	Q13751	OTTHUMG00000036360	ENST00000356082.4:c.2673A>G	1.37:g.209795909T>C		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	100	51	0.51	NM_000228	D3DT88|O14947|Q14733|Q9UJK4|Q9UJL1	Silent	SNP	ENST00000356082.4	37	CCDS1487.1																																																																																			T|0.896;C|0.104	0.104	strong		0.597	LAMB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088525.2	NM_000228	
ERMARD	55780	hgsc.bcm.edu	37	6	170176647	170176647	+	Silent	SNP	C	C	T	rs386708934|rs4716399	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:170176647C>T	ENST00000366773.3	+	16	1650	c.1617C>T	c.(1615-1617)atC>atT	p.I539I	ERMARD_ENST00000392095.4_Silent_p.I413I|ERMARD_ENST00000588451.1_Silent_p.I403I|ERMARD_ENST00000366772.2_Intron|ERMARD_ENST00000418781.3_Intron	NM_001278532.1|NM_018341.1	NP_001265461.1|NP_060811.1	Q5T6L9	EMARD_HUMAN	ER membrane-associated RNA degradation	539					multicellular organismal development (GO:0007275)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)											TCCGAAGCATCAGCGAACAGT	0.632													C|||	1721	0.34365	0.497	0.304	5008	,	,		21048	0.3304		0.2366	False		,,,				2504	0.2883				p.I539I		Atlas-SNP	.											.	C6orf70	63	.	0			c.C1617T						PASS	.	C		2113,2293	572.6+/-383.4	503,1107,593	95.0	72.0	80.0		1617	1.3	0.0	6	dbSNP_111	80	1913,6687	335.9+/-321.6	235,1443,2622	no	coding-synonymous	C6orf70	NM_018341.1		738,2550,3215	TT,TC,CC		22.2442,47.9573,30.9549		539/679	170176647	4026,8980	2203	4300	6503	SO:0001819	synonymous_variant	55780	exon16			AAGCATCAGCGAA	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.1617C>T	6.37:g.170176647C>T		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	44	13	0.295455	NM_018341	B4DFH0|F8WAF1|Q3ZCS8|Q5T6L8|Q9NUT5|Q9NVU2	Silent	SNP	ENST00000366773.3	37	CCDS34576.1																																																																																			C|0.694;T|0.306	0.306	strong		0.632	ERMARD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043238.2	NM_018341	
PTPRQ	374462	hgsc.bcm.edu	37	12	80890246	80890246	+	Silent	SNP	T	T	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:80890246T>G	ENST00000266688.5	+	19	2196	c.2196T>G	c.(2194-2196)tcT>tcG	p.S732S				Q9UMZ3	PTPRQ_HUMAN	protein tyrosine phosphatase, receptor type, Q	778	Fibronectin type-III 8. {ECO:0000255|PROSITE-ProRule:PRU00316}.				regulation of fat cell differentiation (GO:0045598)	integral component of membrane (GO:0016021)	protein tyrosine phosphatase activity (GO:0004725)			breast(1)|endometrium(7)|kidney(9)|lung(2)|prostate(1)|skin(2)|stomach(2)	24						CTGTAAGGTCTTACACCAGAT	0.328																																					p.S564S		Atlas-SNP	.											.	PTPRQ	119	.	0			c.T1692G						PASS	.						102.0	91.0	95.0					12																	80890246		692	1591	2283	SO:0001819	synonymous_variant	374462	exon11			AAGGTCTTACACC	AF169351	CCDS73501.1	12q21.31	2013-02-11	2001-12-04		ENSG00000139304	ENSG00000139304		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9679	protein-coding gene	gene with protein product		603317	"""deafness, autosomal recessive 84"""	DFNB84		20346435	Standard	NM_001145026		Approved		uc001sze.2	Q9UMZ3	OTTHUMG00000170171	ENST00000266688.5:c.2196T>G	12.37:g.80890246T>G		Somatic	316	0	0		WXS	Illumina HiSeq	Phase_I	277	60	0.216606	NM_001145026		Silent	SNP	ENST00000266688.5	37		.	.	.	.	.	.	.	.	.	.	T	1.028	-0.682677	0.03353	.	.	ENSG00000139304	ENST00000532722	.	.	.	5.74	-11.5	0.00074	.	.	.	.	.	T	0.30978	0.0782	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.40496	-0.9560	4	.	.	.	.	1.5	0.02474	0.2724:0.0888:0.2754:0.3634	.	.	.	.	R	433	.	.	L	+	2	0	PTPRQ	79414377	0.000000	0.05858	0.094000	0.20943	0.124000	0.20399	-1.949000	0.01532	-1.866000	0.01145	-0.649000	0.03915	CTT	.	.	none		0.328	PTPRQ-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001145026	
TTC21A	199223	hgsc.bcm.edu	37	3	39152345	39152345	+	Missense_Mutation	SNP	G	G	A	rs1112438	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:39152345G>A	ENST00000431162.2	+	4	406	c.272G>A	c.(271-273)cGa>cAa	p.R91Q	GORASP1_ENST00000319283.3_5'Flank|TTC21A_ENST00000301819.6_Missense_Mutation_p.R91Q|TTC21A_ENST00000440121.1_Missense_Mutation_p.R91Q			Q8NDW8	TT21A_HUMAN	tetratricopeptide repeat domain 21A	91			R -> Q (in dbSNP:rs1112438).							NS(1)|breast(2)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(9)|lung(23)|ovary(1)|prostate(1)|skin(3)	50				KIRC - Kidney renal clear cell carcinoma(284;0.0588)|Kidney(284;0.0738)		TTTACAGACCGAGAAGCAATT	0.542													G|||	1741	0.347644	0.5681	0.2911	5008	,	,		22574	0.252		0.2714	False		,,,				2504	0.2669				p.R91Q		Atlas-SNP	.											TTC21A,caecum,carcinoma,0,1	TTC21A	96	1	0			c.G272A						PASS	.	G	GLN/ARG,GLN/ARG	1928,1994		483,962,516	59.0	61.0	60.0		272,272	0.6	0.8	3	dbSNP_86	60	2377,5959		360,1657,2151	yes	missense,missense	TTC21A	NM_001105513.2,NM_145755.2	43,43	843,2619,2667	AA,AG,GG		28.5149,49.1586,35.1199	benign,benign	91/1273,91/1321	39152345	4305,7953	1961	4168	6129	SO:0001583	missense	199223	exon4			CAGACCGAGAAGC	AJ487015	CCDS43068.1, CCDS46800.1, CCDS43068.2	3p22.2	2014-09-04			ENSG00000168026	ENSG00000168026		"""Tetratricopeptide (TTC) repeat domain containing"""	30761	protein-coding gene	gene with protein product		611430					Standard	NM_145755		Approved	STI2	uc003cjc.2	Q8NDW8	OTTHUMG00000155973	ENST00000431162.2:c.272G>A	3.37:g.39152345G>A	ENSP00000398211:p.Arg91Gln	Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	137	65	0.474453	NM_001105513	A1L388|B4DYF6|B4DYJ3|D3YTE7|D4PHA5|Q6P5W8|Q8N7G5|Q8NA02	Missense_Mutation	SNP	ENST00000431162.2	37	CCDS46800.1	733	0.3356227106227106	264	0.5365853658536586	111	0.30662983425414364	154	0.2692307692307692	204	0.2691292875989446	G	15.81	2.943055	0.53079	0.491586	0.285149	ENSG00000168026	ENST00000301819;ENST00000424305;ENST00000431162;ENST00000440121	T;T;T	0.63096	0.34;0.34;-0.02	5.74	0.555	0.17247	Tetratricopeptide-like helical (1);	1.254700	0.05507	N	0.559506	T	0.00012	0.0000	L	0.45137	1.4	0.80722	P	0.0	B;B;B;B;B	0.27416	0.178;0.068;0.116;0.07;0.068	B;B;B;B;B	0.17433	0.018;0.008;0.008;0.003;0.008	T	0.42050	-0.9474	9	0.25106	T	0.35	3.0433	2.0891	0.03652	0.2241:0.2337:0.4224:0.1198	rs1112438;rs4557093;rs17855762;rs52803003;rs59061178;rs1112438	91;91;91;91;91	Q8NDW8-6;Q8NDW8-5;Q8NDW8-7;Q8NDW8;F5H6V8	.;.;.;TT21A_HUMAN;.	Q	91	ENSP00000301819:R91Q;ENSP00000398211:R91Q;ENSP00000410882:R91Q	ENSP00000301819:R91Q	R	+	2	0	TTC21A	39127349	0.349000	0.24870	0.838000	0.33150	0.989000	0.77384	0.487000	0.22356	-0.189000	0.10482	0.655000	0.94253	CGA	G|0.662;A|0.338	0.338	strong		0.542	TTC21A-021	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000377829.1	NM_145755	
SENP2	59343	hgsc.bcm.edu	37	3	185331165	185331165	+	Missense_Mutation	SNP	C	C	A	rs6762208	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:185331165C>A	ENST00000296257.5	+	10	1142	c.902C>A	c.(901-903)aCg>aAg	p.T301K	SENP2_ENST00000545472.1_Missense_Mutation_p.T291K|SENP2_ENST00000427465.2_Missense_Mutation_p.T125K	NM_021627.2	NP_067640.2	Q9HC62	SENP2_HUMAN	SUMO1/sentrin/SMT3 specific peptidase 2	301			T -> K (in dbSNP:rs6762208). {ECO:0000269|PubMed:10718198, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:17974005, ECO:0000269|Ref.1}.		cellular protein metabolic process (GO:0044267)|dorsal/ventral axis specification (GO:0009950)|heart development (GO:0007507)|labyrinthine layer development (GO:0060711)|mRNA transport (GO:0051028)|negative regulation of chromatin binding (GO:0035562)|negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518)|negative regulation of protein binding (GO:0032091)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-translational protein modification (GO:0043687)|protein desumoylation (GO:0016926)|protein sumoylation (GO:0016925)|protein transport (GO:0015031)|regulation of DNA endoreduplication (GO:0032875)|regulation of G1/S transition of mitotic cell cycle (GO:2000045)|regulation of Wnt signaling pathway (GO:0030111)|spongiotrophoblast layer development (GO:0060712)|trophoblast giant cell differentiation (GO:0060707)|Wnt signaling pathway (GO:0016055)	cytoplasmic vesicle (GO:0031410)|nuclear pore (GO:0005643)|nucleoplasm (GO:0005654)|PML body (GO:0016605)	SUMO-specific protease activity (GO:0016929)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(5)|skin(3)	12	all_cancers(143;1.28e-10)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(80;1.31e-21)			GATACAGAGACGATGGTCGGA	0.333													A|||	2138	0.426917	0.5121	0.3444	5008	,	,		17598	0.3165		0.3221	False		,,,				2504	0.592				p.T301K		Atlas-SNP	.											.	SENP2	88	.	0			c.C902A						PASS	.	A	LYS/THR	2082,2324	604.0+/-390.2	490,1102,611	128.0	141.0	137.0		902	3.4	0.7	3	dbSNP_116	137	2952,5648	667.3+/-402.5	504,1944,1852	yes	missense	SENP2	NM_021627.2	78	994,3046,2463	AA,AC,CC		34.3256,47.2537,38.7052	benign	301/590	185331165	5034,7972	2203	4300	6503	SO:0001583	missense	59343	exon10			CAGAGACGATGGT	AF151697	CCDS33902.1	3q28	2005-08-17	2005-08-17		ENSG00000163904	ENSG00000163904			23116	protein-coding gene	gene with protein product		608261	"""SUMO1/sentrin/SMT3 specific protease 2"""			11896061, 11489887	Standard	XM_005247690		Approved	SMT3IP2, KIAA1331, DKFZp762A2316, AXAM2	uc003fpn.3	Q9HC62	OTTHUMG00000156658	ENST00000296257.5:c.902C>A	3.37:g.185331165C>A	ENSP00000296257:p.Thr301Lys	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	68	67	0.985294	NM_021627	B4DQ42|Q8IW97|Q96SR2|Q9P2L5	Missense_Mutation	SNP	ENST00000296257.5	37	CCDS33902.1	792	0.3626373626373626	246	0.5	129	0.356353591160221	174	0.3041958041958042	243	0.32058047493403696	A	0.013	-1.637506	0.00799	0.472537	0.343256	ENSG00000163904	ENST00000545472;ENST00000296257;ENST00000437107;ENST00000427465;ENST00000444509	T;T;T;T	0.24350	2.24;2.27;2.25;1.86	5.8	3.44	0.39384	.	0.102716	0.42053	N	0.000767	T	0.00012	0.0000	N	0.01874	-0.695	0.58432	P	1.999999999946489E-6	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.48305	-0.9047	9	0.02654	T	1	-9.8691	4.9115	0.13823	0.6804:0.1574:0.1622:0.0	rs6762208;rs56530709;rs58977663;rs6762208	291;301	B4DQ42;Q9HC62	.;SENP2_HUMAN	K	291;301;172;125;8	ENSP00000439653:T291K;ENSP00000296257:T301K;ENSP00000394562:T125K;ENSP00000399201:T8K	ENSP00000296257:T301K	T	+	2	0	SENP2	186813859	0.997000	0.39634	0.738000	0.30950	0.015000	0.08874	1.376000	0.34306	0.135000	0.18707	-0.362000	0.07510	ACG	C|0.610;A|0.390	0.390	strong		0.333	SENP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345159.1	NM_021627	
GPR112	139378	hgsc.bcm.edu	37	X	135496398	135496398	+	Silent	SNP	G	G	A	rs5930942	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:135496398G>A	ENST00000394143.1	+	25	9408	c.9117G>A	c.(9115-9117)acG>acA	p.T3039T	GPR112_ENST00000412101.1_Silent_p.T2834T|GPR112_ENST00000370652.1_Silent_p.T3039T|GPR112_ENST00000287534.4_Silent_p.T2758T|GPR112_ENST00000394141.1_Silent_p.T2834T	NM_153834.3	NP_722576.3	Q8IZF6	GP112_HUMAN	G protein-coupled receptor 112	3039					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(13)|central_nervous_system(2)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(33)|lung(97)|ovary(5)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(2)	199	Acute lymphoblastic leukemia(192;0.000127)					AACTGTTGACGCCATCTCTCA	0.408													A|||	2894	0.766623	0.5991	0.5994	3775	,	,		12714	0.7024		0.4821	False		,,,				2504	0.5041				p.T3039T		Atlas-SNP	.											.	GPR112	459	.	0			c.G9117A						PASS	.	A		2956,879		960,588,448,84,123	141.0	140.0	140.0		9117	-0.1	0.1	X	dbSNP_114	140	4080,2648		895,1155,1135,378,737	no	coding-synonymous	GPR112	NM_153834.3		1855,1743,1583,462,860	AA,AG,A,GG,G		39.3579,22.9205,33.3901		3039/3081	135496398	7036,3527	2203	4300	6503	SO:0001819	synonymous_variant	139378	exon25			GTTGACGCCATCT	AY140954	CCDS35409.1	Xq26.3	2014-08-08			ENSG00000156920	ENSG00000156920		"""-"", ""GPCR / Class B : Orphans"""	18992	protein-coding gene	gene with protein product						12435584	Standard	XM_005262367		Approved	RP1-299I16, PGR17	uc004ezu.1	Q8IZF6	OTTHUMG00000022508	ENST00000394143.1:c.9117G>A	X.37:g.135496398G>A		Somatic	293	0	0		WXS	Illumina HiSeq	Phase_I	209	204	0.976077	NM_153834	A2A2J1|A2A2J2|Q5EGP2|Q86SM6	Silent	SNP	ENST00000394143.1	37	CCDS35409.1																																																																																			0|0.003;A|0.709	0.709	strong		0.408	GPR112-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000286639.1		
HTT	3064	hgsc.bcm.edu	37	4	3162056	3162056	+	Silent	SNP	C	C	T	rs363099	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:3162056C>T	ENST00000355072.5	+	29	3946	c.3801C>T	c.(3799-3801)ctC>ctT	p.L1267L		NM_002111.6	NP_002102	P42858	HD_HUMAN	huntingtin	1267					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)		GAGGGTTTCTCCGCTCAGCCT	0.507													C|||	1071	0.213858	0.0113	0.2882	5008	,	,		19711	0.3442		0.3121	False		,,,				2504	0.1994				p.L1267L		Atlas-SNP	.											HTT,NS,carcinoma,0,1	HTT	221	1	0			c.C3801T						scavenged	.	C		256,3662		16,224,1719	171.0	165.0	167.0		3801	0.1	1.0	4	dbSNP_79	167	2331,5887		331,1669,2109	no	coding-synonymous	HTT	NM_002111.6		347,1893,3828	TT,TC,CC		28.3646,6.5339,21.3167		1267/3143	3162056	2587,9549	1959	4109	6068	SO:0001819	synonymous_variant	3064	exon29			GTTTCTCCGCTCA	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.3801C>T	4.37:g.3162056C>T		Somatic	157	1	0.00636943		WXS	Illumina HiSeq	Phase_I	175	87	0.497143	NM_002111	Q9UQB7	Silent	SNP	ENST00000355072.5	37	CCDS43206.1																																																																																			T|0.148;G|0.337	0.148	strong		0.507	HTT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358234.2	NM_002111	
KIAA1109	84162	hgsc.bcm.edu	37	4	123280860	123280860	+	Silent	SNP	T	T	C	rs1127348	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:123280860T>C	ENST00000264501.4	+	85	15157	c.14784T>C	c.(14782-14784)caT>caC	p.H4928H	KIAA1109_ENST00000388738.3_Silent_p.H4928H			Q2LD37	K1109_HUMAN	KIAA1109	4928					regulation of cell growth (GO:0001558)|regulation of epithelial cell differentiation (GO:0030856)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(7)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(6)|large_intestine(33)|liver(4)|lung(74)|ovary(9)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(6)|urinary_tract(3)	172						ATACATGGCATCTAGAACCTA	0.323													T|||	610	0.121805	0.0068	0.1311	5008	,	,		19004	0.123		0.2416	False		,,,				2504	0.1462				p.H4928H		Atlas-SNP	.											KIAA1109,colon,carcinoma,0,1	KIAA1109	424	1	0			c.T14784C						PASS	.	T		142,3558		5,132,1713	119.0	106.0	110.0		14784	5.9	1.0	4	dbSNP_86	110	1764,6428		193,1378,2525	no	coding-synonymous	KIAA1109	NM_015312.3		198,1510,4238	CC,CT,TT		21.5332,3.8378,16.0276		4928/5006	123280860	1906,9986	1850	4096	5946	SO:0001819	synonymous_variant	84162	exon83			ATGGCATCTAGAA	AL137384	CCDS43267.1	4q28.1	2012-07-09			ENSG00000138688	ENSG00000138688			26953	protein-coding gene	gene with protein product	"""fragile site-associated"""	611565				16386706	Standard	NM_015312		Approved	FLJ21404, FSA, KIAA1371, Tweek	uc003ieh.3	Q2LD37	OTTHUMG00000150116	ENST00000264501.4:c.14784T>C	4.37:g.123280860T>C		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	85	33	0.388235	NM_015312	Q4W598|Q5CZA9|Q6ZS70|Q6ZV75|Q86XA5|Q8WVD8|Q9H742|Q9NT48|Q9NTC3|Q9NTI4|Q9P2H6|Q9UPP3	Silent	SNP	ENST00000264501.4	37	CCDS43267.1	310	0.14194139194139194	3	0.006097560975609756	51	0.1408839779005525	75	0.13111888111888112	181	0.23878627968337732	T	7.423	0.637044	0.14386	0.038378	0.215332	ENSG00000138688	ENST00000306802	.	.	.	5.94	5.94	0.96194	.	.	.	.	.	T	0.00039	0.0001	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.06661	-1.0814	3	.	.	.	.	12.2461	0.54571	0.0:0.0678:0.0:0.9322	rs1127348;rs2306366;rs17388140;rs60969099;rs1127348	.	.	.	T	1304	.	.	I	+	2	0	KIAA1109	123500310	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.379000	0.44318	2.282000	0.76494	0.528000	0.53228	ATC	T|0.843;C|0.157	0.157	strong		0.323	KIAA1109-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316415.1	NM_020797	
KDM2B	84678	hgsc.bcm.edu	37	12	121878659	121878659	+	Silent	SNP	C	C	T	rs1064951	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:121878659C>T	ENST00000377071.4	-	21	3642	c.3570G>A	c.(3568-3570)caG>caA	p.Q1190Q	KDM2B_ENST00000542973.1_Silent_p.Q558Q|KDM2B_ENST00000377069.4_Silent_p.Q1121Q|KDM2B_ENST00000536437.1_Intron	NM_032590.4	NP_115979.3	Q8NHM5	KDM2B_HUMAN	lysine (K)-specific demethylase 2B	1190					embryonic camera-type eye morphogenesis (GO:0048596)|forebrain development (GO:0030900)|fourth ventricle development (GO:0021592)|hindbrain development (GO:0030902)|histone demethylation (GO:0016577)|histone H2A monoubiquitination (GO:0035518)|initiation of neural tube closure (GO:0021993)|lateral ventricle development (GO:0021670)|midbrain development (GO:0030901)|midbrain-hindbrain boundary morphogenesis (GO:0021555)|negative regulation of neural precursor cell proliferation (GO:2000178)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|spermatogenesis (GO:0007283)|third ventricle development (GO:0021678)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone demethylase activity (GO:0032452)|histone demethylase activity (H3-K36 specific) (GO:0051864)|rRNA binding (GO:0019843)|zinc ion binding (GO:0008270)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	19						GATCCCGCATCTGGGCATCCT	0.632													C|||	1675	0.334465	0.1573	0.4006	5008	,	,		16903	0.4514		0.4046	False		,,,				2504	0.3344				p.Q1190Q		Atlas-SNP	.											.	KDM2B	218	.	0			c.G3570A						PASS	.	C	,	783,3405		80,623,1391	37.0	44.0	42.0		3363,3570	4.1	1.0	12	dbSNP_86	42	3208,5234		606,1996,1619	no	coding-synonymous,coding-synonymous	KDM2B	NM_001005366.1,NM_032590.4	,	686,2619,3010	TT,TC,CC		38.0005,18.6963,31.5994	,	1121/1266,1190/1337	121878659	3991,8639	2094	4221	6315	SO:0001819	synonymous_variant	84678	exon21			CCGCATCTGGGCA	AJ459424	CCDS41849.1, CCDS41850.1	12q24.31	2014-02-18	2009-04-06	2009-04-06	ENSG00000089094	ENSG00000089094		"""F-boxes / Leucine-rich repeats"", ""Chromatin-modifying enzymes / K-demethylases"""	13610	protein-coding gene	gene with protein product	"""jumonji C domain-containing histone demethylase 1B"""	609078	"""F-box and leucine-rich repeat protein 10"""	FBXL10		10799292	Standard	NM_032590		Approved	PCCX2, CXXC2, Fbl10, JHDM1B	uc001uat.3	Q8NHM5	OTTHUMG00000169071	ENST00000377071.4:c.3570G>A	12.37:g.121878659C>T		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	88	37	0.420455	NM_032590	A8MRS1|Q8NCI2|Q96HC7|Q96SL0|Q96T03|Q9NS96|Q9UF75	Silent	SNP	ENST00000377071.4	37	CCDS41850.1																																																																																			C|0.667;T|0.333	0.333	strong		0.632	KDM2B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000402132.2	NM_032590	
TANC2	26115	hgsc.bcm.edu	37	17	61315272	61315272	+	Silent	SNP	G	G	A	rs2460111	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:61315272G>A	ENST00000424789.2	+	6	649	c.645G>A	c.(643-645)caG>caA	p.Q215Q	AC037445.1_ENST00000581421.1_RNA|TANC2_ENST00000389520.4_Silent_p.Q215Q	NM_025185.3	NP_079461.2	Q9HCD6	TANC2_HUMAN	tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 2	215					in utero embryonic development (GO:0001701)			p.Q215Q(2)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(15)|ovary(2)|upper_aerodigestive_tract(3)	44						AACCTTGGCAGTCTCAAAAAT	0.393													A|||	2677	0.534545	0.9281	0.4827	5008	,	,		17601	0.1667		0.4911	False		,,,				2504	0.4632				p.Q215Q		Atlas-SNP	.											TANC2_ENST00000389520,NS,lymphoid_neoplasm,0,2	TANC2	266	2	2	Substitution - coding silent(2)	haematopoietic_and_lymphoid_tissue(2)	c.G645A						PASS	.	A		3152,522		1371,410,56	47.0	45.0	46.0		645	0.8	1.0	17	dbSNP_100	46	4195,3997		1083,2029,984	no	coding-synonymous	TANC2	NM_025185.3		2454,2439,1040	AA,AG,GG		48.7915,14.2079,38.0836		215/1991	61315272	7347,4519	1837	4096	5933	SO:0001819	synonymous_variant	26115	exon6			TTGGCAGTCTCAA	AB032974	CCDS45754.1	17q23.3	2013-01-11				ENSG00000170921		"""Ankyrin repeat domain containing"", ""Tetratricopeptide (TTC) repeat domain containing"""	30212	protein-coding gene	gene with protein product	"""rolling pebbles homolog B (Drosophila)"""	615047					Standard	NM_025185		Approved	DKFZP564D166, FLJ10215, FLJ11824, KIAA1148, KIAA1636, rols, ROLSA	uc002jal.4	Q9HCD6		ENST00000424789.2:c.645G>A	17.37:g.61315272G>A		Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	115	114	0.991304	NM_025185	Q9HAC3|Q9NW88|Q9NXY9|Q9ULS2	Silent	SNP	ENST00000424789.2	37	CCDS45754.1																																																																																			G|0.463;A|0.537	0.537	strong		0.393	TANC2-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444765.1		
FDX1L	112812	hgsc.bcm.edu	37	19	10426597	10426597	+	Missense_Mutation	SNP	T	T	C	rs62640397	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:10426597T>C	ENST00000393708.3	-	1	94	c.76A>G	c.(76-78)Aga>Gga	p.R26G	FDX1L_ENST00000541276.1_Missense_Mutation_p.R29G|FDX1L_ENST00000494368.1_Intron|CTD-2369P2.10_ENST00000452032.2_Missense_Mutation_p.R26G|CTD-2369P2.12_ENST00000586529.1_Intron|FDX1L_ENST00000492239.1_5'Flank	NM_001031734.2	NP_001026904.1	Q6P4F2	ADXL_HUMAN	ferredoxin 1-like	26					oxidation-reduction process (GO:0055114)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)	2 iron, 2 sulfur cluster binding (GO:0051537)|electron carrier activity (GO:0009055)|metal ion binding (GO:0046872)			NS(2)|endometrium(1)|large_intestine(1)|lung(3)|skin(2)|upper_aerodigestive_tract(1)	10			OV - Ovarian serous cystadenocarcinoma(20;9.5e-10)|Epithelial(33;2.11e-06)|all cancers(31;5.06e-06)			CCCCCAGGTCTGTTCCACCAG	0.677													T|||	106	0.0211661	0.0015	0.0058	5008	,	,		11423	0.0397		0.0328	False		,,,				2504	0.0276				p.R26G		Atlas-SNP	.											.	FDX1L	21	.	0			c.A76G						PASS	.	T	GLY/ARG	36,4366		0,36,2165	19.0	22.0	21.0		76	-2.5	0.0	19	dbSNP_129	21	269,8329		5,259,4035	yes	missense	FDX1L	NM_001031734.2	125	5,295,6200	CC,CT,TT		3.1286,0.8178,2.3462	benign	26/184	10426597	305,12695	2201	4299	6500	SO:0001583	missense	112812	exon1			CAGGTCTGTTCCA	AK097022	CCDS32905.1	19p13.2	2012-10-09			ENSG00000267673	ENSG00000267673			30546	protein-coding gene	gene with protein product		614585				12477932	Standard	NM_001031734		Approved	MGC19604	uc002mny.1	Q6P4F2	OTTHUMG00000141299	ENST00000393708.3:c.76A>G	19.37:g.10426597T>C	ENSP00000377311:p.Arg26Gly	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	70	31	0.442857	NM_001031734	Q8N8B8	Missense_Mutation	SNP	ENST00000393708.3	37	CCDS32905.1	56	0.02564102564102564	1	0.0020325203252032522	2	0.0055248618784530384	26	0.045454545454545456	27	0.03562005277044855	T	10.47	1.359917	0.24598	0.008178	0.031286	ENSG00000167807	ENST00000541276;ENST00000393708	.	.	.	4.14	-2.54	0.06307	.	0.296563	0.29956	N	0.010774	T	0.01976	0.0062	N	0.08118	0	0.19775	N	0.999957	B	0.06786	0.001	B	0.04013	0.001	T	0.06935	-1.0799	9	0.87932	D	0	-10.9532	3.6387	0.08158	0.11:0.0955:0.4395:0.355	.	26	Q6P4F2	ADXL_HUMAN	G	29;26	.	ENSP00000341665:R26G	R	-	1	2	FDX1L	10287597	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.952000	0.03881	-0.744000	0.04778	-2.293000	0.00265	AGA	T|0.980;C|0.020	0.020	strong		0.677	FDX1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280567.2		
NOL6	65083	hgsc.bcm.edu	37	9	33466219	33466219	+	Silent	SNP	A	A	C	rs3739681	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:33466219A>C	ENST00000379471.2	-	18	2301	c.2214T>G	c.(2212-2214)gtT>gtG	p.V738V	NOL6_ENST00000455041.2_Silent_p.V686V|NOL6_ENST00000464829.1_Intron			Q9H6R4	NOL6_HUMAN	nucleolar protein 6 (RNA-associated)	738					rRNA processing (GO:0006364)	condensed nuclear chromosome (GO:0000794)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			endometrium(4)|kidney(4)|large_intestine(5)|lung(8)|ovary(2)|prostate(2)|skin(2)	27			LUSC - Lung squamous cell carcinoma(29;0.00788)	GBM - Glioblastoma multiforme(74;0.152)		CCAGGTGACAAACCACTGAGG	0.627													A|||	861	0.171925	0.174	0.1398	5008	,	,		17424	0.2262		0.1412	False		,,,				2504	0.1677				p.V738V		Atlas-SNP	.											.	NOL6	85	.	0			c.T2214G						PASS	.	A	,	710,3696	290.4+/-280.9	49,612,1542	53.0	54.0	54.0		2214,	-2.9	1.0	9	dbSNP_107	54	1337,7263	256.9+/-281.2	114,1109,3077	no	coding-synonymous,intron	NOL6	NM_022917.4,NM_139235.3	,	163,1721,4619	CC,CA,AA		15.5465,16.1144,15.7389	,	738/1147,	33466219	2047,10959	2203	4300	6503	SO:0001819	synonymous_variant	65083	exon18			GTGACAAACCACT	AF361079	CCDS6543.1, CCDS6544.1	9p12	2013-02-22	2013-02-22		ENSG00000165271	ENSG00000165271			19910	protein-coding gene	gene with protein product		611532	"""nucleolar protein family 6 (RNA-associated)"""			11895476, 15590835	Standard	NM_022917		Approved	bA311H10.1, Nrap, FLJ21959, MGC14896, MGC14921, MGC20838, UTP22	uc003zsz.3	Q9H6R4	OTTHUMG00000000394	ENST00000379471.2:c.2214T>G	9.37:g.33466219A>C		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	56	29	0.517857	NM_022917	Q5T5M3|Q5T5M4|Q7L4G6|Q8N6I0|Q8TEY9|Q8TEZ0|Q8TEZ1|Q9H675	Silent	SNP	ENST00000379471.2	37																																																																																				A|0.831;C|0.169	0.169	strong		0.627	NOL6-005	NOVEL	non_canonical_TEC|basic	protein_coding	protein_coding	OTTHUMT00000001019.2	NM_022917	
ADAMTS18	170692	hgsc.bcm.edu	37	16	77327018	77327018	+	Silent	SNP	G	G	A	rs35296483	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:77327018G>A	ENST00000282849.5	-	20	3562	c.3144C>T	c.(3142-3144)tgC>tgT	p.C1048C	RP11-538I12.3_ENST00000561672.1_RNA	NM_199355.2	NP_955387.1	Q8TE60	ATS18_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 18	1048	TSP type-1 3. {ECO:0000255|PROSITE- ProRule:PRU00210}.				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						TGTTCTTGGGGCATCGTCCAA	0.587													G|||	622	0.124201	0.0061	0.2507	5008	,	,		15862	0.1935		0.1262	False		,,,				2504	0.1207				p.C1048C		Atlas-SNP	.											.	ADAMTS18	270	.	0			c.C3144T						PASS	.	G		103,4293	80.9+/-119.3	3,97,2098	86.0	79.0	82.0		3144	1.6	1.0	16	dbSNP_126	82	1125,7475	233.6+/-266.8	71,983,3246	no	coding-synonymous	ADAMTS18	NM_199355.2		74,1080,5344	AA,AG,GG		13.0814,2.343,9.4491		1048/1222	77327018	1228,11768	2198	4300	6498	SO:0001819	synonymous_variant	170692	exon20			CTTGGGGCATCGT	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.3144C>T	16.37:g.77327018G>A		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	70	23	0.328571	NM_199355	Q6P4R5|Q6ZWJ9	Silent	SNP	ENST00000282849.5	37	CCDS10926.1																																																																																			G|0.891;A|0.109	0.109	strong		0.587	ADAMTS18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269037.1		
DTHD1	401124	hgsc.bcm.edu	37	4	36296443	36296443	+	Silent	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:36296443G>A	ENST00000456874.2	+	4	1108	c.1050G>A	c.(1048-1050)gtG>gtA	p.V350V	DTHD1_ENST00000507598.1_Silent_p.V390V|DTHD1_ENST00000357504.3_Silent_p.V185V	NM_001170700.2	NP_001164171.1	Q6ZMT9	DTHD1_HUMAN	death domain containing 1	350					signal transduction (GO:0007165)					breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|stomach(1)	8						CAGCTCTGGTGGCACATTTAA	0.368																																					p.V350V		Atlas-SNP	.											.	DTHD1	63	.	0			c.G1050A						PASS	.						153.0	122.0	131.0					4																	36296443		692	1591	2283	SO:0001819	synonymous_variant	401124	exon4			TCTGGTGGCACAT	AK094684	CCDS54754.1	4p14	2009-10-02			ENSG00000197057	ENSG00000197057			37261	protein-coding gene	gene with protein product							Standard	NM_001170700		Approved	FLJ16686	uc021xne.2	Q6ZMT9	OTTHUMG00000160371	ENST00000456874.2:c.1050G>A	4.37:g.36296443G>A		Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	134	60	0.447761	NM_001170700	B2RXK4|B4E2N7	Silent	SNP	ENST00000456874.2	37	CCDS54754.1																																																																																			.	.	none		0.368	DTHD1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001136536	
CCDC157	550631	hgsc.bcm.edu	37	22	30762035	30762035	+	Missense_Mutation	SNP	A	A	G	rs9606721	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:30762035A>G	ENST00000405659.1	+	3	755	c.46A>G	c.(46-48)Aca>Gca	p.T16A	CCDC157_ENST00000399824.2_Missense_Mutation_p.T16A|CCDC157_ENST00000338306.3_Missense_Mutation_p.T16A			Q569K6	CC157_HUMAN	coiled-coil domain containing 157	16				T -> A (in Ref. 2; AAH92419/AAI19800/ AAI27256). {ECO:0000305}.						central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(5)|skin(3)|upper_aerodigestive_tract(1)	15						GAGCCTGCGCACAGACCTCAC	0.667													A|||	36	0.0071885	0.0015	0.0043	5008	,	,		18645	0.0		0.0288	False		,,,				2504	0.002				p.T16A		Atlas-SNP	.											.	CCDC157	86	.	0			c.A46G						PASS	.	A	ALA/THR	3,1381		0,3,689	41.0	48.0	46.0		46	1.8	1.0	22	dbSNP_119	46	68,3114		0,68,1523	yes	missense	CCDC157	NM_001017437.2	58	0,71,2212	GG,GA,AA		2.137,0.2168,1.555	benign	16/753	30762035	71,4495	692	1591	2283	SO:0001583	missense	550631	exon3			CTGCGCACAGACC	BC018040	CCDS33632.2	22q12.2	2009-03-05			ENSG00000187860	ENSG00000187860			33854	protein-coding gene	gene with protein product							Standard	NM_001017437		Approved		uc011aku.2	Q569K6	OTTHUMG00000151007	ENST00000405659.1:c.46A>G	22.37:g.30762035A>G	ENSP00000385357:p.Thr16Ala	Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	49	19	0.387755	NM_001017437	Q0VD76|Q9BYA4	Missense_Mutation	SNP	ENST00000405659.1	37	CCDS33632.2	27	0.012362637362637362	2	0.0040650406504065045	1	0.0027624309392265192	0	0.0	24	0.0316622691292876	A	13.54	2.268147	0.40095	0.002168	0.02137	ENSG00000187860	ENST00000399824;ENST00000405659;ENST00000338306;ENST00000445005;ENST00000430839	T;T;T;T;T	0.40756	1.02;2.02;2.02;1.6;1.6	5.36	1.76	0.24704	.	.	.	.	.	T	0.07098	0.0180	N	0.08118	0	0.58432	D	0.999999	B	0.06786	0.001	B	0.08055	0.003	T	0.04178	-1.0971	9	0.33141	T	0.24	-18.4701	7.5038	0.27532	0.5034:0.4206:0.076:0.0	rs9606721	16	Q569K6	CC157_HUMAN	A	16	ENSP00000382720:T16A;ENSP00000385357:T16A;ENSP00000343087:T16A;ENSP00000387491:T16A;ENSP00000401837:T16A	ENSP00000343087:T16A	T	+	1	0	CCDC157	29092035	1.000000	0.71417	0.969000	0.41365	0.651000	0.38670	3.752000	0.55172	0.406000	0.25560	-0.666000	0.03841	ACA	A|0.987;G|0.013	0.013	strong		0.667	CCDC157-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320936.1	NM_001017437	
WDR41	55255	hgsc.bcm.edu	37	5	76734084	76734084	+	Missense_Mutation	SNP	C	C	T	rs33204	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:76734084C>T	ENST00000296679.4	-	10	1360	c.985G>A	c.(985-987)Gtt>Att	p.V329I	WDR41_ENST00000507029.1_Missense_Mutation_p.V274I|WDR41_ENST00000512033.1_5'Flank|WDR41_ENST00000414719.2_Missense_Mutation_p.V75I	NM_018268.2	NP_060738.2	Q9HAD4	WDR41_HUMAN	WD repeat domain 41	329			V -> I (in dbSNP:rs33204). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:17974005}.			lysosomal membrane (GO:0005765)				NS(1)|autonomic_ganglia(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(5)	14		all_lung(232;0.000961)|Lung NSC(167;0.0011)|Ovarian(174;0.0105)|Prostate(461;0.059)		OV - Ovarian serous cystadenocarcinoma(54;6.3e-50)|Epithelial(54;2.04e-44)|all cancers(79;6.84e-40)		AGTCTGGCAACGTGCAGGACA	0.463													T|||	2646	0.528355	0.6362	0.611	5008	,	,		21138	0.4603		0.4205	False		,,,				2504	0.5051				p.V329I		Atlas-SNP	.											.	WDR41	29	.	0			c.G985A						PASS	.	T	ILE/VAL	2590,1816	532.2+/-373.4	761,1068,374	228.0	214.0	218.0		985	-2.4	0.0	5	dbSNP_76	218	3902,4698	604.5+/-394.8	914,2074,1312	yes	missense	WDR41	NM_018268.2	29	1675,3142,1686	TT,TC,CC		45.3721,41.2165,49.9154	benign	329/460	76734084	6492,6514	2203	4300	6503	SO:0001583	missense	55255	exon10			TGGCAACGTGCAG	AF115511	CCDS4038.1	5q14	2013-01-09			ENSG00000164253	ENSG00000164253		"""WD repeat domain containing"""	25601	protein-coding gene	gene with protein product						12477932	Standard	NM_018268		Approved	FLJ10904	uc003kff.1	Q9HAD4	OTTHUMG00000102169	ENST00000296679.4:c.985G>A	5.37:g.76734084C>T	ENSP00000296679:p.Val329Ile	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	140	75	0.535714	NM_018268	B4DT55|Q7Z792|Q8IWG3|Q8IXA9|Q8NDA7|Q9NV62	Missense_Mutation	SNP	ENST00000296679.4	37	CCDS4038.1	1102	0.5045787545787546	318	0.6463414634146342	212	0.585635359116022	270	0.47202797202797203	302	0.39841688654353563	T	0.196	-1.048825	0.01981	0.587835	0.453721	ENSG00000164253	ENST00000296679;ENST00000414719;ENST00000515253;ENST00000507029;ENST00000507654	T;T;T;T;T	0.61040	0.14;0.14;0.14;0.14;0.14	5.75	-2.41	0.06562	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.335923	0.35096	N	0.003446	T	0.00012	0.0000	N	0.04387	-0.21	0.80722	P	0.0	B;B;B	0.06786	0.001;0.001;0.0	B;B;B	0.04013	0.001;0.001;0.001	T	0.47548	-0.9109	9	0.34782	T	0.22	-1.4621	12.8081	0.57626	0.0:0.4274:0.0:0.5726	rs33204;rs1128214;rs3184901;rs11550077;rs17409156;rs17856058;rs52790159;rs59230263;rs33204	274;75;329	B4DT55;B4E2L4;Q9HAD4	.;.;WDR41_HUMAN	I	329;75;264;274;100	ENSP00000296679:V329I;ENSP00000392931:V75I;ENSP00000426499:V264I;ENSP00000424287:V274I;ENSP00000427291:V100I	ENSP00000296679:V329I	V	-	1	0	WDR41	76769840	0.999000	0.42202	0.031000	0.17742	0.239000	0.25481	0.529000	0.23019	-0.623000	0.05618	-1.007000	0.02485	GTT	C|0.490;T|0.510	0.510	strong		0.463	WDR41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000220014.2	NM_018268	
OR10AD1	121275	hgsc.bcm.edu	37	12	48596546	48596546	+	Missense_Mutation	SNP	C	C	T	rs75531856	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:48596546C>T	ENST00000310248.2	-	1	624	c.530G>A	c.(529-531)aGc>aAc	p.S177N		NM_001004134.1	NP_001004134.1	Q8NGE0	O10AD_HUMAN	olfactory receptor, family 10, subfamily AD, member 1	177						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(2)|lung(3)|ovary(1)|stomach(1)|urinary_tract(1)	9						ACAGAAGAAGCTTTCTATGTG	0.507													T|||	213	0.0425319	0.059	0.036	5008	,	,		21070	0.006		0.0924	False		,,,				2504	0.0112				p.S177N		Atlas-SNP	.											.	OR10AD1	24	.	0			c.G530A						PASS	.	T	ASN/SER	275,4131	800.4+/-415.6	8,259,1936	51.0	42.0	45.0		530	3.7	0.6	12	dbSNP_131	45	762,7838	784.1+/-407.6	30,702,3568	yes	missense	OR10AD1	NM_001004134.1	46	38,961,5504	TT,TC,CC		8.8605,6.2415,7.9732	benign	177/318	48596546	1037,11969	2203	4300	6503	SO:0001583	missense	121275	exon1			AAGAAGCTTTCTA		CCDS31787.1	12q13.11	2013-09-24	2002-11-13	2002-11-15	ENSG00000172640	ENSG00000172640		"""GPCR / Class A : Olfactory receptors"""	14819	protein-coding gene	gene with protein product			"""olfactory receptor, family 10, subfamily AD, member 1 pseudogene"""	OR10AD1P			Standard	NM_001004134		Approved		uc001rrl.1	Q8NGE0	OTTHUMG00000168027	ENST00000310248.2:c.530G>A	12.37:g.48596546C>T	ENSP00000308689:p.Ser177Asn	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	124	55	0.443548	NM_001004134	B9EGT9|Q6IFA8	Missense_Mutation	SNP	ENST00000310248.2	37	CCDS31787.1	99	0.04532967032967033	21	0.042682926829268296	9	0.024861878453038673	3	0.005244755244755245	66	0.0870712401055409	T	9.976	1.226799	0.22542	0.062415	0.088605	ENSG00000172640	ENST00000310248	T	0.00137	8.68	4.83	3.69	0.42338	GPCR, rhodopsin-like superfamily (1);	0.000000	0.42682	N	0.000680	T	0.00012	0.0000	N	0.02345	-0.59	0.19775	N	0.999958	B	0.02656	0.0	B	0.01281	0.0	T	0.31447	-0.9943	10	0.66056	D	0.02	-26.1844	7.8654	0.29535	0.0:0.1739:0.0:0.8261	.	177	Q8NGE0	O10AD_HUMAN	N	177	ENSP00000308689:S177N	ENSP00000308689:S177N	S	-	2	0	OR10AD1	46882813	1.000000	0.71417	0.627000	0.29227	0.469000	0.32828	2.446000	0.44908	0.439000	0.26476	-0.361000	0.07541	AGC	C|0.935;T|0.065	0.065	strong		0.507	OR10AD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397577.1		
CCDC9	26093	hgsc.bcm.edu	37	19	47774680	47774680	+	Silent	SNP	C	C	G	rs117519030	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:47774680C>G	ENST00000221922.6	+	12	1563	c.1341C>G	c.(1339-1341)gcC>gcG	p.A447A		NM_015603.2	NP_056418.1	Q9Y3X0	CCDC9_HUMAN	coiled-coil domain containing 9	447							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)		aggaACCAGCCCAAGACCACC	0.612													C|||	36	0.0071885	0.0023	0.0043	5008	,	,		14944	0.0		0.0249	False		,,,				2504	0.0051				p.A447A		Atlas-SNP	.											.	CCDC9	37	.	0			c.C1341G						PASS	.	C		23,4383		0,23,2180	109.0	105.0	106.0		1341	-1.1	0.0	19	dbSNP_132	106	311,8287		7,297,3995	no	coding-synonymous	CCDC9	NM_015603.2		7,320,6175	GG,GC,CC		3.6171,0.522,2.5684		447/532	47774680	334,12670	2203	4299	6502	SO:0001819	synonymous_variant	26093	exon12			ACCAGCCCAAGAC	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.1341C>G	19.37:g.47774680C>G		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	55	30	0.545455	NM_015603		Silent	SNP	ENST00000221922.6	37	CCDS12698.1																																																																																			C|0.978;G|0.022	0.022	strong		0.612	CCDC9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466917.1	NM_015603	
IRF3	3661	hgsc.bcm.edu	37	19	50162909	50162909	+	Missense_Mutation	SNP	C	C	G	rs7251	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:50162909C>G	ENST00000597198.1	-	8	1661	c.1280G>C	c.(1279-1281)aGc>aCc	p.S427T	IRF3_ENST00000599223.1_Missense_Mutation_p.S300T|IRF3_ENST00000600022.1_Missense_Mutation_p.S154T|IRF3_ENST00000596822.1_Missense_Mutation_p.E115D|IRF3_ENST00000309877.7_Missense_Mutation_p.S427T|IRF3_ENST00000599144.1_Missense_Mutation_p.S281T|IRF3_ENST00000600911.1_Missense_Mutation_p.E388D|IRF3_ENST00000377139.3_Missense_Mutation_p.S427T|IRF3_ENST00000599680.1_5'UTR|IRF3_ENST00000377135.4_Missense_Mutation_p.S300T|IRF3_ENST00000593922.1_Missense_Mutation_p.S281T|IRF3_ENST00000598808.1_Missense_Mutation_p.S281T|IRF3_ENST00000601291.1_Missense_Mutation_p.E432D|IRF3_ENST00000596765.1_Missense_Mutation_p.S154T			Q14653	IRF3_HUMAN	interferon regulatory factor 3	427			S -> T (in dbSNP:rs7251). {ECO:0000269|PubMed:14702039, ECO:0000269|Ref.5}.		apoptotic process (GO:0006915)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to dsRNA (GO:0071359)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|innate immune response (GO:0045087)|interferon-gamma-mediated signaling pathway (GO:0060333)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|macrophage apoptotic process (GO:0071888)|MDA-5 signaling pathway (GO:0039530)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of defense response to virus by host (GO:0050689)|negative regulation of interferon-beta biosynthetic process (GO:0045358)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of type I interferon production (GO:0032480)|positive regulation of cytokine secretion (GO:0050715)|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 type I interferon production (GO:0032481)|positive regulation of type I interferon-mediated signaling pathway (GO:0060340)|programmed necrotic cell death (GO:0097300)|response to exogenous dsRNA (GO:0043330)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|transcription from RNA polymerase II promoter (GO:0006366)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|type I interferon biosynthetic process (GO:0045351)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription cofactor activity (GO:0003712)|transcription regulatory region DNA binding (GO:0044212)	p.S427T(1)		breast(1)|large_intestine(2)|lung(4)|ovary(2)|stomach(1)	10		all_lung(116;3.24e-07)|Lung NSC(112;1.6e-06)|all_neural(266;0.0459)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.0011)|GBM - Glioblastoma multiforme(134;0.02)		GAGGGCTCAGCTCTCCCCAGG	0.587													G|||	2427	0.484625	0.708	0.4409	5008	,	,		17387	0.3571		0.333	False		,,,				2504	0.501				p.E432D		Atlas-SNP	.											IRF3,NS,carcinoma,0,1	IRF3	27	1	1	Substitution - Missense(1)	stomach(1)	c.G1296C						scavenged	.	G	ASP/GLU,THR/SER,THR/SER,THR/SER,THR/SER,THR/SER,THR/SER,THR/SER	2920,1484	467.0+/-354.7	986,948,268	108.0	91.0	97.0		1296,1175,899,842,842,461,461,1280	-1.1	0.0	19	dbSNP_52	97	2715,5879	670.6+/-402.8	431,1853,2013	yes	missense,missense,missense,missense,missense,missense,missense,missense	IRF3	NM_001197122.1,NM_001197123.1,NM_001197124.1,NM_001197125.1,NM_001197126.1,NM_001197127.1,NM_001197128.1,NM_001571.5	45,58,58,58,58,58,58,58	1417,2801,2281	GG,GC,CC		31.5918,33.6966,43.3528	benign,benign,benign,benign,benign,benign,benign,benign	432/453,392/393,300/301,281/282,281/282,154/155,154/155,427/428	50162909	5635,7363	2202	4297	6499	SO:0001583	missense	3661	exon8			GCTCAGCTCTCCC		CCDS12775.1, CCDS56099.1, CCDS59407.1, CCDS59408.1, CCDS59409.1	19q13.3-q13.4	2008-07-16				ENSG00000126456			6118	protein-coding gene	gene with protein product		603734				8524823	Standard	NM_001571		Approved		uc002pow.3	Q14653		ENST00000597198.1:c.1280G>C	19.37:g.50162909C>G	ENSP00000469113:p.Ser427Thr	Somatic	73	1	0.0136986		WXS	Illumina HiSeq	Phase_I	70	35	0.5	NM_001197122	A8K7L2|B2RAZ3|Q5FBY1|Q5FBY2|Q5FBY4|Q7Z5G6	Missense_Mutation	SNP	ENST00000597198.1	37	CCDS12775.1	971	0.44459706959706957	355	0.7215447154471545	153	0.42265193370165743	220	0.38461538461538464	243	0.32058047493403696	G	0.062	-1.221020	0.01530	0.663034	0.315918	ENSG00000126456	ENST00000377139;ENST00000309877;ENST00000377135	D;D;D	0.96554	-4.05;-4.05;-3.94	4.25	-1.13	0.09775	SMAD/FHA domain (1);	.	.	.	.	T	0.00012	0.0000	N	0.02011	-0.69	0.40695	P	0.017568999999999946	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.31779	-0.9931	8	0.02654	T	1	.	4.4658	0.11689	0.3207:0.3403:0.3389:0.0	rs7251;rs17713;rs3170560;rs12976242;rs17856307;rs59032938;rs7251	427;300	Q14653;Q5FBY1	IRF3_HUMAN;.	T	427;427;300	ENSP00000366344:S427T;ENSP00000310127:S427T;ENSP00000366339:S300T	ENSP00000310127:S427T	S	-	2	0	IRF3	54854721	0.000000	0.05858	0.002000	0.10522	0.001000	0.01503	-0.481000	0.06552	-0.168000	0.10853	-0.225000	0.12378	AGC	C|0.546;G|0.454	0.454	strong		0.587	IRF3-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465962.1	NM_001571	
BRD2	6046	hgsc.bcm.edu	37	6	32946133	32946133	+	Silent	SNP	T	T	C	rs206781	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:32946133T>C	ENST00000374825.4	+	10	3510	c.1809T>C	c.(1807-1809)tcT>tcC	p.S603S	BRD2_ENST00000395287.1_Silent_p.S603S|BRD2_ENST00000395289.2_Silent_p.S603S|BRD2_ENST00000449085.2_Silent_p.S556S|BRD2_ENST00000443797.2_Silent_p.S483S|BRD2_ENST00000374831.4_Silent_p.S603S	NM_005104.3	NP_005095.1	P25440	BRD2_HUMAN	bromodomain containing 2	603					chromatin modification (GO:0016568)|nucleosome assembly (GO:0006334)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|lysine-acetylated histone binding (GO:0070577)			central_nervous_system(3)|stomach(2)	5						TAGGCCCTTCTGGCTTTGGAC	0.537													T|||	1323	0.264177	0.171	0.2911	5008	,	,		17525	0.1964		0.3748	False		,,,				2504	0.3272				p.S603S		Atlas-SNP	.											.	BRD2	70	.	0			c.T1809C						PASS	.	T	,,,	646,2372		62,522,925	153.0	164.0	160.0		1809,1809,1668,1809	1.5	1.0	6	dbSNP_79	160	2009,3409		381,1247,1081	yes	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	BRD2	NM_001113182.2,NM_001199455.1,NM_001199456.1,NM_005104.3	,,,	443,1769,2006	CC,CT,TT		37.0801,21.4049,31.4723	,,,	603/802,603/837,556/755,603/802	32946133	2655,5781	1509	2709	4218	SO:0001819	synonymous_variant	6046	exon10			CCCTTCTGGCTTT	X96670	CCDS4762.1, CCDS56420.1, CCDS56421.1	6p21.3	2010-12-23	2002-01-14		ENSG00000204256	ENSG00000204256			1103	protein-coding gene	gene with protein product		601540	"""bromodomain-containing 2"""			1352711, 8781126	Standard	NM_005104		Approved	KIAA9001, RING3, D6S113E, NAT, FSRG1	uc021ywf.1	P25440	OTTHUMG00000031241	ENST00000374825.4:c.1809T>C	6.37:g.32946133T>C		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	97	51	0.525773	NM_005104	A2AAU0|B0S7P0|B1AZT1|O00699|O00700|Q15310|Q5STC9|Q63HQ9|Q658Y7|Q6P3U2|Q969U4	Silent	SNP	ENST00000374825.4	37	CCDS4762.1	597	0.2733516483516483	89	0.18089430894308944	100	0.27624309392265195	111	0.19405594405594406	297	0.391820580474934	T	10.96	1.499210	0.26861	0.214049	0.370801	ENSG00000204256	ENST00000449025	.	.	.	5.37	1.48	0.22813	.	.	.	.	.	T	0.12050	0.0293	.	.	.	0.09310	P	0.9999999999999775	.	.	.	.	.	.	T	0.20371	-1.0277	3	.	.	.	-6.2398	2.2795	0.04111	0.1549:0.0857:0.1614:0.5979	rs206781;rs209471;rs622332;rs1049374;rs1265601;rs2070267;rs3189519;rs6919815;rs17416379;rs17508857;rs17855228;rs206781	.	.	.	P	609	.	.	L	+	2	0	BRD2	33054111	0.445000	0.25657	0.993000	0.49108	0.968000	0.65278	-0.043000	0.12043	0.446000	0.26666	-0.307000	0.09154	CTG	T|0.705;C|0.295	0.295	strong		0.537	BRD2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076503.2		
TSEN54	283989	hgsc.bcm.edu	37	17	73513289	73513289	+	Silent	SNP	C	C	G	rs6501818	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:73513289C>G	ENST00000333213.6	+	4	369	c.333C>G	c.(331-333)cgC>cgG	p.R111R	CASKIN2_ENST00000581870.1_5'Flank|CASKIN2_ENST00000321617.3_5'Flank|TSEN54_ENST00000580013.1_3'UTR	NM_207346.2	NP_997229.2	Q7Z6J9	SEN54_HUMAN	TSEN54 tRNA splicing endonuclease subunit	111					mRNA processing (GO:0006397)|tRNA splicing, via endonucleolytic cleavage and ligation (GO:0006388)	nucleus (GO:0005634)				endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(1)|lung(5)|ovary(2)	13	all_cancers(13;3.15e-09)|all_epithelial(9;5.78e-10)|Breast(9;5.8e-10)|all_lung(278;0.246)		all cancers(21;4.57e-07)|Epithelial(20;2.92e-06)|Lung(188;0.0809)|LUSC - Lung squamous cell carcinoma(166;0.154)			GCCGGCAGCGCCTTCACCCGG	0.612													G|||	817	0.163139	0.351	0.1066	5008	,	,		15203	0.0298		0.1421	False		,,,				2504	0.1084				p.R111R		Atlas-SNP	.											.	TSEN54	27	.	0			c.C333G						PASS	.	G		1452,2942		260,932,1005	20.0	23.0	22.0		333	2.0	1.0	17	dbSNP_116	22	1130,7468		70,990,3239	no	coding-synonymous	TSEN54	NM_207346.2		330,1922,4244	GG,GC,CC		13.1426,33.0451,19.8738		111/527	73513289	2582,10410	2197	4299	6496	SO:0001819	synonymous_variant	283989	exon4			GCAGCGCCTTCAC	AK097583	CCDS11724.1	17q25.1	2013-08-06	2013-08-06		ENSG00000182173	ENSG00000182173		"""tRNA splicing endonuclease subunits"""	27561	protein-coding gene	gene with protein product		608755	"""tRNA splicing endonuclease 54 homolog (SEN54, S. cerevisiae)"", ""tRNA splicing endonuclease 54 homolog (S. cerevisiae)"""			15109492	Standard	NM_207346		Approved	SEN54, SEN54L	uc002jof.1	Q7Z6J9		ENST00000333213.6:c.333C>G	17.37:g.73513289C>G		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	90	47	0.522222	NM_207346	Q86WV3|Q86XE4|Q8N9H2	Silent	SNP	ENST00000333213.6	37	CCDS11724.1																																																																																			C|0.822;G|0.178	0.178	strong		0.612	TSEN54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447618.1	NM_207346	
PRDM1	639	hgsc.bcm.edu	37	6	106547372	106547372	+	Missense_Mutation	SNP	C	C	G	rs811925	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:106547372C>G	ENST00000369096.4	+	4	843	c.609C>G	c.(607-609)gaC>gaG	p.D203E	PRDM1_ENST00000369089.3_Missense_Mutation_p.D69E|PRDM1_ENST00000369091.2_Missense_Mutation_p.D167E|RP1-134E15.3_ENST00000602426.1_RNA	NM_001198.3	NP_001189.2	O75626	PRDM1_HUMAN	PR domain containing 1, with ZNF domain	203			D -> E (in dbSNP:rs811925).		cell fate commitment (GO:0045165)|eye photoreceptor cell development (GO:0042462)|germ cell development (GO:0007281)|intestinal epithelial cell development (GO:0060576)|maternal placenta development (GO:0001893)|negative regulation of B cell proliferation (GO:0030889)|negative regulation of lipopolysaccharide-mediated signaling pathway (GO:0031665)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of B cell differentiation (GO:0045579)|positive regulation of gene expression (GO:0010628)|post-embryonic development (GO:0009791)|transcription, DNA-templated (GO:0006351)|trophoblast giant cell differentiation (GO:0060707)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(59)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|skin(5)|urinary_tract(2)	94	Breast(9;0.022)	all_cancers(87;2.2e-31)|all_epithelial(87;2.03e-21)|Acute lymphoblastic leukemia(125;4.99e-11)|all_lung(197;7.55e-09)|all_hematologic(75;5.82e-08)|Lung NSC(302;1.28e-06)|Colorectal(196;0.0112)|Ovarian(999;0.0365)		all cancers(137;1.83e-46)|Epithelial(106;5.59e-35)|OV - Ovarian serous cystadenocarcinoma(136;1.99e-20)|GBM - Glioblastoma multiforme(226;3.72e-11)|BRCA - Breast invasive adenocarcinoma(108;1.38e-05)		ATTGTCGGGACTTTGCAGAAA	0.443			"""D, N, Mis, F, S"""		DLBCL								C|||	752	0.15016	0.1558	0.1513	5008	,	,		19653	0.0208		0.2048	False		,,,				2504	0.2188				p.D203E		Atlas-SNP	.		Rec	yes		6	6q21	639	"""PR domain containing 1, with ZNF domain"""		L	.	PRDM1	195	.	0			c.C609G						PASS	.	C	GLU/ASP,GLU/ASP	717,3689	296.7+/-284.4	62,593,1548	96.0	83.0	87.0		609,207	5.9	1.0	6	dbSNP_86	87	1457,7143	278.4+/-293.4	108,1241,2951	yes	missense,missense	PRDM1	NM_001198.3,NM_182907.1	45,45	170,1834,4499	GG,GC,CC		16.9419,16.2733,16.7154	probably-damaging,probably-damaging	203/826,69/692	106547372	2174,10832	2203	4300	6503	SO:0001583	missense	639	exon4			TCGGGACTTTGCA		CCDS5054.2, CCDS34505.1	6q21	2013-01-08			ENSG00000057657	ENSG00000057657		"""Zinc fingers, C2H2-type"""	9346	protein-coding gene	gene with protein product		603423		BLIMP1		1851123	Standard	NM_001198		Approved	PRDI-BF1	uc003prd.2	O75626	OTTHUMG00000015299	ENST00000369096.4:c.609C>G	6.37:g.106547372C>G	ENSP00000358092:p.Asp203Glu	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	103	43	0.417476	NM_001198	B2REA6|E1P5E0|Q86WM7	Missense_Mutation	SNP	ENST00000369096.4	37	CCDS5054.2	297	0.13598901098901098	70	0.14227642276422764	61	0.1685082872928177	10	0.017482517482517484	156	0.20580474934036938	C	5.903	0.350657	0.11182	0.162733	0.169419	ENSG00000057657	ENST00000369091;ENST00000369096;ENST00000456278;ENST00000450060;ENST00000369089	D;D;D;D	0.89343	-2.5;-2.5;-2.5;-2.5	5.94	5.94	0.96194	SET domain (2);	0.091905	0.85682	D	0.000000	T	0.64713	0.2623	N	0.02708	-0.52	0.22873	P	0.99862732	P;P	0.39116	0.66;0.568	B;B	0.35971	0.215;0.046	T	0.73972	-0.3814	9	0.09843	T	0.71	-48.4594	20.3736	0.98901	0.0:1.0:0.0:0.0	rs811925;rs17440760;rs811925	69;203	Q86WM7;O75626	.;PRDM1_HUMAN	E	167;203;167;82;69	ENSP00000358087:D167E;ENSP00000358092:D203E;ENSP00000399772:D82E;ENSP00000358085:D69E	ENSP00000358085:D69E	D	+	3	2	PRDM1	106654065	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.723000	0.38053	2.820000	0.97059	0.650000	0.86243	GAC	C|0.843;G|0.157	0.157	strong		0.443	PRDM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041661.3		
CCDC8	83987	hgsc.bcm.edu	37	19	46915702	46915702	+	Silent	SNP	C	C	T	rs35262679	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:46915702C>T	ENST00000307522.3	-	1	1139	c.366G>A	c.(364-366)cgG>cgA	p.R122R		NM_032040.4	NP_114429.2	Q9H0W5	CCDC8_HUMAN	coiled-coil domain containing 8	122					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)		TCTTGCCCCGCCGCGGGCCCT	0.647													C|||	210	0.0419329	0.0575	0.0447	5008	,	,		12883	0.0099		0.0577	False		,,,				2504	0.0358				p.R122R		Atlas-SNP	.											.	CCDC8	56	.	0			c.G366A						PASS	.	C		231,4173	136.9+/-172.8	4,223,1975	48.0	54.0	52.0		366	-1.1	0.0	19	dbSNP_126	52	541,8059	147.7+/-203.1	15,511,3774	no	coding-synonymous	CCDC8	NM_032040.3		19,734,5749	TT,TC,CC		6.2907,5.2452,5.9366		122/539	46915702	772,12232	2202	4300	6502	SO:0001819	synonymous_variant	83987	exon1			GCCCCGCCGCGGG	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.366G>A	19.37:g.46915702C>T		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	59	25	0.423729	NM_032040	Q8TB26	Silent	SNP	ENST00000307522.3	37	CCDS12685.1																																																																																			C|0.941;T|0.059	0.059	strong		0.647	CCDC8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368598.1	NM_032040	
AXIN1	8312	hgsc.bcm.edu	37	16	347184	347184	+	Silent	SNP	A	A	G	rs214252	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	49	0	0		WXS	Illumina HiSeq	Phase_I	76	13	0.171053	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		
PDXK	8566	hgsc.bcm.edu	37	21	45168884	45168884	+	Silent	SNP	G	G	A	rs11539534	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:45168884G>A	ENST00000291565.4	+	6	570	c.387G>A	c.(385-387)ccG>ccA	p.P129P	PDXK_ENST00000468090.1_Silent_p.P101P|PDXK_ENST00000467908.1_Silent_p.P89P	NM_003681.4	NP_003672.1	O00764	PDXK_HUMAN	pyridoxal (pyridoxine, vitamin B6) kinase	129					cell proliferation (GO:0008283)|pyridoxal 5'-phosphate salvage (GO:0009443)|pyridoxal phosphate biosynthetic process (GO:0042823)|small molecule metabolic process (GO:0044281)|vitamin B6 metabolic process (GO:0042816)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|lithium ion binding (GO:0031403)|magnesium ion binding (GO:0000287)|potassium ion binding (GO:0030955)|protein homodimerization activity (GO:0042803)|pyridoxal kinase activity (GO:0008478)|pyridoxal phosphate binding (GO:0030170)|sodium ion binding (GO:0031402)|zinc ion binding (GO:0008270)			endometrium(1)|lung(2)|ovary(1)|urinary_tract(1)	5				Colorectal(79;0.109)|READ - Rectum adenocarcinoma(84;0.161)|STAD - Stomach adenocarcinoma(101;0.18)	Pyridoxal(DB00147)|Pyridoxine(DB00165)	AGTACGTCCCGGAGGACCTCC	0.557													G|||	756	0.150958	0.0726	0.2075	5008	,	,		16291	0.2123		0.0905	False		,,,				2504	0.2157				p.P129P		Atlas-SNP	.											.	PDXK	17	.	0			c.G387A						PASS	.	G		246,4160	144.2+/-179.2	9,228,1966	88.0	83.0	85.0		387	-9.5	0.0	21	dbSNP_120	85	796,7804	187.4+/-234.7	36,724,3540	no	coding-synonymous	PDXK	NM_003681.4		45,952,5506	AA,AG,GG		9.2558,5.5833,8.0117		129/313	45168884	1042,11964	2203	4300	6503	SO:0001819	synonymous_variant	8566	exon6			CGTCCCGGAGGAC	U89606	CCDS13699.1	21q22.3	2007-05-10			ENSG00000160209	ENSG00000160209	2.7.1.35		8819	protein-coding gene	gene with protein product		179020	"""chromosome 21 open reading frame 97"", ""chromosome 21 open reading frame 124"""	C21orf97, C21orf124		9099727	Standard	NM_003681		Approved	PNK, PKH, FLJ21324, PRED79, FLJ31940, MGC15873	uc002zdm.4	O00764	OTTHUMG00000086870	ENST00000291565.4:c.387G>A	21.37:g.45168884G>A		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	57	23	0.403509	NM_003681	Q7Z2Y0|Q9BS02	Silent	SNP	ENST00000291565.4	37	CCDS13699.1																																																																																			G|0.906;A|0.094	0.094	strong		0.557	PDXK-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195636.1	NM_003681	
SGK223	157285	hgsc.bcm.edu	37	8	8235523	8235523	+	Silent	SNP	G	G	A	rs55993234	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:8235523G>A	ENST00000520004.1	-	3	660	c.396C>T	c.(394-396)taC>taT	p.Y132Y	SGK223_ENST00000330777.4_Silent_p.Y132Y			Q86YV5	SG223_HUMAN		132							ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)										AGCTGCCCAGGTAGACGACGG	0.587													G|||	80	0.0159744	0.0015	0.0187	5008	,	,		16855	0.001		0.0278	False		,,,				2504	0.0368				p.Y132Y	GBM(34;731 755 10259 33573 33867)	Atlas-SNP	.											.	.	.	.	0			c.C396T						PASS	.	G		27,3893		0,27,1933	55.0	59.0	58.0		396	1.5	0.9	8	dbSNP_129	58	389,7905		10,369,3768	no	coding-synonymous	SGK223	NM_001080826.1		10,396,5701	AA,AG,GG		4.6901,0.6888,3.4059		132/1403	8235523	416,11798	1960	4147	6107	SO:0001819	synonymous_variant	0	exon2			GCCCAGGTAGACG																												ENST00000520004.1:c.396C>T	8.37:g.8235523G>A		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	51	7	0.137255	NM_001080826	Q8N3N5	Silent	SNP	ENST00000520004.1	37	CCDS43706.1																																																																																			G|0.974;A|0.026	0.026	strong		0.587	SGK223-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374864.1		
PTPRN2	5799	hgsc.bcm.edu	37	7	157959879	157959879	+	Silent	SNP	C	C	T	rs1130497	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:157959879C>T	ENST00000389418.4	-	6	663	c.654G>A	c.(652-654)ccG>ccA	p.P218P	PTPRN2_ENST00000409483.1_Silent_p.P180P|PTPRN2_ENST00000389416.4_Silent_p.P201P|PTPRN2_ENST00000389413.3_Silent_p.P218P|PTPRN2_ENST00000404321.2_Silent_p.P241P	NM_002847.3	NP_002838.2	Q92932	PTPR2_HUMAN	protein tyrosine phosphatase, receptor type, N polypeptide 2	218					negative regulation of GTPase activity (GO:0034260)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	endoplasmic reticulum lumen (GO:0005788)|integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)|secretory granule (GO:0030141)|terminal bouton (GO:0043195)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|liver(1)|lung(42)|ovary(4)|pleura(1)|prostate(2)|skin(10)|upper_aerodigestive_tract(1)	86	all_neural(206;0.181)	all_cancers(7;8.99e-13)|all_epithelial(9;2.4e-06)|all_hematologic(28;0.0155)|Breast(660;0.132)	OV - Ovarian serous cystadenocarcinoma(82;0.00463)	STAD - Stomach adenocarcinoma(7;0.0875)		CGAGGGTCCGCGGCAGGAGGT	0.657													c|||	1698	0.339058	0.1399	0.4179	5008	,	,		16229	0.4087		0.4533	False		,,,				2504	0.363				p.P218P		Atlas-SNP	.											.	PTPRN2	243	.	0			c.G654A						PASS	.		,,	743,3659	298.7+/-285.4	74,595,1532	39.0	39.0	39.0		654,603,654	-0.4	0.0	7	dbSNP_86	39	3730,4870	518.5+/-379.3	790,2150,1360	no	coding-synonymous,coding-synonymous,coding-synonymous	PTPRN2	NM_002847.3,NM_130842.2,NM_130843.2	,,	864,2745,2892	TT,TC,CC		43.3721,16.8787,34.4024	,,	218/1016,201/999,218/987	157959879	4473,8529	2201	4300	6501	SO:0001819	synonymous_variant	5799	exon6			GGTCCGCGGCAGG	AB002385	CCDS5947.1, CCDS5948.1, CCDS5949.1	7q36	2011-06-09			ENSG00000155093	ENSG00000155093		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"""	9677	protein-coding gene	gene with protein product	"""IAR PTPRP"""	601698				8954911, 9220540	Standard	NM_130842		Approved	KIAA0387, phogrin, ICAAR, IA-2beta	uc003wno.3	Q92932	OTTHUMG00000152646	ENST00000389418.4:c.654G>A	7.37:g.157959879C>T		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	59	58	0.983051	NM_130843	E9PC57|Q8N4I5|Q92662|Q9Y4F8|Q9Y4I6	Silent	SNP	ENST00000389418.4	37	CCDS5947.1																																																																																			C|0.659;T|0.341	0.341	strong		0.657	PTPRN2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000353214.1		
PREP	5550	hgsc.bcm.edu	37	6	105776792	105776792	+	Silent	SNP	G	G	A	rs6902415	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:105776792G>A	ENST00000369110.3	-	9	1317	c.1125C>T	c.(1123-1125)ttC>ttT	p.F375F		NM_002726.4	NP_002717.3	P48147	PPCE_HUMAN	prolyl endopeptidase	375					proteolysis (GO:0006508)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	serine-type endopeptidase activity (GO:0004252)|serine-type exopeptidase activity (GO:0070008)|serine-type peptidase activity (GO:0008236)			breast(1)|endometrium(2)|large_intestine(7)|lung(12)|ovary(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	29		all_cancers(87;0.000128)|Acute lymphoblastic leukemia(125;1.9e-08)|all_hematologic(75;9.25e-07)|all_epithelial(87;0.0344)|Lung NSC(302;0.191)|Colorectal(196;0.202)			Oxytocin(DB00107)	CATCGAGCGGGAAGGTCTTAA	0.463													G|||	1158	0.23123	0.6241	0.0735	5008	,	,		17509	0.0704		0.0676	False		,,,				2504	0.1462				p.F375F		Atlas-SNP	.											.	PREP	65	.	0			c.C1125T						PASS	.	G		2312,2094	604.8+/-390.4	618,1076,509	128.0	126.0	127.0		1125	1.6	1.0	6	dbSNP_116	127	540,8060	149.1+/-204.2	20,500,3780	no	coding-synonymous	PREP	NM_002726.4		638,1576,4289	AA,AG,GG		6.2791,47.5261,21.9283		375/711	105776792	2852,10154	2203	4300	6503	SO:0001819	synonymous_variant	5550	exon9			GAGCGGGAAGGTC		CCDS5053.1	6q22	2008-02-05			ENSG00000085377	ENSG00000085377	3.4.21.26		9358	protein-coding gene	gene with protein product		600400				7959018	Standard	NM_002726		Approved		uc003prc.3	P48147	OTTHUMG00000015297	ENST00000369110.3:c.1125C>T	6.37:g.105776792G>A		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	102	43	0.421569	NM_002726	Q8N6D4	Silent	SNP	ENST00000369110.3	37	CCDS5053.1																																																																																			G|0.789;A|0.211	0.211	strong		0.463	PREP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041658.1		
TDRD9	122402	hgsc.bcm.edu	37	14	104481083	104481083	+	Silent	SNP	T	T	C	rs11160779	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:104481083T>C	ENST00000409874.4	+	21	2176	c.2128T>C	c.(2128-2130)Ttg>Ctg	p.L710L	RN7SL634P_ENST00000485467.2_RNA|TDRD9_ENST00000339063.5_Silent_p.L710L	NM_153046.2	NP_694591.2	Q8NDG6	TDRD9_HUMAN	tudor domain containing 9	710					cell differentiation (GO:0030154)|DNA methylation involved in gamete generation (GO:0043046)|fertilization (GO:0009566)|gene silencing by RNA (GO:0031047)|male meiosis (GO:0007140)|multicellular organismal development (GO:0007275)|piRNA metabolic process (GO:0034587)|spermatogenesis (GO:0007283)	nucleus (GO:0005634)|piP-body (GO:0071547)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)	p.L425L(1)|p.L710L(1)		breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(10)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)	33		all_cancers(154;0.109)|Melanoma(154;0.0525)|all_epithelial(191;0.0768)				ATATGAAGAATTGAAGACTAG	0.378													T|||	1604	0.320288	0.2769	0.3444	5008	,	,		18980	0.3393		0.3479	False		,,,				2504	0.3139				p.L710L		Atlas-SNP	.											TDRD9_ENST00000409874,NS,carcinoma,-1,4	TDRD9	175	4	2	Substitution - coding silent(2)	stomach(2)	c.T2128C						PASS	.	T		1323,3083	446.9+/-348.2	188,947,1068	128.0	127.0	128.0		2128	-3.2	0.0	14	dbSNP_120	128	2888,5712	451.8+/-362.8	481,1926,1893	no	coding-synonymous	TDRD9	NM_153046.2		669,2873,2961	CC,CT,TT		33.5814,30.0272,32.3774		710/1383	104481083	4211,8795	2203	4300	6503	SO:0001819	synonymous_variant	122402	exon21			GAAGAATTGAAGA	AK093483	CCDS9987.2	14q32.33	2013-01-23	2004-04-01	2004-04-02	ENSG00000156414	ENSG00000156414		"""Tudor domain containing"""	20122	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 75"""	C14orf75			Standard	NM_153046		Approved	DKFZp434N0820, FLJ36164, NET54	uc001yom.4	Q8NDG6	OTTHUMG00000152876	ENST00000409874.4:c.2128T>C	14.37:g.104481083T>C		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	65	36	0.553846	NM_153046	A1A4S7|Q6ZU54|Q8N7T3|Q8N827|Q8N9V5|Q96AS9	Silent	SNP	ENST00000409874.4	37	CCDS9987.2	698	0.31959706959706957	131	0.266260162601626	114	0.3149171270718232	187	0.3269230769230769	266	0.35092348284960423	T	3.482	-0.105587	0.06967	0.300272	0.335814	ENSG00000156414	ENST00000557332	.	.	.	5.09	-3.15	0.05233	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999855393	.	.	.	.	.	.	T	0.23904	-1.0175	3	.	.	.	.	14.7852	0.69796	0.0:0.3035:0.0:0.6965	rs11160779;rs11160779	.	.	.	T	436	.	.	I	+	2	0	TDRD9	103550836	0.000000	0.05858	0.033000	0.17914	0.595000	0.36748	-0.448000	0.06820	-0.934000	0.03733	-0.376000	0.06991	ATT	T|0.678;C|0.322	0.322	strong		0.378	TDRD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328325.3	NM_153046	
OR5D14	219436	hgsc.bcm.edu	37	11	55563602	55563602	+	Missense_Mutation	SNP	G	G	A	rs68042892	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:55563602G>A	ENST00000335605.1	+	1	571	c.571G>A	c.(571-573)Ggc>Agc	p.G191S		NM_001004735.1	NP_001004735.1	Q8NGL3	OR5DE_HUMAN	olfactory receptor, family 5, subfamily D, member 14	191						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.G191S(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(30)|ovary(2)|prostate(1)|skin(2)|stomach(3)|urinary_tract(1)	48		all_epithelial(135;0.196)				CTCTGTGTCTGGCTCTGATAT	0.438													N|||	525	0.104832	0.1884	0.0461	5008	,	,		20460	0.0813		0.0924	False		,,,				2504	0.0706				p.G191S		Atlas-SNP	.											OR5D14,NS,carcinoma,0,1	OR5D14	116	1	1	Substitution - Missense(1)	stomach(1)	c.G571A						PASS	.	A	SER/GLY	670,3730	763.2+/-413.2	63,544,1593	213.0	207.0	209.0		571	-1.0	0.0	11	dbSNP_130	209	727,7865	786.0+/-407.6	32,663,3601	yes	missense	OR5D14	NM_001004735.1	56	95,1207,5194	AA,AG,GG		8.4614,15.2273,10.7528	benign	191/315	55563602	1397,11595	2200	4296	6496	SO:0001583	missense	219436	exon1			GTGTCTGGCTCTG	AB065779	CCDS31508.1	11q11	2012-08-09			ENSG00000186113	ENSG00000186113		"""GPCR / Class A : Olfactory receptors"""	15281	protein-coding gene	gene with protein product							Standard	NM_001004735		Approved		uc010rim.2	Q8NGL3	OTTHUMG00000166809	ENST00000335605.1:c.571G>A	11.37:g.55563602G>A	ENSP00000334456:p.Gly191Ser	Somatic	286	0	0		WXS	Illumina HiSeq	Phase_I	249	189	0.759036	NM_001004735	Q6IF69|Q6IFD4|Q96RB5	Missense_Mutation	SNP	ENST00000335605.1	37	CCDS31508.1	213	0.09752747252747253	92	0.18699186991869918	21	0.058011049723756904	35	0.06118881118881119	65	0.08575197889182058	a	6.430	0.447491	0.12223	0.152273	0.084614	ENSG00000186113	ENST00000335605	T	0.00048	8.82	5.08	-0.978	0.10279	GPCR, rhodopsin-like superfamily (1);	0.566189	0.16176	N	0.226056	T	0.00012	0.0000	N	0.01576	-0.805	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.05115	-1.0905	9	0.59425	D	0.04	-3.1471	7.6783	0.28499	0.2259:0.0:0.0843:0.6898	.	191	Q8NGL3	OR5DE_HUMAN	S	191	ENSP00000334456:G191S	ENSP00000334456:G191S	G	+	1	0	OR5D14	55320178	0.021000	0.18746	0.000000	0.03702	0.000000	0.00434	0.417000	0.21214	-0.350000	0.08262	-1.237000	0.01550	GGC	G|0.896;A|0.104	0.104	strong		0.438	OR5D14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391513.1	NM_001004735	
TNS1	7145	hgsc.bcm.edu	37	2	218683368	218683368	+	Silent	SNP	C	C	T	rs34144104	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:218683368C>T	ENST00000171887.4	-	24	3827	c.3375G>A	c.(3373-3375)ccG>ccA	p.P1125P	TNS1_ENST00000419504.1_Silent_p.P1112P|TNS1_ENST00000430930.1_Silent_p.P1104P	NM_022648.4	NP_072174.3	Q9HBL0	TENS1_HUMAN	tensin 1	1125	Ser-rich.				cell-substrate junction assembly (GO:0007044)|fibroblast migration (GO:0010761)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)	poly(A) RNA binding (GO:0044822)	p.P1125P(1)		breast(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(23)|liver(1)|lung(24)|ovary(3)|pancreas(1)|prostate(3)|skin(5)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	79		Renal(207;0.0483)|Lung NSC(271;0.213)		Epithelial(149;4.43e-06)|all cancers(144;0.000653)|LUSC - Lung squamous cell carcinoma(224;0.0091)|Lung(261;0.013)		TCTGGGCAGACGGGCTGGGCT	0.632													C|||	1078	0.215256	0.0643	0.3156	5008	,	,		17264	0.2292		0.2654	False		,,,				2504	0.2822				p.P1125P		Atlas-SNP	.											TNS1,NS,carcinoma,0,2	TNS1	251	2	1	Substitution - coding silent(1)	prostate(1)	c.G3375A						PASS	.	C		401,4005	197.1+/-221.3	19,363,1821	45.0	50.0	48.0		3375	-1.6	0.3	2	dbSNP_126	48	2547,6053	413.0+/-351.0	376,1795,2129	no	coding-synonymous	TNS1	NM_022648.4		395,2158,3950	TT,TC,CC		29.6163,9.1012,22.6665		1125/1736	218683368	2948,10058	2203	4300	6503	SO:0001819	synonymous_variant	7145	exon24			GGCAGACGGGCTG	AB209238	CCDS2407.1	2q35-q36	2014-06-13	2005-05-13	2005-05-13	ENSG00000079308	ENSG00000079308		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"", ""SH2 domain containing"""	11973	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 155"""	600076	"""tensin"", ""matrix-remodelling associated 6"""	TNS, MXRA6			Standard	NM_022648		Approved	DKFZp586K0617, PPP1R155	uc002vgt.2	Q9HBL0	OTTHUMG00000133056	ENST00000171887.4:c.3375G>A	2.37:g.218683368C>T		Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	132	71	0.537879	NM_022648	Q4ZG71|Q6IPI5	Silent	SNP	ENST00000171887.4	37	CCDS2407.1																																																																																			C|0.774;T|0.226	0.226	strong		0.632	TNS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256672.2	NM_022648	
CCDC146	57639	hgsc.bcm.edu	37	7	76916819	76916819	+	Silent	SNP	G	G	A	rs3763402	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	179	0	0		WXS	Illumina HiSeq	Phase_I	185	182	0.983784	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	
ZNF48	197407	hgsc.bcm.edu	37	16	30408961	30408961	+	Silent	SNP	C	C	T	rs61978578	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:30408961C>T	ENST00000320159.2	+	2	766	c.390C>T	c.(388-390)caC>caT	p.H130H	SEPT1_ENST00000570039.1_5'Flank	NM_001214906.1|NM_001214907.1|NM_001214909.1|NM_152652.2	NP_001201835.1|NP_001201836.1|NP_001201838.1|NP_689865.2	Q96MX3	ZNF48_HUMAN	zinc finger protein 48	130					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(1)|large_intestine(1)|lung(11)|ovary(2)|pancreas(1)|skin(1)	21						TGGTGAAACACCAGCGGACCC	0.582													C|||	547	0.109225	0.0053	0.0115	5008	,	,		18304	0.0774		0.0328	False		,,,				2504	0.4305				p.H130H		Atlas-SNP	.											.	ZNF48	34	.	0			c.C390T						PASS	.	C	,,,	38,4356	43.8+/-77.6	0,38,2159	47.0	55.0	53.0		390,21,390,390	4.8	1.0	16	dbSNP_129	53	335,8265	115.5+/-175.4	7,321,3972	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ZNF48	NM_001214906.1,NM_001214907.1,NM_001214909.1,NM_152652.2	,,,	7,359,6131	TT,TC,CC		3.8953,0.8648,2.8706	,,,	130/619,7/496,130/619,130/619	30408961	373,12621	2197	4300	6497	SO:0001819	synonymous_variant	197407	exon3			GAAACACCAGCGG	M88358, AK056313	CCDS10679.1, CCDS73868.1	16p11.2	2013-01-08			ENSG00000180035	ENSG00000180035		"""Zinc fingers, C2H2-type"""	13114	protein-coding gene	gene with protein product			"""zinc finger protein 553"""	ZNF553		1505991	Standard	NM_152652		Approved	DKFZp762K013, FLJ31751, MGC43952	uc021tgi.1	Q96MX3	OTTHUMG00000048195	ENST00000320159.2:c.390C>T	16.37:g.30408961C>T		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	52	19	0.365385	NM_001214906	Q15920|Q4G0R3|Q69YP3|Q96IL9	Silent	SNP	ENST00000320159.2	37	CCDS10679.1																																																																																			C|0.966;T|0.034	0.034	strong		0.582	ZNF48-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255549.2	NM_152652	
OR5H2	79310	hgsc.bcm.edu	37	3	98002419	98002419	+	Missense_Mutation	SNP	A	A	G	rs16839214	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:98002419A>G	ENST00000355273.2	+	1	688	c.688A>G	c.(688-690)Atc>Gtc	p.I230V	RP11-325B23.2_ENST00000508616.1_lincRNA	NM_001005482.1	NP_001005482.1	Q8NGV7	OR5H2_HUMAN	olfactory receptor, family 5, subfamily H, member 2	230			I -> V (in dbSNP:rs16839214).			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						TCTTTTCACAATCCTAAAAAA	0.363													A|||	819	0.163538	0.1641	0.1715	5008	,	,		18698	0.2609		0.1004	False		,,,				2504	0.1217				p.I230V		Atlas-SNP	.											.	OR5H2	63	.	0			c.A688G						PASS	.	A	VAL/ILE	664,3742	279.6+/-274.9	50,564,1589	86.0	88.0	87.0		688	-6.1	0.0	3	dbSNP_123	87	1037,7563	219.2+/-257.4	67,903,3330	yes	missense	OR5H2	NM_001005482.1	29	117,1467,4919	GG,GA,AA		12.0581,15.0704,13.0786	benign	230/315	98002419	1701,11305	2203	4300	6503	SO:0001583	missense	79310	exon1			TTCACAATCCTAA		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.688A>G	3.37:g.98002419A>G	ENSP00000347418:p.Ile230Val	Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	135	69	0.511111	NM_001005482	Q6IF87	Missense_Mutation	SNP	ENST00000355273.2	37	CCDS33801.1	346	0.15842490842490842	75	0.1524390243902439	71	0.19613259668508287	126	0.2202797202797203	74	0.09762532981530343	A	6.885	0.532668	0.13127	0.150704	0.120581	ENSG00000197938	ENST00000355273	T	0.00024	8.98	3.03	-6.07	0.02158	GPCR, rhodopsin-like superfamily (1);	0.377483	0.18850	N	0.129422	T	0.00012	0.0000	L	0.33245	0.995	0.80722	P	0.0	B	0.23249	0.082	B	0.30495	0.116	T	0.41574	-0.9501	9	0.54805	T	0.06	.	6.5644	0.22503	0.5252:0.1257:0.3491:0.0	rs16839214;rs52834668;rs59137991;rs16839214	230	Q8NGV7	OR5H2_HUMAN	V	230	ENSP00000347418:I230V	ENSP00000347418:I230V	I	+	1	0	OR5H2	99485109	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.601000	0.02081	-2.134000	0.00812	-1.509000	0.00949	ATC	A|0.855;G|0.145	0.145	strong		0.363	OR5H2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359113.2		
SKIV2L2	23517	hgsc.bcm.edu	37	5	54645455	54645455	+	Missense_Mutation	SNP	C	C	G	rs142958762	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:54645455C>G	ENST00000230640.5	+	12	1549	c.1295C>G	c.(1294-1296)tCc>tGc	p.S432C	SKIV2L2_ENST00000545714.1_Missense_Mutation_p.S331C	NM_015360.4	NP_056175.3	P42285	SK2L2_HUMAN	superkiller viralicidic activity 2-like 2 (S. cerevisiae)	432	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				maturation of 5.8S rRNA (GO:0000460)|mRNA splicing, via spliceosome (GO:0000398)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)			NS(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(5)|lung(12)|ovary(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	41		Lung NSC(810;0.000744)|Breast(144;0.181)|Prostate(74;0.194)				GATTGCTTATCCGATGAAGAT	0.313													C|||	11	0.00219649	0.0	0.0014	5008	,	,		19133	0.0		0.0099	False		,,,				2504	0.0				p.S432C	Melanoma(2;92 134 23744 29976 33782)	Atlas-SNP	.											.	SKIV2L2	104	.	0			c.C1295G						PASS	.	C	CYS/SER	8,4398	14.3+/-33.2	0,8,2195	72.0	77.0	76.0		1295	5.5	1.0	5	dbSNP_134	76	40,8560	26.3+/-74.7	0,40,4260	yes	missense	SKIV2L2	NM_015360.4	112	0,48,6455	GG,GC,CC		0.4651,0.1816,0.3691	probably-damaging	432/1043	54645455	48,12958	2203	4300	6503	SO:0001583	missense	23517	exon12			GCTTATCCGATGA	D29641	CCDS3967.1	5q11.2	2008-11-25	2005-02-18	2005-02-18	ENSG00000039123	ENSG00000039123			18734	protein-coding gene	gene with protein product	"""functional spliceosome-associated protein 118"""		"""KIAA0052"""	KIAA0052			Standard	NM_015360		Approved	Mtr4, Dob1, fSAP118	uc003jpy.4	P42285	OTTHUMG00000097019	ENST00000230640.5:c.1295C>G	5.37:g.54645455C>G	ENSP00000230640:p.Ser432Cys	Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	171	98	0.573099	NM_015360	Q2M386|Q6MZZ8|Q6P170|Q8N5R0|Q8TAG2	Missense_Mutation	SNP	ENST00000230640.5	37	CCDS3967.1	9	0.004120879120879121	0	0.0	1	0.0027624309392265192	0	0.0	8	0.010554089709762533	C	26.5	4.743788	0.89663	0.001816	0.004651	ENSG00000039123	ENST00000230640;ENST00000545714	T;T	0.45276	0.9;0.9	5.53	5.53	0.82687	Helicase, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.65964	0.2742	M	0.90650	3.135	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.74023	0.982;0.947	T	0.76000	-0.3119	10	0.87932	D	0	-21.515	19.8173	0.96576	0.0:1.0:0.0:0.0	.	331;432	F5H7E2;P42285	.;SK2L2_HUMAN	C	432;331	ENSP00000230640:S432C;ENSP00000442583:S331C	ENSP00000230640:S432C	S	+	2	0	SKIV2L2	54681212	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	5.850000	0.69473	2.763000	0.94921	0.585000	0.79938	TCC	C|0.995;G|0.005	0.005	strong		0.313	SKIV2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214108.1		
GHRL	51738	hgsc.bcm.edu	37	3	10331519	10331519	+	Missense_Mutation	SNP	C	C	T	rs34911341	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:10331519C>T	ENST00000335542.8	-	4	1022	c.152G>A	c.(151-153)cGa>cAa	p.R51Q	GHRL_ENST00000422159.1_Missense_Mutation_p.R51Q|GHRL_ENST00000457360.1_Missense_Mutation_p.R51Q|GHRLOS_ENST00000605014.1_RNA|GHRL_ENST00000450603.1_Missense_Mutation_p.R51Q|GHRLOS_ENST00000439539.3_RNA|GHRL_ENST00000449554.2_Missense_Mutation_p.R50Q|GHRL_ENST00000287656.7_Missense_Mutation_p.R50Q|GHRL_ENST00000439975.2_Intron|GHRLOS_ENST00000603771.1_RNA|GHRL_ENST00000449238.2_Missense_Mutation_p.R38Q|GHRL_ENST00000446937.2_Intron|GHRLOS_ENST00000605105.1_RNA|GHRL_ENST00000430179.1_Missense_Mutation_p.R50Q|GHRL_ENST00000476283.1_5'Flank|GHRL_ENST00000429122.1_Missense_Mutation_p.R51Q|GHRL_ENST00000437422.2_Missense_Mutation_p.R39Q			Q9UBU3	GHRL_HUMAN	ghrelin/obestatin prepropeptide	51					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						TGCTAGAGCTCGGGGCTGCAG	0.567													C|||	13	0.00259585	0.0	0.0014	5008	,	,		17746	0.005		0.007	False		,,,				2504	0.0				p.R51Q		Atlas-SNP	.											.	GHRL	8	.	0			c.G152A	GRCh37	CM012814	GHRL	M	rs34911341	PASS	.	C	GLN/ARG,GLN/ARG,GLN/ARG,,GLN/ARG	7,4399	14.3+/-33.2	0,7,2196	140.0	150.0	147.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	149,116,113,,152	4.9	1.0	3	dbSNP_126	147	53,8547	34.8+/-89.0	0,53,4247	yes	missense,missense,missense,intron,missense	GHRL	NM_001134941.1,NM_001134944.1,NM_001134945.1,NM_001134946.1,NM_016362.3	43,43,43,,43	0,60,6443	TT,TC,CC		0.6163,0.1589,0.4613	probably-damaging,probably-damaging,probably-damaging,,probably-damaging	50/117,39/106,38/105,,51/118	10331519	60,12946	2203	4300	6503	SO:0001583	missense	51738	exon3			AGAGCTCGGGGCT	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.152G>A	3.37:g.10331519C>T	ENSP00000335074:p.Arg51Gln	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	110	57	0.518182	NM_016362	A8CF34|A8CF38|A8CF42|A8DN29|A8DN30|Q86YP8|Q8TAT9|Q9H3R3	Missense_Mutation	SNP	ENST00000335542.8	37	CCDS33700.1	6	0.0027472527472527475	0	0.0	0	0.0	1	0.0017482517482517483	5	0.006596306068601583	C	26.4	4.737997	0.89573	0.001589	0.006163	ENSG00000157017	ENST00000335542;ENST00000430179;ENST00000450603;ENST00000449554;ENST00000422159;ENST00000449238;ENST00000437422;ENST00000287656;ENST00000457360;ENST00000429122	T;T;T;T;T;T;T;T;T;T	0.62364	0.63;0.63;0.63;0.63;0.03;0.43;0.42;0.63;0.63;0.63	4.88	4.88	0.63580	Motilin/ghrelin (1);	0.000000	0.49305	D	0.000160	T	0.68796	0.3040	M	0.62088	1.915	0.43003	D	0.994528	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.91635	0.998;0.996;0.998;0.996;0.999	T	0.73329	-0.4017	10	0.48119	T	0.1	-12.7683	13.3995	0.60874	0.0:1.0:0.0:0.0	rs34911341	38;39;51;50;51	Q9UBU3-4;Q9UBU3-3;Q9UBU3;Q9UBU3-2;Q86YP8	.;.;GHRL_HUMAN;.;.	Q	51;50;51;50;51;38;39;50;51;51	ENSP00000335074:R51Q;ENSP00000399922:R50Q;ENSP00000389192:R51Q;ENSP00000415521:R50Q;ENSP00000405464:R51Q;ENSP00000388145:R38Q;ENSP00000416768:R39Q;ENSP00000287656:R50Q;ENSP00000391406:R51Q;ENSP00000414819:R51Q	ENSP00000287656:R50Q	R	-	2	0	GHRL	10306519	0.997000	0.39634	0.981000	0.43875	0.957000	0.61999	3.731000	0.55013	2.531000	0.85337	0.655000	0.94253	CGA	C|0.996;T|0.004	0.004	strong		0.567	GHRL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000339625.1	NM_016362	
TNN	63923	hgsc.bcm.edu	37	1	175097864	175097864	+	Silent	SNP	G	G	A	rs12022593	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:175097864G>A	ENST00000239462.4	+	15	3425	c.3312G>A	c.(3310-3312)acG>acA	p.T1104T		NM_022093.1	NP_071376.1	Q9UQP3	TENN_HUMAN	tenascin N	1104	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				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)		ACATGGAAACGGACGGAGGTG	0.592													G|||	879	0.175519	0.1082	0.1643	5008	,	,		17883	0.2609		0.1948	False		,,,				2504	0.1667				p.T1104T		Atlas-SNP	.											TNN,right_upper_lobe,carcinoma,+1,1	TNN	297	1	0			c.G3312A						PASS	.	G		525,3881	240.6+/-251.3	24,477,1702	97.0	92.0	94.0		3312	-2.3	0.9	1	dbSNP_120	94	1856,6744	331.6+/-319.7	212,1432,2656	no	coding-synonymous	TNN	NM_022093.1		236,1909,4358	AA,AG,GG		21.5814,11.9156,18.3069		1104/1300	175097864	2381,10625	2203	4300	6503	SO:0001819	synonymous_variant	63923	exon15			GGAAACGGACGGA	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.3312G>A	1.37:g.175097864G>A		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	91	47	0.516484	NM_022093	B9EGP3|Q5R360	Silent	SNP	ENST00000239462.4	37	CCDS30943.1																																																																																			G|0.813;A|0.187	0.187	strong		0.592	TNN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084422.1	XM_040527	
ZC3HAV1	56829	hgsc.bcm.edu	37	7	138740037	138740037	+	Missense_Mutation	SNP	G	G	C	rs2297236	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	46	0	0		WXS	Illumina HiSeq	Phase_I	38	38	1	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	
YEATS2	55689	hgsc.bcm.edu	37	3	183476685	183476685	+	Missense_Mutation	SNP	G	G	A	rs262993	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:183476685G>A	ENST00000305135.5	+	13	1783	c.1588G>A	c.(1588-1590)Gtc>Atc	p.V530I		NM_018023.4	NP_060493.3	Q9ULM3	YETS2_HUMAN	YEATS domain containing 2	530			V -> I (in dbSNP:rs262993).		chromatin organization (GO:0006325)|histone H3 acetylation (GO:0043966)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)	Ada2/Gcn5/Ada3 transcription activator complex (GO:0005671)|mitotic spindle (GO:0072686)	TBP-class protein binding (GO:0017025)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(24)|ovary(3)|prostate(2)|skin(3)	49	all_cancers(143;6.55e-10)|Ovarian(172;0.0303)		all cancers(12;2.38e-42)|Epithelial(37;1.9e-36)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)			GGCTTCTCAGGTCTCCCAAGG	0.363													G|||	2132	0.425719	0.261	0.4467	5008	,	,		18474	0.5188		0.4533	False		,,,				2504	0.5092				p.V530I		Atlas-SNP	.											YEATS2,NS,carcinoma,-1,1	YEATS2	111	1	0			c.G1588A						PASS	.	G	ILE/VAL	1039,2615		149,741,937	129.0	118.0	121.0		1588	4.2	1.0	3	dbSNP_79	121	3602,4572		784,2034,1269	yes	missense	YEATS2	NM_018023.4	29	933,2775,2206	AA,AG,GG		44.0666,28.4346,39.2374	benign	530/1423	183476685	4641,7187	1827	4087	5914	SO:0001583	missense	55689	exon13			TCTCAGGTCTCCC	AB033023	CCDS43175.1	3q27.3	2004-08-18			ENSG00000163872	ENSG00000163872			25489	protein-coding gene	gene with protein product		613373				10574462	Standard	NM_018023		Approved	FLJ10201, FLJ12841, FLJ13308, KIAA1197	uc003fly.2	Q9ULM3	OTTHUMG00000156898	ENST00000305135.5:c.1588G>A	3.37:g.183476685G>A	ENSP00000306983:p.Val530Ile	Somatic	367	0	0		WXS	Illumina HiSeq	Phase_I	330	137	0.415152	NM_018023	A7E2B9|D3DNS9|Q641P6|Q9NW96	Missense_Mutation	SNP	ENST00000305135.5	37	CCDS43175.1	927	0.42445054945054944	117	0.23780487804878048	164	0.4530386740331492	309	0.5402097902097902	337	0.4445910290237467	G	16.01	3.001348	0.54254	0.284346	0.440666	ENSG00000163872	ENST00000421660;ENST00000305135	T	0.28895	1.59	5.22	4.15	0.48705	.	0.448888	0.20667	N	0.087912	T	0.00012	0.0000	N	0.08118	0	0.53005	P	3.100000000000325E-5	B	0.23937	0.094	B	0.14023	0.01	T	0.40308	-0.9570	9	0.72032	D	0.01	-1.2302	14.6752	0.68975	0.082:0.0:0.918:0.0	rs262993;rs58123380;rs262993	530	Q9ULM3	YETS2_HUMAN	I	530	ENSP00000306983:V530I	ENSP00000306983:V530I	V	+	1	0	YEATS2	184959379	1.000000	0.71417	0.990000	0.47175	0.979000	0.70002	5.373000	0.66162	2.449000	0.82847	0.585000	0.79938	GTC	G|0.576;A|0.424	0.424	strong		0.363	YEATS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346507.2	NM_018023	
DEGS2	123099	hgsc.bcm.edu	37	14	100615961	100615961	+	Missense_Mutation	SNP	C	C	T	rs4905937	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:100615961C>T	ENST00000305631.5	-	2	744	c.169G>A	c.(169-171)Gcc>Acc	p.A57T	DEGS2_ENST00000553834.1_Intron|DEGS2_ENST00000557117.1_5'UTR	NM_206918.2	NP_996801.2			delta(4)-desaturase, sphingolipid 2											breast(1)|lung(6)|skin(1)	8		Melanoma(154;0.212)				AGCCAGCAGGCCAGCATCTGC	0.672													C|||	713	0.142372	0.0749	0.1599	5008	,	,		16363	0.1825		0.167	False		,,,				2504	0.1544				p.A57T		Atlas-SNP	.											.	DEGS2	25	.	0			c.G169A						PASS	.	C	THR/ALA	380,4014		17,346,1834	23.0	26.0	25.0		169	4.4	1.0	14	dbSNP_111	25	1376,7212		105,1166,3023	no	missense	DEGS2	NM_206918.2	58	122,1512,4857	TT,TC,CC		16.0224,8.6482,13.5264	possibly-damaging	57/324	100615961	1756,11226	2197	4294	6491	SO:0001583	missense	123099	exon2			AGCAGGCCAGCAT		CCDS9956.1	14q32.2	2013-09-02	2011-12-09	2004-12-14	ENSG00000168350	ENSG00000168350		"""Fatty acid desaturases"""	20113	protein-coding gene	gene with protein product	"""sphingolipid delta(4)-desaturase 2"", ""dihydroceramide desaturase 2"""	610862	"""chromosome 14 open reading frame 66"", ""degenerative spermatocyte homolog 2, lipid desaturase (Drosophila)"""	C14orf66			Standard	NM_206918		Approved	DES2, FADS8	uc001ygx.2	Q6QHC5	OTTHUMG00000171537	ENST00000305631.5:c.169G>A	14.37:g.100615961C>T	ENSP00000307126:p.Ala57Thr	Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	41	26	0.634146	NM_206918		Missense_Mutation	SNP	ENST00000305631.5	37	CCDS9956.1	314	0.14377289377289376	37	0.07520325203252033	56	0.15469613259668508	97	0.16958041958041958	124	0.16358839050131926	C	17.99	3.521991	0.64747	0.086482	0.160224	ENSG00000168350	ENST00000305631	T	0.33216	1.42	4.4	4.4	0.53042	.	0.000000	0.85682	D	0.000000	T	0.00109	0.0003	L	0.48260	1.515	0.09310	P	1.0	P	0.48294	0.908	P	0.44422	0.449	T	0.11867	-1.0570	9	0.22706	T	0.39	-25.8571	17.3127	0.87214	0.0:1.0:0.0:0.0	rs4905937;rs17855855;rs4905937	57	Q6QHC5	DEGS2_HUMAN	T	57	ENSP00000307126:A57T	ENSP00000307126:A57T	A	-	1	0	DEGS2	99685714	1.000000	0.71417	1.000000	0.80357	0.941000	0.58515	5.961000	0.70356	2.154000	0.67381	0.561000	0.74099	GCC	C|0.864;T|0.136	0.136	strong		0.672	DEGS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414003.1	NM_206918	
GFRA1	2674	hgsc.bcm.edu	37	10	117849353	117849353	+	Missense_Mutation	SNP	T	T	C	rs2072276	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:117849353T>C	ENST00000355422.6	-	9	1646	c.1096A>G	c.(1096-1098)Act>Gct	p.T366A	GFRA1_ENST00000439649.3_Missense_Mutation_p.T361A|GFRA1_ENST00000369236.1_Missense_Mutation_p.T361A|GFRA1_ENST00000544592.1_Missense_Mutation_p.T245A	NM_005264.4	NP_005255.1	P56159	GFRA1_HUMAN	GDNF family receptor alpha 1	366	Poly-Thr.		T -> A (in dbSNP:rs2072276). {ECO:0000269|PubMed:14566559, ECO:0000269|PubMed:9545641}.		axon guidance (GO:0007411)|cell surface receptor signaling pathway (GO:0007166)|glial cell-derived neurotrophic factor receptor signaling pathway (GO:0035860)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|plasma membrane (GO:0005886)	glial cell-derived neurotrophic factor receptor activity (GO:0016167)|receptor binding (GO:0005102)			endometrium(2)|large_intestine(10)|liver(1)|lung(8)|ovary(2)|pancreas(1)|prostate(1)|stomach(1)	26		Lung NSC(174;0.21)		all cancers(201;0.0337)		GTGGTGGTAGTGGCAGTGGTG	0.527													T|||	577	0.115216	0.0809	0.1282	5008	,	,		16729	0.1647		0.0855	False		,,,				2504	0.1319				p.T366A	Ovarian(128;329 1725 45498 46808 50759)	Atlas-SNP	.											.	GFRA1	107	.	0			c.A1096G						PASS	.						65.0	64.0	64.0					10																	117849353		2203	4300	6503	SO:0001583	missense	2674	exon9			TGGTAGTGGCAGT	AF038421	CCDS7593.1, CCDS44481.1	10q25-q26	2011-01-25			ENSG00000151892	ENSG00000151892			4243	protein-coding gene	gene with protein product		601496		GDNFRA		9465905, 9545641	Standard	NM_005264		Approved	RETL1, GDNFR, GFR-ALPHA-1, RET1L, TRNR1	uc001lcj.3	P56159	OTTHUMG00000019097	ENST00000355422.6:c.1096A>G	10.37:g.117849353T>C	ENSP00000347591:p.Thr366Ala	Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	33	11	0.333333	NM_005264	A8KA21|O15507|O43912	Missense_Mutation	SNP	ENST00000355422.6	37	CCDS44481.1	255	0.11675824175824176	42	0.08536585365853659	51	0.1408839779005525	104	0.18181818181818182	58	0.07651715039577836	T	5.264	0.234096	0.09969	.	.	ENSG00000151892	ENST00000439649;ENST00000369236;ENST00000355422;ENST00000544592;ENST00000369234	T;T	0.44881	1.52;0.91	6.17	5.04	0.67666	.	0.193681	0.56097	N	0.000038	T	0.00073	0.0002	L	0.54323	1.7	0.24301	P	0.99512591	B;B	0.32467	0.255;0.372	B;B	0.30316	0.053;0.114	T	0.13282	-1.0515	9	0.08381	T	0.77	-19.8837	6.7944	0.23717	0.1343:0.0706:0.0:0.7951	rs2072276;rs8192665;rs52818520;rs60239356;rs2072276	366;361	P56159;P56159-2	GFRA1_HUMAN;.	A	366;361;361;245;361	ENSP00000358239:T361A;ENSP00000442179:T245A	ENSP00000347591:T361A	T	-	1	0	GFRA1	117839343	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	3.743000	0.55104	1.151000	0.42436	0.533000	0.62120	ACT	T|0.878;G|0.015	.	strong		0.527	GFRA1-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050512.2	NM_145793	
BRCA2	675	hgsc.bcm.edu	37	13	32929232	32929232	+	Silent	SNP	A	A	G	rs1799955	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:32929232A>G	ENST00000380152.3	+	14	7475	c.7242A>G	c.(7240-7242)tcA>tcG	p.S2414S	BRCA2_ENST00000544455.1_Silent_p.S2414S			P51587	BRCA2_HUMAN	breast cancer 2, early onset	2414	Interaction with FANCD2.				brain development (GO:0007420)|cell aging (GO:0007569)|centrosome duplication (GO:0051298)|cytokinesis (GO:0000910)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|female gonad development (GO:0008585)|hemopoiesis (GO:0030097)|histone H3 acetylation (GO:0043966)|histone H4 acetylation (GO:0043967)|inner cell mass cell proliferation (GO:0001833)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|male meiosis I (GO:0007141)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|nucleotide-excision repair (GO:0006289)|oocyte maturation (GO:0001556)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokinesis (GO:0032465)|replication fork protection (GO:0048478)|response to gamma radiation (GO:0010332)|response to UV-C (GO:0010225)|response to X-ray (GO:0010165)|spermatogenesis (GO:0007283)	BRCA2-MAGE-D1 complex (GO:0033593)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)|secretory granule (GO:0030141)	gamma-tubulin binding (GO:0043015)|H3 histone acetyltransferase activity (GO:0010484)|H4 histone acetyltransferase activity (GO:0010485)|protease binding (GO:0002020)|single-stranded DNA binding (GO:0003697)			NS(3)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(32)|liver(1)|lung(41)|oesophagus(5)|ovary(22)|pancreas(4)|prostate(3)|salivary_gland(1)|skin(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	183		Lung SC(185;0.0262)		all cancers(112;7.13e-07)|Epithelial(112;1.59e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000732)|BRCA - Breast invasive adenocarcinoma(63;0.0291)|GBM - Glioblastoma multiforme(144;0.0704)		AAACTAAATCACATTTTCACA	0.333			"""D, Mis, N, F, S"""		"""breast, ovarian, pancreatic"""	"""breast, ovarian, pancreatic, leukemia  (FANCB, FANCD1)"""		Homologous recombination	Pancreatic Cancer, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Prostate Cancer;Hereditary Breast-Ovarian Cancer, BRCA2 type;Fanconi Anemia type D1, bi-allelic BRCA2 mutations;Fanconi Anemia	TCGA Ovarian(8;0.087)			A|||	1165	0.232628	0.2073	0.1988	5008	,	,		20134	0.369		0.2087	False		,,,				2504	0.1748				p.S2414S	Esophageal Squamous(138;838 1285 7957 30353 30468 36915 49332)	Atlas-SNP	.	yes	Rec	yes	Hereditary breast/ovarian cancer	13	13q12	675	familial breast/ovarian cancer gene 2		"""L, E"""	.	BRCA2	812	.	0			c.A7242G						PASS	.	A		915,3491	350.3+/-310.7	85,745,1373	74.0	73.0	74.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	7242	-2.2	0.5	13	dbSNP_89	74	1834,6766	328.4+/-318.3	188,1458,2654	no	coding-synonymous	BRCA2	NM_000059.3		273,2203,4027	GG,GA,AA		21.3256,20.7671,21.1364		2414/3419	32929232	2749,10257	2203	4300	6503	SO:0001819	synonymous_variant	675	exon14	Familial Cancer Database	incl.: Hereditary Pancreatic Adenocarcinoma, Insulin-Dependent Diabetes Mellitus - Exocrine Insufficiency - Familial Pancreatic Cancer, PNCA1;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;HPC; ;FANCD1;Pancytopenia Dysmelia, FA (several complementation groups)	TAAATCACATTTT	U43746	CCDS9344.1	13q12-q13	2014-09-17	2003-10-14		ENSG00000139618	ENSG00000139618		"""Fanconi anemia, complementation groups"""	1101	protein-coding gene	gene with protein product	"""BRCA1/BRCA2-containing complex, subunit 2"""	600185	"""Fanconi anemia, complementation group D1"""	FANCD1, FACD, FANCD		8091231, 7581463, 15057823	Standard	NM_000059		Approved	FAD, FAD1, BRCC2	uc001uub.1	P51587	OTTHUMG00000017411	ENST00000380152.3:c.7242A>G	13.37:g.32929232A>G		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	91	49	0.538462	NM_000059	O00183|O15008|Q13879|Q5TBJ7	Silent	SNP	ENST00000380152.3	37	CCDS9344.1																																																																																			A|0.772;G|0.228	0.228	strong		0.333	BRCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046000.2	NM_000059	
CNTN6	27255	hgsc.bcm.edu	37	3	1418753	1418753	+	Silent	SNP	G	G	A	rs17038365	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:1418753G>A	ENST00000446702.2	+	17	2787	c.2160G>A	c.(2158-2160)acG>acA	p.T720T	CNTN6_ENST00000539053.1_Silent_p.T648T|CNTN6_ENST00000350110.2_Silent_p.T720T			Q9UQ52	CNTN6_HUMAN	contactin 6	720	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|central nervous system development (GO:0007417)|Notch signaling pathway (GO:0007219)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)				breast(6)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(25)|lung(34)|ovary(1)|pancreas(1)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	90		all_cancers(2;0.000164)|all_epithelial(2;0.107)		Epithelial(13;0.000233)|all cancers(10;0.0013)|OV - Ovarian serous cystadenocarcinoma(96;0.0139)		TCGTCATTACGTGGGAGGTAA	0.383													G|||	365	0.0728834	0.1029	0.0749	5008	,	,		18561	0.0268		0.0785	False		,,,				2504	0.0726				p.T720T		Atlas-SNP	.											.	CNTN6	245	.	0			c.G2160A						PASS	.	G		405,4001	201.5+/-224.5	17,371,1815	171.0	163.0	166.0		2160	-3.2	1.0	3	dbSNP_123	166	773,7827	183.7+/-231.9	38,697,3565	no	coding-synonymous	CNTN6	NM_014461.2		55,1068,5380	AA,AG,GG		8.9884,9.192,9.0574		720/1029	1418753	1178,11828	2203	4300	6503	SO:0001819	synonymous_variant	27255	exon17			CATTACGTGGGAG	AB003592	CCDS2557.1	3p26-p25	2013-02-11			ENSG00000134115	ENSG00000134115		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	2176	protein-coding gene	gene with protein product	"""neural adhesion molecule"""	607220				9486763	Standard	NM_014461		Approved	NB-3	uc003bpa.3	Q9UQ52	OTTHUMG00000119030	ENST00000446702.2:c.2160G>A	3.37:g.1418753G>A		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	87	43	0.494253	NM_014461	Q2KHM2	Silent	SNP	ENST00000446702.2	37	CCDS2557.1																																																																																			G|0.918;A|0.082	0.082	strong		0.383	CNTN6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239235.2	NM_014461	
AP3D1	8943	hgsc.bcm.edu	37	19	2138654	2138654	+	Silent	SNP	T	T	G	rs25672	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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_ENST00000355272.6_Silent_p.I52I|AP3D1_ENST00000350812.6_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	73	0	0		WXS	Illumina HiSeq	Phase_I	102	102	1	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		
TSHZ1	10194	hgsc.bcm.edu	37	18	72998524	72998524	+	Missense_Mutation	SNP	C	C	T	rs200266026		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:72998524C>T	ENST00000580243.1	+	2	1510	c.1162C>T	c.(1162-1164)Ccg>Tcg	p.P388S	TSHZ1_ENST00000322038.5_Missense_Mutation_p.P343S			Q6ZSZ6	TSH1_HUMAN	teashirt zinc finger homeobox 1	388					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)		AGCAGCGAACCCGTACGTCAC	0.627																																					p.P343S		Atlas-SNP	.											.	TSHZ1	104	.	0			c.C1027T						PASS	.						104.0	109.0	107.0					18																	72998524		2203	4300	6503	SO:0001583	missense	10194	exon2			GCGAACCCGTACG	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.1162C>T	18.37:g.72998524C>T	ENSP00000464391:p.Pro388Ser	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	98	35	0.357143	NM_005786	O60534|Q4LE29|Q53EU4	Missense_Mutation	SNP	ENST00000580243.1	37		.	.	.	.	.	.	.	.	.	.	C	7.820	0.717534	0.15372	.	.	ENSG00000179981	ENST00000322038	T	0.12569	2.67	5.27	5.27	0.74061	.	0.000000	0.85682	D	0.000000	T	0.19846	0.0477	M	0.66939	2.045	0.58432	D	0.999994	P	0.48503	0.911	B	0.39840	0.311	T	0.03354	-1.1045	10	0.54805	T	0.06	-26.8549	18.8997	0.92437	0.0:1.0:0.0:0.0	.	388	Q6ZSZ6	TSH1_HUMAN	S	343	ENSP00000323584:P343S	ENSP00000323584:P343S	P	+	1	0	TSHZ1	71127512	1.000000	0.71417	0.995000	0.50966	0.313000	0.28021	7.343000	0.79319	2.452000	0.82932	0.561000	0.74099	CCG	.	.	weak		0.627	TSHZ1-005	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000444913.1	NM_005786	
PHLDB3	653583	hgsc.bcm.edu	37	19	43990795	43990795	+	Missense_Mutation	SNP	G	G	A	rs117243018	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:43990795G>A	ENST00000292140.5	-	12	1754	c.1394C>T	c.(1393-1395)gCc>gTc	p.A465V		NM_198850.3	NP_942147.3	Q6NSJ2	PHLB3_HUMAN	pleckstrin homology-like domain, family B, member 3	465							enzyme binding (GO:0019899)			breast(1)|central_nervous_system(1)|lung(5)	7		Prostate(69;0.0153)				CTCCGCCATGGCCTGCTGCAG	0.657													G|||	49	0.00978435	0.0008	0.0072	5008	,	,		14217	0.0		0.0308	False		,,,				2504	0.0123				p.A465V		Atlas-SNP	.											.	PHLDB3	30	.	0			c.C1394T						PASS	.	G	VAL/ALA	21,4051		0,21,2015	26.0	29.0	28.0		1394	4.0	1.0	19	dbSNP_132	28	261,8097		4,253,3922	yes	missense	PHLDB3	NM_198850.3	64	4,274,5937	AA,AG,GG		3.1228,0.5157,2.2687	probably-damaging	465/641	43990795	282,12148	2036	4179	6215	SO:0001583	missense	653583	exon12			GCCATGGCCTGCT		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.1394C>T	19.37:g.43990795G>A	ENSP00000292140:p.Ala465Val	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	43	18	0.418605	NM_198850	Q8N7Z4	Missense_Mutation	SNP	ENST00000292140.5	37	CCDS12621.2	32	0.014652014652014652	1	0.0020325203252032522	5	0.013812154696132596	0	0.0	26	0.03430079155672823	G	16.53	3.149195	0.57151	0.005157	0.031228	ENSG00000176531	ENST00000292140	T	0.56941	0.43	4.01	4.01	0.46588	.	0.000000	0.44285	U	0.000478	T	0.18002	0.0432	L	0.29908	0.895	0.58432	D	0.999992	B;B	0.30793	0.295;0.131	B;B	0.26310	0.068;0.027	T	0.34079	-0.9843	10	0.72032	D	0.01	.	14.0682	0.64844	0.0:0.0:1.0:0.0	.	169;465	B2RXH3;Q6NSJ2	.;PHLB3_HUMAN	V	465	ENSP00000292140:A465V	ENSP00000292140:A465V	A	-	2	0	PHLDB3	48682635	1.000000	0.71417	0.981000	0.43875	0.819000	0.46315	6.294000	0.72738	2.252000	0.74401	0.465000	0.42564	GCC	G|0.984;A|0.016	0.016	strong		0.657	PHLDB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319643.2		
EP400	57634	hgsc.bcm.edu	37	12	132562126	132562126	+	Missense_Mutation	SNP	G	G	A	rs73164912	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:132562126G>A	ENST00000333577.4	+	54	9497	c.9388G>A	c.(9388-9390)Gcc>Acc	p.A3130T	EP400_ENST00000389561.2_Missense_Mutation_p.A3094T|EP400_ENST00000330386.6_Missense_Mutation_p.A3013T|EP400_ENST00000332482.4_Missense_Mutation_p.A3057T|EP400_ENST00000389562.2_Missense_Mutation_p.A3093T|RP13-820C6.2_ENST00000542422.1_RNA			Q96L91	EP400_HUMAN	E1A binding protein p400	3130					chromatin organization (GO:0006325)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)	NuA4 histone acetyltransferase complex (GO:0035267)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|Swr1 complex (GO:0000812)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			NS(1)|breast(6)|central_nervous_system(10)|cervix(1)|endometrium(21)|kidney(13)|large_intestine(25)|lung(56)|ovary(5)|prostate(8)|skin(6)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	161	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.198)		OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06)		CCAGGTGCCCGCCAGCTCCGA	0.632													G|||	409	0.0816693	0.143	0.072	5008	,	,		13730	0.0119		0.1213	False		,,,				2504	0.0368				p.A3094T		Atlas-SNP	.											.	EP400	370	.	0			c.G9280A						PASS	.	G	THR/ALA	584,3822	247.2+/-255.5	41,502,1660	25.0	29.0	28.0		9280	1.7	0.0	12	dbSNP_131	28	1201,7399	236.8+/-268.9	90,1021,3189	yes	missense	EP400	NM_015409.4	58	131,1523,4849	AA,AG,GG		13.9651,13.2547,13.7244	possibly-damaging	3094/3124	132562126	1785,11221	2203	4300	6503	SO:0001583	missense	57634	exon53			GTGCCCGCCAGCT	U80743	CCDS31929.1, CCDS31929.2	12q24.33	2008-02-01	2002-02-05	2002-02-08		ENSG00000183495			11958	protein-coding gene	gene with protein product		606265	"""trinucleotide repeat containing 12"""	TNRC12		9225980, 11509179	Standard	NM_015409		Approved	CAGH32, KIAA1498, P400, KIAA1818, DKFZP434I225	uc001ujn.3	Q96L91		ENST00000333577.4:c.9388G>A	12.37:g.132562126G>A	ENSP00000333602:p.Ala3130Thr	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	65	38	0.584615	NM_015409	O15411|Q6P2F5|Q8N8Q7|Q8NE05|Q96JK7|Q9P230	Missense_Mutation	SNP	ENST00000333577.4	37		201	0.09203296703296704	71	0.1443089430894309	29	0.08011049723756906	5	0.008741258741258742	96	0.1266490765171504	G	4.653	0.121436	0.08881	0.132547	0.139651	ENSG00000183495	ENST00000333577;ENST00000389561;ENST00000389562;ENST00000332482;ENST00000330386;ENST00000541296	D;D;D;D;D	0.91068	-2.78;-2.77;-2.73;-2.75;-2.76	5.62	1.66	0.24008	.	0.251619	0.39407	N	0.001380	T	0.02649	0.0080	N	0.24115	0.695	0.58432	P	1.0000000000287557E-6	B;B;B;B	0.19331	0.001;0.035;0.035;0.035	B;B;B;B	0.14023	0.001;0.01;0.01;0.01	T	0.47420	-0.9119	9	0.51188	T	0.08	.	9.7951	0.40731	0.1811:0.0:0.7155:0.1035	.	3130;3094;3013;3093	Q96L91;Q96L91-2;Q96L91-4;Q96L91-5	EP400_HUMAN;.;.;.	T	3130;3094;3093;3057;3013;3094	ENSP00000333602:A3130T;ENSP00000374212:A3094T;ENSP00000374213:A3093T;ENSP00000331737:A3057T;ENSP00000330620:A3013T	ENSP00000330620:A3013T	A	+	1	0	EP400	131128079	0.728000	0.28080	0.001000	0.08648	0.029000	0.11900	2.010000	0.40913	-0.162000	0.10964	-0.797000	0.03246	GCC	G|0.875;A|0.125	0.125	strong		0.632	EP400-203	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015409	
SH3PXD2A	9644	hgsc.bcm.edu	37	10	105363289	105363289	+	Silent	SNP	T	T	C	rs3740471	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:105363289T>C	ENST00000369774.4	-	15	1962	c.1686A>G	c.(1684-1686)gcA>gcG	p.A562A	SH3PXD2A_ENST00000427662.2_Intron|SH3PXD2A_ENST00000315994.6_5'UTR|SH3PXD2A_ENST00000540321.1_Silent_p.A429A|SH3PXD2A_ENST00000538130.1_Silent_p.A397A|SH3PXD2A_ENST00000355946.2_Silent_p.A534A			Q5TCZ1	SPD2A_HUMAN	SH3 and PX domains 2A	562					superoxide metabolic process (GO:0006801)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|podosome (GO:0002102)	phosphatidylinositol binding (GO:0035091)			breast(1)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(8)|lung(18)|ovary(1)|skin(1)|urinary_tract(1)	38		Colorectal(252;0.0815)|Breast(234;0.131)		Epithelial(162;4.09e-10)|all cancers(201;2.73e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0119)		CAAAGCCGAATGCAGGGATGT	0.677													T|||	679	0.135583	0.0643	0.1628	5008	,	,		15829	0.1548		0.1998	False		,,,				2504	0.1268				p.A534A		Atlas-SNP	.											.	SH3PXD2A	90	.	0			c.A1602G						PASS	.	T		389,4017	191.9+/-217.4	21,347,1835	42.0	46.0	45.0		1602	1.3	1.0	10	dbSNP_107	45	1922,6678	333.3+/-320.5	216,1490,2594	yes	coding-synonymous	SH3PXD2A	NM_014631.2		237,1837,4429	CC,CT,TT		22.3488,8.8289,17.7687		534/1106	105363289	2311,10695	2203	4300	6503	SO:0001819	synonymous_variant	9644	exon14			GCCGAATGCAGGG	AB007878	CCDS31278.1	10q25.1	2006-02-13	2006-02-13	2006-02-13	ENSG00000107957	ENSG00000107957			23664	protein-coding gene	gene with protein product	"""five SH3 domains"""		"""SH3 multiple domains 1"""	SH3MD1		9687503	Standard	XM_005270297		Approved	FISH, KIAA0418	uc001kxj.1	Q5TCZ1	OTTHUMG00000018997	ENST00000369774.4:c.1686A>G	10.37:g.105363289T>C		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	66	34	0.515152	NM_014631	D3DR98|O43302|Q5TCZ2|Q5TDQ8	Silent	SNP	ENST00000369774.4	37		333	0.15247252747252749	22	0.044715447154471545	53	0.1464088397790055	98	0.17132867132867133	160	0.21108179419525067	T	0.325	-0.959357	0.02267	0.088289	0.223488	ENSG00000107957	ENST00000420222	.	.	.	5.47	1.31	0.21738	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999847	.	.	.	.	.	.	T	0.22521	-1.0214	3	.	.	.	-30.7092	2.7623	0.05310	0.1377:0.114:0.4585:0.2898	rs3740471;rs17738234;rs56448553;rs3740471	.	.	.	V	489	.	.	I	-	1	0	SH3PXD2A	105353279	1.000000	0.71417	0.994000	0.49952	0.225000	0.24961	1.815000	0.38981	0.211000	0.20683	-0.441000	0.05720	ATT	T|0.835;C|0.165	0.165	strong		0.677	SH3PXD2A-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000050178.1	NM_014631	
ZNF91	7644	hgsc.bcm.edu	37	19	23542291	23542291	+	Missense_Mutation	SNP	G	G	C	rs386808073|rs385750	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:23542291G>C	ENST00000300619.7	-	4	3695	c.3490C>G	c.(3490-3492)Cta>Gta	p.L1164V	ZNF91_ENST00000599743.1_Intron|ZNF91_ENST00000596528.1_5'Flank|ZNF91_ENST00000397082.2_Missense_Mutation_p.L1132V	NM_003430.2	NP_003421.2	Q05481	ZNF91_HUMAN	zinc finger protein 91	1164			L -> P (in dbSNP:rs428549).|L -> V (in dbSNP:rs385750).	L -> A (in Ref. 2; BAF83945). {ECO:0000305}.	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)				tcccaaagtagtgggattaca	0.428													C|||	1832	0.365815	0.5915	0.1787	5008	,	,		16656	0.369		0.2505	False		,,,				2504	0.3088				p.L1164V		Atlas-SNP	.											.	ZNF91	349	.	0			c.C3490G						PASS	.	C	VAL/LEU	57,4067		6,45,2011	30.0	36.0	34.0		3490		0.0	19	dbSNP_80	34	28,8416		1,26,4195	no	missense	ZNF91	NM_003430.2	32	7,71,6206	CC,CG,GG		0.3316,1.3822,0.6763	benign	1164/1192	23542291	85,12483	2062	4222	6284	SO:0001583	missense	7644	exon4			AAAGTAGTGGGAT	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.3490C>G	19.37:g.23542291G>C	ENSP00000300619:p.Leu1164Val	Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	19	7	0.368421	NM_003430	A8K5E1|B7Z6G6	Missense_Mutation	SNP	ENST00000300619.7	37	CCDS42541.1	624	0.2857142857142857	230	0.46747967479674796	69	0.19060773480662985	182	0.3181818181818182	143	0.18865435356200527	C	0.094	-1.161904	0.01673	0.013822	0.003316	ENSG00000167232	ENST00000300619;ENST00000397082	T;T	0.05319	3.5;3.46	.	.	.	.	.	.	.	.	T	0.00012	0.0000	N	0.03608	-0.345	0.80722	P	0.0	B;B	0.18863	0.005;0.031	B;B	0.06405	0.0;0.002	T	0.45716	-0.9242	7	0.33940	T	0.23	.	5.7282	0.18024	0.0:0.3358:0.6642:0.0	rs56958500	1132;1164	Q05481-2;Q05481	.;ZNF91_HUMAN	V	1164;1132	ENSP00000300619:L1164V;ENSP00000380272:L1132V	ENSP00000300619:L1164V	L	-	1	2	ZNF91	23334131	0.267000	0.24122	0.005000	0.12908	0.006000	0.05464	0.923000	0.28757	-1.966000	0.01009	-1.954000	0.00483	CTA	G|0.713;C|0.287	0.287	strong		0.428	ZNF91-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465891.1	NM_003430	
EAPP	55837	hgsc.bcm.edu	37	14	34985658	34985658	+	Missense_Mutation	SNP	C	C	T	rs17856037	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:34985658C>T	ENST00000250454.3	-	6	797	c.716G>A	c.(715-717)cGg>cAg	p.R239Q		NM_018453.3	NP_060923.2	Q56P03	EAPP_HUMAN	E2F-associated phosphoprotein	239				R -> Q (in Ref. 2; AAX63200 and 6; AAH01245). {ECO:0000305}.	negative regulation of transcription elongation from RNA polymerase II promoter (GO:0034244)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)				breast(1)|endometrium(1)|large_intestine(3)|lung(4)|ovary(1)|urinary_tract(2)	12	Breast(36;0.0473)|Hepatocellular(127;0.158)		LUAD - Lung adenocarcinoma(48;0.00169)|Lung(238;0.00342)|Epithelial(34;0.18)	GBM - Glioblastoma multiforme(112;0.0196)		AGCATCTTCCCGGTTAGACCT	0.438													T|||	293	0.0585064	0.1808	0.0346	5008	,	,		18471	0.003		0.0209	False		,,,				2504	0.0061				p.R239Q		Atlas-SNP	.											.	EAPP	28	.	0			c.G716A						PASS	.	T	GLN/ARG	658,3290		56,546,1372	250.0	246.0	248.0		716	-4.5	0.0	14	dbSNP_123	248	209,8075		5,199,3938	yes	missense	EAPP	NM_018453.3	43	61,745,5310	TT,TC,CC		2.5229,16.6667,7.088	benign	239/286	34985658	867,11365	1974	4142	6116	SO:0001583	missense	55837	exon6			TCTTCCCGGTTAG	AF217512	CCDS41941.1	14q13	2007-03-26	2007-03-26	2007-03-26		ENSG00000129518			19312	protein-coding gene	gene with protein product		609486	"""chromosome 14 open reading frame 11"""	C14orf11		15716352	Standard	NM_018453		Approved	BM036, FLJ20578	uc001wsd.1	Q56P03		ENST00000250454.3:c.716G>A	14.37:g.34985658C>T	ENSP00000250454:p.Arg239Gln	Somatic	241	0	0		WXS	Illumina HiSeq	Phase_I	212	94	0.443396	NM_018453	Q9BVF4|Q9NWV5|Q9NZ86	Missense_Mutation	SNP	ENST00000250454.3	37	CCDS41941.1	132	0.06043956043956044	98	0.1991869918699187	15	0.04143646408839779	3	0.005244755244755245	16	0.021108179419525065	T	1.890	-0.455790	0.04540	0.166667	0.025229	ENSG00000129518	ENST00000250454	T	0.39787	1.06	5.44	-4.46	0.03536	.	1.542390	0.03076	N	0.157818	T	0.00012	0.0000	N	0.00823	-1.155	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.13442	-1.0509	9	0.14656	T	0.56	3.8818	9.2874	0.37766	0.0:0.4138:0.1912:0.395	rs17856037	239	Q56P03	EAPP_HUMAN	Q	239	ENSP00000250454:R239Q	ENSP00000250454:R239Q	R	-	2	0	EAPP	34055409	0.000000	0.05858	0.000000	0.03702	0.051000	0.14879	0.285000	0.18883	-1.106000	0.03008	-1.103000	0.02113	CGG	C|0.950;T|0.050	0.050	strong		0.438	EAPP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409847.1	NM_018453	
FAM160B1	57700	hgsc.bcm.edu	37	10	116602805	116602805	+	Silent	SNP	A	A	G	rs17092491	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:116602805A>G	ENST00000369248.4	+	6	971	c.636A>G	c.(634-636)gaA>gaG	p.E212E	FAM160B1_ENST00000369250.3_Silent_p.E212E	NM_020940.3	NP_065991.3	Q5W0V3	F16B1_HUMAN	family with sequence similarity 160, member B1	212										NS(1)|central_nervous_system(3)|endometrium(2)|kidney(1)|large_intestine(5)|lung(13)	25						AACCAGAGGAACTATCTGGTG	0.448													A|||	494	0.0986422	0.0227	0.1455	5008	,	,		13286	0.1974		0.0875	False		,,,				2504	0.0777				p.E212E		Atlas-SNP	.											.	FAM160B1	107	.	0			c.A636G						PASS	.	A	,	211,4195	129.0+/-165.8	5,201,1997	136.0	110.0	119.0		636,636	-6.6	0.0	10	dbSNP_123	119	860,7740	195.6+/-240.8	48,764,3488	no	coding-synonymous,coding-synonymous	FAM160B1	NM_001135051.1,NM_020940.3	,	53,965,5485	GG,GA,AA		10.0,4.7889,8.2347	,	212/739,212/766	116602805	1071,11935	2203	4300	6503	SO:0001819	synonymous_variant	57700	exon6			AGAGGAACTATCT	AB046820	CCDS31290.1, CCDS44480.1	10q26.11	2008-06-05	2008-06-05	2008-06-05	ENSG00000151553	ENSG00000151553			29320	protein-coding gene	gene with protein product			"""KIAA1600"""	KIAA1600		10997877	Standard	NM_020940		Approved	bA106M7.3	uc001lcb.3	Q5W0V3	OTTHUMG00000019092	ENST00000369248.4:c.636A>G	10.37:g.116602805A>G		Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	143	73	0.51049	NM_020940	Q5H9P7|Q5W0V2|Q8IY76|Q9HCH2	Silent	SNP	ENST00000369248.4	37	CCDS31290.1																																																																																			A|0.908;G|0.092	0.092	strong		0.448	FAM160B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050499.1	XM_049351	
GPR133	283383	hgsc.bcm.edu	37	12	131475607	131475607	+	Missense_Mutation	SNP	C	C	A	rs137909892	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:131475607C>A	ENST00000261654.5	+	7	1353	c.794C>A	c.(793-795)tCc>tAc	p.S265Y	RP11-76C10.5_ENST00000542980.1_lincRNA|GPR133_ENST00000535015.1_Missense_Mutation_p.S297Y	NM_198827.3	NP_942122.2	Q6QNK2	GP133_HUMAN	G protein-coupled receptor 133	265					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)		TTCATGACATCCACAGCAAGC	0.473													C|||	16	0.00319489	0.0	0.0	5008	,	,		19824	0.0		0.006	False		,,,				2504	0.0102				p.S265Y		Atlas-SNP	.											.	GPR133	136	.	0			c.C794A						PASS	.	C	TYR/SER	4,4402	8.1+/-20.4	0,4,2199	140.0	105.0	117.0		794	3.4	0.0	12	dbSNP_134	117	53,8547	34.3+/-88.2	1,51,4248	yes	missense	GPR133	NM_198827.3	144	1,55,6447	AA,AC,CC		0.6163,0.0908,0.4383	possibly-damaging	265/875	131475607	57,12949	2203	4300	6503	SO:0001583	missense	283383	exon7			TGACATCCACAGC	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.794C>A	12.37:g.131475607C>A	ENSP00000261654:p.Ser265Tyr	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	144	75	0.520833	NM_198827	B2CKK9|B7ZLF7|Q2M1L3|Q6ZMQ1|Q7Z7M2|Q86SM4	Missense_Mutation	SNP	ENST00000261654.5	37	CCDS9272.1	6	0.0027472527472527475	0	0.0	0	0.0	0	0.0	6	0.0079155672823219	C	10.74	1.435607	0.25813	9.08E-4	0.006163	ENSG00000111452	ENST00000261654;ENST00000542091;ENST00000535015;ENST00000537600	T;T	0.46063	0.88;0.88	4.4	3.41	0.39046	.	0.630854	0.15230	N	0.273456	T	0.20292	0.0488	N	0.19112	0.55	0.22571	N	0.998973	B;P	0.35600	0.343;0.511	B;B	0.31751	0.116;0.135	T	0.18808	-1.0325	10	0.72032	D	0.01	.	11.8911	0.52630	0.0:0.8233:0.1767:0.0	.	297;265	B7ZLF7;Q6QNK2	.;GP133_HUMAN	Y	265;205;297;24	ENSP00000261654:S265Y;ENSP00000444425:S297Y	ENSP00000261654:S265Y	S	+	2	0	GPR133	130041560	0.001000	0.12720	0.006000	0.13384	0.002000	0.02628	0.878000	0.28126	2.395000	0.81488	0.557000	0.71058	TCC	C|0.997;A|0.003	0.003	strong		0.473	GPR133-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399356.1	NM_198827	
KIF2B	84643	hgsc.bcm.edu	37	17	51901244	51901244	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:51901244G>A	ENST00000268919.4	+	1	1006	c.850G>A	c.(850-852)Gcc>Acc	p.A284T		NM_032559.4	NP_115948.4	Q8N4N8	KIF2B_HUMAN	kinesin family member 2B	284	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|metabolic process (GO:0008152)|microtubule depolymerization (GO:0007019)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|regulation of chromosome segregation (GO:0051983)	cytosol (GO:0005829)|kinesin complex (GO:0005871)|kinetochore (GO:0000776)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(1)|breast(2)|endometrium(7)|kidney(2)|large_intestine(15)|lung(58)|ovary(5)|prostate(4)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	104						CCAGTTCACCGCCCAGCCACT	0.572																																					p.A284T		Atlas-SNP	.											.	KIF2B	254	.	0			c.G850A						PASS	.						91.0	79.0	83.0					17																	51901244		2203	4300	6503	SO:0001583	missense	84643	exon1			TTCACCGCCCAGC	AF333335	CCDS32685.1	17q22	2014-08-12			ENSG00000141200	ENSG00000141200		"""Kinesins"""	29443	protein-coding gene	gene with protein product		615142				11416179	Standard	NM_032559		Approved		uc002iua.2	Q8N4N8	OTTHUMG00000177756	ENST00000268919.4:c.850G>A	17.37:g.51901244G>A	ENSP00000268919:p.Ala284Thr	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	86	27	0.313953	NM_032559	Q96MA2|Q9BXG6	Missense_Mutation	SNP	ENST00000268919.4	37	CCDS32685.1	.	.	.	.	.	.	.	.	.	.	G	25.9	4.686847	0.88639	.	.	ENSG00000141200	ENST00000268919;ENST00000416491	T	0.18502	2.21	5.52	5.52	0.82312	Kinesin, motor domain (4);	0.000000	0.51477	D	0.000092	T	0.18425	0.0442	L	0.43923	1.385	0.58432	D	0.999998	P	0.41784	0.762	B	0.38880	0.284	T	0.01127	-1.1443	10	0.35671	T	0.21	.	18.3543	0.90352	0.0:0.0:1.0:0.0	.	284	Q8N4N8	KIF2B_HUMAN	T	284;172	ENSP00000268919:A284T	ENSP00000268919:A284T	A	+	1	0	KIF2B	49256243	1.000000	0.71417	0.964000	0.40570	0.833000	0.47200	5.606000	0.67641	2.739000	0.93911	0.655000	0.94253	GCC	.	.	none		0.572	KIF2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438854.1	NM_032559	
CDHR1	92211	hgsc.bcm.edu	37	10	85960395	85960395	+	Silent	SNP	A	A	G	rs4933975	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:85960395A>G	ENST00000372117.3	+	6	580	c.477A>G	c.(475-477)gcA>gcG	p.A159A	CDHR1_ENST00000440770.2_5'Flank|CDHR1_ENST00000332904.3_Silent_p.A159A	NM_033100.2	NP_149091.1	Q96JP9	CDHR1_HUMAN	cadherin-related family member 1	159	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cellular process (GO:0009987)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)	integral component of plasma membrane (GO:0005887)|photoreceptor outer segment membrane (GO:0042622)	calcium ion binding (GO:0005509)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(21)|ovary(1)|prostate(1)|skin(1)	36						AGGTCCATGCAGTGGACAGGG	0.597													G|||	2584	0.515974	0.711	0.5202	5008	,	,		19219	0.3948		0.4612	False		,,,				2504	0.4305				p.A159A		Atlas-SNP	.											CDHR1,NS,carcinoma,+2,1	CDHR1	122	1	0			c.A477G						scavenged	.	G	,	2949,1457	466.0+/-354.4	1006,937,260	112.0	79.0	90.0		477,477	-10.6	0.0	10	dbSNP_111	90	3878,4722	604.6+/-394.8	859,2160,1281	no	coding-synonymous,coding-synonymous	CDHR1	NM_001171971.1,NM_033100.2	,	1865,3097,1541	GG,GA,AA		45.093,33.0685,47.5088	,	159/746,159/860	85960395	6827,6179	2203	4300	6503	SO:0001819	synonymous_variant	92211	exon6			CCATGCAGTGGAC	AB053448	CCDS7372.1, CCDS53548.1	10q23.1	2014-01-28	2010-01-25	2010-01-25	ENSG00000148600	ENSG00000148600		"""Cadherins / Cadherin-related"""	14550	protein-coding gene	gene with protein product		609502	"""protocadherin 21"""	PCDH21		11597768	Standard	NM_001171971		Approved	KIAA1775, CORD15, RP65	uc001kcv.3	Q96JP9	OTTHUMG00000018634	ENST00000372117.3:c.477A>G	10.37:g.85960395A>G		Somatic	218	2	0.00917431		WXS	Illumina HiSeq	Phase_I	212	109	0.514151	NM_001171971	Q69YZ8|Q8IXY5	Silent	SNP	ENST00000372117.3	37	CCDS7372.1																																																																																			A|0.487;G|0.513	0.513	strong		0.597	CDHR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049111.1	NM_033100	
RNF111	54778	hgsc.bcm.edu	37	15	59368167	59368167	+	Silent	SNP	G	G	A	rs7178935	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:59368167G>A	ENST00000557998.1	+	7	1988	c.1701G>A	c.(1699-1701)gtG>gtA	p.V567V	RNF111_ENST00000561186.1_Silent_p.V567V|RNF111_ENST00000434298.1_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	63	0	0		WXS	Illumina HiSeq	Phase_I	64	35	0.546875	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	
C9orf89	84270	hgsc.bcm.edu	37	9	95869981	95869981	+	Silent	SNP	G	G	A	rs74414352	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:95869981G>A	ENST00000375464.2	+	2	161	c.33G>A	c.(31-33)gtG>gtA	p.V11V		NM_032310.3	NP_115686.3	Q96LW7	BINCA_HUMAN	chromosome 9 open reading frame 89	11	CARD.				negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	CARD domain binding (GO:0050700)			endometrium(1)|kidney(1)|lung(3)|ovary(1)|skin(1)	7						ACCGCCTGGTGCAGGACACGC	0.562													G|||	18	0.00359425	0.0	0.0072	5008	,	,		21851	0.001		0.0099	False		,,,				2504	0.002				p.V11V		Atlas-SNP	.											.	C9orf89	12	.	0			c.G33A						PASS	.	G		3,4403	6.2+/-15.9	0,3,2200	92.0	68.0	76.0		33	-5.4	0.9	9	dbSNP_132	76	39,8561	26.3+/-74.7	0,39,4261	no	coding-synonymous	C9orf89	NM_032310.3		0,42,6461	AA,AG,GG		0.4535,0.0681,0.3229		11/184	95869981	42,12964	2203	4300	6503	SO:0001819	synonymous_variant	84270	exon2			CCTGGTGCAGGAC	AK057716	CCDS6702.2	9q22.32	2012-03-16			ENSG00000165233	ENSG00000165233			28148	protein-coding gene	gene with protein product	"""Bcl10-interacting protein with CARD"""					12477932	Standard	XM_005252273		Approved	MGC11115, bA370F5.1, BinCARD	uc004atd.3	Q96LW7	OTTHUMG00000020243	ENST00000375464.2:c.33G>A	9.37:g.95869981G>A		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	78	34	0.435897	NM_032310	Q5BJH8|Q9BSY2	Silent	SNP	ENST00000375464.2	37	CCDS6702.2																																																																																			G|0.997;A|0.003	0.003	strong		0.562	C9orf89-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053128.1	NM_032310	
PDXDC1	23042	hgsc.bcm.edu	37	16	15111218	15111218	+	Missense_Mutation	SNP	C	C	T	rs4985162	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:15111218C>T	ENST00000396410.4	+	11	999	c.902C>T	c.(901-903)cCg>cTg	p.P301L	PDXDC1_ENST00000450288.2_Missense_Mutation_p.P273L|PDXDC1_ENST00000447912.2_Missense_Mutation_p.P210L|RP11-680G24.5_ENST00000565178.1_RNA|PDXDC1_ENST00000325823.7_Missense_Mutation_p.P286L|PDXDC1_ENST00000563679.1_Missense_Mutation_p.P319L|PDXDC1_ENST00000535621.2_Missense_Mutation_p.P301L|PDXDC1_ENST00000455313.2_Missense_Mutation_p.P278L|PDXDC1_ENST00000569715.1_Missense_Mutation_p.P274L	NM_015027.2	NP_055842.2	Q6P996	PDXD1_HUMAN	pyridoxal-dependent decarboxylase domain containing 1	301			P -> L (in dbSNP:rs4985162). {ECO:0000269|PubMed:14702039}.		carboxylic acid metabolic process (GO:0019752)	Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)	carboxy-lyase activity (GO:0016831)|pyridoxal phosphate binding (GO:0030170)			central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(2)|liver(1)|lung(10)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						ACTCCTGGCCCGTGGCTGGGT	0.502																																					p.P301L		Atlas-SNP	.											.	PDXDC1	59	.	0			c.C902T						PASS	.	C	LEU/PRO	639,3755		23,593,1581	86.0	91.0	89.0		902	4.5	0.5	16	dbSNP_111	89	1574,7020		29,1516,2752	no	missense	PDXDC1	NM_015027.2	98	52,2109,4333	TT,TC,CC		18.3151,14.5426,17.0388	benign	301/789	15111218	2213,10775	2197	4297	6494	SO:0001583	missense	23042	exon11			CTGGCCCGTGGCT	AK025504, BX647809	CCDS32393.1, CCDS66954.1, CCDS66957.1, CCDS73830.1, CCDS73831.1	16p13.11	2008-02-05							28995	protein-coding gene	gene with protein product		614244					Standard	XM_005255173		Approved	KIAA0251	uc002dda.4	Q6P996	OTTHUMG00000166304	ENST00000396410.4:c.902C>T	16.37:g.15111218C>T	ENSP00000379691:p.Pro301Leu	Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	144	12	0.0833333	NM_015027	B4DR55|B4DSL3|E7EMH5|E7EPL4|H3BNZ1|O00236|Q4F6X7|Q6PID7|Q86YF1|Q8N4Q9|Q8TBS5	Missense_Mutation	SNP	ENST00000396410.4	37	CCDS32393.1	583	0.26694139194139194	58	0.11788617886178862	127	0.35082872928176795	246	0.43006993006993005	152	0.20052770448548812	C	13.70	2.316841	0.40996	0.145426	0.183151	ENSG00000179889	ENST00000325823;ENST00000447912;ENST00000535621;ENST00000396410;ENST00000450288;ENST00000537781;ENST00000455313	T;T;T;T;T;T	0.37584	1.19;1.19;1.19;1.19;1.19;1.19	5.45	4.49	0.54785	Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.261616	0.44285	N	0.000468	T	0.00012	0.0000	N	0.19112	0.55	0.22479	P	0.999063953	B;B;B;B;B	0.15930	0.006;0.015;0.006;0.006;0.0	B;B;B;B;B	0.16722	0.006;0.016;0.01;0.01;0.001	T	0.46317	-0.9200	9	0.25106	T	0.35	-12.0274	12.4403	0.55621	0.0:0.9177:0.0:0.0823	rs4985162	273;210;301;301;278	E7EPL4;E7EMH5;Q86XE2;Q6P996;Q6P996-2	.;.;.;PDXD1_HUMAN;.	L	286;210;301;301;273;7;278	ENSP00000322807:P286L;ENSP00000400310:P210L;ENSP00000437835:P301L;ENSP00000379691:P301L;ENSP00000391147:P273L;ENSP00000406703:P278L	ENSP00000322807:P286L	P	+	2	0	PDXDC1	15018719	0.931000	0.31567	0.484000	0.27391	0.957000	0.61999	3.082000	0.50128	1.260000	0.44134	0.542000	0.68232	CCG	.	.	weak		0.502	PDXDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389065.2	NM_015027	
GABBR2	9568	hgsc.bcm.edu	37	9	101068580	101068580	+	Silent	SNP	G	G	A	rs2304389	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:101068580G>A	ENST00000259455.2	-	15	2511	c.2052C>T	c.(2050-2052)ccC>ccT	p.P684P		NM_005458.7	NP_005449.5	O75899	GABR2_HUMAN	gamma-aminobutyric acid (GABA) B receptor, 2	684					G-protein coupled receptor signaling pathway (GO:0007186)|gamma-aminobutyric acid signaling pathway (GO:0007214)|negative regulation of adenylate cyclase activity (GO:0007194)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|G-protein coupled receptor heterodimeric complex (GO:0038039)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	G-protein coupled GABA receptor activity (GO:0004965)		NOTCH1_ENST00000277541/GABBR2(2)	breast(4)|endometrium(4)|large_intestine(12)|lung(21)|ovary(2)|skin(4)|stomach(1)|urinary_tract(1)	49		Acute lymphoblastic leukemia(62;0.0527)			Baclofen(DB00181)	CGTTGAGTGCGGGGATGCTGA	0.557													G|||	970	0.19369	0.1815	0.2061	5008	,	,		19497	0.1925		0.17	False		,,,				2504	0.227				p.P684P		Atlas-SNP	.											GABBR2,NS,malignant_melanoma,-1,1	GABBR2	126	1	0			c.C2052T						PASS	.	G		737,3669	303.2+/-287.8	63,611,1529	119.0	80.0	93.0		2052	-10.3	0.1	9	dbSNP_100	93	1427,7173	273.0+/-290.4	122,1183,2995	no	coding-synonymous	GABBR2	NM_005458.7		185,1794,4524	AA,AG,GG		16.593,16.7272,16.6385		684/942	101068580	2164,10842	2203	4300	6503	SO:0001819	synonymous_variant	9568	exon15			GAGTGCGGGGATG	AF069755	CCDS6736.1	9q22.1-q22.3	2012-08-29	2006-02-16	2006-02-16	ENSG00000136928	ENSG00000136928		"""GABA receptors"", ""GPCR / Class C : GABA(B) receptors"""	4507	protein-coding gene	gene with protein product		607340	"""G protein-coupled receptor 51"""	GPR51		10087195	Standard	NM_005458		Approved	HG20, GABABR2, GPRC3B	uc004ays.3	O75899	OTTHUMG00000020345	ENST00000259455.2:c.2052C>T	9.37:g.101068580G>A		Somatic	210	1	0.0047619		WXS	Illumina HiSeq	Phase_I	208	116	0.557692	NM_005458	O75974|O75975|Q5VXZ2|Q8WX04|Q9P1R2|Q9UNR1|Q9UNS9	Silent	SNP	ENST00000259455.2	37	CCDS6736.1																																																																																			G|0.831;A|0.169	0.169	strong		0.557	GABBR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053373.1		
LAMB1	3912	hgsc.bcm.edu	37	7	107615506	107615506	+	Silent	SNP	C	C	T	rs11770141	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:107615506C>T	ENST00000222399.6	-	12	1637	c.1407G>A	c.(1405-1407)ggG>ggA	p.G469G	LAMB1_ENST00000393561.1_Silent_p.G493G|LAMB1_ENST00000393560.1_Silent_p.G469G	NM_002291.2	NP_002282.2	P07942	LAMB1_HUMAN	laminin, beta 1	469	Laminin EGF-like 4. {ECO:0000255|PROSITE- ProRule:PRU00460}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|embryo implantation (GO:0007566)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of cell adhesion (GO:0007162)|neuron projection development (GO:0031175)|neuronal-glial interaction involved in cerebral cortex radial glia guided migration (GO:0021812)|odontogenesis (GO:0042476)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell proliferation (GO:0050679)|substrate adhesion-dependent cell spreading (GO:0034446)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-2 complex (GO:0005607)|laminin-8 complex (GO:0043257)|perinuclear region of cytoplasm (GO:0048471)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)|structural molecule activity (GO:0005198)			NS(3)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(4)|large_intestine(11)|lung(37)|ovary(6)|prostate(5)|skin(5)|upper_aerodigestive_tract(3)	82						CACAAGGATTCCCTCCAGGAA	0.458													C|||	487	0.0972444	0.1104	0.1182	5008	,	,		19617	0.0714		0.0964	False		,,,				2504	0.092				p.G469G		Atlas-SNP	.											.	LAMB1	185	.	0			c.G1407A						PASS	.	C		431,3975	210.5+/-231.0	27,377,1799	76.0	71.0	73.0		1407	3.8	1.0	7	dbSNP_120	73	803,7797	187.0+/-234.4	36,731,3533	no	coding-synonymous	LAMB1	NM_002291.2		63,1108,5332	TT,TC,CC		9.3372,9.7821,9.4879		469/1787	107615506	1234,11772	2203	4300	6503	SO:0001819	synonymous_variant	3912	exon12			AGGATTCCCTCCA	M61916	CCDS5750.1	7q22	2013-03-01			ENSG00000091136	ENSG00000091136		"""Laminins"""	6486	protein-coding gene	gene with protein product		150240	"""cutis laxa with marfanoid phenotype"""	CLM		2563160, 2704655, 1864606	Standard	NM_002291		Approved		uc003vew.2	P07942	OTTHUMG00000149966	ENST00000222399.6:c.1407G>A	7.37:g.107615506C>T		Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	23	13	0.565217	NM_002291	Q14D91	Silent	SNP	ENST00000222399.6	37	CCDS5750.1																																																																																			C|0.903;T|0.097	0.097	strong		0.458	LAMB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314584.1	NM_002291	
NAGK	55577	hgsc.bcm.edu	37	2	71304738	71304738	+	Silent	SNP	G	G	A	rs1043701	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:71304738G>A	ENST00000244204.6	+	9	878	c.816G>A	c.(814-816)gtG>gtA	p.V272V	NAGK_ENST00000443938.2_Silent_p.V268V|NAGK_ENST00000443872.2_Silent_p.V124V|NAGK_ENST00000455662.2_Silent_p.V318V|NAGK_ENST00000418807.3_Silent_p.V221V			Q9UJ70	NAGK_HUMAN	N-acetylglucosamine kinase	272					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)	TGGGCTCTGTGTGGAAGAGCT	0.612													G|||	250	0.0499201	0.0068	0.049	5008	,	,		16621	0.002		0.1153	False		,,,				2504	0.091				p.V318V		Atlas-SNP	.											.	NAGK	34	.	0			c.G954A						PASS	.	G		85,4321	68.7+/-106.4	2,81,2120	54.0	47.0	50.0		954	3.8	1.0	2	dbSNP_86	50	964,7636	201.1+/-244.7	56,852,3392	no	coding-synonymous	NAGK	NM_017567.4		58,933,5512	AA,AG,GG		11.2093,1.9292,8.0655		318/391	71304738	1049,11957	2203	4300	6503	SO:0001819	synonymous_variant	55577	exon9			CTCTGTGTGGAAG	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.816G>A	2.37:g.71304738G>A		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	97	53	0.546392	NM_017567	B4DLZ5|Q53HD5|Q6IA84|Q9BS29|Q9BVP0|Q9NV37	Silent	SNP	ENST00000244204.6	37		108|108	0.04945054945054945|0.04945054945054945	3|3	0.006097560975609756|0.006097560975609756	19|19	0.052486187845303865|0.052486187845303865	0|0	0.0|0.0	86|86	0.11345646437994723|0.11345646437994723	G|G	10.65|10.65	1.410214|1.410214	0.25465|0.25465	0.019292|0.019292	0.112093|0.112093	ENSG00000124357|ENSG00000124357	ENST00000443938|ENST00000524537	.|.	.|.	.|.	5.63|5.63	3.81|3.81	0.43845|0.43845	.|.	.|0.060021	.|0.64402	.|D	.|0.000003	T|T	0.02727|0.02727	0.0082|0.0082	.|.	.|.	.|.	0.09310|0.09310	P|P	1.0|1.0	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.52283|0.52283	-0.8596|-0.8596	3|5	.|0.87932	.|D	.|0	-36.4269|-36.4269	10.4487|10.4487	0.44509|0.44509	0.1623:0.0:0.8377:0.0|0.1623:0.0:0.8377:0.0	rs1043701;rs3171860;rs1043701|rs1043701;rs3171860;rs1043701	.|.	.|.	.|.	Y|M	290|37	.|.	.|ENSP00000437192:V37M	C|V	+|+	2|1	0|0	NAGK|NAGK	71158246|71158246	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.942000|0.942000	0.58702|0.58702	2.907000|2.907000	0.48743|0.48743	1.376000|1.376000	0.46267|0.46267	0.655000|0.655000	0.94253|0.94253	TGT|GTG	G|0.935;A|0.065	0.065	strong		0.612	NAGK-032	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000471889.1		
FSTL5	56884	hgsc.bcm.edu	37	4	162680603	162680603	+	Silent	SNP	A	A	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:162680603A>T	ENST00000306100.5	-	6	1123	c.687T>A	c.(685-687)gcT>gcA	p.A229A	FSTL5_ENST00000427802.2_Silent_p.A228A|FSTL5_ENST00000379164.4_Silent_p.A228A|FSTL5_ENST00000536695.1_Silent_p.A228A	NM_001128427.2|NM_020116.4	NP_001121899.1|NP_064501.2	Q8N475	FSTL5_HUMAN	follistatin-like 5	229	EF-hand 2. {ECO:0000255|PROSITE- ProRule:PRU00448}.					extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(18)|lung(43)|ovary(4)|pancreas(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	91	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.179)		GGTGCTTGTCAGCATTAAAAT	0.333																																					p.A229A		Atlas-SNP	.											.	FSTL5	207	.	0			c.T687A						PASS	.						93.0	101.0	98.0					4																	162680603		2203	4300	6503	SO:0001819	synonymous_variant	56884	exon6			CTTGTCAGCATTA	BC036502	CCDS3802.1, CCDS47157.1, CCDS47158.1	4q32.3	2013-01-11			ENSG00000168843	ENSG00000168843		"""EF-hand domain containing"", ""Immunoglobulin superfamily / I-set domain containing"""	21386	protein-coding gene	gene with protein product						10574462, 15527507	Standard	NM_020116		Approved	DKFZp566D234, KIAA1263	uc003iqh.4	Q8N475	OTTHUMG00000161397	ENST00000306100.5:c.687T>A	4.37:g.162680603A>T		Somatic	239	0	0		WXS	Illumina HiSeq	Phase_I	210	52	0.247619	NM_020116	E9PCP6|Q9NSW7|Q9ULF7	Silent	SNP	ENST00000306100.5	37	CCDS3802.1																																																																																			.	.	none		0.333	FSTL5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364773.2	NM_020116	
LEPREL1	55214	hgsc.bcm.edu	37	3	189712010	189712010	+	Silent	SNP	G	G	A	rs1719600	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:189712010G>A	ENST00000319332.5	-	3	893	c.696C>T	c.(694-696)caC>caT	p.H232H	LEPREL1_ENST00000427335.2_Silent_p.H51H	NM_018192.3	NP_060662.2	Q8IVL5	P3H2_HUMAN	leprecan-like 1	232					collagen metabolic process (GO:0032963)|extracellular matrix organization (GO:0030198)|negative regulation of cell proliferation (GO:0008285)|peptidyl-proline hydroxylation (GO:0019511)	basement membrane (GO:0005604)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|Golgi apparatus (GO:0005794)	iron ion binding (GO:0005506)|L-ascorbic acid binding (GO:0031418)|procollagen-proline 3-dioxygenase activity (GO:0019797)			NS(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(10)|liver(1)|lung(8)|ovary(2)|prostate(2)|skin(5)	41	all_cancers(143;4.01e-10)|Ovarian(172;0.0925)		Lung(62;4.35e-05)	GBM - Glioblastoma multiforme(93;0.02)	L-Proline(DB00172)|Succinic acid(DB00139)|Vitamin C(DB00126)	CTTGTTCGAAGTGCCTGATAG	0.398													G|||	809	0.161542	0.0545	0.1571	5008	,	,		15915	0.1577		0.2763	False		,,,				2504	0.1953				p.H232H		Atlas-SNP	.											.	LEPREL1	95	.	0			c.C696T						PASS	.	G	,	382,4024	188.5+/-214.9	17,348,1838	87.0	85.0	86.0		153,696	2.0	1.0	3	dbSNP_89	86	2238,6362	378.8+/-339.0	290,1658,2352	no	coding-synonymous,coding-synonymous	LEPREL1	NM_001134418.1,NM_018192.3	,	307,2006,4190	AA,AG,GG		26.0233,8.67,20.1445	,	51/528,232/709	189712010	2620,10386	2203	4300	6503	SO:0001819	synonymous_variant	55214	exon3			TTCGAAGTGCCTG		CCDS3294.1, CCDS46981.1	3q29	2014-01-28			ENSG00000090530	ENSG00000090530	1.14.11.7		19317	protein-coding gene	gene with protein product	"""prolyl 3-hydroxylase 2"""	610341				15063763, 21885030	Standard	NM_018192		Approved	FLJ10718, MLAT4, P3H2	uc011bsk.2	Q8IVL5	OTTHUMG00000156312	ENST00000319332.5:c.696C>T	3.37:g.189712010G>A		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	57	27	0.473684	NM_018192	B3KPK0|B3KWI9|D3DNV8|Q9NVI2	Silent	SNP	ENST00000319332.5	37	CCDS3294.1																																																																																			G|0.812;A|0.188	0.188	strong		0.398	LEPREL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343855.1	NM_018192	
SOCS5	9655	hgsc.bcm.edu	37	2	46986716	46986716	+	Silent	SNP	C	C	G	rs41489952	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	159	0	0		WXS	Illumina HiSeq	Phase_I	323	249	0.770898	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		
ZNF721	170960	hgsc.bcm.edu	37	4	437831	437831	+	Missense_Mutation	SNP	C	C	T	rs72501950	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:437831C>T	ENST00000338977.5	-	2	437	c.389G>A	c.(388-390)cGt>cAt	p.R130H	ZNF721_ENST00000507078.1_Intron|ABCA11P_ENST00000451020.2_RNA|ZNF721_ENST00000506646.1_Intron|ZNF721_ENST00000511833.2_Missense_Mutation_p.R142H			Q8TF20	ZN721_HUMAN	zinc finger protein 721	130					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						GTCTTTGCCACGTTCTTCACA	0.383													C|||	818	0.163339	0.3101	0.085	5008	,	,		21420	0.1141		0.1064	False		,,,				2504	0.1299				p.S142Y		Atlas-SNP	.											.	ZNF721	205	.	0			c.C425A						PASS	.	C	HIS/ARG	1122,3152		143,836,1158	160.0	172.0	168.0		425	-0.7	0.0	4	dbSNP_130	168	828,7716		45,738,3489	no	missense	ZNF721	NM_133474.2	29	188,1574,4647	TT,TC,CC		9.691,26.2518,15.213	possibly-damaging	142/924	437831	1950,10868	2137	4272	6409	SO:0001583	missense	170960	exon3			TTGCCACGTTCTT	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.389G>A	4.37:g.437831C>T	ENSP00000340524:p.Arg130His	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	82	44	0.536585	NM_133474	Q69YG7	Missense_Mutation	SNP	ENST00000338977.5	37		333	0.15247252747252749	142	0.2886178861788618	35	0.09668508287292818	81	0.14160839160839161	75	0.09894459102902374	C	14.66	2.601449	0.46423	0.262518	0.09691	ENSG00000182903	ENST00000338977;ENST00000511833	T;T	0.15017	2.46;2.46	0.723	-0.679	0.11350	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	N	0.19112	0.55	0.53688	P	2.6999999999999247E-5	P;B;B	0.49358	0.923;0.092;0.149	B;B;B	0.35859	0.212;0.002;0.005	T	0.47535	-0.9110	8	0.59425	D	0.04	.	6.1646	0.20384	0.0:0.6815:0.3185:0.0	.	130;142;142	Q8TF20;D9N162;Q8TF20-2	ZN721_HUMAN;.;.	H	130;142	ENSP00000340524:R130H;ENSP00000428878:R142H	ENSP00000340524:R130H	R	-	2	0	ZNF721	427831	0.007000	0.16637	0.001000	0.08648	0.012000	0.07955	1.391000	0.34475	-0.280000	0.09154	0.205000	0.17691	CGT	C|0.855;T|0.145	0.145	strong		0.383	ZNF721-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000357939.1	NM_133474	
RNASET2	8635	hgsc.bcm.edu	37	6	167344583	167344583	+	Silent	SNP	A	A	G	rs13213697	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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_ENST00000496851.2_5'Flank|RNASET2_ENST00000476238.2_Silent_p.L172L|RP11-514O12.4_ENST00000507747.1_Intron	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	80	0	0		WXS	Illumina HiSeq	Phase_I	78	40	0.512821	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	
NSD1	64324	hgsc.bcm.edu	37	5	176638506	176638506	+	Missense_Mutation	SNP	G	G	C	rs28932179	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:176638506G>C	ENST00000439151.2	+	5	3151	c.3106G>C	c.(3106-3108)Gcc>Ccc	p.A1036P	NSD1_ENST00000361032.4_Missense_Mutation_p.A933P|NSD1_ENST00000347982.4_Missense_Mutation_p.A767P|NSD1_ENST00000354179.4_Missense_Mutation_p.A767P	NM_022455.4	NP_071900.2	Q96L73	NSD1_HUMAN	nuclear receptor binding SET domain protein 1	1036			A -> P (in dbSNP:rs28932179). {ECO:0000269|PubMed:12464997}.		gastrulation with mouth forming second (GO:0001702)|histone H3-K36 methylation (GO:0010452)|histone H4-K20 methylation (GO:0034770)|histone methylation (GO:0016571)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|estrogen receptor binding (GO:0030331)|histone methyltransferase activity (H3-K36 specific) (GO:0046975)|histone methyltransferase activity (H4-K20 specific) (GO:0042799)|retinoic acid receptor binding (GO:0042974)|retinoid X receptor binding (GO:0046965)|thyroid hormone receptor binding (GO:0046966)|transcription cofactor activity (GO:0003712)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(18)|lung(24)|ovary(2)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(3)	96	all_cancers(89;1.57e-05)|Renal(175;0.000269)|Lung NSC(126;0.00111)|all_lung(126;0.002)	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)|Epithelial(233;0.198)	Kidney(146;0.235)		TGCTTTTTCAGCCCAAATGGT	0.458			T	NUP98	AML		Sotos Syndrome		Weaver syndrome;Sotos syndrome;Beckwith-Wiedemann syndrome	HNSCC(47;0.14)																											p.A1036P		Atlas-SNP	.		Dom	yes		5	5q35	64324	nuclear receptor binding SET domain protein 1	yes	L	NSD1_ENST00000439151,NS,carcinoma,-2,2	NSD1	416	2	0			c.G3106C						PASS	.	G	PRO/ALA,PRO/ALA	133,4273	94.8+/-133.5	3,127,2073	122.0	121.0	121.0		3106,2299	-7.9	0.0	5	dbSNP_125	121	209,8391	89.9+/-152.1	2,205,4093	yes	missense,missense	NSD1	NM_022455.4,NM_172349.2	27,27	5,332,6166	CC,CG,GG		2.4302,3.0186,2.6296	possibly-damaging,possibly-damaging	1036/2697,767/2428	176638506	342,12664	2203	4300	6503	SO:0001583	missense	64324	exon5	Familial Cancer Database	Weaver-Smith syndrome;Cerebral Gigantism;BWS, Exomphalos-Macroglossia-Gigantism (EMG) syndrome, Wiedemann-Beckwith syndrome, WBS	TTTTCAGCCCAAA	AK026066	CCDS4412.1, CCDS4413.1	5q35	2014-09-17	2003-03-12		ENSG00000165671	ENSG00000165671		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	14234	protein-coding gene	gene with protein product		606681	"""Sotos syndrome"""	STO		9628876, 11896389	Standard	NM_022455		Approved	ARA267, FLJ22263, KMT3B	uc003mfr.4	Q96L73	OTTHUMG00000130846	ENST00000439151.2:c.3106G>C	5.37:g.176638506G>C	ENSP00000395929:p.Ala1036Pro	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	144	67	0.465278	NM_022455	Q96PD8|Q96RN7	Missense_Mutation	SNP	ENST00000439151.2	37	CCDS4412.1	49	0.022435897435897436	24	0.04878048780487805	4	0.011049723756906077	0	0.0	21	0.027704485488126648	G	3.407	-0.121106	0.06838	0.030186	0.024302	ENSG00000165671	ENST00000354179;ENST00000439151;ENST00000347982;ENST00000361032	D;D;D;D	0.93547	-3.13;-3.13;-3.13;-3.24	4.58	-7.92	0.01160	.	0.885835	0.09644	N	0.774583	T	0.52869	0.1761	N	0.24115	0.695	0.09310	N	0.999999	P;P;B	0.40875	0.731;0.729;0.38	B;P;B	0.45232	0.277;0.474;0.147	T	0.72597	-0.4245	9	.	.	.	.	0.8308	0.01130	0.3731:0.1058:0.1991:0.3219	rs28932179	767;933;1036	Q96L73-2;Q96L73-3;Q96L73	.;.;NSD1_HUMAN	P	767;1036;767;933	ENSP00000346111:A767P;ENSP00000395929:A1036P;ENSP00000343209:A767P;ENSP00000354310:A933P	.	A	+	1	0	NSD1	176571112	0.005000	0.15991	0.008000	0.14137	0.473000	0.32948	-0.404000	0.07205	-2.092000	0.00857	0.467000	0.42956	GCC	G|0.975;C|0.025	0.025	strong		0.458	NSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253412.2	NM_172349	
CCR8	1237	hgsc.bcm.edu	37	3	39374151	39374151	+	Missense_Mutation	SNP	C	C	T	rs144913149		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:39374151C>T	ENST00000326306.4	+	2	467	c.329C>T	c.(328-330)tCt>tTt	p.S110F	CCR8_ENST00000545843.1_Missense_Mutation_p.S27F|CCR8_ENST00000414803.1_Silent_p.V52V	NM_005201.3	NP_005192.1	P51685	CCR8_HUMAN	chemokine (C-C motif) receptor 8	110					cell adhesion (GO:0007155)|chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|positive regulation of cytosolic calcium ion concentration (GO:0007204)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	C-C chemokine receptor activity (GO:0016493)|chemokine receptor activity (GO:0004950)|coreceptor activity (GO:0015026)			NS(3)|breast(1)|endometrium(3)|large_intestine(5)|lung(7)|ovary(1)|skin(1)	21				KIRC - Kidney renal clear cell carcinoma(284;0.0504)|Kidney(284;0.0635)		AAAGTGGTGTCTGGCTTTTAT	0.493													C|||	1	0.000199681	0.0	0.0	5008	,	,		24185	0.0		0.001	False		,,,				2504	0.0				p.S110F		Atlas-SNP	.											.	CCR8	34	.	0			c.C329T						PASS	.	C	PHE/SER	1,4405	2.1+/-5.4	0,1,2202	248.0	223.0	231.0		329	4.7	1.0	3	dbSNP_134	231	15,8585	10.5+/-38.8	0,15,4285	yes	missense	CCR8	NM_005201.3	155	0,16,6487	TT,TC,CC		0.1744,0.0227,0.123	probably-damaging	110/356	39374151	16,12990	2203	4300	6503	SO:0001583	missense	1237	exon2			TGGTGTCTGGCTT	D49919	CCDS2684.1	3p22	2012-08-08			ENSG00000179934	ENSG00000179934		"""GPCR / Class A : Chemokine receptors : C-C motif"", ""CD molecules"""	1609	protein-coding gene	gene with protein product		601834		CMKBRL2, CMKBR8		8816377, 8886020	Standard	NM_005201		Approved	CY6, TER1, CKR-L1, GPR-CY6, CDw198	uc010hhr.2	P51685	OTTHUMG00000131290	ENST00000326306.4:c.329C>T	3.37:g.39374151C>T	ENSP00000326432:p.Ser110Phe	Somatic	416	0	0		WXS	Illumina HiSeq	Phase_I	354	180	0.508475	NM_005201	B2RC64|Q3KNQ8|Q3KNR3|Q9BYX5	Missense_Mutation	SNP	ENST00000326306.4	37	CCDS2684.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	15.81	2.941871	0.53079	2.27E-4	0.001744	ENSG00000179934	ENST00000326306;ENST00000545843	T;T	0.37584	1.19;1.19	4.67	4.67	0.58626	GPCR, rhodopsin-like superfamily (1);	0.316313	0.30142	N	0.010316	T	0.59252	0.2180	M	0.79343	2.45	0.36556	D	0.872118	D;D	0.71674	0.998;0.998	D;D	0.80764	0.994;0.994	T	0.69676	-0.5081	10	0.87932	D	0	.	12.254	0.54613	0.1705:0.8294:0.0:0.0	.	110;27	P51685;Q3KNR3	CCR8_HUMAN;.	F	110;27	ENSP00000326432:S110F;ENSP00000440474:S27F	ENSP00000326432:S110F	S	+	2	0	CCR8	39349155	0.000000	0.05858	1.000000	0.80357	0.981000	0.71138	0.375000	0.20518	2.429000	0.82318	0.563000	0.77884	TCT	C|0.999;T|0.001	0.001	strong		0.493	CCR8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254058.2	NM_005201	
CALML5	51806	hgsc.bcm.edu	37	10	5541230	5541230	+	Missense_Mutation	SNP	T	T	C	rs11546426	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:5541230T>C	ENST00000380332.3	-	1	303	c.172A>G	c.(172-174)Agc>Ggc	p.S58G		NM_017422.4	NP_059118.2	Q9NZT1	CALL5_HUMAN	calmodulin-like 5	58	EF-hand 2. {ECO:0000255|PROSITE- ProRule:PRU00448}.		S -> G (polymorphism confirmed at protein level; dbSNP:rs11546426). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17488105}.		epidermis development (GO:0008544)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			biliary_tract(1)|large_intestine(2)|lung(2)|ovary(1)|skin(1)|stomach(1)	8						TCGCCGTCGCTGTCAACCTCG	0.652													T|||	1487	0.296925	0.4493	0.2133	5008	,	,		17834	0.2014		0.2972	False		,,,				2504	0.2485				p.S58G	GBM(149;1055 3356 43077)	Atlas-SNP	.											.	CALML5	25	.	0			c.A172G						PASS	.	T	GLY/SER	1804,2602	530.3+/-372.9	367,1070,766	73.0	74.0	74.0		172	0.6	0.0	10	dbSNP_120	74	2610,5990	422.1+/-353.9	433,1744,2123	yes	missense	CALML5	NM_017422.4	56	800,2814,2889	CC,CT,TT		30.3488,40.9442,33.9382	possibly-damaging	58/147	5541230	4414,8592	2203	4300	6503	SO:0001583	missense	51806	exon1			CGTCGCTGTCAAC	AF172852	CCDS7068.1	10p15.1	2013-01-10			ENSG00000178372	ENSG00000178372		"""EF-hand domain containing"""	18180	protein-coding gene	gene with protein product	"""calmodulin-like skin protein"""	605183				10777582	Standard	NM_017422		Approved	CLSP	uc001iic.2	Q9NZT1	OTTHUMG00000017598	ENST00000380332.3:c.172A>G	10.37:g.5541230T>C	ENSP00000369689:p.Ser58Gly	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	83	37	0.445783	NM_017422	Q5SQI3|Q8IXU8	Missense_Mutation	SNP	ENST00000380332.3	37	CCDS7068.1	632	0.2893772893772894	218	0.44308943089430897	82	0.2265193370165746	112	0.1958041958041958	220	0.29023746701846964	T	14.35	2.509974	0.44660	0.409442	0.303488	ENSG00000178372	ENST00000380332	T	0.72505	-0.66	4.6	0.628	0.17681	EF-hand-like domain (1);	0.913192	0.09252	N	0.827796	T	0.00012	0.0000	L	0.31578	0.945	0.80722	P	0.0	B	0.13145	0.007	B	0.12837	0.008	T	0.32508	-0.9904	9	0.87932	D	0	-10.236	3.7075	0.08407	0.1584:0.2953:0.0:0.5463	rs11546426;rs17853880	58	Q9NZT1	CALL5_HUMAN	G	58	ENSP00000369689:S58G	ENSP00000369689:S58G	S	-	1	0	CALML5	5531230	0.649000	0.27322	0.001000	0.08648	0.000000	0.00434	0.567000	0.23608	-0.000000	0.14550	-0.408000	0.06270	AGC	T|0.677;C|0.323;A|0.000	0.323	strong		0.652	CALML5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046556.1	NM_017422	
BSCL2	26580	hgsc.bcm.edu	37	11	62458275	62458275	+	Silent	SNP	T	T	C	rs6856	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:62458275T>C	ENST00000403550.1	-	9	1368	c.945A>G	c.(943-945)gaA>gaG	p.E315E	BSCL2_ENST00000405837.1_Silent_p.E381E|BSCL2_ENST00000407022.3_Silent_p.E315E|BSCL2_ENST00000433053.1_Silent_p.E379E|BSCL2_ENST00000278893.7_Missense_Mutation_p.K268R|LRRN4CL_ENST00000317449.4_5'Flank|BSCL2_ENST00000421906.1_Silent_p.E315E|BSCL2_ENST00000360796.5_Silent_p.E379E|HNRNPUL2-BSCL2_ENST00000403734.2_3'UTR			Q96G97	BSCL2_HUMAN	Berardinelli-Seip congenital lipodystrophy 2 (seipin)	315					cell death (GO:0008219)|fat cell differentiation (GO:0045444)|lipid catabolic process (GO:0016042)|lipid particle organization (GO:0034389)|lipid storage (GO:0019915)|negative regulation of lipid catabolic process (GO:0050995)	integral component of endoplasmic reticulum membrane (GO:0030176)				endometrium(2)|kidney(2)|large_intestine(2)|lung(4)|prostate(1)|skin(1)	12						CTGAGGGATCTTCAGGGCTCT	0.567													T|||	676	0.134984	0.084	0.1556	5008	,	,		19992	0.0853		0.1928	False		,,,				2504	0.181				p.K268R		Atlas-SNP	.											.	BSCL2	35	.	0			c.A803G						PASS	.	T	,ARG/LYS,	492,3912	231.0+/-245.0	29,434,1739	90.0	81.0	84.0		1137,803,945	-3.9	0.0	11	dbSNP_52	84	1891,6707	336.3+/-321.8	215,1461,2623	yes	coding-synonymous,missense,coding-synonymous	BSCL2	NM_001122955.3,NM_001130702.2,NM_032667.6	,26,	244,1895,4362	CC,CT,TT		21.9935,11.1717,18.3279	,,	379/463,268/288,315/399	62458275	2383,10619	2202	4299	6501	SO:0001819	synonymous_variant	26580	exon8			GGGATCTTCAGGG		CCDS8031.1, CCDS44627.1, CCDS55769.1	11q13	2014-09-17	2009-07-30		ENSG00000168000	ENSG00000168000			15832	protein-coding gene	gene with protein product		606158	"""spastic paraplegia 17 (Silver syndrome)"""	GNG3LG, SPG17		11479539, 14981520	Standard	NM_001122955		Approved		uc001nur.4	Q96G97	OTTHUMG00000150624	ENST00000403550.1:c.945A>G	11.37:g.62458275T>C		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	47	10	0.212766	NM_001130702	G3XAE4|Q567S1|Q96SV1|Q9BSQ0	Missense_Mutation	SNP	ENST00000403550.1	37	CCDS8031.1	321	0.14697802197802198	52	0.10569105691056911	70	0.19337016574585636	50	0.08741258741258741	149	0.19656992084432717	T	18.17	3.563743	0.65651	0.111717	0.219935	ENSG00000168000	ENST00000278893	D	0.90324	-2.65	4.96	-3.94	0.04130	.	.	.	.	.	T	0.00178	0.0005	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.13495	-1.0507	7	0.56958	D	0.05	-3.8108	6.2679	0.20939	0.1468:0.4889:0.0:0.3643	rs6856;rs1128631;rs3185757;rs11558434;rs17294661;rs17353223;rs17848888;rs17849878;rs52801011	268	Q96G97-3	.	R	268	ENSP00000278893:K268R	ENSP00000278893:K268R	K	-	2	0	BSCL2	62214851	0.017000	0.18338	0.005000	0.12908	0.974000	0.67602	-0.325000	0.07976	-0.967000	0.03582	0.459000	0.35465	AAG	T|0.825;C|0.175	0.175	strong		0.567	BSCL2-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000319185.1	NM_032667	
KRT27	342574	hgsc.bcm.edu	37	17	38938591	38938591	+	Missense_Mutation	SNP	C	C	G	rs2469826	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:38938591C>G	ENST00000301656.3	-	1	195	c.155G>C	c.(154-156)aGc>aCc	p.S52T		NM_181537.3	NP_853515.2			keratin 27									p.S52T(1)		NS(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(6)|ovary(1)|prostate(3)|skin(1)|stomach(1)	21		Breast(137;0.000812)				TGCAGATGAGCTGCCCCCAAA	0.602													C|||	1543	0.308107	0.3737	0.3977	5008	,	,		16787	0.2361		0.2773	False		,,,				2504	0.2618				p.S52T		Atlas-SNP	.											KRT27,NS,carcinoma,0,1	KRT27	41	1	1	Substitution - Missense(1)	stomach(1)	c.G155C						PASS	.	C	THR/SER	1594,2812	492.7+/-362.5	300,994,909	65.0	59.0	61.0		155	3.4	1.0	17	dbSNP_100	61	2244,6356	377.8+/-338.7	305,1634,2361	yes	missense	KRT27	NM_181537.3	58	605,2628,3270	GG,GC,CC		26.093,36.1779,29.5095	possibly-damaging	52/460	38938591	3838,9168	2203	4300	6503	SO:0001583	missense	342574	exon1			GATGAGCTGCCCC	AJ564206	CCDS11375.1	17q21.2	2013-01-16	2006-07-17	2006-07-17	ENSG00000171446	ENSG00000171446		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	30841	protein-coding gene	gene with protein product			"""keratin 25C"""	KRT25C		16831889	Standard	NM_181537		Approved		uc002hvg.3	Q7Z3Y8	OTTHUMG00000133371	ENST00000301656.3:c.155G>C	17.37:g.38938591C>G	ENSP00000301656:p.Ser52Thr	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	62	28	0.451613	NM_181537		Missense_Mutation	SNP	ENST00000301656.3	37	CCDS11375.1	677	0.309981684981685	190	0.3861788617886179	134	0.3701657458563536	152	0.26573426573426573	201	0.26517150395778366	C	10.22	1.291162	0.23564	0.361779	0.26093	ENSG00000171446	ENST00000301656	D	0.83591	-1.74	5.43	3.41	0.39046	.	0.089857	0.49305	D	0.000147	T	0.00012	0.0000	L	0.60455	1.87	0.36333	P	0.14099700000000004	B	0.31485	0.325	B	0.32677	0.15	T	0.09862	-1.0655	9	0.27082	T	0.32	.	10.227	0.43231	0.0:0.788:0.1368:0.0752	rs2469826;rs56419417;rs2469826	52	Q7Z3Y8	K1C27_HUMAN	T	52	ENSP00000301656:S52T	ENSP00000301656:S52T	S	-	2	0	KRT27	36192117	0.000000	0.05858	0.972000	0.41901	0.401000	0.30781	1.215000	0.32431	0.749000	0.32854	0.655000	0.94253	AGC	C|0.685;G|0.315	0.315	strong		0.602	KRT27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257216.1	NM_181537	
TGIF1	7050	hgsc.bcm.edu	37	18	3457695	3457695	+	Silent	SNP	C	C	T	rs2229335	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:3457695C>T	ENST00000330513.5	+	3	1266	c.963C>T	c.(961-963)gtC>gtT	p.V321V	TGIF1_ENST00000551541.1_Silent_p.V172V|TGIF1_ENST00000401449.1_Silent_p.V172V|TGIF1_ENST00000405385.3_Silent_p.V172V|TGIF1_ENST00000400167.2_Silent_p.V172V|TGIF1_ENST00000548489.2_Silent_p.V206V|TGIF1_ENST00000407501.2_Silent_p.V192V|TGIF1_ENST00000345133.5_Silent_p.V172V|TGIF1_ENST00000472042.1_Silent_p.V172V|TGIF1_ENST00000343820.5_Silent_p.V192V	NM_170695.2	NP_733796.2	Q15583	TGIF1_HUMAN	TGFB-induced factor homeobox 1	321					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)				GCCAGTCGGTCGGTGTGGGAC	0.498													T|||	210	0.0419329	0.1354	0.0231	5008	,	,		18497	0.003		0.0089	False		,,,				2504	0.0031				p.V321V		Atlas-SNP	.											.	TGIF1	41	.	0			c.C963T						PASS	.	T	,,,,,,,	560,3846	774.5+/-414.0	31,498,1674	116.0	101.0	106.0		576,963,618,576,516,516,516,516	-4.1	0.0	18	dbSNP_98	106	39,8561	817.5+/-406.9	0,39,4261	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TGIF1	NM_003244.2,NM_170695.2,NM_173207.1,NM_173208.1,NM_173209.1,NM_173210.1,NM_173211.1,NM_174886.1	,,,,,,,	31,537,5935	TT,TC,CC		0.4535,12.7099,4.6056	,,,,,,,	192/273,321/402,206/287,192/273,172/253,172/253,172/253,172/253	3457695	599,12407	2203	4300	6503	SO:0001819	synonymous_variant	7050	exon3			GTCGGTCGGTGTG	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.963C>T	18.37:g.3457695C>T		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	90	47	0.522222	NM_170695	A6NE42|A6NLU7|F8VZB6|Q6ICR0|Q8N5X9|Q9NRS0	Silent	SNP	ENST00000330513.5	37	CCDS11834.1																																																																																			C|0.955;T|0.045	0.045	strong		0.498	TGIF1-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254368.4	NM_170695	
OTUD4	54726	hgsc.bcm.edu	37	4	146058966	146058966	+	Silent	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:146058966G>A	ENST00000447906.2	-	21	3148	c.2961C>T	c.(2959-2961)agC>agT	p.S987S	OTUD4_ENST00000454497.2_Silent_p.S922S|OTUD4_ENST00000455611.2_Intron			Q01804	OTUD4_HUMAN	OTU deubiquitinase 4	987					protein K48-linked deubiquitination (GO:0071108)		poly(A) RNA binding (GO:0044822)|ubiquitin-specific protease activity (GO:0004843)			breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(10)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	33	all_hematologic(180;0.151)					TTTCTTTCAGGCTTTGAATGG	0.453																																					p.S922S		Atlas-SNP	.											OTUD4_ENST00000447906,NS,malignant_melanoma,0,2	OTUD4	120	2	0			c.C2766T						scavenged	.						127.0	134.0	131.0					4																	146058966		2203	4300	6503	SO:0001819	synonymous_variant	54726	exon21			TTTCAGGCTTTGA		CCDS3764.1, CCDS47139.1	4q31.21	2014-02-24	2014-02-24		ENSG00000164164	ENSG00000164164		"""OTU domain containing"""	24949	protein-coding gene	gene with protein product		611744	"""OTU domain containing 4"""			1475186, 12727813, 19996094	Standard	NM_001102653		Approved	HSHIN1, KIAA1046, DUBA6	uc003ika.4	Q01804	OTTHUMG00000161480	ENST00000447906.2:c.2961C>T	4.37:g.146058966G>A		Somatic	261	1	0.00383142		WXS	Illumina HiSeq	Phase_I	239	3	0.0125523	NM_001102653	B4DYS4|Q147U2|Q1ZYK1|Q6PG39|Q96MQ5|Q9NT94|Q9UPV6	Silent	SNP	ENST00000447906.2	37																																																																																				.	.	none		0.453	OTUD4-004	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000365117.2	NM_017493	
PSG8	440533	hgsc.bcm.edu	37	19	43262267	43262267	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:43262267T>C	ENST00000306511.4	-	3	693	c.596A>G	c.(595-597)aAc>aGc	p.N199S	PSG8_ENST00000401467.2_Intron|PSG8_ENST00000404209.4_Missense_Mutation_p.N199S|PSG8_ENST00000600709.1_5'UTR|PSG8_ENST00000406636.3_Missense_Mutation_p.N77S	NM_182707.2	NP_874366.1	Q9UQ74	PSG8_HUMAN	pregnancy specific beta-1-glycoprotein 8	199	Ig-like C2-type 1.					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)				GAGGGTCCTGTTGGTTTCAGA	0.517																																					p.N199S		Atlas-SNP	.											.	PSG8	101	.	0			c.A596G						PASS	.						269.0	276.0	274.0					19																	43262267		2203	4299	6502	SO:0001583	missense	440533	exon3			GTCCTGTTGGTTT	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.596A>G	19.37:g.43262267T>C	ENSP00000305005:p.Asn199Ser	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	90	39	0.433333	NM_001130167	A5PKV3|B2RPL4|B4DTI6|O60410|Q68CR6	Missense_Mutation	SNP	ENST00000306511.4	37	CCDS33037.1	.	.	.	.	.	.	.	.	.	.	t	11.57	1.678127	0.29783	.	.	ENSG00000124467	ENST00000404209;ENST00000292109;ENST00000406636;ENST00000426252;ENST00000306511	T;T;T	0.15017	2.46;2.46;2.46	1.53	1.53	0.23141	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.36936	0.0985	M	0.83223	2.63	0.09310	N	1	P;P;P;P	0.48089	0.624;0.683;0.884;0.905	P;P;P;P	0.62089	0.516;0.73;0.836;0.898	T	0.10291	-1.0636	9	0.87932	D	0	.	5.1071	0.14790	0.0:0.0:0.0:1.0	.	77;199;199;199	Q9UQ74-2;Q9UQ74;Q9UQ74-3;A5PKV3	.;PSG8_HUMAN;.;.	S	199;74;77;11;199	ENSP00000385869:N199S;ENSP00000385081:N77S;ENSP00000305005:N199S	ENSP00000292109:N74S	N	-	2	0	PSG8	47954107	0.019000	0.18553	0.023000	0.16930	0.028000	0.11728	1.962000	0.40442	0.697000	0.31718	0.248000	0.18094	AAC	.	.	none		0.517	PSG8-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464526.1		
MED24	9862	hgsc.bcm.edu	37	17	38175866	38175866	+	Silent	SNP	G	G	A	rs11555254	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:38175866G>A	ENST00000394128.2	-	26	2967	c.2886C>T	c.(2884-2886)tcC>tcT	p.S962S	MED24_ENST00000394127.2_Silent_p.S949S|MED24_ENST00000501516.3_Silent_p.S981S|MED24_ENST00000394126.1_Silent_p.S987S|MED24_ENST00000356271.3_Silent_p.S949S	NM_014815.3	NP_055630.2	O75448	MED24_HUMAN	mediator complex subunit 24	962					androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of transcription, DNA-templated (GO:0045893)|protein heterooligomerization (GO:0051291)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|receptor activity (GO:0004872)|RNA polymerase II transcription cofactor activity (GO:0001104)|thyroid hormone receptor binding (GO:0046966)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			autonomic_ganglia(1)|breast(2)|endometrium(9)|large_intestine(10)|lung(14)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	41	Colorectal(19;0.000442)					CCTTGGGGCTGGACATGGCTG	0.647													G|||	557	0.111222	0.1762	0.1225	5008	,	,		17624	0.006		0.162	False		,,,				2504	0.0716				p.S962S		Atlas-SNP	.											.	MED24	89	.	0			c.C2886T						PASS	.	G	,	798,3608	316.9+/-294.8	72,654,1477	71.0	61.0	64.0		2847,2886	4.1	1.0	17	dbSNP_120	64	1405,7195	268.7+/-288.0	114,1177,3009	no	coding-synonymous,coding-synonymous	MED24	NM_001079518.1,NM_014815.3	,	186,1831,4486	AA,AG,GG		16.3372,18.1117,16.9383	,	949/977,962/990	38175866	2203,10803	2203	4300	6503	SO:0001819	synonymous_variant	9862	exon26			GGGGCTGGACATG	AF055995	CCDS11359.1, CCDS42315.1	17q21.2	2007-07-30	2007-07-30	2007-07-30	ENSG00000008838	ENSG00000008838			22963	protein-coding gene	gene with protein product		607000	"""thyroid hormone receptor associated protein 4"", ""cofactor required for Sp1 transcriptional activation, subunit 4, 100kDa"""	THRAP4, CRSP4			Standard	NM_001079518		Approved	TRAP100, KIAA0130, DRIP100, CRSP100	uc002htt.3	O75448	OTTHUMG00000133329	ENST00000394128.2:c.2886C>T	17.37:g.38175866G>A		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	123	63	0.512195	NM_014815	A8K4S5|B3KMR9|Q14143|Q9NNY5	Silent	SNP	ENST00000394128.2	37	CCDS11359.1	272	0.12454212454212454	91	0.18495934959349594	48	0.13259668508287292	3	0.005244755244755245	130	0.17150395778364116	G	10.91	1.484460	0.26598	0.181117	0.163372	ENSG00000008838	ENST00000422942	.	.	.	5.08	4.09	0.47781	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	.	.	.	.	.	.	.	-16.2844	14.4219	0.67190	0.0753:0.0:0.9247:0.0	rs11555254;rs17850738;rs11555254	.	.	.	X	260	.	.	Q	-	1	0	MED24	35429392	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	3.006000	0.49529	2.506000	0.84524	0.650000	0.86243	CAG	G|0.850;A|0.150	0.150	strong		0.647	MED24-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257147.2	NM_014815	
S1PR5	53637	hgsc.bcm.edu	37	19	10624838	10624838	+	Missense_Mutation	SNP	C	C	T	rs150461309	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:10624838C>T	ENST00000439028.3	-	2	975	c.850G>A	c.(850-852)Gta>Ata	p.V284I	S1PR5_ENST00000333430.4_Missense_Mutation_p.V284I	NM_001166215.1	NP_001159687.1	Q9H228	S1PR5_HUMAN	sphingosine-1-phosphate receptor 5	284					regulation of neuron differentiation (GO:0045664)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sphingosine-1-phosphate receptor activity (GO:0038036)			central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(5)|ovary(1)|pancreas(1)|prostate(1)	12					Fingolimod(DB08868)	TGCAGGAGTACAGGACAGGTG	0.657													C|||	24	0.00479233	0.0	0.0014	5008	,	,		15614	0.0169		0.004	False		,,,				2504	0.002				p.V284I		Atlas-SNP	.											.	S1PR5	33	.	0			c.G850A						PASS	.	C	ILE/VAL,ILE/VAL	2,4392	2.1+/-5.4	0,2,2195	34.0	32.0	32.0		850,850	1.8	0.2	19	dbSNP_134	32	9,8591	6.4+/-24.3	0,9,4291	yes	missense,missense	S1PR5	NM_001166215.1,NM_030760.4	29,29	0,11,6486	TT,TC,CC		0.1047,0.0455,0.0847	benign,benign	284/399,284/399	10624838	11,12983	2197	4300	6497	SO:0001583	missense	53637	exon2			GGAGTACAGGACA	AK074661	CCDS12240.1	19p13.2	2012-08-08	2008-04-30	2008-04-30		ENSG00000180739		"""GPCR / Class A : Lysophospholipid receptors : Sphingosine 1-phosphate"""	14299	protein-coding gene	gene with protein product		605146	"""endothelial differentiation, sphingolipid G-protein-coupled receptor, 8"""	EDG8		10799507	Standard	NM_030760		Approved	Edg-8	uc002mou.2	Q9H228		ENST00000439028.3:c.850G>A	19.37:g.10624838C>T	ENSP00000416915:p.Val284Ile	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	63	30	0.47619	NM_030760	Q6NW11	Missense_Mutation	SNP	ENST00000439028.3	37	CCDS12240.1	17|17	0.007783882783882784|0.007783882783882784	0|0	0.0|0.0	0|0	0.0|0.0	14|14	0.024475524475524476|0.024475524475524476	3|3	0.00395778364116095|0.00395778364116095	C|C	0.204|0.204	-1.041896|-1.041896	0.01997|0.01997	4.55E-4|4.55E-4	0.001047|0.001047	ENSG00000180739|ENSG00000180739	ENST00000359134|ENST00000439028;ENST00000333430	.|T;T	.|0.36878	.|1.23;1.23	5.21|5.21	1.84|1.84	0.25277|0.25277	.|GPCR, rhodopsin-like superfamily (1);	.|0.440276	.|0.20594	.|U	.|0.089285	T|T	0.05318|0.05318	0.0141|0.0141	N|N	0.05230|0.05230	-0.09|-0.09	0.09310|0.09310	N|N	0.999994|0.999994	.|B	.|0.20459	.|0.045	.|B	.|0.18263	.|0.021	T|T	0.25363|0.25363	-1.0134|-1.0134	6|10	0.87932|0.02654	D|T	0|1	.|.	1.7218|1.7218	0.02913|0.02913	0.147:0.4824:0.143:0.2276|0.147:0.4824:0.143:0.2276	.|.	.|284	.|Q9H228	.|S1PR5_HUMAN	Y|I	252|284	.|ENSP00000416915:V284I;ENSP00000328472:V284I	ENSP00000352045:C252Y|ENSP00000328472:V284I	C|V	-|-	2|1	0|0	S1PR5|S1PR5	10485838|10485838	0.000000|0.000000	0.05858|0.05858	0.163000|0.163000	0.22734|0.22734	0.520000|0.520000	0.34377|0.34377	-0.726000|-0.726000	0.04936|0.04936	0.194000|0.194000	0.20326|0.20326	0.491000|0.491000	0.48974|0.48974	TGT|GTA	C|0.997;T|0.003	0.003	strong		0.657	S1PR5-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452015.1	NM_030760	
GRK4	2868	hgsc.bcm.edu	37	4	2990499	2990499	+	Missense_Mutation	SNP	G	G	T	rs2960306	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:2990499G>T	ENST00000398052.4	+	3	537	c.194G>T	c.(193-195)cGt>cTt	p.R65L	GRK4_ENST00000345167.6_Missense_Mutation_p.R33L|GRK4_ENST00000504933.1_Missense_Mutation_p.R65L|GRK4_ENST00000398051.4_Missense_Mutation_p.R33L	NM_182982.2	NP_892027.2	P32298	GRK4_HUMAN	G protein-coupled receptor kinase 4	65	N-terminal.|RGS. {ECO:0000255|PROSITE- ProRule:PRU00171}.		R -> L (in dbSNP:rs2960306). {ECO:0000269|PubMed:17344846}.		G-protein coupled receptor internalization (GO:0002031)|receptor internalization (GO:0031623)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|signal transduction (GO:0007165)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytosol (GO:0005829)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)	ATP binding (GO:0005524)|G-protein coupled receptor kinase activity (GO:0004703)|rhodopsin kinase activity (GO:0050254)			lung(1)|upper_aerodigestive_tract(1)	2				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)		ATAGGAAGACGTCTCTTCAGG	0.433													.|||	1565	0.3125	0.5371	0.3285	5008	,	,		20266	0.0942		0.3777	False		,,,				2504	0.1554				p.R65L		Atlas-SNP	.											.	GRK4	72	.	0			c.G194T	GRCh37	CM025429	GRK4	M	rs2960306	PASS	.	T	LEU/ARG,LEU/ARG,LEU/ARG	2167,2239	594.5+/-388.2	508,1151,544	144.0	143.0	143.0		98,194,194	5.6	1.0	4	dbSNP_101	143	3086,5514	659.9+/-401.7	581,1924,1795	yes	missense,missense,missense	GRK4	NM_001004056.1,NM_001004057.1,NM_182982.2	102,102,102	1089,3075,2339	TT,TG,GG		35.8837,49.1829,40.3891	benign,benign,benign	33/547,65/533,65/579	2990499	5253,7753	2203	4300	6503	SO:0001583	missense	2868	exon3			GAAGACGTCTCTT		CCDS33946.1, CCDS33947.1, CCDS47002.1, CCDS68656.1	4p16.3	2008-02-05	2004-02-04	2004-02-06	ENSG00000125388	ENSG00000125388			4543	protein-coding gene	gene with protein product		137026	"""G protein-coupled receptor kinase 2-like (Drosophila)"""	GPRK2L		1338872	Standard	NM_182982		Approved	GPRK4	uc003ggn.1	P32298	OTTHUMG00000159914	ENST00000398052.4:c.194G>T	4.37:g.2990499G>T	ENSP00000381129:p.Arg65Leu	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	60	60	1	NM_182982	O00641|O00642|Q13293|Q13294|Q13295|Q14453|Q14725|Q15313|Q15314|Q15315|Q15316|Q17RH6|Q53EQ8	Missense_Mutation	SNP	ENST00000398052.4	37	CCDS33946.1	736	0.336996336996337	264	0.5365853658536586	124	0.3425414364640884	57	0.09965034965034965	291	0.3839050131926121	T	10.94	1.492816	0.26774	0.491829	0.358837	ENSG00000125388	ENST00000398051;ENST00000398052;ENST00000345167;ENST00000504933	T;T;T;T	0.01902	4.57;4.57;4.57;4.57	5.56	5.56	0.83823	Regulator of G protein signalling (3);Regulator of G protein signalling superfamily (1);	0.089250	0.47093	N	0.000243	T	0.00012	0.0000	N	0.00114	-2.085	0.09310	P	1.0	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;0.001	T	0.14671	-1.0464	9	0.15952	T	0.53	-12.4212	11.1954	0.48709	0.0:0.0:0.1541:0.8459	rs2960306;rs57066640;rs2960306	33;33;65;65	P32298-3;P32298-2;P32298-4;P32298	.;.;.;GRK4_HUMAN	L	33;65;33;65	ENSP00000381128:R33L;ENSP00000381129:R65L;ENSP00000264764:R33L;ENSP00000427445:R65L	ENSP00000264764:R33L	R	+	2	0	GRK4	2960297	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	3.228000	0.51270	0.934000	0.37316	-0.376000	0.06991	CGT	G|0.638;T|0.362	0.362	strong		0.433	GRK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358176.2	NM_005307	
MIOX	55586	hgsc.bcm.edu	37	22	50926768	50926768	+	Silent	SNP	C	C	T	rs2232883	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:50926768C>T	ENST00000216075.6	+	5	479	c.405C>T	c.(403-405)ccC>ccT	p.P135P	MIOX_ENST00000395732.3_Silent_p.P135P|MIOX_ENST00000395733.3_Missense_Mutation_p.P146L	NM_017584.5	NP_060054.4	Q9UGB7	MIOX_HUMAN	myo-inositol oxygenase	135					inositol catabolic process (GO:0019310)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|inclusion body (GO:0016234)	aldo-keto reductase (NADP) activity (GO:0004033)|ferric iron binding (GO:0008199)|inositol oxygenase activity (GO:0050113)|NADP binding (GO:0050661)|oxidoreductase activity, acting on NAD(P)H (GO:0016651)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen (GO:0016701)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	13		all_cancers(38;4.58e-14)|all_epithelial(38;1.12e-12)|all_lung(38;3.07e-05)|Breast(42;6.27e-05)|Lung NSC(38;0.000813)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)		TCGGGGAGCCCCAGGTAAGAG	0.647													c|||	427	0.0852636	0.093	0.0908	5008	,	,		14186	0.0278		0.1392	False		,,,				2504	0.0746				p.P135P		Atlas-SNP	.											.	MIOX	21	.	0			c.C405T						PASS	.	C		450,3956	211.5+/-231.7	30,390,1783	55.0	57.0	56.0		405	-2.2	1.0	22	dbSNP_98	56	1244,7356	245.7+/-274.4	101,1042,3157	no	coding-synonymous	MIOX	NM_017584.5		131,1432,4940	TT,TC,CC		14.4651,10.2133,13.0248		135/286	50926768	1694,11312	2203	4300	6503	SO:0001819	synonymous_variant	55586	exon5			GGAGCCCCAGGTA	AF197129	CCDS14092.1	22q13.3	2008-06-11	2005-06-15	2005-06-15	ENSG00000100253	ENSG00000100253			14522	protein-coding gene	gene with protein product	"""kidney-specific protein 32"""	606774	"""aldehyde reductase (aldose reductase) like 6"""	ALDRL6		10944187, 11716759	Standard	NM_017584		Approved		uc003bll.1	Q9UGB7	OTTHUMG00000150207	ENST00000216075.6:c.405C>T	22.37:g.50926768C>T		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	96	37	0.385417	NM_017584	Q05DJ6|Q5S8C9|Q9BZZ1|Q9UHB8	Silent	SNP	ENST00000216075.6	37	CCDS14092.1	212	0.09706959706959707	48	0.0975609756097561	38	0.10497237569060773	16	0.027972027972027972	110	0.14511873350923482	C	10.08	1.251662	0.22880	0.102133	0.144651	ENSG00000100253	ENST00000395733	.	.	.	4.29	-2.17	0.07059	.	0.057262	0.64402	D	0.000001	T	0.00109	0.0003	.	.	.	0.09310	P	1.0	B	0.09022	0.002	B	0.09377	0.004	T	0.07366	-1.0776	7	0.72032	D	0.01	-9.7685	0.8144	0.01099	0.163:0.2381:0.3211:0.2778	rs2232883	146	Q9UGB7-2	.	L	146	.	ENSP00000379082:P146L	P	+	2	0	MIOX	49273634	0.009000	0.17119	1.000000	0.80357	0.751000	0.42716	-0.849000	0.04322	0.058000	0.16222	0.436000	0.28706	CCC	C|0.878;T|0.122	0.122	strong		0.647	MIOX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316835.1	NM_017584	
ZNF419	79744	hgsc.bcm.edu	37	19	58002859	58002859	+	Silent	SNP	T	T	C	rs62126198	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:58002859T>C	ENST00000221735.7	+	3	279	c.93T>C	c.(91-93)gaT>gaC	p.D31D	ZNF419_ENST00000424930.2_Silent_p.D32D|AC003005.4_ENST00000601674.1_Silent_p.D18D|ZNF419_ENST00000347466.6_Silent_p.D32D|ZNF419_ENST00000415379.2_Silent_p.D18D|ZNF419_ENST00000354197.4_Silent_p.D19D|ZNF419_ENST00000518999.1_Silent_p.D32D|ZNF419_ENST00000520540.1_Silent_p.D19D|ZNF419_ENST00000442920.2_Silent_p.D18D|ZNF419_ENST00000426954.2_Silent_p.D19D			Q96HQ0	ZN419_HUMAN	zinc finger protein 419	31	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.D32D(1)|p.D11D(1)		central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(10)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	26		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0694)|Breast(46;0.0848)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0252)|Lung(386;0.171)		CCTTTGAGGATGTGGCTGTCT	0.498																																					p.D32D		Atlas-SNP	.											ZNF419_ENST00000284020,colon,carcinoma,0,2	ZNF419	134	2	2	Substitution - coding silent(2)	large_intestine(2)	c.T96C						scavenged	.						174.0	165.0	168.0					19																	58002859		2203	4300	6503	SO:0001819	synonymous_variant	79744	exon3			TGAGGATGTGGCT	AK026886	CCDS42637.1, CCDS46211.1, CCDS54325.1, CCDS54326.1, CCDS54327.1, CCDS54328.1	19q13.43	2013-01-08	2006-12-15	2006-12-15	ENSG00000105136	ENSG00000105136		"""Zinc fingers, C2H2-type"", ""-"""	20648	protein-coding gene	gene with protein product			"""zinc finger protein 419A"""	ZNF419A			Standard	NM_001098492		Approved		uc010ety.1	Q96HQ0	OTTHUMG00000037073	ENST00000221735.7:c.93T>C	19.37:g.58002859T>C		Somatic	216	0	0		WXS	Illumina HiSeq	Phase_I	225	12	0.0533333	NM_001098494	B4DXU7|B4E348|B7ZA41|E9PCP4|E9PED0|E9PET3|E9PFX9|Q9H5P0	Silent	SNP	ENST00000221735.7	37	CCDS54326.1																																																																																			T|0.996;C|0.004	0.004	strong		0.498	ZNF419-006	KNOWN	NAGNAG_splice_site|non_canonical_polymorphism|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000378506.1	NM_024691	
YWHAE	7531	hgsc.bcm.edu	37	17	1265285	1265285	+	Silent	SNP	C	C	T	rs34137556	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:1265285C>T	ENST00000264335.8	-	3	549	c.282G>A	c.(280-282)aaG>aaA	p.K94K	YWHAE_ENST00000575977.1_Intron|YWHAE_ENST00000573026.1_Intron|YWHAE_ENST00000571732.1_Silent_p.K72K	NM_006761.4	NP_006752.1	P62258	1433E_HUMAN	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, epsilon	94					apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cerebral cortex development (GO:0021987)|G2/M transition of mitotic cell cycle (GO:0000086)|hippo signaling (GO:0035329)|hippocampus development (GO:0021766)|intracellular signal transduction (GO:0035556)|intrinsic apoptotic signaling pathway (GO:0097193)|membrane organization (GO:0061024)|membrane repolarization during cardiac muscle cell action potential (GO:0086013)|mitotic cell cycle (GO:0000278)|negative regulation of peptidyl-serine dephosphorylation (GO:1902309)|neuron migration (GO:0001764)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|protein targeting (GO:0006605)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of heart rate by hormone (GO:0003064)|regulation of membrane repolarization (GO:0060306)|regulation of potassium ion transmembrane transporter activity (GO:1901016)|substantia nigra development (GO:0021762)|viral process (GO:0016032)	cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|kinesin complex (GO:0005871)|membrane (GO:0016020)|mitochondrion (GO:0005739)	enzyme binding (GO:0019899)|histone deacetylase binding (GO:0042826)|ion channel binding (GO:0044325)|MHC class II protein complex binding (GO:0023026)|phosphoprotein binding (GO:0051219)|phosphoserine binding (GO:0050815)|poly(A) RNA binding (GO:0044822)|potassium channel regulator activity (GO:0015459)|protein heterodimerization activity (GO:0046982)			kidney(2)|large_intestine(4)|lung(5)|ovary(2)|pancreas(1)	14			OV - Ovarian serous cystadenocarcinoma(18;0.203)	UCEC - Uterine corpus endometrioid carcinoma (25;0.0887)		AACAGATTAACTTTAGCTCAG	0.318			T	"""FAM22a, FAM22B"""	edometrial stromal sarcoma		Miller-Dieker lissencephaly syndrome						C|||	79	0.0157748	0.0015	0.0231	5008	,	,		14398	0.0		0.0258	False		,,,				2504	0.0358				p.K94K		Atlas-SNP	.		Dom	yes		17	17p13.3	7531	"""tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, epsilon polypeptide (14-3-3 epsilon)"""	yes	M	.	YWHAE	50	.	0			c.G282A						PASS	.	C		24,4382		0,24,2179	29.0	28.0	29.0		282	3.0	1.0	17	dbSNP_126	29	265,8333		2,261,4036	no	coding-synonymous	YWHAE	NM_006761.4		2,285,6215	TT,TC,CC		3.0821,0.5447,2.2224		94/256	1265285	289,12715	2203	4299	6502	SO:0001819	synonymous_variant	7531	exon3			GATTAACTTTAGC	U54778	CCDS11001.1	17p13.3	2013-12-03	2013-12-03		ENSG00000108953	ENSG00000108953			12851	protein-coding gene	gene with protein product	"""14-3-3 epsilon"""	605066	"""tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, epsilon polypeptide"""			9371399	Standard	NM_006761		Approved	FLJ45465	uc002fsj.3	P62258	OTTHUMG00000134316	ENST00000264335.8:c.282G>A	17.37:g.1265285C>T		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	65	37	0.569231	NM_006761	B3KY71|D3DTH5|P29360|P42655|Q4VJB6|Q53XZ5|Q63631|Q7M4R4	Silent	SNP	ENST00000264335.8	37	CCDS11001.1																																																																																			C|0.981;T|0.019	0.019	strong		0.318	YWHAE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259354.3	NM_006761	
TRIM49C	642612	hgsc.bcm.edu	37	11	89768577	89768577	+	Silent	SNP	C	C	T	rs61903674	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:89768577C>T	ENST00000448984.1	+	3	527	c.198C>T	c.(196-198)acC>acT	p.T66T	TRIM49C_ENST00000432771.1_Silent_p.T66T	NM_001195234.1	NP_001182163.1	P0CI26	TR49C_HUMAN	tripartite motif containing 49C	66						intracellular (GO:0005622)	zinc ion binding (GO:0008270)			endometrium(3)|kidney(1)|lung(4)	8						ACCTCAAAACCAACATTCATT	0.458													c|||	231	0.0461262	0.003	0.0605	5008	,	,		16161	0.002		0.1054	False		,,,				2504	0.0787				p.T66T		Atlas-SNP	.											.	TRIM49C	48	.	0			c.C198T						PASS	.																																			SO:0001819	synonymous_variant	642612	exon3			CAAAACCAACATT	BC126470	CCDS53694.1	11q14.3	2014-02-17	2012-05-18	2012-05-18	ENSG00000204449	ENSG00000204449		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	38877	protein-coding gene	gene with protein product			"""tripartite motif containing 49-like 2"""	TRIM49L2			Standard	NM_001195234		Approved		uc010rua.2	P0CI26		ENST00000448984.1:c.198C>T	11.37:g.89768577C>T		Somatic	322	0	0		WXS	Illumina HiSeq	Phase_I	369	101	0.273713	NM_001195234	A0AVR7|A0AVR9|Q6DJV1|Q9NS80	Silent	SNP	ENST00000448984.1	37	CCDS53694.1																																																																																			.	.	weak		0.458	TRIM49C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395455.1	NM_001195234	
KIF17	57576	hgsc.bcm.edu	37	1	21044151	21044151	+	Nonsense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:21044151G>A	ENST00000247986.2	-	1	359	c.49C>T	c.(49-51)Cag>Tag	p.Q17*	SH2D5_ENST00000460804.1_5'Flank|KIF17_ENST00000400463.3_Nonsense_Mutation_p.Q17*|KIF17_ENST00000375044.1_5'Flank			Q9P2E2	KIF17_HUMAN	kinesin family member 17	17	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|cell projection organization (GO:0030030)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|neurogenesis (GO:0022008)|protein complex localization (GO:0031503)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|intraciliary transport particle B (GO:0030992)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|plus-end-directed microtubule motor activity (GO:0008574)			NS(2)|endometrium(3)|kidney(3)|large_intestine(9)|liver(1)|lung(23)|ovary(4)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	50		all_lung(284;2.99e-05)|Lung NSC(340;3.26e-05)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00179)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|COAD - Colon adenocarcinoma(152;1.43e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000168)|Kidney(64;0.000221)|GBM - Glioblastoma multiforme(114;0.000651)|KIRC - Kidney renal clear cell carcinoma(64;0.0031)|STAD - Stomach adenocarcinoma(196;0.00336)|READ - Rectum adenocarcinoma(331;0.0686)|Lung(427;0.209)		CGCTCCCGCTGGTTCATGGGA	0.741																																					p.Q17X		Atlas-SNP	.											.	KIF17	130	.	0			c.C49T						PASS	.						11.0	12.0	12.0					1																	21044151		2178	4261	6439	SO:0001587	stop_gained	57576	exon1			CCCGCTGGTTCAT	AB037826	CCDS213.1, CCDS44079.1, CCDS72722.1	1p36.13	2012-08-01			ENSG00000117245	ENSG00000117245		"""Kinesins"""	19167	protein-coding gene	gene with protein product	"""kinesin-like protein KIF17"", ""KIF3-related motor protein"", ""KIF17 variant protein"""	605037				10846156	Standard	XR_241202		Approved	KIAA1405, KIF3X, KIF17B, OSM-3, KLP-2	uc001bdr.4	Q9P2E2	OTTHUMG00000002863	ENST00000247986.2:c.49C>T	1.37:g.21044151G>A	ENSP00000247986:p.Gln17*	Somatic	13	0	0		WXS	Illumina HiSeq	Phase_I	13	6	0.461538	NM_001122819	A2A3Q7|A2A3Q8|O95077|Q53YS6|Q5VWA9|Q6GSA8|Q8N411	Nonsense_Mutation	SNP	ENST00000247986.2	37	CCDS213.1	.	.	.	.	.	.	.	.	.	.	G	39	7.498382	0.98322	.	.	ENSG00000117245	ENST00000400463;ENST00000247986	.	.	.	4.11	3.16	0.36331	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.09590	T	0.72	.	2.572	0.04797	0.1049:0.1814:0.5104:0.2033	.	.	.	.	X	17	.	ENSP00000247986:Q17X	Q	-	1	0	KIF17	20916738	0.969000	0.33509	1.000000	0.80357	0.824000	0.46624	1.130000	0.31393	0.865000	0.35603	0.485000	0.47835	CAG	.	.	none		0.741	KIF17-009	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276995.1	NM_020816	
MLC1	23209	hgsc.bcm.edu	37	22	50502491	50502491	+	Missense_Mutation	SNP	T	T	C	rs11568188	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:50502491T>C	ENST00000311597.5	-	11	1637	c.1031A>G	c.(1030-1032)aAc>aGc	p.N344S	MLC1_ENST00000535444.1_Missense_Mutation_p.N265S|MLC1_ENST00000450140.2_Missense_Mutation_p.N292S|MLC1_ENST00000538737.1_Missense_Mutation_p.N310S|MLC1_ENST00000431262.2_Missense_Mutation_p.N314S|MLC1_ENST00000483836.1_5'UTR|MLC1_ENST00000395876.2_Missense_Mutation_p.N344S	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						scavenged	.		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	136	1	0.00735294		WXS	Illumina HiSeq	Phase_I	56	12	0.214286	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	
PLEK	5341	hgsc.bcm.edu	37	2	68592496	68592496	+	Missense_Mutation	SNP	C	C	T	rs17035364	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:68592496C>T	ENST00000234313.7	+	1	192	c.13C>T	c.(13-15)Cgg>Tgg	p.R5W	AC015969.3_ENST00000366218.2_RNA	NM_002664.2	NP_002655.2	P08567	PLEK_HUMAN	pleckstrin	5	PH 1. {ECO:0000255|PROSITE- ProRule:PRU00145}.		R -> W (in dbSNP:rs17035364).		actin cytoskeleton reorganization (GO:0031532)|blood coagulation (GO:0007596)|cell projection organization (GO:0030030)|cortical actin cytoskeleton organization (GO:0030866)|hematopoietic progenitor cell differentiation (GO:0002244)|integrin-mediated signaling pathway (GO:0007229)|negative regulation of calcium-mediated signaling (GO:0050849)|negative regulation of G-protein coupled receptor protein signaling pathway (GO:0045744)|negative regulation of inositol phosphate biosynthetic process (GO:0010920)|phosphatidylinositol metabolic process (GO:0046488)|phospholipase C-inhibiting G-protein coupled receptor signaling pathway (GO:0030845)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of actin filament bundle assembly (GO:0032233)|positive regulation of actin filament depolymerization (GO:0030836)|positive regulation of inositol-polyphosphate 5-phosphatase activity (GO:0010925)|positive regulation of integrin activation (GO:0033625)|positive regulation of platelet activation (GO:0010572)|protein kinase C signaling (GO:0070528)|protein secretion by platelet (GO:0070560)|regulation of cell diameter (GO:0060305)|ruffle organization (GO:0031529)|thrombin receptor signaling pathway (GO:0070493)|vesicle docking involved in exocytosis (GO:0006904)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|membrane (GO:0016020)|ruffle membrane (GO:0032587)	phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|protein homodimerization activity (GO:0042803)|protein kinase C binding (GO:0005080)			autonomic_ganglia(1)|endometrium(3)|large_intestine(6)|lung(12)|ovary(1)|skin(1)	24		Ovarian(717;0.0129)		STAD - Stomach adenocarcinoma(1183;0.00159)|READ - Rectum adenocarcinoma(193;0.0419)		GGAACCAAAGCGGATCAGAGA	0.597													C|||	261	0.0521166	0.1036	0.085	5008	,	,		19549	0.0258		0.0219	False		,,,				2504	0.0174				p.R5W		Atlas-SNP	.											.	PLEK	64	.	0			c.C13T						PASS	.	C	TRP/ARG	433,3973	210.2+/-230.7	12,409,1782	134.0	111.0	119.0		13	3.8	1.0	2	dbSNP_123	119	218,8382	91.1+/-153.3	3,212,4085	yes	missense	PLEK	NM_002664.2	101	15,621,5867	TT,TC,CC		2.5349,9.8275,5.0054	probably-damaging	5/351	68592496	651,12355	2203	4300	6503	SO:0001583	missense	5341	exon1			CCAAAGCGGATCA	X07743	CCDS1887.1	2p13.3	2013-01-10			ENSG00000115956	ENSG00000115956		"""Pleckstrin homology (PH) domain containing"""	9070	protein-coding gene	gene with protein product		173570				2897630, 12054651	Standard	NM_002664		Approved	P47	uc002sen.4	P08567	OTTHUMG00000129562	ENST00000234313.7:c.13C>T	2.37:g.68592496C>T	ENSP00000234313:p.Arg5Trp	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	106	33	0.311321	NM_002664	B2R9E8|Q53SU8|Q6FGM8|Q6FGQ1|Q8WV81	Missense_Mutation	SNP	ENST00000234313.7	37	CCDS1887.1	99	0.04532967032967033	48	0.0975609756097561	25	0.06906077348066299	11	0.019230769230769232	15	0.01978891820580475	C	21.7	4.185141	0.78677	0.098275	0.025349	ENSG00000115956	ENST00000234313	T	0.12255	2.7	5.85	3.83	0.44106	Pleckstrin homology-type (1);Pleckstrin homology domain (2);	0.684013	0.15170	N	0.276712	T	0.00384	0.0012	N	0.08118	0	0.40181	D	0.977297	D;D	0.67145	0.996;0.99	P;P	0.59056	0.851;0.674	T	0.32851	-0.9891	10	0.66056	D	0.02	.	12.1627	0.54113	0.3222:0.6778:0.0:0.0	rs17035364;rs52792076;rs57290355;rs17035364	23;5	Q59GZ2;P08567	.;PLEK_HUMAN	W	5	ENSP00000234313:R5W	ENSP00000234313:R5W	R	+	1	2	PLEK	68446000	0.956000	0.32656	1.000000	0.80357	0.974000	0.67602	0.047000	0.14056	1.435000	0.47434	0.563000	0.77884	CGG	C|0.952;T|0.048	0.048	strong		0.597	PLEK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251755.1	NM_002664	
HIST1H1B	3009	hgsc.bcm.edu	37	6	27835272	27835272	+	Silent	SNP	T	T	C	rs200948	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:27835272T>C	ENST00000331442.3	-	1	87	c.36A>G	c.(34-36)ccA>ccG	p.P12P		NM_005322.2	NP_005313.1	P16401	H15_HUMAN	histone cluster 1, H1b	12					chromatin organization (GO:0006325)|establishment of protein localization to chromatin (GO:0071169)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nucleosome assembly (GO:0006334)|positive regulation of cell growth (GO:0030307)|positive regulation of histone H3-K9 methylation (GO:0051574)|protein stabilization (GO:0050821)	extracellular vesicular exosome (GO:0070062)|nuclear chromatin (GO:0000790)|nuclear heterochromatin (GO:0005720)|nucleosome (GO:0000786)	chromatin DNA binding (GO:0031490)|histone deacetylase binding (GO:0042826)|poly(A) RNA binding (GO:0044822)			endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(5)|lung(12)|prostate(2)|upper_aerodigestive_tract(2)	24						CCACCGGCGCTGGGGTGGCTG	0.587													T|||	561	0.112021	0.1793	0.1383	5008	,	,		15202	0.0645		0.0875	False		,,,				2504	0.0767				p.P12P		Atlas-SNP	.											.	HIST1H1B	54	.	0			c.A36G						PASS	.	T		580,3690		40,500,1595	20.0	25.0	23.0		36	-1.9	0.4	6	dbSNP_79	23	830,7498		44,742,3378	no	coding-synonymous	HIST1H1B	NM_005322.2		84,1242,4973	CC,CT,TT		9.9664,13.5831,11.1923		12/227	27835272	1410,11188	2135	4164	6299	SO:0001819	synonymous_variant	3009	exon1			CGGCGCTGGGGTG	AF531304	CCDS4635.1	6p22.1	2012-05-04	2006-10-11	2003-02-14	ENSG00000184357	ENSG00000184357		"""Histones / Replication-dependent"""	4719	protein-coding gene	gene with protein product		142711	"""H1 histone family, member 5"", ""histone 1, H1b"""	H1F5		9031620, 9119399, 12408966	Standard	NM_005322		Approved	H1.5, H1b, H1s-3	uc003njx.3	P16401	OTTHUMG00000016139	ENST00000331442.3:c.36A>G	6.37:g.27835272T>C		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	63	30	0.47619	NM_005322	Q14529|Q3MJ42	Silent	SNP	ENST00000331442.3	37	CCDS4635.1																																																																																			T|0.896;C|0.104	0.104	strong		0.587	HIST1H1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043371.1	NM_005322	
PLA2G4C	8605	hgsc.bcm.edu	37	19	48558286	48558286	+	Silent	SNP	G	G	A	rs2307281	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:48558286G>A	ENST00000599921.1	-	15	1635	c.1278C>T	c.(1276-1278)gaC>gaT	p.D426D	PLA2G4C_ENST00000599111.1_Silent_p.D436D|PLA2G4C_ENST00000596510.1_5'UTR|PLA2G4C_ENST00000354276.3_Silent_p.D426D|PLA2G4C_ENST00000413144.2_Silent_p.D426D			Q9UP65	PA24C_HUMAN	phospholipase A2, group IVC (cytosolic, calcium-independent)	426	PLA2c. {ECO:0000255|PROSITE- ProRule:PRU00555}.				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)		GGCGGCAGTAGTCAGTGGTAG	0.572													g|||	562	0.11222	0.0197	0.2046	5008	,	,		13343	0.0159		0.2286	False		,,,				2504	0.1513				p.D436D		Atlas-SNP	.											.	PLA2G4C	76	.	0			c.C1308T						PASS	.	G	,,	226,4180	135.7+/-171.8	3,220,1980	68.0	69.0	69.0		1308,1278,1278	0.6	0.1	19	dbSNP_100	69	1927,6673	340.0+/-323.4	201,1525,2574	no	coding-synonymous,coding-synonymous,coding-synonymous	PLA2G4C	NM_001159322.1,NM_001159323.1,NM_003706.2	,,	204,1745,4554	AA,AG,GG		22.407,5.1294,16.5539	,,	436/552,426/528,426/542	48558286	2153,10853	2203	4300	6503	SO:0001819	synonymous_variant	8605	exon15			GCAGTAGTCAGTG	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.1278C>T	19.37:g.48558286G>A		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	76	44	0.578947	NM_001159322	B2RB71|B4DI40|O75457|Q6IBI8|Q9UG68	Silent	SNP	ENST00000599921.1	37	CCDS12710.1																																																																																			G|0.854;A|0.146	0.146	strong		0.572	PLA2G4C-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000465551.1		
PCDH15	65217	hgsc.bcm.edu	37	10	55955485	55955485	+	Silent	SNP	A	A	G	rs7921598	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:55955485A>G	ENST00000320301.6	-	11	1657	c.1263T>C	c.(1261-1263)acT>acC	p.T421T	PCDH15_ENST00000409834.1_Silent_p.T25T|PCDH15_ENST00000395432.2_Silent_p.T384T|PCDH15_ENST00000395433.1_Silent_p.T399T|PCDH15_ENST00000395445.1_Silent_p.T421T|PCDH15_ENST00000373957.3_Silent_p.T399T|PCDH15_ENST00000395442.1_Intron|PCDH15_ENST00000395438.1_Silent_p.T421T|PCDH15_ENST00000373965.2_Silent_p.T421T|PCDH15_ENST00000395430.1_Silent_p.T421T|PCDH15_ENST00000395440.1_Silent_p.T421T|PCDH15_ENST00000395446.1_Silent_p.T421T|PCDH15_ENST00000373955.1_Silent_p.T421T|PCDH15_ENST00000414778.1_Silent_p.T426T|PCDH15_ENST00000437009.1_Silent_p.T421T|PCDH15_ENST00000361849.3_Silent_p.T421T	NM_033056.3	NP_149045.3	Q96QU1	PCD15_HUMAN	protocadherin-related 15	421	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|synapse (GO:0045202)	calcium ion binding (GO:0005509)			NS(3)|breast(6)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(39)|lung(108)|ovary(5)|pancreas(6)|prostate(6)|skin(12)|upper_aerodigestive_tract(12)|urinary_tract(1)	237		Melanoma(3;0.117)|Lung SC(717;0.238)				TTAAAGGTGAAGTCAAATTGA	0.358										HNSCC(58;0.16)			G|||	1282	0.25599	0.5348	0.2118	5008	,	,		17037	0.0863		0.1382	False		,,,				2504	0.2065				p.T426T		Atlas-SNP	.											.	PCDH15	1715	.	0			c.T1278C						PASS	.	G	,,,,,,,,,,,	2108,2298	601.9+/-389.8	506,1096,601	124.0	116.0	119.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1278,1263,1263,1263,1152,1197,1278,1263,1278,1263,1197,1263	4.1	0.9	10	dbSNP_116	119	1102,7498	768.6+/-407.6	65,972,3263	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	PCDH15	NM_001142763.1,NM_001142764.1,NM_001142765.1,NM_001142766.1,NM_001142767.1,NM_001142768.1,NM_001142769.1,NM_001142770.1,NM_001142771.1,NM_001142772.1,NM_001142773.1,NM_033056.3	,,,,,,,,,,,	571,2068,3864	GG,GA,AA		12.814,47.8438,24.6809	,,,,,,,,,,,	426/1963,421/1958,421/1887,421/1953,384/1916,399/1936,426/1791,421/1540,426/1683,421/1678,399/1933,421/1956	55955485	3210,9796	2203	4300	6503	SO:0001819	synonymous_variant	65217	exon12			AGGTGAAGTCAAA	AY029205	CCDS7248.1, CCDS44400.1, CCDS44401.1, CCDS44403.1, CCDS44404.1, CCDS73134.1, CCDS73135.1, CCDS73136.1, CCDS73137.1, CCDS73138.1	10q21.1	2013-01-08	2010-01-25		ENSG00000150275	ENSG00000150275		"""Cadherins / Cadherin-related"""	14674	protein-coding gene	gene with protein product	"""cadherin-related family member 15"""	605514	"""deafness, autosomal recessive 23"", ""protocadherin 15"""	USH1F, DFNB23		11398101, 14570705	Standard	NM_033056		Approved	CDHR15	uc010qhy.1	Q96QU1	OTTHUMG00000018259	ENST00000320301.6:c.1263T>C	10.37:g.55955485A>G		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	92	48	0.521739	NM_001142763	A6NL19|C6ZEF5|C6ZEF6|C6ZEF7|Q5VY38|Q5VY39|Q6TRH8|Q8NDB9|Q96QT8	Silent	SNP	ENST00000320301.6	37	CCDS7248.1																																																																																			A|0.756;G|0.244	0.244	strong		0.358	PCDH15-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000048121.2	NM_033056	
TRIM66	9866	hgsc.bcm.edu	37	11	8668082	8668082	+	Missense_Mutation	SNP	C	C	T	rs61741649	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:8668082C>T	ENST00000299550.6	-	6	628	c.434G>A	c.(433-435)aGg>aAg	p.R145K	TRIM66_ENST00000402157.2_Missense_Mutation_p.R143K|TRIM66_ENST00000531498.1_5'UTR	NM_014818.1	NP_055633.1	O15016	TRI66_HUMAN	tripartite motif containing 66	145						aggresome (GO:0016235)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(4)|kidney(1)|lung(1)|skin(2)	9						TTCCACCTTCCTATGCTGATG	0.408													C|||	161	0.0321486	0.003	0.0533	5008	,	,		23209	0.0		0.0577	False		,,,				2504	0.0634				p.R145K		Atlas-SNP	.											.	TRIM66	45	.	0			c.G434A						PASS	.	C	LYS/ARG	14,1370		0,14,678	373.0	272.0	302.0		434	6.2	1.0	11	dbSNP_129	302	226,2956		7,212,1372	yes	missense	TRIM66	NM_014818.1	26	7,226,2050	TT,TC,CC		7.1025,1.0116,5.2562	possibly-damaging	145/1217	8668082	240,4326	692	1591	2283	SO:0001583	missense	9866	exon6			ACCTTCCTATGCT	AB002296		11p15.4	2013-01-28	2011-01-25		ENSG00000166436	ENSG00000166436		"""Tripartite motif containing / Tripartite motif containing"", ""Zinc fingers, PHD-type"""	29005	protein-coding gene	gene with protein product		612000	"""chromosome 11 open reading frame 29"", ""tripartite motif-containing 66"""	C11orf29		9205841	Standard	NM_014818		Approved	KIAA0298, TIF1D	uc010rbo.2	O15016	OTTHUMG00000150481	ENST00000299550.6:c.434G>A	11.37:g.8668082C>T	ENSP00000299550:p.Arg145Lys	Somatic	352	0	0		WXS	Illumina HiSeq	Phase_I	410	341	0.831707	NM_014818	Q9BQQ4	Missense_Mutation	SNP	ENST00000299550.6	37		63	0.028846153846153848	1	0.0020325203252032522	13	0.03591160220994475	0	0.0	49	0.06464379947229551	C	15.27	2.782641	0.49891	0.010116	0.071025	ENSG00000166436	ENST00000299550;ENST00000402157	T;T	0.61274	0.12;0.13	6.16	6.16	0.99307	B-box, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.02267	0.0070	N	0.04959	-0.14	0.28531	N	0.912561	B;P	0.36027	0.282;0.533	B;B	0.27796	0.076;0.083	T	0.09840	-1.0656	10	0.02654	T	1	-25.5523	14.3908	0.66978	0.0:0.925:0.0:0.075	.	145;143	O15016;B5MCJ9	TRI66_HUMAN;.	K	145;143	ENSP00000299550:R145K;ENSP00000384876:R143K	ENSP00000299550:R145K	R	-	2	0	TRIM66	8624658	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.518000	0.53451	2.937000	0.99478	0.650000	0.86243	AGG	C|0.963;T|0.037	0.037	strong		0.408	TRIM66-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		XM_084529	
TRPC1	7220	hgsc.bcm.edu	37	3	142523349	142523349	+	Silent	SNP	G	G	A	rs3821647	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:142523349G>A	ENST00000476941.1	+	12	2517	c.2031G>A	c.(2029-2031)acG>acA	p.T677T	TRPC1_ENST00000273482.6_Silent_p.T643T	NM_001251845.1	NP_001238774.1	P48995	TRPC1_HUMAN	transient receptor potential cation channel, subfamily C, member 1	677					axon guidance (GO:0007411)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|response to calcium ion (GO:0051592)|saliva secretion (GO:0046541)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|costamere (GO:0043034)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|sarcomere (GO:0030017)	calcium channel activity (GO:0005262)|cation channel activity (GO:0005261)|inositol 1,4,5 trisphosphate binding (GO:0070679)|ion channel binding (GO:0044325)|store-operated calcium channel activity (GO:0015279)	p.T643T(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(18)|ovary(2)|skin(2)|stomach(3)|urinary_tract(1)	37						ACAAATGTACGTTACCTCCAC	0.368													G|||	972	0.194089	0.2186	0.1354	5008	,	,		16060	0.2391		0.2038	False		,,,				2504	0.1462				p.T677T		Atlas-SNP	.											TRPC1,NS,carcinoma,0,1	TRPC1	82	1	1	Substitution - coding silent(1)	stomach(1)	c.G2031A						PASS	.	G		928,3478	352.6+/-311.8	97,734,1372	100.0	95.0	97.0		1929	-3.1	1.0	3	dbSNP_107	97	1578,7022	294.8+/-302.1	163,1252,2885	no	coding-synonymous	TRPC1	NM_003304.4		260,1986,4257	AA,AG,GG		18.3488,21.0622,19.268		643/760	142523349	2506,10500	2203	4300	6503	SO:0001819	synonymous_variant	7220	exon12			ATGTACGTTACCT	X89066	CCDS3126.1, CCDS58856.1	3q23	2011-12-14			ENSG00000144935	ENSG00000144935		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	12333	protein-coding gene	gene with protein product		602343				7568191, 16382100	Standard	NM_001251845		Approved	HTRP-1	uc003evc.3	P48995	OTTHUMG00000159301	ENST00000476941.1:c.2031G>A	3.37:g.142523349G>A		Somatic	220	0	0		WXS	Illumina HiSeq	Phase_I	232	108	0.465517	NM_001251845	Q14CE4	Silent	SNP	ENST00000476941.1	37	CCDS58856.1																																																																																			G|0.806;A|0.194	0.194	strong		0.368	TRPC1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354520.1	NM_003304	
JAK1	3716	hgsc.bcm.edu	37	1	65311214	65311214	+	Silent	SNP	G	G	C	rs3737139	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:65311214G>C	ENST00000342505.4	-	15	2345	c.2097C>G	c.(2095-2097)gcC>gcG	p.A699A	JAK1_ENST00000465376.1_5'UTR	NM_002227.2	NP_002218.2	P23458	JAK1_HUMAN	Janus kinase 1	699	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)	TCAGGGCACTGGCCAGCTGTT	0.532			Mis		ALL								G|||	194	0.038738	0.0015	0.1311	5008	,	,		20122	0.0069		0.0408	False		,,,				2504	0.0542				p.A699A		Atlas-SNP	.		Dom	yes		1	1p32.3-p31.3	3716	Janus kinase 1		L	.	JAK1	209	.	0			c.C2097G						PASS	.	G		44,3910		1,42,1934	171.0	176.0	174.0		2097	5.2	1.0	1	dbSNP_107	174	504,7816		13,478,3669	no	coding-synonymous	JAK1	NM_002227.2		14,520,5603	CC,CG,GG		6.0577,1.1128,4.4647		699/1155	65311214	548,11726	1977	4160	6137	SO:0001819	synonymous_variant	3716	exon15			GGCACTGGCCAGC	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.2097C>G	1.37:g.65311214G>C		Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	153	73	0.477124	NM_002227	Q59GQ2|Q9UD26	Silent	SNP	ENST00000342505.4	37	CCDS41346.1																																																																																			G|0.958;C|0.042	0.042	strong		0.532	JAK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025791.1	NM_002227	
CLEC18C	283971	hgsc.bcm.edu	37	16	70211370	70211370	+	Missense_Mutation	SNP	C	C	G	rs3869428	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:70211370C>G	ENST00000569347.2	+	3	697	c.443C>G	c.(442-444)aCc>aGc	p.T148S	CLEC18C_ENST00000536907.2_Missense_Mutation_p.T148S|CLEC18C_ENST00000541793.2_Missense_Mutation_p.T148S|CLEC18C_ENST00000561612.1_Intron|CLEC18C_ENST00000314151.8_Missense_Mutation_p.T148S	NM_173619.2	NP_775890.2	Q8NCF0	CL18C_HUMAN	C-type lectin domain family 18, member C	148	SCP.					extracellular region (GO:0005576)	carbohydrate binding (GO:0030246)	p.T148S(1)		endometrium(3)|large_intestine(6)|lung(1)	10						GCCACCTGCACCCACTACACG	0.602																																					p.T148S		Atlas-SNP	.											CLEC18C,rectum,carcinoma,0,1	CLEC18C	15	1	1	Substitution - Missense(1)	large_intestine(1)	c.C443G						scavenged	.						12.0	11.0	11.0					16																	70211370		2072	4009	6081	SO:0001583	missense	283971	exon3			CCTGCACCCACTA	AL833339	CCDS32473.1	16q22.1	2010-04-27	2009-03-10	2009-03-10		ENSG00000157335		"""C-type lectin domain containing"""	28538	protein-coding gene	gene with protein product						12477932	Standard	XM_005255906		Approved	MGC34761		Q8NCF0		ENST00000569347.2:c.443C>G	16.37:g.70211370C>G	ENSP00000455920:p.Thr148Ser	Somatic	529	0	0		WXS	Illumina HiSeq	Phase_I	545	98	0.179817	NM_173619	Q8IUW8	Missense_Mutation	SNP	ENST00000569347.2	37	CCDS32473.1	.	.	.	.	.	.	.	.	.	.	c	6.117	0.389845	0.11581	.	.	ENSG00000157335	ENST00000541793;ENST00000314151;ENST00000433156;ENST00000539438;ENST00000536907	T;T;T	0.07688	3.17;3.17;3.17	4.32	2.09	0.27110	CAP domain (3);	0.557277	0.19650	N	0.109248	T	0.06508	0.0167	L	0.28344	0.845	0.21802	N	0.999531	B	0.10296	0.003	B	0.12837	0.008	T	0.30851	-0.9964	10	0.51188	T	0.08	.	10.1296	0.42672	0.0:0.6029:0.3971:0.0	.	148	Q8NCF0	CL18C_HUMAN	S	148;148;148;144;148	ENSP00000444875:T148S;ENSP00000326538:T148S;ENSP00000444726:T148S	ENSP00000326538:T148S	T	+	2	0	CLEC18C	68768871	0.141000	0.22595	1.000000	0.80357	0.135000	0.20990	1.141000	0.31528	0.903000	0.36546	0.298000	0.19748	ACC	.	.	weak		0.602	CLEC18C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000434588.2	NM_173619	
MUC4	4585	hgsc.bcm.edu	37	3	195507915	195507915	+	Silent	SNP	T	T	C	rs71635073		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195507915T>C	ENST00000463781.3	-	2	10995	c.10536A>G	c.(10534-10536)tcA>tcG	p.S3512S	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Silent_p.S3512S	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.S3512S(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)		CGGTGGATGCTGAGGAAGCGC	0.587																																					p.S3512S		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	1	Substitution - coding silent(1)	kidney(1)	c.A10536G						PASS	.						45.0	38.0	40.0					3																	195507915		649	1586	2235	SO:0001819	synonymous_variant	4585	exon2			GGATGCTGAGGAA	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.10536A>G	3.37:g.195507915T>C		Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	203	55	0.270936	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Silent	SNP	ENST00000463781.3	37	CCDS54700.1																																																																																			C|1.000;|0.000	1.000	weak		0.587	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
ME3	10873	hgsc.bcm.edu	37	11	86267714	86267714	+	Silent	SNP	C	C	A	rs12287767	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:86267714C>A	ENST00000393324.3	-	3	601	c.348G>T	c.(346-348)cgG>cgT	p.R116R	ME3_ENST00000323418.6_Silent_p.R54R|ME3_ENST00000359636.2_Silent_p.R116R|RP11-317J19.1_ENST00000524610.1_RNA|ME3_ENST00000543262.1_Silent_p.R116R	NM_001014811.1	NP_001014811.1	Q16798	MAON_HUMAN	malic enzyme 3, NADP(+)-dependent, mitochondrial	116					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)				GCTTCTCGTTCCGGTCTTGGA	0.537													C|||	1383	0.276158	0.1921	0.3487	5008	,	,		20697	0.5327		0.1799	False		,,,				2504	0.1728				p.R116R		Atlas-SNP	.											.	ME3	70	.	0			c.G348T						PASS	.	C	,,	819,3585	326.1+/-299.4	67,685,1450	114.0	95.0	102.0		348,348,348	5.2	1.0	11	dbSNP_120	102	1449,7149	278.6+/-293.5	110,1229,2960	no	coding-synonymous,coding-synonymous,coding-synonymous	ME3	NM_001014811.1,NM_001161586.1,NM_006680.2	,,	177,1914,4410	AA,AC,CC		16.8528,18.5967,17.4435	,,	116/605,116/605,116/605	86267714	2268,10734	2202	4299	6501	SO:0001819	synonymous_variant	10873	exon4			CTCGTTCCGGTCT	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.348G>T	11.37:g.86267714C>A		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	93	23	0.247312	NM_006680	B7Z6V0|Q8TBJ0	Silent	SNP	ENST00000393324.3	37	CCDS8277.1																																																																																			C|0.774;A|0.226	0.226	strong		0.537	ME3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393767.2		
LRRIQ1	84125	hgsc.bcm.edu	37	12	85438499	85438499	+	Missense_Mutation	SNP	G	G	A	rs3765044	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:85438499G>A	ENST00000393217.2	+	4	309	c.248G>A	c.(247-249)tGt>tAt	p.C83Y		NM_001079910.1	NP_001073379.1	Q96JM4	LRIQ1_HUMAN	leucine-rich repeats and IQ motif containing 1	83			C -> Y (in dbSNP:rs3765044). {ECO:0000269|PubMed:14702039}.							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)		TCTCTAGGCTGTAGTTATGGA	0.274													G|||	1035	0.206669	0.0446	0.3112	5008	,	,		12725	0.2222		0.2604	False		,,,				2504	0.2802				p.C83Y		Atlas-SNP	.											.	LRRIQ1	512	.	0			c.G248A						PASS	.	G	TYR/CYS	334,4042		15,304,1869	55.0	59.0	57.0		248	-2.9	0.0	12	dbSNP_107	57	2303,6175		317,1669,2253	yes	missense	LRRIQ1	NM_001079910.1	194	332,1973,4122	AA,AG,GG		27.1644,7.6325,20.515	benign	83/1723	85438499	2637,10217	2188	4239	6427	SO:0001583	missense	84125	exon4			TAGGCTGTAGTTA	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.248G>A	12.37:g.85438499G>A	ENSP00000376910:p.Cys83Tyr	Somatic	244	0	0		WXS	Illumina HiSeq	Phase_I	206	101	0.490291	NM_001079910	Q567P4|Q9BS17|Q9HA36	Missense_Mutation	SNP	ENST00000393217.2	37	CCDS41816.1	461	0.21108058608058608	23	0.046747967479674794	110	0.30386740331491713	128	0.22377622377622378	200	0.2638522427440633	G	0.001	-3.383939	0.00015	0.076325	0.271644	ENSG00000133640	ENST00000256007;ENST00000378580;ENST00000393212;ENST00000393217	T;T	0.50001	0.95;0.76	4.79	-2.93	0.05598	.	1.279600	0.05313	N	0.525186	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	0.01281	0.0;0.0	T	0.25950	-1.0117	9	0.02654	T	1	.	9.2091	0.37306	0.245:0.1252:0.6298:0.0	rs3765044;rs52836945;rs60065129;rs3765044	83;83	Q96JM4;C9JI57	LRIQ1_HUMAN;.	Y	83	ENSP00000376906:C83Y;ENSP00000376910:C83Y	ENSP00000256007:C83Y	C	+	2	0	LRRIQ1	83962630	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-0.698000	0.05092	-0.584000	0.05913	-1.641000	0.00772	TGT	G|0.796;A|0.204	0.204	strong		0.274	LRRIQ1-004	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388249.2	NM_032165	
CPAMD8	27151	hgsc.bcm.edu	37	19	17100550	17100550	+	Missense_Mutation	SNP	A	A	T	rs61744414	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	103	0	0		WXS	Illumina HiSeq	Phase_I	68	29	0.426471	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	
KRTAP4-8	728224	hgsc.bcm.edu	37	17	39254133	39254133	+	Missense_Mutation	SNP	G	G	T	rs200462175		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:39254133G>T	ENST00000333822.4	-	1	260	c.204C>A	c.(202-204)agC>agA	p.S68R		NM_031960.2	NP_114166.1	Q9BYQ9	KRA48_HUMAN	keratin associated protein 4-8	68	25 X 5 AA repeats of C-C-[IKRQVHEC]- [SPRT]-[STCVQPR].				aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)				endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(1)|prostate(1)	11						ACACACAGCAGCTGGGGCGAC	0.667																																					p.S68R		Atlas-SNP	.											.	KRTAP4-8	57	.	0			c.C204A						PASS	.						6.0	9.0	8.0					17																	39254133		616	1426	2042	SO:0001583	missense	728224	exon1			ACAGCAGCTGGGG	AJ406940	CCDS45674.1	17q21.2	2013-06-25			ENSG00000204880	ENSG00000204880		"""Keratin associated proteins"""	17230	protein-coding gene	gene with protein product						11279113	Standard	NM_031960		Approved	KAP4.8	uc010wfo.2	Q9BYQ9	OTTHUMG00000133580	ENST00000333822.4:c.204C>A	17.37:g.39254133G>T	ENSP00000328444:p.Ser68Arg	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	40	4	0.1	NM_031960	A8MSH3	Missense_Mutation	SNP	ENST00000333822.4	37	CCDS45674.1	.	.	.	.	.	.	.	.	.	.	.	13.88	2.368333	0.42003	.	.	ENSG00000204880	ENST00000333822;ENST00000332991	T	0.01963	4.53	3.73	-3.02	0.05446	.	2.601200	0.02242	U	0.065854	T	0.05135	0.0137	M	0.89658	3.05	0.20307	N	0.999915	B	0.11235	0.004	B	0.10450	0.005	T	0.47774	-0.9091	10	0.46703	T	0.11	.	0.2646	0.00223	0.277:0.1441:0.2848:0.2941	.	68	Q9BYQ9	KRA48_HUMAN	R	68	ENSP00000328444:S68R	ENSP00000414561:S68R	S	-	3	2	KRTAP4-8	36507659	0.949000	0.32298	0.011000	0.14972	0.444000	0.32077	1.355000	0.34068	-0.877000	0.04012	0.449000	0.29647	AGC	.	.	weak		0.667	KRTAP4-8-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257684.1	NM_031960	
RPGRIP1	57096	hgsc.bcm.edu	37	14	21770681	21770681	+	Silent	SNP	A	A	G	rs17792599	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:21770681A>G	ENST00000400017.2	+	4	525	c.525A>G	c.(523-525)ccA>ccG	p.P175P	RPGRIP1_ENST00000206660.6_Silent_p.P175P|RPGRIP1_ENST00000556336.1_Silent_p.P175P|RPGRIP1_ENST00000557771.1_Silent_p.P175P	NM_020366.3	NP_065099.3	Q96KN7	RPGR1_HUMAN	retinitis pigmentosa GTPase regulator interacting protein 1	175					eye photoreceptor cell development (GO:0042462)|response to stimulus (GO:0050896)|retina development in camera-type eye (GO:0060041)|visual perception (GO:0007601)	axoneme (GO:0005930)|nonmotile primary cilium (GO:0031513)				breast(3)|endometrium(2)|kidney(4)|large_intestine(11)|lung(10)|ovary(4)|pancreas(1)|prostate(3)|stomach(1)	39	all_cancers(95;0.0017)	all_cancers(140;0.0973)	Epithelial(56;6.24e-07)|all cancers(55;6.56e-06)	GBM - Glioblastoma multiforme(265;0.00888)		CAGCCCCTCCATCGTTTAAGG	0.478													A|||	678	0.135383	0.1362	0.1527	5008	,	,		18254	0.0933		0.1889	False		,,,				2504	0.1104				p.P175P		Atlas-SNP	.											.	RPGRIP1	213	.	0			c.A525G						PASS	.	A		476,3398		26,424,1487	51.0	51.0	51.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	525	-4.8	0.0	14	dbSNP_123	51	1565,6715		163,1239,2738	no	coding-synonymous	RPGRIP1	NM_020366.3		189,1663,4225	GG,GA,AA		18.901,12.287,16.7928		175/1287	21770681	2041,10113	1937	4140	6077	SO:0001819	synonymous_variant	57096	exon4			CCCTCCATCGTTT	AF227257	CCDS45080.1	14q11.2	2013-06-06			ENSG00000092200	ENSG00000092200			13436	protein-coding gene	gene with protein product		605446		RPGRIP		10958647, 10958648	Standard	NM_020366		Approved	RGI1, LCA6, CORD13	uc001wag.3	Q96KN7	OTTHUMG00000170758	ENST00000400017.2:c.525A>G	14.37:g.21770681A>G		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	86	49	0.569767	NM_020366	Q7Z2W6|Q8IXV5|Q96QA8|Q9HB94|Q9HB95|Q9HBK6|Q9NR40	Silent	SNP	ENST00000400017.2	37	CCDS45080.1																																																																																			A|0.857;G|0.142	0.142	strong		0.478	RPGRIP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410258.1	NM_020366	
ULK4	54986	hgsc.bcm.edu	37	3	41831203	41831203	+	Missense_Mutation	SNP	C	C	T	rs17215589	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:41831203C>T	ENST00000301831.4	-	21	2605	c.2143G>A	c.(2143-2145)Gct>Act	p.A715T		NM_017886.2	NP_060356.2	Q96C45	ULK4_HUMAN	unc-51 like kinase 4	715			A -> T (in dbSNP:rs17215589).		cilium morphogenesis (GO:0060271)|epithelial cilium movement (GO:0003351)|microtubule cytoskeleton organization (GO:0000226)|regulation of JNK cascade (GO:0046328)|regulation of MAPK cascade (GO:0043408)|regulation of neuron migration (GO:2001222)|regulation of neuron projection development (GO:0010975)|regulation of p38MAPK cascade (GO:1900744)|regulation of protein kinase C signaling (GO:0090036)|ventricular system development (GO:0021591)		ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|cervix(1)|large_intestine(6)|lung(7)|prostate(5)|skin(1)	22				KIRC - Kidney renal clear cell carcinoma(284;0.214)		AACATGGCAGCGAATAAGGTC	0.393													T|||	408	0.0814696	0.0552	0.0879	5008	,	,		19692	0.002		0.166	False		,,,				2504	0.1074				p.A715T		Atlas-SNP	.											.	ULK4	150	.	0			c.G2143A						PASS	.	T	THR/ALA	254,3610		9,236,1687	112.0	109.0	110.0		2143	2.3	0.0	3	dbSNP_123	110	1240,7006		90,1060,2973	yes	missense	ULK4	NM_017886.2	58	99,1296,4660	TT,TC,CC		15.0376,6.5735,12.3369	benign	715/1276	41831203	1494,10616	1932	4123	6055	SO:0001583	missense	54986	exon21			TGGCAGCGAATAA	AK000581	CCDS43071.1	3p22.1	2013-07-02	2013-07-02		ENSG00000168038	ENSG00000168038			15784	protein-coding gene	gene with protein product			"""unc-51-like kinase 4 (C. elegans)"""			12477932	Standard	NM_017886		Approved	FLJ20574, REC01035, FAM7C1	uc003ckv.4	Q96C45	OTTHUMG00000156210	ENST00000301831.4:c.2143G>A	3.37:g.41831203C>T	ENSP00000301831:p.Ala715Thr	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	93	46	0.494624	NM_017886	A6NF15|Q8IW79|Q9NWV6|Q9UF96	Missense_Mutation	SNP	ENST00000301831.4	37	CCDS43071.1	194	0.08882783882783883	29	0.05894308943089431	30	0.08287292817679558	2	0.0034965034965034965	133	0.17546174142480211	T	2.507	-0.313897	0.05422	0.065735	0.150376	ENSG00000168038	ENST00000301831	T	0.66099	-0.19	5.91	2.31	0.28768	Armadillo-like helical (1);Armadillo-type fold (2);	0.222920	0.38272	N	0.001755	T	0.00039	0.0001	N	0.02802	-0.49	0.09310	P	0.999999898638	B	0.06786	0.001	B	0.06405	0.002	T	0.12066	-1.0562	9	0.02654	T	1	.	4.5461	0.12081	0.2099:0.287:0.0:0.5031	rs17215589;rs17215589	715	Q96C45	ULK4_HUMAN	T	715	ENSP00000301831:A715T	ENSP00000301831:A715T	A	-	1	0	ULK4	41806207	0.719000	0.27986	0.028000	0.17463	0.890000	0.51754	-0.189000	0.09629	-0.047000	0.13423	-0.254000	0.11334	GCT	C|0.898;T|0.102	0.102	strong		0.393	ULK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343490.1	XM_929989	
KRTAP5-5	439915	hgsc.bcm.edu	37	11	1651625	1651625	+	Silent	SNP	G	G	A	rs576867883|rs200756510|rs71025765	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:1651625G>A	ENST00000399676.2	+	1	593	c.555G>A	c.(553-555)caG>caA	p.Q185Q		NM_001001480.2	NP_001001480.2	Q701N2	KRA55_HUMAN	keratin associated protein 5-5	185	8 X 4 AA repeats of C-C-X-P.					keratin filament (GO:0045095)		p.Y182_P191delYCCQSSCCKP(1)		endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(17)|ovary(2)|prostate(5)|urinary_tract(1)	33		all_epithelial(84;0.00018)|Ovarian(85;0.0014)|Breast(177;0.00147)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.000614)|Lung(200;0.0681)|LUSC - Lung squamous cell carcinoma(625;0.082)		ACTGCTGCCAGTCCAGCTGCT	0.597																																					p.Q185Q		Atlas-SNP	.											KRTAP5-5,NS,carcinoma,+2,1	KRTAP5-5	86	1	1	Deletion - In frame(1)	urinary_tract(1)	c.G555A						PASS	.						67.0	73.0	71.0					11																	1651625		2200	4292	6492	SO:0001819	synonymous_variant	439915	exon1			CTGCCAGTCCAGC	AB125074	CCDS41592.1	11p15.5	2008-10-30			ENSG00000185940	ENSG00000185940		"""Keratin associated proteins"""	23601	protein-coding gene	gene with protein product						15144888	Standard	NM_001001480		Approved	KRTAP5.5, KRTAP5-11	uc001lty.3	Q701N2	OTTHUMG00000057554	ENST00000399676.2:c.555G>A	11.37:g.1651625G>A		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	56	17	0.303571	NM_001001480	A8MWN2	Silent	SNP	ENST00000399676.2	37	CCDS41592.1																																																																																			G|0.988;A|0.011	0.011	strong		0.597	KRTAP5-5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127919.1		
NEB	4703	hgsc.bcm.edu	37	2	152389991	152389991	+	Intron	SNP	A	A	G	rs114218081	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:152389991A>G	ENST00000172853.10	-	115	16462				NEB_ENST00000427231.2_Intron|NEB_ENST00000603639.1_Silent_p.L7128L|NEB_ENST00000409198.1_Intron|NEB_ENST00000397345.3_Silent_p.L7128L|NEB_ENST00000604864.1_Intron			P20929	NEBU_HUMAN	nebulin						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)		AGAGCAGTCAACATATCTGGA	0.413													A|||	88	0.0175719	0.0393	0.0072	5008	,	,		22891	0.0		0.0268	False		,,,				2504	0.0041				p.L7163L		Atlas-SNP	.											.	NEB	1697	.	0			c.T21487C						PASS	.	A	,,	55,1329		3,49,640	218.0	170.0	185.0		,21382,	6.2	1.0	2	dbSNP_132	185	66,3116		0,66,1525	no	intron,coding-synonymous,intron	NEB	NM_001164507.1,NM_001164508.1,NM_004543.4	,,	3,115,2165	GG,GA,AA		2.0742,3.974,2.65	,,	,7128/8526,	152389991	121,4445	692	1591	2283	SO:0001627	intron_variant	4703	exon144			CAGTCAACATATC	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.16314+737T>C	2.37:g.152389991A>G		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	102	46	0.45098	NM_001271208	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Silent	SNP	ENST00000172853.10	37																																																																																				A|0.979;G|0.021	0.021	strong		0.413	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543	
C6orf223	221416	hgsc.bcm.edu	37	6	43968814	43968814	+	Missense_Mutation	SNP	A	A	G	rs2295333	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:43968814A>G	ENST00000336600.5	+	2	162	c.142A>G	c.(142-144)Aag>Gag	p.K48E	C6orf223_ENST00000439969.2_Missense_Mutation_p.Q62R|C6orf223_ENST00000448947.2_Intron|RP5-1120P11.1_ENST00000422059.1_RNA|C6orf223_ENST00000442114.2_Missense_Mutation_p.K28E|RP5-1120P11.1_ENST00000607590.1_RNA	NM_001171992.1|NM_153246.4	NP_001165463.1|NP_694978.2	Q8N319	CF223_HUMAN	chromosome 6 open reading frame 223	48			K -> E (in dbSNP:rs2295333).							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)			AAGAAGTGGCAAGACTTCAGC	0.537													G|||	977	0.195088	0.233	0.0951	5008	,	,		18234	0.3571		0.0696	False		,,,				2504	0.1769				p.Q62R		Atlas-SNP	.											.	C6orf223	14	.	0			c.A185G						PASS	.	G	GLU/LYS,ARG/GLN	926,3480	738.4+/-411.0	100,726,1377	120.0	118.0	119.0		142,185	1.2	0.0	6	dbSNP_100	119	493,8107	797.5+/-407.4	16,461,3823	yes	missense,missense	C6orf223	NM_153246.4,NM_001171992.1	56,43	116,1187,5200	GG,GA,AA		5.7326,21.0168,10.9103	benign,benign	48/243,62/106	43968814	1419,11587	2203	4300	6503	SO:0001583	missense	221416	exon2			AGTGGCAAGACTT	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.142A>G	6.37:g.43968814A>G	ENSP00000426159:p.Lys48Glu	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	75	42	0.56	NM_001171992	E9PB59|Q8N575	Missense_Mutation	SNP	ENST00000336600.5	37	CCDS34459.1	446|446	0.2042124542124542|0.2042124542124542	129|129	0.2621951219512195|0.2621951219512195	43|43	0.11878453038674033|0.11878453038674033	221|221	0.38636363636363635|0.38636363636363635	53|53	0.06992084432717678|0.06992084432717678	G|G	4.835|4.835	0.155188|0.155188	0.09236|0.09236	0.210168|0.210168	0.057326|0.057326	ENSG00000181577|ENSG00000181577	ENST00000336600|ENST00000439969	T|.	0.38560|.	1.13|.	2.09|2.09	1.18|1.18	0.20946|0.20946	.|.	.|.	.|.	.|.	.|.	T|T	0.07143|0.07143	0.0181|0.0181	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	0.20538|0.20538	-1.0272|-1.0272	8|5	0.87932|0.87932	D|D	0|0	.|.	3.4135|3.4135	0.07366|0.07366	0.168:0.2706:0.5615:0.0|0.168:0.2706:0.5615:0.0	rs2295333;rs58327156;rs2295333|rs2295333;rs58327156;rs2295333	48|.	Q8N319|.	CF223_HUMAN|.	E|R	48|62	ENSP00000426159:K48E|.	ENSP00000426159:K48E|ENSP00000423262:Q62R	K|Q	+|+	1|2	0|0	C6orf223|C6orf223	44076792|44076792	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.025000|0.025000	0.11179|0.11179	-0.202000|-0.202000	0.09451|0.09451	0.035000|0.035000	0.15519|0.15519	-1.473000|-1.473000	0.01005|0.01005	AAG|CAA	A|0.833;G|0.167	0.167	strong		0.537	C6orf223-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040702.3	NM_153246	
IQCF1	132141	hgsc.bcm.edu	37	3	51929183	51929183	+	Missense_Mutation	SNP	C	C	T	rs11927897	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:51929183C>T	ENST00000310914.5	-	4	403	c.341G>A	c.(340-342)cGg>cAg	p.R114Q		NM_152397.2	NP_689610.2	Q8N6M8	IQCF1_HUMAN	IQ motif containing F1	114			R -> Q (in dbSNP:rs11927897).							central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(3)|ovary(1)|prostate(1)	12				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.000541)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)		CGCTGCCTGCCGCCTCTTCTT	0.632													C|||	114	0.0227636	0.0121	0.0231	5008	,	,		17682	0.0		0.0457	False		,,,				2504	0.0368				p.R114Q		Atlas-SNP	.											.	IQCF1	26	.	0			c.G341A						PASS	.	C	GLN/ARG	93,4313	73.1+/-111.1	2,89,2112	42.0	40.0	41.0		341	3.9	0.6	3	dbSNP_120	41	399,8201	121.5+/-180.6	11,377,3912	yes	missense	IQCF1	NM_152397.2	43	13,466,6024	TT,TC,CC		4.6395,2.1108,3.7829	probably-damaging	114/206	51929183	492,12514	2203	4300	6503	SO:0001583	missense	132141	exon4			GCCTGCCGCCTCT	BC029595	CCDS2836.1	3p21.31	2008-02-05			ENSG00000173389	ENSG00000173389			28607	protein-coding gene	gene with protein product						12477932	Standard	NM_152397		Approved	MGC39725	uc003dbv.3	Q8N6M8	OTTHUMG00000156908	ENST00000310914.5:c.341G>A	3.37:g.51929183C>T	ENSP00000307958:p.Arg114Gln	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	85	51	0.6	NM_152397	Q8N711	Missense_Mutation	SNP	ENST00000310914.5	37	CCDS2836.1	43	0.019688644688644688	5	0.01016260162601626	8	0.022099447513812154	0	0.0	30	0.0395778364116095	C	23.9	4.470041	0.84533	0.021108	0.046395	ENSG00000173389	ENST00000310914	T	0.28895	1.59	4.75	3.87	0.44632	.	0.128181	0.36167	N	0.002757	T	0.04770	0.0129	L	0.58101	1.795	0.20873	N	0.999834	D	0.57899	0.981	B	0.41088	0.347	T	0.05419	-1.0886	10	0.38643	T	0.18	-3.7108	9.2785	0.37714	0.0:0.9012:0.0:0.0988	rs11927897;rs52814630;rs59031146;rs11927897	114	Q8N6M8	IQCF1_HUMAN	Q	114	ENSP00000307958:R114Q	ENSP00000307958:R114Q	R	-	2	0	IQCF1	51904223	0.024000	0.19004	0.575000	0.28536	0.412000	0.31113	1.522000	0.35921	1.358000	0.45922	0.549000	0.68633	CGG	C|0.968;T|0.032	0.032	strong		0.632	IQCF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346568.1	NM_152397	
ARFRP1	10139	hgsc.bcm.edu	37	20	62331989	62331989	+	Silent	SNP	T	T	G	rs1048665	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:62331989T>G	ENST00000359715.5	-	6	1049	c.483A>C	c.(481-483)cgA>cgC	p.R161R	ARFRP1_ENST00000324228.2_Silent_p.R161R|ARFRP1_ENST00000485858.1_5'UTR|ARFRP1_ENST00000440854.1_Silent_p.R161R|ARFRP1_ENST00000607873.1_Silent_p.R114R|ARFRP1_ENST00000609142.1_Silent_p.R161R			Q13795	ARFRP_HUMAN	ADP-ribosylation factor related protein 1	161					gastrulation (GO:0007369)|Golgi to plasma membrane protein transport (GO:0043001)|GTP catabolic process (GO:0006184)|protein localization to Golgi apparatus (GO:0034067)|retrograde transport, endosome to Golgi (GO:0042147)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	Golgi apparatus (GO:0005794)|membrane (GO:0016020)|trans-Golgi network (GO:0005802)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|skin(1)	7	all_cancers(38;9.53e-13)|all_epithelial(29;2.64e-14)|Lung NSC(23;7e-10)|all_lung(23;2.53e-09)		Epithelial(9;4.09e-08)|all cancers(9;1.7e-07)|OV - Ovarian serous cystadenocarcinoma(5;0.0102)			TCAGGCAATCTCGCCTGCCGA	0.672													C|||	1326	0.264776	0.025	0.2637	5008	,	,		14320	0.6498		0.2048	False		,,,				2504	0.2546				p.R161R		Atlas-SNP	.											.	ARFRP1	17	.	0			c.A483C						PASS	.	C	,	308,4084		12,284,1900	53.0	44.0	47.0		483,483	-10.8	0.0	20	dbSNP_86	47	1968,6612		230,1508,2552	no	coding-synonymous,coding-synonymous	ARFRP1	NM_001134758.1,NM_003224.3	,	242,1792,4452	GG,GT,TT		22.9371,7.0128,17.5455	,	161/174,161/202	62331989	2276,10696	2196	4290	6486	SO:0001819	synonymous_variant	10139	exon7			GCAATCTCGCCTG	X91504	CCDS13533.1, CCDS46630.1, CCDS68172.1, CCDS68173.1	20q13.3	2014-05-09			ENSG00000101246	ENSG00000101246		"""ADP-ribosylation factors"""	662	protein-coding gene	gene with protein product		604699				8530503	Standard	NM_003224		Approved	ARP, Arp1, ARL18	uc031rup.1	Q13795	OTTHUMG00000032993	ENST00000359715.5:c.483A>C	20.37:g.62331989T>G		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	76	35	0.460526	NM_001134758	B7ZKX7|E1P5J9|Q6IBQ0	Silent	SNP	ENST00000359715.5	37	CCDS13533.1																																																																																			T|0.790;G|0.200;C|0.001;A|0.009	0.200	strong		0.672	ARFRP1-007	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000472024.1		
PTH1R	5745	hgsc.bcm.edu	37	3	46939575	46939575	+	Silent	SNP	C	C	A	rs143863124	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:46939575C>A	ENST00000313049.5	+	5	639	c.436C>A	c.(436-438)Cga>Aga	p.R146R	PTH1R_ENST00000490109.1_3'UTR|PTH1R_ENST00000430002.2_Silent_p.R146R|PTH1R_ENST00000449590.1_Silent_p.R146R|PTH1R_ENST00000418619.1_Silent_p.R146R			Q03431	PTH1R_HUMAN	parathyroid hormone 1 receptor	146					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)	CCATGCCTACCGACGCTGTGA	0.607													C|||	9	0.00179712	0.0	0.0	5008	,	,		18086	0.0		0.0089	False		,,,				2504	0.0				p.R146R		Atlas-SNP	.											.	PTH1R	49	.	0			c.C436A						PASS	.	C	,	4,4402	8.1+/-20.4	0,4,2199	109.0	109.0	109.0		436,436	3.2	1.0	3	dbSNP_134	109	43,8557	28.5+/-78.6	1,41,4258	no	coding-synonymous,coding-synonymous	PTH1R	NM_000316.2,NM_001184744.1	,	1,45,6457	AA,AC,CC		0.5,0.0908,0.3614	,	146/594,146/594	46939575	47,12959	2203	4300	6503	SO:0001819	synonymous_variant	5745	exon6			GCCTACCGACGCT		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.436C>A	3.37:g.46939575C>A		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	119	56	0.470588	NM_001184744	Q2M1U3	Silent	SNP	ENST00000313049.5	37	CCDS2747.1																																																																																			C|0.996;A|0.004	0.004	strong		0.607	PTH1R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257481.1	NM_000316	
ATF6	22926	hgsc.bcm.edu	37	1	161751741	161751741	+	Missense_Mutation	SNP	A	A	G	rs1058405	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:161751741A>G	ENST00000367942.3	+	3	266	c.199A>G	c.(199-201)Atg>Gtg	p.M67V		NM_007348.3	NP_031374.2	P18850	ATF6A_HUMAN	activating transcription factor 6	67	Transcription activation.		M -> L (in dbSNP:rs1058405). {ECO:0000269|PubMed:9271374}.|M -> V (in dbSNP:rs1058405). {ECO:0000269|PubMed:15489334}.		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)|positive regulation of transcription from RNA polymerase II promoter involved in unfolded protein response (GO:0006990)|protein folding (GO:0006457)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to stress (GO:0006950)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	endoplasmic reticulum membrane (GO:0005789)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			breast(2)|endometrium(3)|kidney(2)|large_intestine(8)|lung(14)|ovary(3)|skin(1)|stomach(1)	34	all_hematologic(112;0.156)		BRCA - Breast invasive adenocarcinoma(70;0.00953)		Pseudoephedrine(DB00852)	TTTGGATTTGATGCCTTGGGA	0.284													A|||	836	0.166933	0.0113	0.17	5008	,	,		18662	0.2629		0.2724	False		,,,				2504	0.1677				p.M67V		Atlas-SNP	.											.	ATF6	84	.	0			c.A199G	GRCh37	CM077506	ATF6	M	rs1058405	PASS	.	A	VAL/MET	250,4156	145.0+/-179.8	6,238,1959	94.0	91.0	92.0		199	3.8	1.0	1	dbSNP_86	92	2505,6095	409.7+/-349.9	336,1833,2131	yes	missense	ATF6	NM_007348.3	21	342,2071,4090	GG,GA,AA		29.1279,5.6741,21.1825	possibly-damaging	67/671	161751741	2755,10251	2203	4300	6503	SO:0001583	missense	22926	exon3			GATTTGATGCCTT	AB015856	CCDS1235.1	1q22-q23	2013-01-10			ENSG00000118217	ENSG00000118217		"""basic leucine zipper proteins"""	791	protein-coding gene	gene with protein product	"""activating transcription factor 6 alpha"""	605537				9837962, 9271374, 11256944	Standard	NM_007348		Approved	ATF6A	uc001gbs.3	P18850	OTTHUMG00000023961	ENST00000367942.3:c.199A>G	1.37:g.161751741A>G	ENSP00000356919:p.Met67Val	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	56	18	0.321429	NM_007348	O15139|Q5VW62|Q6IPB5|Q9UEC9	Missense_Mutation	SNP	ENST00000367942.3	37	CCDS1235.1	462	0.21153846153846154	11	0.022357723577235773	74	0.20441988950276244	169	0.29545454545454547	208	0.27440633245382584	A	9.163	1.019228	0.19355	0.056741	0.291279	ENSG00000118217	ENST00000367942	T	0.13901	2.55	5.04	3.83	0.44106	.	0.093620	0.85682	D	0.000000	T	0.05456	0.0144	L	0.53249	1.67	0.38764	P	0.04560299999999995	B	0.20887	0.049	B	0.22386	0.039	T	0.15752	-1.0426	9	0.27785	T	0.31	-7.2503	8.4476	0.32852	0.8028:0.1972:0.0:0.0	rs1058405;rs17407301;rs17845445;rs17858317;rs52823149;rs61419510;rs1058405	67	P18850	ATF6A_HUMAN	V	67	ENSP00000356919:M67V	ENSP00000356919:M67V	M	+	1	0	ATF6	160018365	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.129000	0.42055	2.023000	0.59567	0.454000	0.30748	ATG	A|0.793;G|0.207	0.207	strong		0.284	ATF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060304.2	NM_007348	
MTTP	4547	hgsc.bcm.edu	37	4	100503136	100503136	+	Missense_Mutation	SNP	C	C	G	rs141736123	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:100503136C>G	ENST00000265517.5	+	2	339	c.136C>G	c.(136-138)Cgg>Ggg	p.R46G	MTTP_ENST00000511045.1_Missense_Mutation_p.R73G|MTTP_ENST00000422897.2_Missense_Mutation_p.R46G|MTTP_ENST00000457717.1_Missense_Mutation_p.R46G			P55157	MTP_HUMAN	microsomal triglyceride transfer protein	46	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)	TCTTCTTGATCGGGGCAAAGG	0.468													C|||	63	0.0125799	0.0015	0.0115	5008	,	,		19440	0.0		0.0219	False		,,,				2504	0.0317				p.R46G		Atlas-SNP	.											.	MTTP	127	.	0			c.C136G						PASS	.	C	GLY/ARG	13,4393	20.2+/-43.8	0,13,2190	180.0	151.0	161.0		136	4.0	1.0	4	dbSNP_134	161	151,8449	73.2+/-135.9	1,149,4150	yes	missense	MTTP	NM_000253.2	125	1,162,6340	GG,GC,CC		1.7558,0.2951,1.261	benign	46/895	100503136	164,12842	2203	4300	6503	SO:0001583	missense	4547	exon3			CTTGATCGGGGCA		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.136C>G	4.37:g.100503136C>G	ENSP00000265517:p.Arg46Gly	Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	151	70	0.463576	NM_000253	A8K428|Q08AM4|Q6P5T3	Missense_Mutation	SNP	ENST00000265517.5	37	CCDS3651.1	19	0.0086996336996337	1	0.0020325203252032522	3	0.008287292817679558	0	0.0	15	0.01978891820580475	C	11.83	1.754473	0.31046	0.002951	0.017558	ENSG00000138823	ENST00000506883;ENST00000511045;ENST00000457717;ENST00000265517;ENST00000422897;ENST00000538053	T;T;T;T;T	0.40476	1.03;1.03;1.03;1.03;1.03	5.76	3.98	0.46160	Lipid transport protein, beta-sheet shell (1);Lipid transport protein, N-terminal (3);Vitellinogen, beta-sheet N-terminal (1);	0.458166	0.26052	N	0.026639	T	0.16642	0.0400	L	0.38838	1.175	0.33153	D	0.546014	B;B;B	0.09022	0.001;0.001;0.002	B;B;B	0.15484	0.005;0.001;0.013	T	0.25606	-1.0127	10	0.21014	T	0.42	-12.0949	9.6418	0.39844	0.1303:0.5146:0.3551:0.0	.	73;46;46	E9PBP6;P55157;Q6P5T3	.;MTP_HUMAN;.	G	56;73;46;46;46;46	ENSP00000426755:R56G;ENSP00000427679:R73G;ENSP00000400821:R46G;ENSP00000265517:R46G;ENSP00000407350:R46G	ENSP00000265517:R46G	R	+	1	2	MTTP	100722159	1.000000	0.71417	0.996000	0.52242	0.629000	0.37895	1.216000	0.32443	0.733000	0.32492	0.655000	0.94253	CGG	C|0.989;G|0.010;T|0.000	0.010	strong		0.468	MTTP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253662.3		
ALMS1	7840	hgsc.bcm.edu	37	2	73680508	73680508	+	Missense_Mutation	SNP	G	G	C	rs6546839	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:73680508G>C	ENST00000264448.6	+	8	6962	c.6851G>C	c.(6850-6852)cGt>cCt	p.R2284P	ALMS1_ENST00000377715.1_Missense_Mutation_p.R2284P|ALMS1_ENST00000409009.1_Missense_Mutation_p.R2242P	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	2284			R -> P (in dbSNP:rs6546839).		endosomal transport (GO:0016197)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of stress fiber assembly (GO:0051492)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)				breast(4)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(31)|lung(68)|ovary(4)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	147						CCCCTTGCCCGTTTCAGAGAT	0.398													C|||	1825	0.364417	0.8782	0.3919	5008	,	,		20366	0.0089		0.2276	False		,,,				2504	0.1575				p.R2284P		Atlas-SNP	.											.	ALMS1	384	.	0			c.G6851C						PASS	.	C	PRO/ARG	2723,947		1024,675,136	72.0	73.0	73.0		6851	5.5	1.0	2	dbSNP_116	73	1952,6200		222,1508,2346	yes	missense	ALMS1	NM_015120.4	103	1246,2183,2482	CC,CG,GG		23.945,25.8038,39.5449	benign	2284/4168	73680508	4675,7147	1835	4076	5911	SO:0001583	missense	7840	exon8			TTGCCCGTTTCAG	AB002326	CCDS42697.1	2p13.1	2014-09-17			ENSG00000116127	ENSG00000116127			428	protein-coding gene	gene with protein product		606844				9063741	Standard	NM_015120		Approved	KIAA0328	uc002sje.1	Q8TCU4	OTTHUMG00000152812	ENST00000264448.6:c.6851G>C	2.37:g.73680508G>C	ENSP00000264448:p.Arg2284Pro	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	66	66	1	NM_015120	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Missense_Mutation	SNP	ENST00000264448.6	37	CCDS42697.1	737	0.3374542124542125	425	0.8638211382113821	126	0.34806629834254144	8	0.013986013986013986	178	0.23482849604221637	C	3.609	-0.079949	0.07141	0.741962	0.23945	ENSG00000116127	ENST00000409009;ENST00000264448;ENST00000377715	T;T;T	0.11385	3.65;3.65;2.78	5.49	5.49	0.81192	.	0.132997	0.35291	N	0.003301	T	0.00012	0.0000	N	0.00413	-1.525	0.49299	P	2.2900000000003473E-4	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.32295	-0.9912	9	0.02654	T	1	.	12.855	0.57880	0.0:0.8363:0.1637:0.0	rs6546839;rs17434138;rs17848860;rs61596780;rs6546839	2284;2242;2284	Q8TCU4-3;B8ZZJ3;Q8TCU4	.;.;ALMS1_HUMAN	P	2242;2284;2284	ENSP00000386627:R2242P;ENSP00000264448:R2284P;ENSP00000366944:R2284P	ENSP00000264448:R2284P	R	+	2	0	ALMS1	73534016	0.983000	0.35010	1.000000	0.80357	0.958000	0.62258	2.660000	0.46749	1.481000	0.48307	-0.120000	0.15030	CGT	G|0.687;C|0.313	0.313	strong		0.398	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120	
TPX2	22974	hgsc.bcm.edu	37	20	30381700	30381700	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:30381700G>A	ENST00000300403.6	+	14	2087	c.1559G>A	c.(1558-1560)gGg>gAg	p.G520E	TPX2_ENST00000340513.4_Missense_Mutation_p.G556E	NM_012112.4	NP_036244.2	Q9ULW0	TPX2_HUMAN	TPX2, microtubule-associated	520					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)			CCACATTATGGGGTGCCTTTT	0.443																																					p.G520E		Atlas-SNP	.											.	TPX2	61	.	0			c.G1559A						PASS	.						171.0	176.0	174.0					20																	30381700		2203	4300	6503	SO:0001583	missense	22974	exon14			ATTATGGGGTGCC	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.1559G>A	20.37:g.30381700G>A	ENSP00000300403:p.Gly520Glu	Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	158	38	0.240506	NM_012112	Q9H1R4|Q9NRA3|Q9UFN9|Q9UL00|Q9Y2M1	Missense_Mutation	SNP	ENST00000300403.6	37	CCDS13190.1	.	.	.	.	.	.	.	.	.	.	G	27.4	4.831487	0.91036	.	.	ENSG00000088325	ENST00000300403;ENST00000340513	T	0.35236	1.32	6.03	6.03	0.97812	.	0.000000	0.85682	D	0.000000	T	0.63674	0.2531	M	0.81682	2.555	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.997	T	0.57015	-0.7883	10	0.25751	T	0.34	-20.3066	19.545	0.95291	0.0:0.0:1.0:0.0	.	556;520	Q96RR5;Q9ULW0	.;TPX2_HUMAN	E	520;556	ENSP00000341145:G556E	ENSP00000300403:G520E	G	+	2	0	TPX2	29845361	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	5.527000	0.67123	2.861000	0.98227	0.655000	0.94253	GGG	.	.	none		0.443	TPX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078569.2		
PCDHGA12	26025	hgsc.bcm.edu	37	5	140810773	140810773	+	Silent	SNP	G	G	A	rs17097300	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:140810773G>A	ENST00000252085.3	+	1	589	c.447G>A	c.(445-447)gaG>gaA	p.E149E	PCDHGA3_ENST00000253812.6_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGB8P_ENST00000502926.1_RNA|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA10_ENST00000398610.2_Intron|PCDHGA11_ENST00000518882.1_Intron|PCDHGB7_ENST00000398594.2_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA11_ENST00000398587.2_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA8_ENST00000398604.2_Intron	NM_003735.2|NM_032094.1	NP_003726.1|NP_115265.1	O60330	PCDGC_HUMAN	protocadherin gamma subfamily A, 12	149	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(2)|cervix(1)|endometrium(7)|kidney(1)|large_intestine(10)|lung(23)|ovary(5)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)	58			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CAGCCACTGAGATGCGGTTCC	0.473													g|||	338	0.067492	0.0038	0.2219	5008	,	,		19627	0.0952		0.0219	False		,,,				2504	0.0624				p.E149E		Atlas-SNP	.											.	PCDHGA12	271	.	0			c.G447A						PASS	.	G	,,,,,,,,,,,,,,,,,,,,	31,4375	33.5+/-64.1	0,31,2172	92.0	105.0	101.0		447,,,,,,,,,,,,,,,,,,,,447	-0.9	0.9	5	dbSNP_123	101	230,8370	91.6+/-153.7	3,224,4073	no	coding-synonymous,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,coding-synonymous	PCDHGB4,PCDHGA8,PCDHGA12,PCDHGB7,PCDHGB6,PCDHGB5,PCDHGB3,PCDHGB2,PCDHGB1,PCDHGA11,PCDHGA10,PCDHGA9,PCDHGA7,PCDHGA6,PCDHGA5,PCDHGA4,PCDHGA3,PCDHGA2,PCDHGA1	NM_003735.2,NM_003736.2,NM_018912.2,NM_018913.2,NM_018914.2,NM_018915.2,NM_018916.3,NM_018917.2,NM_018918.2,NM_018919.2,NM_018920.2,NM_018921.2,NM_018922.2,NM_018923.2,NM_018924.2,NM_018925.2,NM_018926.2,NM_018927.3,NM_032088.1,NM_032092.1,NM_032094.1	,,,,,,,,,,,,,,,,,,,,	3,255,6245	AA,AG,GG		2.6744,0.7036,2.0068	,,,,,,,,,,,,,,,,,,,,	149/933,,,,,,,,,,,,,,,,,,,,149/821	140810773	261,12745	2203	4300	6503	SO:0001819	synonymous_variant	26025	exon1			CACTGAGATGCGG	AF152506	CCDS4260.1, CCDS75346.1	5q31	2010-01-26	2002-05-23		ENSG00000253159	ENSG00000253159		"""Cadherins / Protocadherins : Clustered"""	8699	other	protocadherin	"""fibroblast cadherin FIB3"""	603059	"""cadherin 21"""	CDH21		10380929	Standard	NM_003735		Approved	KIAA0588, FIB3, PCDH-GAMMA-A12		O60330	OTTHUMG00000129611	ENST00000252085.3:c.447G>A	5.37:g.140810773G>A		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	50	25	0.5	NM_032094	O15100|Q6UW70|Q9Y5D7	Silent	SNP	ENST00000252085.3	37	CCDS4260.1																																																																																			G|0.959;A|0.041	0.041	strong		0.473	PCDHGA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251806.2	NM_003735	
CDRT15L2	256223	hgsc.bcm.edu	37	17	20483255	20483255	+	Missense_Mutation	SNP	G	G	A	rs150637113	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:20483255G>A	ENST00000399044.1	+	1	219	c.199G>A	c.(199-201)Ggg>Agg	p.G67R	RP11-434D2.12_ENST00000580931.1_lincRNA	NM_001190790.1	NP_001177719.1	A8MXV6	CD15L_HUMAN	CMT1A duplicated region transcript 15-like 2	67						integral component of membrane (GO:0016021)				central_nervous_system(1)	1						GATCCCATCGGGGCTGCCTCT	0.642													.|||	68	0.0135783	0.0008	0.0072	5008	,	,		17868	0.0288		0.0089	False		,,,				2504	0.0245				p.G67R		Atlas-SNP	.											.	CDRT15L2	5	.	0			c.G199A						PASS	.																																			SO:0001583	missense	256223	exon1			CCATCGGGGCTGC		CCDS54096.1	17p11.2	2008-10-30			ENSG00000214819	ENSG00000214819			34075	protein-coding gene	gene with protein product							Standard	NM_001190790		Approved		uc021tsn.1	A8MXV6	OTTHUMG00000059557	ENST00000399044.1:c.199G>A	17.37:g.20483255G>A	ENSP00000382000:p.Gly67Arg	Somatic	334	0	0		WXS	Illumina HiSeq	Phase_I	292	140	0.479452	NM_001190790		Missense_Mutation	SNP	ENST00000399044.1	37	CCDS54096.1	33	0.01510989010989011	0	0.0	3	0.008287292817679558	24	0.04195804195804196	6	0.0079155672823219	.	10.99	1.506723	0.26949	.	.	ENSG00000214819	ENST00000399044	T	0.60797	0.16	0.783	0.783	0.18572	.	.	.	.	.	T	0.14141	0.0342	N	0.24115	0.695	0.09310	N	1	.	.	.	.	.	.	T	0.24119	-1.0169	7	0.72032	D	0.01	.	4.8613	0.13585	0.0:0.0:1.0:0.0	.	.	.	.	R	67	ENSP00000382000:G67R	ENSP00000382000:G67R	G	+	1	0	CDRT15L2	20423847	0.003000	0.15002	0.001000	0.08648	0.034000	0.12701	1.294000	0.33365	0.710000	0.31997	0.205000	0.17691	GGG	G|0.986;A|0.014	0.014	strong		0.642	CDRT15L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132432.3	XM_170840	
KANK2	25959	hgsc.bcm.edu	37	19	11304498	11304498	+	Silent	SNP	C	C	T	rs755238	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:11304498C>T	ENST00000586659.1	-	4	572	c.258G>A	c.(256-258)tcG>tcA	p.S86S	KANK2_ENST00000432929.2_Silent_p.S86S|KANK2_ENST00000589359.1_Silent_p.S86S|KANK2_ENST00000589894.1_Silent_p.S86S|KANK2_ENST00000355150.5_Silent_p.S86S			Q63ZY3	KANK2_HUMAN	KN motif and ankyrin repeat domains 2	86					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						TGGAGCACAGCGACTCAGTGG	0.682													C|||	252	0.0503195	0.0461	0.1052	5008	,	,		13819	0.0129		0.0706	False		,,,				2504	0.0348				p.S86S		Atlas-SNP	.											KANK2,NS,carcinoma,0,1	KANK2	47	1	0			c.G258A						PASS	.	C	,	246,4160		5,236,1962	36.0	38.0	37.0		258,258	-8.8	0.6	19	dbSNP_86	37	717,7879		30,657,3611	no	coding-synonymous,coding-synonymous	KANK2	NM_001136191.2,NM_015493.6	,	35,893,5573	TT,TC,CC		8.3411,5.5833,7.4066	,	86/852,86/860	11304498	963,12039	2203	4298	6501	SO:0001819	synonymous_variant	25959	exon2			GCACAGCGACTCA	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.258G>A	19.37:g.11304498C>T		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	46	18	0.391304	NM_015493	B0I1P4|Q3KQZ3|Q6GUF5|Q9H8S4|Q9NUP0|Q9P210	Silent	SNP	ENST00000586659.1	37	CCDS12255.1																																																																																			C|0.934;T|0.066	0.066	strong		0.682	KANK2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000453066.2	NM_015493	
ZNF701	55762	hgsc.bcm.edu	37	19	53086598	53086598	+	Missense_Mutation	SNP	G	G	A	rs3745102	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:53086598G>A	ENST00000540331.1	+	5	1709	c.1484G>A	c.(1483-1485)cGt>cAt	p.R495H	ZNF701_ENST00000391785.3_Missense_Mutation_p.R429H|CTD-3099C6.7_ENST00000599222.1_RNA|ZNF701_ENST00000301093.2_Missense_Mutation_p.R495H	NM_001172655.1	NP_001166126.1	Q9NV72	ZN701_HUMAN	zinc finger protein 701	495			R -> H (in dbSNP:rs67702454). {ECO:0000269|PubMed:14702039}.		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(5)|kidney(1)|large_intestine(2)|lung(6)	14				OV - Ovarian serous cystadenocarcinoma(262;0.0105)|GBM - Glioblastoma multiforme(134;0.0402)		GCATGTCATCGTAGACTTCAT	0.363													g|||	1417	0.282947	0.0522	0.2839	5008	,	,		22708	0.3373		0.3598	False		,,,				2504	0.4591				p.R495H	NSCLC(89;451 1475 9611 20673 52284)	Atlas-SNP	.											.	ZNF701	44	.	0			c.G1484A						PASS	.						50.0	41.0	44.0					19																	53086598		2203	4291	6494	SO:0001583	missense	55762	exon5			GTCATCGTAGACT	AK001753	CCDS33092.1, CCDS54311.1	19q13.41	2013-01-08				ENSG00000167562		"""Zinc fingers, C2H2-type"", ""-"""	25597	protein-coding gene	gene with protein product							Standard	NM_018260		Approved	FLJ10891	uc021uyw.1	Q9NV72		ENST00000540331.1:c.1484G>A	19.37:g.53086598G>A	ENSP00000444339:p.Arg495His	Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	111	110	0.990991	NM_001172655	A2RRM8|B9EGF2|F5GZM6|Q66K42	Missense_Mutation	SNP	ENST00000540331.1	37	CCDS54311.1	581	0.266025641025641	27	0.054878048780487805	106	0.292817679558011	182	0.3181818181818182	266	0.35092348284960423	N	4.277	0.050616	0.08243	.	.	ENSG00000167562	ENST00000391785;ENST00000301093;ENST00000540331	T;T;T	0.18502	2.21;2.21;2.21	1.98	-2.21	0.06973	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	L	0.42487	1.325	0.80722	P	0.0	B;B	0.09022	0.002;0.001	B;B	0.08055	0.003;0.001	T	0.47275	-0.9130	8	0.24483	T	0.36	.	7.8679	0.29547	0.4668:0.0:0.5332:0.0	rs3745102	495;429	F5GZM6;Q9NV72	.;ZN701_HUMAN	H	429;495;495	ENSP00000375662:R429H;ENSP00000301093:R495H;ENSP00000444339:R495H	ENSP00000301093:R495H	R	+	2	0	ZNF701	57778410	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.539000	0.02202	-0.969000	0.03573	-0.598000	0.04106	CGT	G|0.686;A|0.314	0.314	strong		0.363	ZNF701-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000463467.1	NM_018260	
KCNS3	3790	hgsc.bcm.edu	37	2	18113508	18113508	+	Silent	SNP	G	G	A	rs3747516	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:18113508G>A	ENST00000403915.1	+	3	1684	c.1233G>A	c.(1231-1233)aaG>aaA	p.K411K	KCNS3_ENST00000304101.4_Silent_p.K411K|KCNS3_ENST00000465292.1_Intron	NM_001282428.1	NP_001269357.1	Q9BQ31	KCNS3_HUMAN	potassium voltage-gated channel, delayed-rectifier, subfamily S, member 3	411					energy reserve metabolic process (GO:0006112)|potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|potassium channel regulator activity (GO:0015459)			endometrium(5)|kidney(1)|large_intestine(7)|lung(11)|ovary(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)					AGTTTTCCAAGTACTACCAGA	0.478													G|||	1788	0.357029	0.3343	0.3833	5008	,	,		24317	0.4702		0.164	False		,,,				2504	0.4509				p.K411K		Atlas-SNP	.											.	KCNS3	85	.	0			c.G1233A						PASS	.	G		1266,3140	433.3+/-343.5	188,890,1125	191.0	169.0	176.0		1233	4.1	1.0	2	dbSNP_107	176	1359,7241	266.1+/-286.5	91,1177,3032	no	coding-synonymous	KCNS3	NM_002252.3		279,2067,4157	AA,AG,GG		15.8023,28.7335,20.183		411/492	18113508	2625,10381	2203	4300	6503	SO:0001819	synonymous_variant	3790	exon3			TTCCAAGTACTAC	AF043472	CCDS1692.1	2p24	2011-07-05			ENSG00000170745	ENSG00000170745		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6302	protein-coding gene	gene with protein product		603888				10484328, 16382104	Standard	NM_002252		Approved	Kv9.3	uc002rcw.3	Q9BQ31	OTTHUMG00000044150	ENST00000403915.1:c.1233G>A	2.37:g.18113508G>A		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	145	61	0.42069	NM_002252	D6W520|O43651|Q4ZFY1|Q96B56	Silent	SNP	ENST00000403915.1	37	CCDS1692.1																																																																																			G|0.744;A|0.256	0.256	strong		0.478	KCNS3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323808.1	NM_002252	
ABCA13	154664	hgsc.bcm.edu	37	7	48311658	48311658	+	Missense_Mutation	SNP	G	G	A	rs17547816	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:48311658G>A	ENST00000435803.1	+	17	2419	c.2395G>A	c.(2395-2397)Gaa>Aaa	p.E799K		NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	799			E -> K (in dbSNP:rs17547816).		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						ATTTGGCAACGAAGTGATTTG	0.348													G|||	139	0.0277556	0.0008	0.0303	5008	,	,		14622	0.0298		0.0646	False		,,,				2504	0.0225				p.E799K		Atlas-SNP	.											.	ABCA13	1192	.	0			c.G2395A						PASS	.	G	LYS/GLU	29,3647		0,29,1809	41.0	41.0	41.0		2395	1.4	0.0	7	dbSNP_123	41	363,7835		5,353,3741	yes	missense	ABCA13	NM_152701.3	56	5,382,5550	AA,AG,GG		4.4279,0.7889,3.3013	benign	799/5059	48311658	392,11482	1838	4099	5937	SO:0001583	missense	154664	exon17			GGCAACGAAGTGA	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.2395G>A	7.37:g.48311658G>A	ENSP00000411096:p.Glu799Lys	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	31	22	0.709677	NM_152701	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Missense_Mutation	SNP	ENST00000435803.1	37	CCDS47584.1	71	0.03250915750915751	1	0.0020325203252032522	14	0.03867403314917127	10	0.017482517482517484	46	0.06068601583113457	G	9.173	1.021597	0.19433	0.007889	0.044279	ENSG00000179869	ENST00000435803	D	0.85556	-2.0	5.81	1.36	0.22044	.	0.962437	0.08523	N	0.933115	T	0.33469	0.0864	L	0.46157	1.445	0.80722	P	0.0	B	0.25486	0.127	B	0.12837	0.008	T	0.57412	-0.7816	9	0.52906	T	0.07	.	5.5862	0.17275	0.2184:0.2306:0.551:0.0	rs17547816;rs52811397;rs17547816	799	Q86UQ4	ABCAD_HUMAN	K	799	ENSP00000411096:E799K	ENSP00000411096:E799K	E	+	1	0	ABCA13	48282204	0.093000	0.21703	0.000000	0.03702	0.014000	0.08584	1.097000	0.30988	-0.037000	0.13646	0.585000	0.79938	GAA	G|0.965;A|0.035	0.035	strong		0.348	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701	
SUSD1	64420	hgsc.bcm.edu	37	9	114804173	114804173	+	Silent	SNP	G	G	A	rs3849117	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:114804173G>A	ENST00000374270.3	-	16	2389	c.2217C>T	c.(2215-2217)ctC>ctT	p.L739L	SUSD1_ENST00000374263.3_3'UTR|SUSD1_ENST00000374264.2_3'UTR	NM_022486.3	NP_071931.2	Q6UWL2	SUSD1_HUMAN	sushi domain containing 1	739						integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)		SUSD1/ROD1(2)	central_nervous_system(1)|endometrium(4)|large_intestine(8)|lung(11)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	28						AGAGGAATGTGAGAATGATCA	0.522													G|||	343	0.0684904	0.0053	0.0346	5008	,	,		22479	0.0625		0.0815	False		,,,				2504	0.1708				p.L739L		Atlas-SNP	.											.	SUSD1	51	.	0			c.C2217T						PASS	.	G		68,4338	61.7+/-98.7	1,66,2136	174.0	153.0	160.0		2217	-5.2	0.0	9	dbSNP_108	160	708,7892	174.5+/-224.7	28,652,3620	no	coding-synonymous	SUSD1	NM_022486.3		29,718,5756	AA,AG,GG		8.2326,1.5433,5.9665		739/748	114804173	776,12230	2203	4300	6503	SO:0001819	synonymous_variant	64420	exon16			GAATGTGAGAATG	AL137432	CCDS6783.1, CCDS65105.1, CCDS65106.1	9q31.3-q33.1	2008-02-05			ENSG00000106868	ENSG00000106868			25413	protein-coding gene	gene with protein product						12975309	Standard	NM_022486		Approved	DKFZP761E1824	uc004bfu.3	Q6UWL2	OTTHUMG00000020499	ENST00000374270.3:c.2217C>T	9.37:g.114804173G>A		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	96	49	0.510417	NM_022486	A1A4C5|A8KA03|Q5T8V6|Q5T8V7|Q6P9G7|Q8WU83|Q96DM9|Q9H6V2|Q9NTA7	Silent	SNP	ENST00000374270.3	37	CCDS6783.1																																																																																			G|0.943;A|0.057	0.057	strong		0.522	SUSD1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053668.3	NM_022486	
RNF39	80352	hgsc.bcm.edu	37	6	30039240	30039240	+	Missense_Mutation	SNP	G	G	T	rs2301753	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	10	0	0		WXS	Illumina HiSeq	Phase_I	17	8	0.470588	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	
ADAMTS7	11173	hgsc.bcm.edu	37	15	79064143	79064143	+	Silent	SNP	C	C	G	rs11635870	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:79064143C>G	ENST00000388820.4	-	15	2370	c.2160G>C	c.(2158-2160)gcG>gcC	p.A720A	ADAMTS7_ENST00000566303.1_Intron	NM_014272.3	NP_055087.2	Q9UKP4	ATS7_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 7	720	Spacer.				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						CGCGTGCGCCCGCTGGGATCA	0.617													G|||	932	0.186102	0.0454	0.2579	5008	,	,		18925	0.0188		0.4185	False		,,,				2504	0.2587				p.A720A		Atlas-SNP	.											.	ADAMTS7	142	.	0			c.G2160C						PASS	.	G		469,3923	777.1+/-414.2	37,395,1764	49.0	36.0	41.0		2160	-8.1	0.0	15	dbSNP_120	41	3668,4918	608.6+/-395.4	815,2038,1440	no	coding-synonymous	ADAMTS7	NM_014272.3		852,2433,3204	GG,GC,CC		42.7207,10.6785,31.877		720/1687	79064143	4137,8841	2196	4293	6489	SO:0001819	synonymous_variant	11173	exon15			TGCGCCCGCTGGG	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.2160G>C	15.37:g.79064143C>G		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	86	49	0.569767	NM_014272	Q14F51|Q6P7J9	Silent	SNP	ENST00000388820.4	37	CCDS32303.1																																																																																			C|0.715;G|0.285	0.285	strong		0.617	ADAMTS7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421331.1	NM_014272	
ZNF417	147687	hgsc.bcm.edu	37	19	58420162	58420162	+	Missense_Mutation	SNP	T	T	C	rs10416584	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:58420162T>C	ENST00000312026.5	-	3	1648	c.1484A>G	c.(1483-1485)aAt>aGt	p.N495S	ZNF417_ENST00000536263.1_Missense_Mutation_p.N296S|ZNF417_ENST00000595559.1_Missense_Mutation_p.N494S|CTD-2583A14.9_ENST00000602124.1_Intron	NM_152475.2	NP_689688.2	Q8TAU3	ZN417_HUMAN	zinc finger protein 417	495			N -> S (in dbSNP:rs10416584). {ECO:0000269|PubMed:15489334}.		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|stomach(3)|upper_aerodigestive_tract(1)	18		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0151)		CCCACATTCATTGCATTCATA	0.408													C|||	1576	0.314696	0.2943	0.2882	5008	,	,		21501	0.2996		0.3698	False		,,,				2504	0.32				p.N495S		Atlas-SNP	.											.	ZNF417	44	.	0			c.A1484G						PASS	.	C	SER/ASN	951,3455		164,623,1416	111.0	91.0	98.0		1484	-4.8	0.0	19	dbSNP_119	98	2498,6098		564,1370,2364	no	missense	ZNF417	NM_152475.2	46	728,1993,3780	CC,CT,TT		29.06,21.5842,26.5267	benign	495/576	58420162	3449,9553	2203	4298	6501	SO:0001583	missense	147687	exon3			CATTCATTGCATT	BC025783	CCDS12965.1, CCDS74469.1	19q13.43	2013-01-08				ENSG00000173480		"""Zinc fingers, C2H2-type"", ""-"""	20646	protein-coding gene	gene with protein product							Standard	NM_152475		Approved	MGC34079	uc002qqq.3	Q8TAU3		ENST00000312026.5:c.1484A>G	19.37:g.58420162T>C	ENSP00000311319:p.Asn495Ser	Somatic	239	0	0		WXS	Illumina HiSeq	Phase_I	215	97	0.451163	NM_152475	B4DEU1	Missense_Mutation	SNP	ENST00000312026.5	37	CCDS12965.1	607	0.27793040293040294	110	0.22357723577235772	110	0.30386740331491713	141	0.2465034965034965	246	0.3245382585751979	.	0.125	-1.120845	0.01785	0.215842	0.2906	ENSG00000173480	ENST00000312026;ENST00000536263	T;T	0.07216	3.21;3.21	2.38	-4.76	0.03229	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	N	0.12611	0.24	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.42413	-0.9453	8	0.02654	T	1	.	1.0708	0.01621	0.205:0.1385:0.2171:0.4394	rs10416584;rs17856733	495	Q8TAU3	ZN417_HUMAN	S	495;296	ENSP00000311319:N495S;ENSP00000442760:N296S	ENSP00000311319:N495S	N	-	2	0	ZNF417	63111974	0.000000	0.05858	0.000000	0.03702	0.166000	0.22503	-8.711000	0.00017	-3.048000	0.00261	-0.665000	0.03846	AAT	T|0.053;C|0.947	0.947	strong		0.408	ZNF417-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466860.1	NM_152475	
MPHOSPH9	10198	hgsc.bcm.edu	37	12	123705962	123705962	+	Missense_Mutation	SNP	C	C	T	rs36121382	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:123705962C>T	ENST00000606320.1	-	5	1035	c.829G>A	c.(829-831)Ggt>Agt	p.G277S	MPHOSPH9_ENST00000539639.1_5'Flank|MPHOSPH9_ENST00000392425.3_Missense_Mutation_p.G125S|MPHOSPH9_ENST00000302349.5_Missense_Mutation_p.G125S|MPHOSPH9_ENST00000541076.2_Missense_Mutation_p.G247S			Q99550	MPP9_HUMAN	M-phase phosphoprotein 9	277			G -> S (in dbSNP:rs36121382). {ECO:0000269|PubMed:14702039}.			centriole (GO:0005814)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|plasma membrane (GO:0005886)				NS(1)|breast(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(18)|prostate(2)|skin(1)	33	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000182)|Epithelial(86;0.00046)|BRCA - Breast invasive adenocarcinoma(302;0.169)		TTATTTTCACCAAGAAAATTA	0.313													C|||	463	0.0924521	0.0424	0.0663	5008	,	,		18744	0.2679		0.0487	False		,,,				2504	0.0429				p.G125S		Atlas-SNP	.											.	MPHOSPH9	75	.	0			c.G373A						PASS	.	C	SER/GLY	191,4211	115.4+/-153.4	0,191,2010	44.0	47.0	46.0		373	1.0	1.0	12	dbSNP_126	46	317,8281	106.0+/-166.9	11,295,3993	yes	missense	MPHOSPH9	NM_022782.2	56	11,486,6003	TT,TC,CC		3.6869,4.3389,3.9077	benign	125/1032	123705962	508,12492	2201	4299	6500	SO:0001583	missense	10198	exon1			TTTCACCAAGAAA	X98258	CCDS9243.1, CCDS9243.2	12q24	2008-03-03			ENSG00000051825	ENSG00000051825			7215	protein-coding gene	gene with protein product		605501				8885239	Standard	NM_022782		Approved	MPP9	uc001uel.3	Q99550	OTTHUMG00000168849	ENST00000606320.1:c.829G>A	12.37:g.123705962C>T	ENSP00000475489:p.Gly277Ser	Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	150	72	0.48	NM_022782	A1L486|A6NEE2|B3KR87|Q9H976|U3KQ28	Missense_Mutation	SNP	ENST00000606320.1	37		225|225	0.10302197802197802|0.10302197802197802	18|18	0.036585365853658534|0.036585365853658534	19|19	0.052486187845303865|0.052486187845303865	163|163	0.28496503496503495|0.28496503496503495	25|25	0.032981530343007916|0.032981530343007916	C|C	10.18|10.18	1.280125|1.280125	0.23392|0.23392	0.043389|0.043389	0.036869|0.036869	ENSG00000051825|ENSG00000257076	ENST00000302349;ENST00000541076|ENST00000539336	T;T|.	0.29142|.	1.58;1.59|.	5.43|5.43	1.04|1.04	0.20106|0.20106	.|.	0.791890|.	0.11830|.	N|.	0.525354|.	T|.	0.00012|.	0.0000|.	L|L	0.54323|0.54323	1.7|1.7	0.44454|0.44454	P|P	0.002615000000000034|0.002615000000000034	B|.	0.14012|.	0.009|.	B|.	0.12156|.	0.007|.	T|.	0.18116|.	-1.0347|.	9|.	0.30854|.	T|.	0.27|.	-2.8431|-2.8431	5.8606|5.8606	0.18745|0.18745	0.1272:0.4856:0.0:0.3872|0.1272:0.4856:0.0:0.3872	rs36121382|rs36121382	125|.	Q99550|.	MPP9_HUMAN|.	S|X	125|134	ENSP00000303597:G125S;ENSP00000445859:G125S|.	ENSP00000303597:G125S|.	G|W	-|-	1|2	0|0	MPHOSPH9|RP11-546D6.2	122271915|122271915	0.034000|0.034000	0.19679|0.19679	0.975000|0.975000	0.42487|0.42487	0.986000|0.986000	0.74619|0.74619	0.194000|0.194000	0.17135|0.17135	0.279000|0.279000	0.22186|0.22186	0.455000|0.455000	0.32223|0.32223	GGT|TGG	C|0.942;T|0.058	0.058	strong		0.313	MPHOSPH9-030	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000471390.2		
HNRNPH3	3189	hgsc.bcm.edu	37	10	70101417	70101417	+	Missense_Mutation	SNP	G	G	C	rs16925347	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:70101417G>C	ENST00000265866.7	+	8	1016	c.851G>C	c.(850-852)gGc>gCc	p.G284A	HNRNPH3_ENST00000441000.2_Missense_Mutation_p.G176A|HNRNPH3_ENST00000469172.1_3'UTR|HNRNPH3_ENST00000354695.5_Missense_Mutation_p.G269A	NM_012207.2|NM_021644.3	NP_036339.1|NP_067676.2	P31942	HNRH3_HUMAN	heterogeneous nuclear ribonucleoprotein H3 (2H9)	284	Gly-rich.		G -> A (in dbSNP:rs16925347).		epithelial cell differentiation (GO:0030855)|mRNA splicing, via spliceosome (GO:0000398)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)	nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(5)|ovary(2)|prostate(2)	11						GGAATGGGAGGCTACGGAAGA	0.368													G|||	183	0.0365415	0.003	0.098	5008	,	,		17232	0.001		0.0845	False		,,,				2504	0.0256				p.G284A		Atlas-SNP	.											.	HNRNPH3	33	.	0			c.G851C						PASS	.	G	ALA/GLY,ALA/GLY	89,4317	74.1+/-112.3	2,85,2116	95.0	101.0	99.0		851,806	4.8	1.0	10	dbSNP_123	99	787,7813	185.3+/-233.1	39,709,3552	yes	missense,missense	HNRNPH3	NM_012207.2,NM_021644.3	60,60	41,794,5668	CC,CG,GG		9.1512,2.02,6.7354	probably-damaging,probably-damaging	284/347,269/332	70101417	876,12130	2203	4300	6503	SO:0001583	missense	3189	exon8			TGGGAGGCTACGG		CCDS7278.1, CCDS7279.1	10q22	2013-02-12		2008-04-18	ENSG00000096746	ENSG00000096746		"""RNA binding motif (RRM) containing"""	5043	protein-coding gene	gene with protein product		602324		HNRPH3		8999868	Standard	NM_021644		Approved	2H9	uc001jnw.4	P31942	OTTHUMG00000018349	ENST00000265866.7:c.851G>C	10.37:g.70101417G>C	ENSP00000265866:p.Gly284Ala	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	83	41	0.493976	NM_012207	A8K682|B3KRE1|Q9BSX1|Q9NP53|Q9NP96|Q9NPA7|Q9NPI4|Q9UFU4|Q9Y4J5	Missense_Mutation	SNP	ENST00000265866.7	37	CCDS7278.1	113	0.051739926739926737	1	0.0020325203252032522	41	0.1132596685082873	1	0.0017482517482517483	70	0.09234828496042216	G	11.23	1.577265	0.28092	0.0202	0.091512	ENSG00000096746	ENST00000265866;ENST00000441000;ENST00000354695	T;T;T	0.16196	2.7;2.36;2.55	5.68	4.77	0.60923	Nucleotide-binding, alpha-beta plait (1);	0.071468	0.64402	D	0.000018	T	0.00356	0.0011	L	0.52011	1.625	0.09310	P	0.9999999999804431	B;B;B	0.10296	0.001;0.003;0.002	B;B;B	0.08055	0.001;0.003;0.002	T	0.11842	-1.0571	9	0.20046	T	0.44	.	16.8329	0.85949	0.0:0.1285:0.8715:0.0	rs16925347;rs52833498;rs16925347	176;269;284	B4DHY1;P31942-2;P31942	.;.;HNRH3_HUMAN	A	284;176;269	ENSP00000265866:G284A;ENSP00000409869:G176A;ENSP00000346726:G269A	ENSP00000265866:G284A	G	+	2	0	HNRNPH3	69771423	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	3.872000	0.56085	1.390000	0.46547	0.563000	0.77884	GGC	G|0.943;C|0.057	0.057	strong		0.368	HNRNPH3-012	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090165.1		
PRKAR1B	5575	hgsc.bcm.edu	37	7	590199	590199	+	Silent	SNP	A	A	G	rs11545042	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:590199A>G	ENST00000406797.1	-	11	1188	c.1014T>C	c.(1012-1014)acT>acC	p.T338T	AC147651.2_ENST00000517177.1_RNA|PRKAR1B_ENST00000403562.1_Silent_p.T338T|PRKAR1B_ENST00000537384.1_Silent_p.T338T|PRKAR1B_ENST00000360274.4_Silent_p.T338T|PRKAR1B_ENST00000544935.1_Silent_p.T338T	NM_001164761.1	NP_001158233.1	P31321	KAP1_HUMAN	protein kinase, cAMP-dependent, regulatory, type I, beta	338					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|blood coagulation (GO:0007596)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|learning or memory (GO:0007611)|negative regulation of cAMP-dependent protein kinase activity (GO:2000480)|neurotrophin TRK receptor signaling pathway (GO:0048011)|protein phosphorylation (GO:0006468)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cAMP-dependent protein kinase complex (GO:0005952)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	cAMP binding (GO:0030552)|cAMP-dependent protein kinase inhibitor activity (GO:0004862)|cAMP-dependent protein kinase regulator activity (GO:0008603)|protein kinase A catalytic subunit binding (GO:0034236)			endometrium(4)|large_intestine(1)|liver(1)|lung(10)|prostate(1)	17		Ovarian(82;0.0779)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0181)|Epithelial(4;5.75e-19)|OV - Ovarian serous cystadenocarcinoma(56;2.01e-18)|all cancers(6;3.96e-16)|BRCA - Breast invasive adenocarcinoma(126;0.152)		GGGCCACGACAGTGGCCGCCC	0.672													.|||	795	0.158746	0.2322	0.1124	5008	,	,		11673	0.2391		0.1123	False		,,,				2504	0.0573				p.T338T		Atlas-SNP	.											.	PRKAR1B	32	.	0			c.T1014C						PASS	.	G	,,,,,	885,3459		93,699,1380	21.0	20.0	20.0		1014,1014,1014,1014,1014,1014	-2.0	1.0	7	dbSNP_120	20	967,7557		46,875,3341	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PRKAR1B	NM_001164758.1,NM_001164759.1,NM_001164760.1,NM_001164761.1,NM_001164762.1,NM_002735.2	,,,,,	139,1574,4721	GG,GA,AA		11.3444,20.3729,14.3923	,,,,,	338/382,338/382,338/382,338/382,338/382,338/382	590199	1852,11016	2172	4262	6434	SO:0001819	synonymous_variant	5575	exon11			CACGACAGTGGCC	M65066	CCDS34579.1	7p22.3	2013-09-19			ENSG00000188191	ENSG00000188191	2.7.11.1		9390	protein-coding gene	gene with protein product		176911				1358799, 3479018	Standard	NM_002735		Approved		uc003siw.2	P31321	OTTHUMG00000151411	ENST00000406797.1:c.1014T>C	7.37:g.590199A>G		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	35	10	0.285714	NM_001164760	Q8N422	Silent	SNP	ENST00000406797.1	37	CCDS34579.1	379	0.17353479853479853	126	0.25609756097560976	44	0.12154696132596685	130	0.22727272727272727	79	0.10422163588390501	a	3.749	-0.051904	0.07362	0.203729	0.113444	ENSG00000188191	ENST00000400758	.	.	.	4.65	-1.96	0.07525	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999987	.	.	.	.	.	.	T	0.26780	-1.0093	3	.	.	.	-1.4289	8.2013	0.31426	0.5175:0.2625:0.2199:0.0	rs11545042;rs28722665	.	.	.	P	199	.	.	L	-	2	0	PRKAR1B	556725	0.000000	0.05858	0.964000	0.40570	0.529000	0.34654	-2.186000	0.01251	-0.857000	0.04115	-2.296000	0.00263	CTG	A|0.826;G|0.174	0.174	strong		0.672	PRKAR1B-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322525.1		
LAMA2	3908	hgsc.bcm.edu	37	6	129571272	129571272	+	Missense_Mutation	SNP	G	G	A	rs36044314	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:129571272G>A	ENST00000421865.2	+	13	1847	c.1798G>A	c.(1798-1800)Gga>Aga	p.G600R		NM_000426.3|NM_001079823.1	NP_000417|NP_001073291.1	P24043	LAMA2_HUMAN	laminin, alpha 2	600	Laminin IV type A 1. {ECO:0000255|PROSITE-ProRule:PRU00458}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|myelination in peripheral nervous system (GO:0022011)|positive regulation of synaptic transmission, cholinergic (GO:0032224)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basement membrane (GO:0005604)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|sarcolemma (GO:0042383)	structural molecule activity (GO:0005198)			NS(2)|biliary_tract(2)|breast(10)|central_nervous_system(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(35)|lung(84)|ovary(10)|prostate(4)|skin(9)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(2)	194				OV - Ovarian serous cystadenocarcinoma(136;0.178)|all cancers(137;0.245)		AGCAGTAGGAGGACAGTTGAC	0.373													G|||	48	0.00958466	0.0008	0.0115	5008	,	,		19659	0.0		0.0139	False		,,,				2504	0.0256				p.G600R		Atlas-SNP	.											.	LAMA2	481	.	0			c.G1798A	GRCh37	CD085944	LAMA2	D	rs36044314	PASS	.	G	ARG/GLY,ARG/GLY	13,4393	20.2+/-43.8	0,13,2190	165.0	149.0	155.0		1798,1798	5.7	1.0	6	dbSNP_126	155	177,8423	79.8+/-142.4	0,177,4123	yes	missense,missense	LAMA2	NM_000426.3,NM_001079823.1	125,125	0,190,6313	AA,AG,GG		2.0581,0.2951,1.4609	probably-damaging,probably-damaging	600/3123,600/3119	129571272	190,12816	2203	4300	6503	SO:0001583	missense	3908	exon13			GTAGGAGGACAGT	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.1798G>A	6.37:g.129571272G>A	ENSP00000400365:p.Gly600Arg	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	53	12	0.226415	NM_000426	Q14736|Q5VUM2|Q93022	Missense_Mutation	SNP	ENST00000421865.2	37	CCDS5138.1	16	0.007326007326007326	1	0.0020325203252032522	3	0.008287292817679558	0	0.0	12	0.0158311345646438	G	20.8	4.057221	0.76074	0.002951	0.020581	ENSG00000196569	ENST00000358023;ENST00000354729;ENST00000421865	T	0.39056	1.1	5.69	5.69	0.88448	Laminin B type IV (2);Laminin B, subgroup (1);	0.000000	0.85682	D	0.000000	T	0.61714	0.2369	M	0.77313	2.365	0.58432	D	0.999999	D;D	0.76494	0.999;0.999	D;D	0.75020	0.985;0.985	T	0.62562	-0.6828	10	0.59425	D	0.04	.	18.9514	0.92642	0.0:0.0:1.0:0.0	rs36044314	600;600	A6NF00;P24043	.;LAMA2_HUMAN	R	600	ENSP00000400365:G600R	ENSP00000346769:G600R	G	+	1	0	LAMA2	129612965	1.000000	0.71417	1.000000	0.80357	0.914000	0.54420	6.032000	0.70918	2.840000	0.97914	0.655000	0.94253	GGA	G|0.987;A|0.013	0.013	strong		0.373	LAMA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042180.1		
PPFIA4	8497	hgsc.bcm.edu	37	1	203044777	203044777	+	Missense_Mutation	SNP	G	G	A	rs12130501	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:203044777G>A	ENST00000447715.2	+	34	3841	c.3400G>A	c.(3400-3402)Ggc>Agc	p.G1134S	PPFIA4_ENST00000414050.2_Missense_Mutation_p.G863S|PPFIA4_ENST00000272198.6_Missense_Mutation_p.G650S|PPFIA4_ENST00000367240.2_Missense_Mutation_p.G1135S|PPFIA4_ENST00000599966.1_Missense_Mutation_p.G641S|PPFIA4_ENST00000295706.4_Missense_Mutation_p.G641S			O75335	LIPA4_HUMAN	protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 4	1134				G -> A (in Ref. 5; AAC26102). {ECO:0000305}.	cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intracellular (GO:0005622)|presynaptic active zone (GO:0048786)				NS(1)|autonomic_ganglia(1)|breast(3)|endometrium(6)|kidney(2)|large_intestine(8)|lung(20)|ovary(4)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	50						CCACGGTCGCGGCGGCATGCT	0.716													g|||	32	0.00638978	0.0	0.0115	5008	,	,		11140	0.0		0.0189	False		,,,				2504	0.0051				p.G650S		Atlas-SNP	.											PPFIA4_ENST00000272198,colon,carcinoma,-1,2	PPFIA4	139	2	0			c.G1948A						PASS	.		SER/GLY	15,3733		0,15,1859	11.0	14.0	13.0		1948	-0.2	0.0	1	dbSNP_120	13	228,7910		2,224,3843	no	missense	PPFIA4	NM_015053.1	56	2,239,5702	AA,AG,GG		2.8017,0.4002,2.0444	benign	650/702	203044777	243,11643	1874	4069	5943	SO:0001583	missense	8497	exon16			GGTCGCGGCGGCA	AF034801	CCDS44296.1	1q32.1	2013-01-10			ENSG00000143847	ENSG00000143847		"""Sterile alpha motif (SAM) domain containing"""	9248	protein-coding gene	gene with protein product	"""Liprin-alpha4"""	603145				9624153	Standard	XM_005245553		Approved		uc009xaj.3	O75335	OTTHUMG00000042123	ENST00000447715.2:c.3400G>A	1.37:g.203044777G>A	ENSP00000402576:p.Gly1134Ser	Somatic	13	0	0		WXS	Illumina HiSeq	Phase_I	26	12	0.461538	NM_015053	A2RUJ5|B1APN8|B1N949|B7ZM43|O94971	Missense_Mutation	SNP	ENST00000447715.2	37		16	0.007326007326007326	0	0.0	5	0.013812154696132596	0	0.0	11	0.014511873350923483	g	12.32	1.901775	0.33535	0.004002	0.028017	ENSG00000143847	ENST00000367240;ENST00000447715;ENST00000295706;ENST00000414050;ENST00000272198	T;T;T;T;T	0.21734	2.32;2.0;1.99;2.0;1.99	4.58	-0.158	0.13383	.	1.035160	0.07805	U	0.957214	T	0.03564	0.0102	N	0.17474	0.49	0.09310	N	1	B;B;B;B;B	0.17038	0.0;0.0;0.005;0.02;0.012	B;B;B;B;B	0.16722	0.0;0.0;0.002;0.016;0.007	T	0.34875	-0.9811	10	0.32370	T	0.25	-0.3686	4.4121	0.11438	0.4118:0.2651:0.3231:0.0	rs12130501	863;1134;336;641;650	B4DIS5;B1N949;B3KN22;O75335-2;O75335	.;.;.;.;LIPA4_HUMAN	S	1135;1134;641;863;650	ENSP00000356209:G1135S;ENSP00000402576:G1134S;ENSP00000295706:G641S;ENSP00000400379:G863S;ENSP00000272198:G650S	ENSP00000272198:G650S	G	+	1	0	PPFIA4	201311400	0.948000	0.32251	0.014000	0.15608	0.413000	0.31143	1.380000	0.34351	-0.369000	0.08028	0.298000	0.19748	GGC	G|0.992;A|0.008	0.008	strong		0.716	PPFIA4-005	NOVEL	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000462949.1	NM_015053	
HLA-A	3105	hgsc.bcm.edu	37	6	29910622	29910622	+	Silent	SNP	C	C	T	rs199501996	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:29910622C>T	ENST00000396634.1	+	4	503	c.162C>T	c.(160-162)gaC>gaT	p.D54D	HLA-A_ENST00000376802.2_Silent_p.D54D|HLA-A_ENST00000376809.5_Silent_p.D54D|HLA-A_ENST00000376806.5_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						scavenged	.						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	105	0	0		WXS	Illumina HiSeq	Phase_I	141	19	0.134752	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	
ANO7	50636	hgsc.bcm.edu	37	2	242151585	242151585	+	Silent	SNP	C	C	T	rs7593101	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	124	0	0		WXS	Illumina HiSeq	Phase_I	123	66	0.536585	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	
MYPOP	339344	hgsc.bcm.edu	37	19	46394187	46394187	+	Silent	SNP	C	C	T	rs62111265	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:46394187C>T	ENST00000322217.5	-	3	980	c.894G>A	c.(892-894)ctG>ctA	p.L298L		NM_001012643.2	NP_001012661.1	Q86VE0	MYPOP_HUMAN	Myb-related transcription factor, partner of profilin	298	Pro-rich.					nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)			large_intestine(2)|lung(1)|skin(1)	4						GGGTTCCTGGCAGAAGGGGCA	0.711													C|||	628	0.125399	0.025	0.2161	5008	,	,		4314	0.0992		0.1779	False		,,,				2504	0.1697				p.L298L		Atlas-SNP	.											.	MYPOP	23	.	0			c.G894A						PASS	.	C		210,4064		8,194,1935	7.0	6.0	6.0		894	3.1	1.0	19	dbSNP_129	6	1360,7006		99,1162,2922	no	coding-synonymous	MYPOP	NM_001012643.2		107,1356,4857	TT,TC,CC		16.2563,4.9134,12.4209		298/400	46394187	1570,11070	2137	4183	6320	SO:0001819	synonymous_variant	339344	exon3			TCCTGGCAGAAGG	BC044311	CCDS33055.1	19q13.32	2014-06-13			ENSG00000176182	ENSG00000176182			20178	protein-coding gene	gene with protein product	"""p42 Myb-related transcription factor, partner of profilin"""					15615774	Standard	NM_001012643		Approved	P42pop	uc002pdt.3	Q86VE0	OTTHUMG00000182486	ENST00000322217.5:c.894G>A	19.37:g.46394187C>T		Somatic	24	0	0		WXS	Illumina HiSeq	Phase_I	19	13	0.684211	NM_001012643		Silent	SNP	ENST00000322217.5	37	CCDS33055.1																																																																																			C|0.872;G|0.000;T|0.128	0.128	strong		0.711	MYPOP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461684.1	NM_001012643	
MCPH1	79648	hgsc.bcm.edu	37	8	6338306	6338306	+	Missense_Mutation	SNP	C	C	A	rs12674488	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:6338306C>A	ENST00000344683.5	+	11	2121	c.2045C>A	c.(2044-2046)aCc>aAc	p.T682N		NM_024596.3	NP_078872	Q8NEM0	MCPH1_HUMAN	microcephalin 1	682	BRCT 2. {ECO:0000255|PROSITE- ProRule:PRU00033}.		T -> N (in dbSNP:rs12674488).		cerebral cortex development (GO:0021987)|mitotic cell cycle (GO:0000278)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleoplasm (GO:0005654)	identical protein binding (GO:0042802)		AGPAT5/MCPH1(2)	central_nervous_system(1)|large_intestine(4)|skin(1)	6		Hepatocellular(245;0.0663)		Colorectal(4;0.0505)		GTCTGTGAGACCACGACTCAC	0.488													C|||	733	0.146366	0.0938	0.1153	5008	,	,		18435	0.1806		0.163	False		,,,				2504	0.1871				p.T682N	Colon(95;1448 1467 8277 34473 35819)	Atlas-SNP	.											.	MCPH1	65	.	0			c.C2045A						PASS	.	C	ASN/THR	335,3637		14,307,1665	126.0	121.0	123.0		2045	0.7	0.0	8	dbSNP_120	123	1301,7031		96,1109,2961	yes	missense	MCPH1	NM_024596.3	65	110,1416,4626	AA,AC,CC		15.6145,8.434,13.2965	probably-damaging	682/836	6338306	1636,10668	1986	4166	6152	SO:0001583	missense	79648	exon11			GTGAGACCACGAC	AK022909	CCDS43689.1, CCDS55190.1, CCDS55191.1	8p23.1	2012-11-26	2007-11-26		ENSG00000147316	ENSG00000147316			6954	protein-coding gene	gene with protein product	"""BRCT-repeat inhibitor of TERT expression 1"""	607117	"""microcephaly, primary autosomal recessive 1"""			9683597, 17925396	Standard	NM_024596		Approved	FLJ12847, BRIT1	uc003wqi.3	Q8NEM0	OTTHUMG00000163618	ENST00000344683.5:c.2045C>A	8.37:g.6338306C>A	ENSP00000342924:p.Thr682Asn	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	80	13	0.1625	NM_024596	B4DWW2|E9PGU5|E9PH63|Q66GU1|Q9H9C7	Missense_Mutation	SNP	ENST00000344683.5	37	CCDS43689.1	304	0.1391941391941392	41	0.08333333333333333	42	0.11602209944751381	104	0.18181818181818182	117	0.15435356200527706	C	13.12	2.140912	0.37825	0.08434	0.156145	ENSG00000147316	ENST00000344683	T	0.28666	1.6	5.91	0.673	0.17941	BRCT (3);	0.466822	0.27019	N	0.021330	T	0.00109	0.0003	L	0.49126	1.545	0.58432	P	6.999999999979245E-6	D	0.57899	0.981	P	0.60345	0.873	T	0.04140	-1.0974	9	0.44086	T	0.13	-3.8872	18.5762	0.91155	0.0:0.372:0.628:0.0	rs12674488;rs52795475;rs61269664;rs12674488	682	Q8NEM0	MCPH1_HUMAN	N	682	ENSP00000342924:T682N	ENSP00000342924:T682N	T	+	2	0	MCPH1	6325714	0.731000	0.28111	0.000000	0.03702	0.135000	0.20990	1.013000	0.29937	-0.152000	0.11156	0.655000	0.94253	ACC	C|0.850;A|0.150	0.150	strong		0.488	MCPH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374532.2	NM_024596	
ERMARD	55780	hgsc.bcm.edu	37	6	170176648	170176648	+	Missense_Mutation	SNP	A	A	G	rs386708934|rs4716346	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:170176648A>G	ENST00000366773.3	+	16	1651	c.1618A>G	c.(1618-1620)Agc>Ggc	p.S540G	ERMARD_ENST00000392095.4_Missense_Mutation_p.S414G|ERMARD_ENST00000588451.1_Missense_Mutation_p.S404G|ERMARD_ENST00000366772.2_Intron|ERMARD_ENST00000418781.3_Intron	NM_001278532.1|NM_018341.1	NP_001265461.1|NP_060811.1	Q5T6L9	EMARD_HUMAN	ER membrane-associated RNA degradation	540			S -> G (in dbSNP:rs4716346). {ECO:0000269|PubMed:14702039}.		multicellular organismal development (GO:0007275)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)											CCGAAGCATCAGCGAACAGTG	0.627													G|||	1721	0.34365	0.497	0.304	5008	,	,		21067	0.3304		0.2366	False		,,,				2504	0.2883				p.S540G		Atlas-SNP	.											.	C6orf70	63	.	0			c.A1618G						PASS	.	G	GLY/SER	2113,2293	600.2+/-389.4	503,1107,593	94.0	71.0	79.0		1618	-6.8	0.0	6	dbSNP_111	79	1913,6687	726.4+/-406.6	235,1443,2622	yes	missense	C6orf70	NM_018341.1	56	738,2550,3215	GG,GA,AA		22.2442,47.9573,30.9549	benign	540/679	170176648	4026,8980	2203	4300	6503	SO:0001583	missense	55780	exon16			AGCATCAGCGAAC	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.1618A>G	6.37:g.170176648A>G	ENSP00000355735:p.Ser540Gly	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	44	13	0.295455	NM_018341	B4DFH0|F8WAF1|Q3ZCS8|Q5T6L8|Q9NUT5|Q9NVU2	Missense_Mutation	SNP	ENST00000366773.3	37	CCDS34576.1	573	0.2623626373626374	178	0.3617886178861789	92	0.2541436464088398	159	0.27797202797202797	144	0.18997361477572558	G	12.19	1.863197	0.32884	0.479573	0.222442	ENSG00000130023	ENST00000366773;ENST00000392095;ENST00000366771	T;T	0.47528	0.84;0.84	5.37	-6.82	0.01698	.	0.716909	0.14165	N	0.337097	T	0.12008	0.0292	L	0.46885	1.475	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.10917	-1.0609	9	0.22109	T	0.4	.	5.928	0.19122	0.5017:0.0:0.3028:0.1955	rs4716346;rs17860646;rs59930119;rs4716346	540	Q5T6L9	CF070_HUMAN	G	540;414;188	ENSP00000355735:S540G;ENSP00000375945:S414G	ENSP00000355733:S188G	S	+	1	0	C6orf70	169918573	0.000000	0.05858	0.000000	0.03702	0.019000	0.09904	-0.628000	0.05515	-1.767000	0.01300	-1.485000	0.00982	AGC	A|0.706;G|0.294	0.294	strong		0.627	ERMARD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043238.2	NM_018341	
CEP170B	283638	hgsc.bcm.edu	37	14	105350178	105350178	+	Silent	SNP	C	C	T	rs45449696	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:105350178C>T	ENST00000414716.3	+	9	1290	c.1062C>T	c.(1060-1062)caC>caT	p.H354H	CEP170B_ENST00000453495.1_Silent_p.H355H|CEP170B_ENST00000418279.1_Silent_p.H284H|CEP170B_ENST00000556508.1_Silent_p.H284H	NM_001112726.2	NP_001106197.1	Q9Y4F5	C170B_HUMAN	centrosomal protein 170B	354						cytoplasm (GO:0005737)|microtubule (GO:0005874)											GCCACAAGCACGAGGACGGCA	0.667													C|||	1100	0.219649	0.1853	0.3242	5008	,	,		14088	0.003		0.3618	False		,,,				2504	0.2689				p.H354H		Atlas-SNP	.											.	.	.	.	0			c.C1062T						PASS	.	C	,	739,3217		74,591,1313	6.0	7.0	7.0		1062,852	-5.3	0.8	14	dbSNP_127	7	2964,5248		574,1816,1716	no	coding-synonymous,coding-synonymous	KIAA0284	NM_001112726.2,NM_015005.2	,	648,2407,3029	TT,TC,CC		36.0935,18.6805,30.4323	,	354/1555,284/1520	105350178	3703,8465	1978	4106	6084	SO:0001819	synonymous_variant	283638	exon9			CAAGCACGAGGAC	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.1062C>T	14.37:g.105350178C>T		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	71	29	0.408451	NM_001112726	Q2KHR7|Q86TI7	Silent	SNP	ENST00000414716.3	37	CCDS45175.1																																																																																			C|0.760;T|0.240	0.240	strong		0.667	CEP170B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000410289.2	NM_001112726	
PKD1L1	168507	hgsc.bcm.edu	37	7	47869038	47869038	+	Silent	SNP	T	T	C	rs7788583	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:47869038T>C	ENST00000289672.2	-	44	6770	c.6720A>G	c.(6718-6720)gcA>gcG	p.A2240A		NM_138295.3	NP_612152.1	Q8TDX9	PK1L1_HUMAN	polycystic kidney disease 1 like 1	2240					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)	p.A2240A(1)	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						CAACCTCGCCTGCACAGTCAG	0.408													T|||	981	0.195887	0.3359	0.1297	5008	,	,		18191	0.0704		0.174	False		,,,				2504	0.2055				p.A2240A		Atlas-SNP	.											PKD1L1,NS,carcinoma,0,1	PKD1L1	328	1	1	Substitution - coding silent(1)	stomach(1)	c.A6720G						PASS	.	T		1357,3049	447.9+/-348.5	206,945,1052	91.0	98.0	96.0		6720	-7.0	0.0	7	dbSNP_116	96	1519,7081	285.8+/-297.4	121,1277,2902	no	coding-synonymous	PKD1L1	NM_138295.3		327,2222,3954	CC,CT,TT		17.6628,30.7989,22.1129		2240/2850	47869038	2876,10130	2203	4300	6503	SO:0001819	synonymous_variant	168507	exon44			CTCGCCTGCACAG	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.6720A>G	7.37:g.47869038T>C		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	36	20	0.555556	NM_138295	Q6UWK1	Silent	SNP	ENST00000289672.2	37	CCDS34633.1																																																																																			T|0.785;C|0.215	0.215	strong		0.408	PKD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340974.1	NM_138295	
WFDC10A	140832	hgsc.bcm.edu	37	20	44259549	44259549	+	Silent	SNP	G	G	A	rs2272961	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:44259549G>A	ENST00000372643.3	+	2	420	c.132G>A	c.(130-132)caG>caA	p.Q44Q	WFDC9_ENST00000326000.1_Intron	NM_080753.2	NP_542791.1	Q9H1F0	WF10A_HUMAN	WAP four-disulfide core domain 10A	44	WAP. {ECO:0000255|PROSITE- ProRule:PRU00722}.					extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)			large_intestine(2)	2		Myeloproliferative disorder(115;0.0122)				GCCAGCAGCAGCCTAAACTAT	0.403													G|||	1034	0.20647	0.1785	0.3012	5008	,	,		24775	0.2917		0.174	False		,,,				2504	0.1227				p.Q44Q		Atlas-SNP	.											.	WFDC10A	7	.	0			c.G132A						PASS	.	G	,	799,3607	318.8+/-295.8	61,677,1465	111.0	91.0	97.0		132,	-3.0	0.0	20	dbSNP_100	97	1368,7232	266.5+/-286.8	104,1160,3036	no	coding-synonymous,intron	WFDC10A,WFDC9	NM_080753.2,NM_147198.3	,	165,1837,4501	AA,AG,GG		15.907,18.1344,16.6615	,	44/80,	44259549	2167,10839	2203	4300	6503	SO:0001819	synonymous_variant	140832	exon2			GCAGCAGCCTAAA	AL031671	CCDS13363.1	20q13.11	2013-01-21	2003-02-21	2003-02-21	ENSG00000180305	ENSG00000180305		"""WAP four-disulfide core domain containing"""	16139	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 146"""	C20orf146		12206714	Standard	NM_080753		Approved	dJ688G8.3, WAP10	uc002xoz.3	Q9H1F0	OTTHUMG00000046331	ENST00000372643.3:c.132G>A	20.37:g.44259549G>A		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	122	64	0.52459	NM_080753	A2RRE9|Q5TGZ7	Silent	SNP	ENST00000372643.3	37	CCDS13363.1																																																																																			G|0.807;A|0.193	0.193	strong		0.403	WFDC10A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106944.2		
AMZ1	155185	hgsc.bcm.edu	37	7	2752330	2752330	+	Missense_Mutation	SNP	C	C	T	rs111981479	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:2752330C>T	ENST00000312371.4	+	7	1683	c.1315C>T	c.(1315-1317)Cgc>Tgc	p.R439C	AMZ1_ENST00000489665.1_Intron|AMZ1_ENST00000407112.1_3'UTR	NM_133463.1	NP_597720.1	Q400G9	AMZ1_HUMAN	archaelysin family metallopeptidase 1	439							metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(2)|kidney(1)|large_intestine(4)|lung(8)|skin(1)	16		Ovarian(82;0.0779)		OV - Ovarian serous cystadenocarcinoma(56;5.03e-14)		CGCCCTCGACCGCTGGGAGAT	0.682													C|||	57	0.0113818	0.0257	0.0058	5008	,	,		16717	0.003		0.004	False		,,,				2504	0.0123				p.R439C		Atlas-SNP	.											.	AMZ1	41	.	0			c.C1315T						PASS	.	C	CYS/ARG	109,4295	78.3+/-116.7	4,101,2097	44.0	42.0	43.0		1315	2.6	0.0	7	dbSNP_132	43	44,8548	29.0+/-79.6	0,44,4252	yes	missense	AMZ1	NM_133463.1	180	4,145,6349	TT,TC,CC		0.5121,2.475,1.1773	probably-damaging	439/499	2752330	153,12843	2202	4296	6498	SO:0001583	missense	155185	exon7			CTCGACCGCTGGG	AB075830	CCDS34589.1, CCDS64582.1	7p22.3	2008-01-17			ENSG00000174945	ENSG00000174945			22231	protein-coding gene	gene with protein product	"""archaemetzincin-1"""	615168				15972818	Standard	NM_133463		Approved	KIAA1950	uc003smr.1	Q400G9	OTTHUMG00000152111	ENST00000312371.4:c.1315C>T	7.37:g.2752330C>T	ENSP00000308149:p.Arg439Cys	Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	115	87	0.756522	NM_133463	B3KRS0|Q8TF51	Missense_Mutation	SNP	ENST00000312371.4	37	CCDS34589.1	17	0.007783882783882784	11	0.022357723577235773	1	0.0027624309392265192	1	0.0017482517482517483	4	0.005277044854881266	C	9.560	1.118113	0.20877	0.02475	0.005121	ENSG00000174945	ENST00000312371	T	0.29397	1.57	4.67	2.61	0.31194	.	0.343057	0.24132	N	0.041258	T	0.11793	0.0287	L	0.42245	1.32	0.09310	N	1	D	0.56287	0.975	B	0.40565	0.333	T	0.09335	-1.0679	10	0.66056	D	0.02	-18.9727	7.8987	0.29721	0.2349:0.6271:0.138:0.0	.	439	Q400G9	AMZ1_HUMAN	C	439	ENSP00000308149:R439C	ENSP00000308149:R439C	R	+	1	0	AMZ1	2718856	0.027000	0.19231	0.002000	0.10522	0.090000	0.18270	1.543000	0.36147	0.933000	0.37291	0.462000	0.41574	CGC	C|0.990;T|0.010	0.010	strong		0.682	AMZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325244.1	NM_133463	
SVIL	6840	hgsc.bcm.edu	37	10	29839798	29839798	+	Silent	SNP	A	A	G	rs17834991	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:29839798A>G	ENST00000355867.4	-	6	1307	c.555T>C	c.(553-555)taT>taC	p.Y185Y	SVIL_ENST00000375400.3_Silent_p.Y185Y|SVIL_ENST00000375398.2_Silent_p.Y185Y	NM_021738.2	NP_068506.2	O95425	SVIL_HUMAN	supervillin	185					cytoskeleton organization (GO:0007010)|skeletal muscle tissue development (GO:0007519)	actin cytoskeleton (GO:0015629)|cell projection (GO:0042995)|costamere (GO:0043034)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)	p.Y185Y(1)		breast(1)|central_nervous_system(3)|cervix(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(24)|lung(35)|ovary(8)|prostate(2)|skin(4)|stomach(7)|upper_aerodigestive_tract(2)|urinary_tract(2)	112		Breast(68;0.103)				CATGGAGGGCATAGTCCTTGG	0.572													A|||	791	0.157947	0.0348	0.2839	5008	,	,		18876	0.1637		0.2147	False		,,,				2504	0.1708				p.Y185Y		Atlas-SNP	.											SVIL,NS,carcinoma,0,1	SVIL	226	1	1	Substitution - coding silent(1)	stomach(1)	c.T555C						PASS	.	A	,	282,4124	157.0+/-190.0	10,262,1931	93.0	94.0	94.0		555,555	-0.5	0.0	10	dbSNP_123	94	1734,6866	315.8+/-312.4	180,1374,2746	no	coding-synonymous,coding-synonymous	SVIL	NM_003174.3,NM_021738.2	,	190,1636,4677	GG,GA,AA		20.1628,6.4004,15.5005	,	185/1789,185/2215	29839798	2016,10990	2203	4300	6503	SO:0001819	synonymous_variant	6840	exon8			GAGGGCATAGTCC	AF051851	CCDS7163.1, CCDS7164.1	10p11.2	2008-07-29			ENSG00000197321	ENSG00000197321			11480	protein-coding gene	gene with protein product	"""archvillin"""	604126				9382871	Standard	NM_003174		Approved		uc001iut.1	O95425	OTTHUMG00000017882	ENST00000355867.4:c.555T>C	10.37:g.29839798A>G		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	75	30	0.4	NM_003174	D3DRW9|M1J557|O60611|O60612|Q5VZK5|Q5VZK6|Q9H1R7	Silent	SNP	ENST00000355867.4	37	CCDS7164.1																																																																																			A|0.839;G|0.161;T|0.000	0.161	strong		0.572	SVIL-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047395.1		
NTAN1	123803	hgsc.bcm.edu	37	16	15131962	15131962	+	Missense_Mutation	SNP	A	A	G	rs1135999	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:15131962A>G	ENST00000287706.3	-	10	951	c.859T>C	c.(859-861)Tct>Cct	p.S287P	PDXDC1_ENST00000535621.2_Intron	NM_001270766.1|NM_173474.3	NP_001257695.1|NP_775745.1	Q96AB6	NTAN1_HUMAN	N-terminal asparagine amidase	287			S -> P (in dbSNP:rs1135999).		adult locomotory behavior (GO:0008344)|memory (GO:0007613)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein-N-terminal asparagine amidohydrolase activity (GO:0008418)			endometrium(1)|large_intestine(4)|lung(3)	8						TTATTTCCAGAAAACAGTGTG	0.393													G|||	1723	0.34405	0.1838	0.5331	5008	,	,		17634	0.37		0.3072	False		,,,				2504	0.4376				p.S287P		Atlas-SNP	.											.	NTAN1	21	.	0			c.T859C						PASS	.	G	PRO/SER	985,3409	720.3+/-409.0	118,749,1330	80.0	82.0	82.0		859	5.9	1.0	16	dbSNP_86	82	2565,6035	682.5+/-403.8	359,1847,2094	yes	missense	NTAN1	NM_173474.2	74	477,2596,3424	GG,GA,AA		29.8256,22.4169,27.3203	benign	287/311	15131962	3550,9444	2197	4300	6497	SO:0001583	missense	123803	exon10			TTCCAGAAAACAG	AF092440	CCDS10558.1, CCDS73832.1	16p13	2008-02-05			ENSG00000157045	ENSG00000157045			29909	protein-coding gene	gene with protein product		615367				8910481	Standard	NM_173474		Approved		uc002ddd.4	Q96AB6	OTTHUMG00000129849	ENST00000287706.3:c.859T>C	16.37:g.15131962A>G	ENSP00000287706:p.Ser287Pro	Somatic	178	1	0.00561798		WXS	Illumina HiSeq	Phase_I	109	76	0.697248	NM_173474	Q7Z4Z0	Missense_Mutation	SNP	ENST00000287706.3	37	CCDS10558.1	727	0.33287545787545786	94	0.1910569105691057	174	0.48066298342541436	216	0.3776223776223776	243	0.32058047493403696	G	7.877	0.729487	0.15507	0.224169	0.298256	ENSG00000157045	ENST00000287706	T	0.23552	1.9	5.87	5.87	0.94306	.	0.000000	0.85682	N	0.000000	T	0.00012	0.0000	N	0.00036	-2.54	0.48762	P	2.950000000000452E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.45101	-0.9284	9	0.02654	T	1	-10.699	14.696	0.69121	0.0692:0.0:0.9308:0.0	rs1135999;rs3087673;rs3199047;rs17841256;rs58432330;rs1135999	287	Q96AB6	NTAN1_HUMAN	P	287	ENSP00000287706:S287P	ENSP00000287706:S287P	S	-	1	0	NTAN1	15039463	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	5.104000	0.64584	1.644000	0.50603	-0.119000	0.15052	TCT	A|0.707;G|0.293	0.293	strong		0.393	NTAN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252089.1	NM_173474	
GABRG3	2567	hgsc.bcm.edu	37	15	27772676	27772676	+	Silent	SNP	C	C	T	rs140679	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:27772676C>T	ENST00000333743.6	+	8	1217	c.963C>T	c.(961-963)acC>acT	p.T321T	RP11-100M12.3_ENST00000556642.1_RNA	NM_033223.4	NP_150092.2	Q99928	GBRG3_HUMAN	gamma-aminobutyric acid (GABA) A receptor, gamma 3	321					gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|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)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(23)|skin(1)|upper_aerodigestive_tract(4)	42		all_lung(180;4.58e-12)|Breast(32;0.000625)|Colorectal(260;0.235)		all cancers(64;3.15e-07)|Epithelial(43;1.17e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0261)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|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)	TTTTTGTGACCGTGTGCTTCC	0.557													C|||	2586	0.516374	0.3026	0.6844	5008	,	,		20370	0.6577		0.5467	False		,,,				2504	0.5092				p.T321T	NSCLC(114;800 1656 7410 37729 45293)	Atlas-SNP	.											.	GABRG3	115	.	0			c.C963T						PASS	.	C		1351,2995		231,889,1053	139.0	127.0	131.0		963	-8.3	0.5	15	dbSNP_78	131	4580,3972		1233,2114,929	no	coding-synonymous	GABRG3	NM_033223.4		1464,3003,1982	TT,TC,CC		46.4453,31.0861,45.9839		321/468	27772676	5931,6967	2173	4276	6449	SO:0001819	synonymous_variant	2567	exon8			TGTGACCGTGTGC		CCDS45195.1, CCDS59251.1	15q12	2012-06-22			ENSG00000182256	ENSG00000182256		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	4088	protein-coding gene	gene with protein product	"""GABA(G) receptor, gamma 3"""	600233				7601451	Standard	NM_033223		Approved		uc001zbg.2	Q99928	OTTHUMG00000044462	ENST00000333743.6:c.963C>T	15.37:g.27772676C>T		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	122	58	0.47541	NM_033223	G3V594|Q9HD46|Q9NYT2	Silent	SNP	ENST00000333743.6	37	CCDS45195.1	1190	0.5448717948717948	150	0.3048780487804878	238	0.6574585635359116	394	0.6888111888111889	408	0.5382585751978892	C	9.780	1.175068	0.21704	0.310861	0.535547	ENSG00000182256	ENST00000451330	.	.	.	5.48	-8.26	0.01021	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.00995	-1.1487	3	.	.	.	.	18.8379	0.92169	0.0:0.1181:0.0:0.8819	rs140679;rs17649404;rs140679	.	.	.	L	84	.	.	P	+	2	0	GABRG3	25446271	0.001000	0.12720	0.503000	0.27626	0.903000	0.53119	-1.707000	0.01893	-2.099000	0.00849	-0.251000	0.11542	CCG	C|0.472;T|0.528	0.528	strong		0.557	GABRG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103584.2		
C7	730	hgsc.bcm.edu	37	5	40964852	40964852	+	Missense_Mutation	SNP	A	A	C	rs13157656	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:40964852A>C	ENST00000313164.9	+	14	2118	c.1759A>C	c.(1759-1761)Aca>Cca	p.T587P		NM_000587.2	NP_000578.2	P10643	CO7_HUMAN	complement component 7	587	CCP 1.|Sushi 1. {ECO:0000255|PROSITE- ProRule:PRU00302}.		T -> P (polymorphism confirmed at protein level; dbSNP:rs13157656). {ECO:0000269|PubMed:22028381, ECO:0000269|PubMed:3335508}.		cellular sodium ion homeostasis (GO:0006883)|complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|complement activation, classical pathway (GO:0006958)|cytolysis (GO:0019835)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane attack complex (GO:0005579)							Ovarian(839;0.0112)				GGATGAAGGTACAATGTTTCC	0.353													A|||	965	0.192692	0.0265	0.2089	5008	,	,		18703	0.2133		0.2207	False		,,,				2504	0.3558				p.T587P		Atlas-SNP	.											.	C7	136	.	0			c.A1759C						PASS	.	A	PRO/THR	239,3489		6,227,1631	143.0	141.0	142.0		1759	-4.7	0.0	5	dbSNP_121	142	1927,6279		231,1465,2407	yes	missense	C7	NM_000587.2	38	237,1692,4038	CC,CA,AA		23.4828,6.4109,18.1498	benign	587/844	40964852	2166,9768	1864	4103	5967	SO:0001583	missense	730	exon14			GAAGGTACAATGT	J03507	CCDS47201.1	5p13.1	2014-09-17			ENSG00000112936	ENSG00000112936		"""Complement system"""	1346	protein-coding gene	gene with protein product		217070					Standard	NM_000587		Approved		uc003jmh.3	P10643	OTTHUMG00000150340	ENST00000313164.9:c.1759A>C	5.37:g.40964852A>C	ENSP00000322061:p.Thr587Pro	Somatic	206	0	0		WXS	Illumina HiSeq	Phase_I	203	110	0.541872	NM_000587	Q6P3T5|Q92489	Missense_Mutation	SNP	ENST00000313164.9	37	CCDS47201.1	395	0.18086080586080586	21	0.042682926829268296	81	0.22375690607734808	123	0.21503496503496503	170	0.22427440633245382	A	13.95	2.391395	0.42410	0.064109	0.234828	ENSG00000112936	ENST00000313164;ENST00000440677	T	0.63913	-0.07	6.17	-4.69	0.03299	Complement control module (2);Sushi/SCR/CCP (3);	0.765086	0.12472	N	0.465951	T	0.00012	0.0000	L	0.28192	0.835	0.80722	P	0.0	B	0.06786	0.001	B	0.10450	0.005	T	0.14420	-1.0473	9	0.37606	T	0.19	0.0778	0.5007	0.00579	0.3586:0.1501:0.2454:0.2459	rs13157656;rs17176312;rs52828491;rs13157656	587	P10643	CO7_HUMAN	P	587;427	ENSP00000322061:T587P	ENSP00000322061:T587P	T	+	1	0	C7	41000609	0.000000	0.05858	0.040000	0.18447	0.625000	0.37756	-1.442000	0.02407	-0.366000	0.08064	-0.327000	0.08410	ACA	A|0.817;C|0.182	0.182	strong		0.353	C7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317680.1		
CALHM1	255022	hgsc.bcm.edu	37	10	105218254	105218254	+	Silent	SNP	C	C	T	rs4918016|rs386747134	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:105218254C>T	ENST00000329905.5	-	1	391	c.255G>A	c.(253-255)ccG>ccA	p.P85P	RP11-225H22.4_ENST00000411906.1_RNA	NM_001001412.3	NP_001001412.3	Q8IU99	CAHM1_HUMAN	calcium homeostasis modulator 1	85					ATP transport (GO:0015867)|cation transport (GO:0006812)|protein homooligomerization (GO:0051260)|regulation of ion transmembrane transport (GO:0034765)|sensory perception of bitter taste (GO:0050913)|sensory perception of sweet taste (GO:0050916)|sensory perception of umami taste (GO:0050917)	endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)	calcium activated cation channel activity (GO:0005227)|calcium channel activity (GO:0005262)|identical protein binding (GO:0042802)|voltage-gated ion channel activity (GO:0005244)			large_intestine(2)|liver(1)|lung(5)|ovary(1)	9						GGCGGCCCAGCGGCCGCTTCC	0.672													C|||	1521	0.303714	0.1997	0.4063	5008	,	,		14923	0.4137		0.2992	False		,,,				2504	0.2628				p.P85P		Atlas-SNP	.											.	CALHM1	33	.	0			c.G255A						PASS	.	C		951,3449		112,727,1361	21.0	27.0	25.0		255	-10.8	0.0	10	dbSNP_111	25	2724,5866		440,1844,2011	no	coding-synonymous	CALHM1	NM_001001412.3		552,2571,3372	TT,TC,CC		31.7113,21.6136,28.291		85/347	105218254	3675,9315	2200	4295	6495	SO:0001819	synonymous_variant	255022	exon1			GCCCAGCGGCCGC	BC036208	CCDS7550.1	10q24.33	2008-07-02	2008-07-02	2008-07-02	ENSG00000185933	ENSG00000185933			23494	protein-coding gene	gene with protein product		612234	"""family with sequence similarity 26, member C"""	FAM26C		18585350	Standard	NM_001001412		Approved		uc001kxe.2	Q8IU99	OTTHUMG00000018991	ENST00000329905.5:c.255G>A	10.37:g.105218254C>T		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	142	75	0.528169	NM_001001412	Q5W091	Silent	SNP	ENST00000329905.5	37	CCDS7550.1																																																																																			C|0.702;T|0.298	0.298	strong		0.672	CALHM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050165.1	NM_001001412	
HLA-A	3105	hgsc.bcm.edu	37	6	29910607	29910607	+	Silent	SNP	G	G	C	rs72555397		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:29910607G>C	ENST00000396634.1	+	4	488	c.147G>C	c.(145-147)gtG>gtC	p.V49V	HLA-A_ENST00000376802.2_Silent_p.V49V|HLA-A_ENST00000376809.5_Silent_p.V49V|HLA-A_ENST00000376806.5_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						scavenged	.																																			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	83	0	0		WXS	Illumina HiSeq	Phase_I	115	16	0.13913	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	
HTT	3064	hgsc.bcm.edu	37	4	3227419	3227419	+	Silent	SNP	A	A	G	rs362273	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:3227419A>G	ENST00000355072.5	+	57	7942	c.7797A>G	c.(7795-7797)ctA>ctG	p.L2599L		NM_002111.6	NP_002102	P42858	HD_HUMAN	huntingtin	2599					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)		AGCTGCTGCTACAGATCAACC	0.647													G|||	1234	0.246406	0.1218	0.304	5008	,	,		14498	0.3393		0.3191	False		,,,				2504	0.2035				p.L2599L		Atlas-SNP	.											HTT,caecum,carcinoma,0,1	HTT	221	1	0			c.A7797G						PASS	.	G		636,3396		56,524,1436	28.0	32.0	31.0		7797	3.1	1.0	4	dbSNP_79	31	2492,5908		355,1782,2063	no	coding-synonymous	HTT	NM_002111.6		411,2306,3499	GG,GA,AA		29.6667,15.7738,25.1609		2599/3143	3227419	3128,9304	2016	4200	6216	SO:0001819	synonymous_variant	3064	exon57			GCTGCTACAGATC	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.7797A>G	4.37:g.3227419A>G		Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	174	83	0.477012	NM_002111	Q9UQB7	Silent	SNP	ENST00000355072.5	37	CCDS43206.1																																																																																			A|0.737;G|0.263	0.263	strong		0.647	HTT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358234.2	NM_002111	
HSPA4	3308	hgsc.bcm.edu	37	5	132412424	132412424	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:132412424T>C	ENST00000304858.2	+	7	1031	c.742T>C	c.(742-744)Ttt>Ctt	p.F248L	HSPA4_ENST00000504328.1_3'UTR	NM_002154.3	NP_002145.3	P34932	HSP74_HUMAN	heat shock 70kDa protein 4	248					chaperone-mediated protein complex assembly (GO:0051131)|protein import into mitochondrial outer membrane (GO:0045040)|response to unfolded protein (GO:0006986)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(10)|stomach(1)	32			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			CTGTGAAGAATTTGGGAAGAA	0.373																																					p.F248L	Colon(114;1299 1588 6063 12302 48757)	Atlas-SNP	.											.	HSPA4	68	.	0			c.T742C						PASS	.						106.0	108.0	107.0					5																	132412424		2203	4300	6503	SO:0001583	missense	3308	exon7			GAAGAATTTGGGA	AB023420	CCDS4166.1	5q31.1	2011-09-07	2002-08-29		ENSG00000170606	ENSG00000170606		"""Heat shock proteins / HSP70"""	5237	protein-coding gene	gene with protein product	"""hsp70 RY"""	601113	"""heat shock 70kD protein 4"""			8335910	Standard	NM_002154		Approved	HS24/P52, HSPH2	uc003kyj.3	P34932	OTTHUMG00000129012	ENST00000304858.2:c.742T>C	5.37:g.132412424T>C	ENSP00000302961:p.Phe248Leu	Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	109	19	0.174312	NM_002154	O95756|Q2TAL4|Q9BUK9	Missense_Mutation	SNP	ENST00000304858.2	37	CCDS4166.1	.	.	.	.	.	.	.	.	.	.	T	34	5.399231	0.96030	.	.	ENSG00000170606	ENST00000304858;ENST00000537974	T	0.01295	5.04	5.67	5.67	0.87782	.	0.000000	0.85682	D	0.000000	T	0.12263	0.0298	M	0.91561	3.22	0.80722	D	1	D	0.69078	0.997	D	0.77004	0.989	T	0.00403	-1.1761	10	0.87932	D	0	-10.5177	16.1924	0.82000	0.0:0.0:0.0:1.0	.	248	P34932	HSP74_HUMAN	L	248	ENSP00000302961:F248L	ENSP00000302961:F248L	F	+	1	0	HSPA4	132440323	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.565000	0.82337	2.287000	0.76781	0.482000	0.46254	TTT	.	.	none		0.373	HSPA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251011.1	NM_002154, NM_198431	
ZFP64	55734	hgsc.bcm.edu	37	20	50769379	50769379	+	Missense_Mutation	SNP	C	C	T	rs3746414	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:50769379C>T	ENST00000216923.4	-	6	1701	c.1352G>A	c.(1351-1353)aGt>aAt	p.S451N	ZFP64_ENST00000346617.4_Missense_Mutation_p.S397N|ZFP64_ENST00000371515.4_Missense_Mutation_p.S449N|ZFP64_ENST00000477786.1_Intron|ZFP64_ENST00000361387.2_Intron|ZFP64_ENST00000371518.2_Intron	NM_018197.2|NM_199426.1	NP_060667.2|NP_955458.1	Q9NPA5	ZF64A_HUMAN	ZFP64 zinc finger protein	451			S -> N (in dbSNP:rs3746414). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(5)|large_intestine(8)|lung(11)|ovary(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	33						CTTACTCTCACTGTACTCACT	0.582													T|||	848	0.169329	0.1498	0.2781	5008	,	,		20551	0.0843		0.2137	False		,,,				2504	0.1605				p.S451N		Atlas-SNP	.											.	ZFP64	240	.	0			c.G1352A						PASS	.	T	ASN/SER,ASN/SER,ASN/SER,	675,3731	751.0+/-412.2	56,563,1584	73.0	53.0	60.0		1352,1190,1346,	-10.5	0.0	20	dbSNP_107	60	1863,6737	719.1+/-406.2	193,1477,2630	yes	missense,missense,missense,intron	ZFP64	NM_018197.2,NM_022088.4,NM_199426.1,NM_199427.2	46,46,46,	249,2040,4214	TT,TC,CC		21.6628,15.32,19.5141	benign,benign,benign,	451/682,397/628,449/680,	50769379	2538,10468	2203	4300	6503	SO:0001583	missense	55734	exon6			CTCTCACTGTACT	AK001596	CCDS13439.1, CCDS13440.1, CCDS13441.1, CCDS13442.1	20q13.11-q13.13	2013-01-08	2012-11-27		ENSG00000020256	ENSG00000020256		"""Zinc fingers, C2H2-type"""	15940	protein-coding gene	gene with protein product			"""zinc finger protein 338"", ""zinc finger protein 64 homolog (mouse)"", ""zinc finger protein 64"""	ZNF338		9034307	Standard	NM_199427		Approved	FLJ10734, dJ831D17.1, FLJ12628, dJ548G19.1	uc002xwl.3	Q9NPA5	OTTHUMG00000032756	ENST00000216923.4:c.1352G>A	20.37:g.50769379C>T	ENSP00000216923:p.Ser451Asn	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	83	43	0.518072	NM_018197	Q9NTS7|Q9NVH4	Missense_Mutation	SNP	ENST00000216923.4	37	CCDS13440.1	385	0.1762820512820513	62	0.12601626016260162	104	0.287292817679558	57	0.09965034965034965	162	0.21372031662269128	T	1.446	-0.566451	0.03910	0.1532	0.216628	ENSG00000020256	ENST00000216923;ENST00000346617;ENST00000371515;ENST00000546083;ENST00000371516	T;T;T	0.07327	3.21;3.25;3.2	5.49	-10.5	0.00291	Zinc finger, C2H2 (1);	1.054690	0.07392	N	0.889223	T	0.00012	0.0000	N	0.12182	0.205	0.80722	P	0.0	B;B;B	0.06786	0.001;0.0;0.0	B;B;B	0.08055	0.003;0.0;0.0	T	0.40079	-0.9582	9	0.34782	T	0.22	-0.1662	17.7348	0.88389	0.0741:0.7041:0.0:0.2218	rs3746414;rs17845354;rs17858201;rs17859339;rs58513527;rs3746414	397;449;451	Q9NPA5-2;Q5JWM1;Q9NPA5	.;.;ZF64A_HUMAN	N	451;397;449;293;604	ENSP00000216923:S451N;ENSP00000344615:S397N;ENSP00000360570:S449N	ENSP00000216923:S451N	S	-	2	0	ZFP64	50202786	0.000000	0.05858	0.000000	0.03702	0.149000	0.21700	-2.377000	0.01069	-2.527000	0.00494	-1.178000	0.01721	AGT	C|0.848;T|0.152	0.152	strong		0.582	ZFP64-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000079744.1	NM_018197	
PECR	55825	hgsc.bcm.edu	37	2	216908679	216908679	+	Silent	SNP	C	C	T	rs2303842	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:216908679C>T	ENST00000265322.7	-	7	848	c.774G>A	c.(772-774)tcG>tcA	p.S258S		NM_018441.5	NP_060911.2	Q9BY49	PECR_HUMAN	peroxisomal trans-2-enoyl-CoA reductase	258					fatty acid biosynthetic process (GO:0006633)|oxidation-reduction process (GO:0055114)|phytol metabolic process (GO:0033306)	intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	receptor binding (GO:0005102)|trans-2-enoyl-CoA reductase (NADPH) activity (GO:0019166)	p.S258S(1)		endometrium(2)|kidney(1)|liver(1)|lung(9)|stomach(1)	14		Renal(323;0.0327)		Epithelial(149;3.8e-06)|all cancers(144;0.000272)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)	Adenine(DB00173)	CCACATCCACCGACTGTCCAG	0.502													C|||	703	0.140375	0.0431	0.1455	5008	,	,		18933	0.12		0.2346	False		,,,				2504	0.1922				p.S258S		Atlas-SNP	.											PECR,NS,carcinoma,0,1	PECR	22	1	1	Substitution - coding silent(1)	stomach(1)	c.G774A						PASS	.	C		347,4059	180.5+/-208.7	13,321,1869	71.0	65.0	67.0		774	2.7	0.9	2	dbSNP_100	67	2150,6450	367.0+/-334.5	292,1566,2442	no	coding-synonymous	PECR	NM_018441.5		305,1887,4311	TT,TC,CC		25.0,7.8756,19.1988		258/304	216908679	2497,10509	2203	4300	6503	SO:0001819	synonymous_variant	55825	exon7			ATCCACCGACTGT	AF119841	CCDS33375.1	2q35	2011-09-14			ENSG00000115425	ENSG00000115425	1.3.1.38	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"""	18281	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 29C, member 1"""	605843				10811639, 11669066, 19027726	Standard	NM_018441		Approved	HSA250303, TERP, SDR29C1	uc002vft.3	Q9BY49	OTTHUMG00000154825	ENST00000265322.7:c.774G>A	2.37:g.216908679C>T		Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	156	68	0.435897	NM_018441	B2RE42|Q53TC4|Q6IAK9|Q9NRD4|Q9NY60|Q9P1A4	Silent	SNP	ENST00000265322.7	37	CCDS33375.1																																																																																			C|0.838;T|0.161	0.161	strong		0.502	PECR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337277.1	NM_018441	
IDO2	169355	hgsc.bcm.edu	37	8	39840234	39840234	+	Missense_Mutation	SNP	A	A	G	rs4736794	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:39840234A>G	ENST00000389060.4	+	4	379	c.379A>G	c.(379-381)Atc>Gtc	p.I127V	IDO2_ENST00000343295.4_3'UTR|RP11-44K6.3_ENST00000517623.1_RNA|IDO2_ENST00000502986.2_Missense_Mutation_p.I140V			Q6ZQW0	I23O2_HUMAN	indoleamine 2,3-dioxygenase 2	127					cellular nitrogen compound metabolic process (GO:0034641)|small molecule metabolic process (GO:0044281)|tryptophan catabolic process (GO:0006569)|tryptophan catabolic process to kynurenine (GO:0019441)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	heme binding (GO:0020037)|indoleamine 2,3-dioxygenase activity (GO:0033754)|metal ion binding (GO:0046872)|tryptophan 2,3-dioxygenase activity (GO:0004833)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(6)|ovary(2)|upper_aerodigestive_tract(1)	18						GCTCCCTCCTATCCTGGTCCA	0.463													A|||	800	0.159744	0.0227	0.2118	5008	,	,		17762	0.3343		0.1014	False		,,,				2504	0.1881				p.I140V		Atlas-SNP	.											.	IDO2	78	.	0			c.A418G						PASS	.	A	VAL/ILE	115,3659		3,109,1775	66.0	66.0	66.0		418	5.3	1.0	8	dbSNP_111	66	780,7436		28,724,3356	yes	missense	IDO2	NM_194294.2	29	31,833,5131	GG,GA,AA		9.4937,3.0472,7.4646	probably-damaging	140/421	39840234	895,11095	1887	4108	5995	SO:0001583	missense	169355	exon5			CCTCCTATCCTGG	AK128691		8p11.21	2012-04-19	2009-01-07	2009-01-07	ENSG00000188676	ENSG00000188676			27269	protein-coding gene	gene with protein product		612129	"""indoleamine-pyrrole 2,3 dioxygenase-like 1"""	INDOL1			Standard	NM_194294		Approved		uc010lwy.1	Q6ZQW0	OTTHUMG00000141271	ENST00000389060.4:c.379A>G	8.37:g.39840234A>G	ENSP00000426447:p.Ile127Val	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	59	38	0.644068	NM_194294	A4UD41	Missense_Mutation	SNP	ENST00000389060.4	37		358	0.16391941391941392	10	0.02032520325203252	67	0.1850828729281768	207	0.3618881118881119	74	0.09762532981530343	A	20.8	4.056992	0.76074	0.030472	0.094937	ENSG00000188676	ENST00000502986;ENST00000389060	T;T	0.41758	0.99;0.99	5.29	5.29	0.74685	.	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	L	0.37850	1.14	0.25863	P	0.9838042	D	0.76494	0.999	D	0.83275	0.996	T	0.38757	-0.9646	8	.	.	.	.	11.6398	0.51227	1.0:0.0:0.0:0.0	rs4736794;rs52790922;rs57148239;rs4736794	140	F5H5G0	.	V	140;127	ENSP00000443432:I140V;ENSP00000426447:I127V	.	I	+	1	0	IDO2	39959391	1.000000	0.71417	0.998000	0.56505	0.994000	0.84299	6.903000	0.75703	2.009000	0.58944	0.377000	0.23210	ATC	A|0.845;G|0.155	0.155	strong		0.463	IDO2-004	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000372742.1	NM_194294	
TRIM11	81559	hgsc.bcm.edu	37	1	228589861	228589861	+	Splice_Site	SNP	G	G	A	rs143926476		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:228589861G>A	ENST00000284551.6	-	2	688	c.410C>T	c.(409-411)gCg>gTg	p.A137V	TRIM11_ENST00000366699.3_Splice_Site_p.A137V|TRIM11_ENST00000493030.2_Missense_Mutation_p.A12V|TRIM11_ENST00000460651.1_5'Flank	NM_145214.2	NP_660215.1	Q96F44	TRI11_HUMAN	tripartite motif containing 11	137					defense response to virus (GO:0051607)|innate immune response (GO:0045087)|negative regulation of neurogenesis (GO:0050768)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of viral entry into host cell (GO:0046597)|negative regulation of viral release from host cell (GO:1902187)|negative regulation of viral transcription (GO:0032897)|positive regulation of viral entry into host cell (GO:0046598)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(12)|ovary(1)|skin(1)	18		Prostate(94;0.0724)				CTCCAGCTTCGCCTGCGGGAG	0.597																																					p.A137V		Atlas-SNP	.											.	TRIM11	38	.	0			c.C410T						PASS	.	G	VAL/ALA	2,4404	4.2+/-10.8	0,2,2201	57.0	48.0	51.0		410	0.3	0.4	1	dbSNP_134	51	0,8600		0,0,4300	no	missense-near-splice	TRIM11	NM_145214.2	64	0,2,6501	AA,AG,GG		0.0,0.0454,0.0154	benign	137/469	228589861	2,13004	2203	4300	6503	SO:0001630	splice_region_variant	81559	exon2			AGCTTCGCCTGCG	AF220125	CCDS31048.1	1q42.13	2013-01-09	2011-01-25		ENSG00000154370	ENSG00000154370		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	16281	protein-coding gene	gene with protein product		607868	"""tripartite motif-containing 11"""			11331580	Standard	NM_145214		Approved	RNF92, BIA1	uc001hss.3	Q96F44	OTTHUMG00000039773	ENST00000284551.6:c.409-1C>T	1.37:g.228589861G>A		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	132	31	0.234848	NM_145214	A6NKE2|B2RB82|B3KUS3|B4DX88|Q5VSU1|Q8NCA6|Q9C022	Missense_Mutation	SNP	ENST00000284551.6	37	CCDS31048.1	.	.	.	.	.	.	.	.	.	.	G	10.19	1.281017	0.23392	4.54E-4	0.0	ENSG00000154370	ENST00000284551;ENST00000366699	T;T	0.57436	0.4;0.4	4.56	0.332	0.15938	.	0.734180	0.11649	N	0.542981	T	0.16342	0.0393	N	0.00605	-1.335	0.09310	N	0.999998	B;B;B	0.17465	0.0;0.022;0.0	B;B;B	0.14578	0.001;0.011;0.0	T	0.18085	-1.0348	10	0.34782	T	0.22	.	1.8017	0.03073	0.3285:0.3588:0.2048:0.1079	.	137;137;137	Q96F44-3;Q96F44-2;Q96F44	.;.;TRI11_HUMAN	V	137	ENSP00000284551:A137V;ENSP00000355660:A137V	ENSP00000284551:A137V	A	-	2	0	TRIM11	226656484	0.001000	0.12720	0.445000	0.26908	0.054000	0.15201	-0.571000	0.05889	0.469000	0.27268	-0.252000	0.11476	GCG	G|1.000;A|0.000	0.000	weak		0.597	TRIM11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095995.3	NM_145214	Missense_Mutation
SLC5A8	160728	hgsc.bcm.edu	37	12	101561940	101561940	+	Silent	SNP	A	A	T	rs9634221	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:101561940A>T	ENST00000536262.2	-	11	1812	c.1254T>A	c.(1252-1254)ggT>ggA	p.G418G		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						CACCAACCATACCAAATACGC	0.383													A|||	966	0.192891	0.0703	0.0807	5008	,	,		20688	0.5427		0.1362	False		,,,				2504	0.136				p.G418G	GBM(60;420 1056 13605 22380 47675)	Atlas-SNP	.											.	SLC5A8	102	.	0			c.T1254A						PASS	.	A		306,4100	160.3+/-192.7	13,280,1910	87.0	73.0	78.0		1254	0.3	1.0	12	dbSNP_119	78	1141,7459	227.3+/-262.8	76,989,3235	no	coding-synonymous	SLC5A8	NM_145913.3		89,1269,5145	TT,TA,AA		13.2674,6.9451,11.1256		418/611	101561940	1447,11559	2203	4300	6503	SO:0001819	synonymous_variant	160728	exon11			AACCATACCAAAT	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.1254T>A	12.37:g.101561940A>T		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	120	63	0.525	NM_145913		Silent	SNP	ENST00000536262.2	37	CCDS9080.1																																																																																			A|0.847;T|0.153	0.153	strong		0.383	SLC5A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409401.1	NM_145913	
LARGE	9215	hgsc.bcm.edu	37	22	34022284	34022284	+	Silent	SNP	G	G	A	rs86487	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:34022284G>A	ENST00000354992.2	-	5	1006	c.435C>T	c.(433-435)gcC>gcT	p.A145A	LARGE_ENST00000337431.2_Silent_p.A145A|LARGE_ENST00000402320.1_Silent_p.A145A|LARGE_ENST00000437602.2_Silent_p.A145A|LARGE_ENST00000397394.2_Silent_p.A145A	NM_004737.4	NP_004728.1	O95461	LARGE_HUMAN	like-glycosyltransferase	145					glycoprotein biosynthetic process (GO:0009101)|glycosphingolipid biosynthetic process (GO:0006688)|muscle cell cellular homeostasis (GO:0046716)|N-acetylglucosamine metabolic process (GO:0006044)|protein glycosylation (GO:0006486)	integral component of Golgi membrane (GO:0030173)	acetylglucosaminyltransferase activity (GO:0008375)|transferase activity, transferring glycosyl groups (GO:0016757)			breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(23)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	51		Lung NSC(1;0.219)				CATTGTATCCGGCGCAGACAA	0.537													G|||	2068	0.412939	0.1082	0.4841	5008	,	,		19458	0.5615		0.505	False		,,,				2504	0.5266				p.A145A	Colon(70;397 1175 4573 19089 45288)	Atlas-SNP	.											LARGE,NS,carcinoma,-2,1	LARGE	98	1	0			c.C435T						PASS	.	G	,	721,3685	302.1+/-287.2	42,637,1524	104.0	83.0	90.0		435,435	0.2	1.0	22	dbSNP_79	90	4159,4441	566.6+/-388.7	1007,2145,1148	no	coding-synonymous,coding-synonymous	LARGE	NM_004737.4,NM_133642.3	,	1049,2782,2672	AA,AG,GG		48.3605,16.364,37.5211	,	145/757,145/757	34022284	4880,8126	2203	4300	6503	SO:0001819	synonymous_variant	9215	exon5			GTATCCGGCGCAG	AJ007583	CCDS13912.1	22q12.3	2013-02-22			ENSG00000133424	ENSG00000133424		"""Glycosyltransferase family 8 domain containing"""	6511	protein-coding gene	gene with protein product		603590				9892679, 10591208, 12966029	Standard	NM_004737		Approved	KIAA0609	uc003ane.4	O95461	OTTHUMG00000150914	ENST00000354992.2:c.435C>T	22.37:g.34022284G>A		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	73	35	0.479452	NM_004737	B0QXZ7|O60348|Q17R80|Q9UGD1|Q9UGE7|Q9UGG3|Q9UGZ8|Q9UH22	Silent	SNP	ENST00000354992.2	37	CCDS13912.1																																																																																			G|0.597;A|0.403	0.403	strong		0.537	LARGE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320515.2	NM_133642	
MUSK	4593	hgsc.bcm.edu	37	9	113449489	113449489	+	Missense_Mutation	SNP	C	C	T	rs35142681	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:113449489C>T	ENST00000374448.4	+	3	433	c.299C>T	c.(298-300)aCg>aTg	p.T100M	MUSK_ENST00000189978.5_Missense_Mutation_p.T100M|MUSK_ENST00000374440.3_5'UTR|MUSK_ENST00000416899.2_Missense_Mutation_p.T100M|MUSK_ENST00000374439.1_5'Flank	NM_001166281.1|NM_005592.3	NP_001159753.1|NP_005583.1	O15146	MUSK_HUMAN	muscle, skeletal, receptor tyrosine kinase	100	Ig-like 1.		T -> M (in dbSNP:rs35142681). {ECO:0000269|PubMed:17344846}.		cell differentiation (GO:0030154)|extracellular matrix organization (GO:0030198)|memory (GO:0007613)|multicellular organismal development (GO:0007275)|neuromuscular junction development (GO:0007528)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of gene expression (GO:0010628)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of protein geranylgeranylation (GO:2000541)|positive regulation of protein phosphorylation (GO:0001934)|protein autophosphorylation (GO:0046777)|regulation of synaptic growth at neuromuscular junction (GO:0008582)|regulation of transcription, DNA-templated (GO:0006355)|skeletal muscle acetylcholine-gated channel clustering (GO:0071340)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|neuromuscular junction (GO:0031594)|postsynaptic membrane (GO:0045211)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(7)|lung(23)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	49						TACTGCTGCACGGCCAACAAT	0.517													C|||	49	0.00978435	0.0015	0.0216	5008	,	,		17374	0.0		0.0308	False		,,,				2504	0.001				p.T100M		Atlas-SNP	.											.	MUSK	112	.	0			c.C299T						PASS	.	C	MET/THR,MET/THR,MET/THR	29,4035		1,27,2004	181.0	187.0	185.0		299,299,299	-7.1	0.0	9	dbSNP_126	185	254,8152		3,248,3952	yes	missense,missense,missense	MUSK	NM_001166280.1,NM_001166281.1,NM_005592.3	81,81,81	4,275,5956	TT,TC,CC		3.0217,0.7136,2.2694	benign,benign,benign	100/784,100/774,100/870	113449489	283,12187	2032	4203	6235	SO:0001583	missense	4593	exon3			GCTGCACGGCCAA	AF006464	CCDS48005.1, CCDS75874.1	9q31.3-q32	2013-01-29			ENSG00000030304	ENSG00000030304		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	7525	protein-coding gene	gene with protein product		601296				7546737	Standard	NM_005592		Approved		uc022blv.1	O15146	OTTHUMG00000020485	ENST00000374448.4:c.299C>T	9.37:g.113449489C>T	ENSP00000363571:p.Thr100Met	Somatic	212	0	0		WXS	Illumina HiSeq	Phase_I	157	157	1	NM_001166281	Q32MJ8|Q32MJ9|Q5VZW7|Q5VZW8	Missense_Mutation	SNP	ENST00000374448.4	37	CCDS48005.1	29	0.013278388278388278	1	0.0020325203252032522	6	0.016574585635359115	0	0.0	22	0.029023746701846966	C	11.55	1.672850	0.29693	0.007136	0.030217	ENSG00000030304	ENST00000189978;ENST00000374448;ENST00000543335;ENST00000374447;ENST00000545907;ENST00000416899	T	0.68765	-0.35	6.05	-7.08	0.01558	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.734616	0.13377	N	0.392447	T	0.22322	0.0538	N	0.25245	0.725	0.33065	D	0.534608	B;B	0.28233	0.164;0.204	B;B	0.24701	0.055;0.053	T	0.07462	-1.0771	10	0.48119	T	0.1	.	13.5019	0.61462	0.0999:0.6723:0.0:0.2278	rs35142681	100;100	O15146;F5H6T2	MUSK_HUMAN;.	M	100	ENSP00000363571:T100M	ENSP00000189978:T100M	T	+	2	0	MUSK	112489310	0.014000	0.17966	0.006000	0.13384	0.988000	0.76386	0.205000	0.17356	-1.188000	0.02705	-0.355000	0.07637	ACG	C|0.983;T|0.017	0.017	strong		0.517	MUSK-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding			
PCDHB16	57717	hgsc.bcm.edu	37	5	140564214	140564214	+	Silent	SNP	T	T	C	rs61739446	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	58	0	0		WXS	Illumina HiSeq	Phase_I	58	22	0.37931	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	
FAS	355	hgsc.bcm.edu	37	10	90771767	90771767	+	Missense_Mutation	SNP	G	G	A	rs56006128	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:90771767G>A	ENST00000355279.2	+	7	580	c.580G>A	c.(580-582)Gaa>Aaa	p.E194K	FAS_ENST00000357339.2_Missense_Mutation_p.E173K|FAS_ENST00000355740.2_Missense_Mutation_p.E194K|FAS_ENST00000313771.5_3'UTR|FAS_ENST00000352159.4_Missense_Mutation_p.E194K			P49327	FAS_HUMAN	Fas cell surface death receptor	0	Beta-ketoacyl synthase. {ECO:0000250}.				acetyl-CoA metabolic process (GO:0006084)|cellular lipid metabolic process (GO:0044255)|cellular response to interleukin-4 (GO:0071353)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|fatty acid metabolic process (GO:0006631)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|osteoblast differentiation (GO:0001649)|pantothenate metabolic process (GO:0015939)|positive regulation of cellular metabolic process (GO:0031325)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|glycogen granule (GO:0042587)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	3-hydroxyoctanoyl-[acyl-carrier-protein] dehydratase activity (GO:0047451)|3-hydroxypalmitoyl-[acyl-carrier-protein] dehydratase activity (GO:0004317)|3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity (GO:0004316)|3-oxoacyl-[acyl-carrier-protein] synthase activity (GO:0004315)|[acyl-carrier-protein] S-acetyltransferase activity (GO:0004313)|[acyl-carrier-protein] S-malonyltransferase activity (GO:0004314)|drug binding (GO:0008144)|enoyl-[acyl-carrier-protein] reductase (NADPH, A-specific) activity (GO:0047117)|enoyl-[acyl-carrier-protein] reductase (NADPH, B-specific) activity (GO:0004319)|fatty acid synthase activity (GO:0004312)|myristoyl-[acyl-carrier-protein] hydrolase activity (GO:0016295)|NADPH binding (GO:0070402)|oleoyl-[acyl-carrier-protein] hydrolase activity (GO:0004320)|palmitoyl-[acyl-carrier-protein] hydrolase activity (GO:0016296)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(1)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(3)|lung(5)|upper_aerodigestive_tract(2)	18		Colorectal(252;0.0161)		Colorectal(12;0.000136)|COAD - Colon adenocarcinoma(12;0.000193)	Cerulenin(DB01034)|Orlistat(DB01083)	GAAGAGAAAGGAAGTACAGAA	0.358													G|||	3	0.000599042	0.0	0.0014	5008	,	,		20137	0.0		0.002	False		,,,				2504	0.0				p.E194K		Atlas-SNP	.											.	FAS	47	.	0			c.G580A	GRCh37	CM065175	FAS	M	rs56006128	PASS	.	G	LYS/GLU,LYS/GLU,LYS/GLU	3,4403	6.2+/-15.9	0,3,2200	104.0	107.0	106.0		580,517,580		0.0	10	dbSNP_129	106	29,8571	19.8+/-62.0	0,29,4271	yes	missense,missense,missense	FAS	NM_000043.4,NM_152871.2,NM_152872.2	56,56,56	0,32,6471	AA,AG,GG		0.3372,0.0681,0.246	benign,benign,benign	194/336,173/315,194/221	90771767	32,12974	2203	4300	6503	SO:0001583	missense	355	exon7			AGAAAGGAAGTAC	M67454	CCDS7393.1, CCDS7394.1, CCDS7395.1	10q24.1	2014-09-17	2013-05-22	2005-01-07	ENSG00000026103	ENSG00000026103		"""Tumor necrosis factor receptor superfamily"", ""CD molecules"""	11920	protein-coding gene	gene with protein product	"""TNF receptor superfamily member 6"""	134637	"""tumor necrosis factor receptor superfamily, member 6"", ""Fas (TNF receptor superfamily, member 6)"""	FAS1, APT1, TNFRSF6		1385299, 1385309	Standard	NM_000043		Approved	CD95, APO-1	uc001kfr.3	P25445	OTTHUMG00000018701	ENST00000355279.2:c.580G>A	10.37:g.90771767G>A	ENSP00000347426:p.Glu194Lys	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	54	27	0.5	NM_152872	Q13479|Q16702|Q4LE83|Q6P4U5|Q6SS02|Q969R1|Q96C68|Q96IT0	Missense_Mutation	SNP	ENST00000355279.2	37	CCDS7395.1	3	0.0013736263736263737	0	0.0	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	G	0.005	-2.233006	0.00277	6.81E-4	0.003372	ENSG00000026103	ENST00000540197;ENST00000355740;ENST00000352159;ENST00000357339;ENST00000355279;ENST00000371875	D;T;D;T	0.92595	-3.07;-0.6;-2.09;-0.49	.	.	.	.	1209.270000	0.00166	U	0.000004	T	0.74489	0.3723	N	0.00583	-1.355	0.09310	N	1	B;B;B	0.14805	0.001;0.0;0.011	B;B;B	0.01281	0.0;0.0;0.0	T	0.69895	-0.5021	8	0.28530	T	0.3	.	.	.	.	rs56006128	173;194;194	P25445-6;Q5T9P3;P25445	.;.;TNR6_HUMAN	K	221;194;194;173;194;194	ENSP00000347979:E194K;ENSP00000345601:E194K;ENSP00000349896:E173K;ENSP00000347426:E194K	ENSP00000345601:E194K	E	+	1	0	FAS	90761747	.	.	0.010000	0.14722	0.014000	0.08584	.	.	0.119000	0.18210	0.121000	0.15741	GAA	G|0.999;A|0.001	0.001	strong		0.358	FAS-011	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000049280.2		
CDH2	1000	hgsc.bcm.edu	37	18	25593740	25593740	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:25593740G>T	ENST00000269141.3	-	3	729	c.306C>A	c.(304-306)ttC>ttA	p.F102L	CDH2_ENST00000399380.3_Missense_Mutation_p.F71L	NM_001792.3	NP_001783.2	P19022	CADH2_HUMAN	cadherin 2, type 1, N-cadherin (neuronal)	102					adherens junction organization (GO:0034332)|blood vessel morphogenesis (GO:0048514)|calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell migration (GO:0016477)|cell-cell adhesion mediated by cadherin (GO:0044331)|cell-cell junction organization (GO:0045216)|glial cell differentiation (GO:0010001)|heterophilic cell-cell adhesion (GO:0007157)|homophilic cell adhesion (GO:0007156)|muscle cell differentiation (GO:0042692)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|neuronal stem cell maintenance (GO:0097150)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of muscle cell differentiation (GO:0051149)|striated muscle cell differentiation (GO:0051146)	apical plasma membrane (GO:0016324)|catenin complex (GO:0016342)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intercalated disc (GO:0014704)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|synapse (GO:0045202)	alpha-catenin binding (GO:0045294)|beta-catenin binding (GO:0008013)|calcium ion binding (GO:0005509)|gamma-catenin binding (GO:0045295)			NS(1)|breast(5)|cervix(2)|endometrium(7)|kidney(3)|large_intestine(22)|lung(32)|ovary(4)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	82						CATATATCAGGAACTTGGCAT	0.458																																					p.F102L		Atlas-SNP	.											CDH2,NS,carcinoma,-1,1	CDH2	194	1	0			c.C306A						scavenged	.						181.0	170.0	174.0					18																	25593740		2203	4300	6503	SO:0001583	missense	1000	exon3			TATCAGGAACTTG	S42303	CCDS11891.1	18q12.1	2010-01-26			ENSG00000170558	ENSG00000170558		"""CD molecules"", ""Cadherins / Major cadherins"""	1759	protein-coding gene	gene with protein product	"""N-cadherin"""	114020		NCAD		2384753, 7731968, 2216790	Standard	NM_001792		Approved	CDHN, CD325	uc002kwg.2	P19022	OTTHUMG00000059940	ENST00000269141.3:c.306C>A	18.37:g.25593740G>T	ENSP00000269141:p.Phe102Leu	Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	131	5	0.0381679	NM_001792	A8MWK3|B0YIY6|Q14923|Q8N173	Missense_Mutation	SNP	ENST00000269141.3	37	CCDS11891.1	.	.	.	.	.	.	.	.	.	.	G	15.78	2.935194	0.52866	.	.	ENSG00000170558	ENST00000269141;ENST00000399380;ENST00000418492;ENST00000430882;ENST00000413878	T;T;T;T;T	0.58506	0.33;0.33;0.33;0.33;0.33	5.55	5.55	0.83447	Cadherin prodomain-like (1);Cadherin-like (1);	0.052264	0.85682	D	0.000000	T	0.52917	0.1764	L	0.54965	1.715	0.44214	D	0.997045	B;B	0.17465	0.022;0.002	B;B	0.26864	0.074;0.005	T	0.52601	-0.8554	10	0.51188	T	0.08	.	9.7395	0.40409	0.159:0.0:0.841:0.0	.	71;102	A8MWK3;P19022	.;CADH2_HUMAN	L	102;71;51;17;17	ENSP00000269141:F102L;ENSP00000382312:F71L;ENSP00000411360:F51L;ENSP00000412120:F17L;ENSP00000414269:F17L	ENSP00000269141:F102L	F	-	3	2	CDH2	23847738	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.749000	0.38319	2.616000	0.88540	0.585000	0.79938	TTC	.	.	none		0.458	CDH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133246.3	NM_001792	
CATSPER3	347732	hgsc.bcm.edu	37	5	134343661	134343661	+	Silent	SNP	C	C	T	rs10044000	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:134343661C>T	ENST00000282611.6	+	4	593	c.507C>T	c.(505-507)gcC>gcT	p.A169A		NM_178019.2	NP_821138.1	Q86XQ3	CTSR3_HUMAN	cation channel, sperm associated 3	169					calcium ion import (GO:0070509)|membrane depolarization during action potential (GO:0086010)|multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|single fertilization (GO:0007338)|sodium ion transport (GO:0006814)|sperm capacitation (GO:0048240)|sperm motility (GO:0030317)|sperm-egg recognition (GO:0035036)	acrosomal vesicle (GO:0001669)|CatSper complex (GO:0036128)|endoplasmic reticulum (GO:0005783)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|voltage-gated calcium channel activity (GO:0005245)	p.A169A(1)		NS(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|stomach(1)|urinary_tract(1)	18			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			TGATCACCGCCGTGGGGCAGA	0.592													C|||	1358	0.271166	0.1467	0.2911	5008	,	,		13373	0.2569		0.4254	False		,,,				2504	0.2812				p.A169A		Atlas-SNP	.											CATSPER3,NS,carcinoma,0,1	CATSPER3	38	1	1	Substitution - coding silent(1)	stomach(1)	c.C507T						PASS	.	C		813,3593	324.8+/-298.8	65,683,1455	190.0	138.0	156.0		507	-2.0	0.0	5	dbSNP_119	156	3585,5015	518.2+/-379.2	751,2083,1466	no	coding-synonymous	CATSPER3	NM_178019.2		816,2766,2921	TT,TC,CC		41.686,18.4521,33.8152		169/399	134343661	4398,8608	2203	4300	6503	SO:0001819	synonymous_variant	347732	exon4			CACCGCCGTGGGG	AF432876	CCDS4181.1	5q31.2	2011-07-05			ENSG00000152705	ENSG00000152705		"""Voltage-gated ion channels / Cation channels, sperm associated"""	20819	protein-coding gene	gene with protein product		609120				12646162, 12932298, 17227845, 16382101	Standard	NM_178019		Approved	CACRC	uc003lag.3	Q86XQ3	OTTHUMG00000129137	ENST00000282611.6:c.507C>T	5.37:g.134343661C>T		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	126	58	0.460317	NM_178019	Q86XS6	Silent	SNP	ENST00000282611.6	37	CCDS4181.1																																																																																			C|0.678;T|0.322	0.322	strong		0.592	CATSPER3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251191.2	NM_178019	
AFAP1L1	134265	hgsc.bcm.edu	37	5	148680717	148680717	+	Missense_Mutation	SNP	G	G	A	rs61734415	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:148680717G>A	ENST00000296721.4	+	4	349	c.251G>A	c.(250-252)cGg>cAg	p.R84Q	AFAP1L1_ENST00000515000.1_Missense_Mutation_p.R84Q|AFAP1L1_ENST00000522492.1_3'UTR	NM_001146337.1|NM_152406.2	NP_001139809.1|NP_689619.1	Q8TED9	AF1L1_HUMAN	actin filament associated protein 1-like 1	84				R -> Q (in Ref. 2; BAC04664). {ECO:0000305}.		cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(1)|endometrium(3)|kidney(1)|large_intestine(6)|liver(1)|lung(10)|ovary(1)|pancreas(1)|skin(2)	26			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AGTGACCTTCGGGACATGCCA	0.592													G|||	46	0.0091853	0.0015	0.0101	5008	,	,		16787	0.0		0.0338	False		,,,				2504	0.0031				p.R84Q		Atlas-SNP	.											AFAP1L1,NS,carcinoma,+1,1	AFAP1L1	86	1	0			c.G251A						PASS	.	G	GLN/ARG,GLN/ARG	43,4363	46.0+/-80.4	0,43,2160	105.0	99.0	101.0		251,251	0.6	1.0	5	dbSNP_129	101	384,8216	126.0+/-184.5	8,368,3924	yes	missense,missense	AFAP1L1	NM_001146337.1,NM_152406.2	43,43	8,411,6084	AA,AG,GG		4.4651,0.9759,3.2831	benign,benign	84/726,84/769	148680717	427,12579	2203	4300	6503	SO:0001583	missense	134265	exon4			ACCTTCGGGACAT	AK094067	CCDS34274.1, CCDS54932.1	5q33.1	2013-01-10			ENSG00000157510	ENSG00000157510		"""Pleckstrin homology (PH) domain containing"""	26714	protein-coding gene	gene with protein product		614410					Standard	NM_152406		Approved	FLJ36748	uc003lqh.3	Q8TED9	OTTHUMG00000163441	ENST00000296721.4:c.251G>A	5.37:g.148680717G>A	ENSP00000296721:p.Arg84Gln	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	70	35	0.5	NM_001146337	Q08AN4|Q08AN5|Q8IW82|Q8N8Z5|Q8N9Q4	Missense_Mutation	SNP	ENST00000296721.4	37	CCDS34274.1	38	0.0173992673992674	2	0.0040650406504065045	6	0.016574585635359115	0	0.0	30	0.0395778364116095	G	8.165	0.790456	0.16258	0.009759	0.044651	ENSG00000157510	ENST00000296721;ENST00000515000	T;T	0.40476	1.03;1.03	5.01	0.557	0.17260	.	0.349373	0.29522	N	0.011911	T	0.06325	0.0163	L	0.33485	1.01	0.34167	D	0.669394	B;B;B	0.21147	0.002;0.001;0.052	B;B;B	0.12156	0.007;0.001;0.003	T	0.26155	-1.0111	10	0.08837	T	0.75	-13.3407	10.3008	0.43650	0.487:0.0:0.513:0.0	rs61734415	84;84;84	Q8TED9-2;Q8TED9;Q8TED9-3	.;AF1L1_HUMAN;.	Q	84	ENSP00000296721:R84Q;ENSP00000424427:R84Q	ENSP00000296721:R84Q	R	+	2	0	AFAP1L1	148660910	0.995000	0.38212	0.995000	0.50966	0.906000	0.53458	0.499000	0.22546	0.162000	0.19483	-0.254000	0.11334	CGG	G|0.972;A|0.028	0.028	strong		0.592	AFAP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373443.1	NM_152406	
CABLES2	81928	hgsc.bcm.edu	37	20	60966374	60966374	+	Silent	SNP	G	G	C	rs13042761	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:60966374G>C	ENST00000279101.5	-	9	1235	c.1227C>G	c.(1225-1227)ggC>ggG	p.G409G		NM_031215.2	NP_112492.2	Q9BTV7	CABL2_HUMAN	Cdk5 and Abl enzyme substrate 2	409					cell cycle (GO:0007049)|cell division (GO:0051301)|regulation of cell cycle (GO:0051726)|regulation of cell division (GO:0051302)		cyclin-dependent protein serine/threonine kinase regulator activity (GO:0016538)			endometrium(2)|kidney(1)|lung(6)|pancreas(1)|skin(1)	11	Breast(26;2.05e-08)		BRCA - Breast invasive adenocarcinoma(19;4.36e-06)			GCACGCAGGCGCCAGCGCACA	0.647													G|||	447	0.0892572	0.2141	0.0677	5008	,	,		18046	0.001		0.0646	False		,,,				2504	0.0521				p.G409G		Atlas-SNP	.											.	CABLES2	30	.	0			c.C1227G						PASS	.	G		788,3618	313.3+/-293.0	66,656,1481	75.0	76.0	76.0		1227	-5.4	0.8	20	dbSNP_121	76	615,7985	160.1+/-213.3	27,561,3712	no	coding-synonymous	CABLES2	NM_031215.2		93,1217,5193	CC,CG,GG		7.1512,17.8847,10.7873		409/479	60966374	1403,11603	2203	4300	6503	SO:0001819	synonymous_variant	81928	exon9			GCAGGCGCCAGCG	BC003122	CCDS33503.1	20q13.33	2004-01-09	2004-01-09	2004-01-09	ENSG00000149679	ENSG00000149679			16143	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 150"""	C20orf150		12477932	Standard	NM_031215		Approved	dJ908M14.2, ik3-2	uc002ycv.2	Q9BTV7	OTTHUMG00000032912	ENST00000279101.5:c.1227C>G	20.37:g.60966374G>C		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	61	27	0.442623	NM_031215	Q5JWL0|Q9BYK0	Silent	SNP	ENST00000279101.5	37	CCDS33503.1	197	0.0902014652014652	121	0.2459349593495935	29	0.08011049723756906	1	0.0017482517482517483	46	0.06068601583113457	G	9.632	1.136688	0.21123	0.178847	0.071512	ENSG00000149679	ENST00000453274	.	.	.	5.56	-5.4	0.02656	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999792	.	.	.	.	.	.	T	0.35500	-0.9786	3	.	.	.	-36.4946	4.0011	0.09580	0.1792:0.5061:0.113:0.2016	rs13042761;rs60915086	.	.	.	G	203	.	.	A	-	2	0	CABLES2	60399769	0.003000	0.15002	0.803000	0.32268	0.917000	0.54804	-1.346000	0.02634	-0.706000	0.05028	-1.157000	0.01802	GCG	G|0.891;C|0.109	0.109	strong		0.647	CABLES2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080027.2	XM_037265	
MLC1	23209	hgsc.bcm.edu	37	22	50515273	50515273	+	Silent	SNP	G	G	A	rs267607236|rs6010165	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:50515273G>A	ENST00000311597.5	-	7	1200	c.594C>T	c.(592-594)taC>taT	p.Y198Y	MLC1_ENST00000535444.1_Silent_p.Y119Y|MLC1_ENST00000450140.2_Silent_p.Y146Y|MLC1_ENST00000538737.1_Silent_p.Y164Y|MLC1_ENST00000431262.2_Silent_p.Y168Y|MLC1_ENST00000395876.2_Silent_p.Y198Y	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	65	0	0		WXS	Illumina HiSeq	Phase_I	53	26	0.490566	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	
C5orf60	285679	hgsc.bcm.edu	37	5	179071836	179071836	+	Silent	SNP	C	C	T	rs4990391	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:179071836C>T	ENST00000448248.2	-	1	211	c.186G>A	c.(184-186)ccG>ccA	p.P62P	C5orf60_ENST00000506142.1_Intron	NM_001142306.1	NP_001135778.1	A6NFR6	CE060_HUMAN	chromosome 5 open reading frame 60	62						integral component of membrane (GO:0016021)				NS(1)|breast(1)|kidney(5)	7						GCACTGAGGACGGCTCCCTGG	0.532													-|||	717	0.143171	0.171	0.0951	5008	,	,		22464	0.0546		0.2256	False		,,,				2504	0.1462				p.P62P		Atlas-SNP	.											C5orf60,colon,carcinoma,0,1	C5orf60	24	1	0			c.G186A						PASS	.						64.0	60.0	62.0					5																	179071836		692	1591	2283	SO:0001819	synonymous_variant	285679	exon1			TGAGGACGGCTCC	BC043435	CCDS47353.1	5q35.3	2010-08-19			ENSG00000204661	ENSG00000204661			27753	protein-coding gene	gene with protein product						12477932	Standard	NM_001142306		Approved		uc003mki.3	A6NFR6	OTTHUMG00000163221	ENST00000448248.2:c.186G>A	5.37:g.179071836C>T		Somatic	248	0	0		WXS	Illumina HiSeq	Phase_I	150	149	0.993333	NM_001142306	A1L488|B7ZM52|B7ZM53	Silent	SNP	ENST00000448248.2	37	CCDS47353.1																																																																																			C|0.848;T|0.152	0.152	strong		0.532	C5orf60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372148.2	NM_001142306	
DUSP2	1844	hgsc.bcm.edu	37	2	96810609	96810609	+	Missense_Mutation	SNP	C	C	T	rs572028879		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:96810609C>T	ENST00000288943.4	-	2	486	c.401G>A	c.(400-402)gGc>gAc	p.G134D	AC012307.2_ENST00000449242.1_lincRNA	NM_004418.3	NP_004409.1	Q05923	DUS2_HUMAN	dual specificity phosphatase 2	134	Rhodanese. {ECO:0000255|PROSITE- ProRule:PRU00173}.				endoderm formation (GO:0001706)|inactivation of MAPK activity (GO:0000188)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	nucleus (GO:0005634)	MAP kinase tyrosine/serine/threonine phosphatase activity (GO:0017017)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)|protein tyrosine/threonine phosphatase activity (GO:0008330)			NS(1)|breast(1)|lung(2)|skin(1)	5		Ovarian(717;0.0228)				GCCCTGGAAGCCGTCGAAGCC	0.697													C|||	1	0.000199681	0.0008	0.0	5008	,	,		11195	0.0		0.0	False		,,,				2504	0.0				p.G134D		Atlas-SNP	.											.	DUSP2	20	.	0			c.G401A						PASS	.						15.0	20.0	18.0					2																	96810609		2094	4175	6269	SO:0001583	missense	1844	exon2			TGGAAGCCGTCGA	L11329	CCDS2016.1	2q11	2011-06-09			ENSG00000158050	ENSG00000158050		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : MAP kinase phosphatases"""	3068	protein-coding gene	gene with protein product		603068				7806236, 7590752, 12673251	Standard	NM_004418		Approved	PAC-1	uc002svk.4	Q05923	OTTHUMG00000130456	ENST00000288943.4:c.401G>A	2.37:g.96810609C>T	ENSP00000288943:p.Gly134Asp	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	80	26	0.325	NM_004418	Q53T45	Missense_Mutation	SNP	ENST00000288943.4	37	CCDS2016.1	.	.	.	.	.	.	.	.	.	.	C	3.560	-0.089892	0.07053	.	.	ENSG00000158050	ENST00000288943	T	0.26373	1.74	4.31	2.38	0.29361	Rhodanese-like (5);	0.285507	0.32736	N	0.005712	T	0.26774	0.0655	L	0.58101	1.795	0.25586	N	0.986743	B	0.31459	0.324	B	0.37091	0.241	T	0.14504	-1.0470	10	0.28530	T	0.3	.	10.6808	0.45813	0.0:0.5226:0.4774:0.0	.	134	Q05923	DUS2_HUMAN	D	134	ENSP00000288943:G134D	ENSP00000288943:G134D	G	-	2	0	DUSP2	96174336	0.037000	0.19845	0.471000	0.27229	0.207000	0.24258	0.181000	0.16880	0.349000	0.23975	0.456000	0.33151	GGC	.	.	none		0.697	DUSP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252847.1	NM_004418	
SERGEF	26297	hgsc.bcm.edu	37	11	17981047	17981047	+	Silent	SNP	C	C	T	rs211146	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:17981047C>T	ENST00000265965.5	-	9	1132	c.981G>A	c.(979-981)tcG>tcA	p.S327S	SERGEF_ENST00000528200.1_Intron|SERGEF_ENST00000532265.1_Intron	NM_012139.2	NP_036271.1	Q9UGK8	SRGEF_HUMAN	secretion regulating guanine nucleotide exchange factor	327					negative regulation of protein secretion (GO:0050709)|positive regulation of Ran GTPase activity (GO:0032853)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|nucleolus (GO:0005730)|nucleus (GO:0005634)	Ran guanyl-nucleotide exchange factor activity (GO:0005087)			autonomic_ganglia(1)|central_nervous_system(1)|large_intestine(5)|lung(5)	12						AATGCGGAGACGAAGGCATGC	0.453													T|||	3448	0.688498	0.9221	0.5836	5008	,	,		22490	0.4881		0.6044	False		,,,				2504	0.7403				p.S327S		Atlas-SNP	.											.	SERGEF	38	.	0			c.G981A						PASS	.	T		3811,589	258.3+/-262.4	1653,505,42	106.0	100.0	102.0		981	-12.3	0.0	11	dbSNP_79	102	5264,3322	495.1+/-374.0	1623,2018,652	no	coding-synonymous	SERGEF	NM_012139.2		3276,2523,694	TT,TC,CC		38.6909,13.3864,30.117		327/459	17981047	9075,3911	2200	4293	6493	SO:0001819	synonymous_variant	26297	exon9			CGGAGACGAAGGC	AJ243950	CCDS7828.1	11p14.3	2006-03-09			ENSG00000129158	ENSG00000129158			17499	protein-coding gene	gene with protein product		606051				10571079, 12459492	Standard	NM_012139		Approved	DelGEF, Gnefr	uc001mnm.3	Q9UGK8	OTTHUMG00000166420	ENST00000265965.5:c.981G>A	11.37:g.17981047C>T		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	44	44	1	NM_012139	Q9UGK9	Silent	SNP	ENST00000265965.5	37	CCDS7828.1	1383|1383	0.6332417582417582|0.6332417582417582	447|447	0.9085365853658537|0.9085365853658537	211|211	0.5828729281767956|0.5828729281767956	271|271	0.4737762237762238|0.4737762237762238	454|454	0.5989445910290238|0.5989445910290238	T|T	13.34|13.34	2.209462|2.209462	0.39003|0.39003	0.866136|0.866136	0.613091|0.613091	ENSG00000129158|ENSG00000129158	ENST00000529151|ENST00000533241	.|.	.|.	.|.	6.17|6.17	-12.3|-12.3	0.00002|0.00002	.|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.48185|0.48185	P|P	3.950000000000342E-4|3.950000000000342E-4	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.16571|0.16571	-1.0398|-1.0398	3|3	.|.	.|.	.|.	-5.0328|-5.0328	7.6256|7.6256	0.28210|0.28210	0.0709:0.417:0.3637:0.1485|0.0709:0.417:0.3637:0.1485	rs211146;rs502846;rs17793954;rs57664433;rs211146|rs211146;rs502846;rs17793954;rs57664433;rs211146	.|.	.|.	.|.	H|I	191|100	.|.	.|.	R|V	-|-	2|1	0|0	SERGEF|SERGEF	17937623|17937623	0.000000|0.000000	0.05858|0.05858	0.002000|0.002000	0.10522|0.10522	0.921000|0.921000	0.55340|0.55340	-4.254000|-4.254000	0.00265|0.00265	-3.475000|-3.475000	0.00156|0.00156	-0.254000|-0.254000	0.11334|0.11334	CGT|GTC	C|0.326;T|0.674	0.674	strong		0.453	SERGEF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389538.1	NM_012139	
AHNAK	79026	hgsc.bcm.edu	37	11	62284888	62284888	+	Silent	SNP	G	G	A	rs11555628	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:62284888G>A	ENST00000378024.4	-	5	17275	c.17001C>T	c.(16999-17001)acC>acT	p.T5667T	AHNAK_ENST00000257247.7_Intron|AHNAK_ENST00000525875.1_5'Flank|AHNAK_ENST00000530124.1_Intron	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	139	0	0		WXS	Illumina HiSeq	Phase_I	126	21	0.166667	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	
TMPRSS4	56649	hgsc.bcm.edu	37	11	117979606	117979606	+	Missense_Mutation	SNP	G	G	C	rs45441097	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:117979606G>C	ENST00000437212.3	+	7	792	c.578G>C	c.(577-579)tGt>tCt	p.C193S	TMPRSS4_ENST00000534111.1_Missense_Mutation_p.C191S|TMPRSS4_ENST00000522824.1_Missense_Mutation_p.C188S|TMPRSS4_ENST00000522307.1_Missense_Mutation_p.C46S|TMPRSS4_ENST00000523251.1_Missense_Mutation_p.C153S			Q9NRS4	TMPS4_HUMAN	transmembrane protease, serine 4	193	SRCR. {ECO:0000255|PROSITE- ProRule:PRU00196}.				proteolysis (GO:0006508)	integral component of membrane (GO:0016021)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)			breast(2)|central_nervous_system(2)|large_intestine(3)|lung(8)|ovary(1)|prostate(2)|skin(1)	19	all_hematologic(175;0.0487)	Medulloblastoma(222;0.0431)|all_hematologic(192;0.164)|Breast(348;0.183)|all_neural(223;0.238)		BRCA - Breast invasive adenocarcinoma(274;4.16e-05)|Epithelial(105;0.00204)		TCCCTGCACTGTCTTGGTGAG	0.567													G|||	13	0.00259585	0.0	0.0086	5008	,	,		20409	0.0		0.006	False		,,,				2504	0.001				p.C193S		Atlas-SNP	.											.	TMPRSS4	46	.	0			c.G578C						PASS	.	G	SER/CYS,SER/CYS,SER/CYS,SER/CYS	4,4396	8.1+/-20.4	0,4,2196	108.0	92.0	97.0		563,572,458,578	4.9	1.0	11	dbSNP_127	97	44,8548	28.5+/-78.6	0,44,4252	yes	missense,missense,missense,missense	TMPRSS4	NM_001083947.1,NM_001173551.1,NM_001173552.1,NM_019894.3	112,112,112,112	0,48,6448	CC,CG,GG		0.5121,0.0909,0.3695	probably-damaging,probably-damaging,probably-damaging,probably-damaging	188/433,191/436,153/398,193/438	117979606	48,12944	2200	4296	6496	SO:0001583	missense	56649	exon7			TGCACTGTCTTGG	AF179224	CCDS31684.1, CCDS44743.1, CCDS53716.1, CCDS53717.1	11q23.3	2010-04-13			ENSG00000137648	ENSG00000137648		"""Serine peptidases / Transmembrane"""	11878	protein-coding gene	gene with protein product	"""transmembrane serine protease 3"", ""membrane-type serine protease 2"", ""type II membrane serine protease"""	606565				10825129	Standard	NM_001083947		Approved	TMPRSS3, MT-SP2	uc021qrd.1	Q9NRS4	OTTHUMG00000164122	ENST00000437212.3:c.578G>C	11.37:g.117979606G>C	ENSP00000416037:p.Cys193Ser	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	63	42	0.666667	NM_019894	A8MU84|B0YJB0|B7Z8C5|E7ERX8|Q5XKQ6|Q6UX37|Q9NZA5	Missense_Mutation	SNP	ENST00000437212.3	37	CCDS31684.1	7	0.003205128205128205	0	0.0	3	0.008287292817679558	0	0.0	4	0.005277044854881266	G	20.7	4.036391	0.75617	9.09E-4	0.005121	ENSG00000137648	ENST00000534111;ENST00000522307;ENST00000523251;ENST00000437212;ENST00000522824;ENST00000522151	D;T;D;D;D;D	0.98926	-5.24;0.26;-5.24;-5.24;-5.24;-5.24	4.93	4.93	0.64822	Speract/scavenger receptor-related (2);	0.000000	0.64402	D	0.000007	D	0.98839	0.9608	M	0.88640	2.97	0.58432	D	0.999999	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.91635	0.997;0.996;0.997;0.999;0.998	D	0.95989	0.8984	10	0.87932	D	0	.	15.1719	0.72881	0.0:0.0:1.0:0.0	rs45441097	168;153;46;193;191	B7Z900;E7ERX8;E7ESG9;Q9NRS4;Q9NRS4-3	.;.;.;TMPS4_HUMAN;.	S	191;46;153;193;188;140	ENSP00000435184:C191S;ENSP00000428814:C46S;ENSP00000429209:C153S;ENSP00000416037:C193S;ENSP00000430547:C188S;ENSP00000428407:C140S	ENSP00000416037:C193S	C	+	2	0	TMPRSS4	117484816	0.998000	0.40836	0.964000	0.40570	0.803000	0.45373	5.377000	0.66184	2.564000	0.86499	0.561000	0.74099	TGT	G|0.997;C|0.003	0.003	strong		0.567	TMPRSS4-004	KNOWN	non_canonical_polymorphism|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000377328.2	NM_019894	
TES	26136	hgsc.bcm.edu	37	7	115897392	115897392	+	Silent	SNP	G	G	C	rs4710	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:115897392G>C	ENST00000358204.4	+	7	1337	c.1122G>C	c.(1120-1122)cgG>cgC	p.R374R	AC073130.3_ENST00000444244.1_RNA|AC002066.1_ENST00000446355.2_RNA|TES_ENST00000537767.1_Silent_p.R132R|TES_ENST00000393481.2_Silent_p.R365R	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	161	0	0		WXS	Illumina HiSeq	Phase_I	158	158	1	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	
DEF8	54849	hgsc.bcm.edu	37	16	90015960	90015960	+	Silent	SNP	G	G	C	rs6500462	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:90015960G>C	ENST00000268676.7	+	2	176	c.87G>C	c.(85-87)ggG>ggC	p.G29G	DEF8_ENST00000418391.2_Intron|DEF8_ENST00000567874.1_Intron|DEF8_ENST00000569453.1_Intron|DEF8_ENST00000563795.1_Intron|DEF8_ENST00000563594.1_Intron|DEF8_ENST00000570182.1_Intron	NM_207514.2	NP_997397.1	Q6ZN54	DEFI8_HUMAN	differentially expressed in FDCP 8 homolog (mouse)	29					intracellular signal transduction (GO:0035556)		zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(1)|large_intestine(1)|lung(8)|upper_aerodigestive_tract(1)	12		all_cancers(9;7.59e-13)|Lung NSC(15;1.56e-06)|all_lung(18;2.18e-06)|all_neural(9;0.0019)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.0274)		CGCACACCGGGGTGACTTCTC	0.677													G|||	135	0.0269569	0.0061	0.0202	5008	,	,		13884	0.001		0.0775	False		,,,				2504	0.0348				p.G29G		Atlas-SNP	.											.	DEF8	28	.	0			c.G87C						PASS	.	G	,,,,,,,,	81,4315	69.8+/-107.6	2,77,2119	67.0	66.0	66.0		,,,,,,,,87	0.8	0.0	16	dbSNP_116	66	784,7816	183.5+/-231.7	35,714,3551	no	intron,intron,intron,intron,intron,intron,intron,intron,coding-synonymous	DEF8	NM_001242816.1,NM_001242817.1,NM_001242818.1,NM_001242819.1,NM_001242820.1,NM_001242821.1,NM_001242822.1,NM_017702.3,NM_207514.2	,,,,,,,,	37,791,5670	CC,CG,GG		9.1163,1.8426,6.6559	,,,,,,,,	,,,,,,,,29/513	90015960	865,12131	2198	4300	6498	SO:0001819	synonymous_variant	54849	exon2			CACCGGGGTGACT	AK131370	CCDS10989.1, CCDS45555.1, CCDS58493.1, CCDS58494.1, CCDS58495.1, CCDS58496.1	16q24.3	2011-01-31			ENSG00000140995	ENSG00000140995			25969	protein-coding gene	gene with protein product						12477932	Standard	NM_207514		Approved	FLJ20186	uc002fpn.2	Q6ZN54	OTTHUMG00000138989	ENST00000268676.7:c.87G>C	16.37:g.90015960G>C		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	132	33	0.25	NM_207514	B3KT65|B4DK62|B4E0S9|B7Z3H6|H3BUG7|Q8N8N3|Q9NXL0	Silent	SNP	ENST00000268676.7	37	CCDS10989.1																																																																																			G|0.947;C|0.053	0.053	strong		0.677	DEF8-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000272878.1	NM_207514	
BRDT	676	hgsc.bcm.edu	37	1	92442695	92442695	+	Missense_Mutation	SNP	A	A	C	rs1156281	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:92442695A>C	ENST00000362005.3	+	7	1132	c.714A>C	c.(712-714)aaA>aaC	p.K238N	BRDT_ENST00000394530.3_Missense_Mutation_p.K192N|BRDT_ENST00000484781.1_3'UTR|BRDT_ENST00000370389.2_Missense_Mutation_p.K165N|BRDT_ENST00000402388.1_Missense_Mutation_p.K238N|BRDT_ENST00000399546.2_Missense_Mutation_p.K238N	NM_001242805.1	NP_001229734	Q58F21	BRDT_HUMAN	bromodomain, testis-specific	238			K -> N (in dbSNP:rs1156281). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17344846}.		cell differentiation (GO:0030154)|chromatin remodeling (GO:0006338)|histone displacement (GO:0001207)|male meiosis (GO:0007140)|male meiosis I (GO:0007141)|mRNA processing (GO:0006397)|positive regulation of transcription during meiosis (GO:0051039)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	histone binding (GO:0042393)|lysine-acetylated histone binding (GO:0070577)|transcription coactivator activity (GO:0003713)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(24)|ovary(1)|prostate(4)|skin(2)|stomach(2)|urinary_tract(2)	56		all_lung(203;0.00531)|Lung NSC(277;0.0194)		all cancers(265;0.0228)|Epithelial(280;0.133)		TCACAGAAAAATCAGTGGCAC	0.368													A|||	947	0.189097	0.1513	0.134	5008	,	,		19037	0.3859		0.0755	False		,,,				2504	0.1933				p.K242N		Atlas-SNP	.											.	BRDT	133	.	0			c.A726C						PASS	.	A	ASN/LYS,ASN/LYS,ASN/LYS,ASN/LYS,ASN/LYS,ASN/LYS,ASN/LYS	562,3844	244.3+/-253.7	39,484,1680	58.0	56.0	57.0		714,726,576,576,495,714,714	3.2	0.2	1	dbSNP_87	57	497,8103	142.2+/-198.4	18,461,3821	yes	missense,missense,missense,missense,missense,missense,missense	BRDT	NM_001242805.1,NM_001242806.1,NM_001242807.1,NM_001242808.1,NM_001242810.1,NM_001726.3,NM_207189.2	94,94,94,94,94,94,94	57,945,5501	CC,CA,AA		5.7791,12.7553,8.1424	benign,benign,benign,benign,benign,benign,benign	238/948,242/952,192/902,192/902,165/875,238/948,238/948	92442695	1059,11947	2203	4300	6503	SO:0001583	missense	676	exon6			AGAAAAATCAGTG	AF019085	CCDS735.1, CCDS55615.1, CCDS55616.1, CCDS72820.1	1p22.1	2010-12-23			ENSG00000137948	ENSG00000137948			1105	protein-coding gene	gene with protein product	"""cancer/testis antigen 9"""	602144				9367677	Standard	NM_001726		Approved	BRD6, CT9	uc010osz.2	Q58F21	OTTHUMG00000010113	ENST00000362005.3:c.714A>C	1.37:g.92442695A>C	ENSP00000354568:p.Lys238Asn	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	102	50	0.490196	NM_001242806	A6NF68|B7Z811|B7Z890|B7ZAX7|D3DT32|O14789|Q05DQ4|Q6P5T1|Q7Z4A6|Q8IWI6	Missense_Mutation	SNP	ENST00000362005.3	37	CCDS735.1	405	0.18543956043956045	63	0.12804878048780488	41	0.1132596685082873	241	0.42132867132867136	60	0.079155672823219	A	13.80	2.344740	0.41498	0.127553	0.057791	ENSG00000137948	ENST00000362005;ENST00000370389;ENST00000399546;ENST00000539070;ENST00000394530;ENST00000426141;ENST00000402388	T;T;T;T;T;T	0.11063	3.1;3.1;3.1;3.14;2.81;3.1	5.58	3.21	0.36854	.	1.092130	0.06940	N	0.812580	T	0.06962	0.0177	L	0.34521	1.04	0.42066	P	0.008811000000000013	D;D;P;D	0.53312	0.959;0.959;0.944;0.959	P;P;P;P	0.52343	0.503;0.503;0.696;0.503	T	0.25882	-1.0119	9	0.72032	D	0.01	-3.2232	7.8455	0.29422	0.7881:0.1391:0.0727:0.0	rs1156281;rs52816607;rs58411058;rs1156281	192;192;242;238	B7ZAX7;B7Z811;B7Z890;Q58F21	.;.;.;BRDT_HUMAN	N	238;165;238;238;192;238;238	ENSP00000354568:K238N;ENSP00000359416:K165N;ENSP00000387822:K238N;ENSP00000378038:K192N;ENSP00000404969:K238N;ENSP00000384051:K238N	ENSP00000354568:K238N	K	+	3	2	BRDT	92215283	0.991000	0.36638	0.150000	0.22450	0.181000	0.23173	2.784000	0.47774	0.467000	0.27218	0.533000	0.62120	AAA	A|0.865;C|0.135	0.135	strong		0.368	BRDT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027980.2	NM_207189	
PCDHB3	56132	hgsc.bcm.edu	37	5	140480852	140480852	+	Missense_Mutation	SNP	G	G	A	rs12515688	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:140480852G>A	ENST00000231130.2	+	1	619	c.619G>A	c.(619-621)Gaa>Aaa	p.E207K	AC005754.7_ENST00000607216.1_RNA	NM_018937.2	NP_061760.1	Q9Y5E6	PCDB3_HUMAN	protocadherin beta 3	207	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.		E -> K (in dbSNP:rs12515688).		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(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(19)|lung(24)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	72			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			GGAGCAGCCGGAACTCAGCTT	0.567													G|||	746	0.148962	0.1672	0.1974	5008	,	,		17622	0.122		0.159	False		,,,				2504	0.1074				p.E207K		Atlas-SNP	.											.	PCDHB3	208	.	0			c.G619A						PASS	.	G	LYS/GLU	887,3519	330.7+/-301.6	78,731,1394	57.0	55.0	56.0		619	4.2	0.0	5	dbSNP_120	56	1517,7083	273.7+/-290.8	143,1231,2926	yes	missense	PCDHB3	NM_018937.2	56	221,1962,4320	AA,AG,GG		17.6395,20.1316,18.4838	benign	207/797	140480852	2404,10602	2203	4300	6503	SO:0001583	missense	56132	exon1			CAGCCGGAACTCA	AF152496	CCDS4245.1	5q31	2010-01-26			ENSG00000113205	ENSG00000113205		"""Cadherins / Protocadherins : Clustered"""	8688	other	protocadherin		606329				10380929	Standard	NM_018937		Approved	PCDH-BETA3	uc003lio.3	Q9Y5E6	OTTHUMG00000129622	ENST00000231130.2:c.619G>A	5.37:g.140480852G>A	ENSP00000231130:p.Glu207Lys	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	61	25	0.409836	NM_018937	B2R8P2	Missense_Mutation	SNP	ENST00000231130.2	37	CCDS4245.1	344	0.1575091575091575	93	0.18902439024390244	67	0.1850828729281768	64	0.11188811188811189	120	0.158311345646438	G	14.21	2.467224	0.43839	0.201316	0.176395	ENSG00000113205	ENST00000231130	T	0.52526	0.66	5.08	4.2	0.49525	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.00144	0.0004	M	0.87827	2.91	0.80722	P	0.0	D	0.55385	0.971	P	0.56278	0.795	T	0.03212	-1.1060	8	0.38643	T	0.18	.	14.7293	0.69368	0.0:0.2749:0.7251:0.0	rs12515688;rs17844389;rs12515688	207	Q9Y5E6	PCDB3_HUMAN	K	207	ENSP00000231130:E207K	ENSP00000231130:E207K	E	+	1	0	PCDHB3	140461036	0.002000	0.14202	0.005000	0.12908	0.220000	0.24768	1.282000	0.33226	1.236000	0.43740	0.655000	0.94253	GAA	G|0.822;A|0.178	0.178	strong		0.567	PCDHB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251817.2	NM_018937	
CCL14	6358	hgsc.bcm.edu	37	17	34313674	34313674	+	Silent	SNP	G	G	A	rs113937434	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:34313674G>A	ENST00000394509.4	-	1	120	c.12C>T	c.(10-12)tcC>tcT	p.S4S	CTB-186H2.3_ENST00000591669.1_Silent_p.T40T|CCL14_ENST00000480944.2_5'UTR|CCL15-CCL14_ENST00000481427.2_3'UTR|CCL14_ENST00000435911.2_Silent_p.S4S|CTB-186H2.3_ENST00000593057.1_3'UTR|CCL14_ENST00000586216.1_Silent_p.S4S|CCL14_ENST00000536149.1_Silent_p.S4S			Q16627	CCL14_HUMAN	chemokine (C-C motif) ligand 14	4					cell chemotaxis (GO:0060326)|cellular calcium ion homeostasis (GO:0006874)|immune response (GO:0006955)|positive regulation of cell proliferation (GO:0008284)	extracellular space (GO:0005615)				large_intestine(1)|lung(6)	7		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		TGGCAGCCACGGAGATCTTCA	0.537													G|||	106	0.0211661	0.003	0.0144	5008	,	,		16096	0.0476		0.0358	False		,,,				2504	0.0082				p.S4S		Atlas-SNP	.											.	CCL14	22	.	0			c.C12T						PASS	.	G	,	46,4360	48.2+/-83.0	0,46,2157	194.0	137.0	157.0		12,12	0.2	0.0	17	dbSNP_132	157	252,8348	99.9+/-161.4	0,252,4048	no	coding-synonymous,coding-synonymous	CCL14	NM_032962.4,NM_032963.3	,	0,298,6205	AA,AG,GG		2.9302,1.044,2.2913	,	4/110,4/94	34313674	298,12708	2203	4300	6503	SO:0001819	synonymous_variant	6358	exon1			AGCCACGGAGATC	Z49270	CCDS32624.1, CCDS45652.1	17q11.2	2014-04-10	2002-08-22	2002-08-23	ENSG00000213494	ENSG00000276409		"""Chemokine ligands"", ""Endogenous ligands"""	10612	protein-coding gene	gene with protein product		601392	"""small inducible cytokine subfamily A (Cys-Cys), member 14"""	SCYA14		8661057	Standard	NM_032963		Approved	HCC-1, HCC-3, NCC-2, SCYL2, CKb1, MCIF	uc010wcq.1	Q16627	OTTHUMG00000188403	ENST00000394509.4:c.12C>T	17.37:g.34313674G>A		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	119	61	0.512605	NM_032962	E1P649|E1P650|Q13954	Silent	SNP	ENST00000394509.4	37	CCDS32624.1																																																																																			G|0.977;A|0.023	0.023	strong		0.537	CCL14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000272892.2	NM_032962	
BCOR	54880	hgsc.bcm.edu	37	X	39932949	39932949	+	Silent	SNP	G	G	A	rs17145653	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:39932949G>A	ENST00000378444.4	-	4	1878	c.1650C>T	c.(1648-1650)acC>acT	p.T550T	BCOR_ENST00000397354.3_Silent_p.T550T|BCOR_ENST00000342274.4_Silent_p.T550T|BCOR_ENST00000378455.4_Silent_p.T550T	NM_001123385.1	NP_001116857.1	Q6W2J9	BCOR_HUMAN	BCL6 corepressor	550					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						TGACAGCATCGGTGCCGCCCA	0.572			"""F, N, S, T"""	RARA	"""retinoblastoma, AML, APL(translocation)"""		oculo-facio-cardio-dental genetic						G|||	11	0.00291391	0.0015	0.0014	3775	,	,		14756	0.0		0.007	False		,,,				2504	0.001				p.T550T		Atlas-SNP	.		Rec	yes		X	Xp11.4	54880	BCL6 corepressor	yes		.	BCOR	351	.	0			c.C1650T						PASS	.	G	,,,	5,3828		0,5,0,1626,571	110.0	70.0	84.0		1650,1650,1650,1650	-11.2	0.0	X	dbSNP_123	84	76,6652		0,58,18,2370,1854	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	BCOR	NM_001123383.1,NM_001123384.1,NM_001123385.1,NM_017745.5	,,,	0,63,18,3996,2425	AA,AG,A,GG,G		1.1296,0.1304,0.767	,,,	550/1722,550/1704,550/1756,550/1722	39932949	81,10480	2202	4300	6502	SO:0001819	synonymous_variant	54880	exon4			AGCATCGGTGCCG	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.1650C>T	X.37:g.39932949G>A		Somatic	119	1	0.00840336		WXS	Illumina HiSeq	Phase_I	74	73	0.986486	NM_001123385	D3DWB3|D3DWB4|Q29RF6|Q6P4B6|Q7Z2K7|Q8TEB4|Q96DB3|Q9H232|Q9H233|Q9HCJ7|Q9NXF2	Silent	SNP	ENST00000378444.4	37	CCDS48093.1																																																																																			0|0.004;A|0.006	0.006	strong		0.572	BCOR-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000060666.2	NM_017745	
OR4C16	219428	hgsc.bcm.edu	37	11	55339652	55339652	+	Nonsense_Mutation	SNP	C	C	T	rs1459101	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:55339652C>T	ENST00000314634.3	+	1	49	c.49C>T	c.(49-51)Cag>Tag	p.Q17*		NM_001004701.2	NP_001004701.2	Q8NGL9	OR4CG_HUMAN	olfactory receptor, family 4, subfamily C, member 16 (gene/pseudogene)	17						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)				TGGATTGACACAGGATCCTTT	0.388													c|||	1265	0.252596	0.1014	0.3242	5008	,	,		18829	0.3909		0.2843	False		,,,				2504	0.2311				p.Q17X		Atlas-SNP	.											OR4C16,NS,carcinoma,-2,1	OR4C16	104	1	0			c.C49T						PASS	.	C	stop/GLN	561,3841	252.1+/-258.6	27,507,1667	132.0	122.0	125.0		49	0.8	0.0	11	dbSNP_88	125	2290,6302	386.3+/-341.8	329,1632,2335	yes	stop-gained	OR4C16	NM_001004701.2		356,2139,4002	TT,TC,CC		26.6527,12.7442,21.9409		17/311	55339652	2851,10143	2201	4296	6497	SO:0001587	stop_gained	219428	exon1			TTGACACAGGATC	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.49C>T	11.37:g.55339652C>T	ENSP00000324913:p.Gln17*	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	138	31	0.224638	NM_001004701	Q6IEV8	Nonsense_Mutation	SNP	ENST00000314634.3	37	CCDS31502.1	605	0.27701465201465203	47	0.09552845528455285	126	0.34806629834254144	214	0.3741258741258741	218	0.287598944591029	C	15.62	2.886232	0.51908	0.127442	0.266527	ENSG00000181935	ENST00000314634	.	.	.	4.98	0.756	0.18421	.	0.325431	0.26677	N	0.023065	.	.	.	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	.	5.4911	0.16777	0.0:0.5122:0.3092:0.1786	rs1459101;rs52825307;rs60632881;rs1459101	.	.	.	X	17	.	ENSP00000324913:Q17X	Q	+	1	0	OR4C16	55096228	0.000000	0.05858	0.017000	0.16124	0.810000	0.45777	-1.242000	0.02908	0.253000	0.21552	0.549000	0.68633	CAG	C|0.759;T|0.241	0.241	strong		0.388	OR4C16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382627.1	NM_001004701	
GPR113	165082	hgsc.bcm.edu	37	2	26536694	26536694	+	Missense_Mutation	SNP	C	C	T	rs2052937	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:26536694C>T	ENST00000311519.1	-	8	1209	c.1210G>A	c.(1210-1212)Gct>Act	p.A404T	GPR113_ENST00000333478.6_Missense_Mutation_p.A205T|GPR113_ENST00000459892.1_5'UTR|GPR113_ENST00000421160.2_Missense_Mutation_p.A335T|GPR113_ENST00000541401.1_Missense_Mutation_p.A7T	NM_001145168.1	NP_001138640.1	Q8IZF5	GP113_HUMAN	G protein-coupled receptor 113	404			A -> T (in dbSNP:rs2052937). {ECO:0000269|PubMed:12975309}.		G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(5)|ovary(4)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	24	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					AGGTCACAAGCGTACGTGGTG	0.617													T|||	3322	0.663339	0.6974	0.7133	5008	,	,		19849	0.6687		0.6938	False		,,,				2504	0.545				p.A404T		Atlas-SNP	.											.	GPR113	134	.	0			c.G1210A						PASS	.	T	THR/ALA,THR/ALA,THR/ALA	2980,1426	466.2+/-354.4	997,986,220	84.0	82.0	82.0		1210,1003,613	3.5	0.0	2	dbSNP_94	82	5992,2608	422.7+/-354.1	2085,1822,393	yes	missense,missense,missense	GPR113	NM_001145168.1,NM_001145169.1,NM_153835.3	58,58,58	3082,2808,613	TT,TC,CC		30.3256,32.365,31.0165	benign,benign,benign	404/1080,335/998,205/874	26536694	8972,4034	2203	4300	6503	SO:0001583	missense	165082	exon8			CACAAGCGTACGT	AB083619	CCDS33159.2, CCDS46238.1, CCDS46239.1	2p24.1	2014-08-08			ENSG00000173567	ENSG00000173567		"""-"", ""GPCR / Class B : Orphans"""	18989	protein-coding gene	gene with protein product						12435584	Standard	NM_153835		Approved	hGPCR37, PGR23	uc002rhe.4	Q8IZF5	OTTHUMG00000150225	ENST00000311519.1:c.1210G>A	2.37:g.26536694C>T	ENSP00000307831:p.Ala404Thr	Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	152	150	0.986842	NM_001145168	B4DF15|E9PEV1|Q53TA5|Q6UXT7|Q6UXX3|Q86SL7|Q8IXD8|Q8TDT3	Missense_Mutation	SNP	ENST00000311519.1	37	CCDS46239.1	1544	0.706959706959707	336	0.6829268292682927	251	0.6933701657458563	423	0.7395104895104895	534	0.7044854881266491	T	0.038	-1.297136	0.01364	0.67635	0.696744	ENSG00000173567	ENST00000541401;ENST00000333478;ENST00000421160;ENST00000311519	T;T;T;T	0.26660	1.72;3.25;3.25;3.25	5.8	3.47	0.39725	.	.	.	.	.	T	0.00012	0.0000	N	0.00538	-1.39	0.58432	P	1.0000000000287557E-6	B;B;B;B	0.22211	0.0;0.066;0.0;0.0	B;B;B;B	0.12156	0.0;0.007;0.0;0.0	T	0.38415	-0.9662	8	0.02654	T	1	-6.7019	6.8577	0.24050	0.0:0.2588:0.0:0.7412	rs2052937;rs56672489;rs2052937	335;205;404;7	E9PEV1;Q8IZF5-2;Q8IZF5;F5H1E4	.;.;GP113_HUMAN;.	T	7;205;335;404	ENSP00000445729:A7T;ENSP00000327396:A205T;ENSP00000388537:A335T;ENSP00000307831:A404T	ENSP00000307831:A404T	A	-	1	0	GPR113	26390198	0.040000	0.19996	0.007000	0.13788	0.070000	0.16714	0.581000	0.23819	0.478000	0.27488	-0.254000	0.11334	GCT	C|0.313;T|0.687	0.687	strong		0.617	GPR113-004	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000316892.1	NM_153835	
TXNDC2	84203	hgsc.bcm.edu	37	18	9887857	9887857	+	Missense_Mutation	SNP	G	G	A	rs17732496	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:9887857G>A	ENST00000306084.6	+	2	1580	c.1381G>A	c.(1381-1383)Gca>Aca	p.A461T	TXNDC2_ENST00000536353.2_3'UTR|TXNDC2_ENST00000357775.5_Missense_Mutation_p.A394T	NM_001098529.1	NP_001091999.1	Q86VQ3	TXND2_HUMAN	thioredoxin domain containing 2 (spermatozoa)	461	Thioredoxin. {ECO:0000255|PROSITE- ProRule:PRU00691}.		A -> T (in dbSNP:rs17732496). {ECO:0000269|PubMed:11230166}.		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						GGACTTTGAGGCATCACTGAA	0.577													G|||	565	0.112819	0.0696	0.1729	5008	,	,		20611	0.0119		0.1511	False		,,,				2504	0.1933				p.A461T		Atlas-SNP	.											.	TXNDC2	168	.	0			c.G1381A						PASS	.	G	THR/ALA,THR/ALA	354,4052	181.5+/-209.5	18,318,1867	61.0	53.0	56.0		1381,1180	-3.0	0.0	18	dbSNP_123	56	1231,7369	246.8+/-275.1	80,1071,3149	yes	missense,missense	TXNDC2	NM_001098529.1,NM_032243.5	58,58	98,1389,5016	AA,AG,GG		14.314,8.0345,12.1867	benign,benign	461/554,394/487	9887857	1585,11421	2203	4300	6503	SO:0001583	missense	84203	exon2			TTTGAGGCATCAC	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.1381G>A	18.37:g.9887857G>A	ENSP00000304908:p.Ala461Thr	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	112	55	0.491071	NM_001098529	A5YM73|Q8N7U4|Q96RX3|Q9H0L8	Missense_Mutation	SNP	ENST00000306084.6	37	CCDS42414.1	227	0.10393772893772894	37	0.07520325203252033	65	0.17955801104972377	9	0.015734265734265736	116	0.15303430079155672	G	5.661	0.306519	0.10733	0.080345	0.14314	ENSG00000168454	ENST00000536353;ENST00000357775;ENST00000306084;ENST00000426718	T;T	0.13538	2.58;2.58	4.05	-3.03	0.05429	Thioredoxin domain (1);Thioredoxin-like fold (3);	0.751915	0.11711	N	0.536894	T	0.00012	0.0000	L	0.38175	1.15	0.80722	P	0.0	B	0.22080	0.064	B	0.22152	0.038	T	0.42799	-0.9430	8	.	.	.	-0.2557	2.7506	0.05280	0.0868:0.2456:0.2687:0.3989	rs17732496;rs17732496	461	Q86VQ3	TXND2_HUMAN	T	259;394;461;446	ENSP00000350419:A394T;ENSP00000304908:A461T	.	A	+	1	0	TXNDC2	9877857	0.000000	0.05858	0.000000	0.03702	0.261000	0.26267	-1.457000	0.02374	-0.669000	0.05289	0.650000	0.86243	GCA	G|0.887;A|0.113	0.113	strong		0.577	TXNDC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254487.1		
CHAT	1103	hgsc.bcm.edu	37	10	50824619	50824619	+	Missense_Mutation	SNP	G	G	A	rs3810950	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:50824619G>A	ENST00000337653.2	+	2	511	c.358G>A	c.(358-360)Gca>Aca	p.A120T	CHAT_ENST00000395562.2_Missense_Mutation_p.A38T|CHAT_ENST00000455728.2_Missense_Mutation_p.A2T|CHAT_ENST00000395559.2_Missense_Mutation_p.A2T|CHAT_ENST00000339797.1_Missense_Mutation_p.A2T|CHAT_ENST00000460699.1_3'UTR|CHAT_ENST00000351556.3_Missense_Mutation_p.A2T	NM_001142929.1|NM_020549.4	NP_001136401.1|NP_065574	P28329	CLAT_HUMAN	choline O-acetyltransferase	120			A -> T (in dbSNP:rs3810950). {ECO:0000269|PubMed:11172068, ECO:0000269|PubMed:1388731, ECO:0000269|PubMed:15489334}.		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)	CCGTAAGATGGCAGCAAAAAC	0.557													G|||	804	0.160543	0.0053	0.1671	5008	,	,		18114	0.1696		0.2316	False		,,,				2504	0.2832				p.A120T		Atlas-SNP	.											CHAT,NS,carcinoma,-1,1	CHAT	162	1	0			c.G358A	GRCh37	CM025920	CHAT	M	rs3810950	PASS	.	G	THR/ALA,THR/ALA,THR/ALA,THR/ALA,THR/ALA,THR/ALA,THR/ALA	228,4178	131.4+/-167.9	7,214,1982	114.0	85.0	95.0		4,112,4,358,4,4,4	3.0	0.0	10	dbSNP_107	95	2144,6456	354.6+/-329.6	263,1618,2419	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	58,58,58,58,58,58,58	270,1832,4401	AA,AG,GG		24.9302,5.1748,18.2377	benign,benign,benign,benign,benign,benign,benign	2/631,38/667,2/631,120/749,2/631,2/631,2/631	50824619	2372,10634	2203	4300	6503	SO:0001583	missense	1103	exon2			AAGATGGCAGCAA	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.358G>A	10.37:g.50824619G>A	ENSP00000337103:p.Ala120Thr	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	46	22	0.478261	NM_020549	A2BDF4|A2BDF5|Q16488|Q9BQ23|Q9BQ35|Q9BQE1	Missense_Mutation	SNP	ENST00000337653.2	37	CCDS7232.1	332	0.152014652014652	5	0.01016260162601626	77	0.212707182320442	87	0.1520979020979021	163	0.21503957783641162	G	6.004	0.369097	0.11352	0.051748	0.249302	ENSG00000070748	ENST00000339797;ENST00000351556;ENST00000395559;ENST00000337653;ENST00000395562;ENST00000455728	D;D;D;D;D;D	0.85955	-2.05;-2.05;-2.05;-1.9;-1.95;-1.92	3.96	3.03	0.35002	.	0.678932	0.14323	N	0.326861	T	0.00039	0.0001	N	0.08118	0	0.80722	P	0.0	B;B	0.25609	0.13;0.014	B;B	0.29942	0.109;0.005	T	0.05386	-1.0888	9	0.17369	T	0.5	-2.7401	5.388	0.16227	0.1117:0.222:0.6664:0.0	rs3810950;rs17775591;rs60084580;rs3810950	2;120	F8W8I2;P28329	.;CLAT_HUMAN	T	2;2;2;120;38;2	ENSP00000343486:A2T;ENSP00000345878:A2T;ENSP00000378926:A2T;ENSP00000337103:A120T;ENSP00000378929:A38T;ENSP00000390521:A2T	ENSP00000337103:A120T	A	+	1	0	CHAT	50494625	0.048000	0.20356	0.004000	0.12327	0.745000	0.42441	2.188000	0.42612	1.229000	0.43630	0.655000	0.94253	GCA	G|0.762;A|0.237	0.237	strong		0.557	CHAT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047997.1	NM_020549	
FHAD1	114827	hgsc.bcm.edu	37	1	15723843	15723843	+	Silent	SNP	G	G	A	rs2294490	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:15723843G>A	ENST00000375998.4	+	30	4173	c.4173G>A	c.(4171-4173)ctG>ctA	p.L1391L	FHAD1_ENST00000471347.1_3'UTR|FHAD1_ENST00000314740.8_Silent_p.L662L|FHAD1_ENST00000358897.4_Silent_p.L1391L|FHAD1_ENST00000417793.1_Silent_p.L1355L			B1AJZ9	FHAD1_HUMAN	forkhead-associated (FHA) phosphopeptide binding domain 1	1391										skin(1)|stomach(1)	2						GAGAGATGCTGAGGAAAGAGA	0.478													G|||	1556	0.310703	0.0983	0.2925	5008	,	,		14855	0.4504		0.4533	False		,,,				2504	0.32				p.L1391L		Atlas-SNP	.											.	FHAD1	78	.	0			c.G4173A						PASS	.	G		195,1189		10,175,507	119.0	114.0	116.0		4173	1.2	0.4	1	dbSNP_100	116	1470,1712		337,796,458	no	coding-synonymous	FHAD1	NM_052929.1		347,971,965	AA,AG,GG		46.1974,14.0896,36.4652		1391/1413	15723843	1665,2901	692	1591	2283	SO:0001819	synonymous_variant	114827	exon31			GATGCTGAGGAAA	AK093300		1p36.21	2012-04-19			ENSG00000142621	ENSG00000142621			29408	protein-coding gene	gene with protein product						11572484	Standard	NM_052929		Approved	KIAA1937	uc001awb.2	B1AJZ9	OTTHUMG00000002088	ENST00000375998.4:c.4173G>A	1.37:g.15723843G>A		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	74	74	1	NM_052929	Q0P6F5|Q8N8D3|Q8N9T6|Q8NA05	Silent	SNP	ENST00000375998.4	37																																																																																				G|0.663;A|0.337	0.337	strong		0.478	FHAD1-026	PUTATIVE	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000393400.2	NM_052929	
ACAN	176	hgsc.bcm.edu	37	15	89415247	89415247	+	Missense_Mutation	SNP	C	C	G	rs3817428	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:89415247C>G	ENST00000561243.1	+	14	7119	c.7119C>G	c.(7117-7119)gaC>gaG	p.D2373E	ACAN_ENST00000439576.2_Missense_Mutation_p.D2373E|ACAN_ENST00000559004.1_Missense_Mutation_p.D2335E|ACAN_ENST00000352105.7_Missense_Mutation_p.D2335E			P16112	PGCA_HUMAN	aggrecan	2258	G3.|Sushi. {ECO:0000255|PROSITE- ProRule:PRU00302}.				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|proteolysis (GO:0006508)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)	carbohydrate binding (GO:0030246)|extracellular matrix structural constituent (GO:0005201)|hyaluronic acid binding (GO:0005540)|metal ion binding (GO:0046872)	p.D2259E(1)		NS(1)|central_nervous_system(4)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(15)|liver(2)|lung(40)|ovary(2)|prostate(5)|skin(5)|stomach(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	93	Lung NSC(78;0.0392)|all_lung(78;0.077)		BRCA - Breast invasive adenocarcinoma(143;0.146)			ATGCCCAAGACTACCAGTGGA	0.592													C|||	572	0.114217	0.0477	0.1268	5008	,	,		22065	0.123		0.2445	False		,,,				2504	0.0521				p.D2373E		Atlas-SNP	.											ACAN,NS,carcinoma,0,1	ACAN	220	1	1	Substitution - Missense(1)	stomach(1)	c.C7119G						scavenged	.	C	GLU/ASP,GLU/ASP	307,4045	151.4+/-185.3	15,277,1884	110.0	114.0	112.0		7119,7005	3.9	1.0	15	dbSNP_107	112	2308,6282	380.0+/-339.5	298,1712,2285	yes	missense,missense	ACAN	NM_013227.3,NM_001135.3	45,45	313,1989,4169	GG,GC,CC		26.8685,7.0542,20.2055	benign,benign	2373/2531,2335/2432	89415247	2615,10327	2176	4295	6471	SO:0001583	missense	176	exon15			CCAAGACTACCAG	M55172	CCDS53970.1, CCDS53971.1	15q26.1	2013-05-07	2007-02-16	2007-02-16	ENSG00000157766	ENSG00000157766		"""Immunoglobulin superfamily / V-set domain containing"", ""Proteoglycans / Extracellular Matrix : Hyalectans"""	319	protein-coding gene	gene with protein product	"""aggrecan proteoglycan"""	155760	"""chondroitin sulfate proteoglycan 1"", ""aggrecan 1"""	MSK16, CSPG1, AGC1		1985970	Standard	NM_013227		Approved	CSPGCP	uc010upo.1	P16112	OTTHUMG00000171989	ENST00000561243.1:c.7119C>G	15.37:g.89415247C>G	ENSP00000453342:p.Asp2373Glu	Somatic	122	1	0.00819672		WXS	Illumina HiSeq	Phase_I	140	76	0.542857	NM_013227	Q13650|Q9UCD3|Q9UCP4|Q9UCP5|Q9UDE0	Missense_Mutation	SNP	ENST00000561243.1	37	CCDS53970.1	342	0.1565934065934066	25	0.0508130081300813	57	0.1574585635359116	63	0.11013986013986014	197	0.2598944591029024	C	13.69	2.311104	0.40895	0.070542	0.268685	ENSG00000157766	ENST00000439576;ENST00000352105;ENST00000268134	T;T	0.18338	2.22;2.22	5.76	3.89	0.44902	.	0.000000	0.34386	N	0.004011	T	0.00012	0.0000	N	0.04705	-0.18	0.38965	P	0.04137299999999999	P;B	0.35493	0.505;0.286	B;B	0.35607	0.161;0.206	T	0.50389	-0.8834	9	0.23891	T	0.37	-28.3785	11.615	0.51083	0.0:0.8564:0.0:0.1436	rs3817428;rs17201667;rs52795578;rs3817428	2335;2373	E7ENV9;E7EX88	.;.	E	2373;2335;2259	ENSP00000387356:D2373E;ENSP00000341615:D2335E	ENSP00000268134:D2259E	D	+	3	2	ACAN	87216251	0.991000	0.36638	1.000000	0.80357	0.979000	0.70002	0.384000	0.20668	0.796000	0.33947	-0.192000	0.12808	GAC	C|0.854;G|0.146	0.146	strong		0.592	ACAN-006	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416267.2	NM_001135	
RNF213	57674	hgsc.bcm.edu	37	17	78261730	78261730	+	Silent	SNP	G	G	A	rs17853714	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:78261730G>A	ENST00000582970.1	+	4	521	c.378G>A	c.(376-378)ccG>ccA	p.P126P	RNF213_ENST00000456466.1_Silent_p.P126P|RNF213_ENST00000508628.2_Silent_p.P175P|RNF213_ENST00000319921.4_Silent_p.P126P	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	109	0	0		WXS	Illumina HiSeq	Phase_I	105	63	0.6	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	
GPR114	221188	hgsc.bcm.edu	37	16	57601792	57601792	+	Silent	SNP	C	C	T	rs9937918	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:57601792C>T	ENST00000340339.4	+	9	1369	c.846C>T	c.(844-846)cgC>cgT	p.R282R	GPR114_ENST00000394361.4_3'UTR|GPR114_ENST00000349457.3_Silent_p.R282R	NM_153837.1	NP_722579.1	Q8IZF4	GP114_HUMAN	G protein-coupled receptor 114	282					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(5)|lung(5)|ovary(2)|stomach(1)|urinary_tract(1)	23						CCTTAACACGCATCCACATGA	0.597													c|||	2275	0.454273	0.3759	0.5029	5008	,	,		23261	0.7123		0.2783	False		,,,				2504	0.4407				p.R282R		Atlas-SNP	.											.	GPR114	52	.	0			c.C846T						PASS	.			1618,2778	499.8+/-364.5	299,1020,879	94.0	76.0	82.0		846	-4.1	0.1	16	dbSNP_119	82	2432,6168	398.2+/-346.0	342,1748,2210	no	coding-synonymous	GPR114	NM_153837.1		641,2768,3089	TT,TC,CC		28.2791,36.8062,31.1634		282/529	57601792	4050,8946	2198	4300	6498	SO:0001819	synonymous_variant	221188	exon9			AACACGCATCCAC	AY140956	CCDS10785.1	16q13	2014-08-08			ENSG00000159618	ENSG00000159618		"""-"", ""GPCR / Class B : Orphans"""	19010	protein-coding gene	gene with protein product						12435584	Standard	NM_153837		Approved	PGR27	uc002ely.3	Q8IZF4	OTTHUMG00000133461	ENST00000340339.4:c.846C>T	16.37:g.57601792C>T		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	75	51	0.68	NM_153837	B3KXZ5|Q6ZMH7|Q6ZML4|Q86SL8|Q8IZ14	Silent	SNP	ENST00000340339.4	37	CCDS10785.1																																																																																			C|0.625;T|0.375	0.375	strong		0.597	GPR114-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257336.3	NM_153837	
THBS1	7057	hgsc.bcm.edu	37	15	39880358	39880358	+	Silent	SNP	C	C	T	rs2228261	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:39880358C>T	ENST00000260356.5	+	9	1575	c.1410C>T	c.(1408-1410)aaC>aaT	p.N470N		NM_003246.2	NP_003237.2	P07996	TSP1_HUMAN	thrombospondin 1	470	TSP type-1 2. {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)	p.N470N(1)		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)		CCCAGATGAACGGGAAACCCT	0.597													C|||	1336	0.266773	0.4493	0.1383	5008	,	,		20241	0.2897		0.1312	False		,,,				2504	0.227				p.N470N		Atlas-SNP	.											THBS1,NS,carcinoma,0,1	THBS1	106	1	1	Substitution - coding silent(1)	stomach(1)	c.C1410T						PASS	.	C		1702,2698	513.4+/-368.3	331,1040,829	83.0	78.0	80.0		1410	-12.0	0.0	15	dbSNP_98	80	1130,7464	232.5+/-266.1	64,1002,3231	no	coding-synonymous	THBS1	NM_003246.2		395,2042,4060	TT,TC,CC		13.1487,38.6818,21.7947		470/1171	39880358	2832,10162	2200	4297	6497	SO:0001819	synonymous_variant	7057	exon9			GATGAACGGGAAA		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.1410C>T	15.37:g.39880358C>T		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	103	59	0.572816	NM_003246	A8K6H4|B4E3J7|B9EGH6|Q15667|Q59E99	Silent	SNP	ENST00000260356.5	37	CCDS32194.1																																																																																			C|0.766;T|0.234	0.234	strong		0.597	THBS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257831.2	NM_003246	
ARSD	414	hgsc.bcm.edu	37	X	2836084	2836084	+	Silent	SNP	C	C	G	rs73632973	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:2836084C>G	ENST00000381154.1	-	5	699	c.624G>C	c.(622-624)gcG>gcC	p.A208A	ARSD_ENST00000217890.6_5'UTR	NM_001669.3	NP_001660.2	P51689	ARSD_HUMAN	arylsulfatase D	208					cellular protein metabolic process (GO:0044267)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	arylsulfatase activity (GO:0004065)|metal ion binding (GO:0046872)			large_intestine(3)|lung(3)	6		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				GAATCCCCAGCGCCAGGAACT	0.657																																					p.A208A		Atlas-SNP	.											.	ARSD	47	.	0			c.G624C						PASS	.						16.0	19.0	18.0					X																	2836084		2199	4294	6493	SO:0001819	synonymous_variant	414	exon5			CCCCAGCGCCAGG	X83572	CCDS35196.1	Xp22.3	2013-02-14			ENSG00000006756	ENSG00000006756		"""Arylsulfatase family"""	717	protein-coding gene	gene with protein product		300002				7720070	Standard	NM_001669		Approved		uc004cqy.3	P51689	OTTHUMG00000021077	ENST00000381154.1:c.624G>C	X.37:g.2836084C>G		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	84	10	0.119048	NM_001669	Q9UHJ8	Silent	SNP	ENST00000381154.1	37	CCDS35196.1																																																																																			C|0.928;G|0.072	0.072	strong		0.657	ARSD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055636.1		
PTPRG	5793	hgsc.bcm.edu	37	3	62278938	62278938	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:62278938G>A	ENST00000474889.1	+	30	4671	c.4294G>A	c.(4294-4296)Gca>Aca	p.A1432T	PTPRG-AS1_ENST00000498655.1_RNA|PTPRG-AS1_ENST00000479018.1_RNA|PTPRG-AS1_ENST00000462497.1_RNA|PTPRG-AS1_ENST00000474795.1_RNA|PTPRG-AS1_ENST00000495542.1_RNA|PTPRG-AS1_ENST00000475371.1_RNA|PTPRG_ENST00000295874.10_Missense_Mutation_p.A1403T|PTPRG-AS1_ENST00000466893.1_RNA|PTPRG-AS1_ENST00000490916.1_RNA	NM_002841.3	NP_002832.3	P23470	PTPRG_HUMAN	protein tyrosine phosphatase, receptor type, G	1432					brain development (GO:0007420)|negative regulation of epithelial cell migration (GO:0010633)|negative regulation of neuron projection development (GO:0010977)|peptidyl-tyrosine dephosphorylation (GO:0035335)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	identical protein binding (GO:0042802)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(12)|liver(2)|lung(15)|ovary(7)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	62				BRCA - Breast invasive adenocarcinoma(55;0.000376)|KIRC - Kidney renal clear cell carcinoma(10;0.0499)|Kidney(10;0.065)		TGTTCTTATTGCAGATGAATC	0.403																																					p.A1432T		Atlas-SNP	.											PTPRG,NS,carcinoma,-1,1	PTPRG	153	1	0			c.G4294A						scavenged	.						132.0	125.0	127.0					3																	62278938		2203	4299	6502	SO:0001583	missense	5793	exon30			CTTATTGCAGATG	L09247	CCDS2895.1	3p21-p14	2013-02-11			ENSG00000144724	ENSG00000144724		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9671	protein-coding gene	gene with protein product		176886		PTPG		1711217	Standard	NM_002841		Approved	RPTPG	uc003dlb.3	P23470	OTTHUMG00000158660	ENST00000474889.1:c.4294G>A	3.37:g.62278938G>A	ENSP00000418112:p.Ala1432Thr	Somatic	218	0	0		WXS	Illumina HiSeq	Phase_I	196	2	0.0102041	NM_002841	B2RU12|B7ZLX5|Q15623|Q59EE0|Q68DU5	Missense_Mutation	SNP	ENST00000474889.1	37	CCDS2895.1	.	.	.	.	.	.	.	.	.	.	G	11.20	1.569534	0.28003	.	.	ENSG00000144724	ENST00000474889;ENST00000295874	T;T	0.50001	0.76;0.78	5.45	4.57	0.56435	.	0.298040	0.36932	N	0.002323	T	0.30070	0.0753	N	0.22421	0.69	0.09310	N	1	B;B;B	0.13145	0.0;0.007;0.002	B;B;B	0.12156	0.0;0.007;0.002	T	0.10730	-1.0617	10	0.66056	D	0.02	.	5.1695	0.15103	0.2831:0.0:0.7169:0.0	.	678;1403;1432	B7Z3T1;P23470-2;P23470	.;.;PTPRG_HUMAN	T	1432;1403	ENSP00000418112:A1432T;ENSP00000295874:A1403T	ENSP00000295874:A1403T	A	+	1	0	PTPRG	62253978	0.031000	0.19500	0.832000	0.32986	0.982000	0.71751	2.373000	0.44266	2.581000	0.87130	0.650000	0.86243	GCA	.	.	none		0.403	PTPRG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351674.1	NM_002841	
ITGB1	3688	hgsc.bcm.edu	37	10	33214802	33214802	+	Silent	SNP	A	A	G	rs2298141	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:33214802A>G	ENST00000396033.2	-	6	918	c.783T>C	c.(781-783)tgT>tgC	p.C261C	ITGB1_ENST00000484088.1_5'Flank|ITGB1_ENST00000423113.1_Silent_p.C261C|ITGB1_ENST00000374956.4_Silent_p.C261C|ITGB1_ENST00000302278.3_Silent_p.C261C	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	107	0	0		WXS	Illumina HiSeq	Phase_I	80	39	0.4875	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	
TRAIP	10293	hgsc.bcm.edu	37	3	49866584	49866584	+	Silent	SNP	T	T	G	rs35129566	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:49866584T>G	ENST00000331456.2	-	15	1475	c.1362A>C	c.(1360-1362)acA>acC	p.T454T		NM_005879.2	NP_005870.2	Q9BWF2	TRAIP_HUMAN	TRAF interacting protein	454	Interaction with CYLD.				apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|receptor signaling protein activity (GO:0005057)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|kidney(2)|large_intestine(2)|liver(2)|lung(9)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	24				BRCA - Breast invasive adenocarcinoma(193;4.71e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		GAGAAGGCACTGTCTTCACCC	0.537													T|||	677	0.135184	0.2746	0.1412	5008	,	,		22461	0.0129		0.166	False		,,,				2504	0.0368				p.T454T		Atlas-SNP	.											.	TRAIP	47	.	0			c.A1362C						PASS	.	T		1155,3251	408.9+/-334.8	145,865,1193	266.0	195.0	219.0		1362	1.3	0.0	3	dbSNP_126	219	1579,7021	295.0+/-302.2	141,1297,2862	no	coding-synonymous	TRAIP	NM_005879.2		286,2162,4055	GG,GT,TT		18.3605,26.2143,21.0211		454/470	49866584	2734,10272	2203	4300	6503	SO:0001819	synonymous_variant	10293	exon15			AGGCACTGTCTTC	BC019283	CCDS2806.1	3p21.31	2013-01-09			ENSG00000183763	ENSG00000183763		"""RING-type (C3HC4) zinc fingers"""	30764	protein-coding gene	gene with protein product	"""ring finger protein 206"""	605958				9104814	Standard	NM_005879		Approved	TRIP, RNF206	uc003cxs.1	Q9BWF2	OTTHUMG00000158269	ENST00000331456.2:c.1362A>C	3.37:g.49866584T>G		Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	121	69	0.570248	NM_005879	B5BU84|B5BUL3|O00467	Silent	SNP	ENST00000331456.2	37	CCDS2806.1																																																																																			T|0.809;G|0.191	0.191	strong		0.537	TRAIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350518.1	NM_005879	
C10orf10	11067	hgsc.bcm.edu	37	10	45473317	45473317	+	Silent	SNP	C	C	T	rs3740094	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:45473317C>T	ENST00000298295.3	-	2	379	c.162G>A	c.(160-162)ctG>ctA	p.L54L	RASSF4_ENST00000374417.2_Intron|C10orf10_ENST00000496638.1_Intron|RASSF4_ENST00000340258.5_Intron|RASSF4_ENST00000472561.1_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	50	0	0		WXS	Illumina HiSeq	Phase_I	43	24	0.55814	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	
LRPPRC	10128	hgsc.bcm.edu	37	2	44201376	44201376	+	Silent	SNP	T	T	C	rs4953042	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:44201376T>C	ENST00000260665.7	-	9	1125	c.1068A>G	c.(1066-1068)caA>caG	p.Q356Q	LRPPRC_ENST00000409659.1_Silent_p.Q356Q|LRPPRC_ENST00000409946.1_Silent_p.Q356Q	NM_133259.3	NP_573566.2	P42704	LPPRC_HUMAN	leucine-rich pentatricopeptide repeat containing	356					mitochondrion transport along microtubule (GO:0047497)|mRNA transport (GO:0051028)|negative regulation of mitochondrial RNA catabolic process (GO:0000961)|regulation of mitochondrial translation (GO:0070129)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	condensed nuclear chromosome (GO:0000794)|cytoskeleton (GO:0005856)|membrane (GO:0016020)|microtubule (GO:0005874)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|ribonucleoprotein complex (GO:0030529)	beta-tubulin binding (GO:0048487)|microtubule binding (GO:0008017)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)			breast(3)|endometrium(3)|kidney(5)|large_intestine(9)|lung(15)|ovary(2)|prostate(2)|skin(2)	41		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)				CTAGTAAAATTTGCAACGCTA	0.373													T|||	1281	0.255791	0.025	0.2666	5008	,	,		19268	0.5198		0.1521	False		,,,				2504	0.3947				p.Q356Q		Atlas-SNP	.											.	LRPPRC	105	.	0			c.A1068G						PASS	.	T		212,4194	129.4+/-166.1	4,204,1995	76.0	76.0	76.0		1068	-3.3	0.0	2	dbSNP_111	76	1286,7314	254.0+/-279.5	89,1108,3103	no	coding-synonymous	LRPPRC	NM_133259.3		93,1312,5098	CC,CT,TT		14.9535,4.8116,11.5178		356/1395	44201376	1498,11508	2203	4300	6503	SO:0001819	synonymous_variant	10128	exon9			TAAAATTTGCAAC	M92439	CCDS33189.1	2p21	2012-02-24	2012-02-24		ENSG00000138095	ENSG00000138095			15714	protein-coding gene	gene with protein product		607544	"""Leigh syndrome, French-Canadian type (cytochrome oxidase deficiency)"""	LSFC		8012652, 8619474, 22045337	Standard	NM_133259		Approved	GP130, LRP130	uc002rtr.2	P42704	OTTHUMG00000152782	ENST00000260665.7:c.1068A>G	2.37:g.44201376T>C		Somatic	396	2	0.00505051		WXS	Illumina HiSeq	Phase_I	708	549	0.775424	NM_133259	A0PJE3|A8K1V1|Q53PC0|Q53QN7|Q6ZUD8|Q7Z7A6|Q96D84	Silent	SNP	ENST00000260665.7	37	CCDS33189.1																																																																																			T|0.840;C|0.160	0.160	strong		0.373	LRPPRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327823.1	NM_133259	
CCDC18	343099	hgsc.bcm.edu	37	1	93676478	93676478	+	Missense_Mutation	SNP	A	A	C	rs76148185	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:93676478A>C	ENST00000343253.7	+	10	1831	c.1329A>C	c.(1327-1329)gaA>gaC	p.E443D	CCDC18_ENST00000338949.4_Missense_Mutation_p.E242D|CCDC18_ENST00000557479.1_Missense_Mutation_p.E561D|CCDC18_ENST00000334652.5_5'UTR|CCDC18_ENST00000401026.3_Missense_Mutation_p.E443D			Q5T9S5	CCD18_HUMAN	coiled-coil domain containing 18	443										breast(5)|endometrium(3)|kidney(1)|large_intestine(6)|lung(19)|ovary(3)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	42		all_lung(203;0.00196)|Lung NSC(277;0.00903)|Melanoma(281;0.099)|all_neural(321;0.185)|Glioma(108;0.203)		all cancers(265;0.00166)|GBM - Glioblastoma multiforme(16;0.00551)|Epithelial(280;0.0967)		TGATTTCGGAATTGAGGTACA	0.383													A|||	47	0.00938498	0.0008	0.013	5008	,	,		17506	0.0		0.0278	False		,,,				2504	0.0092				p.E443D		Atlas-SNP	.											.	CCDC18	93	.	0			c.A1329C						PASS	.	A	ASP/GLU	17,3673		0,17,1828	82.0	78.0	79.0		1329	1.2	1.0	1	dbSNP_131	79	225,7975		2,221,3877	yes	missense	CCDC18	NM_206886.3	45	2,238,5705	CC,CA,AA		2.7439,0.4607,2.0353	benign	443/1300	93676478	242,11648	1845	4100	5945	SO:0001583	missense	343099	exon10			TTCGGAATTGAGG			1p22.1	2008-02-05			ENSG00000122483	ENSG00000122483			30370	protein-coding gene	gene with protein product						12601173	Standard	XM_006710609		Approved	NY-SAR-41	uc021opx.1	Q5T9S5	OTTHUMG00000010598	ENST00000343253.7:c.1329A>C	1.37:g.93676478A>C	ENSP00000343377:p.Glu443Asp	Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	153	80	0.522876	NM_206886	Q6ZU17	Missense_Mutation	SNP	ENST00000343253.7	37		24|24	0.01098901098901099|0.01098901098901099	1|1	0.0020325203252032522|0.0020325203252032522	5|5	0.013812154696132596|0.013812154696132596	0|0	0.0|0.0	18|18	0.023746701846965697|0.023746701846965697	A|A	10.40|10.40	1.339270|1.339270	0.24339|0.24339	0.004607|0.004607	0.027439|0.027439	ENSG00000122483|ENSG00000122483	ENST00000343253;ENST00000401026;ENST00000557479;ENST00000338949;ENST00000455267|ENST00000370276	T;T;T;T;T|.	0.19394|.	2.15;2.15;2.15;2.15;2.15|.	6.04|6.04	1.23|1.23	0.21249|0.21249	.|.	0.416730|.	0.25296|.	N|.	0.031686|.	T|T	0.21186|0.21186	0.0510|0.0510	L|L	0.27053|0.27053	0.805|0.805	0.80722|0.80722	D|D	1|1	B;B|.	0.18013|.	0.009;0.025|.	B;B|.	0.14023|.	0.006;0.01|.	T|T	0.05517|0.05517	-1.0880|-1.0880	10|5	0.16896|.	T|.	0.51|.	.|.	5.0648|5.0648	0.14576|0.14576	0.498:0.2315:0.2705:0.0|0.498:0.2315:0.2705:0.0	.|.	443;561|.	Q5T9S5;G3V388|.	CCD18_HUMAN;.|.	D|T	443;443;561;242;163|497	ENSP00000343377:E443D;ENSP00000383808:E443D;ENSP00000451099:E561D;ENSP00000344380:E242D;ENSP00000391151:E163D|.	ENSP00000344380:E242D|.	E|N	+|+	3|2	2|0	CCDC18|CCDC18	93449066|93449066	1.000000|1.000000	0.71417|0.71417	0.995000|0.995000	0.50966|0.50966	0.936000|0.936000	0.57629|0.57629	1.123000|1.123000	0.31308|0.31308	0.190000|0.190000	0.20209|0.20209	0.459000|0.459000	0.35465|0.35465	GAA|AAT	A|0.982;C|0.018	0.018	strong		0.383	CCDC18-008	PUTATIVE	basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000382327.1	NM_206886	
PCYOX1L	78991	hgsc.bcm.edu	37	5	148747902	148747902	+	Missense_Mutation	SNP	G	G	C	rs4705336	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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						scavenged	.	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	163	1	0.00613497	1719	WXS	Illumina HiSeq	Phase_I	141	70	0.496454	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	
DHX33	56919	hgsc.bcm.edu	37	17	5356913	5356913	+	Silent	SNP	C	C	T	rs16954697	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:5356913C>T	ENST00000225296.3	-	8	1583	c.1383G>A	c.(1381-1383)tcG>tcA	p.S461S	DHX33_ENST00000433302.3_Silent_p.S237S	NM_001199699.1|NM_020162.3	NP_001186628.1|NP_064547.2	Q9H6R0	DHX33_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 33	461					positive regulation of transcription from RNA polymerase I promoter (GO:0045943)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)|rDNA binding (GO:0000182)			breast(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(2)|lung(2)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17						GAGATGGCTTCGACATGAAGT	0.443													G|||	1042	0.208067	0.2413	0.0994	5008	,	,		19550	0.2331		0.162	False		,,,				2504	0.2618				p.S461S		Atlas-SNP	.											.	DHX33	41	.	0			c.G1383A						PASS	.	G	,	1075,3331		136,803,1264	134.0	120.0	124.0		864,1383	0.3	1.0	17	dbSNP_123	124	1120,7480		76,968,3256	no	coding-synonymous,coding-synonymous	DHX33	NM_001199699.1,NM_020162.3	,	212,1771,4520	TT,TC,CC		13.0233,24.3985,16.8768	,	288/535,461/708	5356913	2195,10811	2203	4300	6503	SO:0001819	synonymous_variant	56919	exon8			TGGCTTCGACATG	AL359945	CCDS11072.1	17p13	2003-06-13	2003-06-13	2003-06-13	ENSG00000005100	ENSG00000005100		"""DEAH-boxes"""	16718	protein-coding gene	gene with protein product		614405	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 33"""	DDX33			Standard	NM_020162		Approved	FLJ21972, DKFZp762F2011	uc002gca.3	Q9H6R0	OTTHUMG00000102041	ENST00000225296.3:c.1383G>A	17.37:g.5356913C>T		Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	98	45	0.459184	NM_020162	B4DHF9|Q4G149|Q5CZ73|Q9H5M9	Silent	SNP	ENST00000225296.3	37	CCDS11072.1																																																																																			C|0.819;N|0.001	.	strong		0.443	DHX33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219826.2	NM_020162	
KRTAP4-6	81871	hgsc.bcm.edu	37	17	39296412	39296412	+	Missense_Mutation	SNP	T	T	A	rs200470462		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:39296412T>A	ENST00000345847.4	-	1	327	c.328A>T	c.(328-330)Agc>Tgc	p.S110C		NM_030976.1	NP_112238.1	Q9BYQ5	KRA46_HUMAN	keratin associated protein 4-6	110	30 X 5 AA repeats of C-C-[IRQVEL]-[SPTR]- [STVQRCP].					keratin filament (GO:0045095)		p.S110C(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|lung(1)|prostate(1)|urinary_tract(1)	9						CTGGAGATGCTGCAGCTGGGA	0.657																																					p.S110C		Atlas-SNP	.											KRTAP4-6,NS,carcinoma,0,2	KRTAP4-6	46	2	1	Substitution - Missense(1)	endometrium(1)	c.A328T						scavenged	.																																			SO:0001583	missense	81871	exon1			AGATGCTGCAGCT	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.328A>T	17.37:g.39296412T>A	ENSP00000328270:p.Ser110Cys	Somatic	64	1	0.015625		WXS	Illumina HiSeq	Phase_I	59	8	0.135593	NM_030976	Q9BYR1	Missense_Mutation	SNP	ENST00000345847.4	37	CCDS54125.1	.	.	.	.	.	.	.	.	.	.	.	2.702	-0.270707	0.05716	.	.	ENSG00000198090	ENST00000345847	T	0.00832	5.64	5.04	2.75	0.32379	.	.	.	.	.	T	0.00210	0.0006	N	0.00010	-3.04	0.19300	N	0.999971	.	.	.	.	.	.	T	0.44667	-0.9313	7	0.02654	T	1	.	3.2614	0.06850	0.543:0.0:0.1598:0.2972	.	.	.	.	C	110	ENSP00000328270:S110C	ENSP00000328270:S110C	S	-	1	0	KRTAP4-6	36549938	0.149000	0.22717	0.661000	0.29709	0.064000	0.16182	0.179000	0.16840	0.259000	0.21709	-0.319000	0.08680	AGC	.	.	weak		0.657	KRTAP4-6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257779.1		
TBC1D1	23216	hgsc.bcm.edu	37	4	38022219	38022219	+	Missense_Mutation	SNP	G	G	A	rs112261209	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:38022219G>A	ENST00000261439.4	+	5	1335	c.980G>A	c.(979-981)aGa>aAa	p.R327K	TBC1D1_ENST00000508802.1_Missense_Mutation_p.R327K	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	327	PID. {ECO:0000255|PROSITE- ProRule:PRU00148}.				membrane organization (GO:0061024)|regulation of protein localization (GO:0032880)	cytosol (GO:0005829)|nucleus (GO:0005634)	Rab GTPase activator activity (GO:0005097)			NS(1)|breast(3)|kidney(1)|large_intestine(5)|lung(19)|ovary(2)|prostate(2)|skin(2)|urinary_tract(1)	36						CAGGGCATCAGACACGTGGAC	0.473													G|||	8	0.00159744	0.0008	0.0	5008	,	,		18624	0.0		0.007	False		,,,				2504	0.0				p.R327K		Atlas-SNP	.											.	TBC1D1	94	.	0			c.G980A						PASS	.	G	LYS/ARG	12,4394	19.1+/-41.9	0,12,2191	281.0	268.0	272.0		980	5.4	1.0	4	dbSNP_132	272	115,8485	61.0+/-122.8	1,113,4186	yes	missense	TBC1D1	NM_015173.2	26	1,125,6377	AA,AG,GG		1.3372,0.2724,0.9765	benign	327/1169	38022219	127,12879	2203	4300	6503	SO:0001583	missense	23216	exon5			GCATCAGACACGT	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.980G>A	4.37:g.38022219G>A	ENSP00000261439:p.Arg327Lys	Somatic	235	0	0		WXS	Illumina HiSeq	Phase_I	250	115	0.46	NM_015173	B7Z3D9|E9PGH8|Q96K82|Q9UPP4	Missense_Mutation	SNP	ENST00000261439.4	37	CCDS33972.1	5	0.0022893772893772895	0	0.0	0	0.0	0	0.0	5	0.006596306068601583	G	12.08	1.830008	0.32329	0.002724	0.013372	ENSG00000065882	ENST00000508802;ENST00000261439;ENST00000446803	T;T;T	0.12879	2.64;2.64;2.64	5.41	5.41	0.78517	Phosphotyrosine interaction domain (3);Pleckstrin homology-type (1);	0.000000	0.50627	D	0.000107	T	0.04048	0.0113	N	0.01140	-0.99	0.80722	D	1	B;P;B	0.45957	0.379;0.869;0.379	B;P;B	0.48425	0.124;0.577;0.124	T	0.39121	-0.9629	10	0.02654	T	1	-22.2465	12.5429	0.56182	0.0763:0.0:0.9237:0.0	.	327;327;327	B9A6J6;E9PGH8;Q86TI0	.;.;TBCD1_HUMAN	K	327;327;198	ENSP00000423651:R327K;ENSP00000261439:R327K;ENSP00000396877:R198K	ENSP00000261439:R327K	R	+	2	0	TBC1D1	37698614	0.402000	0.25311	0.976000	0.42696	0.769000	0.43574	2.794000	0.47853	2.533000	0.85409	0.467000	0.42956	AGA	G|0.992;A|0.008	0.008	strong		0.473	TBC1D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317443.2	NM_015173	
DCHS2	54798	hgsc.bcm.edu	37	4	155287535	155287535	+	Missense_Mutation	SNP	T	T	C	rs10017772	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:155287535T>C	ENST00000357232.4	-	5	520	c.521A>G	c.(520-522)cAt>cGt	p.H174R	DCHS2_ENST00000339452.1_Missense_Mutation_p.H768R	NM_017639.3	NP_060109.2	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	174	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.		H -> R (in dbSNP:rs10017772). {ECO:0000269|PubMed:15489334}.		homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(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)		AAACACAGGATGATTATCATT	0.502													T|||	2313	0.461861	0.3873	0.4078	5008	,	,		20150	0.4474		0.492	False		,,,				2504	0.5849				p.H768R		Atlas-SNP	.											.	DCHS2	594	.	0			c.A2303G						PASS	.	T	ARG/HIS,ARG/HIS	1826,2580	533.3+/-373.7	382,1062,759	151.0	123.0	133.0		2303,521	2.1	0.0	4	dbSNP_119	133	3991,4609	552.7+/-386.2	938,2115,1247	yes	missense,missense	DCHS2	NM_001142552.1,NM_017639.3	29,29	1320,3177,2006	CC,CT,TT		46.407,41.4435,44.7255	benign,benign	768/1370,174/2917	155287535	5817,7189	2203	4300	6503	SO:0001583	missense	54798	exon3			ACAGGATGATTAT	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.521A>G	4.37:g.155287535T>C	ENSP00000349768:p.His174Arg	Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	177	80	0.451977	NM_001142552	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Missense_Mutation	SNP	ENST00000357232.4	37	CCDS3785.1	977	0.44734432234432236	187	0.3800813008130081	166	0.4585635359116022	248	0.43356643356643354	376	0.49604221635883905	T	0.331	-0.955864	0.02267	0.414435	0.46407	ENSG00000197410	ENST00000357232;ENST00000339452;ENST00000544161	T;T	0.58358	0.34;0.34	5.83	2.1	0.27182	Cadherin (3);Cadherin conserved site (1);Cadherin-like (1);	0.904858	0.09284	N	0.823281	T	0.00012	0.0000	N	0.01493	-0.835	0.54753	P	1.399999999995849E-5	B;B	0.13145	0.007;0.001	B;B	0.08055	0.003;0.0	T	0.47086	-0.9144	9	0.11182	T	0.66	.	5.1022	0.14766	0.0:0.1599:0.2882:0.5519	rs10017772;rs52822806;rs59714068;rs10017772	768;174	E9PC11;Q6V1P9	.;PCD23_HUMAN	R	174;768;768	ENSP00000349768:H174R;ENSP00000345062:H768R	ENSP00000345062:H768R	H	-	2	0	DCHS2	155506985	0.025000	0.19082	0.001000	0.08648	0.656000	0.38851	0.289000	0.18957	0.126000	0.18424	0.533000	0.62120	CAT	C|0.446;N|0.000	0.446	strong		0.502	DCHS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365281.2	NM_001142552	
ENG	2022	hgsc.bcm.edu	37	9	130616621	130616621	+	Missense_Mutation	SNP	G	G	A	rs35400405	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:130616621G>A	ENST00000373203.4	-	1	414	c.14C>T	c.(13-15)aCg>aTg	p.T5M	ENG_ENST00000344849.3_Missense_Mutation_p.T5M	NM_000118.2|NM_001114753.1|NM_001278138.1	NP_000109.1|NP_001108225.1|NP_001265067.1	P17813	EGLN_HUMAN	endoglin	5			T -> M (in dbSNP:rs35400405). {ECO:0000269|PubMed:9245986}.		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						CAGAGGGAGCGTGCCGCGGTC	0.721									Juvenile Polyposis;Hereditary Hemorrhagic Telangiectasia				g|||	204	0.0407348	0.1256	0.0231	5008	,	,		13491	0.0		0.0199	False		,,,				2504	0.002				p.T5M		Atlas-SNP	.											.	ENG	44	.	0			c.C14T	GRCh37	CM004889	ENG	M	rs35400405	PASS	.		MET/THR,MET/THR	445,3945		20,405,1770	33.0	35.0	34.0		14,14	0.1	0.0	9	dbSNP_126	34	196,8378		4,188,4095	yes	missense,missense	ENG	NM_000118.2,NM_001114753.1	81,81	24,593,5865	AA,AG,GG		2.286,10.1367,4.9445	possibly-damaging,possibly-damaging	5/626,5/659	130616621	641,12323	2195	4287	6482	SO:0001583	missense	2022	exon1	Familial Cancer Database	incl.: Juvenile Polyposis of the Stomach;HHT, Rendu-Osler-Weber disease, incl.: Pulmonary arteriovenous malformations, hypertrophic osteoarthropathy and juvenile polyposis,	GGGAGCGTGCCGC	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.14C>T	9.37:g.130616621G>A	ENSP00000362299:p.Thr5Met	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	117	61	0.521368	NM_001114753	Q14248|Q14926|Q5T9C0	Missense_Mutation	SNP	ENST00000373203.4	37	CCDS48029.1	91	0.041666666666666664	66	0.13414634146341464	10	0.027624309392265192	0	0.0	15	0.01978891820580475	G	3.401	-0.122326	0.06795	0.101367	0.02286	ENSG00000106991	ENST00000373203;ENST00000344849;ENST00000545345	T;T	0.42900	0.96;1.54	5.27	0.0968	0.14491	.	1.824350	0.02663	N	0.107751	T	0.00271	0.0008	N	0.08118	0	0.58432	P	4.000000000004E-6	B;B	0.09022	0.002;0.002	B;B	0.04013	0.001;0.001	T	0.11324	-1.0592	9	0.39692	T	0.17	-15.5952	8.2349	0.31620	0.4735:0.0:0.5265:0.0	rs35400405	5;5	Q5T9B9;P17813	.;EGLN_HUMAN	M	5	ENSP00000362299:T5M;ENSP00000341917:T5M	ENSP00000341917:T5M	T	-	2	0	ENG	129656442	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.362000	0.07602	0.037000	0.15575	-0.265000	0.10407	ACG	G|0.950;A|0.050	0.050	strong		0.721	ENG-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054313.1		
NPC1L1	29881	hgsc.bcm.edu	37	7	44579180	44579180	+	Silent	SNP	G	G	C	rs2072183	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:44579180G>C	ENST00000289547.4	-	2	871	c.816C>G	c.(814-816)ctC>ctG	p.L272L	NPC1L1_ENST00000423141.1_Silent_p.L272L|NPC1L1_ENST00000381160.3_Silent_p.L272L|NPC1L1_ENST00000546276.1_Silent_p.L272L	NM_013389.2	NP_037521.2	Q9UHC9	NPCL1_HUMAN	NPC1-like 1	272					cholesterol biosynthetic process (GO:0006695)|cholesterol transport (GO:0030301)|intestinal cholesterol absorption (GO:0030299)|lipoprotein metabolic process (GO:0042157)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)|sterol transport (GO:0015918)	brush border membrane (GO:0031526)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	drug binding (GO:0008144)|hedgehog receptor activity (GO:0008158)|myosin V binding (GO:0031489)|Rab GTPase binding (GO:0017137)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(4)|large_intestine(7)|lung(27)|ovary(6)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	57					Ezetimibe(DB00973)	AGGTGGAGTCGAGGGCCTGGG	0.612													C|||	1238	0.247204	0.1952	0.245	5008	,	,		20275	0.374		0.2336	False		,,,				2504	0.2025				p.L272L		Atlas-SNP	.											.	NPC1L1	141	.	0			c.C816G						PASS	.	C	,	971,3435		108,755,1340	50.0	54.0	53.0	http://www.ncbi.nlm.nih.gov/pubmed?term	816,816	4.0	0.4	7	dbSNP_96	53	1928,6672		234,1460,2606	yes	coding-synonymous,coding-synonymous	NPC1L1	NM_001101648.1,NM_013389.2	,	342,2215,3946	CC,CG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	22.4186,22.0381,22.2897	,	272/1333,272/1360	44579180	2899,10107	2203	4300	6503	SO:0001819	synonymous_variant	29881	exon2			GGAGTCGAGGGCC		CCDS5491.1, CCDS43575.1, CCDS75587.1	7p13	2012-11-15	2012-11-15		ENSG00000015520	ENSG00000015520			7898	protein-coding gene	gene with protein product		608010	"""NPC1 (Niemann-Pick disease, type C1, gene)-like 1"""			10783261	Standard	NM_013389		Approved		uc003tlb.3	Q9UHC9	OTTHUMG00000023691	ENST00000289547.4:c.816C>G	7.37:g.44579180G>C		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	101	73	0.722772	NM_001101648	A4D2J7|B7ZLE6|D3DVK9|Q17RV5|Q6R3Q4|Q9UHC8	Silent	SNP	ENST00000289547.4	37	CCDS5491.1																																																																																			G|0.762;C|0.238;A|0.000	0.238	strong		0.612	NPC1L1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251256.1	NM_013389	
WWP2	11060	hgsc.bcm.edu	37	16	69967897	69967897	+	Silent	SNP	T	T	C	rs2270841	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:69967897T>C	ENST00000359154.2	+	17	1808	c.1707T>C	c.(1705-1707)caT>caC	p.H569H	WWP2_ENST00000568684.1_Silent_p.H130H|WWP2_ENST00000544162.1_3'UTR|WWP2_ENST00000448661.1_Silent_p.H569H|MIR140_ENST00000385282.1_RNA|WWP2_ENST00000356003.2_Silent_p.H569H|WWP2_ENST00000542271.1_Silent_p.H453H	NM_001270454.1|NM_007014.4	NP_001257383.1|NP_008945.2	O00308	WWP2_HUMAN	WW domain containing E3 ubiquitin protein ligase 2	569	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						TCCTGTCTCATGAGGTGCTCA	0.483													C|||	4280	0.854633	0.947	0.7507	5008	,	,		23109	0.9683		0.7525	False		,,,				2504	0.7914				p.H569H		Atlas-SNP	.											WWP2,NS,carcinoma,0,1	WWP2	88	1	0			c.T1707C						PASS	.	C	,	3941,455	218.1+/-236.3	1767,407,24	186.0	170.0	175.0		1707,390	-3.6	0.8	16	dbSNP_100	175	6380,2220	378.8+/-339.0	2378,1624,298	no	coding-synonymous,coding-synonymous	WWP2	NM_007014.3,NM_199424.1	,	4145,2031,322	CC,CT,TT		25.814,10.3503,20.5833	,	569/871,130/432	69967897	10321,2675	2198	4300	6498	SO:0001819	synonymous_variant	11060	exon17			GTCTCATGAGGTG	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.1707T>C	16.37:g.69967897T>C		Somatic	187	0	0		WXS	Illumina HiSeq	Phase_I	180	179	0.994444	NM_001270454	A6NEP1|B2R706|B4DTL5|F5H213|H3BRF3|I3RSG8|Q6ZTQ5|Q96CZ2|Q9BWN6	Silent	SNP	ENST00000359154.2	37	CCDS10885.1																																																																																			T|0.194;C|0.806	0.806	strong		0.483	WWP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268954.1	NM_007014	
ZFP64	55734	hgsc.bcm.edu	37	20	50769549	50769549	+	Silent	SNP	A	A	G	rs3746413	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:50769549A>G	ENST00000216923.4	-	6	1531	c.1182T>C	c.(1180-1182)caT>caC	p.H394H	ZFP64_ENST00000346617.4_Silent_p.H340H|ZFP64_ENST00000371515.4_Silent_p.H392H|ZFP64_ENST00000477786.1_Intron|ZFP64_ENST00000361387.2_Intron|ZFP64_ENST00000371518.2_Intron	NM_018197.2|NM_199426.1	NP_060667.2|NP_955458.1	Q9NPA5	ZF64A_HUMAN	ZFP64 zinc finger protein	394					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(5)|large_intestine(8)|lung(11)|ovary(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	33						CCATGTCCCCATGGAACTTCT	0.567													A|||	840	0.167732	0.1445	0.2767	5008	,	,		20214	0.0843		0.2137	False		,,,				2504	0.1605				p.H394H		Atlas-SNP	.											.	ZFP64	240	.	0			c.T1182C						PASS	.	A	,,,	659,3747	281.6+/-276.1	52,555,1596	116.0	96.0	103.0		1182,1020,1176,	-0.1	0.4	20	dbSNP_107	103	1867,6733	332.4+/-320.1	193,1481,2626	no	coding-synonymous,coding-synonymous,coding-synonymous,intron	ZFP64	NM_018197.2,NM_022088.4,NM_199426.1,NM_199427.2	,,,	245,2036,4222	GG,GA,AA		21.7093,14.9569,19.4218	,,,	394/682,340/628,392/680,	50769549	2526,10480	2203	4300	6503	SO:0001819	synonymous_variant	55734	exon6			GTCCCCATGGAAC	AK001596	CCDS13439.1, CCDS13440.1, CCDS13441.1, CCDS13442.1	20q13.11-q13.13	2013-01-08	2012-11-27		ENSG00000020256	ENSG00000020256		"""Zinc fingers, C2H2-type"""	15940	protein-coding gene	gene with protein product			"""zinc finger protein 338"", ""zinc finger protein 64 homolog (mouse)"", ""zinc finger protein 64"""	ZNF338		9034307	Standard	NM_199427		Approved	FLJ10734, dJ831D17.1, FLJ12628, dJ548G19.1	uc002xwl.3	Q9NPA5	OTTHUMG00000032756	ENST00000216923.4:c.1182T>C	20.37:g.50769549A>G		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	69	34	0.492754	NM_018197	Q9NTS7|Q9NVH4	Silent	SNP	ENST00000216923.4	37	CCDS13440.1																																																																																			A|0.821;G|0.179	0.179	strong		0.567	ZFP64-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000079744.1	NM_018197	
MMS22L	253714	hgsc.bcm.edu	37	6	97613299	97613299	+	Missense_Mutation	SNP	G	G	A	rs10484830	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:97613299G>A	ENST00000275053.4	-	21	3309	c.3044C>T	c.(3043-3045)cCg>cTg	p.P1015L	MMS22L_ENST00000369251.2_Missense_Mutation_p.P975L	NM_198468.2	NP_940870.2	Q6ZRQ5	MMS22_HUMAN	MMS22-like, DNA repair protein	1015			P -> L (in dbSNP:rs10484830).		double-strand break repair via homologous recombination (GO:0000724)|replication fork processing (GO:0031297)	nuclear replication fork (GO:0043596)				breast(1)|endometrium(9)|kidney(2)|large_intestine(12)|lung(20)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	50						ATAGGCATTCGGATTTTGAGA	0.353													G|||	486	0.0970447	0.2935	0.0317	5008	,	,		17448	0.001		0.0298	False		,,,				2504	0.046				p.P1015L		Atlas-SNP	.											.	MMS22L	102	.	0			c.C3044T						PASS	.	G	LEU/PRO	1079,3327	389.3+/-327.3	136,807,1260	86.0	78.0	81.0		3044	4.7	1.0	6	dbSNP_119	81	346,8254	117.7+/-177.3	3,340,3957	yes	missense	MMS22L	NM_198468.2	98	139,1147,5217	AA,AG,GG		4.0233,24.4893,10.9565	benign	1015/1244	97613299	1425,11581	2203	4300	6503	SO:0001583	missense	253714	exon21			GCATTCGGATTTT		CCDS5039.1	6q16.3	2010-11-11	2010-11-11	2010-11-11	ENSG00000146263	ENSG00000146263			21475	protein-coding gene	gene with protein product		615614	"""chromosome 6 open reading frame 167"""	C6orf167		21055983, 21055984	Standard	NM_198468		Approved	dJ39B17.2	uc003ppb.3	Q6ZRQ5	OTTHUMG00000015248	ENST00000275053.4:c.3044C>T	6.37:g.97613299G>A	ENSP00000275053:p.Pro1015Leu	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	78	30	0.384615	NM_198468	D6R9Y8|D6RBQ4|E1P529|Q5THT2|Q68CQ6|Q68D32	Missense_Mutation	SNP	ENST00000275053.4	37	CCDS5039.1	181	0.08287545787545787	138	0.2804878048780488	14	0.03867403314917127	1	0.0017482517482517483	28	0.036939313984168866	G	14.46	2.541625	0.45280	0.244893	0.040233	ENSG00000146263	ENST00000275053;ENST00000369251	T;T	0.28255	1.62;1.62	5.65	4.7	0.59300	.	0.288860	0.38720	N	0.001593	T	0.10723	0.0262	L	0.40543	1.245	0.31635	P	0.648543	B;B	0.31680	0.335;0.335	B;B	0.25614	0.062;0.038	T	0.08764	-1.0706	9	0.41790	T	0.15	-3.6329	8.0473	0.30557	0.0:0.1139:0.4797:0.4064	rs10484830;rs52811524;rs10484830	975;1015	E2QRD4;Q6ZRQ5	.;MMS22_HUMAN	L	1015;975	ENSP00000275053:P1015L;ENSP00000358254:P975L	ENSP00000275053:P1015L	P	-	2	0	MMS22L	97720020	0.999000	0.42202	0.999000	0.59377	0.913000	0.54294	2.661000	0.46758	2.647000	0.89833	0.655000	0.94253	CCG	G|0.898;A|0.102	0.102	strong		0.353	MMS22L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041573.3	NM_198468	
KIAA1683	80726	hgsc.bcm.edu	37	19	18375563	18375563	+	Intron	SNP	G	G	A	rs12608744	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:18375563G>A	ENST00000600328.3	-	3	2810				KIAA1683_ENST00000392413.4_Silent_p.P929P|KIAA1683_ENST00000600359.3_Intron			Q9H0B3	K1683_HUMAN	KIAA1683							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						GCATGCTCTGGGGCAGGGCTT	0.667													G|||	911	0.181909	0.0121	0.3271	5008	,	,		18402	0.2341		0.2704	False		,,,				2504	0.1636				p.P929P		Atlas-SNP	.											.	KIAA1683	190	.	0			c.C2787T						PASS	.	G	,,	76,1308		0,76,616	27.0	31.0	30.0		2787,,	-5.0	0.0	19	dbSNP_120	30	847,2335		114,619,858	yes	coding-synonymous,intron,intron	KIAA1683	NM_001145304.1,NM_001145305.1,NM_025249.3	,,	114,695,1474	AA,AG,GG		26.6185,5.4913,20.2146	,,	929/1368,,	18375563	923,3643	692	1591	2283	SO:0001627	intron_variant	80726	exon3			GCTCTGGGGCAGG	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.2616+170C>T	19.37:g.18375563G>A		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	50	29	0.58	NM_001145304	B4DYH2|E9PDE0|E9PH54|Q2KHR5|Q8N4G8|Q96M14|Q9C0I0	Silent	SNP	ENST00000600328.3	37	CCDS32958.1																																																																																			G|0.789;A|0.211	0.211	strong		0.667	KIAA1683-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000466312.3		
CUTC	51076	hgsc.bcm.edu	37	10	101502968	101502968	+	Silent	SNP	A	A	G	rs3740076	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:101502968A>G	ENST00000370476.5	+	4	381	c.252A>G	c.(250-252)ccA>ccG	p.P84P	CUTC_ENST00000493385.1_3'UTR	NM_015960.2	NP_057044.2	Q9NTM9	CUTC_HUMAN	cutC copper transporter	84					copper ion homeostasis (GO:0055070)|copper ion transport (GO:0006825)|protein tetramerization (GO:0051262)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	copper ion binding (GO:0005507)			breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	14		Colorectal(252;0.234)		Epithelial(162;3e-10)|all cancers(201;2.37e-08)		TGATTCGGCCACGGGGAGGTG	0.418													A|||	320	0.0638978	0.0053	0.1499	5008	,	,		19471	0.0228		0.1083	False		,,,				2504	0.0787				p.P84P		Atlas-SNP	.											.	CUTC	32	.	0			c.A252G						PASS	.	A		81,4325	69.2+/-107.0	1,79,2123	215.0	198.0	204.0		252	0.7	1.0	10	dbSNP_107	204	928,7672	204.0+/-246.8	49,830,3421	no	coding-synonymous	CUTC	NM_015960.2		50,909,5544	GG,GA,AA		10.7907,1.8384,7.758		84/274	101502968	1009,11997	2203	4300	6503	SO:0001819	synonymous_variant	51076	exon4			TCGGCCACGGGGA	AF132966	CCDS7483.1	10q24.31	2013-07-31	2013-07-31		ENSG00000119929	ENSG00000119929			24271	protein-coding gene	gene with protein product		610101	"""cutC copper transporter homolog (E. coli)"""			16182249	Standard	NM_015960		Approved	CGI-32	uc001kqd.4	Q9NTM9	OTTHUMG00000018889	ENST00000370476.5:c.252A>G	10.37:g.101502968A>G		Somatic	321	0	0		WXS	Illumina HiSeq	Phase_I	255	114	0.447059	NM_015960	Q5TCZ8|Q9Y321	Silent	SNP	ENST00000370476.5	37	CCDS7483.1																																																																																			A|0.931;G|0.069	0.069	strong		0.418	CUTC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049811.1	NM_015960	
MUC4	4585	hgsc.bcm.edu	37	3	195507077	195507077	+	Missense_Mutation	SNP	G	G	A	rs76343663	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195507077G>A	ENST00000463781.3	-	2	11833	c.11374C>T	c.(11374-11376)Cct>Tct	p.P3792S	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.P3792S	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)		ACAGGAAGAGGGGTGGTGTCA	0.597																																					p.P3792S		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,+1,1	MUC4	1505	1	0			c.C11374T						scavenged	.						7.0	7.0	7.0					3																	195507077		624	1491	2115	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.11374C>T	3.37:g.195507077G>A	ENSP00000417498:p.Pro3792Ser	Somatic	22	3	0.136364		WXS	Illumina HiSeq	Phase_I	82	7	0.0853659	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	7.542	0.660889	0.14645	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.37058	1.43;1.22	.	.	.	.	0.555598	0.09973	N	0.732028	T	0.19485	0.0468	N	0.19112	0.55	0.19575	N	0.999969	B	0.15141	0.012	B	0.04013	0.001	T	0.27157	-1.0082	8	.	.	.	.	5.844	0.18652	9.0E-4:0.0:0.9991:0.0	.	3664	E7ESK3	.	S	3792	ENSP00000417498:P3792S;ENSP00000420243:P3792S	.	P	-	1	0	MUC4	196991856	0.000000	0.05858	0.110000	0.21437	0.110000	0.19582	-0.857000	0.04286	0.064000	0.16427	0.064000	0.15345	CCT	G|0.991;A|0.009	0.009	strong		0.597	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
OR51B4	79339	hgsc.bcm.edu	37	11	5322737	5322737	+	Missense_Mutation	SNP	A	A	G	rs10837771	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:5322737A>G	ENST00000380224.1	-	1	489	c.440T>C	c.(439-441)aTg>aCg	p.M147T	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	147			M -> T (in dbSNP:rs10837771). {ECO:0000269|PubMed:15489334}.		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)		AAAACCTCTCATCAGTACCCC	0.458													A|||	2215	0.442292	0.1195	0.4582	5008	,	,		21763	0.747		0.4473	False		,,,				2504	0.5481				p.M147T		Atlas-SNP	.											.	OR51B4	64	.	0			c.T440C						PASS	.	A	THR/MET	730,3672	300.1+/-286.2	63,604,1534	147.0	139.0	142.0		440	2.6	0.0	11	dbSNP_120	142	3745,4849	534.2+/-382.6	801,2143,1353	yes	missense	OR51B4	NM_033179.2	81	864,2747,2887	GG,GA,AA		43.5769,16.5834,34.4337	benign	147/311	5322737	4475,8521	2201	4297	6498	SO:0001583	missense	79339	exon1			CCTCTCATCAGTA	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.440T>C	11.37:g.5322737A>G	ENSP00000369573:p.Met147Thr	Somatic	216	1	0.00462963		WXS	Illumina HiSeq	Phase_I	213	156	0.732394	NM_033179	A7MAV5|Q6NTD7	Missense_Mutation	SNP	ENST00000380224.1	37	CCDS7757.1	1016	0.4652014652014652	76	0.15447154471544716	173	0.47790055248618785	435	0.7604895104895105	332	0.43799472295514513	A	0.539	-0.854514	0.02630	0.165834	0.435769	ENSG00000183251	ENST00000380224	T	0.35973	1.28	4.93	2.63	0.31362	GPCR, rhodopsin-like superfamily (1);	1.310660	0.05269	N	0.517263	T	0.00012	0.0000	L	0.28192	0.835	0.80722	P	0.0	B	0.16166	0.016	B	0.16289	0.015	T	0.40905	-0.9538	9	0.22109	T	0.4	.	8.3225	0.32136	0.8362:0.0:0.1638:0.0	rs10837771;rs52828011;rs60441744;rs10837771	147	Q9Y5P0	O51B4_HUMAN	T	147	ENSP00000369573:M147T	ENSP00000369573:M147T	M	-	2	0	OR51B4	5279313	0.000000	0.05858	0.001000	0.08648	0.055000	0.15305	0.397000	0.20883	0.386000	0.24997	0.533000	0.62120	ATG	A|0.589;G|0.411	0.411	strong		0.458	OR51B4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142956.2	NM_033179	
LTBP1	4052	hgsc.bcm.edu	37	2	33623567	33623567	+	Silent	SNP	G	G	A	rs138835287		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:33623567G>A	ENST00000404816.2	+	34	5474	c.5121G>A	c.(5119-5121)ccG>ccA	p.P1707P	LTBP1_ENST00000407925.1_Silent_p.P1381P|LTBP1_ENST00000402934.1_Silent_p.P1326P|LTBP1_ENST00000272273.5_Silent_p.P605P|LTBP1_ENST00000418533.2_Silent_p.P1339P|LTBP1_ENST00000404525.1_Silent_p.P1328P|LTBP1_ENST00000390003.4_Silent_p.P1382P|LTBP1_ENST00000354476.3_Silent_p.P1708P			Q14766	LTBP1_HUMAN	latent transforming growth factor beta binding protein 1	1707					extracellular matrix organization (GO:0030198)|sequestering of TGFbeta in extracellular matrix (GO:0035583)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|transforming growth factor beta binding (GO:0050431)|transforming growth factor beta-activated receptor activity (GO:0005024)	p.P1708P(1)		breast(2)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(13)|lung(60)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(3)	108	all_hematologic(175;0.115)	Medulloblastoma(90;0.215)				ACTGCACTCCGTTGAATACCG	0.458													G|||	1	0.000199681	0.0	0.0014	5008	,	,		21600	0.0		0.0	False		,,,				2504	0.0				p.P1707P		Atlas-SNP	.											LTBP1_ENST00000407925,NS,carcinoma,0,3	LTBP1	317	3	1	Substitution - coding silent(1)	lung(1)	c.G5121A						PASS	.	G	,,,,	0,4406		0,0,2203	123.0	99.0	107.0		4143,4017,3984,3858,5121	-9.1	0.0	2	dbSNP_134	107	21,8579	15.3+/-51.7	0,21,4279	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	LTBP1	NM_000627.3,NM_001166264.1,NM_001166265.1,NM_001166266.1,NM_206943.2	,,,,	0,21,6482	AA,AG,GG		0.2442,0.0,0.1615	,,,,	1381/1396,1339/1354,1328/1343,1286/1301,1707/1722	33623567	21,12985	2203	4300	6503	SO:0001819	synonymous_variant	4052	exon34			CACTCCGTTGAAT		CCDS33177.1, CCDS33178.1, CCDS33177.2, CCDS33178.2, CCDS54344.1, CCDS54345.1	2p22-p21	2008-05-23			ENSG00000049323	ENSG00000049323		"""Latent transforming growth factor, beta binding proteins"""	6714	protein-coding gene	gene with protein product	"""TGF-beta1-BP-1"""	150390				2350783, 11104663	Standard	NM_206943		Approved		uc021vft.1	Q14766	OTTHUMG00000152118	ENST00000404816.2:c.5121G>A	2.37:g.33623567G>A		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	107	55	0.514019	NM_206943	A1L3V1|P22064|Q53SD8|Q53SF3|Q53SG1|Q59HF7|Q8TD95	Silent	SNP	ENST00000404816.2	37	CCDS33177.2																																																																																			G|0.999;A|0.001	0.001	strong		0.458	LTBP1-014	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326227.2	NM_206943	
DDX19A	55308	hgsc.bcm.edu	37	16	70395387	70395387	+	Silent	SNP	C	C	T	rs1134074	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:70395387C>T	ENST00000302243.7	+	5	523	c.360C>T	c.(358-360)aaC>aaT	p.N120N	DDX19A_ENST00000417604.2_Intron|DDX19A_ENST00000562509.1_3'UTR|DDX19A_ENST00000443119.2_Silent_p.N30N|RP11-529K1.3_ENST00000567706.1_Intron	NM_018332.3	NP_060802.1	Q9NUU7	DD19A_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 19A	120	N-terminal lobe. {ECO:0000250}.				mRNA transport (GO:0051028)|positive regulation of apoptotic process (GO:0043065)|protein transport (GO:0015031)|response to zinc ion (GO:0010043)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear pore (GO:0005643)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|RNA binding (GO:0003723)			breast(1)|endometrium(1)|large_intestine(5)|lung(3)|urinary_tract(1)	11		Ovarian(137;0.221)				TACAAGAGAACGCATTACCCA	0.498													C|||	1130	0.225639	0.0234	0.3184	5008	,	,		19485	0.3036		0.3996	False		,,,				2504	0.1738				p.N120N		Atlas-SNP	.											.	DDX19A	39	.	0			c.C360T						PASS	.	C		368,4028	188.1+/-214.6	18,332,1848	145.0	112.0	123.0		360	-9.3	0.0	16	dbSNP_86	123	3273,5327	491.2+/-373.0	623,2027,1650	no	coding-synonymous	DDX19A	NM_018332.3		641,2359,3498	TT,TC,CC		38.0581,8.3712,28.0163		120/479	70395387	3641,9355	2198	4300	6498	SO:0001819	synonymous_variant	55308	exon5			AGAGAACGCATTA	AF183422	CCDS10889.1	16q22.1	2012-02-23	2012-02-23	2005-07-13	ENSG00000168872	ENSG00000168872		"""DEAD-boxes"""	25628	protein-coding gene	gene with protein product			"""DEAD (Asp-Glu-Ala-As) box polypeptide 19-like"""	DDX19L		12477932	Standard	NM_018332		Approved	FLJ11126		Q9NUU7	OTTHUMG00000137579	ENST00000302243.7:c.360C>T	16.37:g.70395387C>T		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	60	39	0.65	NM_018332	B2RPL0|B4DRZ7|Q53FM0	Silent	SNP	ENST00000302243.7	37	CCDS10889.1																																																																																			C|0.732;T|0.268	0.268	strong		0.498	DDX19A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268967.2	NM_018332	
SPATA31E1	286234	hgsc.bcm.edu	37	9	90503451	90503451	+	Missense_Mutation	SNP	G	G	A	rs11142017	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:90503451G>A	ENST00000325643.5	+	4	4115	c.4049G>A	c.(4048-4050)cGc>cAc	p.R1350H		NM_178828.4	NP_849150.3	Q6ZUB1	S31E1_HUMAN	SPATA31 subfamily E, member 1	1350			R -> H (in dbSNP:rs11142017). {ECO:0000269|PubMed:14702039}.		cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											GGTGACTTCCGCGCCCAGGAG	0.592													.|||	2304	0.460064	0.5151	0.4049	5008	,	,		19039	0.3373		0.5179	False		,,,				2504	0.4918				p.R1350H		Atlas-SNP	.											.	.	.	.	0			c.G4049A						PASS	.	A	HIS/ARG	2192,2214	589.5+/-387.1	542,1108,553	86.0	77.0	80.0		4049	1.2	0.0	9	dbSNP_120	80	4226,4374	583.5+/-391.6	1067,2092,1141	yes	missense	C9orf79	NM_178828.4	29	1609,3200,1694	AA,AG,GG		49.1395,49.7503,49.3465	benign	1350/1446	90503451	6418,6588	2203	4300	6503	SO:0001583	missense	286234	exon4			ACTTCCGCGCCCA	AK093185	CCDS6676.1	9q22.1-q22.2	2012-10-12	2012-10-12	2012-10-12	ENSG00000177992	ENSG00000177992			26672	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 79"", ""family with sequence similarity 75, member E1"""	C9orf79, FAM75E1			Standard	NM_178828		Approved	FLJ35866	uc004app.4	Q6ZUB1	OTTHUMG00000020157	ENST00000325643.5:c.4049G>A	9.37:g.90503451G>A	ENSP00000322640:p.Arg1350His	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	106	47	0.443396	NM_178828	B2RPB1|Q5SQC9|Q8NA41|Q8ND27	Missense_Mutation	SNP	ENST00000325643.5	37	CCDS6676.1	982	0.44963369963369965	245	0.49796747967479676	157	0.43370165745856354	192	0.3356643356643357	388	0.5118733509234829	a	7.370	0.626610	0.14257	0.497503	0.491395	ENSG00000177992	ENST00000325643	T	0.03717	3.83	2.47	1.25	0.21368	.	2.244580	0.02369	N	0.077687	T	0.00012	0.0000	N	0.01352	-0.895	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.43956	-0.9359	9	0.42905	T	0.14	.	2.9167	0.05755	0.586:0.2613:0.1527:0.0	rs11142017;rs11142017	1350	Q6ZUB1	CI079_HUMAN	H	1350	ENSP00000322640:R1350H	ENSP00000322640:R1350H	R	+	2	0	C9orf79	89693271	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	0.117000	0.15583	-0.023000	0.13963	-0.254000	0.11334	CGC	G|0.532;A|0.468	0.468	strong		0.592	SPATA31E1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052954.2	NM_178828	
NPC1L1	29881	hgsc.bcm.edu	37	7	44553238	44553238	+	Silent	SNP	A	A	G	rs217434	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:44553238A>G	ENST00000289547.4	-	20	3943	c.3888T>C	c.(3886-3888)gtT>gtC	p.V1296V	NPC1L1_ENST00000546276.1_Silent_p.V1223V|NPC1L1_ENST00000381160.3_Silent_p.V1269V	NM_013389.2	NP_037521.2	Q9UHC9	NPCL1_HUMAN	NPC1-like 1	1296					cholesterol biosynthetic process (GO:0006695)|cholesterol transport (GO:0030301)|intestinal cholesterol absorption (GO:0030299)|lipoprotein metabolic process (GO:0042157)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)|sterol transport (GO:0015918)	brush border membrane (GO:0031526)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	drug binding (GO:0008144)|hedgehog receptor activity (GO:0008158)|myosin V binding (GO:0031489)|Rab GTPase binding (GO:0017137)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(4)|large_intestine(7)|lung(27)|ovary(6)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	57					Ezetimibe(DB00973)	GAGCCGGGTTAACGTCAGGCC	0.607													G|||	583	0.116414	0.1483	0.1153	5008	,	,		18730	0.005		0.1789	False		,,,				2504	0.1247				p.V1296V		Atlas-SNP	.											NPC1L1,right_lower_lobe,carcinoma,-2,1	NPC1L1	141	1	0			c.T3888C						PASS	.	G	,	741,3665	756.4+/-412.6	61,619,1523	53.0	55.0	55.0		3807,3888	1.0	0.3	7	dbSNP_79	55	1733,6867	736.0+/-407.0	177,1379,2744	no	coding-synonymous,coding-synonymous	NPC1L1	NM_001101648.1,NM_013389.2	,	238,1998,4267	GG,GA,AA		20.1512,16.818,19.022	,	1269/1333,1296/1360	44553238	2474,10532	2203	4300	6503	SO:0001819	synonymous_variant	29881	exon20			CGGGTTAACGTCA		CCDS5491.1, CCDS43575.1, CCDS75587.1	7p13	2012-11-15	2012-11-15		ENSG00000015520	ENSG00000015520			7898	protein-coding gene	gene with protein product		608010	"""NPC1 (Niemann-Pick disease, type C1, gene)-like 1"""			10783261	Standard	NM_013389		Approved		uc003tlb.3	Q9UHC9	OTTHUMG00000023691	ENST00000289547.4:c.3888T>C	7.37:g.44553238A>G		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	39	34	0.871795	NM_013389	A4D2J7|B7ZLE6|D3DVK9|Q17RV5|Q6R3Q4|Q9UHC8	Silent	SNP	ENST00000289547.4	37	CCDS5491.1																																																																																			A|0.838;G|0.162	0.162	strong		0.607	NPC1L1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251256.1	NM_013389	
ELSPBP1	64100	hgsc.bcm.edu	37	19	48519205	48519205	+	Silent	SNP	C	C	T	rs34647554	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:48519205C>T	ENST00000339841.2	+	4	442	c.264C>T	c.(262-264)tgC>tgT	p.C88C	ELSPBP1_ENST00000597519.1_Intron	NM_022142.4	NP_071425.3	Q96BH3	ESPB1_HUMAN	epididymal sperm binding protein 1	88	Fibronectin type-II 2. {ECO:0000255|PROSITE-ProRule:PRU00479}.				single fertilization (GO:0007338)	extracellular region (GO:0005576)				NS(1)|breast(1)|kidney(1)|large_intestine(1)|lung(6)	10		all_cancers(25;8.7e-09)|all_lung(116;1.15e-06)|all_epithelial(76;1.17e-06)|Lung NSC(112;2.56e-06)|all_neural(266;0.0138)|Ovarian(192;0.0261)|Breast(70;0.203)		OV - Ovarian serous cystadenocarcinoma(262;0.000253)|all cancers(93;0.00129)|Epithelial(262;0.0314)|GBM - Glioblastoma multiforme(486;0.0606)		ATAACAGCTGCATCTCCCAGG	0.483													c|||	473	0.0944489	0.0129	0.0937	5008	,	,		21102	0.0685		0.1352	False		,,,				2504	0.1902				p.C88C		Atlas-SNP	.											.	ELSPBP1	29	.	0			c.C264T						PASS	.	C		153,4253	106.9+/-145.3	2,149,2052	121.0	100.0	107.0		264	2.3	0.3	19	dbSNP_126	107	1145,7455	235.7+/-268.2	74,997,3229	no	coding-synonymous	ELSPBP1	NM_022142.4		76,1146,5281	TT,TC,CC		13.314,3.4725,9.98		88/224	48519205	1298,11708	2203	4300	6503	SO:0001819	synonymous_variant	64100	exon4			CAGCTGCATCTCC	AJ278478	CCDS12708.1	19q13.33	2009-09-17							14417	protein-coding gene	gene with protein product	"""epididymal protein 12"""	607443					Standard	NM_022142		Approved	HE12, E12, EDDM12	uc002pht.3	Q96BH3		ENST00000339841.2:c.264C>T	19.37:g.48519205C>T		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	77	41	0.532468	NM_022142	Q96RT0|Q9H4C8	Silent	SNP	ENST00000339841.2	37	CCDS12708.1																																																																																			C|0.902;T|0.098	0.098	strong		0.483	ELSPBP1-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465207.1		
PCNT	5116	hgsc.bcm.edu	37	21	47860110	47860110	+	Missense_Mutation	SNP	G	G	A	rs563489032		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:47860110G>A	ENST00000359568.5	+	42	9495	c.9388G>A	c.(9388-9390)Gtc>Atc	p.V3130I	PCNT_ENST00000480896.1_3'UTR	NM_006031.5	NP_006022.3	O95613	PCNT_HUMAN	pericentrin	3130	Interaction with NEK2.				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)					CACCAGCAATGTCAAGGTAGG	0.542																																					p.V3130I		Atlas-SNP	.											.	PCNT	283	.	0			c.G9388A						PASS	.						59.0	66.0	63.0					21																	47860110		2203	4299	6502	SO:0001583	missense	5116	exon42			AGCAATGTCAAGG	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.9388G>A	21.37:g.47860110G>A	ENSP00000352572:p.Val3130Ile	Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	35	12	0.342857	NM_006031	O43152|Q7Z7C9	Missense_Mutation	SNP	ENST00000359568.5	37	CCDS33592.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	5.094|5.094	0.202944|0.202944	0.09704|0.09704	.|.	.|.	ENSG00000160299|ENSG00000160299	ENST00000418394|ENST00000359568	.|T	.|0.01505	.|4.82	4.3|4.3	-4.62|-4.62	0.03370|0.03370	.|.	.|.	.|.	.|.	.|.	T|T	0.01092|0.01092	0.0036|0.0036	N|N	0.17474|0.17474	0.49|0.49	0.09310|0.09310	N|N	1|1	.|B;B	.|0.17038	.|0.02;0.012	.|B;B	.|0.14578	.|0.011;0.005	T|T	0.48269|0.48269	-0.9050|-0.9050	5|9	.|0.16420	.|T	.|0.52	.|.	6.8565|6.8565	0.24044|0.24044	0.5669:0.0:0.3097:0.1234|0.5669:0.0:0.3097:0.1234	.|.	.|2933;3130	.|O95613-2;O95613	.|.;PCNT_HUMAN	I|I	110|3130	.|ENSP00000352572:V3130I	.|ENSP00000352572:V3130I	M|V	+|+	3|1	0|0	PCNT|PCNT	46684538|46684538	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.005000|0.005000	0.04900|0.04900	-1.051000|-1.051000	0.03507|0.03507	-1.138000|-1.138000	0.02884|0.02884	-0.136000|-0.136000	0.14681|0.14681	ATG|GTC	.	.	none		0.542	PCNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207336.1	NM_006031	
CCDC66	285331	hgsc.bcm.edu	37	3	56628031	56628031	+	Missense_Mutation	SNP	G	G	A	rs7637449	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:56628031G>A	ENST00000394672.3	+	10	1449	c.1379G>A	c.(1378-1380)cGa>cAa	p.R460Q	CCDC66_ENST00000326595.7_Missense_Mutation_p.R426Q|CCDC66_ENST00000436465.2_Missense_Mutation_p.R460Q	NM_001012506.4|NM_001141947.1	NP_001012524.4|NP_001135419.1	A2RUB6	CCD66_HUMAN	coiled-coil domain containing 66	460			R -> Q (in dbSNP:rs7637449). {ECO:0000269|PubMed:15489334}.		post-embryonic retina morphogenesis in camera-type eye (GO:0060060)|retinal rod cell development (GO:0046548)					breast(1)|kidney(1)|large_intestine(2)|liver(1)|lung(4)|skin(2)|urinary_tract(1)	12				KIRC - Kidney renal clear cell carcinoma(284;0.0478)|Kidney(284;0.0597)|OV - Ovarian serous cystadenocarcinoma(275;0.233)		CGAGACAGACGACGACAAAAA	0.378													G|||	1077	0.215056	0.0741	0.2839	5008	,	,		20188	0.0486		0.5388	False		,,,				2504	0.1953				p.R460Q		Atlas-SNP	.											.	CCDC66	145	.	0			c.G1379A						PASS	.	G	GLN/ARG,GLN/ARG	678,3728	287.2+/-279.2	66,546,1591	181.0	169.0	173.0		1277,1379	5.8	0.9	3	dbSNP_116	173	4621,3979	600.5+/-394.2	1241,2139,920	yes	missense,missense	CCDC66	NM_001012506.4,NM_001141947.1	43,43	1307,2685,2511	AA,AG,GG		46.2674,15.3881,40.7427	probably-damaging,probably-damaging	426/915,460/949	56628031	5299,7707	2203	4300	6503	SO:0001583	missense	285331	exon10			ACAGACGACGACA	AL832692	CCDS33770.2, CCDS46852.1	3p14.3	2006-03-27			ENSG00000180376	ENSG00000180376			27709	protein-coding gene	gene with protein product						14702039	Standard	NR_024460		Approved	DKFZp686C0433	uc003dhz.3	A2RUB6	OTTHUMG00000155748	ENST00000394672.3:c.1379G>A	3.37:g.56628031G>A	ENSP00000378167:p.Arg460Gln	Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	120	120	1	NM_001141947	B3KWL8|Q4VC34|Q8N949	Missense_Mutation	SNP	ENST00000394672.3	37	CCDS46852.1	617	0.2825091575091575	42	0.08536585365853659	118	0.3259668508287293	34	0.05944055944055944	423	0.558047493403694	G	29.8	5.038495	0.93630	0.153881	0.537326	ENSG00000180376	ENST00000422222;ENST00000394672;ENST00000326595;ENST00000436465	T;T;T;T	0.55930	0.49;0.49;0.49;0.49	5.81	5.81	0.92471	.	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	M	0.66939	2.045	0.09310	P	1.0	D	0.89917	1.0	D	0.91635	0.999	T	0.51521	-0.8695	9	0.72032	D	0.01	-9.6521	17.8518	0.88748	0.0:0.0:1.0:0.0	rs7637449;rs52797312;rs58163850;rs7637449	460	A2RUB6	CCD66_HUMAN	Q	416;460;426;460	ENSP00000401451:R416Q;ENSP00000378167:R460Q;ENSP00000326050:R426Q;ENSP00000404320:R460Q	ENSP00000326050:R426Q	R	+	2	0	CCDC66	56603071	0.998000	0.40836	0.875000	0.34327	0.968000	0.65278	4.880000	0.63107	2.739000	0.93911	0.585000	0.79938	CGA	G|0.660;A|0.340	0.340	strong		0.378	CCDC66-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341473.1	NM_001012506	
MYO9B	4650	hgsc.bcm.edu	37	19	17305440	17305440	+	Silent	SNP	T	T	C	rs1064305	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:17305440T>C	ENST00000594824.1	+	22	3351	c.3204T>C	c.(3202-3204)ggT>ggC	p.G1068G	MYO9B_ENST00000595618.1_Silent_p.G1068G|MYO9B_ENST00000397274.2_Silent_p.G1068G			Q13459	MYO9B_HUMAN	myosin IXB	1068	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						CAAGAGCAGGTGCTGAGGAGG	0.642													C|||	3226	0.644169	0.7905	0.7046	5008	,	,		16150	0.7401		0.3877	False		,,,				2504	0.5685				p.G1068G		Atlas-SNP	.											.	MYO9B	264	.	0			c.T3204C						PASS	.	C	,	3162,1184		1162,838,173	18.0	23.0	21.0		3204,3204	-8.2	0.0	19	dbSNP_86	21	3437,5121		723,1991,1565	no	coding-synonymous,coding-synonymous	MYO9B	NM_001130065.1,NM_004145.3	,	1885,2829,1738	CC,CT,TT		40.1613,27.2434,48.8608	,	1068/2023,1068/2158	17305440	6599,6305	2173	4279	6452	SO:0001819	synonymous_variant	4650	exon22			AGCAGGTGCTGAG		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.3204T>C	19.37:g.17305440T>C		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	93	42	0.451613	NM_001130065	O75314|Q9NUJ2|Q9UHN0	Silent	SNP	ENST00000594824.1	37																																																																																				T|0.392;C|0.608	0.608	strong		0.642	MYO9B-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000463236.1		
GPR112	139378	hgsc.bcm.edu	37	X	135426693	135426693	+	Missense_Mutation	SNP	A	A	G	rs4829829	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:135426693A>G	ENST00000394143.1	+	6	1119	c.828A>G	c.(826-828)atA>atG	p.I276M	GPR112_ENST00000412101.1_Missense_Mutation_p.I71M|GPR112_ENST00000370652.1_Missense_Mutation_p.I276M|GPR112_ENST00000287534.4_Missense_Mutation_p.I213M|GPR112_ENST00000394141.1_Missense_Mutation_p.I71M	NM_153834.3	NP_722576.3	Q8IZF6	GP112_HUMAN	G protein-coupled receptor 112	276			I -> M (in dbSNP:rs4829829). {ECO:0000269|Ref.2}.		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(13)|central_nervous_system(2)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(33)|lung(97)|ovary(5)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(2)	199	Acute lymphoblastic leukemia(192;0.000127)					GCATACCTATATTTGCAACTG	0.363													a|||	1702	0.450861	0.4228	0.3545	3775	,	,		15401	0.2024		0.3738	False		,,,				2504	0.3241				p.I276M		Atlas-SNP	.											.	GPR112	459	.	0			c.A828G						PASS	.		MET/ILE	2087,1748		484,812,307,336,264	199.0	154.0	169.0		828	-8.6	0.0	X	dbSNP_111	169	3203,3525		555,1185,908,688,964	yes	missense	GPR112	NM_153834.3	10	1039,1997,1215,1024,1228	GG,GA,G,AA,A		47.607,45.5802,49.9195	benign	276/3081	135426693	5290,5273	2203	4300	6503	SO:0001583	missense	139378	exon6			ACCTATATTTGCA	AY140954	CCDS35409.1	Xq26.3	2014-08-08			ENSG00000156920	ENSG00000156920		"""-"", ""GPCR / Class B : Orphans"""	18992	protein-coding gene	gene with protein product						12435584	Standard	XM_005262367		Approved	RP1-299I16, PGR17	uc004ezu.1	Q8IZF6	OTTHUMG00000022508	ENST00000394143.1:c.828A>G	X.37:g.135426693A>G	ENSP00000377699:p.Ile276Met	Somatic	283	0	0		WXS	Illumina HiSeq	Phase_I	153	153	1	NM_153834	A2A2J1|A2A2J2|Q5EGP2|Q86SM6	Missense_Mutation	SNP	ENST00000394143.1	37	CCDS35409.1	710	0.4279686558167571	138	0.372972972972973	80	0.27972027972027974	76	0.15702479338842976	187	0.3191126279863481	a	2.435	-0.329891	0.05314	0.544198	0.47607	ENSG00000156920	ENST00000394143;ENST00000370652;ENST00000412101;ENST00000287534;ENST00000394141	T;T;T;T;T	0.30448	1.55;1.55;1.53;1.66;1.53	4.27	-8.55	0.00908	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B;B	0.11235	0.004;0.002;0.001	B;B;B	0.09377	0.004;0.004;0.002	T	0.43228	-0.9404	8	0.37606	T	0.19	.	0.3544	0.00354	0.2435:0.2422:0.2647:0.2496	rs4829829;rs59872615;rs4829829	213;71;276	Q8IZF6-2;Q8IZF6-3;Q8IZF6	.;.;GP112_HUMAN	M	276;276;71;213;71	ENSP00000377699:I276M;ENSP00000359686:I276M;ENSP00000416526:I71M;ENSP00000287534:I213M;ENSP00000377697:I71M	ENSP00000287534:I213M	I	+	3	3	GPR112	135254359	0.001000	0.12720	0.000000	0.03702	0.050000	0.14768	-0.872000	0.04219	-2.190000	0.00757	-0.485000	0.04761	ATA	A|0.517;0|0.025	.	strong		0.363	GPR112-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000286639.1		
OR10AD1	121275	hgsc.bcm.edu	37	12	48597064	48597064	+	Silent	SNP	A	A	G	rs17224828	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:48597064A>G	ENST00000310248.2	-	1	106	c.12T>C	c.(10-12)aaT>aaC	p.N4N		NM_001004134.1	NP_001004134.1	Q8NGE0	O10AD_HUMAN	olfactory receptor, family 10, subfamily AD, member 1	4						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(2)|lung(3)|ovary(1)|stomach(1)|urinary_tract(1)	9						CTATGCTGCCATTCCTTAGCA	0.517													G|||	212	0.0423323	0.059	0.036	5008	,	,		22556	0.006		0.0915	False		,,,				2504	0.0112				p.N4N		Atlas-SNP	.											.	OR10AD1	24	.	0			c.T12C						PASS	.	G		271,4135	767.2+/-413.5	7,257,1939	44.0	42.0	43.0		12	-5.8	0.0	12	dbSNP_123	43	761,7839	754.1+/-407.5	28,705,3567	no	coding-synonymous	OR10AD1	NM_001004134.1		35,962,5506	GG,GA,AA		8.8488,6.1507,7.9348		4/318	48597064	1032,11974	2203	4300	6503	SO:0001819	synonymous_variant	121275	exon1			GCTGCCATTCCTT		CCDS31787.1	12q13.11	2013-09-24	2002-11-13	2002-11-15	ENSG00000172640	ENSG00000172640		"""GPCR / Class A : Olfactory receptors"""	14819	protein-coding gene	gene with protein product			"""olfactory receptor, family 10, subfamily AD, member 1 pseudogene"""	OR10AD1P			Standard	NM_001004134		Approved		uc001rrl.1	Q8NGE0	OTTHUMG00000168027	ENST00000310248.2:c.12T>C	12.37:g.48597064A>G		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	41	25	0.609756	NM_001004134	B9EGT9|Q6IFA8	Silent	SNP	ENST00000310248.2	37	CCDS31787.1																																																																																			A|0.939;G|0.061	0.061	strong		0.517	OR10AD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397577.1		
ENGASE	64772	hgsc.bcm.edu	37	17	77079576	77079576	+	Silent	SNP	A	A	G	rs61756761	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:77079576A>G	ENST00000579016.1	+	9	1155	c.1155A>G	c.(1153-1155)cgA>cgG	p.R385R	ENGASE_ENST00000584568.1_3'UTR	NM_001042573.2	NP_001036038.1	Q8NFI3	ENASE_HUMAN	endo-beta-N-acetylglucosaminidase	385						cytoplasm (GO:0005737)	mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase activity (GO:0033925)			breast(2)|endometrium(4)|large_intestine(1)|lung(15)|prostate(2)|skin(1)	25						TCTGGGGCCGACTGGAGCGTT	0.612													G|||	682	0.136182	0.357	0.0677	5008	,	,		20375	0.0476		0.0577	False		,,,				2504	0.0583				p.R385R		Atlas-SNP	.											ENGASE,NS,carcinoma,+1,1	ENGASE	55	1	0			c.A1155G						scavenged	.	G		1152,3078		150,852,1113	92.0	102.0	99.0		1155	5.5	0.9	17	dbSNP_129	99	481,7973		9,463,3755	no	coding-synonymous	ENGASE	NM_001042573.1		159,1315,4868	GG,GA,AA		5.6896,27.234,12.8745		385/744	77079576	1633,11051	2115	4227	6342	SO:0001819	synonymous_variant	64772	exon9			GGGCCGACTGGAG	AF512564	CCDS42394.1	17q25.3	2009-03-03			ENSG00000167280	ENSG00000167280	3.2.1.96		24622	protein-coding gene	gene with protein product	"""Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase"", ""Di-N-acetylchitobiosyl beta-N-acetylglucosaminidase"""	611898				12114544, 18586680	Standard	NM_001042573		Approved	FLJ21865	uc002jwv.4	Q8NFI3	OTTHUMG00000167714	ENST00000579016.1:c.1155A>G	17.37:g.77079576A>G		Somatic	131	1	0.00763359		WXS	Illumina HiSeq	Phase_I	120	59	0.491667	NM_001042573	Q659F0|Q8TB86|Q9H6U4	Silent	SNP	ENST00000579016.1	37	CCDS42394.1																																																																																			A|0.902;G|0.098	0.098	strong		0.612	ENGASE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395807.1	NM_022759	
AMZ1	155185	hgsc.bcm.edu	37	7	2752456	2752456	+	Nonsense_Mutation	SNP	C	C	T	rs145687592	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:2752456C>T	ENST00000312371.4	+	7	1809	c.1441C>T	c.(1441-1443)Cga>Tga	p.R481*	AMZ1_ENST00000489665.1_Intron|AMZ1_ENST00000407112.1_3'UTR	NM_133463.1	NP_597720.1	Q400G9	AMZ1_HUMAN	archaelysin family metallopeptidase 1	481							metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(2)|kidney(1)|large_intestine(4)|lung(8)|skin(1)	16		Ovarian(82;0.0779)		OV - Ovarian serous cystadenocarcinoma(56;5.03e-14)		GCTGAGTGCCCGAAAACTCGC	0.657													C|||	4	0.000798722	0.0008	0.0029	5008	,	,		18095	0.0		0.001	False		,,,				2504	0.0				p.R481X		Atlas-SNP	.											.	AMZ1	41	.	0			c.C1441T						PASS	.	C	stop/ARG	2,4396		0,2,2197	30.0	33.0	32.0		1441	2.5	0.0	7	dbSNP_134	32	30,8562		0,30,4266	no	stop-gained	AMZ1	NM_133463.1		0,32,6463	TT,TC,CC		0.3492,0.0455,0.2463		481/499	2752456	32,12958	2199	4296	6495	SO:0001587	stop_gained	155185	exon7			AGTGCCCGAAAAC	AB075830	CCDS34589.1, CCDS64582.1	7p22.3	2008-01-17			ENSG00000174945	ENSG00000174945			22231	protein-coding gene	gene with protein product	"""archaemetzincin-1"""	615168				15972818	Standard	NM_133463		Approved	KIAA1950	uc003smr.1	Q400G9	OTTHUMG00000152111	ENST00000312371.4:c.1441C>T	7.37:g.2752456C>T	ENSP00000308149:p.Arg481*	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	100	21	0.21	NM_133463	B3KRS0|Q8TF51	Nonsense_Mutation	SNP	ENST00000312371.4	37	CCDS34589.1	.	.	.	.	.	.	.	.	.	.	C	37	6.264480	0.97426	4.55E-4	0.003492	ENSG00000174945	ENST00000312371	.	.	.	4.68	2.5	0.30297	.	0.125168	0.34025	N	0.004323	.	.	.	.	.	.	0.09310	N	0.999996	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-23.2544	6.85	0.24010	0.3424:0.5583:0.0:0.0993	.	.	.	.	X	481	.	ENSP00000308149:R481X	R	+	1	2	AMZ1	2718982	0.042000	0.20092	0.001000	0.08648	0.011000	0.07611	0.315000	0.19451	0.459000	0.27016	0.561000	0.74099	CGA	C|0.998;T|0.002	0.002	strong		0.657	AMZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325244.1	NM_133463	
CCL3	6348	hgsc.bcm.edu	37	17	34416537	34416537	+	Silent	SNP	G	G	A	rs1130371	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:34416537G>A	ENST00000225245.5	-	2	262	c.180C>T	c.(178-180)ccC>ccT	p.P60P	AC069363.1_ENST00000441575.1_RNA|AC069363.1_ENST00000590992.1_RNA|AC069363.1_ENST00000592728.1_RNA	NM_002983.2	NP_002974.1	P10147	CCL3_HUMAN	chemokine (C-C motif) ligand 3	60					astrocyte cell migration (GO:0043615)|behavior (GO:0007610)|calcium ion transport (GO:0006816)|calcium-mediated signaling (GO:0019722)|cell activation (GO:0001775)|cell-cell signaling (GO:0007267)|cellular calcium ion homeostasis (GO:0006874)|cellular response to interferon-gamma (GO:0071346)|cellular response to interleukin-1 (GO:0071347)|cellular response to organic cyclic compound (GO:0071407)|cellular response to tumor necrosis factor (GO:0071356)|chemotaxis (GO:0006935)|cytoskeleton organization (GO:0007010)|eosinophil chemotaxis (GO:0048245)|eosinophil degranulation (GO:0043308)|exocytosis (GO:0006887)|granulocyte chemotaxis (GO:0071621)|inflammatory response (GO:0006954)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|lymphocyte chemotaxis (GO:0048247)|macrophage chemotaxis (GO:0048246)|MAPK cascade (GO:0000165)|monocyte chemotaxis (GO:0002548)|negative regulation by host of viral transcription (GO:0043922)|negative regulation of bone mineralization (GO:0030502)|negative regulation of gene expression (GO:0010629)|negative regulation of osteoclast differentiation (GO:0045671)|neutrophil chemotaxis (GO:0030593)|osteoblast differentiation (GO:0001649)|positive chemotaxis (GO:0050918)|positive regulation of calcium ion import (GO:0090280)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of catalytic activity (GO:0043085)|positive regulation of cell migration (GO:0030335)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of gene expression (GO:0010628)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interleukin-1 beta secretion (GO:0050718)|positive regulation of natural killer cell chemotaxis (GO:2000503)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of tumor necrosis factor production (GO:0032760)|protein kinase B signaling (GO:0043491)|protein phosphorylation (GO:0006468)|regulation of cell shape (GO:0008360)|regulation of sensory perception of pain (GO:0051930)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to cholesterol (GO:0070723)|response to toxic substance (GO:0009636)|signaling (GO:0023052)|T cell chemotaxis (GO:0010818)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|intracellular (GO:0005622)	calcium-dependent protein kinase C activity (GO:0004698)|CCR1 chemokine receptor binding (GO:0031726)|CCR5 chemokine receptor binding (GO:0031730)|chemoattractant activity (GO:0042056)|chemokine activity (GO:0008009)|identical protein binding (GO:0042802)|kinase activity (GO:0016301)|phospholipase activator activity (GO:0016004)|protein kinase activity (GO:0004672)			breast(2)|lung(3)|urinary_tract(1)	6		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		ACATGACACCGGGCTTGGAGC	0.582													G|||	1107	0.221046	0.1331	0.1182	5008	,	,		18931	0.3532		0.2505	False		,,,				2504	0.2464				p.P60P		Atlas-SNP	.											.	CCL3	8	.	0			c.C180T						PASS	.	G		611,3795		40,531,1632	155.0	150.0	152.0		180	-10.8	1.0	17	dbSNP_86	152	2001,6599		243,1515,2542	no	coding-synonymous	CCL3	NM_002983.2		283,2046,4174	AA,AG,GG		23.2674,13.8675,20.083		60/93	34416537	2612,10394	2203	4300	6503	SO:0001819	synonymous_variant	6348	exon2			GACACCGGGCTTG	M23178	CCDS11307.1	17q12	2014-05-06	2002-08-22	2002-08-23	ENSG00000006075	ENSG00000277632		"""Chemokine ligands"", ""Endogenous ligands"""	10627	protein-coding gene	gene with protein product		182283	"""small inducible cytokine A3 (homologous to mouse Mip-1a)"""	SCYA3			Standard	NM_002983		Approved	G0S19-1, LD78ALPHA, MIP-1-alpha	uc002hkv.3	P10147	OTTHUMG00000188413	ENST00000225245.5:c.180C>T	17.37:g.34416537G>A		Somatic	288	0	0		WXS	Illumina HiSeq	Phase_I	321	166	0.517134	NM_002983		Silent	SNP	ENST00000225245.5	37	CCDS11307.1																																																																																			G|0.795;A|0.205	0.205	strong		0.582	CCL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256581.1	NM_002983	
MCPH1	79648	hgsc.bcm.edu	37	8	6478986	6478986	+	Silent	SNP	C	C	T	rs2912010	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:6478986C>T	ENST00000344683.5	+	13	2302	c.2226C>T	c.(2224-2226)agC>agT	p.S742S	MCPH1_ENST00000521175.1_3'UTR|CTD-2541M15.1_ENST00000522897.1_RNA|CTD-2541M15.1_ENST00000515608.1_RNA	NM_024596.3	NP_078872	Q8NEM0	MCPH1_HUMAN	microcephalin 1	742					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)		TGTGCCGAAGCGAGTGCCACT	0.577													c|||	2268	0.452875	0.3449	0.3516	5008	,	,		17581	0.6776		0.4076	False		,,,				2504	0.4857				p.S742S	Colon(95;1448 1467 8277 34473 35819)	Atlas-SNP	.											.	MCPH1	65	.	0			c.C2226T						PASS	.	T		1477,2755		275,927,914	53.0	58.0	56.0		2226	-4.8	0.0	8	dbSNP_101	56	3284,5194		630,2024,1585	no	coding-synonymous	MCPH1	NM_024596.3		905,2951,2499	TT,TC,CC		38.7356,34.9008,37.4587		742/836	6478986	4761,7949	2116	4239	6355	SO:0001819	synonymous_variant	79648	exon13			CCGAAGCGAGTGC	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.2226C>T	8.37:g.6478986C>T		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	25	24	0.96	NM_024596	B4DWW2|E9PGU5|E9PH63|Q66GU1|Q9H9C7	Silent	SNP	ENST00000344683.5	37	CCDS43689.1																																																																																			C|0.558;T|0.442	0.442	strong		0.577	MCPH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374532.2	NM_024596	
NLRP5	126206	hgsc.bcm.edu	37	19	56569629	56569629	+	Missense_Mutation	SNP	C	C	G	rs12462795	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:56569629C>G	ENST00000390649.3	+	14	3323	c.3323C>G	c.(3322-3324)tCt>tGt	p.S1108C		NM_153447.4	NP_703148.4	P59047	NALP5_HUMAN	NLR family, pyrin domain containing 5	1108			S -> C (in dbSNP:rs12462795).		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)		GGACTGACTTCTGATTGCTGT	0.493													C|||	858	0.171326	0.0726	0.1167	5008	,	,		19105	0.3383		0.1362	False		,,,				2504	0.2076				p.S1108C		Atlas-SNP	.											.	NLRP5	217	.	0			c.C3323G						PASS	.	C	CYS/SER	297,3739		10,277,1731	189.0	179.0	182.0		3323	2.3	0.0	19	dbSNP_120	182	1231,7149		94,1043,3053	yes	missense	NLRP5	NM_153447.4	112	104,1320,4784	GG,GC,CC		14.6897,7.3588,12.3067	probably-damaging	1108/1201	56569629	1528,10888	2018	4190	6208	SO:0001583	missense	126206	exon14			TGACTTCTGATTG	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.3323C>G	19.37:g.56569629C>G	ENSP00000375063:p.Ser1108Cys	Somatic	195	0	0		WXS	Illumina HiSeq	Phase_I	153	74	0.48366	NM_153447	A8MTY4|Q86W29	Missense_Mutation	SNP	ENST00000390649.3	37	CCDS12938.1	374	0.17124542124542125	25	0.0508130081300813	41	0.1132596685082873	205	0.3583916083916084	103	0.1358839050131926	C	12.37	1.917549	0.33815	0.073588	0.146897	ENSG00000171487	ENST00000390649	T	0.54866	0.55	3.36	2.32	0.28847	.	0.000000	0.33144	N	0.005238	T	0.00012	0.0000	M	0.91038	3.17	0.80722	P	0.0	D	0.76494	0.999	D	0.65987	0.94	T	0.08953	-1.0697	9	0.72032	D	0.01	.	6.6416	0.22913	0.0:0.8685:0.0:0.1315	rs12462795;rs52831139;rs56605543;rs59402599;rs12462795	1108	P59047	NALP5_HUMAN	C	1108	ENSP00000375063:S1108C	ENSP00000375063:S1108C	S	+	2	0	NLRP5	61261441	0.001000	0.12720	0.001000	0.08648	0.001000	0.01503	0.525000	0.22956	0.992000	0.38840	0.561000	0.74099	TCT	C|0.827;G|0.173	0.173	strong		0.493	NLRP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313735.1	NM_153447	
AGAP11	119385	hgsc.bcm.edu	37	10	88768657	88768657	+	RNA	SNP	C	C	T	rs1745901	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:88768657C>T	ENST00000444431.1	+	0	3257				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)										CCAATTCAGACATCGGGCTGG	0.557													C|||	3895	0.777756	0.8116	0.7522	5008	,	,		17731	0.9286		0.7038	False		,,,				2504	0.6708				p.D216D		Atlas-SNP	.											.	.	.	.	0			c.C648T						PASS	.	C		3451,955	733.1+/-410.4	1347,757,99	92.0	102.0	99.0		648		0.0	10	dbSNP_89	99	5858,2742	680.4+/-403.6	1971,1916,413	no	coding-synonymous	AGAP11	NM_133447.1		3318,2673,512	TT,TC,CC		31.8837,21.675,28.4253		216/551	88768657	9309,3697	2203	4300	6503			119385	exon12			TTCAGACATCGGG			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.88768657C>T		Somatic	397	1	0.00251889		WXS	Illumina HiSeq	Phase_I	335	142	0.423881	NM_133447	B9EIP7|D3DWE4	Silent	SNP	ENST00000444431.1	37																																																																																				C|0.222;T|0.778	0.778	strong		0.557	AGAP11-001	KNOWN	basic|readthrough_transcript	processed_transcript	processed_transcript	OTTHUMT00000049193.1	NM_133447	
GSTP1	2950	hgsc.bcm.edu	37	11	67353970	67353970	+	Silent	SNP	T	T	C	rs4891	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:67353970T>C	ENST00000398606.3	+	7	804	c.555T>C	c.(553-555)agT>agC	p.S185S	GSTP1_ENST00000498765.1_3'UTR|GSTP1_ENST00000398603.1_Silent_p.S149S	NM_000852.3	NP_000843.1	P09211	GSTP1_HUMAN	glutathione S-transferase pi 1	185	GST C-terminal.				cellular response to lipopolysaccharide (GO:0071222)|central nervous system development (GO:0007417)|common myeloid progenitor cell proliferation (GO:0035726)|glutathione derivative biosynthetic process (GO:1901687)|glutathione metabolic process (GO:0006749)|negative regulation of acute inflammatory response (GO:0002674)|negative regulation of apoptotic process (GO:0043066)|negative regulation of biosynthetic process (GO:0009890)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of interleukin-1 beta production (GO:0032691)|negative regulation of JUN kinase activity (GO:0043508)|negative regulation of leukocyte proliferation (GO:0070664)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of monocyte chemotactic protein-1 production (GO:0071638)|negative regulation of nitric-oxide synthase biosynthetic process (GO:0051771)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of stress-activated MAPK cascade (GO:0032873)|negative regulation of tumor necrosis factor production (GO:0032720)|negative regulation of tumor necrosis factor-mediated signaling pathway (GO:0010804)|nitric oxide storage (GO:0035732)|positive regulation of superoxide anion generation (GO:0032930)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of stress-activated MAPK cascade (GO:0032872)|response to reactive oxygen species (GO:0000302)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|TRAF2-GSTP1 complex (GO:0097057)|vesicle (GO:0031982)	dinitrosyl-iron complex binding (GO:0035731)|glutathione transferase activity (GO:0004364)|JUN kinase binding (GO:0008432)|kinase regulator activity (GO:0019207)|nitric oxide binding (GO:0070026)|S-nitrosoglutathione binding (GO:0035730)			central_nervous_system(1)|cervix(1)|endometrium(4)|lung(2)|ovary(1)	9					Busulfan(DB01008)|Carboplatin(DB00958)|Chlorambucil(DB00291)|Cisplatin(DB00515)|Clomipramine(DB01242)|Etoposide(DB00773)|Glutathione(DB00143)|Oxaliplatin(DB00526)|Vitamin E(DB00163)	GGCGCCTCAGTGCCCGGCCCA	0.622													C|||	1783	0.35603	0.5182	0.4885	5008	,	,		18460	0.1736		0.337	False		,,,				2504	0.2505				p.S185S		Atlas-SNP	.											.	GSTP1	21	.	0			c.T555C						PASS	.	C		1846,2220		420,1006,607	40.0	43.0	42.0		555	-8.6	0.0	11	dbSNP_52	42	2844,5488		513,1818,1835	no	coding-synonymous	GSTP1	NM_000852.3		933,2824,2442	CC,CT,TT		34.1335,45.4009,37.8287		185/211	67353970	4690,7708	2033	4166	6199	SO:0001819	synonymous_variant	2950	exon7			CCTCAGTGCCCGG	U12472	CCDS41679.1	11q13.2	2014-09-17	2008-07-18		ENSG00000084207	ENSG00000084207	2.5.1.18	"""Glutathione S-transferases / Soluble"""	4638	protein-coding gene	gene with protein product		134660		FAEES3, GST3		1885604, 7587384, 19915149	Standard	NM_000852		Approved	GSTP	uc001omf.3	P09211	OTTHUMG00000137430	ENST00000398606.3:c.555T>C	11.37:g.67353970T>C		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	51	14	0.27451	NM_000852	O00460|Q15690|Q5TZY3	Silent	SNP	ENST00000398606.3	37	CCDS41679.1																																																																																			T|0.688;C|0.312	0.312	strong		0.622	GSTP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268504.1	NM_000852	
OR10AD1	121275	hgsc.bcm.edu	37	12	48596579	48596579	+	Missense_Mutation	SNP	C	C	T	rs17224674	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:48596579C>T	ENST00000310248.2	-	1	591	c.497G>A	c.(496-498)cGa>cAa	p.R166Q		NM_001004134.1	NP_001004134.1	Q8NGE0	O10AD_HUMAN	olfactory receptor, family 10, subfamily AD, member 1	166			R -> Q (in dbSNP:rs17224674).			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(2)|lung(3)|ovary(1)|stomach(1)|urinary_tract(1)	9						GAAGGGCTCTCGGAATGAAAT	0.507													C|||	123	0.0245607	0.0076	0.0317	5008	,	,		21550	0.0		0.0815	False		,,,				2504	0.0092				p.R166Q		Atlas-SNP	.											.	OR10AD1	24	.	0			c.G497A						PASS	.	C	GLN/ARG	90,4316	76.2+/-114.5	0,90,2113	53.0	46.0	48.0		497	0.7	0.0	12	dbSNP_123	48	713,7887	173.9+/-224.3	27,659,3614	yes	missense	OR10AD1	NM_001004134.1	43	27,749,5727	TT,TC,CC		8.2907,2.0427,6.1741	probably-damaging	166/318	48596579	803,12203	2203	4300	6503	SO:0001583	missense	121275	exon1			GGCTCTCGGAATG		CCDS31787.1	12q13.11	2013-09-24	2002-11-13	2002-11-15	ENSG00000172640	ENSG00000172640		"""GPCR / Class A : Olfactory receptors"""	14819	protein-coding gene	gene with protein product			"""olfactory receptor, family 10, subfamily AD, member 1 pseudogene"""	OR10AD1P			Standard	NM_001004134		Approved		uc001rrl.1	Q8NGE0	OTTHUMG00000168027	ENST00000310248.2:c.497G>A	12.37:g.48596579C>T	ENSP00000308689:p.Arg166Gln	Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	139	55	0.395683	NM_001004134	B9EGT9|Q6IFA8	Missense_Mutation	SNP	ENST00000310248.2	37	CCDS31787.1	70	0.03205128205128205	4	0.008130081300813009	8	0.022099447513812154	0	0.0	58	0.07651715039577836	C	3.399	-0.122722	0.06795	0.020427	0.082907	ENSG00000172640	ENST00000310248	T	0.00145	8.67	4.83	0.729	0.18266	GPCR, rhodopsin-like superfamily (1);	0.538596	0.14094	N	0.341831	T	0.00012	0.0000	N	0.05199	-0.095	0.09310	N	1	B	0.22346	0.068	B	0.13407	0.009	T	0.01316	-1.1387	10	0.15499	T	0.54	-0.4284	3.3589	0.07179	0.1804:0.5273:0.0:0.2923	rs17224674;rs56500145;rs17224674	166	Q8NGE0	O10AD_HUMAN	Q	166	ENSP00000308689:R166Q	ENSP00000308689:R166Q	R	-	2	0	OR10AD1	46882846	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.917000	0.00695	0.348000	0.23949	0.561000	0.74099	CGA	C|0.954;T|0.046	0.046	strong		0.507	OR10AD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397577.1		
MYH11	4629	hgsc.bcm.edu	37	16	15839034	15839034	+	Silent	SNP	G	G	A	rs587781048|rs1050113	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:15839034G>A	ENST00000300036.5	-	20	2581	c.2472C>T	c.(2470-2472)gcC>gcT	p.A824A	MYH11_ENST00000576790.2_Silent_p.A824A|MYH11_ENST00000452625.2_Silent_p.A831A|MYH11_ENST00000396324.3_Silent_p.A831A	NM_002474.2	NP_002465.1	P35749	MYH11_HUMAN	myosin, heavy chain 11, smooth muscle	824					axon guidance (GO:0007411)|cardiac muscle fiber development (GO:0048739)|elastic fiber assembly (GO:0048251)|muscle contraction (GO:0006936)|skeletal muscle myosin thick filament assembly (GO:0030241)|smooth muscle contraction (GO:0006939)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|smooth muscle contractile fiber (GO:0030485)|stress fiber (GO:0001725)	ATP binding (GO:0005524)|motor activity (GO:0003774)|structural constituent of muscle (GO:0008307)			NS(2)|breast(7)|central_nervous_system(1)|endometrium(11)|kidney(5)|large_intestine(34)|liver(1)|lung(37)|ovary(9)|pancreas(1)|prostate(7)|skin(7)|upper_aerodigestive_tract(1)	123						TGAGGTAGGCGGCGCAGTTCC	0.627			T	CBFB	AML								G|||	1270	0.253594	0.1112	0.2695	5008	,	,		18020	0.3542		0.339	False		,,,				2504	0.2434				p.A831A		Atlas-SNP	.		Dom	yes		16	16p13.13-p13.12	4629	"""myosin, heavy polypeptide 11, smooth muscle"""		L	MYH11_ENST00000396324,NS,carcinoma,-2,4	MYH11	520	4	0			c.C2493T						PASS	.	G	,,,	651,3743	279.9+/-275.1	53,545,1599	82.0	80.0	81.0		2493,2493,2472,2472	-9.6	0.3	16	dbSNP_86	81	2769,5831	440.5+/-359.5	471,1827,2002	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	MYH11	NM_001040113.1,NM_001040114.1,NM_002474.2,NM_022844.2	,,,	524,2372,3601	AA,AG,GG		32.1977,14.8157,26.3198	,,,	831/1946,831/1980,824/1973,824/1939	15839034	3420,9574	2197	4300	6497	SO:0001819	synonymous_variant	4629	exon21			GTAGGCGGCGCAG	X69292	CCDS10565.1, CCDS10566.1, CCDS45423.1, CCDS45424.1	16p13.11	2011-09-27	2006-09-29		ENSG00000133392	ENSG00000133392		"""Myosins / Myosin superfamily : Class II"""	7569	protein-coding gene	gene with protein product		160745	"""myosin, heavy polypeptide 11, smooth muscle"""			7684189	Standard	NM_001040113		Approved	SMMHC, SMHC	uc002ddx.3	P35749	OTTHUMG00000129935	ENST00000300036.5:c.2472C>T	16.37:g.15839034G>A		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	60	12	0.2	NM_001040114	D2JYH7|O00396|O94944|P78422|Q3MIV8|Q3MNF0|Q3MNF1	Silent	SNP	ENST00000300036.5	37	CCDS10565.1																																																																																			T|0.000;G|0.726;C|0.000;A|0.274	0.274	strong		0.627	MYH11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252192.2	NM_001040113	
PPP6R2	9701	hgsc.bcm.edu	37	22	50877166	50877166	+	Silent	SNP	G	G	C	rs4824131	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:50877166G>C	ENST00000216061.5	+	20	2473	c.2103G>C	c.(2101-2103)gcG>gcC	p.A701A	PPP6R2_ENST00000395744.3_Silent_p.A674A|PPP6R2_ENST00000395741.3_Silent_p.A675A|PPP6R2_ENST00000359139.3_Silent_p.A674A			O75170	PP6R2_HUMAN	protein phosphatase 6, regulatory subunit 2	701						cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)				NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(2)|liver(1)|lung(6)|ovary(2)|skin(1)|urinary_tract(1)	22						AGAAGGAAGCGCCCCCTGTGG	0.672													C|||	3351	0.669129	0.4697	0.7478	5008	,	,		16752	0.9345		0.661	False		,,,				2504	0.6176				p.A701A		Atlas-SNP	.											.	PPP6R2	71	.	0			c.G2103C						PASS	.	C	,,,	2169,2225		557,1055,585	18.0	19.0	19.0		2103,2025,2022,2022	-6.0	0.0	22	dbSNP_111	19	5506,3090		1832,1842,624	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PPP6R2	NM_001242898.1,NM_001242899.1,NM_001242900.1,NM_014678.4	,,,	2389,2897,1209	CC,CG,GG		35.947,49.3628,40.9161	,,,	701/960,675/934,674/928,674/933	50877166	7675,5315	2197	4298	6495	SO:0001819	synonymous_variant	9701	exon19			GGAAGCGCCCCCT	AB014585	CCDS33681.1, CCDS56235.1, CCDS56236.1, CCDS74881.1	22q13.33	2012-04-17	2010-06-28	2010-06-28	ENSG00000100239	ENSG00000100239		"""Serine/threonine phosphatases / Protein phosphatase 6, regulatory subunits"""	19253	protein-coding gene	gene with protein product		610877	"""KIAA0685"", ""SAPS domain family, member 2"""	KIAA0685, SAPS2		16769727	Standard	NM_014678		Approved	dJ579N16.1, SAP190	uc003blc.3	O75170	OTTHUMG00000150199	ENST00000216061.5:c.2103G>C	22.37:g.50877166G>C		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	56	30	0.535714	NM_001242898	A6PVG3|B7Z7T3|Q5U5P3|Q7Z2L2|Q7Z5G5|Q7Z731|Q9UGB9	Silent	SNP	ENST00000216061.5	37																																																																																				G|0.367;C|0.633	0.633	strong		0.672	PPP6R2-004	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000316809.1	NM_014678	
AMPD1	270	hgsc.bcm.edu	37	1	115221116	115221116	+	Missense_Mutation	SNP	C	C	A	rs61752478	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:115221116C>A	ENST00000520113.2	-	8	1044	c.1029G>T	c.(1027-1029)atG>atT	p.M343I	AMPD1_ENST00000369538.3_Missense_Mutation_p.M339I|AMPD1_ENST00000353928.6_Missense_Mutation_p.M310I			P23109	AMPD1_HUMAN	adenosine monophosphate deaminase 1	343					IMP salvage (GO:0032264)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase metabolic process (GO:0006144)|purine-containing compound salvage (GO:0043101)|response to organic substance (GO:0010033)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	AMP deaminase activity (GO:0003876)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(17)|ovary(3)|pancreas(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	45	all_epithelial(7;7.83e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;4.64e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)	Adenosine monophosphate(DB00131)	GTTTCTGGTTCATGCAAGCGG	0.393													C|||	13	0.00259585	0.0008	0.0072	5008	,	,		21444	0.0		0.007	False		,,,				2504	0.0				p.M343I		Atlas-SNP	.											.	AMPD1	223	.	0			c.G1029T	GRCh37	CM041236	AMPD1	M	rs61752478	PASS	.	C	ILE/MET,ILE/MET	4,4402	8.1+/-20.4	0,4,2199	98.0	96.0	97.0		1029,1017	5.1	1.0	1	dbSNP_129	97	46,8554	30.7+/-82.3	0,46,4254	yes	missense,missense	AMPD1	NM_000036.2,NM_001172626.1	10,10	0,50,6453	AA,AC,CC		0.5349,0.0908,0.3844	probably-damaging,probably-damaging	343/781,339/777	115221116	50,12956	2203	4300	6503	SO:0001583	missense	270	exon8			CTGGTTCATGCAA	M60092	CCDS876.1, CCDS876.2, CCDS53349.1	1p13	2010-02-10	2010-02-10		ENSG00000116748	ENSG00000116748	3.5.4.6		468	protein-coding gene	gene with protein product	"""AMPD isoform M"", ""skeletal muscle AMPD"""	102770	"""adenosine monophosphate deaminase 1 (isoform M)"""			1400401	Standard	NM_001172626		Approved	MAD, MADA	uc001efe.2	P23109	OTTHUMG00000011892	ENST00000520113.2:c.1029G>T	1.37:g.115221116C>A	ENSP00000430075:p.Met343Ile	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	77	40	0.519481	NM_000036	A8K5N4|B2RAM1|F2Z3B3|Q5TF00|Q5TF02	Missense_Mutation	SNP	ENST00000520113.2	37	CCDS876.2	5	0.0022893772893772895	1	0.0020325203252032522	2	0.0055248618784530384	0	0.0	2	0.002638522427440633	C	28.9	4.960280	0.92791	9.08E-4	0.005349	ENSG00000116748	ENST00000520113;ENST00000369538;ENST00000353928	D;D;D	0.95482	-3.72;-3.72;-3.72	5.1	5.1	0.69264	Adenosine/AMP deaminase (1);	0.000000	0.85682	D	0.000000	D	0.97573	0.9205	M	0.83384	2.64	0.80722	D	1	P;D	0.57899	0.759;0.981	P;D	0.65773	0.576;0.938	D	0.98134	1.0432	10	0.87932	D	0	-20.3493	18.8767	0.92341	0.0:1.0:0.0:0.0	rs61752478	339;310	Q5TF02;P23109	.;AMPD1_HUMAN	I	343;339;310	ENSP00000430075:M343I;ENSP00000358551:M339I;ENSP00000316520:M310I	ENSP00000316520:M310I	M	-	3	0	AMPD1	115022639	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.776000	0.85560	2.539000	0.85634	0.561000	0.74099	ATG	C|0.997;A|0.003	0.003	strong		0.393	AMPD1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000032860.4		
PDCD6IP	10015	hgsc.bcm.edu	37	3	33893987	33893987	+	Missense_Mutation	SNP	A	A	G	rs9813017	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:33893987A>G	ENST00000307296.3	+	13	2026	c.1649A>G	c.(1648-1650)aAt>aGt	p.N550S	PDCD6IP_ENST00000457054.2_Missense_Mutation_p.N555S			Q8WUM4	PDC6I_HUMAN	programmed cell death 6 interacting protein	550	Interaction with EIAV p9.|Self-association.		N -> S (in dbSNP:rs9813017). {ECO:0000269|PubMed:10718198, ECO:0000269|PubMed:11683497}.		apoptotic process (GO:0006915)|cell cycle (GO:0007049)|cell division (GO:0051301)|protein transport (GO:0015031)|viral life cycle (GO:0019058)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|immunological synapse (GO:0001772)|membrane (GO:0016020)|vesicle (GO:0031982)	calcium-dependent protein binding (GO:0048306)|protein homodimerization activity (GO:0042803)			central_nervous_system(3)|endometrium(1)|kidney(2)|large_intestine(7)|lung(6)|ovary(2)|skin(1)|stomach(1)	23						TAGGTTGTAAATGTCTTAAAA	0.313													A|||	413	0.0824681	0.1362	0.0922	5008	,	,		13897	0.0218		0.0994	False		,,,				2504	0.0481				p.N555S		Atlas-SNP	.											.	PDCD6IP	62	.	0			c.A1664G						PASS	.	A	SER/ASN,SER/ASN	610,3788		41,528,1630	30.0	31.0	31.0		1664,1649	4.2	1.0	3	dbSNP_119	31	955,7641		56,843,3399	no	missense,missense	PDCD6IP	NM_001162429.1,NM_013374.4	46,46	97,1371,5029	GG,GA,AA		11.1098,13.8699,12.044	benign,benign	555/874,550/869	33893987	1565,11429	2199	4298	6497	SO:0001583	missense	10015	exon13			TTGTAAATGTCTT	BC020066	CCDS2660.1, CCDS54561.1	3p22.3	2012-08-30	2001-11-29		ENSG00000170248	ENSG00000170248			8766	protein-coding gene	gene with protein product	"""ALG-2 interacting protein X"""	608074	"""programmed cell death 6-interacting protein"""			9880530	Standard	NM_001162429		Approved	Alix, AIP1, Hp95	uc003cfy.4	Q8WUM4	OTTHUMG00000130751	ENST00000307296.3:c.1649A>G	3.37:g.33893987A>G	ENSP00000307387:p.Asn550Ser	Somatic	190	0	0		WXS	Illumina HiSeq	Phase_I	176	79	0.448864	NM_001162429	C5MQH7|E9PFU1|Q6NUS1|Q9BX86|Q9NUN0|Q9P2H2|Q9UKL5	Missense_Mutation	SNP	ENST00000307296.3	37	CCDS2660.1	170	0.07783882783882784	66	0.13414634146341464	34	0.09392265193370165	8	0.013986013986013986	62	0.08179419525065963	A	6.915	0.538385	0.13250	0.138699	0.111098	ENSG00000170248	ENST00000307296;ENST00000457054	T;T	0.27256	1.68;1.68	5.33	4.17	0.49024	.	0.191499	0.56097	N	0.000039	T	0.00109	0.0003	L	0.28274	0.84	0.23361	P	0.99783538	B;B;B	0.06786	0.001;0.0;0.0	B;B;B	0.06405	0.0;0.002;0.002	T	0.22941	-1.0202	9	0.07644	T	0.81	-8.7419	8.1568	0.31173	0.8446:0.0:0.1554:0.0	rs9813017;rs52832450;rs9813017	331;555;550	B7Z5C1;E9PFU1;Q8WUM4	.;.;PDC6I_HUMAN	S	550;555	ENSP00000307387:N550S;ENSP00000411825:N555S	ENSP00000307387:N550S	N	+	2	0	PDCD6IP	33868991	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.475000	0.45162	0.858000	0.35431	0.383000	0.25322	AAT	A|0.901;G|0.099	0.099	strong		0.313	PDCD6IP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253251.2		
IZUMO1	284359	hgsc.bcm.edu	37	19	49244219	49244219	+	Silent	SNP	C	C	A	rs66877153|rs2307018|rs386810061	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:49244219C>A	ENST00000332955.2	-	10	1546	c.999G>T	c.(997-999)gcG>gcT	p.A333A	RASIP1_ENST00000222145.4_5'Flank|RASIP1_ENST00000594232.1_5'Flank	NM_182575.2	NP_872381.2	Q8IYV9	IZUM1_HUMAN	izumo sperm-egg fusion 1	333			A -> V (in dbSNP:rs2307019). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:15759005, ECO:0000269|PubMed:18082733}.		cell adhesion (GO:0007155)|fusion of sperm to egg plasma membrane (GO:0007342)|multicellular organism reproduction (GO:0032504)|single fertilization (GO:0007338)|sperm-egg recognition (GO:0035036)	acrosomal membrane (GO:0002080)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)			endometrium(4)|kidney(3)|large_intestine(4)|lung(2)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	17		all_lung(116;0.000156)|Lung NSC(112;0.000251)|all_epithelial(76;0.000761)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000134)|all cancers(93;0.000348)|Epithelial(262;0.019)|GBM - Glioblastoma multiforme(486;0.022)		TTTGCTCGGCCGCTCCACTGC	0.512													C|||	2573	0.513778	0.3162	0.5461	5008	,	,		18325	0.8323		0.4473	False		,,,				2504	0.498				p.A333A		Atlas-SNP	.											.	IZUMO1	30	.	0			c.G999T						PASS	.	C		1423,2983	463.2+/-353.5	246,931,1026	113.0	98.0	103.0		999	-6.3	0.0	19	dbSNP_100	103	3754,4846	529.3+/-381.6	794,2166,1340	no	coding-synonymous	IZUMO1	NM_182575.2		1040,3097,2366	AA,AC,CC		43.6512,32.2969,39.8047		333/351	49244219	5177,7829	2203	4300	6503	SO:0001819	synonymous_variant	284359	exon10			CTCGGCCGCTCCA	BC034769	CCDS12732.1	19q13.33	2014-07-23			ENSG00000182264	ENSG00000182264		"""-"""	28539	protein-coding gene	gene with protein product	"""oocyte binding/fusion factor"""	609278				15759005, 18952059, 19658160, 22957301	Standard	NM_182575		Approved	IZUMO, MGC34799, OBF	uc002pkj.3	Q8IYV9	OTTHUMG00000183324	ENST00000332955.2:c.999G>T	19.37:g.49244219C>A		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	104	54	0.519231	NM_182575	Q6Q8P6|Q6Q8P7	Silent	SNP	ENST00000332955.2	37	CCDS12732.1																																																																																			C|0.585;A|0.415	0.415	strong		0.512	IZUMO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466189.1	NM_182575	
ITPRIPL1	150771	hgsc.bcm.edu	37	2	96993757	96993757	+	Missense_Mutation	SNP	C	C	T	rs2279105	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:96993757C>T	ENST00000439118.2	+	3	1639	c.1388C>T	c.(1387-1389)aCg>aTg	p.T463M	ITPRIPL1_ENST00000542887.1_Missense_Mutation_p.T455M|ITPRIPL1_ENST00000536814.1_Missense_Mutation_p.T455M|ITPRIPL1_ENST00000361124.4_Missense_Mutation_p.T471M	NM_001008949.2	NP_001008949.1	Q6GPH6	IPIL1_HUMAN	inositol 1,4,5-trisphosphate receptor interacting protein-like 1	463			T -> M (in dbSNP:rs2279105).			integral component of membrane (GO:0016021)|membrane (GO:0016020)				breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(7)|ovary(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27						CTGCCCCTCACGGACTGGGCC	0.567													C|||	1806	0.360623	0.2421	0.3141	5008	,	,		19389	0.2312		0.3191	False		,,,				2504	0.7301				p.T471M		Atlas-SNP	.											.	ITPRIPL1	58	.	0			c.C1412T						PASS	.	C	MET/THR,MET/THR,MET/THR,MET/THR	1099,3307	395.4+/-329.6	133,833,1237	90.0	90.0	90.0		1388,1364,1364,1412	5.5	0.4	2	dbSNP_100	90	2883,5717	451.4+/-362.6	507,1869,1924	yes	missense,missense,missense,missense	ITPRIPL1	NM_001008949.2,NM_001163523.1,NM_001163524.1,NM_178495.5	81,81,81,81	640,2702,3161	TT,TC,CC		33.5233,24.9433,30.6166	probably-damaging,probably-damaging,probably-damaging,probably-damaging	463/556,455/548,455/548,471/564	96993757	3982,9024	2203	4300	6503	SO:0001583	missense	150771	exon1			CCCTCACGGACTG		CCDS33250.1, CCDS46360.1, CCDS54378.1	2q11.2	2011-04-28	2011-04-28	2008-08-11	ENSG00000198885	ENSG00000198885			29371	protein-coding gene	gene with protein product			"""KIAA1754-like"", ""inositol 1,4,5-triphosphate receptor interacting protein-like 1"""	KIAA1754L		12477932	Standard	NM_178495		Approved		uc010yul.2	Q6GPH6	OTTHUMG00000155230	ENST00000439118.2:c.1388C>T	2.37:g.96993757C>T	ENSP00000389308:p.Thr463Met	Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	116	50	0.431034	NM_178495	F5H1L8|Q8NE61	Missense_Mutation	SNP	ENST00000439118.2	37	CCDS46360.1	582|582	0.2664835164835165|0.2664835164835165	107|107	0.21747967479674796|0.21747967479674796	112|112	0.30939226519337015|0.30939226519337015	121|121	0.21153846153846154|0.21153846153846154	242|242	0.31926121372031663|0.31926121372031663	C|C	13.57|13.57	2.275854|2.275854	0.40294|0.40294	0.249433|0.249433	0.335233|0.335233	ENSG00000198885|ENSG00000198885	ENST00000420728|ENST00000536814;ENST00000439118;ENST00000361124;ENST00000542887	.|T;T;T;T	.|0.08282	.|3.11;3.11;3.11;3.11	5.5|5.5	5.5|5.5	0.81552|0.81552	.|.	.|0.299368	.|0.23750	.|N	.|0.044930	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.12182|0.12182	0.205|0.205	0.80722|0.80722	P|P	0.0|0.0	.|D;D	.|0.71674	.|0.998;0.998	.|P;P	.|0.51266	.|0.534;0.664	T|T	0.60409|0.60409	-0.7269|-0.7269	4|9	.|0.45353	.|T	.|0.12	-6.5149|-6.5149	18.332|18.332	0.90272|0.90272	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	rs2279105;rs52800255;rs58471167;rs2279105|rs2279105;rs52800255;rs58471167;rs2279105	.|471;463	.|Q6GPH6-2;Q6GPH6	.|.;IPIL1_HUMAN	W|M	495|455;463;471;455	.|ENSP00000439566:T455M;ENSP00000389308:T463M;ENSP00000355121:T471M;ENSP00000438212:T455M	.|ENSP00000355121:T471M	R|T	+|+	1|2	2|0	ITPRIPL1|ITPRIPL1	96357484|96357484	0.143000|0.143000	0.22626|0.22626	0.363000|0.363000	0.25875|0.25875	0.875000|0.875000	0.50365|0.50365	2.765000|2.765000	0.47621|0.47621	2.861000|2.861000	0.98227|0.98227	0.655000|0.655000	0.94253|0.94253	CGG|ACG	C|0.705;T|0.295	0.295	strong		0.567	ITPRIPL1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000338896.1	NM_178495	
SUN1	23353	hgsc.bcm.edu	37	7	883105	883105	+	Silent	SNP	C	C	T	rs113652875	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:883105C>T	ENST00000405266.1	+	5	630	c.606C>T	c.(604-606)ccC>ccT	p.P202P	SUN1_ENST00000389574.3_Silent_p.P152P|SUN1_ENST00000457378.2_Silent_p.P223P|SUN1_ENST00000456758.2_Silent_p.P260P|SUN1_ENST00000452783.2_Intron|SUN1_ENST00000403868.1_Silent_p.P202P|SUN1_ENST00000401592.1_Silent_p.P202P|SUN1_ENST00000425407.2_Silent_p.P152P			O94901	SUN1_HUMAN	Sad1 and UNC84 domain containing 1	202					cytoskeletal anchoring at nuclear membrane (GO:0090286)|nuclear envelope organization (GO:0006998)|nuclear matrix anchoring at nuclear membrane (GO:0090292)	acrosomal membrane (GO:0002080)|integral component of nuclear inner membrane (GO:0005639)|nuclear envelope (GO:0005635)|SUN-KASH complex (GO:0034993)		p.P152P(1)|p.P223P(1)|p.P202P(1)		NS(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(17)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						CGGCGCACCCCGCGGCCCCCG	0.577													.|||	108	0.0215655	0.0318	0.0303	5008	,	,		14218	0.0		0.0368	False		,,,				2504	0.0082				p.P223P		Atlas-SNP	.											.	SUN1	157	.	3	Substitution - coding silent(3)	lung(3)	c.C669T						PASS	.	C	,,,,	123,3783		3,117,1833	93.0	110.0	105.0		606,,669,606,456	-8.3	0.0	7	dbSNP_132	105	395,7857		5,385,3736	no	coding-synonymous,intron,coding-synonymous,coding-synonymous,coding-synonymous	SUN1	NM_001130965.2,NM_001171944.1,NM_001171945.1,NM_001171946.1,NM_025154.5	,,,,	8,502,5569	TT,TC,CC		4.7867,3.149,4.2606	,,,,	202/786,,223/279,202/258,152/703	883105	518,11640	1953	4126	6079	SO:0001819	synonymous_variant	23353	exon7			GCACCCCGCGGCC	AF202724	CCDS43533.1, CCDS47525.1, CCDS55078.1, CCDS55079.1, CCDS55080.1	7p22.3	2010-01-27	2010-01-27	2010-01-27	ENSG00000164828	ENSG00000164828			18587	protein-coding gene	gene with protein product	"""Sad1 unc-84 domain protein 1"""	607723	"""unc-84 homolog A (C. elegans)"""	UNC84A		11593002	Standard	NM_001130965		Approved	KIAA0810, FLJ12407	uc021zym.1	O94901	OTTHUMG00000151426	ENST00000405266.1:c.606C>T	7.37:g.883105C>T		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	70	23	0.328571	NM_001171945	A5PL20|B3KMV7|B4DZF7|B7WNY4|B7WP53|E9PDU4|E9PF23|F8WD13|Q96CZ7|Q9HA14|Q9UH98	Silent	SNP	ENST00000405266.1	37		54	0.024725274725274724	10	0.02032520325203252	19	0.052486187845303865	0	0.0	25	0.032981530343007916	C	5.914	0.352670	0.11182	0.03149	0.047867	ENSG00000164828	ENST00000419312	T	0.45668	0.89	4.16	-8.32	0.00996	.	0.484707	0.23375	N	0.048878	T	0.07188	0.0182	.	.	.	0.09310	N	0.999992	.	.	.	.	.	.	T	0.35251	-0.9796	7	0.72032	D	0.01	-0.6632	8.7454	0.34583	0.0929:0.1:0.0927:0.7143	.	.	.	.	L	43	ENSP00000414279:P43L	ENSP00000414279:P43L	P	+	2	0	SUN1	849631	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.997000	0.01470	-2.012000	0.00950	-0.218000	0.12543	CCG	C|0.969;T|0.031	0.031	strong		0.577	SUN1-001	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000322566.1	NM_025154	
ZSCAN9	7746	hgsc.bcm.edu	37	6	28195521	28195521	+	Silent	SNP	A	A	G	rs12197427	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:28195521A>G	ENST00000252207.5	+	3	622	c.474A>G	c.(472-474)ctA>ctG	p.L158L	ZSCAN9_ENST00000531979.1_Silent_p.L158L|ZSCAN9_ENST00000425468.2_Silent_p.L158L|ZSCAN9_ENST00000531981.1_3'UTR|ZSCAN9_ENST00000527436.1_Silent_p.L158L	NM_006299.4	NP_006290.1	O15535	ZSC9_HUMAN	zinc finger and SCAN domain containing 9	158					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)										TGGTGCCTCTAGCAGAGCAGA	0.488													A|||	78	0.0155751	0.0	0.0274	5008	,	,		18815	0.0129		0.0278	False		,,,				2504	0.0184				p.L158L		Atlas-SNP	.											ZNF193,NS,carcinoma,+2,1	.	.	1	0			c.A474G						PASS	.	A	,,	26,4380	32.6+/-62.9	0,26,2177	70.0	64.0	66.0		474,474,474	-3.5	0.0	6	dbSNP_120	66	313,8287	112.0+/-172.2	8,297,3995	no	coding-synonymous,coding-synonymous,coding-synonymous	ZNF193	NM_001199479.1,NM_001199480.1,NM_006299.4	,,	8,323,6172	GG,GA,AA		3.6395,0.5901,2.6065	,,	158/446,158/395,158/395	28195521	339,12667	2203	4300	6503	SO:0001819	synonymous_variant	7746	exon3			GCCTCTAGCAGAG	U62392	CCDS4646.1, CCDS56407.1	6p21	2013-01-09	2013-01-09	2013-01-09	ENSG00000137185	ENSG00000137185		"""-"", ""Zinc fingers, C2H2-type"""	12984	protein-coding gene	gene with protein product		602246	"""zinc finger protein 193"""	ZNF193			Standard	NM_001199479		Approved	PRD51	uc003nkq.2	O15535	OTTHUMG00000014515	ENST00000252207.5:c.474A>G	6.37:g.28195521A>G		Somatic	200	0	0		WXS	Illumina HiSeq	Phase_I	160	77	0.48125	NM_006299	B4E1W6|E7EVQ2|Q2TTR1	Silent	SNP	ENST00000252207.5	37	CCDS4646.1																																																																																			A|0.971;G|0.029	0.029	strong		0.488	ZSCAN9-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000040183.2	NM_006299	
UGT2A1	10941	hgsc.bcm.edu	37	4	70455231	70455231	+	Silent	SNP	G	G	A	rs41292305	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:70455231G>A	ENST00000503640.1	-	6	1498	c.1443C>T	c.(1441-1443)ctC>ctT	p.L481L	UGT2A2_ENST00000457664.2_Silent_p.L490L|UGT2A1_ENST00000286604.4_Silent_p.L481L|UGT2A1_ENST00000514019.1_Silent_p.L647L|UGT2A1_ENST00000512704.1_Silent_p.L437L|UGT2A1_ENST00000502343.1_5'Flank	NM_006798.3	NP_006789.2	Q9Y4X1	UD2A1_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide A1, complex locus	481					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						GGAACCAGGTGAGGTCATGGG	0.483													G|||	71	0.0141773	0.0023	0.0216	5008	,	,		15765	0.001		0.0417	False		,,,				2504	0.0102				p.L647L		Atlas-SNP	.											UGT2A1_ENST00000457664,colon,carcinoma,-1,2	UGT2A1	131	2	0			c.C1941T						PASS	.	G	,	40,4366	43.8+/-77.6	0,40,2163	133.0	130.0	131.0		1470,1443	3.8	1.0	4	dbSNP_127	131	328,8272	115.0+/-174.9	5,318,3977	no	coding-synonymous,coding-synonymous	UGT2A1,UGT2A2	NM_001105677.2,NM_006798.2	,	5,358,6140	AA,AG,GG		3.814,0.9079,2.8295	,	490/537,481/528	70455231	368,12638	2203	4300	6503	SO:0001819	synonymous_variant	10941	exon7			CCAGGTGAGGTCA	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.1443C>T	4.37:g.70455231G>A		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	131	46	0.351145	NM_001252274	B4E2F4|D3GER1|D3GER2|E9PDM7|J3KNA3	Silent	SNP	ENST00000503640.1	37	CCDS3529.1																																																																																			G|0.973;A|0.027	0.027	strong		0.483	UGT2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251554.3	NM_006798	
MYH10	4628	hgsc.bcm.edu	37	17	8416901	8416901	+	Silent	SNP	C	C	T	rs11374	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:8416901C>T	ENST00000269243.4	-	21	2745	c.2607G>A	c.(2605-2607)acG>acA	p.T869T	RNU7-43P_ENST00000516554.1_RNA|MYH10_ENST00000379980.4_Silent_p.T885T|MYH10_ENST00000360416.3_Silent_p.T900T|MYH10_ENST00000396239.1_Silent_p.T890T	NM_005964.3	NP_005955.3	P35580	MYH10_HUMAN	myosin, heavy chain 10, non-muscle	869					actin filament-based movement (GO:0030048)|actomyosin structure organization (GO:0031032)|adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cardiac myofibril assembly (GO:0055003)|cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|cerebellar Purkinje cell layer development (GO:0021680)|exocytosis (GO:0006887)|fourth ventricle development (GO:0021592)|in utero embryonic development (GO:0001701)|lateral ventricle development (GO:0021670)|mitotic cytokinesis (GO:0000281)|neuromuscular process controlling balance (GO:0050885)|neuron migration (GO:0001764)|nuclear migration (GO:0007097)|plasma membrane repair (GO:0001778)|regulation of cell shape (GO:0008360)|retina development in camera-type eye (GO:0060041)|substrate-dependent cell migration, cell extension (GO:0006930)|third ventricle development (GO:0021678)|ventricular cardiac muscle cell development (GO:0055015)	actomyosin (GO:0042641)|axon (GO:0030424)|cell cortex (GO:0005938)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|midbody (GO:0030496)|myosin complex (GO:0016459)|myosin II complex (GO:0016460)|myosin II filament (GO:0097513)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|spindle (GO:0005819)|stress fiber (GO:0001725)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)	p.T869T(1)		breast(5)|endometrium(9)|kidney(2)|large_intestine(16)|lung(9)|ovary(3)|prostate(3)|skin(4)|stomach(1)	52						CTTCCACCTTCGTCTGCTTCT	0.507													C|||	2120	0.423323	0.3835	0.4323	5008	,	,		18617	0.502		0.3519	False		,,,				2504	0.4632				p.T900T		Atlas-SNP	.											MYH10,NS,carcinoma,0,1	MYH10	148	1	1	Substitution - coding silent(1)	prostate(1)	c.G2700A						PASS	.	C		1685,2721	510.4+/-367.5	316,1053,834	188.0	146.0	160.0		2607	-10.2	0.2	17	dbSNP_52	160	3299,5301	494.0+/-373.7	626,2047,1627	no	coding-synonymous	MYH10	NM_005964.1		942,3100,2461	TT,TC,CC		38.3605,38.2433,38.3208		869/1977	8416901	4984,8022	2203	4300	6503	SO:0001819	synonymous_variant	4628	exon23			CACCTTCGTCTGC	M69181	CCDS11144.1, CCDS58515.1, CCDS73984.1	17p13	2011-09-27	2006-09-29		ENSG00000133026	ENSG00000133026		"""Myosins / Myosin superfamily : Class II"""	7568	protein-coding gene	gene with protein product		160776	"""myosin, heavy polypeptide 10, non-muscle"""			1860190	Standard	NM_001256012		Approved	NMMHCB	uc002glm.4	P35580	OTTHUMG00000108195	ENST00000269243.4:c.2607G>A	17.37:g.8416901C>T		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	70	39	0.557143	NM_001256012	B2RWP9|D3DTS1|F8VTL3|Q12989|Q149N3|Q149N4|Q16087|Q4LE45|Q6PK16|Q9BWG0	Silent	SNP	ENST00000269243.4	37	CCDS11144.1																																																																																			A|0.000;C|0.606;G|0.000;T|0.394	0.394	strong		0.507	MYH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000227001.2		
C6orf223	221416	hgsc.bcm.edu	37	6	43970827	43970827	+	Silent	SNP	G	G	A	rs2295334	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:43970827G>A	ENST00000336600.5	+	4	713	c.693G>A	c.(691-693)gcG>gcA	p.A231A	C6orf223_ENST00000439969.2_3'UTR|C6orf223_ENST00000448947.2_3'UTR|RP5-1120P11.1_ENST00000422059.1_RNA|C6orf223_ENST00000442114.2_Silent_p.A211A|RP5-1120P11.1_ENST00000607590.1_RNA	NM_001171992.1|NM_153246.4	NP_001165463.1|NP_694978.2	Q8N319	CF223_HUMAN	chromosome 6 open reading frame 223	231										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)			TGTCATCCGCGGCGCTCCGCG	0.667													G|||	462	0.0922524	0.0605	0.0187	5008	,	,		12712	0.251		0.0318	False		,,,				2504	0.0859				p.A231A		Atlas-SNP	.											.	C6orf223	14	.	0			c.G693A						PASS	.	G	,	188,4190		2,184,2003	19.0	25.0	23.0		,693	-2.0	0.0	6	dbSNP_100	23	155,8409		3,149,4130	yes	utr-3,coding-synonymous	C6orf223	NM_001171992.1,NM_153246.4	,	5,333,6133	AA,AG,GG		1.8099,4.2942,2.6503	,	,231/243	43970827	343,12599	2189	4282	6471	SO:0001819	synonymous_variant	221416	exon4			ATCCGCGGCGCTC	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.693G>A	6.37:g.43970827G>A		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	102	49	0.480392	NM_153246	E9PB59|Q8N575	Silent	SNP	ENST00000336600.5	37	CCDS34459.1																																																																																			G|0.927;A|0.073	0.073	strong		0.667	C6orf223-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040702.3	NM_153246	
SLC45A1	50651	hgsc.bcm.edu	37	1	8390888	8390888	+	Silent	SNP	G	G	A	rs2289731	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:8390888G>A	ENST00000471889.1	+	5	1720	c.1335G>A	c.(1333-1335)ccG>ccA	p.P445P	SLC45A1_ENST00000377479.2_Silent_p.P479P|SLC45A1_ENST00000289877.8_Silent_p.P445P|SLC45A1_ENST00000481265.1_3'UTR|Y_RNA_ENST00000516445.1_RNA			Q9Y2W3	S45A1_HUMAN	solute carrier family 45, member 1	445					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)		CCTCTAAGCCGAGGTCATCAG	0.622													G|||	1705	0.340455	0.5363	0.2911	5008	,	,		15582	0.1746		0.325	False		,,,				2504	0.2975				p.P445P		Atlas-SNP	.											SLC45A1,NS,carcinoma,0,2	SLC45A1	85	2	0			c.G1335A						PASS	.	G		2265,2141	578.1+/-384.6	579,1107,517	50.0	57.0	55.0		1335	-10.2	0.0	1	dbSNP_100	55	2780,5820	422.9+/-354.2	454,1872,1974	yes	coding-synonymous	SLC45A1	NM_001080397.1		1033,2979,2491	AA,AG,GG		32.3256,48.5928,38.7898		445/749	8390888	5045,7961	2203	4300	6503	SO:0001819	synonymous_variant	50651	exon4			TAAGCCGAGGTCA	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.1335G>A	1.37:g.8390888G>A		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	61	31	0.508197	NM_001080397	Q5VY46|Q5VY49	Silent	SNP	ENST00000471889.1	37	CCDS30577.1																																																																																			G|0.636;A|0.364	0.364	strong		0.622	SLC45A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001245.5		
C1QTNF1	114897	hgsc.bcm.edu	37	17	77040185	77040185	+	Silent	SNP	G	G	C	rs4789853	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:77040185G>C	ENST00000339142.2	+	3	690	c.135G>C	c.(133-135)tcG>tcC	p.S45S	C1QTNF1_ENST00000392445.2_Silent_p.S45S|C1QTNF1_ENST00000583904.1_Silent_p.S45S|C1QTNF1_ENST00000354124.3_Silent_p.S55S|C1QTNF1_ENST00000311661.4_Intron|C1QTNF1_ENST00000581774.1_Silent_p.S45S|C1QTNF1_ENST00000580454.1_Silent_p.S45S|C1QTNF1_ENST00000579760.1_Silent_p.S45S|C1QTNF1_ENST00000578229.1_5'UTR|C1QTNF1_ENST00000580474.1_Silent_p.S45S	NM_198593.3	NP_940995.1	Q9BXJ1	C1QT1_HUMAN	C1q and tumor necrosis factor related protein 1	45					negative regulation of platelet activation (GO:0010544)|negative regulation of platelet aggregation (GO:0090331)|positive regulation of aldosterone secretion (GO:2000860)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of gene expression (GO:0010628)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of protein kinase B signaling (GO:0051897)|protein heterotrimerization (GO:0070208)|protein homooligomerization (GO:0051260)|regulation of glucose metabolic process (GO:0010906)	collagen trimer (GO:0005581)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)	collagen binding (GO:0005518)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(5)|ovary(2)	14			BRCA - Breast invasive adenocarcinoma(99;0.0294)|OV - Ovarian serous cystadenocarcinoma(97;0.201)			AGCTGCCGTCGCCTCCGGACC	0.677													C|||	2303	0.459864	0.5499	0.4928	5008	,	,		19352	0.5387		0.2883	False		,,,				2504	0.41				p.S45S		Atlas-SNP	.											.	C1QTNF1	62	.	0			c.G135C						PASS	.	C	,,	2253,2153	573.6+/-383.6	593,1067,543	40.0	34.0	36.0		135,135,	-1.8	0.0	17	dbSNP_111	36	2554,6046	682.2+/-403.8	392,1770,2138	no	coding-synonymous,coding-synonymous,intron	C1QTNF1	NM_030968.2,NM_198593.2,NM_198594.1	,,	985,2837,2681	CC,CG,GG		29.6977,48.8652,36.9599	,,	45/282,45/282,	77040185	4807,8199	2203	4300	6503	SO:0001819	synonymous_variant	114897	exon2			GCCGTCGCCTCCG	AF329840	CCDS11761.1, CCDS11762.1	17q25	2012-07-02			ENSG00000173918	ENSG00000173918			14324	protein-coding gene	gene with protein product	"""G protein coupled receptor interacting protein"""	610365				12409230	Standard	NM_198593		Approved	CTRP1, ZSIG37, GIP, FLJ90694	uc002jwp.4	Q9BXJ1	OTTHUMG00000177533	ENST00000339142.2:c.135G>C	17.37:g.77040185G>C		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	29	17	0.586207	NM_030968	Q6ZMH6|Q96NF2|Q9GZR4	Silent	SNP	ENST00000339142.2	37	CCDS11761.1																																																																																			G|0.616;C|0.384	0.384	strong		0.677	C1QTNF1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437388.2	NM_030968	
ACOT11	26027	hgsc.bcm.edu	37	1	55060251	55060251	+	Missense_Mutation	SNP	C	C	T	rs2304306	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:55060251C>T	ENST00000371316.3	+	6	576	c.494C>T	c.(493-495)cCg>cTg	p.P165L	ACOT11_ENST00000481208.1_3'UTR|ACOT11_ENST00000343744.2_Missense_Mutation_p.P165L	NM_015547.3	NP_056362.1	Q8WXI4	ACO11_HUMAN	acyl-CoA thioesterase 11	165			P -> L (in dbSNP:rs2304306).		fatty acid metabolic process (GO:0006631)|intracellular signal transduction (GO:0035556)|response to cold (GO:0009409)|response to temperature stimulus (GO:0009266)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	acyl-CoA hydrolase activity (GO:0047617)|carboxylic ester hydrolase activity (GO:0052689)|lipid binding (GO:0008289)			NS(1)|central_nervous_system(1)|endometrium(6)|large_intestine(3)|lung(5)|ovary(1)	17						CAGATCACGCCGCGGACAGAA	0.617													C|||	405	0.0808706	0.0295	0.1412	5008	,	,		19363	0.1776		0.0278	False		,,,				2504	0.0624				p.P165L	Ovarian(148;1440 1861 22015 32453 51933)	Atlas-SNP	.											.	ACOT11	105	.	0			c.C494T						PASS	.	C	LEU/PRO,LEU/PRO	147,4259	101.2+/-139.8	1,145,2057	43.0	41.0	42.0		494,494	4.9	0.1	1	dbSNP_100	42	185,8415	82.6+/-145.2	1,183,4116	yes	missense,missense	ACOT11	NM_015547.3,NM_147161.3	98,98	2,328,6173	TT,TC,CC		2.1512,3.3364,2.5527	benign,benign	165/608,165/595	55060251	332,12674	2203	4300	6503	SO:0001583	missense	26027	exon6			TCACGCCGCGGAC	AB014607	CCDS592.1, CCDS593.1	1p32.3	2011-09-13	2005-09-08	2005-09-08	ENSG00000162390	ENSG00000162390	3.1.2.-	"""Acyl CoA thioesterases"", ""StAR-related lipid transfer (START) domain containing"""	18156	protein-coding gene	gene with protein product	"""StAR-related lipid transfer (START) domain containing 14"""	606803	"""thioesterase, adipose associated"""	THEA		11696000, 16103133, 16940157	Standard	NM_015547		Approved	STARD14, BFIT, KIAA0707, BFIT1, THEM1	uc001cxl.2	Q8WXI4	OTTHUMG00000009891	ENST00000371316.3:c.494C>T	1.37:g.55060251C>T	ENSP00000360366:p.Pro165Leu	Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	135	56	0.414815	NM_147161	B1AQ22|D3DQ50|O75187|Q52LP1|Q53ER9|Q96DI1|Q9H883	Missense_Mutation	SNP	ENST00000371316.3	37	CCDS592.1	188	0.08608058608058608	13	0.026422764227642278	48	0.13259668508287292	104	0.18181818181818182	23	0.030343007915567283	C	13.72	2.321705	0.41096	0.033364	0.021512	ENSG00000162390	ENST00000343744;ENST00000371316	T;T	0.48522	0.81;0.81	4.93	4.93	0.64822	.	0.000000	0.85682	D	0.000000	T	0.00109	0.0003	L	0.50847	1.595	0.09310	P	0.9999999999763491	P;P	0.47409	0.675;0.895	B;B	0.39299	0.155;0.296	T	0.12426	-1.0548	9	0.12103	T	0.63	-16.8503	18.5484	0.91055	0.0:1.0:0.0:0.0	rs2304306;rs52793120;rs2304306	165;165	Q8WXI4;Q8WXI4-2	ACO11_HUMAN;.	L	165	ENSP00000340260:P165L;ENSP00000360366:P165L	ENSP00000340260:P165L	P	+	2	0	ACOT11	54832839	1.000000	0.71417	0.075000	0.20258	0.384000	0.30261	7.360000	0.79487	2.448000	0.82819	0.561000	0.74099	CCG	C|0.950;T|0.050	0.050	strong		0.617	ACOT11-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000027356.1	NM_015547	
FCGR3A	2214	hgsc.bcm.edu	37	1	161518286	161518286	+	Missense_Mutation	SNP	C	C	T	rs200727785		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:161518286C>T	ENST00000436743.1	-	4	398	c.244G>A	c.(244-246)Gac>Aac	p.D82N	RP11-25K21.6_ENST00000537821.2_RNA|FCGR3A_ENST00000443193.1_Missense_Mutation_p.D117N|FCGR3A_ENST00000540048.1_Missense_Mutation_p.D82N|FCGR3A_ENST00000367969.3_Missense_Mutation_p.D118N|FCGR3A_ENST00000476031.1_5'UTR	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)	82	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)	CCACTGTCGTCGACTGTGGCA	0.547																																					p.D118N		Atlas-SNP	.											FCGR3A,colon,carcinoma,+2,1	FCGR3A	38	1	0			c.G352A						scavenged	.						282.0	257.0	266.0					1																	161518286		2203	4300	6503	SO:0001583	missense	2214	exon3			TGTCGTCGACTGT	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.244G>A	1.37:g.161518286C>T	ENSP00000416607:p.Asp82Asn	Somatic	714	0	0		WXS	Illumina HiSeq	Phase_I	428	83	0.193925	NM_000569	A2N6W9|Q53FJ0|Q53FL6|Q5EBR4|Q65ZM6|Q6PIJ0	Missense_Mutation	SNP	ENST00000436743.1	37	CCDS44266.1	.	.	.	.	.	.	.	.	.	.	T	0.254	-1.004529	0.02112	.	.	ENSG00000203747	ENST00000367969;ENST00000443193;ENST00000436743;ENST00000367967;ENST00000540048;ENST00000442336	T;T;T;T;T;T	0.12255	2.7;2.7;2.7;2.7;2.7;2.7	4.42	-8.84	0.00803	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	1.472120	0.04313	N	0.349334	T	0.01061	0.0035	N	0.11756	0.17	0.09310	A	2.22055e-13	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.30937	-0.9961	9	0.02654	T	1	.	6.7583	0.23526	0.0842:0.2147:0.084:0.6171	.	82;117	P08637;E9PG94	FCG3A_HUMAN;.	N	118;117;82;82;82;81	ENSP00000356946:D118N;ENSP00000392047:D117N;ENSP00000416607:D82N;ENSP00000356944:D82N;ENSP00000444971:D82N;ENSP00000396567:D81N	ENSP00000356944:D82N	D	-	1	0	FCGR3A	159784910	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.472000	0.00459	-3.122000	0.00238	-3.646000	0.00026	GAC	C|0.667;T|0.333	0.333	strong		0.547	FCGR3A-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102169.2	NM_000569	
PCDHB8	56128	hgsc.bcm.edu	37	5	140559849	140559849	+	Missense_Mutation	SNP	G	G	A	rs17096961	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:140559849G>A	ENST00000239444.2	+	1	2479	c.2234G>A	c.(2233-2235)aGc>aAc	p.S745N	PCDHB16_ENST00000361016.2_5'Flank	NM_019120.3	NP_061993.2	Q9UN66	PCDB8_HUMAN	protocadherin beta 8	745			S -> N (in dbSNP:rs17096961).		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)			GGCACCGGGAGCCTGTCTCAG	0.597													G|||	758	0.151358	0.2572	0.1902	5008	,	,		15316	0.0407		0.1531	False		,,,				2504	0.093				p.S745N		Atlas-SNP	.											.	PCDHB8	199	.	0			c.G2234A						PASS	.	G	ASN/SER	1039,3367	384.4+/-325.3	116,807,1280	89.0	91.0	91.0		2234	3.7	0.2	5	dbSNP_123	91	1429,7171	275.0+/-291.5	126,1177,2997	yes	missense	PCDHB8	NM_019120.3	46	242,1984,4277	AA,AG,GG		16.6163,23.5815,18.9759	benign	745/802	140559849	2468,10538	2203	4300	6503	SO:0001583	missense	56128	exon1			CCGGGAGCCTGTC	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.2234G>A	5.37:g.140559849G>A	ENSP00000239444:p.Ser745Asn	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	98	59	0.602041	NM_019120	B9EGV1	Missense_Mutation	SNP	ENST00000239444.2	37	CCDS4250.1	327	0.14972527472527472	122	0.24796747967479674	63	0.17403314917127072	26	0.045454545454545456	116	0.15303430079155672	g	11.20	1.567178	0.28003	0.235815	0.166163	ENSG00000120322	ENST00000239444	T	0.49432	0.78	4.53	3.66	0.41972	.	.	.	.	.	T	0.00012	0.0000	L	0.50333	1.59	0.40933	P	0.015599999999999947	B	0.02656	0.0	B	0.04013	0.001	T	0.07597	-1.0764	8	0.66056	D	0.02	.	14.1857	0.65605	0.0:0.8474:0.1526:0.0	rs17096961;rs17844509;rs17096961	745	Q9UN66	PCDB8_HUMAN	N	745	ENSP00000239444:S745N	ENSP00000239444:S745N	S	+	2	0	PCDHB8	140540033	0.626000	0.27120	0.220000	0.23810	0.001000	0.01503	3.667000	0.54547	0.895000	0.36342	-0.241000	0.12123	AGC	G|0.827;A|0.173	0.173	strong		0.597	PCDHB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251816.2	NM_019120	
PLD1	5337	hgsc.bcm.edu	37	3	171404478	171404478	+	Missense_Mutation	SNP	C	C	A	rs2290480	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:171404478C>A	ENST00000351298.4	-	16	1990	c.1864G>T	c.(1864-1866)Gct>Tct	p.A622S	PLD1_ENST00000342215.6_Intron|PLD1_ENST00000356327.5_Intron|PLD1_ENST00000340989.4_Missense_Mutation_p.A622S	NM_002662.4	NP_002653.1	Q13393	PLD1_HUMAN	phospholipase D1, phosphatidylcholine-specific	622	Catalytic.		A -> S (in dbSNP:rs2290480).		chemotaxis (GO:0006935)|defense response to Gram-positive bacterium (GO:0050830)|glycerophospholipid biosynthetic process (GO:0046474)|lipid catabolic process (GO:0016042)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylglycerol biosynthetic process (GO:0006655)|phospholipid metabolic process (GO:0006644)|Ras protein signal transduction (GO:0007265)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	N-acylphosphatidylethanolamine-specific phospholipase D activity (GO:0070290)|phosphatidylinositol binding (GO:0035091)|phospholipase D activity (GO:0004630)			breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(15)|lung(27)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	63	all_cancers(22;4.53e-19)|Ovarian(172;0.00197)|Breast(254;0.186)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)		Choline(DB00122)	TACTTACCAGCATGAGGTCTA	0.438													C|||	829	0.165535	0.1384	0.1052	5008	,	,		17750	0.13		0.1988	False		,,,				2504	0.2474				p.A622S	NSCLC(149;2174 3517 34058)	Atlas-SNP	.											PLD1,NS,carcinoma,0,2	PLD1	134	2	0			c.G1864T						PASS	.	C	,SER/ALA	564,3842	252.4+/-258.8	34,496,1673	132.0	136.0	135.0		,1864	-8.8	0.0	3	dbSNP_100	135	1762,6838	319.1+/-314.0	195,1372,2733	yes	intron,missense	PLD1	NM_001130081.2,NM_002662.4	,99	229,1868,4406	AA,AC,CC		20.4884,12.8007,17.8841	,benign	,622/1075	171404478	2326,10680	2203	4300	6503	SO:0001583	missense	5337	exon16			TACCAGCATGAGG	U38545	CCDS3216.1, CCDS46957.1	3q26	2013-01-10	2006-02-17		ENSG00000075651	ENSG00000075651	3.1.4.4	"""Pleckstrin homology (PH) domain containing"""	9067	protein-coding gene	gene with protein product	"""choline phosphatase 1"""	602382				9858822, 8530346	Standard	NM_002662		Approved		uc003fhs.3	Q13393	OTTHUMG00000156947	ENST00000351298.4:c.1864G>T	3.37:g.171404478C>A	ENSP00000342793:p.Ala622Ser	Somatic	202	0	0		WXS	Illumina HiSeq	Phase_I	186	71	0.38172	NM_002662		Missense_Mutation	SNP	ENST00000351298.4	37	CCDS3216.1	326	0.14926739926739926	65	0.13211382113821138	42	0.11602209944751381	67	0.11713286713286714	152	0.20052770448548812	C	6.267	0.417295	0.11870	0.128007	0.204884	ENSG00000075651	ENST00000351298;ENST00000340989	T;T	0.06528	3.43;3.29	5.46	-8.81	0.00813	.	3.181240	0.00582	N	0.000327	T	0.00012	0.0000	N	0.03608	-0.345	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.38950	-0.9637	9	0.07482	T	0.82	.	9.5572	0.39346	0.095:0.3045:0.0:0.6005	rs2290480;rs2290480	622	Q13393	PLD1_HUMAN	S	622	ENSP00000342793:A622S;ENSP00000340326:A622S	ENSP00000340326:A622S	A	-	1	0	PLD1	172887172	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-3.644000	0.00405	-2.053000	0.00901	0.557000	0.71058	GCT	C|0.841;A|0.159	0.159	strong		0.438	PLD1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000346730.2	NM_002662	
CEP131	22994	hgsc.bcm.edu	37	17	79170576	79170576	+	Silent	SNP	C	C	T	rs1542961	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:79170576C>T	ENST00000269392.4	-	15	2080	c.1833G>A	c.(1831-1833)gcG>gcA	p.A611A	AZI1_ENST00000374782.3_Silent_p.A608A|AZI1_ENST00000450824.2_Silent_p.A608A|RP11-455O6.2_ENST00000571085.1_RNA|AZI1_ENST00000575907.1_Silent_p.A611A	NM_014984.2	NP_055799.2	Q9UPN4	CP131_HUMAN		611					cell differentiation (GO:0030154)|G2/M transition of mitotic cell cycle (GO:0000086)|intraciliary transport involved in cilium morphogenesis (GO:0035735)|mitotic cell cycle (GO:0000278)|multicellular organismal development (GO:0007275)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular protein transport (GO:0090316)|regulation of centrosome duplication (GO:0010824)|spermatogenesis (GO:0007283)	BBSome (GO:0034464)|cell projection (GO:0042995)|centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)	protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(3)|endometrium(6)|kidney(3)|large_intestine(1)|lung(12)|ovary(2)|prostate(3)|urinary_tract(5)	36	all_neural(118;0.0804)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0272)|OV - Ovarian serous cystadenocarcinoma(97;0.117)			GCCGGCTCAGCGCCTTCTCTG	0.701													C|||	1108	0.221246	0.2927	0.2622	5008	,	,		12663	0.0149		0.4036	False		,,,				2504	0.1207				p.A608A		Atlas-SNP	.											AZI1_ENST00000450824,NS,carcinoma,0,2	AZI1	145	2	0			c.G1824A						scavenged	.	C	,	1300,3068		187,926,1071	23.0	22.0	22.0		1824,1824	0.6	0.1	17	dbSNP_88	22	3373,5197		688,1997,1600	no	coding-synonymous,coding-synonymous	AZI1	NM_001009811.2,NM_014984.2	,	875,2923,2671	TT,TC,CC		39.3582,29.7619,36.1184	,	608/1045,608/1081	79170576	4673,8265	2184	4285	6469	SO:0001819	synonymous_variant	22994	exon15			GCTCAGCGCCTTC																												ENST00000269392.4:c.1833G>A	17.37:g.79170576C>T		Somatic	92	1	0.0108696		WXS	Illumina HiSeq	Phase_I	110	110	1	NM_014984	A6NHI8|B2RN11|Q96F50	Silent	SNP	ENST00000269392.4	37																																																																																				C|0.699;T|0.301	0.301	strong		0.701	AZI1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000256070.1		
GPR75-ASB3	100302652	hgsc.bcm.edu	37	2	53955850	53955850	+	Splice_Site	SNP	C	C	T	rs17521008	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:53955850C>T	ENST00000263634.3	-	5	737	c.603G>A	c.(601-603)tcG>tcA	p.S201S	GPR75-ASB3_ENST00000482829.1_5'UTR|GPR75-ASB3_ENST00000352846.3_Splice_Site_p.S239S|GPR75-ASB3_ENST00000406687.1_Splice_Site_p.S128S|ASB3_ENST00000498475.2_5'UTR|GPR75-ASB3_ENST00000394717.2_Splice_Site_p.S128S|ASB3_ENST00000406625.2_Splice_Site_p.S236S	NM_016115.4	NP_057199.1			GPR75-ASB3 readthrough									p.S201S(1)									TAATCTTACCCGATGAAATAA	0.368													C|||	860	0.171725	0.1074	0.2046	5008	,	,		18067	0.1637		0.1799	False		,,,				2504	0.2352				p.S239S		Atlas-SNP	.											ASB3,NS,carcinoma,0,1	.	.	1	1	Substitution - coding silent(1)	stomach(1)	c.G717A						PASS	.	C	,,,	518,3888	236.8+/-248.8	36,446,1721	85.0	84.0	84.0		717,384,603,384	-11.4	0.0	2	dbSNP_123	84	1641,6959	302.0+/-305.7	161,1319,2820	yes	coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice	ASB3,GPR75-ASB3	NM_001164165.1,NM_001201965.1,NM_016115.4,NM_145863.2	,,,	197,1765,4541	TT,TC,CC		19.0814,11.7567,16.6	,,,	239/557,128/446,201/519,128/446	53955850	2159,10847	2203	4300	6503	SO:0001630	splice_region_variant	100302652	exon5			CTTACCCGATGAA		CCDS54361.1	2p16	2013-01-23			ENSG00000115239	ENSG00000115239			40043	other	readthrough							Standard	NM_001164165		Approved				OTTHUMG00000129279	ENST00000263634.3:c.604+1G>A	2.37:g.53955850C>T		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	120	94	0.783333	NM_001164165		Silent	SNP	ENST00000263634.3	37	CCDS1846.1	348	0.15934065934065933	65	0.13211382113821138	74	0.20441988950276244	85	0.1486013986013986	124	0.16358839050131926	C	0.049	-1.254936	0.01457	0.117567	0.190814	ENSG00000115239	ENST00000406053	.	.	.	5.72	-11.4	0.00090	.	.	.	.	.	T	0.00012	0.0000	.	.	.	.	.	.	.	.	.	.	.	.	T	0.03306	-1.1050	3	.	.	.	.	2.567	0.04785	0.2366:0.0914:0.2099:0.4621	rs17521008	.	.	.	R	194	.	.	G	-	1	0	ASB3	53809354	0.000000	0.05858	0.003000	0.11579	0.836000	0.47400	-4.365000	0.00245	-4.807000	0.00031	-2.943000	0.00086	GGG	C|0.834;T|0.166	0.166	strong		0.368	GPR75-ASB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251402.3		Silent
GRIN3B	116444	hgsc.bcm.edu	37	19	1003172	1003172	+	Missense_Mutation	SNP	C	C	T	rs2240154	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:1003172C>T	ENST00000234389.3	+	2	489	c.470C>T	c.(469-471)aCg>aTg	p.T157M	AC004528.4_ENST00000588380.1_RNA	NM_138690.1	NP_619635.1	O60391	NMD3B_HUMAN	glutamate receptor, ionotropic, N-methyl-D-aspartate 3B	157			T -> M (in dbSNP:rs2240154).		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)	CCCCTGGAGACGCTGCTGGAT	0.692													c|||	904	0.180511	0.0053	0.2478	5008	,	,		13218	0.4415		0.1252	False		,,,				2504	0.1575				p.T157M		Atlas-SNP	.											GRIN3B,colon,carcinoma,-1,1	GRIN3B	46	1	0			c.C470T						scavenged	.	C	MET/THR	120,4112		4,112,2000	8.0	9.0	9.0		470	3.4	0.9	19	dbSNP_98	9	1154,7198		74,1006,3096	yes	missense	GRIN3B	NM_138690.1	81	78,1118,5096	TT,TC,CC		13.817,2.8355,10.124	probably-damaging	157/1044	1003172	1274,11310	2116	4176	6292	SO:0001583	missense	116444	exon2			TGGAGACGCTGCT		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.470C>T	19.37:g.1003172C>T	ENSP00000234389:p.Thr157Met	Somatic	46	1	0.0217391		WXS	Illumina HiSeq	Phase_I	66	66	1	NM_138690	Q5EAK7|Q7RTW9	Missense_Mutation	SNP	ENST00000234389.3	37	CCDS32861.1	461	0.21108058608058608	6	0.012195121951219513	80	0.22099447513812154	271	0.4737762237762238	104	0.13720316622691292	c	12.89	2.073457	0.36566	0.028355	0.13817	ENSG00000116032	ENST00000234389	T	0.11495	2.77	3.38	3.38	0.38709	.	0.873177	0.09050	U	0.856029	T	0.00012	0.0000	L	0.56769	1.78	0.44946	P	0.0020400000000000418	D	0.89917	1.0	D	0.64410	0.925	T	0.48536	-0.9027	9	0.66056	D	0.02	.	9.1853	0.37168	0.2175:0.7825:0.0:0.0	rs2240154;rs58215190;rs2240154	157	O60391	NMD3B_HUMAN	M	157	ENSP00000234389:T157M	ENSP00000234389:T157M	T	+	2	0	GRIN3B	954172	0.738000	0.28186	0.869000	0.34112	0.749000	0.42624	1.365000	0.34182	1.748000	0.51833	0.449000	0.29647	ACG	C|0.842;T|0.158	0.158	strong		0.692	GRIN3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103923.2		
MAP1A	4130	hgsc.bcm.edu	37	15	43818115	43818115	+	Missense_Mutation	SNP	G	G	A	rs145659671	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:43818115G>A	ENST00000300231.5	+	4	4894	c.4444G>A	c.(4444-4446)Gac>Aac	p.D1482N	MAP1A_ENST00000399453.1_Missense_Mutation_p.D1482N|MAP1A_ENST00000382031.1_Missense_Mutation_p.D1720N			P78559	MAP1A_HUMAN	microtubule-associated protein 1A	1482					microtubule cytoskeleton organization (GO:0000226)|sensory perception of sound (GO:0007605)	cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)	structural molecule activity (GO:0005198)	p.D1482N(1)		breast(5)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(11)|liver(2)|lung(19)|ovary(5)|pancreas(3)|prostate(2)|skin(6)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	66		all_cancers(109;1.03e-14)|all_epithelial(112;2.23e-12)|Lung NSC(122;2.76e-08)|all_lung(180;3.1e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;3.05e-06)	Estramustine(DB01196)	GGAACAAAAGGACAGGGTCCT	0.448													G|||	11	0.00219649	0.0008	0.0086	5008	,	,		20845	0.0		0.003	False		,,,				2504	0.001				p.D1482N		Atlas-SNP	.											MAP1A,NS,carcinoma,0,1	MAP1A	189	1	1	Substitution - Missense(1)	pancreas(1)	c.G4444A						scavenged	.	G	ASN/ASP	14,3740		0,14,1863	92.0	92.0	92.0		4444	3.9	0.5	15	dbSNP_134	92	124,8086		0,124,3981	yes	missense	MAP1A	NM_002373.5	23	0,138,5844	AA,AG,GG		1.5104,0.3729,1.1535	probably-damaging	1482/2804	43818115	138,11826	1877	4105	5982	SO:0001583	missense	4130	exon4			CAAAAGGACAGGG	U38292	CCDS42031.1	15q15.3	2006-06-15			ENSG00000166963	ENSG00000166963			6835	protein-coding gene	gene with protein product		600178		MAP1L		7806212, 7629894	Standard	XM_005254385		Approved		uc001zrt.3	P78559	OTTHUMG00000059756	ENST00000300231.5:c.4444G>A	15.37:g.43818115G>A	ENSP00000300231:p.Asp1482Asn	Somatic	54	1	0.0185185		WXS	Illumina HiSeq	Phase_I	83	53	0.638554	NM_002373	O95643|Q12973|Q15882|Q9UJT4	Missense_Mutation	SNP	ENST00000300231.5	37	CCDS42031.1	7	0.003205128205128205	1	0.0020325203252032522	3	0.008287292817679558	0	0.0	3	0.00395778364116095	G	12.86	2.064968	0.36470	0.003729	0.015104	ENSG00000166963	ENST00000382031;ENST00000399453;ENST00000300231	T;T;T	0.23552	2.25;1.9;1.9	3.94	3.94	0.45596	.	.	.	.	.	T	0.32793	0.0841	M	0.71581	2.175	0.09310	N	1	D	0.67145	0.996	D	0.79784	0.993	T	0.12041	-1.0563	9	0.56958	D	0.05	-7.9541	13.1289	0.59369	0.0:0.1622:0.8377:0.0	.	1482	P78559	MAP1A_HUMAN	N	1720;1482;1482	ENSP00000371462:D1720N;ENSP00000382380:D1482N;ENSP00000300231:D1482N	ENSP00000300231:D1482N	D	+	1	0	MAP1A	41605407	0.002000	0.14202	0.509000	0.27700	0.039000	0.13416	0.567000	0.23608	2.166000	0.68216	0.563000	0.77884	GAC	G|0.992;A|0.008	0.008	strong		0.448	MAP1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000132894.5	NM_002373	
ACER3	55331	hgsc.bcm.edu	37	11	76637680	76637680	+	Silent	SNP	G	G	A	rs4479014	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:76637680G>A	ENST00000532485.1	+	2	287	c.183G>A	c.(181-183)aaG>aaA	p.K61K	ACER3_ENST00000530182.1_3'UTR|ACER3_ENST00000526597.1_5'UTR|ACER3_ENST00000538157.1_Silent_p.K19K|ACER3_ENST00000533873.1_Intron	NM_018367.5	NP_060837.3	Q9NUN7	ACER3_HUMAN	alkaline ceramidase 3	61					ceramide metabolic process (GO:0006672)|phytosphingosine biosynthetic process (GO:0071602)|positive regulation of cell proliferation (GO:0008284)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|sphingosine biosynthetic process (GO:0046512)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of Golgi membrane (GO:0030173)	phytoceramidase activity (GO:0070774)			endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|prostate(1)	9						GTCTGGAAAAGCGGTACATTG	0.363													A|||	2523	0.503794	0.1876	0.4726	5008	,	,		15568	0.5903		0.7127	False		,,,				2504	0.6493				p.K61K		Atlas-SNP	.											.	ACER3	19	.	0			c.G183A						PASS	.	A		1274,3126	699.8+/-406.5	205,864,1131	154.0	130.0	138.0		183	1.6	1.0	11	dbSNP_111	138	6292,2292	384.5+/-341.1	2313,1666,313	no	coding-synonymous	ACER3	NM_018367.5		2518,2530,1444	AA,AG,GG		26.7008,28.9545,41.7283		61/268	76637680	7566,5418	2200	4292	6492	SO:0001819	synonymous_variant	55331	exon2			GGAAAAGCGGTAC	AF214454	CCDS8247.1, CCDS73352.1	11q13.5	2013-01-25	2008-12-19	2008-12-19	ENSG00000078124	ENSG00000078124	3.5.1.23	"""Alkaline ceramidase"""	16066	protein-coding gene	gene with protein product	"""alkaline phytoceramidase"""		"""phytoceramidase, alkaline"""	PHCA		11356846, 18619555	Standard	XM_005274090		Approved	FLJ11238, APHC	uc009yum.1	Q9NUN7	OTTHUMG00000165225	ENST00000532485.1:c.183G>A	11.37:g.76637680G>A		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	111	15	0.135135	NM_018367	B2RC99	Silent	SNP	ENST00000532485.1	37	CCDS8247.1																																																																																			G|0.422;A|0.578	0.578	strong		0.363	ACER3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382770.2	NM_018367	
FRMD4B	23150	hgsc.bcm.edu	37	3	69299233	69299233	+	Missense_Mutation	SNP	C	C	G	rs4361282	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:69299233C>G	ENST00000398540.3	-	6	602	c.519G>C	c.(517-519)gaG>gaC	p.E173D	FRMD4B_ENST00000542259.1_Missense_Mutation_p.E119D	NM_015123.1	NP_055938	Q9Y2L6	FRM4B_HUMAN	FERM domain containing 4B	173	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				establishment of epithelial cell polarity (GO:0090162)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular space (GO:0005615)|ruffle (GO:0001726)				NS(2)|central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(3)|lung(1)|ovary(3)|prostate(3)|skin(2)	19		Lung NSC(201;0.0138)|Prostate(884;0.11)		BRCA - Breast invasive adenocarcinoma(55;0.000201)|Epithelial(33;0.00141)|LUSC - Lung squamous cell carcinoma(21;0.00999)|Lung(16;0.0182)		TGGTTTCGCTCTCTACTTCGA	0.433													G|||	1237	0.247005	0.3457	0.2133	5008	,	,		18600	0.2649		0.2237	False		,,,				2504	0.1431				p.E173D		Atlas-SNP	.											.	FRMD4B	90	.	0			c.G519C						PASS	.	G	ASP/GLU	1174,2712		165,844,934	279.0	271.0	273.0		519	4.3	1.0	3	dbSNP_111	273	1816,6458		195,1426,2516	yes	missense	FRMD4B	NM_015123.1	45	360,2270,3450	GG,GC,CC		21.9483,30.211,24.5888	benign	173/1035	69299233	2990,9170	1943	4137	6080	SO:0001583	missense	23150	exon6			TTCGCTCTCTACT	AL832231	CCDS46863.1	3p14.2	2006-04-12			ENSG00000114541	ENSG00000114541			24886	protein-coding gene	gene with protein product						10231032, 11445584	Standard	XM_005264720		Approved	KIAA1013, GRSP1	uc003dnv.2	Q9Y2L6	OTTHUMG00000158772	ENST00000398540.3:c.519G>C	3.37:g.69299233C>G	ENSP00000381549:p.Glu173Asp	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	94	55	0.585106	NM_015123	Q8TAI3	Missense_Mutation	SNP	ENST00000398540.3	37	CCDS46863.1	577	0.2641941391941392	176	0.35772357723577236	73	0.20165745856353592	143	0.25	185	0.24406332453825857	G	1.525	-0.545949	0.04024	0.30211	0.219483	ENSG00000114541	ENST00000398540;ENST00000542259;ENST00000493880;ENST00000473029;ENST00000460709	T;T;T;T;T	0.77358	-1.09;-1.09;-1.09;-1.09;-1.09	5.33	4.33	0.51752	Band 4.1 domain (1);FERM central domain (2);FERM domain (1);FERM/acyl-CoA-binding protein, 3-helical bundle (1);	0.106811	0.64402	N	0.000007	T	0.00012	0.0000	N	0.11560	0.145	0.51233	P	8.60000000000305E-5	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.10474	-1.0628	9	0.02654	T	1	-15.1785	7.5424	0.27746	0.0:0.1412:0.5798:0.279	rs4361282;rs52807668;rs4361282	17;173	B4DHD5;Q9Y2L6	.;FRM4B_HUMAN	D	173;119;64;119;119	ENSP00000381549:E173D;ENSP00000437658:E119D;ENSP00000418962:E64D;ENSP00000418373:E119D;ENSP00000418023:E119D	ENSP00000381549:E173D	E	-	3	2	FRMD4B	69381923	1.000000	0.71417	0.999000	0.59377	0.706000	0.40770	1.131000	0.31406	1.400000	0.46741	-0.187000	0.12897	GAG	C|0.742;G|0.258	0.258	strong		0.433	FRMD4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352111.1		
GRIN3A	116443	hgsc.bcm.edu	37	9	104449098	104449098	+	Missense_Mutation	SNP	C	C	T	rs10989591	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	95	0	0		WXS	Illumina HiSeq	Phase_I	71	36	0.507042	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		
TATDN1	83940	hgsc.bcm.edu	37	8	125498547	125498547	+	IGR	SNP	C	C	T	rs3812471	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:125498547C>T	ENST00000276692.6	-	0	1018				RP11-158K1.3_ENST00000518639.1_RNA|RNF139_ENST00000303545.3_Silent_p.Y219Y	NM_032026.3	NP_114415.1	Q6P1N9	TATD1_HUMAN	TatD DNase domain containing 1						DNA catabolic process (GO:0006308)	intracellular organelle (GO:0043229)|nucleus (GO:0005634)	deoxyribonuclease activity (GO:0004536)|endodeoxyribonuclease activity, producing 5'-phosphomonoesters (GO:0016888)|metal ion binding (GO:0046872)			endometrium(1)|kidney(2)|large_intestine(3)|lung(6)|prostate(2)|upper_aerodigestive_tract(1)	15	Ovarian(258;0.00438)|all_neural(195;0.0779)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.00288)			ATCGAATTTACGGATTACAGT	0.398													T|||	2859	0.570887	0.7912	0.4755	5008	,	,		22796	0.4355		0.494	False		,,,				2504	0.5593				p.Y219Y		Atlas-SNP	.											.	RNF139	57	.	0			c.C657T						PASS	.	T		3097,1309	439.6+/-345.7	1095,907,201	208.0	210.0	209.0		657	0.4	1.0	8	dbSNP_107	209	3997,4603	599.4+/-394.1	908,2181,1211	no	coding-synonymous	RNF139	NM_007218.3		2003,3088,1412	TT,TC,CC		46.4767,29.7095,45.4559		219/665	125498547	7094,5912	2203	4300	6503	SO:0001628	intergenic_variant	11236	exon2			AATTTACGGATTA	AF212250	CCDS6351.1, CCDS55273.1	8q24.13	2004-06-07			ENSG00000147687	ENSG00000147687			24220	protein-coding gene	gene with protein product						12477932	Standard	NM_032026		Approved	CDA11	uc003yrd.2	Q6P1N9	OTTHUMG00000165068		8.37:g.125498547C>T		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	81	81	1	NM_007218	B2R5J0|Q8TD02|Q9BY40	Silent	SNP	ENST00000276692.6	37	CCDS6351.1																																																																																			C|0.445;T|0.555	0.555	strong		0.398	TATDN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381655.1	NM_032026	
KRTAP4-8	728224	hgsc.bcm.edu	37	17	39253815	39253815	+	Silent	SNP	G	G	A	rs77163010	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:39253815G>A	ENST00000333822.4	-	1	578	c.522C>T	c.(520-522)tgC>tgT	p.C174C		NM_031960.2	NP_114166.1	Q9BYQ9	KRA48_HUMAN	keratin associated protein 4-8	174					aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)				endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(1)|prostate(1)	11						CGGGGCGGGGGCAGGTGGAGA	0.632													G|||	2819	0.562899	0.6536	0.6081	5008	,	,		16773	0.4127		0.6183	False		,,,				2504	0.5061				p.C174C		Atlas-SNP	.											.	KRTAP4-8	57	.	0			c.C522T						PASS	.						52.0	63.0	60.0					17																	39253815		691	1591	2282	SO:0001819	synonymous_variant	728224	exon1			GCGGGGGCAGGTG	AJ406940	CCDS45674.1	17q21.2	2013-06-25			ENSG00000204880	ENSG00000204880		"""Keratin associated proteins"""	17230	protein-coding gene	gene with protein product						11279113	Standard	NM_031960		Approved	KAP4.8	uc010wfo.2	Q9BYQ9	OTTHUMG00000133580	ENST00000333822.4:c.522C>T	17.37:g.39253815G>A		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	118	55	0.466102	NM_031960	A8MSH3	Silent	SNP	ENST00000333822.4	37	CCDS45674.1																																																																																			G|0.983;A|0.017	0.017	strong		0.632	KRTAP4-8-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257684.1	NM_031960	
CPQ	10404	hgsc.bcm.edu	37	8	98041698	98041698	+	Silent	SNP	C	C	T	rs113729124	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:98041698C>T	ENST00000220763.5	+	6	1239	c.1029C>T	c.(1027-1029)gcC>gcT	p.A343A		NM_016134.2	NP_057218.1	Q9Y646	CBPQ_HUMAN	carboxypeptidase Q	343					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)										GAGTTGGTGCCTTCCAGTATT	0.413													C|||	10	0.00199681	0.0	0.0014	5008	,	,		17784	0.0		0.004	False		,,,				2504	0.0051				p.A343A		Atlas-SNP	.											.	.	.	.	0			c.C1029T						PASS	.	C		8,4398	14.3+/-33.2	0,8,2195	84.0	80.0	81.0		1029	0.5	0.8	8	dbSNP_132	81	116,8484	55.2+/-116.2	0,116,4184	no	coding-synonymous	PGCP	NM_016134.2		0,124,6379	TT,TC,CC		1.3488,0.1816,0.9534		343/473	98041698	124,12882	2203	4300	6503	SO:0001819	synonymous_variant	10404	exon6			TGGTGCCTTCCAG	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.1029C>T	8.37:g.98041698C>T		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	92	19	0.206522	NM_016134	B2RD88|Q8NBZ1|Q9UNM8|Q9Y5X6	Silent	SNP	ENST00000220763.5	37	CCDS6273.1	4	0.0018315018315018315	0	0.0	0	0.0	0	0.0	4	0.005277044854881266	C	9.628	1.135542	0.21123	0.001816	0.013488	ENSG00000104324	ENST00000522617	.	.	.	5.64	0.527	0.17084	.	.	.	.	.	T	0.42562	0.1208	.	.	.	0.52501	D	0.999951	.	.	.	.	.	.	T	0.32268	-0.9913	4	.	.	.	-29.2346	4.6998	0.12822	0.0:0.5093:0.1507:0.34	.	.	.	.	L	1	.	.	P	+	2	0	AC010859.1	98110874	0.011000	0.17503	0.819000	0.32651	0.914000	0.54420	-0.025000	0.12413	0.319000	0.23209	-0.140000	0.14226	CCT	C|0.993;G|0.000;T|0.007	0.007	strong		0.413	CPQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379757.2	NM_016134	
PABPC4L	132430	hgsc.bcm.edu	37	4	135121601	135121601	+	Missense_Mutation	SNP	C	C	T	rs10009368	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:135121601C>T	ENST00000421491.3	-	2	830	c.574G>A	c.(574-576)Gtt>Att	p.V192I	PABPC4L_ENST00000529122.2_Missense_Mutation_p.V250I			P0CB38	PAB4L_HUMAN	poly(A) binding protein, cytoplasmic 4-like	192	RRM 3. {ECO:0000255|PROSITE- ProRule:PRU00176}.		V -> I (in dbSNP:rs10009368).				nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			breast(1)|endometrium(2)	3						TTTATGTAAACATTGGTGAAT	0.403													T|||	3189	0.636781	0.7179	0.5403	5008	,	,		20019	0.9841		0.329	False		,,,				2504	0.5542				p.V250I		Atlas-SNP	.											.	PABPC4L	60	.	0			c.G748A						PASS	.	T	ILE/VAL	925,459		310,305,77	133.0	114.0	120.0		748	-1.0	0.0	4	dbSNP_119	120	981,2201		143,695,753	yes	missense	PABPC4L	NM_001114734.1	29	453,1000,830	TT,TC,CC		30.8297,33.1647,41.7433	benign	250/429	135121601	1906,2660	692	1591	2283	SO:0001583	missense	132430	exon2			TGTAAACATTGGT	AY672099		4q28.3	2013-02-12				ENSG00000254535		"""RNA binding motif (RRM) containing"""	31955	protein-coding gene	gene with protein product							Standard	NM_001114734		Approved		uc010ioe.3	P0CB38		ENST00000421491.3:c.574G>A	4.37:g.135121601C>T	ENSP00000463233:p.Val192Ile	Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	156	154	0.987179	NM_001114734		Missense_Mutation	SNP	ENST00000421491.3	37																																																																																				C|0.348;T|0.652	0.652	strong		0.403	PABPC4L-001	KNOWN	upstream_ATG|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000364399.2	NM_001114734	
ZPR1	8882	hgsc.bcm.edu	37	11	116655600	116655600	+	Missense_Mutation	SNP	G	G	A	rs35120633	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:116655600G>A	ENST00000227322.3	-	8	850	c.791C>T	c.(790-792)gCc>gTc	p.A264V		NM_003904.3	NP_003895.1	O75312	ZPR1_HUMAN		264			A -> V (in dbSNP:rs35120633).		apoptotic process involved in development (GO:1902742)|axon development (GO:0061564)|Cajal body organization (GO:0030576)|cell proliferation (GO:0008283)|cellular response to epidermal growth factor stimulus (GO:0071364)|DNA endoreduplication (GO:0042023)|inner cell mass cell proliferation (GO:0001833)|microtubule cytoskeleton organization (GO:0000226)|mRNA processing (GO:0006397)|negative regulation of motor neuron apoptotic process (GO:2000672)|positive regulation of gene expression (GO:0010628)|positive regulation of growth (GO:0045927)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of RNA splicing (GO:0033120)|positive regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0071931)|pre-mRNA catabolic process (GO:1990261)|regulation of myelination (GO:0031641)|RNA splicing (GO:0008380)|signal transduction (GO:0007165)|spinal cord development (GO:0021510)|trophectodermal cell proliferation (GO:0001834)	axon (GO:0030424)|Cajal body (GO:0015030)|cytoplasm (GO:0005737)|Gemini of coiled bodies (GO:0097504)|growth cone (GO:0030426)|neuronal cell body (GO:0043025)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perikaryon (GO:0043204)|SMN complex (GO:0032797)	translation initiation factor binding (GO:0031369)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|large_intestine(2)|lung(4)|upper_aerodigestive_tract(1)	9	all_hematologic(175;0.0487)	all_cancers(61;1.72e-06)|all_epithelial(67;0.000735)|Melanoma(852;0.022)|Acute lymphoblastic leukemia(157;0.0255)|Medulloblastoma(222;0.0523)|Breast(348;0.056)|all_hematologic(158;0.0588)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|Epithelial(105;5.61e-06)|all cancers(92;0.000139)|OV - Ovarian serous cystadenocarcinoma(223;0.153)		CTGAGCGGGGGCATTGCATTC	0.507													G|||	234	0.0467252	0.0333	0.1153	5008	,	,		22892	0.0		0.0666	False		,,,				2504	0.044				p.A264V		Atlas-SNP	.											.	ZNF259	27	.	0			c.C791T						PASS	.	G	VAL/ALA	130,4272	95.7+/-134.4	0,130,2071	121.0	105.0	111.0		791	5.9	1.0	11	dbSNP_126	111	556,8036	151.6+/-206.3	20,516,3760	yes	missense	ZNF259	NM_003904.3	64	20,646,5831	AA,AG,GG		6.4711,2.9532,5.2794	benign	264/460	116655600	686,12308	2201	4296	6497	SO:0001583	missense	8882	exon8			GCGGGGGCATTGC																												ENST00000227322.3:c.791C>T	11.37:g.116655600G>A	ENSP00000227322:p.Ala264Val	Somatic	227	0	0		WXS	Illumina HiSeq	Phase_I	206	53	0.257282	NM_003904	Q2TAA0	Missense_Mutation	SNP	ENST00000227322.3	37	CCDS8375.1	89|89	0.04075091575091575|0.04075091575091575	16|16	0.032520325203252036|0.032520325203252036	31|31	0.0856353591160221|0.0856353591160221	0|0	0.0|0.0	42|42	0.055408970976253295|0.055408970976253295	G|G	16.56|16.56	3.157904|3.157904	0.57368|0.57368	0.029532|0.029532	0.064711|0.064711	ENSG00000109917|ENSG00000109917	ENST00000227322|ENST00000444935	T|.	0.44881|.	0.91|.	5.92|5.92	5.92|5.92	0.95590|0.95590	Zinc finger, ZPR1-type (3);|.	0.046340|.	0.85682|.	D|.	0.000000|.	T|T	0.06005|0.06005	0.0156|0.0156	L|L	0.54965|0.54965	1.715|1.715	0.80722|0.80722	D|D	1|1	B;B|.	0.25772|.	0.062;0.134|.	B;B|.	0.23419|.	0.046;0.046|.	T|T	0.03750|0.03750	-1.1007|-1.1007	10|5	0.41790|.	T|.	0.15|.	-14.1729|-14.1729	13.4996|13.4996	0.61447|0.61447	0.0711:0.0:0.9289:0.0|0.0711:0.0:0.9289:0.0	rs35120633;rs61905118|rs35120633;rs61905118	213;264|.	B4DVT8;O75312|.	.;ZPR1_HUMAN|.	V|S	264|264	ENSP00000227322:A264V|.	ENSP00000227322:A264V|.	A|P	-|-	2|1	0|0	ZNF259|ZNF259	116160810|116160810	1.000000|1.000000	0.71417|0.71417	0.990000|0.990000	0.47175|0.47175	0.435000|0.435000	0.31806|0.31806	6.269000|6.269000	0.72558|0.72558	2.795000|2.795000	0.96236|0.96236	0.655000|0.655000	0.94253|0.94253	GCC|CCC	G|0.948;A|0.052	0.052	strong		0.507	ZNF259-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106283.2		
C9orf114	51490	hgsc.bcm.edu	37	9	131586374	131586374	+	Silent	SNP	G	G	A	rs7033070	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:131586374G>A	ENST00000361256.5	-	10	931	c.891C>T	c.(889-891)gcC>gcT	p.A297A		NM_016390.3	NP_057474.2	Q5T280	CI114_HUMAN	chromosome 9 open reading frame 114	297							poly(A) RNA binding (GO:0044822)			kidney(2)|large_intestine(4)|ovary(1)	7						GCTGGGCAGAGGCCACATCTG	0.637													G|||	1802	0.359824	0.559	0.2032	5008	,	,		14427	0.2669		0.2535	False		,,,				2504	0.407				p.A297A		Atlas-SNP	.											C9orf114,NS,carcinoma,0,1	C9orf114	28	1	0			c.C891T						PASS	.	G		2166,2240	551.4+/-378.3	544,1078,581	43.0	38.0	40.0		891	0.9	1.0	9	dbSNP_116	40	2138,6462	346.9+/-326.4	253,1632,2415	no	coding-synonymous	C9orf114	NM_016390.2		797,2710,2996	AA,AG,GG		24.8605,49.1602,33.0924		297/377	131586374	4304,8702	2203	4300	6503	SO:0001819	synonymous_variant	51490	exon10			GGCAGAGGCCACA		CCDS6913.1	9q34.11	2014-05-29			ENSG00000198917	ENSG00000198917			26933	protein-coding gene	gene with protein product	"""centromere protein 32"""					20813266	Standard	NM_016390		Approved	HSPC109, CENP-32	uc004bwd.3	Q5T280	OTTHUMG00000020762	ENST00000361256.5:c.891C>T	9.37:g.131586374G>A		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	81	47	0.580247	NM_016390	Q0D2P6|Q6P469|Q6PGP9|Q6PIJ1|Q6PJV9	Silent	SNP	ENST00000361256.5	37	CCDS6913.1																																																																																			G|0.671;A|0.329	0.329	strong		0.637	C9orf114-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054500.1	NM_016390	
MAP1A	4130	hgsc.bcm.edu	37	15	43820423	43820423	+	Missense_Mutation	SNP	C	C	T	rs28438815	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:43820423C>T	ENST00000300231.5	+	4	7202	c.6752C>T	c.(6751-6753)gCc>gTc	p.A2251V	MAP1A_ENST00000399453.1_Missense_Mutation_p.A2251V|MAP1A_ENST00000382031.1_Missense_Mutation_p.A2489V			P78559	MAP1A_HUMAN	microtubule-associated protein 1A	2251					microtubule cytoskeleton organization (GO:0000226)|sensory perception of sound (GO:0007605)	cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)	structural molecule activity (GO:0005198)			breast(5)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(11)|liver(2)|lung(19)|ovary(5)|pancreas(3)|prostate(2)|skin(6)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	66		all_cancers(109;1.03e-14)|all_epithelial(112;2.23e-12)|Lung NSC(122;2.76e-08)|all_lung(180;3.1e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;3.05e-06)	Estramustine(DB01196)	CCACGACCTGCCTCACCAGCC	0.622													C|||	53	0.0105831	0.0	0.0231	5008	,	,		17552	0.0		0.0348	False		,,,				2504	0.002				p.A2251V		Atlas-SNP	.											.	MAP1A	189	.	0			c.C6752T						PASS	.	C	VAL/ALA	22,3884		0,22,1931	67.0	72.0	70.0		6752	4.3	1.0	15	dbSNP_125	70	186,8070		5,176,3947	yes	missense	MAP1A	NM_002373.5	64	5,198,5878	TT,TC,CC		2.2529,0.5632,1.7102	probably-damaging	2251/2804	43820423	208,11954	1953	4128	6081	SO:0001583	missense	4130	exon4			GACCTGCCTCACC	U38292	CCDS42031.1	15q15.3	2006-06-15			ENSG00000166963	ENSG00000166963			6835	protein-coding gene	gene with protein product		600178		MAP1L		7806212, 7629894	Standard	XM_005254385		Approved		uc001zrt.3	P78559	OTTHUMG00000059756	ENST00000300231.5:c.6752C>T	15.37:g.43820423C>T	ENSP00000300231:p.Ala2251Val	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	69	21	0.304348	NM_002373	O95643|Q12973|Q15882|Q9UJT4	Missense_Mutation	SNP	ENST00000300231.5	37	CCDS42031.1	30	0.013736263736263736	0	0.0	9	0.024861878453038673	0	0.0	21	0.027704485488126648	C	12.50	1.955544	0.34471	0.005632	0.022529	ENSG00000166963	ENST00000382031;ENST00000399453;ENST00000300231	T;T;T	0.01548	4.78;4.78;4.78	4.32	4.32	0.51571	.	0.000000	0.33875	N	0.004464	T	0.01189	0.0039	L	0.36672	1.1	0.37166	D	0.902822	P	0.46142	0.873	P	0.50352	0.638	T	0.58329	-0.7655	10	0.52906	T	0.07	-9.2631	15.166	0.72825	0.0:1.0:0.0:0.0	rs28438815;rs28438815	2251	P78559	MAP1A_HUMAN	V	2489;2251;2251	ENSP00000371462:A2489V;ENSP00000382380:A2251V;ENSP00000300231:A2251V	ENSP00000300231:A2251V	A	+	2	0	MAP1A	41607715	1.000000	0.71417	0.982000	0.44146	0.892000	0.51952	1.507000	0.35758	2.241000	0.73720	0.561000	0.74099	GCC	C|0.977;T|0.023	0.023	strong		0.622	MAP1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000132894.5	NM_002373	
PTGS1	5742	hgsc.bcm.edu	37	9	125154660	125154660	+	Missense_Mutation	SNP	C	C	T	rs200295924		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:125154660C>T	ENST00000362012.2	+	11	1642	c.1637C>T	c.(1636-1638)cCg>cTg	p.P546L	PTGS1_ENST00000223423.4_Missense_Mutation_p.P509L|PTGS1_ENST00000540753.1_Missense_Mutation_p.P484L|PTGS1_ENST00000373698.5_Missense_Mutation_p.P437L	NM_000962.3|NM_001271164.1|NM_001271367.1|NM_080591.2	NP_000953.2|NP_001258093.1|NP_001258296.1|NP_542158.1	P23219	PGH1_HUMAN	prostaglandin-endoperoxide synthase 1 (prostaglandin G/H synthase and cyclooxygenase)	546					arachidonic acid metabolic process (GO:0019369)|cyclooxygenase pathway (GO:0019371)|inflammatory response (GO:0006954)|lipid metabolic process (GO:0006629)|prostaglandin biosynthetic process (GO:0001516)|regulation of blood pressure (GO:0008217)|regulation of cell proliferation (GO:0042127)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|photoreceptor outer segment (GO:0001750)	dioxygenase activity (GO:0051213)|heme binding (GO:0020037)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)|prostaglandin-endoperoxide synthase activity (GO:0004666)			large_intestine(3)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	8					Acetaminophen(DB00316)|Acetylsalicylic acid(DB00945)|Antipyrine(DB01435)|Antrafenine(DB01419)|Balsalazide(DB01014)|Bortezomib(DB00188)|Bromfenac(DB00963)|Candesartan(DB00796)|Carprofen(DB00821)|Carvedilol(DB01136)|Chlorpropamide(DB00672)|Dapsone(DB00250)|Desmopressin(DB00035)|Diazepam(DB00829)|Diclofenac(DB00586)|Diethylcarbamazine(DB00711)|Diflunisal(DB00861)|Dihomo-gamma-linolenic acid(DB00154)|Diphenhydramine(DB01075)|Dronabinol(DB00470)|Eletriptan(DB00216)|Eszopiclone(DB00402)|Etodolac(DB00749)|Etoposide(DB00773)|Fenoprofen(DB00573)|Flurbiprofen(DB00712)|Hexobarbital(DB01355)|Hydromorphone(DB00327)|Ibuprofen(DB01050)|Icosapent(DB00159)|Ifosfamide(DB01181)|Imatinib(DB00619)|Indomethacin(DB00328)|Irbesartan(DB01029)|Ketamine(DB01221)|Ketobemidone(DB06738)|Ketoprofen(DB01009)|Ketorolac(DB00465)|Lornoxicam(DB06725)|Lumiracoxib(DB01283)|Magnesium salicylate(DB01397)|Meclofenamic acid(DB00939)|Mefenamic acid(DB00784)|Meloxicam(DB00814)|Mesalazine(DB00244)|Minoxidil(DB00350)|Montelukast(DB00471)|Nabumetone(DB00461)|Naproxen(DB00788)|Nateglinide(DB00731)|Nepafenac(DB06802)|Niflumic Acid(DB04552)|Nortriptyline(DB00540)|Oxaprozin(DB00991)|Phenylbutazone(DB00812)|Pioglitazone(DB01132)|Piroxicam(DB00554)|Rosiglitazone(DB00412)|Salicylate-sodium(DB01398)|Salicylic acid(DB00936)|Salsalate(DB01399)|Sulfamethoxazole(DB01015)|Sulfasalazine(DB00795)|Sulindac(DB00605)|Suprofen(DB00870)|Tenoxicam(DB00469)|Terbinafine(DB00857)|Thalidomide(DB01041)|Tiaprofenic acid(DB01600)|Tolmetin(DB00500)|Torasemide(DB00214)|Trabectedin(DB05109)|Triflusal(DB08814)|Trisalicylate-choline(DB01401)|Valproic Acid(DB00313)|Voriconazole(DB00582)|Zafirlukast(DB00549)|Zileuton(DB00744)|Zolpidem(DB00425)|Zopiclone(DB01198)	TACTGGAAGCCGAGCACATTT	0.527																																					p.P546L		Atlas-SNP	.											.	PTGS1	84	.	0			c.C1637T						PASS	.						112.0	111.0	112.0					9																	125154660		2203	4300	6503	SO:0001583	missense	5742	exon11			GGAAGCCGAGCAC	M59979	CCDS6842.1, CCDS6843.1, CCDS59520.1, CCDS59521.1, CCDS75895.1	9q32-q33.3	2008-02-05			ENSG00000095303	ENSG00000095303	1.14.99.1		9604	protein-coding gene	gene with protein product		176805				2512924, 1907252	Standard	NM_000962		Approved	COX1, PGHS-1, PTGHS	uc004bmg.2	P23219	OTTHUMG00000020605	ENST00000362012.2:c.1637C>T	9.37:g.125154660C>T	ENSP00000354612:p.Pro546Leu	Somatic	272	0	0		WXS	Illumina HiSeq	Phase_I	230	57	0.247826	NM_000962	A8K1V7|B4DHQ2|B4E2S5|Q15122|Q3HY28|Q3HY29|Q5T7T6|Q5T7T7|Q5T7T8	Missense_Mutation	SNP	ENST00000362012.2	37	CCDS6842.1	.	.	.	.	.	.	.	.	.	.	C	32	5.178609	0.94846	.	.	ENSG00000095303	ENST00000540753;ENST00000362012;ENST00000223423;ENST00000373698	T;T;T;T	0.71103	-0.54;-0.54;-0.54;-0.54	5.41	5.41	0.78517	.	0.096182	0.64402	D	0.000001	D	0.87370	0.6160	M	0.91920	3.255	0.80722	D	1	P;D;D	0.69078	0.939;0.995;0.997	P;D;D	0.68621	0.71;0.959;0.931	D	0.90078	0.4168	10	0.87932	D	0	-4.3937	18.2032	0.89846	0.0:1.0:0.0:0.0	.	484;546;509	B4DHQ2;P23219;P23219-2	.;PGH1_HUMAN;.	L	484;546;509;437	ENSP00000437709:P484L;ENSP00000354612:P546L;ENSP00000223423:P509L;ENSP00000362802:P437L	ENSP00000223423:P509L	P	+	2	0	PTGS1	124194481	1.000000	0.71417	0.878000	0.34440	0.935000	0.57460	7.814000	0.86154	2.539000	0.85634	0.655000	0.94253	CCG	.	.	weak		0.527	PTGS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053933.1		
CHFR	55743	hgsc.bcm.edu	37	12	133423662	133423662	+	Missense_Mutation	SNP	C	C	T	rs2306536	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:133423662C>T	ENST00000432561.2	-	15	1811	c.1738G>A	c.(1738-1740)Gtg>Atg	p.V580M	CHFR_ENST00000541341.1_Missense_Mutation_p.V7M|CHFR_ENST00000537522.1_Missense_Mutation_p.V202M|CHFR_ENST00000266880.7_Missense_Mutation_p.V579M|CHFR_ENST00000443047.2_Missense_Mutation_p.V488M|CHFR_ENST00000450056.2_Missense_Mutation_p.V568M|CHFR_ENST00000315585.7_Missense_Mutation_p.V539M|CHFR_ENST00000541837.2_5'UTR			Q96EP1	CHFR_HUMAN	checkpoint with forkhead and ring finger domains, E3 ubiquitin protein ligase	580			V -> M (common polymorphism; dbSNP:rs2306536). {ECO:0000269|PubMed:10935642, ECO:0000269|PubMed:11948416, ECO:0000269|PubMed:14702039}.		mitotic cell cycle checkpoint (GO:0007093)|mitotic nuclear division (GO:0007067)|modification-dependent protein catabolic process (GO:0019941)|protein polyubiquitination (GO:0000209)|ubiquitin-dependent protein catabolic process (GO:0006511)	nucleus (GO:0005634)|PML body (GO:0016605)	ligase activity (GO:0016874)|nucleotide binding (GO:0000166)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	26	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_cancers(7;0.00552)|all_epithelial(31;0.226)		OV - Ovarian serous cystadenocarcinoma(86;2.59e-08)|Epithelial(86;6.38e-07)|all cancers(50;1.56e-05)		TGGAGAGCCACGAGGCTCTCG	0.507													C|||	1000	0.199681	0.2753	0.1427	5008	,	,		18582	0.0665		0.2058	False		,,,				2504	0.2689				p.V580M		Atlas-SNP	.											CHFR_ENST00000432561,colon,carcinoma,0,2	CHFR	83	2	0			c.G1738A	GRCh37	CM084783	CHFR	M	rs2306536	PASS	.	C	MET/VAL,MET/VAL,MET/VAL,MET/VAL,MET/VAL	1238,3168	426.4+/-341.1	187,864,1152	133.0	138.0	137.0		1738,1735,1702,1462,1615	-2.6	0.0	12	dbSNP_100	137	1673,6927	308.2+/-308.8	160,1353,2787	yes	missense,missense,missense,missense,missense	CHFR	NM_001161344.1,NM_001161345.1,NM_001161346.1,NM_001161347.1,NM_018223.2	21,21,21,21,21	347,2217,3939	TT,TC,CC		19.4535,28.098,22.382	benign,benign,benign,benign,benign	580/665,579/664,568/653,488/573,539/624	133423662	2911,10095	2203	4300	6503	SO:0001583	missense	55743	exon15			GAGCCACGAGGCT	AK001658	CCDS31937.1, CCDS53847.1, CCDS53848.1, CCDS53849.1	12q24.33	2012-02-23	2012-02-23			ENSG00000072609		"""RING-type (C3HC4) zinc fingers"""	20455	protein-coding gene	gene with protein product		605209	"""checkpoint with forkhead and ring finger domains"""			10935642, 11807090	Standard	NM_001161344		Approved	FLJ10796, RNF196	uc001ulf.2	Q96EP1		ENST00000432561.2:c.1738G>A	12.37:g.133423662C>T	ENSP00000392395:p.Val580Met	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	42	29	0.690476	NM_001161344	A6NEN5|B4DZ77|B4E2L6|Q96SL3|Q9NRT4|Q9NT32|Q9NVD5	Missense_Mutation	SNP	ENST00000432561.2	37	CCDS53849.1	364	0.16666666666666666	121	0.2459349593495935	55	0.15193370165745856	35	0.06118881118881119	153	0.20184696569920843	C	6.429	0.447239	0.12223	0.28098	0.194535	ENSG00000072609	ENST00000315585;ENST00000443047;ENST00000450056;ENST00000266880;ENST00000537522;ENST00000432561	T;T;T;T;T;T	0.30714	1.52;1.52;1.52;1.52;1.52;1.52	5.64	-2.61	0.06171	.	0.724852	0.13465	N	0.385827	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	B;B;B;B;B	0.24186	0.06;0.061;0.036;0.061;0.099	B;B;B;B;B	0.22601	0.04;0.03;0.013;0.03;0.04	T	0.38950	-0.9637	9	0.48119	T	0.1	-13.553	1.7815	0.03032	0.1432:0.2711:0.3167:0.269	rs2306536;rs3210617;rs52806127;rs60167259;rs2306536	488;579;580;568;539	Q96EP1-5;Q96EP1-4;Q96EP1;Q96EP1-2;Q96EP1-3	.;.;CHFR_HUMAN;.;.	M	539;488;568;579;202;580	ENSP00000320557:V539M;ENSP00000416431:V488M;ENSP00000398735:V568M;ENSP00000266880:V579M;ENSP00000442327:V202M;ENSP00000392395:V580M	ENSP00000266880:V579M	V	-	1	0	CHFR	131933735	0.035000	0.19736	0.012000	0.15200	0.117000	0.20001	0.255000	0.18333	-0.397000	0.07691	-0.258000	0.10820	GTG	C|0.795;T|0.205	0.205	strong		0.507	CHFR-002	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397130.2		
ZNF682	91120	hgsc.bcm.edu	37	19	20117685	20117685	+	Missense_Mutation	SNP	G	G	A	rs2075090	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:20117685G>A	ENST00000397165.2	-	4	786	c.626C>T	c.(625-627)aCc>aTc	p.T209I	ZNF682_ENST00000597972.1_Missense_Mutation_p.T215I|ZNF682_ENST00000397162.1_Missense_Mutation_p.T177I|ZNF682_ENST00000595736.1_Missense_Mutation_p.T133I|ZNF682_ENST00000358523.5_Missense_Mutation_p.T177I|ZNF682_ENST00000596019.1_Intron	NM_033196.2	NP_149973.1	O95780	ZN682_HUMAN	zinc finger protein 682	209			T -> I (in dbSNP:rs2075090). {ECO:0000269|PubMed:14702039}.		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(2)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|stomach(1)|urinary_tract(1)	14						CCACTTAAAGGTTTTGCCACA	0.378													g|||	621	0.124002	0.1316	0.17	5008	,	,		19963	0.1954		0.0378	False		,,,				2504	0.0961				p.T209I		Atlas-SNP	.											.	ZNF682	51	.	0			c.C626T						PASS	.	G	ILE/THR,ILE/THR	456,3668		29,398,1635	50.0	52.0	52.0		530,626	-0.6	0.0	19	dbSNP_96	52	283,8185		5,273,3956	yes	missense,missense	ZNF682	NM_001077349.1,NM_033196.2	89,89	34,671,5591	AA,AG,GG		3.342,11.0572,5.8688	possibly-damaging,possibly-damaging	177/467,209/499	20117685	739,11853	2062	4234	6296	SO:0001583	missense	91120	exon4			TTAAAGGTTTTGC	AC006539	CCDS42533.1, CCDS42534.1	19p12	2014-02-13			ENSG00000197124	ENSG00000197124		"""Zinc fingers, C2H2-type"", ""-"""	28857	protein-coding gene	gene with protein product							Standard	NM_033196		Approved	BC39498_3	uc002noq.3	O95780	OTTHUMG00000182650	ENST00000397165.2:c.626C>T	19.37:g.20117685G>A	ENSP00000380351:p.Thr209Ile	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	35	16	0.457143	NM_033196	B3KU64|E9PFJ5|Q96JV9	Missense_Mutation	SNP	ENST00000397165.2	37	CCDS42533.1	252	0.11538461538461539	72	0.14634146341463414	50	0.13812154696132597	105	0.18356643356643357	25	0.032981530343007916	G	6.697	0.497203	0.12762	0.110572	0.03342	ENSG00000197124	ENST00000397165;ENST00000397162;ENST00000358523	T;T;T	0.36157	1.27;1.27;1.27	1.08	-0.578	0.11724	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00073	0.0002	M	0.64080	1.96	0.58432	P	5.999999999950489E-6	B	0.23249	0.082	B	0.25987	0.065	T	0.12785	-1.0534	8	0.72032	D	0.01	.	5.2114	0.15318	0.244:0.0:0.756:0.0	rs2075090;rs60679185;rs2075090	209	O95780	ZN682_HUMAN	I	209;177;177	ENSP00000380351:T209I;ENSP00000380348:T177I;ENSP00000351324:T177I	ENSP00000351324:T177I	T	-	2	0	ZNF682	19978685	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	-0.410000	0.07151	-0.354000	0.08212	-0.350000	0.07774	ACC	G|0.895;A|0.105	0.105	strong		0.378	ZNF682-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462888.1	NM_033196	
CHRD	8646	hgsc.bcm.edu	37	3	184099378	184099378	+	Silent	SNP	C	C	A	rs35929225	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:184099378C>A	ENST00000204604.1	+	4	723	c.477C>A	c.(475-477)ggC>ggA	p.G159G	CHRD_ENST00000348986.3_Silent_p.G159G|EIF2B5_ENST00000444495.1_Intron|CHRD_ENST00000482805.1_3'UTR|CHRD_ENST00000450923.1_Silent_p.G159G|CHRD_ENST00000545352.1_5'Flank	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	66	0	0		WXS	Illumina HiSeq	Phase_I	81	47	0.580247	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	
DCAF12	25853	hgsc.bcm.edu	37	9	34125258	34125258	+	Silent	SNP	C	C	G	rs61735450	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:34125258C>G	ENST00000361264.4	-	2	437	c.96G>C	c.(94-96)tcG>tcC	p.S32S	DCAF12_ENST00000463286.1_5'UTR	NM_015397.3	NP_056212.1	Q5T6F0	DCA12_HUMAN	DDB1 and CUL4 associated factor 12	32					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						TTTTGTGAAGCGAGTGATCCC	0.433													C|||	55	0.0109824	0.0015	0.0187	5008	,	,		20770	0.0		0.0328	False		,,,				2504	0.0072				p.S32S		Atlas-SNP	.											.	DCAF12	37	.	0			c.G96C						PASS	.	C		36,4370	40.8+/-73.8	0,36,2167	74.0	70.0	72.0		96	-9.1	0.5	9	dbSNP_129	72	297,8303	107.8+/-168.5	5,287,4008	no	coding-synonymous	DCAF12	NM_015397.3		5,323,6175	GG,GC,CC		3.4535,0.8171,2.5604		32/454	34125258	333,12673	2203	4300	6503	SO:0001819	synonymous_variant	25853	exon2			GTGAAGCGAGTGA	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.96G>C	9.37:g.34125258C>G		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	65	32	0.492308	NM_015397	A8KA70|D3DRL6|Q5T6E9|Q5T6F1|Q6P3V0|Q7L4F8|Q96PZ5|Q9NXA9|Q9UFJ1	Silent	SNP	ENST00000361264.4	37	CCDS6549.1																																																																																			C|0.969;G|0.031	0.031	strong		0.433	DCAF12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052133.2	NM_015397	
MUC17	140453	hgsc.bcm.edu	37	7	100681211	100681211	+	Missense_Mutation	SNP	G	G	C	rs147094151	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:100681211G>C	ENST00000306151.4	+	3	6578	c.6514G>C	c.(6514-6516)Gtg>Ctg	p.V2172L		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	2172	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)					CAGCACCACAGTGGTGGCCAG	0.468																																					p.V2172L		Atlas-SNP	.											.	MUC17	804	.	0			c.G6514C						PASS	.	C	LEU/VAL	33,4373		0,33,2170	246.0	241.0	243.0		6514	-1.4	0.0	7	dbSNP_134	243	373,8227		6,361,3933	no	missense	MUC17	NM_001040105.1	32	6,394,6103	CC,CG,GG		4.3372,0.749,3.1216	benign	2172/4494	100681211	406,12600	2203	4300	6503	SO:0001583	missense	140453	exon3			ACCACAGTGGTGG	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.6514G>C	7.37:g.100681211G>C	ENSP00000302716:p.Val2172Leu	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	69	36	0.521739	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	N	0.655	-0.807913	0.02819	0.00749	0.043372	ENSG00000169876	ENST00000306151	T	0.02446	4.29	0.683	-1.37	0.09056	.	.	.	.	.	T	0.00328	0.0010	N	0.03608	-0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.44667	-0.9313	9	0.24483	T	0.36	.	3.5846	0.07966	0.3877:0.2157:0.3965:0.0	.	2172	Q685J3	MUC17_HUMAN	L	2172	ENSP00000302716:V2172L	ENSP00000302716:V2172L	V	+	1	0	MUC17	100467931	.	.	0.000000	0.03702	0.000000	0.00434	.	.	-2.419000	0.00565	-1.314000	0.01303	GTG	G|0.968;C|0.032	0.032	strong		0.468	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
CC2D1B	200014	hgsc.bcm.edu	37	1	52822722	52822722	+	Missense_Mutation	SNP	G	G	A	rs201266966		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:52822722G>A	ENST00000371586.2	-	16	1985	c.1847C>T	c.(1846-1848)gCg>gTg	p.A616V	CC2D1B_ENST00000460261.1_5'UTR|CC2D1B_ENST00000438831.1_5'UTR|CC2D1B_ENST00000284376.3_Missense_Mutation_p.A610V	NM_032449.2	NP_115825.1	Q5T0F9	C2D1B_HUMAN	coiled-coil and C2 domain containing 1B	616						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)			breast(1)|large_intestine(6)|lung(13)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	27						CACCTCCTCCGCCTTCTGGGA	0.607													G|||	1	0.000199681	0.0	0.0	5008	,	,		19738	0.0		0.0	False		,,,				2504	0.001				p.A616V		Atlas-SNP	.											CC2D1B,NS,carcinoma,0,1	CC2D1B	73	1	0			c.C1847T						PASS	.						59.0	57.0	58.0					1																	52822722		2202	4300	6502	SO:0001583	missense	200014	exon16			TCCTCCGCCTTCT	AB058739	CCDS30714.1	1p32.3	2008-02-05			ENSG00000154222	ENSG00000154222			29386	protein-coding gene	gene with protein product						11347906	Standard	NM_032449		Approved	KIAA1836	uc001ctq.2	Q5T0F9	OTTHUMG00000008102	ENST00000371586.2:c.1847C>T	1.37:g.52822722G>A	ENSP00000360642:p.Ala616Val	Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	173	84	0.485549	NM_032449	Q49AE8|Q5T0F8|Q5T0G0|Q6ZNQ1|Q96AP3|Q96I04|Q96JJ1	Missense_Mutation	SNP	ENST00000371586.2	37	CCDS30714.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	12.17|12.17	1.858338|1.858338	0.32791|0.32791	.|.	.|.	ENSG00000154222|ENSG00000154222	ENST00000371586;ENST00000284376;ENST00000371573|ENST00000438021;ENST00000450942	T;T|.	0.28895|.	1.59;1.59|.	5.65|5.65	4.73|4.73	0.59995|0.59995	.|.	0.170245|.	0.51477|.	N|.	0.000082|.	T|T	0.71685|0.71685	0.3369|0.3369	M|M	0.61703|0.61703	1.905|1.905	0.80722|0.80722	D|D	1|1	B;B;B|.	0.21688|.	0.059;0.041;0.024|.	B;B;B|.	0.16722|.	0.012;0.016;0.008|.	T|T	0.69687|0.69687	-0.5078|-0.5078	10|5	0.59425|.	D|.	0.04|.	-3.3081|-3.3081	16.7669|16.7669	0.85526|0.85526	0.0692:0.0:0.9308:0.0|0.0692:0.0:0.9308:0.0	.|.	396;610;616|.	Q5T0G1;Q5T0F9-2;Q5T0F9|.	.;.;C2D1B_HUMAN|.	V|W	616;610;524|397;530	ENSP00000360642:A616V;ENSP00000284376:A610V|.	ENSP00000284376:A610V|.	A|R	-|-	2|1	0|2	CC2D1B|CC2D1B	52595310|52595310	1.000000|1.000000	0.71417|0.71417	0.797000|0.797000	0.32132|0.32132	0.144000|0.144000	0.21451|0.21451	5.830000|5.830000	0.69324|0.69324	0.953000|0.953000	0.37825|0.37825	-0.797000|-0.797000	0.03246|0.03246	GCG|CGG	G|0.997;A|0.003	0.003	weak		0.607	CC2D1B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000022189.1	NM_032449	
IL11	3589	hgsc.bcm.edu	37	19	55879872	55879872	+	Silent	SNP	C	C	T	rs1126757	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:55879872C>T	ENST00000264563.2	-	3	308	c.246G>A	c.(244-246)gcG>gcA	p.A82A	IL11_ENST00000585513.1_Silent_p.A82A|IL11_ENST00000590625.1_Silent_p.A3A	NM_000641.3	NP_000632.1	P20809	IL11_HUMAN	interleukin 11	82					B cell differentiation (GO:0030183)|cell-cell signaling (GO:0007267)|fat cell differentiation (GO:0045444)|megakaryocyte differentiation (GO:0030219)|negative regulation of hormone secretion (GO:0046888)|positive regulation of cell proliferation (GO:0008284)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	growth factor activity (GO:0008083)|interleukin-11 receptor binding (GO:0005142)			large_intestine(1)|skin(1)	2	Breast(117;0.191)	Renal(1328;0.245)	BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.044)		CCAGTGCCCCCGCACTCATGG	0.652													C|||	1975	0.394369	0.0234	0.4452	5008	,	,		12524	0.7093		0.4722	False		,,,				2504	0.455				p.A82A		Atlas-SNP	.											.	IL11	16	.	0			c.G246A						PASS	.	C		420,3986	198.7+/-222.5	21,378,1804	49.0	50.0	49.0	http://www.ncbi.nlm.nih.gov/pubmed?term	246	-7.7	0.0	19	dbSNP_86	49	4037,4563	538.2+/-383.4	954,2129,1217	yes	coding-synonymous	IL11	NM_000641.2		975,2507,3021	TT,TC,CC	http://www.ncbi.nlm.nih.gov/pubmed?term	46.9419,9.5325,34.2688		82/200	55879872	4457,8549	2203	4300	6503	SO:0001819	synonymous_variant	3589	exon3			TGCCCCCGCACTC	X58377	CCDS12923.1, CCDS59423.1	19q13.3-q13.4	2014-01-30			ENSG00000095752	ENSG00000095752		"""Interleukins and interleukin receptors"", ""Endogenous ligands"""	5966	protein-coding gene	gene with protein product	"""adipogenesis inhibitory factor"", ""oprelvekin"""	147681				1386338	Standard	NM_001267718		Approved	IL-11, AGIF	uc002qks.2	P20809		ENST00000264563.2:c.246G>A	19.37:g.55879872C>T		Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	145	77	0.531034	NM_000641	B4DQV5|Q96EB4	Silent	SNP	ENST00000264563.2	37	CCDS12923.1																																																																																			C|0.636;T|0.364	0.364	strong		0.652	IL11-003	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453027.1	NM_000641	
FAM129A	116496	hgsc.bcm.edu	37	1	184801065	184801065	+	Silent	SNP	T	T	C	rs487675	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:184801065T>C	ENST00000367511.3	-	6	826	c.633A>G	c.(631-633)caA>caG	p.Q211Q	FAM129A_ENST00000487074.1_5'UTR	NM_052966.2	NP_443198.1	Q9BZQ8	NIBAN_HUMAN	family with sequence similarity 129, member A	211					negative regulation of protein phosphorylation (GO:0001933)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of translation (GO:0045727)|response to endoplasmic reticulum stress (GO:0034976)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)				autonomic_ganglia(1)|breast(1)|cervix(2)|endometrium(4)|large_intestine(6)|liver(1)|lung(22)|ovary(3)|skin(3)|upper_aerodigestive_tract(2)	45						CTAAAAAGGCTTGGGCTTCAA	0.418													T|||	1421	0.283746	0.3812	0.2363	5008	,	,		19811	0.1558		0.3429	False		,,,				2504	0.2566				p.Q211Q		Atlas-SNP	.											FAM129A,colon,carcinoma,0,1	FAM129A	98	1	0			c.A633G						PASS	.	T		1616,2790	494.5+/-363.0	291,1034,878	88.0	88.0	88.0		633	5.5	1.0	1	dbSNP_83	88	2927,5673	452.1+/-362.9	488,1951,1861	no	coding-synonymous	FAM129A	NM_052966.2		779,2985,2739	CC,CT,TT		34.0349,36.6773,34.93		211/929	184801065	4543,8463	2203	4300	6503	SO:0001819	synonymous_variant	116496	exon6			AAAGGCTTGGGCT	AF288391	CCDS1364.1	1q25	2008-10-08	2006-11-23	2006-11-23	ENSG00000135842	ENSG00000135842			16784	protein-coding gene	gene with protein product	"""cell growth inhibiting protein 39"""		"""chromosome 1 open reading frame 24"""	C1orf24		15085203, 16444351	Standard	NM_052966		Approved	NIBAN, GIG39	uc001gra.4	Q9BZQ8	OTTHUMG00000035388	ENST00000367511.3:c.633A>G	1.37:g.184801065T>C		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	94	93	0.989362	NM_052966	Q2TTR2|Q5TEM8|Q8TEI5|Q9H593|Q9H9Y8|Q9HCB9	Silent	SNP	ENST00000367511.3	37	CCDS1364.1																																																																																			T|0.682;C|0.318	0.318	strong		0.418	FAM129A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085786.1		
ZFHX4	79776	hgsc.bcm.edu	37	8	77765865	77765865	+	Silent	SNP	C	C	T	rs2728455	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:77765865C>T	ENST00000521891.2	+	10	7156	c.6708C>T	c.(6706-6708)taC>taT	p.Y2236Y	ZFHX4_ENST00000050961.6_Silent_p.Y2191Y|ZFHX4_ENST00000455469.2_Silent_p.Y2191Y|ZFHX4_ENST00000518282.1_Silent_p.Y2210Y	NM_024721.4	NP_078997.4	Q86UP3	ZFHX4_HUMAN	zinc finger homeobox 4	2191					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)			TTACTGACTACCAGCTTAGGG	0.398										HNSCC(33;0.089)			C|||	707	0.141174	0.0431	0.1311	5008	,	,		18934	0.0327		0.2555	False		,,,				2504	0.2751				p.Y2236Y		Atlas-SNP	.											.	ZFHX4	878	.	0			c.C6708T						PASS	.	C		306,3446		11,284,1581	68.0	64.0	65.0		6708	3.2	1.0	8	dbSNP_100	65	2122,6080		253,1616,2232	no	coding-synonymous	ZFHX4	NM_024721.4		264,1900,3813	TT,TC,CC		25.8717,8.1557,20.3112		2236/3617	77765865	2428,9526	1876	4101	5977	SO:0001819	synonymous_variant	79776	exon10			TGACTACCAGCTT		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.6708C>T	8.37:g.77765865C>T		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	90	90	1	NM_024721	G3V138|Q18PS0|Q6ZN20	Silent	SNP	ENST00000521891.2	37	CCDS47878.2																																																																																			C|0.867;T|0.133	0.133	strong		0.398	ZFHX4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379197.2	NM_024721	
NSUN2	54888	hgsc.bcm.edu	37	5	6600064	6600064	+	Missense_Mutation	SNP	G	G	T	rs61744358	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:6600064G>T	ENST00000264670.6	-	19	2590	c.2279C>A	c.(2278-2280)cCg>cAg	p.P760Q	NSUN2_ENST00000539938.1_Missense_Mutation_p.P524Q|NSUN2_ENST00000506139.1_Missense_Mutation_p.P725Q	NM_017755.5	NP_060225.4	Q08J23	NSUN2_HUMAN	NOP2/Sun RNA methyltransferase family, member 2	760					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)	p.P760L(1)		breast(1)|endometrium(6)|kidney(2)|large_intestine(5)|lung(23)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	41						GACCCCCGCCGGGTCACAGCC	0.627													G|||	276	0.0551118	0.0915	0.0432	5008	,	,		15965	0.001		0.0666	False		,,,				2504	0.0583				p.P760Q		Atlas-SNP	.											NSUN2,colon,carcinoma,0,1	NSUN2	82	1	1	Substitution - Missense(1)	large_intestine(1)	c.C2279A						PASS	.	G	GLN/PRO,GLN/PRO	261,4145	148.8+/-183.1	3,255,1945	133.0	120.0	124.0		2174,2279	1.6	0.0	5	dbSNP_129	124	596,8004	158.8+/-212.2	26,544,3730	yes	missense,missense	NSUN2	NM_001193455.1,NM_017755.5	76,76	29,799,5675	TT,TG,GG		6.9302,5.9237,6.5893	possibly-damaging,possibly-damaging	725/733,760/768	6600064	857,12149	2203	4300	6503	SO:0001583	missense	54888	exon19			CCCGCCGGGTCAC	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.2279C>A	5.37:g.6600064G>T	ENSP00000264670:p.Pro760Gln	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	41	25	0.609756	NM_017755	A8K529|B2RNR4|B3KP09|B4DQW2|G3V1R4|Q9BVN4|Q9H858|Q9NXD9	Missense_Mutation	SNP	ENST00000264670.6	37	CCDS3869.1	118	0.05402930402930403	46	0.09349593495934959	17	0.04696132596685083	1	0.0017482517482517483	54	0.0712401055408971	G	10.71	1.425970	0.25726	0.059237	0.069302	ENSG00000037474	ENST00000264670;ENST00000539938;ENST00000506139	T;T;T	0.54479	1.31;0.57;1.31	4.44	1.59	0.23543	.	1.998300	0.01889	N	0.038397	T	0.02156	0.0067	L	0.47716	1.5	0.09310	N	1	B;B;B	0.10296	0.003;0.003;0.003	B;B;B	0.14578	0.003;0.004;0.011	T	0.01982	-1.1235	10	0.17369	T	0.5	-3.3591	4.279	0.10824	0.2004:0.0:0.6189:0.1806	rs61744358	725;760;760	B4DQW2;Q08J23;A8K529	.;NSUN2_HUMAN;.	Q	760;524;725	ENSP00000264670:P760Q;ENSP00000444338:P524Q;ENSP00000420957:P725Q	ENSP00000264670:P760Q	P	-	2	0	NSUN2	6653064	0.003000	0.15002	0.000000	0.03702	0.003000	0.03518	0.602000	0.24134	0.191000	0.20236	-0.216000	0.12614	CCG	C|0.000;G|0.932;T|0.067	0.067	strong		0.627	NSUN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206902.1	NM_017755	
PIAS4	51588	hgsc.bcm.edu	37	19	4037723	4037723	+	Silent	SNP	G	G	A	rs140558761	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:4037723G>A	ENST00000262971.2	+	11	1498	c.1383G>A	c.(1381-1383)ccG>ccA	p.P461P		NM_015897.2	NP_056981.2	Q8N2W9	PIAS4_HUMAN	protein inhibitor of activated STAT, 4	461					negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902231)|positive regulation of keratinocyte apoptotic process (GO:1902174)|positive regulation of protein sumoylation (GO:0033235)|protein sumoylation (GO:0016925)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	DNA binding (GO:0003677)|SUMO ligase activity (GO:0019789)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(1)|lung(3)|pancreas(1)|skin(3)	17				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00461)|STAD - Stomach adenocarcinoma(1328;0.18)		ATGGGAAGCCGGGCGCCGATG	0.697													.|||	4	0.000798722	0.0	0.0	5008	,	,		12829	0.0		0.004	False		,,,				2504	0.0				p.P461P		Atlas-SNP	.											.	PIAS4	40	.	0			c.G1383A						PASS	.			1,4391		0,1,2195	22.0	23.0	23.0		1383	-8.8	0.0	19	dbSNP_134	23	26,8560		0,26,4267	no	coding-synonymous	PIAS4	NM_015897.2		0,27,6462	AA,AG,GG		0.3028,0.0228,0.208		461/511	4037723	27,12951	2196	4293	6489	SO:0001819	synonymous_variant	51588	exon11			GAAGCCGGGCGCC	AF077952	CCDS12118.1	19p13.3	2011-10-11						"""Zinc fingers, MIZ-type"""	17002	protein-coding gene	gene with protein product	"""zinc finger, MIZ-type containing 6"""	605989				9724754	Standard	NM_015897		Approved	Piasg, PIASY, FLJ12419, ZMIZ6	uc002lzg.3	Q8N2W9		ENST00000262971.2:c.1383G>A	19.37:g.4037723G>A		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	80	43	0.5375	NM_015897	O75926|Q96G19|Q9UN16	Silent	SNP	ENST00000262971.2	37	CCDS12118.1																																																																																			G|0.998;A|0.002	0.002	strong		0.697	PIAS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457496.1	NM_015897	
NOS2	4843	hgsc.bcm.edu	37	17	26125743	26125743	+	Silent	SNP	G	G	A	rs3730014	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:26125743G>A	ENST00000313735.6	-	2	326	c.93C>T	c.(91-93)gcC>gcT	p.A31A		NM_000625.4	NP_000616.3	P35228	NOS2_HUMAN	nitric oxide synthase 2, inducible	31					arginine catabolic process (GO:0006527)|blood coagulation (GO:0007596)|cellular response to interferon-gamma (GO:0071346)|cellular response to lipopolysaccharide (GO:0071222)|circadian rhythm (GO:0007623)|defense response to bacterium (GO:0042742)|defense response to Gram-negative bacterium (GO:0050829)|inflammatory response (GO:0006954)|innate immune response in mucosa (GO:0002227)|interaction with host (GO:0051701)|negative regulation of blood pressure (GO:0045776)|negative regulation of gene expression (GO:0010629)|negative regulation of protein catabolic process (GO:0042177)|nitric oxide biosynthetic process (GO:0006809)|nitric oxide mediated signal transduction (GO:0007263)|peptidyl-cysteine S-nitrosylation (GO:0018119)|phagosome maturation (GO:0090382)|positive regulation of guanylate cyclase activity (GO:0031284)|positive regulation of killing of cells of other organism (GO:0051712)|positive regulation of leukocyte mediated cytotoxicity (GO:0001912)|positive regulation of vasodilation (GO:0045909)|regulation of cell proliferation (GO:0042127)|regulation of cellular respiration (GO:0043457)|regulation of insulin secretion (GO:0050796)|response to bacterium (GO:0009617)|response to hypoxia (GO:0001666)|superoxide metabolic process (GO:0006801)	cortical cytoskeleton (GO:0030863)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular (GO:0005622)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|peroxisome (GO:0005777)	arginine binding (GO:0034618)|flavin adenine dinucleotide binding (GO:0050660)|FMN binding (GO:0010181)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|NADP binding (GO:0050661)|NADPH-hemoprotein reductase activity (GO:0003958)|nitric-oxide synthase activity (GO:0004517)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|tetrahydrobiopterin binding (GO:0034617)			autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(8)|lung(28)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	56					Dexamethasone(DB01234)|Doxorubicin(DB00997)|L-Arginine(DB00125)|L-Citrulline(DB00155)|Miconazole(DB01110)|Triflusal(DB08814)	TGGCACAGGGGGCTTTCTCCA	0.512													G|||	45	0.00898562	0.0	0.0043	5008	,	,		19189	0.0		0.0129	False		,,,				2504	0.0297				p.A31A		Atlas-SNP	.											.	NOS2	113	.	0			c.C93T						PASS	.	G		12,4394	17.9+/-39.9	0,12,2191	217.0	204.0	208.0		93	3.7	0.0	17	dbSNP_107	208	150,8450	73.5+/-136.2	1,148,4151	no	coding-synonymous	NOS2	NM_000625.4		1,160,6342	AA,AG,GG		1.7442,0.2724,1.2456		31/1154	26125743	162,12844	2203	4300	6503	SO:0001819	synonymous_variant	4843	exon2			ACAGGGGGCTTTC	U20141	CCDS11223.1	17q11.2	2014-06-12	2008-09-16	2008-09-16	ENSG00000007171	ENSG00000007171	1.14.13.39		7873	protein-coding gene	gene with protein product		163730	"""nitric oxide synthase 2A (inducible, hepatocytes)"""	NOS2A		7682706	Standard	NM_000625		Approved	iNOS, NOS, HEP-NOS	uc002gzu.3	P35228	OTTHUMG00000132445	ENST00000313735.6:c.93C>T	17.37:g.26125743G>A		Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	118	67	0.567797	NM_000625	A1L3U5|B7ZLY2|O60757|O94994|Q16263|Q16692|Q4TTS5|Q9UD42	Silent	SNP	ENST00000313735.6	37	CCDS11223.1																																																																																			G|0.988;A|0.012	0.012	strong		0.512	NOS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255597.1	NM_000625	
SLFN14	342618	hgsc.bcm.edu	37	17	33881631	33881631	+	Missense_Mutation	SNP	T	T	C	rs321612	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:33881631T>C	ENST00000415846.3	-	2	1188	c.1153A>G	c.(1153-1155)Aaa>Gaa	p.K385E	RP11-1094M14.12_ENST00000588445.1_RNA	NM_001129820.1	NP_001123292.1	P0C7P3	SLN14_HUMAN	schlafen family member 14	385			K -> E (in dbSNP:rs321612). {ECO:0000269|PubMed:15489334}.				ATP binding (GO:0005524)			breast(3)|central_nervous_system(1)|endometrium(2)|kidney(3)	9						TCCTTAAATTTGTGGACTTTT	0.418													C|||	3141	0.627196	0.7163	0.6556	5008	,	,		10937	0.6885		0.5805	False		,,,				2504	0.4714				p.K385E		Atlas-SNP	.											.	SLFN14	43	.	0			c.A1153G						PASS	.	C	GLU/LYS	957,427		326,305,61	95.0	82.0	86.0		1153	1.5	0.9	17	dbSNP_79	86	1920,1262		577,766,248	yes	missense	SLFN14	NM_001129820.1	56	903,1071,309	CC,CT,TT		39.6606,30.8526,36.9908	benign	385/913	33881631	2877,1689	692	1591	2283	SO:0001583	missense	342618	exon2			TAAATTTGTGGAC		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.1153A>G	17.37:g.33881631T>C	ENSP00000391101:p.Lys385Glu	Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	107	56	0.523364	NM_001129820	B2RTW9	Missense_Mutation	SNP	ENST00000415846.3	37	CCDS45650.1	1406	0.6437728937728938	338	0.6869918699186992	245	0.6767955801104972	391	0.6835664335664335	432	0.5699208443271768	C	0.011	-1.728039	0.00694	0.691474	0.603394	ENSG00000236320	ENST00000415846	T	0.55052	0.54	4.88	1.51	0.23008	.	.	.	.	.	T	0.00012	0.0000	N	0.00170	-1.935	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.43798	-0.9369	8	0.02654	T	1	-3.9053	5.1052	0.14781	0.0:0.4889:0.327:0.1842	rs321612;rs1280800;rs17550394;rs52824305;rs58358968;rs321612	385	P0C7P3	SLN14_HUMAN	E	385	ENSP00000391101:K385E	ENSP00000391101:K385E	K	-	1	0	SLFN14	30905744	0.015000	0.18098	0.902000	0.35471	0.003000	0.03518	0.169000	0.16641	0.336000	0.23639	-0.128000	0.14901	AAA	C|0.651;N|0.000	0.651	strong		0.418	SLFN14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448928.1	NM_001129820	
PLCD1	5333	hgsc.bcm.edu	37	3	38051941	38051941	+	Silent	SNP	T	T	C	rs9857730	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:38051941T>C	ENST00000334661.4	-	6	1125	c.903A>G	c.(901-903)ccA>ccG	p.P301P	PLCD1_ENST00000463876.1_Silent_p.P322P|PLCD1_ENST00000479619.1_5'Flank	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	144	0	0		WXS	Illumina HiSeq	Phase_I	172	84	0.488372	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		
METTL21B	25895	hgsc.bcm.edu	37	12	58174306	58174306	+	Silent	SNP	T	T	C	rs923829	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:58174306T>C	ENST00000300209.8	+	3	683	c.558T>C	c.(556-558)caT>caC	p.H186H	RP11-571M6.15_ENST00000553083.1_Intron|METTL21B_ENST00000551420.1_Silent_p.H5H|TSFM_ENST00000540550.1_5'Flank|TSFM_ENST00000323833.8_5'Flank|TSFM_ENST00000548851.1_5'Flank|TSFM_ENST00000454289.3_5'Flank|TSFM_ENST00000543727.1_5'Flank|TSFM_ENST00000350762.5_5'Flank|TSFM_ENST00000550559.1_5'Flank|METTL21B_ENST00000333012.5_3'UTR|RP11-571M6.15_ENST00000471530.1_Intron	NM_015433.2	NP_056248.2	Q96AZ1	MT21B_HUMAN	methyltransferase like 21B	186						cytoplasm (GO:0005737)|intracellular (GO:0005622)	methyltransferase activity (GO:0008168)			endometrium(1)|lung(1)	2						GAAAGGAGCATGGGACAGAGA	0.567													t|||	2024	0.404153	0.2141	0.2767	5008	,	,		21672	0.6468		0.3191	False		,,,				2504	0.589				p.H186H		Atlas-SNP	.											.	METTL21B	16	.	0			c.T558C						PASS	.	T	,	1018,3388	377.5+/-322.5	116,786,1301	69.0	60.0	63.0		558,	-2.5	1.0	12	dbSNP_86	63	2755,5845	438.5+/-358.9	456,1843,2001	no	coding-synonymous,utr-3	METTL21B	NM_015433.2,NM_206914.1	,	572,2629,3302	CC,CT,TT		32.0349,23.1049,29.0097	,	186/227,	58174306	3773,9233	2203	4300	6503	SO:0001819	synonymous_variant	25895	exon3			GGAGCATGGGACA	AL050100, AF455816	CCDS8957.1, CCDS31848.1	12q14.1	2011-03-03	2011-03-03	2011-03-03	ENSG00000123427	ENSG00000123427			24936	protein-coding gene	gene with protein product		615258	"""family with sequence similarity 119, member B"""	FAM119B		12477932	Standard	NM_015433		Approved	DKFZP586D0919	uc001sqg.3	Q96AZ1	OTTHUMG00000170459	ENST00000300209.8:c.558T>C	12.37:g.58174306T>C		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	60	29	0.483333	NM_015433	Q9H749|Q9Y3W2	Silent	SNP	ENST00000300209.8	37	CCDS8957.1																																																																																			T|0.672;C|0.328	0.328	strong		0.567	METTL21B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409268.1	NM_015433	
CMTR2	55783	hgsc.bcm.edu	37	16	71319539	71319539	+	Silent	SNP	C	C	T	rs3826247	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:71319539C>T	ENST00000338099.5	-	3	621	c.285G>A	c.(283-285)gcG>gcA	p.A95A	CMTR2_ENST00000434935.2_Silent_p.A95A			Q8IYT2	CMTR2_HUMAN	cap methyltransferase 2	95					7-methylguanosine mRNA capping (GO:0006370)|cap2 mRNA methylation (GO:0097310)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	mRNA (nucleoside-2'-O-)-methyltransferase activity (GO:0004483)										TGATTTTCCCCGCTTTATTAG	0.373													T|||	2314	0.462061	0.3714	0.6628	5008	,	,		20347	0.245		0.675	False		,,,				2504	0.4468				p.A95A		Atlas-SNP	.											.	FTSJD1	70	.	0			c.G285A						PASS	.	T	,	1766,2630	640.0+/-397.2	352,1062,784	102.0	97.0	99.0		285,285	0.6	1.0	16	dbSNP_107	99	5609,2991	461.7+/-365.5	1836,1937,527	no	coding-synonymous,coding-synonymous	FTSJD1	NM_001099642.1,NM_018348.5	,	2188,2999,1311	TT,TC,CC		34.7791,40.1729,43.2518	,	95/771,95/771	71319539	7375,5621	2198	4300	6498	SO:0001819	synonymous_variant	55783	exon3			TTTCCCCGCTTTA	BC035005	CCDS10898.1	16q22.2	2013-07-23	2013-07-23	2013-07-23	ENSG00000180917	ENSG00000180917			25635	protein-coding gene	gene with protein product	"""adrift homolog (Drosophila)"""		"""FtsJ methyltransferase domain containing 1"""	FTSJD1		21310715	Standard	NM_018348		Approved	FLJ11171, AFT, MTr2	uc010cga.3	Q8IYT2	OTTHUMG00000137587	ENST00000338099.5:c.285G>A	16.37:g.71319539C>T		Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	161	161	1	NM_018348	B2RCD5|D3DWS1|Q8NE77|Q8NFR5|Q9H8Z4|Q9NUS3|Q9NXF5	Silent	SNP	ENST00000338099.5	37	CCDS10898.1																																																																																			C|0.460;T|0.540	0.540	strong		0.373	CMTR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268984.2	NM_018348	
AHNAK2	113146	hgsc.bcm.edu	37	14	105418170	105418170	+	Silent	SNP	G	G	C	rs200879546	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:105418170G>C	ENST00000333244.5	-	7	3737	c.3618C>G	c.(3616-3618)ctC>ctG	p.L1206L	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	1206						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)			CAGTGGTCTTGAGGTCCCCCT	0.657													.|||	304	0.0607029	0.0938	0.0159	5008	,	,		15598	0.1002		0.0099	False		,,,				2504	0.0593				p.L1206L		Atlas-SNP	.											AHNAK2_ENST00000333244,NS,carcinoma,0,2	AHNAK2	719	2	0			c.C3618G						scavenged	.						111.0	88.0	96.0					14																	105418170		1937	4041	5978	SO:0001819	synonymous_variant	113146	exon7			GGTCTTGAGGTCC	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.3618C>G	14.37:g.105418170G>C		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	126	18	0.142857	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Silent	SNP	ENST00000333244.5	37	CCDS45177.1																																																																																			G|0.993;C|0.007	0.007	strong		0.657	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
CACNA1C	775	hgsc.bcm.edu	37	12	2791132	2791132	+	Missense_Mutation	SNP	A	A	G	rs10774053|rs71441836	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:2791132A>G	ENST00000399617.1	+	43	5461	c.5461A>G	c.(5461-5463)Atg>Gtg	p.M1821V	CACNA1C_ENST00000335762.5_Intron|CACNA1C_ENST00000399621.1_Intron|CACNA1C_ENST00000399644.1_Intron|CACNA1C_ENST00000347598.4_Intron|CACNA1C_ENST00000399634.1_Intron|CACNA1C_ENST00000399603.1_Intron|CACNA1C_ENST00000399649.1_Intron|CACNA1C_ENST00000327702.7_Missense_Mutation_p.M1821V|CACNA1C_ENST00000399655.1_Intron|CACNA1C_ENST00000406454.3_Intron|CACNA1C_ENST00000399637.1_Intron|CACNA1C_ENST00000399591.1_Intron|CACNA1C_ENST00000399641.1_Intron|CACNA1C_ENST00000399606.1_Intron|CACNA1C-AS1_ENST00000501371.1_RNA|CACNA1C_ENST00000399601.1_Intron|CACNA1C_ENST00000399629.1_Intron|CACNA1C_ENST00000402845.3_Intron|CACNA1C_ENST00000344100.3_Intron|CACNA1C_ENST00000399638.1_Intron|CACNA1C_ENST00000399595.1_Intron|CACNA1C_ENST00000399597.1_Intron	NM_001167624.1	NP_001161096.1	Q13936	CAC1C_HUMAN	calcium channel, voltage-dependent, L type, alpha 1C subunit	1869					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)	GCACGTTCCGATGTGTGAGGA	0.567													G|||	3859	0.770567	0.7844	0.7651	5008	,	,		21122	0.6081		0.83	False		,,,				2504	0.862				p.M1869V		Atlas-SNP	.											.	CACNA1C	1023	.	0			c.A5605G						PASS	.	G	,,,VAL/MET,,,,,,,,,,,,,,,,,VAL/MET,,VAL/MET	2489,647		991,507,70	129.0	108.0	114.0		,,,5461,,,,,,,,,,,,,,,,,5461,,5605	0.9	0.0	12	dbSNP_120	114	5953,1211		2490,973,119	yes	intron,intron,intron,missense,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,missense,intron,missense	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	,,,21,,,,,,,,,,,,,,,,,21,,21	3481,1480,189	GG,GA,AA		16.904,20.6314,18.0388	,,,,,,,,,,,,,,,,,,,,,,	,,,1821/2174,,,,,,,,,,,,,,,,,1821/2174,,1869/2222	2791132	8442,1858	1568	3582	5150	SO:0001583	missense	775	exon45			GTTCCGATGTGTG	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	ENST00000399617.1:c.5461A>G	12.37:g.2791132A>G	ENSP00000382526:p.Met1821Val	Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	41	41	1	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	ENST00000399617.1	37	CCDS53733.1	1651	0.7559523809523809	371	0.7540650406504065	285	0.787292817679558	363	0.6346153846153846	632	0.8337730870712401	G	0.601	-0.828983	0.02734	0.793686	0.83096	ENSG00000151067	ENST00000327702;ENST00000399617	D;D	0.95307	-3.57;-3.67	2.99	0.908	0.19326	.	.	.	.	.	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	0.37430	-0.9706	8	0.02654	T	1	.	5.4803	0.16719	0.4638:0.0:0.5362:0.0	rs10774053;rs17761283	1869;1821;1821	Q13936;Q13936-33;E9PDJ0	CAC1C_HUMAN;.;.	V	1821	ENSP00000329877:M1821V;ENSP00000382526:M1821V	ENSP00000329877:M1821V	M	+	1	0	CACNA1C	2661393	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.383000	0.07398	-0.044000	0.13491	-0.962000	0.02626	ATG	A|0.230;G|0.770	0.770	strong		0.567	CACNA1C-013	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317031.1	NM_000719	
AP2B1	163	hgsc.bcm.edu	37	17	33998802	33998802	+	Silent	SNP	G	G	C	rs1049379	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:33998802G>C	ENST00000262325.7	+	15	2572	c.2019G>C	c.(2017-2019)gtG>gtC	p.V673V	AP2B1_ENST00000545922.2_3'UTR|AP2B1_ENST00000537622.2_Silent_p.V687V|AP2B1_ENST00000312678.8_Silent_p.V687V|AP2B1_ENST00000592545.1_Silent_p.V649V|AP2B1_ENST00000538556.1_Silent_p.V616V|AP2B1_ENST00000589344.1_Silent_p.V687V	NM_001282.2	NP_001273.1	P63010	AP2B1_HUMAN	adaptor-related protein complex 2, beta 1 subunit	673	Pro-rich (stalk region).				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|axon guidance (GO:0007411)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|intracellular protein transport (GO:0006886)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of defense response to virus by virus (GO:0050690)|synaptic transmission (GO:0007268)|viral process (GO:0016032)	clathrin adaptor complex (GO:0030131)|clathrin-coated endocytic vesicle membrane (GO:0030669)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|plasma membrane (GO:0005886)	clathrin binding (GO:0030276)|protein transporter activity (GO:0008565)			NS(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(6)|ovary(3)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	28		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0227)		CATCATCGGTGCCTGCAACCT	0.483													G|||	2359	0.471046	0.4644	0.4798	5008	,	,		16898	0.5317		0.4672	False		,,,				2504	0.4151				p.V687V		Atlas-SNP	.											.	AP2B1	70	.	0			c.G2061C						PASS	.	G	,	2180,2226	584.5+/-386.0	536,1108,559	163.0	164.0	164.0		2061,2019	3.0	1.0	17	dbSNP_86	164	4239,4361	572.0+/-389.6	1053,2133,1114	no	coding-synonymous,coding-synonymous	AP2B1	NM_001030006.1,NM_001282.2	,	1589,3241,1673	CC,CG,GG		49.2907,49.478,49.3541	,	687/952,673/938	33998802	6419,6587	2203	4300	6503	SO:0001819	synonymous_variant	163	exon16			ATCGGTGCCTGCA	M34175	CCDS32621.1, CCDS32622.1	17q11.2-q12	2010-06-18			ENSG00000006125	ENSG00000006125			563	protein-coding gene	gene with protein product		601025		ADTB2, CLAPB1		8262066, 8595912	Standard	XM_005257937		Approved		uc002hjq.3	P63010		ENST00000262325.7:c.2019G>C	17.37:g.33998802G>C		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	73	34	0.465753	NM_001030006	A6NJP3|P21851|Q7Z451|Q96J19	Silent	SNP	ENST00000262325.7	37	CCDS32622.1																																																																																			G|0.518;C|0.482	0.482	strong		0.483	AP2B1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000448969.1		
APLF	200558	hgsc.bcm.edu	37	2	68753240	68753240	+	Missense_Mutation	SNP	T	T	A	rs35002937	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:68753240T>A	ENST00000303795.4	+	6	841	c.670T>A	c.(670-672)Tcc>Acc	p.S224T		NM_173545.2	NP_775816.1	Q8IW19	APLF_HUMAN	aprataxin and PNKP like factor	224			S -> T (in dbSNP:rs35002937).		cellular response to DNA damage stimulus (GO:0006974)|DNA catabolic process, endonucleolytic (GO:0000737)|double-strand break repair (GO:0006302)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|positive regulation of DNA ligation (GO:0051106)|regulation of isotype switching (GO:0045191)|single strand break repair (GO:0000012)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|site of double-strand break (GO:0035861)	3'-5' exonuclease activity (GO:0008408)|DNA-(apurinic or apyrimidinic site) lyase activity (GO:0003906)|endodeoxyribonuclease activity (GO:0004520)|metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)			autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|liver(2)|lung(9)|ovary(3)|prostate(1)|skin(1)	25						CAAAGATAAATCCCAGCTAAA	0.348													A|||	1150	0.229633	0.5991	0.1182	5008	,	,		16373	0.0367		0.1213	False		,,,				2504	0.1196				p.S224T		Atlas-SNP	.											APLF,colon,carcinoma,0,1	APLF	69	1	0			c.T670A						PASS	.	A	THR/SER	2385,2021	561.6+/-380.8	667,1051,485	85.0	88.0	87.0		670	3.6	0.1	2	dbSNP_126	87	1147,7453	766.1+/-407.6	81,985,3234	yes	missense	APLF	NM_173545.2	58	748,2036,3719	AA,AT,TT		13.3372,45.8693,27.1567	benign	224/512	68753240	3532,9474	2203	4300	6503	SO:0001583	missense	200558	exon6			GATAAATCCCAGC	BC030711	CCDS1888.1	2p14	2014-02-20	2008-10-01	2008-10-01	ENSG00000169621	ENSG00000169621			28724	protein-coding gene	gene with protein product	"""XRCC1-interacting protein 1"", ""zinc finger, CX5CX6HX5H motif containing 1"""	611035	"""chromosome 2 open reading frame 13"""	C2orf13		18474613, 18077224, 17353262	Standard	NM_173545		Approved	MGC47799, Xip1, ZCCHH1	uc002sep.3	Q8IW19	OTTHUMG00000129566	ENST00000303795.4:c.670T>A	2.37:g.68753240T>A	ENSP00000307004:p.Ser224Thr	Somatic	174	1	0.00574713		WXS	Illumina HiSeq	Phase_I	135	79	0.585185	NM_173545	A8K476|Q53P47|Q53PB9|Q53QU0	Missense_Mutation	SNP	ENST00000303795.4	37	CCDS1888.1	447	0.20467032967032966	290	0.5894308943089431	43	0.11878453038674033	22	0.038461538461538464	92	0.12137203166226913	a	0.004	-2.284029	0.00251	0.541307	0.133372	ENSG00000169621	ENST00000303795	T	0.22336	1.96	4.75	3.6	0.41247	.	0.790106	0.11661	N	0.541829	T	0.00012	0.0000	N	0.00119	-2.075	0.80722	P	0.0	B;B	0.06786	0.001;0.0	B;B	0.04013	0.001;0.0	T	0.45687	-0.9244	9	0.02654	T	1	.	4.1048	0.10032	0.7239:0.0:0.0962:0.1799	rs35002937	224;224	F8WET0;Q8IW19	.;APLF_HUMAN	T	224	ENSP00000307004:S224T	ENSP00000307004:S224T	S	+	1	0	APLF	68606744	0.270000	0.24152	0.145000	0.22337	0.037000	0.13140	0.150000	0.16263	0.421000	0.25980	-0.344000	0.07964	TCC	T|0.754;A|0.246	0.246	strong		0.348	APLF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251759.1	NM_173545	
MUC5B	727897	hgsc.bcm.edu	37	11	1264772	1264772	+	Missense_Mutation	SNP	T	T	C	rs2943500		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:1264772T>C	ENST00000529681.1	+	31	6720	c.6662T>C	c.(6661-6663)aTc>aCc	p.I2221T	MUC5B_ENST00000447027.1_Missense_Mutation_p.I2224T|RP11-532E4.2_ENST00000532061.2_RNA	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	222	2	0.00900901		WXS	Illumina HiSeq	Phase_I	324	8	0.0246914	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	
DENND4A	10260	hgsc.bcm.edu	37	15	65994733	65994733	+	Silent	SNP	C	C	T	rs17810074	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:65994733C>T	ENST00000431932.2	-	17	2548	c.2340G>A	c.(2338-2340)gtG>gtA	p.V780V	DENND4A_ENST00000443035.3_Silent_p.V780V	NM_005848.3	NP_005839.3	Q7Z401	MYCPP_HUMAN	DENN/MADD domain containing 4A	780					positive regulation of Rab GTPase activity (GO:0032851)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(17)|lung(11)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	51						GACAGACTTTCACATAAGCTG	0.408													C|||	1234	0.246406	0.0711	0.3977	5008	,	,		18286	0.1935		0.326	False		,,,				2504	0.3487				p.V780V		Atlas-SNP	.											.	DENND4A	217	.	0			c.G2340A						PASS	.	C	,	357,3345		18,321,1512	62.0	54.0	56.0		2340,2340	4.8	1.0	15	dbSNP_123	56	2417,5779		363,1691,2044	no	coding-synonymous,coding-synonymous	DENND4A	NM_001144823.1,NM_005848.3	,	381,2012,3556	TT,TC,CC		29.49,9.6434,23.3148	,	780/1907,780/1864	65994733	2774,9124	1851	4098	5949	SO:0001819	synonymous_variant	10260	exon17			GACTTTCACATAA	AF534403	CCDS45285.1, CCDS53949.1	15q22.31	2012-10-03	2006-01-27	2006-01-27				"""DENN/MADD domain containing"""	24321	protein-coding gene	gene with protein product		600382	"""c-myc promoter binding protein"""	MYCPBP		8056341, 12906859	Standard	NM_005848		Approved	IRLB	uc002api.3	Q7Z401		ENST00000431932.2:c.2340G>A	15.37:g.65994733C>T		Somatic	234	0	0		WXS	Illumina HiSeq	Phase_I	237	130	0.548523	NM_001144823	E7EPL3|Q14655|Q86T77|Q8IVX2|Q8NB93	Silent	SNP	ENST00000431932.2	37	CCDS45285.1																																																																																			C|0.761;T|0.239	0.239	strong		0.408	DENND4A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419611.1	NM_005848	
TBXAS1	6916	hgsc.bcm.edu	37	7	139706915	139706915	+	Missense_Mutation	SNP	G	G	A	rs3735354	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:139706915G>A	ENST00000336425.5	+	14	1548	c.1159G>A	c.(1159-1161)Gag>Aag	p.E387K	TBXAS1_ENST00000411653.1_Missense_Mutation_p.E387K|TBXAS1_ENST00000425687.1_Missense_Mutation_p.E320K|TBXAS1_ENST00000263552.6_Missense_Mutation_p.E388K|TBXAS1_ENST00000414508.2_Missense_Mutation_p.E388K|TBXAS1_ENST00000462275.1_3'UTR|TBXAS1_ENST00000448866.1_Missense_Mutation_p.E387K|TBXAS1_ENST00000416849.2_Missense_Mutation_p.E434K|TBXAS1_ENST00000436047.2_Missense_Mutation_p.E388K|TBXAS1_ENST00000458722.1_Missense_Mutation_p.E433K			P24557	THAS_HUMAN	thromboxane A synthase 1 (platelet)	387			E -> K (in dbSNP:rs3735354).		arachidonic acid metabolic process (GO:0019369)|cellular chloride ion homeostasis (GO:0030644)|cyclooxygenase pathway (GO:0019371)|icosanoid metabolic process (GO:0006690)|positive regulation of vasoconstriction (GO:0045907)|small molecule metabolic process (GO:0044281)|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)|monooxygenase activity (GO:0004497)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen (GO:0016705)|thromboxane-A synthase activity (GO:0004796)			breast(3)|endometrium(1)|kidney(1)|large_intestine(5)|lung(11)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	28	Melanoma(164;0.0142)				Ridogrel(DB01207)|Sulfasalazine(DB00795)	CTGCAGCCTCGAGGAAGGCCT	0.552													g|||	13	0.00259585	0.0	0.0	5008	,	,		16000	0.0119		0.0	False		,,,				2504	0.001				p.E434K		Atlas-SNP	.											.	TBXAS1	121	.	0			c.G1300A						PASS	.	A	LYS/GLU,LYS/GLU,LYS/GLU,LYS/GLU,LYS/GLU	1,4405	2.1+/-5.4	0,1,2202	158.0	152.0	154.0		1162,1162,1300,958,1162	1.2	0.9	7	dbSNP_107	154	4,8596	3.7+/-12.6	0,4,4296	yes	missense,missense,missense,missense,missense	TBXAS1	NM_001061.4,NM_001130966.2,NM_001166253.1,NM_001166254.1,NM_030984.3	56,56,56,56,56	0,5,6498	AA,AG,GG		0.0465,0.0227,0.0384	benign,benign,benign,benign,benign	388/535,388/535,434/581,320/467,388/461	139706915	5,13001	2203	4300	6503	SO:0001583	missense	6916	exon11			AGCCTCGAGGAAG	L36085	CCDS5855.1, CCDS5856.1, CCDS55174.1, CCDS55175.1	7q34-q35	2014-09-17	2008-07-31		ENSG00000059377	ENSG00000059377	5.3.99.5	"""Cytochrome P450s"""	11609	protein-coding gene	gene with protein product	"""cytochrome P450, family 5, subfamily A, polypeptide 1"""	274180	"""thromboxane A synthase 1 (platelet, cytochrome P450, subfamily V)"""			1714723, 8964509	Standard	NM_001061		Approved	CYP5, CYP5A1, THAS, TXS, TXAS, TS	uc011kqv.2	P24557	OTTHUMG00000157302	ENST00000336425.5:c.1159G>A	7.37:g.139706915G>A	ENSP00000338087:p.Glu387Lys	Somatic	194	0	0		WXS	Illumina HiSeq	Phase_I	184	88	0.478261	NM_001166253	B4DJG6|E7EMU9|E7EP08|E7ESB5|O14987|Q16843|Q16844|Q8IUN1|Q96CN2|Q9GZW4|Q9HD77|Q9HD78|Q9HD79|Q9HD80|Q9HD81|Q9HD82|Q9HD83|Q9HD84	Missense_Mutation	SNP	ENST00000336425.5	37		10	0.004578754578754579	0	0.0	0	0.0	10	0.017482517482517484	0	0.0	g	11.35	1.612042	0.28712	2.27E-4	4.65E-4	ENSG00000059377	ENST00000425687;ENST00000263552;ENST00000336425;ENST00000416849;ENST00000436047;ENST00000414508;ENST00000448866;ENST00000458722;ENST00000411653	T;T;T;T;T;T;T;T;T	0.67698	-0.28;-0.28;-0.28;-0.28;-0.28;-0.28;-0.28;-0.28;-0.28	4.27	1.21	0.21127	.	0.345598	0.30949	N	0.008554	T	0.23611	0.0571	N	0.04705	-0.18	0.53688	D	0.999974	B;B;B;B;B;B;B	0.34255	0.003;0.006;0.037;0.445;0.005;0.002;0.002	B;B;B;B;B;B;B	0.32533	0.007;0.006;0.003;0.147;0.003;0.001;0.0	T	0.05784	-1.0864	10	0.32370	T	0.25	.	8.8391	0.35131	0.1489:0.5364:0.3147:0.0	rs3735354;rs52807697;rs60013190;rs3735354	368;434;339;320;388;388;387	B4DVP1;E7EP08;B4E0M5;E7ESB5;E7EMU9;Q53F23;P24557	.;.;.;.;.;.;THAS_HUMAN	K	320;388;387;434;388;388;387;433;387	ENSP00000388736:E320K;ENSP00000263552:E388K;ENSP00000338087:E387K;ENSP00000389414:E434K;ENSP00000392361:E388K;ENSP00000392702:E388K;ENSP00000402536:E387K;ENSP00000411274:E433K;ENSP00000411326:E387K	ENSP00000263552:E388K	E	+	1	0	TBXAS1	139353384	0.981000	0.34729	0.949000	0.38748	0.620000	0.37586	1.384000	0.34396	0.374000	0.24650	-0.847000	0.03039	GAG	G|0.998;A|0.002	0.002	strong		0.552	TBXAS1-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000348373.1		
SLC17A3	10786	hgsc.bcm.edu	37	6	25850845	25850845	+	Missense_Mutation	SNP	C	C	T	rs56027330	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:25850845C>T	ENST00000360657.3	-	7	886	c.601G>A	c.(601-603)Ggg>Agg	p.G201R	SLC17A3_ENST00000361703.6_Missense_Mutation_p.G201R|SLC17A3_ENST00000397060.4_Missense_Mutation_p.G279R			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	54	0	0		WXS	Illumina HiSeq	Phase_I	62	30	0.483871	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		
MYO9B	4650	hgsc.bcm.edu	37	19	17283657	17283657	+	Silent	SNP	C	C	T	rs2279006	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:17283657C>T	ENST00000594824.1	+	13	2172	c.2025C>T	c.(2023-2025)atC>atT	p.I675I	MYO9B_ENST00000595618.1_Silent_p.I675I|MYO9B_ENST00000397274.2_Silent_p.I675I			Q13459	MYO9B_HUMAN	myosin IXB	675	Myosin motor.				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						GGGAGCTCATCGGCATGGACC	0.692													C|||	708	0.141374	0.2927	0.0865	5008	,	,		15230	0.0933		0.0785	False		,,,				2504	0.09				p.I675I		Atlas-SNP	.											.	MYO9B	264	.	0			c.C2025T						PASS	.	C	,	1119,3123		130,859,1132	52.0	60.0	57.0		2025,2025	-9.0	0.7	19	dbSNP_100	57	624,7820		20,584,3618	no	coding-synonymous,coding-synonymous	MYO9B	NM_001130065.1,NM_004145.3	,	150,1443,4750	TT,TC,CC		7.3899,26.3791,13.7396	,	675/2023,675/2158	17283657	1743,10943	2121	4222	6343	SO:0001819	synonymous_variant	4650	exon13			GCTCATCGGCATG		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.2025C>T	19.37:g.17283657C>T		Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	47	16	0.340426	NM_001130065	O75314|Q9NUJ2|Q9UHN0	Silent	SNP	ENST00000594824.1	37																																																																																				C|0.845;T|0.155	0.155	strong		0.692	MYO9B-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000463236.1		
CCDC109B	55013	hgsc.bcm.edu	37	4	110581363	110581363	+	Missense_Mutation	SNP	T	T	A	rs4698744	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:110581363T>A	ENST00000394650.4	+	3	321	c.188T>A	c.(187-189)aTt>aAt	p.I63N	CCDC109B_ENST00000515114.1_3'UTR	NM_017918.4	NP_060388.2	Q9NWR8	MCUB_HUMAN	coiled-coil domain containing 109B	63			I -> N (in dbSNP:rs4698744).		mitochondrial calcium ion homeostasis (GO:0051560)|mitochondrial calcium ion transport (GO:0006851)	calcium channel complex (GO:0034704)|integral component of mitochondrial inner membrane (GO:0031305)|intrinsic component of membrane (GO:0031224)|mitochondrion (GO:0005739)|uniplex complex (GO:1990246)	calcium channel inhibitor activity (GO:0019855)			breast(1)|endometrium(1)|kidney(4)|large_intestine(2)|lung(1)	9				OV - Ovarian serous cystadenocarcinoma(123;6.65e-06)		ATAACAGTTATTTATAGACAT	0.308													A|||	1477	0.294928	0.1346	0.3804	5008	,	,		15650	0.4802		0.3201	False		,,,				2504	0.2342				p.I63N		Atlas-SNP	.											.	CCDC109B	47	.	0			c.T188A						PASS	.	A	ASN/ILE	199,1185		15,169,508	74.0	57.0	62.0		188	-7.5	0.0	4	dbSNP_111	62	983,2199		156,671,764	yes	missense	CCDC109B	NM_017918.4	149	171,840,1272	AA,AT,TT		30.8925,14.3786,25.887	benign	63/337	110581363	1182,3384	692	1591	2283	SO:0001583	missense	55013	exon3			CAGTTATTTATAG	BC002633	CCDS3683.2	4q25	2011-05-24			ENSG00000005059	ENSG00000005059			26076	protein-coding gene	gene with protein product						12477932	Standard	NM_017918		Approved	FLJ20647	uc011cfs.2	Q9NWR8	OTTHUMG00000161103	ENST00000394650.4:c.188T>A	4.37:g.110581363T>A	ENSP00000378145:p.Ile63Asn	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	112	47	0.419643	NM_017918	A8K4Y3|Q6IAC1	Missense_Mutation	SNP	ENST00000394650.4	37	CCDS3683.2	727	0.33287545787545786	80	0.16260162601626016	138	0.3812154696132597	270	0.47202797202797203	239	0.3153034300791557	A	6.289	0.421491	0.11928	0.143786	0.308925	ENSG00000005059	ENST00000394650;ENST00000452915	T;T	0.45276	0.9;0.9	5.28	-7.51	0.01346	.	0.868148	0.09770	N	0.758169	T	0.00012	0.0000	N	0.02247	-0.625	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.37267	-0.9713	9	0.13470	T	0.59	-0.215	5.0765	0.14634	0.3719:0.1008:0.4294:0.0979	rs4698744;rs17619522;rs58266701;rs4698744	63;42	Q9NWR8;C9JTJ6	C109B_HUMAN;.	N	63;42	ENSP00000378145:I63N;ENSP00000414591:I42N	ENSP00000378145:I63N	I	+	2	0	CCDC109B	110800812	0.126000	0.22350	0.000000	0.03702	0.820000	0.46376	0.094000	0.15107	-2.463000	0.00535	-1.099000	0.02127	ATT	T|0.669;A|0.331	0.331	strong		0.308	CCDC109B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254865.1	NM_017918	
NAT10	55226	hgsc.bcm.edu	37	11	34130342	34130342	+	Silent	SNP	A	A	G	rs11552143	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:34130342A>G	ENST00000257829.3	+	3	368	c.162A>G	c.(160-162)tcA>tcG	p.S54S	NAT10_ENST00000531159.2_Intron|NAT10_ENST00000527971.1_Silent_p.S54S	NM_024662.2	NP_078938	Q9H0A0	NAT10_HUMAN	N-acetyltransferase 10 (GCN5-related)	54						membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|N-acetyltransferase activity (GO:0008080)|poly(A) RNA binding (GO:0044822)			endometrium(4)|large_intestine(8)|lung(8)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	23		Acute lymphoblastic leukemia(5;0.0119)|all_hematologic(20;0.0231)				CTCGGCCTTCAGTGCTGTGGT	0.413													A|||	325	0.0648962	0.1127	0.0461	5008	,	,		20024	0.0		0.0775	False		,,,				2504	0.0675				p.S54S		Atlas-SNP	.											.	NAT10	78	.	0			c.A162G						PASS	.	A	,	398,4006	198.1+/-222.0	21,356,1825	147.0	135.0	139.0		,162	-3.6	1.0	11	dbSNP_120	139	796,7800	186.6+/-234.0	34,728,3536	no	intron,coding-synonymous	NAT10	NM_001144030.1,NM_024662.2	,	55,1084,5361	GG,GA,AA		9.2601,9.0372,9.1846	,	,54/1026	34130342	1194,11806	2202	4298	6500	SO:0001819	synonymous_variant	55226	exon3			GCCTTCAGTGCTG	AF489535	CCDS7889.1, CCDS44568.1	11p13	2011-11-16	2008-09-24		ENSG00000135372	ENSG00000135372	2.3.1.-		29830	protein-coding gene	gene with protein product		609221	"""N-acetyltransferase 10"""			14592445, 21177859	Standard	NM_024662		Approved	hALP, FLJ10774, FLJ12179, NET43, KIAA1709	uc001mvk.3	Q9H0A0	OTTHUMG00000166249	ENST00000257829.3:c.162A>G	11.37:g.34130342A>G		Somatic	191	0	0		WXS	Illumina HiSeq	Phase_I	162	125	0.771605	NM_024662	B4DFD5|E7ESU4|E9PMN9|Q86WK5|Q9C0F4|Q9HA61|Q9NVF2	Silent	SNP	ENST00000257829.3	37	CCDS7889.1																																																																																			A|0.913;G|0.087	0.087	strong		0.413	NAT10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388693.1	NM_024662	
KPRP	448834	hgsc.bcm.edu	37	1	152732567	152732567	+	Missense_Mutation	SNP	G	G	A	rs16834461	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:152732567G>A	ENST00000606109.1	+	1	531	c.503G>A	c.(502-504)cGt>cAt	p.R168H	KPRP_ENST00000368773.1_Missense_Mutation_p.R168H			Q5T749	KPRP_HUMAN	keratinocyte proline-rich protein	168	Gln-rich.		R -> H (in dbSNP:rs16834461).			cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)				NS(1)|breast(1)|endometrium(9)|kidney(1)|large_intestine(10)|lung(21)|ovary(6)|pancreas(1)|prostate(6)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	60	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)			TATAGAGGGCGTCCTGCAGTG	0.522													G|||	1265	0.252596	0.3585	0.2464	5008	,	,		19803	0.3442		0.1123	False		,,,				2504	0.1636				p.R168H		Atlas-SNP	.											.	KPRP	152	.	0			c.G503A						PASS	.	G	HIS/ARG	1320,3086	445.5+/-347.7	205,910,1088	115.0	117.0	117.0		503	-2.4	0.0	1	dbSNP_123	117	964,7636	210.0+/-251.0	66,832,3402	yes	missense	KPRP	NM_001025231.1	29	271,1742,4490	AA,AG,GG		11.2093,29.9591,17.5611	possibly-damaging	168/580	152732567	2284,10722	2203	4300	6503	SO:0001583	missense	448834	exon2			GAGGGCGTCCTGC	AY960854	CCDS30862.1	1q21.3	2008-02-05	2007-02-02	2006-12-07	ENSG00000203786	ENSG00000203786			31823	protein-coding gene	gene with protein product		613260	"""chromosome 1 open reading frame 45"""	C1orf45		16297201	Standard	NM_001025231		Approved		uc001fal.1	Q5T749	OTTHUMG00000012402	ENST00000606109.1:c.503G>A	1.37:g.152732567G>A	ENSP00000475216:p.Arg168His	Somatic	232	0	0		WXS	Illumina HiSeq	Phase_I	163	75	0.460123	NM_001025231		Missense_Mutation	SNP	ENST00000606109.1	37	CCDS30862.1	543	0.24862637362637363	174	0.35365853658536583	91	0.2513812154696133	200	0.34965034965034963	78	0.10290237467018469	G	0.603	-0.828055	0.02734	0.299591	0.112093	ENSG00000203786	ENST00000368773	T	0.11821	2.74	5.63	-2.44	0.06502	.	1.434680	0.04174	N	0.325356	T	0.01730	0.0055	N	0.08118	0	0.80722	P	0.0	P	0.42039	0.769	B	0.36186	0.219	T	0.32955	-0.9887	9	0.28530	T	0.3	0.8042	6.7297	0.23377	0.4528:0.1216:0.4256:0.0	rs16834461;rs56757678;rs16834461	168	Q5T749	KPRP_HUMAN	H	168	ENSP00000357762:R168H	ENSP00000357762:R168H	R	+	2	0	KPRP	150999191	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.040000	0.12104	-0.360000	0.08138	-0.126000	0.14955	CGT	G|0.798;A|0.202	0.202	strong		0.522	KPRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034522.2	NM_001025231	
SIRT3	23410	hgsc.bcm.edu	37	11	233212	233212	+	Silent	SNP	C	C	A	rs11555236	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:233212C>A	ENST00000382743.4	-	3	579	c.477G>T	c.(475-477)tcG>tcT	p.S159S	SIRT3_ENST00000528702.1_5'UTR|SIRT3_ENST00000532956.1_Silent_p.S159S|SIRT3_ENST00000529382.1_Silent_p.S17S|SIRT3_ENST00000525319.1_Silent_p.S78S|SIRT3_ENST00000524564.1_Silent_p.S95S	NM_001017524.2|NM_012239.5	NP_001017524.1|NP_036371.1	Q9NTG7	SIR3_HUMAN	sirtuin 3	159	Deacetylase sirtuin-type. {ECO:0000255|PROSITE-ProRule:PRU00236}.				aerobic respiration (GO:0009060)|peptidyl-lysine deacetylation (GO:0034983)|protein ADP-ribosylation (GO:0006471)|protein deacetylation (GO:0006476)	membrane (GO:0016020)|mitochondrion (GO:0005739)	NAD+ ADP-ribosyltransferase activity (GO:0003950)|NAD+ binding (GO:0070403)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|zinc ion binding (GO:0008270)			endometrium(1)|lung(5)|urinary_tract(1)	7		all_cancers(49;1.58e-09)|all_epithelial(84;2.71e-06)|Breast(177;0.000162)|Ovarian(85;0.000626)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.0538)|all_lung(207;0.0713)		all cancers(45;3.66e-27)|Epithelial(43;2.02e-26)|OV - Ovarian serous cystadenocarcinoma(40;2.9e-21)|BRCA - Breast invasive adenocarcinoma(625;3.88e-05)|Lung(200;0.111)|LUSC - Lung squamous cell carcinoma(625;0.129)		CACTCCCCGGCGATCTGCAGG	0.572													A|||	576	0.115016	0.0159	0.1484	5008	,	,		17030	0.0942		0.2048	False		,,,				2504	0.1544				p.S159S		Atlas-SNP	.											.	SIRT3	28	.	0			c.G477T						PASS	.		,	192,4214	808.3+/-415.9	6,180,2017	45.0	48.0	47.0		51,477	0.3	0.2	11	dbSNP_120	47	1830,6770	731.2+/-406.8	178,1474,2648	no	coding-synonymous,coding-synonymous	SIRT3	NM_001017524.2,NM_012239.5	,	184,1654,4665	AA,AC,CC		21.2791,4.3577,15.5467	,	17/258,159/400	233212	2022,10984	2203	4300	6503	SO:0001819	synonymous_variant	23410	exon3			CCCCGGCGATCTG	AF083108	CCDS7691.1, CCDS53590.1	11p15.5	2010-06-25	2010-06-25		ENSG00000142082	ENSG00000142082			14931	protein-coding gene	gene with protein product		604481	"""sirtuin (silent mating type information regulation 2, S.cerevisiae, homolog) 3"", ""sirtuin (silent mating type information regulation 2 homolog) 3 (S. cerevisiae)"""			10381378, 18215119	Standard	NM_012239		Approved	SIR2L3	uc001lok.4	Q9NTG7	OTTHUMG00000119074	ENST00000382743.4:c.477G>T	11.37:g.233212C>A		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	81	66	0.814815	NM_012239	B7Z5U6|Q9Y6E8	Silent	SNP	ENST00000382743.4	37	CCDS7691.1																																																																																			C|0.849;A|0.151	0.151	strong		0.572	SIRT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239288.3		
LILRB3	11025	hgsc.bcm.edu	37	19	54724457	54724457	+	Missense_Mutation	SNP	T	T	C	rs1052995	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:54724457T>C	ENST00000391750.1	-	7	1335	c.1199A>G	c.(1198-1200)tAc>tGc	p.Y400C	LILRB3_ENST00000424807.1_Missense_Mutation_p.Y400C|LILRB3_ENST00000346401.6_Missense_Mutation_p.Y400C|LILRA6_ENST00000440558.2_Missense_Mutation_p.Y400C|LILRA6_ENST00000270464.5_Missense_Mutation_p.Y400C|LILRB3_ENST00000407860.2_Missense_Mutation_p.Y400C|LILRB3_ENST00000469273.1_5'UTR|LILRA6_ENST00000419410.2_Intron|LILRA6_ENST00000391735.3_Intron|LILRB3_ENST00000245620.9_Missense_Mutation_p.Y400C			O75022	LIRB3_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 3	400	Ig-like C2-type 4.		Y -> F (in dbSNP:rs8105096).|Y -> H (in dbSNP:rs1052992).|Y -> R (requires 2 nucleotide substitutions). {ECO:0000269|PubMed:9548455, ECO:0000269|Ref.3}.		cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)|immune system process (GO:0002376)|negative regulation of osteoclast differentiation (GO:0045671)	integral component of plasma membrane (GO:0005887)	receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			endometrium(3)|kidney(13)|large_intestine(1)|lung(6)|ovary(2)|prostate(5)|skin(2)|stomach(1)|urinary_tract(1)	34	all_cancers(19;0.00723)|all_epithelial(19;0.00389)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		GTTGGAGCTGTATGAGCCGTA	0.602													.|||	1376	0.27476	0.3306	0.2522	5008	,	,		9425	0.0476		0.2883	False		,,,				2504	0.4356				p.Y400C		Atlas-SNP	.											.	LILRB3	67	.	0			c.A1199G						PASS	.						19.0	12.0	14.0					19																	54724457		2178	3945	6123	SO:0001583	missense	11025	exon6			GAGCTGTATGAGC	U91928	CCDS33105.1, CCDS46175.1	19q13.4	2013-01-11			ENSG00000204577	ENSG00000204577		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6607	protein-coding gene	gene with protein product		604820				9278324, 9382880	Standard	NM_006864		Approved	LIR-3, HL9, ILT5, LIR3, CD85a	uc002qee.1	O75022	OTTHUMG00000066626	ENST00000391750.1:c.1199A>G	19.37:g.54724457T>C	ENSP00000375630:p.Tyr400Cys	Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	57	31	0.54386	NM_006864	C9J1P3|C9JIP1|O15471|Q86U49	Missense_Mutation	SNP	ENST00000391750.1	37	CCDS33105.1	368	0.1684981684981685	146	0.2967479674796748	74	0.20441988950276244	20	0.03496503496503497	128	0.16886543535620052	C	8.457	0.854468	0.17106	.	.	ENSG00000204577;ENSG00000204577;ENSG00000204577;ENSG00000204577;ENSG00000204577;ENSG00000244482;ENSG00000244482	ENST00000391750;ENST00000424807;ENST00000346401;ENST00000245620;ENST00000407860;ENST00000440558;ENST00000270464	T;T;T;T;T;T;T	0.00753	5.74;5.74;5.74;5.74;5.74;5.74;5.74	2.88	-5.77	0.02369	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	6.834670	0.00465	N	0.000119	T	0.00012	0.0000	M	0.69823	2.125	0.80722	P	0.0	B;B;B;B;B;B	0.30870	0.298;0.001;0.001;0.108;0.053;0.004	P;B;B;B;B;B	0.56343	0.796;0.007;0.021;0.093;0.1;0.009	T	0.42682	-0.9437	9	0.39692	T	0.17	.	3.7917	0.08722	0.3774:0.2784:0.0:0.3442	rs1052995;rs2361812;rs3193479	400;400;400;400;400;400	B5MCX0;F8WCY4;F8W6G6;O75022-2;O75022;O75022-3	.;.;.;.;LIRB3_HUMAN;.	C	400	ENSP00000375630:Y400C;ENSP00000412771:Y400C;ENSP00000345184:Y400C;ENSP00000245620:Y400C;ENSP00000384274:Y400C;ENSP00000390120:Y400C;ENSP00000270464:Y400C	ENSP00000270464:Y400C	Y	-	2	0	LILRB3;LILRA6	59416269	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-8.592000	0.00019	-2.477000	0.00525	-4.852000	0.00002	TAC	T|1.000;|0.000	.	strong		0.602	LILRB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000142844.5	NM_006864	
CCDC110	256309	hgsc.bcm.edu	37	4	186381165	186381165	+	Silent	SNP	G	G	A	rs7699724	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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_ENST00000393540.3_Silent_p.D155D|CCDC110_ENST00000507501.1_5'UTR	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	162	0	0		WXS	Illumina HiSeq	Phase_I	135	50	0.37037	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	
DHX38	9785	hgsc.bcm.edu	37	16	72130815	72130815	+	Silent	SNP	C	C	A	rs1050362	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:72130815C>A	ENST00000268482.3	+	3	927	c.418C>A	c.(418-420)Cgg>Agg	p.R140R	TXNL4B_ENST00000426362.2_5'Flank|DHX38_ENST00000536867.1_Intron	NM_014003.3	NP_054722.2	Q92620	PRP16_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 38	140					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)				GCGGGAGCGGCGGGAACATGG	0.537													C|||	2395	0.478235	0.7874	0.3156	5008	,	,		19363	0.3105		0.3549	False		,,,				2504	0.4755				p.R140R	Melanoma(97;711 1442 7855 13832 28836)	Atlas-SNP	.											DHX38,right_upper_lobe,carcinoma,-2,2	DHX38	91	2	0			c.C418A						PASS	.	C		3048,1348	692.2+/-405.5	1072,904,222	151.0	146.0	148.0		418	4.1	1.0	16	dbSNP_86	148	3214,5386	484.9+/-371.5	591,2032,1677	no	coding-synonymous	DHX38	NM_014003.3		1663,2936,1899	AA,AC,CC		37.3721,30.6642,48.1841		140/1228	72130815	6262,6734	2198	4300	6498	SO:0001819	synonymous_variant	9785	exon3			GAGCGGCGGGAAC	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.418C>A	16.37:g.72130815C>A		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	113	36	0.318584	NM_014003	B4DVG8|D3DWS7|O75212|Q96HN7	Silent	SNP	ENST00000268482.3	37	CCDS10907.1																																																																																			C|0.529;A|0.471	0.471	strong		0.537	DHX38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269004.3	NM_014003	
NUP210L	91181	hgsc.bcm.edu	37	1	153982536	153982536	+	Missense_Mutation	SNP	C	C	T	rs199611847		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:153982536C>T	ENST00000368559.3	-	35	4913	c.4842G>A	c.(4840-4842)atG>atA	p.M1614I	NUP210L_ENST00000271854.3_Missense_Mutation_p.M1614I|NUP210L_ENST00000368553.1_Missense_Mutation_p.M547I	NM_207308.2	NP_997191.2	Q5VU65	P210L_HUMAN	nucleoporin 210kDa-like	1614					Sertoli cell development (GO:0060009)|spermatid development (GO:0007286)	integral component of membrane (GO:0016021)				NS(1)|breast(6)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(12)|lung(34)|ovary(4)|pancreas(1)|prostate(2)|skin(6)|urinary_tract(2)	80	all_lung(78;9.35e-31)|Lung NSC(65;1.33e-28)|Hepatocellular(266;0.0877)|Melanoma(130;0.128)		LUSC - Lung squamous cell carcinoma(543;0.151)|Colorectal(543;0.198)			CATGGCACAGCATGAGGGTCG	0.423																																					p.M1614I		Atlas-SNP	.											.	NUP210L	181	.	0			c.G4842A						PASS	.	T	ILE/MET,ILE/MET	0,3736		0,0,1868	148.0	141.0	143.0		4842,4842	2.4	0.2	1		143	3,8209		0,3,4103	yes	missense,missense	NUP210L	NM_001159484.1,NM_207308.2	10,10	0,3,5971	TT,TC,CC		0.0365,0.0,0.0251	benign,benign	1614/1737,1614/1889	153982536	3,11945	1868	4106	5974	SO:0001583	missense	91181	exon35			GCACAGCATGAGG	AK125924	CCDS41399.1, CCDS53370.1	1q21.3	2008-02-05			ENSG00000143552	ENSG00000143552			29915	protein-coding gene	gene with protein product							Standard	NM_207308		Approved		uc001fdw.3	Q5VU65	OTTHUMG00000035852	ENST00000368559.3:c.4842G>A	1.37:g.153982536C>T	ENSP00000357547:p.Met1614Ile	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	67	29	0.432836	NM_001159484	E7EP56|Q5T4L7|Q6ZRN1|Q6ZRT4|Q6ZU81|Q8NDI6|Q9UF31	Missense_Mutation	SNP	ENST00000368559.3	37	CCDS41399.1	.	.	.	.	.	.	.	.	.	.	c	0.029	-1.345824	0.01266	0.0	3.65E-4	ENSG00000143552	ENST00000368559;ENST00000368553;ENST00000271854	T;T;T	0.18810	3.68;2.19;3.5	5.24	2.39	0.29439	.	1.290600	0.05075	N	0.482321	T	0.04092	0.0114	L	0.39898	1.24	0.20403	N	0.999903	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.31586	-0.9938	10	0.02654	T	1	-12.129	5.8719	0.18809	0.1534:0.6865:0.0:0.1601	.	1614;1614	E7EP56;Q5VU65	.;P210L_HUMAN	I	1614;547;1614	ENSP00000357547:M1614I;ENSP00000357541:M547I;ENSP00000271854:M1614I	ENSP00000271854:M1614I	M	-	3	0	NUP210L	152249160	0.666000	0.27475	0.235000	0.24058	0.484000	0.33280	0.687000	0.25407	0.370000	0.24538	-0.224000	0.12420	ATG	.	.	weak		0.423	NUP210L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087270.3	NM_207308	
ANKMY1	51281	hgsc.bcm.edu	37	2	241463639	241463639	+	Missense_Mutation	SNP	C	C	T	rs3796119	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:241463639C>T	ENST00000272972.3	-	7	1442	c.1228G>A	c.(1228-1230)Gag>Aag	p.E410K	ANKMY1_ENST00000401804.1_Missense_Mutation_p.E499K|ANKMY1_ENST00000403283.1_Missense_Mutation_p.E348K|ANKMY1_ENST00000391987.1_Missense_Mutation_p.E410K|ANKMY1_ENST00000406958.1_Intron|ANKMY1_ENST00000405002.1_Missense_Mutation_p.E180K|ANKMY1_ENST00000462004.1_5'Flank|ANKMY1_ENST00000361678.4_Missense_Mutation_p.E269K|ANKMY1_ENST00000405523.3_Missense_Mutation_p.E269K|ANKMY1_ENST00000536462.1_Missense_Mutation_p.E222K|ANKMY1_ENST00000373318.2_Missense_Mutation_p.E269K|ANKMY1_ENST00000373320.4_Missense_Mutation_p.E180K	NM_016552.2	NP_057636.2	Q9P2S6	ANKY1_HUMAN	ankyrin repeat and MYND domain containing 1	410							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)		TGGCCGCCCTCGTGGCTGCCT	0.642													C|||	155	0.0309505	0.0	0.0086	5008	,	,		17207	0.0109		0.0129	False		,,,				2504	0.1278				p.E410K		Atlas-SNP	.											ANKMY1_ENST00000361678,NS,carcinoma,+2,2	ANKMY1	112	2	0			c.G1228A						scavenged	.	C	LYS/GLU,LYS/GLU	14,4392	21.2+/-45.6	0,14,2189	52.0	53.0	53.0		1228,805	0.4	0.0	2	dbSNP_107	53	109,8491	57.9+/-119.4	1,107,4192	yes	missense,missense	ANKMY1	NM_016552.2,NM_017844.2	56,56	1,121,6381	TT,TC,CC		1.2674,0.3177,0.9457	possibly-damaging,possibly-damaging	410/942,269/718	241463639	123,12883	2203	4300	6503	SO:0001583	missense	51281	exon7			CGCCCTCGTGGCT	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.1228G>A	2.37:g.241463639C>T	ENSP00000272972:p.Glu410Lys	Somatic	102	1	0.00980392		WXS	Illumina HiSeq	Phase_I	80	33	0.4125	NM_016552	B2RB78|Q4ZFV3|Q8IYX5|Q8NDK5|Q9H0V8|Q9NX10	Missense_Mutation	SNP	ENST00000272972.3	37	CCDS2536.1	22	0.010073260073260074	0	0.0	3	0.008287292817679558	8	0.013986013986013986	11	0.014511873350923483	C	11.65	1.702216	0.30232	0.003177	0.012674	ENSG00000144504	ENST00000373318;ENST00000272972;ENST00000361678;ENST00000391987;ENST00000373320;ENST00000403283;ENST00000401804;ENST00000536462;ENST00000405523;ENST00000405002	T;T;T;T;T;T;T;T;T;T	0.59772	2.59;0.27;1.89;0.27;4.12;2.13;0.24;1.75;1.77;2.03	2.39	0.356	0.16074	Ankyrin repeat-containing domain (1);	0.821330	0.10129	U	0.712362	T	0.33673	0.0871	N	0.14661	0.345	0.09310	N	1	P;D;D;P;D;P	0.60575	0.913;0.966;0.981;0.799;0.988;0.913	B;B;B;B;P;B	0.50754	0.158;0.293;0.43;0.129;0.649;0.158	T	0.17228	-1.0376	10	0.35671	T	0.21	.	2.7648	0.05317	0.2754:0.5575:0.0:0.167	rs3796119	410;222;180;269;269;410	Q4ZFV3;F5H558;Q9P2S6-4;Q6GPI0;Q9P2S6-2;Q9P2S6	.;.;.;.;.;ANKY1_HUMAN	K	269;410;269;410;180;348;499;222;269;180	ENSP00000362415:E269K;ENSP00000272972:E410K;ENSP00000355097:E269K;ENSP00000375847:E410K;ENSP00000362417:E180K;ENSP00000383968:E348K;ENSP00000385887:E499K;ENSP00000444707:E222K;ENSP00000385635:E269K;ENSP00000385145:E180K	ENSP00000272972:E410K	E	-	1	0	ANKMY1	241112312	0.004000	0.15560	0.000000	0.03702	0.003000	0.03518	0.616000	0.24344	0.071000	0.16664	0.491000	0.48974	GAG	C|0.990;T|0.010	0.010	strong		0.642	ANKMY1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000257187.2	NM_017844	
UGT2B11	10720	hgsc.bcm.edu	37	4	70080139	70080139	+	Missense_Mutation	SNP	C	C	T	rs7688262	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:70080139C>T	ENST00000446444.1	-	1	310	c.302G>A	c.(301-303)cGa>cAa	p.R101Q	RP11-704M14.1_ENST00000504301.1_RNA|RP11-704M14.1_ENST00000505646.1_RNA	NM_001073.1	NP_001064.1	O75310	UDB11_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide B11	101					estrogen metabolic process (GO:0008210)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	glucuronosyltransferase activity (GO:0015020)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(18)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	42						GCTATCTTTTCGAATGTCTGA	0.303													.|||	839	0.167532	0.3033	0.1801	5008	,	,		20947	0.0486		0.1064	False		,,,				2504	0.1605				p.R101Q		Atlas-SNP	.											UGT2B11,NS,carcinoma,-1,2	UGT2B11	92	2	0			c.G302A						PASS	.	C	GLN/ARG	825,3549		123,579,1485	63.0	79.0	73.0		302	-3.5	0.0	4	dbSNP_116	73	585,7997		28,529,3734	no	missense	UGT2B11	NM_001073.1	43	151,1108,5219	TT,TC,CC		6.8166,18.8615,10.883	benign	101/530	70080139	1410,11546	2187	4291	6478	SO:0001583	missense	10720	exon1			TCTTTTCGAATGT	AF016492	CCDS3527.1	4q13.3	2008-02-05	2005-07-20		ENSG00000213759	ENSG00000213759		"""UDP glucuronosyltransferases"""	12545	protein-coding gene	gene with protein product		603064	"""UDP glycosyltransferase 2 family, polypeptide B11"""			9675083	Standard	NM_001073		Approved		uc003heh.3	O75310	OTTHUMG00000129395	ENST00000446444.1:c.302G>A	4.37:g.70080139C>T	ENSP00000387683:p.Arg101Gln	Somatic	557	1	0.00179533		WXS	Illumina HiSeq	Phase_I	393	157	0.399491	NM_001073	Q3KNV9	Missense_Mutation	SNP	ENST00000446444.1	37	CCDS3527.1	318	0.14560439560439561	150	0.3048780487804878	63	0.17403314917127072	32	0.055944055944055944	73	0.09630606860158311	-	1.849	-0.465491	0.04476	0.188615	0.068166	ENSG00000213759	ENST00000446444	T	0.59364	0.27	1.77	-3.54	0.04653	.	0.644350	0.13601	U	0.375824	T	0.00012	0.0000	L	0.36672	1.1	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.20605	-1.0270	9	0.32370	T	0.25	.	4.6393	0.12541	0.0:0.1842:0.2599:0.5558	rs7688262	101	O75310	UDB11_HUMAN	Q	101	ENSP00000387683:R101Q	ENSP00000387683:R101Q	R	-	2	0	UGT2B11	70114728	0.007000	0.16637	0.000000	0.03702	0.004000	0.04260	0.000000	0.12993	-1.062000	0.03181	-1.398000	0.01145	CGA	C|0.886;T|0.114	0.114	strong		0.303	UGT2B11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251551.2	NM_001073	
ZNF91	7644	hgsc.bcm.edu	37	19	23543834	23543834	+	Silent	SNP	C	C	T	rs7255296	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:23543834C>T	ENST00000300619.7	-	4	2152	c.1947G>A	c.(1945-1947)aaG>aaA	p.K649K	ZNF91_ENST00000599743.1_Intron|ZNF91_ENST00000596528.1_5'Flank|ZNF91_ENST00000397082.2_Silent_p.K617K	NM_003430.2	NP_003421.2	Q05481	ZNF91_HUMAN	zinc finger protein 91	649					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)				TATGAATTCTCTTATGTTTAG	0.388													C|||	696	0.138978	0.2171	0.1153	5008	,	,		5248	0.0218		0.1849	False		,,,				2504	0.1237				p.K649K		Atlas-SNP	.											.	ZNF91	349	.	0			c.G1947A						PASS	.	C		853,3345		93,667,1339	58.0	61.0	60.0		1947	-2.2	0.0	19	dbSNP_116	60	1769,6713		175,1419,2647	no	coding-synonymous	ZNF91	NM_003430.2		268,2086,3986	TT,TC,CC		20.8559,20.3192,20.6782		649/1192	23543834	2622,10058	2099	4241	6340	SO:0001819	synonymous_variant	7644	exon4			AATTCTCTTATGT	M61871	CCDS42541.1, CCDS74322.1	19p12	2014-02-04	2006-05-12		ENSG00000167232	ENSG00000167232		"""Zinc fingers, C2H2-type"", ""-"""	13166	protein-coding gene	gene with protein product		603971	"""zinc finger protein 91 (HPF7, HTF10)"""			2023909, 2505992	Standard	XR_430154		Approved	HPF7, HTF10	uc002nre.3	Q05481	OTTHUMG00000183268	ENST00000300619.7:c.1947G>A	19.37:g.23543834C>T		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	49	18	0.367347	NM_003430	A8K5E1|B7Z6G6	Silent	SNP	ENST00000300619.7	37	CCDS42541.1																																																																																			C|0.854;T|0.146	0.146	strong		0.388	ZNF91-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465891.1	NM_003430	
KIFC1	3833	hgsc.bcm.edu	37	6	33374015	33374015	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:33374015G>A	ENST00000428849.2	+	8	2029	c.1579G>A	c.(1579-1581)Gcc>Acc	p.A527T		NM_002263.3	NP_002254.2	Q9BW19	KIFC1_HUMAN	kinesin family member C1	527	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)			endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|prostate(3)|skin(1)	13						TCGGGCTGTGGCCCGCACAGC	0.597																																					p.A527T		Atlas-SNP	.											.	KIFC1	47	.	0			c.G1579A						PASS	.						60.0	71.0	67.0					6																	33374015		2202	4300	6502	SO:0001583	missense	3833	exon8			GCTGTGGCCCGCA	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.1579G>A	6.37:g.33374015G>A	ENSP00000393963:p.Ala527Thr	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	120	52	0.433333	NM_002263	O60887|Q14834|Q4KMP0|Q5SU09|Q6GMS7|Q6P4A5|Q9UQP7	Missense_Mutation	SNP	ENST00000428849.2	37	CCDS34430.1	.	.	.	.	.	.	.	.	.	.	g	25.6	4.651805	0.88056	.	.	ENSG00000237649	ENST00000428849	T	0.49139	0.79	5.29	4.43	0.53597	Kinesin, motor domain (4);	0.000000	0.85682	D	0.000000	T	0.67192	0.2867	M	0.92833	3.35	0.80722	D	1	D;D	0.76494	0.999;0.997	D;D	0.72982	0.979;0.965	T	0.76225	-0.3037	10	0.87932	D	0	-5.1694	11.577	0.50866	0.0857:0.0:0.9143:0.0	.	519;527	B4E063;Q9BW19	.;KIFC1_HUMAN	T	527	ENSP00000393963:A527T	ENSP00000393963:A527T	A	+	1	0	KIFC1	33481993	1.000000	0.71417	0.999000	0.59377	0.871000	0.50021	6.592000	0.74095	1.461000	0.47929	0.558000	0.71614	GCC	.	.	none		0.597	KIFC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076417.1	NM_002263	
WBSCR28	135886	hgsc.bcm.edu	37	7	73279413	73279413	+	Missense_Mutation	SNP	C	C	T	rs118088869	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:73279413C>T	ENST00000320531.2	+	2	199	c.163C>T	c.(163-165)Cgg>Tgg	p.R55W		NM_182504.3	NP_872310.2	Q6UE05	WBS28_HUMAN	Williams-Beuren syndrome chromosome region 28	55						integral component of membrane (GO:0016021)		p.R55R(1)		breast(2)|kidney(2)|lung(6)|skin(1)	11		Lung NSC(55;0.159)				CCAGGAGGCCCGGGGGTCCTG	0.617													C|||	53	0.0105831	0.0038	0.013	5008	,	,		15897	0.0		0.0328	False		,,,				2504	0.0061				p.R55W		Atlas-SNP	.											.	WBSCR28	24	.	1	Substitution - coding silent(1)	lung(1)	c.C163T						PASS	.	C	TRP/ARG	32,3674		0,32,1821	138.0	146.0	143.0		163	1.5	0.4	7	dbSNP_132	143	264,7930		5,254,3838	yes	missense	WBSCR28	NM_182504.3	101	5,286,5659	TT,TC,CC		3.2219,0.8635,2.4874	probably-damaging	55/266	73279413	296,11604	1853	4097	5950	SO:0001583	missense	135886	exon2			GAGGCCCGGGGGT	BC030643	CCDS43597.1	7q11.23	2006-07-04			ENSG00000175877	ENSG00000175877			23018	protein-coding gene	gene with protein product		612547				8812460	Standard	NM_182504		Approved	MGC26719	uc003tzk.2	Q6UE05	OTTHUMG00000157243	ENST00000320531.2:c.163C>T	7.37:g.73279413C>T	ENSP00000316775:p.Arg55Trp	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	107	65	0.607477	NM_182504	Q6UE04|Q8NHP4	Missense_Mutation	SNP	ENST00000320531.2	37	CCDS43597.1	31	0.014194139194139194	2	0.0040650406504065045	9	0.024861878453038673	0	0.0	20	0.026385224274406333	C	5.956	0.360297	0.11296	0.008635	0.032219	ENSG00000175877	ENST00000320531	T	0.19532	2.14	4.43	1.45	0.22620	.	1.221350	0.06077	N	0.661182	T	0.03520	0.0101	N	0.08118	0	0.09310	N	1	B	0.18310	0.027	B	0.10450	0.005	T	0.28267	-1.0049	10	0.46703	T	0.11	-13.413	6.1732	0.20429	0.0:0.4923:0.4005:0.1072	.	55	Q6UE05	WBS28_HUMAN	W	55	ENSP00000316775:R55W	ENSP00000316775:R55W	R	+	1	2	WBSCR28	72917349	0.000000	0.05858	0.377000	0.26055	0.064000	0.16182	-0.549000	0.06041	0.529000	0.28599	-0.273000	0.10243	CGG	C|0.983;T|0.017	0.017	strong		0.617	WBSCR28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348130.1	NM_182504	
GIMAP8	155038	hgsc.bcm.edu	37	7	150164155	150164155	+	Silent	SNP	T	T	C	rs61748320	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:150164155T>C	ENST00000307271.3	+	2	943	c.369T>C	c.(367-369)gcT>gcC	p.A123A		NM_175571.2	NP_783161.1	Q8ND71	GIMA8_HUMAN	GTPase, IMAP family member 8	123	AIG1-type G 1.					cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	GTP binding (GO:0005525)			breast(3)|central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(11)|lung(26)|ovary(2)|skin(7)|stomach(1)|urinary_tract(1)	62			OV - Ovarian serous cystadenocarcinoma(82;0.0218)	UCEC - Uterine corpus endometrioid carcinoma (81;0.17)		TGTTTGGAGCTGAAGCCAGGA	0.483													T|||	31	0.0061901	0.0	0.0159	5008	,	,		21448	0.0		0.0159	False		,,,				2504	0.0041				p.A123A		Atlas-SNP	.											.	GIMAP8	136	.	0			c.T369C						PASS	.	T		24,4382	31.7+/-61.6	0,24,2179	83.0	78.0	79.0		369	-8.9	0.0	7	dbSNP_129	79	226,8374	93.5+/-155.5	2,222,4076	no	coding-synonymous	GIMAP8	NM_175571.2		2,246,6255	CC,CT,TT		2.6279,0.5447,1.9222		123/666	150164155	250,12756	2203	4300	6503	SO:0001819	synonymous_variant	155038	exon2			TGGAGCTGAAGCC	AL834361	CCDS34777.1	7q36.1	2014-04-04			ENSG00000171115	ENSG00000171115		"""GTPases, IMAP"""	21792	protein-coding gene	gene with protein product	"""immune-associated nucleotide-binding protein 9"""					15474311	Standard	XM_005249951		Approved	DKFZp667I133, hIAN6, IAN9	uc003whj.3	Q8ND71	OTTHUMG00000158327	ENST00000307271.3:c.369T>C	7.37:g.150164155T>C		Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	138	54	0.391304	NM_175571		Silent	SNP	ENST00000307271.3	37	CCDS34777.1																																																																																			T|0.985;C|0.015	0.015	strong		0.483	GIMAP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350701.1	NM_175571	
SLC22A24	283238	hgsc.bcm.edu	37	11	62848445	62848445	+	Silent	SNP	A	A	G	rs11231340	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:62848445A>G	ENST00000417740.1	-	9	1986	c.1545T>C	c.(1543-1545)ctT>ctC	p.L515L		NM_001136506.2	NP_001129978.2	Q8N4F4	S22AO_HUMAN	solute carrier family 22, member 24	273					ion transport (GO:0006811)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)		p.L515L(1)		kidney(1)|stomach(1)	2						TGGTTTCTGGAAGGAGGAGGA	0.507													A|||	2222	0.44369	0.3442	0.4914	5008	,	,		22919	0.4196		0.5109	False		,,,				2504	0.5				p.L515L		Atlas-SNP	.											SLC22A24_ENST00000417740,NS,carcinoma,0,1	SLC22A24	31	1	1	Substitution - coding silent(1)	kidney(1)	c.T1545C						scavenged	.	A		491,893		86,319,287	155.0	133.0	139.0		1545	1.1	1.0	11	dbSNP_120	139	1692,1490		447,798,346	no	coding-synonymous	SLC22A24	NM_001136506.2		533,1117,633	GG,GA,AA		46.8259,35.4769,47.8099		515/553	62848445	2183,2383	692	1591	2283	SO:0001819	synonymous_variant	283238	exon9			TTCTGGAAGGAGG		CCDS73308.1	11q12.3	2013-05-22			ENSG00000197658	ENSG00000197658		"""Solute carriers"""	28542	protein-coding gene	gene with protein product		611698				17714910	Standard	NM_001136506		Approved	MGC34821, NET46	uc021qkp.1	Q8N4F4	OTTHUMG00000165372	ENST00000417740.1:c.1545T>C	11.37:g.62848445A>G		Somatic	132	1	0.00757576		WXS	Illumina HiSeq	Phase_I	129	33	0.255814	NM_001136506		Silent	SNP	ENST00000417740.1	37																																																																																				A|0.539;G|0.460	0.460	strong		0.507	SLC22A24-003	PUTATIVE	non_canonical_polymorphism|basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000383747.1	NM_173586	
BPIFB4	149954	hgsc.bcm.edu	37	20	31678534	31678534	+	Silent	SNP	T	T	C	rs2070326	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:31678534T>C	ENST00000375483.3	+	8	1072	c.1072T>C	c.(1072-1074)Ttg>Ctg	p.L358L		NM_182519.2	NP_872325.2	P59827	BPIB4_HUMAN	BPI fold containing family B, member 4	358						cytoplasm (GO:0005737)|extracellular region (GO:0005576)	lipid binding (GO:0008289)										TCTGGGGATATTGGGAAGTGT	0.592													T|||	1090	0.217652	0.1732	0.3127	5008	,	,		19342	0.1607		0.2366	False		,,,				2504	0.2495				p.L358L		Atlas-SNP	.											.	.	.	.	0			c.T1072C						PASS	.	T		858,3548	334.9+/-303.7	95,668,1440	119.0	96.0	104.0		1072	0.4	1.0	20	dbSNP_96	104	2000,6600	349.3+/-327.4	222,1556,2522	no	coding-synonymous	BPIFB4	NM_182519.2		317,2224,3962	CC,CT,TT		23.2558,19.4734,21.9745		358/615	31678534	2858,10148	2203	4300	6503	SO:0001819	synonymous_variant	149954	exon8			GGGATATTGGGAA	AF549190	CCDS13213.2	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000186191	ENSG00000186191		"""BPI fold containing"""	16179	protein-coding gene	gene with protein product		615718	"""chromosome 20 open reading frame 186"""	C20orf186		11971875, 21787333	Standard	NM_182519		Approved	dJ726C3.5, LPLUNC4	uc010zue.2	P59827	OTTHUMG00000032235	ENST00000375483.3:c.1072T>C	20.37:g.31678534T>C		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	121	50	0.413223	NM_182519	Q5TDX6	Silent	SNP	ENST00000375483.3	37	CCDS13213.2																																																																																			T|0.784;C|0.216	0.216	strong		0.592	BPIFB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078655.5	NM_182519	
MEPE	56955	hgsc.bcm.edu	37	4	88766969	88766969	+	Missense_Mutation	SNP	A	A	G	rs61731014	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:88766969A>G	ENST00000424957.3	+	4	1022	c.949A>G	c.(949-951)Att>Gtt	p.I317V	MEPE_ENST00000361056.3_Missense_Mutation_p.I317V|MEPE_ENST00000560249.1_Missense_Mutation_p.I204V|MEPE_ENST00000540395.1_Missense_Mutation_p.I204V|MEPE_ENST00000497649.2_Missense_Mutation_p.I293V|MEPE_ENST00000508016.1_3'UTR|MEPE_ENST00000395102.4_Missense_Mutation_p.I348V	NM_001184694.1	NP_001171623.1	Q9NQ76	MEPE_HUMAN	matrix extracellular phosphoglycoprotein	317					biomineral tissue development (GO:0031214)|negative regulation of bone mineralization (GO:0030502)|regulation of bone remodeling (GO:0046850)|skeletal system development (GO:0001501)	proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)			cervix(1)|endometrium(1)|kidney(3)|large_intestine(5)|lung(19)|ovary(1)|skin(5)|upper_aerodigestive_tract(1)	36		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000432)		TGGAAATACCATTGGAACTAG	0.448													A|||	53	0.0105831	0.0	0.0187	5008	,	,		20945	0.001		0.0268	False		,,,				2504	0.0123				p.I317V		Atlas-SNP	.											.	MEPE	86	.	0			c.A949G						PASS	.	A	VAL/ILE,VAL/ILE,VAL/ILE,VAL/ILE,VAL/ILE	23,4383	30.8+/-60.4	0,23,2180	65.0	66.0	65.0		949,610,610,610,949	-4.5	0.0	4	dbSNP_129	65	203,8397	87.4+/-149.7	5,193,4102	yes	missense,missense,missense,missense,missense	MEPE	NM_001184694.1,NM_001184695.1,NM_001184696.1,NM_001184697.1,NM_020203.3	29,29,29,29,29	5,216,6282	GG,GA,AA		2.3605,0.522,1.7377	benign,benign,benign,benign,benign	317/526,204/413,204/413,204/413,317/526	88766969	226,12780	2203	4300	6503	SO:0001583	missense	56955	exon4			AATACCATTGGAA	AJ276396	CCDS3625.1, CCDS54776.1	4q21.1	2008-08-29	2008-08-29		ENSG00000152595	ENSG00000152595			13361	protein-coding gene	gene with protein product		605912	"""matrix, extracellular phosphoglycoprotein with ASARM motif (bone)"""			10945470	Standard	NM_020203		Approved		uc003hqy.3	Q9NQ76	OTTHUMG00000130592	ENST00000424957.3:c.949A>G	4.37:g.88766969A>G	ENSP00000416984:p.Ile317Val	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	33	13	0.393939	NM_020203	A1A4X9|A8MTA3|D2CFR4|F5H5C5	Missense_Mutation	SNP	ENST00000424957.3	37	CCDS3625.1	31	0.014194139194139194	0	0.0	9	0.024861878453038673	1	0.0017482517482517483	21	0.027704485488126648	A	6.730	0.503419	0.12822	0.00522	0.023605	ENSG00000152595	ENST00000424957;ENST00000395102;ENST00000497649;ENST00000540395;ENST00000361056	T;T;T;T;T	0.43688	0.94;0.94;0.94;0.96;0.94	4.99	-4.51	0.03483	.	1.439880	0.04269	N	0.341765	T	0.08313	0.0207	L	0.28274	0.84	0.09310	N	1	B	0.18863	0.031	B	0.14578	0.011	T	0.06481	-1.0824	10	0.28530	T	0.3	-0.3564	0.3973	0.00420	0.2932:0.1333:0.2641:0.3095	rs61731014	317	Q9NQ76	MEPE_HUMAN	V	317;348;293;204;317	ENSP00000416984:I317V;ENSP00000378534:I348V;ENSP00000422747:I293V;ENSP00000443491:I204V;ENSP00000354341:I317V	ENSP00000354341:I317V	I	+	1	0	MEPE	88985993	0.000000	0.05858	0.000000	0.03702	0.022000	0.10575	-0.044000	0.12023	-0.960000	0.03613	-0.290000	0.09829	ATT	A|0.983;G|0.017	0.017	strong		0.448	MEPE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253038.1		
FASN	2194	hgsc.bcm.edu	37	17	80045086	80045086	+	Silent	SNP	G	G	C	rs4485435	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	91	0	0		WXS	Illumina HiSeq	Phase_I	83	40	0.481928	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	
STOX2	56977	hgsc.bcm.edu	37	4	184931818	184931818	+	Silent	SNP	G	G	A	rs4861597	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:184931818G>A	ENST00000308497.4	+	3	3262	c.1827G>A	c.(1825-1827)acG>acA	p.T609T	STOX2_ENST00000438269.1_Silent_p.T609T	NM_020225.1	NP_064610.1	Q9P2F5	STOX2_HUMAN	storkhead box 2	609					embryo development (GO:0009790)|maternal placenta development (GO:0001893)					breast(1)|endometrium(7)|lung(6)	14		all_lung(41;1.89e-12)|Lung NSC(41;3.48e-12)|Colorectal(36;0.00435)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|all_hematologic(60;0.027)|Prostate(90;0.0283)		all cancers(43;2.85e-26)|Epithelial(43;2.27e-22)|OV - Ovarian serous cystadenocarcinoma(60;3.4e-10)|Colorectal(24;8.23e-06)|GBM - Glioblastoma multiforme(59;1.64e-05)|STAD - Stomach adenocarcinoma(60;3.6e-05)|COAD - Colon adenocarcinoma(29;4.37e-05)|LUSC - Lung squamous cell carcinoma(40;0.008)|READ - Rectum adenocarcinoma(43;0.227)		CTAGTGAGACGGTGCTCACGG	0.502													G|||	2144	0.428115	0.4123	0.3156	5008	,	,		20530	0.6022		0.2972	False		,,,				2504	0.4847				p.T609T		Atlas-SNP	.											.	STOX2	142	.	0			c.G1827A						PASS	.	G		1533,2383		301,931,726	54.0	55.0	55.0		1827	-7.6	0.1	4	dbSNP_111	55	2232,6076		318,1596,2240	no	coding-synonymous	STOX2	NM_020225.1		619,2527,2966	AA,AG,GG		26.8657,39.1471,30.8001		609/927	184931818	3765,8459	1958	4154	6112	SO:0001819	synonymous_variant	56977	exon3			TGAGACGGTGCTC	AB037813	CCDS47167.1	4q35.1	2014-09-11			ENSG00000173320	ENSG00000173320			25450	protein-coding gene	gene with protein product							Standard	XM_005263142		Approved	DKFZp762K222	uc003ivz.1	Q9P2F5	OTTHUMG00000160618	ENST00000308497.4:c.1827G>A	4.37:g.184931818G>A		Somatic	208	0	0		WXS	Illumina HiSeq	Phase_I	228	120	0.526316	NM_020225	A6H8U4|Q9NPS8	Silent	SNP	ENST00000308497.4	37	CCDS47167.1																																																																																			G|0.583;A|0.417	0.417	strong		0.502	STOX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361433.3	NM_020225	
MUC6	4588	hgsc.bcm.edu	37	11	1016849	1016849	+	Missense_Mutation	SNP	C	C	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:1016849C>G	ENST00000421673.2	-	31	6002	c.5952G>C	c.(5950-5952)atG>atC	p.M1984I		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming	1984	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.M1984I(2)		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)		ATGTTGCAGTCATAGGACCTG	0.582																																					p.M1984I		Atlas-SNP	.											MUC6_ENST00000421673,NS,carcinoma,0,2	MUC6	408	2	2	Substitution - Missense(2)	lung(2)	c.G5952C						scavenged	.						1544.0	1533.0	1537.0					11																	1016849		2203	4298	6501	SO:0001583	missense	4588	exon31			TGCAGTCATAGGA	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.5952G>C	11.37:g.1016849C>G	ENSP00000406861:p.Met1984Ile	Somatic	758	23	0.030343		WXS	Illumina HiSeq	Phase_I	1074	35	0.0325885	NM_005961	O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	Missense_Mutation	SNP	ENST00000421673.2	37	CCDS44513.1	.	.	.	.	.	.	.	.	.	.	c	0.326	-0.959077	0.02267	.	.	ENSG00000184956	ENST00000421673	T	0.17691	2.26	2.64	-5.29	0.02747	.	.	.	.	.	T	0.09598	0.0236	L	0.43152	1.355	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.27839	-1.0062	9	0.14656	T	0.56	.	1.5757	0.02624	0.1743:0.1847:0.3717:0.2692	.	1984	Q6W4X9	MUC6_HUMAN	I	1984	ENSP00000406861:M1984I	ENSP00000406861:M1984I	M	-	3	0	MUC6	1006849	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.496000	0.02291	-4.003000	0.00082	-2.547000	0.00178	ATG	.	.	none		0.582	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382120.2	XM_290540	
NAV2	89797	hgsc.bcm.edu	37	11	19970501	19970501	+	Silent	SNP	T	T	C	rs11025335	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:19970501T>C	ENST00000396087.3	+	11	2688	c.2589T>C	c.(2587-2589)caT>caC	p.H863H	NAV2_ENST00000527559.2_Silent_p.H792H|NAV2_ENST00000540292.1_Silent_p.H794H|NAV2_ENST00000360655.4_Silent_p.H776H|NAV2_ENST00000349880.4_Silent_p.H840H|NAV2_ENST00000396085.1_Silent_p.H840H	NM_001244963.1	NP_001231892.1	Q8IVL1	NAV2_HUMAN	neuron navigator 2	863					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						GTGTCTGCCATGTGGACGTCT	0.587													T|||	1308	0.261182	0.1036	0.2608	5008	,	,		18337	0.4395		0.2406	False		,,,				2504	0.3119				p.H863H		Atlas-SNP	.											.	NAV2	255	.	0			c.T2589C						PASS	.	T	,,	505,3893	231.7+/-245.5	26,453,1720	76.0	72.0	73.0		2328,2520,2520	-4.9	0.8	11	dbSNP_120	73	1906,6680	335.9+/-321.6	213,1480,2600	no	coding-synonymous,coding-synonymous,coding-synonymous	NAV2	NM_001111018.1,NM_145117.4,NM_182964.5	,,	239,1933,4320	CC,CT,TT		22.1989,11.4825,18.569	,,	776/2366,840/2430,840/2433	19970501	2411,10573	2199	4293	6492	SO:0001819	synonymous_variant	89797	exon11			CTGCCATGTGGAC	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.2589T>C	11.37:g.19970501T>C		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	109	21	0.192661	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|0.792;C|0.208	0.208	strong		0.587	NAV2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324112.1	NM_145117	
P2RY8	286530	hgsc.bcm.edu	37	X	1584817	1584817	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:1584817C>T	ENST00000381297.4	-	2	845	c.635G>A	c.(634-636)tGt>tAt	p.C212Y	P2RY8_ENST00000460672.1_5'Flank	NM_178129.4	NP_835230.1	Q86VZ1	P2RY8_HUMAN	purinergic receptor P2Y, G-protein coupled, 8	212						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled purinergic nucleotide receptor activity (GO:0045028)			endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(2)|lung(13)|prostate(1)	23		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				GGCCGTGTAACAAGCCACGGT	0.657			T	CRLF2	"""B-ALL, Downs associated ALL"""																																p.C212Y		Atlas-SNP	.		Dom	yes		"""X,Y"""	Xp22.3; Yp11.3	286530	"""purinergic receptor P2Y, G-protein coupled, 8"""		L	.	P2RY8	53	.	0			c.G635A						PASS	.						102.0	55.0	71.0					X																	1584817		2203	4295	6498	SO:0001583	missense	286530	exon2			GTGTAACAAGCCA	AA804531	CCDS14115.1	Xp22.33 and Yp11.3	2012-08-08			ENSG00000182162	ENSG00000182162		"""Pseudoautosomal regions / PAR1"", ""Purinergic receptors"", ""GPCR / Class A : Purinergic receptors, P2Y"""	15524	protein-coding gene	gene with protein product		300525				11004484	Standard	NM_178129		Approved	P2Y8	uc004cpz.2	Q86VZ1	OTTHUMG00000021060	ENST00000381297.4:c.635G>A	X.37:g.1584817C>T	ENSP00000370697:p.Cys212Tyr	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	68	27	0.397059	NM_178129		Missense_Mutation	SNP	ENST00000381297.4	37	CCDS14115.1	.	.	.	.	.	.	.	.	.	.	c	13.10	2.136811	0.37728	.	.	ENSG00000182162	ENST00000381297	T	0.42131	0.98	2.41	2.41	0.29592	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	U	0.000000	T	0.66557	0.2801	M	0.87682	2.9	0.09310	N	1	D	0.89917	1.0	D	0.97110	1.0	T	0.61436	-0.7063	10	0.87932	D	0	.	12.9335	0.58301	0.0:1.0:0.0:0.0	.	212	Q86VZ1	P2RY8_HUMAN	Y	212	ENSP00000370697:C212Y	ENSP00000370697:C212Y	C	-	2	0	P2RY8	1544817	1.000000	0.71417	0.993000	0.49108	0.058000	0.15608	6.011000	0.70760	0.838000	0.34948	0.279000	0.19357	TGT	.	.	none		0.657	P2RY8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055602.1	NM_178129	
OR5D16	390144	hgsc.bcm.edu	37	11	55606818	55606818	+	Silent	SNP	C	C	T	rs11231253	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:55606818C>T	ENST00000378396.1	+	1	591	c.591C>T	c.(589-591)agC>agT	p.S197S		NM_001005496.1	NP_001005496.1	Q8NGK9	OR5DG_HUMAN	olfactory receptor, family 5, subfamily D, member 16	197						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(2)|large_intestine(4)|lung(26)|ovary(5)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	44		all_epithelial(135;0.208)				CTTATCTCAGCCAGTTGCTTC	0.383													-|||	2269	0.453075	0.2746	0.4957	5008	,	,		22120	0.626		0.3638	False		,,,				2504	0.5777				p.S197S		Atlas-SNP	.											OR5D16,NS,adenoma,0,1	OR5D16	94	1	0			c.C591T						PASS	.	C		1342,3060		207,928,1066	191.0	165.0	174.0		591	-4.6	0.0	11	dbSNP_120	174	3174,5418		607,1960,1729	yes	coding-synonymous	OR5D16	NM_001005496.1		814,2888,2795	TT,TC,CC		36.9413,30.4861,34.7545		197/329	55606818	4516,8478	2201	4296	6497	SO:0001819	synonymous_variant	390144	exon1			TCTCAGCCAGTTG	AB065783	CCDS31512.1	11q11	2012-08-09			ENSG00000205029	ENSG00000205029		"""GPCR / Class A : Olfactory receptors"""	15283	protein-coding gene	gene with protein product							Standard	NM_001005496		Approved		uc010rio.2	Q8NGK9	OTTHUMG00000154233	ENST00000378396.1:c.591C>T	11.37:g.55606818C>T		Somatic	254	0	0		WXS	Illumina HiSeq	Phase_I	219	43	0.196347	NM_001005496	Q6IF65|Q96RB4	Silent	SNP	ENST00000378396.1	37	CCDS31512.1																																																																																			C|0.619;T|0.381	0.381	strong		0.383	OR5D16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334506.1	NM_001005496	
HDLBP	3069	hgsc.bcm.edu	37	2	242179134	242179134	+	Silent	SNP	G	G	A	rs10153800	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:242179134G>A	ENST00000391975.1	-	19	2720	c.2493C>T	c.(2491-2493)ggC>ggT	p.G831G	HDLBP_ENST00000391976.2_Silent_p.G831G|HDLBP_ENST00000310931.4_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	105	0	0		WXS	Illumina HiSeq	Phase_I	92	42	0.456522	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	
SYT16	83851	hgsc.bcm.edu	37	14	62463214	62463214	+	Silent	SNP	C	C	T	rs1889806	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:62463214C>T	ENST00000430451.2	+	1	674	c.477C>T	c.(475-477)gaC>gaT	p.D159D	SYT16_ENST00000446982.2_Silent_p.D159D	NM_031914.2	NP_114120.2	Q17RD7	SYT16_HUMAN	synaptotagmin XVI	159					exocytosis (GO:0006887)					central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(11)|lung(12)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	35				OV - Ovarian serous cystadenocarcinoma(108;0.0438)|BRCA - Breast invasive adenocarcinoma(234;0.118)		ATGGCTTTGACAGCCAGCTCC	0.453													C|||	2806	0.560304	0.6195	0.5879	5008	,	,		20252	0.749		0.4036	False		,,,				2504	0.4274				p.D159D		Atlas-SNP	.											SYT16,NS,carcinoma,+2,1	SYT16	144	1	0			c.C477T						PASS	.	C		2098,1630		592,914,358	119.0	115.0	116.0		477	2.3	1.0	14	dbSNP_92	116	3356,4864		687,1982,1441	no	coding-synonymous	SYT16	NM_031914.2		1279,2896,1799	TT,TC,CC		40.8273,43.7232,45.6478		159/646	62463214	5454,6494	1864	4110	5974	SO:0001819	synonymous_variant	83851	exon1			CTTTGACAGCCAG	BC040924	CCDS45121.1	14q23.2	2014-07-02	2005-07-15	2005-07-15	ENSG00000139973	ENSG00000139973		"""Synaptotagmins"""	23142	protein-coding gene	gene with protein product	"""synaptotagmin XIV-related"", "" chr14 synaptotagmin"""	610950	"""synaptotagmin XIV-like"""	SYT14L		11543631	Standard	NM_031914		Approved	yt14r, CHR14SYT, Strep14	uc001xfu.1	Q17RD7	OTTHUMG00000171106	ENST00000430451.2:c.477C>T	14.37:g.62463214C>T		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	82	41	0.5	NM_031914	B4DZH2|B7ZL60|C9J8I3|Q707N2|Q7Z441|Q8IUU0|Q9BQR8	Silent	SNP	ENST00000430451.2	37	CCDS45121.1																																																																																			C|0.433;T|0.567	0.567	strong		0.453	SYT16-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000411700.1	NM_031914	
BRCA2	675	hgsc.bcm.edu	37	13	32911888	32911888	+	Silent	SNP	A	A	G	rs1801406	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:32911888A>G	ENST00000380152.3	+	11	3629	c.3396A>G	c.(3394-3396)aaA>aaG	p.K1132K	BRCA2_ENST00000544455.1_Silent_p.K1132K			P51587	BRCA2_HUMAN	breast cancer 2, early onset	1132					brain development (GO:0007420)|cell aging (GO:0007569)|centrosome duplication (GO:0051298)|cytokinesis (GO:0000910)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|female gonad development (GO:0008585)|hemopoiesis (GO:0030097)|histone H3 acetylation (GO:0043966)|histone H4 acetylation (GO:0043967)|inner cell mass cell proliferation (GO:0001833)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|male meiosis I (GO:0007141)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|nucleotide-excision repair (GO:0006289)|oocyte maturation (GO:0001556)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokinesis (GO:0032465)|replication fork protection (GO:0048478)|response to gamma radiation (GO:0010332)|response to UV-C (GO:0010225)|response to X-ray (GO:0010165)|spermatogenesis (GO:0007283)	BRCA2-MAGE-D1 complex (GO:0033593)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)|secretory granule (GO:0030141)	gamma-tubulin binding (GO:0043015)|H3 histone acetyltransferase activity (GO:0010484)|H4 histone acetyltransferase activity (GO:0010485)|protease binding (GO:0002020)|single-stranded DNA binding (GO:0003697)			NS(3)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(32)|liver(1)|lung(41)|oesophagus(5)|ovary(22)|pancreas(4)|prostate(3)|salivary_gland(1)|skin(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	183		Lung SC(185;0.0262)		all cancers(112;7.13e-07)|Epithelial(112;1.59e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000732)|BRCA - Breast invasive adenocarcinoma(63;0.0291)|GBM - Glioblastoma multiforme(144;0.0704)		AGTTTAGAAAACCAAGCTACA	0.358			"""D, Mis, N, F, S"""		"""breast, ovarian, pancreatic"""	"""breast, ovarian, pancreatic, leukemia  (FANCB, FANCD1)"""		Homologous recombination	Pancreatic Cancer, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Prostate Cancer;Hereditary Breast-Ovarian Cancer, BRCA2 type;Fanconi Anemia type D1, bi-allelic BRCA2 mutations;Fanconi Anemia	TCGA Ovarian(8;0.087)			A|||	1336	0.266773	0.2095	0.2378	5008	,	,		19807	0.3681		0.2753	False		,,,				2504	0.2515				p.K1132K	Esophageal Squamous(138;838 1285 7957 30353 30468 36915 49332)	Atlas-SNP	.	yes	Rec	yes	Hereditary breast/ovarian cancer	13	13q12	675	familial breast/ovarian cancer gene 2		"""L, E"""	.	BRCA2	812	.	0			c.A3396G						PASS	.	A		996,3410	351.1+/-311.1	107,782,1314	60.0	61.0	61.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	3396	-3.1	0.7	13	dbSNP_89	61	2643,5955	415.9+/-351.9	400,1843,2056	no	coding-synonymous	BRCA2	NM_000059.3		507,2625,3370	GG,GA,AA		30.7397,22.6055,27.9837		1132/3419	32911888	3639,9365	2203	4299	6502	SO:0001819	synonymous_variant	675	exon11	Familial Cancer Database	incl.: Hereditary Pancreatic Adenocarcinoma, Insulin-Dependent Diabetes Mellitus - Exocrine Insufficiency - Familial Pancreatic Cancer, PNCA1;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;HPC; ;FANCD1;Pancytopenia Dysmelia, FA (several complementation groups)	TAGAAAACCAAGC	U43746	CCDS9344.1	13q12-q13	2014-09-17	2003-10-14		ENSG00000139618	ENSG00000139618		"""Fanconi anemia, complementation groups"""	1101	protein-coding gene	gene with protein product	"""BRCA1/BRCA2-containing complex, subunit 2"""	600185	"""Fanconi anemia, complementation group D1"""	FANCD1, FACD, FANCD		8091231, 7581463, 15057823	Standard	NM_000059		Approved	FAD, FAD1, BRCC2	uc001uub.1	P51587	OTTHUMG00000017411	ENST00000380152.3:c.3396A>G	13.37:g.32911888A>G		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	63	63	1	NM_000059	O00183|O15008|Q13879|Q5TBJ7	Silent	SNP	ENST00000380152.3	37	CCDS9344.1																																																																																			A|0.722;G|0.278	0.278	strong		0.358	BRCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046000.2	NM_000059	
SCIN	85477	hgsc.bcm.edu	37	7	12610451	12610451	+	Silent	SNP	G	G	A	rs76096341	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:12610451G>A	ENST00000297029.5	+	1	140	c.39G>A	c.(37-39)gcG>gcA	p.A13A	AC005281.2_ENST00000433040.1_RNA	NM_001112706.2	NP_001106177.1	Q9Y6U3	ADSV_HUMAN	scinderin	13	Actin-severing. {ECO:0000255}.				actin filament capping (GO:0051693)|actin filament severing (GO:0051014)|actin nucleation (GO:0045010)|calcium ion-dependent exocytosis (GO:0017156)|negative regulation of cell proliferation (GO:0008285)|positive regulation of apoptotic process (GO:0043065)|positive regulation of megakaryocyte differentiation (GO:0045654)|positive regulation of secretion (GO:0051047)|regulation of chondrocyte differentiation (GO:0032330)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)	1-phosphatidylinositol binding (GO:0005545)|actin binding (GO:0003779)|actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylserine binding (GO:0001786)			endometrium(3)|kidney(1)|large_intestine(2)|lung(9)|ovary(2)	17				UCEC - Uterine corpus endometrioid carcinoma (126;0.195)		TCGCCCGGGCGGGCAAGCAGG	0.652													G|||	115	0.0229633	0.0045	0.0317	5008	,	,		15575	0.0		0.0696	False		,,,				2504	0.0174				p.A13A		Atlas-SNP	.											.	SCIN	105	.	0			c.G39A						PASS	.	G		22,1360		0,22,669	17.0	27.0	24.0		39	-7.9	0.1	7	dbSNP_132	24	149,3031		5,139,1446	no	coding-synonymous	SCIN	NM_001112706.2		5,161,2115	AA,AG,GG		4.6855,1.5919,3.7484		13/716	12610451	171,4391	691	1590	2281	SO:0001819	synonymous_variant	85477	exon1			CCGGGCGGGCAAG	AF276507	CCDS47545.1, CCDS47546.1	7p21.3	2006-04-25			ENSG00000006747	ENSG00000006747			21695	protein-coding gene	gene with protein product		613416					Standard	NM_033128		Approved	adseverin, KIAA1905	uc003ssn.4	Q9Y6U3	OTTHUMG00000152385	ENST00000297029.5:c.39G>A	7.37:g.12610451G>A		Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	112	30	0.267857	NM_001112706	A8K2U8|Q8NBZ6|Q8WU97|Q96JC7|Q96PY2	Silent	SNP	ENST00000297029.5	37	CCDS47545.1																																																																																			G|0.970;A|0.030	0.030	strong		0.652	SCIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326041.1	NM_033128	
AP3B1	8546	hgsc.bcm.edu	37	5	77473165	77473165	+	Silent	SNP	A	A	G	rs4532349	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:77473165A>G	ENST00000255194.6	-	9	1213	c.1038T>C	c.(1036-1038)aaT>aaC	p.N346N	AP3B1_ENST00000519295.1_Silent_p.N297N	NM_001271769.1	NP_001258698.1	O00203	AP3B1_HUMAN	adaptor-related protein complex 3, beta 1 subunit	346					anterograde axon cargo transport (GO:0008089)|anterograde synaptic vesicle transport (GO:0048490)|antigen processing and presentation, exogenous lipid antigen via MHC class Ib (GO:0048007)|blood coagulation (GO:0007596)|intracellular protein transport (GO:0006886)|melanosome organization (GO:0032438)|positive regulation of NK T cell differentiation (GO:0051138)|protein targeting to lysosome (GO:0006622)	AP-3 adaptor complex (GO:0030123)|cytoplasmic vesicle (GO:0031410)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	GTP-dependent protein binding (GO:0030742)|protein phosphatase binding (GO:0019903)			breast(5)|central_nervous_system(2)|cervix(1)|endometrium(3)|large_intestine(12)|lung(12)|prostate(1)|skin(2)|urinary_tract(1)	39		all_lung(232;0.000397)|Lung NSC(167;0.00106)|Ovarian(174;0.0105)|Prostate(461;0.215)		OV - Ovarian serous cystadenocarcinoma(54;8.23e-47)|Epithelial(54;2.74e-41)|all cancers(79;4.8e-36)		TGACCTACCTATTGCTACGAA	0.328									Hermansky-Pudlak syndrome				A|||	715	0.142772	0.0968	0.3026	5008	,	,		17278	0.0724		0.1968	False		,,,				2504	0.1084				p.N346N		Atlas-SNP	.											AP3B1,colon,carcinoma,0,1	AP3B1	94	1	0			c.T1038C						PASS	.	A		529,3877	240.9+/-251.5	39,451,1713	96.0	92.0	94.0		1038	3.0	1.0	5	dbSNP_111	94	1905,6695	338.0+/-322.5	232,1441,2627	no	coding-synonymous	AP3B1	NM_003664.3		271,1892,4340	GG,GA,AA		22.1512,12.0064,18.7144		346/1095	77473165	2434,10572	2203	4300	6503	SO:0001819	synonymous_variant	8546	exon9	Familial Cancer Database	HPS, HPS1-8	CTACCTATTGCTA	U81504	CCDS4041.1, CCDS64186.1	5q14.1	2014-09-17			ENSG00000132842	ENSG00000132842			566	protein-coding gene	gene with protein product		603401				9182526, 9151686	Standard	NM_003664		Approved	ADTB3A, HPS2	uc003kfj.4	O00203	OTTHUMG00000106919	ENST00000255194.6:c.1038T>C	5.37:g.77473165A>G		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	149	103	0.691275	NM_003664	E5RJ68|O00580|Q7Z393|Q9HD66	Silent	SNP	ENST00000255194.6	37	CCDS4041.1																																																																																			A|0.832;G|0.168	0.168	strong		0.328	AP3B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000225548.2		
MUC4	4585	hgsc.bcm.edu	37	3	195509879	195509879	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195509879A>G	ENST00000463781.3	-	2	9031	c.8572T>C	c.(8572-8574)Tcc>Ccc	p.S2858P	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.S2858P	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.S2858P(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)		TGACCTGTGGACACTGAGGAA	0.587																																					p.S2858P		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	2	Substitution - Missense(2)	endometrium(2)	c.T8572C						PASS	.						43.0	30.0	34.0					3																	195509879		682	1572	2254	SO:0001583	missense	4585	exon2			CTGTGGACACTGA	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.8572T>C	3.37:g.195509879A>G	ENSP00000417498:p.Ser2858Pro	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	131	13	0.0992366	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	a	4.416	0.076953	0.08485	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.38887	1.11;1.34	.	.	.	.	.	.	.	.	T	0.37892	0.1020	N	0.19112	0.55	0.09310	N	1	D	0.53885	0.963	D	0.65874	0.939	T	0.17289	-1.0374	7	.	.	.	.	1.4356	0.02342	0.333:0.0:0.3289:0.3381	.	2730	E7ESK3	.	P	2858	ENSP00000417498:S2858P;ENSP00000420243:S2858P	.	S	-	1	0	MUC4	196994658	0.001000	0.12720	0.000000	0.03702	0.000000	0.00434	-0.006000	0.12833	-0.000000	0.14550	0.000000	0.15137	TCC	.	.	none		0.587	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
FUNDC1	139341	hgsc.bcm.edu	37	X	44401295	44401295	+	Silent	SNP	T	T	G	rs41298452	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:44401295T>G	ENST00000378045.4	-	2	249	c.81A>C	c.(79-81)gcA>gcC	p.A27A	FUNDC1_ENST00000483115.1_5'UTR	NM_173794.3	NP_776155.1	Q8IVP5	FUND1_HUMAN	FUN14 domain containing 1	27					mitochondrion degradation (GO:0000422)|response to hypoxia (GO:0001666)	integral component of mitochondrial outer membrane (GO:0031307)|mitochondrial outer membrane (GO:0005741)				breast(1)|large_intestine(2)|lung(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	6						GGTGTCTTCTTGCATACTCAG	0.393													T|||	343	0.0908609	0.1233	0.0346	3775	,	,		14088	0.0665		0.0268	False		,,,				2504	0.0634				p.A27A		Atlas-SNP	.											.	FUNDC1	15	.	0			c.A81C						PASS	.	T		560,3275		34,406,86,1192,485	74.0	58.0	64.0		81	-1.0	1.0	X	dbSNP_127	64	270,6458		5,182,78,2241,1794	no	coding-synonymous	FUNDC1	NM_173794.3		39,588,164,3433,2279	GG,GT,G,TT,T		4.0131,14.6023,7.8576		27/156	44401295	830,9733	2203	4300	6503	SO:0001819	synonymous_variant	139341	exon2			TCTTCTTGCATAC	BC042813	CCDS14263.1	Xp11.4	2005-09-22			ENSG00000069509	ENSG00000069509			28746	protein-coding gene	gene with protein product		300871				12477932	Standard	NM_173794		Approved	MGC51029	uc004dgc.3	Q8IVP5	OTTHUMG00000021399	ENST00000378045.4:c.81A>C	X.37:g.44401295T>G		Somatic	309	2	0.00647249		WXS	Illumina HiSeq	Phase_I	207	205	0.990338	NM_173794		Silent	SNP	ENST00000378045.4	37	CCDS14263.1																																																																																			T|0.917;G|0.083	0.083	strong		0.393	FUNDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056320.1	NM_173794	
STPG2	285555	hgsc.bcm.edu	37	4	98893476	98893476	+	Silent	SNP	C	C	T	rs783959	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:98893476C>T	ENST00000295268.3	-	7	977	c.888G>A	c.(886-888)tcG>tcA	p.S296S		NM_174952.2	NP_777612.1	Q8N412	STPG2_HUMAN	sperm-tail PG-rich repeat containing 2	296								p.S296S(2)									CTTTCTGAACCGAGAAGAAAG	0.363													C|||	2050	0.409345	0.3714	0.5403	5008	,	,		15237	0.2431		0.4751	False		,,,				2504	0.4714				p.S296S		Atlas-SNP	.											C4orf37,NS,carcinoma,0,2	.	.	2	2	Substitution - coding silent(2)	prostate(1)|stomach(1)	c.G888A						scavenged	.	C		1577,2829	492.5+/-362.4	296,985,922	82.0	82.0	82.0		888	0.3	0.0	4	dbSNP_86	82	4000,4600	552.9+/-386.2	937,2126,1237	no	coding-synonymous	C4orf37	NM_174952.2		1233,3111,2159	TT,TC,CC		46.5116,35.7921,42.8802		296/460	98893476	5577,7429	2203	4300	6503	SO:0001819	synonymous_variant	285555	exon7			CTGAACCGAGAAG	BC036870	CCDS3645.1	4q22.3-q23	2013-10-11	2012-07-30	2012-07-30	ENSG00000163116	ENSG00000163116			28712	protein-coding gene	gene with protein product			"""chromosome 4 open reading frame 37"""	C4orf37		23031811	Standard	NM_174952		Approved	MGC46496	uc003htt.2	Q8N412	OTTHUMG00000131009	ENST00000295268.3:c.888G>A	4.37:g.98893476C>T		Somatic	261	2	0.00766284		WXS	Illumina HiSeq	Phase_I	198	196	0.989899	NM_174952		Silent	SNP	ENST00000295268.3	37	CCDS3645.1																																																																																			C|0.581;T|0.419	0.419	strong		0.363	STPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253642.1	NM_174952	
BCL2L14	79370	hgsc.bcm.edu	37	12	12247616	12247616	+	Silent	SNP	T	T	C	rs11054683	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:12247616T>C	ENST00000308721.5	+	5	903	c.697T>C	c.(697-699)Ttg>Ctg	p.L233L	BCL2L14_ENST00000266434.4_3'UTR|BCL2L14_ENST00000396367.1_Silent_p.L233L|BCL2L14_ENST00000586576.1_Silent_p.L266L|BCL2L14_ENST00000589718.1_Silent_p.L233L|BCL2L14_ENST00000396369.1_Intron	NM_138723.1	NP_620049.1	Q9BZR8	B2L14_HUMAN	BCL2-like 14 (apoptosis facilitator)	233					apoptotic process (GO:0006915)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|regulation of apoptotic process (GO:0042981)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular organelle (GO:0043229)|membrane (GO:0016020)	protein kinase binding (GO:0019901)			large_intestine(1)|lung(2)|skin(3)	6		Prostate(47;0.0872)		BRCA - Breast invasive adenocarcinoma(232;0.154)		AGATAAGGCTTTGATGGGCCA	0.483													T|||	802	0.160144	0.2216	0.1671	5008	,	,		20506	0.0188		0.2525	False		,,,				2504	0.1227				p.L233L		Atlas-SNP	.											.	BCL2L14	47	.	0			c.T697C						PASS	.	T	,,	928,3478	356.6+/-313.6	99,730,1374	124.0	123.0	123.0		,697,697	0.3	0.1	12	dbSNP_120	123	2121,6479	366.1+/-334.2	262,1597,2441	no	utr-3,coding-synonymous,coding-synonymous	BCL2L14	NM_030766.1,NM_138722.1,NM_138723.1	,,	361,2327,3815	CC,CT,TT		24.6628,21.0622,23.443	,,	,233/328,233/328	12247616	3049,9957	2203	4300	6503	SO:0001819	synonymous_variant	79370	exon5			AAGGCTTTGATGG	AF281254	CCDS8645.1, CCDS8646.1	12p13-p12	2014-03-07			ENSG00000121380	ENSG00000121380			16657	protein-coding gene	gene with protein product		606126				11054413	Standard	NM_030766		Approved	BCLG, BCL-G	uc001rac.3	Q9BZR8	OTTHUMG00000159528	ENST00000308721.5:c.697T>C	12.37:g.12247616T>C		Somatic	246	0	0		WXS	Illumina HiSeq	Phase_I	195	77	0.394872	NM_138723	A8KAD0|Q96QR5|Q9BZR7	Silent	SNP	ENST00000308721.5	37	CCDS8645.1																																																																																			T|0.781;C|0.219	0.219	strong		0.483	BCL2L14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355994.3	NM_030766	
SLC7A10	56301	hgsc.bcm.edu	37	19	33700281	33700281	+	Silent	SNP	C	C	A	rs2303094	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:33700281C>A	ENST00000253188.4	-	10	1520	c.1374G>T	c.(1372-1374)acG>acT	p.T458T	CTD-2540B15.13_ENST00000609744.1_RNA	NM_019849.2	NP_062823.1	Q9NS82	AAA1_HUMAN	solute carrier family 7 (neutral amino acid transporter light chain, asc system), member 10	458					amino acid transport (GO:0006865)|blood coagulation (GO:0007596)|D-alanine transport (GO:0042941)|D-serine transport (GO:0042942)|ion transport (GO:0006811)|L-serine transport (GO:0015825)|leukocyte migration (GO:0050900)|neutral amino acid transport (GO:0015804)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	L-serine transmembrane transporter activity (GO:0015194)|neutral amino acid transmembrane transporter activity (GO:0015175)	p.T458T(1)		central_nervous_system(1)|kidney(1)|large_intestine(4)|lung(8)|ovary(2)|skin(1)|stomach(1)	18	Esophageal squamous(110;0.137)					TGGGCACCCCCGTAAGGATGA	0.567													C|||	250	0.0499201	0.0076	0.0764	5008	,	,		16772	0.122		0.0427	False		,,,				2504	0.0215				p.T458T		Atlas-SNP	.											SLC7A10,NS,carcinoma,0,1	SLC7A10	43	1	1	Substitution - coding silent(1)	stomach(1)	c.G1374T						PASS	.	C		84,4322	70.9+/-108.8	0,84,2119	84.0	84.0	84.0		1374	-9.5	0.4	19	dbSNP_100	84	459,8141	137.1+/-194.1	16,427,3857	no	coding-synonymous	SLC7A10	NM_019849.2		16,511,5976	AA,AC,CC		5.3372,1.9065,4.175		458/524	33700281	543,12463	2203	4300	6503	SO:0001819	synonymous_variant	56301	exon10			CACCCCCGTAAGG	AB037670	CCDS12431.1	19q13.11	2013-05-28	2011-07-12		ENSG00000130876	ENSG00000130876		"""Solute carriers"""	11058	protein-coding gene	gene with protein product		607959				10734121, 10863037	Standard	NM_019849		Approved	asc-1	uc002num.2	Q9NS82	OTTHUMG00000180344	ENST00000253188.4:c.1374G>T	19.37:g.33700281C>A		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	69	39	0.565217	NM_019849	B2RE84	Silent	SNP	ENST00000253188.4	37	CCDS12431.1																																																																																			C|0.956;A|0.044	0.044	strong		0.567	SLC7A10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450846.2	NM_019849	
KRTAP10-10	353333	hgsc.bcm.edu	37	21	46057958	46057958	+	Silent	SNP	C	C	T	rs4818951	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:46057958C>T	ENST00000380095.1	+	1	686	c.624C>T	c.(622-624)tcC>tcT	p.S208S	TSPEAR_ENST00000323084.4_Intron	NM_181688.1	NP_859016.1	P60014	KR10A_HUMAN	keratin associated protein 10-10	208	15 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				NS(1)|endometrium(2)|kidney(1)|lung(6)|prostate(1)|skin(2)	13						CCGTCCCCTCCTGCGGTGCCT	0.697													C|||	3206	0.640176	0.4092	0.6931	5008	,	,		18953	0.6687		0.7594	False		,,,				2504	0.7628				p.S208S		Atlas-SNP	.											.	KRTAP10-10	37	.	0			c.C624T						PASS	.	C	,	1952,2454	547.0+/-377.2	407,1138,658	86.0	91.0	89.0		,624	2.3	0.5	21	dbSNP_111	89	6136,2464	691.7+/-404.5	2207,1722,371	no	intron,coding-synonymous	TSPEAR,KRTAP10-10	NM_144991.2,NM_181688.1	,	2614,2860,1029	TT,TC,CC		28.6512,44.3032,37.8133	,	,208/252	46057958	8088,4918	2203	4300	6503	SO:0001819	synonymous_variant	353333	exon1			CCCCTCCTGCGGT	AJ566387	CCDS33585.1	21q22.3	2006-03-13			ENSG00000221859	ENSG00000221859		"""Keratin associated proteins"""	22972	protein-coding gene	gene with protein product							Standard	NM_181688		Approved	KAP10.10, KAP18.10, KRTAP18-10	uc002zfq.3	P60014	OTTHUMG00000057631	ENST00000380095.1:c.624C>T	21.37:g.46057958C>T		Somatic	194	0	0		WXS	Illumina HiSeq	Phase_I	195	192	0.984615	NM_181688		Silent	SNP	ENST00000380095.1	37	CCDS33585.1																																																																																			C|0.368;T|0.632	0.632	strong		0.697	KRTAP10-10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128034.1	NM_181688	
OR10C1	442194	hgsc.bcm.edu	37	6	29408528	29408528	+	Missense_Mutation	SNP	A	A	G	rs2074464	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:29408528A>G	ENST00000444197.2	+	1	1446	c.736A>G	c.(736-738)Atg>Gtg	p.M246V	OR11A1_ENST00000377149.1_Intron	NM_013941.3	NP_039229.3	Q96KK4	O10C1_HUMAN	olfactory receptor, family 10, subfamily C, member 1 (gene/pseudogene)	246			M -> V (in dbSNP:rs2074464). {ECO:0000269|PubMed:12213199, ECO:0000269|PubMed:14574404}.			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(2)|kidney(1)|large_intestine(3)|liver(2)|lung(14)|ovary(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	27						CCACCTGATCATGGTCTCCCT	0.582													G|||	2963	0.591653	0.6346	0.5303	5008	,	,		18506	0.5774		0.5338	False		,,,				2504	0.6513				p.M246V		Atlas-SNP	.											.	OR10C1	58	.	0			c.A736G						PASS	.	G	VAL/MET	2071,951		730,611,170	272.0	306.0	294.0		736	3.5	0.2	6	dbSNP_96	294	2978,2438		841,1296,571	yes	missense	OR10C1	NM_013941.3	21	1571,1907,741	GG,GA,AA		45.0148,31.4692,40.1635	benign	246/313	29408528	5049,3389	1511	2708	4219	SO:0001583	missense	442194	exon1			CTGATCATGGTCT		CCDS34364.1	6p22.2-p21.31	2013-10-10	2013-10-10		ENSG00000206474	ENSG00000206474		"""GPCR / Class A : Olfactory receptors"""	8165	protein-coding gene	gene with protein product			"""olfactory receptor, family 10, subfamily C, member 2"", ""olfactory receptor, family 10, subfamily C, member 1"""	OR10C2			Standard	NM_013941		Approved	hs6M1-17, OR10C1P	uc011dlp.2	Q96KK4	OTTHUMG00000031207	ENST00000444197.2:c.736A>G	6.37:g.29408528A>G	ENSP00000419119:p.Met246Val	Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	155	68	0.43871	NM_013941	Q5SUN7|Q96R18	Missense_Mutation	SNP	ENST00000444197.2	37	CCDS34364.1	1300	0.5952380952380952	381	0.774390243902439	201	0.5552486187845304	302	0.527972027972028	416	0.5488126649076517	G	0.172	-1.070339	0.01918	0.685308	0.549852	ENSG00000206474	ENST00000444197	T	0.00015	9.15	3.49	3.49	0.39957	GPCR, rhodopsin-like superfamily (1);	0.000000	0.35407	N	0.003229	T	0.00012	0.0000	N	0.00003	-3.48	0.50467	P	1.2999999999996348E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.16247	-1.0409	9	0.02654	T	1	.	10.6625	0.45710	0.0971:0.0:0.9029:0.0	rs2074464;rs17177660;rs52805749;rs58298350;rs2074464	246	Q96KK4	O10C1_HUMAN	V	246	ENSP00000419119:M246V	ENSP00000419119:M246V	M	+	1	0	OR10C1	29516507	0.001000	0.12720	0.170000	0.22879	0.665000	0.39181	0.331000	0.19733	0.695000	0.31675	-0.172000	0.13284	ATG	T|0.005;G|0.594;A|0.401	0.594	strong		0.582	OR10C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076415.2		
DSG1	1828	hgsc.bcm.edu	37	18	28934681	28934681	+	Missense_Mutation	SNP	A	A	T	rs3752095	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:28934681A>T	ENST00000257192.4	+	15	2734	c.2522A>T	c.(2521-2523)tAc>tTc	p.Y841F	RP11-534N16.1_ENST00000578119.1_RNA|RP11-534N16.1_ENST00000581856.1_RNA|RP11-534N16.1_ENST00000578477.1_RNA|DSG1_ENST00000462981.2_Missense_Mutation_p.Y200F|RP11-534N16.1_ENST00000581452.1_RNA	NM_001942.2	NP_001933.2	Q02413	DSG1_HUMAN	desmoglein 1	841			Y -> F (in dbSNP:rs3752095).		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)			ACCGAGTCTTACACCACCTCT	0.527													A|||	578	0.115415	0.1256	0.0836	5008	,	,		21622	0.0813		0.1412	False		,,,				2504	0.1329				p.Y841F		Atlas-SNP	.											.	DSG1	176	.	0			c.A2522T						PASS	.	A	PHE/TYR	611,3795	265.9+/-266.9	39,533,1631	223.0	187.0	199.0		2522	5.8	1.0	18	dbSNP_107	199	1169,7431	239.9+/-270.8	70,1029,3201	yes	missense	DSG1	NM_001942.2	22	109,1562,4832	TT,TA,AA		13.593,13.8675,13.686	probably-damaging	841/1050	28934681	1780,11226	2203	4300	6503	SO:0001583	missense	1828	exon15			AGTCTTACACCAC	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.2522A>T	18.37:g.28934681A>T	ENSP00000257192:p.Tyr841Phe	Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	155	86	0.554839	NM_001942	B7Z845	Missense_Mutation	SNP	ENST00000257192.4	37	CCDS11896.1	254	0.1163003663003663	65	0.13211382113821138	36	0.09944751381215469	48	0.08391608391608392	105	0.13852242744063326	A	13.18	2.158766	0.38119	0.138675	0.13593	ENSG00000134760	ENST00000257192	T	0.69175	-0.38	5.76	5.76	0.90799	.	0.000000	0.64402	D	0.000011	T	0.03348	0.0097	M	0.88775	2.98	0.22185	P	0.999301881	D	0.76494	0.999	D	0.72982	0.979	T	0.50423	-0.8830	9	0.72032	D	0.01	.	16.0817	0.81010	1.0:0.0:0.0:0.0	rs3752095;rs17715907;rs52827858;rs59956720;rs3752095	841	Q02413	DSG1_HUMAN	F	841	ENSP00000257192:Y841F	ENSP00000257192:Y841F	Y	+	2	0	DSG1	27188679	1.000000	0.71417	0.998000	0.56505	0.847000	0.48162	6.414000	0.73318	2.206000	0.71126	0.383000	0.25322	TAC	A|0.864;T|0.136	0.136	strong		0.527	DSG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254947.1	NM_001942	
CHGA	1113	hgsc.bcm.edu	37	14	93398849	93398849	+	Missense_Mutation	SNP	G	G	A	rs9658664	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:93398849G>A	ENST00000216492.5	+	7	1223	c.943G>A	c.(943-945)Ggc>Agc	p.G315S	CHGA_ENST00000334654.4_Missense_Mutation_p.G164S	NM_001275.3	NP_001266.1	P10645	CMGA_HUMAN	chromogranin A (parathyroid secretory protein 1)	315			G -> S (in dbSNP:rs9658664).		regulation of blood pressure (GO:0008217)	extracellular region (GO:0005576)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|secretory granule (GO:0030141)				cervix(1)|large_intestine(1)|lung(3)|skin(3)	8		all_cancers(154;0.0843)		Epithelial(152;0.102)|COAD - Colon adenocarcinoma(157;0.208)|all cancers(159;0.224)		GGTCCCGCAAGGCCTCTTCCG	0.637													G|||	67	0.0133786	0.0008	0.0	5008	,	,		17786	0.0		0.0089	False		,,,				2504	0.0583				p.G315S	Colon(31;154 822 45066 49155)|NSCLC(28;804 1157 13734 25204)	Atlas-SNP	.											.	CHGA	32	.	0			c.G943A						PASS	.	G	SER/GLY	8,4344		0,8,2168	36.0	21.0	26.0		943	3.1	0.0	14	dbSNP_119	26	69,8443		0,69,4187	yes	missense	CHGA	NM_001275.3	56	0,77,6355	AA,AG,GG		0.8106,0.1838,0.5986	benign	315/458	93398849	77,12787	2176	4256	6432	SO:0001583	missense	1113	exon7			CCGCAAGGCCTCT		CCDS9906.1	14q32	2012-10-02			ENSG00000100604	ENSG00000100604			1929	protein-coding gene	gene with protein product	"""vasostatin"", ""pancreastatin"", ""parastatin"""	118910				3403545	Standard	NM_001275		Approved		uc001ybc.4	P10645		ENST00000216492.5:c.943G>A	14.37:g.93398849G>A	ENSP00000216492:p.Gly315Ser	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	45	20	0.444444	NM_001275	B2R9E9|Q53FA8|Q6NR84|Q96E84|Q96GL7|Q9BQB5	Missense_Mutation	SNP	ENST00000216492.5	37	CCDS9906.1	10	0.004578754578754579	2	0.0040650406504065045	0	0.0	0	0.0	8	0.010554089709762533	G	8.995	0.978781	0.18812	0.001838	0.008106	ENSG00000100604	ENST00000216492;ENST00000334654	T;T	0.01474	4.85;4.85	4.95	3.07	0.35406	.	0.771697	0.11631	N	0.544808	T	0.01835	0.0058	L	0.50333	1.59	0.09310	N	1	B;B	0.23442	0.004;0.085	B;B	0.31614	0.009;0.133	T	0.46857	-0.9161	10	0.06236	T	0.91	-2.2368	14.2623	0.66092	0.0:0.284:0.716:0.0	rs9658664;rs52795344;rs9658664	164;315	G5E968;P10645	.;CMGA_HUMAN	S	315;164	ENSP00000216492:G315S;ENSP00000334023:G164S	ENSP00000216492:G315S	G	+	1	0	CHGA	92468602	0.898000	0.30612	0.003000	0.11579	0.333000	0.28666	3.882000	0.56160	0.461000	0.27071	0.555000	0.69702	GGC	G|0.992;A|0.008	0.008	strong		0.637	CHGA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412411.1	NM_001275	
ROCK2	9475	hgsc.bcm.edu	37	2	11359120	11359120	+	Missense_Mutation	SNP	G	G	T	rs2230774	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:11359120G>T	ENST00000315872.6	-	10	1740	c.1292C>A	c.(1291-1293)aCt>aAt	p.T431N	ROCK2_ENST00000401753.1_Missense_Mutation_p.T188N	NM_004850.3	NP_004841.2	O75116	ROCK2_HUMAN	Rho-associated, coiled-coil containing protein kinase 2	431	Interaction with PPP1R12A.		T -> N (in dbSNP:rs2230774). {ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:9734811, ECO:0000269|PubMed:9933571}.		actin cytoskeleton organization (GO:0030036)|axon guidance (GO:0007411)|centrosome duplication (GO:0051298)|cytokinesis (GO:0000910)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|intracellular signal transduction (GO:0035556)|negative regulation of angiogenesis (GO:0016525)|neural tube closure (GO:0001843)|positive regulation of centrosome duplication (GO:0010825)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell adhesion (GO:0030155)|regulation of cell motility (GO:2000145)|regulation of circadian rhythm (GO:0042752)|regulation of establishment of cell polarity (GO:2000114)|regulation of focal adhesion assembly (GO:0051893)|regulation of keratinocyte differentiation (GO:0045616)|regulation of stress fiber assembly (GO:0051492)|rhythmic process (GO:0048511)|smooth muscle contraction (GO:0006939)	centrosome (GO:0005813)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|spindle pole centrosome (GO:0031616)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|protein serine/threonine kinase activity (GO:0004674)|structural molecule activity (GO:0005198)	p.T431N(1)		breast(2)|central_nervous_system(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(6)|lung(10)|prostate(1)|skin(4)|stomach(3)|urinary_tract(2)	43	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.137)|OV - Ovarian serous cystadenocarcinoma(76;0.162)		TATGGAATCAGTTTCTCTACA	0.284													T|||	2002	0.39976	0.2035	0.5634	5008	,	,		16818	0.3889		0.5268	False		,,,				2504	0.4294				p.T431N		Atlas-SNP	.											ROCK2_ENST00000315872,NS,carcinoma,0,1	ROCK2	224	1	1	Substitution - Missense(1)	stomach(1)	c.C1292A						PASS	.	T	ASN/THR	979,2621		142,695,963	77.0	69.0	72.0		1292	4.4	1.0	2	dbSNP_98	72	4295,3811		1146,2003,904	yes	missense	ROCK2	NM_004850.3	65	1288,2698,1867	TT,TG,GG		47.0146,27.1944,45.0538	benign	431/1389	11359120	5274,6432	1800	4053	5853	SO:0001583	missense	9475	exon10			GAATCAGTTTCTC	D87931	CCDS42654.1	2p24	2013-01-10			ENSG00000134318	ENSG00000134318	2.7.11.1	"""Pleckstrin homology (PH) domain containing"""	10252	protein-coding gene	gene with protein product		604002				9933571	Standard	NM_004850		Approved		uc002rbd.1	O75116	OTTHUMG00000149916	ENST00000315872.6:c.1292C>A	2.37:g.11359120G>T	ENSP00000317985:p.Thr431Asn	Somatic	296	1	0.00337838		WXS	Illumina HiSeq	Phase_I	301	119	0.395349	NM_004850	Q53QZ0|Q53SJ7|Q9UQN5	Missense_Mutation	SNP	ENST00000315872.6	37	CCDS42654.1	931	0.42628205128205127	100	0.2032520325203252	200	0.5524861878453039	234	0.4090909090909091	397	0.5237467018469657	T	3.282	-0.146893	0.06627	0.271944	0.529854	ENSG00000134318	ENST00000315872;ENST00000401753	T;T	0.62498	0.02;1.05	5.54	4.39	0.52855	.	0.397066	0.27172	N	0.020589	T	0.00012	0.0000	N	0.00230	-1.795	0.45837	P	0.0012950000000000461	B	0.02656	0.0	B	0.01281	0.0	T	0.46442	-0.9191	9	0.11794	T	0.64	.	6.4363	0.21825	0.0:0.0809:0.1581:0.761	rs2230774;rs9808232;rs17366763;rs52790024;rs9808232	431	O75116	ROCK2_HUMAN	N	431;188	ENSP00000317985:T431N;ENSP00000385509:T188N	ENSP00000261535:T431N	T	-	2	0	ROCK2	11276571	1.000000	0.71417	0.997000	0.53966	0.807000	0.45602	1.218000	0.32467	0.396000	0.25283	-0.335000	0.08231	ACT	T|0.320;G|0.373;C|0.181;N|0.000;A|0.127	0.320	strong		0.284	ROCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313886.3		
BTBD16	118663	hgsc.bcm.edu	37	10	124096041	124096041	+	Silent	SNP	T	T	C	rs1129973	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	120	1	0.00833333		WXS	Illumina HiSeq	Phase_I	74	30	0.405405	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	
CEP192	55125	hgsc.bcm.edu	37	18	13068132	13068132	+	Missense_Mutation	SNP	T	T	C	rs578208	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:13068132T>C	ENST00000325971.8	+	21	4459	c.2866T>C	c.(2866-2868)Tcc>Ccc	p.S956P	CEP192_ENST00000430049.2_Missense_Mutation_p.S1077P|CEP192_ENST00000506447.1_Missense_Mutation_p.S1552P			Q8TEP8	CE192_HUMAN	centrosomal protein 192kDa	956			S -> P (in dbSNP:rs578208). {ECO:0000269|PubMed:11230166, ECO:0000269|PubMed:12693554, ECO:0000269|PubMed:15498874}.		centrosome duplication (GO:0051298)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|negative regulation of phosphatase activity (GO:0010923)|spindle assembly (GO:0051225)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)	phosphatase binding (GO:0019902)			NS(1)|breast(4)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(36)|ovary(4)|pancreas(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	71						TTCCAAGGAATCCGTCCGAGC	0.488													C|||	3742	0.747204	0.8669	0.6354	5008	,	,		17132	0.8105		0.6203	False		,,,				2504	0.7301				p.S1552P		Atlas-SNP	.											.	CEP192	340	.	0			c.T4654C						PASS	.	C	PRO/SER	3568,838	328.0+/-300.3	1451,666,86	97.0	103.0	101.0		4654	5.4	0.8	18	dbSNP_83	101	5325,3275	489.6+/-372.6	1662,2001,637	yes	missense	CEP192	NM_032142.3	74	3113,2667,723	CC,CT,TT		38.0814,19.0195,31.6239	benign	1552/2538	13068132	8893,4113	2203	4300	6503	SO:0001583	missense	55125	exon23			AAGGAATCCGTCC	AK074074	CCDS32792.1, CCDS32792.2	18p11.21	2014-02-20				ENSG00000101639		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	25515	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 62"""					11230166, 14654843	Standard	NM_032142		Approved	KIAA1569, FLJ10352, PPP1R62	uc010xac.2	Q8TEP8		ENST00000325971.8:c.2866T>C	18.37:g.13068132T>C	ENSP00000317156:p.Ser956Pro	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	53	29	0.54717	NM_032142	A0A060A9S4|E9PF99|Q8WYT8|Q9H0F4|Q9NW27	Missense_Mutation	SNP	ENST00000325971.8	37		1607	0.7358058608058609	435	0.8841463414634146	236	0.6519337016574586	464	0.8111888111888111	472	0.6226912928759895	C	6.879	0.531696	0.13127	0.809805	0.619186	ENSG00000101639	ENST00000506447;ENST00000325971;ENST00000399863;ENST00000430049	T;T;T	0.24350	1.86;1.86;1.86	5.37	5.37	0.77165	.	0.000000	0.85682	N	0.000000	T	0.00012	0.0000	N	0.00082	-2.215	0.42656	P	0.006533000000000011	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.39354	-0.9618	9	0.02654	T	1	-8.0771	14.6427	0.68737	0.0:0.9298:0.0:0.0702	rs578208;rs1787012;rs17660892;rs52836713;rs60741171;rs578208	1077;1552	C9JT09;E9PF99	.;.	P	1552;956;956;1077	ENSP00000427550:S1552P;ENSP00000317156:S956P;ENSP00000389190:S1077P	ENSP00000317156:S956P	S	+	1	0	CEP192	13058132	1.000000	0.71417	0.796000	0.32109	0.247000	0.25773	4.296000	0.59055	1.415000	0.47037	-0.119000	0.15052	TCC	A|0.001;C|0.718	0.718	strong		0.488	CEP192-201	KNOWN	basic	protein_coding	protein_coding		NM_032142	
SLC9C1	285335	hgsc.bcm.edu	37	3	111981849	111981849	+	Silent	SNP	C	C	T	rs9860819	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:111981849C>T	ENST00000305815.5	-	10	1371	c.1119G>A	c.(1117-1119)aaG>aaA	p.K373K	SLC9C1_ENST00000487372.1_Silent_p.K325K	NM_183061.1	NP_898884.1	Q4G0N8	SL9C1_HUMAN	solute carrier family 9, subfamily C (Na+-transporting carboxylic acid decarboxylase), member 1	373					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)										TAGGCATCCCCTTCATTTCAC	0.378													T|||	3220	0.642971	0.4849	0.7118	5008	,	,		16323	0.7738		0.5964	False		,,,				2504	0.7209				p.K373K		Atlas-SNP	.											.	.	.	.	0			c.G1119A						PASS	.	T		2215,2191	582.8+/-385.7	535,1145,523	103.0	100.0	101.0		1119	3.3	1.0	3	dbSNP_119	101	5324,3276	485.6+/-371.7	1657,2010,633	no	coding-synonymous	SLC9A10	NM_183061.1		2192,3155,1156	TT,TC,CC		38.093,49.7276,42.0344		373/1178	111981849	7539,5467	2203	4300	6503	SO:0001819	synonymous_variant	285335	exon10			CATCCCCTTCATT	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.1119G>A	3.37:g.111981849C>T		Somatic	354	0	0		WXS	Illumina HiSeq	Phase_I	269	269	1	NM_183061	Q6ZRP4|Q7RTP2	Silent	SNP	ENST00000305815.5	37	CCDS33817.1																																																																																			C|0.400;T|0.600	0.600	strong		0.378	SLC9C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354066.1	NM_183061	
LILRA6	79168	hgsc.bcm.edu	37	19	54746380	54746380	+	Missense_Mutation	SNP	C	C	T	rs150628522	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:54746380C>T	ENST00000396365.2	-	2	100	c.61G>A	c.(61-63)Gtg>Atg	p.V21M	LILRA6_ENST00000245621.5_Missense_Mutation_p.V21M|LILRA6_ENST00000440558.2_Missense_Mutation_p.V21M|LILRA6_ENST00000270464.5_Missense_Mutation_p.V21M|LILRB3_ENST00000407860.2_Missense_Mutation_p.V21M|LILRA6_ENST00000419410.2_Missense_Mutation_p.V21M|LILRA6_ENST00000391735.3_Missense_Mutation_p.V21M	NM_024318.2	NP_077294	Q6PI73	LIRA6_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 6	21					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)		CCTGCCTGCACGCGGGTCCTG	0.657																																					p.V21M		Atlas-SNP	.											LILRA6,NS,carcinoma,0,2	LILRA6	75	2	0			c.G61A						scavenged	.						5.0	6.0	6.0					19																	54746380		1873	3940	5813	SO:0001583	missense	79168	exon2			CCTGCACGCGGGT	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.61G>A	19.37:g.54746380C>T	ENSP00000379651:p.Val21Met	Somatic	274	0	0		WXS	Illumina HiSeq	Phase_I	199	62	0.311558	NM_024318		Missense_Mutation	SNP	ENST00000396365.2	37	CCDS42610.1	.	.	.	.	.	.	.	.	.	.	C	9.815	1.184124	0.21870	.	.	ENSG00000204577;ENSG00000244482;ENSG00000244482;ENSG00000244482;ENSG00000244482;ENSG00000244482;ENSG00000244482;ENSG00000244482	ENST00000407860;ENST00000440558;ENST00000270464;ENST00000419410;ENST00000391735;ENST00000421123;ENST00000396365;ENST00000245621	T;T;T;T;T;T;T	0.00523	7.02;7.06;7.06;7.09;6.83;6.91;6.83	3.4	1.18	0.20946	Immunoglobulin-like fold (1);	0.896200	0.09207	N	0.833786	T	0.00998	0.0033	M	0.69823	2.125	0.80722	P	0.0	D;D;P;P;P;D;P;P;D;D	0.71674	0.983;0.964;0.826;0.78;0.801;0.989;0.927;0.954;0.971;0.998	P;P;B;B;P;P;B;B;P;P	0.58391	0.546;0.597;0.284;0.185;0.475;0.581;0.342;0.284;0.674;0.838	T	0.48456	-0.9034	9	0.52906	T	0.07	.	3.693	0.08353	0.0:0.545:0.2077:0.2473	.	21;21;21;21;21;21;21;21;21;21	C9JFH3;Q6PI73-2;B5MCX0;B5ME96;Q6PI73;F8WCY4;F8WD89;D3YTC4;F8W6G6;O75022-2	.;.;.;.;LIRA6_HUMAN;.;.;.;.;.	M	21	ENSP00000384274:V21M;ENSP00000390120:V21M;ENSP00000270464:V21M;ENSP00000411227:V21M;ENSP00000375615:V21M;ENSP00000379651:V21M;ENSP00000245621:V21M	ENSP00000245621:V21M	V	-	1	0	LILRB3;LILRA6	59438192	0.000000	0.05858	0.000000	0.03702	0.070000	0.16714	0.138000	0.16016	0.266000	0.21894	0.184000	0.17185	GTG	C|0.795;T|0.205	0.205	strong		0.657	LILRA6-003	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000313725.1	NM_024318	
LAMA1	284217	hgsc.bcm.edu	37	18	7049171	7049171	+	Missense_Mutation	SNP	C	C	T	rs140718292	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:7049171C>T	ENST00000389658.3	-	5	767	c.674G>A	c.(673-675)cGc>cAc	p.R225H		NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	225	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)				CAAGCGAAGGCGAATATATCG	0.468													C|||	11	0.00219649	0.0	0.0058	5008	,	,		16222	0.0		0.006	False		,,,				2504	0.001				p.R225H		Atlas-SNP	.											LAMA1,scalp,carcinoma,-1,1	LAMA1	458	1	0			c.G674A						scavenged	.	C	HIS/ARG	7,4399	12.9+/-30.5	0,7,2196	149.0	123.0	132.0		674	5.0	1.0	18	dbSNP_134	132	87,8513	50.6+/-110.7	0,87,4213	yes	missense	LAMA1	NM_005559.3	29	0,94,6409	TT,TC,CC		1.0116,0.1589,0.7227	probably-damaging	225/3076	7049171	94,12912	2203	4300	6503	SO:0001583	missense	284217	exon5			CGAAGGCGAATAT	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.674G>A	18.37:g.7049171C>T	ENSP00000374309:p.Arg225His	Somatic	109	1	0.00917431		WXS	Illumina HiSeq	Phase_I	104	50	0.480769	NM_005559		Missense_Mutation	SNP	ENST00000389658.3	37	CCDS32787.1	10	0.004578754578754579	0	0.0	3	0.008287292817679558	0	0.0	7	0.009234828496042216	C	33	5.214689	0.95104	0.001589	0.010116	ENSG00000101680	ENST00000389658	D	0.84800	-1.9	5.85	4.97	0.65823	Laminin, N-terminal (3);	0.064020	0.64402	D	0.000007	D	0.93520	0.7932	H	0.96861	3.895	0.58432	D	0.999996	D	0.89917	1.0	D	0.97110	1.0	D	0.95070	0.8203	10	0.87932	D	0	.	16.9089	0.86135	0.0:0.872:0.128:0.0	.	225	P25391	LAMA1_HUMAN	H	225	ENSP00000374309:R225H	ENSP00000374309:R225H	R	-	2	0	LAMA1	7039171	1.000000	0.71417	0.992000	0.48379	0.944000	0.59088	7.818000	0.86416	1.436000	0.47453	0.557000	0.71058	CGC	C|0.993;T|0.007	0.007	strong		0.468	LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1	NM_005559	
OR10H2	26538	hgsc.bcm.edu	37	19	15838972	15838972	+	Missense_Mutation	SNP	T	T	A	rs4569397	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:15838972T>A	ENST00000305899.3	+	1	139	c.119T>A	c.(118-120)cTg>cAg	p.L40Q		NM_013939.2	NP_039227.1	O60403	O10H2_HUMAN	olfactory receptor, family 10, subfamily H, member 2	40			L -> Q (in dbSNP:rs4569397).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(2)|skin(3)|stomach(1)	27	all_hematologic(1;0.0517)|Acute lymphoblastic leukemia(2;0.074)					TTCACGCTGCTGGGCAACCTG	0.582													T|||	1310	0.261581	0.4319	0.2752	5008	,	,		22562	0.0119		0.3131	False		,,,				2504	0.226				p.L40Q		Atlas-SNP	.											OR10H2,NS,carcinoma,-1,1	OR10H2	59	1	0			c.T119A						scavenged	.	T	GLN/LEU	1798,2608		372,1054,777	228.0	189.0	202.0		119	2.9	1.0	19	dbSNP_111	202	2471,6125		379,1713,2206	no	missense	OR10H2	NM_013939.2	113	751,2767,2983	AA,AT,TT		28.7459,40.808,32.8334	probably-damaging	40/316	15838972	4269,8733	2203	4298	6501	SO:0001583	missense	26538	exon1			CGCTGCTGGGCAA	AC004597	CCDS12333.1	19p13.1	2012-08-09				ENSG00000171942		"""GPCR / Class A : Olfactory receptors"""	8173	protein-coding gene	gene with protein product							Standard	NM_013939		Approved		uc002nbm.2	O60403		ENST00000305899.3:c.119T>A	19.37:g.15838972T>A	ENSP00000306095:p.Leu40Gln	Somatic	140	1	0.00714286		WXS	Illumina HiSeq	Phase_I	203	83	0.408867	NM_013939	Q6IFQ1|Q96R58	Missense_Mutation	SNP	ENST00000305899.3	37	CCDS12333.1	563	0.25778388278388276	198	0.4024390243902439	115	0.31767955801104975	11	0.019230769230769232	239	0.3153034300791557	.	16.52	3.146455	0.57044	0.40808	0.287459	ENSG00000171942	ENST00000305899	T	0.00625	6.14	2.88	2.88	0.33553	.	0.000000	0.38720	N	0.001598	T	0.00012	0.0000	M	0.93016	3.37	0.29061	P	0.88391	D	0.89917	1.0	D	0.91635	0.999	T	0.40646	-0.9552	9	0.40728	T	0.16	.	4.5583	0.12147	0.0:0.1544:0.0:0.8456	rs4569397	40	O60403	O10H2_HUMAN	Q	40	ENSP00000306095:L40Q	ENSP00000306095:L40Q	L	+	2	0	OR10H2	15699972	0.000000	0.05858	1.000000	0.80357	0.990000	0.78478	0.639000	0.24690	1.186000	0.42985	0.438000	0.28831	CTG	T|0.581;A|0.419	0.419	strong		0.582	OR10H2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460917.1		
XPC	7508	hgsc.bcm.edu	37	3	14199887	14199887	+	Missense_Mutation	SNP	G	G	A	rs2228000	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:14199887G>A	ENST00000285021.7	-	9	1710	c.1496C>T	c.(1495-1497)gCg>gTg	p.A499V	XPC_ENST00000449060.2_Missense_Mutation_p.A462V	NM_001145769.1|NM_004628.4	NP_001139241.1|NP_004619.3	Q01831	XPC_HUMAN	xeroderma pigmentosum, complementation group C	499	Interaction with RAD23B.		A -> V (in dbSNP:rs2228000). {ECO:0000269|PubMed:12177305, ECO:0000269|PubMed:8168482, ECO:0000269|Ref.4}.		DNA repair (GO:0006281)|intra-S DNA damage checkpoint (GO:0031573)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage recognition (GO:0000715)|nucleotide-excision repair, DNA damage removal (GO:0000718)|regulation of mitotic cell cycle phase transition (GO:1901990)|response to drug (GO:0042493)|response to UV-B (GO:0010224)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|XPC complex (GO:0071942)	bubble DNA binding (GO:0000405)|damaged DNA binding (GO:0003684)|heteroduplex DNA loop binding (GO:0000404)|single-stranded DNA binding (GO:0003697)			NS(1)|breast(2)|endometrium(1)|kidney(3)|large_intestine(4)|lung(5)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						TGAGGATGCCGCTGGCAAGCT	0.537			"""Mis, N, F, S"""			"""skin basal cell, skin squamous cell, melanoma"""		Nucleotide excision repair (NER)	Xeroderma Pigmentosum				G|||	1167	0.233027	0.093	0.245	5008	,	,		20742	0.4127		0.2584	False		,,,				2504	0.2025				p.A499V		Atlas-SNP	.	yes	Rec		Xeroderma pigmentosum (C)	3	3p25	7508	"""xeroderma pigmentosum, complementation group C"""		E	XPC,caecum,carcinoma,+1,1	XPC	60	1	0			c.C1496T	GRCh37	CM057944	XPC	M	rs2228000	PASS	.	G	VAL/ALA,VAL/ALA	288,2848		18,252,1298	71.0	64.0	66.0		1385,1496	-1.0	0.0	3	dbSNP_98	66	1778,5386		219,1340,2023	yes	missense,missense	XPC	NM_001145769.1,NM_004628.4	64,64	237,1592,3321	AA,AG,GG		24.8185,9.1837,20.0583	benign,benign	462/904,499/941	14199887	2066,8234	1568	3582	5150	SO:0001583	missense	7508	exon9	Familial Cancer Database	incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV	GATGCCGCTGGCA		CCDS46763.1	3p25.1	2014-09-17			ENSG00000154767	ENSG00000154767			12816	protein-coding gene	gene with protein product	"""xeroderma pigmentosum group C protein"""	613208				1522891	Standard	NM_004628		Approved	XPCC, RAD4	uc011ave.2	Q01831	OTTHUMG00000155526	ENST00000285021.7:c.1496C>T	3.37:g.14199887G>A	ENSP00000285021:p.Ala499Val	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	53	26	0.490566	NM_004628	B4DIP3|E9PB96|E9PH69|Q53GT7|Q96AX0	Missense_Mutation	SNP	ENST00000285021.7	37	CCDS46763.1	541	0.24771062271062272	39	0.07926829268292683	93	0.2569060773480663	210	0.36713286713286714	199	0.262532981530343	G	9.045	0.990686	0.18966	0.091837	0.248185	ENSG00000154767	ENST00000285021;ENST00000449060	T;T	0.36699	1.24;1.26	5.34	-1.03	0.10102	.	0.809781	0.11805	N	0.527757	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	B;B	0.23185	0.081;0.004	B;B	0.19946	0.027;0.004	T	0.45745	-0.9240	9	0.30854	T	0.27	0.064	4.6128	0.12411	0.1193:0.0886:0.4136:0.3785	rs2228000;rs3729586;rs52792520;rs2228000	462;499	E9PH69;Q01831	.;XPC_HUMAN	V	499;462	ENSP00000285021:A499V;ENSP00000404002:A462V	ENSP00000285021:A499V	A	-	2	0	XPC	14174889	.	.	0.000000	0.03702	0.000000	0.00434	.	.	-0.927000	0.03766	-0.797000	0.03246	GCG	G|0.772;A|0.228	0.228	strong		0.537	XPC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000340517.3	NM_004628	
OR52E2	119678	hgsc.bcm.edu	37	11	5080234	5080234	+	Silent	SNP	T	T	C	rs2445333	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:5080234T>C	ENST00000321522.2	-	1	623	c.624A>G	c.(622-624)ctA>ctG	p.L208L		NM_001005164.2	NP_001005164.2	Q8NGJ4	O52E2_HUMAN	olfactory receptor, family 52, subfamily E, member 2	208						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)		TGTCAAACACTAGATTACAAA	0.413													T|||	1525	0.304513	0.4054	0.1599	5008	,	,		23141	0.1746		0.2853	False		,,,				2504	0.4243				p.L208L		Atlas-SNP	.											.	OR52E2	63	.	0			c.A624G						PASS	.	T		1605,2797	497.4+/-363.8	294,1017,890	90.0	79.0	83.0		624	-7.5	0.0	11	dbSNP_100	83	2538,6058	414.1+/-351.3	379,1780,2139	no	coding-synonymous	OR52E2	NM_001005164.2		673,2797,3029	CC,CT,TT		29.5254,36.4607,31.8741		208/326	5080234	4143,8855	2201	4298	6499	SO:0001819	synonymous_variant	119678	exon1			AAACACTAGATTA	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.624A>G	11.37:g.5080234T>C		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	97	74	0.762887	NM_001005164		Silent	SNP	ENST00000321522.2	37	CCDS31371.1																																																																																			T|0.698;C|0.302	0.302	strong		0.413	OR52E2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142815.1	NM_001005164	
CAMKV	79012	hgsc.bcm.edu	37	3	49898273	49898273	+	Silent	SNP	A	A	G	rs2681781	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:49898273A>G	ENST00000477224.1	-	8	1129	c.651T>C	c.(649-651)aaT>aaC	p.N217N	CAMKV_ENST00000466940.1_Silent_p.N174N|CAMKV_ENST00000463537.1_Silent_p.N217N|CAMKV_ENST00000488336.1_Silent_p.N217N|CAMKV_ENST00000296471.7_Silent_p.N189N|CAMKV_ENST00000498324.1_5'Flank|RN7SL217P_ENST00000584520.1_RNA|CAMKV_ENST00000467248.1_Silent_p.N142N			Q8NCB2	CAMKV_HUMAN	CaM kinase-like vesicle-associated	217	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.					cytoplasmic vesicle (GO:0031410)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)			central_nervous_system(1)|large_intestine(2)|lung(2)|ovary(2)	7				BRCA - Breast invasive adenocarcinoma(193;4.62e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.00551)|Kidney(197;0.00621)		AGAAAGGTGGATTGCCTGAAA	0.507													G|||	2019	0.403155	0.6914	0.3703	5008	,	,		16605	0.1448		0.4911	False		,,,				2504	0.2127				p.N217N		Atlas-SNP	.											.	CAMKV	84	.	0			c.T651C						PASS	.	G		2797,1609	497.6+/-363.9	894,1009,300	154.0	157.0	156.0		651	0.7	1.0	3	dbSNP_100	156	4271,4329	579.4+/-390.9	1060,2151,1089	no	coding-synonymous	CAMKV	NM_024046.3		1954,3160,1389	GG,GA,AA		49.6628,36.5184,45.6559		217/502	49898273	7068,5938	2203	4300	6503	SO:0001819	synonymous_variant	79012	exon8			AGGTGGATTGCCT	BC017363	CCDS33762.1	3p21.31	2005-03-04			ENSG00000164076	ENSG00000164076			28788	protein-coding gene	gene with protein product		614993				12477932	Standard	XM_005265478		Approved	MGC8407, VACAMKL	uc003cxt.1	Q8NCB2	OTTHUMG00000158288	ENST00000477224.1:c.651T>C	3.37:g.49898273A>G		Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	98	66	0.673469	NM_024046	A6NFD4|Q6FIB8|Q8NBS8|Q8NC85|Q8NDU4|Q8WTT8|Q9BQC9|Q9H0Q5	Silent	SNP	ENST00000477224.1	37	CCDS33762.1																																																																																			A|0.515;G|0.485	0.485	strong		0.507	CAMKV-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350584.4	NM_024046	
TUBG1	7283	hgsc.bcm.edu	37	17	40766546	40766546	+	Silent	SNP	C	C	G	rs1045710	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:40766546C>G	ENST00000251413.3	+	10	1091	c.1029C>G	c.(1027-1029)cgC>cgG	p.R343R		NM_001070.4	NP_001061.2	P23258	TBG1_HUMAN	tubulin, gamma 1	343					cytoplasmic microtubule organization (GO:0031122)|G2/M transition of mitotic cell cycle (GO:0000086)|meiotic spindle organization (GO:0000212)|microtubule cytoskeleton organization (GO:0000226)|microtubule nucleation (GO:0007020)|mitotic cell cycle (GO:0000278)	apical part of cell (GO:0045177)|cell leading edge (GO:0031252)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|gamma-tubulin complex (GO:0000930)|nonmotile primary cilium (GO:0031513)|pericentriolar material (GO:0000242)|polar microtubule (GO:0005827)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)			endometrium(2)|kidney(2)|large_intestine(2)|lung(4)|ovary(1)|prostate(1)	12		Breast(137;0.00116)		BRCA - Breast invasive adenocarcinoma(366;0.129)	Vinblastine(DB00570)	TCCGGGAACGCAAGTTGGCCA	0.657													c|||	2960	0.591054	0.7171	0.5159	5008	,	,		16066	0.4673		0.5239	False		,,,				2504	0.6708				p.R343R	Colon(20;114 698 11420 22864)	Atlas-SNP	.											.	TUBG1	25	.	0			c.C1029G						PASS	.	C		2995,1409		1053,889,260	37.0	44.0	42.0		1029	-2.2	0.7	17	dbSNP_86	42	4507,4079		1270,1967,1056	no	coding-synonymous	TUBG1	NM_001070.4		2323,2856,1316	GG,GC,CC		47.5076,31.9936,42.2479		343/452	40766546	7502,5488	2202	4293	6495	SO:0001819	synonymous_variant	7283	exon10			GGAACGCAAGTTG	BC000619	CCDS11433.1	17q21.31	2010-03-15	2000-01-20		ENSG00000131462	ENSG00000131462		"""Tubulins"""	12417	protein-coding gene	gene with protein product		191135	"""tubulin, gamma polypeptide"""	TUBG		1904010	Standard	NM_001070		Approved	TUBGCP1	uc002ian.3	P23258		ENST00000251413.3:c.1029C>G	17.37:g.40766546C>G		Somatic	246	0	0		WXS	Illumina HiSeq	Phase_I	184	69	0.375	NM_001070	Q53X79|Q9BW59	Silent	SNP	ENST00000251413.3	37	CCDS11433.1																																																																																			G|1.000;|0.000	1.000	weak		0.657	TUBG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450548.1	NM_001070	
ADI1	55256	hgsc.bcm.edu	37	2	3504687	3504687	+	Silent	SNP	A	A	G	rs9950	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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						PASS	.	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	152	1	0.00657895		WXS	Illumina HiSeq	Phase_I	198	198	1	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	
HLA-DRB5	3127	hgsc.bcm.edu	37	6	32497900	32497900	+	Splice_Site	SNP	A	A	G	rs78612727	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:32497900A>G	ENST00000374975.3	-	1	163		c.e1+1			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						ATGTGCACTTACGTCGGGTGT	0.522																																					.		Atlas-SNP	.											.	HLA-DRB5	31	.	0			c.100+2T>C						PASS	.						99.0	102.0	101.0					6																	32497900		2203	4300	6503	SO:0001630	splice_region_variant	3127	exon2			GCACTTACGTCGG		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.100+1T>C	6.37:g.32497900A>G		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	86	14	0.162791	NM_002125		Splice_Site	SNP	ENST00000374975.3	37	CCDS4751.1	.	.	.	.	.	.	.	.	.	.	.	8.839	0.941693	0.18281	.	.	ENSG00000198502	ENST00000374975	.	.	.	4.54	3.3	0.37823	.	.	.	.	.	.	.	.	.	.	.	0.35921	D	0.831832	.	.	.	.	.	.	.	.	.	.	.	.	.	.	7.4495	0.27229	0.8084:0.0:0.0:0.1916	.	.	.	.	.	-1	.	.	.	-	.	.	HLA-DRB5	32605878	0.985000	0.35326	0.199000	0.23439	0.019000	0.09904	2.123000	0.41996	1.909000	0.55274	0.397000	0.26171	.	A|0.994;G|0.006	0.006	strong		0.522	HLA-DRB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076022.2	NM_002125	Intron
PYGB	5834	hgsc.bcm.edu	37	20	25259006	25259006	+	Missense_Mutation	SNP	G	G	T	rs2228976	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	104	0	0		WXS	Illumina HiSeq	Phase_I	107	52	0.485981	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	
KIAA0368	23392	hgsc.bcm.edu	37	9	114174384	114174384	+	Silent	SNP	C	C	T	rs16916079	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:114174384C>T	ENST00000338205.5	-	20	2343	c.2124G>A	c.(2122-2124)gcG>gcA	p.A708A	RNA5SP294_ENST00000411306.1_RNA|KIAA0368_ENST00000259335.4_Silent_p.A886A			Q5VYK3	ECM29_HUMAN	KIAA0368	714					ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)	centrosome (GO:0005813)|cytoplasmic membrane-bounded vesicle (GO:0016023)|early endosome (GO:0005769)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle (GO:0030134)|late endosome (GO:0005770)|membrane (GO:0016020)|multivesicular body (GO:0005771)|nucleus (GO:0005634)|proteasome complex (GO:0000502)		p.A886A(1)		NS(2)|breast(3)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(23)|prostate(3)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	65						AATAAAACAACGCTGCCAGTT	0.358													C|||	307	0.0613019	0.0756	0.0072	5008	,	,		18160	0.1637		0.0109	False		,,,				2504	0.0266				p.A886A		Atlas-SNP	.											KIAA0368,NS,carcinoma,0,1	KIAA0368	144	1	1	Substitution - coding silent(1)	stomach(1)	c.G2658A						PASS	.	C		182,3478		7,168,1655	90.0	84.0	86.0		2658	-11.0	0.1	9	dbSNP_123	86	107,8093		0,107,3993	no	coding-synonymous	KIAA0368	NM_001080398.1		7,275,5648	TT,TC,CC		1.3049,4.9727,2.4368		886/2018	114174384	289,11571	1830	4100	5930	SO:0001819	synonymous_variant	23392	exon22			AAACAACGCTGCC	AK025689	CCDS48006.1	9q32	2012-11-29	2006-11-23	2006-11-23	ENSG00000136813	ENSG00000136813			29020	protein-coding gene	gene with protein product	"""ECM29 homolog (S. cerevisiae)"""					9205841, 15496406, 20682791	Standard	NM_001080398		Approved	FLJ22036, ECM29	uc004bfe.1	Q5VYK3	OTTHUMG00000020489	ENST00000338205.5:c.2124G>A	9.37:g.114174384C>T		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	67	29	0.432836	NM_001080398	O15074|Q8WU82	Silent	SNP	ENST00000338205.5	37																																																																																				C|0.943;T|0.057	0.057	strong		0.358	KIAA0368-001	NOVEL	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000053637.2	NM_014686	
ANKRD22	118932	hgsc.bcm.edu	37	10	90585819	90585819	+	Silent	SNP	G	G	A	rs7893917	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:90585819G>A	ENST00000371930.4	-	4	585	c.375C>T	c.(373-375)ggC>ggT	p.G125G	ANKRD22_ENST00000476963.1_5'Flank	NM_144590.2	NP_653191.2	Q5VYY1	ANR22_HUMAN	ankyrin repeat domain 22	125										NS(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|skin(3)	10		Colorectal(252;0.0163)		Colorectal(12;6.29e-05)|COAD - Colon adenocarcinoma(12;7.69e-05)		TAACTTCGACGCCAGCATCAA	0.323													G|||	1709	0.341254	0.1619	0.3458	5008	,	,		18691	0.4365		0.4115	False		,,,				2504	0.41				p.G125G		Atlas-SNP	.											.	ANKRD22	23	.	0			c.C375T						PASS	.	G		944,3462	359.4+/-314.8	104,736,1363	101.0	96.0	98.0		375	-10.8	0.0	10	dbSNP_116	98	3324,5276	495.3+/-374.0	659,2006,1635	no	coding-synonymous	ANKRD22	NM_144590.2		763,2742,2998	AA,AG,GG		38.6512,21.4253,32.8156		125/192	90585819	4268,8738	2203	4300	6503	SO:0001819	synonymous_variant	118932	exon4			TTCGACGCCAGCA	BC021671	CCDS7390.1	10q23.31	2013-09-20			ENSG00000152766	ENSG00000152766		"""Ankyrin repeat domain containing"""	28321	protein-coding gene	gene with protein product						12477932	Standard	NM_144590		Approved	MGC22805	uc001kfj.4	Q5VYY1	OTTHUMG00000018699	ENST00000371930.4:c.375C>T	10.37:g.90585819G>A		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	70	35	0.5	NM_144590	B2R9Y7|Q8WU06	Silent	SNP	ENST00000371930.4	37	CCDS7390.1																																																																																			G|0.659;A|0.341	0.341	strong		0.323	ANKRD22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049262.1	NM_144590	
PRKD1	5587	hgsc.bcm.edu	37	14	30046511	30046511	+	Missense_Mutation	SNP	T	T	C	rs45582934	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:30046511T>C	ENST00000331968.5	-	18	2901	c.2672A>G	c.(2671-2673)cAc>cGc	p.H891R	PRKD1_ENST00000415220.2_Missense_Mutation_p.H899R	NM_002742.2	NP_002733.2	Q15139	KPCD1_HUMAN	protein kinase D1	891			H -> R (in dbSNP:rs45582934). {ECO:0000269|PubMed:17344846}.		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)		AGTGTCACTGTGGCTAGCACT	0.512													T|||	26	0.00519169	0.0	0.0101	5008	,	,		19205	0.0		0.0159	False		,,,				2504	0.0031				p.H891R		Atlas-SNP	.											.	PRKD1	316	.	0			c.A2672G						PASS	.	T	ARG/HIS	8,4398	14.3+/-33.2	0,8,2195	145.0	120.0	129.0		2672	3.5	0.9	14	dbSNP_127	129	114,8486	61.0+/-122.8	0,114,4186	yes	missense	PRKD1	NM_002742.2	29	0,122,6381	CC,CT,TT		1.3256,0.1816,0.938	benign	891/913	30046511	122,12884	2203	4300	6503	SO:0001583	missense	5587	exon18			TCACTGTGGCTAG		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.2672A>G	14.37:g.30046511T>C	ENSP00000333568:p.His891Arg	Somatic	306	1	0.00326797		WXS	Illumina HiSeq	Phase_I	255	108	0.423529	NM_002742	A6NL64|B2RAF6	Missense_Mutation	SNP	ENST00000331968.5	37	CCDS9637.1	19	0.0086996336996337	0	0.0	4	0.011049723756906077	0	0.0	15	0.01978891820580475	T	8.126	0.782077	0.16189	0.001816	0.013256	ENSG00000184304	ENST00000331968;ENST00000415220	T;T	0.64260	-0.09;-0.09	6.03	3.52	0.40303	Protein kinase-like domain (1);	0.268929	0.35436	N	0.003219	T	0.23094	0.0558	N	0.22421	0.69	0.09310	N	0.999997	B	0.02656	0.0	B	0.01281	0.0	T	0.06516	-1.0822	10	0.15066	T	0.55	-13.0063	3.4153	0.07373	0.1367:0.0719:0.1431:0.6483	rs45582934;rs61732494	891	Q15139	KPCD1_HUMAN	R	891;899	ENSP00000333568:H891R;ENSP00000390535:H899R	ENSP00000333568:H891R	H	-	2	0	PRKD1	29116262	0.999000	0.42202	0.939000	0.37840	0.977000	0.68977	0.530000	0.23036	1.072000	0.40860	0.533000	0.62120	CAC	T|0.992;C|0.008	0.008	strong		0.512	PRKD1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000276611.2	NM_002742	
PKHD1L1	93035	hgsc.bcm.edu	37	8	110420384	110420384	+	Silent	SNP	T	T	C	rs13254245	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:110420384T>C	ENST00000378402.5	+	18	2024	c.1920T>C	c.(1918-1920)aaT>aaC	p.N640N		NM_177531.4	NP_803875.2	Q86WI1	PKHL1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1	640					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)			TCACACTGAATTGGGATGGGA	0.438										HNSCC(38;0.096)			T|||	1573	0.314097	0.1551	0.4741	5008	,	,		14681	0.3929		0.3111	False		,,,				2504	0.3374				p.N640N		Atlas-SNP	.											.	PKHD1L1	522	.	0			c.T1920C						PASS	.	T		729,3143		76,577,1283	118.0	119.0	119.0		1920	-8.1	0.0	8	dbSNP_121	119	2633,5641		428,1777,1932	no	coding-synonymous	PKHD1L1	NM_177531.4		504,2354,3215	CC,CT,TT		31.8226,18.8275,27.6799		640/4244	110420384	3362,8784	1936	4137	6073	SO:0001819	synonymous_variant	93035	exon18			ACTGAATTGGGAT	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.1920T>C	8.37:g.110420384T>C		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	90	66	0.733333	NM_177531	Q567P2|Q9UF27	Silent	SNP	ENST00000378402.5	37	CCDS47911.1																																																																																			T|0.689;C|0.311	0.311	strong		0.438	PKHD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381017.1	NM_177531	
RNF32	140545	hgsc.bcm.edu	37	7	156469179	156469179	+	Missense_Mutation	SNP	C	C	T	rs2302146	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:156469179C>T	ENST00000405335.1	+	10	1328	c.919C>T	c.(919-921)Cgc>Tgc	p.R307C	RNF32_ENST00000317955.5_Missense_Mutation_p.R307C|LMBR1_ENST00000430825.2_5'UTR|RNF32_ENST00000392743.2_Missense_Mutation_p.R307C|RNF32_ENST00000311822.8_3'UTR|RNF32_ENST00000432459.2_Missense_Mutation_p.R307C|RNF32_ENST00000343665.4_Missense_Mutation_p.R283C			Q9H0A6	RNF32_HUMAN	ring finger protein 32	307			R -> C (in dbSNP:rs2302146).			aggresome (GO:0016235)|endosome (GO:0005768)	zinc ion binding (GO:0008270)			cervix(2)|endometrium(3)|kidney(1)|large_intestine(2)|lung(5)|upper_aerodigestive_tract(2)	15	Ovarian(565;0.218)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.00291)	UCEC - Uterine corpus endometrioid carcinoma (81;0.169)		TGGCGGTCAGCGCGTGGGTGC	0.672													C|||	2016	0.402556	0.531	0.415	5008	,	,		12678	0.4058		0.3559	False		,,,				2504	0.2648				p.R307C		Atlas-SNP	.											.	RNF32	77	.	0			c.C919T						PASS	.	C	CYS/ARG,CYS/ARG,CYS/ARG	2153,2253	578.9+/-384.8	551,1051,601	45.0	40.0	41.0		919,919,919	-0.6	0.0	7	dbSNP_100	41	2967,5633	457.6+/-364.4	519,1929,1852	yes	missense,missense,missense	RNF32	NM_001184996.1,NM_001184997.1,NM_030936.3	180,180,180	1070,2980,2453	TT,TC,CC		34.5,48.8652,39.3664	probably-damaging,probably-damaging,probably-damaging	307/363,307/363,307/363	156469179	5120,7886	2203	4300	6503	SO:0001583	missense	140545	exon9			GGTCAGCGCGTGG		CCDS5944.1	7q36	2013-08-05			ENSG00000105982	ENSG00000105982		"""RING-type (C3HC4) zinc fingers"""	17118	protein-coding gene	gene with protein product		610241				11890671	Standard	NM_001184996		Approved	FKSG33, HSD15, LMBR2	uc003wmr.3	Q9H0A6	OTTHUMG00000151440	ENST00000405335.1:c.919C>T	7.37:g.156469179C>T	ENSP00000385285:p.Arg307Cys	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	70	40	0.571429	NM_001184996	Q6FIB3|Q6X7T4|Q8N6V8|Q8TDG0|Q96BM5|Q9Y6U1	Missense_Mutation	SNP	ENST00000405335.1	37	CCDS5944.1	919	0.4207875457875458	263	0.5345528455284553	136	0.3756906077348066	233	0.40734265734265734	287	0.3786279683377309	C	13.73	2.323027	0.41096	0.488652	0.345	ENSG00000105982	ENST00000432459;ENST00000317955;ENST00000405335;ENST00000392743;ENST00000343665	T;T;T;T;T	0.67345	-0.26;-0.26;-0.26;-0.26;-0.26	3.66	-0.589	0.11683	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (2);Zinc finger, C3HC4 RING-type (1);	2.027620	0.02567	N	0.097404	T	0.00012	0.0000	L	0.29908	0.895	0.80722	P	0.0	D	0.59767	0.986	P	0.48901	0.594	T	0.29579	-1.0007	9	0.59425	D	0.04	0.3209	2.1958	0.03910	0.1602:0.4725:0.1589:0.2083	rs2302146;rs10372978;rs2302146	307	Q9H0A6	RNF32_HUMAN	C	307;307;307;307;283	ENSP00000405588:R307C;ENSP00000315950:R307C;ENSP00000385285:R307C;ENSP00000376499:R307C;ENSP00000341185:R283C	ENSP00000315950:R307C	R	+	1	0	RNF32	156161940	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	0.486000	0.22340	-0.157000	0.11059	0.563000	0.77884	CGC	C|0.600;T|0.400	0.400	strong		0.672	RNF32-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322660.2	NM_030936	
C12orf40	283461	hgsc.bcm.edu	37	12	40085906	40085906	+	Missense_Mutation	SNP	A	A	T	rs73270414	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:40085906A>T	ENST00000324616.5	+	11	1557	c.1403A>T	c.(1402-1404)aAg>aTg	p.K468M	C12orf40_ENST00000405531.3_Missense_Mutation_p.K468M	NM_001031748.2	NP_001026918.2	Q86WS4	CL040_HUMAN	chromosome 12 open reading frame 40	468										breast(4)|central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(14)|ovary(6)|prostate(1)|skin(2)	38						ATATCTACTAAGAAAATCTGT	0.244													A|||	650	0.129792	0.0658	0.098	5008	,	,		13634	0.1766		0.162	False		,,,				2504	0.1575				p.K468M		Atlas-SNP	.											C12orf40,fourth_ventricle,glioma,0,1	C12orf40	118	1	0			c.A1403T						PASS	.	A	MET/LYS	277,3257		11,255,1501	28.0	26.0	27.0		1403	1.7	0.4	12	dbSNP_130	27	1306,6626		108,1090,2768	yes	missense	C12orf40	NM_001031748.2	95	119,1345,4269	TT,TA,AA		16.465,7.8381,13.806	benign	468/653	40085906	1583,9883	1767	3966	5733	SO:0001583	missense	283461	exon11			CTACTAAGAAAAT	AK097445	CCDS41770.1	12q12	2008-08-04			ENSG00000180116	ENSG00000180116			26846	protein-coding gene	gene with protein product						12477932	Standard	XM_005268806		Approved	FLJ40126	uc001rmc.3	Q86WS4	OTTHUMG00000133567	ENST00000324616.5:c.1403A>T	12.37:g.40085906A>T	ENSP00000317671:p.Lys468Met	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	122	52	0.42623	NM_001031748	B7WNU1|Q8IXY6|Q8N818|V9HW02	Missense_Mutation	SNP	ENST00000324616.5	37	CCDS41770.1	281	0.12866300366300365	29	0.05894308943089431	40	0.11049723756906077	97	0.16958041958041958	115	0.1517150395778364	A	4.175	0.031040	0.08101	0.078381	0.16465	ENSG00000180116	ENST00000405531;ENST00000324616	T;T	0.53206	0.63;0.72	2.84	1.66	0.24008	.	0.915548	0.09122	N	0.845588	T	0.00109	0.0003	N	0.24115	0.695	0.33319	P	0.432906	B	0.16603	0.018	B	0.20767	0.031	T	0.12760	-1.0535	9	0.38643	T	0.18	.	5.995	0.19489	0.7306:0.2694:0.0:0.0	.	468	Q86WS4	CL040_HUMAN	M	468	ENSP00000383897:K468M;ENSP00000317671:K468M	ENSP00000317671:K468M	K	+	2	0	C12orf40	38372173	0.046000	0.20272	0.429000	0.26710	0.178000	0.23041	0.308000	0.19314	0.475000	0.27415	0.379000	0.24179	AAG	A|0.858;T|0.142	0.142	strong		0.244	C12orf40-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257664.2	NM_173599	
TESPA1	9840	hgsc.bcm.edu	37	12	55368291	55368291	+	Missense_Mutation	SNP	C	C	T	rs62623446	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:55368291C>T	ENST00000449076.1	-	2	188	c.56G>A	c.(55-57)cGt>cAt	p.R19H	TESPA1_ENST00000524622.1_5'Flank|TESPA1_ENST00000532804.1_5'Flank|TESPA1_ENST00000316577.8_Missense_Mutation_p.R19H|TESPA1_ENST00000524959.1_5'Flank|TESPA1_ENST00000531122.1_5'Flank	NM_001136030.2	NP_001129502.1	A2RU30	TESP1_HUMAN	thymocyte expressed, positive selection associated 1	19					COP9 signalosome assembly (GO:0010387)|positive regulation of T cell differentiation in thymus (GO:0033089)|positive regulation of T cell receptor signaling pathway (GO:0050862)	COP9 signalosome (GO:0008180)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)											ACGGCTCTGACGGAGCCAGGC	0.632													C|||	116	0.0231629	0.0038	0.0346	5008	,	,		15839	0.0		0.0686	False		,,,				2504	0.0184				p.R19H		Atlas-SNP	.											.	.	.	.	0			c.G56A						PASS	.	C	HIS/ARG,HIS/ARG	37,3795		0,37,1879	17.0	20.0	19.0		56,56	3.9	0.5	12	dbSNP_129	19	574,7658		18,538,3560	yes	missense,missense	KIAA0748	NM_001098815.1,NM_001136030.1	29,29	18,575,5439	TT,TC,CC		6.9728,0.9656,5.0647	probably-damaging,probably-damaging	19/522,19/522	55368291	611,11453	1916	4116	6032	SO:0001583	missense	9840	exon2			CTCTGACGGAGCC	AB018291	CCDS44913.1, CCDS58240.1	12q13.2	2012-03-21	2012-03-21	2012-03-21	ENSG00000135426	ENSG00000135426			29109	protein-coding gene	gene with protein product		615664	"""KIAA0748"""	KIAA0748		9872452	Standard	NM_001136030		Approved		uc001sgn.4	A2RU30	OTTHUMG00000165407	ENST00000449076.1:c.56G>A	12.37:g.55368291C>T	ENSP00000400892:p.Arg19His	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	108	58	0.537037	NM_001098815	B4DPM3|B4E048|B7Z9K7|O94849|Q4G0P2|Q9P0C4	Missense_Mutation	SNP	ENST00000449076.1	37	CCDS44913.1	67	0.030677655677655676	6	0.012195121951219513	7	0.019337016574585635	0	0.0	54	0.0712401055408971	C	15.59	2.879890	0.51801	0.009656	0.069728	ENSG00000135426	ENST00000449076;ENST00000316577;ENST00000524668;ENST00000533607	T;T	0.52754	0.65;0.65	4.84	3.94	0.45596	.	.	.	.	.	T	0.08223	0.0205	L	0.36672	1.1	0.26708	N	0.971021	D	0.89917	1.0	D	0.63703	0.917	T	0.02751	-1.1115	9	0.51188	T	0.08	.	11.161	0.48516	0.1845:0.8155:0.0:0.0	rs62623446	19	A2RU30	K0748_HUMAN	H	19	ENSP00000400892:R19H;ENSP00000312679:R19H	ENSP00000312679:R19H	R	-	2	0	KIAA0748	53654558	0.504000	0.26123	0.509000	0.27700	0.994000	0.84299	0.735000	0.26115	1.332000	0.45431	0.655000	0.94253	CGT	C|0.968;T|0.032	0.032	strong		0.632	TESPA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000383822.1	NM_001098815	
COL11A2	1302	hgsc.bcm.edu	37	6	33144243	33144243	+	Silent	SNP	T	T	A	rs1799908	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:33144243T>A	ENST00000374708.4	-	25	2136	c.1878A>T	c.(1876-1878)ggA>ggT	p.G626G	COL11A2_ENST00000395197.1_Silent_p.G652G|COL11A2_ENST00000357486.1_Silent_p.G691G|COL11A2_ENST00000477772.1_Intron|COL11A2_ENST00000341947.2_Silent_p.G712G|COL11A2_ENST00000374714.1_Silent_p.G686G|COL11A2_ENST00000374713.1_Silent_p.G665G|COL11A2_ENST00000374712.1_Silent_p.G631G|COL11A2_ENST00000361917.1_Silent_p.G605G	NM_080681.2	NP_542412.2	P13942	COBA2_HUMAN	collagen, type XI, alpha 2	712	Triple-helical region.				cartilage development (GO:0051216)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|palate development (GO:0060021)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|soft palate development (GO:0060023)	collagen type XI trimer (GO:0005592)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)|metal ion binding (GO:0046872)|protein binding, bridging (GO:0030674)			biliary_tract(1)|breast(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|liver(1)|lung(27)|ovary(5)|prostate(5)|skin(6)	68						ATCCTAGAGGTCCCTGAGGTC	0.562													A|||	2740	0.547125	0.5242	0.5144	5008	,	,		17786	0.7192		0.4414	False		,,,				2504	0.5327				p.G712G	Melanoma(1;90 116 3946 5341 17093)	Atlas-SNP	.											COL11A2,NS,carcinoma,0,2	COL11A2	124	2	0			c.A2136T						PASS	.	A	,,	1490,1532		365,760,386	36.0	39.0	38.0		1815,2136,1878	1.1	1.0	6	dbSNP_89	38	2209,3207		447,1315,946	yes	coding-synonymous,coding-synonymous,coding-synonymous	COL11A2	NM_080679.2,NM_080680.2,NM_080681.2	,,	812,2075,1332	AA,AT,TT		40.7866,49.3051,43.8374	,,	605/1630,712/1737,626/1651	33144243	3699,4739	1511	2708	4219	SO:0001819	synonymous_variant	1302	exon27			TAGAGGTCCCTGA	U32169	CCDS43452.1, CCDS54992.1	6p21.3	2013-01-16			ENSG00000204248	ENSG00000204248		"""Collagens"""	2187	protein-coding gene	gene with protein product		120290		DFNA13, DFNB53		7559422, 10581026	Standard	NM_080679		Approved	HKE5	uc003ocx.1	P13942	OTTHUMG00000031036	ENST00000374708.4:c.1878A>T	6.37:g.33144243T>A		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	67	66	0.985075	NM_080680	A6NLX2|E7ER90|Q07751|Q13271|Q13272|Q13273|Q5JP94|Q5SUI8|Q7Z6C3|Q99866|Q9UIP9	Silent	SNP	ENST00000374708.4	37	CCDS43452.1																																																																																			T|0.527;A|0.473	0.473	strong		0.562	COL11A2-001	KNOWN	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076032.2		
FMN2	56776	hgsc.bcm.edu	37	1	240492734	240492734	+	Missense_Mutation	SNP	G	G	A	rs3795677	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:240492734G>A	ENST00000319653.9	+	10	4633	c.4403G>A	c.(4402-4404)cGt>cAt	p.R1468H	FMN2_ENST00000545751.1_Missense_Mutation_p.R64H	NM_020066.4	NP_064450.3	Q9NZ56	FMN2_HUMAN	formin 2	1468	FH2. {ECO:0000255|PROSITE- ProRule:PRU00774}.		R -> H (in dbSNP:rs3795677). {ECO:0000269|Ref.3}.		cellular response to DNA damage stimulus (GO:0006974)|cellular response to hypoxia (GO:0071456)|establishment of meiotic spindle localization (GO:0051295)|formin-nucleated actin cable assembly (GO:0070649)|homologous chromosome movement towards spindle pole involved in homologous chromosome segregation (GO:0051758)|intracellular signal transduction (GO:0035556)|intracellular transport (GO:0046907)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein catabolic process (GO:0042177)|oogenesis (GO:0048477)|polar body extrusion after meiotic divisions (GO:0040038)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	cell cortex (GO:0005938)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|microvillus (GO:0005902)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|spindle (GO:0005819)	actin binding (GO:0003779)			NS(1)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(13)|lung(87)|ovary(6)|pancreas(3)|prostate(12)|skin(7)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(2)	178	Ovarian(103;0.127)	all_cancers(173;0.013)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)			TGCTCAATTCGTCGCAAACTG	0.408													G|||	1607	0.320887	0.3381	0.3588	5008	,	,		18670	0.3185		0.2883	False		,,,				2504	0.3067				p.R1468H		Atlas-SNP	.											FMN2,NS,carcinoma,+1,1	FMN2	451	1	0			c.G4403A						PASS	.	G	HIS/ARG	1380,3026	456.3+/-351.3	201,978,1024	144.0	136.0	138.0		4403	1.7	1.0	1	dbSNP_107	138	2363,6237	394.1+/-344.6	308,1747,2245	yes	missense	FMN2	NM_020066.4	29	509,2725,3269	AA,AG,GG		27.4767,31.3209,28.779	possibly-damaging	1468/1723	240492734	3743,9263	2203	4300	6503	SO:0001583	missense	56776	exon10			CAATTCGTCGCAA	AF218942	CCDS31069.2	1q43	2008-02-05			ENSG00000155816	ENSG00000155816			14074	protein-coding gene	gene with protein product		606373				10781961	Standard	NM_020066		Approved		uc010pyd.2	Q9NZ56	OTTHUMG00000039883	ENST00000319653.9:c.4403G>A	1.37:g.240492734G>A	ENSP00000318884:p.Arg1468His	Somatic	266	0	0		WXS	Illumina HiSeq	Phase_I	224	115	0.513393	NM_020066	B0QZA7|B4DP05|Q59GF6|Q5VU37|Q9NZ55	Missense_Mutation	SNP	ENST00000319653.9	37	CCDS31069.2	705	0.3228021978021978	158	0.32113821138211385	127	0.35082872928176795	196	0.34265734265734266	224	0.2955145118733509	G	7.918	0.737991	0.15574	0.313209	0.274767	ENSG00000155816	ENST00000319653;ENST00000545751;ENST00000537355	T;T	0.18502	2.21;2.21	5.65	1.72	0.24424	Actin-binding FH2/DRF autoregulatory (1);Actin-binding FH2 (3);	0.324081	0.26065	N	0.026552	T	0.00012	0.0000	N	0.25890	0.77	0.09310	P	0.9999999999949641	B;B;B;P	0.34837	0.002;0.005;0.008;0.472	B;B;B;B	0.37780	0.002;0.005;0.008;0.258	T	0.31586	-0.9938	9	0.06365	T	0.9	.	11.8887	0.52616	0.2878:0.0:0.7122:0.0	rs3795677;rs17679152;rs56984583;rs3795677	64;114;97;1468	B4DP05;F5H2C1;B4DN09;Q9NZ56	.;.;.;FMN2_HUMAN	H	1468;64;95	ENSP00000318884:R1468H;ENSP00000437918:R64H	ENSP00000318884:R1468H	R	+	2	0	FMN2	238559357	0.000000	0.05858	0.998000	0.56505	0.979000	0.70002	-0.225000	0.09151	0.059000	0.16252	-0.940000	0.02684	CGT	G|0.684;A|0.316	0.316	strong		0.408	FMN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096217.2	XM_371352	
SLFN11	91607	hgsc.bcm.edu	37	17	33680807	33680807	+	Silent	SNP	G	G	A	rs9897352	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:33680807G>A	ENST00000394566.1	-	6	1742	c.1470C>T	c.(1468-1470)acC>acT	p.T490T	SLFN11_ENST00000308377.4_Silent_p.T490T	NM_001104587.1|NM_001104588.1|NM_001104589.1|NM_001104590.1	NP_001098057.1|NP_001098058.1|NP_001098059.1|NP_001098060.1	Q7Z7L1	SLN11_HUMAN	schlafen family member 11	490					defense response to virus (GO:0051607)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|tRNA binding (GO:0000049)	p.T490T(1)		autonomic_ganglia(1)|breast(1)|kidney(3)|large_intestine(14)|lung(17)|ovary(1)|prostate(4)|skin(2)|stomach(5)|upper_aerodigestive_tract(2)	50		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		AAGTAAAGGCGGTGCGAGTGC	0.562													G|||	3783	0.755391	0.7148	0.7291	5008	,	,		9874	0.9107		0.6769	False		,,,				2504	0.7495				p.T490T		Atlas-SNP	.											SLFN11,NS,carcinoma,0,1	SLFN11	112	1	1	Substitution - coding silent(1)	stomach(1)	c.C1470T						scavenged	.						15.0	13.0	14.0					17																	33680807		2176	4237	6413	SO:0001819	synonymous_variant	91607	exon4			AAAGGCGGTGCGA	AK074184	CCDS11294.1	17q12	2006-04-05			ENSG00000172716	ENSG00000172716			26633	protein-coding gene	gene with protein product		614953				12477932	Standard	NM_001104587		Approved	FLJ34922	uc010ctr.3	Q7Z7L1	OTTHUMG00000132948	ENST00000394566.1:c.1470C>T	17.37:g.33680807G>A		Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	133	89	0.669173	NM_152270	E1P643|Q8N3S8|Q8N762|Q8TEE0	Silent	SNP	ENST00000394566.1	37	CCDS11294.1																																																																																			G|0.234;A|0.766	0.766	strong		0.562	SLFN11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256480.1	NM_152270	
C15orf32	145858	hgsc.bcm.edu	37	15	93015427	93015427	+	Missense_Mutation	SNP	G	G	A	rs1455773	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:93015427G>A	ENST00000333334.2	+	1	544	c.49G>A	c.(49-51)Gct>Act	p.A17T	C15orf32_ENST00000556865.1_Missense_Mutation_p.A17T|RP11-763K15.1_ENST00000554440.1_lincRNA	NM_153040.2	NP_694585.1	Q32M92	CO032_HUMAN	chromosome 15 open reading frame 32	17			A -> T (in dbSNP:rs1455773).							endometrium(1)|large_intestine(2)|lung(5)|ovary(1)|prostate(1)|skin(2)	12	Lung NSC(78;0.0893)|all_lung(78;0.125)		BRCA - Breast invasive adenocarcinoma(143;0.0493)|OV - Ovarian serous cystadenocarcinoma(32;0.125)			CTTGCACCCGGCTGACCCCCA	0.532													G|||	2128	0.42492	0.4728	0.4135	5008	,	,		19913	0.4772		0.336	False		,,,				2504	0.4059				p.A17T		Atlas-SNP	.											.	C15orf32	22	.	0			c.G49A						PASS	.	G	THR/ALA	1943,2453	550.6+/-378.1	420,1103,675	52.0	54.0	53.0		49	-0.1	0.0	15	dbSNP_88	53	2623,5973	424.3+/-354.6	389,1845,2064	yes	missense	C15orf32	NM_153040.2	58	809,2948,2739	AA,AG,GG		30.5142,44.1993,35.1447	benign	17/179	93015427	4566,8426	2198	4298	6496	SO:0001583	missense	145858	exon1			CACCCGGCTGACC		CCDS10373.1, CCDS73784.1	15q26.1	2014-09-10			ENSG00000183643	ENSG00000183643			26549	protein-coding gene	gene with protein product							Standard	NM_153040		Approved	FLJ32831	uc002brc.1	Q32M92	OTTHUMG00000149844	ENST00000333334.2:c.49G>A	15.37:g.93015427G>A	ENSP00000330267:p.Ala17Thr	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	87	53	0.609195	NM_153040	C5HTZ8|Q96M45	Missense_Mutation	SNP	ENST00000333334.2	37	CCDS10373.1	893	0.4088827838827839	229	0.4654471544715447	148	0.4088397790055249	261	0.4562937062937063	255	0.33641160949868076	G	9.624	1.134609	0.21123	0.441993	0.305142	ENSG00000183643	ENST00000333334	T	0.54866	0.55	2.29	-0.0883	0.13674	.	.	.	.	.	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B	0.14012	0.009	B	0.10450	0.005	T	0.43393	-0.9394	8	0.87932	D	0	.	4.381	0.11293	0.6211:0.0:0.3789:0.0	rs1455773;rs60165357;rs1455773	17	Q32M92	CO032_HUMAN	T	17	ENSP00000330267:A17T	ENSP00000330267:A17T	A	+	1	0	C15orf32	90816431	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.335000	0.07873	-0.045000	0.13468	-0.471000	0.05019	GCT	G|0.616;N|0.000	.	strong		0.532	C15orf32-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313527.2	NM_153040	
ELSPBP1	64100	hgsc.bcm.edu	37	19	48519158	48519158	+	Missense_Mutation	SNP	C	C	T	rs34129198	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:48519158C>T	ENST00000339841.2	+	4	395	c.217C>T	c.(217-219)Cgc>Tgc	p.R73C	ELSPBP1_ENST00000597519.1_Intron	NM_022142.4	NP_071425.3	Q96BH3	ESPB1_HUMAN	epididymal sperm binding protein 1	73	Fibronectin type-II 2. {ECO:0000255|PROSITE-ProRule:PRU00479}.				single fertilization (GO:0007338)	extracellular region (GO:0005576)				NS(1)|breast(1)|kidney(1)|large_intestine(1)|lung(6)	10		all_cancers(25;8.7e-09)|all_lung(116;1.15e-06)|all_epithelial(76;1.17e-06)|Lung NSC(112;2.56e-06)|all_neural(266;0.0138)|Ovarian(192;0.0261)|Breast(70;0.203)		OV - Ovarian serous cystadenocarcinoma(262;0.000253)|all cancers(93;0.00129)|Epithelial(262;0.0314)|GBM - Glioblastoma multiforme(486;0.0606)		AGATTACCCACGCTGTATCTT	0.463													c|||	810	0.161741	0.2103	0.1254	5008	,	,		20377	0.0724		0.1531	False		,,,				2504	0.2229				p.R73C		Atlas-SNP	.											.	ELSPBP1	29	.	0			c.C217T						PASS	.	C	CYS/ARG	884,3522	343.3+/-307.6	86,712,1405	106.0	83.0	91.0		217	2.2	0.9	19	dbSNP_126	91	1294,7306	256.1+/-280.7	91,1112,3097	yes	missense	ELSPBP1	NM_022142.4	180	177,1824,4502	TT,TC,CC		15.0465,20.0635,16.7461	probably-damaging	73/224	48519158	2178,10828	2203	4300	6503	SO:0001583	missense	64100	exon4			TACCCACGCTGTA	AJ278478	CCDS12708.1	19q13.33	2009-09-17							14417	protein-coding gene	gene with protein product	"""epididymal protein 12"""	607443					Standard	NM_022142		Approved	HE12, E12, EDDM12	uc002pht.3	Q96BH3		ENST00000339841.2:c.217C>T	19.37:g.48519158C>T	ENSP00000340660:p.Arg73Cys	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	82	38	0.463415	NM_022142	Q96RT0|Q9H4C8	Missense_Mutation	SNP	ENST00000339841.2	37	CCDS12708.1	325	0.1488095238095238	107	0.21747967479674796	59	0.16298342541436464	47	0.08216783216783216	112	0.14775725593667546	C	9.088	1.000976	0.19121	0.200635	0.150465	ENSG00000169393	ENST00000339841	T	0.10005	2.92	3.4	2.21	0.28008	Fibronectin, type II, collagen-binding (3);Kringle-like fold (1);	0.186449	0.24554	N	0.037536	T	0.00012	0.0000	L	0.35414	1.06	0.40606	P	0.018378000000000005	P	0.35226	0.491	B	0.27608	0.081	T	0.45425	-0.9262	9	0.38643	T	0.18	.	7.0708	0.25177	0.2693:0.7306:0.0:0.0	rs34129198	73	Q96BH3	ESPB1_HUMAN	C	73	ENSP00000340660:R73C	ENSP00000340660:R73C	R	+	1	0	ELSPBP1	53210970	0.868000	0.29978	0.938000	0.37757	0.306000	0.27790	1.077000	0.30741	1.817000	0.53016	0.543000	0.68304	CGC	C|0.837;T|0.163	0.163	strong		0.463	ELSPBP1-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465207.1		
PLEKHD1	400224	hgsc.bcm.edu	37	14	69995112	69995112	+	Silent	SNP	G	G	A	rs55727771	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:69995112G>A	ENST00000322564.7	+	13	1709	c.1497G>A	c.(1495-1497)tcG>tcA	p.S499S		NM_001161498.1	NP_001154970.1	A6NEE1	PLHD1_HUMAN	pleckstrin homology domain containing, family D (with coiled-coil domains) member 1	499										breast(1)|endometrium(1)|kidney(2)	4						GAGCCCCCTCGGCACTCTCCC	0.662													G|||	511	0.102037	0.0484	0.0865	5008	,	,		15213	0.1508		0.1243	False		,,,				2504	0.1125				p.S499S		Atlas-SNP	.											.	PLEKHD1	24	.	0			c.G1497A						PASS	.	G		82,1302		4,74,614	35.0	43.0	41.0		1497	-10.5	0.0	14	dbSNP_129	41	393,2789		20,353,1218	no	coding-synonymous	PLEKHD1	NM_001161498.1		24,427,1832	AA,AG,GG		12.3507,5.9249,10.403		499/507	69995112	475,4091	692	1591	2283	SO:0001819	synonymous_variant	400224	exon13			CCCCTCGGCACTC	AK126770	CCDS53903.1	14q24.1	2013-01-10	2011-05-04		ENSG00000175985	ENSG00000175985		"""Pleckstrin homology (PH) domain containing"""	20148	protein-coding gene	gene with protein product			"""pleckstrin homology domain containing, family D (with M protein repeats) member 1"""				Standard	NM_001161498		Approved	UPF0639	uc010ttf.1	A6NEE1		ENST00000322564.7:c.1497G>A	14.37:g.69995112G>A		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	64	62	0.96875	NM_001161498	B9EJC2	Silent	SNP	ENST00000322564.7	37	CCDS53903.1																																																																																			G|0.895;A|0.105	0.105	strong		0.662	PLEKHD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412451.2	NM_001161498	
C5orf55	116349	hgsc.bcm.edu	37	5	442586	442586	+	Missense_Mutation	SNP	G	G	C	rs10035612	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:442586G>C	ENST00000408966.2	-	1	672	c.352C>G	c.(352-354)Cgg>Ggg	p.R118G	EXOC3_ENST00000512944.1_5'Flank	NM_138464.2	NP_612473.1	Q8N2X6	CE055_HUMAN	chromosome 5 open reading frame 55	118			R -> G (in dbSNP:rs10035612).			extracellular region (GO:0005576)				large_intestine(1)|lung(2)	3						ACTCAGGACCGGCCCTCTGCA	0.637													G|||	428	0.0854633	0.031	0.147	5008	,	,		18305	0.1339		0.0736	False		,,,				2504	0.0777				p.R118G		Atlas-SNP	.											.	C5orf55	11	.	0			c.C352G						PASS	.	G	GLY/ARG	141,3709		3,135,1787	30.0	32.0	32.0		352	-1.7	0.0	5	dbSNP_119	32	685,7567		34,617,3475	yes	missense	C5orf55	NM_138464.2	125	37,752,5262	CC,CG,GG		8.301,3.6623,6.8253	benign	118/120	442586	826,11276	1925	4126	6051	SO:0001583	missense	116349	exon1			AGGACCGGCCCTC	BC014011	CCDS43298.1	5p15.33	2012-02-24			ENSG00000221990	ENSG00000221990			25175	protein-coding gene	gene with protein product						12477932	Standard	NM_138464		Approved		uc010ita.3	Q8N2X6	OTTHUMG00000162235	ENST00000408966.2:c.352C>G	5.37:g.442586G>C	ENSP00000386139:p.Arg118Gly	Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	27	14	0.518519	NM_138464	Q96CR9	Missense_Mutation	SNP	ENST00000408966.2	37	CCDS43298.1	188	0.08608058608058608	22	0.044715447154471545	47	0.1298342541436464	54	0.0944055944055944	65	0.08575197889182058	G	3.483	-0.105384	0.06967	0.036623	0.08301	ENSG00000221990	ENST00000408966	T	0.39787	1.06	0.849	-1.7	0.08159	.	.	.	.	.	T	0.00178	0.0005	N	0.08118	0	0.80722	P	0.0	B	0.12013	0.005	B	0.06405	0.002	T	0.11842	-1.0571	8	0.87932	D	0	.	2.6537	0.05005	0.2923:0.3923:0.3154:0.0	rs10035612;rs10035612	118	Q8N2X6	CE055_HUMAN	G	118	ENSP00000386139:R118G	ENSP00000386139:R118G	R	-	1	2	C5orf55	495586	0.000000	0.05858	0.002000	0.10522	0.430000	0.31655	-1.365000	0.02587	-1.033000	0.03299	0.205000	0.17691	CGG	G|0.925;C|0.075	0.075	strong		0.637	C5orf55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368033.1	NM_138464	
ECE2	9718	hgsc.bcm.edu	37	3	183996068	183996068	+	Silent	SNP	C	C	T	rs3752904	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:183996068C>T	ENST00000402825.3	+	6	1071	c.1071C>T	c.(1069-1071)gcC>gcT	p.A357A	ECE2_ENST00000357474.5_Silent_p.A285A|EIF2B5_ENST00000444495.1_Intron|ECE2_ENST00000404464.3_Silent_p.A239A|ECE2_ENST00000359140.4_Silent_p.A210A	NM_014693.3	NP_055508.3	O60344	ECE2_HUMAN	endothelin converting enzyme 2	357	Endothelin-converting enzyme 2 region.				brain development (GO:0007420)|cardioblast differentiation (GO:0010002)|cell-cell signaling (GO:0007267)|heart development (GO:0007507)|peptide hormone processing (GO:0016486)	cytoplasmic vesicle membrane (GO:0030659)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)|methyltransferase activity (GO:0008168)			breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(11)|lung(13)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(4)	49	all_cancers(143;1.39e-10)|Ovarian(172;0.0339)		Epithelial(37;8.28e-34)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			ACATCAGTGCCGACTCTAAGA	0.542													C|||	2514	0.501997	0.593	0.6095	5008	,	,		16408	0.4157		0.5308	False		,,,				2504	0.362				p.A357A		Atlas-SNP	.											.	ECE2	303	.	0			c.C1071T						PASS	.	C	,,,	2666,1740	647.2+/-398.5	823,1020,360	75.0	73.0	73.0		630,855,717,1071	-7.3	0.7	3	dbSNP_107	73	4504,4096	591.6+/-392.9	1175,2154,971	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ECE2	NM_001037324.2,NM_001100120.1,NM_001100121.1,NM_014693.3	,,,	1998,3174,1331	TT,TC,CC		47.6279,39.4916,44.8716	,,,	210/737,285/812,239/766,357/884	183996068	7170,5836	2203	4300	6503	SO:0001819	synonymous_variant	9718	exon6			CAGTGCCGACTCT	AF428263	CCDS3255.1, CCDS33899.1, CCDS3256.2, CCDS43179.1, CCDS46969.1	3q27.1	2007-07-26			ENSG00000145194	ENSG00000145194			13275	protein-coding gene	gene with protein product		610145				11718899	Standard	NM_032331		Approved	KIAA0604, MGC2408	uc003fni.4	O60344	OTTHUMG00000150551	ENST00000402825.3:c.1071C>T	3.37:g.183996068C>T		Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	132	66	0.5	NM_014693	A5PLK8|Q6NTG7|Q6UW36|Q8NFD7|Q96NX3|Q96NX4|Q9BRZ8	Silent	SNP	ENST00000402825.3	37	CCDS3256.2																																																																																			C|0.451;T|0.549	0.549	strong		0.542	ECE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318874.3	NM_014693	
HCFC1R1	54985	hgsc.bcm.edu	37	16	3073240	3073240	+	Missense_Mutation	SNP	G	G	T	rs10508	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:3073240G>T	ENST00000248089.3	-	3	579	c.275C>A	c.(274-276)cCa>cAa	p.P92Q	HCFC1R1_ENST00000574151.1_Missense_Mutation_p.P73Q|THOC6_ENST00000574549.1_5'Flank|HCFC1R1_ENST00000396916.1_Missense_Mutation_p.P92Q|HCFC1R1_ENST00000574980.1_Missense_Mutation_p.P92Q|HCFC1R1_ENST00000354679.3_Missense_Mutation_p.P90Q|HCFC1R1_ENST00000572355.1_Missense_Mutation_p.P52Q|THOC6_ENST00000575576.1_5'Flank|THOC6_ENST00000326266.8_5'Flank|THOC6_ENST00000253952.9_5'Flank	NM_017885.2	NP_060355.1	Q9NWW0	HPIP_HUMAN	host cell factor C1 regulator 1 (XPO1 dependent)	92			P -> Q (in dbSNP:rs10508). {ECO:0000269|PubMed:15489334}.			cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|large_intestine(1)|upper_aerodigestive_tract(1)	3						CTACCTGAGTGGGGGCAGGGC	0.597													G|||	947	0.189097	0.1354	0.1916	5008	,	,		15819	0.1181		0.2356	False		,,,				2504	0.2853				p.P92Q		Atlas-SNP	.											HCFC1R1_ENST00000248089,NS,carcinoma,0,2	HCFC1R1	17	2	0			c.C275A						scavenged	.	G	GLN/PRO,GLN/PRO,GLN/PRO	606,3790	260.1+/-263.5	46,514,1638	38.0	43.0	41.0		218,275,275	3.1	1.0	16	dbSNP_52	41	1976,6624	342.7+/-324.6	227,1522,2551	yes	missense,missense,missense	HCFC1R1	NM_001002017.1,NM_001002018.1,NM_017885.2	76,76,76	273,2036,4189	TT,TG,GG		22.9767,13.7853,19.8677	benign,benign,benign	73/120,92/139,92/139	3073240	2582,10414	2198	4300	6498	SO:0001583	missense	54985	exon3			CTGAGTGGGGGCA	AK000575	CCDS10490.1, CCDS32375.1, CCDS73815.1	16p13.3	2008-02-05	2005-12-01			ENSG00000103145			21198	protein-coding gene	gene with protein product			"""host cell factor C1 regulator 1 (XPO1 dependant)"""			12235138	Standard	NM_001002018		Approved	HPIP, FLJ20568	uc002csy.1	Q9NWW0		ENST00000248089.3:c.275C>A	16.37:g.3073240G>T	ENSP00000248089:p.Pro92Gln	Somatic	55	1	0.0181818		WXS	Illumina HiSeq	Phase_I	67	50	0.746269	NM_017885	D3DUA7|Q68EN7	Missense_Mutation	SNP	ENST00000248089.3	37	CCDS10490.1	366	0.16758241758241757	54	0.10975609756097561	75	0.20718232044198895	59	0.10314685314685315	178	0.23482849604221637	G	9.981	1.228065	0.22542	0.137853	0.229767	ENSG00000103145	ENST00000248089;ENST00000354679;ENST00000396916	T;T	0.44881	0.91;0.91	5.16	3.14	0.36123	.	1.204350	0.06110	N	0.667046	T	0.00012	0.0000	N	0.19112	0.55	0.25564	P	0.9869678	P;B	0.36837	0.571;0.037	B;B	0.34452	0.183;0.012	T	0.14364	-1.0475	9	0.49607	T	0.09	0.0011	7.4927	0.27471	0.0927:0.1666:0.7407:0.0	rs10508;rs1130914;rs1804992;rs2285974;rs3177831;rs3190341;rs11558417;rs17342478;rs17350124;rs58574567;rs10508	73;92	Q9NWW0-2;Q9NWW0	.;HPIP_HUMAN	Q	92;73;92	ENSP00000248089:P92Q;ENSP00000380123:P92Q	ENSP00000248089:P92Q	P	-	2	0	HCFC1R1	3013241	0.946000	0.32159	0.999000	0.59377	0.630000	0.37929	2.458000	0.45014	1.172000	0.42781	0.558000	0.71614	CCA	G|0.817;T|0.183	0.183	strong		0.597	HCFC1R1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000436969.1	NM_017885	
FPR3	2359	hgsc.bcm.edu	37	19	52327784	52327784	+	Silent	SNP	C	C	T	rs3752125	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:52327784C>T	ENST00000339223.4	+	2	962	c.783C>T	c.(781-783)ggC>ggT	p.G261G	FPR3_ENST00000595991.1_Silent_p.G261G	NM_002030.3	NP_002021.3	P25089	FPR3_HUMAN	formyl peptide receptor 3	261					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						AACTAATTGGCATTCTAATGG	0.413													C|||	1135	0.226637	0.0998	0.2997	5008	,	,		21535	0.2649		0.2763	False		,,,				2504	0.2556				p.G261G		Atlas-SNP	.											.	FPR3	66	.	0			c.C783T						PASS	.	C		577,3829		38,501,1664	149.0	134.0	139.0		783	1.0	0.0	19	dbSNP_107	139	2638,5962		402,1834,2064	no	coding-synonymous	FPR3	NM_002030.3		440,2335,3728	TT,TC,CC		30.6744,13.0958,24.7194		261/354	52327784	3215,9791	2203	4300	6503	SO:0001819	synonymous_variant	2359	exon2			AATTGGCATTCTA		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.783C>T	19.37:g.52327784C>T		Somatic	350	0	0		WXS	Illumina HiSeq	Phase_I	320	133	0.415625	NM_002030		Silent	SNP	ENST00000339223.4	37	CCDS12841.1																																																																																			C|0.753;T|0.247	0.247	strong		0.413	FPR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466914.1	NM_002030	
SRGAP3	9901	hgsc.bcm.edu	37	3	9099989	9099989	+	Silent	SNP	A	A	G	rs61747289	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:9099989A>G	ENST00000383836.3	-	7	1396	c.969T>C	c.(967-969)aaT>aaC	p.N323N	SRGAP3_ENST00000360413.3_Silent_p.N323N|SRGAP3_ENST00000433332.3_5'UTR	NM_014850.3	NP_055665.1	O43295	SRGP3_HUMAN	SLIT-ROBO Rho GTPase activating protein 3	323	F-BAR domain.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)		SRGAP3/RAF1(6)	breast(1)|endometrium(2)|kidney(21)|large_intestine(7)|lung(13)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	54				OV - Ovarian serous cystadenocarcinoma(96;0.0563)		AGAAGACTTGATTGCACATGT	0.567			T	RAF1	pilocytic astrocytoma								A|||	84	0.0167732	0.0015	0.0476	5008	,	,		20339	0.0		0.0328	False		,,,				2504	0.0164				p.N323N		Atlas-SNP	.		Dom	yes		3	3p25.3	9901	SLIT-ROBO Rho GTPase activating protein 3		M	.	SRGAP3	146	.	0			c.T969C						PASS	.	A	,	46,4360	48.2+/-83.0	1,44,2158	239.0	193.0	209.0		969,969	2.7	1.0	3	dbSNP_129	209	440,8160	134.9+/-192.2	12,416,3872	no	coding-synonymous,coding-synonymous	SRGAP3	NM_001033117.1,NM_014850.2	,	13,460,6030	GG,GA,AA		5.1163,1.044,3.7367	,	323/1076,323/1100	9099989	486,12520	2203	4300	6503	SO:0001819	synonymous_variant	9901	exon7			GACTTGATTGCAC	AB007871	CCDS2572.1, CCDS33689.1	3p25.3	2011-07-04	2004-11-12	2004-11-12	ENSG00000196220	ENSG00000196220		"""Rho GTPase activating proteins"""	19744	protein-coding gene	gene with protein product		606525	"""SLIT-ROBO Rho GTPase activating protein 2"""	SRGAP2		12195014	Standard	NM_014850		Approved	KIAA0411, MEGAP, WRP, ARHGAP14	uc003brf.2	O43295	OTTHUMG00000090589	ENST00000383836.3:c.969T>C	3.37:g.9099989A>G		Somatic	244	0	0		WXS	Illumina HiSeq	Phase_I	177	75	0.423729	NM_014850	Q8IX13|Q8IZV8	Silent	SNP	ENST00000383836.3	37	CCDS2572.1																																																																																			A|0.967;G|0.033	0.033	strong		0.567	SRGAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207137.3		
C2orf16	84226	hgsc.bcm.edu	37	2	27801403	27801403	+	Missense_Mutation	SNP	C	C	G	rs1919125	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:27801403C>G	ENST00000408964.2	+	1	2015	c.1964C>G	c.(1963-1965)aCt>aGt	p.T655S		NM_032266.3	NP_115642.3	Q68DN1	CB016_HUMAN	chromosome 2 open reading frame 16	655			T -> S (in dbSNP:rs1919125).			extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(33)|urinary_tract(1)	47	Acute lymphoblastic leukemia(172;0.155)					AGTCCATGTACTCAAGTGAAG	0.393													T|||	3303	0.659545	0.7368	0.6888	5008	,	,		21823	0.8462		0.498	False		,,,				2504	0.5082				p.T655S		Atlas-SNP	.											.	C2orf16	357	.	0			c.C1964G						PASS	.	T	SER/THR	2616,1152		902,812,170	97.0	95.0	95.0		1964	-0.7	0.0	2	dbSNP_92	95	4085,4151		1029,2027,1062	yes	missense	C2orf16	NM_032266.3	58	1931,2839,1232	GG,GC,CC		49.5993,30.5732,44.1769	benign	655/1985	27801403	6701,5303	1884	4118	6002	SO:0001583	missense	84226	exon1			CATGTACTCAAGT	AL136898	CCDS42666.1	2p23.3	2013-09-20			ENSG00000221843	ENSG00000221843			25275	protein-coding gene	gene with protein product	"""P-S-E-R-S-H-H-S repeats containing"""						Standard	NM_032266		Approved	DKFZp434G118	uc002rkz.4	Q68DN1	OTTHUMG00000159099	ENST00000408964.2:c.1964C>G	2.37:g.27801403C>G	ENSP00000386190:p.Thr655Ser	Somatic	320	0	0		WXS	Illumina HiSeq	Phase_I	350	349	0.997143	NM_032266	B9EIQ4|Q53S01|Q8ND64|Q9H088	Missense_Mutation	SNP	ENST00000408964.2	37	CCDS42666.1	1448	0.663003663003663	359	0.7296747967479674	229	0.6325966850828729	490	0.8566433566433567	370	0.48812664907651715	T	0.082	-1.181599	0.01633	0.694268	0.495993	ENSG00000221843	ENST00000408964	T	0.05649	3.41	4.27	-0.677	0.11357	.	.	.	.	.	T	0.00012	0.0000	N	0.12182	0.205	0.80722	P	0.0	B	0.06786	0.001	B	0.04013	0.001	T	0.12218	-1.0556	8	0.10377	T	0.69	.	5.683	0.17786	0.0:0.2722:0.5177:0.2101	rs1919125;rs17756208;rs60093522;rs1919125	655	Q68DN1	CB016_HUMAN	S	655	ENSP00000386190:T655S	ENSP00000386190:T655S	T	+	2	0	C2orf16	27654907	0.001000	0.12720	0.040000	0.18447	0.033000	0.12548	-0.497000	0.06428	-0.356000	0.08187	-1.482000	0.00985	ACT	C|0.375;G|0.625	0.625	strong		0.393	C2orf16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353292.1	NM_032266	
DGKB	1607	hgsc.bcm.edu	37	7	14217673	14217673	+	Silent	SNP	G	G	A	rs6966154	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:14217673G>A	ENST00000403951.2	-	24	2648	c.2229C>T	c.(2227-2229)tgC>tgT	p.C743C	DGKB_ENST00000444700.2_Silent_p.C724C|DGKB_ENST00000407950.1_Silent_p.C735C|DGKB_ENST00000402815.1_Silent_p.C742C|DGKB_ENST00000399322.3_Silent_p.C743C|DGKB_ENST00000406247.3_Silent_p.C743C|DGKB_ENST00000258767.5_Silent_p.C743C			Q9Y6T7	DGKB_HUMAN	diacylglycerol kinase, beta 90kDa	743					blood coagulation (GO:0007596)|intracellular signal transduction (GO:0035556)|platelet activation (GO:0030168)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|diacylglycerol kinase activity (GO:0004143)|NAD+ kinase activity (GO:0003951)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|liver(1)|lung(34)|ovary(4)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	72						CCACGCAGGAGCACTGAGCCA	0.507													G|||	1454	0.290335	0.5378	0.2003	5008	,	,		14132	0.2659		0.2078	False		,,,				2504	0.1299				p.C743C		Atlas-SNP	.											.	DGKB	166	.	0			c.C2229T						PASS	.	G	,	1910,2292		444,1022,635	53.0	62.0	59.0		2229,2229	3.1	1.0	7	dbSNP_116	59	1488,7060		122,1244,2908	no	coding-synonymous,coding-synonymous	DGKB	NM_004080.2,NM_145695.2	,	566,2266,3543	AA,AG,GG		17.4076,45.4545,26.651	,	743/805,743/774	14217673	3398,9352	2101	4274	6375	SO:0001819	synonymous_variant	1607	exon23			GCAGGAGCACTGA	AB018261	CCDS47547.1, CCDS47548.1	7p21.2	2013-01-10	2002-08-29		ENSG00000136267	ENSG00000136267	2.7.1.107	"""EF-hand domain containing"""	2850	protein-coding gene	gene with protein product		604070	"""diacylglycerol kinase, beta (90kD)"""	DAGK2		7689223	Standard	NM_004080		Approved	KIAA0718, DGK, DGK-BETA	uc003ssz.3	Q9Y6T7	OTTHUMG00000152477	ENST00000403951.2:c.2229C>T	7.37:g.14217673G>A		Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	37	29	0.783784	NM_145695	A4D116|A4D117|A8MXU2|O75241|Q2M377|Q75MF9|Q75MU7|Q86UI5|Q86UM9|Q9UQ29	Silent	SNP	ENST00000403951.2	37	CCDS47547.1																																																																																			G|0.720;A|0.280	0.280	strong		0.507	DGKB-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000326356.2	NM_004080	
ARMC12	221481	hgsc.bcm.edu	37	6	35705892	35705892	+	Silent	SNP	T	T	C	rs386700146|rs2817041	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:35705892T>C	ENST00000373866.3	+	2	274	c.252T>C	c.(250-252)taT>taC	p.Y84Y	RP3-510O8.4_ENST00000452048.1_RNA|ARMC12_ENST00000373869.3_Silent_p.Y84Y|ARMC12_ENST00000288065.2_Silent_p.Y111Y			Q5T9G4	ARM12_HUMAN	armadillo repeat containing 12	84						nucleus (GO:0005634)											AGGATGAGTATGCCAAGAGCA	0.617											OREG0017379	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	3803	0.759385	0.8086	0.8473	5008	,	,		17563	0.5794		0.8002	False		,,,				2504	0.774				p.Y111Y		Atlas-SNP	.											.	.	.	.	0			c.T333C						PASS	.	C		3439,967	364.6+/-317.1	1340,759,104	90.0	90.0	90.0		333	4.4	0.3	6	dbSNP_100	90	6923,1677	308.9+/-309.1	2764,1395,141	no	coding-synonymous	C6orf81	NM_145028.3		4104,2154,245	CC,CT,TT		19.5,21.9473,20.3291		111/368	35705892	10362,2644	2203	4300	6503	SO:0001819	synonymous_variant	221481	exon2			TGAGTATGCCAAG	AK058119	CCDS4809.1, CCDS69093.1, CCDS69094.1	6p21.31	2013-02-14	2011-12-14	2011-12-14	ENSG00000157343	ENSG00000157343		"""Armadillo repeat containing"""	21099	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 81"""	C6orf81			Standard	XM_005248920		Approved	FLJ25390	uc003ola.3	Q5T9G4	OTTHUMG00000014577	ENST00000373866.3:c.252T>C	6.37:g.35705892T>C		Somatic	61	0	0	857	WXS	Illumina HiSeq	Phase_I	76	76	1	NM_145028	Q8NEB2|Q96LL8	Silent	SNP	ENST00000373866.3	37																																																																																				T|0.216;C|0.784	0.784	strong		0.617	ARMC12-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000040311.2	NM_145028	
DNHD1	144132	hgsc.bcm.edu	37	11	6588228	6588228	+	Missense_Mutation	SNP	G	G	A	rs10769699	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:6588228G>A	ENST00000527990.2	+	34	11489	c.11489G>A	c.(11488-11490)cGt>cAt	p.R3830H	DNHD1_ENST00000254579.6_Missense_Mutation_p.R3830H			Q96M86	DNHD1_HUMAN	dynein heavy chain domain 1	3830			R -> H (in dbSNP:rs10769699).		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)		TGCCAGCTGCGTGCTCATTGT	0.537													G|||	1167	0.233027	0.0734	0.3098	5008	,	,		22346	0.2222		0.4095	False		,,,				2504	0.2239				p.R3830H		Atlas-SNP	.											.	DNHD1	198	.	0			c.G11489A						PASS	.	G	HIS/ARG	448,3592		24,400,1596	79.0	82.0	81.0		11489	-0.1	0.7	11	dbSNP_120	81	3213,5139		620,1973,1583	yes	missense	DNHD1	NM_144666.2	29	644,2373,3179	AA,AG,GG		38.4698,11.0891,29.5433	benign	3830/4754	6588228	3661,8731	2020	4176	6196	SO:0001583	missense	144132	exon36			AGCTGCGTGCTCA	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.11489G>A	11.37:g.6588228G>A	ENSP00000436180:p.Arg3830His	Somatic	137	1	0.00729927		WXS	Illumina HiSeq	Phase_I	175	174	0.994286	NM_144666	Q2NKK8|Q6UWI9|Q8NAA2|Q8TEE6|Q9NSZ9	Missense_Mutation	SNP	ENST00000527990.2	37	CCDS44532.1	603	0.2760989010989011	28	0.056910569105691054	119	0.3287292817679558	151	0.263986013986014	305	0.4023746701846966	G	7.681	0.689026	0.14973	0.110891	0.384698	ENSG00000179532	ENST00000254579;ENST00000527990;ENST00000525883;ENST00000530197	T;T	0.26810	1.71;1.71	4.82	-0.0996	0.13624	.	1.110500	0.06919	N	0.808972	T	0.00012	0.0000	N	0.12182	0.205	0.80722	P	0.0	B;B;B	0.18610	0.013;0.013;0.029	B;B;B	0.10450	0.002;0.002;0.005	T	0.47947	-0.9077	9	0.37606	T	0.19	-0.2341	7.1096	0.25382	0.6282:0.0:0.3718:0.0	rs10769699;rs52822986;rs60470898;rs10769699	2918;98;3830	B0I1S4;D3DQT9;Q96M86	.;.;DNHD1_HUMAN	H	3830;3830;98;98	ENSP00000254579:R3830H;ENSP00000436180:R3830H	ENSP00000254579:R3830H	R	+	2	0	DNHD1	6544804	0.656000	0.27385	0.718000	0.30602	0.611000	0.37282	0.300000	0.19156	0.103000	0.17682	0.655000	0.94253	CGT	G|0.727;A|0.273	0.273	strong		0.537	DNHD1-007	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384673.2	NM_144666	
MED14	9282	hgsc.bcm.edu	37	X	40573157	40573157	+	Silent	SNP	G	G	A	rs6520683	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:40573157G>A	ENST00000324817.1	-	5	643	c.525C>T	c.(523-525)gaC>gaT	p.D175D		NM_004229.3	NP_004220.2	O60244	MED14_HUMAN	mediator complex subunit 14	175					androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|receptor activity (GO:0004872)|RNA polymerase II transcription cofactor activity (GO:0001104)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			NS(2)|breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(7)|lung(8)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						GAATAATTTTGTCCTGCAAAA	0.338													A|||	1136	0.300927	0.4584	0.1124	3775	,	,		12488	0.1538		0.1352	False		,,,				2504	0.1646				p.D175D		Atlas-SNP	.											.	MED14	108	.	0			c.C525T						PASS	.	A		1994,1841		442,809,301,381,270	122.0	122.0	122.0		525	3.2	1.0	X	dbSNP_116	122	1203,5525		74,735,320,1619,1552	no	coding-synonymous	MED14	NM_004229.3		516,1544,621,2000,1822	AA,AG,A,GG,G		17.8805,48.0052,30.266		175/1455	40573157	3197,7366	2203	4300	6503	SO:0001819	synonymous_variant	9282	exon5			AATTTTGTCCTGC	AB006651	CCDS14254.1	Xp11.4	2008-05-14	2007-07-30	2007-07-30	ENSG00000180182	ENSG00000180182			2370	protein-coding gene	gene with protein product		300182	"""cofactor required for Sp1 transcriptional activation, subunit 2, 150kDa"""	CXorf4, CRSP2		9989412, 9598311	Standard	NM_004229		Approved	EXLM1, CRSP150, TRAP170, RGR1, CSRP	uc004dex.4	O60244	OTTHUMG00000024107	ENST00000324817.1:c.525C>T	X.37:g.40573157G>A		Somatic	219	0	0		WXS	Illumina HiSeq	Phase_I	171	169	0.988304	NM_004229	Q4KMR7|Q9UNB3	Silent	SNP	ENST00000324817.1	37	CCDS14254.1																																																																																			G|0.693;A|0.307	0.307	strong		0.338	MED14-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060692.1	NM_004229	
PIGR	5284	hgsc.bcm.edu	37	1	207109116	207109116	+	Missense_Mutation	SNP	C	C	T	rs2275531	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:207109116C>T	ENST00000356495.4	-	5	1276	c.1093G>A	c.(1093-1095)Ggc>Agc	p.G365S		NM_002644.3	NP_002635.2	P01833	PIGR_HUMAN	polymeric immunoglobulin receptor	365	Ig-like V-type 4.		G -> S (in dbSNP:rs2275531). {ECO:0000269|PubMed:1355431, ECO:0000269|PubMed:1682231, ECO:0000269|PubMed:17974005, ECO:0000269|PubMed:1859628, ECO:0000269|PubMed:2920039, ECO:0000269|PubMed:6526384}.		detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc receptor signaling pathway (GO:0038093)|immunoglobulin transcytosis in epithelial cells mediated by polymeric immunoglobulin receptor (GO:0002415)|receptor clustering (GO:0043113)|retina homeostasis (GO:0001895)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	polymeric immunoglobulin receptor activity (GO:0001792)			central_nervous_system(2)|endometrium(5)|kidney(3)|large_intestine(7)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	45						GCCACAGAGCCTCCTGCCACC	0.612											OREG0014186	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	1484	0.296326	0.1944	0.3271	5008	,	,		19680	0.3284		0.4563	False		,,,				2504	0.2147				p.G365S		Atlas-SNP	.											PIGR,NS,carcinoma,0,1	PIGR	98	1	0			c.G1093A						PASS	.	C	SER/GLY	963,3441		114,735,1353	31.0	34.0	33.0		1093	4.6	1.0	1	dbSNP_100	33	3938,4662		920,2098,1282	yes	missense	PIGR	NM_002644.3	56	1034,2833,2635	TT,TC,CC		45.7907,21.8665,37.6884	probably-damaging	365/765	207109116	4901,8103	2202	4300	6502	SO:0001583	missense	5284	exon5			CAGAGCCTCCTGC		CCDS1474.1	1q31-q41	2013-01-11			ENSG00000162896	ENSG00000162896		"""Immunoglobulin superfamily / V-set domain containing"""	8968	protein-coding gene	gene with protein product		173880					Standard	NM_002644		Approved		uc001hez.3	P01833	OTTHUMG00000036581	ENST00000356495.4:c.1093G>A	1.37:g.207109116C>T	ENSP00000348888:p.Gly365Ser	Somatic	86	0	0	2165	WXS	Illumina HiSeq	Phase_I	76	29	0.381579	NM_002644	Q68D81|Q8IZY7	Missense_Mutation	SNP	ENST00000356495.4	37	CCDS1474.1	764	0.3498168498168498	111	0.22560975609756098	134	0.3701657458563536	179	0.3129370629370629	340	0.44854881266490765	C	15.25	2.777910	0.49786	0.218665	0.457907	ENSG00000162896	ENST00000356495	T	0.04275	3.66	5.55	4.64	0.57946	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like fold (1);	0.169823	0.42172	N	0.000742	T	0.00012	0.0000	M	0.75615	2.305	0.31681	P	0.643169	D	0.89917	1.0	D	0.97110	1.0	T	0.47509	-0.9112	9	0.44086	T	0.13	-22.293	8.6869	0.34243	0.0:0.8266:0.0:0.1734	rs2275531;rs2275531	365	P01833	PIGR_HUMAN	S	365	ENSP00000348888:G365S	ENSP00000348888:G365S	G	-	1	0	PIGR	205175739	0.755000	0.28372	1.000000	0.80357	0.242000	0.25591	0.601000	0.24119	1.352000	0.45808	-0.140000	0.14226	GGC	C|0.639;T|0.361	0.361	strong		0.612	PIGR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088975.1	NM_002644	
INSL3	3640	hgsc.bcm.edu	37	19	17932190	17932190	+	Silent	SNP	T	T	C	rs1047233	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:17932190T>C	ENST00000317306.7	-	1	142	c.126A>G	c.(124-126)ctA>ctG	p.L42L	INSL3_ENST00000379695.5_Silent_p.L42L	NM_005543.3	NP_005534.2	P51460	INSL3_HUMAN	insulin-like 3 (Leydig cell)	42					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						ACACGCGCACTAGCGCGCGTA	0.721													C|||	1288	0.257188	0.3941	0.3127	5008	,	,		12303	0.005		0.4076	False		,,,				2504	0.138				p.L42L		Atlas-SNP	.											INSL3,NS,carcinoma,0,1	INSL3	8	1	0			c.A126G						PASS	.	C		1224,2548		247,730,909	4.0	7.0	6.0		126	-1.9	1.0	19	dbSNP_86	6	2298,4938		486,1326,1806	no	coding-synonymous	INSL3	NM_005543.2		733,2056,2715	CC,CT,TT		31.7579,32.4496,31.9949		42/132	17932190	3522,7486	1886	3618	5504	SO:0001819	synonymous_variant	3640	exon1			GCGCACTAGCGCG		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.126A>G	19.37:g.17932190T>C		Somatic	7	0	0		WXS	Illumina HiSeq	Phase_I	16	7	0.4375	NM_005543	B4DZ72|G3XAG0|Q3KPI5|Q3KPI6|Q6YNB5|Q9UEA2|Q9UPH6	Silent	SNP	ENST00000317306.7	37	CCDS12365.1																																																																																			T|0.715;G|0.000;C|0.284;A|0.000	0.284	strong		0.721	INSL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466836.1	NM_005543	
ADAMTS7	11173	hgsc.bcm.edu	37	15	79064080	79064080	+	Silent	SNP	G	G	A	rs11635931	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:79064080G>A	ENST00000388820.4	-	15	2433	c.2223C>T	c.(2221-2223)agC>agT	p.S741S	ADAMTS7_ENST00000566303.1_Intron	NM_014272.3	NP_055087.2	Q9UKP4	ATS7_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 7	741	Spacer.				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						CCGGGTCCTCGCTCCGCAGTG	0.632													G|||	932	0.186102	0.0454	0.2579	5008	,	,		18538	0.0188		0.4185	False		,,,				2504	0.2587				p.S741S		Atlas-SNP	.											.	ADAMTS7	142	.	0			c.C2223T						PASS	.	G		470,3922	219.4+/-237.2	37,396,1763	73.0	55.0	61.0		2223	-1.7	1.0	15	dbSNP_120	61	3669,4917	515.0+/-378.5	798,2073,1422	no	coding-synonymous	ADAMTS7	NM_014272.3		835,2469,3185	AA,AG,GG		42.7324,10.7013,31.8924		741/1687	79064080	4139,8839	2196	4293	6489	SO:0001819	synonymous_variant	11173	exon15			GTCCTCGCTCCGC	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.2223C>T	15.37:g.79064080G>A		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	69	34	0.492754	NM_014272	Q14F51|Q6P7J9	Silent	SNP	ENST00000388820.4	37	CCDS32303.1																																																																																			G|0.721;A|0.279	0.279	strong		0.632	ADAMTS7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421331.1	NM_014272	
ADPRH	141	hgsc.bcm.edu	37	3	119305379	119305379	+	Silent	SNP	T	T	A	rs25676	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:119305379T>A	ENST00000478399.1	+	3	1951	c.546T>A	c.(544-546)gcT>gcA	p.A182A	ADPRH_ENST00000478927.1_Silent_p.A182A|ADPRH_ENST00000357003.3_Silent_p.A182A|ADPRH_ENST00000465513.1_Silent_p.A182A|ADPRH_ENST00000471850.1_3'UTR			P54922	ADPRH_HUMAN	ADP-ribosylarginine hydrolase	182					cellular protein modification process (GO:0006464)|protein de-ADP-ribosylation (GO:0051725)		ADP-ribosylarginine hydrolase activity (GO:0003875)|magnesium ion binding (GO:0000287)			breast(1)|kidney(1)|lung(10)|ovary(1)	13		Lung NSC(201;0.0977)		GBM - Glioblastoma multiforme(114;0.23)		CAGCCTATGCTGTGAATAGCA	0.512													T|||	2065	0.41234	0.4372	0.281	5008	,	,		19874	0.5089		0.2634	False		,,,				2504	0.5256				p.A182A	GBM(133;579 1804 5989 9967 40052)	Atlas-SNP	.											.	ADPRH	33	.	0			c.T546A						PASS	.	T		1754,2652	521.9+/-370.6	359,1036,808	103.0	106.0	105.0		546	-1.0	1.0	3	dbSNP_72	105	2533,6067	414.2+/-351.4	379,1775,2146	no	coding-synonymous	ADPRH	NM_001125.2		738,2811,2954	AA,AT,TT		29.4535,39.8094,32.9617		182/358	119305379	4287,8719	2203	4300	6503	SO:0001819	synonymous_variant	141	exon4			CTATGCTGTGAAT	L13291	CCDS2990.1	3q13.31-q13.33	2004-02-27			ENSG00000144843	ENSG00000144843			269	protein-coding gene	gene with protein product		603081				8349667, 12070318	Standard	NM_001125		Approved	ARH1	uc003ecs.3	P54922	OTTHUMG00000159420	ENST00000478399.1:c.546T>A	3.37:g.119305379T>A		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	86	54	0.627907	NM_001125	B2R8H1|D3DN83	Silent	SNP	ENST00000478399.1	37	CCDS2990.1																																																																																			T|0.650;A|0.350	0.350	strong		0.512	ADPRH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355199.1	NM_001125	
ACTR1B	10120	hgsc.bcm.edu	37	2	98275354	98275354	+	Missense_Mutation	SNP	G	G	A	rs11692435	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	85	0	0		WXS	Illumina HiSeq	Phase_I	55	28	0.509091	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	
DHDH	27294	hgsc.bcm.edu	37	19	49438363	49438363	+	Missense_Mutation	SNP	G	G	A	rs2270941	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:49438363G>A	ENST00000221403.2	+	2	237	c.197G>A	c.(196-198)aGc>aAc	p.S66N	DHDH_ENST00000522614.1_Missense_Mutation_p.S66N|DHDH_ENST00000523250.1_Missense_Mutation_p.S66N	NM_014475.3	NP_055290.1	Q9UQ10	DHDH_HUMAN	dihydrodiol dehydrogenase (dimeric)	66			S -> N (in dbSNP:rs2270941).		carbohydrate metabolic process (GO:0005975)|D-xylose catabolic process (GO:0042843)		D-xylose 1-dehydrogenase (NADP+) activity (GO:0047837)|electron carrier activity (GO:0009055)|NAD(P)+ transhydrogenase activity (GO:0008746)|trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity (GO:0047115)			central_nervous_system(1)|large_intestine(3)|lung(3)|ovary(1)|soft_tissue(1)	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;0.000158)|all cancers(93;0.000258)|Epithelial(262;0.0173)|GBM - Glioblastoma multiforme(486;0.0179)		AAGGACCCGAGCGTGGGTGAG	0.692													A|||	2561	0.511382	0.7958	0.4308	5008	,	,		14256	0.5456		0.2535	False		,,,				2504	0.4141				p.S66N		Atlas-SNP	.											DHDH,NS,carcinoma,0,1	DHDH	35	1	0			c.G197A						PASS	.	A	ASN/SER	3081,1311		1099,883,214	22.0	17.0	19.0		197	4.7	0.3	19	dbSNP_100	19	1842,6740		209,1424,2658	yes	missense	DHDH	NM_014475.3	46	1308,2307,2872	AA,AG,GG		21.4635,29.8497,37.9451	benign	66/335	49438363	4923,8051	2196	4291	6487	SO:0001583	missense	27294	exon2			ACCCGAGCGTGGG	AB021933	CCDS12741.1	19q13.3	2008-02-05			ENSG00000104808	ENSG00000104808	1.3.1.20		17887	protein-coding gene	gene with protein product		606377				10477285	Standard	NM_014475		Approved	HUM2DD	uc002ple.1	Q9UQ10	OTTHUMG00000165029	ENST00000221403.2:c.197G>A	19.37:g.49438363G>A	ENSP00000221403:p.Ser66Asn	Somatic	6	0	0		WXS	Illumina HiSeq	Phase_I	19	6	0.315789	NM_014475		Missense_Mutation	SNP	ENST00000221403.2	37	CCDS12741.1	1018	0.4661172161172161	367	0.7459349593495935	141	0.38950276243093923	305	0.5332167832167832	205	0.2704485488126649	A	8.755	0.922187	0.17982	0.701503	0.214635	ENSG00000104808	ENST00000221403;ENST00000523250;ENST00000522614	T;T;T	0.21361	2.01;2.01;2.01	4.74	4.74	0.60224	Oxidoreductase, N-terminal (1);NAD(P)-binding domain (1);	0.254938	0.43919	N	0.000502	T	0.00012	0.0000	N	0.00966	-1.09	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.38045	-0.9679	9	0.02654	T	1	-20.6016	8.936	0.35700	0.9105:0.0:0.0895:0.0	rs2270941;rs17239182;rs52799839;rs58054167;rs2270941	66	Q9UQ10	DHDH_HUMAN	N	66	ENSP00000221403:S66N;ENSP00000428935:S66N;ENSP00000428672:S66N	ENSP00000221403:S66N	S	+	2	0	DHDH	54130175	0.322000	0.24634	0.282000	0.24776	0.680000	0.39746	4.951000	0.63610	0.951000	0.37770	-0.556000	0.04195	AGC	G|0.533;A|0.467	0.467	strong		0.692	DHDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381477.1	NM_014475	
ACAP1	9744	hgsc.bcm.edu	37	17	7254315	7254315	+	Missense_Mutation	SNP	G	G	A	rs35985803	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:7254315G>A	ENST00000158762.3	+	21	2325	c.2119G>A	c.(2119-2121)Gca>Aca	p.A707T	ACAP1_ENST00000571471.1_Missense_Mutation_p.A11T|ACAP1_ENST00000575415.1_Missense_Mutation_p.A11T|ACAP1_ENST00000574499.1_Missense_Mutation_p.A32T|KCTD11_ENST00000333751.3_5'Flank|RP11-542C16.1_ENST00000572417.1_RNA|ACAP1_ENST00000570504.1_Missense_Mutation_p.A11T	NM_014716.3	NP_055531.1	Q15027	ACAP1_HUMAN	ArfGAP with coiled-coil, ankyrin repeat and PH domains 1	707	Required for interaction with GULP1.				protein transport (GO:0015031)|regulation of ARF GTPase activity (GO:0032312)	endosome (GO:0005768)|membrane (GO:0016020)	ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)			NS(1)|breast(5)|cervix(3)|endometrium(4)|kidney(1)|large_intestine(7)|liver(1)|lung(6)|prostate(3)|skin(1)|urinary_tract(1)	33						CCAGGGGCAGGCAGGTAAAGA	0.587													g|||	214	0.0427316	0.0151	0.0389	5008	,	,		14235	0.0357		0.0716	False		,,,				2504	0.0603				p.A707T		Atlas-SNP	.											.	ACAP1	66	.	0			c.G2119A						PASS	.		THR/ALA	119,4287	90.2+/-128.9	3,113,2087	81.0	80.0	80.0		2119	0.2	1.0	17	dbSNP_126	80	728,7872	176.6+/-226.4	25,678,3597	yes	missense	ACAP1	NM_014716.3	58	28,791,5684	AA,AG,GG		8.4651,2.7009,6.5124	benign	707/741	7254315	847,12159	2203	4300	6503	SO:0001583	missense	9744	exon21			GGGCAGGCAGGTA	D30758	CCDS11101.1	17p13.1	2013-01-11	2008-09-22	2008-09-22	ENSG00000072818	ENSG00000072818		"""ADP-ribosylation factor GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"", ""Ankyrin repeat domain containing"""	16467	protein-coding gene	gene with protein product		607763	"""centaurin, beta 1"""	CENTB1		11050434, 11062263	Standard	NM_014716		Approved	KIAA0050	uc002ggd.2	Q15027	OTTHUMG00000102199	ENST00000158762.3:c.2119G>A	17.37:g.7254315G>A	ENSP00000158762:p.Ala707Thr	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	115	63	0.547826	NM_014716	Q53XN9	Missense_Mutation	SNP	ENST00000158762.3	37	CCDS11101.1	97	0.044413919413919416	12	0.024390243902439025	20	0.055248618784530384	13	0.022727272727272728	52	0.06860158311345646	g	12.55	1.972076	0.34754	0.027009	0.084651	ENSG00000072818	ENST00000158762	T	0.73152	-0.72	4.53	0.24	0.15489	.	0.666605	0.15127	N	0.279041	T	0.03520	0.0101	N	0.12746	0.255	0.28933	N	0.891457	B	0.02656	0.0	B	0.04013	0.001	T	0.03000	-1.1084	10	0.23891	T	0.37	.	7.096	0.25309	0.3837:0.0:0.6163:0.0	rs35985803;rs35985803	707	Q15027	ACAP1_HUMAN	T	707	ENSP00000158762:A707T	ENSP00000158762:A707T	A	+	1	0	ACAP1	7195039	1.000000	0.71417	0.996000	0.52242	0.310000	0.27922	0.407000	0.21049	-0.061000	0.13110	-0.461000	0.05368	GCA	G|0.944;A|0.056	0.056	strong		0.587	ACAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000220049.4	NM_014716	
LTBP2	4053	hgsc.bcm.edu	37	14	75019002	75019002	+	Silent	SNP	C	C	T	rs61738025	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:75019002C>T	ENST00000261978.4	-	6	1673	c.1287G>A	c.(1285-1287)ctG>ctA	p.L429L	LTBP2_ENST00000556690.1_Silent_p.L429L|LTBP2_ENST00000557425.1_Intron|CTD-2207P18.1_ENST00000554552.1_lincRNA	NM_000428.2	NP_000419.1	Q14767	LTBP2_HUMAN	latent transforming growth factor beta binding protein 2	429					protein secretion (GO:0009306)|protein targeting (GO:0006605)|transforming growth factor beta receptor signaling pathway (GO:0007179)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|heparin binding (GO:0008201)			breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(9)|liver(1)|lung(29)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	58				BRCA - Breast invasive adenocarcinoma(234;0.00219)|READ - Rectum adenocarcinoma(1;0.0649)		GCGGGATAGGCAGGTGGCAGA	0.657													c|||	353	0.0704872	0.0915	0.0634	5008	,	,		16437	0.0952		0.0457	False		,,,				2504	0.047				p.L429L		Atlas-SNP	.											.	LTBP2	158	.	0			c.G1287A						PASS	.			393,4013	188.1+/-214.6	12,369,1822	39.0	41.0	40.0		1287	4.9	1.0	14	dbSNP_129	40	475,8121	137.9+/-194.8	15,445,3838	no	coding-synonymous	LTBP2	NM_000428.2		27,814,5660	TT,TC,CC		5.5258,8.9197,6.6759		429/1822	75019002	868,12134	2203	4298	6501	SO:0001819	synonymous_variant	4053	exon6			GATAGGCAGGTGG		CCDS9831.1	14q24.3	2011-10-20	2001-12-04			ENSG00000119681		"""Latent transforming growth factor, beta binding proteins"""	6715	protein-coding gene	gene with protein product		602091	"""chromosome 14 open reading frame 141"""	LTBP3, C14orf141		7798248	Standard	NM_000428		Approved		uc001xqa.3	Q14767		ENST00000261978.4:c.1287G>A	14.37:g.75019002C>T		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	80	38	0.475	NM_000428	Q99907|Q9NS51	Silent	SNP	ENST00000261978.4	37	CCDS9831.1																																																																																			C|0.928;T|0.072	0.072	strong		0.657	LTBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413595.1	NM_000428	
ZNF469	84627	hgsc.bcm.edu	37	16	88494603	88494603	+	Missense_Mutation	SNP	G	G	T	rs536586591	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:88494603G>T	ENST00000437464.1	+	1	725	c.725G>T	c.(724-726)aGc>aTc	p.S242I	ZNF469_ENST00000565624.1_Missense_Mutation_p.S242I	NM_001127464.1	NP_001120936.1	Q96JG9	ZN469_HUMAN	zinc finger protein 469	242	Pro-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(4)|endometrium(6)|kidney(3)|large_intestine(1)|skin(6)	20						GCTGAGAATAGCTTCCCAGGT	0.677													G|||	4	0.000798722	0.0	0.0	5008	,	,		11181	0.0		0.002	False		,,,				2504	0.002				p.S242I		Atlas-SNP	.											.	ZNF469	121	.	0			c.G725T						PASS	.						8.0	12.0	11.0					16																	88494603		688	1589	2277	SO:0001583	missense	84627	exon1			AGAATAGCTTCCC	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.725G>T	16.37:g.88494603G>T	ENSP00000402343:p.Ser242Ile	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	101	66	0.653465	NM_001127464		Missense_Mutation	SNP	ENST00000437464.1	37	CCDS45544.1	.	.	.	.	.	.	.	.	.	.	G	12.78	2.041088	0.35989	.	.	ENSG00000225614	ENST00000437464	T	0.10288	2.89	4.34	1.27	0.21489	.	.	.	.	.	T	0.12646	0.0307	N	0.19112	0.55	0.22435	N	0.999101	D	0.61697	0.99	P	0.56398	0.797	T	0.20874	-1.0262	9	0.87932	D	0	.	7.2383	0.26082	0.3662:0.0:0.6338:0.0	.	242	Q96JG9	ZN469_HUMAN	I	242	ENSP00000402343:S242I	ENSP00000402343:S242I	S	+	2	0	ZNF469	87022104	0.993000	0.37304	0.755000	0.31263	0.617000	0.37484	0.285000	0.18883	0.003000	0.14656	0.462000	0.41574	AGC	.	.	none		0.677	ZNF469-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NG_012236	
DSG3	1830	hgsc.bcm.edu	37	18	29056063	29056063	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:29056063C>T	ENST00000257189.4	+	16	2923	c.2840C>T	c.(2839-2841)tCc>tTc	p.S947F		NM_001944.2	NP_001935.2	P32926	DSG3_HUMAN	desmoglein 3	947					apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|homophilic cell adhesion (GO:0007156)	cell junction (GO:0030054)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(2)|cervix(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(28)|ovary(4)|prostate(1)|skin(8)|upper_aerodigestive_tract(1)	62			OV - Ovarian serous cystadenocarcinoma(10;0.00504)			GTGCAACCTTCCACTGCAGGC	0.517																																					p.S947F		Atlas-SNP	.											.	DSG3	172	.	0			c.C2840T						PASS	.						156.0	141.0	146.0					18																	29056063		2203	4300	6503	SO:0001583	missense	1830	exon16			AACCTTCCACTGC	M76482	CCDS11898.1	18q12.1	2010-06-24	2010-06-24		ENSG00000134757	ENSG00000134757		"""Cadherins / Major cadherins"""	3050	protein-coding gene	gene with protein product	"""pemphigus vulgaris antigen"""	169615	"""desmoglein 3 (pemphigus vulgaris antigen)"""			1601426	Standard	NM_001944		Approved	CDHF6	uc002kws.3	P32926	OTTHUMG00000131985	ENST00000257189.4:c.2840C>T	18.37:g.29056063C>T	ENSP00000257189:p.Ser947Phe	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	67	16	0.238806	NM_001944	A8K2V2	Missense_Mutation	SNP	ENST00000257189.4	37	CCDS11898.1	.	.	.	.	.	.	.	.	.	.	C	19.04	3.750220	0.69533	.	.	ENSG00000134757	ENST00000257189	T	0.80480	-1.38	5.54	5.54	0.83059	.	0.756022	0.11629	N	0.545016	D	0.85066	0.5612	L	0.58510	1.815	0.09310	N	0.999999	D	0.53619	0.961	P	0.57548	0.823	T	0.76553	-0.2917	10	0.87932	D	0	.	10.1776	0.42948	0.0:0.9051:0.0:0.0949	.	947	P32926	DSG3_HUMAN	F	947	ENSP00000257189:S947F	ENSP00000257189:S947F	S	+	2	0	DSG3	27310061	0.016000	0.18221	0.812000	0.32479	0.925000	0.55904	2.776000	0.47709	2.779000	0.95612	0.655000	0.94253	TCC	.	.	none		0.517	DSG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254949.1	NM_001944	
DSPP	1834	hgsc.bcm.edu	37	4	88537035	88537035	+	Missense_Mutation	SNP	A	A	G	rs202210195		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:88537035A>G	ENST00000282478.7	+	4	3254	c.3221A>G	c.(3220-3222)gAc>gGc	p.D1074G	RP11-742B18.1_ENST00000506480.1_RNA|DSPP_ENST00000399271.1_Missense_Mutation_p.D1074G			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	1074	Asp/Ser-rich.				biomineral tissue development (GO:0031214)|cellular response to cell-matrix adhesion (GO:0071460)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|skin(3)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Hepatocellular(203;0.114)|all_hematologic(202;0.236)		OV - Ovarian serous cystadenocarcinoma(123;0.000508)		gacagcagtgacagcagcgac	0.542																																					p.D1074G		Atlas-SNP	.											DSPP,NS,carcinoma,-1,1	DSPP	174	1	0			c.A3221G						PASS	.						58.0	65.0	62.0					4																	88537035		1567	2848	4415	SO:0001583	missense	1834	exon5			GCAGTGACAGCAG	AF163151	CCDS43248.1	4q21.3	2008-02-05			ENSG00000152591	ENSG00000152591			3054	protein-coding gene	gene with protein product		125485		DFNA39, DGI1		8995371, 9533027	Standard	NM_014208		Approved	DMP3	uc003hqu.3	Q9NZW4	OTTHUMG00000161061	ENST00000282478.7:c.3221A>G	4.37:g.88537035A>G	ENSP00000282478:p.Asp1074Gly	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	94	34	0.361702	NM_014208	A8MUI0|O95815	Missense_Mutation	SNP	ENST00000282478.7	37	CCDS43248.1	.	.	.	.	.	.	.	.	.	.	a	3.083	-0.188481	0.06299	.	.	ENSG00000152591	ENST00000399271;ENST00000282478	D;D	0.88741	-2.42;-2.42	1.51	1.51	0.23008	.	.	.	.	.	D	0.83468	0.5261	L	0.34521	1.04	0.58432	P	4.000000000004E-6	D	0.58620	0.983	P	0.48598	0.583	T	0.81771	-0.0780	8	0.48119	T	0.1	.	5.1866	0.15187	1.0:0.0:0.0:0.0	.	1074	Q9NZW4	DSPP_HUMAN	G	1074	ENSP00000382213:D1074G;ENSP00000282478:D1074G	ENSP00000282478:D1074G	D	+	2	0	DSPP	88756059	0.407000	0.25352	0.138000	0.22173	0.004000	0.04260	1.380000	0.34351	0.963000	0.38082	0.242000	0.17961	GAC	.	.	weak		0.542	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208	
B3GALNT2	148789	hgsc.bcm.edu	37	1	235652513	235652513	+	Silent	SNP	T	T	C	rs291396	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:235652513T>C	ENST00000366600.3	-	3	549	c.321A>G	c.(319-321)gaA>gaG	p.E107E	B3GALNT2_ENST00000494378.1_Intron|B3GALNT2_ENST00000313984.3_Silent_p.E148E	NM_152490.2	NP_689703.1	Q8NCR0	B3GL2_HUMAN	beta-1,3-N-acetylgalactosaminyltransferase 2	107					protein glycosylation (GO:0006486)|protein O-linked glycosylation (GO:0006493)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	acetylgalactosaminyltransferase activity (GO:0008376)|acetylglucosaminyltransferase activity (GO:0008375)|galactosyltransferase activity (GO:0008378)			NS(1)|breast(2)|endometrium(5)|kidney(1)|large_intestine(2)|lung(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	18	Ovarian(103;0.0634)|Breast(184;0.23)	all_cancers(173;0.0539)|Prostate(94;0.0353)	OV - Ovarian serous cystadenocarcinoma(106;0.000117)			AATAAGGATCTTCCCTGTCTT	0.413													C|||	3399	0.678714	0.5893	0.7104	5008	,	,		17359	0.8413		0.5139	False		,,,				2504	0.7791				p.E107E		Atlas-SNP	.											.	B3GALNT2	36	.	0			c.A321G						PASS	.	C		2488,1918	546.6+/-377.1	697,1094,412	226.0	195.0	206.0		321	-0.3	0.4	1	dbSNP_79	206	4287,4313	578.3+/-390.7	1082,2123,1095	no	coding-synonymous	B3GALNT2	NM_152490.2		1779,3217,1507	CC,CT,TT		49.8488,43.5315,47.9087		107/501	235652513	6775,6231	2203	4300	6503	SO:0001819	synonymous_variant	148789	exon3			AGGATCTTCCCTG	BC029564	CCDS1606.1, CCDS60453.1	1q42.3	2013-02-19	2006-06-14		ENSG00000162885	ENSG00000162885		"""Beta 3-glycosyltransferases"""	28596	protein-coding gene	gene with protein product		610194	"""UDP-GalNAc:betaGlcNAc beta-1,3-galactosaminyltransferase, polypeptide 2"""			14724282	Standard	NM_001277155		Approved	MGC39558	uc001hxc.3	Q8NCR0	OTTHUMG00000040468	ENST00000366600.3:c.321A>G	1.37:g.235652513T>C		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	59	35	0.59322	NM_152490	Q59GR3|Q5TCI3|Q96AL7	Silent	SNP	ENST00000366600.3	37	CCDS1606.1																																																																																			T|0.416;C|0.584	0.584	strong		0.413	B3GALNT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097376.1	NM_152490	
MAP1A	4130	hgsc.bcm.edu	37	15	43817406	43817406	+	Silent	SNP	T	T	C	rs71471869|rs480108	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:43817406T>C	ENST00000300231.5	+	4	4185	c.3735T>C	c.(3733-3735)gaT>gaC	p.D1245D	MAP1A_ENST00000399453.1_Silent_p.D1245D|MAP1A_ENST00000382031.1_Silent_p.D1483D			P78559	MAP1A_HUMAN	microtubule-associated protein 1A	1245			D -> N (in dbSNP:rs12912505).		microtubule cytoskeleton organization (GO:0000226)|sensory perception of sound (GO:0007605)	cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)	structural molecule activity (GO:0005198)			breast(5)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(11)|liver(2)|lung(19)|ovary(5)|pancreas(3)|prostate(2)|skin(6)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	66		all_cancers(109;1.03e-14)|all_epithelial(112;2.23e-12)|Lung NSC(122;2.76e-08)|all_lung(180;3.1e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;3.05e-06)	Estramustine(DB01196)	AGGCCGAGGATACCTCTCACC	0.547													C|||	2649	0.528954	0.9728	0.3329	5008	,	,		18861	0.4177		0.2962	False		,,,				2504	0.4223				p.D1245D		Atlas-SNP	.											.	MAP1A	189	.	0			c.T3735C						PASS	.	C		3579,723		1500,579,72	94.0	110.0	105.0		3735	0.9	0.1	15	dbSNP_83	105	2490,5988		361,1768,2110	no	coding-synonymous	MAP1A	NM_002373.5		1861,2347,2182	CC,CT,TT		29.3701,16.8061,47.4883		1245/2804	43817406	6069,6711	2151	4239	6390	SO:0001819	synonymous_variant	4130	exon4			CGAGGATACCTCT	U38292	CCDS42031.1	15q15.3	2006-06-15			ENSG00000166963	ENSG00000166963			6835	protein-coding gene	gene with protein product		600178		MAP1L		7806212, 7629894	Standard	XM_005254385		Approved		uc001zrt.3	P78559	OTTHUMG00000059756	ENST00000300231.5:c.3735T>C	15.37:g.43817406T>C		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	138	41	0.297101	NM_002373	O95643|Q12973|Q15882|Q9UJT4	Silent	SNP	ENST00000300231.5	37	CCDS42031.1																																																																																			T|0.539;C|0.461	0.461	strong		0.547	MAP1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000132894.5	NM_002373	
HELT	391723	hgsc.bcm.edu	37	4	185940952	185940952	+	Missense_Mutation	SNP	C	C	G	rs1078461	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:185940952C>G	ENST00000515777.1	+	3	272	c.184C>G	c.(184-186)Ctg>Gtg	p.L62V	HELT_ENST00000338875.4_Missense_Mutation_p.L147V|HELT_ENST00000505610.1_Missense_Mutation_p.L62V			A6NFD8	HELT_HUMAN	helt bHLH transcription factor	62	bHLH. {ECO:0000255|PROSITE- ProRule:PRU00981}.		L -> V (in dbSNP:rs1078461).		central nervous system development (GO:0007417)|GABAergic neuron differentiation in basal ganglia (GO:0021858)|multicellular organism growth (GO:0035264)|multicellular organismal aging (GO:0010259)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|suckling behavior (GO:0001967)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|endometrium(3)|large_intestine(3)|lung(4)|skin(1)|urinary_tract(2)	14		all_lung(41;9.65e-12)|Lung NSC(41;1.64e-11)|Colorectal(36;0.0215)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|Prostate(90;0.0283)|all_hematologic(60;0.0749)		all cancers(43;8.92e-26)|Epithelial(43;3.02e-23)|OV - Ovarian serous cystadenocarcinoma(60;2.59e-11)|Colorectal(24;4.79e-05)|BRCA - Breast invasive adenocarcinoma(30;7.72e-05)|GBM - Glioblastoma multiforme(59;0.000274)|COAD - Colon adenocarcinoma(29;0.000362)|STAD - Stomach adenocarcinoma(60;0.000756)|LUSC - Lung squamous cell carcinoma(40;0.00902)|READ - Rectum adenocarcinoma(43;0.155)		CGTTCAGTACCTGAGAGCACT	0.642													c|||	559	0.111621	0.0862	0.1354	5008	,	,		16083	0.1885		0.0924	False		,,,				2504	0.0695				p.L147V		Atlas-SNP	.											.	HELT	34	.	0			c.C439G						PASS	.	C	VAL/LEU	425,3981	193.3+/-218.5	21,383,1799	30.0	31.0	31.0		439	3.1	1.0	4	dbSNP_86	31	819,7781	180.6+/-229.5	39,741,3520	yes	missense	HELT	NM_001029887.1	32	60,1124,5319	GG,GC,CC		9.5233,9.6459,9.5648	probably-damaging	147/328	185940952	1244,11762	2203	4300	6503	SO:0001583	missense	391723	exon3			CAGTACCTGAGAG	BC144567	CCDS75214.1, CCDS75215.1	4q35.1	2014-07-17	2011-09-12		ENSG00000187821	ENSG00000187821		"""Basic helix-loop-helix proteins"""	33783	protein-coding gene	gene with protein product	"""megane bHLH factor"", ""HES-like"""		"""Hey-like transcription factor (zebrafish)"", ""HES/HEY-like transcription factor"""			14764602, 17611227	Standard	XM_005262989		Approved	HESL, HCM1228, Mgn, bHLHb44, MEGANE	uc011ckq.2	A6NFD8	OTTHUMG00000160484	ENST00000515777.1:c.184C>G	4.37:g.185940952C>G	ENSP00000426033:p.Leu62Val	Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	171	78	0.45614	NM_001029887	B2RTS5|B7ZMI7|B7ZMI8	Missense_Mutation	SNP	ENST00000515777.1	37		264	0.12087912087912088	41	0.08333333333333333	41	0.1132596685082873	109	0.19055944055944055	73	0.09630606860158311	C	19.49	3.837382	0.71373	0.096459	0.095233	ENSG00000187821	ENST00000505610;ENST00000515777;ENST00000338875	D;D;D	0.98060	-4.69;-4.69;-4.69	4.89	3.12	0.35913	Helix-loop-helix DNA-binding (5);	0.000000	0.64402	D	0.000010	T	0.04770	0.0129	L	0.39566	1.225	0.20975	P	0.999819995	D;P;P	0.57899	0.981;0.937;0.923	P;P;P	0.59948	0.866;0.794;0.69	T	0.05852	-1.0860	9	0.56958	D	0.05	.	9.7352	0.40384	0.0:0.7691:0.0:0.2309	rs1078461;rs4359954;rs17631598;rs1078461	147;62;62	A6NFD8;B7ZMI7;A6NFD8-2	HELT_HUMAN;.;.	V	62;62;147	ENSP00000422140:L62V;ENSP00000426033:L62V;ENSP00000343464:L147V	ENSP00000343464:L147V	L	+	1	2	HELT	186177946	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	2.880000	0.48530	1.288000	0.44600	0.561000	0.74099	CTG	C|0.898;G|0.102	0.102	strong		0.642	HELT-002	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000360792.1	NM_001300781	
PYGB	5834	hgsc.bcm.edu	37	20	25260931	25260931	+	Silent	SNP	A	A	G	rs2227890	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:25260931A>G	ENST00000216962.4	+	10	1232	c.1122A>G	c.(1120-1122)gcA>gcG	p.A374A		NM_002862.3	NP_002853.2	P11216	PYGB_HUMAN	phosphorylase, glycogen; brain	374					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						AGACCTGTGCATACACCAACC	0.537													G|||	2690	0.537141	0.4523	0.3473	5008	,	,		21077	0.9107		0.4334	False		,,,				2504	0.5082				p.A374A		Atlas-SNP	.											PYGB,NS,carcinoma,0,1	PYGB	84	1	0			c.A1122G						PASS	.	G		1903,2503	628.7+/-395.1	401,1101,701	136.0	122.0	126.0		1122	-7.7	0.6	20	dbSNP_98	126	3754,4846	616.5+/-396.5	813,2128,1359	no	coding-synonymous	PYGB	NM_002862.3		1214,3229,2060	GG,GA,AA		43.6512,43.1911,43.4953		374/844	25260931	5657,7349	2203	4300	6503	SO:0001819	synonymous_variant	5834	exon10			CTGTGCATACACC		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.1122A>G	20.37:g.25260931A>G		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	152	72	0.473684	NM_002862	Q96AK1|Q9NPX8	Silent	SNP	ENST00000216962.4	37	CCDS13171.1																																																																																			A|0.513;G|0.487	0.487	strong		0.537	PYGB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078415.2	NM_002862	
OR10AD1	121275	hgsc.bcm.edu	37	12	48596890	48596890	+	Silent	SNP	G	G	A	rs17823193	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:48596890G>A	ENST00000310248.2	-	1	280	c.186C>T	c.(184-186)ttC>ttT	p.F62F		NM_001004134.1	NP_001004134.1	Q8NGE0	O10AD_HUMAN	olfactory receptor, family 10, subfamily AD, member 1	62						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(2)|lung(3)|ovary(1)|stomach(1)|urinary_tract(1)	9						GGCCGAGGAAGAAGTACATGG	0.537													G|||	213	0.0425319	0.059	0.036	5008	,	,		21794	0.006		0.0924	False		,,,				2504	0.0112				p.F62F		Atlas-SNP	.											.	OR10AD1	24	.	0			c.C186T						PASS	.	G		273,4133	154.4+/-187.8	8,257,1938	118.0	95.0	103.0		186	3.1	1.0	12	dbSNP_123	103	762,7838	181.3+/-230.0	29,704,3567	yes	coding-synonymous	OR10AD1	NM_001004134.1		37,961,5505	AA,AG,GG		8.8605,6.1961,7.9579		62/318	48596890	1035,11971	2203	4300	6503	SO:0001819	synonymous_variant	121275	exon1			GAGGAAGAAGTAC		CCDS31787.1	12q13.11	2013-09-24	2002-11-13	2002-11-15	ENSG00000172640	ENSG00000172640		"""GPCR / Class A : Olfactory receptors"""	14819	protein-coding gene	gene with protein product			"""olfactory receptor, family 10, subfamily AD, member 1 pseudogene"""	OR10AD1P			Standard	NM_001004134		Approved		uc001rrl.1	Q8NGE0	OTTHUMG00000168027	ENST00000310248.2:c.186C>T	12.37:g.48596890G>A		Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	152	82	0.539474	NM_001004134	B9EGT9|Q6IFA8	Silent	SNP	ENST00000310248.2	37	CCDS31787.1																																																																																			G|0.939;A|0.061	0.061	strong		0.537	OR10AD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397577.1		
HLA-G	3135	hgsc.bcm.edu	37	6	29795636	29795636	+	Silent	SNP	G	G	A	rs1630223	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:29795636G>A	ENST00000360323.6	+	1	39	c.15G>A	c.(13-15)gcG>gcA	p.A5A	HLA-G_ENST00000376818.3_Silent_p.A5A|HLA-G_ENST00000376815.3_Silent_p.A5A|HLA-G_ENST00000428701.1_Silent_p.A5A|HLA-G_ENST00000376828.2_Silent_p.A10A			P17693	HLAG_HUMAN	major histocompatibility complex, class I, G	5					antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular defense response (GO:0006968)|cytokine-mediated signaling pathway (GO:0019221)|immune response-inhibiting cell surface receptor signaling pathway (GO:0002767)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of dendritic cell differentiation (GO:2001199)|negative regulation of T cell proliferation (GO:0042130)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of regulatory T cell differentiation (GO:0045591)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|positive regulation of T cell tolerance induction (GO:0002666)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)	early endosome membrane (GO:0031901)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|membrane (GO:0016020)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	peptide antigen binding (GO:0042605)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)			central_nervous_system(1)|endometrium(1)|large_intestine(5)|lung(4)|ovary(3)|pancreas(1)|prostate(5)|skin(1)	21						TGGTCATGGCGCCCCGAACCC	0.652													g|||	2726	0.544329	0.5083	0.4654	5008	,	,		14134	0.6032		0.4324	False		,,,				2504	0.7035				p.A5A		Atlas-SNP	.											.	HLA-G	90	.	0			c.G15A						PASS	.	G		1538,1484		392,754,365	42.0	47.0	45.0		15	1.7	0.0	6	dbSNP_89	45	2507,2911		598,1311,800	no	coding-synonymous	HLA-G	NM_002127.5		990,2065,1165	AA,AG,GG		46.2717,49.1066,47.9265		5/339	29795636	4045,4395	1511	2709	4220	SO:0001819	synonymous_variant	3135	exon2			CATGGCGCCCCGA		CCDS4668.1	6p21.3	2013-01-11	2007-12-12		ENSG00000204632	ENSG00000204632		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4964	protein-coding gene	gene with protein product	"""b2 microglobulin"""	142871	"""HLA-G histocompatibility antigen, class I, G"""				Standard	NM_002127		Approved		uc003nnw.2	P17693	OTTHUMG00000031157	ENST00000360323.6:c.15G>A	6.37:g.29795636G>A		Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	143	132	0.923077	NM_002127		Silent	SNP	ENST00000360323.6	37	CCDS4668.1																																																																																			G|0.509;A|0.491	0.491	strong		0.652	HLA-G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076286.2	NM_002127	
FAM149A	25854	hgsc.bcm.edu	37	4	187078819	187078819	+	Silent	SNP	C	C	G	rs2276923	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:187078819C>G	ENST00000356371.5	+	8	1548	c.1548C>G	c.(1546-1548)tcC>tcG	p.S516S	FAM149A_ENST00000514153.1_Silent_p.S225S|FAM149A_ENST00000227065.4_Silent_p.S225S|FAM149A_ENST00000502970.1_Silent_p.S225S|FAM149A_ENST00000514829.1_3'UTR|FAM149A_ENST00000503432.1_Silent_p.S225S|FAM149A_ENST00000389354.5_Silent_p.S225S			A5PLN7	F149A_HUMAN	family with sequence similarity 149, member A	516										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)		GCCCCCCGTCCGGACACGCCG	0.587													C|||	917	0.183107	0.1929	0.2421	5008	,	,		17100	0.2024		0.1501	False		,,,				2504	0.1421				p.S225S		Atlas-SNP	.											.	FAM149A	52	.	0			c.C675G						PASS	.	C	,	835,3571	328.5+/-300.6	70,695,1438	63.0	68.0	66.0		675,675	0.9	0.7	4	dbSNP_100	66	1231,7369	244.9+/-273.9	91,1049,3160	no	coding-synonymous,coding-synonymous	FAM149A	NM_001006655.2,NM_015398.2	,	161,1744,4598	GG,GC,CC		14.314,18.9514,15.885	,	225/483,225/483	187078819	2066,10940	2203	4300	6503	SO:0001819	synonymous_variant	25854	exon7			CCCGTCCGGACAC	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.1548C>G	4.37:g.187078819C>G		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	49	17	0.346939	NM_001006655	B5MDB8|Q2TAN6|Q7Z2S5|Q9Y4T9	Silent	SNP	ENST00000356371.5	37																																																																																				C|0.839;G|0.161	0.161	strong		0.587	FAM149A-201	KNOWN	basic	protein_coding	protein_coding		NM_001006655	
SCN10A	6336	hgsc.bcm.edu	37	3	38739416	38739416	+	Silent	SNP	C	C	T	rs145313578	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:38739416C>T	ENST00000449082.2	-	27	5294	c.5295G>A	c.(5293-5295)tcG>tcA	p.S1765S		NM_006514.2	NP_006505.2	Q9Y5Y9	SCNAA_HUMAN	sodium channel, voltage-gated, type X, alpha subunit	1765					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)	CTGCAAAGTCCGAGAGAGCAG	0.498													C|||	4	0.000798722	0.0	0.0014	5008	,	,		19894	0.0		0.001	False		,,,				2504	0.002				p.S1765S		Atlas-SNP	.											SCN10A,NS,carcinoma,-1,2	SCN10A	359	2	0			c.G5295A						scavenged	.	C		1,4405	2.1+/-5.4	0,1,2202	76.0	80.0	79.0		5295	-10.8	0.2	3	dbSNP_134	79	12,8588	8.4+/-32.0	0,12,4288	no	coding-synonymous	SCN10A	NM_006514.2		0,13,6490	TT,TC,CC		0.1395,0.0227,0.1		1765/1957	38739416	13,12993	2203	4300	6503	SO:0001819	synonymous_variant	6336	exon27			AAAGTCCGAGAGA	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.5295G>A	3.37:g.38739416C>T		Somatic	166	2	0.0120482		WXS	Illumina HiSeq	Phase_I	165	80	0.484848	NM_006514	A6NDQ1	Silent	SNP	ENST00000449082.2	37	CCDS33736.1																																																																																			C|0.999;T|0.001	0.001	strong		0.498	SCN10A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109745.3	NM_006514	
KIAA1147	57189	hgsc.bcm.edu	37	7	141362558	141362558	+	Silent	SNP	G	G	T	rs375569681		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:141362558G>T	ENST00000536163.1	-	9	1265	c.1266C>A	c.(1264-1266)ggC>ggA	p.G422G	KIAA1147_ENST00000482493.1_Silent_p.G318G|RP5-894A10.6_ENST00000602609.1_RNA	NM_001080392.1	NP_001073861.1	A4D1U4	LCHN_HUMAN	KIAA1147	422										breast(3)|endometrium(4)|kidney(2)|large_intestine(1)|ovary(1)|skin(1)	12	Melanoma(164;0.0171)					CTAGGCCCATGCCCCGGGCAT	0.527																																					p.G422G		Atlas-SNP	.											.	KIAA1147	32	.	0			c.C1266A						PASS	.	G		0,3818		0,0,1909	37.0	39.0	38.0		1266	5.4	1.0	7		38	2,8234		0,2,4116	no	coding-synonymous	KIAA1147	NM_001080392.1		0,2,6025	TT,TG,GG		0.0243,0.0,0.0166		422/456	141362558	2,12052	1909	4118	6027	SO:0001819	synonymous_variant	57189	exon9			GCCCATGCCCCGG	AB032973	CCDS47726.1	7q34	2012-10-04			ENSG00000257093	ENSG00000257093			29472	protein-coding gene	gene with protein product							Standard	NM_001080392		Approved	LCHN	uc003vwk.3	A4D1U4	OTTHUMG00000157539	ENST00000536163.1:c.1266C>A	7.37:g.141362558G>T		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	62	37	0.596774	NM_001080392	Q9ULS3	Silent	SNP	ENST00000536163.1	37	CCDS47726.1																																																																																			.	.	weak		0.527	KIAA1147-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349104.1		
MYO18A	399687	hgsc.bcm.edu	37	17	27424316	27424316	+	Silent	SNP	G	G	A	rs8067806	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:27424316G>A	ENST00000527372.1	-	27	4335	c.4155C>T	c.(4153-4155)acC>acT	p.T1385T	MYO18A_ENST00000531253.1_Silent_p.T1385T|MYO18A_ENST00000533112.1_Silent_p.T1385T|MYO18A_ENST00000354329.4_Silent_p.T1385T	NM_078471.3	NP_510880.2	Q92614	MY18A_HUMAN	myosin XVIIIA	1385					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)			GCCGTTTCTTGGTGAAGTCCA	0.632													G|||	1320	0.263578	0.1755	0.1571	5008	,	,		15890	0.5833		0.167	False		,,,				2504	0.228				p.T1385T	Esophageal Squamous(182;472 2015 7001 15270 22562)	Atlas-SNP	.											.	MYO18A	217	.	0			c.C4155T						PASS	.	G	,	724,3438		69,586,1426	53.0	57.0	56.0		4155,4155	4.8	1.0	17	dbSNP_116	56	1292,7086		85,1122,2982	no	coding-synonymous,coding-synonymous	MYO18A	NM_078471.3,NM_203318.1	,	154,1708,4408	AA,AG,GG		15.4213,17.3955,16.0766	,	1385/2055,1385/2040	27424316	2016,10524	2081	4189	6270	SO:0001819	synonymous_variant	399687	exon27			TTTCTTGGTGAAG	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.4155C>T	17.37:g.27424316G>A		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	50	12	0.24	NM_078471	Q5H9U3|Q5W9F9|Q5W9G1|Q8IXP8	Silent	SNP	ENST00000527372.1	37	CCDS45642.1																																																																																			G|0.745;A|0.255	0.255	strong		0.632	MYO18A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389396.1	NM_078471	
TAAR6	319100	hgsc.bcm.edu	37	6	132892332	132892332	+	Missense_Mutation	SNP	G	G	A	rs8192625	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:132892332G>A	ENST00000275198.1	+	1	872	c.872G>A	c.(871-873)tGt>tAt	p.C291Y		NM_175067.1	NP_778237.1	Q96RI8	TAAR6_HUMAN	trace amine associated receptor 6	291			C -> Y (in dbSNP:rs8192625). {ECO:0000269|PubMed:15329799}.		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)|trace-amine receptor activity (GO:0001594)			cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(2)|lung(19)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	41	Breast(56;0.112)			OV - Ovarian serous cystadenocarcinoma(155;0.006)|GBM - Glioblastoma multiforme(226;0.00792)		ACCCCTGCCTGTATTTATGAG	0.358													A|||	309	0.0617013	0.1067	0.0476	5008	,	,		18898	0.0169		0.0507	False		,,,				2504	0.0685				p.C291Y		Atlas-SNP	.											.	TAAR6	68	.	0			c.G872A						PASS	.	A	TYR/CYS	456,3950	784.3+/-414.7	22,412,1769	119.0	120.0	120.0		872	3.9	0.4	6	dbSNP_117	120	582,8018	793.1+/-407.5	19,544,3737	yes	missense	TAAR6	NM_175067.1	194	41,956,5506	AA,AG,GG		6.7674,10.3495,7.9809	benign	291/346	132892332	1038,11968	2203	4300	6503	SO:0001583	missense	319100	exon1			CTGCCTGTATTTA	AF380192	CCDS5155.1	6q23.1	2012-08-08	2005-02-23	2005-02-24	ENSG00000146383	ENSG00000146383		"""GPCR / Class A : Trace amine associated receptors"""	20978	protein-coding gene	gene with protein product		608923	"""trace amine receptor 4"""	TRAR4		11459929, 15718104	Standard	NM_175067		Approved	TA4	uc011eck.2	Q96RI8	OTTHUMG00000015579	ENST00000275198.1:c.872G>A	6.37:g.132892332G>A	ENSP00000275198:p.Cys291Tyr	Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	93	61	0.655914	NM_175067	Q5VUQ4	Missense_Mutation	SNP	ENST00000275198.1	37	CCDS5155.1	116	0.05311355311355311	43	0.08739837398373984	18	0.049723756906077346	13	0.022727272727272728	42	0.055408970976253295	A	0.539	-0.854571	0.02630	0.103495	0.067674	ENSG00000146383	ENST00000275198;ENST00000539228	T	0.35236	1.32	5.11	3.94	0.45596	GPCR, rhodopsin-like superfamily (1);	0.117627	0.34802	N	0.003677	T	0.00936	0.0031	N	0.00021	-2.755	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.43686	-0.9376	10	0.02654	T	1	-4.0137	3.1411	0.06456	0.6364:0.1193:0.0768:0.1675	rs8192625;rs17061415;rs8192625	291	Q96RI8	TAAR6_HUMAN	Y	291;266	ENSP00000275198:C291Y	ENSP00000275198:C291Y	C	+	2	0	TAAR6	132934025	0.000000	0.05858	0.379000	0.26080	0.548000	0.35241	0.687000	0.25407	0.402000	0.25451	-1.172000	0.01736	TGT	G|0.930;A|0.070	0.070	strong		0.358	TAAR6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042255.1	NM_175067	
MINK1	50488	hgsc.bcm.edu	37	17	4797910	4797910	+	Missense_Mutation	SNP	G	G	A	rs79940062	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:4797910G>A	ENST00000355280.6	+	24	3095	c.2899G>A	c.(2899-2901)Gac>Aac	p.D967N	MINK1_ENST00000347992.7_Missense_Mutation_p.D938N|MINK1_ENST00000453408.3_Missense_Mutation_p.D947N	NM_001024937.3|NM_015716.4|NM_153827.4	NP_001020108.1|NP_056531.1|NP_722549.2			misshapen-like kinase 1											central_nervous_system(2)|large_intestine(1)|lung(1)|skin(1)|stomach(1)	6						AGGCAGTGGGGACAGCATCCC	0.612													G|||	28	0.00559105	0.0008	0.0029	5008	,	,		20491	0.001		0.0179	False		,,,				2504	0.0061				p.D967N		Atlas-SNP	.											.	MINK1	110	.	0			c.G2899A						PASS	.	G	ASN/ASP,ASN/ASP,ASN/ASP,ASN/ASP	16,4312		0,16,2148	47.0	51.0	50.0		2839,2788,2899,2812	5.3	1.0	17	dbSNP_133	50	160,8386		1,158,4114	yes	missense,missense,missense,missense	MINK1	NM_001024937.3,NM_015716.4,NM_153827.4,NM_170663.4	23,23,23,23	1,174,6262	AA,AG,GG		1.8722,0.3697,1.3671	benign,benign,benign,benign	947/1313,930/1296,967/1333,938/1304	4797910	176,12698	2164	4273	6437	SO:0001583	missense	50488	exon24			AGTGGGGACAGCA	AY775058	CCDS45588.1, CCDS45589.1, CCDS45590.1	17p13.2	2011-04-14	2010-06-24		ENSG00000141503	ENSG00000141503			17565	protein-coding gene	gene with protein product	"""misshapen/NIK-related kinase"""	609426	"""misshapen-like kinase 1 (zebrafish)"""			10708748, 12087176	Standard	NM_015716		Approved	B55, MINK, ZC3, MAP4K6, YSK2	uc010vsl.2	Q8N4C8		ENST00000355280.6:c.2899G>A	17.37:g.4797910G>A	ENSP00000347427:p.Asp967Asn	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	95	40	0.421053	NM_153827		Missense_Mutation	SNP	ENST00000355280.6	37	CCDS45588.1	13	0.005952380952380952	1	0.0020325203252032522	1	0.0027624309392265192	1	0.0017482517482517483	10	0.013192612137203167	G	21.1	4.091253	0.76756	0.003697	0.018722	ENSG00000141503	ENST00000355280;ENST00000453408;ENST00000347992	T;T;T	0.74315	-0.83;-0.83;-0.83	5.26	5.26	0.73747	.	0.053262	0.64402	D	0.000001	T	0.73497	0.3594	M	0.65498	2.005	0.58432	D	0.999999	P;D;D;D	0.67145	0.952;0.996;0.993;0.996	P;D;D;D	0.73708	0.643;0.981;0.956;0.981	T	0.75451	-0.3313	10	0.22109	T	0.4	.	16.4095	0.83703	0.0:0.0:1.0:0.0	.	930;947;967;938	Q8N4C8-2;Q8N4C8-4;Q8N4C8;Q8N4C8-3	.;.;MINK1_HUMAN;.	N	967;947;938	ENSP00000347427:D967N;ENSP00000406487:D947N;ENSP00000269296:D938N	ENSP00000269296:D938N	D	+	1	0	MINK1	4738686	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.679000	0.74513	2.735000	0.93741	0.655000	0.94253	GAC	G|0.993;A|0.007	0.007	strong		0.612	MINK1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439801.1	NM_015716	
CD83	9308	hgsc.bcm.edu	37	6	14131804	14131804	+	Silent	SNP	G	G	A	rs7743206	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:14131804G>A	ENST00000379153.3	+	3	378	c.207G>A	c.(205-207)agG>agA	p.R69R		NM_001040280.1|NM_001251901.1|NM_004233.3	NP_001035370.1|NP_001238830.1|NP_004224.1	Q01151	CD83_HUMAN	CD83 molecule	69	Ig-like V-type.				defense response (GO:0006952)|humoral immune response (GO:0006959)|negative regulation of interleukin-4 production (GO:0032713)|positive regulation of CD4-positive, alpha-beta T cell differentiation (GO:0043372)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of interleukin-2 production (GO:0032743)|response to organic cyclic compound (GO:0014070)|signal transduction (GO:0007165)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				breast(2)|endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(1)	12	Breast(50;0.00245)|Ovarian(93;0.137)	all_hematologic(90;0.117)				ACCACCTCAGGGGACAGCACT	0.537													G|||	654	0.130591	0.146	0.0908	5008	,	,		20460	0.1766		0.1302	False		,,,				2504	0.091				p.R69R		Atlas-SNP	.											.	CD83	23	.	0			c.G207A						PASS	.	G	,	624,3782	271.3+/-270.1	53,518,1632	108.0	99.0	102.0		207,207	-3.4	0.0	6	dbSNP_116	102	1204,7396	243.9+/-273.3	98,1008,3194	no	coding-synonymous,coding-synonymous	CD83	NM_001040280.1,NM_004233.3	,	151,1526,4826	AA,AG,GG		14.0,14.1625,14.0551	,	69/205,69/206	14131804	1828,11178	2203	4300	6503	SO:0001819	synonymous_variant	9308	exon3			CCTCAGGGGACAG	Z11697	CCDS4532.1, CCDS75403.1	6p23	2013-01-11	2006-03-31		ENSG00000112149	ENSG00000112149		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"""	1703	protein-coding gene	gene with protein product		604534	"""CD83 antigen (activated B lymphocytes, immunoglobulin superfamily)"", ""CD83 molecule """			1378080, 8422464	Standard	NM_001251901		Approved	HB15, BL11	uc003nbi.3	Q01151	OTTHUMG00000014283	ENST00000379153.3:c.207G>A	6.37:g.14131804G>A		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	89	40	0.449438	NM_004233	Q5THX9	Silent	SNP	ENST00000379153.3	37	CCDS4532.1																																																																																			G|0.859;A|0.141	0.141	strong		0.537	CD83-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039916.1		
GPRIN2	9721	hgsc.bcm.edu	37	10	46999863	46999863	+	Missense_Mutation	SNP	C	C	G	rs4445576	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:46999863C>G	ENST00000374317.1	+	3	1256	c.983C>G	c.(982-984)tCc>tGc	p.S328C	GPRIN2_ENST00000374314.4_Missense_Mutation_p.S328C	NM_014696.3	NP_055511.2	O60269	GRIN2_HUMAN	G protein regulated inducer of neurite outgrowth 2	328			S -> C (in dbSNP:rs4445576).							breast(2)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(1)|lung(6)|prostate(1)	18						GCAGAGGCATCCCCGCTGTCA	0.652													C|||	825	0.164736	0.1021	0.3285	5008	,	,		36299	0.004		0.3042	False		,,,				2504	0.1554				p.S328C		Atlas-SNP	.											GPRIN2,NS,carcinoma,0,3	GPRIN2	94	3	0			c.C983G						PASS	.	C	CYS/SER	471,3935		0,471,1732	56.0	59.0	58.0		983	3.2	0.0	10	dbSNP_111	58	2030,6570		1,2028,2271	yes	missense	GPRIN2	NM_014696.3	112	1,2499,4003	GG,GC,CC		23.6047,10.69,19.2296	probably-damaging	328/459	46999863	2501,10505	2203	4300	6503	SO:0001583	missense	9721	exon3			AGGCATCCCCGCT	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.983C>G	10.37:g.46999863C>G	ENSP00000363436:p.Ser328Cys	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	106	22	0.207547	NM_014696	Q5SVF0	Missense_Mutation	SNP	ENST00000374317.1	37	CCDS31192.1	386	0.17673992673992675	56	0.11382113821138211	102	0.281767955801105	0	0.0	228	0.3007915567282322	C	11.15	1.553761	0.27739	0.1069	0.236047	ENSG00000204175	ENST00000374317;ENST00000374314	T;T	0.03889	3.77;3.77	3.15	3.15	0.36227	.	0.474723	0.15845	N	0.241802	T	0.00012	0.0000	L	0.51422	1.61	0.09310	N	1	D	0.65815	0.995	P	0.55824	0.785	T	0.47959	-0.9076	10	0.54805	T	0.06	.	12.1335	0.53957	0.0:1.0:0.0:0.0	rs4445576	328	O60269	GRIN2_HUMAN	C	328	ENSP00000363436:S328C;ENSP00000363433:S328C	ENSP00000363433:S328C	S	+	2	0	GPRIN2	46419869	.	.	0.005000	0.12908	0.392000	0.30506	.	.	1.788000	0.52465	0.313000	0.20887	TCC	C|0.822;G|0.178	0.178	strong		0.652	GPRIN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047836.1	NM_014696	
SMCHD1	23347	hgsc.bcm.edu	37	18	2724930	2724930	+	Missense_Mutation	SNP	A	A	T	rs633422	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:2724930A>T	ENST00000320876.6	+	21	2975	c.2637A>T	c.(2635-2637)aaA>aaT	p.K879N	SMCHD1_ENST00000261598.8_Missense_Mutation_p.K879N|RP11-703M24.5_ENST00000583546.1_RNA	NM_015295.2	NP_056110.2	A6NHR9	SMHD1_HUMAN	structural maintenance of chromosomes flexible hinge domain containing 1	879			K -> N (in dbSNP:rs633422).		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						AAATAACCAAAGGACCAAATT	0.358													A|||	1033	0.20627	0.0166	0.2925	5008	,	,		15014	0.1915		0.4553	False		,,,				2504	0.1605				p.K879N		Atlas-SNP	.											.	SMCHD1	88	.	0			c.A2637T						PASS	.	A	ASN/LYS	299,3319		16,267,1526	61.0	55.0	57.0		2637	3.1	1.0	18	dbSNP_83	57	3562,4564		786,1990,1287	yes	missense	SMCHD1	NM_015295.2	94	802,2257,2813	TT,TA,AA		43.8346,8.2642,32.8764	benign	879/2006	2724930	3861,7883	1809	4063	5872	SO:0001583	missense	23347	exon21			AACCAAAGGACCA	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.2637A>T	18.37:g.2724930A>T	ENSP00000326603:p.Lys879Asn	Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	27	11	0.407407	NM_015295	O75141|Q6AHX6|Q6ZTQ8|Q9H6Q2|Q9UG39	Missense_Mutation	SNP	ENST00000320876.6	37	CCDS45822.1	607	0.27793040293040294	11	0.022357723577235773	120	0.3314917127071823	139	0.243006993006993	337	0.4445910290237467	A	12.57	1.976754	0.34848	0.082642	0.438346	ENSG00000101596	ENST00000320876;ENST00000261598	T;T	0.25414	1.8;1.8	5.6	3.1	0.35709	.	0.228496	0.43747	D	0.000539	T	0.00012	0.0000	L	0.27053	0.805	0.31040	P	0.71645	B	0.02656	0.0	B	0.01281	0.0	T	0.48433	-0.9036	9	0.30078	T	0.28	-11.9875	5.7568	0.18178	0.7265:0.0:0.1505:0.123	rs633422;rs17551379;rs633422	879	A6NHR9	SMHD1_HUMAN	N	879	ENSP00000326603:K879N;ENSP00000261598:K879N	ENSP00000261598:K879N	K	+	3	2	SMCHD1	2714930	0.993000	0.37304	1.000000	0.80357	0.999000	0.98932	1.045000	0.30341	0.363000	0.24346	0.533000	0.62120	AAA	A|0.748;T|0.252	0.252	strong		0.358	SMCHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441082.2		
HTR3D	200909	hgsc.bcm.edu	37	3	183756702	183756702	+	Missense_Mutation	SNP	G	G	A	rs6789754	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:183756702G>A	ENST00000382489.3	+	8	1304	c.1304G>A	c.(1303-1305)cGc>cAc	p.R435H	HTR3D_ENST00000334128.2_Missense_Mutation_p.R260H|HTR3D_ENST00000453435.1_Missense_Mutation_p.R214H|HTR3D_ENST00000428798.2_Missense_Mutation_p.R385H	NM_001163646.1	NP_001157118.1	Q70Z44	5HT3D_HUMAN	5-hydroxytryptamine (serotonin) receptor 3D, ionotropic	435			R -> H (in dbSNP:rs6789754). {ECO:0000269|PubMed:15489334}.		ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	extracellular ligand-gated ion channel activity (GO:0005230)			large_intestine(3)|lung(3)|prostate(1)|skin(1)|stomach(2)	10	all_cancers(143;2.33e-10)|Ovarian(172;0.0303)		Epithelial(37;6.23e-36)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)		Ergoloid mesylate(DB01049)	CTGCTCTTCCGCCTCTACCTG	0.582													G|||	3398	0.678514	0.8351	0.6455	5008	,	,		18643	0.754		0.5905	False		,,,				2504	0.5031				p.R435H		Atlas-SNP	.											.	HTR3D	65	.	0			c.G1304A						PASS	.	G	HIS/ARG,HIS/ARG,HIS/ARG	3453,953		1354,745,104	174.0	158.0	163.0		1154,1304,779	1.2	0.9	3	dbSNP_116	163	5051,3549		1485,2081,734	no	missense,missense,missense	HTR3D	NM_001145143.1,NM_001163646.1,NM_182537.2	29,29,29	2839,2826,838	AA,AG,GG		41.2674,21.6296,34.6148	possibly-damaging,possibly-damaging,possibly-damaging	385/405,435/455,260/280	183756702	8504,4502	2203	4300	6503	SO:0001583	missense	200909	exon8			TCTTCCGCCTCTA	AY159812	CCDS3249.1, CCDS46966.1, CCDS54685.1	3q27	2012-05-22	2012-02-03		ENSG00000186090	ENSG00000186090		"""5-HT (serotonin) receptors"", ""Ligand-gated ion channels / 5-HT (serotonin) receptors, ionotropic"""	24004	protein-coding gene	gene with protein product		610122	"""5-hydroxytryptamine (serotonin) receptor 3 family member D"""			12801637	Standard	NM_001145143		Approved		uc011bqv.2	Q70Z44	OTTHUMG00000156858	ENST00000382489.3:c.1304G>A	3.37:g.183756702G>A	ENSP00000371929:p.Arg435His	Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	154	72	0.467532	NM_001163646	C9J2I6|J3QT78|Q495N5|Q495N6|Q7Z6B3	Missense_Mutation	SNP	ENST00000382489.3	37	CCDS54685.1	1487	0.6808608058608059	393	0.7987804878048781	216	0.5966850828729282	427	0.7465034965034965	451	0.5949868073878628	.	11.41	1.629459	0.28978	0.783704	0.587326	ENSG00000186090	ENST00000334128;ENST00000428798;ENST00000382489;ENST00000453435	D;D;D;D	0.81908	-1.55;-1.55;-1.55;-1.55	4.11	1.16	0.20824	Neurotransmitter-gated ion-channel transmembrane domain (1);	0.813114	0.10601	N	0.655669	T	0.00012	0.0000	L	0.53249	1.67	0.80722	P	0.0	P;B;B;B	0.42973	0.796;0.006;0.006;0.03	B;B;B;B	0.33254	0.16;0.017;0.006;0.052	T	0.46884	-0.9159	9	0.28530	T	0.3	-6.0501	4.1452	0.10212	0.2203:0.1932:0.5864:0.0	rs6789754;rs58875341	435;260;214;260	Q70Z44;Q70Z44-2;Q70Z44-3;F6WC43	5HT3D_HUMAN;.;.;.	H	260;385;435;214	ENSP00000334315:R260H;ENSP00000405409:R385H;ENSP00000371929:R435H;ENSP00000389268:R214H	ENSP00000334315:R260H	R	+	2	0	HTR3D	185239396	0.024000	0.19004	0.916000	0.36221	0.944000	0.59088	2.087000	0.41653	0.107000	0.17824	0.563000	0.77884	CGC	G|0.341;A|0.659	0.659	strong		0.582	HTR3D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000346289.1	NM_182537	
STAMBPL1	57559	hgsc.bcm.edu	37	10	90673047	90673047	+	Missense_Mutation	SNP	G	G	A	rs34270879	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:90673047G>A	ENST00000371926.3	+	6	1568	c.610G>A	c.(610-612)Gag>Aag	p.E204K	STAMBPL1_ENST00000371927.3_Missense_Mutation_p.E204K|STAMBPL1_ENST00000371922.1_Missense_Mutation_p.E38K|STAMBPL1_ENST00000371924.1_Missense_Mutation_p.E204K	NM_020799.3	NP_065850.1	Q96FJ0	STALP_HUMAN	STAM binding protein-like 1	204			E -> K (in dbSNP:rs34270879).			membrane (GO:0016020)	metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)			breast(2)|endometrium(1)|large_intestine(2)|liver(2)|lung(2)|ovary(1)|skin(1)	11		Colorectal(252;0.0381)		Colorectal(12;6.38e-05)|COAD - Colon adenocarcinoma(12;7.75e-05)		AGGGCTGTCAGAGCAGATTGA	0.453													G|||	70	0.0139776	0.0038	0.0231	5008	,	,		20978	0.0		0.0348	False		,,,				2504	0.0143				p.E204K		Atlas-SNP	.											.	STAMBPL1	63	.	0			c.G610A						PASS	.	G	LYS/GLU	33,4373	38.4+/-70.7	0,33,2170	131.0	120.0	124.0		610	6.0	1.0	10	dbSNP_126	124	369,8231	122.0+/-181.0	5,359,3936	yes	missense	STAMBPL1	NM_020799.2	56	5,392,6106	AA,AG,GG		4.2907,0.749,3.0909	possibly-damaging	204/437	90673047	402,12604	2203	4300	6503	SO:0001583	missense	57559	exon6			CTGTCAGAGCAGA	AB037794	CCDS7391.1	10q23.32	2006-11-08			ENSG00000138134	ENSG00000138134			24105	protein-coding gene	gene with protein product	"""associated molecule with the SH3 domain of STAM (AMSH) like protein"", ""associated molecule with the SH3 domain of STAM (AMSH) - Family Protein"""	612352				12810066, 12943674	Standard	NM_020799		Approved	AMSH-LP, KIAA1373, AMSH-FP, FLJ31524, ALMalpha, bA399O19.2	uc001kfk.4	Q96FJ0	OTTHUMG00000018702	ENST00000371926.3:c.610G>A	10.37:g.90673047G>A	ENSP00000360994:p.Glu204Lys	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	177	81	0.457627	NM_020799	B3KPA7|Q5T9N4|Q5T9N9|Q7Z420|Q9P2H4	Missense_Mutation	SNP	ENST00000371926.3	37	CCDS7391.1	39	0.017857142857142856	4	0.008130081300813009	11	0.03038674033149171	0	0.0	24	0.0316622691292876	G	21.4	4.144961	0.77888	0.00749	0.042907	ENSG00000138134	ENST00000371926;ENST00000371927;ENST00000371924;ENST00000371922	T;T;T;T	0.23348	1.95;1.93;1.95;1.91	5.97	5.97	0.96955	.	0.264086	0.31347	N	0.007805	T	0.07234	0.0183	N	0.08118	0	0.49798	D	0.999825	P;D	0.69078	0.845;0.997	P;D	0.75020	0.458;0.985	T	0.03025	-1.1081	10	0.06757	T	0.87	-5.0108	17.1443	0.86762	0.0:0.0:1.0:0.0	rs34270879	204;204	Q96FJ0-2;Q96FJ0	.;STALP_HUMAN	K	204;204;204;38	ENSP00000360994:E204K;ENSP00000360995:E204K;ENSP00000360992:E204K;ENSP00000360990:E38K	ENSP00000360990:E38K	E	+	1	0	STAMBPL1	90663027	1.000000	0.71417	0.970000	0.41538	0.912000	0.54170	5.019000	0.64060	2.829000	0.97493	0.650000	0.86243	GAG	G|0.970;A|0.030	0.030	strong		0.453	STAMBPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049283.1	NM_020799	
MGME1	92667	hgsc.bcm.edu	37	20	17968923	17968923	+	Silent	SNP	T	T	C	rs28455091	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:17968923T>C	ENST00000377710.5	+	4	1134	c.846T>C	c.(844-846)gaT>gaC	p.D282D	MGME1_ENST00000467391.1_3'UTR|MGME1_ENST00000377704.4_Intron|MGME1_ENST00000377709.1_Silent_p.D202D	NM_052865.2	NP_443097.1			mitochondrial genome maintenance exonuclease 1																		TGAACCATGATACCAACTACA	0.443													C|||	1562	0.311901	0.1823	0.2349	5008	,	,		19600	0.4345		0.2624	False		,,,				2504	0.4663				p.D282D		Atlas-SNP	.											.	.	.	.	0			c.T846C						PASS	.	C		953,3453	735.6+/-410.7	114,725,1364	104.0	93.0	97.0		846	0.7	0.9	20	dbSNP_125	97	2500,6100	695.0+/-404.8	350,1800,2150	no	coding-synonymous	C20orf72	NM_052865.2		464,2525,3514	CC,CT,TT		29.0698,21.6296,26.5493		282/345	17968923	3453,9553	2203	4300	6503	SO:0001819	synonymous_variant	92667	exon4			CCATGATACCAAC		CCDS13131.1	20p11.23	2013-08-29	2013-01-11	2013-01-11	ENSG00000125871	ENSG00000125871			16205	protein-coding gene	gene with protein product		615076	"""chromosome 20 open reading frame 72"""	C20orf72		23313956, 23358826, 23434322	Standard	NM_052865		Approved	bA504H3.4, DDK1	uc002wqh.3	Q9BQP7	OTTHUMG00000031955	ENST00000377710.5:c.846T>C	20.37:g.17968923T>C		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	89	42	0.47191	NM_052865		Silent	SNP	ENST00000377710.5	37	CCDS13131.1																																																																																			T|0.732;C|0.268	0.268	strong		0.443	MGME1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078139.1	NM_052865	
PRRC2C	23215	hgsc.bcm.edu	37	1	171557600	171557600	+	Missense_Mutation	SNP	A	A	G	rs2421847	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:171557600A>G	ENST00000338920.4	+	33	8386	c.8149A>G	c.(8149-8151)Act>Gct	p.T2717A	PRRC2C_ENST00000367742.3_Missense_Mutation_p.T2719A|PRRC2C_ENST00000426496.2_Missense_Mutation_p.T2652A|PRRC2C_ENST00000392078.3_Missense_Mutation_p.T2719A	NM_015172.3	NP_055987.2	Q9Y520	PRC2C_HUMAN	proline-rich coiled-coil 2C	2717			T -> A (in dbSNP:rs2421847).		hematopoietic progenitor cell differentiation (GO:0002244)	membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)										AGCCCCTGCCACTGTGAGAAT	0.428													A|||	95	0.0189696	0.0015	0.0259	5008	,	,		16401	0.0		0.0388	False		,,,				2504	0.0368				p.T2717A		Atlas-SNP	.											.	.	.	.	0			c.A8149G						PASS	.	A	ALA/THR	31,4375	37.6+/-69.7	1,29,2173	83.0	86.0	85.0		8149	2.5	1.0	1	dbSNP_100	85	334,8266	115.7+/-175.5	2,330,3968	yes	missense	PRRC2C	NM_015172.3	58	3,359,6141	GG,GA,AA		3.8837,0.7036,2.8064	probably-damaging	2717/2818	171557600	365,12641	2203	4300	6503	SO:0001583	missense	23215	exon33			CCTGCCACTGTGA	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.8149A>G	1.37:g.171557600A>G	ENSP00000343629:p.Thr2717Ala	Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	148	59	0.398649	NM_015172	Q05DM8|Q49A39|Q6PD54|Q9H2N2|Q9HA05|Q9NSM8|Q9NXL3|Q9UF29|Q9UPQ6	Missense_Mutation	SNP	ENST00000338920.4	37	CCDS1296.2	42	0.019230769230769232	1	0.0020325203252032522	9	0.024861878453038673	0	0.0	32	0.04221635883905013	A	9.336	1.061898	0.19987	0.007036	0.038837	ENSG00000117523	ENST00000392078;ENST00000451306;ENST00000426496;ENST00000367742;ENST00000338920;ENST00000392080	T;T;T;T	0.01821	4.62;4.62;4.64;4.64	6.06	2.49	0.30216	.	0.741361	0.10991	N	0.611633	T	0.00328	0.0010	N	0.19112	0.55	0.23320	N	0.997917	B;B	0.11235	0.0;0.004	B;B	0.08055	0.0;0.003	T	0.45818	-0.9235	10	0.02654	T	1	.	4.7266	0.12943	0.616:0.0:0.2524:0.1316	rs2421847;rs58232543;rs2421847	2652;2717	B7WNZ6;Q9Y520-4	.;.	A	2719;2671;2652;2719;2717;2474	ENSP00000375928:T2719A;ENSP00000410219:T2652A;ENSP00000356716:T2719A;ENSP00000343629:T2717A	ENSP00000343629:T2717A	T	+	1	0	PRRC2C	169824223	1.000000	0.71417	0.999000	0.59377	0.961000	0.63080	3.312000	0.51927	0.174000	0.19809	-0.301000	0.09380	ACT	A|0.977;G|0.023	0.023	strong		0.428	PRRC2C-010	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000314826.4	NM_015172	
PRMT9	90826	hgsc.bcm.edu	37	4	148560210	148560210	+	Silent	SNP	G	G	A	rs34852471	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:148560210G>A	ENST00000322396.6	-	11	2465	c.2223C>T	c.(2221-2223)gaC>gaT	p.D741D	PRMT10_ENST00000541232.1_Silent_p.D628D|TMEM184C_ENST00000508208.1_Intron	NM_138364.2	NP_612373.2	Q6P2P2	ANM9_HUMAN		741	SAM-dependent MTase PRMT-type 2. {ECO:0000255|PROSITE-ProRule:PRU01015}.					cytoplasm (GO:0005737)	protein methyltransferase activity (GO:0008276)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	28						ATGAGGATAGGTCCAAAAATA	0.363													G|||	65	0.0129792	0.0008	0.0072	5008	,	,		16503	0.003		0.0447	False		,,,				2504	0.0112				p.D741D		Atlas-SNP	.											.	PRMT10	68	.	0			c.C2223T						PASS	.	G		32,4374	37.6+/-69.7	0,32,2171	93.0	94.0	93.0		2223	0.5	0.1	4	dbSNP_126	93	322,8278	113.3+/-173.4	9,304,3987	no	coding-synonymous	PRMT10	NM_138364.2		9,336,6158	AA,AG,GG		3.7442,0.7263,2.7218		741/846	148560210	354,12652	2203	4300	6503	SO:0001819	synonymous_variant	90826	exon11			GGATAGGTCCAAA																												ENST00000322396.6:c.2223C>T	4.37:g.148560210G>A		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	84	39	0.464286	NM_138364	A8KA39|B3KU92|Q6ZR58|Q8N383|Q9BT55|Q9NT98	Silent	SNP	ENST00000322396.6	37	CCDS3771.1																																																																																			G|0.976;A|0.024	0.024	strong		0.363	PRMT10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364650.1		
NRCAM	4897	hgsc.bcm.edu	37	7	107834613	107834613	+	Missense_Mutation	SNP	G	G	C	rs6958498	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:107834613G>C	ENST00000425651.2	-	14	1632	c.1633C>G	c.(1633-1635)Cct>Gct	p.P545A	NRCAM_ENST00000351718.4_Missense_Mutation_p.P539A|NRCAM_ENST00000413765.2_Missense_Mutation_p.P526A|NRCAM_ENST00000379022.4_Missense_Mutation_p.P545A|NRCAM_ENST00000379024.4_Missense_Mutation_p.P526A|NRCAM_ENST00000379028.3_Missense_Mutation_p.P545A	NM_001037132.2	NP_001032209.1	Q92823	NRCAM_HUMAN	neuronal cell adhesion molecule	545	Ig-like 6.		P -> A (in dbSNP:rs6958498). {ECO:0000269|PubMed:12690205, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9205841, ECO:0000269|Ref.7}.	Missing (in Ref. 1; AAC50765). {ECO:0000305}.	angiogenesis (GO:0001525)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|axonogenesis (GO:0007409)|central nervous system development (GO:0007417)|clustering of voltage-gated sodium channels (GO:0045162)|heterotypic cell-cell adhesion (GO:0034113)|neuron migration (GO:0001764)|neuronal action potential propagation (GO:0019227)|positive regulation of neuron differentiation (GO:0045666)|protein localization (GO:0008104)|regulation of axon extension (GO:0030516)|retinal ganglion cell axon guidance (GO:0031290)|single organismal cell-cell adhesion (GO:0016337)|synapse assembly (GO:0007416)	axon initial segment (GO:0043194)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|synapse (GO:0045202)	ankyrin binding (GO:0030506)			breast(4)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(8)|liver(1)|lung(36)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(4)	65						ATCCATGTAGGATCTGAAATG	0.393													G|||	3500	0.698882	0.441	0.8012	5008	,	,		21767	0.8839		0.7992	False		,,,				2504	0.681				p.P545A		Atlas-SNP	.											.	NRCAM	267	.	0			c.C1633G						PASS	.	G	ALA/PRO,ALA/PRO,ALA/PRO,ALA/PRO,ALA/PRO	2232,2174	593.7+/-388.1	564,1104,535	164.0	131.0	142.0		1633,1633,1576,1576,1615	4.8	1.0	7	dbSNP_116	142	6706,1894	727.9+/-406.7	2611,1484,205	yes	missense,missense,missense,missense,missense	NRCAM	NM_001037132.2,NM_001193582.1,NM_001193583.1,NM_001193584.1,NM_005010.4	27,27,27,27,27	3175,2588,740	CC,CG,GG		22.0233,49.3418,31.2779	benign,benign,benign,benign,benign	545/1305,545/1212,526/1193,526/1181,539/1184	107834613	8938,4068	2203	4300	6503	SO:0001583	missense	4897	exon14			ATGTAGGATCTGA		CCDS5751.1, CCDS47686.1, CCDS55153.1, CCDS75652.1	7q31	2013-02-11			ENSG00000091129	ENSG00000091129		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	7994	protein-coding gene	gene with protein product	"""NgCAM-related cell adhesion molecule"""	601581				8812479	Standard	NM_001037132		Approved	KIAA0343, Bravo	uc022aka.1	Q92823	OTTHUMG00000154973	ENST00000425651.2:c.1633C>G	7.37:g.107834613G>C	ENSP00000401244:p.Pro545Ala	Somatic	281	0	0		WXS	Illumina HiSeq	Phase_I	195	193	0.989744	NM_001037132	A4D0S3|E9PDA4|O15051|O15179|Q14BM2|Q9UHI3|Q9UHI4	Missense_Mutation	SNP	ENST00000425651.2	37	CCDS47686.1	1604	0.7344322344322345	197	0.40040650406504064	290	0.8011049723756906	509	0.8898601398601399	608	0.8021108179419525	G	14.11	2.438335	0.43326	0.506582	0.779767	ENSG00000091129	ENST00000379032;ENST00000379028;ENST00000413765;ENST00000537765;ENST00000351718;ENST00000379024;ENST00000425651;ENST00000379022;ENST00000445979	T;T;T;T;T;T	0.31769	1.48;1.48;1.48;1.48;1.48;1.48	5.7	4.82	0.62117	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.049754	0.85682	N	0.000000	T	0.00012	0.0000	L	0.39085	1.19	0.09310	P	0.999999999806525	B;B;B;B;B	0.30511	0.044;0.282;0.035;0.059;0.003	B;B;B;B;B	0.39617	0.086;0.278;0.305;0.139;0.013	T	0.04153	-1.0973	9	0.19590	T	0.45	.	16.7949	0.85599	0.0:0.1288:0.8712:0.0	rs6958498;rs52825382;rs57776386;rs6958498	545;526;526;539;545	Q92823-5;Q92823-3;E9PDA4;Q92823-4;Q92823	.;.;.;.;NRCAM_HUMAN	A	545;545;526;545;539;526;545;545;539	ENSP00000368314:P545A;ENSP00000407858:P526A;ENSP00000325269:P539A;ENSP00000368310:P526A;ENSP00000401244:P545A;ENSP00000368308:P545A	ENSP00000325269:P539A	P	-	1	0	NRCAM	107621849	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	7.583000	0.82559	1.381000	0.46364	0.655000	0.94253	CCT	G|0.295;C|0.705	0.705	strong		0.393	NRCAM-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337942.2	NM_001037132	
CAMKV	79012	hgsc.bcm.edu	37	3	49899795	49899795	+	Silent	SNP	G	G	A	rs3796386	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:49899795G>A	ENST00000477224.1	-	2	505	c.27C>T	c.(25-27)ggC>ggT	p.G9G	CAMKV_ENST00000466940.1_Silent_p.G9G|CAMKV_ENST00000463537.1_Silent_p.G9G|CAMKV_ENST00000488336.1_Silent_p.G9G|CAMKV_ENST00000296471.7_Silent_p.G9G|CAMKV_ENST00000498324.1_5'UTR|RN7SL217P_ENST00000584520.1_RNA|CAMKV_ENST00000467248.1_5'UTR			Q8NCB2	CAMKV_HUMAN	CaM kinase-like vesicle-associated	9						cytoplasmic vesicle (GO:0031410)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)			central_nervous_system(1)|large_intestine(2)|lung(2)|ovary(2)	7				BRCA - Breast invasive adenocarcinoma(193;4.62e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.00551)|Kidney(197;0.00621)		TCTTCTTGTCGCCCAGAGTCA	0.552													G|||	1397	0.278954	0.3631	0.3141	5008	,	,		20204	0.124		0.4145	False		,,,				2504	0.1605				p.G9G		Atlas-SNP	.											.	CAMKV	84	.	0			c.C27T						PASS	.	G		1597,2809	496.4+/-363.5	294,1009,900	123.0	109.0	114.0		27	-9.8	0.8	3	dbSNP_107	114	3600,5000	521.0+/-379.8	724,2152,1424	no	coding-synonymous	CAMKV	NM_024046.3		1018,3161,2324	AA,AG,GG		41.8605,36.246,39.9585		9/502	49899795	5197,7809	2203	4300	6503	SO:0001819	synonymous_variant	79012	exon2			CTTGTCGCCCAGA	BC017363	CCDS33762.1	3p21.31	2005-03-04			ENSG00000164076	ENSG00000164076			28788	protein-coding gene	gene with protein product		614993				12477932	Standard	XM_005265478		Approved	MGC8407, VACAMKL	uc003cxt.1	Q8NCB2	OTTHUMG00000158288	ENST00000477224.1:c.27C>T	3.37:g.49899795G>A		Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	116	66	0.568965	NM_024046	A6NFD4|Q6FIB8|Q8NBS8|Q8NC85|Q8NDU4|Q8WTT8|Q9BQC9|Q9H0Q5	Silent	SNP	ENST00000477224.1	37	CCDS33762.1																																																																																			G|0.650;A|0.350	0.350	strong		0.552	CAMKV-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350584.4	NM_024046	
SLC6A17	388662	hgsc.bcm.edu	37	1	110709720	110709720	+	Missense_Mutation	SNP	G	G	A	rs12737742|rs35600013	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:110709720G>A	ENST00000331565.4	+	2	654	c.169G>A	c.(169-171)Gca>Aca	p.A57T	RP5-1028L10.1_ENST00000430098.1_RNA|RP5-1028L10.1_ENST00000443008.1_RNA|RP5-1028L10.1_ENST00000418579.1_RNA	NM_001010898.2	NP_001010898.1	Q9H1V8	S6A17_HUMAN	solute carrier family 6 (neutral amino acid transporter), member 17	57			A -> T (in dbSNP:rs12737742). {ECO:0000269|PubMed:15489334}.		alanine transport (GO:0032328)|glycine transport (GO:0015816)|leucine transport (GO:0015820)|neutral amino acid transport (GO:0015804)|proline transport (GO:0015824)	cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|synaptic vesicle (GO:0008021)	neurotransmitter:sodium symporter activity (GO:0005328)			breast(1)|endometrium(4)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	37		all_cancers(81;9.9e-06)|all_epithelial(167;3.24e-06)|all_lung(203;0.000116)|Lung NSC(277;0.000233)		Lung(183;0.0282)|Epithelial(280;0.0372)|all cancers(265;0.0378)|Colorectal(144;0.0438)|LUSC - Lung squamous cell carcinoma(189;0.151)|COAD - Colon adenocarcinoma(174;0.151)		GGAGCTGGATGCAGAGGACCG	0.612													G|||	1253	0.2502	0.0333	0.2608	5008	,	,		14238	0.2143		0.4652	False		,,,				2504	0.3517				p.A57T		Atlas-SNP	.											.	SLC6A17	86	.	0			c.G169A						PASS	.	G	THR/ALA,	477,3929		30,417,1756	71.0	58.0	62.0		169,291	2.6	0.0	1	dbSNP_121	62	3831,4769		935,1961,1404	yes	missense,coding-synonymous	SLC6A17,LOC100130800	NM_001010898.2,XM_001719118.1	58,	965,2378,3160	AA,AG,GG		44.5465,10.8261,33.1232	benign,	57/728,97/154	110709720	4308,8698	2203	4300	6503	SO:0001583	missense	388662	exon2			CTGGATGCAGAGG		CCDS30799.1	1p13.2	2013-07-19	2013-07-19		ENSG00000197106	ENSG00000197106		"""Solute carriers"""	31399	protein-coding gene	gene with protein product		610299	"""solute carrier family 6 (neurotransmitter transporter), member 17"", ""solute carrier family 6, member 17"""				Standard	NM_001010898		Approved		uc009wfq.3	Q9H1V8	OTTHUMG00000011761	ENST00000331565.4:c.169G>A	1.37:g.110709720G>A	ENSP00000330199:p.Ala57Thr	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	90	44	0.488889	NM_001010898	A6NEA8|A8K1R7|B9EIR5|Q5T5Q9	Missense_Mutation	SNP	ENST00000331565.4	37	CCDS30799.1	500	0.22893772893772893	15	0.03048780487804878	100	0.27624309392265195	108	0.1888111888111888	277	0.3654353562005277	G	13.10	2.134875	0.37728	0.108261	0.445465	ENSG00000197106	ENST00000331565;ENST00000450985	T	0.74209	-0.82	4.44	2.57	0.30868	.	0.616662	0.17593	N	0.168698	T	0.28830	0.0715	N	0.08118	0	0.80722	P	0.0	B	0.20887	0.049	B	0.23275	0.045	T	0.03325	-1.1048	9	0.22706	T	0.39	.	6.0414	0.19736	0.1679:0.1554:0.6768:0.0	rs12737742	57	Q9H1V8	S6A17_HUMAN	T	57	ENSP00000330199:A57T	ENSP00000330199:A57T	A	+	1	0	SLC6A17	110511243	0.000000	0.05858	0.042000	0.18584	0.914000	0.54420	0.538000	0.23160	0.504000	0.28082	0.655000	0.94253	GCA	A|0.305;C|0.000;G|0.695	0.305	strong		0.612	SLC6A17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032550.2	XM_371280	
NSD1	64324	hgsc.bcm.edu	37	5	176637471	176637471	+	Missense_Mutation	SNP	G	G	A	rs28932177	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:176637471G>A	ENST00000439151.2	+	5	2116	c.2071G>A	c.(2071-2073)Gcc>Acc	p.A691T	NSD1_ENST00000361032.4_Missense_Mutation_p.A588T|NSD1_ENST00000347982.4_Missense_Mutation_p.A422T|NSD1_ENST00000354179.4_Missense_Mutation_p.A422T	NM_022455.4	NP_071900.2	Q96L73	NSD1_HUMAN	nuclear receptor binding SET domain protein 1	691			A -> T (in dbSNP:rs28932177). {ECO:0000269|PubMed:12464997}.		gastrulation with mouth forming second (GO:0001702)|histone H3-K36 methylation (GO:0010452)|histone H4-K20 methylation (GO:0034770)|histone methylation (GO:0016571)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|estrogen receptor binding (GO:0030331)|histone methyltransferase activity (H3-K36 specific) (GO:0046975)|histone methyltransferase activity (H4-K20 specific) (GO:0042799)|retinoic acid receptor binding (GO:0042974)|retinoid X receptor binding (GO:0046965)|thyroid hormone receptor binding (GO:0046966)|transcription cofactor activity (GO:0003712)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(18)|lung(24)|ovary(2)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(3)	96	all_cancers(89;1.57e-05)|Renal(175;0.000269)|Lung NSC(126;0.00111)|all_lung(126;0.002)	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)|Epithelial(233;0.198)	Kidney(146;0.235)		TAGGTTTGCTGCCACAAACAC	0.393			T	NUP98	AML		Sotos Syndrome		Weaver syndrome;Sotos syndrome;Beckwith-Wiedemann syndrome	HNSCC(47;0.14)			G|||	65	0.0129792	0.0045	0.0086	5008	,	,		20290	0.0		0.0249	False		,,,				2504	0.0286				p.A691T		Atlas-SNP	.		Dom	yes		5	5q35	64324	nuclear receptor binding SET domain protein 1	yes	L	.	NSD1	416	.	0			c.G2071A						PASS	.	G	THR/ALA,THR/ALA	28,4378	35.2+/-66.4	1,26,2176	53.0	56.0	55.0		2071,1264	3.3	1.0	5	dbSNP_125	55	207,8393	89.7+/-151.9	2,203,4095	yes	missense,missense	NSD1	NM_022455.4,NM_172349.2	58,58	3,229,6271	AA,AG,GG		2.407,0.6355,1.8069	benign,benign	691/2697,422/2428	176637471	235,12771	2203	4300	6503	SO:0001583	missense	64324	exon5	Familial Cancer Database	Weaver-Smith syndrome;Cerebral Gigantism;BWS, Exomphalos-Macroglossia-Gigantism (EMG) syndrome, Wiedemann-Beckwith syndrome, WBS	TTTGCTGCCACAA	AK026066	CCDS4412.1, CCDS4413.1	5q35	2014-09-17	2003-03-12		ENSG00000165671	ENSG00000165671		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	14234	protein-coding gene	gene with protein product		606681	"""Sotos syndrome"""	STO		9628876, 11896389	Standard	NM_022455		Approved	ARA267, FLJ22263, KMT3B	uc003mfr.4	Q96L73	OTTHUMG00000130846	ENST00000439151.2:c.2071G>A	5.37:g.176637471G>A	ENSP00000395929:p.Ala691Thr	Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	185	69	0.372973	NM_022455	Q96PD8|Q96RN7	Missense_Mutation	SNP	ENST00000439151.2	37	CCDS4412.1	27	0.012362637362637362	2	0.0040650406504065045	4	0.011049723756906077	0	0.0	21	0.027704485488126648	G	10.58	1.390030	0.25118	0.006355	0.02407	ENSG00000165671	ENST00000354179;ENST00000355783;ENST00000439151;ENST00000347982;ENST00000361032	D;D;D;D	0.92752	-2.98;-2.98;-2.98;-3.1	5.1	3.31	0.37934	.	0.621198	0.16033	N	0.232761	T	0.59362	0.2188	N	0.08118	0	0.21822	N	0.999526	B;B;B	0.12630	0.006;0.006;0.001	B;B;B	0.12156	0.004;0.007;0.002	T	0.58719	-0.7587	9	.	.	.	.	4.2978	0.10910	0.182:0.0:0.592:0.226	rs28932177;rs28932177	422;588;691	Q96L73-2;Q96L73-3;Q96L73	.;.;NSD1_HUMAN	T	422;422;691;422;588	ENSP00000346111:A422T;ENSP00000395929:A691T;ENSP00000343209:A422T;ENSP00000354310:A588T	.	A	+	1	0	NSD1	176570077	0.188000	0.23250	1.000000	0.80357	0.984000	0.73092	0.269000	0.18589	1.504000	0.48704	0.655000	0.94253	GCC	G|0.983;A|0.017	0.017	strong		0.393	NSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253412.2	NM_172349	
MED12L	116931	hgsc.bcm.edu	37	3	151090424	151090424	+	Missense_Mutation	SNP	G	G	A	rs3732765	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:151090424G>A	ENST00000474524.1	+	25	3667	c.3629G>A	c.(3628-3630)cGa>cAa	p.R1210Q	P2RY12_ENST00000302632.3_Intron|MED12L_ENST00000273432.4_Missense_Mutation_p.R1070Q	NM_053002.4	NP_443728.3	Q86YW9	MD12L_HUMAN	mediator complex subunit 12-like	1210			R -> Q (in dbSNP:rs3732765).			mediator complex (GO:0016592)	RNA polymerase II transcription cofactor activity (GO:0001104)	p.R1210Q(1)		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)			AGAGGTTTGCGATGTGATGGG	0.388													G|||	1018	0.203275	0.0287	0.3055	5008	,	,		18878	0.1389		0.3807	False		,,,				2504	0.2505				p.R1210Q		Atlas-SNP	.											MED12L,NS,carcinoma,0,1	MED12L	271	1	1	Substitution - Missense(1)	stomach(1)	c.G3629A						PASS	.	G	,GLN/ARG	361,4045	185.0+/-212.2	15,331,1857	126.0	117.0	120.0		,3629	4.9	0.5	3	dbSNP_107	120	3235,5365	487.5+/-372.1	582,2071,1647	yes	intron,missense	P2RY12,MED12L	NM_022788.3,NM_053002.4	,43	597,2402,3504	AA,AG,GG		37.6163,8.1934,27.6488	,benign	,1210/2146	151090424	3596,9410	2203	4300	6503	SO:0001583	missense	116931	exon25			GTTTGCGATGTGA	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.3629G>A	3.37:g.151090424G>A	ENSP00000417235:p.Arg1210Gln	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	82	41	0.5	NM_053002	Q96PC7|Q96PC8|Q9H9M5|Q9HCD7|Q9UI69	Missense_Mutation	SNP	ENST00000474524.1	37	CCDS33876.1	494	0.2261904761904762	16	0.032520325203252036	120	0.3314917127071823	73	0.12762237762237763	285	0.3759894459102902	G	10.71	1.425534	0.25639	0.081934	0.376163	ENSG00000144893	ENST00000474524;ENST00000273432	T;T	0.60040	0.44;0.22	5.9	4.95	0.65309	.	0.073163	0.56097	D	0.000028	T	0.00012	0.0000	N	0.19112	0.55	0.21762	P	0.999551663	P;B;B	0.44195	0.828;0.431;0.305	B;B;B	0.42959	0.403;0.028;0.068	T	0.36792	-0.9733	9	0.36615	T	0.2	-22.3073	11.0701	0.47997	0.0:0.0:0.7064:0.2936	rs3732765;rs17282989;rs52828592;rs61340099;rs3732765	1070;1209;1210	F8WAE6;Q86YW9-4;Q86YW9	.;.;MD12L_HUMAN	Q	1210;1070	ENSP00000417235:R1210Q;ENSP00000273432:R1070Q	ENSP00000273432:R1070Q	R	+	2	0	MED12L	152573114	0.956000	0.32656	0.518000	0.27811	0.971000	0.66376	3.813000	0.55636	2.788000	0.95919	0.650000	0.86243	CGA	G|0.766;A|0.234	0.234	strong		0.388	MED12L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357707.2	NM_053002	
NR0B1	190	hgsc.bcm.edu	37	X	30326983	30326983	+	Silent	SNP	C	C	T	rs2269345	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:30326983C>T	ENST00000378970.4	-	1	732	c.498G>A	c.(496-498)cgG>cgA	p.R166R	NR0B1_ENST00000453287.1_Silent_p.R166R|NR0B1_ENST00000378963.1_5'Flank	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	52	0	0	816	WXS	Illumina HiSeq	Phase_I	56	55	0.982143	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	
KRT37	8688	hgsc.bcm.edu	37	17	39580660	39580660	+	Missense_Mutation	SNP	T	T	C	rs9916724	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:39580660T>C	ENST00000225550.3	-	1	115	c.116A>G	c.(115-117)aAt>aGt	p.N39S	AC003958.2_ENST00000432258.1_RNA	NM_003770.4	NP_003761.3	O76014	KRT37_HUMAN	keratin 37	39	Head.		N -> S (in dbSNP:rs9916724).			extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(9)|lung(6)|skin(3)	25		Breast(137;0.000496)				GGAGGCAGCATTGGCCTCTGC	0.622													T|||	1960	0.391374	0.1846	0.3415	5008	,	,		20684	0.4067		0.4592	False		,,,				2504	0.6207				p.N39S		Atlas-SNP	.											.	KRT37	61	.	0			c.A116G						PASS	.	T	SER/ASN	983,3423		111,761,1331	52.0	53.0	53.0		116	2.9	0.0	17	dbSNP_119	53	4170,4430		1019,2132,1149	yes	missense	KRT37	NM_003770.4	46	1130,2893,2480	CC,CT,TT		48.4884,22.3105,39.6202	benign	39/450	39580660	5153,7853	2203	4300	6503	SO:0001583	missense	8688	exon1			GCAGCATTGGCCT	Y16793	CCDS32653.1	17q21.2	2013-06-20	2006-07-17	2006-07-17	ENSG00000108417	ENSG00000108417		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6455	protein-coding gene	gene with protein product		604541	"""keratin, hair, acidic, 7"""	KRTHA7		9756910, 16831889	Standard	NM_003770		Approved		uc002hwp.1	O76014	OTTHUMG00000133606	ENST00000225550.3:c.116A>G	17.37:g.39580660T>C	ENSP00000225550:p.Asn39Ser	Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	117	60	0.512821	NM_003770		Missense_Mutation	SNP	ENST00000225550.3	37	CCDS32653.1	812	0.3717948717948718	101	0.20528455284552846	145	0.4005524861878453	227	0.3968531468531469	339	0.4472295514511873	.	5.186	0.219886	0.09863	0.223105	0.484884	ENSG00000108417	ENST00000225550	T	0.81247	-1.47	2.94	2.94	0.34122	.	0.677290	0.12593	N	0.455396	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.35919	-0.9769	9	0.10377	T	0.69	.	6.4153	0.21714	0.0:0.1301:0.0:0.8699	rs9916724;rs59188249	39	O76014	KRT37_HUMAN	S	39	ENSP00000225550:N39S	ENSP00000225550:N39S	N	-	2	0	KRT37	36834186	0.000000	0.05858	0.002000	0.10522	0.004000	0.04260	-0.252000	0.08806	1.127000	0.42034	0.383000	0.25322	AAT	T|0.619;C|0.381	0.381	strong		0.622	KRT37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257714.2	NM_003770	
ALMS1	7840	hgsc.bcm.edu	37	2	73829372	73829372	+	Silent	SNP	C	C	T	rs1052162	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:73829372C>T	ENST00000264448.6	+	20	12283	c.12172C>T	c.(12172-12174)Ctg>Ttg	p.L4058L	ALMS1_ENST00000409009.1_Silent_p.L4016L|ALMS1_ENST00000464408.2_3'UTR	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	4058	ALMS motif.				endosomal transport (GO:0016197)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of stress fiber assembly (GO:0051492)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)				breast(4)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(31)|lung(68)|ovary(4)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	147						GATAAAGCGCCTGAAGTTAAT	0.493													C|||	1711	0.341653	0.8011	0.3804	5008	,	,		20743	0.0089		0.2276	False		,,,				2504	0.1534				p.L4058L		Atlas-SNP	.											.	ALMS1	384	.	0			c.C12172T						PASS	.	C		3092,1314	677.6+/-403.4	1083,926,194	53.0	58.0	56.0		12172	3.6	1.0	2	dbSNP_86	56	2027,6573	351.2+/-328.2	228,1571,2501	no	coding-synonymous	ALMS1	NM_015120.4		1311,2497,2695	TT,TC,CC		23.5698,29.823,39.3588		4058/4168	73829372	5119,7887	2203	4300	6503	SO:0001819	synonymous_variant	7840	exon20			AAGCGCCTGAAGT	AB002326	CCDS42697.1	2p13.1	2014-09-17			ENSG00000116127	ENSG00000116127			428	protein-coding gene	gene with protein product		606844				9063741	Standard	NM_015120		Approved	KIAA0328	uc002sje.1	Q8TCU4	OTTHUMG00000152812	ENST00000264448.6:c.12172C>T	2.37:g.73829372C>T		Somatic	287	0	0		WXS	Illumina HiSeq	Phase_I	187	184	0.983957	NM_015120	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Silent	SNP	ENST00000264448.6	37	CCDS42697.1																																																																																			C|0.663;T|0.337	0.337	strong		0.493	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120	
SLFN11	91607	hgsc.bcm.edu	37	17	33680811	33680811	+	Missense_Mutation	SNP	C	C	A	rs9898983	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:33680811C>A	ENST00000394566.1	-	6	1738	c.1466G>T	c.(1465-1467)cGc>cTc	p.R489L	SLFN11_ENST00000308377.4_Missense_Mutation_p.R489L	NM_001104587.1|NM_001104588.1|NM_001104589.1|NM_001104590.1	NP_001098057.1|NP_001098058.1|NP_001098059.1|NP_001098060.1	Q7Z7L1	SLN11_HUMAN	schlafen family member 11	489			R -> L (in dbSNP:rs9898983).		defense response to virus (GO:0051607)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|tRNA binding (GO:0000049)	p.R489L(2)		autonomic_ganglia(1)|breast(1)|kidney(3)|large_intestine(14)|lung(17)|ovary(1)|prostate(4)|skin(2)|stomach(5)|upper_aerodigestive_tract(2)	50		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		AAAGGCGGTGCGAGTGCAGTA	0.562													C|||	1707	0.340855	0.4266	0.3415	5008	,	,		9159	0.4464		0.159	False		,,,				2504	0.3027				p.R489L		Atlas-SNP	.											SLFN11,NS,carcinoma,0,2	SLFN11	112	2	2	Substitution - Missense(2)	stomach(2)	c.G1466T						scavenged	.						16.0	14.0	15.0					17																	33680811		2181	4250	6431	SO:0001583	missense	91607	exon4			GCGGTGCGAGTGC	AK074184	CCDS11294.1	17q12	2006-04-05			ENSG00000172716	ENSG00000172716			26633	protein-coding gene	gene with protein product		614953				12477932	Standard	NM_001104587		Approved	FLJ34922	uc010ctr.3	Q7Z7L1	OTTHUMG00000132948	ENST00000394566.1:c.1466G>T	17.37:g.33680811C>A	ENSP00000378067:p.Arg489Leu	Somatic	149	1	0.00671141		WXS	Illumina HiSeq	Phase_I	122	42	0.344262	NM_152270	E1P643|Q8N3S8|Q8N762|Q8TEE0	Missense_Mutation	SNP	ENST00000394566.1	37	CCDS11294.1	709	0.32463369963369965	229	0.4654471544715447	113	0.31215469613259667	239	0.4178321678321678	128	0.16886543535620052	c	1.872	-0.460031	0.04508	.	.	ENSG00000172716	ENST00000308377;ENST00000394566	T;T	0.02032	4.49;4.49	3.69	-7.38	0.01407	.	1.539480	0.03869	N	0.275369	T	0.00012	0.0000	L	0.48362	1.52	0.80722	P	0.0	B	0.17667	0.023	B	0.13407	0.009	T	0.47114	-0.9142	9	0.10636	T	0.68	.	4.2916	0.10881	0.1177:0.1683:0.1165:0.5975	rs9898983	489	Q7Z7L1	SLN11_HUMAN	L	489	ENSP00000312402:R489L;ENSP00000378067:R489L	ENSP00000312402:R489L	R	-	2	0	SLFN11	30704924	0.000000	0.05858	0.000000	0.03702	0.039000	0.13416	-6.906000	0.00050	-1.990000	0.00978	-0.903000	0.02851	CGC	C|0.694;A|0.306	0.306	strong		0.562	SLFN11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256480.1	NM_152270	
DAAM2	23500	hgsc.bcm.edu	37	6	39864730	39864730	+	Silent	SNP	C	C	T	rs3008815	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:39864730C>T	ENST00000398904.2	+	20	2666	c.2484C>T	c.(2482-2484)atC>atT	p.I828I	RP11-61I13.3_ENST00000430595.1_RNA|DAAM2_ENST00000538976.1_Silent_p.I828I|RP11-61I13.3_ENST00000437947.1_RNA|RP11-61I13.3_ENST00000606829.1_RNA|RP11-61I13.3_ENST00000420293.1_RNA|DAAM2_ENST00000274867.4_Silent_p.I828I			Q86T65	DAAM2_HUMAN	dishevelled associated activator of morphogenesis 2	828	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)					TCAACAAGATCGCTGACACCA	0.582													C|||	2316	0.46246	0.4213	0.4827	5008	,	,		18846	0.3244		0.5288	False		,,,				2504	0.5777				p.I828I		Atlas-SNP	.											.	DAAM2	101	.	0			c.C2484T						PASS	.	C	,	1622,2474		325,972,751	41.0	47.0	45.0		2484,2484	-3.2	0.9	6	dbSNP_101	45	4336,4036		1166,2004,1016	no	coding-synonymous,coding-synonymous	DAAM2	NM_001201427.1,NM_015345.3	,	1491,2976,1767	TT,TC,CC		48.2083,39.5996,47.7863	,	828/1069,828/1068	39864730	5958,6510	2048	4186	6234	SO:0001819	synonymous_variant	23500	exon20			CAAGATCGCTGAC	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.2484C>T	6.37:g.39864730C>T		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	49	29	0.591837	NM_015345	G5EA45|Q5T4T8|Q5T4U0|Q9NQI5|Q9Y4G0	Silent	SNP	ENST00000398904.2	37	CCDS56426.1																																																																																			C|0.551;T|0.449	0.449	strong		0.582	DAAM2-003	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000280648.1		
LPL	4023	hgsc.bcm.edu	37	8	19818436	19818436	+	Silent	SNP	C	C	A	rs316	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:19818436C>A	ENST00000311322.8	+	8	1634	c.1164C>A	c.(1162-1164)acC>acA	p.T388T		NM_000237.2	NP_000228.1	P06858	LIPL_HUMAN	lipoprotein lipase	388	Heparin-binding. {ECO:0000250}.|PLAT. {ECO:0000255|PROSITE- ProRule:PRU00152}.				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)	CAAATAAGACCTACTCCTTCC	0.403													A|||	764	0.152556	0.2368	0.1455	5008	,	,		14705	0.1121		0.1203	False		,,,				2504	0.1186				p.T388T		Atlas-SNP	.											.	LPL	78	.	0			c.C1164A						PASS	.	A		1008,3398	728.4+/-409.9	116,776,1311	104.0	103.0	104.0		1164	-11.3	0.4	8	dbSNP_36	104	1055,7545	770.4+/-407.7	56,943,3301	no	coding-synonymous	LPL	NM_000237.2		172,1719,4612	AA,AC,CC		12.2674,22.8779,15.8619		388/476	19818436	2063,10943	2203	4300	6503	SO:0001819	synonymous_variant	4023	exon8			TAAGACCTACTCC		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.1164C>A	8.37:g.19818436C>A		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	63	11	0.174603	NM_000237	B2R5T9|Q16282|Q16283|Q96FC4	Silent	SNP	ENST00000311322.8	37	CCDS6012.1																																																																																			C|0.846;A|0.154	0.154	strong		0.403	LPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089113.3		
TRAPPC10	7109	hgsc.bcm.edu	37	21	45503121	45503121	+	Missense_Mutation	SNP	G	G	A	rs2071152	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:45503121G>A	ENST00000291574.4	+	14	2351	c.2176G>A	c.(2176-2178)Gtg>Atg	p.V726M		NM_003274.4	NP_003265.3	P48553	TPC10_HUMAN	trafficking protein particle complex 10	726			V -> M (common polymorphism; dbSNP:rs2071152). {ECO:0000269|PubMed:9370297}.		sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|vesicle-mediated transport (GO:0016192)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	sodium ion transmembrane transporter activity (GO:0015081)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(8)|ovary(1)|prostate(2)|skin(2)|urinary_tract(4)	41						GGGTGCCCACGTGCTGAGGTG	0.562													G|||	1974	0.394169	0.6664	0.3012	5008	,	,		19366	0.2976		0.1541	False		,,,				2504	0.4387				p.V726M		Atlas-SNP	.											.	TRAPPC10	109	.	0			c.G2176A						PASS	.	G	MET/VAL	2696,1710	643.0+/-397.8	836,1024,343	102.0	99.0	100.0		2176	-1.1	0.0	21	dbSNP_96	100	1395,7205	264.6+/-285.7	140,1115,3045	yes	missense	TRAPPC10	NM_003274.4	21	976,2139,3388	AA,AG,GG		16.2209,38.8107,31.4547	benign	726/1260	45503121	4091,8915	2203	4300	6503	SO:0001583	missense	7109	exon14			GCCCACGTGCTGA	U19252	CCDS13704.1	21q22.3	2008-05-07	2008-05-07	2008-05-07	ENSG00000160218	ENSG00000160218		"""Trafficking protein particle complex"""	11868	protein-coding gene	gene with protein product	"""trafficking protein particle complex subunit 130"", ""TRAPP 130 kDa subunit"""	602103	"""transmembrane protein 1"""	TMEM1		7633421	Standard	NM_003274		Approved	EHOC-1, TRS130	uc002zea.3	P48553	OTTHUMG00000086894	ENST00000291574.4:c.2176G>A	21.37:g.45503121G>A	ENSP00000291574:p.Val726Met	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	60	60	1	NM_003274	Q3MIR2|Q86SI7|Q9UMD4|Q9Y4L3	Missense_Mutation	SNP	ENST00000291574.4	37	CCDS13704.1	696	0.31868131868131866	313	0.6361788617886179	95	0.26243093922651933	169	0.29545454545454547	119	0.15699208443271767	G	4.979	0.181776	0.09495	0.611893	0.162209	ENSG00000160218	ENST00000291574	T	0.23348	1.91	5.73	-1.09	0.09904	.	0.504277	0.23874	N	0.043713	T	0.00012	0.0000	N	0.11560	0.145	0.45634	P	0.00143099999999996	B;B	0.17852	0.024;0.011	B;B	0.13407	0.009;0.003	T	0.35126	-0.9801	9	0.39692	T	0.17	.	6.6404	0.22906	0.3741:0.2141:0.4119:0.0	rs2071152;rs58410301;rs2071152	26;726	B4DI17;P48553	.;TPC10_HUMAN	M	726	ENSP00000291574:V726M	ENSP00000291574:V726M	V	+	1	0	TRAPPC10	44327549	0.951000	0.32395	0.013000	0.15412	0.003000	0.03518	1.941000	0.40233	-0.108000	0.12066	-0.773000	0.03387	GTG	G|0.661;A|0.339	0.339	strong		0.562	TRAPPC10-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000195737.1	NM_003274	
MRPS30	10884	hgsc.bcm.edu	37	5	44809162	44809162	+	Missense_Mutation	SNP	G	G	C	rs3747479	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:44809162G>C	ENST00000507110.1	+	1	136	c.98G>C	c.(97-99)tGc>tCc	p.C33S	RP11-53O19.1_ENST00000505401.1_RNA|RP11-53O19.1_ENST00000505637.1_RNA|RP11-53O19.1_ENST00000508945.1_RNA|RP11-53O19.1_ENST00000505302.1_RNA|RP11-53O19.1_ENST00000503452.1_RNA|RP11-53O19.1_ENST00000503179.1_RNA|RP11-53O19.1_ENST00000514597.1_RNA|RP11-53O19.1_ENST00000508123.1_RNA	NM_016640.3	NP_057724.2	Q9NP92	RT30_HUMAN	mitochondrial ribosomal protein S30	33			C -> S (in dbSNP:rs3747479). {ECO:0000269|PubMed:10640817, ECO:0000269|PubMed:11230166, ECO:0000269|Ref.2}.		apoptotic process (GO:0006915)|translation (GO:0006412)	mitochondrion (GO:0005739)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			central_nervous_system(1)|cervix(1)|endometrium(4)|large_intestine(2)|lung(11)|prostate(1)	20	Lung NSC(6;8.08e-07)					GAAACGACCTGCCAAGACGTC	0.672													G|||	1996	0.398562	0.2466	0.4553	5008	,	,		12993	0.5357		0.3738	False		,,,				2504	0.4479				p.C33S		Atlas-SNP	.											MRPS30_ENST00000507110,NS,carcinoma,0,4	MRPS30	90	4	0			c.G98C						scavenged	.	G	SER/CYS	1150,3158		202,746,1206	10.0	12.0	11.0		98	-0.5	0.0	5	dbSNP_107	11	3110,5358		629,1852,1753	yes	missense	MRPS30	NM_016640.3	112	831,2598,2959	CC,CG,GG		36.7265,26.6945,33.3438	benign	33/440	44809162	4260,8516	2154	4234	6388	SO:0001583	missense	10884	exon1			CGACCTGCCAAGA	AF146192	CCDS3951.1	5q11	2012-09-13		2001-11-09	ENSG00000112996	ENSG00000112996		"""Mitochondrial ribosomal proteins / small subunits"""	8769	protein-coding gene	gene with protein product		611991		PDCD9		10640817, 11279123	Standard	NM_016640		Approved	PAP	uc003joh.3	Q9NP92	OTTHUMG00000096967	ENST00000507110.1:c.98G>C	5.37:g.44809162G>C	ENSP00000424328:p.Cys33Ser	Somatic	82	3	0.0365854		WXS	Illumina HiSeq	Phase_I	75	40	0.533333	NM_016640	Q96I91|Q96Q19|Q9H0P8|Q9NSF9|Q9NZ76	Missense_Mutation	SNP	ENST00000507110.1	37	CCDS3951.1	887	0.40613553113553114	139	0.28252032520325204	157	0.43370165745856354	306	0.534965034965035	285	0.3759894459102902	G	5.819	0.335379	0.11013	0.266945	0.367265	ENSG00000112996	ENST00000507110	T	0.16324	2.35	5.14	-0.478	0.12093	.	2.286390	0.01507	N	0.017754	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.06405	0.002	T	0.45891	-0.9230	9	0.13853	T	0.58	2.2095	4.9665	0.14093	0.0754:0.3817:0.3416:0.2013	rs3747479	33	Q9NP92	RT30_HUMAN	S	33	ENSP00000424328:C33S	ENSP00000424328:C33S	C	+	2	0	MRPS30	44844919	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	0.300000	0.19156	0.066000	0.16515	0.655000	0.94253	TGC	A|0.000;C|0.396;G|0.604	0.396	strong		0.672	MRPS30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214033.2	NM_016640	
KIF17	57576	hgsc.bcm.edu	37	1	21044161	21044161	+	Silent	SNP	A	A	G	rs601329	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:21044161A>G	ENST00000247986.2	-	1	349	c.39T>C	c.(37-39)cgT>cgC	p.R13R	SH2D5_ENST00000460804.1_5'Flank|KIF17_ENST00000400463.3_Silent_p.R13R|KIF17_ENST00000375044.1_5'Flank			Q9P2E2	KIF17_HUMAN	kinesin family member 17	13	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|cell projection organization (GO:0030030)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|neurogenesis (GO:0022008)|protein complex localization (GO:0031503)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|intraciliary transport particle B (GO:0030992)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|plus-end-directed microtubule motor activity (GO:0008574)			NS(2)|endometrium(3)|kidney(3)|large_intestine(9)|liver(1)|lung(23)|ovary(4)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	50		all_lung(284;2.99e-05)|Lung NSC(340;3.26e-05)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00179)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|COAD - Colon adenocarcinoma(152;1.43e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000168)|Kidney(64;0.000221)|GBM - Glioblastoma multiforme(114;0.000651)|KIRC - Kidney renal clear cell carcinoma(64;0.0031)|STAD - Stomach adenocarcinoma(196;0.00336)|READ - Rectum adenocarcinoma(331;0.0686)|Lung(427;0.209)		GGTTCATGGGACGGCAGCGCA	0.736													G|||	3566	0.712061	0.6006	0.621	5008	,	,		7917	0.8879		0.7167	False		,,,				2504	0.7413				p.R13R		Atlas-SNP	.											.	KIF17	130	.	0			c.T39C						PASS	.	G	,	2733,1611		903,927,342	10.0	11.0	11.0		39,39	-5.0	0.9	1	dbSNP_83	11	5867,2633		2078,1711,461	no	coding-synonymous,coding-synonymous	KIF17	NM_001122819.1,NM_020816.2	,	2981,2638,803	GG,GA,AA		30.9765,37.0856,33.0427	,	13/1029,13/1030	21044161	8600,4244	2172	4250	6422	SO:0001819	synonymous_variant	57576	exon1			CATGGGACGGCAG	AB037826	CCDS213.1, CCDS44079.1, CCDS72722.1	1p36.13	2012-08-01			ENSG00000117245	ENSG00000117245		"""Kinesins"""	19167	protein-coding gene	gene with protein product	"""kinesin-like protein KIF17"", ""KIF3-related motor protein"", ""KIF17 variant protein"""	605037				10846156	Standard	XR_241202		Approved	KIAA1405, KIF3X, KIF17B, OSM-3, KLP-2	uc001bdr.4	Q9P2E2	OTTHUMG00000002863	ENST00000247986.2:c.39T>C	1.37:g.21044161A>G		Somatic	13	0	0		WXS	Illumina HiSeq	Phase_I	11	11	1	NM_001122819	A2A3Q7|A2A3Q8|O95077|Q53YS6|Q5VWA9|Q6GSA8|Q8N411	Silent	SNP	ENST00000247986.2	37	CCDS213.1																																																																																			A|0.268;G|0.732	0.732	strong		0.736	KIF17-009	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276995.1	NM_020816	
FERMT3	83706	hgsc.bcm.edu	37	11	63979162	63979162	+	Silent	SNP	C	C	T	rs17851033	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:63979162C>T	ENST00000279227.5	+	6	824	c.729C>T	c.(727-729)gcC>gcT	p.A243A	FERMT3_ENST00000345728.5_Silent_p.A243A	NM_178443.2	NP_848537.1	Q86UX7	URP2_HUMAN	fermitin family member 3	243	FERM.				integrin activation (GO:0033622)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|platelet aggregation (GO:0070527)|regulation of cell-cell adhesion mediated by integrin (GO:0033632)|substrate adhesion-dependent cell spreading (GO:0034446)	cell junction (GO:0030054)|cell projection (GO:0042995)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|podosome (GO:0002102)	integrin binding (GO:0005178)			breast(1)|cervix(1)|endometrium(4)|large_intestine(2)|lung(6)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	18						GCATCAAGGCCGGGGACGCAC	0.647													C|||	364	0.0726837	0.0189	0.1297	5008	,	,		12585	0.0466		0.0636	False		,,,				2504	0.1411				p.A243A		Atlas-SNP	.											.	FERMT3	51	.	0			c.C729T						PASS	.	C	,	135,4267	97.1+/-135.8	1,133,2067	102.0	96.0	98.0		729,729	-6.7	0.7	11	dbSNP_123	98	593,8001	157.5+/-211.1	22,549,3726	no	coding-synonymous,coding-synonymous	FERMT3	NM_031471.5,NM_178443.2	,	23,682,5793	TT,TC,CC		6.9002,3.0668,5.6017	,	243/664,243/668	63979162	728,12268	2201	4297	6498	SO:0001819	synonymous_variant	83706	exon6			CAAGGCCGGGGAC	L25343	CCDS8059.1, CCDS8060.1	11q13.1	2014-09-17	2010-06-24		ENSG00000149781	ENSG00000149781		"""Fermitins"", ""Pleckstrin homology (PH) domain containing"""	23151	protein-coding gene	gene with protein product	"""kindlin-3"""	607901	"""fermitin family homolog 3 (Drosophila)"""				Standard	NM_178443		Approved	URP2, KIND3, MIG2B, MGC10966, MIG-2, UNC112C	uc001nym.2	Q86UX7	OTTHUMG00000167790	ENST00000279227.5:c.729C>T	11.37:g.63979162C>T		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	90	65	0.722222	NM_031471	Q8IUA1|Q8N207|Q9BT48	Silent	SNP	ENST00000279227.5	37	CCDS8060.1																																																																																			C|0.944;T|0.056	0.056	strong		0.647	FERMT3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000396297.1	NM_031471	
C4A	720	hgsc.bcm.edu	37	6	31963559	31963559	+	Missense_Mutation	SNP	A	A	G	rs147162052		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:31963559A>G	ENST00000428956.2	+	25	3302	c.3218A>G	c.(3217-3219)gAc>gGc	p.D1073G	C4A_ENST00000498271.1_Missense_Mutation_p.D1073G	NM_007293.2	NP_009224.2	P0C0L4	CO4A_HUMAN	complement component 4A (Rodgers blood group)	1073			D -> G (in allotype C4A1, allotype C4A2; dbSNP:rs147162052). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:3696167, ECO:0000269|Ref.8}.		complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|positive regulation of apoptotic cell clearance (GO:2000427)|regulation of complement activation (GO:0030449)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	complement component C1q binding (GO:0001849)|endopeptidase inhibitor activity (GO:0004866)									Intravenous Immunoglobulin(DB00028)	TTGTCACGGGACAGCAGCACC	0.612																																					p.G1073G		Atlas-SNP	.											C4B,right_upper_lobe,carcinoma,0,2	C4A	15	2	0			c.G3218G						scavenged	.						101.0	86.0	91.0					6																	31963559		1499	2656	4155	SO:0001583	missense	720	exon25			CACGGGACAGCAG	L26261, M14823, X77491, AY224378	CCDS47404.1, CCDS59005.1	6p21.3	2014-09-17	2006-01-19		ENSG00000244731	ENSG00000244731		"""Blood group antigens"", ""Complement system"""	1323	protein-coding gene	gene with protein product		120810	"""complement component 4A"""				Standard	NM_001252204		Approved	CPAMD2, C4S, CO4, C4, C4A3, C4A2, C4A4, C4A6, C4B, RG		P0C0L4	OTTHUMG00000031186	ENST00000428956.2:c.3218A>G	6.37:g.31963559A>G	ENSP00000396688:p.Asp1073Gly	Somatic	1276	19	0.0148903		WXS	Illumina HiSeq	Phase_I	230	10	0.0434783	NM_007293	A6H8M8|A6NHJ5|A7E2V2|B0QZR6|B0V2C8|B2RUT6|B7ZVZ6|P01028|P78445|Q13160|Q13906|Q14033|Q14835|Q4LE82|Q5JNX2|Q5JQM8|Q6P4R1|Q6U2E5|Q6U2E8|Q6U2F0|Q6U2F3|Q6U2F4|Q6U2F6|Q6U2F8|Q6U2G0|Q96EG2|Q96SA8|Q9NPK5|Q9UIP5	Silent	SNP	ENST00000428956.2	37	CCDS47404.1	.	.	.	.	.	.	.	.	.	.	A	1.712	-0.498842	0.04291	.	.	ENSG00000244731	ENST00000428956;ENST00000498271	T;T	0.37915	1.17;1.17	3.11	1.88	0.25563	Terpenoid cylases/protein prenyltransferase alpha-alpha toroid (1);A-macroglobulin complement component (1);	.	.	.	.	T	0.16642	0.0400	M	0.64170	1.965	0.80722	D	1	B;B	0.19200	0.015;0.034	B;B	0.23150	0.026;0.044	T	0.04885	-1.0920	9	0.46703	T	0.11	.	5.4739	0.16686	0.8606:0.0:0.1394:0.0	.	1073;1073	A6H8M8;P0C0L4	.;CO4A_HUMAN	G	1073	ENSP00000396688:D1073G;ENSP00000420212:D1073G	ENSP00000396688:D1073G	D	+	2	0	C4A	32071538	0.168000	0.22989	0.910000	0.35882	0.043000	0.13939	0.471000	0.22100	0.399000	0.25367	-1.226000	0.01582	GAC	A|0.500;G|0.500	0.500	strong		0.612	C4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076364.3	NM_007293	
MAG	4099	hgsc.bcm.edu	37	19	35793589	35793589	+	Silent	SNP	C	C	T	rs1126770	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:35793589C>T	ENST00000392213.3	+	7	1368	c.1209C>T	c.(1207-1209)acC>acT	p.T403T	MAG_ENST00000537831.2_Silent_p.T378T|MAG_ENST00000361922.4_Silent_p.T403T	NM_002361.3	NP_002352.1	P20916	MAG_HUMAN	myelin associated glycoprotein	403	Ig-like C2-type 3.				blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|leukocyte migration (GO:0050900)|negative regulation of axonogenesis (GO:0050771)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of axonogenesis (GO:0050770)|substantia nigra development (GO:0021762)	integral component of membrane (GO:0016021)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|Schmidt-Lanterman incisure (GO:0043220)	carbohydrate binding (GO:0030246)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(3)|large_intestine(10)|lung(11)|skin(2)|upper_aerodigestive_tract(2)	34	all_lung(56;2.37e-08)|Lung NSC(56;3.66e-08)|Esophageal squamous(110;0.162)	Renal(1328;0.242)	Epithelial(14;3.14e-19)|OV - Ovarian serous cystadenocarcinoma(14;1.5e-18)|all cancers(14;1.5e-16)|LUSC - Lung squamous cell carcinoma(66;0.0417)			AGAGGGCCACCGCCTTCAACC	0.622													C|||	1183	0.236222	0.174	0.3271	5008	,	,		16814	0.1677		0.3191	False		,,,				2504	0.2413				p.T403T		Atlas-SNP	.											.	MAG	172	.	0			c.C1209T						PASS	.	C	,,	882,3524	342.3+/-307.1	78,726,1399	92.0	75.0	81.0		1134,1209,1209	-10.5	0.3	19	dbSNP_86	81	2794,5806	443.1+/-360.3	458,1878,1964	no	coding-synonymous,coding-synonymous,coding-synonymous	MAG	NM_001199216.1,NM_002361.3,NM_080600.2	,,	536,2604,3363	TT,TC,CC		32.4884,20.0182,28.2639	,,	378/602,403/627,403/583	35793589	3676,9330	2203	4300	6503	SO:0001819	synonymous_variant	4099	exon7			GGCCACCGCCTTC	M29273	CCDS12455.1, CCDS12456.1, CCDS56090.1	19q13.1	2013-01-29			ENSG00000105695	ENSG00000105695		"""Sialic acid binding Ig-like lectins"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6783	protein-coding gene	gene with protein product	"""sialic acid binding Ig-like lectin 4A"""	159460		GMA		2476987, 8432525	Standard	NM_080600		Approved	SIGLEC4A, SIGLEC-4A, S-MAG	uc002nyy.2	P20916		ENST00000392213.3:c.1209C>T	19.37:g.35793589C>T		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	58	28	0.482759	NM_080600	B7Z2E5|F5GYC0|Q567S4	Silent	SNP	ENST00000392213.3	37	CCDS12455.1																																																																																			C|0.728;T|0.272	0.272	strong		0.622	MAG-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000466071.1	NM_080600	
SPTBN4	57731	hgsc.bcm.edu	37	19	41038574	41038574	+	Missense_Mutation	SNP	G	G	A	rs814501	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:41038574G>A	ENST00000352632.3	+	19	4077	c.3991G>A	c.(3991-3993)Ggc>Agc	p.G1331S	SPTBN4_ENST00000338932.3_Missense_Mutation_p.G1331S|SPTBN4_ENST00000392025.1_Missense_Mutation_p.G74S|SPTBN4_ENST00000392023.1_Missense_Mutation_p.G7S|SPTBN4_ENST00000595535.1_Missense_Mutation_p.G1331S|SPTBN4_ENST00000598249.1_Missense_Mutation_p.G1331S			Q9H254	SPTN4_HUMAN	spectrin, beta, non-erythrocytic 4	1331			G -> S (in dbSNP:rs814501). {ECO:0000269|PubMed:11294830}.		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)			GGCGCGGGATGGCACGCGGGA	0.607													G|||	1616	0.322684	0.441	0.2867	5008	,	,		18358	0.0595		0.4722	False		,,,				2504	0.3057				p.G1331S		Atlas-SNP	.											.	SPTBN4	213	.	0			c.G3991A						PASS	.	G	SER/GLY,SER/GLY	1933,2473	550.2+/-378.0	414,1105,684	76.0	64.0	68.0		3991,19	2.6	1.0	19	dbSNP_86	68	4448,4152	589.0+/-392.4	1121,2206,973	yes	missense,missense	SPTBN4	NM_020971.2,NM_025213.2	56,56	1535,3311,1657	AA,AG,GG		48.2791,43.872,49.062	benign,benign	1331/2565,7/679	41038574	6381,6625	2203	4300	6503	SO:0001583	missense	57731	exon19			CGGGATGGCACGC	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.3991G>A	19.37:g.41038574G>A	ENSP00000263373:p.Gly1331Ser	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	80	38	0.475	NM_020971	E9PGQ5|Q9H1K7|Q9H1K8|Q9H1K9|Q9H253|Q9H3G8|Q9HCD0	Missense_Mutation	SNP	ENST00000352632.3	37	CCDS12559.1	757	0.3466117216117216	242	0.491869918699187	119	0.3287292817679558	34	0.05944055944055944	362	0.47757255936675463	G	9.364	1.068837	0.20147	0.43872	0.517209	ENSG00000160460	ENST00000428507;ENST00000352632;ENST00000338932;ENST00000392025;ENST00000392023	T;T;T;T	0.58358	0.78;0.78;0.78;0.34	4.86	2.62	0.31277	.	0.275219	0.29152	N	0.012981	T	0.00012	0.0000	N	0.12569	0.235	0.34208	P	0.32599599999999995	B;B;P;B;P;B	0.48089	0.057;0.041;0.659;0.004;0.905;0.033	B;B;B;B;B;B	0.43331	0.032;0.016;0.228;0.008;0.416;0.104	T	0.44574	-0.9319	9	0.31617	T	0.26	.	7.6838	0.28528	0.2814:0.0:0.7185:0.0	rs814501;rs52802515;rs814501	1331;74;74;7;1331;1331	E9PDB1;Q9H254-3;C9JY79;E9PGQ5;Q9H254;Q71S06	.;.;.;.;SPTN4_HUMAN;.	S	1331;1331;1331;74;7	ENSP00000263373:G1331S;ENSP00000340345:G1331S;ENSP00000375879:G74S;ENSP00000375877:G7S	ENSP00000340345:G1331S	G	+	1	0	SPTBN4	45730414	0.983000	0.35010	0.986000	0.45419	0.993000	0.82548	1.662000	0.37418	1.252000	0.44001	0.561000	0.74099	GGC	G|0.572;A|0.428	0.428	strong		0.607	SPTBN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462559.2		
LCE3D	84648	hgsc.bcm.edu	37	1	152552285	152552285	+	Missense_Mutation	SNP	C	C	A	rs512208	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:152552285C>A	ENST00000368787.3	-	2	184	c.128G>T	c.(127-129)gGc>gTc	p.G43V		NM_032563.1	NP_115952.1	Q9BYE3	LCE3D_HUMAN	late cornified envelope 3D	43			G -> V (in dbSNP:rs512208). {ECO:0000269|PubMed:15489334}.		keratinization (GO:0031424)			p.G43V(1)		breast(1)|endometrium(1)|large_intestine(2)|lung(7)|pancreas(1)|skin(1)|stomach(2)	15	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)	UCEC - Uterine corpus endometrioid carcinoma (5;0.153)|KIRC - Kidney renal clear cell carcinoma(4;0.0323)|Kidney(5;0.0378)		AGGGCCACAGCCCCCAGAGCT	0.662													C|||	1386	0.276757	0.1384	0.2853	5008	,	,		15854	0.3264		0.3827	False		,,,				2504	0.2975				p.G43V		Atlas-SNP	.											LCE3D,NS,carcinoma,0,1	LCE3D	28	1	1	Substitution - Missense(1)	stomach(1)	c.G128T						scavenged	.	C	VAL/GLY	789,3617	316.1+/-294.4	78,633,1492	57.0	66.0	63.0		128	0.3	0.6	1	dbSNP_83	63	3138,5454	473.4+/-368.6	598,1942,1756	no	missense	LCE3D	NM_032563.1	109	676,2575,3248	AA,AC,CC		36.5223,17.9074,30.2123	benign	43/93	152552285	3927,9071	2203	4296	6499	SO:0001583	missense	84648	exon2			CCACAGCCCCCAG	BI670519	CCDS1014.1	1q21	2008-02-05	2004-05-21	2004-10-15	ENSG00000163202	ENSG00000163202		"""Late cornified envelopes"""	16615	protein-coding gene	gene with protein product		612616	"""small proline rich-like (epidermal differentiation complex) 6B"""	SPRL6B, SPRL6A		11698679	Standard	NM_032563		Approved	LEP16	uc001fab.3	Q9BYE3	OTTHUMG00000012384	ENST00000368787.3:c.128G>T	1.37:g.152552285C>A	ENSP00000357776:p.Gly43Val	Somatic	154	1	0.00649351		WXS	Illumina HiSeq	Phase_I	140	63	0.45	NM_032563	Q3MIL1	Missense_Mutation	SNP	ENST00000368787.3	37	CCDS1014.1	655	0.2999084249084249	68	0.13821138211382114	103	0.2845303867403315	188	0.32867132867132864	296	0.39050131926121373	C	0.190	-1.053864	0.01965	0.179074	0.365223	ENSG00000163202	ENST00000368787	T	0.03982	3.74	3.63	0.259	0.15583	.	.	.	.	.	T	0.01222	0.0040	.	.	.	0.48135	P	4.089999999999927E-4	B	0.34181	0.44	B	0.33750	0.169	T	0.50294	-0.8845	7	0.34782	T	0.22	.	6.4364	0.21825	0.1979:0.4157:0.3864:0.0	rs512208	43	Q9BYE3	LCE3D_HUMAN	V	43	ENSP00000357776:G43V	ENSP00000357776:G43V	G	-	2	0	LCE3D	150818909	0.111000	0.22076	0.642000	0.29436	0.005000	0.04900	0.010000	0.13242	0.318000	0.23185	-0.929000	0.02709	GGC	C|0.986;A|0.014	0.014	weak		0.662	LCE3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034504.1	NM_032563	
MAML3	55534	hgsc.bcm.edu	37	4	140640703	140640703	+	Missense_Mutation	SNP	G	G	T	rs61747885	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:140640703G>T	ENST00000509479.2	-	5	4047	c.3191C>A	c.(3190-3192)cCc>cAc	p.P1064H	MGST2_ENST00000515137.1_Intron	NM_018717.4	NP_061187			mastermind-like 3 (Drosophila)											breast(1)|endometrium(7)|kidney(2)|large_intestine(1)|lung(9)|ovary(1)|prostate(2)|urinary_tract(2)	25	all_hematologic(180;0.162)					CTGTGCTGGGGGCTGGCTGAA	0.617													G|||	548	0.109425	0.0378	0.0922	5008	,	,		19107	0.1567		0.1412	False		,,,				2504	0.137				p.P1060H		Atlas-SNP	.											.	MAML3	192	.	0			c.C3179A						PASS	.	G	,,HIS/PRO	233,4165	118.0+/-155.7	5,223,1971	32.0	36.0	35.0		,,3191	4.8	1.0	4	dbSNP_129	35	1342,7250	253.9+/-279.4	104,1134,3058	yes	intron,intron,missense	MGST2,MAML3	NM_001204366.1,NM_001204367.1,NM_018717.4	,,77	109,1357,5029	TT,TG,GG		15.6192,5.2979,12.1247	,,possibly-damaging	,,1064/1139	140640703	1575,11415	2199	4296	6495	SO:0001583	missense	55534	exon6			GCTGGGGGCTGGC	AB058719	CCDS54805.1	4q31.1	2014-08-12	2003-09-24		ENSG00000196782	ENSG00000196782			16272	protein-coding gene	gene with protein product	"""mastermind (drosophila)-like 3"""	608991	"""trinucleotide repeat containing 3"""	TNRC3		12370315, 12386158	Standard	NM_018717		Approved	KIAA1816, MAM2, CAGH3, GDN	uc021xsg.1	Q96JK9	OTTHUMG00000161441	ENST00000509479.2:c.3191C>A	4.37:g.140640703G>T	ENSP00000421180:p.Pro1064His	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	65	31	0.476923	NM_018717		Missense_Mutation	SNP	ENST00000509479.2	37	CCDS54805.1	260	0.11904761904761904	20	0.04065040650406504	47	0.1298342541436464	81	0.14160839160839161	112	0.14775725593667546	G	13.86	2.363105	0.41902	0.052979	0.156192	ENSG00000196782	ENST00000509479;ENST00000538400	T	0.24350	1.86	4.78	4.78	0.61160	.	0.642458	0.15615	N	0.253161	T	0.00144	0.0004	M	0.70595	2.14	0.09310	P	1.0	P;P	0.45348	0.856;0.856	B;B	0.40101	0.319;0.319	T	0.11743	-1.0575	9	0.44086	T	0.13	.	18.1787	0.89769	0.0:0.0:1.0:0.0	rs61747885	1064;1060	E7EVW8;Q96JK9	.;MAML3_HUMAN	H	1064;371	ENSP00000421180:P1064H	ENSP00000421180:P1064H	P	-	2	0	MAML3	140860153	1.000000	0.71417	0.995000	0.50966	0.948000	0.59901	5.774000	0.68906	2.342000	0.79632	0.591000	0.81541	CCC	G|0.877;T|0.123	0.123	strong		0.617	MAML3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364934.2		
HIST1H1C	3006	hgsc.bcm.edu	37	6	26056277	26056277	+	Missense_Mutation	SNP	T	T	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:26056277T>G	ENST00000343677.2	-	1	422	c.380A>C	c.(379-381)aAa>aCa	p.K127T		NM_005319.3	NP_005310.1	P16403	H12_HUMAN	histone cluster 1, H1c	127					nucleosome assembly (GO:0006334)|nucleosome positioning (GO:0016584)	nuclear euchromatin (GO:0005719)|nucleosome (GO:0000786)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(6)|kidney(1)|large_intestine(1)|lung(8)|ovary(4)|prostate(3)|skin(3)|upper_aerodigestive_tract(3)	34						CTTCTTAGGTTTGGTTCCGCC	0.557																																					p.K127T		Atlas-SNP	.											.	HIST1H1C	80	.	0			c.A380C						PASS	.						57.0	68.0	65.0					6																	26056277		2202	4299	6501	SO:0001583	missense	3006	exon1			TTAGGTTTGGTTC	X57129	CCDS4577.1	6p21.3	2012-10-02	2006-10-11	2003-02-21	ENSG00000187837	ENSG00000187837		"""Histones / Replication-dependent"""	4716	protein-coding gene	gene with protein product		142710	"""H1 histone family, member 2"", ""histone 1, H1c"""	H1F2		2759094, 12408966	Standard	NM_005319		Approved	H1.2, H1s-1, H1c	uc003nfw.3	P16403	OTTHUMG00000016140	ENST00000343677.2:c.380A>C	6.37:g.26056277T>G	ENSP00000339566:p.Lys127Thr	Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	127	36	0.283465	NM_005319	A8K4I2	Missense_Mutation	SNP	ENST00000343677.2	37	CCDS4577.1	.	.	.	.	.	.	.	.	.	.	T	12.28	1.890388	0.33348	.	.	ENSG00000187837	ENST00000343677	T	0.19532	2.14	5.54	5.54	0.83059	.	0.120538	0.53938	D	0.000047	T	0.06325	0.0163	N	0.08118	0	0.58432	D	0.999999	B	0.25719	0.132	B	0.25759	0.063	T	0.14392	-1.0474	10	0.62326	D	0.03	-6.0558	15.1351	0.72558	0.0:0.0:0.0:1.0	.	127	P16403	H12_HUMAN	T	127	ENSP00000339566:K127T	ENSP00000339566:K127T	K	-	2	0	HIST1H1C	26164256	1.000000	0.71417	0.961000	0.40146	0.109000	0.19521	3.997000	0.57016	2.229000	0.72834	0.533000	0.62120	AAA	.	.	none		0.557	HIST1H1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043372.1	NM_005319	
CELA2A	63036	hgsc.bcm.edu	37	1	15789297	15789297	+	Silent	SNP	A	A	C	rs3815787	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:15789297A>C	ENST00000359621.4	+	4	322	c.297A>C	c.(295-297)gcA>gcC	p.A99A		NM_033440.2	NP_254275.1	P08217	CEL2A_HUMAN	chymotrypsin-like elastase family, member 2A	99	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)|keratohyalin granule (GO:0036457)	serine hydrolase activity (GO:0017171)|serine-type endopeptidase activity (GO:0004252)	p.A99A(1)		central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(7)|ovary(2)|prostate(1)	16						GCTCGCTGGCAGTCAGTGTCT	0.602													C|||	1997	0.398762	0.6762	0.3213	5008	,	,		15780	0.2321		0.3161	False		,,,				2504	0.3354				p.A99A		Atlas-SNP	.											CELA2A,brain,primitive_neuroectodermal_tumour-medulloblastoma,0,1	CELA2A	32	1	1	Substitution - coding silent(1)	central_nervous_system(1)	c.A297C						scavenged	.	C		2681,1725	516.5+/-369.2	827,1027,349	98.0	104.0	102.0		297	-6.5	0.0	1	dbSNP_107	102	2851,5749	673.3+/-403.0	473,1905,1922	no	coding-synonymous	CELA2A	NM_033440.2		1300,2932,2271	CC,CA,AA		33.1512,39.1512,42.5342		99/270	15789297	5532,7474	2203	4300	6503	SO:0001819	synonymous_variant	63036	exon4			GCTGGCAGTCAGT		CCDS157.1	1p36.21	2009-07-09			ENSG00000142615	ENSG00000142615	3.4.21.71		24609	protein-coding gene	gene with protein product	"""elastase 2A"""	609443				3646943, 2834346	Standard	NM_033440		Approved	ELA2A	uc001awk.3	P08217	OTTHUMG00000002258	ENST00000359621.4:c.297A>C	1.37:g.15789297A>C		Somatic	190	2	0.0105263		WXS	Illumina HiSeq	Phase_I	155	151	0.974194	NM_033440	B2R5I4|Q14243	Silent	SNP	ENST00000359621.4	37	CCDS157.1																																																																																			.	.	weak		0.602	CELA2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006445.1	NM_033440	
NUP210L	91181	hgsc.bcm.edu	37	1	154031134	154031134	+	Missense_Mutation	SNP	C	C	A	rs201928881		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:154031134C>A	ENST00000368559.3	-	21	2957	c.2886G>T	c.(2884-2886)gaG>gaT	p.E962D	NUP210L_ENST00000271854.3_Missense_Mutation_p.E962D|NUP210L_ENST00000368553.1_5'Flank	NM_207308.2	NP_997191.2	Q5VU65	P210L_HUMAN	nucleoporin 210kDa-like	962					Sertoli cell development (GO:0060009)|spermatid development (GO:0007286)	integral component of membrane (GO:0016021)				NS(1)|breast(6)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(12)|lung(34)|ovary(4)|pancreas(1)|prostate(2)|skin(6)|urinary_tract(2)	80	all_lung(78;9.35e-31)|Lung NSC(65;1.33e-28)|Hepatocellular(266;0.0877)|Melanoma(130;0.128)		LUSC - Lung squamous cell carcinoma(543;0.151)|Colorectal(543;0.198)			GATCATAGACCTCCAAGGTAA	0.433																																					p.E962D		Atlas-SNP	.											.	NUP210L	181	.	0			c.G2886T						PASS	.	C	ASP/GLU,ASP/GLU	3,3683		0,3,1840	92.0	82.0	85.0		2886,2886	-0.5	1.0	1		85	19,8163		0,19,4072	yes	missense,missense	NUP210L	NM_001159484.1,NM_207308.2	45,45	0,22,5912	AA,AC,CC		0.2322,0.0814,0.1854	benign,benign	962/1737,962/1889	154031134	22,11846	1843	4091	5934	SO:0001583	missense	91181	exon21			ATAGACCTCCAAG	AK125924	CCDS41399.1, CCDS53370.1	1q21.3	2008-02-05			ENSG00000143552	ENSG00000143552			29915	protein-coding gene	gene with protein product							Standard	NM_207308		Approved		uc001fdw.3	Q5VU65	OTTHUMG00000035852	ENST00000368559.3:c.2886G>T	1.37:g.154031134C>A	ENSP00000357547:p.Glu962Asp	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	66	32	0.484848	NM_001159484	E7EP56|Q5T4L7|Q6ZRN1|Q6ZRT4|Q6ZU81|Q8NDI6|Q9UF31	Missense_Mutation	SNP	ENST00000368559.3	37	CCDS41399.1	.	.	.	.	.	.	.	.	.	.	C	9.212	1.031090	0.19590	8.14E-4	0.002322	ENSG00000143552	ENST00000368559;ENST00000271854	T;T	0.07021	3.49;3.23	4.44	-0.504	0.11997	.	0.135069	0.33959	N	0.004391	T	0.02012	0.0063	L	0.44542	1.39	0.34482	D	0.703977	P;P	0.39665	0.651;0.682	B;B	0.32980	0.115;0.156	T	0.51787	-0.8661	10	0.33141	T	0.24	-24.0406	7.5347	0.27704	0.0:0.4383:0.0:0.5617	.	962;962	E7EP56;Q5VU65	.;P210L_HUMAN	D	962	ENSP00000357547:E962D;ENSP00000271854:E962D	ENSP00000271854:E962D	E	-	3	2	NUP210L	152297758	0.993000	0.37304	0.999000	0.59377	0.737000	0.42083	0.083000	0.14871	-0.010000	0.14271	0.591000	0.81541	GAG	.	.	weak		0.433	NUP210L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087270.3	NM_207308	
UGT2B11	10720	hgsc.bcm.edu	37	4	70079975	70079975	+	Missense_Mutation	SNP	A	A	G	rs7697037	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:70079975A>G	ENST00000446444.1	-	1	474	c.466T>C	c.(466-468)Tgt>Cgt	p.C156R	RP11-704M14.1_ENST00000504301.1_RNA|RP11-704M14.1_ENST00000505646.1_RNA	NM_001073.1	NP_001064.1	O75310	UDB11_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide B11	156					estrogen metabolic process (GO:0008210)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	glucuronosyltransferase activity (GO:0015020)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(18)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	42						AGCTCACCACAGGGAAAAACA	0.393													.|||	824	0.164537	0.2935	0.1787	5008	,	,		18927	0.0476		0.1064	False		,,,				2504	0.1605				p.C156R		Atlas-SNP	.											.	UGT2B11	92	.	0			c.T466C						PASS	.	A	ARG/CYS	1129,3277		152,825,1226	128.0	126.0	126.0		466	2.0	0.8	4	dbSNP_116	126	826,7772		36,754,3509	no	missense	UGT2B11	NM_001073.1	180	188,1579,4735	GG,GA,AA		9.6069,25.6241,15.0338	probably-damaging	156/530	70079975	1955,11049	2203	4299	6502	SO:0001583	missense	10720	exon1			CACCACAGGGAAA	AF016492	CCDS3527.1	4q13.3	2008-02-05	2005-07-20		ENSG00000213759	ENSG00000213759		"""UDP glucuronosyltransferases"""	12545	protein-coding gene	gene with protein product		603064	"""UDP glycosyltransferase 2 family, polypeptide B11"""			9675083	Standard	NM_001073		Approved		uc003heh.3	O75310	OTTHUMG00000129395	ENST00000446444.1:c.466T>C	4.37:g.70079975A>G	ENSP00000387683:p.Cys156Arg	Somatic	405	0	0		WXS	Illumina HiSeq	Phase_I	317	160	0.504732	NM_001073	Q3KNV9	Missense_Mutation	SNP	ENST00000446444.1	37	CCDS3527.1	339	0.15521978021978022	157	0.31910569105691056	66	0.18232044198895028	36	0.06293706293706294	80	0.10554089709762533	-	8.678	0.904384	0.17760	0.256241	0.096069	ENSG00000213759	ENST00000446444	T	0.63744	-0.06	1.96	1.96	0.26148	.	0.083414	0.49916	U	0.000138	T	0.00012	0.0000	H	0.97732	4.065	0.24325	P	0.99502787	D	0.89917	1.0	D	0.76575	0.988	T	0.02450	-1.1157	9	0.87932	D	0	.	7.5503	0.27793	1.0:0.0:0.0:0.0	rs7697037;rs60116346	156	O75310	UDB11_HUMAN	R	156	ENSP00000387683:C156R	ENSP00000387683:C156R	C	-	1	0	UGT2B11	70114564	0.000000	0.05858	0.752000	0.31206	0.013000	0.08279	-0.102000	0.10956	0.898000	0.36418	0.155000	0.16302	TGT	A|0.840;G|0.160	0.160	strong		0.393	UGT2B11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251551.2	NM_001073	
F5	2153	hgsc.bcm.edu	37	1	169521849	169521849	+	Silent	SNP	T	T	C	rs6035	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:169521849T>C	ENST00000367797.3	-	8	1443	c.1242A>G	c.(1240-1242)aaA>aaG	p.K414K	F5_ENST00000546081.1_Silent_p.K277K|F5_ENST00000367796.3_Silent_p.K414K	NM_000130.4	NP_000121	P12259	FA5_HUMAN	coagulation factor V (proaccelerin, labile factor)	414	F5/8 type A 2.|Plastocyanin-like 3.				blood circulation (GO:0008015)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)|vesicle (GO:0031982)	copper ion binding (GO:0005507)			NS(1)|breast(4)|central_nervous_system(4)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(24)|lung(55)|ovary(3)|prostate(4)|skin(5)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(1)	128	all_hematologic(923;0.208)				ART-123(DB05777)|Drotrecogin alfa(DB00055)	TCCCATCTTCTTTCATATTGG	0.348													T|||	416	0.0830671	0.0847	0.0735	5008	,	,		15504	0.0714		0.0865	False		,,,				2504	0.0961				p.K414K		Atlas-SNP	.											.	F5	301	.	0			c.A1242G	GRCh37	CM070088	F5	M	rs6035	PASS	.	T		399,4007	197.7+/-221.8	30,339,1834	154.0	153.0	154.0		1242	0.8	0.0	1	dbSNP_52	154	743,7857	179.5+/-228.6	42,659,3599	no	coding-synonymous	F5	NM_000130.4		72,998,5433	CC,CT,TT		8.6395,9.0558,8.7806		414/2225	169521849	1142,11864	2203	4300	6503	SO:0001819	synonymous_variant	2153	exon8			ATCTTCTTTCATA	M14335	CCDS1281.1	1q23	2012-10-02			ENSG00000198734	ENSG00000198734			3542	protein-coding gene	gene with protein product		612309					Standard	NM_000130		Approved		uc001ggg.1	P12259	OTTHUMG00000034595	ENST00000367797.3:c.1242A>G	1.37:g.169521849T>C		Somatic	209	1	0.00478469		WXS	Illumina HiSeq	Phase_I	202	101	0.5	NM_000130	A8K6E8|Q14285|Q2EHR5|Q5R346|Q5R347|Q6UPU6|Q8WWQ6	Silent	SNP	ENST00000367797.3	37	CCDS1281.1																																																																																			T|0.917;C|0.083	0.083	strong		0.348	F5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083712.1	NM_000130	
TRIM39	56658	hgsc.bcm.edu	37	6	30297529	30297529	+	Silent	SNP	T	T	C	rs2057727	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:30297529T>C	ENST00000396547.1	+	2	595	c.435T>C	c.(433-435)gaT>gaC	p.D145D	TRIM39_ENST00000376656.4_Silent_p.D145D|TRIM39-RPP21_ENST00000513556.1_Silent_p.D57D|HCG18_ENST00000426882.1_RNA|TRIM39_ENST00000396548.1_Silent_p.D145D|HCG18_ENST00000413358.2_RNA|TRIM39_ENST00000396551.3_Silent_p.D145D|TRIM39_ENST00000540416.1_Silent_p.D145D|TRIM39_ENST00000376659.5_Silent_p.D145D|HCG18_ENST00000412685.2_RNA			Q9HCM9	TRI39_HUMAN	tripartite motif containing 39	145					apoptotic process (GO:0006915)|negative regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000059)|positive regulation of apoptotic signaling pathway (GO:2001235)|protein ubiquitination (GO:0016567)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	identical protein binding (GO:0042802)|ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			ovary(3)	3						CACTGGACGATGCTACACAGG	0.537													C|||	1907	0.380791	0.3222	0.4539	5008	,	,		20492	0.506		0.2525	False		,,,				2504	0.411				p.D145D		Atlas-SNP	.											.	TRIM39	56	.	0			c.T435C						PASS	.	C	,,	879,2137		122,635,751	60.0	64.0	63.0		435,435,435	-1.6	0.6	6	dbSNP_94	63	1357,4057		165,1027,1515	yes	coding-synonymous,coding-synonymous,coding-synonymous	TRIM39,TRIM39-RPP21	NM_001199119.1,NM_021253.3,NM_172016.2	,,	287,1662,2266	CC,CT,TT		25.0646,29.1446,26.5243	,,	145/504,145/519,145/489	30297529	2236,6194	1508	2707	4215	SO:0001819	synonymous_variant	56658	exon3			GGACGATGCTACA	BC034985	CCDS34377.1, CCDS34378.1	6p22.1	2013-01-09	2011-01-25	2002-06-07	ENSG00000204599	ENSG00000204599		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	10065	protein-coding gene	gene with protein product		605700	"""ring finger protein 23"", ""tripartite motif-containing 39"""	RNF23		11006080	Standard	NM_021253		Approved			Q9HCM9	OTTHUMG00000031066	ENST00000396547.1:c.435T>C	6.37:g.30297529T>C		Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	120	58	0.483333	NM_172016	Q5STG3|Q5STG4|Q76BL3|Q8IYT9|Q96IB6	Silent	SNP	ENST00000396547.1	37	CCDS34377.1	746	0.3415750915750916	156	0.3170731707317073	147	0.40607734806629836	270	0.47202797202797203	173	0.22823218997361477	C	9.049	0.991596	0.18966	0.291446	0.250646	ENSG00000204599	ENST00000420746	.	.	.	5.35	-1.57	0.08506	.	.	.	.	.	T	0.17704	0.0425	.	.	.	0.09310	P	0.9999999999999996	.	.	.	.	.	.	T	0.18241	-1.0343	3	.	.	.	.	6.5398	0.22375	0.118:0.3956:0.0:0.4864	rs2057727;rs6939906;rs17194831;rs17850232;rs61139874;rs2057727	.	.	.	T	75	.	.	M	+	2	0	TRIM39	30405508	0.037000	0.19845	0.565000	0.28409	0.944000	0.59088	-1.096000	0.03353	-0.658000	0.05366	-0.227000	0.12334	ATG	T|0.696;C|0.304	0.304	strong		0.537	TRIM39-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000076086.2	NM_172016	
DAB2	1601	hgsc.bcm.edu	37	5	39381618	39381618	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:39381618G>A	ENST00000320816.6	-	11	1909	c.1442C>T	c.(1441-1443)cCc>cTc	p.P481L	DAB2_ENST00000339788.6_Missense_Mutation_p.P263L|DAB2_ENST00000509337.1_Missense_Mutation_p.P460L|DAB2_ENST00000545653.1_Missense_Mutation_p.P460L	NM_001343.3	NP_001334.2	P98082	DAB2_HUMAN	Dab, mitogen-responsive phosphoprotein, homolog 2 (Drosophila)	481					activation of JUN kinase activity (GO:0007257)|apoptotic process (GO:0006915)|cell morphogenesis involved in differentiation (GO:0000904)|cell proliferation (GO:0008283)|cellular response to transforming growth factor beta stimulus (GO:0071560)|clathrin coat assembly (GO:0048268)|endoderm development (GO:0007492)|excretion (GO:0007588)|in utero embryonic development (GO:0001701)|leading edge cell differentiation (GO:0035026)|membrane organization (GO:0061024)|myeloid cell differentiation (GO:0030099)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of protein binding (GO:0032091)|negative regulation of protein localization to plasma membrane (GO:1903077)|negative regulation of transcription, DNA-templated (GO:0045892)|pinocytosis (GO:0006907)|positive regulation of cell migration (GO:0030335)|positive regulation of clathrin-mediated endocytosis (GO:2000370)|positive regulation of early endosome to late endosome transport (GO:2000643)|positive regulation of endocytosis (GO:0045807)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of integrin-mediated signaling pathway (GO:2001046)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of receptor recycling (GO:0001921)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of Wnt signaling pathway, planar cell polarity pathway (GO:2000096)|protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)|Wnt signaling pathway (GO:0016055)	apical plasma membrane (GO:0016324)|clathrin coat of coated pit (GO:0030132)|clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal membrane (GO:0005765)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	cargo receptor activity (GO:0038024)|clathrin adaptor activity (GO:0035615)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|protein C-terminus binding (GO:0008022)|SMAD binding (GO:0046332)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(1)|kidney(5)|large_intestine(9)|lung(19)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)	47	all_lung(31;0.000197)		Epithelial(62;0.137)			CAGAGGGTTGGGCTGCAGGGC	0.532																																					p.P481L		Atlas-SNP	.											.	DAB2	124	.	0			c.C1442T						PASS	.						118.0	123.0	121.0					5																	39381618		2203	4300	6503	SO:0001583	missense	1601	exon11			GGGTTGGGCTGCA	U53446	CCDS34149.1, CCDS58946.1	5p13.1	2013-10-03	2013-03-08		ENSG00000153071	ENSG00000153071			2662	protein-coding gene	gene with protein product		601236	"""disabled (Drosophila) homolog 2 (mitogen-responsive phosphoprotein)"", ""disabled homolog 2, mitogen-responsive phosphoprotein (Drosophila)"""			8660969, 9620555	Standard	NM_001343		Approved	DOC-2	uc003jlx.3	P98082	OTTHUMG00000162043	ENST00000320816.6:c.1442C>T	5.37:g.39381618G>A	ENSP00000313391:p.Pro481Leu	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	123	43	0.349593	NM_001343	A6NES5|Q13598|Q9BTY0|Q9UK04	Missense_Mutation	SNP	ENST00000320816.6	37	CCDS34149.1	.	.	.	.	.	.	.	.	.	.	G	13.36	2.212852	0.39102	.	.	ENSG00000153071	ENST00000320816;ENST00000339788;ENST00000545653;ENST00000509337	T;T;T;T	0.37752	1.32;1.18;1.31;1.31	5.87	3.96	0.45880	.	0.775909	0.12796	N	0.438417	T	0.28200	0.0696	L	0.29908	0.895	0.44908	D	0.99792	B;B	0.15719	0.014;0.014	B;B	0.17979	0.013;0.02	T	0.04400	-1.0954	10	0.23891	T	0.37	-1.2282	13.2306	0.59941	0.0:0.1217:0.7521:0.1262	.	481;460	P98082;P98082-3	DAB2_HUMAN;.	L	481;263;460;460	ENSP00000313391:P481L;ENSP00000345508:P263L;ENSP00000439919:P460L;ENSP00000426245:P460L	ENSP00000313391:P481L	P	-	2	0	DAB2	39417375	1.000000	0.71417	0.991000	0.47740	0.841000	0.47740	2.304000	0.43655	1.587000	0.49959	0.655000	0.94253	CCC	.	.	none		0.532	DAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367014.1	NM_001343	
KRTAP4-9	100132386	hgsc.bcm.edu	37	17	39262122	39262122	+	Missense_Mutation	SNP	G	G	A	rs200757692|rs188946528	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:39262122G>A	ENST00000391415.1	+	1	539	c.482G>A	c.(481-483)cGc>cAc	p.R161H		NM_001146041.1	NP_001139513.1	Q9BYQ8	KRA49_HUMAN	keratin associated protein 4-9	161	29 X 5 AA repeats of C-C-[RQVHIEK]- [SPTR]-[VSTQCRNP].				aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)				central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(1)|urinary_tract(3)	14						agctgctgccgcccctcttgc	0.652													g|||	92	0.0183706	0.0038	0.0331	5008	,	,		17570	0.001		0.0616	False		,,,				2504	0.001				p.R161H		Atlas-SNP	.											KRTAP4-9_ENST00000377734,NS,carcinoma,+1,2	KRTAP4-9	110	2	0			c.G482A						PASS	.						8.0	13.0	11.0					17																	39262122		684	1580	2264	SO:0001583	missense	100132386	exon1			GCTGCCGCCCCTC	AJ406941	CCDS54124.1	17q21.2	2013-06-25			ENSG00000212722	ENSG00000212722		"""Keratin associated proteins"""	18910	protein-coding gene	gene with protein product							Standard	NM_001146041		Approved	KAP4.9	uc010wfp.2	Q9BYQ8	OTTHUMG00000133584	ENST00000391415.1:c.482G>A	17.37:g.39262122G>A	ENSP00000375234:p.Arg161His	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	42	12	0.285714	NM_001146041		Missense_Mutation	SNP	ENST00000391415.1	37	CCDS54124.1	61	0.027930402930402932	3	0.006097560975609756	12	0.03314917127071823	1	0.0017482517482517483	45	0.059366754617414245	.	12.11	1.839141	0.32513	.	.	ENSG00000212722	ENST00000377734;ENST00000391415;ENST00000333994	T	0.00599	6.3	2.87	-2.78	0.05859	.	0.000000	0.40640	U	0.001042	T	0.00109	0.0003	M	0.74881	2.28	0.09310	N	1	B	0.22080	0.064	B	0.12837	0.008	T	0.47598	-0.9105	10	0.56958	D	0.05	.	4.4035	0.11399	0.3381:0.1654:0.4965:0.0	.	161	Q9BYQ8	KRA49_HUMAN	H	149;161;152	ENSP00000375234:R161H	ENSP00000334461:R152H	R	+	2	0	KRTAP4-9	36515648	0.000000	0.05858	0.312000	0.25196	0.222000	0.24845	-0.253000	0.08794	-0.966000	0.03587	-1.073000	0.02249	CGC	G|0.972;A|0.028	0.028	strong		0.652	KRTAP4-9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257688.1	NM_001146041	
TXLNB	167838	hgsc.bcm.edu	37	6	139581461	139581461	+	Silent	SNP	C	C	T	rs6904970	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:139581461C>T	ENST00000358430.3	-	6	1228	c.996G>A	c.(994-996)aaG>aaA	p.K332K		NM_153235.3	NP_694967.3	Q8N3L3	TXLNB_HUMAN	taxilin beta	332						cytoplasm (GO:0005737)				breast(2)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(5)|lung(14)|ovary(2)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)	37				OV - Ovarian serous cystadenocarcinoma(155;0.000185)|GBM - Glioblastoma multiforme(68;0.000235)		ATACATATTCCTTTTCTCGTT	0.388													C|||	399	0.0796725	0.2141	0.0476	5008	,	,		18813	0.001		0.0517	False		,,,				2504	0.0307				p.K332K		Atlas-SNP	.											.	TXLNB	96	.	0			c.G996A						PASS	.	C		759,3647	304.4+/-288.4	78,603,1522	103.0	89.0	94.0		996	5.6	1.0	6	dbSNP_116	94	446,8154	132.3+/-190.0	14,418,3868	no	coding-synonymous	TXLNB	NM_153235.3		92,1021,5390	TT,TC,CC		5.186,17.2265,9.265		332/685	139581461	1205,11801	2203	4300	6503	SO:0001819	synonymous_variant	167838	exon6			ATATTCCTTTTCT		CCDS34545.1	6q23.3	2008-02-05	2005-07-29	2005-07-29	ENSG00000164440	ENSG00000164440			21617	protein-coding gene	gene with protein product		611438	"""chromosome 6 open reading frame 198"""	C6orf198		15184072	Standard	NM_153235		Approved	DKFZp451A175, MDP77, dJ522B19.2	uc021zfy.1	Q8N3L3	OTTHUMG00000015688	ENST00000358430.3:c.996G>A	6.37:g.139581461C>T		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	80	25	0.3125	NM_153235	Q5VTF3|Q76L25|Q86T52|Q8N3S2	Silent	SNP	ENST00000358430.3	37	CCDS34545.1	146	0.06684981684981685	91	0.18495934959349594	14	0.03867403314917127	1	0.0017482517482517483	40	0.052770448548812667	C	8.483	0.860121	0.17178	0.172265	0.05186	ENSG00000164440	ENST00000367652	.	.	.	5.64	5.64	0.86602	.	.	.	.	.	T	0.53045	0.1772	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.55121	-0.8190	3	.	.	.	-22.4848	12.9619	0.58464	0.0:0.9261:0.0:0.0739	rs6904970	.	.	.	R	45	.	.	G	-	1	0	TXLNB	139623154	1.000000	0.71417	1.000000	0.80357	0.788000	0.44548	1.579000	0.36536	2.676000	0.91093	0.591000	0.81541	GGA	C|0.915;T|0.085	0.085	strong		0.388	TXLNB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042458.1	NM_153235	
MFAP3	4238	hgsc.bcm.edu	37	5	153429459	153429459	+	Silent	SNP	T	T	C	rs690592	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:153429459T>C	ENST00000436816.1	+	2	396	c.177T>C	c.(175-177)gaT>gaC	p.D59D	MFAP3_ENST00000322602.5_Silent_p.D59D|MFAP3_ENST00000439768.2_Intron	NM_001242336.1|NM_005927.4	NP_001229265.1|NP_005918.1	P55082	MFAP3_HUMAN	microfibrillar-associated protein 3	59	Ig-like C2-type.				extracellular matrix organization (GO:0030198)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|kidney(2)|large_intestine(1)|lung(2)|pancreas(1)	7	Renal(175;0.00488)	Lung NSC(249;0.00145)|all_lung(500;0.00226)|all_neural(177;0.122)|Breast(839;0.14)	Kidney(363;0.000173)|KIRC - Kidney renal clear cell carcinoma(527;0.000785)	OV - Ovarian serous cystadenocarcinoma(192;9.69e-06)|GBM - Glioblastoma multiforme(465;0.0201)		CGGATGATGATGTCATCATAG	0.438													T|||	3581	0.715056	0.6203	0.7147	5008	,	,		19293	0.8581		0.6272	False		,,,				2504	0.7863				p.D59D		Atlas-SNP	.											.	MFAP3	20	.	0			c.T177C						PASS	.	T	,,	2854,1552	668.3+/-402.0	929,996,278	88.0	78.0	81.0		,177,177	3.6	1.0	5	dbSNP_83	81	5351,3249	649.0+/-400.6	1665,2021,614	no	intron,coding-synonymous,coding-synonymous	MFAP3	NM_001135037.1,NM_001242336.1,NM_005927.4	,,	2594,3017,892	CC,CT,TT		37.7791,35.2247,36.9137	,,	,59/363,59/363	153429459	8205,4801	2203	4300	6503	SO:0001819	synonymous_variant	4238	exon2			TGATGATGTCATC		CCDS4324.1, CCDS47319.1	5q32-q33.2	2013-01-11			ENSG00000037749	ENSG00000037749		"""Immunoglobulin superfamily / I-set domain containing"""	7034	protein-coding gene	gene with protein product		600491				7782085	Standard	NM_005927		Approved		uc010jib.2	P55082	OTTHUMG00000130149	ENST00000436816.1:c.177T>C	5.37:g.153429459T>C		Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	170	73	0.429412	NM_005927	B2RDK0|B4DKA1|Q9NXA7	Silent	SNP	ENST00000436816.1	37	CCDS4324.1																																																																																			T|0.355;C|0.645	0.645	strong		0.438	MFAP3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252457.2	NM_005927	
C1QTNF2	114898	hgsc.bcm.edu	37	5	159776637	159776637	+	Silent	SNP	C	C	T	rs10053189	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:159776637C>T	ENST00000393975.3	-	3	534	c.531G>A	c.(529-531)aaG>aaA	p.K177K		NM_031908.4	NP_114114.2	Q9BXJ5	C1QT2_HUMAN	C1q and tumor necrosis factor related protein 2	132	C1q. {ECO:0000255|PROSITE- ProRule:PRU00368}.				activation of MAPK activity (GO:0000187)|positive regulation of fatty acid oxidation (GO:0046321)|positive regulation of glucose import (GO:0046326)|positive regulation of glycogen biosynthetic process (GO:0045725)|protein heterotrimerization (GO:0070208)|protein homooligomerization (GO:0051260)	collagen trimer (GO:0005581)|extracellular space (GO:0005615)				breast(2)|endometrium(2)|large_intestine(1)|lung(4)|prostate(1)|skin(3)	13	Renal(175;0.00196)	Medulloblastoma(196;0.0354)|all_neural(177;0.116)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			CTGGCTCCCCCTTCTTGCCCT	0.692													c|||	1696	0.338658	0.2133	0.4063	5008	,	,		18204	0.3284		0.4781	False		,,,				2504	0.3272				p.K177K		Atlas-SNP	.											.	C1QTNF2	33	.	0			c.G531A						PASS	.	T		1099,3307	375.1+/-321.5	144,811,1248	96.0	106.0	103.0		531	1.8	1.0	5	dbSNP_119	103	4016,4584	538.4+/-383.4	956,2104,1240	no	coding-synonymous	C1QTNF2	NM_031908.4		1100,2915,2488	TT,TC,CC		46.6977,24.9433,39.328		177/331	159776637	5115,7891	2203	4300	6503	SO:0001819	synonymous_variant	114898	exon3			CTCCCCCTTCTTG	AF329836	CCDS4351.2	5q33.3	2008-05-15			ENSG00000145861	ENSG00000145861			14325	protein-coding gene	gene with protein product							Standard	XM_005265815		Approved	CTRP2	uc003lyd.3	Q9BXJ5	OTTHUMG00000130323	ENST00000393975.3:c.531G>A	5.37:g.159776637C>T		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	65	28	0.430769	NM_031908		Silent	SNP	ENST00000393975.3	37	CCDS4351.2																																																																																			C|0.626;T|0.374	0.374	strong		0.692	C1QTNF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252672.2		
SLC35G6	643664	hgsc.bcm.edu	37	17	7386217	7386217	+	Missense_Mutation	SNP	T	T	C	rs200349946	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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						scavenged	.						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	164	0	0		WXS	Illumina HiSeq	Phase_I	148	38	0.256757	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	
RNF213	57674	hgsc.bcm.edu	37	17	78263514	78263514	+	Silent	SNP	G	G	A	rs17853713	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:78263514G>A	ENST00000582970.1	+	6	1133	c.990G>A	c.(988-990)aaG>aaA	p.K330K	RNF213_ENST00000456466.1_Silent_p.K330K|RNF213_ENST00000508628.2_Silent_p.K379K|RNF213_ENST00000319921.4_Silent_p.K330K	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	102	0	0		WXS	Illumina HiSeq	Phase_I	101	49	0.485149	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	
BTN2A1	11120	hgsc.bcm.edu	37	6	26463575	26463575	+	Missense_Mutation	SNP	G	G	T	rs34505465|rs13195402	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:26463575G>T	ENST00000312541.5	+	4	782	c.534G>T	c.(532-534)tgG>tgT	p.W178C	BTN2A1_ENST00000469185.1_Missense_Mutation_p.W178C|BTN2A1_ENST00000541522.1_Missense_Mutation_p.W117C|BTN2A1_ENST00000429381.1_Missense_Mutation_p.W178C	NM_007049.3|NM_078476.2	NP_008980.1|NP_510961.1	Q7KYR7	BT2A1_HUMAN	butyrophilin, subfamily 2, member A1	178			W -> C (in dbSNP:rs13195402).|W -> L (in dbSNP:rs13195401).		lipid metabolic process (GO:0006629)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)				breast(3)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(2)|lung(9)|ovary(2)|prostate(1)|skin(3)|urinary_tract(3)	27						TCACAGTGTGGAGGGACCCCT	0.587													G|||	120	0.0239617	0.0227	0.0303	5008	,	,		17982	0.0		0.0686	False		,,,				2504	0.0				p.W178C		Atlas-SNP	.											.	BTN2A1	118	.	0			c.G534T						PASS	.	G	CYS/TRP,CYS/TRP,CYS/TRP,CYS/TRP	136,4270	88.7+/-127.4	3,130,2070	83.0	78.0	79.0		351,534,534,534	2.9	0.4	6	dbSNP_121	79	686,7914	160.0+/-213.2	29,628,3643	yes	missense,missense,missense,missense	BTN2A1	NM_001197233.1,NM_001197234.1,NM_007049.3,NM_078476.2	215,215,215,215	32,758,5713	TT,TG,GG		7.9767,3.0867,6.3202	probably-damaging,probably-damaging,probably-damaging,probably-damaging	117/467,178/331,178/528,178/335	26463575	822,12184	2203	4300	6503	SO:0001583	missense	11120	exon4			AGTGTGGAGGGAC	U90543	CCDS4613.1, CCDS47390.1, CCDS56404.1, CCDS56405.1	6p22.1	2014-01-14			ENSG00000112763	ENSG00000112763		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Butyrophilins"""	1136	protein-coding gene	gene with protein product		613590				9382921, 9149941	Standard	NM_007049		Approved	BT2.1, BTF1, BTN2.1	uc003nib.2	Q7KYR7	OTTHUMG00000014457	ENST00000312541.5:c.534G>T	6.37:g.26463575G>T	ENSP00000312158:p.Trp178Cys	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	61	29	0.47541	NM_001197234	B4DLP9|E9PGR4|O00475|P78408|Q59EN4|Q7KYQ7|Q7Z386|Q96AV7|Q9NU62	Missense_Mutation	SNP	ENST00000312541.5	37	CCDS4613.1	61	0.027930402930402932	8	0.016260162601626018	10	0.027624309392265192	0	0.0	43	0.05672823218997362	G	11.93	1.784342	0.31593	0.030867	0.079767	ENSG00000112763	ENST00000312541;ENST00000541522;ENST00000429381;ENST00000265424;ENST00000469185	T;T;T;T	0.67698	-0.28;-0.28;-0.28;-0.28	2.88	2.88	0.33553	CD80-like, immunoglobulin C2-set (1);	0.000000	0.50627	D	0.000118	T	0.79879	0.4522	M	0.89658	3.05	0.51482	D	0.999928	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.83168	-0.0095	10	0.62326	D	0.03	.	11.9438	0.52915	0.0:0.0:1.0:0.0	rs13195402;rs13195402	178;178	Q96AV7;Q7KYR7	.;BT2A1_HUMAN	C	178;117;178;178;178	ENSP00000312158:W178C;ENSP00000443909:W117C;ENSP00000416945:W178C;ENSP00000419043:W178C	ENSP00000265424:W178C	W	+	3	0	BTN2A1	26571554	1.000000	0.71417	0.394000	0.26270	0.142000	0.21351	5.311000	0.65786	1.896000	0.54893	0.561000	0.74099	TGG	G|0.952;T|0.048	0.048	strong		0.587	BTN2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040122.2	NM_007049	
RAPGEF3	10411	hgsc.bcm.edu	37	12	48151822	48151822	+	Missense_Mutation	SNP	C	C	G	rs11168230	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:48151822C>G	ENST00000449771.2	-	2	134	c.46G>C	c.(46-48)Gct>Cct	p.A16P	RAPGEF3_ENST00000171000.4_5'UTR|RAPGEF3_ENST00000549347.1_5'UTR|RAPGEF3_ENST00000389212.3_Missense_Mutation_p.A16P|RAPGEF3_ENST00000548919.1_5'UTR|SLC48A1_ENST00000547002.1_5'Flank|RAPGEF3_ENST00000395358.3_Missense_Mutation_p.A16P|RAPGEF3_ENST00000549151.1_5'UTR|RAPGEF3_ENST00000405493.2_5'UTR			O95398	RPGF3_HUMAN	Rap guanine nucleotide exchange factor (GEF) 3	16			A -> P (in dbSNP:rs11168230). {ECO:0000269|PubMed:15489334}.		angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cAMP-mediated signaling (GO:0019933)|cell proliferation (GO:0008283)|cellular response to cAMP (GO:0071320)|energy reserve metabolic process (GO:0006112)|establishment of endothelial barrier (GO:0061028)|platelet activation (GO:0030168)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cAMP catabolic process (GO:0030822)|positive regulation of Rap GTPase activity (GO:0032854)|positive regulation of stress fiber assembly (GO:0051496)|Rap protein signal transduction (GO:0032486)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cAMP-dependent protein kinase complex (GO:0005952)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cAMP binding (GO:0030552)|cAMP-dependent protein kinase regulator activity (GO:0008603)|guanyl-nucleotide exchange factor activity (GO:0005085)|Rap guanyl-nucleotide exchange factor activity (GO:0017034)			endometrium(1)|kidney(2)|large_intestine(4)|lung(9)|pancreas(1)|prostate(1)|skin(7)	25	Lung SC(27;0.192)			GBM - Glioblastoma multiforme(48;0.0375)		TCCTCCACAGCCAGGCCCACC	0.657													C|||	1487	0.296925	0.2988	0.2709	5008	,	,		16982	0.2004		0.335	False		,,,				2504	0.3732				p.A16P		Atlas-SNP	.											.	RAPGEF3	98	.	0			c.G46C						PASS	.	C	PRO/ALA,,	1187,3177		185,817,1180	13.0	14.0	14.0		46,,	2.0	0.9	12	dbSNP_120	14	2586,5970		408,1770,2100	no	missense,utr-5,utr-5	RAPGEF3	NM_001098531.2,NM_001098532.2,NM_006105.5	27,,	593,2587,3280	GG,GC,CC		30.2244,27.1998,29.2028	possibly-damaging,,	16/924,,	48151822	3773,9147	2182	4278	6460	SO:0001583	missense	10411	exon2			CCACAGCCAGGCC	AK092448	CCDS31784.1, CCDS41775.1	12q13.1	2006-04-12	2004-03-26		ENSG00000079337	ENSG00000079337			16629	protein-coding gene	gene with protein product	"""exchange protein directly activated by cAMP 1"""	606057	"""RAP guanine-nucleotide-exchange factor (GEF) 3"""			10777494, 9856955	Standard	NM_001098531		Approved	cAMP-GEFI, EPAC, bcm910	uc001rpz.4	O95398	OTTHUMG00000133667	ENST00000449771.2:c.46G>C	12.37:g.48151822C>G	ENSP00000395708:p.Ala16Pro	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	122	70	0.57377	NM_001098531	A8K2G5|E7EQC8|O95634|Q8WVN0	Missense_Mutation	SNP	ENST00000449771.2	37	CCDS41775.1	611	0.27976190476190477	138	0.2804878048780488	103	0.2845303867403315	122	0.21328671328671328	248	0.32717678100263853	C	16.11	3.029273	0.54790	0.271998	0.302244	ENSG00000079337	ENST00000449771;ENST00000389212;ENST00000397089;ENST00000395358	T;T;T	0.62498	0.02;0.02;0.02	5.12	1.99	0.26369	.	.	.	.	.	T	0.00012	0.0000	N	0.19112	0.55	0.22240	P	0.999267639	B;B;B	0.09022	0.0;0.002;0.0	B;B;B	0.09377	0.0;0.004;0.001	T	0.26430	-1.0103	8	0.30078	T	0.28	.	4.294	0.10892	0.0:0.5898:0.1857:0.2245	rs11168230;rs11168230	28;16;16	B7Z5J6;O95398-2;O95398	.;.;RPGF3_HUMAN	P	16;16;28;16	ENSP00000395708:A16P;ENSP00000373864:A16P;ENSP00000378764:A16P	ENSP00000373864:A16P	A	-	1	0	RAPGEF3	46438089	0.037000	0.19845	0.918000	0.36340	0.989000	0.77384	0.843000	0.27640	0.540000	0.28808	0.591000	0.81541	GCT	C|0.721;G|0.279	0.279	strong		0.657	RAPGEF3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257848.1	NM_006105	
KRT9	3857	hgsc.bcm.edu	37	17	39727894	39727894	+	Silent	SNP	A	A	G	rs115965791	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:39727894A>G	ENST00000246662.4	-	1	416	c.351T>C	c.(349-351)ggT>ggC	p.G117G	KRT9_ENST00000588431.1_Intron	NM_000226.3	NP_000217.2	P35527	K1C9_HUMAN	keratin 9	117	Head.				epidermis development (GO:0008544)|intermediate filament organization (GO:0045109)|skin development (GO:0043588)|spermatogenesis (GO:0007283)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|membrane (GO:0016020)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(4)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	25		Breast(137;0.000307)				ctccagaaccaccaccaaagc	0.567													A|||	28	0.00559105	0.0015	0.0043	5008	,	,		12499	0.0		0.0129	False		,,,				2504	0.0102				p.G117G		Atlas-SNP	.											.	KRT9	78	.	0			c.T351C						PASS	.	A		8,4394		0,8,2193	142.0	171.0	161.0		351	-9.1	0.0	17	dbSNP_132	161	53,8537		0,53,4242	yes	coding-synonymous	KRT9	NM_000226.3		0,61,6435	GG,GA,AA		0.617,0.1817,0.4695		117/624	39727894	61,12931	2201	4295	6496	SO:0001819	synonymous_variant	3857	exon1			AGAACCACCACCA		CCDS32654.1	17q21.2	2013-06-20	2008-08-01		ENSG00000171403	ENSG00000171403		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6447	protein-coding gene	gene with protein product	"""cytokeratin 9"", ""type I cytoskeletal 9"", ""epidermolytic palmoplantar keratoderma"""	607606				7512862, 16831889	Standard	NM_000226		Approved	EPPK, K9, CK-9	uc002hxe.4	P35527	OTTHUMG00000133599	ENST00000246662.4:c.351T>C	17.37:g.39727894A>G		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	75	37	0.493333	NM_000226	O00109|Q0IJ47|Q14665	Silent	SNP	ENST00000246662.4	37	CCDS32654.1																																																																																			A|0.995;G|0.005	0.005	strong		0.567	KRT9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257707.1	NM_000226	
CAV3	859	hgsc.bcm.edu	37	3	8775589	8775589	+	Silent	SNP	C	C	T	rs1974763	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:8775589C>T	ENST00000343849.2	+	1	104	c.27C>T	c.(25-27)ctC>ctT	p.L9L	CAV3_ENST00000397368.2_Silent_p.L9L|SSUH2_ENST00000478513.1_Intron|CAV3_ENST00000472766.1_3'UTR	NM_001234.4|NM_033337.2	NP_001225.1|NP_203123.1	P56539	CAV3_HUMAN	caveolin 3	9					actin filament organization (GO:0007015)|cardiac muscle cell development (GO:0055013)|caveola assembly (GO:0070836)|cell differentiation (GO:0030154)|cell growth (GO:0016049)|cholesterol homeostasis (GO:0042632)|cytoplasmic microtubule organization (GO:0031122)|endocytosis (GO:0006897)|establishment of protein localization to plasma membrane (GO:0090002)|glucose homeostasis (GO:0042593)|heart trabecula formation (GO:0060347)|membrane raft organization (GO:0031579)|muscle cell cellular homeostasis (GO:0046716)|muscle organ development (GO:0007517)|myoblast fusion (GO:0007520)|negative regulation of calcium ion transport (GO:0051926)|negative regulation of cardiac muscle hypertrophy (GO:0010614)|negative regulation of cell growth involved in cardiac muscle cell development (GO:0061052)|negative regulation of cell size (GO:0045792)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of nitric-oxide synthase activity (GO:0051001)|negative regulation of potassium ion transmembrane transport (GO:1901380)|negative regulation of potassium ion transmembrane transporter activity (GO:1901017)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein localization to cell surface (GO:2000009)|negative regulation of sarcomere organization (GO:0060299)|nucleus localization (GO:0051647)|plasma membrane organization (GO:0007009)|plasma membrane repair (GO:0001778)|positive regulation of caveolin-mediated endocytosis (GO:2001288)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of myotube differentiation (GO:0010831)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|protein localization (GO:0008104)|protein localization to plasma membrane (GO:0072659)|regulation of branching involved in mammary gland duct morphogenesis (GO:0060762)|regulation of calcium ion import (GO:0090279)|regulation of calcium ion transmembrane transporter activity (GO:1901019)|regulation of cardiac muscle contraction (GO:0055117)|regulation of heart contraction (GO:0008016)|regulation of heart rate (GO:0002027)|regulation of membrane depolarization during cardiac muscle cell action potential (GO:1900825)|regulation of membrane potential (GO:0042391)|regulation of nerve growth factor receptor activity (GO:0051394)|regulation of p38MAPK cascade (GO:1900744)|regulation of protein kinase B signaling (GO:0051896)|regulation of signal transduction by receptor internalization (GO:0038009)|regulation of skeletal muscle contraction (GO:0014819)|regulation of sodium ion transmembrane transporter activity (GO:2000649)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|regulation of ventricular cardiac muscle cell membrane depolarization (GO:0060373)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|T-tubule organization (GO:0033292)|triglyceride metabolic process (GO:0006641)|ventricular cardiac muscle cell action potential (GO:0086005)	caveola (GO:0005901)|cell surface (GO:0009986)|dystrophin-associated glycoprotein complex (GO:0016010)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|membrane raft (GO:0045121)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|vesicle (GO:0031982)	calcium channel regulator activity (GO:0005246)|connexin binding (GO:0071253)|ion channel binding (GO:0044325)|potassium channel inhibitor activity (GO:0019870)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)|protein complex scaffold (GO:0032947)|sodium channel regulator activity (GO:0017080)			breast(1)|kidney(2)|large_intestine(4)|lung(3)|prostate(1)	11						ACACAGATCTCGAGGCCCAGA	0.557													C|||	213	0.0425319	0.0053	0.062	5008	,	,		15414	0.006		0.1302	False		,,,				2504	0.0266				p.L9L		Atlas-SNP	.											.	CAV3	20	.	0			c.C27T						PASS	.	C	,	117,4289	87.3+/-125.9	3,111,2089	114.0	98.0	103.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	27,27	0.7	1.0	3	dbSNP_92	103	1073,7527	224.3+/-260.7	62,949,3289	no	coding-synonymous,coding-synonymous	CAV3	NM_001234.3,NM_033337.2	,	65,1060,5378	TT,TC,CC		12.4767,2.6555,9.1496	,	9/152,9/152	8775589	1190,11816	2203	4300	6503	SO:0001819	synonymous_variant	859	exon1			AGATCTCGAGGCC	AF043101	CCDS2569.1	3p25	2014-09-17			ENSG00000182533	ENSG00000182533			1529	protein-coding gene	gene with protein product	"""M-caveolin"""	601253				9536092, 9537420	Standard	NM_033337		Approved	VIP-21, LGMD1C, VIP21, LQT9	uc003brb.3	P56539	OTTHUMG00000090519	ENST00000343849.2:c.27C>T	3.37:g.8775589C>T		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	98	56	0.571429	NM_033337	A8K777|Q3T1A4	Silent	SNP	ENST00000343849.2	37	CCDS2569.1																																																																																			C|0.925;T|0.075	0.075	strong		0.557	CAV3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207008.2	NM_033337	
STAG1	10274	hgsc.bcm.edu	37	3	136088038	136088038	+	Silent	SNP	G	G	A	rs9860801	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:136088038G>A	ENST00000383202.2	-	24	2713	c.2457C>T	c.(2455-2457)ttC>ttT	p.F819F	STAG1_ENST00000536929.1_Silent_p.F403F|STAG1_ENST00000236698.5_Silent_p.F819F|STAG1_ENST00000434713.2_Silent_p.F593F	NM_005862.2	NP_005853.2	Q8WVM7	STAG1_HUMAN	stromal antigen 1	819					chromosome segregation (GO:0007059)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	cell junction (GO:0030054)|chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(16)|lung(16)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	58						TATCTGGATTGAACACCAAAG	0.448													A|||	1517	0.302915	0.5522	0.2017	5008	,	,		15257	0.0585		0.3022	False		,,,				2504	0.2904				p.F819F		Atlas-SNP	.											.	STAG1	135	.	0			c.C2457T						PASS	.	A		2295,2111	576.3+/-384.2	609,1077,517	90.0	89.0	90.0		2457	3.0	1.0	3	dbSNP_119	90	2836,5764	675.1+/-403.2	465,1906,1929	no	coding-synonymous	STAG1	NM_005862.2		1074,2983,2446	AA,AG,GG		32.9767,47.9119,39.451		819/1259	136088038	5131,7875	2203	4300	6503	SO:0001819	synonymous_variant	10274	exon24			TGGATTGAACACC	Z75330	CCDS3090.1	3q22.2-q22.3	2011-08-12			ENSG00000118007	ENSG00000118007			11354	protein-coding gene	gene with protein product		604358				9305759	Standard	XM_006713471		Approved	SA-1, SCC3A	uc003era.1	Q8WVM7	OTTHUMG00000159798	ENST00000383202.2:c.2457C>T	3.37:g.136088038G>A		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	142	61	0.429577	NM_005862	O00539|Q6P275	Silent	SNP	ENST00000383202.2	37	CCDS3090.1																																																																																			G|0.655;A|0.344	0.344	strong		0.448	STAG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357366.1	NM_005862	
HLA-A	3105	hgsc.bcm.edu	37	6	29910801	29910801	+	Missense_Mutation	SNP	C	C	A	rs1136692	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:29910801C>A	ENST00000396634.1	+	4	682	c.341C>A	c.(340-342)gCc>gAc	p.A114D	HLA-A_ENST00000376802.2_Missense_Mutation_p.A114D|HLA-A_ENST00000376809.5_Missense_Mutation_p.A114D|HLA-A_ENST00000376806.5_Missense_Mutation_p.A114D			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	114	Alpha-1.		A -> D (in allele A*31:03).		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						CAGAGCGAGGCCGGTGAGTGA	0.682									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|||	1484	0.296326	0.2413	0.1744	5008	,	,		10398	0.3929		0.2475	False		,,,				2504	0.408				p.A114D		Atlas-SNP	.											.	HLA-A	89	.	0			c.C341A						PASS	.	A	ASP/ALA	802,3598		84,634,1482	40.0	43.0	42.0		341	-6.5	0.0	6	dbSNP_131	42	2513,6069		461,1591,2239	no	missense	HLA-A	NM_002116.7	126	545,2225,3721	AA,AC,CC		29.2822,18.2273,25.5354	benign	114/366	29910801	3315,9667	2200	4291	6491	SO:0001583	missense	3105	exon2	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	GCGAGGCCGGTGA	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.341C>A	6.37:g.29910801C>A	ENSP00000379873:p.Ala114Asp	Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	101	98	0.970297	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Missense_Mutation	SNP	ENST00000396634.1	37	CCDS34373.1	514	0.23534798534798534	95	0.19308943089430894	51	0.1408839779005525	175	0.30594405594405594	193	0.2546174142480211	.	7.188	0.590993	0.13812	0.182273	0.292822	ENSG00000206503	ENST00000396634;ENST00000376806;ENST00000376809;ENST00000355767;ENST00000376802	T;T;T;T	0.00009	9.49;9.49;9.49;9.49	3.57	-6.48	0.01896	MHC class I, alpha chain, alpha1/alpha2 (2);MHC classes I/II-like antigen recognition protein (2);MHC class I-like antigen recognition (2);	.	.	.	.	T	0.00039	0.0001	M	0.73319	2.225	0.80722	P	0.0	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.06405	0.002;0.0;0.0;0.0	T	0.14783	-1.0460	8	0.37606	T	0.19	.	7.6397	0.28286	0.3552:0.3375:0.3073:0.0	rs1136692;rs2231013;rs2308561;rs3177886;rs3179185;rs12721825;rs17433758;rs41557214	114;114;114;114	Q5SRN7;P16188;Q5SRN5;P04439	.;1A30_HUMAN;.;1A03_HUMAN	D	114	ENSP00000379873:A114D;ENSP00000366002:A114D;ENSP00000366005:A114D;ENSP00000365998:A114D	ENSP00000348012:A114D	A	+	2	0	HLA-A	30018780	0.000000	0.05858	0.002000	0.10522	0.012000	0.07955	-1.881000	0.01626	-1.395000	0.02074	-4.609000	0.00004	GCC	A|0.278;C|0.722	0.278	strong		0.682	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
TTN	7273	hgsc.bcm.edu	37	2	179479245	179479245	+	Silent	SNP	C	C	T	rs72677244	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:179479245C>T	ENST00000591111.1	-	211	44297	c.44073G>A	c.(44071-44073)gaG>gaA	p.E14691E	TTN_ENST00000359218.5_Silent_p.E7392E|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000589830.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000589487.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000589234.1_RNA|RP11-171I2.4_ENST00000605334.1_lincRNA|TTN_ENST00000342992.6_Silent_p.E13764E|TTN_ENST00000460472.2_Silent_p.E7267E|TTN_ENST00000589042.1_Silent_p.E16332E|TTN_ENST00000342175.6_Silent_p.E7459E|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000592630.1_RNA			Q8WZ42	TITIN_HUMAN	titin	14691	Ig-like 96.				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)			CATTCACAGCCTCAATGATAT	0.418													C|||	363	0.072484	0.0847	0.0231	5008	,	,		18504	0.1567		0.0209	False		,,,				2504	0.0573				p.E16332E		Atlas-SNP	.											.	TTN	18412	.	0			c.G48996A						PASS	.	C	,,,	251,3699		7,237,1731	96.0	92.0	94.0		21801,41292,22176,22377	2.9	1.0	2	dbSNP_130	94	105,8175		1,103,4036	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	,,,	8,340,5767	TT,TC,CC		1.2681,6.3544,2.9109	,,,	7267/26927,13764/33424,7392/27052,7459/27119	179479245	356,11874	1975	4140	6115	SO:0001819	synonymous_variant	7273	exon261			CACAGCCTCAATG	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.44073G>A	2.37:g.179479245C>T		Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	123	66	0.536585	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	37																																																																																				C|0.941;T|0.059	0.059	strong		0.418	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
MUC4	4585	hgsc.bcm.edu	37	3	195512343	195512343	+	Silent	SNP	G	G	A	rs113457754		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195512343G>A	ENST00000463781.3	-	2	6567	c.6108C>T	c.(6106-6108)acC>acT	p.T2036T	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Silent_p.T2036T	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.T2036T(2)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		AGGAAGTATCGGTGACAGGAA	0.567																																					p.T2036T		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,4	MUC4	1505	4	2	Substitution - coding silent(2)	stomach(2)	c.C6108T						PASS	.						29.0	25.0	26.0					3																	195512343		688	1575	2263	SO:0001819	synonymous_variant	4585	exon2			AGTATCGGTGACA	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.6108C>T	3.37:g.195512343G>A		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	95	20	0.210526	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Silent	SNP	ENST00000463781.3	37	CCDS54700.1																																																																																			G|0.500;A|0.500	0.500	weak		0.567	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
KRT84	3890	hgsc.bcm.edu	37	12	52777578	52777578	+	Missense_Mutation	SNP	C	C	T	rs386763043|rs1613931	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	116	0	0		WXS	Illumina HiSeq	Phase_I	91	46	0.505495	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	
ZNF30	90075	hgsc.bcm.edu	37	19	35435589	35435589	+	Silent	SNP	C	C	T	rs3761066	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:35435589C>T	ENST00000601142.1	+	5	1956	c.1719C>T	c.(1717-1719)tgC>tgT	p.C573C	ZNF30_ENST00000439785.1_Silent_p.C574C|ZNF30_ENST00000601957.1_3'UTR|ZNF30_ENST00000426813.2_Silent_p.C492C|ZNF30_ENST00000303586.7_Silent_p.C574C			P17039	ZNF30_HUMAN	zinc finger protein 30	573					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(3)|ovary(1)|prostate(2)	16	all_lung(56;8.38e-08)|Lung NSC(56;1.31e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0849)	GBM - Glioblastoma multiforme(1328;0.0265)		GTAAGGAATGCGGGAAGGCCT	0.393													C|||	1214	0.242412	0.2284	0.1945	5008	,	,		22802	0.3869		0.1849	False		,,,				2504	0.2055				p.C574C		Atlas-SNP	.											.	ZNF30	44	.	0			c.C1722T						PASS	.	C	,,	957,3419	324.0+/-298.4	107,743,1338	51.0	58.0	56.0		1722,1722,1719	1.0	0.2	19	dbSNP_107	56	1505,7089	277.5+/-292.9	123,1259,2915	no	coding-synonymous,coding-synonymous,coding-synonymous	ZNF30	NM_001099437.1,NM_001099438.1,NM_194325.2	,,	230,2002,4253	TT,TC,CC		17.5122,21.8693,18.9823	,,	574/625,574/625,573/624	35435589	2462,10508	2188	4297	6485	SO:0001819	synonymous_variant	90075	exon5			GGAATGCGGGAAG	X52359	CCDS46044.1, CCDS46045.1	19q13.13	2013-01-08	2006-05-10			ENSG00000168661		"""Zinc fingers, C2H2-type"", ""-"""	13090	protein-coding gene	gene with protein product			"""zinc finger protein 30 (KOX 28)"""				Standard	NM_001099437		Approved	KOX28, DKFZp686N19164, FLJ20562	uc010edq.1	P17039		ENST00000601142.1:c.1719C>T	19.37:g.35435589C>T		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	46	31	0.673913	NM_001099438	A5PLP1|A8K320|B4DIC0|Q6N068	Silent	SNP	ENST00000601142.1	37	CCDS46045.1																																																																																			C|0.747;T|0.253	0.253	strong		0.393	ZNF30-003	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464432.1	NM_194325	
CLCN2	1181	hgsc.bcm.edu	37	3	184075047	184075047	+	Silent	SNP	A	A	G	rs2228291	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:184075047A>G	ENST00000265593.4	-	9	1077	c.906T>C	c.(904-906)atT>atC	p.I302I	CLCN2_ENST00000344937.7_Silent_p.I302I|CLCN2_ENST00000475279.1_5'Flank|EIF2B5_ENST00000444495.1_Intron|CLCN2_ENST00000434054.2_Silent_p.I258I|CLCN2_ENST00000423355.2_5'UTR|CLCN2_ENST00000457512.1_Silent_p.I302I	NM_004366.5	NP_004357.3	P51788	CLCN2_HUMAN	chloride channel, voltage-sensitive 2	302					cell differentiation involved in salivary gland development (GO:0060689)|ion transmembrane transport (GO:0034220)|regulation of anion transport (GO:0044070)|retina development in camera-type eye (GO:0060041)|transmembrane transport (GO:0055085)|transport (GO:0006810)	chloride channel complex (GO:0034707)|plasma membrane (GO:0005886)	adenyl nucleotide binding (GO:0030554)|voltage-gated chloride channel activity (GO:0005247)			breast(2)|central_nervous_system(4)|endometrium(1)|kidney(3)|large_intestine(4)|lung(9)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	27	all_cancers(143;6.66e-11)|Ovarian(172;0.0339)		Epithelial(37;2.22e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)		Lubiprostone(DB01046)	AGAGGGCTGTAATAGTCTCTA	0.627													A|||	1778	0.355032	0.4735	0.4352	5008	,	,		16498	0.373		0.2356	False		,,,				2504	0.2423				p.I302I		Atlas-SNP	.											.	CLCN2	74	.	0			c.T906C						PASS	.	A	,,,	1931,2475	545.8+/-376.9	426,1079,698	51.0	56.0	54.0		906,774,906,906	-8.3	0.1	3	dbSNP_98	54	2045,6555	352.5+/-328.7	239,1567,2494	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CLCN2	NM_001171087.1,NM_001171088.1,NM_001171089.1,NM_004366.4	,,,	665,2646,3192	GG,GA,AA		23.7791,43.8266,30.5705	,,,	302/882,258/855,302/870,302/899	184075047	3976,9030	2203	4300	6503	SO:0001819	synonymous_variant	1181	exon9			GGCTGTAATAGTC	S77770	CCDS3263.1, CCDS54690.1, CCDS54691.1, CCDS54692.1	3q27.1	2013-09-19	2012-02-23		ENSG00000114859	ENSG00000114859		"""Ion channels / Chloride channels : Voltage-sensitive"""	2020	protein-coding gene	gene with protein product		600570	"""chloride channel 2"""			7795595	Standard	NM_004366		Approved	CLC2, EJM6, ClC-2	uc003foi.4	P51788	OTTHUMG00000156747	ENST00000265593.4:c.906T>C	3.37:g.184075047A>G		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	38	22	0.578947	NM_001171087	B4DQT9|B4DZ58|E9PBD9|E9PCD2|O14864|Q6IPA9|Q8WU13	Silent	SNP	ENST00000265593.4	37	CCDS3263.1																																																																																			A|0.659;G|0.341	0.341	strong		0.627	CLCN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000345571.1		
BNIPL	149428	hgsc.bcm.edu	37	1	151015564	151015564	+	Missense_Mutation	SNP	G	G	A	rs61751620	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:151015564G>A	ENST00000368931.3	+	5	722	c.566G>A	c.(565-567)cGc>cAc	p.R189H	BNIPL_ENST00000295294.7_Missense_Mutation_p.R107H	NM_138278.3	NP_612122.2	Q7Z465	BNIPL_HUMAN	BCL2/adenovirus E1B 19kD interacting protein like	189					apoptotic process (GO:0006915)|negative regulation of cell proliferation (GO:0008285)|regulation of growth rate (GO:0040009)	cytosol (GO:0005829)|nucleus (GO:0005634)	identical protein binding (GO:0042802)			autonomic_ganglia(1)|endometrium(3)|large_intestine(1)|lung(4)|skin(1)	10	Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.211)			CGGGAGCAGCGCGTAGACATG	0.493													G|||	35	0.00698882	0.0015	0.0115	5008	,	,		19426	0.0		0.0239	False		,,,				2504	0.001				p.R189H		Atlas-SNP	.											.	BNIPL	45	.	0			c.G566A						PASS	.	G	HIS/ARG,HIS/ARG	21,4385	28.1+/-56.4	0,21,2182	150.0	132.0	138.0		320,566	4.4	1.0	1	dbSNP_129	138	224,8376	93.1+/-155.1	1,222,4077	yes	missense,missense	BNIPL	NM_001159642.1,NM_138278.3	29,29	1,243,6259	AA,AG,GG		2.6047,0.4766,1.8837	probably-damaging,probably-damaging	107/276,189/358	151015564	245,12761	2203	4300	6503	SO:0001583	missense	149428	exon5			AGCAGCGCGTAGA	AF193056	CCDS978.2, CCDS53362.1	1q21.2	2008-02-05			ENSG00000163141	ENSG00000163141			16976	protein-coding gene	gene with protein product		611275				12681488, 11741952	Standard	NM_138278		Approved	BNIPl-1, BNIPL-2, PP753	uc001ewl.2	Q7Z465	OTTHUMG00000035157	ENST00000368931.3:c.566G>A	1.37:g.151015564G>A	ENSP00000357927:p.Arg189His	Somatic	207	0	0		WXS	Illumina HiSeq	Phase_I	184	98	0.532609	NM_138278	Q6DK43|Q8TCY7|Q8WYG2	Missense_Mutation	SNP	ENST00000368931.3	37	CCDS978.2	23	0.010531135531135532	1	0.0020325203252032522	5	0.013812154696132596	0	0.0	17	0.022427440633245383	G	15.19	2.760407	0.49468	0.004766	0.026047	ENSG00000163141	ENST00000368931;ENST00000361277;ENST00000295294	T;T;T	0.59502	0.96;0.96;0.26	5.3	4.39	0.52855	.	0.398705	0.26407	N	0.024547	T	0.44767	0.1309	M	0.87827	2.91	0.30896	N	0.729787	B	0.19583	0.037	B	0.15484	0.013	T	0.52034	-0.8629	10	0.54805	T	0.06	.	9.7811	0.40649	0.0953:0.0:0.9047:0.0	rs61751620	189	Q7Z465	BNIPL_HUMAN	H	189;187;107	ENSP00000357927:R189H;ENSP00000355333:R187H;ENSP00000295294:R107H	ENSP00000295294:R107H	R	+	2	0	BNIPL	149282188	0.123000	0.22298	1.000000	0.80357	0.497000	0.33675	1.183000	0.32041	1.260000	0.44134	0.505000	0.49811	CGC	G|0.985;A|0.015	0.015	strong		0.493	BNIPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085092.1	NM_138279	
USH2A	7399	hgsc.bcm.edu	37	1	215956140	215956140	+	Missense_Mutation	SNP	T	T	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:215956140T>G	ENST00000307340.3	-	53	10911	c.10525A>C	c.(10525-10527)Aaa>Caa	p.K3509Q	USH2A_ENST00000366943.2_Missense_Mutation_p.K3509Q	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	3509	Fibronectin type-III 20. {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)		TTGTCTATTTTGGTCCACGTA	0.403										HNSCC(13;0.011)																											p.K3509Q		Atlas-SNP	.											.	USH2A	1168	.	0			c.A10525C						PASS	.						99.0	94.0	95.0					1																	215956140		2203	4300	6503	SO:0001583	missense	7399	exon53			CTATTTTGGTCCA	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.10525A>C	1.37:g.215956140T>G	ENSP00000305941:p.Lys3509Gln	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	97	30	0.309278	NM_206933	Q5VVM9|Q6S362|Q9NS27	Missense_Mutation	SNP	ENST00000307340.3	37	CCDS31025.1	.	.	.	.	.	.	.	.	.	.	T	14.66	2.602549	0.46423	.	.	ENSG00000042781	ENST00000307340;ENST00000366943	T;T	0.53206	0.63;0.63	5.43	5.43	0.79202	Fibronectin, type III (3);Immunoglobulin-like fold (1);	0.313381	0.22314	U	0.061685	T	0.42359	0.1199	L	0.45137	1.4	0.23739	N	0.996979	P	0.50272	0.933	B	0.42386	0.386	T	0.35624	-0.9781	10	0.22706	T	0.39	.	15.4862	0.75569	0.0:0.0:0.0:1.0	.	3509	O75445	USH2A_HUMAN	Q	3509	ENSP00000305941:K3509Q;ENSP00000355910:K3509Q	ENSP00000305941:K3509Q	K	-	1	0	USH2A	214022763	1.000000	0.71417	0.021000	0.16686	0.401000	0.30781	3.818000	0.55678	2.063000	0.61619	0.533000	0.62120	AAA	.	.	none		0.403	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123	
LRP1	4035	hgsc.bcm.edu	37	12	57597023	57597023	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:57597023C>T	ENST00000243077.3	+	69	11237	c.10771C>T	c.(10771-10773)Cgc>Tgc	p.R3591C		NM_002332.2	NP_002323.2	Q07954	LRP1_HUMAN	low density lipoprotein receptor-related protein 1	3591	LDL-receptor class A 27. {ECO:0000255|PROSITE-ProRule:PRU00124}.				aging (GO:0007568)|aorta morphogenesis (GO:0035909)|apoptotic cell clearance (GO:0043277)|beta-amyloid clearance (GO:0097242)|cell proliferation (GO:0008283)|cholesterol metabolic process (GO:0008203)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of platelet-derived growth factor receptor-beta signaling pathway (GO:2000587)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of Wnt signaling pathway (GO:0030178)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of lipid transport (GO:0032370)|positive regulation of protein transport (GO:0051222)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|receptor-mediated endocytosis (GO:0006898)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cholesterol transport (GO:0032374)|regulation of phospholipase A2 activity (GO:0032429)|retinoid metabolic process (GO:0001523)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	apolipoprotein binding (GO:0034185)|calcium ion binding (GO:0005509)|lipoprotein particle receptor binding (GO:0070325)|lipoprotein transporter activity (GO:0042954)|poly(A) RNA binding (GO:0044822)|protein complex binding (GO:0032403)|receptor activity (GO:0004872)			NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(33)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(26)|lung(58)|ovary(10)|pancreas(2)|prostate(11)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	184				BRCA - Breast invasive adenocarcinoma(357;0.0103)	Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031)	CATCGCGGGGCGCTGGAAATG	0.672																																					p.R3591C		Atlas-SNP	.											LRP1,bladder,carcinoma,-1,1	LRP1	428	1	0			c.C10771T						PASS	.						36.0	34.0	35.0					12																	57597023		2199	4298	6497	SO:0001583	missense	4035	exon69			GCGGGGCGCTGGA	X13916	CCDS8932.1	12q13.3	2013-05-28	2010-01-26		ENSG00000123384	ENSG00000123384		"""CD molecules"", ""Low density lipoprotein receptors"""	6692	protein-coding gene	gene with protein product		107770	"""alpha-2-macroglobulin receptor"""	APR, A2MR		2548950	Standard	NM_002332		Approved	LRP, CD91, LRP1A, APOER	uc001snd.3	Q07954	OTTHUMG00000044412	ENST00000243077.3:c.10771C>T	12.37:g.57597023C>T	ENSP00000243077:p.Arg3591Cys	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	89	25	0.280899	NM_002332	Q2PP12|Q86SW0|Q8IVG8	Missense_Mutation	SNP	ENST00000243077.3	37	CCDS8932.1	.	.	.	.	.	.	.	.	.	.	C	15.80	2.939225	0.52972	.	.	ENSG00000123384	ENST00000243077;ENST00000555124	D;D	0.95656	-3.77;-3.77	5.06	4.15	0.48705	Low-density lipoprotein (LDL) receptor class A, conserved site (1);	0.151987	0.40385	N	0.001116	D	0.98197	0.9404	H	0.94658	3.565	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.98813	1.0744	10	0.59425	D	0.04	.	13.6941	0.62567	0.1557:0.8443:0.0:0.0	.	3591	Q07954	LRP1_HUMAN	C	3591;172	ENSP00000243077:R3591C;ENSP00000451012:R172C	ENSP00000243077:R3591C	R	+	1	0	LRP1	55883290	0.172000	0.23043	1.000000	0.80357	0.384000	0.30261	0.760000	0.26475	1.325000	0.45301	0.650000	0.86243	CGC	.	.	none		0.672	LRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412772.2	NM_002332	
KIAA0226L	80183	hgsc.bcm.edu	37	13	46946157	46946157	+	Missense_Mutation	SNP	C	C	T	rs1408184	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:46946157C>T	ENST00000429979.1	-	3	1058	c.454G>A	c.(454-456)Ggg>Agg	p.G152R	KIAA0226L_ENST00000378787.3_Missense_Mutation_p.G152R|KIAA0226L_ENST00000480935.1_5'Flank|KIAA0226L_ENST00000378781.3_Missense_Mutation_p.G152R|KIAA0226L_ENST00000378784.4_Missense_Mutation_p.G85R|KIAA0226L_ENST00000409879.2_Intron|KIAA0226L_ENST00000534925.1_Missense_Mutation_p.G17R|KIAA0226L_ENST00000389908.3_Missense_Mutation_p.G152R|KIAA0226L_ENST00000322896.6_Intron|KIAA0226L_ENST00000378797.2_Missense_Mutation_p.G152R|RNU2-6P_ENST00000411404.1_RNA	NM_025113.2	NP_079389.2	Q9H714	K226L_HUMAN	KIAA0226-like	152			G -> R (in dbSNP:rs1408184). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.							NS(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(7)|pancreas(1)	26						GCCAAAATCCCAGGGCTTGTG	0.512													T|||	2261	0.451478	0.5295	0.4121	5008	,	,		20853	0.5923		0.3469	False		,,,				2504	0.3364				p.G152R		Atlas-SNP	.											.	KIAA0226L	63	.	0			c.G454A						PASS	.	T	ARG/GLY	2128,2278	599.7+/-389.3	523,1082,598	69.0	68.0	68.0		454	1.0	0.0	13	dbSNP_88	68	2817,5783	675.5+/-403.2	456,1905,1939	yes	missense	KIAA0226L	NM_025113.2	125	979,2987,2537	TT,TC,CC		32.7558,48.2978,38.0209	benign	152/663	46946157	4945,8061	2203	4300	6503	SO:0001583	missense	80183	exon3			AAATCCCAGGGCT	AK025215	CCDS31970.2, CCDS66543.1, CCDS66544.1, CCDS66545.1, CCDS73569.1	13q14.11	2011-08-09	2011-08-09	2011-08-09	ENSG00000102445	ENSG00000102445			20420	protein-coding gene	gene with protein product			"""chromosome 13 open reading frame 18"""	C13orf18			Standard	NM_001286766		Approved	FLJ21562	uc010acl.3	Q9H714	OTTHUMG00000016868	ENST00000429979.1:c.454G>A	13.37:g.46946157C>T	ENSP00000396935:p.Gly152Arg	Somatic	231	0	0		WXS	Illumina HiSeq	Phase_I	167	77	0.461078	NM_025113	A8KAG9|A8XR19|B3KS87|Q5W051|Q5W053|Q6PJ74|Q6PK94|Q86XH7|Q8N5J6	Missense_Mutation	SNP	ENST00000429979.1	37	CCDS31970.2	1031	0.47206959706959706	280	0.5691056910569106	152	0.4198895027624309	341	0.5961538461538461	258	0.3403693931398417	T	7.723	0.697533	0.15106	0.482978	0.327558	ENSG00000102445	ENST00000378781;ENST00000429979;ENST00000378797;ENST00000378784;ENST00000389908;ENST00000378787;ENST00000534925;ENST00000417405;ENST00000439642	T;T;T;T;T;T;T;T;T	0.41758	0.99;1.02;0.99;1.01;1.02;0.99;1.03;1.0;0.99	5.83	0.984	0.19773	.	0.718736	0.13469	N	0.385568	T	0.00012	0.0000	N	0.00926	-1.1	0.80722	P	0.0	B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0	B;B;B;B;B	0.01281	0.0;0.0;0.0;0.0;0.0	T	0.44636	-0.9315	9	0.08837	T	0.75	-2.1112	8.5131	0.33229	0.0:0.404:0.0:0.596	rs1408184;rs3742267;rs17857288;rs52811841;rs57945176;rs1408184	152;152;152;85;152	E7EMA2;Q9H714-1;Q9H714;Q9H714-3;Q9H714-4	.;.;K226L_HUMAN;.;.	R	152;152;152;85;152;152;17;17;152	ENSP00000368057:G152R;ENSP00000396935:G152R;ENSP00000368074:G152R;ENSP00000368061:G85R;ENSP00000374558:G152R;ENSP00000368064:G152R;ENSP00000437501:G17R;ENSP00000402357:G17R;ENSP00000414579:G152R	ENSP00000368057:G152R	G	-	1	0	KIAA0226L	45844158	0.000000	0.05858	0.004000	0.12327	0.003000	0.03518	-0.213000	0.09305	0.153000	0.19213	-0.254000	0.11334	GGG	T|0.432;G|0.002	0.432	strong		0.512	KIAA0226L-204	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044809.2	NM_025113	
OTOP1	133060	hgsc.bcm.edu	37	4	4199760	4199760	+	Silent	SNP	G	G	A	rs17697262	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	146	1	0.00684932		WXS	Illumina HiSeq	Phase_I	94	41	0.43617	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	
CA6	765	hgsc.bcm.edu	37	1	9009444	9009444	+	Missense_Mutation	SNP	A	A	C	rs2274328	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:9009444A>C	ENST00000377443.2	+	2	206	c.202A>C	c.(202-204)Atg>Ctg	p.M68L	CA6_ENST00000476083.1_Intron|CA6_ENST00000377436.3_Missense_Mutation_p.M68L|CA6_ENST00000377442.2_Intron|CA6_ENST00000480186.3_Missense_Mutation_p.M68L	NM_001215.3	NP_001206.2	P23280	CAH6_HUMAN	carbonic anhydrase VI	68			M -> L (in dbSNP:rs2274328).		bicarbonate transport (GO:0015701)|detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|one-carbon metabolic process (GO:0006730)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	carbonate dehydratase activity (GO:0004089)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(2)|prostate(1)|skin(5)	16	Ovarian(185;0.112)|all_lung(157;0.143)	all_epithelial(116;1.02e-19)|all_lung(118;3.6e-06)|Lung NSC(185;7.94e-06)|Renal(390;0.000147)|Breast(348;0.00123)|Colorectal(325;0.00205)|Hepatocellular(190;0.00825)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.9e-07)|COAD - Colon adenocarcinoma(227;8.28e-05)|Kidney(185;0.000268)|KIRC - Kidney renal clear cell carcinoma(229;0.000971)|STAD - Stomach adenocarcinoma(132;0.00184)|BRCA - Breast invasive adenocarcinoma(304;0.00192)|READ - Rectum adenocarcinoma(331;0.0649)	Mafenide(DB06795)|Zonisamide(DB00909)	GGGGCTCAATATGACAGGCTA	0.607													C|||	2511	0.501398	0.5598	0.4712	5008	,	,		20063	0.4127		0.5358	False		,,,				2504	0.5				p.M68L		Atlas-SNP	.											CA6_ENST00000319474,brain,glioma,0,2	CA6	47	2	0			c.A202C						PASS	.	C	LEU/MET	2403,2003	559.0+/-380.1	666,1071,466	59.0	49.0	52.0		202	2.4	0.0	1	dbSNP_100	52	4505,4095	560.6+/-387.6	1192,2121,987	yes	missense	CA6	NM_001215.2	15	1858,3192,1453	CC,CA,AA		47.6163,45.4607,46.8861	benign	68/309	9009444	6908,6098	2203	4300	6503	SO:0001583	missense	765	exon2			CTCAATATGACAG	M57892	CCDS30578.1, CCDS57970.1, CCDS57971.1	1p36.2	2008-02-05			ENSG00000131686	ENSG00000131686	4.2.1.1	"""Carbonic anhydrases"""	1380	protein-coding gene	gene with protein product		114780				9691177	Standard	NM_001215		Approved		uc031plc.1	P23280	OTTHUMG00000001763	ENST00000377443.2:c.202A>C	1.37:g.9009444A>C	ENSP00000366662:p.Met68Leu	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	110	55	0.5	NM_001270500	E7EMQ1|Q5FBW3|Q5FC00|Q96QX8|Q9UF03	Missense_Mutation	SNP	ENST00000377443.2	37	CCDS30578.1	1079	0.49404761904761907	264	0.5365853658536586	182	0.5027624309392266	243	0.42482517482517484	390	0.5145118733509235	C	1.753	-0.488725	0.04352	0.545393	0.523837	ENSG00000131686	ENST00000319474;ENST00000377443;ENST00000377436	T;T;T	0.61859	0.07;0.07;0.07	5.32	2.4	0.29515	Carbonic anhydrase, alpha-class, catalytic domain (4);	0.080431	0.52532	N	0.000076	T	0.00012	0.0000	N	0.00138	-2.015	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.45086	-0.9285	8	.	.	.	.	4.5988	0.12343	0.3068:0.5279:0.0:0.1653	rs2274328;rs60130913;rs2274328	68	P23280	CAH6_HUMAN	L	68	ENSP00000325786:M68L;ENSP00000366662:M68L;ENSP00000366654:M68L	.	M	+	1	0	CA6	8932031	0.188000	0.23250	0.001000	0.08648	0.006000	0.05464	0.497000	0.22514	0.058000	0.16222	-0.121000	0.15023	ATG	A|0.488;C|0.511	0.511	strong		0.607	CA6-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000004911.1		
KATNB1	10300	hgsc.bcm.edu	37	16	57787027	57787027	+	Silent	SNP	C	C	T	rs12922275	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:57787027C>T	ENST00000379661.3	+	11	1286	c.894C>T	c.(892-894)taC>taT	p.Y298Y		NM_005886.2	NP_005877.2			katanin p80 (WD repeat containing) subunit B 1											cervix(1)|endometrium(3)|kidney(2)|large_intestine(1)|lung(6)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	16		all_neural(199;0.223)				TCTCCTCCTACGTGGTGGATC	0.672													C|||	504	0.100639	0.1324	0.072	5008	,	,		14456	0.0883		0.0497	False		,,,				2504	0.1431				p.Y298Y		Atlas-SNP	.											.	KATNB1	35	.	0			c.C894T						PASS	.	C		516,3850		30,456,1697	58.0	53.0	55.0		894	-4.1	1.0	16	dbSNP_121	55	444,8056		10,424,3816	no	coding-synonymous	KATNB1	NM_005886.2		40,880,5513	TT,TC,CC		5.2235,11.8186,7.4615		298/656	57787027	960,11906	2183	4250	6433	SO:0001819	synonymous_variant	10300	exon11			CTCCTACGTGGTG	AF052432	CCDS10788.1	16q12.2	2013-01-09	2003-03-13		ENSG00000140854	ENSG00000140854		"""WD repeat domain containing"""	6217	protein-coding gene	gene with protein product		602703	"""katanin p80 (WD40-containing) subunit B 1"""			9568719	Standard	XM_006721121		Approved		uc002eml.1	Q9BVA0	OTTHUMG00000133467	ENST00000379661.3:c.894C>T	16.37:g.57787027C>T		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	70	59	0.842857	NM_005886		Silent	SNP	ENST00000379661.3	37	CCDS10788.1																																																																																			C|0.918;T|0.082	0.082	strong		0.672	KATNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257343.3		
STON1	11037	hgsc.bcm.edu	37	2	48808882	48808882	+	Silent	SNP	T	T	A	rs3749144	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:48808882T>A	ENST00000406226.1	+	3	1305	c.1110T>A	c.(1108-1110)ccT>ccA	p.P370P	STON1_ENST00000309835.3_Silent_p.P370P|STON1_ENST00000404752.1_Silent_p.P370P|STON1-GTF2A1L_ENST00000394754.1_Silent_p.P370P|STON1-GTF2A1L_ENST00000309827.2_Silent_p.P370P|STON1-GTF2A1L_ENST00000402114.2_Silent_p.P370P|STON1-GTF2A1L_ENST00000394751.3_Silent_p.P370P|STON1-GTF2A1L_ENST00000405008.1_Silent_p.P370P	NM_001198595.1	NP_001185524.1	Q9Y6Q2	STON1_HUMAN	stonin 1	370	SHD. {ECO:0000255|PROSITE- ProRule:PRU00403}.				endocytosis (GO:0006897)|intracellular protein transport (GO:0006886)|regulation of endocytosis (GO:0030100)	clathrin adaptor complex (GO:0030131)				NS(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(19)|prostate(3)|skin(2)	37		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			TTCATGAACCTGACATAGAGC	0.428													A|||	1683	0.336062	0.2784	0.3112	5008	,	,		20805	0.3879		0.3201	False		,,,				2504	0.3947				p.P370P		Atlas-SNP	.											.	STON1	100	.	0			c.T1110A						PASS	.	A	,,,,	1308,3098	693.8+/-405.7	193,922,1088	68.0	68.0	68.0		1110,1110,1110,1110,1110	-4.4	0.0	2	dbSNP_107	68	2750,5850	678.0+/-403.4	457,1836,2007	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	STON1,STON1-GTF2A1L	NM_001198593.1,NM_001198594.1,NM_001198595.1,NM_006873.3,NM_172311.2	,,,,	650,2758,3095	AA,AT,TT		31.9767,29.6868,31.201	,,,,	370/1159,370/1136,370/736,370/736,370/1183	48808882	4058,8948	2203	4300	6503	SO:0001819	synonymous_variant	11037	exon3			TGAACCTGACATA	AF026169	CCDS1841.1	2p16.3	2008-02-05			ENSG00000243244	ENSG00000243244			17003	protein-coding gene	gene with protein product	"""stoned B homolog 1 (Drosophila)"""	605357				14504226, 10364255	Standard	NM_001198595		Approved	SBLF, stoned-b1		Q9Y6Q2	OTTHUMG00000129169	ENST00000406226.1:c.1110T>A	2.37:g.48808882T>A		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	196	43	0.219388	NM_001198595	A8MXJ1|B5MCF5|B7ZL16|Q96JE3|Q9BYX3	Silent	SNP	ENST00000406226.1	37	CCDS1841.1																																																																																			T|0.678;A|0.322	0.322	strong		0.428	STON1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323848.2	NM_006873	
ITGA8	8516	hgsc.bcm.edu	37	10	15649698	15649698	+	Missense_Mutation	SNP	T	T	G	rs9333269	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:15649698T>G	ENST00000378076.3	-	17	2095	c.1742A>C	c.(1741-1743)cAg>cCg	p.Q581P		NM_003638.1	NP_003629	P53708	ITA8_HUMAN	integrin, alpha 8	581			Q -> P (in dbSNP:rs9333269). {ECO:0000269|PubMed:15579315, ECO:0000269|Ref.1}.		brain development (GO:0007420)|cell projection organization (GO:0030030)|cell-matrix adhesion (GO:0007160)|establishment of protein localization (GO:0045184)|extracellular matrix organization (GO:0030198)|inner ear morphogenesis (GO:0042472)|integrin-mediated signaling pathway (GO:0007229)|kidney development (GO:0001822)|memory (GO:0007613)|mesodermal cell differentiation (GO:0048333)|metanephros development (GO:0001656)|positive regulation of transcription from RNA polymerase II promoter involved in smooth muscle cell differentiation (GO:2000721)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle tissue development (GO:0048745)|substrate adhesion-dependent cell spreading (GO:0034446)	apical part of cell (GO:0045177)|cell surface (GO:0009986)|dendritic spine membrane (GO:0032591)|endoplasmic reticulum (GO:0005783)|focal adhesion (GO:0005925)|integrin alpha8-beta1 complex (GO:0034678)|integrin complex (GO:0008305)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	metal ion binding (GO:0046872)	p.Q581P(1)		NS(2)|breast(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(57)|ovary(3)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	96						GATGAAATCCTGGCACTGGTG	0.428													T|||	163	0.0325479	0.0053	0.0591	5008	,	,		18247	0.0		0.0974	False		,,,				2504	0.0174				p.Q581P		Atlas-SNP	.											ITGA8,NS,carcinoma,0,1	ITGA8	230	1	1	Substitution - Missense(1)	stomach(1)	c.A1742C						PASS	.	T	PRO/GLN	69,4337	62.3+/-99.4	0,69,2134	214.0	223.0	220.0		1742	-2.0	0.1	10	dbSNP_119	220	777,7823	183.5+/-231.7	30,717,3553	yes	missense	ITGA8	NM_003638.1	76	30,786,5687	GG,GT,TT		9.0349,1.566,6.5047	benign	581/1064	15649698	846,12160	2203	4300	6503	SO:0001583	missense	8516	exon17			AAATCCTGGCACT	L36531	CCDS31155.1	10p13	2010-03-23			ENSG00000077943	ENSG00000077943		"""Integrins"""	6144	protein-coding gene	gene with protein product		604063				7768999	Standard	XM_005252633		Approved		uc001ioc.1	P53708	OTTHUMG00000017733	ENST00000378076.3:c.1742A>C	10.37:g.15649698T>G	ENSP00000367316:p.Gln581Pro	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	127	59	0.464567	NM_003638	B0YJ31|Q5VX94	Missense_Mutation	SNP	ENST00000378076.3	37	CCDS31155.1	108	0.04945054945054945	4	0.008130081300813009	30	0.08287292817679558	0	0.0	74	0.09762532981530343	T	8.908	0.958115	0.18507	0.01566	0.090349	ENSG00000077943	ENST00000378076;ENST00000538044	T	0.49432	0.78	5.84	-2.03	0.07365	Integrin alpha-2 (1);	0.585017	0.19111	N	0.122450	T	0.01287	0.0042	L	0.56769	1.78	0.25234	N	0.989803	P;P	0.36249	0.49;0.545	B;B	0.41646	0.247;0.362	T	0.05937	-1.0855	10	0.30854	T	0.27	.	7.9534	0.30027	0.0974:0.3569:0.0:0.5457	rs9333269;rs52803309;rs9333269	566;581	F5H818;P53708	.;ITA8_HUMAN	P	581;566	ENSP00000367316:Q581P	ENSP00000367316:Q581P	Q	-	2	0	ITGA8	15689704	0.986000	0.35501	0.136000	0.22124	0.041000	0.13682	0.007000	0.13174	-1.017000	0.03367	-1.431000	0.01090	CAG	T|0.949;G|0.051	0.051	strong		0.428	ITGA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046987.1	NM_003638	
ACBD5	91452	hgsc.bcm.edu	37	10	27508758	27508758	+	Silent	SNP	T	T	C	rs10764690	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:27508758T>C	ENST00000375888.1	-	6	610	c.546A>G	c.(544-546)ccA>ccG	p.P182P	ACBD5_ENST00000396271.3_Silent_p.P173P|ACBD5_ENST00000476758.1_5'UTR|ACBD5_ENST00000375901.1_Silent_p.P64P|ACBD5_ENST00000375897.3_Silent_p.P64P|ACBD5_ENST00000375905.4_Silent_p.P138P			Q5T8D3	ACBD5_HUMAN	acyl-CoA binding domain containing 5	182					peroxisome degradation (GO:0030242)|transport (GO:0006810)	integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)|peroxisome (GO:0005777)	fatty-acyl-CoA binding (GO:0000062)|lipid binding (GO:0008289)			breast(1)|endometrium(1)|large_intestine(3)|lung(7)|prostate(1)	13						TTTTGGCGTTTGGAGTAGAAG	0.388													T|||	1592	0.317891	0.0696	0.3905	5008	,	,		4066	0.4147		0.4652	False		,,,				2504	0.3507				p.P173P		Atlas-SNP	.											ACBD5_ENST00000396271,NS,adenoma,0,2	ACBD5	75	2	0			c.A519G						PASS	.	T	,	714,3692	297.3+/-284.7	54,606,1543	131.0	114.0	119.0		414,519	2.0	1.0	10	dbSNP_120	119	4408,4192	584.9+/-391.8	1149,2110,1041	no	coding-synonymous,coding-synonymous	ACBD5	NM_001042473.2,NM_145698.3	,	1203,2716,2584	CC,CT,TT		48.7442,16.2052,39.3818	,	138/491,173/526	27508758	5122,7884	2203	4300	6503	SO:0001819	synonymous_variant	91452	exon6			GGCGTTTGGAGTA	AF505653	CCDS7154.1, CCDS44368.1, CCDS73079.1	10p12.1	2010-04-30	2010-04-30		ENSG00000107897	ENSG00000107897			23338	protein-coding gene	gene with protein product			"""acyl-Coenzyme A binding domain containing 5"""			12056414	Standard	NR_024150		Approved	DKFZp434A2417, KIAA1996	uc010qdp.2	Q5T8D3	OTTHUMG00000017854	ENST00000375888.1:c.546A>G	10.37:g.27508758T>C		Somatic	159	1	0.00628931		WXS	Illumina HiSeq	Phase_I	114	114	1	NM_145698	B3KQ56|D3DRW0|Q5T8D4|Q5T8E1|Q5T8E2|Q86UV1|Q8N6E3|Q9UFB5	Silent	SNP	ENST00000375888.1	37																																																																																				T|0.634;C|0.366	0.366	strong		0.388	ACBD5-005	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000047314.1	NM_145698	
CCIN	881	hgsc.bcm.edu	37	9	36171092	36171092	+	Silent	SNP	G	G	A	rs61735202	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:36171092G>A	ENST00000335119.2	+	1	1704	c.1593G>A	c.(1591-1593)ggG>ggA	p.G531G		NM_005893.2	NP_005884.2	Q13939	CALI_HUMAN	calicin	531					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)				breast(3)|endometrium(2)|large_intestine(4)|liver(2)|lung(5)|ovary(1)|skin(4)	21			STAD - Stomach adenocarcinoma(86;0.228)			TTGTATGTGGGGGTGTCACCA	0.537													G|||	71	0.0141773	0.0113	0.0159	5008	,	,		20466	0.0		0.0427	False		,,,				2504	0.002				p.G531G		Atlas-SNP	.											.	CCIN	56	.	0			c.G1593A						PASS	.	G		63,4343	58.7+/-95.3	0,63,2140	127.0	101.0	110.0		1593	-4.6	0.9	9	dbSNP_129	110	273,8327	102.9+/-164.1	5,263,4032	yes	coding-synonymous	CCIN	NM_005893.2		5,326,6172	AA,AG,GG		3.1744,1.4299,2.5834		531/589	36171092	336,12670	2203	4300	6503	SO:0001819	synonymous_variant	881	exon1			ATGTGGGGGTGTC	Z46967	CCDS6599.1	9p13.1	2013-10-02			ENSG00000185972	ENSG00000185972		"""BTB/POZ domain containing"""	1568	protein-coding gene	gene with protein product		603960				7641791	Standard	NM_005893		Approved	KBTBD14, BTBD20	uc003zzb.4	Q13939	OTTHUMG00000019901	ENST00000335119.2:c.1593G>A	9.37:g.36171092G>A		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	53	22	0.415094	NM_005893	Q9BXG7	Silent	SNP	ENST00000335119.2	37	CCDS6599.1																																																																																			G|0.975;A|0.025	0.025	strong		0.537	CCIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052418.1	NM_005893	
CHRM3	1131	hgsc.bcm.edu	37	1	240070855	240070855	+	Missense_Mutation	SNP	C	C	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:240070855C>G	ENST00000255380.4	+	5	883	c.104C>G	c.(103-105)aCt>aGt	p.T35S		NM_000740.2	NP_000731.1	P20309	ACM3_HUMAN	cholinergic receptor, muscarinic 3	35					cell proliferation (GO:0008283)|cellular protein modification process (GO:0006464)|energy reserve metabolic process (GO:0006112)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|G-protein coupled receptor signaling pathway (GO:0007186)|nervous system development (GO:0007399)|positive regulation of smooth muscle contraction (GO:0045987)|regulation of insulin secretion (GO:0050796)|regulation of vascular smooth muscle contraction (GO:0003056)|saliva secretion (GO:0046541)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|smooth muscle contraction (GO:0006939)	asymmetric synapse (GO:0032279)|axon terminus (GO:0043679)|cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|drug binding (GO:0008144)|G-protein coupled acetylcholine receptor activity (GO:0016907)|phosphatidylinositol phospholipase C activity (GO:0004435)|receptor activity (GO:0004872)			breast(3)|endometrium(5)|kidney(2)|large_intestine(4)|lung(19)|ovary(4)|prostate(1)|skin(12)|upper_aerodigestive_tract(1)	51	Ovarian(103;0.127)	all_cancers(173;0.00567)|all_neural(198;0.203)	OV - Ovarian serous cystadenocarcinoma(106;0.00989)		Aclidinium(DB08897)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Anisotropine Methylbromide(DB00517)|Aripiprazole(DB01238)|Atropine(DB00572)|Brompheniramine(DB00835)|Cevimeline(DB00185)|Chlorpromazine(DB00477)|Chlorprothixene(DB01239)|Cinnarizine(DB00568)|Clozapine(DB00363)|Cryptenamine(DB00785)|Cyproheptadine(DB00434)|Darifenacin(DB00496)|Desipramine(DB01151)|Diphemanil Methylsulfate(DB00729)|Diphenidol(DB01231)|Disopyramide(DB00280)|Doxepin(DB01142)|Fesoterodine(DB06702)|Glycopyrrolate(DB00986)|Homatropine Methylbromide(DB00725)|Hyoscyamine(DB00424)|Imipramine(DB00458)|Ipratropium bromide(DB00332)|Isopropamide(DB01625)|Ketamine(DB01221)|Loxapine(DB00408)|Maprotiline(DB00934)|Mepenzolate(DB04843)|Methacholine(DB06709)|Methotrimeprazine(DB01403)|Methylscopolamine bromide(DB00462)|Metixene(DB00340)|Mivacurium(DB01226)|Nicardipine(DB00622)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Oxybutynin(DB01062)|Oxyphencyclimine(DB00383)|Pancuronium(DB01337)|Paroxetine(DB00715)|Pethidine(DB00454)|Pilocarpine(DB01085)|Pipecuronium(DB01338)|Procyclidine(DB00387)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Quetiapine(DB01224)|Scopolamine(DB00747)|Solifenacin(DB01591)|Succinylcholine(DB00202)|Tiotropium(DB01409)|Tolterodine(DB01036)|Tramadol(DB00193)|Trihexyphenidyl(DB00376)|Trimipramine(DB00726)|Tropicamide(DB00809)|Ziprasidone(DB00246)	GGAACCGTCACTCATTTCGGC	0.552																																					p.T35S		Atlas-SNP	.											.	CHRM3	118	.	0			c.C104G						PASS	.						77.0	77.0	77.0					1																	240070855		2203	4300	6503	SO:0001583	missense	1131	exon5			CCGTCACTCATTT	U29589	CCDS1616.1	1q43	2012-09-20			ENSG00000133019	ENSG00000133019		"""Cholinergic receptors"", ""GPCR / Class A : Cholinergic receptors, muscarinic"""	1952	protein-coding gene	gene with protein product	"""acetylcholine receptor, muscarinic 3"""	118494					Standard	XM_005273032		Approved		uc001hyp.3	P20309	OTTHUMG00000039649	ENST00000255380.4:c.104C>G	1.37:g.240070855C>G	ENSP00000255380:p.Thr35Ser	Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	123	32	0.260163	NM_000740	Q0VAJ8|Q4QRI3|Q5VXY2|Q9HB60	Missense_Mutation	SNP	ENST00000255380.4	37	CCDS1616.1	.	.	.	.	.	.	.	.	.	.	C	3.466	-0.108946	0.06924	.	.	ENSG00000133019	ENST00000255380;ENST00000448020	T;T	0.58210	0.35;1.64	5.6	5.6	0.85130	.	0.663883	0.14104	N	0.341213	T	0.29882	0.0747	N	0.02011	-0.69	0.09310	N	0.999999	B	0.02656	0.0	B	0.01281	0.0	T	0.06338	-1.0832	10	0.19590	T	0.45	-4.5748	18.1624	0.89712	0.0:1.0:0.0:0.0	.	35	P20309	ACM3_HUMAN	S	35	ENSP00000255380:T35S;ENSP00000404764:T35S	ENSP00000255380:T35S	T	+	2	0	CHRM3	238137478	0.026000	0.19158	0.441000	0.26858	0.202000	0.24057	2.791000	0.47829	2.788000	0.95919	0.650000	0.86243	ACT	.	.	none		0.552	CHRM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095644.2	NM_000740	
CCPG1	9236	hgsc.bcm.edu	37	15	55653031	55653031	+	Silent	SNP	A	A	G	rs501231	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:55653031A>G	ENST00000310958.6	-	8	1238	c.940T>C	c.(940-942)Ttg>Ctg	p.L314L	DYX1C1-CCPG1_ENST00000565113.1_RNA|CCPG1_ENST00000569205.1_Silent_p.L314L|CCPG1_ENST00000442196.3_Silent_p.L314L|CCPG1_ENST00000425574.3_Intron	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	314					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)		p.L314L(1)		autonomic_ganglia(1)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(8)|lung(10)|ovary(1)|stomach(3)	30				all cancers(107;0.0354)		TCCTTCTCCAAGGATACTCTT	0.358													G|||	2281	0.455471	0.6672	0.3329	5008	,	,		18212	0.256		0.5209	False		,,,				2504	0.3947				p.L314L		Atlas-SNP	.											CCPG1,NS,carcinoma,0,1	CCPG1	74	1	1	Substitution - coding silent(1)	stomach(1)	c.T940C						PASS	.	G	,,,	2419,1217		786,847,185	88.0	82.0	84.0		940,,940,940	4.8	1.0	15	dbSNP_83	84	4166,3990		1078,2010,990	no	coding-synonymous,intron,coding-synonymous,coding-synonymous	CCPG1	NM_001204450.1,NM_001204451.1,NM_004748.4,NM_020739.3	,,,	1864,2857,1175	GG,GA,AA		48.921,33.4708,44.1571	,,,	314/808,,314/758,314/758	55653031	6585,5207	1818	4078	5896	SO:0001819	synonymous_variant	9236	exon8			TCTCCAAGGATAC	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.940T>C	15.37:g.55653031A>G		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	122	61	0.5	NM_020739	A0PJH3|A8K9T0|O14712|Q05DG4|Q5U5S7|Q8IYV8|Q9BY53|Q9HA17	Silent	SNP	ENST00000310958.6	37	CCDS42039.1																																																																																			A|0.518;G|0.482	0.482	strong		0.358	CCPG1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000419850.1	NM_004748	
OAF	220323	hgsc.bcm.edu	37	11	120099791	120099791	+	Silent	SNP	C	C	T	rs2465654	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	138	0	0		WXS	Illumina HiSeq	Phase_I	99	75	0.757576	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	
PMS1	5378	hgsc.bcm.edu	37	2	190728798	190728798	+	Missense_Mutation	SNP	A	A	G	rs201205478		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:190728798A>G	ENST00000441310.2	+	10	2419	c.2186A>G	c.(2185-2187)aAt>aGt	p.N729S	PMS1_ENST00000421722.1_3'UTR|PMS1_ENST00000409823.3_Missense_Mutation_p.N690S|PMS1_ENST00000432292.3_Missense_Mutation_p.N553S|PMS1_ENST00000447232.2_Intron|PMS1_ENST00000418224.3_Missense_Mutation_p.N553S	NM_000534.4	NP_000525.1	P54277	PMS1_HUMAN	PMS1 postmeiotic segregation increased 1 (S. cerevisiae)	729					ATP catabolic process (GO:0006200)|mismatch repair (GO:0006298)|response to drug (GO:0042493)	MutLalpha complex (GO:0032389)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|mismatched DNA binding (GO:0030983)|single-stranded DNA binding (GO:0003697)			breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(5)|lung(16)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	36			OV - Ovarian serous cystadenocarcinoma(117;0.0013)|Epithelial(96;0.0263)|all cancers(119;0.0751)			TTGATCCACAATCTCAGGTTT	0.333			"""Mis, N"""			"""colorectal, endometrial, ovarian"""		Direct reversal of damage;Mismatch excision repair (MMR)																													p.N729S		Atlas-SNP	.	yes	Rec		Hereditary non-polyposis colorectal cancer	2	2q31-q33	5378	PMS1 postmeiotic segregation increased 1 (S. cerevisiae)		E	.	PMS1	78	.	0			c.A2186G						PASS	.	A	SER/ASN,SER/ASN,	0,4406		0,0,2203	113.0	122.0	119.0		2186,2069,	3.1	1.0	2		119	2,8598	2.2+/-6.3	0,2,4298	yes	missense,missense,intron	PMS1	NM_000534.4,NM_001128143.1,NM_001128144.1	46,46,	0,2,6501	GG,GA,AA		0.0233,0.0,0.0154	benign,benign,	729/933,690/894,	190728798	2,13004	2203	4300	6503	SO:0001583	missense	5378	exon10			TCCACAATCTCAG		CCDS2302.1, CCDS46473.1, CCDS46474.1, CCDS74615.1	2q31-q33	2014-09-17	2001-11-28		ENSG00000064933	ENSG00000064933			9121	protein-coding gene	gene with protein product		600258	"""postmeiotic segregation increased (S. cerevisiae) 1"""	PMSL1		8072530	Standard	NM_000534		Approved		uc002urh.4	P54277	OTTHUMG00000132664	ENST00000441310.2:c.2186A>G	2.37:g.190728798A>G	ENSP00000406490:p.Asn729Ser	Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	186	85	0.456989	NM_000534	D3DPI1|Q4VAL4|Q5FBZ3|Q5FBZ6|Q5FBZ8	Missense_Mutation	SNP	ENST00000441310.2	37	CCDS2302.1	.	.	.	.	.	.	.	.	.	.	A	9.300	1.052870	0.19907	0.0	2.33E-4	ENSG00000064933	ENST00000392338;ENST00000441310;ENST00000418224;ENST00000409823;ENST00000432292;ENST00000424307;ENST00000452382	T;T;T;T;D;T	0.85955	2.0;2.0;2.0;2.0;-2.05;2.02	5.45	3.11	0.35812	.	0.489617	0.25535	N	0.030017	T	0.64338	0.2589	N	0.04043	-0.29	0.19300	N	0.999974	B;B;B	0.06786	0.0;0.001;0.0	B;B;B	0.04013	0.0;0.001;0.0	T	0.52449	-0.8574	10	0.36615	T	0.2	-11.736	4.1444	0.10209	0.6036:0.0:0.2516:0.1448	.	729;690;729	Q4VAL4;Q5FBZ3;P54277	.;.;PMS1_HUMAN	S	553;729;553;690;553;668;117	ENSP00000406490:N729S;ENSP00000404492:N553S;ENSP00000387125:N690S;ENSP00000398378:N553S;ENSP00000389938:N668S;ENSP00000396232:N117S	ENSP00000376149:N553S	N	+	2	0	PMS1	190437043	0.996000	0.38824	1.000000	0.80357	0.975000	0.68041	0.494000	0.22467	0.528000	0.28580	0.524000	0.50904	AAT	.	.	weak		0.333	PMS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255918.2		
POM121L12	285877	hgsc.bcm.edu	37	7	53103371	53103371	+	Missense_Mutation	SNP	G	G	T	rs72598684	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:53103371G>T	ENST00000408890.4	+	1	23	c.7G>T	c.(7-9)Gct>Tct	p.A3S		NM_182595.3	NP_872401.3	Q8N7R1	P1L12_HUMAN	POM121 transmembrane nucleoporin-like 12	3										endometrium(5)|kidney(1)|large_intestine(5)|lung(44)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	61						AGCCATGGGCGCTGCAGCTCC	0.706													G|||	1509	0.301318	0.1377	0.2334	5008	,	,		13585	0.4315		0.2833	False		,,,				2504	0.455				p.A3S		Atlas-SNP	.											.	POM121L12	146	.	0			c.G7T						PASS	.	G	SER/ALA	555,3451		48,459,1496	6.0	9.0	8.0		7	-0.3	0.0	7	dbSNP_130	8	1999,6175		239,1521,2327	no	missense	POM121L12	NM_182595.3	99	287,1980,3823	TT,TG,GG		24.4556,13.8542,20.9688	benign	3/297	53103371	2554,9626	2003	4087	6090	SO:0001583	missense	285877	exon1			ATGGGCGCTGCAG		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.7G>T	7.37:g.53103371G>T	ENSP00000386133:p.Ala3Ser	Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	48	24	0.5	NM_182595	Q8NDI9	Missense_Mutation	SNP	ENST00000408890.4	37	CCDS43584.1	624	0.2857142857142857	70	0.14227642276422764	94	0.2596685082872928	250	0.4370629370629371	210	0.2770448548812665	G	9.531	1.110853	0.20714	0.138542	0.244556	ENSG00000221900	ENST00000408890	T	0.29397	1.57	1.66	-0.285	0.12866	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	D	0.59357	0.985	P	0.55824	0.785	T	0.43637	-0.9379	8	0.41790	T	0.15	.	4.0677	0.09868	0.421:0.0:0.579:0.0	.	3	Q8N7R1	P1L12_HUMAN	S	3	ENSP00000386133:A3S	ENSP00000386133:A3S	A	+	1	0	POM121L12	53070865	0.000000	0.05858	0.003000	0.11579	0.008000	0.06430	-1.106000	0.03319	-0.090000	0.12462	0.462000	0.41574	GCT	G|0.715;T|0.285	0.285	strong		0.706	POM121L12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342656.1	NM_182595	
EPS8L2	64787	hgsc.bcm.edu	37	11	720197	720197	+	Silent	SNP	C	C	T	rs3087546	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:720197C>T	ENST00000533256.1	+	6	676	c.301C>T	c.(301-303)Ctg>Ttg	p.L101L	EPS8L2_ENST00000530636.1_Silent_p.L101L|EPS8L2_ENST00000526198.1_Silent_p.L101L|EPS8L2_ENST00000318562.8_Silent_p.L101L|AP006621.9_ENST00000527021.2_RNA			Q9H6S3	ES8L2_HUMAN	EPS8-like 2	101	PID. {ECO:0000255|PROSITE- ProRule:PRU00148}.				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)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|ruffle membrane (GO:0032587)|vesicle (GO:0031982)	actin binding (GO:0003779)			NS(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(2)|pancreas(1)|prostate(2)|soft_tissue(1)|urinary_tract(1)	13		all_cancers(49;1.24e-08)|all_epithelial(84;1.87e-05)|Breast(177;0.000286)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.106)|all_lung(207;0.136)		all cancers(45;4.37e-27)|Epithelial(43;2.81e-26)|OV - Ovarian serous cystadenocarcinoma(40;1.33e-20)|BRCA - Breast invasive adenocarcinoma(625;4.29e-05)|Lung(200;0.0582)|LUSC - Lung squamous cell carcinoma(625;0.0703)		CGACCAGTCGCTGCGGCTGCT	0.657													C|||	2463	0.491813	0.5651	0.647	5008	,	,		17050	0.2222		0.5457	False		,,,				2504	0.5051				p.L101L		Atlas-SNP	.											EPS8L2,rectum,carcinoma,0,1	EPS8L2	42	1	0			c.C301T						PASS	.	C		2361,2045	601.6+/-389.7	622,1117,464	58.0	49.0	52.0		301	0.3	0.4	11	dbSNP_102	52	5037,3563	623.5+/-397.5	1480,2077,743	no	coding-synonymous	EPS8L2	NM_022772.3		2102,3194,1207	TT,TC,CC		41.4302,46.414,43.1186		101/716	720197	7398,5608	2203	4300	6503	SO:0001819	synonymous_variant	64787	exon5			CAGTCGCTGCGGC	AF318331	CCDS31328.1	11p15.5	2008-02-05				ENSG00000177106			21296	protein-coding gene	gene with protein product		614988				12620401	Standard	NM_022772		Approved	FLJ21935, FLJ22171, MGC3088	uc001lqt.3	Q9H6S3		ENST00000533256.1:c.301C>T	11.37:g.720197C>T		Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	202	45	0.222772	NM_022772	B3KSX1|B7ZKL3|Q53GM8|Q8WYW7|Q96K06|Q9H6K9	Silent	SNP	ENST00000533256.1	37	CCDS31328.1																																																																																			C|0.473;T|0.527	0.527	strong		0.657	EPS8L2-003	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382344.1	NM_022772	
SGK2	10110	hgsc.bcm.edu	37	20	42199296	42199296	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:42199296C>T	ENST00000341458.4	+	6	799	c.580C>T	c.(580-582)Ccc>Tcc	p.P194S	SGK2_ENST00000423407.3_Missense_Mutation_p.P134S|SGK2_ENST00000485914.1_3'UTR|SGK2_ENST00000426287.1_Missense_Mutation_p.P160S|SGK2_ENST00000373100.1_Missense_Mutation_p.P134S|SGK2_ENST00000373077.1_Missense_Mutation_p.P133S|SGK2_ENST00000373092.3_Missense_Mutation_p.P134S	NM_016276.3	NP_057360.2	Q9HBY8	SGK2_HUMAN	serum/glucocorticoid regulated kinase 2	194	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				intracellular signal transduction (GO:0035556)|ion transmembrane transport (GO:0034220)|positive regulation of transporter activity (GO:0032411)|protein phosphorylation (GO:0006468)|regulation of cell growth (GO:0001558)|regulation of cell proliferation (GO:0042127)|response to oxidative stress (GO:0006979)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|potassium channel regulator activity (GO:0015459)|protein serine/threonine kinase activity (GO:0004674)|sodium channel regulator activity (GO:0017080)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(11)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27		Myeloproliferative disorder(115;0.00452)	COAD - Colon adenocarcinoma(18;0.0031)			GTTCCTGGAGCCCCGGGCCAG	0.627																																					p.P194S		Atlas-SNP	.											.	SGK2	50	.	0			c.C580T						PASS	.						59.0	61.0	61.0					20																	42199296		2203	4300	6503	SO:0001583	missense	10110	exon6			CTGGAGCCCCGGG	AF169034	CCDS13320.1, CCDS13321.1	20q13.2	2008-07-04			ENSG00000101049	ENSG00000101049			13900	protein-coding gene	gene with protein product		607589				10548550	Standard	NM_016276		Approved		uc002xkv.3	Q9HBY8	OTTHUMG00000033054	ENST00000341458.4:c.580C>T	20.37:g.42199296C>T	ENSP00000340608:p.Pro194Ser	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	87	4	0.045977	NM_016276	Q52PK5|Q5H8Y6|Q5H8Z1|Q5TZR3|Q9UKG6	Missense_Mutation	SNP	ENST00000341458.4	37	CCDS13320.1	.	.	.	.	.	.	.	.	.	.	C	15.50	2.852794	0.51270	.	.	ENSG00000101049	ENST00000373100;ENST00000373092;ENST00000373077;ENST00000412111;ENST00000423407;ENST00000341458;ENST00000426287	T;T;T;T;T;T;T	0.63913	-0.07;-0.07;-0.07;-0.07;-0.07;-0.07;-0.07	4.92	4.92	0.64577	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.047564	0.85682	N	0.000000	T	0.48114	0.1482	N	0.17764	0.52	0.80722	D	1	B;B;P	0.37015	0.181;0.241;0.578	B;B;B	0.35971	0.049;0.143;0.215	T	0.44559	-0.9320	10	0.24483	T	0.36	.	17.7648	0.88475	0.0:1.0:0.0:0.0	.	160;194;134	Q9HBY8-3;Q9HBY8;Q9HBY8-2	.;SGK2_HUMAN;.	S	134;134;133;133;134;194;160	ENSP00000362192:P134S;ENSP00000362184:P134S;ENSP00000362168:P133S;ENSP00000396222:P133S;ENSP00000392795:P134S;ENSP00000340608:P194S;ENSP00000412214:P160S	ENSP00000340608:P194S	P	+	1	0	SGK2	41632710	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	7.643000	0.83403	2.658000	0.90341	0.655000	0.94253	CCC	.	.	none		0.627	SGK2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080383.1		
TTC21B	79809	hgsc.bcm.edu	37	2	166771842	166771842	+	Silent	SNP	A	A	G	rs138449110		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:166771842A>G	ENST00000243344.7	-	15	2144	c.2007T>C	c.(2005-2007)gaT>gaC	p.D669D		NM_024753.4	NP_079029.3	Q7Z4L5	TT21B_HUMAN	tetratricopeptide repeat domain 21B	669				D -> G (in Ref. 4; BAB71404). {ECO:0000305}.	forebrain dorsal/ventral pattern formation (GO:0021798)|intraciliary retrograde transport (GO:0035721)|intraciliary transport involved in cilium morphogenesis (GO:0035735)|protein localization to cilium (GO:0061512)|regulation of smoothened signaling pathway (GO:0008589)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|smoothened signaling pathway (GO:0007224)|ventricular system development (GO:0021591)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|intraciliary transport particle A (GO:0030991)|nuclear chromatin (GO:0000790)				breast(2)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(9)|lung(28)|ovary(2)|pancreas(2)|skin(2)|urinary_tract(1)	58						CCCGTTCAATATCTCCTTGGG	0.413																																					p.D669D		Atlas-SNP	.											.	TTC21B	130	.	0			c.T2007C						PASS	.	A		0,4406		0,0,2203	153.0	154.0	154.0		2007	0.6	0.6	2	dbSNP_134	154	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	TTC21B	NM_024753.3		0,2,6501	GG,GA,AA		0.0233,0.0,0.0154		669/1317	166771842	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	79809	exon15			TTCAATATCTCCT	AB082523	CCDS33315.1	2q24.3	2014-09-04			ENSG00000123607	ENSG00000123607		"""Tetratricopeptide (TTC) repeat domain containing"", ""Intraflagellar transport homologs"""	25660	protein-coding gene	gene with protein product		612014				12056414, 21258341	Standard	NM_024753		Approved	FLJ11457, JBTS11, NPHP12, IFT139, THM1	uc002udk.3	Q7Z4L5	OTTHUMG00000154083	ENST00000243344.7:c.2007T>C	2.37:g.166771842A>G		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	86	37	0.430233	NM_024753	A8MUZ3|Q3LIE4|Q53T84|Q6P4A1|Q6PIF5|Q8NCN3|Q96MA4|Q9HAK8	Silent	SNP	ENST00000243344.7	37	CCDS33315.1																																																																																			A|1.000;G|0.000	0.000	weak		0.413	TTC21B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333770.1	NM_024753	
ARHGAP21	57584	hgsc.bcm.edu	37	10	24889664	24889664	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:24889664C>T	ENST00000396432.2	-	14	3529	c.3043G>A	c.(3043-3045)Gac>Aac	p.D1015N	ARHGAP21_ENST00000320481.6_Missense_Mutation_p.D802N|ARHGAP21_ENST00000493154.1_5'UTR	NM_020824.3	NP_065875.3	Q5T5U3	RHG21_HUMAN	Rho GTPase activating protein 21	1014	Interaction with ARF1 and ARF6.|PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				establishment of Golgi localization (GO:0051683)|Golgi organization (GO:0007030)|maintenance of Golgi location (GO:0051684)|organelle transport along microtubule (GO:0072384)|signal transduction (GO:0007165)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)			NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(11)|kidney(4)|large_intestine(17)|lung(21)|ovary(7)|pancreas(1)|prostate(5)|skin(2)|stomach(2)|urinary_tract(1)	78						CATTCACAGTCGGACGTGGTG	0.478																																					p.D1015N		Atlas-SNP	.											.	ARHGAP21	185	.	0			c.G3043A						PASS	.						118.0	112.0	114.0					10																	24889664		2203	4298	6501	SO:0001583	missense	57584	exon14			CACAGTCGGACGT	AF480466	CCDS7144.2	10p12.31	2013-01-10			ENSG00000107863	ENSG00000107863		"""Rho GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"""	23725	protein-coding gene	gene with protein product		609870				12056806	Standard	NM_020824		Approved	KIAA1424, ARHGAP10	uc001isb.2	Q5T5U3	OTTHUMG00000017825	ENST00000396432.2:c.3043G>A	10.37:g.24889664C>T	ENSP00000379709:p.Asp1015Asn	Somatic	214	0	0		WXS	Illumina HiSeq	Phase_I	194	38	0.195876	NM_020824	Q0VF98|Q7Z3P7|Q8N3A2|Q8NI19|Q8TBV5|Q9P2C3	Missense_Mutation	SNP	ENST00000396432.2	37	CCDS7144.2	.	.	.	.	.	.	.	.	.	.	C	23.5	4.427131	0.83667	.	.	ENSG00000107863	ENST00000396432;ENST00000320481;ENST00000376410;ENST00000446003;ENST00000445703	T;T;T;T	0.80033	-1.33;-1.33;-1.33;-1.33	6.02	6.02	0.97574	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.000000	0.85682	D	0.000000	D	0.86961	0.6059	L	0.39467	1.215	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.995;1.0	D	0.86018	0.1505	10	0.52906	T	0.07	.	20.5407	0.99260	0.0:1.0:0.0:0.0	.	1005;1014	F8W9U9;Q5T5U3	.;RHG21_HUMAN	N	1015;802;1005;1015;850	ENSP00000379709:D1015N;ENSP00000365604:D802N;ENSP00000365592:D1005N;ENSP00000405018:D1015N	ENSP00000365604:D802N	D	-	1	0	ARHGAP21	24929670	1.000000	0.71417	0.892000	0.35008	0.258000	0.26162	7.767000	0.85331	2.865000	0.98341	0.655000	0.94253	GAC	.	.	none		0.478	ARHGAP21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047229.4	NM_020824	
MYBBP1A	10514	hgsc.bcm.edu	37	17	4446457	4446457	+	Silent	SNP	G	G	A	rs751670	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:4446457G>A	ENST00000254718.4	-	20	2949	c.2643C>T	c.(2641-2643)caC>caT	p.H881H	MYBBP1A_ENST00000381556.2_Silent_p.H881H			Q9BQG0	MBB1A_HUMAN	MYB binding protein (P160) 1a	881					cellular response to glucose starvation (GO:0042149)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleocytoplasmic transport (GO:0006913)|osteoblast differentiation (GO:0001649)|positive regulation of cell cycle arrest (GO:0071158)|regulation of transcription, DNA-templated (GO:0006355)|respiratory electron transport chain (GO:0022904)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|NLS-dependent protein nuclear import complex (GO:0042564)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA-directed DNA polymerase activity (GO:0003887)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding (GO:0043565)|transcription factor binding (GO:0008134)			breast(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(7)|ovary(3)|prostate(2)|skin(2)|stomach(1)	24						GGCACAGGTGGTGCCTGTGGG	0.657													G|||	1165	0.232628	0.0234	0.2061	5008	,	,		17316	0.5496		0.1571	False		,,,				2504	0.2853				p.H881H		Atlas-SNP	.											.	MYBBP1A	69	.	0			c.C2643T						PASS	.	G	,	207,4189		10,187,2001	14.0	16.0	15.0		2643,2643	-4.4	0.5	17	dbSNP_86	15	1333,7223		117,1099,3062	no	coding-synonymous,coding-synonymous	MYBBP1A	NM_001105538.1,NM_014520.3	,	127,1286,5063	AA,AG,GG		15.5797,4.7088,11.8901	,	881/1333,881/1329	4446457	1540,11412	2198	4278	6476	SO:0001819	synonymous_variant	10514	exon20			CAGGTGGTGCCTG	AF147709	CCDS11046.1, CCDS42238.1	17p13.3	2008-07-18			ENSG00000132382	ENSG00000132382			7546	protein-coding gene	gene with protein product	"""p53-activated protein-2"""	604885				10644447	Standard	NM_014520		Approved	P160, PAP2, FLJ37886	uc002fxz.4	Q9BQG0	OTTHUMG00000090747	ENST00000254718.4:c.2643C>T	17.37:g.4446457G>A		Somatic	6	0	0		WXS	Illumina HiSeq	Phase_I	5	5	1	NM_014520	Q86VM3|Q9BW49|Q9P0V5|Q9UF99	Silent	SNP	ENST00000254718.4	37	CCDS11046.1																																																																																			G|0.812;A|0.188	0.188	strong		0.657	MYBBP1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000207488.2	NM_014520	
KRTAP4-6	81871	hgsc.bcm.edu	37	17	39296167	39296167	+	Silent	SNP	A	A	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:39296167A>G	ENST00000345847.4	-	1	572	c.573T>C	c.(571-573)atT>atC	p.I191I		NM_030976.1	NP_112238.1	Q9BYQ5	KRA46_HUMAN	keratin associated protein 4-6	191						keratin filament (GO:0045095)				endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|lung(1)|prostate(1)|urinary_tract(1)	9						GGCAGGTGGAAATGACACAGG	0.627																																					p.I191I		Atlas-SNP	.											KRTAP4-6,bladder,carcinoma,0,9	KRTAP4-6	46	9	0			c.T573C						scavenged	.																																			SO:0001819	synonymous_variant	81871	exon1			GGTGGAAATGACA	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.573T>C	17.37:g.39296167A>G		Somatic	122	1	0.00819672		WXS	Illumina HiSeq	Phase_I	132	5	0.0378788	NM_030976	Q9BYR1	Silent	SNP	ENST00000345847.4	37	CCDS54125.1																																																																																			.	.	none		0.627	KRTAP4-6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257779.1		
CROCC	9696	hgsc.bcm.edu	37	1	17265507	17265507	+	Missense_Mutation	SNP	C	C	T	rs201951425	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:17265507C>T	ENST00000375541.5	+	12	1547	c.1478C>T	c.(1477-1479)cCg>cTg	p.P493L	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)		CAGCGGACCCCGTCCCCACCG	0.736																																					p.P493L		Atlas-SNP	.											CROCC,NS,carcinoma,0,1	CROCC	185	1	0			c.C1478T						scavenged	.	C	LEU/PRO	55,4215		0,55,2080	11.0	11.0	11.0		1478	5.4	1.0	1	dbSNP_134	11	247,8075		0,247,3914	no	missense	CROCC	NM_014675.3	98	0,302,5994	TT,TC,CC		2.968,1.2881,2.3983	probably-damaging	493/2018	17265507	302,12290	2135	4161	6296	SO:0001583	missense	9696	exon12			GGACCCCGTCCCC	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.1478C>T	1.37:g.17265507C>T	ENSP00000364691:p.Pro493Leu	Somatic	3	0	0		WXS	Illumina HiSeq	Phase_I	9	5	0.555556	NM_014675		Missense_Mutation	SNP	ENST00000375541.5	37	CCDS30616.1	36	0.016483516483516484	9	0.018292682926829267	7	0.019337016574585635	0	0.0	20	0.026385224274406333	C	15.49	2.847709	0.51164	0.012881	0.02968	ENSG00000058453	ENST00000375541;ENST00000445545	T	0.11385	2.78	5.39	5.39	0.77823	.	.	.	.	.	T	0.08268	0.0206	L	0.55481	1.735	0.50813	D	0.99989	D;P;D	0.65815	0.981;0.803;0.995	B;B;P	0.59115	0.421;0.095;0.852	T	0.00200	-1.1927	9	0.27785	T	0.31	.	14.606	0.68478	0.0:0.8534:0.1466:0.0	.	356;356;493	A1L0S8;A1L0S9;Q5TZA2	.;.;CROCC_HUMAN	L	493;374	ENSP00000364691:P493L	ENSP00000364691:P493L	P	+	2	0	CROCC	17138094	0.934000	0.31675	0.991000	0.47740	0.293000	0.27360	5.113000	0.64640	2.702000	0.92279	0.561000	0.74099	CCG	C|0.983;T|0.017	0.017	strong		0.736	CROCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006249.2	NM_014675	
SYNE1	23345	hgsc.bcm.edu	37	6	152671865	152671865	+	Missense_Mutation	SNP	T	T	G	rs13210127	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:152671865T>G	ENST00000367255.5	-	71	12222	c.11621A>C	c.(11620-11622)aAg>aCg	p.K3874T	SYNE1_ENST00000265368.4_Missense_Mutation_p.K3874T|SYNE1_ENST00000448038.1_Missense_Mutation_p.K3859T|SYNE1_ENST00000423061.1_Missense_Mutation_p.K3859T|SYNE1_ENST00000341594.5_Missense_Mutation_p.K3798T	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	3874			K -> T (in dbSNP:rs13210127).		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)		TCTCACTGACTTTACTGATGG	0.418										HNSCC(10;0.0054)			T|||	272	0.0543131	0.0159	0.0216	5008	,	,		18027	0.1359		0.0139	False		,,,				2504	0.0869				p.K3874T		Atlas-SNP	.											.	SYNE1	3227	.	0			c.A11621C						PASS	.	T	THR/LYS,THR/LYS	33,4373	38.4+/-70.7	0,33,2170	193.0	179.0	184.0		11576,11621	2.3	0.4	6	dbSNP_121	184	173,8427	80.1+/-142.7	2,169,4129	yes	missense,missense	SYNE1	NM_033071.3,NM_182961.3	78,78	2,202,6299	GG,GT,TT		2.0116,0.749,1.5839	benign,benign	3859/8750,3874/8798	152671865	206,12800	2203	4300	6503	SO:0001583	missense	23345	exon71			ACTGACTTTACTG	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.11621A>C	6.37:g.152671865T>G	ENSP00000356224:p.Lys3874Thr	Somatic	299	0	0		WXS	Illumina HiSeq	Phase_I	161	110	0.68323	NM_182961	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Missense_Mutation	SNP	ENST00000367255.5	37	CCDS5236.2	130	0.05952380952380952	7	0.014227642276422764	11	0.03038674033149171	101	0.17657342657342656	11	0.014511873350923483	T	12.12	1.842220	0.32513	0.00749	0.020116	ENSG00000131018	ENST00000367255;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594	T;T;T;T;T	0.36157	1.3;1.3;1.3;1.3;1.27	6.03	2.3	0.28687	.	0.504604	0.19609	N	0.110200	T	0.10294	0.0252	L	0.31065	0.9	0.09310	P	1.0	B;B;B;B	0.20988	0.05;0.05;0.05;0.019	B;B;B;B	0.24269	0.052;0.052;0.052;0.022	T	0.12863	-1.0531	9	0.37606	T	0.19	.	7.2625	0.26212	0.0:0.1281:0.1228:0.7491	rs13210127;rs52813805;rs59972232;rs13210127	3874;3874;3874;3859	B7ZBC3;Q8NF91;E7EQI5;Q8NF91-4	.;SYNE1_HUMAN;.;.	T	3874;3859;3874;3859;3798	ENSP00000356224:K3874T;ENSP00000396024:K3859T;ENSP00000265368:K3874T;ENSP00000390975:K3859T;ENSP00000341887:K3798T	ENSP00000265368:K3874T	K	-	2	0	SYNE1	152713558	0.868000	0.29978	0.377000	0.26055	0.944000	0.59088	0.452000	0.21795	0.158000	0.19367	0.533000	0.62120	AAG	T|0.963;G|0.037	0.037	strong		0.418	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961	
OTOP1	133060	hgsc.bcm.edu	37	4	4199261	4199261	+	Missense_Mutation	SNP	C	C	T	rs11736799	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:4199261C>T	ENST00000296358.4	-	5	1324	c.1300G>A	c.(1300-1302)Gtg>Atg	p.V434M		NM_177998.1	NP_819056.1	Q7RTM1	OTOP1_HUMAN	otopetrin 1	434			V -> M (in dbSNP:rs11736799).		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)		TACTTCTCCACGATCGCCAGG	0.547													C|||	77	0.0153754	0.0008	0.0202	5008	,	,		18403	0.0		0.0328	False		,,,				2504	0.0297				p.V434M		Atlas-SNP	.											.	OTOP1	118	.	0			c.G1300A						PASS	.	C	MET/VAL	24,4382	29.9+/-59.1	0,24,2179	64.0	67.0	66.0		1300	0.3	0.0	4	dbSNP_120	66	292,8308	106.6+/-167.4	2,288,4010	no	missense	OTOP1	NM_177998.1	21	2,312,6189	TT,TC,CC		3.3953,0.5447,2.4296	possibly-damaging	434/613	4199261	316,12690	2203	4300	6503	SO:0001583	missense	133060	exon5			TCTCCACGATCGC	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.1300G>A	4.37:g.4199261C>T	ENSP00000296358:p.Val434Met	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	68	33	0.485294	NM_177998	A1L476	Missense_Mutation	SNP	ENST00000296358.4	37	CCDS3372.1	31	0.014194139194139194	0	0.0	10	0.027624309392265192	0	0.0	21	0.027704485488126648	C	9.089	1.001247	0.19121	0.005447	0.033953	ENSG00000163982	ENST00000296358	T	0.26810	1.71	4.76	0.289	0.15723	.	0.562723	0.18293	N	0.145644	T	0.08358	0.0208	L	0.46157	1.445	0.09310	N	1	D	0.56968	0.978	P	0.47075	0.536	T	0.05903	-1.0857	10	0.48119	T	0.1	-1.6525	6.6074	0.22734	0.0:0.2043:0.5397:0.256	rs11736799;rs11736799	434	Q7RTM1	OTOP1_HUMAN	M	434	ENSP00000296358:V434M	ENSP00000296358:V434M	V	-	1	0	OTOP1	4250162	0.000000	0.05858	0.000000	0.03702	0.209000	0.24338	0.315000	0.19451	0.148000	0.19059	0.195000	0.17529	GTG	C|0.980;T|0.020	0.020	strong		0.547	OTOP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206661.2	NM_177998	
IQCE	23288	hgsc.bcm.edu	37	7	2649686	2649686	+	Missense_Mutation	SNP	C	C	T	rs368687600		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:2649686C>T	ENST00000402050.2	+	22	2162	c.1978C>T	c.(1978-1980)Ccc>Tcc	p.P660S	IQCE_ENST00000325979.7_Missense_Mutation_p.P595S|IQCE_ENST00000438376.2_Missense_Mutation_p.P644S|IQCE_ENST00000404984.1_Missense_Mutation_p.P609S	NM_001100390.1|NM_152558.3	NP_001093860.1|NP_689771.3	Q6IPM2	IQCE_HUMAN	IQ motif containing E	660						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)		AGACCCCTCTCCCTCAGGGCC	0.597																																					p.P660S		Atlas-SNP	.											.	IQCE	66	.	0			c.C1978T						PASS	.	C	SER/PRO,SER/PRO	0,4082		0,0,2041	65.0	67.0	66.0		1930,1978	0.9	0.0	7		66	2,8352		0,2,4175	no	missense,missense	IQCE	NM_001100390.1,NM_152558.3	74,74	0,2,6216	TT,TC,CC		0.0239,0.0,0.0161	probably-damaging,probably-damaging	644/680,660/696	2649686	2,12434	2041	4177	6218	SO:0001583	missense	23288	exon22			CCCTCTCCCTCAG	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.1978C>T	7.37:g.2649686C>T	ENSP00000385597:p.Pro660Ser	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	95	73	0.768421	NM_152558	Q4G0P7|Q6P7T4|Q9H0H7|Q9UPX7	Missense_Mutation	SNP	ENST00000402050.2	37	CCDS43542.1	.	.	.	.	.	.	.	.	.	.	C	3.946	-0.013165	0.07727	0.0	2.39E-4	ENSG00000106012	ENST00000402050;ENST00000404984;ENST00000438376;ENST00000325979	T;T;T;T	0.11712	2.77;2.75;2.76;2.76	4.9	0.875	0.19130	.	2.223160	0.02320	N	0.072870	T	0.07413	0.0187	N	0.22421	0.69	0.09310	N	1	B;B	0.13145	0.004;0.007	B;B	0.12837	0.004;0.008	T	0.32745	-0.9895	10	0.09590	T	0.72	.	5.0459	0.14483	0.0:0.4788:0.3314:0.1899	.	660;644	Q6IPM2;Q6IPM2-4	IQCE_HUMAN;.	S	660;609;644;595	ENSP00000385597:P660S;ENSP00000385945:P609S;ENSP00000396178:P644S;ENSP00000313772:P595S	ENSP00000313772:P595S	P	+	1	0	IQCE	2616212	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.116000	0.10724	-0.128000	0.11641	0.561000	0.74099	CCC	.	.	weak		0.597	IQCE-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000325063.2	NM_152558	
ZNF85	7639	hgsc.bcm.edu	37	19	21131728	21131728	+	Silent	SNP	A	A	G	rs12972502	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:21131728A>G	ENST00000328178.8	+	4	521	c.408A>G	c.(406-408)caA>caG	p.Q136Q	ZNF85_ENST00000601023.1_Silent_p.Q77Q|ZNF85_ENST00000345030.6_Silent_p.Q103Q	NM_001256173.1|NM_003429.4	NP_001243102.1|NP_003420.2	Q03923	ZNF85_HUMAN	zinc finger protein 85	136					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						GACTTAACCAATGTCTCACAG	0.328													.|||	278	0.0555112	0.0053	0.0634	5008	,	,		17503	0.001		0.1402	False		,,,				2504	0.0869				p.Q166Q		Atlas-SNP	.											.	ZNF85	72	.	0			c.A498G						PASS	.	A		100,4306		2,96,2105	67.0	70.0	69.0		408	-2.5	0.0	19	dbSNP_121	69	1039,7561		53,933,3314	no	coding-synonymous	ZNF85	NM_003429.4		55,1029,5419	GG,GA,AA		12.0814,2.2696,8.7575		136/596	21131728	1139,11867	2203	4300	6503	SO:0001819	synonymous_variant	7639	exon5			TAACCAATGTCTC	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.408A>G	19.37:g.21131728A>G		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	67	66	0.985075	NM_001256171	B9ZVP4|Q6NVI0	Silent	SNP	ENST00000328178.8	37	CCDS32977.1																																																																																			A|0.919;G|0.081	0.081	strong		0.328	ZNF85-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463430.1	NM_003429	
TMEM8A	58986	hgsc.bcm.edu	37	16	427784	427784	+	Silent	SNP	G	G	A	rs11641742	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:427784G>A	ENST00000431232.2	-	2	346	c.186C>T	c.(184-186)taC>taT	p.Y62Y	TMEM8A_ENST00000476735.1_5'UTR|TMEM8A_ENST00000250930.3_De_novo_Start_OutOfFrame	NM_021259.2	NP_067082.2	Q9HCN3	TMM8A_HUMAN	transmembrane protein 8A	62					cell adhesion (GO:0007155)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)				central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|pancreas(1)|prostate(1)	14						TGGCACTGCCGTACCAGCTGT	0.677													G|||	2663	0.531749	0.6188	0.4712	5008	,	,		15053	0.2996		0.5378	False		,,,				2504	0.6902				p.Y62Y		Atlas-SNP	.											.	TMEM8A	49	.	0			c.C186T						PASS	.	G		2723,1635		850,1023,306	36.0	42.0	40.0		186	-8.8	0.7	16	dbSNP_120	40	4854,3714		1426,2002,856	no	coding-synonymous	TMEM8A	NM_021259.2		2276,3025,1162	AA,AG,GG		43.3473,37.5172,41.3817		62/772	427784	7577,5349	2179	4284	6463	SO:0001819	synonymous_variant	58986	exon2			ACTGCCGTACCAG	AB045292	CCDS10407.1	16p13.3	2009-06-12	2009-06-12	2009-06-12	ENSG00000129925	ENSG00000129925			17205	protein-coding gene	gene with protein product			"""transmembrane protein 6"", ""transmembrane protein 8 (five membrane-spanning domains)"""	TMEM6, TMEM8		11006113	Standard	NM_021259		Approved	M83	uc002cgu.4	Q9HCN3	OTTHUMG00000047996	ENST00000431232.2:c.186C>T	16.37:g.427784G>A		Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	136	136	1	NM_021259	D3DU49|Q4TT35|Q8WU24|Q96S25|Q9BR03|Q9BT97|Q9H7B9	Silent	SNP	ENST00000431232.2	37	CCDS10407.1																																																																																			G|0.455;A|0.545	0.545	strong		0.677	TMEM8A-001	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000109257.2	NM_021259	
OR10H4	126541	hgsc.bcm.edu	37	19	16060248	16060248	+	Missense_Mutation	SNP	A	A	G	rs16980822	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:16060248A>G	ENST00000322107.1	+	1	431	c.431A>G	c.(430-432)cAt>cGt	p.H144R		NM_001004465.1	NP_001004465.1	Q8NGA5	O10H4_HUMAN	olfactory receptor, family 10, subfamily H, member 4	144			H -> R (in dbSNP:rs16980822).			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)|large_intestine(3)|lung(8)|ovary(1)|pancreas(1)|urinary_tract(1)	17						GACTGTGCCCATCTTGTGGCC	0.537													.|||	1211	0.241813	0.4622	0.1772	5008	,	,		23626	0.0546		0.2644	False		,,,				2504	0.1595				p.H144R		Atlas-SNP	.											OR10H4,NS,carcinoma,+1,1	OR10H4	48	1	0			c.A431G						PASS	.	G	ARG/HIS	1849,2557		384,1081,738	183.0	157.0	166.0		431	0.4	0.0	19	dbSNP_123	166	2049,6551		235,1579,2486	yes	missense	OR10H4	NM_001004465.1	29	619,2660,3224	GG,GA,AA		23.8256,41.9655,29.9708	benign	144/317	16060248	3898,9108	2203	4300	6503	SO:0001583	missense	126541	exon1			GTGCCCATCTTGT	AC011517	CCDS32941.1	19p13.12	2013-09-24			ENSG00000176231	ENSG00000176231		"""GPCR / Class A : Olfactory receptors"""	15388	protein-coding gene	gene with protein product							Standard	NM_001004465		Approved		uc010xov.2	Q8NGA5	OTTHUMG00000182268	ENST00000322107.1:c.431A>G	19.37:g.16060248A>G	ENSP00000318834:p.His144Arg	Somatic	200	0	0		WXS	Illumina HiSeq	Phase_I	190	104	0.547368	NM_001004465	Q6IFJ2|Q96R57	Missense_Mutation	SNP	ENST00000322107.1	37	CCDS32941.1	549	0.25137362637362637	237	0.4817073170731707	82	0.2265193370165746	40	0.06993006993006994	190	0.25065963060686014	N	0.676	-0.799908	0.02841	0.419655	0.238256	ENSG00000176231	ENST00000322107	T	0.35789	1.29	1.53	0.441	0.16577	GPCR, rhodopsin-like superfamily (1);	0.568736	0.13060	N	0.416993	T	0.00012	0.0000	N	0.02842	-0.48	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.47849	-0.9085	9	0.18710	T	0.47	.	4.571	0.12210	0.6061:0.0:0.3939:0.0	rs16980822;rs52815203;rs59896686;rs16980822	144	Q8NGA5	O10H4_HUMAN	R	144	ENSP00000318834:H144R	ENSP00000318834:H144R	H	+	2	0	OR10H4	15921248	0.000000	0.05858	0.001000	0.08648	0.069000	0.16628	-2.003000	0.01463	-0.004000	0.14419	-0.392000	0.06488	CAT	A|0.724;G|0.276	0.276	strong		0.537	OR10H4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460311.1		
MYO18B	84700	hgsc.bcm.edu	37	22	26388337	26388337	+	Silent	SNP	C	C	T	rs916425	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:26388337C>T	ENST00000407587.2	+	40	6337	c.6168C>T	c.(6166-6168)taC>taT	p.Y2056Y	MYO18B_ENST00000335473.7_Silent_p.Y2055Y|MYO18B_ENST00000536101.1_Silent_p.Y2055Y			Q8IUG5	MY18B_HUMAN	myosin XVIIIB	2055	Tail.					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						AGGAGAAGTACGTGGAGGAAC	0.577													C|||	571	0.114018	0.1997	0.1066	5008	,	,		21990	0.001		0.1759	False		,,,				2504	0.0562				p.Y2055Y		Atlas-SNP	.											.	MYO18B	322	.	0			c.C6165T						PASS	.	C		770,3384		72,626,1379	61.0	64.0	63.0		6165	-6.9	0.7	22	dbSNP_86	63	1363,7089		110,1143,2973	no	coding-synonymous	MYO18B	NM_032608.5		182,1769,4352	TT,TC,CC		16.1264,18.5364,16.9205		2055/2568	26388337	2133,10473	2077	4226	6303	SO:0001819	synonymous_variant	84700	exon40			GAAGTACGTGGAG	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.6168C>T	22.37:g.26388337C>T		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	64	28	0.4375	NM_032608	B2RWP3|F5GYU7|Q8NDI8|Q8TE65|Q8WWS0|Q96KH2|Q96KR8|Q96KR9	Silent	SNP	ENST00000407587.2	37		268	0.1227106227106227	92	0.18699186991869918	42	0.11602209944751381	1	0.0017482517482517483	133	0.17546174142480211	C	1.337	-0.595152	0.03771	0.185364	0.161264	ENSG00000133454	ENST00000543971	.	.	.	5.17	-6.94	0.01633	.	.	.	.	.	T	0.00073	0.0002	.	.	.	0.09310	P	0.9999999883998	.	.	.	.	.	.	T	0.13361	-1.0512	3	.	.	.	.	11.1467	0.48434	0.0:0.3209:0.088:0.5911	rs916425;rs916425	.	.	.	M	20	.	.	T	+	2	0	MYO18B	24718337	0.149000	0.22717	0.692000	0.30179	0.288000	0.27193	-0.838000	0.04372	-1.610000	0.01583	-1.934000	0.00508	ACG	C|0.866;T|0.134	0.134	strong		0.577	MYO18B-006	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000400691.1	NM_032608	
AHNAK2	113146	hgsc.bcm.edu	37	14	105415577	105415577	+	Silent	SNP	G	G	A	rs375265904		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:105415577G>A	ENST00000333244.5	-	7	6330	c.6211C>T	c.(6211-6213)Ctg>Ttg	p.L2071L	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	2071						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.L2071V(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)			ACCTTGGGCAGGTGCCCTTTG	0.617																																					p.L2071L		Atlas-SNP	.											AHNAK2_ENST00000333244,NS,carcinoma,0,1	AHNAK2	719	1	1	Substitution - Missense(1)	lung(1)	c.C6211T						scavenged	.						107.0	76.0	87.0					14																	105415577		1793	3071	4864	SO:0001819	synonymous_variant	113146	exon7			TGGGCAGGTGCCC	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.6211C>T	14.37:g.105415577G>A		Somatic	1	0	0		WXS	Illumina HiSeq	Phase_I	55	8	0.145455	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Silent	SNP	ENST00000333244.5	37	CCDS45177.1																																																																																			.	.	weak		0.617	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
TBC1D1	23216	hgsc.bcm.edu	37	4	38016395	38016395	+	Missense_Mutation	SNP	T	T	G	rs10501	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	40	0	0		WXS	Illumina HiSeq	Phase_I	38	13	0.342105	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	
FMN2	56776	hgsc.bcm.edu	37	1	240256822	240256822	+	Silent	SNP	C	C	A	rs10926124	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:240256822C>A	ENST00000319653.9	+	1	1643	c.1413C>A	c.(1411-1413)gcC>gcA	p.A471A		NM_020066.4	NP_064450.3	Q9NZ56	FMN2_HUMAN	formin 2	471					cellular response to DNA damage stimulus (GO:0006974)|cellular response to hypoxia (GO:0071456)|establishment of meiotic spindle localization (GO:0051295)|formin-nucleated actin cable assembly (GO:0070649)|homologous chromosome movement towards spindle pole involved in homologous chromosome segregation (GO:0051758)|intracellular signal transduction (GO:0035556)|intracellular transport (GO:0046907)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein catabolic process (GO:0042177)|oogenesis (GO:0048477)|polar body extrusion after meiotic divisions (GO:0040038)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	cell cortex (GO:0005938)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|microvillus (GO:0005902)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|spindle (GO:0005819)	actin binding (GO:0003779)			NS(1)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(13)|lung(87)|ovary(6)|pancreas(3)|prostate(12)|skin(7)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(2)	178	Ovarian(103;0.127)	all_cancers(173;0.013)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)			AGCACCGGGCCGACGGCGGCC	0.741													C|||	1652	0.329872	0.09	0.3357	5008	,	,		11042	0.3006		0.5249	False		,,,				2504	0.4796				p.A471A		Atlas-SNP	.											FMN2,NS,carcinoma,+1,1	FMN2	451	1	0			c.C1413A						scavenged	.	C		701,3587		91,519,1534	10.0	14.0	13.0		1413	-7.9	0.0	1	dbSNP_120	13	4311,4019		1186,1939,1040	no	coding-synonymous	FMN2	NM_020066.4		1277,2458,2574	AA,AC,CC		48.2473,16.3479,39.721		471/1723	240256822	5012,7606	2144	4165	6309	SO:0001819	synonymous_variant	56776	exon1			CCGGGCCGACGGC	AF218942	CCDS31069.2	1q43	2008-02-05			ENSG00000155816	ENSG00000155816			14074	protein-coding gene	gene with protein product		606373				10781961	Standard	NM_020066		Approved		uc010pyd.2	Q9NZ56	OTTHUMG00000039883	ENST00000319653.9:c.1413C>A	1.37:g.240256822C>A		Somatic	9	0	0		WXS	Illumina HiSeq	Phase_I	13	8	0.615385	NM_020066	B0QZA7|B4DP05|Q59GF6|Q5VU37|Q9NZ55	Silent	SNP	ENST00000319653.9	37	CCDS31069.2																																																																																			C|0.617;A|0.383	0.383	strong		0.741	FMN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096217.2	XM_371352	
KANK2	25959	hgsc.bcm.edu	37	19	11303554	11303554	+	Missense_Mutation	SNP	A	A	G	rs17616661	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:11303554A>G	ENST00000586659.1	-	4	1516	c.1202T>C	c.(1201-1203)aTg>aCg	p.M401T	KANK2_ENST00000432929.2_Missense_Mutation_p.M401T|KANK2_ENST00000589359.1_Missense_Mutation_p.M401T|KANK2_ENST00000589894.1_Missense_Mutation_p.M401T|KANK2_ENST00000355150.5_Missense_Mutation_p.M401T			Q63ZY3	KANK2_HUMAN	KN motif and ankyrin repeat domains 2	401			M -> T (in dbSNP:rs17616661).		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						CTTCTTCACCATATGGACGTT	0.617													A|||	259	0.0517173	0.0499	0.1052	5008	,	,		16912	0.0129		0.0716	False		,,,				2504	0.0358				p.M401T		Atlas-SNP	.											.	KANK2	47	.	0			c.T1202C						PASS	.	A	THR/MET,THR/MET	253,4153	145.4+/-180.2	5,243,1955	82.0	84.0	84.0		1202,1202	-0.5	0.0	19	dbSNP_123	84	771,7829	182.5+/-230.9	34,703,3563	yes	missense,missense	KANK2	NM_001136191.2,NM_015493.6	81,81	39,946,5518	GG,GA,AA		8.9651,5.7422,7.8733	benign,benign	401/852,401/860	11303554	1024,11982	2203	4300	6503	SO:0001583	missense	25959	exon2			TTCACCATATGGA	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.1202T>C	19.37:g.11303554A>G	ENSP00000465650:p.Met401Thr	Somatic	212	0	0		WXS	Illumina HiSeq	Phase_I	176	81	0.460227	NM_015493	B0I1P4|Q3KQZ3|Q6GUF5|Q9H8S4|Q9NUP0|Q9P210	Missense_Mutation	SNP	ENST00000586659.1	37	CCDS12255.1	124	0.056776556776556776	23	0.046747967479674794	38	0.10497237569060773	9	0.015734265734265736	54	0.0712401055408971	A	7.875	0.728997	0.15507	0.057422	0.089651	ENSG00000197256	ENST00000432929;ENST00000355150	T;T	0.34667	1.35;1.35	4.11	-0.526	0.11913	.	2.300800	0.01860	N	0.036548	T	0.00300	0.0009	N	0.00926	-1.1	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	0.11227	-1.0596	9	0.11485	T	0.65	-32.8339	1.0732	0.01626	0.3953:0.156:0.2963:0.1523	rs17616661;rs56647164;rs17616661	401;401;401	Q63ZY3-3;Q63ZY3;Q63ZY3-2	.;KANK2_HUMAN;.	T	401	ENSP00000395650:M401T;ENSP00000347276:M401T	ENSP00000347276:M401T	M	-	2	0	KANK2	11164554	0.000000	0.05858	0.007000	0.13788	0.223000	0.24884	0.245000	0.18142	-0.218000	0.10018	0.379000	0.24179	ATG	A|0.936;G|0.064	0.064	strong		0.617	KANK2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000453066.2	NM_015493	
UMODL1	89766	hgsc.bcm.edu	37	21	43557698	43557698	+	Missense_Mutation	SNP	A	A	C	rs3819142	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:43557698A>C	ENST00000408910.2	+	22	3925	c.3925A>C	c.(3925-3927)Aac>Cac	p.N1309H	UMODL1_ENST00000400427.1_Missense_Mutation_p.N1365H|UMODL1_ENST00000400424.2_Missense_Mutation_p.N1237H|UMODL1_ENST00000408989.2_Missense_Mutation_p.N1437H|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	128	0	0		WXS	Illumina HiSeq	Phase_I	146	96	0.657534	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		
POLD3	10714	hgsc.bcm.edu	37	11	74329615	74329615	+	Silent	SNP	T	T	C	rs4944052	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:74329615T>C	ENST00000263681.2	+	6	555	c.426T>C	c.(424-426)ccT>ccC	p.P142P	POLD3_ENST00000527458.1_Silent_p.P103P|POLD3_ENST00000532497.1_Silent_p.P36P	NM_006591.2	NP_006582.1	Q15054	DPOD3_HUMAN	polymerase (DNA-directed), delta 3, accessory subunit	142					base-excision repair (GO:0006284)|DNA repair (GO:0006281)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA synthesis involved in DNA repair (GO:0000731)|mismatch repair (GO:0006298)|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)	delta DNA polymerase complex (GO:0043625)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA-directed DNA polymerase activity (GO:0003887)	p.P142P(1)		breast(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(6)|ovary(1)|skin(1)|stomach(1)	18	Breast(11;3.21e-06)					CTGCCGTCCCTAGAGCTCCTG	0.428													T|||	2249	0.449081	0.5703	0.4424	5008	,	,		19675	0.3204		0.3221	False		,,,				2504	0.5532				p.P142P		Atlas-SNP	.											POLD3,NS,carcinoma,0,1	POLD3	87	1	1	Substitution - coding silent(1)	stomach(1)	c.T426C						PASS	.	T		2500,1900	625.9+/-394.6	694,1112,394	126.0	128.0	127.0		426	-4.0	0.9	11	dbSNP_111	127	2773,5813	438.7+/-359.0	480,1813,2000	no	coding-synonymous	POLD3	NM_006591.1		1174,2925,2394	CC,CT,TT		32.2968,43.1818,40.6053		142/467	74329615	5273,7713	2200	4293	6493	SO:0001819	synonymous_variant	10714	exon6			CGTCCCTAGAGCT	D26018	CCDS8233.1	11q14	2014-06-13			ENSG00000077514	ENSG00000077514		"""DNA polymerases"""	20932	protein-coding gene	gene with protein product	"""DNA polymerase delta subunit p66"", ""Pol delta C subunit (p66)"", ""protein phosphatase 1, regulatory subunit 128"""	611415				10219083	Standard	NM_006591		Approved	P66, KIAA0039, P68, PPP1R128	uc001ovf.2	Q15054	OTTHUMG00000165621	ENST00000263681.2:c.426T>C	11.37:g.74329615T>C		Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	129	128	0.992248	NM_006591	B7ZAI6|Q32MZ9|Q32N00	Silent	SNP	ENST00000263681.2	37	CCDS8233.1																																																																																			T|0.602;C|0.398	0.398	strong		0.428	POLD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385376.1	NM_006591	
ANKRD32	84250	hgsc.bcm.edu	37	5	93987532	93987532	+	Missense_Mutation	SNP	C	C	A	rs6891545	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:93987532C>A	ENST00000265140.5	+	7	1283	c.864C>A	c.(862-864)agC>agA	p.S288R		NM_032290.3	NP_115666.2	Q9BQI6	ANR32_HUMAN	ankyrin repeat domain 32	288			S -> R (in dbSNP:rs6891545).			centrosome (GO:0005813)|nucleus (GO:0005634)				NS(1)|breast(2)|endometrium(2)|large_intestine(1)|lung(3)|ovary(2)|prostate(1)|skin(1)	13		all_cancers(142;1.51e-09)|all_epithelial(76;4.68e-12)|all_lung(232;5.94e-05)|Ovarian(174;0.000953)|Lung NSC(167;0.00105)|Colorectal(57;0.122)|Lung SC(612;0.152)		all cancers(79;3.88e-18)		CCTTTGGAAGCCATACATATG	0.229													g|||	1176	0.234824	0.1967	0.2983	5008	,	,		13098	0.3095		0.1909	False		,,,				2504	0.2096				p.S288R		Atlas-SNP	.											.	ANKRD32	117	.	0			c.C864A						PASS	.	A	ARG/SER	283,1101		26,231,435	54.0	45.0	48.0		864	-2.7	0.0	5	dbSNP_116	48	734,2434		80,574,930	yes	missense	ANKRD32	NM_032290.3	110	106,805,1365	AA,AC,CC		23.1692,20.448,22.3418	benign	288/1059	93987532	1017,3535	692	1584	2276	SO:0001583	missense	84250	exon7			TGGAAGCCATACA	AL136560	CCDS4071.2	5q15	2013-01-10			ENSG00000133302	ENSG00000133302		"""Ankyrin repeat domain containing"""	25408	protein-coding gene	gene with protein product			"""BRCT domain containing 1"""	BRCTD1			Standard	NM_032290		Approved	DKFZp761C121, DKFZp564C0469	uc003kkr.4	Q9BQI6	OTTHUMG00000121133	ENST00000265140.5:c.864C>A	5.37:g.93987532C>A	ENSP00000265140:p.Ser288Arg	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	77	76	0.987013	NM_032290	B4DMG4|Q3B7K4|Q6NSA5|Q6PHW9|Q9Y402	Missense_Mutation	SNP	ENST00000265140.5	37	CCDS4071.2	482	0.2206959706959707	70	0.14227642276422764	85	0.23480662983425415	178	0.3111888111888112	149	0.19656992084432717	g	0.001	-5.900514	0.00000	0.20448	0.231692	ENSG00000133302	ENST00000265140	T	0.42131	0.98	3.78	-2.65	0.06095	.	0.428985	0.17307	N	0.179005	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	0.07868	-1.0750	9	0.02654	T	1	.	1.0319	0.01540	0.3262:0.1117:0.3331:0.229	rs6891545;rs52811552;rs6891545	288	Q9BQI6	ANR32_HUMAN	R	288	ENSP00000265140:S288R	ENSP00000265140:S288R	S	+	3	2	ANKRD32	94013288	0.008000	0.16893	0.001000	0.08648	0.002000	0.02628	-1.459000	0.02370	-1.437000	0.01967	-6.496000	0.00000	AGC	C|0.778;A|0.222	0.222	strong		0.229	ANKRD32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241610.1	NM_032290	
DUSP15	128853	hgsc.bcm.edu	37	20	30452782	30452782	+	Silent	SNP	C	C	T	rs4911536	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:30452782C>T	ENST00000278979.3	-	4	229	c.153G>A	c.(151-153)ccG>ccA	p.P51P	DUSP15_ENST00000398084.2_5'UTR|DUSP15_ENST00000486996.1_5'UTR|DUSP15_ENST00000339738.5_Silent_p.P54P|DUSP15_ENST00000375966.4_Silent_p.P51P|DUSP15_ENST00000493115.1_5'UTR|DUSP15_ENST00000398083.1_5'UTR			Q9H1R2	DUS15_HUMAN	dual specificity phosphatase 15	51					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)|plasma membrane (GO:0005886)	protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.P54P(1)		large_intestine(1)|lung(4)|pancreas(1)|stomach(1)	7			Colorectal(19;0.00306)|COAD - Colon adenocarcinoma(19;0.0347)			TATCAGCGACCGGGATGCGAA	0.587													C|||	1427	0.284944	0.149	0.3069	5008	,	,		20586	0.372		0.2773	False		,,,				2504	0.3712				p.P54P		Atlas-SNP	.											DUSP15,NS,carcinoma,0,1	DUSP15	28	1	1	Substitution - coding silent(1)	stomach(1)	c.G162A						PASS	.	C	,,	813,3593	325.3+/-299.0	73,667,1463	148.0	131.0	137.0		,162,	-4.8	1.0	20	dbSNP_111	137	2491,6109	409.1+/-349.7	371,1749,2180	no	utr-5,coding-synonymous,utr-5	DUSP15	NM_001012644.1,NM_080611.3,NM_177991.1	,,	444,2416,3643	TT,TC,CC		28.9651,18.4521,25.4037	,,	,54/236,	30452782	3304,9702	2203	4300	6503	SO:0001819	synonymous_variant	128853	exon4			AGCGACCGGGATG		CCDS13193.1, CCDS42862.1	20q11.21	2011-06-09	2005-03-09		ENSG00000149599	ENSG00000149599		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Atypical dual specificity phosphatases"""	16236	protein-coding gene	gene with protein product			"""dual specificity phosphatase-like 15"""			15138252	Standard	NM_080611		Approved	bA243J16.6, VHY	uc002wwx.1	Q9H1R2	OTTHUMG00000032182	ENST00000278979.3:c.153G>A	20.37:g.30452782C>T		Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	118	118	1	NM_080611	A6NH79|A8MVC8|Q5QP62|Q5QP63|Q5QP65|Q6PGN7|Q8N826|Q9BX24	Silent	SNP	ENST00000278979.3	37		607	0.27793040293040294	78	0.15853658536585366	109	0.3011049723756906	215	0.3758741258741259	205	0.2704485488126649	C	13.25	2.180570	0.38511	0.184521	0.289651	ENSG00000149599	ENST00000375953;ENST00000428829	.	.	.	5.63	-4.79	0.03200	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999996912	.	.	.	.	.	.	T	0.40887	-0.9539	4	0.87932	D	0	.	0.4065	0.00434	0.3674:0.2264:0.2159:0.1903	rs4911536;rs56871761;rs4911536	.	.	.	Q	43	.	ENSP00000365120:R43Q	R	-	2	0	DUSP15	29916443	0.526000	0.26298	0.955000	0.39395	0.967000	0.64934	-0.642000	0.05427	-0.849000	0.04158	-0.397000	0.06425	CGG	C|0.733;T|0.267	0.267	strong		0.587	DUSP15-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000078555.3	NM_080611	
RSF1	51773	hgsc.bcm.edu	37	11	77378388	77378388	+	Silent	SNP	T	T	C	rs4945197	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:77378388T>C	ENST00000308488.6	-	16	4202	c.3900A>G	c.(3898-3900)ctA>ctG	p.L1300L	RSF1_ENST00000360355.2_Silent_p.L1269L|RSF1_ENST00000480887.1_Silent_p.L1048L			Q96T23	RSF1_HUMAN	remodeling and spacing factor 1	1300					CENP-A containing nucleosome assembly (GO:0034080)|chromatin remodeling (GO:0006338)|DNA-templated transcription, initiation (GO:0006352)|negative regulation of DNA binding (GO:0043392)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome assembly (GO:0006334)|nucleosome positioning (GO:0016584)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of viral transcription (GO:0050434)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|RSF complex (GO:0031213)	histone binding (GO:0042393)|zinc ion binding (GO:0008270)	p.L1300L(1)		breast(3)|central_nervous_system(2)|endometrium(3)|kidney(4)|large_intestine(9)|lung(14)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	43	all_cancers(14;1.54e-17)|all_epithelial(13;4.06e-20)|Ovarian(111;0.152)		Epithelial(5;3e-50)|all cancers(3;6.37e-47)|BRCA - Breast invasive adenocarcinoma(5;9.82e-31)			CAATCCGGTGTAGCCGTTTGC	0.562													T|||	983	0.196286	0.329	0.2147	5008	,	,		20309	0.1736		0.0984	False		,,,				2504	0.1278				p.L1300L		Atlas-SNP	.											RSF1,NS,carcinoma,0,1	RSF1	105	1	1	Substitution - coding silent(1)	stomach(1)	c.A3900G						PASS	.	T		1335,3065	446.7+/-348.1	204,927,1069	113.0	100.0	105.0		3900	0.0	1.0	11	dbSNP_111	105	831,7753	191.8+/-238.0	36,759,3497	yes	coding-synonymous	RSF1	NM_016578.3		240,1686,4566	CC,CT,TT		9.6808,30.3409,16.6821		1300/1442	77378388	2166,10818	2200	4292	6492	SO:0001819	synonymous_variant	51773	exon16			CCGGTGTAGCCGT	AF380176, AF227948	CCDS8253.1	11q14.1	2013-01-28	2006-05-25	2006-05-25	ENSG00000048649	ENSG00000048649		"""Zinc fingers, PHD-type"""	18118	protein-coding gene	gene with protein product		608522	"""hepatitis B virus x associated protein"""	HBXAP		11788598, 12972596	Standard	NM_016578		Approved	XAP8, RSF-1, p325	uc001oyn.3	Q96T23	OTTHUMG00000150433	ENST00000308488.6:c.3900A>G	11.37:g.77378388T>C		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	94	79	0.840426	NM_016578	Q86X86|Q9H3L8|Q9NVZ8|Q9NYU0	Silent	SNP	ENST00000308488.6	37	CCDS8253.1																																																																																			T|0.813;C|0.187	0.187	strong		0.562	RSF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318075.2	NM_016578	
SLC12A6	9990	hgsc.bcm.edu	37	15	34542872	34542872	+	Silent	SNP	C	C	G	rs17236798	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:34542872C>G	ENST00000354181.3	-	12	2043	c.1551G>C	c.(1549-1551)ccG>ccC	p.P517P	SLC12A6_ENST00000290209.5_Silent_p.P466P|SLC12A6_ENST00000560164.1_Silent_p.P329P|SLC12A6_ENST00000397707.2_Silent_p.P502P|SLC12A6_ENST00000458406.2_Silent_p.P458P|SLC12A6_ENST00000397702.2_Silent_p.P458P|SLC12A6_ENST00000451844.2_Silent_p.P329P|SLC12A6_ENST00000558667.1_Silent_p.P517P|SLC12A6_ENST00000560611.1_Silent_p.P517P|SLC12A6_ENST00000558589.1_Silent_p.P508P			Q9UHW9	S12A6_HUMAN	solute carrier family 12 (potassium/chloride transporter), member 6	517					angiogenesis (GO:0001525)|cellular hypotonic response (GO:0071476)|cellular hypotonic salinity response (GO:0071477)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transport (GO:0006811)|potassium ion import (GO:0010107)|potassium ion transport (GO:0006813)|rubidium ion transport (GO:0035826)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	potassium ion transmembrane transporter activity (GO:0015079)|potassium:chloride symporter activity (GO:0015379)|protein kinase binding (GO:0019901)|rubidium ion transmembrane transporter activity (GO:0035827)			central_nervous_system(5)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(8)|lung(17)|ovary(4)|skin(3)	45		all_lung(180;2.78e-08)		all cancers(64;3.43e-17)|GBM - Glioblastoma multiforme(113;2.6e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0301)	Potassium Chloride(DB00761)	TAGTACCAATCGGAATAGACT	0.418													G|||	1038	0.207268	0.1263	0.2017	5008	,	,		19869	0.2827		0.2068	False		,,,				2504	0.2434				p.P517P		Atlas-SNP	.											.	SLC12A6	205	.	0			c.G1551C						PASS	.	G	,,,,,	563,3839	773.7+/-414.0	36,491,1674	124.0	116.0	119.0		1374,1374,1524,1506,1398,1551	3.0	1.0	15	dbSNP_123	119	1465,7131	749.9+/-407.4	123,1219,2956	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SLC12A6	NM_001042494.1,NM_001042495.1,NM_001042496.1,NM_001042497.1,NM_005135.2,NM_133647.1	,,,,,	159,1710,4630	GG,GC,CC		17.0428,12.7896,15.6024	,,,,,	458/1092,458/1092,508/1142,502/1136,466/1100,517/1151	34542872	2028,10970	2201	4298	6499	SO:0001819	synonymous_variant	9990	exon11			ACCAATCGGAATA	AF108831	CCDS10036.1, CCDS42010.1, CCDS42011.1, CCDS42012.1, CCDS58352.1	15q13	2014-09-17	2013-07-18		ENSG00000140199	ENSG00000140199		"""Solute carriers"""	10914	protein-coding gene	gene with protein product		604878	"""agenesis of corpus callosum and peripheral neuropathy (Andermann syndrome)"""	KCC3, ACCPN		10187864, 10347194	Standard	NM_133647		Approved		uc001zhw.3	Q9UHW9	OTTHUMG00000129441	ENST00000354181.3:c.1551G>C	15.37:g.34542872C>G		Somatic	263	0	0		WXS	Illumina HiSeq	Phase_I	220	108	0.490909	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	
SMARCA5	8467	hgsc.bcm.edu	37	4	144471249	144471249	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:144471249A>G	ENST00000283131.3	+	23	3547	c.3085A>G	c.(3085-3087)Aag>Gag	p.K1029E		NM_003601.3	NP_003592.3	O60264	SMCA5_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 5	1029					ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|CENP-A containing nucleosome assembly (GO:0034080)|chromatin remodeling (GO:0006338)|chromatin silencing at rDNA (GO:0000183)|DNA-templated transcription, initiation (GO:0006352)|double-strand break repair (GO:0006302)|nucleosome assembly (GO:0006334)|nucleosome positioning (GO:0016584)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	chromatin silencing complex (GO:0005677)|condensed chromosome (GO:0000793)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|NURF complex (GO:0016589)|RSF complex (GO:0031213)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)		EWSR1/SMARCA5(2)	endometrium(2)|kidney(2)|large_intestine(9)|lung(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	21	all_hematologic(180;0.158)					ACGAGGACCAAAGCCTTCAGT	0.358																																					p.K1029E		Atlas-SNP	.											.	SMARCA5	73	.	0			c.A3085G						PASS	.						67.0	63.0	64.0					4																	144471249		2203	4300	6503	SO:0001583	missense	8467	exon23			GGACCAAAGCCTT	AB010882	CCDS3761.1	4q31.1-q31.2	2011-04-20			ENSG00000153147	ENSG00000153147			11101	protein-coding gene	gene with protein product		603375				9730600	Standard	NM_003601		Approved	hSNF2H, hISWI, ISWI	uc003ijg.3	O60264	OTTHUMG00000161474	ENST00000283131.3:c.3085A>G	4.37:g.144471249A>G	ENSP00000283131:p.Lys1029Glu	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	66	14	0.212121	NM_003601		Missense_Mutation	SNP	ENST00000283131.3	37	CCDS3761.1	.	.	.	.	.	.	.	.	.	.	A	16.07	3.017568	0.54576	.	.	ENSG00000153147	ENST00000283131;ENST00000536484;ENST00000535006	D	0.91011	-2.77	5.62	5.62	0.85841	.	0.000000	0.85682	D	0.000000	T	0.81973	0.4936	N	0.08118	0	0.46586	D	0.999116	B	0.26400	0.148	B	0.30029	0.11	T	0.78375	-0.2228	10	0.21014	T	0.42	-12.3435	16.1203	0.81346	1.0:0.0:0.0:0.0	.	1029	O60264	SMCA5_HUMAN	E	1029;972;972	ENSP00000283131:K1029E	ENSP00000283131:K1029E	K	+	1	0	SMARCA5	144690699	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.877000	0.69675	2.274000	0.75844	0.533000	0.62120	AAG	.	.	none		0.358	SMARCA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365077.3		
DHDH	27294	hgsc.bcm.edu	37	19	49445774	49445774	+	Nonsense_Mutation	SNP	C	C	T	rs10423255	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:49445774C>T	ENST00000221403.2	+	5	737	c.697C>T	c.(697-699)Cag>Tag	p.Q233*	DHDH_ENST00000522614.1_Intron|DHDH_ENST00000523250.1_Nonsense_Mutation_p.Q94*	NM_014475.3	NP_055290.1	Q9UQ10	DHDH_HUMAN	dihydrodiol dehydrogenase (dimeric)	233					carbohydrate metabolic process (GO:0005975)|D-xylose catabolic process (GO:0042843)		D-xylose 1-dehydrogenase (NADP+) activity (GO:0047837)|electron carrier activity (GO:0009055)|NAD(P)+ transhydrogenase activity (GO:0008746)|trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity (GO:0047115)			central_nervous_system(1)|large_intestine(3)|lung(3)|ovary(1)|soft_tissue(1)	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;0.000158)|all cancers(93;0.000258)|Epithelial(262;0.0173)|GBM - Glioblastoma multiforme(486;0.0179)		CATCACCGTGCAGCTCTCCAA	0.637													C|||	276	0.0551118	0.0681	0.0461	5008	,	,		17972	0.0506		0.0606	False		,,,				2504	0.0429				p.Q233X		Atlas-SNP	.											.	DHDH	35	.	0			c.C697T						PASS	.	C	stop/GLN	261,4145	150.7+/-184.7	13,235,1955	67.0	55.0	59.0		697	-8.6	0.0	19	dbSNP_119	59	513,8087	145.6+/-201.3	13,487,3800	yes	stop-gained	DHDH	NM_014475.3		26,722,5755	TT,TC,CC		5.9651,5.9237,5.9511		233/335	49445774	774,12232	2203	4300	6503	SO:0001587	stop_gained	27294	exon5			ACCGTGCAGCTCT	AB021933	CCDS12741.1	19q13.3	2008-02-05			ENSG00000104808	ENSG00000104808	1.3.1.20		17887	protein-coding gene	gene with protein product		606377				10477285	Standard	NM_014475		Approved	HUM2DD	uc002ple.1	Q9UQ10	OTTHUMG00000165029	ENST00000221403.2:c.697C>T	19.37:g.49445774C>T	ENSP00000221403:p.Gln233*	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	92	50	0.543478	NM_014475		Nonsense_Mutation	SNP	ENST00000221403.2	37	CCDS12741.1	130	0.05952380952380952	28	0.056910569105691054	20	0.055248618784530384	35	0.06118881118881119	47	0.06200527704485488	C	10.04	1.240374	0.22711	0.059237	0.059651	ENSG00000104808	ENST00000221403;ENST00000523250	.	.	.	4.3	-8.61	0.00885	.	1.784800	0.02394	N	0.080029	.	.	.	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-0.4623	14.3564	0.66740	0.2382:0.6084:0.1534:0.0	rs10423255;rs10423255	.	.	.	X	233;94	.	ENSP00000221403:Q233X	Q	+	1	0	DHDH	54137586	0.000000	0.05858	0.000000	0.03702	0.256000	0.26092	-4.283000	0.00260	-3.996000	0.00083	0.484000	0.47621	CAG	C|0.938;T|0.062	0.062	strong		0.637	DHDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381477.1	NM_014475	
GABRB1	2560	hgsc.bcm.edu	37	4	47408709	47408709	+	Silent	SNP	A	A	G	rs6289	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	192	0	0		WXS	Illumina HiSeq	Phase_I	135	56	0.414815	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		
DOPEY2	9980	hgsc.bcm.edu	37	21	37661405	37661405	+	Missense_Mutation	SNP	G	G	A	rs3827183	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:37661405G>A	ENST00000399151.3	+	35	6501	c.6416G>A	c.(6415-6417)gGg>gAg	p.G2139E		NM_005128.2	NP_005119.2	Q9Y3R5	DOP2_HUMAN	dopey family member 2	2139			G -> E (in dbSNP:rs3827183). {ECO:0000269|PubMed:10231032}.		cognition (GO:0050890)|endoplasmic reticulum organization (GO:0007029)|Golgi to endosome transport (GO:0006895)|multicellular organismal development (GO:0007275)|protein transport (GO:0015031)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)		p.G2139E(1)		autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(6)|lung(25)|ovary(2)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58						CCCTCAGTGGGGGAGATACCC	0.398													G|||	724	0.144569	0.115	0.111	5008	,	,		18023	0.126		0.1223	False		,,,				2504	0.2505				p.G2139E		Atlas-SNP	.											DOPEY2,NS,carcinoma,0,1	DOPEY2	184	1	1	Substitution - Missense(1)	stomach(1)	c.G6416A						PASS	.	G	GLU/GLY	525,3881	239.9+/-250.9	30,465,1708	110.0	106.0	108.0		6416	2.9	0.2	21	dbSNP_107	108	1026,7574	219.0+/-257.2	70,886,3344	yes	missense	DOPEY2	NM_005128.2	98	100,1351,5052	AA,AG,GG		11.9302,11.9156,11.9253	benign	2139/2299	37661405	1551,11455	2203	4300	6503	SO:0001583	missense	9980	exon35			CAGTGGGGGAGAT	AJ237839	CCDS13643.1	21q22.2	2013-03-05	2006-02-02	2006-02-02	ENSG00000142197	ENSG00000142197			1291	protein-coding gene	gene with protein product		604803	"""chromosome 21 open reading frame 5"""	C21orf5		16301316, 16303751, 10931277	Standard	NM_005128		Approved	KIAA0933	uc002yvg.3	Q9Y3R5	OTTHUMG00000086619	ENST00000399151.3:c.6416G>A	21.37:g.37661405G>A	ENSP00000382104:p.Gly2139Glu	Somatic	197	0	0		WXS	Illumina HiSeq	Phase_I	218	132	0.605505	NM_005128	D3DSG5|Q6PJQ7|Q9UEZ3	Missense_Mutation	SNP	ENST00000399151.3	37	CCDS13643.1	265	0.12133699633699634	57	0.11585365853658537	41	0.1132596685082873	71	0.12412587412587413	96	0.1266490765171504	G	15.39	2.819449	0.50633	0.119156	0.119302	ENSG00000142197	ENST00000399151	T	0.41758	0.99	4.81	2.87	0.33458	.	0.436973	0.24249	N	0.040199	T	0.00356	0.0011	L	0.56769	1.78	0.32167	P	0.582177	B;B	0.28552	0.191;0.215	B;B	0.29942	0.109;0.051	T	0.09143	-1.0688	9	0.11485	T	0.65	.	9.9191	0.41453	0.0825:0.1407:0.7768:0.0	rs3827183;rs58599312;rs3827183	2132;2139	Q9Y3R5-2;Q9Y3R5	.;DOP2_HUMAN	E	2139	ENSP00000382104:G2139E	ENSP00000382104:G2139E	G	+	2	0	DOPEY2	36583275	0.515000	0.26210	0.199000	0.23439	0.733000	0.41908	2.524000	0.45589	1.387000	0.46486	0.563000	0.77884	GGG	G|0.873;A|0.127	0.127	strong		0.398	DOPEY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194636.1	NM_005128	
ANXA10	11199	hgsc.bcm.edu	37	4	169098914	169098914	+	Silent	SNP	A	A	G	rs477897	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:169098914A>G	ENST00000359299.3	+	7	690	c.504A>G	c.(502-504)acA>acG	p.T168T		NM_007193.4	NP_009124.2	Q9UJ72	ANX10_HUMAN	annexin A10	168				T -> S (in Ref. 1; CAB51917). {ECO:0000305}.		mitochondrion (GO:0005739)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)			endometrium(1)|kidney(2)|large_intestine(4)|lung(6)|prostate(1)|stomach(2)	16		Prostate(90;0.00876)|Renal(120;0.0183)|all_neural(102;0.0837)|Melanoma(52;0.132)		GBM - Glioblastoma multiforme(119;0.0325)		AAGGATATACAGACCCTGCGA	0.453													A|||	575	0.114816	0.1067	0.1326	5008	,	,		19645	0.0476		0.2256	False		,,,				2504	0.0685				p.T168T		Atlas-SNP	.											.	ANXA10	44	.	0			c.A504G						PASS	.	A		510,3896	238.0+/-249.6	33,444,1726	123.0	119.0	120.0		504	-10.0	0.0	4	dbSNP_83	120	1813,6787	325.4+/-316.9	197,1419,2684	no	coding-synonymous	ANXA10	NM_007193.4		230,1863,4410	GG,GA,AA		21.0814,11.5751,17.861		168/325	169098914	2323,10683	2203	4300	6503	SO:0001819	synonymous_variant	11199	exon7			ATATACAGACCCT	AJ238979	CCDS34096.1	4q32.3	2008-02-05			ENSG00000109511	ENSG00000109511		"""Annexins"""	534	protein-coding gene	gene with protein product		608008				10458909	Standard	NM_007193		Approved	ANX14	uc003irm.3	Q9UJ72	OTTHUMG00000161275	ENST00000359299.3:c.504A>G	4.37:g.169098914A>G		Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	152	86	0.565789	NM_007193	Q96IQ5|Q9UJV4	Silent	SNP	ENST00000359299.3	37	CCDS34096.1																																																																																			A|0.841;G|0.159	0.159	strong		0.453	ANXA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364348.2	NM_007193	
HLA-A	3105	hgsc.bcm.edu	37	6	29910761	29910761	+	Missense_Mutation	SNP	G	G	A	rs1136688	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:29910761G>A	ENST00000396634.1	+	4	642	c.301G>A	c.(301-303)Gac>Aac	p.D101N	HLA-A_ENST00000376802.2_Missense_Mutation_p.D101N|HLA-A_ENST00000376809.5_Missense_Mutation_p.D101N|HLA-A_ENST00000376806.5_Missense_Mutation_p.D101N			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	101	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						TGACCGAGTGGACCTGGGGAC	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)			a|||	1928	0.384984	0.3812	0.3963	5008	,	,		10355	0.3115		0.3936	False		,,,				2504	0.4489				p.D101N		Atlas-SNP	.											.	HLA-A	89	.	0			c.G301A						PASS	.	A	ASN/ASP	1178,3210		254,670,1270	60.0	64.0	62.0		301	-7.2	0.0	6	dbSNP_86	62	2688,5880		672,1344,2268	no	missense	HLA-A	NM_002116.7	23	926,2014,3538	AA,AG,GG		31.3725,26.8459,29.8395	benign	101/366	29910761	3866,9090	2194	4284	6478	SO:0001583	missense	3105	exon2	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	CGAGTGGACCTGG	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.301G>A	6.37:g.29910761G>A	ENSP00000379873:p.Asp101Asn	Somatic	227	0	0		WXS	Illumina HiSeq	Phase_I	142	140	0.985915	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Missense_Mutation	SNP	ENST00000396634.1	37	CCDS34373.1	631	0.2889194139194139	145	0.29471544715447157	127	0.35082872928176795	124	0.21678321678321677	235	0.3100263852242744	.	6.812	0.518999	0.13005	0.268459	0.313725	ENSG00000206503	ENST00000396634;ENST00000376806;ENST00000376809;ENST00000355767;ENST00000376802	T;T;T;T	0.00682	5.86;5.86;5.86;5.86	3.57	-7.15	0.01521	MHC class I, alpha chain, alpha1/alpha2 (6);MHC classes I/II-like antigen recognition protein (3);MHC class I-like antigen recognition (3);	2.561180	0.02614	N	0.102464	T	0.00073	0.0002	N	0.00670	-1.27	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	0.12156	0.002;0.007;0.002;0.003;0.002	T	0.43540	-0.9385	9	0.07325	T	0.83	.	9.8047	0.40786	0.1773:0.0:0.5959:0.2268	rs1136688;rs2231003;rs3179183;rs3200156;rs9260135;rs16896601;rs17423978;rs41563415	101;101;101;101;101	P13746;Q5SRN7;P16188;Q5SRN5;P04439	1A11_HUMAN;.;1A30_HUMAN;.;1A03_HUMAN	N	101	ENSP00000379873:D101N;ENSP00000366002:D101N;ENSP00000366005:D101N;ENSP00000365998:D101N	ENSP00000348012:D101N	D	+	1	0	HLA-A	30018740	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-5.635000	0.00108	-3.195000	0.00218	-4.015000	0.00013	GAC	A|0.386;G|0.614	0.386	strong		0.687	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
AHNAK2	113146	hgsc.bcm.edu	37	14	105417894	105417894	+	Missense_Mutation	SNP	C	C	G	rs2819440	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:105417894C>G	ENST00000333244.5	-	7	4013	c.3894G>C	c.(3892-3894)atG>atC	p.M1298I	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	1298			M -> I (in dbSNP:rs2819440).			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)			CCGGGGCCTGCATGTCCACCT	0.607													.|||	3924	0.783546	0.9909	0.6758	5008	,	,		13772	0.5982		0.7694	False		,,,				2504	0.7853				p.M1298I		Atlas-SNP	.											.	AHNAK2	719	.	0			c.G3894C						PASS	.	G	ILE/MET	3661,165		1781,99,33	73.0	66.0	68.0		3894	-0.2	0.0	14	dbSNP_100	68	4770,1700		2138,494,603	no	missense	AHNAK2	NM_138420.2	10	3919,593,636	GG,GC,CC		26.2751,4.3126,18.1138	benign	1298/5796	105417894	8431,1865	1913	3235	5148	SO:0001583	missense	113146	exon7			GGCCTGCATGTCC	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.3894G>C	14.37:g.105417894C>G	ENSP00000353114:p.Met1298Ile	Somatic	0	0	.		WXS	Illumina HiSeq	Phase_I	84	83	0.988095	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	1639	0.7504578754578755	486	0.9878048780487805	245	0.6767955801104972	332	0.5804195804195804	576	0.7598944591029023	N	0.196	-1.048798	0.01981	0.956874	0.737249	ENSG00000185567	ENST00000333244	T	0.00606	6.26	4.21	-0.191	0.13252	.	.	.	.	.	T	0.00012	0.0000	N	0.00140	-2.01	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.27157	-1.0082	8	0.26408	T	0.33	-3.3979	3.7716	0.08643	0.1777:0.48:0.219:0.1234	rs57546342	1298	Q8IVF2	AHNK2_HUMAN	I	1298	ENSP00000353114:M1298I	ENSP00000353114:M1298I	M	-	3	0	AHNAK2	104488939	0.947000	0.32204	0.000000	0.03702	0.000000	0.00434	-0.516000	0.06282	-0.810000	0.04375	-1.145000	0.01858	ATG	C|0.249;G|0.751	0.751	strong		0.607	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
UHRF1BP1	54887	hgsc.bcm.edu	37	6	34826663	34826663	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:34826663G>A	ENST00000192788.5	+	14	2701	c.2530G>A	c.(2530-2532)Gtg>Atg	p.V844M	UHRF1BP1_ENST00000452449.2_Missense_Mutation_p.V844M	NM_017754.3	NP_060224.3	Q6BDS2	URFB1_HUMAN	UHRF1 binding protein 1	844							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						CCTGAAGGAGGTGCTGCAGAG	0.537																																					p.V844M		Atlas-SNP	.											.	UHRF1BP1	102	.	0			c.G2530A						PASS	.						123.0	120.0	121.0					6																	34826663		2021	4193	6214	SO:0001583	missense	54887	exon14			AAGGAGGTGCTGC	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.2530G>A	6.37:g.34826663G>A	ENSP00000192788:p.Val844Met	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	130	32	0.246154	NM_017754	Q9NXE0	Missense_Mutation	SNP	ENST00000192788.5	37	CCDS43455.1	.	.	.	.	.	.	.	.	.	.	G	12.55	1.972845	0.34848	.	.	ENSG00000065060	ENST00000192788;ENST00000452449	T;T	0.17370	2.28;2.28	5.17	5.17	0.71159	.	0.207707	0.41396	D	0.000890	T	0.06600	0.0169	L	0.34521	1.04	0.31062	N	0.713971	B	0.31581	0.329	B	0.27170	0.077	T	0.10870	-1.0611	10	0.52906	T	0.07	-16.6036	13.7912	0.63143	0.0:0.0:0.8469:0.1531	.	844	Q6BDS2	URFB1_HUMAN	M	844	ENSP00000192788:V844M;ENSP00000400628:V844M	ENSP00000192788:V844M	V	+	1	0	UHRF1BP1	34934641	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	2.028000	0.41088	2.692000	0.91855	0.591000	0.81541	GTG	.	.	none		0.537	UHRF1BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040260.1	NM_017754	
NAV2	89797	hgsc.bcm.edu	37	11	20112417	20112417	+	Silent	SNP	A	A	C	rs2243624	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:20112417A>C	ENST00000396087.3	+	30	5781	c.5682A>C	c.(5680-5682)tcA>tcC	p.S1894S	NAV2_ENST00000527559.2_Silent_p.S1823S|NAV2_ENST00000540292.1_Silent_p.S1825S|NAV2_ENST00000360655.4_Silent_p.S1771S|NAV2_ENST00000533917.1_Silent_p.S899S|NAV2_ENST00000349880.4_Silent_p.S1835S|NAV2_ENST00000311043.8_Silent_p.S899S|NAV2_ENST00000396085.1_Silent_p.S1838S	NM_001244963.1	NP_001231892.1	Q8IVL1	NAV2_HUMAN	neuron navigator 2	1894					glossopharyngeal nerve development (GO:0021563)|locomotory behavior (GO:0007626)|optic nerve development (GO:0021554)|regulation of systemic arterial blood pressure by baroreceptor feedback (GO:0003025)|sensory perception of smell (GO:0007608)|sensory perception of sound (GO:0007605)|vagus nerve development (GO:0021564)	interstitial matrix (GO:0005614)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|heparin binding (GO:0008201)			NS(1)|breast(2)|central_nervous_system(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(26)|lung(38)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	116						CTAGAATTTCAGAATGCATGG	0.438													A|||	2038	0.406949	0.4592	0.4467	5008	,	,		19772	0.6349		0.3101	False		,,,				2504	0.1728				p.S1894S		Atlas-SNP	.											.	NAV2	255	.	0			c.A5682C						PASS	.	A	,,,	1805,2601	531.5+/-373.2	358,1089,756	85.0	70.0	75.0		5313,2697,5505,5514	-11.1	0.0	11	dbSNP_100	75	2748,5852	439.1+/-359.1	457,1834,2009	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NAV2	NM_001111018.1,NM_001111019.1,NM_145117.4,NM_182964.5	,,,	815,2923,2765	CC,CA,AA		31.9535,40.9669,35.0069	,,,	1771/2366,899/1494,1835/2430,1838/2433	20112417	4553,8453	2203	4300	6503	SO:0001819	synonymous_variant	89797	exon29			AATTTCAGAATGC	AB037840	CCDS7850.1, CCDS7851.2, CCDS44552.1, CCDS53612.1, CCDS58126.1	11p15.1	2008-07-18			ENSG00000166833	ENSG00000166833	3.6.1.1		15997	protein-coding gene	gene with protein product	"""pore membrane and/or filament interacting like protein 2"", ""retinoic acid inducible gene in neuroblastoma 1"", ""helicase, APC down-regulated 1"""	607026				12079279, 12062803	Standard	NM_145117		Approved	FLJ10633, FLJ11030, HELAD1, KIAA1419, POMFIL2, RAINB1, FLJ23707	uc010rdm.2	Q8IVL1	OTTHUMG00000151837	ENST00000396087.3:c.5682A>C	11.37:g.20112417A>C		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	76	13	0.171053	NM_001244963	A6NEC1|Q8IVK3|Q8IVK4|Q8IVK5|Q8IVK6|Q8IVK7|Q8IVK8|Q8NHC9|Q8NHD0|Q8TDE9|Q8TDF0|Q8TEB3|Q96B30|Q9NUZ6|Q9NVM7|Q9P2C8	Silent	SNP	ENST00000396087.3	37	CCDS58126.1																																																																																			A|0.618;C|0.382	0.382	strong		0.438	NAV2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324112.1	NM_145117	
RNF32	140545	hgsc.bcm.edu	37	7	156469133	156469133	+	Missense_Mutation	SNP	C	C	G	rs2302147	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:156469133C>G	ENST00000405335.1	+	10	1282	c.873C>G	c.(871-873)caC>caG	p.H291Q	RNF32_ENST00000317955.5_Missense_Mutation_p.H291Q|LMBR1_ENST00000430825.2_5'UTR|RNF32_ENST00000392743.2_Missense_Mutation_p.H291Q|RNF32_ENST00000311822.8_3'UTR|RNF32_ENST00000432459.2_Missense_Mutation_p.H291Q|RNF32_ENST00000343665.4_Missense_Mutation_p.H267Q			Q9H0A6	RNF32_HUMAN	ring finger protein 32	291			H -> Q (in dbSNP:rs2302147).			aggresome (GO:0016235)|endosome (GO:0005768)	zinc ion binding (GO:0008270)			cervix(2)|endometrium(3)|kidney(1)|large_intestine(2)|lung(5)|upper_aerodigestive_tract(2)	15	Ovarian(565;0.218)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.00291)	UCEC - Uterine corpus endometrioid carcinoma (81;0.169)		GGGAGACCCACGAGTGCTCCA	0.617													C|||	2009	0.401158	0.5303	0.4121	5008	,	,		13424	0.4097		0.3479	False		,,,				2504	0.2648				p.H291Q		Atlas-SNP	.											.	RNF32	77	.	0			c.C873G						PASS	.	C	GLN/HIS,GLN/HIS,GLN/HIS	2153,2253	569.4+/-382.6	550,1053,600	38.0	37.0	37.0		873,873,873	-3.8	0.0	7	dbSNP_100	37	2970,5630	451.5+/-362.7	519,1932,1849	no	missense,missense,missense	RNF32	NM_001184996.1,NM_001184997.1,NM_030936.3	24,24,24	1069,2985,2449	GG,GC,CC		34.5349,48.8652,39.3895	benign,benign,benign	291/363,291/363,291/363	156469133	5123,7883	2203	4300	6503	SO:0001583	missense	140545	exon9			GACCCACGAGTGC		CCDS5944.1	7q36	2013-08-05			ENSG00000105982	ENSG00000105982		"""RING-type (C3HC4) zinc fingers"""	17118	protein-coding gene	gene with protein product		610241				11890671	Standard	NM_001184996		Approved	FKSG33, HSD15, LMBR2	uc003wmr.3	Q9H0A6	OTTHUMG00000151440	ENST00000405335.1:c.873C>G	7.37:g.156469133C>G	ENSP00000385285:p.His291Gln	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	74	44	0.594595	NM_001184996	Q6FIB3|Q6X7T4|Q8N6V8|Q8TDG0|Q96BM5|Q9Y6U1	Missense_Mutation	SNP	ENST00000405335.1	37	CCDS5944.1	911	0.41712454212454214	262	0.532520325203252	134	0.3701657458563536	236	0.4125874125874126	279	0.36807387862796836	C	8.510	0.866371	0.17250	0.488652	0.345349	ENSG00000105982	ENST00000432459;ENST00000317955;ENST00000405335;ENST00000392743;ENST00000343665	T;T;T;T;T	0.40756	1.02;1.02;1.02;1.02;1.02	4.71	-3.84	0.04256	Zinc finger, RING/FYVE/PHD-type (1);	1.357730	0.04194	N	0.328751	T	0.00012	0.0000	N	0.02315	-0.6	0.09310	P	0.99999542511	B	0.19073	0.033	B	0.11329	0.006	T	0.39522	-0.9610	9	0.27785	T	0.31	0.9631	12.4771	0.55821	0.0:0.2759:0.0:0.7241	rs2302147;rs10372879;rs2302147	291	Q9H0A6	RNF32_HUMAN	Q	291;291;291;291;267	ENSP00000405588:H291Q;ENSP00000315950:H291Q;ENSP00000385285:H291Q;ENSP00000376499:H291Q;ENSP00000341185:H267Q	ENSP00000315950:H291Q	H	+	3	2	RNF32	156161894	0.000000	0.05858	0.001000	0.08648	0.018000	0.09664	-1.452000	0.02385	-0.967000	0.03582	-0.222000	0.12452	CAC	C|0.601;G|0.399	0.399	strong		0.617	RNF32-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322660.2	NM_030936	
PRPH	5630	hgsc.bcm.edu	37	12	49689009	49689009	+	Missense_Mutation	SNP	G	G	A	rs57451017	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:49689009G>A	ENST00000257860.4	+	1	1525	c.26G>A	c.(25-27)cGg>cAg	p.R9Q	RP11-161H23.9_ENST00000553259.1_RNA	NM_006262.3	NP_006253.2	P23942	PRPH2_HUMAN	peripherin	0					cell adhesion (GO:0007155)|retina development in camera-type eye (GO:0060041)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)				kidney(1)|large_intestine(2)|lung(8)|skin(1)	12						TCGGGCCTCCGGGCCGGCTTC	0.692													G|||	73	0.0145767	0.0008	0.0101	5008	,	,		14471	0.0139		0.0169	False		,,,				2504	0.0348				p.R9Q		Atlas-SNP	.											.	PRPH	26	.	0			c.G26A						PASS	.	G	GLN/ARG	15,4377		0,15,2181	14.0	15.0	15.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	26	3.7	1.0	12	dbSNP_129	15	99,8473		0,99,4187	yes	missense	PRPH	NM_006262.3	43	0,114,6368	AA,AG,GG		1.1549,0.3415,0.8794	possibly-damaging	9/471	49689009	114,12850	2196	4286	6482	SO:0001583	missense	5630	exon1			GCCTCCGGGCCGG		CCDS8783.1	12q12-q13	2013-01-16						"""Intermediate filaments type III"""	9461	protein-coding gene	gene with protein product		170710		NEF4		1378416	Standard	XM_005269025		Approved	PRPH1	uc001rtu.3	P41219		ENST00000257860.4:c.26G>A	12.37:g.49689009G>A	ENSP00000257860:p.Arg9Gln	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	135	67	0.496296	NM_006262	Q5TFH5|Q6DK65	Missense_Mutation	SNP	ENST00000257860.4	37	CCDS8783.1	33	0.01510989010989011	2	0.0040650406504065045	5	0.013812154696132596	14	0.024475524475524476	12	0.0158311345646438	G	23.8	4.454808	0.84209	0.003415	0.011549	ENSG00000135406	ENST00000257860	D	0.83673	-1.75	4.55	3.66	0.41972	.	0.000000	0.34531	N	0.003900	T	0.49983	0.1589	N	0.19112	0.55	0.39071	D	0.96072	P	0.36495	0.556	B	0.24394	0.053	T	0.62364	-0.6870	10	0.39692	T	0.17	.	10.2584	0.43412	0.0974:0.0:0.9026:0.0	rs57451017	9	P41219	PERI_HUMAN	Q	9	ENSP00000257860:R9Q	ENSP00000257860:R9Q	R	+	2	0	PRPH	47975276	.	.	1.000000	0.80357	0.776000	0.43924	.	.	1.129000	0.42072	0.563000	0.77884	CGG	G|0.986;A|0.014	0.014	strong		0.692	PRPH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393381.1	NM_006262	
TBC1D13	54662	hgsc.bcm.edu	37	9	131565554	131565554	+	Missense_Mutation	SNP	T	T	C	rs1572912	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:131565554T>C	ENST00000372648.5	+	8	719	c.569T>C	c.(568-570)gTg>gCg	p.V190A	TBC1D13_ENST00000539497.1_Missense_Mutation_p.V9A|TBC1D13_ENST00000223865.8_Intron|TBC1D13_ENST00000466056.1_3'UTR	NM_018201.3	NP_060671.3	Q9NVG8	TBC13_HUMAN	TBC1 domain family, member 13	190	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.		V -> A (in dbSNP:rs1572912). {ECO:0000269|PubMed:15489334}.				Rab GTPase activator activity (GO:0005097)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)	6						AAGAACTCTGTGCCATCATCC	0.552													C|||	2520	0.503195	0.9206	0.2637	5008	,	,		19402	0.3571		0.2863	False		,,,				2504	0.4826				p.V190A		Atlas-SNP	.											.	TBC1D13	27	.	0			c.T569C						PASS	.	C	ALA/VAL	3576,830	328.3+/-300.5	1455,666,82	102.0	93.0	96.0		569	2.5	0.0	9	dbSNP_88	96	2434,6166	698.7+/-405.0	322,1790,2188	yes	missense	TBC1D13	NM_018201.3	64	1777,2456,2270	CC,CT,TT		28.3023,18.8379,46.2094	benign	190/401	131565554	6010,6996	2203	4300	6503	SO:0001583	missense	54662	exon8			ACTCTGTGCCATC	AK001605	CCDS6911.1, CCDS69677.1	9q34.13	2013-07-09			ENSG00000107021	ENSG00000107021			25571	protein-coding gene	gene with protein product						22762500	Standard	XM_005252060		Approved	FLJ10743	uc010myj.3	Q9NVG8	OTTHUMG00000020760	ENST00000372648.5:c.569T>C	9.37:g.131565554T>C	ENSP00000361731:p.Val190Ala	Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	137	61	0.445255	NM_018201	A7E2E7|B3KW04|B9EGJ8|Q5T270|Q5T271	Missense_Mutation	SNP	ENST00000372648.5	37	CCDS6911.1	928	0.4249084249084249	435	0.8841463414634146	103	0.2845303867403315	206	0.36013986013986016	184	0.24274406332453827	C	0.579	-0.838026	0.02692	0.811621	0.283023	ENSG00000107021	ENST00000372648;ENST00000539497	T;T	0.41758	0.99;1.55	5.36	2.49	0.30216	Rab-GAP/TBC domain (3);	0.812882	0.11683	N	0.539641	T	0.00012	0.0000	N	0.16656	0.425	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.37430	-0.9706	9	0.07030	T	0.85	0.5411	6.3238	0.21232	0.0:0.6384:0.1326:0.229	rs1572912;rs52793555;rs60746730;rs1572912	190	Q9NVG8	TBC13_HUMAN	A	190;9	ENSP00000361731:V190A;ENSP00000437751:V9A	ENSP00000361731:V190A	V	+	2	0	TBC1D13	130605375	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.664000	0.25068	0.013000	0.14918	-1.536000	0.00914	GTG	T|0.535;C|0.464	0.464	strong		0.552	TBC1D13-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054496.1	NM_018201	
ACAN	176	hgsc.bcm.edu	37	15	89400080	89400080	+	Missense_Mutation	SNP	A	A	G	rs35546357	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:89400080A>G	ENST00000561243.1	+	11	4264	c.4264A>G	c.(4264-4266)Act>Gct	p.T1422A	ACAN_ENST00000439576.2_Missense_Mutation_p.T1422A|ACAN_ENST00000559004.1_Missense_Mutation_p.T1422A|ACAN_ENST00000352105.7_Missense_Mutation_p.T1422A			P16112	PGCA_HUMAN	aggrecan	1423	29 X 19 AA approximate tandem repeats of E-[IVDG]-[LV]-[EV]-[GTI]-[STA]-[ATV]- [SP]-[GA]-[VIFAD]-[GEDL]-[DE]-[LVI]-[SG]- [GERK]-[LV]-P-S-G.|CS-1.				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|proteolysis (GO:0006508)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)	carbohydrate binding (GO:0030246)|extracellular matrix structural constituent (GO:0005201)|hyaluronic acid binding (GO:0005540)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(4)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(15)|liver(2)|lung(40)|ovary(2)|prostate(5)|skin(5)|stomach(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	93	Lung NSC(78;0.0392)|all_lung(78;0.077)		BRCA - Breast invasive adenocarcinoma(143;0.146)			TCTAGAGACTACTGCCCCTGG	0.537																																					p.T1422A		Atlas-SNP	.											.	ACAN	220	.	0			c.A4264G						PASS	.	A	ALA/THR,ALA/THR	40,3654		0,40,1807	129.0	133.0	132.0		4264,4264	-0.5	0.0	15	dbSNP_126	132	168,7992		2,164,3914	no	missense,missense	ACAN	NM_013227.3,NM_001135.3	58,58	2,204,5721	GG,GA,AA		2.0588,1.0828,1.7547	benign,benign	1422/2531,1422/2432	89400080	208,11646	1847	4080	5927	SO:0001583	missense	176	exon12			GAGACTACTGCCC	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.4264A>G	15.37:g.89400080A>G	ENSP00000453342:p.Thr1422Ala	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	53	28	0.528302	NM_001135	Q13650|Q9UCD3|Q9UCP4|Q9UCP5|Q9UDE0	Missense_Mutation	SNP	ENST00000561243.1	37	CCDS53970.1	.	.	.	.	.	.	.	.	.	.	-	11.27	1.589124	0.28357	0.010828	0.020588	ENSG00000157766	ENST00000439576;ENST00000352105;ENST00000268134	D;D	0.94828	-3.53;-3.5	3.81	-0.463	0.12164	.	0.556823	0.13655	N	0.371970	T	0.72326	0.3446	N	0.02539	-0.55	0.09310	N	1	P;B	0.37663	0.604;0.397	B;B	0.41299	0.353;0.147	T	0.74748	-0.3560	10	0.33141	T	0.24	.	4.2067	0.10491	0.2792:0.0:0.3464:0.3744	rs35546357	1422;1422	E7ENV9;E7EX88	.;.	A	1422;1422;1308	ENSP00000387356:T1422A;ENSP00000341615:T1422A	ENSP00000268134:T1308A	T	+	1	0	ACAN	87201084	0.075000	0.21258	0.008000	0.14137	0.533000	0.34776	-0.241000	0.08940	0.141000	0.18875	-0.892000	0.02923	ACT	A|0.983;G|0.017	0.017	strong		0.537	ACAN-006	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416267.2	NM_001135	
TBC1D9B	23061	hgsc.bcm.edu	37	5	179290845	179290845	+	Missense_Mutation	SNP	T	T	G	rs30386	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:179290845T>G	ENST00000356834.3	-	22	3393	c.3356A>C	c.(3355-3357)aAa>aCa	p.K1119T	TBC1D9B_ENST00000518085.1_5'UTR|TBC1D9B_ENST00000355235.3_Missense_Mutation_p.K1102T|TBC1D9B_ENST00000444477.2_Missense_Mutation_p.K260T|TBC1D9B_ENST00000519746.1_Missense_Mutation_p.K278T	NM_198868.2	NP_942568.2	Q66K14	TBC9B_HUMAN	TBC1 domain family, member 9B (with GRAM domain)	1119			K -> T (in dbSNP:rs30386). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005, ECO:0000269|PubMed:9734811, ECO:0000269|Ref.5}.			integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|Rab GTPase activator activity (GO:0005097)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(9)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	28	all_cancers(89;0.000197)|all_epithelial(37;6.84e-05)|Renal(175;0.000159)|Lung NSC(126;0.00136)|all_lung(126;0.00243)	all_cancers(40;0.0236)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CTGTGGGGCTTTTCCGAGGTG	0.647													T|||	2887	0.576478	0.4289	0.67	5008	,	,		17713	0.7748		0.4493	False		,,,				2504	0.636				p.K1119T		Atlas-SNP	.											.	TBC1D9B	157	.	0			c.A3356C						PASS	.	T	THR/LYS,THR/LYS	2023,2383	554.0+/-378.9	497,1029,677	66.0	70.0	69.0		3305,3356	5.4	0.9	5	dbSNP_76	69	3951,4649	537.1+/-383.1	903,2145,1252	yes	missense,missense	TBC1D9B	NM_015043.3,NM_198868.2	78,78	1400,3174,1929	GG,GT,TT		45.9419,45.9147,45.9326	benign,benign	1102/1234,1119/1251	179290845	5974,7032	2203	4300	6503	SO:0001583	missense	23061	exon22			GGGGCTTTTCCGA	AB014576	CCDS4450.1, CCDS43408.1	5q35.3	2013-01-10			ENSG00000197226	ENSG00000197226		"""EF-hand domain containing"""	29097	protein-coding gene	gene with protein product						9734811	Standard	NM_198868		Approved	KIAA0676	uc003mlh.3	Q66K14	OTTHUMG00000130911	ENST00000356834.3:c.3356A>C	5.37:g.179290845T>G	ENSP00000349291:p.Lys1119Thr	Somatic	116	1	0.00862069		WXS	Illumina HiSeq	Phase_I	138	138	1	NM_198868	D3DWQ5|D3DWQ6|O75163|Q53EY0|Q6MZI2|Q96H49	Missense_Mutation	SNP	ENST00000356834.3	37	CCDS43408.1	1187|1187	0.5434981684981685|0.5434981684981685	193|193	0.39227642276422764|0.39227642276422764	224|224	0.6187845303867403|0.6187845303867403	444|444	0.7762237762237763|0.7762237762237763	326|326	0.43007915567282323|0.43007915567282323	T|T	1.164|1.164	-0.642875|-0.642875	0.03531|0.03531	0.459147|0.459147	0.459419|0.459419	ENSG00000197226|ENSG00000197226	ENST00000524222|ENST00000356834;ENST00000355235;ENST00000519746;ENST00000444477;ENST00000544438	T|T;T;T;T	0.42131|0.41400	0.98|1.0;1.0;1.0;1.0	5.37|5.37	5.37|5.37	0.77165|0.77165	.|.	0.301605|0.301605	0.32015|0.32015	N|N	0.006703|0.006703	T|T	0.00012|0.00012	0.0000|0.0000	L|L	0.47716|0.47716	1.5|1.5	0.58432|0.58432	P|P	4.000000000004E-6|4.000000000004E-6	.|B;B;B;B;P	.|0.40970	.|0.007;0.013;0.009;0.256;0.734	.|B;B;B;B;B	.|0.35470	.|0.009;0.02;0.007;0.039;0.203	T|T	0.18398|0.18398	-1.0338|-1.0338	7|9	0.18276|0.30854	T|T	0.48|0.27	-18.4965|-18.4965	11.3822|11.3822	0.49763|0.49763	0.0:0.0:0.1513:0.8487|0.0:0.0:0.1513:0.8487	rs30386;rs1301867;rs3734004;rs17079713;rs17844858;rs17857573;rs58733153;rs30386|rs30386;rs1301867;rs3734004;rs17079713;rs17844858;rs17857573;rs58733153;rs30386	.|1101;1102;1119;318;193	.|A1L3A9;Q66K14-2;Q66K14;B3KM54;F5H5B8	.|.;.;TBC9B_HUMAN;.;.	Q|T	162|1119;1102;278;260;193	ENSP00000428724:K162Q|ENSP00000349291:K1119T;ENSP00000347375:K1102T;ENSP00000430293:K278T;ENSP00000401585:K260T	ENSP00000428724:K162Q|ENSP00000347375:K1102T	K|K	-|-	1|2	0|0	TBC1D9B|TBC1D9B	179223451|179223451	0.835000|0.835000	0.29415|0.29415	0.884000|0.884000	0.34674|0.34674	0.024000|0.024000	0.10985|0.10985	1.367000|1.367000	0.34204|0.34204	2.027000|2.027000	0.59764|0.59764	0.459000|0.459000	0.35465|0.35465	AAG|AAA	T|0.501;G|0.499	0.499	strong		0.647	TBC1D9B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253501.3	NM_015043	
XPO5	57510	hgsc.bcm.edu	37	6	43514382	43514382	+	Silent	SNP	A	A	G	rs567618901		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:43514382A>G	ENST00000265351.7	-	20	2478	c.2268T>C	c.(2266-2268)agT>agC	p.S756S	SCARNA15_ENST00000516409.1_RNA	NM_020750.2	NP_065801.1	Q9HAV4	XPO5_HUMAN	exportin 5	756					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)			TTGGATTTCCACTGGATGTAT	0.458													A|||	1	0.000199681	0.0	0.0	5008	,	,		15773	0.001		0.0	False		,,,				2504	0.0				p.S756S		Atlas-SNP	.											XPO5,NS,carcinoma,-1,1	XPO5	79	1	0			c.T2268C						PASS	.						54.0	53.0	53.0					6																	43514382		1873	4102	5975	SO:0001819	synonymous_variant	57510	exon20			ATTTCCACTGGAT	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.2268T>C	6.37:g.43514382A>G		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	98	43	0.438776	NM_020750	Q5JTE6|Q96G48|Q96HN3|Q9BWM6|Q9BZV5|Q9H9M4|Q9NT89|Q9NW39|Q9ULC9	Silent	SNP	ENST00000265351.7	37	CCDS47430.1																																																																																			.	.	none		0.458	XPO5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040657.2	NM_020750	
MYO7A	4647	hgsc.bcm.edu	37	11	76912636	76912636	+	Missense_Mutation	SNP	A	A	T	rs2276288	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:76912636A>T	ENST00000409709.3	+	36	5268	c.4996A>T	c.(4996-4998)Agt>Tgt	p.S1666C	MYO7A_ENST00000458637.2_Missense_Mutation_p.S1628C|MYO7A_ENST00000409619.2_Missense_Mutation_p.S1617C	NM_000260.3	NP_000251.3	Q13402	MYO7A_HUMAN	myosin VIIA	1666	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.		S -> C (in dbSNP:rs2276288). {ECO:0000269|PubMed:8622919, ECO:0000269|PubMed:8884267}.|S -> G.		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						CCCCACCGACAGTGTGTACGT	0.607													a|||	2763	0.551717	0.7254	0.6455	5008	,	,		17830	0.4524		0.5656	False		,,,				2504	0.3384				p.S1666C		Atlas-SNP	.											.	MYO7A	164	.	0			c.A4996T						PASS	.	A	CYS/SER,CYS/SER	2919,1367		1017,885,241	70.0	75.0	73.0		4996,4882	3.5	0.6	11	dbSNP_100	73	4591,3871		1259,2073,899	yes	missense,missense	MYO7A	NM_000260.3,NM_001127180.1	112,112	2276,2958,1140	TT,TA,AA		45.7457,31.8945,41.0888	benign,benign	1666/2216,1628/2176	76912636	7510,5238	2143	4231	6374	SO:0001583	missense	4647	exon36			ACCGACAGTGTGT	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.4996A>T	11.37:g.76912636A>T	ENSP00000386331:p.Ser1666Cys	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	71	71	1	NM_000260	B9A011|F8VUN5|P78427|Q13321|Q14785|Q92821|Q92822	Missense_Mutation	SNP	ENST00000409709.3	37	CCDS53683.1	1295	0.592948717948718	365	0.741869918699187	227	0.6270718232044199	260	0.45454545454545453	443	0.5844327176781002	T	0.981	-0.697003	0.03279	0.681055	0.542543	ENSG00000137474	ENST00000409709;ENST00000458637;ENST00000409619;ENST00000545136;ENST00000358342;ENST00000343356;ENST00000341717;ENST00000458169;ENST00000544424	T;T;T;T	0.28895	1.59;1.59;1.59;1.59	4.58	3.46	0.39613	.	0.216755	0.49305	N	0.000153	T	0.00012	0.0000	.	.	.	0.43583	P	0.004076999999999997	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.41106	-0.9527	8	0.02654	T	1	.	9.0084	0.36127	0.2964:0.0:0.0:0.7036	rs2276288;rs57060436	1617;1628	B9A011;F8VUN5	.;.	C	1666;1628;1617;839;1665;1635;1542;808;281	ENSP00000386331:S1666C;ENSP00000392185:S1628C;ENSP00000386635:S1617C;ENSP00000417017:S808C	ENSP00000345075:S1542C	S	+	1	0	MYO7A	76590284	1.000000	0.71417	0.581000	0.28614	0.784000	0.44337	2.920000	0.48844	0.791000	0.33826	-0.372000	0.07161	AGT	A|0.422;T|0.578	0.578	strong		0.607	MYO7A-001	KNOWN	non_canonical_conserved|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000328133.1	NM_000260	
DSP	1832	hgsc.bcm.edu	37	6	7584617	7584617	+	Silent	SNP	C	C	T	rs2076300	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:7584617C>T	ENST00000379802.3	+	24	7463	c.7122C>T	c.(7120-7122)acC>acT	p.T2374T	DSP_ENST00000418664.2_Silent_p.T1775T	NM_004415.2	NP_004406.2	P15924	DESP_HUMAN	desmoplakin	2374	4.5 X 38 AA tandem repeats (Domain B).|Globular 2.				adherens junction organization (GO:0034332)|apoptotic process (GO:0006915)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|desmosome organization (GO:0002934)|epidermis development (GO:0008544)|intermediate filament organization (GO:0045109)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)|protein localization to adherens junction (GO:0071896)|regulation of heart rate by cardiac conduction (GO:0086091)|single organismal cell-cell adhesion (GO:0016337)|ventricular cardiac muscle cell action potential (GO:0086005)|ventricular compact myocardium morphogenesis (GO:0003223)|wound healing (GO:0042060)	basolateral plasma membrane (GO:0016323)|cornified envelope (GO:0001533)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|intercalated disc (GO:0014704)|intermediate filament (GO:0005882)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)|protein binding, bridging (GO:0030674)|protein kinase C binding (GO:0005080)|scaffold protein binding (GO:0097110)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)	p.T2374T(1)		biliary_tract(1)|breast(6)|central_nervous_system(7)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(16)|liver(2)|lung(27)|ovary(4)|prostate(1)|skin(8)|stomach(3)|upper_aerodigestive_tract(7)|urinary_tract(5)	101	Ovarian(93;0.0584)	all_hematologic(90;0.236)		OV - Ovarian serous cystadenocarcinoma(45;0.000508)		AGATCGCAACCGGGGGGATCA	0.448													C|||	1060	0.211661	0.1369	0.2421	5008	,	,		21083	0.0744		0.3797	False		,,,				2504	0.2597				p.T2374T		Atlas-SNP	.											DSP,NS,carcinoma,0,1	DSP	306	1	1	Substitution - coding silent(1)	stomach(1)	c.C7122T						PASS	.	C	,	758,3648	308.0+/-290.3	71,616,1516	71.0	72.0	72.0		5325,7122	-11.2	0.1	6	dbSNP_96	72	3173,5427	480.6+/-370.4	595,1983,1722	no	coding-synonymous,coding-synonymous	DSP	NM_001008844.1,NM_004415.2	,	666,2599,3238	TT,TC,CC		36.8953,17.2038,30.2245	,	1775/2273,2374/2872	7584617	3931,9075	2203	4300	6503	SO:0001819	synonymous_variant	1832	exon24			CGCAACCGGGGGG	J05211	CCDS4501.1, CCDS47368.1	6p24.3	2014-09-17	2003-05-20		ENSG00000096696	ENSG00000096696			3052	protein-coding gene	gene with protein product		125647	"""desmoplakin (DPI, DPII)"""			1889810	Standard	NM_004415		Approved	KPPS2, PPKS2, DPI, DPII	uc003mxp.1	P15924	OTTHUMG00000014212	ENST00000379802.3:c.7122C>T	6.37:g.7584617C>T		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	143	84	0.587413	NM_004415	B2RTT2|D7RX09|O75993|Q14189|Q9UHN4	Silent	SNP	ENST00000379802.3	37	CCDS4501.1																																																																																			C|0.732;T|0.268	0.268	strong		0.448	DSP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039786.2	NM_004415	
ADAMTS7	11173	hgsc.bcm.edu	37	15	79058090	79058090	+	Missense_Mutation	SNP	A	A	G	rs2929158	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	72	0	0		WXS	Illumina HiSeq	Phase_I	97	10	0.103093	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	
HAO1	54363	hgsc.bcm.edu	37	20	7894999	7894999	+	Silent	SNP	C	C	T	rs373499154		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:7894999C>T	ENST00000378789.3	-	3	408	c.357G>A	c.(355-357)gcG>gcA	p.A119A		NM_017545.2	NP_060015.1	Q9UJM8	HAOX1_HUMAN	hydroxyacid oxidase (glycolate oxidase) 1	119	FMN hydroxy acid dehydrogenase. {ECO:0000255|PROSITE-ProRule:PRU00683}.				cellular nitrogen compound metabolic process (GO:0034641)|fatty acid alpha-oxidation (GO:0001561)|glycolate catabolic process (GO:0046296)|glyoxylate metabolic process (GO:0046487)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)	peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	(S)-2-hydroxy-acid oxidase activity (GO:0003973)|FMN binding (GO:0010181)|glycolate oxidase activity (GO:0008891)|glyoxylate oxidase activity (GO:0047969)|long-chain-(S)-2-hydroxy-long-chain-acid oxidase activity (GO:0052853)|medium-chain-(S)-2-hydroxy-acid oxidase activity (GO:0052854)|receptor binding (GO:0005102)|very-long-chain-(S)-2-hydroxy-acid oxidase activity (GO:0052852)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(19)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	36						GACCAGCTTCCGCCACTTCTT	0.537																																					p.A119A		Atlas-SNP	.											HAO1,colon,carcinoma,0,1	HAO1	71	1	0			c.G357A						scavenged	.						98.0	68.0	78.0					20																	7894999		2203	4300	6503	SO:0001819	synonymous_variant	54363	exon3			AGCTTCCGCCACT	AL021879	CCDS13100.1	20p12	2005-01-10			ENSG00000101323	ENSG00000101323	1.1.3.15		4809	protein-coding gene	gene with protein product		605023		GOX1		9891009	Standard	NM_017545		Approved	GOX	uc002wmw.1	Q9UJM8	OTTHUMG00000031841	ENST00000378789.3:c.357G>A	20.37:g.7894999C>T		Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	160	2	0.0125	NM_017545	Q14CQ0|Q9UPZ0|Q9Y3I7	Silent	SNP	ENST00000378789.3	37	CCDS13100.1																																																																																			.	.	weak		0.537	HAO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077926.2		
LILRB3	11025	hgsc.bcm.edu	37	19	54723030	54723030	+	Missense_Mutation	SNP	C	C	A	rs61734493	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:54723030C>A	ENST00000391750.1	-	9	1530	c.1394G>T	c.(1393-1395)cGa>cTa	p.R465L	LILRB3_ENST00000424807.1_Missense_Mutation_p.R465L|LILRB3_ENST00000346401.6_Missense_Mutation_p.R477L|LILRA6_ENST00000440558.2_Missense_Mutation_p.R465L|LILRA6_ENST00000270464.5_Missense_Mutation_p.R465L|LILRB3_ENST00000407860.2_Missense_Mutation_p.R482L|LILRB3_ENST00000469273.1_5'UTR|LILRA6_ENST00000419410.2_Missense_Mutation_p.R465L|LILRA6_ENST00000391735.3_3'UTR|LILRB3_ENST00000245620.9_Missense_Mutation_p.R465L			O75022	LIRB3_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 3	465					cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)|immune system process (GO:0002376)|negative regulation of osteoclast differentiation (GO:0045671)	integral component of plasma membrane (GO:0005887)	receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			endometrium(3)|kidney(13)|large_intestine(1)|lung(6)|ovary(2)|prostate(5)|skin(2)|stomach(1)|urinary_tract(1)	34	all_cancers(19;0.00723)|all_epithelial(19;0.00389)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		ACGCTGACGTCggaggaggag	0.607													.|||	102	0.0203674	0.0023	0.0259	5008	,	,		16344	0.0		0.0785	False		,,,				2504	0.002				p.R465L		Atlas-SNP	.											.	LILRB3	67	.	0			c.G1394T						PASS	.	C	LEU/ARG,LEU/ARG	55,4351		2,51,2150	165.0	119.0	134.0		1394,1394	0.7	0.0	19	dbSNP_129	134	515,8085		40,435,3825	no	missense,missense	LILRB3	NM_001081450.1,NM_006864.2	102,102	42,486,5975	AA,AC,CC		5.9884,1.2483,4.3826	possibly-damaging,possibly-damaging	465/633,465/632	54723030	570,12436	2203	4300	6503	SO:0001583	missense	11025	exon8			TGACGTCGGAGGA	U91928	CCDS33105.1, CCDS46175.1	19q13.4	2013-01-11			ENSG00000204577	ENSG00000204577		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6607	protein-coding gene	gene with protein product		604820				9278324, 9382880	Standard	NM_006864		Approved	LIR-3, HL9, ILT5, LIR3, CD85a	uc002qee.1	O75022	OTTHUMG00000066626	ENST00000391750.1:c.1394G>T	19.37:g.54723030C>A	ENSP00000375630:p.Arg465Leu	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	58	27	0.465517	NM_006864	C9J1P3|C9JIP1|O15471|Q86U49	Missense_Mutation	SNP	ENST00000391750.1	37	CCDS33105.1	56	0.02564102564102564	0	0.0	10	0.027624309392265192	0	0.0	46	0.06068601583113457	C	10.70	1.424541	0.25639	0.012483	0.059884	ENSG00000204577;ENSG00000204577;ENSG00000204577;ENSG00000204577;ENSG00000204577;ENSG00000244482;ENSG00000244482;ENSG00000244482	ENST00000391750;ENST00000424807;ENST00000346401;ENST00000245620;ENST00000407860;ENST00000440558;ENST00000270464;ENST00000419410	T;T;T;T;T;T;T;T	0.00498	7.04;7.04;6.97;7.04;6.99;7.02;7.02;7.04	2.82	0.67	0.17923	.	2586.710000	0.00166	N	0.000000	T	0.00109	0.0003	L	0.58428	1.81	0.09310	N	1	B;B;B;B;B;B;B	0.30179	0.271;0.107;0.031;0.017;0.052;0.207;0.032	B;B;B;B;B;B;B	0.31869	0.137;0.062;0.008;0.013;0.039;0.051;0.036	T	0.47086	-0.9144	10	0.38643	T	0.18	.	4.9124	0.13829	0.0:0.7061:0.0:0.2939	.	482;465;465;477;482;465;465	B5MCX0;F8WCY4;D3YTC4;F8W6G6;O75022-2;O75022;O75022-3	.;.;.;.;.;LIRB3_HUMAN;.	L	465;465;477;465;482;465;465;465	ENSP00000375630:R465L;ENSP00000412771:R465L;ENSP00000345184:R477L;ENSP00000245620:R465L;ENSP00000384274:R482L;ENSP00000390120:R465L;ENSP00000270464:R465L;ENSP00000411227:R465L	ENSP00000270464:R465L	R	-	2	0	LILRB3;LILRA6	59414842	0.000000	0.05858	0.000000	0.03702	0.042000	0.13812	-0.092000	0.11129	0.294000	0.22547	-0.424000	0.05967	CGA	C|0.956;A|0.044	0.044	strong		0.607	LILRB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000142844.5	NM_006864	
CHGB	1114	hgsc.bcm.edu	37	20	5903932	5903932	+	Missense_Mutation	SNP	G	G	T	rs142841879	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:5903932G>T	ENST00000378961.4	+	4	1346	c.1142G>T	c.(1141-1143)tGg>tTg	p.W381L		NM_001819.2	NP_001810.2	P05060	SCG1_HUMAN	chromogranin B (secretogranin 1)	381						extracellular region (GO:0005576)|secretory granule (GO:0030141)	hormone activity (GO:0005179)			breast(7)|kidney(2)|large_intestine(8)|lung(19)|ovary(1)|pancreas(2)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)	47						GAGGAGAGTTGGGATGAGGAG	0.547													G|||	16	0.00319489	0.0008	0.0058	5008	,	,		19943	0.0		0.0099	False		,,,				2504	0.001				p.W381L		Atlas-SNP	.											.	CHGB	112	.	0			c.G1142T						PASS	.	G	LEU/TRP	2,4404	4.2+/-10.8	0,2,2201	115.0	113.0	114.0		1142	-3.4	0.0	20	dbSNP_134	114	35,8565	23.4+/-69.3	0,35,4265	yes	missense	CHGB	NM_001819.2	61	0,37,6466	TT,TG,GG		0.407,0.0454,0.2845	benign	381/678	5903932	37,12969	2203	4300	6503	SO:0001583	missense	1114	exon4			AGAGTTGGGATGA		CCDS13092.1	20p12.3	2013-09-19			ENSG00000089199	ENSG00000089199			1930	protein-coding gene	gene with protein product	"""secretogranin B"""	118920		SCG1		3608978	Standard	NM_001819		Approved		uc002wmg.3	P05060	OTTHUMG00000031821	ENST00000378961.4:c.1142G>T	20.37:g.5903932G>T	ENSP00000368244:p.Trp381Leu	Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	23	12	0.521739	NM_001819	A8K021|Q59EU9|Q6IBS6|Q9BQV6|Q9UC25|Q9UJA6	Missense_Mutation	SNP	ENST00000378961.4	37	CCDS13092.1	12	0.005494505494505495	1	0.0020325203252032522	3	0.008287292817679558	0	0.0	8	0.010554089709762533	G	0.005	-2.221686	0.00283	4.54E-4	0.00407	ENSG00000089199	ENST00000378961	T	0.01406	4.93	5.45	-3.43	0.04810	.	2.071020	0.01949	N	0.042447	T	0.00496	0.0016	N	0.03115	-0.41	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.41324	-0.9515	10	0.02654	T	1	2.2596	3.0644	0.06210	0.2183:0.2311:0.4368:0.1138	.	381	P05060	SCG1_HUMAN	L	381	ENSP00000368244:W381L	ENSP00000368244:W381L	W	+	2	0	CHGB	5851932	0.000000	0.05858	0.000000	0.03702	0.059000	0.15707	0.033000	0.13754	-1.015000	0.03375	-0.253000	0.11424	TGG	G|0.997;T|0.003	0.003	strong		0.547	CHGB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077897.2	NM_001819	
OR52J3	119679	hgsc.bcm.edu	37	11	5068661	5068661	+	Silent	SNP	A	A	G	rs2500019|rs386750099	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:5068661A>G	ENST00000380370.1	+	1	906	c.906A>G	c.(904-906)gaA>gaG	p.E302E		NM_001001916.2	NP_001001916.2	Q8NH60	O52J3_HUMAN	olfactory receptor, family 52, subfamily J, member 3	302						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)		AGATTCGAGAACGAGTGCTCT	0.383													G|||	2444	0.488019	0.5923	0.4971	5008	,	,		21199	0.2619		0.508	False		,,,				2504	0.5532				p.E302E		Atlas-SNP	.											.	OR52J3	77	.	0			c.A906G						PASS	.	G		2432,1970		689,1054,458	58.0	55.0	56.0		906	-0.4	0.0	11	dbSNP_100	56	4226,4370		1065,2096,1137	no	coding-synonymous	OR52J3	NM_001001916.2		1754,3150,1595	GG,GA,AA		49.1624,44.7524,48.7767		302/312	5068661	6658,6340	2201	4298	6499	SO:0001819	synonymous_variant	119679	exon1			TCGAGAACGAGTG	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.906A>G	11.37:g.5068661A>G		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	70	70	1	NM_001001916	Q6IFE4	Silent	SNP	ENST00000380370.1	37	CCDS31370.1																																																																																			A|0.493;G|0.507	0.507	strong		0.383	OR52J3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142807.1	NM_001001916	
FRZB	2487	hgsc.bcm.edu	37	2	183731193	183731193	+	Missense_Mutation	SNP	C	C	A	rs36077496	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:183731193C>A	ENST00000295113.4	-	1	697	c.88G>T	c.(88-90)Gct>Tct	p.A30S		NM_001463.3	NP_001454.2	Q92765	SFRP3_HUMAN	frizzled-related protein	30					brain development (GO:0007420)|cochlea morphogenesis (GO:0090103)|convergent extension involved in organogenesis (GO:0060029)|epithelium development (GO:0060429)|gonad development (GO:0008406)|mammary gland involution (GO:0060056)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cartilage development (GO:0061037)|negative regulation of cell development (GO:0010721)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of hepatocyte differentiation (GO:0070367)|negative regulation of Wnt signaling pathway (GO:0030178)|neural crest cell differentiation (GO:0014033)|positive regulation of apoptotic process (GO:0043065)|positive regulation of fat cell differentiation (GO:0045600)|skeletal system development (GO:0001501)|somite development (GO:0061053)|vasculature development (GO:0001944)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|membrane (GO:0016020)	PDZ domain binding (GO:0030165)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(12)|ovary(2)|prostate(1)|skin(1)	21			OV - Ovarian serous cystadenocarcinoma(117;0.109)|Epithelial(96;0.231)			GCAGCCCGAGCCCCGGGCACC	0.692													C|||	83	0.0165735	0.0015	0.0375	5008	,	,		12541	0.0		0.0408	False		,,,				2504	0.0143				p.A30S		Atlas-SNP	.											.	FRZB	42	.	0			c.G88T						PASS	.	C	SER/ALA	26,4378		0,26,2176	17.0	17.0	17.0		88	3.9	0.8	2	dbSNP_126	17	346,8248		2,342,3953	yes	missense	FRZB	NM_001463.3	99	2,368,6129	AA,AC,CC		4.0261,0.5904,2.862	possibly-damaging	30/326	183731193	372,12626	2202	4297	6499	SO:0001583	missense	2487	exon1			CCCGAGCCCCGGG	U24163	CCDS2286.1	2q32.1	2013-09-19			ENSG00000162998	ENSG00000162998		"""Secreted frizzled-related proteins"""	3959	protein-coding gene	gene with protein product		605083				8824257, 9118218	Standard	NM_001463		Approved	FRZB-PEN, FRZB1, SRFP3, FRP-3, SFRP3, FRE, FRITZ, FRZB-1, FZRB, hFIZ	uc002upa.2	Q92765	OTTHUMG00000132597	ENST00000295113.4:c.88G>T	2.37:g.183731193C>A	ENSP00000295113:p.Ala30Ser	Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	37	22	0.594595	NM_001463	O00181|Q99686	Missense_Mutation	SNP	ENST00000295113.4	37	CCDS2286.1	45	0.020604395604395604	0	0.0	15	0.04143646408839779	0	0.0	30	0.0395778364116095	C	10.79	1.448352	0.26074	0.005904	0.040261	ENSG00000162998	ENST00000295113	T	0.72615	-0.67	4.8	3.88	0.44766	Frizzled domain (1);	0.275162	0.33772	N	0.004574	T	0.19846	0.0477	N	0.08118	0	0.35248	D	0.77846	P	0.47677	0.899	B	0.43478	0.421	T	0.49771	-0.8904	10	0.19590	T	0.45	.	14.1532	0.65401	0.1503:0.8497:0.0:0.0	rs36077496	30	Q92765	SFRP3_HUMAN	S	30	ENSP00000295113:A30S	ENSP00000295113:A30S	A	-	1	0	FRZB	183439438	0.993000	0.37304	0.830000	0.32933	0.211000	0.24417	2.961000	0.49168	2.494000	0.84150	0.491000	0.48974	GCT	C|0.973;A|0.027	0.027	strong		0.692	FRZB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255808.1	NM_001463	
MUC4	4585	hgsc.bcm.edu	37	3	195511556	195511556	+	Missense_Mutation	SNP	T	T	A	rs79961534		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195511556T>A	ENST00000463781.3	-	2	7354	c.6895A>T	c.(6895-6897)Aca>Tca	p.T2299S	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.T2299S	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.T2299S(2)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GCGTGACCTGTGGATGCTGAG	0.587																																					p.T2299S		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	2	Substitution - Missense(2)	stomach(2)	c.A6895T						PASS	.						7.0	7.0	7.0					3																	195511556		545	1393	1938	SO:0001583	missense	4585	exon2			GACCTGTGGATGC	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.6895A>T	3.37:g.195511556T>A	ENSP00000417498:p.Thr2299Ser	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	39	19	0.487179	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	T	4.627	0.116607	0.08881	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.42900	0.96;1.12	.	.	.	.	0.395708	0.11245	U	0.584203	T	0.12433	0.0302	N	0.02539	-0.55	0.09310	N	1	B	0.33494	0.414	B	0.22386	0.039	T	0.13818	-1.0495	8	.	.	.	.	2.7352	0.05238	0.0:0.3911:0.0:0.6089	.	2299	E7ESK3	.	S	2299	ENSP00000417498:T2299S;ENSP00000420243:T2299S	.	T	-	1	0	MUC4	196995951	0.000000	0.05858	0.007000	0.13788	0.015000	0.08874	-0.430000	0.06973	0.408000	0.25621	0.055000	0.15244	ACA	T|0.996;A|0.004	0.004	weak		0.587	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
DISC1	27185	hgsc.bcm.edu	37	1	232144887	232144887	+	3'UTR	SNP	A	A	G	rs821617	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:232144887A>G	ENST00000535983.1	+	0	2391				DISC1_ENST00000366637.3_Intron|DISC1_ENST00000439617.2_Intron|DISC1_ENST00000537876.1_3'UTR	NM_001164538.1|NM_001164541.1	NP_001158010.1|NP_001158013.1	Q9NRI5	DISC1_HUMAN	disrupted in schizophrenia 1						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)				AATATTGGGAAGGCTTCCCAT	0.363													G|||	1250	0.249601	0.3775	0.1369	5008	,	,		15515	0.1052		0.2853	False		,,,				2504	0.2689				p.K800R		Atlas-SNP	.											.	DISC1	207	.	0			c.A2399G						PASS	.	G	,,ARG/LYS,,,,	506,878		89,328,275	18.0	18.0	18.0		,,2399,,,,	1.5	0.0	1	dbSNP_86	18	891,2291		125,641,825	yes	intron,intron,missense,intron,utr-3,utr-3,intron	DISC1	NM_001012957.1,NM_001164537.1,NM_001164538.1,NM_001164540.1,NM_001164541.1,NM_001164547.1,NM_018662.2	,,26,,,,	214,969,1100	GG,GA,AA		28.0013,36.5607,30.5957	,,,,,,	,,800/804,,,,	232144887	1397,3169	692	1591	2283	SO:0001624	3_prime_UTR_variant	27185	exon11			TTGGGAAGGCTTC	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	ENST00000535983.1:c.*250A>G	1.37:g.232144887A>G		Somatic	20	0	0		WXS	Illumina HiSeq	Phase_I	22	12	0.545455	NM_001164538	A6NLH2|C4P091|C4P095|C4P0A1|C4P0A3|C4P0B3|C4P0B6|C4P0C1|C9J6D0|O75045|Q5VT44|Q5VT45|Q8IXJ0|Q8IXJ1|Q9BX19|Q9NRI3|Q9NRI4	Missense_Mutation	SNP	ENST00000535983.1	37	CCDS53483.1	542	0.24816849816849818	193	0.39227642276422764	64	0.17679558011049723	63	0.11013986013986014	222	0.2928759894459103	G	8.426	0.847445	0.17034	0.365607	0.280013	ENSG00000162946	ENST00000422590	.	.	.	4.42	1.54	0.23209	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	.	.	.	.	.	.	T	0.48091	-0.9065	4	.	.	.	.	6.6707	0.23066	0.4009:0.0:0.5991:0.0	rs821617;rs9431781;rs57773369	.	.	.	G	203	.	.	R	+	1	2	DISC1	230211510	0.000000	0.05858	0.000000	0.03702	0.098000	0.18820	0.025000	0.13577	0.004000	0.14682	-0.128000	0.14901	AGG	A|0.764;G|0.236	0.236	strong		0.363	DISC1-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_018662	
MBD3L3	653657	hgsc.bcm.edu	37	19	7056537	7056537	+	Silent	SNP	G	G	A	rs201991311	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:7056537G>A	ENST00000333843.4	-	2	457	c.423C>T	c.(421-423)ccC>ccT	p.P141P		NM_001164425.1	NP_001157897.1	A6NE82	MB3L3_HUMAN	methyl-CpG binding domain protein 3-like 3	141					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)			p.P141P(1)		central_nervous_system(1)|lung(5)|stomach(1)	7						GCCCAGGGGTGGGCTCAAGCG	0.632																																					p.P141P		Atlas-SNP	.											MBD3L3,brain,primitive_neuroectodermal_tumour-medulloblastoma,0,1	MBD3L3	12	1	1	Substitution - coding silent(1)	central_nervous_system(1)	c.C423T						scavenged	.						15.0	23.0	20.0					19																	7056537		692	1587	2279	SO:0001819	synonymous_variant	653657	exon2			AGGGGTGGGCTCA		CCDS45944.1	19p13.2	2014-04-01			ENSG00000182315	ENSG00000182315			37205	protein-coding gene	gene with protein product							Standard	NM_001164425		Approved		uc021uns.1	A6NE82	OTTHUMG00000181976	ENST00000333843.4:c.423C>T	19.37:g.7056537G>A		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	139	22	0.158273	NM_001164425		Silent	SNP	ENST00000333843.4	37	CCDS45944.1																																																																																			G|0.975;A|0.025	0.025	strong		0.632	MBD3L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458500.1	NM_001164425	
CCDC185	164127	hgsc.bcm.edu	37	1	223566859	223566859	+	Silent	SNP	T	T	C	rs111306873	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:223566859T>C	ENST00000366875.3	+	1	145	c.42T>C	c.(40-42)gaT>gaC	p.D14D		NM_152610.2	NP_689823.2	Q8N715	CC185_HUMAN		14										breast(4)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(12)|skin(3)	29				GBM - Glioblastoma multiforme(131;0.0704)		CCTACCGGGATCTCTGGGAAC	0.731													C|||	460	0.091853	0.1218	0.0692	5008	,	,		10160	0.131		0.0398	False		,,,				2504	0.0808				p.D14D		Atlas-SNP	.											.	C1orf65	71	.	0			c.T42C						PASS	.	C		331,3661		4,323,1669	4.0	5.0	5.0		42	1.7	0.2	1	dbSNP_132	5	244,7760		0,244,3758	no	coding-synonymous	C1orf65	NM_152610.2		4,567,5427	CC,CT,TT		3.0485,8.2916,4.7933		14/624	223566859	575,11421	1996	4002	5998	SO:0001819	synonymous_variant	164127	exon1			CCGGGATCTCTGG																												ENST00000366875.3:c.42T>C	1.37:g.223566859T>C		Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	17	10	0.588235	NM_152610	Q8N746|Q8NA93	Silent	SNP	ENST00000366875.3	37	CCDS1537.1																																																																																			T|0.930;C|0.070	0.070	strong		0.731	C1orf65-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092718.1		
RFC2	5982	hgsc.bcm.edu	37	7	73663362	73663362	+	Silent	SNP	T	T	C	rs1805395	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:73663362T>C	ENST00000055077.3	-	4	372	c.312A>G	c.(310-312)gaA>gaG	p.E104E	RFC2_ENST00000352131.3_Silent_p.E104E	NM_181471.1	NP_852136.1	P35250	RFC2_HUMAN	replication factor C (activator 1) 2, 40kDa	104					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)			central_nervous_system(1)|endometrium(2)|large_intestine(1)|liver(1)|lung(3)	8						AAGCATTGAGTTCCAACATGG	0.537													T|||	59	0.0117812	0.0	0.0216	5008	,	,		16046	0.0		0.0368	False		,,,				2504	0.0072				p.E104E		Atlas-SNP	.											.	RFC2	27	.	0			c.A312G						PASS	.	T	,	43,4363	43.8+/-77.6	0,43,2160	93.0	100.0	98.0		312,312	-5.7	0.9	7	dbSNP_98	98	405,8195	128.2+/-186.4	10,385,3905	no	coding-synonymous,coding-synonymous	RFC2	NM_002914.3,NM_181471.1	,	10,428,6065	CC,CT,TT		4.7093,0.9759,3.4446	,	104/321,104/355	73663362	448,12558	2203	4300	6503	SO:0001819	synonymous_variant	5982	exon4			ATTGAGTTCCAAC		CCDS5567.1, CCDS5568.1, CCDS75618.1	7q11.23	2010-04-21	2002-08-29		ENSG00000049541	ENSG00000049541		"""ATPases / AAA-type"""	9970	protein-coding gene	gene with protein product	"""activator 1"""	600404	"""replication factor C (activator 1) 2 (40kD)"""			1313560, 7774928	Standard	NM_181471		Approved	A1, RFC40	uc003uaj.3	P35250	OTTHUMG00000023239	ENST00000055077.3:c.312A>G	7.37:g.73663362T>C		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	35	19	0.542857	NM_181471	B5BU07|D3DXG3|P32846|Q9BU93	Silent	SNP	ENST00000055077.3	37	CCDS5568.1																																																																																			T|0.971;C|0.029	0.029	strong		0.537	RFC2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252459.2	NM_181471	
LRRC8C	84230	hgsc.bcm.edu	37	1	90179532	90179532	+	Missense_Mutation	SNP	A	A	G	rs12032393	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:90179532A>G	ENST00000370454.4	+	3	1658	c.1403A>G	c.(1402-1404)aAt>aGt	p.N468S	LRRC8C_ENST00000479252.1_Intron|RP11-302M6.4_ENST00000370453.5_Intron	NM_032270.4	NP_115646	Q8TDW0	LRC8C_HUMAN	leucine rich repeat containing 8 family, member C	468			N -> S (in dbSNP:rs12032393).		fat cell differentiation (GO:0045444)|ion transport (GO:0006811)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|large_intestine(5)|lung(10)|ovary(3)|pancreas(1)|prostate(1)|skin(5)|urinary_tract(1)	28		all_lung(203;0.126)		all cancers(265;0.00756)|Epithelial(280;0.0313)		CAGCTAGACAATCTTCAAGAG	0.438													A|||	754	0.150559	0.0325	0.2089	5008	,	,		20196	0.25		0.1531	False		,,,				2504	0.1636				p.N468S		Atlas-SNP	.											.	LRRC8C	73	.	0			c.A1403G						PASS	.	A	SER/ASN	203,4203	127.0+/-164.0	7,189,2007	94.0	89.0	91.0		1403	4.8	1.0	1	dbSNP_120	91	1235,7365	248.7+/-276.3	71,1093,3136	yes	missense	LRRC8C	NM_032270.4	46	78,1282,5143	GG,GA,AA		14.3605,4.6074,11.0564	benign	468/804	90179532	1438,11568	2203	4300	6503	SO:0001583	missense	84230	exon3			TAGACAATCTTCA		CCDS725.1	1p22.2	2011-02-10			ENSG00000171488	ENSG00000171488			25075	protein-coding gene	gene with protein product	"""hypothetical protein AD158"""	612889				11230166	Standard	NM_032270		Approved	AD158	uc001dnl.4	Q8TDW0	OTTHUMG00000010305	ENST00000370454.4:c.1403A>G	1.37:g.90179532A>G	ENSP00000359483:p.Asn468Ser	Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	48	21	0.4375	NM_032270	B3KXS9|Q29RV6|Q9H075	Missense_Mutation	SNP	ENST00000370454.4	37	CCDS725.1	358	0.16391941391941392	22	0.044715447154471545	64	0.17679558011049723	152	0.26573426573426573	120	0.158311345646438	A	8.862	0.947264	0.18356	0.046074	0.143605	ENSG00000171488	ENST00000370454	T	0.17213	2.29	5.95	4.83	0.62350	.	0.085066	0.85682	D	0.000000	T	0.06188	0.0160	L	0.35793	1.09	0.26258	P	0.9786276	B	0.24483	0.104	B	0.21708	0.036	T	0.12863	-1.0531	9	0.39692	T	0.17	.	12.0658	0.53588	0.933:0.0:0.067:0.0	rs12032393;rs52828026;rs56419062;rs57211627;rs12032393	468	Q8TDW0	LRC8C_HUMAN	S	468	ENSP00000359483:N468S	ENSP00000359483:N468S	N	+	2	0	LRRC8C	89952120	0.997000	0.39634	0.979000	0.43373	0.989000	0.77384	3.287000	0.51732	1.078000	0.41014	0.528000	0.53228	AAT	A|0.869;G|0.131	0.131	strong		0.438	LRRC8C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028435.2	NM_032270	
EML2	24139	hgsc.bcm.edu	37	19	46127999	46127999	+	Silent	SNP	C	C	T	rs36013288	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:46127999C>T	ENST00000245925.3	-	9	869	c.819G>A	c.(817-819)ggG>ggA	p.G273G	EML2_ENST00000587152.1_Silent_p.G474G|EML2_ENST00000536630.1_Silent_p.G420G|EML2_ENST00000589876.1_Silent_p.G273G|EML2_ENST00000586902.1_5'UTR	NM_012155.2	NP_036287.1	O95834	EMAL2_HUMAN	echinoderm microtubule associated protein like 2	273	Tandem atypical propeller in EMLs. {ECO:0000250}.				negative regulation of microtubule polymerization (GO:0031115)|regulation of microtubule nucleation (GO:0010968)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)	microtubule binding (GO:0008017)|tubulin binding (GO:0015631)			NS(1)|breast(2)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(8)|lung(13)|ovary(1)|urinary_tract(1)	31		Ovarian(192;0.179)|all_neural(266;0.224)		OV - Ovarian serous cystadenocarcinoma(262;0.00553)|GBM - Glioblastoma multiforme(486;0.131)|Epithelial(262;0.197)		CATAGAGGTTCCCCCCAGAGT	0.532													C|||	37	0.00738818	0.0	0.0115	5008	,	,		20477	0.0		0.0089	False		,,,				2504	0.0204				p.G474G		Atlas-SNP	.											EML2,NS,carcinoma,-1,1	EML2	64	1	0			c.G1422A						scavenged	.		,,	15,4391	21.2+/-45.6	0,15,2188	86.0	64.0	71.0		1422,1260,819	-0.9	1.0	19	dbSNP_126	71	70,8530	39.8+/-96.3	2,66,4232	no	coding-synonymous,coding-synonymous,coding-synonymous	EML2	NM_001193268.1,NM_001193269.1,NM_012155.2	,,	2,81,6420	TT,TC,CC		0.814,0.3404,0.6535	,,	474/851,420/797,273/650	46127999	85,12921	2203	4300	6503	SO:0001819	synonymous_variant	24139	exon12			GAGGTTCCCCCCA	AF103939	CCDS12670.1, CCDS54280.1, CCDS59399.1	19q13.32	2013-01-10				ENSG00000125746		"""WD repeat domain containing"""	18035	protein-coding gene	gene with protein product	"""echinoderm MT-associated protein (EMAP)-like protein 70"", ""microtubule-associated protein like echinoderm EMAP"""					11694528, 10521658	Standard	NM_012155		Approved	EMAP2, ELP70, EMAP-2	uc010xxm.2	O95834		ENST00000245925.3:c.819G>A	19.37:g.46127999C>T		Somatic	85	1	0.0117647		WXS	Illumina HiSeq	Phase_I	72	34	0.472222	NM_001193268	B7Z3I2|B7Z3Q9|K7ERL7|Q59EN8|Q8N5A2|Q9UG50	Silent	SNP	ENST00000245925.3	37	CCDS12670.1																																																																																			C|0.993;T|0.007	0.007	strong		0.532	EML2-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000459608.1	NM_012155	
PCDHB7	56129	hgsc.bcm.edu	37	5	140552558	140552558	+	Silent	SNP	T	T	C	rs17096945	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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						PASS	.	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	150	0	0		WXS	Illumina HiSeq	Phase_I	121	65	0.53719	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	
GJA9	81025	hgsc.bcm.edu	37	1	39340282	39340282	+	Missense_Mutation	SNP	C	C	T	rs880303	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:39340282C>T	ENST00000360786.3	-	1	1741	c.1489G>A	c.(1489-1491)Gta>Ata	p.V497I	MYCBP_ENST00000489803.1_5'UTR|RP5-864K19.4_ENST00000443161.1_RNA|GJA9_ENST00000454994.2_Intron|MYCBP_ENST00000397572.2_5'Flank|GJA9_ENST00000357771.3_Missense_Mutation_p.V497I|RP5-864K19.4_ENST00000433671.2_RNA|RP5-864K19.4_ENST00000456813.1_RNA			P57773	CXA9_HUMAN	gap junction protein, alpha 9, 59kDa	497			V -> I (in dbSNP:rs880303). {ECO:0000269|Ref.1}.		cell communication (GO:0007154)	connexon complex (GO:0005922)|integral component of membrane (GO:0016021)				breast(3)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	19	Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)	OV - Ovarian serous cystadenocarcinoma(33;8.23e-17)			AGGGACACTACGTGATTTGGA	0.433													C|||	1557	0.310903	0.1452	0.4813	5008	,	,		19898	0.2718		0.4523	False		,,,				2504	0.3088				p.V497I		Atlas-SNP	.											.	GJA9	55	.	0			c.G1489A						PASS	.	C	ILE/VAL	827,3579	328.0+/-300.3	81,665,1457	93.0	90.0	91.0		1489	-4.7	0.0	1	dbSNP_86	91	3914,4686	546.7+/-385.0	880,2154,1266	yes	missense	GJA9	NM_030772.4	29	961,2819,2723	TT,TC,CC		45.5116,18.7699,36.4524	benign	497/516	39340282	4741,8265	2203	4300	6503	SO:0001583	missense	81025	exon2			ACACTACGTGATT	AF179597	CCDS432.1	1p34	2008-02-05	2007-11-06	2007-11-06	ENSG00000131233	ENSG00000131233		"""Ion channels / Gap junction proteins (connexins)"""	19155	protein-coding gene	gene with protein product	"""connexin 59"""	611923	"""gap junction protein, alpha 10, 59kDa"""	GJA10			Standard	NM_030772		Approved	CX59, CX58	uc021olr.1	P57773	OTTHUMG00000000482	ENST00000360786.3:c.1489G>A	1.37:g.39340282C>T	ENSP00000354020:p.Val497Ile	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	81	47	0.580247	NM_030772	B2R722|B3KVQ2|Q5TA63|Q96KG0	Missense_Mutation	SNP	ENST00000360786.3	37	CCDS432.1	756	0.34615384615384615	74	0.15040650406504066	171	0.4723756906077348	168	0.2937062937062937	343	0.4525065963060686	C	8.017	0.758789	0.15846	0.187699	0.455116	ENSG00000131233	ENST00000357771;ENST00000360786	D;D	0.97378	-4.36;-4.36	4.16	-4.7	0.03288	.	672.406000	0.00649	N	0.000558	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.50808	-0.8784	9	0.19590	T	0.45	.	1.938	0.03341	0.1411:0.4103:0.1402:0.3084	rs880303;rs17499686;rs52793287;rs58889690;rs880303	497	P57773	CXA9_HUMAN	I	497	ENSP00000350415:V497I;ENSP00000354020:V497I	ENSP00000350415:V497I	V	-	1	0	GJA9	39112869	0.000000	0.05858	0.000000	0.03702	0.038000	0.13279	0.499000	0.22546	-0.846000	0.04174	-0.471000	0.05019	GTA	C|0.662;N|0.000	.	strong		0.433	GJA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001205.1	NM_030772	
CATSPERD	257062	hgsc.bcm.edu	37	19	5748257	5748257	+	Missense_Mutation	SNP	A	A	G	rs139627891	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:5748257A>G	ENST00000381624.3	+	10	956	c.895A>G	c.(895-897)Att>Gtt	p.I299V	CATSPERD_ENST00000381614.2_5'UTR	NM_152784.3	NP_689997.3	Q86XM0	CTSRD_HUMAN	catsper channel auxiliary subunit delta	299					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)											CATCCACAACATTGCTGTCAG	0.498													A|||	25	0.00499201	0.0023	0.0115	5008	,	,		17217	0.0		0.0129	False		,,,				2504	0.001				p.I299V		Atlas-SNP	.											.	.	.	.	0			c.A895G						PASS	.	A	VAL/ILE	9,3897		0,9,1944	93.0	97.0	96.0		895	-1.9	0.0	19	dbSNP_134	96	120,8172		0,120,4026	yes	missense	TMEM146	NM_152784.3	29	0,129,5970	GG,GA,AA		1.4472,0.2304,1.0576	benign	299/799	5748257	129,12069	1953	4146	6099	SO:0001583	missense	257062	exon10			CACAACATTGCTG	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.895A>G	19.37:g.5748257A>G	ENSP00000371037:p.Ile299Val	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	79	35	0.443038	NM_152784	Q6ZRP1	Missense_Mutation	SNP	ENST00000381624.3	37	CCDS12149.2	20	0.009157509157509158	1	0.0020325203252032522	9	0.024861878453038673	0	0.0	10	0.013192612137203167	A	0.734	-0.778673	0.02929	0.002304	0.014472	ENSG00000174898	ENST00000394548;ENST00000381624	T	0.19669	2.13	3.0	-1.94	0.07571	.	0.346149	0.16676	N	0.204156	T	0.03915	0.0110	N	0.19112	0.55	0.19300	N	0.999973	B	0.20887	0.049	B	0.15484	0.013	T	0.37776	-0.9691	10	0.02654	T	1	-5.7467	8.0291	0.30454	0.3318:0.0:0.6682:0.0	.	299	Q86XM0	TM146_HUMAN	V	225;299	ENSP00000371037:I299V	ENSP00000371037:I299V	I	+	1	0	TMEM146	5699257	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.544000	0.06077	-0.482000	0.06782	-0.911000	0.02809	ATT	A|0.989;G|0.011	0.011	strong		0.498	CATSPERD-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000286953.2	NM_152784	
LRGUK	136332	hgsc.bcm.edu	37	7	133812351	133812351	+	Silent	SNP	T	T	C	rs61732215	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:133812351T>C	ENST00000285928.2	+	1	300	c.231T>C	c.(229-231)gaT>gaC	p.D77D	LRGUK_ENST00000473068.1_3'UTR	NM_144648.1	NP_653249.1	Q96M69	LRGUK_HUMAN	leucine-rich repeats and guanylate kinase domain containing	77						cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|kinase activity (GO:0016301)			breast(1)|endometrium(2)|kidney(2)|large_intestine(12)|lung(23)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	49						CGGACGGAGATGAGGACCAGG	0.607													C|||	284	0.0567093	0.1717	0.0274	5008	,	,		16505	0.001		0.005	False		,,,				2504	0.0327				p.D77D		Atlas-SNP	.											.	LRGUK	113	.	0			c.T231C						PASS	.	C		710,3696	760.6+/-413.0	61,588,1554	82.0	79.0	80.0		231	-7.9	0.0	7	dbSNP_129	80	43,8557	817.4+/-406.9	0,43,4257	no	coding-synonymous	LRGUK	NM_144648.1		61,631,5811	CC,CT,TT		0.5,16.1144,5.7896		77/826	133812351	753,12253	2203	4300	6503	SO:0001819	synonymous_variant	136332	exon1			CGGAGATGAGGAC	AK057348	CCDS5830.1	7q33	2006-10-27			ENSG00000155530	ENSG00000155530			21964	protein-coding gene	gene with protein product							Standard	NM_144648		Approved	FLJ32786	uc003vrm.1	Q96M69	OTTHUMG00000155320	ENST00000285928.2:c.231T>C	7.37:g.133812351T>C		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	147	73	0.496599	NM_144648	Q2M3I1	Silent	SNP	ENST00000285928.2	37	CCDS5830.1																																																																																			T|0.945;C|0.055	0.055	strong		0.607	LRGUK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339442.1	NM_144648	
NRBF2	29982	hgsc.bcm.edu	37	10	64913517	64913517	+	Missense_Mutation	SNP	G	G	A	rs145813277	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:64913517G>A	ENST00000277746.6	+	4	584	c.403G>A	c.(403-405)Gac>Aac	p.D135N	NRBF2_ENST00000435510.2_Missense_Mutation_p.D125N	NM_030759.3	NP_110386.2	Q96F24	NRBF2_HUMAN	nuclear receptor binding factor 2	135					gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)		p.D135N(1)		large_intestine(2)|lung(3)|skin(1)	6	Prostate(12;0.0119)|all_hematologic(501;0.191)					GGGGATCTTTGACAGGGATCC	0.468																																					p.D135N		Atlas-SNP	.											NRBF2,trunk,malignant_melanoma,0,1	NRBF2	18	1	1	Substitution - Missense(1)	skin(1)	c.G403A						scavenged	.						21.0	22.0	22.0					10																	64913517		2194	4287	6481	SO:0001583	missense	29982	exon4			ATCTTTGACAGGG	D82519	CCDS7268.1, CCDS60537.1	10q22.1	2012-11-01			ENSG00000148572	ENSG00000148572			19692	protein-coding gene	gene with protein product	"""comodulator of PPAR and RXR 1"", ""comodulator of PPAR and RXR 2"""					10786636	Standard	NM_001282405		Approved	DKFZp564C1664, FLJ30395, COPR1, COPR2	uc001jmj.4	Q96F24	OTTHUMG00000018309	ENST00000277746.6:c.403G>A	10.37:g.64913517G>A	ENSP00000277746:p.Asp135Asn	Somatic	196	0	0		WXS	Illumina HiSeq	Phase_I	180	26	0.144444	NM_030759	A6PW36|B4DWS0|Q86UR2|Q96NP6|Q9H0S9|Q9H2I2	Missense_Mutation	SNP	ENST00000277746.6	37	CCDS7268.1	.	.	.	.	.	.	.	.	.	.	G	24.1	4.495538	0.85069	.	.	ENSG00000148572	ENST00000277746;ENST00000435510	.	.	.	5.78	5.78	0.91487	.	0.044270	0.85682	D	0.000000	T	0.79551	0.4465	M	0.74881	2.28	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.79784	0.985;0.993	T	0.75442	-0.3316	9	0.30854	T	0.27	-19.7372	20.0118	0.97458	0.0:0.0:1.0:0.0	.	125;135	B4DWS0;Q96F24	.;NRBF2_HUMAN	N	135;125	.	ENSP00000277746:D135N	D	+	1	0	NRBF2	64583523	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	5.599000	0.67592	2.744000	0.94065	0.563000	0.77884	GAC	G|0.998;A|0.002	0.002	strong		0.468	NRBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048247.1	NM_030759	
RPAP1	26015	hgsc.bcm.edu	37	15	41819466	41819466	+	Missense_Mutation	SNP	G	G	A	rs35981448	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:41819466G>A	ENST00000304330.4	-	13	1761	c.1645C>T	c.(1645-1647)Cgc>Tgc	p.R549C	RPAP1_ENST00000568413.1_5'Flank|RPAP1_ENST00000561603.1_Missense_Mutation_p.R549C	NM_015540.2	NP_056355.2	Q9BWH6	RPAP1_HUMAN	RNA polymerase II associated protein 1	549						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)		AGCACGTAGCGCAGCCGAGGC	0.617													G|||	14	0.00279553	0.0008	0.0014	5008	,	,		18252	0.0		0.006	False		,,,				2504	0.0061				p.R549C		Atlas-SNP	.											.	RPAP1	111	.	0			c.C1645T						PASS	.	G	CYS/ARG	7,4399	12.9+/-30.5	0,7,2196	38.0	42.0	41.0		1645	5.3	1.0	15	dbSNP_126	41	49,8551	30.1+/-81.4	0,49,4251	yes	missense	RPAP1	NM_015540.2	180	0,56,6447	AA,AG,GG		0.5698,0.1589,0.4306	probably-damaging	549/1394	41819466	56,12950	2203	4300	6503	SO:0001583	missense	26015	exon13			CGTAGCGCAGCCG	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.1645C>T	15.37:g.41819466G>A	ENSP00000306123:p.Arg549Cys	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	74	37	0.5	NM_015540	Q9H9I2|Q9NSQ5|Q9P2E4|Q9UFS7	Missense_Mutation	SNP	ENST00000304330.4	37	CCDS10079.1	5	0.0022893772893772895	1	0.0020325203252032522	0	0.0	0	0.0	4	0.005277044854881266	G	20.3	3.958716	0.74016	0.001589	0.005698	ENSG00000103932	ENST00000304330	T	0.17691	2.26	5.35	5.35	0.76521	.	0.000000	0.85682	D	0.000000	T	0.32793	0.0841	M	0.69523	2.12	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.10590	-1.0623	10	0.87932	D	0	-18.6742	13.8344	0.63400	0.0:0.0:0.8466:0.1534	rs35981448	549	Q9BWH6	RPAP1_HUMAN	C	549	ENSP00000306123:R549C	ENSP00000306123:R549C	R	-	1	0	RPAP1	39606758	1.000000	0.71417	0.996000	0.52242	0.877000	0.50540	5.777000	0.68931	2.659000	0.90383	0.655000	0.94253	CGC	G|0.996;A|0.004	0.004	strong		0.617	RPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252694.2	NM_015540	
DIP2A	23181	hgsc.bcm.edu	37	21	47910523	47910523	+	Silent	SNP	A	A	G	rs7279002	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:47910523A>G	ENST00000417564.2	+	3	195	c.174A>G	c.(172-174)ccA>ccG	p.P58P	DIP2A_ENST00000318711.7_Silent_p.P58P|DIP2A_ENST00000427143.2_Intron|DIP2A_ENST00000457905.3_Silent_p.P58P|DIP2A_ENST00000400274.1_Silent_p.P58P|DIP2A_ENST00000466639.1_Silent_p.P58P|DIP2A_ENST00000435722.3_Silent_p.P58P			Q14689	DIP2A_HUMAN	DIP2 disco-interacting protein 2 homolog A (Drosophila)	58	DMAP-interaction.				multicellular organismal development (GO:0007275)|negative regulation of gene expression (GO:0010629)|regulation of apoptotic process (GO:0042981)	cell surface (GO:0009986)|nucleus (GO:0005634)	catalytic activity (GO:0003824)			cervix(1)|endometrium(7)|kidney(2)|large_intestine(6)|lung(22)|ovary(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	43	Breast(49;0.0933)			Epithelial(3;3.12e-06)|OV - Ovarian serous cystadenocarcinoma(3;5.68e-06)|all cancers(3;4.08e-05)|Colorectal(79;0.0129)|COAD - Colon adenocarcinoma(84;0.0824)		GAATAGACCCATCTCTGCAAG	0.463													A|||	1797	0.358826	0.5053	0.1988	5008	,	,		19194	0.4067		0.2545	False		,,,				2504	0.3323				p.P58P		Atlas-SNP	.											.	DIP2A	332	.	0			c.A174G						PASS	.	A	,,,,,,	1640,2134		358,924,605	37.0	39.0	38.0		,174,174,174,174,174,174	-10.3	0.0	21	dbSNP_116	38	1911,6281		243,1425,2428	no	intron,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	DIP2A	NM_001146114.1,NM_001146115.1,NM_001146116.1,NM_015151.3,NM_206889.2,NM_206890.2,NM_206891.2	,,,,,,	601,2349,3033	GG,GA,AA		23.3276,43.4552,29.6757	,,,,,,	,58/799,58/1568,58/1572,58/890,58/842,58/813	47910523	3551,8415	1887	4096	5983	SO:0001819	synonymous_variant	23181	exon3			AGACCCATCTCTG	AF490768	CCDS46655.1, CCDS46656.1, CCDS46657.1, CCDS54490.1, CCDS54491.1	21q22.3	2010-08-20	2006-01-13	2006-01-13	ENSG00000160305	ENSG00000160305			17217	protein-coding gene	gene with protein product		607711	"""chromosome 21 open reading frame 106"""	C21orf106			Standard	NM_015151		Approved	Dip2, KIAA0184	uc002zjo.2	Q14689	OTTHUMG00000090717	ENST00000417564.2:c.174A>G	21.37:g.47910523A>G		Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	194	74	0.381443	NM_206891	A6P4T3|B4E0F0|E7EMA5|Q8IVA3|Q8N4S2|Q8TD89|Q96ML9	Silent	SNP	ENST00000417564.2	37	CCDS46655.1																																																																																			A|0.634;G|0.366	0.366	strong		0.463	DIP2A-012	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000376736.1	NM_015151	
MSL1	339287	hgsc.bcm.edu	37	17	38282624	38282624	+	Silent	SNP	C	C	T	rs28526298	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:38282624C>T	ENST00000398532.4	+	2	1272	c.957C>T	c.(955-957)ccC>ccT	p.P319P	MSL1_ENST00000577454.1_Silent_p.P319P|MSL1_ENST00000578648.1_Silent_p.P319P|MSL1_ENST00000579565.1_Silent_p.P56P	NM_001012241.1	NP_001012241.1	Q68DK7	MSL1_HUMAN	male-specific lethal 1 homolog (Drosophila)	319					chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)	MSL complex (GO:0072487)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				endometrium(1)|kidney(2)|large_intestine(2)|lung(2)	7						CTCCCAAGCCCTTCTCATGTG	0.478													T|||	410	0.081869	0.27	0.0403	5008	,	,		17773	0.0		0.0219	False		,,,				2504	0.0031				p.P56P		Atlas-SNP	.											.	MSL1	21	.	0			c.C168T						PASS	.	T		876,3026		83,710,1158	67.0	69.0	69.0		168	3.7	1.0	17	dbSNP_125	69	205,8073		3,199,3937	no	coding-synonymous	MSL1	NM_001012241.1		86,909,5095	TT,TC,CC		2.4764,22.45,8.8752		56/352	38282624	1081,11099	1951	4139	6090	SO:0001819	synonymous_variant	339287	exon3			CAAGCCCTTCTCA		CCDS45670.1	17q21.1	2011-03-21			ENSG00000188895	ENSG00000188895			27905	protein-coding gene	gene with protein product		614801				16227571, 16543150	Standard	NM_001012241		Approved	hMSL1, MSL-1, DKFZp686P24239	uc002hua.4	Q68DK7		ENST00000398532.4:c.957C>T	17.37:g.38282624C>T		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	100	47	0.47	NM_001012241	Q0VF46|Q69Z03	Silent	SNP	ENST00000398532.4	37																																																																																				C|0.938;T|0.062	0.062	strong		0.478	MSL1-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000447409.2	NM_001012241	
LINGO1	84894	hgsc.bcm.edu	37	15	77907145	77907145	+	Silent	SNP	G	G	A	rs3743481	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:77907145G>A	ENST00000355300.6	-	2	1278	c.1104C>T	c.(1102-1104)tcC>tcT	p.S368S	LINGO1_ENST00000561030.1_Silent_p.S362S	NM_032808.5	NP_116197.4	Q96FE5	LIGO1_HUMAN	leucine rich repeat and Ig domain containing 1	368					central nervous system neuron development (GO:0021954)|negative regulation of axonogenesis (GO:0050771)|negative regulation of oligodendrocyte differentiation (GO:0048715)|neuron projection development (GO:0031175)|neurotrophin TRK receptor signaling pathway (GO:0048011)|protein kinase B signaling (GO:0043491)|regulation of axonogenesis (GO:0050770)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(16)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	31						CCAGCGGGTTGGAGTCCAGGA	0.637													G|||	2604	0.519968	0.5666	0.4164	5008	,	,		17828	0.5952		0.4056	False		,,,				2504	0.5706				p.S368S		Atlas-SNP	.											LINGO1,rectum,carcinoma,0,1	LINGO1	76	1	0			c.C1104T						PASS	.	G		2162,2064		575,1012,526	42.0	45.0	44.0		1104	4.9	1.0	15	dbSNP_107	44	3157,5271		564,2029,1621	no	coding-synonymous	LINGO1	NM_032808.5		1139,3041,2147	AA,AG,GG		37.4585,48.8405,42.0341		368/621	77907145	5319,7335	2113	4214	6327	SO:0001819	synonymous_variant	84894	exon2			CGGGTTGGAGTCC	AK027500	CCDS45313.1, CCDS73766.1	15q24	2013-01-11	2007-02-01	2007-02-01		ENSG00000169783		"""Immunoglobulin superfamily / I-set domain containing"""	21205	protein-coding gene	gene with protein product		609791	"""leucine rich repeat neuronal 6A"""	LRRN6A		14686891	Standard	XM_006720723		Approved	FLJ14594, LERN1	uc002bct.1	Q96FE5		ENST00000355300.6:c.1104C>T	15.37:g.77907145G>A		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	152	86	0.565789	NM_032808	D3DW80|Q6NUK3|Q6UXM3|Q6VVG0|Q6VVG1|Q6VVG2|Q8N3K5|Q96K52	Silent	SNP	ENST00000355300.6	37	CCDS45313.1																																																																																			G|0.496;A|0.504	0.504	strong		0.637	LINGO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419546.1	NM_032808	
HTR1B	3351	hgsc.bcm.edu	37	6	78172260	78172260	+	Silent	SNP	C	C	G	rs6296	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:78172260C>G	ENST00000369947.2	-	1	1230	c.861G>C	c.(859-861)gtG>gtC	p.V287V		NM_000863.1	NP_000854.1	P28222	5HT1B_HUMAN	5-hydroxytryptamine (serotonin) receptor 1B, G protein-coupled	287					adenylate cyclase-inhibiting serotonin receptor signaling pathway (GO:0007198)|bone remodeling (GO:0046849)|cellular response to alkaloid (GO:0071312)|cellular response to drug (GO:0035690)|cellular response to temperature stimulus (GO:0071502)|drinking behavior (GO:0042756)|G-protein coupled receptor internalization (GO:0002031)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|negative regulation of cAMP biosynthetic process (GO:0030818)|negative regulation of serotonin secretion (GO:0014063)|negative regulation of synaptic transmission, GABAergic (GO:0032229)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of behavior (GO:0050795)|regulation of dopamine secretion (GO:0014059)|response to cocaine (GO:0042220)|response to ethanol (GO:0045471)|response to mineralocorticoid (GO:0051385)|synaptic transmission (GO:0007268)|vasoconstriction (GO:0042310)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	drug binding (GO:0008144)|serotonin binding (GO:0051378)|serotonin receptor activity (GO:0004993)			NS(1)|breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(9)|prostate(2)|upper_aerodigestive_tract(2)	25		all_cancers(76;0.0867)|Acute lymphoblastic leukemia(125;0.00119)|all_hematologic(105;0.0332)		BRCA - Breast invasive adenocarcinoma(397;0.205)	Almotriptan(DB00918)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Apomorphine(DB00714)|Aripiprazole(DB01238)|Asenapine(DB06216)|Bopindolol(DB08807)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Clozapine(DB00363)|Dihydroergotamine(DB00320)|Eletriptan(DB00216)|Ergoloid mesylate(DB01049)|Ergotamine(DB00696)|Frovatriptan(DB00998)|Ketamine(DB01221)|Lisuride(DB00589)|Loxapine(DB00408)|Methysergide(DB00247)|Naratriptan(DB00952)|Olanzapine(DB00334)|Ondansetron(DB00904)|Penbutolol(DB01359)|Pergolide(DB01186)|Pindolol(DB00960)|Pramipexole(DB00413)|Propranolol(DB00571)|Quetiapine(DB01224)|Rizatriptan(DB00953)|Ropinirole(DB00268)|Sumatriptan(DB00669)|Yohimbine(DB01392)|Ziprasidone(DB00246)|Zolmitriptan(DB00315)	TGACTTGGTTCACATACACAG	0.577													C|||	1693	0.338059	0.2436	0.4049	5008	,	,		16718	0.5089		0.2634	False		,,,				2504	0.319				p.V287V		Atlas-SNP	.											.	HTR1B	55	.	0			c.G861C						PASS	.	C		987,3419	364.9+/-317.2	124,739,1340	134.0	147.0	143.0		861	4.2	1.0	6	dbSNP_52	143	2257,6343	381.2+/-339.9	311,1635,2354	no	coding-synonymous	HTR1B	NM_000863.1		435,2374,3694	GG,GC,CC		26.2442,22.4013,24.9423		287/391	78172260	3244,9762	2203	4300	6503	SO:0001819	synonymous_variant	3351	exon1			TTGGTTCACATAC	BC069065	CCDS4986.1	6q13	2012-08-08	2012-02-03		ENSG00000135312	ENSG00000135312		"""5-HT (serotonin) receptors"", ""GPCR / Class A : 5-HT (serotonin) receptors, GPCR only"""	5287	protein-coding gene	gene with protein product		182131	"""5-hydroxytryptamine (serotonin) receptor 1B"""			1348246, 11247661	Standard	NM_000863		Approved	S12, 5-HT1B, HTR1D2, 5-HT1DB	uc003pil.1	P28222	OTTHUMG00000015066	ENST00000369947.2:c.861G>C	6.37:g.78172260C>G		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	49	25	0.510204	NM_000863	Q4VAY7	Silent	SNP	ENST00000369947.2	37	CCDS4986.1																																																																																			C|0.709;G|0.291	0.291	strong		0.577	HTR1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041292.1	NM_000863	
MUC4	4585	hgsc.bcm.edu	37	3	195507226	195507226	+	Missense_Mutation	SNP	A	A	G	rs201269328|rs74187968	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195507226A>G	ENST00000463781.3	-	2	11684	c.11225T>C	c.(11224-11226)gTc>gCc	p.V3742A	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.V3742A	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)		AAGAGGGGTGACGTGACCTGT	0.587													.|||	1722	0.34385	0.4713	0.2594	5008	,	,		9294	0.3819		0.2913	False		,,,				2504	0.2464				p.V3742A		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,-1,2	MUC4	1505	2	0			c.T11225C						scavenged	.						26.0	26.0	26.0					3																	195507226		670	1583	2253	SO:0001583	missense	4585	exon2			GGGGTGACGTGAC	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.11225T>C	3.37:g.195507226A>G	ENSP00000417498:p.Val3742Ala	Somatic	65	9	0.138462		WXS	Illumina HiSeq	Phase_I	76	66	0.868421	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	6.544	0.468647	0.12461	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.47869	1.13;0.83	0.885	-1.77	0.07982	.	0.000000	0.25514	U	0.030158	T	0.17916	0.0430	N	0.08118	0	0.09310	N	1	B	0.19200	0.034	B	0.14023	0.01	T	0.12630	-1.0540	9	.	.	.	.	1.6977	0.02866	0.4856:0.0:0.2321:0.2823	.	3614	E7ESK3	.	A	3742	ENSP00000417498:V3742A;ENSP00000420243:V3742A	.	V	-	2	0	MUC4	196992005	0.000000	0.05858	0.020000	0.16555	0.037000	0.13140	-2.220000	0.01217	-1.811000	0.01229	-2.094000	0.00368	GTC	A|0.001;G|0.999	0.999	weak		0.587	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
LRP1	4035	hgsc.bcm.edu	37	12	57550588	57550588	+	Silent	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:57550588G>A	ENST00000243077.3	+	10	1912	c.1446G>A	c.(1444-1446)caG>caA	p.Q482Q		NM_002332.2	NP_002323.2	Q07954	LRP1_HUMAN	low density lipoprotein receptor-related protein 1	482	EGF-like 3. {ECO:0000255|PROSITE- ProRule:PRU00076}.				aging (GO:0007568)|aorta morphogenesis (GO:0035909)|apoptotic cell clearance (GO:0043277)|beta-amyloid clearance (GO:0097242)|cell proliferation (GO:0008283)|cholesterol metabolic process (GO:0008203)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of platelet-derived growth factor receptor-beta signaling pathway (GO:2000587)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of Wnt signaling pathway (GO:0030178)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of lipid transport (GO:0032370)|positive regulation of protein transport (GO:0051222)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|receptor-mediated endocytosis (GO:0006898)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cholesterol transport (GO:0032374)|regulation of phospholipase A2 activity (GO:0032429)|retinoid metabolic process (GO:0001523)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	apolipoprotein binding (GO:0034185)|calcium ion binding (GO:0005509)|lipoprotein particle receptor binding (GO:0070325)|lipoprotein transporter activity (GO:0042954)|poly(A) RNA binding (GO:0044822)|protein complex binding (GO:0032403)|receptor activity (GO:0004872)			NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(33)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(26)|lung(58)|ovary(10)|pancreas(2)|prostate(11)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	184				BRCA - Breast invasive adenocarcinoma(357;0.0103)	Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031)	AAAACGACCAGTATGGGAAGC	0.632																																					p.Q482Q		Atlas-SNP	.											.	LRP1	428	.	0			c.G1446A						PASS	.						44.0	40.0	42.0					12																	57550588		2203	4300	6503	SO:0001819	synonymous_variant	4035	exon10			CGACCAGTATGGG	X13916	CCDS8932.1	12q13.3	2013-05-28	2010-01-26		ENSG00000123384	ENSG00000123384		"""CD molecules"", ""Low density lipoprotein receptors"""	6692	protein-coding gene	gene with protein product		107770	"""alpha-2-macroglobulin receptor"""	APR, A2MR		2548950	Standard	NM_002332		Approved	LRP, CD91, LRP1A, APOER	uc001snd.3	Q07954	OTTHUMG00000044412	ENST00000243077.3:c.1446G>A	12.37:g.57550588G>A		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	47	5	0.106383	NM_002332	Q2PP12|Q86SW0|Q8IVG8	Silent	SNP	ENST00000243077.3	37	CCDS8932.1																																																																																			.	.	none		0.632	LRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412772.2	NM_002332	
GPAT2	150763	hgsc.bcm.edu	37	2	96688916	96688916	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:96688916G>A	ENST00000434632.1	-	20	2546	c.2087C>T	c.(2086-2088)cCg>cTg	p.P696L	GPAT2_ENST00000453542.1_Missense_Mutation_p.P625L|GPAT2_ENST00000359548.4_Missense_Mutation_p.P696L|GPAT2_ENST00000377137.3_Intron|FAHD2CP_ENST00000607780.1_RNA			Q6NUI2	GPAT2_HUMAN	glycerol-3-phosphate acyltransferase 2, mitochondrial	696					CDP-diacylglycerol biosynthetic process (GO:0016024)|glycerol-3-phosphate metabolic process (GO:0006072)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	glycerol-3-phosphate O-acyltransferase activity (GO:0004366)			NS(1)|breast(1)|cervix(1)|endometrium(4)|large_intestine(1)|lung(5)|skin(3)	16						CTTGAGCAGCGGGCTGAGCAG	0.652																																					p.P696L		Atlas-SNP	.											GPAT2,NS,carcinoma,+1,1	GPAT2	46	1	0			c.C2087T						scavenged	.						12.0	15.0	14.0					2																	96688916		1813	4047	5860	SO:0001583	missense	150763	exon19			AGCAGCGGGCTGA	BC042847	CCDS42714.1	2q11.2	2010-05-04			ENSG00000186281	ENSG00000186281			27168	protein-coding gene	gene with protein product	"""cancer/testis antigen 123"""					12477932	Standard	NM_207328		Approved	CT123	uc010yuf.1	Q6NUI2	OTTHUMG00000155208	ENST00000434632.1:c.2087C>T	2.37:g.96688916G>A	ENSP00000389395:p.Pro696Leu	Somatic	339	1	0.00294985		WXS	Illumina HiSeq	Phase_I	264	29	0.109848	NM_207328	Q6P2E4|Q6ZNI3|Q6ZNI5|Q6ZWJ4	Missense_Mutation	SNP	ENST00000434632.1	37	CCDS42714.1	.	.	.	.	.	.	.	.	.	.	g	23.0	4.365252	0.82463	.	.	ENSG00000186281	ENST00000359548;ENST00000434632;ENST00000453542	D;D;T	0.83419	-1.72;-1.72;-0.81	5.44	5.44	0.79542	.	0.141914	0.49916	D	0.000123	D	0.89894	0.6847	M	0.64404	1.975	0.80722	D	1	D;D;D;D	0.89917	1.0;0.999;1.0;1.0	D;D;D;D	0.91635	0.996;0.932;0.999;0.995	D	0.90665	0.4593	10	0.87932	D	0	-13.903	16.7485	0.85479	0.0:0.0:1.0:0.0	.	625;702;696;625	E9PE95;Q6NUI2-4;Q6NUI2;B4DNZ9	.;.;GPAT2_HUMAN;.	L	696;696;625	ENSP00000352547:P696L;ENSP00000389395:P696L;ENSP00000393770:P625L	ENSP00000352547:P696L	P	-	2	0	GPAT2	96052643	1.000000	0.71417	0.905000	0.35620	0.705000	0.40729	7.030000	0.76484	2.569000	0.86673	0.637000	0.83480	CCG	.	.	none		0.652	GPAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338786.1	NM_207328	
SLC29A3	55315	hgsc.bcm.edu	37	10	73082563	73082563	+	Missense_Mutation	SNP	A	A	G	rs2277257	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	129	0	0		WXS	Illumina HiSeq	Phase_I	121	60	0.495868	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	
CDH6	1004	hgsc.bcm.edu	37	5	31317952	31317952	+	Silent	SNP	T	T	C	rs2229575	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:31317952T>C	ENST00000265071.2	+	11	2068	c.1803T>C	c.(1801-1803)caT>caC	p.H601H	CDH6_ENST00000514738.1_Silent_p.H546H	NM_004932.3	NP_004923.1	P55285	CADH6_HUMAN	cadherin 6, type 2, K-cadherin (fetal kidney)	601	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(3)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(42)|ovary(4)|prostate(6)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(1)	77						AATCCTGCCATGCGGAGGCGC	0.572													T|||	1950	0.389377	0.062	0.5043	5008	,	,		19805	0.4931		0.5616	False		,,,				2504	0.4663				p.H601H		Atlas-SNP	.											.	CDH6	175	.	0			c.T1803C						PASS	.	T		657,3749	276.9+/-273.4	53,551,1599	61.0	54.0	56.0		1803	-10.6	0.3	5	dbSNP_98	56	4623,3977	595.4+/-393.5	1279,2065,956	no	coding-synonymous	CDH6	NM_004932.3		1332,2616,2555	CC,CT,TT		46.2442,14.9115,40.5966		601/791	31317952	5280,7726	2203	4300	6503	SO:0001819	synonymous_variant	1004	exon11			CTGCCATGCGGAG	D31784	CCDS3894.1	5p13.3	2010-01-26			ENSG00000113361	ENSG00000113361		"""Cadherins / Major cadherins"""	1765	protein-coding gene	gene with protein product	"""K-Cadherin"""	603007				7743525, 10191097	Standard	NM_004932		Approved		uc003jhe.2	P55285	OTTHUMG00000090673	ENST00000265071.2:c.1803T>C	5.37:g.31317952T>C		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	68	67	0.985294	NM_004932	A8K5H5|Q9BWS0	Silent	SNP	ENST00000265071.2	37	CCDS3894.1																																																																																			T|0.595;C|0.405	0.405	strong		0.572	CDH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207355.2	NM_004932	
TRIAP1	51499	hgsc.bcm.edu	37	12	120884328	120884328	+	5'Flank	SNP	C	C	T	rs2235217	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:120884328C>T	ENST00000546954.1	-	0	0				TRIAP1_ENST00000302432.3_5'Flank|GATC_ENST00000551765.1_Silent_p.G15G|AL021546.6_ENST00000551806.1_Intron	NM_016399.2	NP_057483.1	O43715	TRIA1_HUMAN	TP53 regulated inhibitor of apoptosis 1						cellular response to UV (GO:0034644)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:1902166)|negative regulation of release of cytochrome c from mitochondria (GO:0090201)|phospholipid transport (GO:0015914)|positive regulation of phospholipid transport (GO:2001140)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of membrane lipid distribution (GO:0097035)	mitochondrial intermembrane space (GO:0005758)|mitochondrion (GO:0005739)|protein complex (GO:0043234)	p53 binding (GO:0002039)					all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					CCCCTCTGGGCGGGCGCCAGG	0.706													C|||	1299	0.259385	0.0794	0.2579	5008	,	,		14028	0.4901		0.2783	False		,,,				2504	0.2464				p.G15G		Atlas-SNP	.											.	GATC	12	.	0			c.C45T						PASS	.	C		466,3940	217.8+/-236.0	23,420,1760	46.0	52.0	50.0		45	-0.2	0.0	12	dbSNP_98	50	2719,5877	419.6+/-353.1	426,1867,2005	no	coding-synonymous	GATC	NM_176818.2		449,2287,3765	TT,TC,CC		31.631,10.5765,24.4962		15/137	120884328	3185,9817	2203	4298	6501	SO:0001631	upstream_gene_variant	283459	exon1			TCTGGGCGGGCGC		CCDS9198.1	12q24.31	2012-10-15			ENSG00000170855	ENSG00000170855			26937	protein-coding gene	gene with protein product	"""p53-inducible cell-survival factor"", ""mitochondrial distribution and morphology 35 homolog (S. cerevisiae)"""	614943				11042152, 15735003	Standard	NM_016399		Approved	P53CSV, WF-1, HSPC132, p53CSV, MDM35	uc001tyg.3	O43715	OTTHUMG00000047787		12.37:g.120884328C>T	Exception_encountered	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	61	38	0.622951	NM_176818	B2R4Z7|Q5RKS5|Q6LCA7	Silent	SNP	ENST00000546954.1	37	CCDS9198.1																																																																																			C|0.744;T|0.256	0.256	strong		0.706	TRIAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000108980.3	NM_016399	
ORAI1	84876	hgsc.bcm.edu	37	12	122079348	122079348	+	Silent	SNP	T	T	C	rs3741597	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:122079348T>C	ENST00000330079.7	+	2	904	c.711T>C	c.(709-711)gcT>gcC	p.A237A		NM_032790.3	NP_116179	Q96D31	CRCM1_HUMAN	ORAI calcium release-activated calcium modulator 1	235					blood coagulation (GO:0007596)|immune system process (GO:0002376)|positive regulation of calcium ion transport (GO:0051928)|regulation of calcium ion transport (GO:0051924)|store-operated calcium entry (GO:0002115)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|protein complex (GO:0043234)	identical protein binding (GO:0042802)|store-operated calcium channel activity (GO:0015279)			breast(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(3)|upper_aerodigestive_tract(1)	11	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)			OV - Ovarian serous cystadenocarcinoma(86;0.000415)|Epithelial(86;0.00148)		GCCAGGCAGCTGCCATCGCCT	0.637													T|||	237	0.0473243	0.0787	0.0043	5008	,	,		18007	0.1131		0.0089	False		,,,				2504	0.0072				p.A237A		Atlas-SNP	.											.	ORAI1	66	.	0			c.T711C						PASS	.	T		315,4073		5,305,1884	51.0	67.0	62.0		711	-11.0	0.0	12	dbSNP_107	62	53,8519		0,53,4233	no	coding-synonymous	ORAI1	NM_032790.3		5,358,6117	CC,CT,TT		0.6183,7.1787,2.8395		237/304	122079348	368,12592	2194	4286	6480	SO:0001819	synonymous_variant	84876	exon2			GGCAGCTGCCATC	AK027372		12q24.31	2014-09-17	2007-08-14	2007-08-14	ENSG00000182500	ENSG00000276045		"""ORAI calcium release-activated calcium modulators"""	25896	protein-coding gene	gene with protein product	"""calcium release-activated calcium modulator 1"""	610277	"""transmembrane protein 142A"""	TMEM142A		16582901	Standard	NM_032790		Approved	FLJ14466, CRACM1	uc021rff.1	Q96D31		ENST00000330079.7:c.711T>C	12.37:g.122079348T>C		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	112	45	0.401786	NM_032790	Q3MHV3|Q6DHX2|Q96BP7|Q96K71	Silent	SNP	ENST00000330079.7	37	CCDS41851.1																																																																																			T|0.942;C|0.058	0.058	strong		0.637	ORAI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402151.1	NM_032790	
SFSWAP	6433	hgsc.bcm.edu	37	12	132250712	132250712	+	Silent	SNP	G	G	C	rs1051233	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:132250712G>C	ENST00000261674.4	+	13	2142	c.2001G>C	c.(1999-2001)ctG>ctC	p.L667L	SFSWAP_ENST00000541286.1_Silent_p.L667L	NM_004592.3	NP_004583.2	Q12872	SFSWA_HUMAN	splicing factor, suppressor of white-apricot family	667					mRNA processing (GO:0006397)|mRNA splice site selection (GO:0006376)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	RNA binding (GO:0003723)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(8)|ovary(1)|skin(2)	25						GGGAAAAGCTGGCCCAGGCGT	0.443													G|||	508	0.101438	0.0091	0.2291	5008	,	,		18099	0.0		0.2366	False		,,,				2504	0.1012				p.L667L		Atlas-SNP	.											.	SFSWAP	69	.	0			c.G2001C						PASS	.	G		206,4200	127.0+/-164.0	7,192,2004	104.0	119.0	114.0		2001	-9.3	0.5	12	dbSNP_86	114	2198,6402	375.7+/-337.9	275,1648,2377	no	coding-synonymous	SFSWAP	NM_004592.2		282,1840,4381	CC,CG,GG		25.5581,4.6754,18.4838		667/952	132250712	2404,10602	2203	4300	6503	SO:0001819	synonymous_variant	6433	exon13			AAAGCTGGCCCAG	U08377	CCDS9273.1, CCDS58290.1	12q24.33	2014-04-14	2014-04-14	2010-09-15	ENSG00000061936	ENSG00000061936			10790	protein-coding gene	gene with protein product		601945	"""splicing factor, arginine/serine-rich 8 (suppressor-of-white-apricot, Drosophila homolog)"", ""splicing factor, arginine/serine-rich 8 (suppressor-of-white-apricot homolog, Drosophila)"", ""splicing factor, suppressor of white-apricot homolog (Drosophila)"""	SFRS8		8940107	Standard	NM_004592		Approved	SWAP	uc010tbn.2	Q12872	OTTHUMG00000168319	ENST00000261674.4:c.2001G>C	12.37:g.132250712G>C		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	41	18	0.439024	NM_001261411	B2RN45|B7ZM97|F5H6B8|Q6PJF7	Silent	SNP	ENST00000261674.4	37	CCDS9273.1	284	0.13003663003663005	8	0.016260162601626018	98	0.27071823204419887	0	0.0	178	0.23482849604221637	G	9.674	1.147491	0.21288	0.046754	0.255581	ENSG00000061936	ENST00000537164	.	.	.	5.73	-9.28	0.00656	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999998	.	.	.	.	.	.	T	0.30650	-0.9971	3	.	.	.	-17.2187	1.6034	0.02679	0.2261:0.1231:0.2084:0.4424	rs1051233;rs3191598;rs17678095;rs1051233	.	.	.	S	230	.	.	W	+	2	0	SFSWAP	130816665	0.879000	0.30193	0.539000	0.28077	0.987000	0.75469	-0.165000	0.09968	-1.785000	0.01271	0.591000	0.81541	TGG	G|0.840;C|0.160	0.160	strong		0.443	SFSWAP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399276.1	NM_004592	
ACTL7B	10880	hgsc.bcm.edu	37	9	111618209	111618209	+	Start_Codon_SNP	SNP	A	A	G	rs17728850	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:111618209A>G	ENST00000374667.3	-	1	1030	c.2T>C	c.(1-3)aTg>aCg	p.M1T		NM_006686.3	NP_006677.1	Q9Y614	ACL7B_HUMAN	actin-like 7B	1						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						CCTTGTCGCCATCTGCCTCCC	0.657													A|||	350	0.0698882	0.0651	0.1354	5008	,	,		17466	0.0		0.1074	False		,,,				2504	0.0634				p.M1T		Atlas-SNP	.											.	ACTL7B	57	.	0			c.T2C						PASS	.	A	THR/MET	306,4100	165.4+/-196.9	13,280,1910	50.0	50.0	50.0		2	4.0	1.0	9	dbSNP_123	50	888,7712	200.2+/-244.0	47,794,3459	yes	missense	ACTL7B	NM_006686.3	81	60,1074,5369	GG,GA,AA		10.3256,6.9451,9.1804	benign	1/416	111618209	1194,11812	2203	4300	6503	SO:0001582	initiator_codon_variant	10880	exon1			GTCGCCATCTGCC	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.2T>C	9.37:g.111618209A>G	ENSP00000363799:p.Met1Thr	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	41	10	0.243902	NM_006686	B2R9Q2|Q5JSV1	Missense_Mutation	SNP	ENST00000374667.3	37	CCDS6771.1	178	0.0815018315018315	48	0.0975609756097561	44	0.12154696132596685	0	0.0	86	0.11345646437994723	A	11.81	1.748987	0.30955	0.069451	0.103256	ENSG00000148156	ENST00000374667	D	0.94931	-3.56	3.99	3.99	0.46301	.	0.556195	0.13318	N	0.396957	T	0.33498	0.0865	.	.	.	0.37717	P	0.075206	P	0.50156	0.932	P	0.55391	0.775	T	0.68788	-0.5316	8	0.87932	D	0	.	9.2214	0.37379	1.0:0.0:0.0:0.0	rs17728850;rs17728850	1	Q9Y614	ACL7B_HUMAN	T	1	ENSP00000363799:M1T	ENSP00000363799:M1T	M	-	2	0	ACTL7B	110658030	0.119000	0.22226	1.000000	0.80357	0.155000	0.21991	1.905000	0.39878	1.685000	0.51034	0.459000	0.35465	ATG	A|0.915;G|0.085	0.085	strong		0.657	ACTL7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053571.1	NM_006686	Missense_Mutation
ATXN1	6310	hgsc.bcm.edu	37	6	16327897	16327897	+	Missense_Mutation	SNP	C	C	A	rs184327938		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	48	0	0		WXS	Illumina HiSeq	Phase_I	51	19	0.372549	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	
CDKL4	344387	hgsc.bcm.edu	37	2	39440541	39440541	+	Splice_Site	SNP	G	G	A	rs375514414		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:39440541G>A	ENST00000395035.3	-	3	362	c.363C>T	c.(361-363)aaC>aaT	p.N121N	CDKL4_ENST00000378803.1_Splice_Site_p.N121N			Q5MAI5	CDKL4_HUMAN	cyclin-dependent kinase-like 4	121	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.					cytoplasm (GO:0005737)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)			breast(1)|large_intestine(2)|liver(1)|lung(7)|ovary(1)	12		all_hematologic(82;0.248)				TGTTACTTACGTTATGTATAT	0.328													G|||	1	0.000199681	0.0	0.0	5008	,	,		18274	0.001		0.0	False		,,,				2504	0.0				p.N121N		Atlas-SNP	.											CDKL4,NS,carcinoma,0,1	CDKL4	30	1	0			c.C363T						PASS	.	G		1,4405	2.1+/-5.4	0,1,2202	71.0	78.0	75.0		363	-4.6	0.9	2		75	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous-near-splice	CDKL4	NM_001009565.1		0,2,6501	AA,AG,GG		0.0116,0.0227,0.0154		121/316	39440541	2,13004	2203	4300	6503	SO:0001630	splice_region_variant	344387	exon3			ACTTACGTTATGT		CCDS33184.1	2p22.3	2011-11-04			ENSG00000205111	ENSG00000205111		"""Cyclin-dependent kinases"""	19287	protein-coding gene	gene with protein product							Standard	NM_001009565		Approved		uc002rrm.3	Q5MAI5	OTTHUMG00000133574	ENST00000395035.3:c.363+1C>T	2.37:g.39440541G>A		Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	328	67	0.204268	NM_001009565	Q2NME9	Silent	SNP	ENST00000395035.3	37																																																																																				.	.	weak		0.328	CDKL4-002	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000331655.1	XM_293029	Silent
HPS1	3257	hgsc.bcm.edu	37	10	100189568	100189568	+	Missense_Mutation	SNP	C	C	A	rs11592273	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:100189568C>A	ENST00000325103.6	-	9	1080	c.847G>T	c.(847-849)Ggg>Tgg	p.G283W	HPS1_ENST00000338546.5_Missense_Mutation_p.G283W|HPS1_ENST00000467246.1_Intron|MIR4685_ENST00000578185.1_RNA|HPS1_ENST00000361490.4_Missense_Mutation_p.G283W	NM_000195.3	NP_000186.2	Q92902	HPS1_HUMAN	Hermansky-Pudlak syndrome 1	283			G -> W (in dbSNP:rs11592273).		blood coagulation (GO:0007596)|eye pigmentation (GO:0048069)|lysosome organization (GO:0007040)|melanocyte differentiation (GO:0030318)|positive regulation of natural killer cell activation (GO:0032816)|retina development in camera-type eye (GO:0060041)|secretion of lysosomal enzymes (GO:0033299)|visual perception (GO:0007601)	BLOC-3 complex (GO:0031085)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)	protein dimerization activity (GO:0046983)			breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|liver(1)|lung(9)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	23		Colorectal(252;0.234)		Epithelial(162;3.87e-12)|all cancers(201;5.63e-10)		GAGCTCCCCCCAGTTGGGCCC	0.692									Hermansky-Pudlak syndrome				C|||	128	0.0255591	0.0144	0.0331	5008	,	,		18046	0.0		0.0726	False		,,,				2504	0.0133				p.G283W		Atlas-SNP	.											.	HPS1	65	.	0			c.G847T						PASS	.	C	TRP/GLY,TRP/GLY	133,4273	93.0+/-131.7	3,127,2073	79.0	84.0	83.0		847,847	-5.5	0.0	10	dbSNP_120	83	652,7948	161.9+/-214.7	23,606,3671	yes	missense,missense	HPS1	NM_000195.3,NM_182639.2	184,184	26,733,5744	AA,AC,CC		7.5814,3.0186,6.0357	possibly-damaging,possibly-damaging	283/701,283/325	100189568	785,12221	2203	4300	6503	SO:0001583	missense	3257	exon9	Familial Cancer Database	HPS, HPS1-8	TCCCCCCAGTTGG	U79136	CCDS7475.1, CCDS7476.1	10q23.1-q23.3	2014-06-18		2002-05-01	ENSG00000107521	ENSG00000107521			5163	protein-coding gene	gene with protein product		604982	"""Hermansky-Pudlak syndrome"""	HPS		8541858, 7573033	Standard	NM_182639		Approved		uc021pwv.1	Q92902	OTTHUMG00000018876	ENST00000325103.6:c.847G>T	10.37:g.100189568C>A	ENSP00000326649:p.Gly283Trp	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	63	33	0.52381	NM_000195	A8MRT2|O15402|O15502|Q5TAA3|Q8WXE5	Missense_Mutation	SNP	ENST00000325103.6	37	CCDS7475.1	79	0.036172161172161175	6	0.012195121951219513	14	0.03867403314917127	0	0.0	59	0.07783641160949868	C	12.04	1.818877	0.32145	0.030186	0.075814	ENSG00000107521	ENST00000325103;ENST00000361490;ENST00000338546	T;T;T	0.44083	1.54;1.54;0.93	4.15	-5.53	0.02552	.	2.870320	0.00819	N	0.001574	T	0.02688	0.0081	N	0.22421	0.69	0.09310	N	1	D;P;D	0.61697	0.99;0.932;0.99	P;P;P	0.56278	0.688;0.795;0.694	T	0.34054	-0.9844	10	0.52906	T	0.07	.	7.2775	0.26292	0.0:0.4246:0.1287:0.4467	rs11592273;rs58352354;rs11592273	283;283;283	Q92902;Q92902-3;D3DR62	HPS1_HUMAN;.;.	W	283	ENSP00000326649:G283W;ENSP00000355310:G283W;ENSP00000343638:G283W	ENSP00000326649:G283W	G	-	1	0	HPS1	100179558	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.787000	0.01764	-1.507000	0.01803	-3.959000	0.00015	GGG	.	.	none		0.692	HPS1-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049776.1	NM_000195, NM_182637, NM_182638, NM_182639	
KRT17	3872	hgsc.bcm.edu	37	17	39777895	39777895	+	Nonsense_Mutation	SNP	T	T	A	rs146900210	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:39777895T>A	ENST00000311208.8	-	4	851	c.784A>T	c.(784-786)Aag>Tag	p.K262*	JUP_ENST00000540235.1_Nonsense_Mutation_p.K421*	NM_000422.2	NP_000413.1	Q04695	K1C17_HUMAN	keratin 17	262	Coil 2.|Rod.				epidermis development (GO:0008544)|intermediate filament organization (GO:0045109)|keratinization (GO:0031424)|morphogenesis of an epithelium (GO:0002009)|positive regulation of cell growth (GO:0030307)|positive regulation of hair follicle development (GO:0051798)|positive regulation of translation (GO:0045727)|signal transduction (GO:0007165)	cell periphery (GO:0071944)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	MHC class II protein binding (GO:0042289)|MHC class II receptor activity (GO:0032395)|structural constituent of cytoskeleton (GO:0005200)			central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(5)|ovary(1)|skin(1)	12		Breast(137;0.000307)				TCTGCCATCTTCTCATACTGG	0.617																																					p.K262X	Pancreas(92;1242 2086 39193 50508)	Atlas-SNP	.											.	KRT17	57	.	0			c.A784T						PASS	.	T	stop/LYS	0,4406		0,0,2203	122.0	105.0	111.0		784	1.5	1.0	17	dbSNP_134	111	5,8595	4.3+/-15.6	0,5,4295	no	stop-gained	KRT17	NM_000422.2		0,5,6498	AA,AT,TT		0.0581,0.0,0.0384		262/433	39777895	5,13001	2203	4300	6503	SO:0001587	stop_gained	3872	exon4			CCATCTTCTCATA	X62571	CCDS11402.1	17q21.2	2014-06-12			ENSG00000128422	ENSG00000128422		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6427	protein-coding gene	gene with protein product		148069		PCHC1		7539673, 1281771, 16831889	Standard	NM_000422		Approved		uc002hxh.2	Q04695	OTTHUMG00000133505	ENST00000311208.8:c.784A>T	17.37:g.39777895T>A	ENSP00000308452:p.Lys262*	Somatic	307	1	0.00325733		WXS	Illumina HiSeq	Phase_I	347	172	0.495677	NM_000422	A5Z1M9|A5Z1N0|A5Z1N1|A5Z1N2|A6NDV6|A6NKQ2|Q6IP98|Q8N1P6	Nonsense_Mutation	SNP	ENST00000311208.8	37	CCDS11402.1	.	.	.	.	.	.	.	.	.	.	T	26.3	4.726067	0.89298	0.0	5.81E-4	ENSG00000128422;ENSG00000173801	ENST00000311208;ENST00000540235	.	.	.	3.82	1.49	0.22878	.	0.000000	0.49305	D	0.000147	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	4.9636	0.14080	0.0:0.1718:0.1573:0.6709	.	.	.	.	X	262;421	.	.	K	-	1	0	JUP;KRT17	37031421	0.014000	0.17966	0.998000	0.56505	0.970000	0.65996	0.145000	0.16157	0.160000	0.19432	0.533000	0.62120	AAG	T|1.000;A|0.000	0.000	strong		0.617	KRT17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257460.1	NM_000422	
ZNF750	79755	hgsc.bcm.edu	37	17	80789628	80789628	+	Missense_Mutation	SNP	T	T	C	rs8074277	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:80789628T>C	ENST00000269394.3	-	2	1536	c.703A>G	c.(703-705)Atg>Gtg	p.M235V	TBCD_ENST00000355528.4_Intron|ZNF750_ENST00000572562.1_Intron|TBCD_ENST00000539345.2_Intron|TBCD_ENST00000397466.2_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	169	0	0		WXS	Illumina HiSeq	Phase_I	144	56	0.388889	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	
ZSCAN1	284312	hgsc.bcm.edu	37	19	58549366	58549366	+	Silent	SNP	C	C	G	rs159870	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:58549366C>G	ENST00000282326.1	+	3	409	c.162C>G	c.(160-162)ctC>ctG	p.L54L	ZSCAN1_ENST00000391700.1_Silent_p.L54L|ZSCAN1_ENST00000601162.1_Silent_p.L54L	NM_182572.3	NP_872378.3	Q8NBB4	ZSCA1_HUMAN	zinc finger and SCAN domain containing 1	54	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)|transcription coactivator activity (GO:0003713)			NS(1)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(25)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	48		Colorectal(82;5.46e-05)|all_neural(62;0.0182)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0152)		GGCCGCACCTCGCGCTGGGCC	0.701													C|||	3217	0.642372	0.6725	0.7305	5008	,	,		10937	0.4345		0.7346	False		,,,				2504	0.6585				p.L54L		Atlas-SNP	.											.	ZSCAN1	102	.	0			c.C162G						PASS	.	C		2875,1491		959,957,267	14.0	15.0	15.0		162	-3.9	0.0	19	dbSNP_79	15	6111,2457		2210,1691,383	no	coding-synonymous	ZSCAN1	NM_182572.3		3169,2648,650	GG,GC,CC		28.6765,34.1503,30.5242		54/409	58549366	8986,3948	2183	4284	6467	SO:0001819	synonymous_variant	284312	exon3			GCACCTCGCGCTG	AK091098	CCDS12969.1	19q13.43	2013-06-13	2004-04-21		ENSG00000152467	ENSG00000152467		"""-"", ""Zinc fingers, C2H2-type"""	23712	protein-coding gene	gene with protein product			"""zinc finger with SCAN domain 1"""			12477932	Standard	NM_182572		Approved	FLJ33779, ZNF915	uc002qrc.1	Q8NBB4	OTTHUMG00000183381	ENST00000282326.1:c.162C>G	19.37:g.58549366C>G		Somatic	9	0	0		WXS	Illumina HiSeq	Phase_I	18	6	0.333333	NM_182572	Q3B798|Q6WLH8|Q86WS8	Silent	SNP	ENST00000282326.1	37	CCDS12969.1																																																																																			C|0.331;G|0.669	0.669	strong		0.701	ZSCAN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466427.1	NM_182572	
PANX2	56666	hgsc.bcm.edu	37	22	50615556	50615556	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:50615556G>A	ENST00000395842.2	+	2	415	c.415G>A	c.(415-417)Gcg>Acg	p.A139T	PANX2_ENST00000159647.5_Missense_Mutation_p.A139T	NM_052839.3	NP_443071.2	Q96RD6	PANX2_HUMAN	pannexin 2	139					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)		GTACGTGCCCGCGCTGGGCTG	0.687																																					p.A139T		Atlas-SNP	.											PANX2_ENST00000395842,colon,carcinoma,0,2	PANX2	69	2	0			c.G415A						scavenged	.						36.0	28.0	31.0					22																	50615556		2195	4298	6493	SO:0001583	missense	56666	exon2			GTGCCCGCGCTGG		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.415G>A	22.37:g.50615556G>A	ENSP00000379183:p.Ala139Thr	Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	181	4	0.0220994	NM_052839	B7Z684|Q96RD5|Q9UGX8	Missense_Mutation	SNP	ENST00000395842.2	37	CCDS14085.2	.	.	.	.	.	.	.	.	.	.	G	23.9	4.465657	0.84425	.	.	ENSG00000073150	ENST00000159647;ENST00000395842	T;T	0.29655	1.56;1.56	4.54	3.5	0.40072	.	0.064589	0.64402	D	0.000008	T	0.22859	0.0552	L	0.36672	1.1	0.58432	D	0.999997	P;P	0.42757	0.597;0.789	B;B	0.37015	0.089;0.239	T	0.08086	-1.0739	10	0.54805	T	0.06	-13.0858	12.2486	0.54585	0.0843:0.0:0.9157:0.0	.	139;139	Q96RD6-1;Q96RD6	.;PANX2_HUMAN	T	139	ENSP00000159647:A139T;ENSP00000379183:A139T	ENSP00000159647:A139T	A	+	1	0	PANX2	48957683	1.000000	0.71417	0.880000	0.34516	0.988000	0.76386	7.571000	0.82399	2.251000	0.74343	0.555000	0.69702	GCG	.	.	none		0.687	PANX2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075010.3	NM_052839	
PPP1R26	9858	hgsc.bcm.edu	37	9	138377657	138377657	+	Missense_Mutation	SNP	T	T	C	rs1808998	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:138377657T>C	ENST00000356818.2	+	4	1850	c.1301T>C	c.(1300-1302)aTg>aCg	p.M434T	PPP1R26_ENST00000604351.1_Missense_Mutation_p.M434T|PPP1R26_ENST00000401470.3_Missense_Mutation_p.M434T|PPP1R26_ENST00000602993.1_Intron|PPP1R26_ENST00000605660.1_Missense_Mutation_p.M434T|PPP1R26_ENST00000605286.1_Missense_Mutation_p.M434T	NM_014811.3	NP_055626.3	Q5T8A7	PPR26_HUMAN	protein phosphatase 1, regulatory subunit 26	434			M -> T (in dbSNP:rs1808998). {ECO:0000269|PubMed:15489334}.		negative regulation of phosphatase activity (GO:0010923)	nucleus (GO:0005634)	phosphatase binding (GO:0019902)|protein phosphatase inhibitor activity (GO:0004864)										ACCAAGACCATGGACCCTGGT	0.592													C|||	2324	0.464058	0.4183	0.5231	5008	,	,		18270	0.6825		0.2147	False		,,,				2504	0.5153				p.M434T		Atlas-SNP	.											.	.	.	.	0			c.T1301C						PASS	.	C	THR/MET	1645,2761	636.1+/-396.5	304,1037,862	33.0	37.0	36.0		1301	-2.0	0.0	9	dbSNP_92	36	1822,6778	713.3+/-405.9	201,1420,2679	yes	missense	KIAA0649	NM_014811.3	81	505,2457,3541	CC,CT,TT		21.186,37.3355,26.6569	benign	434/1210	138377657	3467,9539	2203	4300	6503	SO:0001583	missense	9858	exon4			AGACCATGGACCC	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.1301T>C	9.37:g.138377657T>C	ENSP00000349274:p.Met434Thr	Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	22	14	0.636364	NM_014811	Q86WU0|Q8WVV0|Q9Y4D3	Missense_Mutation	SNP	ENST00000356818.2	37	CCDS6988.1	908	0.4157509157509158	168	0.34146341463414637	163	0.45027624309392267	416	0.7272727272727273	161	0.21240105540897097	C	0.016	-1.520221	0.00967	0.373355	0.21186	ENSG00000196422	ENST00000356818	T	0.08102	3.13	5.06	-1.98	0.07480	.	1.322620	0.05171	N	0.499637	T	0.00012	0.0000	N	0.00729	-1.24	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.39921	-0.9590	9	0.02654	T	1	0.4383	1.8933	0.03252	0.1239:0.3712:0.1217:0.3833	rs1808998;rs3748193;rs17846421;rs17859466;rs1808998	434	Q5T8A7	PPR26_HUMAN	T	434	ENSP00000349274:M434T	ENSP00000349274:M434T	M	+	2	0	KIAA0649	137517478	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.935000	0.03950	-1.293000	0.02362	-1.859000	0.00561	ATG	T|0.653;C|0.347	0.347	strong		0.592	PPP1R26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054987.1	NM_014811	
IDI2	91734	hgsc.bcm.edu	37	10	1065458	1065458	+	Silent	SNP	C	C	T	rs17851563	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:1065458C>T	ENST00000277517.1	-	5	747	c.683G>A	c.(682-684)tGa>tAa	p.*228*	GTPBP4_ENST00000360803.4_3'UTR	NM_033261.2	NP_150286.1	Q9BXS1	IDI2_HUMAN	isopentenyl-diphosphate delta isomerase 2	0					cholesterol biosynthetic process (GO:0006695)|dimethylallyl diphosphate biosynthetic process (GO:0050992)|isopentenyl diphosphate metabolic process (GO:0046490)|isoprenoid biosynthetic process (GO:0008299)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|peroxisome (GO:0005777)	hydrolase activity (GO:0016787)|isopentenyl-diphosphate delta-isomerase activity (GO:0004452)|metal ion binding (GO:0046872)	p.*228*(1)		kidney(1)|large_intestine(3)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	9		Colorectal(49;0.235)	OV - Ovarian serous cystadenocarcinoma(33;0.143)	Epithelial(11;0.067)|OV - Ovarian serous cystadenocarcinoma(14;0.169)|all cancers(11;0.192)		CCCTGCCTCTCACACTCTGTG	0.542													C|||	55	0.0109824	0.0015	0.0159	5008	,	,		19684	0.0		0.0408	False		,,,				2504	0.001				p.X228X		Atlas-SNP	.											IDI2,caecum,carcinoma,0,1	IDI2	20	1	1	Substitution - coding silent(1)	large_intestine(1)	c.G683A						PASS	.	C		29,4377	36.0+/-67.5	0,29,2174	39.0	39.0	39.0		683	-0.8	0.0	10	dbSNP_123	39	310,8290	109.0+/-169.6	5,300,3995	no	coding-synonymous	IDI2	NM_033261.2		5,329,6169	TT,TC,CC		3.6047,0.6582,2.6065		228/228	1065458	339,12667	2203	4300	6503	SO:0001819	synonymous_variant	91734	exon5			GCCTCTCACACTC	AF271725	CCDS7055.1	10p15.3	2003-11-19			ENSG00000148377	ENSG00000148377			23487	protein-coding gene	gene with protein product		615389				12477932	Standard	NM_033261		Approved	IPPI2	uc001ifv.1	Q9BXS1	OTTHUMG00000017537	ENST00000277517.1:c.683G>A	10.37:g.1065458C>T		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	52	29	0.557692	NM_033261		Silent	SNP	ENST00000277517.1	37	CCDS7055.1																																																																																			C|0.978;T|0.022	0.022	strong		0.542	IDI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046411.1	NM_033261	
FBLIM1	54751	hgsc.bcm.edu	37	1	16095031	16095031	+	Silent	SNP	G	G	A	rs140170023	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:16095031G>A	ENST00000375766.3	+	5	1087	c.447G>A	c.(445-447)gcG>gcA	p.A149A	FBLIM1_ENST00000441801.2_Silent_p.A149A|FBLIM1_ENST00000400773.1_Intron|FBLIM1_ENST00000375771.1_Silent_p.A149A|FBLIM1_ENST00000332305.5_Intron	NM_017556.2	NP_060026.2	Q8WUP2	FBLI1_HUMAN	filamin binding LIM protein 1	149	Pro-rich.				cell junction assembly (GO:0034329)|regulation of cell shape (GO:0008360)|regulation of integrin activation (GO:0033623)|single organismal cell-cell adhesion (GO:0016337)	cytosol (GO:0005829)|focal adhesion (GO:0005925)|stress fiber (GO:0001725)	filamin binding (GO:0031005)|zinc ion binding (GO:0008270)			large_intestine(2)|lung(4)|prostate(4)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	16		Colorectal(325;0.000257)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		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)|READ - Rectum adenocarcinoma(331;0.0649)|STAD - Stomach adenocarcinoma(313;0.138)		AGGCCCCAGCGGAGGGACCTT	0.627													G|||	28	0.00559105	0.0015	0.0086	5008	,	,		14787	0.0		0.0189	False		,,,				2504	0.001				p.A149A		Atlas-SNP	.											.	FBLIM1	46	.	0			c.G447A						PASS	.	G	,,	16,4390		0,16,2187	28.0	30.0	29.0		447,,447	-6.5	0.0	1	dbSNP_134	29	154,8442		0,154,4144	no	coding-synonymous,intron,coding-synonymous	FBLIM1	NM_001024215.1,NM_001024216.1,NM_017556.2	,,	0,170,6331	AA,AG,GG		1.7915,0.3631,1.3075	,,	149/375,,149/374	16095031	170,12832	2203	4298	6501	SO:0001819	synonymous_variant	54751	exon4			CCCAGCGGAGGGA		CCDS163.1, CCDS30609.1, CCDS44064.1	1p36.13	2014-04-07			ENSG00000162458	ENSG00000162458			24686	protein-coding gene	gene with protein product		607747				12679033, 12496242	Standard	XM_005245900		Approved	FBLP-1, CAL, migfilin	uc001axe.1	Q8WUP2	OTTHUMG00000003079	ENST00000375766.3:c.447G>A	1.37:g.16095031G>A		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	120	55	0.458333	NM_001024215	B3KNY0|Q5VVE0|Q5VVE1|Q8IX23|Q96T00|Q9UFD6	Silent	SNP	ENST00000375766.3	37	CCDS163.1																																																																																			G|0.989;A|0.011	0.011	strong		0.627	FBLIM1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008511.3	NM_001024215	
LAMA4	3910	hgsc.bcm.edu	37	6	112435912	112435912	+	Silent	SNP	A	A	T	rs1050353	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:112435912A>T	ENST00000230538.7	-	37	5557	c.5160T>A	c.(5158-5160)gtT>gtA	p.V1720V	LAMA4_ENST00000389463.4_Silent_p.V1713V|LAMA4_ENST00000522006.1_Silent_p.V1713V|LAMA4_ENST00000424408.2_Silent_p.V1713V	NM_001105206.2	NP_001098676.2	Q16363	LAMA4_HUMAN	laminin, alpha 4	1720	Laminin G-like 5. {ECO:0000255|PROSITE- ProRule:PRU00122}.				blood vessel development (GO:0001568)|brown fat cell differentiation (GO:0050873)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)	extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(42)|ovary(4)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(8)	100		all_cancers(87;0.000196)|all_hematologic(75;0.000114)|all_epithelial(87;0.00542)|Colorectal(196;0.0209)		all cancers(137;0.0335)|OV - Ovarian serous cystadenocarcinoma(136;0.0578)|Epithelial(106;0.0748)|BRCA - Breast invasive adenocarcinoma(108;0.242)		GCTTGGGTGTAACTGAGGTGG	0.423													T|||	1411	0.281749	0.3419	0.2392	5008	,	,		17779	0.3571		0.2634	False		,,,				2504	0.1718				p.V1720V		Atlas-SNP	.											.	LAMA4	227	.	0			c.T5160A						PASS	.	T	,,	1477,2929	678.8+/-403.6	258,961,984	146.0	129.0	135.0		5160,5139,5139	-12.1	0.1	6	dbSNP_86	135	2489,6111	695.2+/-404.8	341,1807,2152	no	coding-synonymous,coding-synonymous,coding-synonymous	LAMA4	NM_001105206.1,NM_001105207.1,NM_002290.3	,,	599,2768,3136	TT,TA,AA		28.9419,33.5225,30.4936	,,	1720/1824,1713/1817,1713/1817	112435912	3966,9040	2203	4300	6503	SO:0001819	synonymous_variant	3910	exon37			GGGTGTAACTGAG		CCDS34514.1, CCDS43491.1, CCDS43492.1	6q21	2014-09-17			ENSG00000112769	ENSG00000112769		"""Laminins"""	6484	protein-coding gene	gene with protein product		600133				7959779	Standard	NM_001105206		Approved	LAMA3	uc003pvu.3	Q16363	OTTHUMG00000015386	ENST00000230538.7:c.5160T>A	6.37:g.112435912A>T		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	115	57	0.495652	NM_001105206	Q14731|Q14735|Q15335|Q4LE44|Q5SZG8|Q9BTB8|Q9UE18|Q9UJN9	Silent	SNP	ENST00000230538.7	37	CCDS43491.1																																																																																			A|0.701;T|0.299	0.299	strong		0.423	LAMA4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041876.2	NM_001105206	
OR7A10	390892	hgsc.bcm.edu	37	19	14951898	14951898	+	Silent	SNP	G	G	T	rs3752195	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:14951898G>T	ENST00000248058.1	-	1	791	c.792C>A	c.(790-792)gcC>gcA	p.A264A		NM_001005190.1	NP_001005190.1	O76100	OR7AA_HUMAN	olfactory receptor, family 7, subfamily A, member 10	264						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)|kidney(2)|large_intestine(4)|lung(9)|stomach(1)	19	Ovarian(108;0.203)					AATTGTGGGTGGCAGCAGAAC	0.478													.|||	1159	0.23143	0.1694	0.2464	5008	,	,		19853	0.1776		0.2097	False		,,,				2504	0.3824				p.A264A		Atlas-SNP	.											OR7A10,NS,carcinoma,-2,1	OR7A10	33	1	0			c.C792A						PASS	.	T		829,3577	747.7+/-411.9	90,649,1464	96.0	87.0	90.0		792	-3.8	0.0	19	dbSNP_107	90	1967,6633	723.8+/-406.5	208,1551,2541	no	coding-synonymous	OR7A10	NM_001005190.1		298,2200,4005	TT,TG,GG		22.8721,18.8153,21.4978		264/310	14951898	2796,10210	2203	4300	6503	SO:0001819	synonymous_variant	390892	exon1			GTGGGTGGCAGCA		CCDS32936.1	19p13.1	2012-08-09						"""GPCR / Class A : Olfactory receptors"""	8356	protein-coding gene	gene with protein product							Standard	NM_001005190		Approved		uc002mzx.1	O76100		ENST00000248058.1:c.792C>A	19.37:g.14951898G>T		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	53	28	0.528302	NM_001005190	Q6IFP0|Q96R97	Silent	SNP	ENST00000248058.1	37	CCDS32936.1																																																																																			G|0.787;T|0.213	0.213	strong		0.478	OR7A10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466520.1	NM_001005190	
CETN3	1070	hgsc.bcm.edu	37	5	89703535	89703535	+	Missense_Mutation	SNP	A	A	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:89703535A>C	ENST00000283122.3	-	2	258	c.134T>G	c.(133-135)aTa>aGa	p.I45R	CETN3_ENST00000522083.1_Missense_Mutation_p.I45R|CETN3_ENST00000522864.1_Missense_Mutation_p.I45R|CETN3_ENST00000522842.1_Missense_Mutation_p.I45R|CETN3_ENST00000522565.1_Missense_Mutation_p.I45R	NM_004365.2	NP_004356.2	O15182	CETN3_HUMAN	centrin, EF-hand protein, 3	45	EF-hand 1. {ECO:0000255|PROSITE- ProRule:PRU00448}.				centrosome cycle (GO:0007098)|mitotic nuclear division (GO:0007067)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|ciliary transition zone (GO:0035869)|cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|photoreceptor connecting cilium (GO:0032391)	calcium ion binding (GO:0005509)			lung(3)	3		all_cancers(142;7.93e-09)|all_epithelial(76;2.13e-11)|Lung NSC(167;2.46e-05)|all_lung(232;3.25e-05)|Ovarian(174;0.00832)|Colorectal(57;0.122)|Breast(839;0.198)		OV - Ovarian serous cystadenocarcinoma(54;1.42e-32)|Epithelial(54;1.45e-26)|all cancers(79;2.87e-23)		ATGATAATCTATTGCTTCATC	0.269																																					p.I45R		Atlas-SNP	.											.	CETN3	16	.	0			c.T134G						PASS	.						100.0	96.0	97.0					5																	89703535		2200	4291	6491	SO:0001583	missense	1070	exon2			TAATCTATTGCTT	Y12473	CCDS4066.1, CCDS75274.1	5q14.3	2013-01-10	2010-06-24		ENSG00000153140	ENSG00000153140		"""EF-hand domain containing"""	1868	protein-coding gene	gene with protein product	"""CDC31 yeast homolog"", ""EF-hand superfamily member"""	602907	"""centrin, EF-hand protein, 3 (CDC31 yeast homolog)"""			9256449	Standard	XM_006714521		Approved	CEN3	uc003kjo.3	O15182	OTTHUMG00000131326	ENST00000283122.3:c.134T>G	5.37:g.89703535A>C	ENSP00000283122:p.Ile45Arg	Somatic	342	0	0		WXS	Illumina HiSeq	Phase_I	332	122	0.36747	NM_004365	Q53YD2|Q9BS23	Missense_Mutation	SNP	ENST00000283122.3	37	CCDS4066.1	.	.	.	.	.	.	.	.	.	.	A	19.53	3.845429	0.71603	.	.	ENSG00000153140	ENST00000283122;ENST00000522083;ENST00000522864;ENST00000522565;ENST00000522842	T;T;T;T;T	0.78246	-1.16;-1.16;-1.16;-1.16;-1.16	5.65	4.5	0.54988	EF-hand-like domain (1);	0.000000	0.85682	D	0.000000	D	0.92156	0.7513	H	0.98738	4.315	0.80722	D	1	D	0.89917	1.0	D	0.75484	0.986	D	0.93002	0.6424	10	0.87932	D	0	.	10.5918	0.45314	0.925:0.0:0.075:0.0	.	45	O15182	CETN3_HUMAN	R	45	ENSP00000283122:I45R;ENSP00000428259:I45R;ENSP00000430361:I45R;ENSP00000430409:I45R;ENSP00000429875:I45R	ENSP00000283122:I45R	I	-	2	0	CETN3	89739291	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.065000	0.93941	0.975000	0.38392	0.459000	0.35465	ATA	.	.	none		0.269	CETN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254097.1	NM_004365	
ARHGAP26	23092	hgsc.bcm.edu	37	5	142254679	142254679	+	Silent	SNP	A	A	G	rs185200	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:142254679A>G	ENST00000274498.4	+	3	633	c.255A>G	c.(253-255)agA>agG	p.R85R	ARHGAP26_ENST00000378004.3_Silent_p.R85R	NM_015071.4	NP_055886.1	Q9UNA1	RHG26_HUMAN	Rho GTPase activating protein 26	85					actin cytoskeleton organization (GO:0030036)|filopodium assembly (GO:0046847)|nervous system development (GO:0007399)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell junction (GO:0030054)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)	phospholipid binding (GO:0005543)|Rho GTPase activator activity (GO:0005100)			autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(6)|lung(7)|ovary(1)	25		all_hematologic(541;0.0416)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			TTCCAGCAAGATCTTTGCAGG	0.483													G|||	3374	0.673722	0.8979	0.5058	5008	,	,		19158	0.8581		0.3091	False		,,,				2504	0.6748				p.R85R		Atlas-SNP	.											.	ARHGAP26	57	.	0			c.A255G						PASS	.	G	,	3440,966	362.4+/-316.1	1350,740,113	114.0	103.0	107.0		255,255	2.6	1.0	5	dbSNP_79	107	2569,6031	690.7+/-404.5	378,1813,2109	no	coding-synonymous,coding-synonymous	ARHGAP26	NM_001135608.1,NM_015071.4	,	1728,2553,2222	GG,GA,AA		29.8721,21.9246,46.2018	,	85/760,85/815	142254679	6009,6997	2203	4300	6503	SO:0001819	synonymous_variant	23092	exon3			AGCAAGATCTTTG	AB014521	CCDS4277.1, CCDS47297.1	5q31	2011-06-29			ENSG00000145819	ENSG00000145819		"""Rho GTPase activating proteins"""	17073	protein-coding gene	gene with protein product	"""GTPase regulator associated with the focal adhesion kinase pp125"""	605370				9858476, 8649427	Standard	NM_001135608		Approved	GRAF, KIAA0621, OPHN1L, OPHN1L1	uc011dbj.2	Q9UNA1	OTTHUMG00000059705	ENST00000274498.4:c.255A>G	5.37:g.142254679A>G		Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	91	44	0.483516	NM_015071	O75117|Q5D035|Q9BYS6|Q9BYS7|Q9UJ00	Silent	SNP	ENST00000274498.4	37	CCDS4277.1																																																																																			A|0.466;G|0.534	0.534	strong		0.483	ARHGAP26-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000132744.3	NM_015071	
PKN1	5585	hgsc.bcm.edu	37	19	14582539	14582539	+	Silent	SNP	C	C	T	rs8598	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:14582539C>T	ENST00000242783.6	+	22	2937	c.2772C>T	c.(2770-2772)ctC>ctT	p.L924L	PKN1_ENST00000342216.4_Silent_p.L930L	NM_002741.3	NP_002732.3	Q16512	PKN1_HUMAN	protein kinase N1	924	AGC-kinase C-terminal.				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						CGCGGCCCCTCACAGCCGCGG	0.726													C|||	567	0.113219	0.0514	0.1571	5008	,	,		9008	0.0089		0.2465	False		,,,				2504	0.136				p.L930L	NSCLC(185;2539 2965 10733 52867)	Atlas-SNP	.											.	PKN1	99	.	0			c.C2790T						PASS	.	C	,	298,3504		18,262,1621	6.0	8.0	7.0		2772,2790	1.5	0.6	19	dbSNP_52	7	2128,5922		302,1524,2199	no	coding-synonymous,coding-synonymous	PKN1	NM_002741.3,NM_213560.1	,	320,1786,3820	TT,TC,CC		26.4348,7.838,20.4691	,	924/943,930/949	14582539	2426,9426	1901	4025	5926	SO:0001819	synonymous_variant	5585	exon22			GCCCCTCACAGCC	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.2772C>T	19.37:g.14582539C>T		Somatic	19	0	0		WXS	Illumina HiSeq	Phase_I	22	17	0.772727	NM_213560	A8K7W5|B2R9R4|B3KVN3|Q15143|Q504U4|Q8IUV5|Q9UD44	Silent	SNP	ENST00000242783.6	37	CCDS42513.1																																																																																			C|0.867;T|0.133	0.133	strong		0.726	PKN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095510.1	NM_002741, NM_213560	
C9orf129	445577	hgsc.bcm.edu	37	9	96080699	96080699	+	Missense_Mutation	SNP	C	C	T	rs36081907	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:96080699C>T	ENST00000375419.1	-	5	935	c.572G>A	c.(571-573)cGt>cAt	p.R191H	WNK2_ENST00000356055.3_Intron|WNK2_ENST00000471076.1_Intron|WNK2_ENST00000395475.2_Intron|WNK2_ENST00000349097.3_Intron|WNK2_ENST00000395477.2_Intron	NM_001098808.1	NP_001092278.1	Q5T035	CI129_HUMAN	chromosome 9 open reading frame 129	191			R -> H (in dbSNP:rs36081907).							endometrium(2)|large_intestine(1)|lung(1)|ovary(2)	6						GGCTGAGAGACGGCGGGACGC	0.567													C|||	494	0.0986422	0.1762	0.0937	5008	,	,		17538	0.001		0.1402	False		,,,				2504	0.0552				p.R191H		Atlas-SNP	.											.	C9orf129	18	.	0			c.G572A						PASS	.	C	HIS/ARG,	606,3386		47,512,1437	72.0	79.0	77.0		572,	-3.1	0.0	9	dbSNP_126	77	923,7437		56,811,3313	yes	missense,intron	WNK2,C9orf129	NM_001098808.1,NM_006648.3	29,	103,1323,4750	TT,TC,CC		11.0407,15.1804,12.3786	possibly-damaging,	191/197,	96080699	1529,10823	1996	4180	6176	SO:0001583	missense	445577	exon5			GAGAGACGGCGGG		CCDS43850.1	9q22.31	2012-04-02			ENSG00000204352	ENSG00000204352			31116	protein-coding gene	gene with protein product							Standard	NM_001098808		Approved	bA165J3.3	uc010mre.3	Q5T035	OTTHUMG00000020248	ENST00000375419.1:c.572G>A	9.37:g.96080699C>T	ENSP00000364568:p.Arg191His	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	71	34	0.478873	NM_001098808		Missense_Mutation	SNP	ENST00000375419.1	37	CCDS43850.1	237	0.10851648351648352	90	0.18292682926829268	39	0.10773480662983426	1	0.0017482517482517483	107	0.14116094986807387	C	12.95	2.091402	0.36855	0.151804	0.110407	ENSG00000204352	ENST00000375419	T	0.53423	0.62	1.54	-3.08	0.05347	.	.	.	.	.	T	0.00039	0.0001	N	0.08118	0	0.80722	P	0.0	P	0.50066	0.931	B	0.29176	0.099	T	0.13415	-1.0510	8	0.87932	D	0	.	3.4845	0.07614	0.2975:0.3528:0.3497:0.0	rs36081907;rs57634506;rs62574762	191	Q5T035	CI129_HUMAN	H	191	ENSP00000364568:R191H	ENSP00000364568:R191H	R	-	2	0	C9orf129	95120520	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.366000	0.02585	-0.978000	0.03533	-0.302000	0.09304	CGT	C|0.886;T|0.114	0.114	strong		0.567	C9orf129-001	KNOWN	mRNA_end_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053147.1	NM_001098808	
NEIL3	55247	hgsc.bcm.edu	37	4	178262683	178262683	+	Silent	SNP	T	T	C	rs17676249	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:178262683T>C	ENST00000264596.3	+	6	874	c.756T>C	c.(754-756)ccT>ccC	p.P252P	RP11-376O6.2_ENST00000506895.1_RNA	NM_018248.2	NP_060718	Q8TAT5	NEIL3_HUMAN	nei endonuclease VIII-like 3 (E. coli)	252					base-excision repair (GO:0006284)|DNA catabolic process, endonucleolytic (GO:0000737)|nucleotide-excision repair (GO:0006289)	nucleus (GO:0005634)	bubble DNA binding (GO:0000405)|damaged DNA binding (GO:0003684)|DNA N-glycosylase activity (GO:0019104)|DNA-(apurinic or apyrimidinic site) lyase activity (GO:0003906)|double-stranded DNA binding (GO:0003690)|single-stranded DNA binding (GO:0003697)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(14)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	29		Breast(14;6.27e-05)|Melanoma(52;0.00102)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|all_neural(102;0.164)		all cancers(43;1.96e-23)|Epithelial(43;2.52e-20)|OV - Ovarian serous cystadenocarcinoma(60;1.89e-11)|GBM - Glioblastoma multiforme(59;9.49e-05)|Colorectal(24;0.00013)|COAD - Colon adenocarcinoma(29;0.000696)|STAD - Stomach adenocarcinoma(60;0.00308)|LUSC - Lung squamous cell carcinoma(193;0.0398)|READ - Rectum adenocarcinoma(43;0.191)		ACAAGCGTCCTAATTGTGGTC	0.388								Base excision repair (BER), DNA glycosylases					T|||	728	0.145367	0.1437	0.1268	5008	,	,		16258	0.1091		0.2048	False		,,,				2504	0.137				p.P252P		Atlas-SNP	.											.	NEIL3	89	.	0			c.T756C						PASS	.	T		753,3653	309.1+/-290.9	69,615,1519	90.0	84.0	86.0		756	3.0	1.0	4	dbSNP_123	86	1837,6763	328.8+/-318.4	194,1449,2657	no	coding-synonymous	NEIL3	NM_018248.2		263,2064,4176	CC,CT,TT		21.3605,17.0903,19.9139		252/606	178262683	2590,10416	2203	4300	6503	SO:0001819	synonymous_variant	55247	exon6			GCGTCCTAATTGT	AB079071	CCDS3828.1	4q34	2014-02-18			ENSG00000109674	ENSG00000109674			24573	protein-coding gene	gene with protein product	"""zinc finger, GRF-type containing 3"""	608934				12713815, 12509226	Standard	NM_018248		Approved	FLJ10858, hFPG2, FPG2, hNEI3, ZGRF3	uc003iut.2	Q8TAT5	OTTHUMG00000160722	ENST00000264596.3:c.756T>C	4.37:g.178262683T>C		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	53	25	0.471698	NM_018248	Q2PPJ3|Q8NG51|Q9NV95	Silent	SNP	ENST00000264596.3	37	CCDS3828.1																																																																																			T|0.826;C|0.174	0.174	strong		0.388	NEIL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361914.1	NM_018248	
APH1B	83464	hgsc.bcm.edu	37	15	63569902	63569902	+	Missense_Mutation	SNP	C	C	T	rs117618017	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:63569902C>T	ENST00000261879.5	+	1	150	c.80C>T	c.(79-81)aCc>aTc	p.T27I	APH1B_ENST00000380343.4_Missense_Mutation_p.T27I	NM_001145646.1|NM_031301.3	NP_001139118.1|NP_112591.2	Q8WW43	APH1B_HUMAN	APH1B gamma secretase subunit	27				T -> I (in Ref. 4; AAQ89061). {ECO:0000305}.	apoptotic signaling pathway (GO:0097190)|membrane protein intracellular domain proteolysis (GO:0031293)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|positive regulation of apoptotic process (GO:0043065)|positive regulation of catalytic activity (GO:0043085)|protein processing (GO:0016485)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|transport vesicle (GO:0030133)	peptidase activity (GO:0008233)	p.T27I(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|stomach(1)|upper_aerodigestive_tract(1)	12						ACCATCGCCACCGAGCCGTTG	0.682													C|||	222	0.0443291	0.0045	0.0879	5008	,	,		8198	0.0		0.1352	False		,,,				2504	0.0194				p.T27I		Atlas-SNP	.											APH1B,NS,lymphoid_neoplasm,0,3	APH1B	27	3	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.C80T						PASS	.	C	ILE/THR,ILE/THR	129,4277	93.0+/-131.7	4,121,2078	49.0	49.0	49.0		80,80	1.0	0.0	15	dbSNP_132	49	1099,7501	226.9+/-262.5	68,963,3269	yes	missense,missense	APH1B	NM_001145646.1,NM_031301.3	89,89	72,1084,5347	TT,TC,CC		12.7791,2.9278,9.4418	probably-damaging,probably-damaging	27/217,27/258	63569902	1228,11778	2203	4300	6503	SO:0001583	missense	83464	exon1			TCGCCACCGAGCC	AY358698	CCDS10184.1, CCDS45276.1	15q22.2	2013-05-01	2013-05-01		ENSG00000138613	ENSG00000138613			24080	protein-coding gene	gene with protein product		607630	"""anterior pharynx defective 1 homolog B (C. elegans)"""			12110170, 11230166	Standard	NM_031301		Approved	PSFL, APH-1B, DKFZp564D0372	uc002ama.3	Q8WW43	OTTHUMG00000132863	ENST00000261879.5:c.80C>T	15.37:g.63569902C>T	ENSP00000261879:p.Thr27Ile	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	130	85	0.653846	NM_001145646	A8K589|Q564N3|Q6UWQ1|Q9H0S0	Missense_Mutation	SNP	ENST00000261879.5	37	CCDS10184.1	138	0.06318681318681318	5	0.01016260162601626	35	0.09668508287292818	0	0.0	98	0.12928759894459102	C	7.955	0.745633	0.15710	0.029278	0.127791	ENSG00000138613	ENST00000380343;ENST00000261879;ENST00000380340	T;T;T	0.43688	0.94;0.94;0.94	4.11	0.961	0.19638	.	0.534132	0.18319	N	0.144870	T	0.00328	0.0010	M	0.62723	1.935	0.80722	P	0.0	P;P	0.38677	0.642;0.521	B;B	0.37650	0.193;0.255	T	0.04029	-1.0983	9	0.37606	T	0.19	-2.1163	1.1628	0.01809	0.1834:0.4361:0.1783:0.2022	.	27;27	Q564N3;Q8WW43	.;APH1B_HUMAN	I	27	ENSP00000369700:T27I;ENSP00000261879:T27I;ENSP00000369697:T27I	ENSP00000261879:T27I	T	+	2	0	APH1B	61356955	0.013000	0.17824	0.005000	0.12908	0.350000	0.29205	1.171000	0.31896	0.098000	0.17522	-0.719000	0.03609	ACC	C|0.915;T|0.085	0.085	strong		0.682	APH1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256337.1	NM_031301	
MUC4	4585	hgsc.bcm.edu	37	3	195507323	195507323	+	Missense_Mutation	SNP	T	T	C	rs201618076		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195507323T>C	ENST00000463781.3	-	2	11587	c.11128A>G	c.(11128-11130)Acc>Gcc	p.T3710A	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.T3710A	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		AGAGGGGTGGTGTGACCTGAG	0.572																																					p.T3710A		Atlas-SNP	.											MUC4_ENST00000463781,uveal_tract,malignant_melanoma,0,1	MUC4	1505	1	0			c.A11128G						scavenged	.						67.0	57.0	60.0					3																	195507323		660	1591	2251	SO:0001583	missense	4585	exon2			GGGTGGTGTGACC	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.11128A>G	3.37:g.195507323T>C	ENSP00000417498:p.Thr3710Ala	Somatic	80	1	0.0125		WXS	Illumina HiSeq	Phase_I	96	13	0.135417	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	t	5.476	0.272841	0.10349	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.31510	1.51;1.49	0.885	-1.77	0.07982	.	.	.	.	.	T	0.11067	0.0270	N	0.14661	0.345	0.09310	N	1	P	0.37985	0.613	B	0.25140	0.058	T	0.14062	-1.0486	8	.	.	.	.	3.5153	0.07722	0.0:0.2995:0.0:0.7005	.	3582	E7ESK3	.	A	3710	ENSP00000417498:T3710A;ENSP00000420243:T3710A	.	T	-	1	0	MUC4	196992102	0.927000	0.31430	0.003000	0.11579	0.039000	0.13416	0.650000	0.24858	-1.812000	0.01227	-2.075000	0.00382	ACC	.	.	weak		0.572	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
TRIM51	84767	hgsc.bcm.edu	37	11	55653164	55653164	+	Missense_Mutation	SNP	G	G	A	rs10897403	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:55653164G>A	ENST00000449290.2	+	2	352	c.260G>A	c.(259-261)aGc>aAc	p.S87N	TRIM51_ENST00000244891.3_5'Flank	NM_032681.3	NP_116070.2	Q9BSJ1	TRI51_HUMAN	tripartite motif-containing 51	87						intracellular (GO:0005622)	zinc ion binding (GO:0008270)										CAATTCCTTAGCTCTGAGGAG	0.483													N|||	2125	0.424321	0.1672	0.4928	5008	,	,		21418	0.621		0.3628	False		,,,				2504	0.5838				p.S87N		Atlas-SNP	.											.	.	.	.	0			c.G260A						PASS	.	G	ASN/SER	278,1106		31,216,445	14.0	13.0	13.0		260	0.8	0.0	11	dbSNP_120	13	1132,2048		219,694,677	no	missense	SPRYD5	NM_032681.3	46	250,910,1122	AA,AG,GG		35.5975,20.0867,30.894	possibly-damaging	87/453	55653164	1410,3154	692	1590	2282	SO:0001583	missense	84767	exon2			TCCTTAGCTCTGA	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.260G>A	11.37:g.55653164G>A	ENSP00000395086:p.Ser87Asn	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	62	15	0.241935	NM_032681	A6NMG2	Missense_Mutation	SNP	ENST00000449290.2	37		850	0.3891941391941392	70	0.14227642276422764	174	0.48066298342541436	341	0.5961538461538461	265	0.3496042216358839	.	6.212	0.407193	0.11754	0.200867	0.355975	ENSG00000124900	ENST00000449290	T	0.57436	0.4	0.803	0.803	0.18691	Zinc finger, RING/FYVE/PHD-type (1);	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.50632	P	1.1099999999997223E-4	B	0.31989	0.35	B	0.30105	0.111	T	0.45948	-0.9226	8	0.21014	T	0.42	.	7.5005	0.27516	1.0E-4:0.0:0.9999:0.0	rs10897403;rs57159508	87	Q9BSJ1	SPRY5_HUMAN	N	87	ENSP00000395086:S87N	ENSP00000395086:S87N	S	+	2	0	SPRYD5	55409740	0.000000	0.05858	0.038000	0.18304	0.141000	0.21300	-0.576000	0.05854	0.752000	0.32923	0.152000	0.16155	AGC	G|0.613;A|0.387	0.387	strong		0.483	TRIM51-004	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000391522.1	NM_032681	
CACNA1I	8911	hgsc.bcm.edu	37	22	40057273	40057273	+	Silent	SNP	T	T	C	rs136852	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:40057273T>C	ENST00000402142.3	+	16	2859	c.2859T>C	c.(2857-2859)agT>agC	p.S953S	CACNA1I_ENST00000407673.1_Silent_p.S918S|CACNA1I_ENST00000401624.1_Silent_p.S953S|CACNA1I_ENST00000336649.4_Silent_p.S959S|CACNA1I_ENST00000404898.1_Silent_p.S918S|CACNA1I_ENST00000400164.3_Silent_p.S918S	NM_021096.3	NP_066919.2	Q9P0X4	CAC1I_HUMAN	calcium channel, voltage-dependent, T type, alpha 1I subunit	953					axon guidance (GO:0007411)|calcium ion import (GO:0070509)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|signal transduction (GO:0007165)|sleep (GO:0030431)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	voltage-gated calcium channel activity (GO:0005245)			breast(2)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|liver(2)|lung(27)|ovary(1)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	60	Melanoma(58;0.0749)				Cinnarizine(DB00568)|Flunarizine(DB04841)|Paramethadione(DB00617)|Spironolactone(DB00421)|Verapamil(DB00661)|Zonisamide(DB00909)	GAAAGAGCAGTGTCATGTCTC	0.667													C|||	3690	0.736821	0.792	0.7363	5008	,	,		18175	0.994		0.5527	False		,,,				2504	0.5869				p.S953S		Atlas-SNP	.											.	CACNA1I	264	.	0			c.T2859C						PASS	.	C	,	3008,930		1153,702,114	32.0	37.0	35.0		2754,2859	-5.4	0.8	22	dbSNP_78	35	4417,3857		1187,2043,907	no	coding-synonymous,coding-synonymous	CACNA1I	NM_001003406.1,NM_021096.3	,	2340,2745,1021	CC,CT,TT		46.6159,23.616,39.1991	,	918/2189,953/2224	40057273	7425,4787	1969	4137	6106	SO:0001819	synonymous_variant	8911	exon16			GAGCAGTGTCATG	AF129133	CCDS46710.1, CCDS46711.1	22q13.1	2012-03-07	2007-02-16		ENSG00000100346	ENSG00000100346		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1396	protein-coding gene	gene with protein product		608230				10454147, 16382099	Standard	NM_021096		Approved	Cav3.3	uc003ayd.3	Q9P0X4	OTTHUMG00000151096	ENST00000402142.3:c.2859T>C	22.37:g.40057273T>C		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	59	37	0.627119	NM_021096	B0QY12|B0QY13|B0QY14|O95504|Q5JZ88|Q7Z6S9|Q8NFX6|Q9NZC8|Q9UH15|Q9UH30|Q9ULU9|Q9UNE6	Silent	SNP	ENST00000402142.3	37	CCDS46710.1																																																																																			T|0.284;C|0.716	0.716	strong		0.667	CACNA1I-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000321290.1	NM_001003406	
OR1L8	138881	hgsc.bcm.edu	37	9	125330240	125330240	+	Missense_Mutation	SNP	T	T	G	rs72751258	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:125330240T>G	ENST00000304865.2	-	1	598	c.517A>C	c.(517-519)Aat>Cat	p.N173H		NM_001004454.1	NP_001004454.1	Q8NGR8	OR1L8_HUMAN	olfactory receptor, family 1, subfamily L, member 8	173						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(5)|lung(6)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	20						TGGATAACATTGGAGTCACAG	0.493													T|||	25	0.00499201	0.0015	0.0072	5008	,	,		23469	0.0		0.0119	False		,,,				2504	0.0061				p.N173H		Atlas-SNP	.											.	OR1L8	90	.	0			c.A517C						PASS	.	T	HIS/ASN	18,4388	24.3+/-50.5	0,18,2185	144.0	113.0	123.0		517	2.0	0.9	9	dbSNP_130	123	131,8469	67.3+/-129.8	1,129,4170	yes	missense	OR1L8	NM_001004454.1	68	1,147,6355	GG,GT,TT		1.5233,0.4085,1.1456	probably-damaging	173/310	125330240	149,12857	2203	4300	6503	SO:0001583	missense	138881	exon1			TAACATTGGAGTC		CCDS35124.1	9q33.2	2013-09-20			ENSG00000171496	ENSG00000171496		"""GPCR / Class A : Olfactory receptors"""	15110	protein-coding gene	gene with protein product							Standard	NM_001004454		Approved		uc004bmp.1	Q8NGR8	OTTHUMG00000020609	ENST00000304865.2:c.517A>C	9.37:g.125330240T>G	ENSP00000306607:p.Asn173His	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	114	66	0.578947	NM_001004454	A3KFM3|B9EIR6|Q6IF15|Q96R79	Missense_Mutation	SNP	ENST00000304865.2	37	CCDS35124.1	14	0.00641025641025641	2	0.0040650406504065045	2	0.0055248618784530384	0	0.0	10	0.013192612137203167	T	12.79	2.043930	0.36085	0.004085	0.015233	ENSG00000171496	ENST00000304865	T	0.00256	8.42	4.49	1.95	0.26073	GPCR, rhodopsin-like superfamily (1);	0.283555	0.25096	N	0.033176	T	0.00073	0.0002	L	0.31926	0.97	0.09310	N	1	B	0.17038	0.02	B	0.25405	0.06	T	0.15752	-1.0426	10	0.26408	T	0.33	-9.7633	6.2416	0.20793	0.0:0.091:0.2517:0.6573	.	173	Q8NGR8	OR1L8_HUMAN	H	173	ENSP00000306607:N173H	ENSP00000306607:N173H	N	-	1	0	OR1L8	124370061	0.004000	0.15560	0.911000	0.35937	0.942000	0.58702	1.334000	0.33827	0.889000	0.36185	0.369000	0.22263	AAT	T|0.989;G|0.011	0.011	strong		0.493	OR1L8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053939.1		
NFXL1	152518	hgsc.bcm.edu	37	4	47901476	47901476	+	Missense_Mutation	SNP	G	G	A	rs12651301	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	174	0	0		WXS	Illumina HiSeq	Phase_I	138	72	0.521739	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	
HIST1H2BG	8339	hgsc.bcm.edu	37	6	26216656	26216656	+	Silent	SNP	T	T	C	rs41266811	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:26216656T>C	ENST00000244601.3	-	1	216	c.216A>G	c.(214-216)gaA>gaG	p.E72E	HIST1H2AE_ENST00000303910.2_5'Flank	NM_003518.3	NP_003509.1	P62807	H2B1C_HUMAN	histone cluster 1, H2bg	72					antibacterial humoral response (GO:0019731)|chromatin organization (GO:0006325)|defense response to Gram-positive bacterium (GO:0050830)|innate immune response in mucosa (GO:0002227)|nucleosome assembly (GO:0006334)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	8		all_hematologic(11;0.196)				CTGCGATGCGTTCGAAGATGT	0.562													C|||	507	0.101238	0.1498	0.0562	5008	,	,		20268	0.0407		0.1054	False		,,,				2504	0.1258				p.E72E		Atlas-SNP	.											.	HIST1H2BG	25	.	0			c.A216G						PASS	.	C		558,3848		35,488,1680	172.0	157.0	162.0		216	3.1	1.0	6	dbSNP_127	162	736,7864		21,694,3585	no	coding-synonymous	HIST1H2BG	NM_003518.3		56,1182,5265	CC,CT,TT		8.5581,12.6645,9.9493		72/127	26216656	1294,11712	2203	4300	6503	SO:0001819	synonymous_variant	8339	exon1			GATGCGTTCGAAG	M60750	CCDS4594.1	6p21.3	2011-01-27	2006-10-11	2003-02-14	ENSG00000187990	ENSG00000273802		"""Histones / Replication-dependent"""	4746	protein-coding gene	gene with protein product		602798	"""H2B histone family, member A"", ""histone 1, H2bg"""	H2BFA		1916825, 12408966	Standard	NM_003518		Approved	H2B/a, H2B.1A	uc003ngz.2	P62807	OTTHUMG00000014446	ENST00000244601.3:c.216A>G	6.37:g.26216656T>C		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	115	58	0.504348	NM_003518	P02278|Q3B872|Q4VB69|Q93078|Q93080	Silent	SNP	ENST00000244601.3	37	CCDS4594.1																																																																																			T|0.903;C|0.097	0.097	strong		0.562	HIST1H2BG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040109.2	NM_003518	
OR51F1	256892	hgsc.bcm.edu	37	11	4790268	4790268	+	Missense_Mutation	SNP	C	C	A	rs1030726	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:4790268C>A	ENST00000380383.1	-	1	900	c.901G>T	c.(901-903)Gac>Tac	p.D301Y	OR51F1_ENST00000343430.3_Missense_Mutation_p.D294Y|MMP26_ENST00000477339.1_Intron|MMP26_ENST00000380390.1_Intron			A6NGY5	O51F1_HUMAN	olfactory receptor, family 51, subfamily F, member 1	301			D -> Y (in dbSNP:rs1030726).			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)		TTTACACTGTCGATGATGGGG	0.448													A|||	1080	0.215655	0.4569	0.2017	5008	,	,		21026	0.0		0.2704	False		,,,				2504	0.0654				p.D294Y		Atlas-SNP	.											.	OR51F1	60	.	0			c.G880T						PASS	.	A	TYR/ASP	1967,2435	618.7+/-393.2	444,1079,678	95.0	92.0	93.0		880	5.4	1.0	11	dbSNP_86	93	2178,6418	712.3+/-405.9	291,1596,2411	yes	missense	OR51F1	NM_001004752.1	160	735,2675,3089	AA,AC,CC		25.3374,44.6842,31.8895	benign	294/313	4790268	4145,8853	2201	4298	6499	SO:0001583	missense	256892	exon1			CACTGTCGATGAT	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.901G>T	11.37:g.4790268C>A	ENSP00000369744:p.Asp301Tyr	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	118	13	0.110169	NM_001004752		Missense_Mutation	SNP	ENST00000380383.1	37		494	0.2261904761904762	225	0.4573170731707317	82	0.2265193370165746	0	0.0	187	0.24670184696569922	A	1.713	-0.498507	0.04291	0.446842	0.253374	ENSG00000188069	ENST00000343430;ENST00000380383	T;T	0.15718	2.4;2.4	5.43	5.43	0.79202	GPCR, rhodopsin-like superfamily (1);	0.000000	0.50627	N	0.000106	T	0.00012	0.0000	N	0.00000	-3.91	0.38500	P	0.05178700000000003	B	0.02656	0.0	B	0.01281	0.0	T	0.47911	-0.9080	9	0.02654	T	1	.	11.8333	0.52307	0.8531:0.1469:0.0:0.0	rs1030726;rs52801059;rs60846270;rs1030726	301	A6NGY5	O51F1_HUMAN	Y	294;301	ENSP00000345163:D294Y;ENSP00000369744:D301Y	ENSP00000345163:D294Y	D	-	1	0	OR51F1	4746844	1.000000	0.71417	0.992000	0.48379	0.617000	0.37484	6.611000	0.74183	1.085000	0.41206	-0.256000	0.11100	GAC	C|0.712;A|0.288	0.288	strong		0.448	OR51F1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001004752	
OR5L1	219437	hgsc.bcm.edu	37	11	55579102	55579102	+	Missense_Mutation	SNP	C	C	T	rs34961497	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:55579102C>T	ENST00000333973.2	+	1	249	c.160C>T	c.(160-162)Cgg>Tgg	p.R54W		NM_001004738.1	NP_001004738.1	Q8NGL2	OR5L1_HUMAN	olfactory receptor, family 5, subfamily L, member 1	54			R -> W (in dbSNP:rs34961497).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(2)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(4)|liver(4)|lung(36)|ovary(2)|pancreas(1)|prostate(5)|skin(9)|stomach(4)|upper_aerodigestive_tract(3)	78		all_epithelial(135;0.208)				GGTCAGCTCTCGGCTCCACAC	0.468													N|||	448	0.0894569	0.1309	0.0432	5008	,	,		20175	0.0813		0.0924	False		,,,				2504	0.0716				p.R54W		Atlas-SNP	.											OR5L1,NS,carcinoma,-1,1	OR5L1	145	1	0			c.C160T						PASS	.	C	TRP/ARG	518,3882	235.5+/-248.0	32,454,1714	311.0	273.0	286.0		160	-4.8	0.0	11	dbSNP_126	286	716,7876	175.0+/-225.2	26,664,3606	no	missense	OR5L1	NM_001004738.1	101	58,1118,5320	TT,TC,CC		8.3333,11.7727,9.4982	probably-damaging	54/312	55579102	1234,11758	2200	4296	6496	SO:0001583	missense	219437	exon1			AGCTCTCGGCTCC	AB065780	CCDS31509.1	11q11	2012-08-09			ENSG00000186117	ENSG00000186117		"""GPCR / Class A : Olfactory receptors"""	8350	protein-coding gene	gene with protein product							Standard	NM_001004738		Approved	OST262	uc001nhw.1	Q8NGL2	OTTHUMG00000166810	ENST00000333973.2:c.160C>T	11.37:g.55579102C>T	ENSP00000335529:p.Arg54Trp	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	167	103	0.616766	NM_001004738	B2RNK6|Q6IFD0	Missense_Mutation	SNP	ENST00000333973.2	37	CCDS31509.1	199	0.09111721611721611	78	0.15853658536585366	20	0.055248618784530384	36	0.06293706293706294	65	0.08575197889182058	c	14.43	2.533746	0.45073	0.117727	0.083333	ENSG00000186117	ENST00000333973	T	0.01152	5.26	4.32	-4.81	0.03180	GPCR, rhodopsin-like superfamily (1);	1.504320	0.04361	N	0.357399	T	0.00012	0.0000	M	0.87097	2.86	0.80722	P	0.0	D	0.59767	0.986	P	0.46339	0.513	T	0.33979	-0.9847	9	0.87932	D	0	9.4321	9.3255	0.37990	0.4691:0.2081:0.3227:0.0	rs34961497;rs61998195	54	Q8NGL2	OR5L1_HUMAN	W	54	ENSP00000335529:R54W	ENSP00000335529:R54W	R	+	1	2	OR5L1	55335678	0.000000	0.05858	0.000000	0.03702	0.019000	0.09904	-0.488000	0.06497	-0.824000	0.04295	-0.575000	0.04146	CGG	C|0.907;T|0.093	0.093	strong		0.468	OR5L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391514.1	NM_001004738	
CLASRP	11129	hgsc.bcm.edu	37	19	45563695	45563695	+	Silent	SNP	G	G	A	rs147776329	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:45563695G>A	ENST00000221455.3	+	9	857	c.759G>A	c.(757-759)aaG>aaA	p.K253K	CLASRP_ENST00000544944.2_Silent_p.K253K|CLASRP_ENST00000391953.4_Silent_p.K191K	NM_007056.2	NP_008987	Q8N2M8	CLASR_HUMAN	CLK4-associating serine/arginine rich protein	253					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)				breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(6)|pancreas(2)|prostate(1)	16						AGCATGCCAAGGCTCTTGAGG	0.602													G|||	20	0.00399361	0.0038	0.0058	5008	,	,		18973	0.0		0.0109	False		,,,				2504	0.0				p.K253K		Atlas-SNP	.											.	CLASRP	44	.	0			c.G759A						PASS	.	G		19,4387	26.2+/-53.5	0,19,2184	126.0	102.0	110.0		759	3.6	1.0	19	dbSNP_134	110	114,8486	61.0+/-122.8	1,112,4187	no	coding-synonymous	CLASRP	NM_007056.2		1,131,6371	AA,AG,GG		1.3256,0.4312,1.0226		253/675	45563695	133,12873	2203	4300	6503	SO:0001819	synonymous_variant	11129	exon9			TGCCAAGGCTCTT	AF042800	CCDS12652.2, CCDS62710.1	19q13.3	2010-09-21	2010-09-21	2010-09-21	ENSG00000104859	ENSG00000104859			17731	protein-coding gene	gene with protein product	"""Clk4 associating SR-related protein"""		"""splicing factor, arginine/serine-rich 16"""	SFRS16		12169693	Standard	NM_007056		Approved	SWAP2, CLASP	uc002pak.3	Q8N2M8	OTTHUMG00000150189	ENST00000221455.3:c.759G>A	19.37:g.45563695G>A		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	86	33	0.383721	NM_007056	B4DDT8|F8WAG9|O96026|Q6UW71|Q96DX2	Silent	SNP	ENST00000221455.3	37	CCDS12652.2																																																																																			G|0.991;A|0.009	0.009	strong		0.602	CLASRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316749.1	NM_007056	
OPLAH	26873	hgsc.bcm.edu	37	8	145114924	145114924	+	Silent	SNP	G	G	C	rs7003860	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:145114924G>C	ENST00000426825.1	-	2	93	c.12C>G	c.(10-12)ccC>ccG	p.P4P	OPLAH_ENST00000534424.1_5'UTR	NM_017570.3	NP_060040.1	O14841	OPLA_HUMAN	5-oxoprolinase (ATP-hydrolysing)	4					glutathione biosynthetic process (GO:0006750)|glutathione derivative biosynthetic process (GO:1901687)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	5-oxoprolinase (ATP-hydrolyzing) activity (GO:0017168)|ATP binding (GO:0005524)			breast(1)|central_nervous_system(1)|endometrium(1)|lung(13)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	20	all_cancers(97;1.06e-10)|all_epithelial(106;1.5e-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;6.79e-41)|Epithelial(56;1.02e-39)|all cancers(56;2.24e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			AGCGGCCCTCGGGGCTGCCCA	0.652													G|||	605	0.120807	0.3404	0.0663	5008	,	,		14509	0.001		0.0795	False		,,,				2504	0.0286				p.P4P		Atlas-SNP	.											.	OPLAH	78	.	0			c.C12G						PASS	.	G		1125,2657		172,781,938	15.0	17.0	17.0		12	-9.8	0.0	8	dbSNP_116	17	565,7665		17,531,3567	no	coding-synonymous	OPLAH	NM_017570.3		189,1312,4505	CC,CG,GG		6.8651,29.7462,14.0693		4/1289	145114924	1690,10322	1891	4115	6006	SO:0001819	synonymous_variant	26873	exon2			GCCCTCGGGGCTG	AF024672, AB122018	CCDS75802.1	8q24.3	2010-11-23			ENSG00000178814	ENSG00000178814	3.5.2.9		8149	protein-coding gene	gene with protein product		614243				14993790	Standard	NM_017570		Approved	OPLA, 5-Opase	uc003zar.3	O14841		ENST00000426825.1:c.12C>G	8.37:g.145114924G>C		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	61	59	0.967213	NM_017570	A5PKY8|Q75W65|Q9Y4Q0	Silent	SNP	ENST00000426825.1	37																																																																																				G|0.894;C|0.106	0.106	strong		0.652	OPLAH-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_017570	
DTHD1	401124	hgsc.bcm.edu	37	4	36310049	36310049	+	Missense_Mutation	SNP	C	C	T	rs12507599	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:36310049C>T	ENST00000456874.2	+	6	1712	c.1654C>T	c.(1654-1656)Cgt>Tgt	p.R552C	RP11-431M7.2_ENST00000504344.1_RNA|DTHD1_ENST00000507598.1_Missense_Mutation_p.R592C|DTHD1_ENST00000357504.3_Missense_Mutation_p.R387C	NM_001170700.2	NP_001164171.1	Q6ZMT9	DTHD1_HUMAN	death domain containing 1	552			R -> C (in dbSNP:rs12507599). {ECO:0000269|PubMed:15489334}.		signal transduction (GO:0007165)					breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|stomach(1)	8						AGAGCCATCTCGTCATTTCCA	0.373													C|||	1571	0.313698	0.2526	0.3141	5008	,	,		18858	0.369		0.2416	False		,,,				2504	0.4131				p.R552C		Atlas-SNP	.											.	DTHD1	63	.	0			c.C1654T						PASS	.	C	CYS/ARG,CYS/ARG	340,1044		32,276,384	77.0	67.0	70.0		1159,1654	2.0	0.0	4	dbSNP_120	70	823,2359		102,619,870	yes	missense,missense	DTHD1	NM_001136536.3,NM_001170700.1	180,180	134,895,1254	TT,TC,CC		25.8642,24.5665,25.4709	benign,benign	387/617,552/782	36310049	1163,3403	692	1591	2283	SO:0001583	missense	401124	exon6			CCATCTCGTCATT	AK094684	CCDS54754.1	4p14	2009-10-02			ENSG00000197057	ENSG00000197057			37261	protein-coding gene	gene with protein product							Standard	NM_001170700		Approved	FLJ16686	uc021xne.2	Q6ZMT9	OTTHUMG00000160371	ENST00000456874.2:c.1654C>T	4.37:g.36310049C>T	ENSP00000401597:p.Arg552Cys	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	67	37	0.552239	NM_001170700	B2RXK4|B4E2N7	Missense_Mutation	SNP	ENST00000456874.2	37	CCDS54754.1	594	0.27197802197802196	118	0.23983739837398374	119	0.3287292817679558	179	0.3129370629370629	178	0.23482849604221637	C	2.482	-0.319388	0.05386	0.245665	0.258642	ENSG00000197057	ENST00000357504;ENST00000507598;ENST00000456874	T;T;T	0.79141	-1.24;-1.24;-1.24	4.8	2.05	0.26809	.	0.666605	0.15021	N	0.284984	T	0.00012	0.0000	L	0.36672	1.1	0.80722	P	0.0	B	0.11235	0.004	B	0.04013	0.001	T	0.08889	-1.0700	9	0.49607	T	0.09	-2.7289	3.213	0.06689	0.1457:0.5709:0.1328:0.1506	rs12507599;rs56422944;rs12507599	387	Q6ZMT9-2	.	C	387;592;552	ENSP00000350103:R387C;ENSP00000424426:R592C;ENSP00000401597:R552C	ENSP00000350103:R387C	R	+	1	0	DTHD1	35986444	0.000000	0.05858	0.001000	0.08648	0.004000	0.04260	0.404000	0.20999	0.306000	0.22856	-0.137000	0.14449	CGT	C|0.725;T|0.275	0.275	strong		0.373	DTHD1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001136536	
VPRBP	9730	hgsc.bcm.edu	37	3	51458204	51458204	+	Silent	SNP	G	G	A	rs150385433	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:51458204G>A	ENST00000335891.5	-	7	882	c.873C>T	c.(871-873)tcC>tcT	p.S291S				Q9Y4B6	VPRBP_HUMAN	Vpr (HIV-1) binding protein	740	Protein kinase-like.				B cell differentiation (GO:0030183)|cell competition in a multicellular organism (GO:0035212)|histone H2A-T120 phosphorylation (GO:1990245)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|protein ubiquitination (GO:0016567)|transcription, DNA-templated (GO:0006351)|V(D)J recombination (GO:0033151)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|histone kinase activity (H2A-T120 specific) (GO:1990244)			breast(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(6)|lung(12)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	41				BRCA - Breast invasive adenocarcinoma(193;0.000272)|Kidney(197;0.000729)|KIRC - Kidney renal clear cell carcinoma(197;0.000875)		TGGACAGTAAGGACAGGAGCA	0.557													G|||	16	0.00319489	0.0015	0.0058	5008	,	,		20267	0.0		0.0099	False		,,,				2504	0.0				p.S687S		Atlas-SNP	.											.	VPRBP	107	.	0			c.C2061T						PASS	.	G	,	3,4027		0,3,2012	224.0	213.0	217.0		2058,2061	-3.6	1.0	3	dbSNP_134	217	66,8310		0,66,4122	no	coding-synonymous,coding-synonymous	VPRBP	NM_001171904.1,NM_014703.2	,	0,69,6134	AA,AG,GG		0.788,0.0744,0.5562	,	686/1454,687/1455	51458204	69,12337	2015	4188	6203	SO:0001819	synonymous_variant	9730	exon14			CAGTAAGGACAGG	AB018343	CCDS74943.1, CCDS74944.1	3p21.2	2011-06-17			ENSG00000145041	ENSG00000145041		"""DDB1 and CUL4 associated factors"""	30911	protein-coding gene	gene with protein product	"""DDB1 and CUL4 associated factor 1"""					8195203, 11223251	Standard	NM_014703		Approved	KIAA0800, MGC102804, DCAF1	uc003dbe.2	Q9Y4B6	OTTHUMG00000156895	ENST00000335891.5:c.873C>T	3.37:g.51458204G>A		Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	121	69	0.570248	NM_014703	Q2YD74|Q8TBD9|Q9HCA1|Q9UG37	Silent	SNP	ENST00000335891.5	37																																																																																				G|0.995;A|0.005	0.005	strong		0.557	VPRBP-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_014703	
CD70	970	hgsc.bcm.edu	37	19	6586268	6586268	+	Silent	SNP	G	G	A	rs1862511	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:6586268G>A	ENST00000245903.3	-	3	494	c.345C>T	c.(343-345)tgC>tgT	p.C115C	CD70_ENST00000423145.3_Silent_p.C115C	NM_001252.3	NP_001243.1	P32970	CD70_HUMAN	CD70 molecule	115					cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|extrinsic apoptotic signaling pathway (GO:0097191)|immune response (GO:0006955)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	protease binding (GO:0002020)|receptor binding (GO:0005102)			endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(6)|skin(1)	11						TCGTGGAGGAGCAGATGGCCA	0.632													g|||	1756	0.350639	0.1876	0.2464	5008	,	,		16154	0.6756		0.3022	False		,,,				2504	0.3599				p.C115C	Pancreas(183;2617 2876 10173 34193)	Atlas-SNP	.											.	CD70	24	.	0			c.C345T						PASS	.			947,3459	358.4+/-314.3	99,749,1355	125.0	90.0	102.0		345	1.7	0.7	19	dbSNP_92	102	2476,6124	407.8+/-349.3	368,1740,2192	no	coding-synonymous	CD70	NM_001252.3		467,2489,3547	AA,AG,GG		28.7907,21.4934,26.3186		115/194	6586268	3423,9583	2203	4300	6503	SO:0001819	synonymous_variant	970	exon3			GGAGGAGCAGATG	L08096	CCDS12170.1	19p13	2013-05-22	2006-10-27	2006-10-27		ENSG00000125726		"""Tumor necrosis factor (ligand) superfamily"", ""CD molecules"""	11937	protein-coding gene	gene with protein product		602840	"""tumor necrosis factor (ligand) superfamily, member 7"""	CD27LG, TNFSF7		8387892, 8120384	Standard	NM_001252		Approved	CD27L	uc002mfi.3	P32970		ENST00000245903.3:c.345C>T	19.37:g.6586268G>A		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	106	105	0.990566	NM_001252	B4DPR8|Q53XX4|Q96J57	Silent	SNP	ENST00000245903.3	37	CCDS12170.1																																																																																			G|0.695;A|0.305	0.305	strong		0.632	CD70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457860.1		
STT3A	3703	hgsc.bcm.edu	37	11	125478126	125478126	+	Silent	SNP	C	C	T	rs149906495		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:125478126C>T	ENST00000529196.1	+	10	1109	c.903C>T	c.(901-903)agC>agT	p.S301S	STT3A_ENST00000392708.4_Silent_p.S301S|STT3A_ENST00000531491.1_Silent_p.S209S			P46977	STT3A_HUMAN	STT3A, subunit of the oligosaccharyltransferase complex (catalytic)	301					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)		TTTTCCGGAGCGTCATCTCTC	0.478																																					p.S301S		Atlas-SNP	.											STT3A,NS,carcinoma,0,1	STT3A	52	1	0			c.C903T						scavenged	.	C		1,4401	2.1+/-5.4	0,1,2200	123.0	116.0	118.0		903	-1.9	1.0	11	dbSNP_134	118	0,8598		0,0,4299	no	coding-synonymous	STT3A	NM_152713.3		0,1,6499	TT,TC,CC		0.0,0.0227,0.0077		301/706	125478126	1,12999	2201	4299	6500	SO:0001819	synonymous_variant	3703	exon9			CCGGAGCGTCATC	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.903C>T	11.37:g.125478126C>T		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	96	2	0.0208333	NM_152713	B4DJ24|E9PNQ1|Q86XU9|Q8TE35|Q8WUB4	Silent	SNP	ENST00000529196.1	37	CCDS8458.1	.	.	.	.	.	.	.	.	.	.	C	10.18	1.279257	0.23307	2.27E-4	0.0	ENSG00000134910	ENST00000526726	.	.	.	5.82	-1.87	0.07737	.	.	.	.	.	T	0.57257	0.2041	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.54309	-0.8313	4	.	.	.	-14.4912	11.1318	0.48351	0.0:0.3973:0.0:0.6027	.	.	.	.	V	59	.	.	A	+	2	0	STT3A	124983336	0.349000	0.24870	0.993000	0.49108	0.947000	0.59692	-0.323000	0.07997	-0.328000	0.08539	-1.004000	0.02495	GCG	C|1.000;T|0.000	0.000	weak		0.478	STT3A-002	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000386691.1	NM_152713	
CETN3	1070	hgsc.bcm.edu	37	5	89703641	89703641	+	Missense_Mutation	SNP	C	C	G	rs4873	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:89703641C>G	ENST00000283122.3	-	2	152	c.28G>C	c.(28-30)Gta>Cta	p.V10L	CETN3_ENST00000522083.1_Missense_Mutation_p.V10L|CETN3_ENST00000522864.1_Missense_Mutation_p.V10L|CETN3_ENST00000522842.1_Missense_Mutation_p.V10L|CETN3_ENST00000522565.1_Missense_Mutation_p.V10L	NM_004365.2	NP_004356.2	O15182	CETN3_HUMAN	centrin, EF-hand protein, 3	10			V -> L (in dbSNP:rs4873). {ECO:0000269|PubMed:9256449}.		centrosome cycle (GO:0007098)|mitotic nuclear division (GO:0007067)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|ciliary transition zone (GO:0035869)|cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|photoreceptor connecting cilium (GO:0032391)	calcium ion binding (GO:0005509)			lung(3)	3		all_cancers(142;7.93e-09)|all_epithelial(76;2.13e-11)|Lung NSC(167;2.46e-05)|all_lung(232;3.25e-05)|Ovarian(174;0.00832)|Colorectal(57;0.122)|Breast(839;0.198)		OV - Ovarian serous cystadenocarcinoma(54;1.42e-32)|Epithelial(54;1.45e-26)|all cancers(79;2.87e-23)		TTGTCCACTACAAGCTCACTT	0.308													C|||	928	0.185304	0.0628	0.1585	5008	,	,		15964	0.2034		0.2565	False		,,,				2504	0.2781				p.V10L		Atlas-SNP	.											.	CETN3	16	.	0			c.G28C						PASS	.	C	LEU/VAL	412,3990	201.5+/-224.5	20,372,1809	110.0	105.0	107.0		28	3.6	1.0	5	dbSNP_52	107	2314,6276	386.4+/-341.8	302,1710,2283	yes	missense	CETN3	NM_004365.2	32	322,2082,4092	GG,GC,CC		26.9383,9.3594,20.9821	benign	10/168	89703641	2726,10266	2201	4295	6496	SO:0001583	missense	1070	exon2			CCACTACAAGCTC	Y12473	CCDS4066.1, CCDS75274.1	5q14.3	2013-01-10	2010-06-24		ENSG00000153140	ENSG00000153140		"""EF-hand domain containing"""	1868	protein-coding gene	gene with protein product	"""CDC31 yeast homolog"", ""EF-hand superfamily member"""	602907	"""centrin, EF-hand protein, 3 (CDC31 yeast homolog)"""			9256449	Standard	XM_006714521		Approved	CEN3	uc003kjo.3	O15182	OTTHUMG00000131326	ENST00000283122.3:c.28G>C	5.37:g.89703641C>G	ENSP00000283122:p.Val10Leu	Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	138	64	0.463768	NM_004365	Q53YD2|Q9BS23	Missense_Mutation	SNP	ENST00000283122.3	37	CCDS4066.1	384	0.17582417582417584	21	0.042682926829268296	62	0.1712707182320442	115	0.20104895104895104	186	0.24538258575197888	C	12.02	1.812032	0.32053	0.093594	0.269383	ENSG00000153140	ENST00000283122;ENST00000522083;ENST00000522864;ENST00000522565;ENST00000522842	T;T;T;T;T	0.73575	-0.13;-0.68;-0.76;-0.52;-0.57	5.44	3.64	0.41730	.	0.482638	0.19205	N	0.120077	T	0.00012	0.0000	N	0.08118	0	0.39683	P	0.029067999999999983	B	0.02656	0.0	B	0.04013	0.001	T	0.05099	-1.0906	9	0.08599	T	0.76	.	8.0433	0.30534	0.2979:0.6252:0.0:0.0769	rs4873;rs12243;rs1129126;rs3186654;rs11554604;rs17342999;rs17354731;rs52803027;rs4873	10	O15182	CETN3_HUMAN	L	10	ENSP00000283122:V10L;ENSP00000428259:V10L;ENSP00000430361:V10L;ENSP00000430409:V10L;ENSP00000429875:V10L	ENSP00000283122:V10L	V	-	1	0	CETN3	89739397	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	2.485000	0.45250	0.643000	0.30638	0.561000	0.74099	GTA	C|0.804;G|0.196	0.196	strong		0.308	CETN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254097.1	NM_004365	
ATAD5	79915	hgsc.bcm.edu	37	17	29161202	29161202	+	Missense_Mutation	SNP	A	A	T	rs9910051	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:29161202A>T	ENST00000321990.4	+	2	481	c.103A>T	c.(103-105)Acc>Tcc	p.T35S	CTD-2349P21.11_ENST00000580873.1_RNA	NM_024857.3	NP_079133.3	Q96QE3	ATAD5_HUMAN	ATPase family, AAA domain containing 5	35			T -> S (in dbSNP:rs9910051).		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)				TGACACATCTACCTGCAAAAC	0.308													T|||	1442	0.287939	0.5681	0.2305	5008	,	,		17249	0.1359		0.1163	False		,,,				2504	0.2832				p.T35S		Atlas-SNP	.											.	ATAD5	150	.	0			c.A103T						PASS	.	T	SER/THR	2097,2303	549.6+/-377.8	501,1095,604	75.0	82.0	80.0		103	5.5	1.0	17	dbSNP_119	80	960,7638	761.2+/-407.6	45,870,3384	yes	missense	ATAD5	NM_024857.3	58	546,1965,3988	TT,TA,AA		11.1654,47.6591,23.519	benign	35/1845	29161202	3057,9941	2200	4299	6499	SO:0001583	missense	79915	exon2			ACATCTACCTGCA		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.103A>T	17.37:g.29161202A>T	ENSP00000313171:p.Thr35Ser	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	88	49	0.556818	NM_024857	Q05DH0|Q69YR6|Q9H9I1	Missense_Mutation	SNP	ENST00000321990.4	37	CCDS11260.1	518	0.23717948717948717	269	0.5467479674796748	81	0.22375690607734808	90	0.15734265734265734	78	0.10290237467018469	T	11.35	1.612102	0.28712	0.476591	0.111654	ENSG00000176208	ENST00000321990	T	0.05855	3.38	5.47	5.47	0.80525	.	0.556987	0.18338	N	0.144288	T	0.00012	0.0000	N	0.00112	-2.095	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.40194	-0.9576	9	0.02654	T	1	.	6.5206	0.22272	0.1388:0.0722:0.0:0.789	rs9910051;rs52830976;rs9910051	35	Q96QE3	ATAD5_HUMAN	S	35	ENSP00000313171:T35S	ENSP00000313171:T35S	T	+	1	0	ATAD5	26185328	0.998000	0.40836	0.974000	0.42286	0.914000	0.54420	1.019000	0.30014	0.911000	0.36747	-0.257000	0.10917	ACC	A|0.786;N|0.000	.	strong		0.308	ATAD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256206.2	NM_024857	
SIPA1L2	57568	hgsc.bcm.edu	37	1	232574921	232574921	+	Missense_Mutation	SNP	T	T	C	rs2275307	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:232574921T>C	ENST00000366630.1	-	14	4322	c.3964A>G	c.(3964-3966)Acc>Gcc	p.T1322A	SIPA1L2_ENST00000262861.4_Missense_Mutation_p.T1322A|SIPA1L2_ENST00000308942.4_Missense_Mutation_p.T396A			Q9P2F8	SI1L2_HUMAN	signal-induced proliferation-associated 1 like 2	1322	Ser-rich.		T -> A (in dbSNP:rs2275307). {ECO:0000269|PubMed:10718198, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.1, ECO:0000269|Ref.4}.		regulation of small GTPase mediated signal transduction (GO:0051056)		GTPase activator activity (GO:0005096)			NS(1)|breast(5)|central_nervous_system(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(13)|lung(49)|ovary(2)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	103		all_cancers(173;0.00605)|Prostate(94;0.128)|all_epithelial(177;0.186)				GCGGAGATGGTGGACGCGTAG	0.607													C|||	1764	0.352236	0.41	0.3473	5008	,	,		19452	0.4643		0.2008	False		,,,				2504	0.318				p.T1322A		Atlas-SNP	.											.	SIPA1L2	218	.	0			c.A3964G						PASS	.	C	ALA/THR	1603,2551		312,979,786	32.0	35.0	34.0		3964	-1.9	0.0	1	dbSNP_100	34	1823,6619		204,1415,2602	yes	missense	SIPA1L2	NM_020808.3	58	516,2394,3388	CC,CT,TT		21.5944,38.5893,27.1991	benign	1322/1723	232574921	3426,9170	2077	4221	6298	SO:0001583	missense	57568	exon13			AGATGGTGGACGC	AB037810	CCDS41474.1	1q42.2	2008-02-05			ENSG00000116991	ENSG00000116991			23800	protein-coding gene	gene with protein product		611609					Standard	NM_020808		Approved	KIAA1389	uc001hvg.3	Q9P2F8	OTTHUMG00000037820	ENST00000366630.1:c.3964A>G	1.37:g.232574921T>C	ENSP00000355589:p.Thr1322Ala	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	64	27	0.421875	NM_020808	Q2TV88|Q5VXR7|Q5VXR8|Q641Q4|Q8NA38|Q96DZ3|Q9H9F6	Missense_Mutation	SNP	ENST00000366630.1	37	CCDS41474.1	745	0.3411172161172161	206	0.4186991869918699	118	0.3259668508287293	274	0.479020979020979	147	0.19393139841688653	C	0.008	-1.930233	0.00488	0.385893	0.215944	ENSG00000116991	ENST00000366630;ENST00000262861;ENST00000308942	T;T;T	0.76968	-1.06;-1.06;2.89	5.16	-1.91	0.07641	.	0.762839	0.12744	N	0.442752	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	0.17048	-1.0382	9	0.02654	T	1	-1.9707	7.3522	0.26697	0.0:0.3717:0.1155:0.5127	rs2275307;rs2275307	1322;396	Q9P2F8;Q9P2F8-2	SI1L2_HUMAN;.	A	1322;1322;396	ENSP00000355589:T1322A;ENSP00000262861:T1322A;ENSP00000309102:T396A	ENSP00000262861:T1322A	T	-	1	0	SIPA1L2	230641544	0.487000	0.25988	0.000000	0.03702	0.037000	0.13140	1.127000	0.31357	-0.905000	0.03871	-0.213000	0.12676	ACC	T|0.688;C|0.311	0.311	strong		0.607	SIPA1L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092318.1	XM_045839	
SOGA1	140710	hgsc.bcm.edu	37	20	35443768	35443768	+	Missense_Mutation	SNP	G	G	A	rs201600310		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:35443768G>A	ENST00000357779.3	-	5	1689	c.1363C>T	c.(1363-1365)Cgg>Tgg	p.R455W	SOGA1_ENST00000456801.2_Missense_Mutation_p.R296W|SOGA1_ENST00000279034.6_Missense_Mutation_p.R455W|SOGA1_ENST00000237536.4_Missense_Mutation_p.R693W			O94964	SOGA1_HUMAN	suppressor of glucose, autophagy associated 1	455					insulin receptor signaling pathway (GO:0008286)|negative regulation of gluconeogenesis (GO:0045721)|regulation of autophagy (GO:0010506)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				endometrium(5)|kidney(1)|lung(21)|urinary_tract(1)	28						TCATGCAGCCGGAAGTCAGCA	0.642																																					p.R693W		Atlas-SNP	.											.	SOGA1	136	.	0			c.C2077T						PASS	.						38.0	40.0	39.0					20																	35443768		2203	4300	6503	SO:0001583	missense	140710	exon5			GCAGCCGGAAGTC	AK126630	CCDS46598.1, CCDS54459.1	20q11.23	2012-03-01	2012-02-27	2012-02-27	ENSG00000149639	ENSG00000149639			16111	protein-coding gene	gene with protein product	"""suppressor of glucose by autophagy"", ""suppressor of glucose from autophagy"""		"""chromosome 20 open reading frame 117"", ""KIAA0889"""	C20orf117, KIAA0889		20813965	Standard	NM_080627		Approved	dJ132F21.1, FLJ44670, SOGA	uc021wcx.1	O94964	OTTHUMG00000032395	ENST00000357779.3:c.1363C>T	20.37:g.35443768G>A	ENSP00000350424:p.Arg455Trp	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	82	36	0.439024	NM_080627	A6NK10|Q14DB2|Q5JW51|Q6ZTG8	Missense_Mutation	SNP	ENST00000357779.3	37		.	.	.	.	.	.	.	.	.	.	G	12.03	1.815128	0.32053	.	.	ENSG00000149639	ENST00000237536;ENST00000279034;ENST00000456801;ENST00000357779	T;T;T;T	0.18960	2.18;2.19;2.18;2.19	4.6	2.45	0.29901	.	0.356930	0.24426	N	0.038636	T	0.28400	0.0702	L	0.29908	0.895	0.22185	N	0.999303	D	0.76494	0.999	D	0.69307	0.963	T	0.02037	-1.1225	10	0.66056	D	0.02	-35.7471	8.495	0.33123	0.0:0.1348:0.5622:0.3029	.	455	O94964-4	.	W	693;455;296;455	ENSP00000237536:R693W;ENSP00000279034:R455W;ENSP00000413886:R296W;ENSP00000350424:R455W	ENSP00000237536:R693W	R	-	1	2	KIAA0889	34877182	0.915000	0.31059	0.960000	0.40013	0.382000	0.30200	1.264000	0.33015	1.137000	0.42214	0.313000	0.20887	CGG	G|0.998;A|0.002	0.002	weak		0.642	SOGA1-201	KNOWN	basic	protein_coding	protein_coding		NM_199181	
KIAA1549	57670	hgsc.bcm.edu	37	7	138545996	138545996	+	Silent	SNP	G	G	A	rs12707399	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:138545996G>A	ENST00000422774.1	-	16	5184	c.5136C>T	c.(5134-5136)ccC>ccT	p.P1712P	KIAA1549_ENST00000440172.1_Silent_p.P1712P|KIAA1549_ENST00000242365.4_Silent_p.P1662P			Q9HCM3	K1549_HUMAN	KIAA1549	1712						integral component of membrane (GO:0016021)			KIAA1549/BRAF(703)	large_intestine(4)|pancreas(1)|upper_aerodigestive_tract(2)	7						GTGGGACTCCGGGGCCTACAC	0.692			O	BRAF	pilocytic astrocytoma								G|||	423	0.0844649	0.0439	0.0706	5008	,	,		14566	0.0129		0.162	False		,,,				2504	0.1431				p.P1712P	NSCLC(119;1534 1718 44213 46230 50068)	Atlas-SNP	.		Dom	yes		7	7q34	57670	KIAA1549		O	.	KIAA1549	314	.	0			c.C5136T						PASS	.	G	,	203,3839		6,191,1824	33.0	40.0	38.0		5136,5136	-8.8	0.0	7	dbSNP_121	38	1016,7312		64,888,3212	no	coding-synonymous,coding-synonymous	KIAA1549	NM_001164665.1,NM_020910.2	,	70,1079,5036	AA,AG,GG		12.1998,5.0223,9.8545	,	1712/1951,1712/1935	138545996	1219,11151	2021	4164	6185	SO:0001819	synonymous_variant	57670	exon16			GACTCCGGGGCCT		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.5136C>T	7.37:g.138545996G>A		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	40	17	0.425	NM_020910	B6HY55|B6HY56|B6HY58|B6HY60|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q5BJD6|Q8IY15|Q9H0M3	Silent	SNP	ENST00000422774.1	37	CCDS56513.1																																																																																			G|0.913;A|0.087	0.087	strong		0.692	KIAA1549-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348092.1		
DDX27	55661	hgsc.bcm.edu	37	20	47859217	47859217	+	Splice_Site	SNP	G	G	A	rs1130146	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:47859217G>A	ENST00000371764.4	+	19	2305	c.2296G>A	c.(2296-2298)Ggc>Agc	p.G766S	ZNFX1_ENST00000469991.1_Intron|ZNFX1_ENST00000371754.4_Intron|DDX27_ENST00000484427.1_3'UTR	NM_017895.7	NP_060365.7	Q96GQ7	DDX27_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 27	766			G -> S (in dbSNP:rs1130146). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.			nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(1)|endometrium(2)|kidney(3)|large_intestine(12)|lung(19)|ovary(1)|prostate(2)|skin(3)|urinary_tract(1)	45			BRCA - Breast invasive adenocarcinoma(12;0.000899)|COAD - Colon adenocarcinoma(4;0.14)|Colorectal(8;0.166)			GTATCGAGCTGGGTAGGATTT	0.443													G|||	1365	0.272564	0.0567	0.3271	5008	,	,		18301	0.3234		0.4085	False		,,,				2504	0.3333				p.G766S		Atlas-SNP	.											.	DDX27	74	.	0			c.G2296A						PASS	.	G	SER/GLY	468,3938	220.7+/-238.1	26,416,1761	114.0	118.0	116.0		2296	4.9	1.0	20	dbSNP_86	116	3283,5317	491.9+/-373.2	631,2021,1648	yes	missense-near-splice	DDX27	NM_017895.7	56	657,2437,3409	AA,AG,GG		38.1744,10.6219,28.8405	possibly-damaging	766/797	47859217	3751,9255	2203	4300	6503	SO:0001630	splice_region_variant	55661	exon19			CGAGCTGGGTAGG	AL049766	CCDS13416.1	20q13.13	2010-07-06	2003-06-13		ENSG00000124228	ENSG00000124228		"""DEAD-boxes"""	15837	protein-coding gene	gene with protein product			"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 27"""				Standard	NM_017895		Approved	dJ686N3.1, DRS1	uc002xuh.3	Q96GQ7	OTTHUMG00000033072	ENST00000371764.4:c.2297+1G>A	20.37:g.47859217G>A		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	126	67	0.531746	NM_017895	A0AVB6|B7ZLY1|Q5VXM7|Q8WYG4|Q969N7|Q96F57|Q96L97|Q9BWY9|Q9BXF0|Q9H990|Q9NWU3|Q9P0C2|Q9UGD6	Missense_Mutation	SNP	ENST00000371764.4	37	CCDS13416.1	634	0.2902930402930403	32	0.06504065040650407	124	0.3425414364640884	165	0.28846153846153844	313	0.4129287598944591	G	27.8	4.860053	0.91433	0.106219	0.381744	ENSG00000124228	ENST00000371764	T	0.01438	4.89	5.91	4.95	0.65309	.	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	L	0.34521	1.04	0.09310	P	1.0	D	0.58620	0.983	P	0.54312	0.748	T	0.63954	-0.6520	9	0.23891	T	0.37	-21.6264	14.2585	0.66067	0.0:0.0:0.8498:0.1502	rs1130146;rs3188714;rs6063377;rs8116791;rs11553386;rs17416057;rs17722253;rs52796221;rs58594349;rs6063377	766	Q96GQ7	DDX27_HUMAN	S	766	ENSP00000360828:G766S	ENSP00000360828:G766S	G	+	1	0	DDX27	47292624	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	7.104000	0.77024	1.487000	0.48415	0.655000	0.94253	GGC	G|0.716;A|0.284	0.284	strong		0.443	DDX27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080485.1		Missense_Mutation
C10orf113	387638	hgsc.bcm.edu	37	10	21414892	21414892	+	Missense_Mutation	SNP	C	C	G	rs625223	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:21414892C>G	ENST00000534331.1	-	2	378	c.328G>C	c.(328-330)Gat>Cat	p.D110H	NEBL_ENST00000417816.2_Intron|C10orf113_ENST00000529198.1_3'UTR|C10orf113_ENST00000377118.4_Missense_Mutation_p.D100H	NM_001010896.2	NP_001010896.2	Q5VZT2	CJ113_HUMAN	chromosome 10 open reading frame 113	110			D -> H (in dbSNP:rs625223). {ECO:0000269|PubMed:15489334}.							endometrium(1)|large_intestine(1)|lung(1)|ovary(3)|pancreas(1)	7						TTGCCTGGATCTGGTTCAGGA	0.542													C|||	2719	0.542931	0.6657	0.3847	5008	,	,		16457	0.7063		0.3181	False		,,,				2504	0.5521				p.D110H		Atlas-SNP	.											.	C10orf113	32	.	0			c.G328C						PASS	.	C	,,,HIS/ASP	2636,1770	644.5+/-398.0	789,1058,356	67.0	69.0	68.0		,,,328	2.6	0.8	10	dbSNP_83	68	2896,5704	454.0+/-363.4	507,1882,1911	yes	intron,utr-3,intron,missense	NEBL,C10orf113	NM_001173484.1,NM_001177483.1,NM_213569.2,NM_001010896.2	,,,81	1296,2940,2267	GG,GC,CC		33.6744,40.1725,42.5342	,,,benign	,,,110/156	21414892	5532,7474	2203	4300	6503	SO:0001583	missense	387638	exon2			CTGGATCTGGTTC		CCDS31162.1, CCDS31162.2, CCDS53496.1	10p12.31	2012-06-12			ENSG00000204683	ENSG00000204683			31447	protein-coding gene	gene with protein product							Standard	NM_001010896		Approved	bA165O3.1	uc001iqm.3	Q5VZT2	OTTHUMG00000017786	ENST00000534331.1:c.328G>C	10.37:g.21414892C>G	ENSP00000433646:p.Asp110His	Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	97	47	0.484536	NM_001010896	B9EIM9|E9PRX7	Missense_Mutation	SNP	ENST00000534331.1	37	CCDS31162.2	1069	0.48946886446886445	317	0.6443089430894309	127	0.35082872928176795	389	0.6800699300699301	236	0.3113456464379947	C	11.97	1.796893	0.31777	0.598275	0.336744	ENSG00000204683	ENST00000534331;ENST00000377118	T;T	0.41065	1.01;1.01	4.51	2.6	0.31112	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.52099	P	5.299999999996974E-5	B	0.23735	0.09	B	0.20767	0.031	T	0.33163	-0.9879	8	0.87932	D	0	-0.1856	10.9676	0.47421	0.0:0.5718:0.4282:0.0	rs625223;rs979004;rs52825206;rs625223	110	Q5VZT2	CJ113_HUMAN	H	110;100	ENSP00000433646:D110H;ENSP00000366322:D100H	ENSP00000366322:D100H	D	-	1	0	C10orf113	21454898	0.969000	0.33509	0.775000	0.31657	0.991000	0.79684	0.708000	0.25719	0.589000	0.29677	0.460000	0.39030	GAT	C|0.539;G|0.461	0.461	strong		0.542	C10orf113-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047108.3	NM_001010896	
ARAP3	64411	hgsc.bcm.edu	37	5	141033870	141033870	+	Missense_Mutation	SNP	T	T	G	rs61749636	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:141033870T>G	ENST00000239440.4	-	33	4347	c.4282A>C	c.(4282-4284)Aca>Cca	p.T1428P	ARAP3_ENST00000512390.1_5'UTR|FCHSD1_ENST00000519800.1_5'Flank|FCHSD1_ENST00000435817.2_5'Flank|FCHSD1_ENST00000522783.1_5'Flank|ARAP3_ENST00000513878.1_Missense_Mutation_p.T1077P|ARAP3_ENST00000508305.1_Missense_Mutation_p.T1259P	NM_022481.5	NP_071926.4	Q8WWN8	ARAP3_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 3	1428			T -> P (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		cytoskeleton organization (GO:0007010)|negative regulation of cell migration (GO:0030336)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of Rho protein signal transduction (GO:0035024)|regulation of ARF GTPase activity (GO:0032312)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	ARF GTPase activator activity (GO:0008060)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|Rho GTPase activator activity (GO:0005100)|zinc ion binding (GO:0008270)	p.T1428P(1)		NS(1)|breast(7)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(14)|ovary(1)|prostate(2)|skin(4)|stomach(1)	53						CACTCCCGTGTGGTGGAGAAG	0.567													T|||	131	0.0261581	0.003	0.0519	5008	,	,		17472	0.0		0.0795	False		,,,				2504	0.0112				p.T1428P		Atlas-SNP	.											ARAP3,colon,carcinoma,+2,4	ARAP3	139	4	1	Substitution - Missense(1)	breast(1)	c.A4282C						PASS	.	T	PRO/THR	74,4332	65.3+/-102.7	1,72,2130	118.0	115.0	116.0		4282	0.0	0.0	5	dbSNP_129	116	650,7950	166.4+/-218.3	25,600,3675	yes	missense	ARAP3	NM_022481.5	38	26,672,5805	GG,GT,TT		7.5581,1.6795,5.5667	benign	1428/1545	141033870	724,12282	2203	4300	6503	SO:0001583	missense	64411	exon33			CCCGTGTGGTGGA	AJ310567	CCDS4266.1	5q31.3	2013-01-11	2008-09-22	2008-09-22	ENSG00000120318	ENSG00000120318		"""ADP-ribosylation factor GTPase activating proteins"", ""Sterile alpha motif (SAM) domain containing"", ""Pleckstrin homology (PH) domain containing"", ""Ankyrin repeat domain containing"""	24097	protein-coding gene	gene with protein product		606647	"""centaurin, delta 3"""	CENTD3		11804589, 12015138	Standard	XM_005268497		Approved	FLJ21065, DRAG1	uc003llm.3	Q8WWN8	OTTHUMG00000129610	ENST00000239440.4:c.4282A>C	5.37:g.141033870T>G	ENSP00000239440:p.Thr1428Pro	Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	167	81	0.48503	NM_022481	B4DIT1|D3DQE3	Missense_Mutation	SNP	ENST00000239440.4	37	CCDS4266.1	88	0.040293040293040296	2	0.0040650406504065045	21	0.058011049723756904	0	0.0	65	0.08575197889182058	T	1.173	-0.640433	0.03557	0.016795	0.075581	ENSG00000120318	ENST00000508305;ENST00000239440;ENST00000513878	T;T;T	0.45668	0.89;0.89;0.89	4.01	0.00808	0.14073	.	0.594286	0.14268	N	0.330342	T	0.00724	0.0024	N	0.14661	0.345	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	0.10314	-1.0635	10	0.28530	T	0.3	.	6.0483	0.19772	0.1528:0.0:0.317:0.5302	rs61749636	1077;1259;1428	B4DIT1;G5E9Y3;Q8WWN8	.;.;ARAP3_HUMAN	P	1259;1428;1077	ENSP00000421826:T1259P;ENSP00000239440:T1428P;ENSP00000421468:T1077P	ENSP00000239440:T1428P	T	-	1	0	ARAP3	141014054	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	0.295000	0.19065	0.002000	0.14630	0.533000	0.62120	ACA	T|0.952;G|0.048	0.048	strong		0.567	ARAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251805.1	NM_022481	
CCM2	83605	hgsc.bcm.edu	37	7	45077978	45077978	+	Missense_Mutation	SNP	G	G	A	rs2107732	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:45077978G>A	ENST00000258781.6	+	2	306	c.157G>A	c.(157-159)Gtc>Atc	p.V53I	CCM2_ENST00000475551.1_Missense_Mutation_p.V47I|CCM2_ENST00000461377.1_3'UTR|CCM2_ENST00000544363.1_Missense_Mutation_p.V53I|CCM2_ENST00000541586.1_Intron|CCM2_ENST00000474617.1_Missense_Mutation_p.V47I|CCM2_ENST00000381112.3_Missense_Mutation_p.V74I	NM_031443.3	NP_113631.1	Q9BSQ5	CCM2_HUMAN	cerebral cavernous malformation 2	53			V -> I (in dbSNP:rs2107732). {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						GCCTGAGCGCGTCGAGCCAGA	0.517													G|||	165	0.0329473	0.0015	0.0562	5008	,	,		19226	0.0		0.1024	False		,,,				2504	0.0215				p.V74I		Atlas-SNP	.											.	CCM2	42	.	0			c.G220A						PASS	.	G	ILE/VAL,,ILE/VAL,ILE/VAL	75,4331	67.6+/-105.2	0,75,2128	123.0	113.0	116.0		220,,157,157	5.4	1.0	7	dbSNP_96	116	771,7829	182.8+/-231.1	34,703,3563	yes	missense,intron,missense,missense	CCM2	NM_001029835.2,NM_001167934.1,NM_001167935.1,NM_031443.3	29,,29,29	34,778,5691	AA,AG,GG		8.9651,1.7022,6.5047	benign,,benign,benign	74/466,,53/354,53/445	45077978	846,12160	2203	4300	6503	SO:0001583	missense	83605	exon2			GAGCGCGTCGAGC	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.157G>A	7.37:g.45077978G>A	ENSP00000258781:p.Val53Ile	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	57	17	0.298246	NM_001029835	A4D2L4|B3KUV0|D3DVL4|E9PDJ3|F5H0E1|F5H551|Q71RE5|Q8TAT4	Missense_Mutation	SNP	ENST00000258781.6	37	CCDS5500.1	102	0.046703296703296704	0	0.0	27	0.07458563535911603	0	0.0	75	0.09894459102902374	G	9.324	1.058697	0.19987	0.017022	0.089651	ENSG00000136280	ENST00000258781;ENST00000544363;ENST00000543541;ENST00000475551;ENST00000381112;ENST00000474617	T;T;T;T;T	0.28069	1.63;1.63;1.63;1.63;1.63	5.36	5.36	0.76844	.	0.060069	0.64402	D	0.000002	T	0.00440	0.0014	N	0.17872	0.535	0.43183	D	0.995003	P;P;B;B	0.38048	0.616;0.48;0.178;0.178	B;B;B;B	0.23574	0.047;0.043;0.025;0.043	T	0.18272	-1.0342	10	0.13108	T	0.6	-40.3143	17.6903	0.88267	0.0:0.0:1.0:0.0	rs2107732;rs17576937;rs52830810;rs2107732	74;74;53;53	B7Z5A6;E9PDJ3;F5H0E1;Q9BSQ5	.;.;.;CCM2_HUMAN	I	53;53;53;47;74;47	ENSP00000258781:V53I;ENSP00000438035:V53I;ENSP00000417180:V47I;ENSP00000370503:V74I;ENSP00000419474:V47I	ENSP00000258781:V53I	V	+	1	0	CCM2	45044503	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.014000	0.76380	2.523000	0.85059	0.655000	0.94253	GTC	G|0.938;A|0.062	0.062	strong		0.517	CCM2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251348.1	NM_031443	
ZNF185	7739	hgsc.bcm.edu	37	X	152083059	152083059	+	Missense_Mutation	SNP	G	G	A	rs6526142	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:152083059G>A	ENST00000370268.4	+	1	63	c.26G>A	c.(25-27)cGc>cAc	p.R9H	ZNF185_ENST00000318504.7_Missense_Mutation_p.R9H|ZNF185_ENST00000535861.1_Missense_Mutation_p.R9H|ZNF185_ENST00000370270.2_Missense_Mutation_p.R9H|ZNF185_ENST00000539731.1_Missense_Mutation_p.R9H|ZNF185_ENST00000449285.2_Missense_Mutation_p.R9H|ZNF185_ENST00000324823.6_5'UTR			O15231	ZN185_HUMAN	zinc finger protein 185 (LIM domain)	9						actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)	zinc ion binding (GO:0008270)			NS(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(3)|ovary(3)	12	Acute lymphoblastic leukemia(192;6.56e-05)					CTTGGAGGCCGCACCAAAGGT	0.572													G|||	962	0.254834	0.2708	0.1095	3775	,	,		13133	0.0982		0.2316	False		,,,				2504	0.2004				p.R9H		Atlas-SNP	.											.	ZNF185	92	.	0			c.G26A						PASS	.	G	HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG	1081,2154		137,606,201,594,360	44.0	43.0	43.0		26,26,26,26,26,26	2.3	0.0	X	dbSNP_116	43	1874,4523		204,946,520,1164,1249	yes	missense,missense,missense,missense,missense,missense	ZNF185	NM_001178106.1,NM_001178107.1,NM_001178108.1,NM_001178109.1,NM_001178110.1,NM_007150.3	29,29,29,29,29,29	341,1552,721,1758,1609	AA,AG,A,GG,G		29.295,33.4158,30.679	benign,benign,benign,benign,benign,benign	9/722,9/693,9/691,9/661,9/631,9/690	152083059	2955,6677	1898	4083	5981	SO:0001583	missense	7739	exon1			GAGGCCGCACCAA	AK056517	CCDS48184.1, CCDS55528.1, CCDS55529.1, CCDS55530.1, CCDS55531.1, CCDS55532.1, CCDS69832.1	Xq28	2012-08-08			ENSG00000147394	ENSG00000147394		"""Zinc fingers, C2H2-type"""	12976	protein-coding gene	gene with protein product		300381				9268636	Standard	NM_001178106		Approved		uc011myg.2	O15231	OTTHUMG00000024187	ENST00000370268.4:c.26G>A	X.37:g.152083059G>A	ENSP00000359291:p.Arg9His	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	70	69	0.985714	NM_001178109	A4FTV3|A6NME5|B4DLE9|B7Z771|B8K2L9|B8K2M0|B8K2M1|B8K2M2|E9PFR6|F5GXF7|F5GZL4|F8W8V7|H0Y4M8|O00345|Q8N1R8|Q9NSD2	Missense_Mutation	SNP	ENST00000370268.4	37	CCDS48184.1	412	0.24834237492465341	108	0.2727272727272727	22	0.06395348837209303	32	0.05925925925925926	118	0.18553459119496854	G	5.653	0.305112	0.10678	0.334158	0.29295	ENSG00000147394	ENST00000535861;ENST00000539731;ENST00000449285;ENST00000318504;ENST00000370268	T;T;T;T;T	0.46063	0.88;0.88;0.89;0.89;0.88	4.17	2.32	0.28847	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	P;P;B;P;P;B	0.43094	0.524;0.524;0.3;0.799;0.799;0.3	B;B;B;B;B;B	0.34722	0.121;0.067;0.085;0.188;0.121;0.085	T	0.38023	-0.9680	8	0.40728	T	0.16	.	4.1622	0.10289	0.124:0.0:0.6406:0.2354	rs6526142;rs59608332	9;9;9;9;9;9	O15231-3;B8K2L9;B8K2M0;F5GZL4;F5GXF7;O15231	.;.;.;.;.;ZN185_HUMAN	H	9	ENSP00000440847:R9H;ENSP00000444367:R9H;ENSP00000395228:R9H;ENSP00000312782:R9H;ENSP00000359291:R9H	ENSP00000312782:R9H	R	+	2	0	ZNF185	151833715	0.008000	0.16893	0.002000	0.10522	0.272000	0.26649	1.256000	0.32921	0.494000	0.27859	0.529000	0.55759	CGC	G|0.750;A|0.250	0.250	strong		0.572	ZNF185-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000377480.1	NM_007150	
ZNF679	168417	hgsc.bcm.edu	37	7	63726678	63726678	+	Missense_Mutation	SNP	T	T	A	rs1830036	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:63726678T>A	ENST00000421025.1	+	5	936	c.667T>A	c.(667-669)Tgc>Agc	p.C223S	ZNF679_ENST00000255746.4_Missense_Mutation_p.C223S	NM_001159524.1|NM_153363.2	NP_001152996.1|NP_699194.2	Q8IYX0	ZN679_HUMAN	zinc finger protein 679	223			C -> S (in dbSNP:rs1830036).		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						ACCCTTCAACTGCTCTTCAAC	0.403													.|||	701	0.139976	0.3003	0.1354	5008	,	,		19655	0.0685		0.0378	False		,,,				2504	0.1053				p.C223S		Atlas-SNP	.											.	ZNF679	80	.	0			c.T667A						PASS	.	T	SER/CYS	337,1047		48,241,403	55.0	56.0	56.0		667	0.8	0.0	7	dbSNP_92	56	146,3036		8,130,1453	no	missense	ZNF679	NM_153363.2	112	56,371,1856	AA,AT,TT		4.5883,24.3497,10.5782	benign	223/412	63726678	483,4083	692	1591	2283	SO:0001583	missense	168417	exon5			TTCAACTGCTCTT	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.667T>A	7.37:g.63726678T>A	ENSP00000416809:p.Cys223Ser	Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	32	8	0.25	NM_153363		Missense_Mutation	SNP	ENST00000421025.1	37	CCDS47592.1	225	0.10302197802197802	127	0.258130081300813	33	0.09116022099447514	42	0.07342657342657342	23	0.030343007915567283	T	0.742	-0.775919	0.02951	0.243497	0.045883	ENSG00000197123	ENST00000421025;ENST00000255746	T;T	0.07114	3.22;3.22	0.819	0.819	0.18785	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	N	0.00563	-1.375	0.80722	P	0.0	B	0.27791	0.189	B	0.28011	0.085	T	0.45205	-0.9277	8	0.21014	T	0.42	.	5.4486	0.16550	0.0:0.0:0.0:1.0	rs1830036;rs1830036	223	Q8IYX0	ZN679_HUMAN	S	223	ENSP00000416809:C223S;ENSP00000255746:C223S	ENSP00000255746:C223S	C	+	1	0	ZNF679	63364113	0.000000	0.05858	0.044000	0.18714	0.044000	0.14063	-6.354000	0.00069	0.165000	0.19558	0.163000	0.16589	TGC	T|0.900;A|0.100	0.100	strong		0.403	ZNF679-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344317.2	NM_153363	
MFI2	4241	hgsc.bcm.edu	37	3	196743130	196743130	+	Silent	SNP	T	T	C	rs6779362	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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						PASS	.	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	110	0	0		WXS	Illumina HiSeq	Phase_I	76	34	0.447368	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		
CLCN6	1185	hgsc.bcm.edu	37	1	11906068	11906068	+	IGR	SNP	A	A	G	rs5065	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:11906068A>G	ENST00000346436.6	+	0	5583				NPPA_ENST00000376476.1_Nonstop_Mutation_p.*102R|NPPA_ENST00000376480.3_Nonstop_Mutation_p.*152R|NPPA-AS1_ENST00000400892.2_RNA|NPPA-AS1_ENST00000446542.1_RNA	NM_001286.3	NP_001277	P51797	CLCN6_HUMAN	chloride channel, voltage-sensitive 6						cell volume homeostasis (GO:0006884)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|regulation of anion transport (GO:0044070)|response to mechanical stimulus (GO:0009612)|signal transduction (GO:0007165)|transmembrane transport (GO:0055085)	endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)	antiporter activity (GO:0015297)|ATP binding (GO:0005524)|voltage-gated chloride channel activity (GO:0005247)			cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(12)|prostate(2)|skin(4)	36	Ovarian(185;0.249)	Lung NSC(185;8.69e-05)|all_lung(284;9.87e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.13e-06)|COAD - Colon adenocarcinoma(227;0.000274)|BRCA - Breast invasive adenocarcinoma(304;0.000311)|Kidney(185;0.000816)|KIRC - Kidney renal clear cell carcinoma(229;0.00268)|STAD - Stomach adenocarcinoma(313;0.00743)|READ - Rectum adenocarcinoma(331;0.0649)		TGTTATCTTCAGTACTGCAAA	0.517													G|||	897	0.179113	0.4183	0.1138	5008	,	,		18871	0.0129		0.1233	False		,,,				2504	0.1309				p.X152R		Atlas-SNP	.											.	NPPA	14	.	0			c.T454C	GRCh37	CM040788	NPPA	M	rs5065	PASS	.	G	ARG/stop	1800,2606	641.4+/-397.5	380,1040,783	151.0	136.0	141.0		454	0.9	1.0	1	dbSNP_52	141	1335,7265	756.5+/-407.5	97,1141,3062	yes	stop-lost	NPPA	NM_006172.3		477,2181,3845	GG,GA,AA		15.5233,40.8534,24.1043		152/152	11906068	3135,9871	2203	4300	6503	SO:0001628	intergenic_variant	4878	exon3			ATCTTCAGTACTG	X83378	CCDS138.1, CCDS57972.1	1p36	2012-09-26	2012-02-23		ENSG00000011021	ENSG00000011021		"""Ion channels / Chloride channels : Voltage-sensitive"""	2024	protein-coding gene	gene with protein product		602726	"""chloride channel 6"""			8543009	Standard	NM_001286		Approved	CLC-6, KIAA0046, ClC-6	uc001ate.5	P51797	OTTHUMG00000002299		1.37:g.11906068A>G		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	122	51	0.418033	NM_006172	A8K1T4|B4DGT7|F8W9R3|O60818|O60819|O60820|O60821|P78520|P78521|Q17R81|Q5SNW2|Q5SNW3|Q5SNX1|Q5SNX2|Q5SNX3|Q99427|Q99428|Q99429	Missense_Mutation	SNP	ENST00000346436.6	37	CCDS138.1	304	0.1391941391941392	174	0.35365853658536583	41	0.1132596685082873	4	0.006993006993006993	85	0.11213720316622691	G	5.706	0.314728	0.10789	0.408534	0.155233	ENSG00000175206	ENST00000376480;ENST00000376476	.	.	.	5.47	0.954	0.19595	.	.	.	.	.	.	.	.	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	2.1248	0.03735	0.2569:0.1343:0.4715:0.1373	rs5065;rs198363;rs1130764;rs3189984;rs17413194;rs17856153;rs57081035;rs5065	.	.	.	R	152;102	.	.	X	-	1	0	NPPA	11828655	0.997000	0.39634	0.976000	0.42696	0.154000	0.21943	0.306000	0.19279	0.041000	0.15688	-0.128000	0.14901	TGA	A|0.796;G|0.204	0.204	strong		0.517	CLCN6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006639.2	NM_001286	
PODXL	5420	hgsc.bcm.edu	37	7	131194255	131194255	+	Missense_Mutation	SNP	G	G	C	rs35893129|rs36086597	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:131194255G>C	ENST00000378555.3	-	4	1139	c.892C>G	c.(892-894)Ccc>Gcc	p.P298A	PODXL_ENST00000537928.1_Missense_Mutation_p.P266A|PODXL_ENST00000322985.9_Missense_Mutation_p.P266A|PODXL_ENST00000465001.1_5'Flank|PODXL_ENST00000541194.1_Missense_Mutation_p.P300A			O00592	PODXL_HUMAN	podocalyxin-like	298	Thr-rich.		P -> A (in dbSNP:rs35893129).		cell adhesion (GO:0007155)|cell migration (GO:0016477)|epithelial tube formation (GO:0072175)|glomerular visceral epithelial cell development (GO:0072015)|leukocyte migration (GO:0050900)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell-cell adhesion (GO:0022408)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-cell adhesion mediated by integrin (GO:0033634)|regulation of microvillus assembly (GO:0032534)	apical plasma membrane (GO:0016324)|cell body (GO:0044297)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|microvillus membrane (GO:0031528)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|slit diaphragm (GO:0036057)				NS(1)|breast(3)|endometrium(3)|kidney(3)|large_intestine(4)|lung(4)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	24	Melanoma(18;0.162)					GGGCTCGTGGGCTGCACTGTC	0.587													G|||	139	0.0277556	0.0083	0.0331	5008	,	,		18222	0.0		0.0795	False		,,,				2504	0.0256				p.P298A		Atlas-SNP	.											.	PODXL	53	.	0			c.C892G						PASS	.	G	ALA/PRO,ALA/PRO	74,4332	66.4+/-103.9	2,70,2131	221.0	206.0	211.0		892,796	2.7	0.0	7	dbSNP_126	211	659,7941	167.4+/-219.2	29,601,3670	yes	missense,missense	PODXL	NM_001018111.2,NM_005397.3	27,27	31,671,5801	CC,CG,GG		7.6628,1.6795,5.6359	probably-damaging,probably-damaging	298/559,266/527	131194255	733,12273	2203	4300	6503	SO:0001583	missense	5420	exon4			TCGTGGGCTGCAC		CCDS34755.1, CCDS47714.1	7q32-q33	2008-07-18			ENSG00000128567	ENSG00000128567			9171	protein-coding gene	gene with protein product		602632					Standard	NM_001018111		Approved	PCLP, Gp200, PC	uc003vqx.4	O00592	OTTHUMG00000154918	ENST00000378555.3:c.892C>G	7.37:g.131194255G>C	ENSP00000367817:p.Pro298Ala	Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	178	95	0.533708	NM_001018111	A6NHX8|Q52LZ7|Q53ER6	Missense_Mutation	SNP	ENST00000378555.3	37	CCDS34755.1	74	0.03388278388278388	6	0.012195121951219513	10	0.027624309392265192	0	0.0	58	0.07651715039577836	G	14.36	2.513213	0.44660	0.016795	0.076628	ENSG00000128567	ENST00000541194;ENST00000537928;ENST00000544955;ENST00000378555;ENST00000322985	T;T;T;T	0.12147	2.82;2.71;2.82;2.87	3.62	2.71	0.32032	.	48.005600	0.00166	N	0.000001	T	0.00754	0.0025	N	0.24115	0.695	0.09310	N	1	P;P	0.51057	0.932;0.941	P;B	0.47470	0.548;0.346	T	0.16247	-1.0409	10	0.48119	T	0.1	-11.6227	7.4932	0.27473	0.1195:0.0:0.8805:0.0	rs35893129	266;298	O00592-2;O00592	.;PODXL_HUMAN	A	300;266;256;298;266	ENSP00000440518:P300A;ENSP00000442655:P266A;ENSP00000367817:P298A;ENSP00000319782:P266A	ENSP00000319782:P266A	P	-	1	0	PODXL	130844795	0.003000	0.15002	0.014000	0.15608	0.019000	0.09904	0.352000	0.20113	1.076000	0.40961	0.650000	0.86243	CCC	G|0.949;C|0.051	0.051	strong		0.587	PODXL-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000337627.2	NM_001018111	
ZKSCAN4	387032	hgsc.bcm.edu	37	6	28219661	28219661	+	Missense_Mutation	SNP	G	G	A	rs9986596	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:28219661G>A	ENST00000377294.2	-	1	341	c.98C>T	c.(97-99)tCc>tTc	p.S33F	ZKSCAN4_ENST00000423974.2_Intron	NM_019110.3	NP_061983.2	Q969J2	ZKSC4_HUMAN	zinc finger with KRAB and SCAN domains 4	33			S -> F (in dbSNP:rs9986596).		transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|large_intestine(2)|lung(10)|ovary(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	18						CGTCAAGGCGGAGGCTTCCTC	0.667													G|||	698	0.139377	0.2179	0.1225	5008	,	,		14031	0.128		0.1143	False		,,,				2504	0.0828				p.S33F		Atlas-SNP	.											.	ZKSCAN4	42	.	0			c.C98T						PASS	.	G	PHE/SER	953,3425		113,727,1349	44.0	49.0	47.0		98	-0.4	0.0	6	dbSNP_119	47	1180,7360		100,980,3190	yes	missense	ZKSCAN4	NM_019110.3	155	213,1707,4539	AA,AG,GG		13.8173,21.7679,16.5118	benign	33/546	28219661	2133,10785	2189	4270	6459	SO:0001583	missense	387032	exon1			AAGGCGGAGGCTT	AK056698	CCDS4647.1	6p21	2013-01-09	2007-02-20	2007-02-20	ENSG00000187626	ENSG00000187626		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	13854	protein-coding gene	gene with protein product		611643	"""zinc finger protein 307"", ""zinc finger protein 427"""	ZNF307, ZNF427		12477932	Standard	NM_019110		Approved	p373c6.1, P1P373C6, FLJ32136, ZSCAN36	uc003nks.1	Q969J2	OTTHUMG00000014511	ENST00000377294.2:c.98C>T	6.37:g.28219661G>A	ENSP00000366509:p.Ser33Phe	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	48	34	0.708333	NM_019110	B2RE32|Q5U7L4	Missense_Mutation	SNP	ENST00000377294.2	37	CCDS4647.1	310	0.14194139194139194	97	0.19715447154471544	44	0.12154696132596685	79	0.1381118881118881	90	0.11873350923482849	G	10.35	1.325696	0.24080	0.217679	0.138173	ENSG00000187626	ENST00000377294	T	0.05786	3.39	4.61	-0.381	0.12485	.	.	.	.	.	T	0.00875	0.0029	N	0.19112	0.55	0.58432	P	4.000000000004E-6	B	0.12630	0.006	B	0.10450	0.005	T	0.47799	-0.9089	8	0.10111	T	0.7	.	3.8039	0.08768	0.0885:0.1234:0.4709:0.3172	rs9986596	33	Q969J2	ZKSC4_HUMAN	F	33	ENSP00000366509:S33F	ENSP00000366509:S33F	S	-	2	0	ZKSCAN4	28327640	0.000000	0.05858	0.000000	0.03702	0.164000	0.22412	0.730000	0.26043	0.092000	0.17331	0.563000	0.77884	TCC	G|0.842;A|0.158	0.158	strong		0.667	ZKSCAN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040179.1	NM_019110	
GK5	256356	hgsc.bcm.edu	37	3	141884493	141884493	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:141884493G>A	ENST00000392993.2	-	16	1712	c.1561C>T	c.(1561-1563)Cgc>Tgc	p.R521C		NM_001039547.2	NP_001034636.1	Q6ZS86	GLPK5_HUMAN	glycerol kinase 5 (putative)	521					glycerol catabolic process (GO:0019563)		ATP binding (GO:0005524)|glycerol kinase activity (GO:0004370)			kidney(1)|large_intestine(1)|lung(7)|urinary_tract(1)	10						TTCATGGAGCGTTTCACTGCT	0.393																																					p.R521C		Atlas-SNP	.											GK5,NS,carcinoma,+1,1	GK5	45	1	0			c.C1561T						PASS	.						218.0	199.0	205.0					3																	141884493		2203	4300	6503	SO:0001583	missense	256356	exon16			TGGAGCGTTTCAC	BX648681	CCDS33871.1	3q23	2014-02-12	2006-09-21		ENSG00000175066	ENSG00000175066		"""Glycerol kinases"""	28635	protein-coding gene	gene with protein product						12477932	Standard	NM_001039547		Approved	MGC40579	uc003euq.2	Q6ZS86	OTTHUMG00000133572	ENST00000392993.2:c.1561C>T	3.37:g.141884493G>A	ENSP00000418001:p.Arg521Cys	Somatic	396	0	0		WXS	Illumina HiSeq	Phase_I	303	148	0.488449	NM_001039547	B2R9I2|D3DNG2|Q8N2A7|Q8N5E6	Missense_Mutation	SNP	ENST00000392993.2	37	CCDS33871.1	.	.	.	.	.	.	.	.	.	.	G	24.1	4.493597	0.84962	.	.	ENSG00000175066	ENST00000392993	D	0.91407	-2.84	5.98	5.11	0.69529	.	0.049681	0.85682	D	0.000000	D	0.93216	0.7839	M	0.84948	2.725	0.80722	D	1	D	0.59767	0.986	P	0.50537	0.643	D	0.93320	0.6692	10	0.49607	T	0.09	-12.3259	14.3523	0.66711	0.0723:0.0:0.9277:0.0	.	521	Q6ZS86	GLPK5_HUMAN	C	521	ENSP00000418001:R521C	ENSP00000418001:R521C	R	-	1	0	GK5	143367183	1.000000	0.71417	0.989000	0.46669	0.972000	0.66771	6.503000	0.73699	1.537000	0.49254	0.591000	0.81541	CGC	.	.	none		0.393	GK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353999.1	NM_001039547	
CRISPLD2	83716	hgsc.bcm.edu	37	16	84906098	84906098	+	Missense_Mutation	SNP	C	C	G	rs721005	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:84906098C>G	ENST00000262424.5	+	9	1189	c.965C>G	c.(964-966)aCt>aGt	p.T322S	CRISPLD2_ENST00000564567.1_Missense_Mutation_p.T322S|CRISPLD2_ENST00000567845.1_Missense_Mutation_p.T321S	NM_031476.3	NP_113664.1	Q9H0B8	CRLD2_HUMAN	cysteine-rich secretory protein LCCL domain containing 2	322	LCCL 1. {ECO:0000255|PROSITE- ProRule:PRU00123}.		T -> S (in dbSNP:rs721005). {ECO:0000269|PubMed:12975309, ECO:0000269|PubMed:15489334}.		extracellular matrix organization (GO:0030198)|face morphogenesis (GO:0060325)|lung development (GO:0030324)	extracellular matrix (GO:0031012)|extracellular vesicular exosome (GO:0070062)|transport vesicle (GO:0030133)	heparin binding (GO:0008201)	p.T322S(1)		endometrium(3)|large_intestine(5)|lung(8)|prostate(1)|stomach(1)	18						ATCTTTGGAACTCTGTTCTAT	0.468													C|||	2429	0.485024	0.5703	0.2911	5008	,	,		20109	0.6488		0.3857	False		,,,				2504	0.4407				p.T322S		Atlas-SNP	.											CRISPLD2,NS,carcinoma,0,1	CRISPLD2	36	1	1	Substitution - Missense(1)	stomach(1)	c.C965G						PASS	.	C	SER/THR	2403,1995	616.0+/-392.7	666,1071,462	164.0	135.0	145.0		965	5.0	0.2	16	dbSNP_86	145	3337,5263	496.7+/-374.4	648,2041,1611	yes	missense	CRISPLD2	NM_031476.3	58	1314,3112,2073	GG,GC,CC		38.8023,45.3615,44.1606	benign	322/498	84906098	5740,7258	2199	4300	6499	SO:0001583	missense	83716	exon9			TTGGAACTCTGTT	AL136861	CCDS10949.1	16q24.1	2008-02-05	2005-02-16	2005-02-16	ENSG00000103196	ENSG00000103196			25248	protein-coding gene	gene with protein product		612434	"""LCCL domain containing cysteine-rich secretory protein 2"""	LCRISP2		11230166	Standard	NM_031476		Approved	DKFZP434B044	uc010voh.1	Q9H0B8	OTTHUMG00000137644	ENST00000262424.5:c.965C>G	16.37:g.84906098C>G	ENSP00000262424:p.Thr322Ser	Somatic	286	0	0		WXS	Illumina HiSeq	Phase_I	338	337	0.997041	NM_031476	D3DUM0|Q6P590|Q6UWH0|Q6UXC6|Q96IB1|Q96K61	Missense_Mutation	SNP	ENST00000262424.5	37	CCDS10949.1	1033	0.47298534798534797	269	0.5467479674796748	104	0.287292817679558	378	0.6608391608391608	282	0.3720316622691293	C	3.694	-0.062909	0.07273	0.546385	0.388023	ENSG00000103196	ENST00000262424	D	0.88896	-2.44	5.01	5.01	0.66863	LCCL (5);	0.051171	0.85682	N	0.000000	T	0.00012	0.0000	N	0.21508	0.67	0.09310	P	1.0	P;B;B	0.34629	0.46;0.208;0.173	B;B;B	0.38880	0.284;0.108;0.038	T	0.33929	-0.9849	9	0.07990	T	0.79	.	14.2014	0.65707	0.0:1.0:0.0:0.0	rs721005;rs3803629;rs17186723;rs17855776;rs52828946;rs60503314;rs721005	322;322;322	Q9H0B8;Q9H0B8-2;Q9H0B8-3	CRLD2_HUMAN;.;.	S	322	ENSP00000262424:T322S	ENSP00000262424:T322S	T	+	2	0	CRISPLD2	83463599	0.954000	0.32549	0.202000	0.23494	0.084000	0.17831	5.047000	0.64232	2.481000	0.83766	0.561000	0.74099	ACT	C|0.539;G|0.461	0.461	strong		0.468	CRISPLD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269086.2	NM_031476	
C2orf16	84226	hgsc.bcm.edu	37	2	27802805	27802805	+	Silent	SNP	A	A	G	rs3811644	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:27802805A>G	ENST00000408964.2	+	1	3417	c.3366A>G	c.(3364-3366)ctA>ctG	p.L1122L	AC074091.1_ENST00000408604.1_RNA	NM_032266.3	NP_115642.3	Q68DN1	CB016_HUMAN	chromosome 2 open reading frame 16	1122						extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(33)|urinary_tract(1)	47	Acute lymphoblastic leukemia(172;0.155)					CTATCTGCCTACAGTGTGGCC	0.463													A|||	1025	0.204673	0.0499	0.111	5008	,	,		20009	0.3383		0.2137	False		,,,				2504	0.3333				p.L1122L		Atlas-SNP	.											.	C2orf16	357	.	0			c.A3366G						PASS	.	A		293,3591		6,281,1655	108.0	109.0	109.0		3366	2.5	1.0	2	dbSNP_107	109	1677,6613		169,1339,2637	no	coding-synonymous	C2orf16	NM_032266.3		175,1620,4292	GG,GA,AA		20.2292,7.5438,16.182		1122/1985	27802805	1970,10204	1942	4145	6087	SO:0001819	synonymous_variant	84226	exon1			CTGCCTACAGTGT	AL136898	CCDS42666.1	2p23.3	2013-09-20			ENSG00000221843	ENSG00000221843			25275	protein-coding gene	gene with protein product	"""P-S-E-R-S-H-H-S repeats containing"""						Standard	NM_032266		Approved	DKFZp434G118	uc002rkz.4	Q68DN1	OTTHUMG00000159099	ENST00000408964.2:c.3366A>G	2.37:g.27802805A>G		Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	200	78	0.39	NM_032266	B9EIQ4|Q53S01|Q8ND64|Q9H088	Silent	SNP	ENST00000408964.2	37	CCDS42666.1																																																																																			A|0.811;G|0.189	0.189	strong		0.463	C2orf16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353292.1	NM_032266	
MYOF	26509	hgsc.bcm.edu	37	10	95095792	95095792	+	Silent	SNP	A	A	G	rs79155397	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:95095792A>G	ENST00000359263.4	-	41	4448	c.4449T>C	c.(4447-4449)tgT>tgC	p.C1483C	MYOF_ENST00000358334.5_Silent_p.C1470C|MYOF_ENST00000371502.4_Silent_p.C1502C|MYOF_ENST00000371501.4_Silent_p.C1483C	NM_013451.3	NP_038479.1	Q9NZM1	MYOF_HUMAN	myoferlin	1483					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)			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						TTTCTAGTTCACAATTATATA	0.403													G|||	261	0.0521166	0.0711	0.049	5008	,	,		19168	0.0		0.1024	False		,,,				2504	0.0307				p.C1483C		Atlas-SNP	.											.	MYOF	177	.	0			c.T4449C						PASS	.	G	,	311,3399		16,279,1560	119.0	109.0	112.0		4449,4410	0.8	1.0	10	dbSNP_132	112	552,7628		20,512,3558	no	coding-synonymous,coding-synonymous	MYOF	NM_013451.3,NM_133337.2	,	36,791,5118	GG,GA,AA		6.7482,8.3827,7.2582	,	1483/2062,1470/2049	95095792	863,11027	1855	4090	5945	SO:0001819	synonymous_variant	26509	exon41			TAGTTCACAATTA	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.4449T>C	10.37:g.95095792A>G		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	114	50	0.438596	NM_013451	B3KQN5|Q5VWW2|Q5VWW3|Q5VWW4|Q5VWW5|Q7Z642|Q8IWH0|Q9HBU3|Q9NZM0|Q9ULL3|Q9Y4U4	Silent	SNP	ENST00000359263.4	37	CCDS41551.1																																																																																			A|0.936;G|0.064	0.064	strong		0.403	MYOF-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000049423.2	NM_013451	
KRTAP10-10	353333	hgsc.bcm.edu	37	21	46057422	46057422	+	Missense_Mutation	SNP	T	T	A	rs112205018|rs386819192	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:46057422T>A	ENST00000380095.1	+	1	150	c.88T>A	c.(88-90)Tgc>Agc	p.C30S	TSPEAR_ENST00000323084.4_Intron	NM_181688.1	NP_859016.1	P60014	KR10A_HUMAN	keratin associated protein 10-10	30	15 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				NS(1)|endometrium(2)|kidney(1)|lung(6)|prostate(1)|skin(2)	13						CTGCGAGCCCTGCTGCTGTGC	0.677													T|||	1453	0.290136	0.2337	0.2075	5008	,	,		16831	0.253		0.3101	False		,,,				2504	0.4427				p.C30S		Atlas-SNP	.											KRTAP10-10,caecum,carcinoma,0,1	KRTAP10-10	37	1	0			c.T88A						PASS	.						64.0	70.0	68.0					21																	46057422		2203	4299	6502	SO:0001583	missense	353333	exon1			GAGCCCTGCTGCT	AJ566387	CCDS33585.1	21q22.3	2006-03-13			ENSG00000221859	ENSG00000221859		"""Keratin associated proteins"""	22972	protein-coding gene	gene with protein product							Standard	NM_181688		Approved	KAP10.10, KAP18.10, KRTAP18-10	uc002zfq.3	P60014	OTTHUMG00000057631	ENST00000380095.1:c.88T>A	21.37:g.46057422T>A	ENSP00000369438:p.Cys30Ser	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	84	16	0.190476	NM_181688		Missense_Mutation	SNP	ENST00000380095.1	37	CCDS33585.1	540	0.24725274725274726	93	0.18902439024390244	74	0.20441988950276244	138	0.24125874125874125	235	0.3100263852242744	t	0.004	-2.351941	0.00217	.	.	ENSG00000221859	ENST00000380095	T	0.09911	2.93	3.09	0.455	0.16649	.	.	.	.	.	T	0.00012	0.0000	N	0.01686	-0.76	0.50313	P	1.3399999999996748E-4	B	0.16166	0.016	B	0.10450	0.005	T	0.45948	-0.9226	8	0.06365	T	0.9	.	5.6129	0.17416	0.0:0.6006:0.0:0.3994	.	30	P60014	KR10A_HUMAN	S	30	ENSP00000369438:C30S	ENSP00000369438:C30S	C	+	1	0	KRTAP10-10	44881850	.	.	0.910000	0.35882	0.005000	0.04900	.	.	-0.062000	0.13088	-0.407000	0.06327	TGC	T|0.742;A|0.258	0.258	strong		0.677	KRTAP10-10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128034.1	NM_181688	
MAGEC3	139081	hgsc.bcm.edu	37	X	140983103	140983103	+	Silent	SNP	C	C	T	rs176025	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:140983103C>T	ENST00000298296.1	+	5	958	c.958C>T	c.(958-960)Ctg>Ttg	p.L320L	MAGEC3_ENST00000448920.1_Silent_p.L72L|MAGEC3_ENST00000409007.1_5'Flank|MAGEC3_ENST00000544766.1_5'UTR|MAGEC3_ENST00000483584.1_3'UTR|MAGEC3_ENST00000536088.1_Intron|MAGEC3_ENST00000443323.2_Intron	NM_138702.1	NP_619647.1	Q8TD91	MAGC3_HUMAN	melanoma antigen family C, 3	320	MAGE 1. {ECO:0000255|PROSITE- ProRule:PRU00127}.									NS(2)|breast(3)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(6)|liver(1)|lung(32)|ovary(1)|prostate(1)|skin(5)|stomach(1)|urinary_tract(2)	69	Acute lymphoblastic leukemia(192;6.56e-05)					CCGACTTGCACTGTGGGAGTC	0.597													-|||	843	0.223311	0.3359	0.1354	3775	,	,		7497	0.0427		0.2058	False		,,,				2504	0.0562				p.L320L		Atlas-SNP	.											.	MAGEC3	228	.	0			c.C958T						PASS	.	T	,	1712,2123		318,812,264,502,307	123.0	112.0	116.0		958,	-1.4	0.0	X	dbSNP_79	116	1769,4959		188,910,483,1330,1389	no	coding-synonymous,utr-5	MAGEC3	NM_138702.1,NM_177456.2	,	506,1722,747,1832,1696	TT,TC,T,CC,C		26.2931,44.6415,32.9547	,	320/644,	140983103	3481,7082	2203	4300	6503	SO:0001819	synonymous_variant	139081	exon5			CTTGCACTGTGGG	AF490508	CCDS14676.1, CCDS14677.1	Xq27.2	2009-03-25			ENSG00000165509	ENSG00000165509			23798	protein-coding gene	gene with protein product	"""cancer/testis antigen family 7, member 2"""	300469				10861452	Standard	NM_138702		Approved	HCA2, MAGE-C3, CT7.2	uc011mwp.2	Q8TD91	OTTHUMG00000022570	ENST00000298296.1:c.958C>T	X.37:g.140983103C>T		Somatic	201	1	0.00497512		WXS	Illumina HiSeq	Phase_I	150	148	0.986667	NM_138702	Q3SYA7|Q5JZ43|Q9BZ80	Silent	SNP	ENST00000298296.1	37	CCDS14676.1																																																																																			C|0.685;T|0.315	0.315	strong		0.597	MAGEC3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058606.1	NM_138702	
SIGLEC6	946	hgsc.bcm.edu	37	19	52033158	52033158	+	Missense_Mutation	SNP	C	C	T	rs35931837	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:52033158C>T	ENST00000425629.3	-	5	986	c.832G>A	c.(832-834)Ggc>Agc	p.G278S	SIGLEC6_ENST00000436458.1_Missense_Mutation_p.G226S|SIGLEC6_ENST00000474054.1_5'Flank|SIGLEC6_ENST00000343300.4_Missense_Mutation_p.G278S|SIGLEC6_ENST00000391797.3_Missense_Mutation_p.G267S|SIGLEC6_ENST00000359982.4_Missense_Mutation_p.G289S|SIGLEC6_ENST00000346477.3_Missense_Mutation_p.G262S	NM_001245.5	NP_001236.4	O43699	SIGL6_HUMAN	sialic acid binding Ig-like lectin 6	278	Ig-like C2-type 2.				cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)			endometrium(3)|kidney(1)|large_intestine(6)|liver(1)|lung(15)|ovary(1)|stomach(1)	28		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.00115)|OV - Ovarian serous cystadenocarcinoma(262;0.0165)		GGGGGGTTGCCGTCAGCATCA	0.622													C|||	368	0.0734824	0.0038	0.2363	5008	,	,		15730	0.002		0.1183	False		,,,				2504	0.0798				p.G289S		Atlas-SNP	.											SIGLEC6_ENST00000425629,NS,carcinoma,+2,2	SIGLEC6	142	2	0			c.G865A						PASS	.	C	SER/GLY,SER/GLY,SER/GLY,SER/GLY,SER/GLY,SER/GLY	116,4288	82.9+/-121.4	2,112,2088	76.0	86.0	83.0		676,865,799,832,784,832	1.5	0.9	19	dbSNP_126	83	938,7662	203.2+/-246.3	62,814,3424	no	missense,missense,missense,missense,missense,missense	SIGLEC6	NM_001177547.1,NM_001177548.1,NM_001177549.1,NM_001245.5,NM_198845.4,NM_198846.4	56,56,56,56,56,56	64,926,5512	TT,TC,CC		10.907,2.634,8.1052	benign,benign,benign,benign,benign,benign	226/402,289/390,267/343,278/454,262/438,278/354	52033158	1054,11950	2202	4300	6502	SO:0001583	missense	946	exon5			GGTTGCCGTCAGC	D86358	CCDS12834.3, CCDS12835.3, CCDS12836.3, CCDS54307.1, CCDS54308.1, CCDS59417.1	19q13.3	2013-01-29			ENSG00000105492	ENSG00000105492		"""Sialic acid binding Ig-like lectins"", ""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	10875	protein-coding gene	gene with protein product		604405		CD33L, CD33L1		9465907	Standard	NM_001245		Approved	OB-BP1, SIGLEC-6, CD327	uc002pwy.3	O43699	OTTHUMG00000133571	ENST00000425629.3:c.832G>A	19.37:g.52033158C>T	ENSP00000401502:p.Gly278Ser	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	109	44	0.40367	NM_001177548	A8MV71|B2RTS8|C9JBE5|F8WA78|O15388|O43700	Missense_Mutation	SNP	ENST00000425629.3	37	CCDS12834.3	178	0.0815018315018315	4	0.008130081300813009	71	0.19613259668508287	0	0.0	103	0.1358839050131926	C	0.011	-1.691978	0.00731	0.02634	0.10907	ENSG00000105492	ENST00000346477;ENST00000391797;ENST00000425629;ENST00000359982;ENST00000436458;ENST00000343300	T;T;T;T;T	0.81163	-1.46;-1.29;-1.29;-1.29;-1.29	3.71	1.55	0.23275	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.297955	0.23995	N	0.042527	T	0.00073	0.0002	N	0.03917	-0.325	0.38054	P	0.06411100000000003	B;B;B;B;B;B	0.17852	0.002;0.0;0.016;0.007;0.024;0.009	B;B;B;B;B;B	0.09377	0.002;0.002;0.004;0.003;0.004;0.002	T	0.05451	-1.0884	9	0.02654	T	1	.	5.3372	0.15965	0.0:0.254:0.0:0.746	rs35931837	289;226;267;278;262;278	F8WA78;C9JBE5;O43699-4;O43699-2;O43699-3;O43699	.;.;.;.;.;SIGL6_HUMAN	S	251;262;278;289;226;278	ENSP00000344064:G251S;ENSP00000401502:G278S;ENSP00000353071:G289S;ENSP00000410679:G226S;ENSP00000345907:G278S	ENSP00000345907:G278S	G	-	1	0	SIGLEC6	56724970	0.083000	0.21467	0.902000	0.35471	0.038000	0.13279	-0.302000	0.08221	0.150000	0.19136	-0.492000	0.04666	GGC	C|0.914;T|0.086	0.086	strong		0.622	SIGLEC6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257670.3	NM_001245	
MTUS1	57509	hgsc.bcm.edu	37	8	17611886	17611886	+	Silent	SNP	G	G	A	rs2979788	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:17611886G>A	ENST00000262102.6	-	2	1655	c.1431C>T	c.(1429-1431)ccC>ccT	p.P477P	MTUS1_ENST00000519263.1_Silent_p.P477P|MTUS1_ENST00000381862.3_Silent_p.P477P|MTUS1_ENST00000381869.3_Silent_p.P477P	NM_001001924.2	NP_001001924.1	Q9ULD2	MTUS1_HUMAN	microtubule associated tumor suppressor 1	477					cellular response to peptide hormone stimulus (GO:0071375)|regulation of macrophage chemotaxis (GO:0010758)	extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(14)|lung(8)|ovary(1)|skin(2)|urinary_tract(1)	36				Colorectal(111;0.0778)		TTCCTAAACTGGGTTTACACA	0.403													A|||	3344	0.667732	0.3661	0.8228	5008	,	,		19432	0.5942		0.8519	False		,,,				2504	0.8517				p.P477P		Atlas-SNP	.											.	MTUS1	144	.	0			c.C1431T						PASS	.	A	,	1707,1981		386,935,523	157.0	148.0	151.0		1431,1431	-2.7	0.0	8	dbSNP_101	151	6879,1329		2867,1145,92	no	coding-synonymous,coding-synonymous	MTUS1	NM_001001924.2,NM_001001925.2	,	3253,2080,615	AA,AG,GG		16.1915,46.2852,27.8245	,	477/1271,477/1217	17611886	8586,3310	1844	4104	5948	SO:0001819	synonymous_variant	57509	exon2			TAAACTGGGTTTA	AL096842	CCDS43716.1, CCDS43717.1, CCDS43718.1, CCDS43719.1, CCDS55204.1	8p22	2013-01-17	2009-10-20		ENSG00000129422	ENSG00000129422			29789	protein-coding gene	gene with protein product	"""AT2 receptor-interacting protein"", ""AT2R binding protein"", ""mitochondrial tumor suppressor gene 1"""	609589	"""mitochondrial tumor suppressor 1"""			10574462, 12692079	Standard	NM_001001931		Approved	MTSG1, KIAA1288, DKFZp586D1519, FLJ14295, ATIP1, MP44, ATBP, ICIS	uc003wxv.3	Q9ULD2	OTTHUMG00000163756	ENST00000262102.6:c.1431C>T	8.37:g.17611886G>A		Somatic	219	0	0		WXS	Illumina HiSeq	Phase_I	139	139	1	NM_001001924	A8K135|B2RBJ6|B3KWJ9|B4DH03|B9EGA1|D3DSP8|Q63HJ6|Q659F4|Q6PK49|Q6URW7|Q8N4M6|Q8WTT9|Q9H7T2	Silent	SNP	ENST00000262102.6	37	CCDS43717.1																																																																																			G|0.311;A|0.689	0.689	strong		0.403	MTUS1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000375247.1	XM_372031	
TSHZ3	57616	hgsc.bcm.edu	37	19	31769763	31769763	+	Silent	SNP	G	G	A	rs12461253	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:31769763G>A	ENST00000240587.4	-	2	1263	c.936C>T	c.(934-936)gtC>gtT	p.V312V		NM_020856.2	NP_065907.2	Q63HK5	TSH3_HUMAN	teashirt zinc finger homeobox 3	312					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)					TTTTGGCGGCGACAGGAGTGA	0.537													G|||	1753	0.35004	0.236	0.3098	5008	,	,		14828	0.5734		0.2962	False		,,,				2504	0.3579				p.V312V		Atlas-SNP	.											.	TSHZ3	549	.	0			c.C936T						PASS	.	G		994,3412	369.3+/-319.0	118,758,1327	85.0	86.0	86.0		936	-10.2	0.0	19	dbSNP_120	86	2506,6094	410.2+/-350.1	367,1772,2161	no	coding-synonymous	TSHZ3	NM_020856.2		485,2530,3488	AA,AG,GG		29.1395,22.5601,26.9107		312/1082	31769763	3500,9506	2203	4300	6503	SO:0001819	synonymous_variant	57616	exon2			GGCGGCGACAGGA	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.936C>T	19.37:g.31769763G>A		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	89	43	0.483146	NM_020856	Q9H0G6|Q9P254	Silent	SNP	ENST00000240587.4	37	CCDS12421.2																																																																																			G|0.689;A|0.311	0.311	strong		0.537	TSHZ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316743.2	NM_020856	
PDE4DIP	9659	hgsc.bcm.edu	37	1	144922523	144922523	+	Missense_Mutation	SNP	C	C	T	rs2455994	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:144922523C>T	ENST00000369354.3	-	7	1073	c.884G>A	c.(883-885)cGt>cAt	p.R295H	PDE4DIP_ENST00000369359.4_Missense_Mutation_p.R432H|PDE4DIP_ENST00000369349.3_Missense_Mutation_p.R295H|PDE4DIP_ENST00000313382.9_Missense_Mutation_p.R361H|PDE4DIP_ENST00000479408.2_Missense_Mutation_p.R82H|PDE4DIP_ENST00000529945.1_Missense_Mutation_p.R458H|PDE4DIP_ENST00000369356.4_Missense_Mutation_p.R295H|PDE4DIP_ENST00000530740.1_Missense_Mutation_p.R432H|PDE4DIP_ENST00000313431.9_Missense_Mutation_p.R458H|PDE4DIP_ENST00000369351.3_Missense_Mutation_p.R295H			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	295					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)		TGTTACCTCACGTTCCCTGCT	0.378			T	PDGFRB	MPD																																p.R458H		Atlas-SNP	.		Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	.	PDE4DIP	817	.	0			c.G1373A						PASS	.	C	HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG	1506,2900		0,1506,697	314.0	323.0	320.0		884,884,1082,884,1373	2.1	1.0	1	dbSNP_100	320	2953,5643		0,2953,1345	yes	missense,missense,missense,missense,missense	PDE4DIP	NM_014644.4,NM_001198834.2,NM_001198832.1,NM_001002812.1,NM_001002811.1	29,29,29,29,29	0,4459,2042	TT,TC,CC		34.3532,34.1807,34.2947	benign,benign,benign,benign,benign	295/2347,295/2363,361/2241,295/970,458/1133	144922523	4459,8543	2203	4298	6501	SO:0001583	missense	9659	exon3			ACCTCACGTTCCC	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.884G>A	1.37:g.144922523C>T	ENSP00000358360:p.Arg295His	Somatic	229	0	0		WXS	Illumina HiSeq	Phase_I	160	34	0.2125	NM_001002811	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	572	0.2619047619047619	186	0.3780487804878049	95	0.26243093922651933	25	0.043706293706293704	266	0.35092348284960423	C	15.33	2.800371	0.50315	0.341807	0.343532	ENSG00000178104	ENST00000313382;ENST00000369354;ENST00000369356;ENST00000369353;ENST00000530740;ENST00000369359;ENST00000369351;ENST00000369349;ENST00000313431;ENST00000529945;ENST00000479408	T;T;T;T;T;T;T;T;T;T	0.12039	4.72;4.82;4.82;4.82;4.82;3.81;3.82;2.72;2.72;2.73	6.06	2.07	0.26955	.	.	.	.	.	T	0.02688	0.0081	N	0.14661	0.345	0.80722	D	1	B;B;B;B;B	0.22414	0.045;0.067;0.069;0.015;0.018	B;B;B;B;B	0.18561	0.005;0.022;0.006;0.0;0.002	T	0.39396	-0.9616	9	0.40728	T	0.16	.	8.9819	0.35970	0.0:0.6854:0.0:0.3146	rs2455994;rs58012659	458;295;458;361;295	E9PL24;Q5VU43-7;Q5VU43-2;Q5VU43-3;Q5VU43	.;.;.;.;MYOME_HUMAN	H	361;295;295;458;432;432;295;295;458;458;82	ENSP00000327209:R361H;ENSP00000358360:R295H;ENSP00000358363:R295H;ENSP00000435654:R432H;ENSP00000358366:R432H;ENSP00000358357:R295H;ENSP00000358355:R295H;ENSP00000316434:R458H;ENSP00000433392:R458H;ENSP00000436791:R82H	ENSP00000327209:R361H	R	-	2	0	PDE4DIP	143633880	0.480000	0.25933	0.999000	0.59377	0.967000	0.64934	0.055000	0.14229	0.129000	0.18514	0.650000	0.86243	CGT	C|0.738;T|0.262	0.262	strong		0.378	PDE4DIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000038858.2	NM_022359	
BCAT2	587	hgsc.bcm.edu	37	19	49309776	49309776	+	Missense_Mutation	SNP	G	G	C	rs117048185	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:49309776G>C	ENST00000316273.6	-	3	310	c.298C>G	c.(298-300)Cag>Gag	p.Q100E	BCAT2_ENST00000402551.1_Missense_Mutation_p.Q60E|BCAT2_ENST00000601496.1_5'Flank|BCAT2_ENST00000599246.1_Intron|BCAT2_ENST00000597011.1_Missense_Mutation_p.Q60E|BCAT2_ENST00000545387.2_Intron|BCAT2_ENST00000598162.1_Missense_Mutation_p.Q100E	NM_001190.3	NP_001181.2	O15382	BCAT2_HUMAN	branched chain amino-acid transaminase 2, mitochondrial	100					branched-chain amino acid biosynthetic process (GO:0009082)|branched-chain amino acid catabolic process (GO:0009083)|cellular nitrogen compound metabolic process (GO:0034641)|isoleucine catabolic process (GO:0006550)|leucine metabolic process (GO:0006551)|regulation of hormone levels (GO:0010817)|small molecule metabolic process (GO:0044281)|valine metabolic process (GO:0006573)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	branched-chain-amino-acid transaminase activity (GO:0004084)|L-isoleucine transaminase activity (GO:0052656)|L-leucine transaminase activity (GO:0052654)|L-valine transaminase activity (GO:0052655)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(5)|ovary(2)|skin(1)	12		all_epithelial(76;7e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000138)|all cancers(93;0.000366)|Epithelial(262;0.0195)|GBM - Glioblastoma multiforme(486;0.0224)	L-Isoleucine(DB00167)|L-Leucine(DB00149)	CATGCCACCTGCAGGGAGTAG	0.607													G|||	30	0.00599042	0.0008	0.0072	5008	,	,		16606	0.0		0.0229	False		,,,				2504	0.001				p.Q100E		Atlas-SNP	.											.	BCAT2	35	.	0			c.C298G						PASS	.	G	,GLU/GLN	10,4396	15.5+/-35.6	0,10,2193	63.0	74.0	71.0		,298	5.3	1.0	19	dbSNP_132	71	120,8480	61.7+/-123.6	1,118,4181	yes	intron,missense	BCAT2	NM_001164773.1,NM_001190.3	,29	1,128,6374	CC,CG,GG		1.3953,0.227,0.9995	,benign	,100/393	49309776	130,12876	2203	4300	6503	SO:0001583	missense	587	exon3			CCACCTGCAGGGA	U68418	CCDS12735.1, CCDS54290.1, CCDS74416.1	19q13.33	2013-09-20	2010-05-07		ENSG00000105552	ENSG00000105552	2.6.1.42		977	protein-coding gene	gene with protein product		113530	"""branched chain aminotransferase 2, mitochondrial"""	BCT2		9165094	Standard	NM_001190		Approved	BCAM	uc002pkr.3	O15382	OTTHUMG00000183327	ENST00000316273.6:c.298C>G	19.37:g.49309776G>C	ENSP00000322991:p.Gln100Glu	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	85	45	0.529412	NM_001190	B2RB87|O00269|Q96KG1|Q9BTB6|Q9BUU6	Missense_Mutation	SNP	ENST00000316273.6	37	CCDS12735.1	22	0.010073260073260074	1	0.0020325203252032522	5	0.013812154696132596	0	0.0	16	0.021108179419525065	G	1.762	-0.486562	0.04352	0.00227	0.013953	ENSG00000105552	ENST00000316273;ENST00000402551	T;T	0.30448	1.53;1.53	5.26	5.26	0.73747	.	0.056271	0.64402	D	0.000001	T	0.05410	0.0143	N	0.02721	-0.515	0.43959	D	0.996633	B;B	0.23377	0.084;0.084	B;B	0.18263	0.021;0.021	T	0.13098	-1.0522	10	0.02654	T	1	-20.0097	12.4651	0.55753	0.0:0.1688:0.8312:0.0	.	100;100	Q53EW7;O15382	.;BCAT2_HUMAN	E	100;60	ENSP00000322991:Q100E;ENSP00000385161:Q60E	ENSP00000322991:Q100E	Q	-	1	0	BCAT2	54001588	0.995000	0.38212	1.000000	0.80357	0.499000	0.33736	2.479000	0.45197	2.627000	0.88993	0.555000	0.69702	CAG	G|0.990;C|0.010	0.010	strong		0.607	BCAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466202.1		
RPTN	126638	hgsc.bcm.edu	37	1	152129100	152129100	+	Missense_Mutation	SNP	C	C	T	rs200003389	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:152129100C>T	ENST00000316073.3	-	3	539	c.475G>A	c.(475-477)Ggt>Agt	p.G159S		NM_001122965.1	NP_001116437.1	Q6XPR3	RPTN_HUMAN	repetin	159	Gln-rich.					cornified envelope (GO:0001533)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)	p.G159_H170delGQSEKQDRDSHH(1)		breast(2)|central_nervous_system(1)|endometrium(14)|kidney(2)|large_intestine(1)|lung(32)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	59						TCAGACTGACCATGGTGGGAA	0.502																																					p.G159S		Atlas-SNP	.											RPTN,NS,carcinoma,0,1	RPTN	123	1	1	Deletion - In frame(1)	stomach(1)	c.G475A						scavenged	.	C	SER/GLY	0,3128		0,0,1564	469.0	409.0	427.0		475	-0.8	0.0	1	dbSNP_134	427	1,7133		0,1,3566	yes	missense	RPTN	NM_001122965.1	56	0,1,5130	TT,TC,CC		0.014,0.0,0.0097	benign	159/785	152129100	1,10261	1564	3567	5131	SO:0001583	missense	126638	exon3			ACTGACCATGGTG	AK096436	CCDS41397.1	1q21.3	2013-01-10			ENSG00000215853	ENSG00000215853		"""EF-hand domain containing"""	26809	protein-coding gene	gene with protein product		613259				15854042	Standard	NM_001122965		Approved	FLJ39117	uc001ezs.1	Q6XPR3	OTTHUMG00000154095	ENST00000316073.3:c.475G>A	1.37:g.152129100C>T	ENSP00000317895:p.Gly159Ser	Somatic	273	1	0.003663		WXS	Illumina HiSeq	Phase_I	179	32	0.178771	NM_001122965	B7ZBZ3	Missense_Mutation	SNP	ENST00000316073.3	37	CCDS41397.1	.	.	.	.	.	.	.	.	.	.	C	10.44	1.350341	0.24512	0.0	1.4E-4	ENSG00000215853	ENST00000316073	T	0.12569	2.67	4.57	-0.815	0.10843	.	0.522245	0.14186	U	0.335665	T	0.02418	0.0074	L	0.33245	0.995	0.09310	N	1	P	0.47350	0.894	B	0.38500	0.275	T	0.39820	-0.9595	10	0.33940	T	0.23	0.6761	4.3811	0.11295	0.0:0.4509:0.1612:0.3879	.	159	Q6XPR3	RPTN_HUMAN	S	159	ENSP00000317895:G159S	ENSP00000317895:G159S	G	-	1	0	RPTN	150395724	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.352000	0.07701	-0.522000	0.06417	-0.272000	0.10252	GGT	C|0.966;T|0.034	0.034	strong		0.502	RPTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333867.1	XM_371312	
TET1	80312	hgsc.bcm.edu	37	10	70405539	70405539	+	Missense_Mutation	SNP	A	A	G	rs16925541|rs71483917	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:70405539A>G	ENST00000373644.4	+	4	3262	c.3053A>G	c.(3052-3054)aAt>aGt	p.N1018S		NM_030625.2	NP_085128.2	Q8NFU7	TET1_HUMAN	tet methylcytosine dioxygenase 1	1018			N -> S (in dbSNP:rs16925541).		chromatin modification (GO:0016568)|DNA demethylation (GO:0080111)|inner cell mass cell differentiation (GO:0001826)|negative regulation of methylation-dependent chromatin silencing (GO:0090310)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein O-linked glycosylation (GO:0006493)|regulation of DNA methylation (GO:0044030)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	iron ion binding (GO:0005506)|methylcytosine dioxygenase activity (GO:0070579)|structure-specific DNA binding (GO:0043566)|zinc ion binding (GO:0008270)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(2)|ovary(5)|prostate(1)|upper_aerodigestive_tract(2)	21						ATTGACACCAATAAAAGTATT	0.333													A|||	417	0.0832668	0.0038	0.0692	5008	,	,		22340	0.1052		0.0636	False		,,,				2504	0.1984				p.N1018S		Atlas-SNP	.											.	TET1	255	.	0			c.A3053G						PASS	.	A	SER/ASN	70,4336	64.1+/-101.4	1,68,2134	70.0	70.0	70.0		3053	0.5	0.1	10	dbSNP_123	70	633,7967	163.0+/-215.7	25,583,3692	yes	missense	TET1	NM_030625.2	46	26,651,5826	GG,GA,AA		7.3605,1.5887,5.4052	benign	1018/2137	70405539	703,12303	2203	4300	6503	SO:0001583	missense	80312	exon4			ACACCAATAAAAG	AF430147	CCDS7281.1	10q21	2014-02-18	2011-09-30	2008-03-12	ENSG00000138336	ENSG00000138336			29484	protein-coding gene	gene with protein product	"""leukemia-associated protein with a CXXC domain"", ""ten-eleven translocation-1"""	607790	"""CXXC zinc finger 6"", ""tet oncogene 1"""	CXXC6		12124344, 12646957	Standard	NM_030625		Approved	LCX, KIAA1676, bA119F7.1	uc001jok.4	Q8NFU7	OTTHUMG00000018359	ENST00000373644.4:c.3053A>G	10.37:g.70405539A>G	ENSP00000362748:p.Asn1018Ser	Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	157	69	0.43949	NM_030625	Q5VUP7|Q7Z6B6|Q8TCR1|Q9C0I7	Missense_Mutation	SNP	ENST00000373644.4	37	CCDS7281.1	182	0.08333333333333333	4	0.008130081300813009	35	0.09668508287292818	67	0.11713286713286714	76	0.10026385224274406	A	6.009	0.370042	0.11352	0.015887	0.073605	ENSG00000138336	ENST00000373644	T	0.08546	3.08	5.46	0.475	0.16774	.	6.431470	0.00166	N	0.000002	T	0.00144	0.0004	L	0.29908	0.895	0.54753	P	1.2000000000012001E-5	B	0.17852	0.024	B	0.15484	0.013	T	0.38824	-0.9643	9	0.45353	T	0.12	.	8.239	0.31650	0.6781:0.0:0.3219:0.0	rs16925541;rs58250080;rs16925541	1018	Q8NFU7	TET1_HUMAN	S	1018	ENSP00000362748:N1018S	ENSP00000362748:N1018S	N	+	2	0	TET1	70075545	0.051000	0.20477	0.119000	0.21687	0.364000	0.29643	0.237000	0.17985	-0.157000	0.11059	-0.376000	0.06991	AAT	ATA|0.500;GTG|0.500	.	alt		0.333	TET1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048354.1	NM_030625	
LILRB3	11025	hgsc.bcm.edu	37	19	54722275	54722275	+	Silent	SNP	G	G	A	rs1132609	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:54722275G>A	ENST00000391750.1	-	12	1684	c.1548C>T	c.(1546-1548)gcC>gcT	p.A516A	LILRB3_ENST00000424807.1_Silent_p.A516A|LILRB3_ENST00000346401.6_Silent_p.A528A|LILRA6_ENST00000440558.2_Silent_p.A516A|LILRA6_ENST00000270464.5_Silent_p.A516A|LILRB3_ENST00000407860.2_Silent_p.A533A|LILRB3_ENST00000469273.1_5'UTR|LILRA6_ENST00000419410.2_Silent_p.A516A|LILRA6_ENST00000391735.3_Intron|LILRB3_ENST00000245620.9_Silent_p.A516A			O75022	LIRB3_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 3	516					cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)|immune system process (GO:0002376)|negative regulation of osteoclast differentiation (GO:0045671)	integral component of plasma membrane (GO:0005887)	receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			endometrium(3)|kidney(13)|large_intestine(1)|lung(6)|ovary(2)|prostate(5)|skin(2)|stomach(1)|urinary_tract(1)	34	all_cancers(19;0.00723)|all_epithelial(19;0.00389)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		TGTCCTTCACGGCAGCATCTG	0.632													.|||	1152	0.230032	0.0166	0.2262	5008	,	,		17986	0.252		0.2883	False		,,,				2504	0.4387				p.A516A		Atlas-SNP	.											.	LILRB3	67	.	0			c.C1548T						PASS	.	G	,	246,4160	142.7+/-177.9	14,218,1971	115.0	100.0	105.0		1548,1548	-6.2	0.0	19	dbSNP_86	105	2593,6007	420.0+/-353.3	403,1787,2110	no	coding-synonymous,coding-synonymous	LILRB3	NM_001081450.1,NM_006864.2	,	417,2005,4081	AA,AG,GG		30.1512,5.5833,21.8284	,	516/633,516/632	54722275	2839,10167	2203	4300	6503	SO:0001819	synonymous_variant	11025	exon11			CTTCACGGCAGCA	U91928	CCDS33105.1, CCDS46175.1	19q13.4	2013-01-11			ENSG00000204577	ENSG00000204577		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6607	protein-coding gene	gene with protein product		604820				9278324, 9382880	Standard	NM_006864		Approved	LIR-3, HL9, ILT5, LIR3, CD85a	uc002qee.1	O75022	OTTHUMG00000066626	ENST00000391750.1:c.1548C>T	19.37:g.54722275G>A		Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	144	65	0.451389	NM_006864	C9J1P3|C9JIP1|O15471|Q86U49	Silent	SNP	ENST00000391750.1	37	CCDS33105.1																																																																																			.	.	weak		0.632	LILRB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000142844.5	NM_006864	
DCPS	28960	hgsc.bcm.edu	37	11	126174164	126174164	+	Silent	SNP	C	C	T	rs695029	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:126174164C>T	ENST00000263579.4	+	1	518	c.189C>T	c.(187-189)ttC>ttT	p.F63F	RP11-712L6.5_ENST00000524964.1_5'UTR	NM_014026.3	NP_054745.1	Q96C86	DCPS_HUMAN	decapping enzyme, scavenger	63					cellular response to menadione (GO:0036245)|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 cis splicing, via spliceosome (GO:0045292)|mRNA metabolic process (GO:0016071)|negative regulation of programmed cell death (GO:0043069)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	m7G(5')pppN diphosphatase activity (GO:0050072)|RNA 7-methylguanosine cap binding (GO:0000340)			endometrium(3)|large_intestine(4)|lung(6)|ovary(1)|skin(2)|urinary_tract(1)	17	all_hematologic(175;0.145)	Breast(109;0.00156)|Lung NSC(97;0.00949)|all_lung(97;0.0101)|Medulloblastoma(222;0.0425)|all_neural(223;0.0604)		BRCA - Breast invasive adenocarcinoma(274;1.15e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.08)		AAATCATTTTCCTACACGGGA	0.547													C|||	1531	0.305711	0.0749	0.3905	5008	,	,		17744	0.624		0.2008	False		,,,				2504	0.3374				p.F63F		Atlas-SNP	.											DCPS,NS,carcinoma,+2,1	DCPS	33	1	0			c.C189T						PASS	.	C		466,3936	218.1+/-236.3	26,414,1761	72.0	71.0	71.0		189	3.8	0.9	11	dbSNP_83	71	1723,6873	311.4+/-310.3	160,1403,2735	no	coding-synonymous	DCPS	NM_014026.3		186,1817,4496	TT,TC,CC		20.0442,10.5861,16.8411		63/338	126174164	2189,10809	2201	4298	6499	SO:0001819	synonymous_variant	28960	exon1			CATTTTCCTACAC	AF077201	CCDS8473.1	11q24	2008-02-05			ENSG00000110063	ENSG00000110063			29812	protein-coding gene	gene with protein product		610534				12198172, 14523240	Standard	NM_014026		Approved	HSPC015, HINT-5, HSL1	uc001qdp.3	Q96C86	OTTHUMG00000165829	ENST00000263579.4:c.189C>T	11.37:g.126174164C>T		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	80	63	0.7875	NM_014026	Q8NHL8|Q9Y2S5	Silent	SNP	ENST00000263579.4	37	CCDS8473.1																																																																																			C|0.772;T|0.228	0.228	strong		0.547	DCPS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386455.1	NM_014026	
C4orf17	84103	hgsc.bcm.edu	37	4	100443800	100443800	+	Missense_Mutation	SNP	G	G	A	rs17029087	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:100443800G>A	ENST00000326581.4	+	3	633	c.271G>A	c.(271-273)Gag>Aag	p.E91K	C4orf17_ENST00000514652.1_Missense_Mutation_p.E91K|C4orf17_ENST00000503257.1_3'UTR	NM_032149.2	NP_115525.2	Q53FE4	CD017_HUMAN	chromosome 4 open reading frame 17	91			E -> K (in dbSNP:rs17029087). {ECO:0000269|PubMed:11230166, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.2}.							central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(9)|prostate(1)|urinary_tract(3)	18				OV - Ovarian serous cystadenocarcinoma(123;2.08e-08)		TGCAGTCCAGGAGAGCCCTGT	0.498													G|||	1032	0.20607	0.1838	0.1873	5008	,	,		16608	0.1161		0.2744	False		,,,				2504	0.272				p.E91K		Atlas-SNP	.											.	C4orf17	42	.	0			c.G271A						PASS	.	G	LYS/GLU	885,3521	342.0+/-307.0	101,683,1419	92.0	88.0	89.0		271	0.5	0.0	4	dbSNP_123	89	2356,6244	392.0+/-343.8	328,1700,2272	yes	missense	C4orf17	NM_032149.2	56	429,2383,3691	AA,AG,GG		27.3953,20.0862,24.9193	benign	91/360	100443800	3241,9765	2203	4300	6503	SO:0001583	missense	84103	exon3			GTCCAGGAGAGCC	AL136838	CCDS3649.1	4q23	2008-02-05			ENSG00000138813	ENSG00000138813			25274	protein-coding gene	gene with protein product						11230166	Standard	NM_032149		Approved	DKFZP434G072	uc003huw.3	Q53FE4	OTTHUMG00000131027	ENST00000326581.4:c.271G>A	4.37:g.100443800G>A	ENSP00000322582:p.Glu91Lys	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	92	40	0.434783	NM_032149	Q6FI84|Q6IS77|Q8NA78|Q9H0D9	Missense_Mutation	SNP	ENST00000326581.4	37	CCDS3649.1	399	0.18269230769230768	64	0.13008130081300814	70	0.19337016574585636	66	0.11538461538461539	199	0.262532981530343	G	11.57	1.677464	0.29783	0.200862	0.273953	ENSG00000138813	ENST00000326581;ENST00000514652	T;T	0.17854	2.25;2.25	4.41	0.478	0.16789	.	2.099710	0.01389	N	0.013186	T	0.00012	0.0000	L	0.59436	1.845	0.80722	P	0.0	B	0.20164	0.042	B	0.26310	0.068	T	0.37888	-0.9686	9	0.27785	T	0.31	0.2327	7.6519	0.28352	0.0955:0.4981:0.4064:0.0	rs17029087;rs52812387;rs17029087	91	Q53FE4	CD017_HUMAN	K	91	ENSP00000322582:E91K;ENSP00000427663:E91K	ENSP00000322582:E91K	E	+	1	0	C4orf17	100662823	0.001000	0.12720	0.000000	0.03702	0.000000	0.00434	0.370000	0.20433	0.048000	0.15891	-0.894000	0.02916	GAG	G|0.780;A|0.220	0.220	strong		0.498	C4orf17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253670.2	NM_032149	
THOC5	8563	hgsc.bcm.edu	37	22	29913272	29913272	+	Missense_Mutation	SNP	C	C	T	rs737976	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:29913272C>T	ENST00000490103.1	-	16	1695	c.1573G>A	c.(1573-1575)Gtt>Att	p.V525I	CTA-256D12.11_ENST00000411969.1_RNA|THOC5_ENST00000397871.1_Missense_Mutation_p.V525I|THOC5_ENST00000397872.1_Missense_Mutation_p.V525I|THOC5_ENST00000397873.2_Missense_Mutation_p.V525I	NM_003678.4	NP_003669.4	Q13769	THOC5_HUMAN	THO complex 5	525			V -> I (in dbSNP:rs737976). {ECO:0000269|PubMed:10231032, ECO:0000269|PubMed:15461802, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:8242058}.		blastocyst development (GO:0001824)|cell morphogenesis (GO:0000902)|monocyte differentiation (GO:0030224)|mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|negative regulation of DNA damage checkpoint (GO:2000002)|negative regulation of macrophage differentiation (GO:0045650)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|primitive hemopoiesis (GO:0060215)|regulation of mRNA export from nucleus (GO:0010793)|regulation of stem cell division (GO:2000035)|RNA splicing (GO:0008380)|stem cell division (GO:0017145)|viral mRNA export from host cell nucleus (GO:0046784)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|THO complex (GO:0000347)|THO complex part of transcription export complex (GO:0000445)|transcription export complex (GO:0000346)	mRNA binding (GO:0003729)			NS(1)|breast(4)|cervix(1)|endometrium(2)|large_intestine(4)|lung(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	21						TCATGGGCAACTGTCACCCAT	0.502													T|||	2232	0.445687	0.3298	0.379	5008	,	,		23280	0.7242		0.5129	False		,,,				2504	0.2935				p.V525I		Atlas-SNP	.											.	THOC5	58	.	0			c.G1573A						PASS	.	T	ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL	1556,2850	668.9+/-402.1	277,1002,924	132.0	107.0	116.0		1573,1573,1573,1573	-2.5	0.0	22	dbSNP_86	116	4320,4280	576.4+/-390.4	1046,2228,1026	yes	missense,missense,missense,missense	THOC5	NM_001002877.1,NM_001002878.1,NM_001002879.1,NM_003678.4	29,29,29,29	1323,3230,1950	TT,TC,CC		49.7674,35.3155,45.1791	benign,benign,benign,benign	525/684,525/684,525/684,525/684	29913272	5876,7130	2203	4300	6503	SO:0001583	missense	8563	exon17			GGGCAACTGTCAC	AB023200	CCDS13859.1	22q12	2013-02-11			ENSG00000100296	ENSG00000100296		"""THO complex subunits"""	19074	protein-coding gene	gene with protein product	"""functional spliceosome-associated protein 79"""	612733	"""chromosome 22 open reading frame 19"""	C22orf19		11979277, 8242058, 10231032, 19015024, 18373705	Standard	NM_003678		Approved	PK1.3, KIAA0983, Fmip, fSAP79	uc003afs.3	Q13769	OTTHUMG00000151291	ENST00000490103.1:c.1573G>A	22.37:g.29913272C>T	ENSP00000420306:p.Val525Ile	Somatic	205	0	0		WXS	Illumina HiSeq	Phase_I	169	77	0.455621	NM_001002878	O60839|Q9UPZ5	Missense_Mutation	SNP	ENST00000490103.1	37	CCDS13859.1	1135	0.5196886446886447	180	0.36585365853658536	147	0.40607734806629836	417	0.7290209790209791	391	0.5158311345646438	T	0.016	-1.518513	0.00967	0.353155	0.502326	ENSG00000100296	ENST00000490103;ENST00000397872;ENST00000397871;ENST00000397873	T;T;T;T	0.23552	1.9;1.9;1.9;1.9	5.35	-2.49	0.06403	.	0.472153	0.26338	N	0.024946	T	0.00012	0.0000	N	0.02539	-0.55	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.27331	-1.0077	9	0.02654	T	1	-25.8597	7.0418	0.25025	0.0:0.1903:0.3011:0.5086	rs737976;rs1130637;rs3189712;rs11546950;rs17416425;rs17536969;rs17856090;rs52793971;rs60269391;rs737976	525	Q13769	THOC5_HUMAN	I	525	ENSP00000420306:V525I;ENSP00000380970:V525I;ENSP00000380969:V525I;ENSP00000380971:V525I	ENSP00000380969:V525I	V	-	1	0	THOC5	28243272	0.040000	0.19996	0.005000	0.12908	0.283000	0.27025	0.249000	0.18216	-1.032000	0.03304	-2.134000	0.00341	GTT	C|0.516;T|0.484	0.484	strong		0.502	THOC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322097.1	NM_003678	
LMO2	4005	hgsc.bcm.edu	37	11	33881016	33881016	+	Silent	SNP	T	T	C	rs3740617	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:33881016T>C	ENST00000395833.3	-	3	792	c.363A>G	c.(361-363)aaA>aaG	p.K121K	LMO2_ENST00000257818.2_Silent_p.K190K	NM_001142315.1|NM_001142316.1	NP_001135787.1|NP_001135788.1	P25791	RBTN2_HUMAN	LIM domain only 2 (rhombotin-like 1)	121	LIM zinc-binding 2. {ECO:0000255|PROSITE- ProRule:PRU00125}.				cellular response to thyroid hormone stimulus (GO:0097067)|embryonic hemopoiesis (GO:0035162)|mRNA transcription from RNA polymerase II promoter (GO:0042789)|multicellular organismal development (GO:0007275)|negative regulation of erythrocyte differentiation (GO:0045647)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	bHLH transcription factor binding (GO:0043425)|chromatin binding (GO:0003682)|cofactor binding (GO:0048037)|E-box binding (GO:0070888)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|zinc ion binding (GO:0008270)	p.K121K(1)		NS(1)|endometrium(2)|large_intestine(1)|lung(7)|prostate(1)|stomach(1)|urinary_tract(1)	14						AGGCGGCGCATTTGAAACATT	0.488			T	TRD@	T-ALL								T|||	2817	0.5625	0.4682	0.7291	5008	,	,		20105	0.4921		0.5954	False		,,,				2504	0.6104				p.K190K		Atlas-SNP	.		Dom	yes		11	11p13	4005	LIM domain only 2 (rhombotin-like 1) (RBTN2)		L	LMO2,NS,carcinoma,-2,2	LMO2	21	2	1	Substitution - coding silent(1)	stomach(1)	c.A570G						PASS	.	T	,,	2231,2173	591.8+/-387.6	554,1123,525	137.0	115.0	123.0		363,363,570	-0.1	1.0	11	dbSNP_107	123	5207,3389	641.0+/-399.6	1599,2009,690	no	coding-synonymous,coding-synonymous,coding-synonymous	LMO2	NM_001142315.1,NM_001142316.1,NM_005574.3	,,	2153,3132,1215	CC,CT,TT		39.4253,49.3415,42.7846	,,	121/159,121/159,190/228	33881016	7438,5562	2202	4298	6500	SO:0001819	synonymous_variant	4005	exon6			GGCGCATTTGAAA	X61118	CCDS7888.2, CCDS44567.1	11p13	2008-07-18			ENSG00000135363	ENSG00000135363			6642	protein-coding gene	gene with protein product	"""T-cell translocation gene 2"", ""rhombotin-like 1"""	180385		RBTNL1		2034676	Standard	NM_005574		Approved	TTG2, RHOM2, RBTN2	uc010rem.2	P25791	OTTHUMG00000157176	ENST00000395833.3:c.363A>G	11.37:g.33881016T>C		Somatic	196	1	0.00510204		WXS	Illumina HiSeq	Phase_I	145	145	1	NM_005574	Q9HD58	Silent	SNP	ENST00000395833.3	37	CCDS44567.1																																																																																			A|0.005;C|0.553	0.553	strong		0.488	LMO2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347777.1	NM_005574	
SLC4A5	57835	hgsc.bcm.edu	37	2	74460685	74460685	+	Silent	SNP	C	C	T	rs3796109	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:74460685C>T	ENST00000377634.4	-	23	2838	c.2439G>A	c.(2437-2439)acG>acA	p.T813T	SLC4A5_ENST00000357822.5_Silent_p.T813T|SLC4A5_ENST00000346834.4_Silent_p.T813T|SLC4A5_ENST00000359484.4_Silent_p.T711T|SLC4A5_ENST00000358683.4_Silent_p.T711T|SLC4A5_ENST00000483195.1_5'UTR|SLC4A5_ENST00000394019.2_Silent_p.T813T|SLC4A5_ENST00000423644.1_Silent_p.T813T|RP11-287D1.3_ENST00000451608.2_3'UTR|SLC4A5_ENST00000377632.1_Silent_p.T813T					solute carrier family 4 (sodium bicarbonate cotransporter), member 5											breast(5)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(12)|lung(13)|ovary(5)|pancreas(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	48						GGTCAGGCCGCGTTGGCTGAG	0.627													C|||	543	0.108427	0.1589	0.2262	5008	,	,		18172	0.1071		0.0268	False		,,,				2504	0.0419				p.T813T		Atlas-SNP	.											.	SLC4A5	215	.	0			c.G2439A						PASS	.	C	,	592,3814	254.0+/-259.7	40,512,1651	26.0	28.0	27.0		2439,2439	-8.4	0.8	2	dbSNP_107	27	261,8339	100.1+/-161.6	4,253,4043	no	coding-synonymous,coding-synonymous	SLC4A5	NM_021196.3,NM_133478.2	,	44,765,5694	TT,TC,CC		3.0349,13.4362,6.5585	,	813/1138,813/1122	74460685	853,12153	2203	4300	6503	SO:0001819	synonymous_variant	57835	exon18			AGGCCGCGTTGGC	AF243499	CCDS1936.1, CCDS1937.1	2p13.1	2013-07-19	2013-07-19		ENSG00000188687	ENSG00000188687		"""Solute carriers"""	18168	protein-coding gene	gene with protein product		606757	"""solute carrier family 4, sodium bicarbonate cotransporter, member 5"""			10978526, 11087115	Standard	NM_133478		Approved	NBC4	uc002sko.1	Q9BY07	OTTHUMG00000090263	ENST00000377634.4:c.2439G>A	2.37:g.74460685C>T		Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	28	12	0.428571	NM_021196		Silent	SNP	ENST00000377634.4	37	CCDS1936.1																																																																																			C|0.917;T|0.083	0.083	strong		0.627	SLC4A5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206583.3		
NCOA6	23054	hgsc.bcm.edu	37	20	33328372	33328372	+	Silent	SNP	C	C	T	rs141863711		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:33328372C>T	ENST00000374796.2	-	12	8258	c.5688G>A	c.(5686-5688)ccG>ccA	p.P1896P	NCOA6_ENST00000359003.2_Silent_p.P1896P			Q14686	NCOA6_HUMAN	nuclear receptor coactivator 6	1896	EP300/CRSP3-binding region.				brain development (GO:0007420)|cellular lipid metabolic process (GO:0044255)|cellular response to DNA damage stimulus (GO:0006974)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA-templated transcription, initiation (GO:0006352)|glucocorticoid receptor signaling pathway (GO:0042921)|heart development (GO:0007507)|intracellular estrogen receptor signaling pathway (GO:0030520)|labyrinthine layer blood vessel development (GO:0060716)|myeloid cell differentiation (GO:0030099)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|response to hormone (GO:0009725)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)	histone methyltransferase complex (GO:0035097)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|retinoid X receptor binding (GO:0046965)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)			NS(2)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(9)|kidney(8)|large_intestine(16)|lung(37)|ovary(4)|prostate(5)|skin(13)|upper_aerodigestive_tract(2)|urinary_tract(1)	107						AGGCAGTGCCCGGGCCCACAG	0.602																																					p.P1896P		Atlas-SNP	.											.	NCOA6	219	.	0			c.G5688A						PASS	.	C	,	1,4405	2.1+/-5.4	0,1,2202	53.0	53.0	53.0		,5688	-11.3	0.0	20	dbSNP_134	53	0,8600		0,0,4300	no	intron,coding-synonymous	NCOA6	NM_001242539.1,NM_014071.3	,	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	,	,1896/2064	33328372	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	23054	exon11			AGTGCCCGGGCCC	AF128458	CCDS13241.1, CCDS74720.1	20q11	2008-08-01			ENSG00000198646	ENSG00000198646			15936	protein-coding gene	gene with protein product	"""nuclear receptor coactivator RAP250"", ""activating signal cointegrator-2"", ""peroxisome proliferator-activated receptor interacting protein"""	605299				8724849, 8263591	Standard	NM_014071		Approved	KIAA0181, RAP250, ASC2, AIB3, PRIP, TRBP, NRC	uc002xaw.3	Q14686	OTTHUMG00000032311	ENST00000374796.2:c.5688G>A	20.37:g.33328372C>T		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	45	16	0.355556	NM_014071	A6NLF1|B2RMN5|E1P5P7|Q9NTZ9|Q9UH74|Q9UK86	Silent	SNP	ENST00000374796.2	37	CCDS13241.1																																																																																			C|1.000;T|0.000	0.000	weak		0.602	NCOA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078811.2	NM_014071	
ZNF217	7764	hgsc.bcm.edu	37	20	52192417	52192417	+	Silent	SNP	C	C	T	rs45439395	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:52192417C>T	ENST00000371471.2	-	4	3311	c.2886G>A	c.(2884-2886)ccG>ccA	p.P962P	ZNF217_ENST00000302342.3_Silent_p.P962P|RP4-724E16.2_ENST00000424252.1_RNA			O75362	ZN217_HUMAN	zinc finger protein 217	962					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)			GCGCCTGCGACGGATACACAC	0.562													C|||	11	0.00219649	0.0	0.0014	5008	,	,		20692	0.0		0.0099	False		,,,				2504	0.0				p.P962P		Atlas-SNP	.											.	ZNF217	227	.	0			c.G2886A						PASS	.	C		2,4404	4.2+/-10.8	0,2,2201	141.0	113.0	122.0		2886	-7.8	0.0	20	dbSNP_127	122	63,8537	39.8+/-96.3	0,63,4237	no	coding-synonymous	ZNF217	NM_006526.2		0,65,6438	TT,TC,CC		0.7326,0.0454,0.4998		962/1049	52192417	65,12941	2203	4300	6503	SO:0001819	synonymous_variant	7764	exon3			CTGCGACGGATAC	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.2886G>A	20.37:g.52192417C>T		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	99	55	0.555556	NM_006526	E1P5Y6|Q14DB8	Silent	SNP	ENST00000371471.2	37	CCDS13443.1																																																																																			C|0.997;T|0.003	0.003	strong		0.562	ZNF217-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079757.2	NM_006526	
WDR33	55339	hgsc.bcm.edu	37	2	128522207	128522207	+	Intron	SNP	C	C	T	rs17534123	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:128522207C>T	ENST00000322313.4	-	6	785				WDR33_ENST00000393006.1_Intron|WDR33_ENST00000409658.3_Missense_Mutation_p.R274Q	NM_018383.4	NP_060853.3	Q9C0J8	WDR33_HUMAN	WD repeat domain 33						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)		AGGCTGATACCGGGACAACAC	0.368													C|||	288	0.057508	0.0575	0.0533	5008	,	,		21216	0.0427		0.0716	False		,,,				2504	0.0613				p.R274Q		Atlas-SNP	.											.	WDR33	136	.	0			c.G821A						PASS	.	C	GLN/ARG,,	150,2336		6,138,1099	39.0	42.0	41.0		821,,	1.3	0.9	2	dbSNP_123	41	372,4154		16,340,1907	yes	missense,intron,intron	WDR33	NM_001006622.2,NM_001006623.2,NM_018383.4	43,,	22,478,3006	TT,TC,CC		8.2192,6.0338,7.4444	,,	274/327,,	128522207	522,6490	1243	2263	3506	SO:0001627	intron_variant	55339	exon6			TGATACCGGGACA		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.626+194G>A	2.37:g.128522207C>T		Somatic	383	0	0		WXS	Illumina HiSeq	Phase_I	294	145	0.493197	NM_001006622	Q05DP8|Q53FG9|Q587J1|Q69YF7|Q6NUQ0|Q9NUL1	Missense_Mutation	SNP	ENST00000322313.4	37	CCDS2150.1	115	0.052655677655677656	30	0.06097560975609756	16	0.04419889502762431	13	0.022727272727272728	56	0.07387862796833773	C	4.696	0.129357	0.08981	0.060338	0.082192	ENSG00000136709	ENST00000409658	T	0.38722	1.12	5.7	1.26	0.21427	.	.	.	.	.	T	0.01061	0.0035	.	.	.	0.48696	P	3.0200000000002447E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.15521	-1.0434	7	0.21014	T	0.42	.	3.1906	0.06615	0.0:0.3346:0.2213:0.4441	rs17534123;rs17534123	274	Q9C0J8-2	.	Q	274	ENSP00000387186:R274Q	ENSP00000387186:R274Q	R	-	2	0	WDR33	128238677	0.980000	0.34600	0.927000	0.36925	0.992000	0.81027	0.314000	0.19432	0.325000	0.23359	-0.140000	0.14226	CGG	C|0.943;T|0.057	0.057	strong		0.368	WDR33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331141.2	NM_018383	
DPYSL4	10570	hgsc.bcm.edu	37	10	134017388	134017388	+	Silent	SNP	C	C	G	rs1052556	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:134017388C>G	ENST00000338492.4	+	13	1748	c.1584C>G	c.(1582-1584)gtC>gtG	p.V528V	DPYSL4_ENST00000368629.1_Silent_p.V368V|DPYSL4_ENST00000368627.1_Silent_p.V368V	NM_006426.2	NP_006417.2	O14531	DPYL4_HUMAN	dihydropyrimidinase-like 4	528					axon guidance (GO:0007411)|nervous system development (GO:0007399)|pyrimidine nucleobase catabolic process (GO:0006208)	cytosol (GO:0005829)	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides (GO:0016812)			NS(1)|central_nervous_system(2)|endometrium(5)|kidney(1)|large_intestine(4)|lung(12)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	32		all_cancers(35;4.33e-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;7.21e-05)|Epithelial(32;8.01e-05)|all cancers(32;9.29e-05)|BRCA - Breast invasive adenocarcinoma(275;0.206)		AGATCTCCGTCCCTCCTGTGC	0.682													C|||	761	0.151957	0.0756	0.1153	5008	,	,		16346	0.372		0.1262	False		,,,				2504	0.0808				p.V528V		Atlas-SNP	.											.	DPYSL4	91	.	0			c.C1584G						PASS	.	C		434,3972	208.8+/-229.8	22,390,1791	98.0	94.0	95.0		1584	-0.6	0.3	10	dbSNP_86	95	999,7601	215.2+/-254.6	64,871,3365	no	coding-synonymous	DPYSL4	NM_006426.2		86,1261,5156	GG,GC,CC		11.6163,9.8502,11.018		528/573	134017388	1433,11573	2203	4300	6503	SO:0001819	synonymous_variant	10570	exon13			CTCCGTCCCTCCT	AB006713	CCDS7665.1	10q25.2-q26	2008-05-14			ENSG00000151640	ENSG00000151640			3016	protein-coding gene	gene with protein product		608407				8973361, 9652388	Standard	NM_006426		Approved	ULIP4, DRP-4	uc009ybb.3	O14531	OTTHUMG00000019283	ENST00000338492.4:c.1584C>G	10.37:g.134017388C>G		Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	169	85	0.502959	NM_006426	B2RMQ1|D3DRG5|O00240|Q5T0Q7	Silent	SNP	ENST00000338492.4	37	CCDS7665.1																																																																																			C|0.865;G|0.135	0.135	strong		0.682	DPYSL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051050.2		
Unknown	0	hgsc.bcm.edu	37	7	63680401	63680401	+	IGR	SNP	C	C	T	rs10258764	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:63680401C>T								GUSBP6 (69302 upstream) : ZNF679 (8450 downstream)																							GAGAGAAACCCTACACATGTG	0.418													.|||	469	0.0936502	0.1672	0.0591	5008	,	,		21570	0.122		0.0189	False		,,,				2504	0.0665				p.P324P		Atlas-SNP	.											.	.	.	.	0			c.C972T						PASS	.	C		179,1205		12,155,525	28.0	31.0	30.0		972	-1.6	0.5	7	dbSNP_119	30	84,3098		2,80,1509	no	coding-synonymous	ZNF735	NM_001159524.1		14,235,2034	TT,TC,CC		2.6398,12.9335,5.76		324/413	63680401	263,4303	692	1591	2283	SO:0001628	intergenic_variant	730291	exon4			GAAACCCTACACA																													7.37:g.63680401C>T		Somatic	20	0	0		WXS	Illumina HiSeq	Phase_I	15	10	0.666667	NM_001159524		Silent	SNP		37																																																																																				C|0.910;T|0.090	0.090	strong	0	0.418								
PLA2R1	22925	hgsc.bcm.edu	37	2	160885418	160885418	+	Missense_Mutation	SNP	G	G	C	rs35771982	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:160885418G>C	ENST00000283243.7	-	5	1104	c.898C>G	c.(898-900)Cac>Gac	p.H300D	PLA2R1_ENST00000392771.1_Missense_Mutation_p.H300D	NM_001195641.1|NM_007366.4	NP_001182570.1|NP_031392.3	Q13018	PLA2R_HUMAN	phospholipase A2 receptor 1, 180kDa	300	C-type lectin 1. {ECO:0000255|PROSITE- ProRule:PRU00040}.		H -> D (in dbSNP:rs35771982). {ECO:0000269|PubMed:7721806}.		cytokine production (GO:0001816)|negative regulation of arachidonic acid secretion (GO:1900139)|negative regulation of phospholipase A2 activity (GO:1900138)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of arachidonic acid secretion (GO:0090238)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|reactive oxygen species metabolic process (GO:0072593)|receptor-mediated endocytosis (GO:0006898)|replicative senescence (GO:0090399)	cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	carbohydrate binding (GO:0030246)|phospholipase binding (GO:0043274)|receptor activity (GO:0004872)		PLA2R1/RBMS1(2)	central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(17)|lung(20)|ovary(1)|pancreas(1)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)	60						CAGCCAGCGTGTTCATCCAGC	0.478													G|||	1257	0.250998	0.0371	0.268	5008	,	,		19325	0.3532		0.4702	False		,,,				2504	0.1973				p.H300D		Atlas-SNP	.											.	PLA2R1	153	.	0			c.C898G						PASS	.	G	ASP/HIS,ASP/HIS,ASP/HIS	442,3964	213.1+/-232.8	23,396,1784	123.0	96.0	105.0		898,898,898	-0.9	0.0	2	dbSNP_126	105	4200,4400	569.8+/-389.2	1057,2086,1157	yes	missense,missense,missense	PLA2R1	NM_001007267.2,NM_001195641.1,NM_007366.4	81,81,81	1080,2482,2941	CC,CG,GG		48.8372,10.0318,35.6912	benign,benign,benign	300/1325,300/1462,300/1464	160885418	4642,8364	2203	4300	6503	SO:0001583	missense	22925	exon5			CAGCGTGTTCATC	U17033	CCDS33309.1, CCDS42767.1	2q23-q24	2011-08-30	2002-08-29		ENSG00000153246	ENSG00000153246		"""C-type lectin domain containing"""	9042	protein-coding gene	gene with protein product		604939	"""phospholipase A2 receptor 1, 180kD"""			7721806, 7925459	Standard	NM_007366		Approved	PLA2G1R, PLA2IR, PLA2-R, CLEC13C	uc002ube.2	Q13018	OTTHUMG00000154087	ENST00000283243.7:c.898C>G	2.37:g.160885418G>C	ENSP00000283243:p.His300Asp	Somatic	277	0	0		WXS	Illumina HiSeq	Phase_I	244	116	0.47541	NM_001195641	B2RTU9|D3DPB1|Q13019|Q15095|Q53R45|Q53RR7	Missense_Mutation	SNP	ENST00000283243.7	37	CCDS33309.1	697	0.3191391941391941	23	0.046747967479674794	109	0.3011049723756906	201	0.3513986013986014	364	0.48021108179419525	G	0.014	-1.576005	0.00887	0.100318	0.488372	ENSG00000153246	ENST00000283243;ENST00000392771	T;T	0.15017	2.46;2.46	5.83	-0.954	0.10359	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	0.824431	0.11259	N	0.582814	T	0.00012	0.0000	N	0.02247	-0.625	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.44605	-0.9317	9	0.11794	T	0.64	.	5.4776	0.16704	0.0:0.3217:0.2728:0.4055	rs35771982;rs60910735;rs62175486	300;300;300	B7ZML4;Q13018-2;Q13018	.;.;PLA2R_HUMAN	D	300	ENSP00000283243:H300D;ENSP00000376524:H300D	ENSP00000283243:H300D	H	-	1	0	PLA2R1	160593664	0.000000	0.05858	0.000000	0.03702	0.029000	0.11900	-0.203000	0.09438	-0.102000	0.12197	-1.036000	0.02392	CAC	G|0.655;C|0.345	0.345	strong		0.478	PLA2R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333820.1		
OR5L1	219437	hgsc.bcm.edu	37	11	55579801	55579801	+	Missense_Mutation	SNP	T	T	C	rs12790505	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:55579801T>C	ENST00000333973.2	+	1	948	c.859T>C	c.(859-861)Tct>Cct	p.S287P		NM_001004738.1	NP_001004738.1	Q8NGL2	OR5L1_HUMAN	olfactory receptor, family 5, subfamily L, member 1	287			S -> P (in dbSNP:rs12790505).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.S287P(1)		NS(1)|breast(2)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(4)|liver(4)|lung(36)|ovary(2)|pancreas(1)|prostate(5)|skin(9)|stomach(4)|upper_aerodigestive_tract(3)	78		all_epithelial(135;0.208)				TATGCTGAACTCTGTGATCTA	0.433													N|||	525	0.104832	0.1884	0.0461	5008	,	,		15985	0.0813		0.0924	False		,,,				2504	0.0706				p.S287P		Atlas-SNP	.											OR5L1,NS,carcinoma,0,1	OR5L1	145	1	1	Substitution - Missense(1)	stomach(1)	c.T859C						PASS	.	C	PRO/SER	669,3731		63,543,1594	56.0	54.0	55.0		859	4.1	0.9	11	dbSNP_121	55	726,7866		32,662,3602	yes	missense	OR5L1	NM_001004738.1	74	95,1205,5196	CC,CT,TT		8.4497,15.2045,10.7374	benign	287/312	55579801	1395,11597	2200	4296	6496	SO:0001583	missense	219437	exon1			CTGAACTCTGTGA	AB065780	CCDS31509.1	11q11	2012-08-09			ENSG00000186117	ENSG00000186117		"""GPCR / Class A : Olfactory receptors"""	8350	protein-coding gene	gene with protein product							Standard	NM_001004738		Approved	OST262	uc001nhw.1	Q8NGL2	OTTHUMG00000166810	ENST00000333973.2:c.859T>C	11.37:g.55579801T>C	ENSP00000335529:p.Ser287Pro	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	98	75	0.765306	NM_001004738	B2RNK6|Q6IFD0	Missense_Mutation	SNP	ENST00000333973.2	37	CCDS31509.1	213	0.09752747252747253	92	0.18699186991869918	21	0.058011049723756904	35	0.06118881118881119	65	0.08575197889182058	N	0.453	-0.892792	0.02491	0.152045	0.084497	ENSG00000186117	ENST00000333973	T	0.14516	2.5	4.12	4.12	0.48240	GPCR, rhodopsin-like superfamily (1);	0.000000	0.52532	N	0.000079	T	0.00012	0.0000	N	0.00001	-3.64	0.49213	P	2.4000000000001798E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.37663	-0.9696	9	0.02654	T	1	-51.3685	11.1525	0.48466	0.0:0.9065:0.0:0.0935	rs12790505;rs52821601;rs12790505	287	Q8NGL2	OR5L1_HUMAN	P	287	ENSP00000335529:S287P	ENSP00000335529:S287P	S	+	1	0	OR5L1	55336377	0.997000	0.39634	0.884000	0.34674	0.299000	0.27559	3.578000	0.53892	0.738000	0.32606	-0.984000	0.02558	TCT	T|0.888;C|0.112	0.112	strong		0.433	OR5L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391514.1	NM_001004738	
MC1R	4157	hgsc.bcm.edu	37	16	89985950	89985950	+	Missense_Mutation	SNP	C	C	T	rs34158934	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:89985950C>T	ENST00000555147.1	+	1	1664	c.284C>T	c.(283-285)aCg>aTg	p.T95M	TUBB3_ENST00000556922.1_Missense_Mutation_p.T95M|RP11-566K11.7_ENST00000570217.1_RNA|TUBB3_ENST00000554444.1_5'Flank|MC1R_ENST00000555427.1_Missense_Mutation_p.T95M|RP11-566K11.4_ENST00000554623.1_RNA	NM_002386.3	NP_002377.4	Q01726	MSHR_HUMAN	melanocortin 1 receptor (alpha melanocyte stimulating hormone receptor)	95			T -> M (in dbSNP:rs34158934).		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)		GTGCTGGAGACGGCCGTCATC	0.627									Melanoma, Familial Clustering of				C|||	4	0.000798722	0.0023	0.0014	5008	,	,		19710	0.0		0.0	False		,,,				2504	0.0				p.T95M		Atlas-SNP	.											.	MC1R	20	.	0			c.C284T	GRCh37	CM062826	MC1R	M	rs34158934	PASS	.	C	MET/THR	3,4379		0,3,2188	46.0	56.0	52.0		284	3.9	0.8	16	dbSNP_126	52	5,8569		0,5,4282	yes	missense	MC1R	NM_002386.3	81	0,8,6470	TT,TC,CC		0.0583,0.0685,0.0617		95/318	89985950	8,12948	2191	4287	6478	SO:0001583	missense	4157	exon1	Familial Cancer Database		TGGAGACGGCCGT		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.284C>T	16.37:g.89985950C>T	ENSP00000451605:p.Thr95Met	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	115	67	0.582609	NM_002386	Q66K38|Q6UR93|Q8WWX6|Q8WWX7|Q96I33|Q96RU4|Q9UBF7|Q9UN58|Q9UN59|Q9UN60|Q9UN61|Q9UN62	Missense_Mutation	SNP	ENST00000555147.1	37	CCDS56011.1	.	.	.	.	.	.	.	.	.	.	C	15.03	2.711952	0.48517	6.85E-4	5.83E-4	ENSG00000258947;ENSG00000258947;ENSG00000258839	ENST00000555427;ENST00000556922;ENST00000555147	T;T;T	0.01505	4.82;4.82;4.82	4.86	3.91	0.45181	GPCR, rhodopsin-like superfamily (1);	0.000000	0.38959	U	0.001519	T	0.02727	0.0082	L	0.41824	1.3	0.45914	D	0.998756	P	0.47034	0.889	P	0.46796	0.527	T	0.64368	-0.6424	9	.	.	.	.	10.5142	0.44879	0.0:0.836:0.0:0.164	rs34158934	95	Q01726	MSHR_HUMAN	M	95	ENSP00000451760:T95M;ENSP00000451560:T95M;ENSP00000451605:T95M	.	T	+	2	0	MC1R;RP11-566K11.2	88513451	0.902000	0.30710	0.785000	0.31869	0.215000	0.24574	1.867000	0.39499	1.057000	0.40506	0.455000	0.32223	ACG	C|0.995;T|0.005	0.005	strong		0.627	MC1R-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412014.1	NM_002386	
PITPNM3	83394	hgsc.bcm.edu	37	17	6406883	6406883	+	Missense_Mutation	SNP	C	C	T	rs3809835	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:6406883C>T	ENST00000262483.8	-	4	325	c.238G>A	c.(238-240)Gcg>Acg	p.A80T	PITPNM3_ENST00000421306.3_Missense_Mutation_p.A44T	NM_031220.3	NP_112497.2	Q9BZ71	PITM3_HUMAN	PITPNM family member 3	80			A -> T (in dbSNP:rs3809835). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.5}.		phosphatidylinositol metabolic process (GO:0046488)|phospholipid transport (GO:0015914)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)	calcium ion binding (GO:0005509)|lipid binding (GO:0008289)|phosphatidylinositol transporter activity (GO:0008526)|receptor tyrosine kinase binding (GO:0030971)			autonomic_ganglia(1)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(9)|lung(10)|ovary(3)|prostate(3)|skin(2)	36				Colorectal(2;0.000372)|READ - Rectum adenocarcinoma(2;0.0276)|LUAD - Lung adenocarcinoma(2;0.0836)|COAD - Colon adenocarcinoma(228;0.185)		GTGCACGGCGCGGTCCCTTCT	0.562													C|||	1370	0.273562	0.2927	0.1988	5008	,	,		21036	0.252		0.3618	False		,,,				2504	0.2321				p.A80T		Atlas-SNP	.											.	PITPNM3	91	.	0			c.G238A						PASS	.	C	THR/ALA,THR/ALA	1224,3182	425.7+/-340.9	173,878,1152	77.0	61.0	66.0		130,238	-1.5	0.0	17	dbSNP_107	66	2890,5710	452.5+/-363.0	492,1906,1902	yes	missense,missense	PITPNM3	NM_001165966.1,NM_031220.3	58,58	665,2784,3054	TT,TC,CC		33.6047,27.7803,31.6316	benign,benign	44/939,80/975	6406883	4114,8892	2203	4300	6503	SO:0001583	missense	83394	exon4			ACGGCGCGGTCCC	AF334586	CCDS11076.1, CCDS54080.1	17p13	2013-07-18	2013-07-18	2013-07-18	ENSG00000091622	ENSG00000091622		"""GPCR / Class A : Chemokine receptors : Atypical"""	21043	protein-coding gene	gene with protein product	"""atypical chemokine receptor 6"""	608921	"""cone rod dystrophy 5"""	CORD5		10022914	Standard	NM_031220		Approved	NIR1, RDGBA3, ACKR6	uc002gdd.4	Q9BZ71	OTTHUMG00000102039	ENST00000262483.8:c.238G>A	17.37:g.6406883C>T	ENSP00000262483:p.Ala80Thr	Somatic	19	0	0		WXS	Illumina HiSeq	Phase_I	25	10	0.4	NM_031220	A1A5D0|F8WEW5|Q59GH9|Q9NPQ4	Missense_Mutation	SNP	ENST00000262483.8	37	CCDS11076.1	626	0.2866300366300366	128	0.2601626016260163	80	0.22099447513812154	147	0.256993006993007	271	0.3575197889182058	C	9.413	1.080943	0.20309	0.277803	0.336047	ENSG00000091622	ENST00000262483;ENST00000421306	T;T	0.41400	2.1;1.0	3.83	-1.55	0.08558	.	1.013940	0.07908	N	0.973856	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B;B	0.09022	0.001;0.002	B;B	0.08055	0.003;0.0	T	0.42732	-0.9434	9	0.08837	T	0.75	-13.9644	7.2358	0.26070	0.0:0.457:0.0:0.543	rs3809835;rs17731176;rs57510419;rs3809835	44;80	F8WEW5;Q9BZ71	.;PITM3_HUMAN	T	80;44	ENSP00000262483:A80T;ENSP00000407882:A44T	ENSP00000262483:A80T	A	-	1	0	PITPNM3	6347607	0.000000	0.05858	0.000000	0.03702	0.127000	0.20565	-1.150000	0.03178	-0.243000	0.09653	-0.136000	0.14681	GCG	C|0.696;T|0.304	0.304	strong		0.562	PITPNM3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000219824.2	NM_031220	
PTBP1	5725	hgsc.bcm.edu	37	19	804396	804396	+	Silent	SNP	C	C	T	rs3180287	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:804396C>T	ENST00000349038.4	+	5	466	c.393C>T	c.(391-393)tcC>tcT	p.S131S	MIR4745_ENST00000577608.1_RNA|PTBP1_ENST00000350092.4_Intron|PTBP1_ENST00000356948.6_Silent_p.S131S|PTBP1_ENST00000394601.4_Silent_p.S131S	NM_031991.3	NP_114368.1	P26599	PTBP1_HUMAN	polypyrimidine tract binding protein 1	131	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				alternative mRNA splicing, via spliceosome (GO:0000380)|gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|negative regulation of muscle cell differentiation (GO:0051148)|negative regulation of RNA splicing (GO:0033119)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing (GO:0008380)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|poly-pyrimidine tract binding (GO:0008187)|pre-mRNA binding (GO:0036002)|RNA binding (GO:0003723)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|skin(2)|upper_aerodigestive_tract(4)	19		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;6.59e-06)|all_lung(49;9.97e-06)|Breast(49;0.000172)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		TCCAGTTCTCCAACCACAAGG	0.662													C|||	807	0.161142	0.1331	0.268	5008	,	,		14794	0.0228		0.1451	False		,,,				2504	0.2822				p.S131S		Atlas-SNP	.											.	PTBP1	43	.	0			c.C393T						PASS	.	C	,,,	571,3833	251.8+/-258.4	46,479,1677	65.0	56.0	59.0		393,393,393,	1.1	1.0	19	dbSNP_105	59	1274,7326	251.1+/-277.7	86,1102,3112	no	coding-synonymous,coding-synonymous,coding-synonymous,intron	PTBP1	NM_002819.4,NM_031990.3,NM_031991.3,NM_175847.2	,,,	132,1581,4789	TT,TC,CC		14.814,12.9655,14.1879	,,,	131/558,131/551,131/532,	804396	1845,11159	2202	4300	6502	SO:0001819	synonymous_variant	5725	exon5			GTTCTCCAACCAC	X60648	CCDS32859.1, CCDS42456.1, CCDS45892.1	19p13.3	2013-07-16	2002-01-25	2002-01-25	ENSG00000011304	ENSG00000011304		"""RNA binding motif (RRM) containing"""	9583	protein-coding gene	gene with protein product	"""heterogeneous nuclear ribonucleoprotein I"""	600693	"""polypyrimidine tract binding protein (heterogeneous nuclear ribonucleoprotein I)"""	PTB		1906036, 11024286	Standard	NM_002819		Approved	HNRPI, HNRNP-I, PTB2, PTB3, PTB-1, PTB4, pPTB	uc002lpp.2	P26599		ENST00000349038.4:c.393C>T	19.37:g.804396C>T		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	31	31	1	NM_031990	Q9BUQ0	Silent	SNP	ENST00000349038.4	37	CCDS32859.1																																																																																			C|0.862;G|0.000;T|0.138	0.138	strong		0.662	PTBP1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457605.1		
A2ML1	144568	hgsc.bcm.edu	37	12	8995756	8995756	+	Silent	SNP	A	A	G	rs7308106	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:8995756A>G	ENST00000299698.7	+	12	1455	c.1275A>G	c.(1273-1275)gtA>gtG	p.V425V	A2ML1_ENST00000539547.1_5'Flank	NM_001282424.1|NM_144670.4	NP_001269353.1|NP_653271			alpha-2-macroglobulin-like 1											NS(2)|breast(5)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|liver(2)|lung(36)|ovary(2)|skin(4)|stomach(1)|urinary_tract(1)	80						AAGACTTAGTATATAATCCGG	0.468													A|||	187	0.0373403	0.0045	0.0706	5008	,	,		-128	0.001		0.1103	False		,,,				2504	0.0204				p.V425V		Atlas-SNP	.											.	A2ML1	199	.	0			c.A1275G						PASS	.	A		66,3806		3,60,1873	84.0	85.0	84.0		1275	0.5	0.0	12	dbSNP_116	84	866,7408		38,790,3309	no	coding-synonymous	A2ML1	NM_144670.3		41,850,5182	GG,GA,AA		10.4665,1.7045,7.6733		425/1455	8995756	932,11214	1936	4137	6073	SO:0001819	synonymous_variant	144568	exon12			CTTAGTATATAAT	AK057908	CCDS8596.2, CCDS73439.1	12p13	2010-12-14	2005-09-01	2005-09-01	ENSG00000166535	ENSG00000166535			23336	protein-coding gene	gene with protein product		610627	"""C3 and PZP-like, alpha-2-macroglobulin domain containing 9"""	CPAMD9		16298998	Standard	NM_144670		Approved	FLJ25179	uc001quz.5	A8K2U0	OTTHUMG00000128499	ENST00000299698.7:c.1275A>G	12.37:g.8995756A>G		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	55	27	0.490909	NM_144670		Silent	SNP	ENST00000299698.7	37	CCDS8596.2																																																																																			A|0.939;G|0.061	0.061	strong		0.468	A2ML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250304.3	NM_144670	
CBR3	874	hgsc.bcm.edu	37	21	37507769	37507769	+	Silent	SNP	C	C	T	rs881712	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:37507769C>T	ENST00000290354.5	+	1	560	c.279C>T	c.(277-279)gtC>gtT	p.V93V	CBR3-AS1_ENST00000608641.1_RNA|CBR3-AS1_ENST00000608632.1_RNA|CBR3-AS1_ENST00000608622.1_RNA|CBR3-AS1_ENST00000608690.1_RNA|CBR3-AS1_ENST00000413862.1_RNA|CBR3-AS1_ENST00000453159.1_RNA	NM_001236.3	NP_001227.1	O75828	CBR3_HUMAN	carbonyl reductase 3	93			V -> I (in dbSNP:rs2835285).		cognition (GO:0050890)|phylloquinone catabolic process (GO:0042376)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|nucleus (GO:0005634)	3-keto sterol reductase activity (GO:0000253)|carbonyl reductase (NADPH) activity (GO:0004090)|NADPH binding (GO:0070402)			kidney(1)|large_intestine(1)|lung(1)	3					Doxorubicin(DB00997)	ACGCGGCCGTCGCCTTCAAGA	0.667													C|||	1545	0.308506	0.0673	0.4524	5008	,	,		14412	0.4276		0.4304	False		,,,				2504	0.2843				p.V93V		Atlas-SNP	.											.	CBR3	11	.	0			c.C279T						PASS	.	C		600,3806		50,500,1653	26.0	32.0	30.0		279	4.3	1.0	21	dbSNP_86	30	3809,4789		834,2141,1324	no	coding-synonymous	CBR3	NM_001236.3		884,2641,2977	TT,TC,CC		44.301,13.6178,33.905		93/278	37507769	4409,8595	2203	4299	6502	SO:0001819	synonymous_variant	874	exon1			GGCCGTCGCCTTC	AB004854	CCDS13642.1	21q22.2	2011-09-14			ENSG00000159231	ENSG00000159231	1.1.1.184	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"""	1549	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 21C, member 2"""	603608				9740676, 19027726	Standard	NM_001236		Approved	SDR21C2	uc002yve.3	O75828	OTTHUMG00000086617	ENST00000290354.5:c.279C>T	21.37:g.37507769C>T		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	132	70	0.530303	NM_001236	Q6FHP2	Silent	SNP	ENST00000290354.5	37	CCDS13642.1																																																																																			C|0.666;T|0.334	0.334	strong		0.667	CBR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194632.1		
LILRA4	23547	hgsc.bcm.edu	37	19	54848741	54848741	+	Silent	SNP	T	T	C	rs12985462	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:54848741T>C	ENST00000291759.4	-	5	938	c.882A>G	c.(880-882)agA>agG	p.R294R	AC008984.2_ENST00000507363.1_RNA	NM_012276.3	NP_036408.3	P59901	LIRA4_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 4	294	Ig-like C2-type 3.				immune system process (GO:0002376)	integral component of membrane (GO:0016021)				NS(2)|breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(5)|lung(13)|prostate(3)|skin(1)|upper_aerodigestive_tract(3)	32	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.0565)		CGCCGTAGCATCTGTACTGGC	0.692													T|||	872	0.174121	0.0204	0.2262	5008	,	,		13206	0.2143		0.1978	False		,,,				2504	0.2791				p.R294R		Atlas-SNP	.											LILRA4,NS,carcinoma,0,1	LILRA4	91	1	0			c.A882G						PASS	.	T		199,4207		5,189,2009	32.0	32.0	32.0		882	-0.7	0.0	19	dbSNP_121	32	1570,7030		144,1282,2874	no	coding-synonymous	LILRA4	NM_012276.3		149,1471,4883	CC,CT,TT		18.2558,4.5166,13.6014		294/500	54848741	1769,11237	2203	4300	6503	SO:0001819	synonymous_variant	23547	exon5			GTAGCATCTGTAC	AF041261	CCDS12890.1	19q13.4	2013-01-11			ENSG00000239961	ENSG00000239961		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	15503	protein-coding gene	gene with protein product		607517				10941842	Standard	NM_012276		Approved	ILT7, CD85g	uc002qfj.3	P59901	OTTHUMG00000065355	ENST00000291759.4:c.882A>G	19.37:g.54848741T>C		Somatic	205	0	0		WXS	Illumina HiSeq	Phase_I	164	77	0.469512	NM_012276	Q32MC4	Silent	SNP	ENST00000291759.4	37	CCDS12890.1																																																																																			T|0.855;C|0.145	0.145	strong		0.692	LILRA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140229.2	NM_012276	
RGS3	5998	hgsc.bcm.edu	37	9	116356776	116356776	+	Silent	SNP	C	C	T	rs61749208	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:116356776C>T	ENST00000374140.2	+	23	3356	c.3147C>T	c.(3145-3147)ccC>ccT	p.P1049P	RGS3_ENST00000350696.5_Silent_p.P1049P|RGS3_ENST00000394646.3_Silent_p.P442P|RGS3_ENST00000462143.1_Silent_p.P370P|RGS3_ENST00000342620.5_Silent_p.P19P|RGS3_ENST00000343817.5_Silent_p.P768P|RGS3_ENST00000462403.1_Silent_p.P162P|RGS3_ENST00000374134.3_Silent_p.P370P	NM_001282923.1|NM_144488.4	NP_001269852.1|NP_652759.3	P49796	RGS3_HUMAN	regulator of G-protein signaling 3	1049					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						GAGCCCCTCCCGCGGGCAAGG	0.587													C|||	194	0.038738	0.0197	0.0476	5008	,	,		16194	0.001		0.0934	False		,,,				2504	0.0409				p.P1049P		Atlas-SNP	.											.	RGS3	251	.	0			c.C3147T						PASS	.	C	,,,,	144,4262	98.5+/-137.1	5,134,2064	56.0	67.0	63.0		1110,2304,57,3147,486	-7.5	0.7	9	dbSNP_129	63	853,7747	192.7+/-238.6	37,779,3484	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	RGS3	NM_021106.3,NM_130795.2,NM_134427.1,NM_144488.4,NM_144489.2	,,,,	42,913,5548	TT,TC,CC		9.9186,3.2683,7.6657	,,,,	370/520,768/918,19/169,1049/1199,162/312	116356776	997,12009	2203	4300	6503	SO:0001819	synonymous_variant	5998	exon23			CCCTCCCGCGGGC	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.3147C>T	9.37:g.116356776C>T		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	151	81	0.536424	NM_144488	A6NHA0|A8K0V1|B3KUB2|Q5VXB8|Q5VXC1|Q5VZ05|Q5VZ06|Q6ZRM5|Q8IUQ1|Q8NC47|Q8NFN4|Q8NFN5|Q8NFN6|Q8TD59|Q8TD68|Q8WV02|Q8WXA0	Silent	SNP	ENST00000374140.2	37	CCDS43869.1																																																																																			C|0.933;G|0.000;T|0.067	0.067	strong		0.587	RGS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055561.3	NM_017790	
TPRX1	284355	hgsc.bcm.edu	37	19	48305602	48305602	+	Silent	SNP	C	C	T	rs147608412	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:48305602C>T	ENST00000322175.3	-	2	821	c.666G>A	c.(664-666)ccG>ccA	p.P222P	TPRX1_ENST00000535759.1_Silent_p.P319P|TPRX1_ENST00000543508.1_Silent_p.P212P	NM_198479.2	NP_940881.2	Q8N7U7	TPRX1_HUMAN	tetra-peptide repeat homeobox 1	222	Gly-rich.					nucleus (GO:0005634)	DNA binding (GO:0003677)	p.P228_I231delPGPI(1)		endometrium(5)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|prostate(2)|skin(1)	18		all_cancers(25;3.02e-09)|all_epithelial(76;7e-07)|all_lung(116;2.48e-06)|Lung NSC(112;5.15e-06)|Ovarian(192;0.0139)|all_neural(266;0.0146)|Breast(70;0.133)		OV - Ovarian serous cystadenocarcinoma(262;0.000241)|all cancers(93;0.00036)|Epithelial(262;0.0127)|GBM - Glioblastoma multiforme(486;0.048)		ggcctgggatcgggcctgggt	0.667													C|||	221	0.0441294	0.0295	0.0476	5008	,	,		12917	0.001		0.1103	False		,,,				2504	0.0378				p.P222P	Esophageal Squamous(123;175 2281 3051 32395)	Atlas-SNP	.											TPRX1,NS,carcinoma,-1,1	TPRX1	46	1	1	Deletion - In frame(1)	prostate(1)	c.G666A						PASS	.	T		79,3765		0,79,1843	12.0	10.0	10.0		666	-0.8	0.0	19	dbSNP_134	10	659,7001		14,631,3185	no	coding-synonymous	TPRX1	NM_198479.2		14,710,5028	TT,TC,CC		8.6031,2.0552,6.4152		222/412	48305602	738,10766	1922	3830	5752	SO:0001819	synonymous_variant	284355	exon2			TGGGATCGGGCCT		CCDS33066.1	19q13.33	2011-07-08			ENSG00000178928	ENSG00000178928		"""Homeoboxes / PRD class"""	32174	protein-coding gene	gene with protein product		611166					Standard	XM_005258788		Approved	FLJ40321	uc002php.2	Q8N7U7		ENST00000322175.3:c.666G>A	19.37:g.48305602C>T		Somatic	20	0	0		WXS	Illumina HiSeq	Phase_I	26	7	0.269231	NM_198479	A5D8Y3|B2RPL5	Silent	SNP	ENST00000322175.3	37	CCDS33066.1																																																																																			C|0.943;T|0.057	0.057	strong		0.667	TPRX1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000409868.1	NM_198479	
PTOV1	53635	hgsc.bcm.edu	37	19	50358133	50358133	+	Silent	SNP	T	T	G	rs75478119	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:50358133T>G	ENST00000601675.1	+	4	542	c.438T>G	c.(436-438)ccT>ccG	p.P146P	PTOV1_ENST00000221557.9_Silent_p.P114P|PTOV1_ENST00000598325.1_3'UTR|PTOV1_ENST00000600603.1_Silent_p.P114P|AC018766.5_ENST00000593654.1_RNA|PTOV1_ENST00000601638.1_Silent_p.P114P|AC018766.6_ENST00000601211.1_RNA|MIR4749_ENST00000578197.1_RNA|PTOV1_ENST00000391842.1_Silent_p.P146P|PTOV1_ENST00000599732.1_Silent_p.P146P			Q86YD1	PTOV1_HUMAN	prostate tumor overexpressed 1	146					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				endometrium(5)|kidney(3)|large_intestine(2)|lung(5)|ovary(1)	16		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;0.0116)|OV - Ovarian serous cystadenocarcinoma(262;0.0132)		AGCTGATCCCTCAGCAGCTGC	0.657													G|||	1800	0.359425	0.4123	0.2392	5008	,	,		10608	0.2877		0.3171	False		,,,				2504	0.4908				p.P146P		Atlas-SNP	.											PTOV1,NS,carcinoma,+1,1	PTOV1	41	1	0			c.T438G						PASS	.	G		1777,2629	611.4+/-391.8	361,1055,787	32.0	33.0	33.0		438	-2.8	1.0	19	dbSNP_131	33	2922,5676	653.3+/-401.0	499,1924,1876	no	coding-synonymous	PTOV1	NM_017432.3		860,2979,2663	GG,GT,TT		33.9846,40.3314,36.135		146/417	50358133	4699,8305	2203	4299	6502	SO:0001819	synonymous_variant	53635	exon4			GATCCCTCAGCAG	AF238381	CCDS12782.1	19q13.33	2014-08-28	2008-09-12		ENSG00000104960	ENSG00000104960			9632	protein-coding gene	gene with protein product		610195				12598323, 15713644	Standard	XM_005258998		Approved		uc002pqf.1	Q86YD1	OTTHUMG00000183162	ENST00000601675.1:c.438T>G	19.37:g.50358133T>G		Somatic	152	1	0.00657895		WXS	Illumina HiSeq	Phase_I	110	109	0.990909	NM_017432	Q6UXX7|Q96BU3|Q9HBN4|Q9NYL1	Silent	SNP	ENST00000601675.1	37	CCDS12782.1																																																																																			T|0.654;G|0.346	0.346	strong		0.657	PTOV1-007	KNOWN	alternative_3_UTR|NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465347.1	NM_017432	
FAT1	2195	hgsc.bcm.edu	37	4	187531022	187531022	+	Missense_Mutation	SNP	A	A	G	rs28647489	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:187531022A>G	ENST00000441802.2	-	15	10210	c.10001T>C	c.(10000-10002)gTg>gCg	p.V3334A		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	3334	Cadherin 30. {ECO:0000255|PROSITE- ProRule:PRU00043}.				actin filament organization (GO:0007015)|anatomical structure morphogenesis (GO:0009653)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.V3334A(2)|p.V3337A(1)		NS(1)|breast(3)|central_nervous_system(3)|endometrium(38)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(33)|lung(88)|ovary(13)|pancreas(2)|prostate(16)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	228						TTGGCTGAACACAGGGGTATT	0.463										HNSCC(5;0.00058)			A|||	964	0.192492	0.1921	0.1902	5008	,	,		17034	0.3819		0.1103	False		,,,				2504	0.0838				p.V3334A	Colon(197;1040 2055 4143 4984 49344)	Atlas-SNP	.											FAT1,NS,carcinoma,0,2	FAT1	500	2	3	Substitution - Missense(3)	prostate(3)	c.T10001C						scavenged	.	A	ALA/VAL	588,3466		52,484,1491	126.0	132.0	130.0		10001	2.8	0.6	4	dbSNP_125	130	1004,7342		69,866,3238	yes	missense	FAT1	NM_005245.3	64	121,1350,4729	GG,GA,AA		12.0297,14.5042,12.8387	possibly-damaging	3334/4589	187531022	1592,10808	2027	4173	6200	SO:0001583	missense	2195	exon15			CTGAACACAGGGG	X87241	CCDS47177.1	4q35.2	2013-05-31	2013-05-31	2008-10-30	ENSG00000083857	ENSG00000083857		"""Cadherins / Cadherin-related"""	3595	protein-coding gene	gene with protein product	"""cadherin-related family member 8"""	600976	"""FAT tumor suppressor (Drosophila) homolog"", ""FAT tumor suppressor homolog 1 (Drosophila)"""	FAT		8586420	Standard	XM_005262834		Approved	CDHF7, CDHR8	uc003izf.3	Q14517	OTTHUMG00000160320	ENST00000441802.2:c.10001T>C	4.37:g.187531022A>G	ENSP00000406229:p.Val3334Ala	Somatic	165	2	0.0121212		WXS	Illumina HiSeq	Phase_I	170	80	0.470588	NM_005245		Missense_Mutation	SNP	ENST00000441802.2	37	CCDS47177.1	477	0.2184065934065934	93	0.18902439024390244	71	0.19613259668508287	226	0.3951048951048951	87	0.11477572559366754	A	4.568	0.105461	0.08780	0.145042	0.120297	ENSG00000083857	ENST00000441802;ENST00000260147	T	0.03124	4.04	5.22	2.77	0.32553	Cadherin (2);Cadherin-like (1);	0.116821	0.56097	N	0.000021	T	0.00012	0.0000	L	0.45285	1.41	0.20074	P	0.9999339666	B	0.06786	0.001	B	0.09377	0.004	T	0.44832	-0.9302	9	0.10636	T	0.68	.	7.0552	0.25095	0.7965:0.0:0.0715:0.132	rs28647489;rs28647489	3334	Q14517	FAT1_HUMAN	A	3334;3336	ENSP00000406229:V3334A	ENSP00000260147:V3336A	V	-	2	0	FAT1	187768016	0.974000	0.33945	0.573000	0.28510	0.210000	0.24377	3.445000	0.52921	0.443000	0.26582	0.528000	0.53228	GTG	A|0.797;G|0.203	0.203	strong		0.463	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245	
VPS13C	54832	hgsc.bcm.edu	37	15	62202482	62202482	+	Missense_Mutation	SNP	C	C	T	rs10851704	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:62202482C>T	ENST00000261517.5	-	64	8811	c.8738G>A	c.(8737-8739)aGt>aAt	p.S2913N	VPS13C_ENST00000249837.3_Missense_Mutation_p.S2870N|VPS13C_ENST00000395896.4_Missense_Mutation_p.S2913N|VPS13C_ENST00000395898.3_Missense_Mutation_p.S2870N	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						GCCTGACAAACTTTCTGGCCA	0.338													T|||	2586	0.516374	0.4841	0.6671	5008	,	,		9613	0.4732		0.5517	False		,,,				2504	0.4611				p.S2913N		Atlas-SNP	.											.	VPS13C	506	.	0			c.G8738A						PASS	.	T	ASN/SER,ASN/SER,ASN/SER,ASN/SER	2198,2208	586.2+/-386.4	563,1072,568	50.0	52.0	51.0		8738,8609,8609,8738	3.5	1.0	15	dbSNP_120	51	4603,3997	552.6+/-386.1	1235,2133,932	yes	missense,missense,missense,missense	VPS13C	NM_001018088.2,NM_017684.4,NM_018080.3,NM_020821.2	46,46,46,46	1798,3205,1500	TT,TC,CC		46.4767,49.8865,47.7087	benign,benign,benign,benign	2913/3629,2870/3711,2870/3586,2913/3754	62202482	6801,6205	2203	4300	6503	SO:0001583	missense	54832	exon64			GACAAACTTTCTG	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.8738G>A	15.37:g.62202482C>T	ENSP00000261517:p.Ser2913Asn	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	46	46	1	NM_020821		Missense_Mutation	SNP	ENST00000261517.5	37	CCDS32257.1	1177	0.5389194139194139	242	0.491869918699187	231	0.638121546961326	281	0.49125874125874125	423	0.558047493403694	T	4.368	0.067920	0.08436	0.498865	0.535233	ENSG00000129003	ENST00000249837;ENST00000261517;ENST00000395896;ENST00000395898	T;T;T	0.27720	1.65;1.65;1.65	5.85	3.54	0.40534	Vacuolar protein sorting-associated protein (1);	0.145640	0.64402	N	0.000014	T	0.00012	0.0000	N	0.01656	-0.775	0.54753	P	1.3000000000040757E-5	B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0	B;B;B;B;B	0.04013	0.001;0.001;0.001;0.001;0.001	T	0.47182	-0.9137	9	0.02654	T	1	.	9.5913	0.39548	0.0:0.2007:0.0:0.7993	rs10851704;rs52801554;rs59009682;rs10851704	2913;2870;2913;2870;2913	F5GZG8;Q709C8-4;Q709C8-2;Q709C8-3;Q709C8	.;.;.;.;VP13C_HUMAN	N	2870;2913;2913;2913	ENSP00000249837:S2870N;ENSP00000261517:S2913N;ENSP00000379233:S2913N	ENSP00000249837:S2870N	S	-	2	0	VPS13C	59989774	1.000000	0.71417	0.971000	0.41717	0.983000	0.72400	0.853000	0.27777	0.133000	0.18654	-0.254000	0.11334	AGT	C|0.476;T|0.524	0.524	strong		0.338	VPS13C-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000415997.1	NM_017684	
TSPYL4	23270	hgsc.bcm.edu	37	6	116575116	116575116	+	Missense_Mutation	SNP	G	G	T	rs17524614	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:116575116G>T	ENST00000420283.1	-	1	145	c.56C>A	c.(55-57)gCt>gAt	p.A19D	DSE_ENST00000540275.1_5'Flank|RP3-486I3.7_ENST00000448740.2_lincRNA	NM_021648.4	NP_067680.3	Q9UJ04	TSYL4_HUMAN	TSPY-like 4	19					nucleosome assembly (GO:0006334)	nucleus (GO:0005634)				endometrium(2)|large_intestine(4)|lung(3)|upper_aerodigestive_tract(2)	11		all_cancers(87;0.0144)|all_epithelial(87;0.021)|Colorectal(196;0.234)		all cancers(137;0.045)|OV - Ovarian serous cystadenocarcinoma(136;0.0666)|GBM - Glioblastoma multiforme(226;0.095)|Epithelial(106;0.125)		GTCGGGAGCAGCCAGGCCGCC	0.622													G|||	509	0.101637	0.0106	0.2089	5008	,	,		16134	0.1101		0.1501	False		,,,				2504	0.09				p.A19D		Atlas-SNP	.											.	TSPYL4	18	.	0			c.C56A						PASS	.	G	ASP/ALA	108,3832		3,102,1865	19.0	23.0	21.0		56	1.3	0.0	6	dbSNP_123	21	1016,7262		57,902,3180	yes	missense	TSPYL4	NM_021648.4	126	60,1004,5045	TT,TG,GG		12.2735,2.7411,9.1995	benign	19/415	116575116	1124,11094	1970	4139	6109	SO:0001583	missense	23270	exon1			GGAGCAGCCAGGC		CCDS5106.1	6q22.1	2010-05-12			ENSG00000187189	ENSG00000187189			21559	protein-coding gene	gene with protein product							Standard	NM_021648		Approved	dJ486I3.2, KIAA0721	uc003pwn.3	Q9UJ04	OTTHUMG00000015429	ENST00000420283.1:c.56C>A	6.37:g.116575116G>T	ENSP00000410943:p.Ala19Asp	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	104	104	1	NM_021648	B4DYQ2|O94828|Q96GW8	Missense_Mutation	SNP	ENST00000420283.1	37	CCDS5106.1	276	0.12637362637362637	8	0.016260162601626018	73	0.20165745856353592	71	0.12412587412587413	124	0.16358839050131926	G	12.35	1.911171	0.33721	0.027411	0.122735	ENSG00000187189	ENST00000420283	T	0.26660	1.72	4.12	1.34	0.21922	.	.	.	.	.	T	0.08358	0.0208	L	0.55481	1.735	0.80722	P	0.0	P	0.42409	0.779	B	0.36885	0.235	T	0.14144	-1.0483	8	0.52906	T	0.07	-0.0586	4.1276	0.10134	0.2135:0.1949:0.5916:0.0	rs17524614	19	Q9UJ04	TSYL4_HUMAN	D	19	ENSP00000410943:A19D	ENSP00000410943:A19D	A	-	2	0	TSPYL4	116681809	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.137000	0.15995	0.285000	0.22329	0.462000	0.41574	GCT	G|0.876;T|0.124	0.124	strong		0.622	TSPYL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041934.2		
ZNF142	7701	hgsc.bcm.edu	37	2	219513782	219513782	+	Silent	SNP	T	T	C	rs4674322	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	57	0	0	2259	WXS	Illumina HiSeq	Phase_I	49	21	0.428571	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	
ADAM33	80332	hgsc.bcm.edu	37	20	3652365	3652365	+	Missense_Mutation	SNP	T	T	C	rs55687415	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:3652365T>C	ENST00000356518.2	-	16	2009	c.1768A>G	c.(1768-1770)Atg>Gtg	p.M590V	ADAM33_ENST00000466620.1_5'UTR|ADAM33_ENST00000350009.2_Missense_Mutation_p.M590V|ADAM33_ENST00000379861.4_Missense_Mutation_p.M590V	NM_025220.2	NP_079496.1	Q9BZ11	ADA33_HUMAN	ADAM metallopeptidase domain 33	590	Cys-rich.				proteolysis (GO:0006508)	integral component of membrane (GO:0016021)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(17)|ovary(1)|skin(3)	29						ACTGGCACCATGTGCGGTGCG	0.637													T|||	33	0.00658946	0.0227	0.0043	5008	,	,		20795	0.0		0.0	False		,,,				2504	0.0				p.M590V		Atlas-SNP	.											.	ADAM33	76	.	0			c.A1768G						PASS	.	T	VAL/MET,VAL/MET	82,4324		0,82,2121	42.0	33.0	36.0		1768,1768	0.5	0.0	20	dbSNP_129	36	4,8588		0,4,4292	yes	missense,missense	ADAM33	NM_025220.2,NM_153202.1	21,21	0,86,6413	CC,CT,TT		0.0466,1.8611,0.6616	benign,benign	590/814,590/788	3652365	86,12912	2203	4296	6499	SO:0001583	missense	80332	exon16			GCACCATGTGCGG	AL117415, AB055891	CCDS13058.1, CCDS63219.1	20p13	2010-04-06	2005-08-18		ENSG00000149451	ENSG00000149451		"""ADAM metallopeptidase domain containing"""	15478	protein-coding gene	gene with protein product		607114	"""a disintegrin and metalloproteinase domain 33"", ""chromosome 20 open reading frame 153"""	C20orf153		11814695	Standard	XM_005260843		Approved	DKFZp434K0521, dJ964F7.1	uc002wit.3	Q9BZ11	OTTHUMG00000031758	ENST00000356518.2:c.1768A>G	20.37:g.3652365T>C	ENSP00000348912:p.Met590Val	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	53	22	0.415094	NM_025220	A0A1K6|Q5JT75|Q5JT76|Q8N0W6	Missense_Mutation	SNP	ENST00000356518.2	37	CCDS13058.1	14	0.00641025641025641	13	0.026422764227642278	1	0.0027624309392265192	0	0.0	0	0.0	T	4.955	0.177362	0.09443	0.018611	4.66E-4	ENSG00000149451	ENST00000356518;ENST00000379861;ENST00000350009;ENST00000428784;ENST00000439201	T;T;T	0.21031	2.03;2.03;2.03	5.46	0.539	0.17156	ADAM, cysteine-rich (2);	.	.	.	.	T	0.01835	0.0058	N	0.00926	-1.1	0.09310	N	0.999999	B;B;B;B	0.19073	0.033;0.001;0.001;0.001	B;B;B;B	0.14578	0.011;0.002;0.004;0.004	T	0.41520	-0.9504	9	0.16420	T	0.52	.	9.2387	0.37481	0.0:0.3775:0.0:0.6225	rs55687415;rs61753555	106;590;590;590	E9PEB2;Q9BZ11-2;Q9BZ11;A2A2L3	.;.;ADA33_HUMAN;.	V	590;590;590;106;470	ENSP00000348912:M590V;ENSP00000369190:M590V;ENSP00000322550:M590V	ENSP00000322550:M590V	M	-	1	0	ADAM33	3600365	0.620000	0.27068	0.003000	0.11579	0.082000	0.17680	0.249000	0.18216	-0.185000	0.10550	0.459000	0.35465	ATG	T|0.992;C|0.008	0.008	strong		0.637	ADAM33-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000077763.2	NM_025220	
CISD3	284106	hgsc.bcm.edu	37	17	36889559	36889559	+	Missense_Mutation	SNP	C	C	T	rs2879097	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:36889559C>T	ENST00000439660.2	+	4	359	c.235C>T	c.(235-237)Cgc>Tgc	p.R79C	CISD3_ENST00000578573.1_3'UTR|RNA5SP440_ENST00000363245.1_RNA	NM_001136498.1	NP_001129970.1	P0C7P0	CISD3_HUMAN	CDGSH iron sulfur domain 3	79						mitochondrion (GO:0005739)	2 iron, 2 sulfur cluster binding (GO:0051537)|metal ion binding (GO:0046872)			endometrium(2)	2						CTTCTTCCAACGCACTGGCCT	0.622													C|||	755	0.150759	0.0439	0.2925	5008	,	,		17132	0.1468		0.2167	False		,,,				2504	0.1309				p.R79C		Atlas-SNP	.											.	CISD3	12	.	0			c.C235T						PASS	.						65.0	53.0	57.0					17																	36889559		692	1591	2283	SO:0001583	missense	284106	exon4			TTCCAACGCACTG	AK097047	CCDS45662.1	17q12	2007-08-10				ENSG00000277972		"""CDGSH iron sulfur domain containing"""	27578	protein-coding gene	gene with protein product	"""mitoNEET related 2"""	611933				17376863, 17584744	Standard	NM_001136498		Approved	Miner2	uc010wds.1	P0C7P0		ENST00000439660.2:c.235C>T	17.37:g.36889559C>T	ENSP00000391402:p.Arg79Cys	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	76	33	0.434211	NM_001136498		Missense_Mutation	SNP	ENST00000439660.2	37	CCDS45662.1	356	0.163003663003663	25	0.0508130081300813	95	0.26243093922651933	75	0.13111888111888112	161	0.21240105540897097	C	19.18	3.777203	0.70107	.	.	ENSG00000230055	ENST00000439660	.	.	.	5.41	3.31	0.37934	.	.	.	.	.	T	0.00012	0.0000	L	0.43923	1.385	0.26437	P	0.9758395	D	0.69078	0.997	P	0.50490	0.642	T	0.08597	-1.0714	7	0.59425	D	0.04	-11.4689	9.4137	0.38507	0.1578:0.6886:0.1536:0.0	rs2879097;rs35161534;rs58181077;rs2879097	79	P0C7P0	CISD3_HUMAN	C	79	.	ENSP00000391402:R79C	R	+	1	0	CISD3	34143085	0.386000	0.25180	1.000000	0.80357	0.975000	0.68041	1.441000	0.35035	2.527000	0.85204	0.455000	0.32223	CGC	C|0.849;T|0.151	0.151	strong		0.622	CISD3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441921.1		
LMNA	4000	hgsc.bcm.edu	37	1	156084760	156084760	+	Silent	SNP	C	C	T	rs11549668	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:156084760C>T	ENST00000368300.4	+	1	263	c.51C>T	c.(49-51)agC>agT	p.S17S	LMNA_ENST00000361308.4_Silent_p.S17S|LMNA_ENST00000347559.2_Silent_p.S17S|LMNA_ENST00000368299.3_Silent_p.S17S|LMNA_ENST00000368301.2_Silent_p.S17S	NM_170707.3	NP_733821.1	P02545	LMNA_HUMAN	lamin A/C	17	Head.|Interaction with MLIP.				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)					CGCAGGCCAGCTCCACTCCGC	0.721									Werner syndrome;Hutchinson-Gilford Progeria Syndrome				C|||	34	0.00678914	0.0008	0.0187	5008	,	,		12738	0.0		0.0139	False		,,,				2504	0.0061				p.S17S		Atlas-SNP	.											.	LMNA	31	.	0			c.C51T						PASS	.	C	,,	14,4348		0,14,2167	18.0	17.0	17.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	51,51,51	2.9	1.0	1	dbSNP_120	17	108,8434		1,106,4164	no	coding-synonymous,coding-synonymous,coding-synonymous	LMNA	NM_005572.3,NM_170707.2,NM_170708.2	,,	1,120,6331	TT,TC,CC		1.2643,0.321,0.9454	,,	17/573,17/665,17/635	156084760	122,12782	2181	4271	6452	SO:0001819	synonymous_variant	4000	exon1	Familial Cancer Database	WS, Adult Progeria;HGPS, Progeria	GGCCAGCTCCACT	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.51C>T	1.37:g.156084760C>T		Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	25	20	0.8	NM_170707	B4DI32|D3DVB0|D6RAQ3|E7EUI9|P02546|Q5I6Y4|Q5I6Y6|Q5TCJ2|Q5TCJ3|Q6UYC3|Q969I8|Q96JA2	Silent	SNP	ENST00000368300.4	37	CCDS1129.1																																																																																			C|0.991;T|0.009	0.009	strong		0.721	LMNA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039200.2	NM_170707	
SOX5	6660	hgsc.bcm.edu	37	12	23687354	23687354	+	Silent	SNP	G	G	A	rs61756181	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:23687354G>A	ENST00000451604.2	-	15	2192	c.2091C>T	c.(2089-2091)agC>agT	p.S697S	SOX5_ENST00000396007.2_Silent_p.S311S|SOX5_ENST00000541536.1_Silent_p.S576S|SOX5_ENST00000546136.1_Silent_p.S684S|SOX5_ENST00000381381.2_Silent_p.S576S|SOX5_ENST00000309359.1_Silent_p.S684S|SOX5_ENST00000545921.1_Silent_p.S687S|SOX5_ENST00000537393.1_Silent_p.S662S			P35711	SOX5_HUMAN	SRY (sex determining region Y)-box 5	697					cartilage development (GO:0051216)|cell fate commitment (GO:0045165)|cellular response to transforming growth factor beta stimulus (GO:0071560)|central nervous system neuron differentiation (GO:0021953)|in utero embryonic development (GO:0001701)|negative regulation of transcription, DNA-templated (GO:0045892)|oligodendrocyte differentiation (GO:0048709)|positive regulation of cartilage development (GO:0061036)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of mesenchymal stem cell differentiation (GO:2000741)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of timing of neuron differentiation (GO:0060164)|transcription from RNA polymerase II promoter (GO:0006366)	nuclear transcription factor complex (GO:0044798)	sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(25)|ovary(5)|skin(2)|upper_aerodigestive_tract(3)	57						TGCTAGACACGCTTGAGTGCT	0.572													G|||	353	0.0704872	0.028	0.0591	5008	,	,		17855	0.1081		0.0109	False		,,,				2504	0.1585				p.S697S		Atlas-SNP	.											.	SOX5	134	.	0			c.C2091T						PASS	.	G	,,	140,4266	99.8+/-138.5	3,134,2066	99.0	85.0	90.0		2091,2052,933	-0.5	1.0	12	dbSNP_129	90	86,8514	49.8+/-109.6	0,86,4214	no	coding-synonymous,coding-synonymous,coding-synonymous	SOX5	NM_006940.4,NM_152989.2,NM_178010.1	,,	3,220,6280	AA,AG,GG		1.0,3.1775,1.7377	,,	697/764,684/751,311/378	23687354	226,12780	2203	4300	6503	SO:0001819	synonymous_variant	6660	exon15			AGACACGCTTGAG	AB081589	CCDS8699.1, CCDS41761.1, CCDS44844.1, CCDS58216.1, CCDS58217.1	12p12.1	2010-04-20			ENSG00000134532	ENSG00000134532		"""SRY (sex determining region Y)-boxes"""	11201	protein-coding gene	gene with protein product		604975				8812465	Standard	NM_006940		Approved	L-SOX5, MGC35153	uc001rfw.3	P35711	OTTHUMG00000169026	ENST00000451604.2:c.2091C>T	12.37:g.23687354G>A		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	80	35	0.4375	NM_006940	B7Z8V0|F5H5B0|Q86UK8|Q8J017|Q8J018|Q8J019|Q8J020|Q8N1D9|Q8N7E0|Q8TEA4	Silent	SNP	ENST00000451604.2	37	CCDS8699.1																																																																																			G|0.977;A|0.023	0.023	strong		0.572	SOX5-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000402006.2	NM_006940	
C7	730	hgsc.bcm.edu	37	5	40964885	40964885	+	Missense_Mutation	SNP	A	A	T	rs60714178	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:40964885A>T	ENST00000313164.9	+	14	2151	c.1792A>T	c.(1792-1794)Act>Tct	p.T598S		NM_000587.2	NP_000578.2	P10643	CO7_HUMAN	complement component 7	598	CCP 1.|Sushi 1. {ECO:0000255|PROSITE- ProRule:PRU00302}.				cellular sodium ion homeostasis (GO:0006883)|complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|complement activation, classical pathway (GO:0006958)|cytolysis (GO:0019835)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane attack complex (GO:0005579)							Ovarian(839;0.0112)				TGTAGTGTACACTTGCAATGA	0.403													A|||	331	0.0660942	0.0272	0.1081	5008	,	,		18463	0.001		0.1481	False		,,,				2504	0.0716				p.T598S		Atlas-SNP	.											.	C7	136	.	0			c.A1792T						PASS	.	A	SER/THR	180,3684		6,168,1758	163.0	161.0	162.0		1792	-0.2	0.6	5	dbSNP_129	162	1278,6984		83,1112,2936	yes	missense	C7	NM_000587.2	58	89,1280,4694	TT,TA,AA		15.4684,4.6584,12.0238	benign	598/844	40964885	1458,10668	1932	4131	6063	SO:0001583	missense	730	exon14			GTGTACACTTGCA	J03507	CCDS47201.1	5p13.1	2014-09-17			ENSG00000112936	ENSG00000112936		"""Complement system"""	1346	protein-coding gene	gene with protein product		217070					Standard	NM_000587		Approved		uc003jmh.3	P10643	OTTHUMG00000150340	ENST00000313164.9:c.1792A>T	5.37:g.40964885A>T	ENSP00000322061:p.Thr598Ser	Somatic	220	0	0		WXS	Illumina HiSeq	Phase_I	230	113	0.491304	NM_000587	Q6P3T5|Q92489	Missense_Mutation	SNP	ENST00000313164.9	37	CCDS47201.1	177	0.08104395604395605	15	0.03048780487804878	37	0.10220994475138122	1	0.0017482517482517483	124	0.16358839050131926	A	11.28	1.591300	0.28357	0.046584	0.154684	ENSG00000112936	ENST00000313164;ENST00000440677	T	0.63744	-0.06	6.04	-0.173	0.13322	Complement control module (2);Sushi/SCR/CCP (3);	0.363303	0.29100	N	0.013144	T	0.00144	0.0004	N	0.20304	0.555	0.45118	P	0.0018700000000000383	B	0.20550	0.046	B	0.23574	0.047	T	0.04178	-1.0971	9	0.16420	T	0.52	-8.1559	4.3042	0.10938	0.3711:0.0:0.1734:0.4555	rs60714178;rs61741887	598	P10643	CO7_HUMAN	S	598;438	ENSP00000322061:T598S	ENSP00000322061:T598S	T	+	1	0	C7	41000642	0.340000	0.24792	0.595000	0.28798	0.893000	0.52053	0.756000	0.26419	0.035000	0.15519	0.460000	0.39030	ACT	A|0.902;T|0.098	0.098	strong		0.403	C7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317680.1		
MAP7D1	55700	hgsc.bcm.edu	37	1	36636774	36636774	+	Silent	SNP	G	G	A	rs139650826	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:36636774G>A	ENST00000373151.2	+	2	465	c.249G>A	c.(247-249)caG>caA	p.Q83Q	MAP7D1_ENST00000373150.4_Silent_p.Q83Q|MAP7D1_ENST00000316156.4_Silent_p.Q83Q	NM_018067.3	NP_060537.3	Q3KQU3	MA7D1_HUMAN	MAP7 domain containing 1	83	Pro-rich.				microtubule cytoskeleton organization (GO:0000226)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)				breast(2)|cervix(1)|endometrium(2)|large_intestine(3)|lung(3)|ovary(3)|prostate(3)|skin(1)|urinary_tract(1)	19		Myeloproliferative disorder(586;0.0393)				CCCCCCCGCAGGAAGAGTCCC	0.642													G|||	23	0.00459265	0.0008	0.0043	5008	,	,		13296	0.0		0.0179	False		,,,				2504	0.001				p.Q83Q		Atlas-SNP	.											.	MAP7D1	62	.	0			c.G249A						PASS	.	G		12,4394	19.1+/-41.9	0,12,2191	39.0	43.0	41.0		249	2.2	1.0	1	dbSNP_134	41	125,8475	62.4+/-124.4	1,123,4176	no	coding-synonymous	MAP7D1	NM_018067.3		1,135,6367	AA,AG,GG		1.4535,0.2724,1.0534		83/842	36636774	137,12869	2203	4300	6503	SO:0001819	synonymous_variant	55700	exon2			CCCGCAGGAAGAG	AK096341	CCDS30673.1, CCDS65492.1, CCDS65493.1	1p34.3	2008-02-05	2007-02-08	2007-02-08	ENSG00000116871	ENSG00000116871			25514	protein-coding gene	gene with protein product			"""proline arginine rich coiled coil 1"", ""arginine/proline rich coiled-coil 1"""	PARCC1, RPRC1		10574461	Standard	XM_005271024		Approved	FLJ10350, FLJ39022	uc001bzz.3	Q3KQU3	OTTHUMG00000007714	ENST00000373151.2:c.249G>A	1.37:g.36636774G>A		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	82	39	0.47561	NM_018067	D3DPS4|Q7L8J5|Q8N905|Q8TAK0|Q9HBQ2|Q9NW29|Q9ULN3	Silent	SNP	ENST00000373151.2	37	CCDS30673.1																																																																																			G|0.992;A|0.008	0.008	strong		0.642	MAP7D1-009	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382095.1	NM_018067	
APCDD1	147495	hgsc.bcm.edu	37	18	10471764	10471764	+	Silent	SNP	C	C	T	rs3748414	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:10471764C>T	ENST00000355285.5	+	3	834	c.480C>T	c.(478-480)gcC>gcT	p.A160A	APCDD1_ENST00000578882.1_Intron	NM_153000.4	NP_694545.1			adenomatosis polyposis coli down-regulated 1											NS(1)|breast(1)|endometrium(3)|large_intestine(5)|lung(7)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22				READ - Rectum adenocarcinoma(15;0.08)		AGGCGGTGGCCGAGAAGCTCG	0.667													C|||	518	0.103435	0.0325	0.0778	5008	,	,		14254	0.1528		0.1123	False		,,,				2504	0.1575				p.A160A		Atlas-SNP	.											.	APCDD1	57	.	0			c.C480T						PASS	.	C		241,4165	134.9+/-171.1	6,229,1968	40.0	48.0	45.0		480	-7.7	0.1	18	dbSNP_107	45	1032,7568	213.9+/-253.7	60,912,3328	no	coding-synonymous	APCDD1	NM_153000.4		66,1141,5296	TT,TC,CC		12.0,5.4698,9.7878		160/515	10471764	1273,11733	2203	4300	6503	SO:0001819	synonymous_variant	147495	exon3			GGTGGCCGAGAAG	AB056722	CCDS11849.1	18p11.21	2006-07-07			ENSG00000154856	ENSG00000154856			15718	protein-coding gene	gene with protein product		607479				12384519	Standard	NM_153000		Approved	B7323	uc002kom.4	Q8J025	OTTHUMG00000131635	ENST00000355285.5:c.480C>T	18.37:g.10471764C>T		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	51	29	0.568627	NM_153000		Silent	SNP	ENST00000355285.5	37	CCDS11849.1																																																																																			T|0.102;G|0.000;C|0.898	0.102	strong		0.667	APCDD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254529.2	NM_153000	
MUC4	4585	hgsc.bcm.edu	37	3	195507925	195507925	+	Missense_Mutation	SNP	C	C	T	rs71635074		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195507925C>T	ENST00000463781.3	-	2	10985	c.10526G>A	c.(10525-10527)gGc>gAc	p.G3509D	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.G3509D	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.G3509D(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)		TGAGGAAGCGCCGGTGACAGG	0.597																																					p.G3509D		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	1	Substitution - Missense(1)	kidney(1)	c.G10526A						PASS	.						42.0	37.0	38.0					3																	195507925		644	1582	2226	SO:0001583	missense	4585	exon2			GAAGCGCCGGTGA	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.10526G>A	3.37:g.195507925C>T	ENSP00000417498:p.Gly3509Asp	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	186	36	0.193548	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	1.142	-0.649185	0.03506	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.30182	1.54;1.54	0.743	-1.49	0.08718	.	.	.	.	.	T	0.09905	0.0243	N	0.03608	-0.345	0.09310	N	1	B	0.10296	0.003	B	0.08055	0.003	T	0.22243	-1.0222	8	.	.	.	.	1.8613	0.03189	0.3063:0.4305:0.0:0.2632	.	3381	E7ESK3	.	D	3509	ENSP00000417498:G3509D;ENSP00000420243:G3509D	.	G	-	2	0	MUC4	196992704	0.000000	0.05858	0.003000	0.11579	0.003000	0.03518	-2.451000	0.01006	-1.862000	0.01151	-1.862000	0.00560	GGC	T|1.000;|0.000	1.000	weak		0.597	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
NAT2	10	hgsc.bcm.edu	37	8	18258370	18258370	+	Missense_Mutation	SNP	G	G	A	rs1799931	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:18258370G>A	ENST00000286479.3	+	2	964	c.857G>A	c.(856-858)gGa>gAa	p.G286E	NAT2_ENST00000520116.1_Missense_Mutation_p.G156E	NM_000015.2	NP_000006.2	P11245	ARY2_HUMAN	N-acetyltransferase 2 (arylamine N-acetyltransferase)	286			G -> E (in allele NAT2*7A and allele NAT2*7B; a slow acetylator; dbSNP:rs1799931). {ECO:0000269|PubMed:1381364, ECO:0000269|PubMed:16416399, ECO:0000269|PubMed:1968463, ECO:0000269|Ref.14}.	G -> R (in Ref. 9; AAG34181). {ECO:0000305}.	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)	CCTGGTGATGGATCCCTTACT	0.383									Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of				G|||	387	0.0772764	0.0287	0.1124	5008	,	,		15535	0.1796		0.0229	False		,,,				2504	0.0685				p.G286E		Atlas-SNP	.											.	NAT2	34	.	0			c.G857A	GRCh37	CM900170	NAT2	M	rs1799931	PASS	.	G	GLU/GLY	126,4252		0,126,2063	43.0	47.0	46.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	857	-5.1	0.0	8	dbSNP_89	46	170,8354		1,168,4093	yes	missense	NAT2	NM_000015.2	98	1,294,6156	AA,AG,GG		1.9944,2.878,2.2942	benign	286/291	18258370	296,12606	2189	4262	6451	SO:0001583	missense	10	exon2	Familial Cancer Database	incl.: Familial Head and Neck Cancer	GTGATGGATCCCT	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.857G>A	8.37:g.18258370G>A	ENSP00000286479:p.Gly286Glu	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	75	13	0.173333	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	155	0.07097069597069597	16	0.032520325203252036	34	0.09392265193370165	90	0.15734265734265734	15	0.01978891820580475	G	0.010	-1.795156	0.00617	0.02878	0.019944	ENSG00000156006	ENST00000286479;ENST00000520116	T;T	0.02280	4.8;4.36	2.55	-5.09	0.02920	.	1.633550	0.03660	N	0.242391	T	0.00012	0.0000	L	0.39898	1.24	0.80722	P	0.0	B	0.31274	0.317	B	0.28784	0.094	T	0.45571	-0.9252	9	0.05351	T	0.99	.	2.9625	0.05897	0.2935:0.0:0.2623:0.4442	rs1799931;rs4646270;rs17693862;rs52802193;rs58803786;rs1799931	286	A4Z6T7	.	E	286;156	ENSP00000286479:G286E;ENSP00000428416:G156E	ENSP00000286479:G286E	G	+	2	0	NAT2	18302650	0.000000	0.05858	0.000000	0.03702	0.089000	0.18198	-1.316000	0.02710	-1.374000	0.02131	0.205000	0.17691	GGA	G|0.949;A|0.051	0.051	strong		0.383	NAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253380.1	NM_000015	
C1orf27	54953	hgsc.bcm.edu	37	1	186363119	186363119	+	Missense_Mutation	SNP	C	C	G	rs12084264	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:186363119C>G	ENST00000287859.6	+	9	877	c.752C>G	c.(751-753)tCt>tGt	p.S251C	C1orf27_ENST00000419367.3_Missense_Mutation_p.S219C|C1orf27_ENST00000432021.3_Intron|C1orf27_ENST00000367470.3_Intron	NM_017847.5	NP_060317.3	Q5SWX8	ODR4_HUMAN	chromosome 1 open reading frame 27	251			S -> C (in dbSNP:rs12084264). {ECO:0000269|PubMed:14702039}.			integral component of membrane (GO:0016021)	oxidoreductase activity (GO:0016491)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(2)|lung(3)|ovary(1)	9						ACTAGTCATTCTTTTGATGTC	0.279													C|||	1164	0.232428	0.149	0.4078	5008	,	,		14393	0.127		0.335	False		,,,				2504	0.2239				p.S251C		Atlas-SNP	.											C1orf27_ENST00000287859,NS,carcinoma,0,2	C1orf27	41	2	0			c.C752G						PASS	.	C	,CYS/SER,CYS/SER	581,2775		48,485,1145	27.0	24.0	25.0		,656,752	3.4	0.9	1	dbSNP_120	25	2399,5149		385,1629,1760	yes	intron,missense,missense	C1orf27	NM_001164245.1,NM_001164246.1,NM_017847.5	,112,112	433,2114,2905	GG,GC,CC		31.7833,17.3123,27.3294	,benign,benign	,219/423,251/455	186363119	2980,7924	1678	3774	5452	SO:0001583	missense	54953	exon9			GTCATTCTTTTGA	BC003397	CCDS53448.1, CCDS53449.1, CCDS53450.1	1q25	2012-06-25			ENSG00000157181	ENSG00000157181			24299	protein-coding gene	gene with protein product	"""transactivated by recombinant transforming growth factor beta"""	609335				12868032	Standard	NM_017847		Approved	FLJ20505, odr-4, TTG1	uc021pgj.1	Q5SWX8	OTTHUMG00000035579	ENST00000287859.6:c.752C>G	1.37:g.186363119C>G	ENSP00000287859:p.Ser251Cys	Somatic	273	0	0		WXS	Illumina HiSeq	Phase_I	214	211	0.985981	NM_017847	B4DNY0|E9PFR7|Q19CC6|Q8WYB6|Q9BTS2|Q9H6A6|Q9NX06	Missense_Mutation	SNP	ENST00000287859.6	37	CCDS53448.1	557	0.25503663003663	65	0.13211382113821138	148	0.4088397790055249	77	0.1346153846153846	267	0.35224274406332456	C	15.80	2.939210	0.52972	0.173123	0.317833	ENSG00000157181	ENST00000419367;ENST00000432021;ENST00000287859	T;T	0.46451	0.87;0.87	5.34	3.43	0.39272	.	0.556512	0.18307	N	0.145224	T	0.00012	0.0000	L	0.50333	1.59	0.09310	P	0.99999999387866	D;B	0.57899	0.981;0.0	P;B	0.53062	0.717;0.003	T	0.43702	-0.9375	9	0.37606	T	0.19	-3.9611	6.5884	0.22634	0.0:0.5515:0.3334:0.1151	rs12084264;rs17521893;rs12084264	219;251	E9PFR7;Q5SWX8	.;ODR4_HUMAN	C	219;251;251	ENSP00000395084:S219C;ENSP00000287859:S251C	ENSP00000287859:S251C	S	+	2	0	C1orf27	184629742	0.008000	0.16893	0.940000	0.37924	0.976000	0.68499	0.050000	0.14120	0.605000	0.29947	-0.300000	0.09419	TCT	C|0.756;G|0.244	0.244	strong		0.279	C1orf27-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086352.2	NM_017847	
SERPINA5	5104	hgsc.bcm.edu	37	14	95054012	95054012	+	Missense_Mutation	SNP	A	A	G	rs6119	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:95054012A>G	ENST00000554866.1	+	2	427	c.313A>G	c.(313-315)Aag>Gag	p.K105E	SERPINA5_ENST00000554276.1_Missense_Mutation_p.K105E|SERPINA5_ENST00000553780.1_Missense_Mutation_p.K105E|SERPINA5_ENST00000329597.7_Missense_Mutation_p.K105E			P05154	IPSP_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 5	105			K -> E (in allele PCI*B; dbSNP:rs6119). {ECO:0000269|PubMed:10391209, ECO:0000269|PubMed:8713781, ECO:0000269|Ref.6}.		fusion of sperm to egg plasma membrane (GO:0007342)|lipid transport (GO:0006869)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of proteolysis (GO:0045861)|regulation of proteolysis (GO:0030162)|spermatogenesis (GO:0007283)	acrosomal membrane (GO:0002080)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|platelet alpha granule (GO:0031091)|platelet dense tubular network (GO:0031094)|protein C inhibitor-coagulation factor V complex (GO:0097181)|protein C inhibitor-coagulation factor Xa complex (GO:0097182)|protein C inhibitor-coagulation factor XI complex (GO:0097183)|protein C inhibitor-KLK3 complex (GO:0036029)|protein C inhibitor-plasma kallikrein complex (GO:0036030)|protein C inhibitor-PLAT complex (GO:0036026)|protein C inhibitor-PLAU complex (GO:0036027)|protein C inhibitor-thrombin complex (GO:0036028)|protein C inhibitor-TMPRSS11E complex (GO:0036025)|protein C inhibitor-TMPRSS7 complex (GO:0036024)|protein complex (GO:0043234)	acrosin binding (GO:0032190)|glycosaminoglycan binding (GO:0005539)|heparin binding (GO:0008201)|phosphatidylcholine binding (GO:0031210)|protease binding (GO:0002020)|retinoic acid binding (GO:0001972)|serine-type endopeptidase inhibitor activity (GO:0004867)			endometrium(3)|large_intestine(5)|lung(18)|ovary(2)|skin(5)|upper_aerodigestive_tract(3)	36				COAD - Colon adenocarcinoma(157;0.21)	Drotrecogin alfa(DB00055)|Urokinase(DB00013)	AAGCTCAGAGAAGGAGCTGCA	0.592													G|||	1347	0.26897	0.615	0.1182	5008	,	,		19503	0.25		0.0905	False		,,,				2504	0.1115				p.K105E		Atlas-SNP	.											.	SERPINA5	69	.	0			c.A313G						PASS	.	G	GLU/LYS	2260,2146	574.6+/-383.8	585,1090,528	33.0	32.0	32.0		313	2.0	0.0	14	dbSNP_52	32	813,7787	779.3+/-407.7	41,731,3528	yes	missense	SERPINA5	NM_000624.4	56	626,1821,4056	GG,GA,AA		9.4535,48.7063,23.6276	benign	105/407	95054012	3073,9933	2203	4300	6503	SO:0001583	missense	5104	exon3			TCAGAGAAGGAGC	M68516	CCDS9928.1	14q32.1	2014-02-18	2005-08-18		ENSG00000188488	ENSG00000188488		"""Serine (or cysteine) peptidase inhibitors"""	8723	protein-coding gene	gene with protein product		601841	"""serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 5"""	PLANH3, PCI		1714450, 8381582, 24172014	Standard	NM_000624		Approved	PAI3, PROCI	uc001ydm.3	P05154	OTTHUMG00000170860	ENST00000554866.1:c.313A>G	14.37:g.95054012A>G	ENSP00000451126:p.Lys105Glu	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	37	17	0.459459	NM_000624	Q07616|Q9UG30	Missense_Mutation	SNP	ENST00000554866.1	37	CCDS9928.1	532	0.24358974358974358	289	0.5873983739837398	48	0.13259668508287292	125	0.21853146853146854	70	0.09234828496042216	G	0.126	-1.119664	0.01785	0.512937	0.094535	ENSG00000188488	ENST00000554220;ENST00000553780;ENST00000554760;ENST00000554866;ENST00000329597;ENST00000556775;ENST00000555681;ENST00000554276;ENST00000557598	D;D;D;D;D;D;D;D;D	0.83673	-1.75;-1.75;-1.75;-1.75;-1.75;-1.75;-1.75;-1.75;-1.75	3.94	2.01	0.26516	Serpin domain (3);	0.758820	0.12020	N	0.507024	T	0.00012	0.0000	N	0.00599	-1.345	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.40664	-0.9551	9	0.02654	T	1	.	4.9873	0.14196	0.08:0.2673:0.5152:0.1375	rs6119;rs3190222;rs61244877;rs6119	105;105	G3V5Q9;P05154	.;IPSP_HUMAN	E	105	ENSP00000450484:K105E;ENSP00000450837:K105E;ENSP00000452469:K105E;ENSP00000451126:K105E;ENSP00000333203:K105E;ENSP00000450745:K105E;ENSP00000451650:K105E;ENSP00000451610:K105E;ENSP00000450485:K105E	ENSP00000333203:K105E	K	+	1	0	SERPINA5	94123765	0.000000	0.05858	0.003000	0.11579	0.011000	0.07611	-0.520000	0.06252	0.085000	0.17107	-0.231000	0.12243	AAG	A|0.750;G|0.250	0.250	strong		0.592	SERPINA5-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410726.1	NM_000624	
OR5H2	79310	hgsc.bcm.edu	37	3	98002429	98002429	+	Missense_Mutation	SNP	A	A	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:98002429A>T	ENST00000355273.2	+	1	698	c.698A>T	c.(697-699)aAg>aTg	p.K233M	RP11-325B23.2_ENST00000508616.1_lincRNA	NM_001005482.1	NP_001005482.1	Q8NGV7	OR5H2_HUMAN	olfactory receptor, family 5, subfamily H, member 2	233						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						ATCCTAAAAAAGAAGTCTGTT	0.368																																					p.K233M		Atlas-SNP	.											OR5H2,NS,carcinoma,0,1	OR5H2	63	1	0			c.A698T						PASS	.						84.0	86.0	85.0					3																	98002429		2203	4300	6503	SO:0001583	missense	79310	exon1			TAAAAAAGAAGTC		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.698A>T	3.37:g.98002429A>T	ENSP00000347418:p.Lys233Met	Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	137	39	0.284672	NM_001005482	Q6IF87	Missense_Mutation	SNP	ENST00000355273.2	37	CCDS33801.1	.	.	.	.	.	.	.	.	.	.	A	0.025	-1.380780	0.01204	.	.	ENSG00000197938	ENST00000355273	T	0.00032	8.88	3.03	-5.67	0.02444	GPCR, rhodopsin-like superfamily (1);	0.347490	0.20667	N	0.087917	T	0.00039	0.0001	N	0.00642	-1.3	0.09310	N	1	B	0.29232	0.238	B	0.32211	0.142	T	0.47923	-0.9079	10	0.02654	T	1	.	0.6655	0.00849	0.2024:0.1404:0.235:0.4222	.	233	Q8NGV7	OR5H2_HUMAN	M	233	ENSP00000347418:K233M	ENSP00000347418:K233M	K	+	2	0	OR5H2	99485119	0.000000	0.05858	0.003000	0.11579	0.036000	0.12997	-0.051000	0.11885	-0.806000	0.04398	0.338000	0.21704	AAG	.	.	none		0.368	OR5H2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359113.2		
NOS1AP	9722	hgsc.bcm.edu	37	1	162335256	162335256	+	Silent	SNP	C	C	T	rs348624	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:162335256C>T	ENST00000361897.5	+	9	1404	c.1002C>T	c.(1000-1002)cgC>cgT	p.R334R	RP11-565P22.6_ENST00000431696.1_Silent_p.R20R|NOS1AP_ENST00000493151.1_Silent_p.R39R|NOS1AP_ENST00000530878.1_Silent_p.R329R	NM_001164757.1|NM_014697.2	NP_001158229.1|NP_055512.1	O75052	CAPON_HUMAN	nitric oxide synthase 1 (neuronal) adaptor protein	334					regulation of apoptotic process (GO:0042981)|regulation of nitric oxide biosynthetic process (GO:0045428)|regulation of nitric-oxide synthase activity (GO:0050999)		nitric-oxide synthase binding (GO:0050998)			NS(1)|breast(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(12)|skin(1)|upper_aerodigestive_tract(2)	32	all_hematologic(112;0.203)		BRCA - Breast invasive adenocarcinoma(70;0.0537)			CCCAGGCTCGCGTGCATCAGC	0.592													C|||	1256	0.250799	0.4342	0.2161	5008	,	,		18697	0.123		0.1193	False		,,,				2504	0.2945				p.R334R		Atlas-SNP	.											.	NOS1AP	139	.	0			c.C1002T						PASS	.	C	,,	1761,2645	521.9+/-370.6	339,1083,781	69.0	63.0	65.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	117,987,1002	-7.3	0.9	1	dbSNP_79	65	1031,7569	219.4+/-257.5	60,911,3329	no	coding-synonymous,coding-synonymous,coding-synonymous	NOS1AP	NM_001126060.1,NM_001164757.1,NM_014697.2	,,	399,1994,4110	TT,TC,CC		11.9884,39.9682,21.467	,,	39/212,329/502,334/507	162335256	2792,10214	2203	4300	6503	SO:0001819	synonymous_variant	9722	exon9			GGCTCGCGTGCAT	AB007933	CCDS1237.1, CCDS44267.1, CCDS53421.1	1q23.3	2010-08-20			ENSG00000198929	ENSG00000198929			16859	protein-coding gene	gene with protein product	"""C-terminal PDZ domain ligand of neuronal nitric oxide synthase"""	605551				9455484, 9459447	Standard	NM_001126060		Approved	KIAA0464, CAPON	uc001gbv.2	O75052	OTTHUMG00000024049	ENST00000361897.5:c.1002C>T	1.37:g.162335256C>T		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	89	34	0.382022	NM_014697	B7ZLF5|O43564|Q3T551|Q5VU95	Silent	SNP	ENST00000361897.5	37	CCDS1237.1																																																																																			C|0.779;T|0.221	0.221	strong		0.592	NOS1AP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000060555.2	NM_014697	
MYOF	26509	hgsc.bcm.edu	37	10	95082894	95082894	+	Silent	SNP	G	G	A	rs35527060	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:95082894G>A	ENST00000359263.4	-	48	5396	c.5397C>T	c.(5395-5397)gaC>gaT	p.D1799D	MYOF_ENST00000358334.5_Silent_p.D1786D|MYOF_ENST00000371502.4_Silent_p.D1789D|MYOF_ENST00000485212.1_5'Flank|MYOF_ENST00000371501.4_Silent_p.D1799D	NM_013451.3	NP_038479.1	Q9NZM1	MYOF_HUMAN	myoferlin	1799					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)			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						CCAAGATAACGTCCTTGGTGT	0.478													G|||	130	0.0259585	0.0015	0.0504	5008	,	,		21158	0.0		0.0765	False		,,,				2504	0.0164				p.D1799D		Atlas-SNP	.											MYOF,caecum,carcinoma,-1,1	MYOF	177	1	0			c.C5397T						PASS	.	G	,	38,3914		0,38,1938	299.0	280.0	286.0		5397,5358	-6.6	0.2	10	dbSNP_126	286	530,7792		21,488,3652	no	coding-synonymous,coding-synonymous	MYOF	NM_013451.3,NM_133337.2	,	21,526,5590	AA,AG,GG		6.3687,0.9615,4.6277	,	1799/2062,1786/2049	95082894	568,11706	1976	4161	6137	SO:0001819	synonymous_variant	26509	exon48			GATAACGTCCTTG	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.5397C>T	10.37:g.95082894G>A		Somatic	226	0	0		WXS	Illumina HiSeq	Phase_I	163	82	0.503067	NM_013451	B3KQN5|Q5VWW2|Q5VWW3|Q5VWW4|Q5VWW5|Q7Z642|Q8IWH0|Q9HBU3|Q9NZM0|Q9ULL3|Q9Y4U4	Silent	SNP	ENST00000359263.4	37	CCDS41551.1																																																																																			G|0.960;A|0.040	0.040	strong		0.478	MYOF-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000049423.2	NM_013451	
CHST4	10164	hgsc.bcm.edu	37	16	71570847	71570847	+	Missense_Mutation	SNP	G	G	A	rs148657245	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:71570847G>A	ENST00000338482.5	+	3	610	c.267G>A	c.(265-267)atG>atA	p.M89I	RP11-510M2.5_ENST00000568523.1_RNA|ZNF19_ENST00000568446.1_Intron|CHST4_ENST00000539698.3_Missense_Mutation_p.M89I|CHST4_ENST00000572450.1_Missense_Mutation_p.M89I			Q8NCG5	CHST4_HUMAN	carbohydrate (N-acetylglucosamine 6-O) sulfotransferase 4	89					carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|cellular component movement (GO:0006928)|immune response (GO:0006955)|inflammatory response (GO:0006954)|leukocyte tethering or rolling (GO:0050901)|N-acetylglucosamine metabolic process (GO:0006044)|protein sulfation (GO:0006477)|sulfur compound metabolic process (GO:0006790)	integral component of membrane (GO:0016021)|intrinsic component of Golgi membrane (GO:0031228)|trans-Golgi network (GO:0005802)	N-acetylglucosamine 6-O-sulfotransferase activity (GO:0001517)|sulfotransferase activity (GO:0008146)			cervix(1)|kidney(3)|large_intestine(9)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)	21						CCGCCTGGATGCTGCACATGG	0.582													G|||	17	0.00339457	0.0	0.0	5008	,	,		17368	0.0		0.0129	False		,,,				2504	0.0041				p.M89I		Atlas-SNP	.											.	CHST4	47	.	0			c.G267A						PASS	.	G	ILE/MET,ILE/MET	7,4389	12.9+/-30.5	0,7,2191	90.0	93.0	92.0		267,267	-2.5	0.0	16	dbSNP_134	92	95,8505	54.0+/-114.7	1,93,4206	yes	missense,missense	CHST4	NM_001166395.1,NM_005769.2	10,10	1,100,6397	AA,AG,GG		1.1047,0.1592,0.7849	benign,benign	89/387,89/387	71570847	102,12894	2198	4300	6498	SO:0001583	missense	10164	exon2			CTGGATGCTGCAC	AF131235	CCDS10902.1	16q22.2	2008-02-05			ENSG00000140835	ENSG00000140835		"""Sulfotransferases, membrane-bound"""	1972	protein-coding gene	gene with protein product						10330415	Standard	NM_001166395		Approved	HEC-GLCNAC-6-ST, LSST	uc002fao.3	Q8NCG5	OTTHUMG00000137592	ENST00000338482.5:c.267G>A	16.37:g.71570847G>A	ENSP00000341206:p.Met89Ile	Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	205	131	0.639024	NM_001166395	Q8IV46|Q9Y5R3	Missense_Mutation	SNP	ENST00000338482.5	37	CCDS10902.1	11	0.005036630036630037	0	0.0	0	0.0	0	0.0	11	0.014511873350923483	G	3.265	-0.150351	0.06585	0.001592	0.011047	ENSG00000140835	ENST00000338482;ENST00000539698	D;D	0.81499	-1.5;-1.5	6.0	-2.45	0.06481	Sulfotransferase domain (1);	1.694150	0.02602	N	0.101171	T	0.55353	0.1915	N	0.14661	0.345	0.09310	N	1	B	0.12013	0.005	B	0.08055	0.003	T	0.43845	-0.9366	10	0.34782	T	0.22	-3.2597	3.7124	0.08425	0.1301:0.4236:0.2298:0.2165	.	89	Q8NCG5	CHST4_HUMAN	I	89	ENSP00000341206:M89I;ENSP00000441204:M89I	ENSP00000341206:M89I	M	+	3	0	CHST4	70128348	0.002000	0.14202	0.001000	0.08648	0.002000	0.02628	0.112000	0.15479	-0.681000	0.05204	-0.878000	0.02970	ATG	G|0.993;A|0.007	0.007	strong		0.582	CHST4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268992.4	NM_005769	
HIBADH	11112	hgsc.bcm.edu	37	7	27702390	27702390	+	Silent	SNP	C	C	A	rs11550134	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:27702390C>A	ENST00000265395.2	-	1	224	c.18G>T	c.(16-18)cgG>cgT	p.R6R		NM_152740.3	NP_689953.1	P31937	3HIDH_HUMAN	3-hydroxyisobutyrate dehydrogenase	6					branched-chain amino acid catabolic process (GO:0009083)|cellular nitrogen compound metabolic process (GO:0034641)|pentose-phosphate shunt (GO:0006098)|small molecule metabolic process (GO:0044281)|valine catabolic process (GO:0006574)	mitochondrial matrix (GO:0005759)	3-hydroxyisobutyrate dehydrogenase activity (GO:0008442)|NAD binding (GO:0051287)|phosphogluconate dehydrogenase (decarboxylating) activity (GO:0004616)			endometrium(4)|kidney(2)|lung(3)|ovary(2)|prostate(1)	12			GBM - Glioblastoma multiforme(3;0.0368)			CTCCGAGGAGCCGTAAGGAGG	0.736													C|||	1415	0.282548	0.0734	0.255	5008	,	,		9029	0.5397		0.2475	False		,,,				2504	0.3558				p.R6R		Atlas-SNP	.											.	HIBADH	28	.	0			c.G18T						PASS	.	C		268,2718		19,230,1244	3.0	4.0	4.0		18	4.4	1.0	7	dbSNP_120	4	1157,4723		112,933,1895	no	coding-synonymous	HIBADH	NM_152740.3		131,1163,3139	AA,AC,CC		19.6769,8.9752,16.0726		6/337	27702390	1425,7441	1493	2940	4433	SO:0001819	synonymous_variant	11112	exon1			GAGGAGCCGTAAG	AF529362	CCDS5414.1	7p15	2009-06-12			ENSG00000106049	ENSG00000106049	1.1.1.31		4907	protein-coding gene	gene with protein product		608475					Standard	NM_152740		Approved	NS5ATP1	uc003szf.3	P31937	OTTHUMG00000097035	ENST00000265395.2:c.18G>T	7.37:g.27702390C>A		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	50	39	0.78	NM_152740	Q546Z2|Q9UDN3	Silent	SNP	ENST00000265395.2	37	CCDS5414.1																																																																																			C|0.727;A|0.273	0.273	strong		0.736	HIBADH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214132.1	NM_152740	
KRTAP12-4	386684	hgsc.bcm.edu	37	21	46074202	46074202	+	Silent	SNP	A	A	G	rs9984726	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:46074202A>G	ENST00000391618.1	-	1	374	c.330T>C	c.(328-330)acT>acC	p.T110T	TSPEAR_ENST00000323084.4_Intron	NM_198698.1	NP_941971.1	P60329	KR124_HUMAN	keratin associated protein 12-4	110						keratin filament (GO:0045095)				lung(4)|ovary(1)|prostate(1)	6						CTCAGCAGCCAGTGGGGGTGC	0.617													G|||	3932	0.785144	0.9191	0.7493	5008	,	,		17808	0.6458		0.7624	False		,,,				2504	0.7965				p.T110T		Atlas-SNP	.											.	KRTAP12-4	10	.	0			c.T330C						PASS	.	G	,	3598,422		1616,366,28	27.0	33.0	31.0		,330	0.9	0.0	21	dbSNP_119	31	5942,2410		2151,1640,385	no	intron,coding-synonymous	TSPEAR,KRTAP12-4	NM_144991.2,NM_198698.1	,	3767,2006,413	GG,GA,AA		28.8554,10.4975,22.8904	,	,110/113	46074202	9540,2832	2010	4176	6186	SO:0001819	synonymous_variant	386684	exon1			GCAGCCAGTGGGG	AB076360	CCDS42963.1	21q22.3	2006-03-13			ENSG00000212933	ENSG00000212933		"""Keratin associated proteins"""	20532	protein-coding gene	gene with protein product							Standard	NM_198698		Approved	KRTAP12.4	uc002zfs.1	P60329	OTTHUMG00000057633	ENST00000391618.1:c.330T>C	21.37:g.46074202A>G		Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	148	148	1	NM_198698	Q08AF5	Silent	SNP	ENST00000391618.1	37	CCDS42963.1																																																																																			A|0.264;G|0.736	0.736	strong		0.617	KRTAP12-4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128036.1		
HLA-C	3107	hgsc.bcm.edu	37	6	31238995	31238995	+	Silent	SNP	G	G	A	rs41553316	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:31238995G>A	ENST00000376228.5	-	3	488	c.474C>T	c.(472-474)acC>acT	p.T158T	HLA-C_ENST00000383329.3_Silent_p.T158T	NM_002117.5	NP_002108.4	Q95604	1C17_HUMAN	major histocompatibility complex, class I, C	158	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						TGTCCGCGGCGGTCCAGGAGC	0.706																																					p.T158T		Atlas-SNP	.											.	HLA-C	92	.	0			c.C474T						PASS	.	G		56,4268		0,56,2106	32.0	24.0	27.0		474	-5.6	0.0	6	dbSNP_127	27	293,8131		0,293,3919	no	coding-synonymous	HLA-C	NM_002117.5		0,349,6025	AA,AG,GG		3.4782,1.2951,2.7377		158/367	31238995	349,12399	2162	4212	6374	SO:0001819	synonymous_variant	3107	exon3			CGCGGCGGTCCAG	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.474C>T	6.37:g.31238995G>A		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	149	48	0.322148	NM_002117	O02864|O02958|Q29643|Q9MY30	Silent	SNP	ENST00000376228.5	37	CCDS34393.1	.	.	.	.	.	.	.	.	.	.	.	5.917	0.353241	0.11182	0.012951	0.034782	ENSG00000204525	ENST00000415537	.	.	.	2.81	-5.62	0.02481	.	.	.	.	.	T	0.08714	0.0216	.	.	.	0.20074	N	0.999938	.	.	.	.	.	.	T	0.14254	-1.0479	4	.	.	.	.	5.0919	0.14713	0.1703:0.5184:0.2055:0.1058	rs41553316	.	.	.	C	158	.	.	R	-	1	0	HLA-C	31346974	0.000000	0.05858	0.004000	0.12327	0.036000	0.12997	-2.190000	0.01247	-2.555000	0.00477	-2.311000	0.00256	CGC	G|0.972;A|0.028	0.028	strong		0.706	HLA-C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076281.3	NM_002117	
NOD1	10392	hgsc.bcm.edu	37	7	30492550	30492550	+	Silent	SNP	G	G	A	rs2235099|rs72551114	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:30492550G>A	ENST00000222823.4	-	6	1008	c.483C>T	c.(481-483)gaC>gaT	p.D161D	NOD1_ENST00000423334.2_Silent_p.D161D	NM_006092.2	NP_006083.1	Q9Y239	NOD1_HUMAN	nucleotide-binding oligomerization domain containing 1	161					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of MAPK activity (GO:0000187)|apoptotic process (GO:0006915)|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)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interleukin-8 biosynthetic process (GO:0042228)|intracellular signal transduction (GO:0035556)|JNK cascade (GO:0007254)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of dendritic cell antigen processing and presentation (GO:0002606)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of JNK cascade (GO:0046330)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of tumor necrosis factor production (GO:0032760)|protein oligomerization (GO:0051259)|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)	basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|cytosol (GO:0005829)	ATP binding (GO:0005524)|CARD domain binding (GO:0050700)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|identical protein binding (GO:0042802)|peptidoglycan binding (GO:0042834)|protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(17)|ovary(2)|prostate(1)|skin(2)	39						CCATGATGGTGTCCATGTAGA	0.597													G|||	1693	0.338059	0.4024	0.1758	5008	,	,		19153	0.3869		0.2326	False		,,,				2504	0.4243				p.D161D		Atlas-SNP	.											.	NOD1	79	.	0			c.C483T						PASS	.	G		1679,2727	510.4+/-367.5	323,1033,847	119.0	99.0	106.0		483	2.5	1.0	7	dbSNP_98	106	2119,6481	365.1+/-333.8	281,1557,2462	no	coding-synonymous	NOD1	NM_006092.2		604,2590,3309	AA,AG,GG		24.6395,38.1071,29.2019		161/954	30492550	3798,9208	2203	4300	6503	SO:0001819	synonymous_variant	10392	exon6			GATGGTGTCCATG	AF126484	CCDS5427.1	7p15-p14	2006-12-08	2006-12-08	2006-12-08	ENSG00000106100	ENSG00000106100		"""Nucleotide-binding domain and leucine rich repeat containing"""	16390	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 1"", ""NLR family, CARD domain containing 1"""	605980	"""caspase recruitment domain family, member 4"""	CARD4		10224040, 10329646	Standard	NM_006092		Approved	NLRC1, CLR7.1	uc003tav.3	Q9Y239	OTTHUMG00000023923	ENST00000222823.4:c.483C>T	7.37:g.30492550G>A		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	66	21	0.318182	NM_006092	B4DTU3|Q549U4|Q8IWF5	Silent	SNP	ENST00000222823.4	37	CCDS5427.1																																																																																			G|0.895;A|0.105	0.105	strong		0.597	NOD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250443.2		
DNAH1	25981	hgsc.bcm.edu	37	3	52391735	52391735	+	Silent	SNP	A	A	C	rs11714402	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:52391735A>C	ENST00000420323.2	+	23	4225	c.3964A>C	c.(3964-3966)Agg>Cgg	p.R1322R		NM_015512.4	NP_056327	Q9P2D7	DYH1_HUMAN	dynein, axonemal, heavy chain 1	1322	Stem. {ECO:0000250}.				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)		GGAGACCAAGAGGAGCGCCTT	0.632													C|||	807	0.161142	0.3101	0.1542	5008	,	,		17029	0.0238		0.165	False		,,,				2504	0.1022				p.R1322R		Atlas-SNP	.											DNAH1_ENST00000420323,NS,carcinoma,0,2	DNAH1	534	2	0			c.A3964C						scavenged	.	C		885,3197		102,681,1258	29.0	32.0	31.0		3964	-1.0	0.6	3	dbSNP_120	31	1421,6957		112,1197,2880	no	coding-synonymous	DNAH1	NM_015512.4		214,1878,4138	CC,CA,AA		16.9611,21.6805,18.5072		1322/4266	52391735	2306,10154	2041	4189	6230	SO:0001819	synonymous_variant	25981	exon23			ACCAAGAGGAGCG	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.3964A>C	3.37:g.52391735A>C		Somatic	144	1	0.00694444		WXS	Illumina HiSeq	Phase_I	142	72	0.507042	NM_015512	B0I1R6|O00436|O15435|O95491|Q6ZU48|Q86YK7|Q8TEJ4|Q92863|Q9H8E6|Q9UFW6|Q9Y4Z7	Silent	SNP	ENST00000420323.2	37	CCDS46842.1																																																																																			A|0.837;C|0.163	0.163	strong		0.632	DNAH1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350816.1	NM_015512	
NME8	51314	hgsc.bcm.edu	37	7	37934146	37934146	+	Missense_Mutation	SNP	T	T	C	rs56128139|rs386712272	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:37934146T>C	ENST00000199447.4	+	16	1850	c.1478T>C	c.(1477-1479)aTa>aCa	p.I493T	EPDR1_ENST00000476620.1_Intron|NME8_ENST00000440017.1_Missense_Mutation_p.I493T	NM_016616.4	NP_057700.3	Q8N427	TXND3_HUMAN	NME/NM23 family member 8	493	NDK 3.		I -> T (in dbSNP:rs56128139). {ECO:0000269|PubMed:15489334}.		cell differentiation (GO:0030154)|cell redox homeostasis (GO:0045454)|CTP biosynthetic process (GO:0006241)|GTP biosynthetic process (GO:0006183)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)|UTP biosynthetic process (GO:0006228)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|nucleoside diphosphate kinase activity (GO:0004550)										CCTGAGCAAATAGAGAAAATT	0.303													T|||	790	0.157748	0.0151	0.2291	5008	,	,		17475	0.1359		0.3419	False		,,,				2504	0.1329				p.I493T		Atlas-SNP	.											.	.	.	.	0			c.T1478C						PASS	.	T	THR/ILE	5,4401		2,1,2200	61.0	63.0	63.0		1478	1.1	0.0	7	dbSNP_129	63	77,8521		12,53,4234	yes	missense	TXNDC3	NM_016616.4	89	14,54,6434	CC,CT,TT		0.8956,0.1135,0.6306	benign	493/589	37934146	82,12922	2203	4299	6502	SO:0001583	missense	51314	exon16			AGCAAATAGAGAA	AF202051	CCDS5452.1	7p15.2	2012-05-18	2012-05-18	2012-05-18	ENSG00000086288	ENSG00000086288			16473	protein-coding gene	gene with protein product	"""sperm-specific thioredoxin 2"""	607421	"""thioredoxin domain containing 3 (spermatozoa)"""	TXNDC3		11737268, 11768308, 19852809	Standard	NM_016616		Approved	CILD6, SPTRX2, NM23-H8	uc003tfn.3	Q8N427	OTTHUMG00000023716	ENST00000199447.4:c.1478T>C	7.37:g.37934146T>C	ENSP00000199447:p.Ile493Thr	Somatic	268	0	0		WXS	Illumina HiSeq	Phase_I	242	190	0.785124	NM_016616	Q9NZH1	Missense_Mutation	SNP	ENST00000199447.4	37	CCDS5452.1	343	0.15705128205128205	11	0.022357723577235773	73	0.20165745856353592	70	0.12237762237762238	189	0.24934036939313983	T	6.406	0.442939	0.12164	0.001135	0.008956	ENSG00000086288	ENST00000199447;ENST00000440017	T;T	0.43688	0.94;0.94	4.05	1.11	0.20524	.	0.568879	0.14595	N	0.310022	T	0.00012	0.0000	N	0.11201	0.11	0.80722	P	0.0	B	0.14438	0.01	B	0.23275	0.045	T	0.26360	-1.0105	9	0.52906	T	0.07	-4.655	5.9615	0.19303	0.0:0.6617:0.0:0.3383	rs56128139;rs62001871	493	Q8N427	TXND3_HUMAN	T	493	ENSP00000199447:I493T;ENSP00000397063:I493T	ENSP00000199447:I493T	I	+	2	0	TXNDC3	37900671	0.012000	0.17670	0.000000	0.03702	0.002000	0.02628	0.098000	0.15189	0.265000	0.21872	-0.621000	0.04028	ATA	T|0.761;C|0.239	0.239	strong		0.303	NME8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219946.1	NM_016616	
MICA	100507436	hgsc.bcm.edu	37	6	31380194	31380194	+	Missense_Mutation	SNP	T	T	C	rs41554412	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:31380194T>C	ENST00000449934.2	+	5	1039	c.985T>C	c.(985-987)Tgt>Cgt	p.C329R	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)				TTATTTTCTATGTCCGTTGTT	0.468													t|||	1266	0.252796	0.3616	0.2853	5008	,	,		18607	0.1776		0.1779	False		,,,				2504	0.2372				p.C329R		Atlas-SNP	.											MICA,NS,carcinoma,-2,1	MICA	21	1	0			c.T985C						PASS	.						163.0	154.0	156.0					6																	31380194		692	1591	2283	SO:0001583	missense	100507436	exon5			TTTCTATGTCCGT	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.985T>C	6.37:g.31380194T>C	ENSP00000413079:p.Cys329Arg	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	44	24	0.545455	NM_001177519		Missense_Mutation	SNP	ENST00000449934.2	37	CCDS56412.1	528	0.24175824175824176	172	0.34959349593495936	113	0.31215469613259667	94	0.16433566433566432	149	0.19656992084432717	-	7.095	0.572964	0.13623	.	.	ENSG00000204520	ENST00000376222;ENST00000364810;ENST00000399172;ENST00000449934;ENST00000421350	T;T	0.01438	5.44;4.89	1.49	0.201	0.15186	.	.	.	.	.	T	0.01029	0.0034	L	0.34521	1.04	0.80722	P	0.0	D;D	0.63046	0.992;0.992	P;P	0.59703	0.74;0.862	T	0.54098	-0.8344	8	0.87932	D	0	.	3.6509	0.08203	0.3419:0.0:0.0:0.6581	rs41554412;rs61738276	191;329	Q5SS58;Q96QC4	.;.	R	191;329;286;329;220	ENSP00000413079:C329R;ENSP00000402410:C220R	ENSP00000365394:C329R	C	+	1	0	MICA	31488173	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-0.397000	0.07269	0.086000	0.17137	0.310000	0.20435	TGT	T|0.773;C|0.227	0.227	strong		0.468	MICA-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076101.7	NM_001177519	
KLHDC7B	113730	hgsc.bcm.edu	37	22	50988062	50988062	+	Silent	SNP	G	G	T	rs140519	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:50988062G>T	ENST00000395676.2	+	1	1601	c.1467G>T	c.(1465-1467)gtG>gtT	p.V489V	CTA-384D8.31_ENST00000434237.1_RNA	NM_138433.3	NP_612442.2	Q96G42	KLD7B_HUMAN	kelch domain containing 7B	489										central_nervous_system(1)|cervix(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	14		all_cancers(38;1.53e-10)|all_epithelial(38;1.82e-09)|Breast(42;0.000448)|all_lung(38;0.000665)|Lung NSC(38;0.0104)|Ovarian(80;0.104)|Lung SC(80;0.162)|Hepatocellular(38;0.178)		OV - Ovarian serous cystadenocarcinoma(4;7.49e-69)|all cancers(3;9.79e-66)|Epithelial(4;1.3e-63)|GBM - Glioblastoma multiforme(4;0.000399)|Lung(4;0.125)|BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)		GCGACATCGTGGCACTGGGGG	0.667													G|||	2029	0.405152	0.1936	0.4366	5008	,	,		13461	0.5784		0.495	False		,,,				2504	0.3978				p.V489V		Atlas-SNP	.											KLHDC7B,extremity,malignant_melanoma,+2,1	KLHDC7B	39	1	0			c.G1467T						PASS	.	G		1017,3389		119,779,1305	48.0	54.0	52.0		1467	3.2	1.0	22	dbSNP_78	52	4137,4459		1014,2109,1175	no	coding-synonymous	KLHDC7B	NM_138433.3		1133,2888,2480	TT,TG,GG		48.127,23.0822,39.6401		489/595	50988062	5154,7848	2203	4298	6501	SO:0001819	synonymous_variant	113730	exon1			CATCGTGGCACTG	BC009980	CCDS14097.2	22q13.33	2006-11-29		2005-12-13	ENSG00000130487	ENSG00000130487			25145	protein-coding gene	gene with protein product							Standard	NM_138433		Approved	MGC16635	uc003bmi.3	Q96G42	OTTHUMG00000150250	ENST00000395676.2:c.1467G>T	22.37:g.50988062G>T		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	70	38	0.542857	NM_138433		Silent	SNP	ENST00000395676.2	37	CCDS14097.2																																																																																			G|0.594;T|0.406	0.406	strong		0.667	KLHDC7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317089.2	NM_138433	
SFRP2	6423	hgsc.bcm.edu	37	4	154709854	154709854	+	Missense_Mutation	SNP	G	G	A	rs386680891|rs4643790	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	91	0	0		WXS	Illumina HiSeq	Phase_I	110	50	0.454545	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		
SIGLEC12	89858	hgsc.bcm.edu	37	19	52001485	52001485	+	Missense_Mutation	SNP	G	G	A	rs11668530	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:52001485G>A	ENST00000291707.3	-	5	1247	c.1192C>T	c.(1192-1194)Cac>Tac	p.H398Y	SIGLEC12_ENST00000598614.1_Missense_Mutation_p.H280Y	NM_053003.2	NP_443729.1	Q96PQ1	SIG12_HUMAN	sialic acid binding Ig-like lectin 12 (gene/pseudogene)	398	Ig-like C2-type 2.		H -> Y (in dbSNP:rs11668530).		cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			NS(2)|biliary_tract(1)|breast(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(8)|liver(1)|lung(23)|ovary(4)|prostate(2)|skin(8)|stomach(3)|upper_aerodigestive_tract(2)	61		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.00161)|OV - Ovarian serous cystadenocarcinoma(262;0.0102)		CAGACAAGGTGCAGGGACTGG	0.597													g|||	1770	0.353435	0.0605	0.513	5008	,	,		17523	0.2728		0.498	False		,,,				2504	0.5706				p.H398Y		Atlas-SNP	.											.	SIGLEC12	243	.	0			c.C1192T						PASS	.	G	TYR/HIS,TYR/HIS	631,3775		52,527,1624	39.0	35.0	36.0		838,1192	1.4	0.2	19	dbSNP_120	36	4457,4143		1169,2119,1012	yes	missense,missense	SIGLEC12	NM_033329.1,NM_053003.2	83,83	1221,2646,2636	AA,AG,GG		48.1744,14.3214,39.1204	benign,benign	280/478,398/596	52001485	5088,7918	2203	4300	6503	SO:0001583	missense	89858	exon5			CAAGGTGCAGGGA	AF282256	CCDS12833.1, CCDS59416.1	19q13.41	2013-01-29	2011-06-29	2004-10-20	ENSG00000254521	ENSG00000254521		"""Sialic acid binding Ig-like lectins"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	15482	protein-coding gene	gene with protein product		606094	"""SIGLEC-like 1"", ""sialic acid binding Ig-like lectin 12"""	SIGLECL1		11409877, 11328818, 21555517	Standard	NM_053003		Approved	SLG, S2V, Siglec-XII, Siglec-12, Siglec-L1	uc002pwx.1	Q96PQ1	OTTHUMG00000165524	ENST00000291707.3:c.1192C>T	19.37:g.52001485G>A	ENSP00000291707:p.His398Tyr	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	42	42	1	NM_053003	Q8IYH7	Missense_Mutation	SNP	ENST00000291707.3	37	CCDS12833.1	740	0.33882783882783885	40	0.08130081300813008	174	0.48066298342541436	145	0.2534965034965035	381	0.5026385224274407	.	5.039	0.192805	0.09599	0.143214	0.518256	ENSG00000254521	ENST00000291707	T	0.11930	2.73	1.39	1.39	0.22231	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.407398	0.18126	U	0.150893	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B;B	0.22983	0.078;0.024	B;B	0.30401	0.115;0.022	T	0.42103	-0.9471	9	0.27082	T	0.32	.	6.2185	0.20667	0.0:0.0:1.0:0.0	rs11668530;rs56924805;rs11668530	398;280	Q96PQ1;Q96PQ1-2	SIG12_HUMAN;.	Y	398	ENSP00000291707:H398Y	ENSP00000291707:H398Y	H	-	1	0	SIGLEC12	56693297	0.087000	0.21565	0.164000	0.22755	0.025000	0.11179	0.197000	0.17197	1.076000	0.40961	0.393000	0.25936	CAC	G|0.640;A|0.360	0.360	strong		0.597	SIGLEC12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384641.2	NM_053003	
MYH7B	57644	hgsc.bcm.edu	37	20	33565755	33565755	+	Missense_Mutation	SNP	G	G	A	rs11906160	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:33565755G>A	ENST00000262873.7	+	3	165	c.73G>A	c.(73-75)Gcc>Acc	p.A25T		NM_020884.3	NP_065935.2	A7E2Y1	MYH7B_HUMAN	myosin, heavy chain 7B, cardiac muscle, beta	0						membrane (GO:0016020)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(2)|breast(5)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(19)|ovary(5)|prostate(3)|upper_aerodigestive_tract(2)|urinary_tract(3)	54			BRCA - Breast invasive adenocarcinoma(18;0.00691)			GCCTTGGGCCGCCTTGAACCT	0.602													G|||	782	0.15615	0.3041	0.1052	5008	,	,		13720	0.0863		0.1034	False		,,,				2504	0.1186				p.A25T		Atlas-SNP	.											.	MYH7B	145	.	0			c.G73A						PASS	.	G	THR/ALA	1039,3285		115,809,1238	119.0	129.0	126.0	http://www.ncbi.nlm.nih.gov/pubmed?term	73	-9.1	0.0	20	dbSNP_120	126	950,7582		50,850,3366	yes	missense	MYH7B	NM_020884.3	58	165,1659,4604	AA,AG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	11.1346,24.0287,15.4714		25/1984	33565755	1989,10867	2162	4266	6428	SO:0001583	missense	57644	exon5			TGGGCCGCCTTGA	AB040945	CCDS42869.1	20q11	2011-09-27	2006-09-29		ENSG00000078814	ENSG00000078814		"""Myosins / Myosin superfamily : Class II"""	15906	protein-coding gene	gene with protein product		609928	"""myosin, heavy polypeptide 7B, cardiac muscle, beta"""			11919279, 15014174	Standard	XM_006723839		Approved	KIAA1512, dJ756N5.1, MYH14, MHC14	uc002xbi.2	A7E2Y1	OTTHUMG00000032320	ENST00000262873.7:c.73G>A	20.37:g.33565755G>A	ENSP00000262873:p.Ala25Thr	Somatic	22	0	0		WXS	Illumina HiSeq	Phase_I	28	9	0.321429	NM_020884	Q5JVW7|Q6NT44|Q6NT57|Q6WG75|Q96I57|Q9NWE2|Q9P216	Missense_Mutation	SNP	ENST00000262873.7	37	CCDS42869.1	311	0.1423992673992674	138	0.2804878048780488	46	0.1270718232044199	40	0.06993006993006994	87	0.11477572559366754	G	10.14	1.268479	0.23136	0.240287	0.111346	ENSG00000078814	ENST00000262873	D	0.86097	-2.07	4.52	-9.05	0.00730	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.02821	-1.1106	5	0.07030	T	0.85	.	10.2475	0.43350	0.5764:0.0:0.3366:0.087	rs11906160;rs61678150;rs11906160	.	.	.	T	25	ENSP00000262873:A25T	ENSP00000262873:A25T	A	+	1	0	MYH7B	33029416	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-3.052000	0.00627	-2.137000	0.00809	-1.421000	0.01109	GCC	G|0.858;A|0.142	0.142	strong		0.602	MYH7B-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000078833.2	NM_020884	
ACTR3C	653857	hgsc.bcm.edu	37	7	149983565	149983565	+	Missense_Mutation	SNP	T	T	C	rs28634863|rs71531433	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:149983565T>C	ENST00000539352.1	-	5	613	c.362A>G	c.(361-363)cAg>cGg	p.Q121R	ACTR3C_ENST00000252071.4_Missense_Mutation_p.Q121R	NM_001164458.1	NP_001157930.1	Q9C0K3	ARP3C_HUMAN	ARP3 actin-related protein 3 homolog C (yeast)	121						extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)	p.Q121R(1)									GATCCACTTCTGGGGATCCAC	0.413													C|||	1445	0.288538	0.559	0.1023	5008	,	,		18724	0.1974		0.0954	False		,,,				2504	0.3476				p.Q121R		Atlas-SNP	.											Q9C0K3_HUMAN,NS,carcinoma,0,1	.	.	1	1	Substitution - Missense(1)	stomach(1)	c.A362G						scavenged	.						179.0	210.0	201.0					7																	149983565		692	1591	2283	SO:0001583	missense	653857	exon5			CACTTCTGGGGAT		CCDS47744.1	7q36.1	2009-09-23			ENSG00000106526	ENSG00000106526			37282	protein-coding gene	gene with protein product						11162478, 14651955	Standard	NM_001164458		Approved	ARP11	uc022aps.1	Q9C0K3	OTTHUMG00000158323	ENST00000539352.1:c.362A>G	7.37:g.149983565T>C	ENSP00000440990:p.Gln121Arg	Somatic	201	0	0		WXS	Illumina HiSeq	Phase_I	120	30	0.25	NM_001164459	Q5CZI4	Missense_Mutation	SNP	ENST00000539352.1	37	CCDS47744.1	364	0.16666666666666666	191	0.3882113821138211	26	0.0718232044198895	87	0.1520979020979021	60	0.079155672823219	C	0	-2.711141	0.00094	.	.	ENSG00000106526	ENST00000478393;ENST00000252071;ENST00000539352;ENST00000477871	T;T;T;D	0.96619	3.31;3.31;3.31;-4.07	2.42	1.51	0.23008	.	0.175232	0.37761	N	0.001946	T	0.00012	0.0000	N	0.05177	-0.1	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.25641	-1.0126	8	.	.	.	-0.2029	3.2015	0.06651	0.0:0.4921:0.2256:0.2823	rs28634863	121	Q9C0K3	ARP3C_HUMAN	R	119;121;121;220	ENSP00000417426:Q119R;ENSP00000252071:Q121R;ENSP00000440990:Q121R;ENSP00000418635:Q220R	.	Q	-	2	0	ACTR3C	149614498	0.000000	0.05858	0.697000	0.30258	0.172000	0.22775	-0.100000	0.10990	0.131000	0.18576	-1.160000	0.01791	CAG	T|0.500;C|0.500	0.500	weak		0.413	ACTR3C-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350676.2		
GDPGP1	390637	hgsc.bcm.edu	37	15	90785060	90785060	+	Missense_Mutation	SNP	C	C	T	rs10153004	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:90785060C>T	ENST00000558017.1	+	4	1340	c.920C>T	c.(919-921)aCa>aTa	p.T307I	GDPGP1_ENST00000329600.6_Missense_Mutation_p.T307I	NM_001013657.2	NP_001013679.2	Q6ZNW5	GDPP1_HUMAN	GDP-D-glucose phosphorylase 1	307			T -> I (in dbSNP:rs10153004). {ECO:0000269|PubMed:14702039}.		glucose metabolic process (GO:0006006)	cytoplasm (GO:0005737)	GDP-D-glucose phosphorylase activity (GO:0080048)|guanyl-nucleotide exchange factor activity (GO:0005085)|hydrolase activity (GO:0016787)|nucleotide binding (GO:0000166)|nucleotidyltransferase activity (GO:0016779)										TCAGCCCTCACAGGGGTCCGA	0.557													C|||	658	0.13139	0.2405	0.1398	5008	,	,		19012	0.0		0.1789	False		,,,				2504	0.0644				p.T307I		Atlas-SNP	.											.	.	.	.	0			c.C920T						PASS	.	C	ILE/THR	869,3529	339.9+/-306.0	88,693,1418	92.0	90.0	91.0		920	3.7	0.0	15	dbSNP_119	91	1433,7163	275.0+/-291.5	131,1171,2996	yes	missense	C15orf58	NM_001013657.2	89	219,1864,4414	TT,TC,CC		16.6705,19.759,17.7159	benign	307/386	90785060	2302,10692	2199	4298	6497	SO:0001583	missense	390637	exon4			CCCTCACAGGGGT		CCDS32327.1	15q26.1	2012-05-04	2012-05-04	2012-05-04	ENSG00000183208	ENSG00000183208	2.7.7.78		34360	protein-coding gene	gene with protein product			"""chromosome 15 open reading frame 58"""	C15orf58		21507950	Standard	NM_001013657		Approved		uc002bpc.3	Q6ZNW5		ENST00000558017.1:c.920C>T	15.37:g.90785060C>T	ENSP00000452793:p.Thr307Ile	Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	180	74	0.411111	NM_001013657		Missense_Mutation	SNP	ENST00000558017.1	37	CCDS32327.1	311	0.1423992673992674	114	0.23170731707317074	61	0.1685082872928177	0	0.0	136	0.17941952506596306	C	10.97	1.501071	0.26861	0.19759	0.166705	ENSG00000183208	ENST00000329600	T	0.23147	1.92	5.62	3.71	0.42584	.	0.493880	0.19174	N	0.120863	T	0.00012	0.0000	L	0.38175	1.15	0.80722	P	0.0	B	0.27656	0.184	B	0.21151	0.033	T	0.28299	-1.0048	9	0.38643	T	0.18	-0.9139	8.6185	0.33847	0.0:0.7589:0.1583:0.0829	rs10153004;rs52820774;rs10153004	307	Q6ZNW5	VTC2_HUMAN	I	307	ENSP00000368405:T307I	ENSP00000368405:T307I	T	+	2	0	C15orf58	88586064	0.000000	0.05858	0.025000	0.17156	0.889000	0.51656	0.164000	0.16542	0.709000	0.31976	0.655000	0.94253	ACA	C|0.835;T|0.165	0.165	strong		0.557	GDPGP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416973.1	NM_001013657	
STON1	11037	hgsc.bcm.edu	37	2	48808898	48808898	+	Silent	SNP	C	C	T	rs3749145	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:48808898C>T	ENST00000406226.1	+	3	1321	c.1126C>T	c.(1126-1128)Ctg>Ttg	p.L376L	STON1_ENST00000309835.3_Silent_p.L376L|STON1_ENST00000404752.1_Silent_p.L376L|STON1-GTF2A1L_ENST00000394754.1_Silent_p.L376L|STON1-GTF2A1L_ENST00000309827.2_Silent_p.L376L|STON1-GTF2A1L_ENST00000402114.2_Silent_p.L376L|STON1-GTF2A1L_ENST00000394751.3_Silent_p.L376L|STON1-GTF2A1L_ENST00000405008.1_Silent_p.L376L	NM_001198595.1	NP_001185524.1	Q9Y6Q2	STON1_HUMAN	stonin 1	376	SHD. {ECO:0000255|PROSITE- ProRule:PRU00403}.				endocytosis (GO:0006897)|intracellular protein transport (GO:0006886)|regulation of endocytosis (GO:0030100)	clathrin adaptor complex (GO:0030131)				NS(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(19)|prostate(3)|skin(2)	37		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			AGAGCAGATGCTGAAGTTGGG	0.408													C|||	1673	0.334065	0.2791	0.3098	5008	,	,		21013	0.3879		0.3191	False		,,,				2504	0.3855				p.L376L		Atlas-SNP	.											.	STON1	100	.	0			c.C1126T						PASS	.	C	,,,,	1311,3095	437.6+/-345.0	195,921,1087	69.0	69.0	69.0		1126,1126,1126,1126,1126	2.2	1.0	2	dbSNP_107	69	2751,5849	437.4+/-358.6	456,1839,2005	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	STON1,STON1-GTF2A1L	NM_001198593.1,NM_001198594.1,NM_001198595.1,NM_006873.3,NM_172311.2	,,,,	651,2760,3092	TT,TC,CC		31.9884,29.7549,31.2317	,,,,	376/1159,376/1136,376/736,376/736,376/1183	48808898	4062,8944	2203	4300	6503	SO:0001819	synonymous_variant	11037	exon3			CAGATGCTGAAGT	AF026169	CCDS1841.1	2p16.3	2008-02-05			ENSG00000243244	ENSG00000243244			17003	protein-coding gene	gene with protein product	"""stoned B homolog 1 (Drosophila)"""	605357				14504226, 10364255	Standard	NM_001198595		Approved	SBLF, stoned-b1		Q9Y6Q2	OTTHUMG00000129169	ENST00000406226.1:c.1126C>T	2.37:g.48808898C>T		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	226	53	0.234513	NM_001198595	A8MXJ1|B5MCF5|B7ZL16|Q96JE3|Q9BYX3	Silent	SNP	ENST00000406226.1	37	CCDS1841.1																																																																																			C|0.681;T|0.319	0.319	strong		0.408	STON1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323848.2	NM_006873	
MFHAS1	9258	hgsc.bcm.edu	37	8	8749318	8749318	+	Silent	SNP	A	A	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:8749318A>G	ENST00000276282.6	-	1	1837	c.1251T>C	c.(1249-1251)caT>caC	p.H417H		NM_004225.2	NP_004216.2	Q9Y4C4	MFHA1_HUMAN	malignant fibrous histiocytoma amplified sequence 1	417	Roc. {ECO:0000255|PROSITE- ProRule:PRU00758}.									endometrium(1)|kidney(3)|large_intestine(7)|lung(6)|ovary(1)|prostate(2)|stomach(1)	21		Hepatocellular(245;0.217)		COAD - Colon adenocarcinoma(149;0.124)		CTGCAGCCTTATGCCCCATCA	0.617																																					p.H417H	Melanoma(103;1201 2045 17515 28966)	Atlas-SNP	.											.	MFHAS1	58	.	0			c.T1251C						PASS	.						48.0	43.0	44.0					8																	8749318		2203	4300	6503	SO:0001819	synonymous_variant	9258	exon1			AGCCTTATGCCCC	AB016816	CCDS34844.1	8p23.1	2014-03-07			ENSG00000147324	ENSG00000147324			16982	protein-coding gene	gene with protein product	"""leucine rich repeat containing 65"", ""malignant fibrous histiocytoma-amplified sequences with leucine-rich tandem repeats 1"""	605352				9973190	Standard	NM_004225		Approved	MASL1, LRRC65	uc003wsj.1	Q9Y4C4	OTTHUMG00000163676	ENST00000276282.6:c.1251T>C	8.37:g.8749318A>G		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	36	17	0.472222	NM_004225	Q96CI0	Silent	SNP	ENST00000276282.6	37	CCDS34844.1																																																																																			.	.	none		0.617	MFHAS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374724.2	NM_004225	
HLA-A	3105	hgsc.bcm.edu	37	6	29910731	29910731	+	Missense_Mutation	SNP	G	G	A	rs79361534|rs281864737	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:29910731G>A	ENST00000396634.1	+	4	612	c.271G>A	c.(271-273)Gtg>Atg	p.V91M	HLA-A_ENST00000376802.2_Missense_Mutation_p.V91M|HLA-A_ENST00000376809.5_Missense_Mutation_p.V91M|HLA-A_ENST00000376806.5_Missense_Mutation_p.V91M			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	91	Alpha-1.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	beta-2-microglobulin binding (GO:0030881)|peptide antigen binding (GO:0042605)|TAP binding (GO:0046977)			central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	30						GACACGGAATGTGAAGGCCCA	0.687									Osteosarcoma, Familial Clustering of;Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of;Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of	Multiple Myeloma(9;0.094)			g|||	454	0.090655	0.0847	0.0476	5008	,	,		12317	0.0188		0.1262	False		,,,				2504	0.1667				p.V91M		Atlas-SNP	.											.	HLA-A	89	.	0			c.G271A						PASS	.	G	MET/VAL	353,4047		18,317,1865	80.0	84.0	82.0		271	-6.4	0.0	6	dbSNP_127	82	1485,7097		170,1145,2976	no	missense	HLA-A	NM_002116.7	21	188,1462,4841	AA,AG,GG		17.3037,8.0227,14.1581	benign	91/366	29910731	1838,11144	2200	4291	6491	SO:0001583	missense	3105	exon2	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	CGGAATGTGAAGG	D32129	CCDS34373.1	6p21.3	2013-01-11			ENSG00000206503	ENSG00000206503		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4931	protein-coding gene	gene with protein product		142800				8838351	Standard	NM_001242758		Approved		uc003nol.3	P01891	OTTHUMG00000130501	ENST00000396634.1:c.271G>A	6.37:g.29910731G>A	ENSP00000379873:p.Val91Met	Somatic	274	0	0		WXS	Illumina HiSeq	Phase_I	179	108	0.603352	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Missense_Mutation	SNP	ENST00000396634.1	37	CCDS34373.1	198	0.09065934065934066	45	0.09146341463414634	19	0.052486187845303865	12	0.02097902097902098	122	0.16094986807387862	.	5.403	0.259593	0.10239	0.080227	0.173037	ENSG00000206503	ENST00000396634;ENST00000376806;ENST00000376809;ENST00000355767;ENST00000376802	T;T;T;T	0.00010	9.4;9.4;9.4;9.4	3.2	-6.41	0.01938	MHC class I, alpha chain, alpha1/alpha2 (6);MHC classes I/II-like antigen recognition protein (3);MHC class I-like antigen recognition (3);	754.410000	0.00447	U	0.000088	T	0.00039	0.0001	L	0.28054	0.825	0.80722	P	0.0	B;B;B;B;B	0.17667	0.002;0.023;0.002;0.011;0.002	B;B;B;B;B	0.23419	0.005;0.046;0.005;0.012;0.005	T	0.09207	-1.0685	9	0.41790	T	0.15	.	4.2384	0.10637	0.2942:0.0:0.1814:0.5244	rs41564215	91;91;91;91;91	P13746;Q5SRN7;P16188;Q5SRN5;P04439	1A11_HUMAN;.;1A30_HUMAN;.;1A03_HUMAN	M	91	ENSP00000379873:V91M;ENSP00000366002:V91M;ENSP00000366005:V91M;ENSP00000365998:V91M	ENSP00000348012:V91M	V	+	1	0	HLA-A	30018710	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-4.711000	0.00195	-1.498000	0.01824	-1.251000	0.01509	GTG	A|0.124;G|0.876	0.124	strong		0.687	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
PKHD1	5314	hgsc.bcm.edu	37	6	51914956	51914956	+	Splice_Site	SNP	G	G	A	rs9370096	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:51914956G>A	ENST00000371117.3	-	22	2553	c.2278C>T	c.(2278-2280)Cgc>Tgc	p.R760C	PKHD1_ENST00000340994.4_Splice_Site_p.R760C	NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	760			R -> C (in dbSNP:rs9370096). {ECO:0000269|PubMed:11919560, ECO:0000269|PubMed:12846734, ECO:0000269|PubMed:12874454}.|R -> H (in ARPKD). {ECO:0000269|PubMed:11898128, ECO:0000269|PubMed:12506140}.|R -> W (in dbSNP:rs9370096).		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)					ACTCCTTACCGTGCAGTGATG	0.542											OREG0017493	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	1782	0.355831	0.1097	0.6009	5008	,	,		19454	0.4048		0.503	False		,,,				2504	0.3129				p.R760C		Atlas-SNP	.											.	PKHD1	927	.	0			c.C2278T						PASS	.	G	CYS/ARG,CYS/ARG	667,3739	282.2+/-276.4	53,561,1589	59.0	54.0	56.0		2278,2278	-6.3	0.8	6	dbSNP_119	56	4388,4212	583.5+/-391.6	1137,2114,1049	yes	missense-near-splice,missense-near-splice	PKHD1	NM_138694.3,NM_170724.2	180,180	1190,2675,2638	AA,AG,GG		48.9767,15.1384,38.8667	benign,benign	760/4075,760/3397	51914956	5055,7951	2203	4300	6503	SO:0001630	splice_region_variant	5314	exon22			CTTACCGTGCAGT	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.2279+1C>T	6.37:g.51914956G>A		Somatic	109	0	0	981	WXS	Illumina HiSeq	Phase_I	108	108	1	NM_170724	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Missense_Mutation	SNP	ENST00000371117.3	37	CCDS4935.1	897	0.4107142857142857	62	0.12601626016260162	214	0.5911602209944752	233	0.40734265734265734	388	0.5118733509234829	G	13.42	2.230413	0.39399	0.151384	0.510233	ENSG00000170927	ENST00000371117;ENST00000340994;ENST00000393616	D;D	0.87571	-2.06;-2.27	5.64	-6.31	0.02001	.	0.515347	0.19974	N	0.101902	T	0.42291	0.1196	N	0.02391	-0.57	0.24758	P	0.99294784	B;B	0.15473	0.013;0.007	B;B	0.09377	0.004;0.002	T	0.25398	-1.0133	9	0.37606	T	0.19	.	7.0585	0.25113	0.4834:0.0:0.1262:0.3904	rs9370096;rs52833131;rs58979956;rs9370096	760;760	P08F94-2;P08F94	.;PKHD1_HUMAN	C	760	ENSP00000360158:R760C;ENSP00000341097:R760C	ENSP00000341097:R760C	R	-	1	0	PKHD1	52022915	0.003000	0.15002	0.834000	0.33040	0.875000	0.50365	-0.487000	0.06505	-0.738000	0.04817	-0.140000	0.14226	CGC	G|0.620;A|0.380	0.380	strong		0.542	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694	Missense_Mutation
RNF17	56163	hgsc.bcm.edu	37	13	25440318	25440318	+	Missense_Mutation	SNP	G	G	A	rs9507425	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:25440318G>A	ENST00000255324.5	+	30	4190	c.4138G>A	c.(4138-4140)Gaa>Aaa	p.E1380K	RNF17_ENST00000339524.3_Missense_Mutation_p.E390K|RNF17_ENST00000381921.1_Missense_Mutation_p.E1338K	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	274	0	0		WXS	Illumina HiSeq	Phase_I	227	103	0.453745	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	
KRTAP10-9	386676	hgsc.bcm.edu	37	21	46047857	46047857	+	Missense_Mutation	SNP	C	C	T	rs9980129	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:46047857C>T	ENST00000397911.3	+	1	818	c.769C>T	c.(769-771)Cgc>Tgc	p.R257C	TSPEAR_ENST00000323084.4_Intron|KRTAP10-9_ENST00000484861.1_Intron	NM_198690.2	NP_941963.2	P60411	KR109_HUMAN	keratin associated protein 10-9	257			R -> C (in dbSNP:rs9980129). {ECO:0000269|PubMed:14962103, ECO:0000269|PubMed:15489334}.			keratin filament (GO:0045095)				endometrium(1)|kidney(1)|large_intestine(1)|lung(6)	9						CACCTCCTCCCGCCAGCCCAG	0.692													T|||	3138	0.626597	0.5076	0.6744	5008	,	,		18439	0.6488		0.7068	False		,,,				2504	0.6483				p.R257C		Atlas-SNP	.											.	KRTAP10-9	24	.	0			c.C769T						PASS	.	T	,CYS/ARG	2317,2085	528.4+/-372.4	626,1065,510	61.0	78.0	72.0		,769	1.2	1.0	21	dbSNP_119	72	5788,2798	430.3+/-356.5	1953,1882,458	yes	intron,missense	TSPEAR,KRTAP10-9	NM_144991.2,NM_198690.2	,180	2579,2947,968	TT,TC,CC		32.5879,47.3648,37.5962	,benign	,257/293	46047857	8105,4883	2201	4293	6494	SO:0001583	missense	386676	exon1			TCCTCCCGCCAGC	AJ566386	CCDS42961.1	21q22.3	2007-10-05			ENSG00000221837	ENSG00000221837		"""Keratin associated proteins"""	22971	protein-coding gene	gene with protein product				KRTAP18-9			Standard	NM_198690		Approved	KAP10.9, KAP18.9	uc002zfp.4	P60411	OTTHUMG00000057637	ENST00000397911.3:c.769C>T	21.37:g.46047857C>T	ENSP00000381009:p.Arg257Cys	Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	185	183	0.989189	NM_198690	A2RRG1|A6NIR9|Q70LJ1	Missense_Mutation	SNP	ENST00000397911.3	37	CCDS42961.1	1384	0.6336996336996337	252	0.5121951219512195	245	0.6767955801104972	353	0.6171328671328671	534	0.7044854881266491	t	0.033	-1.322386	0.01320	0.526352	0.674121	ENSG00000221837	ENST00000397911	T	0.00635	6.06	2.6	1.24	0.21308	.	.	.	.	.	T	0.00012	0.0000	N	0.00043	-2.465	0.36089	P	0.15666400000000003	B	0.20052	0.041	B	0.18871	0.023	T	0.06935	-1.0799	7	.	.	.	.	3.9932	0.09546	0.0:0.1389:0.2108:0.6503	rs9980129	257	P60411	KR109_HUMAN	C	257	ENSP00000381009:R257C	.	R	+	1	0	KRTAP10-9	44872285	0.190000	0.23276	0.997000	0.53966	0.734000	0.41952	0.165000	0.16564	0.229000	0.21039	-0.360000	0.07572	CGC	C|0.352;T|0.648	0.648	strong		0.692	KRTAP10-9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128040.1		
SLC16A9	220963	hgsc.bcm.edu	37	10	61414176	61414176	+	Missense_Mutation	SNP	G	G	A	rs56370926	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:61414176G>A	ENST00000395348.3	-	5	1244	c.608C>T	c.(607-609)gCt>gTt	p.A203V	SLC16A9_ENST00000395347.1_Missense_Mutation_p.A203V	NM_194298.2	NP_919274.1	Q7RTY1	MOT9_HUMAN	solute carrier family 16, member 9	203			A -> V (in dbSNP:rs56370926).		urate metabolic process (GO:0046415)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	symporter activity (GO:0015293)			kidney(3)|large_intestine(5)|lung(5)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	23						ATCTTCTGGAGCTATTTTTTT	0.378													G|||	159	0.0317492	0.0023	0.0173	5008	,	,		18499	0.0		0.0616	False		,,,				2504	0.0838				p.A203V		Atlas-SNP	.											.	SLC16A9	58	.	0			c.C608T						PASS	.	G	VAL/ALA	46,4360	50.2+/-85.5	0,46,2157	106.0	112.0	110.0		608	1.9	0.7	10	dbSNP_129	110	461,8139	136.7+/-193.7	14,433,3853	yes	missense	SLC16A9	NM_194298.2	64	14,479,6010	AA,AG,GG		5.3605,1.044,3.8982	benign	203/510	61414176	507,12499	2203	4300	6503	SO:0001583	missense	220963	exon5			TCTGGAGCTATTT	AK125791	CCDS7256.1	10q21.3	2013-07-18	2013-07-18	2004-01-21	ENSG00000165449	ENSG00000165449		"""Solute carriers"""	23520	protein-coding gene	gene with protein product	"""monocarboxylic acid transporter 9"""	614242	"""chromosome 10 open reading frame 36"", ""solute carrier family 16 (monocarboxylic acid transporters), member 9"", ""solute carrier family 16, member 9 (monocarboxylic acid transporter 9)"""	C10orf36			Standard	NM_194298		Approved	FLJ43803, MCT9	uc010qig.1	Q7RTY1	OTTHUMG00000018283	ENST00000395348.3:c.608C>T	10.37:g.61414176G>A	ENSP00000378757:p.Ala203Val	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	49	21	0.428571	NM_194298	Q6ZMI2|Q9UFH8	Missense_Mutation	SNP	ENST00000395348.3	37	CCDS7256.1	55	0.025183150183150184	1	0.0020325203252032522	6	0.016574585635359115	0	0.0	48	0.0633245382585752	G	1.699	-0.502086	0.04261	0.01044	0.053605	ENSG00000165449	ENST00000395348;ENST00000395347	D;D	0.81579	-1.51;-1.51	5.12	1.94	0.25998	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.526148	0.17511	N	0.171612	T	0.17704	0.0425	N	0.20986	0.625	0.09310	N	1	B	0.28128	0.201	B	0.28232	0.087	T	0.17198	-1.0377	10	0.30854	T	0.27	.	6.5243	0.22293	0.2549:0.2418:0.5033:0.0	rs56370926	203	Q7RTY1	MOT9_HUMAN	V	203	ENSP00000378757:A203V;ENSP00000378756:A203V	ENSP00000378756:A203V	A	-	2	0	SLC16A9	61084182	0.004000	0.15560	0.673000	0.29887	0.020000	0.10135	0.456000	0.21859	1.147000	0.42369	-0.216000	0.12614	GCT	G|0.965;A|0.035	0.035	strong		0.378	SLC16A9-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048174.2	NM_194298	
CYP4F2	8529	hgsc.bcm.edu	37	19	16006413	16006413	+	Silent	SNP	G	G	A	rs3093114	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:16006413G>A	ENST00000221700.6	-	3	341	c.246C>T	c.(244-246)gcC>gcT	p.A82A	CYP4F2_ENST00000011989.7_Intron	NM_001082.3	NP_001073.3			cytochrome P450, family 4, subfamily F, polypeptide 2											NS(2)|breast(1)|endometrium(6)|kidney(2)|large_intestine(9)|liver(1)|lung(18)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	46						GGGGGTAGGTGGCCACCAGCT	0.557													.|||	609	0.121605	0.1135	0.1239	5008	,	,		16944	0.0556		0.1759	False		,,,				2504	0.1431				p.A82A		Atlas-SNP	.											.	CYP4F2	97	.	0			c.C246T						PASS	.	G		595,3811	263.1+/-265.3	43,509,1651	94.0	99.0	97.0		246	-0.4	0.3	19	dbSNP_103	97	1471,7129	280.5+/-294.5	124,1223,2953	no	coding-synonymous	CYP4F2	NM_001082.3		167,1732,4604	AA,AG,GG		17.1047,13.5043,15.885		82/521	16006413	2066,10940	2203	4300	6503	SO:0001819	synonymous_variant	8529	exon3			GTAGGTGGCCACC	U02388	CCDS12336.1	19p13.12	2013-11-11	2003-01-14		ENSG00000186115	ENSG00000186115		"""Cytochrome P450s"""	2645	protein-coding gene	gene with protein product		604426	"""cytochrome P450, subfamily IVF, polypeptide 2"""			8424651, 8026587	Standard	NM_001082		Approved		uc002nbs.1	P78329	OTTHUMG00000185995	ENST00000221700.6:c.246C>T	19.37:g.16006413G>A		Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	33	21	0.636364	NM_001082		Silent	SNP	ENST00000221700.6	37	CCDS12336.1																																																																																			G|0.861;A|0.139	0.139	strong		0.557	CYP4F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460372.3	NM_001082	
MYH9	4627	hgsc.bcm.edu	37	22	36684354	36684354	+	Missense_Mutation	SNP	T	T	C	rs2269529	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:36684354T>C	ENST00000216181.5	-	34	5106	c.4876A>G	c.(4876-4878)Atc>Gtc	p.I1626V	MYH9_ENST00000475726.1_5'Flank	NM_002473.4	NP_002464.1	P35579	MYH9_HUMAN	myosin, heavy chain 9, non-muscle	1626			I -> V (in dbSNP:rs2269529). {ECO:0000269|PubMed:11776386}.		actin cytoskeleton reorganization (GO:0031532)|actin filament-based movement (GO:0030048)|actomyosin structure organization (GO:0031032)|angiogenesis (GO:0001525)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|blood vessel endothelial cell migration (GO:0043534)|cytokinesis (GO:0000910)|establishment of meiotic spindle localization (GO:0051295)|establishment of T cell polarity (GO:0001768)|in utero embryonic development (GO:0001701)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|meiotic spindle organization (GO:0000212)|membrane protein ectodomain proteolysis (GO:0006509)|monocyte differentiation (GO:0030224)|myoblast fusion (GO:0007520)|platelet aggregation (GO:0070527)|platelet formation (GO:0030220)|protein transport (GO:0015031)|regulation of cell shape (GO:0008360)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|uropod organization (GO:0032796)	actin cytoskeleton (GO:0015629)|actomyosin (GO:0042641)|actomyosin contractile ring (GO:0005826)|cell leading edge (GO:0031252)|cell-cell adherens junction (GO:0005913)|cleavage furrow (GO:0032154)|cortical cytoskeleton (GO:0030863)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|immunological synapse (GO:0001772)|membrane (GO:0016020)|myosin II complex (GO:0016460)|myosin II filament (GO:0097513)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|ruffle (GO:0001726)|spindle (GO:0005819)|stress fiber (GO:0001725)|uropod (GO:0001931)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)|motor activity (GO:0003774)|poly(A) RNA binding (GO:0044822)|protein anchor (GO:0043495)|protein homodimerization activity (GO:0042803)			NS(1)|breast(8)|central_nervous_system(3)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(16)|lung(29)|ovary(4)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(6)|urinary_tract(3)	86						GCCGAGTCGATGTGCGCCTCC	0.652			T	ALK	ALCL		"""Deafness, autosomal dominant 17, Epstein syndrome, Fechtner syndrome, May-Hegglin anomaly, Sebastian syndrome"""		Hereditary Macrothrombocytopenia, MYH9-associated				.|||	1473	0.294129	0.0431	0.2118	5008	,	,		16121	0.5952		0.2078	False		,,,				2504	0.4703				p.I1626V		Atlas-SNP	.		Dom	yes		22	22q13.1	4627	"""myosin, heavy polypeptide 9, non-muscle"""	yes	L	.	MYH9	225	.	0			c.A4876G						PASS	.	T	VAL/ILE	319,4087	168.0+/-198.9	12,295,1896	125.0	101.0	109.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	4876	4.5	0.9	22	dbSNP_100	109	1704,6896	311.4+/-310.3	194,1316,2790	yes	missense	MYH9	NM_002473.4	29	206,1611,4686	CC,CT,TT		19.814,7.2401,15.5544	benign	1626/1961	36684354	2023,10983	2203	4300	6503	SO:0001583	missense	4627	exon34	Familial Cancer Database	MYHIIA syndrome, incl. Fechtner Syndrome, FTNS, and May-Hegglin Anomaly, MHA	AGTCGATGTGCGC		CCDS13927.1	22q13.1	2014-09-17	2006-09-29		ENSG00000100345	ENSG00000100345		"""Myosins / Myosin superfamily : Class II"""	7579	protein-coding gene	gene with protein product	"""nonmuscle myosin heavy chain II-A"""	160775	"""myosin, heavy polypeptide 9, non-muscle"""	DFNA17		1860190, 11023810	Standard	NM_002473		Approved	NMMHCA, NMHC-II-A, MHA, FTNS, EPSTS	uc003apg.3	P35579	OTTHUMG00000030429	ENST00000216181.5:c.4876A>G	22.37:g.36684354T>C	ENSP00000216181:p.Ile1626Val	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	89	42	0.47191	NM_002473	A8K6E4|O60805|Q60FE2|Q86T83	Missense_Mutation	SNP	ENST00000216181.5	37	CCDS13927.1	621	0.28434065934065933	42	0.08536585365853659	78	0.2154696132596685	354	0.6188811188811189	147	0.19393139841688653	T	5.367	0.252980	0.10185	0.072401	0.19814	ENSG00000100345	ENST00000337818;ENST00000397231;ENST00000216181	T	0.76839	-1.05	5.5	4.47	0.54385	Myosin tail (1);	0.051153	0.85682	N	0.000000	T	0.00012	0.0000	N	0.21240	0.645	0.09310	P	1.0	B	0.20164	0.042	B	0.22753	0.041	T	0.47497	-0.9113	9	0.59425	D	0.04	.	11.6753	0.51425	0.0:0.0696:0.0:0.9304	rs2269529;rs56717084;rs2269529	1626	P35579	MYH9_HUMAN	V	1048;228;1626	ENSP00000216181:I1626V	ENSP00000216181:I1626V	I	-	1	0	MYH9	35014300	1.000000	0.71417	0.914000	0.36105	0.254000	0.26022	4.186000	0.58337	1.013000	0.39391	0.533000	0.62120	ATC	T|0.784;C|0.216	0.216	strong		0.652	MYH9-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000259110.3	NM_002473	
WDR25	79446	hgsc.bcm.edu	37	14	100996337	100996337	+	Missense_Mutation	SNP	G	G	A	rs144754220		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:100996337G>A	ENST00000335290.6	+	7	1820	c.1594G>A	c.(1594-1596)Gcc>Acc	p.A532T	WDR25_ENST00000554998.1_Missense_Mutation_p.A532T|WDR25_ENST00000542471.2_Missense_Mutation_p.A275T|WDR25_ENST00000557502.1_3'UTR|WDR25_ENST00000402312.3_Missense_Mutation_p.A532T	NM_024515.4	NP_078791.3	Q64LD2	WDR25_HUMAN	WD repeat domain 25	532										central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(5)|lung(8)|skin(1)	20		Melanoma(154;0.212)				CTCCGTCCTCGCCACCTGCTC	0.617																																					p.A532T		Atlas-SNP	.											.	WDR25	37	.	0			c.G1594A						PASS	.	G	THR/ALA,THR/ALA	1,4405	2.1+/-5.4	0,1,2202	75.0	68.0	71.0		1594,1594	4.8	1.0	14	dbSNP_134	71	0,8600		0,0,4300	no	missense,missense	WDR25	NM_001161476.1,NM_024515.4	58,58	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	possibly-damaging,possibly-damaging	532/545,532/545	100996337	1,13005	2203	4300	6503	SO:0001583	missense	79446	exon7			GTCCTCGCCACCT	BC007953	CCDS32157.1	14q32.32	2013-01-09				ENSG00000176473		"""WD repeat domain containing"""	21064	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 67"""	C14orf67		15587985	Standard	NM_001161476		Approved	MGC4645	uc001yhn.3	Q64LD2		ENST00000335290.6:c.1594G>A	14.37:g.100996337G>A	ENSP00000334148:p.Ala532Thr	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	91	20	0.21978	NM_001161476	A8K7E5|Q6NVV6|Q86TQ4|Q9BTK5	Missense_Mutation	SNP	ENST00000335290.6	37	CCDS32157.1	.	.	.	.	.	.	.	.	.	.	G	26.0	4.693621	0.88735	2.27E-4	0.0	ENSG00000176473	ENST00000554998;ENST00000402312;ENST00000335290;ENST00000542471	T;T;T;T	0.70282	4.69;4.69;4.69;-0.47	4.83	4.83	0.62350	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.133172	0.49305	D	0.000150	D	0.85982	0.5824	M	0.92077	3.27	0.58432	D	0.999996	D;D	0.89917	1.0;0.997	P;P	0.59546	0.859;0.834	D	0.89565	0.3809	10	0.62326	D	0.03	-12.8885	17.0452	0.86500	0.0:0.0:1.0:0.0	.	275;532	Q64LD2-2;Q64LD2	.;WDR25_HUMAN	T	532;532;532;275	ENSP00000450661:A532T;ENSP00000385540:A532T;ENSP00000334148:A532T;ENSP00000441903:A275T	ENSP00000334148:A532T	A	+	1	0	WDR25	100066090	1.000000	0.71417	0.964000	0.40570	0.626000	0.37791	9.336000	0.96533	2.388000	0.81334	0.655000	0.94253	GCC	G|1.000;A|0.000	0.000	weak		0.617	WDR25-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414312.1	NM_024515	
DNMT1	1786	hgsc.bcm.edu	37	19	10265725	10265725	+	Silent	SNP	G	G	A	rs75443147	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:10265725G>A	ENST00000340748.4	-	19	1687	c.1452C>T	c.(1450-1452)gcC>gcT	p.A484A	DNMT1_ENST00000359526.4_Silent_p.A500A|DNMT1_ENST00000540357.1_Silent_p.A484A			P26358	DNMT1_HUMAN	DNA (cytosine-5-)-methyltransferase 1	484	DNA replication foci-targeting sequence. {ECO:0000250}.|Homodimerization.|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)	GAATGTATTCGGCAAATGCTG	0.532													G|||	43	0.00858626	0.0	0.0	5008	,	,		20399	0.0268		0.005	False		,,,				2504	0.0112				p.A500A		Atlas-SNP	.											.	DNMT1	148	.	0			c.C1500T						PASS	.	G	,	2,4404	4.2+/-10.8	0,2,2201	78.0	76.0	77.0		1500,1452	-11.9	0.1	19	dbSNP_131	77	6,8594	5.0+/-18.6	0,6,4294	no	coding-synonymous,coding-synonymous	DNMT1	NM_001130823.1,NM_001379.2	,	0,8,6495	AA,AG,GG		0.0698,0.0454,0.0615	,	500/1633,484/1617	10265725	8,12998	2203	4300	6503	SO:0001819	synonymous_variant	1786	exon20			GTATTCGGCAAAT	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.1452C>T	19.37:g.10265725G>A		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	45	27	0.6	NM_001130823	A0AV63|B7ZLW6|Q9UHG5|Q9ULA2|Q9UMZ6	Silent	SNP	ENST00000340748.4	37	CCDS12228.1																																																																																			G|0.997;A|0.003	0.003	strong		0.532	DNMT1-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451166.1	NM_001379	
ACRV1	56	hgsc.bcm.edu	37	11	125547869	125547869	+	Missense_Mutation	SNP	C	C	T	rs34788353	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:125547869C>T	ENST00000533904.1	-	2	718	c.376G>A	c.(376-378)Gga>Aga	p.G126R	ACRV1_ENST00000453509.1_Missense_Mutation_p.G56R|ACRV1_ENST00000315608.3_Missense_Mutation_p.G126R|ACRV1_ENST00000530048.1_Missense_Mutation_p.G71R|ACRV1_ENST00000353070.1_Intron|ACRV1_ENST00000527795.1_Missense_Mutation_p.G56R|ACRV1_ENST00000345274.1_Missense_Mutation_p.G56R|ACRV1_ENST00000445562.1_Intron|ACRV1_ENST00000425431.1_Intron|ACRV1_ENST00000348856.3_Intron			P26436	ASPX_HUMAN	acrosomal vesicle protein 1	126	4 X 4 AA repeats of S-G-E-H.|9 X 5 AA repeats of [SV]-G-E-Q-[PSA].		G -> R (in dbSNP:rs34788353). {ECO:0000269|PubMed:8373955, ECO:0000269|Ref.4}.		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)		GGCTGTTCTCCGGAGAGGTGT	0.552													C|||	312	0.0623003	0.1286	0.0476	5008	,	,		21433	0.002		0.0706	False		,,,				2504	0.0368				p.G126R		Atlas-SNP	.											.	ACRV1	21	.	0			c.G376A						PASS	.	C	ARG/GLY,ARG/GLY,ARG/GLY,ARG/GLY	500,3902	232.0+/-245.7	26,448,1727	176.0	156.0	163.0		376,376,211,166	-0.5	0.0	11	dbSNP_126	163	573,8025	154.3+/-208.6	17,539,3743	yes	missense,missense,missense,missense	ACRV1	NM_001612.5,NM_020069.4,NM_020107.4,NM_020108.4	125,125,125,125	43,987,5470	TT,TC,CC		6.6643,11.3585,8.2538	benign,benign,benign,benign	126/266,126/247,71/211,56/196	125547869	1073,11927	2201	4299	6500	SO:0001583	missense	56	exon2			GTTCTCCGGAGAG	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.376G>A	11.37:g.125547869C>T	ENSP00000432816:p.Gly126Arg	Somatic	200	1	0.005		WXS	Illumina HiSeq	Phase_I	180	118	0.655556	NM_001612	Q53FF4	Missense_Mutation	SNP	ENST00000533904.1	37	CCDS8460.1	139	0.06364468864468864	69	0.1402439024390244	17	0.04696132596685083	0	0.0	53	0.06992084432717678	C	9.975	1.226415	0.22542	0.113585	0.066643	ENSG00000134940	ENST00000533904;ENST00000433875;ENST00000257382;ENST00000426183;ENST00000453509;ENST00000345274;ENST00000315608;ENST00000530048;ENST00000527795	T;T;T;T;T;T;T;T;T	0.49432	2.01;2.04;2.08;2.11;2.12;0.78;2.04;2.08;2.11	4.57	-0.493	0.12038	.	0.565262	0.17237	N	0.181698	T	0.00524	0.0017	L	0.43923	1.385	0.47153	P	6.690000000000307E-4	B;B;B;B;B;D	0.65815	0.02;0.391;0.345;0.008;0.099;0.995	B;B;B;B;B;D	0.66497	0.016;0.034;0.16;0.018;0.035;0.944	T	0.13764	-1.0497	9	0.45353	T	0.12	-1.6082	8.327	0.32162	0.0:0.5456:0.0:0.4544	rs34788353	126;126;56;71;56;56	P26436;P26436-2;P26436-8;P26436-3;P26436-4;P26436-5	ASPX_HUMAN;.;.;.;.;.	R	126;126;71;56;56;56;126;71;56	ENSP00000432816:G126R;ENSP00000407846:G126R;ENSP00000257382:G71R;ENSP00000411583:G56R;ENSP00000397448:G56R;ENSP00000257383:G56R;ENSP00000317684:G126R;ENSP00000433720:G71R;ENSP00000436819:G56R	ENSP00000257382:G71R	G	-	1	0	ACRV1	125053079	0.000000	0.05858	0.004000	0.12327	0.010000	0.07245	-0.479000	0.06567	0.006000	0.14734	-0.855000	0.03028	GGA	C|0.924;T|0.076	0.076	strong		0.552	ACRV1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386722.1	NM_001612	
POM121L12	285877	hgsc.bcm.edu	37	7	53104078	53104078	+	Silent	SNP	G	G	A	rs72598686	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:53104078G>A	ENST00000408890.4	+	1	730	c.714G>A	c.(712-714)ccG>ccA	p.P238P		NM_182595.3	NP_872401.3	Q8N7R1	P1L12_HUMAN	POM121 transmembrane nucleoporin-like 12	238										endometrium(5)|kidney(1)|large_intestine(5)|lung(44)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	61						CTCTGAAGCCGAGCCTCGGCC	0.647													G|||	1659	0.33127	0.2209	0.2464	5008	,	,		12613	0.4315		0.2982	False		,,,				2504	0.4714				p.P238P		Atlas-SNP	.											POM121L12,NS,carcinoma,0,1	POM121L12	146	1	0			c.G714A						PASS	.	G		847,3087		94,659,1214	44.0	52.0	50.0		714	-3.7	0.0	7	dbSNP_130	50	2247,6031		281,1685,2173	no	coding-synonymous	POM121L12	NM_182595.3		375,2344,3387	AA,AG,GG		27.1442,21.5302,25.3357		238/297	53104078	3094,9118	1967	4139	6106	SO:0001819	synonymous_variant	285877	exon1			GAAGCCGAGCCTC		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.714G>A	7.37:g.53104078G>A		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	61	35	0.57377	NM_182595	Q8NDI9	Silent	SNP	ENST00000408890.4	37	CCDS43584.1																																																																																			G|0.706;A|0.294	0.294	strong		0.647	POM121L12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342656.1	NM_182595	
ICAM3	3385	hgsc.bcm.edu	37	19	10449358	10449358	+	Splice_Site	SNP	T	T	C	rs7258015	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:10449358T>C	ENST00000160262.5	-	2	551	c.343A>G	c.(343-345)Agg>Ggg	p.R115G	ICAM3_ENST00000589261.1_Splice_Site_p.R38G	NM_002162.3	NP_002153.2	P32942	ICAM3_HUMAN	intercellular adhesion molecule 3	115			R -> G (in dbSNP:rs7258015). {ECO:0000269|PubMed:1448174, ECO:0000269|PubMed:8459213}.		extracellular matrix organization (GO:0030198)|regulation of immune response (GO:0050776)|single organismal cell-cell adhesion (GO:0016337)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	integrin binding (GO:0005178)|receptor binding (GO:0005102)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(7)|ovary(1)|upper_aerodigestive_tract(2)	13			OV - Ovarian serous cystadenocarcinoma(20;6.13e-09)|Epithelial(33;9.69e-06)|all cancers(31;2.05e-05)			GTCGACTCACTGTACACGGTG	0.547													T|||	896	0.178914	0.1392	0.1744	5008	,	,		19949	0.1141		0.2356	False		,,,				2504	0.2444				p.R115G		Atlas-SNP	.											ICAM3,colon,carcinoma,0,1	ICAM3	29	1	0			c.A343G						scavenged	.	T	GLY/ARG	745,3661	304.1+/-288.3	56,633,1514	76.0	59.0	65.0		343	-11.5	0.0	19	dbSNP_116	65	1967,6633	344.9+/-325.5	238,1491,2571	yes	missense-near-splice	ICAM3	NM_002162.3	125	294,2124,4085	CC,CT,TT		22.8721,16.9088,20.8519	benign	115/548	10449358	2712,10294	2203	4300	6503	SO:0001630	splice_region_variant	3385	exon2			ACTCACTGTACAC		CCDS12235.1	19p13.3-p13.2	2013-01-11				ENSG00000076662		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5346	protein-coding gene	gene with protein product		146631				1448174	Standard	NM_002162		Approved	CDW50, ICAM-R, CD50	uc002mob.2	P32942		ENST00000160262.5:c.343+1A>G	19.37:g.10449358T>C		Somatic	140	2	0.0142857		WXS	Illumina HiSeq	Phase_I	129	47	0.364341	NM_002162	Q6PD68	Missense_Mutation	SNP	ENST00000160262.5	37	CCDS12235.1	382	0.1749084249084249	58	0.11788617886178862	69	0.19060773480662985	70	0.12237762237762238	185	0.24406332453825857	T	12.32	1.901485	0.33535	0.169088	0.228721	ENSG00000076662	ENST00000160262	T	0.24350	1.86	5.75	-11.5	0.00074	Intercellular adhesion molecule/vascular cell adhesion molecule, N-terminal (1);Intercellular adhesion molecule, N-terminal (1);Immunoglobulin-like fold (1);	0.854576	0.10072	N	0.719602	T	0.00012	0.0000	L	0.27053	0.805	0.09310	P	1.0	B;B	0.02656	0.0;0.0	B;B	0.08055	0.003;0.002	T	0.20739	-1.0266	8	.	.	.	-3.8943	6.787	0.23679	0.0633:0.391:0.1209:0.4248	rs7258015;rs58067369;rs7258015	38;115	B7Z6W6;P32942	.;ICAM3_HUMAN	G	115	ENSP00000160262:R115G	.	R	-	1	2	ICAM3	10310358	0.022000	0.18835	0.001000	0.08648	0.172000	0.22775	-2.406000	0.01044	-2.000000	0.00965	-0.213000	0.12676	AGG	T|0.809;C|0.191	0.191	strong		0.547	ICAM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451234.1		Missense_Mutation
PEX14	5195	hgsc.bcm.edu	37	1	10596341	10596341	+	Silent	SNP	C	C	T	rs12375	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:10596341C>T	ENST00000356607.4	+	3	236	c.156C>T	c.(154-156)ttC>ttT	p.F52F	PEX14_ENST00000538836.1_Intron|PEX14_ENST00000492696.1_3'UTR	NM_004565.2	NP_004556.1	O75381	PEX14_HUMAN	peroxisomal biogenesis factor 14	52					microtubule anchoring (GO:0034453)|negative regulation of protein binding (GO:0032091)|negative regulation of protein homotetramerization (GO:1901094)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription, DNA-templated (GO:0045892)|peroxisome organization (GO:0007031)|peroxisome transport along microtubule (GO:0036250)|protein complex assembly (GO:0006461)|protein homooligomerization (GO:0051260)|protein import into peroxisome matrix (GO:0016558)|protein import into peroxisome matrix, substrate release (GO:0044721)|protein import into peroxisome matrix, translocation (GO:0016561)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)|protein complex (GO:0043234)	beta-tubulin binding (GO:0048487)|microtubule binding (GO:0008017)|protein N-terminus binding (GO:0047485)|receptor binding (GO:0005102)|transcription corepressor activity (GO:0003714)			breast(3)|endometrium(1)|large_intestine(3)|lung(5)|prostate(1)	13	Ovarian(185;0.203)	all_lung(284;6.02e-06)|Lung NSC(185;9.62e-06)|Renal(390;0.000147)|Breast(348;0.000932)|Colorectal(325;0.00215)|Hepatocellular(190;0.00913)|Ovarian(437;0.023)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0292)|Colorectal(212;9.13e-08)|COAD - Colon adenocarcinoma(227;2.07e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000482)|Kidney(185;0.00174)|KIRC - Kidney renal clear cell carcinoma(229;0.00457)|STAD - Stomach adenocarcinoma(132;0.0249)|READ - Rectum adenocarcinoma(331;0.0419)		GGAGAGCATTCCTAAAGAAGA	0.562													C|||	1142	0.228035	0.0658	0.4265	5008	,	,		16571	0.2004		0.3141	False		,,,				2504	0.2464				p.F52F		Atlas-SNP	.											.	PEX14	40	.	0			c.C156T						PASS	.	C		472,3934	220.7+/-238.1	30,412,1761	52.0	50.0	51.0		156	3.4	1.0	1	dbSNP_52	51	2770,5830	432.8+/-357.2	469,1832,1999	no	coding-synonymous	PEX14	NM_004565.2		499,2244,3760	TT,TC,CC		32.2093,10.7127,24.927		52/378	10596341	3242,9764	2203	4300	6503	SO:0001819	synonymous_variant	5195	exon3			AGCATTCCTAAAG	AF045186	CCDS30582.1	1p36.22	2008-05-14			ENSG00000142655	ENSG00000142655			8856	protein-coding gene	gene with protein product		601791				9653144	Standard	NM_004565		Approved		uc001arn.3	O75381	OTTHUMG00000001908	ENST00000356607.4:c.156C>T	1.37:g.10596341C>T		Somatic	218	0	0		WXS	Illumina HiSeq	Phase_I	181	86	0.475138	NM_004565	B2R7N1|B3KML6|B7Z1N2|Q8WX51	Silent	SNP	ENST00000356607.4	37	CCDS30582.1																																																																																			C|0.770;T|0.230	0.230	strong		0.562	PEX14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005414.1		
IL4I1	259307	hgsc.bcm.edu	37	19	50393269	50393269	+	Silent	SNP	A	A	G	rs56359967	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:50393269A>G	ENST00000391826.2	-	8	1504	c.1362T>C	c.(1360-1362)ttT>ttC	p.F454F	MIR4750_ENST00000584564.1_RNA|IL4I1_ENST00000341114.3_Silent_p.F476F|IL4I1_ENST00000595948.1_Silent_p.F476F	NM_152899.1	NP_690863.1	Q96RQ9	OXLA_HUMAN	interleukin 4 induced 1	454						extracellular region (GO:0005576)|lysosome (GO:0005764)	L-amino-acid oxidase activity (GO:0001716)			endometrium(3)|large_intestine(3)|lung(6)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	16		all_lung(116;1.47e-05)|all_neural(266;0.0459)|Ovarian(192;0.0481)		GBM - Glioblastoma multiforme(134;0.00245)|OV - Ovarian serous cystadenocarcinoma(262;0.0169)	Flavin adenine dinucleotide(DB03147)	GCTGTACCACAAAGCCACCCT	0.667											OREG0025629	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	659	0.131589	0.1566	0.1945	5008	,	,		15075	0.1885		0.0169	False		,,,				2504	0.1125				p.F476F		Atlas-SNP	.											.	IL4I1	50	.	0			c.T1428C						PASS	.	G	,	545,3703		28,489,1607	22.0	9.0	13.0		1362,1428	2.1	1.0	19	dbSNP_129	13	178,8150		4,170,3990	no	coding-synonymous,coding-synonymous	IL4I1	NM_152899.1,NM_172374.1	,	32,659,5597	GG,GA,AA		2.1374,12.8296,5.749	,	454/568,476/590	50393269	723,11853	2124	4164	6288	SO:0001819	synonymous_variant	259307	exon10			TACCACAAAGCCA	AF293462	CCDS12786.1, CCDS12787.1	19q13.3-q13.4	2014-06-26				ENSG00000104951			19094	protein-coding gene	gene with protein product		609742				12031486	Standard	NM_152899		Approved	FIG1	uc002pqt.1	Q96RQ9		ENST00000391826.2:c.1362T>C	19.37:g.50393269A>G		Somatic	45	0	0	969	WXS	Illumina HiSeq	Phase_I	34	16	0.470588	NM_172374	Q1WMJ3|Q4GZN1|Q4GZN2|Q6P2Q3|Q8TEM5|Q96RQ8	Silent	SNP	ENST00000391826.2	37	CCDS12787.1																																																																																			A|0.881;G|0.119	0.119	strong		0.667	IL4I1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466413.1		
RPS14	6208	hgsc.bcm.edu	37	5	149826526	149826526	+	Splice_Site	SNP	C	C	T	rs4841	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:149826526C>T	ENST00000401695.3	-	3	196	c.150G>A	c.(148-150)aaG>aaA	p.K50K	RPS14_ENST00000312037.5_Splice_Site_p.K50K|RPS14_ENST00000407193.1_Splice_Site_p.K50K			P62263	RS14_HUMAN	ribosomal protein S14	50					cellular protein metabolic process (GO:0044267)|erythrocyte differentiation (GO:0030218)|gene expression (GO:0010467)|maturation of SSU-rRNA (GO:0030490)|mRNA metabolic process (GO:0016071)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of translation (GO:0006417)|ribosomal small subunit assembly (GO:0000028)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytosol (GO:0005829)|cytosolic small ribosomal subunit (GO:0022627)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)	mRNA 5'-UTR binding (GO:0048027)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)|translation regulator activity (GO:0045182)			central_nervous_system(1)|lung(1)|skin(1)	3		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			AGATGGTTTCCCTGGGGACAA	0.517													T|||	1344	0.268371	0.2027	0.2161	5008	,	,		20873	0.2669		0.2575	False		,,,				2504	0.407				p.K50K		Atlas-SNP	.											.	RPS14	11	.	0			c.G150A						PASS	.	T	,,	947,3459	736.7+/-410.8	96,755,1352	98.0	86.0	90.0		150,150,150	2.0	1.0	5	dbSNP_52	90	2293,6307	705.7+/-405.5	285,1723,2292	yes	coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice	RPS14	NM_001025070.1,NM_001025071.1,NM_005617.3	,,	381,2478,3644	TT,TC,CC		26.6628,21.4934,24.9116	,,	50/152,50/152,50/152	149826526	3240,9766	2203	4300	6503	SO:0001630	splice_region_variant	6208	exon3			GGTTTCCCTGGGG		CCDS4307.1	5q31-q33	2012-10-02			ENSG00000164587	ENSG00000164587		"""S ribosomal proteins"""	10387	protein-coding gene	gene with protein product	"""emetine resistance"", ""40S ribosomal protein S14"""	130620				3785212, 1549121	Standard	XM_006714790		Approved	EMTB, S14	uc003lsj.3	P62263	OTTHUMG00000130080	ENST00000401695.3:c.150-1G>A	5.37:g.149826526C>T		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	54	23	0.425926	NM_001025071	B2R5G5|D3DQG5|P06366|Q5BJI0	Silent	SNP	ENST00000401695.3	37	CCDS4307.1																																																																																			T|0.198;G|0.151;C|0.606;A|0.044	0.198	strong		0.517	RPS14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252373.1	NM_001025071	Silent
C5orf47	133491	hgsc.bcm.edu	37	5	173426709	173426709	+	Missense_Mutation	SNP	G	G	T	rs56138314	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:173426709G>T	ENST00000340147.6	+	3	523	c.418G>T	c.(418-420)Gta>Tta	p.V140L	C5orf47_ENST00000522195.1_Intron	NM_001144954.1	NP_001138426.1	Q569G3	CE047_HUMAN	chromosome 5 open reading frame 47	140										kidney(1)|prostate(1)	2						TAAGGTTTTAGTATGGAATAG	0.343													G|||	104	0.0207668	0.0386	0.0231	5008	,	,		20040	0.003		0.0298	False		,,,				2504	0.0041				p.V140L		Atlas-SNP	.											C5orf47,NS,carcinoma,-1,1	C5orf47	14	1	0			c.G418T						PASS	.	G	LEU/VAL	51,1333		1,49,642	144.0	116.0	125.0		418	3.6	0.1	5	dbSNP_129	125	110,3068		3,104,1482	yes	missense	C5orf47	NM_001144954.1	32	4,153,2124	TT,TG,GG		3.4613,3.685,3.5292	possibly-damaging	140/177	173426709	161,4401	692	1589	2281	SO:0001583	missense	133491	exon3			GTTTTAGTATGGA		CCDS47343.1	5q35.2	2012-02-24			ENSG00000185056	ENSG00000185056			27026	protein-coding gene	gene with protein product						12477932	Standard	NM_001144954		Approved	LOC133491	uc003mcw.4	Q569G3	OTTHUMG00000163349	ENST00000340147.6:c.418G>T	5.37:g.173426709G>T	ENSP00000340887:p.Val140Leu	Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	125	51	0.408	NM_001144954	Q8IYU7	Missense_Mutation	SNP	ENST00000340147.6	37	CCDS47343.1	58	0.026556776556776556	20	0.04065040650406504	11	0.03038674033149171	3	0.005244755244755245	24	0.0316622691292876	G	11.21	1.573044	0.28092	0.03685	0.034613	ENSG00000185056	ENST00000340147	.	.	.	4.5	3.63	0.41609	.	.	.	.	.	T	0.10637	0.0260	L	0.34521	1.04	0.09310	N	1	D	0.56035	0.974	P	0.51135	0.66	T	0.02766	-1.1113	8	0.87932	D	0	-5.6429	8.4289	0.32746	0.1069:0.0:0.8931:0.0	rs56138314	140	Q569G3	CE047_HUMAN	L	140	.	ENSP00000340887:V140L	V	+	1	0	C5orf47	173359315	0.814000	0.29104	0.092000	0.20876	0.424000	0.31475	3.254000	0.51477	1.257000	0.44085	0.650000	0.86243	GTA	G|0.971;T|0.029	0.029	strong		0.343	C5orf47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372926.1	NM_001144954	
SLC28A1	9154	hgsc.bcm.edu	37	15	85478729	85478729	+	Missense_Mutation	SNP	G	G	A	rs2242046	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:85478729G>A	ENST00000286749.3	+	14	1651	c.1561G>A	c.(1561-1563)Gac>Aac	p.D521N	SLC28A1_ENST00000538177.1_Intron|SLC28A1_ENST00000537624.1_Missense_Mutation_p.D521N|SLC28A1_ENST00000537216.1_Missense_Mutation_p.D521N|RNU6-339P_ENST00000384310.1_RNA|SLC28A1_ENST00000394573.1_Missense_Mutation_p.D521N			O00337	S28A1_HUMAN	solute carrier family 28 (concentrative nucleoside transporter), member 1	521			D -> N (in B and C; dbSNP:rs2242046). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:9124315}.		nucleobase-containing compound metabolic process (GO:0006139)|nucleoside transmembrane transport (GO:1901642)|nucleoside transport (GO:0015858)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	nucleoside binding (GO:0001882)|nucleoside transmembrane transporter activity (GO:0005337)|nucleoside:sodium symporter activity (GO:0005415)			breast(2)|endometrium(4)|kidney(2)|large_intestine(4)|lung(17)|ovary(1)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)	41			BRCA - Breast invasive adenocarcinoma(143;0.0587)		Gemcitabine(DB00441)|Stavudine(DB00649)|Zidovudine(DB00495)	GTGGGTCGGCGACAGGAAGCA	0.627													G|||	1042	0.208067	0.0325	0.2622	5008	,	,		21265	0.0605		0.503	False		,,,				2504	0.2556				p.D521N		Atlas-SNP	.											.	SLC28A1	118	.	0			c.G1561A						PASS	.	G	ASN/ASP	456,3950	217.4+/-235.8	39,378,1786	98.0	95.0	96.0		1561	-0.1	0.0	15	dbSNP_98	96	4278,4320	576.3+/-390.4	1066,2146,1087	yes	missense	SLC28A1	NM_004213.3	23	1105,2524,2873	AA,AG,GG		49.7558,10.3495,36.4042	benign	521/650	85478729	4734,8270	2203	4299	6502	SO:0001583	missense	9154	exon15			GTCGGCGACAGGA	U62967	CCDS10334.1, CCDS10335.1, CCDS73777.1	15q25.3	2013-07-17	2013-07-17		ENSG00000156222	ENSG00000156222		"""Solute carriers"""	11001	protein-coding gene	gene with protein product		606207	"""solute carrier family 28 (sodium-coupled nucleoside transporter), member 1"""			9124315	Standard	NM_004213		Approved	CNT1	uc002blg.3	O00337	OTTHUMG00000148668	ENST00000286749.3:c.1561G>A	15.37:g.85478729G>A	ENSP00000286749:p.Asp521Asn	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	74	73	0.986486	NM_004213	A0AV42|A8K7I2|O00335|O00336|Q5U5S6|Q5U648|Q9UEZ9	Missense_Mutation	SNP	ENST00000286749.3	37	CCDS10334.1	561	0.25686813186813184	25	0.0508130081300813	105	0.2900552486187845	42	0.07342657342657342	389	0.5131926121372031	G	8.616	0.890211	0.17613	0.103495	0.497558	ENSG00000156222	ENST00000537216;ENST00000537624;ENST00000286749;ENST00000394573	T;T;T;T	0.02015	4.5;4.67;4.68;4.68	5.19	-0.144	0.13440	Na dependent nucleoside transporter, C-terminal (1);	0.994708	0.08157	N	0.989064	T	0.00012	0.0000	L	0.27053	0.805	0.58432	P	1.999999999946489E-6	B;B;B	0.21821	0.061;0.005;0.025	B;B;B	0.13407	0.009;0.002;0.009	T	0.32428	-0.9907	9	0.48119	T	0.1	-20.7634	2.0739	0.03619	0.1564:0.1197:0.4171:0.3067	rs2242046;rs17216003;rs17609392;rs57854627;rs2242046	521;521;521	B7Z533;F5H560;O00337	.;.;S28A1_HUMAN	N	521	ENSP00000440546:D521N;ENSP00000444700:D521N;ENSP00000286749:D521N;ENSP00000378074:D521N	ENSP00000286749:D521N	D	+	1	0	SLC28A1	83279733	0.000000	0.05858	0.000000	0.03702	0.023000	0.10783	0.816000	0.27267	-0.177000	0.10690	-0.391000	0.06502	GAC	G|0.690;A|0.310	0.310	strong		0.627	SLC28A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000308998.2		
BRD7	29117	hgsc.bcm.edu	37	16	50368663	50368663	+	Silent	SNP	G	G	A	rs1062348	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:50368663G>A	ENST00000394688.3	-	7	1005	c.846C>T	c.(844-846)gcC>gcT	p.A282A	BRD7_ENST00000394689.2_Silent_p.A282A			Q9NPI1	BRD7_HUMAN	bromodomain containing 7	282					cell cycle (GO:0007049)|negative regulation of cell proliferation (GO:0008285)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of histone acetylation (GO:0035066)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	histone binding (GO:0042393)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(7)|prostate(2)|urinary_tract(2)	22		all_cancers(37;0.0127)				CGTGTGCTTCGGCATCTCCAG	0.473													G|||	1254	0.250399	0.2943	0.0893	5008	,	,		17016	0.497		0.1083	False		,,,				2504	0.1973				p.A282A		Atlas-SNP	.											.	BRD7	61	.	0			c.C846T						PASS	.	G	,	1156,3240	400.1+/-331.5	119,918,1161	135.0	141.0	139.0		846,846	-10.9	0.0	16	dbSNP_86	139	876,7724	195.8+/-240.9	41,794,3465	no	coding-synonymous,coding-synonymous	BRD7	NM_001173984.2,NM_013263.4	,	160,1712,4626	AA,AG,GG		10.186,26.2966,15.6356	,	282/653,282/652	50368663	2032,10964	2198	4300	6498	SO:0001819	synonymous_variant	29117	exon7			TGCTTCGGCATCT	AF213969	CCDS10742.1, CCDS54007.1	16q12.1	2008-11-18	2002-01-14		ENSG00000166164	ENSG00000166164			14310	protein-coding gene	gene with protein product			"""bromodomain-containing 7"""			10526152, 18809673	Standard	NM_013263		Approved	CELTIX1, BP75	uc002ege.2	Q9NPI1	OTTHUMG00000133170	ENST00000394688.3:c.846C>T	16.37:g.50368663G>A		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	127	78	0.614173	NM_013263	Q4VC09|Q8N2L9|Q96KA4|Q9BV48|Q9UH59	Silent	SNP	ENST00000394688.3	37	CCDS10742.1																																																																																			G|0.826;A|0.174	0.174	strong		0.473	BRD7-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000256874.3	NM_013263	
STK31	56164	hgsc.bcm.edu	37	7	23751736	23751736	+	Silent	SNP	A	A	G	rs7779633	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:23751736A>G	ENST00000355870.3	+	2	188	c.69A>G	c.(67-69)caA>caG	p.Q23Q	STK31_ENST00000354639.3_5'UTR|STK31_ENST00000433467.2_Silent_p.Q23Q|STK31_ENST00000428484.1_5'UTR	NM_031414.4	NP_113602.2	Q9BXU1	STK31_HUMAN	serine/threonine kinase 31	23						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						GAATTGTTCAAATGGATGAAG	0.279													A|||	1928	0.384984	0.503	0.353	5008	,	,		17811	0.3571		0.3519	False		,,,				2504	0.3108				p.Q23Q		Atlas-SNP	.											STK31,NS,carcinoma,+1,1	STK31	175	1	0			c.A69G						PASS	.	A	,,	2059,2347	565.2+/-381.6	493,1073,637	138.0	139.0	138.0		,69,	-2.3	1.0	7	dbSNP_116	138	2910,5690	452.7+/-363.0	472,1966,1862	no	utr-5,coding-synonymous,utr-5	STK31	NM_001122833.1,NM_031414.3,NM_032944.2	,,	965,3039,2499	GG,GA,AA		33.8372,46.7317,38.2054	,,	,23/1020,	23751736	4969,8037	2203	4300	6503	SO:0001819	synonymous_variant	56164	exon2			TGTTCAAATGGAT	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.69A>G	7.37:g.23751736A>G		Somatic	188	1	0.00531915		WXS	Illumina HiSeq	Phase_I	150	109	0.726667	NM_031414	B4DZ06|B7WPP5|C9J4F9|Q6PCD3|Q9BXH8	Silent	SNP	ENST00000355870.3	37	CCDS5386.1																																																																																			A|0.618;G|0.382	0.382	strong		0.279	STK31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214036.2	NM_031414	
IQGAP2	10788	hgsc.bcm.edu	37	5	75948650	75948650	+	Missense_Mutation	SNP	A	A	G	rs2431363	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:75948650A>G	ENST00000274364.6	+	18	2467	c.2170A>G	c.(2170-2172)Att>Gtt	p.I724V	IQGAP2_ENST00000502745.1_Missense_Mutation_p.I220V|IQGAP2_ENST00000396234.3_Missense_Mutation_p.I220V|IQGAP2_ENST00000379730.3_Missense_Mutation_p.I226V	NM_006633.2	NP_006624	Q13576	IQGA2_HUMAN	IQ motif containing GTPase activating protein 2	724	IQ 2. {ECO:0000255|PROSITE- ProRule:PRU00116}.		I -> V (in dbSNP:rs2431363). {ECO:0000269|PubMed:8756646, ECO:0000269|Ref.2}.		negative regulation of catalytic activity (GO:0043086)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|microvillus (GO:0005902)	actin binding (GO:0003779)|GTPase inhibitor activity (GO:0005095)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|Ras GTPase activator activity (GO:0005099)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(15)|lung(23)|ovary(6)|prostate(1)|skin(3)|stomach(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	68		all_lung(232;0.000514)|Lung NSC(167;0.00135)|Prostate(461;0.00838)|Ovarian(174;0.0149)		all cancers(79;1.38e-36)		TACTGATTCTATTGTGAAGGT	0.393													A|||	2036	0.40655	0.3888	0.4107	5008	,	,		21944	0.2163		0.5626	False		,,,				2504	0.4632				p.I724V		Atlas-SNP	.											.	IQGAP2	186	.	0			c.A2170G						PASS	.	A	VAL/ILE	1795,2611	529.0+/-372.6	351,1093,759	117.0	109.0	112.0		2170	1.1	0.3	5	dbSNP_100	112	4802,3798	613.6+/-396.1	1321,2160,819	yes	missense	IQGAP2	NM_006633.2	29	1672,3253,1578	GG,GA,AA		44.1628,40.7399,49.2773	benign	724/1576	75948650	6597,6409	2203	4300	6503	SO:0001583	missense	10788	exon18			GATTCTATTGTGA	U51903	CCDS34188.1, CCDS68897.1, CCDS68898.1, CCDS75262.1	5q	2008-07-18			ENSG00000145703	ENSG00000145703			6111	protein-coding gene	gene with protein product		605401				8756646	Standard	XM_005248409		Approved		uc003kek.3	Q13576	OTTHUMG00000162432	ENST00000274364.6:c.2170A>G	5.37:g.75948650A>G	ENSP00000274364:p.Ile724Val	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	122	122	1	NM_006633	A8K4V1|B7Z8A4|J3KR91	Missense_Mutation	SNP	ENST00000274364.6	37	CCDS34188.1	886	0.4056776556776557	173	0.3516260162601626	157	0.43370165745856354	132	0.23076923076923078	424	0.5593667546174143	A	0.219	-1.030512	0.02045	0.407399	0.558372	ENSG00000145703	ENST00000274364;ENST00000379730;ENST00000514350;ENST00000505766;ENST00000514001;ENST00000396234;ENST00000545384;ENST00000502745	T;T;T;T;T;T;T	0.27104	1.69;1.69;1.69;1.69;1.69;1.69;1.69	5.31	1.14	0.20703	.	0.228647	0.44902	N	0.000402	T	0.00012	0.0000	N	0.13235	0.315	0.52099	P	5.3999999999998494E-5	B;B;B;B	0.06786	0.0;0.001;0.0;0.0	B;B;B;B	0.15052	0.007;0.012;0.005;0.006	T	0.46857	-0.9161	9	0.02654	T	1	-9.1742	8.5428	0.33404	0.5631:0.0:0.4369:0.0	rs2431363;rs3815769;rs52796908;rs58637816;rs2431363	226;674;220;724	F5H7S7;E7EWC2;Q13576-2;Q13576	.;.;.;IQGA2_HUMAN	V	724;226;697;674;277;220;277;220	ENSP00000274364:I724V;ENSP00000442313:I226V;ENSP00000423672:I697V;ENSP00000421097:I674V;ENSP00000422661:I277V;ENSP00000379535:I220V;ENSP00000426027:I220V	ENSP00000274364:I724V	I	+	1	0	IQGAP2	75984406	0.004000	0.15560	0.311000	0.25182	0.716000	0.41182	0.075000	0.14686	0.018000	0.15052	0.533000	0.62120	ATT	G|0.459;N|0.000	0.459	strong		0.393	IQGAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368877.1	NM_006633	
PCDHGC5	56097	hgsc.bcm.edu	37	5	140870516	140870516	+	Missense_Mutation	SNP	A	A	G	rs2074912	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:140870516A>G	ENST00000252087.1	+	1	1709	c.1709A>G	c.(1708-1710)gAc>gGc	p.D570G	PCDHGA3_ENST00000253812.6_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGC3_ENST00000308177.3_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA10_ENST00000398610.2_Intron|PCDHGA11_ENST00000518882.1_Intron|PCDHGB7_ENST00000398594.2_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA11_ENST00000398587.2_Intron|PCDHGA12_ENST00000252085.3_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGC4_ENST00000306593.1_Intron	NM_018929.2|NM_032403.2|NM_032407.1	NP_061752.1|NP_115779.1|NP_115783.1	Q9Y5F6	PCDGM_HUMAN	protocadherin gamma subfamily C, 5	570			D -> G (in dbSNP:rs2074912).		homophilic cell adhesion (GO:0007156)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(2)|endometrium(6)|kidney(4)|large_intestine(4)|lung(10)|ovary(4)|prostate(1)|urinary_tract(2)	35			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CCACGGCCAGACTGGGAACAC	0.602													G|||	936	0.186901	0.1437	0.3545	5008	,	,		20886	0.129		0.2127	False		,,,				2504	0.1595				p.D570G		Atlas-SNP	.											.	PCDHGC5	199	.	0			c.A1709G						PASS	.	G	,,,,,,,,,,,,,,,,,,,,GLY/ASP,,,,GLY/ASP	706,3700	757.9+/-412.8	58,590,1555	61.0	57.0	58.0		,,,,,,,,,,,,,,,,,,,,1709,,,,1709	5.4	0.1	5	dbSNP_96	58	1696,6904	736.3+/-407.0	156,1384,2760	yes	intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,missense,intron,intron,intron,missense	PCDHGC3,PCDHGB4,PCDHGA8,PCDHGA12,PCDHGC5,PCDHGC4,PCDHGB7,PCDHGB6,PCDHGB5,PCDHGB3,PCDHGB2,PCDHGB1,PCDHGA11,PCDHGA10,PCDHGA9,PCDHGA7,PCDHGA6,PCDHGA5,PCDHGA4,PCDHGA3,PCDHGA2,PCDHGA1	NM_002588.2,NM_003735.2,NM_003736.2,NM_018912.2,NM_018913.2,NM_018914.2,NM_018915.2,NM_018916.3,NM_018917.2,NM_018918.2,NM_018919.2,NM_018920.2,NM_018921.2,NM_018922.2,NM_018923.2,NM_018924.2,NM_018925.2,NM_018926.2,NM_018927.3,NM_018928.2,NM_018929.2,NM_032088.1,NM_032092.1,NM_032403.1,NM_032407.1	,,,,,,,,,,,,,,,,,,,,94,,,,94	214,1974,4315	GG,GA,AA		19.7209,16.0236,18.4684	,,,,,,,,,,,,,,,,,,,,benign,,,,benign	,,,,,,,,,,,,,,,,,,,,570/945,,,,570/879	140870516	2402,10604	2203	4300	6503	SO:0001583	missense	56097	exon1			GGCCAGACTGGGA	AF152526	CCDS4263.1, CCDS75350.1	5q31	2010-01-26			ENSG00000240764	ENSG00000240764		"""Cadherins / Protocadherins : Clustered"""	8718	other	protocadherin		606306				10380929	Standard	NM_018929		Approved	PCDH-GAMMA-C5	uc003lla.2	Q9Y5F6	OTTHUMG00000129624	ENST00000252087.1:c.1709A>G	5.37:g.140870516A>G	ENSP00000252087:p.Asp570Gly	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	64	64	1	NM_018929	Q9Y5C2	Missense_Mutation	SNP	ENST00000252087.1	37	CCDS4263.1	430	0.19688644688644688	70	0.14227642276422764	120	0.3314917127071823	77	0.1346153846153846	163	0.21503957783641162	G	0.787	-0.760117	0.03019	0.160236	0.197209	ENSG00000240764	ENST00000252087	T	0.48836	0.8	5.45	5.45	0.79879	Cadherin-like (1);	0.000000	0.64402	N	0.000019	T	0.00012	0.0000	N	0.10685	0.025	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.38023	-0.9680	9	0.16420	T	0.52	.	6.1051	0.20069	0.0738:0.1326:0.6568:0.1368	rs2074912;rs60363178;rs2074912	570;570	Q9Y5F6-2;Q9Y5F6	.;PCDGM_HUMAN	G	570	ENSP00000252087:D570G	ENSP00000252087:D570G	D	+	2	0	PCDHGC5	140850700	0.978000	0.34361	0.145000	0.22337	0.992000	0.81027	2.437000	0.44828	1.550000	0.49438	-0.119000	0.15052	GAC	A|0.821;G|0.179	0.179	strong		0.602	PCDHGC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251819.1	NM_018929	
GPAM	57678	hgsc.bcm.edu	37	10	113926224	113926224	+	Missense_Mutation	SNP	A	A	G	rs35019520	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:113926224A>G	ENST00000348367.4	-	12	1354	c.1157T>C	c.(1156-1158)aTt>aCt	p.I386T	GPAM_ENST00000369425.1_Missense_Mutation_p.I386T|GPAM_ENST00000423155.1_Missense_Mutation_p.I386T			Q9HCL2	GPAT1_HUMAN	glycerol-3-phosphate acyltransferase, mitochondrial	386			I -> T (in dbSNP:rs35019520).		acyl-CoA metabolic process (GO:0006637)|CDP-diacylglycerol biosynthetic process (GO:0016024)|cellular lipid metabolic process (GO:0044255)|defense response to virus (GO:0051607)|fatty acid homeostasis (GO:0055089)|fatty acid metabolic process (GO:0006631)|glycerophospholipid biosynthetic process (GO:0046474)|interleukin-2 secretion (GO:0070970)|negative regulation of activation-induced cell death of T cells (GO:0070236)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid homeostasis (GO:0055091)|phospholipid metabolic process (GO:0006644)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of multicellular organism growth (GO:0040018)|regulation of cytokine secretion (GO:0050707)|response to glucose (GO:0009749)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial outer membrane (GO:0005741)|plasma membrane (GO:0005886)	glycerol-3-phosphate O-acyltransferase activity (GO:0004366)			breast(2)|central_nervous_system(2)|endometrium(8)|kidney(2)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	31				Epithelial(162;0.0306)|all cancers(201;0.123)		TAACATTCTAATAACACCTCT	0.388													A|||	37	0.00738818	0.0008	0.0086	5008	,	,		20081	0.0		0.0219	False		,,,				2504	0.0082				p.I386T	Ovarian(161;1017 2606 18293 52943)	Atlas-SNP	.											.	GPAM	68	.	0			c.T1157C						PASS	.	A	THR/ILE	11,4395	17.9+/-39.9	0,11,2192	240.0	207.0	218.0		1157	4.7	1.0	10	dbSNP_126	218	109,8491	59.1+/-120.7	1,107,4192	yes	missense	GPAM	NM_020918.4	89	1,118,6384	GG,GA,AA		1.2674,0.2497,0.9227	benign	386/829	113926224	120,12886	2203	4300	6503	SO:0001583	missense	57678	exon12			ATTCTAATAACAC	AL832464	CCDS7570.1	10q25.3	2009-07-15			ENSG00000119927	ENSG00000119927			24865	protein-coding gene	gene with protein product	"""glycerol-3-phosphate acyltransferase 1, mitochondrial"""	602395				10997877, 8369314	Standard	NM_020918		Approved	KIAA1560, MGC26846, GPAT1	uc001kzp.3	Q9HCL2	OTTHUMG00000019055	ENST00000348367.4:c.1157T>C	10.37:g.113926224A>G	ENSP00000265276:p.Ile386Thr	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	108	38	0.351852	NM_001244949	Q5VW51|Q86TA3	Missense_Mutation	SNP	ENST00000348367.4	37	CCDS7570.1	20	0.009157509157509158	0	0.0	7	0.019337016574585635	0	0.0	13	0.017150395778364115	A	14.69	2.610145	0.46527	0.002497	0.012674	ENSG00000119927	ENST00000348367;ENST00000423155;ENST00000369425	T;T;T	0.42900	0.96;0.96;0.96	5.87	4.69	0.59074	.	0.159420	0.56097	D	0.000036	T	0.12305	0.0299	N	0.08118	0	0.29156	N	0.878052	B;B	0.19817	0.039;0.039	B;B	0.18871	0.023;0.023	T	0.04737	-1.0930	10	0.22706	T	0.39	-19.2312	14.4037	0.67068	0.8693:0.1307:0.0:0.0	rs35019520	386;386	Q5VW52;Q9HCL2	.;GPAT1_HUMAN	T	386	ENSP00000265276:I386T;ENSP00000409242:I386T;ENSP00000358433:I386T	ENSP00000265276:I386T	I	-	2	0	GPAM	113916214	1.000000	0.71417	0.993000	0.49108	0.998000	0.95712	5.730000	0.68546	2.247000	0.74100	0.523000	0.50628	ATT	A|0.990;G|0.010	0.010	strong		0.388	GPAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050377.1	NM_020918	
NDUFA9	4704	hgsc.bcm.edu	37	12	4768290	4768290	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:4768290G>A	ENST00000266544.5	+	5	519	c.499G>A	c.(499-501)Gtt>Att	p.V167I	RP11-500M8.7_ENST00000536588.1_3'UTR	NM_005002.4	NP_004993.1	Q16795	NDUA9_HUMAN	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 9, 39kDa	167					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)|sodium ion transport (GO:0006814)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial membrane (GO:0031966)|mitochondrial respiratory chain complex I (GO:0005747)|nucleus (GO:0005634)	coenzyme binding (GO:0050662)|NADH dehydrogenase (ubiquinone) activity (GO:0008137)|NADH dehydrogenase activity (GO:0003954)|protein complex binding (GO:0032403)			NS(1)|breast(1)|endometrium(3)|large_intestine(4)|lung(9)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	21						ATTCATTCATGTTTCACATCT	0.358																																					p.V167I	Colon(75;996 1244 23946 25294 29232)	Atlas-SNP	.											.	NDUFA9	45	.	0			c.G499A						PASS	.						69.0	73.0	72.0					12																	4768290		2203	4300	6503	SO:0001583	missense	4704	exon5			ATTCATGTTTCAC	AF050641	CCDS8532.1	12p13.3	2011-09-14	2002-08-29		ENSG00000139180	ENSG00000139180		"""Mitochondrial respiratory chain complex / Complex I"", ""Short chain dehydrogenase/reductase superfamily / Extended SDR fold"""	7693	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 22E, member 1"", ""complex I 39kDa subunit"""	603834	"""NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 9 (39kD)"""	NDUFS2L		8486360, 19027726	Standard	NM_005002		Approved	SDR22E1, CI-39k	uc001qnc.3	Q16795		ENST00000266544.5:c.499G>A	12.37:g.4768290G>A	ENSP00000266544:p.Val167Ile	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	67	30	0.447761	NM_005002	Q14076|Q2NKX0	Missense_Mutation	SNP	ENST00000266544.5	37	CCDS8532.1	.	.	.	.	.	.	.	.	.	.	G	11.75	1.731929	0.30684	.	.	ENSG00000139180	ENST00000266544	D	0.93189	-3.18	5.26	3.43	0.39272	NAD(P)-binding domain (1);NmrA-like (1);	0.304583	0.38005	N	0.001857	D	0.85898	0.5804	N	0.17922	0.545	0.80722	D	1	B;B	0.15473	0.013;0.013	B;B	0.25987	0.065;0.065	T	0.76515	-0.2931	10	0.27082	T	0.32	-11.9884	7.2226	0.25997	0.3375:0.0:0.6625:0.0	.	167;167	A8K4V2;Q16795	.;NDUA9_HUMAN	I	167	ENSP00000266544:V167I	ENSP00000266544:V167I	V	+	1	0	NDUFA9	4638551	0.989000	0.36119	0.984000	0.44739	0.576000	0.36127	0.932000	0.28884	0.707000	0.31934	0.585000	0.79938	GTT	.	.	none		0.358	NDUFA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398900.2	NM_005002	
BAIAP3	8938	hgsc.bcm.edu	37	16	1389222	1389222	+	Silent	SNP	C	C	T	rs61742684	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:1389222C>T	ENST00000324385.5	+	4	540	c.382C>T	c.(382-384)Ctg>Ttg	p.L128L	BAIAP3_ENST00000426824.3_Silent_p.L93L|BAIAP3_ENST00000562208.1_Silent_p.L93L|BAIAP3_ENST00000421665.2_Silent_p.L93L|BAIAP3_ENST00000397488.2_Silent_p.L110L|BAIAP3_ENST00000397489.1_Silent_p.L110L|BAIAP3_ENST00000568887.1_Silent_p.L93L	NM_003933.4	NP_003924.2	O94812	BAIP3_HUMAN	BAI1-associated protein 3	128					G-protein coupled receptor signaling pathway (GO:0007186)|neurotransmitter secretion (GO:0007269)		protein C-terminus binding (GO:0008022)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(1)|lung(25)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	42		Hepatocellular(780;0.0893)				CAGCCTCGGCCTGAGAGCCCT	0.687													C|||	105	0.0209665	0.0083	0.0447	5008	,	,		13161	0.0		0.0547	False		,,,				2504	0.0082				p.L128L		Atlas-SNP	.											.	BAIAP3	88	.	0			c.C382T						PASS	.	C	,,,,	57,4221		0,57,2082	7.0	9.0	8.0		277,277,277,277,382	3.4	0.4	16	dbSNP_129	8	437,8021		9,419,3801	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	BAIAP3	NM_001199096.1,NM_001199097.1,NM_001199098.1,NM_001199099.1,NM_003933.4	,,,,	9,476,5883	TT,TC,CC		5.1667,1.3324,3.8788	,,,,	93/1117,93/1153,93/1130,93/1125,128/1188	1389222	494,12242	2139	4229	6368	SO:0001819	synonymous_variant	8938	exon4			CTCGGCCTGAGAG	AB017111	CCDS10434.1, CCDS55978.1, CCDS55979.1, CCDS58402.1, CCDS58403.1, CCDS66894.1	16p13.3	2008-07-04			ENSG00000007516	ENSG00000007516			948	protein-coding gene	gene with protein product		604009				9790924	Standard	NM_003933		Approved	BAP3, KIAA0734	uc002clk.2	O94812	OTTHUMG00000047833	ENST00000324385.5:c.382C>T	16.37:g.1389222C>T		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	43	42	0.976744	NM_003933	A2A2B2|B2RCD7|B4DGS5|B4DIK3|B4DRK9|B4DRP1|E7EUB9|H3BUH8|H3BVI3|H7C2Q1|O94839|Q2M226|Q658J2|Q76N05|Q96RZ3|Q9UJK1	Silent	SNP	ENST00000324385.5	37	CCDS10434.1																																																																																			C|0.973;T|0.027	0.027	strong		0.687	BAIAP3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000109056.3		
GLB1L	79411	hgsc.bcm.edu	37	2	220101974	220101974	+	Silent	SNP	A	A	G	rs61733623	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:220101974A>G	ENST00000295759.7	-	17	2098	c.1785T>C	c.(1783-1785)ccT>ccC	p.P595P	GLB1L_ENST00000409640.1_Silent_p.P505P|GLB1L_ENST00000356283.3_Silent_p.P505P|GLB1L_ENST00000392089.2_Silent_p.P595P|GLB1L_ENST00000497855.1_5'UTR			Q6UWU2	GLB1L_HUMAN	galactosidase, beta 1-like	595					carbohydrate metabolic process (GO:0005975)	extracellular region (GO:0005576)	beta-galactosidase activity (GO:0004565)			breast(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(7)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	22		all_lung(227;1.19e-05)|Lung NSC(271;2.76e-05)|Medulloblastoma(418;0.0208)|Esophageal squamous(248;0.0559)		Epithelial(149;1.3e-11)|all cancers(144;2.07e-10)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		GGGCTCCCCTAGGAAACAGCA	0.498													a|||	22	0.00439297	0.0023	0.0058	5008	,	,		18170	0.0		0.0139	False		,,,				2504	0.001				p.P595P		Atlas-SNP	.											GLB1L,colon,carcinoma,-1,1	GLB1L	52	1	0			c.T1785C						scavenged	.	A		19,4387	25.3+/-52.1	0,19,2184	109.0	107.0	108.0		1785	3.0	0.4	2	dbSNP_129	108	135,8465	68.4+/-130.8	1,133,4166	no	coding-synonymous	GLB1L	NM_024506.3		1,152,6350	GG,GA,AA		1.5698,0.4312,1.1841		595/655	220101974	154,12852	2203	4300	6503	SO:0001819	synonymous_variant	79411	exon17			TCCCCTAGGAAAC		CCDS2437.1, CCDS74657.1	2q36.1	2008-02-05			ENSG00000163521	ENSG00000163521			28129	protein-coding gene	gene with protein product						12975309	Standard	XM_005246850		Approved	MGC10771	uc002vkm.3	Q6UWU2	OTTHUMG00000133133	ENST00000295759.7:c.1785T>C	2.37:g.220101974A>G		Somatic	169	1	0.00591716		WXS	Illumina HiSeq	Phase_I	149	80	0.536913	NM_024506	Q96DR0	Silent	SNP	ENST00000295759.7	37	CCDS2437.1																																																																																			A|0.990;G|0.010	0.010	strong		0.498	GLB1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256822.2	NM_024506	
RAD54B	25788	hgsc.bcm.edu	37	8	95423464	95423464	+	Silent	SNP	A	A	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:95423464A>G	ENST00000336148.5	-	4	508	c.384T>C	c.(382-384)gtT>gtC	p.V128V		NM_012415.3	NP_036547.1	Q9Y620	RA54B_HUMAN	RAD54 homolog B (S. cerevisiae)	128					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)			TACACCAAACAACACTGAAAT	0.328								Direct reversal of damage;Homologous recombination																													p.V128V		Atlas-SNP	.											.	RAD54B	88	.	0			c.T384C						PASS	.						100.0	101.0	101.0					8																	95423464		2202	4297	6499	SO:0001819	synonymous_variant	25788	exon4			CCAAACAACACTG	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.384T>C	8.37:g.95423464A>G		Somatic	259	0	0		WXS	Illumina HiSeq	Phase_I	240	111	0.4625	NM_012415	F6WBS8	Silent	SNP	ENST00000336148.5	37	CCDS6262.1																																																																																			.	.	none		0.328	RAD54B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257806.3	NM_012415	
ACTN1	87	hgsc.bcm.edu	37	14	69352230	69352230	+	Silent	SNP	G	G	A	rs15993	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:69352230G>A	ENST00000193403.6	-	12	1680	c.1297C>T	c.(1297-1299)Ctg>Ttg	p.L433L	ACTN1_ENST00000438964.2_Silent_p.L433L|ACTN1_ENST00000394419.4_Silent_p.L433L|ACTN1_ENST00000538545.2_Silent_p.L433L|ACTN1_ENST00000376839.3_Silent_p.L368L	NM_001102.3	NP_001093.1	P12814	ACTN1_HUMAN	actinin, alpha 1	433	Interaction with DDN.				actin crosslink formation (GO:0051764)|actin filament bundle assembly (GO:0051017)|blood coagulation (GO:0007596)|cell junction assembly (GO:0034329)|extracellular matrix organization (GO:0030198)|focal adhesion assembly (GO:0048041)|negative regulation of cellular component movement (GO:0051271)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of apoptotic process (GO:0042981)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)|pseudopodium (GO:0031143)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|double-stranded RNA binding (GO:0003725)|integrin binding (GO:0005178)|ion channel binding (GO:0044325)|vinculin binding (GO:0017166)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|lung(9)|prostate(2)|urinary_tract(1)	27				BRCA - Breast invasive adenocarcinoma(234;0.00605)|all cancers(60;0.00846)|OV - Ovarian serous cystadenocarcinoma(108;0.0654)		TTCTTGAGCAGGGCCTTGATC	0.612													g|||	1160	0.231629	0.149	0.3991	5008	,	,		16779	0.1796		0.1918	False		,,,				2504	0.319				p.L433L		Atlas-SNP	.											.	ACTN1	77	.	0			c.C1297T						PASS	.	G	,,	635,3771	273.7+/-271.5	52,531,1620	137.0	103.0	114.0		1297,1297,1297	3.3	1.0	14	dbSNP_52	114	1753,6847	319.2+/-314.1	166,1421,2713	no	coding-synonymous,coding-synonymous,coding-synonymous	ACTN1	NM_001102.3,NM_001130004.1,NM_001130005.1	,,	218,1952,4333	AA,AG,GG		20.3837,14.4122,18.3608	,,	433/893,433/915,433/888	69352230	2388,10618	2203	4300	6503	SO:0001819	synonymous_variant	87	exon12			TGAGCAGGGCCTT	M95178	CCDS9792.1, CCDS45129.1, CCDS45130.1	14q24.1	2014-08-08			ENSG00000072110	ENSG00000072110		"""EF-hand domain containing"""	163	protein-coding gene	gene with protein product		102575				2349951	Standard	NM_001102		Approved		uc001xkm.3	P12814	OTTHUMG00000171386	ENST00000193403.6:c.1297C>T	14.37:g.69352230G>A		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	75	28	0.373333	NM_001102	B3V8S3|B4DHH3|B7TY16|Q1HE25|Q9BTN1	Silent	SNP	ENST00000193403.6	37	CCDS9792.1																																																																																			G|0.811;A|0.189	0.189	strong		0.612	ACTN1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000413233.3	NM_001102	
TRIOBP	11078	hgsc.bcm.edu	37	22	38122122	38122122	+	Missense_Mutation	SNP	T	T	C	rs5756795	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	55	0	0		WXS	Illumina HiSeq	Phase_I	47	26	0.553191	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		
FHAD1	114827	hgsc.bcm.edu	37	1	15616139	15616139	+	Missense_Mutation	SNP	G	G	A	rs486557	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:15616139G>A	ENST00000375998.4	+	3	545	c.545G>A	c.(544-546)cGc>cAc	p.R182H	FHAD1_ENST00000375999.3_Missense_Mutation_p.R182H|FHAD1_ENST00000358897.4_Missense_Mutation_p.R182H|FHAD1_ENST00000417793.1_Missense_Mutation_p.R182H			B1AJZ9	FHAD1_HUMAN	forkhead-associated (FHA) phosphopeptide binding domain 1	182										skin(1)|stomach(1)	2						GACGACGCCCGCAAGCCACCC	0.612													G|||	1042	0.208067	0.2073	0.2089	5008	,	,		16676	0.0417		0.326	False		,,,				2504	0.2587				p.R182H		Atlas-SNP	.											.	FHAD1	78	.	0			c.G545A						PASS	.						28.0	36.0	34.0					1																	15616139		692	1591	2283	SO:0001583	missense	114827	exon4			ACGCCCGCAAGCC	AK093300		1p36.21	2012-04-19			ENSG00000142621	ENSG00000142621			29408	protein-coding gene	gene with protein product						11572484	Standard	NM_052929		Approved	KIAA1937	uc001awb.2	B1AJZ9	OTTHUMG00000002088	ENST00000375998.4:c.545G>A	1.37:g.15616139G>A	ENSP00000365166:p.Arg182His	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	68	32	0.470588	NM_052929	Q0P6F5|Q8N8D3|Q8N9T6|Q8NA05	Missense_Mutation	SNP	ENST00000375998.4	37		473	0.21657509157509158	110	0.22357723577235772	100	0.27624309392265195	22	0.038461538461538464	241	0.3179419525065963	G	5.490	0.275364	0.10403	.	.	ENSG00000142621	ENST00000358897;ENST00000417793;ENST00000375999;ENST00000375998	T;T;T;T	0.46819	0.88;0.87;0.86;0.88	3.77	-7.54	0.01332	.	1.620530	0.04279	N	0.343560	T	0.00012	0.0000	N	0.02539	-0.55	0.50313	P	1.36000000000025E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.17228	-1.0376	9	0.36615	T	0.2	-1.7323	12.0544	0.53527	0.1394:0.6827:0.178:0.0	rs486557;rs3765352;rs52797627;rs60426766;rs486557	182	B1AJZ9	FHAD1_HUMAN	H	182	ENSP00000351770:R182H;ENSP00000407615:R182H;ENSP00000365167:R182H;ENSP00000365166:R182H	ENSP00000351770:R182H	R	+	2	0	FHAD1	15488726	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.847000	0.04331	-1.849000	0.01171	-1.154000	0.01816	CGC	G|0.777;A|0.223	0.223	strong		0.612	FHAD1-026	PUTATIVE	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000393400.2	NM_052929	
IQGAP2	10788	hgsc.bcm.edu	37	5	75932965	75932965	+	Missense_Mutation	SNP	G	G	C	rs2455230	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:75932965G>C	ENST00000274364.6	+	16	2184	c.1887G>C	c.(1885-1887)ttG>ttC	p.L629F	IQGAP2_ENST00000502745.1_Missense_Mutation_p.L182F|IQGAP2_ENST00000396234.3_Missense_Mutation_p.L182F|IQGAP2_ENST00000379730.3_Missense_Mutation_p.L188F	NM_006633.2	NP_006624	Q13576	IQGA2_HUMAN	IQ motif containing GTPase activating protein 2	629			L -> F (in dbSNP:rs2455230). {ECO:0000269|PubMed:21269460, ECO:0000269|PubMed:8756646, ECO:0000269|Ref.2}.		negative regulation of catalytic activity (GO:0043086)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|microvillus (GO:0005902)	actin binding (GO:0003779)|GTPase inhibitor activity (GO:0005095)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|Ras GTPase activator activity (GO:0005099)	p.L629F(1)		NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(15)|lung(23)|ovary(6)|prostate(1)|skin(3)|stomach(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	68		all_lung(232;0.000514)|Lung NSC(167;0.00135)|Prostate(461;0.00838)|Ovarian(174;0.0149)		all cancers(79;1.38e-36)		AATCATGCTTGTATAAAGAAT	0.378													G|||	2771	0.553315	0.5537	0.4928	5008	,	,		18374	0.4722		0.6083	False		,,,				2504	0.6227				p.L629F		Atlas-SNP	.											IQGAP2,NS,carcinoma,0,1	IQGAP2	186	1	1	Substitution - Missense(1)	stomach(1)	c.G1887C						PASS	.	G	PHE/LEU	2454,1952	620.3+/-393.5	655,1144,404	107.0	104.0	105.0		1887	0.2	0.0	5	dbSNP_100	105	5082,3518	631.4+/-398.5	1479,2124,697	yes	missense	IQGAP2	NM_006633.2	22	2134,3268,1101	CC,CG,GG		40.907,44.3032,42.0575	possibly-damaging	629/1576	75932965	7536,5470	2203	4300	6503	SO:0001583	missense	10788	exon16			ATGCTTGTATAAA	U51903	CCDS34188.1, CCDS68897.1, CCDS68898.1, CCDS75262.1	5q	2008-07-18			ENSG00000145703	ENSG00000145703			6111	protein-coding gene	gene with protein product		605401				8756646	Standard	XM_005248409		Approved		uc003kek.3	Q13576	OTTHUMG00000162432	ENST00000274364.6:c.1887G>C	5.37:g.75932965G>C	ENSP00000274364:p.Leu629Phe	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	85	85	1	NM_006633	A8K4V1|B7Z8A4|J3KR91	Missense_Mutation	SNP	ENST00000274364.6	37	CCDS34188.1	1191	0.5453296703296703	261	0.5304878048780488	183	0.505524861878453	293	0.5122377622377622	454	0.5989445910290238	G	10.87	1.473117	0.26423	0.556968	0.59093	ENSG00000145703	ENST00000274364;ENST00000379730;ENST00000514350;ENST00000505766;ENST00000514001;ENST00000396234;ENST00000545384;ENST00000502745	T;T;T;T;T;T;T	0.60672	0.17;0.17;0.17;0.17;0.17;0.17;0.17	5.72	0.233	0.15386	.	1.161090	0.06276	N	0.696452	T	0.00012	0.0000	M	0.67953	2.075	0.80722	P	0.0	B;B;B;B	0.22541	0.071;0.004;0.071;0.004	B;B;B;B	0.35899	0.213;0.017;0.213;0.017	T	0.47749	-0.9093	9	0.14656	T	0.56	3.0E-4	4.8888	0.13717	0.353:0.1597:0.4873:0.0	rs2455230;rs3797458;rs17748849;rs52806612;rs2455230	188;579;182;629	F5H7S7;E7EWC2;Q13576-2;Q13576	.;.;.;IQGA2_HUMAN	F	629;188;602;579;182;182;182;182	ENSP00000274364:L629F;ENSP00000442313:L188F;ENSP00000423672:L602F;ENSP00000421097:L579F;ENSP00000422661:L182F;ENSP00000379535:L182F;ENSP00000426027:L182F	ENSP00000274364:L629F	L	+	3	2	IQGAP2	75968721	0.000000	0.05858	0.000000	0.03702	0.066000	0.16364	0.145000	0.16157	0.018000	0.15052	-0.203000	0.12734	TTG	G|0.436;C|0.563	0.563	strong		0.378	IQGAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368877.1	NM_006633	
DEFB129	140881	hgsc.bcm.edu	37	20	210061	210061	+	Silent	SNP	G	G	A	rs13045643	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	73	0	0		WXS	Illumina HiSeq	Phase_I	70	70	1	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	
MUC4	4585	hgsc.bcm.edu	37	3	195505838	195505838	+	Missense_Mutation	SNP	G	G	C	rs59101491		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195505838G>C	ENST00000463781.3	-	2	13072	c.12613C>G	c.(12613-12615)Cac>Gac	p.H4205D	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.H4205D	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.H4205D(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)		GGGGTGGCGTGACCTGTGGAT	0.597																																					p.H4205D		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,+2,19	MUC4	1505	19	2	Substitution - Missense(2)	prostate(2)	c.C12613G						scavenged	.						15.0	14.0	14.0					3																	195505838		689	1578	2267	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.12613C>G	3.37:g.195505838G>C	ENSP00000417498:p.His4205Asp	Somatic	72	3	0.0416667		WXS	Illumina HiSeq	Phase_I	116	6	0.0517241	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	0.851	-0.738678	0.03111	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.29142	1.58;1.6	.	.	.	.	.	.	.	.	T	0.16685	0.0401	N	0.19112	0.55	0.22684	N	0.998851	B	0.30236	0.274	B	0.29267	0.1	T	0.25187	-1.0139	6	.	.	.	.	.	.	.	rs59101491	4077	E7ESK3	.	D	4205	ENSP00000417498:H4205D;ENSP00000420243:H4205D	.	H	-	1	0	MUC4	196990617	.	.	0.017000	0.16124	0.048000	0.14542	.	.	0.452000	0.26830	0.074000	0.15403	CAC	.	.	weak		0.597	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
EXT1	2131	hgsc.bcm.edu	37	8	118819578	118819578	+	Silent	SNP	C	C	T	rs7837891	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:118819578C>T	ENST00000378204.2	-	9	2567	c.1761G>A	c.(1759-1761)gaG>gaA	p.E587E		NM_000127.2	NP_000118.2	Q16394	EXT1_HUMAN	exostosin glycosyltransferase 1	587					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)			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)			CCACAATCCTCTCAGGGAAGC	0.502			"""Mis, N, F, S"""			"""exostoses, osteosarcoma"""			Langer-Giedion syndrome;Hereditary Multiple Exostoses				C|||	1695	0.338458	0.1634	0.549	5008	,	,		17366	0.38		0.4185	False		,,,				2504	0.3006				p.E587E		Atlas-SNP	.	yes	Rec		Multiple Exostoses Type 1	8	8q24.11-q24.13	2131	multiple exostoses type 1 gene		M	.	EXT1	98	.	0			c.G1761A						PASS	.	C		935,3471	357.6+/-314.0	104,727,1372	73.0	65.0	68.0		1761	5.9	1.0	8	dbSNP_116	68	3631,4969	524.4+/-380.5	771,2089,1440	no	coding-synonymous	EXT1	NM_000127.2		875,2816,2812	TT,TC,CC		42.2209,21.2211,35.1069		587/747	118819578	4566,8440	2203	4300	6503	SO:0001819	synonymous_variant	2131	exon9	Familial Cancer Database	Trichorhinophalangeal syndrome type 2, TRPS II;HME, Hereditary Exostoses, Multiple Osteochondromatosis, Multiple Cartilaginous Exostoses	AATCCTCTCAGGG	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.1761G>A	8.37:g.118819578C>T		Somatic	116	1	0.00862069		WXS	Illumina HiSeq	Phase_I	101	99	0.980198	NM_000127	B2R7V2|Q9BVI9	Silent	SNP	ENST00000378204.2	37	CCDS6324.1																																																																																			C|0.659;T|0.341	0.341	strong		0.502	EXT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132768.3	NM_000127	
FAM151A	338094	hgsc.bcm.edu	37	1	55075122	55075122	+	Missense_Mutation	SNP	C	C	G	rs11206394	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:55075122C>G	ENST00000302250.2	-	8	1737	c.1577G>C	c.(1576-1578)gGc>gCc	p.G526A	ACOT11_ENST00000371316.3_Intron|ACOT11_ENST00000481208.1_3'UTR|ACOT11_ENST00000343744.2_3'UTR|FAM151A_ENST00000371304.2_Missense_Mutation_p.G339A	NM_176782.2	NP_788954.2	Q8WW52	F151A_HUMAN	family with sequence similarity 151, member A	526			G -> A (in dbSNP:rs11206394).			extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(2)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	12						CAGCAGCCTGCCTATGGCTCC	0.627													G|||	685	0.136781	0.1422	0.1599	5008	,	,		18324	0.2292		0.0487	False		,,,				2504	0.1084				p.G526A		Atlas-SNP	.											.	FAM151A	58	.	0			c.G1577C						PASS	.	G	,,ALA/GLY	673,3733		44,585,1574	54.0	54.0	54.0		,,1577	3.4	0.7	1	dbSNP_120	54	392,8202		17,358,3922	yes	intron,utr-3,missense	ACOT11,FAM151A	NM_015547.3,NM_147161.3,NM_176782.2	,,60	61,943,5496	GG,GC,CC		4.5613,15.2746,8.1923	,,benign	,,526/586	55075122	1065,11935	2203	4297	6500	SO:0001583	missense	338094	exon8			AGCCTGCCTATGG	AK091901	CCDS594.1	1p32.3	2008-02-05	2007-12-18	2007-12-18	ENSG00000162391	ENSG00000162391			25032	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 179"""	C1orf179		17273976	Standard	NM_176782		Approved	MGC27169	uc001cxn.3	Q8WW52	OTTHUMG00000009888	ENST00000302250.2:c.1577G>C	1.37:g.55075122C>G	ENSP00000306888:p.Gly526Ala	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	72	34	0.472222	NM_176782	Q5VUG5|Q6DKH5|Q6UWV0|Q8NAX9|Q96KY5	Missense_Mutation	SNP	ENST00000302250.2	37	CCDS594.1	297	0.13598901098901098	64	0.13008130081300814	56	0.15469613259668508	135	0.23601398601398602	42	0.055408970976253295	G	0.009	-1.833065	0.00579	0.152746	0.045613	ENSG00000162391	ENST00000302250;ENST00000294370	T	0.10477	2.87	4.28	3.36	0.38483	.	0.360829	0.23995	N	0.042535	T	0.00012	0.0000	N	0.00077	-2.24	0.09310	P	0.9999999999282506	B	0.02656	0.0	B	0.01281	0.0	T	0.39961	-0.9588	9	0.02654	T	1	-15.6326	3.2166	0.06701	0.0936:0.1779:0.5439:0.1847	rs11206394;rs11206394	526	Q8WW52	F151A_HUMAN	A	526;339	ENSP00000306888:G526A	ENSP00000294370:G339A	G	-	2	0	FAM151A	54847710	0.993000	0.37304	0.663000	0.29738	0.127000	0.20565	1.996000	0.40776	0.752000	0.32923	-0.120000	0.15030	GGC	C|0.901;G|0.099	0.099	strong		0.627	FAM151A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027342.1	NM_176782	
ABCC3	8714	hgsc.bcm.edu	37	17	48745345	48745345	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:48745345C>T	ENST00000285238.8	+	13	1837	c.1757C>T	c.(1756-1758)cCc>cTc	p.P586L		NM_003786.3	NP_003777.2	O15438	MRP3_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 3	586	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)	AACATGCTGCCCCAGTTAATC	0.532																																					p.P586L		Atlas-SNP	.											ABCC3,caecum,carcinoma,+1,1	ABCC3	138	1	0			c.C1757T						scavenged	.						151.0	131.0	138.0					17																	48745345		2203	4300	6503	SO:0001583	missense	8714	exon13			TGCTGCCCCAGTT	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.1757C>T	17.37:g.48745345C>T	ENSP00000285238:p.Pro586Leu	Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	115	3	0.026087	NM_003786	B2RPA9|D3DTX9|O60265|O60922|O75621|O95078|O95289|O95290|Q86X85|Q9UN52	Missense_Mutation	SNP	ENST00000285238.8	37	CCDS32681.1	.	.	.	.	.	.	.	.	.	.	C	27.8	4.859862	0.91433	.	.	ENSG00000108846	ENST00000285238	T	0.55052	0.54	4.32	4.32	0.51571	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);	0.000000	0.85682	D	0.000000	T	0.80732	0.4679	H	0.97962	4.115	0.80722	D	1	D	0.58620	0.983	P	0.59056	0.851	D	0.88950	0.3386	10	0.87932	D	0	-21.3117	17.385	0.87413	0.0:1.0:0.0:0.0	.	586	O15438	MRP3_HUMAN	L	586	ENSP00000285238:P586L	ENSP00000285238:P586L	P	+	2	0	ABCC3	46100344	1.000000	0.71417	0.789000	0.31954	0.900000	0.52787	7.651000	0.83577	2.406000	0.81754	0.591000	0.81541	CCC	.	.	none		0.532	ABCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368083.2	NM_020038	
PLCH2	9651	hgsc.bcm.edu	37	1	2430617	2430617	+	Silent	SNP	C	C	T	rs2296442	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:2430617C>T	ENST00000419816.2	+	19	2803	c.2529C>T	c.(2527-2529)atC>atT	p.I843I	PLCH2_ENST00000449969.1_Silent_p.I816I|PLCH2_ENST00000378486.3_Silent_p.I843I|PLCH2_ENST00000378488.3_Silent_p.I807I|PLCH2_ENST00000288766.5_Silent_p.I131I			O75038	PLCH2_HUMAN	phospholipase C, eta 2	843	C2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				inositol phosphate metabolic process (GO:0043647)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|phosphatidylinositol metabolic process (GO:0046488)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|phosphatidylinositol phospholipase C activity (GO:0004435)|signal transducer activity (GO:0004871)			central_nervous_system(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(8)|ovary(1)|prostate(3)|skin(1)	20	all_cancers(77;0.000161)|all_epithelial(69;5.98e-05)|all_lung(157;0.016)|Lung NSC(156;0.0376)|Ovarian(185;0.0634)	all_epithelial(116;7.32e-16)|all_lung(118;1.15e-06)|Lung NSC(185;6.26e-05)|Renal(390;0.00571)|Breast(487;0.00832)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Medulloblastoma(700;0.151)|Lung SC(97;0.217)		Epithelial(90;1.44e-37)|OV - Ovarian serous cystadenocarcinoma(86;6.78e-23)|GBM - Glioblastoma multiforme(42;2.8e-08)|Colorectal(212;4.19e-05)|COAD - Colon adenocarcinoma(227;0.000195)|Kidney(185;0.00034)|BRCA - Breast invasive adenocarcinoma(365;0.00443)|KIRC - Kidney renal clear cell carcinoma(229;0.00548)|STAD - Stomach adenocarcinoma(132;0.00644)|Lung(427;0.2)		ACGATCCCATCGGGCGTGACT	0.657													C|||	1836	0.366613	0.1725	0.4481	5008	,	,		20117	0.4812		0.4821	False		,,,				2504	0.3344				p.I843I		Atlas-SNP	.											.	PLCH2	131	.	0			c.C2529T						PASS	.	C		934,3406		107,720,1343	46.0	49.0	48.0		2529	-1.7	1.0	1	dbSNP_100	48	4049,4499		959,2131,1184	no	coding-synonymous	PLCH2	NM_014638.2		1066,2851,2527	TT,TC,CC		47.3678,21.5207,38.6639		843/1417	2430617	4983,7905	2170	4274	6444	SO:0001819	synonymous_variant	9651	exon19			TCCCATCGGGCGT	AB007919	CCDS59959.1	1p36.32	2013-01-10	2006-03-16	2006-03-16	ENSG00000149527	ENSG00000149527	3.1.4.11	"""EF-hand domain containing"""	29037	protein-coding gene	gene with protein product		612836	"""phospholipase C-like 4"""	PLCL4		15899900	Standard	XM_006711054		Approved	KIAA0450, PLCeta2, RP3-395M20.1, PLC-eta2	uc001aji.1	O75038	OTTHUMG00000000719	ENST00000419816.2:c.2529C>T	1.37:g.2430617C>T		Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	101	100	0.990099	NM_014638	A2VCM3|B9DI80|Q3LUA8|Q86XJ2|Q86XU1|Q86YU7|Q8TEH5|Q8WUS6	Silent	SNP	ENST00000419816.2	37		951	0.43543956043956045	97	0.19715447154471544	168	0.46408839779005523	316	0.5524475524475524	370	0.48812664907651715	c	4.641	0.119174	0.08881	0.215207	0.473678	ENSG00000149527	ENST00000419816	.	.	.	5.03	-1.71	0.08133	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.45101	-0.9284	3	.	.	.	.	11.3627	0.49653	0.0:0.396:0.0:0.604	rs2296442;rs57851129;rs2296442	.	.	.	L	138	.	.	S	+	2	0	PLCH2	2420477	0.003000	0.15002	0.965000	0.40720	0.773000	0.43773	-1.564000	0.02152	-0.659000	0.05359	-0.227000	0.12334	TCG	C|0.593;T|0.407	0.407	strong		0.657	PLCH2-009	KNOWN	non_canonical_conserved|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000467514.1	NM_014638	
VIPR2	7434	hgsc.bcm.edu	37	7	158828692	158828692	+	Missense_Mutation	SNP	C	C	T	rs145308657		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:158828692C>T	ENST00000262178.2	-	8	945	c.760G>A	c.(760-762)Gtc>Atc	p.V254I	VIPR2_ENST00000402066.1_Missense_Mutation_p.V395I|VIPR2_ENST00000377633.3_Missense_Mutation_p.V238I	NM_003382.4	NP_003373.2	P41587	VIPR2_HUMAN	vasoactive intestinal peptide receptor 2	254					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)		CCGATGCAGACGGTGGGGAGG	0.612																																					p.V254I	Pancreas(154;1876 1931 2329 17914 20079)	Atlas-SNP	.											.	VIPR2	53	.	0			c.G760A						PASS	.	T	ILE/VAL	0,4406		0,0,2203	66.0	50.0	55.0		760	-2.9	0.0	7	dbSNP_134	55	2,8598	2.2+/-6.3	0,2,4298	yes	missense	VIPR2	NM_003382.4	29	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	benign	254/439	158828692	2,13004	2203	4300	6503	SO:0001583	missense	7434	exon8			TGCAGACGGTGGG	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.760G>A	7.37:g.158828692C>T	ENSP00000262178:p.Val254Ile	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	56	29	0.517857	NM_003382	Q13053|Q15870|Q53Y09|Q6ZN22|Q9UCW0	Missense_Mutation	SNP	ENST00000262178.2	37	CCDS5950.1	.	.	.	.	.	.	.	.	.	.	c	4.973	0.180779	0.09443	0.0	2.33E-4	ENSG00000106018	ENST00000262178;ENST00000377633;ENST00000402066	T;T;T	0.51574	0.7;0.7;0.7	4.72	-2.87	0.05700	GPCR, family 2-like (1);	0.479321	0.17044	N	0.189218	T	0.23133	0.0559	N	0.16602	0.42	0.09310	N	0.999991	B	0.24882	0.113	B	0.22880	0.042	T	0.16305	-1.0407	9	.	.	.	.	6.6287	0.22845	0.0:0.3749:0.1336:0.4915	.	254	P41587	VIPR2_HUMAN	I	254;238;395	ENSP00000262178:V254I;ENSP00000366860:V238I;ENSP00000384497:V395I	.	V	-	1	0	VIPR2	158521453	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.497000	0.02289	-0.616000	0.05671	-1.616000	0.00795	GTC	C|1.000;T|0.000	0.000	weak		0.612	VIPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322675.1	NM_003382	
PLCD4	84812	hgsc.bcm.edu	37	2	219492952	219492952	+	Splice_Site	SNP	C	C	T	rs61733653	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:219492952C>T	ENST00000450993.2	+	7	1312	c.973C>T	c.(973-975)Cgg>Tgg	p.R325W	PLCD4_ENST00000417849.1_Splice_Site_p.R325W|PLCD4_ENST00000432688.1_Splice_Site_p.R325W	NM_032726.3	NP_116115.1	Q9BRC7	PLCD4_HUMAN	phospholipase C, delta 4	325	PI-PLC X-box. {ECO:0000255|PROSITE- ProRule:PRU00270}.				acrosome reaction (GO:0007340)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|phosphatidylinositol metabolic process (GO:0046488)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|phosphatidylinositol phospholipase C activity (GO:0004435)|signal transducer activity (GO:0004871)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(2)|lung(7)|ovary(3)|prostate(1)|urinary_tract(3)	23		Renal(207;0.0915)		Epithelial(149;5.11e-07)|all cancers(144;0.000104)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)		GGGATATATACGGTGCAGTGG	0.517													C|||	17	0.00339457	0.0008	0.0058	5008	,	,		20599	0.0		0.0089	False		,,,				2504	0.0031				p.R325W		Atlas-SNP	.											.	PLCD4	51	.	0			c.C973T						PASS	.	C	TRP/ARG	17,4047		0,17,2015	121.0	116.0	117.0		973	2.9	1.0	2	dbSNP_129	117	95,8281		1,93,4094	yes	missense-near-splice	PLCD4	NM_032726.3	101	1,110,6109	TT,TC,CC		1.1342,0.4183,0.9003	probably-damaging	325/763	219492952	112,12328	2032	4188	6220	SO:0001630	splice_region_variant	84812	exon7			TATATACGGTGCA	AI366170	CCDS46516.1	2q35	2013-01-10			ENSG00000115556	ENSG00000115556	3.1.4.11	"""EF-hand domain containing"""	9062	protein-coding gene	gene with protein product		605939				10702683, 9056492	Standard	NM_032726		Approved		uc021vwx.1	Q9BRC7	OTTHUMG00000154743	ENST00000450993.2:c.974+1C>T	2.37:g.219492952C>T		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	80	45	0.5625	NM_032726	Q53FS8	Missense_Mutation	SNP	ENST00000450993.2	37	CCDS46516.1	7	0.003205128205128205	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	5	0.006596306068601583	C	17.58	3.425437	0.62733	0.004183	0.011342	ENSG00000115556	ENST00000450993;ENST00000251959;ENST00000417849;ENST00000432688	T;T;T	0.64618	-0.11;-0.11;-0.11	4.7	2.91	0.33838	PLC-like phosphodiesterase, TIM beta/alpha-barrel domain (2);Phospholipase C, phosphatidylinositol-specific , X domain (3);	0.112622	0.56097	N	0.000021	T	0.70613	0.3244	M	0.86651	2.83	0.38031	D	0.935157	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	T	0.74717	-0.3571	10	0.87932	D	0	.	4.4431	0.11584	0.2899:0.5284:0.0:0.1817	rs61733653	325;325	B7Z5V4;Q9BRC7	.;PLCD4_HUMAN	W	325	ENSP00000388631:R325W;ENSP00000396942:R325W;ENSP00000396185:R325W	ENSP00000251959:R325W	R	+	1	2	PLCD4	219201196	1.000000	0.71417	1.000000	0.80357	0.900000	0.52787	1.641000	0.37197	0.600000	0.29862	-0.262000	0.10625	CGG	C|0.994;T|0.006	0.006	strong		0.517	PLCD4-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336876.1		Missense_Mutation
OR7A17	26333	hgsc.bcm.edu	37	19	14992031	14992031	+	Missense_Mutation	SNP	A	A	G	rs10405129	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	82	0	0		WXS	Illumina HiSeq	Phase_I	58	28	0.482759	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	
PSME4	23198	hgsc.bcm.edu	37	2	54115904	54115904	+	Silent	SNP	A	A	G	rs805400	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:54115904A>G	ENST00000404125.1	-	38	4397	c.4342T>C	c.(4342-4344)Ttg>Ctg	p.L1448L	PSME4_ENST00000476586.1_5'Flank|PSME4_ENST00000421748.2_Silent_p.L592L	NM_014614.2	NP_055429.2	Q14997	PSME4_HUMAN	proteasome (prosome, macropain) activator subunit 4	1448					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)			GGTGATTCCAACAGCAGTTCA	0.368													A|||	1763	0.352037	0.2201	0.2579	5008	,	,		17217	0.4742		0.3072	False		,,,				2504	0.5174				p.L1448L		Atlas-SNP	.											.	PSME4	247	.	0			c.T4342C						PASS	.	A		949,3457	360.6+/-315.3	91,767,1345	126.0	123.0	124.0		4342	2.0	0.8	2	dbSNP_86	124	2667,5933	428.8+/-356.0	401,1865,2034	no	coding-synonymous	PSME4	NM_014614.2		492,2632,3379	GG,GA,AA		31.0116,21.5388,27.8026		1448/1844	54115904	3616,9390	2203	4300	6503	SO:0001819	synonymous_variant	23198	exon38			ATTCCAACAGCAG	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.4342T>C	2.37:g.54115904A>G		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	199	147	0.738693	NM_014614	Q1XBG4|Q1XBG5|Q1XBG6|Q2M1Z0|Q6IPR2|Q86XF8	Silent	SNP	ENST00000404125.1	37	CCDS33197.2																																																																																			A|0.711;G|0.289	0.289	strong		0.368	PSME4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324163.1	XM_040158	
YEATS2	55689	hgsc.bcm.edu	37	3	183521939	183521939	+	Silent	SNP	C	C	T	rs34612765	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:183521939C>T	ENST00000305135.5	+	27	3942	c.3747C>T	c.(3745-3747)tcC>tcT	p.S1249S	AC131160.1_ENST00000401347.1_RNA|YEATS2-AS1_ENST00000425008.3_RNA	NM_018023.4	NP_060493.3	Q9ULM3	YETS2_HUMAN	YEATS domain containing 2	1249					chromatin organization (GO:0006325)|histone H3 acetylation (GO:0043966)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)	Ada2/Gcn5/Ada3 transcription activator complex (GO:0005671)|mitotic spindle (GO:0072686)	TBP-class protein binding (GO:0017025)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(24)|ovary(3)|prostate(2)|skin(3)	49	all_cancers(143;6.55e-10)|Ovarian(172;0.0303)		all cancers(12;2.38e-42)|Epithelial(37;1.9e-36)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)			ACGGGGACTCCATCGAGGACG	0.617													C|||	121	0.0241613	0.0045	0.0303	5008	,	,		15926	0.0		0.0646	False		,,,				2504	0.0297				p.S1249S		Atlas-SNP	.											.	YEATS2	111	.	0			c.C3747T						PASS	.	C		36,4172		0,36,2068	91.0	92.0	92.0		3747	-2.3	0.6	3	dbSNP_126	92	471,7983		11,449,3767	no	coding-synonymous	YEATS2	NM_018023.4		11,485,5835	TT,TC,CC		5.5713,0.8555,4.0041		1249/1423	183521939	507,12155	2104	4227	6331	SO:0001819	synonymous_variant	55689	exon27			GGACTCCATCGAG	AB033023	CCDS43175.1	3q27.3	2004-08-18			ENSG00000163872	ENSG00000163872			25489	protein-coding gene	gene with protein product		613373				10574462	Standard	NM_018023		Approved	FLJ10201, FLJ12841, FLJ13308, KIAA1197	uc003fly.2	Q9ULM3	OTTHUMG00000156898	ENST00000305135.5:c.3747C>T	3.37:g.183521939C>T		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	89	36	0.404494	NM_018023	A7E2B9|D3DNS9|Q641P6|Q9NW96	Silent	SNP	ENST00000305135.5	37	CCDS43175.1																																																																																			C|0.962;T|0.038	0.038	strong		0.617	YEATS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346507.2	NM_018023	
ADCK4	79934	hgsc.bcm.edu	37	19	41209477	41209477	+	Silent	SNP	C	C	T	rs11538385	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:41209477C>T	ENST00000324464.3	-	9	1069	c.768G>A	c.(766-768)gcG>gcA	p.A256A	ADCK4_ENST00000243583.6_Silent_p.A215A|ADCK4_ENST00000450541.1_Silent_p.A215A	NM_024876.3	NP_079152.3	Q96D53	ADCK4_HUMAN	aarF domain containing kinase 4	256	Protein kinase.					integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|endometrium(3)|large_intestine(3)|lung(6)|stomach(2)|urinary_tract(1)	17			Lung(22;9.49e-05)|LUSC - Lung squamous cell carcinoma(20;0.000219)			TCTTGAGTACCGCCAGCAGGT	0.622													C|||	1149	0.229433	0.084	0.196	5008	,	,		17506	0.2361		0.3032	False		,,,				2504	0.3671				p.A256A		Atlas-SNP	.											ADCK4_ENST00000324464,colon,carcinoma,-1,6	ADCK4	92	6	0			c.G768A						scavenged	.	C	,	543,3863	240.9+/-251.5	35,473,1695	55.0	57.0	56.0		645,768	-10.1	0.5	19	dbSNP_120	56	2474,6126	404.1+/-348.0	353,1768,2179	no	coding-synonymous,coding-synonymous	ADCK4	NM_001142555.2,NM_024876.3	,	388,2241,3874	TT,TC,CC		28.7674,12.3241,23.197	,	215/504,256/545	41209477	3017,9989	2203	4300	6503	SO:0001819	synonymous_variant	79934	exon9			GAGTACCGCCAGC	AK022291	CCDS12562.1, CCDS46081.1	19q13.2	2008-02-05				ENSG00000123815			19041	protein-coding gene	gene with protein product		615567					Standard	NM_024876		Approved	FLJ12229, COQ8	uc002oor.2	Q96D53		ENST00000324464.3:c.768G>A	19.37:g.41209477C>T		Somatic	106	1	0.00943396		WXS	Illumina HiSeq	Phase_I	96	53	0.552083	NM_024876	Q8TAJ1|Q9HA52	Silent	SNP	ENST00000324464.3	37	CCDS12562.1																																																																																			C|0.773;T|0.227	0.227	strong		0.622	ADCK4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462731.1	NM_024876	
SLC13A3	64849	hgsc.bcm.edu	37	20	45242269	45242269	+	Silent	SNP	G	G	C	rs2273024	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:45242269G>C	ENST00000279027.4	-	2	225	c.207C>G	c.(205-207)ctC>ctG	p.L69L	SLC13A3_ENST00000290317.5_Silent_p.L22L|SLC13A3_ENST00000435032.1_5'UTR|SLC13A3_ENST00000495082.1_Silent_p.L22L|SLC13A3_ENST00000417157.2_Silent_p.L22L|SLC13A3_ENST00000396360.1_Silent_p.L22L|SLC13A3_ENST00000372121.1_Silent_p.L69L|SLC13A3_ENST00000339636.3_Silent_p.L69L|SLC13A3_ENST00000413164.2_Silent_p.L69L|SLC13A3_ENST00000472148.1_Silent_p.L22L	NM_001193342.1|NM_022829.5	NP_001180271.1|NP_073740.2	Q8WWT9	S13A3_HUMAN	solute carrier family 13 (sodium-dependent dicarboxylate transporter), member 3	69					transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	high-affinity sodium:dicarboxylate symporter activity (GO:0015362)			breast(2)|endometrium(2)|kidney(2)|large_intestine(9)|lung(12)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	31		Myeloproliferative disorder(115;0.0122)			Succinic acid(DB00139)	TGAAGGGGAAGAGGACGATGG	0.612													G|||	1548	0.309105	0.2088	0.3617	5008	,	,		14974	0.2798		0.3539	False		,,,				2504	0.3916				p.L69L		Atlas-SNP	.											.	SLC13A3	88	.	0			c.C207G						PASS	.	G	,,,,	1028,3378	373.4+/-320.8	116,796,1291	74.0	55.0	61.0		66,207,66,,207	-0.3	1.0	20	dbSNP_100	61	2852,5748	440.6+/-359.6	451,1950,1899	no	coding-synonymous,coding-synonymous,coding-synonymous,intron,coding-synonymous	SLC13A3	NM_001011554.2,NM_001193339.1,NM_001193340.1,NM_001193342.1,NM_022829.5	,,,,	567,2746,3190	CC,CG,GG		33.1628,23.3318,29.8324	,,,,	22/556,69/553,22/521,,69/603	45242269	3880,9126	2203	4300	6503	SO:0001819	synonymous_variant	64849	exon2			GGGGAAGAGGACG	AF154121	CCDS13400.1, CCDS42886.1, CCDS54469.1, CCDS54470.1	20q13.12	2013-05-22			ENSG00000158296	ENSG00000158296		"""Solute carriers"""	14430	protein-coding gene	gene with protein product		606411				10794676, 10992006	Standard	NM_001011554		Approved	NADC3, SDCT2	uc002xsf.2	Q8WWT9	OTTHUMG00000033042	ENST00000279027.4:c.207C>G	20.37:g.45242269G>C		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	106	55	0.518868	NM_022829	B4DIR8|E1P5U4|F6WI18|Q5JYC9|Q5JYD0|Q5JYD1|Q5TCQ2|Q8IVB1|Q8N8K4|Q96MM5|Q9BR25|Q9H1G1|Q9H3W4|Q9NQN5|Q9NS04	Silent	SNP	ENST00000279027.4	37	CCDS13400.1																																																																																			G|0.680;C|0.320	0.320	strong		0.612	SLC13A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080329.2		
RRP12	23223	hgsc.bcm.edu	37	10	99141205	99141205	+	Silent	SNP	A	A	G	rs2275089	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:99141205A>G	ENST00000370992.4	-	12	1467	c.1356T>C	c.(1354-1356)gcT>gcC	p.A452A	RRP12_ENST00000315563.6_Silent_p.A352A|RRP12_ENST00000536831.1_Silent_p.A170A|RRP12_ENST00000414986.1_Silent_p.A391A	NM_015179.3	NP_055994.2	Q5JTH9	RRP12_HUMAN	ribosomal RNA processing 12 homolog (S. cerevisiae)	452						integral component of membrane (GO:0016021)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(5)|large_intestine(2)|lung(13)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	37		Colorectal(252;0.162)		Epithelial(162;2.72e-09)|all cancers(201;1.76e-07)		AGCCAATGTCAGCCATGTGGG	0.607													G|||	2027	0.404752	0.553	0.3415	5008	,	,		18385	0.3125		0.337	False		,,,				2504	0.4141				p.A452A		Atlas-SNP	.											.	RRP12	97	.	0			c.T1356C						PASS	.	G	,	2176,2230	586.8+/-386.5	547,1082,574	70.0	56.0	60.0		1173,1356	-10.2	0.0	10	dbSNP_100	60	2738,5862	677.6+/-403.4	436,1866,1998	no	coding-synonymous,coding-synonymous	RRP12	NM_001145114.1,NM_015179.3	,	983,2948,2572	GG,GA,AA		31.8372,49.3872,37.7826	,	391/1237,452/1298	99141205	4914,8092	2203	4300	6503	SO:0001819	synonymous_variant	23223	exon12			AATGTCAGCCATG		CCDS7457.1, CCDS44467.1, CCDS60605.1	10q24.2	2006-11-06	2006-11-06	2006-11-06	ENSG00000052749	ENSG00000052749			29100	protein-coding gene	gene with protein product			"""KIAA0690"""	KIAA0690		9734811	Standard	NM_015179		Approved		uc001knf.3	Q5JTH9	OTTHUMG00000018855	ENST00000370992.4:c.1356T>C	10.37:g.99141205A>G		Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	161	94	0.583851	NM_015179	B4DK00|E9PCK7|Q5JTH8|Q69YK4|Q96E87|Q9BUH3|Q9Y4C7	Silent	SNP	ENST00000370992.4	37	CCDS7457.1																																																																																			A|0.622;G|0.378	0.378	strong		0.607	RRP12-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049699.4	NM_015179	
CPAMD8	27151	hgsc.bcm.edu	37	19	17100552	17100552	+	Silent	SNP	A	A	G	rs1973093	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	103	0	0		WXS	Illumina HiSeq	Phase_I	69	68	0.985507	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	
C20orf96	140680	hgsc.bcm.edu	37	20	256727	256727	+	Splice_Site	SNP	T	T	A	rs3827147	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:256727T>A	ENST00000360321.2	-	10	1051	c.913A>T	c.(913-915)Att>Ttt	p.I305F	C20orf96_ENST00000382369.5_Splice_Site_p.I270F	NM_080571.1|NM_153269.2	NP_542138.1|NP_695001.2	Q9NUD7	CT096_HUMAN	chromosome 20 open reading frame 96	305			I -> F (in dbSNP:rs3827147). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.3}.							endometrium(3)|large_intestine(2)|lung(4)|prostate(1)|skin(1)|urinary_tract(1)	12		all_cancers(10;0.00959)|Lung NSC(37;0.227)	OV - Ovarian serous cystadenocarcinoma(29;0.149)			TGGTCAATAATCTGAGAGGAA	0.527													A|||	3181	0.635184	0.7383	0.4942	5008	,	,		20974	0.6935		0.6262	False		,,,				2504	0.545				p.I305F		Atlas-SNP	.											.	C20orf96	28	.	0			c.A913T						PASS	.	A	PHE/ILE,PHE/ILE	3202,1204	419.3+/-338.6	1161,880,162	61.0	64.0	63.0		910,913	-1.1	0.2	20	dbSNP_107	63	5310,3290	491.7+/-373.1	1642,2026,632	yes	missense-near-splice,missense-near-splice	C20orf96	NM_080571.1,NM_153269.2	21,21	2803,2906,794	AA,AT,TT		38.2558,27.3264,34.5533	benign,benign	304/363,305/364	256727	8512,4494	2203	4300	6503	SO:0001630	splice_region_variant	140680	exon10			CAATAATCTGAGA	AL034548	CCDS12994.1, CCDS74685.1	20p13	2012-10-30			ENSG00000196476	ENSG00000196476			16227	protein-coding gene	gene with protein product							Standard	NM_153269		Approved	dJ1103G7.2	uc002wde.2	Q9NUD7	OTTHUMG00000031626	ENST00000360321.2:c.913-1A>T	20.37:g.256727T>A		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	97	39	0.402062	NM_153269	A3KPE0|B2RPH9|Q8N840|Q8NAX5	Missense_Mutation	SNP	ENST00000360321.2	37	CCDS12994.1	1434	0.6565934065934066	363	0.7378048780487805	182	0.5027624309392266	401	0.701048951048951	488	0.6437994722955145	A	1.003	-0.690171	0.03303	0.726736	0.617442	ENSG00000196476	ENST00000382369;ENST00000360321	T;T	0.39056	1.1;1.1	4.7	-1.09	0.09904	.	0.930757	0.08962	N	0.868581	T	0.00012	0.0000	N	0.00583	-1.355	0.31184	P	0.7017599999999999	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.32929	-0.9888	9	0.25106	T	0.35	-8.4372	3.58	0.07949	0.2786:0.0:0.3895:0.3319	rs3827147;rs56599014;rs60970895;rs3827147	305;270	Q9NUD7;Q5JYC3	CT096_HUMAN;.	F	270;305	ENSP00000371806:I270F;ENSP00000353470:I305F	ENSP00000353470:I305F	I	-	1	0	C20orf96	204727	0.287000	0.24315	0.223000	0.23860	0.073000	0.16967	0.171000	0.16685	-0.364000	0.08088	-0.569000	0.04157	ATT	T|0.339;A|0.661	0.661	strong		0.527	C20orf96-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077439.2	NM_153269	Missense_Mutation
TRIM21	6737	hgsc.bcm.edu	37	11	4411241	4411241	+	Silent	SNP	C	C	T	rs926101	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:4411241C>T	ENST00000254436.7	-	2	511	c.399G>A	c.(397-399)caG>caA	p.Q133Q	TRIM21_ENST00000543625.1_Silent_p.Q133Q	NM_003141.3	NP_003132.2	P19474	RO52_HUMAN	tripartite motif containing 21	133					cell cycle (GO:0007049)|innate immune response (GO:0045087)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein deubiquitination (GO:0090086)|negative regulation of viral release from host cell (GO:1902187)|negative regulation of viral transcription (GO:0032897)|positive regulation of cell cycle (GO:0045787)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of type I interferon production (GO:0032481)|positive regulation of viral entry into host cell (GO:0046598)|protein autoubiquitination (GO:0051865)|protein destabilization (GO:0031648)|protein monoubiquitination (GO:0006513)|protein polyubiquitination (GO:0000209)|protein trimerization (GO:0070206)|protein ubiquitination (GO:0016567)|regulation of type I interferon production (GO:0032479)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	DNA binding (GO:0003677)|ligase activity (GO:0016874)|RNA binding (GO:0003723)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(8)|ovary(3)	16		Medulloblastoma(188;0.0025)|Breast(177;0.0101)|all_neural(188;0.0227)		Epithelial(150;2.08e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0851)|LUSC - Lung squamous cell carcinoma(625;0.194)		CCTGGTACTCCTGTGCAGCCT	0.557													C|||	1054	0.210463	0.1921	0.1254	5008	,	,		19787	0.2837		0.1233	False		,,,				2504	0.3098				p.Q133Q		Atlas-SNP	.											.	TRIM21	45	.	0			c.G399A						PASS	.	C		646,3316		47,552,1382	43.0	45.0	44.0		399	2.1	1.0	11	dbSNP_86	44	1036,7308		77,882,3213	no	coding-synonymous	TRIM21	NM_003141.3		124,1434,4595	TT,TC,CC		12.4161,16.3049,13.6681		133/476	4411241	1682,10624	1981	4172	6153	SO:0001819	synonymous_variant	6737	exon2			GTACTCCTGTGCA	AF391283	CCDS44525.1	11p15.5-p15.3	2014-02-14	2011-01-25	2004-11-26		ENSG00000132109		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	11312	protein-coding gene	gene with protein product		109092	"""Sjogren syndrome antigen A1 (52kDa, ribonucleoprotein autoantigen SS-A/Ro)"", ""tripartite motif-containing 21"""	SSA1		8094596	Standard	NM_003141		Approved	RNF81, RO52, Ro/SSA	uc001lyy.1	P19474		ENST00000254436.7:c.399G>A	11.37:g.4411241C>T		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	90	13	0.144444	NM_003141	Q5XPV5|Q96RF8	Silent	SNP	ENST00000254436.7	37	CCDS44525.1																																																																																			C|0.811;T|0.189	0.189	strong		0.557	TRIM21-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000385842.1	NM_003141	
ZFP64	55734	hgsc.bcm.edu	37	20	50803573	50803573	+	Silent	SNP	G	G	A	rs34351592	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:50803573G>A	ENST00000216923.4	-	2	433	c.84C>T	c.(82-84)ccC>ccT	p.P28P	ZFP64_ENST00000346617.4_Silent_p.P28P|ZFP64_ENST00000371515.4_Silent_p.P26P|ZFP64_ENST00000361387.2_Silent_p.P28P|ZFP64_ENST00000371518.2_Silent_p.P28P	NM_018197.2|NM_199426.1	NP_060667.2|NP_955458.1	Q9NPA5	ZF64A_HUMAN	ZFP64 zinc finger protein	28					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(5)|large_intestine(8)|lung(11)|ovary(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	33						TATGGATGTCGGGAGTCAGCT	0.512													G|||	846	0.16893	0.3185	0.1643	5008	,	,		19634	0.1736		0.0706	False		,,,				2504	0.0665				p.P28P		Atlas-SNP	.											.	ZFP64	240	.	0			c.C84T						PASS	.	G	,,,	1206,3200	418.5+/-338.3	170,866,1167	66.0	59.0	62.0		84,84,78,84	-10.6	0.1	20	dbSNP_126	62	493,8107	142.0+/-198.3	9,475,3816	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ZFP64	NM_018197.2,NM_022088.4,NM_199426.1,NM_199427.2	,,,	179,1341,4983	AA,AG,GG		5.7326,27.3718,13.0632	,,,	28/682,28/628,26/680,28/646	50803573	1699,11307	2203	4300	6503	SO:0001819	synonymous_variant	55734	exon2			GATGTCGGGAGTC	AK001596	CCDS13439.1, CCDS13440.1, CCDS13441.1, CCDS13442.1	20q13.11-q13.13	2013-01-08	2012-11-27		ENSG00000020256	ENSG00000020256		"""Zinc fingers, C2H2-type"""	15940	protein-coding gene	gene with protein product			"""zinc finger protein 338"", ""zinc finger protein 64 homolog (mouse)"", ""zinc finger protein 64"""	ZNF338		9034307	Standard	NM_199427		Approved	FLJ10734, dJ831D17.1, FLJ12628, dJ548G19.1	uc002xwl.3	Q9NPA5	OTTHUMG00000032756	ENST00000216923.4:c.84C>T	20.37:g.50803573G>A		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	69	31	0.449275	NM_018197	Q9NTS7|Q9NVH4	Silent	SNP	ENST00000216923.4	37	CCDS13440.1																																																																																			G|0.864;A|0.136	0.136	strong		0.512	ZFP64-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000079744.1	NM_018197	
GYS2	2998	hgsc.bcm.edu	37	12	21713402	21713402	+	Missense_Mutation	SNP	T	T	C	rs2306180	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:21713402T>C	ENST00000261195.2	-	8	1341	c.1087A>G	c.(1087-1089)Atg>Gtg	p.M363V		NM_021957.3	NP_068776.2	P54840	GYS2_HUMAN	glycogen synthase 2 (liver)	363			M -> V (in dbSNP:rs2306180). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:8203908, ECO:0000269|PubMed:9691087, ECO:0000269|Ref.3}.		carbohydrate metabolic process (GO:0005975)|generation of precursor metabolites and energy (GO:0006091)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|response to glucose (GO:0009749)|small molecule metabolic process (GO:0044281)	cell cortex (GO:0005938)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|ectoplasm (GO:0043265)	glycogen (starch) synthase activity (GO:0004373)|glycogen synthase activity, transferring glucose-1-phosphate (GO:0061547)|protein homodimerization activity (GO:0042803)			NS(1)|breast(2)|endometrium(5)|kidney(1)|large_intestine(14)|lung(14)|prostate(6)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	48						AAAAACACCATCACTGTGATG	0.368													C|||	3709	0.740615	0.6407	0.7579	5008	,	,		16384	0.7629		0.7704	False		,,,				2504	0.8098				p.M363V	Colon(149;9 1820 3690 10544 50424)	Atlas-SNP	.											.	GYS2	110	.	0			c.A1087G						PASS	.	C	VAL/MET	2980,1426	463.8+/-353.7	1018,944,241	178.0	162.0	167.0		1087	4.0	1.0	12	dbSNP_100	167	6680,1920	341.3+/-324.0	2609,1462,229	yes	missense	GYS2	NM_021957.3	21	3627,2406,470	CC,CT,TT		22.3256,32.365,25.7266	benign	363/704	21713402	9660,3346	2203	4300	6503	SO:0001583	missense	2998	exon8			ACACCATCACTGT		CCDS8690.1	12p12.2-p11.2	2013-02-22			ENSG00000111713	ENSG00000111713	2.4.1.11	"""Glycosyltransferase group 1 domain containing"""	4707	protein-coding gene	gene with protein product		138571					Standard	NM_021957		Approved		uc001rfb.3	P54840	OTTHUMG00000169135	ENST00000261195.2:c.1087A>G	12.37:g.21713402T>C	ENSP00000261195:p.Met363Val	Somatic	177	1	0.00564972		WXS	Illumina HiSeq	Phase_I	116	115	0.991379	NM_021957	A0AVD8	Missense_Mutation	SNP	ENST00000261195.2	37	CCDS8690.1	1644	0.7527472527472527	334	0.6788617886178862	271	0.7486187845303868	441	0.7709790209790209	598	0.7889182058047494	C	1.365	-0.587682	0.03799	0.67635	0.776744	ENSG00000111713	ENST00000261195	T	0.54866	0.55	4.87	3.98	0.46160	.	0.067832	0.64402	N	0.000012	T	0.00012	0.0000	N	0.00006	-3.19	0.51767	P	6.20000000000065E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.45086	-0.9285	9	0.02654	T	1	-9.4095	10.3642	0.44012	0.0:0.7804:0.0:0.2196	rs2306180;rs17849028;rs61057006;rs2306180	363	P54840	GYS2_HUMAN	V	363	ENSP00000261195:M363V	ENSP00000261195:M363V	M	-	1	0	GYS2	21604669	0.998000	0.40836	0.998000	0.56505	0.905000	0.53344	2.620000	0.46410	0.675000	0.31264	-0.213000	0.12676	ATG	C|0.742;N|0.000	0.742	strong		0.368	GYS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402396.1	NM_021957	
USP36	57602	hgsc.bcm.edu	37	17	76814782	76814782	+	Silent	SNP	G	G	A	rs35273233	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:76814782G>A	ENST00000542802.3	-	10	1433	c.990C>T	c.(988-990)cgC>cgT	p.R330R	USP36_ENST00000312010.6_Silent_p.R330R|USP36_ENST00000449938.2_Silent_p.R30R|USP36_ENST00000588467.1_5'UTR			Q9P275	UBP36_HUMAN	ubiquitin specific peptidase 36	330	USP.				protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)	nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|ubiquitin-specific protease activity (GO:0004843)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(12)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	34			BRCA - Breast invasive adenocarcinoma(99;0.000842)|OV - Ovarian serous cystadenocarcinoma(97;0.151)			AGTTGGCAAAGCGCTTGAGGG	0.532													G|||	579	0.115615	0.0855	0.1297	5008	,	,		18769	0.0863		0.1988	False		,,,				2504	0.091				p.R330R		Atlas-SNP	.											.	USP36	243	.	0			c.C990T						PASS	.	G		438,3968	210.8+/-231.2	10,418,1775	187.0	162.0	170.0		990	3.1	1.0	17	dbSNP_126	170	1639,6961	303.7+/-306.6	150,1339,2811	no	coding-synonymous	USP36	NM_025090.3		160,1757,4586	AA,AG,GG		19.0581,9.941,15.9696		330/1124	76814782	2077,10929	2203	4300	6503	SO:0001819	synonymous_variant	57602	exon10			GGCAAAGCGCTTG	AB040886	CCDS32755.1	17q25.3	2008-02-05	2005-08-08			ENSG00000055483		"""Ubiquitin-specific peptidases"""	20062	protein-coding gene	gene with protein product		612543	"""ubiquitin specific protease 36"""			12838346	Standard	NM_025090		Approved	KIAA1453, FLJ12851	uc002jvz.1	Q9P275		ENST00000542802.3:c.990C>T	17.37:g.76814782G>A		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	148	66	0.445946	NM_025090	Q05C98|Q05DD0|Q6IQ38|Q8NDM8|Q9NVC8	Silent	SNP	ENST00000542802.3	37	CCDS32755.1																																																																																			G|0.848;A|0.152	0.152	strong		0.532	USP36-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437472.3	NM_025090	
GSPT1	2935	hgsc.bcm.edu	37	16	11981487	11981487	+	Silent	SNP	G	G	A	rs3752426	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:11981487G>A	ENST00000563468.1	-	5	509	c.483C>T	c.(481-483)ggC>ggT	p.G161G	RP11-166B2.8_ENST00000574364.1_RNA|GSPT1_ENST00000434724.2_Silent_p.G299G|GSPT1_ENST00000420576.2_Silent_p.G161G|GSPT1_ENST00000439887.2_Silent_p.G298G|GSPT1_ENST00000564790.1_5'Flank			P15170	ERF3A_HUMAN	G1 to S phase transition 1	161	G3. {ECO:0000255|PROSITE- ProRule:PRU01059}.|tr-type G. {ECO:0000255|PROSITE- ProRule:PRU01059}.				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						AACTCTTGTGGCCAGGGGCAT	0.423													G|||	601	0.120008	0.0257	0.2075	5008	,	,		16284	0.0109		0.3211	False		,,,				2504	0.091				p.G299G		Atlas-SNP	.											.	GSPT1	71	.	0			c.C897T						PASS	.	G	,,	335,4057	157.0+/-190.0	14,307,1875	148.0	152.0	151.0		894,483,897	2.3	1.0	16	dbSNP_107	151	2912,5684	447.6+/-361.6	475,1962,1861	no	coding-synonymous,coding-synonymous,coding-synonymous	GSPT1	NM_001130006.1,NM_001130007.1,NM_002094.3	,,	489,2269,3736	AA,AG,GG		33.8762,7.6275,25.0	,,	298/637,161/500,299/638	11981487	3247,9741	2196	4298	6494	SO:0001819	synonymous_variant	2935	exon7			CTTGTGGCCAGGG	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.483C>T	16.37:g.11981487G>A		Somatic	209	0	0		WXS	Illumina HiSeq	Phase_I	207	156	0.753623	NM_002094	J3KQG6|Q96GF2	Silent	SNP	ENST00000563468.1	37	CCDS45414.1																																																																																			G|0.830;A|0.170	0.170	strong		0.423	GSPT1-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000421513.1	NM_002094	
C8A	731	hgsc.bcm.edu	37	1	57340727	57340727	+	Missense_Mutation	SNP	C	C	A	rs652785	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:57340727C>A	ENST00000361249.3	+	3	373	c.277C>A	c.(277-279)Caa>Aaa	p.Q93K		NM_000562.2	NP_000553.1	P07357	CO8A_HUMAN	complement component 8, alpha polypeptide	93			Q -> K (in allele C8A*B; dbSNP:rs652785). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:7649542}.		complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|complement activation, classical pathway (GO:0006958)|cytolysis (GO:0019835)|immune response (GO:0006955)|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)|membrane (GO:0016020)|membrane attack complex (GO:0005579)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(25)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	43						TTGTGTAAGGCAAGCACAGTG	0.493													C|||	1721	0.34365	0.1755	0.2507	5008	,	,		20376	0.496		0.3439	False		,,,				2504	0.4796				p.Q93K		Atlas-SNP	.											.	C8A	103	.	0			c.C277A						PASS	.	C	LYS/GLN	935,3471	357.1+/-313.8	91,753,1359	92.0	82.0	85.0		277	3.4	0.5	1	dbSNP_83	85	3239,5361	487.5+/-372.1	641,1957,1702	yes	missense	C8A	NM_000562.2	53	732,2710,3061	AA,AC,CC		37.6628,21.2211,32.0929	benign	93/585	57340727	4174,8832	2203	4300	6503	SO:0001583	missense	731	exon3			GTAAGGCAAGCAC	M16974	CCDS606.1	1p32.2	2014-09-17			ENSG00000157131	ENSG00000157131		"""Complement system"""	1352	protein-coding gene	gene with protein product		120950					Standard	NM_000562		Approved		uc001cyo.2	P07357	OTTHUMG00000008306	ENST00000361249.3:c.277C>A	1.37:g.57340727C>A	ENSP00000354458:p.Gln93Lys	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	69	30	0.434783	NM_000562	A2RUI4|A2RUI5|Q13668|Q9H130	Missense_Mutation	SNP	ENST00000361249.3	37	CCDS606.1	716	0.32783882783882784	95	0.19308943089430894	103	0.2845303867403315	251	0.4388111888111888	267	0.35224274406332456	C	1.011	-0.687821	0.03328	0.212211	0.376628	ENSG00000157131	ENST00000361249	T	0.75154	-0.91	5.42	3.42	0.39159	.	0.780783	0.12304	N	0.480872	T	0.00012	0.0000	L	0.54323	1.7	0.80722	P	0.0	B	0.20780	0.048	B	0.15052	0.012	T	0.32322	-0.9911	9	0.25106	T	0.35	-1.4146	10.1215	0.42623	0.3548:0.5267:0.1185:0.0	rs652785;rs3738562;rs17372660;rs52793830;rs61616553;rs652785	93	P07357	CO8A_HUMAN	K	93	ENSP00000354458:Q93K	ENSP00000354458:Q93K	Q	+	1	0	C8A	57113315	0.000000	0.05858	0.490000	0.27465	0.013000	0.08279	0.109000	0.15417	1.478000	0.48253	0.650000	0.86243	CAA	C|0.671;N|0.000	.	strong		0.493	C8A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022890.1	NM_000562	
PDE4DIP	9659	hgsc.bcm.edu	37	1	144854645	144854645	+	Silent	SNP	T	T	C	rs143461294	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:144854645T>C	ENST00000369354.3	-	42	7014	c.6825A>G	c.(6823-6825)acA>acG	p.T2275T	PDE4DIP_ENST00000369359.4_Silent_p.T2411T|PDE4DIP_ENST00000313382.9_Silent_p.T2169T|PDE4DIP_ENST00000369356.4_Silent_p.T2275T|PDE4DIP_ENST00000530740.1_Silent_p.T2360T|PDE4DIP_ENST00000524974.1_5'UTR			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	2275					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)		GTTCCCTTTCTGTTGATTCTC	0.478			T	PDGFRB	MPD																																p.T2275T		Atlas-SNP	.		Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	.	PDE4DIP	817	.	0			c.A6825G						PASS	.	T	,,	3,4403		0,3,2200	231.0	201.0	211.0		6507,6825,6825	2.0	0.0	1	dbSNP_134	211	9,8591		0,9,4291	no	coding-synonymous,coding-synonymous,coding-synonymous	PDE4DIP	NM_001198832.1,NM_001198834.2,NM_014644.4	,,	0,12,6491	CC,CT,TT		0.1047,0.0681,0.0923	,,	2169/2241,2275/2363,2275/2347	144854645	12,12994	2203	4300	6503	SO:0001819	synonymous_variant	9659	exon42			CCTTTCTGTTGAT	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.6825A>G	1.37:g.144854645T>C		Somatic	206	0	0		WXS	Illumina HiSeq	Phase_I	210	31	0.147619	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																																																																																			T|0.999;C|0.001	0.001	strong		0.478	PDE4DIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000038858.2	NM_022359	
DLST	1743	hgsc.bcm.edu	37	14	75367807	75367807	+	Silent	SNP	C	C	T	rs20578	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:75367807C>T	ENST00000334220.4	+	14	1159	c.1098C>T	c.(1096-1098)ggC>ggT	p.G366G	DLST_ENST00000334212.6_Silent_p.G280G	NM_001933.4	NP_001924.2	P36957	ODO2_HUMAN	dihydrolipoamide S-succinyltransferase (E2 component of 2-oxo-glutarate complex)	366					cellular metabolic process (GO:0044237)|cellular nitrogen compound metabolic process (GO:0034641)|generation of precursor metabolites and energy (GO:0006091)|L-lysine catabolic process to acetyl-CoA via saccharopine (GO:0033512)|lysine catabolic process (GO:0006554)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrial matrix (GO:0005759)|nucleus (GO:0005634)|oxoglutarate dehydrogenase complex (GO:0045252)	dihydrolipoyllysine-residue succinyltransferase activity (GO:0004149)			breast(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(4)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18				BRCA - Breast invasive adenocarcinoma(234;0.00698)		ATATGGATGGCGGTACCTTCA	0.458													C|||	1423	0.284145	0.3404	0.2349	5008	,	,		20960	0.2202		0.2962	False		,,,				2504	0.2965				p.G366G		Atlas-SNP	.											.	DLST	42	.	0			c.C1098T						PASS	.	C		1500,2906	479.2+/-358.4	262,976,965	151.0	145.0	147.0		1098	-6.7	0.8	14	dbSNP_67	147	2653,5947	428.1+/-355.8	420,1813,2067	no	coding-synonymous	DLST	NM_001933.4		682,2789,3032	TT,TC,CC		30.8488,34.0445,31.9314		366/454	75367807	4153,8853	2203	4300	6503	SO:0001819	synonymous_variant	1743	exon14			GGATGGCGGTACC		CCDS9833.1	14q23.1	2008-08-11			ENSG00000119689	ENSG00000119689	2.3.1.61		2911	protein-coding gene	gene with protein product		126063		DLTS		8009371	Standard	NM_001933		Approved		uc001xqv.2	P36957		ENST00000334220.4:c.1098C>T	14.37:g.75367807C>T		Somatic	239	0	0		WXS	Illumina HiSeq	Phase_I	172	85	0.494186	NM_001933	B7Z5W8|E7ESY5|Q7LDY7|Q9BQ32	Silent	SNP	ENST00000334220.4	37	CCDS9833.1																																																																																			C|0.690;T|0.310	0.310	strong		0.458	DLST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413637.1		
TPX2	22974	hgsc.bcm.edu	37	20	30382315	30382315	+	Silent	SNP	A	A	G	rs3203770	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	79	0	0		WXS	Illumina HiSeq	Phase_I	73	37	0.506849	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		
STXBP5L	9515	hgsc.bcm.edu	37	3	120976051	120976051	+	Missense_Mutation	SNP	C	C	G	rs17249244	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:120976051C>G	ENST00000273666.6	+	17	1974	c.1703C>G	c.(1702-1704)aCc>aGc	p.T568S	STXBP5L_ENST00000472879.1_Missense_Mutation_p.T568S|STXBP5L_ENST00000471454.1_Missense_Mutation_p.T568S|STXBP5L_ENST00000492541.1_Missense_Mutation_p.T568S|STXBP5L_ENST00000497029.1_Missense_Mutation_p.T568S	NM_014980.2	NP_055795.1	Q9Y2K9	STB5L_HUMAN	syntaxin binding protein 5-like	568			T -> S (in dbSNP:rs17249244).		exocytosis (GO:0006887)|glucose homeostasis (GO:0042593)|negative regulation of insulin secretion (GO:0046676)|positive regulation of protein secretion (GO:0050714)|protein transport (GO:0015031)|regulation of exocytosis (GO:0017157)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|breast(3)|endometrium(3)|kidney(3)|large_intestine(12)|lung(28)|ovary(7)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	68				GBM - Glioblastoma multiforme(114;0.0694)		GATATTATTACCCCTGAACCA	0.368													C|||	450	0.0898562	0.0908	0.1023	5008	,	,		14776	0.004		0.2048	False		,,,				2504	0.0501				p.T568S		Atlas-SNP	.											.	STXBP5L	159	.	0			c.C1703G						PASS	.	C	SER/THR	381,3289		17,347,1471	121.0	117.0	118.0		1703	5.5	1.0	3	dbSNP_123	118	1515,6641		158,1199,2721	yes	missense	STXBP5L	NM_014980.2	58	175,1546,4192	GG,GC,CC		18.5753,10.3815,16.0325	benign	568/1187	120976051	1896,9930	1835	4078	5913	SO:0001583	missense	9515	exon17			TTATTACCCCTGA	AB023223	CCDS43137.1	3q13.33-q21.1	2013-01-10			ENSG00000145087	ENSG00000145087		"""WD repeat domain containing"""	30757	protein-coding gene	gene with protein product		609381				10231032, 14767561	Standard	NM_014980		Approved	KIAA1006, LLGL4	uc003eec.4	Q9Y2K9	OTTHUMG00000159426	ENST00000273666.6:c.1703C>G	3.37:g.120976051C>G	ENSP00000273666:p.Thr568Ser	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	62	32	0.516129	NM_014980	Q4G1B4|Q6PIC3	Missense_Mutation	SNP	ENST00000273666.6	37	CCDS43137.1	228	0.1043956043956044	35	0.07113821138211382	43	0.11878453038674033	1	0.0017482517482517483	149	0.19656992084432717	C	7.387	0.629960	0.14257	0.103815	0.185753	ENSG00000145087	ENST00000273666;ENST00000471454;ENST00000472879;ENST00000497029;ENST00000492541;ENST00000471262	T;T;T;T;T;T	0.29655	1.56;1.56;1.56;1.56;1.56;1.56	5.49	5.49	0.81192	WD40 repeat-like-containing domain (1);	0.110117	0.64402	D	0.000007	T	0.00012	0.0000	N	0.02266	-0.62	0.23501	P	0.99754522	B;B	0.15473	0.013;0.013	B;B	0.11329	0.006;0.006	T	0.11542	-1.0583	9	0.02654	T	1	-2.3276	16.0333	0.80597	0.0:0.8657:0.1343:0.0	rs17249244;rs52832788;rs17249244	568;568	E9PFI2;Q9Y2K9	.;STB5L_HUMAN	S	568	ENSP00000273666:T568S;ENSP00000420019:T568S;ENSP00000419627:T568S;ENSP00000420287:T568S;ENSP00000420666:T568S;ENSP00000420167:T568S	ENSP00000273666:T568S	T	+	2	0	STXBP5L	122458741	1.000000	0.71417	0.996000	0.52242	0.996000	0.88848	4.931000	0.63469	2.732000	0.93576	0.585000	0.79938	ACC	C|0.880;G|0.120	0.120	strong		0.368	STXBP5L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355256.3		
CRACR2A	84766	hgsc.bcm.edu	37	12	3788145	3788145	+	Missense_Mutation	SNP	C	C	T	rs242018	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	107	0	0		WXS	Illumina HiSeq	Phase_I	102	51	0.5	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		
ZFAT	57623	hgsc.bcm.edu	37	8	135614972	135614972	+	Silent	SNP	A	A	G	rs3739422	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:135614972A>G	ENST00000377838.3	-	6	1164	c.990T>C	c.(988-990)taT>taC	p.Y330Y	ZFAT_ENST00000520214.1_Silent_p.Y318Y|ZFAT_ENST00000523399.1_Silent_p.Y268Y|ZFAT_ENST00000520356.1_Silent_p.Y318Y|ZFAT_ENST00000520727.1_Silent_p.Y318Y|ZFAT-AS1_ENST00000505776.1_RNA|ZFAT_ENST00000429442.2_Silent_p.Y318Y	NM_001174157.1|NM_020863.3	NP_001167628.1|NP_065914.2	Q9P243	ZFAT_HUMAN	zinc finger and AT hook domain containing	330					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)			TGAACGAGCAATAGTCGCAGG	0.557													A|||	1936	0.386581	0.2859	0.3948	5008	,	,		18510	0.5476		0.2813	False		,,,				2504	0.4591				p.Y330Y		Atlas-SNP	.											.	ZFAT	265	.	0			c.T990C						PASS	.	A	,,,,	1043,3155		123,797,1179	61.0	68.0	66.0		954,954,804,954,990	3.2	0.3	8	dbSNP_107	66	2308,6140		306,1696,2222	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	,,,,	429,2493,3401	GG,GA,AA		27.3201,24.8452,26.4985	,,,,	318/1232,318/1232,268/1182,318/1146,330/1244	135614972	3351,9295	2099	4224	6323	SO:0001819	synonymous_variant	57623	exon6			CGAGCAATAGTCG	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.990T>C	8.37:g.135614972A>G		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	108	105	0.972222	NM_020863	B7ZL15|E9PER3|Q3MIM5|Q6PJ01|Q75PJ6|Q75PJ7|Q75PJ9|Q86X64	Silent	SNP	ENST00000377838.3	37	CCDS47924.1																																																																																			A|0.643;G|0.357	0.357	strong		0.557	ZFAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378272.1	NM_001029939	
LONRF3	79836	hgsc.bcm.edu	37	X	118148229	118148229	+	Silent	SNP	A	A	G	rs2278954	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:118148229A>G	ENST00000371628.3	+	10	2065	c.2034A>G	c.(2032-2034)gcA>gcG	p.A678A	LONRF3_ENST00000304778.7_Silent_p.A637A|LONRF3_ENST00000472173.1_3'UTR|LONRF3_ENST00000422289.2_Silent_p.A422A	NM_001031855.1	NP_001027026.1	Q496Y0	LONF3_HUMAN	LON peptidase N-terminal domain and ring finger 3	678	Lon.						ATP-dependent peptidase activity (GO:0004176)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(4)|lung(17)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	36						ATCAGCAAGCATCATTGTGGT	0.433													G|||	1746	0.462517	0.6021	0.2421	3775	,	,		17899	0.1359		0.2843	False		,,,				2504	0.3671				p.A678A		Atlas-SNP	.											.	LONRF3	138	.	0			c.A2034G						PASS	.	G	,	2781,1054		871,616,423,145,148	306.0	249.0	268.0		2034,1911	-6.8	0.0	X	dbSNP_100	268	2550,4178		359,1101,731,968,1141	no	coding-synonymous,coding-synonymous	LONRF3	NM_001031855.1,NM_024778.4	,	1230,1717,1154,1113,1289	GG,GA,G,AA,A		37.9013,27.4837,49.5314	,	678/760,637/719	118148229	5331,5232	2203	4300	6503	SO:0001819	synonymous_variant	79836	exon10			GCAAGCATCATTG	AK026265	CCDS14575.1, CCDS35374.1, CCDS76014.1	Xq24	2013-01-09	2005-08-19	2005-08-19	ENSG00000175556	ENSG00000175556		"""RING-type (C3HC4) zinc fingers"""	21152	protein-coding gene	gene with protein product			"""ring finger protein 127"""	RNF127			Standard	XM_005262476		Approved	FLJ22612	uc004eqw.3	Q496Y0	OTTHUMG00000022262	ENST00000371628.3:c.2034A>G	X.37:g.118148229A>G		Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	112	112	1	NM_001031855	Q5JPN6|Q8NB00|Q9H647	Silent	SNP	ENST00000371628.3	37	CCDS35374.1	673	0.405666063893912	200	0.6329113924050633	62	0.2108843537414966	52	0.09961685823754789	141	0.2288961038961039	G	7.787	0.710819	0.15239	0.725163	0.379013	ENSG00000175556	ENST00000439603	.	.	.	5.7	-6.8	0.01709	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.999999580202	.	.	.	.	.	.	T	0.28744	-1.0034	3	.	.	.	-63.1	2.3441	0.04267	0.5401:0.1472:0.1646:0.148	rs2278954;rs17326906;rs56528694;rs60466076;rs2278954	.	.	.	V	444	.	.	I	+	1	0	LONRF3	118032257	0.000000	0.05858	0.006000	0.13384	0.809000	0.45718	-3.583000	0.00423	-2.585000	0.00460	-0.871000	0.02989	ATC	0|0.014;G|0.475	0.475	strong		0.433	LONRF3-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355124.2	NM_024778	
KRTAP3-2	83897	hgsc.bcm.edu	37	17	39156027	39156027	+	Missense_Mutation	SNP	G	G	A	rs3829598	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	131	0	0		WXS	Illumina HiSeq	Phase_I	118	55	0.466102	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		
LRRC56	115399	hgsc.bcm.edu	37	11	551235	551235	+	Silent	SNP	G	G	A	rs35537971	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:551235G>A	ENST00000270115.7	+	9	1229	c.729G>A	c.(727-729)ccG>ccA	p.P243P		NM_198075.3	NP_932341.1	Q8IYG6	LRC56_HUMAN	leucine rich repeat containing 56	243	LRRCT.									kidney(1)|lung(4)|skin(1)	6		all_cancers(49;2.16e-06)|all_epithelial(84;0.000256)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;7.63e-28)|Epithelial(43;7.29e-27)|OV - Ovarian serous cystadenocarcinoma(40;7.15e-21)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0375)|LUSC - Lung squamous cell carcinoma(625;0.0703)		CGGCCCCCCCGCGGCTGAGCC	0.687													G|||	758	0.151358	0.2277	0.2435	5008	,	,		10391	0.0188		0.1879	False		,,,				2504	0.0818				p.P243P		Atlas-SNP	.											.	LRRC56	23	.	0			c.G729A						PASS	.	G		817,3135		88,641,1247	21.0	17.0	19.0		729	3.6	0.0	11	dbSNP_126	19	1473,6373		141,1191,2591	no	coding-synonymous	LRRC56	NM_198075.3		229,1832,3838	AA,AG,GG		18.7739,20.6731,19.4101		243/543	551235	2290,9508	1976	3923	5899	SO:0001819	synonymous_variant	115399	exon9			CCCCCCGCGGCTG		CCDS7700.1	11p15.5	2005-10-18			ENSG00000161328	ENSG00000161328			25430	protein-coding gene	gene with protein product						12477932	Standard	NM_198075		Approved	FLJ00101, DKFZp761L1518	uc010qvz.2	Q8IYG6	OTTHUMG00000132003	ENST00000270115.7:c.729G>A	11.37:g.551235G>A		Somatic	205	0	0		WXS	Illumina HiSeq	Phase_I	229	174	0.759825	NM_198075	Q8N3Q4	Silent	SNP	ENST00000270115.7	37	CCDS7700.1																																																																																			G|0.835;A|0.165	0.165	strong		0.687	LRRC56-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254969.1	NM_198075	
KCNIP4	80333	hgsc.bcm.edu	37	4	20852244	20852244	+	Silent	SNP	A	A	G	rs3765122	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:20852244A>G	ENST00000382152.2	-	3	377	c.210T>C	c.(208-210)ccT>ccC	p.P70P	KCNIP4_ENST00000447367.2_Silent_p.P36P|KCNIP4_ENST00000359001.5_Silent_p.P8P|KCNIP4_ENST00000509207.1_Silent_p.P8P|KCNIP4_ENST00000382149.4_5'UTR|KCNIP4_ENST00000382148.3_Silent_p.P45P|KCNIP4_ENST00000382150.4_Silent_p.P49P	NM_025221.5	NP_079497.2	Q6PIL6	KCIP4_HUMAN	Kv channel interacting protein 4	70	EF-hand 1; degenerate. {ECO:0000255|PROSITE-ProRule:PRU00448}.					dendrite (GO:0030425)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|potassium channel activity (GO:0005267)|voltage-gated ion channel activity (GO:0005244)			NS(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)	13		Breast(46;0.134)				CAAGGGCTTCAGGCCGATGCC	0.468													G|||	1749	0.349241	0.121	0.4755	5008	,	,		18316	0.4335		0.4274	False		,,,				2504	0.4008				p.P50P		Atlas-SNP	.											.	KCNIP4	85	.	0			c.T150C						PASS	.	G	,,,,,	749,3657	756.2+/-412.6	69,611,1523	70.0	70.0	70.0		135,24,210,108,24,147	-10.8	0.7	4	dbSNP_107	70	3482,5118	634.8+/-398.9	703,2076,1521	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	KCNIP4	NM_001035003.1,NM_001035004.1,NM_025221.5,NM_147181.3,NM_147182.3,NM_147183.3	,,,,,	772,2687,3044	GG,GA,AA		40.4884,16.9995,32.5311	,,,,,	45/226,8/189,70/251,36/217,8/189,49/230	20852244	4231,8775	2203	4300	6503	SO:0001819	synonymous_variant	80333	exon2			GGCTTCAGGCCGA	AF453244	CCDS3428.1, CCDS43215.1, CCDS43216.1, CCDS43217.1, CCDS47035.1	4p15.32	2013-01-10			ENSG00000185774	ENSG00000185774		"""EF-hand domain containing"""	30083	protein-coding gene	gene with protein product		608182				11805342, 11847232	Standard	XM_005248190		Approved	CALP, KCHIP4, MGC44947	uc003gqh.1	Q6PIL6	OTTHUMG00000128557	ENST00000382152.2:c.210T>C	4.37:g.20852244A>G		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	47	21	0.446809	NM_025221	Q3YAB8|Q3YAB9|Q3YAC0|Q3YAC1|Q3YAC2|Q4W5G8|Q8NEU0|Q9BWT2|Q9H294|Q9H2A4	Silent	SNP	ENST00000382152.2	37	CCDS43216.1																																																																																			A|0.672;G|0.328	0.328	strong		0.468	KCNIP4-004	KNOWN	non_canonical_conserved|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000360407.3	NM_025221	
UGT2B7	7364	hgsc.bcm.edu	37	4	69972949	69972949	+	Silent	SNP	C	C	G	rs4292394	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:69972949C>G	ENST00000508661.1	+	4	1086	c.1059C>G	c.(1057-1059)ctC>ctG	p.L353L	UGT2B7_ENST00000305231.7_Silent_p.L353L|UGT2B7_ENST00000509763.1_3'UTR			P16662	UD2B7_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide B7	353					androgen metabolic process (GO:0008209)|cellular glucuronidation (GO:0052695)|lipid metabolic process (GO:0006629)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	glucuronosyltransferase activity (GO:0015020)			autonomic_ganglia(1)|endometrium(3)|kidney(4)|large_intestine(6)|lung(16)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	38					Atorvastatin(DB01076)|Carbamazepine(DB00564)|Chenodeoxycholic acid(DB06777)|Codeine(DB00318)|Dabigatran etexilate(DB06695)|Dapagliflozin(DB06292)|Diclofenac(DB00586)|Epirubicin(DB00445)|Etodolac(DB00749)|Ezetimibe(DB00973)|Flunitrazepam(DB01544)|Flurbiprofen(DB00712)|Fluvastatin(DB01095)|Ibuprofen(DB01050)|Indomethacin(DB00328)|Losartan(DB00678)|Lovastatin(DB00227)|Mitiglinide(DB01252)|Morphine(DB00295)|Mycophenolate mofetil(DB00688)|Mycophenolic acid(DB01024)|Naproxen(DB00788)|Oxazepam(DB00842)|Pitavastatin(DB08860)|Silodosin(DB06207)|Simvastatin(DB00641)|Suprofen(DB00870)|Tapentadol(DB06204)|Valproic Acid(DB00313)|Zidovudine(DB00495)	ATACTCGGCTCTACAAGTGGA	0.358													c|||	3360	0.670927	0.8298	0.6859	5008	,	,		16163	0.7242		0.5149	False		,,,				2504	0.5511				p.L353L		Atlas-SNP	.											.	UGT2B7	79	.	0			c.C1059G						PASS	.	C		3321,1085	717.4+/-408.7	1259,803,141	132.0	131.0	131.0		1059	-5.9	0.0	4	dbSNP_111	131	4124,4476	561.8+/-387.8	987,2150,1163	no	coding-synonymous	UGT2B7	NM_001074.2		2246,2953,1304	GG,GC,CC		47.9535,24.6255,42.7572		353/530	69972949	7445,5561	2203	4300	6503	SO:0001819	synonymous_variant	7364	exon4			TCGGCTCTACAAG	BC030974	CCDS3526.1	4q13	2008-02-05	2005-07-20		ENSG00000171234	ENSG00000171234		"""UDP glucuronosyltransferases"""	12554	protein-coding gene	gene with protein product		600068	"""UDP glycosyltransferase 2 family, polypeptide B7"""			2159463, 7835904	Standard	NM_001074		Approved	UGT2B9	uc003heg.4	P16662	OTTHUMG00000129404	ENST00000508661.1:c.1059C>G	4.37:g.69972949C>G		Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	106	44	0.415094	NM_001074	B2R810|Q6GTW0	Silent	SNP	ENST00000508661.1	37																																																																																				C|0.420;G|0.580	0.580	strong		0.358	UGT2B7-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000362103.1	NM_001074	
OR2T3	343173	hgsc.bcm.edu	37	1	248637381	248637381	+	Missense_Mutation	SNP	G	G	A	rs139789199	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:248637381G>A	ENST00000359594.2	+	1	755	c.730G>A	c.(730-732)Gcc>Acc	p.A244T		NM_001005495.1	NP_001005495.1	Q8NH03	OR2T3_HUMAN	olfactory receptor, family 2, subfamily T, member 3	244						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|endometrium(5)|lung(19)|ovary(1)|prostate(1)|skin(3)	31	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			GAAGGCCTTGGCCACCTGCTC	0.562																																					p.A244T		Atlas-SNP	.											OR2T3,NS,carcinoma,0,3	OR2T3	79	3	0			c.G730A						scavenged	.	G	THR/ALA	108,4298	63.5+/-100.7	4,100,2099	200.0	168.0	179.0		730	-4.7	0.0	1	dbSNP_134	179	4,8596	3.0+/-9.4	0,4,4296	no	missense	OR2T3	NM_001005495.1	58	4,104,6395	AA,AG,GG		0.0465,2.4512,0.8611	benign	244/319	248637381	112,12894	2203	4300	6503	SO:0001583	missense	343173	exon1			GCCTTGGCCACCT		CCDS31117.1	1q44	2012-08-09			ENSG00000196539	ENSG00000196539		"""GPCR / Class A : Olfactory receptors"""	14727	protein-coding gene	gene with protein product							Standard	NM_001005495		Approved		uc001iel.1	Q8NH03	OTTHUMG00000040452	ENST00000359594.2:c.730G>A	1.37:g.248637381G>A	ENSP00000352604:p.Ala244Thr	Somatic	482	0	0		WXS	Illumina HiSeq	Phase_I	491	51	0.10387	NM_001005495	B2RNJ1	Missense_Mutation	SNP	ENST00000359594.2	37	CCDS31117.1	56	0.02564102564102564	16	0.032520325203252036	7	0.019337016574585635	21	0.03671328671328671	12	0.0158311345646438	g	8.134	0.783767	0.16189	0.024512	4.65E-4	ENSG00000196539	ENST00000359594	T	0.00063	8.78	2.37	-4.74	0.03249	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00039	0.0001	L	0.32530	0.975	0.09310	N	1	B	0.29531	0.247	B	0.37888	0.26	T	0.02167	-1.1202	9	0.27082	T	0.32	.	3.8534	0.08965	0.2803:0.0:0.43:0.2897	.	244	Q8NH03	OR2T3_HUMAN	T	244	ENSP00000352604:A244T	ENSP00000352604:A244T	A	+	1	0	OR2T3	246704004	0.000000	0.05858	0.001000	0.08648	0.247000	0.25773	-1.692000	0.01918	-1.238000	0.02535	0.186000	0.17326	GCC	G|0.987;A|0.013	0.013	strong		0.562	OR2T3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097348.1	NM_001005495	
TPH2	121278	hgsc.bcm.edu	37	12	72372862	72372862	+	Silent	SNP	A	A	G	rs7305115	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	58	0	0		WXS	Illumina HiSeq	Phase_I	57	57	1	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	
TRPC4AP	26133	hgsc.bcm.edu	37	20	33657126	33657126	+	Silent	SNP	G	G	A	rs1998233	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:33657126G>A	ENST00000252015.2	-	3	476	c.387C>T	c.(385-387)taC>taT	p.Y129Y	TRPC4AP_ENST00000432634.2_Intron|TRPC4AP_ENST00000451813.2_Silent_p.Y129Y			Q8TEL6	TP4AP_HUMAN	transient receptor potential cation channel, subfamily C, member 4 associated protein	129	Interaction with TNFRSF1A. {ECO:0000250}.				calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|protein ubiquitination (GO:0016567)|transmembrane transport (GO:0055085)|ubiquitin-dependent protein catabolic process (GO:0006511)	Cul4A-RING E3 ubiquitin ligase complex (GO:0031464)|plasma membrane (GO:0005886)	phosphatase binding (GO:0019902)			breast(3)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(13)|skin(1)|stomach(1)|urinary_tract(1)	32			BRCA - Breast invasive adenocarcinoma(18;0.00936)			AGTCAAAAATGTAAGTATTTG	0.348													A|||	3943	0.78734	0.8381	0.8646	5008	,	,		17478	0.7847		0.7684	False		,,,				2504	0.6861				p.Y129Y		Atlas-SNP	.											.	TRPC4AP	64	.	0			c.C387T						PASS	.	A	,	3579,827	327.2+/-299.9	1454,671,78	129.0	133.0	131.0		387,387	2.0	1.0	20	dbSNP_92	131	6244,2356	393.4+/-344.3	2268,1708,324	no	coding-synonymous,coding-synonymous	TRPC4AP	NM_015638.2,NM_199368.1	,	3722,2379,402	AA,AG,GG		27.3953,18.7699,24.4733	,	129/798,129/790	33657126	9823,3183	2203	4300	6503	SO:0001819	synonymous_variant	26133	exon3			AAAAATGTAAGTA	AF055022	CCDS13246.1, CCDS46591.1	20q11.23	2014-06-13	2003-10-06	2003-10-08	ENSG00000100991	ENSG00000100991			16181	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 158"""	608430	"""chromosome 20 open reading frame 188"""	C20orf188			Standard	NM_015638		Approved	DKFZP727M231, DKFZp586C1223, dJ756N5.2, TRRP4AP, PPP1R158	uc002xbk.3	Q8TEL6	OTTHUMG00000032319	ENST00000252015.2:c.387C>T	20.37:g.33657126G>A		Somatic	316	1	0.00316456		WXS	Illumina HiSeq	Phase_I	227	226	0.995595	NM_199368	E1P5Q0|E1P5Q1|Q96H82|Q9BVB8|Q9H429|Q9UFS6	Silent	SNP	ENST00000252015.2	37	CCDS13246.1																																																																																			G|0.223;A|0.777	0.777	strong		0.348	TRPC4AP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078832.2	NM_015638	
MYC	4609	hgsc.bcm.edu	37	8	128750540	128750540	+	Missense_Mutation	SNP	A	A	G	rs4645959	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:128750540A>G	ENST00000259523.6	+	2	1237	c.32A>G	c.(31-33)aAc>aGc	p.N11S	MYC_ENST00000524013.1_Missense_Mutation_p.N25S|MYC_ENST00000377970.2_Missense_Mutation_p.N26S			P01106	MYC_HUMAN	v-myc avian myelocytomatosis viral oncogene homolog	11			N -> S (in dbSNP:rs4645959). {ECO:0000269|Ref.11}.		branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|cell cycle arrest (GO:0007050)|cellular iron ion homeostasis (GO:0006879)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to UV (GO:0034644)|chromatin remodeling (GO:0006338)|chromosome organization (GO:0051276)|energy reserve metabolic process (GO:0006112)|fibroblast apoptotic process (GO:0044346)|gene expression (GO:0010467)|MAPK cascade (GO:0000165)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell division (GO:0051782)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of monocyte differentiation (GO:0045656)|negative regulation of stress-activated MAPK cascade (GO:0032873)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|oxygen transport (GO:0015671)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of metanephric cap mesenchymal cell proliferation (GO:0090096)|positive regulation of response to DNA damage stimulus (GO:2001022)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of gene expression (GO:0010468)|regulation of telomere maintenance (GO:0032204)|response to drug (GO:0042493)|response to gamma radiation (GO:0010332)|response to growth factor (GO:0070848)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|E-box binding (GO:0070888)|protein complex binding (GO:0032403)|repressing transcription factor binding (GO:0070491)|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)|transcription factor binding (GO:0008134)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|lung(7)|ovary(1)|pancreas(1)|skin(1)|urinary_tract(1)	16	all_cancers(1;6.19e-134)|all_epithelial(1;1.75e-119)|all_lung(1;5.66e-51)|Breast(1;1.08e-22)|all_neural(1;4.45e-21)|Medulloblastoma(1;1.88e-20)|Colorectal(1;1.92e-09)|Lung SC(1;4.52e-07)|Ovarian(5;0.000122)|Esophageal squamous(12;0.000995)|Renal(1;0.0921)|Hepatocellular(40;0.108)|Myeloproliferative disorder(2;0.135)|Melanoma(291;0.185)	Myeloproliferative disorder(644;0.0255)|Ovarian(118;0.0654)|Breast(495;0.212)|Acute lymphoblastic leukemia(644;0.22)	Epithelial(1;1.63e-94)|all cancers(1;5.82e-87)|OV - Ovarian serous cystadenocarcinoma(1;2.12e-71)|BRCA - Breast invasive adenocarcinoma(1;4.3e-14)|Lung(2;0.000381)|Colorectal(2;0.0102)|LUAD - Lung adenocarcinoma(14;0.0172)|READ - Rectum adenocarcinoma(2;0.0723)|LUSC - Lung squamous cell carcinoma(258;0.151)	KIRC - Kidney renal clear cell carcinoma(542;0.248)	Nadroparin(DB08813)	ACCAACAGGAACTATGACCTC	0.602		3	"""A, T"""	"""IGK@, BCL5, BCL7A , BTG1, TRA@, IGH@"""	"""Burkitt lymphoma,  amplified in other cancers, B-CLL"""						OREG0018982	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	A|||	76	0.0151757	0.0045	0.0288	5008	,	,		16470	0.0		0.0467	False		,,,				2504	0.0031				p.N26S		Atlas-SNP	.		Dom	yes		8	8q24.12-q24.13	4609	v-myc myelocytomatosis viral oncogene homolog (avian)		"""L, E"""	.	MYC	168	.	0			c.A77G	GRCh37	CM057723	MYC	M	rs4645959	PASS	.	A	SER/ASN	35,4371	40.8+/-73.8	0,35,2168	72.0	72.0	72.0		77	3.9	1.0	8	dbSNP_111	72	341,8259	117.2+/-176.8	8,325,3967	yes	missense	MYC	NM_002467.4	46	8,360,6135	GG,GA,AA		3.9651,0.7944,2.891	possibly-damaging	26/455	128750540	376,12630	2203	4300	6503	SO:0001583	missense	4609	exon2			ACAGGAACTATGA		CCDS6359.2	8q24	2013-07-09	2013-07-09		ENSG00000136997	ENSG00000136997		"""Basic helix-loop-helix proteins"""	7553	protein-coding gene	gene with protein product		190080					Standard	NM_002467		Approved	c-Myc, bHLHe39, MYCC	uc003ysi.3	P01106	OTTHUMG00000128475	ENST00000259523.6:c.32A>G	8.37:g.128750540A>G	ENSP00000259523:p.Asn11Ser	Somatic	72	0	0	1567	WXS	Illumina HiSeq	Phase_I	47	34	0.723404	NM_002467	A8WFE7|P01107|Q14026	Missense_Mutation	SNP	ENST00000259523.6	37		42	0.019230769230769232	1	0.0020325203252032522	12	0.03314917127071823	0	0.0	29	0.03825857519788918	A	21.3	4.128161	0.77549	0.007944	0.039651	ENSG00000136997	ENST00000259523;ENST00000517291;ENST00000377970;ENST00000524013;ENST00000454617	T;T;T;T	0.29655	1.56;1.56;1.56;1.56	5.08	3.91	0.45181	Transcription regulator Myc, N-terminal (1);	0.042412	0.85682	D	0.000000	T	0.12305	0.0299	L	0.45352	1.415	0.52501	D	0.999959	D	0.56746	0.977	P	0.57152	0.814	T	0.01337	-1.1381	10	0.51188	T	0.08	-52.1751	12.2988	0.54862	0.8496:0.1504:0.0:0.0	rs4645959;rs17187550;rs59953828;rs4645959	11	P01106	MYC_HUMAN	S	11;25;26;25;11	ENSP00000259523:N11S;ENSP00000429441:N25S;ENSP00000367207:N26S;ENSP00000430235:N25S	ENSP00000259523:N11S	N	+	2	0	MYC	128819722	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	5.877000	0.69675	2.144000	0.66660	0.459000	0.35465	AAC	A|0.974;G|0.026	0.026	strong		0.602	MYC-002	PUTATIVE	basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000250278.1		
PFDN1	5201	hgsc.bcm.edu	37	5	139680027	139680027	+	Silent	SNP	A	A	G	rs145830713	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:139680027A>G	ENST00000261813.4	-	2	221	c.174T>C	c.(172-174)acT>acC	p.T58T	PFDN1_ENST00000514611.1_5'UTR|PFDN1_ENST00000524074.1_Silent_p.T58T|PFDN1_ENST00000510217.1_Intron	NM_002622.4	NP_002613.2	O60925	PFD1_HUMAN	prefoldin subunit 1	58					'de novo' posttranslational protein folding (GO:0051084)|actin cytoskeleton organization (GO:0030036)|B cell activation (GO:0042113)|cell cycle (GO:0007049)|cellular protein metabolic process (GO:0044267)|cerebellum development (GO:0021549)|protein folding (GO:0006457)|regulation of transcription, DNA-templated (GO:0006355)|telencephalon development (GO:0021537)	prefoldin complex (GO:0016272)	sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|large_intestine(3)|prostate(1)	6			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CATACATGTTAGTCTCATCTA	0.368													A|||	108	0.0215655	0.0	0.072	5008	,	,		24235	0.001		0.0089	False		,,,				2504	0.0491				p.T58T		Atlas-SNP	.											.	PFDN1	10	.	0			c.T174C						PASS	.	A		15,4391	23.3+/-48.9	0,15,2188	252.0	223.0	233.0		174	3.5	1.0	5	dbSNP_134	233	121,8479	63.5+/-125.6	0,121,4179	no	coding-synonymous	PFDN1	NM_002622.4		0,136,6367	GG,GA,AA		1.407,0.3404,1.0457		58/123	139680027	136,12870	2203	4300	6503	SO:0001819	synonymous_variant	5201	exon2			CATGTTAGTCTCA	Y17392	CCDS4222.1	5q31	2008-02-05	2006-02-24		ENSG00000113068	ENSG00000113068			8866	protein-coding gene	gene with protein product		604897	"""prefoldin 1"""			9630229	Standard	XM_005268465		Approved	PFD1	uc003lff.1	O60925	OTTHUMG00000129249	ENST00000261813.4:c.174T>C	5.37:g.139680027A>G		Somatic	312	0	0		WXS	Illumina HiSeq	Phase_I	291	151	0.5189	NM_002622	B2RD02|Q53F95|Q96EX6	Silent	SNP	ENST00000261813.4	37	CCDS4222.1																																																																																			A|0.989;G|0.011	0.011	strong		0.368	PFDN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251354.3	NM_002622	
USP48	84196	hgsc.bcm.edu	37	1	22033020	22033020	+	Silent	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:22033020C>T	ENST00000308271.9	-	17	2799	c.2151G>A	c.(2149-2151)aaG>aaA	p.K717K	USP48_ENST00000400301.1_Silent_p.K717K|USP48_ENST00000529637.1_Silent_p.K729K|USP48_ENST00000374732.3_Silent_p.K255K	NM_032236.5	NP_115612.4	Q86UV5	UBP48_HUMAN	ubiquitin specific peptidase 48	717	DUSP 3. {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)			NS(1)|endometrium(6)|kidney(2)|large_intestine(11)|lung(14)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	42		Colorectal(325;3.46e-05)|all_lung(284;4.29e-05)|Lung NSC(340;4.66e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|OV - Ovarian serous cystadenocarcinoma(117;4.74e-26)|COAD - Colon adenocarcinoma(152;1.3e-05)|GBM - Glioblastoma multiforme(114;1.86e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000614)|STAD - Stomach adenocarcinoma(196;0.00644)|KIRC - Kidney renal clear cell carcinoma(1967;0.00711)|Lung(427;0.0327)|READ - Rectum adenocarcinoma(331;0.0657)|LUSC - Lung squamous cell carcinoma(448;0.0753)		GGAGAGAAGTCTTTTGCTCGT	0.388																																					p.K717K		Atlas-SNP	.											USP48,colon,carcinoma,0,1	USP48	91	1	0			c.G2151A						PASS	.						131.0	133.0	132.0					1																	22033020		2203	4300	6503	SO:0001819	synonymous_variant	84196	exon17			AGAAGTCTTTTGC	AF502942	CCDS30623.1, CCDS44084.1	1p36.12	2008-02-05	2005-08-08	2004-04-07	ENSG00000090686	ENSG00000090686		"""Ubiquitin-specific peptidases"""	18533	protein-coding gene	gene with protein product			"""ubiquitin specific protease 31"", ""ubiquitin specific protease 48"""	USP31		12838346	Standard	XM_005246009		Approved	FLJ23277, FLJ11328, FLJ20103, FLJ23054, MGC14879	uc001bfb.3	Q86UV5	OTTHUMG00000007798	ENST00000308271.9:c.2151G>A	1.37:g.22033020C>T		Somatic	198	0	0		WXS	Illumina HiSeq	Phase_I	199	63	0.316583	NM_032236	B7ZKS7|Q2M3I4|Q5SZI4|Q5T3T5|Q6NX53|Q8N3F6|Q96F64|Q96IQ3|Q9H5N3|Q9H5T7|Q9NUJ6|Q9NXR0	Silent	SNP	ENST00000308271.9	37	CCDS30623.1																																																																																			.	.	none		0.388	USP48-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021372.1	NM_032236	
PGLYRP2	114770	hgsc.bcm.edu	37	19	15587185	15587185	+	Missense_Mutation	SNP	C	C	T	rs733731	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	222	0	0		WXS	Illumina HiSeq	Phase_I	175	80	0.457143	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	
FBXO38	81545	hgsc.bcm.edu	37	5	147805120	147805120	+	Missense_Mutation	SNP	T	T	C	rs10043775	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:147805120T>C	ENST00000340253.5	+	14	1942	c.1774T>C	c.(1774-1776)Tca>Cca	p.S592P	FBXO38_ENST00000296701.6_Missense_Mutation_p.S592P|FBXO38_ENST00000394370.3_Missense_Mutation_p.S592P|FBXO38_ENST00000513826.1_Missense_Mutation_p.S592P			Q6PIJ6	FBX38_HUMAN	F-box protein 38	592			S -> P (in dbSNP:rs10043775). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.2}.		cell death (GO:0008219)	cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.S592P(1)	ATG4C/FBXO38(2)	NS(1)|breast(2)|endometrium(7)|kidney(5)|large_intestine(9)|lung(15)|ovary(5)|prostate(2)|skin(2)|stomach(2)|urinary_tract(1)	51			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AAAACCAACCTCAATTACTGT	0.418													C|||	1365	0.272564	0.3086	0.2651	5008	,	,		21042	0.248		0.2346	False		,,,				2504	0.2935				p.S592P		Atlas-SNP	.											FBXO38,NS,carcinoma,0,1	FBXO38	115	1	1	Substitution - Missense(1)	stomach(1)	c.T1774C						PASS	.	C	PRO/SER,PRO/SER	1284,3122	699.9+/-406.5	203,878,1122	124.0	121.0	122.0		1774,1774	4.9	1.0	5	dbSNP_119	122	2267,6333	707.9+/-405.6	281,1705,2314	yes	missense,missense	FBXO38	NM_030793.3,NM_205836.1	74,74	484,2583,3436	CC,CT,TT	http://www.ncbi.nlm.nih.gov/pubmed?term	26.3605,29.1421,27.3028	benign,benign	592/1114,592/1189	147805120	3551,9455	2203	4300	6503	SO:0001583	missense	81545	exon14			CCAACCTCAATTA	BC005873	CCDS43384.1, CCDS64285.1	5q33.1	2008-02-05			ENSG00000145868	ENSG00000145868		"""F-boxes /  ""other"""""	28844	protein-coding gene	gene with protein product		608533				12477932	Standard	NM_030793		Approved	MOKA, SP329, FLJ13962, Fbx38	uc003lpg.2	Q6PIJ6	OTTHUMG00000129929	ENST00000340253.5:c.1774T>C	5.37:g.147805120T>C	ENSP00000342023:p.Ser592Pro	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	107	52	0.485981	NM_001271723	Q6PK72|Q7Z2U0|Q86VN3|Q9BXY6|Q9H837|Q9HC40	Missense_Mutation	SNP	ENST00000340253.5	37		560	0.2564102564102564	155	0.3150406504065041	97	0.26795580110497236	124	0.21678321678321677	184	0.24274406332453827	C	6.949	0.544999	0.13312	0.291421	0.263605	ENSG00000145868	ENST00000340253;ENST00000296701;ENST00000394370;ENST00000513826	T;T;T;T	0.28895	1.62;1.59;1.61;1.59	5.76	4.88	0.63580	.	0.049595	0.85682	N	0.000000	T	0.00012	0.0000	N	0.02539	-0.55	0.44807	P	0.0021900000000000253	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.37641	-0.9697	9	0.06494	T	0.89	-4.0317	10.8718	0.46887	0.0:0.7983:0.1305:0.0712	rs10043775;rs17358782;rs52826607;rs56937554;rs10043775	592;592;592	Q6PIJ6-3;Q6PIJ6-2;Q6PIJ6	.;.;FBX38_HUMAN	P	592	ENSP00000342023:S592P;ENSP00000296701:S592P;ENSP00000377895:S592P;ENSP00000426410:S592P	ENSP00000296701:S592P	S	+	1	0	FBXO38	147785313	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	3.368000	0.52357	0.878000	0.35920	-0.128000	0.14901	TCA	T|0.734;C|0.266	0.266	strong		0.418	FBXO38-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000252185.2	NM_030793	
TM6SF2	53345	hgsc.bcm.edu	37	19	19380996	19380996	+	Silent	SNP	G	G	T	rs2074300	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:19380996G>T	ENST00000389363.4	-	4	459	c.387C>A	c.(385-387)ggC>ggA	p.G129G	AC138430.4_ENST00000586064.2_RNA|TM6SF2_ENST00000586107.1_5'UTR	NM_001001524.2	NP_001001524.2	Q9BZW4	TM6S2_HUMAN	transmembrane 6 superfamily member 2	129						integral component of membrane (GO:0016021)				breast(2)|kidney(1)|large_intestine(1)|lung(8)|skin(1)|upper_aerodigestive_tract(1)	14			Epithelial(12;0.0151)			TGCAGATGGCGCCGGCCATGG	0.637													G|||	1331	0.265775	0.211	0.3141	5008	,	,		16900	0.3065		0.1501	False		,,,				2504	0.3824				p.G129G		Atlas-SNP	.											.	TM6SF2	39	.	0			c.C387A						PASS	.	G		822,3316		79,664,1326	38.0	41.0	40.0		387	-8.2	0.3	19	dbSNP_96	40	1467,6937		130,1207,2865	no	coding-synonymous	TM6SF2	NM_001001524.2		209,1871,4191	TT,TG,GG		17.456,19.8647,18.2507		129/378	19380996	2289,10253	2069	4202	6271	SO:0001819	synonymous_variant	53345	exon4			GATGGCGCCGGCC	AF255923	CCDS42528.1	19p13.3-p12	2008-02-05							11861	protein-coding gene	gene with protein product		606563				11124529	Standard	NM_001001524		Approved	Lpr4	uc002nmd.1	Q9BZW4		ENST00000389363.4:c.387C>A	19.37:g.19380996G>T		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	114	114	1	NM_001001524	Q0IJ64	Silent	SNP	ENST00000389363.4	37	CCDS42528.1	500	0.22893772893772893	102	0.2073170731707317	100	0.27624309392265195	178	0.3111888111888112	120	0.158311345646438	G	10.72	1.430186	0.25726	0.198647	0.17456	ENSG00000213996	ENST00000431465	.	.	.	4.74	-8.25	0.01025	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.49582	P	1.9700000000000273E-4	.	.	.	.	.	.	T	0.36504	-0.9745	4	0.87932	D	0	-8.7426	1.1726	0.01829	0.235:0.2013:0.3962:0.1674	rs2074300	.	.	.	E	152	.	ENSP00000391180:A152E	A	-	2	0	TM6SF2	19241996	0.000000	0.05858	0.332000	0.25469	0.729000	0.41735	-1.731000	0.01853	-1.096000	0.03046	0.505000	0.49811	GCG	G|0.794;T|0.206	0.206	strong		0.637	TM6SF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460122.2	NM_203510	
TAP2	6891	hgsc.bcm.edu	37	6	32800412	32800412	+	Missense_Mutation	SNP	C	C	T	rs1800454	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:32800412C>T	ENST00000452392.2	-	6	1308	c.1135G>A	c.(1135-1137)Gta>Ata	p.V379I	TAP2_ENST00000374899.4_Missense_Mutation_p.V379I|TAP2_ENST00000374897.2_Missense_Mutation_p.V379I|TAP2_ENST00000485701.1_5'UTR			Q9UDX4	S14L3_HUMAN	transporter 2, ATP-binding cassette, sub-family B (MDR/TAP)	0	GOLD. {ECO:0000255|PROSITE- ProRule:PRU00096}.					extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)	lipid binding (GO:0008289)|transporter activity (GO:0005215)									Vitamin E(DB00163)	ACCCTCCTTACGAGCAGGTAC	0.552													C|||	731	0.145966	0.152	0.1369	5008	,	,		18457	0.1905		0.1531	False		,,,				2504	0.091				p.V379I		Atlas-SNP	.											TAP2_ENST00000458336,NS,carcinoma,0,4	TAP2	98	4	0			c.G1135A	GRCh37	CM920658	TAP2	M	rs1800454	PASS	.	C	ILE/VAL,ILE/VAL	450,2570		32,386,1092	89.0	78.0	82.0		1135,1135	-9.9	0.0	6	dbSNP_89	82	742,4676		58,626,2025	yes	missense,missense	TAP2	NM_000544.3,NM_018833.2	29,29	90,1012,3117	TT,TC,CC		13.6951,14.9007,14.1266	benign,benign	379/704,379/654	32800412	1192,7246	1510	2709	4219	SO:0001583	missense	6891	exon6			TCCTTACGAGCAG	M74447	CCDS4755.1	6p21.3	2014-09-17			ENSG00000204267	ENSG00000204267		"""ATP binding cassette transporters / subfamily B"""	44	protein-coding gene	gene with protein product		170261		ABCB3		1529427, 1946428, 16395595	Standard	NM_001290043		Approved	PSF2, RING11, D6S217E	uc003ocd.3	Q03519	OTTHUMG00000031068	ENST00000452392.2:c.1135G>A	6.37:g.32800412C>T	ENSP00000391806:p.Val379Ile	Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	111	33	0.297297	NM_018833	E7EN74|E9PE57|Q495V8|Q495W0|Q495W1	Missense_Mutation	SNP	ENST00000452392.2	37		335	0.1533882783882784	67	0.13617886178861788	49	0.13535911602209943	97	0.16958041958041958	122	0.16094986807387862	C	0.866	-0.733797	0.03111	0.149007	0.136951	ENSG00000204267;ENSG00000204267;ENSG00000204267;ENSG00000250264	ENST00000556934;ENST00000374899;ENST00000374897;ENST00000452392	D;D;D	0.88509	-2.39;-2.39;-2.39	4.96	-9.93	0.00452	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1);	2.160830	0.02792	N	0.122180	T	0.29223	0.0727	N	0.00985	-1.075	0.09310	P	0.999993	B;B;B;B	0.20780	0.048;0.029;0.029;0.029	B;B;B;B	0.20955	0.032;0.012;0.012;0.012	T	0.48525	-0.9028	9	0.02654	T	1	-57.7115	1.346	0.02163	0.1525:0.1691:0.2177:0.4608	rs1800454;rs2228392;rs4148873;rs59850737;rs1800454	379;380;379;379	E7ENX8;Q59H06;Q03519;Q9UP03	.;.;TAP2_HUMAN;.	I	379	ENSP00000364034:V379I;ENSP00000364032:V379I;ENSP00000391806:V379I	ENSP00000364032:V379I	V	-	1	0	XXbac-BPG246D15.9;TAP2	32908390	0.000000	0.05858	0.000000	0.03702	0.258000	0.26162	-1.955000	0.01523	-2.988000	0.00280	-2.275000	0.00273	GTA	C|0.860;T|0.140	0.140	strong		0.552	TAP2-001	NOVEL	mRNA_end_NF|cds_end_NF|basic|appris_principal|readthrough_transcript|exp_conf	protein_coding	protein_coding	OTTHUMT00000361828.1	NM_000544	
FAT3	120114	hgsc.bcm.edu	37	11	92088524	92088524	+	Silent	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:92088524C>T	ENST00000298047.6	+	1	3263	c.3246C>T	c.(3244-3246)atC>atT	p.I1082I	FAT3_ENST00000525166.1_Silent_p.I932I|FAT3_ENST00000409404.2_Silent_p.I1082I|FAT3_ENST00000541502.1_Silent_p.I1082I			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	1082	Cadherin 10. {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)				AGTACTCCATCAGGGATGGCA	0.463										TCGA Ovarian(4;0.039)																											p.I1082I		Atlas-SNP	.											.	FAT3	1822	.	0			c.C3246T						PASS	.						108.0	105.0	106.0					11																	92088524		2055	4207	6262	SO:0001819	synonymous_variant	120114	exon1			CTCCATCAGGGAT	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.3246C>T	11.37:g.92088524C>T		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	102	32	0.313726	NM_001008781	B5MDB0|Q96AU6	Silent	SNP	ENST00000298047.6	37																																																																																				.	.	none		0.463	FAT3-201	KNOWN	basic	protein_coding	protein_coding		NM_001008781	
DTX1	1840	hgsc.bcm.edu	37	12	113496151	113496151	+	Missense_Mutation	SNP	C	C	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:113496151C>G	ENST00000257600.3	+	1	657	c.154C>G	c.(154-156)Ctg>Gtg	p.L52V		NM_004416.2	NP_004407.2	Q86Y01	DTX1_HUMAN	deltex 1, E3 ubiquitin ligase	52	WWE 1. {ECO:0000255|PROSITE- ProRule:PRU00248}.				cell surface receptor signaling pathway (GO:0007166)|glial cell differentiation (GO:0010001)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of T cell differentiation (GO:0045581)|Notch signaling pathway (GO:0007219)|protein ubiquitination (GO:0016567)|regulation of Notch signaling pathway (GO:0008593)|regulation of RNA biosynthetic process (GO:2001141)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ligase activity (GO:0016874)|Notch binding (GO:0005112)|transcription coactivator activity (GO:0003713)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(2)|lung(11)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	32						TGAGAACGTGCTGAAGGAGGA	0.647																																					p.L52V		Atlas-SNP	.											.	DTX1	83	.	0			c.C154G						PASS	.						121.0	106.0	111.0					12																	113496151		2203	4300	6503	SO:0001583	missense	1840	exon1			AACGTGCTGAAGG	AF053700	CCDS9164.1	12q24	2014-01-28	2014-01-28			ENSG00000135144			3060	protein-coding gene	gene with protein product		602582	"""deltex homolog 1 (Drosophila)"""			9590294, 12670957	Standard	NM_004416		Approved	hDx-1	uc001tuk.1	Q86Y01	OTTHUMG00000169610	ENST00000257600.3:c.154C>G	12.37:g.113496151C>G	ENSP00000257600:p.Leu52Val	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	79	13	0.164557	NM_004416	O60630|Q9BS04	Missense_Mutation	SNP	ENST00000257600.3	37	CCDS9164.1	.	.	.	.	.	.	.	.	.	.	C	18.19	3.569791	0.65765	.	.	ENSG00000135144	ENST00000257600	T	0.46819	0.86	3.9	3.9	0.45041	WWE domain (2);WWE domain, subgroup (1);	0.093779	0.43919	U	0.000507	T	0.31606	0.0802	N	0.16478	0.41	0.39022	D	0.95976	B	0.29481	0.245	B	0.28305	0.088	T	0.19128	-1.0315	10	0.25106	T	0.35	-0.2273	14.8783	0.70513	0.0:1.0:0.0:0.0	.	52	Q86Y01	DTX1_HUMAN	V	52	ENSP00000257600:L52V	ENSP00000257600:L52V	L	+	1	2	DTX1	111980534	1.000000	0.71417	1.000000	0.80357	0.907000	0.53573	3.362000	0.52314	2.021000	0.59480	0.555000	0.69702	CTG	.	.	none		0.647	DTX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405045.2		
KIAA1614	57710	hgsc.bcm.edu	37	1	180886216	180886216	+	Missense_Mutation	SNP	C	C	T	rs77695365	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:180886216C>T	ENST00000367588.4	+	2	1032	c.977C>T	c.(976-978)tCc>tTc	p.S326F		NM_020950.1	NP_066001.1	Q5VZ46	K1614_HUMAN	KIAA1614	326										NS(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(12)|ovary(5)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	33						TGGACTCCATCCTGGGACACA	0.627													C|||	204	0.0407348	0.0393	0.0331	5008	,	,		19151	0.001		0.0646	False		,,,				2504	0.0644				p.S326F		Atlas-SNP	.											.	KIAA1614	75	.	0			c.C977T						PASS	.	C	PHE/SER	120,3780		3,114,1833	19.0	21.0	20.0		977	2.2	0.8	1	dbSNP_131	20	466,7814		11,444,3685	yes	missense	KIAA1614	NM_020950.1	155	14,558,5518	TT,TC,CC		5.628,3.0769,4.8112	probably-damaging	326/1191	180886216	586,11594	1950	4140	6090	SO:0001583	missense	57710	exon2			CTCCATCCTGGGA	AB046834	CCDS41442.1	1q25.3	2008-02-05			ENSG00000135835	ENSG00000135835			29327	protein-coding gene	gene with protein product							Standard	NM_020950		Approved		uc001gok.2	Q5VZ46	OTTHUMG00000035183	ENST00000367588.4:c.977C>T	1.37:g.180886216C>T	ENSP00000356560:p.Ser326Phe	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	108	56	0.518519	NM_020950	Q5VZ45|Q9HCF8	Missense_Mutation	SNP	ENST00000367588.4	37	CCDS41442.1	78	0.03571428571428571	22	0.044715447154471545	10	0.027624309392265192	1	0.0017482517482517483	45	0.059366754617414245	C	10.54	1.379164	0.24944	0.030769	0.05628	ENSG00000135835	ENST00000367588	T	0.21191	2.02	4.21	2.25	0.28309	.	0.836895	0.10118	N	0.713838	T	0.04318	0.0119	L	0.44542	1.39	0.27493	N	0.952222	D	0.69078	0.997	P	0.60345	0.873	T	0.19943	-1.0290	9	0.72032	D	0.01	-8.3197	10.4802	0.44689	0.0:0.6146:0.3854:0.0	.	326	Q5VZ46	K1614_HUMAN	F	326	ENSP00000356560:S326F	ENSP00000356560:S326F	S	+	2	0	KIAA1614	179152839	0.211000	0.23529	0.819000	0.32651	0.025000	0.11179	0.415000	0.21181	0.494000	0.27859	-0.300000	0.09419	TCC	C|0.955;T|0.045	0.045	strong		0.627	KIAA1614-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000085151.1	XM_046531	
PLCB4	5332	hgsc.bcm.edu	37	20	9288522	9288522	+	Missense_Mutation	SNP	G	G	A	rs6077510	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:9288522G>A	ENST00000378493.1	+	1	76	c.61G>A	c.(61-63)Gca>Aca	p.A21T	PLCB4_ENST00000378473.3_Missense_Mutation_p.A21T|PLCB4_ENST00000492632.1_3'UTR|PLCB4_ENST00000378501.2_Missense_Mutation_p.A21T|PLCB4_ENST00000278655.4_Missense_Mutation_p.A21T|PLCB4_ENST00000414679.2_Missense_Mutation_p.A21T|PLCB4_ENST00000334005.3_Missense_Mutation_p.A21T			Q15147	PLCB4_HUMAN	phospholipase C, beta 4	21			A -> T (in dbSNP:rs6077510). {ECO:0000269|PubMed:15489334}.		inositol phosphate metabolic process (GO:0043647)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|dendrite (GO:0030425)|nucleus (GO:0005634)|postsynaptic density (GO:0014069)|smooth endoplasmic reticulum (GO:0005790)	calcium ion binding (GO:0005509)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|signal transducer activity (GO:0004871)			NS(2)|breast(4)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(11)|liver(4)|lung(34)|ovary(3)|pancreas(1)|prostate(1)|skin(19)|upper_aerodigestive_tract(1)	87						GCAAGAAGGAGCAGTTTTTGA	0.303													G|||	2361	0.471446	0.1203	0.5922	5008	,	,		15339	0.4692		0.6819	False		,,,				2504	0.6462				p.A21T		Atlas-SNP	.											.	PLCB4	204	.	0			c.G61A						PASS	.	G	THR/ALA,THR/ALA,THR/ALA	930,3476	350.5+/-310.9	104,722,1377	64.0	59.0	61.0		61,61,61	5.9	1.0	20	dbSNP_114	61	5785,2809	670.3+/-402.7	1968,1849,480	yes	missense,missense,missense	PLCB4	NM_000933.3,NM_001172646.1,NM_182797.2	58,58,58	2072,2571,1857	AA,AG,GG		32.6856,21.1076,48.3462	benign,benign,benign	21/1195,21/1188,21/1176	9288522	6715,6285	2203	4297	6500	SO:0001583	missense	5332	exon2			GAAGGAGCAGTTT		CCDS13104.1, CCDS13105.1, CCDS54447.1	20p12	2008-03-18			ENSG00000101333	ENSG00000101333	3.1.4.11		9059	protein-coding gene	gene with protein product		600810				8530101	Standard	NM_000933		Approved		uc021wam.1	Q15147	OTTHUMG00000031853	ENST00000378493.1:c.61G>A	20.37:g.9288522G>A	ENSP00000367754:p.Ala21Thr	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	64	36	0.5625	NM_182797	B7ZLK6|E2QRH8|Q17R56|Q5JYS8|Q5JYS9|Q5JYT0|Q5JYT3|Q5JYT4|Q9BQW5|Q9BQW6|Q9BQW8|Q9UJQ2	Missense_Mutation	SNP	ENST00000378493.1	37	CCDS13105.1	1053	0.48214285714285715	73	0.1483739837398374	215	0.5939226519337016	268	0.46853146853146854	497	0.6556728232189973	G	12.93	2.085975	0.36758	0.211076	0.673144	ENSG00000101333	ENST00000407043;ENST00000441846;ENST00000334005;ENST00000378473;ENST00000437503;ENST00000416836;ENST00000278655;ENST00000378493;ENST00000378501	T;T;T;T;T;T;T;T;T	0.42900	0.96;0.96;0.96;0.96;0.96;0.96;0.96;0.96;0.96	5.86	5.86	0.93980	Pleckstrin homology-type (1);	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	L	0.39020	1.185	0.19300	P	0.9999724842	P;D;P	0.63880	0.506;0.993;0.928	B;D;P	0.68192	0.083;0.956;0.546	T	0.07868	-1.0750	9	0.02654	T	1	.	18.9701	0.92711	0.0:0.0:1.0:0.0	rs6077510;rs52833495;rs57612679;rs6077510	21;21;21	E2QRH8;Q15147;Q15147-4	.;PLCB4_HUMAN;.	T	21	ENSP00000385805:A21T;ENSP00000412982:A21T;ENSP00000334105:A21T;ENSP00000367734:A21T;ENSP00000391614:A21T;ENSP00000395753:A21T;ENSP00000278655:A21T;ENSP00000367754:A21T;ENSP00000367762:A21T	ENSP00000278655:A21T	A	+	1	0	PLCB4	9236522	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.072000	0.76777	2.781000	0.95711	0.650000	0.86243	GCA	G|0.505;A|0.495	0.495	strong		0.303	PLCB4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000077948.2		
SLC9C2	284525	hgsc.bcm.edu	37	1	173472465	173472465	+	Splice_Site	SNP	G	G	A	rs72709309	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:173472465G>A	ENST00000367714.3	-	27	3733	c.3311C>T	c.(3310-3312)gCc>gTc	p.A1104V	SLC9C2_ENST00000466087.1_5'UTR	NM_178527.3	NP_848622.2	Q5TAH2	SL9C2_HUMAN	solute carrier family 9, member C2 (putative)	1104					sodium ion transport (GO:0006814)	integral component of membrane (GO:0016021)	solute:proton antiporter activity (GO:0015299)										GTTGACTGAGGCTAACCAAAT	0.308													G|||	76	0.0151757	0.0008	0.0346	5008	,	,		17650	0.0		0.0417	False		,,,				2504	0.0092				p.A1104V		Atlas-SNP	.											.	.	.	.	0			c.C3311T						PASS	.	G	VAL/ALA	36,4370	40.8+/-73.8	0,36,2167	109.0	98.0	102.0		3311	1.2	0.0	1	dbSNP_130	102	360,8240	119.4+/-178.7	9,342,3949	yes	missense-near-splice	SLC9A11	NM_178527.3	64	9,378,6116	AA,AG,GG		4.186,0.8171,3.0447	benign	1104/1125	173472465	396,12610	2203	4300	6503	SO:0001630	splice_region_variant	284525	exon27			ACTGAGGCTAACC	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.3311-1C>T	1.37:g.173472465G>A		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	122	69	0.565574	NM_178527	Q86UF3	Missense_Mutation	SNP	ENST00000367714.3	37	CCDS1308.1	51	0.023351648351648352	1	0.0020325203252032522	14	0.03867403314917127	0	0.0	36	0.047493403693931395	G	9.015	0.983365	0.18889	0.008171	0.04186	ENSG00000162753	ENST00000367714	T	0.05081	3.5	4.03	1.17	0.20885	.	2.115000	0.01969	N	0.043930	T	0.01454	0.0047	N	0.22421	0.69	0.09310	N	1	B	0.30068	0.267	B	0.30495	0.116	T	0.43956	-0.9359	10	0.24483	T	0.36	.	5.0227	0.14369	0.0:0.3097:0.3909:0.2995	.	1104	Q5TAH2	S9A11_HUMAN	V	1104	ENSP00000356687:A1104V	ENSP00000356687:A1104V	A	-	2	0	SLC9A11	171739088	0.000000	0.05858	0.001000	0.08648	0.004000	0.04260	-1.336000	0.02660	0.276000	0.22118	0.655000	0.94253	GCC	G|0.973;A|0.027	0.027	strong		0.308	SLC9C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084205.1	NM_178527	Missense_Mutation
EAF1	85403	hgsc.bcm.edu	37	3	15476011	15476011	+	Silent	SNP	C	C	G	rs1563415	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:15476011C>G	ENST00000396842.2	+	4	917	c.492C>G	c.(490-492)ccC>ccG	p.P164P	EAF1_ENST00000432764.2_Silent_p.P63P|RNU6-1024P_ENST00000384199.1_RNA|EAF1-AS1_ENST00000597949.1_RNA	NM_033083.6	NP_149074.3	Q96JC9	EAF1_HUMAN	ELL associated factor 1	164	Pro-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|ELL-EAF complex (GO:0032783)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)				central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(1)|prostate(1)|urinary_tract(1)	7						AAGATAACCCCTCACCTGAAC	0.478													C|||	1040	0.207668	0.0144	0.2363	5008	,	,		19515	0.2917		0.2485	False		,,,				2504	0.32				p.P164P		Atlas-SNP	.											.	EAF1	16	.	0			c.C492G						PASS	.	C		245,4161	142.7+/-177.9	6,233,1964	231.0	218.0	222.0		492	0.2	1.0	3	dbSNP_88	222	2268,6332	384.1+/-341.0	278,1712,2310	no	coding-synonymous	EAF1	NM_033083.6		284,1945,4274	GG,GC,CC		26.3721,5.5606,19.3219		164/269	15476011	2513,10493	2203	4300	6503	SO:0001819	synonymous_variant	85403	exon4			TAACCCCTCACCT	AF272973	CCDS2626.1	3p25.1	2011-06-10			ENSG00000144597	ENSG00000144597			20907	protein-coding gene	gene with protein product		608315				11418481	Standard	NM_033083		Approved		uc003bzu.3	Q96JC9	OTTHUMG00000162544	ENST00000396842.2:c.492C>G	3.37:g.15476011C>G		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	82	34	0.414634	NM_033083	B4E3F5|Q8IW10	Silent	SNP	ENST00000396842.2	37	CCDS2626.1																																																																																			C|0.796;G|0.204	0.204	strong		0.478	EAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252100.4	NM_033083	
ZNF880	400713	hgsc.bcm.edu	37	19	52887437	52887437	+	Missense_Mutation	SNP	A	A	C	rs8104812	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:52887437A>C	ENST00000422689.2	+	4	619	c.604A>C	c.(604-606)Aat>Cat	p.N202H		NM_001145434.1	NP_001138906.1	Q6PDB4	ZN880_HUMAN	zinc finger protein 880	202					regulation of transcription, DNA-templated (GO:0006355)	intracellular (GO:0005622)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(2)|skin(1)	10						ACTTGCTAACAATCAAGTAAT	0.373													C|||	1897	0.378794	0.2405	0.379	5008	,	,		20813	0.3462		0.4205	False		,,,				2504	0.5562				p.N202H		Atlas-SNP	.											.	ZNF880	45	.	0			c.A604C						PASS	.	C	HIS/ASN	392,992		53,286,353	47.0	46.0	46.0		604	0.7	0.0	19	dbSNP_116	46	1214,1968		222,770,599	yes	missense	ZNF880	NM_001145434.1	68	275,1056,952	CC,CA,AA		38.1521,28.3237,35.173	benign	202/578	52887437	1606,2960	692	1591	2283	SO:0001583	missense	400713	exon4			GCTAACAATCAAG	BC058819	CCDS46164.1	19q13.41	2013-01-08			ENSG00000221923	ENSG00000221923		"""Zinc fingers, C2H2-type"", ""-"""	37249	protein-coding gene	gene with protein product							Standard	NM_001145434		Approved		uc002pzc.3	Q6PDB4	OTTHUMG00000167972	ENST00000422689.2:c.604A>C	19.37:g.52887437A>C	ENSP00000406318:p.Asn202His	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	67	67	1	NM_001145434	B4DNA6	Missense_Mutation	SNP	ENST00000422689.2	37	CCDS46164.1	745	0.3411172161172161	119	0.241869918699187	138	0.3812154696132597	177	0.3094405594405594	311	0.4102902374670185	C	0.005	-2.223193	0.00283	0.283237	0.381521	ENSG00000221923	ENST00000422689	T	0.12879	2.64	1.84	0.682	0.17992	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	N	0.00005	-3.26	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.41698	-0.9494	7	.	.	.	.	5.3499	0.16030	0.2302:0.5451:0.2247:0.0	rs8104812;rs17736363;rs8104812	202	Q6PDB4	ZN880_HUMAN	H	202	ENSP00000406318:N202H	.	N	+	1	0	ZNF880	57579249	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.069000	0.14552	-0.288000	0.09051	-1.160000	0.01791	AAT	A|0.655;C|0.345	0.345	strong		0.373	ZNF880-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397374.1	NM_001145434	
LRPPRC	10128	hgsc.bcm.edu	37	2	44201315	44201315	+	Missense_Mutation	SNP	A	A	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:44201315A>T	ENST00000260665.7	-	9	1186	c.1129T>A	c.(1129-1131)Tta>Ata	p.L377I	LRPPRC_ENST00000409659.1_Missense_Mutation_p.L377I|LRPPRC_ENST00000409946.1_Missense_Mutation_p.L377I	NM_133259.3	NP_573566.2	P42704	LPPRC_HUMAN	leucine-rich pentatricopeptide repeat containing	377					mitochondrion transport along microtubule (GO:0047497)|mRNA transport (GO:0051028)|negative regulation of mitochondrial RNA catabolic process (GO:0000961)|regulation of mitochondrial translation (GO:0070129)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	condensed nuclear chromosome (GO:0000794)|cytoskeleton (GO:0005856)|membrane (GO:0016020)|microtubule (GO:0005874)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|ribonucleoprotein complex (GO:0030529)	beta-tubulin binding (GO:0048487)|microtubule binding (GO:0008017)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)			breast(3)|endometrium(3)|kidney(5)|large_intestine(9)|lung(15)|ovary(2)|prostate(2)|skin(2)	41		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)				CAGTGTTGTAAAAAGAAACTG	0.358																																					p.L377I		Atlas-SNP	.											.	LRPPRC	105	.	0			c.T1129A						PASS	.						98.0	96.0	97.0					2																	44201315		2203	4300	6503	SO:0001583	missense	10128	exon9			GTTGTAAAAAGAA	M92439	CCDS33189.1	2p21	2012-02-24	2012-02-24		ENSG00000138095	ENSG00000138095			15714	protein-coding gene	gene with protein product		607544	"""Leigh syndrome, French-Canadian type (cytochrome oxidase deficiency)"""	LSFC		8012652, 8619474, 22045337	Standard	NM_133259		Approved	GP130, LRP130	uc002rtr.2	P42704	OTTHUMG00000152782	ENST00000260665.7:c.1129T>A	2.37:g.44201315A>T	ENSP00000260665:p.Leu377Ile	Somatic	342	0	0		WXS	Illumina HiSeq	Phase_I	550	65	0.118182	NM_133259	A0PJE3|A8K1V1|Q53PC0|Q53QN7|Q6ZUD8|Q7Z7A6|Q96D84	Missense_Mutation	SNP	ENST00000260665.7	37	CCDS33189.1	.	.	.	.	.	.	.	.	.	.	A	15.67	2.901542	0.52227	.	.	ENSG00000138095	ENST00000465633;ENST00000260665;ENST00000409946;ENST00000409659;ENST00000447246	T;T;T;T	0.70399	0.32;0.26;0.29;-0.48	6.08	1.21	0.21127	.	0.000000	0.64402	D	0.000004	T	0.69753	0.3146	L	0.46157	1.445	0.47621	D	0.999471	P;B;D	0.67145	0.955;0.097;0.996	P;B;P	0.59703	0.753;0.054;0.862	T	0.64659	-0.6355	10	0.40728	T	0.16	-13.0937	4.796	0.13272	0.5914:0.0:0.2803:0.1283	.	277;351;377	F5H4J6;C9JCA9;P42704	.;.;LPPRC_HUMAN	I	277;377;377;377;351	ENSP00000260665:L377I;ENSP00000386234:L377I;ENSP00000386562:L377I;ENSP00000403637:L351I	ENSP00000260665:L377I	L	-	1	2	LRPPRC	44054819	1.000000	0.71417	0.456000	0.27044	0.944000	0.59088	3.419000	0.52728	0.194000	0.20326	0.482000	0.46254	TTA	.	.	none		0.358	LRPPRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327823.1	NM_133259	
PRLHR	2834	hgsc.bcm.edu	37	10	120353843	120353843	+	Missense_Mutation	SNP	G	G	A	rs8192524	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:120353843G>A	ENST00000369169.1	-	1	913	c.914C>T	c.(913-915)cCc>cTc	p.P305L	PRLHR_ENST00000239032.2_Missense_Mutation_p.P305L			P49683	PRLHR_HUMAN	prolactin releasing hormone receptor	305					feeding behavior (GO:0007631)|female pregnancy (GO:0007565)|G-protein coupled receptor signaling pathway (GO:0007186)|hormone metabolic process (GO:0042445)|neuropeptide signaling pathway (GO:0007218)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|neuropeptide receptor activity (GO:0008188)|neuropeptide Y receptor activity (GO:0004983)			large_intestine(2)|lung(8)|ovary(1)|skin(1)	12		Colorectal(252;0.0429)|Lung NSC(174;0.142)|all_lung(145;0.175)		all cancers(201;0.0166)		GATGGCGTGGGGGTCGAGGTC	0.657													G|||	159	0.0317492	0.0015	0.0706	5008	,	,		17349	0.003		0.0537	False		,,,				2504	0.0521				p.P305L		Atlas-SNP	.											.	PRLHR	41	.	0			c.C914T	GRCh37	CM030884	PRLHR	M	rs8192524	PASS	.	G	LEU/PRO	39,4367	40.8+/-73.8	0,39,2164	45.0	45.0	45.0		914	4.4	1.0	10	dbSNP_117	45	382,8218	119.9+/-179.2	11,360,3929	yes	missense	PRLHR	NM_004248.2	98	11,399,6093	AA,AG,GG		4.4419,0.8852,3.237	possibly-damaging	305/371	120353843	421,12585	2203	4300	6503	SO:0001583	missense	2834	exon2			GCGTGGGGGTCGA	AB048946	CCDS7606.1	10q25.3-q26	2014-02-21	2005-11-24	2005-11-24	ENSG00000119973	ENSG00000119973		"""GPCR / Class A : RF amide peptide receptors"""	4464	protein-coding gene	gene with protein product		600895	"""G protein-coupled receptor 10"""	GPR10		8666380, 15885496	Standard	NM_004248		Approved	PrRPR	uc001ldp.1	P49683	OTTHUMG00000019136	ENST00000369169.1:c.914C>T	10.37:g.120353843G>A	ENSP00000358167:p.Pro305Leu	Somatic	22	0	0		WXS	Illumina HiSeq	Phase_I	18	9	0.5	NM_004248	O75194|Q502U8|Q5VXR9	Missense_Mutation	SNP	ENST00000369169.1	37	CCDS7606.1	58	0.026556776556776556	1	0.0020325203252032522	21	0.058011049723756904	0	0.0	36	0.047493403693931395	G	15.33	2.801158	0.50315	0.008852	0.044419	ENSG00000119973	ENST00000239032;ENST00000369169	T;T	0.50001	0.76;0.76	4.38	4.38	0.52667	GPCR, rhodopsin-like superfamily (1);	0.125039	0.52532	D	0.000074	T	0.03651	0.0104	L	0.41124	1.26	0.51233	D	0.999919	P	0.36633	0.562	B	0.31191	0.125	T	0.02109	-1.1212	10	0.26408	T	0.33	.	5.1894	0.15201	0.2578:0.0:0.7422:0.0	rs8192524	305	P49683	PRLHR_HUMAN	L	305	ENSP00000239032:P305L;ENSP00000358167:P305L	ENSP00000239032:P305L	P	-	2	0	PRLHR	120343833	1.000000	0.71417	0.990000	0.47175	0.938000	0.57974	7.439000	0.80444	2.255000	0.74692	0.561000	0.74099	CCC	G|0.968;A|0.032	0.032	strong		0.657	PRLHR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050610.1	NM_004248	
PTBP2	58155	hgsc.bcm.edu	37	1	97272456	97272456	+	Silent	SNP	A	A	G	rs6699932	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:97272456A>G	ENST00000426398.2	+	11	1156	c.1113A>G	c.(1111-1113)ttA>ttG	p.L371L	PTBP2_ENST00000394184.3_Silent_p.L387L|PTBP2_ENST00000370198.1_Silent_p.L376L|PTBP2_ENST00000609116.1_Silent_p.L371L|PTBP2_ENST00000541987.1_3'UTR|PTBP2_ENST00000370197.1_Silent_p.L376L|PTBP2_ENST00000482253.1_3'UTR	NM_021190.2	NP_067013.1	Q9UKA9	PTBP2_HUMAN	polypyrimidine tract binding protein 2	371	RRM 3. {ECO:0000255|PROSITE- ProRule:PRU00176}.				mRNA splice site selection (GO:0006376)|negative regulation of RNA splicing (GO:0033119)|regulation of neural precursor cell proliferation (GO:2000177)	spliceosomal complex (GO:0005681)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(15)|skin(1)	26		all_epithelial(167;2.95e-05)|all_lung(203;0.000396)|Lung NSC(277;0.00171)		all cancers(265;0.0582)|Epithelial(280;0.0716)|Colorectal(170;0.0879)|KIRC - Kidney renal clear cell carcinoma(1967;0.202)		TGAAGATTTTATACAATAAGA	0.358													G|||	1392	0.277955	0.5408	0.1499	5008	,	,		17431	0.2103		0.2117	False		,,,				2504	0.1513				p.L371L		Atlas-SNP	.											.	PTBP2	62	.	0			c.A1113G						PASS	.	G		2194,2212	590.6+/-387.4	547,1100,556	134.0	132.0	133.0		1113	3.3	1.0	1	dbSNP_116	133	1604,6996	743.0+/-407.2	133,1338,2829	no	coding-synonymous	PTBP2	NM_021190.2		680,2438,3385	GG,GA,AA		18.6512,49.7957,29.2019		371/532	97272456	3798,9208	2203	4300	6503	SO:0001819	synonymous_variant	58155	exon11			GATTTTATACAAT	AB051232	CCDS754.1, CCDS72828.1, CCDS72829.1, CCDS72830.1	1p21.3	2013-07-16			ENSG00000117569	ENSG00000117569		"""RNA binding motif (RRM) containing"""	17662	protein-coding gene	gene with protein product		608449				11003644	Standard	XM_005271084		Approved	brPTB, nPTB, PTB, PTBLP	uc001drq.3	Q9UKA9	OTTHUMG00000010685	ENST00000426398.2:c.1113A>G	1.37:g.97272456A>G		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	81	80	0.987654	NM_021190	Q8N0Z1|Q8N160|Q8NFB0|Q8NFB1|Q969N9|Q96Q76	Silent	SNP	ENST00000426398.2	37	CCDS754.1																																																																																			A|0.707;G|0.293	0.293	strong		0.358	PTBP2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000029453.1		
ARHGEF28	64283	hgsc.bcm.edu	37	5	73207372	73207372	+	Missense_Mutation	SNP	T	T	A	rs1478453	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:73207372T>A	ENST00000426542.2	+	34	4940	c.4920T>A	c.(4918-4920)caT>caA	p.H1640Q	ARHGEF28_ENST00000512883.1_Missense_Mutation_p.H560Q|ARHGEF28_ENST00000296794.6_Missense_Mutation_p.H1640Q|ARHGEF28_ENST00000287898.5_Missense_Mutation_p.H1596Q|ARHGEF28_ENST00000513042.2_Missense_Mutation_p.H1640Q|ARHGEF28_ENST00000296799.4_Missense_Mutation_p.H1327Q|ARHGEF28_ENST00000545377.1_Missense_Mutation_p.H1640Q|ARHGEF28_ENST00000437974.1_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	122	0	0		WXS	Illumina HiSeq	Phase_I	122	122	1	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		
DCLRE1C	64421	hgsc.bcm.edu	37	10	14987181	14987181	+	Missense_Mutation	SNP	C	C	A	rs138077101	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:14987181C>A	ENST00000378278.2	-	3	206	c.169G>T	c.(169-171)Gtt>Ttt	p.V57F	DCLRE1C_ENST00000453695.2_5'UTR|DCLRE1C_ENST00000396817.2_5'UTR|DCLRE1C_ENST00000357717.2_Intron|DCLRE1C_ENST00000378254.1_5'UTR|DCLRE1C_ENST00000378255.1_5'UTR|DCLRE1C_ENST00000378249.1_5'UTR|DCLRE1C_ENST00000378289.4_Missense_Mutation_p.V57F|DCLRE1C_ENST00000378246.2_5'UTR|DCLRE1C_ENST00000378258.1_5'UTR			Q96SD1	DCR1C_HUMAN	DNA cross-link repair 1C	57					B cell differentiation (GO:0030183)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA recombination (GO:0006310)|double-strand break repair (GO:0006302)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|response to ionizing radiation (GO:0010212)|telomere maintenance (GO:0000723)	nucleus (GO:0005634)	5'-3' exonuclease activity (GO:0008409)|single-stranded DNA endodeoxyribonuclease activity (GO:0000014)			breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)	17						TATAGATAAACCTTCAAGCTG	0.308								Non-homologous end-joining																													p.V57F		Atlas-SNP	.											.	DCLRE1C	136	.	0			c.G169T						PASS	.	C	PHE/VAL,,,	0,4406		0,0,2203	45.0	46.0	46.0		169,,,	5.2	1.0	10	dbSNP_134	46	8,8592	5.7+/-21.5	0,8,4292	yes	missense,utr-5,utr-5,utr-5	DCLRE1C	NM_001033855.1,NM_001033857.1,NM_001033858.1,NM_022487.2	50,,,	0,8,6495	AA,AC,CC		0.093,0.0,0.0615	probably-damaging,,,	57/693,,,	14987181	8,12998	2203	4300	6503	SO:0001583	missense	64421	exon3			GATAAACCTTCAA	BC022254	CCDS7105.1, CCDS31149.1, CCDS31150.1	10p13	2014-09-17	2010-06-24		ENSG00000152457	ENSG00000152457			17642	protein-coding gene	gene with protein product	"""PSO2 homolog (S. cerevisiae)"""	605988	"""severe combined immunodeficiency, type a (Athabascan)"", ""DNA cross-link repair 1C (PSO2 homolog, S. cerevisiae)"""	SCIDA		11336668, 9443881	Standard	XM_005252558		Approved	ARTEMIS, FLJ11360, SNM1C, A-SCID	uc001inn.3	Q96SD1	OTTHUMG00000017716	ENST00000378278.2:c.169G>T	10.37:g.14987181C>A	ENSP00000367527:p.Val57Phe	Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	117	53	0.452991	NM_001033855	D3DRT6|Q1HCL2|Q5JSR4|Q5JSR5|Q5JSR7|Q5JSR8|Q5JSR9|Q5JSS0|Q5JSS7|Q6PK14|Q8N101|Q8N132|Q8TBW9|Q9BVW9|Q9HAM4	Missense_Mutation	SNP	ENST00000378278.2	37	CCDS31149.1	.	.	.	.	.	.	.	.	.	.	C	27.6	4.843519	0.91197	0.0	9.3E-4	ENSG00000152457	ENST00000378289;ENST00000378278	T;T	0.76316	-1.01;-1.01	5.19	5.19	0.71726	Beta-lactamase-like (1);	0.115748	0.64402	D	0.000016	D	0.83774	0.5327	L	0.47078	1.49	0.80722	D	1	P;P	0.48350	0.897;0.909	P;P	0.60789	0.712;0.879	T	0.82967	-0.0194	10	0.44086	T	0.13	.	18.7242	0.91708	0.0:1.0:0.0:0.0	.	57;57	Q96SD1-4;Q96SD1	.;DCR1C_HUMAN	F	57	ENSP00000367538:V57F;ENSP00000367527:V57F	ENSP00000367527:V57F	V	-	1	0	DCLRE1C	15027187	1.000000	0.71417	0.997000	0.53966	0.941000	0.58515	2.687000	0.46976	2.604000	0.88044	0.573000	0.79308	GTT	C|1.000;A|0.000	0.000	strong		0.308	DCLRE1C-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046934.1	NM_022487	
COL5A1	1289	hgsc.bcm.edu	37	9	137619195	137619195	+	Silent	SNP	C	C	T	rs3124299	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:137619195C>T	ENST00000371817.3	+	5	1152	c.738C>T	c.(736-738)acC>acT	p.T246T		NM_000093.3|NM_001278074.1	NP_000084.3|NP_001265003.1	P20908	CO5A1_HUMAN	collagen, type V, alpha 1	246	Nonhelical region.				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)		ACTGTGACACCGCAGTACCTG	0.537													C|||	1716	0.342652	0.0424	0.5519	5008	,	,		18306	0.4077		0.4652	False		,,,				2504	0.407				p.T246T		Atlas-SNP	.											.	COL5A1	323	.	0			c.C738T						PASS	.	C		427,3979	204.8+/-226.9	33,361,1809	107.0	94.0	98.0		738	-8.4	0.0	9	dbSNP_103	98	3893,4707	545.0+/-384.7	895,2103,1302	yes	coding-synonymous	COL5A1	NM_000093.3		928,2464,3111	TT,TC,CC		45.2674,9.6913,33.2154		246/1839	137619195	4320,8686	2203	4300	6503	SO:0001819	synonymous_variant	1289	exon5			TGACACCGCAGTA	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.738C>T	9.37:g.137619195C>T		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	108	58	0.537037	NM_000093	Q15094|Q5SUX4	Silent	SNP	ENST00000371817.3	37	CCDS6982.1																																																																																			C|0.665;T|0.335	0.335	strong		0.537	COL5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054954.2	NM_000093	
CEACAM6	4680	hgsc.bcm.edu	37	19	42260569	42260569	+	Silent	SNP	G	G	A	rs1805223	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:42260569G>A	ENST00000199764.6	+	2	344	c.126G>A	c.(124-126)ccG>ccA	p.P42P	CEA_ENST00000598976.1_Intron|AC011513.4_ENST00000601409.1_RNA	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	151	0	0		WXS	Illumina HiSeq	Phase_I	131	75	0.572519	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		
REV1	51455	hgsc.bcm.edu	37	2	100055158	100055158	+	Missense_Mutation	SNP	T	T	C	rs3087399	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:100055158T>C	ENST00000258428.3	-	6	1346	c.1118A>G	c.(1117-1119)aAt>aGt	p.N373S	REV1_ENST00000393445.3_Missense_Mutation_p.N373S|REV1_ENST00000465835.1_5'UTR	NM_001037872.1|NM_016316.2	NP_001032961.1|NP_057400.1	Q9UBZ9	REV1_HUMAN	REV1, polymerase (DNA directed)	373			N -> S (in dbSNP:rs3087399).		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						TTGTAGGGTATTGACAAACTC	0.368								Direct reversal of damage					.|||	841	0.167931	0.2859	0.0576	5008	,	,		18937	0.0536		0.1193	False		,,,				2504	0.2546				p.N373S		Atlas-SNP	.											.	REV1	100	.	0			c.A1118G						PASS	.	T	SER/ASN,SER/ASN	1125,3281	399.5+/-331.2	136,853,1214	97.0	103.0	101.0		1118,1118	-0.6	0.8	2	dbSNP_102	101	1028,7572	220.6+/-258.3	59,910,3331	yes	missense,missense	REV1	NM_001037872.1,NM_016316.2	46,46	195,1763,4545	CC,CT,TT		11.9535,25.5334,16.5539	benign,benign	373/1251,373/1252	100055158	2153,10853	2203	4300	6503	SO:0001583	missense	51455	exon6			AGGGTATTGACAA	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.1118A>G	2.37:g.100055158T>C	ENSP00000258428:p.Asn373Ser	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	94	44	0.468085	NM_001037872	O95941|Q53SI7|Q9C0J4|Q9NUP2	Missense_Mutation	SNP	ENST00000258428.3	37	CCDS2045.1	290	0.13278388278388278	150	0.3048780487804878	20	0.055248618784530384	16	0.027972027972027972	104	0.13720316622691292	T	9.343	1.063410	0.20067	0.255334	0.119535	ENSG00000135945	ENST00000393445;ENST00000258428;ENST00000450415	T;T;T	0.53423	1.55;1.56;0.62	5.99	-0.648	0.11464	.	0.214602	0.56097	N	0.000031	T	0.00012	0.0000	L	0.49350	1.555	0.22918	P	0.99856913	B;B;B	0.22414	0.069;0.001;0.036	B;B;B	0.28991	0.086;0.008;0.097	T	0.34204	-0.9838	9	0.11485	T	0.65	.	10.7703	0.46319	0.0:0.3803:0.0:0.6197	rs3087399;rs52791165;rs57440453;rs3087399	352;373;373	Q9UBZ9-3;Q9UBZ9;Q9UBZ9-2	.;REV1_HUMAN;.	S	373;373;11	ENSP00000377091:N373S;ENSP00000258428:N373S;ENSP00000414875:N11S	ENSP00000258428:N373S	N	-	2	0	REV1	99421590	1.000000	0.71417	0.794000	0.32065	0.977000	0.68977	1.404000	0.34623	-0.321000	0.08627	-0.250000	0.11733	AAT	T|0.866;C|0.134	0.134	strong		0.368	REV1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253123.2	NM_016316	
TBL3	10607	hgsc.bcm.edu	37	16	2025678	2025678	+	Silent	SNP	C	C	A	rs17602	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:2025678C>A	ENST00000568546.1	+	10	1082	c.954C>A	c.(952-954)ctC>ctA	p.L318L		NM_006453.2	NP_006444.2	Q12788	TBL3_HUMAN	transducin (beta)-like 3	318					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						ACCTGTTGCTCTACGAGGCTC	0.692													C|||	534	0.106629	0.0045	0.1787	5008	,	,		18419	0.0387		0.1143	False		,,,				2504	0.2556				p.L318L	Melanoma(118;616 1651 35077 38081 48633)	Atlas-SNP	.											.	TBL3	54	.	0			c.C954A						PASS	.	C		112,4282	83.9+/-122.4	2,108,2087	35.0	35.0	35.0		954	-2.6	0.7	16	dbSNP_63	35	975,7621	198.7+/-243.0	56,863,3379	no	coding-synonymous	TBL3	NM_006453.2		58,971,5466	AA,AC,CC		11.3425,2.5489,8.368		318/809	2025678	1087,11903	2197	4298	6495	SO:0001819	synonymous_variant	10607	exon10			GTTGCTCTACGAG	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.954C>A	16.37:g.2025678C>A		Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	46	37	0.804348	NM_006453	Q59GD6|Q8IVB7|Q96A78	Silent	SNP	ENST00000568546.1	37	CCDS10453.1																																																																																			C|0.921;A|0.079	0.079	strong		0.692	TBL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250615.3	NM_006453	
GDF15	9518	hgsc.bcm.edu	37	19	18499151	18499151	+	Silent	SNP	C	C	T	rs1059022	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:18499151C>T	ENST00000252809.3	+	2	365	c.333C>T	c.(331-333)ccC>ccT	p.P111P	MIR3189_ENST00000578735.1_RNA	NM_004864.2	NP_004855.2	Q99988	GDF15_HUMAN	growth differentiation factor 15	111					cell-cell signaling (GO:0007267)|signal transduction (GO:0007165)|transforming growth factor beta receptor signaling pathway (GO:0007179)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	cytokine activity (GO:0005125)			kidney(2)|large_intestine(1)|liver(1)|lung(5)|prostate(2)|skin(1)	12						CCGCCCTTCCCGAGGGGCTCC	0.701											OREG0025363	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	863	0.172324	0.3601	0.1556	5008	,	,		12390	0.0069		0.175	False		,,,				2504	0.0982				p.P111P		Atlas-SNP	.											GDF15,NS,carcinoma,0,1	GDF15	31	1	0			c.C333T						PASS	.	C		1414,2934		255,904,1015	17.0	21.0	19.0		333	-8.6	0.0	19	dbSNP_86	19	1497,7063		143,1211,2926	no	coding-synonymous	GDF15	NM_004864.2		398,2115,3941	TT,TC,CC		17.4883,32.5207,22.5519		111/309	18499151	2911,9997	2174	4280	6454	SO:0001819	synonymous_variant	9518	exon2			CCTTCCCGAGGGG	BC008962	CCDS12376.1	19p13.11	2008-05-14				ENSG00000130513			30142	protein-coding gene	gene with protein product	"""prostate differentiation factor"""	605312				11895857, 9593718	Standard	NM_004864		Approved	PLAB, MIC-1, PDF, MIC1, NAG-1, PTGFB	uc002niv.2	Q99988		ENST00000252809.3:c.333C>T	19.37:g.18499151C>T		Somatic	134	0	0	726	WXS	Illumina HiSeq	Phase_I	120	74	0.616667	NM_004864	O14629|P78360|Q9BWA0|Q9NRT0	Silent	SNP	ENST00000252809.3	37	CCDS12376.1																																																																																			C|0.799;T|0.201	0.201	strong		0.701	GDF15-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466340.2	NM_004864	
KLHL3	26249	hgsc.bcm.edu	37	5	136969793	136969793	+	Silent	SNP	C	C	T	rs2301708	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:136969793C>T	ENST00000309755.4	-	12	1826	c.1383G>A	c.(1381-1383)gaG>gaA	p.E461E	KLHL3_ENST00000506491.1_Silent_p.E379E|KLHL3_ENST00000506873.1_5'UTR|KLHL3_ENST00000508657.1_Silent_p.E429E|KLHL3_ENST00000541417.1_Intron	NM_017415.2	NP_059111.2	Q9UH77	KLHL3_HUMAN	kelch-like family member 3	461					distal tubule morphogenesis (GO:0072156)|ion homeostasis (GO:0050801)|protein K48-linked ubiquitination (GO:0070936)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|renal sodium ion absorption (GO:0070294)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)	structural molecule activity (GO:0005198)	p.E461E(1)		breast(2)|endometrium(3)|kidney(2)|large_intestine(4)|lung(8)|stomach(1)|upper_aerodigestive_tract(1)	21		all_hematologic(541;3.67e-07)|Breast(839;7.61e-05)|Prostate(281;0.000825)|Ovarian(839;0.0481)|all_lung(232;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)	GBM - Glioblastoma multiforme(465;0.0223)		GGTTGTACTGCTCCACAGTGC	0.567													C|||	1134	0.226438	0.0855	0.2118	5008	,	,		16929	0.4583		0.175	False		,,,				2504	0.2413				p.E461E		Atlas-SNP	.											KLHL3,NS,carcinoma,0,1	KLHL3	54	1	1	Substitution - coding silent(1)	stomach(1)	c.G1383A						PASS	.	C		398,4008	198.4+/-222.2	17,364,1822	119.0	106.0	110.0		1383	2.3	1.0	5	dbSNP_100	110	1623,6977	303.2+/-306.3	167,1289,2844	no	coding-synonymous	KLHL3	NM_017415.2		184,1653,4666	TT,TC,CC		18.8721,9.0331,15.539		461/588	136969793	2021,10985	2203	4300	6503	SO:0001819	synonymous_variant	26249	exon12			GTACTGCTCCACA	AB032955	CCDS4192.1, CCDS58969.1, CCDS58970.1	5q31	2013-01-30	2013-01-30		ENSG00000146021	ENSG00000146021		"""Kelch-like"", ""BTB/POZ domain containing"""	6354	protein-coding gene	gene with protein product		605775	"""kelch (Drosophila)-like 3"", ""kelch-like 3 (Drosophila)"""			10843806	Standard	NM_017415		Approved	KIAA1129	uc010jek.3	Q9UH77	OTTHUMG00000129155	ENST00000309755.4:c.1383G>A	5.37:g.136969793C>T		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	65	35	0.538462	NM_017415	B2RBK7|Q9UH75|Q9UH76|Q9ULU0|Q9Y6V6	Silent	SNP	ENST00000309755.4	37	CCDS4192.1																																																																																			C|0.814;T|0.186	0.186	strong		0.567	KLHL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251220.2		
INSR	3643	hgsc.bcm.edu	37	19	7150532	7150532	+	Missense_Mutation	SNP	G	G	A	rs143523271	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:7150532G>A	ENST00000302850.5	-	11	2385	c.2243C>T	c.(2242-2244)tCa>tTa	p.S748L	INSR_ENST00000341500.5_Intron	NM_000208.2	NP_000199.2	P06213	INSR_HUMAN	insulin receptor	748					activation of MAPK activity (GO:0000187)|activation of protein kinase activity (GO:0032147)|activation of protein kinase B activity (GO:0032148)|carbohydrate metabolic process (GO:0005975)|cellular response to growth factor stimulus (GO:0071363)|cellular response to insulin stimulus (GO:0032869)|epidermis development (GO:0008544)|exocrine pancreas development (GO:0031017)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|heart morphogenesis (GO:0003007)|insulin receptor signaling pathway (GO:0008286)|male sex determination (GO:0030238)|peptidyl-tyrosine autophosphorylation (GO:0038083)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of developmental growth (GO:0048639)|positive regulation of DNA replication (GO:0045740)|positive regulation of glucose import (GO:0046326)|positive regulation of glycogen biosynthetic process (GO:0045725)|positive regulation of glycolytic process (GO:0045821)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mitosis (GO:0045840)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of respiratory burst (GO:0060267)|protein autophosphorylation (GO:0046777)|protein heterotetramerization (GO:0051290)|regulation of embryonic development (GO:0045995)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction by phosphorylation (GO:0023014)|transformation of host cell by virus (GO:0019087)	caveola (GO:0005901)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|insulin receptor complex (GO:0005899)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|insulin binding (GO:0043559)|insulin receptor substrate binding (GO:0043560)|insulin-activated receptor activity (GO:0005009)|insulin-like growth factor I binding (GO:0031994)|insulin-like growth factor II binding (GO:0031995)|insulin-like growth factor receptor binding (GO:0005159)|phosphatidylinositol 3-kinase binding (GO:0043548)|protein tyrosine kinase activity (GO:0004713)|PTB domain binding (GO:0051425)|receptor signaling protein tyrosine kinase activity (GO:0004716)			breast(1)|central_nervous_system(4)|endometrium(6)|kidney(2)|large_intestine(13)|lung(25)|ovary(4)|prostate(4)|skin(3)|stomach(2)|urinary_tract(2)	66					"""""""Insulin(DB00071)|""""Insulin(DB08914)|Insulin Aspart(DB01306)|Insulin Detemir(DB01307)|Insulin Glargine(DB00047)|Insulin Glulisine(DB01309)|Insulin Lispro(DB00046)|Insulin Regular(DB00030)|Mecasermin(DB01277)"""	ACCAGTGCCTGAAGAGGTTTT	0.592																																					p.S748L		Atlas-SNP	.											.	INSR	265	.	0			c.C2243T						PASS	.	G	LEU/SER,	1,4405	2.1+/-5.4	0,1,2202	77.0	68.0	71.0		2243,	4.2	0.5	19	dbSNP_134	71	12,8588	9.1+/-34.3	0,12,4288	yes	missense,intron	INSR	NM_000208.2,NM_001079817.1	145,	0,13,6490	AA,AG,GG		0.1395,0.0227,0.1	benign,	748/1383,	7150532	13,12993	2203	4300	6503	SO:0001583	missense	3643	exon11			GTGCCTGAAGAGG	M10051	CCDS12176.1, CCDS42487.1	19p13.3-p13.2	2013-02-11				ENSG00000171105		"""CD molecules"", ""Fibronectin type III domain containing"""	6091	protein-coding gene	gene with protein product		147670				2983222	Standard	NM_000208		Approved	CD220	uc002mgd.1	P06213		ENST00000302850.5:c.2243C>T	19.37:g.7150532G>A	ENSP00000303830:p.Ser748Leu	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	51	21	0.411765	NM_000208	Q17RW0|Q59H98|Q9UCB7|Q9UCB8|Q9UCB9	Missense_Mutation	SNP	ENST00000302850.5	37	CCDS12176.1	.	.	.	.	.	.	.	.	.	.	G	5.384	0.256032	0.10185	2.27E-4	0.001395	ENSG00000171105	ENST00000302850	T	0.75704	-0.96	5.23	4.2	0.49525	Fibronectin, type III (2);	0.753844	0.10277	U	0.693994	T	0.63954	0.2555	L	0.34521	1.04	0.80722	D	1	B	0.02656	0.0	B	0.06405	0.002	T	0.54316	-0.8312	10	0.33940	T	0.23	.	9.578	0.39470	0.0959:0.0:0.9041:0.0	.	748	P06213	INSR_HUMAN	L	748	ENSP00000303830:S748L	ENSP00000303830:S748L	S	-	2	0	INSR	7101532	0.977000	0.34250	0.504000	0.27639	0.048000	0.14542	2.692000	0.47018	1.202000	0.43218	0.643000	0.83706	TCA	G|0.999;A|0.001	0.001	strong		0.592	INSR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458544.1		
HLA-C	3107	hgsc.bcm.edu	37	6	31238925	31238925	+	Missense_Mutation	SNP	C	C	T	rs141142418	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:31238925C>T	ENST00000376228.5	-	3	558	c.544G>A	c.(544-546)Gcc>Acc	p.A182T	HLA-C_ENST00000383329.3_Missense_Mutation_p.A182T	NM_002117.5	NP_002108.4	Q95604	1C17_HUMAN	major histocompatibility complex, class I, C	182	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						TCCAGGTAGGCTCTCAGCTGC	0.697																																					p.A182T		Atlas-SNP	.											.	HLA-C	92	.	0			c.G544A						PASS	.	C	THR/ALA	47,4349		0,47,2151	47.0	33.0	38.0		544	-2.6	0.0	6	dbSNP_134	38	265,8319		0,265,4027	no	missense	HLA-C	NM_002117.5	58	0,312,6178	TT,TC,CC		3.0871,1.0692,2.4037	possibly-damaging	182/367	31238925	312,12668	2198	4292	6490	SO:0001583	missense	3107	exon3			GGTAGGCTCTCAG	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.544G>A	6.37:g.31238925C>T	ENSP00000365402:p.Ala182Thr	Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	174	49	0.281609	NM_002117	O02864|O02958|Q29643|Q9MY30	Missense_Mutation	SNP	ENST00000376228.5	37	CCDS34393.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	12.87|12.87	2.068156|2.068156	0.36470|0.36470	0.010692|0.010692	0.030871|0.030871	ENSG00000204525|ENSG00000204525	ENST00000376228;ENST00000383329;ENST00000396254;ENST00000539307|ENST00000415537	T;T|.	0.00816|.	5.66;5.66|.	2.81|2.81	-2.58|-2.58	0.06228|0.06228	MHC class I, alpha chain, alpha1/alpha2 (2);MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);|.	1.179000|.	0.06837|.	U|.	0.795036|.	T|T	0.22044|0.22044	0.0531|0.0531	M|M	0.74881|0.74881	2.28|2.28	0.09310|0.09310	N|N	1|1	P;P;P;P|.	0.43938|.	0.822;0.684;0.713;0.822|.	P;B;B;B|.	0.46389|.	0.515;0.293;0.419;0.419|.	T|T	0.38222|0.38222	-0.9671|-0.9671	10|5	0.40728|.	T|.	0.16|.	.|.	0.9152|0.9152	0.01303|0.01303	0.1642:0.2513:0.162:0.4225|0.1642:0.2513:0.162:0.4225	.|.	182;182;182;182|.	A2AEA4;A6H578;A2AEA2;P10321|.	.;.;.;1C07_HUMAN|.	T|N	182;182;182;219|181	ENSP00000365402:A182T;ENSP00000372819:A182T|.	ENSP00000365402:A182T|.	A|S	-|-	1|2	0|0	HLA-C|HLA-C	31346904|31346904	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.004000|0.004000	0.04260|0.04260	-1.272000|-1.272000	0.02826|0.02826	-0.698000|-0.698000	0.05085|0.05085	0.305000|0.305000	0.20034|0.20034	GCC|AGC	C|0.971;T|0.029	0.029	strong		0.697	HLA-C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076281.3	NM_002117	
SH3BP4	23677	hgsc.bcm.edu	37	2	235949877	235949877	+	Missense_Mutation	SNP	T	T	C	rs3731644	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:235949877T>C	ENST00000409212.1	+	4	971	c.464T>C	c.(463-465)aTg>aCg	p.M155T	SH3BP4_ENST00000344528.4_Missense_Mutation_p.M155T|SH3BP4_ENST00000392011.2_Missense_Mutation_p.M155T			Q9P0V3	SH3B4_HUMAN	SH3-domain binding protein 4	155			M -> T (in dbSNP:rs3731644). {ECO:0000269|PubMed:16325581}.		cellular response to amino acid stimulus (GO:0071230)|endocytosis (GO:0006897)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of GTPase activity (GO:0034260)|negative regulation of TOR signaling (GO:0032007)|positive regulation of autophagy (GO:0010508)|protein localization to lysosome (GO:0061462)|regulation of catalytic activity (GO:0050790)	coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	GDP-dissociation inhibitor activity (GO:0005092)|identical protein binding (GO:0042802)|Ras GTPase binding (GO:0017016)	p.M155T(1)		central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(6)|lung(13)|ovary(4)|prostate(2)|skin(6)|stomach(3)|urinary_tract(2)	44		Breast(86;0.000332)|Renal(207;0.00339)|all_lung(227;0.00458)|all_hematologic(139;0.0296)|Lung NSC(271;0.0419)		Epithelial(121;7.66e-20)|BRCA - Breast invasive adenocarcinoma(100;0.000402)|Lung(119;0.00299)|LUSC - Lung squamous cell carcinoma(224;0.00645)|GBM - Glioblastoma multiforme(43;0.237)		CCAGGCAGAATGTACAGTAAT	0.507													C|||	1711	0.341653	0.4002	0.4092	5008	,	,		20531	0.4117		0.0964	False		,,,				2504	0.3947				p.M155T		Atlas-SNP	.											SH3BP4,NS,carcinoma,0,1	SH3BP4	109	1	1	Substitution - Missense(1)	stomach(1)	c.T464C						PASS	.	C	THR/MET	1622,2784	661.5+/-400.9	314,994,895	100.0	103.0	102.0		464	2.5	0.0	2	dbSNP_107	102	950,7650	775.6+/-407.7	49,852,3399	yes	missense	SH3BP4	NM_014521.2	81	363,1846,4294	CC,CT,TT		11.0465,36.8134,19.7755	benign	155/964	235949877	2572,10434	2203	4300	6503	SO:0001583	missense	23677	exon4			GCAGAATGTACAG	AF147747	CCDS2513.1	2q37.1-q37.2	2008-05-15			ENSG00000130147	ENSG00000130147			10826	protein-coding gene	gene with protein product		605611				10644451	Standard	NM_014521		Approved		uc002vvp.3	Q9P0V3	OTTHUMG00000133292	ENST00000409212.1:c.464T>C	2.37:g.235949877T>C	ENSP00000386862:p.Met155Thr	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	39	12	0.307692	NM_014521	O95082|Q309A3|Q53QD0|Q53TD1	Missense_Mutation	SNP	ENST00000409212.1	37	CCDS2513.1	660	0.3021978021978022	200	0.4065040650406504	130	0.35911602209944754	253	0.4423076923076923	77	0.10158311345646438	C	3.825	-0.036980	0.07497	0.368134	0.110465	ENSG00000130147	ENST00000392011;ENST00000420127;ENST00000409212;ENST00000344528;ENST00000446904	T;T;T;T	0.24350	3.06;3.06;3.06;1.86	5.35	2.53	0.30540	.	1.323390	0.04695	N	0.414885	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	0.46317	-0.9200	9	0.12103	T	0.63	-17.0704	3.1836	0.06593	0.1268:0.4588:0.2683:0.1461	rs3731644;rs52831227;rs61554763;rs3731644	155;155	A8K594;Q9P0V3	.;SH3B4_HUMAN	T	155	ENSP00000375867:M155T;ENSP00000386862:M155T;ENSP00000340237:M155T;ENSP00000415391:M155T	ENSP00000340237:M155T	M	+	2	0	SH3BP4	235614616	0.004000	0.15560	0.000000	0.03702	0.198000	0.23893	1.295000	0.33377	-0.001000	0.14495	-0.761000	0.03458	ATG	T|0.747;C|0.253	0.253	strong		0.507	SH3BP4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329763.1		
EXO1	9156	hgsc.bcm.edu	37	1	242035438	242035438	+	Missense_Mutation	SNP	G	G	A	rs4149965	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:242035438G>A	ENST00000366548.3	+	12	1965	c.1372G>A	c.(1372-1374)Gtg>Atg	p.V458M	EXO1_ENST00000348581.5_Missense_Mutation_p.V458M|EXO1_ENST00000518483.1_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	286	0	0		WXS	Illumina HiSeq	Phase_I	223	109	0.488789	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	
TEP1	7011	hgsc.bcm.edu	37	14	20850093	20850093	+	Missense_Mutation	SNP	C	C	T	rs1713456	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:20850093C>T	ENST00000262715.5	-	30	4443	c.4403G>A	c.(4402-4404)tGc>tAc	p.C1468Y	TEP1_ENST00000545983.1_5'UTR|TEP1_ENST00000556935.1_Missense_Mutation_p.C1360Y	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						PASS	.	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	80	0	0		WXS	Illumina HiSeq	Phase_I	94	48	0.510638	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	
PARL	55486	hgsc.bcm.edu	37	3	183551309	183551309	+	Silent	SNP	C	C	T	rs140027735		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:183551309C>T	ENST00000317096.4	-	9	1059	c.999G>A	c.(997-999)gcG>gcA	p.A333A	PARL_ENST00000435888.1_Silent_p.A249A|PARL_ENST00000311101.5_Silent_p.A283A	NM_018622.5	NP_061092.3	Q9H300	PARL_HUMAN	presenilin associated, rhomboid-like	333					membrane protein proteolysis (GO:0033619)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|negative regulation of release of cytochrome c from mitochondria (GO:0090201)|proteolysis (GO:0006508)|regulation of protein targeting to mitochondrion (GO:1903214)|regulation of reactive oxygen species metabolic process (GO:2000377)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	endopeptidase activity (GO:0004175)|serine-type endopeptidase activity (GO:0004252)			endometrium(2)|large_intestine(3)|liver(1)|lung(6)|prostate(1)|skin(1)|stomach(2)|urinary_tract(1)	17	all_cancers(143;6.55e-10)|Ovarian(172;0.0303)		all cancers(12;2.21e-41)|Epithelial(37;1.34e-36)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)			CAAGATGTGCCGCATGATCAA	0.488																																					p.A333A		Atlas-SNP	.											PARL,NS,carcinoma,-2,1	PARL	32	1	0			c.G999A						PASS	.						117.0	101.0	106.0					3																	183551309		2203	4300	6503	SO:0001819	synonymous_variant	55486	exon9			ATGTGCCGCATGA	AF116692	CCDS3248.1, CCDS33897.1	3q27.3	2008-02-05		2006-02-28	ENSG00000175193	ENSG00000175193			18253	protein-coding gene	gene with protein product	"""rhomboid 7 homolog 1 (Drosophila)"""	607858		PSARL			Standard	XM_005247587		Approved	PRO2207, PSARL1, RHBDS1	uc003fmd.3	Q9H300	OTTHUMG00000156890	ENST00000317096.4:c.999G>A	3.37:g.183551309C>T		Somatic	272	0	0		WXS	Illumina HiSeq	Phase_I	249	79	0.317269	NM_018622	Q96CQ4|Q9BTJ6|Q9P1E3	Silent	SNP	ENST00000317096.4	37	CCDS3248.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	9.958|9.958	1.222020|1.222020	0.22457|0.22457	.|.	.|.	ENSG00000175193|ENSG00000175193	ENST00000417784|ENST00000418450	.|.	.|.	.|.	5.63|5.63	0.535|0.535	0.17133|0.17133	.|.	.|.	.|.	.|.	.|.	T|T	0.42131|0.42131	0.1189|0.1189	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.24297|0.24297	-1.0164|-1.0164	4|4	.|.	.|.	.|.	-14.8538|-14.8538	1.496|1.496	0.02467|0.02467	0.1357:0.2209:0.1255:0.5179|0.1357:0.2209:0.1255:0.5179	.|.	.|.	.|.	.|.	S|Q	125|66	.|.	.|.	G|R	-|-	1|2	0|0	PARL|PARL	185034003|185034003	0.871000|0.871000	0.30034|0.30034	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	-0.009000|-0.009000	0.12765|0.12765	0.149000|0.149000	0.19098|0.19098	-0.238000|-0.238000	0.12139|0.12139	GGC|CGG	C|1.000;A|0.000	.	alt		0.488	PARL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346465.1	NM_018622	
SIPA1	6494	hgsc.bcm.edu	37	11	65408937	65408937	+	Missense_Mutation	SNP	C	C	T	rs3741378	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:65408937C>T	ENST00000394224.3	+	2	841	c.545C>T	c.(544-546)tCc>tTc	p.S182F	SIPA1_ENST00000534313.1_Missense_Mutation_p.S182F|SIPA1_ENST00000394227.3_Missense_Mutation_p.S182F|SIPA1_ENST00000527525.1_Missense_Mutation_p.S182F	NM_153253.29	NP_694985.29	Q96FS4	SIPA1_HUMAN	signal-induced proliferation-associated 1	182			S -> F (in dbSNP:rs3741378). {ECO:0000269|PubMed:9346962}.		cell proliferation (GO:0008283)|cellular response to water deprivation (GO:0042631)|cytoskeleton organization (GO:0007010)|intracellular signal transduction (GO:0035556)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell growth (GO:0030308)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Rap GTPase activity (GO:0032854)|signal transduction (GO:0007165)	cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|protein complex (GO:0043234)|transport vesicle (GO:0030133)	GTPase activator activity (GO:0005096)|Rap GTPase activator activity (GO:0046582)			cervix(1)|endometrium(2)|large_intestine(2)|lung(3)|prostate(1)|urinary_tract(1)	10						GGACCAGCATCCCCACCTGTG	0.677													C|||	1050	0.209665	0.3048	0.1412	5008	,	,		16826	0.3522		0.1312	False		,,,				2504	0.0634				p.S182F		Atlas-SNP	.											.	SIPA1	45	.	0			c.C545T						PASS	.	C	PHE/SER,PHE/SER	1167,3233	404.9+/-333.3	156,855,1189	50.0	52.0	51.0		545,545	2.7	0.1	11	dbSNP_107	51	1126,7468	231.1+/-265.2	78,970,3249	yes	missense,missense	SIPA1	NM_006747.3,NM_153253.29	155,155	234,1825,4438	TT,TC,CC		13.1022,26.5227,17.6466	possibly-damaging,possibly-damaging	182/1043,182/1043	65408937	2293,10701	2200	4297	6497	SO:0001583	missense	6494	exon2			CAGCATCCCCACC	AH006363, BC010492, BM677738	CCDS8108.1	11q13.3	2008-09-12	2008-09-12		ENSG00000213445	ENSG00000213445			10885	protein-coding gene	gene with protein product		602180				9027487	Standard	NM_006747		Approved	SPA1	uc001ofb.2	Q96FS4	OTTHUMG00000166541	ENST00000394224.3:c.545C>T	11.37:g.65408937C>T	ENSP00000377771:p.Ser182Phe	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	58	35	0.603448	NM_006747	O14518|O60484|O60618|Q2YD83	Missense_Mutation	SNP	ENST00000394224.3	37	CCDS8108.1	504	0.23076923076923078	158	0.32113821138211385	50	0.13812154696132597	201	0.3513986013986014	95	0.12532981530343007	C	11.84	1.758463	0.31137	0.265227	0.131022	ENSG00000213445	ENST00000534313;ENST00000527525;ENST00000394224;ENST00000394227	D;D;D;D	0.83250	-1.69;-1.7;-1.69;-1.7	4.78	2.65	0.31530	.	0.828298	0.10021	U	0.726013	T	0.00012	0.0000	L	0.55481	1.735	0.80722	P	0.0	B;B	0.31351	0.32;0.214	B;B	0.34931	0.192;0.094	T	0.04930	-1.0917	9	0.72032	D	0.01	-10.8171	12.2808	0.54762	0.0:0.6725:0.3275:0.0	rs3741378;rs3741378	182;182	F6RY50;Q96FS4	.;SIPA1_HUMAN	F	182	ENSP00000436269:S182F;ENSP00000433686:S182F;ENSP00000377771:S182F;ENSP00000377774:S182F	ENSP00000377771:S182F	S	+	2	0	SIPA1	65165513	0.004000	0.15560	0.104000	0.21259	0.212000	0.24457	1.961000	0.40432	1.071000	0.40834	0.555000	0.69702	TCC	C|0.800;T|0.200	0.200	strong		0.677	SIPA1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390356.1	NM_006747	
SLC16A7	9194	hgsc.bcm.edu	37	12	60168491	60168491	+	Missense_Mutation	SNP	T	T	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:60168491T>G	ENST00000261187.4	+	4	579	c.415T>G	c.(415-417)Ttc>Gtc	p.F139V	SLC16A7_ENST00000547379.1_Missense_Mutation_p.F139V|SLC16A7_ENST00000552432.1_Missense_Mutation_p.F139V|SLC16A7_ENST00000552024.1_Missense_Mutation_p.F139V|SLC16A7_ENST00000543448.1_Missense_Mutation_p.F40V	NM_004731.4	NP_004722.2	O60669	MOT2_HUMAN	solute carrier family 16 (monocarboxylate transporter), member 7	139					lactate transmembrane transport (GO:0035873)|pyruvate transmembrane transport (GO:1901475)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	lactate transmembrane transporter activity (GO:0015129)|pyruvate secondary active transmembrane transporter activity (GO:0005477)|pyruvate transmembrane transporter activity (GO:0050833)|secondary active monocarboxylate transmembrane transporter activity (GO:0015355)|symporter activity (GO:0015293)			endometrium(1)|large_intestine(14)|liver(2)|lung(11)|ovary(1)|skin(1)	30				GBM - Glioblastoma multiforme(3;0.0303)	Gamma Hydroxybutyric Acid(DB01440)|Niflumic Acid(DB04552)|Probenecid(DB01032)|Pyruvic acid(DB00119)	TGGCAAATACTTCTATAGGAA	0.398																																					p.F139V		Atlas-SNP	.											.	SLC16A7	82	.	0			c.T415G						PASS	.						77.0	73.0	74.0					12																	60168491		2203	4300	6503	SO:0001583	missense	9194	exon5			AAATACTTCTATA	AF049608	CCDS8961.1	12q14.1	2013-07-18	2013-07-18		ENSG00000118596	ENSG00000118596		"""Solute carriers"""	10928	protein-coding gene	gene with protein product		603654	"""solute carrier family 16 (monocarboxylic acid transporters), member 7"""			9786900	Standard	NM_004731		Approved	MCT2	uc001sqt.4	O60669	OTTHUMG00000169923	ENST00000261187.4:c.415T>G	12.37:g.60168491T>G	ENSP00000261187:p.Phe139Val	Somatic	257	0	0		WXS	Illumina HiSeq	Phase_I	209	44	0.210526	NM_001270622	Q8NEM3|Q9UPB3	Missense_Mutation	SNP	ENST00000261187.4	37	CCDS8961.1	.	.	.	.	.	.	.	.	.	.	T	25.0	4.592137	0.86953	.	.	ENSG00000118596	ENST00000552432;ENST00000547379;ENST00000552024;ENST00000548610;ENST00000261187;ENST00000543448;ENST00000548444	T;T;T;T;T;T;T	0.60299	0.2;0.2;0.2;0.2;0.2;0.2;0.2	5.87	5.87	0.94306	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.85682	D	0.000000	D	0.83087	0.5178	H	0.95745	3.715	0.80722	D	1	D	0.71674	0.998	D	0.74023	0.982	D	0.88302	0.2950	9	.	.	.	.	16.2631	0.82557	0.0:0.0:0.0:1.0	.	139	O60669	MOT2_HUMAN	V	139;139;139;139;139;40;24	ENSP00000449547:F139V;ENSP00000448071:F139V;ENSP00000448742:F139V;ENSP00000446722:F139V;ENSP00000261187:F139V;ENSP00000443731:F40V;ENSP00000447814:F24V	.	F	+	1	0	SLC16A7	58454758	1.000000	0.71417	1.000000	0.80357	0.837000	0.47467	8.040000	0.89188	2.239000	0.73571	0.528000	0.53228	TTC	.	.	none		0.398	SLC16A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406587.1	NM_004731	
MUC4	4585	hgsc.bcm.edu	37	3	195512531	195512531	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195512531C>T	ENST00000463781.3	-	2	6379	c.5920G>A	c.(5920-5922)Gct>Act	p.A1974T	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_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	63	1	0.015873		WXS	Illumina HiSeq	Phase_I	134	6	0.0447761	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	
FERMT1	55612	hgsc.bcm.edu	37	20	6069723	6069723	+	Silent	SNP	G	G	A	rs35413391	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:6069723G>A	ENST00000217289.4	-	10	1941	c.1153C>T	c.(1153-1155)Cta>Tta	p.L385L	FERMT1_ENST00000478194.1_5'UTR|FERMT1_ENST00000536936.1_Silent_p.L128L	NM_017671.4	NP_060141.3	Q9BQL6	FERM1_HUMAN	fermitin family member 1	385	FERM.|PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				cell adhesion (GO:0007155)|establishment of epithelial cell polarity (GO:0090162)|keratinocyte migration (GO:0051546)|keratinocyte proliferation (GO:0043616)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytosol (GO:0005829)|filamentous actin (GO:0031941)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)				NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|pancreas(1)|prostate(2)|skin(2)	17						GCTTTTGGTAGTAACTTCTTG	0.358													g|||	159	0.0317492	0.0038	0.0749	5008	,	,		18431	0.0		0.0825	False		,,,				2504	0.0194				p.L385L		Atlas-SNP	.											.	FERMT1	106	.	0			c.C1153T						PASS	.	G		65,4341	61.7+/-98.7	0,65,2138	113.0	121.0	118.0		1153	-4.5	0.1	20	dbSNP_126	118	658,7942	165.7+/-217.8	20,618,3662	yes	coding-synonymous	FERMT1	NM_017671.4		20,683,5800	AA,AG,GG		7.6512,1.4753,5.559		385/678	6069723	723,12283	2203	4300	6503	SO:0001819	synonymous_variant	55612	exon10			TTGGTAGTAACTT	AK000123	CCDS13098.1	20p12.3	2013-01-10	2010-06-24	2007-12-14	ENSG00000101311	ENSG00000101311		"""Fermitins"", ""Pleckstrin homology (PH) domain containing"""	15889	protein-coding gene	gene with protein product	"""kindlin-1"", ""kinderlin"""	607900	"""chromosome 20 open reading frame 42"", ""fermitin family homolog 1 (Drosophila)"""	C20orf42		12697302, 12789646	Standard	NM_017671		Approved	FLJ20116, URP1, KIND1, UNC112A	uc002wmr.3	Q9BQL6	OTTHUMG00000031826	ENST00000217289.4:c.1153C>T	20.37:g.6069723G>A		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	71	28	0.394366	NM_017671	D3DW10|Q8IX34|Q8IYH2|Q9NWM2|Q9NXQ3	Silent	SNP	ENST00000217289.4	37	CCDS13098.1																																																																																			G|0.949;A|0.051	0.051	strong		0.358	FERMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077908.2	NM_017671	
ANO1	55107	hgsc.bcm.edu	37	11	70007770	70007770	+	Missense_Mutation	SNP	T	T	C	rs2186797	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:70007770T>C	ENST00000355303.5	+	18	2128	c.1823T>C	c.(1822-1824)tTc>tCc	p.F608S	ANO1_ENST00000316296.5_Missense_Mutation_p.F550S|ANO1_ENST00000531349.1_Missense_Mutation_p.F317S|ANO1_ENST00000538023.1_Missense_Mutation_p.F608S|ANO1_ENST00000530676.1_Missense_Mutation_p.F462S|ANO1_ENST00000398543.2_Missense_Mutation_p.F462S	NM_018043.5	NP_060513.5	Q5XXA6	ANO1_HUMAN	anoctamin 1, calcium activated chloride channel	608			F -> S (in dbSNP:rs2186797).		cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|regulation of membrane potential (GO:0042391)|trachea development (GO:0060438)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|chloride channel complex (GO:0034707)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|intracellular calcium activated chloride channel activity (GO:0005229)			central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(12)|ovary(3)|pancreas(1)|upper_aerodigestive_tract(1)	29					Crofelemer(DB04941)	AGGCTGATCTTCAAGGCTTTC	0.537													T|||	101	0.0201677	0.003	0.0418	5008	,	,		20880	0.0		0.0636	False		,,,				2504	0.0041				p.F608S		Atlas-SNP	.											.	ANO1	156	.	0			c.T1823C						PASS	.	T	SER/PHE	59,3825		0,59,1883	189.0	196.0	194.0		1823	5.0	1.0	11	dbSNP_96	194	549,7727		24,501,3613	yes	missense	ANO1	NM_018043.5	155	24,560,5496	CC,CT,TT		6.6336,1.5191,5.0	possibly-damaging	608/987	70007770	608,11552	1942	4138	6080	SO:0001583	missense	55107	exon18			TGATCTTCAAGGC	BC033036	CCDS44663.1	11q13.2	2014-04-09	2008-08-28	2008-08-28	ENSG00000131620	ENSG00000131620		"""Ion channels / Chloride channels : Calcium activated : Anoctamins"""	21625	protein-coding gene	gene with protein product		610108	"""oral cancer overexpressed 2"", ""transmembrane protein 16A"""	ORAOV2, TMEM16A		15067359, 18724360, 24692353	Standard	NM_018043		Approved	TAOS2, FLJ10261, DOG1	uc001opj.3	Q5XXA6	OTTHUMG00000167204	ENST00000355303.5:c.1823T>C	11.37:g.70007770T>C	ENSP00000347454:p.Phe608Ser	Somatic	256	0	0		WXS	Illumina HiSeq	Phase_I	212	39	0.183962	NM_018043	A8KAM3|Q8IYY8|Q8N7V3	Missense_Mutation	SNP	ENST00000355303.5	37	CCDS44663.1	69	0.03159340659340659	2	0.0040650406504065045	16	0.04419889502762431	0	0.0	51	0.06728232189973615	T	18.84	3.709394	0.68615	0.015191	0.066336	ENSG00000131620	ENST00000355303;ENST00000538023;ENST00000398543;ENST00000546327;ENST00000316296;ENST00000530676;ENST00000531349	T;T;T;T;T;T	0.63096	-0.02;-0.02;-0.02;-0.02;-0.02;-0.02	5.01	5.01	0.66863	.	0.000000	0.85682	D	0.000000	T	0.17365	0.0417	M	0.74467	2.265	0.09310	P	0.999999884589	B;P;P	0.40731	0.205;0.515;0.728	B;B;P	0.48524	0.217;0.1;0.58	T	0.60566	-0.7238	8	.	.	.	.	14.7301	0.69374	0.0:0.0:0.0:1.0	rs2186797;rs17424050;rs60058467;rs2186797	317;550;608	E9PNA7;Q5XXA6-3;Q5XXA6	.;.;ANO1_HUMAN	S	608;608;462;366;550;462;317	ENSP00000347454:F608S;ENSP00000444689:F608S;ENSP00000381551:F462S;ENSP00000319477:F550S;ENSP00000435797:F462S;ENSP00000432843:F317S	.	F	+	2	0	ANO1	69685418	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.586000	0.82596	1.888000	0.54679	0.459000	0.35465	TTC	T|0.969;C|0.031	0.031	strong		0.537	ANO1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000393685.1	NM_018043	
TTC30A	92104	hgsc.bcm.edu	37	2	178482771	178482771	+	Missense_Mutation	SNP	C	C	T	rs59353759	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:178482771C>T	ENST00000355689.5	-	1	923	c.659G>A	c.(658-660)cGc>cAc	p.R220H	AC073834.3_ENST00000357045.4_RNA	NM_152275.3	NP_689488.3	Q86WT1	TT30A_HUMAN	tetratricopeptide repeat domain 30A	220					cilium assembly (GO:0042384)|intraciliary transport (GO:0042073)	cilium (GO:0005929)|intraciliary transport particle B (GO:0030992)				autonomic_ganglia(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(8)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	30			OV - Ovarian serous cystadenocarcinoma(117;0.000423)|Epithelial(96;0.00373)|all cancers(119;0.0169)			AGGATGCTGGCGGATGCCACG	0.542													C|||	171	0.0341454	0.0408	0.013	5008	,	,		21101	0.0109		0.0199	False		,,,				2504	0.0787				p.R220H		Atlas-SNP	.											.	TTC30A	60	.	0			c.G659A						PASS	.	C	HIS/ARG	184,4222	119.6+/-157.3	4,176,2023	71.0	70.0	70.0		659	5.8	1.0	2	dbSNP_129	70	154,8446	73.8+/-136.5	2,150,4148	no	missense	TTC30A	NM_152275.3	29	6,326,6171	TT,TC,CC		1.7907,4.1761,2.5988	benign	220/666	178482771	338,12668	2203	4300	6503	SO:0001583	missense	92104	exon1			TGCTGGCGGATGC	AK024008	CCDS2276.1	2q31.2	2013-01-11			ENSG00000197557	ENSG00000197557		"""Tetratricopeptide (TTC) repeat domain containing"""	25853	protein-coding gene	gene with protein product						12477932	Standard	NM_152275		Approved	FLJ13946	uc002ulo.3	Q86WT1	OTTHUMG00000132528	ENST00000355689.5:c.659G>A	2.37:g.178482771C>T	ENSP00000347915:p.Arg220His	Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	166	81	0.487952	NM_152275	A8K8N0|Q8IVP2	Missense_Mutation	SNP	ENST00000355689.5	37	CCDS2276.1	40	0.018315018315018316	14	0.028455284552845527	7	0.019337016574585635	5	0.008741258741258742	14	0.018469656992084433	C	11.45	1.642016	0.29157	0.041761	0.017907	ENSG00000197557	ENST00000355689	T	0.21543	2.0	5.78	5.78	0.91487	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.138754	0.64402	D	0.000006	T	0.05731	0.0150	M	0.71920	2.185	0.51482	D	0.99992	B	0.28512	0.214	B	0.21917	0.037	T	0.01626	-1.1309	10	0.59425	D	0.04	.	9.433	0.38622	0.0:0.8764:0.0:0.1236	rs59353759;rs61997200	220	Q86WT1	TT30A_HUMAN	H	220	ENSP00000347915:R220H	ENSP00000347915:R220H	R	-	2	0	TTC30A	178191017	1.000000	0.71417	1.000000	0.80357	0.692000	0.40212	2.932000	0.48940	2.755000	0.94549	0.549000	0.68633	CGC	C|0.974;T|0.026	0.026	strong		0.542	TTC30A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255728.2	NM_152275	
NKTR	4820	hgsc.bcm.edu	37	3	42679497	42679497	+	Silent	SNP	C	C	T	rs35890296	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:42679497C>T	ENST00000232978.8	+	13	2489	c.2301C>T	c.(2299-2301)agC>agT	p.S767S	RP4-613B23.1_ENST00000438017.1_RNA|RP4-613B23.1_ENST00000434363.1_RNA|RP4-613B23.1_ENST00000445452.1_RNA	NM_005385.3	NP_005376.2	P30414	NKTR_HUMAN	natural killer cell triggering receptor	767	Arg/Ser-rich.				protein folding (GO:0006457)	membrane (GO:0016020)	cyclosporin A binding (GO:0016018)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			breast(3)|central_nervous_system(1)|endometrium(7)|kidney(2)|large_intestine(6)|lung(10)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	41				KIRC - Kidney renal clear cell carcinoma(284;0.24)		AAAAAAATAGCGTTTCACATA	0.388													T|||	971	0.19389	0.32	0.0735	5008	,	,		20890	0.1101		0.1402	False		,,,				2504	0.2505				p.S767S		Atlas-SNP	.											.	NKTR	116	.	0			c.C2301T						PASS	.	T		1276,3130	698.4+/-406.3	182,912,1109	88.0	89.0	89.0		2301	-1.2	0.0	3	dbSNP_126	89	1061,7539	769.1+/-407.6	58,945,3297	no	coding-synonymous	NKTR	NM_005385.3		240,1857,4406	TT,TC,CC		12.3372,28.9605,17.9686		767/1463	42679497	2337,10669	2203	4300	6503	SO:0001819	synonymous_variant	4820	exon13			AAATAGCGTTTCA		CCDS2702.1	3p22.1	2014-01-20	2014-01-20		ENSG00000114857	ENSG00000114857			7833	protein-coding gene	gene with protein product	"""NK-tumor recognition protein"", ""natural-killer cells cyclophilin-related protein"", ""NK-TR protein"""	161565	"""natural killer-tumor recognition sequence"""			8314596, 8144875	Standard	XM_005265173		Approved	p104	uc003clo.3	P30414	OTTHUMG00000133037	ENST00000232978.8:c.2301C>T	3.37:g.42679497C>T		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	101	50	0.49505	NM_005385		Silent	SNP	ENST00000232978.8	37	CCDS2702.1																																																																																			C|0.823;T|0.177	0.177	strong		0.388	NKTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256642.2	NM_005385	
BOD1	91272	hgsc.bcm.edu	37	5	173036257	173036257	+	Silent	SNP	A	A	G	rs77014290	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:173036257A>G	ENST00000311086.4	-	3	766	c.543T>C	c.(541-543)tcT>tcC	p.S181S	BOD1_ENST00000285908.5_Intron|BOD1_ENST00000480951.1_Intron|BOD1_ENST00000471339.1_5'Flank	NM_138369.2	NP_612378.1	Q96IK1	BOD1_HUMAN	biorientation of chromosomes in cell division 1	181					mitotic nuclear division (GO:0007067)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|kinetochore (GO:0000776)		p.S181S(1)		endometrium(1)|large_intestine(2)|lung(2)|ovary(2)	7						AAGTGTCCTGAGATGGAGCTG	0.512																																					p.S181S		Atlas-SNP	.											BOD1,NS,carcinoma,0,1	BOD1	15	1	1	Substitution - coding silent(1)	lung(1)	c.T543C						scavenged	.						92.0	91.0	91.0					5																	173036257		2203	4300	6503	SO:0001819	synonymous_variant	91272	exon3			GTCCTGAGATGGA	AY303777	CCDS4389.1, CCDS54951.1	5q35.2	2013-10-11	2009-03-04	2009-03-04	ENSG00000145919	ENSG00000145919			25114	protein-coding gene	gene with protein product	"""biorientation defective 1"""		"""family with sequence similarity 44, member B"""	FAM44B		17938248	Standard	NM_138369		Approved		uc003mcq.2	Q96IK1	OTTHUMG00000130540	ENST00000311086.4:c.543T>C	5.37:g.173036257A>G		Somatic	146	1	0.00684932		WXS	Illumina HiSeq	Phase_I	197	17	0.0862944	NM_138369	B4DXH8|Q9BTW1	Silent	SNP	ENST00000311086.4	37	CCDS4389.1	.	.	.	.	.	.	.	.	.	.	A	10.16	1.274704	0.23307	.	.	ENSG00000145919	ENST00000477985	.	.	.	5.86	2.54	0.30619	.	0.220881	0.48767	D	0.000172	T	0.46580	0.1400	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.40701	-0.9549	6	0.39692	T	0.17	-11.0788	1.6489	0.02767	0.2536:0.1527:0.4384:0.1553	.	.	.	.	P	114	.	ENSP00000420005:S114P	S	-	1	0	BOD1	172968863	0.999000	0.42202	0.962000	0.40283	0.898000	0.52572	0.891000	0.28309	0.806000	0.34183	-0.177000	0.13119	TCA	A|0.981;G|0.019	0.019	strong		0.512	BOD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252963.1	NM_138369	
MTSS1	9788	hgsc.bcm.edu	37	8	125568485	125568485	+	Silent	SNP	C	C	T	rs145509745		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:125568485C>T	ENST00000518547.1	-	12	1865	c.1392G>A	c.(1390-1392)tcG>tcA	p.S464S	MTSS1_ENST00000378017.3_Silent_p.S439S|MTSS1_ENST00000395508.2_Silent_p.S238S|MTSS1_ENST00000325064.5_Silent_p.S468S|MTSS1_ENST00000431961.2_Silent_p.S182S|NDUFB9_ENST00000522532.1_Intron|MTSS1_ENST00000354184.4_Silent_p.S182S|MTSS1_ENST00000523587.1_5'UTR|MTSS1_ENST00000524090.1_Silent_p.S354S	NM_001282971.1|NM_014751.4	NP_001269900.1|NP_055566.3	O43312	MTSS1_HUMAN	metastasis suppressor 1	464					actin cytoskeleton organization (GO:0030036)|actin filament polymerization (GO:0030041)|adherens junction maintenance (GO:0034334)|bone mineralization (GO:0030282)|cell adhesion (GO:0007155)|cellular component movement (GO:0006928)|cellular response to fluid shear stress (GO:0071498)|epithelial cell proliferation involved in renal tubule morphogenesis (GO:2001013)|filopodium assembly (GO:0046847)|glomerulus morphogenesis (GO:0072102)|in utero embryonic development (GO:0001701)|magnesium ion homeostasis (GO:0010960)|microspike assembly (GO:0030035)|negative regulation of epithelial cell proliferation (GO:0050680)|nephron tubule epithelial cell differentiation (GO:0072160)|positive regulation of actin filament bundle assembly (GO:0032233)|renal tubule morphogenesis (GO:0061333)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	actin cytoskeleton (GO:0015629)|adherens junction (GO:0005912)|cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|ruffle (GO:0001726)	actin monomer binding (GO:0003785)|identical protein binding (GO:0042802)|receptor binding (GO:0005102)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(5)|lung(14)|ovary(1)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	37	Ovarian(258;0.00438)|all_neural(195;0.00459)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.00288)			TGGTGGCAGCCGATACAGTCA	0.642																																					p.S464S	Esophageal Squamous(160;622 1893 3862 8546 12509)	Atlas-SNP	.											.	MTSS1	79	.	0			c.G1392A						PASS	.	C		0,4406		0,0,2203	78.0	66.0	70.0		1392	-6.7	0.8	8	dbSNP_134	70	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	MTSS1	NM_014751.4		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		464/756	125568485	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	9788	exon12			GGCAGCCGATACA	AF086645	CCDS6353.1, CCDS64968.1, CCDS64969.1	8p22	2008-02-05			ENSG00000170873	ENSG00000170873			20443	protein-coding gene	gene with protein product		608486				12482861, 12082544	Standard	XM_005251111		Approved	KIAA0429, MIMA, MIMB, MIM	uc003yrk.2	O43312	OTTHUMG00000048189	ENST00000518547.1:c.1392G>A	8.37:g.125568485C>T		Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	131	68	0.519084	NM_014751	J3KNK6|Q8TCA2|Q96RX2	Silent	SNP	ENST00000518547.1	37	CCDS6353.1	.	.	.	.	.	.	.	.	.	.	C	8.528	0.870352	0.17322	0.0	1.16E-4	ENSG00000170873	ENST00000519168;ENST00000523179	.	.	.	4.65	-6.73	0.01749	.	.	.	.	.	T	0.37839	0.1018	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.39663	-0.9603	4	.	.	.	-9.0128	3.2915	0.06950	0.2562:0.1322:0.0856:0.526	.	.	.	.	S	252;247	.	.	G	-	1	0	MTSS1	125637666	0.000000	0.05858	0.803000	0.32268	0.967000	0.64934	-3.210000	0.00556	-1.401000	0.02058	-0.538000	0.04264	GGC	C|1.000;T|0.000	0.000	weak		0.642	MTSS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109625.3	NM_014751	
DDX60L	91351	hgsc.bcm.edu	37	4	169299528	169299528	+	Missense_Mutation	SNP	T	T	C	rs13110927	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:169299528T>C	ENST00000511577.1	-	33	4709	c.4462A>G	c.(4462-4464)Aat>Gat	p.N1488D	DDX60L_ENST00000260184.7_Missense_Mutation_p.N1488D			Q5H9U9	DDX6L_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60-like	1488				N -> D (in Ref. 1; AL832950). {ECO:0000305}.			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)		AAACTTAAATTAGCATTTTGG	0.303													T|||	2255	0.45028	0.202	0.5288	5008	,	,		14971	0.6339		0.498	False		,,,				2504	0.4918				p.N1488D		Atlas-SNP	.											.	DDX60L	116	.	0			c.A4462G						PASS	.	T	ASP/ASN	896,2662		126,644,1009	39.0	34.0	35.0		4462	-2.2	0.0	4	dbSNP_121	35	4073,3987		1074,1925,1031	yes	missense	DDX60L	NM_001012967.1	23	1200,2569,2040	CC,CT,TT		49.4665,25.1827,42.7698	benign	1488/1707	169299528	4969,6649	1779	4030	5809	SO:0001583	missense	91351	exon33			TTAAATTAGCATT	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.4462A>G	4.37:g.169299528T>C	ENSP00000422423:p.Asn1488Asp	Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	152	151	0.993421	NM_001012967	Q96ND6	Missense_Mutation	SNP	ENST00000511577.1	37		1036	0.47435897435897434	87	0.17682926829268292	193	0.5331491712707183	371	0.6486013986013986	385	0.5079155672823219	T	0.058	-1.232019	0.01505	0.251827	0.505335	ENSG00000181381	ENST00000260184;ENST00000511577	T;T	0.17213	2.29;2.29	3.14	-2.16	0.07080	.	.	.	.	.	T	0.00012	0.0000	L	0.44542	1.39	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.39683	-0.9602	8	0.13853	T	0.58	.	8.1605	0.31196	0.0:0.0922:0.4846:0.4232	rs13110927;rs17612081;rs52827582;rs60464051;rs13110927	1488	Q5H9U9	DDX6L_HUMAN	D	1488	ENSP00000260184:N1488D;ENSP00000422423:N1488D	ENSP00000260184:N1488D	N	-	1	0	DDX60L	169536103	0.000000	0.05858	0.000000	0.03702	0.062000	0.15995	-0.476000	0.06591	-1.279000	0.02405	-2.160000	0.00327	AAT	T|0.533;C|0.467	0.467	strong		0.303	DDX60L-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000364839.1	NM_001012967	
PCDHB11	56125	hgsc.bcm.edu	37	5	140579358	140579358	+	Missense_Mutation	SNP	A	A	G	rs3756323	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	65	0	0		WXS	Illumina HiSeq	Phase_I	44	20	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	
TRIM27	5987	hgsc.bcm.edu	37	6	28891176	28891176	+	Silent	SNP	T	T	C	rs2230683	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:28891176T>C	ENST00000377199.3	-	1	590	c.234A>G	c.(232-234)gtA>gtG	p.V78V	TRIM27_ENST00000377194.3_Silent_p.V78V|TRIM27_ENST00000498117.1_5'Flank	NM_006510.4	NP_006501.1	P14373	TRI27_HUMAN	tripartite motif containing 27	78					Arp2/3 complex-mediated actin nucleation (GO:0034314)|cell proliferation (GO:0008283)|innate immune response (GO:0045087)|interferon-gamma secretion (GO:0072643)|negative regulation of adaptive immune response (GO:0002820)|negative regulation of calcium ion import (GO:0090281)|negative regulation of gene expression, epigenetic (GO:0045814)|negative regulation of interleukin-2 secretion (GO:1900041)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of tumor necrosis factor production (GO:0032720)|negative regulation of viral release from host cell (GO:1902187)|negative regulation of viral transcription (GO:0032897)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein K63-linked ubiquitination (GO:0070534)|protein trimerization (GO:0070206)|retrograde transport, endosome to Golgi (GO:0042147)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ligase activity (GO:0016874)|metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(2)|lung(6)|ovary(1)	10						GCAGCTGCTTTACCAGTTGGG	0.687			T	RET	papillary thyroid								T|||	93	0.0185703	0.0045	0.0245	5008	,	,		13739	0.0		0.0696	False		,,,				2504	0.0				p.V78V		Atlas-SNP	.		Dom	yes		6	6p22	5987	tripartite motif-containing 27		E	.	TRIM27	26	.	0			c.A234G						PASS	.	T		101,4299		3,95,2102	27.0	27.0	27.0		234	2.3	1.0	6	dbSNP_98	27	769,7825		40,689,3568	no	coding-synonymous	TRIM27	NM_006510.4		43,784,5670	CC,CT,TT		8.9481,2.2955,6.6954		78/514	28891176	870,12124	2200	4297	6497	SO:0001819	synonymous_variant	5987	exon1			CTGCTTTACCAGT	Z58939	CCDS4654.1	6p22	2013-01-09	2011-01-25	2006-09-26	ENSG00000204713	ENSG00000204713		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	9975	protein-coding gene	gene with protein product		602165	"""ret finger protein"", ""tripartite motif-containing 27"""	RFP		8114113	Standard	NM_006510		Approved	RNF76	uc003nlr.3	P14373	OTTHUMG00000031215	ENST00000377199.3:c.234A>G	6.37:g.28891176T>C		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	45	19	0.422222	NM_006510	A2BE15|Q5RJA8|Q5ST26|Q6LA73|Q6NXR9|Q9BZY6|Q9UJL3	Silent	SNP	ENST00000377199.3	37	CCDS4654.1																																																																																			T|0.950;C|0.050	0.050	strong		0.687	TRIM27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076442.2	NM_030950	
NRCAM	4897	hgsc.bcm.edu	37	7	107849908	107849908	+	Silent	SNP	G	G	A	rs1269621	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:107849908G>A	ENST00000425651.2	-	9	1031	c.1032C>T	c.(1030-1032)aaC>aaT	p.N344N	NRCAM_ENST00000351718.4_Silent_p.N338N|NRCAM_ENST00000413765.2_Silent_p.N325N|NRCAM_ENST00000379022.4_Silent_p.N344N|NRCAM_ENST00000379024.4_Silent_p.N325N|NRCAM_ENST00000379028.3_Silent_p.N344N	NM_001037132.2	NP_001032209.1	Q92823	NRCAM_HUMAN	neuronal cell adhesion molecule	344	Ig-like 3.				angiogenesis (GO:0001525)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|axonogenesis (GO:0007409)|central nervous system development (GO:0007417)|clustering of voltage-gated sodium channels (GO:0045162)|heterotypic cell-cell adhesion (GO:0034113)|neuron migration (GO:0001764)|neuronal action potential propagation (GO:0019227)|positive regulation of neuron differentiation (GO:0045666)|protein localization (GO:0008104)|regulation of axon extension (GO:0030516)|retinal ganglion cell axon guidance (GO:0031290)|single organismal cell-cell adhesion (GO:0016337)|synapse assembly (GO:0007416)	axon initial segment (GO:0043194)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|synapse (GO:0045202)	ankyrin binding (GO:0030506)			breast(4)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(8)|liver(1)|lung(36)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(4)	65						CTCCTAATGCGTTTTTTGCTA	0.353													G|||	2929	0.584864	0.5408	0.6066	5008	,	,		17628	0.8155		0.508	False		,,,				2504	0.4703				p.N344N		Atlas-SNP	.											.	NRCAM	267	.	0			c.C1032T						PASS	.	G	,,,,	2411,1995	615.6+/-392.6	638,1135,430	164.0	157.0	159.0		1032,1032,975,975,1014	2.2	0.3	7	dbSNP_87	159	4368,4232	583.1+/-391.5	1127,2114,1059	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NRCAM	NM_001037132.2,NM_001193582.1,NM_001193583.1,NM_001193584.1,NM_005010.4	,,,,	1765,3249,1489	AA,AG,GG		49.2093,45.2792,47.8779	,,,,	344/1305,344/1212,325/1193,325/1181,338/1184	107849908	6779,6227	2203	4300	6503	SO:0001819	synonymous_variant	4897	exon9			TAATGCGTTTTTT		CCDS5751.1, CCDS47686.1, CCDS55153.1, CCDS75652.1	7q31	2013-02-11			ENSG00000091129	ENSG00000091129		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	7994	protein-coding gene	gene with protein product	"""NgCAM-related cell adhesion molecule"""	601581				8812479	Standard	NM_001037132		Approved	KIAA0343, Bravo	uc022aka.1	Q92823	OTTHUMG00000154973	ENST00000425651.2:c.1032C>T	7.37:g.107849908G>A		Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	108	106	0.981481	NM_001037132	A4D0S3|E9PDA4|O15051|O15179|Q14BM2|Q9UHI3|Q9UHI4	Silent	SNP	ENST00000425651.2	37	CCDS47686.1																																																																																			G|0.434;A|0.566	0.566	strong		0.353	NRCAM-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337942.2	NM_001037132	
TLN2	83660	hgsc.bcm.edu	37	15	63111778	63111778	+	Missense_Mutation	SNP	G	G	A	rs138463845	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:63111778G>A	ENST00000561311.1	+	52	7065	c.6835G>A	c.(6835-6837)Ggc>Agc	p.G2279S	TLN2_ENST00000306829.6_Missense_Mutation_p.G2279S			Q9Y4G6	TLN2_HUMAN	talin 2	2279					cell adhesion (GO:0007155)|cell-cell junction assembly (GO:0007043)|cytoskeletal anchoring at plasma membrane (GO:0007016)	actin cytoskeleton (GO:0015629)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|synapse (GO:0045202)	actin binding (GO:0003779)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			NS(3)|breast(6)|central_nervous_system(3)|endometrium(8)|kidney(8)|large_intestine(20)|lung(34)|ovary(6)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)	99						GCGAGTCGCCGGCGCTGTGAC	0.562													G|||	8	0.00159744	0.0008	0.0029	5008	,	,		18034	0.0		0.005	False		,,,				2504	0.0				p.G2279S		Atlas-SNP	.											TLN2,NS,carcinoma,-2,2	TLN2	253	2	0			c.G6835A						scavenged	.	G	SER/GLY	8,4398	14.3+/-33.2	0,8,2195	57.0	60.0	59.0		6835	4.5	0.0	15	dbSNP_134	59	64,8536	39.3+/-95.6	0,64,4236	yes	missense	TLN2	NM_015059.2	56	0,72,6431	AA,AG,GG		0.7442,0.1816,0.5536	benign	2279/2543	63111778	72,12934	2203	4300	6503	SO:0001583	missense	83660	exon50			GTCGCCGGCGCTG	AB002318	CCDS32261.1	15q15-q21	2008-07-03			ENSG00000171914	ENSG00000171914			15447	protein-coding gene	gene with protein product		607349				9205841, 11527381	Standard	NM_015059		Approved	KIAA0320, ILWEQ	uc002alb.4	Q9Y4G6	OTTHUMG00000133679	ENST00000561311.1:c.6835G>A	15.37:g.63111778G>A	ENSP00000453508:p.Gly2279Ser	Somatic	45	2	0.0444444		WXS	Illumina HiSeq	Phase_I	49	29	0.591837	NM_015059	A6NLB8	Missense_Mutation	SNP	ENST00000561311.1	37	CCDS32261.1	5	0.0022893772893772895	0	0.0	2	0.0055248618784530384	0	0.0	3	0.00395778364116095	G	4.821	0.152577	0.09185	0.001816	0.007442	ENSG00000171914	ENST00000306829	T	0.64803	-0.12	5.38	4.46	0.54185	.	0.218055	0.45361	D	0.000378	T	0.23806	0.0576	N	0.02916	-0.46	0.09310	N	0.999999	B	0.14438	0.01	B	0.06405	0.002	T	0.15009	-1.0452	10	0.05620	T	0.96	-15.6397	10.7611	0.46266	0.2001:0.0:0.7999:0.0	.	2279	Q9Y4G6	TLN2_HUMAN	S	2279	ENSP00000303476:G2279S	ENSP00000303476:G2279S	G	+	1	0	TLN2	60898831	0.994000	0.37717	0.029000	0.17559	0.423000	0.31445	4.826000	0.62715	1.270000	0.44297	0.561000	0.74099	GGC	G|0.995;A|0.005	0.005	strong		0.562	TLN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257878.2		
PRF1	5551	hgsc.bcm.edu	37	10	72360457	72360457	+	Missense_Mutation	SNP	G	G	A	rs151232299		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:72360457G>A	ENST00000441259.1	-	2	362	c.202C>T	c.(202-204)Cgg>Tgg	p.R68W	PRF1_ENST00000373209.2_Missense_Mutation_p.R68W	NM_001083116.1|NM_005041.4	NP_001076585.1|NP_005032.2	P14222	PERF_HUMAN	perforin 1 (pore forming protein)	68	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						CCGTCGGGCCGCAGGAACCTT	0.682			M			"""various leukaemia, lymphoma"""	Type 2 familial hemophagocytic lymphohistiocytosis		Familial Hemophagocytic Lymphohistiocytosis																												p.R68W		Atlas-SNP	.	yes	Rec			10	10q22	5551	perforin 1 (pore forming protein)		L	PRF1,right_upper_lobe,carcinoma,+2,1	PRF1	64	1	0			c.C202T						PASS	.	G	TRP/ARG,TRP/ARG	1,4405	2.1+/-5.4	0,1,2202	41.0	41.0	41.0		202,202	1.6	0.9	10	dbSNP_134	41	0,8600		0,0,4300	yes	missense,missense	PRF1	NM_001083116.1,NM_005041.4	101,101	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging,probably-damaging	68/556,68/556	72360457	1,13005	2203	4300	6503	SO:0001583	missense	5551	exon2	Familial Cancer Database	FHLH, FHL, Familial Hemophagocytic Reticulosis, FHR	CGGGCCGCAGGAA	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.202C>T	10.37:g.72360457G>A	ENSP00000398568:p.Arg68Trp	Somatic	252	0	0		WXS	Illumina HiSeq	Phase_I	239	91	0.380753	NM_001083116	B2R6X4|Q59F57|Q86WX7	Missense_Mutation	SNP	ENST00000441259.1	37	CCDS7305.1	.	.	.	.	.	.	.	.	.	.	G	16.75	3.210912	0.58343	2.27E-4	0.0	ENSG00000180644	ENST00000373209;ENST00000441259;ENST00000318971	D;D	0.91740	-2.9;-2.9	5.7	1.58	0.23477	Membrane attack complex component/perforin (MACPF) domain (1);	0.257519	0.37530	N	0.002057	D	0.93523	0.7933	M	0.83692	2.655	0.18873	N	0.999984	D	0.89917	1.0	P	0.61722	0.893	D	0.86042	0.1520	10	0.87932	D	0	-20.3888	1.6559	0.02782	0.161:0.1295:0.3914:0.3181	.	68	P14222	PERF_HUMAN	W	68	ENSP00000362305:R68W;ENSP00000398568:R68W	ENSP00000316746:R68W	R	-	1	2	PRF1	72030463	0.000000	0.05858	0.910000	0.35882	0.562000	0.35680	0.342000	0.19926	0.014000	0.14944	0.655000	0.94253	CGG	G|1.000;A|0.000	0.000	weak		0.682	PRF1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048517.2	NM_005041	
MPHOSPH10	10199	hgsc.bcm.edu	37	2	71360282	71360282	+	Missense_Mutation	SNP	G	G	A	rs13010513	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:71360282G>A	ENST00000244230.2	+	2	696	c.344G>A	c.(343-345)cGt>cAt	p.R115H	MCEE_ENST00000244217.5_5'Flank|MPHOSPH10_ENST00000468427.1_3'UTR|MPHOSPH10_ENST00000498451.2_Missense_Mutation_p.R115H	NM_005791.2	NP_005782.1	O00566	MPP10_HUMAN	M-phase phosphoprotein 10 (U3 small nucleolar ribonucleoprotein)	115			R -> H (in dbSNP:rs13010513).		negative regulation of phosphatase activity (GO:0010923)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)|rRNA processing (GO:0006364)	chromosome (GO:0005694)|nucleolus (GO:0005730)|small nucleolar ribonucleoprotein complex (GO:0005732)	poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(2)|pancreas(2)|skin(2)|stomach(1)	26						GAACAGGAACGTGAAGAGGAT	0.403													G|||	957	0.191094	0.1891	0.1729	5008	,	,		19641	0.2282		0.1342	False		,,,				2504	0.227				p.R115H		Atlas-SNP	.											.	MPHOSPH10	81	.	0			c.G344A						PASS	.	G	HIS/ARG	862,3544	335.2+/-303.8	83,696,1424	71.0	69.0	70.0		344	2.8	0.0	2	dbSNP_121	70	1450,7150	276.9+/-292.6	121,1208,2971	yes	missense	MPHOSPH10	NM_005791.2	29	204,1904,4395	AA,AG,GG		16.8605,19.5642,17.7764	benign	115/682	71360282	2312,10694	2203	4300	6503	SO:0001583	missense	10199	exon2			AGGAACGTGAAGA	X98494	CCDS1916.1	2p13.3	2014-06-12			ENSG00000124383	ENSG00000124383			7213	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 106"""	605503				8885239, 9450966	Standard	NM_005791		Approved	MPP10, MPP10P, CT90, PPP1R106	uc002sht.2	O00566	OTTHUMG00000129715	ENST00000244230.2:c.344G>A	2.37:g.71360282G>A	ENSP00000244230:p.Arg115His	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	108	59	0.546296	NM_005791	A0AVJ8	Missense_Mutation	SNP	ENST00000244230.2	37	CCDS1916.1	365	0.1671245421245421	95	0.19308943089430894	61	0.1685082872928177	103	0.18006993006993008	106	0.13984168865435356	G	5.476	0.272902	0.10349	0.195642	0.168605	ENSG00000124383	ENST00000244230	T	0.10288	2.89	4.61	2.81	0.32909	.	0.722586	0.14295	N	0.328668	T	0.00012	0.0000	N	0.14661	0.345	0.29172	P	0.877071	P;P	0.40250	0.709;0.455	B;B	0.28638	0.092;0.083	T	0.47302	-0.9128	9	0.45353	T	0.12	.	5.0267	0.14389	0.1887:0.1724:0.6389:0.0	rs13010513;rs52815322;rs13010513	115;115	B3KPV5;O00566	.;MPP10_HUMAN	H	115	ENSP00000244230:R115H	ENSP00000244230:R115H	R	+	2	0	MPHOSPH10	71213790	0.137000	0.22531	0.003000	0.11579	0.632000	0.37999	0.394000	0.20834	0.696000	0.31696	-0.228000	0.12330	CGT	G|0.825;A|0.175	0.175	strong		0.403	MPHOSPH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251924.2	NM_005791	
KCNQ1	3784	hgsc.bcm.edu	37	11	2869188	2869188	+	Silent	SNP	C	C	T	rs11601907	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:2869188C>T	ENST00000155840.5	+	16	2094	c.1986C>T	c.(1984-1986)taC>taT	p.Y662Y	KCNQ1_ENST00000335475.5_Silent_p.Y535Y|KCNQ1_ENST00000526095.1_3'UTR|KCNQ1-AS1_ENST00000440887.2_RNA	NM_000218.2	NP_000209.2	P51787	KCNQ1_HUMAN	potassium voltage-gated channel, KQT-like subfamily, member 1	662					atrial cardiac muscle cell action potential (GO:0086014)|cardiac muscle contraction (GO:0060048)|cardiovascular system development (GO:0072358)|cellular response to cAMP (GO:0071320)|cellular response to drug (GO:0035690)|cellular response to epinephrine stimulus (GO:0071872)|gene silencing (GO:0016458)|male gonad development (GO:0008584)|membrane repolarization during action potential (GO:0086011)|membrane repolarization during cardiac muscle cell action potential (GO:0086013)|negative regulation of insulin secretion (GO:0046676)|positive regulation of gastric acid secretion (GO:0060454)|positive regulation of potassium ion transmembrane transport (GO:1901381)|potassium ion export (GO:0071435)|potassium ion transmembrane transport (GO:0071805)|regulation of atrial cardiac muscle cell membrane repolarization (GO:0060372)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of heart contraction (GO:0008016)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of membrane repolarization (GO:0060306)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|sensory perception of sound (GO:0007605)|synaptic transmission (GO:0007268)|ventricular cardiac muscle cell action potential (GO:0086005)	basolateral plasma membrane (GO:0016323)|early endosome (GO:0005769)|late endosome (GO:0005770)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|voltage-gated potassium channel complex (GO:0008076)|zymogen granule membrane (GO:0042589)	calmodulin binding (GO:0005516)|delayed rectifier potassium channel activity (GO:0005251)|ion channel binding (GO:0044325)|outward rectifier potassium channel activity (GO:0015271)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|protein phosphatase 1 binding (GO:0008157)|scaffold protein binding (GO:0097110)|voltage-gated potassium channel activity (GO:0005249)|voltage-gated potassium channel activity involved in atrial cardiac muscle cell action potential repolarization (GO:0086089)|voltage-gated potassium channel activity involved in cardiac muscle cell action potential repolarization (GO:0086008)|voltage-gated potassium channel activity involved in ventricular cardiac muscle cell action potential repolarization (GO:1902282)			endometrium(1)|kidney(1)|large_intestine(2)|lung(9)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(2)	21		all_epithelial(84;3.26e-05)|Breast(177;0.001)|Medulloblastoma(188;0.00111)|Ovarian(85;0.00158)|all_neural(188;0.00725)|all_lung(207;0.11)|Lung NSC(207;0.159)		BRCA - Breast invasive adenocarcinoma(625;0.00251)|Lung(200;0.131)	Bepridil(DB01244)|Indapamide(DB00808)	TGCCCACCTACGAGCAGCTGA	0.716													C|||	417	0.0832668	0.0242	0.1081	5008	,	,		13923	0.0		0.2386	False		,,,				2504	0.0716				p.Y662Y		Atlas-SNP	.											.	KCNQ1	60	.	0			c.C1986T						PASS	.	C	,	241,4067		10,221,1923	10.0	10.0	10.0		1986,1605	-2.3	1.0	11	dbSNP_120	10	1984,6538		231,1522,2508	no	coding-synonymous,coding-synonymous	KCNQ1	NM_000218.2,NM_181798.1	,	241,1743,4431	TT,TC,CC		23.2809,5.5942,17.3422	,	662/677,535/550	2869188	2225,10605	2154	4261	6415	SO:0001819	synonymous_variant	3784	exon16			CACCTACGAGCAG	AF000571	CCDS7736.1	11p15.5	2014-09-17			ENSG00000053918	ENSG00000053918		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6294	protein-coding gene	gene with protein product	"""Jervell and Lange-Nielsen syndrome 1"""	607542		LQT, KCNA9		8528244, 16382104	Standard	NM_181798		Approved	Kv7.1, KCNA8, KVLQT1, JLNS1, LQT1	uc001lwn.3	P51787	OTTHUMG00000009900	ENST00000155840.5:c.1986C>T	11.37:g.2869188C>T		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	124	33	0.266129	NM_000218	O00347|O60607|O94787|Q14D14|Q7Z6G9|Q92960|Q9UMN8|Q9UMN9	Silent	SNP	ENST00000155840.5	37	CCDS7736.1																																																																																			C|0.892;T|0.108	0.108	strong		0.716	KCNQ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027382.2	NM_000218	
EDDM3A	10876	hgsc.bcm.edu	37	14	21215923	21215923	+	Missense_Mutation	SNP	G	G	T	rs34552133	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	178	0	0		WXS	Illumina HiSeq	Phase_I	146	74	0.506849	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		
BAI2	576	hgsc.bcm.edu	37	1	32221612	32221612	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:32221612C>T	ENST00000373658.3	-	4	1167	c.826G>A	c.(826-828)Gag>Aag	p.E276K	MIR4254_ENST00000581063.1_RNA|BAI2_ENST00000373655.2_Missense_Mutation_p.E276K|BAI2_ENST00000257070.4_Missense_Mutation_p.E276K|BAI2_ENST00000398556.3_Missense_Mutation_p.E279K|BAI2_ENST00000398547.1_Missense_Mutation_p.E264K|BAI2_ENST00000398538.1_Missense_Mutation_p.E264K|BAI2_ENST00000398542.1_Missense_Mutation_p.E264K|BAI2_ENST00000527361.1_Missense_Mutation_p.E276K	NM_001703.2	NP_001694.2	O60241	BAI2_HUMAN	brain-specific angiogenesis inhibitor 2	276					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)		TATCTCATCTCGGTTGTGAAC	0.642																																					p.E276K		Atlas-SNP	.											.	BAI2	128	.	0			c.G826A						PASS	.						61.0	65.0	64.0					1																	32221612		2203	4300	6503	SO:0001583	missense	576	exon4			TCATCTCGGTTGT	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.826G>A	1.37:g.32221612C>T	ENSP00000362762:p.Glu276Lys	Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	121	54	0.446281	NM_001703	B9EGK9|Q5T6K0|Q8NGW8|Q96GZ9	Missense_Mutation	SNP	ENST00000373658.3	37	CCDS346.2	.	.	.	.	.	.	.	.	.	.	C	11.52	1.662416	0.29515	.	.	ENSG00000121753	ENST00000398556;ENST00000398547;ENST00000373658;ENST00000373655;ENST00000398542;ENST00000257070;ENST00000527361;ENST00000398538;ENST00000420125;ENST00000533175	T;T;T;T;T;T;T;T;T;T	0.44083	1.61;1.81;0.99;0.99;1.97;0.93;0.93;1.01;1.59;1.45	5.33	5.33	0.75918	.	0.000000	0.42053	D	0.000761	T	0.30479	0.0766	N	0.22421	0.69	0.80722	D	1	B;B;B;B;B;B	0.24426	0.103;0.06;0.012;0.012;0.001;0.007	B;B;B;B;B;B	0.15052	0.01;0.012;0.001;0.006;0.0;0.0	T	0.04870	-1.0921	10	0.29301	T	0.29	.	16.3081	0.82856	0.0:1.0:0.0:0.0	.	264;276;264;264;276;276	A2A3C3;O60241-4;O60241-3;A2A3C1;O60241-2;O60241	.;.;.;.;.;BAI2_HUMAN	K	279;264;276;276;264;276;276;264;269;310	ENSP00000381564:E279K;ENSP00000381555:E264K;ENSP00000362762:E276K;ENSP00000362759:E276K;ENSP00000381550:E264K;ENSP00000257070:E276K;ENSP00000435397:E276K;ENSP00000381548:E264K;ENSP00000410921:E269K;ENSP00000437219:E310K	ENSP00000257070:E276K	E	-	1	0	BAI2	31994199	0.978000	0.34361	1.000000	0.80357	0.996000	0.88848	2.427000	0.44740	2.667000	0.90743	0.561000	0.74099	GAG	.	.	none		0.642	BAI2-015	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000381838.1	NM_001703	
STARD7	56910	hgsc.bcm.edu	37	2	96861159	96861159	+	Missense_Mutation	SNP	C	C	G	rs2276650	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:96861159C>G	ENST00000337288.5	-	2	802	c.419G>C	c.(418-420)cGt>cCt	p.R140P	STARD7_ENST00000462501.1_5'UTR	NM_020151.3	NP_064536.2	Q9NQZ5	STAR7_HUMAN	StAR-related lipid transfer (START) domain containing 7	140	START. {ECO:0000255|PROSITE- ProRule:PRU00197}.		R -> P (in dbSNP:rs2276650). {ECO:0000269|PubMed:15489334}.			mitochondrion (GO:0005739)	lipid binding (GO:0008289)	p.R65P(1)		endometrium(2)|kidney(1)|large_intestine(1)|lung(8)|stomach(2)	14						CATTTCCCAACGTTGCTCTTT	0.498													N|||	660	0.131789	0.0454	0.134	5008	,	,		19125	0.124		0.17	False		,,,				2504	0.2157				p.R140P		Atlas-SNP	.											STARD7,NS,carcinoma,0,1	STARD7	49	1	1	Substitution - Missense(1)	stomach(1)	c.G419C						PASS	.	G	PRO/ARG	294,4112	797.8+/-415.4	10,274,1919	151.0	116.0	128.0		419	4.7	0.0	2	dbSNP_100	128	1418,7182	746.9+/-407.3	122,1174,3004	yes	missense	STARD7	NM_020151.3	103	132,1448,4923	GG,GC,CC		16.4884,6.6727,13.1632	benign	140/371	96861159	1712,11294	2203	4300	6503	SO:0001583	missense	56910	exon2			TCCCAACGTTGCT	AF270647	CCDS2017.2	2p11.1	2011-09-12	2007-08-16		ENSG00000084090	ENSG00000084090		"""StAR-related lipid transfer (START) domain containing"""	18063	protein-coding gene	gene with protein product			"""START domain containing 7"""				Standard	NM_020151		Approved	GTT1	uc002svm.4	Q9NQZ5	OTTHUMG00000130457	ENST00000337288.5:c.419G>C	2.37:g.96861159C>G	ENSP00000338030:p.Arg140Pro	Somatic	228	0	0		WXS	Illumina HiSeq	Phase_I	213	111	0.521127	NM_020151	D3DXG9|Q53T44|Q6GU43|Q969M6	Missense_Mutation	SNP	ENST00000337288.5	37	CCDS2017.2	266	0.12179487179487179	21	0.042682926829268296	46	0.1270718232044199	66	0.11538461538461539	133	0.17546174142480211	G	0.772	-0.765499	0.02996	0.066727	0.164884	ENSG00000084090	ENST00000337288;ENST00000443962	T;T	0.03094	4.05;4.05	5.62	4.73	0.59995	Lipid-binding START (3);START-like domain (1);	0.264075	0.36972	N	0.002307	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	0.48502	-0.9030	9	0.17832	T	0.49	-4.41	9.4979	0.38999	0.0:0.2954:0.5518:0.1529	rs2276650;rs17419527;rs17845138;rs17856446;rs17857941;rs17858069;rs52838299;rs2276650	140	Q9NQZ5	STAR7_HUMAN	P	140;39	ENSP00000338030:R140P;ENSP00000409410:R39P	ENSP00000338030:R140P	R	-	2	0	STARD7	96224886	0.927000	0.31430	0.014000	0.15608	0.676000	0.39594	2.586000	0.46119	0.708000	0.31955	-0.120000	0.15030	CGT	C|0.878;G|0.122	0.122	strong		0.498	STARD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252848.2		
INSR	3643	hgsc.bcm.edu	37	19	7125519	7125519	+	Silent	SNP	G	G	A	rs1799815	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:7125519G>A	ENST00000302850.5	-	17	3175	c.3033C>T	c.(3031-3033)taC>taT	p.Y1011Y	INSR_ENST00000341500.5_Silent_p.Y999Y	NM_000208.2	NP_000199.2	P06213	INSR_HUMAN	insulin receptor	1011					activation of MAPK activity (GO:0000187)|activation of protein kinase activity (GO:0032147)|activation of protein kinase B activity (GO:0032148)|carbohydrate metabolic process (GO:0005975)|cellular response to growth factor stimulus (GO:0071363)|cellular response to insulin stimulus (GO:0032869)|epidermis development (GO:0008544)|exocrine pancreas development (GO:0031017)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|heart morphogenesis (GO:0003007)|insulin receptor signaling pathway (GO:0008286)|male sex determination (GO:0030238)|peptidyl-tyrosine autophosphorylation (GO:0038083)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of developmental growth (GO:0048639)|positive regulation of DNA replication (GO:0045740)|positive regulation of glucose import (GO:0046326)|positive regulation of glycogen biosynthetic process (GO:0045725)|positive regulation of glycolytic process (GO:0045821)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mitosis (GO:0045840)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of respiratory burst (GO:0060267)|protein autophosphorylation (GO:0046777)|protein heterotetramerization (GO:0051290)|regulation of embryonic development (GO:0045995)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction by phosphorylation (GO:0023014)|transformation of host cell by virus (GO:0019087)	caveola (GO:0005901)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|insulin receptor complex (GO:0005899)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|insulin binding (GO:0043559)|insulin receptor substrate binding (GO:0043560)|insulin-activated receptor activity (GO:0005009)|insulin-like growth factor I binding (GO:0031994)|insulin-like growth factor II binding (GO:0031995)|insulin-like growth factor receptor binding (GO:0005159)|phosphatidylinositol 3-kinase binding (GO:0043548)|protein tyrosine kinase activity (GO:0004713)|PTB domain binding (GO:0051425)|receptor signaling protein tyrosine kinase activity (GO:0004716)			breast(1)|central_nervous_system(4)|endometrium(6)|kidney(2)|large_intestine(13)|lung(25)|ovary(4)|prostate(4)|skin(3)|stomach(2)|urinary_tract(2)	66					"""""""Insulin(DB00071)|""""Insulin(DB08914)|Insulin Aspart(DB01306)|Insulin Detemir(DB01307)|Insulin Glargine(DB00047)|Insulin Glulisine(DB01309)|Insulin Lispro(DB00046)|Insulin Regular(DB00030)|Mecasermin(DB01277)"""	CGTCCGGCACGTACACAGAGC	0.572													G|||	83	0.0165735	0.0038	0.0231	5008	,	,		21903	0.0		0.0527	False		,,,				2504	0.0092				p.Y1011Y		Atlas-SNP	.											.	INSR	265	.	0			c.C3033T						PASS	.	G	,	61,4345	59.3+/-96.0	0,61,2142	84.0	70.0	74.0		3033,2997	-6.2	0.9	19	dbSNP_89	74	613,7987	161.0+/-214.0	21,571,3708	no	coding-synonymous,coding-synonymous	INSR	NM_000208.2,NM_001079817.1	,	21,632,5850	AA,AG,GG		7.1279,1.3845,5.1822	,	1011/1383,999/1371	7125519	674,12332	2203	4300	6503	SO:0001819	synonymous_variant	3643	exon17			CGGCACGTACACA	M10051	CCDS12176.1, CCDS42487.1	19p13.3-p13.2	2013-02-11				ENSG00000171105		"""CD molecules"", ""Fibronectin type III domain containing"""	6091	protein-coding gene	gene with protein product		147670				2983222	Standard	NM_000208		Approved	CD220	uc002mgd.1	P06213		ENST00000302850.5:c.3033C>T	19.37:g.7125519G>A		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	45	25	0.555556	NM_000208	Q17RW0|Q59H98|Q9UCB7|Q9UCB8|Q9UCB9	Silent	SNP	ENST00000302850.5	37	CCDS12176.1																																																																																			G|0.956;A|0.044	0.044	strong		0.572	INSR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458544.1		
MUC6	4588	hgsc.bcm.edu	37	11	1017974	1017974	+	Missense_Mutation	SNP	C	C	G	rs200353019		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:1017974C>G	ENST00000421673.2	-	31	4877	c.4827G>C	c.(4825-4827)caG>caC	p.Q1609H		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming	1609	Approximate repeats.|Pro-rich.|Thr-rich.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)	extracellular matrix structural constituent (GO:0005201)	p.Q1609H(2)		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)		GAAGTGTGGTCTGAGGGTGTG	0.547																																					p.Q1609H		Atlas-SNP	.											MUC6_ENST00000421673,colon,carcinoma,0,2	MUC6	408	2	2	Substitution - Missense(2)	large_intestine(2)	c.G4827C						scavenged	.						473.0	441.0	452.0					11																	1017974		2186	4282	6468	SO:0001583	missense	4588	exon31			TGTGGTCTGAGGG	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.4827G>C	11.37:g.1017974C>G	ENSP00000406861:p.Gln1609His	Somatic	357	11	0.0308123		WXS	Illumina HiSeq	Phase_I	440	34	0.0772727	NM_005961	O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	Missense_Mutation	SNP	ENST00000421673.2	37	CCDS44513.1	.	.	.	.	.	.	.	.	.	.	C	5.277	0.236564	0.10023	.	.	ENSG00000184956	ENST00000421673	T	0.35421	1.31	2.39	0.333	0.15943	.	.	.	.	.	T	0.26702	0.0653	L	0.52011	1.625	0.09310	N	1	B	0.25486	0.127	B	0.27715	0.082	T	0.28681	-1.0036	9	0.22109	T	0.4	.	3.4702	0.07565	0.0:0.5042:0.2173:0.2785	.	1609	Q6W4X9	MUC6_HUMAN	H	1609	ENSP00000406861:Q1609H	ENSP00000406861:Q1609H	Q	-	3	2	MUC6	1007974	0.000000	0.05858	0.003000	0.11579	0.027000	0.11550	-2.394000	0.01054	-0.057000	0.13199	-0.710000	0.03640	CAG	.	.	weak		0.547	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382120.2	XM_290540	
LPPR3	79948	hgsc.bcm.edu	37	19	814680	814680	+	Intron	SNP	G	G	T	rs56944467	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:814680G>T	ENST00000520876.3	-	6	736				LPPR3_ENST00000359894.2_Silent_p.A223A|MIR3187_ENST00000583431.1_RNA	NM_001270366.1	NP_001257295.1	Q6T4P5	LPPR3_HUMAN								integral component of membrane (GO:0016021)	phosphatidate phosphatase activity (GO:0008195)										GGCAGTGAGGGGCCGGACTCA	0.662													G|||	676	0.134984	0.0764	0.2565	5008	,	,		14874	0.0208		0.1312	False		,,,				2504	0.2495				p.A223A		Atlas-SNP	.											.	.	.	.	0			c.C669A						PASS	.	G		359,4033	179.7+/-208.2	15,329,1852	54.0	50.0	51.0		669	0.9	0.0	19	dbSNP_129	51	1094,7502	225.7+/-261.6	62,970,3266	no	coding-synonymous	LPPR3	NM_024888.1		77,1299,5118	TT,TG,GG		12.7268,8.174,11.1872		223/747	814680	1453,11535	2196	4298	6494	SO:0001627	intron_variant	0	exon6			GTGAGGGGCCGGA																												ENST00000520876.3:c.657+11C>A	19.37:g.814680G>T		Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	23	14	0.608696	NM_024888	Q86XQ4|Q96EH1|Q9BQF9|Q9HAJ4	Silent	SNP	ENST00000520876.3	37	CCDS58636.1																																																																																			G|0.886;T|0.114	0.114	strong		0.662	LPPR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379096.3		
GNAT2	2780	hgsc.bcm.edu	37	1	110148974	110148974	+	Silent	SNP	C	C	T	rs1799875	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:110148974C>T	ENST00000351050.3	-	5	732	c.546G>A	c.(544-546)acG>acA	p.T182T		NM_005272.3	NP_005263.1	P19087	GNAT2_HUMAN	guanine nucleotide binding protein (G protein), alpha transducing activity polypeptide 2	182					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|detection of light stimulus involved in visual perception (GO:0050908)|G-protein coupled receptor signaling pathway (GO:0007186)|phototransduction (GO:0007602)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|response to light intensity (GO:0009642)|retinal cone cell development (GO:0046549)|visual perception (GO:0007601)	heterotrimeric G-protein complex (GO:0005834)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|photoreceptor outer segment membrane (GO:0042622)|plasma membrane (GO:0005886)	G-protein beta/gamma-subunit complex binding (GO:0031683)|G-protein coupled photoreceptor activity (GO:0008020)|G-protein coupled receptor binding (GO:0001664)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(2)|prostate(1)|upper_aerodigestive_tract(1)	14		all_epithelial(167;2.5e-05)|all_lung(203;0.000135)|Lung NSC(277;0.000269)|Breast(1374;0.244)		Lung(183;0.0422)|Colorectal(144;0.108)|Epithelial(280;0.125)|all cancers(265;0.129)|LUSC - Lung squamous cell carcinoma(189;0.227)		CAATGATGCCCGTGGTTTTGA	0.458													C|||	1896	0.378594	0.056	0.5375	5008	,	,		21137	0.626		0.4602	False		,,,				2504	0.363				p.T182T		Atlas-SNP	.											.	GNAT2	31	.	0			c.G546A						PASS	.	C		495,3911	229.1+/-243.8	26,443,1734	152.0	139.0	143.0		546	-1.3	1.0	1	dbSNP_89	143	3805,4795	538.7+/-383.5	837,2131,1332	no	coding-synonymous	GNAT2	NM_005272.3		863,2574,3066	TT,TC,CC		44.2442,11.2347,33.0617		182/355	110148974	4300,8706	2203	4300	6503	SO:0001819	synonymous_variant	2780	exon5			GATGCCCGTGGTT	BC000233	CCDS803.1	1p13	2013-01-08			ENSG00000134183	ENSG00000134183			4394	protein-coding gene	gene with protein product		139340				8406495	Standard	NM_005272		Approved	ACHM4	uc001dya.3	P19087	OTTHUMG00000011639	ENST00000351050.3:c.546G>A	1.37:g.110148974C>T		Somatic	209	0	0		WXS	Illumina HiSeq	Phase_I	202	89	0.440594	NM_005272		Silent	SNP	ENST00000351050.3	37	CCDS803.1																																																																																			C|0.630;T|0.370	0.370	strong		0.458	GNAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032181.1	NM_005272	
BAG5	9529	hgsc.bcm.edu	37	14	104028270	104028270	+	Intron	SNP	T	T	C	rs7148456	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:104028270T>C	ENST00000445922.2	-	1	219				APOPT1_ENST00000556253.2_5'Flank|APOPT1_ENST00000247618.4_5'Flank|BAG5_ENST00000299204.4_Intron|BAG5_ENST00000337322.4_Silent_p.P25P|APOPT1_ENST00000409074.2_5'Flank|RP11-73M18.2_ENST00000472726.2_5'Flank|RP11-894P9.2_ENST00000556332.1_RNA	NM_004873.3	NP_004864.1	Q9UL15	BAG5_HUMAN	BCL2-associated athanogene 5						negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|negative regulation of protein refolding (GO:0061084)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of ubiquitin-protein transferase activity (GO:0051444)|neuron death (GO:0070997)|protein folding (GO:0006457)|regulation of inclusion body assembly (GO:0090083)	inclusion body (GO:0016234)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	chaperone binding (GO:0051087)|protein kinase binding (GO:0019901)|ubiquitin protein ligase binding (GO:0031625)			endometrium(5)|large_intestine(4)|lung(7)|ovary(2)|prostate(2)|skin(2)|urinary_tract(2)	24		Melanoma(154;0.155)	Epithelial(46;0.144)			GAGTCCACAATGGCCTAATGC	0.488													T|||	1282	0.25599	0.2322	0.3357	5008	,	,		20177	0.3502		0.2634	False		,,,				2504	0.1268				p.P25P	NSCLC(171;1832 2055 18950 31566 41632)	Atlas-SNP	.											.	BAG5	47	.	0			c.A75G						PASS	.	T	,,	883,2949		93,697,1126	106.0	106.0	106.0		,75,	-5.3	0.0	14	dbSNP_116	106	2215,6043		289,1637,2203	no	intron,coding-synonymous,intron	BAG5	NM_001015048.2,NM_001015049.2,NM_004873.3	,,	382,2334,3329	CC,CT,TT		26.8225,23.0428,25.6245	,,	,25/489,	104028270	3098,8992	1916	4129	6045	SO:0001627	intron_variant	9529	exon1			CCACAATGGCCTA	AF095195	CCDS9982.1, CCDS41995.1	14q32	2008-08-01				ENSG00000166170			941	protein-coding gene	gene with protein product		603885				9873016, 15603737	Standard	NM_001015048		Approved		uc001ynh.2	Q9UL15		ENST00000445922.2:c.27+166A>G	14.37:g.104028270T>C		Somatic	227	0	0		WXS	Illumina HiSeq	Phase_I	187	89	0.475936	NM_001015049	O94950|Q86W59	Silent	SNP	ENST00000445922.2	37	CCDS9982.1																																																																																			T|0.730;C|0.270	0.270	strong		0.488	BAG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414990.1		
AHNAK2	113146	hgsc.bcm.edu	37	14	105417396	105417396	+	Missense_Mutation	SNP	C	C	G	rs144323040	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:105417396C>G	ENST00000333244.5	-	7	4511	c.4392G>C	c.(4390-4392)gaG>gaC	p.E1464D	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	1464						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)			CTCCTGGGGCCTCGACATCCA	0.572													.|||	181	0.0361422	0.0023	0.0331	5008	,	,		12711	0.0228		0.0586	False		,,,				2504	0.0746				p.E1464D		Atlas-SNP	.											.	AHNAK2	719	.	0			c.G4392C						PASS	.	C	ASP/GLU	34,3766		7,20,1873	122.0	95.0	105.0		4392	2.3	0.0	14	dbSNP_134	105	418,5542		156,106,2718	no	missense	AHNAK2	NM_138420.2	45	163,126,4591	GG,GC,CC		7.0134,0.8947,4.6311	benign	1464/5796	105417396	452,9308	1900	2980	4880	SO:0001583	missense	113146	exon7			TGGGGCCTCGACA	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.4392G>C	14.37:g.105417396C>G	ENSP00000353114:p.Glu1464Asp	Somatic	0	0	.		WXS	Illumina HiSeq	Phase_I	75	74	0.986667	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	57	0.0260989010989011	1	0.0020325203252032522	11	0.03038674033149171	18	0.03146853146853147	27	0.03562005277044855	c	10.83	1.461863	0.26248	0.008947	0.070134	ENSG00000185567	ENST00000333244	T	0.00730	5.77	4.16	2.31	0.28768	.	.	.	.	.	T	0.00073	0.0002	N	0.11064	0.09	0.09310	N	1	B	0.23990	0.095	B	0.21917	0.037	T	0.49322	-0.8952	9	0.30854	T	0.27	-23.502	5.8092	0.18457	0.0:0.6082:0.1408:0.251	.	1464	Q8IVF2	AHNK2_HUMAN	D	1464	ENSP00000353114:E1464D	ENSP00000353114:E1464D	E	-	3	2	AHNAK2	104488441	0.000000	0.05858	0.009000	0.14445	0.035000	0.12851	-0.624000	0.05540	0.237000	0.21200	0.485000	0.47835	GAG	C|0.975;G|0.025	0.025	strong		0.572	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
ADAMTS18	170692	hgsc.bcm.edu	37	16	77328895	77328895	+	Silent	SNP	C	C	T	rs12935229	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:77328895C>T	ENST00000282849.5	-	19	3349	c.2931G>A	c.(2929-2931)gtG>gtA	p.V977V		NM_199355.2	NP_955387.1	Q8TE60	ATS18_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 18	977	TSP type-1 2. {ECO:0000255|PROSITE- ProRule:PRU00210}.				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						TGGGTGTGCTCACTGGACAGA	0.552													C|||	574	0.114617	0.0053	0.1873	5008	,	,		17738	0.1935		0.1262	False		,,,				2504	0.1176				p.V977V		Atlas-SNP	.											.	ADAMTS18	270	.	0			c.G2931A						PASS	.	C		95,4301	77.8+/-116.1	2,91,2105	147.0	91.0	110.0		2931	5.6	1.0	16	dbSNP_121	110	1124,7476	233.2+/-266.6	70,984,3246	no	coding-synonymous	ADAMTS18	NM_199355.2		72,1075,5351	TT,TC,CC		13.0698,2.1611,9.3798		977/1222	77328895	1219,11777	2198	4300	6498	SO:0001819	synonymous_variant	170692	exon19			TGTGCTCACTGGA	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.2931G>A	16.37:g.77328895C>T		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	196	89	0.454082	NM_199355	Q6P4R5|Q6ZWJ9	Silent	SNP	ENST00000282849.5	37	CCDS10926.1																																																																																			C|0.890;T|0.110	0.110	strong		0.552	ADAMTS18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269037.1		
CNTN2	6900	hgsc.bcm.edu	37	1	205031116	205031116	+	Missense_Mutation	SNP	C	C	T	rs2229866	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:205031116C>T	ENST00000331830.4	+	9	1381	c.1097C>T	c.(1096-1098)cCt>cTt	p.P366L	AL583832.1_ENST00000515887.1_RNA	NM_005076.3	NP_005067.1	Q02246	CNTN2_HUMAN	contactin 2 (axonal)	366	Ig-like C2-type 4.		P -> L (in dbSNP:rs2229866).		adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|cell adhesion (GO:0007155)|cellular protein localization (GO:0034613)|central nervous system myelination (GO:0022010)|cerebral cortex GABAergic interneuron migration (GO:0021853)|clustering of voltage-gated potassium channels (GO:0045163)|establishment of protein localization to juxtaparanode region of axon (GO:0071206)|learning (GO:0007612)|microtubule cytoskeleton organization (GO:0000226)|negative regulation of neuron differentiation (GO:0045665)|positive regulation of adenosine receptor signaling pathway (GO:0060168)|positive regulation of protein processing (GO:0010954)|presynaptic membrane organization (GO:0097090)|receptor internalization (GO:0031623)|regulation of astrocyte differentiation (GO:0048710)|regulation of axon diameter (GO:0031133)|regulation of neuronal synaptic plasticity (GO:0048168)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|juxtaparanode region of axon (GO:0044224)|myelin sheath (GO:0043209)|neuronal cell body (GO:0043025)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|synapse (GO:0045202)|voltage-gated potassium channel complex (GO:0008076)	carbohydrate binding (GO:0030246)|identical protein binding (GO:0042802)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(11)|lung(23)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	54	all_cancers(21;0.144)|Breast(84;0.0437)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.158)			AACGGGGAGCCTCTGGCCTCC	0.652											OREG0014144	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	2760	0.551118	0.323	0.5591	5008	,	,		15503	0.876		0.339	False		,,,				2504	0.7372				p.P366L	Melanoma(183;2548 2817 37099 41192)	Atlas-SNP	.											.	CNTN2	116	.	0			c.C1097T						PASS	.	C	LEU/PRO	1480,2924		251,978,973	16.0	18.0	17.0		1097	4.9	1.0	1	dbSNP_98	17	2953,5641		552,1849,1896	yes	missense	CNTN2	NM_005076.3	98	803,2827,2869	TT,TC,CC		34.3612,33.6058,34.1052	benign	366/1041	205031116	4433,8565	2202	4297	6499	SO:0001583	missense	6900	exon9			GGGAGCCTCTGGC	X67734	CCDS1449.1	1q32.1	2013-02-11			ENSG00000184144	ENSG00000184144		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	2172	protein-coding gene	gene with protein product		190197		TAX, AXT		8307567, 8586965	Standard	NM_005076		Approved	TAG-1, TAX1	uc001hbr.3	Q02246	OTTHUMG00000037105	ENST00000331830.4:c.1097C>T	1.37:g.205031116C>T	ENSP00000330633:p.Pro366Leu	Somatic	71	0	0	2149	WXS	Illumina HiSeq	Phase_I	65	34	0.523077	NM_005076	P78432|Q5T054	Missense_Mutation	SNP	ENST00000331830.4	37	CCDS1449.1	1085	0.4967948717948718	153	0.31097560975609756	182	0.5027624309392266	498	0.8706293706293706	252	0.3324538258575198	C	20.8	4.055142	0.75960	0.336058	0.343612	ENSG00000184144	ENST00000331830	T	0.68025	-0.3	4.94	4.94	0.65067	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.52532	D	0.000078	T	0.00012	0.0000	M	0.66560	2.04	0.09310	P	0.999999999241044	B;B	0.18610	0.029;0.013	B;B	0.18871	0.023;0.014	T	0.40289	-0.9571	9	0.62326	D	0.03	.	17.7437	0.88414	0.0:1.0:0.0:0.0	rs2229866;rs4951164	366;366	A1L3A3;Q02246	.;CNTN2_HUMAN	L	366	ENSP00000330633:P366L	ENSP00000330633:P366L	P	+	2	0	CNTN2	203297739	1.000000	0.71417	0.999000	0.59377	0.994000	0.84299	4.643000	0.61390	2.284000	0.76573	0.557000	0.71058	CCT	C|0.586;T|0.414	0.414	strong		0.652	CNTN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090080.3	NM_005076	
COL6A5	256076	hgsc.bcm.edu	37	3	130098349	130098349	+	Silent	SNP	G	G	A	rs16845861	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:130098349G>A	ENST00000432398.2	+	4	1250	c.756G>A	c.(754-756)agG>agA	p.R252R	COL6A5_ENST00000265379.6_Silent_p.R252R	NM_153264.5	NP_694996.5	A8TX70	CO6A5_HUMAN	collagen, type VI, alpha 5	252	Nonhelical region.|VWFA 2. {ECO:0000255|PROSITE- ProRule:PRU00219}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				endometrium(6)|kidney(4)|large_intestine(8)|lung(19)|pancreas(2)|prostate(3)|stomach(1)|urinary_tract(1)	44						GAAATTTAAGGCATCTTCAGA	0.468													G|||	1956	0.390575	0.4697	0.4553	5008	,	,		20494	0.5099		0.2008	False		,,,				2504	0.3098				p.R252R		Atlas-SNP	.											COL6A5,colon,carcinoma,+1,1	COL6A5	205	1	0			c.G756A						PASS	.	G		583,801		114,355,223	95.0	85.0	88.0		756	4.2	0.0	3	dbSNP_123	88	696,2486		84,528,979	no	coding-synonymous	COL6A5	NM_153264.5		198,883,1202	AA,AG,GG		21.873,42.1243,28.0114		252/2527	130098349	1279,3287	692	1591	2283	SO:0001819	synonymous_variant	256076	exon4			TTTAAGGCATCTT	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.756G>A	3.37:g.130098349G>A		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	119	61	0.512605	NM_153264	A9J6L2|A9J6L4|A9J6L6|A9J6L7|A9J6M0|A9J6M1|A9J6M2|B5MEA7|Q6ZW26|Q8NA36	Silent	SNP	ENST00000432398.2	37																																																																																				G|0.632;A|0.368	0.368	strong		0.468	COL6A5-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_153264	
DYNC2H1	79659	hgsc.bcm.edu	37	11	102980324	102980324	+	Silent	SNP	C	C	T	rs17301028	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:102980324C>T	ENST00000375735.2	+	1	165	c.21C>T	c.(19-21)gaC>gaT	p.D7D	DYNC2H1_ENST00000398093.3_Silent_p.D7D|DYNC2H1_ENST00000334267.7_Silent_p.D7D	NM_001080463.1|NM_001377.2	NP_001073932.1|NP_001368.2	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1	7	Stem. {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)		GGACTGCGGACGTTCGGAAGC	0.522													C|||	206	0.0411342	0.003	0.0476	5008	,	,		19324	0.001		0.0795	False		,,,				2504	0.09				p.D7D		Atlas-SNP	.											.	DYNC2H1	246	.	0			c.C21T						PASS	.	C	,	71,3673		1,69,1802	51.0	48.0	49.0		21,21	1.7	0.2	11	dbSNP_123	49	788,7422		41,706,3358	no	coding-synonymous,coding-synonymous	DYNC2H1	NM_001080463.1,NM_001377.2	,	42,775,5160	TT,TC,CC		9.5981,1.8964,7.1859	,	7/4315,7/4308	102980324	859,11095	1872	4105	5977	SO:0001819	synonymous_variant	79659	exon1			TGCGGACGTTCGG	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.21C>T	11.37:g.102980324C>T		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	72	55	0.763889	NM_001377	O00432|Q16693|Q3C1U8|Q4AC93|Q6ZMX7|Q6ZUM6|Q7Z363|Q8N977|Q92815|Q9HAE4	Silent	SNP	ENST00000375735.2	37	CCDS53701.1																																																																																			C|0.950;T|0.050	0.050	strong		0.522	DYNC2H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387196.1	XM_370652	
CFAP44	55779	hgsc.bcm.edu	37	3	113146130	113146130	+	Missense_Mutation	SNP	T	T	C	rs386664769|rs59722850	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:113146130T>C	ENST00000295868.2	-	3	319	c.157A>G	c.(157-159)Aaa>Gaa	p.K53E	WDR52-AS1_ENST00000498480.1_RNA|WDR52_ENST00000393845.2_Missense_Mutation_p.K53E|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						CCTTCCCCTTTGGTAAATGTT	0.323													C|||	1365	0.272564	0.0734	0.268	5008	,	,		18333	0.5129		0.2555	False		,,,				2504	0.3149				p.K53E		Atlas-SNP	.											.	WDR52	151	.	0			c.A157G						PASS	.	C	GLU/LYS,GLU/LYS	514,3892	777.6+/-414.2	38,438,1727	161.0	140.0	147.0		157,157	3.5	0.5	3	dbSNP_129	147	1974,6626	722.6+/-406.4	233,1508,2559	yes	missense,missense	WDR52	NM_001164496.1,NM_018338.3	56,56	271,1946,4286	CC,CT,TT		22.9535,11.6659,19.1296	benign,benign	53/1855,53/983	113146130	2488,10518	2203	4300	6503	SO:0001583	missense	55779	exon3			CCCCTTTGGTAAA																												ENST00000295868.2:c.157A>G	3.37:g.113146130T>C	ENSP00000295868:p.Lys53Glu	Somatic	248	0	0		WXS	Illumina HiSeq	Phase_I	221	116	0.524887	NM_001164496		Missense_Mutation	SNP	ENST00000295868.2	37	CCDS2972.1	600	0.27472527472527475	38	0.07723577235772358	82	0.2265193370165746	288	0.5034965034965035	192	0.2532981530343008	C	1.365	-0.587740	0.03799	0.116659	0.229535	ENSG00000206530	ENST00000393845;ENST00000295868;ENST00000473143	T;T;T	0.44482	2.98;1.07;0.92	4.43	3.53	0.40419	.	.	.	.	.	T	0.00012	0.0000	N	0.01352	-0.895	0.21220	P	0.999758682	B	0.02656	0.0	B	0.01281	0.0	T	0.47182	-0.9137	8	0.02654	T	1	.	6.2418	0.20795	0.0:0.7138:0.1866:0.0996	rs59722850	53	Q96MT7	WDR52_HUMAN	E	53	ENSP00000377428:K53E;ENSP00000295868:K53E;ENSP00000419671:K53E	ENSP00000295868:K53E	K	-	1	0	WDR52	114628820	0.618000	0.27051	0.548000	0.28192	0.006000	0.05464	1.006000	0.29847	0.771000	0.33359	-0.128000	0.14901	AAA	T|0.784;C|0.216	0.216	strong		0.323	WDR52-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000354128.3		
NOXO1	124056	hgsc.bcm.edu	37	16	2030127	2030127	+	Missense_Mutation	SNP	G	G	A	rs61729118	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:2030127G>A	ENST00000397280.4	-	5	475	c.472C>T	c.(472-474)Ctc>Ttc	p.L158F	TBL3_ENST00000568546.1_3'UTR|NOXO1_ENST00000354249.4_Missense_Mutation_p.L152F|NOXO1_ENST00000356120.4_Missense_Mutation_p.L153F|AC005606.1_ENST00000598236.1_5'Flank|NOXO1_ENST00000566005.1_Missense_Mutation_p.L157F			Q8NFA2	NOXO1_HUMAN	NADPH oxidase organizer 1	158					extracellular matrix disassembly (GO:0022617)|regulation of hydrogen peroxide metabolic process (GO:0010310)|regulation of respiratory burst (GO:0060263)|superoxide metabolic process (GO:0006801)	NADPH oxidase complex (GO:0043020)	enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|phosphatidylinositol binding (GO:0035091)|phospholipid binding (GO:0005543)|superoxide-generating NADPH oxidase activator activity (GO:0016176)			lung(2)	2					Ecabet(DB05265)	TGGATGGAGAGGCGGCCCGCA	0.672													G|||	537	0.107228	0.003	0.1816	5008	,	,		15896	0.0357		0.1183	False		,,,				2504	0.2577				p.L158F	Pancreas(104;2811 2841 4129)|Esophageal Squamous(25;910 1225 43728)	Atlas-SNP	.											.	NOXO1	13	.	0			c.C472T						PASS	.	G	PHE/LEU,PHE/LEU,PHE/LEU	106,4280		3,100,2090	14.0	20.0	18.0		454,457,472	3.1	0.0	16	dbSNP_129	18	956,7624		56,844,3390	yes	missense,missense,missense	NOXO1	NM_144603.2,NM_172167.1,NM_172168.1	22,22,22	59,944,5480	AA,AG,GG		11.1422,2.4168,8.1907	possibly-damaging,possibly-damaging,possibly-damaging	152/371,153/372,158/377	2030127	1062,11904	2193	4290	6483	SO:0001583	missense	124056	exon5			TGGAGAGGCGGCC	AF532985	CCDS10454.1, CCDS10455.1, CCDS42101.1, CCDS58406.1	16p13.3	2008-02-05			ENSG00000196408	ENSG00000196408			19404	protein-coding gene	gene with protein product		611256					Standard	NM_144603		Approved	P41NOXA, P41NOXB, P41NOXC, SH3PXD5, SNX28	uc002cnx.4	Q8NFA2	OTTHUMG00000128707	ENST00000397280.4:c.472C>T	16.37:g.2030127G>A	ENSP00000380450:p.Leu158Phe	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	89	76	0.853933	NM_172168	Q86YM1|Q8NFA3|Q96B73	Missense_Mutation	SNP	ENST00000397280.4	37	CCDS42101.1	153	0.07005494505494506	5	0.01016260162601626	47	0.1298342541436464	19	0.033216783216783216	82	0.10817941952506596	G	16.98	3.272639	0.59649	0.024168	0.111422	ENSG00000196408	ENST00000354249;ENST00000356120;ENST00000397280	T;T;T	0.70631	-0.5;-0.5;-0.49	4.06	3.09	0.35607	Src homology-3 domain (1);	0.597434	0.18323	N	0.144731	T	0.01940	0.0061	M	0.63428	1.95	0.09310	P	0.9999969323	D;D;D;D	0.63880	0.993;0.993;0.993;0.988	P;P;P;P	0.49953	0.627;0.627;0.627;0.563	T	0.49133	-0.8971	9	0.56958	D	0.05	-2.9127	11.4727	0.50280	0.0914:0.0:0.9086:0.0	.	157;152;153;158	Q8NFA2-2;Q8NFA2-4;Q8NFA2-3;Q8NFA2	.;.;.;NOXO1_HUMAN	F	152;153;158	ENSP00000346195:L152F;ENSP00000348435:L153F;ENSP00000380450:L158F	ENSP00000346195:L152F	L	-	1	0	NOXO1	1970128	0.097000	0.21791	0.023000	0.16930	0.674000	0.39518	0.958000	0.29227	0.998000	0.38996	0.462000	0.41574	CTC	G|0.928;A|0.072	0.072	strong		0.672	NOXO1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250612.1		
ADAMTSL3	57188	hgsc.bcm.edu	37	15	84539619	84539619	+	Missense_Mutation	SNP	C	C	G	rs4144691	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:84539619C>G	ENST00000286744.5	+	9	1092	c.868C>G	c.(868-870)Ctc>Gtc	p.L290V	ADAMTSL3_ENST00000567476.1_Missense_Mutation_p.L290V	NM_207517.2	NP_997400.2	P82987	ATL3_HUMAN	ADAMTS-like 3	290			L -> V (in dbSNP:rs4144691). {ECO:0000269|PubMed:14667842}.			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)			CGGCGTCTTTCTCGTAGAAAA	0.388													G|||	4044	0.807508	0.9629	0.9078	5008	,	,		15806	0.7232		0.7833	False		,,,				2504	0.638				p.L290V		Atlas-SNP	.											.	ADAMTSL3	290	.	0			c.C868G						PASS	.	G	VAL/LEU	4133,273	150.7+/-184.7	1945,243,15	62.0	68.0	66.0		868	1.7	0.0	15	dbSNP_110	66	6900,1700	308.6+/-309.0	2754,1392,154	yes	missense	ADAMTSL3	NM_207517.2	32	4699,1635,169	GG,GC,CC		19.7674,6.1961,15.1699	benign	290/1692	84539619	11033,1973	2203	4300	6503	SO:0001583	missense	57188	exon9			GTCTTTCTCGTAG	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.868C>G	15.37:g.84539619C>G	ENSP00000286744:p.Leu290Val	Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	29	29	1	NM_207517	A1A566|A1A567|Q9ULI7	Missense_Mutation	SNP	ENST00000286744.5	37	CCDS10326.1	1787	0.8182234432234432	467	0.9491869918699187	320	0.8839779005524862	414	0.7237762237762237	586	0.7730870712401056	G	0	-2.816932	0.00072	0.938039	0.802326	ENSG00000156218	ENST00000286744	T	0.63744	-0.06	4.69	1.68	0.24146	.	1.092520	0.07042	N	0.830385	T	0.00012	0.0000	N	0.05414	-0.055	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.39623	-0.9605	9	0.02654	T	1	.	5.542	0.17043	0.3257:0.1359:0.5384:0.0	rs4144691;rs17841183;rs52823048;rs59718593;rs4144691	290;290	P82987-2;P82987	.;ATL3_HUMAN	V	290	ENSP00000286744:L290V	ENSP00000286744:L290V	L	+	1	0	ADAMTSL3	82330623	0.998000	0.40836	0.002000	0.10522	0.021000	0.10359	1.054000	0.30455	-0.175000	0.10725	-0.357000	0.07601	CTC	C|0.164;G|0.836	0.836	strong		0.388	ADAMTSL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304007.2	NM_207517	
PRKAR2B	5577	hgsc.bcm.edu	37	7	106799997	106799997	+	Silent	SNP	G	G	A	rs257376	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:106799997G>A	ENST00000265717.4	+	11	1486	c.1227G>A	c.(1225-1227)acG>acA	p.T409T		NM_002736.2	NP_002727.2	P31323	KAP3_HUMAN	protein kinase, cAMP-dependent, regulatory, type II, beta	409					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|blood coagulation (GO:0007596)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fatty acid metabolic process (GO:0006631)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G2/M transition of mitotic cell cycle (GO:0000086)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|learning (GO:0007612)|mitotic cell cycle (GO:0000278)|negative regulation of cAMP-dependent protein kinase activity (GO:2000480)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cAMP-dependent protein kinase complex (GO:0005952)|centrosome (GO:0005813)|ciliary base (GO:0097546)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	cAMP binding (GO:0030552)|cAMP-dependent protein kinase inhibitor activity (GO:0004862)|cAMP-dependent protein kinase regulator activity (GO:0008603)|protein kinase A catalytic subunit binding (GO:0034236)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|kidney(2)|large_intestine(5)|lung(5)|ovary(1)	14						TGTTTGGAACGAACATGGATA	0.418													A|||	2352	0.469649	0.5083	0.4597	5008	,	,		16877	0.4514		0.5408	False		,,,				2504	0.3701				p.T409T		Atlas-SNP	.											.	PRKAR2B	34	.	0			c.G1227A						PASS	.	A		2197,2209	590.7+/-387.4	544,1109,550	146.0	127.0	133.0		1227	-0.9	1.0	7	dbSNP_79	133	4627,3973	553.1+/-386.2	1253,2121,926	yes	coding-synonymous	PRKAR2B	NM_002736.2		1797,3230,1476	AA,AG,GG		46.1977,49.8638,47.5319		409/419	106799997	6824,6182	2203	4300	6503	SO:0001819	synonymous_variant	5577	exon11			TGGAACGAACATG		CCDS5740.1	7q22.3	2010-04-22			ENSG00000005249	ENSG00000005249	2.7.11.1		9392	protein-coding gene	gene with protein product		176912		PRKAR2		1358799	Standard	NM_002736		Approved		uc003vdx.3	P31323	OTTHUMG00000137418	ENST00000265717.4:c.1227G>A	7.37:g.106799997G>A		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	82	38	0.463415	NM_002736	A4D0R9	Silent	SNP	ENST00000265717.4	37	CCDS5740.1																																																																																			G|0.497;A|0.503	0.503	strong		0.418	PRKAR2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268386.1		
MAP1A	4130	hgsc.bcm.edu	37	15	43818052	43818052	+	Missense_Mutation	SNP	G	G	A	rs2245715	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:43818052G>A	ENST00000300231.5	+	4	4831	c.4381G>A	c.(4381-4383)Gat>Aat	p.D1461N	MAP1A_ENST00000399453.1_Missense_Mutation_p.D1461N|MAP1A_ENST00000382031.1_Missense_Mutation_p.D1699N			P78559	MAP1A_HUMAN	microtubule-associated protein 1A	1461			D -> N (in dbSNP:rs2245715).		microtubule cytoskeleton organization (GO:0000226)|sensory perception of sound (GO:0007605)	cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)	structural molecule activity (GO:0005198)			breast(5)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(11)|liver(2)|lung(19)|ovary(5)|pancreas(3)|prostate(2)|skin(6)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	66		all_cancers(109;1.03e-14)|all_epithelial(112;2.23e-12)|Lung NSC(122;2.76e-08)|all_lung(180;3.1e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;3.05e-06)	Estramustine(DB01196)	AGAACAAAAGGATACAGCCCT	0.448													G|||	1837	0.366813	0.6831	0.2147	5008	,	,		20781	0.4167		0.1044	False		,,,				2504	0.2658				p.D1461N		Atlas-SNP	.											.	MAP1A	189	.	0			c.G4381A						PASS	.	G	ASN/ASP	2194,1530		656,882,324	81.0	82.0	82.0		4381	3.0	0.1	15	dbSNP_100	82	839,7353		48,743,3305	yes	missense	MAP1A	NM_002373.5	23	704,1625,3629	AA,AG,GG		10.2417,41.0849,25.4532	possibly-damaging	1461/2804	43818052	3033,8883	1862	4096	5958	SO:0001583	missense	4130	exon4			CAAAAGGATACAG	U38292	CCDS42031.1	15q15.3	2006-06-15			ENSG00000166963	ENSG00000166963			6835	protein-coding gene	gene with protein product		600178		MAP1L		7806212, 7629894	Standard	XM_005254385		Approved		uc001zrt.3	P78559	OTTHUMG00000059756	ENST00000300231.5:c.4381G>A	15.37:g.43818052G>A	ENSP00000300231:p.Asp1461Asn	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	86	29	0.337209	NM_002373	O95643|Q12973|Q15882|Q9UJT4	Missense_Mutation	SNP	ENST00000300231.5	37	CCDS42031.1	747	0.34203296703296704	329	0.6686991869918699	76	0.20994475138121546	270	0.47202797202797203	72	0.09498680738786279	G	14.00	2.405007	0.42613	0.589151	0.102417	ENSG00000166963	ENST00000382031;ENST00000399453;ENST00000300231	T;T;T	0.21543	2.31;2.0;2.0	3.98	3.02	0.34903	.	.	.	.	.	T	0.00012	0.0000	L	0.49126	1.545	0.80722	P	0.0	B	0.26195	0.144	B	0.33042	0.157	T	0.21143	-1.0254	8	0.37606	T	0.19	-0.0114	13.2141	0.59849	0.0:0.1619:0.8381:0.0	rs2245715;rs60336985;rs2245715	1461	P78559	MAP1A_HUMAN	N	1699;1461;1461	ENSP00000371462:D1699N;ENSP00000382380:D1461N;ENSP00000300231:D1461N	ENSP00000300231:D1461N	D	+	1	0	MAP1A	41605344	0.004000	0.15560	0.077000	0.20336	0.498000	0.33706	1.414000	0.34736	0.947000	0.37659	0.563000	0.77884	GAT	G|0.669;A|0.331	0.331	strong		0.448	MAP1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000132894.5	NM_002373	
MUC4	4585	hgsc.bcm.edu	37	3	195507717	195507717	+	Silent	SNP	G	G	T	rs376353447		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195507717G>T	ENST00000463781.3	-	2	11193	c.10734C>A	c.(10732-10734)tcC>tcA	p.S3578S	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Silent_p.S3578S	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.S3578S(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	0.587																																					p.S3578S		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	1	Substitution - coding silent(1)	kidney(1)	c.C10734A						PASS	.						8.0	8.0	8.0					3																	195507717		621	1507	2128	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.10734C>A	3.37:g.195507717G>T		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	92	39	0.423913	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		0.587	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
ZNF554	115196	hgsc.bcm.edu	37	19	2833802	2833802	+	Missense_Mutation	SNP	A	A	G	rs867168	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:2833802A>G	ENST00000317243.5	+	5	767	c.569A>G	c.(568-570)gAg>gGg	p.E190G	ZNF554_ENST00000591265.1_3'UTR	NM_001102651.1	NP_001096121.1	Q86TJ5	ZN554_HUMAN	zinc finger protein 554	190			E -> G (in dbSNP:rs867168).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|liver(3)|lung(10)|ovary(1)|upper_aerodigestive_tract(1)	23		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		AAGCAGTTAGAGGACAGCCAT	0.502													A|||	1150	0.229633	0.0204	0.4164	5008	,	,		18096	0.4425		0.2127	False		,,,				2504	0.1779				p.E190G		Atlas-SNP	.											.	ZNF554	47	.	0			c.A569G						PASS	.	A	GLY/GLU	171,3611		0,171,1720	85.0	88.0	87.0		569	1.4	0.0	19	dbSNP_86	87	1451,6789		119,1213,2788	yes	missense	ZNF554	NM_001102651.1	98	119,1384,4508	GG,GA,AA		17.6092,4.5214,13.4919	possibly-damaging	190/539	2833802	1622,10400	1891	4120	6011	SO:0001583	missense	115196	exon5			AGTTAGAGGACAG	AK027860	CCDS42462.1	19p13.3	2013-09-20			ENSG00000172006	ENSG00000172006		"""Zinc fingers, C2H2-type"", ""-"""	26629	protein-coding gene	gene with protein product						12477932	Standard	NM_001102651		Approved	FLJ34817	uc002lwm.2	Q86TJ5	OTTHUMG00000180493	ENST00000317243.5:c.569A>G	19.37:g.2833802A>G	ENSP00000321132:p.Glu190Gly	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	73	37	0.506849	NM_001102651	Q8NAT3|Q9BWN3	Missense_Mutation	SNP	ENST00000317243.5	37	CCDS42462.1	572	0.2619047619047619	12	0.024390243902439025	141	0.38950276243093923	249	0.4353146853146853	170	0.22427440633245382	A	8.935	0.964366	0.18583	0.045214	0.176092	ENSG00000172006	ENST00000317243	T	0.08807	3.05	2.57	1.39	0.22231	.	.	.	.	.	T	0.00012	0.0000	L	0.29908	0.895	0.80722	P	0.0	B	0.11235	0.004	B	0.06405	0.002	T	0.48293	-0.9048	8	0.23302	T	0.38	.	1.8775	0.03221	0.5646:0.0:0.1624:0.273	rs867168;rs17763848;rs52831157;rs58761543;rs867168	190	Q86TJ5	ZN554_HUMAN	G	190	ENSP00000321132:E190G	ENSP00000321132:E190G	E	+	2	0	ZNF554	2784802	.	.	0.025000	0.17156	0.028000	0.11728	.	.	1.200000	0.43188	0.448000	0.29417	GAG	A|0.773;G|0.227	0.227	strong		0.502	ZNF554-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451598.3	NM_152303	
UNC13A	23025	hgsc.bcm.edu	37	19	17716896	17716896	+	Silent	SNP	G	G	T	rs3746198	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:17716896G>T	ENST00000519716.2	-	44	5078	c.5079C>A	c.(5077-5079)tcC>tcA	p.S1693S	UNC13A_ENST00000550896.1_Silent_p.S1666S|UNC13A_ENST00000552293.1_Silent_p.S1687S|UNC13A_ENST00000252773.7_Silent_p.S1693S|UNC13A_ENST00000551649.1_Silent_p.S1712S|UNC13A_ENST00000428389.2_Silent_p.S1781S	NM_001080421.2	NP_001073890.2	Q9UPW8	UN13A_HUMAN	unc-13 homolog A (C. elegans)	1693					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						CCTCCTCGGCGGAGCGCGTGT	0.726													G|||	476	0.0950479	0.2171	0.0548	5008	,	,		12444	0.0179		0.0984	False		,,,				2504	0.0348				p.S1693S		Atlas-SNP	.											.	UNC13A	299	.	0			c.C5079A						PASS	.	G		622,3120		54,514,1303	9.0	8.0	8.0		5079	-6.0	0.9	19	dbSNP_107	8	643,7373		27,589,3392	no	coding-synonymous	UNC13A	NM_001080421.2		81,1103,4695	TT,TG,GG		8.0215,16.6221,10.7586		1693/1704	17716896	1265,10493	1871	4008	5879	SO:0001819	synonymous_variant	23025	exon42			CTCGGCGGAGCGC	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.5079C>A	19.37:g.17716896G>T		Somatic	22	0	0		WXS	Illumina HiSeq	Phase_I	24	15	0.625	NM_001080421	E5RHY9	Silent	SNP	ENST00000519716.2	37	CCDS46013.2																																																																																			G|0.909;T|0.091	0.091	strong		0.726	UNC13A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000376169.2	XM_038604	
KIAA0930	23313	hgsc.bcm.edu	37	22	45608215	45608215	+	Intron	SNP	G	G	A	rs150665432	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:45608215G>A	ENST00000336156.5	-	2	130				KIAA0930_ENST00000391627.2_Intron|KIAA0930_ENST00000251993.7_Nonsense_Mutation_p.Q4*|KIAA0930_ENST00000496226.1_5'UTR|KIAA0930_ENST00000443310.3_Intron|KIAA0930_ENST00000492273.1_Nonsense_Mutation_p.Q4*	NM_001009880.1	NP_001009880.1	Q6ICG6	K0930_HUMAN	KIAA0930											endometrium(1)|kidney(4)|large_intestine(2)|lung(7)|urinary_tract(1)	15						GCAGCAGCCTGAGAGCCCATG	0.637													G|||	10	0.00199681	0.0015	0.0029	5008	,	,		16127	0.0		0.004	False		,,,				2504	0.002				p.Q4X		Atlas-SNP	.											.	KIAA0930	43	.	0			c.C10T						PASS	.	G	,stop/GLN	3,4401	6.2+/-15.9	0,3,2199	32.0	32.0	32.0		,10	-1.5	0.0	22	dbSNP_134	32	35,8563	23.4+/-69.3	1,33,4265	yes	intron,stop-gained	KIAA0930	NM_001009880.1,NM_015264.1	,	1,36,6464	AA,AG,GG		0.4071,0.0681,0.2923	,	,4/410	45608215	38,12964	2202	4299	6501	SO:0001627	intron_variant	23313	exon1			CAGCCTGAGAGCC	AK025608	CCDS33665.1, CCDS33666.1	22q13.31	2011-02-23	2011-02-23	2011-02-23	ENSG00000100364	ENSG00000100364			1314	protein-coding gene	gene with protein product			"""chromosome 22 open reading frame 9"""	C22orf9		10231032	Standard	NM_015264		Approved	bK268H5.C22.1	uc003bfw.1	Q6ICG6	OTTHUMG00000151263	ENST00000336156.5:c.65-227C>T	22.37:g.45608215G>A		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	85	47	0.552941	NM_015264	B0QY17|B0QY19|B3KT48|Q6ZVE5|Q7Z6K9|Q8IZ76|Q9Y2E2	Nonsense_Mutation	SNP	ENST00000336156.5	37	CCDS33665.1	10	0.004578754578754579	2	0.0040650406504065045	2	0.0055248618784530384	1	0.0017482517482517483	5	0.006596306068601583	G	15.73	2.919233	0.52546	6.81E-4	0.004071	ENSG00000100364	ENST00000251993	.	.	.	2.41	-1.47	0.08772	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	0.23302	T	0.38	.	4.8647	0.13602	0.1506:0.3861:0.4633:0.0	.	.	.	.	X	4	.	ENSP00000251993:Q4X	Q	-	1	0	KIAA0930	43986879	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.788000	0.04614	-0.192000	0.10432	-0.258000	0.10820	CAG	G|0.996;A|0.004	0.004	strong		0.637	KIAA0930-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321975.2	NM_001009880	
FAT2	2196	hgsc.bcm.edu	37	5	150930205	150930205	+	Silent	SNP	C	C	T	rs35489594	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:150930205C>T	ENST00000261800.5	-	7	4536	c.4524G>A	c.(4522-4524)acG>acA	p.T1508T		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	1508	Cadherin 13. {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)			ATTTTCCCACCGTTACCAGGA	0.522													C|||	6	0.00119808	0.0	0.0014	5008	,	,		21811	0.0		0.004	False		,,,				2504	0.001				p.T1508T		Atlas-SNP	.											.	FAT2	465	.	0			c.G4524A						PASS	.	C		11,4395	15.5+/-35.6	0,11,2192	96.0	87.0	90.0		4524	-10.5	0.8	5	dbSNP_126	90	73,8527	43.6+/-101.6	0,73,4227	no	coding-synonymous	FAT2	NM_001447.2		0,84,6419	TT,TC,CC		0.8488,0.2497,0.6459		1508/4350	150930205	84,12922	2203	4300	6503	SO:0001819	synonymous_variant	2196	exon7			TCCCACCGTTACC	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.4524G>A	5.37:g.150930205C>T		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	134	60	0.447761	NM_001447	O75091|Q9NSR7	Silent	SNP	ENST00000261800.5	37	CCDS4317.1																																																																																			C|0.995;T|0.005	0.005	strong		0.522	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447	
LTN1	26046	hgsc.bcm.edu	37	21	30339234	30339234	+	Missense_Mutation	SNP	T	T	C	rs61735768	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:30339234T>C	ENST00000361371.5	-	10	1658	c.1579A>G	c.(1579-1581)Agc>Ggc	p.S527G	LTN1_ENST00000389195.2_Missense_Mutation_p.S573G|LTN1_ENST00000389194.2_Missense_Mutation_p.S573G			O94822	LTN1_HUMAN	listerin E3 ubiquitin protein ligase 1	527					protein ubiquitination (GO:0016567)		ligase activity (GO:0016874)|zinc ion binding (GO:0008270)	p.S527G(1)		NS(1)|central_nervous_system(1)|endometrium(4)|kidney(5)|large_intestine(12)|lung(19)|ovary(5)|pancreas(1)|prostate(2)|skin(6)|stomach(2)|upper_aerodigestive_tract(2)	60						TTCAATGAGCTCTTCGGCTTC	0.383													T|||	769	0.153554	0.0424	0.2233	5008	,	,		17681	0.3839		0.1233	False		,,,				2504	0.0481				p.S573G		Atlas-SNP	.											LTN1,NS,carcinoma,0,1	LTN1	141	1	1	Substitution - Missense(1)	stomach(1)	c.A1717G						PASS	.	T	GLY/SER	278,4128	154.4+/-187.8	14,250,1939	76.0	72.0	73.0		1717	4.8	0.5	21	dbSNP_129	73	978,7622	211.3+/-251.9	55,868,3377	yes	missense	LTN1	NM_015565.2	56	69,1118,5316	CC,CT,TT		11.3721,6.3096,9.6571	benign	573/1813	30339234	1256,11750	2203	4300	6503	SO:0001583	missense	26046	exon10			ATGAGCTCTTCGG	AK001915	CCDS33527.1, CCDS33527.2	21q21.3	2013-01-09	2010-09-17	2010-09-17	ENSG00000198862	ENSG00000198862		"""RING-type (C3HC4) zinc fingers"""	13082	protein-coding gene	gene with protein product	"""listerin"""	613083	"""chromosome 21 open reading frame 98"", ""zinc finger protein 294"", ""ring finger protein 160"""	C21orf98, C21orf10, ZNF294, RNF160		20835226, 19196968	Standard	NM_015565		Approved	KIAA0714, FLJ11053, LISTERIN	uc002ymr.2	O94822	OTTHUMG00000078803	ENST00000361371.5:c.1579A>G	21.37:g.30339234T>C	ENSP00000354977:p.Ser527Gly	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	95	30	0.315789	NM_015565	A6NL41|A7E2D0|B2RTS0|C9J7U3|J3KPL4|Q05C47|Q9H8M4|Q9NUY5|Q9P0E9	Missense_Mutation	SNP	ENST00000361371.5	37		427	0.1955128205128205	21	0.042682926829268296	74	0.20441988950276244	233	0.40734265734265734	99	0.13060686015831136	T	12.03	1.814859	0.32053	0.063096	0.113721	ENSG00000198862	ENST00000389194;ENST00000361371;ENST00000389195	T;T;T	0.24723	2.18;2.19;1.84	4.83	4.83	0.62350	Armadillo-type fold (1);	0.304482	0.38164	N	0.001788	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.40887	-0.9539	9	0.62326	D	0.03	.	10.1603	0.42847	0.1487:0.0:0.0:0.8513	.	527	O94822	LTN1_HUMAN	G	573;527;573	ENSP00000373846:S573G;ENSP00000354977:S527G;ENSP00000373847:S573G	ENSP00000354977:S527G	S	-	1	0	LTN1	29261105	0.005000	0.15991	0.478000	0.27316	0.651000	0.38670	1.358000	0.34102	2.145000	0.66743	0.528000	0.53228	AGC	T|0.880;C|0.120	0.120	strong		0.383	LTN1-008	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000472108.1	NM_015565	
MYH8	4626	hgsc.bcm.edu	37	17	10304500	10304500	+	Silent	SNP	C	C	T	rs3744553	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:10304500C>T	ENST00000403437.2	-	25	3211	c.3117G>A	c.(3115-3117)ggG>ggA	p.G1039G	CTC-297N7.11_ENST00000587182.2_RNA|RP11-799N11.1_ENST00000399342.2_RNA|RP11-799N11.1_ENST00000581304.1_RNA	NM_002472.2	NP_002463.2	P13535	MYH8_HUMAN	myosin, heavy chain 8, skeletal muscle, perinatal	1039					ATP catabolic process (GO:0006200)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|skeletal muscle contraction (GO:0003009)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|sarcomere (GO:0030017)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)|myosin light chain binding (GO:0032027)|structural constituent of muscle (GO:0008307)			NS(3)|breast(8)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(61)|ovary(3)|prostate(3)|skin(10)|upper_aerodigestive_tract(2)|urinary_tract(2)	134						GTTCCAGAGACCCTTCAAGCT	0.348									Trismus-Pseudocamptodactyly Syndrome with Cardiac Myxoma and Freckling				C|||	253	0.0505192	0.0121	0.0346	5008	,	,		16654	0.0288		0.0547	False		,,,				2504	0.1319				p.G1039G		Atlas-SNP	.											.	MYH8	346	.	0			c.G3117A						PASS	.	C		93,4313	76.2+/-114.5	0,93,2110	96.0	85.0	89.0		3117	-4.2	1.0	17	dbSNP_107	89	545,8055	149.7+/-204.7	16,513,3771	no	coding-synonymous	MYH8	NM_002472.2		16,606,5881	TT,TC,CC		6.3372,2.1108,4.9054		1039/1938	10304500	638,12368	2203	4300	6503	SO:0001819	synonymous_variant	4626	exon25	Familial Cancer Database	Carney Complex Variant	CAGAGACCCTTCA		CCDS11153.1	17p13.1	2013-09-19	2006-09-29		ENSG00000133020	ENSG00000133020		"""Myosins / Myosin superfamily : Class II"""	7578	protein-coding gene	gene with protein product		160741	"""myosin, heavy polypeptide 8, skeletal muscle, perinatal"""			2373371	Standard	NM_002472		Approved	MyHC-peri, MyHC-pn	uc002gmm.2	P13535	OTTHUMG00000130361	ENST00000403437.2:c.3117G>A	17.37:g.10304500C>T		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	93	41	0.44086	NM_002472	Q14910	Silent	SNP	ENST00000403437.2	37	CCDS11153.1																																																																																			C|0.949;T|0.051	0.051	strong		0.348	MYH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252724.2	NM_002472	
LIMK1	3984	hgsc.bcm.edu	37	7	73520264	73520264	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:73520264T>C	ENST00000336180.2	+	6	719	c.668T>C	c.(667-669)aTc>aCc	p.I223T	LIMK1_ENST00000418310.1_Missense_Mutation_p.I253T|LIMK1_ENST00000538333.3_Missense_Mutation_p.I189T	NM_002314.3	NP_002305.1	P53667	LIMK1_HUMAN	LIM domain kinase 1	223	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				actin cytoskeleton organization (GO:0030036)|axon guidance (GO:0007411)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|negative regulation of ubiquitin-protein transferase activity (GO:0051444)|nervous system development (GO:0007399)|positive regulation of actin filament bundle assembly (GO:0032233)|positive regulation of axon extension (GO:0045773)|positive regulation of stress fiber assembly (GO:0051496)|protein phosphorylation (GO:0006468)|Rho protein signal transduction (GO:0007266)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|neuron projection (GO:0043005)|nucleus (GO:0005634)	ATP binding (GO:0005524)|heat shock protein binding (GO:0031072)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|ovary(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	21		Lung NSC(55;0.137)			Dabrafenib(DB08912)	GGAGACCGGATCTTGGAAATC	0.607																																					p.I223T		Atlas-SNP	.											.	LIMK1	55	.	0			c.T668C						PASS	.						104.0	89.0	94.0					7																	73520264		2203	4300	6503	SO:0001583	missense	3984	exon6			ACCGGATCTTGGA	D26309	CCDS5563.1, CCDS56491.1	7q11.23	2005-01-21			ENSG00000106683	ENSG00000106683			6613	protein-coding gene	gene with protein product		601329				8673124, 8812460	Standard	NM_002314		Approved	LIMK	uc003uaa.2	P53667	OTTHUMG00000023448	ENST00000336180.2:c.668T>C	7.37:g.73520264T>C	ENSP00000336740:p.Ile223Thr	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	78	16	0.205128	NM_002314	B7Z6I8|D3DXF4|D3DXF5|O15283|Q15820|Q15821|Q75MU3|Q9Y5Q1	Missense_Mutation	SNP	ENST00000336180.2	37	CCDS5563.1	.	.	.	.	.	.	.	.	.	.	T	23.0	4.363859	0.82353	.	.	ENSG00000106683	ENST00000418310;ENST00000419043;ENST00000336180;ENST00000423685;ENST00000538333	T;T;T;T	0.56941	0.43;0.43;0.43;0.43	4.97	4.97	0.65823	PDZ/DHR/GLGF (4);	0.051007	0.85682	D	0.000000	T	0.71685	0.3369	M	0.81341	2.54	0.80722	D	1	P;D;D	0.63046	0.852;0.992;0.992	B;D;D	0.68483	0.433;0.958;0.958	T	0.76356	-0.2989	10	0.87932	D	0	-30.7731	12.6805	0.56918	0.0:0.0:0.0:1.0	.	118;189;223	Q59FA3;B7Z6I8;P53667	.;.;LIMK1_HUMAN	T	253;223;223;189;189	ENSP00000409717:I253T;ENSP00000336740:I223T;ENSP00000396480:I189T;ENSP00000444452:I189T	ENSP00000336740:I223T	I	+	2	0	LIMK1	73158200	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	7.676000	0.84012	1.898000	0.54952	0.524000	0.50904	ATC	.	.	none		0.607	LIMK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252335.2	NM_002314	
THEG	51298	hgsc.bcm.edu	37	19	372689	372689	+	Missense_Mutation	SNP	G	G	A	rs35119230	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:372689G>A	ENST00000342640.4	-	5	619	c.577C>T	c.(577-579)Cgc>Tgc	p.R193C	THEG_ENST00000346878.2_Missense_Mutation_p.R169C	NM_016585.4	NP_057669.1	Q9P2T0	THEG_HUMAN	theg spermatid protein	193					cell differentiation (GO:0030154)|chaperone-mediated protein complex assembly (GO:0051131)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	nucleus (GO:0005634)				NS(1)|breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(9)|ovary(1)|prostate(1)|skin(2)|soft_tissue(1)	29		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)		TCCTCCACGCGGCGGGACACC	0.547													G|||	46	0.0091853	0.0015	0.0101	5008	,	,		20029	0.0		0.0338	False		,,,				2504	0.0031				p.R193C		Atlas-SNP	.											.	THEG	58	.	0			c.C577T						PASS	.	G	CYS/ARG,CYS/ARG	40,4366	43.1+/-76.7	0,40,2163	116.0	100.0	105.0		577,505	3.3	0.0	19	dbSNP_126	105	346,8254	117.9+/-177.5	8,330,3962	yes	missense,missense	THEG	NM_016585.3,NM_199202.1	180,180	8,370,6125	AA,AG,GG		4.0233,0.9079,2.9679	probably-damaging,probably-damaging	193/380,169/356	372689	386,12620	2203	4300	6503	SO:0001583	missense	51298	exon5			CCACGCGGCGGGA	AF268610	CCDS12025.1, CCDS12026.1	19p13.3	2012-02-24	2012-02-24		ENSG00000105549	ENSG00000105549			13706	protein-coding gene	gene with protein product	"""cancer/testis antigen 56"""	609503	"""Theg homolog (mouse)"""			11173852	Standard	NM_016585		Approved	CT56, THEG1	uc002lol.3	Q9P2T0	OTTHUMG00000165491	ENST00000342640.4:c.577C>T	19.37:g.372689G>A	ENSP00000340088:p.Arg193Cys	Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	164	74	0.451219	NM_016585	A6NMJ8	Missense_Mutation	SNP	ENST00000342640.4	37	CCDS12025.1	26	0.011904761904761904	1	0.0020325203252032522	3	0.008287292817679558	0	0.0	22	0.029023746701846966	G	11.49	1.653400	0.29425	0.009079	0.040233	ENSG00000105549	ENST00000342640;ENST00000346878	T;T	0.34859	1.37;1.34	3.31	3.31	0.37934	.	0.000000	0.52532	D	0.000061	T	0.25121	0.0610	M	0.79123	2.44	0.22424	N	0.999111	D;D	0.89917	1.0;1.0	D;D	0.87578	0.997;0.998	T	0.10730	-1.0617	10	0.87932	D	0	-19.2655	10.3558	0.43962	0.0:0.0:1.0:0.0	rs35119230	169;193	Q9P2T0-2;Q9P2T0	.;THEG_HUMAN	C	193;169	ENSP00000340088:R193C;ENSP00000264820:R169C	ENSP00000340088:R193C	R	-	1	0	THEG	323689	0.047000	0.20315	0.041000	0.18516	0.153000	0.21895	1.195000	0.32186	2.168000	0.68352	0.561000	0.74099	CGC	G|0.976;A|0.024	0.024	strong		0.547	THEG-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384431.2		
SPOCK1	6695	hgsc.bcm.edu	37	5	136834138	136834138	+	Missense_Mutation	SNP	T	T	C	rs111393448	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:136834138T>C	ENST00000394945.1	-	2	279	c.110A>G	c.(109-111)aAt>aGt	p.N37S	SPOCK1_ENST00000282223.7_Missense_Mutation_p.N37S	NM_004598.3	NP_004589.1	Q08629	TICN1_HUMAN	sparc/osteonectin, cwcv and kazal-like domains proteoglycan (testican) 1	37					cell adhesion (GO:0007155)|central nervous system neuron differentiation (GO:0021953)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of neuron projection development (GO:0010977)|nervous system development (GO:0007399)|neurogenesis (GO:0022008)|neuron migration (GO:0001764)|regulation of cell growth (GO:0001558)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|neuromuscular junction (GO:0031594)|node of Ranvier (GO:0033268)|postsynaptic density (GO:0014069)|proteinaceous extracellular matrix (GO:0005578)|sarcoplasm (GO:0016528)	calcium ion binding (GO:0005509)|cysteine-type endopeptidase inhibitor activity (GO:0004869)|metalloendopeptidase inhibitor activity (GO:0008191)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|liver(2)|lung(4)|ovary(1)|pancreas(1)|stomach(1)	18			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			GTCTAGGAAATTGCCGTGGTT	0.682													T|||	19	0.00379393	0.0	0.0058	5008	,	,		9286	0.0		0.0129	False		,,,				2504	0.002				p.N37S		Atlas-SNP	.											.	SPOCK1	58	.	0			c.A110G						PASS	.	T	SER/ASN	9,4397		0,9,2194	22.0	21.0	22.0		110	3.7	1.0	5	dbSNP_132	22	106,8492		3,100,4196	yes	missense	SPOCK1	NM_004598.3	46	3,109,6390	CC,CT,TT		1.2328,0.2043,0.8843	benign	37/440	136834138	115,12889	2203	4299	6502	SO:0001583	missense	6695	exon2			AGGAAATTGCCGT	AF231124	CCDS4191.1	5q31.2	2008-02-05	2005-11-04	2005-11-04	ENSG00000152377	ENSG00000152377			11251	protein-coding gene	gene with protein product		602264	"""sparc/osteonectin, cwcv and kazal-like domains proteoglycan (testican)"""	TIC1, SPOCK		9545645	Standard	NM_004598		Approved	testican-1	uc003lbp.3	Q08629	OTTHUMG00000129157	ENST00000394945.1:c.110A>G	5.37:g.136834138T>C	ENSP00000378401:p.Asn37Ser	Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	40	23	0.575	NM_004598	B3KSW3|Q59EW0|Q8N630|Q9UCL8	Missense_Mutation	SNP	ENST00000394945.1	37	CCDS4191.1	14	0.00641025641025641	0	0.0	2	0.0055248618784530384	0	0.0	12	0.0158311345646438	T	24.2	4.510460	0.85389	0.002043	0.012328	ENSG00000152377	ENST00000394945;ENST00000282223;ENST00000505690	T;T;T	0.58940	0.3;0.3;0.34	3.66	3.66	0.41972	.	0.344437	0.23803	N	0.044419	T	0.33498	0.0865	L	0.51914	1.62	0.27215	N	0.959807	B	0.15930	0.015	B	0.14578	0.011	T	0.44112	-0.9349	10	0.56958	D	0.05	.	10.3639	0.44012	0.0:0.0:0.0:1.0	.	37	Q08629	TICN1_HUMAN	S	37	ENSP00000378401:N37S;ENSP00000282223:N37S;ENSP00000424517:N37S	ENSP00000282223:N37S	N	-	2	0	SPOCK1	136862037	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	3.481000	0.53179	1.439000	0.47511	0.379000	0.24179	AAT	T|0.991;C|0.009	0.009	strong		0.682	SPOCK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251222.1	NM_004598	
SYNE1	23345	hgsc.bcm.edu	37	6	152708310	152708310	+	Missense_Mutation	SNP	G	G	A	rs214950	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:152708310G>A	ENST00000367255.5	-	54	8985	c.8384C>T	c.(8383-8385)gCg>gTg	p.A2795V	SYNE1_ENST00000265368.4_Missense_Mutation_p.A2795V|SYNE1_ENST00000448038.1_Missense_Mutation_p.A2802V|SYNE1_ENST00000423061.1_Missense_Mutation_p.A2802V|SYNE1_ENST00000341594.5_Missense_Mutation_p.A2834V	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	2795			A -> V (in dbSNP:rs214950).		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)		CCTGGACTTCGCAATTAGACG	0.493										HNSCC(10;0.0054)			G|||	1247	0.249002	0.152	0.1614	5008	,	,		16439	0.4018		0.2167	False		,,,				2504	0.318				p.A2802V		Atlas-SNP	.											.	SYNE1	3227	.	0			c.C8405T						PASS	.	G	VAL/ALA,VAL/ALA	698,3708	292.1+/-281.9	55,588,1560	186.0	166.0	173.0		8405,8384	1.5	0.0	6	dbSNP_79	173	1883,6717	335.0+/-321.2	218,1447,2635	yes	missense,missense	SYNE1	NM_033071.3,NM_182961.3	64,64	273,2035,4195	AA,AG,GG		21.8953,15.842,19.8447	benign,benign	2802/8750,2795/8798	152708310	2581,10425	2203	4300	6503	SO:0001583	missense	23345	exon54			GACTTCGCAATTA	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.8384C>T	6.37:g.152708310G>A	ENSP00000356224:p.Ala2795Val	Somatic	207	0	0		WXS	Illumina HiSeq	Phase_I	145	49	0.337931	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	560	0.2564102564102564	73	0.1483739837398374	71	0.19613259668508287	249	0.4353146853146853	167	0.22031662269129287	G	4.484	0.089763	0.08632	0.15842	0.218953	ENSG00000131018	ENST00000367255;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594	T;T;T;T;T	0.36157	1.27;1.27;1.27;1.27;1.27	5.7	1.51	0.23008	.	0.311325	0.27147	N	0.020718	T	0.06735	0.0172	N	0.22421	0.69	0.40549	P	0.018894999999999995	B;B;B;B	0.23937	0.007;0.033;0.033;0.094	B;B;B;B	0.15052	0.001;0.003;0.003;0.012	T	0.19844	-1.0293	9	0.35671	T	0.21	.	2.1478	0.03791	0.159:0.1006:0.3035:0.4369	rs214950;rs535611;rs52790834;rs58051739;rs214950	2778;2795;2795;2802	B3W695;Q8NF91;E7EQI5;Q8NF91-4	.;SYNE1_HUMAN;.;.	V	2795;2802;2795;2802;2834	ENSP00000356224:A2795V;ENSP00000396024:A2802V;ENSP00000265368:A2795V;ENSP00000390975:A2802V;ENSP00000341887:A2834V	ENSP00000265368:A2795V	A	-	2	0	SYNE1	152750003	0.998000	0.40836	0.000000	0.03702	0.007000	0.05969	4.552000	0.60747	0.350000	0.24002	-0.822000	0.03109	GCG	G|0.776;A|0.224	0.224	strong		0.493	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961	
CCDC79	283847	hgsc.bcm.edu	37	16	66812797	66812797	+	Silent	SNP	C	C	T	rs363162	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:66812797C>T	ENST00000558713.2	-	9	894	c.822G>A	c.(820-822)acG>acA	p.T274T	CCDC79_ENST00000415744.1_Silent_p.T274T|CCDC79_ENST00000561333.1_5'UTR|CCDC79_ENST00000433574.1_Silent_p.T274T|CCDC79_ENST00000432602.1_Silent_p.T274T|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	104	0	0		WXS	Illumina HiSeq	Phase_I	108	108	1	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		
CXXC5	51523	hgsc.bcm.edu	37	5	139060486	139060486	+	Silent	SNP	G	G	A	rs356445	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:139060486G>A	ENST00000302517.3	+	2	1092	c.378G>A	c.(376-378)gcG>gcA	p.A126A	CXXC5_ENST00000511048.1_Silent_p.A126A	NM_016463.7	NP_057547.5	Q7LFL8	CXXC5_HUMAN	CXXC finger protein 5	126					positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)	DNA binding (GO:0003677)|signal transducer activity (GO:0004871)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(7)|upper_aerodigestive_tract(1)	12			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CGGCCATGGCGGTGGACAAAA	0.652													G|||	957	0.191094	0.5015	0.0634	5008	,	,		16819	0.0585		0.0517	False		,,,				2504	0.1421				p.A126A		Atlas-SNP	.											CXXC5,NS,carcinoma,0,1	CXXC5	27	1	0			c.G378A						PASS	.						68.0	83.0	78.0					5																	139060486		2111	4242	6353	SO:0001819	synonymous_variant	51523	exon2			CATGGCGGTGGAC	AK024338	CCDS43370.1	5q31.3	2014-02-18	2011-12-01						26943	protein-coding gene	gene with protein product	"""retinoid-inducible nuclear factor"", ""WT1-induced Inhibitor of Dishevelled"""	612752				11042152, 19001364, 19182210, 20220130	Standard	NM_016463		Approved	HSPC195, RINF, WID	uc010jfg.1	Q7LFL8		ENST00000302517.3:c.378G>A	5.37:g.139060486G>A		Somatic	21	0	0		WXS	Illumina HiSeq	Phase_I	16	6	0.375	NM_016463	B3KND0|C8CBA8|Q8TB79|Q9NV51|Q9P0S8	Silent	SNP	ENST00000302517.3	37	CCDS43370.1																																																																																			G|0.837;A|0.163	0.163	strong		0.652	CXXC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372744.1	NM_016463	
CYP2C9	1559	hgsc.bcm.edu	37	10	96702047	96702047	+	Missense_Mutation	SNP	C	C	T	rs1799853	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:96702047C>T	ENST00000260682.6	+	3	442	c.430C>T	c.(430-432)Cgt>Tgt	p.R144C	CYP2C9_ENST00000461906.1_3'UTR	NM_000771.3	NP_000762.2	P11712	CP2C9_HUMAN	cytochrome P450, family 2, subfamily C, polypeptide 9	144			R -> C (in allele CYP2C9*2; dbSNP:rs1799853). {ECO:0000269|PubMed:15469410, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:2827463, ECO:0000269|PubMed:3697070, ECO:0000269|PubMed:8946475, ECO:0000269|PubMed:9110362, ECO:0000269|Ref.3}.		arachidonic acid metabolic process (GO:0019369)|cellular amide metabolic process (GO:0043603)|drug catabolic process (GO:0042737)|drug metabolic process (GO:0017144)|epoxygenase P450 pathway (GO:0019373)|exogenous drug catabolic process (GO:0042738)|monocarboxylic acid metabolic process (GO:0032787)|monoterpenoid metabolic process (GO:0016098)|omega-hydroxylase P450 pathway (GO:0097267)|oxidation-reduction process (GO:0055114)|oxidative demethylation (GO:0070989)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|urea metabolic process (GO:0019627)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|intracellular membrane-bounded organelle (GO:0043231)	(R)-limonene 6-monooxygenase activity (GO:0052741)|(S)-limonene 6-monooxygenase activity (GO:0018675)|(S)-limonene 7-monooxygenase activity (GO:0018676)|caffeine oxidase activity (GO:0034875)|drug binding (GO:0008144)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity (GO:0016491)|steroid hydroxylase activity (GO:0008395)			breast(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(9)|ovary(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	34		Colorectal(252;0.0902)		all cancers(201;6.93e-05)	Acenocoumarol(DB01418)|Acetaminophen(DB00316)|Acetylsalicylic acid(DB00945)|Agomelatine(DB06594)|Alosetron(DB00969)|Alprazolam(DB00404)|Aminophenazone(DB01424)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amlodipine(DB00381)|Amodiaquine(DB00613)|Amprenavir(DB00701)|Anastrozole(DB01217)|Antipyrine(DB01435)|Apixaban(DB06605)|Aprepitant(DB00673)|Arformoterol(DB01274)|Artemether(DB06697)|Atazanavir(DB01072)|Atorvastatin(DB01076)|Atovaquone(DB01117)|Azelastine(DB00972)|Bexarotene(DB00307)|Bicalutamide(DB01128)|Bortezomib(DB00188)|Bosentan(DB00559)|Brompheniramine(DB00835)|Buprenorphine(DB00921)|Bupropion(DB01156)|Cabozantinib(DB08875)|Caffeine(DB00201)|Candesartan(DB00796)|Capecitabine(DB01101)|Carbamazepine(DB00564)|Carbinoxamine(DB00748)|Carvedilol(DB01136)|Celecoxib(DB00482)|Chloramphenicol(DB00446)|Chlorpropamide(DB00672)|Cholecalciferol(DB00169)|Cimetidine(DB00501)|Cinnarizine(DB00568)|Cisapride(DB00604)|Cisplatin(DB00515)|Clevidipine(DB04920)|Clopidogrel(DB00758)|Clotrimazole(DB00257)|Clozapine(DB00363)|Cocaine(DB00907)|Colchicine(DB01394)|Cyclizine(DB01176)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dapagliflozin(DB06292)|Dapsone(DB00250)|Delavirdine(DB00705)|Desloratadine(DB00967)|Dexamethasone(DB01234)|Dexfenfluramine(DB01191)|Dextromethorphan(DB00514)|Dextropropoxyphene(DB00647)|Diazepam(DB00829)|Diclofenac(DB00586)|Diclofenamide(DB01144)|Dicoumarol(DB00266)|Diethylstilbestrol(DB00255)|Diltiazem(DB00343)|Diphenhydramine(DB01075)|Disulfiram(DB00822)|Dolasetron(DB00757)|Donepezil(DB00843)|Dopamine(DB00988)|Dorzolamide(DB00869)|Doxepin(DB01142)|Dronabinol(DB00470)|Efavirenz(DB00625)|Eletriptan(DB00216)|Enzalutamide(DB08899)|Epinephrine(DB00668)|Epoprostenol(DB01240)|Eprosartan(DB00876)|Estradiol(DB00783)|Estrone(DB00655)|Estropipate(DB04574)|Eszopiclone(DB00402)|Ethanol(DB00898)|Etodolac(DB00749)|Etoricoxib(DB01628)|Etravirine(DB06414)|Felodipine(DB01023)|Fenofibrate(DB01039)|Flecainide(DB01195)|Fluconazole(DB00196)|Flunarizine(DB04841)|Flunitrazepam(DB01544)|Fluorouracil(DB00544)|Fluoxetine(DB00472)|Flurbiprofen(DB00712)|Fluvastatin(DB01095)|Fluvoxamine(DB00176)|Formoterol(DB00983)|Fosphenytoin(DB01320)|Gefitinib(DB00317)|Gemfibrozil(DB01241)|Ginkgo biloba(DB01381)|Gliclazide(DB01120)|Glimepiride(DB00222)|Glipizide(DB01067)|Glyburide(DB01016)|Guanfacine(DB01018)|Haloperidol(DB00502)|Halothane(DB01159)|Hexobarbital(DB01355)|Histamine Phosphate(DB00667)|Human Serum Albumin(DB00062)|Hydromorphone(DB00327)|Ibuprofen(DB01050)|Idarubicin(DB01177)|Ifosfamide(DB01181)|Imatinib(DB00619)|Indinavir(DB00224)|Indomethacin(DB00328)|Irbesartan(DB01029)|Isoniazid(DB00951)|Ketamine(DB01221)|Ketobemidone(DB06738)|Ketoconazole(DB01026)|Ketoprofen(DB01009)|Lansoprazole(DB00448)|Leflunomide(DB01097)|Lidocaine(DB00281)|Lopinavir(DB01601)|Loratadine(DB00455)|Lornoxicam(DB06725)|Losartan(DB00678)|Lovastatin(DB00227)|Lumiracoxib(DB01283)|Medroxyprogesterone Acetate(DB00603)|Mefenamic acid(DB00784)|Melatonin(DB01065)|Meloxicam(DB00814)|Mestranol(DB01357)|Methadone(DB00333)|Methazolamide(DB00703)|Methimazole(DB00763)|Methoxyflurane(DB01028)|Metronidazole(DB00916)|Miconazole(DB01110)|Mirtazapine(DB00370)|Moclobemide(DB01171)|Modafinil(DB00745)|Montelukast(DB00471)|Naproxen(DB00788)|Nateglinide(DB00731)|Nelfinavir(DB00220)|Nevirapine(DB00238)|Nicardipine(DB00622)|Niclosamide(DB06803)|Nicotine(DB00184)|Nifedipine(DB01115)|Nilotinib(DB04868)|Nilutamide(DB00665)|Nilvadipine(DB06712)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Omeprazole(DB00338)|Ondansetron(DB00904)|Ospemifene(DB04938)|Oxaprozin(DB00991)|Paclitaxel(DB01229)|Pantoprazole(DB00213)|Paramethadione(DB00617)|Paroxetine(DB00715)|Perphenazine(DB00850)|Phenobarbital(DB01174)|Phenprocoumon(DB00946)|Phentermine(DB00191)|Phenylbutazone(DB00812)|Phenytoin(DB00252)|Pioglitazone(DB01132)|Piroxicam(DB00554)|Pitavastatin(DB08860)|Pranlukast(DB01411)|Prasugrel(DB06209)|Pravastatin(DB00175)|Primidone(DB00794)|Probenecid(DB01032)|Progesterone(DB00396)|Proguanil(DB01131)|Promazine(DB00420)|Promethazine(DB01069)|Propafenone(DB01182)|Propofol(DB00818)|Pyrimethamine(DB00205)|Quazepam(DB01589)|Quinidine(DB00908)|Quinine(DB00468)|Rabeprazole(DB01129)|Regorafenib(DB08896)|Rifampicin(DB01045)|Rifapentine(DB01201)|Ritonavir(DB00503)|Rosiglitazone(DB00412)|Rosuvastatin(DB01098)|Salicylic acid(DB00936)|Saquinavir(DB01232)|Secobarbital(DB00418)|Selegiline(DB01037)|Sertraline(DB01104)|Sildenafil(DB00203)|Simvastatin(DB00641)|Sitaxentan(DB06268)|Sorafenib(DB00398)|Sulfadiazine(DB00359)|Sulfadimethoxine(DB06150)|Sulfamethizole(DB00576)|Sulfamethoxazole(DB01015)|Sulfamoxole(DB08798)|Sulfanilamide(DB00259)|Sulfaphenazole(DB06729)|Sulfapyridine(DB00891)|Sulfinpyrazone(DB01138)|Sulfisoxazole(DB00263)|Suprofen(DB00870)|Tamoxifen(DB00675)|Tapentadol(DB06204)|Temazepam(DB00231)|Teniposide(DB00444)|Tenoxicam(DB00469)|Terbinafine(DB00857)|Testosterone(DB00624)|Thalidomide(DB01041)|Theophylline(DB00277)|Thiamylal(DB01154)|Thioridazine(DB00679)|Ticlopidine(DB00208)|Tioconazole(DB01007)|Tolbutamide(DB01124)|Tolcapone(DB00323)|Tolterodine(DB01036)|Torasemide(DB00214)|Trabectedin(DB05109)|Tranylcypromine(DB00752)|Treprostinil(DB00374)|Tretinoin(DB00755)|Triazolam(DB00897)|Trimethadione(DB00347)|Trimethoprim(DB00440)|Trimipramine(DB00726)|Troleandomycin(DB01361)|Valproic Acid(DB00313)|Valsartan(DB00177)|Venlafaxine(DB00285)|Verapamil(DB00661)|Vismodegib(DB08828)|Voriconazole(DB00582)|Warfarin(DB00682)|Ximelagatran(DB04898)|Zafirlukast(DB00549)|Zalcitabine(DB00943)|Zidovudine(DB00495)|Zileuton(DB00744)|Zolpidem(DB00425)|Zopiclone(DB01198)	CATTGAGGACCGTGTTCAAGA	0.498													C|||	240	0.0479233	0.0083	0.0994	5008	,	,		20423	0.001		0.1243	False		,,,				2504	0.0348				p.R144C	Ovarian(54;1266 1406 16072 35076)	Atlas-SNP	.											.	CYP2C9	82	.	0			c.C430T	GRCh37	CM994193	CYP2C9	M	rs1799853	PASS	.	C	CYS/ARG	118,4288		4,110,2089	154.0	146.0	149.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	430	1.4	0.1	10	dbSNP_89	149	1124,7470		75,974,3248	yes	missense	CYP2C9	NM_000771.3	180	79,1084,5337	TT,TC,CC	http://www.ncbi.nlm.nih.gov/pubmed?term	13.0789,2.6782,9.5538	probably-damaging	144/491	96702047	1242,11758	2203	4297	6500	SO:0001583	missense	1559	exon3			GAGGACCGTGTTC	M61855	CCDS7437.1	10q24.1	2007-12-14	2003-01-14		ENSG00000138109	ENSG00000138109		"""Cytochrome P450s"""	2623	protein-coding gene	gene with protein product		601130	"""cytochrome P450, subfamily IIC (mephenytoin 4-hydroxylase), polypeptide 9"""	CYP2C10		2009263, 7841444	Standard	NM_000771		Approved	P450IIC9	uc001kka.4	P11712	OTTHUMG00000018805	ENST00000260682.6:c.430C>T	10.37:g.96702047C>T	ENSP00000260682:p.Arg144Cys	Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	137	67	0.489051	NM_000771	P11713|Q16756|Q16872|Q5VX92|Q6IRV8|Q8WW80	Missense_Mutation	SNP	ENST00000260682.6	37	CCDS7437.1	149	0.06822344322344322	9	0.018292682926829267	45	0.12430939226519337	2	0.0034965034965034965	93	0.12269129287598944	.	16.06	3.014845	0.54468	0.026782	0.130789	ENSG00000138109	ENST00000545448;ENST00000260682	T	0.69926	-0.44	3.54	1.42	0.22433	.	0.089345	0.47093	U	0.000246	T	0.02418	0.0074	M	0.74647	2.275	0.23144	P	0.99822706	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.81914	0.989;0.989;0.995	T	0.51810	-0.8658	9	0.72032	D	0.01	.	5.9087	0.19016	0.4066:0.4141:0.1794:0.0	rs1799853;rs17110268;rs60690363;rs1799853	144;144;144	Q5VX92;P11712;Q8WW80	.;CP2C9_HUMAN;.	C	144	ENSP00000260682:R144C	ENSP00000260682:R144C	R	+	1	0	CYP2C9	96692037	0.000000	0.05858	0.125000	0.21846	0.884000	0.51177	-0.307000	0.08167	0.194000	0.20326	0.484000	0.47621	CGT	C|1.000;|0.000	.	weak		0.498	CYP2C9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049501.1	NM_000771	
SLC22A23	63027	hgsc.bcm.edu	37	6	3273457	3273457	+	Silent	SNP	A	A	G	rs9503518	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:3273457A>G	ENST00000406686.3	-	10	1892	c.1893T>C	c.(1891-1893)tcT>tcC	p.S631S	SLC22A23_ENST00000436008.2_Silent_p.S639S|PSMG4_ENST00000451246.2_Intron|SLC22A23_ENST00000380302.4_Silent_p.S350S|SLC22A23_ENST00000490273.1_Silent_p.S350S	NM_015482.1	NP_056297.1	A1A5C7	S22AN_HUMAN	solute carrier family 22, member 23	631					ion transport (GO:0006811)	integral component of membrane (GO:0016021)	transmembrane transporter activity (GO:0022857)			endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)	14	Ovarian(93;0.0493)	all_hematologic(90;0.0905)				GCTCCCCGTTAGAAATGTTCT	0.612													G|||	524	0.104633	0.1362	0.0793	5008	,	,		16721	0.121		0.0606	False		,,,				2504	0.1084				p.S631S		Atlas-SNP	.											.	SLC22A23	89	.	0			c.T1893C						PASS	.	G	,	579,3827	771.2+/-413.8	36,507,1660	89.0	91.0	90.0		1893,1050	4.1	1.0	6	dbSNP_119	90	633,7967	789.5+/-407.6	27,579,3694	no	coding-synonymous,coding-synonymous	SLC22A23	NM_015482.1,NM_021945.5	,	63,1086,5354	GG,GA,AA		7.3605,13.1412,9.3188	,	631/687,350/406	3273457	1212,11794	2203	4300	6503	SO:0001819	synonymous_variant	63027	exon10			CCCGTTAGAAATG	AJ420525	CCDS34331.1, CCDS47363.1, CCDS75389.1	6p25.2	2013-05-22	2008-01-11	2008-01-11	ENSG00000137266	ENSG00000137266		"""Solute carriers"""	21106	protein-coding gene	gene with protein product		611697	"""chromosome 6 open reading frame 85"""	C6orf85		17714910	Standard	NM_015482		Approved	FLJ22174	uc003mvm.3	A1A5C7	OTTHUMG00000014144	ENST00000406686.3:c.1893T>C	6.37:g.3273457A>G		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	124	67	0.540323	NM_015482	A1A5C8|Q5T8B8|Q6ZMH3|Q8IW73	Silent	SNP	ENST00000406686.3	37	CCDS47363.1																																																																																			A|0.899;G|0.101	0.101	strong		0.612	SLC22A23-006	KNOWN	not_organism_supported|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000353059.1	NM_021945	
CEACAM8	1088	hgsc.bcm.edu	37	19	43093033	43093033	+	Silent	SNP	G	G	A	rs35599593	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:43093033G>A	ENST00000244336.5	-	4	962	c.861C>T	c.(859-861)ccC>ccT	p.P287P	LIPE-AS1_ENST00000594688.1_RNA|LIPE-AS1_ENST00000594624.2_RNA|CEACAM8_ENST00000599005.1_Intron	NM_001816.3	NP_001807.2	P31997	CEAM8_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 8	287	Ig-like C2-type 2.				immune response (GO:0006955)	anchored component of membrane (GO:0031225)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				endometrium(1)|large_intestine(5)|lung(5)|ovary(1)|pancreas(1)|prostate(2)|skin(1)	16		Prostate(69;0.00899)				TAGTGATGTTGGGGATAAAGA	0.502													G|||	62	0.0123802	0.0023	0.013	5008	,	,		17688	0.0		0.0427	False		,,,				2504	0.0072				p.P287P		Atlas-SNP	.											.	CEACAM8	44	.	0			c.C861T						PASS	.	G		43,4363	46.0+/-80.4	0,43,2160	230.0	206.0	214.0		861	-0.5	0.9	19	dbSNP_126	214	473,8127	138.7+/-195.5	10,453,3837	no	coding-synonymous	CEACAM8	NM_001816.3		10,496,5997	AA,AG,GG		5.5,0.9759,3.9674		287/350	43093033	516,12490	2203	4300	6503	SO:0001819	synonymous_variant	1088	exon4			GATGTTGGGGATA	D90064	CCDS12610.1	19q13.2	2013-01-29			ENSG00000124469	ENSG00000124469		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	1820	protein-coding gene	gene with protein product		615747		CGM6		2208113, 2306228	Standard	NM_001816		Approved	CD66b	uc002oud.2	P31997	OTTHUMG00000151124	ENST00000244336.5:c.861C>T	19.37:g.43093033G>A		Somatic	339	0	0		WXS	Illumina HiSeq	Phase_I	301	153	0.508306	NM_001816	O60399|Q16574	Silent	SNP	ENST00000244336.5	37	CCDS12610.1																																																																																			G|0.969;A|0.031	0.031	strong		0.502	CEACAM8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321430.1		
NBPF10	100132406	hgsc.bcm.edu	37	1	145302704	145302704	+	Missense_Mutation	SNP	A	A	G	rs3926769	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:145302704A>G	ENST00000369339.3	+	5	582	c.329A>G	c.(328-330)aAg>aGg	p.K110R	RP11-458D21.5_ENST00000468030.1_3'UTR|NBPF10_ENST00000369338.1_Missense_Mutation_p.K110R|NBPF10_ENST00000342960.5_Missense_Mutation_p.K381R			Q6P3W6	NBPFA_HUMAN	neuroblastoma breakpoint family, member 10	381						cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)			NS(3)|breast(1)|central_nervous_system(3)|endometrium(12)|kidney(23)|lung(15)|ovary(1)|prostate(7)|skin(6)|urinary_tract(2)	73	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		ACCCAGTTAAAGGAGAAGTTA	0.522													.|||	2571	0.513379	0.5408	0.5317	5008	,	,		13159	0.4841		0.5089	False		,,,				2504	0.498				p.K381R		Atlas-SNP	.											NBPF10_ENST00000369338,NS,neuroblastoma,0,2	NBPF10	221	2	0			c.A1142G						scavenged	.																																			SO:0001583	missense	100132406	exon8			AGTTAAAGGAGAA	BC021111		1q21.1	2013-01-17			ENSG00000163386	ENSG00000271425		"""neuroblastoma breakpoint family"""	31992	protein-coding gene	gene with protein product		614000				16079250	Standard	NM_001039703		Approved	AG1		Q6P3W6	OTTHUMG00000013757	ENST00000369339.3:c.329A>G	1.37:g.145302704A>G	ENSP00000358345:p.Lys110Arg	Somatic	53	2	0.0377358		WXS	Illumina HiSeq	Phase_I	16	9	0.5625	NM_001039703	Q5RHC0|Q9NWN6	Missense_Mutation	SNP	ENST00000369339.3	37		.	.	.	.	.	.	.	.	.	.	.	0.005	-2.236338	0.00277	.	.	ENSG00000163386	ENST00000448873;ENST00000369338;ENST00000369334;ENST00000342960	T;T	0.09911	2.93;4.61	0.712	-0.599	0.11645	.	.	.	.	.	T	0.00815	0.0027	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.09377	0.004	T	0.47484	-0.9114	7	0.02654	T	1	.	.	.	.	.	110	A8MQ30	.	R	306;110;110;381	ENSP00000358344:K110R;ENSP00000345684:K381R	ENSP00000345684:K381R	K	+	2	0	NBPF10	144014061	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	-1.782000	0.01772	-0.240000	0.09696	0.336000	0.21669	AAG	G|1.000;|0.000	1.000	weak		0.522	NBPF10-001	KNOWN	not_best_in_genome_evidence|basic	protein_coding	protein_coding	OTTHUMT00000038550.3	NM_001039703	
ZNF512	84450	hgsc.bcm.edu	37	2	27838058	27838058	+	Silent	SNP	C	C	A	rs11127071	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:27838058C>A	ENST00000355467.4	+	11	1238	c.1155C>A	c.(1153-1155)ctC>ctA	p.L385L	ZNF512_ENST00000416005.2_Silent_p.L356L|ZNF512_ENST00000413371.2_Silent_p.L308L|RP11-158I13.2_ENST00000505973.1_RNA|ZNF512_ENST00000556601.1_Silent_p.L254L|ZNF512_ENST00000379717.1_Silent_p.L384L	NM_001271287.1|NM_001271288.1|NM_001271289.1|NM_001271318.1|NM_032434.3	NP_001258216.1|NP_001258217.1|NP_001258218.1|NP_001258247.1|NP_115810.2	Q96ME7	ZN512_HUMAN	zinc finger protein 512	385					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(5)|large_intestine(3)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24	Acute lymphoblastic leukemia(172;0.155)					GTCCAGGGCTCCCTACCTTCA	0.378													A|||	3269	0.652756	0.7148	0.6873	5008	,	,		17541	0.8452		0.497	False		,,,				2504	0.5061				p.L385L		Atlas-SNP	.											.	ZNF512	54	.	0			c.C1155A						PASS	.	A		2965,1441	466.0+/-354.4	979,1007,217	176.0	168.0	170.0		1155	-6.0	0.4	2	dbSNP_120	170	4252,4348	581.1+/-391.2	1064,2124,1112	no	coding-synonymous	ZNF512	NM_032434.2		2043,3131,1329	AA,AC,CC		49.4419,32.7054,44.5102		385/568	27838058	7217,5789	2203	4300	6503	SO:0001819	synonymous_variant	84450	exon11			AGGGCTCCCTACC	AL833748	CCDS1758.1, CCDS59428.1, CCDS59429.1	2p23	2008-02-05			ENSG00000243943	ENSG00000243943		"""Zinc fingers, C2H2-type"""	29380	protein-coding gene	gene with protein product						11347906	Standard	NM_032434		Approved	KIAA1805	uc002rla.4	Q96ME7	OTTHUMG00000097786	ENST00000355467.4:c.1155C>A	2.37:g.27838058C>A		Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	158	157	0.993671	NM_032434	B4DSM5|Q53RZ7|Q86XK6|Q96JM0	Silent	SNP	ENST00000355467.4	37	CCDS1758.1																																																																																			C|0.399;A|0.601	0.601	strong		0.378	ZNF512-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000215029.2	NM_032434	
AP1G1	164	hgsc.bcm.edu	37	16	71773190	71773190	+	Missense_Mutation	SNP	G	G	T	rs904763	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:71773190G>T	ENST00000299980.4	-	20	2495	c.2054C>A	c.(2053-2055)cCc>cAc	p.P685H	AP1G1_ENST00000423132.2_Missense_Mutation_p.P688H|AP1G1_ENST00000569748.1_Missense_Mutation_p.P685H|AP1G1_ENST00000393512.3_Missense_Mutation_p.P688H|AP1G1_ENST00000433195.2_Missense_Mutation_p.P708H|AP1G1_ENST00000564155.1_Missense_Mutation_p.P110H	NM_001128.5	NP_001119.3	O43747	AP1G1_HUMAN	adaptor-related protein complex 1, gamma 1 subunit	685			P -> H (in dbSNP:rs904763). {ECO:0000269|PubMed:9733768}.		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|endosome to melanosome transport (GO:0035646)|Golgi to lysosome transport (GO:0090160)|intracellular protein transport (GO:0006886)|melanosome organization (GO:0032438)|membrane organization (GO:0061024)|positive regulation of natural killer cell degranulation (GO:0043323)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of defense response to virus by virus (GO:0050690)|viral process (GO:0016032)	AP-type membrane coat adaptor complex (GO:0030119)|clathrin adaptor complex (GO:0030131)|clathrin-coated vesicle (GO:0030136)|clathrin-coated vesicle membrane (GO:0030665)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|recycling endosome (GO:0055037)|trans-Golgi network membrane (GO:0032588)	GTP-dependent protein binding (GO:0030742)|kinesin binding (GO:0019894)|protein transporter activity (GO:0008565)|Rab GTPase binding (GO:0017137)|transporter activity (GO:0005215)			breast(1)|endometrium(8)|large_intestine(6)|lung(7)|ovary(4)|pancreas(1)|urinary_tract(1)	28		Ovarian(137;0.125)				CAACAAGAAGGGGGGCTGGGA	0.473													G|||	1206	0.240815	0.1112	0.1945	5008	,	,		17689	0.1895		0.2127	False		,,,				2504	0.5307				p.P688H		Atlas-SNP	.											.	AP1G1	83	.	0			c.C2063A						PASS	.	G	HIS/PRO,HIS/PRO	553,3843	247.2+/-255.5	40,473,1685	78.0	79.0	79.0		2063,2054	5.7	1.0	16	dbSNP_86	79	1712,6888	312.0+/-310.6	188,1336,2776	yes	missense,missense	AP1G1	NM_001030007.1,NM_001128.5	77,77	228,1809,4461	TT,TG,GG		19.907,12.5796,17.4284	benign,benign	688/826,685/823	71773190	2265,10731	2198	4300	6498	SO:0001583	missense	164	exon21			AAGAAGGGGGGCT	Y12226	CCDS32480.1, CCDS45522.1	16q23	2009-08-03				ENSG00000166747			555	protein-coding gene	gene with protein product	"""gamma1-adaptin"""	603533		CLAPG1, ADTG		9653655, 9733768	Standard	NM_001128		Approved		uc010cgg.3	O43747		ENST00000299980.4:c.2054C>A	16.37:g.71773190G>T	ENSP00000299980:p.Pro685His	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	202	115	0.569307	NM_001030007	O75709|O75842|Q9UG09|Q9Y3U4	Missense_Mutation	SNP	ENST00000299980.4	37	CCDS32480.1	403	0.18452380952380953	58	0.11788617886178862	80	0.22099447513812154	115	0.20104895104895104	150	0.19788918205804748	G	16.36	3.100175	0.56183	0.125796	0.19907	ENSG00000166747	ENST00000299980;ENST00000393512;ENST00000423132;ENST00000433195	T;T;T;T	0.15487	2.43;2.43;2.43;2.42	5.65	5.65	0.86999	Clathrin adaptor, gamma-adaptin, appendage (1);	0.161882	0.56097	D	0.000024	T	0.00012	0.0000	L	0.38175	1.15	0.21184	P	0.999763743	B;B;B	0.32203	0.075;0.36;0.259	B;B;B	0.34418	0.129;0.182;0.136	T	0.47381	-0.9122	9	0.19147	T	0.46	-2.506	14.5426	0.68005	0.0:0.0:0.8536:0.1464	rs904763;rs3794690;rs52820202;rs61682139;rs904763	685;708;688	O43747;B3KXW5;O43747-2	AP1G1_HUMAN;.;.	H	685;688;688;708	ENSP00000299980:P685H;ENSP00000377148:P688H;ENSP00000409153:P688H;ENSP00000403259:P708H	ENSP00000299980:P685H	P	-	2	0	AP1G1	70330691	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	6.138000	0.71717	2.658000	0.90341	0.650000	0.86243	CCC	G|0.820;T|0.180	0.180	strong		0.473	AP1G1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434147.1		
PTPRN2	5799	hgsc.bcm.edu	37	7	157929370	157929370	+	Missense_Mutation	SNP	C	C	T	rs55645575	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:157929370C>T	ENST00000389418.4	-	8	1159	c.1150G>A	c.(1150-1152)Gac>Aac	p.D384N	PTPRN2_ENST00000409483.1_Missense_Mutation_p.D346N|PTPRN2_ENST00000389416.4_Missense_Mutation_p.D367N|PTPRN2_ENST00000389413.3_Missense_Mutation_p.D384N|PTPRN2_ENST00000404321.2_Missense_Mutation_p.D407N	NM_002847.3	NP_002838.2	Q92932	PTPR2_HUMAN	protein tyrosine phosphatase, receptor type, N polypeptide 2	384					negative regulation of GTPase activity (GO:0034260)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	endoplasmic reticulum lumen (GO:0005788)|integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)|secretory granule (GO:0030141)|terminal bouton (GO:0043195)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|liver(1)|lung(42)|ovary(4)|pleura(1)|prostate(2)|skin(10)|upper_aerodigestive_tract(1)	86	all_neural(206;0.181)	all_cancers(7;8.99e-13)|all_epithelial(9;2.4e-06)|all_hematologic(28;0.0155)|Breast(660;0.132)	OV - Ovarian serous cystadenocarcinoma(82;0.00463)	STAD - Stomach adenocarcinoma(7;0.0875)		CTATCATCGTCGTCCTGCACT	0.443													C|||	27	0.00539137	0.0	0.0072	5008	,	,		17715	0.0		0.0159	False		,,,				2504	0.0061				p.D384N		Atlas-SNP	.											.	PTPRN2	243	.	0			c.G1150A						PASS	.		ASN/ASP,ASN/ASP,ASN/ASP	13,4393	20.2+/-43.8	0,13,2190	194.0	151.0	166.0		1150,1099,1150	-0.7	0.0	7	dbSNP_129	166	130,8470	66.3+/-128.7	1,128,4171	yes	missense,missense,missense	PTPRN2	NM_002847.3,NM_130842.2,NM_130843.2	23,23,23	1,141,6361	TT,TC,CC		1.5116,0.2951,1.0995	benign,benign,benign	384/1016,367/999,384/987	157929370	143,12863	2203	4300	6503	SO:0001583	missense	5799	exon8			CATCGTCGTCCTG	AB002385	CCDS5947.1, CCDS5948.1, CCDS5949.1	7q36	2011-06-09			ENSG00000155093	ENSG00000155093		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"""	9677	protein-coding gene	gene with protein product	"""IAR PTPRP"""	601698				8954911, 9220540	Standard	NM_130842		Approved	KIAA0387, phogrin, ICAAR, IA-2beta	uc003wno.3	Q92932	OTTHUMG00000152646	ENST00000389418.4:c.1150G>A	7.37:g.157929370C>T	ENSP00000374069:p.Asp384Asn	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	88	32	0.363636	NM_130843	E9PC57|Q8N4I5|Q92662|Q9Y4F8|Q9Y4I6	Missense_Mutation	SNP	ENST00000389418.4	37	CCDS5947.1	14	0.00641025641025641	0	0.0	2	0.0055248618784530384	0	0.0	12	0.0158311345646438	C	4.357	0.065672	0.08388	0.002951	0.015116	ENSG00000155093	ENST00000409483;ENST00000389413;ENST00000389416;ENST00000389418;ENST00000404321	T;T;T;T;T	0.02916	4.13;4.11;4.13;4.13;4.12	4.47	-0.709	0.11237	.	.	.	.	.	T	0.00695	0.0023	N	0.08118	0	0.09310	N	1	B;B;B;B;B	0.10296	0.003;0.002;0.003;0.002;0.002	B;B;B;B;B	0.06405	0.002;0.001;0.002;0.001;0.001	T	0.49194	-0.8965	9	0.17832	T	0.49	.	4.3322	0.11069	0.1523:0.4773:0.0:0.3704	rs55645575	407;346;384;367;384	Q92932-3;E7EM83;Q92932-2;E9PC57;Q92932	.;.;.;.;PTPR2_HUMAN	N	346;384;367;384;407	ENSP00000387114:D346N;ENSP00000374064:D384N;ENSP00000374067:D367N;ENSP00000374069:D384N;ENSP00000385464:D407N	ENSP00000374064:D384N	D	-	1	0	PTPRN2	157622131	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.080000	0.14802	-0.123000	0.11745	-1.747000	0.00681	GAC	C|0.989;T|0.011	0.011	strong		0.443	PTPRN2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000353214.1		
ZBBX	79740	hgsc.bcm.edu	37	3	167051726	167051726	+	Silent	SNP	A	A	G	rs10936530	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:167051726A>G	ENST00000392766.2	-	10	916	c.576T>C	c.(574-576)ttT>ttC	p.F192F	ZBBX_ENST00000469220.1_Intron|ZBBX_ENST00000392764.1_Silent_p.F163F|ZBBX_ENST00000392767.2_Silent_p.F192F|ZBBX_ENST00000455345.2_Silent_p.F192F|ZBBX_ENST00000307529.5_Silent_p.F192F	NM_001199201.1|NM_024687.3	NP_001186130.1|NP_078963.2	A8MT70	ZBBX_HUMAN	zinc finger, B-box domain containing	192						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						CATCCTTTATAAACTGATGGG	0.308													A|||	2306	0.460463	0.4584	0.4395	5008	,	,		14921	0.6637		0.341	False		,,,				2504	0.3916				p.F192F		Atlas-SNP	.											ZBBX_ENST00000455345,NS,carcinoma,-2,2	ZBBX	299	2	0			c.T576C						PASS	.	A	,,	1533,2057		322,889,584	107.0	94.0	98.0		576,489,576	-1.6	0.5	3	dbSNP_120	98	2668,5474		422,1824,1825	no	coding-synonymous,coding-synonymous,coding-synonymous	ZBBX	NM_001199201.1,NM_001199202.1,NM_024687.3	,,	744,2713,2409	GG,GA,AA		32.7684,42.7019,35.808	,,	192/840,163/772,192/801	167051726	4201,7531	1795	4071	5866	SO:0001819	synonymous_variant	79740	exon10			CTTTATAAACTGA	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.576T>C	3.37:g.167051726A>G		Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	119	56	0.470588	NM_024687	A8MV69|B3KSC1|B5MDJ6|F2Z370|Q9H5T8	Silent	SNP	ENST00000392766.2	37	CCDS3199.2																																																																																			A|0.557;G|0.443	0.443	strong		0.308	ZBBX-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000257657.3	NM_024687	
SLC24A2	25769	hgsc.bcm.edu	37	9	19786217	19786217	+	Silent	SNP	G	G	A	rs1536517	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:19786217G>A	ENST00000341998.2	-	1	709	c.648C>T	c.(646-648)atC>atT	p.I216I	SLC24A2_ENST00000286344.3_Silent_p.I216I	NM_001193288.2|NM_020344.3	NP_001180217.1|NP_065077.1	Q9UI40	NCKX2_HUMAN	solute carrier family 24 (sodium/potassium/calcium exchanger), member 2	216					cellular calcium ion homeostasis (GO:0006874)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|learning (GO:0007612)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|memory (GO:0007613)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|intrinsic component of plasma membrane (GO:0031226)|plasma membrane (GO:0005886)	cadmium ion binding (GO:0046870)|calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium, potassium:sodium antiporter activity (GO:0008273)|manganese ion binding (GO:0030145)|nickel cation binding (GO:0016151)|potassium ion binding (GO:0030955)|sodium ion binding (GO:0031402)|symporter activity (GO:0015293)	p.I216I(1)		endometrium(3)|kidney(1)|large_intestine(9)|lung(13)|ovary(3)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	33				GBM - Glioblastoma multiforme(1;1.67e-55)|Lung(42;0.0443)		TAACAAAGAGGATGTTGAATA	0.438													G|||	757	0.151158	0.1868	0.0764	5008	,	,		22564	0.4077		0.0119	False		,,,				2504	0.0348				p.I216I		Atlas-SNP	.											SLC24A2,NS,carcinoma,0,1	SLC24A2	93	1	1	Substitution - coding silent(1)	stomach(1)	c.C648T						PASS	.	G	,	708,3698	295.3+/-283.6	60,588,1555	106.0	99.0	102.0		648,648	4.1	1.0	9	dbSNP_88	102	96,8504	52.7+/-113.3	1,94,4205	no	coding-synonymous,coding-synonymous	SLC24A2	NM_001193288.2,NM_020344.3	,	61,682,5760	AA,AG,GG		1.1163,16.069,6.1818	,	216/645,216/662	19786217	804,12202	2203	4300	6503	SO:0001819	synonymous_variant	25769	exon1			AAAGAGGATGTTG	AF097366	CCDS6493.1, CCDS55297.1	9p22.1	2013-05-22			ENSG00000155886	ENSG00000155886		"""Solute carriers"""	10976	protein-coding gene	gene with protein product		609838				10662833	Standard	NM_020344		Approved	NCKX2	uc003zoa.2	Q9UI40	OTTHUMG00000019646	ENST00000341998.2:c.648C>T	9.37:g.19786217G>A		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	79	30	0.379747	NM_001193288	B7ZLL8|Q9NTN5|Q9NZQ4	Silent	SNP	ENST00000341998.2	37	CCDS6493.1																																																																																			G|0.882;A|0.118	0.118	strong		0.438	SLC24A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051866.2	NM_020344	
TNS1	7145	hgsc.bcm.edu	37	2	218695102	218695102	+	Missense_Mutation	SNP	G	G	A	rs3796028	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:218695102G>A	ENST00000171887.4	-	21	3462	c.3010C>T	c.(3010-3012)Cgg>Tgg	p.R1004W	TNS1_ENST00000419504.1_Missense_Mutation_p.R1004W|TNS1_ENST00000430930.1_Intron	NM_022648.4	NP_072174.3	Q9HBL0	TENS1_HUMAN	tensin 1	1004			R -> W (in dbSNP:rs3796028).		cell-substrate junction assembly (GO:0007044)|fibroblast migration (GO:0010761)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)	poly(A) RNA binding (GO:0044822)			breast(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(23)|liver(1)|lung(24)|ovary(3)|pancreas(1)|prostate(3)|skin(5)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	79		Renal(207;0.0483)|Lung NSC(271;0.213)		Epithelial(149;4.43e-06)|all cancers(144;0.000653)|LUSC - Lung squamous cell carcinoma(224;0.0091)|Lung(261;0.013)		GGCTGGATCCGTCTTCTGGTA	0.567													G|||	1880	0.375399	0.32	0.4308	5008	,	,		19019	0.4276		0.3648	False		,,,				2504	0.3681				p.R1004W		Atlas-SNP	.											.	TNS1	251	.	0			c.C3010T						PASS	.	G	TRP/ARG	1375,3031	455.5+/-351.0	201,973,1029	84.0	73.0	77.0		3010	-1.2	1.0	2	dbSNP_107	77	2946,5654	457.3+/-364.3	501,1944,1855	yes	missense	TNS1	NM_022648.4	101	702,2917,2884	AA,AG,GG		34.2558,31.2074,33.2231	possibly-damaging	1004/1736	218695102	4321,8685	2203	4300	6503	SO:0001583	missense	7145	exon21			GGATCCGTCTTCT	AB209238	CCDS2407.1	2q35-q36	2014-06-13	2005-05-13	2005-05-13	ENSG00000079308	ENSG00000079308		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"", ""SH2 domain containing"""	11973	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 155"""	600076	"""tensin"", ""matrix-remodelling associated 6"""	TNS, MXRA6			Standard	NM_022648		Approved	DKFZp586K0617, PPP1R155	uc002vgt.2	Q9HBL0	OTTHUMG00000133056	ENST00000171887.4:c.3010C>T	2.37:g.218695102G>A	ENSP00000171887:p.Arg1004Trp	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	58	34	0.586207	NM_022648	Q4ZG71|Q6IPI5	Missense_Mutation	SNP	ENST00000171887.4	37	CCDS2407.1	842	0.38553113553113555	175	0.3556910569105691	144	0.39779005524861877	256	0.44755244755244755	267	0.35224274406332456	G	3.509	-0.100132	0.07010	0.312074	0.342558	ENSG00000079308	ENST00000171887;ENST00000419504	D;D	0.91407	-2.84;-2.83	4.4	-1.23	0.09465	.	7739.210000	0.00166	N	0.000000	T	0.00012	0.0000	N	0.08118	0	0.09310	P	0.999999888189	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.34725	-0.9817	9	0.59425	D	0.04	.	4.2296	0.10597	0.0938:0.2993:0.47:0.1369	rs3796028;rs17789579;rs3796028	1004;1004	Q9HBL0;E9PF55	TENS1_HUMAN;.	W	1004	ENSP00000171887:R1004W;ENSP00000408724:R1004W	ENSP00000171887:R1004W	R	-	1	2	TNS1	218403347	0.797000	0.28877	0.993000	0.49108	0.017000	0.09413	-0.422000	0.07043	-0.055000	0.13244	-2.034000	0.00421	CGG	G|0.646;A|0.354	0.354	strong		0.567	TNS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256672.2	NM_022648	
NOP14	8602	hgsc.bcm.edu	37	4	2951804	2951804	+	Missense_Mutation	SNP	A	A	G	rs2515960	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:2951804A>G	ENST00000314262.6	-	8	1187	c.1139T>C	c.(1138-1140)tTg>tCg	p.L380S	NOP14_ENST00000416614.2_Missense_Mutation_p.L380S|NOP14-AS1_ENST00000503709.1_RNA|NOP14-AS1_ENST00000505731.1_RNA|NOP14_ENST00000398071.4_Missense_Mutation_p.L380S|NOP14_ENST00000502735.1_Missense_Mutation_p.L380S|NOP14-AS1_ENST00000515194.1_RNA	NM_003703.1	NP_003694.1	P78316	NOP14_HUMAN	NOP14 nucleolar protein	380			L -> S (in dbSNP:rs2515960). {ECO:0000269|Ref.2}.		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)|maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000462)|ribosomal small subunit biogenesis (GO:0042274)|rRNA processing (GO:0006364)	90S preribosome (GO:0030686)|membrane (GO:0016020)|mitochondrion (GO:0005739)|Noc4p-Nop14p complex (GO:0030692)|nucleolus (GO:0005730)|nucleus (GO:0005634)|small-subunit processome (GO:0032040)	enzyme binding (GO:0019899)|poly(A) RNA binding (GO:0044822)|snoRNA binding (GO:0030515)			NS(1)|endometrium(2)|kidney(3)|large_intestine(9)|lung(12)|pancreas(1)|skin(1)|urinary_tract(1)	30						TTCCAGGTCCAAGTGGCTATC	0.547													G|||	2041	0.407548	0.6815	0.415	5008	,	,		20210	0.1915		0.4433	False		,,,				2504	0.2178				p.L380S		Atlas-SNP	.											.	NOP14	69	.	0			c.T1139C						PASS	.	G	SER/LEU	2761,1645	505.2+/-366.1	862,1037,304	315.0	311.0	312.0		1139	5.4	1.0	4	dbSNP_100	312	3694,4906	621.0+/-397.1	826,2042,1432	yes	missense	NOP14	NM_003703.1	145	1688,3079,1736	GG,GA,AA		42.9535,37.3355,49.6309	benign	380/858	2951804	6455,6551	2203	4300	6503	SO:0001583	missense	8602	exon8			AGGTCCAAGTGGC	AB000467	CCDS33945.1	4p16.3	2012-12-10	2012-12-10	2008-10-13	ENSG00000087269	ENSG00000087269			16821	protein-coding gene	gene with protein product	"""NOP14 homolog (S. cerevisiae)"""	611526	"""chromosome 4 open reading frame 9"", ""nucleolar protein 14"", ""nucleolar protein 14 homolog (yeast)"", ""NOP14 nucleolar protein homolog (yeast)"""	C4orf9, NOL14		9734812, 11694595	Standard	XR_241655		Approved	RES4-25, UTP2	uc003ggj.1	P78316	OTTHUMG00000159911	ENST00000314262.6:c.1139T>C	4.37:g.2951804A>G	ENSP00000315674:p.Leu380Ser	Somatic	256	1	0.00390625		WXS	Illumina HiSeq	Phase_I	202	199	0.985148	NM_003703	D3DVR6|Q7LGI5|Q7Z6K0|Q8TBR6	Missense_Mutation	SNP	ENST00000314262.6	37	CCDS33945.1	925	0.42353479853479853	332	0.6747967479674797	153	0.42265193370165743	104	0.18181818181818182	336	0.44327176781002636	G	2.803	-0.248704	0.05867	0.626645	0.429535	ENSG00000087269	ENST00000416614;ENST00000314262;ENST00000502735;ENST00000398071;ENST00000546137	T;T;T;T	0.28454	1.61;1.61;1.61;1.61	5.43	5.43	0.79202	.	0.230549	0.37906	N	0.001898	T	0.00012	0.0000	N	0.00026	-2.66	0.41445	P	0.012051000000000034	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.37384	-0.9708	9	0.87932	D	0	-5.1055	13.1764	0.59629	0.0771:0.0:0.9229:0.0	rs2515960;rs13126429;rs52813409;rs61659094;rs2515960	380;380	E9PFK5;P78316	.;NOP14_HUMAN	S	380;380;380;380;279	ENSP00000405068:L380S;ENSP00000315674:L380S;ENSP00000427415:L380S;ENSP00000381146:L380S	ENSP00000315674:L380S	L	-	2	0	NOP14	2921602	1.000000	0.71417	0.955000	0.39395	0.104000	0.19210	3.876000	0.56115	1.309000	0.44985	-0.119000	0.15052	TTG	A|0.537;G|0.463	0.463	strong		0.547	NOP14-002	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000358135.2	NM_003703	
FAT4	79633	hgsc.bcm.edu	37	4	126402890	126402890	+	Silent	SNP	G	G	A	rs6824160	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:126402890G>A	ENST00000394329.3	+	15	12826	c.12813G>A	c.(12811-12813)gtG>gtA	p.V4271V	FAT4_ENST00000335110.5_Silent_p.V2512V	NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	4271	Laminin G-like 2. {ECO:0000255|PROSITE- ProRule:PRU00122}.				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						ACACTACTGTGAAGGTGAGAT	0.403													G|||	673	0.134385	0.0068	0.1124	5008	,	,		18179	0.2579		0.1302	False		,,,				2504	0.1994				p.V4271V		Atlas-SNP	.											.	FAT4	1752	.	0			c.G12813A						PASS	.	G		124,4282	92.0+/-130.7	5,114,2084	70.0	65.0	67.0		12813	4.9	1.0	4	dbSNP_116	67	1039,7561	219.2+/-257.4	59,921,3320	no	coding-synonymous	FAT4	NM_024582.4		64,1035,5404	AA,AG,GG		12.0814,2.8143,8.942		4271/4982	126402890	1163,11843	2203	4300	6503	SO:0001819	synonymous_variant	79633	exon15			TACTGTGAAGGTG	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.12813G>A	4.37:g.126402890G>A		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	90	37	0.411111	NM_024582	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Silent	SNP	ENST00000394329.3	37	CCDS3732.3																																																																																			G|0.890;A|0.110	0.110	strong		0.403	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582	
OSCP1	127700	hgsc.bcm.edu	37	1	36889005	36889005	+	Silent	SNP	G	G	A	rs16822954	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:36889005G>A	ENST00000356637.5	-	6	672	c.609C>T	c.(607-609)tcC>tcT	p.S203S	OSCP1_ENST00000315643.9_Silent_p.S203S|OSCP1_ENST00000235532.5_Silent_p.S193S|OSCP1_ENST00000495222.1_5'UTR|OSCP1_ENST00000433045.2_Silent_p.S148S			Q8WVF1	OSCP1_HUMAN	organic solute carrier partner 1	203					transport (GO:0006810)	plasma membrane (GO:0005886)				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						GAACAGGCCCGGACACCGGCA	0.433													g|||	674	0.134585	0.0726	0.1297	5008	,	,		16851	0.3065		0.0905	False		,,,				2504	0.09				p.S193S		Atlas-SNP	.											.	OSCP1	48	.	0			c.C579T						PASS	.	G		359,4047	184.3+/-211.7	8,343,1852	89.0	93.0	92.0		579	-9.5	0.4	1	dbSNP_123	92	815,7785	189.3+/-236.1	31,753,3516	no	coding-synonymous	OSCP1	NM_145047.4		39,1096,5368	AA,AG,GG		9.4767,8.148,9.0266		193/380	36889005	1174,11832	2203	4300	6503	SO:0001819	synonymous_variant	127700	exon5			AGGCCCGGACACC		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.609C>T	1.37:g.36889005G>A		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	66	34	0.515152	NM_145047	A6NHM5|A6NHS9|A6NIN9|Q4AEJ0|Q8N7G2|Q8TDF1	Silent	SNP	ENST00000356637.5	37																																																																																				G|0.890;A|0.110	0.110	strong		0.433	OSCP1-010	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000389759.1	NM_145047	
ARHGEF5	7984	hgsc.bcm.edu	37	7	144062222	144062222	+	Silent	SNP	G	G	A	rs201478085		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:144062222G>A	ENST00000056217.5	+	2	2634	c.2460G>A	c.(2458-2460)ccG>ccA	p.P820P	ARHGEF5_ENST00000471847.2_5'Flank	NM_005435.3	NP_005426.2	Q12774	ARHG5_HUMAN	Rho guanine nucleotide exchange factor (GEF) 5	820					actin cytoskeleton organization (GO:0030036)|intracellular signal transduction (GO:0035556)|myeloid dendritic cell chemotaxis (GO:0002408)|positive regulation of podosome assembly (GO:0071803)|regulation of Rho GTPase activity (GO:0032319)		GTP binding (GO:0005525)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.P820P(1)		breast(1)|endometrium(6)|kidney(8)|large_intestine(9)|liver(1)|lung(8)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	40	Melanoma(164;0.14)					CTGATTTGCCGCAGCCCCACC	0.607																																					p.P820P		Atlas-SNP	.											ARHGEF5,NS,carcinoma,+2,2	ARHGEF5	73	2	1	Substitution - coding silent(1)	large_intestine(1)	c.G2460A						scavenged	.						2.0	3.0	3.0					7																	144062222		1307	2929	4236	SO:0001819	synonymous_variant	7984	exon2			TTTGCCGCAGCCC	U02082	CCDS34771.1	7q35	2012-09-20			ENSG00000050327	ENSG00000050327		"""Rho guanine nucleotide exchange factors"""	13209	protein-coding gene	gene with protein product	"""transforming immortalized mammary oncogene"", ""guanine nucleotide regulatory protein TIM"""	600888				8134109, 7656213	Standard	NM_005435		Approved	TIM, TIM1, GEF5, P60	uc003wel.3	Q12774	OTTHUMG00000158004	ENST00000056217.5:c.2460G>A	7.37:g.144062222G>A		Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	151	27	0.178808	NM_005435	A6NNJ2|Q6ZML7	Silent	SNP	ENST00000056217.5	37	CCDS34771.1	.	.	.	.	.	.	.	.	.	.	G	0.015	-1.555218	0.00918	.	.	ENSG00000050327	ENST00000474817	.	.	.	3.89	-7.77	0.01227	.	.	.	.	.	T	0.16171	0.0389	.	.	.	0.19575	N	0.999965	.	.	.	.	.	.	T	0.16129	-1.0413	4	.	.	.	0.9342	2.0231	0.03513	0.2015:0.1496:0.4066:0.2422	.	.	.	.	H	74	.	.	R	+	2	0	ARHGEF5	143693155	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-3.255000	0.00538	-2.388000	0.00588	-1.365000	0.01206	CGC	G|0.995;A|0.005	0.005	weak		0.607	ARHGEF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349981.1	NM_005435	
LRP1B	53353	hgsc.bcm.edu	37	2	141259283	141259283	+	Silent	SNP	G	G	A	rs35296183	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:141259283G>A	ENST00000389484.3	-	55	9794	c.8823C>T	c.(8821-8823)gaC>gaT	p.D2941D		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	2941	EGF-like 11. {ECO:0000255|PROSITE- ProRule:PRU00076}.				protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)			NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		GGTCTTGACAGTCTTGAGAAC	0.378										TSP Lung(27;0.18)			G|||	523	0.104433	0.0401	0.1066	5008	,	,		16546	0.0188		0.1988	False		,,,				2504	0.181				p.D2941D	Colon(99;50 2074 2507 20106)	Atlas-SNP	.											.	LRP1B	1315	.	0			c.C8823T						PASS	.	G		283,4123	158.5+/-191.2	7,269,1927	115.0	118.0	117.0		8823	1.2	1.0	2	dbSNP_126	117	1947,6653	343.9+/-325.1	215,1517,2568	no	coding-synonymous	LRP1B	NM_018557.2		222,1786,4495	AA,AG,GG		22.6395,6.4231,17.1459		2941/4600	141259283	2230,10776	2203	4300	6503	SO:0001819	synonymous_variant	53353	exon55			TTGACAGTCTTGA	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.8823C>T	2.37:g.141259283G>A		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	72	32	0.444444	NM_018557	Q8WY29|Q8WY30|Q8WY31	Silent	SNP	ENST00000389484.3	37	CCDS2182.1																																																																																			G|0.847;A|0.153	0.153	strong		0.378	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557	
PLCB3	5331	hgsc.bcm.edu	37	11	64026685	64026685	+	Silent	SNP	C	C	T	rs28395882	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:64026685C>T	ENST00000540288.1	+	13	1597	c.1494C>T	c.(1492-1494)tcC>tcT	p.S498S	PLCB3_ENST00000325234.5_Silent_p.S431S|PLCB3_ENST00000279230.6_Silent_p.S498S	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						scavenged	.	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	13	0	0		WXS	Illumina HiSeq	Phase_I	10	3	0.3	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		
PRR11	55771	hgsc.bcm.edu	37	17	57247133	57247133	+	Missense_Mutation	SNP	G	G	A	rs145780567	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:57247133G>A	ENST00000262293.4	+	2	332	c.20G>A	c.(19-21)cGa>cAa	p.R7Q		NM_018304.3	NP_060774.2	Q96HE9	PRR11_HUMAN	proline rich 11	7						cytoplasm (GO:0005737)|membrane (GO:0016020)				breast(1)|kidney(1)|large_intestine(2)|lung(8)|ovary(3)|pancreas(1)	16	Medulloblastoma(34;0.0922)|all_neural(34;0.101)					TTCAAACAACGAAGACGAAAG	0.338													G|||	15	0.00299521	0.0	0.0058	5008	,	,		14982	0.001		0.0099	False		,,,				2504	0.0				p.R7Q		Atlas-SNP	.											PRR11,NS,carcinoma,+1,1	PRR11	36	1	0			c.G20A						PASS	.	G	GLN/ARG	11,4395	17.9+/-39.9	0,11,2192	62.0	60.0	61.0		20	1.2	0.4	17	dbSNP_134	61	78,8522	43.6+/-101.6	0,78,4222	yes	missense	PRR11	NM_018304.3	43	0,89,6414	AA,AG,GG		0.907,0.2497,0.6843	benign	7/361	57247133	89,12917	2203	4300	6503	SO:0001583	missense	55771	exon2			AACAACGAAGACG		CCDS11614.1	17q23.2	2005-12-13				ENSG00000068489			25619	protein-coding gene	gene with protein product		615920				11799066	Standard	NM_018304		Approved	FLJ11029	uc002ixf.2	Q96HE9		ENST00000262293.4:c.20G>A	17.37:g.57247133G>A	ENSP00000262293:p.Arg7Gln	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	86	47	0.546512	NM_018304	Q9NUZ7|Q9NXE9	Missense_Mutation	SNP	ENST00000262293.4	37	CCDS11614.1	11	0.005036630036630037	0	0.0	4	0.011049723756906077	0	0.0	7	0.009234828496042216	G	4.777	0.144546	0.09134	0.002497	0.00907	ENSG00000068489	ENST00000262293	.	.	.	4.38	1.17	0.20885	.	0.450854	0.18874	N	0.128767	T	0.19765	0.0475	L	0.32530	0.975	0.18873	N	0.999986	B	0.23490	0.086	B	0.14578	0.011	T	0.12319	-1.0552	9	0.49607	T	0.09	-2.239	6.1076	0.20081	0.3479:0.0:0.6521:0.0	.	7	Q96HE9	PRR11_HUMAN	Q	7	.	ENSP00000262293:R7Q	R	+	2	0	PRR11	54601915	1.000000	0.71417	0.357000	0.25798	0.008000	0.06430	0.486000	0.22340	0.182000	0.20032	0.561000	0.74099	CGA	G|0.994;A|0.006	0.006	strong		0.338	PRR11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445949.1	NM_018304	
MUC4	4585	hgsc.bcm.edu	37	3	195506990	195506990	+	Missense_Mutation	SNP	C	C	G	rs200783894	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195506990C>G	ENST00000463781.3	-	2	11920	c.11461G>C	c.(11461-11463)Gac>Cac	p.D3821H	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.D3821H	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)		GGGGTGGTGTCACCTGTGGAT	0.587													.|||	203	0.0405351	0.0537	0.0476	5008	,	,		9160	0.0188		0.0368	False		,,,				2504	0.044				p.D3821H		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	0			c.G11461C						scavenged	.						4.0	4.0	4.0					3																	195506990		522	1378	1900	SO:0001583	missense	4585	exon2			TGGTGTCACCTGT	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.11461G>C	3.37:g.195506990C>G	ENSP00000417498:p.Asp3821His	Somatic	70	5	0.0714286		WXS	Illumina HiSeq	Phase_I	59	10	0.169492	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	c	3.752	-0.051387	0.07407	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.35048	1.4;1.33	.	.	.	.	.	.	.	.	T	0.16727	0.0402	N	0.19112	0.55	0.09310	N	1	B	0.26876	0.162	B	0.09377	0.004	T	0.18935	-1.0321	7	.	.	.	.	2.6646	0.05037	0.0:0.5037:0.0:0.4962	rs3107751;rs28520424	3693	E7ESK3	.	H	3821	ENSP00000417498:D3821H;ENSP00000420243:D3821H	.	D	-	1	0	MUC4	196991769	0.001000	0.12720	0.109000	0.21407	0.109000	0.19521	-0.170000	0.09897	0.064000	0.16427	0.064000	0.15345	GAC	C|0.746;G|0.253	0.253	strong		0.587	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
PRKCQ	5588	hgsc.bcm.edu	37	10	6498723	6498723	+	Silent	SNP	G	G	A	rs11258943	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:6498723G>A	ENST00000263125.5	-	15	1659	c.1560C>T	c.(1558-1560)atC>atT	p.I520I	PRKCQ_ENST00000397176.2_Silent_p.I520I|PRKCQ_ENST00000539722.1_Silent_p.I395I	NM_001282644.1|NM_006257.3	NP_001269573.1|NP_006248.1	Q04759	KPCT_HUMAN	protein kinase C, theta	520	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|Fc-epsilon receptor signaling pathway (GO:0038095)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|membrane protein ectodomain proteolysis (GO:0006509)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of T cell apoptotic process (GO:0070233)|phototransduction, visible light (GO:0007603)|platelet activation (GO:0030168)|positive regulation of interleukin-17 production (GO:0032740)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of interleukin-4 production (GO:0032753)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of T-helper 17 type immune response (GO:2000318)|positive regulation of T-helper 2 cell activation (GO:2000570)|protein ubiquitination (GO:0016567)|regulation of cell growth (GO:0001558)|regulation of platelet aggregation (GO:0090330)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|regulation of transcription, DNA-templated (GO:0006355)|rhodopsin mediated signaling pathway (GO:0016056)|T cell receptor signaling pathway (GO:0050852)	cytosol (GO:0005829)|immunological synapse (GO:0001772)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)|ubiquitin-protein transferase activity (GO:0004842)			NS(1)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|liver(1)|lung(13)|ovary(4)|prostate(1)|skin(4)|stomach(2)	45					Tamoxifen(DB00675)	CAAAATCCGCGATCTTGATAT	0.418													G|||	708	0.141374	0.1551	0.1153	5008	,	,		20609	0.0645		0.2187	False		,,,				2504	0.1411				p.I520I	Ovarian(50;572 1126 10530 25349 30594)	Atlas-SNP	.											.	PRKCQ	113	.	0			c.C1560T						PASS	.	G	,	701,3705	291.0+/-281.2	56,589,1558	247.0	198.0	215.0		1560,1560	-9.7	0.0	10	dbSNP_120	215	1869,6731	333.1+/-320.4	186,1497,2617	no	coding-synonymous,coding-synonymous	PRKCQ	NM_001242413.1,NM_006257.3	,	242,2086,4175	AA,AG,GG		21.7326,15.9101,19.7601	,	520/644,520/707	6498723	2570,10436	2203	4300	6503	SO:0001819	synonymous_variant	5588	exon15			ATCCGCGATCTTG	L07032	CCDS7079.1, CCDS55701.1, CCDS60482.1	10p15	2009-07-10			ENSG00000065675	ENSG00000065675	2.7.11.1		9410	protein-coding gene	gene with protein product		600448				8444877	Standard	NM_001282645		Approved		uc001ijj.2	Q04759	OTTHUMG00000017623	ENST00000263125.5:c.1560C>T	10.37:g.6498723G>A		Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	121	53	0.438017	NM_006257	B4DF52|Q14DH6|Q3MJF1|Q64FY5|Q9H508|Q9H549	Silent	SNP	ENST00000263125.5	37	CCDS7079.1	315	0.14423076923076922	70	0.14227642276422764	47	0.1298342541436464	29	0.050699300699300696	169	0.22295514511873352	G	0.028	-1.352505	0.01256	0.159101	0.217326	ENSG00000065675	ENST00000397178	.	.	.	5.55	-9.67	0.00531	.	.	.	.	.	T	0.00039	0.0001	.	.	.	0.09310	P	0.9999999999999992	.	.	.	.	.	.	T	0.10706	-1.0618	3	.	.	.	.	12.5145	0.56024	0.2922:0.0:0.5408:0.167	rs11258943;rs11258943	.	.	.	L	293	.	.	S	-	2	0	PRKCQ	6538729	0.012000	0.17670	0.026000	0.17262	0.001000	0.01503	-1.264000	0.02847	-2.746000	0.00377	-2.811000	0.00111	TCG	G|0.837;A|0.163	0.163	strong		0.418	PRKCQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046665.1	NM_006257	
CHI3L2	1117	hgsc.bcm.edu	37	1	111783982	111783982	+	Silent	SNP	C	C	A	rs13721	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:111783982C>A	ENST00000445067.2	+	11	1723	c.952C>A	c.(952-954)Cgg>Agg	p.R318R	CHI3L2_ENST00000369748.4_Silent_p.R318R|CHI3L2_ENST00000466741.1_Silent_p.R239R|CHI3L2_ENST00000369744.2_Silent_p.R308R|CHI3L2_ENST00000524472.1_Silent_p.R239R|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	76	0	0		WXS	Illumina HiSeq	Phase_I	80	80	1	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	
PDZD8	118987	hgsc.bcm.edu	37	10	119043295	119043295	+	Silent	SNP	C	C	T	rs41314485	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:119043295C>T	ENST00000334464.5	-	5	3188	c.2949G>A	c.(2947-2949)gaG>gaA	p.E983E	PDZD8_ENST00000482496.1_5'Flank	NM_173791.3	NP_776152.1	Q8NEN9	PDZD8_HUMAN	PDZ domain containing 8	983					cytoskeleton organization (GO:0007010)|intracellular signal transduction (GO:0035556)|regulation of cell morphogenesis (GO:0022604)|viral process (GO:0016032)	membrane (GO:0016020)	metal ion binding (GO:0046872)			kidney(3)|large_intestine(8)|lung(24)|upper_aerodigestive_tract(3)	38		Colorectal(252;0.19)		all cancers(201;0.0121)		GACCACAGACCTCCGTGTCAC	0.468													C|||	12	0.00239617	0.0008	0.0	5008	,	,		20619	0.0		0.0099	False		,,,				2504	0.001				p.E983E		Atlas-SNP	.											.	PDZD8	85	.	0			c.G2949A						PASS	.	C		6,4400	11.4+/-27.6	0,6,2197	286.0	283.0	284.0		2949	0.9	1.0	10	dbSNP_127	284	81,8519	47.2+/-106.3	0,81,4219	no	coding-synonymous	PDZD8	NM_173791.3		0,87,6416	TT,TC,CC		0.9419,0.1362,0.6689		983/1155	119043295	87,12919	2203	4300	6503	SO:0001819	synonymous_variant	118987	exon5			ACAGACCTCCGTG	AL122051	CCDS7600.1	10q26.12	2006-01-24		2006-01-24	ENSG00000165650	ENSG00000165650			26974	protein-coding gene	gene with protein product		614235		PDZK8		12477932	Standard	NM_173791		Approved	bA129M16.2, FLJ34427	uc001lde.1	Q8NEN9	OTTHUMG00000019122	ENST00000334464.5:c.2949G>A	10.37:g.119043295C>T		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	131	70	0.534351	NM_173791	Q86WE0|Q86WE5|Q9UFF1	Silent	SNP	ENST00000334464.5	37	CCDS7600.1																																																																																			C|0.993;T|0.007	0.007	strong		0.468	PDZD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050565.1	NM_173791	
INPP5F	22876	hgsc.bcm.edu	37	10	121551581	121551581	+	Silent	SNP	A	A	C	rs2289306	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:121551581A>C	ENST00000369081.1	+	3	475	c.357A>C	c.(355-357)gcA>gcC	p.A119A	INPP5F_ENST00000361976.2_Intron|INPP5F_ENST00000369083.3_Intron			Q01968	OCRL_HUMAN	inositol polyphosphate-5-phosphatase F	0	PH.				cilium assembly (GO:0042384)|in utero embryonic development (GO:0001701)|inositol phosphate metabolic process (GO:0043647)|lipid metabolic process (GO:0006629)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|positive regulation of Rac GTPase activity (GO:0032855)|regulation of Rac GTPase activity (GO:0032314)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|extracellular vesicular exosome (GO:0070062)|Golgi stack (GO:0005795)|Golgi-associated vesicle (GO:0005798)|nucleus (GO:0005634)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	inositol phosphate phosphatase activity (GO:0052745)|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity (GO:0004439)|Rac GTPase activator activity (GO:0030675)|Rac GTPase binding (GO:0048365)	p.A119A(1)		breast(1)|cervix(1)|endometrium(7)|kidney(4)|large_intestine(9)|lung(5)|ovary(5)|pancreas(1)|prostate(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	42		Lung NSC(174;0.109)|all_lung(145;0.142)		all cancers(201;0.00205)|BRCA - Breast invasive adenocarcinoma(275;0.158)		CAGGGTTTGCACTTGGGAAGA	0.502													C|||	2069	0.413139	0.329	0.3501	5008	,	,		17327	0.2341		0.4463	False		,,,				2504	0.7219				p.A215A		Atlas-SNP	.											INPP5F_ENST00000369081,NS,carcinoma,0,1	INPP5F	112	1	1	Substitution - coding silent(1)	stomach(1)	c.A645C						scavenged	.	C		1521,2885	672.5+/-402.6	250,1021,932	116.0	121.0	119.0			3.3	0.2	10	dbSNP_100	119	3820,4780	610.9+/-395.7	886,2048,1366	no	intron	INPP5F	NM_014937.3		1136,3069,2298	CC,CA,AA		44.4186,34.5211,41.0657			121551581	5341,7665	2203	4300	6503	SO:0001819	synonymous_variant	22876	exon5			GTTTGCACTTGGG	AB023183	CCDS7616.1, CCDS58098.1	10q26.13	2009-02-03			ENSG00000198825	ENSG00000198825			17054	protein-coding gene	gene with protein product		609389				10231032, 11274189	Standard	NM_014937		Approved	SAC2, KIAA0966, hSac2	uc001leo.3	Q9Y2H2	OTTHUMG00000019158	ENST00000369081.1:c.357A>C	10.37:g.121551581A>C		Somatic	152	2	0.0131579		WXS	Illumina HiSeq	Phase_I	99	47	0.474747	NM_001243195	A6NKI1|A8KAP2|B7ZLX2|O60800|Q15684|Q15774|Q4VY09|Q4VY10|Q5JQF1|Q5JQF2|Q9UJG5|Q9UMA5	Silent	SNP	ENST00000369081.1	37																																																																																				A|0.616;C|0.384	0.384	strong		0.502	INPP5F-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000050682.1	NM_014937	
OR9G1	390174	hgsc.bcm.edu	37	11	56468258	56468258	+	Missense_Mutation	SNP	C	C	T	rs78340277	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:56468258C>T	ENST00000312153.1	+	1	395	c.395C>T	c.(394-396)gCc>gTc	p.A132V		NM_001005213.1	NP_001005213.1	Q8NH87	OR9G1_HUMAN	olfactory receptor, family 9, subfamily G, member 1	132						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|kidney(1)|lung(25)|stomach(2)|upper_aerodigestive_tract(1)	31						CTGCTTTATGCCCAGGCCATG	0.498													C|||	31	0.0061901	0.0015	0.0029	5008	,	,		19708	0.0		0.0239	False		,,,				2504	0.0031				p.A132V		Atlas-SNP	.											.	.	.	.	0			c.C395T						PASS	.	C	VAL/ALA	16,4386	21.2+/-45.6	0,16,2185	186.0	171.0	176.0		395	4.4	0.8	11	dbSNP_131	176	171,8421	67.7+/-130.1	0,171,4125	yes	missense	OR9G1	NM_001005213.1	64	0,187,6310	TT,TC,CC		1.9902,0.3635,1.4391	possibly-damaging	132/306	56468258	187,12807	2201	4296	6497	SO:0001583	missense	504191	exon1			TTTATGCCCAGGC	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.395C>T	11.37:g.56468258C>T	ENSP00000309012:p.Ala132Val	Somatic	257	0	0		WXS	Illumina HiSeq	Phase_I	227	85	0.374449	NM_001013358	Q6IEU9|Q8NGQ0	Missense_Mutation	SNP	ENST00000312153.1	37	CCDS31536.1	16	0.007326007326007326	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	14	0.018469656992084433	C	11.81	1.748637	0.30955	0.003635	0.019902	ENSG00000174914	ENST00000312153	T	0.01572	4.76	4.43	4.43	0.53597	GPCR, rhodopsin-like superfamily (1);	0.696787	0.13040	N	0.418614	T	0.00998	0.0033	L	0.31120	0.905	0.09310	N	1	B	0.02656	0.0	B	0.10450	0.005	T	0.40117	-0.9580	10	0.66056	D	0.02	-6.4294	10.827	0.46638	0.0:0.9106:0.0:0.0894	.	132	Q8NH87	OR9G1_HUMAN	V	132	ENSP00000309012:A132V	ENSP00000309012:A132V	A	+	2	0	OR9G1	56224834	0.000000	0.05858	0.813000	0.32504	0.681000	0.39784	-0.197000	0.09518	2.430000	0.82344	0.585000	0.79938	GCC	C|0.987;T|0.013	0.013	strong		0.498	OR9G1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393253.1	NM_001005213	
CACNA1C	775	hgsc.bcm.edu	37	12	2794937	2794937	+	Missense_Mutation	SNP	C	C	T	rs201777030		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:2794937C>T	ENST00000347598.4	+	46	5753	c.5753C>T	c.(5752-5754)aCg>aTg	p.T1918M	CACNA1C_ENST00000335762.5_Missense_Mutation_p.T1895M|CACNA1C_ENST00000399621.1_Missense_Mutation_p.T1889M|CACNA1C_ENST00000399617.1_Missense_Mutation_p.T1905M|CACNA1C_ENST00000399644.1_Missense_Mutation_p.T1870M|CACNA1C_ENST00000399634.1_Missense_Mutation_p.T1941M|CACNA1C_ENST00000399603.1_Missense_Mutation_p.T1870M|CACNA1C_ENST00000399649.1_Missense_Mutation_p.T1876M|CACNA1C_ENST00000327702.7_Missense_Mutation_p.T1905M|CACNA1C_ENST00000399655.1_Missense_Mutation_p.T1870M|CACNA1C_ENST00000406454.3_Missense_Mutation_p.T1941M|CACNA1C_ENST00000399637.1_Missense_Mutation_p.T1889M|CACNA1C_ENST00000399591.1_Missense_Mutation_p.T1878M|CACNA1C_ENST00000399641.1_Missense_Mutation_p.T1870M|CACNA1C_ENST00000399606.1_Missense_Mutation_p.T1890M|CACNA1C-AS1_ENST00000501371.1_RNA|CACNA1C_ENST00000399601.1_Missense_Mutation_p.T1870M|CACNA1C_ENST00000399629.1_Missense_Mutation_p.T1887M|CACNA1C_ENST00000402845.3_Missense_Mutation_p.T1889M|CACNA1C_ENST00000344100.3_Missense_Mutation_p.T1911M|CACNA1C_ENST00000399638.1_Missense_Mutation_p.T1898M|CACNA1C_ENST00000399595.1_Missense_Mutation_p.T1878M|CACNA1C_ENST00000399597.1_Missense_Mutation_p.T1870M	NM_001129827.1|NM_199460.2	NP_001123299.1|NP_955630.2	Q13936	CAC1C_HUMAN	calcium channel, voltage-dependent, L type, alpha 1C subunit	1953					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.T1911M(1)|p.T1983M(1)|p.T1405M(1)		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)	CGGCAACTGACGCTCCCAGAG	0.582																																					p.T1953M		Atlas-SNP	.											Q6YL47_HUMAN,trunk,malignant_melanoma,0,3	CACNA1C	1023	3	3	Substitution - Missense(3)	skin(3)	c.C5858T						scavenged	.						49.0	49.0	49.0					12																	2794937		2012	4159	6171	SO:0001583	missense	775	exon47			AACTGACGCTCCC	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.5753C>T	12.37:g.2794937C>T	ENSP00000266376:p.Thr1918Met	Somatic	110	2	0.0181818		WXS	Illumina HiSeq	Phase_I	118	16	0.135593	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	.	.	.	.	.	.	.	.	.	.	C	15.33	2.802724	0.50315	.	.	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	0.54866	0.55;0.55;0.55;0.55;0.55;0.55;0.55;0.55;0.55;0.55;0.55;0.55;0.55;0.55;0.55;0.55;0.55;0.55;0.55;0.55;0.55;0.55	4.26	4.26	0.50523	.	29.029300	0.00550	N	0.000258	T	0.70133	0.3189	L	0.56769	1.78	0.34775	D	0.734153	P;P;D;P;P;D;D;P;P;D;P;D;P;P;D;P;P;B;P;P;D;P;P;D;D	0.65815	0.863;0.922;0.995;0.664;0.934;0.988;0.992;0.869;0.638;0.966;0.922;0.989;0.927;0.783;0.992;0.677;0.927;0.317;0.922;0.485;0.985;0.869;0.869;0.981;0.995	B;P;P;B;P;P;P;P;B;P;P;P;P;P;P;B;P;B;P;B;P;P;P;P;P	0.56916	0.238;0.595;0.809;0.146;0.756;0.647;0.795;0.595;0.282;0.553;0.595;0.736;0.521;0.595;0.65;0.391;0.521;0.299;0.595;0.229;0.542;0.595;0.595;0.46;0.809	T	0.60281	-0.7294	10	0.38643	T	0.18	.	16.9179	0.86156	0.0:1.0:0.0:0.0	.	561;1911;1867;1953;1905;1889;1870;1887;1898;1870;1890;1870;1901;1918;1870;1905;1941;1878;1876;1878;1859;1889;1889;1870;1870	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;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.	M	1895;1870;1870;1898;1870;1889;1889;1878;1870;1918;1890;1870;1911;1887;1905;1876;1889;1870;1941;1905;1941;1878;1771	ENSP00000336982:T1895M;ENSP00000382563:T1870M;ENSP00000382552:T1870M;ENSP00000382547:T1898M;ENSP00000382506:T1870M;ENSP00000382530:T1889M;ENSP00000382546:T1889M;ENSP00000382500:T1878M;ENSP00000382549:T1870M;ENSP00000266376:T1918M;ENSP00000382515:T1890M;ENSP00000382510:T1870M;ENSP00000341092:T1911M;ENSP00000382537:T1887M;ENSP00000329877:T1905M;ENSP00000382557:T1876M;ENSP00000385724:T1889M;ENSP00000382512:T1870M;ENSP00000382542:T1941M;ENSP00000382526:T1905M;ENSP00000385896:T1941M;ENSP00000382504:T1878M	ENSP00000323129:T1771M	T	+	2	0	CACNA1C	2665198	1.000000	0.71417	0.106000	0.21319	0.488000	0.33401	5.733000	0.68571	2.202000	0.70862	0.449000	0.29647	ACG	.	.	weak		0.582	CACNA1C-017	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317035.1	NM_000719	
PKD1L2	114780	hgsc.bcm.edu	37	16	81249954	81249954	+	RNA	SNP	T	T	A	rs7191351	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:81249954T>A	ENST00000525539.1	-	0	358				PKD1L2_ENST00000337114.4_RNA	NM_052892.3	NP_443124.3	Q7Z442	PK1L2_HUMAN	polycystic kidney disease 1-like 2						ion transport (GO:0006811)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(20)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44						AGCGGCGGCCTGCCCTCCATG	0.632													T|||	2351	0.469449	0.351	0.5519	5008	,	,		16693	0.4425		0.6541	False		,,,				2504	0.409				p.Q120L		Atlas-SNP	.											.	PKD1L2	361	.	0			c.A359T						PASS	.	T	LEU/GLN,LEU/GLN	1866,2212		433,1000,606	50.0	63.0	59.0		359,359	1.4	0.0	16	dbSNP_116	59	5288,3060		1664,1960,550	yes	missense,missense	PKD1L2	NM_001076780.1,NM_052892.3	113,113	2097,2960,1156	AA,AT,TT		36.6555,45.7577,42.4272	probably-damaging,probably-damaging	120/992,120/2460	81249954	7154,5272	2039	4174	6213			114780	exon2			GCGGCCTGCCCTC	AY164483	CCDS61998.1, CCDS61999.1	16q23.2	2014-09-11			ENSG00000166473	ENSG00000166473			21715	protein-coding gene	gene with protein product		607894				12782129	Standard	NM_052892		Approved	KIAA1879	uc002fgf.1	Q7Z442	OTTHUMG00000166126		16.37:g.81249954T>A		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	95	95	1	NM_001076780	Q6UEE1|Q6ZN46|Q6ZSP2|Q8N1H9|Q96CL2|Q96Q08	Missense_Mutation	SNP	ENST00000525539.1	37		1129	0.516941391941392	176	0.35772357723577236	224	0.6187845303867403	234	0.4090909090909091	495	0.6530343007915568	T	13.46	2.245031	0.39697	0.457577	0.633445	ENSG00000166473	ENST00000337114	T	0.20069	2.1	5.09	1.37	0.22104	C-type lectin fold (1);C-type lectin (3);	0.501380	0.20678	N	0.087718	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	P;P	0.41848	0.763;0.491	P;B	0.44897	0.463;0.187	T	0.31280	-0.9949	8	0.87932	D	0	-0.6228	7.8882	0.29663	0.0:0.0723:0.3877:0.54	rs7191351;rs7191351	120;120	Q7Z442-3;Q7Z442	.;PK1L2_HUMAN	L	120	ENSP00000337397:Q120L	ENSP00000337397:Q120L	Q	-	2	0	PKD1L2	79807455	0.462000	0.25791	0.011000	0.14972	0.008000	0.06430	1.173000	0.31920	0.292000	0.22492	-0.320000	0.08662	CAG	A|0.526;N|0.001	0.526	strong		0.632	PKD1L2-001	KNOWN	non_canonical_polymorphism|basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000387972.2		
FAM208B	54906	hgsc.bcm.edu	37	10	5803349	5803349	+	Silent	SNP	A	A	C	rs543461908	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:5803349A>C	ENST00000328090.5	+	19	7714	c.7089A>C	c.(7087-7089)cgA>cgC	p.R2363R		NM_017782.4	NP_060252	Q5VWN6	F208B_HUMAN	family with sequence similarity 208, member B	2363																	GTGACTCTCGATCATCAACAA	0.388																																					p.R2363R		Atlas-SNP	.											C10orf18,NS,carcinoma,+2,2	.	.	2	0			c.A7089C						PASS	.						128.0	120.0	122.0					10																	5803349		1889	4118	6007	SO:0001819	synonymous_variant	54906	exon19			CTCTCGATCATCA	BX649177	CCDS41485.1	10p15.1	2011-09-14	2011-09-14	2011-09-14	ENSG00000108021	ENSG00000108021			23484	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 18"""	C10orf18		12477932	Standard	NM_017782		Approved	FLJ20360, bA318E3.2, KIAA2006	uc001iij.3	Q5VWN6	OTTHUMG00000017605	ENST00000328090.5:c.7089A>C	10.37:g.5803349A>C		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	120	28	0.233333	NM_017782	Q2YD91|Q5VWN5|Q6ZRQ8|Q8IVG4|Q9BUZ7|Q9H5J9|Q9H7A4|Q9H996|Q9NXA1	Silent	SNP	ENST00000328090.5	37	CCDS41485.1																																																																																			.	.	none		0.388	FAM208B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046571.2	NM_017782	
PADI6	353238	hgsc.bcm.edu	37	1	17708528	17708528	+	RNA	SNP	G	G	A	rs61766772	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:17708528G>A	ENST00000434762.2	+	0	670							Q6TGC4	PADI6_HUMAN	peptidyl arginine deiminase, type VI						cytoplasm organization (GO:0007028)|cytoskeleton organization (GO:0007010)|protein citrullination (GO:0018101)|regulation of translation by machinery localization (GO:0043143)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|protein-arginine deiminase activity (GO:0004668)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(9)|lung(9)|ovary(2)	29		Colorectal(325;3.46e-05)|Breast(348;0.000162)|all_lung(284;0.000337)|Lung NSC(340;0.000419)|Renal(390;0.000518)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00488)|BRCA - Breast invasive adenocarcinoma(304;7.59e-06)|COAD - Colon adenocarcinoma(227;1.18e-05)|Kidney(64;0.000186)|KIRC - Kidney renal clear cell carcinoma(64;0.00272)|STAD - Stomach adenocarcinoma(196;0.0134)|READ - Rectum adenocarcinoma(331;0.0655)|Lung(427;0.189)	L-Citrulline(DB00155)	AAGAAATATCGGCTAGTCCTC	0.483													G|||	122	0.024361	0.0015	0.036	5008	,	,		20649	0.0		0.0606	False		,,,				2504	0.0348				p.R207Q		Atlas-SNP	.											.	PADI6	51	.	0			c.G620A						PASS	.	G	GLN/ARG	33,3827		0,33,1897	78.0	80.0	79.0		620	0.9	0.3	1	dbSNP_129	79	520,7718		9,502,3608	yes	missense	PADI6	NM_207421.3	43	9,535,5505	AA,AG,GG		6.3122,0.8549,4.571	benign	207/695	17708528	553,11545	1930	4119	6049			353238	exon6			AATATCGGCTAGT	AY422079	CCDS72715.1	1p36.13	2014-07-10			ENSG00000256049	ENSG00000276747	3.5.3.15	"""Peptidyl arginine deiminases"""	20449	protein-coding gene	gene with protein product		610363				15087120	Standard	NM_207421		Approved		uc001bak.1	Q6TGC4	OTTHUMG00000002372		1.37:g.17708528G>A		Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	128	59	0.460938	NM_207421	Q330K5|Q70SX3	Missense_Mutation	SNP	ENST00000434762.2	37																																																																																				G|0.963;A|0.037	0.037	strong		0.483	PADI6-001	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000006804.4	NM_207421	
FAM205A	259308	hgsc.bcm.edu	37	9	34726821	34726821	+	Missense_Mutation	SNP	A	A	C	rs117956208	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:34726821A>C	ENST00000378788.3	-	4	455	c.416T>G	c.(415-417)cTa>cGa	p.L139R		NM_001141917.1	NP_001135389.1	Q6ZU69	F205A_HUMAN	family with sequence similarity 205, member A	139						integral component of membrane (GO:0016021)|nucleus (GO:0005634)				breast(1)|endometrium(2)|kidney(1)	4						CAGCATCTCTAGGCAAGAGGA	0.493													A|||	61	0.0121805	0.0	0.0245	5008	,	,		19454	0.0109		0.0109	False		,,,				2504	0.0225				p.L139R		Atlas-SNP	.											.	FAM205A	45	.	0			c.T416G						PASS	.	A	ARG/LEU	7,1377		0,7,685	60.0	54.0	56.0		416	1.7	0.0	9	dbSNP_132	56	53,3129		0,53,1538	yes	missense	FAM205A	NM_001141917.1	102	0,60,2223	CC,CA,AA		1.6656,0.5058,1.3141	probably-damaging	139/1336	34726821	60,4506	692	1591	2283	SO:0001583	missense	259308	exon4			ATCTCTAGGCAAG		CCDS55305.1	9p13.3	2014-05-16			ENSG00000205108	ENSG00000205108			41911	protein-coding gene	gene with protein product							Standard	NM_001141917		Approved	C9orf144B	uc011lor.2	Q6ZU69	OTTHUMG00000000448	ENST00000378788.3:c.416T>G	9.37:g.34726821A>C	ENSP00000417711:p.Leu139Arg	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	90	53	0.588889	NM_001141917	A8MVW7	Missense_Mutation	SNP	ENST00000378788.3	37	CCDS55305.1	22	0.010073260073260074	0	0.0	7	0.019337016574585635	8	0.013986013986013986	7	0.009234828496042216	A	13.77	2.335402	0.41398	0.005058	0.016656	ENSG00000205108	ENST00000378788	T	0.30981	1.51	4.17	1.73	0.24493	.	21.267300	0.00357	U	0.000026	T	0.33206	0.0855	M	0.67397	2.05	0.09310	N	1	D	0.67145	0.996	P	0.62740	0.906	T	0.03077	-1.1075	10	0.59425	D	0.04	.	3.1708	0.06551	0.6786:0.0:0.1141:0.2073	.	139	Q6ZU69	F205A_HUMAN	R	139	ENSP00000417711:L139R	ENSP00000417711:L139R	L	-	2	0	RP11-195F19.10	34716821	0.003000	0.15002	0.004000	0.12327	0.013000	0.08279	0.550000	0.23345	0.236000	0.21180	0.528000	0.53228	CTA	A|0.987;C|0.013	0.013	strong		0.493	FAM205A-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001150.2	NM_001141917	
MPC2	25874	hgsc.bcm.edu	37	1	167893759	167893759	+	Silent	SNP	G	G	A	rs9618	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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						PASS	.	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	160	1	0.00625		WXS	Illumina HiSeq	Phase_I	102	102	1	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	
CASC1	55259	hgsc.bcm.edu	37	12	25311489	25311489	+	Missense_Mutation	SNP	G	G	T	rs10842496	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:25311489G>T	ENST00000320267.9	-	3	178	c.97C>A	c.(97-99)Cgt>Agt	p.R33S	CASC1_ENST00000545133.1_Intron|CASC1_ENST00000557684.1_5'UTR|CASC1_ENST00000395990.2_5'UTR|CASC1_ENST00000395987.3_Missense_Mutation_p.R39S|CASC1_ENST00000537577.1_Intron|CASC1_ENST00000354189.5_Missense_Mutation_p.R97S	NM_001082973.1	NP_001076442	Q6TDU7	CASC1_HUMAN	cancer susceptibility candidate 1	33	Glu-rich.		R -> S (in dbSNP:rs10842496). {ECO:0000269|PubMed:16410263}.							breast(3)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|liver(1)|lung(3)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	31	Acute lymphoblastic leukemia(6;0.00112)|all_hematologic(7;0.00152)|Melanoma(3;0.0301)|Colorectal(261;0.11)		OV - Ovarian serous cystadenocarcinoma(3;7.42e-20)|Epithelial(3;7.58e-16)|all cancers(3;1.07e-13)			TATTTCAAACGGGCTTCCTCT	0.303													G|||	1271	0.253794	0.1293	0.3487	5008	,	,		19737	0.1925		0.3757	False		,,,				2504	0.2924				p.R97S		Atlas-SNP	.											.	CASC1	146	.	0			c.C289A						PASS	.	G	SER/ARG,SER/ARG,SER/ARG,,	681,3725	284.6+/-277.7	52,577,1574	79.0	77.0	78.0		289,97,115,,	5.4	1.0	12	dbSNP_120	78	3109,5487	470.9+/-367.9	564,1981,1753	yes	missense,missense,missense,intron,utr-5	CASC1	NM_001082972.1,NM_001082973.1,NM_018272.3,NM_001204101.1,NM_001204102.1	110,110,110,,	616,2558,3327	TT,TG,GG		36.168,15.4562,29.1494	probably-damaging,probably-damaging,probably-damaging,,	97/691,33/717,39/723,,	25311489	3790,9212	2203	4298	6501	SO:0001583	missense	55259	exon4			TCAAACGGGCTTC	AK093102	CCDS31759.2, CCDS41762.1, CCDS41763.1, CCDS55810.1, CCDS55811.1	12p12.1	2012-04-17			ENSG00000118307	ENSG00000118307		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	29599	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 54"""					14583591	Standard	NM_018272		Approved	LAS1, FLJ10921, PPP1R54	uc001rgk.3	Q6TDU7	OTTHUMG00000150195	ENST00000320267.9:c.97C>A	12.37:g.25311489G>T	ENSP00000313141:p.Arg33Ser	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	59	58	0.983051	NM_001082972	B4DNP2|F5H6T6|Q17RL2|Q4G171|Q5U5K5|Q9NV50	Missense_Mutation	SNP	ENST00000320267.9	37	CCDS41762.1	598|598	0.27380952380952384|0.27380952380952384	67|67	0.13617886178861788|0.13617886178861788	111|111	0.30662983425414364|0.30662983425414364	138|138	0.24125874125874125|0.24125874125874125	282|282	0.3720316622691293|0.3720316622691293	G|G	17.49|17.49	3.401556|3.401556	0.62288|0.62288	0.154562|0.154562	0.36168|0.36168	ENSG00000118307|ENSG00000118307	ENST00000556006|ENST00000354189;ENST00000395987;ENST00000320267;ENST00000395992	.|T;T;T	.|0.44881	.|1.99;0.91;0.92	5.42|5.42	5.42|5.42	0.78866|0.78866	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.00012|0.00012	0.0000|0.0000	M|M	0.69823|0.69823	2.125|2.125	0.09310|0.09310	P|P	1.0|1.0	.|D;D;D	.|0.89917	.|1.0;1.0;1.0	.|D;D;D	.|0.91635	.|0.999;0.997;0.999	T|T	0.20706|0.20706	-1.0267|-1.0267	4|9	.|0.66056	.|D	.|0.02	-17.9944|-17.9944	14.7255|14.7255	0.69341|0.69341	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	rs10842496;rs10842496|rs10842496;rs10842496	.|97;33;39	.|Q6TDU7-3;Q6TDU7;F8W8F9	.|.;CASC1_HUMAN;.	Q|S	8|97;39;33;39	.|ENSP00000346126:R97S;ENSP00000379310:R39S;ENSP00000313141:R33S	.|ENSP00000313141:R33S	P|R	-|-	2|1	0|0	CASC1|CASC1	25202756|25202756	1.000000|1.000000	0.71417|0.71417	0.971000|0.971000	0.41717|0.41717	0.990000|0.990000	0.78478|0.78478	3.836000|3.836000	0.55813|0.55813	2.535000|2.535000	0.85469|0.85469	0.573000|0.573000	0.79308|0.79308	CCG|CGT	G|0.728;T|0.272	0.272	strong		0.303	CASC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000316761.1	NM_018272	
CCDC92	80212	hgsc.bcm.edu	37	12	124427306	124427306	+	Missense_Mutation	SNP	T	T	A	rs11057401	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:124427306T>A	ENST00000238156.3	-	4	562	c.208A>T	c.(208-210)Agt>Tgt	p.S70C	CCDC92_ENST00000545891.1_Missense_Mutation_p.S53C|CCDC92_ENST00000545135.1_Missense_Mutation_p.S53C|CCDC92_ENST00000544798.1_5'UTR	NM_025140.1	NP_079416.1	Q53HC0	CCD92_HUMAN	coiled-coil domain containing 92	70			S -> C (in dbSNP:rs11057401).			centriole (GO:0005814)				large_intestine(5)|lung(2)	7	all_neural(191;0.101)|Medulloblastoma(191;0.163)			Epithelial(86;0.0002)|OV - Ovarian serous cystadenocarcinoma(86;0.000222)|all cancers(50;0.00129)|BRCA - Breast invasive adenocarcinoma(302;0.242)		TGTTCCGAACTTTTGACTGTC	0.373													T|||	1254	0.250399	0.3109	0.3184	5008	,	,		22215	0.0794		0.3489	False		,,,				2504	0.1953				p.S70C		Atlas-SNP	.											CCDC92,colon,carcinoma,0,1	CCDC92	18	1	0			c.A208T						PASS	.	T	CYS/SER	1429,2977	465.5+/-354.2	212,1005,986	188.0	168.0	175.0		208	3.4	0.7	12	dbSNP_120	175	2661,5939	428.1+/-355.8	404,1853,2043	yes	missense	CCDC92	NM_025140.1	112	616,2858,3029	AA,AT,TT		30.9419,32.433,31.447	probably-damaging	70/332	124427306	4090,8916	2203	4300	6503	SO:0001583	missense	80212	exon4			CCGAACTTTTGAC	AK026124	CCDS9256.1	12q24.31	2011-09-02			ENSG00000119242	ENSG00000119242			29563	protein-coding gene	gene with protein product	"""limkain beta 2"""					12477932	Standard	NM_025140		Approved	FLJ22471	uc001ufw.1	Q53HC0	OTTHUMG00000168725	ENST00000238156.3:c.208A>T	12.37:g.124427306T>A	ENSP00000238156:p.Ser70Cys	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	131	62	0.473282	NM_025140	B3KNQ0|Q9H697	Missense_Mutation	SNP	ENST00000238156.3	37	CCDS9256.1	574	0.26282051282051283	153	0.31097560975609756	111	0.30662983425414364	51	0.08916083916083917	259	0.341688654353562	T	23.5	4.429598	0.83776	0.32433	0.309419	ENSG00000119242	ENST00000238156;ENST00000545135;ENST00000545891;ENST00000539761;ENST00000535556;ENST00000539551	T;T;T;T;T;T	0.46819	0.86;0.86;0.86;0.86;0.86;0.86	5.76	3.44	0.39384	.	0.312818	0.42548	D	0.000694	T	0.00012	0.0000	M	0.79123	2.44	0.09310	P	0.99999343041	D	0.89917	1.0	D	0.70935	0.971	T	0.12167	-1.0558	9	0.72032	D	0.01	-19.3809	9.4934	0.38974	0.0:0.1428:0.0:0.8572	rs11057401;rs11544975;rs17882962;rs11057401	70	Q53HC0	CCD92_HUMAN	C	70;53;53;70;53;70	ENSP00000238156:S70C;ENSP00000439526:S53C;ENSP00000440024:S53C;ENSP00000439441:S70C;ENSP00000438281:S53C;ENSP00000442369:S70C	ENSP00000238156:S70C	S	-	1	0	CCDC92	122993259	1.000000	0.71417	0.670000	0.29842	0.968000	0.65278	3.019000	0.49635	0.469000	0.27268	0.533000	0.62120	AGT	T|0.710;A|0.290	0.290	strong		0.373	CCDC92-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000400780.2	NM_025140	
SLFN11	91607	hgsc.bcm.edu	37	17	33690466	33690466	+	Missense_Mutation	SNP	C	C	A	rs12453150	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:33690466C>A	ENST00000394566.1	-	4	633	c.361G>T	c.(361-363)Gtc>Ttc	p.V121F	SLFN11_ENST00000308377.4_Missense_Mutation_p.V121F	NM_001104587.1|NM_001104588.1|NM_001104589.1|NM_001104590.1	NP_001098057.1|NP_001098058.1|NP_001098059.1|NP_001098060.1	Q7Z7L1	SLN11_HUMAN	schlafen family member 11	121			V -> F (in dbSNP:rs12453150). {ECO:0000269|PubMed:14702039}.		defense response to virus (GO:0051607)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|tRNA binding (GO:0000049)			autonomic_ganglia(1)|breast(1)|kidney(3)|large_intestine(14)|lung(17)|ovary(1)|prostate(4)|skin(2)|stomach(5)|upper_aerodigestive_tract(2)	50		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		CGGGGCTTGACAGAGCGATCT	0.468													C|||	2084	0.416134	0.1543	0.5202	5008	,	,		18643	0.4821		0.5547	False		,,,				2504	0.4857				p.V121F		Atlas-SNP	.											.	SLFN11	112	.	0			c.G361T						PASS	.	C	PHE/VAL,PHE/VAL,PHE/VAL,PHE/VAL,PHE/VAL	1015,3391	373.9+/-321.0	101,813,1289	58.0	57.0	57.0		361,361,361,361,361	-8.4	0.0	17	dbSNP_120	57	4725,3875	605.0+/-394.9	1311,2103,886	yes	missense,missense,missense,missense,missense	SLFN11	NM_001104587.1,NM_001104588.1,NM_001104589.1,NM_001104590.1,NM_152270.3	50,50,50,50,50	1412,2916,2175	AA,AC,CC		45.0581,23.0368,44.1335	benign,benign,benign,benign,benign	121/902,121/902,121/902,121/902,121/902	33690466	5740,7266	2203	4300	6503	SO:0001583	missense	91607	exon2			GCTTGACAGAGCG	AK074184	CCDS11294.1	17q12	2006-04-05			ENSG00000172716	ENSG00000172716			26633	protein-coding gene	gene with protein product		614953				12477932	Standard	NM_001104587		Approved	FLJ34922	uc010ctr.3	Q7Z7L1	OTTHUMG00000132948	ENST00000394566.1:c.361G>T	17.37:g.33690466C>A	ENSP00000378067:p.Val121Phe	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	62	33	0.532258	NM_152270	E1P643|Q8N3S8|Q8N762|Q8TEE0	Missense_Mutation	SNP	ENST00000394566.1	37	CCDS11294.1	972	0.44505494505494503	76	0.15447154471544716	184	0.5082872928176796	287	0.5017482517482518	425	0.5606860158311345	C	6.914	0.538262	0.13188	0.230368	0.549419	ENSG00000172716	ENST00000308377;ENST00000394566	T;T	0.01981	4.52;4.52	4.18	-8.36	0.00980	.	3.322670	0.01114	N	0.005654	T	0.00012	0.0000	N	0.17082	0.46	0.80722	P	0.0	B	0.06786	0.001	B	0.06405	0.002	T	0.45906	-0.9229	9	0.08381	T	0.77	.	1.5129	0.02500	0.2034:0.4249:0.1856:0.1861	rs12453150;rs52821683;rs57680721;rs12453150	121	Q7Z7L1	SLN11_HUMAN	F	121	ENSP00000312402:V121F;ENSP00000378067:V121F	ENSP00000312402:V121F	V	-	1	0	SLFN11	30714579	0.000000	0.05858	0.000000	0.03702	0.024000	0.10985	-1.838000	0.01687	-3.775000	0.00108	-0.150000	0.13652	GTC	C|0.564;A|0.436	0.436	strong		0.468	SLFN11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256480.1	NM_152270	
OXNAD1	92106	hgsc.bcm.edu	37	3	16327855	16327855	+	Missense_Mutation	SNP	T	T	G	rs842274	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:16327855T>G	ENST00000285083.5	+	5	655	c.190T>G	c.(190-192)Tca>Gca	p.S64A	OXNAD1_ENST00000606098.1_Missense_Mutation_p.S64A|OXNAD1_ENST00000605932.1_Missense_Mutation_p.S64A|OXNAD1_ENST00000544043.1_Missense_Mutation_p.S82A|OXNAD1_ENST00000435829.2_Missense_Mutation_p.S82A	NM_138381.3	NP_612390.1	Q96HP4	OXND1_HUMAN	oxidoreductase NAD-binding domain containing 1	64	FAD-binding FR-type. {ECO:0000255|PROSITE-ProRule:PRU00716}.		S -> A (in dbSNP:rs842274). {ECO:0000269|Ref.1}.			mitochondrion (GO:0005739)	oxidoreductase activity (GO:0016491)			endometrium(3)|kidney(1)|large_intestine(2)|lung(5)|skin(2)	13						TTAGATTGTGTCAGCAGCTAA	0.478													T|||	2169	0.433107	0.3056	0.4712	5008	,	,		17571	0.4762		0.4334	False		,,,				2504	0.5337				p.S64A		Atlas-SNP	.											.	OXNAD1	31	.	0			c.T190G						PASS	.	T	ALA/SER	1547,2859	484.4+/-360.0	274,999,930	179.0	154.0	162.0		190	2.9	0.6	3	dbSNP_86	162	3655,4945	524.7+/-380.6	788,2079,1433	yes	missense	OXNAD1	NM_138381.3	99	1062,3078,2363	GG,GT,TT		42.5,35.1112,39.9969	benign	64/313	16327855	5202,7804	2203	4300	6503	SO:0001583	missense	92106	exon5			ATTGTGTCAGCAG	AL832787	CCDS2630.1	3p25-p24	2010-03-19			ENSG00000154814	ENSG00000154814			25128	protein-coding gene	gene with protein product						12477932	Standard	NM_138381		Approved	MGC15763	uc003caw.3	Q96HP4	OTTHUMG00000129867	ENST00000285083.5:c.190T>G	3.37:g.16327855T>G	ENSP00000285083:p.Ser64Ala	Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	142	141	0.992958	NM_138381	Q2HYC7|Q59FA4	Missense_Mutation	SNP	ENST00000285083.5	37	CCDS2630.1	908	0.4157509157509158	136	0.2764227642276423	170	0.4696132596685083	284	0.4965034965034965	318	0.41952506596306066	T	13.47	2.248105	0.39697	0.351112	0.425	ENSG00000154814	ENST00000285083;ENST00000435829;ENST00000544043	T;T;T	0.22336	2.29;1.96;2.28	5.26	2.89	0.33648	Riboflavin synthase-like beta-barrel (1);Ferredoxin reductase-type FAD-binding domain (1);	0.235250	0.44902	N	0.000405	T	0.00012	0.0000	L	0.29908	0.895	0.33960	P	0.354468	B;B	0.10296	0.003;0.001	B;B	0.11329	0.006;0.001	T	0.47471	-0.9115	9	0.20519	T	0.43	-5.9895	6.6934	0.23185	0.235:0.0:0.1618:0.6031	rs842274;rs3821707;rs17330471;rs52798805;rs58580702;rs842274	82;64	F5H620;Q96HP4	.;OXND1_HUMAN	A	64;64;82	ENSP00000285083:S64A;ENSP00000389872:S64A;ENSP00000437967:S82A	ENSP00000285083:S64A	S	+	1	0	OXNAD1	16302859	1.000000	0.71417	0.602000	0.28890	0.827000	0.46813	1.867000	0.39499	0.317000	0.23160	0.533000	0.62120	TCA	T|0.589;G|0.405	0.405	strong		0.478	OXNAD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252109.1	NM_138381	
AMELX	265	hgsc.bcm.edu	37	X	11316742	11316742	+	Silent	SNP	C	C	T	rs2106416	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:11316742C>T	ENST00000380714.3	+	5	287	c.219C>T	c.(217-219)caC>caT	p.H73H	ARHGAP6_ENST00000413512.3_Intron|ARHGAP6_ENST00000380736.1_Intron|ARHGAP6_ENST00000380718.1_Intron|ARHGAP6_ENST00000380732.3_Intron|AMELX_ENST00000380712.3_Silent_p.H87H|AMELX_ENST00000348912.4_Silent_p.H57H|ARHGAP6_ENST00000337414.4_Intron	NM_001142.2	NP_001133.1	Q99217	AMELX_HUMAN	amelogenin, X-linked	73					biomineral tissue development (GO:0031214)|cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|chondrocyte differentiation (GO:0002062)|enamel mineralization (GO:0070166)|epithelial to mesenchymal transition (GO:0001837)|ion homeostasis (GO:0050801)|odontogenesis of dentin-containing tooth (GO:0042475)|osteoblast differentiation (GO:0001649)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of tooth mineralization (GO:0070172)|signal transduction (GO:0007165)|tooth mineralization (GO:0034505)	cell surface (GO:0009986)|proteinaceous extracellular matrix (GO:0005578)	growth factor activity (GO:0008083)|hydroxyapatite binding (GO:0046848)|identical protein binding (GO:0042802)|structural constituent of tooth enamel (GO:0030345)			endometrium(3)|kidney(2)|large_intestine(1)|lung(9)	15						CCCAACAGCACCCCCCGACTC	0.597													C|||	622	0.164768	0.2133	0.0865	3775	,	,		11178	0.0149		0.168	False		,,,				2504	0.0982				p.H87H		Atlas-SNP	.											.	AMELX	31	.	0			c.C261T						PASS	.	C	,,,,	1114,2721		134,679,167,819,404	140.0	121.0	128.0		219,,,261,171	-3.8	0.9	X	dbSNP_96	128	1475,5253		94,850,437,1484,1435	no	coding-synonymous,intron,intron,coding-synonymous,coding-synonymous	AMELX,ARHGAP6	NM_001142.2,NM_006125.2,NM_013427.2,NM_182680.1,NM_182681.1	,,,,	228,1529,604,2303,1839	TT,TC,T,CC,C		21.9233,29.0482,24.5101	,,,,	73/192,,,87/206,57/176	11316742	2589,7974	2203	4300	6503	SO:0001819	synonymous_variant	265	exon6			ACAGCACCCCCCG		CCDS14144.1, CCDS14145.1, CCDS14146.1	Xp22.31-p22.1	2010-04-20	2010-04-20		ENSG00000125363	ENSG00000125363			461	protein-coding gene	gene with protein product	"""amelogenesis imperfecta 1"""	300391	"""amelogenin (X chromosome, amelogenesis imperfecta 1)"""	AMG, AIH1		1734713	Standard	NM_182680		Approved		uc004cus.3	Q99217	OTTHUMG00000021130	ENST00000380714.3:c.219C>T	X.37:g.11316742C>T		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	68	68	1	NM_182680	Q96NW6|Q9UCA7	Silent	SNP	ENST00000380714.3	37	CCDS14144.1																																																																																			C|0.765;T|0.235	0.235	strong		0.597	AMELX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055746.1	NM_001142	
XRN1	54464	hgsc.bcm.edu	37	3	142123841	142123841	+	Silent	SNP	C	C	T	rs2306700	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:142123841C>T	ENST00000264951.4	-	16	1908	c.1791G>A	c.(1789-1791)gaG>gaA	p.E597E	XRN1_ENST00000392981.2_Silent_p.E597E|RNU6-1294P_ENST00000515995.1_RNA	NM_019001.3	NP_061874.3	Q8IZH2	XRN1_HUMAN	5'-3' exoribonuclease 1	597					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|histone mRNA catabolic process (GO:0071044)|mRNA metabolic process (GO:0016071)|nuclear mRNA surveillance (GO:0071028)|nuclear-transcribed mRNA catabolic process (GO:0000956)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|RNA metabolic process (GO:0016070)|rRNA catabolic process (GO:0016075)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|membrane (GO:0016020)	5'-3' exonuclease activity (GO:0008409)|DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(3)|endometrium(6)|kidney(12)|large_intestine(11)|liver(1)|lung(17)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	61						ACATTAGGCACTCACTATGTT	0.408													C|||	609	0.121605	0.1604	0.0965	5008	,	,		18450	0.1002		0.1481	False		,,,				2504	0.0818				p.E597E		Atlas-SNP	.											.	XRN1	138	.	0			c.G1791A						PASS	.	C	,	645,3761	277.8+/-273.9	46,553,1604	169.0	152.0	158.0		1791,1791	-0.4	1.0	3	dbSNP_100	158	1196,7404	242.6+/-272.5	79,1038,3183	no	coding-synonymous,coding-synonymous	XRN1	NM_001042604.1,NM_019001.3	,	125,1591,4787	TT,TC,CC		13.907,14.6391,14.155	,	597/1694,597/1707	142123841	1841,11165	2203	4300	6503	SO:0001819	synonymous_variant	54464	exon16			TAGGCACTCACTA	AY137776	CCDS3123.1, CCDS63801.1, CCDS75028.1	3q23	2008-02-05			ENSG00000114127	ENSG00000114127			30654	protein-coding gene	gene with protein product		607994				12515382	Standard	XM_005247544		Approved	SEP1	uc003eus.3	Q8IZH2	OTTHUMG00000159251	ENST00000264951.4:c.1791G>A	3.37:g.142123841C>T		Somatic	339	0	0		WXS	Illumina HiSeq	Phase_I	275	140	0.509091	NM_001042604	Q4G0S3|Q68D88|Q6AI24|Q6MZS8|Q86WS7|Q8N8U4|Q9UF39	Silent	SNP	ENST00000264951.4	37	CCDS3123.1																																																																																			C|0.867;T|0.133	0.133	strong		0.408	XRN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000354087.2	NM_019001	
KANSL1	284058	hgsc.bcm.edu	37	17	44248499	44248499	+	Silent	SNP	G	G	C	rs2240758	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:44248499G>C	ENST00000262419.6	-	2	1481	c.1011C>G	c.(1009-1011)tcC>tcG	p.S337S	KANSL1_ENST00000574590.1_Silent_p.S337S|KANSL1_ENST00000575318.1_Silent_p.S337S|KANSL1_ENST00000576248.1_5'Flank|KANSL1_ENST00000572904.1_Silent_p.S337S|KANSL1_ENST00000432791.1_Silent_p.S337S|KANSL1_ENST00000393476.3_5'UTR	NM_001193466.1	NP_001180395	Q7Z3B3	KANL1_HUMAN	KAT8 regulatory NSL complex subunit 1	337					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)											GTGGTCTCAAGGATTCCAAGT	0.493													G|||	957	0.191094	0.0076	0.2968	5008	,	,		25316	0.4097		0.1928	False		,,,				2504	0.137				p.S337S		Atlas-SNP	.											KIAA1267,NS,carcinoma,-1,3	.	.	3	0			c.C1011G						PASS	.	G	,,	169,4237	112.5+/-150.6	6,157,2040	78.0	95.0	89.0		1011,1011,1011	3.9	1.0	17	dbSNP_98	89	1441,7159	276.0+/-292.1	128,1185,2987	no	coding-synonymous,coding-synonymous,coding-synonymous	KIAA1267	NM_001193465.1,NM_001193466.1,NM_015443.3	,,	134,1342,5027	CC,CG,GG		16.7558,3.8357,12.3789	,,	337/1105,337/1106,337/1106	44248499	1610,11396	2203	4300	6503	SO:0001819	synonymous_variant	284058	exon2			TCTCAAGGATTCC	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.1011C>G	17.37:g.44248499G>C		Somatic	207	0	0		WXS	Illumina HiSeq	Phase_I	86	41	0.476744	NM_001193466	A8K5E4|Q6AW85|Q8IYH1|Q9BRH0|Q9NTE7|Q9UFT0|Q9ULF3	Silent	SNP	ENST00000262419.6	37	CCDS11503.1																																																																																			G|0.432;C|0.568	0.568	strong		0.493	KANSL1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440274.1	NM_015443	
KRTAP10-9	386676	hgsc.bcm.edu	37	21	46047633	46047633	+	Missense_Mutation	SNP	A	A	G	rs8127342	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:46047633A>G	ENST00000397911.3	+	1	594	c.545A>G	c.(544-546)tAc>tGc	p.Y182C	TSPEAR_ENST00000323084.4_Intron|KRTAP10-9_ENST00000484861.1_Intron	NM_198690.2	NP_941963.2	P60411	KR109_HUMAN	keratin associated protein 10-9	182	25 X 5 AA repeats of C-C-X(3).		Y -> C (in dbSNP:rs8127342). {ECO:0000269|PubMed:15489334}.			keratin filament (GO:0045095)				endometrium(1)|kidney(1)|large_intestine(1)|lung(6)	9						CAGCAGTCCTACTGTGTGCCT	0.592													G|||	3191	0.637181	0.5219	0.6772	5008	,	,		22988	0.6667		0.7167	False		,,,				2504	0.6524				p.Y182C		Atlas-SNP	.											.	KRTAP10-9	24	.	0			c.A545G						PASS	.	G	,CYS/TYR	2344,2062	568.0+/-382.3	633,1078,492	248.0	264.0	259.0		,545	1.3	0.0	21	dbSNP_116	259	5810,2790	442.8+/-360.2	1958,1894,448	no	intron,missense	TSPEAR,KRTAP10-9	NM_144991.2,NM_198690.2	,194	2591,2972,940	GG,GA,AA		32.4419,46.7998,37.3059	,benign	,182/293	46047633	8154,4852	2203	4300	6503	SO:0001583	missense	386676	exon1			AGTCCTACTGTGT	AJ566386	CCDS42961.1	21q22.3	2007-10-05			ENSG00000221837	ENSG00000221837		"""Keratin associated proteins"""	22971	protein-coding gene	gene with protein product				KRTAP18-9			Standard	NM_198690		Approved	KAP10.9, KAP18.9	uc002zfp.4	P60411	OTTHUMG00000057637	ENST00000397911.3:c.545A>G	21.37:g.46047633A>G	ENSP00000381009:p.Tyr182Cys	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	164	164	1	NM_198690	A2RRG1|A6NIR9|Q70LJ1	Missense_Mutation	SNP	ENST00000397911.3	37	CCDS42961.1	1408	0.6446886446886447	259	0.5264227642276422	245	0.6767955801104972	364	0.6363636363636364	540	0.712401055408971	g	0	-2.837910	0.00069	0.532002	0.675581	ENSG00000221837	ENST00000397911	T	0.00768	5.72	3.45	1.28	0.21552	.	.	.	.	.	T	0.00012	0.0000	N	0.00000	-4.235	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.35425	-0.9789	7	.	.	.	.	6.7087	0.23264	0.1159:0.5079:0.3762:0.0	rs8127342	182	P60411	KR109_HUMAN	C	182	ENSP00000381009:Y182C	.	Y	+	2	0	KRTAP10-9	44872061	0.001000	0.12720	0.004000	0.12327	0.010000	0.07245	0.351000	0.20096	0.092000	0.17331	-0.176000	0.13171	TAC	A|0.343;G|0.657	0.657	strong		0.592	KRTAP10-9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128040.1		
DFFB	1677	hgsc.bcm.edu	37	1	3800242	3800242	+	Silent	SNP	A	A	G	rs3205087	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:3800242A>G	ENST00000378209.3	+	7	1277	c.954A>G	c.(952-954)ccA>ccG	p.P318P	AL691523.1_ENST00000579705.1_RNA	NM_004402.2	NP_004393.1	O76075	DFFB_HUMAN	DNA fragmentation factor, 40kDa, beta polypeptide (caspase-activated DNase)	318					apoptotic chromosome condensation (GO:0030263)|apoptotic DNA fragmentation (GO:0006309)|apoptotic process (GO:0006915)|brain development (GO:0007420)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)	cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	deoxyribonuclease activity (GO:0004536)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)			endometrium(1)|large_intestine(3)|lung(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	12	all_cancers(77;0.0395)|Ovarian(185;0.0634)|all_lung(157;0.222)|Lung NSC(156;0.227)	all_cancers(23;2.05e-30)|all_epithelial(116;6.22e-21)|all_lung(118;2.65e-08)|Lung NSC(185;6.25e-06)|Breast(487;0.000659)|Renal(390;0.00121)|all_neural(13;0.0019)|Hepatocellular(190;0.00705)|Colorectal(325;0.0113)|all_hematologic(16;0.0194)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0308)|Lung SC(97;0.0548)|Medulloblastoma(700;0.211)		Epithelial(90;1.18e-39)|OV - Ovarian serous cystadenocarcinoma(86;7.28e-23)|GBM - Glioblastoma multiforme(42;2.95e-17)|Colorectal(212;1.23e-05)|COAD - Colon adenocarcinoma(227;5.94e-05)|Kidney(185;0.000371)|BRCA - Breast invasive adenocarcinoma(365;0.00038)|KIRC - Kidney renal clear cell carcinoma(229;0.00571)|STAD - Stomach adenocarcinoma(132;0.00645)|Lung(427;0.124)		ACTGTGACCCAAGCAGAATCT	0.488													A|||	1782	0.355831	0.3124	0.3256	5008	,	,		16180	0.3482		0.4105	False		,,,				2504	0.3875				p.P318P		Atlas-SNP	.											.	DFFB	30	.	0			c.A954G						PASS	.	A		1491,2915	477.4+/-357.9	251,989,963	136.0	130.0	132.0		954	-10.9	0.0	1	dbSNP_105	132	3879,4721	544.4+/-384.6	868,2143,1289	no	coding-synonymous	DFFB	NM_004402.2		1119,3132,2252	GG,GA,AA		45.1047,33.8402,41.2886		318/339	3800242	5370,7636	2203	4300	6503	SO:0001819	synonymous_variant	1677	exon7			TGACCCAAGCAGA		CCDS52.1, CCDS72693.1	1p36.3	2014-03-06	2002-08-29		ENSG00000169598	ENSG00000169598			2773	protein-coding gene	gene with protein product		601883				9108473, 9560346	Standard	NM_004402		Approved	CAD, CPAN, DFF-40, DFF40	uc001alc.3	O76075	OTTHUMG00000003525	ENST00000378209.3:c.954A>G	1.37:g.3800242A>G		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	95	94	0.989474	NM_004402	O60521|Q5SR22|Q9BYI4|Q9BYI5|Q9BYI6	Silent	SNP	ENST00000378209.3	37	CCDS52.1																																																																																			A|0.607;G|0.393	0.393	strong		0.488	DFFB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009821.2	NM_001282669	
ING4	51147	hgsc.bcm.edu	37	12	6760367	6760367	+	Silent	SNP	C	C	T	rs76327967	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:6760367C>T	ENST00000396807.4	-	8	782	c.744G>A	c.(742-744)aaG>aaA	p.K248K	ING4_ENST00000341550.4_Silent_p.K247K|ING4_ENST00000423703.2_3'UTR|ING4_ENST00000486287.1_5'UTR|ING4_ENST00000446105.2_Silent_p.K244K|ING4_ENST00000444704.2_Silent_p.K224K|ING4_ENST00000412586.2_Silent_p.K245K	NM_001127582.1|NM_001127585.1|NM_001127586.1|NM_016162.3	NP_001121054.1|NP_001121057.1|NP_001121058.1|NP_057246.2	Q9UNL4	ING4_HUMAN	inhibitor of growth family, member 4	248					apoptotic process (GO:0006915)|cell cycle arrest (GO:0007050)|chromatin organization (GO:0006325)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA replication (GO:0006260)|histone H3 acetylation (GO:0043966)|histone H4-K12 acetylation (GO:0043983)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)|negative regulation of cell proliferation (GO:0008285)|negative regulation of growth (GO:0045926)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of apoptotic process (GO:0043065)|protein acetylation (GO:0006473)	histone acetyltransferase complex (GO:0000123)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	methylated histone binding (GO:0035064)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			central_nervous_system(3)|endometrium(1)|large_intestine(2)|lung(3)|ovary(1)	10						TTATCTATTTCTTCTTCCGTT	0.527													C|||	361	0.0720847	0.1815	0.0677	5008	,	,		20926	0.0179		0.0298	False		,,,				2504	0.0266				p.K248K		Atlas-SNP	.											.	ING4	31	.	0			c.G744A						PASS	.	C	,,,,,	762,3644	310.0+/-291.3	54,654,1495	98.0	89.0	92.0		744,735,732,672,,741	4.0	1.0	12	dbSNP_131	92	327,8273	113.5+/-173.5	4,319,3977	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,utr-3,coding-synonymous	ING4	NM_001127582.1,NM_001127583.1,NM_001127584.1,NM_001127585.1,NM_001127586.1,NM_016162.3	,,,,,	58,973,5472	TT,TC,CC		3.8023,17.2946,8.3731	,,,,,	248/250,245/247,244/246,224/226,,247/249	6760367	1089,11917	2203	4300	6503	SO:0001819	synonymous_variant	51147	exon8			CTATTTCTTCTTC	AF063594	CCDS8555.1, CCDS44812.1, CCDS44813.1, CCDS44814.1, CCDS44815.1, CCDS44816.1	12p13.32	2013-01-28			ENSG00000111653	ENSG00000111653		"""Zinc fingers, PHD-type"""	19423	protein-coding gene	gene with protein product		608524				12750254	Standard	NM_001127582		Approved	p29ING4, my036	uc001qpw.4	Q9UNL4	OTTHUMG00000141274	ENST00000396807.4:c.744G>A	12.37:g.6760367C>T		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	110	45	0.409091	NM_001127582	A4KYM4|A4KYM6|D3DUR8|Q0EF62|Q0EF63|Q4VBQ6|Q96E15|Q9H3J0	Silent	SNP	ENST00000396807.4	37	CCDS44813.1																																																																																			C|0.923;T|0.077	0.077	strong		0.527	ING4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000280467.2	NM_198287	
CHD5	26038	hgsc.bcm.edu	37	1	6202245	6202245	+	De_novo_Start_OutOfFrame	SNP	G	G	A	rs2273032	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:6202245G>A	ENST00000378021.1	-	0	2478				CHD5_ENST00000262450.3_Silent_p.N793N			O00258	WRB_HUMAN	chromodomain helicase DNA binding protein 5						tail-anchored membrane protein insertion into ER membrane (GO:0071816)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)				breast(3)|central_nervous_system(3)|liver(1)|lung(1)|ovary(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)	16	Ovarian(185;0.0634)	all_cancers(23;5.36e-32)|all_epithelial(116;2.32e-17)|all_neural(13;3.68e-06)|all_lung(118;3.94e-06)|all_hematologic(16;2.39e-05)|Lung NSC(185;5.33e-05)|Acute lymphoblastic leukemia(12;0.000372)|Glioma(11;0.00127)|Renal(390;0.00188)|Colorectal(325;0.00342)|Breast(487;0.00373)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.15)		Epithelial(90;3.08e-37)|GBM - Glioblastoma multiforme(13;1.36e-31)|OV - Ovarian serous cystadenocarcinoma(86;7.7e-19)|Colorectal(212;9.97e-08)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(185;6.16e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.00109)|BRCA - Breast invasive adenocarcinoma(365;0.0012)|STAD - Stomach adenocarcinoma(132;0.00346)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.193)		AGGAAAACTCGTTCTCCCGAA	0.572													G|||	665	0.132788	0.0371	0.0605	5008	,	,		18718	0.3323		0.1113	False		,,,				2504	0.1299				p.N793N		Atlas-SNP	.											CHD5_ENST00000262450,NS,carcinoma,0,1	CHD5	267	1	0			c.C2379T						PASS	.	G		250,4156	144.6+/-179.5	10,230,1963	162.0	152.0	155.0		2379	-4.8	1.0	1	dbSNP_100	155	983,7617	213.8+/-253.6	53,877,3370	no	coding-synonymous	CHD5	NM_015557.2		63,1107,5333	AA,AG,GG		11.4302,5.6741,9.4802		793/1955	6202245	1233,11773	2203	4300	6503			26038	exon15			AAACTCGTTCTCC	AF425231	CCDS57.1	1p36.3	2013-01-28			ENSG00000116254	ENSG00000116254		"""Zinc fingers, PHD-type"""	16816	protein-coding gene	gene with protein product		610771				11889561, 12592387	Standard	NM_015557		Approved		uc001amb.2	Q8TDI0	OTTHUMG00000000952	ENST00000378021.1:c.-1051C>T	1.37:g.6202245G>A		Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	100	37	0.37	NM_015557	A8KAP8|A8MQ44|D3DSH9|O60740	Silent	SNP	ENST00000378021.1	37																																																																																				G|0.879;N|0.001	.	strong		0.572	CHD5-201	KNOWN	basic	protein_coding	protein_coding		NM_015557	
MUC4	4585	hgsc.bcm.edu	37	3	195508982	195508982	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195508982C>T	ENST00000463781.3	-	2	9928	c.9469G>A	c.(9469-9471)Gac>Aac	p.D3157N	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_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	36	1	0.0277778		WXS	Illumina HiSeq	Phase_I	49	4	0.0816327	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	
EMC1	23065	hgsc.bcm.edu	37	1	19565344	19565344	+	Missense_Mutation	SNP	C	C	G	rs709683	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:19565344C>G	ENST00000477853.1	-	10	1076	c.1034G>C	c.(1033-1035)aGt>aCt	p.S345T	RP1-43E13.2_ENST00000437898.1_RNA|EMC1_ENST00000375208.3_Missense_Mutation_p.S323T|EMC1_ENST00000375199.3_Missense_Mutation_p.S344T	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	345			S -> T (in dbSNP:rs709683). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:16303743}.			ER membrane protein complex (GO:0072546)|integral component of membrane (GO:0016021)											AGAACTGCTACTTTTCTGCTA	0.458													G|||	2866	0.572284	0.7315	0.5101	5008	,	,		18872	0.7401		0.3469	False		,,,				2504	0.4601				p.S345T		Atlas-SNP	.											.	.	.	.	0			c.G1034C						PASS	.	G	THR/SER	3012,1394	458.0+/-351.8	1047,918,238	116.0	124.0	121.0		1034	5.2	0.9	1	dbSNP_86	121	3095,5505	659.4+/-401.7	566,1963,1771	yes	missense	KIAA0090	NM_015047.1	58	1613,2881,2009	GG,GC,CC		35.9884,31.6387,46.9553	benign	345/994	19565344	6107,6899	2203	4300	6503	SO:0001583	missense	23065	exon10			CTGCTACTTTTCT		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.1034G>C	1.37:g.19565344C>G	ENSP00000420608:p.Ser345Thr	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	89	89	1	NM_001271428	A8K6F3|Q14700|Q5TG62|Q63HL0|Q63HL3|Q8NBH8	Missense_Mutation	SNP	ENST00000477853.1	37	CCDS190.1	1224|1224	0.5604395604395604|0.5604395604395604	361|361	0.733739837398374|0.733739837398374	167|167	0.4613259668508287|0.4613259668508287	431|431	0.7534965034965035|0.7534965034965035	265|265	0.3496042216358839|0.3496042216358839	G|G	7.688|7.688	0.690412|0.690412	0.15039|0.15039	0.683613|0.683613	0.359884|0.359884	ENSG00000127463|ENSG00000127463	ENST00000375197|ENST00000477853;ENST00000375199;ENST00000375208	.|T;T;T	.|0.23147	.|1.98;1.92;1.98	6.17|6.17	5.22|5.22	0.72569|0.72569	.|.	.|0.708347	.|0.15080	.|N	.|0.281698	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.08118|0.08118	0|0	0.58432|0.58432	P|P	4.000000000004E-6|4.000000000004E-6	.|B;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	0.16217|0.16217	-1.0410|-1.0410	5|9	0.39692|0.12430	T|T	0.17|0.62	-7.2019|-7.2019	16.2834|16.2834	0.82708|0.82708	0.0:0.2663:0.7337:0.0|0.0:0.2663:0.7337:0.0	rs709683;rs57408009;rs709683|rs709683;rs57408009;rs709683	.|323;344;345;345	.|Q8N766-4;Q8N766-2;Q8N766-3;Q8N766	.|.;.;.;K0090_HUMAN	N|T	78|345;344;323	.|ENSP00000420608:S345T;ENSP00000364345:S344T;ENSP00000364354:S323T	ENSP00000364343:K78N|ENSP00000364345:S344T	K|S	-|-	3|2	2|0	KIAA0090|KIAA0090	19437931|19437931	0.934000|0.934000	0.31675|0.31675	0.868000|0.868000	0.34077|0.34077	0.804000|0.804000	0.45430|0.45430	2.667000|2.667000	0.46808|0.46808	1.643000|1.643000	0.50594|0.50594	-0.120000|-0.120000	0.15030|0.15030	AAG|AGT	C|0.506;G|0.494	0.494	strong		0.458	EMC1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000007076.2	NM_015047	
GFM2	84340	hgsc.bcm.edu	37	5	74037386	74037386	+	Missense_Mutation	SNP	T	T	A	rs16872235	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:74037386T>A	ENST00000296805.3	-	11	1355	c.898A>T	c.(898-900)Agt>Tgt	p.S300C	GFM2_ENST00000345239.2_Missense_Mutation_p.S300C|GFM2_ENST00000427854.2_Missense_Mutation_p.S300C|GFM2_ENST00000509430.1_Missense_Mutation_p.S300C	NM_032380.3	NP_115756.2			G elongation factor, mitochondrial 2											breast(2)|endometrium(2)|large_intestine(4)|lung(5)|prostate(1)	14		all_lung(232;0.00101)|Lung NSC(167;0.00278)|Ovarian(174;0.0129)|Breast(144;0.231)		OV - Ovarian serous cystadenocarcinoma(47;1.86e-56)		AAATTCTCACTAAATTCTTCT	0.289													T|||	543	0.108427	0.1732	0.1066	5008	,	,		15709	0.0208		0.1382	False		,,,				2504	0.0818				p.S300C		Atlas-SNP	.											.	GFM2	38	.	0			c.A898T						PASS	.	T	CYS/SER,CYS/SER,CYS/SER	798,3594	289.8+/-280.6	65,668,1463	44.0	46.0	46.0		898,898,898	5.9	1.0	5	dbSNP_123	46	1051,7519	206.1+/-248.3	63,925,3297	yes	missense,missense,missense	GFM2	NM_032380.3,NM_170681.1,NM_170691.1	112,112,112	128,1593,4760	AA,AT,TT		12.2637,18.1694,14.2648	possibly-damaging,possibly-damaging,possibly-damaging	300/780,300/514,300/733	74037386	1849,11113	2196	4285	6481	SO:0001583	missense	84340	exon11			TCTCACTAAATTC	AF111808	CCDS4023.1, CCDS4024.1, CCDS47232.1	5q13	2008-02-05			ENSG00000164347	ENSG00000164347			29682	protein-coding gene	gene with protein product		606544				11735030	Standard	NM_001281302		Approved	EFG2, FLJ21661	uc003kdh.1	Q969S9	OTTHUMG00000102058	ENST00000296805.3:c.898A>T	5.37:g.74037386T>A	ENSP00000296805:p.Ser300Cys	Somatic	328	1	0.00304878		WXS	Illumina HiSeq	Phase_I	274	161	0.587591	NM_032380		Missense_Mutation	SNP	ENST00000296805.3	37	CCDS4023.1	233	0.10668498168498168	87	0.17682926829268292	45	0.12430939226519337	14	0.024475524475524476	87	0.11477572559366754	T	18.66	3.671118	0.67814	0.181694	0.122637	ENSG00000164347	ENST00000296805;ENST00000345239;ENST00000546082;ENST00000509430;ENST00000427854;ENST00000509097	T;T;T;T;T	0.74421	-0.02;0.11;-0.02;-0.84;-0.14	5.88	5.88	0.94601	Protein synthesis factor, GTP-binding (1);	0.074495	0.85682	D	0.000000	T	0.00552	0.0018	L	0.39898	1.24	0.18873	P	0.9999851399	D;D;D;D;D	0.71674	0.998;0.99;0.996;0.997;0.992	P;P;P;D;P	0.64144	0.893;0.849;0.849;0.922;0.907	T	0.14282	-1.0478	9	0.87932	D	0	-20.6679	16.2868	0.82725	0.0:0.0:0.0:1.0	rs16872235;rs16872235	300;300;300;300;300	F5H687;Q969S9-3;Q969S9-5;Q969S9-2;Q969S9	.;.;.;.;RRF2M_HUMAN	C	300;300;300;300;300;258	ENSP00000296805:S300C;ENSP00000296804:S300C;ENSP00000427004:S300C;ENSP00000405808:S300C;ENSP00000421717:S258C	ENSP00000296805:S300C	S	-	1	0	GFM2	74073142	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.039000	0.57325	2.244000	0.73946	0.460000	0.39030	AGT	T|0.878;A|0.122	0.122	strong		0.289	GFM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219860.2	NM_032380	
TRPM8	79054	hgsc.bcm.edu	37	2	234863788	234863788	+	Missense_Mutation	SNP	G	G	A	rs7593557	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:234863788G>A	ENST00000324695.4	+	11	1296	c.1256G>A	c.(1255-1257)aGt>aAt	p.S419N	TRPM8_ENST00000433712.2_Missense_Mutation_p.S107N|AC005538.5_ENST00000455991.1_RNA	NM_024080.4	NP_076985.4	Q7Z2W7	TRPM8_HUMAN	transient receptor potential cation channel, subfamily M, member 8	419			S -> N (in dbSNP:rs7593557).		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)	p.S419N(1)		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)	TTCAGCACCAGTGAGCAAGAC	0.488													A|||	1725	0.344449	0.6362	0.1571	5008	,	,		21237	0.4444		0.0527	False		,,,				2504	0.2802				p.S419N		Atlas-SNP	.											TRPM8,NS,carcinoma,0,1	TRPM8	146	1	1	Substitution - Missense(1)	stomach(1)	c.G1256A						PASS	.	A	ASN/SER	2336,2070	569.8+/-382.7	617,1102,484	89.0	86.0	87.0		1256	6.0	0.9	2	dbSNP_116	87	499,8101	797.0+/-407.5	14,471,3815	yes	missense	TRPM8	NM_024080.4	46	631,1573,4299	AA,AG,GG		5.8023,46.9814,21.7976	benign	419/1105	234863788	2835,10171	2203	4300	6503	SO:0001583	missense	79054	exon11			GCACCAGTGAGCA	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.1256G>A	2.37:g.234863788G>A	ENSP00000323926:p.Ser419Asn	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	92	37	0.402174	NM_024080	A0AVG2|Q3YFM7|Q6QNH9|Q8TAC3|Q8TDX8|Q9BVK1	Missense_Mutation	SNP	ENST00000324695.4	37	CCDS33407.1	658	0.30128205128205127	298	0.6056910569105691	71	0.19613259668508287	247	0.4318181818181818	42	0.055408970976253295	A	13.05	2.121907	0.37436	0.530186	0.058023	ENSG00000144481	ENST00000324695;ENST00000433712	T;T	0.35789	1.29;1.29	5.99	5.99	0.97316	.	0.207539	0.42682	N	0.000679	T	0.00012	0.0000	N	0.15975	0.35	0.58432	P	5.999999999950489E-6	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.37934	-0.9684	9	0.08599	T	0.76	-25.8811	11.2408	0.48968	0.9284:0.0:0.0716:0.0	rs7593557;rs52800345;rs59539312;rs7593557	107;419	A0AVG2;Q7Z2W7	.;TRPM8_HUMAN	N	419;107	ENSP00000323926:S419N;ENSP00000404423:S107N	ENSP00000323926:S419N	S	+	2	0	TRPM8	234528527	0.999000	0.42202	0.908000	0.35775	0.586000	0.36452	3.631000	0.54280	1.092000	0.41356	-0.254000	0.11334	AGT	G|0.732;A|0.268	0.268	strong		0.488	TRPM8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131005.4	NM_024080	
ASB11	140456	hgsc.bcm.edu	37	X	15332558	15332558	+	Intron	SNP	A	A	G	rs5935944	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:15332558A>G	ENST00000480796.1	-	1	232				ASB11_ENST00000344384.4_Silent_p.R17R|ASB11_ENST00000537676.1_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	100	0	0		WXS	Illumina HiSeq	Phase_I	85	85	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		
COL4A1	1282	hgsc.bcm.edu	37	13	110827580	110827580	+	Silent	SNP	C	C	T	rs874204	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:110827580C>T	ENST00000375820.4	-	37	3304	c.3183G>A	c.(3181-3183)ggG>ggA	p.G1061G		NM_001845.4	NP_001836.2	P02462	CO4A1_HUMAN	collagen, type IV, alpha 1	1061	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)			CACCTCGCAGCCCTGGGATGC	0.572													C|||	1593	0.318091	0.2549	0.353	5008	,	,		21894	0.2788		0.3668	False		,,,				2504	0.3691				p.G1061G		Atlas-SNP	.											.	COL4A1	372	.	0			c.G3183A						PASS	.	C		1251,3155	430.6+/-342.6	181,889,1133	153.0	117.0	129.0		3183	-5.6	0.8	13	dbSNP_86	129	3118,5482	475.8+/-369.2	568,1982,1750	no	coding-synonymous	COL4A1	NM_001845.4		749,2871,2883	TT,TC,CC		36.2558,28.3931,33.5922		1061/1670	110827580	4369,8637	2203	4300	6503	SO:0001819	synonymous_variant	1282	exon37			TCGCAGCCCTGGG	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.3183G>A	13.37:g.110827580C>T		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	104	53	0.509615	NM_001845	A7E2W4|B1AM70|Q1P9S9|Q5VWF6|Q86X41|Q8NF88|Q9NYC5	Silent	SNP	ENST00000375820.4	37	CCDS9511.1																																																																																			C|0.658;A|0.001	.	strong		0.572	COL4A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045759.3		
Unknown	0	hgsc.bcm.edu	37	17	17326363	17326363	+	IGR	SNP	G	G	A	rs35590625	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:17326363G>A								NT5M (75388 upstream) : Y_RNA (37394 downstream)																							AGCTTTGAGTGTTCTTCGAAG	0.458													G|||	1288	0.257188	0.354	0.1744	5008	,	,		24040	0.1647		0.2555	False		,,,				2504	0.2822				p.V60I		Atlas-SNP	.											.	.	.	.	0			c.G178A						PASS	.																																			SO:0001628	intergenic_variant	140776	exon3			TTGAGTGTTCTTC																													17.37:g.17326363G>A		Somatic	11	0	0		WXS	Illumina HiSeq	Phase_I	15	6	0.4	NM_001243312		Missense_Mutation	SNP		37																																																																																				G|0.747;A|0.253	0.253	strong	0	0.458								
C4orf17	84103	hgsc.bcm.edu	37	4	100443782	100443782	+	Missense_Mutation	SNP	T	T	C	rs13119384|rs201447915|rs386677740|rs35156523	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:100443782T>C	ENST00000326581.4	+	3	615	c.253T>C	c.(253-255)Tcc>Ccc	p.S85P	C4orf17_ENST00000514652.1_Missense_Mutation_p.S85P|C4orf17_ENST00000503257.1_3'UTR	NM_032149.2	NP_115525.2	Q53FE4	CD017_HUMAN	chromosome 4 open reading frame 17	85			S -> P (in dbSNP:rs13119384). {ECO:0000269|PubMed:11230166, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.2}.							central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(9)|prostate(1)|urinary_tract(3)	18				OV - Ovarian serous cystadenocarcinoma(123;2.08e-08)		CAGTTACCCCTCCAGCACTGC	0.498													C|||	2881	0.57528	0.9319	0.3516	5008	,	,		16590	0.4018		0.3638	False		,,,				2504	0.6483				p.S85P		Atlas-SNP	.											.	C4orf17	42	.	0			c.T253C						PASS	.	C	PRO/SER	3504,902		1523,458,222	119.0	109.0	112.0		253	3.3	0.1	4	dbSNP_121	112	1806,6794		567,672,3061	yes	missense	C4orf17	NM_032149.2	74	2090,1130,3283	CC,CT,TT		21.0,20.4721,40.8273	benign	85/360	100443782	5310,7696	2203	4300	6503	SO:0001583	missense	84103	exon3			TACCCCTCCAGCA	AL136838	CCDS3649.1	4q23	2008-02-05			ENSG00000138813	ENSG00000138813			25274	protein-coding gene	gene with protein product						11230166	Standard	NM_032149		Approved	DKFZP434G072	uc003huw.3	Q53FE4	OTTHUMG00000131027	ENST00000326581.4:c.253T>C	4.37:g.100443782T>C	ENSP00000322582:p.Ser85Pro	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	90	90	1	NM_032149	Q6FI84|Q6IS77|Q8NA78|Q9H0D9	Missense_Mutation	SNP	ENST00000326581.4	37	CCDS3649.1	1053	0.48214285714285715	457	0.9288617886178862	135	0.3729281767955801	194	0.33916083916083917	267	0.35224274406332456	C	0.713	-0.786566	0.02907	0.795279	0.21	ENSG00000138813	ENST00000326581;ENST00000514652	T;T	0.16196	2.36;2.36	5.27	3.34	0.38264	.	0.707304	0.13253	N	0.401895	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	0.24261	-1.0165	9	0.24483	T	0.36	-3.704	3.2687	0.06874	0.1889:0.5555:0.1618:0.0938	rs33968283	85	Q53FE4	CD017_HUMAN	P	85	ENSP00000322582:S85P;ENSP00000427663:S85P	ENSP00000322582:S85P	S	+	1	0	C4orf17	100662805	0.001000	0.12720	0.052000	0.19188	0.001000	0.01503	0.160000	0.16462	0.778000	0.33520	-0.128000	0.14901	TCC	T|0.458;C|0.542	0.542	strong		0.498	C4orf17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253670.2	NM_032149	
PIGW	284098	hgsc.bcm.edu	37	17	34893655	34893655	+	Missense_Mutation	SNP	C	C	G	rs61755368	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:34893655C>G	ENST00000592983.1	+	2	1285	c.705C>G	c.(703-705)caC>caG	p.H235Q	MYO19_ENST00000590081.1_Intron|MYO19_ENST00000544606.1_5'Flank|MYO19_ENST00000431794.3_5'Flank|MYO19_ENST00000268852.9_5'Flank|MYO19_ENST00000586007.1_5'Flank|PIGW_ENST00000328396.2_Missense_Mutation_p.H235Q			Q7Z7B1	PIGW_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class W	235					C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	transferase activity, transferring acyl groups (GO:0016746)			breast(2)|endometrium(3)|kidney(1)|large_intestine(1)|lung(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	13		Breast(25;0.00957)|Ovarian(249;0.17)	Kidney(155;0.104)	UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		ATGGAGTTCACTGGAACTTTT	0.368													C|||	5	0.000998403	0.0	0.0	5008	,	,		20498	0.0		0.005	False		,,,				2504	0.0				p.H235Q		Atlas-SNP	.											.	PIGW	50	.	0			c.C705G						PASS	.	C	GLN/HIS	6,4390	9.9+/-24.2	0,6,2192	75.0	79.0	77.0		705	2.7	1.0	17	dbSNP_129	77	60,8538	35.3+/-89.8	0,60,4239	yes	missense	PIGW	NM_178517.3	24	0,66,6431	GG,GC,CC		0.6978,0.1365,0.5079	probably-damaging	235/505	34893655	66,12928	2198	4299	6497	SO:0001583	missense	284098	exon2			AGTTCACTGGAAC	AB097818	CCDS11313.1	17q21.1	2014-05-06	2006-06-28		ENSG00000184886	ENSG00000277161		"""Phosphatidylinositol glycan anchor biosynthesis"""	23213	protein-coding gene	gene with protein product		610275	"""phosphatidylinositol glycan, class W"""			14517336, 12714589	Standard	XM_005257238		Approved	Gwt1, FLJ37433	uc002hmz.1	Q7Z7B1	OTTHUMG00000188438	ENST00000592983.1:c.705C>G	17.37:g.34893655C>G	ENSP00000468778:p.His235Gln	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	114	57	0.5	NM_178517	Q8N9G3	Missense_Mutation	SNP	ENST00000592983.1	37	CCDS11313.1	5	0.0022893772893772895	0	0.0	0	0.0	0	0.0	5	0.006596306068601583	C	16.95	3.262679	0.59431	0.001365	0.006978	ENSG00000184886	ENST00000328396	.	.	.	5.79	2.71	0.32032	.	0.000000	0.85682	D	0.000000	T	0.76543	0.4002	M	0.92604	3.325	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.82206	-0.0572	8	.	.	.	-6.0044	10.914	0.47124	0.0:0.793:0.0:0.207	rs61755368	235	Q7Z7B1	PIGW_HUMAN	Q	235	.	.	H	+	3	2	PIGW	31967768	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	0.970000	0.29383	0.802000	0.34089	0.561000	0.74099	CAC	C|0.995;G|0.005	0.005	strong		0.368	PIGW-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451318.1	NM_178517	
ZNF816	125893	hgsc.bcm.edu	37	19	53454543	53454543	+	Missense_Mutation	SNP	G	G	A	rs11084210	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:53454543G>A	ENST00000357666.4	-	5	785	c.485C>T	c.(484-486)tCg>tTg	p.S162L	ZNF321P_ENST00000391777.3_Intron|ZNF816_ENST00000444460.2_Missense_Mutation_p.S162L|ZNF816_ENST00000434371.2_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	86	0	0		WXS	Illumina HiSeq	Phase_I	66	34	0.515152	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	
FAM214A	56204	hgsc.bcm.edu	37	15	52901284	52901284	+	Silent	SNP	T	T	C	rs58018557|rs386783993	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:52901284T>C	ENST00000261844.7	-	6	1979	c.1827A>G	c.(1825-1827)tcA>tcG	p.S609S	FAM214A_ENST00000546305.2_Silent_p.S616S	NM_019600.2	NP_062546.2	Q32MH5	F214A_HUMAN	family with sequence similarity 214, member A	609																	TTGAGGAAGTTGATAAACTAG	0.338													C|||	2472	0.49361	0.6233	0.317	5008	,	,		17171	0.8869		0.17	False		,,,				2504	0.3712				p.S609S		Atlas-SNP	.											.	.	.	.	0			c.A1827G						PASS	.	C		1897,1773		487,923,425	110.0	118.0	115.0		1827	-0.1	0.0	15	dbSNP_129	115	1271,6885		119,1033,2926	no	coding-synonymous	KIAA1370	NM_019600.2		606,1956,3351	CC,CT,TT		15.5836,48.3106,26.7884		609/1077	52901284	3168,8658	1835	4078	5913	SO:0001819	synonymous_variant	56204	exon6			GGAAGTTGATAAA	AB037791	CCDS45263.1, CCDS66773.1	15q21.2-q21.3	2011-12-01	2011-12-01	2011-12-01	ENSG00000047346	ENSG00000047346			25609	protein-coding gene	gene with protein product			"""KIAA1370"""	KIAA1370		10718198	Standard	XM_005254547		Approved	FLJ10980	uc002acg.4	Q32MH5		ENST00000261844.7:c.1827A>G	15.37:g.52901284T>C		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	83	51	0.614458	NM_019600	A8KA52|B4DEP5|B4DF40|F5H8G0|Q32MH6|Q4G0R7|Q5XJ16|Q6PDA3|Q9NV24|Q9P2H7	Silent	SNP	ENST00000261844.7	37	CCDS45263.1																																																																																			T|0.652;C|0.348	0.348	strong		0.338	FAM214A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419914.1	NM_019600	
S100PBP	64766	hgsc.bcm.edu	37	1	33292008	33292008	+	Missense_Mutation	SNP	G	G	A	rs61739743	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:33292008G>A	ENST00000373475.5	+	3	562	c.308G>A	c.(307-309)aGc>aAc	p.S103N	S100PBP_ENST00000356689.3_3'UTR|S100PBP_ENST00000398243.3_Missense_Mutation_p.S103N|S100PBP_ENST00000373476.1_Missense_Mutation_p.S103N	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)				TCATCGTACAGCCTGGGACCA	0.473													G|||	35	0.00698882	0.0182	0.0072	5008	,	,		19748	0.0		0.006	False		,,,				2504	0.0				p.S103N		Atlas-SNP	.											.	S100PBP	31	.	0			c.G308A						PASS	.	G	ASN/SER,ASN/SER	72,4334	62.3+/-99.4	1,70,2132	56.0	52.0	53.0		308,308	0.1	0.1	1	dbSNP_129	53	65,8535	39.8+/-96.3	0,65,4235	yes	missense,missense	S100PBP	NM_001017406.1,NM_022753.2	46,46	1,135,6367	AA,AG,GG		0.7558,1.6341,1.0534	benign,benign	103/342,103/409	33292008	137,12869	2203	4300	6503	SO:0001583	missense	64766	exon3			CGTACAGCCTGGG	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.308G>A	1.37:g.33292008G>A	ENSP00000362574:p.Ser103Asn	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	82	36	0.439024	NM_001256121		Missense_Mutation	SNP	ENST00000373475.5	37	CCDS30666.1	16	0.007326007326007326	11	0.022357723577235773	3	0.008287292817679558	0	0.0	2	0.002638522427440633	G	4.857	0.159396	0.09236	0.016341	0.007558	ENSG00000116497	ENST00000530710;ENST00000373476;ENST00000373475;ENST00000531123;ENST00000398243;ENST00000356689;ENST00000526230;ENST00000531256;ENST00000482212	.	.	.	5.32	0.136	0.14780	.	0.673278	0.15732	N	0.247367	T	0.12860	0.0312	N	0.20986	0.625	0.09310	N	0.999997	B;B	0.19583	0.037;0.008	B;B	0.22386	0.039;0.009	T	0.12066	-1.0562	9	0.45353	T	0.12	-0.1643	5.5651	0.17167	0.2246:0.2654:0.51:0.0	rs61739743	103;103	A8MTZ6;Q96BU1	.;S1PBP_HUMAN	N	103	.	ENSP00000349117:S103N	S	+	2	0	S100PBP	33064595	0.603000	0.26924	0.082000	0.20525	0.073000	0.16967	0.412000	0.21131	-0.034000	0.13713	0.655000	0.94253	AGC	G|0.990;A|0.010	0.010	strong		0.473	S100PBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011266.1	NM_022753	
CCAR2	57805	hgsc.bcm.edu	37	8	22463623	22463623	+	Silent	SNP	C	C	T	rs7843828	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:22463623C>T	ENST00000308511.4	+	3	333	c.84C>T	c.(82-84)ggC>ggT	p.G28G	CCAR2_ENST00000521301.1_Silent_p.G28G|CCAR2_ENST00000520861.1_5'Flank|CCAR2_ENST00000389279.3_Silent_p.G28G			Q8N163	CCAR2_HUMAN	cell cycle and apoptosis regulator 2	28					cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|mRNA processing (GO:0006397)|negative regulation of catalytic activity (GO:0043086)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902230)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA damage checkpoint (GO:2000003)|regulation of circadian rhythm (GO:0042752)|regulation of DNA-templated transcription, elongation (GO:0032784)|regulation of protein stability (GO:0031647)|response to UV (GO:0009411)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|DBIRD complex (GO:0044609)|mitochondrial matrix (GO:0005759)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)|poly(A) RNA binding (GO:0044822)|RNA polymerase II core binding (GO:0000993)										CTCTTCTGGGCCCTCCTCCTG	0.537													C|||	1520	0.303514	0.264	0.3285	5008	,	,		19386	0.2103		0.336	False		,,,				2504	0.4018				p.G28G		Atlas-SNP	.											KIAA1967,colon,carcinoma,+1,1	KIAA1967	72	1	0			c.C84T						PASS	.	C		1248,3158	431.2+/-342.8	189,870,1144	270.0	277.0	275.0		84	-7.6	0.5	8	dbSNP_116	275	2806,5794	442.4+/-360.1	459,1888,1953	no	coding-synonymous	KIAA1967	NM_021174.5		648,2758,3097	TT,TC,CC		32.6279,28.325,31.1702		28/924	22463623	4054,8952	2203	4300	6503	SO:0001819	synonymous_variant	57805	exon3			TCTGGGCCCTCCT	AL834351	CCDS34863.1	8p22	2013-08-22	2013-08-22	2013-08-22		ENSG00000158941			23360	protein-coding gene	gene with protein product	"""deleted in breast cancer"""	607359	"""KIAA1967"""	KIAA1967		12370419	Standard	NM_021174		Approved	DBC-1, DBC1, NET35	uc003xci.3	Q8N163		ENST00000308511.4:c.84C>T	8.37:g.22463623C>T		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	98	74	0.755102	NM_021174	A6NL03|B2RB79|D3DSR6|Q6P0Q9|Q8N3G7|Q8N8M1|Q8TF34|Q9H9Q9|Q9HD12|Q9NT55	Silent	SNP	ENST00000308511.4	37	CCDS34863.1	620	0.2838827838827839	123	0.25	121	0.3342541436464088	130	0.22727272727272727	246	0.3245382585751979	C	10.08	1.252727	0.22965	0.28325	0.326279	ENSG00000158941	ENST00000523801	.	.	.	5.45	-7.62	0.01294	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.999999190523	.	.	.	.	.	.	T	0.16041	-1.0416	3	.	.	.	-19.6607	9.4666	0.38817	0.169:0.5618:0.0:0.2691	rs7843828;rs17855314;rs57777354;rs7843828	.	.	.	S	36	.	.	P	+	1	0	KIAA1967	22519568	0.029000	0.19370	0.529000	0.27951	0.995000	0.86356	-1.986000	0.01484	-1.730000	0.01362	-0.152000	0.13540	CCC	C|0.705;T|0.295	0.295	strong		0.537	CCAR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375865.1	NM_021174	
SPTA1	6708	hgsc.bcm.edu	37	1	158624528	158624528	+	Missense_Mutation	SNP	G	G	T	rs35948326	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	80	0	0		WXS	Illumina HiSeq	Phase_I	45	25	0.555556	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	
SLCO1A2	6579	hgsc.bcm.edu	37	12	21457434	21457434	+	Missense_Mutation	SNP	T	T	G	rs11568563	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:21457434T>G	ENST00000307378.6	-	7	1236	c.516A>C	c.(514-516)gaA>gaC	p.E172D	SLCO1A2_ENST00000452078.1_Missense_Mutation_p.E172D|SLCO1A2_ENST00000390670.3_Missense_Mutation_p.E170D|SLCO1A2_ENST00000458504.1_Missense_Mutation_p.E40D|SLCO1A2_ENST00000537524.1_Missense_Mutation_p.E40D	NM_134431.3	NP_602307.1	P46721	SO1A2_HUMAN	solute carrier organic anion transporter family, member 1A2	172			E -> D (in dbSNP:rs11568563). {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)	GGATGGGAGTTTCACCCATTC	0.348													T|||	132	0.0263578	0.0144	0.0403	5008	,	,		18757	0.0		0.0686	False		,,,				2504	0.0164				p.E172D		Atlas-SNP	.											SLCO1A2,lymph_node,lymphoid_neoplasm,0,1	SLCO1A2	107	1	0			c.A516C	GRCh37	CM051637	SLCO1A2	M	rs11568563	PASS	.	T	ASP/GLU,ASP/GLU	82,4324	69.8+/-107.6	0,82,2121	96.0	91.0	92.0	http://www.ncbi.nlm.nih.gov/pubmed?term	516,516	3.6	1.0	12	dbSNP_126	92	480,8120	140.8+/-197.2	8,464,3828	yes	missense,missense	SLCO1A2	NM_021094.3,NM_134431.3	45,45	8,546,5949	GG,GT,TT	http://www.ncbi.nlm.nih.gov/pubmed?term	5.5814,1.8611,4.3211	probably-damaging,probably-damaging	172/671,172/671	21457434	562,12444	2203	4300	6503	SO:0001583	missense	6579	exon7			GGGAGTTTCACCC		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.516A>C	12.37:g.21457434T>G	ENSP00000305974:p.Glu172Asp	Somatic	231	0	0		WXS	Illumina HiSeq	Phase_I	169	82	0.485207	NM_134431	Q9UGP7|Q9UL38	Missense_Mutation	SNP	ENST00000307378.6	37	CCDS8686.1	73	0.033424908424908424	5	0.01016260162601626	15	0.04143646408839779	0	0.0	53	0.06992084432717678	T	19.91	3.915407	0.73098	0.018611	0.055814	ENSG00000084453	ENST00000307378;ENST00000452078;ENST00000458504;ENST00000537524;ENST00000390670	T;T;T;T;T	0.41065	1.01;1.01;1.01;1.01;1.01	4.75	3.6	0.41247	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.85682	D	0.000000	T	0.15739	0.0379	M	0.92738	3.34	0.36436	D	0.86518	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.998;0.999	T	0.61382	-0.7074	10	0.44086	T	0.13	.	10.4978	0.44788	0.0:0.077:0.0:0.923	rs11568563;rs52838223;rs57550534;rs11568563	152;170;172	Q8IV69;P46721-2;P46721	.;.;SO1A2_HUMAN	D	172;172;40;40;170	ENSP00000305974:E172D;ENSP00000393973:E172D;ENSP00000394854:E40D;ENSP00000439401:E40D;ENSP00000375088:E170D	ENSP00000305974:E172D	E	-	3	2	SLCO1A2	21348701	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	2.341000	0.43983	0.838000	0.34948	0.482000	0.46254	GAA	T|0.964;G|0.036	0.036	strong		0.348	SLCO1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343648.3	NM_021094	
ICAM1	3383	hgsc.bcm.edu	37	19	10395248	10395248	+	Silent	SNP	C	C	T	rs13306429	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:10395248C>T	ENST00000264832.3	+	5	1420	c.1095C>T	c.(1093-1095)aaC>aaT	p.N365N	ICAM4_ENST00000393717.2_5'Flank|ICAM1_ENST00000423829.2_Silent_p.N143N|CTD-2369P2.8_ENST00000589379.1_RNA|CTD-2369P2.5_ENST00000592893.1_RNA|ICAM4_ENST00000340992.4_5'Flank|ICAM4_ENST00000380770.3_5'Flank	NM_000201.2	NP_000192.2	P05362	ICAM1_HUMAN	intercellular adhesion molecule 1	365	Ig-like C2-type 4.				adhesion of symbiont to host (GO:0044406)|cell adhesion (GO:0007155)|cell adhesion mediated by integrin (GO:0033627)|cell aging (GO:0007569)|cellular response to alkaloid (GO:0071312)|cellular response to glucose stimulus (GO:0071333)|cellular response to hypoxia (GO:0071456)|cellular response to interleukin-1 (GO:0071347)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to nutrient levels (GO:0031669)|cellular response to tumor necrosis factor (GO:0071356)|cytokine-mediated signaling pathway (GO:0019221)|establishment of endothelial barrier (GO:0061028)|extracellular matrix organization (GO:0030198)|heterophilic cell-cell adhesion (GO:0007157)|interferon-gamma-mediated signaling pathway (GO:0060333)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|membrane to membrane docking (GO:0022614)|negative regulation of calcium ion transport (GO:0051926)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|ovarian follicle development (GO:0001541)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cellular extravasation (GO:0002693)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of vasoconstriction (GO:0045907)|receptor-mediated virion attachment to host cell (GO:0046813)|regulation of cell adhesion (GO:0030155)|regulation of cell shape (GO:0008360)|regulation of immune response (GO:0050776)|regulation of leukocyte mediated cytotoxicity (GO:0001910)|regulation of ruffle assembly (GO:1900027)|response to amino acid (GO:0043200)|response to amphetamine (GO:0001975)|response to copper ion (GO:0046688)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to gonadotropin (GO:0034698)|response to ionizing radiation (GO:0010212)|response to organic cyclic compound (GO:0014070)|response to sulfur dioxide (GO:0010477)|T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell (GO:0002291)|T cell antigen processing and presentation (GO:0002457)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|immunological synapse (GO:0001772)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	integrin binding (GO:0005178)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)|virus receptor activity (GO:0001618)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(4)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	14			OV - Ovarian serous cystadenocarcinoma(20;1.39e-09)|Epithelial(33;2.81e-06)|all cancers(31;6.56e-06)		Hyaluronan(DB08818)|Natalizumab(DB00108)	CAGAGGACAACGGGCGCAGCT	0.652													C|||	55	0.0109824	0.0	0.0	5008	,	,		13810	0.0466		0.003	False		,,,				2504	0.0051				p.N365N		Atlas-SNP	.											.	ICAM1	32	.	0			c.C1095T						PASS	.	C		1,4405	2.1+/-5.4	0,1,2202	40.0	47.0	45.0		1095	-2.0	0.0	19	dbSNP_121	45	7,8593	5.7+/-21.5	0,7,4293	no	coding-synonymous	ICAM1	NM_000201.2		0,8,6495	TT,TC,CC		0.0814,0.0227,0.0615		365/533	10395248	8,12998	2203	4300	6503	SO:0001819	synonymous_variant	3383	exon5			GGACAACGGGCGC		CCDS12231.1	19p13.3-p13.2	2014-01-30	2008-07-18			ENSG00000090339		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Endogenous ligands"""	5344	protein-coding gene	gene with protein product	"""human rhinovirus receptor"""	147840				2453850, 3871395	Standard	NM_000201		Approved	BB2, CD54	uc002mnq.2	P05362		ENST00000264832.3:c.1095C>T	19.37:g.10395248C>T		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	62	28	0.451613	NM_000201	B2R6M3|Q5NKV7|Q96B50	Silent	SNP	ENST00000264832.3	37	CCDS12231.1																																																																																			C|0.994;T|0.006	0.006	strong		0.652	ICAM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451207.1		
IGFN1	91156	hgsc.bcm.edu	37	1	201163305	201163305	+	De_novo_Start_OutOfFrame	SNP	C	C	A	rs189690117	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:201163305C>A	ENST00000295591.8	+	0	161				IGFN1_ENST00000451870.2_Missense_Mutation_p.P11T|IGFN1_ENST00000335211.4_Missense_Mutation_p.P11T			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						GTCCCACATCCCTGGAGTGAG	0.607													C|||	7	0.00139776	0.0015	0.0014	5008	,	,		18650	0.0		0.004	False		,,,				2504	0.0				p.P11T		Atlas-SNP	.											.	IGFN1	220	.	0			c.C31A						PASS	.						30.0	36.0	34.0					1																	201163305		692	1591	2283			91156	exon3			CACATCCCTGGAG	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.-8490C>A	1.37:g.201163305C>A		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	116	116	1	NM_001164586	F8WAI1|Q9NT72	Missense_Mutation	SNP	ENST00000295591.8	37		2	9.157509157509158E-4	1	0.0020325203252032522	0	0.0	0	0.0	1	0.0013192612137203166	C	15.73	2.921085	0.52653	.	.	ENSG00000163395	ENST00000335211;ENST00000451870	T;T	0.63096	0.23;-0.02	4.55	4.55	0.56014	.	.	.	.	.	T	0.69287	0.3094	L	0.55481	1.735	0.80722	D	1	.	.	.	.	.	.	T	0.72620	-0.4238	7	0.62326	D	0.03	.	14.2363	0.65929	0.0:1.0:0.0:0.0	.	.	.	.	T	11	ENSP00000334714:P11T;ENSP00000398386:P11T	ENSP00000334714:P11T	P	+	1	0	IGFN1	199429928	0.289000	0.24334	0.730000	0.30809	0.517000	0.34286	2.800000	0.47900	2.058000	0.61347	0.637000	0.83480	CCT	C|0.999;A|0.001	0.001	strong		0.607	IGFN1-201	KNOWN	basic	protein_coding	protein_coding		NM_178275	
PCDHB6	56130	hgsc.bcm.edu	37	5	140531374	140531374	+	Silent	SNP	T	T	C	rs17844437	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	171	0	0		WXS	Illumina HiSeq	Phase_I	167	70	0.419162	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	
CCDC185	164127	hgsc.bcm.edu	37	1	223567808	223567808	+	Missense_Mutation	SNP	C	C	T	rs6682552	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:223567808C>T	ENST00000366875.3	+	1	1094	c.991C>T	c.(991-993)Cgg>Tgg	p.R331W		NM_152610.2	NP_689823.2	Q8N715	CC185_HUMAN		331			R -> W (in dbSNP:rs6682552).							breast(4)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(12)|skin(3)	29				GBM - Glioblastoma multiforme(131;0.0704)		GCGCGGCCTGCGGCGGGACAG	0.701													C|||	403	0.0804712	0.0825	0.0634	5008	,	,		14331	0.13		0.0408	False		,,,				2504	0.0798				p.R331W		Atlas-SNP	.											.	C1orf65	71	.	0			c.C991T						PASS	.	C	TRP/ARG	302,3938		10,282,1828	11.0	10.0	10.0		991	1.6	0.0	1	dbSNP_116	10	291,8107		7,277,3915	yes	missense	C1orf65	NM_152610.2	101	17,559,5743	TT,TC,CC		3.4651,7.1226,4.6922	probably-damaging	331/624	223567808	593,12045	2120	4199	6319	SO:0001583	missense	164127	exon1			GGCCTGCGGCGGG																												ENST00000366875.3:c.991C>T	1.37:g.223567808C>T	ENSP00000355840:p.Arg331Trp	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	115	54	0.469565	NM_152610	Q8N746|Q8NA93	Missense_Mutation	SNP	ENST00000366875.3	37	CCDS1537.1	137	0.06272893772893773	26	0.052845528455284556	17	0.04696132596685083	66	0.11538461538461539	28	0.036939313984168866	C	11.09	1.535969	0.27475	0.071226	0.034651	ENSG00000178395	ENST00000366875	T	0.27890	1.64	2.59	1.63	0.23807	.	.	.	.	.	T	0.00666	0.0022	M	0.62723	1.935	0.53688	P	2.5000000000052758E-5	D	0.76494	0.999	P	0.56343	0.796	T	0.12167	-1.0558	8	0.54805	T	0.06	.	9.2985	0.37831	0.0:0.7768:0.2232:0.0	rs6682552;rs6682552	331	Q8N715	CA065_HUMAN	W	331	ENSP00000355840:R331W	ENSP00000355840:R331W	R	+	1	2	C1orf65	221634431	0.000000	0.05858	0.009000	0.14445	0.097000	0.18754	-0.154000	0.10130	0.625000	0.30304	0.650000	0.86243	CGG	C|0.933;T|0.067	0.067	strong		0.701	C1orf65-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092718.1		
KRT28	162605	hgsc.bcm.edu	37	17	38955991	38955991	+	Missense_Mutation	SNP	C	C	T	rs7209228	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:38955991C>T	ENST00000306658.7	-	1	220	c.155G>A	c.(154-156)gGc>gAc	p.G52D		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)				ACTGCCCAAGCCCCCTCCCAA	0.567													C|||	521	0.104034	0.1256	0.1124	5008	,	,		17892	0.004		0.1829	False		,,,				2504	0.091				p.G52D	Melanoma(19;789 869 15380 26882 39836)	Atlas-SNP	.											.	KRT28	65	.	0			c.G155A						PASS	.	C	ASP/GLY	496,3910	230.7+/-244.8	31,434,1738	71.0	75.0	74.0		155	3.5	0.8	17	dbSNP_116	74	1518,7082	286.9+/-297.9	131,1256,2913	yes	missense	KRT28	NM_181535.3	94	162,1690,4651	TT,TC,CC		17.6512,11.2574,15.4852	benign	52/465	38955991	2014,10992	2203	4300	6503	SO:0001583	missense	162605	exon1			CCCAAGCCCCCTC	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.155G>A	17.37:g.38955991C>T	ENSP00000305263:p.Gly52Asp	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	42	13	0.309524	NM_181535		Missense_Mutation	SNP	ENST00000306658.7	37	CCDS11376.1	239	0.10943223443223443	65	0.13211382113821138	47	0.1298342541436464	0	0.0	127	0.16754617414248021	C	14.98	2.696528	0.48202	0.112574	0.176512	ENSG00000173908	ENST00000306658	D	0.88354	-2.37	5.52	3.47	0.39725	.	0.453405	0.18702	N	0.133542	T	0.00580	0.0019	L	0.29908	0.895	0.41216	P	0.01352500000000001	P	0.43477	0.808	B	0.34590	0.186	T	0.24154	-1.0168	9	0.45353	T	0.12	.	14.9934	0.71412	0.0:0.7198:0.2802:0.0	rs7209228;rs52810060;rs59201813;rs7209228	52	Q7Z3Y7	K1C28_HUMAN	D	52	ENSP00000305263:G52D	ENSP00000305263:G52D	G	-	2	0	KRT28	36209517	0.015000	0.18098	0.846000	0.33378	0.886000	0.51366	2.612000	0.46343	0.765000	0.33221	0.650000	0.86243	GGC	C|0.859;T|0.141	0.141	strong		0.567	KRT28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257201.2	NM_181535	
KRT32	3882	hgsc.bcm.edu	37	17	39622068	39622068	+	Missense_Mutation	SNP	G	G	T	rs2071561	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	120	0	0		WXS	Illumina HiSeq	Phase_I	121	121	1	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	
NFIX	4784	hgsc.bcm.edu	37	19	13183882	13183882	+	Nonsense_Mutation	SNP	C	C	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:13183882C>G	ENST00000592199.1	+	3	581	c.581C>G	c.(580-582)tCa>tGa	p.S194*	NFIX_ENST00000397661.2_Nonsense_Mutation_p.S194*|NFIX_ENST00000360105.4_Nonsense_Mutation_p.S197*|NFIX_ENST00000358552.3_Nonsense_Mutation_p.S193*|NFIX_ENST00000587760.1_Nonsense_Mutation_p.S186*|NFIX_ENST00000588680.1_3'UTR|NFIX_ENST00000587260.1_Nonsense_Mutation_p.S193*|NFIX_ENST00000588228.1_Nonsense_Mutation_p.S147*|NFIX_ENST00000585575.1_Nonsense_Mutation_p.S186*|AC007787.2_ENST00000588095.1_RNA			Q14938	NFIX_HUMAN	nuclear factor I/X (CCAAT-binding transcription factor)	194					astrocyte differentiation (GO:0048708)|cerebellar granule cell differentiation (GO:0021707)|cerebellar Purkinje cell layer development (GO:0021680)|DNA replication (GO:0006260)|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)	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)|endometrium(3)|kidney(2)|large_intestine(1)|lung(1)|skin(1)|urinary_tract(1)	11			OV - Ovarian serous cystadenocarcinoma(19;8.2e-22)			TCAGATAGTTCAAACCAGCAA	0.557																																					p.S202X		Atlas-SNP	.											.	NFIX	61	.	0			c.C605G						PASS	.						142.0	144.0	143.0					19																	13183882		2032	4166	6198	SO:0001587	stop_gained	4784	exon3			ATAGTTCAAACCA	U18761	CCDS45996.1, CCDS59359.1	19p13.3	2008-02-05				ENSG00000008441			7788	protein-coding gene	gene with protein product		164005				8340106, 7590749	Standard	NM_001271043		Approved	NF1A	uc010xmx.2	Q14938		ENST00000592199.1:c.581C>G	19.37:g.13183882C>G	ENSP00000467512:p.Ser194*	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	105	27	0.257143	NM_001271043	B4DM25|O60413|Q0VG09|Q12859|Q13050|Q13052|Q5U094|Q9UPH1|Q9Y6R8	Nonsense_Mutation	SNP	ENST00000592199.1	37		.	.	.	.	.	.	.	.	.	.	C	35	5.568508	0.96540	.	.	ENSG00000008441	ENST00000397661;ENST00000360105;ENST00000264825;ENST00000438869;ENST00000358552	.	.	.	4.59	4.59	0.56863	.	0.156010	0.44483	D	0.000442	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.40728	T	0.16	.	14.6799	0.69009	0.0:1.0:0.0:0.0	.	.	.	.	X	194;194;197;147;193	.	ENSP00000264825:S197X	S	+	2	0	NFIX	13044882	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.505000	0.73708	2.280000	0.76307	0.462000	0.41574	TCA	.	.	none		0.557	NFIX-013	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000452763.1	NM_002501	
ETS2	2114	hgsc.bcm.edu	37	21	40191431	40191431	+	Silent	SNP	T	T	G	rs457705	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:40191431T>G	ENST00000360214.3	+	9	1276	c.816T>G	c.(814-816)acT>acG	p.T272T	ETS2_ENST00000360938.3_Silent_p.T272T	NM_001256295.1	NP_001243224.1	P15036	ETS2_HUMAN	v-ets avian erythroblastosis virus E26 oncogene homolog 2	272					cell differentiation (GO:0030154)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|skeletal system development (GO:0001501)|transcription from RNA polymerase II promoter (GO:0006366)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(2)|endometrium(1)|large_intestine(3)|lung(5)|ovary(1)|pancreas(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	18		Prostate(19;6.33e-08)|all_epithelial(19;0.123)				TGCCAGGGACTCCCAAAGACC	0.547													G|||	2910	0.58107	0.5628	0.5778	5008	,	,		18814	0.4563		0.838	False		,,,				2504	0.4724				p.T412T		Atlas-SNP	.											ETS2_ENST00000360214,NS,carcinoma,0,2	ETS2	87	2	0			c.T1236G						scavenged	.	G		2739,1667	509.6+/-367.3	872,995,336	71.0	64.0	66.0		816	-0.9	0.1	21	dbSNP_80	66	7292,1308	257.6+/-281.6	3085,1122,93	no	coding-synonymous	ETS2	NM_005239.4		3957,2117,429	GG,GT,TT		15.2093,37.8348,22.8741		272/470	40191431	10031,2975	2203	4300	6503	SO:0001819	synonymous_variant	2114	exon9			AGGGACTCCCAAA		CCDS13659.1	21q22.3	2013-07-09	2013-07-09		ENSG00000157557	ENSG00000157557			3489	protein-coding gene	gene with protein product		164740	"""v-ets erythroblastosis virus E26 oncogene homolog 2 (avian)"""			17986575	Standard	NM_001256295		Approved		uc002yxf.3	P15036	OTTHUMG00000090769	ENST00000360214.3:c.816T>G	21.37:g.40191431T>G		Somatic	68	1	0.0147059		WXS	Illumina HiSeq	Phase_I	62	62	1	NM_001256295	A6NM68|D3DSH6|Q53Y89	Silent	SNP	ENST00000360214.3	37	CCDS13659.1																																																																																			T|0.298;G|0.702	0.702	strong		0.547	ETS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207544.1		
SLC24A2	25769	hgsc.bcm.edu	37	9	19622268	19622268	+	Silent	SNP	T	T	C	rs4977308	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:19622268T>C	ENST00000341998.2	-	2	1021	c.960A>G	c.(958-960)ccA>ccG	p.P320P	SLC24A2_ENST00000286344.3_Silent_p.P320P	NM_001193288.2|NM_020344.3	NP_001180217.1|NP_065077.1	Q9UI40	NCKX2_HUMAN	solute carrier family 24 (sodium/potassium/calcium exchanger), member 2	320					cellular calcium ion homeostasis (GO:0006874)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|learning (GO:0007612)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|memory (GO:0007613)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|intrinsic component of plasma membrane (GO:0031226)|plasma membrane (GO:0005886)	cadmium ion binding (GO:0046870)|calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium, potassium:sodium antiporter activity (GO:0008273)|manganese ion binding (GO:0030145)|nickel cation binding (GO:0016151)|potassium ion binding (GO:0030955)|sodium ion binding (GO:0031402)|symporter activity (GO:0015293)			endometrium(3)|kidney(1)|large_intestine(9)|lung(13)|ovary(3)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	33				GBM - Glioblastoma multiforme(1;1.67e-55)|Lung(42;0.0443)		CCGGTAGAGTTGGTTCATCCT	0.473													C|||	3914	0.78155	0.7542	0.8156	5008	,	,		19936	0.8671		0.7227	False		,,,				2504	0.7669				p.P320P		Atlas-SNP	.											.	SLC24A2	93	.	0			c.A960G						PASS	.	C	,	3336,1070	390.0+/-327.5	1264,808,131	109.0	86.0	94.0		960,960	1.0	0.3	9	dbSNP_111	94	6195,2405	398.7+/-346.2	2243,1709,348	no	coding-synonymous,coding-synonymous	SLC24A2	NM_001193288.2,NM_020344.3	,	3507,2517,479	CC,CT,TT		27.9651,24.2851,26.7184	,	320/645,320/662	19622268	9531,3475	2203	4300	6503	SO:0001819	synonymous_variant	25769	exon2			TAGAGTTGGTTCA	AF097366	CCDS6493.1, CCDS55297.1	9p22.1	2013-05-22			ENSG00000155886	ENSG00000155886		"""Solute carriers"""	10976	protein-coding gene	gene with protein product		609838				10662833	Standard	NM_020344		Approved	NCKX2	uc003zoa.2	Q9UI40	OTTHUMG00000019646	ENST00000341998.2:c.960A>G	9.37:g.19622268T>C		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	70	36	0.514286	NM_001193288	B7ZLL8|Q9NTN5|Q9NZQ4	Silent	SNP	ENST00000341998.2	37	CCDS6493.1																																																																																			T|0.231;C|0.769	0.769	strong		0.473	SLC24A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051866.2	NM_020344	
TUBG2	27175	hgsc.bcm.edu	37	17	40811919	40811919	+	Silent	SNP	A	A	G	rs525911	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:40811919A>G	ENST00000251412.7	+	2	316	c.117A>G	c.(115-117)gaA>gaG	p.E39E		NM_016437.2	NP_057521.1	Q9NRH3	TBG2_HUMAN	tubulin, gamma 2	39					cytoplasmic microtubule organization (GO:0031122)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule nucleation (GO:0007020)|mitotic cell cycle (GO:0000278)	cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|gamma-tubulin complex (GO:0000930)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|pericentriolar material (GO:0000242)|spindle microtubule (GO:0005876)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)	15		Breast(137;0.00116)		BRCA - Breast invasive adenocarcinoma(366;0.141)		TCGTGGAGGAATTCGCCACCG	0.662																																					p.E39E		Atlas-SNP	.											.	TUBG2	43	.	0			c.A117G						PASS	.						44.0	58.0	53.0					17																	40811919		2200	4290	6490	SO:0001819	synonymous_variant	27175	exon2			GGAGGAATTCGCC	AF225971	CCDS32658.1	17q21.2	2014-09-04			ENSG00000037042	ENSG00000037042		"""Tubulins"""	12419	protein-coding gene	gene with protein product		605785					Standard	NM_016437		Approved		uc010wgr.2	Q9NRH3	OTTHUMG00000180640	ENST00000251412.7:c.117A>G	17.37:g.40811919A>G		Somatic	282	0	0		WXS	Illumina HiSeq	Phase_I	229	83	0.362445	NM_016437	A6NDI4|Q32NB2	Silent	SNP	ENST00000251412.7	37	CCDS32658.1																																																																																			A|0.485;G|0.515	0.515	strong		0.662	TUBG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452326.1	NM_016437	
ABI3BP	25890	hgsc.bcm.edu	37	3	100617668	100617668	+	Silent	SNP	G	G	T	rs34999788	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:100617668G>T	ENST00000284322.5	-	4	529	c.420C>A	c.(418-420)tcC>tcA	p.S140S	ABI3BP_ENST00000532144.1_5'Flank|ABI3BP_ENST00000495063.1_Silent_p.S140S|ABI3BP_ENST00000471714.1_Silent_p.S140S	NM_015429.3	NP_056244.2	Q7Z7G0	TARSH_HUMAN	ABI family, member 3 (NESH) binding protein	140	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						GGAAACCCCAGGACAGGAAGA	0.478													G|||	270	0.0539137	0.0076	0.072	5008	,	,		20097	0.002		0.1541	False		,,,				2504	0.0542				p.S140S		Atlas-SNP	.											.	ABI3BP	305	.	0			c.C420A						PASS	.	G		126,4102		4,118,1992	88.0	97.0	94.0		420	4.6	1.0	3	dbSNP_126	94	1250,7252		93,1064,3094	no	coding-synonymous	ABI3BP	NM_015429.3		97,1182,5086	TT,TG,GG		14.7024,2.9801,10.8091		140/1076	100617668	1376,11354	2114	4251	6365	SO:0001819	synonymous_variant	25890	exon4			ACCCCAGGACAGG	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.420C>A	3.37:g.100617668G>T		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	67	22	0.328358	NM_015429	B3KSL4|Q6ZW20|Q6ZW22|Q9C082|Q9UFI6	Silent	SNP	ENST00000284322.5	37	CCDS46880.1																																																																																			G|0.913;T|0.087	0.087	strong		0.478	ABI3BP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000353260.1		
HLA-DPB1	3115	hgsc.bcm.edu	37	6	33053609	33053609	+	Missense_Mutation	SNP	G	G	A	rs11551421	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:33053609G>A	ENST00000418931.2	+	4	816	c.700G>A	c.(700-702)Gtg>Atg	p.V234M		NM_002121.5	NP_002112.3	P04440	DPB1_HUMAN	major histocompatibility complex, class II, DP beta 1	234			V -> M (in allele DPB1*05:01 and allele DPB1*19:01; dbSNP:rs11551421).		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell proliferation (GO:0042102)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	peptide antigen binding (GO:0042605)			cervix(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(3)|ovary(1)|skin(1)	11						TGGGGGCTTCGTGCTGGGGCT	0.582													.|||	575	0.114816	0.0363	0.0504	5008	,	,		19453	0.4018		0.0567	False		,,,				2504	0.0307				p.V234M		Atlas-SNP	.											.	HLA-DPB1	28	.	0			c.G700A						PASS	.	G	MET/VAL	192,4214	121.3+/-158.8	4,184,2015	107.0	95.0	99.0		700	2.2	0.4	6	dbSNP_120	99	375,8225	122.4+/-181.4	8,359,3933	yes	missense	HLA-DPB1	NM_002121.5	21	12,543,5948	AA,AG,GG		4.3605,4.3577,4.3595	benign	234/259	33053609	567,12439	2203	4300	6503	SO:0001583	missense	3115	exon4			GGCTTCGTGCTGG		CCDS4765.1	6p21.3	2013-01-11			ENSG00000223865	ENSG00000223865		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4940	protein-coding gene	gene with protein product		142858		HLA-DP1B			Standard	NM_002121		Approved		uc003ocu.2	P04440	OTTHUMG00000031076	ENST00000418931.2:c.700G>A	6.37:g.33053609G>A	ENSP00000408146:p.Val234Met	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	90	46	0.511111	NM_002121	A0PFJ7|A5I886|A8YPB3|B5U8B4|B7VF80|B7VF87|B8ZX68|B8ZYT0|B9W5S8|B9W6F7|B9W6F9|C0MPP5|C0MPQ2|C0MPQ3|C0MPQ5|C0MPQ6|C0MPQ7|C4R9J5|C5IZL1|O00259|O19698|O19700|O19702|O19749|O46884|O77952|O98215|O98216|O98217|O98218|O98219|O98222|O98223|P01916|P04232|P13763|P79493|P79608|Q0P0L4|Q0ZFN3|Q14279|Q27S71|Q29682|Q29684|Q29698|Q29714|Q29775|Q29776|Q29778|Q29779|Q29781|Q29827|Q29828|Q29879|Q29880|Q29898|Q29977|Q2MGW3|Q30015|Q30031|Q30032|Q30033|Q30034|Q30050|Q30051|Q30052|Q30053|Q30054|Q30055|Q30174|Q4GY31|Q4JHD8|Q5ENE0|Q5ENE1|Q5ENW3|Q5EP46|Q5EP47|Q5EP49|Q5EP51|Q5EP52|Q5EP53|Q5EP56|Q5I4H8|Q5I4H9|Q5ISH4|Q5ISH5|Q5SQ73|Q5STP2|Q5YLA6|Q6IVX1|Q6LBX2|Q6LBX3|Q6LBX4|Q6LBX5|Q6LBX6|Q6LBX7|Q6PWX6|Q6TAS4|Q714U1|Q714U2|Q7YQ10|Q860Z7|Q8HWL7|Q8HWT5|Q8SNC4|Q95HC1|Q95IT7|Q95IT8|Q9BD13|Q9GIM2|Q9GIM4|Q9GIX6|Q9GJ41|Q9MY67|Q9TNT7|Q9TQE2|Q9XS11|Q9XS12	Missense_Mutation	SNP	ENST00000418931.2	37	CCDS4765.1	298|298	0.13644688644688643|0.13644688644688643	20|20	0.04065040650406504|0.04065040650406504	22|22	0.06077348066298342|0.06077348066298342	212|212	0.3706293706293706|0.3706293706293706	44|44	0.05804749340369393|0.05804749340369393	G|G	7.651|7.651	0.682915|0.682915	0.14907|0.14907	0.043577|0.043577	0.043605|0.043605	ENSG00000223865|ENSG00000223865	ENST00000422592|ENST00000418931;ENST00000411942;ENST00000428835	.|T;T	.|0.00801	.|5.78;5.68	4.02|4.02	2.16|2.16	0.27623|0.27623	.|Immunoglobulin-like fold (1);	.|0.235256	.|0.34555	.|N	.|0.003880	T|T	0.00666|0.00666	0.0022|0.0022	M|M	0.84773|0.84773	2.715|2.715	0.09310|0.09310	P|P	0.99999290789|0.99999290789	.|B;B;B	.|0.30709	.|0.291;0.228;0.076	.|B;B;B	.|0.29598	.|0.104;0.066;0.022	T|T	0.39057|0.39057	-0.9632|-0.9632	5|9	0.87932|0.62326	D|D	0|0.03	.|.	5.3636|5.3636	0.16101|0.16101	0.1141:0.2077:0.6782:0.0|0.1141:0.2077:0.6782:0.0	rs11551421;rs29029545;rs11551421|rs11551421;rs29029545;rs11551421	.|200;244;234	.|A2ALJ6;Q59GY1;P04440	.|.;.;DPB1_HUMAN	H|M	44|234;204;211	.|ENSP00000408146:V234M;ENSP00000412654:V211M	ENSP00000413559:R44H|ENSP00000389210:V204M	R|V	+|+	2|1	0|0	HLA-DPB1|HLA-DPB1	33161587|33161587	0.455000|0.455000	0.25736|0.25736	0.441000|0.441000	0.26858|0.26858	0.185000|0.185000	0.23345|0.23345	0.294000|0.294000	0.19047|0.19047	0.441000|0.441000	0.26529|0.26529	0.637000|0.637000	0.83480|0.83480	CGT|GTG	G|0.913;A|0.087	0.087	strong		0.582	HLA-DPB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076106.2	NM_002121	
HELZ2	85441	hgsc.bcm.edu	37	20	62191937	62191937	+	Silent	SNP	G	G	A	rs11551685	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:62191937G>A	ENST00000467148.1	-	16	7464	c.7395C>T	c.(7393-7395)tgC>tgT	p.C2465C	HELZ2_ENST00000427522.2_Silent_p.C1896C	NM_001037335.2	NP_001032412.2	Q9BYK8	HELZ2_HUMAN	helicase with zinc finger 2, transcriptional coactivator	2465	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)										AGATGACAGGGCAGCTCTCCT	0.642													G|||	1097	0.21905	0.1823	0.2954	5008	,	,		15975	0.2569		0.0984	False		,,,				2504	0.2996				p.C2465C		Atlas-SNP	.											.	.	.	.	0			c.C7395T						PASS	.	G	,	753,3653	308.3+/-290.5	71,611,1521	112.0	108.0	109.0		7395,5688	1.0	0.8	20	dbSNP_120	109	874,7726	197.8+/-242.3	44,786,3470	no	coding-synonymous,coding-synonymous	PRIC285	NM_001037335.2,NM_033405.3	,	115,1397,4991	AA,AG,GG		10.1628,17.0903,12.5096	,	2465/2650,1896/2081	62191937	1627,11379	2203	4300	6503	SO:0001819	synonymous_variant	85441	exon17			GACAGGGCAGCTC	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.7395C>T	20.37:g.62191937G>A		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	61	33	0.540984	NM_001037335	Q3C2G2|Q4VXQ1|Q8TEF3|Q96ND3|Q9C094	Silent	SNP	ENST00000467148.1	37	CCDS33508.1																																																																																			G|0.842;A|0.158	0.158	strong		0.642	HELZ2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354127.1	NM_001037335	
LGR6	59352	hgsc.bcm.edu	37	1	202183308	202183308	+	Intron	SNP	C	C	T	rs10920362	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:202183308C>T	ENST00000367278.3	+	2	301				LGR6_ENST00000255432.7_Intron|LGR6_ENST00000439764.2_Missense_Mutation_p.S9L	NM_001017403.1	NP_001017403.1	Q9HBX8	LGR6_HUMAN	leucine-rich repeat containing G protein-coupled receptor 6						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						GAGGGCCGCTCAGCGAGGGCG	0.697													T|||	2005	0.400359	0.472	0.4366	5008	,	,		11015	0.3095		0.4791	False		,,,				2504	0.2904				p.S9L		Atlas-SNP	.											.	LGR6	102	.	0			c.C26T						PASS	.	T	,LEU/SER,	2028,2338		478,1072,633	14.0	15.0	15.0		,26,	-2.7	0.0	1	dbSNP_120	15	3918,4670		919,2080,1295	no	intron,missense,intron	LGR6	NM_001017403.1,NM_001017404.1,NM_021636.2	,145,	1397,3152,1928	TT,TC,CC		45.6218,46.4498,45.9009	,,	,9/829,	202183308	5946,7008	2183	4294	6477	SO:0001627	intron_variant	59352	exon1			GCCGCTCAGCGAG	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.213-11243C>T	1.37:g.202183308C>T		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	107	57	0.53271	NM_001017404	Q5T509|Q5T512|Q6UY15|Q86VU0|Q96K69|Q9BYD7	Missense_Mutation	SNP	ENST00000367278.3	37	CCDS30971.1	927	0.42445054945054944	249	0.5060975609756098	172	0.47513812154696133	152	0.26573426573426573	354	0.46701846965699206	T	4.644	0.119782	0.08881	0.464498	0.456218	ENSG00000133067	ENST00000439764	T	0.52295	0.67	1.99	-2.73	0.05950	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.10296	0.003	B	0.04013	0.001	T	0.44298	-0.9337	7	0.66056	D	0.02	.	3.838	0.08902	0.1722:0.4257:0.0:0.402	rs10920362;rs60483425;rs10920362	9	Q9HBX8-1	.	L	9	ENSP00000387869:S9L	ENSP00000387869:S9L	S	+	2	0	LGR6	200449931	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.816000	0.00752	-1.333000	0.02247	-2.879000	0.00098	TCA	C|0.563;T|0.437	0.437	strong		0.697	LGR6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099143.1	NM_021636	
CCRL2	9034	hgsc.bcm.edu	37	3	46450297	46450297	+	Missense_Mutation	SNP	A	A	G	rs3204850	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:46450297A>G	ENST00000399036.3	+	2	1079	c.727A>G	c.(727-729)Ata>Gta	p.I243V	CCRL2_ENST00000400880.3_Missense_Mutation_p.I243V|CCRL2_ENST00000400882.2_Missense_Mutation_p.I243V|CCRL2_ENST00000357392.4_Missense_Mutation_p.I255V|RP11-24F11.2_ENST00000451485.1_RNA	NM_003965.4	NP_003956.2	O00421	CCRL2_HUMAN	chemokine (C-C motif) receptor-like 2	243			I -> V (in dbSNP:rs3204850). {ECO:0000269|Ref.3}.		chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	CCR chemokine receptor binding (GO:0048020)|chemokine receptor activity (GO:0004950)|chemokine receptor binding (GO:0042379)			lung(3)|ovary(1)|urinary_tract(1)	5				BRCA - Breast invasive adenocarcinoma(193;0.00112)|KIRC - Kidney renal clear cell carcinoma(197;0.017)|Kidney(197;0.02)		TGTTTTTGCCATAATGGTAGT	0.418													A|||	353	0.0704872	0.003	0.0403	5008	,	,		21215	0.0288		0.0934	False		,,,				2504	0.2025				p.I255V		Atlas-SNP	.											.	CCRL2	23	.	0			c.A763G						PASS	.	A	VAL/ILE,VAL/ILE	66,3808		2,62,1873	246.0	243.0	244.0		763,727	0.2	0.0	3	dbSNP_105	244	690,7562		27,636,3463	yes	missense,missense	CCRL2	NM_001130910.1,NM_003965.4	29,29	29,698,5336	GG,GA,AA		8.3616,1.7037,6.2345	benign,benign	255/357,243/345	46450297	756,11370	1937	4126	6063	SO:0001583	missense	9034	exon2			TTTGCCATAATGG	AF014958	CCDS43079.1, CCDS46814.1	3p21	2013-07-18	2013-07-18	2013-07-18	ENSG00000121797	ENSG00000121797		"""GPCR / Class A : Chemokine receptors : Atypical"""	1612	protein-coding gene	gene with protein product	"""atypical chemokine receptor 5"""	608379				9473515	Standard	NM_001130910		Approved	HCR, CRAM-B, CKRX, CRAM-A, ACKR5	uc003cpp.4	O00421	OTTHUMG00000156318	ENST00000399036.3:c.727A>G	3.37:g.46450297A>G	ENSP00000381994:p.Ile243Val	Somatic	219	0	0		WXS	Illumina HiSeq	Phase_I	234	111	0.474359	NM_001130910	B4DKQ8|O75307|Q4VBB0|Q6IPX0|Q7KYQ9|Q96KP5|Q9UPG0	Missense_Mutation	SNP	ENST00000399036.3	37	CCDS43079.1	111	0.050824175824175824	4	0.008130081300813009	11	0.03038674033149171	21	0.03671328671328671	75	0.09894459102902374	A	14.23	2.473282	0.43942	0.017037	0.083616	ENSG00000121797	ENST00000399036;ENST00000357392;ENST00000400880;ENST00000400882	T;T;T;T	0.34072	1.38;1.38;1.38;1.38	5.24	0.16	0.14972	GPCR, rhodopsin-like superfamily (1);	0.356870	0.25636	N	0.029306	T	0.00637	0.0021	L	0.37630	1.12	0.80722	P	0.0	B;B	0.24258	0.1;0.046	B;B	0.22152	0.022;0.038	T	0.06006	-1.0851	9	0.48119	T	0.1	.	8.7445	0.34578	0.5761:0.0:0.4239:0.0	rs3204850;rs17715546;rs35223756;rs61754204	255;243	O00421-2;O00421	.;CCRL2_HUMAN	V	243;255;243;243	ENSP00000381994:I243V;ENSP00000349967:I255V;ENSP00000383677:I243V;ENSP00000383678:I243V	ENSP00000349967:I255V	I	+	1	0	CCRL2	46425301	0.002000	0.14202	0.011000	0.14972	0.917000	0.54804	-0.076000	0.11412	-0.202000	0.10268	0.397000	0.26171	ATA	A|0.948;G|0.052	0.052	strong		0.418	CCRL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343909.2		
NCAPH2	29781	hgsc.bcm.edu	37	22	50960682	50960682	+	Splice_Site	SNP	C	C	T	rs140524	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:50960682C>T	ENST00000420993.2	+	14	1355		c.e14+2		CTA-384D8.36_ENST00000608319.1_RNA|NCAPH2_ENST00000520297.1_Splice_Site|NCAPH2_ENST00000299821.11_Splice_Site|NCAPH2_ENST00000395701.3_Splice_Site	NM_001185011.1|NM_152299.3	NP_001171940.1|NP_689512.2	Q6IBW4	CNDH2_HUMAN	non-SMC condensin II complex, subunit H2						chromosome condensation (GO:0030261)|mitotic cell cycle (GO:0000278)	chromosome (GO:0005694)|membrane (GO:0016020)|nucleoplasm (GO:0005654)		p.?(1)		breast(1)|cervix(1)|endometrium(2)|kidney(3)|lung(10)|ovary(1)|prostate(2)|skin(3)|stomach(1)	24		all_cancers(38;4.58e-14)|all_epithelial(38;1.12e-12)|all_lung(38;3.07e-05)|Breast(42;6.27e-05)|Lung NSC(38;0.000813)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.212)		AGGAGGGAGGCAAGTCCCAGC	0.592													C|||	1153	0.230232	0.2315	0.2378	5008	,	,		17582	0.2986		0.1551	False		,,,				2504	0.2301				.		Atlas-SNP	.											NCAPH2,NS,carcinoma,0,1	NCAPH2	69	1	1	Unknown(1)	stomach(1)	c.1233+2C>T						scavenged	.	C	,	1026,3380	380.9+/-323.9	115,796,1292	76.0	79.0	78.0		,	-1.7	0.9	22	dbSNP_78	78	1408,7192	271.7+/-289.7	119,1170,3011	yes	splice-5,splice-5	NCAPH2	NM_001185011.1,NM_152299.3	,	234,1966,4303	TT,TC,CC		16.3721,23.2864,18.7144	,	,	50960682	2434,10572	2203	4300	6503	SO:0001630	splice_region_variant	29781	exon14			GGGAGGCAAGTCC	BC001937	CCDS14094.2, CCDS43038.1, CCDS54546.1	22q13.33	2008-02-04			ENSG00000025770	ENSG00000025770			25071	protein-coding gene	gene with protein product	"""kleisin beta"", ""CAP-H2 subunit of the condensin II complex"""	611230				10493829	Standard	NM_014551		Approved	384D8-2, hCAP-H2, CAP-H2	uc003blx.4	Q6IBW4	OTTHUMG00000150205	ENST00000420993.2:c.1233+2C>T	22.37:g.50960682C>T		Somatic	71	1	0.0140845		WXS	Illumina HiSeq	Phase_I	75	37	0.493333	NM_001185011	B7WPH1|O43788|Q13391|Q96C14|Q96GJ0|Q9BQ71|Q9BUT3|Q9BVD1	Splice_Site	SNP	ENST00000420993.2	37	CCDS14094.2	457	0.20924908424908426	108	0.21951219512195122	87	0.24033149171270718	145	0.2534965034965035	117	0.15435356200527706	C	11.97	1.798696	0.31777	0.232864	0.163721	ENSG00000025770	ENST00000420993;ENST00000395701;ENST00000299821	.	.	.	4.93	-1.73	0.08081	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	0.9999999999999993	.	.	.	.	.	.	.	.	.	.	.	.	.	.	4.3457	0.11131	0.1726:0.2524:0.0:0.575	rs140524;rs57584715;rs140524	.	.	.	.	-1	.	.	.	+	.	.	NCAPH2	49307548	0.036000	0.19791	0.853000	0.33588	0.792000	0.44763	-0.585000	0.05794	0.110000	0.17919	0.591000	0.81541	.	C|0.810;T|0.190	0.190	strong		0.592	NCAPH2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317012.1	NM_152299	Intron
TYK2	7297	hgsc.bcm.edu	37	19	10477206	10477206	+	Silent	SNP	G	G	A	rs280523	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:10477206G>A	ENST00000525621.1	-	6	997	c.516C>T	c.(514-516)acC>acT	p.T172T	TYK2_ENST00000529370.1_Silent_p.T172T|TYK2_ENST00000524462.1_5'UTR|TYK2_ENST00000264818.6_Silent_p.T172T	NM_003331.4	NP_003322.3	P29597	TYK2_HUMAN	tyrosine kinase 2	172	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				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)			TCTCCTCCTCGGTCGACAGCT	0.562													G|||	417	0.0832668	0.1634	0.0403	5008	,	,		17246	0.0308		0.0775	False		,,,				2504	0.0654				p.T172T		Atlas-SNP	.											.	TYK2	126	.	0			c.C516T						PASS	.	G		776,3630	314.7+/-293.7	58,660,1485	171.0	157.0	162.0		516	-2.5	0.0	19	dbSNP_79	162	566,8034	154.3+/-208.6	22,522,3756	no	coding-synonymous	TYK2	NM_003331.4		80,1182,5241	AA,AG,GG		6.5814,17.6123,10.3183		172/1188	10477206	1342,11664	2203	4300	6503	SO:0001819	synonymous_variant	7297	exon6			CTCCTCGGTCGAC		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.516C>T	19.37:g.10477206G>A		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	134	51	0.380597	NM_003331	Q6QB10|Q96CH0	Silent	SNP	ENST00000525621.1	37	CCDS12236.1																																																																																			G|0.905;A|0.095	0.095	strong		0.562	TYK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389443.1		
KIF18B	146909	hgsc.bcm.edu	37	17	43008970	43008970	+	Splice_Site	SNP	T	T	C	rs17546822	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:43008970T>C	ENST00000593135.1	-	11	1614	c.1517A>G	c.(1516-1518)cAg>cGg	p.Q506R	KIF18B_ENST00000587309.1_Splice_Site_p.Q518R|KIF18B_ENST00000339151.4_Splice_Site_p.Q518R|KIF18B_ENST00000438933.2_Splice_Site_p.Q518R|KIF18B_ENST00000590129.1_Splice_Site_p.Q527R	NM_001265577.1	NP_001252506.1	Q86Y91	KI18B_HUMAN	kinesin family member 18B	527					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)				AGATACCTACTGCTTAGAACG	0.567													T|||	119	0.023762	0.0045	0.0274	5008	,	,		22248	0.0		0.0716	False		,,,				2504	0.0225				p.Q518R		Atlas-SNP	.											.	KIF18B	63	.	0			c.A1553G						PASS	.	T	ARG/GLN	88,3940		1,86,1927	101.0	102.0	101.0		1553	1.1	0.4	17	dbSNP_123	101	596,7764		22,552,3606	yes	missense-near-splice	KIF18B	NM_001080443.1	43	23,638,5533	CC,CT,TT		7.1292,2.1847,5.5215	benign	518/856	43008970	684,11704	2014	4180	6194	SO:0001630	splice_region_variant	146909	exon11			ACCTACTGCTTAG		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.1517+1A>G	17.37:g.43008970T>C		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	87	37	0.425287	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	T	0.879	-0.729286	0.03135	0.021847	0.071292	ENSG00000186185	ENST00000438933;ENST00000339151;ENST00000376982	T;T	0.63580	-0.05;-0.05	4.62	1.07	0.20283	.	.	.	.	.	T	0.04588	0.0125	L	0.35288	1.05	0.09310	N	0.999994	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.06405	0.001;0.001;0.002	T	0.04621	-1.0938	8	.	.	.	.	2.3826	0.04357	0.2094:0.2453:0.0:0.5453	rs17546822;rs56528092;rs17546822	527;515;527	Q86Y91;Q86Y91-3;Q86Y91-2	KI18B_HUMAN;.;.	R	518	ENSP00000412798:Q518R;ENSP00000341466:Q518R	.	Q	-	2	0	KIF18B	40364496	0.598000	0.26882	0.412000	0.26496	0.038000	0.13279	-0.038000	0.12144	0.331000	0.23511	0.533000	0.62120	CAG	T|0.964;C|0.036	0.036	strong		0.567	KIF18B-001	PUTATIVE	basic|appris_candidate|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000448724.1	NM_001080443	Missense_Mutation
NOL9	79707	hgsc.bcm.edu	37	1	6585956	6585956	+	Silent	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:6585956C>T	ENST00000377705.5	-	12	2099	c.2067G>A	c.(2065-2067)gaG>gaA	p.E689E		NM_024654.4	NP_078930	Q5SY16	NOL9_HUMAN	nucleolar protein 9	689					maturation of 5.8S rRNA (GO:0000460)	membrane (GO:0016020)|nucleolus (GO:0005730)	ATP binding (GO:0005524)|polynucleotide 5'-hydroxyl-kinase activity (GO:0051731)|RNA binding (GO:0003723)			central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(9)|skin(2)|urinary_tract(1)	19	Ovarian(185;0.0212)|all_lung(157;0.154)	all_cancers(23;2.46e-35)|all_epithelial(116;1.41e-22)|all_lung(118;7.59e-07)|Lung NSC(185;4.28e-06)|Colorectal(325;4.52e-05)|Breast(487;0.000353)|Renal(390;0.0007)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0443)		Colorectal(212;1.47e-07)|COAD - Colon adenocarcinoma(227;1.47e-05)|Kidney(185;5.27e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000971)|BRCA - Breast invasive adenocarcinoma(365;0.00113)|STAD - Stomach adenocarcinoma(132;0.0017)|READ - Rectum adenocarcinoma(331;0.0649)		GGTATGGTTTCTCTTTATGTG	0.413																																					p.E689E		Atlas-SNP	.											NOL9,bladder,carcinoma,0,1	NOL9	49	1	0			c.G2067A						scavenged	.						198.0	192.0	194.0					1																	6585956		2203	4300	6503	SO:0001819	synonymous_variant	79707	exon12			TGGTTTCTCTTTA	AK091284	CCDS80.1	1p36.31	2012-05-02			ENSG00000162408	ENSG00000162408			26265	protein-coding gene	gene with protein product	"""polynucleotide 5'-kinase"""					21063389	Standard	NM_024654		Approved	FLJ23323, NET6, Grc3	uc001ans.3	Q5SY16	OTTHUMG00000000904	ENST00000377705.5:c.2067G>A	1.37:g.6585956C>T		Somatic	246	0	0		WXS	Illumina HiSeq	Phase_I	251	4	0.0159363	NM_024654	Q2NL84|Q4VBY3|Q6P472|Q7L4D6|Q96EE0|Q9H5L4	Silent	SNP	ENST00000377705.5	37	CCDS80.1																																																																																			.	.	none		0.413	NOL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002625.1	NM_024654	
KIAA1755	85449	hgsc.bcm.edu	37	20	36869516	36869516	+	Missense_Mutation	SNP	C	C	A	rs1205434	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	65	0	0		WXS	Illumina HiSeq	Phase_I	66	34	0.515152	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	
MTHFR	4524	hgsc.bcm.edu	37	1	11863057	11863057	+	Silent	SNP	G	G	A	rs2066470	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:11863057G>A	ENST00000376592.1	-	1	245	c.117C>T	c.(115-117)ccC>ccT	p.P39P	MTHFR_ENST00000376590.3_Silent_p.P39P|MTHFR_ENST00000376583.3_Silent_p.P80P|MTHFR_ENST00000376585.1_Silent_p.P80P			P42898	MTHR_HUMAN	methylenetetrahydrofolate reductase (NAD(P)H)	39					blood circulation (GO:0008015)|cellular amino acid metabolic process (GO:0006520)|folic acid metabolic process (GO:0046655)|homocysteine metabolic process (GO:0050667)|methionine biosynthetic process (GO:0009086)|response to drug (GO:0042493)|response to folic acid (GO:0051593)|response to hypoxia (GO:0001666)|response to interleukin-1 (GO:0070555)|response to vitamin B2 (GO:0033274)|S-adenosylmethionine metabolic process (GO:0046500)|small molecule metabolic process (GO:0044281)|tetrahydrofolate interconversion (GO:0035999)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|neuron projection (GO:0043005)	flavin adenine dinucleotide binding (GO:0050660)|methylenetetrahydrofolate reductase (NAD(P)H) activity (GO:0004489)|modified amino acid binding (GO:0072341)|NADP binding (GO:0050661)			NS(4)|breast(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(6)|prostate(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	33	Ovarian(185;0.249)	Lung NSC(185;8.69e-05)|all_lung(284;9.87e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00826)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.66e-06)|COAD - Colon adenocarcinoma(227;0.000261)|BRCA - Breast invasive adenocarcinoma(304;0.000304)|Kidney(185;0.000777)|KIRC - Kidney renal clear cell carcinoma(229;0.00261)|STAD - Stomach adenocarcinoma(313;0.0073)|READ - Rectum adenocarcinoma(331;0.0649)	Benazepril(DB00542)|Cyanocobalamin(DB00115)|Fluorouracil(DB00544)|Folic Acid(DB00158)|L-Methionine(DB00134)|Menadione(DB00170)|Methotrexate(DB00563)|Riboflavin(DB00140)|Tetrahydrofolic acid(DB00116)	CATGCCGCTCGGGGTCCAGGC	0.592													G|||	509	0.101637	0.0719	0.0548	5008	,	,		18607	0.123		0.0984	False		,,,				2504	0.1564				p.P39P		Atlas-SNP	.											.	MTHFR	65	.	0			c.C117T						PASS	.	G		345,4061	180.1+/-208.5	15,315,1873	60.0	57.0	58.0		117	-11.3	0.0	1	dbSNP_94	58	822,7778	190.8+/-237.2	41,740,3519	no	coding-synonymous	MTHFR	NM_005957.4		56,1055,5392	AA,AG,GG		9.5581,7.8302,8.9728		39/657	11863057	1167,11839	2203	4300	6503	SO:0001819	synonymous_variant	4524	exon2			CCGCTCGGGGTCC	BC053509	CCDS137.1	1p36.3	2014-09-17	2010-05-04		ENSG00000177000	ENSG00000177000	1.5.1.20		7436	protein-coding gene	gene with protein product		607093	"""5,10-methylenetetrahydrofolate reductase (NADPH)"""			7920641	Standard	NM_005957		Approved		uc001atc.2	P42898	OTTHUMG00000002277	ENST00000376592.1:c.117C>T	1.37:g.11863057G>A		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	112	65	0.580357	NM_005957	B2R7A6|Q5SNW6|Q5SNW9|Q7Z6M6|Q8IU73|Q9UQR2	Silent	SNP	ENST00000376592.1	37	CCDS137.1																																																																																			G|0.910;A|0.090	0.090	strong		0.592	MTHFR-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000006538.1	NM_005957	
PDS5A	23244	hgsc.bcm.edu	37	4	39921942	39921942	+	Silent	SNP	A	A	G	rs28449663	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:39921942A>G	ENST00000303538.8	-	7	1271	c.732T>C	c.(730-732)gcT>gcC	p.A244A	PDS5A_ENST00000503396.1_Silent_p.A244A	NM_001100399.1	NP_001093869.1			PDS5, regulator of cohesion maintenance, homolog A (S. cerevisiae)											breast(2)|cervix(1)|endometrium(4)|kidney(4)|large_intestine(9)|lung(14)|prostate(3)|skin(1)|urinary_tract(1)	39						TACATACATTAGCAATGCATG	0.264													G|||	1990	0.397364	0.1407	0.2882	5008	,	,		16228	0.6637		0.4115	False		,,,				2504	0.5327				p.A244A		Atlas-SNP	.											PDS5A_ENST00000503396,NS,carcinoma,0,2	PDS5A	114	2	0			c.T732C						PASS	.	G	,	616,2984		50,516,1234	73.0	70.0	71.0		732,732	2.6	1.0	4	dbSNP_125	71	3331,4767		691,1949,1409	no	coding-synonymous,coding-synonymous	PDS5A	NM_001100399.1,NM_001100400.1	,	741,2465,2643	GG,GA,AA		41.1336,17.1111,33.7408	,	244/1338,244/601	39921942	3947,7751	1800	4049	5849	SO:0001819	synonymous_variant	23244	exon7			TACATTAGCAATG	AF294791	CCDS47045.1, CCDS54759.1	4p14	2007-06-20			ENSG00000121892	ENSG00000121892			29088	protein-coding gene	gene with protein product		613200				11076961, 15855230	Standard	NM_001100399		Approved	KIAA0648, PIG54, SCC-112	uc003guv.4	Q29RF7	OTTHUMG00000160582	ENST00000303538.8:c.732T>C	4.37:g.39921942A>G		Somatic	205	0	0		WXS	Illumina HiSeq	Phase_I	173	72	0.416185	NM_001100399		Silent	SNP	ENST00000303538.8	37	CCDS47045.1																																																																																			A|0.598;G|0.402	0.402	strong		0.264	PDS5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361287.1	NM_015200	
NEK9	91754	hgsc.bcm.edu	37	14	75590846	75590846	+	Silent	SNP	A	A	T	rs175449	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:75590846A>T	ENST00000238616.5	-	2	458	c.300T>A	c.(298-300)atT>atA	p.I100I		NM_033116.4	NP_149107.4	Q8TD19	NEK9_HUMAN	NIMA-related kinase 9	100	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope disassembly (GO:0007077)	cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)			endometrium(4)|kidney(2)|large_intestine(4)|lung(13)|ovary(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)	31				BRCA - Breast invasive adenocarcinoma(234;0.00718)		CCAGAATAACAATCTCATTCA	0.453													A|||	2143	0.427915	0.5847	0.3631	5008	,	,		20412	0.1528		0.4911	False		,,,				2504	0.4806				p.I100I		Atlas-SNP	.											.	NEK9	64	.	0			c.T300A						PASS	.	A		2461,1945	622.2+/-393.9	686,1089,428	202.0	155.0	171.0		300	3.8	1.0	14	dbSNP_79	171	4358,4242	581.7+/-391.3	1105,2148,1047	no	coding-synonymous	NEK9	NM_033116.4		1791,3237,1475	TT,TA,AA		49.3256,44.1443,47.5704		100/980	75590846	6819,6187	2203	4300	6503	SO:0001819	synonymous_variant	91754	exon2			AATAACAATCTCA	AY048580	CCDS9839.1	14q24.2	2012-11-15	2012-11-15		ENSG00000119638	ENSG00000119638			18591	protein-coding gene	gene with protein product		609798	"""NIMA (never in mitosis gene a)- related kinase 9"""			11864968	Standard	NM_033116		Approved	Nek8, NERCC, DKFZp434D0935, MGC16714	uc001xrl.3	Q8TD19	OTTHUMG00000171768	ENST00000238616.5:c.300T>A	14.37:g.75590846A>T		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	139	77	0.553957	NM_033116	Q52LK6|Q8NCN0|Q8TCY4|Q9UPI4|Q9Y6S4|Q9Y6S5|Q9Y6S6	Silent	SNP	ENST00000238616.5	37	CCDS9839.1																																																																																			A|0.436;T|0.564	0.564	strong		0.453	NEK9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415021.1	NM_033116	
CYP4F2	8529	hgsc.bcm.edu	37	19	16008257	16008257	+	Silent	SNP	T	T	C	rs3093106	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:16008257T>C	ENST00000221700.6	-	2	260	c.165A>G	c.(163-165)ccA>ccG	p.P55P	CYP4F2_ENST00000011989.7_5'UTR	NM_001082.3	NP_001073.3			cytochrome P450, family 4, subfamily F, polypeptide 2											NS(2)|breast(1)|endometrium(6)|kidney(2)|large_intestine(9)|liver(1)|lung(18)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	46						AGTTCCGTCTTGGGGGTTGTG	0.612													.|||	902	0.180112	0.32	0.1427	5008	,	,		17842	0.0585		0.1769	False		,,,				2504	0.1462				p.P55P		Atlas-SNP	.											.	CYP4F2	97	.	0			c.A165G						PASS	.	C		1389,3017	458.0+/-351.8	234,921,1048	105.0	99.0	101.0		165	-4.0	0.0	19	dbSNP_103	101	1484,7116	282.1+/-295.4	124,1236,2940	no	coding-synonymous	CYP4F2	NM_001082.3		358,2157,3988	CC,CT,TT		17.2558,31.5252,22.0898		55/521	16008257	2873,10133	2203	4300	6503	SO:0001819	synonymous_variant	8529	exon2			CCGTCTTGGGGGT	U02388	CCDS12336.1	19p13.12	2013-11-11	2003-01-14		ENSG00000186115	ENSG00000186115		"""Cytochrome P450s"""	2645	protein-coding gene	gene with protein product		604426	"""cytochrome P450, subfamily IVF, polypeptide 2"""			8424651, 8026587	Standard	NM_001082		Approved		uc002nbs.1	P78329	OTTHUMG00000185995	ENST00000221700.6:c.165A>G	19.37:g.16008257T>C		Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	155	78	0.503226	NM_001082		Silent	SNP	ENST00000221700.6	37	CCDS12336.1																																																																																			T|0.799;C|0.201	0.201	strong		0.612	CYP4F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460372.3	NM_001082	
HLA-DOB	3112	hgsc.bcm.edu	37	6	32781554	32781554	+	Missense_Mutation	SNP	G	G	A	rs2070121	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:32781554G>A	ENST00000438763.2	-	4	796	c.700C>T	c.(700-702)Ctt>Ttt	p.L234F	TAP2_ENST00000452392.2_Missense_Mutation_p.L841F	NM_002120.3	NP_002111.1	P13765	DOB_HUMAN	major histocompatibility complex, class II, DO beta	234			L -> F (in allele DOB*01:04; dbSNP:rs2070121).		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|immune response (GO:0006955)|negative regulation of antigen processing and presentation of peptide antigen via MHC class II (GO:0002587)|signal transduction (GO:0007165)	endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|MHC class II protein complex (GO:0042613)	MHC class II protein complex binding (GO:0023026)|MHC class II receptor activity (GO:0032395)			endometrium(2)|large_intestine(1)|lung(2)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	9						ATTAGCCCAAGTAGGAAGGCT	0.468													G|||	472	0.0942492	0.1853	0.0461	5008	,	,		19018	0.0645		0.0845	False		,,,				2504	0.046				p.L234F		Atlas-SNP	.											.	HLA-DOB	17	.	0			c.C700T						PASS	.	G	PHE/LEU	586,3816		40,506,1655	44.0	39.0	41.0		700	-1.4	0.2	6	dbSNP_96	41	644,7946		22,600,3673	yes	missense	HLA-DOB	NM_002120.3	22	62,1106,5328	AA,AG,GG		7.4971,13.3121,9.4674		234/274	32781554	1230,11762	2201	4295	6496	SO:0001583	missense	3112	exon4			GCCCAAGTAGGAA		CCDS4754.1	6p21.3	2013-01-11			ENSG00000241106	ENSG00000241106		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4937	protein-coding gene	gene with protein product		600629					Standard	NM_002120		Approved			P13765	OTTHUMG00000031213	ENST00000438763.2:c.700C>T	6.37:g.32781554G>A	ENSP00000390020:p.Leu234Phe	Somatic	187	0	0		WXS	Illumina HiSeq	Phase_I	101	33	0.326733	NM_002120	B0V0Y0|Q29746|Q29825|Q6FHC2	Missense_Mutation	SNP	ENST00000438763.2	37	CCDS4754.1	185	0.08470695970695971	67	0.13617886178861788	22	0.06077348066298342	33	0.057692307692307696	63	0.08311345646437995	G	10.31	1.314401	0.23908	0.133121	0.074971	ENSG00000241106;ENSG00000250264	ENST00000438763;ENST00000452392	T;T	0.75154	5.74;-0.91	4.06	-1.36	0.09085	Immunoglobulin-like fold (1);	0.409391	0.24836	N	0.035216	T	0.46268	0.1384	L	0.60845	1.875	0.37026	P	0.103572	B;B	0.15141	0.003;0.012	B;B	0.09377	0.003;0.004	T	0.20505	-1.0273	9	0.87932	D	0	.	5.3487	0.16024	0.4433:0.1568:0.3999:0.0	rs2070121;rs7749688;rs17220115;rs17220122;rs17885054;rs45465200;rs59116190;rs2070121	841;234	E7ENX8;P13765	.;DOB_HUMAN	F	234;841	ENSP00000390020:L234F;ENSP00000391806:L841F	ENSP00000390020:L234F	L	-	1	0	XXbac-BPG246D15.9;HLA-DOB	32889532	0.023000	0.18921	0.173000	0.22940	0.062000	0.15995	-0.234000	0.09028	-0.289000	0.09038	-0.149000	0.13747	CTT	G|0.912;A|0.088	0.088	strong		0.468	HLA-DOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076439.1	NM_002120	
SLC30A5	64924	hgsc.bcm.edu	37	5	68419054	68419054	+	Silent	SNP	A	A	T	rs164572	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	73	0	0		WXS	Illumina HiSeq	Phase_I	69	24	0.347826	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		
OVCH1	341350	hgsc.bcm.edu	37	12	29648275	29648275	+	Missense_Mutation	SNP	G	G	A	rs10843438	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:29648275G>A	ENST00000318184.5	-	4	396	c.397C>T	c.(397-399)Cgt>Tgt	p.R133C		NM_183378.2	NP_899234.2	Q7RTY7	OVCH1_HUMAN	ovochymase 1	133	Peptidase S1 1. {ECO:0000255|PROSITE- ProRule:PRU00274}.		R -> C (in dbSNP:rs10843438).			extracellular region (GO:0005576)	metal ion binding (GO:0046872)|serine-type endopeptidase activity (GO:0004252)			NS(2)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(15)|lung(43)|ovary(5)|pancreas(3)|prostate(2)|skin(1)|soft_tissue(1)|stomach(3)	92	Lung NSC(12;1.84e-09)|Acute lymphoblastic leukemia(23;0.00885)|all_hematologic(23;0.0155)					ATATATTCACGGCTGTTGTAT	0.373													g|||	2241	0.447484	0.3185	0.3689	5008	,	,		17661	0.5347		0.5716	False		,,,				2504	0.4601				p.R133C		Atlas-SNP	.											OVCH1,NS,carcinoma,+1,1	OVCH1	195	1	0			c.C397T						PASS	.	A	CYS/ARG	1168,2506		182,804,851	188.0	176.0	180.0		397	0.6	0.0	12	dbSNP_120	180	4371,3797		1163,2045,876	yes	missense	OVCH1	NM_183378.2	180	1345,2849,1727	AA,AG,GG		46.4863,31.791,46.7742	probably-damaging	133/1135	29648275	5539,6303	1837	4084	5921	SO:0001583	missense	341350	exon4			ATTCACGGCTGTT	BN000128		12p11.23	2012-11-08			ENSG00000187950	ENSG00000187950			23080	protein-coding gene	gene with protein product						12838346	Standard	NM_183378		Approved	OVCH	uc001rix.1	Q7RTY7	OTTHUMG00000167741	ENST00000318184.5:c.397C>T	12.37:g.29648275G>A	ENSP00000326708:p.Arg133Cys	Somatic	251	0	0		WXS	Illumina HiSeq	Phase_I	186	86	0.462366	NM_183378		Missense_Mutation	SNP	ENST00000318184.5	37		1022	0.46794871794871795	164	0.3333333333333333	126	0.34806629834254144	304	0.5314685314685315	428	0.5646437994722955	g	1.438	-0.568535	0.03910	0.31791	0.535137	ENSG00000187950	ENST00000318184	D	0.89270	-2.49	2.68	0.63	0.17693	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	.	.	.	.	T	0.00012	0.0000	L	0.42245	1.32	0.80722	P	0.0	P	0.45283	0.855	B	0.38921	0.285	T	0.37126	-0.9719	8	0.38643	T	0.18	.	5.5032	0.16840	0.335:0.0:0.665:0.0	rs10843438;rs17661258;rs52809981;rs56547749;rs60594525;rs10843438	133	Q7RTY7	OVCH1_HUMAN	C	133	ENSP00000326708:R133C	ENSP00000326708:R133C	R	-	1	0	OVCH1	29539542	0.000000	0.05858	0.001000	0.08648	0.159000	0.22180	-0.544000	0.06077	0.151000	0.19162	-0.119000	0.15052	CGT	G|0.534;A|0.466	0.466	strong		0.373	OVCH1-001	KNOWN	non_canonical_TEC|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000395997.2	NM_183378	
MUC4	4585	hgsc.bcm.edu	37	3	195507242	195507242	+	Missense_Mutation	SNP	C	C	A	rs567957149|rs74187968	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195507242C>A	ENST00000463781.3	-	2	11668	c.11209G>T	c.(11209-11211)Gca>Tca	p.A3737S	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.A3737S	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		CCTGTGGATGCTGAGGAAGGG	0.572													.|||	53	0.0105831	0.0136	0.0086	5008	,	,		10241	0.0069		0.0139	False		,,,				2504	0.0082				p.A3737S		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	0			c.G11209T						PASS	.						35.0	34.0	34.0					3																	195507242		619	1580	2199	SO:0001583	missense	4585	exon2			TGGATGCTGAGGA	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.11209G>T	3.37:g.195507242C>A	ENSP00000417498:p.Ala3737Ser	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	83	28	0.337349	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	c	2.940	-0.219185	0.06101	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.32515	1.56;1.45	.	.	.	.	0.435754	0.11199	U	0.589055	T	0.12561	0.0305	N	0.14661	0.345	0.09310	N	1	B	0.11235	0.004	B	0.04013	0.001	T	0.26155	-1.0111	8	.	.	.	.	2.155	0.03810	0.0:0.332:0.3413:0.3266	.	3609	E7ESK3	.	S	3737	ENSP00000417498:A3737S;ENSP00000420243:A3737S	.	A	-	1	0	MUC4	196992021	0.000000	0.05858	0.005000	0.12908	0.022000	0.10575	-0.526000	0.06207	-0.927000	0.03766	0.064000	0.15345	GCA	A|1.000;|0.000	1.000	weak		0.572	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
C8orf74	203076	hgsc.bcm.edu	37	8	10532188	10532188	+	Silent	SNP	T	T	C	rs61729951	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:10532188T>C	ENST00000304519.5	+	2	110	c.81T>C	c.(79-81)ctT>ctC	p.L27L	C8orf74_ENST00000524025.1_3'UTR|RP1L1_ENST00000329335.3_Intron	NM_001040032.1	NP_001035121	Q6P047	CH074_HUMAN	chromosome 8 open reading frame 74	27										central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(5)|urinary_tract(1)	13				COAD - Colon adenocarcinoma(149;0.0811)		TGCGGAGGCTTCTGAACTGGG	0.577													T|||	23	0.00459265	0.0008	0.0072	5008	,	,		16259	0.0		0.0149	False		,,,				2504	0.002				p.L27L		Atlas-SNP	.											.	C8orf74	28	.	0			c.T81C						PASS	.	T		17,3793		0,17,1888	39.0	43.0	42.0		81	-1.6	0.4	8	dbSNP_129	42	163,8101		3,157,3972	no	coding-synonymous	C8orf74	NM_001040032.1		3,174,5860	CC,CT,TT		1.9724,0.4462,1.4908		27/295	10532188	180,11894	1905	4132	6037	SO:0001819	synonymous_variant	203076	exon2			GAGGCTTCTGAAC	BC038534	CCDS47800.1	8p23.1	2012-04-17			ENSG00000171060	ENSG00000171060			32296	protein-coding gene	gene with protein product							Standard	NM_001040032		Approved		uc003wtd.1	Q6P047	OTTHUMG00000163807	ENST00000304519.5:c.81T>C	8.37:g.10532188T>C		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	137	105	0.766423	NM_001040032	A2RUD6	Silent	SNP	ENST00000304519.5	37	CCDS47800.1	11	0.005036630036630037	0	0.0	3	0.008287292817679558	0	0.0	8	0.010554089709762533	T	1.640	-0.516781	0.04200	0.004462	0.019724	ENSG00000171060	ENST00000521818	.	.	.	5.06	-1.65	0.08291	.	.	.	.	.	T	0.16854	0.0405	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.26950	-1.0088	4	.	.	.	.	7.5808	0.27963	0.0:0.3943:0.3278:0.2779	rs61729951	.	.	.	P	26	.	.	S	+	1	0	C8orf74	10569598	0.002000	0.14202	0.397000	0.26308	0.201000	0.24016	-0.558000	0.05978	-0.316000	0.08690	-0.495000	0.04643	TCT	T|0.992;C|0.008	0.008	strong		0.577	C8orf74-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375675.1	NM_001040032	
FAR1	84188	hgsc.bcm.edu	37	11	13743325	13743325	+	Silent	SNP	A	A	G	rs34341612	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:13743325A>G	ENST00000354817.3	+	10	1320	c.1176A>G	c.(1174-1176)gaA>gaG	p.E392E	FAR1_ENST00000532502.1_Silent_p.E16E	NM_032228.5	NP_115604.1	Q8WVX9	FACR1_HUMAN	fatty acyl CoA reductase 1	392					cellular lipid metabolic process (GO:0044255)|ether lipid biosynthetic process (GO:0008611)|glycerophospholipid biosynthetic process (GO:0046474)|long-chain fatty-acyl-CoA metabolic process (GO:0035336)|small molecule metabolic process (GO:0044281)|wax biosynthetic process (GO:0010025)	integral component of membrane (GO:0016021)|peroxisomal matrix (GO:0005782)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	fatty-acyl-CoA reductase (alcohol-forming) activity (GO:0080019)|long-chain-fatty-acyl-CoA reductase activity (GO:0050062)			breast(1)|endometrium(1)|kidney(3)|large_intestine(1)|liver(1)|lung(3)|ovary(1)|prostate(1)|skin(1)	13						TGTTTCTTGAATATTTCACAA	0.303													A|||	31	0.0061901	0.0008	0.0058	5008	,	,		16434	0.0		0.0119	False		,,,				2504	0.0143				p.E392E		Atlas-SNP	.											.	FAR1	40	.	0			c.A1176G						PASS	.	A		9,4387	15.5+/-35.6	0,9,2189	85.0	84.0	84.0		1176	0.2	1.0	11	dbSNP_126	84	123,8459	63.5+/-125.6	0,123,4168	no	coding-synonymous	FAR1	NM_032228.5		0,132,6357	GG,GA,AA		1.4332,0.2047,1.0171		392/516	13743325	132,12846	2198	4291	6489	SO:0001819	synonymous_variant	84188	exon10			TCTTGAATATTTC	AK026381	CCDS7813.1	11p15.2	2011-09-14	2008-06-06	2008-06-06	ENSG00000197601	ENSG00000197601	1.2.1.-	"""Short chain dehydrogenase/reductase superfamily / Atypical members"""	26222	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 10E, member 1"""		"""male sterility domain containing 2"""	MLSTD2		15220348, 15220349, 19027726	Standard	NM_032228		Approved	FLJ22728, SDR10E1	uc001mld.3	Q8WVX9	OTTHUMG00000165743	ENST00000354817.3:c.1176A>G	11.37:g.13743325A>G		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	49	32	0.653061	NM_032228	D3DQW8|Q5CZA3	Silent	SNP	ENST00000354817.3	37	CCDS7813.1																																																																																			A|0.990;G|0.010	0.010	strong		0.303	FAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385990.2	NM_032228	
UGT1A1	54658	hgsc.bcm.edu	37	2	234527118	234527118	+	Silent	SNP	A	A	G	rs1042605	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:234527118A>G	ENST00000373450.4	+	1	828	c.765A>G	c.(763-765)acA>acG	p.T255T		NM_019076.4	NP_061949.3	P22309	UD11_HUMAN	UDP glucuronosyltransferase 1 family, polypeptide A1	258					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)	TGTTGCGAACAGACTTTGTTT	0.428													-|||	655	0.130791	0.2163	0.0692	5008	,	,		19448	0.1081		0.16	False		,,,				2504	0.0521				p.T255T		Atlas-SNP	.											.	UGT1A8	69	.	0			c.A765G						PASS	.	G		910,3496	737.9+/-410.9	108,694,1401	254.0	253.0	254.0		765	-4.2	0.0	2	dbSNP_86	254	1326,7274	756.7+/-407.5	108,1110,3082	no	coding-synonymous	UGT1A8	NM_019076.4		216,1804,4483	GG,GA,AA		15.4186,20.6537,17.1921		255/531	234527118	2236,10770	2203	4300	6503	SO:0001819	synonymous_variant	54576	exon1			GCGAACAGACTTT	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.765A>G	2.37:g.234527118A>G		Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	154	79	0.512987	NM_019076	A6NJC3|B8K286	Silent	SNP	ENST00000373450.4	37	CCDS33402.1																																																																																			A|0.856;G|0.144	0.144	strong		0.428	UGT1A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000130994.1		
ESYT2	57488	hgsc.bcm.edu	37	7	158528254	158528254	+	Silent	SNP	G	G	A	rs34974906	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:158528254G>A	ENST00000251527.5	-	20	2591	c.2526C>T	c.(2524-2526)ctC>ctT	p.L842L	ESYT2_ENST00000435514.2_Silent_p.L277L	NM_020728.2	NP_065779.1	A0FGR8	ESYT2_HUMAN	extended synaptotagmin-like protein 2	870	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)	p.L842L(1)		breast(1)|central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(16)|prostate(2)	32						CGGCAACGTCGAGCGTTCTCC	0.458													G|||	446	0.0890575	0.1233	0.0591	5008	,	,		19168	0.0427		0.1252	False		,,,				2504	0.0746				p.L842L		Atlas-SNP	.											ESYT2,NS,malignant_melanoma,0,3	ESYT2	70	3	1	Substitution - coding silent(1)	central_nervous_system(1)	c.C2526T						PASS	.			514,3892	236.1+/-248.4	24,466,1713	153.0	158.0	156.0		2526	1.8	0.2	7	dbSNP_126	156	1087,7513	226.8+/-262.4	62,963,3275	no	coding-synonymous	ESYT2	NM_020728.2		86,1429,4988	AA,AG,GG		12.6395,11.6659,12.3097		842/894	158528254	1601,11405	2203	4300	6503	SO:0001819	synonymous_variant	57488	exon20			AACGTCGAGCGTT	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.2526C>T	7.37:g.158528254G>A		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	66	25	0.378788	NM_020728	A4D229|Q69YJ2|Q6UKI4|Q6ZTU0|Q6ZVU1|Q9BQS0|Q9NW47|Q9ULJ2	Silent	SNP	ENST00000251527.5	37	CCDS34791.1																																																																																			G|0.884;A|0.116	0.116	strong		0.458	ESYT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322647.1	NM_020728	
STOX1	219736	hgsc.bcm.edu	37	10	70641785	70641785	+	Missense_Mutation	SNP	T	T	C	rs377656965		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:70641785T>C	ENST00000298596.6	+	2	465	c.382T>C	c.(382-384)Tgt>Cgt	p.C128R	STOX1_ENST00000421961.2_Missense_Mutation_p.C18R|STOX1_ENST00000399169.4_Missense_Mutation_p.C128R|STOX1_ENST00000399162.2_Missense_Mutation_p.C128R|STOX1_ENST00000399165.4_Missense_Mutation_p.C128R	NM_152709.4	NP_689922.3	Q6ZVD7	STOX1_HUMAN	storkhead box 1	128						cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(5)|endometrium(2)|kidney(2)|large_intestine(5)|liver(2)|lung(8)|prostate(1)|skin(3)	28						AGTTCTTTGCTGTGCTATATC	0.368																																					p.C128R		Atlas-SNP	.											.	STOX1	75	.	0			c.T382C						PASS	.	T	ARG/CYS,ARG/CYS,ARG/CYS,ARG/CYS,ARG/CYS	0,3730		0,0,1865	166.0	152.0	156.0		382,382,382,52,382	5.6	1.0	10		156	1,8199		0,1,4099	no	missense,missense,missense,missense,missense	STOX1	NM_001130159.2,NM_001130160.2,NM_001130161.2,NM_001130162.2,NM_152709.4	180,180,180,180,180	0,1,5964	CC,CT,TT		0.0122,0.0,0.0084	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	128/228,128/170,128/990,18/880,128/990	70641785	1,11929	1865	4100	5965	SO:0001583	missense	219736	exon2			CTTTGCTGTGCTA	AK057891	CCDS41535.1, CCDS44416.1, CCDS44417.1	10q22.1	2005-11-29	2005-04-04	2005-04-04	ENSG00000165730	ENSG00000165730			23508	protein-coding gene	gene with protein product		609397	"""chromosome 10 open reading frame 24"""	C10orf24			Standard	NM_152709		Approved	FLJ25162	uc001joq.3	Q6ZVD7	OTTHUMG00000018367	ENST00000298596.6:c.382T>C	10.37:g.70641785T>C	ENSP00000298596:p.Cys128Arg	Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	160	73	0.45625	NM_001130160	A2A3Q9|A5D6Y7|B0QZA4|B0QZA5|B0QZA6|Q4F8Q6|Q5I946|Q5I947|Q5I948|Q5VX38|Q5VX39|Q6ZRY3|Q96LR3|Q96LS0	Missense_Mutation	SNP	ENST00000298596.6	37	CCDS41535.1	.	.	.	.	.	.	.	.	.	.	T	13.74	2.328142	0.41197	0.0	1.22E-4	ENSG00000165730	ENST00000399169;ENST00000298596;ENST00000399165;ENST00000399162;ENST00000421961	T;T;T;T;T	0.75938	-0.98;-0.98;-0.98;-0.98;-0.98	5.57	5.57	0.84162	Storkhead-box protein, winged-helix domain (1);	0.149142	0.45867	U	0.000336	T	0.68970	0.3059	L	0.36672	1.1	0.80722	D	1	P;P;P	0.48503	0.627;0.911;0.627	B;P;B	0.45753	0.216;0.492;0.14	T	0.72381	-0.4311	10	0.59425	D	0.04	.	11.934	0.52864	0.0:0.0702:0.0:0.9298	.	128;128;128	Q6ZVD7-3;Q6ZVD7;Q6ZVD7-2	.;STOX1_HUMAN;.	R	128;128;128;128;18	ENSP00000382121:C128R;ENSP00000298596:C128R;ENSP00000382118:C128R;ENSP00000382115:C128R;ENSP00000394509:C18R	ENSP00000298596:C128R	C	+	1	0	STOX1	70311791	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.709000	0.47160	2.242000	0.73789	0.482000	0.46254	TGT	.	.	none		0.368	STOX1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276849.3	NM_152709	
MUC4	4585	hgsc.bcm.edu	37	3	195511668	195511668	+	Silent	SNP	G	G	A	rs71291861|rs3107748	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195511668G>A	ENST00000463781.3	-	2	7242	c.6783C>T	c.(6781-6783)gaC>gaT	p.D2261D	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Silent_p.D2261D	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		CTGAGGAAGCGTCGGTGACAG	0.582													.|||	2203	0.439896	0.236	0.4352	5008	,	,		10401	0.7054		0.4602	False		,,,				2504	0.4243				p.D2261D		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,5	MUC4	1505	5	0			c.C6783T						PASS	.						34.0	33.0	33.0					3																	195511668		679	1584	2263	SO:0001819	synonymous_variant	4585	exon2			GGAAGCGTCGGTG	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.6783C>T	3.37:g.195511668G>A		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	117	29	0.247863	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Silent	SNP	ENST00000463781.3	37	CCDS54700.1																																																																																			G|0.762;A|0.238	0.238	strong		0.582	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
KRT86	3892	hgsc.bcm.edu	37	12	52695787	52695787	+	Silent	SNP	C	C	T	rs112261068	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:52695787C>T	ENST00000423955.2	+	3	265	c.87C>T	c.(85-87)gcC>gcT	p.A29A	KRT86_ENST00000293525.5_Silent_p.A29A|KRT86_ENST00000544024.1_Silent_p.A29A			O43790	KRT86_HUMAN	keratin 86	29	Head.					extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			breast(1)|cervix(1)|large_intestine(1)|lung(5)|ovary(1)|skin(1)	10				BRCA - Breast invasive adenocarcinoma(357;0.189)		GCATCACCGCCGCCCCCTACC	0.701													c|||	778	0.155351	0.1717	0.1354	5008	,	,		12144	0.0903		0.1282	False		,,,				2504	0.2423				p.A29A		Atlas-SNP	.											.	KRT86	33	.	0			c.C87T						PASS	.	C		686,3466		52,582,1442	20.0	25.0	24.0		87	2.0	1.0	12	dbSNP_132	24	1225,7155		102,1021,3067	no	coding-synonymous	KRT86	NM_002284.3		154,1603,4509	TT,TC,CC		14.6181,16.5222,15.249		29/487	52695787	1911,10621	2076	4190	6266	SO:0001819	synonymous_variant	3892	exon1			CACCGCCGCCCCC	X99142	CCDS41785.1	12q13	2013-01-16	2006-07-17	2006-07-17		ENSG00000170442		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6463	protein-coding gene	gene with protein product	"""hard keratin type II 6"""	601928	"""keratin, hair, basic, 6 (monilethrix)"""	KRTHB6		9241275, 16831889	Standard	NM_002284		Approved	MNX, Hb6	uc001sad.3	O43790		ENST00000423955.2:c.87C>T	12.37:g.52695787C>T		Somatic	5	0	0		WXS	Illumina HiSeq	Phase_I	17	15	0.882353	NM_002284	P78387	Silent	SNP	ENST00000423955.2	37	CCDS41785.1																																																																																			C|0.873;T|0.127	0.127	strong		0.701	KRT86-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404911.1	NM_002284	
MSRB2	22921	hgsc.bcm.edu	37	10	23408278	23408278	+	Silent	SNP	C	C	T	rs7427	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	114	0	0		WXS	Illumina HiSeq	Phase_I	132	60	0.454545	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	
COL6A3	1293	hgsc.bcm.edu	37	2	238249630	238249630	+	Silent	SNP	C	C	T	rs4433949	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:238249630C>T	ENST00000295550.4	-	38	8381	c.7929G>A	c.(7927-7929)gcG>gcA	p.A2643A	COL6A3_ENST00000346358.4_Silent_p.A2443A|COL6A3_ENST00000347401.3_Silent_p.A2442A|COL6A3_ENST00000472056.1_Silent_p.A2036A|COL6A3_ENST00000353578.4_Silent_p.A2437A|COL6A3_ENST00000409809.1_Silent_p.A2437A	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	2643	Nonhelical region.|VWFA 12. {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)		TGACCAGGTACGCTATGTACT	0.567													C|||	1715	0.342452	0.2133	0.3329	5008	,	,		21379	0.4802		0.4284	False		,,,				2504	0.2935				p.A2643A		Atlas-SNP	.											.	COL6A3	608	.	0			c.G7929A						PASS	.	C	,,	1138,3268	405.1+/-333.4	155,828,1220	158.0	146.0	150.0		7929,6108,7311	-5.4	0.0	2	dbSNP_111	150	3646,4954	524.7+/-380.6	769,2108,1423	no	coding-synonymous,coding-synonymous,coding-synonymous	COL6A3	NM_004369.3,NM_057166.4,NM_057167.3	,,	924,2936,2643	TT,TC,CC		42.3953,25.8284,36.783	,,	2643/3178,2036/2571,2437/2972	238249630	4784,8222	2203	4300	6503	SO:0001819	synonymous_variant	1293	exon38			CAGGTACGCTATG	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.7929G>A	2.37:g.238249630C>T		Somatic	206	0	0		WXS	Illumina HiSeq	Phase_I	195	93	0.476923	NM_004369	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Silent	SNP	ENST00000295550.4	37	CCDS33412.1																																																																																			C|0.625;T|0.375	0.375	strong		0.567	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369	
DIAPH3	81624	hgsc.bcm.edu	37	13	60413550	60413550	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:60413550G>T	ENST00000400324.4	-	23	2990	c.2770C>A	c.(2770-2772)Cag>Aag	p.Q924K	DIAPH3_ENST00000465066.1_5'UTR|DIAPH3_ENST00000400320.1_Missense_Mutation_p.Q878K|DIAPH3_ENST00000377908.2_Missense_Mutation_p.Q913K|DIAPH3_ENST00000400319.1_Missense_Mutation_p.Q854K|DIAPH3_ENST00000267215.4_Missense_Mutation_p.Q924K|DIAPH3_ENST00000400330.1_Missense_Mutation_p.Q924K	NM_001042517.1|NM_001258366.1	NP_001035982.1|NP_001245295.1	Q9NSV4	DIAP3_HUMAN	diaphanous-related formin 3	924	FH2. {ECO:0000255|PROSITE- ProRule:PRU00774}.				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)		CTTCCCATCTGCCTCAAATTC	0.403																																					p.Q924K		Atlas-SNP	.											.	DIAPH3	139	.	0			c.C2770A						PASS	.						82.0	77.0	79.0					13																	60413550		1842	4094	5936	SO:0001583	missense	81624	exon23			CCATCTGCCTCAA	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.2770C>A	13.37:g.60413550G>T	ENSP00000383178:p.Gln924Lys	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	52	10	0.192308	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	.	.	.	.	.	.	.	.	.	.	G	23.9	4.470488	0.84533	.	.	ENSG00000139734	ENST00000400324;ENST00000400330;ENST00000400327;ENST00000413168;ENST00000400329;ENST00000377908;ENST00000400319;ENST00000400320;ENST00000267215;ENST00000267214;ENST00000453990	T;T;T;T;T;T	0.16073	2.37;2.37;2.37;2.37;2.37;2.37	5.19	5.19	0.71726	Actin-binding FH2/DRF autoregulatory (1);Actin-binding FH2 (3);	0.058535	0.64402	D	0.000001	T	0.29223	0.0727	L	0.58969	1.84	0.51482	D	0.999927	B;D	0.55605	0.014;0.972	B;P	0.49361	0.01;0.608	T	0.01397	-1.1365	10	0.48119	T	0.1	.	19.0719	0.93143	0.0:0.0:1.0:0.0	.	661;924	Q9NSV4-1;Q9NSV4	.;DIAP3_HUMAN	K	924;924;913;878;854;913;854;878;924;661;924	ENSP00000383178:Q924K;ENSP00000383184:Q924K;ENSP00000367141:Q913K;ENSP00000383173:Q854K;ENSP00000383174:Q878K;ENSP00000267215:Q924K	ENSP00000267214:Q661K	Q	-	1	0	DIAPH3	59311551	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	9.414000	0.97362	2.585000	0.87301	0.591000	0.81541	CAG	.	.	none		0.403	DIAPH3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045166.3	NM_001042517	
DENND5B	160518	hgsc.bcm.edu	37	12	31605044	31605044	+	Missense_Mutation	SNP	G	G	T	rs1056320	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:31605044G>T	ENST00000389082.5	-	5	1723	c.1459C>A	c.(1459-1461)Cat>Aat	p.H487N	DENND5B_ENST00000536562.1_Missense_Mutation_p.H522N|DENND5B_ENST00000354285.4_Missense_Mutation_p.H509N|snoU13_ENST00000458765.1_RNA|DENND5B_ENST00000306833.6_Missense_Mutation_p.H522N	NM_144973.3	NP_659410.3	Q6ZUT9	DEN5B_HUMAN	DENN/MADD domain containing 5B	487			H -> N (in dbSNP:rs1056320). {ECO:0000269|PubMed:14702039, ECO:0000269|Ref.5}.		positive regulation of Rab GTPase activity (GO:0032851)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			NS(2)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(8)|lung(17)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	38						TCTTCACAATGCAGTTTTAAA	0.473													G|||	888	0.177316	0.2284	0.1052	5008	,	,		19727	0.247		0.1233	False		,,,				2504	0.1431				p.H487N		Atlas-SNP	.											.	DENND5B	114	.	0			c.C1459A						PASS	.	G	ASN/HIS	770,3092		77,616,1238	167.0	167.0	167.0		1459	4.7	1.0	12	dbSNP_86	167	867,7403		54,759,3322	yes	missense	DENND5B	NM_144973.3	68	131,1375,4560	TT,TG,GG		10.4837,19.9379,13.4932	benign	487/1275	31605044	1637,10495	1931	4135	6066	SO:0001583	missense	160518	exon5			CACAATGCAGTTT	AF086301	CCDS44857.1	12p11.21	2012-10-03			ENSG00000170456	ENSG00000170456		"""DENN/MADD domain containing"""	28338	protein-coding gene	gene with protein product						12477932	Standard	NM_144973		Approved	MGC24039	uc001rki.1	Q6ZUT9	OTTHUMG00000169034	ENST00000389082.5:c.1459C>A	12.37:g.31605044G>T	ENSP00000373734:p.His487Asn	Somatic	236	0	0		WXS	Illumina HiSeq	Phase_I	175	86	0.491429	NM_144973	B5ME75|Q59FW8|Q68CZ7|Q6NUJ0|Q7Z3F9|Q8N973|Q8WUC8	Missense_Mutation	SNP	ENST00000389082.5	37	CCDS44857.1	394	0.1804029304029304	122	0.24796747967479674	42	0.11602209944751381	139	0.243006993006993	91	0.12005277044854881	G	10.69	1.420867	0.25639	0.199379	0.104837	ENSG00000170456	ENST00000389082;ENST00000306833;ENST00000536562;ENST00000354285;ENST00000546299	T;T;T;T;T	0.39997	1.05;1.05;1.05;1.05;1.05	4.67	4.67	0.58626	.	0.346390	0.26804	N	0.022409	T	0.00012	0.0000	N	0.14661	0.345	0.45239	P	0.0017559999999999798	B;B;B;B	0.12630	0.001;0.006;0.0;0.0	B;B;B;B	0.19666	0.001;0.026;0.0;0.001	T	0.19516	-1.0303	9	0.19147	T	0.46	-18.0088	13.191	0.59711	0.0791:0.0:0.9209:0.0	rs1056320;rs3168408;rs16916263;rs52832424;rs58342800;rs1056320	409;509;487;522	Q6ZUT9-3;Q6ZUT9-4;Q6ZUT9;G3V1S3	.;.;DEN5B_HUMAN;.	N	487;522;522;509;439	ENSP00000373734:H487N;ENSP00000306482:H522N;ENSP00000444889:H522N;ENSP00000346238:H509N;ENSP00000442938:H439N	ENSP00000306482:H522N	H	-	1	0	DENND5B	31496311	1.000000	0.71417	1.000000	0.80357	0.818000	0.46254	5.975000	0.70475	2.421000	0.82119	0.563000	0.77884	CAT	G|0.818;T|0.182	0.182	strong		0.473	DENND5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402040.1	NM_144973	
KIF4A	24137	hgsc.bcm.edu	37	X	69573639	69573639	+	Silent	SNP	C	C	T	rs1199429	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:69573639C>T	ENST00000374403.3	+	15	1738	c.1656C>T	c.(1654-1656)ccC>ccT	p.P552P	KIF4A_ENST00000374388.3_Silent_p.P552P	NM_012310.4	NP_036442.3	O95239	KIF4A_HUMAN	kinesin family member 4A	552					anterograde axon cargo transport (GO:0008089)|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)|organelle organization (GO:0006996)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|membrane (GO:0016020)|midbody (GO:0030496)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)			breast(6)|endometrium(9)|kidney(3)|large_intestine(8)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	51						AACTGCAGCCCATTCAGTACC	0.428													C|||	450	0.119205	0.2791	0.0375	3775	,	,		13843	0.0		0.0398	False		,,,				2504	0.0153				p.P552P		Atlas-SNP	.											.	KIF4A	118	.	0			c.C1656T						PASS	.	C		1337,2496		210,717,200,705,369	46.0	39.0	41.0		1656	-0.2	1.0	X	dbSNP_87	41	323,6400		4,225,90,2199,1777	no	coding-synonymous	KIF4A	NM_012310.4		214,942,290,2904,2146	TT,TC,T,CC,C		4.8044,34.8813,15.7257		552/1233	69573639	1660,8896	2201	4295	6496	SO:0001819	synonymous_variant	24137	exon15			GCAGCCCATTCAG	AF179308	CCDS14401.1	Xq13.1	2008-08-11			ENSG00000090889	ENSG00000090889		"""Kinesins"""	13339	protein-coding gene	gene with protein product	"""chromokinesin"""	300521				10773663	Standard	NM_012310		Approved	KIF4-G1, KIF4, HSA271784, FLJ12530, FLJ12655, FLJ14204, FLJ20631	uc004dyg.3	O95239	OTTHUMG00000021775	ENST00000374403.3:c.1656C>T	X.37:g.69573639C>T		Somatic	238	0	0		WXS	Illumina HiSeq	Phase_I	175	175	1	NM_012310	B2R7V5|D3DVU4|Q86TN3|Q86XX7|Q9NNY6|Q9NY24|Q9UMW3	Silent	SNP	ENST00000374403.3	37	CCDS14401.1																																																																																			0|0.003;T|0.145	0.145	strong		0.428	KIF4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057068.1	NM_012310	
MCM3	4172	hgsc.bcm.edu	37	6	52129484	52129484	+	Missense_Mutation	SNP	C	C	T	rs2230240	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:52129484C>T	ENST00000229854.7	-	17	2405	c.2329G>A	c.(2329-2331)Gaa>Aaa	p.E777K	MCM3_ENST00000419835.2_Missense_Mutation_p.E731K|MCM3_ENST00000596288.1_Missense_Mutation_p.E822K			P25205	MCM3_HUMAN	minichromosome maintenance complex component 3	777			E -> K (in dbSNP:rs2230240). {ECO:0000269|Ref.5}.		DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA strand elongation involved in DNA replication (GO:0006271)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)	alpha DNA polymerase:primase complex (GO:0005658)|centrosome (GO:0005813)|intracellular membrane-bounded organelle (GO:0043231)|MCM complex (GO:0042555)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)			endometrium(4)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	20	Lung NSC(77;0.0931)					AAGGGCTCTTCGCTGTCCCGG	0.532													C|||	573	0.114417	0.0151	0.1686	5008	,	,		21520	0.002		0.2883	False		,,,				2504	0.1472				p.E822K		Atlas-SNP	.											.	MCM3	63	.	0			c.G2464A						PASS	.	C	LYS/GLU	205,4201	126.1+/-163.2	5,195,2003	212.0	184.0	193.0		2329	4.5	0.9	6	dbSNP_98	193	2223,6377	376.9+/-338.3	264,1695,2341	yes	missense	MCM3	NM_002388.3	56	269,1890,4344	TT,TC,CC		25.8488,4.6527,18.6683	benign	777/809	52129484	2428,10578	2203	4300	6503	SO:0001583	missense	4172	exon17			GCTCTTCGCTGTC	X62153	CCDS4940.1, CCDS4940.2, CCDS75468.1	6p12	2008-02-05	2007-04-04		ENSG00000112118	ENSG00000112118			6945	protein-coding gene	gene with protein product		602693	"""minichromosome maintenance deficient (S. cerevisiae) 3"", ""MCM3 minichromosome maintenance deficient 3 (S. cerevisiae)"""			1549468	Standard	NM_002388		Approved		uc011dwu.2	P25205	OTTHUMG00000014844	ENST00000229854.7:c.2329G>A	6.37:g.52129484C>T	ENSP00000229854:p.Glu777Lys	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	113	62	0.548673	NM_002388	B4DWW4|Q92660|Q9BTR3|Q9NUE7	Missense_Mutation	SNP	ENST00000229854.7	37		301|301	0.13782051282051283|0.13782051282051283	11|11	0.022357723577235773|0.022357723577235773	68|68	0.1878453038674033|0.1878453038674033	1|1	0.0017482517482517483|0.0017482517482517483	221|221	0.29155672823219|0.29155672823219	C|C	9.414|9.414	1.081380|1.081380	0.20309|0.20309	0.046527|0.046527	0.258488|0.258488	ENSG00000112118|ENSG00000112118	ENST00000229854;ENST00000419835|ENST00000340349;ENST00000421471	T;T|T	0.60040|0.34667	0.22;0.22|1.35	5.39|5.39	4.53|4.53	0.55603|0.55603	.|.	0.546643|.	0.21374|.	N|.	0.075591|.	T|T	0.28366|0.28366	0.0701|0.0701	L|L	0.46157|0.46157	1.445|1.445	0.51767|0.51767	P|P	6.300000000003525E-5|6.300000000003525E-5	B;B|.	0.23591|.	0.082;0.088|.	B;B|.	0.18871|.	0.005;0.023|.	T|T	0.22417|0.22417	-1.0217|-1.0217	9|6	0.08837|0.87932	T|D	0.75|0	-14.6083|-14.6083	10.3857|10.3857	0.44138|0.44138	0.0:0.7525:0.1704:0.0771|0.0:0.7525:0.1704:0.0771	rs2230240;rs3208353;rs17240266;rs17581678;rs52808543;rs61476086;rs2230240|rs2230240;rs3208353;rs17240266;rs17581678;rs52808543;rs61476086;rs2230240	731;777|.	B4DUQ9;P25205|.	.;MCM3_HUMAN|.	K|Q	777;731|324;322	ENSP00000229854:E777K;ENSP00000388647:E731K|ENSP00000407651:R322Q	ENSP00000229854:E777K|ENSP00000340566:R324Q	E|R	-|-	1|2	0|0	MCM3|MCM3	52237443|52237443	0.894000|0.894000	0.30519|0.30519	0.895000|0.895000	0.35142|0.35142	0.239000|0.239000	0.25481|0.25481	1.996000|1.996000	0.40776|0.40776	1.515000|1.515000	0.48885|0.48885	-0.137000|-0.137000	0.14449|0.14449	GAA|CGA	C|0.841;T|0.159	0.159	strong		0.532	MCM3-006	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000470784.1		
UGT1A7	54577	hgsc.bcm.edu	37	2	234590970	234590970	+	Missense_Mutation	SNP	T	T	G	rs71405712|rs17868323	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:234590970T>G	ENST00000373426.3	+	1	387	c.387T>G	c.(385-387)aaT>aaG	p.N129K	UGT1A1_ENST00000373450.4_Intron|UGT1A10_ENST00000373445.1_Intron|UGT1A9_ENST00000354728.4_Intron|UGT1A10_ENST00000344644.5_Intron|UGT1A1_ENST00000609637.1_Intron	NM_019077.2	NP_061950.2	Q9HAW7	UD17_HUMAN	UDP glucuronosyltransferase 1 family, polypeptide A7	129			N -> K (in allele UGT1A7*2 and allele UGT1A7*3; dbSNP:rs17868323). {ECO:0000269|PubMed:11037804, ECO:0000269|PubMed:11434514, ECO:0000269|PubMed:19204906, ECO:0000269|Ref.3}.		cellular glucuronidation (GO:0052695)|coumarin metabolic process (GO:0009804)|drug metabolic process (GO:0017144)|excretion (GO:0007588)|flavone metabolic process (GO:0051552)|flavonoid glucuronidation (GO:0052696)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cellular glucuronidation (GO:2001030)|negative regulation of fatty acid metabolic process (GO:0045922)|retinoic acid metabolic process (GO:0042573)|xenobiotic glucuronidation (GO:0052697)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	drug binding (GO:0008144)|enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)|glucuronosyltransferase activity (GO:0015020)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase C binding (GO:0005080)|retinoic acid binding (GO:0001972)			NS(1)|endometrium(6)|kidney(5)|large_intestine(5)|liver(1)|lung(12)|ovary(1)|prostate(1)|skin(1)	33		Breast(86;0.000765)|all_lung(227;0.00267)|Renal(207;0.00339)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0328)|Lung NSC(271;0.0457)|Lung SC(224;0.128)		Epithelial(121;8.93e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000412)|Lung(119;0.00333)|LUSC - Lung squamous cell carcinoma(224;0.00746)	Mycophenolate mofetil(DB00688)|Mycophenolic acid(DB01024)	GTTTGTTTAATGACCGAAAAT	0.368													G|||	2886	0.576278	0.6097	0.5072	5008	,	,		19279	0.4385		0.6034	False		,,,				2504	0.6943				p.N129K		Atlas-SNP	.											.	UGT1A7	74	.	0			c.T387G	GRCh37	CM024576	UGT1A7	M	rs17868323	PASS	.						70.0	76.0	74.0					2																	234590970		2201	4300	6501	SO:0001583	missense	54577	exon1			GTTTAATGACCGA	U39570	CCDS2506.1	2q37	2010-03-05	2005-07-20		ENSG00000244122	ENSG00000244122		"""UDP glucuronosyltransferases"""	12539	other	complex locus constituent		606432	"""UDP glycosyltransferase 1 family, polypeptide A6"""			9295054, 11434514	Standard	NM_019077		Approved	UGT1G		Q9HAW7	OTTHUMG00000059004	ENST00000373426.3:c.387T>G	2.37:g.234590970T>G	ENSP00000362525:p.Asn129Lys	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	72	23	0.319444	NM_019077	B8K293|O00473	Missense_Mutation	SNP	ENST00000373426.3	37	CCDS2506.1	1095	0.5013736263736264	265	0.5386178861788617	185	0.511049723756906	220	0.38461538461538464	425	0.5606860158311345	G	0.103	-1.149935	0.01714	.	.	ENSG00000244122	ENST00000373426	T	0.05855	3.38	4.51	-9.01	0.00744	.	.	.	.	.	T	0.00012	0.0000	N	0.04994	-0.135	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.42582	-0.9443	8	0.27785	T	0.31	.	8.2035	0.31438	0.0617:0.3453:0.391:0.202	rs17868323	129;129	Q5DSZ7;Q9HAW7	.;UD17_HUMAN	K	129	ENSP00000362525:N129K	ENSP00000362525:N129K	N	+	3	2	UGT1A7	234255709	0.000000	0.05858	0.001000	0.08648	0.037000	0.13140	-13.134000	0.00001	-3.135000	0.00235	-1.473000	0.01005	AAT	.	.	weak		0.368	UGT1A7-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000130614.1	NM_019077	
OR4X1	390113	hgsc.bcm.edu	37	11	48286234	48286234	+	Silent	SNP	A	A	G	rs61732322	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:48286234A>G	ENST00000320048.1	+	1	822	c.822A>G	c.(820-822)acA>acG	p.T274T		NM_001004726.1	NP_001004726.1	Q8NH49	OR4X1_HUMAN	olfactory receptor, family 4, subfamily X, member 1 (gene/pseudogene)	274						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)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(11)|ovary(1)|pancreas(1)|prostate(1)|skin(5)|stomach(1)	28						TATTTTATACAGTGGTCACAC	0.428													A|||	122	0.024361	0.0023	0.0504	5008	,	,		22286	0.003		0.0586	False		,,,				2504	0.0225				p.T274T		Atlas-SNP	.											.	OR4X1	75	.	0			c.A822G						PASS	.	A		47,4355	51.6+/-87.1	1,45,2155	115.0	106.0	109.0		822	-5.8	0.2	11	dbSNP_129	109	515,8081	145.7+/-201.4	12,491,3795	no	coding-synonymous	OR4X1	NM_001004726.1		13,536,5950	GG,GA,AA		5.9912,1.0677,4.3237		274/306	48286234	562,12436	2201	4298	6499	SO:0001819	synonymous_variant	390113	exon1			TTATACAGTGGTC	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.822A>G	11.37:g.48286234A>G		Somatic	199	0	0		WXS	Illumina HiSeq	Phase_I	224	49	0.21875	NM_001004726	Q6IF74	Silent	SNP	ENST00000320048.1	37	CCDS31487.1																																																																																			A|0.962;G|0.038	0.038	strong		0.428	OR4X1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383373.1	NM_001004726	
C17orf74	201243	hgsc.bcm.edu	37	17	7330290	7330290	+	Missense_Mutation	SNP	C	C	T	rs78371599	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:7330290C>T	ENST00000333870.3	+	3	1054	c.980C>T	c.(979-981)tCg>tTg	p.S327L	RP11-104H15.7_ENST00000575310.1_RNA|C17orf74_ENST00000574034.1_3'UTR	NM_175734.4	NP_783861.3	Q0P670	CQ074_HUMAN	chromosome 17 open reading frame 74	327						integral component of membrane (GO:0016021)				cervix(1)|endometrium(5)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|skin(3)	22		Prostate(122;0.157)				CCCCCTGCCTCGGTGTCCCGG	0.697													T|||	115	0.0229633	0.0068	0.0519	5008	,	,		14412	0.0		0.0417	False		,,,				2504	0.0286				p.S327L		Atlas-SNP	.											.	C17orf74	56	.	0			c.C980T						PASS	.	T	LEU/SER	35,3873		0,35,1919	18.0	21.0	20.0		980	1.0	0.0	17	dbSNP_131	20	283,7975		5,273,3851	no	missense	C17orf74	NM_175734.4	145	5,308,5770	TT,TC,CC		3.427,0.8956,2.6138	benign	327/502	7330290	318,11848	1954	4129	6083	SO:0001583	missense	201243	exon3			CTGCCTCGGTGTC	BC044816	CCDS42255.1	17p13.1	2012-05-30			ENSG00000184560	ENSG00000184560			27315	protein-coding gene	gene with protein product						12477932	Standard	NM_175734		Approved		uc002ggw.3	Q0P670	OTTHUMG00000178190	ENST00000333870.3:c.980C>T	17.37:g.7330290C>T	ENSP00000328061:p.Ser327Leu	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	128	75	0.585938	NM_175734		Missense_Mutation	SNP	ENST00000333870.3	37	CCDS42255.1	57	0.0260989010989011	8	0.016260162601626018	20	0.055248618784530384	0	0.0	29	0.03825857519788918	T	0.004	-2.257882	0.00265	0.008956	0.03427	ENSG00000184560	ENST00000333870	T	0.30182	1.54	4.59	0.992	0.19819	.	0.885507	0.09178	N	0.837814	T	0.00784	0.0026	N	0.01352	-0.895	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.30851	-0.9964	10	0.02654	T	1	-11.5194	3.8518	0.08959	0.0:0.3191:0.1941:0.4868	.	327	Q0P670	CQ074_HUMAN	L	327	ENSP00000328061:S327L	ENSP00000328061:S327L	S	+	2	0	C17orf74	7271014	0.000000	0.05858	0.002000	0.10522	0.007000	0.05969	-0.504000	0.06375	0.246000	0.21394	-1.305000	0.01319	TCG	C|0.968;T|0.032	0.032	strong		0.697	C17orf74-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440933.2	NM_175734	
IL17REL	400935	hgsc.bcm.edu	37	22	50439194	50439194	+	Missense_Mutation	SNP	C	C	T	rs9617090	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:50439194C>T	ENST00000389983.2	-	5	472	c.208G>A	c.(208-210)Ggg>Agg	p.G70R	IL17REL_ENST00000341280.5_Missense_Mutation_p.G70R	NM_001001694.2	NP_001001694.2	Q6ZVW7	I17EL_HUMAN	interleukin 17 receptor E-like	70			G -> R (in dbSNP:rs9617090).	GGQ -> RGR (in Ref. 1; BAC85743). {ECO:0000305}.						endometrium(1)|large_intestine(1)|lung(3)|pancreas(1)	6		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;0.2)|LUAD - Lung adenocarcinoma(64;0.247)		TGCTGCCCCCCCTGCTGCCGG	0.701													C|||	1328	0.265176	0.1384	0.2968	5008	,	,		17292	0.3343		0.4115	False		,,,				2504	0.1922				p.G70R		Atlas-SNP	.											.	IL17REL	21	.	0			c.G208A						PASS	.		ARG/GLY	810,3588		87,636,1476	15.0	18.0	17.0		208	-0.7	0.0	22	dbSNP_119	17	3580,5004		761,2058,1473	yes	missense	IL17REL	NM_001001694.2	125	848,2694,2949	TT,TC,CC		41.7055,18.4175,33.8161	benign	70/337	50439194	4390,8592	2199	4292	6491	SO:0001583	missense	400935	exon5			GCCCCCCCTGCTG	AK123987	CCDS33679.1	22q13.33	2009-01-13			ENSG00000188263	ENSG00000188263			33808	protein-coding gene	gene with protein product		613414					Standard	NM_001001694		Approved	FLJ41993	uc003bje.1	Q6ZVW7	OTTHUMG00000150242	ENST00000389983.2:c.208G>A	22.37:g.50439194C>T	ENSP00000374633:p.Gly70Arg	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	94	50	0.531915	NM_001001694	A6NCN4|A6PVC1	Missense_Mutation	SNP	ENST00000389983.2	37	CCDS33679.1	672	0.3076923076923077	66	0.13414634146341464	106	0.292817679558011	198	0.34615384615384615	302	0.39841688654353563	c	4.275	0.050173	0.08243	0.184175	0.417055	ENSG00000188263	ENST00000389983;ENST00000341280	T;T	0.13420	2.59;2.59	3.36	-0.699	0.11277	.	1.046010	0.07618	U	0.926515	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	0.48258	-0.9051	9	0.15952	T	0.53	.	3.7209	0.08456	0.4232:0.4475:0.0:0.1293	rs9617090	70	Q6ZVW7	I17EL_HUMAN	R	70	ENSP00000374633:G70R;ENSP00000342520:G70R	ENSP00000342520:G70R	G	-	1	0	IL17REL	48781321	0.000000	0.05858	0.000000	0.03702	0.028000	0.11728	-0.148000	0.10219	0.068000	0.16574	-0.127000	0.14921	GGG	C|0.696;T|0.304	0.304	strong		0.701	IL17REL-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317011.1	NM_001001694	
TRIAP1	51499	hgsc.bcm.edu	37	12	120884291	120884291	+	5'Flank	SNP	C	C	T	rs17431446	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:120884291C>T	ENST00000546954.1	-	0	0				TRIAP1_ENST00000302432.3_5'Flank|GATC_ENST00000551765.1_Missense_Mutation_p.S3L|AL021546.6_ENST00000551806.1_Intron	NM_016399.2	NP_057483.1	O43715	TRIA1_HUMAN	TP53 regulated inhibitor of apoptosis 1						cellular response to UV (GO:0034644)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:1902166)|negative regulation of release of cytochrome c from mitochondria (GO:0090201)|phospholipid transport (GO:0015914)|positive regulation of phospholipid transport (GO:2001140)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of membrane lipid distribution (GO:0097035)	mitochondrial intermembrane space (GO:0005758)|mitochondrion (GO:0005739)|protein complex (GO:0043234)	p53 binding (GO:0002039)					all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					GAAATGTGGTCGCGGTTGGTG	0.687													C|||	203	0.0405351	0.0008	0.0447	5008	,	,		16318	0.0089		0.0606	False		,,,				2504	0.1033				p.S3L		Atlas-SNP	.											.	GATC	12	.	0			c.C8T						PASS	.	C	LEU/SER	42,4364	46.7+/-81.2	1,40,2162	71.0	74.0	73.0		8	2.2	1.0	12	dbSNP_123	73	491,8105	140.0+/-196.6	15,461,3822	yes	missense	GATC	NM_176818.2	145	16,501,5984	TT,TC,CC		5.712,0.9532,4.0994	benign	3/137	120884291	533,12469	2203	4298	6501	SO:0001631	upstream_gene_variant	283459	exon1			TGTGGTCGCGGTT		CCDS9198.1	12q24.31	2012-10-15			ENSG00000170855	ENSG00000170855			26937	protein-coding gene	gene with protein product	"""p53-inducible cell-survival factor"", ""mitochondrial distribution and morphology 35 homolog (S. cerevisiae)"""	614943				11042152, 15735003	Standard	NM_016399		Approved	P53CSV, WF-1, HSPC132, p53CSV, MDM35	uc001tyg.3	O43715	OTTHUMG00000047787		12.37:g.120884291C>T	Exception_encountered	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	82	31	0.378049	NM_176818	B2R4Z7|Q5RKS5|Q6LCA7	Missense_Mutation	SNP	ENST00000546954.1	37	CCDS9198.1	65	0.02976190476190476	1	0.0020325203252032522	21	0.058011049723756904	1	0.0017482517482517483	42	0.055408970976253295	C	12.49	1.953388	0.34471	0.009532	0.05712	ENSG00000257218	ENST00000551765	T	0.52295	0.67	5.16	2.23	0.28157	.	0.429262	0.25529	N	0.030049	T	0.02571	0.0078	N	0.08118	0	0.18873	N	0.999986	B	0.02656	0.0	B	0.01281	0.0	T	0.08371	-1.0725	10	0.72032	D	0.01	-8.8394	6.0097	0.19569	0.0:0.6282:0.1383:0.2336	rs17431446;rs52822087;rs17431446	3	O43716	GATC_HUMAN	L	3	ENSP00000446872:S3L	ENSP00000448397:S3L	S	+	2	0	AL021546.1	119368674	0.960000	0.32886	0.954000	0.39281	0.048000	0.14542	0.573000	0.23699	0.767000	0.33267	0.644000	0.83932	TCG	C|0.963;T|0.037	0.037	strong		0.687	TRIAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000108980.3	NM_016399	
GCAT	23464	hgsc.bcm.edu	37	22	38204089	38204089	+	Missense_Mutation	SNP	C	C	T	rs397839522|rs710187	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	74	0	0		WXS	Illumina HiSeq	Phase_I	88	52	0.590909	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	
SLC12A7	10723	hgsc.bcm.edu	37	5	1073802	1073802	+	Silent	SNP	C	C	T	rs547552720		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:1073802C>T	ENST00000264930.5	-	17	2230	c.2187G>A	c.(2185-2187)tcG>tcA	p.S729S		NM_006598.2	NP_006589.2	Q9Y666	S12A7_HUMAN	solute carrier family 12 (potassium/chloride transporter), member 7	729					cell volume homeostasis (GO:0006884)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transport (GO:0006811)|potassium ion transport (GO:0006813)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	potassium:chloride symporter activity (GO:0015379)|protein kinase binding (GO:0019901)			breast(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(14)|ovary(2)|prostate(1)|skin(4)|urinary_tract(2)	32	Lung NSC(6;2.47e-13)|all_lung(6;1.67e-12)|all_epithelial(6;5.44e-09)		Epithelial(17;0.000497)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|all cancers(22;0.00241)|Lung(60;0.165)		Potassium Chloride(DB00761)	CCTCCAGCACCGAGCCCACGA	0.697																																					p.S729S		Atlas-SNP	.											SLC12A7,caecum,carcinoma,-1,1	SLC12A7	97	1	0			c.G2187A						scavenged	.						58.0	61.0	60.0					5																	1073802		2202	4295	6497	SO:0001819	synonymous_variant	10723	exon17			CAGCACCGAGCCC	AF105365	CCDS34129.1	5p15	2013-07-18	2013-07-18		ENSG00000113504	ENSG00000113504		"""Solute carriers"""	10915	protein-coding gene	gene with protein product		604879				10347194	Standard	NM_006598		Approved	KCC4, DKFZP434F076	uc003jbu.3	Q9Y666	OTTHUMG00000161931	ENST00000264930.5:c.2187G>A	5.37:g.1073802C>T		Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	131	3	0.0229008	NM_006598	A6NDS8|Q4G0F3|Q96I81|Q9H7I3|Q9H7I7|Q9UFW2	Silent	SNP	ENST00000264930.5	37	CCDS34129.1	.	.	.	.	.	.	.	.	.	.	c	8.351	0.830918	0.16820	.	.	ENSG00000113504	ENST00000513223	.	.	.	4.04	-4.84	0.03151	.	.	.	.	.	T	0.35941	0.0949	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.35001	-0.9806	4	.	.	.	.	1.3088	0.02094	0.5059:0.1284:0.1428:0.2228	.	.	.	.	S	87	.	.	G	-	1	0	SLC12A7	1126802	0.000000	0.05858	0.960000	0.40013	0.627000	0.37826	-3.130000	0.00591	-0.983000	0.03511	-0.350000	0.07774	GGT	.	.	none		0.697	SLC12A7-001	KNOWN	non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366446.2	NM_006598	
HS3ST3A1	9955	hgsc.bcm.edu	37	17	13399616	13399616	+	Silent	SNP	A	A	T	rs62057033	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:13399616A>T	ENST00000284110.1	-	2	1916	c.1119T>A	c.(1117-1119)ccT>ccA	p.P373P	HS3ST3A1_ENST00000578576.1_Silent_p.P171P	NM_006042.1	NP_006033.1	Q9Y663	HS3SA_HUMAN	heparan sulfate (glucosamine) 3-O-sulfotransferase 3A1	373					carbohydrate metabolic process (GO:0005975)|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 3 activity (GO:0033872)|sulfotransferase activity (GO:0008146)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	16		all_lung(20;0.114)		UCEC - Uterine corpus endometrioid carcinoma (92;0.101)		GGTCGATCTCAGGATGGGTCC	0.607													A|||	2091	0.417532	0.1823	0.5144	5008	,	,		13730	0.5585		0.3459	False		,,,				2504	0.5951				p.P373P		Atlas-SNP	.											.	HS3ST3A1	39	.	0			c.T1119A						PASS	.						20.0	21.0	20.0					17																	13399616		2194	4261	6455	SO:0001819	synonymous_variant	9955	exon2			GATCTCAGGATGG	AF105376	CCDS11165.1	17p12	2007-04-02			ENSG00000153976	ENSG00000153976	2.8.2.23	"""Sulfotransferases, membrane-bound"""	5196	protein-coding gene	gene with protein product		604057				9988767	Standard	NM_006042		Approved	3OST3A1, 30ST3A1	uc002gob.1	Q9Y663	OTTHUMG00000058768	ENST00000284110.1:c.1119T>A	17.37:g.13399616A>T		Somatic	381	1	0.00262467		WXS	Illumina HiSeq	Phase_I	287	95	0.33101	NM_006042	A8K7N2	Silent	SNP	ENST00000284110.1	37	CCDS11165.1																																																																																			A|0.615;T|0.385	0.385	strong		0.607	HS3ST3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129952.1	NM_006042	
ZBTB3	79842	hgsc.bcm.edu	37	11	62521475	62521475	+	Silent	SNP	T	T	C	rs201229122|rs72929471	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:62521475T>C	ENST00000394807.3	-	1	185	c.60A>G	c.(58-60)cgA>cgG	p.R20R		NM_024784.3	NP_079060.1	Q9H5J0	ZBTB3_HUMAN	zinc finger and BTB domain containing 3	20					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(4)|endometrium(3)|kidney(1)|large_intestine(2)|liver(1)|lung(9)|ovary(2)|prostate(2)	24						GAGATCTTTTTCGCTCCCAGG	0.622													T|||	690	0.13778	0.0968	0.1556	5008	,	,		14457	0.0853		0.1938	False		,,,				2504	0.1769				p.R20R		Atlas-SNP	.											.	ZBTB3	47	.	0			c.A60G						PASS	.	T		534,3870	244.7+/-253.9	33,468,1701	99.0	88.0	92.0		60	1.4	0.1	11	dbSNP_130	92	1901,6697	336.2+/-321.7	221,1459,2619	no	coding-synonymous	ZBTB3	NM_024784.3		254,1927,4320	CC,CT,TT		22.1098,12.1253,18.7279		20/575	62521475	2435,10567	2202	4299	6501	SO:0001819	synonymous_variant	79842	exon1			TCTTTTTCGCTCC	AK027045	CCDS8034.1	11q12.3	2013-01-09				ENSG00000185670		"""-"", ""BTB/POZ domain containing"", ""Zinc fingers, C2H2-type"""	22918	protein-coding gene	gene with protein product							Standard	NM_024784		Approved	FLJ23392	uc001nuz.3	Q9H5J0		ENST00000394807.3:c.60A>G	11.37:g.62521475T>C		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	93	14	0.150538	NM_024784		Silent	SNP	ENST00000394807.3	37	CCDS8034.1																																																																																			T|0.821;C|0.179	0.179	strong		0.622	ZBTB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395342.1	NM_024784	
TTLL4	9654	hgsc.bcm.edu	37	2	219602819	219602819	+	Silent	SNP	G	G	A	rs3731876	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:219602819G>A	ENST00000392102.1	+	3	760	c.420G>A	c.(418-420)ccG>ccA	p.P140P	TTLL4_ENST00000258398.4_Silent_p.P140P|TTLL4_ENST00000442769.1_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	64	0	0		WXS	Illumina HiSeq	Phase_I	36	36	1	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	
PCDHB8	56128	hgsc.bcm.edu	37	5	140559058	140559058	+	Silent	SNP	G	G	A	rs17844495		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:140559058G>A	ENST00000239444.2	+	1	1688	c.1443G>A	c.(1441-1443)tcG>tcA	p.S481S	PCDHB16_ENST00000361016.2_5'Flank	NM_019120.3	NP_061993.2	Q9UN66	PCDB8_HUMAN	protocadherin beta 8	481	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)			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)			ACAGAGACTCGGGCACCAACG	0.662																																					p.S481S		Atlas-SNP	.											.	PCDHB8	199	.	0			c.G1443A						PASS	.						85.0	131.0	115.0					5																	140559058		2203	4296	6499	SO:0001819	synonymous_variant	56128	exon1			AGACTCGGGCACC	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.1443G>A	5.37:g.140559058G>A		Somatic	228	0	0		WXS	Illumina HiSeq	Phase_I	261	41	0.157088	NM_019120	B9EGV1	Silent	SNP	ENST00000239444.2	37	CCDS4250.1																																																																																			G|0.680;A|0.320	0.320	strong		0.662	PCDHB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251816.2	NM_019120	
TGM7	116179	hgsc.bcm.edu	37	15	43569097	43569097	+	Missense_Mutation	SNP	C	C	T	rs146833656	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:43569097C>T	ENST00000452443.2	-	12	1940	c.1936G>A	c.(1936-1938)Gaa>Aaa	p.E646K		NM_052955.2	NP_443187.1	Q96PF1	TGM7_HUMAN	transglutaminase 7	646					peptide cross-linking (GO:0018149)		metal ion binding (GO:0046872)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(8)|lung(16)|ovary(2)|prostate(4)|skin(1)	39		all_cancers(109;2.12e-14)|all_epithelial(112;1.99e-12)|Lung NSC(122;2.46e-08)|all_lung(180;2.75e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;9.14e-07)	L-Glutamine(DB00130)	CCGCTTCCTTCCAGCACCATC	0.592													C|||	12	0.00239617	0.0008	0.0086	5008	,	,		21418	0.0		0.004	False		,,,				2504	0.001				p.E646K		Atlas-SNP	.											.	TGM7	86	.	0			c.G1936A						PASS	.	C	LYS/GLU	15,4389	22.3+/-47.3	0,15,2187	111.0	90.0	97.0		1936	5.1	1.0	15	dbSNP_134	97	104,8494	56.8+/-118.0	0,104,4195	yes	missense	TGM7	NM_052955.2	56	0,119,6382	TT,TC,CC		1.2096,0.3406,0.9152	probably-damaging	646/711	43569097	119,12883	2202	4299	6501	SO:0001583	missense	116179	exon12			TTCCTTCCAGCAC	AF363393	CCDS32213.1	15q15.2	2004-07-01				ENSG00000159495		"""Transglutaminases"""	30790	protein-coding gene	gene with protein product	"""transglutaminase Z"""	606776				11390390	Standard	NM_052955		Approved	TGMZ	uc001zrf.1	Q96PF1		ENST00000452443.2:c.1936G>A	15.37:g.43569097C>T	ENSP00000389466:p.Glu646Lys	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	84	63	0.75	NM_052955		Missense_Mutation	SNP	ENST00000452443.2	37	CCDS32213.1	7	0.003205128205128205	1	0.0020325203252032522	3	0.008287292817679558	0	0.0	3	0.00395778364116095	C	23.4	4.409135	0.83340	0.003406	0.012096	ENSG00000159495	ENST00000452443	T	0.37584	1.19	5.13	5.13	0.70059	Transglutaminase, C-terminal (2);Immunoglobulin-like fold (1);	0.233909	0.35378	N	0.003260	T	0.55273	0.1910	M	0.86864	2.845	0.44668	D	0.997653	D	0.67145	0.996	D	0.63192	0.912	T	0.68443	-0.5407	10	0.72032	D	0.01	-23.3696	16.0633	0.80853	0.0:1.0:0.0:0.0	.	646	Q96PF1	TGM7_HUMAN	K	646	ENSP00000389466:E646K	ENSP00000389466:E646K	E	-	1	0	TGM7	41356389	1.000000	0.71417	1.000000	0.80357	0.573000	0.36030	5.641000	0.67881	2.375000	0.81037	0.585000	0.79938	GAA	C|0.992;T|0.008	0.008	strong		0.592	TGM7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432489.1	NM_052955	
SLC9C1	285335	hgsc.bcm.edu	37	3	111918215	111918215	+	Missense_Mutation	SNP	C	C	T	rs386664658|rs28516377	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:111918215C>T	ENST00000305815.5	-	20	2728	c.2476G>A	c.(2476-2478)Ggc>Agc	p.G826S	SLC9C1_ENST00000487372.1_Missense_Mutation_p.G778S	NM_183061.1	NP_898884.1	Q4G0N8	SL9C1_HUMAN	solute carrier family 9, subfamily C (Na+-transporting carboxylic acid decarboxylase), member 1	826			G -> S (in dbSNP:rs28516377). {ECO:0000269|PubMed:14702039}.		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)										CCTTTTAAGCCAAAAGCCTTA	0.308													T|||	1682	0.335863	0.3699	0.4049	5008	,	,		17248	0.3393		0.2376	False		,,,				2504	0.3384				p.G826S		Atlas-SNP	.											SLC9A10,NS,carcinoma,0,1	.	.	1	0			c.G2476A						PASS	.	T	SER/GLY	1595,2807	650.4+/-399.0	307,981,913	75.0	82.0	80.0		2476	-3.0	0.0	3	dbSNP_125	80	2317,6279	697.4+/-404.9	321,1675,2302	yes	missense	SLC9A10	NM_183061.1	56	628,2656,3215	TT,TC,CC		26.9544,36.2335,30.0969	benign	826/1178	111918215	3912,9086	2201	4298	6499	SO:0001583	missense	285335	exon20			TTAAGCCAAAAGC	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.2476G>A	3.37:g.111918215C>T	ENSP00000306627:p.Gly826Ser	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	66	66	1	NM_183061	Q6ZRP4|Q7RTP2	Missense_Mutation	SNP	ENST00000305815.5	37	CCDS33817.1	540	0.24725274725274726	114	0.23170731707317074	121	0.3342541436464088	160	0.27972027972027974	145	0.19129287598944592	T	0.024	-1.394455	0.01175	0.362335	0.269544	ENSG00000172139	ENST00000305815;ENST00000487372	T;T	0.76060	-0.98;-0.99	5.55	-3.0	0.05480	.	1.049680	0.07428	N	0.895123	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B;B	0.29716	0.004;0.255	B;B	0.24394	0.006;0.053	T	0.05683	-1.0870	9	0.15952	T	0.53	.	8.7266	0.34474	0.0:0.4304:0.1116:0.458	rs28516377	778;826	Q4G0N8-2;Q4G0N8	.;S9A10_HUMAN	S	826;778	ENSP00000306627:G826S;ENSP00000420688:G778S	ENSP00000306627:G826S	G	-	1	0	SLC9A10	113400905	0.006000	0.16342	0.000000	0.03702	0.000000	0.00434	0.009000	0.13219	-0.760000	0.04677	-3.067000	0.00067	GGC	C|0.725;T|0.275	0.275	strong		0.308	SLC9C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354066.1	NM_183061	
PAK2	5062	hgsc.bcm.edu	37	3	196530022	196530022	+	Silent	SNP	C	C	T	rs115224945	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:196530022C>T	ENST00000327134.3	+	4	745	c.423C>T	c.(421-423)agC>agT	p.S141S		NM_002577.4	NP_002568.2	Q13177	PAK2_HUMAN	p21 protein (Cdc42/Rac)-activated kinase 2	141					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)		AATATCTGAGCTTTACTCCTC	0.418																																					p.S141S		Atlas-SNP	.											PAK2_ENST00000327134,rectum,carcinoma,0,2	PAK2	113	2	0			c.C423T						scavenged	.						85.0	79.0	81.0					3																	196530022		2203	4300	6503	SO:0001819	synonymous_variant	5062	exon4			TCTGAGCTTTACT	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.423C>T	3.37:g.196530022C>T		Somatic	75	3	0.04		WXS	Illumina HiSeq	Phase_I	66	4	0.0606061	NM_002577	Q13154|Q6ISC3	Silent	SNP	ENST00000327134.3	37	CCDS3321.1																																																																																			C|0.986;T|0.015	0.015	strong		0.418	PAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340548.1	NM_002577	
ZCCHC3	85364	hgsc.bcm.edu	37	20	278806	278806	+	Silent	SNP	C	C	T	rs1057189	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	37	0	0		WXS	Illumina HiSeq	Phase_I	38	18	0.473684	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		
OR11H4	390442	hgsc.bcm.edu	37	14	20711852	20711852	+	Missense_Mutation	SNP	C	C	G	rs17277270	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:20711852C>G	ENST00000315409.2	+	1	955	c.902C>G	c.(901-903)aCt>aGt	p.T301S		NM_001004479.1	NP_001004479.1	Q8NGC9	O11H4_HUMAN	olfactory receptor, family 11, subfamily H, member 4	301			T -> S (in dbSNP:rs17277270).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(3)|lung(11)|ovary(1)|upper_aerodigestive_tract(1)	29	all_cancers(95;0.000888)		Epithelial(56;1.75e-06)|all cancers(55;1.22e-05)	GBM - Glioblastoma multiforme(265;0.0146)		CTGATCTATACTCTTCGTAAT	0.383													c|||	346	0.0690895	0.0234	0.0922	5008	,	,		21401	0.0208		0.166	False		,,,				2504	0.0644				p.T301S		Atlas-SNP	.											.	OR11H4	63	.	0			c.C902G						PASS	.	C	SER/THR	190,4216	120.0+/-157.7	3,184,2016	105.0	105.0	105.0		902	3.8	1.0	14	dbSNP_123	105	1350,7250	263.9+/-285.3	108,1134,3058	yes	missense	OR11H4	NM_001004479.1	58	111,1318,5074	GG,GC,CC		15.6977,4.3123,11.8407	benign	301/325	20711852	1540,11466	2203	4300	6503	SO:0001583	missense	390442	exon1			TCTATACTCTTCG		CCDS32034.1	14q11.2	2013-09-24			ENSG00000176198	ENSG00000176198		"""GPCR / Class A : Olfactory receptors"""	15347	protein-coding gene	gene with protein product							Standard	NM_001004479		Approved		uc010tld.2	Q8NGC9	OTTHUMG00000170852	ENST00000315409.2:c.902C>G	14.37:g.20711852C>G	ENSP00000318997:p.Thr301Ser	Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	88	47	0.534091	NM_001004479	B2RNQ4|Q6IF07	Missense_Mutation	SNP	ENST00000315409.2	37	CCDS32034.1	189	0.08653846153846154	17	0.034552845528455285	36	0.09944751381215469	8	0.013986013986013986	128	0.16886543535620052	c	2.561	-0.301898	0.05495	0.043123	0.156977	ENSG00000176198	ENST00000315409	T	0.36157	1.27	4.7	3.81	0.43845	.	0.093112	0.46758	N	0.000270	T	0.00039	0.0001	N	0.03253	-0.375	0.41546	P	0.011454999999999993	B	0.02656	0.0	B	0.04013	0.001	T	0.14980	-1.0453	9	0.02654	T	1	-9.5805	12.8336	0.57761	0.0:0.1661:0.8338:0.0	rs17277270;rs17277270	301	Q8NGC9	O11H4_HUMAN	S	301	ENSP00000318997:T301S	ENSP00000318997:T301S	T	+	2	0	OR11H4	19781692	0.981000	0.34729	1.000000	0.80357	0.970000	0.65996	2.055000	0.41345	1.207000	0.43291	-0.128000	0.14901	ACT	C|0.896;G|0.104	0.104	strong		0.383	OR11H4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410678.1		
SNAPC4	6621	hgsc.bcm.edu	37	9	139276407	139276407	+	Missense_Mutation	SNP	C	C	T	rs34569521	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:139276407C>T	ENST00000298532.2	-	17	2554	c.2186G>A	c.(2185-2187)cGg>cAg	p.R729Q		NM_003086.2	NP_003077.2			small nuclear RNA activating complex, polypeptide 4, 190kDa											biliary_tract(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(13)|ovary(1)|prostate(3)|skin(2)|urinary_tract(1)	33		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;5.31e-06)|Epithelial(140;7.13e-06)		TCTCCAGCGCCGCTGCCCACT	0.677													C|||	199	0.0397364	0.0023	0.0504	5008	,	,		16704	0.001		0.0785	False		,,,				2504	0.0828				p.R729Q		Atlas-SNP	.											.	SNAPC4	82	.	0			c.G2186A						PASS	.	C	GLN/ARG	75,4323		3,69,2127	23.0	23.0	23.0		2186	-0.4	0.0	9	dbSNP_126	23	745,7839		35,675,3582	no	missense	SNAPC4	NM_003086.2	43	38,744,5709	TT,TC,CC		8.6789,1.7053,6.3164	probably-damaging	729/1470	139276407	820,12162	2199	4292	6491	SO:0001583	missense	6621	exon17			CAGCGCCGCTGCC	AF032387	CCDS6998.1	9q34.3	2008-07-21	2002-08-29		ENSG00000165684	ENSG00000165684			11137	protein-coding gene	gene with protein product		602777	"""small nuclear RNA activating complex, polypeptide 4, 190kD"""			9418884	Standard	XM_005266096		Approved	SNAP190, PTFalpha, FLJ13451	uc004chh.3	Q5SXM2	OTTHUMG00000020929	ENST00000298532.2:c.2186G>A	9.37:g.139276407C>T	ENSP00000298532:p.Arg729Gln	Somatic	187	0	0		WXS	Illumina HiSeq	Phase_I	136	57	0.419118	NM_003086		Missense_Mutation	SNP	ENST00000298532.2	37	CCDS6998.1	92	0.04212454212454213	0	0.0	26	0.0718232044198895	1	0.0017482517482517483	65	0.08575197889182058	C	17.20	3.329431	0.60743	0.017053	0.086789	ENSG00000165684	ENST00000298532	T	0.29397	1.57	4.72	-0.4	0.12411	.	0.481200	0.18390	N	0.142684	T	0.00580	0.0019	L	0.43152	1.355	0.80722	P	0.0	P	0.40360	0.714	B	0.22753	0.041	T	0.08046	-1.0741	9	0.49607	T	0.09	-18.275	7.1507	0.25608	0.0:0.4766:0.0:0.5234	rs34569521	729	Q5SXM2	SNPC4_HUMAN	Q	729	ENSP00000298532:R729Q	ENSP00000298532:R729Q	R	-	2	0	SNAPC4	138396228	0.000000	0.05858	0.000000	0.03702	0.674000	0.39518	-0.812000	0.04496	-0.143000	0.11334	0.462000	0.41574	CGG	C|0.942;T|0.058	0.058	strong		0.677	SNAPC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055071.1	NM_003086	
SLC30A5	64924	hgsc.bcm.edu	37	5	68417643	68417643	+	Silent	SNP	C	C	T	rs164578	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:68417643C>T	ENST00000396591.3	+	13	2302	c.1692C>T	c.(1690-1692)caC>caT	p.H564H	CTC-498J12.3_ENST00000504129.1_RNA	NM_022902.4	NP_075053.2	Q8TAD4	ZNT5_HUMAN	solute carrier family 30 (zinc transporter), member 5	564	His-rich loop.				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)		GCCATTCACACCATATGCATG	0.493													T|||	2122	0.423722	0.326	0.4207	5008	,	,		15173	0.5397		0.4245	False		,,,				2504	0.4376				p.H564H		Atlas-SNP	.											.	SLC30A5	54	.	0			c.C1692T						PASS	.	T		1472,2934	677.5+/-403.4	239,994,970	94.0	79.0	84.0		1692	2.1	1.0	5	dbSNP_79	84	3722,4878	614.5+/-396.2	830,2062,1408	no	coding-synonymous	SLC30A5	NM_022902.3		1069,3056,2378	TT,TC,CC		43.2791,33.409,39.9354		564/766	68417643	5194,7812	2203	4300	6503	SO:0001819	synonymous_variant	64924	exon13			TTCACACCATATG	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.1692C>T	5.37:g.68417643C>T		Somatic	271	0	0		WXS	Illumina HiSeq	Phase_I	249	92	0.369478	NM_022902	B7ZM89|Q6UX54|Q7L4M4|Q8TDG3|Q9BVY8|Q9H9H1	Silent	SNP	ENST00000396591.3	37	CCDS3996.1																																																																																			C|0.589;T|0.411	0.411	strong		0.493	SLC30A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254017.2		
FAM135A	57579	hgsc.bcm.edu	37	6	71238105	71238105	+	Missense_Mutation	SNP	A	A	G	rs2747701	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:71238105A>G	ENST00000418814.2	+	16	4339	c.3725A>G	c.(3724-3726)gAt>gGt	p.D1242G	FAM135A_ENST00000505868.1_Missense_Mutation_p.D1242G|FAM135A_ENST00000370479.3_Missense_Mutation_p.D1029G|FAM135A_ENST00000505769.1_Missense_Mutation_p.D822G|FAM135A_ENST00000457062.2_Missense_Mutation_p.D1029G|FAM135A_ENST00000361499.3_Missense_Mutation_p.D1046G	NM_001105531.2|NM_001162529.1	NP_001099001.1|NP_001156001.1	Q9P2D6	F135A_HUMAN	family with sequence similarity 135, member A	1242			D -> G (in dbSNP:rs2747701). {ECO:0000269|PubMed:11230166, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:16192744}.							breast(2)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(12)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	38						GAAGAAGAGGATGGTTCTGAA	0.403													A|||	1699	0.339257	0.0189	0.2507	5008	,	,		16392	0.5427		0.4761	False		,,,				2504	0.4847				p.D1242G		Atlas-SNP	.											.	FAM135A	181	.	0			c.A3725G						PASS	.	A	GLY/ASP,GLY/ASP,GLY/ASP	381,4025	192.3+/-217.7	13,355,1835	215.0	183.0	194.0		3137,3725,3086	3.8	0.7	6	dbSNP_100	194	4138,4462	564.9+/-388.4	1003,2132,1165	yes	missense,missense,missense	FAM135A	NM_001105531.2,NM_001162529.1,NM_020819.4	94,94,94	1016,2487,3000	GG,GA,AA		48.1163,8.6473,34.7455	benign,benign,benign	1046/1320,1242/1516,1029/1303	71238105	4519,8487	2203	4300	6503	SO:0001583	missense	57579	exon14			AAGAGGATGGTTC	AK000183	CCDS34481.1, CCDS47448.1, CCDS55028.1	6q13	2008-10-30	2007-05-11	2007-05-11	ENSG00000082269	ENSG00000082269			21084	protein-coding gene	gene with protein product			"""KIAA1411"""	KIAA1411		10718198	Standard	NM_001105531		Approved	FLJ20176	uc003pfj.3	Q9P2D6	OTTHUMG00000014991	ENST00000418814.2:c.3725A>G	6.37:g.71238105A>G	ENSP00000410768:p.Asp1242Gly	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	149	83	0.557047	NM_001162529	A2RRQ5|Q3C0H3|Q5JXK0|Q5JXK1|Q68DW0|Q6P081|Q9H0F2|Q9NU48|Q9NUQ5|Q9NXL5	Missense_Mutation	SNP	ENST00000418814.2	37	CCDS55028.1	779	0.3566849816849817	12	0.024390243902439025	98	0.27071823204419887	305	0.5332167832167832	364	0.48021108179419525	A	12.22	1.872457	0.33069	0.086473	0.481163	ENSG00000082269	ENST00000418814;ENST00000370479;ENST00000505769;ENST00000457062;ENST00000361499;ENST00000505868	T;T;T;T;T;T	0.24538	2.16;2.16;1.85;2.16;2.16;2.15	4.92	3.77	0.43336	.	0.230845	0.51477	N	0.000093	T	0.14874	0.0359	M	0.67953	2.075	0.09310	P	0.99999351703	B;B;B;B;B	0.31040	0.305;0.11;0.067;0.076;0.11	B;B;B;B;B	0.33042	0.109;0.157;0.075;0.047;0.157	T	0.04053	-1.0981	9	0.59425	D	0.04	.	10.304	0.43670	0.9221:0.0:0.0779:0.0	rs2747701;rs3736753;rs60825985;rs2747701	822;1242;1242;1046;1029	D6RCC7;Q9P2D6-4;Q9P2D6;Q9P2D6-2;Q9P2D6-3	.;.;F135A_HUMAN;.;.	G	1242;1029;822;1029;1046;1242	ENSP00000410768:D1242G;ENSP00000359510:D1029G;ENSP00000423785:D822G;ENSP00000409201:D1029G;ENSP00000354913:D1046G;ENSP00000423307:D1242G	ENSP00000354913:D1046G	D	+	2	0	FAM135A	71294826	1.000000	0.71417	0.723000	0.30687	0.305000	0.27757	6.153000	0.71819	0.843000	0.35070	0.482000	0.46254	GAT	A|0.647;G|0.353	0.353	strong		0.403	FAM135A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000041137.2	NM_020819	
ZNF714	148206	hgsc.bcm.edu	37	19	21300964	21300964	+	Silent	SNP	T	T	C	rs111456417	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:21300964T>C	ENST00000596143.1	+	5	1819	c.1494T>C	c.(1492-1494)caT>caC	p.H498H	ZNF714_ENST00000601416.1_3'UTR|ZNF714_ENST00000596053.1_Intron|ZNF714_ENST00000291770.7_3'UTR	NM_182515.3	NP_872321	Q96N38	ZN714_HUMAN	zinc finger protein 714	498					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)|urinary_tract(2)	18						TTACTAAACATAGGAAAATTC	0.423													.|||	232	0.0463259	0.0348	0.0389	5008	,	,		19554	0.001		0.1133	False		,,,				2504	0.045				p.H498H		Atlas-SNP	.											.	ZNF714	121	.	0			c.T1494C						PASS	.	T		156,4250		5,146,2052	74.0	82.0	80.0		1494	-0.3	0.0	19	dbSNP_132	80	703,7897		26,651,3623	no	coding-synonymous	ZNF714	NM_182515.3		31,797,5675	CC,CT,TT		8.1744,3.5406,6.6046		498/555	21300964	859,12147	2203	4300	6503	SO:0001819	synonymous_variant	148206	exon5			TAAACATAGGAAA	AK056006	CCDS54239.1	19p12	2013-01-08				ENSG00000160352		"""Zinc fingers, C2H2-type"""	27124	protein-coding gene	gene with protein product						12477932	Standard	NM_182515		Approved		uc002npo.4	Q96N38		ENST00000596143.1:c.1494T>C	19.37:g.21300964T>C		Somatic	23	0	0		WXS	Illumina HiSeq	Phase_I	13	13	1	NM_182515	Q49AI1|Q86W65|Q8ND40	Silent	SNP	ENST00000596143.1	37	CCDS54239.1																																																																																			T|0.935;C|0.065	0.065	strong		0.423	ZNF714-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463930.1	NM_182515	
TMEM44	93109	hgsc.bcm.edu	37	3	194353875	194353875	+	Missense_Mutation	SNP	G	G	T	rs1675955	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:194353875G>T	ENST00000392432.2	-	1	275	c.70C>A	c.(70-72)Cac>Aac	p.H24N	TMEM44_ENST00000473092.1_Missense_Mutation_p.H24N|TMEM44_ENST00000381975.3_Missense_Mutation_p.H24N|TMEM44_ENST00000273580.7_Missense_Mutation_p.H24N|TMEM44_ENST00000347147.4_Missense_Mutation_p.H24N|TMEM44_ENST00000330115.3_Intron|AC046143.3_ENST00000447139.1_RNA	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	74	0	0		WXS	Illumina HiSeq	Phase_I	165	70	0.424242	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	
TDG	6996	hgsc.bcm.edu	37	12	104380734	104380734	+	Missense_Mutation	SNP	G	G	A	rs2888805	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:104380734G>A	ENST00000392872.3	+	10	1333	c.1099G>A	c.(1099-1101)Gtg>Atg	p.V367M	TDG_ENST00000536395.1_3'UTR|TDG_ENST00000544861.1_Missense_Mutation_p.V224M|AC078819.1_ENST00000401157.1_RNA|TDG_ENST00000542036.1_Missense_Mutation_p.V163M|TDG_ENST00000266775.9_Missense_Mutation_p.V363M	NM_003211.4	NP_003202.3	Q13569	TDG_HUMAN	thymine-DNA glycosylase	367			V -> L (in dbSNP:rs2888805).|V -> M (in dbSNP:rs2888805). {ECO:0000269|Ref.2}.		base-excision repair (GO:0006284)|base-excision repair, AP site formation (GO:0006285)|chromatin modification (GO:0016568)|depyrimidination (GO:0045008)|DNA demethylation (GO:0080111)|DNA repair (GO:0006281)|embryo development (GO:0009790)|mismatch repair (GO:0006298)|negative regulation of chromatin binding (GO:0035562)|negative regulation of protein binding (GO:0032091)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of gene expression, epigenetic (GO:0040029)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|PML body (GO:0016605)	damaged DNA binding (GO:0003684)|DNA N-glycosylase activity (GO:0019104)|double-stranded DNA binding (GO:0003690)|mismatched DNA binding (GO:0030983)|protein homodimerization activity (GO:0042803)|pyrimidine-specific mismatch base pair DNA N-glycosylase activity (GO:0008263)|RNA polymerase II transcription cofactor activity (GO:0001104)|structure-specific DNA binding (GO:0043566)			large_intestine(2)|lung(14)|ovary(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	24				BRCA - Breast invasive adenocarcinoma(302;0.00114)		AGTTGAGAGCGTGGAGTTAAG	0.408								Base excision repair (BER), DNA glycosylases					G|||	563	0.11242	0.0053	0.111	5008	,	,		26412	0.2927		0.0944	False		,,,				2504	0.091				p.V367M		Atlas-SNP	.											.	TDG	43	.	0			c.G1099A						PASS	.	G	MET/VAL	97,4309	78.3+/-116.7	0,97,2106	151.0	129.0	136.0		1099	0.2	0.0	12	dbSNP_101	136	836,7764	191.8+/-238.0	26,784,3490	yes	missense	TDG	NM_003211.4	21	26,881,5596	AA,AG,GG		9.7209,2.2015,7.1736	benign	367/411	104380734	933,12073	2203	4300	6503	SO:0001583	missense	6996	exon10			GAGAGCGTGGAGT	U51166	CCDS9095.1	12q24.1	2014-05-14			ENSG00000139372	ENSG00000139372	3.2.2.29		11700	protein-coding gene	gene with protein product	"""G/T mismatch-specific thymine DNA glycosylase"""	601423				8662714, 9299239	Standard	NM_003211		Approved		uc001tkg.3	Q13569	OTTHUMG00000168418	ENST00000392872.3:c.1099G>A	12.37:g.104380734G>A	ENSP00000376611:p.Val367Met	Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	55	10	0.181818	NM_003211	Q8IUZ6|Q8IZM3	Missense_Mutation	SNP	ENST00000392872.3	37	CCDS9095.1	290	0.13278388278388278	4	0.008130081300813009	40	0.11049723756906077	174	0.3041958041958042	72	0.09498680738786279	G	8.454	0.853700	0.17106	0.022015	0.097209	ENSG00000139372	ENST00000392872;ENST00000266775;ENST00000544861;ENST00000542036	T;T;T;T	0.22945	2.27;2.27;2.27;1.93	4.59	0.23	0.15372	.	2.260350	0.01803	N	0.033010	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	P;B;B	0.44344	0.833;0.074;0.074	B;B;B	0.31191	0.125;0.003;0.004	T	0.27806	-1.0063	9	0.46703	T	0.11	-1.0119	1.0514	0.01581	0.177:0.308:0.2758:0.2392	rs2888805;rs4135140;rs52799886;rs59502858	163;367;367	B4DI29;B2R848;Q13569	.;.;TDG_HUMAN	M	367;363;224;163	ENSP00000376611:V367M;ENSP00000266775:V363M;ENSP00000445899:V224M;ENSP00000439054:V163M	ENSP00000266775:V363M	V	+	1	0	TDG	102904864	0.026000	0.19158	0.001000	0.08648	0.002000	0.02628	0.257000	0.18369	0.022000	0.15160	-0.152000	0.13540	GTG	G|0.908;A|0.092	0.092	strong		0.408	TDG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399673.2		
SSC5D	284297	hgsc.bcm.edu	37	19	56002329	56002329	+	Silent	SNP	C	C	T	rs4801305	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:56002329C>T	ENST00000389623.6	+	6	800	c.777C>T	c.(775-777)ccC>ccT	p.P259P	SSC5D_ENST00000587166.1_Silent_p.P259P	NM_001144950.1	NP_001138422.1	A1L4H1	SRCRL_HUMAN	scavenger receptor cysteine rich family, 5 domains	259	SRCR 2. {ECO:0000255|PROSITE- ProRule:PRU00196}.				defense response to Gram-negative bacterium (GO:0050829)|defense response to Gram-positive bacterium (GO:0050830)|detection of bacterial lipoprotein (GO:0042494)|innate immune response (GO:0045087)|multicellular organismal development (GO:0007275)|negative regulation of interleukin-8 secretion (GO:2000483)|receptor-mediated endocytosis (GO:0006898)	cytoplasm (GO:0005737)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|intracellular (GO:0005622)|membrane (GO:0016020)	extracellular matrix binding (GO:0050840)|fibronectin binding (GO:0001968)|laminin binding (GO:0043236)|scavenger receptor activity (GO:0005044)			NS(1)|breast(1)|skin(2)	4						GTGCAGGGCCCGTGTGGATGG	0.711													c|||	322	0.0642971	0.056	0.1326	5008	,	,		14067	0.0556		0.0497	False		,,,				2504	0.0511				p.P259P		Atlas-SNP	.											.	SSC5D	65	.	0			c.C777T						PASS	.	C	,	52,1332		1,50,641	40.0	54.0	50.0		777,777	-8.4	0.3	19	dbSNP_111	50	163,3017		6,151,1433	no	coding-synonymous,coding-synonymous	SSC5D	NM_001144950.1,NM_001195267.1	,	7,201,2074	TT,TC,CC		5.1258,3.7572,4.7108	,	259/1574,259/952	56002329	215,4349	692	1590	2282	SO:0001819	synonymous_variant	284297	exon6			AGGGCCCGTGTGG		CCDS46196.1, CCDS59424.1	19q13.42	2014-07-09	2014-07-09		ENSG00000179954	ENSG00000179954			26641	protein-coding gene	gene with protein product	"""soluble scavenger with 5 domains"""		"""scavenger receptor cysteine rich domain containing (5 domains)"""			19535143	Standard	NM_001144950		Approved	FLJ35258	uc002qlg.4	A1L4H1		ENST00000389623.6:c.777C>T	19.37:g.56002329C>T		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	164	72	0.439024	NM_001195267	B5MDQ5|C7S7T9|C7S7U0|K7EP70	Silent	SNP	ENST00000389623.6	37	CCDS46196.1																																																																																			C|0.947;T|0.053	0.053	strong		0.711	SSC5D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000453345.2	XM_001718392	
TPST2	8459	hgsc.bcm.edu	37	22	26936897	26936897	+	Silent	SNP	G	G	A	rs12169509	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:26936897G>A	ENST00000338754.4	-	3	970	c.700C>T	c.(700-702)Ctg>Ttg	p.L234L	TPST2_ENST00000398110.2_Silent_p.L234L|TPST2_ENST00000403880.1_Silent_p.L234L	NM_003595.3	NP_003586.3	O60704	TPST2_HUMAN	tyrosylprotein sulfotransferase 2	234					fusion of sperm to egg plasma membrane (GO:0007342)|peptidyl-tyrosine sulfation (GO:0006478)|prevention of polyspermy (GO:0060468)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	protein-tyrosine sulfotransferase activity (GO:0008476)			central_nervous_system(1)|large_intestine(1)|lung(5)	7						TACACAGGCAGGCACTTCTCC	0.607													G|||	515	0.102835	0.1059	0.1081	5008	,	,		20781	0.003		0.2386	False		,,,				2504	0.0583				p.L234L		Atlas-SNP	.											.	TPST2	23	.	0			c.C700T						PASS	.	G	,	477,3929	226.2+/-241.8	22,433,1748	92.0	76.0	81.0		700,700	2.5	1.0	22	dbSNP_120	81	1951,6649	344.1+/-325.2	213,1525,2562	no	coding-synonymous,coding-synonymous	TPST2	NM_001008566.1,NM_003595.3	,	235,1958,4310	AA,AG,GG		22.686,10.8261,18.6683	,	234/378,234/378	26936897	2428,10578	2203	4300	6503	SO:0001819	synonymous_variant	8459	exon3			CAGGCAGGCACTT	AF049891	CCDS13839.1	22q12.1	2012-12-13			ENSG00000128294	ENSG00000128294	2.8.2.20	"""Sulfotransferases, membrane-bound"""	12021	protein-coding gene	gene with protein product	"""transport and golgi organization 13 homolog B (Drosophila)"""	603126				9736702, 9733778	Standard	NM_003595		Approved	TANGO13B	uc003acx.3	O60704	OTTHUMG00000150987	ENST00000338754.4:c.700C>T	22.37:g.26936897G>A		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	85	37	0.435294	NM_001008566	B3KQA7|Q6FI98|Q9H0V4	Silent	SNP	ENST00000338754.4	37	CCDS13839.1																																																																																			G|0.823;A|0.177	0.177	strong		0.607	TPST2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320820.3	NM_003595	
MORC1	27136	hgsc.bcm.edu	37	3	108719470	108719470	+	Silent	SNP	C	C	G	rs3762698	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:108719470C>G	ENST00000483760.1	-	20	2101	c.2058G>C	c.(2056-2058)ctG>ctC	p.L686L	MORC1_ENST00000232603.5_Silent_p.L707L					MORC family CW-type zinc finger 1											breast(7)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(14)|lung(47)|ovary(3)|prostate(6)|skin(12)|upper_aerodigestive_tract(3)	105						CTACAAAGTTCAGACTCTGCT	0.358													C|||	1038	0.207268	0.2693	0.2003	5008	,	,		18160	0.0278		0.2694	False		,,,				2504	0.2495				p.L707L		Atlas-SNP	.											.	MORC1	211	.	0			c.G2121C						PASS	.	C		1265,3141	432.0+/-343.1	188,889,1126	177.0	173.0	174.0		2121	-2.0	0.0	3	dbSNP_107	174	2422,6176	400.8+/-346.9	354,1714,2231	no	coding-synonymous	MORC1	NM_014429.3		542,2603,3357	GG,GC,CC		28.1693,28.7108,28.3528		707/985	108719470	3687,9317	2203	4299	6502	SO:0001819	synonymous_variant	27136	exon21			AAAGTTCAGACTC	AF084946	CCDS2955.1	3q13	2011-10-26	2005-06-15	2005-06-15	ENSG00000114487	ENSG00000114487			7198	protein-coding gene	gene with protein product	"""cancer/testis antigen 33"""	603205	"""microrchidia (mouse) homolog"", ""microrchidia homolog (mouse)"""	MORC		10369865	Standard	NM_014429		Approved	ZCW6, CT33	uc003dxl.3	Q86VD1	OTTHUMG00000159209	ENST00000483760.1:c.2058G>C	3.37:g.108719470C>G		Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	118	58	0.491525	NM_014429		Silent	SNP	ENST00000483760.1	37																																																																																				C|0.734;G|0.266	0.266	strong		0.358	MORC1-002	NOVEL	basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000353844.1		
XDH	7498	hgsc.bcm.edu	37	2	31589847	31589847	+	Silent	SNP	G	G	A	rs2295475	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:31589847G>A	ENST00000379416.3	-	21	2259	c.2211C>T	c.(2209-2211)atC>atT	p.I737I		NM_000379.3	NP_000370.2	P47989	XDH_HUMAN	xanthine dehydrogenase	737					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)	CTTGGCCACCGATGTATATCT	0.542													G|||	1353	0.270168	0.0703	0.366	5008	,	,		19611	0.3343		0.3032	False		,,,				2504	0.3722				p.I737I	Colon(66;682 1445 30109 40147)	Atlas-SNP	.											.	XDH	191	.	0			c.C2211T						PASS	.	G		409,3997	200.8+/-224.0	28,353,1822	126.0	101.0	110.0		2211	-11.6	0.2	2	dbSNP_100	110	2628,5972	425.1+/-354.9	397,1834,2069	no	coding-synonymous	XDH	NM_000379.3		425,2187,3891	AA,AG,GG		30.5581,9.2828,23.3508		737/1334	31589847	3037,9969	2203	4300	6503	SO:0001819	synonymous_variant	7498	exon21			GCCACCGATGTAT	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.2211C>T	2.37:g.31589847G>A		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	104	52	0.5	NM_000379	Q16681|Q16712|Q4PJ16	Silent	SNP	ENST00000379416.3	37	CCDS1775.1																																																																																			G|0.765;A|0.235	0.235	strong		0.542	XDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216840.1	NM_000379	
CPA1	1357	hgsc.bcm.edu	37	7	130023561	130023561	+	Missense_Mutation	SNP	G	G	A	rs34474469	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:130023561G>A	ENST00000011292.3	+	6	772	c.622G>A	c.(622-624)Gcc>Acc	p.A208T	CPA1_ENST00000484324.1_Missense_Mutation_p.A120T	NM_001868.2	NP_001859.1	P15085	CBPA1_HUMAN	carboxypeptidase A1 (pancreatic)	208			A -> T (in dbSNP:rs34474469).		proteolysis (GO:0006508)	extracellular space (GO:0005615)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			endometrium(3)|kidney(1)|large_intestine(5)|lung(11)|ovary(1)	21	Melanoma(18;0.0435)					AGCTTTCACCGCCATTCTCGA	0.602													G|||	77	0.0153754	0.0008	0.0187	5008	,	,		20659	0.0		0.0298	False		,,,				2504	0.0337				p.A208T		Atlas-SNP	.											.	CPA1	73	.	0			c.G622A						PASS	.	G	THR/ALA	23,4383	31.7+/-61.6	0,23,2180	181.0	153.0	163.0		622	-2.1	0.0	7	dbSNP_126	163	292,8308	108.2+/-168.9	5,282,4013	yes	missense	CPA1	NM_001868.2	58	5,305,6193	AA,AG,GG		3.3953,0.522,2.422	benign	208/420	130023561	315,12691	2203	4300	6503	SO:0001583	missense	1357	exon6			TTCACCGCCATTC		CCDS5820.1	7q32	2012-02-10			ENSG00000091704	ENSG00000091704	3.4.17.1		2296	protein-coding gene	gene with protein product	"""pancreatic carboxypeptidase A"""	114850		CPA			Standard	NM_001868		Approved		uc003vpx.3	P15085	OTTHUMG00000157826	ENST00000011292.3:c.622G>A	7.37:g.130023561G>A	ENSP00000011292:p.Ala208Thr	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	119	59	0.495798	NM_001868	A4D1M1|Q53XU0|Q9BS67|Q9UCF2	Missense_Mutation	SNP	ENST00000011292.3	37	CCDS5820.1	30	0.013736263736263736	0	0.0	8	0.022099447513812154	0	0.0	22	0.029023746701846966	G	13.32	2.201184	0.38905	0.00522	0.033953	ENSG00000091704	ENST00000011292;ENST00000476062;ENST00000484324	T;T;T	0.10860	2.83;2.83;2.83	5.27	-2.08	0.07254	Peptidase M14, carboxypeptidase A (2);	1.042680	0.07449	N	0.898735	T	0.02571	0.0078	L	0.46819	1.47	0.09310	N	1	P;P	0.42941	0.731;0.794	B;B	0.36464	0.157;0.225	T	0.25641	-1.0126	10	0.41790	T	0.15	.	6.0182	0.19615	0.2234:0.0:0.201:0.5756	rs34474469	120;208	B4DDW9;P15085	.;CBPA1_HUMAN	T	208;120;120	ENSP00000011292:A208T;ENSP00000419408:A120T;ENSP00000419497:A120T	ENSP00000011292:A208T	A	+	1	0	CPA1	129810797	0.000000	0.05858	0.000000	0.03702	0.100000	0.18952	0.104000	0.15313	-0.660000	0.05352	-0.367000	0.07326	GCC	G|0.979;A|0.021	0.021	strong		0.602	CPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349736.2	NM_001868	
DZIP1	22873	hgsc.bcm.edu	37	13	96293759	96293759	+	Silent	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:96293759C>T	ENST00000376829.2	-	5	1238	c.387G>A	c.(385-387)gaG>gaA	p.E129E	DZIP1_ENST00000361156.3_Silent_p.E129E|DZIP1_ENST00000361396.2_Silent_p.E129E|DZIP1_ENST00000466027.1_5'UTR|DZIP1_ENST00000347108.3_Silent_p.E129E	NM_198968.3	NP_945319.1	Q86YF9	DZIP1_HUMAN	DAZ interacting zinc finger protein 1	129					cilium assembly (GO:0042384)|germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)			endometrium(1)|kidney(1)|large_intestine(20)|lung(11)|ovary(2)|pancreas(1)|skin(1)|stomach(1)	38	all_neural(89;0.0878)|Breast(111;0.148)|Medulloblastoma(90;0.163)		BRCA - Breast invasive adenocarcinoma(86;0.141)			GCAGCAAGTACTCGATGGTGA	0.622																																					p.E129E		Atlas-SNP	.											DZIP1_ENST00000347108,NS,neuroblastoma,-2,2	DZIP1	195	2	0			c.G387A						scavenged	.						96.0	74.0	81.0					13																	96293759		2203	4300	6503	SO:0001819	synonymous_variant	22873	exon5			CAAGTACTCGATG	AB023213	CCDS9477.1, CCDS9478.1	13q32.1	2013-05-22	2013-05-22		ENSG00000134874	ENSG00000134874		"""Zinc fingers, C2H2-type"""	20908	protein-coding gene	gene with protein product		608671	"""DAZ interacting protein 1"""				Standard	NM_014934		Approved	KIAA0996, DZIP	uc001vmk.4	Q86YF9	OTTHUMG00000017224	ENST00000376829.2:c.387G>A	13.37:g.96293759C>T		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	102	2	0.0196078	NM_014934	Q5W078|Q5W079|Q8WY45|Q8WY46|Q9UGA5|Q9Y2K0	Silent	SNP	ENST00000376829.2	37	CCDS9478.1																																																																																			.	.	none		0.622	DZIP1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045496.3	NM_014934	
LACTB	114294	hgsc.bcm.edu	37	15	63419699	63419699	+	Missense_Mutation	SNP	A	A	C	rs34536322	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:63419699A>C	ENST00000261893.4	+	4	835	c.763A>C	c.(763-765)Aaa>Caa	p.K255Q	LACTB_ENST00000413507.2_Missense_Mutation_p.K255Q|RPS27L_ENST00000559763.1_Intron	NM_032857.3	NP_116246.2	P83111	LACTB_HUMAN	lactamase, beta	255						cytoplasm (GO:0005737)|mitochondrion (GO:0005739)	hydrolase activity (GO:0016787)			NS(1)|breast(1)|kidney(1)|large_intestine(3)|lung(3)|prostate(1)|skin(1)|stomach(1)	12						AAAAGAAGGCAAAAGTAATGA	0.318													A|||	77	0.0153754	0.0015	0.0259	5008	,	,		18328	0.0		0.0507	False		,,,				2504	0.0061				p.K255Q	Melanoma(85;443 1381 6215 27308 35583)	Atlas-SNP	.											.	LACTB	29	.	0			c.A763C						PASS	.	A	GLN/LYS,GLN/LYS	47,4359	42.3+/-75.8	0,47,2156	51.0	56.0	54.0		763,763	6.1	0.1	15	dbSNP_126	54	406,8188	121.3+/-180.4	11,384,3902	yes	missense,missense	LACTB	NM_032857.3,NM_171846.2	53,53	11,431,6058	CC,CA,AA		4.7242,1.0667,3.4846	benign,benign	255/548,255/374	63419699	453,12547	2203	4297	6500	SO:0001583	missense	114294	exon4			GAAGGCAAAAGTA	AK027808	CCDS10182.1, CCDS45275.1	15q22.1	2012-11-14	2001-12-12	2001-12-14	ENSG00000103642	ENSG00000103642		"""Mitochondrial ribosomal proteins / large subunits"""	16468	protein-coding gene	gene with protein product		608440	"""mitochondrial ribosomal protein L56"""	MRPL56		11707067	Standard	NM_032857		Approved	FLJ14902	uc002alw.3	P83111	OTTHUMG00000132807	ENST00000261893.4:c.763A>C	15.37:g.63419699A>C	ENSP00000261893:p.Lys255Gln	Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	132	72	0.545455	NM_171846	P83096	Missense_Mutation	SNP	ENST00000261893.4	37	CCDS10182.1	48	0.02197802197802198	2	0.0040650406504065045	9	0.024861878453038673	0	0.0	37	0.048812664907651716	A	8.110	0.778652	0.16120	0.010667	0.047242	ENSG00000103642	ENST00000261893;ENST00000413507	T	0.48201	0.82	6.07	6.07	0.98685	Beta-lactamase/transpeptidase-like (1);	0.382752	0.29806	N	0.011159	T	0.06600	0.0169	L	0.27053	0.805	0.38099	D	0.93721	B	0.23735	0.09	B	0.16289	0.015	T	0.07809	-1.0753	10	0.27785	T	0.31	-7.8475	11.6887	0.51503	0.9296:0.0:0.0704:0.0	rs34536322	255	P83111	LACTB_HUMAN	Q	255	ENSP00000261893:K255Q	ENSP00000261893:K255Q	K	+	1	0	LACTB	61206752	1.000000	0.71417	0.112000	0.21494	0.475000	0.33008	2.731000	0.47343	2.330000	0.79161	0.477000	0.44152	AAA	A|0.971;C|0.029	0.029	strong		0.318	LACTB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256224.1	NM_032857	
ZNF485	220992	hgsc.bcm.edu	37	10	44112245	44112245	+	Missense_Mutation	SNP	G	G	A	rs12354886	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:44112245G>A	ENST00000361807.3	+	5	948	c.754G>A	c.(754-756)Gct>Act	p.A252T	ZNF485_ENST00000374437.2_Missense_Mutation_p.A161T|ZNF485_ENST00000374435.3_Missense_Mutation_p.A252T	NM_145312.3	NP_660355.2	Q8NCK3	ZN485_HUMAN	zinc finger protein 485	252			A -> T (in dbSNP:rs12354886).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(8)|skin(1)|urinary_tract(1)	16						GAAAGCCTTCGCTCAGAATGC	0.393													G|||	926	0.184904	0.2943	0.2133	5008	,	,		21170	0.003		0.2177	False		,,,				2504	0.1708				p.A252T		Atlas-SNP	.											.	ZNF485	102	.	0			c.G754A						PASS	.	G	THR/ALA	1183,3223	413.7+/-336.6	169,845,1189	70.0	74.0	73.0		754	0.5	0.0	10	dbSNP_120	73	1995,6605	348.3+/-327.0	222,1551,2527	yes	missense	ZNF485	NM_145312.3	58	391,2396,3716	AA,AG,GG		23.1977,26.8498,24.4349	benign	252/442	44112245	3178,9828	2203	4300	6503	SO:0001583	missense	220992	exon5			GCCTTCGCTCAGA	AK074679	CCDS7205.2	10q11.21	2013-01-08			ENSG00000198298	ENSG00000198298		"""Zinc fingers, C2H2-type"", ""-"""	23440	protein-coding gene	gene with protein product							Standard	NM_145312		Approved		uc010qfc.2	Q8NCK3	OTTHUMG00000018040	ENST00000361807.3:c.754G>A	10.37:g.44112245G>A	ENSP00000354694:p.Ala252Thr	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	79	43	0.544304	NM_145312	B4DSE6|Q96CL0	Missense_Mutation	SNP	ENST00000361807.3	37	CCDS7205.2	366	0.16758241758241757	136	0.2764227642276423	77	0.212707182320442	0	0.0	153	0.20184696569920843	G	0.238	-1.015652	0.02078	0.268498	0.231977	ENSG00000198298	ENST00000361807;ENST00000374437;ENST00000374435	T;T;T	0.07567	3.18;3.18;3.18	2.46	0.496	0.16896	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	N	0.04655	-0.195	0.80722	P	0.0	B	0.06786	0.001	B	0.13407	0.009	T	0.47699	-0.9097	8	0.10902	T	0.67	.	2.3447	0.04269	0.2826:0.0:0.4752:0.2422	rs12354886;rs52806454;rs59867017;rs12354886	252	Q8NCK3	ZN485_HUMAN	T	252;161;252	ENSP00000354694:A252T;ENSP00000363560:A161T;ENSP00000363558:A252T	ENSP00000354694:A252T	A	+	1	0	ZNF485	43432251	0.000000	0.05858	0.000000	0.03702	0.029000	0.11900	-0.058000	0.11750	0.119000	0.18210	-0.521000	0.04368	GCT	G|0.786;A|0.214	0.214	strong		0.393	ZNF485-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047719.2	NM_145312	
RPP40	10799	hgsc.bcm.edu	37	6	4995464	4995464	+	Missense_Mutation	SNP	C	C	T	rs12332997	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:4995464C>T	ENST00000380051.2	-	8	984	c.940G>A	c.(940-942)Gtt>Att	p.V314I	RPP40_ENST00000464646.1_Missense_Mutation_p.V254I|RPP40_ENST00000319533.5_Missense_Mutation_p.V291I	NM_006638.2	NP_006629.2	O75818	RPP40_HUMAN	ribonuclease P/MRP 40kDa subunit	314			V -> I (in dbSNP:rs12332997).		RNA phosphodiester bond hydrolysis (GO:0090501)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|tRNA processing (GO:0008033)	nucleolar ribonuclease P complex (GO:0005655)|nucleus (GO:0005634)	ribonuclease P activity (GO:0004526)			NS(1)|breast(1)|large_intestine(4)|lung(4)|ovary(1)|skin(2)|urinary_tract(1)	14	Ovarian(93;0.11)	all_hematologic(90;0.0895)				AAGCCTTGAACGGACAGTGTA	0.358													C|||	239	0.0477236	0.0484	0.0202	5008	,	,		17533	0.0069		0.0417	False		,,,				2504	0.1145				p.V314I		Atlas-SNP	.											RPP40,colon,carcinoma,0,1	RPP40	36	1	0			c.G940A						PASS	.	C	ILE/VAL	203,4203	126.1+/-163.2	10,183,2010	66.0	65.0	65.0		940	5.0	0.6	6	dbSNP_120	65	247,8353	98.4+/-159.9	2,243,4055	yes	missense	RPP40	NM_006638.2	29	12,426,6065	TT,TC,CC		2.8721,4.6074,3.4599	probably-damaging	314/364	4995464	450,12556	2203	4300	6503	SO:0001583	missense	10799	exon8			CTTGAACGGACAG	U94317	CCDS34333.1, CCDS69040.1, CCDS75391.1	6p25.1	2012-05-21	2007-06-26	2004-03-19	ENSG00000124787	ENSG00000124787			20992	protein-coding gene	gene with protein product		606117	"""ribonuclease P1"", ""ribonuclease P 40kDa subunit"""	RNASEP1		9630247	Standard	NM_006638		Approved	bA428J1.3	uc003mwl.3	O75818	OTTHUMG00000014168	ENST00000380051.2:c.940G>A	6.37:g.4995464C>T	ENSP00000369391:p.Val314Ile	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	80	21	0.2625	NM_006638	Q5VX97|Q8WVK8	Missense_Mutation	SNP	ENST00000380051.2	37	CCDS34333.1	64	0.029304029304029304	24	0.04878048780487805	11	0.03038674033149171	0	0.0	29	0.03825857519788918	C	16.70	3.195693	0.58126	0.046074	0.028721	ENSG00000124787	ENST00000380051;ENST00000319533;ENST00000464646	T;T;T	0.50548	0.74;0.74;0.74	4.96	4.96	0.65561	.	0.000000	0.85682	D	0.000000	T	0.61800	0.2376	M	0.70842	2.15	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.81914	0.995;0.987	T	0.64681	-0.6350	10	0.52906	T	0.07	-0.8184	17.2043	0.86914	0.0:1.0:0.0:0.0	rs12332997;rs52835676;rs57228663;rs12332997	291;314	O75818-2;O75818	.;RPP40_HUMAN	I	314;291;254	ENSP00000369391:V314I;ENSP00000317998:V291I;ENSP00000419431:V254I	ENSP00000317998:V291I	V	-	1	0	RPP40	4940463	1.000000	0.71417	0.586000	0.28679	0.013000	0.08279	6.838000	0.75359	2.294000	0.77228	0.655000	0.94253	GTT	C|0.966;T|0.034	0.034	strong		0.358	RPP40-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039733.2	NM_006638	
TRIM31	11074	hgsc.bcm.edu	37	6	30078330	30078330	+	Silent	SNP	C	C	T	rs2239529	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:30078330C>T	ENST00000376734.3	-	4	764	c.639G>A	c.(637-639)gcG>gcA	p.A213A	TRIM31_ENST00000540829.1_Silent_p.A213A|TRIM31-AS1_ENST00000440874.1_RNA|TRIM31_ENST00000485864.1_5'UTR	NM_007028.3	NP_008959.3	Q9BZY9	TRI31_HUMAN	tripartite motif containing 31	213					innate immune response (GO:0045087)|negative regulation of viral entry into host cell (GO:0046597)|negative regulation of viral transcription (GO:0032897)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein ubiquitination (GO:0016567)|regulation of viral release from host cell (GO:1902186)	mitochondrion (GO:0005739)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(5)|ovary(2)|prostate(2)|skin(2)	15						AGTGTTTCCCCGCTTCCGTTC	0.512													C|||	317	0.0632987	0.0121	0.1138	5008	,	,		19102	0.0486		0.1193	False		,,,				2504	0.0542				p.A213A		Atlas-SNP	.											TRIM31,trunk,malignant_melanoma,-2,2	TRIM31	40	2	0			c.G639A						PASS	.	C		161,4245	107.3+/-145.7	5,151,2047	192.0	172.0	179.0		639	-2.6	0.0	6	dbSNP_98	179	1207,7393	243.9+/-273.3	75,1057,3168	yes	coding-synonymous	TRIM31	NM_007028.3		80,1208,5215	TT,TC,CC		14.0349,3.6541,10.5182		213/426	30078330	1368,11638	2203	4300	6503	SO:0001819	synonymous_variant	11074	exon4			TTTCCCCGCTTCC	AF230386	CCDS34374.1	6p21.3	2013-01-09	2011-01-25		ENSG00000204616	ENSG00000204616		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	16289	protein-coding gene	gene with protein product		609316	"""tripartite motif-containing 31"""			11331580	Standard	XM_006714977		Approved	RNF, HCGI, C6orf13, HCG1	uc003npg.1	Q9BZY9	OTTHUMG00000031064	ENST00000376734.3:c.639G>A	6.37:g.30078330C>T		Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	116	62	0.534483	NM_007028	A6NLX6|A9R9Q4|Q53H52|Q5RI37|Q5SRJ7|Q5SRJ8|Q5SS28|Q96AK4|Q96AP8|Q99579|Q9BZY8	Silent	SNP	ENST00000376734.3	37	CCDS34374.1																																																																																			C|0.907;T|0.093	0.093	strong		0.512	TRIM31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076081.2		
SLC27A2	11001	hgsc.bcm.edu	37	15	50474900	50474900	+	Silent	SNP	C	C	T	rs34490804	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:50474900C>T	ENST00000267842.5	+	1	508	c.276C>T	c.(274-276)gcC>gcT	p.A92A	SLC27A2_ENST00000380902.4_Silent_p.A92A	NM_003645.3	NP_003636.2	O14975	S27A2_HUMAN	solute carrier family 27 (fatty acid transporter), member 2	92					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)		ATCAAGTGGCCCGGGCGCTGC	0.662													C|||	345	0.0688898	0.056	0.0994	5008	,	,		15607	0.0347		0.1223	False		,,,				2504	0.045				p.A92A		Atlas-SNP	.											.	SLC27A2	50	.	0			c.C276T						PASS	.	C	,	315,4077	165.1+/-196.6	9,297,1890	48.0	53.0	51.0		276,276	-6.5	1.0	15	dbSNP_126	51	1031,7559	212.1+/-252.5	73,885,3337	no	coding-synonymous,coding-synonymous	SLC27A2	NM_001159629.1,NM_003645.3	,	82,1182,5227	TT,TC,CC		12.0023,7.1721,10.3682	,	92/568,92/621	50474900	1346,11636	2196	4295	6491	SO:0001819	synonymous_variant	11001	exon1			AGTGGCCCGGGCG	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.276C>T	15.37:g.50474900C>T		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	99	36	0.363636	NM_003645	A8K2J7|Q53FY6|Q6PF09	Silent	SNP	ENST00000267842.5	37	CCDS10133.1																																																																																			C|0.905;T|0.095	0.095	strong		0.662	SLC27A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254539.2	NM_003645	
AURKA	6790	hgsc.bcm.edu	37	20	54961541	54961541	+	Missense_Mutation	SNP	A	A	T	rs2273535	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:54961541A>T	ENST00000347343.2	-	3	358	c.91T>A	c.(91-93)Ttt>Att	p.F31I	AURKA_ENST00000395911.1_Missense_Mutation_p.F31I|AURKA_ENST00000395909.4_Missense_Mutation_p.F31I|AURKA_ENST00000312783.6_Missense_Mutation_p.F31I|AURKA_ENST00000371356.2_Missense_Mutation_p.F31I|AURKA_ENST00000395907.1_Missense_Mutation_p.F31I|AURKA_ENST00000395913.3_Missense_Mutation_p.F31I|AURKA_ENST00000395914.1_Missense_Mutation_p.F31I|AURKA_ENST00000395915.3_Missense_Mutation_p.F31I	NM_003600.2	NP_003591.2	O14965	AURKA_HUMAN	aurora kinase A	31			F -> I (in dbSNP:rs2273535). {ECO:0000269|PubMed:15867347, ECO:0000269|PubMed:16011022, ECO:0000269|PubMed:16762494, ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:9771714}.		anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|anterior/posterior axis specification (GO:0009948)|centrosome localization (GO:0051642)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic centrosome separation (GO:0007100)|mitotic nuclear division (GO:0007067)|mitotic spindle organization (GO:0007052)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein binding (GO:0032091)|negative regulation of spindle checkpoint (GO:0090233)|neuron projection extension (GO:1990138)|positive regulation of mitosis (GO:0045840)|positive regulation of oocyte maturation (GO:1900195)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|protein autophosphorylation (GO:0046777)|protein localization to centrosome (GO:0071539)|protein phosphorylation (GO:0006468)|regulation of centrosome cycle (GO:0046605)|regulation of protein stability (GO:0031647)|spindle assembly involved in female meiosis I (GO:0007057)|spindle stabilization (GO:0043146)	axon hillock (GO:0043203)|centrosome (GO:0005813)|cytosol (GO:0005829)|germinal vesicle (GO:0042585)|meiotic spindle (GO:0072687)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|midbody (GO:0030496)|mitotic spindle (GO:0072686)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|pronucleus (GO:0045120)|spindle (GO:0005819)|spindle pole centrosome (GO:0031616)	ATP binding (GO:0005524)|histone serine kinase activity (GO:0035174)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)			breast(2)|cervix(1)|endometrium(1)|large_intestine(4)|lung(9)|ovary(2)|prostate(1)|skin(2)	22			Colorectal(105;0.202)			TGACAAGGAAATTGCTGAGTC	0.443													A|||	1551	0.309704	0.1339	0.2925	5008	,	,		20638	0.6587		0.2157	False		,,,				2504	0.2965				p.F31I	Melanoma(34;439 1292 51416 52695)|GBM(144;1525 2517 48902 51835)|Esophageal Squamous(191;569 2880 14195 30540)	Atlas-SNP	.											.	AURKA	42	.	0			c.T91A	GRCh37	CM042940	AURKA	M	rs2273535	PASS	.	A	ILE/PHE,ILE/PHE,ILE/PHE,ILE/PHE,ILE/PHE,ILE/PHE	583,3823	255.5+/-260.7	40,503,1660	75.0	74.0	74.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	91,91,91,91,91,91	-7.6	0.0	20	dbSNP_100	74	1865,6735	328.4+/-318.3	196,1473,2631	yes	missense,missense,missense,missense,missense,missense	AURKA	NM_003600.2,NM_198433.1,NM_198434.1,NM_198435.1,NM_198436.1,NM_198437.1	21,21,21,21,21,21	236,1976,4291	TT,TA,AA		21.686,13.232,18.8221	benign,benign,benign,benign,benign,benign	31/404,31/404,31/404,31/404,31/404,31/404	54961541	2448,10558	2203	4300	6503	SO:0001583	missense	6790	exon3			AAGGAAATTGCTG	BC001280	CCDS13451.1	20q13	2012-07-23	2003-07-21	2003-07-23	ENSG00000087586	ENSG00000087586		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	11393	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 47"", ""Aurora-A kinase"""	603072	"""serine/threonine kinase 15"", "" serine/threonine kinase 6"""	STK15, STK6		9174055, 9771714	Standard	NM_003600		Approved	BTAK, AurA, STK7, ARK1, PPP1R47, AIK	uc002xxi.1	O14965	OTTHUMG00000032796	ENST00000347343.2:c.91T>A	20.37:g.54961541A>T	ENSP00000216911:p.Phe31Ile	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	87	40	0.45977	NM_198437	E1P5F9|O60445|O75873|Q9BQD6|Q9UPG5	Missense_Mutation	SNP	ENST00000347343.2	37	CCDS13451.1	690	0.3159340659340659	77	0.1565040650406504	95	0.26243093922651933	363	0.6346153846153846	155	0.20448548812664907	A	1.983	-0.433669	0.04669	0.13232	0.21686	ENSG00000087586	ENST00000395909;ENST00000395914;ENST00000347343;ENST00000395915;ENST00000312783;ENST00000371356;ENST00000395913;ENST00000395911;ENST00000395907;ENST00000441357;ENST00000420474;ENST00000422322;ENST00000456249;ENST00000451915	T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.69040	-0.1;-0.1;-0.1;-0.1;-0.1;-0.1;-0.1;-0.1;-0.37;0.1;2.86;2.65;2.71;2.42	4.28	-7.55	0.01327	.	1.560460	0.03399	N	0.202999	T	0.00012	0.0000	N	0.13043	0.29	0.80722	P	0.0	B;B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0;0.0	B;B;B;B;B;B	0.04013	0.0;0.001;0.0;0.0;0.0;0.0	T	0.32719	-0.9896	9	0.16420	T	0.52	0.1647	1.6559	0.02782	0.1674:0.1141:0.2496:0.4688	rs2273535;rs3171189;rs17007275;rs57597985;rs2273535	31;31;31;31;31;31	Q5QPD1;Q5QPD2;A3KFJ1;Q5QPD4;A3KFJ0;O14965	.;.;.;.;.;AURKA_HUMAN	I	31	ENSP00000379245:F31I;ENSP00000379250:F31I;ENSP00000216911:F31I;ENSP00000379251:F31I;ENSP00000321591:F31I;ENSP00000360407:F31I;ENSP00000379249:F31I;ENSP00000379247:F31I;ENSP00000379243:F31I;ENSP00000393452:F31I;ENSP00000388073:F31I;ENSP00000405042:F31I;ENSP00000405170:F31I;ENSP00000401358:F31I	ENSP00000321591:F31I	F	-	1	0	AURKA	54394948	0.000000	0.05858	0.002000	0.10522	0.061000	0.15899	-0.588000	0.05774	-1.226000	0.02574	-0.371000	0.07208	TTT	A|0.773;T|0.227	0.227	strong		0.443	AURKA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079804.3	NM_003600	
KIDINS220	57498	hgsc.bcm.edu	37	2	8917015	8917015	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:8917015T>C	ENST00000256707.3	-	21	2892	c.2711A>G	c.(2710-2712)tAc>tGc	p.Y904C	KIDINS220_ENST00000319688.5_Missense_Mutation_p.Y905C|KIDINS220_ENST00000473731.1_Missense_Mutation_p.Y904C|KIDINS220_ENST00000427284.1_Missense_Mutation_p.Y904C|KIDINS220_ENST00000418530.1_Missense_Mutation_p.Y862C	NM_020738.2	NP_065789.1	Q9ULH0	KDIS_HUMAN	kinase D-interacting substrate, 220kDa	904	KAP NTPase.				activation of MAPKK activity (GO:0000186)|cellular response to nerve growth factor stimulus (GO:1990090)|cytoplasmic transport (GO:0016482)|dendrite morphogenesis (GO:0048813)|in utero embryonic development (GO:0001701)|nerve growth factor signaling pathway (GO:0038180)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of neuron projection development (GO:0010976)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|membrane (GO:0016020)|protein complex (GO:0043234)	PDZ domain binding (GO:0030165)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(11)|lung(25)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	60	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)					CCTTCTTCGGTAAGTGTCCTG	0.453																																					p.Y904C		Atlas-SNP	.											KIDINS220,caecum,carcinoma,0,1	KIDINS220	136	1	0			c.A2711G						scavenged	.						126.0	118.0	121.0					2																	8917015		1951	4145	6096	SO:0001583	missense	57498	exon21			CTTCGGTAAGTGT	AK025528	CCDS42650.1	2p24	2013-01-10			ENSG00000134313	ENSG00000134313		"""Ankyrin repeat domain containing"""	29508	protein-coding gene	gene with protein product	"""ankyrin repeat-rich membrane-spanning protein"""	615759				10998417, 10574462	Standard	NM_020738		Approved	ARMS	uc002qzc.2	Q9ULH0	OTTHUMG00000151658	ENST00000256707.3:c.2711A>G	2.37:g.8917015T>C	ENSP00000256707:p.Tyr904Cys	Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	160	2	0.0125	NM_020738	A1L4N4|Q4VC08|Q6MZU2|Q9H889|Q9H9E4|Q9NT37|Q9UF42	Missense_Mutation	SNP	ENST00000256707.3	37	CCDS42650.1	.	.	.	.	.	.	.	.	.	.	T	25.5	4.644917	0.87859	.	.	ENSG00000134313	ENST00000496383;ENST00000541927;ENST00000256707;ENST00000427284;ENST00000418530;ENST00000473731;ENST00000489024;ENST00000319688	T;T;T;T;T;T;T	0.67698	0.86;-0.28;-0.24;-0.16;-0.24;-0.2;-0.18	5.62	5.62	0.85841	KAP P-loop (1);	0.177243	0.52532	D	0.000076	T	0.79112	0.4391	L	0.57536	1.79	0.80722	D	1	D;P;P;D	0.76494	0.999;0.901;0.943;0.971	D;P;P;D	0.85130	0.997;0.778;0.866;0.918	T	0.79376	-0.1829	10	0.48119	T	0.1	.	15.8123	0.78573	0.0:0.0:0.0:1.0	.	905;905;862;904	B4DK94;E9PH70;Q9ULH0-2;Q9ULH0	.;.;.;KDIS_HUMAN	C	651;588;904;904;862;904;905;905	ENSP00000420364:Y651C;ENSP00000256707:Y904C;ENSP00000411849:Y904C;ENSP00000414923:Y862C;ENSP00000418974:Y904C;ENSP00000419964:Y905C;ENSP00000319947:Y905C	ENSP00000256707:Y904C	Y	-	2	0	KIDINS220	8834466	1.000000	0.71417	1.000000	0.80357	0.931000	0.56810	7.584000	0.82572	2.127000	0.65507	0.459000	0.35465	TAC	.	.	none		0.453	KIDINS220-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323408.2	NM_020738	
KLHL12	59349	hgsc.bcm.edu	37	1	202888947	202888947	+	Silent	SNP	T	T	C	rs3182429	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:202888947T>C	ENST00000367261.3	-	3	503	c.285A>G	c.(283-285)acA>acG	p.T95T	KLHL12_ENST00000435533.3_Silent_p.T133T	NM_021633.2	NP_067646.1	Q53G59	KLH12_HUMAN	kelch-like family member 12	95	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.				COPII vesicle coating (GO:0048208)|ER to Golgi vesicle-mediated transport (GO:0006888)|protein monoubiquitination (GO:0006513)|Wnt signaling pathway (GO:0016055)	Cul3-RING ubiquitin ligase complex (GO:0031463)|ER to Golgi transport vesicle (GO:0030134)|Golgi membrane (GO:0000139)				NS(3)|breast(2)|endometrium(1)|large_intestine(1)|lung(6)|stomach(1)	14			BRCA - Breast invasive adenocarcinoma(75;0.166)			TCACATGTACTGTTTCTGTGT	0.398													T|||	1461	0.291733	0.0681	0.3271	5008	,	,		18036	0.5208		0.2326	False		,,,				2504	0.3937				p.T95T		Atlas-SNP	.											.	KLHL12	50	.	0			c.A285G						PASS	.	T		508,3898	233.0+/-246.3	35,438,1730	96.0	85.0	88.0		285	-6.0	0.5	1	dbSNP_105	88	1950,6650	344.7+/-325.5	234,1482,2584	no	coding-synonymous	KLHL12	NM_021633.2		269,1920,4314	CC,CT,TT		22.6744,11.5297,18.899		95/569	202888947	2458,10548	2203	4300	6503	SO:0001819	synonymous_variant	59349	exon3			ATGTACTGTTTCT	AF190900	CCDS1429.1	1q32.1	2013-01-30	2013-01-30		ENSG00000117153	ENSG00000117153		"""Kelch-like"", ""BTB/POZ domain containing"""	19360	protein-coding gene	gene with protein product		614522	"""kelch-like 12 (Drosophila)"""			12477932	Standard	NM_021633		Approved	C3IP1	uc001gyo.1	Q53G59	OTTHUMG00000041385	ENST00000367261.3:c.285A>G	1.37:g.202888947T>C		Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	135	54	0.4	NM_021633	A6NEN8|B7Z7B8|Q9HBX5	Silent	SNP	ENST00000367261.3	37	CCDS1429.1																																																																																			T|0.778;C|0.222	0.222	strong		0.398	KLHL12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099151.1	NM_021633	
ALKBH2	121642	hgsc.bcm.edu	37	12	109527872	109527872	+	Missense_Mutation	SNP	T	T	C	rs139644396	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:109527872T>C	ENST00000429722.2	-	3	784	c.421A>G	c.(421-423)Atc>Gtc	p.I141V	ALKBH2_ENST00000343075.3_Missense_Mutation_p.I141V|ALKBH2_ENST00000440112.2_Intron	NM_001145374.1	NP_001138846.1	Q6NS38	ALKB2_HUMAN	alkB, alkylation repair homolog 2 (E. coli)	141					DNA dealkylation involved in DNA repair (GO:0006307)|DNA demethylation (GO:0080111)|DNA repair (GO:0006281)|oxidative demethylation (GO:0070989)|oxidative DNA demethylation (GO:0035511)	nucleoplasm (GO:0005654)	cytosine C-5 DNA demethylase activity (GO:0051747)|DNA-N1-methyladenine dioxygenase activity (GO:0043734)|ferrous iron binding (GO:0008198)			endometrium(1)|kidney(3)|large_intestine(1)|lung(3)	8					Vitamin C(DB00126)	TGATCCCGGATGCGCTCTAGA	0.537								Direct reversal of damage					T|||	47	0.00938498	0.0015	0.0173	5008	,	,		19434	0.001		0.0278	False		,,,				2504	0.0041				p.I141V		Atlas-SNP	.											.	ALKBH2	16	.	0			c.A421G						PASS	.	T	VAL/ILE,VAL/ILE,VAL/ILE,,	18,4388	25.3+/-52.1	0,18,2185	131.0	117.0	122.0		421,421,421,,	-0.1	0.0	12	dbSNP_134	122	224,8376	93.3+/-155.3	5,214,4081	yes	missense,missense,missense,intron,intron	ALKBH2	NM_001001655.2,NM_001145374.1,NM_001145375.1,NM_001205179.1,NM_001205180.1	29,29,29,,	5,232,6266	CC,CT,TT		2.6047,0.4085,1.8607	benign,benign,benign,,	141/262,141/262,141/262,,	109527872	242,12764	2203	4300	6503	SO:0001583	missense	121642	exon3			CCCGGATGCGCTC	AY754389	CCDS31897.1, CCDS55883.1	12q24.11	2008-04-24			ENSG00000189046	ENSG00000189046		"""Alkylation repair homologs"""	32487	protein-coding gene	gene with protein product		610602					Standard	NM_001145374		Approved	MGC90512, ABH2	uc010sxj.1	Q6NS38	OTTHUMG00000169246	ENST00000429722.2:c.421A>G	12.37:g.109527872T>C	ENSP00000398181:p.Ile141Val	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	78	40	0.512821	NM_001001655	A4PET2|Q5XLE3	Missense_Mutation	SNP	ENST00000429722.2	37	CCDS31897.1	27	0.012362637362637362	1	0.0020325203252032522	6	0.016574585635359115	0	0.0	20	0.026385224274406333	T	2.478	-0.320363	0.05386	0.004085	0.026047	ENSG00000189046	ENST00000429722;ENST00000343075;ENST00000435370;ENST00000540305;ENST00000536242	T;T;T	0.13901	2.83;2.83;2.55	5.61	-0.0748	0.13729	.	0.145968	0.64402	N	0.000014	T	0.02970	0.0088	L	0.43598	1.365	0.34502	D	0.706113	B	0.02656	0.0	B	0.08055	0.003	T	0.26950	-1.0088	10	0.22706	T	0.39	-16.551	8.4603	0.32923	0.0:0.3007:0.0:0.6993	.	141	Q6NS38	ALKB2_HUMAN	V	141	ENSP00000398181:I141V;ENSP00000343021:I141V;ENSP00000443042:I141V	ENSP00000343021:I141V	I	-	1	0	ALKBH2	108012255	0.886000	0.30341	0.020000	0.16555	0.215000	0.24574	1.431000	0.34925	0.054000	0.16065	-0.242000	0.12053	ATC	T|0.985;C|0.015	0.015	strong		0.537	ALKBH2-007	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403063.2	NM_001001655	
TSSK2	23617	hgsc.bcm.edu	37	22	19119545	19119545	+	Silent	SNP	C	C	T	rs45604134	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	111	0	0		WXS	Illumina HiSeq	Phase_I	74	42	0.567568	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		
SNF8	11267	hgsc.bcm.edu	37	17	47007963	47007963	+	Silent	SNP	C	C	T	rs2270576	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	39	0	0		WXS	Illumina HiSeq	Phase_I	41	15	0.365854	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	
MUC5B	727897	hgsc.bcm.edu	37	11	1266537	1266537	+	Silent	SNP	G	G	T	rs199659189	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:1266537G>T	ENST00000529681.1	+	31	8485	c.8427G>T	c.(8425-8427)ctG>ctT	p.L2809L	MUC5B_ENST00000447027.1_Silent_p.L2812L|RP11-532E4.2_ENST00000532061.2_RNA	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	327	1	0.0030581		WXS	Illumina HiSeq	Phase_I	393	23	0.0585242	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	
C11orf16	56673	hgsc.bcm.edu	37	11	8947586	8947586	+	Missense_Mutation	SNP	C	C	G	rs11042127	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:8947586C>G	ENST00000326053.5	-	5	734	c.628G>C	c.(628-630)Gtc>Ctc	p.V210L	C11orf16_ENST00000528998.1_5'Flank|C11orf16_ENST00000525780.1_Missense_Mutation_p.V210L	NM_020643.2	NP_065694.2	Q9NQ32	CK016_HUMAN	chromosome 11 open reading frame 16	210			V -> L (in dbSNP:rs11042127). {ECO:0000269|Ref.2}.							central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|stomach(2)|upper_aerodigestive_tract(1)	22				Epithelial(150;4.11e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0234)		ACCGACTGGACCCCACCTAGG	0.502													C|||	1245	0.248602	0.2307	0.2003	5008	,	,		16469	0.377		0.1918	False		,,,				2504	0.2331				p.V210L		Atlas-SNP	.											.	C11orf16	43	.	0			c.G628C						PASS	.	C	LEU/VAL	961,3441	357.9+/-314.1	95,771,1335	75.0	84.0	81.0		628	5.1	0.0	11	dbSNP_120	81	1547,7045	286.3+/-297.7	138,1271,2887	yes	missense	C11orf16	NM_020643.2	32	233,2042,4222	GG,GC,CC		18.0051,21.831,19.3012	probably-damaging	210/468	8947586	2508,10486	2201	4296	6497	SO:0001583	missense	56673	exon5			ACTGGACCCCACC	AJ400877	CCDS7794.1	11p15.3	2008-06-25			ENSG00000176029	ENSG00000176029			1169	protein-coding gene	gene with protein product						11528127	Standard	NM_020643		Approved		uc001mhb.4	Q9NQ32	OTTHUMG00000165654	ENST00000326053.5:c.628G>C	11.37:g.8947586C>G	ENSP00000318999:p.Val210Leu	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	96	13	0.135417	NM_020643	Q53FB2|Q8N6Y9	Missense_Mutation	SNP	ENST00000326053.5	37	CCDS7794.1	548	0.2509157509157509	109	0.22154471544715448	79	0.21823204419889503	213	0.3723776223776224	147	0.19393139841688653	C	11.19	1.567084	0.28003	0.21831	0.180051	ENSG00000176029	ENST00000525780;ENST00000326053	T;T	0.25912	1.77;1.77	6.07	5.14	0.70334	.	0.540684	0.17983	N	0.155467	T	0.00012	0.0000	L	0.59436	1.845	0.80722	P	0.0	B;B	0.28178	0.202;0.202	B;B	0.26202	0.039;0.067	T	0.39722	-0.9600	9	0.40728	T	0.16	-3.3055	15.681	0.77367	0.0:0.8639:0.1361:0.0	rs11042127;rs59695846;rs11042127	210;210	Q9NQ32-2;Q9NQ32	.;CK016_HUMAN	L	210	ENSP00000436818:V210L;ENSP00000318999:V210L	ENSP00000318999:V210L	V	-	1	0	C11orf16	8904162	0.607000	0.26958	0.025000	0.17156	0.196000	0.23810	3.759000	0.55227	1.536000	0.49237	0.655000	0.94253	GTC	C|0.787;G|0.213	0.213	strong		0.502	C11orf16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385626.1	NM_020643	
AMOTL2	51421	hgsc.bcm.edu	37	3	134077470	134077470	+	Missense_Mutation	SNP	C	C	G	rs1353776	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:134077470C>G	ENST00000422605.2	-	9	2359	c.2193G>C	c.(2191-2193)gaG>gaC	p.E731D	AMOTL2_ENST00000514516.1_Missense_Mutation_p.E789D|AMOTL2_ENST00000513145.1_Missense_Mutation_p.E729D|AMOTL2_ENST00000249883.5_Missense_Mutation_p.E732D|RPL39P5_ENST00000273411.2_RNA			Q9Y2J4	AMOL2_HUMAN	angiomotin like 2	731			E -> D (in dbSNP:rs1353776). {ECO:0000269|PubMed:10231032, ECO:0000269|PubMed:12406577, ECO:0000269|PubMed:14702039, ECO:0000269|Ref.3}.		hippo signaling (GO:0035329)|Wnt signaling pathway (GO:0016055)	apical plasma membrane (GO:0016324)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endosome (GO:0005768)|tight junction (GO:0005923)				endometrium(8)|kidney(1)|large_intestine(2)|lung(4)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	19						CTGGGGGGCCCTCAGTCTGGG	0.642											OREG0015814	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	4050	0.808706	0.9357	0.7176	5008	,	,		16022	0.9246		0.6074	False		,,,				2504	0.7894				p.E732D		Atlas-SNP	.											.	AMOTL2	52	.	0			c.G2196C						PASS	.	G	ASP/GLU	3855,551	243.7+/-253.3	1694,467,42	57.0	50.0	52.0		2196	-11.0	0.0	3	dbSNP_88	52	5650,2950	452.8+/-363.1	1858,1934,508	yes	missense	AMOTL2	NM_016201.2	45	3552,2401,550	GG,GC,CC		34.3023,12.5057,26.9183	benign	732/781	134077470	9505,3501	2203	4300	6503	SO:0001583	missense	51421	exon9			GGGGCCCTCAGTC	AF175966	CCDS33860.1, CCDS63783.1, CCDS63784.1	3q21-q22	2008-07-18			ENSG00000114019	ENSG00000114019			17812	protein-coding gene	gene with protein product	"""Leman coiled-coil protein"", ""angiomotin-like protein 2"""	614658					Standard	NM_016201		Approved	LCCP	uc003eqg.1	Q9Y2J4	OTTHUMG00000159777	ENST00000422605.2:c.2193G>C	3.37:g.134077470C>G	ENSP00000409999:p.Glu731Asp	Somatic	66	0	0	1607	WXS	Illumina HiSeq	Phase_I	51	24	0.470588	NM_016201	A8K6F1|B7Z5Q1|E9PHW3|Q53EP1|Q96F99|Q9UKB4	Missense_Mutation	SNP	ENST00000422605.2	37		1690	0.7738095238095238	457	0.9288617886178862	238	0.6574585635359116	530	0.9265734265734266	465	0.6134564643799473	G	0.516	-0.864124	0.02590	0.874943	0.656977	ENSG00000114019	ENST00000249883;ENST00000422605;ENST00000514516;ENST00000513145	T;T;T;T	0.14266	2.6;2.52;2.53;2.52	5.48	-11.0	0.00169	.	0.051644	0.64402	N	0.000001	T	0.00012	0.0000	N	0.00182	-1.905	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;0.0	T	0.52253	-0.8600	9	0.02654	T	1	-12.5176	9.7415	0.40420	0.6518:0.1334:0.1479:0.0669	rs1353776;rs52813761;rs60017682;rs1353776	729;732;789	Q9Y2J4-3;Q9Y2J4-2;E9PHW3	.;.;.	D	732;731;789;729	ENSP00000249883:E732D;ENSP00000409999:E731D;ENSP00000424765:E789D;ENSP00000425475:E729D	ENSP00000249883:E732D	E	-	3	2	AMOTL2	135560160	0.000000	0.05858	0.000000	0.03702	0.057000	0.15508	-2.805000	0.00758	-3.529000	0.00146	-1.556000	0.00890	GAG	C|0.254;G|0.746	0.746	strong		0.642	AMOTL2-014	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000358149.1	NM_016201	
SOCS1	8651	hgsc.bcm.edu	37	16	11348810	11348810	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:11348810C>T	ENST00000332029.2	-	2	676	c.526G>A	c.(526-528)Gag>Aag	p.E176K	RMI2_ENST00000572173.1_Intron	NM_003745.1	NP_003736.1	O15524	SOCS1_HUMAN	suppressor of cytokine signaling 1	176	Interaction with Elongin BC complex. {ECO:0000250}.|SOCS box. {ECO:0000255|PROSITE- ProRule:PRU00194}.				cellular response to amino acid stimulus (GO:0071230)|cytokine-mediated signaling pathway (GO:0019221)|fat cell differentiation (GO:0045444)|interferon-gamma-mediated signaling pathway (GO:0060333)|JAK-STAT cascade (GO:0007259)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of JAK-STAT cascade (GO:0046426)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of tyrosine phosphorylation of Stat3 protein (GO:0042518)|protein ubiquitination (GO:0016567)|regulation of growth (GO:0040008)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of protein phosphorylation (GO:0001932)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|nucleus (GO:0005634)	insulin-like growth factor receptor binding (GO:0005159)|kinase inhibitor activity (GO:0019210)|protein kinase binding (GO:0019901)|protein kinase inhibitor activity (GO:0004860)	p.E176fs*35(3)|p.Y64fs*1(1)|p.R127_*212del(1)|p.V171_R179del(1)|p.0?(1)		breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(66)|lung(3)	71						CGGCACAGCTCCTGCAGCGGC	0.726			"""F, O"""		"""Hodgkin Lymphoma, PMBL"""																																p.E176K	Colon(177;456 3548 27231)	Atlas-SNP	.		Rec	yes		16	16p13.13	8651	suppressor of cytokine signaling 1		L	SOCS1,lymph_node,lymphoid_neoplasm,+2,1	SOCS1	84	1	7	Deletion - Frameshift(4)|Deletion - In frame(2)|Whole gene deletion(1)	haematopoietic_and_lymphoid_tissue(7)	c.G526A						PASS	.						6.0	7.0	7.0					16																	11348810		2122	4174	6296	SO:0001583	missense	8651	exon2			ACAGCTCCTGCAG	U88326	CCDS10546.1	16p13.13	2013-02-14			ENSG00000185338	ENSG00000185338		"""Suppressors of cytokine signaling"", ""SH2 domain containing"""	19383	protein-coding gene	gene with protein product		603597				7796808, 9266833	Standard	NM_003745		Approved	SOCS-1, SSI-1, JAB, TIP3, Cish1	uc002dar.1	O15524	OTTHUMG00000129792	ENST00000332029.2:c.526G>A	16.37:g.11348810C>T	ENSP00000329418:p.Glu176Lys	Somatic	12	0	0		WXS	Illumina HiSeq	Phase_I	17	11	0.647059	NM_003745	O15097|Q9NSA7	Missense_Mutation	SNP	ENST00000332029.2	37	CCDS10546.1	.	.	.	.	.	.	.	.	.	.	C	26.3	4.726616	0.89298	.	.	ENSG00000185338	ENST00000332029	T	0.45276	0.9	4.13	4.13	0.48395	SOCS protein, C-terminal (4);	0.126789	0.51477	U	0.000085	T	0.56746	0.2006	M	0.77616	2.38	0.53688	D	0.999977	P	0.38677	0.642	P	0.48334	0.574	T	0.64863	-0.6307	10	0.72032	D	0.01	-30.4191	15.5539	0.76177	0.0:1.0:0.0:0.0	.	176	O15524	SOCS1_HUMAN	K	176	ENSP00000329418:E176K	ENSP00000329418:E176K	E	-	1	0	SOCS1	11256311	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	2.578000	0.46051	2.141000	0.66446	0.462000	0.41574	GAG	.	.	none		0.726	SOCS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252018.1		
PKD1L1	168507	hgsc.bcm.edu	37	7	47921682	47921682	+	Splice_Site	SNP	A	A	T	rs10951936	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:47921682A>T	ENST00000289672.2	-	20	3317	c.3267T>A	c.(3265-3267)gcT>gcA	p.A1089A		NM_138295.3	NP_612152.1	Q8TDX9	PK1L1_HUMAN	polycystic kidney disease 1 like 1	1089	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						TGGTGTCCTTAGCTAGGAAGA	0.443													T|||	1238	0.247204	0.1914	0.3674	5008	,	,		16918	0.2242		0.334	False		,,,				2504	0.1718				p.A1089A		Atlas-SNP	.											.	PKD1L1	328	.	0			c.T3267A						PASS	.	T		923,3483	738.5+/-411.0	102,719,1382	56.0	50.0	52.0		3267	-0.8	0.0	7	dbSNP_120	52	2847,5753	673.7+/-403.0	457,1933,1910	yes	coding-synonymous-near-splice	PKD1L1	NM_138295.3		559,2652,3292	TT,TA,AA		33.1047,20.9487,28.9866		1089/2850	47921682	3770,9236	2203	4300	6503	SO:0001630	splice_region_variant	168507	exon20			GTCCTTAGCTAGG	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.3266-1T>A	7.37:g.47921682A>T		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	84	21	0.25	NM_138295	Q6UWK1	Silent	SNP	ENST00000289672.2	37	CCDS34633.1																																																																																			A|0.721;T|0.279	0.279	strong		0.443	PKD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340974.1	NM_138295	Silent
UTRN	7402	hgsc.bcm.edu	37	6	144852201	144852201	+	Missense_Mutation	SNP	G	G	A	rs12204734	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:144852201G>A	ENST00000367545.3	+	41	5920	c.5920G>A	c.(5920-5922)Gca>Aca	p.A1974T		NM_007124.2	NP_009055.2	P46939	UTRO_HUMAN	utrophin	1974			A -> T (in dbSNP:rs12204734).		aging (GO:0007568)|muscle cell differentiation (GO:0042692)|muscle contraction (GO:0006936)|muscle organ development (GO:0007517)|neuron projection morphogenesis (GO:0048812)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of sodium ion transmembrane transporter activity (GO:2000649)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dystrophin-associated glycoprotein complex (GO:0016010)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane (GO:0016020)|membrane raft (GO:0045121)|myofibril (GO:0030016)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|protein kinase binding (GO:0019901)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(1)|cervix(2)|endometrium(21)|kidney(10)|large_intestine(29)|lung(56)|ovary(5)|pancreas(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	148		Ovarian(120;0.218)		OV - Ovarian serous cystadenocarcinoma(155;5.72e-07)|GBM - Glioblastoma multiforme(68;4.9e-05)|Colorectal(48;0.213)		TTTTGACAGGGCAATGGAAGA	0.388													G|||	645	0.128794	0.0068	0.0965	5008	,	,		19548	0.0605		0.2018	False		,,,				2504	0.3119				p.A1974T		Atlas-SNP	.											.	UTRN	327	.	0			c.G5920A						PASS	.	G	THR/ALA	152,4254	103.8+/-142.4	2,148,2053	106.0	91.0	96.0		5920	3.6	0.9	6	dbSNP_120	96	1687,6913	309.4+/-309.4	174,1339,2787	yes	missense	UTRN	NM_007124.2	58	176,1487,4840	AA,AG,GG		19.6163,3.4498,14.1396	possibly-damaging	1974/3434	144852201	1839,11167	2203	4300	6503	SO:0001583	missense	7402	exon41			GACAGGGCAATGG	AK023675	CCDS34547.1	6q24	2008-02-05	2006-12-13		ENSG00000152818	ENSG00000152818			12635	protein-coding gene	gene with protein product		128240	"""utrophin (homologous to dystrophin)"""	DMDL		1426262	Standard	NM_007124		Approved	DRP, DRP1	uc003qkt.3	P46939	OTTHUMG00000015746	ENST00000367545.3:c.5920G>A	6.37:g.144852201G>A	ENSP00000356515:p.Ala1974Thr	Somatic	220	0	0		WXS	Illumina HiSeq	Phase_I	121	120	0.991736	NM_007124	Q5SYY1|Q5SZ57|Q9UJ40	Missense_Mutation	SNP	ENST00000367545.3	37	CCDS34547.1	226	0.10347985347985347	4	0.008130081300813009	42	0.11602209944751381	36	0.06293706293706294	144	0.18997361477572558	G	12.56	1.975171	0.34848	0.034498	0.196163	ENSG00000152818	ENST00000367545	T	0.38401	1.14	5.42	3.62	0.41486	.	0.133263	0.33834	N	0.004505	T	0.15782	0.0380	L	0.57536	1.79	0.09310	P	1.0	B	0.09022	0.002	B	0.09377	0.004	T	0.07597	-1.0764	9	0.54805	T	0.06	.	5.9968	0.19499	0.1443:0.0:0.6028:0.2529	rs12204734;rs52835986;rs60168156;rs12204734	1974	P46939	UTRO_HUMAN	T	1974	ENSP00000356515:A1974T	ENSP00000356515:A1974T	A	+	1	0	UTRN	144893894	1.000000	0.71417	0.946000	0.38457	0.624000	0.37722	1.641000	0.37197	1.296000	0.44742	0.591000	0.81541	GCA	G|0.871;A|0.129	0.129	strong		0.388	UTRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042551.1		
PHLDB3	653583	hgsc.bcm.edu	37	19	44001379	44001379	+	Missense_Mutation	SNP	T	T	C	rs11083711	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:44001379T>C	ENST00000292140.5	-	6	1076	c.716A>G	c.(715-717)cAg>cGg	p.Q239R	PHLDB3_ENST00000599242.1_Missense_Mutation_p.Q239R	NM_198850.3	NP_942147.3	Q6NSJ2	PHLB3_HUMAN	pleckstrin homology-like domain, family B, member 3	239			Q -> R (in dbSNP:rs11083711). {ECO:0000269|PubMed:15489334}.				enzyme binding (GO:0019899)			breast(1)|central_nervous_system(1)|lung(5)	7		Prostate(69;0.0153)				CTCCAGTTGCTGGAACTCCAG	0.617													T|||	403	0.0804712	0.0507	0.1859	5008	,	,		18254	0.1131		0.0596	False		,,,				2504	0.0337				p.Q239R		Atlas-SNP	.											.	PHLDB3	30	.	0			c.A716G						PASS	.	T	ARG/GLN	214,4192	128.2+/-165.1	5,204,1994	41.0	39.0	40.0		716	4.5	1.0	19	dbSNP_120	40	468,8132	136.0+/-193.2	15,438,3847	yes	missense	PHLDB3	NM_198850.3	43	20,642,5841	CC,CT,TT		5.4419,4.857,5.2437	possibly-damaging	239/641	44001379	682,12324	2203	4300	6503	SO:0001583	missense	653583	exon6			AGTTGCTGGAACT		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.716A>G	19.37:g.44001379T>C	ENSP00000292140:p.Gln239Arg	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	55	21	0.381818	NM_198850	Q8N7Z4	Missense_Mutation	SNP	ENST00000292140.5	37	CCDS12621.2	166	0.076007326007326	13	0.026422764227642278	52	0.143646408839779	57	0.09965034965034965	44	0.05804749340369393	T	16.09	3.025064	0.54683	0.04857	0.054419	ENSG00000176531	ENST00000292140	T	0.53423	0.62	4.51	4.51	0.55191	.	0.316381	0.25414	N	0.030847	T	0.00845	0.0028	M	0.66297	2.02	0.37189	P	0.09614599999999995	D;D	0.67145	0.996;0.981	D;D	0.75484	0.986;0.932	T	0.35699	-0.9778	9	0.66056	D	0.02	.	10.5883	0.45296	0.0:0.0:0.0:1.0	rs11083711;rs52805800;rs60922596;rs11083711	239;239	Q6NSJ2-2;Q6NSJ2	.;PHLB3_HUMAN	R	239	ENSP00000292140:Q239R	ENSP00000292140:Q239R	Q	-	2	0	PHLDB3	48693219	1.000000	0.71417	1.000000	0.80357	0.940000	0.58332	4.385000	0.59613	1.817000	0.53016	0.254000	0.18369	CAG	T|0.939;C|0.061	0.061	strong		0.617	PHLDB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319643.2		
IDUA	3425	hgsc.bcm.edu	37	4	996165	996165	+	Missense_Mutation	SNP	G	G	A	rs6831280	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:996165G>A	ENST00000247933.4	+	8	1169	c.1081G>A	c.(1081-1083)Gcg>Acg	p.A361T	IDUA_ENST00000514224.1_Missense_Mutation_p.A229T|IDUA_ENST00000453894.1_Missense_Mutation_p.A383T	NM_000203.3	NP_000194.2	P35475	IDUA_HUMAN	iduronidase, alpha-L-	361			A -> T (in dbSNP:rs6831280). {ECO:0000269|PubMed:15300847, ECO:0000269|PubMed:21394825, ECO:0000269|PubMed:8242073}.		carbohydrate metabolic process (GO:0005975)|cell morphogenesis (GO:0000902)|chemical homeostasis (GO:0048878)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate catabolic process (GO:0030209)|disaccharide metabolic process (GO:0005984)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|limb morphogenesis (GO:0035108)|lysosome organization (GO:0007040)|skeletal system morphogenesis (GO:0048705)|small molecule metabolic process (GO:0044281)	coated vesicle (GO:0030135)|extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)	L-iduronidase activity (GO:0003940)			breast(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(5)|upper_aerodigestive_tract(1)	12			OV - Ovarian serous cystadenocarcinoma(23;0.0158)			GCACCCCTTCGCGCAGCGCAC	0.672													G|||	1090	0.217652	0.2481	0.1095	5008	,	,		13248	0.2133		0.166	False		,,,				2504	0.3108				p.A361T		Atlas-SNP	.											.	IDUA	33	.	0			c.G1081A						PASS	.	G	THR/ALA	880,3518	316.6+/-294.7	100,680,1419	62.0	60.0	60.0		1081	-6.4	0.2	4	dbSNP_116	60	1360,7230	254.1+/-279.5	109,1142,3044	yes	missense	IDUA	NM_000203.3	58	209,1822,4463	AA,AG,GG		15.8324,20.0091,17.2467	benign	361/654	996165	2240,10748	2199	4295	6494	SO:0001583	missense	3425	exon8			CCCTTCGCGCAGC	M74715	CCDS3343.1	4p16.3	2012-10-02			ENSG00000127415	ENSG00000127415	3.2.1.76		5391	protein-coding gene	gene with protein product		252800				1832239	Standard	NM_000203		Approved	MPS1	uc003gby.3	P35475	OTTHUMG00000088901	ENST00000247933.4:c.1081G>A	4.37:g.996165G>A	ENSP00000247933:p.Ala361Thr	Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	151	73	0.483444	NM_000203	B3KWK6	Missense_Mutation	SNP	ENST00000247933.4	37	CCDS3343.1	405	0.18543956043956045	120	0.24390243902439024	42	0.11602209944751381	119	0.20804195804195805	124	0.16358839050131926	G	1.283	-0.609829	0.03690	0.200091	0.158324	ENSG00000127415	ENST00000247933;ENST00000453894;ENST00000514224	D;D;D	0.93019	-3.15;-3.15;-3.15	5.35	-6.42	0.01932	Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.644905	0.15664	N	0.250755	T	0.00039	0.0001	N	0.00595	-1.35	0.47009	P	7.200000000000539E-4	B;B	0.16802	0.019;0.004	B;B	0.09377	0.004;0.001	T	0.50750	-0.8791	9	0.05959	T	0.93	-1.0E-4	5.933	0.19150	0.4822:0.0:0.2105:0.3073	rs6831280;rs6831280	383;361	B3KWK6;P35475	.;IDUA_HUMAN	T	361;383;229	ENSP00000247933:A361T;ENSP00000396458:A383T;ENSP00000425081:A229T	ENSP00000247933:A361T	A	+	1	0	IDUA	986165	0.998000	0.40836	0.152000	0.22495	0.006000	0.05464	0.896000	0.28377	-0.673000	0.05259	-0.397000	0.06425	GCG	G|0.821;A|0.179	0.179	strong		0.672	IDUA-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000201812.1	NM_000203	
ANKK1	255239	hgsc.bcm.edu	37	11	113270828	113270828	+	Missense_Mutation	SNP	G	G	A	rs1800497	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:113270828G>A	ENST00000303941.3	+	8	2231	c.2137G>A	c.(2137-2139)Gag>Aag	p.E713K		NM_178510.1	NP_848605.1	Q8NFD2	ANKK1_HUMAN	ankyrin repeat and kinase domain containing 1	713			E -> K (in dbSNP:rs1800497). {ECO:0000269|PubMed:14741327, ECO:0000269|PubMed:17344846}.				ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(2)|lung(14)|ovary(1)|stomach(1)	29		all_cancers(61;1.53e-11)|all_epithelial(67;3e-06)|Melanoma(852;4.04e-05)|all_hematologic(158;0.000315)|Acute lymphoblastic leukemia(157;0.000966)|Breast(348;0.0461)|Medulloblastoma(222;0.0523)|all_neural(223;0.0663)|Prostate(24;0.194)		BRCA - Breast invasive adenocarcinoma(274;4.82e-06)|Epithelial(105;5.41e-05)|all cancers(92;0.000442)|OV - Ovarian serous cystadenocarcinoma(223;0.238)		AGTGCTGGTCGAGGCAGGCGC	0.637													A|||	1631	0.325679	0.385	0.3112	5008	,	,		20348	0.4058		0.1879	False		,,,				2504	0.3149				p.E713K		Atlas-SNP	.											.	ANKK1	83	.	0			c.G2137A	GRCh37	CM041241	ANKK1	M	rs1800497	PASS	.	A	LYS/GLU	1351,2783		230,891,946	21.0	26.0	24.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	2137	2.0	0.1	11	dbSNP_89	24	1598,6796		160,1278,2759	yes	missense	ANKK1	NM_178510.1	56	390,2169,3705	AA,AG,GG		19.0374,32.6802,23.5393	benign	713/766	113270828	2949,9579	2067	4197	6264	SO:0001583	missense	255239	exon8			CTGGTCGAGGCAG	AJ541797	CCDS44734.1	11q23.2	2013-01-10			ENSG00000170209	ENSG00000170209		"""Ankyrin repeat domain containing"""	21027	protein-coding gene	gene with protein product		608774				15146457	Standard	NM_178510		Approved	X-kinase	uc001pny.3	Q8NFD2	OTTHUMG00000167715	ENST00000303941.3:c.2137G>A	11.37:g.113270828G>A	ENSP00000306678:p.Glu713Lys	Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	166	31	0.186747	NM_178510		Missense_Mutation	SNP	ENST00000303941.3	37	CCDS44734.1	647	0.29624542124542125	188	0.3821138211382114	100	0.27624309392265195	222	0.3881118881118881	137	0.18073878627968337	A	0.006	-2.089378	0.00367	0.326802	0.190374	ENSG00000170209	ENST00000303941	T	0.65732	-0.17	4.42	1.98	0.26296	Ankyrin repeat-containing domain (3);	0.914415	0.09102	N	0.848445	T	0.00012	0.0000	N	0.17800	0.525	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.33137	-0.9880	9	0.05833	T	0.94	-2.6564	1.1851	0.01854	0.5313:0.1533:0.1676:0.1478	rs1800497;rs4134623;rs4245144;rs59538675;rs1800497	713	Q8NFD2	ANKK1_HUMAN	K	713	ENSP00000306678:E713K	ENSP00000306678:E713K	E	+	1	0	ANKK1	112776038	0.001000	0.12720	0.054000	0.19295	0.051000	0.14879	0.411000	0.21115	-0.053000	0.13289	-0.439000	0.05793	GAG	G|0.703;A|0.297	0.297	strong		0.637	ANKK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395830.1	NM_178510	
AGAP11	119385	hgsc.bcm.edu	37	10	88768423	88768423	+	RNA	SNP	A	A	G	rs2641562	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	121	0	0		WXS	Illumina HiSeq	Phase_I	86	47	0.546512	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	
HTR1B	3351	hgsc.bcm.edu	37	6	78173018	78173018	+	Missense_Mutation	SNP	C	C	T	rs200659363		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:78173018C>T	ENST00000369947.2	-	1	472	c.103G>A	c.(103-105)Gcc>Acc	p.A35T		NM_000863.1	NP_000854.1	P28222	5HT1B_HUMAN	5-hydroxytryptamine (serotonin) receptor 1B, G protein-coupled	35					adenylate cyclase-inhibiting serotonin receptor signaling pathway (GO:0007198)|bone remodeling (GO:0046849)|cellular response to alkaloid (GO:0071312)|cellular response to drug (GO:0035690)|cellular response to temperature stimulus (GO:0071502)|drinking behavior (GO:0042756)|G-protein coupled receptor internalization (GO:0002031)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|negative regulation of cAMP biosynthetic process (GO:0030818)|negative regulation of serotonin secretion (GO:0014063)|negative regulation of synaptic transmission, GABAergic (GO:0032229)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of behavior (GO:0050795)|regulation of dopamine secretion (GO:0014059)|response to cocaine (GO:0042220)|response to ethanol (GO:0045471)|response to mineralocorticoid (GO:0051385)|synaptic transmission (GO:0007268)|vasoconstriction (GO:0042310)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	drug binding (GO:0008144)|serotonin binding (GO:0051378)|serotonin receptor activity (GO:0004993)	p.A35T(1)		NS(1)|breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(9)|prostate(2)|upper_aerodigestive_tract(2)	25		all_cancers(76;0.0867)|Acute lymphoblastic leukemia(125;0.00119)|all_hematologic(105;0.0332)		BRCA - Breast invasive adenocarcinoma(397;0.205)	Almotriptan(DB00918)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Apomorphine(DB00714)|Aripiprazole(DB01238)|Asenapine(DB06216)|Bopindolol(DB08807)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Clozapine(DB00363)|Dihydroergotamine(DB00320)|Eletriptan(DB00216)|Ergoloid mesylate(DB01049)|Ergotamine(DB00696)|Frovatriptan(DB00998)|Ketamine(DB01221)|Lisuride(DB00589)|Loxapine(DB00408)|Methysergide(DB00247)|Naratriptan(DB00952)|Olanzapine(DB00334)|Ondansetron(DB00904)|Penbutolol(DB01359)|Pergolide(DB01186)|Pindolol(DB00960)|Pramipexole(DB00413)|Propranolol(DB00571)|Quetiapine(DB01224)|Rizatriptan(DB00953)|Ropinirole(DB00268)|Sumatriptan(DB00669)|Yohimbine(DB01392)|Ziprasidone(DB00246)|Zolmitriptan(DB00315)	TAGTCCTTGGCGCTGCAGTTT	0.597																																					p.A35T		Atlas-SNP	.											HTR1B,rectum,carcinoma,0,1	HTR1B	55	1	1	Substitution - Missense(1)	large_intestine(1)	c.G103A						scavenged	.						152.0	136.0	141.0					6																	78173018		2203	4300	6503	SO:0001583	missense	3351	exon1			CCTTGGCGCTGCA	BC069065	CCDS4986.1	6q13	2012-08-08	2012-02-03		ENSG00000135312	ENSG00000135312		"""5-HT (serotonin) receptors"", ""GPCR / Class A : 5-HT (serotonin) receptors, GPCR only"""	5287	protein-coding gene	gene with protein product		182131	"""5-hydroxytryptamine (serotonin) receptor 1B"""			1348246, 11247661	Standard	NM_000863		Approved	S12, 5-HT1B, HTR1D2, 5-HT1DB	uc003pil.1	P28222	OTTHUMG00000015066	ENST00000369947.2:c.103G>A	6.37:g.78173018C>T	ENSP00000358963:p.Ala35Thr	Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	185	4	0.0216216	NM_000863	Q4VAY7	Missense_Mutation	SNP	ENST00000369947.2	37	CCDS4986.1	.	.	.	.	.	.	.	.	.	.	C	0.322	-0.961104	0.02249	.	.	ENSG00000135312	ENST00000369947	T	0.34859	1.34	4.6	-1.32	0.09201	.	1.768550	0.03522	N	0.221110	T	0.06050	0.0157	N	0.12182	0.205	0.09310	N	0.999993	B	0.10296	0.003	B	0.04013	0.001	T	0.18650	-1.0330	9	.	.	.	.	5.1226	0.14867	0.2111:0.5528:0.096:0.1401	.	35	P28222	5HT1B_HUMAN	T	35	ENSP00000358963:A35T	.	A	-	1	0	HTR1B	78229737	0.314000	0.24563	0.079000	0.20413	0.098000	0.18820	0.201000	0.17276	-0.338000	0.08413	-1.134000	0.01955	GCC	.	.	weak		0.597	HTR1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041292.1	NM_000863	
BPIFB2	80341	hgsc.bcm.edu	37	20	31601670	31601670	+	Silent	SNP	C	C	T	rs45589833	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:31601670C>T	ENST00000170150.3	+	5	558	c.363C>T	c.(361-363)cgC>cgT	p.R121R		NM_025227.1	NP_079503.1	Q8N4F0	BPIB2_HUMAN	BPI fold containing family B, member 2	121						extracellular vesicular exosome (GO:0070062)	lipid binding (GO:0008289)										CTGACACCCGCGTGACCCAGA	0.637													C|||	67	0.0133786	0.0023	0.0245	5008	,	,		17585	0.001		0.0348	False		,,,				2504	0.0112				p.R121R		Atlas-SNP	.											.	.	.	.	0			c.C363T						PASS	.	C		37,4369	40.8+/-73.8	0,37,2166	50.0	48.0	49.0		363	-6.7	0.0	20	dbSNP_127	49	354,8246	119.2+/-178.6	11,332,3957	no	coding-synonymous	BPIFB2	NM_025227.1		11,369,6123	TT,TC,CC		4.1163,0.8398,3.0063		121/459	31601670	391,12615	2203	4300	6503	SO:0001819	synonymous_variant	80341	exon5			CACCCGCGTGACC	AF465765	CCDS13210.1	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000078898	ENSG00000078898		"""BPI fold containing"""	16177	protein-coding gene	gene with protein product		614108	"""bactericidal/permeability-increasing protein-like 1"""	C20orf184, BPIL1		12185532, 21787333	Standard	NM_025227		Approved	dJ726C3.2, LPLUNC2	uc002wyj.4	Q8N4F0	OTTHUMG00000032232	ENST00000170150.3:c.363C>T	20.37:g.31601670C>T		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	92	43	0.467391	NM_025227	Q6UWN3|Q6ZME0|Q8NFQ7	Silent	SNP	ENST00000170150.3	37	CCDS13210.1																																																																																			C|0.975;T|0.025	0.025	strong		0.637	BPIFB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078652.2	NM_025227	
LPPR1	54886	hgsc.bcm.edu	37	9	103947810	103947810	+	Missense_Mutation	SNP	T	T	G	rs41296085	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:103947810T>G	ENST00000374874.3	+	2	473	c.34T>G	c.(34-36)Tcc>Gcc	p.S12A	LPPR1_ENST00000395056.2_Missense_Mutation_p.S12A|LPPR1_ENST00000494890.1_3'UTR	NM_207299.1	NP_997182.1	Q8TBJ4	LPPR1_HUMAN		12					nervous system development (GO:0007399)	integral component of membrane (GO:0016021)	catalytic activity (GO:0003824)										ACGAAGTTATTCCATCATCCC	0.338													T|||	42	0.00838658	0.0	0.0144	5008	,	,		16008	0.0		0.0169	False		,,,				2504	0.0153				p.S12A		Atlas-SNP	.											.	.	.	.	0			c.T34G						PASS	.	T	ALA/SER,ALA/SER	17,4389	24.3+/-50.5	0,17,2186	221.0	202.0	208.0		34,34	5.9	1.0	9	dbSNP_127	208	133,8467	67.3+/-129.8	1,131,4168	yes	missense,missense	LPPR1	NM_017753.2,NM_207299.1	99,99	1,148,6354	GG,GT,TT		1.5465,0.3858,1.1533	benign,benign	12/326,12/326	103947810	150,12856	2203	4300	6503	SO:0001583	missense	0	exon2			AGTTATTCCATCA																												ENST00000374874.3:c.34T>G	9.37:g.103947810T>G	ENSP00000364008:p.Ser12Ala	Somatic	246	0	0		WXS	Illumina HiSeq	Phase_I	227	111	0.488987	NM_207299	Q5VX23|Q9NXE2	Missense_Mutation	SNP	ENST00000374874.3	37	CCDS6751.1	20	0.009157509157509158	0	0.0	6	0.016574585635359115	0	0.0	14	0.018469656992084433	T	15.22	2.768539	0.49680	0.003858	0.015465	ENSG00000148123	ENST00000374874;ENST00000456287;ENST00000374871;ENST00000395056	T;T;T	0.38077	1.16;1.16;1.16	5.93	5.93	0.95920	.	0.431258	0.25774	N	0.028386	T	0.23094	0.0558	M	0.65498	2.005	0.34363	D	0.691192	B	0.02656	0.0	B	0.08055	0.003	T	0.40384	-0.9566	10	0.34782	T	0.22	-32.2815	14.3318	0.66561	0.0:0.0:0.0:1.0	rs41296085;rs61755095	12	Q8TBJ4	LPPR1_HUMAN	A	12	ENSP00000364008:S12A;ENSP00000410223:S12A;ENSP00000378496:S12A	ENSP00000364005:S12A	S	+	1	0	RP11-35N6.1	102987631	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.743000	0.62110	2.271000	0.75665	0.533000	0.62120	TCC	T|0.990;G|0.010	0.010	strong		0.338	LPPR1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053425.1		
FMO2	2327	hgsc.bcm.edu	37	1	171154959	171154959	+	Missense_Mutation	SNP	A	A	G	rs2020870	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	119	0	0		WXS	Illumina HiSeq	Phase_I	106	45	0.424528	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	
OBSCN	84033	hgsc.bcm.edu	37	1	228476414	228476414	+	Silent	SNP	G	G	A	rs3795791	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:228476414G>A	ENST00000422127.1	+	38	10208	c.10164G>A	c.(10162-10164)gcG>gcA	p.A3388A	OBSCN_ENST00000284548.11_Silent_p.A3388A|OBSCN_ENST00000359599.6_Silent_p.A2235A|OBSCN_ENST00000570156.2_Silent_p.A3817A|OBSCN_ENST00000366709.4_Silent_p.A507A|OBSCN_ENST00000366707.4_Silent_p.A507A	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	3388	Ig-like 34.				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)				TGAGCAAGGCGGCCCCCGTGG	0.627													G|||	470	0.0938498	0.0439	0.013	5008	,	,		20753	0.3175		0.0258	False		,,,				2504	0.0583				p.A3817A		Atlas-SNP	.											.	OBSCN	2142	.	0			c.G11451A						PASS	.	G	,	193,3981		5,183,1899	88.0	97.0	94.0		10164,10164	-4.2	0.0	1	dbSNP_107	94	156,8232		0,156,4038	no	coding-synonymous,coding-synonymous	OBSCN	NM_001098623.1,NM_052843.2	,	5,339,5937	AA,AG,GG		1.8598,4.6239,2.7782	,	3388/7969,3388/6621	228476414	349,12213	2087	4194	6281	SO:0001819	synonymous_variant	84033	exon43			CAAGGCGGCCCCC	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.10164G>A	1.37:g.228476414G>A		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	96	54	0.5625	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|0.910;A|0.090	0.090	strong		0.627	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
CEP63	80254	hgsc.bcm.edu	37	3	134278270	134278270	+	Splice_Site	SNP	C	C	T	rs1127826	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:134278270C>T	ENST00000337090.3	+	14	2125	c.1952C>T	c.(1951-1953)tCg>tTg	p.S651L	CEP63_ENST00000606977.1_Splice_Site_p.S651L|CEP63_ENST00000513612.2_Splice_Site_p.S651L|CEP63_ENST00000383229.3_Intron|CEP63_ENST00000332047.5_Intron|CEP63_ENST00000354446.3_Intron			Q96MT8	CEP63_HUMAN	centrosomal protein 63kDa	651			S -> L (in dbSNP:rs1127826).		centriole replication (GO:0007099)|DNA damage checkpoint (GO:0000077)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|signal transduction in response to DNA damage (GO:0042770)|spindle assembly (GO:0051225)	centriole (GO:0005814)|centrosome (GO:0005813)|cytosol (GO:0005829)|spindle pole (GO:0000922)				kidney(1)|large_intestine(6)|lung(12)|ovary(1)|prostate(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	27						TTTATATCTTCGGTATGGAAA	0.313													C|||	1638	0.327077	0.0219	0.5288	5008	,	,		19506	0.6002		0.3668	False		,,,				2504	0.274				p.S651L		Atlas-SNP	.											.	CEP63	56	.	0			c.C1952T						PASS	.	C	,,,LEU/SER	402,4004	187.4+/-214.1	17,368,1818	47.0	46.0	47.0		,,,1952	-2.9	0.8	3	dbSNP_86	47	3075,5525	463.1+/-365.9	531,2013,1756	yes	intron,intron,intron,missense-near-splice	CEP63	NM_001042383.1,NM_001042384.1,NM_001042400.1,NM_025180.3	,,,145	548,2381,3574	TT,TC,CC		35.7558,9.1239,26.7338	,,,possibly-damaging	,,,651/704	134278270	3477,9529	2203	4300	6503	SO:0001630	splice_region_variant	80254	exon15			TATCTTCGGTATG	AK056465	CCDS3086.1, CCDS43152.1, CCDS43153.1, CCDS43154.1	3q22.1	2014-02-20			ENSG00000182923	ENSG00000182923			25815	protein-coding gene	gene with protein product		614724				14654843, 24240477	Standard	NM_001042383		Approved	FLJ13386	uc003eqo.1	Q96MT8	OTTHUMG00000159725	ENST00000337090.3:c.1953+1C>T	3.37:g.134278270C>T		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	64	27	0.421875	NM_025180	D3DND8|D3DND9|D3DNE0|Q96CR0|Q9H8F5|Q9H8N0	Missense_Mutation	SNP	ENST00000337090.3	37	CCDS3086.1	796	0.36446886446886445	20	0.04065040650406504	166	0.4585635359116022	341	0.5961538461538461	269	0.3548812664907652	C	12.56	1.975602	0.34848	0.091239	0.357558	ENSG00000182923	ENST00000337090;ENST00000513612	T;T	0.18016	2.24;2.24	5.35	-2.93	0.05598	.	0.948307	0.08789	N	0.893552	T	0.00012	0.0000	L	0.38531	1.155	0.09310	P	0.9999999403245	B	0.06786	0.001	B	0.06405	0.002	T	0.42616	-0.9441	9	0.26408	T	0.33	1.3872	6.7487	0.23475	0.1413:0.1855:0.0:0.6732	rs1127826;rs9868985;rs17352684;rs52808223;rs57512520;rs9868985	651	Q96MT8	CEP63_HUMAN	L	651	ENSP00000336524:S651L;ENSP00000426129:S651L	ENSP00000336524:S651L	S	+	2	0	CEP63	135760960	0.998000	0.40836	0.840000	0.33206	0.950000	0.60333	0.235000	0.17948	-0.737000	0.04824	-0.142000	0.14014	TCG	C|0.695;T|0.305	0.305	strong		0.313	CEP63-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000470139.1	NM_025180	Missense_Mutation
LY75	4065	hgsc.bcm.edu	37	2	160737621	160737621	+	Silent	SNP	C	C	T	rs11675155	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:160737621C>T	ENST00000263636.4	-	8	1404	c.1377G>A	c.(1375-1377)acG>acA	p.T459T	LY75_ENST00000554112.1_Silent_p.T459T|LY75_ENST00000553424.1_Silent_p.T459T|LY75-CD302_ENST00000504764.1_Silent_p.T459T|LY75-CD302_ENST00000505052.1_Silent_p.T459T	NM_002349.3	NP_002340.2	O60449	LY75_HUMAN	lymphocyte antigen 75	459	C-type lectin 2. {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)	p.T459T(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)		CACAGTTGGGCGTCTTATTGT	0.368													C|||	1097	0.21905	0.1218	0.3746	5008	,	,		19539	0.3224		0.165	False		,,,				2504	0.1892				p.T459T		Atlas-SNP	.											LY75,NS,carcinoma,0,1	LY75	151	1	1	Substitution - coding silent(1)	prostate(1)	c.G1377A						PASS	.	C	,,	598,3808	264.1+/-265.8	45,508,1650	171.0	154.0	160.0		1377,1377,1377	-0.8	1.0	2	dbSNP_120	160	1508,7092	285.8+/-297.4	120,1268,2912	no	coding-synonymous,coding-synonymous,coding-synonymous	LY75,LY75-CD302	NM_001198759.1,NM_001198760.1,NM_002349.3	,,	165,1776,4562	TT,TC,CC		17.5349,13.5724,16.1925	,,	459/1874,459/1818,459/1723	160737621	2106,10900	2203	4300	6503	SO:0001819	synonymous_variant	4065	exon8			GTTGGGCGTCTTA	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.1377G>A	2.37:g.160737621C>T		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	105	39	0.371429	NM_002349	O75913|Q53R46|Q53TF5|Q7Z575|Q7Z577	Silent	SNP	ENST00000263636.4	37	CCDS2211.1																																																																																			C|0.818;T|0.182	0.182	strong		0.368	LY75-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255035.1		
FUK	197258	hgsc.bcm.edu	37	16	70512349	70512349	+	Missense_Mutation	SNP	G	G	A	rs17886060	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:70512349G>A	ENST00000288078.6	+	21	3048	c.2816G>A	c.(2815-2817)cGg>cAg	p.R939Q	FUK_ENST00000378912.2_Missense_Mutation_p.R945Q|FUK_ENST00000571514.1_Missense_Mutation_p.R430Q	NM_145059.2	NP_659496.2	Q8N0W3	FUK_HUMAN	fucokinase	939			R -> Q (in dbSNP:rs17886060). {ECO:0000269|Ref.3}.|R -> W (in dbSNP:rs17883248). {ECO:0000269|Ref.3}.			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)				CGCCTGGCTCGGAACCTGCTG	0.647													G|||	22	0.00439297	0.0008	0.0043	5008	,	,		18862	0.0		0.0109	False		,,,				2504	0.0072				p.R939Q		Atlas-SNP	.											.	FUK	72	.	0			c.G2816A						PASS	.	G	GLN/ARG	7,4041		0,7,2017	60.0	65.0	63.0		2816	5.7	1.0	16	dbSNP_124	63	120,8240		1,118,4061	yes	missense	FUK	NM_145059.2	43	1,125,6078	AA,AG,GG		1.4354,0.1729,1.0235	probably-damaging	939/1085	70512349	127,12281	2024	4180	6204	SO:0001583	missense	197258	exon21			TGGCTCGGAACCT		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.2816G>A	16.37:g.70512349G>A	ENSP00000288078:p.Arg939Gln	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	73	49	0.671233	NM_145059	Q5PSM3|Q5XKL6|Q6ZRA0|Q96MT9	Missense_Mutation	SNP	ENST00000288078.6	37	CCDS10891.2	10	0.004578754578754579	0	0.0	1	0.0027624309392265192	0	0.0	9	0.011873350923482849	G	16.72	3.200151	0.58126	0.001729	0.014354	ENSG00000157353	ENST00000288078;ENST00000378912;ENST00000538525	D;D	0.93712	-3.27;-3.27	5.65	5.65	0.86999	.	0.050215	0.85682	D	0.000000	D	0.96021	0.8704	M	0.86028	2.79	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.74348	0.983;0.926;0.926	D	0.95082	0.8214	10	0.59425	D	0.04	-30.887	19.7405	0.96228	0.0:0.0:1.0:0.0	rs17886060;rs17886060	945;845;939	Q8N0W3-2;B2RDL5;Q8N0W3	.;.;FUK_HUMAN	Q	939;945;253	ENSP00000288078:R939Q;ENSP00000368192:R945Q	ENSP00000288078:R939Q	R	+	2	0	FUK	69069850	1.000000	0.71417	0.996000	0.52242	0.977000	0.68977	6.263000	0.72521	2.655000	0.90218	0.655000	0.94253	CGG	G|0.990;A|0.010	0.010	strong		0.647	FUK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157291.2	NM_145059	
SPHKAP	80309	hgsc.bcm.edu	37	2	228882970	228882970	+	Missense_Mutation	SNP	T	T	C	rs3828161	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:228882970T>C	ENST00000392056.3	-	7	2646	c.2600A>G	c.(2599-2601)cAg>cGg	p.Q867R	SPHKAP_ENST00000344657.5_Missense_Mutation_p.Q867R	NM_001142644.1	NP_001136116.1	Q2M3C7	SPKAP_HUMAN	SPHK1 interactor, AKAP domain containing	867			Q -> R (in dbSNP:rs3828161).			extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|Z disc (GO:0030018)	protein kinase A binding (GO:0051018)			NS(5)|breast(5)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(25)|lung(86)|ovary(6)|pancreas(1)|prostate(6)|skin(17)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	185		Renal(207;0.025)|all_hematologic(139;0.15)|all_lung(227;0.204)|Acute lymphoblastic leukemia(138;0.205)|Esophageal squamous(248;0.23)		Epithelial(121;8.17e-11)|all cancers(144;7.92e-08)|Lung(261;0.0168)|LUSC - Lung squamous cell carcinoma(224;0.0232)		ACTTCTGGACTGGCTGACCGT	0.493													T|||	1235	0.246605	0.2874	0.2795	5008	,	,		20550	0.3998		0.1581	False		,,,				2504	0.1012				p.Q867R		Atlas-SNP	.											SPHKAP_ENST00000392056,colon,carcinoma,0,2	SPHKAP	750	2	0			c.A2600G						PASS	.	T	ARG/GLN,ARG/GLN	1280,3126	435.9+/-344.5	195,890,1118	584.0	558.0	567.0		2600,2600	-0.8	0.0	2	dbSNP_107	567	1370,7230	267.6+/-287.4	110,1150,3040	yes	missense,missense	SPHKAP	NM_001142644.1,NM_030623.3	43,43	305,2040,4158	CC,CT,TT		15.9302,29.0513,20.3752	benign,benign	867/1701,867/1672	228882970	2650,10356	2203	4300	6503	SO:0001583	missense	80309	exon7			CTGGACTGGCTGA		CCDS33389.1, CCDS46537.1	2q36.3	2010-08-20			ENSG00000153820	ENSG00000153820		"""A-kinase anchor proteins"""	30619	protein-coding gene	gene with protein product	"""sphingosine kinase type 1-interacting protein"""	611646				12080051, 11214970	Standard	NM_030623		Approved	SKIP	uc002vpq.2	Q2M3C7	OTTHUMG00000153584	ENST00000392056.3:c.2600A>G	2.37:g.228882970T>C	ENSP00000375909:p.Gln867Arg	Somatic	305	0	0		WXS	Illumina HiSeq	Phase_I	214	107	0.5	NM_030623	Q68DA3|Q68DR8|Q9C0I5	Missense_Mutation	SNP	ENST00000392056.3	37	CCDS46537.1	548	0.2509157509157509	138	0.2804878048780488	77	0.212707182320442	218	0.3811188811188811	115	0.1517150395778364	T	0.527	-0.859464	0.02610	0.290513	0.159302	ENSG00000153820	ENST00000392056;ENST00000344657	T;T	0.11169	2.8;2.8	6.17	-0.751	0.11076	.	0.584522	0.18502	N	0.139308	T	0.00012	0.0000	L	0.36672	1.1	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.06405	0.0;0.002	T	0.48547	-0.9026	9	0.22706	T	0.39	.	11.3332	0.49487	0.0:0.3465:0.0:0.6535	rs3828161;rs56528711;rs57833139;rs3828161	867;867	Q2M3C7;Q2M3C7-2	SPKAP_HUMAN;.	R	867	ENSP00000375909:Q867R;ENSP00000339886:Q867R	ENSP00000339886:Q867R	Q	-	2	0	SPHKAP	228591214	0.002000	0.14202	0.000000	0.03702	0.015000	0.08874	1.086000	0.30853	-0.029000	0.13827	0.533000	0.62120	CAG	T|0.776;C|0.224	0.224	strong		0.493	SPHKAP-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331750.1	NM_030623	
LAMC1	3915	hgsc.bcm.edu	37	1	183072701	183072701	+	Silent	SNP	C	C	T	rs2296289	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:183072701C>T	ENST00000258341.4	+	2	914	c.657C>T	c.(655-657)aaC>aaT	p.N219N		NM_002293.3	NP_002284.3	P11047	LAMC1_HUMAN	laminin, gamma 1 (formerly LAMB2)	219	Laminin N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00466}.				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						CTGGGGGCAACGTGGCCTTTT	0.547													C|||	595	0.11881	0.0227	0.2219	5008	,	,		19990	0.1091		0.1064	False		,,,				2504	0.1984				p.N219N		Atlas-SNP	.											.	LAMC1	176	.	0			c.C657T						PASS	.	C		201,4205	124.5+/-161.8	4,193,2006	77.0	70.0	72.0		657	-6.5	0.8	1	dbSNP_100	72	1045,7555	221.3+/-258.8	59,927,3314	no	coding-synonymous	LAMC1	NM_002293.3		63,1120,5320	TT,TC,CC		12.1512,4.562,9.5802		219/1610	183072701	1246,11760	2203	4300	6503	SO:0001819	synonymous_variant	3915	exon2			GGGCAACGTGGCC	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.657C>T	1.37:g.183072701C>T		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	78	46	0.589744	NM_002293	Q5VYE7	Silent	SNP	ENST00000258341.4	37	CCDS1351.1																																																																																			C|0.900;T|0.100	0.100	strong		0.547	LAMC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085954.2	NM_002293	
MATN4	8785	hgsc.bcm.edu	37	20	43933196	43933196	+	Silent	SNP	C	C	T	rs2233093	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:43933196C>T	ENST00000372754.1	-	2	323	c.315G>A	c.(313-315)gtG>gtA	p.V105V	RBPJL_ENST00000343694.3_5'Flank|RBPJL_ENST00000372743.1_5'Flank|MATN4_ENST00000360607.6_Silent_p.V105V|MATN4_ENST00000372751.4_Intron|MATN4_ENST00000372756.1_Silent_p.V105V|MATN4_ENST00000342716.4_Silent_p.V105V|MATN4_ENST00000353917.5_Silent_p.V105V|RBPJL_ENST00000372741.3_5'Flank|MATN4_ENST00000537548.1_Silent_p.V105V			O95460	MATN4_HUMAN	matrilin 4	105	VWFA 1. {ECO:0000255|PROSITE- ProRule:PRU00219}.				extracellular matrix organization (GO:0030198)|response to axon injury (GO:0048678)	extracellular region (GO:0005576)				central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(7)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	27		Myeloproliferative disorder(115;0.0122)				GCGCCAGAGGCACCAGGTCGC	0.662													C|||	858	0.171326	0.295	0.1556	5008	,	,		17451	0.0159		0.2087	False		,,,				2504	0.137				p.V105V		Atlas-SNP	.											.	MATN4	57	.	0			c.G315A						PASS	.	C	,,	1213,3187		174,865,1161	22.0	19.0	20.0		315,315,315	2.7	1.0	20	dbSNP_98	20	1913,6671		215,1483,2594	no	coding-synonymous,coding-synonymous,coding-synonymous	MATN4	NM_003833.3,NM_030590.2,NM_030592.2	,,	389,2348,3755	TT,TC,CC		22.2856,27.5682,24.0758	,,	105/582,105/541,105/500	43933196	3126,9858	2200	4292	6492	SO:0001819	synonymous_variant	8785	exon3			CAGAGGCACCAGG	AJ007581	CCDS13348.1, CCDS46607.1	20q13.1-q13.2	2008-07-07			ENSG00000124159	ENSG00000124159			6910	protein-coding gene	gene with protein product		603897				9827539, 9027493	Standard	NM_003833		Approved		uc002xnn.2	O95460	OTTHUMG00000033043	ENST00000372754.1:c.315G>A	20.37:g.43933196C>T		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	103	70	0.679612	NM_030592	A6NH94|A6NKN5|Q5QPU2|Q5QPU3|Q5QPU4|Q8N2M5|Q8N2M7|Q9H1F8|Q9H1F9	Silent	SNP	ENST00000372754.1	37																																																																																				C|0.801;T|0.199	0.199	strong		0.662	MATN4-002	KNOWN	non_canonical_conserved|non_canonical_U12|not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000080335.1		
DOCK1	1793	hgsc.bcm.edu	37	10	128830409	128830409	+	Silent	SNP	A	A	G	rs2229597	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:128830409A>G	ENST00000280333.6	+	18	1783	c.1674A>G	c.(1672-1674)gcA>gcG	p.A558A		NM_001380.3	NP_001371.1	Q14185	DOCK1_HUMAN	dedicator of cytokinesis 1	558	DHR-1.				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)		AGGCCGAAGCAAAGAAGCTGG	0.512													G|||	631	0.125998	0.0461	0.2003	5008	,	,		19625	0.0873		0.2137	False		,,,				2504	0.1309				p.A558A		Atlas-SNP	.											.	DOCK1	188	.	0			c.A1674G						PASS	.	G		287,3851		7,273,1789	24.0	24.0	24.0		1629	-7.7	0.1	10	dbSNP_98	24	1798,6626		196,1406,2610	no	coding-synonymous	DOCK1	NM_001380.3		203,1679,4399	GG,GA,AA		21.3438,6.9357,16.5977		543/1851	128830409	2085,10477	2069	4212	6281	SO:0001819	synonymous_variant	1793	exon18			CGAAGCAAAGAAG	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.1674A>G	10.37:g.128830409A>G		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	80	49	0.6125	NM_001380	A9Z1Z5	Silent	SNP	ENST00000280333.6	37																																																																																				A|0.857;G|0.143	0.143	strong		0.512	DOCK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050979.2	NM_001380	
EPHA3	2042	hgsc.bcm.edu	37	3	89521725	89521725	+	Silent	SNP	T	T	C	rs1054750	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:89521725T>C	ENST00000336596.2	+	16	3027	c.2802T>C	c.(2800-2802)ggT>ggC	p.G934G	EPHA3_ENST00000494014.1_Intron	NM_005233.5	NP_005224.2	P29320	EPHA3_HUMAN	EPH receptor A3	934	SAM. {ECO:0000255|PROSITE- ProRule:PRU00184}.				cell adhesion (GO:0007155)|cell migration (GO:0016477)|cellular response to retinoic acid (GO:0071300)|ephrin receptor signaling pathway (GO:0048013)|fasciculation of motor neuron axon (GO:0097156)|fasciculation of sensory neuron axon (GO:0097155)|positive regulation of neuron projection development (GO:0010976)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of epithelial to mesenchymal transition (GO:0010717)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule cytoskeleton organization (GO:0070507)|regulation of Rho GTPase activity (GO:0032319)	early endosome (GO:0005769)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|GPI-linked ephrin receptor activity (GO:0005004)			NS(1)|breast(4)|central_nervous_system(4)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(26)|liver(3)|lung(67)|ovary(7)|pancreas(1)|prostate(4)|skin(8)|stomach(1)|upper_aerodigestive_tract(5)	139	all_cancers(8;0.0406)|Melanoma(1;0.00142)|all_epithelial(1;0.0612)	Lung NSC(201;0.0782)		LUSC - Lung squamous cell carcinoma(29;0.00344)|Lung(72;0.00942)		TCTTCACGGGTGTGGAGTACA	0.413										TSP Lung(6;0.00050)			C|||	649	0.129593	0.0688	0.1916	5008	,	,		19868	0.0813		0.2594	False		,,,				2504	0.0838				p.G934G		Atlas-SNP	.											EPHA3,NS,malignant_melanoma,+2,1	EPHA3	501	1	0			c.T2802C						PASS	.	C		390,4016	790.6+/-415.0	21,348,1834	115.0	105.0	109.0		2802	1.7	1.0	3	dbSNP_86	109	2040,6560	720.3+/-406.3	234,1572,2494	no	coding-synonymous	EPHA3	NM_005233.5		255,1920,4328	CC,CT,TT		23.7209,8.8516,18.6837		934/984	89521725	2430,10576	2203	4300	6503	SO:0001819	synonymous_variant	2042	exon16			CACGGGTGTGGAG	M83941	CCDS2922.1, CCDS46875.1	3p11.2	2013-02-11	2004-10-28		ENSG00000044524	ENSG00000044524	2.7.10.1	"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3387	protein-coding gene	gene with protein product		179611	"""EphA3"""	ETK, ETK1, TYRO4		1737782, 1311845	Standard	NM_005233		Approved	HEK, HEK4	uc003dqy.3	P29320	OTTHUMG00000159040	ENST00000336596.2:c.2802T>C	3.37:g.89521725T>C		Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	68	67	0.985294	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	
OBSCN	84033	hgsc.bcm.edu	37	1	228526665	228526665	+	Silent	SNP	T	T	C	rs505629	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:228526665T>C	ENST00000422127.1	+	69	17240	c.17196T>C	c.(17194-17196)gcT>gcC	p.A5732A	OBSCN_ENST00000284548.11_Silent_p.A5732A|OBSCN_ENST00000570156.2_Silent_p.A6689A|OBSCN_ENST00000366709.4_Silent_p.A2851A|OBSCN_ENST00000366707.4_Silent_p.A3366A	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	234	1	0.0042735		WXS	Illumina HiSeq	Phase_I	159	158	0.993711	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	
OR2T34	127068	hgsc.bcm.edu	37	1	248737454	248737454	+	Missense_Mutation	SNP	A	A	G	rs79750523	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:248737454A>G	ENST00000328782.2	-	1	626	c.605T>C	c.(604-606)aTg>aCg	p.M202T		NM_001001821.1	NP_001001821.1	Q8NGX1	O2T34_HUMAN	olfactory receptor, family 2, subfamily T, member 34	202						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(1)|large_intestine(6)|lung(28)|ovary(2)|skin(2)|stomach(3)	43	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			GTACGTGAGCATCTTATAGAG	0.502																																					p.M202T		Atlas-SNP	.											.	OR2T34	72	.	0			c.T605C						PASS	.	G	THR/MET	336,3872		62,212,1830	189.0	206.0	200.0		605	-4.7	0.0	1	dbSNP_131	200	611,7989		5,601,3694	no	missense	OR2T34	NM_001001821.1	81	67,813,5524	GG,GA,AA		7.1047,7.9848,7.3938	benign	202/319	248737454	947,11861	2104	4300	6404	SO:0001583	missense	127068	exon1			GTGAGCATCTTAT	BK004477	CCDS31120.1	1q44	2012-08-09			ENSG00000183310	ENSG00000183310		"""GPCR / Class A : Olfactory receptors"""	31256	protein-coding gene	gene with protein product							Standard	NM_001001821		Approved		uc001iep.1	Q8NGX1	OTTHUMG00000040387	ENST00000328782.2:c.605T>C	1.37:g.248737454A>G	ENSP00000330904:p.Met202Thr	Somatic	529	1	0.00189036		WXS	Illumina HiSeq	Phase_I	201	83	0.412935	NM_001001821	B2RNJ8|Q6IEY5|Q96R31	Missense_Mutation	SNP	ENST00000328782.2	37	CCDS31120.1	404	0.184981684981685	100	0.2032520325203252	48	0.13259668508287292	183	0.31993006993006995	73	0.09630606860158311	.	0	-2.867633	0.00063	0.079848	0.071047	ENSG00000183310	ENST00000328782	T	0.00054	8.8	2.37	-4.74	0.03249	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00012	0.0000	N	0.10945	0.07	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.31503	-0.9941	9	0.02654	T	1	.	5.5169	0.16912	0.3369:0.0:0.4336:0.2295	.	202	Q8NGX1	O2T34_HUMAN	T	202	ENSP00000330904:M202T	ENSP00000330904:M202T	M	-	2	0	OR2T34	246804077	0.000000	0.05858	0.001000	0.08648	0.069000	0.16628	0.183000	0.16919	-2.576000	0.00465	-1.839000	0.00587	ATG	A|0.848;G|0.152	0.152	strong		0.502	OR2T34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097138.1	NM_001001821	
RGS22	26166	hgsc.bcm.edu	37	8	100990177	100990177	+	Silent	SNP	A	A	G	rs7841915	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:100990177A>G	ENST00000360863.6	-	23	3681	c.3487T>C	c.(3487-3489)Ttg>Ctg	p.L1163L	RGS22_ENST00000523287.1_Silent_p.L982L|RGS22_ENST00000523437.1_Silent_p.L1151L	NM_015668.3	NP_056483.3	Q8NE09	RGS22_HUMAN	regulator of G-protein signaling 22	1163					positive regulation of GTPase activity (GO:0043547)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)		RGS22/SYCP1(2)	breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(33)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	68			Epithelial(11;6.71e-08)|all cancers(13;4.19e-06)|OV - Ovarian serous cystadenocarcinoma(57;0.000469)|STAD - Stomach adenocarcinoma(118;0.169)			AGGACTGCCAATTTTTTTTTC	0.313													A|||	375	0.0748802	0.1483	0.0461	5008	,	,		17076	0.0456		0.0477	False		,,,				2504	0.0542				p.L1163L		Atlas-SNP	.											.	RGS22	319	.	0			c.T3487C						PASS	.	A		408,3172		25,358,1407	94.0	86.0	89.0		3487	-10.1	0.0	8	dbSNP_116	89	296,7840		5,286,3777	no	coding-synonymous	RGS22	NM_015668.3		30,644,5184	GG,GA,AA		3.6382,11.3966,6.0089		1163/1265	100990177	704,11012	1790	4068	5858	SO:0001819	synonymous_variant	26166	exon23			CTGCCAATTTTTT	AY009106	CCDS43758.1, CCDS69521.1, CCDS75775.1	8q22.2	2014-01-21	2007-08-14		ENSG00000132554	ENSG00000132554		"""Regulators of G-protein signaling"""	24499	protein-coding gene	gene with protein product		615650	"""regulator of G-protein signalling 22"""				Standard	XM_005250856		Approved	DKFZP434I092, PRTD-NY2, CT145	uc003yjb.1	Q8NE09	OTTHUMG00000164802	ENST00000360863.6:c.3487T>C	8.37:g.100990177A>G		Somatic	303	2	0.00660066		WXS	Illumina HiSeq	Phase_I	232	173	0.74569	NM_015668	A8K944|Q569L2|Q86Y71|Q9BYZ4|Q9UFN6	Silent	SNP	ENST00000360863.6	37	CCDS43758.1																																																																																			A|0.924;G|0.076	0.076	strong		0.313	RGS22-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000380365.1	NM_015668	
ISYNA1	51477	hgsc.bcm.edu	37	19	18545786	18545786	+	Silent	SNP	G	G	T	rs1045631	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:18545786G>T	ENST00000338128.8	-	11	1831	c.1614C>A	c.(1612-1614)acC>acA	p.T538T	ISYNA1_ENST00000457269.4_Silent_p.T484T|ISYNA1_ENST00000317018.6_Silent_p.T336T|ISYNA1_ENST00000578963.1_Silent_p.T410T|ISYNA1_ENST00000545187.1_Silent_p.T388T	NM_001170938.1|NM_016368.4	NP_001164409.1|NP_057452.1	Q9NPH2	INO1_HUMAN	inositol-3-phosphate synthase 1	538					inositol biosynthetic process (GO:0006021)|inositol phosphate metabolic process (GO:0043647)|phospholipid biosynthetic process (GO:0008654)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	inositol-3-phosphate synthase activity (GO:0004512)			breast(1)|endometrium(1)|kidney(2)|lung(4)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(2)	12						TGCAGCCATTGGTGGCAGCGG	0.617																																					p.T538T		Atlas-SNP	.											.	ISYNA1	31	.	0			c.C1614A						PASS	.	G	,,	1037,3369	371.0+/-319.8	126,785,1292	56.0	60.0	59.0		1452,1164,1614	0.9	0.0	19	dbSNP_86	59	1746,6852	310.2+/-309.8	179,1388,2732	no	coding-synonymous,coding-synonymous,coding-synonymous	ISYNA1	NM_001170938.1,NM_001170939.1,NM_016368.4	,,	305,2173,4024	TT,TG,GG		20.307,23.5361,21.4011	,,	484/505,388/409,538/559	18545786	2783,10221	2203	4299	6502	SO:0001819	synonymous_variant	51477	exon11			GCCATTGGTGGCA		CCDS12379.1, CCDS54234.1, CCDS62603.1	19p13.11	2014-09-04			ENSG00000105655	ENSG00000105655	5.5.1.4		29821	protein-coding gene	gene with protein product	"""myo-inositol 1-phosphate synthase"""	611670				15024000, 12941308	Standard	NM_016368		Approved	Ino1, INOS, IPS	uc002njd.2	Q9NPH2	OTTHUMG00000179027	ENST00000338128.8:c.1614C>A	19.37:g.18545786G>T		Somatic	158	1	0.00632911		WXS	Illumina HiSeq	Phase_I	146	145	0.993151	NM_016368	B3KRT1|G5E9U0|Q6NXT5|Q7Z525|Q9BT65|Q9H2Y2|Q9NSU0|Q9NVW7	Silent	SNP	ENST00000338128.8	37	CCDS12379.1																																																																																			G|0.788;T|0.212	0.212	strong		0.617	ISYNA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444469.2	NM_016368	
OR51G1	79324	hgsc.bcm.edu	37	11	4944986	4944986	+	Missense_Mutation	SNP	A	A	G	rs12796015	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:4944986A>G	ENST00000321961.2	-	1	651	c.584T>C	c.(583-585)aTt>aCt	p.I195T	MMP26_ENST00000477339.1_Intron|MMP26_ENST00000380390.1_Intron	NM_001005237.1	NP_001005237.1	Q8NGK1	O51G1_HUMAN	olfactory receptor, family 51, subfamily G, member 1	195			I -> T (in dbSNP:rs12796015).			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)|large_intestine(2)|lung(11)|ovary(2)|prostate(3)|skin(4)|soft_tissue(1)	25		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;2.58e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0284)|LUSC - Lung squamous cell carcinoma(625;0.19)		GTGATTGACAATGATGCTAGA	0.532													A|||	244	0.048722	0.0136	0.0937	5008	,	,		23177	0.0		0.1441	False		,,,				2504	0.0164				p.I195T		Atlas-SNP	.											.	OR51G1	74	.	0			c.T584C						PASS	.	A	THR/ILE	162,4240	108.6+/-147.0	3,156,2042	98.0	87.0	91.0		584	-3.3	0.1	11	dbSNP_121	91	1143,7453	235.3+/-267.9	98,947,3253	yes	missense	OR51G1	NM_001005237.1	89	101,1103,5295	GG,GA,AA		13.2969,3.6801,10.04	benign	195/322	4944986	1305,11693	2201	4298	6499	SO:0001583	missense	79324	exon1			TTGACAATGATGC	AB065793	CCDS31366.1	11p15.4	2012-08-09			ENSG00000176879	ENSG00000176879		"""GPCR / Class A : Olfactory receptors"""	14738	protein-coding gene	gene with protein product				OR51G3P			Standard	NM_001005237		Approved		uc010qyr.2	Q8NGK1	OTTHUMG00000066532	ENST00000321961.2:c.584T>C	11.37:g.4944986A>G	ENSP00000322546:p.Ile195Thr	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	126	20	0.15873	NM_001005237	B9EGW8|Q6IFH6	Missense_Mutation	SNP	ENST00000321961.2	37	CCDS31366.1	163	0.07463369963369963	9	0.018292682926829267	47	0.1298342541436464	0	0.0	107	0.14116094986807387	A	0.001	-3.142373	0.00029	0.036801	0.132969	ENSG00000176879	ENST00000321961	T	0.00076	8.76	4.41	-3.28	0.05033	GPCR, rhodopsin-like superfamily (1);	0.418550	0.17506	U	0.171805	T	0.00012	0.0000	N	0.00399	-1.545	0.80722	P	0.0	B	0.02656	0.0	B	0.06405	0.002	T	0.12967	-1.0527	9	0.25106	T	0.35	.	2.7891	0.05383	0.5473:0.2174:0.1284:0.1068	rs12796015;rs17252996;rs61402395;rs12796015	195	Q8NGK1	O51G1_HUMAN	T	195	ENSP00000322546:I195T	ENSP00000322546:I195T	I	-	2	0	OR51G1	4901562	0.000000	0.05858	0.051000	0.19133	0.016000	0.09150	-3.126000	0.00593	-0.348000	0.08286	-2.128000	0.00344	ATT	A|0.914;G|0.086	0.086	strong		0.532	OR51G1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142345.1	NM_001005237	
GPR126	57211	hgsc.bcm.edu	37	6	142688811	142688811	+	Missense_Mutation	SNP	C	C	T	rs116955726	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:142688811C>T	ENST00000230173.6	+	3	685	c.209C>T	c.(208-210)aCg>aTg	p.T70M	GPR126_ENST00000296932.8_Missense_Mutation_p.T70M|GPR126_ENST00000367608.2_Missense_Mutation_p.T70M|GPR126_ENST00000367609.3_Missense_Mutation_p.T70M|GPR126_ENST00000545477.1_3'UTR	NM_020455.5	NP_065188	Q86SQ4	GP126_HUMAN	G protein-coupled receptor 126	70	CUB. {ECO:0000255|PROSITE- ProRule:PRU00059}.				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)			cervix(1)|endometrium(1)|kidney(3)|large_intestine(12)|lung(10)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	36	Breast(32;0.176)			OV - Ovarian serous cystadenocarcinoma(155;9.33e-06)|GBM - Glioblastoma multiforme(68;0.00121)		TGCATGTGGACGCTCCGAGCC	0.468													C|||	90	0.0179712	0.0212	0.0029	5008	,	,		17237	0.0526		0.001	False		,,,				2504	0.0061				p.T70M		Atlas-SNP	.											.	GPR126	192	.	0			c.C209T						PASS	.	C	MET/THR,MET/THR,MET/THR,MET/THR	65,3801		0,65,1868	82.0	82.0	82.0		209,209,209,209	6.1	1.0	6	dbSNP_132	82	10,8278		0,10,4134	yes	missense,missense,missense,missense	GPR126	NM_001032394.2,NM_001032395.2,NM_020455.5,NM_198569.2	81,81,81,81	0,75,6002	TT,TC,CC		0.1207,1.6813,0.6171	probably-damaging,probably-damaging,probably-damaging,probably-damaging	70/1194,70/1223,70/1222,70/1251	142688811	75,12079	1933	4144	6077	SO:0001583	missense	57211	exon3			TGTGGACGCTCCG	AK027843	CCDS47489.1, CCDS47490.1, CCDS47491.1, CCDS55064.1	6q23.1-q24.3	2014-08-08			ENSG00000112414	ENSG00000112414		"""-"", ""GPCR / Class B : Orphans"""	13841	protein-coding gene	gene with protein product		612243				12565841	Standard	NM_001032395		Approved	FLJ14937	uc010khe.3	Q86SQ4	OTTHUMG00000015709	ENST00000230173.6:c.209C>T	6.37:g.142688811C>T	ENSP00000230173:p.Thr70Met	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	114	30	0.263158	NM_198569	Q5TGN7|Q6DHZ4|Q6F3F5|Q6F3F6|Q6F3F7|Q6F3F8|Q6MZU7|Q8IXA4|Q8NC14|Q96JW0	Missense_Mutation	SNP	ENST00000230173.6	37	CCDS47490.1	47	0.02152014652014652	13	0.026422764227642278	1	0.0027624309392265192	33	0.057692307692307696	0	0.0	C	19.01	3.744059	0.69418	0.016813	0.001207	ENSG00000112414	ENST00000230173;ENST00000367608;ENST00000296932;ENST00000367609;ENST00000541199;ENST00000435011	T;T;T;T;T;T	0.32272	1.46;1.46;1.46;1.46;1.46;1.46	6.06	6.06	0.98353	CUB (5);	0.081206	0.53938	D	0.000060	T	0.41581	0.1165	M	0.68593	2.085	0.32257	N	0.570674	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.73708	0.945;0.945;0.968;0.981;0.973	T	0.49031	-0.8981	10	0.87932	D	0	.	10.5668	0.45177	0.0:0.854:0.0:0.146	.	70;70;70;70;69	Q86SQ4-4;Q86SQ4-3;Q86SQ4-2;Q86SQ4;F5H2L1	.;.;.;GP126_HUMAN;.	M	70;70;70;70;69;70	ENSP00000230173:T70M;ENSP00000356580:T70M;ENSP00000296932:T70M;ENSP00000356581:T70M;ENSP00000446287:T69M;ENSP00000438366:T70M	ENSP00000230173:T70M	T	+	2	0	GPR126	142730504	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	1.888000	0.39708	2.880000	0.98712	0.650000	0.86243	ACG	C|0.977;T|0.023	0.023	strong		0.468	GPR126-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000042487.2		
ADAMTS2	9509	hgsc.bcm.edu	37	5	178700038	178700038	+	Missense_Mutation	SNP	C	C	G	rs146064587		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:178700038C>G	ENST00000251582.7	-	3	663	c.562G>C	c.(562-564)Gag>Cag	p.E188Q	ADAMTS2_ENST00000274609.5_Missense_Mutation_p.E188Q	NM_014244.4	NP_055059.2	O95450	ATS2_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 2	188	Poly-Glu.				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)		ATGAAGAACTCCTCCTCCTCC	0.602																																					p.E188Q		Atlas-SNP	.											.	ADAMTS2	190	.	0			c.G562C						PASS	.	C	GLN/GLU,GLN/GLU	0,4406		0,0,2203	81.0	78.0	79.0		562,562	5.0	1.0	5	dbSNP_134	79	2,8598	2.2+/-6.3	0,2,4298	no	missense,missense	ADAMTS2	NM_014244.4,NM_021599.2	29,29	0,2,6501	GG,GC,CC		0.0233,0.0,0.0154	possibly-damaging,possibly-damaging	188/1212,188/567	178700038	2,13004	2203	4300	6503	SO:0001583	missense	9509	exon3			AGAACTCCTCCTC	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.562G>C	5.37:g.178700038C>G	ENSP00000251582:p.Glu188Gln	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	59	25	0.423729	NM_021599		Missense_Mutation	SNP	ENST00000251582.7	37	CCDS4444.1	.	.	.	.	.	.	.	.	.	.	C	23.6	4.430513	0.83776	0.0	2.33E-4	ENSG00000087116	ENST00000251582;ENST00000274609	T;T	0.07327	3.2;3.2	4.96	4.96	0.65561	Peptidase M12B, propeptide (1);	0.000000	0.37178	N	0.002212	T	0.25568	0.0622	M	0.62154	1.92	0.44660	D	0.997649	D;D	0.89917	0.998;1.0	D;D	0.91635	0.994;0.999	T	0.00389	-1.1770	10	0.59425	D	0.04	.	13.7201	0.62720	0.0:1.0:0.0:0.0	.	188;188	O95450-2;O95450	.;ATS2_HUMAN	Q	188	ENSP00000251582:E188Q;ENSP00000274609:E188Q	ENSP00000251582:E188Q	E	-	1	0	ADAMTS2	178632644	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.753000	0.68736	2.284000	0.76573	0.561000	0.74099	GAG	C|1.000;G|0.000	0.000	weak		0.602	ADAMTS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253507.1	NM_014244	
HLA-A	3105	hgsc.bcm.edu	37	6	29911222	29911222	+	Missense_Mutation	SNP	C	C	T	rs1059535	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:29911222C>T	ENST00000396634.1	+	5	862	c.521C>T	c.(520-522)gCc>gTc	p.A174V	HLA-A_ENST00000376802.2_Missense_Mutation_p.A174V|HLA-A_ENST00000376809.5_Missense_Mutation_p.A174V|HLA-A_ENST00000376806.5_Missense_Mutation_p.A174V			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	174	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						TGGGAGGCGGCCCATGAGGCG	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)			t|||	435	0.086861	0.0817	0.0461	5008	,	,		12539	0.0188		0.1233	False		,,,				2504	0.1554				p.A174V		Atlas-SNP	.											.	HLA-A	89	.	0			c.C521T						PASS	.						37.0	28.0	31.0					6																	29911222		1507	2706	4213	SO:0001583	missense	3105	exon3	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	AGGCGGCCCATGA	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.521C>T	6.37:g.29911222C>T	ENSP00000379873:p.Ala174Val	Somatic	280	0	0		WXS	Illumina HiSeq	Phase_I	135	52	0.385185	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Missense_Mutation	SNP	ENST00000396634.1	37	CCDS34373.1	154|154	0.07051282051282051|0.07051282051282051	36|36	0.07317073170731707|0.07317073170731707	14|14	0.03867403314917127|0.03867403314917127	9|9	0.015734265734265736|0.015734265734265736	95|95	0.12532981530343007|0.12532981530343007	.|.	9.119|9.119	1.008386|1.008386	0.19199|0.19199	.|.	.|.	ENSG00000206503|ENSG00000206503	ENST00000396634;ENST00000376806;ENST00000376809;ENST00000376802|ENST00000355767	T;T;T;T|.	0.00832|.	5.64;5.64;5.64;5.64|.	3.78|3.78	-6.55|-6.55	0.01854|0.01854	MHC class I, alpha chain, alpha1/alpha2 (3);MHC classes I/II-like antigen recognition protein (3);MHC class I-like antigen recognition (3);|.	13.981400|.	0.02424|.	N|.	0.082844|.	T|T	0.47911|0.47911	0.1471|0.1471	M|M	0.90082|0.90082	3.085|3.085	0.80722|0.80722	P|P	0.0|0.0	B;B;B;B;B;B|.	0.12013|.	0.005;0.003;0.002;0.003;0.002;0.003|.	B;B;B;B;B;B|.	0.14578|.	0.002;0.011;0.006;0.005;0.003;0.005|.	T|T	0.56135|0.56135	-0.8029|-0.8029	9|5	0.72032|0.87932	D|D	0.01|0	.|.	5.5436|5.5436	0.17051|0.17051	0.5823:0.1603:0.0:0.2574|0.5823:0.1603:0.0:0.2574	rs1059535;rs2231055;rs3200233;rs9260154;rs16868223;rs41548615|rs1059535;rs2231055;rs3200233;rs9260154;rs16868223;rs41548615	53;174;174;174;174;174|.	B4DVB9;P13746;Q5SRN7;P16188;Q5SRN5;P04439|.	.;1A11_HUMAN;.;1A30_HUMAN;.;1A03_HUMAN|.	V|S	174|149	ENSP00000379873:A174V;ENSP00000366002:A174V;ENSP00000366005:A174V;ENSP00000365998:A174V|.	ENSP00000365998:A174V|ENSP00000348012:P149S	A|P	+|+	2|1	0|0	HLA-A|HLA-A	30019201|30019201	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.007000|0.007000	0.05969|0.05969	-6.247000|-6.247000	0.00074|0.00074	-1.123000|-1.123000	0.02940|0.02940	-1.504000|-1.504000	0.00955|0.00955	GCC|CCC	C|0.912;T|0.088	0.088	strong		0.647	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
KIF17	57576	hgsc.bcm.edu	37	1	21024901	21024901	+	Missense_Mutation	SNP	C	C	T	rs522496	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:21024901C>T	ENST00000247986.2	-	6	1514	c.1204G>A	c.(1204-1206)Gtg>Atg	p.V402M	KIF17_ENST00000400463.3_Missense_Mutation_p.V402M|KIF17_ENST00000490034.1_5'UTR|KIF17_ENST00000375044.1_Missense_Mutation_p.V302M			Q9P2E2	KIF17_HUMAN	kinesin family member 17	402			V -> M (in dbSNP:rs522496). {ECO:0000269|PubMed:10718198, ECO:0000269|PubMed:14673085, ECO:0000269|PubMed:15489334}.		ATP catabolic process (GO:0006200)|cell projection organization (GO:0030030)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|neurogenesis (GO:0022008)|protein complex localization (GO:0031503)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|intraciliary transport particle B (GO:0030992)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|plus-end-directed microtubule motor activity (GO:0008574)			NS(2)|endometrium(3)|kidney(3)|large_intestine(9)|liver(1)|lung(23)|ovary(4)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	50		all_lung(284;2.99e-05)|Lung NSC(340;3.26e-05)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00179)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|COAD - Colon adenocarcinoma(152;1.43e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000168)|Kidney(64;0.000221)|GBM - Glioblastoma multiforme(114;0.000651)|KIRC - Kidney renal clear cell carcinoma(64;0.0031)|STAD - Stomach adenocarcinoma(196;0.00336)|READ - Rectum adenocarcinoma(331;0.0686)|Lung(427;0.209)		TCGGCCTCCACGTCATGCTGG	0.642													T|||	2989	0.596845	0.4455	0.719	5008	,	,		17649	0.6498		0.6869	False		,,,				2504	0.5675				p.V402M		Atlas-SNP	.											KIF17,colon,carcinoma,0,1	KIF17	130	1	0			c.G1204A						PASS	.	T	MET/VAL,MET/VAL	2196,2210	588.0+/-386.8	536,1124,543	88.0	67.0	74.0		1204,1204	2.9	0.0	1	dbSNP_83	74	5496,3104	473.8+/-368.7	1736,2024,540	yes	missense,missense	KIF17	NM_001122819.1,NM_020816.2	21,21	2272,3148,1083	TT,TC,CC		36.093,49.8411,40.8581	benign,benign	402/1029,402/1030	21024901	7692,5314	2203	4300	6503	SO:0001583	missense	57576	exon6			CCTCCACGTCATG	AB037826	CCDS213.1, CCDS44079.1, CCDS72722.1	1p36.13	2012-08-01			ENSG00000117245	ENSG00000117245		"""Kinesins"""	19167	protein-coding gene	gene with protein product	"""kinesin-like protein KIF17"", ""KIF3-related motor protein"", ""KIF17 variant protein"""	605037				10846156	Standard	XR_241202		Approved	KIAA1405, KIF3X, KIF17B, OSM-3, KLP-2	uc001bdr.4	Q9P2E2	OTTHUMG00000002863	ENST00000247986.2:c.1204G>A	1.37:g.21024901C>T	ENSP00000247986:p.Val402Met	Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	35	35	1	NM_001122819	A2A3Q7|A2A3Q8|O95077|Q53YS6|Q5VWA9|Q6GSA8|Q8N411	Missense_Mutation	SNP	ENST00000247986.2	37	CCDS213.1	1356	0.6208791208791209	226	0.45934959349593496	246	0.6795580110497238	360	0.6293706293706294	524	0.6912928759894459	T	6.852	0.526466	0.13066	0.498411	0.63907	ENSG00000117245	ENST00000375044;ENST00000400463;ENST00000247986	T;T;T	0.72282	-0.64;-0.51;-0.51	5.21	2.87	0.33458	.	0.936522	0.08654	N	0.913515	T	0.00012	0.0000	N	0.02539	-0.55	0.80722	P	0.0	B;B	0.12630	0.006;0.003	B;B	0.12837	0.008;0.004	T	0.46569	-0.9182	9	0.38643	T	0.18	.	7.6437	0.28309	0.0:0.3828:0.0:0.6172	rs522496;rs52835247;rs522496	402;402	Q9P2E2-3;Q9P2E2	.;KIF17_HUMAN	M	302;402;402	ENSP00000364184:V302M;ENSP00000383311:V402M;ENSP00000247986:V402M	ENSP00000247986:V402M	V	-	1	0	KIF17	20897488	0.117000	0.22190	0.015000	0.15790	0.057000	0.15508	0.196000	0.17176	0.079000	0.16929	-0.360000	0.07572	GTG	C|0.404;N|0.000	.	strong		0.642	KIF17-009	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276995.1	NM_020816	
OR13C9	286362	hgsc.bcm.edu	37	9	107380396	107380396	+	Silent	SNP	T	T	G	rs36091517	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	299	1	0.00334448		WXS	Illumina HiSeq	Phase_I	231	92	0.398268	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		
KLHDC7A	127707	hgsc.bcm.edu	37	1	18808711	18808711	+	Silent	SNP	G	G	C	rs2992751	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:18808711G>C	ENST00000400664.1	+	1	1288	c.1236G>C	c.(1234-1236)ggG>ggC	p.G412G		NM_152375.2	NP_689588.2	Q5VTJ3	KLD7A_HUMAN	kelch domain containing 7A	412						integral component of membrane (GO:0016021)				endometrium(1)|kidney(1)|large_intestine(4)|lung(11)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)	22		Colorectal(325;3.46e-05)|all_lung(284;0.000152)|Lung NSC(340;0.000185)|Breast(348;0.00046)|Renal(390;0.000518)|Ovarian(437;0.0014)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00462)|BRCA - Breast invasive adenocarcinoma(304;1.41e-05)|Kidney(64;0.00017)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)		CGGTGGCCGGGACCAATTTCT	0.657													G|||	1321	0.263778	0.1725	0.2349	5008	,	,		14427	0.625		0.1173	False		,,,				2504	0.1861				p.G412G		Atlas-SNP	.											.	KLHDC7A	60	.	0			c.G1236C						PASS	.	G		845,3561		85,675,1443	27.0	34.0	32.0		1236	2.2	0.8	1	dbSNP_101	32	1051,7549		54,943,3303	no	coding-synonymous	KLHDC7A	NM_152375.2		139,1618,4746	CC,CG,GG		12.2209,19.1784,14.5779		412/778	18808711	1896,11110	2203	4300	6503	SO:0001819	synonymous_variant	127707	exon1			GGCCGGGACCAAT	AK096072	CCDS185.2	1p36.13	2008-02-05			ENSG00000179023	ENSG00000179023			26791	protein-coding gene	gene with protein product							Standard	NM_152375		Approved	FLJ38753	uc001bax.3	Q5VTJ3	OTTHUMG00000002431	ENST00000400664.1:c.1236G>C	1.37:g.18808711G>C		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	36	12	0.333333	NM_152375	Q8N8W6	Silent	SNP	ENST00000400664.1	37	CCDS185.2																																																																																			G|0.795;C|0.205	0.205	strong		0.657	KLHDC7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006923.3	NM_152375	
C2orf16	84226	hgsc.bcm.edu	37	2	27801759	27801759	+	Missense_Mutation	SNP	A	A	G	rs1919128	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:27801759A>G	ENST00000408964.2	+	1	2371	c.2320A>G	c.(2320-2322)Att>Gtt	p.I774V	AC074091.1_ENST00000408604.1_RNA	NM_032266.3	NP_115642.3	Q68DN1	CB016_HUMAN	chromosome 2 open reading frame 16	774			I -> V (in dbSNP:rs1919128).			extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(33)|urinary_tract(1)	47	Acute lymphoblastic leukemia(172;0.155)					TGGGACAGATATTTTGCAGCC	0.403													A|||	1344	0.268371	0.0318	0.5115	5008	,	,		19920	0.5079		0.2644	False		,,,				2504	0.1728				p.I774V		Atlas-SNP	.											.	C2orf16	357	.	0			c.A2320G						PASS	.	A	VAL/ILE	266,3382		4,258,1562	160.0	158.0	159.0	http://www.ncbi.nlm.nih.gov/pubmed?term	2320	1.2	0.9	2	dbSNP_92	159	2207,5947		300,1607,2170	yes	missense	C2orf16	NM_032266.3	29	304,1865,3732	GG,GA,AA	http://www.ncbi.nlm.nih.gov/pubmed?term	27.0665,7.2917,20.9541	possibly-damaging	774/1985	27801759	2473,9329	1824	4077	5901	SO:0001583	missense	84226	exon1			ACAGATATTTTGC	AL136898	CCDS42666.1	2p23.3	2013-09-20			ENSG00000221843	ENSG00000221843			25275	protein-coding gene	gene with protein product	"""P-S-E-R-S-H-H-S repeats containing"""						Standard	NM_032266		Approved	DKFZp434G118	uc002rkz.4	Q68DN1	OTTHUMG00000159099	ENST00000408964.2:c.2320A>G	2.37:g.27801759A>G	ENSP00000386190:p.Ile774Val	Somatic	256	0	0		WXS	Illumina HiSeq	Phase_I	252	153	0.607143	NM_032266	B9EIQ4|Q53S01|Q8ND64|Q9H088	Missense_Mutation	SNP	ENST00000408964.2	37	CCDS42666.1	713	0.32646520146520147	17	0.034552845528455285	166	0.4585635359116022	323	0.5646853146853147	207	0.27308707124010556	A	12.17	1.857042	0.32791	0.072917	0.270665	ENSG00000221843	ENST00000408964	T	0.05786	3.39	5.39	1.2	0.21068	.	.	.	.	.	T	0.00012	0.0000	L	0.27053	0.805	0.80722	P	0.0	D	0.54601	0.967	P	0.55391	0.775	T	0.41963	-0.9479	8	0.54805	T	0.06	.	2.4677	0.04557	0.5391:0.0:0.2589:0.2021	rs1919128;rs17006147;rs1919128	774	Q68DN1	CB016_HUMAN	V	774	ENSP00000386190:I774V	ENSP00000386190:I774V	I	+	1	0	C2orf16	27655263	0.695000	0.27747	0.866000	0.34008	0.158000	0.22134	2.257000	0.43240	0.893000	0.36288	0.459000	0.35465	ATT	A|0.706;G|0.294	0.294	strong		0.403	C2orf16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353292.1	NM_032266	
NLRP3	114548	hgsc.bcm.edu	37	1	247588053	247588053	+	Silent	SNP	C	C	T	rs34298354	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:247588053C>T	ENST00000336119.3	+	3	2054	c.1308C>T	c.(1306-1308)tcC>tcT	p.S436S	NLRP3_ENST00000366496.2_Silent_p.S436S|NLRP3_ENST00000474792.1_3'UTR|NLRP3_ENST00000366497.2_Silent_p.S436S|NLRP3_ENST00000391827.2_Silent_p.S436S|NLRP3_ENST00000391828.3_Silent_p.S436S|NLRP3_ENST00000348069.2_Silent_p.S436S	NM_001127462.2|NM_001243133.1|NM_004895.4	NP_001120934.1|NP_001230062.1|NP_004886.3	Q96P20	NALP3_HUMAN	NLR family, pyrin domain containing 3	436	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|cellular response to lipopolysaccharide (GO:0071222)|defense response (GO:0006952)|defense response to virus (GO:0051607)|detection of biotic stimulus (GO:0009595)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interleukin-1 beta production (GO:0032611)|interleukin-1 secretion (GO:0050701)|interleukin-18 production (GO:0032621)|negative regulation of acute inflammatory response (GO:0002674)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-1 beta secretion (GO:0050713)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|NLRP3 inflammasome complex assembly (GO:0044546)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of interleukin-1 beta secretion (GO:0050718)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein oligomerization (GO:0051259)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|NLRP3 inflammasome complex (GO:0072559)	ATP binding (GO:0005524)|peptidoglycan binding (GO:0042834)			NS(1)|breast(3)|endometrium(6)|kidney(1)|large_intestine(19)|lung(85)|ovary(9)|pancreas(2)|prostate(4)|skin(8)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	142	all_cancers(71;9.66e-05)|all_epithelial(71;1.85e-05)|Breast(184;0.0226)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)	all_cancers(173;0.0172)	OV - Ovarian serous cystadenocarcinoma(106;0.0141)			CCCAGACATCCAAGACCACCA	0.612													C|||	329	0.0656949	0.0053	0.062	5008	,	,		19956	0.0685		0.1143	False		,,,				2504	0.0971				p.S436S		Atlas-SNP	.											NLRP3,NS,carcinoma,+1,1	NLRP3	286	1	0			c.C1308T						PASS	.	C	,,,,	106,4300	81.9+/-120.4	1,104,2098	97.0	80.0	86.0		1308,1308,1308,1308,1308	1.3	1.0	1	dbSNP_126	86	1051,7549	223.1+/-260.0	59,933,3308	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NLRP3	NM_001079821.2,NM_001127461.2,NM_001127462.2,NM_004895.4,NM_183395.2	,,,,	60,1037,5406	TT,TC,CC		12.2209,2.4058,8.8959	,,,,	436/1037,436/980,436/980,436/1037,436/923	247588053	1157,11849	2203	4300	6503	SO:0001819	synonymous_variant	114548	exon3			GACATCCAAGACC	AF054176	CCDS1632.1, CCDS1633.1, CCDS44346.1, CCDS44347.1	1q44	2014-09-17	2006-12-08	2006-12-08	ENSG00000162711	ENSG00000162711		"""Nucleotide-binding domain and leucine rich repeat containing"""	16400	protein-coding gene	gene with protein product	"""Cryopyrin"", ""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 3"""	606416	"""cold autoinflammatory syndrome 1"""	C1orf7, CIAS1		10741953	Standard	NM_183395		Approved	AGTAVPRL, AII, AVP, FCAS, FCU, NALP3, PYPAF1, MWS, CLR1.1	uc001icr.3	Q96P20	OTTHUMG00000040647	ENST00000336119.3:c.1308C>T	1.37:g.247588053C>T		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	68	39	0.573529	NM_183395	B2RC97|B7ZKS9|B7ZKT2|B7ZKT3|O75434|Q17RS2|Q59H68|Q5JQS8|Q5JQS9|Q6TG35|Q8TCW0|Q8TEU9|Q8WXH9	Silent	SNP	ENST00000336119.3	37	CCDS1632.1																																																																																			C|0.912;T|0.088	0.088	strong		0.612	NLRP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097740.1	NM_004895	
MUC4	4585	hgsc.bcm.edu	37	3	195505247	195505247	+	Silent	SNP	G	G	T	rs76650792	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195505247G>T	ENST00000346145.4	-	2	201	c.162C>A	c.(160-162)atC>atA	p.I54I	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000463781.3_Silent_p.I4290I|MUC4_ENST00000475231.1_Silent_p.I4290I	NM_004532.5	NP_004523.3	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	1047					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)		TGGTGGAAATGATGGTCTGGG	0.592													.|||	112	0.0223642	0.0121	0.0562	5008	,	,		8996	0.005		0.0497	False		,,,				2504	0.002				p.I4290I		Atlas-SNP	.											.	MUC4	1505	.	0			c.C12870A						PASS	.	G	,,	66,4336	60.5+/-97.4	2,62,2137	225.0	175.0	192.0		162,12870,	-4.7	0.0	3	dbSNP_131	192	379,8209	123.9+/-182.7	9,361,3924	no	coding-synonymous,coding-synonymous,intron	MUC4	NM_004532.5,NM_018406.6,NM_138297.4	,,	11,423,6061	TT,TG,GG		4.4131,1.4993,3.4257	,,	54/1177,4290/5413,	195505247	445,12545	2201	4294	6495	SO:0001819	synonymous_variant	4585	exon3			GGAAATGATGGTC	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000346145.4:c.162C>A	3.37:g.195505247G>T		Somatic	296	0	0		WXS	Illumina HiSeq	Phase_I	285	136	0.477193	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Silent	SNP	ENST00000346145.4	37	CCDS3310.1																																																																																			G|0.967;T|0.033	0.033	strong		0.592	MUC4-015	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341862.1	NM_018406	
HJURP	55355	hgsc.bcm.edu	37	2	234749354	234749354	+	Missense_Mutation	SNP	G	G	A	rs12582	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:234749354G>A	ENST00000411486.2	-	8	2137	c.2072C>T	c.(2071-2073)tCc>tTc	p.S691F	HJURP_ENST00000434039.1_5'Flank|HJURP_ENST00000441687.1_Missense_Mutation_p.S606F|HJURP_ENST00000432087.1_Missense_Mutation_p.S637F	NM_018410.3	NP_060880.3	Q8NCD3	HJURP_HUMAN	Holliday junction recognition protein	691			S -> F (in dbSNP:rs12582). {ECO:0000269|PubMed:14702039}.		cell cycle (GO:0007049)|CENP-A containing nucleosome assembly (GO:0034080)|chromosome segregation (GO:0007059)|nucleosome assembly (GO:0006334)|regulation of DNA binding (GO:0051101)|regulation of protein complex assembly (GO:0043254)	chromosome, centromeric region (GO:0000775)|condensed chromosome kinetochore (GO:0000777)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone binding (GO:0042393)|identical protein binding (GO:0042802)			NS(2)|breast(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(3)|lung(11)|ovary(2)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	38		Breast(86;0.00204)|all_lung(227;0.00433)|Renal(207;0.00685)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0719)|Lung SC(224;0.128)		Epithelial(121;2.01e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000186)|Lung(119;0.00521)|LUSC - Lung squamous cell carcinoma(224;0.00829)		CTGGCGTCCGGAGCCCTGGGG	0.597													G|||	793	0.158347	0.2005	0.121	5008	,	,		18776	0.2837		0.0885	False		,,,				2504	0.0706				p.S691F		Atlas-SNP	.											.	HJURP	72	.	0			c.C2072T						PASS	.	G	PHE/SER	692,3714	290.7+/-281.1	53,586,1564	83.0	86.0	85.0		2072	-3.1	0.0	2	dbSNP_52	85	827,7773	190.3+/-236.8	40,747,3513	yes	missense	HJURP	NM_018410.3	155	93,1333,5077	AA,AG,GG		9.6163,15.7059,11.6792	probably-damaging	691/749	234749354	1519,11487	2203	4300	6503	SO:0001583	missense	55355	exon8			CGTCCGGAGCCCT		CCDS33406.1, CCDS63166.1, CCDS63167.1	2q37.1	2007-12-06			ENSG00000123485	ENSG00000123485			25444	protein-coding gene	gene with protein product		612667				17823411	Standard	NM_001282962		Approved	DKFZp762E1312, URLC9, hFLEG1, FAKTS	uc002vvg.3	Q8NCD3	OTTHUMG00000059125	ENST00000411486.2:c.2072C>T	2.37:g.234749354G>A	ENSP00000414109:p.Ser691Phe	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	79	40	0.506329	NM_018410	A8IRH5|B4DWR0|B4DZV4|Q9BUT2|Q9NSL8	Missense_Mutation	SNP	ENST00000411486.2	37	CCDS33406.1	397	0.18177655677655677	97	0.19715447154471544	39	0.10773480662983426	188	0.32867132867132864	73	0.09630606860158311	G	10.41	1.342731	0.24339	0.157059	0.096163	ENSG00000123485	ENST00000411486;ENST00000432087;ENST00000441687	T;T;T	0.08546	3.08;3.08;3.08	4.19	-3.06	0.05379	.	0.946932	0.08763	N	0.897402	T	0.00012	0.0000	L	0.44542	1.39	0.80722	P	0.0	B;B;B	0.31318	0.319;0.141;0.213	B;B;B	0.21917	0.037;0.037;0.028	T	0.47156	-0.9139	9	0.10111	T	0.7	0.0	6.2783	0.20993	0.0:0.288:0.152:0.56	rs12582;rs3172174;rs3821239;rs52802639;rs57951043;rs12582	606;637;691	Q8NCD3-3;Q8NCD3-2;Q8NCD3	.;.;HJURP_HUMAN	F	691;637;606	ENSP00000414109:S691F;ENSP00000407208:S637F;ENSP00000401944:S606F	ENSP00000414109:S691F	S	-	2	0	HJURP	234414093	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.031000	0.03578	-0.734000	0.04843	-0.344000	0.07964	TCC	G|0.846;A|0.154	0.154	strong		0.597	HJURP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000130996.6	NM_018410	
MYO9B	4650	hgsc.bcm.edu	37	19	17312992	17312992	+	Silent	SNP	C	C	T	rs2305765	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:17312992C>T	ENST00000594824.1	+	28	4863	c.4716C>T	c.(4714-4716)gtC>gtT	p.V1572V	MYO9B_ENST00000595618.1_Silent_p.V1572V|MYO9B_ENST00000397274.2_Silent_p.V1572V			Q13459	MYO9B_HUMAN	myosin IXB	1572	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						ACCAGATCGTCGTCAGCAACC	0.577													C|||	3007	0.600439	0.5991	0.6729	5008	,	,		21436	0.746		0.3897	False		,,,				2504	0.6176				p.V1572V		Atlas-SNP	.											MYO9B_ENST00000319396,NS,carcinoma,+2,2	MYO9B	264	2	0			c.C4716T						scavenged	.	C	,	2172,1850		592,988,431	50.0	53.0	52.0		4716,4716	-9.0	0.7	19	dbSNP_100	52	3313,5069		672,1969,1550	no	coding-synonymous,coding-synonymous	MYO9B	NM_001130065.1,NM_004145.3	,	1264,2957,1981	TT,TC,CC		39.5252,45.997,44.2196	,	1572/2023,1572/2158	17312992	5485,6919	2011	4191	6202	SO:0001819	synonymous_variant	4650	exon28			GATCGTCGTCAGC		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.4716C>T	19.37:g.17312992C>T		Somatic	56	1	0.0178571		WXS	Illumina HiSeq	Phase_I	57	29	0.508772	NM_001130065	O75314|Q9NUJ2|Q9UHN0	Silent	SNP	ENST00000594824.1	37																																																																																				C|0.436;T|0.564	0.564	strong		0.577	MYO9B-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000463236.1		
OSBPL3	26031	hgsc.bcm.edu	37	7	24854765	24854765	+	Silent	SNP	G	G	A	rs1044956	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:24854765G>A	ENST00000313367.2	-	19	2536	c.2085C>T	c.(2083-2085)agC>agT	p.S695S	OSBPL3_ENST00000396431.1_Silent_p.S664S|OSBPL3_ENST00000396429.1_Silent_p.S659S|OSBPL3_ENST00000353930.1_Silent_p.S659S|OSBPL3_ENST00000487020.1_5'Flank|OSBPL3_ENST00000352860.1_Silent_p.S664S|OSBPL3_ENST00000409069.1_Silent_p.S628S|OSBPL3_ENST00000431825.2_Silent_p.S628S	NM_015550.2	NP_056365.1	Q9H4L5	OSBL3_HUMAN	oxysterol binding protein-like 3	695					lipid transport (GO:0006869)	cytosol (GO:0005829)|membrane (GO:0016020)|nuclear membrane (GO:0031965)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)	cholesterol binding (GO:0015485)			breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(19)|prostate(1)|skin(3)|urinary_tract(1)	43						ACCTCTGCCCGCTTAAGATGT	0.398													G|||	1920	0.383387	0.1051	0.3646	5008	,	,		21082	0.7371		0.2475	False		,,,				2504	0.5481				p.S695S		Atlas-SNP	.											.	OSBPL3	100	.	0			c.C2085T						PASS	.	G	,,,	626,3780	269.2+/-268.9	39,548,1616	149.0	146.0	147.0		2085,1992,1977,1884	-8.8	0.7	7	dbSNP_86	147	2184,6416	374.7+/-337.5	271,1642,2387	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	OSBPL3	NM_015550.2,NM_145320.1,NM_145321.1,NM_145322.1	,,,	310,2190,4003	AA,AG,GG		25.3953,14.2079,21.6054	,,,	695/888,664/857,659/852,628/821	24854765	2810,10196	2203	4300	6503	SO:0001819	synonymous_variant	26031	exon19			CTGCCCGCTTAAG	AB014604	CCDS5390.1, CCDS5391.1, CCDS5392.1, CCDS47564.1	7p15.3	2013-01-10			ENSG00000070882	ENSG00000070882		"""Oxysterol binding proteins"", ""Pleckstrin homology (PH) domain containing"""	16370	protein-coding gene	gene with protein product		606732		OSBP3		9734811	Standard	XM_005249698		Approved	ORP-3, ORP3, KIAA0704	uc003sxf.3	Q9H4L5	OTTHUMG00000023277	ENST00000313367.2:c.2085C>T	7.37:g.24854765G>A		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	99	18	0.181818	NM_015550	A4D167|A4D168|A4D169|A4D170|A4D171|A4D172|B8ZZ79|B8ZZP0|O14591|O43357|O43358|Q8N702|Q8N703|Q8N704|Q8NFH0|Q8NFH1|Q8NI12|Q8NI13|Q9BZF4|Q9UED6	Silent	SNP	ENST00000313367.2	37	CCDS5390.1																																																																																			G|0.722;A|0.278	0.278	strong		0.398	OSBPL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214085.2		
AGGF1	55109	hgsc.bcm.edu	37	5	76343999	76343999	+	Silent	SNP	T	T	C	rs13155212	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:76343999T>C	ENST00000312916.7	+	7	1597	c.1215T>C	c.(1213-1215)atT>atC	p.I405I		NM_018046.4	NP_060516.2	Q8N302	AGGF1_HUMAN	angiogenic factor with G patch and FHA domains 1	405					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)		AAGACAAAATTTGGCCCCCAT	0.353													T|||	1112	0.222045	0.2352	0.2334	5008	,	,		15147	0.1587		0.2386	False		,,,				2504	0.2444				p.I405I		Atlas-SNP	.											.	AGGF1	71	.	0			c.T1215C						PASS	.	T		970,3436	364.9+/-317.2	107,756,1340	104.0	99.0	101.0		1215	2.2	1.0	5	dbSNP_121	101	2243,6355	378.3+/-338.9	290,1663,2346	no	coding-synonymous	AGGF1	NM_018046.4		397,2419,3686	CC,CT,TT		26.0875,22.0154,24.7078		405/715	76343999	3213,9791	2203	4299	6502	SO:0001819	synonymous_variant	55109	exon7			CAAAATTTGGCCC	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.1215T>C	5.37:g.76343999T>C		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	103	65	0.631068	NM_018046	O00581|Q53YS3|Q9BU84|Q9NW66	Silent	SNP	ENST00000312916.7	37	CCDS4035.1																																																																																			C|0.234;N|0.001	0.234	strong		0.353	AGGF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219971.2	NM_018046	
BBS1	582	hgsc.bcm.edu	37	11	66282095	66282095	+	Silent	SNP	G	G	A	rs2298806	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:66282095G>A	ENST00000318312.7	+	4	429	c.378G>A	c.(376-378)ctG>ctA	p.L126L	BBS1_ENST00000537537.1_Missense_Mutation_p.C30Y|BBS1_ENST00000455748.2_Silent_p.L126L|BBS1_ENST00000529766.1_3'UTR|CTD-3074O7.11_ENST00000419755.3_Silent_p.L163L|BBS1_ENST00000393994.2_Silent_p.L126L	NM_024649.4	NP_078925.3	Q8NFJ9	BBS1_HUMAN	Bardet-Biedl syndrome 1	126					cilium assembly (GO:0042384)|Golgi to plasma membrane protein transport (GO:0043001)|nonmotile primary cilium assembly (GO:0035058)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|retina homeostasis (GO:0001895)|visual perception (GO:0007601)	BBSome (GO:0034464)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)	patched binding (GO:0005113)|RNA polymerase II repressing transcription factor binding (GO:0001103)|smoothened binding (GO:0005119)	p.L126L(1)		NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|kidney(5)|large_intestine(5)|lung(5)|ovary(1)|prostate(2)|skin(2)|stomach(2)|urinary_tract(1)	28						AGTTCAGCCTGCCCCAATTGC	0.498									Bardet-Biedl syndrome				G|||	1060	0.211661	0.1475	0.1614	5008	,	,		20250	0.3036		0.2396	False		,,,				2504	0.2106				p.L126L	GBM(152;173 2612 9770 10137)	Atlas-SNP	.											BBS1,NS,carcinoma,0,1	BBS1	58	1	1	Substitution - coding silent(1)	stomach(1)	c.G378A						PASS	.	G		586,3814	259.8+/-263.3	34,518,1648	103.0	99.0	101.0		378	2.2	1.0	11	dbSNP_100	101	1981,6609	348.1+/-326.9	222,1537,2536	no	coding-synonymous	BBS1	NM_024649.4		256,2055,4184	AA,AG,GG		23.0617,13.3182,19.7614		126/594	66282095	2567,10423	2200	4295	6495	SO:0001819	synonymous_variant	582	exon4	Familial Cancer Database	BBS, Bardet-Biedl syndrome, type 1-12: BBS1-12,Laurence-Moon-Biedl syndrome	CAGCCTGCCCCAA	AF503941	CCDS8142.1	11q13	2013-01-08			ENSG00000174483	ENSG00000174483			966	protein-coding gene	gene with protein product		209901				9039982, 12567324	Standard	NM_024649		Approved	FLJ23590	uc001oij.1	Q8NFJ9	OTTHUMG00000167110	ENST00000318312.7:c.378G>A	11.37:g.66282095G>A		Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	20	17	0.85	NM_024649	Q32MM9|Q32MN0|Q96SN4	Silent	SNP	ENST00000318312.7	37	CCDS8142.1	497	0.22756410256410256	60	0.12195121951219512	73	0.20165745856353592	170	0.2972027972027972	194	0.2559366754617414	G	8.328	0.825914	0.16749	0.133182	0.230617	ENSG00000174483	ENST00000537537	D	0.85861	-2.04	5.09	2.16	0.27623	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.42316	P	0.007762000000000047	.	.	.	.	.	.	T	0.05402	-1.0887	5	0.02654	T	1	.	4.6187	0.12438	0.1659:0.0:0.5317:0.3024	rs2298806;rs17471805;rs58436150;rs2298806	.	.	.	Y	30	ENSP00000439873:C30Y	ENSP00000439873:C30Y	C	+	2	0	BBS1	66038671	1.000000	0.71417	0.966000	0.40874	0.938000	0.57974	1.113000	0.31184	0.261000	0.21753	-0.261000	0.10672	TGC	G|0.793;A|0.207	0.207	strong		0.498	BBS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393235.2		
PAH	5053	hgsc.bcm.edu	37	12	103246700	103246700	+	Silent	SNP	C	C	T	rs1042503	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:103246700C>T	ENST00000553106.1	-	7	1207	c.735G>A	c.(733-735)gtG>gtA	p.V245V	PAH_ENST00000307000.2_Silent_p.V240V|PAH_ENST00000551988.1_5'Flank	NM_000277.1	NP_000268.1	P00439	PH4H_HUMAN	phenylalanine hydroxylase	245			V -> A (in PKU, HPA and non-PKU HPA; haplotypes 3,7). {ECO:0000269|PubMed:12501224, ECO:0000269|PubMed:22513348, ECO:0000269|PubMed:8088845, ECO:0000269|PubMed:8889590}.|V -> E (in PKU; haplotype 11).|V -> L (in PKU).		catecholamine biosynthetic process (GO:0042423)|cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|L-phenylalanine catabolic process (GO:0006559)|neurotransmitter biosynthetic process (GO:0042136)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	amino acid binding (GO:0016597)|iron ion binding (GO:0005506)|phenylalanine 4-monooxygenase activity (GO:0004505)			endometrium(1)|kidney(3)|large_intestine(5)|lung(10)|ovary(5)|skin(2)|urinary_tract(1)	27					Droxidopa(DB06262)|Epinephrine(DB00668)|L-Phenylalanine(DB00120)|Norepinephrine(DB00368)|Tetrahydrobiopterin(DB00360)	GCAGGCCAGCCACAGGTCGGA	0.527													C|||	1577	0.314896	0.0129	0.196	5008	,	,		21210	0.7629		0.2594	False		,,,				2504	0.4029				p.V245V		Atlas-SNP	.											.	PAH	77	.	0			c.G735A	GRCh37	CX056901	PAH	X	rs1042503	PASS	.	C		245,4161	142.7+/-177.9	2,241,1960	69.0	76.0	73.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	735	3.0	1.0	12	dbSNP_86	73	2116,6484	364.1+/-333.4	253,1610,2437	no	coding-synonymous	PAH	NM_000277.1		255,1851,4397	TT,TC,CC		24.6047,5.5606,18.1532		245/453	103246700	2361,10645	2203	4300	6503	SO:0001819	synonymous_variant	5053	exon7			GCCAGCCACAGGT	U49897	CCDS9092.1	12q22-q24.2	2010-04-27				ENSG00000171759	1.14.16.1		8582	protein-coding gene	gene with protein product	"""phenylalanine 4-monooxygenase"""	612349				2063869	Standard	NM_000277		Approved	PH	uc001tjq.1	P00439		ENST00000553106.1:c.735G>A	12.37:g.103246700C>T		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	71	28	0.394366	NM_000277	Q16717|Q8TC14	Silent	SNP	ENST00000553106.1	37	CCDS9092.1																																																																																			C|0.723;T|0.276	0.276	strong		0.527	PAH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406692.1		
TMC1	117531	hgsc.bcm.edu	37	9	75303653	75303653	+	Silent	SNP	C	C	T	rs2589615	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:75303653C>T	ENST00000297784.5	+	6	585	c.45C>T	c.(43-45)gaC>gaT	p.D15D	TMC1_ENST00000396237.3_Silent_p.D15D|TMC1_ENST00000340019.3_Silent_p.D15D	NM_138691.2	NP_619636.2	Q8TDI8	TMC1_HUMAN	transmembrane channel-like 1	15	Arg/Asp/Glu/Lys-rich (highly charged).				auditory receptor cell development (GO:0060117)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|vestibular reflex (GO:0060005)	external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|stereocilium bundle tip (GO:0032426)	voltage-gated calcium channel activity (GO:0005245)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(4)|lung(21)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	36						AAAAAGAAGACGAGACTGAGG	0.368													C|||	2558	0.510783	0.77	0.4496	5008	,	,		19992	0.4187		0.4085	False		,,,				2504	0.4039				p.D15D	Pancreas(75;173 1345 14232 34245 43413)	Atlas-SNP	.											.	TMC1	87	.	0			c.C45T						PASS	.	C		3161,1245	694.7+/-405.8	1149,863,191	90.0	90.0	90.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	45	-5.3	0.2	9	dbSNP_100	90	3698,4902	521.2+/-379.8	775,2148,1377	no	coding-synonymous	TMC1	NM_138691.2		1924,3011,1568	TT,TC,CC		43.0,28.2569,47.2628		15/761	75303653	6859,6147	2203	4300	6503	SO:0001819	synonymous_variant	117531	exon6			AGAAGACGAGACT	AF417578	CCDS6643.1	9q21	2014-01-28			ENSG00000165091	ENSG00000165091			16513	protein-coding gene	gene with protein product		606706	"""transmembrane, cochlear expressed, 1"""	DFNA36, DFNB7, DFNB11		11850618, 11850623	Standard	NM_138691		Approved		uc004aiz.1	Q8TDI8	OTTHUMG00000020014	ENST00000297784.5:c.45C>T	9.37:g.75303653C>T		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	45	22	0.488889	NM_138691	A8MVZ2|B1AM91	Silent	SNP	ENST00000297784.5	37	CCDS6643.1																																																																																			C|0.478;T|0.522	0.522	strong		0.368	TMC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052655.1		
MYH14	79784	hgsc.bcm.edu	37	19	50771511	50771511	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:50771511C>T	ENST00000596571.1	+	21	2797	c.2797C>T	c.(2797-2799)Cgc>Tgc	p.R933C	MYH14_ENST00000440075.2_Missense_Mutation_p.R974C|MYH14_ENST00000262269.8_Missense_Mutation_p.R974C|MYH14_ENST00000425460.1_Missense_Mutation_p.R941C|MYH14_ENST00000376970.2_Missense_Mutation_p.R966C|MYH14_ENST00000601313.1_Missense_Mutation_p.R974C|MYH14_ENST00000598205.1_Missense_Mutation_p.R941C			Q7Z406	MYH14_HUMAN	myosin, heavy chain 14, non-muscle	933			R -> L (in PNMHH). {ECO:0000269|PubMed:21480433}.		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)		GCTGGCAGCCCGCAAGCAGGA	0.657																																					p.R974C		Atlas-SNP	.											.	MYH14	261	.	0			c.C2920T						PASS	.						20.0	29.0	26.0					19																	50771511		2140	4241	6381	SO:0001583	missense	79784	exon24			GCAGCCCGCAAGC	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.2797C>T	19.37:g.50771511C>T	ENSP00000472819:p.Arg933Cys	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	78	47	0.602564	NM_001145809	B0I1S2|C3TTN4|Q5CZ75|Q6XYE4|Q76B62|Q8WV23|Q96I22|Q9BT27|Q9BW35|Q9H882	Missense_Mutation	SNP	ENST00000596571.1	37	CCDS59411.1	.	.	.	.	.	.	.	.	.	.	C	18.37	3.608866	0.66558	.	.	ENSG00000105357	ENST00000301415;ENST00000440075;ENST00000376970;ENST00000425460;ENST00000376965;ENST00000262269	D;D;D;D	0.94232	-3.38;-3.38;-3.38;-3.38	3.9	3.9	0.45041	.	.	.	.	.	D	0.90307	0.6968	M	0.75884	2.315	0.80722	D	1	P;P;P	0.44690	0.713;0.59;0.841	B;B;B	0.34180	0.126;0.059;0.177	D	0.90702	0.4621	9	0.72032	D	0.01	.	9.075	0.36515	0.2192:0.7808:0.0:0.0	.	974;933;941	Q7Z406-2;Q7Z406;Q7Z406-6	.;MYH14_HUMAN;.	C	933;974;966;941;933;974	ENSP00000406273:R974C;ENSP00000366169:R966C;ENSP00000407879:R941C;ENSP00000262269:R974C	ENSP00000262269:R974C	R	+	1	0	MYH14	55463323	0.779000	0.28652	1.000000	0.80357	0.892000	0.51952	2.109000	0.41863	2.180000	0.69256	0.561000	0.74099	CGC	.	.	none		0.657	MYH14-008	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464710.2	NM_024729	
RPTN	126638	hgsc.bcm.edu	37	1	152129115	152129115	+	Missense_Mutation	SNP	T	T	C	rs113327860	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:152129115T>C	ENST00000316073.3	-	3	524	c.460A>G	c.(460-462)Aga>Gga	p.R154G		NM_001122965.1	NP_001116437.1	Q6XPR3	RPTN_HUMAN	repetin	154	Gln-rich.					cornified envelope (GO:0001533)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(1)|endometrium(14)|kidney(2)|large_intestine(1)|lung(32)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	59						TGGGAATCTCTGTCTTGTCTC	0.517																																					p.R154G		Atlas-SNP	.											RPTN,NS,carcinoma,0,2	RPTN	123	2	0			c.A460G						PASS	.	T	GLY/ARG	3,3133		0,3,1565	564.0	480.0	505.0		460	-9.3	0.0	1	dbSNP_132	505	20,7144		0,20,3562	no	missense	RPTN	NM_001122965.1	125	0,23,5127	CC,CT,TT		0.2792,0.0957,0.2233	probably-damaging	154/785	152129115	23,10277	1568	3582	5150	SO:0001583	missense	126638	exon3			AATCTCTGTCTTG	AK096436	CCDS41397.1	1q21.3	2013-01-10			ENSG00000215853	ENSG00000215853		"""EF-hand domain containing"""	26809	protein-coding gene	gene with protein product		613259				15854042	Standard	NM_001122965		Approved	FLJ39117	uc001ezs.1	Q6XPR3	OTTHUMG00000154095	ENST00000316073.3:c.460A>G	1.37:g.152129115T>C	ENSP00000317895:p.Arg154Gly	Somatic	271	0	0		WXS	Illumina HiSeq	Phase_I	169	37	0.218935	NM_001122965	B7ZBZ3	Missense_Mutation	SNP	ENST00000316073.3	37	CCDS41397.1	.	.	.	.	.	.	.	.	.	.	T	13.65	2.299774	0.40694	9.57E-4	0.002792	ENSG00000215853	ENST00000316073	T	0.14391	2.51	5.18	-9.31	0.00646	.	1.021040	0.07904	U	0.973153	T	0.04861	0.0131	M	0.77820	2.39	0.09310	N	1	P	0.41313	0.745	B	0.38562	0.276	T	0.07712	-1.0758	10	0.41790	T	0.15	0.1512	5.4246	0.16419	0.1067:0.1464:0.5432:0.2037	.	154	Q6XPR3	RPTN_HUMAN	G	154	ENSP00000317895:R154G	ENSP00000317895:R154G	R	-	1	2	RPTN	150395739	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.068000	0.14531	-1.180000	0.02734	-0.517000	0.04412	AGA	T|0.940;C|0.060	0.060	strong		0.517	RPTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333867.1	XM_371312	
ATHL1	80162	hgsc.bcm.edu	37	11	290050	290050	+	Silent	SNP	G	G	A	rs139686173	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:290050G>A	ENST00000409548.2	+	2	349	c.234G>A	c.(232-234)gaG>gaA	p.E78E	ATHL1_ENST00000409479.1_Silent_p.E78E|RP11-326C3.2_ENST00000533924.1_RNA|RP11-326C3.2_ENST00000534742.1_RNA|RP11-326C3.2_ENST00000525217.1_RNA|ATHL1_ENST00000409655.1_5'UTR	NM_025092.4	NP_079368.3	Q32M88	ATHL1_HUMAN	ATH1, acid trehalase-like 1 (yeast)	78					carbohydrate metabolic process (GO:0005975)		hydrolase activity, acting on glycosyl bonds (GO:0016798)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|liver(1)|lung(7)|prostate(1)|skin(3)	17		all_cancers(49;1.12e-06)|all_epithelial(84;0.000375)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;5.38e-28)|Epithelial(43;3.25e-27)|OV - Ovarian serous cystadenocarcinoma(40;1.11e-20)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0327)|LUSC - Lung squamous cell carcinoma(625;0.122)		AGCTGACCGAGACCTTCGCCC	0.677													G|||	45	0.00898562	0.0015	0.0187	5008	,	,		14729	0.0		0.0149	False		,,,				2504	0.0153				p.E78E		Atlas-SNP	.											.	ATHL1	88	.	0			c.G234A						PASS	.	G		4,1378		0,4,687	25.0	34.0	31.0		234	3.8	0.4	11	dbSNP_134	31	62,3120		0,62,1529	no	coding-synonymous	ATHL1	NM_025092.4		0,66,2216	AA,AG,GG		1.9485,0.2894,1.4461		78/738	290050	66,4498	691	1591	2282	SO:0001819	synonymous_variant	80162	exon2			GACCGAGACCTTC	AK090428	CCDS31322.2	11p15.5	2005-10-27			ENSG00000142102	ENSG00000142102			26210	protein-coding gene	gene with protein product							Standard	NM_025092		Approved	FLJ22635	uc010qvu.2	Q32M88	OTTHUMG00000153218	ENST00000409548.2:c.234G>A	11.37:g.290050G>A		Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	52	14	0.269231	NM_025092	Q658X8|Q8TEG9|Q9H635	Silent	SNP	ENST00000409548.2	37	CCDS31322.2																																																																																			G|0.986;A|0.014	0.014	strong		0.677	ATHL1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330164.3	NM_025092	
OR2T12	127064	hgsc.bcm.edu	37	1	248458187	248458187	+	Missense_Mutation	SNP	G	G	A	rs200352170		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:248458187G>A	ENST00000317996.1	-	1	693	c.694C>T	c.(694-696)Cgc>Tgc	p.R232C		NM_001004692.1	NP_001004692.1	Q8NG77	O2T12_HUMAN	olfactory receptor, family 2, subfamily T, member 12	232						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(4)|kidney(3)|large_intestine(3)|lung(25)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	43	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0201)			GCCTTCTTGCGGGCTTCTGTA	0.522																																					p.R232C		Atlas-SNP	.											.	OR2T12	113	.	0			c.C694T						PASS	.						100.0	94.0	96.0					1																	248458187		2203	4300	6503	SO:0001583	missense	127064	exon1			TCTTGCGGGCTTC	BK004485	CCDS31110.1	1q44	2012-08-09			ENSG00000177201	ENSG00000177201		"""GPCR / Class A : Olfactory receptors"""	19592	protein-coding gene	gene with protein product							Standard	NM_001004692		Approved		uc010pzj.2	Q8NG77	OTTHUMG00000040457	ENST00000317996.1:c.694C>T	1.37:g.248458187G>A	ENSP00000324583:p.Arg232Cys	Somatic	402	0	0		WXS	Illumina HiSeq	Phase_I	363	97	0.267218	NM_001004692		Missense_Mutation	SNP	ENST00000317996.1	37	CCDS31110.1	.	.	.	.	.	.	.	.	.	.	g	10.81	1.454126	0.26161	.	.	ENSG00000177201	ENST00000317996	T	0.00337	8.05	1.55	0.316	0.15857	GPCR, rhodopsin-like superfamily (1);	0.870947	0.09313	U	0.819284	T	0.00384	0.0012	M	0.85945	2.785	0.09310	N	0.999998	B	0.24368	0.102	B	0.24269	0.052	T	0.31833	-0.9929	10	0.59425	D	0.04	.	7.1649	0.25685	0.0:0.0:0.5344:0.4655	.	232	Q8NG77	O2T12_HUMAN	C	232	ENSP00000324583:R232C	ENSP00000324583:R232C	R	-	1	0	OR2T12	246524810	0.000000	0.05858	0.169000	0.22859	0.670000	0.39368	-0.554000	0.06006	0.645000	0.30675	0.175000	0.17021	CGC	G|0.999;A|0.001	0.001	weak		0.522	OR2T12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097353.1	NM_001004692	
POLQ	10721	hgsc.bcm.edu	37	3	121212484	121212484	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:121212484C>T	ENST00000264233.5	-	15	2491	c.2363G>A	c.(2362-2364)gGc>gAc	p.G788D		NM_199420.3	NP_955452.3	O75417	DPOLQ_HUMAN	polymerase (DNA directed), theta	788					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)		CCTCTGGATGCCAAACGTAAG	0.468								DNA polymerases (catalytic subunits)																													p.G788D	Pancreas(152;907 1925 26081 31236 36904)	Atlas-SNP	.											POLQ,caecum,carcinoma,0,1	POLQ	273	1	0			c.G2363A						scavenged	.						76.0	74.0	75.0					3																	121212484		2203	4300	6503	SO:0001583	missense	10721	exon15			TGGATGCCAAACG	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.2363G>A	3.37:g.121212484C>T	ENSP00000264233:p.Gly788Asp	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	71	3	0.0422535	NM_199420	O95160|Q6VMB5	Missense_Mutation	SNP	ENST00000264233.5	37	CCDS33833.1	.	.	.	.	.	.	.	.	.	.	C	32	5.132722	0.94517	.	.	ENSG00000051341	ENST00000543272;ENST00000264233;ENST00000393672	T	0.72505	-0.66	5.28	5.28	0.74379	.	0.000000	0.85682	D	0.000000	D	0.88779	0.6529	M	0.93939	3.475	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.91345	0.5100	10	0.87932	D	0	.	19.3309	0.94288	0.0:1.0:0.0:0.0	.	788	O75417	DPOLQ_HUMAN	D	411;788;924	ENSP00000264233:G788D	ENSP00000264233:G788D	G	-	2	0	POLQ	122695174	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.337000	0.79256	2.648000	0.89879	0.650000	0.86243	GGC	.	.	none		0.468	POLQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355097.1	NM_199420	
ZADH2	284273	hgsc.bcm.edu	37	18	72913537	72913537	+	Missense_Mutation	SNP	C	C	A	rs17056661	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:72913537C>A	ENST00000322342.3	-	2	1257	c.968G>T	c.(967-969)tGt>tTt	p.C323F	ZADH2_ENST00000537114.2_Missense_Mutation_p.C200F	NM_175907.4	NP_787103.1	Q8N4Q0	ZADH2_HUMAN	zinc binding alcohol dehydrogenase domain containing 2	323			C -> F (in dbSNP:rs17056661).			mitochondrion (GO:0005739)|peroxisome (GO:0005777)	oxidoreductase activity (GO:0016491)|zinc ion binding (GO:0008270)			endometrium(3)|large_intestine(3)|lung(8)|skin(1)	15		Esophageal squamous(42;0.131)|Prostate(75;0.155)		READ - Rectum adenocarcinoma(2;0.0276)|BRCA - Breast invasive adenocarcinoma(31;0.216)		TCCGCTCACACACATCTCGAG	0.507													C|||	75	0.014976	0.0023	0.0288	5008	,	,		19089	0.0		0.0398	False		,,,				2504	0.0123				p.C323F		Atlas-SNP	.											.	ZADH2	25	.	0			c.G968T						PASS	.	C	PHE/CYS	43,4363	46.0+/-80.4	0,43,2160	80.0	77.0	78.0		968	-11.2	0.1	18	dbSNP_123	78	332,8268	115.7+/-175.5	8,316,3976	yes	missense	ZADH2	NM_175907.4	205	8,359,6136	AA,AC,CC		3.8605,0.9759,2.8833	benign	323/378	72913537	375,12631	2203	4300	6503	SO:0001583	missense	284273	exon2			CTCACACACATCT	BC033780	CCDS12008.1	18q22.3	2008-05-29	2008-05-29		ENSG00000180011	ENSG00000180011			28697	protein-coding gene	gene with protein product						12477932	Standard	NM_175907		Approved	MGC45594	uc002llx.3	Q8N4Q0	OTTHUMG00000132858	ENST00000322342.3:c.968G>T	18.37:g.72913537C>A	ENSP00000323678:p.Cys323Phe	Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	112	73	0.651786	NM_175907	A8KA15|B4DZ91	Missense_Mutation	SNP	ENST00000322342.3	37	CCDS12008.1	43	0.019688644688644688	3	0.006097560975609756	14	0.03867403314917127	0	0.0	26	0.03430079155672823	C	1.913	-0.450128	0.04572	0.009759	0.038605	ENSG00000180011	ENST00000322342;ENST00000537114	T;T	0.39406	1.08;1.08	5.61	-11.2	0.00127	NAD(P)-binding domain (1);	1.395860	0.03986	N	0.294069	T	0.02380	0.0073	N	0.01242	-0.935	0.33028	D	0.529801	B	0.02656	0.0	B	0.01281	0.0	T	0.38735	-0.9647	10	0.16896	T	0.51	-2.8008	8.0417	0.30526	0.2388:0.2155:0.0:0.5456	rs17056661;rs17056661	323	Q8N4Q0	ZADH2_HUMAN	F	323;200	ENSP00000323678:C323F;ENSP00000440111:C200F	ENSP00000323678:C323F	C	-	2	0	ZADH2	71042525	0.000000	0.05858	0.094000	0.20943	0.425000	0.31504	-1.033000	0.03571	0.107000	0.17824	0.524000	0.50904	TGT	C|0.973;A|0.027	0.027	strong		0.507	ZADH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256332.1	NM_175907	
LILRB1	10859	hgsc.bcm.edu	37	19	55143083	55143083	+	Missense_Mutation	SNP	T	T	C	rs1061679	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:55143083T>C	ENST00000396331.1	+	5	560	c.203T>C	c.(202-204)cTc>cCc	p.L68P	LILRB1_ENST00000448689.1_Missense_Mutation_p.L68P|LILRB1_ENST00000396315.1_Missense_Mutation_p.L68P|LILRB1_ENST00000396321.2_Missense_Mutation_p.L68P|LILRB1_ENST00000324602.7_Missense_Mutation_p.L68P|LILRB1_ENST00000427581.2_Missense_Mutation_p.L104P|LILRB1_ENST00000396327.3_Missense_Mutation_p.L68P|LILRB1_ENST00000434867.2_Missense_Mutation_p.L68P|LILRB1_ENST00000396317.1_Missense_Mutation_p.L68P|LILRB1_ENST00000418536.2_Missense_Mutation_p.L68P|AC009892.1_ENST00000578908.1_RNA|LILRB1_ENST00000396332.4_Missense_Mutation_p.L68P	NM_006669.3	NP_006660.3	Q8NHL6	LIRB1_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 1	68	Ig-like C2-type 1.		L -> P (in dbSNP:rs1061679). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:20600445, ECO:0000269|PubMed:9285411}.		cellular response to lipopolysaccharide (GO:0071222)|defense response to virus (GO:0051607)|dendritic cell differentiation (GO:0097028)|Fc receptor mediated inhibitory signaling pathway (GO:0002774)|immune response-inhibiting cell surface receptor signaling pathway (GO:0002767)|interferon-gamma production (GO:0032609)|interferon-gamma secretion (GO:0072643)|negative regulation of alpha-beta T cell activation (GO:0046636)|negative regulation of calcium ion transport (GO:0051926)|negative regulation of CD8-positive, alpha-beta T cell activation (GO:2001186)|negative regulation of cell cycle (GO:0045786)|negative regulation of cytokine secretion involved in immune response (GO:0002740)|negative regulation of dendritic cell apoptotic process (GO:2000669)|negative regulation of dendritic cell differentiation (GO:2001199)|negative regulation of endocytosis (GO:0045806)|negative regulation of interferon-beta secretion (GO:0035548)|negative regulation of interferon-gamma biosynthetic process (GO:0045077)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of interleukin-10 secretion (GO:2001180)|negative regulation of interleukin-12 secretion (GO:2001183)|negative regulation of mononuclear cell proliferation (GO:0032945)|negative regulation of natural killer cell mediated cytotoxicity (GO:0045953)|negative regulation of osteoclast development (GO:2001205)|negative regulation of serotonin secretion (GO:0014063)|negative regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell (GO:2001189)|negative regulation of T cell mediated cytotoxicity (GO:0001915)|negative regulation of T cell proliferation (GO:0042130)|negative regulation of transforming growth factor-beta secretion (GO:2001202)|negative regulation of tumor necrosis factor biosynthetic process (GO:0042536)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cytolysis (GO:0045919)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of gamma-delta T cell activation involved in immune response (GO:2001193)|positive regulation of gene expression (GO:0010628)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|receptor internalization (GO:0031623)|regulation of immune response (GO:0050776)|response to virus (GO:0009615)|signal transduction (GO:0007165)|T cell proliferation involved in immune response (GO:0002309)	cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	HLA-A specific inhibitory MHC class I receptor activity (GO:0030107)|HLA-B specific inhibitory MHC class I receptor activity (GO:0030109)|MHC class I protein binding (GO:0042288)|MHC class I receptor activity (GO:0032393)|protein homodimerization activity (GO:0042803)|protein phosphatase 1 binding (GO:0008157)|SH2 domain binding (GO:0042169)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(38)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	74				GBM - Glioblastoma multiforme(193;0.0188)		AAAACAGCACTCTGGATTACA	0.557										HNSCC(37;0.09)			N|||	2345	0.468251	0.618	0.4899	5008	,	,		16994	0.5982		0.3032	False		,,,				2504	0.2863				p.L68P		Atlas-SNP	.											.	LILRB1	140	.	0			c.T203C						PASS	.	C	PRO/LEU,PRO/LEU,PRO/LEU,PRO/LEU	2561,1845	635.3+/-396.4	750,1061,392	156.0	151.0	153.0		203,203,203,203	-3.2	0.0	19	dbSNP_86	153	2761,5839	439.2+/-359.1	430,1901,1969	yes	missense,missense,missense,missense	LILRB1	NM_001081637.1,NM_001081638.1,NM_001081639.1,NM_006669.3	98,98,98,98	1180,2962,2361	CC,CT,TT		32.1047,41.8747,40.9196	benign,benign,benign,benign	68/653,68/652,68/652,68/651	55143083	5322,7684	2203	4300	6503	SO:0001583	missense	10859	exon4			CAGCACTCTGGAT	AF009220	CCDS42614.1, CCDS42615.1, CCDS42616.1, CCDS42617.1, CCDS62803.1	19q13.4	2013-01-11						"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6605	protein-coding gene	gene with protein product		604811				9285411, 9382880	Standard	XM_006726246		Approved	LIR-1, ILT2, MIR-7, CD85, LIR1, CD85j	uc002qgm.3	Q8NHL6		ENST00000396331.1:c.203T>C	19.37:g.55143083T>C	ENSP00000379622:p.Leu68Pro	Somatic	201	0	0		WXS	Illumina HiSeq	Phase_I	151	149	0.986755	NM_001081637	A2IXV4|A8MXT0|O75024|O75025|Q8NHJ9|Q8NHK0	Missense_Mutation	SNP	ENST00000396331.1	37	CCDS42617.1	998	0.45695970695970695	287	0.5833333333333334	161	0.4447513812154696	330	0.5769230769230769	220	0.29023746701846964	T	0.001	-3.114359	0.00032	0.581253	0.321047	ENSG00000104972	ENST00000396321;ENST00000418536;ENST00000448689;ENST00000396331;ENST00000396327;ENST00000324602;ENST00000434867;ENST00000396332;ENST00000427581;ENST00000396317;ENST00000396315	T;T;T;T;T;T;T;T;T;T;T	0.00691	5.84;5.84;5.84;5.84;5.84;5.84;5.84;5.84;5.84;5.84;5.84	1.58	-3.16	0.05217	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	3.065730	0.01064	N	0.004683	T	0.00012	0.0000	N	0.01505	-0.83	0.80722	P	0.0	B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0	B;B;B;B;B	0.04013	0.001;0.001;0.001;0.0;0.001	T	0.36648	-0.9739	9	0.06891	T	0.86	.	0.3542	0.00354	0.1961:0.3113:0.1939:0.2987	rs1061679;rs3202769;rs61439746	68;68;68;68;68	A8MVE2;Q8NHL6-3;A2IXV4;Q8NHL6-2;Q8NHL6	.;.;.;.;LIRB1_HUMAN	P	68;68;68;68;68;68;68;68;104;68;68	ENSP00000379614:L68P;ENSP00000391514:L68P;ENSP00000409968:L68P;ENSP00000379622:L68P;ENSP00000379618:L68P;ENSP00000315997:L68P;ENSP00000405243:L68P;ENSP00000379623:L68P;ENSP00000395004:L104P;ENSP00000379610:L68P;ENSP00000379608:L68P	ENSP00000315997:L68P	L	+	2	0	LILRB1	59834895	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.288000	0.00525	-1.373000	0.02134	-3.790000	0.00020	CTC	T|0.545;C|0.455	0.455	strong		0.557	LILRB1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000140796.4		
SALL1	6299	hgsc.bcm.edu	37	16	51174432	51174432	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:51174432T>C	ENST00000251020.4	-	2	1734	c.1701A>G	c.(1699-1701)atA>atG	p.I567M	SALL1_ENST00000541611.1_Intron|SALL1_ENST00000566102.1_Intron|SALL1_ENST00000440970.1_Missense_Mutation_p.I470M|SALL1_ENST00000562674.1_5'Flank	NM_002968.2	NP_002959.2	Q9NSC2	SALL1_HUMAN	spalt-like transcription factor 1	567					adrenal gland development (GO:0030325)|branching involved in ureteric bud morphogenesis (GO:0001658)|embryonic digestive tract development (GO:0048566)|embryonic digit morphogenesis (GO:0042733)|forelimb morphogenesis (GO:0035136)|gonad development (GO:0008406)|heart development (GO:0007507)|hindlimb morphogenesis (GO:0035137)|histone deacetylation (GO:0016575)|inductive cell-cell signaling (GO:0031129)|kidney development (GO:0001822)|kidney epithelium development (GO:0072073)|limb development (GO:0060173)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube closure (GO:0001843)|olfactory bulb interneuron differentiation (GO:0021889)|olfactory bulb mitral cell layer development (GO:0061034)|olfactory nerve development (GO:0021553)|outer ear morphogenesis (GO:0042473)|pituitary gland development (GO:0021983)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of neural precursor cell proliferation (GO:2000177)|transcription, DNA-templated (GO:0006351)|ureteric bud development (GO:0001657)|ureteric bud invasion (GO:0072092)|ventricular septum development (GO:0003281)	chromocenter (GO:0010369)|cytoplasm (GO:0005737)|heterochromatin (GO:0000792)|nucleus (GO:0005634)|NuRD complex (GO:0016581)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(4)|breast(2)|central_nervous_system(2)|endometrium(3)|kidney(5)|large_intestine(25)|lung(61)|ovary(3)|prostate(6)|skin(12)|upper_aerodigestive_tract(3)	126		all_cancers(37;0.0322)	COAD - Colon adenocarcinoma(2;0.24)			TGATGAAGGGTATGAGGCTTG	0.612																																					p.I567M	GBM(103;1352 1446 1855 4775 8890)	Atlas-SNP	.											.	SALL1	301	.	0			c.A1701G						PASS	.						45.0	50.0	48.0					16																	51174432		2198	4300	6498	SO:0001583	missense	6299	exon2			GAAGGGTATGAGG	X98833	CCDS10747.1, CCDS45483.1	16q12.1	2014-09-17	2013-10-17		ENSG00000103449	ENSG00000103449		"""Zinc fingers, C2H2-type"""	10524	protein-coding gene	gene with protein product		602218	"""sal (Drosophila)-like 1"", ""sal-like 1 (Drosophila)"""	TBS		9425907	Standard	NM_002968		Approved	Hsal1, ZNF794	uc021tie.1	Q9NSC2	OTTHUMG00000133176	ENST00000251020.4:c.1701A>G	16.37:g.51174432T>C	ENSP00000251020:p.Ile567Met	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	64	29	0.453125	NM_002968	Q99881|Q9NSC3|Q9P1R0	Missense_Mutation	SNP	ENST00000251020.4	37	CCDS10747.1	.	.	.	.	.	.	.	.	.	.	T	8.110	0.778639	0.16120	.	.	ENSG00000103449	ENST00000251020;ENST00000440970;ENST00000457559	T;T	0.05996	3.36;3.38	5.32	-10.6	0.00265	.	0.257755	0.45126	D	0.000388	T	0.02156	0.0067	N	0.08118	0	0.09310	N	1	B	0.21225	0.053	B	0.22386	0.039	T	0.29518	-1.0009	10	0.72032	D	0.01	.	6.6511	0.22963	0.0662:0.2679:0.4445:0.2214	.	567	Q9NSC2	SALL1_HUMAN	M	567;470;531	ENSP00000251020:I567M;ENSP00000407914:I470M	ENSP00000251020:I567M	I	-	3	3	SALL1	49731933	0.000000	0.05858	0.164000	0.22755	0.998000	0.95712	-3.833000	0.00355	-2.099000	0.00849	0.455000	0.32223	ATA	.	.	none		0.612	SALL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256883.2	NM_002968	
DHFRL1	200895	hgsc.bcm.edu	37	3	93780109	93780109	+	Missense_Mutation	SNP	G	G	C	rs61739170	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:93780109G>C	ENST00000394221.2	-	2	696	c.247C>G	c.(247-249)Cct>Gct	p.P83A	NSUN3_ENST00000314622.4_5'Flank|DHFRL1_ENST00000481631.1_Intron|DHFRL1_ENST00000314636.2_Missense_Mutation_p.P83A	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	241	0	0		WXS	Illumina HiSeq	Phase_I	161	81	0.503106	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	
NCAPD2	9918	hgsc.bcm.edu	37	12	6638197	6638197	+	Silent	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:6638197C>T	ENST00000315579.5	+	27	4363	c.3564C>T	c.(3562-3564)acC>acT	p.T1188T	NCAPD2_ENST00000545962.1_Silent_p.T1143T	NM_014865.3	NP_055680.3	Q15021	CND1_HUMAN	non-SMC condensin I complex, subunit D2	1188					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						CTTTCCACACCATCATGAAGT	0.527																																					p.T1188T		Atlas-SNP	.											.	NCAPD2	99	.	0			c.C3564T						PASS	.						55.0	61.0	59.0					12																	6638197		2203	4300	6503	SO:0001819	synonymous_variant	9918	exon27			CCACACCATCATG	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.3564C>T	12.37:g.6638197C>T		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	67	23	0.343284	NM_014865	D3DUR4|Q8N6U3	Silent	SNP	ENST00000315579.5	37	CCDS8548.1																																																																																			.	.	none		0.527	NCAPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399964.1	NM_014865	
SQRDL	58472	hgsc.bcm.edu	37	15	45968435	45968435	+	Missense_Mutation	SNP	T	T	C	rs1044032	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:45968435T>C	ENST00000260324.7	+	6	1177	c.791T>C	c.(790-792)aTt>aCt	p.I264T	SQRDL_ENST00000568606.1_Missense_Mutation_p.I264T|RP11-96O20.4_ENST00000564080.1_Missense_Mutation_p.I264T	NM_021199.3	NP_067022.1	Q9Y6N5	SQRD_HUMAN	sulfide quinone reductase-like (yeast)	264			I -> T (in dbSNP:rs1044032). {ECO:0000269|PubMed:10810093}.		cellular nitrogen compound metabolic process (GO:0034641)|small molecule metabolic process (GO:0044281)|sulfide oxidation, using sulfide:quinone oxidoreductase (GO:0070221)|sulfur amino acid catabolic process (GO:0000098)|sulfur amino acid metabolic process (GO:0000096)	mitochondrial inner membrane (GO:0005743)	sulfide:quinone oxidoreductase activity (GO:0070224)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|prostate(2)	11		Lung NSC(122;0.000117)|all_lung(180;0.000737)|Melanoma(134;0.0417)		all cancers(107;5.89e-18)|GBM - Glioblastoma multiforme(94;1.21e-06)|COAD - Colon adenocarcinoma(120;0.17)|Colorectal(133;0.188)		AAAAACCTCATTGAAGTCCGA	0.478													T|||	1323	0.264177	0.1067	0.2046	5008	,	,		17218	0.4276		0.2217	False		,,,				2504	0.3947				p.I264T		Atlas-SNP	.											.	SQRDL	27	.	0			c.T791C						PASS	.	T	THR/ILE	490,3906	228.5+/-243.3	25,440,1733	108.0	111.0	110.0		791	4.6	0.9	15	dbSNP_86	110	1756,6838	318.4+/-313.7	186,1384,2727	yes	missense	SQRDL	NM_021199.2	89	211,1824,4460	CC,CT,TT		20.4329,11.1465,17.2902	benign	264/451	45968435	2246,10744	2198	4297	6495	SO:0001583	missense	58472	exon6			ACCTCATTGAAGT	AF042284	CCDS10127.1	15q21.1	2010-08-05			ENSG00000137767	ENSG00000137767			20390	protein-coding gene	gene with protein product						10810093, 10224084	Standard	NM_021199		Approved	CGI-44	uc001zvu.4	Q9Y6N5	OTTHUMG00000131476	ENST00000260324.7:c.791T>C	15.37:g.45968435T>C	ENSP00000260324:p.Ile264Thr	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	112	41	0.366071	NM_021199	Q9UQM8	Missense_Mutation	SNP	ENST00000260324.7	37	CCDS10127.1	545	0.24954212454212454	57	0.11585365853658537	70	0.19337016574585636	257	0.4493006993006993	161	0.21240105540897097	T	15.76	2.930037	0.52759	0.111465	0.204329	ENSG00000137767	ENST00000260324	T	0.54071	0.59	5.74	4.62	0.57501	Pyridine nucleotide-disulphide oxidoreductase, FAD/NAD(P)-binding domain (1);	0.138279	0.64402	N	0.000006	T	0.00012	0.0000	L	0.39692	1.235	0.19775	P	0.9999502757	B	0.12630	0.006	B	0.18871	0.023	T	0.40942	-0.9536	9	0.41790	T	0.15	.	10.9095	0.47099	0.0:0.0739:0.0:0.9261	rs1044032;rs3183709;rs56504290;rs60998701;rs1044032	264	Q9Y6N5	SQRD_HUMAN	T	264	ENSP00000260324:I264T	ENSP00000260324:I264T	I	+	2	0	SQRDL	43755727	0.990000	0.36364	0.868000	0.34077	0.966000	0.64601	6.252000	0.72447	1.008000	0.39264	-0.261000	0.10672	ATT	T|0.784;C|0.216	0.216	strong		0.478	SQRDL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254319.2		
MVK	4598	hgsc.bcm.edu	37	12	110019338	110019338	+	Silent	SNP	C	C	T	rs104895375|rs2287218|rs104895310	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:110019338C>T	ENST00000228510.3	+	5	586	c.510C>T	c.(508-510)gaC>gaT	p.D170D	MVK_ENST00000539696.1_Intron|MVK_ENST00000392727.3_Intron|MVK_ENST00000535044.1_Intron|MVK_ENST00000541384.1_Intron|MVK_ENST00000539575.1_Intron	NM_000431.2|NM_001114185.1	NP_000422.1|NP_001107657.1	Q03426	KIME_HUMAN	mevalonate kinase	170					cholesterol biosynthetic process (GO:0006695)|isopentenyl diphosphate biosynthetic process, mevalonate pathway (GO:0019287)|isoprenoid biosynthetic process (GO:0008299)|negative regulation of inflammatory response (GO:0050728)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|mevalonate kinase activity (GO:0004496)			endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|prostate(1)|skin(1)	8						CGCTGAAGGACGGGGATTGCG	0.652													C|||	818	0.163339	0.1989	0.1643	5008	,	,		19849	0.128		0.1769	False		,,,				2504	0.137				p.D170D		Atlas-SNP	.											.	MVK	42	.	0			c.C510T						PASS	.	C	,	803,3603	322.1+/-297.4	81,641,1481	86.0	83.0	84.0		510,510	-10.3	0.0	12	dbSNP_100	84	1507,7093	285.5+/-297.2	120,1267,2913	no	coding-synonymous,coding-synonymous	MVK	NM_000431.2,NM_001114185.1	,	201,1908,4394	TT,TC,CC		17.5233,18.2251,17.761	,	170/397,170/397	110019338	2310,10696	2203	4300	6503	SO:0001819	synonymous_variant	4598	exon5			GAAGGACGGGGAT	M88468	CCDS9132.1, CCDS73522.1	12q24	2014-09-17	2008-01-30		ENSG00000110921	ENSG00000110921	2.7.1.36		7530	protein-coding gene	gene with protein product	"""LH receptor mRNA-binding protein"", ""mevalonic aciduria"""	251170	"""mevalonate kinase (mevalonic aciduria)"""			1377680	Standard	XM_005253883		Approved	LRBP, MK	uc001toy.4	Q03426	OTTHUMG00000169256	ENST00000228510.3:c.510C>T	12.37:g.110019338C>T		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	120	61	0.508333	NM_000431		Silent	SNP	ENST00000228510.3	37	CCDS9132.1																																																																																			C|0.831;T|0.169	0.169	strong		0.652	MVK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403143.1	NM_000431	
RALGAPB	57148	hgsc.bcm.edu	37	20	37153554	37153554	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:37153554T>C	ENST00000262879.6	+	11	2037	c.1753T>C	c.(1753-1755)Ttt>Ctt	p.F585L	RALGAPB_ENST00000397040.1_Missense_Mutation_p.F585L|RALGAPB_ENST00000397038.1_Missense_Mutation_p.F363L|RALGAPB_ENST00000397042.3_Missense_Mutation_p.F585L			Q86X10	RLGPB_HUMAN	Ral GTPase activating protein, beta subunit (non-catalytic)	585					activation of Ral GTPase activity (GO:0032859)|membrane organization (GO:0061024)|Ral protein signal transduction (GO:0032484)|regulation of exocyst localization (GO:0060178)		protein heterodimerization activity (GO:0046982)|Ral GTPase activator activity (GO:0017123)			breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(8)|lung(29)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	65						GGTTCCTTACTTTATTTCAGC	0.423																																					p.F585L		Atlas-SNP	.											RALGAPB,NS,carcinoma,0,1	RALGAPB	134	1	0			c.T1753C						scavenged	.						296.0	272.0	280.0					20																	37153554		2203	4300	6503	SO:0001583	missense	57148	exon11			CCTTACTTTATTT	AB033045	CCDS13305.1, CCDS63272.1	20q11.23	2009-09-09	2009-09-09	2009-09-09	ENSG00000170471	ENSG00000170471			29221	protein-coding gene	gene with protein product			"""KIAA1219"""	KIAA1219		19520869	Standard	XM_005260462		Approved	DKFZp781M2411, RalGAPbeta	uc002xiw.3	Q86X10	OTTHUMG00000140270	ENST00000262879.6:c.1753T>C	20.37:g.37153554T>C	ENSP00000262879:p.Phe585Leu	Somatic	404	0	0		WXS	Illumina HiSeq	Phase_I	370	6	0.0162162	NM_020336	A2A2E8|A2A2E9|Q5TG31|Q8N3D1|Q8WWC0|Q9H3X8|Q9UJR1|Q9ULK1|Q9Y3G9	Missense_Mutation	SNP	ENST00000262879.6	37	CCDS13305.1	.	.	.	.	.	.	.	.	.	.	T	35	5.447076	0.96205	.	.	ENSG00000170471	ENST00000262879;ENST00000397042;ENST00000304939;ENST00000397038;ENST00000397040;ENST00000438490	T;T	0.52526	0.66;0.66	5.51	5.51	0.81932	.	0.000000	0.85682	D	0.000000	T	0.62024	0.2394	L	0.49455	1.56	0.80722	D	1	D;P;P;P	0.67145	0.996;0.954;0.954;0.954	D;D;D;D	0.73380	0.98;0.943;0.943;0.943	T	0.58725	-0.7586	10	0.31617	T	0.26	.	15.6243	0.76840	0.0:0.0:0.0:1.0	.	413;585;585;585	A2A2F0;Q86X10-4;A2A2E9;Q86X10	.;.;.;RLGPB_HUMAN	L	585;585;585;363;585;413	ENSP00000262879:F585L;ENSP00000380233:F585L	ENSP00000262879:F585L	F	+	1	0	RALGAPB	36586968	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.040000	0.89188	2.091000	0.63221	0.459000	0.35465	TTT	.	.	none		0.423	RALGAPB-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000079191.1	NM_020336	
CLCN1	1180	hgsc.bcm.edu	37	7	143042837	143042837	+	Silent	SNP	C	C	T	rs2272251	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:143042837C>T	ENST00000343257.2	+	17	2241	c.2154C>T	c.(2152-2154)gaC>gaT	p.D718D		NM_000083.2	NP_000074	P35523	CLCN1_HUMAN	chloride channel, voltage-sensitive 1	718					chloride transmembrane transport (GO:1902476)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|neuronal action potential propagation (GO:0019227)|regulation of anion transport (GO:0044070)|transmembrane transport (GO:0055085)|transport (GO:0006810)	chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)	adenyl nucleotide binding (GO:0030554)|chloride channel activity (GO:0005254)|voltage-gated chloride channel activity (GO:0005247)			breast(4)|central_nervous_system(1)|endometrium(1)|large_intestine(11)|lung(26)|ovary(3)|prostate(2)|skin(7)|stomach(1)|upper_aerodigestive_tract(2)	58	Melanoma(164;0.205)					AGGACGAAGACCTCTCTGGCA	0.677											OREG0018402	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	2395	0.478235	0.3593	0.585	5008	,	,		13451	0.6141		0.4592	False		,,,				2504	0.4427				p.D718D		Atlas-SNP	.											CLCN1,NS,carcinoma,0,1	CLCN1	141	1	0			c.C2154T						PASS	.	C		1498,2778		328,842,968	7.0	8.0	8.0		2154	-1.8	0.1	7	dbSNP_100	8	3583,4875		839,1905,1485	no	coding-synonymous	CLCN1	NM_000083.2		1167,2747,2453	TT,TC,CC		42.3623,35.0327,39.9011		718/989	143042837	5081,7653	2138	4229	6367	SO:0001819	synonymous_variant	1180	exon17			CGAAGACCTCTCT	Z25884	CCDS5881.1	7q12	2012-09-26	2012-02-23		ENSG00000188037	ENSG00000188037		"""Ion channels / Chloride channels : Voltage-sensitive"""	2019	protein-coding gene	gene with protein product	"""Thomsen disease, autosomal dominant"""	118425	"""chloride channel 1, skeletal muscle"""			1379744	Standard	NM_000083		Approved	CLC1, ClC-1	uc003wcr.1	P35523	OTTHUMG00000152695	ENST00000343257.2:c.2154C>T	7.37:g.143042837C>T		Somatic	38	0	0	1676	WXS	Illumina HiSeq	Phase_I	56	32	0.571429	NM_000083	A4D2H5|Q2M202	Silent	SNP	ENST00000343257.2	37	CCDS5881.1																																																																																			C|0.502;T|0.498	0.498	strong		0.677	CLCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327420.1	NM_000083	
MCC	4163	hgsc.bcm.edu	37	5	112823998	112823998	+	Silent	SNP	C	C	T	rs348943	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	86	0	0		WXS	Illumina HiSeq	Phase_I	78	40	0.512821	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	
SPHKAP	80309	hgsc.bcm.edu	37	2	228883029	228883029	+	Missense_Mutation	SNP	A	A	C	rs3811515	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:228883029A>C	ENST00000392056.3	-	7	2587	c.2541T>G	c.(2539-2541)caT>caG	p.H847Q	SPHKAP_ENST00000344657.5_Missense_Mutation_p.H847Q	NM_001142644.1	NP_001136116.1	Q2M3C7	SPKAP_HUMAN	SPHK1 interactor, AKAP domain containing	847			H -> Q (in dbSNP:rs3811515). {ECO:0000269|PubMed:11214970, ECO:0000269|PubMed:17974005}.			extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|Z disc (GO:0030018)	protein kinase A binding (GO:0051018)	p.H847Q(1)		NS(5)|breast(5)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(25)|lung(86)|ovary(6)|pancreas(1)|prostate(6)|skin(17)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	185		Renal(207;0.025)|all_hematologic(139;0.15)|all_lung(227;0.204)|Acute lymphoblastic leukemia(138;0.205)|Esophageal squamous(248;0.23)		Epithelial(121;8.17e-11)|all cancers(144;7.92e-08)|Lung(261;0.0168)|LUSC - Lung squamous cell carcinoma(224;0.0232)		TCTCACTGTGATGAGGGCTTT	0.493													A|||	1115	0.222644	0.0318	0.2464	5008	,	,		21416	0.2242		0.2406	False		,,,				2504	0.4438				p.H847Q		Atlas-SNP	.											SPHKAP,NS,carcinoma,0,1	SPHKAP	750	1	1	Substitution - Missense(1)	stomach(1)	c.T2541G						PASS	.	A	GLN/HIS,GLN/HIS	282,4124	156.3+/-189.4	13,256,1934	745.0	703.0	717.0		2541,2541	1.0	0.0	2	dbSNP_107	717	2167,6433	371.6+/-336.3	287,1593,2420	yes	missense,missense	SPHKAP	NM_001142644.1,NM_030623.3	24,24	300,1849,4354	CC,CA,AA		25.1977,6.4004,18.8298	possibly-damaging,possibly-damaging	847/1701,847/1672	228883029	2449,10557	2203	4300	6503	SO:0001583	missense	80309	exon7			ACTGTGATGAGGG		CCDS33389.1, CCDS46537.1	2q36.3	2010-08-20			ENSG00000153820	ENSG00000153820		"""A-kinase anchor proteins"""	30619	protein-coding gene	gene with protein product	"""sphingosine kinase type 1-interacting protein"""	611646				12080051, 11214970	Standard	NM_030623		Approved	SKIP	uc002vpq.2	Q2M3C7	OTTHUMG00000153584	ENST00000392056.3:c.2541T>G	2.37:g.228883029A>C	ENSP00000375909:p.His847Gln	Somatic	338	0	0		WXS	Illumina HiSeq	Phase_I	281	139	0.494662	NM_030623	Q68DA3|Q68DR8|Q9C0I5	Missense_Mutation	SNP	ENST00000392056.3	37	CCDS46537.1	469	0.21474358974358973	26	0.052845528455284556	96	0.26519337016574585	156	0.2727272727272727	191	0.2519788918205805	A	5.226	0.227206	0.09916	0.064004	0.251977	ENSG00000153820	ENST00000392056;ENST00000344657	T;T	0.11169	2.8;2.8	5.97	0.984	0.19773	.	1.321610	0.04419	N	0.367345	T	0.00012	0.0000	M	0.65975	2.015	0.80722	P	0.0	B;B	0.16802	0.011;0.019	B;B	0.15052	0.003;0.012	T	0.39742	-0.9599	9	0.59425	D	0.04	.	6.0637	0.19852	0.5854:0.2766:0.138:0.0	rs3811515;rs17266858;rs52816852;rs56487013;rs57755256;rs3811515	847;847	Q2M3C7;Q2M3C7-2	SPKAP_HUMAN;.	Q	847	ENSP00000375909:H847Q;ENSP00000339886:H847Q	ENSP00000339886:H847Q	H	-	3	2	SPHKAP	228591273	0.031000	0.19500	0.000000	0.03702	0.414000	0.31173	0.219000	0.17641	0.148000	0.19059	0.533000	0.62120	CAT	A|0.784;C|0.216	0.216	strong		0.493	SPHKAP-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331750.1	NM_030623	
GSG2	83903	hgsc.bcm.edu	37	17	3628212	3628212	+	Missense_Mutation	SNP	T	T	C	rs220461	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:3628212T>C	ENST00000325418.4	+	1	1002	c.983T>C	c.(982-984)aTa>aCa	p.I328T	ITGAE_ENST00000263087.4_Intron|CTD-3195I5.3_ENST00000571741.1_RNA|ITGAE_ENST00000571185.1_Intron	NM_031965.2	NP_114171.2	Q8TF76	HASP_HUMAN	germ cell associated 2 (haspin)	328			I -> T (in dbSNP:rs220461). {ECO:0000269|PubMed:11311556, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17344846}.		histone H3-T3 phosphorylation involved in chromosome passenger complex localization to kinetochore (GO:2000751)|intracellular signal transduction (GO:0035556)|mitotic sister chromatid cohesion (GO:0007064)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|protein localization to chromosome, centromeric region (GO:0071459)|protein phosphorylation (GO:0006468)|regulation of spindle checkpoint (GO:0090231)	centrosome (GO:0005813)|chromosome (GO:0005694)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|spindle (GO:0005819)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|histone kinase activity (H3-T3 specific) (GO:0072354)|protein kinase activity (GO:0004672)										CCAAGGGGAATAGACAGGCTG	0.552													T|||	1270	0.253594	0.0219	0.1556	5008	,	,		19545	0.3006		0.3072	False		,,,				2504	0.5327				p.I328T		Atlas-SNP	.											.	GSG2	48	.	0			c.T983C						PASS	.	T	,THR/ILE	309,4097	162.2+/-194.2	17,275,1911	55.0	51.0	52.0		,983	-8.7	0.0	17	dbSNP_79	52	2743,5857	426.7+/-355.4	435,1873,1992	yes	intron,missense	ITGAE,GSG2	NM_002208.4,NM_031965.2	,89	452,2148,3903	CC,CT,TT		31.8953,7.0132,23.4661	,benign	,328/799	3628212	3052,9954	2203	4300	6503	SO:0001583	missense	83903	exon1			GGGGAATAGACAG	AB039834	CCDS11036.1	17p13	2005-01-19			ENSG00000177602	ENSG00000177602			19682	protein-coding gene	gene with protein product		609240					Standard	NM_031965		Approved	haspin	uc002fwp.3	Q8TF76	OTTHUMG00000090703	ENST00000325418.4:c.983T>C	17.37:g.3628212T>C	ENSP00000325290:p.Ile328Thr	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	37	13	0.351351	NM_031965	Q5U5K3|Q96MN1|Q9BXS7	Missense_Mutation	SNP	ENST00000325418.4	37	CCDS11036.1	494	0.2261904761904762	15	0.03048780487804878	65	0.17955801104972377	177	0.3094405594405594	237	0.31266490765171506	T	1.096	-0.662582	0.03454	0.070132	0.318953	ENSG00000177602	ENST00000325418	T	0.06933	3.24	4.33	-8.67	0.00863	.	0.902637	0.09044	N	0.856810	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	0.49688	-0.8913	9	0.87932	D	0	-23.7501	9.806	0.40792	0.1041:0.6357:0.1141:0.1461	rs220461;rs3809807;rs17463403;rs58374758;rs220461	328	Q8TF76	HASP_HUMAN	T	328	ENSP00000325290:I328T	ENSP00000325290:I328T	I	+	2	0	GSG2	3574961	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.294000	0.01144	-2.050000	0.00905	-1.064000	0.02280	ATA	T|0.769;C|0.230	0.230	strong		0.552	GSG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207391.1	NM_031965	
CYP2W1	54905	hgsc.bcm.edu	37	7	1024855	1024855	+	Missense_Mutation	SNP	G	G	A	rs3735684	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:1024855G>A	ENST00000308919.7	+	4	554	c.541G>A	c.(541-543)Gcg>Acg	p.A181T	CYP2W1_ENST00000340150.6_Missense_Mutation_p.A125T	NM_017781.2	NP_060251.2	Q8TAV3	CP2W1_HUMAN	cytochrome P450, family 2, subfamily W, polypeptide 1	181			A -> T (in dbSNP:rs3735684).		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)		TATCACCTTCGCGCTCCTCTT	0.682													G|||	302	0.0603035	0.0711	0.134	5008	,	,		14229	0.0238		0.0527	False		,,,				2504	0.0389				p.A181T		Atlas-SNP	.											.	CYP2W1	28	.	0			c.G541A						PASS	.	G	THR/ALA	311,3919		14,283,1818	34.0	27.0	29.0		541	-4.1	0.4	7	dbSNP_107	29	446,7924		8,430,3747	yes	missense	CYP2W1	NM_017781.2	58	22,713,5565	AA,AG,GG		5.3286,7.3522,6.0079	benign	181/491	1024855	757,11843	2115	4185	6300	SO:0001583	missense	54905	exon4			ACCTTCGCGCTCC	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.541G>A	7.37:g.1024855G>A	ENSP00000310149:p.Ala181Thr	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	69	56	0.811594	NM_017781		Missense_Mutation	SNP	ENST00000308919.7	37	CCDS5319.2	138	0.06318681318681318	41	0.08333333333333333	40	0.11049723756906077	16	0.027972027972027972	41	0.05408970976253298	G	9.045	0.990712	0.18966	0.073522	0.053286	ENSG00000073067	ENST00000308919;ENST00000340150	T;T	0.68624	-0.34;-0.34	5.06	-4.11	0.03928	.	0.562403	0.20017	N	0.100982	T	0.00754	0.0025	N	0.11698	0.16	0.09310	N	1	B;B	0.14805	0.003;0.011	B;B	0.11329	0.006;0.006	T	0.03043	-1.1079	10	0.52906	T	0.07	.	2.6822	0.05096	0.2581:0.167:0.4017:0.1732	rs3735684;rs17362325;rs3735684	125;181	A6NJ10;Q8TAV3	.;CP2W1_HUMAN	T	181;125	ENSP00000310149:A181T;ENSP00000344178:A125T	ENSP00000310149:A181T	A	+	1	0	CYP2W1	991381	0.000000	0.05858	0.420000	0.26596	0.204000	0.24138	-3.570000	0.00427	-0.238000	0.09724	-1.247000	0.01520	GCG	G|0.936;A|0.064	0.064	strong		0.682	CYP2W1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157249.1	NM_017781	
MLLT3	4300	hgsc.bcm.edu	37	9	20414310	20414310	+	Silent	SNP	A	A	G	rs148318848	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:20414310A>G	ENST00000380338.4	-	5	820	c.534T>C	c.(532-534)agT>agC	p.S178S	MLLT3_ENST00000355930.6_5'UTR|MLLT3_ENST00000475957.1_5'UTR|MLLT3_ENST00000429426.2_Silent_p.S175S	NM_004529.2	NP_004520.2	P42568	AF9_HUMAN	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 3	178	Poly-Ser.				anterior/posterior pattern specification (GO:0009952)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of Wnt signaling pathway, planar cell polarity pathway (GO:2000096)|regulation of transcription, DNA-templated (GO:0006355)|segment specification (GO:0007379)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)				central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(6)|lung(24)|ovary(1)|prostate(4)|skin(1)|urinary_tract(7)	66				GBM - Glioblastoma multiforme(3;4.35e-105)|Lung(42;3.48e-06)|LUSC - Lung squamous cell carcinoma(42;7.92e-05)		tgctgctgctactgctgctgc	0.527			T	MLL	ALL								A|||	169	0.033746	0.0272	0.0231	5008	,	,		12860	0.0169		0.0308	False		,,,				2504	0.0706				p.S178S		Atlas-SNP	.		Dom	yes		9	9p22	4300	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 3 (AF9)"""		L	MLLT3,caecum,carcinoma,0,1	MLLT3	125	1	0			c.T534C						scavenged	.						25.0	33.0	30.0					9																	20414310		2142	4195	6337	SO:0001819	synonymous_variant	4300	exon5			GCTGCTACTGCTG	L13744	CCDS6494.1	9p22	2008-02-05	2001-11-28		ENSG00000171843	ENSG00000171843			7136	protein-coding gene	gene with protein product		159558	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 3"""			8506309, 8414510	Standard	NM_001286691		Approved	AF-9, AF9, YEATS3	uc003zoe.2	P42568	OTTHUMG00000019650	ENST00000380338.4:c.534T>C	9.37:g.20414310A>G		Somatic	103	5	0.0485437		WXS	Illumina HiSeq	Phase_I	105	7	0.0666667	NM_004529	B1AMQ2|B2R7B3|B7Z755|D3DRJ8|Q8IVB0	Silent	SNP	ENST00000380338.4	37	CCDS6494.1																																																																																			.	.	weak		0.527	MLLT3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051872.1	NM_004529	
EIF4G2	1982	hgsc.bcm.edu	37	11	10827592	10827592	+	Missense_Mutation	SNP	T	T	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:10827592T>A	ENST00000526148.1	-	4	620	c.110A>T	c.(109-111)gAg>gTg	p.E37V	EIF4G2_ENST00000525995.1_5'UTR|EIF4G2_ENST00000339995.5_Missense_Mutation_p.E37V|EIF4G2_ENST00000525681.1_Missense_Mutation_p.E37V|EIF4G2_ENST00000396525.2_Missense_Mutation_p.E37V	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)		CCCCAGGAACTCGCTGATTAA	0.403																																					p.E37V		Atlas-SNP	.											.	EIF4G2	89	.	0			c.A110T						PASS	.						97.0	93.0	95.0					11																	10827592		2201	4294	6495	SO:0001583	missense	1982	exon4			AGGAACTCGCTGA	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.110A>T	11.37:g.10827592T>A	ENSP00000433664:p.Glu37Val	Somatic	203	0	0		WXS	Illumina HiSeq	Phase_I	205	48	0.234146	NM_001172705		Missense_Mutation	SNP	ENST00000526148.1	37	CCDS31428.1	.	.	.	.	.	.	.	.	.	.	T	28.8	4.949046	0.92660	.	.	ENSG00000110321	ENST00000526148;ENST00000525681;ENST00000339995;ENST00000396525;ENST00000429377;ENST00000531416;ENST00000532082;ENST00000524932;ENST00000532570;ENST00000526591;ENST00000530211;ENST00000527526;ENST00000530702	T;T;T;T;T;T;T;T	0.49139	2.11;2.11;2.11;2.11;1.79;1.82;1.82;0.79	5.34	5.34	0.76211	.	0.000000	0.85682	D	0.000000	T	0.52435	0.1734	N	0.24115	0.695	0.51233	D	0.999912	D;D	0.65815	0.995;0.995	P;P	0.60682	0.878;0.878	T	0.64533	-0.6385	9	0.87932	D	0	-8.5634	15.356	0.74428	0.0:0.0:0.0:1.0	.	37;110	P78344;B4DZF2	IF4G2_HUMAN;.	V	37;37;37;37;110;37;37;37;37;37;37;37;15	ENSP00000433664:E37V;ENSP00000433371:E37V;ENSP00000340281:E37V;ENSP00000379778:E37V;ENSP00000431583:E37V;ENSP00000433121:E37V;ENSP00000435523:E37V;ENSP00000431511:E37V	ENSP00000340281:E37V	E	-	2	0	EIF4G2	10784168	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	8.040000	0.89188	2.023000	0.59567	0.455000	0.32223	GAG	.	.	none		0.403	EIF4G2-006	KNOWN	alternative_5_UTR|non_ATG_start|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000386603.1	NM_001418	
OTOP2	92736	hgsc.bcm.edu	37	17	72926660	72926660	+	Silent	SNP	C	C	T	rs61746106	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:72926660C>T	ENST00000580223.1	+	5	960	c.930C>T	c.(928-930)taC>taT	p.Y310Y	OTOP2_ENST00000331427.4_Silent_p.Y310Y			Q7RTS6	OTOP2_HUMAN	otopetrin 2	310						integral component of membrane (GO:0016021)				breast(4)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(13)|ovary(3)|prostate(4)|skin(1)|urinary_tract(2)	39	all_lung(278;0.172)|Lung NSC(278;0.207)					TCATCATCTACGAGGTTCAAG	0.602													C|||	89	0.0177716	0.0023	0.0403	5008	,	,		16324	0.0		0.0398	False		,,,				2504	0.0184				p.Y310Y		Atlas-SNP	.											.	OTOP2	81	.	0			c.C930T						PASS	.	C		42,4364	46.7+/-81.2	1,40,2162	44.0	42.0	43.0		930	-3.7	1.0	17	dbSNP_129	43	377,8223	121.0+/-180.1	12,353,3935	no	coding-synonymous	OTOP2	NM_178160.2		13,393,6097	TT,TC,CC		4.3837,0.9532,3.2216		310/563	72926660	419,12587	2203	4300	6503	SO:0001819	synonymous_variant	92736	exon6			CATCTACGAGGTT	BK000567	CCDS11708.1	17q25.3	2006-09-20				ENSG00000183034			19657	protein-coding gene	gene with protein product		607827				12651873	Standard	NM_178160		Approved		uc010wrp.2	Q7RTS6		ENST00000580223.1:c.930C>T	17.37:g.72926660C>T		Somatic	221	0	0		WXS	Illumina HiSeq	Phase_I	175	70	0.4	NM_178160		Silent	SNP	ENST00000580223.1	37	CCDS11708.1																																																																																			C|0.972;T|0.028	0.028	strong		0.602	OTOP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445306.1	NM_178160	
C9orf106	414318	hgsc.bcm.edu	37	9	132084621	132084621	+	RNA	SNP	G	G	A	rs913770	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:132084621G>A	ENST00000316786.1	+	0	582							Q8NAJ2	CI106_HUMAN	chromosome 9 open reading frame 106											large_intestine(1)|lung(1)|ovary(1)|skin(1)	4		Ovarian(14;0.00556)|Medulloblastoma(224;0.235)				GATGCCCGGGGGACACTGCCC	0.592													G|||	940	0.1877	0.4183	0.1167	5008	,	,		20687	0.1538		0.0507	False		,,,				2504	0.1022				p.G177R		Atlas-SNP	.											.	C9orf106	7	.	0			c.G529A						PASS	.	G	ARG/GLY	1424,2536		233,958,789	41.0	45.0	44.0		529	-1.1	0.0	9	dbSNP_86	44	392,7934		5,382,3776	yes	missense	C9orf106	NM_001012715.3	125	238,1340,4565	AA,AG,GG		4.7081,35.9596,14.7811	benign	177/233	132084621	1816,10470	1980	4163	6143			414318	exon2			CCCGGGGGACACT	AK092588		9q34.11	2013-12-05	2013-12-05	2013-12-05	ENSG00000179082	ENSG00000179082			31370	other	unknown							Standard	NM_001012715		Approved	bA65J3.5	uc004bxs.2	Q8NAJ2	OTTHUMG00000020781		9.37:g.132084621G>A		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	40	22	0.55	NM_001012715		Missense_Mutation	SNP	ENST00000316786.1	37																																																																																				G|0.838;A|0.162	0.162	strong		0.592	C9orf106-001	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000054576.2		
EIF4G3	8672	hgsc.bcm.edu	37	1	21268194	21268194	+	Missense_Mutation	SNP	G	G	C	rs142103671	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:21268194G>C	ENST00000264211.8	-	8	1479	c.1285C>G	c.(1285-1287)Cca>Gca	p.P429A	EIF4G3_ENST00000374935.3_Intron|EIF4G3_ENST00000400422.1_Missense_Mutation_p.P429A|EIF4G3_ENST00000602326.1_Missense_Mutation_p.P435A|EIF4G3_ENST00000374937.3_Missense_Mutation_p.P435A|EIF4G3_ENST00000544689.1_5'Flank|EIF4G3_ENST00000536266.1_Missense_Mutation_p.P33A|EIF4G3_ENST00000374927.4_Missense_Mutation_p.P429A|EIF4G3_ENST00000374933.3_5'Flank|EIF4G3_ENST00000356916.3_Missense_Mutation_p.P440A	NM_003760.4	NP_003751.2	O43432	IF4G3_HUMAN	eukaryotic translation initiation factor 4 gamma, 3	429					cytokine-mediated signaling pathway (GO:0019221)|positive regulation of meiosis I (GO:0060903)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of translation (GO:0045727)|regulation of translational initiation (GO:0006446)|spermatogenesis (GO:0007283)|viral process (GO:0016032)	cytosol (GO:0005829)|eukaryotic translation initiation factor 4F complex (GO:0016281)	poly(A) RNA binding (GO:0044822)|RNA cap binding (GO:0000339)|translation factor activity, nucleic acid binding (GO:0008135)|translation initiation factor activity (GO:0003743)			endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(18)|lung(20)|ovary(1)|prostate(4)|skin(3)|stomach(1)|urinary_tract(3)	70		all_lung(284;2.61e-06)|Lung NSC(340;2.81e-06)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00149)|Ovarian(437;0.00338)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.023)|COAD - Colon adenocarcinoma(152;5.42e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000327)|GBM - Glioblastoma multiforme(114;0.000696)|Kidney(64;0.0018)|STAD - Stomach adenocarcinoma(196;0.00644)|KIRC - Kidney renal clear cell carcinoma(64;0.0185)|READ - Rectum adenocarcinoma(331;0.124)|Lung(427;0.191)		ACAATGACTGGAGTGTgagga	0.522													G|||	25	0.00499201	0.0008	0.0101	5008	,	,		17613	0.0		0.0099	False		,,,				2504	0.0072				p.P440A		Atlas-SNP	.											.	EIF4G3	300	.	0			c.C1318G						PASS	.	G	ALA/PRO,ALA/PRO,ALA/PRO,ALA/PRO	17,4389	24.3+/-50.5	0,17,2186	111.0	107.0	108.0		1282,1303,1318,1285	0.6	0.0	1	dbSNP_134	108	114,8486	60.6+/-122.4	0,114,4186	yes	missense,missense,missense,missense	EIF4G3	NM_001198801.1,NM_001198802.1,NM_001198803.1,NM_003760.4	27,27,27,27	0,131,6372	CC,CG,GG		1.3256,0.3858,1.0072	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	428/1622,435/1592,440/516,429/1586	21268194	131,12875	2203	4300	6503	SO:0001583	missense	8672	exon14			TGACTGGAGTGTG	AF012072	CCDS214.1, CCDS55580.1, CCDS59192.1, CCDS72723.1	1p36.12	2008-02-05			ENSG00000075151	ENSG00000075151			3298	protein-coding gene	gene with protein product		603929				9418880	Standard	NM_001198801		Approved	eIF4GII	uc001bef.3	O43432	OTTHUMG00000002624	ENST00000264211.8:c.1285C>G	1.37:g.21268194G>C	ENSP00000264211:p.Pro429Ala	Somatic	206	0	0		WXS	Illumina HiSeq	Phase_I	175	74	0.422857	NM_001198803	B9EGQ7|Q15597|Q504Z1|Q5SWC3|Q8NEN1	Missense_Mutation	SNP	ENST00000264211.8	37	CCDS214.1	13	0.005952380952380952	1	0.0020325203252032522	6	0.016574585635359115	0	0.0	6	0.0079155672823219	G	9.610	1.131111	0.21041	0.003858	0.013256	ENSG00000075151	ENST00000264211;ENST00000400415;ENST00000400422;ENST00000374937;ENST00000536266;ENST00000356916;ENST00000374927;ENST00000537059	T;T;T;T;T	0.19250	2.16;2.16;2.16;2.16;2.16	5.89	0.55	0.17219	.	0.429187	0.26684	N	0.023030	T	0.05410	0.0143	N	0.19112	0.55	0.21220	N	0.999753	B;B;B;B;B;B	0.33940	0.3;0.199;0.433;0.0;0.089;0.0	B;B;B;B;B;B	0.35182	0.197;0.097;0.197;0.001;0.061;0.0	T	0.17623	-1.0363	10	0.39692	T	0.17	0.0335	6.2337	0.20750	0.2391:0.4141:0.3468:0.0	.	429;624;555;33;435;429	B4DXR2;Q59GJ0;B1AN89;F5H564;B9EGQ7;O43432	.;.;.;.;.;IF4G3_HUMAN	A	429;625;429;435;33;555;429;440	ENSP00000264211:P429A;ENSP00000383274:P429A;ENSP00000364073:P435A;ENSP00000444693:P33A;ENSP00000364062:P429A	ENSP00000264211:P429A	P	-	1	0	EIF4G3	21140781	0.016000	0.18221	0.017000	0.16124	0.838000	0.47535	-0.014000	0.12656	-0.148000	0.11234	0.655000	0.94253	CCA	G|0.991;C|0.009	0.009	strong		0.522	EIF4G3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000007467.3	NM_003760	
GIF	2694	hgsc.bcm.edu	37	11	59612859	59612859	+	Missense_Mutation	SNP	T	T	C	rs35211634	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:59612859T>C	ENST00000257248.2	-	1	115	c.68A>G	c.(67-69)cAg>cGg	p.Q23R	GIF_ENST00000541311.1_5'UTR	NM_005142.2	NP_005133.2	P27352	IF_HUMAN	gastric intrinsic factor (vitamin B synthesis)	23			Q -> R (in dbSNP:rs35211634). {ECO:0000269|PubMed:14695536, ECO:0000269|PubMed:15738392}.		cobalamin metabolic process (GO:0009235)|cobalamin transport (GO:0015889)|cobalt ion transport (GO:0006824)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|endosome (GO:0005768)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|lysosomal lumen (GO:0043202)|microvillus (GO:0005902)	cobalamin binding (GO:0031419)			large_intestine(4)|liver(1)|lung(6)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	17					Cyanocobalamin(DB00115)	GCATGAACTCTGGGTCTGGGT	0.537													C|||	514	0.102636	0.2716	0.0331	5008	,	,		17712	0.0417		0.0567	False		,,,				2504	0.0337				p.Q23R	NSCLC(53;1139 1245 16872 38474 42853)	Atlas-SNP	.											.	GIF	43	.	0			c.A68G						PASS	.	C	ARG/GLN	866,3536	744.2+/-411.5	90,686,1425	152.0	149.0	150.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	68	-4.4	0.0	11	dbSNP_126	150	413,8177	800.6+/-407.4	18,377,3900	yes	missense	GIF	NM_005142.2	43	108,1063,5325	CC,CT,TT		4.8079,19.6729,9.8445	benign	23/418	59612859	1279,11713	2201	4295	6496	SO:0001583	missense	2694	exon1			GAACTCTGGGTCT	X76562	CCDS7977.1	11q12.1	2013-09-20			ENSG00000134812	ENSG00000134812			4268	protein-coding gene	gene with protein product		609342				2071148	Standard	NM_005142		Approved	TCN3, IF, IFMH, INF	uc001noi.3	P27352	OTTHUMG00000167399	ENST00000257248.2:c.68A>G	11.37:g.59612859T>C	ENSP00000257248:p.Gln23Arg	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	49	43	0.877551	NM_005142	B2RAN8|B4DVZ1	Missense_Mutation	SNP	ENST00000257248.2	37	CCDS7977.1	185	0.08470695970695971	117	0.23780487804878048	10	0.027624309392265192	13	0.022727272727272728	45	0.059366754617414245	C	2.352	-0.348630	0.05208	0.196729	0.048079	ENSG00000134812	ENST00000257248	T	0.34667	1.35	5.46	-4.43	0.03568	.	0.905508	0.09152	N	0.841440	T	0.00012	0.0000	N	0.01267	-0.92	0.58432	P	1.0000000000287557E-6	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.44528	-0.9322	9	0.11794	T	0.64	2.9968	14.5605	0.68133	0.0:0.2199:0.0:0.7801	rs35211634;rs35211634	23;23	B4DVY6;P27352	.;IF_HUMAN	R	23	ENSP00000257248:Q23R	ENSP00000257248:Q23R	Q	-	2	0	GIF	59369435	0.000000	0.05858	0.000000	0.03702	0.047000	0.14425	-2.402000	0.01047	-1.452000	0.01931	-0.215000	0.12644	CAG	T|0.902;C|0.098	0.098	strong		0.537	GIF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394497.1	NM_005142	
UHRF1BP1	54887	hgsc.bcm.edu	37	6	34826921	34826921	+	Missense_Mutation	SNP	G	G	C	rs61732793	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:34826921G>C	ENST00000192788.5	+	14	2959	c.2788G>C	c.(2788-2790)Gag>Cag	p.E930Q	UHRF1BP1_ENST00000452449.2_Missense_Mutation_p.E930Q	NM_017754.3	NP_060224.3	Q6BDS2	URFB1_HUMAN	UHRF1 binding protein 1	930							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						AGCAAGCCCTGAGAAGGTCTT	0.522													G|||	127	0.0253594	0.0015	0.0346	5008	,	,		24340	0.005		0.0557	False		,,,				2504	0.0409				p.E930Q		Atlas-SNP	.											.	UHRF1BP1	102	.	0			c.G2788C						PASS	.	G	GLN/GLU	33,3907		1,31,1938	40.0	41.0	41.0		2788	2.5	0.2	6	dbSNP_129	41	378,7956		11,356,3800	yes	missense	UHRF1BP1	NM_017754.3	29	12,387,5738	CC,CG,GG		4.5356,0.8376,3.3485	possibly-damaging	930/1441	34826921	411,11863	1970	4167	6137	SO:0001583	missense	54887	exon14			AGCCCTGAGAAGG	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.2788G>C	6.37:g.34826921G>C	ENSP00000192788:p.Glu930Gln	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	73	36	0.493151	NM_017754	Q9NXE0	Missense_Mutation	SNP	ENST00000192788.5	37	CCDS43455.1	61	0.027930402930402932	3	0.006097560975609756	15	0.04143646408839779	3	0.005244755244755245	40	0.052770448548812667	G	2.174	-0.389201	0.04932	0.008376	0.045356	ENSG00000065060	ENST00000192788;ENST00000452449	T;T	0.08720	3.06;3.06	5.7	2.5	0.30297	.	1.138310	0.06182	N	0.679576	T	0.01222	0.0040	N	0.08118	0	0.09310	N	1	B	0.20671	0.047	B	0.19148	0.024	T	0.46898	-0.9158	10	0.25751	T	0.34	-1.3808	4.63	0.12496	0.3302:0.0:0.5186:0.1512	rs61732793	930	Q6BDS2	URFB1_HUMAN	Q	930	ENSP00000192788:E930Q;ENSP00000400628:E930Q	ENSP00000192788:E930Q	E	+	1	0	UHRF1BP1	34934899	0.006000	0.16342	0.197000	0.23402	0.596000	0.36781	1.242000	0.32755	0.758000	0.33059	0.591000	0.81541	GAG	G|0.962;C|0.038	0.038	strong		0.522	UHRF1BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040260.1	NM_017754	
FAT3	120114	hgsc.bcm.edu	37	11	92600266	92600266	+	Silent	SNP	G	G	A	rs75649640	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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_ENST00000409404.2_Silent_p.A4006A|FAT3_ENST00000533797.1_Silent_p.A341A			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	73	0	0		WXS	Illumina HiSeq	Phase_I	49	14	0.285714	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	
HLA-DQA1	3117	hgsc.bcm.edu	37	6	32609147	32609147	+	Missense_Mutation	SNP	A	A	T	rs12722051	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:32609147A>T	ENST00000343139.5	+	2	245	c.143A>T	c.(142-144)tAc>tTc	p.Y48F	HLA-DQA1_ENST00000395363.1_Missense_Mutation_p.Y48F|HLA-DQA1_ENST00000374949.2_Missense_Mutation_p.Y48F	NM_002122.3	NP_002113.2	P01909	DQA1_HUMAN	major histocompatibility complex, class II, DQ alpha 1	48	Alpha-1.		Y -> F (in allele DQA1*02:01, allele DQA1*01:03, allele DQA1*06:01 and allele DQA1*06:02; dbSNP:rs12722051).		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			NS(1)|lung(3)|skin(1)|upper_aerodigestive_tract(1)	6						TCTGGCCAGTACACCCATGAA	0.517													.|||	1285	0.256589	0.1407	0.1729	5008	,	,		14819	0.2798		0.2107	False		,,,				2504	0.4959				p.Y48F		Atlas-SNP	.											.	HLA-DQA1	52	.	0			c.A143T						PASS	.	A	PHE/TYR	424,3982		72,280,1851	135.0	112.0	120.0		143	2.6	0.7	6	dbSNP_126	120	1429,7143		305,819,3162	no	missense	HLA-DQA1	NM_002122.3	22	377,1099,5013	TT,TA,AA		16.6706,9.6232,14.278	benign	48/256	32609147	1853,11125	2203	4286	6489	SO:0001583	missense	3117	exon2			GCCAGTACACCCA		CCDS4752.1	6p21.3	2013-01-11			ENSG00000196735	ENSG00000196735		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4942	protein-coding gene	gene with protein product		146880		HLA-DQA			Standard	NM_002122		Approved	CELIAC1	uc003obr.3	P01909	OTTHUMG00000031106	ENST00000343139.5:c.143A>T	6.37:g.32609147A>T	ENSP00000339398:p.Tyr48Phe	Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	141	82	0.58156	NM_002122	O19630|O19706|P01907|P01908|P04225|P04226|P05536|P79553|Q06751|Q29876|Q29994|Q2Q6Y6|Q2Q6Y7|Q2Q6Y8|Q2WCM3|Q30064|Q30067|Q30068|Q30070|Q30071|Q30072|Q30073|Q30086|Q30101|Q5Y7D5|Q5Y7F5|Q6ICU6|Q6PR46|Q6QDB1|Q860W2|Q860W4|Q9BD37|Q9TPM3|Q9UM31	Missense_Mutation	SNP	ENST00000343139.5	37	CCDS4752.1	414|414	0.18956043956043955|0.18956043956043955	68|68	0.13821138211382114|0.13821138211382114	52|52	0.143646408839779|0.143646408839779	145|145	0.2534965034965035|0.2534965034965035	149|149	0.19656992084432717|0.19656992084432717	.|.	0.924|0.924	-0.715060|-0.715060	0.03206|0.03206	0.096232|0.096232	0.166706|0.166706	ENSG00000196735|ENSG00000196735	ENST00000486548|ENST00000343139;ENST00000395364;ENST00000395363;ENST00000496318;ENST00000374949	.|T;T;T;T	.|0.00753	.|5.74;5.74;5.74;5.74	3.83|3.83	2.64|2.64	0.31445|0.31445	.|.	.|0.737589	.|0.12104	.|N	.|0.499246	T|T	0.00178|0.00178	0.0005|0.0005	.|.	.|.	.|.	0.40416|0.40416	P|P	0.020206999999999975|0.020206999999999975	.|B;B	.|0.16396	.|0.017;0.005	.|B;B	.|0.27262	.|0.078;0.035	T|T	0.18085|0.18085	-1.0348|-1.0348	3|8	.|0.02654	.|T	.|1	.|.	7.9549|7.9549	0.30035|0.30035	0.8168:0.0:0.0:0.1832|0.8168:0.0:0.0:0.1832	rs12722051;rs28383443;rs33909604|rs12722051;rs28383443;rs33909604	.|54;48	.|Q59F33;G4XQK2	.|.;.	S|F	21|48	.|ENSP00000339398:Y48F;ENSP00000378767:Y48F;ENSP00000437302:Y48F;ENSP00000364087:Y48F	.|ENSP00000339398:Y48F	T|Y	+|+	1|2	0|0	HLA-DQA1|HLA-DQA1	32717125|32717125	0.003000|0.003000	0.15002|0.15002	0.739000|0.739000	0.30968|0.30968	0.011000|0.011000	0.07611|0.07611	-0.574000|-0.574000	0.05868|0.05868	0.636000|0.636000	0.30508|0.30508	-0.757000|-0.757000	0.03467|0.03467	ACA|TAC	A|0.805;T|0.195	0.195	strong		0.517	HLA-DQA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076176.3	NM_002122	
SERPINB7	8710	hgsc.bcm.edu	37	18	61471523	61471523	+	Missense_Mutation	SNP	G	G	A	rs17782413	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:61471523G>A	ENST00000398019.2	+	8	1122	c.797G>A	c.(796-798)cGa>cAa	p.R266Q	SERPINB7_ENST00000336429.2_Missense_Mutation_p.R266Q|SERPINB7_ENST00000540675.1_Missense_Mutation_p.R249Q|SERPINB7_ENST00000546027.1_Missense_Mutation_p.R266Q	NM_003784.3	NP_003775.1	O75635	SPB7_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 7	266			R -> Q (in dbSNP:rs17782413).		negative regulation of endopeptidase activity (GO:0010951)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of glomerular mesangial cell proliferation (GO:0072126)|positive regulation of platelet-derived growth factor production (GO:0090362)|positive regulation of transforming growth factor beta1 production (GO:0032914)|regulation of proteolysis (GO:0030162)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	serine-type endopeptidase inhibitor activity (GO:0004867)			central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(3)|lung(14)|prostate(1)|skin(3)	27		Esophageal squamous(42;0.129)				AATCCAAGGCGAATGACCTCT	0.333													G|||	791	0.157947	0.0787	0.2277	5008	,	,		20230	0.1071		0.2247	False		,,,				2504	0.1994				p.R266Q		Atlas-SNP	.											.	SERPINB7	66	.	0			c.G797A						PASS	.	G	GLN/ARG,GLN/ARG	519,3887	233.6+/-246.7	27,465,1711	46.0	45.0	45.0		797,797	1.9	1.0	18	dbSNP_123	45	1992,6608	341.3+/-324.0	225,1542,2533	yes	missense,missense	SERPINB7	NM_001040147.1,NM_003784.2	43,43	252,2007,4244	AA,AG,GG		23.1628,11.7794,19.3065	possibly-damaging,possibly-damaging	266/381,266/381	61471523	2511,10495	2203	4300	6503	SO:0001583	missense	8710	exon8			CAAGGCGAATGAC	AF027866	CCDS11988.1, CCDS58633.1	18q21.33	2014-02-18	2005-08-18		ENSG00000166396	ENSG00000166396		"""Serine (or cysteine) peptidase inhibitors"""	13902	protein-coding gene	gene with protein product		603357	"""serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 7"""			24172014	Standard	NM_003784		Approved	MEGSIN	uc002ljl.4	O75635	OTTHUMG00000060591	ENST00000398019.2:c.797G>A	18.37:g.61471523G>A	ENSP00000381101:p.Arg266Gln	Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	28	14	0.5	NM_001261830	B4DUW8|F5GZC0|Q1ED45|Q3KPG4	Missense_Mutation	SNP	ENST00000398019.2	37	CCDS11988.1	346	0.15842490842490842	48	0.0975609756097561	79	0.21823204419889503	56	0.0979020979020979	163	0.21503957783641162	G	13.79	2.343575	0.41498	0.117794	0.231628	ENSG00000166396	ENST00000336429;ENST00000398019;ENST00000540675;ENST00000546027	D;D;D;D	0.84370	-1.84;-1.84;-1.84;-1.84	5.92	1.9	0.25705	Serpin domain (3);	0.423452	0.22978	N	0.053345	T	0.00073	0.0002	L	0.31578	0.945	0.80722	P	0.0	P;P	0.41524	0.709;0.753	B;B	0.32533	0.091;0.147	T	0.03268	-1.1054	9	0.38643	T	0.18	.	4.6409	0.12548	0.4709:0.0:0.3723:0.1567	rs17782413;rs52800605;rs17782413	249;266	F5GZC0;O75635	.;SPB7_HUMAN	Q	266;266;249;266	ENSP00000337212:R266Q;ENSP00000381101:R266Q;ENSP00000444572:R249Q;ENSP00000444861:R266Q	ENSP00000337212:R266Q	R	+	2	0	SERPINB7	59622503	0.000000	0.05858	0.975000	0.42487	0.866000	0.49608	-0.195000	0.09546	0.495000	0.27882	-0.302000	0.09304	CGA	G|0.824;A|0.176	0.176	strong		0.333	SERPINB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000134007.1	NM_003784	
RASSF6	166824	hgsc.bcm.edu	37	4	74459206	74459206	+	Missense_Mutation	SNP	A	A	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:74459206A>C	ENST00000342081.3	-	4	475	c.345T>G	c.(343-345)ttT>ttG	p.F115L	RASSF6_ENST00000395777.2_Missense_Mutation_p.F83L|RASSF6_ENST00000335049.5_Missense_Mutation_p.F71L|RASSF6_ENST00000307439.5_Missense_Mutation_p.F83L	NM_201431.2	NP_958834.1	Q6ZTQ3	RASF6_HUMAN	Ras association (RalGDS/AF-6) domain family member 6	115					apoptotic process (GO:0006915)|positive regulation of apoptotic process (GO:0043065)|signal transduction (GO:0007165)					breast(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(4)|pancreas(2)|skin(2)	17	Breast(15;0.00102)		all cancers(17;0.00104)|Lung(101;0.128)|LUSC - Lung squamous cell carcinoma(112;0.187)			TCATACTAGTAAAAGAAGAGA	0.363																																					p.F115L		Atlas-SNP	.											.	RASSF6	68	.	0			c.T345G						PASS	.						115.0	115.0	115.0					4																	74459206		2203	4300	6503	SO:0001583	missense	166824	exon4			ACTAGTAAAAGAA	AY217664	CCDS3558.1, CCDS3559.1, CCDS58904.1, CCDS58905.1	4q21.1	2008-02-22	2008-02-22		ENSG00000169435	ENSG00000169435			20796	protein-coding gene	gene with protein product		612620					Standard	NM_177532		Approved		uc003hhd.2	Q6ZTQ3	OTTHUMG00000130007	ENST00000342081.3:c.345T>G	4.37:g.74459206A>C	ENSP00000340578:p.Phe115Leu	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	101	20	0.19802	NM_201431	Q68DT2|Q6PDA6|Q86WG9|Q86WH0	Missense_Mutation	SNP	ENST00000342081.3	37	CCDS3558.1	.	.	.	.	.	.	.	.	.	.	A	6.548	0.469333	0.12461	.	.	ENSG00000169435	ENST00000307439;ENST00000342081;ENST00000395777;ENST00000335049	T;T;T;T	0.37235	1.21;1.21;1.21;1.21	4.87	-1.98	0.07480	.	0.620622	0.17776	N	0.162414	T	0.20700	0.0498	L	0.34521	1.04	0.09310	N	0.999999	B;B;B	0.16166	0.013;0.013;0.016	B;B;B	0.19148	0.024;0.014;0.015	T	0.33624	-0.9861	10	0.10636	T	0.68	-3.5922	9.1491	0.36951	0.4954:0.0:0.5046:0.0	.	71;83;115	Q6ZTQ3-3;Q6ZTQ3-4;Q6ZTQ3	.;.;RASF6_HUMAN	L	83;115;83;71	ENSP00000303877:F83L;ENSP00000340578:F115L;ENSP00000379123:F83L;ENSP00000335582:F71L	ENSP00000303877:F83L	F	-	3	2	RASSF6	74678070	0.159000	0.22864	0.029000	0.17559	0.029000	0.11900	-0.191000	0.09601	-0.624000	0.05611	0.443000	0.29094	TTT	.	.	none		0.363	RASSF6-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252279.1	NM_177532	
CYP4F11	57834	hgsc.bcm.edu	37	19	16032935	16032935	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:16032935G>A	ENST00000402119.4	-	8	1453	c.1027C>T	c.(1027-1029)Cac>Tac	p.H343Y	CYP4F11_ENST00000326742.8_Missense_Mutation_p.H343Y|CYP4F11_ENST00000591841.1_Missense_Mutation_p.H18Y|CYP4F11_ENST00000248041.8_Missense_Mutation_p.H343Y	NM_021187.3	NP_067010.3			cytochrome P450, family 4, subfamily F, polypeptide 11											NS(1)|breast(3)|endometrium(4)|large_intestine(2)|lung(11)|ovary(1)|skin(3)	25						TTTGCAAGGTGGTATAGGACC	0.542																																					p.H343Y		Atlas-SNP	.											CYP4F11,NS,haematopoietic_neoplasm,0,3	CYP4F11	83	3	0			c.C1027T						scavenged	.						114.0	97.0	103.0					19																	16032935		2203	4300	6503	SO:0001583	missense	57834	exon9			CAAGGTGGTATAG	AF236085	CCDS12337.1	19p13.1	2011-07-29	2003-01-14		ENSG00000171903	ENSG00000171903		"""Cytochrome P450s"""	13265	protein-coding gene	gene with protein product		611517	"""cytochrome P450, subfamily IVF, polypeptide 11"""			10964514, 9068972	Standard	NM_021187		Approved		uc002nbu.2	Q9HBI6		ENST00000402119.4:c.1027C>T	19.37:g.16032935G>A	ENSP00000384588:p.His343Tyr	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	85	2	0.0235294	NM_001128932		Missense_Mutation	SNP	ENST00000402119.4	37	CCDS12337.1	.	.	.	.	.	.	.	.	.	.	g	11.02	1.515541	0.27123	.	.	ENSG00000171903	ENST00000402119;ENST00000248041;ENST00000326742	T;T;T	0.77877	-1.13;-1.13;-0.25	2.77	1.71	0.24356	.	0.070458	0.52532	U	0.000066	T	0.69006	0.3063	N	0.21240	0.645	0.28485	N	0.914757	B;P	0.37573	0.002;0.6	B;P	0.46885	0.015;0.53	T	0.64089	-0.6489	10	0.66056	D	0.02	.	7.1013	0.25338	0.0:0.0:0.2473:0.7527	.	343;343	F8W978;Q9HBI6	.;CP4FB_HUMAN	Y	343	ENSP00000384588:H343Y;ENSP00000248041:H343Y;ENSP00000319859:H343Y	ENSP00000248041:H343Y	H	-	1	0	CYP4F11	15893935	1.000000	0.71417	0.980000	0.43619	0.098000	0.18820	3.350000	0.52224	0.284000	0.22305	-0.516000	0.04426	CAC	.	.	none		0.542	CYP4F11-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460385.2	NM_021187	
COL4A3	1285	hgsc.bcm.edu	37	2	228131169	228131169	+	Missense_Mutation	SNP	A	A	G	rs11677877	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:228131169A>G	ENST00000396578.3	+	22	1514	c.1352A>G	c.(1351-1353)cAc>cGc	p.H451R	AC097662.2_ENST00000433324.1_RNA|AC097662.2_ENST00000439598.2_RNA|AC097662.2_ENST00000396588.2_RNA|AC097662.2_ENST00000437673.1_RNA	NM_000091.4	NP_000082.2	Q01955	CO4A3_HUMAN	collagen, type IV, alpha 3 (Goodpasture antigen)	451	Triple-helical region.		H -> R (in dbSNP:rs11677877). {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)		CCTGGAGATCACGGACTGCCA	0.398													G|||	558	0.111422	0.0666	0.183	5008	,	,		17815	0.1577		0.0686	False		,,,				2504	0.1176				p.H451R		Atlas-SNP	.											COL4A3_ENST00000328380,caecum,carcinoma,-1,2	COL4A3	293	2	0			c.A1352G	GRCh37	CM085146	COL4A3	M	rs11677877	scavenged	.	G	ARG/HIS	245,3437		10,225,1606	72.0	70.0	71.0		1352	-4.1	0.0	2	dbSNP_120	71	628,7562		21,586,3488	yes	missense	COL4A3	NM_000091.4	29	31,811,5094	GG,GA,AA		7.6679,6.654,7.3534	benign	451/1671	228131169	873,10999	1841	4095	5936	SO:0001583	missense	1285	exon22			GAGATCACGGACT		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.1352A>G	2.37:g.228131169A>G	ENSP00000379823:p.His451Arg	Somatic	250	3	0.012		WXS	Illumina HiSeq	Phase_I	227	112	0.493392	NM_000091	Q53QQ1|Q53R14|Q53RW8|Q9BQT2|Q9NYC4|Q9UDJ9|Q9UDK9|Q9UDL0|Q9UDL1	Missense_Mutation	SNP	ENST00000396578.3	37	CCDS42829.1	221	0.10119047619047619	25	0.0508130081300813	60	0.16574585635359115	87	0.1520979020979021	49	0.06464379947229551	G	5.410	0.260736	0.10239	0.06654	0.076679	ENSG00000169031	ENST00000396578;ENST00000328380;ENST00000335583;ENST00000396574;ENST00000315699	D	0.96619	-4.07	5.69	-4.09	0.03951	.	1.358520	0.04708	N	0.417004	T	0.00784	0.0026	N	0.00313	-1.665	0.80722	P	0.0	B;B;B;B	0.26258	0.015;0.043;0.043;0.145	B;B;B;B	0.29267	0.019;0.012;0.019;0.1	T	0.63545	-0.6613	9	0.06891	T	0.86	.	4.1959	0.10443	0.5232:0.1033:0.2691:0.1045	rs11677877;rs56438970;rs11677877	451;451;451;451	Q01955-5;Q01955-4;Q01955-2;Q01955	.;.;.;CO4A3_HUMAN	R	451	ENSP00000379823:H451R	ENSP00000323334:H451R	H	+	2	0	COL4A3	227839413	0.000000	0.05858	0.000000	0.03702	0.127000	0.20565	-0.285000	0.08410	-1.113000	0.02981	-1.595000	0.00837	CAC	A|0.908;G|0.092	0.092	strong		0.398	COL4A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331409.2	NM_000091	
KRT73	319101	hgsc.bcm.edu	37	12	53002197	53002197	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:53002197C>T	ENST00000305748.3	-	9	1440	c.1406G>A	c.(1405-1407)gGg>gAg	p.G469E	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	469	Tail.					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)		AAAGCCAGCCCCTGTGCCTGC	0.612																																					p.G469E		Atlas-SNP	.											.	KRT73	101	.	0			c.G1406A						PASS	.						41.0	39.0	40.0					12																	53002197		2203	4300	6503	SO:0001583	missense	319101	exon9			CCAGCCCCTGTGC	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.1406G>A	12.37:g.53002197C>T	ENSP00000307014:p.Gly469Glu	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	69	9	0.130435	NM_175068	Q32MB2	Missense_Mutation	SNP	ENST00000305748.3	37	CCDS8834.1	.	.	.	.	.	.	.	.	.	.	C	18.20	3.570160	0.65765	.	.	ENSG00000186049	ENST00000305748;ENST00000552855	D;D	0.82893	-1.58;-1.66	4.88	4.88	0.63580	.	0.185839	0.26421	N	0.024464	T	0.74473	0.3721	L	0.46819	1.47	0.09310	N	0.999999	P	0.39216	0.664	B	0.35607	0.206	T	0.64287	-0.6443	10	0.09338	T	0.73	.	13.7369	0.62824	0.0:1.0:0.0:0.0	.	469	Q86Y46	K2C73_HUMAN	E	469;214	ENSP00000307014:G469E;ENSP00000449081:G214E	ENSP00000307014:G469E	G	-	2	0	KRT73	51288464	0.031000	0.19500	0.210000	0.23637	0.137000	0.21094	1.906000	0.39887	2.709000	0.92574	0.655000	0.94253	GGG	.	.	none		0.612	KRT73-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405700.1	NM_175068	
IGSF10	285313	hgsc.bcm.edu	37	3	151155620	151155620	+	Silent	SNP	G	G	A	rs6781302	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:151155620G>A	ENST00000282466.3	-	6	6728	c.6729C>T	c.(6727-6729)aaC>aaT	p.N2243N	IGSF10_ENST00000495443.1_5'UTR	NM_001178145.1|NM_001178146.1|NM_178822.4	NP_001171616.1|NP_001171617.1|NP_849144.2	Q6WRI0	IGS10_HUMAN	immunoglobulin superfamily, member 10	2243	Ig-like C2-type 9.			N -> S (in Ref. 3; AAH31063). {ECO:0000305}.	cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)	extracellular region (GO:0005576)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(24)|liver(4)|lung(43)|ovary(8)|prostate(4)|skin(9)|stomach(1)|urinary_tract(3)	116			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			TAACAGTTCTGTTTGTATACA	0.438													G|||	2964	0.591853	0.5015	0.5937	5008	,	,		22139	0.5169		0.7565	False		,,,				2504	0.6207				p.N2243N		Atlas-SNP	.											.	IGSF10	279	.	0			c.C6729T						PASS	.	G	,,	2340,2066	605.2+/-390.5	628,1084,491	110.0	98.0	102.0		810,666,6729	3.7	0.1	3	dbSNP_116	102	6549,2051	720.2+/-406.3	2496,1557,247	no	coding-synonymous,coding-synonymous,coding-synonymous	IGSF10	NM_001178145.1,NM_001178146.1,NM_178822.4	,,	3124,2641,738	AA,AG,GG		23.8488,46.8906,31.6546	,,	270/651,222/603,2243/2624	151155620	8889,4117	2203	4300	6503	SO:0001819	synonymous_variant	285313	exon6			AGTTCTGTTTGTA	AY273815	CCDS3160.1	3q25.1	2013-01-11			ENSG00000152580	ENSG00000152580		"""Immunoglobulin superfamily / I-set domain containing"""	26384	protein-coding gene	gene with protein product						12477932	Standard	NM_178822		Approved	FLJ25972, CMF608	uc011bod.2	Q6WRI0	OTTHUMG00000159856	ENST00000282466.3:c.6729C>T	3.37:g.151155620G>A		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	47	22	0.468085	NM_178822	Q86YJ9|Q8N772|Q8NA84	Silent	SNP	ENST00000282466.3	37	CCDS3160.1																																																																																			G|0.352;A|0.648	0.648	strong		0.438	IGSF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357782.1	NM_178822	
TBC1D26	353149	hgsc.bcm.edu	37	17	15644506	15644506	+	Missense_Mutation	SNP	C	C	T	rs11650318	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:15644506C>T	ENST00000437605.2	+	10	867	c.617C>T	c.(616-618)gCt>gTt	p.A206V	ZNF286A_ENST00000413242.2_3'UTR|AC005324.6_ENST00000580194.1_RNA|AC005324.6_ENST00000434017.1_RNA|AC005324.6_ENST00000433873.1_RNA	NM_178571.4	NP_848666	Q86UD7	TBC26_HUMAN	TBC1 domain family, member 26	206	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.		A -> V (in dbSNP:rs11650318). {ECO:0000269|PubMed:15489334}.				Rab GTPase activator activity (GO:0005097)			endometrium(1)|large_intestine(1)|lung(4)|skin(1)	7				UCEC - Uterine corpus endometrioid carcinoma (92;0.0822)|READ - Rectum adenocarcinoma(1115;0.0222)|BRCA - Breast invasive adenocarcinoma(8;0.078)		GAGGAAGATGCTTTCTGGGCG	0.622													.|||	1235	0.246605	0.0817	0.2651	5008	,	,		21089	0.255		0.3946	False		,,,				2504	0.2955				p.A206V		Atlas-SNP	.											.	TBC1D26	16	.	0			c.C617T						PASS	.	C	VAL/ALA	577,3797	223.0+/-239.6	41,495,1651	91.0	98.0	96.0		617	0.7	0.0	17	dbSNP_120	96	3426,5150	489.3+/-372.6	665,2096,1527	yes	missense	TBC1D26	NM_178571.4	64	706,2591,3178	TT,TC,CC		39.9487,13.1916,30.9112	probably-damaging	206/251	15644506	4003,8947	2187	4288	6475	SO:0001583	missense	353149	exon10			AAGATGCTTTCTG		CCDS42265.1	17p11.2	2008-11-04			ENSG00000214946	ENSG00000214946			28745	protein-coding gene	gene with protein product						11347906	Standard	NM_178571		Approved	MGC51025	uc010cov.3	Q86UD7	OTTHUMG00000059071	ENST00000437605.2:c.617C>T	17.37:g.15644506C>T	ENSP00000410111:p.Ala206Val	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	80	38	0.475	NM_178571	A8K929|Q4G172	Missense_Mutation	SNP	ENST00000437605.2	37	CCDS42265.1																																																																																			C|0.723;T|0.277	0.277	strong		0.622	TBC1D26-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_178571	
PLA2G3	50487	hgsc.bcm.edu	37	22	31536133	31536133	+	Missense_Mutation	SNP	A	A	C	rs2232176	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:31536133A>C	ENST00000215885.3	-	1	460	c.208T>G	c.(208-210)Tca>Gca	p.S70A		NM_015715.3	NP_056530.2	Q9NZ20	PA2G3_HUMAN	phospholipase A2, group III	70			S -> A (in dbSNP:rs2232176). {ECO:0000269|PubMed:10713052, ECO:0000269|PubMed:15489334}.		acrosome assembly (GO:0001675)|cilium morphogenesis (GO:0060271)|glycerophospholipid biosynthetic process (GO:0046474)|lipid catabolic process (GO:0016042)|lipoxygenase pathway (GO:0019372)|mast cell degranulation (GO:0043303)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|sperm axoneme assembly (GO:0007288)	centriole (GO:0005814)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|mast cell granule (GO:0042629)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|calcium-dependent phospholipase A2 activity (GO:0047498)			large_intestine(1)|lung(10)|ovary(1)|prostate(2)|skin(3)|urinary_tract(1)	18						CAGCTACATGACTGCAGCCTC	0.642													C|||	4167	0.832069	0.7231	0.8646	5008	,	,		18627	0.9325		0.7873	False		,,,				2504	0.8988				p.S70A		Atlas-SNP	.											PLA2G3_ENST00000215885,NS,carcinoma,0,4	PLA2G3	85	4	0			c.T208G						scavenged	.	C	ALA/SER	3100,1306	431.6+/-343.0	1086,928,189	66.0	69.0	68.0		208	3.6	0.1	22	dbSNP_98	68	6684,1916	333.3+/-320.5	2596,1492,212	yes	missense	PLA2G3	NM_015715.3	99	3682,2420,401	CC,CA,AA		22.2791,29.6414,24.7732	benign	70/510	31536133	9784,3222	2203	4300	6503	SO:0001583	missense	50487	exon1			TACATGACTGCAG	AF220490	CCDS13889.1	22q12.2	2008-09-19			ENSG00000100078	ENSG00000100078	3.1.1.4		17934	protein-coding gene	gene with protein product		611651				10713052	Standard	NM_015715		Approved	GIII-SPLA2	uc003aka.3	Q9NZ20	OTTHUMG00000151255	ENST00000215885.3:c.208T>G	22.37:g.31536133A>C	ENSP00000215885:p.Ser70Ala	Somatic	49	1	0.0204082		WXS	Illumina HiSeq	Phase_I	37	15	0.405405	NM_015715	O95768	Missense_Mutation	SNP	ENST00000215885.3	37	CCDS13889.1	1786	0.8177655677655677	358	0.7276422764227642	306	0.8453038674033149	529	0.9248251748251748	593	0.7823218997361477	C	1.301	-0.605006	0.03717	0.703586	0.777209	ENSG00000100078	ENST00000215885	T	0.11712	2.75	5.69	3.58	0.41010	.	1.051720	0.07391	N	0.889048	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	0.21348	-1.0248	9	0.06625	T	0.88	-3.9647	7.1186	0.25431	0.3019:0.6191:0.0:0.079	rs2232176;rs17856726;rs61572667;rs2232176	70	Q9NZ20	PA2G3_HUMAN	A	70	ENSP00000215885:S70A	ENSP00000215885:S70A	S	-	1	0	PLA2G3	29866133	0.335000	0.24748	0.103000	0.21229	0.560000	0.35617	0.989000	0.29629	0.342000	0.23796	-0.121000	0.15023	TCA	A|0.211;C|0.789	0.789	strong		0.642	PLA2G3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321938.1	NM_015715	
FKBP15	23307	hgsc.bcm.edu	37	9	115936860	115936860	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:115936860G>A	ENST00000238256.3	-	22	2344	c.2227C>T	c.(2227-2229)Ctc>Ttc	p.L743F		NM_015258.1	NP_056073.1	Q5T1M5	FKB15_HUMAN	FK506 binding protein 15, 133kDa	743					endocytosis (GO:0006897)|negative regulation of phosphatase activity (GO:0010923)|protein folding (GO:0006457)	actin filament (GO:0005884)|axon (GO:0030424)|endosome (GO:0005768)|growth cone (GO:0030426)|membrane (GO:0016020)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(3)|lung(9)|ovary(3)|urinary_tract(1)	26						CTTTCTGAGAGGTTCTTAGGA	0.443																																					p.L743F		Atlas-SNP	.											FKBP15_ENST00000238256,NS,carcinoma,+1,2	FKBP15	128	2	0			c.C2227T						PASS	.						65.0	63.0	64.0					9																	115936860		1882	4104	5986	SO:0001583	missense	23307	exon22			CTGAGAGGTTCTT	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.2227C>T	9.37:g.115936860G>A	ENSP00000238256:p.Leu743Phe	Somatic	219	0	0		WXS	Illumina HiSeq	Phase_I	133	39	0.293233	NM_015258	Q05DK8|Q5T1M2|Q6DD85|Q9Y4D0	Missense_Mutation	SNP	ENST00000238256.3	37	CCDS48007.1	.	.	.	.	.	.	.	.	.	.	g	20.6	4.021430	0.75275	.	.	ENSG00000119321	ENST00000446284;ENST00000238256	T;T	0.29397	1.57;1.58	6.07	6.07	0.98685	.	.	.	.	.	T	0.57227	0.2039	M	0.72894	2.215	0.39987	D	0.974995	D;P	0.89917	1.0;0.788	D;B	0.76575	0.988;0.257	T	0.58194	-0.7679	9	0.72032	D	0.01	-11.325	18.151	0.89674	0.0:0.0:1.0:0.0	.	324;743	B4DVS2;Q5T1M5	.;FKB15_HUMAN	F	768;743	ENSP00000416158:L768F;ENSP00000238256:L743F	ENSP00000238256:L743F	L	-	1	0	FKBP15	114976681	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	4.051000	0.57412	2.890000	0.99128	0.586000	0.80456	CTC	.	.	none		0.443	FKBP15-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_015258	
LHB	3972	hgsc.bcm.edu	37	19	49519883	49519883	+	Missense_Mutation	SNP	A	A	G	rs34349826	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:49519883A>G	ENST00000221421.2	-	2	103	c.104T>C	c.(103-105)aTc>aCc	p.I35T	CTB-60B18.10_ENST00000600007.1_lincRNA	NM_000894.2	NP_000885.1	P01229	LSHB_HUMAN	luteinizing hormone beta polypeptide	35			I -> T (in dbSNP:rs34349826). {ECO:0000269|PubMed:9886510}.		cell-cell signaling (GO:0007267)|cellular protein metabolic process (GO:0044267)|male gonad development (GO:0008584)|peptide hormone processing (GO:0016486)|progesterone biosynthetic process (GO:0006701)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	receptor binding (GO:0005102)			cervix(1)|endometrium(1)|large_intestine(1)|lung(4)|prostate(1)	8		all_epithelial(76;9.62e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		all cancers(93;0.000371)|OV - Ovarian serous cystadenocarcinoma(262;0.000503)|GBM - Glioblastoma multiforme(486;0.00518)|Epithelial(262;0.0427)		GACAGCCAGGATGGCATTGAT	0.657																																					p.I35T		Atlas-SNP	.											LHB,NS,carcinoma,0,1	LHB	20	1	0			c.T104C	GRCh37	CM993949	LHB	M	rs34349826	scavenged	.	G	THR/ILE	78,4328		7,64,2132	92.0	74.0	80.0		104	3.1	1.0	19	dbSNP_126	80	290,8310		21,248,4031	no	missense	LHB	NM_000894.2	89	28,312,6163	GG,GA,AA		3.3721,1.7703,2.8295	benign	35/142	49519883	368,12638	2203	4300	6503	SO:0001583	missense	3972	exon2			GCCAGGATGGCAT		CCDS12748.1	19q13.3	2013-02-26				ENSG00000104826		"""Endogenous ligands"""	6584	protein-coding gene	gene with protein product	"""lutropin, beta chain"", ""interstitial cell stimulating hormone, beta chain"", ""luteinizing hormone beta subunit"""	152780				1191677	Standard	NM_000894		Approved	LSH-B, CGB4, hLHB	uc002plt.3	P01229		ENST00000221421.2:c.104T>C	19.37:g.49519883A>G	ENSP00000221421:p.Ile35Thr	Somatic	374	1	0.0026738		WXS	Illumina HiSeq	Phase_I	260	40	0.153846	NM_000894	Q9UDI0	Missense_Mutation	SNP	ENST00000221421.2	37	CCDS12748.1	.	.	.	.	.	.	.	.	.	.	G	0.004	-2.382431	0.00205	0.017703	0.033721	ENSG00000104826	ENST00000221421;ENST00000391870	D	0.88818	-2.43	4.18	3.14	0.36123	Cystine knot (1);	0.112082	0.64402	N	0.000015	T	0.31918	0.0812	N	0.00179	-1.91	0.52099	P	5.699999999997374E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.57051	-0.7877	9	0.02654	T	1	-22.3916	7.0132	0.24873	0.2118:0.0:0.7882:0.0	rs34349826	35	P01229	LSHB_HUMAN	T	35;51	ENSP00000221421:I35T	ENSP00000221421:I35T	I	-	2	0	LHB	54211695	0.998000	0.40836	0.997000	0.53966	0.049000	0.14656	2.059000	0.41384	0.535000	0.28714	-1.403000	0.01137	ATC	G|1.000;|0.000	1.000	weak		0.657	LHB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466246.1	NM_000894	
FNIP2	57600	hgsc.bcm.edu	37	4	159789441	159789441	+	Missense_Mutation	SNP	C	C	A	rs62001914	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:159789441C>A	ENST00000264433.6	+	13	1728	c.1653C>A	c.(1651-1653)agC>agA	p.S551R	FNIP2_ENST00000379346.3_Missense_Mutation_p.S574R	NM_020840.1	NP_065891.1	Q9P278	FNIP2_HUMAN	folliculin interacting protein 2	551	Interaction with PRKAA1.				intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein phosphorylation (GO:0006468)|regulation of protein phosphorylation (GO:0001932)	cytoplasm (GO:0005737)|microtubule organizing center (GO:0005815)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(3)|prostate(1)	9	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.00936)		TAAATGGGAGCAAGATCATAA	0.502													C|||	46	0.0091853	0.0023	0.0086	5008	,	,		20745	0.0		0.0358	False		,,,				2504	0.001				p.S551R		Atlas-SNP	.											.	FNIP2	90	.	0			c.C1653A						PASS	.	C	ARG/SER	13,4195		0,13,2091	84.0	88.0	87.0		1653	5.8	1.0	4	dbSNP_129	87	276,8190		4,268,3961	yes	missense	FNIP2	NM_020840.1	110	4,281,6052	AA,AC,CC		3.2601,0.3089,2.2803	probably-damaging	551/1115	159789441	289,12385	2104	4233	6337	SO:0001583	missense	57600	exon13			TGGGAGCAAGATC	AB040883	CCDS47155.1	4q32.1	2012-10-31			ENSG00000052795	ENSG00000052795			29280	protein-coding gene	gene with protein product	"""O6-methylguanine-induced apoptosis 1"""	612768				18403135	Standard	NM_020840		Approved	KIAA1450, FNIPL, MAPO1	uc003iqe.4	Q9P278	OTTHUMG00000161983	ENST00000264433.6:c.1653C>A	4.37:g.159789441C>A	ENSP00000264433:p.Ser551Arg	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	72	33	0.458333	NM_020840	Q05DC3|Q96I31|Q9H994	Missense_Mutation	SNP	ENST00000264433.6	37	CCDS47155.1	31	0.014194139194139194	1	0.0020325203252032522	4	0.011049723756906077	0	0.0	26	0.03430079155672823	C	16.79	3.220905	0.58560	0.003089	0.032601	ENSG00000052795	ENST00000264433;ENST00000512986;ENST00000379346	T;T;T	0.32753	1.47;1.5;1.44	5.84	5.84	0.93424	.	.	.	.	.	T	0.17619	0.0423	M	0.78916	2.43	0.41991	D	0.990848	B	0.26400	0.148	B	0.36335	0.222	T	0.08743	-1.0707	8	.	.	.	.	11.4662	0.50241	0.0:0.8618:0.0:0.1382	rs62001914	551	Q9P278	FNIP2_HUMAN	R	551;574;574	ENSP00000264433:S551R;ENSP00000421488:S574R;ENSP00000368651:S574R	.	S	+	3	2	FNIP2	160008891	0.945000	0.32115	1.000000	0.80357	0.947000	0.59692	0.108000	0.15396	2.776000	0.95493	0.650000	0.86243	AGC	C|0.982;A|0.018	0.018	strong		0.502	FNIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366602.1	NM_020840	
EYS	346007	hgsc.bcm.edu	37	6	65300516	65300516	+	Missense_Mutation	SNP	T	T	G	rs57312007	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:65300516T>G	ENST00000370621.3	-	26	5770	c.5244A>C	c.(5242-5244)ttA>ttC	p.L1748F	EYS_ENST00000503581.1_Missense_Mutation_p.L1748F|EYS_ENST00000370616.2_Missense_Mutation_p.L1748F			Q5T1H1	EYS_HUMAN	eyes shut homolog (Drosophila)	1748			L -> F (in dbSNP:rs57312007). {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						TTTGTAAGTTTAACTCAAAAT	0.348													T|||	364	0.0726837	0.0567	0.0548	5008	,	,		19501	0.0228		0.1312	False		,,,				2504	0.0982				p.L1748F		Atlas-SNP	.											.	EYS	527	.	0			c.A5244C						PASS	.	T	PHE/LEU	114,1270		7,100,585	40.0	37.0	38.0		5244	-7.6	0.0	6	dbSNP_129	38	422,2758		23,376,1191	yes	missense	EYS	NM_001142800.1	22	30,476,1776	GG,GT,TT		13.2704,8.237,11.7441	possibly-damaging	1748/3145	65300516	536,4028	692	1590	2282	SO:0001583	missense	346007	exon26			TAAGTTTAACTCA		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.5244A>C	6.37:g.65300516T>G	ENSP00000359655:p.Leu1748Phe	Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	164	82	0.5	NM_001142800	A2RUR2|A8MVE7|B7TYK8|B7UUQ3|B7ZBE7|B7ZBE8|B7ZBR3|B9ZVD2|Q5SZM4|Q5T3C8|Q5T669|Q5TEL3|Q5TEL4|Q5VVG4|Q6UY05|Q9H557|Q9NQ15	Missense_Mutation	SNP	ENST00000370621.3	37		159	0.07280219780219781	29	0.05894308943089431	21	0.058011049723756904	14	0.024475524475524476	95	0.12532981530343007	T	9.392	1.075817	0.20227	0.08237	0.132704	ENSG00000188107	ENST00000503581;ENST00000370621;ENST00000370616	D;D;D	0.85339	-1.97;-1.94;-1.94	5.71	-7.63	0.01290	.	.	.	.	.	T	0.36580	0.0972	N	0.08118	0	0.80722	P	0.0	B;B	0.33171	0.4;0.055	B;B	0.30029	0.11;0.021	T	0.44360	-0.9333	8	0.25106	T	0.35	.	0.4009	0.00426	0.3497:0.1432:0.1903:0.3168	rs57312007	1748;1748	Q5T1H1-1;Q5T1H1	.;EYS_HUMAN	F	1748	ENSP00000424243:L1748F;ENSP00000359655:L1748F;ENSP00000359650:L1748F	ENSP00000359650:L1748F	L	-	3	2	EYS	65357237	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.161000	0.10026	-0.878000	0.04007	-0.353000	0.07706	TTA	T|0.927;G|0.073	0.073	strong		0.348	EYS-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351351.3	XM_294050	
HSD17B11	51170	hgsc.bcm.edu	37	4	88293887	88293887	+	Silent	SNP	G	G	A	rs6531985	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:88293887G>A	ENST00000358290.4	-	4	846	c.531C>T	c.(529-531)gtC>gtT	p.V177V	HSD17B11_ENST00000507518.1_5'UTR|HSD17B11_ENST00000507286.1_Silent_p.V133V	NM_016245.3	NP_057329.2	Q8NBQ5	DHB11_HUMAN	hydroxysteroid (17-beta) dehydrogenase 11	177					androgen catabolic process (GO:0006710)|steroid biosynthetic process (GO:0006694)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|lipid particle (GO:0005811)	estradiol 17-beta-dehydrogenase activity (GO:0004303)|steroid dehydrogenase activity (GO:0016229)			cervix(1)|endometrium(4)|kidney(2)|lung(2)|ovary(2)	11		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.000339)		AGGGGACCGAGACATGTCCAG	0.413													A|||	1429	0.285343	0.5764	0.2882	5008	,	,		14982	0.005		0.327	False		,,,				2504	0.136				p.V177V		Atlas-SNP	.											.	HSD17B11	28	.	0			c.C531T						PASS	.	A		2371,2035	564.7+/-381.5	634,1103,466	159.0	130.0	140.0		531	-8.2	0.0	4	dbSNP_116	140	2700,5900	682.1+/-403.8	406,1888,2006	no	coding-synonymous	HSD17B11	NM_016245.3		1040,2991,2472	AA,AG,GG		31.3953,46.187,38.9897		177/301	88293887	5071,7935	2203	4300	6503	SO:0001819	synonymous_variant	51170	exon4			GACCGAGACATGT	AF126780	CCDS3619.1	4q22.1	2011-09-20	2006-11-22	2006-11-22	ENSG00000198189	ENSG00000198189	1.1.1.-	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 3"""	22960	protein-coding gene	gene with protein product	"""retinal short-chain dehydrogenase/reductase 2"", ""short chain dehydrogenase/reductase family 16C, member 2"""	612831	"""dehydrogenase/reductase (SDR family) member 8"""	DHRS8		11165019, 12697717, 19027726	Standard	XM_006714232		Approved	RetSDR2, 17-BETA-HSD11, 17-BETA-HSDXI, PAN1B, SDR16C2	uc003hqp.2	Q8NBQ5	OTTHUMG00000130594	ENST00000358290.4:c.531C>T	4.37:g.88293887G>A		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	84	44	0.52381	NM_016245	Q96HF6|Q9UKU4	Silent	SNP	ENST00000358290.4	37	CCDS3619.1																																																																																			G|0.645;A|0.355	0.355	strong		0.413	HSD17B11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253041.1	NM_016245	
OXNAD1	92106	hgsc.bcm.edu	37	3	16312564	16312564	+	Silent	SNP	C	C	T	rs842259	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:16312564C>T	ENST00000285083.5	+	3	570	c.105C>T	c.(103-105)caC>caT	p.H35H	OXNAD1_ENST00000606098.1_Silent_p.H35H|OXNAD1_ENST00000605932.1_Silent_p.H35H|OXNAD1_ENST00000544043.1_Silent_p.H53H|OXNAD1_ENST00000435829.2_Silent_p.H53H	NM_138381.3	NP_612390.1	Q96HP4	OXND1_HUMAN	oxidoreductase NAD-binding domain containing 1	35						mitochondrion (GO:0005739)	oxidoreductase activity (GO:0016491)			endometrium(3)|kidney(1)|large_intestine(2)|lung(5)|skin(2)	13						CTTTGCGCCACCTTACTCTAA	0.483													C|||	2107	0.420727	0.2617	0.4654	5008	,	,		17886	0.4752		0.4324	False		,,,				2504	0.5358				p.H35H		Atlas-SNP	.											OXNAD1,rectum,carcinoma,0,1	OXNAD1	31	1	0			c.C105T						PASS	.	C		1361,3045	450.8+/-349.5	221,919,1063	157.0	146.0	150.0		105	3.0	0.5	3	dbSNP_86	150	3655,4945	526.1+/-380.9	787,2081,1432	no	coding-synonymous	OXNAD1	NM_138381.3		1008,3000,2495	TT,TC,CC		42.5,30.8897,38.5668		35/313	16312564	5016,7990	2203	4300	6503	SO:0001819	synonymous_variant	92106	exon3			GCGCCACCTTACT	AL832787	CCDS2630.1	3p25-p24	2010-03-19			ENSG00000154814	ENSG00000154814			25128	protein-coding gene	gene with protein product						12477932	Standard	NM_138381		Approved	MGC15763	uc003caw.3	Q96HP4	OTTHUMG00000129867	ENST00000285083.5:c.105C>T	3.37:g.16312564C>T		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	87	86	0.988506	NM_138381	Q2HYC7|Q59FA4	Silent	SNP	ENST00000285083.5	37	CCDS2630.1																																																																																			C|0.609;T|0.391	0.391	strong		0.483	OXNAD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252109.1	NM_138381	
MSANTD3	91283	hgsc.bcm.edu	37	9	103204577	103204577	+	Silent	SNP	C	C	G	rs35438121	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:103204577C>G	ENST00000395067.2	+	2	628	c.357C>G	c.(355-357)ctC>ctG	p.L119L	TMEFF1_ENST00000334943.6_Silent_p.L6L|MSANTD3_ENST00000489377.1_3'UTR|MSANTD3-TMEFF1_ENST00000502978.1_Missense_Mutation_p.L9V|MSANTD3_ENST00000374885.1_Silent_p.L119L	NM_001198805.1|NM_001198806.1|NM_080655.2	NP_001185734.1|NP_001185735.1|NP_542386.1	Q96H12	MSD3_HUMAN	Myb/SANT-like DNA-binding domain containing 3	119										endometrium(2)|lung(2)	4						CGGAGCAGCTCTACTTCCTGC	0.612													C|||	351	0.0700879	0.0129	0.1239	5008	,	,		15014	0.001		0.167	False		,,,				2504	0.0808				p.L119L		Atlas-SNP	.											MSANTD3,NS,carcinoma,+2,2	MSANTD3	10	2	0			c.C357G						PASS	.	C	,,,,	142,4264	94.8+/-133.5	1,140,2062	44.0	45.0	44.0		357,357,357,357,357	-2.2	1.0	9	dbSNP_126	44	1532,7068	278.6+/-293.5	135,1262,2903	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	C9orf30,C9orf30-TMEFF1	NM_001198805.1,NM_001198806.1,NM_001198807.1,NM_001198812.1,NM_080655.2	,,,,	136,1402,4965	GG,GC,CC		17.814,3.2229,12.871	,,,,	119/276,119/276,119/160,119/455,119/276	103204577	1674,11332	2203	4300	6503	SO:0001819	synonymous_variant	91283	exon2			GCAGCTCTACTTC	BC008993	CCDS6749.1, CCDS56579.1	9q31.1	2012-03-13	2012-03-13	2012-03-13	ENSG00000066697	ENSG00000066697			23370	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 30"""	C9orf30			Standard	NM_080655		Approved	MGC17337		Q96H12	OTTHUMG00000020365	ENST00000395067.2:c.357C>G	9.37:g.103204577C>G		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	36	9	0.25	NM_001198805	B2RC35|Q5T726|Q5T727|Q5T728	Silent	SNP	ENST00000395067.2	37	CCDS6749.1	182	0.08333333333333333	9	0.018292682926829267	52	0.143646408839779	0	0.0	121	0.15963060686015831	C	10.47	1.359305	0.24598	0.032229	0.17814	ENSG00000251349	ENST00000502978	T	0.61627	0.09	5.92	-2.15	0.07102	.	.	.	.	.	T	0.00210	0.0006	.	.	.	0.09310	P	0.9999999999976105	.	.	.	.	.	.	T	0.42816	-0.9429	5	0.72032	D	0.01	-6.7711	10.975	0.47461	0.0877:0.2327:0.6079:0.0717	rs35438121	.	.	.	V	9	ENSP00000424768:L9V	ENSP00000424768:L9V	L	+	1	2	C9orf30-TMEFF1	102244398	0.076000	0.21285	0.994000	0.49952	0.997000	0.91878	-1.163000	0.03138	-0.203000	0.10251	0.655000	0.94253	CTA	C|0.884;G|0.116	0.116	strong		0.612	MSANTD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053410.1	NM_080655	
OBSCN	84033	hgsc.bcm.edu	37	1	228452016	228452016	+	Missense_Mutation	SNP	G	G	C	rs185523702	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:228452016G>C	ENST00000422127.1	+	16	4829	c.4785G>C	c.(4783-4785)gaG>gaC	p.E1595D	OBSCN_ENST00000570156.2_Missense_Mutation_p.E1779D|OBSCN_ENST00000366707.4_5'UTR|OBSCN_ENST00000366709.4_5'UTR|OBSCN_ENST00000284548.11_Missense_Mutation_p.E1595D|OBSCN_ENST00000359599.6_Missense_Mutation_p.E251D	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	1595	Ig-like 16.				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)				TGGTGCAGGAGGCAGGCCAGG	0.642													G|||	20	0.00399361	0.0008	0.0086	5008	,	,		18329	0.0		0.0119	False		,,,				2504	0.001				p.E1779D		Atlas-SNP	.											.	OBSCN	2142	.	0			c.G5337C						PASS	.	G	ASP/GLU,ASP/GLU	12,4228		0,12,2108	44.0	52.0	50.0		4785,4785	3.8	1.0	1		50	165,8287		3,159,4064	no	missense,missense	OBSCN	NM_001098623.1,NM_052843.2	45,45	3,171,6172	CC,CG,GG		1.9522,0.283,1.3946	possibly-damaging,possibly-damaging	1595/7969,1595/6621	228452016	177,12515	2120	4226	6346	SO:0001583	missense	84033	exon18			GCAGGAGGCAGGC	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.4785G>C	1.37:g.228452016G>C	ENSP00000409493:p.Glu1595Asp	Somatic	319	0	0		WXS	Illumina HiSeq	Phase_I	309	147	0.475728	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	15	0.006868131868131868	1	0.0020325203252032522	5	0.013812154696132596	0	0.0	9	0.011873350923482849	.	1.509	-0.549977	0.03996	0.00283	0.019522	ENSG00000154358	ENST00000284548;ENST00000422127;ENST00000359599	T;T;T	0.04317	3.65;3.65;3.65	4.69	3.77	0.43336	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.306226	0.28595	N	0.014790	T	0.01387	0.0045	N	0.16037	0.36	0.80722	D	1	B;B	0.30439	0.018;0.279	B;B	0.23716	0.029;0.048	T	0.52403	-0.8580	10	0.11794	T	0.64	.	13.1743	0.59617	0.1471:0.0:0.8529:0.0	.	1595;1595	Q5VST9;Q5VST9-3	OBSCN_HUMAN;.	D	1595;1595;251	ENSP00000284548:E1595D;ENSP00000409493:E1595D;ENSP00000352613:E251D	ENSP00000284548:E1595D	E	+	3	2	OBSCN	226518639	0.000000	0.05858	0.996000	0.52242	0.001000	0.01503	-0.150000	0.10189	0.601000	0.29879	-1.579000	0.00862	GAG	G|0.990;C|0.010	0.010	strong		0.642	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
USP39	10713	hgsc.bcm.edu	37	2	85843348	85843348	+	Silent	SNP	C	C	T	rs11544042	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:85843348C>T	ENST00000323701.6	+	1	40	c.30C>T	c.(28-30)cgC>cgT	p.R10R	USP39_ENST00000450066.2_Intron|USP39_ENST00000409470.1_Silent_p.R10R|USP39_ENST00000459775.1_Intron|USP39_ENST00000409766.3_Silent_p.R10R|USP39_ENST00000409025.1_Silent_p.R10R	NM_006590.3	NP_006581.2	Q53GS9	SNUT2_HUMAN	ubiquitin specific peptidase 39	10	Arg-rich.				cell cycle (GO:0007049)|cell division (GO:0051301)|mRNA processing (GO:0006397)|RNA splicing (GO:0008380)|spliceosomal complex assembly (GO:0000245)|ubiquitin-dependent protein catabolic process (GO:0006511)	spliceosomal complex (GO:0005681)	ubiquitinyl hydrolase activity (GO:0036459)|zinc ion binding (GO:0008270)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(7)|ovary(1)|prostate(1)|stomach(1)|urinary_tract(1)	19						GGGAGTCTCGCGGTTCCACTC	0.706													C|||	267	0.0533147	0.1036	0.0548	5008	,	,		12680	0.001		0.0775	False		,,,				2504	0.0133				p.R10R		Atlas-SNP	.											.	USP39	33	.	0			c.C30T						PASS	.	C		365,3963		13,339,1812	7.0	8.0	8.0		30	-4.3	1.0	2	dbSNP_120	8	528,7964		12,504,3730	no	coding-synonymous	USP39	NM_006590.2		25,843,5542	TT,TC,CC		6.2176,8.4335,6.9657		10/566	85843348	893,11927	2164	4246	6410	SO:0001819	synonymous_variant	10713	exon1			GTCTCGCGGTTCC	AF132955	CCDS33234.1, CCDS58716.1, CCDS58717.1, CCDS74534.1	2p11.2	2009-01-06	2005-08-08		ENSG00000168883	ENSG00000168883		"""Ubiquitin-specific peptidases"""	20071	protein-coding gene	gene with protein product	"""snRNP assembly defective 1 homolog (S.cerevisiae)"", ""small nuclear ribonucleoprotein 65kDa (U4/U6.U5)"""	611594	"""ubiquitin specific protease 39"""			12838346	Standard	NM_006590		Approved	SAD1, CGI-21, SNRNP65	uc002sqg.4	Q53GS9	OTTHUMG00000153090	ENST00000323701.6:c.30C>T	2.37:g.85843348C>T		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	60	33	0.55	NM_001256725	A8K086|B3KM40|B4DHT4|D6W5L4|G5E9H0|Q6NX47|Q96RK9|Q9BV89|Q9H381|Q9P050|Q9Y310	Silent	SNP	ENST00000323701.6	37	CCDS33234.1																																																																																			C|0.936;T|0.064	0.064	strong		0.706	USP39-009	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329892.1	NM_006590	
ZNF792	126375	hgsc.bcm.edu	37	19	35449082	35449082	+	Silent	SNP	G	G	A	rs3746243	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:35449082G>A	ENST00000404801.1	-	4	2063	c.1677C>T	c.(1675-1677)gaC>gaT	p.D559D	ZNF792_ENST00000605484.1_Silent_p.D492D	NM_175872.4	NP_787068.3	Q3KQV3	ZN792_HUMAN	zinc finger protein 792	559					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			cervix(1)|endometrium(4)|kidney(1)|large_intestine(1)|lung(5)	12	all_lung(56;4.18e-08)|Lung NSC(56;6.62e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0849)			CGTAAGGCCTGTCTGGTTTGT	0.517													A|||	1314	0.26238	0.2277	0.1931	5008	,	,		22050	0.3998		0.1839	False		,,,				2504	0.2975				p.D559D	GBM(1;7 183 21053 22581 22847)	Atlas-SNP	.											.	ZNF792	46	.	0			c.C1677T						PASS	.	A		967,3439	733.5+/-410.5	102,763,1338	117.0	91.0	100.0		1677	-5.6	0.0	19	dbSNP_107	100	1516,7084	747.6+/-407.3	123,1270,2907	no	coding-synonymous	ZNF792	NM_175872.4		225,2033,4245	AA,AG,GG		17.6279,21.9473,19.0912		559/633	35449082	2483,10523	2203	4300	6503	SO:0001819	synonymous_variant	126375	exon4			AGGCCTGTCTGGT	AK095770	CCDS12440.2	19q13.11	2013-01-08			ENSG00000180884	ENSG00000180884		"""Zinc fingers, C2H2-type"", ""-"""	24751	protein-coding gene	gene with protein product						8889548	Standard	NM_175872		Approved	FLJ38451	uc002nxh.1	Q3KQV3	OTTHUMG00000150339	ENST00000404801.1:c.1677C>T	19.37:g.35449082G>A		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	70	36	0.514286	NM_175872	B4E333|Q495L1|Q495L3|Q8N932	Silent	SNP	ENST00000404801.1	37	CCDS12440.2																																																																																			G|0.769;A|0.231	0.231	strong		0.517	ZNF792-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317673.1	NM_175872	
RSF1	51773	hgsc.bcm.edu	37	11	77409568	77409568	+	Silent	SNP	T	T	C	rs4945203	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:77409568T>C	ENST00000308488.6	-	7	2981	c.2679A>G	c.(2677-2679)ccA>ccG	p.P893P	RSF1_ENST00000360355.2_Silent_p.P862P|RSF1_ENST00000480887.1_Silent_p.P641P			Q96T23	RSF1_HUMAN	remodeling and spacing factor 1	893					CENP-A containing nucleosome assembly (GO:0034080)|chromatin remodeling (GO:0006338)|DNA-templated transcription, initiation (GO:0006352)|negative regulation of DNA binding (GO:0043392)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome assembly (GO:0006334)|nucleosome positioning (GO:0016584)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of viral transcription (GO:0050434)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|RSF complex (GO:0031213)	histone binding (GO:0042393)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(2)|endometrium(3)|kidney(4)|large_intestine(9)|lung(14)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	43	all_cancers(14;1.54e-17)|all_epithelial(13;4.06e-20)|Ovarian(111;0.152)		Epithelial(5;3e-50)|all cancers(3;6.37e-47)|BRCA - Breast invasive adenocarcinoma(5;9.82e-31)			ATTTTTTGCATGGTTCATCAT	0.433													C|||	986	0.196885	0.3298	0.2161	5008	,	,		17411	0.1736		0.0984	False		,,,				2504	0.1288				p.P893P		Atlas-SNP	.											.	RSF1	105	.	0			c.A2679G						PASS	.	C		1343,3057	693.4+/-405.7	208,927,1065	223.0	203.0	210.0		2679	-8.3	0.4	11	dbSNP_111	210	832,7752	780.7+/-407.7	36,760,3496	no	coding-synonymous	RSF1	NM_016578.3		244,1687,4561	CC,CT,TT		9.6925,30.5227,16.7514		893/1442	77409568	2175,10809	2200	4292	6492	SO:0001819	synonymous_variant	51773	exon7			TTTGCATGGTTCA	AF380176, AF227948	CCDS8253.1	11q14.1	2013-01-28	2006-05-25	2006-05-25	ENSG00000048649	ENSG00000048649		"""Zinc fingers, PHD-type"""	18118	protein-coding gene	gene with protein product		608522	"""hepatitis B virus x associated protein"""	HBXAP		11788598, 12972596	Standard	NM_016578		Approved	XAP8, RSF-1, p325	uc001oyn.3	Q96T23	OTTHUMG00000150433	ENST00000308488.6:c.2679A>G	11.37:g.77409568T>C		Somatic	390	0	0		WXS	Illumina HiSeq	Phase_I	318	231	0.726415	NM_016578	Q86X86|Q9H3L8|Q9NVZ8|Q9NYU0	Silent	SNP	ENST00000308488.6	37	CCDS8253.1	421	0.19276556776556777	172	0.34959349593495936	67	0.1850828729281768	109	0.19055944055944055	73	0.09630606860158311	C	8.729	0.916226	0.17907	0.305227	0.096925	ENSG00000048649	ENST00000532556	.	.	.	4.68	-8.3	0.01005	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999996607	.	.	.	.	.	.	T	0.33445	-0.9868	3	.	.	.	-7.7615	2.551	0.04749	0.1499:0.3493:0.2269:0.2739	rs4945203;rs4945203	.	.	.	R	147	.	.	H	-	2	0	RSF1	77087216	0.001000	0.12720	0.444000	0.26895	0.979000	0.70002	-1.814000	0.01723	-2.263000	0.00689	-0.930000	0.02707	CAT	T|0.813;C|0.187	0.187	strong		0.433	RSF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318075.2	NM_016578	
LRP1B	53353	hgsc.bcm.edu	37	2	141259376	141259376	+	Silent	SNP	G	G	A	rs35164907	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:141259376G>A	ENST00000389484.3	-	55	9701	c.8730C>T	c.(8728-8730)tgC>tgT	p.C2910C		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	2910	LDL-receptor class A 20. {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)		CCTTATTGTCGCAAAGACCTC	0.383										TSP Lung(27;0.18)			G|||	632	0.126198	0.0613	0.1167	5008	,	,		13824	0.0198		0.2465	False		,,,				2504	0.2065				p.C2910C	Colon(99;50 2074 2507 20106)	Atlas-SNP	.											.	LRP1B	1315	.	0			c.C8730T						PASS	.	G		381,4025	192.3+/-217.7	15,351,1837	80.0	78.0	79.0		8730	3.4	1.0	2	dbSNP_126	79	2307,6293	386.9+/-342.0	309,1689,2302	no	coding-synonymous	LRP1B	NM_018557.2		324,2040,4139	AA,AG,GG		26.8256,8.6473,20.6674		2910/4600	141259376	2688,10318	2203	4300	6503	SO:0001819	synonymous_variant	53353	exon55			ATTGTCGCAAAGA	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.8730C>T	2.37:g.141259376G>A		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	81	36	0.444444	NM_018557	Q8WY29|Q8WY30|Q8WY31	Silent	SNP	ENST00000389484.3	37	CCDS2182.1																																																																																			G|0.818;A|0.182	0.182	strong		0.383	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557	
GUCY1A2	2977	hgsc.bcm.edu	37	11	106849400	106849400	+	Silent	SNP	G	G	A	rs35760785	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:106849400G>A	ENST00000526355.2	-	3	900	c.432C>T	c.(430-432)aaC>aaT	p.N144N	GUCY1A2_ENST00000347596.2_Silent_p.N144N|GUCY1A2_ENST00000282249.2_Silent_p.N144N	NM_000855.2	NP_000846.1	P33402	GCYA2_HUMAN	guanylate cyclase 1, soluble, alpha 2	144					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)	TTTCTTCTTTGTTGGAGTGGT	0.328													G|||	453	0.0904553	0.0431	0.049	5008	,	,		18654	0.1161		0.0885	False		,,,				2504	0.1595				p.N144N		Atlas-SNP	.											.	GUCY1A2	180	.	0			c.C432T						PASS	.	G		236,4166	137.3+/-173.1	13,210,1978	123.0	120.0	121.0		432	4.8	1.0	11	dbSNP_126	121	756,7840	181.3+/-230.0	33,690,3575	no	coding-synonymous	GUCY1A2	NM_000855.1		46,900,5553	AA,AG,GG		8.7948,5.3612,7.6319		144/733	106849400	992,12006	2201	4298	6499	SO:0001819	synonymous_variant	2977	exon3			TTCTTTGTTGGAG	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.432C>T	11.37:g.106849400G>A		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	76	19	0.25	NM_000855	A1L4C4|B7ZLT5	Silent	SNP	ENST00000526355.2	37	CCDS8335.1																																																																																			G|0.920;A|0.080	0.080	strong		0.328	GUCY1A2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389003.2		
SIGLEC6	946	hgsc.bcm.edu	37	19	52033206	52033206	+	Missense_Mutation	SNP	G	G	A	rs2005199	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:52033206G>A	ENST00000425629.3	-	5	938	c.784C>T	c.(784-786)Ctc>Ttc	p.L262F	SIGLEC6_ENST00000436458.1_Missense_Mutation_p.L210F|SIGLEC6_ENST00000474054.1_5'Flank|SIGLEC6_ENST00000343300.4_Missense_Mutation_p.L262F|SIGLEC6_ENST00000391797.3_Missense_Mutation_p.L251F|SIGLEC6_ENST00000359982.4_Missense_Mutation_p.L273F|SIGLEC6_ENST00000346477.3_Missense_Mutation_p.L246F	NM_001245.5	NP_001236.4	O43699	SIGL6_HUMAN	sialic acid binding Ig-like lectin 6	262	Ig-like C2-type 2.		L -> F (in dbSNP:rs2005199).		cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)			endometrium(3)|kidney(1)|large_intestine(6)|liver(1)|lung(15)|ovary(1)|stomach(1)	28		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.00115)|OV - Ovarian serous cystadenocarcinoma(262;0.0165)		AGGACAGGGAGGGACGAGGTG	0.607													G|||	354	0.0706869	0.0144	0.0648	5008	,	,		17592	0.0942		0.0686	False		,,,				2504	0.1288				p.L273F		Atlas-SNP	.											SIGLEC6_ENST00000425629,rectum,carcinoma,0,2	SIGLEC6	142	2	0			c.C817T						PASS	.	G	PHE/LEU,PHE/LEU,PHE/LEU,PHE/LEU,PHE/LEU,PHE/LEU	105,4301	79.9+/-118.3	1,103,2099	99.0	111.0	107.0		628,817,751,784,736,784	-2.2	0.0	19	dbSNP_92	107	577,8015	151.0+/-205.8	20,537,3739	yes	missense,missense,missense,missense,missense,missense	SIGLEC6	NM_001177547.1,NM_001177548.1,NM_001177549.1,NM_001245.5,NM_198845.4,NM_198846.4	22,22,22,22,22,22	21,640,5838	AA,AG,GG		6.7155,2.3831,5.247	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	210/402,273/390,251/343,262/454,246/438,262/354	52033206	682,12316	2203	4296	6499	SO:0001583	missense	946	exon5			CAGGGAGGGACGA	D86358	CCDS12834.3, CCDS12835.3, CCDS12836.3, CCDS54307.1, CCDS54308.1, CCDS59417.1	19q13.3	2013-01-29			ENSG00000105492	ENSG00000105492		"""Sialic acid binding Ig-like lectins"", ""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	10875	protein-coding gene	gene with protein product		604405		CD33L, CD33L1		9465907	Standard	NM_001245		Approved	OB-BP1, SIGLEC-6, CD327	uc002pwy.3	O43699	OTTHUMG00000133571	ENST00000425629.3:c.784C>T	19.37:g.52033206G>A	ENSP00000401502:p.Leu262Phe	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	128	70	0.546875	NM_001177548	A8MV71|B2RTS8|C9JBE5|F8WA78|O15388|O43700	Missense_Mutation	SNP	ENST00000425629.3	37	CCDS12834.3	150	0.06868131868131869	13	0.026422764227642278	30	0.08287292817679558	58	0.10139860139860139	49	0.06464379947229551	G	12.86	2.065950	0.36470	0.023831	0.067155	ENSG00000105492	ENST00000346477;ENST00000391797;ENST00000425629;ENST00000359982;ENST00000436458;ENST00000343300	T;T;T;T	0.68903	-0.36;-0.36;-0.36;-0.36	3.71	-2.15	0.07102	Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.482528	0.15384	N	0.265175	T	0.05364	0.0142	M	0.79926	2.475	0.80722	P	0.0	B;P;P;P;P;P	0.49635	0.451;0.759;0.839;0.839;0.926;0.701	P;P;P;P;P;P	0.55667	0.498;0.513;0.781;0.673;0.781;0.617	T	0.48305	-0.9047	9	0.52906	T	0.07	.	0.4643	0.00521	0.2894:0.1853:0.3361:0.1892	rs2005199;rs17305038;rs52789758;rs59181551;rs2005199	273;210;251;262;246;262	F8WA78;C9JBE5;O43699-4;O43699-2;O43699-3;O43699	.;.;.;.;.;SIGL6_HUMAN	F	235;246;262;273;210;262	ENSP00000401502:L262F;ENSP00000353071:L273F;ENSP00000410679:L210F;ENSP00000345907:L262F	ENSP00000345907:L262F	L	-	1	0	SIGLEC6	56725018	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.232000	0.09055	-0.404000	0.07610	0.514000	0.50259	CTC	G|0.923;A|0.077	0.077	strong		0.607	SIGLEC6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257670.3	NM_001245	
CPT1B	1375	hgsc.bcm.edu	37	22	51011376	51011376	+	Missense_Mutation	SNP	G	G	C	rs8142477	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:51011376G>C	ENST00000360719.2	-	11	1417	c.1280C>G	c.(1279-1281)tCc>tGc	p.S427C	CPT1B_ENST00000312108.7_Missense_Mutation_p.S427C|CPT1B_ENST00000457250.1_Missense_Mutation_p.S393C|CPT1B_ENST00000440709.1_Intron|CPT1B_ENST00000405237.3_Missense_Mutation_p.S427C|CPT1B_ENST00000395650.2_Missense_Mutation_p.S427C|CPT1B_ENST00000434492.2_Missense_Mutation_p.S224C|CHKB-CPT1B_ENST00000453634.1_3'UTR	NM_001145135.1|NM_152245.2	NP_001138607.1|NP_689451.1	Q92523	CPT1B_HUMAN	carnitine palmitoyltransferase 1B (muscle)	427			S -> C (in dbSNP:rs8142477).		carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	carnitine O-palmitoyltransferase activity (GO:0004095)			central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(7)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	22		all_cancers(38;8.8e-15)|all_epithelial(38;1.12e-12)|all_lung(38;3.07e-05)|Breast(42;6.27e-05)|Lung NSC(38;0.000813)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		all cancers(3;3.56e-77)|OV - Ovarian serous cystadenocarcinoma(4;5.39e-74)|Epithelial(4;5.58e-70)|GBM - Glioblastoma multiforme(4;5.59e-08)|LUAD - Lung adenocarcinoma(64;0.0016)|Lung(4;0.00942)|BRCA - Breast invasive adenocarcinoma(115;0.207)		GGGGTCATAGGAGTAGGATTC	0.587													C|||	2118	0.422923	0.6679	0.2997	5008	,	,		18336	0.501		0.1143	False		,,,				2504	0.4162				p.S427C	Esophageal Squamous(170;988 1933 25577 30295 48163)	Atlas-SNP	.											.	CPT1B	61	.	0			c.C1280G						PASS	.	C	CYS/SER,CYS/SER,,CYS/SER,CYS/SER,CYS/SER,CYS/SER	2491,1915	547.2+/-377.2	718,1055,430	123.0	118.0	120.0		1178,1280,,1280,1280,1280,1280	-5.5	0.0	22	dbSNP_116	120	1004,7596	773.3+/-407.7	51,902,3347	yes	missense,missense,intron,missense,missense,missense,missense	CPT1B	NM_001145134.1,NM_001145135.1,NM_001145136.1,NM_001145137.1,NM_004377.3,NM_152245.2,NM_152246.2	112,112,,112,112,112,112	769,1957,3777	CC,CG,GG		11.6744,43.4635,26.8722	benign,benign,,benign,benign,benign,benign	393/739,427/773,,427/773,427/773,427/773,427/773	51011376	3495,9511	2203	4300	6503	SO:0001583	missense	1375	exon11			TCATAGGAGTAGG	U62733	CCDS14098.1, CCDS46734.1	22q13.33	2007-07-26			ENSG00000205560	ENSG00000205560			2329	protein-coding gene	gene with protein product		601987				9070950	Standard	NM_152245		Approved	M-CPT1, CPT1-M	uc003bmm.3	Q92523	OTTHUMG00000137390	ENST00000360719.2:c.1280C>G	22.37:g.51011376G>C	ENSP00000353945:p.Ser427Cys	Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	179	88	0.49162	NM_001145135	B7Z4U4|B7Z5T8|E9PCP2|Q13389|Q99655|Q9BY90	Missense_Mutation	SNP	ENST00000360719.2	37	CCDS14098.1	792	0.3626373626373626	315	0.6402439024390244	93	0.2569060773480663	291	0.5087412587412588	93	0.12269129287598944	C	3.878	-0.026487	0.07589	0.565365	0.116744	ENSG00000205560	ENST00000405237;ENST00000312108;ENST00000360719;ENST00000457250;ENST00000434492;ENST00000395650	D;D;D;D;D;D	0.89746	-2.56;-2.56;-2.56;-2.56;-2.56;-2.56	4.98	-5.54	0.02544	.	1.469010	0.04390	N	0.362247	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.10450	0.005;0.003;0.003	T	0.17930	-1.0353	9	0.35671	T	0.21	0.3286	6.4139	0.21705	0.0:0.2947:0.318:0.3873	rs8142477;rs17836711;rs17848460;rs52832088;rs8142477	393;224;427	B7Z4U4;A2RRE8;Q92523	.;.;CPT1B_HUMAN	C	427;427;427;393;224;427	ENSP00000385486:S427C;ENSP00000312189:S427C;ENSP00000353945:S427C;ENSP00000409342:S393C;ENSP00000410966:S224C;ENSP00000379011:S427C	ENSP00000312189:S427C	S	-	2	0	CPT1B	49358242	0.027000	0.19231	0.000000	0.03702	0.001000	0.01503	0.686000	0.25392	-1.599000	0.01605	-2.174000	0.00321	TCC	G|0.699;C|0.301	0.301	strong		0.587	CPT1B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317264.5	NM_152246	
TFDP2	7029	hgsc.bcm.edu	37	3	141678667	141678667	+	Silent	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:141678667G>A	ENST00000489671.1	-	11	1330	c.900C>T	c.(898-900)ttC>ttT	p.F300F	TFDP2_ENST00000477292.1_Silent_p.F164F|TFDP2_ENST00000467072.1_Silent_p.F240F|TFDP2_ENST00000495310.1_Silent_p.F203F|TFDP2_ENST00000479040.1_Silent_p.F239F|TFDP2_ENST00000499676.2_Silent_p.F240F|TFDP2_ENST00000397991.4_Silent_p.F272F|TFDP2_ENST00000310282.6_Silent_p.F240F|TFDP2_ENST00000317104.7_Silent_p.F224F|TFDP2_ENST00000486111.1_Silent_p.F240F			Q14188	TFDP2_HUMAN	transcription factor Dp-2 (E2F dimerization partner 2)	300	DCB2.				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						TGTCAAAATTGAAAAGATACT	0.403																																					p.F300F		Atlas-SNP	.											.	TFDP2	44	.	0			c.C900T						PASS	.						96.0	91.0	92.0					3																	141678667		1932	4165	6097	SO:0001819	synonymous_variant	7029	exon11			AAAATTGAAAAGA	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.900C>T	3.37:g.141678667G>A		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	87	4	0.045977	NM_001178139	B7Z8C8|B7Z8L5|D3DNG1|E9PFC3|F8WAI2|Q13331|Q14187|Q6R754|Q8WU88|Q9UG28	Silent	SNP	ENST00000489671.1	37	CCDS54650.1	.	.	.	.	.	.	.	.	.	.	G	9.486	1.099510	0.20552	.	.	ENSG00000114126	ENST00000474279	.	.	.	5.69	-4.06	0.03986	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-5.5996	14.6009	0.68441	0.5011:0.0:0.4989:0.0	.	.	.	.	X	14	.	.	Q	-	1	0	TFDP2	143161357	1.000000	0.71417	0.491000	0.27477	0.959000	0.62525	1.103000	0.31062	-0.748000	0.04753	-0.379000	0.06801	CAA	.	.	none		0.403	TFDP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000353294.4	NM_006286	
FAT1	2195	hgsc.bcm.edu	37	4	187557893	187557893	+	Missense_Mutation	SNP	T	T	C	rs328418	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:187557893T>C	ENST00000441802.2	-	5	4027	c.3818A>G	c.(3817-3819)cAc>cGc	p.H1273R		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	1273	Cadherin 11. {ECO:0000255|PROSITE- ProRule:PRU00043}.			H -> R (in Ref. 1; CAA60685). {ECO:0000305}.	actin filament organization (GO:0007015)|anatomical structure morphogenesis (GO:0009653)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(38)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(33)|lung(88)|ovary(13)|pancreas(2)|prostate(16)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	228						GGCTATGACGTGATAGAGCGG	0.488										HNSCC(5;0.00058)			C|||	3234	0.645767	0.8729	0.647	5008	,	,		15938	0.6786		0.5586	False		,,,				2504	0.3937				p.H1273R	Colon(197;1040 2055 4143 4984 49344)	Atlas-SNP	.											.	FAT1	500	.	0			c.A3818G						PASS	.	C	ARG/HIS	3041,701		1235,571,65	206.0	209.0	208.0		3818	5.0	0.0	4	dbSNP_79	208	4535,3677		1247,2041,818	yes	missense	FAT1	NM_005245.3	29	2482,2612,883	CC,CT,TT		44.7759,18.7333,36.6237	benign	1273/4589	187557893	7576,4378	1871	4106	5977	SO:0001583	missense	2195	exon5			ATGACGTGATAGA	X87241	CCDS47177.1	4q35.2	2013-05-31	2013-05-31	2008-10-30	ENSG00000083857	ENSG00000083857		"""Cadherins / Cadherin-related"""	3595	protein-coding gene	gene with protein product	"""cadherin-related family member 8"""	600976	"""FAT tumor suppressor (Drosophila) homolog"", ""FAT tumor suppressor homolog 1 (Drosophila)"""	FAT		8586420	Standard	XM_005262834		Approved	CDHF7, CDHR8	uc003izf.3	Q14517	OTTHUMG00000160320	ENST00000441802.2:c.3818A>G	4.37:g.187557893T>C	ENSP00000406229:p.His1273Arg	Somatic	250	0	0		WXS	Illumina HiSeq	Phase_I	273	130	0.47619	NM_005245		Missense_Mutation	SNP	ENST00000441802.2	37	CCDS47177.1	1481	0.6781135531135531	413	0.8394308943089431	233	0.643646408839779	415	0.7255244755244755	420	0.554089709762533	C	0.854	-0.737484	0.03111	0.812667	0.552241	ENSG00000083857	ENST00000441802;ENST00000260147	T	0.47528	0.84	4.99	4.99	0.66335	Cadherin (3);Cadherin-like (1);	0.056815	0.64402	N	0.000001	T	0.00012	0.0000	N	0.00128	-2.045	0.44136	P	0.0030799999999999716	B	0.02656	0.0	B	0.01281	0.0	T	0.40850	-0.9541	9	0.02654	T	1	.	13.7233	0.62743	0.0:0.9262:0.0:0.0738	rs328418;rs56699278;rs328418	1273	Q14517	FAT1_HUMAN	R	1273	ENSP00000406229:H1273R	ENSP00000260147:H1273R	H	-	2	0	FAT1	187794887	1.000000	0.71417	0.039000	0.18376	0.002000	0.02628	5.940000	0.70187	1.353000	0.45828	-0.215000	0.12644	CAC	T|0.323;G|0.003	.	strong		0.488	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245	
KMT2C	58508	hgsc.bcm.edu	37	7	151949068	151949068	+	Missense_Mutation	SNP	C	C	G	rs3735156	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:151949068C>G	ENST00000262189.6	-	11	1795	c.1577G>C	c.(1576-1578)cGt>cCt	p.R526P	KMT2C_ENST00000355193.2_Missense_Mutation_p.R526P	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	526			R -> P (in dbSNP:rs3735156). {ECO:0000269|PubMed:11891048}.		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)										TGGCTGTAAACGATCCATCTC	0.383													G|||	906	0.180911	0.4977	0.1095	5008	,	,		18528	0.0704		0.0109	False		,,,				2504	0.092				p.R526P		Atlas-SNP	.											.	MLL3	1564	.	0			c.G1577C						PASS	.	G	PRO/ARG	1996,2410	616.3+/-392.7	458,1080,665	106.0	96.0	100.0		1577	5.8	0.0	7	dbSNP_107	100	139,8461	813.0+/-407.0	1,137,4162	yes	missense	MLL3	NM_170606.2	103	459,1217,4827	GG,GC,CC		1.6163,45.3019,16.4155	benign	526/4912	151949068	2135,10871	2203	4300	6503	SO:0001583	missense	58508	exon11			TGTAAACGATCCA	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.1577G>C	7.37:g.151949068C>G	ENSP00000262189:p.Arg526Pro	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	90	45	0.5	NM_170606	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Missense_Mutation	SNP	ENST00000262189.6	37	CCDS5931.1	331	0.15155677655677655	241	0.4898373983739837	37	0.10220994475138122	45	0.07867132867132867	8	0.010554089709762533	G	8.646	0.897097	0.17686	0.453019	0.016163	ENSG00000055609	ENST00000262189;ENST00000355193	D;D	0.82893	-1.66;-1.66	5.75	5.75	0.90469	.	0.321390	0.22057	N	0.065238	T	0.00012	0.0000	N	0.00197	-1.87	0.58432	P	4.000000000004E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.30357	-0.9981	9	0.02654	T	1	.	11.4246	0.50003	0.0:0.2354:0.6285:0.1361	rs3735156;rs10376667;rs61450622;rs3735156	526	Q8NEZ4	MLL3_HUMAN	P	526	ENSP00000262189:R526P;ENSP00000347325:R526P	ENSP00000262189:R526P	R	-	2	0	MLL3	151580001	0.893000	0.30496	0.007000	0.13788	0.948000	0.59901	1.962000	0.40442	1.454000	0.47793	-0.120000	0.15030	CGT	C|0.828;G|0.172	0.172	strong		0.383	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3		
MAGEA4	4103	hgsc.bcm.edu	37	X	151092968	151092968	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:151092968G>T	ENST00000360243.2	+	3	1099	c.832G>T	c.(832-834)Gct>Tct	p.A278S	MAGEA4_ENST00000370335.1_Missense_Mutation_p.A278S|MAGEA4_ENST00000370340.3_Missense_Mutation_p.A278S|MAGEA4_ENST00000393921.1_Missense_Mutation_p.A278S|MAGEA4_ENST00000276344.2_Missense_Mutation_p.A278S|MAGEA4_ENST00000370337.4_Missense_Mutation_p.A278S|MAGEA4_ENST00000393920.1_Missense_Mutation_p.A278S	NM_001011550.1	NP_001011550.1	P43358	MAGA4_HUMAN	melanoma antigen family A, 4	278	MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.									breast(2)|central_nervous_system(4)|endometrium(1)|kidney(1)|large_intestine(3)|lung(14)|ovary(2)	27	Acute lymphoblastic leukemia(192;6.56e-05)					GGGTCCAAGGGCTCTGGCTGA	0.547																																					p.A278S		Atlas-SNP	.											.	MAGEA4	68	.	0			c.G832T						PASS	.						130.0	128.0	129.0					X																	151092968		2203	4300	6503	SO:0001583	missense	4103	exon3			CCAAGGGCTCTGG		CCDS14702.1	Xq28	2009-03-13			ENSG00000147381	ENSG00000147381			6802	protein-coding gene	gene with protein product	"""melanoma-associated antigen 4"", ""cancer/testis antigen family 1, member 4"""	300175		MAGE4		8575766	Standard	XM_005274677		Approved	MAGE4A, MAGE4B, MAGE-41, MAGE-X2, MGC21336, CT1.4	uc004ffa.3	P43358	OTTHUMG00000024174	ENST00000360243.2:c.832G>T	X.37:g.151092968G>T	ENSP00000353379:p.Ala278Ser	Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	95	32	0.336842	NM_001011548	Q14798	Missense_Mutation	SNP	ENST00000360243.2	37	CCDS14702.1	.	.	.	.	.	.	.	.	.	.	G	14.39	2.519751	0.44866	.	.	ENSG00000147381	ENST00000276344;ENST00000393921;ENST00000370337;ENST00000393920;ENST00000370340;ENST00000370335;ENST00000360243	T;T;T;T;T;T;T	0.05717	3.4;3.4;3.4;3.4;3.4;3.4;3.4	2.55	1.68	0.24146	.	0.050169	0.85682	D	0.000000	T	0.19725	0.0474	M	0.83692	2.655	0.09310	N	1	D	0.56968	0.978	D	0.68943	0.961	T	0.02893	-1.1097	9	.	.	.	.	4.7785	0.13190	0.1844:0.0:0.8156:0.0	.	278	P43358	MAGA4_HUMAN	S	278	ENSP00000276344:A278S;ENSP00000377498:A278S;ENSP00000359362:A278S;ENSP00000377497:A278S;ENSP00000359365:A278S;ENSP00000359360:A278S;ENSP00000353379:A278S	.	A	+	1	0	MAGEA4	150843624	0.192000	0.23301	0.009000	0.14445	0.021000	0.10359	0.444000	0.21661	0.500000	0.27991	0.292000	0.19580	GCT	.	.	none		0.547	MAGEA4-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060898.1	NM_002362	
HACL1	26061	hgsc.bcm.edu	37	3	15628040	15628040	+	Missense_Mutation	SNP	T	T	A	rs74637339	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:15628040T>A	ENST00000321169.5	-	6	818	c.451A>T	c.(451-453)Att>Ttt	p.I151F	HACL1_ENST00000451445.2_Intron|HACL1_ENST00000457447.2_Intron|HACL1_ENST00000435217.2_Intron|HACL1_ENST00000456194.2_Missense_Mutation_p.I124F	NM_012260.2	NP_036392.2	Q9UJ83	HACL1_HUMAN	2-hydroxyacyl-CoA lyase 1	151					cellular lipid metabolic process (GO:0044255)|fatty acid alpha-oxidation (GO:0001561)|protein oligomerization (GO:0051259)|small molecule metabolic process (GO:0044281)	peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	carbon-carbon lyase activity (GO:0016830)|cofactor binding (GO:0048037)|identical protein binding (GO:0042802)|magnesium ion binding (GO:0000287)|receptor binding (GO:0005102)|thiamine pyrophosphate binding (GO:0030976)			NS(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(3)|skin(1)	16						ACCTTTTCAATAACAAAAGGA	0.338													T|||	76	0.0151757	0.0008	0.0202	5008	,	,		17140	0.0		0.0567	False		,,,				2504	0.0041				p.I151F		Atlas-SNP	.											.	HACL1	33	.	0			c.A451T						PASS	.	T	PHE/ILE	39,4367	43.1+/-76.7	0,39,2164	72.0	76.0	74.0		451	5.8	1.0	3	dbSNP_131	74	443,8155	133.8+/-191.2	11,421,3867	yes	missense	HACL1	NM_012260.2	21	11,460,6031	AA,AT,TT		5.1524,0.8852,3.7066	probably-damaging	151/579	15628040	482,12522	2203	4299	6502	SO:0001583	missense	26061	exon6			TTTCAATAACAAA	AJ131753	CCDS2627.1, CCDS68360.1, CCDS68361.1, CCDS68362.1	3p24.3	2009-01-14	2006-05-16	2006-05-16	ENSG00000131373	ENSG00000131373	4.1.-.-		17856	protein-coding gene	gene with protein product		604300	"""2-hydroxyphytanoyl-CoA lyase"""	HPCL		10468558, 15644336	Standard	NM_001284416		Approved	2-HPCL, PHYH2	uc003caf.3	Q9UJ83	OTTHUMG00000129862	ENST00000321169.5:c.451A>T	3.37:g.15628040T>A	ENSP00000323811:p.Ile151Phe	Somatic	202	0	0		WXS	Illumina HiSeq	Phase_I	191	84	0.439791	NM_012260	B4DWI1|B4DXI5|E9PEN4|Q9BV42|Q9P0A2	Missense_Mutation	SNP	ENST00000321169.5	37	CCDS2627.1	48	0.02197802197802198	0	0.0	6	0.016574585635359115	0	0.0	42	0.055408970976253295	T	16.39	3.110668	0.56398	0.008852	0.051524	ENSG00000131373	ENST00000321169;ENST00000456194;ENST00000421993;ENST00000414979	T;T	0.37058	1.25;1.22	5.83	5.83	0.93111	Thiamine pyrophosphate enzyme, N-terminal TPP-binding domain (1);	0.101648	0.64402	D	0.000004	T	0.13756	0.0333	M	0.68593	2.085	0.80722	D	1	P;D	0.71674	0.599;0.998	P;D	0.73380	0.596;0.98	T	0.30851	-0.9964	10	0.62326	D	0.03	.	15.1766	0.72916	0.0:0.0:0.0:1.0	.	124;151	B4DWI1;Q9UJ83	.;HACL1_HUMAN	F	151;124;124;86	ENSP00000323811:I151F;ENSP00000390699:I124F	ENSP00000323811:I151F	I	-	1	0	HACL1	15603044	1.000000	0.71417	0.965000	0.40720	0.312000	0.27988	3.550000	0.53691	2.225000	0.72522	0.460000	0.39030	ATT	T|0.970;A|0.030	0.030	strong		0.338	HACL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252104.3	NM_012260	
TLE3	7090	hgsc.bcm.edu	37	15	70351154	70351154	+	Splice_Site	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:70351154C>T	ENST00000558939.1	-	11	2143	c.766G>A	c.(766-768)Gac>Aac	p.D256N	TLE3_ENST00000559191.1_Intron|TLE3_ENST00000539550.1_Splice_Site_p.D200N|TLE3_ENST00000557997.1_Splice_Site_p.D256N|TLE3_ENST00000440567.3_Splice_Site_p.D249N|TLE3_ENST00000559048.1_Splice_Site_p.D261N|TLE3_ENST00000317509.8_Splice_Site_p.D256N|TLE3_ENST00000557907.1_Splice_Site_p.D256N|TLE3_ENST00000558201.1_Splice_Site_p.D262N|TLE3_ENST00000558379.1_Splice_Site_p.D256N|TLE3_ENST00000451782.2_Splice_Site_p.D256N|TLE3_ENST00000560939.1_Splice_Site_p.D261N|TLE3_ENST00000442299.2_Splice_Site_p.D256N|TLE3_ENST00000560589.1_Splice_Site_p.D200N|TLE3_ENST00000559929.1_Splice_Site_p.D266N	NM_001282979.1|NM_001282980.1|NM_001282981.1	NP_001269908.1|NP_001269909.1|NP_001269910.1	Q04726	TLE3_HUMAN	transducin-like enhancer of split 3	256	CCN domain.				Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)				breast(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(16)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	31						GTTGCGGGGTCCTGAAAACAC	0.612																																					p.D256N		Atlas-SNP	.											.	TLE3	104	.	0			c.G766A						PASS	.						17.0	19.0	18.0					15																	70351154		1935	4130	6065	SO:0001630	splice_region_variant	7090	exon11			CGGGGTCCTGAAA	M99438	CCDS45293.1, CCDS45294.1, CCDS58375.1, CCDS61689.1, CCDS61691.1, CCDS61692.1, CCDS73747.1	15q22	2014-03-07	2014-03-07			ENSG00000140332		"""WD repeat domain containing"""	11839	protein-coding gene	gene with protein product		600190	"""transducin-like enhancer of split 3, homolog of Drosophila E(sp1)"", ""transducin-like enhancer of split 3 (E(sp1) homolog, Drosophila)"""			8365415	Standard	XM_005254623		Approved	ESG, ESG3, KIAA1547, HsT18976, GRG3	uc002asm.2	Q04726		ENST00000558939.1:c.766-1G>A	15.37:g.70351154C>T		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	40	15	0.375	NM_001105192	B4DPT0|E9PD64|F8W964|Q6PI57|Q8IVV6|Q8WVR2|Q9HCM5	Missense_Mutation	SNP	ENST00000558939.1	37	CCDS45293.1	.	.	.	.	.	.	.	.	.	.	C	19.84	3.902492	0.72754	.	.	ENSG00000140332	ENST00000442299;ENST00000451782;ENST00000317509;ENST00000440567;ENST00000539550	T;T;T;T;T	0.53857	0.82;0.87;0.92;0.87;0.6	5.3	5.3	0.74995	.	0.000000	0.85682	D	0.000000	T	0.68449	0.3002	L	0.56340	1.77	0.80722	D	1	D;B;B;B;P;B;P;B	0.61080	0.989;0.021;0.264;0.011;0.552;0.053;0.823;0.019	D;B;B;B;B;B;P;B	0.66497	0.944;0.019;0.16;0.02;0.34;0.043;0.733;0.03	T	0.68161	-0.5482	10	0.54805	T	0.06	-0.4451	19.143	0.93452	0.0:1.0:0.0:0.0	.	249;256;256;256;256;256;261;200	F8W964;E9PD64;Q04726-3;Q6PI57;Q04726-2;Q04726;Q04726-4;F5H7D6	.;.;.;.;.;TLE3_HUMAN;.;.	N	256;256;256;249;200	ENSP00000390007:D256N;ENSP00000394717:D256N;ENSP00000319233:D256N;ENSP00000415057:D249N;ENSP00000442594:D200N	ENSP00000319233:D256N	D	-	1	0	TLE3	68138208	1.000000	0.71417	1.000000	0.80357	0.710000	0.40934	7.559000	0.82265	2.764000	0.94973	0.555000	0.69702	GAC	.	.	none		0.612	TLE3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000416913.1	NM_005078	Missense_Mutation
ACAN	176	hgsc.bcm.edu	37	15	89398105	89398105	+	Silent	SNP	C	C	T	rs2351491	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:89398105C>T	ENST00000561243.1	+	11	2289	c.2289C>T	c.(2287-2289)ccC>ccT	p.P763P	ACAN_ENST00000439576.2_Silent_p.P763P|ACAN_ENST00000559004.1_Silent_p.P763P|ACAN_ENST00000352105.7_Silent_p.P763P			P16112	PGCA_HUMAN	aggrecan	762	KS.				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|proteolysis (GO:0006508)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)	carbohydrate binding (GO:0030246)|extracellular matrix structural constituent (GO:0005201)|hyaluronic acid binding (GO:0005540)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(4)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(15)|liver(2)|lung(40)|ovary(2)|prostate(5)|skin(5)|stomach(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	93	Lung NSC(78;0.0392)|all_lung(78;0.077)		BRCA - Breast invasive adenocarcinoma(143;0.146)			CTTGGCCTCCCACTGGCGCAG	0.502													C|||	1753	0.35004	0.1815	0.3746	5008	,	,		19459	0.2083		0.6521	False		,,,				2504	0.3957				p.P763P		Atlas-SNP	.											.	ACAN	220	.	0			c.C2289T						PASS	.	C	,	992,2822		138,716,1053	20.0	21.0	21.0	http://www.ncbi.nlm.nih.gov/pubmed?term	2289,2289	4.6	1.0	15	dbSNP_100	21	5322,2902		1718,1886,508	no	coding-synonymous,coding-synonymous	ACAN	NM_001135.3,NM_013227.3	,	1856,2602,1561	TT,TC,CC	http://www.ncbi.nlm.nih.gov/pubmed?term	35.287,26.0094,47.5494	,	763/2432,763/2531	89398105	6314,5724	1907	4112	6019	SO:0001819	synonymous_variant	176	exon12			GCCTCCCACTGGC	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.2289C>T	15.37:g.89398105C>T		Somatic	195	0	0		WXS	Illumina HiSeq	Phase_I	254	251	0.988189	NM_001135	Q13650|Q9UCD3|Q9UCP4|Q9UCP5|Q9UDE0	Silent	SNP	ENST00000561243.1	37	CCDS53970.1																																																																																			C|0.595;T|0.405	0.405	strong		0.502	ACAN-006	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416267.2	NM_001135	
GRK7	131890	hgsc.bcm.edu	37	3	141535558	141535558	+	Missense_Mutation	SNP	A	A	G	rs36009541	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:141535558A>G	ENST00000264952.2	+	4	1465	c.1328A>G	c.(1327-1329)gAa>gGa	p.E443G		NM_139209.2	NP_631948.1	Q8WTQ7	GRK7_HUMAN	G protein-coupled receptor kinase 7	443	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		E -> G (in dbSNP:rs36009541). {ECO:0000269|PubMed:17344846}.		protein autophosphorylation (GO:0046777)|signal transduction (GO:0007165)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|visual perception (GO:0007601)	membrane (GO:0016020)	ATP binding (GO:0005524)|G-protein coupled receptor kinase activity (GO:0004703)|rhodopsin kinase activity (GO:0050254)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(14)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	26						CTTCACAGAGAAAAGTCTGAT	0.403													A|||	281	0.0561102	0.0522	0.0663	5008	,	,		17513	0.0139		0.1054	False		,,,				2504	0.047				p.E443G		Atlas-SNP	.											.	GRK7	65	.	0			c.A1328G						PASS	.	A	GLY/GLU	286,4120	140.4+/-175.9	10,266,1927	61.0	63.0	62.0		1328	5.4	1.0	3	dbSNP_126	62	1083,7517	200.9+/-244.5	66,951,3283	yes	missense	GRK7	NM_139209.2	98	76,1217,5210	GG,GA,AA		12.593,6.4911,10.5259	benign	443/554	141535558	1369,11637	2203	4300	6503	SO:0001583	missense	131890	exon4			ACAGAGAAAAGTC		CCDS3120.1	3q24	2004-02-04	2004-02-04	2004-02-04	ENSG00000114124	ENSG00000114124			17031	protein-coding gene	gene with protein product		606987		GPRK7		11717351, 11754336	Standard	NM_139209		Approved		uc011bnd.2	Q8WTQ7	OTTHUMG00000159068	ENST00000264952.2:c.1328A>G	3.37:g.141535558A>G	ENSP00000264952:p.Glu443Gly	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	103	56	0.543689	NM_139209		Missense_Mutation	SNP	ENST00000264952.2	37	CCDS3120.1	155	0.07097069597069597	32	0.06504065040650407	33	0.09116022099447514	5	0.008741258741258742	85	0.11213720316622691	A	5.489	0.275185	0.10403	0.064911	0.12593	ENSG00000114124	ENST00000264952	T	0.69806	-0.43	5.4	5.4	0.78164	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.347524	0.29205	N	0.012835	T	0.00384	0.0012	N	0.04297	-0.235	0.80722	P	0.0	B	0.10296	0.003	B	0.10450	0.005	T	0.12811	-1.0533	9	0.02654	T	1	-8.9791	5.9235	0.19096	0.7242:0.1522:0.1236:0.0	rs36009541	443	Q8WTQ7	GRK7_HUMAN	G	443	ENSP00000264952:E443G	ENSP00000264952:E443G	E	+	2	0	GRK7	143018248	0.006000	0.16342	0.997000	0.53966	0.946000	0.59487	0.459000	0.21908	2.052000	0.61016	0.383000	0.25322	GAA	A|0.903;G|0.097	0.097	strong		0.403	GRK7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353168.1	NM_139209	
TRAF1	7185	hgsc.bcm.edu	37	9	123688217	123688217	+	Missense_Mutation	SNP	G	G	A	rs34119250	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:123688217G>A	ENST00000373887.3	-	2	2582	c.137C>T	c.(136-138)cCg>cTg	p.P46L	TRAF1_ENST00000540010.1_Missense_Mutation_p.P46L	NM_005658.4	NP_005649.1	Q13077	TRAF1_HUMAN	TNF receptor-associated factor 1	46					apoptotic process (GO:0006915)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein complex assembly (GO:0006461)|regulation of extrinsic apoptotic signaling pathway (GO:2001236)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)	thioesterase binding (GO:0031996)|tumor necrosis factor receptor binding (GO:0005164)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(9)|ovary(4)|pancreas(1)|skin(2)	22						ACCTCACCTCGGGTTCTCAGA	0.632													G|||	171	0.0341454	0.0068	0.036	5008	,	,		18352	0.003		0.0567	False		,,,				2504	0.0787				p.P46L		Atlas-SNP	.											.	TRAF1	42	.	0			c.C137T						PASS	.	G	LEU/PRO,LEU/PRO	92,4314	75.7+/-113.9	0,92,2111	51.0	51.0	51.0		137,137	0.2	0.3	9	dbSNP_126	51	566,8034	154.5+/-208.7	27,512,3761	yes	missense,missense	TRAF1	NM_001190945.1,NM_005658.4	98,98	27,604,5872	AA,AG,GG		6.5814,2.0881,5.0592	benign,benign	46/417,46/417	123688217	658,12348	2203	4300	6503	SO:0001583	missense	7185	exon2			CACCTCGGGTTCT	AK090468	CCDS6825.1, CCDS55335.1	9q33-q34	2008-02-05			ENSG00000056558	ENSG00000056558			12031	protein-coding gene	gene with protein product		601711				8069916	Standard	NM_001190945		Approved	EBI6	uc010mvl.2	Q13077	OTTHUMG00000020578	ENST00000373887.3:c.137C>T	9.37:g.123688217G>A	ENSP00000362994:p.Pro46Leu	Somatic	194	0	0		WXS	Illumina HiSeq	Phase_I	176	90	0.511364	NM_005658	B4DJ77|Q658U1|Q8NF13	Missense_Mutation	SNP	ENST00000373887.3	37	CCDS6825.1	63	0.028846153846153848	6	0.012195121951219513	13	0.03591160220994475	1	0.0017482517482517483	43	0.05672823218997362	G	4.284	0.051910	0.08291	0.020881	0.065814	ENSG00000056558	ENST00000373887;ENST00000540010	T;T	0.27104	1.69;1.69	5.31	0.251	0.15540	.	0.541665	0.12625	U	0.452676	T	0.00552	0.0018	N	0.01352	-0.895	0.25312	N	0.989199	B	0.02656	0.0	B	0.01281	0.0	T	0.37337	-0.9710	10	0.19147	T	0.46	.	7.7727	0.29019	0.6455:0.0:0.3545:0.0	rs34119250	46	Q13077	TRAF1_HUMAN	L	46	ENSP00000362994:P46L;ENSP00000443183:P46L	ENSP00000362994:P46L	P	-	2	0	TRAF1	122728038	0.050000	0.20438	0.252000	0.24328	0.779000	0.44077	0.266000	0.18534	-0.115000	0.11915	-0.339000	0.08088	CCG	G|0.955;A|0.045	0.045	strong		0.632	TRAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053843.1	NM_005658	
UNC13A	23025	hgsc.bcm.edu	37	19	17741047	17741047	+	Silent	SNP	A	A	G	rs10413821	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:17741047A>G	ENST00000519716.2	-	30	3575	c.3576T>C	c.(3574-3576)gtT>gtC	p.V1192V	UNC13A_ENST00000550896.1_Silent_p.V1190V|UNC13A_ENST00000552293.1_Silent_p.V1192V|UNC13A_ENST00000252773.7_Silent_p.V1192V|UNC13A_ENST00000551649.1_Silent_p.V1192V|UNC13A_ENST00000428389.2_Silent_p.V1280V	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	113	0	0		WXS	Illumina HiSeq	Phase_I	93	93	1	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	
SIGLEC1	6614	hgsc.bcm.edu	37	20	3682149	3682149	+	Silent	SNP	G	G	A	rs13037869	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:3682149G>A	ENST00000344754.4	-	6	1367	c.1368C>T	c.(1366-1368)tcC>tcT	p.S456S	SIGLEC1_ENST00000202578.4_Silent_p.S456S	NM_023068.3	NP_075556.1	Q9BZZ2	SN_HUMAN	sialic acid binding Ig-like lectin 1, sialoadhesin	456	Ig-like C2-type 4.				cell-matrix adhesion (GO:0007160)|endocytosis (GO:0006897)|inflammatory response (GO:0006954)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of T cell apoptotic process (GO:0070234)|single organismal cell-cell adhesion (GO:0016337)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)			NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(4)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(5)|liver(2)|lung(24)|ovary(3)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)	70						CACTGTCCCCGGAGGTGGAGG	0.617													G|||	1384	0.276358	0.1051	0.3804	5008	,	,		20780	0.2123		0.3529	False		,,,				2504	0.4213				p.S456S		Atlas-SNP	.											.	SIGLEC1	210	.	0			c.C1368T						PASS	.	G		609,3797	266.8+/-267.5	51,507,1645	93.0	72.0	79.0		1368	-11.4	0.0	20	dbSNP_121	79	3174,5426	481.3+/-370.6	591,1992,1717	no	coding-synonymous	SIGLEC1	NM_023068.3		642,2499,3362	AA,AG,GG		36.907,13.8221,29.0866		456/1710	3682149	3783,9223	2203	4300	6503	SO:0001819	synonymous_variant	6614	exon6			GTCCCCGGAGGTG	AF230073	CCDS13060.1	20p13	2013-01-29	2006-01-19	2006-01-19	ENSG00000088827	ENSG00000088827		"""CD molecules"", ""Sialic acid binding Ig-like lectins"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	11127	protein-coding gene	gene with protein product		600751	"""sialoadhesin"""	SN		8530048	Standard	XM_006723610		Approved	SIGLEC-1, CD169, FLJ00051, FLJ00055, FLJ00073, FLJ32150, dJ1009E24.1, sialoadhesin	uc002wja.3	Q9BZZ2	OTTHUMG00000031757	ENST00000344754.4:c.1368C>T	20.37:g.3682149G>A		Somatic	182	0	0		WXS	Illumina HiSeq	Phase_I	131	68	0.519084	NM_023068	Q96DL4|Q9GZS5|Q9H1H6|Q9H1H7|Q9H7L7	Silent	SNP	ENST00000344754.4	37	CCDS13060.1																																																																																			G|0.723;A|0.277	0.277	strong		0.617	SIGLEC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077761.2	NM_023068	
OR1L8	138881	hgsc.bcm.edu	37	9	125330184	125330184	+	Silent	SNP	A	A	C	rs10985702	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:125330184A>C	ENST00000304865.2	-	1	654	c.573T>G	c.(571-573)tcT>tcG	p.S191S		NM_001004454.1	NP_001004454.1	Q8NGR8	OR1L8_HUMAN	olfactory receptor, family 1, subfamily L, member 8	191						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(5)|lung(6)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	20						CAAATATGGAAGAGCAGGACA	0.433													A|||	2409	0.48103	0.4508	0.4135	5008	,	,		25550	0.8056		0.3221	False		,,,				2504	0.3988				p.S191S		Atlas-SNP	.											.	OR1L8	90	.	0			c.T573G						PASS	.	A		1937,2469	549.7+/-377.9	430,1077,696	96.0	84.0	88.0		573	-6.1	0.0	9	dbSNP_120	88	2615,5985	423.7+/-354.4	394,1827,2079	no	coding-synonymous	OR1L8	NM_001004454.1		824,2904,2775	CC,CA,AA		30.407,43.9628,34.9992		191/310	125330184	4552,8454	2203	4300	6503	SO:0001819	synonymous_variant	138881	exon1			TATGGAAGAGCAG		CCDS35124.1	9q33.2	2013-09-20			ENSG00000171496	ENSG00000171496		"""GPCR / Class A : Olfactory receptors"""	15110	protein-coding gene	gene with protein product							Standard	NM_001004454		Approved		uc004bmp.1	Q8NGR8	OTTHUMG00000020609	ENST00000304865.2:c.573T>G	9.37:g.125330184A>C		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	84	44	0.52381	NM_001004454	A3KFM3|B9EIR6|Q6IF15|Q96R79	Silent	SNP	ENST00000304865.2	37	CCDS35124.1																																																																																			A|0.580;C|0.420	0.420	strong		0.433	OR1L8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053939.1		
RPP21	79897	hgsc.bcm.edu	37	6	30314566	30314566	+	Silent	SNP	T	T	G	rs35287137|rs1060065	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:30314566T>G	ENST00000442966.2	+	5	457	c.444T>G	c.(442-444)acT>acG	p.T148T	TRIM39-RPP21_ENST00000513556.1_Silent_p.T409T|RPP21_ENST00000428040.2_Silent_p.T171T|RPP21_ENST00000433076.2_Silent_p.T156T|RPP21_ENST00000436442.2_3'UTR			Q9H633	RPP21_HUMAN	ribonuclease P/MRP 21kDa subunit	148					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						AAATGCAGACTCAGGGTTCCA	0.433													T|||	1866	0.372604	0.3018	0.4496	5008	,	,		21469	0.505		0.2435	False		,,,				2504	0.41				p.T497T		Atlas-SNP	.											.	.	.	.	0			c.T1491G						PASS	.	T	,,,	841,2181		114,613,784	161.0	165.0	164.0		1491,468,,444	-0.3	0.0	6	dbSNP_86	164	1311,4107		159,993,1557	no	coding-synonymous,coding-synonymous,utr-3,coding-synonymous	RPP21,TRIM39-RPP21	NM_001199119.1,NM_001199120.1,NM_001199121.1,NM_024839.2	,,,	273,1606,2341	GG,GT,TT		24.1971,27.8293,25.4976	,,,	497/504,156/163,,148/155	30314566	2152,6288	1511	2709	4220	SO:0001819	synonymous_variant	202658	exon10			GCAGACTCAGGGT	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.444T>G	6.37:g.30314566T>G		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	97	41	0.42268	NM_001199119	A2AAZ8|B0S834|B0S835|Q5JPL9|Q5JPM1|Q5STF8|Q5STF9|Q5STG2|Q5SU41|Q5SU42|Q86Y49|Q86Y50|Q86Y51|Q96F16	Silent	SNP	ENST00000442966.2	37	CCDS4679.1																																																																																			.	.	alt		0.433	RPP21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076451.2	NM_024839	
CCDC185	164127	hgsc.bcm.edu	37	1	223567267	223567267	+	Silent	SNP	C	C	T	rs6679661	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:223567267C>T	ENST00000366875.3	+	1	553	c.450C>T	c.(448-450)ccC>ccT	p.P150P		NM_152610.2	NP_689823.2	Q8N715	CC185_HUMAN		150	Pro-rich.									breast(4)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(12)|skin(3)	29				GBM - Glioblastoma multiforme(131;0.0704)		CGCCTTGCCCCGGAGGAGCTG	0.692													C|||	437	0.0872604	0.1067	0.0677	5008	,	,		15567	0.13		0.0398	False		,,,				2504	0.0798				p.P150P		Atlas-SNP	.											.	C1orf65	71	.	0			c.C450T						PASS	.	C		455,3939		25,405,1767	13.0	16.0	15.0		450	-0.4	0.0	1	dbSNP_116	15	321,8275		6,309,3983	no	coding-synonymous	C1orf65	NM_152610.2		31,714,5750	TT,TC,CC		3.7343,10.355,5.9738		150/624	223567267	776,12214	2197	4298	6495	SO:0001819	synonymous_variant	164127	exon1			TTGCCCCGGAGGA																												ENST00000366875.3:c.450C>T	1.37:g.223567267C>T		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	72	36	0.5	NM_152610	Q8N746|Q8NA93	Silent	SNP	ENST00000366875.3	37	CCDS1537.1																																																																																			C|0.924;T|0.076	0.076	strong		0.692	C1orf65-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092718.1		
CD8B	926	hgsc.bcm.edu	37	2	87073852	87073852	+	Missense_Mutation	SNP	C	C	T	rs2228022	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:87073852C>T	ENST00000390655.6	-	4	596	c.538G>A	c.(538-540)Gtc>Atc	p.V180I	CD8B_ENST00000393759.2_Missense_Mutation_p.V180I|CD8B_ENST00000431506.2_Intron|CD8B_ENST00000331469.2_Missense_Mutation_p.V180I|CD8B_ENST00000349455.3_Intron|CD8B_ENST00000393761.2_Intron	NM_004931.4	NP_004922.1	P10966	CD8B_HUMAN	CD8b molecule	180				V -> I (in Ref. 6; AAI00915). {ECO:0000305}.	immune response (GO:0006955)|regulation of defense response to virus by virus (GO:0050690)|regulation of immune response (GO:0050776)|T cell activation (GO:0042110)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|viral process (GO:0016032)	early endosome membrane (GO:0031901)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|T cell receptor complex (GO:0042101)	coreceptor activity (GO:0015026)|MHC class I protein binding (GO:0042288)			NS(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|skin(1)|upper_aerodigestive_tract(1)	13						AGAACCAGGACGCCAGCCACC	0.537													C|||	876	0.17492	0.0764	0.2911	5008	,	,		16088	0.1577		0.2087	False		,,,				2504	0.2086				p.V180I		Atlas-SNP	.											.	CD8B	37	.	0			c.G538A						PASS	.	C	,ILE/VAL,ILE/VAL,,ILE/VAL	437,3931		15,407,1762	54.0	43.0	47.0		,538,538,,538	-0.7	0.0	2	dbSNP_131	47	1742,6818		176,1390,2714	no	intron,missense,missense,intron,missense	CD8B	NM_001178100.1,NM_004931.4,NM_172101.3,NM_172102.3,NM_172213.3	,29,29,,29	191,1797,4476	TT,TC,CC		20.3505,10.0046,16.8549	,benign,benign,,benign	,180/211,180/222,,180/244	87073852	2179,10749	2184	4280	6464	SO:0001583	missense	926	exon4			CCAGGACGCCAGC		CCDS1994.1, CCDS1995.1, CCDS42708.1, CCDS1997.1, CCDS54376.1	2p12	2013-01-11	2006-03-28	2006-03-09	ENSG00000172116	ENSG00000172116		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"""	1707	protein-coding gene	gene with protein product		186730	"""CD8 antigen, beta polypeptide 1 (p37)"""	CD8B1		1541829	Standard	NM_172213		Approved		uc002srw.3	P10966	OTTHUMG00000130264	ENST00000390655.6:c.538G>A	2.37:g.87073852C>T	ENSP00000375070:p.Val180Ile	Somatic	380	1	0.00263158		WXS	Illumina HiSeq	Phase_I	328	146	0.445122	NM_004931	P14860|P14861|Q15980|Q496E0|Q496E1|Q496E2|Q9UDB4|Q9UDB5|Q9UDB6|Q9UDB7|Q9UDB8|Q9UDB9|Q9UDC0|Q9UQ55	Missense_Mutation	SNP	ENST00000390655.6	37	CCDS1997.1	393	0.17994505494505494	42	0.08536585365853659	90	0.24861878453038674	94	0.16433566433566432	167	0.22031662269129287	C	0.008	-1.908834	0.00508	0.100046	0.203505	ENSG00000172116	ENST00000393759;ENST00000331469;ENST00000390655;ENST00000445248	.	.	.	4.91	-0.731	0.11151	.	0.850395	0.10380	N	0.681737	T	0.00012	0.0000	N	0.13098	0.295	0.80722	P	0.0	B;B;B;B	0.15719	0.014;0.003;0.005;0.005	B;B;B;B	0.10450	0.003;0.002;0.005;0.005	T	0.31998	-0.9923	8	0.05620	T	0.96	-5.3481	8.0987	0.30844	0.0:0.4499:0.0:0.5501	.	180;180;180;180	Q53QL8;P10966;P10966-2;P10966-6	.;CD8B_HUMAN;.;.	I	180	.	ENSP00000331172:V180I	V	-	1	0	CD8B	86927363	0.000000	0.05858	0.000000	0.03702	0.018000	0.09664	-1.468000	0.02350	-0.242000	0.09667	-0.137000	0.14449	GTC	C|0.829;T|0.171	0.171	strong		0.537	CD8B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330402.1	NM_172099	
PRSS12	8492	hgsc.bcm.edu	37	4	119219909	119219909	+	Missense_Mutation	SNP	C	C	A	rs28661939	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:119219909C>A	ENST00000296498.3	-	9	2098	c.1816G>T	c.(1816-1818)Gcc>Tcc	p.A606S	PRSS12_ENST00000510903.1_5'UTR	NM_003619.3	NP_003610.2	P56730	NETR_HUMAN	protease, serine, 12 (neurotrypsin, motopsin)	606			A -> S (in dbSNP:rs28661939).		exocytosis (GO:0006887)|zymogen activation (GO:0031638)	axon (GO:0030424)|cytoplasmic vesicle (GO:0031410)|dendrite (GO:0030425)|extracellular region (GO:0005576)|plasma membrane (GO:0005886)|synaptic cleft (GO:0043083)|terminal bouton (GO:0043195)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			endometrium(3)|kidney(1)|large_intestine(9)|lung(11)|prostate(1)|skin(2)|stomach(1)|urinary_tract(1)	29						TTACCTGAGGCCTTCTTGCCA	0.413													C|||	624	0.124601	0.1142	0.111	5008	,	,		20004	0.0476		0.1571	False		,,,				2504	0.1943				p.A606S		Atlas-SNP	.											.	PRSS12	71	.	0			c.G1816T						PASS	.	C	SER/ALA	547,3859	246.2+/-254.9	38,471,1694	148.0	133.0	138.0		1816	1.7	0.9	4	dbSNP_125	138	1289,7311	255.5+/-280.4	96,1097,3107	yes	missense	PRSS12	NM_003619.3	99	134,1568,4801	AA,AC,CC		14.9884,12.4149,14.1166	benign	606/876	119219909	1836,11170	2203	4300	6503	SO:0001583	missense	8492	exon9			CTGAGGCCTTCTT	AJ001531	CCDS3709.1	4q25-q26	2010-05-07			ENSG00000164099	ENSG00000164099		"""Serine peptidases / Serine peptidases"""	9477	protein-coding gene	gene with protein product		606709				9540828, 9245503	Standard	NM_003619		Approved	BSSP-3, MRT1	uc003ica.2	P56730	OTTHUMG00000161166	ENST00000296498.3:c.1816G>T	4.37:g.119219909C>A	ENSP00000296498:p.Ala606Ser	Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	141	61	0.432624	NM_003619	Q9UP16	Missense_Mutation	SNP	ENST00000296498.3	37	CCDS3709.1	244	0.11172161172161173	52	0.10569105691056911	42	0.11602209944751381	30	0.05244755244755245	120	0.158311345646438	C	13.05	2.121411	0.37436	0.124149	0.149884	ENSG00000164099	ENST00000296498	D	0.86297	-2.1	5.46	1.72	0.24424	.	0.829786	0.11144	N	0.594872	T	0.00906	0.0030	L	0.41236	1.265	0.38231	P	0.05898000000000003	B	0.18741	0.03	B	0.15052	0.012	T	0.18178	-1.0345	9	0.08837	T	0.75	.	7.6404	0.28290	0.0:0.6838:0.119:0.1972	rs28661939;rs58619203;rs28661939	606	P56730	NETR_HUMAN	S	606	ENSP00000296498:A606S	ENSP00000296498:A606S	A	-	1	0	PRSS12	119439357	0.992000	0.36948	0.851000	0.33527	0.957000	0.61999	0.812000	0.27211	0.003000	0.14656	0.591000	0.81541	GCC	C|0.873;A|0.127	0.127	strong		0.413	PRSS12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256516.2		
SPAST	6683	hgsc.bcm.edu	37	2	32289034	32289034	+	Missense_Mutation	SNP	C	C	A	rs121908517		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:32289034C>A	ENST00000315285.3	+	1	259	c.134C>A	c.(133-135)cCg>cAg	p.P45Q	SPAST_ENST00000345662.1_Missense_Mutation_p.P45Q	NM_014946.3	NP_055761.2			spastin											breast(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(8)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.208)					cccgAGTCGCCGCATAAGCGG	0.716																																					p.P45Q		Atlas-SNP	.											SPAST,NS,carcinoma,-1,2	SPAST	61	2	0			c.C134A	GRCh37	CM045939	SPAST	M	rs121908517	PASS	.	C	,GLN/PRO,GLN/PRO	0,4402		0,0,2201	24.0	25.0	25.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	,134,134	3.2	1.0	2	dbSNP_133	25	3,8597	2.2+/-6.3	0,3,4297	yes	intron,missense,missense	SPAST,HP11026	XM_003403507.1,NM_199436.1,NM_014946.3	,76,76	0,3,6498	AA,AC,CC		0.0349,0.0,0.0231	,benign,benign	,45/585,45/617	32289034	3,12999	2201	4300	6501	SO:0001583	missense	6683	exon1			AGTCGCCGCATAA	AJ246001	CCDS1778.1, CCDS1779.1	2p24-p21	2014-09-17	2005-03-15	2005-03-17	ENSG00000021574	ENSG00000021574		"""ATPases / AAA-type"""	11233	protein-coding gene	gene with protein product		604277	"""spastic paraplegia 4 (autosomal dominant; spastin)"""	SPG4		10493830, 10610178	Standard	NM_014946		Approved	FSP2, ADPSP, KIAA1083	uc002roc.3	Q9UBP0	OTTHUMG00000128455	ENST00000315285.3:c.134C>A	2.37:g.32289034C>A	ENSP00000320885:p.Pro45Gln	Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	61	25	0.409836	NM_199436		Missense_Mutation	SNP	ENST00000315285.3	37	CCDS1778.1	.	.	.	.	.	.	.	.	.	.	c	10.58	1.390692	0.25118	0.0	3.49E-4	ENSG00000021574	ENST00000345662;ENST00000315285	D;D	0.93426	-3.22;-3.15	4.15	3.25	0.37280	.	0.196102	0.35235	N	0.003354	D	0.84279	0.5437	N	0.14661	0.345	0.35379	A	0.789784	B;B	0.22276	0.067;0.067	B;B	0.14578	0.011;0.011	T	0.81831	-0.0752	9	0.59425	D	0.04	-20.6852	6.4706	0.22005	0.1824:0.722:0.0:0.0957	.	45;45	E5KRP6;Q9UBP0	.;SPAST_HUMAN	Q	45	ENSP00000340817:P45Q;ENSP00000320885:P45Q	ENSP00000320885:P45Q	P	+	2	0	SPAST	32142538	1.000000	0.71417	0.998000	0.56505	0.046000	0.14306	1.604000	0.36804	0.846000	0.35142	0.637000	0.83480	CCG	C|1.000;A|0.000	0.000	weak		0.716	SPAST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250253.1	NM_199436	
CHRNG	1146	hgsc.bcm.edu	37	2	233406178	233406178	+	Missense_Mutation	SNP	G	G	A	rs2289080	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:233406178G>A	ENST00000389494.3	+	5	466	c.445G>A	c.(445-447)Gcc>Acc	p.A149T	CHRNG_ENST00000389492.3_Intron	NM_005199.4	NP_005190.4	P07510	ACHG_HUMAN	cholinergic receptor, nicotinic, gamma (muscle)	149			A -> T (in dbSNP:rs2289080).		muscle contraction (GO:0006936)|regulation of membrane potential (GO:0042391)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|channel activity (GO:0015267)			breast(2)|endometrium(3)|large_intestine(4)|lung(12)|upper_aerodigestive_tract(1)	22		all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0449)|Lung NSC(271;0.132)		Epithelial(121;6.39e-16)|BRCA - Breast invasive adenocarcinoma(100;0.00079)|LUSC - Lung squamous cell carcinoma(224;0.00757)|Lung(119;0.0086)	Galantamine(DB00674)	CTTCCGTTCCGCCTGCTCTAT	0.557													G|||	233	0.0465256	0.034	0.0476	5008	,	,		16616	0.1062		0.0179	False		,,,				2504	0.0307				p.A149T		Atlas-SNP	.											.	CHRNG	54	.	0			c.G445A						PASS	.	G	THR/ALA	101,4305	79.9+/-118.3	1,99,2103	219.0	179.0	193.0		445	2.3	0.8	2	dbSNP_100	193	133,8467	66.3+/-128.7	0,133,4167	yes	missense	CHRNG	NM_005199.4	58	1,232,6270	AA,AG,GG		1.5465,2.2923,1.7992	benign	149/518	233406178	234,12772	2203	4300	6503	SO:0001583	missense	1146	exon5			CGTTCCGCCTGCT	X01715	CCDS33400.1	2q37.1	2012-10-02	2012-02-07		ENSG00000196811	ENSG00000196811		"""Cholinergic receptors"", ""Ligand-gated ion channels / Acetylcholine receptors, nicotinic"""	1967	protein-coding gene	gene with protein product	"""acetylcholine receptor, nicotinic, gamma (muscle)"""	100730	"""cholinergic receptor, nicotinic, gamma"""	ACHRG			Standard	NM_005199		Approved		uc002vsx.1	P07510	OTTHUMG00000153327	ENST00000389494.3:c.445G>A	2.37:g.233406178G>A	ENSP00000374145:p.Ala149Thr	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	142	62	0.43662	NM_005199	B3KWM8|Q14DU4|Q53RG2	Missense_Mutation	SNP	ENST00000389494.3	37	CCDS33400.1	104	0.047619047619047616	16	0.032520325203252036	14	0.03867403314917127	58	0.10139860139860139	16	0.021108179419525065	G	11.02	1.514722	0.27123	0.022923	0.015465	ENSG00000196811	ENST00000389494;ENST00000541596	T	0.79141	-1.24	4.75	2.27	0.28462	Neurotransmitter-gated ion-channel ligand-binding (3);	0.209062	0.42053	D	0.000769	T	0.02929	0.0087	N	0.08118	0	0.22880	N	0.998618	B	0.14438	0.01	B	0.14578	0.011	T	0.02042	-1.1224	10	0.37606	T	0.19	.	13.474	0.61297	0.0:0.0:0.5151:0.4849	rs2289080;rs52797163;rs2289080	149	P07510	ACHG_HUMAN	T	149	ENSP00000374145:A149T	ENSP00000374145:A149T	A	+	1	0	CHRNG	233114422	0.006000	0.16342	0.833000	0.33012	0.961000	0.63080	-0.017000	0.12590	0.172000	0.19760	-0.521000	0.04368	GCC	G|0.968;A|0.032	0.032	strong		0.557	CHRNG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330743.1	NM_005199	
ZDHHC11	79844	hgsc.bcm.edu	37	5	825286	825286	+	Missense_Mutation	SNP	G	G	T	rs2335585	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:825286G>T	ENST00000283441.8	-	8	1399	c.1016C>A	c.(1015-1017)aCg>aAg	p.T339K	ZDHHC11_ENST00000503758.2_5'UTR|ZDHHC11_ENST00000424784.2_Missense_Mutation_p.T339K	NM_024786.2	NP_079062.1	Q9H8X9	ZDH11_HUMAN	zinc finger, DHHC-type containing 11	339						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)			TACCCGTGCCGTCGAATCCCC	0.547																																					p.T339K		Atlas-SNP	.											ZDHHC11_ENST00000424784,NS,carcinoma,0,2	ZDHHC11	97	2	0			c.C1016A						scavenged	.	G	LYS/THR	49,4357		0,49,2154	175.0	127.0	143.0		1016	0.1	0.0	5	dbSNP_100	143	124,8468		2,120,4174	yes	missense	ZDHHC11	NM_024786.2	78	2,169,6328	TT,TG,GG		1.4432,1.1121,1.331	benign	339/413	825286	173,12825	2203	4296	6499	SO:0001583	missense	79844	exon8			CGTGCCGTCGAAT	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.1016C>A	5.37:g.825286G>T	ENSP00000283441:p.Thr339Lys	Somatic	126	1	0.00793651		WXS	Illumina HiSeq	Phase_I	110	14	0.127273	NM_024786	Q6UWR9	Missense_Mutation	SNP	ENST00000283441.8	37	CCDS3857.1	.	.	.	.	.	.	.	.	.	.	N	1.645	-0.515441	0.04200	0.011121	0.014432	ENSG00000188818	ENST00000424784;ENST00000283441	T;T	0.27104	1.69;1.69	0.131	0.131	0.14755	.	.	.	.	.	T	0.06462	0.0166	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.36841	-0.9731	8	0.06099	T	0.92	.	.	.	.	rs2335585;rs16900451;rs52807118;rs59749811;rs2335585	339	Q9H8X9	ZDH11_HUMAN	K	339	ENSP00000397719:T339K;ENSP00000283441:T339K	ENSP00000283441:T339K	T	-	2	0	ZDHHC11	878286	0.001000	0.12720	0.002000	0.10522	0.002000	0.02628	0.529000	0.23019	0.171000	0.19730	0.174000	0.16983	ACG	G|0.985;T|0.015	0.015	strong		0.547	ZDHHC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206681.3	NM_024786	
SLC32A1	140679	hgsc.bcm.edu	37	20	37353743	37353743	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:37353743A>G	ENST00000217420.1	+	1	639	c.376A>G	c.(376-378)Acc>Gcc	p.T126A		NM_080552.2	NP_542119.1	Q9H598	VIAAT_HUMAN	solute carrier family 32 (GABA vesicular transporter), member 1	126					aging (GO:0007568)|ion transport (GO:0006811)|neurotransmitter secretion (GO:0007269)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	cell tip (GO:0051286)|clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane (GO:0061202)|cone cell pedicle (GO:0044316)|dendrite (GO:0030425)|dendrite terminus (GO:0044292)|inhibitory synapse (GO:0060077)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|neuron projection terminus (GO:0044306)|plasma membrane (GO:0005886)|synaptic vesicle membrane (GO:0030672)	gamma-aminobutyric acid:proton symporter activity (GO:0015495)|glycine transmembrane transporter activity (GO:0015187)			breast(2)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(11)|lung(16)|urinary_tract(1)	38		Myeloproliferative disorder(115;0.00878)			Glycine(DB00145)	CTGGAACGTGACCAACGCCAT	0.677																																					p.T126A		Atlas-SNP	.											.	SLC32A1	81	.	0			c.A376G						PASS	.						38.0	40.0	39.0					20																	37353743		2147	4214	6361	SO:0001583	missense	140679	exon1			AACGTGACCAACG	AL133519	CCDS13307.1	20q11	2013-05-22			ENSG00000101438	ENSG00000101438		"""Solute carriers"""	11018	protein-coding gene	gene with protein product			"""vesicular inhibitory amino acid transporter"""	VIAAT		19843525	Standard	NM_080552		Approved	VGAT, bA122O1.1	uc002xjc.3	Q9H598	OTTHUMG00000032457	ENST00000217420.1:c.376A>G	20.37:g.37353743A>G	ENSP00000217420:p.Thr126Ala	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	83	25	0.301205	NM_080552	Q8N489	Missense_Mutation	SNP	ENST00000217420.1	37	CCDS13307.1	.	.	.	.	.	.	.	.	.	.	A	23.6	4.436764	0.83885	.	.	ENSG00000101438	ENST00000217420	T	0.02216	4.39	5.19	4.08	0.47627	.	0.152435	0.64402	N	0.000018	T	0.07458	0.0188	M	0.64170	1.965	0.80722	D	1	P	0.51933	0.949	P	0.58331	0.837	T	0.04885	-1.0920	10	0.59425	D	0.04	-41.9776	9.2152	0.37342	0.9126:0.0:0.0874:0.0	.	126	Q9H598	VIAAT_HUMAN	A	126	ENSP00000217420:T126A	ENSP00000217420:T126A	T	+	1	0	SLC32A1	36787157	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.020000	0.93667	0.811000	0.34303	0.459000	0.35465	ACC	.	.	none		0.677	SLC32A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079206.1	NM_080552	
KIAA1551	55196	hgsc.bcm.edu	37	12	32135938	32135938	+	Silent	SNP	A	A	G	rs11051718	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:32135938A>G	ENST00000312561.4	+	4	2463	c.2049A>G	c.(2047-2049)caA>caG	p.Q683Q	KIAA1551_ENST00000535596.1_Intron	NM_018169.3	NP_060639	Q9HCM1	K1551_HUMAN	KIAA1551	683																	GGAAAAAGCAACCTTCAGATA	0.428													A|||	260	0.0519169	0.0371	0.0893	5008	,	,		21768	0.0149		0.0984	False		,,,				2504	0.0358				p.Q683Q		Atlas-SNP	.											.	.	.	.	0			c.A2049G						PASS	.	A		224,4182	133.7+/-170.0	5,214,1984	63.0	58.0	60.0		2049	-3.3	0.0	12	dbSNP_120	60	1025,7573	219.4+/-257.5	55,915,3329	no	coding-synonymous	C12orf35	NM_018169.3		60,1129,5313	GG,GA,AA		11.9214,5.084,9.6047		683/1748	32135938	1249,11755	2203	4299	6502	SO:0001819	synonymous_variant	55196	exon4			AAAGCAACCTTCA	AK001514	CCDS8725.2	12p11.21	2012-08-14	2012-08-14	2012-08-14	ENSG00000174718	ENSG00000174718			25559	protein-coding gene	gene with protein product			"""chromosome 12 open reading frame 35"""	C12orf35		10997877	Standard	NM_018169		Approved	FLJ20696, FLJ10652	uc001rks.3	Q9HCM1	OTTHUMG00000128501	ENST00000312561.4:c.2049A>G	12.37:g.32135938A>G		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	87	44	0.505747	NM_018169	B2RTU5|Q4KN17|Q9NVL6|Q9NWP9	Silent	SNP	ENST00000312561.4	37	CCDS8725.2																																																																																			A|0.920;G|0.080	0.080	strong		0.428	KIAA1551-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250307.2	NM_018169	
SLC22A24	283238	hgsc.bcm.edu	37	11	62848568	62848568	+	Silent	SNP	C	C	G	rs11231342	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:62848568C>G	ENST00000417740.1	-	9	1863	c.1422G>C	c.(1420-1422)gtG>gtC	p.V474V		NM_001136506.2	NP_001129978.2	Q8N4F4	S22AO_HUMAN	solute carrier family 22, member 24	0					ion transport (GO:0006811)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)				kidney(1)|stomach(1)	2						TCCTACCGGACACTGCATTGA	0.443													C|||	2222	0.44369	0.3442	0.4914	5008	,	,		22267	0.4196		0.5109	False		,,,				2504	0.5				p.V474V		Atlas-SNP	.											.	SLC22A24	31	.	0			c.G1422C						PASS	.	C		491,893		86,319,287	97.0	94.0	95.0		1422	-1.6	0.0	11	dbSNP_120	95	1692,1490		447,798,346	no	coding-synonymous	SLC22A24	NM_001136506.2		533,1117,633	GG,GC,CC		46.8259,35.4769,47.8099		474/553	62848568	2183,2383	692	1591	2283	SO:0001819	synonymous_variant	283238	exon9			ACCGGACACTGCA		CCDS73308.1	11q12.3	2013-05-22			ENSG00000197658	ENSG00000197658		"""Solute carriers"""	28542	protein-coding gene	gene with protein product		611698				17714910	Standard	NM_001136506		Approved	MGC34821, NET46	uc021qkp.1	Q8N4F4	OTTHUMG00000165372	ENST00000417740.1:c.1422G>C	11.37:g.62848568C>G		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	69	14	0.202899	NM_001136506		Silent	SNP	ENST00000417740.1	37																																																																																				C|0.539;G|0.461	0.461	strong		0.443	SLC22A24-003	PUTATIVE	non_canonical_polymorphism|basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000383747.1	NM_173586	
ABCD3	5825	hgsc.bcm.edu	37	1	94930345	94930345	+	Silent	SNP	G	G	A	rs16946	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:94930345G>A	ENST00000370214.4	+	3	186	c.162G>A	c.(160-162)aaG>aaA	p.K54K	ABCD3_ENST00000394233.2_Silent_p.K54K|ABCD3_ENST00000454898.2_Silent_p.K78K|ABCD3_ENST00000315713.5_Silent_p.K54K|ABCD3_ENST00000536817.1_5'UTR	NM_002858.3	NP_002849.1	P28288	ABCD3_HUMAN	ATP-binding cassette, sub-family D (ALD), member 3	54	Interaction with PEX19.|Targeting to peroxisomes.				ATP catabolic process (GO:0006200)|fatty acid beta-oxidation (GO:0006635)|peroxisome organization (GO:0007031)|transmembrane transport (GO:0055085)|very long-chain fatty acid catabolic process (GO:0042760)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|peroxisomal matrix (GO:0005782)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|protein homodimerization activity (GO:0042803)			breast(1)|endometrium(1)|kidney(3)|large_intestine(5)|liver(2)|lung(10)|ovary(1)|pancreas(1)|skin(2)	26		all_lung(203;0.000434)|Lung NSC(277;0.0019)		all cancers(265;0.0261)|Epithelial(280;0.165)		AGGGGAAAAAGGAGCGAGCTG	0.343													G|||	1402	0.279952	0.0998	0.3919	5008	,	,		17199	0.1994		0.502	False		,,,				2504	0.2986				p.K54K		Atlas-SNP	.											.	ABCD3	62	.	0			c.G162A						PASS	.	G	,	696,3710	285.7+/-278.4	52,592,1559	126.0	126.0	126.0		162,162	1.0	1.0	1	dbSNP_60	126	4145,4455	561.4+/-387.8	1021,2103,1176	no	coding-synonymous,coding-synonymous	ABCD3	NM_001122674.1,NM_002858.3	,	1073,2695,2735	AA,AG,GG		48.1977,15.7966,37.2213	,	54/237,54/660	94930345	4841,8165	2203	4300	6503	SO:0001819	synonymous_variant	5825	exon3			GAAAAAGGAGCGA	M81182	CCDS749.1, CCDS44175.1	1p21.3	2012-05-16			ENSG00000117528	ENSG00000117528		"""ATP binding cassette transporters / subfamily D"""	67	protein-coding gene	gene with protein product		170995		PXMP1		1301993, 8449508	Standard	NM_002858		Approved	PMP70, ZWS2	uc001dqn.4	P28288	OTTHUMG00000010717	ENST00000370214.4:c.162G>A	1.37:g.94930345G>A		Somatic	185	1	0.00540541		WXS	Illumina HiSeq	Phase_I	124	123	0.991935	NM_002858	D3DT46|Q15271|Q6NUN5|Q96DA3|Q9H529	Silent	SNP	ENST00000370214.4	37	CCDS749.1																																																																																			G|0.652;A|0.348	0.348	strong		0.343	ABCD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029597.1	NM_002858	
ITSN2	50618	hgsc.bcm.edu	37	2	24432839	24432839	+	Silent	SNP	A	A	G	rs2303296	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:24432839A>G	ENST00000355123.4	-	35	4764	c.4321T>C	c.(4321-4323)Tta>Cta	p.L1441L	ITSN2_ENST00000361999.3_Silent_p.L1414L	NM_006277.2	NP_006268.2	Q9NZM3	ITSN2_HUMAN	intersectin 2	1441	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				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)					GTCTTGTATAATTTCCCACTG	0.443													A|||	707	0.141174	0.0197	0.1354	5008	,	,		19423	0.124		0.2634	False		,,,				2504	0.2014				p.L1441L		Atlas-SNP	.											.	ITSN2	224	.	0			c.T4321C						PASS	.	A	,	267,4139	149.2+/-183.4	9,249,1945	169.0	160.0	163.0		4321,4240	-5.1	0.0	2	dbSNP_100	163	2131,6469	367.2+/-334.6	264,1603,2433	no	coding-synonymous,coding-synonymous	ITSN2	NM_006277.2,NM_019595.3	,	273,1852,4378	GG,GA,AA		24.7791,6.0599,18.4376	,	1441/1698,1414/1671	24432839	2398,10608	2203	4300	6503	SO:0001819	synonymous_variant	50618	exon35			TGTATAATTTCCC	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.4321T>C	2.37:g.24432839A>G		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	105	53	0.504762	NM_006277	O95062|Q15812|Q9HAK4|Q9NXE6|Q9NYG0|Q9NZM2|Q9ULG4	Silent	SNP	ENST00000355123.4	37	CCDS1710.2																																																																																			A|0.824;G|0.176	0.176	strong		0.443	ITSN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207620.2	NM_006277	
RBPJL	11317	hgsc.bcm.edu	37	20	43942698	43942698	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:43942698G>A	ENST00000343694.3	+	8	853	c.781G>A	c.(781-783)Gac>Aac	p.D261N	RBPJL_ENST00000372743.1_Missense_Mutation_p.D261N|RBPJL_ENST00000464504.1_3'UTR|RBPJL_ENST00000372741.3_Missense_Mutation_p.D261N	NM_001281448.1|NM_001281449.1|NM_014276.2	NP_001268377.1|NP_001268378.1|NP_055091.2	Q9UBG7	RBPJL_HUMAN	recombination signal binding protein for immunoglobulin kappa J region-like	261					positive regulation of transcription, DNA-templated (GO:0045893)|signal transduction (GO:0007165)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity (GO:0000982)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(2)|kidney(1)|large_intestine(5)|lung(3)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19		Myeloproliferative disorder(115;0.0122)				TGCCCAAGGAGACTTCCCACC	0.587																																					p.D261N		Atlas-SNP	.											.	RBPJL	67	.	0			c.G781A						PASS	.						129.0	127.0	127.0					20																	43942698		2203	4300	6503	SO:0001583	missense	11317	exon8			CAAGGAGACTTCC	AB024964	CCDS13349.1, CCDS63283.1, CCDS63284.1	20q13.12	2013-10-18	2007-02-26	2007-02-26	ENSG00000124232	ENSG00000124232			13761	protein-coding gene	gene with protein product			"""recombining binding protein suppressor of hairless (Drosophila)-like"""	RBPSUHL		9929984	Standard	NM_014276		Approved	RBP-L, SUH, SUHL	uc002xns.3	Q9UBG7	OTTHUMG00000033055	ENST00000343694.3:c.781G>A	20.37:g.43942698G>A	ENSP00000341243:p.Asp261Asn	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	53	22	0.415094	NM_014276	O95723|Q5QPU9|Q5QPV0|Q9ULV9	Missense_Mutation	SNP	ENST00000343694.3	37	CCDS13349.1	.	.	.	.	.	.	.	.	.	.	G	15.14	2.744830	0.49151	.	.	ENSG00000124232	ENST00000372743;ENST00000372741;ENST00000343694	T;T;T	0.29397	1.57;1.57;1.57	5.25	5.25	0.73442	Beta-trefoil (2);	0.129253	0.51477	D	0.000092	T	0.28962	0.0719	N	0.25485	0.75	0.46260	D	0.998959	P;B	0.47484	0.896;0.303	P;B	0.46172	0.506;0.128	T	0.01334	-1.1382	10	0.36615	T	0.2	-39.329	16.168	0.81785	0.0:0.0:1.0:0.0	.	261;261	Q5QPV1;Q9UBG7	.;RBPJL_HUMAN	N	261	ENSP00000361828:D261N;ENSP00000361826:D261N;ENSP00000341243:D261N	ENSP00000341243:D261N	D	+	1	0	RBPJL	43376112	1.000000	0.71417	1.000000	0.80357	0.313000	0.28021	6.631000	0.74277	2.724000	0.93272	0.563000	0.77884	GAC	.	.	none		0.587	RBPJL-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080391.1	NM_014276	
ZNF462	58499	hgsc.bcm.edu	37	9	109689859	109689859	+	Silent	SNP	T	T	C	rs3814540	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:109689859T>C	ENST00000277225.5	+	3	3955	c.3666T>C	c.(3664-3666)aaT>aaC	p.N1222N	ZNF462_ENST00000457913.1_Silent_p.N1222N|ZNF462_ENST00000441147.2_Silent_p.N67N			Q96JM2	ZN462_HUMAN	zinc finger protein 462	1222					chromatin organization (GO:0006325)|negative regulation of DNA binding (GO:0043392)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|autonomic_ganglia(2)|breast(5)|central_nervous_system(4)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(17)|large_intestine(20)|lung(32)|ovary(5)|prostate(6)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	119						TCAAGGCCAATGCAGATGTGA	0.517													C|||	2598	0.51877	0.7095	0.4481	5008	,	,		15956	0.4802		0.3936	False		,,,				2504	0.4796				p.N1222N		Atlas-SNP	.											.	ZNF462	322	.	0			c.T3666C						PASS	.	C		2798,1608	496.7+/-363.6	890,1018,295	233.0	233.0	233.0		3666	-6.8	0.1	9	dbSNP_107	233	3112,5488	658.0+/-401.5	536,2040,1724	no	coding-synonymous	ZNF462	NM_021224.4		1426,3058,2019	CC,CT,TT		36.186,36.4957,45.4406		1222/2507	109689859	5910,7096	2203	4300	6503	SO:0001819	synonymous_variant	58499	exon3			GGCCAATGCAGAT	AB058706	CCDS35096.1	9q31.3	2008-02-05			ENSG00000148143	ENSG00000148143		"""Zinc fingers, C2H2-type"""	21684	protein-coding gene	gene with protein product							Standard	NM_021224		Approved	DKFZP762N2316, KIAA1803, Zfp462	uc004bcz.3	Q96JM2	OTTHUMG00000020438	ENST00000277225.5:c.3666T>C	9.37:g.109689859T>C		Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	129	69	0.534884	NM_021224	Q5T0T4|Q8N408	Silent	SNP	ENST00000277225.5	37	CCDS35096.1																																																																																			T|0.525;C|0.475	0.475	strong		0.517	ZNF462-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000053532.2	NM_021224	
PREP	5550	hgsc.bcm.edu	37	6	105726036	105726036	+	Missense_Mutation	SNP	C	C	T	rs1051484	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:105726036C>T	ENST00000369110.3	-	15	2308	c.2116G>A	c.(2116-2118)Gtc>Atc	p.V706I	RP3-355L5.4_ENST00000452363.1_RNA	NM_002726.4	NP_002717.3	P48147	PPCE_HUMAN	prolyl endopeptidase	706			V -> I (in dbSNP:rs1051484). {ECO:0000269|PubMed:8089089}.		proteolysis (GO:0006508)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	serine-type endopeptidase activity (GO:0004252)|serine-type exopeptidase activity (GO:0070008)|serine-type peptidase activity (GO:0008236)			breast(1)|endometrium(2)|large_intestine(7)|lung(12)|ovary(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	29		all_cancers(87;0.000128)|Acute lymphoblastic leukemia(125;1.9e-08)|all_hematologic(75;9.25e-07)|all_epithelial(87;0.0344)|Lung NSC(302;0.191)|Colorectal(196;0.202)			Oxytocin(DB00107)	ATCCAGTCGACGTTCAGGCAC	0.552													T|||	1714	0.342252	0.7254	0.2133	5008	,	,		17536	0.1964		0.165	False		,,,				2504	0.2485				p.V706I		Atlas-SNP	.											.	PREP	65	.	0			c.G2116A						PASS	.	T	ILE/VAL	2769,1637	501.5+/-365.0	879,1011,313	187.0	179.0	182.0		2116	4.5	1.0	6	dbSNP_86	182	1332,7268	757.2+/-407.5	93,1146,3061	yes	missense	PREP	NM_002726.4	29	972,2157,3374	TT,TC,CC		15.4884,37.1539,31.5316	benign	706/711	105726036	4101,8905	2203	4300	6503	SO:0001583	missense	5550	exon15			AGTCGACGTTCAG		CCDS5053.1	6q22	2008-02-05			ENSG00000085377	ENSG00000085377	3.4.21.26		9358	protein-coding gene	gene with protein product		600400				7959018	Standard	NM_002726		Approved		uc003prc.3	P48147	OTTHUMG00000015297	ENST00000369110.3:c.2116G>A	6.37:g.105726036C>T	ENSP00000358106:p.Val706Ile	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	62	34	0.548387	NM_002726	Q8N6D4	Missense_Mutation	SNP	ENST00000369110.3	37	CCDS5053.1	675	0.3090659340659341	345	0.7012195121951219	92	0.2541436464088398	119	0.20804195804195805	119	0.15699208443271767	T	6.451	0.451407	0.12223	0.628461	0.154884	ENSG00000085377	ENST00000369110	T	0.28666	1.6	5.77	4.53	0.55603	Peptidase S9, prolyl oligopeptidase, catalytic domain (1);	0.235854	0.44097	N	0.000496	T	0.03608	0.0103	N	0.04373	-0.215	0.54753	P	1.7000000000044757E-5	B	0.02656	0.0	B	0.04013	0.001	T	0.38156	-0.9674	9	0.07644	T	0.81	-12.6298	7.6525	0.28356	0.0:0.0805:0.2879:0.6316	rs1051484;rs3191870;rs3734722;rs56566104;rs58772009;rs1051484	706	P48147	PPCE_HUMAN	I	706	ENSP00000358106:V706I	ENSP00000358106:V706I	V	-	1	0	PREP	105832729	1.000000	0.71417	1.000000	0.80357	0.842000	0.47809	2.614000	0.46359	1.120000	0.41904	-0.269000	0.10298	GTC	C|0.673;T|0.327	0.327	strong		0.552	PREP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041658.1		
GPR112	139378	hgsc.bcm.edu	37	X	135430483	135430483	+	Missense_Mutation	SNP	T	T	C	rs912002	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:135430483T>C	ENST00000394143.1	+	6	4909	c.4618T>C	c.(4618-4620)Tct>Cct	p.S1540P	GPR112_ENST00000412101.1_Missense_Mutation_p.S1335P|GPR112_ENST00000370652.1_Missense_Mutation_p.S1540P|GPR112_ENST00000287534.4_Missense_Mutation_p.S1477P|GPR112_ENST00000394141.1_Missense_Mutation_p.S1335P	NM_153834.3	NP_722576.3	Q8IZF6	GP112_HUMAN	G protein-coupled receptor 112	1540			S -> P (in dbSNP:rs912002).		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(13)|central_nervous_system(2)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(33)|lung(97)|ovary(5)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(2)	199	Acute lymphoblastic leukemia(192;0.000127)					AACTAAATCTTCTAAAACAAT	0.418													t|||	1764	0.467285	0.4251	0.3573	3775	,	,		14599	0.255		0.3797	False		,,,				2504	0.3221				p.S1540P		Atlas-SNP	.											.	GPR112	459	.	0			c.T4618C						PASS	.		PRO/SER	2110,1725		493,813,311,326,260	96.0	94.0	95.0		4618	1.7	0.1	X	dbSNP_86	95	3223,3505		567,1177,912,684,960	yes	missense	GPR112	NM_153834.3	74	1060,1990,1223,1010,1220	CC,CT,C,TT,T		47.9043,44.9804,49.5124	probably-damaging	1540/3081	135430483	5333,5230	2203	4300	6503	SO:0001583	missense	139378	exon6			AAATCTTCTAAAA	AY140954	CCDS35409.1	Xq26.3	2014-08-08			ENSG00000156920	ENSG00000156920		"""-"", ""GPCR / Class B : Orphans"""	18992	protein-coding gene	gene with protein product						12435584	Standard	XM_005262367		Approved	RP1-299I16, PGR17	uc004ezu.1	Q8IZF6	OTTHUMG00000022508	ENST00000394143.1:c.4618T>C	X.37:g.135430483T>C	ENSP00000377699:p.Ser1540Pro	Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	91	91	1	NM_153834	A2A2J1|A2A2J2|Q5EGP2|Q86SM6	Missense_Mutation	SNP	ENST00000394143.1	37	CCDS35409.1	754	0.45449065702230257	137	0.37027027027027026	83	0.2902097902097902	103	0.22391304347826088	190	0.3242320819112628	t	14.52	2.560180	0.45590	0.550196	0.479043	ENSG00000156920	ENST00000394143;ENST00000370652;ENST00000412101;ENST00000287534;ENST00000394141	T;T;T;T;T	0.40756	1.06;1.06;1.02;1.13;1.02	3.02	1.66	0.24008	.	.	.	.	.	T	0.00012	0.0000	L	0.34521	1.04	0.80722	P	0.0	D;D;D	0.76494	0.997;0.999;0.998	D;D;D	0.80764	0.986;0.994;0.987	T	0.44483	-0.9325	8	0.87932	D	0	.	4.2365	0.10628	0.3093:0.0:0.0:0.6907	rs912002;rs52799687;rs61339577;rs912002	1477;1335;1540	Q8IZF6-2;Q8IZF6-3;Q8IZF6	.;.;GP112_HUMAN	P	1540;1540;1335;1477;1335	ENSP00000377699:S1540P;ENSP00000359686:S1540P;ENSP00000416526:S1335P;ENSP00000287534:S1477P;ENSP00000377697:S1335P	ENSP00000287534:S1477P	S	+	1	0	GPR112	135258149	0.316000	0.24580	0.086000	0.20670	0.250000	0.25880	0.927000	0.28818	1.195000	0.43115	0.378000	0.23410	TCT	0|0.015;C|0.478	0.478	strong		0.418	GPR112-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000286639.1		
IL31RA	133396	hgsc.bcm.edu	37	5	55206444	55206444	+	Missense_Mutation	SNP	G	G	A	rs161704	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:55206444G>A	ENST00000447346.2	+	12	1651	c.1586G>A	c.(1585-1587)aGc>aAc	p.S529N	IL31RA_ENST00000354961.4_Missense_Mutation_p.S510N|IL31RA_ENST00000396834.1_Missense_Mutation_p.S510N|IL31RA_ENST00000359040.5_Missense_Mutation_p.S529N|IL31RA_ENST00000490985.1_Missense_Mutation_p.S387N	NM_001242636.1|NM_139017.5	NP_001229565.1|NP_620586.3	Q8NI17	IL31R_HUMAN	interleukin 31 receptor A	497					cytokine-mediated signaling pathway (GO:0019221)|defense response (GO:0006952)|homeostatic process (GO:0042592)|JAK-STAT cascade (GO:0007259)|macrophage differentiation (GO:0030225)|MAPK cascade (GO:0000165)|monocyte differentiation (GO:0030224)|negative regulation of apoptotic process (GO:0043066)|negative regulation of macrophage activation (GO:0043031)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cytokine binding (GO:0019955)|cytokine receptor activity (GO:0004896)|protein kinase binding (GO:0019901)|transcription coactivator activity (GO:0003713)			endometrium(2)|kidney(2)|large_intestine(7)|lung(8)|ovary(1)|stomach(1)	21		Lung NSC(810;6.93e-05)|Prostate(74;0.00741)|Breast(144;0.0544)|Ovarian(174;0.223)				GTCATGGCCAGCACCAGTGCT	0.468													G|||	1552	0.309904	0.3321	0.2176	5008	,	,		22564	0.3254		0.2962	False		,,,				2504	0.3436				p.S529N		Atlas-SNP	.											.	IL31RA	84	.	0			c.G1586A						PASS	.	G	ASN/SER,ASN/SER,ASN/SER,ASN/SER,ASN/SER	1511,2895	480.3+/-358.8	262,987,954	163.0	141.0	148.0		1529,1586,1529,1160,1586	3.3	1.0	5	dbSNP_79	148	2503,6097	410.3+/-350.1	354,1795,2151	yes	missense,missense,missense,missense,missense	IL31RA	NM_001242636.1,NM_001242637.1,NM_001242638.1,NM_001242639.1,NM_139017.5	46,46,46,46,46	616,2782,3105	AA,AG,GG		29.1047,34.2941,30.8627	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	510/746,529/682,510/663,387/623,529/765	55206444	4014,8992	2203	4300	6503	SO:0001583	missense	133396	exon12			TGGCCAGCACCAG	AY499339	CCDS3970.2, CCDS56365.1, CCDS56366.1, CCDS56367.1, CCDS75244.1, CCDS75245.1	5q11.2	2013-02-11			ENSG00000164509	ENSG00000164509		"""Interleukins and interleukin receptors"", ""Fibronectin type III domain containing"""	18969	protein-coding gene	gene with protein product		609510				15184896, 11877449	Standard	NM_139017		Approved	CRL3, GLM-R, CRL, Glmr, IL-31RA	uc003jql.3	Q8NI17	OTTHUMG00000097045	ENST00000447346.2:c.1586G>A	5.37:g.55206444G>A	ENSP00000415900:p.Ser529Asn	Somatic	207	0	0		WXS	Illumina HiSeq	Phase_I	271	165	0.608856	NM_001242637	A6NIF8|Q2TBA1|Q6EBC3|Q6EBC4|Q6EBC5|Q6EBC6|Q6UWL8|Q8WYJ0	Missense_Mutation	SNP	ENST00000447346.2	37	CCDS3970.2	669	0.30631868131868134	147	0.29878048780487804	82	0.2265193370165746	205	0.3583916083916084	235	0.3100263852242744	G	3.877	-0.026766	0.07589	0.342941	0.291047	ENSG00000164509	ENST00000396834;ENST00000447346;ENST00000359040;ENST00000490985;ENST00000354961	T;T;T;T;T	0.57273	0.41;0.41;0.41;0.41;0.41	5.11	3.33	0.38152	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.372887	0.31685	N	0.007222	T	0.00012	0.0000	M	0.71871	2.18	0.09310	P	0.9999999999994192	B;B;B;B	0.27166	0.17;0.037;0.141;0.141	B;B;B;B	0.26310	0.068;0.028;0.041;0.041	T	0.31861	-0.9928	9	0.25751	T	0.34	-19.8536	6.2045	0.20595	0.2609:0.0:0.7391:0.0	rs161704;rs327251;rs52803246;rs58671636;rs161704	497;529;510;529	Q8NI17;Q8NI17-5;Q8NI17-3;Q8NI17-2	IL31R_HUMAN;.;.;.	N	510;529;529;387;510	ENSP00000380046:S510N;ENSP00000415900:S529N;ENSP00000351935:S529N;ENSP00000427533:S387N;ENSP00000347047:S510N	ENSP00000347047:S510N	S	+	2	0	IL31RA	55242201	0.982000	0.34865	1.000000	0.80357	0.987000	0.75469	0.168000	0.16622	1.521000	0.48983	0.557000	0.71058	AGC	G|0.694;N|0.000	.	strong		0.468	IL31RA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214148.1	NM_139017	
VPS13B	157680	hgsc.bcm.edu	37	8	100844758	100844758	+	Silent	SNP	T	T	C	rs36074608	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:100844758T>C	ENST00000358544.2	+	52	9678	c.9567T>C	c.(9565-9567)tcT>tcC	p.S3189S	VPS13B_ENST00000357162.2_Silent_p.S3164S|VPS13B_ENST00000395996.1_3'UTR	NM_017890.4	NP_060360.3	Q7Z7G8	VP13B_HUMAN	vacuolar protein sorting 13 homolog B (yeast)	3189					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)			TGGGCTTTTCTCCTGCCCCAG	0.537													T|||	987	0.197085	0.0514	0.3458	5008	,	,		13808	0.3542		0.174	False		,,,				2504	0.1503				p.S3189S	Colon(161;2205 2542 7338 31318)	Atlas-SNP	.											VPS13B_ENST00000357162,NS,carcinoma,+1,2	VPS13B	811	2	0			c.T9567C						PASS	.	T	,	364,4042	186.4+/-213.3	15,334,1854	77.0	63.0	68.0		9567,9492	0.6	0.3	8	dbSNP_126	68	1493,7107	283.6+/-296.2	121,1251,2928	no	coding-synonymous,coding-synonymous	VPS13B	NM_017890.3,NM_152564.3	,	136,1585,4782	CC,CT,TT		17.3605,8.2615,14.278	,	3189/4023,3164/3998	100844758	1857,11149	2203	4300	6503	SO:0001819	synonymous_variant	157680	exon52			CTTTTCTCCTGCC	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.9567T>C	8.37:g.100844758T>C		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	78	18	0.230769	NM_017890	C9JD30|Q709C6|Q709C7|Q7Z7G4|Q7Z7G5|Q7Z7G6|Q7Z7G7|Q8NB77|Q9NWV1|Q9Y4E7	Silent	SNP	ENST00000358544.2	37	CCDS6280.1																																																																																			T|0.840;C|0.160	0.160	strong		0.537	VPS13B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000277138.1	NM_184042	
OR4A47	403253	hgsc.bcm.edu	37	11	48511050	48511050	+	Missense_Mutation	SNP	T	T	C	rs76991989	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:48511050T>C	ENST00000446524.1	+	1	782	c.706T>C	c.(706-708)Tca>Cca	p.S236P		NM_001005512.2	NP_001005512.2	Q6IF82	O4A47_HUMAN	olfactory receptor, family 4, subfamily A, member 47	236						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(2)|endometrium(1)|kidney(1)|large_intestine(2)|lung(18)|ovary(1)|skin(1)|urinary_tract(2)	29						AAAAGCCCTCTCAACCTGCAG	0.428													T|||	41	0.0081869	0.0015	0.0086	5008	,	,		18021	0.0		0.0268	False		,,,				2504	0.0061				p.S236P		Atlas-SNP	.											OR4A47,bladder,carcinoma,-1,1	OR4A47	72	1	0			c.T706C						PASS	.	T	PRO/SER	23,4379		0,23,2178	148.0	144.0	145.0		706	2.4	0.1	11	dbSNP_131	145	217,8379		3,211,4084	yes	missense	OR4A47	NM_001005512.2	74	3,234,6262	CC,CT,TT		2.5244,0.5225,1.8464	benign	236/310	48511050	240,12758	2201	4298	6499	SO:0001583	missense	403253	exon1			GCCCTCTCAACCT	BK004380	CCDS31490.1	11p11.2	2012-08-09			ENSG00000237388	ENSG00000237388		"""GPCR / Class A : Olfactory receptors"""	31266	protein-coding gene	gene with protein product							Standard	NM_001005512		Approved		uc010rhx.2	Q6IF82	OTTHUMG00000166581	ENST00000446524.1:c.706T>C	11.37:g.48511050T>C	ENSP00000412752:p.Ser236Pro	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	116	90	0.775862	NM_001005512		Missense_Mutation	SNP	ENST00000446524.1	37	CCDS31490.1	23	0.010531135531135532	1	0.0020325203252032522	5	0.013812154696132596	0	0.0	17	0.022427440633245383	N	11.71	1.719811	0.30503	0.005225	0.025244	ENSG00000237388	ENST00000446524	T	0.00309	8.16	4.59	2.36	0.29203	GPCR, rhodopsin-like superfamily (1);	0.553031	0.16377	N	0.217096	T	0.00300	0.0009	H	0.98407	4.225	0.09310	N	0.999997	D	0.53462	0.96	P	0.54965	0.765	T	0.40098	-0.9581	10	0.87932	D	0	.	5.4392	0.16498	0.0:0.2998:0.0:0.7002	.	236	Q6IF82	O4A47_HUMAN	P	236	ENSP00000412752:S236P	ENSP00000412752:S236P	S	+	1	0	OR4A47	48467626	0.000000	0.05858	0.139000	0.22197	0.222000	0.24845	0.081000	0.14823	0.225000	0.20959	0.172000	0.16884	TCA	T|0.981;C|0.019	0.019	strong		0.428	OR4A47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390559.1	NM_001005512	
KREMEN1	83999	hgsc.bcm.edu	37	22	29533499	29533499	+	Silent	SNP	G	G	A	rs35612970	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:29533499G>A	ENST00000407188.1	+	6	795	c.795G>A	c.(793-795)gcG>gcA	p.A265A	KREMEN1_ENST00000400335.4_Silent_p.A267A|KREMEN1_ENST00000327813.5_Silent_p.A267A|KREMEN1_ENST00000400338.2_Silent_p.A267A			Q96MU8	KREM1_HUMAN	kringle containing transmembrane protein 1	265	CUB. {ECO:0000255|PROSITE- ProRule:PRU00059}.				cell communication (GO:0007154)|regulation of canonical Wnt signaling pathway (GO:0060828)|Wnt signaling pathway (GO:0016055)	integral component of membrane (GO:0016021)|membrane (GO:0016020)				breast(1)|endometrium(3)|large_intestine(2)|lung(8)|ovary(3)|prostate(1)|upper_aerodigestive_tract(2)	20						GGGACTCGGCGGACATGGTGG	0.622													G|||	543	0.108427	0.0726	0.111	5008	,	,		15598	0.0427		0.1958	False		,,,				2504	0.1329				p.A267A		Atlas-SNP	.											.	KREMEN1	46	.	0			c.G801A						PASS	.	G	,	317,3549		11,295,1627	64.0	64.0	64.0		801,801	0.2	1.0	22	dbSNP_126	64	1432,6822		129,1174,2824	no	coding-synonymous,coding-synonymous	KREMEN1	NM_001039570.2,NM_032045.4	,	140,1469,4451	AA,AG,GG		17.3492,8.1997,14.4307	,	267/459,267/493	29533499	1749,10371	1933	4127	6060	SO:0001819	synonymous_variant	83999	exon6			CTCGGCGGACATG	AB059618	CCDS43000.1, CCDS13849.1, CCDS43000.2	22q12.1	2008-03-27	2002-11-13	2002-11-15	ENSG00000183762	ENSG00000183762			17550	protein-coding gene	gene with protein product		609898	"""kringle containing transmembrane protein"""	KREMEN		11267660	Standard	NM_001039570		Approved	KRM1	uc011akm.1	Q96MU8	OTTHUMG00000030987	ENST00000407188.1:c.795G>A	22.37:g.29533499G>A		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	82	40	0.487805	NM_001039570	B0QY46|B0QY47|B1AJR5|Q5TIB9|Q6P3X6|Q9BY70|Q9UGS5|Q9UGU1	Silent	SNP	ENST00000407188.1	37	CCDS43000.2																																																																																			G|0.861;A|0.139	0.139	strong		0.622	KREMEN1-004	KNOWN	non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320947.1		
TCTE3	6991	hgsc.bcm.edu	37	6	170144194	170144194	+	Silent	SNP	T	T	C	rs2274954	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:170144194T>C	ENST00000366774.3	-	2	397	c.297A>G	c.(295-297)tcA>tcG	p.S99S		NM_174910.1	NP_777570.1	Q8IZS6	TC1D3_HUMAN	t-complex-associated-testis-expressed 3	99					transport (GO:0006810)	cytoplasm (GO:0005737)|dynein complex (GO:0030286)|membrane (GO:0016020)|microtubule (GO:0005874)	motor activity (GO:0003774)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|prostate(1)	4		Breast(66;0.000338)		OV - Ovarian serous cystadenocarcinoma(33;1.08e-21)|BRCA - Breast invasive adenocarcinoma(81;1.32e-07)|GBM - Glioblastoma multiforme(31;0.00157)		TAGTTTCTACTGAATGAGCTT	0.333													T|||	576	0.115016	0.1331	0.1239	5008	,	,		17831	0.1716		0.0249	False		,,,				2504	0.1186				p.S99S		Atlas-SNP	.											.	TCTE3	13	.	0			c.A297G						PASS	.	T		611,3793	261.9+/-264.6	44,523,1635	64.0	69.0	67.0		297	-6.1	0.8	6	dbSNP_100	67	159,8439	74.2+/-136.8	1,157,4141	no	coding-synonymous	TCTE3	NM_174910.1		45,680,5776	CC,CT,TT		1.8493,13.8738,5.9222		99/199	170144194	770,12232	2202	4299	6501	SO:0001819	synonymous_variant	6991	exon2			TTCTACTGAATGA	AF519569	CCDS5310.1	6q27	2014-06-03			ENSG00000184786	ENSG00000184786			11695	protein-coding gene	gene with protein product	"""Tctex1 domain containing 3"""	186977				1505969, 12584439	Standard	NM_174910		Approved	TCTEX1D3	uc003qxe.1	Q8IZS6	OTTHUMG00000016068	ENST00000366774.3:c.297A>G	6.37:g.170144194T>C		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	32	11	0.34375	NM_174910		Silent	SNP	ENST00000366774.3	37	CCDS5310.1																																																																																			T|0.932;C|0.068	0.068	strong		0.333	TCTE3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043243.1	NM_174910	
LILRA6	79168	hgsc.bcm.edu	37	19	54744794	54744794	+	Missense_Mutation	SNP	G	G	A	rs434127	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:54744794G>A	ENST00000396365.2	-	5	907	c.868C>T	c.(868-870)Cac>Tac	p.H290Y	LILRA6_ENST00000245621.5_Missense_Mutation_p.H290Y|LILRA6_ENST00000440558.2_Missense_Mutation_p.H290Y|LILRA6_ENST00000270464.5_Intron|LILRB3_ENST00000407860.2_Intron|LILRA6_ENST00000419410.2_Missense_Mutation_p.H290Y|LILRA6_ENST00000391735.3_3'UTR	NM_024318.2	NP_077294	Q6PI73	LIRA6_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 6	290	Ig-like C2-type 1.				immune system process (GO:0002376)	integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(20)|ovary(3)|skin(2)|urinary_tract(2)	38	all_cancers(19;0.00723)|all_epithelial(19;0.00389)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		TGGCCCCCGTGGGAGGGGCTC	0.667																																					p.H290Y		Atlas-SNP	.											.	LILRA6	75	.	0			c.C868T						PASS	.						53.0	65.0	61.0					19																	54744794		2203	4300	6503	SO:0001583	missense	79168	exon5			CCCCGTGGGAGGG	AF041262	CCDS42610.1	19q13.4	2013-01-11	2005-05-17	2005-05-17	ENSG00000244482	ENSG00000244482		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	15495	protein-coding gene	gene with protein product			"""leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 6"""	LILRB6		10941842	Standard	NM_024318		Approved	ILT8, CD85b		Q6PI73	OTTHUMG00000066635	ENST00000396365.2:c.868C>T	19.37:g.54744794G>A	ENSP00000379651:p.His290Tyr	Somatic	315	0	0		WXS	Illumina HiSeq	Phase_I	247	71	0.287449	NM_024318		Missense_Mutation	SNP	ENST00000396365.2	37	CCDS42610.1	.	.	.	.	.	.	.	.	.	.	G	4.311	0.057030	0.08339	.	.	ENSG00000244482	ENST00000440558;ENST00000419410;ENST00000421123;ENST00000396365;ENST00000245621	T;T;T;T	0.00824	5.65;5.65;5.65;5.65	1.91	0.716	0.18191	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.760220	0.11527	N	0.555114	T	0.02193	0.0068	M	0.67397	2.05	0.09310	N	0.999999	B;P;B;B	0.52170	0.052;0.951;0.02;0.214	B;P;B;B	0.53954	0.292;0.738;0.049;0.139	T	0.47623	-0.9103	10	0.26408	T	0.33	.	5.2469	0.15502	0.0:0.0:0.6602:0.3398	.	290;290;290;290	C9JFH3;Q6PI73;F8WCY4;D3YTC4	.;LIRA6_HUMAN;.;.	Y	290	ENSP00000390120:H290Y;ENSP00000411227:H290Y;ENSP00000379651:H290Y;ENSP00000245621:H290Y	ENSP00000245621:H290Y	H	-	1	0	LILRA6	59436606	0.000000	0.05858	0.002000	0.10522	0.017000	0.09413	0.093000	0.15086	0.320000	0.23234	0.162000	0.16502	CAC	G|0.857;A|0.143	0.143	strong		0.667	LILRA6-003	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000313725.1	NM_024318	
ZNF598	90850	hgsc.bcm.edu	37	16	2048564	2048564	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:2048564T>C	ENST00000563630.1	-	12	2461	c.2219A>G	c.(2218-2220)tAt>tGt	p.Y740C	AC005606.15_ENST00000567515.1_lincRNA|ZNF598_ENST00000431526.1_Missense_Mutation_p.Y795C|ZNF598_ENST00000562103.1_Missense_Mutation_p.Y740C			Q86UK7	ZN598_HUMAN	zinc finger protein 598	795	Pro-rich.						poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|lung(7)|skin(1)|urinary_tract(1)	16						ACTCTTGTAATACTGGGCTGC	0.652																																					p.Y795C		Atlas-SNP	.											.	ZNF598	55	.	0			c.A2384G						PASS	.						7.0	8.0	8.0					16																	2048564		1863	4080	5943	SO:0001583	missense	90850	exon14			TTGTAATACTGGG	BC029270		16p13.3	2008-05-02				ENSG00000167962		"""Zinc fingers, C2H2-type"""	28079	protein-coding gene	gene with protein product							Standard	NM_178167		Approved	FLJ00086	uc002cof.2	Q86UK7		ENST00000563630.1:c.2219A>G	16.37:g.2048564T>C	ENSP00000455882:p.Tyr740Cys	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	98	49	0.5	NM_178167	Q8IW49|Q8N3D9|Q96FG3|Q9H7J3	Missense_Mutation	SNP	ENST00000563630.1	37		.	.	.	.	.	.	.	.	.	.	.	13.41	2.228427	0.39399	.	.	ENSG00000167962	ENST00000431526	T	0.44881	0.91	5.29	4.2	0.49525	.	0.000000	0.85682	D	0.000000	T	0.67429	0.2892	M	0.90650	3.135	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.996;0.999	T	0.73360	-0.4007	10	0.87932	D	0	-18.8123	9.7829	0.40660	0.0:0.0812:0.0:0.9188	.	795;787	Q86UK7;Q86UK7-2	ZN598_HUMAN;.	C	795	ENSP00000411409:Y795C	ENSP00000411409:Y795C	Y	-	2	0	ZNF598	1988565	1.000000	0.71417	1.000000	0.80357	0.934000	0.57294	7.301000	0.78850	2.000000	0.58554	0.379000	0.24179	TAT	.	.	none		0.652	ZNF598-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000434439.1	NM_178167	
AKAP13	11214	hgsc.bcm.edu	37	15	86123364	86123364	+	Missense_Mutation	SNP	G	G	A	rs7177107	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:86123364G>A	ENST00000394518.2	+	7	2160	c.2065G>A	c.(2065-2067)Gag>Aag	p.E689K	RP11-815J21.2_ENST00000561409.1_RNA|AKAP13_ENST00000361243.2_Missense_Mutation_p.E689K	NM_001270546.1|NM_007200.4	NP_001257475.1|NP_009131.2	Q12802	AKP13_HUMAN	A kinase (PRKA) anchor protein 13	689			E -> K (in dbSNP:rs7177107). {ECO:0000269|Ref.3}.		apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nuclear export (GO:0051168)|positive regulation of apoptotic process (GO:0043065)|protein phosphorylation (GO:0006468)|regulation of cardiac muscle hypertrophy (GO:0010611)|regulation of glucocorticoid mediated signaling pathway (GO:1900169)|regulation of protein kinase activity (GO:0045859)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	cAMP-dependent protein kinase activity (GO:0004691)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|signal transducer activity (GO:0004871)			NS(1)|breast(2)|central_nervous_system(4)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(13)|liver(1)|lung(43)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	98						CATAGTTAGCGAGTCCGAAAG	0.498													G|||	381	0.0760783	0.0091	0.098	5008	,	,		20905	0.001		0.1938	False		,,,				2504	0.1074				p.E689K	Melanoma(94;603 1453 3280 32295 32951)	Atlas-SNP	.											.	AKAP13	394	.	0			c.G2065A						PASS	.	G	LYS/GLU,LYS/GLU	213,4191	128.6+/-165.4	8,197,1997	112.0	97.0	102.0		2065,2065	3.4	0.0	15	dbSNP_116	102	1894,6704	326.2+/-317.3	200,1494,2605	yes	missense,missense	AKAP13	NM_006738.4,NM_007200.3	56,56	208,1691,4602	AA,AG,GG		22.0284,4.8365,16.2052	benign,benign	689/2818,689/2814	86123364	2107,10895	2202	4299	6501	SO:0001583	missense	11214	exon7			GTTAGCGAGTCCG	M90360	CCDS32319.1, CCDS32320.1, CCDS73778.1	15q24-q25	2013-01-10	2002-06-13			ENSG00000170776		"""A-kinase anchor proteins"", ""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	371	protein-coding gene	gene with protein product		604686	"""lymphoid blast crisis oncogene"""	LBC		9627117, 1860836	Standard	NM_007200		Approved	Ht31, BRX, AKAP-Lbc, c-lbc, PROTO-LB, HA-3, ARHGEF13	uc002blu.2	Q12802		ENST00000394518.2:c.2065G>A	15.37:g.86123364G>A	ENSP00000378026:p.Glu689Lys	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	124	45	0.362903	NM_007200	Q14572|Q59FP6|Q86W90|Q8WXQ6|Q96JP6|Q96P79|Q9Y5T0|Q9Y5T6	Missense_Mutation	SNP	ENST00000394518.2	37	CCDS32319.1	197	0.0902014652014652	8	0.016260162601626018	38	0.10497237569060773	1	0.0017482517482517483	150	0.19788918205804748	G	13.21	2.168651	0.38315	0.048365	0.220284	ENSG00000170776	ENST00000361243;ENST00000394518;ENST00000394516;ENST00000458540	T;T	0.09445	2.98;2.98	5.38	3.38	0.38709	.	.	.	.	.	T	0.00012	0.0000	N	0.03608	-0.345	0.53688	P	2.2999999999995246E-5	B;B	0.16802	0.011;0.019	B;B	0.09377	0.002;0.004	T	0.38394	-0.9663	8	0.06625	T	0.88	.	11.9016	0.52687	0.0:0.657:0.343:0.0	rs7177107;rs52836676;rs7177107	689;689	Q12802;Q12802-2	AKP13_HUMAN;.	K	689;689;688;688	ENSP00000354718:E689K;ENSP00000378026:E689K	ENSP00000354718:E689K	E	+	1	0	AKAP13	83924368	0.000000	0.05858	0.002000	0.10522	0.005000	0.04900	0.321000	0.19558	1.405000	0.46838	-0.133000	0.14855	GAG	G|0.875;A|0.125	0.125	strong		0.498	AKAP13-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417318.1	NM_007200	
RABEP1	9135	hgsc.bcm.edu	37	17	5284698	5284698	+	Silent	SNP	A	A	G	rs1143206	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:5284698A>G	ENST00000546142.2	+	17	2572	c.2385A>G	c.(2383-2385)caA>caG	p.Q795Q	RABEP1_ENST00000537505.1_Silent_p.Q752Q|RABEP1_ENST00000408982.2_Silent_p.Q762Q|RABEP1_ENST00000341923.6_Silent_p.Q762Q|NUP88_ENST00000573169.1_Intron|RABEP1_ENST00000262477.6_Silent_p.Q795Q			Q15276	RABE1_HUMAN	rabaptin, RAB GTPase binding effector protein 1	795					apoptotic process (GO:0006915)|endocytosis (GO:0006897)|membrane fusion (GO:0061025)|protein transport (GO:0015031)	early endosome (GO:0005769)|endocytic vesicle (GO:0030139)|endosome (GO:0005768)|intracellular membrane-bounded organelle (GO:0043231)	GTPase activator activity (GO:0005096)|protein homodimerization activity (GO:0042803)			NS(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|ovary(2)|stomach(1)|upper_aerodigestive_tract(1)	8						CCGTTGAACAACTAATGTTTG	0.368													A|||	2765	0.552117	0.3964	0.4251	5008	,	,		22136	0.8254		0.4394	False		,,,				2504	0.6871				p.Q795Q		Atlas-SNP	.											.	RABEP1	59	.	0			c.A2385G						PASS	.	A	,	1519,2169		324,871,649	77.0	76.0	76.0		2286,2385	-2.4	1.0	17	dbSNP_86	76	3199,4981		620,1959,1511	no	coding-synonymous,coding-synonymous	RABEP1	NM_001083585.1,NM_004703.4	,	944,2830,2160	GG,GA,AA		39.1076,41.1876,39.754	,	762/830,795/863	5284698	4718,7150	1844	4090	5934	SO:0001819	synonymous_variant	9135	exon17			TGAACAACTAATG	AF098638	CCDS42243.1, CCDS45592.1	17p13.2	2008-02-05				ENSG00000029725			17677	protein-coding gene	gene with protein product		603616				8521472	Standard	NM_001291582		Approved	neurocrescin, RAB5EP, RABPT5, rabaptin-5	uc002gbm.4	Q15276		ENST00000546142.2:c.2385A>G	17.37:g.5284698A>G		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	70	37	0.528571	NM_004703	B2RAG7|O95369|Q8IVX3	Silent	SNP	ENST00000546142.2	37	CCDS45592.1																																																																																			A|0.519;G|0.481	0.481	strong		0.368	RABEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439349.1	NM_004703	
ATM	472	hgsc.bcm.edu	37	11	108175462	108175462	+	Missense_Mutation	SNP	G	G	A	rs1801516	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:108175462G>A	ENST00000452508.2	+	38	5746	c.5557G>A	c.(5557-5559)Gat>Aat	p.D1853N	ATM_ENST00000278616.4_Missense_Mutation_p.D1853N			Q13315	ATM_HUMAN	ATM serine/threonine kinase	1853			D -> N (common polymorphism; dbSNP:rs1801516). {ECO:0000269|PubMed:10397742, ECO:0000269|PubMed:10425038, ECO:0000269|PubMed:10534763, ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:9711876, ECO:0000269|PubMed:9887333}.|D -> V (might contribute to B-cell chronic lymphocytic leukemia; dbSNP:rs1801673). {ECO:0000269|PubMed:10397742, ECO:0000269|PubMed:10817650, ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:9872980, ECO:0000269|PubMed:9887333}.		brain development (GO:0007420)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|DNA damage induced protein phosphorylation (GO:0006975)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|heart development (GO:0007507)|histone mRNA catabolic process (GO:0071044)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|lipoprotein catabolic process (GO:0042159)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of B cell proliferation (GO:0030889)|neuron apoptotic process (GO:0051402)|oocyte development (GO:0048599)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|positive regulation of neuron apoptotic process (GO:0043525)|pre-B cell allelic exclusion (GO:0002331)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reciprocal meiotic recombination (GO:0007131)|replicative senescence (GO:0090399)|response to hypoxia (GO:0001666)|response to ionizing radiation (GO:0010212)|signal transduction (GO:0007165)|signal transduction involved in mitotic G2 DNA damage checkpoint (GO:0072434)|somitogenesis (GO:0001756)|telomere maintenance (GO:0000723)	cytoplasmic vesicle (GO:0031410)|nucleoplasm (GO:0005654)|spindle (GO:0005819)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent protein kinase activity (GO:0004677)|histone serine kinase activity (GO:0035174)|protein complex binding (GO:0032403)|protein dimerization activity (GO:0046983)|protein N-terminus binding (GO:0047485)|protein serine/threonine kinase activity (GO:0004674)	p.D1853N(10)		NS(4)|breast(23)|central_nervous_system(11)|endometrium(10)|haematopoietic_and_lymphoid_tissue(227)|kidney(19)|large_intestine(53)|liver(5)|lung(62)|ovary(6)|pancreas(4)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	448		all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147)	Caffeine(DB00201)	TTTACTCCAAGATACAAATGA	0.388			"""D, Mis, N, F, S"""		T-PLL	"""leukemia, lymphoma, medulloblastoma, glioma"""		Genes defective in diseases associated with sensitivity to DNA damaging agents	Ataxia Telangiectasia	TSP Lung(14;0.12)			G|||	335	0.066893	0.0083	0.0965	5008	,	,		16727	0.0159		0.162	False		,,,				2504	0.0798				p.D1853N		Atlas-SNP	.	yes	Rec	yes	Ataxia-telangiectasia	11	11q22.3	472	ataxia telangiectasia mutated		"""L, O"""	ATM_ENST00000278616,colon,carcinoma,-1,17	ATM	1657	17	10	Substitution - Missense(10)	breast(9)|skin(1)	c.G5557A	GRCh37	CM077896	ATM	M	rs1801516	PASS	.	G	ASN/ASP	125,4277	92.5+/-131.2	3,119,2079	75.0	72.0	73.0	http://www.ncbi.nlm.nih.gov/pubmed?term	5557	5.5	1.0	11	dbSNP_89	73	1205,7391	241.8+/-272.0	99,1007,3192	yes	missense	ATM	NM_000051.3	23	102,1126,5271	AA,AG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	14.0181,2.8396,10.2323	possibly-damaging	1853/3057	108175462	1330,11668	2201	4298	6499	SO:0001583	missense	472	exon37	Familial Cancer Database	AT, Louis-Bar syndrome	CTCCAAGATACAA	AB209133	CCDS31669.1	11q22-q23	2014-09-17	2014-06-17		ENSG00000149311	ENSG00000149311			795	protein-coding gene	gene with protein product	"""TEL1, telomere maintenance 1, homolog (S. cerevisiae)"""	607585	"""ataxia telangiectasia mutated (includes complementation groups A, C and D)"", ""ataxia telangiectasia mutated"""	ATA, ATDC, ATC, ATD			Standard	XM_005271561		Approved	TEL1, TELO1	uc001pkb.1	Q13315	OTTHUMG00000166480	ENST00000452508.2:c.5557G>A	11.37:g.108175462G>A	ENSP00000388058:p.Asp1853Asn	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	91	15	0.164835	NM_000051	B2RNX5|O15429|Q12758|Q16551|Q93007|Q9NP02|Q9UCX7	Missense_Mutation	SNP	ENST00000452508.2	37	CCDS31669.1	172	0.07875457875457875	5	0.01016260162601626	40	0.11049723756906077	7	0.012237762237762238	120	0.158311345646438	G	17.18	3.324076	0.60634	0.028396	0.140181	ENSG00000149311	ENST00000278616;ENST00000452508	T;T	0.73152	-0.72;-0.72	5.52	5.52	0.82312	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.00580	0.0019	L	0.61036	1.89	0.19945	P	0.9999491241	B	0.20368	0.044	B	0.16289	0.015	T	0.10730	-1.0617	9	0.33940	T	0.23	.	19.8041	0.96521	0.0:0.0:1.0:0.0	rs1801516;rs17503060;rs52821794;rs60879649;rs1801516	1853	Q13315	ATM_HUMAN	N	1853	ENSP00000278616:D1853N;ENSP00000388058:D1853N	ENSP00000278616:D1853N	D	+	1	0	ATM	107680672	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	6.342000	0.72982	2.748000	0.94277	0.591000	0.81541	GAT	G|0.910;A|0.090	0.090	strong		0.388	ATM-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389938.1	NM_000051	
SLC9A5	6553	hgsc.bcm.edu	37	16	67300058	67300058	+	Silent	SNP	G	G	A	rs61744117	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:67300058G>A	ENST00000299798.11	+	15	2213	c.2148G>A	c.(2146-2148)aaG>aaA	p.K716K	CTC-277H1.7_ENST00000573063.1_RNA	NM_004594.2	NP_004585.1	Q14940	SL9A5_HUMAN	solute carrier family 9, subfamily A (NHE5, cation proton antiporter 5), member 5	716					ion transport (GO:0006811)|regulation of pH (GO:0006885)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sodium:proton antiporter activity (GO:0015385)			breast(1)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(3)|lung(9)|ovary(2)|pancreas(1)|prostate(1)	27		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.00376)|Epithelial(162;0.0173)|all cancers(182;0.116)		AGACAGAGAAGGAGGACGATG	0.562													G|||	4	0.000798722	0.0	0.0014	5008	,	,		20520	0.0		0.003	False		,,,				2504	0.0				p.K716K		Atlas-SNP	.											.	SLC9A5	82	.	0			c.G2148A						PASS	.	G		1,4181		0,1,2090	117.0	124.0	121.0		2148	2.2	1.0	16	dbSNP_129	121	23,8393		0,23,4185	no	coding-synonymous	SLC9A5	NM_004594.2		0,24,6275	AA,AG,GG		0.2733,0.0239,0.1905		716/897	67300058	24,12574	2091	4208	6299	SO:0001819	synonymous_variant	6553	exon15			AGAGAAGGAGGAC		CCDS42178.1	16q22.1	2013-05-22	2012-03-22		ENSG00000135740	ENSG00000135740		"""Solute carriers"""	11078	protein-coding gene	gene with protein product		600477	"""solute carrier family 9 (sodium/hydrogen exchanger), isoform 5"", ""solute carrier family 9 (sodium/hydrogen exchanger), member 5"""			7759094, 9933642	Standard	NM_004594		Approved	NHE5	uc002esm.3	Q14940	OTTHUMG00000172935	ENST00000299798.11:c.2148G>A	16.37:g.67300058G>A		Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	200	113	0.565	NM_004594	A5PKY7|Q9Y626	Silent	SNP	ENST00000299798.11	37	CCDS42178.1																																																																																			G|0.998;A|0.002	0.002	strong		0.562	SLC9A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421386.1		
GIMAP4	55303	hgsc.bcm.edu	37	7	150269917	150269917	+	Silent	SNP	G	G	A	rs61741802	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:150269917G>A	ENST00000255945.2	+	3	934	c.759G>A	c.(757-759)gcG>gcA	p.A253A	GIMAP4_ENST00000494750.1_3'UTR|GIMAP4_ENST00000461940.1_Silent_p.A267A	NM_018326.2	NP_060796.1	Q9NUV9	GIMA4_HUMAN	GTPase, IMAP family member 4	253						cytosol (GO:0005829)	GTP binding (GO:0005525)			breast(1)|endometrium(1)|large_intestine(3)|lung(5)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	14			OV - Ovarian serous cystadenocarcinoma(82;0.0179)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		GAGAGAAAGCGCGGATAAGAG	0.458													g|||	63	0.0125799	0.0023	0.0331	5008	,	,		20784	0.0		0.0288	False		,,,				2504	0.0082				p.A253A		Atlas-SNP	.											.	GIMAP4	61	.	0			c.G759A						PASS	.	G		32,4374	37.6+/-69.7	0,32,2171	74.0	75.0	75.0		759	-8.9	0.0	7	dbSNP_129	75	384,8216	124.4+/-183.2	5,374,3921	no	coding-synonymous	GIMAP4	NM_018326.2		5,406,6092	AA,AG,GG		4.4651,0.7263,3.1985		253/330	150269917	416,12590	2203	4300	6503	SO:0001819	synonymous_variant	55303	exon3			GAAAGCGCGGATA	AK001972	CCDS5904.1	7q36.1	2014-04-04			ENSG00000133574	ENSG00000133574		"""GTPases, IMAP"""	21872	protein-coding gene	gene with protein product	"""immune-associated nucleotide-binding protein 1"""	608087				15474311, 18701445	Standard	NM_018326		Approved	HIMAP4, FLJ11110, IMAP4, IAN1	uc003whl.3	Q9NUV9	OTTHUMG00000157475	ENST00000255945.2:c.759G>A	7.37:g.150269917G>A		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	89	40	0.449438	NM_018326		Silent	SNP	ENST00000255945.2	37	CCDS5904.1																																																																																			G|0.972;A|0.028	0.028	strong		0.458	GIMAP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348927.1	NM_018326	
SLC46A2	57864	hgsc.bcm.edu	37	9	115652881	115652881	+	Silent	SNP	G	G	T	rs3802491	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:115652881G>T	ENST00000374228.4	-	1	312	c.81C>A	c.(79-81)gcC>gcA	p.A27A		NM_033051.3	NP_149040.3	Q9BY10	TSCOT_HUMAN	solute carrier family 46, member 2	27					negative regulation of T cell apoptotic process (GO:0070233)|regulation of T cell differentiation (GO:0045580)|T cell homeostasis (GO:0043029)|thymus development (GO:0048538)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	symporter activity (GO:0015293)			central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(11)|pancreas(1)|skin(1)	18						CCTGGGACGAGGCCACCACGG	0.672													G|||	2094	0.418131	0.1906	0.4798	5008	,	,		14846	0.746		0.327	False		,,,				2504	0.4376				p.A27A		Atlas-SNP	.											.	SLC46A2	30	.	0			c.C81A						PASS	.	G		909,3497	332.3+/-302.4	90,729,1384	35.0	38.0	37.0		81	2.1	0.9	9	dbSNP_107	37	2962,5638	442.0+/-360.0	524,1914,1862	no	coding-synonymous	SLC46A2	NM_033051.3		614,2643,3246	TT,TG,GG		34.4419,20.631,29.7632		27/476	115652881	3871,9135	2203	4300	6503	SO:0001819	synonymous_variant	57864	exon1			GGACGAGGCCACC	AF242557	CCDS6786.1	9q32	2013-05-22	2007-03-29	2007-03-29	ENSG00000119457	ENSG00000119457		"""Solute carriers"""	16055	protein-coding gene	gene with protein product		608956	"""thymic stromal co-transporter"""	TSCOT		10978518, 12826694	Standard	NM_033051		Approved	Ly110	uc004bgk.3	Q9BY10	OTTHUMG00000020513	ENST00000374228.4:c.81C>A	9.37:g.115652881G>T		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	18	8	0.444444	NM_033051	B1ALK1|Q86VT0|Q96NE2	Silent	SNP	ENST00000374228.4	37	CCDS6786.1																																																																																			G|0.667;T|0.333	0.333	strong		0.672	SLC46A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053702.1	NM_033051	
NINL	22981	hgsc.bcm.edu	37	20	25456888	25456888	+	Silent	SNP	A	A	G	rs437635	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:25456888A>G	ENST00000278886.6	-	17	3112	c.3039T>C	c.(3037-3039)agT>agC	p.S1013S	NINL_ENST00000422516.1_Intron	NM_025176.4	NP_079452.3	Q9Y2I6	NINL_HUMAN	ninein-like	1013					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						CAACCTCCACACTGTGCTTGT	0.682													G|||	2795	0.558107	0.5356	0.3559	5008	,	,		14219	0.9067		0.4304	False		,,,				2504	0.5041				p.S1013S		Atlas-SNP	.											.	NINL	148	.	0			c.T3039C						PASS	.	G		2241,2165	583.5+/-385.8	552,1137,514	58.0	62.0	60.0		3039	0.2	0.0	20	dbSNP_80	60	3727,4873	615.9+/-396.4	794,2139,1367	no	coding-synonymous	NINL	NM_025176.4		1346,3276,1881	GG,GA,AA		43.3372,49.1375,45.8865		1013/1383	25456888	5968,7038	2203	4300	6503	SO:0001819	synonymous_variant	22981	exon17			CTCCACACTGTGC		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.3039T>C	20.37:g.25456888A>G		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	75	39	0.52	NM_025176	A6NJN0|B3V9H6|B7Z1V8|Q5JYP0|Q8NE38|Q9NQE3	Silent	SNP	ENST00000278886.6	37	CCDS33452.1																																																																																			A|0.506;G|0.494	0.494	strong		0.682	NINL-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078445.3	NM_025176	
ZNF443	10224	hgsc.bcm.edu	37	19	12542772	12542772	+	Missense_Mutation	SNP	C	C	T	rs1134389	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:12542772C>T	ENST00000301547.5	-	4	411	c.214G>A	c.(214-216)Gtt>Att	p.V72I	CTD-3105H18.16_ENST00000595562.1_Intron	NM_005815.4	NP_005806	Q9Y2A4	ZN443_HUMAN	zinc finger protein 443	72	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.			V -> I (in Ref. 1; BAA75543 and 3; AAH32753). {ECO:0000305}.	apoptotic process (GO:0006915)|regulation of transcription, DNA-templated (GO:0006355)|response to stress (GO:0006950)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(3)|endometrium(1)|kidney(1)|large_intestine(11)|lung(10)|pancreas(1)|prostate(1)	28						TTACTTTCAACAAATCTCTCT	0.338													.|||	1308	0.261182	0.171	0.4207	5008	,	,		20498	0.1071		0.496	False		,,,				2504	0.1871				p.V72I		Atlas-SNP	.											.	ZNF443	63	.	0			c.G214A						PASS	.						51.0	43.0	46.0					19																	12542772		2201	4278	6479	SO:0001583	missense	10224	exon4			TTTCAACAAATCT	AB011414	CCDS32918.1	19p13.13	2013-01-08			ENSG00000180855	ENSG00000180855		"""Zinc fingers, C2H2-type"", ""-"""	20878	protein-coding gene	gene with protein product		606697				9731181	Standard	NM_005815		Approved	ZK1	uc002mtu.3	Q9Y2A4	OTTHUMG00000156404	ENST00000301547.5:c.214G>A	19.37:g.12542772C>T	ENSP00000301547:p.Val72Ile	Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	184	74	0.402174	NM_005815		Missense_Mutation	SNP	ENST00000301547.5	37	CCDS32918.1	678	0.31043956043956045	88	0.17886178861788618	157	0.43370165745856354	56	0.0979020979020979	377	0.4973614775725594	C	1.200	-0.632838	0.03584	.	.	ENSG00000180855	ENST00000301547;ENST00000411622	T	0.07327	3.2	1.37	0.266	0.15617	Krueppel-associated box (1);	.	.	.	.	T	0.00012	0.0000	N	0.11560	0.145	0.80722	P	0.0	B	0.17852	0.024	B	0.22601	0.04	T	0.37979	-0.9682	8	0.21540	T	0.41	.	5.5758	0.17222	0.6931:0.3069:0.0:0.0	rs1134389;rs13382105	72	Q9Y2A4	ZN443_HUMAN	I	72	ENSP00000301547:V72I	ENSP00000301547:V72I	V	-	1	0	ZNF443	12403772	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.193000	0.09573	0.039000	0.15632	-0.534000	0.04291	GTT	T|1.000;|0.000	1.000	weak		0.338	ZNF443-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344084.1	NM_005815	
TBC1D31	93594	hgsc.bcm.edu	37	8	124138855	124138855	+	Silent	SNP	G	G	A	rs16898012	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:124138855G>A	ENST00000287380.1	+	13	1902	c.1812G>A	c.(1810-1812)ctG>ctA	p.L604L	TBC1D31_ENST00000518805.1_Silent_p.L237L|TBC1D31_ENST00000327098.5_Silent_p.L604L|TBC1D31_ENST00000522420.1_Silent_p.L499L|TBC1D31_ENST00000309336.3_Silent_p.L604L|TBC1D31_ENST00000521676.1_Silent_p.L481L|TBC1D31_ENST00000378080.2_Silent_p.L499L	NM_145647.3	NP_663622.2	Q96DN5	TBC31_HUMAN	TBC1 domain family, member 31	604						centrosome (GO:0005813)	Rab GTPase activator activity (GO:0005097)										CCTTCCTTCTGATGACTGTTG	0.423													G|||	1490	0.297524	0.3858	0.3732	5008	,	,		15646	0.1815		0.2525	False		,,,				2504	0.2904				p.L604L		Atlas-SNP	.											.	WDR67	97	.	0			c.G1812A						PASS	.	G	,	1691,2715	513.1+/-368.2	325,1041,837	126.0	120.0	122.0		1812,1812	1.8	1.0	8	dbSNP_123	122	2218,6382	378.1+/-338.8	277,1664,2359	no	coding-synonymous,coding-synonymous	WDR67	NM_001145088.1,NM_145647.3	,	602,2705,3196	AA,AG,GG		25.7907,38.3795,30.0554	,	604/971,604/1067	124138855	3909,9097	2203	4300	6503	SO:0001819	synonymous_variant	93594	exon13			CCTTCTGATGACT	AK094612	CCDS6338.1, CCDS47916.1	8q24.13	2013-07-10	2013-07-10	2013-07-10	ENSG00000156787	ENSG00000156787		"""WD repeat domain containing"""	30888	protein-coding gene	gene with protein product			"""WD repeat domain 67"""	WDR67		12477932	Standard	NM_001145088		Approved	MGC21654, Gm85	uc003ypp.2	Q96DN5	OTTHUMG00000165081	ENST00000287380.1:c.1812G>A	8.37:g.124138855G>A		Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	182	40	0.21978	NM_001145088	B7ZL19|Q2M2J9|Q3MIR6|Q8TBP9	Silent	SNP	ENST00000287380.1	37	CCDS6338.1																																																																																			G|0.705;A|0.295	0.295	strong		0.423	TBC1D31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381721.1	NM_145647	
BTN2A1	11120	hgsc.bcm.edu	37	6	26468326	26468326	+	Missense_Mutation	SNP	G	G	A	rs3734542	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:26468326G>A	ENST00000312541.5	+	8	1381	c.1133G>A	c.(1132-1134)cGg>cAg	p.R378Q	BTN2A1_ENST00000469185.1_Intron|BTN2A1_ENST00000541522.1_Missense_Mutation_p.R317Q|BTN2A1_ENST00000429381.1_3'UTR	NM_007049.3|NM_078476.2	NP_008980.1|NP_510961.1	Q7KYR7	BT2A1_HUMAN	butyrophilin, subfamily 2, member A1	378	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.		R -> Q (in dbSNP:rs3734542).		lipid metabolic process (GO:0006629)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)				breast(3)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(2)|lung(9)|ovary(2)|prostate(1)|skin(3)|urinary_tract(3)	27						GTCCTAGGCCGGGAGAGCTTC	0.567													G|||	190	0.0379393	0.0333	0.0346	5008	,	,		22106	0.0099		0.0825	False		,,,				2504	0.0297				p.R378Q		Atlas-SNP	.											BTN2A1_ENST00000265424,NS,carcinoma,-1,2	BTN2A1	118	2	0			c.G1133A						PASS	.	G	GLN/ARG,,GLN/ARG,	189,4217	119.2+/-156.9	4,181,2018	163.0	156.0	158.0		950,,1133,	-3.4	0.0	6	dbSNP_107	158	796,7804	186.2+/-233.7	39,718,3543	yes	missense,intron,missense,utr-3	BTN2A1	NM_001197233.1,NM_001197234.1,NM_007049.3,NM_078476.2	43,,43,	43,899,5561	AA,AG,GG		9.2558,4.2896,7.5734	benign,,benign,	317/467,,378/528,	26468326	985,12021	2203	4300	6503	SO:0001583	missense	11120	exon8			TAGGCCGGGAGAG	U90543	CCDS4613.1, CCDS47390.1, CCDS56404.1, CCDS56405.1	6p22.1	2014-01-14			ENSG00000112763	ENSG00000112763		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Butyrophilins"""	1136	protein-coding gene	gene with protein product		613590				9382921, 9149941	Standard	NM_007049		Approved	BT2.1, BTF1, BTN2.1	uc003nib.2	Q7KYR7	OTTHUMG00000014457	ENST00000312541.5:c.1133G>A	6.37:g.26468326G>A	ENSP00000312158:p.Arg378Gln	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	94	45	0.478723	NM_007049	B4DLP9|E9PGR4|O00475|P78408|Q59EN4|Q7KYQ7|Q7Z386|Q96AV7|Q9NU62	Missense_Mutation	SNP	ENST00000312541.5	37	CCDS4613.1	100	0.045787545787545784	16	0.032520325203252036	11	0.03038674033149171	8	0.013986013986013986	65	0.08575197889182058	G	1.077	-0.668091	0.03428	0.042896	0.092558	ENSG00000112763	ENST00000312541;ENST00000541522;ENST00000265424	T;T	0.11063	2.81;2.81	2.67	-3.36	0.04913	Concanavalin A-like lectin/glucanase (1);SPRY-associated (1);Butyrophylin-like (1);B30.2/SPRY domain (1);	1.455890	0.04492	N	0.379807	T	0.01661	0.0053	L	0.29908	0.895	0.80722	P	0.0	B;B	0.24368	0.102;0.025	B;B	0.19391	0.025;0.015	T	0.43410	-0.9393	9	0.27082	T	0.32	.	1.0184	0.01513	0.3381:0.1348:0.3589:0.1681	rs3734542;rs52798417;rs3734542	317;378	B4DLP9;Q7KYR7	.;BT2A1_HUMAN	Q	378;317;364	ENSP00000312158:R378Q;ENSP00000443909:R317Q	ENSP00000265424:R364Q	R	+	2	0	BTN2A1	26576305	0.000000	0.05858	0.001000	0.08648	0.042000	0.13812	-5.767000	0.00099	-0.907000	0.03862	0.491000	0.48974	CGG	G|0.937;A|0.063	0.063	strong		0.567	BTN2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040122.2	NM_007049	
UMODL1	89766	hgsc.bcm.edu	37	21	43510437	43510437	+	Missense_Mutation	SNP	A	A	C	rs17114359	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:43510437A>C	ENST00000408910.2	+	6	820	c.820A>C	c.(820-822)Aat>Cat	p.N274H	UMODL1_ENST00000400427.1_Missense_Mutation_p.N202H|UMODL1_ENST00000400424.2_Missense_Mutation_p.N202H|UMODL1_ENST00000408989.2_Missense_Mutation_p.N274H	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|||	1206	0.240815	0.0832	0.281	5008	,	,		20658	0.374		0.2018	False		,,,				2504	0.3282				p.N274H	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.A820C						scavenged	.	A	HIS/ASN,HIS/ASN,HIS/ASN,HIS/ASN	371,3907		36,299,1804	133.0	135.0	134.0		820,604,604,820	1.5	0.0	21	dbSNP_123	134	1754,6718		214,1326,2696	yes	missense,missense,missense,missense	UMODL1	NM_001004416.2,NM_001199527.1,NM_001199528.2,NM_173568.3	68,68,68,68	250,1625,4500	CC,CA,AA		20.7035,8.6723,16.6667	probably-damaging,probably-damaging,probably-damaging,probably-damaging	274/1319,202/1375,202/1247,274/1447	43510437	2125,10625	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>C	21.37:g.43510437A>C	ENSP00000386147:p.Asn274His	Somatic	118	1	0.00847458		WXS	Illumina HiSeq	Phase_I	131	55	0.419847	NM_173568	C9JCE6|Q5DIC9|Q6LA40|Q6LA41|Q8N216	Missense_Mutation	SNP	ENST00000408910.2	37	CCDS42936.1	511	0.23397435897435898	45	0.09146341463414634	104	0.287292817679558	209	0.36538461538461536	153	0.20184696569920843	A	6.001	0.368519	0.11352	0.086723	0.207035	ENSG00000177398	ENST00000400427;ENST00000400424;ENST00000408989;ENST00000408910;ENST00000380462;ENST00000400417	D;D;D;D	0.91686	-2.89;-2.89;-2.89;-2.89	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	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B;B	0.30236	0.274;0.007	B;B	0.30782	0.12;0.022	T	0.01488	-1.1342	9	0.44086	T	0.13	-5.2933	8.6932	0.34280	0.4946:0.5054:0.0:0.0	.	274;274	Q5DID0-2;Q5DID0	.;UROL1_HUMAN	H	202;202;274;274;120;120	ENSP00000383279:N202H;ENSP00000383276:N202H;ENSP00000386126:N274H;ENSP00000386147:N274H	ENSP00000369829:N120H	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	0.140	strong		0.557	UMODL1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195292.2		
PGM1	5236	hgsc.bcm.edu	37	1	64095111	64095111	+	Missense_Mutation	SNP	A	A	G	rs855314	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:64095111A>G	ENST00000371084.3	+	2	475	c.262A>G	c.(262-264)Atc>Gtc	p.I88V	PGM1_ENST00000371083.4_Missense_Mutation_p.I106V|PGM1_ENST00000540265.1_5'UTR	NM_002633.2	NP_002624.2	P36871	PGM1_HUMAN	phosphoglucomutase 1	88			I -> V (in dbSNP:rs855314).		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						TCGCTTGGTTATCGGACAGAA	0.468													A|||	650	0.129792	0.2519	0.1138	5008	,	,		16170	0.0109		0.1431	False		,,,				2504	0.0849				p.I106V		Atlas-SNP	.											.	PGM1	75	.	0			c.A316G						PASS	.	A	VAL/ILE,,VAL/ILE	1057,3349	385.6+/-325.8	134,789,1280	144.0	144.0	144.0		316,,262	5.5	1.0	1	dbSNP_86	144	1212,7388	244.0+/-273.4	85,1042,3173	yes	missense,utr-5,missense	PGM1	NM_001172818.1,NM_001172819.1,NM_002633.2	29,,29	219,1831,4453	GG,GA,AA		14.093,23.99,17.4458	benign,,benign	106/581,,88/563	64095111	2269,10737	2203	4300	6503	SO:0001583	missense	5236	exon2			TTGGTTATCGGAC	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.262A>G	1.37:g.64095111A>G	ENSP00000360125:p.Ile88Val	Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	155	75	0.483871	NM_001172818	B2R5N9|B4DPV0|Q16105|Q16106|Q5BKZ9|Q6NW22|Q86U74|Q96J40|Q9NTY4	Missense_Mutation	SNP	ENST00000371084.3	37	CCDS625.1	279	0.12774725274725274	125	0.2540650406504065	41	0.1132596685082873	4	0.006993006993006993	109	0.1437994722955145	A	11.55	1.672935	0.29693	0.2399	0.14093	ENSG00000079739	ENST00000538673;ENST00000371084;ENST00000371083	T;T	0.62498	0.02;0.02	5.48	5.48	0.80851	Alpha-D-phosphohexomutase, alpha/beta/alpha domain I (1);Alpha-D-phosphohexomutase, alpha/beta/alpha I/II/III (2);	0.101891	0.64402	D	0.000003	T	0.17450	0.0419	N	0.02685	-0.53	0.09310	P	1.0	B;B	0.24618	0.022;0.107	B;B	0.25291	0.037;0.059	T	0.14008	-1.0488	9	0.02654	T	1	-23.2235	15.8924	0.79309	1.0:0.0:0.0:0.0	rs855314;rs52835934;rs59193920;rs855314	106;88	P36871-2;P36871	.;PGM1_HUMAN	V	64;88;106	ENSP00000360125:I88V;ENSP00000360124:I106V	ENSP00000360124:I106V	I	+	1	0	PGM1	63867699	1.000000	0.71417	0.991000	0.47740	0.911000	0.54048	9.210000	0.95106	2.210000	0.71456	0.533000	0.62120	ATC	A|0.837;G|0.163	0.163	strong		0.468	PGM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024868.1	NM_002633	
DMD	1756	hgsc.bcm.edu	37	X	32486756	32486756	+	Silent	SNP	C	C	T	rs1800268	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:32486756C>T	ENST00000357033.4	-	23	3227	c.3021G>A	c.(3019-3021)tcG>tcA	p.S1007S	DMD_ENST00000378677.2_Silent_p.S1003S	NM_000109.3|NM_004006.2|NM_004011.3|NM_004012.3|NM_004014.2	NP_000100.2|NP_003997|NP_004002.2|NP_004003.1|NP_004005.1	P11532	DMD_HUMAN	dystrophin	1007					cardiac muscle cell action potential (GO:0086001)|cardiac muscle contraction (GO:0060048)|cellular protein complex assembly (GO:0043623)|cellular protein localization (GO:0034613)|extracellular matrix organization (GO:0030198)|motile cilium assembly (GO:0044458)|muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|negative regulation of peptidyl-cysteine S-nitrosylation (GO:1902083)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|peptide biosynthetic process (GO:0043043)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of heart rate (GO:0002027)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|regulation of skeletal muscle contraction (GO:0014819)|regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion (GO:0014809)|regulation of voltage-gated calcium channel activity (GO:1901385)	cell junction (GO:0030054)|cell surface (GO:0009986)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dystrophin-associated glycoprotein complex (GO:0016010)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|syntrophin complex (GO:0016013)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|dystroglycan binding (GO:0002162)|myosin binding (GO:0017022)|nitric-oxide synthase binding (GO:0050998)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|liver(1)|lung(25)|ovary(3)|pancreas(3)|prostate(2)|skin(1)|urinary_tract(2)	77		all_cancers(2;1.22e-16)|Acute lymphoblastic leukemia(2;4.65e-06)|all_hematologic(2;0.00108)|all_epithelial(3;0.00626)|all_neural(2;0.0189)|all_lung(315;0.182)|Glioma(3;0.203)				GCGCTTTCTTCGACATCTCTT	0.408													C|||	33	0.00874172	0.0	0.013	3775	,	,		11926	0.0		0.0159	False		,,,				2504	0.0082				p.S1007S		Atlas-SNP	.											.	DMD	2127	.	0			c.G3021A						PASS	.	C	,,,,	15,3818		0,12,3,1619,568	75.0	68.0	70.0		2997,3021,2652,3009,2652	-2.5	0.9	X	dbSNP_89	70	112,6616		0,87,25,2341,1847	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	DMD	NM_000109.3,NM_004006.2,NM_004007.2,NM_004009.3,NM_004010.3	,,,,	0,99,28,3960,2415	TT,TC,T,CC,C		1.6647,0.3913,1.2025	,,,,	999/3678,1007/3686,884/3563,1003/3682,884/3563	32486756	127,10434	2202	4300	6502	SO:0001819	synonymous_variant	1756	exon23			TTTCTTCGACATC	AF047505	CCDS14231.1, CCDS14232.1, CCDS14233.1, CCDS14234.1, CCDS48091.1, CCDS55394.1, CCDS55395.1, CCDS75965.1	Xp21.2	2014-09-17	2008-08-01		ENSG00000198947	ENSG00000198947			2928	protein-coding gene	gene with protein product	"""muscular dystrophy, Duchenne and Becker types"""	300377	"""dystrophin (muscular dystrophy, Duchenne and Becker types), includes DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272"", ""mental retardation, X-linked 85"""	MRX85		3282674, 3607877, 23900271	Standard	NM_004019		Approved	BMD, DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272	uc004dda.1	P11532	OTTHUMG00000021336	ENST00000357033.4:c.3021G>A	X.37:g.32486756C>T		Somatic	420	0	0		WXS	Illumina HiSeq	Phase_I	238	238	1	NM_004006	E9PDN1|Q02295|Q14169|Q14170|Q5JYU0|Q6NSJ9|Q7KZ48|Q8N754|Q9UCW3|Q9UCW4	Silent	SNP	ENST00000357033.4	37	CCDS14233.1																																																																																			C|0.989;T|0.011	0.011	strong		0.408	DMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056182.2	NM_004006	
CFHR3	10878	hgsc.bcm.edu	37	1	196757392	196757392	+	Silent	SNP	C	C	T	rs400344	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:196757392C>T	ENST00000367425.4	+	4	569	c.477C>T	c.(475-477)tcC>tcT	p.S159S	CFHR3_ENST00000471440.2_Silent_p.S159S|CFHR3_ENST00000391985.3_Intron	NM_021023.5	NP_066303.2	Q02985	FHR3_HUMAN	complement factor H-related 3	159	Sushi 3. {ECO:0000255|PROSITE- ProRule:PRU00302}.					blood microparticle (GO:0072562)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				breast(1)|central_nervous_system(1)|endometrium(1)|kidney(4)|lung(6)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	18						GATTCATTTCCGAATCTTCCT	0.254													-|||	3252	0.649361	0.646	0.6657	5008	,	,		9863	0.9484		0.501	False		,,,				2504	0.4867				p.S159S		Atlas-SNP	.											CFHR3,NS,carcinoma,0,1	CFHR3	52	1	0			c.C477T						PASS	.						9.0	15.0	13.0					1																	196757392		1478	3842	5320	SO:0001819	synonymous_variant	10878	exon4			CATTTCCGAATCT	X68679	CCDS30958.1, CCDS53453.1	1q32	2014-09-17		2006-02-28	ENSG00000116785	ENSG00000116785		"""Complement system"""	16980	protein-coding gene	gene with protein product	"""complement factor H related 3"""	605336		CFHL3		8428964, 10380701	Standard	NM_021023		Approved	FHR-3, HLF4, FHR3, DOWN16	uc001gtl.3	Q02985	OTTHUMG00000035929	ENST00000367425.4:c.477C>T	1.37:g.196757392C>T		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	49	48	0.979592	NM_021023	B4DPR0|Q9UJ16	Silent	SNP	ENST00000367425.4	37	CCDS30958.1																																																																																			C|0.379;T|0.621	0.621	strong		0.254	CFHR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087505.2	NM_021023	
ZSWIM2	151112	hgsc.bcm.edu	37	2	187698751	187698751	+	Silent	SNP	G	G	A	rs7559533	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:187698751G>A	ENST00000295131.2	-	6	789	c.750C>T	c.(748-750)acC>acT	p.T250T		NM_182521.2	NP_872327.2	Q8NEG5	ZSWM2_HUMAN	zinc finger, SWIM-type containing 2	250					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)			CTATGCATTCGGTACACCTAA	0.368													G|||	983	0.196286	0.0976	0.2464	5008	,	,		19325	0.1131		0.2704	False		,,,				2504	0.3037				p.T250T		Atlas-SNP	.											ZSWIM2,NS,carcinoma,-1,1	ZSWIM2	119	1	0			c.C750T						PASS	.	G		550,3856	247.2+/-255.5	38,474,1691	103.0	90.0	94.0		750	-3.1	0.0	2	dbSNP_116	94	2531,6069	412.7+/-350.9	361,1809,2130	no	coding-synonymous	ZSWIM2	NM_182521.2		399,2283,3821	AA,AG,GG		29.4302,12.483,23.6891		250/634	187698751	3081,9925	2203	4300	6503	SO:0001819	synonymous_variant	151112	exon6			GCATTCGGTACAC	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.750C>T	2.37:g.187698751G>A		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	52	28	0.538462	NM_182521	B3KXV6|Q53SI3|Q57ZY3	Silent	SNP	ENST00000295131.2	37	CCDS33348.1																																																																																			G|0.784;A|0.216	0.216	strong		0.368	ZSWIM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334565.1	NM_182521	
CEP164	22897	hgsc.bcm.edu	37	11	117267884	117267884	+	Missense_Mutation	SNP	A	A	G	rs573455	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:117267884A>G	ENST00000278935.3	+	27	3503	c.3356A>G	c.(3355-3357)cAg>cGg	p.Q1119R	CEP164_ENST00000533706.1_3'UTR	NM_001271933.1|NM_014956.4	NP_001258862.1|NP_055771.4	Q9UPV0	CE164_HUMAN	centrosomal protein 164kDa	1119			Q -> R (in dbSNP:rs573455). {ECO:0000269|PubMed:14702039, 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)		TTCCTTGTGCAGCAGACACGC	0.617													G|||	2320	0.463259	0.5318	0.3386	5008	,	,		20013	0.381		0.5358	False		,,,				2504	0.4693				p.Q1122R		Atlas-SNP	.											.	CEP164	121	.	0			c.A3365G						PASS	.	G	ARG/GLN	2256,2146	581.7+/-385.4	566,1124,511	58.0	53.0	55.0		3356	-1.7	0.0	11	dbSNP_83	55	4681,3911	546.4+/-385.0	1291,2099,906	yes	missense	CEP164	NM_014956.4	43	1857,3223,1417	GG,GA,AA		45.5191,48.7506,46.6138	benign	1119/1461	117267884	6937,6057	2201	4296	6497	SO:0001583	missense	22897	exon26			TTGTGCAGCAGAC	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.3356A>G	11.37:g.117267884A>G	ENSP00000278935:p.Gln1119Arg	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	67	15	0.223881	NM_001271933	Q6PKH9|Q7Z2X9|Q9NVS0|Q9UFJ6	Missense_Mutation	SNP	ENST00000278935.3	37	CCDS31683.1	1010	0.4624542124542125	248	0.5040650406504065	141	0.38950276243093923	219	0.38286713286713286	402	0.5303430079155673	G	0.004	-2.309267	0.00237	0.512494	0.544809	ENSG00000110274	ENST00000278935	T	0.18016	2.24	4.87	-1.69	0.08186	.	0.590552	0.14128	N	0.339568	T	0.00012	0.0000	N	0.03154	-0.405	0.80722	P	0.0	B;B;B	0.06786	0.001;0.0;0.0	B;B;B	0.06405	0.002;0.001;0.001	T	0.41840	-0.9486	9	0.02654	T	1	-3.174	10.3014	0.43654	0.4933:0.0:0.5067:0.0	rs573455;rs3210734;rs17309657;rs52838154;rs59395518;rs573455	893;1119;1122	Q9NTH6;Q9UPV0;Q9UPV0-2	.;CE164_HUMAN;.	R	1119	ENSP00000278935:Q1119R	ENSP00000278935:Q1119R	Q	+	2	0	CEP164	116773094	0.000000	0.05858	0.006000	0.13384	0.032000	0.12392	-0.650000	0.05378	-0.916000	0.03818	-1.861000	0.00560	CAG	A|0.498;G|0.502	0.502	strong		0.617	CEP164-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392893.1	NM_014956	
CSF2RB	1439	hgsc.bcm.edu	37	22	37329999	37329999	+	Silent	SNP	C	C	T	rs1801117	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	43	0	0		WXS	Illumina HiSeq	Phase_I	44	28	0.636364	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	
MUC4	4585	hgsc.bcm.edu	37	3	195507332	195507332	+	Missense_Mutation	SNP	A	A	T	rs200058677		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195507332A>T	ENST00000463781.3	-	2	11578	c.11119T>A	c.(11119-11121)Tca>Aca	p.S3707T	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.S3707T	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)		GTGTGACCTGAGGATGATGAG	0.572																																					p.S3707T		Atlas-SNP	.											.	MUC4	1505	.	0			c.T11119A						PASS	.						65.0	54.0	57.0					3																	195507332		658	1591	2249	SO:0001583	missense	4585	exon2			GACCTGAGGATGA	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.11119T>A	3.37:g.195507332A>T	ENSP00000417498:p.Ser3707Thr	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	86	15	0.174419	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	0.948	-0.707223	0.03230	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.34275	1.39;1.37	.	.	.	.	.	.	.	.	T	0.12135	0.0295	N	0.14661	0.345	0.09310	N	1	P	0.38110	0.618	B	0.28638	0.092	T	0.10497	-1.0627	7	.	.	.	.	1.404	0.02276	0.3909:0.0:0.2806:0.3284	rs28715544	3579	E7ESK3	.	T	3707	ENSP00000417498:S3707T;ENSP00000420243:S3707T	.	S	-	1	0	MUC4	196992111	0.000000	0.05858	0.006000	0.13384	0.012000	0.07955	-4.714000	0.00195	-2.253000	0.00698	-2.525000	0.00183	TCA	.	.	weak		0.572	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
MICAL1	64780	hgsc.bcm.edu	37	6	109770869	109770869	+	Silent	SNP	G	G	A	rs752261	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:109770869G>A	ENST00000358807.3	-	10	1736	c.1425C>T	c.(1423-1425)acC>acT	p.T475T	MICAL1_ENST00000368952.4_Silent_p.T494T|MICAL1_ENST00000358577.3_Silent_p.T389T|MICAL1_ENST00000483856.1_5'Flank	NM_022765.3	NP_073602.3	Q8TDZ2	MICA1_HUMAN	microtubule associated monooxygenase, calponin and LIM domain containing 1	475	Monooxygenase domain. {ECO:0000250}.				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)		CCTGATTGGGGGTCACTGCCC	0.637													G|||	194	0.038738	0.003	0.1715	5008	,	,		15630	0.0		0.0557	False		,,,				2504	0.0153				p.T475T		Atlas-SNP	.											.	MICAL1	79	.	0			c.C1425T						PASS	.	G	,	66,4340	61.1+/-98.1	1,64,2138	59.0	60.0	60.0		1167,1425	-2.4	1.0	6	dbSNP_86	60	545,8055	149.8+/-204.8	21,503,3776	no	coding-synonymous,coding-synonymous	MICAL1	NM_001159291.1,NM_022765.3	,	22,567,5914	AA,AG,GG		6.3372,1.498,4.6978	,	389/982,475/1068	109770869	611,12395	2203	4300	6503	SO:0001819	synonymous_variant	64780	exon10			ATTGGGGGTCACT	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.1425C>T	6.37:g.109770869G>A		Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	29	13	0.448276	NM_022765	B7Z3R5|E1P5F0|Q7Z633|Q8IVS9|Q96G47|Q9H6X6|Q9H7I0|Q9HAA1|Q9UFF7	Silent	SNP	ENST00000358807.3	37	CCDS5076.1	103	0.04716117216117216	5	0.01016260162601626	53	0.1464088397790055	0	0.0	45	0.059366754617414245	G	9.900	1.206611	0.22205	0.01498	0.063372	ENSG00000135596	ENST00000433205	.	.	.	5.24	-2.38	0.06622	.	.	.	.	.	T	0.12987	0.0315	.	.	.	0.09310	P	0.99999120049	.	.	.	.	.	.	T	0.26292	-1.0107	3	.	.	.	.	5.3913	0.16245	0.3166:0.4355:0.248:0.0	rs752261;rs17854786;rs56988467;rs752261	.	.	.	S	40	.	.	P	-	1	0	MICAL1	109877562	0.000000	0.05858	0.985000	0.45067	0.999000	0.98932	-0.905000	0.04075	-0.268000	0.09312	0.655000	0.94253	CCC	G|0.957;A|0.043	0.043	strong		0.637	MICAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041759.2	NM_022765	
OSCP1	127700	hgsc.bcm.edu	37	1	36893968	36893968	+	Intron	SNP	A	A	G	rs61308377	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:36893968A>G	ENST00000356637.5	-	5	610				OSCP1_ENST00000315643.9_Intron|OSCP1_ENST00000235532.5_Intron|OSCP1_ENST00000354267.3_Missense_Mutation_p.Y209H|OSCP1_ENST00000433045.2_Intron			Q8WVF1	OSCP1_HUMAN	organic solute carrier partner 1						transport (GO:0006810)	plasma membrane (GO:0005886)				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						GGGTATACATAATGGAAAGTC	0.398													A|||	675	0.134784	0.0726	0.1297	5008	,	,		15437	0.3075		0.0905	False		,,,				2504	0.09				p.Y209H		Atlas-SNP	.											.	OSCP1	48	.	0			c.T625C						PASS	.	A	,HIS/TYR	359,4047	184.3+/-211.7	8,343,1852	138.0	135.0	136.0		,625	-4.3	0.0	1	dbSNP_129	136	815,7785	189.4+/-236.2	31,753,3516	yes	intron,missense	OSCP1	NM_145047.4,NM_206837.2	,83	39,1096,5368	GG,GA,AA		9.4767,8.148,9.0266	,	,209/224	36893968	1174,11832	2203	4300	6503	SO:0001627	intron_variant	127700	exon5			ATACATAATGGAA		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.546+3434T>C	1.37:g.36893968A>G		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	54	25	0.462963	NM_206837	A6NHM5|A6NHS9|A6NIN9|Q4AEJ0|Q8N7G2|Q8TDF1	Missense_Mutation	SNP	ENST00000356637.5	37		331	0.15155677655677655	52	0.10569105691056911	48	0.13259668508287292	162	0.28321678321678323	69	0.09102902374670185	A	12.61	1.990931	0.35131	0.08148	0.094767	ENSG00000116885	ENST00000354267	T	0.35973	1.28	2.63	-4.35	0.03656	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.36504	-0.9745	7	0.72032	D	0.01	.	5.3488	0.16024	0.267:0.197:0.536:0.0	rs61308377	209	Q8WVF1-4	.	H	209	ENSP00000346216:Y209H	ENSP00000346216:Y209H	Y	-	1	0	OSCP1	36666555	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-0.238000	0.08977	-1.019000	0.03358	0.460000	0.39030	TAT	A|0.891;G|0.109	0.109	strong		0.398	OSCP1-010	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000389759.1	NM_145047	
CTAGE5	4253	hgsc.bcm.edu	37	14	39764176	39764176	+	Missense_Mutation	SNP	G	G	C	rs17855896	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:39764176G>C	ENST00000280083.3	+	8	929	c.615G>C	c.(613-615)aaG>aaC	p.K205N	CTAGE5_ENST00000557038.1_Missense_Mutation_p.K125N|CTAGE5_ENST00000341502.5_Missense_Mutation_p.K205N|CTAGE5_ENST00000553352.1_Missense_Mutation_p.K176N|CTAGE5_ENST00000348007.3_Missense_Mutation_p.K205N|RP11-407N17.3_ENST00000553728.1_Missense_Mutation_p.K740N|CTAGE5_ENST00000341749.3_Missense_Mutation_p.K193N|CTAGE5_ENST00000556148.1_Missense_Mutation_p.K130N|RP11-407N17.3_ENST00000603904.1_Missense_Mutation_p.K176N|CTAGE5_ENST00000396158.2_Missense_Mutation_p.K210N|CTAGE5_ENST00000396165.4_Missense_Mutation_p.K176N			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	210	0	0		WXS	Illumina HiSeq	Phase_I	158	76	0.481013	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	
PKHD1L1	93035	hgsc.bcm.edu	37	8	110413762	110413762	+	Missense_Mutation	SNP	T	T	C	rs964307	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:110413762T>C	ENST00000378402.5	+	14	1422	c.1318T>C	c.(1318-1320)Tat>Cat	p.Y440H		NM_177531.4	NP_803875.2	Q86WI1	PKHL1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1	440			Y -> H (in dbSNP:rs964307).		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)			TGCCAACAGTTATTTTTCCAG	0.348										HNSCC(38;0.096)			T|||	1564	0.3123	0.1483	0.4741	5008	,	,		13464	0.3929		0.3111	False		,,,				2504	0.3374				p.Y440H		Atlas-SNP	.											.	PKHD1L1	522	.	0			c.T1318C						PASS	.	T	HIS/TYR	689,2957		72,545,1206	82.0	76.0	78.0		1318	5.8	1.0	8	dbSNP_86	78	2602,5554		427,1748,1903	yes	missense	PKHD1L1	NM_177531.4	83	499,2293,3109	CC,CT,TT		31.9029,18.8974,27.8851	probably-damaging	440/4244	110413762	3291,8511	1823	4078	5901	SO:0001583	missense	93035	exon14			AACAGTTATTTTT	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.1318T>C	8.37:g.110413762T>C	ENSP00000367655:p.Tyr440His	Somatic	224	0	0		WXS	Illumina HiSeq	Phase_I	178	125	0.702247	NM_177531	Q567P2|Q9UF27	Missense_Mutation	SNP	ENST00000378402.5	37	CCDS47911.1	701	0.320970695970696	78	0.15853658536585366	152	0.4198895027624309	237	0.4143356643356643	234	0.3087071240105541	T	18.78	3.697657	0.68386	0.188974	0.319029	ENSG00000205038	ENST00000378402	T	0.21031	2.03	5.75	5.75	0.90469	PA14 (1);	0.229124	0.37304	N	0.002147	T	0.00012	0.0000	M	0.63843	1.955	0.44168	P	0.003027000000000002	D	0.71674	0.998	D	0.71184	0.972	T	0.46190	-0.9209	9	0.87932	D	0	.	14.007	0.64470	0.0:0.0:0.0:1.0	rs964307;rs52818943;rs59306377;rs964307	440	Q86WI1	PKHL1_HUMAN	H	440	ENSP00000367655:Y440H	ENSP00000367655:Y440H	Y	+	1	0	PKHD1L1	110482938	1.000000	0.71417	0.977000	0.42913	0.844000	0.47949	5.614000	0.67695	2.193000	0.70182	0.477000	0.44152	TAT	T|0.687;C|0.312	0.312	strong		0.348	PKHD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381017.1	NM_177531	
C1orf35	79169	hgsc.bcm.edu	37	1	228290033	228290033	+	Missense_Mutation	SNP	T	T	C	rs61825155	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:228290033T>C	ENST00000272139.4	-	5	659	c.425A>G	c.(424-426)aAa>aGa	p.K142R	C1orf35_ENST00000472617.1_5'UTR	NM_024319.2	NP_077295.1	Q9BU76	MMTA2_HUMAN	chromosome 1 open reading frame 35	142							poly(A) RNA binding (GO:0044822)			large_intestine(1)|lung(1)|skin(1)	3		Prostate(94;0.0488)				CAGCCCCAGTTTGGCGGCCTC	0.701													T|||	28	0.00559105	0.0	0.0072	5008	,	,		11635	0.0		0.0199	False		,,,				2504	0.0031				p.K142R		Atlas-SNP	.											.	C1orf35	17	.	0			c.A425G						PASS	.	T	ARG/LYS	7,4395		0,7,2194	23.0	24.0	23.0		425	4.1	1.0	1	dbSNP_129	23	133,8465		1,131,4167	yes	missense	C1orf35	NM_024319.2	26	1,138,6361	CC,CT,TT		1.5469,0.159,1.0769	probably-damaging	142/264	228290033	140,12860	2201	4299	6500	SO:0001583	missense	79169	exon5			CCCAGTTTGGCGG	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.425A>G	1.37:g.228290033T>C	ENSP00000272139:p.Lys142Arg	Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	33	13	0.393939	NM_024319	Q6P5Y0|Q6ZTZ6|Q6ZWA6|Q8IZH3	Missense_Mutation	SNP	ENST00000272139.4	37	CCDS1566.1	20	0.009157509157509158	0	0.0	2	0.0055248618784530384	0	0.0	18	0.023746701846965697	T	25.3	4.626878	0.87560	0.00159	0.015469	ENSG00000143793	ENST00000272139	.	.	.	4.1	4.1	0.47936	.	0.050943	0.85682	D	0.000000	T	0.54532	0.1864	M	0.68593	2.085	0.58432	D	0.999997	D	0.69078	0.997	D	0.75020	0.985	T	0.61850	-0.6978	9	0.22706	T	0.39	-24.7052	11.773	0.51970	0.0:0.0:0.0:1.0	rs61825155	142	Q9BU76	MMTA2_HUMAN	R	142	.	ENSP00000272139:K142R	K	-	2	0	C1orf35	226356656	1.000000	0.71417	0.998000	0.56505	0.595000	0.36748	4.218000	0.58554	1.861000	0.53984	0.402000	0.26972	AAA	T|0.990;C|0.010	0.010	strong		0.701	C1orf35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092245.1	NM_024319	
HPS3	84343	hgsc.bcm.edu	37	3	148881673	148881673	+	Silent	SNP	C	C	T	rs3732557	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:148881673C>T	ENST00000296051.2	+	14	2666	c.2526C>T	c.(2524-2526)caC>caT	p.H842H	HPS3_ENST00000460120.1_Silent_p.H677H	NM_032383.3	NP_115759.2	Q969F9	HPS3_HUMAN	Hermansky-Pudlak syndrome 3	842					organelle organization (GO:0006996)|pigmentation (GO:0043473)	BLOC-2 complex (GO:0031084)				breast(2)|endometrium(2)|kidney(1)|large_intestine(7)|lung(12)|ovary(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)	34			LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)			CATGGGTTCACGTCGTAATAT	0.279									Hermansky-Pudlak syndrome				C|||	778	0.155351	0.0136	0.1441	5008	,	,		17878	0.2738		0.1799	False		,,,				2504	0.2076				p.H842H		Atlas-SNP	.											.	HPS3	104	.	0			c.C2526T						PASS	.	C		201,4203	120.4+/-158.0	4,193,2005	79.0	78.0	78.0		2526	-2.1	0.1	3	dbSNP_107	78	1627,6969	298.1+/-303.7	162,1303,2833	no	coding-synonymous	HPS3	NM_032383.3		166,1496,4838	TT,TC,CC		18.9274,4.564,14.0615		842/1005	148881673	1828,11172	2202	4298	6500	SO:0001819	synonymous_variant	84343	exon14	Familial Cancer Database	HPS, HPS1-8	GGTTCACGTCGTA	AY033141	CCDS3140.1	3q24	2014-06-18			ENSG00000163755	ENSG00000163755			15597	protein-coding gene	gene with protein product		606118				11455388	Standard	NM_032383		Approved	SUTAL	uc003ewu.1	Q969F9	OTTHUMG00000159548	ENST00000296051.2:c.2526C>T	3.37:g.148881673C>T		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	70	38	0.542857	NM_032383	A8K6G6|Q8WTV6|Q96AP1|Q96MR3|Q9H608	Silent	SNP	ENST00000296051.2	37	CCDS3140.1																																																																																			C|0.849;T|0.151	0.151	strong		0.279	HPS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356151.1	NM_032383	
DNM2	1785	hgsc.bcm.edu	37	19	10870486	10870486	+	Splice_Site	SNP	A	A	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:10870486A>G	ENST00000355667.6	+	2	314	c.234A>G	c.(232-234)acA>acG	p.T78T	DNM2_ENST00000585892.1_Splice_Site_p.T78T|DNM2_ENST00000408974.4_Splice_Site_p.T78T|DNM2_ENST00000314646.5_Splice_Site_p.T78T|DNM2_ENST00000389253.4_Splice_Site_p.T78T|DNM2_ENST00000359692.6_Splice_Site_p.T78T	NM_001005360.2|NM_001190716.1	NP_001005360.1|NP_001177645.1	P50570	DYN2_HUMAN	dynamin 2	78	Dynamin-type G.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell death (GO:0008219)|endocytosis (GO:0006897)|G2/M transition of mitotic cell cycle (GO:0000086)|GTP catabolic process (GO:0006184)|membrane organization (GO:0061024)|nitric oxide metabolic process (GO:0046209)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription, DNA-templated (GO:0045893)|post-Golgi vesicle-mediated transport (GO:0006892)|receptor internalization (GO:0031623)|regulation of nitric-oxide synthase activity (GO:0050999)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic vesicle transport (GO:0048489)|transferrin transport (GO:0033572)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	enzyme binding (GO:0019899)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|microtubule binding (GO:0008017)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(6)|kidney(2)|large_intestine(10)|lung(11)|ovary(2)|skin(3)|upper_aerodigestive_tract(2)	42			Epithelial(33;4.17e-05)|all cancers(31;8.48e-05)			TCTCAAAAACAGGTAAAATGG	0.587			"""F, N, Splice, Mis, O"""		ETP ALL																																p.T78T		Atlas-SNP	.		Rec	yes		19	19p13.2	1785	dynamin 2		L	.	DNM2	175	.	0			c.A234G						PASS	.						101.0	107.0	105.0					19																	10870486		2203	4300	6503	SO:0001630	splice_region_variant	1785	exon2			AAAAACAGGTAAA		CCDS32907.1, CCDS32908.1, CCDS45968.1, CCDS45969.1, CCDS59351.1	19p	2014-09-17						"""Pleckstrin homology (PH) domain containing"""	2974	protein-coding gene	gene with protein product	"""dynamin II"", ""cytoskeletal protein"""	602378				7590285, 9143510	Standard	NM_001190716		Approved	DYNII, DYN2, CMTDIB, CMTDI1, DI-CMTB	uc002mps.2	P50570		ENST00000355667.6:c.235+1A>G	19.37:g.10870486A>G		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	102	43	0.421569	NM_001005361	A8K1B6|E7EV30|E9PEQ4|K7ESI9|Q5I0Y0|Q7Z5S3|Q9UPH4	Silent	SNP	ENST00000355667.6	37	CCDS45968.1																																																																																			.	.	none		0.587	DNM2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000452592.1	NM_004945	Silent
MYO18A	399687	hgsc.bcm.edu	37	17	27442710	27442710	+	Silent	SNP	G	G	C	rs28587908	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:27442710G>C	ENST00000527372.1	-	12	2379	c.2199C>G	c.(2197-2199)ccC>ccG	p.P733P	MYO18A_ENST00000531253.1_Silent_p.P733P|MYO18A_ENST00000533112.1_Silent_p.P733P|MYO18A_ENST00000354329.4_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	104	0	0		WXS	Illumina HiSeq	Phase_I	68	36	0.529412	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	
SUN1	23353	hgsc.bcm.edu	37	7	897496	897496	+	Missense_Mutation	SNP	G	G	A	rs59910530	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:897496G>A	ENST00000405266.1	+	14	1561	c.1537G>A	c.(1537-1539)Gag>Aag	p.E513K	SUN1_ENST00000389574.3_Missense_Mutation_p.E393K|SUN1_ENST00000413514.2_Missense_Mutation_p.E274K|SUN1_ENST00000456758.2_Missense_Mutation_p.E665K|SUN1_ENST00000452783.2_Missense_Mutation_p.E373K|SUN1_ENST00000401592.1_Missense_Mutation_p.E476K|SUN1_ENST00000425407.2_Missense_Mutation_p.E393K			O94901	SUN1_HUMAN	Sad1 and UNC84 domain containing 1	503					cytoskeletal anchoring at nuclear membrane (GO:0090286)|nuclear envelope organization (GO:0006998)|nuclear matrix anchoring at nuclear membrane (GO:0090292)	acrosomal membrane (GO:0002080)|integral component of nuclear inner membrane (GO:0005639)|nuclear envelope (GO:0005635)|SUN-KASH complex (GO:0034993)				NS(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(17)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						GCCCACAGTCGAGCACCTCCA	0.562													G|||	843	0.168331	0.0772	0.2406	5008	,	,		15787	0.1359		0.1849	False		,,,				2504	0.2566				p.E476K		Atlas-SNP	.											.	SUN1	157	.	0			c.G1426A						PASS	.	G	LYS/GLU,LYS/GLU,LYS/GLU	354,3828		19,316,1756	162.0	176.0	171.0		1426,1117,1177	-10.3	0.0	7	dbSNP_129	171	1365,7061		105,1155,2953	yes	missense,missense,missense	SUN1	NM_001130965.2,NM_001171944.1,NM_025154.5	56,56,56	124,1471,4709	AA,AG,GG		16.1999,8.4648,13.6342	benign,benign,benign	476/786,373/683,393/703	897496	1719,10889	2091	4213	6304	SO:0001583	missense	23353	exon13			ACAGTCGAGCACC	AF202724	CCDS43533.1, CCDS47525.1, CCDS55078.1, CCDS55079.1, CCDS55080.1	7p22.3	2010-01-27	2010-01-27	2010-01-27	ENSG00000164828	ENSG00000164828			18587	protein-coding gene	gene with protein product	"""Sad1 unc-84 domain protein 1"""	607723	"""unc-84 homolog A (C. elegans)"""	UNC84A		11593002	Standard	NM_001130965		Approved	KIAA0810, FLJ12407	uc021zym.1	O94901	OTTHUMG00000151426	ENST00000405266.1:c.1537G>A	7.37:g.897496G>A	ENSP00000384116:p.Glu513Lys	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	88	16	0.181818	NM_001130965	A5PL20|B3KMV7|B4DZF7|B7WNY4|B7WP53|E9PDU4|E9PF23|F8WD13|Q96CZ7|Q9HA14|Q9UH98	Missense_Mutation	SNP	ENST00000405266.1	37		359|359	0.16437728937728938|0.16437728937728938	49|49	0.09959349593495935|0.09959349593495935	86|86	0.23756906077348067|0.23756906077348067	89|89	0.1555944055944056|0.1555944055944056	135|135	0.17810026385224276|0.17810026385224276	G|G	8.800|8.800	0.932697|0.932697	0.18131|0.18131	0.084648|0.084648	0.161999|0.161999	ENSG00000164828|ENSG00000164828	ENST00000456758;ENST00000389574;ENST00000452783;ENST00000405266;ENST00000401592;ENST00000297445;ENST00000425407;ENST00000429178;ENST00000413514|ENST00000433212	T;T;T;T;T;T;T;T|.	0.22336|.	2.31;2.31;2.32;2.31;2.31;2.31;1.99;1.96|.	5.15|5.15	-10.3|-10.3	0.00346|0.00346	.|.	1.071220|.	0.06979|.	N|.	0.819504|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.08118|0.08118	0|0	0.80722|0.80722	P|P	0.0|0.0	B;B;B;B;B;B|.	0.17268|.	0.002;0.002;0.003;0.021;0.003;0.005|.	B;B;B;B;B;B|.	0.09377|.	0.002;0.002;0.003;0.004;0.002;0.004|.	T|T	0.22243|0.22243	-1.0222|-1.0222	9|4	0.06236|.	T|.	0.91|.	-4.5311|-4.5311	9.0345|9.0345	0.36280|0.36280	0.2149:0.5051:0.28:0.0|0.2149:0.5051:0.28:0.0	rs59910530;rs61743533|rs59910530;rs61743533	274;373;476;665;503;393|.	E7EP45;E9PDU4;E9PF23;A4D2Q0;O94901;O94901-5|.	.;.;.;.;SUN1_HUMAN;.|.	K|Q	665;393;373;513;476;503;393;401;274|324	ENSP00000388743:E665K;ENSP00000374225:E393K;ENSP00000413439:E373K;ENSP00000384116:E513K;ENSP00000384015:E476K;ENSP00000392309:E393K;ENSP00000409909:E401K;ENSP00000389313:E274K|.	ENSP00000297445:E503K|.	E|R	+|+	1|2	0|0	SUN1|SUN1	864022|864022	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.002000|0.002000	0.02628|0.02628	-0.212000|-0.212000	0.09319|0.09319	-2.067000|-2.067000	0.00885|0.00885	-0.302000|-0.302000	0.09304|0.09304	GAG|CGA	G|0.839;A|0.161	0.161	strong		0.562	SUN1-001	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000322566.1	NM_025154	
NPSR1	387129	hgsc.bcm.edu	37	7	34917702	34917702	+	Missense_Mutation	SNP	G	G	A	rs28480169	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:34917702G>A	ENST00000359791.1	+	9	1168	c.1040G>A	c.(1039-1041)cGt>cAt	p.R347H	NPSR1_ENST00000531252.1_Missense_Mutation_p.R336H	NM_207173.1	NP_997056.1	Q6W5P4	NPSR1_HUMAN	neuropeptide S receptor 1	127						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)	ATCCGTCTCCGTCAGCTCCAG	0.517													G|||	210	0.0419329	0.0129	0.062	5008	,	,		19021	0.0069		0.0974	False		,,,				2504	0.046				p.R347H		Atlas-SNP	.											NPSR1_ENST00000359791,caecum,carcinoma,+1,1	NPSR1	134	1	0			c.G1040A						PASS	.	G	HIS/ARG	111,4295	82.4+/-120.9	1,109,2093	57.0	46.0	50.0		1040	0.5	0.0	7	dbSNP_125	50	750,7850	169.7+/-221.0	26,698,3576	yes	missense	NPSR1	NM_207173.1	29	27,807,5669	AA,AG,GG		8.7209,2.5193,6.62		347/378	34917702	861,12145	2203	4300	6503	SO:0001583	missense	387129	exon9			GTCTCCGTCAGCT	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	ENST00000359791.1:c.1040G>A	7.37:g.34917702G>A	ENSP00000352839:p.Arg347His	Somatic	216	0	0		WXS	Illumina HiSeq	Phase_I	200	42	0.21	NM_207173	A2RTZ4|Q2XP58|Q56H76|Q56H77|Q56H78|Q6JSL4|Q6JSL5|Q6JSL6|Q6JSL7|Q6JSL8|Q6W5P3|Q6ZMB8	Missense_Mutation	SNP	ENST00000359791.1	37	CCDS5443.1	115	0.052655677655677656	12	0.024390243902439025	31	0.0856353591160221	6	0.01048951048951049	66	0.0870712401055409	G	4.311	0.057075	0.08339	0.025193	0.087209	ENSG00000187258	ENST00000359791;ENST00000531252	T;T	0.74002	-0.8;-0.42	2.39	0.484	0.16825	.	.	.	.	.	T	0.02571	0.0078	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	0.09509	-1.0671	8	0.13470	T	0.59	.	7.061	0.25125	0.269:0.0:0.731:0.0	rs28480169	281;336;347	B7ZMA2;Q6W5P4-5;Q6W5P4-4	.;.;.	H	347;336	ENSP00000352839:R347H;ENSP00000433258:R336H	ENSP00000352839:R347H	R	+	2	0	NPSR1	34884227	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.107000	0.15375	-0.137000	0.11455	-1.813000	0.00610	CGT	G|0.940;A|0.060	0.060	strong		0.517	NPSR1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000216838.1	NM_207173	
KRTAP10-2	386679	hgsc.bcm.edu	37	21	45971018	45971018	+	Silent	SNP	C	C	G	rs478947	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:45971018C>G	ENST00000391621.1	-	1	370	c.324G>C	c.(322-324)gtG>gtC	p.V108V	TSPEAR_ENST00000397916.1_Intron|TSPEAR_ENST00000323084.4_Intron|KRTAP10-2_ENST00000498210.1_Intron	NM_198693.2	NP_941966.1	P60368	KR102_HUMAN	keratin associated protein 10-2	108	22 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				large_intestine(1)|lung(4)|skin(1)	6						GCACACAGCACACAGGCTTGC	0.667													G|||	1140	0.227636	0.2179	0.1585	5008	,	,		21167	0.3681		0.2048	False		,,,				2504	0.1687				p.V108V		Atlas-SNP	.											.	KRTAP10-2	21	.	0			c.G324C						PASS	.	G	,	1000,3404	717.3+/-408.7	94,812,1296	109.0	112.0	111.0		,324	-2.6	0.0	21	dbSNP_83	111	1680,6920	732.2+/-406.8	149,1382,2769	no	intron,coding-synonymous	TSPEAR,KRTAP10-2	NM_144991.2,NM_198693.2	,	243,2194,4065	GG,GC,CC		19.5349,22.7066,20.609	,	,108/256	45971018	2680,10324	2202	4300	6502	SO:0001819	synonymous_variant	386679	exon1			ACAGCACACAGGC	AJ566381	CCDS42955.1	21q22.3	2007-10-05			ENSG00000205445	ENSG00000205445		"""Keratin associated proteins"""	22967	protein-coding gene	gene with protein product				KRTAP18-2			Standard	NM_198693		Approved	KAP10.2, KAP18.2	uc002zfi.1	P60368	OTTHUMG00000057625	ENST00000391621.1:c.324G>C	21.37:g.45971018C>G		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	157	67	0.426752	NM_198693	Q70LJ5	Silent	SNP	ENST00000391621.1	37	CCDS42955.1																																																																																			C|0.759;G|0.241	0.241	strong		0.667	KRTAP10-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128027.1		
PIWIL3	440822	hgsc.bcm.edu	37	22	25144912	25144912	+	Missense_Mutation	SNP	C	C	T	rs11703684	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:25144912C>T	ENST00000332271.5	-	12	1827	c.1411G>A	c.(1411-1413)Gtt>Att	p.V471I	PIWIL3_ENST00000527701.1_Missense_Mutation_p.V362I|PIWIL3_ENST00000533313.1_Missense_Mutation_p.V362I|PIWIL3_ENST00000532537.2_5'UTR	NM_001008496.3|NM_001255975.1	NP_001008496.2|NP_001242904.1	Q7Z3Z3	PIWL3_HUMAN	piwi-like RNA-mediated gene silencing 3	471			V -> I (in dbSNP:rs11703684).		cell differentiation (GO:0030154)|gene silencing by RNA (GO:0031047)|meiotic nuclear division (GO:0007126)|multicellular organismal development (GO:0007275)|regulation of translation (GO:0006417)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)	RNA binding (GO:0003723)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(14)|lung(15)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	50						TTTTTCAAAACTCTTCCCGGG	0.358													C|||	1015	0.202676	0.1339	0.3804	5008	,	,		19030	0.1478		0.2097	False		,,,				2504	0.2188				p.V471I		Atlas-SNP	.											.	PIWIL3	115	.	0			c.G1411A						PASS	.	C	ILE/VAL	648,3758	277.2+/-273.6	54,540,1609	118.0	105.0	110.0		1411	-3.9	0.0	22	dbSNP_120	110	1837,6763	328.4+/-318.3	189,1459,2652	yes	missense	PIWIL3	NM_001008496.2	29	243,1999,4261	TT,TC,CC		21.3605,14.7072,19.1066	benign	471/883	25144912	2485,10521	2203	4300	6503	SO:0001583	missense	440822	exon12			TCAAAACTCTTCC	AB079368	CCDS33623.1	22q11.23	2013-02-15	2013-02-15		ENSG00000184571	ENSG00000184571		"""Argonaute/PIWI family"""	18443	protein-coding gene	gene with protein product		610314	"""piwi-like 3 (Drosophila)"""			12906857	Standard	NM_001008496		Approved	HIWI3	uc003abd.2	Q7Z3Z3	OTTHUMG00000150788	ENST00000332271.5:c.1411G>A	22.37:g.25144912C>T	ENSP00000330031:p.Val471Ile	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	66	23	0.348485	NM_001008496		Missense_Mutation	SNP	ENST00000332271.5	37	CCDS33623.1	443	0.20283882783882784	62	0.12601626016260162	137	0.3784530386740331	93	0.16258741258741258	151	0.19920844327176782	C	3.672	-0.067331	0.07273	0.147072	0.213605	ENSG00000184571	ENST00000332271;ENST00000533313;ENST00000527701	T;T;T	0.04156	3.69;3.69;3.69	2.29	-3.89	0.04193	Ribonuclease H-like (1);	0.471570	0.19244	N	0.119081	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	B;B;B	0.24533	0.025;0.105;0.103	B;B;B	0.27796	0.023;0.083;0.061	T	0.45585	-0.9251	9	0.21014	T	0.42	-3.9657	4.2885	0.10867	0.0:0.4058:0.1706:0.4236	rs11703684;rs52807433;rs57708618;rs11703684	362;471;471	E9PIP6;B4DYF7;Q7Z3Z3	.;.;PIWL3_HUMAN	I	471;362;362	ENSP00000330031:V471I;ENSP00000431843:V362I;ENSP00000435718:V362I	ENSP00000330031:V471I	V	-	1	0	PIWIL3	23474912	0.421000	0.25465	0.000000	0.03702	0.078000	0.17371	0.004000	0.13106	-0.807000	0.04393	0.313000	0.20887	GTT	C|0.813;T|0.187	0.187	strong		0.358	PIWIL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320084.2	NM_001008496	
FNDC3A	22862	hgsc.bcm.edu	37	13	49775997	49775997	+	Missense_Mutation	SNP	A	A	G	rs45604939	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:49775997A>G	ENST00000492622.2	+	24	3354	c.3049A>G	c.(3049-3051)Aca>Gca	p.T1017A	FNDC3A_ENST00000398316.3_Missense_Mutation_p.T961A|FNDC3A_ENST00000541916.1_Missense_Mutation_p.T1017A	NM_001079673.1	NP_001073141.1	Q9Y2H6	FND3A_HUMAN	fibronectin type III domain containing 3A	1017	Fibronectin type-III 8. {ECO:0000255|PROSITE-ProRule:PRU00316}.				fertilization (GO:0009566)|Sertoli cell development (GO:0060009)|single organismal cell-cell adhesion (GO:0016337)|spermatid development (GO:0007286)	acrosomal vesicle (GO:0001669)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|vesicle membrane (GO:0012506)	poly(A) RNA binding (GO:0044822)			endometrium(5)|kidney(3)|large_intestine(10)|lung(15)|prostate(5)|skin(2)|urinary_tract(1)	41		all_lung(13;7.44e-08)|Lung NSC(96;4.08e-06)|Breast(56;0.000111)|Prostate(109;0.00174)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|Lung SC(185;0.187)|all_neural(104;0.19)	KIRC - Kidney renal clear cell carcinoma(9;0.206)	GBM - Glioblastoma multiforme(99;2.94e-09)		TAATGAGTCAACATCCTATAA	0.368													A|||	127	0.0253594	0.0008	0.0476	5008	,	,		15155	0.0		0.0676	False		,,,				2504	0.0256				p.T1017A		Atlas-SNP	.											.	FNDC3A	93	.	0			c.A3049G						PASS	.	A	ALA/THR,ALA/THR	52,4354	50.9+/-86.3	0,52,2151	94.0	95.0	94.0		3049,2881	3.7	1.0	13	dbSNP_127	94	602,7996	158.2+/-211.7	19,564,3716	yes	missense,missense	FNDC3A	NM_001079673.1,NM_014923.3	58,58	19,616,5867	GG,GA,AA		7.0016,1.1802,5.0292	possibly-damaging,possibly-damaging	1017/1199,961/1143	49775997	654,12350	2203	4299	6502	SO:0001583	missense	22862	exon24			GAGTCAACATCCT	AB023187	CCDS9413.2, CCDS41886.1	13q14.12	2013-02-11	2005-01-20	2005-01-22	ENSG00000102531	ENSG00000102531		"""Fibronectin type III domain containing"""	20296	protein-coding gene	gene with protein product		615794	"""fibronectin type III domain containing 3"""	FNDC3			Standard	NM_001079673		Approved	bA203I16.5, KIAA0970	uc001vcm.3	Q9Y2H6	OTTHUMG00000016911	ENST00000492622.2:c.3049A>G	13.37:g.49775997A>G	ENSP00000417257:p.Thr1017Ala	Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	141	60	0.425532	NM_001079673	B4DYG1|Q5HYC9|Q5JVF8|Q5JVF9|Q6EVH3|Q6EVH4|Q6N020|Q6P9D5|Q6ZME4|Q9H1W1	Missense_Mutation	SNP	ENST00000492622.2	37	CCDS41886.1	68	0.031135531135531136	1	0.0020325203252032522	18	0.049723756906077346	0	0.0	49	0.06464379947229551	A	22.8	4.334633	0.81801	0.011802	0.070016	ENSG00000102531	ENST00000492622;ENST00000337156;ENST00000541916;ENST00000398316	T;T;T	0.61627	0.09;0.09;0.09	6.16	3.66	0.41972	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.079122	0.52532	D	0.000074	T	0.21509	0.0518	M	0.87547	2.89	0.80722	D	1	D;P	0.64830	0.994;0.597	D;P	0.68765	0.96;0.531	T	0.54794	-0.8240	10	0.48119	T	0.1	-24.27	9.0647	0.36455	0.7455:0.1304:0.0:0.1241	rs45604939	961;1017	Q9Y2H6-2;Q9Y2H6	.;FND3A_HUMAN	A	1017;953;1017;961	ENSP00000417257:T1017A;ENSP00000441831:T1017A;ENSP00000381362:T961A	ENSP00000338579:T953A	T	+	1	0	FNDC3A	48673998	1.000000	0.71417	0.998000	0.56505	0.998000	0.95712	8.904000	0.92590	0.515000	0.28320	0.528000	0.53228	ACA	A|0.954;G|0.046	0.046	strong		0.368	FNDC3A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354845.2	NM_014923	
MUC4	4585	hgsc.bcm.edu	37	3	195515340	195515340	+	Silent	SNP	G	G	A	rs79661483	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195515340G>A	ENST00000463781.3	-	2	3570	c.3111C>T	c.(3109-3111)caC>caT	p.H1037H	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Silent_p.H1037H	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	469	Repeat.				cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GAGGGGTGACGTGACCTGTGG	0.572													.|||	1003	0.20028	0.053	0.2075	5008	,	,		16071	0.37		0.2386	False		,,,				2504	0.18				p.H1037H		Atlas-SNP	.											.	MUC4	1505	.	0			c.C3111T						PASS	.						37.0	20.0	25.0					3																	195515340		692	1591	2283	SO:0001819	synonymous_variant	4585	exon2			GGTGACGTGACCT	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.3111C>T	3.37:g.195515340G>A		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	71	44	0.619718	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Silent	SNP	ENST00000463781.3	37	CCDS54700.1																																																																																			G|0.628;A|0.372	0.372	strong		0.572	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
TRAK2	66008	hgsc.bcm.edu	37	2	202264156	202264156	+	Missense_Mutation	SNP	C	C	T	rs13022344	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:202264156C>T	ENST00000332624.3	-	5	852	c.424G>A	c.(424-426)Gtc>Atc	p.V142I	TRAK2_ENST00000430254.1_Missense_Mutation_p.V142I	NM_015049.2	NP_055864.2	O60296	TRAK2_HUMAN	trafficking protein, kinesin binding 2	142	HAP1 N-terminal.		V -> I (in dbSNP:rs13022344). {ECO:0000269|PubMed:11161814, ECO:0000269|PubMed:14702039}.		protein O-linked glycosylation (GO:0006493)|protein targeting (GO:0006605)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	cytoplasm (GO:0005737)|endosome (GO:0005768)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GABA receptor binding (GO:0050811)|receptor binding (GO:0005102)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(12)|ovary(1)|skin(1)	23						TCAGATAAGACATGGTTCCGC	0.408													C|||	2701	0.539337	0.3495	0.5634	5008	,	,		20096	0.4911		0.663	False		,,,				2504	0.7014				p.V142I		Atlas-SNP	.											.	TRAK2	62	.	0			c.G424A	GRCh37	CM072094	TRAK2	M	rs13022344	PASS	.	C	ILE/VAL	1648,2758	505.9+/-366.3	303,1042,858	113.0	107.0	109.0		424	5.2	1.0	2	dbSNP_121	109	5787,2813	676.2+/-403.3	1935,1917,448	yes	missense	TRAK2	NM_015049.2	29	2238,2959,1306	TT,TC,CC		32.7093,37.4035,42.8341	benign	142/915	202264156	7435,5571	2203	4300	6503	SO:0001583	missense	66008	exon5			ATAAGACATGGTT	AB038951	CCDS2347.1	2q33.1	2012-03-05	2005-12-13	2005-12-13	ENSG00000115993	ENSG00000115993			13206	protein-coding gene	gene with protein product	"""gamma-aminobutyric acid(A) receptor-interacting factor"", ""milton homolog 2 (Drosophila)"", ""O-linked N-acetylglucosamine transferase interacting protein 98"""	607334	"""amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 3"""	ALS2CR3		11161814, 16380713, 20230862	Standard	NM_015049		Approved	CALS-C, KIAA0549, GRIF-1, OIP98, MILT2	uc002uyb.4	O60296	OTTHUMG00000132822	ENST00000332624.3:c.424G>A	2.37:g.202264156C>T	ENSP00000328875:p.Val142Ile	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	93	39	0.419355	NM_015049	E7EV21|Q8WVH7|Q96NS2|Q9C0K5|Q9C0K6	Missense_Mutation	SNP	ENST00000332624.3	37	CCDS2347.1	1148	0.5256410256410257	166	0.33739837398373984	200	0.5524861878453039	272	0.4755244755244755	510	0.6728232189973615	C	12.84	2.058989	0.36373	0.374035	0.672907	ENSG00000115993	ENST00000332624;ENST00000542292;ENST00000430254	T;T	0.18810	2.19;2.19	6.07	5.2	0.72013	.	0.333863	0.28624	N	0.014683	T	0.00012	0.0000	N	0.24115	0.695	0.09310	P	0.9999999999240134	B;B	0.10296	0.0;0.003	B;B	0.12837	0.001;0.008	T	0.33111	-0.9881	9	0.34782	T	0.22	.	6.0626	0.19846	0.0:0.6364:0.1501:0.2135	rs13022344;rs17854051;rs17854102;rs17859473;rs52798654;rs57001181;rs13022344	142;142	E7EV21;O60296	.;TRAK2_HUMAN	I	142;48;142	ENSP00000328875:V142I;ENSP00000409333:V142I	ENSP00000328875:V142I	V	-	1	0	TRAK2	201972401	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	2.282000	0.43461	1.580000	0.49851	-0.150000	0.13652	GTC	C|0.463;T|0.537	0.537	strong		0.408	TRAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256284.3	NM_015049	
PPP1R7	5510	hgsc.bcm.edu	37	2	242122130	242122130	+	Silent	SNP	A	A	G	rs113069444	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:242122130A>G	ENST00000234038.6	+	10	1449	c.975A>G	c.(973-975)acA>acG	p.T325T	PPP1R7_ENST00000272983.8_Silent_p.T282T|PPP1R7_ENST00000407025.1_Silent_p.T325T	NM_001282412.1|NM_001282413.1|NM_002712.1	NP_001269341.1|NP_001269342.1|NP_002703.1	Q15435	PP1R7_HUMAN	protein phosphatase 1, regulatory subunit 7	325					positive regulation of protein dephosphorylation (GO:0035307)|regulation of catalytic activity (GO:0050790)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	enzyme regulator activity (GO:0030234)|protein phosphatase type 1 regulator activity (GO:0008599)			cervix(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(9)|ovary(3)	23		all_cancers(19;6.1e-33)|all_epithelial(40;1.07e-13)|Breast(86;0.000141)|Renal(207;0.00528)|all_lung(227;0.0446)|Ovarian(221;0.104)|Lung NSC(271;0.115)|Esophageal squamous(248;0.131)|all_hematologic(139;0.182)|Melanoma(123;0.238)		Epithelial(32;6.92e-32)|all cancers(36;5.35e-29)|OV - Ovarian serous cystadenocarcinoma(60;3.4e-14)|Kidney(56;4.23e-09)|KIRC - Kidney renal clear cell carcinoma(57;4.24e-08)|BRCA - Breast invasive adenocarcinoma(100;3.56e-06)|Lung(119;0.000588)|LUSC - Lung squamous cell carcinoma(224;0.0048)|Colorectal(34;0.0137)|COAD - Colon adenocarcinoma(134;0.096)		GCCTGGAGACAGTGTACCTGG	0.602													A|||	3	0.000599042	0.0	0.0	5008	,	,		19210	0.0		0.003	False		,,,				2504	0.0				p.T325T	NSCLC(62;446 1299 5417 11238 27640)	Atlas-SNP	.											PPP1R7,NS,carcinoma,+2,1	PPP1R7	35	1	0			c.A975G						PASS	.	A		3,4403	6.2+/-15.9	0,3,2200	127.0	116.0	120.0		975	-10.4	0.1	2	dbSNP_132	120	26,8574	18.5+/-59.3	0,26,4274	no	coding-synonymous	PPP1R7	NM_002712.1		0,29,6474	GG,GA,AA		0.3023,0.0681,0.223		325/361	242122130	29,12977	2203	4300	6503	SO:0001819	synonymous_variant	5510	exon10			GGAGACAGTGTAC	AF067136	CCDS2546.1, CCDS63190.1, CCDS63192.1, CCDS63193.1, CCDS63194.1	2q37.3	2012-04-17	2011-10-04		ENSG00000115685	ENSG00000115685		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	9295	protein-coding gene	gene with protein product		602877	"""protein phosphatase 1, regulatory (inhibitor) subunit 7"""			7498485, 7670491, 10231361	Standard	NM_001282413		Approved	sds22	uc002wat.1	Q15435	OTTHUMG00000133390	ENST00000234038.6:c.975A>G	2.37:g.242122130A>G		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	64	26	0.40625	NM_002712	B4DFD4|B5MCY6|Q9UQE5|Q9UQE6|Q9Y6K4	Silent	SNP	ENST00000234038.6	37	CCDS2546.1	3|3	0.0013736263736263737|0.0013736263736263737	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	3|3	0.00395778364116095|0.00395778364116095	A|A	6.902|6.902	0.536047|0.536047	0.13188|0.13188	6.81E-4|6.81E-4	0.003023|0.003023	ENSG00000115685|ENSG00000115685	ENST00000450367|ENST00000415769	.|.	.|.	.|.	5.19|5.19	-10.4|-10.4	0.00318|0.00318	.|.	.|.	.|.	.|.	.|.	T|T	0.41373|0.41373	0.1156|0.1156	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.54002|0.54002	-0.8358|-0.8358	4|4	.|.	.|.	.|.	-12.923|-12.923	5.0645|5.0645	0.14574|0.14574	0.3682:0.4119:0.0765:0.1434|0.3682:0.4119:0.0765:0.1434	.|.	.|.	.|.	.|.	R|G	300|47	.|.	.|.	Q|S	+|+	2|1	0|0	PPP1R7|PPP1R7	241770803|241770803	0.000000|0.000000	0.05858|0.05858	0.124000|0.124000	0.21820|0.21820	0.701000|0.701000	0.40568|0.40568	-5.138000|-5.138000	0.00147|0.00147	-3.714000|-3.714000	0.00117|0.00117	-1.258000|-1.258000	0.01471|0.01471	CAG|AGT	A|0.997;G|0.002;T|0.000	0.002	strong		0.602	PPP1R7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257244.4	NM_002712	
OBSCN	84033	hgsc.bcm.edu	37	1	228520973	228520973	+	Missense_Mutation	SNP	C	C	G	rs369909	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:228520973C>G	ENST00000422127.1	+	58	15849	c.15805C>G	c.(15805-15807)Ctc>Gtc	p.L5269V	OBSCN_ENST00000284548.11_Missense_Mutation_p.L5269V|OBSCN_ENST00000570156.2_Missense_Mutation_p.L6226V|OBSCN_ENST00000366709.4_Missense_Mutation_p.L2388V|OBSCN_ENST00000366707.4_Missense_Mutation_p.L2903V	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	5269	Ig-like 50.		L -> V (in dbSNP:rs369909).		apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				GCTGAGAGACCTCCAGGTGGC	0.627													C|||	1678	0.335064	0.4183	0.3847	5008	,	,		17947	0.249		0.4205	False		,,,				2504	0.1881				p.L6226V		Atlas-SNP	.											.	OBSCN	2142	.	0			c.C18676G						PASS	.	C	VAL/LEU,VAL/LEU	1383,2607		266,851,878	12.0	15.0	14.0		15805,15805	2.0	1.0	1	dbSNP_80	14	3469,4833		793,1883,1475	yes	missense,missense	OBSCN	NM_001098623.1,NM_052843.2	32,32	1059,2734,2353	GG,GC,CC		41.7851,34.6617,39.4728	possibly-damaging,possibly-damaging	5269/7969,5269/6621	228520973	4852,7440	1995	4151	6146	SO:0001583	missense	84033	exon69			AGAGACCTCCAGG	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"""Rho guanine nucleotide exchange factors"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.15805C>G	1.37:g.228520973C>G	ENSP00000409493:p.Leu5269Val	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	78	36	0.461538	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	
OSBPL6	114880	hgsc.bcm.edu	37	2	179188959	179188959	+	Missense_Mutation	SNP	G	G	A	rs35032920	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:179188959G>A	ENST00000190611.4	+	4	534	c.158G>A	c.(157-159)cGg>cAg	p.R53Q	OSBPL6_ENST00000359685.3_Missense_Mutation_p.R53Q|OSBPL6_ENST00000477097.1_3'UTR|OSBPL6_ENST00000392505.2_Missense_Mutation_p.R53Q|OSBPL6_ENST00000409631.1_Missense_Mutation_p.R53Q|OSBPL6_ENST00000357080.4_Missense_Mutation_p.R53Q|OSBPL6_ENST00000315022.2_Missense_Mutation_p.R32Q|OSBPL6_ENST00000409045.3_Missense_Mutation_p.R53Q	NM_032523.3	NP_115912.1	Q9BZF3	OSBL6_HUMAN	oxysterol binding protein-like 6	53			R -> Q (in dbSNP:rs35032920).		lipid transport (GO:0006869)	cytosol (GO:0005829)|nuclear membrane (GO:0031965)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)	lipid binding (GO:0008289)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(13)|lung(18)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	46			OV - Ovarian serous cystadenocarcinoma(117;0.00578)|Epithelial(96;0.00847)|all cancers(119;0.0335)			TCTGTAAGTCGGCAATTGCTA	0.498													G|||	319	0.0636981	0.0303	0.0519	5008	,	,		18960	0.0278		0.0557	False		,,,				2504	0.1626				p.R53Q		Atlas-SNP	.											.	OSBPL6	178	.	0			c.G158A						PASS	.	G	GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG	138,4268		1,136,2066	76.0	65.0	69.0		158,158,158,158,95	6.0	1.0	2	dbSNP_126	69	367,8233		7,353,3940	yes	missense,missense,missense,missense,missense	OSBPL6	NM_001201480.1,NM_001201481.1,NM_001201482.1,NM_032523.3,NM_145739.2	43,43,43,43,43	8,489,6006	AA,AG,GG		4.2674,3.1321,3.8828	benign,benign,benign,benign,benign	53/960,53/904,53/899,53/935,32/939	179188959	505,12501	2203	4300	6503	SO:0001583	missense	114880	exon4			TAAGTCGGCAATT	AF392448	CCDS2277.1, CCDS2278.1, CCDS56150.1, CCDS56151.1, CCDS56152.1	2q32.1	2008-05-27			ENSG00000079156	ENSG00000079156		"""Oxysterol binding proteins"""	16388	protein-coding gene	gene with protein product	"""OSBP-related protein 6"""	606734				11483621	Standard	NM_001201480		Approved	ORP6	uc002uly.3	Q9BZF3	OTTHUMG00000132579	ENST00000190611.4:c.158G>A	2.37:g.179188959G>A	ENSP00000190611:p.Arg53Gln	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	48	26	0.541667	NM_001201482	B4DTW1|C4AMC0|C4AME4|D3DPF6|D3DPF7|Q4ZG68|Q53T68|Q59H61|Q7Z4Q1|Q86V84|Q8N9T0|Q96SR1	Missense_Mutation	SNP	ENST00000190611.4	37	CCDS2277.1	88	0.040293040293040296	15	0.03048780487804878	22	0.06077348066298342	15	0.026223776223776224	36	0.047493403693931395	G	18.10	3.547563	0.65311	0.031321	0.042674	ENSG00000079156	ENST00000392505;ENST00000359685;ENST00000357080;ENST00000409045;ENST00000190611;ENST00000409631;ENST00000315022	T;T;T;T;T;T;T	0.42131	0.98;0.98;0.98;0.98;0.98;0.98;0.98	5.96	5.96	0.96718	.	0.646123	0.16436	N	0.214505	T	0.02083	0.0065	N	0.08118	0	0.35902	D	0.830474	B;B;B;B;B;P	0.35155	0.104;0.379;0.072;0.379;0.098;0.487	B;B;B;B;B;B	0.27262	0.014;0.078;0.026;0.048;0.007;0.042	T	0.13388	-1.0511	10	0.28530	T	0.3	-17.2325	9.2797	0.37720	0.1189:0.0:0.8811:0.0	rs35032920	53;32;53;53;53;53	Q9BZF3-4;Q9BZF3-3;Q9BZF3-2;Q9BZF3-5;Q9BZF3;Q86V84	.;.;.;.;OSBL6_HUMAN;.	Q	53;53;53;53;53;53;32	ENSP00000376293:R53Q;ENSP00000352713:R53Q;ENSP00000349591:R53Q;ENSP00000387248:R53Q;ENSP00000190611:R53Q;ENSP00000386885:R53Q;ENSP00000318723:R32Q	ENSP00000190611:R53Q	R	+	2	0	OSBPL6	178897205	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	4.069000	0.57541	2.832000	0.97577	0.655000	0.94253	CGG	G|0.960;A|0.040	0.040	strong		0.498	OSBPL6-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000334393.2	NM_032523	
OR9Q2	219957	hgsc.bcm.edu	37	11	57958497	57958497	+	Missense_Mutation	SNP	T	T	C	rs34337292	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:57958497T>C	ENST00000311591.3	+	1	592	c.535T>C	c.(535-537)Tgt>Cgt	p.C179R		NM_001005283.2	NP_001005283.1	Q8NGE9	OR9Q2_HUMAN	olfactory receptor, family 9, subfamily Q, member 2	179			C -> R (in dbSNP:rs34337292).			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(2)|endometrium(1)|large_intestine(3)|lung(24)|ovary(3)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	41		Breast(21;0.0589)				CTTCATTTTCTGTGACCTCCC	0.458													T|||	1021	0.203874	0.2806	0.2939	5008	,	,		22568	0.0734		0.2406	False		,,,				2504	0.1329				p.C179R		Atlas-SNP	.											OR9Q2,NS,carcinoma,-1,1	OR9Q2	78	1	0			c.T535C						PASS	.	T	ARG/CYS	1245,3157	429.5+/-342.2	178,889,1134	112.0	108.0	109.0		535	5.1	1.0	11	dbSNP_126	109	2252,6340	380.7+/-339.8	303,1646,2347	yes	missense	OR9Q2	NM_001005283.2	180	481,2535,3481	CC,CT,TT		26.2104,28.2826,26.9124	probably-damaging	179/315	57958497	3497,9497	2201	4296	6497	SO:0001583	missense	219957	exon1			ATTTTCTGTGACC	AB065859	CCDS31544.1	11q12.1	2012-08-09		2004-03-10	ENSG00000186513	ENSG00000186513		"""GPCR / Class A : Olfactory receptors"""	15328	protein-coding gene	gene with protein product				OR9Q2P			Standard	NM_001005283		Approved		uc010rka.2	Q8NGE9	OTTHUMG00000167414	ENST00000311591.3:c.535T>C	11.37:g.57958497T>C	ENSP00000308714:p.Cys179Arg	Somatic	359	0	0		WXS	Illumina HiSeq	Phase_I	284	212	0.746479	NM_001005283		Missense_Mutation	SNP	ENST00000311591.3	37	CCDS31544.1	480	0.21978021978021978	139	0.28252032520325204	106	0.292817679558011	53	0.09265734265734266	182	0.24010554089709762	T	19.00	3.741288	0.69304	0.282826	0.262104	ENSG00000186513	ENST00000311591	T	0.62498	0.02	5.08	5.08	0.68730	GPCR, rhodopsin-like superfamily (1);	0.000000	0.52532	D	0.000074	T	0.00039	0.0001	H	0.97611	4.04	0.09310	P	0.99999999660194	D	0.63880	0.993	D	0.65573	0.936	T	0.01393	-1.1366	9	0.87932	D	0	-13.7757	14.4675	0.67494	0.0:0.0:0.0:1.0	rs34337292	179	Q8NGE9	OR9Q2_HUMAN	R	179	ENSP00000308714:C179R	ENSP00000308714:C179R	C	+	1	0	OR9Q2	57715073	1.000000	0.71417	1.000000	0.80357	0.859000	0.49053	4.986000	0.63851	2.264000	0.75181	0.533000	0.62120	TGT	T|0.754;C|0.246	0.246	strong		0.458	OR9Q2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394540.1	NM_001005283	
MEGF6	1953	hgsc.bcm.edu	37	1	3428608	3428608	+	Missense_Mutation	SNP	G	G	A	rs11585362	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:3428608G>A	ENST00000356575.4	-	8	1164	c.938C>T	c.(937-939)gCg>gTg	p.A313V	MEGF6_ENST00000294599.4_Missense_Mutation_p.A208V	NM_001409.3	NP_001400.3	O75095	MEGF6_HUMAN	multiple EGF-like-domains 6	313	EGF-like 5; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.		A -> V (in dbSNP:rs11585362).			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)		CTCATAGCCCGCGTGACACAC	0.672													G|||	1278	0.255192	0.3411	0.1945	5008	,	,		18825	0.4048		0.1501	False		,,,				2504	0.136				p.A313V	Ovarian(73;978 3658)	Atlas-SNP	.											.	MEGF6	91	.	0			c.C938T						PASS	.	G	VAL/ALA	1293,2947		193,907,1020	49.0	59.0	56.0		938	3.7	0.0	1	dbSNP_120	56	1229,7197		94,1041,3078	yes	missense	MEGF6	NM_001409.3	64	287,1948,4098	AA,AG,GG		14.5858,30.4953,19.9116	possibly-damaging	313/1542	3428608	2522,10144	2120	4213	6333	SO:0001583	missense	1953	exon8			TAGCCCGCGTGAC	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.938C>T	1.37:g.3428608G>A	ENSP00000348982:p.Ala313Val	Somatic	307	0	0		WXS	Illumina HiSeq	Phase_I	179	122	0.681564	NM_001409	Q4AC86|Q5VV39	Missense_Mutation	SNP	ENST00000356575.4	37	CCDS41237.1	601	0.2751831501831502	179	0.3638211382113821	85	0.23480662983425415	233	0.40734265734265734	104	0.13720316622691292	G	10.15	1.271169	0.23221	0.304953	0.145858	ENSG00000162591	ENST00000294599;ENST00000356575	D;D	0.92299	-3.01;-3.01	4.63	3.71	0.42584	EGF-like region, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	0.130150	0.51477	D	0.000097	T	0.00012	0.0000	L	0.41710	1.295	0.80722	P	0.0	P;P	0.52061	0.95;0.893	B;B	0.41571	0.36;0.3	T	0.02901	-1.1096	9	0.28530	T	0.3	-5.9456	8.4155	0.32668	0.0833:0.0:0.7611:0.1556	rs11585362;rs60818858;rs11585362	313;208	O75095;O75095-2	MEGF6_HUMAN;.	V	208;313	ENSP00000294599:A208V;ENSP00000348982:A313V	ENSP00000294599:A208V	A	-	2	0	MEGF6	3418468	0.969000	0.33509	0.015000	0.15790	0.038000	0.13279	5.545000	0.67237	0.909000	0.36697	-0.448000	0.05591	GCG	G|0.738;A|0.262	0.262	strong		0.672	MEGF6-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354866.1	NM_001409	
MTERF4	130916	hgsc.bcm.edu	37	2	242039198	242039198	+	Missense_Mutation	SNP	T	T	C	rs3796093	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:242039198T>C	ENST00000391980.2	-	2	191	c.133A>G	c.(133-135)Aca>Gca	p.T45A	MTERFD2_ENST00000495694.1_Missense_Mutation_p.T45A|MTERFD2_ENST00000464344.2_Intron|MTERFD2_ENST00000407095.3_Missense_Mutation_p.T45A|MTERFD2_ENST00000406593.1_Intron	NM_182501.3	NP_872307.2	Q7Z6M4	MTEF4_HUMAN		45			T -> A (in dbSNP:rs3796093).		rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|mitochondrial large ribosomal subunit (GO:0005762)|mitochondrion (GO:0005739)	rRNA binding (GO:0019843)			endometrium(3)|large_intestine(6)|lung(5)|ovary(1)|skin(2)|urinary_tract(3)	20		all_cancers(19;4.67e-31)|all_epithelial(40;8.67e-13)|Breast(86;0.000141)|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;2.47e-32)|all cancers(36;1.79e-29)|OV - Ovarian serous cystadenocarcinoma(60;2.59e-14)|Kidney(56;3.21e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;2.81e-06)|Lung(119;0.000509)|LUSC - Lung squamous cell carcinoma(224;0.00442)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0886)		TTGGAGGCTGTAGTCAGTTTG	0.517													T|||	471	0.0940495	0.1369	0.0951	5008	,	,		20220	0.124		0.0626	False		,,,				2504	0.0368				p.T45A		Atlas-SNP	.											.	MTERFD2	33	.	0			c.A133G						PASS	.	T	ALA/THR	625,3781	271.6+/-270.3	51,523,1629	69.0	69.0	69.0		133	0.6	0.0	2	dbSNP_107	69	585,8015	156.4+/-210.3	21,543,3736	yes	missense	MTERFD2	NM_182501.3	58	72,1066,5365	CC,CT,TT		6.8023,14.1852,9.3034	benign	45/382	242039198	1210,11796	2203	4300	6503	SO:0001583	missense	130916	exon2			AGGCTGTAGTCAG																												ENST00000391980.2:c.133A>G	2.37:g.242039198T>C	ENSP00000375840:p.Thr45Ala	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	94	49	0.521277	NM_182501	A8K6K0|Q9P0E0	Missense_Mutation	SNP	ENST00000391980.2	37	CCDS2544.1	227	0.10393772893772894	75	0.1524390243902439	35	0.09668508287292818	70	0.12237762237762238	47	0.06200527704485488	T	20.3	3.965965	0.74131	0.141852	0.068023	ENSG00000122085	ENST00000495694;ENST00000401626;ENST00000391980;ENST00000424798;ENST00000407095;ENST00000434791	T;T;T;T;T;T	0.60797	0.16;0.21;1.94;0.91;0.93;0.32	4.57	0.636	0.17729	.	0.480627	0.17001	N	0.190890	T	0.00241	0.0007	L	0.36672	1.1	0.80722	P	0.0	B;B	0.21452	0.036;0.056	B;B	0.15870	0.012;0.014	T	0.03483	-1.1032	9	0.46703	T	0.11	-22.0028	4.1038	0.10026	0.0:0.2002:0.1768:0.623	rs3796093;rs52805218;rs60253284;rs3796093	45;45	B4DKD5;Q7Z6M4	.;MTER2_HUMAN	A	45;45;45;38;45;24	ENSP00000419315:T45A;ENSP00000385183:T45A;ENSP00000375840:T45A;ENSP00000409023:T38A;ENSP00000385630:T45A;ENSP00000393063:T24A	ENSP00000241527:T45A	T	-	1	0	MTERFD2	241687871	0.001000	0.12720	0.002000	0.10522	0.721000	0.41392	0.055000	0.14229	0.142000	0.18901	0.482000	0.46254	ACA	T|0.899;C|0.101	0.101	strong		0.517	MTERFD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323798.4		
MUC4	4585	hgsc.bcm.edu	37	3	195506983	195506983	+	Missense_Mutation	SNP	G	G	A	rs541438739	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195506983G>A	ENST00000463781.3	-	2	11927	c.11468C>T	c.(11467-11469)aCc>aTc	p.T3823I	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.T3823I	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.T3823I(1)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		AGGAAGAGGGGTGGTGTCACC	0.587													.|||	248	0.0495208	0.1399	0.0317	5008	,	,		9423	0.002		0.0358	False		,,,				2504	0.0031				p.T3823I		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,+1,2	MUC4	1505	2	1	Substitution - Missense(1)	kidney(1)	c.C11468T						scavenged	.						5.0	5.0	5.0					3																	195506983		440	1246	1686	SO:0001583	missense	4585	exon2			AGAGGGGTGGTGT	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.11468C>T	3.37:g.195506983G>A	ENSP00000417498:p.Thr3823Ile	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	51	9	0.176471	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	
RFX6	222546	hgsc.bcm.edu	37	6	117244374	117244374	+	Silent	SNP	T	T	C	rs7770158	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:117244374T>C	ENST00000332958.2	+	14	1558	c.1542T>C	c.(1540-1542)aaT>aaC	p.N514N		NM_173560.3	NP_775831.2	Q8HWS3	RFX6_HUMAN	regulatory factor X, 6	514					endocrine pancreas development (GO:0031018)|glucose homeostasis (GO:0042593)|pancreatic A cell differentiation (GO:0003310)|pancreatic D cell differentiation (GO:0003311)|pancreatic epsilon cell differentiation (GO:0090104)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of insulin secretion (GO:0050796)|transcription, DNA-templated (GO:0006351)|type B pancreatic cell differentiation (GO:0003309)	nucleus (GO:0005634)	transcription regulatory region DNA binding (GO:0044212)			cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(29)|ovary(1)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	59						CCTTGAACAATGCATCCAGTT	0.338													T|||	1702	0.339856	0.2927	0.2896	5008	,	,		20919	0.4236		0.2286	False		,,,				2504	0.4673				p.N514N		Atlas-SNP	.											.	RFX6	141	.	0			c.T1542C						PASS	.	T		1232,3174	424.2+/-340.4	180,872,1151	148.0	136.0	140.0		1542	0.7	1.0	6	dbSNP_116	140	1528,7072	288.1+/-298.6	143,1242,2915	no	coding-synonymous	RFX6	NM_173560.3		323,2114,4066	CC,CT,TT		17.7674,27.9619,21.221		514/929	117244374	2760,10246	2203	4300	6503	SO:0001819	synonymous_variant	222546	exon14			GAACAATGCATCC	BC039248	CCDS5113.1	6q22.31	2008-08-04	2008-08-04	2008-08-04	ENSG00000185002	ENSG00000185002			21478	protein-coding gene	gene with protein product		612659	"""regulatory factor X domain containing 1"""	RFXDC1			Standard	NM_173560		Approved	MGC33442, dJ955L16.1	uc003pxm.3	Q8HWS3	OTTHUMG00000015449	ENST00000332958.2:c.1542T>C	6.37:g.117244374T>C		Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	166	79	0.475904	NM_173560	Q5T6B3	Silent	SNP	ENST00000332958.2	37	CCDS5113.1																																																																																			T|0.747;C|0.253	0.253	strong		0.338	RFX6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041970.2	NM_173560	
ODF2L	57489	hgsc.bcm.edu	37	1	86820267	86820267	+	Silent	SNP	C	C	T	rs1182098	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:86820267C>T	ENST00000359242.3	-	16	1994	c.1713G>A	c.(1711-1713)gaG>gaA	p.E571E	ODF2L_ENST00000524695.1_5'Flank|ODF2L_ENST00000370566.3_Silent_p.E489E|ODF2L_ENST00000394731.1_Silent_p.E411E|ODF2L_ENST00000294678.2_Silent_p.E555E|ODF2L_ENST00000370567.1_Silent_p.E542E|ODF2L_ENST00000317336.7_Silent_p.E571E	NM_001007022.2	NP_001007023.2	Q9ULJ1	ODF2L_HUMAN	outer dense fiber of sperm tails 2-like	571						centrosome (GO:0005813)				endometrium(2)|kidney(2)|large_intestine(10)|lung(6)|ovary(1)|pancreas(1)|skin(1)|stomach(1)	24				all cancers(265;0.0313)|Epithelial(280;0.0611)		ATGCTGTATACTCTGCAGATT	0.373													c|||	3779	0.754593	0.7821	0.67	5008	,	,		17940	0.8284		0.6551	False		,,,				2504	0.8037				p.E571E		Atlas-SNP	.											.	ODF2L	53	.	0			c.G1713A						PASS	.	C	,,,	3413,993	729.3+/-410.0	1332,749,122	141.0	142.0	142.0		1713,1554,1467,1665	-0.4	1.0	1	dbSNP_87	142	5662,2938	668.2+/-402.5	1850,1962,488	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ODF2L	NM_001007022.2,NM_001184765.1,NM_001184766.1,NM_020729.2	,,,	3182,2711,610	TT,TC,CC		34.1628,22.5374,30.2245	,,,	571/637,518/621,489/592,555/621	86820267	9075,3931	2203	4300	6503	SO:0001819	synonymous_variant	57489	exon16			TGTATACTCTGCA		CCDS30763.1, CCDS41354.1, CCDS30763.2, CCDS41354.2, CCDS53339.1	1p22.3	2008-02-05			ENSG00000122417	ENSG00000122417			29225	protein-coding gene	gene with protein product						10574462	Standard	NM_020729		Approved	KIAA1229	uc001dll.2	Q9ULJ1	OTTHUMG00000010080	ENST00000359242.3:c.1713G>A	1.37:g.86820267C>T		Somatic	204	0	0		WXS	Illumina HiSeq	Phase_I	178	86	0.483146	NM_001007022	A8MU56|B4E037|Q05C40|Q5BJG5|Q5TBX3|Q5TBX4|Q86X31	Silent	SNP	ENST00000359242.3	37	CCDS41354.2	1620	0.7417582417582418	394	0.8008130081300813	242	0.6685082872928176	490	0.8566433566433567	494	0.6517150395778364	c	7.819	0.717354	0.15372	0.774626	0.658372	ENSG00000122417	ENST00000459999	.	.	.	6.03	-0.431	0.12295	.	.	.	.	.	T	0.34716	0.0907	.	.	.	0.09310	P	0.999999999996032	.	.	.	.	.	.	T	0.24870	-1.0148	3	.	.	.	-17.7708	11.9193	0.52783	0.0:0.3744:0.0:0.6256	rs1182098;rs17359498;rs1182098	.	.	.	N	338	.	.	S	-	2	0	ODF2L	86592855	0.631000	0.27164	0.956000	0.39512	0.965000	0.64279	-0.014000	0.12656	-0.062000	0.13088	-0.285000	0.09966	AGT	C|0.282;T|0.718	0.718	strong		0.373	ODF2L-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000027873.2		
GRAMD3	65983	hgsc.bcm.edu	37	5	125802027	125802027	+	Intron	SNP	G	G	A	rs62394179	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:125802027G>A	ENST00000285689.3	+	2	664				GRAMD3_ENST00000514932.1_Intron|GRAMD3_ENST00000513040.1_Intron|RP11-517I3.1_ENST00000515808.1_RNA|GRAMD3_ENST00000515200.1_Splice_Site_p.R82K|GRAMD3_ENST00000542322.1_Splice_Site_p.E76K|GRAMD3_ENST00000543198.1_Splice_Site_p.R82K|GRAMD3_ENST00000502348.1_Intron|RP11-517I3.1_ENST00000512779.1_RNA|GRAMD3_ENST00000511134.1_Intron|GRAMD3_ENST00000544396.1_Intron	NM_023927.2	NP_076416.2	Q96HH9	GRAM3_HUMAN	GRAM domain containing 3							cytoplasmic microtubule (GO:0005881)				breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	11		Prostate(80;0.0928)	KIRC - Kidney renal clear cell carcinoma(527;0.0584)|Kidney(363;0.0934)	Epithelial(69;0.0401)|OV - Ovarian serous cystadenocarcinoma(64;0.0604)|all cancers(49;0.108)		TCAGGACCAAGAGTAAGTCTT	0.408													G|||	932	0.186102	0.2436	0.1772	5008	,	,		19851	0.1399		0.2664	False		,,,				2504	0.0798				p.E76K		Atlas-SNP	.											.	GRAMD3	30	.	0			c.G226A						PASS	.	G	,,LYS/GLU,,	334,1050		37,260,395	222.0	168.0	185.0		,,226,,	2.5	0.0	5	dbSNP_129	185	819,2363		93,633,865	yes	intron,intron,missense-near-splice,intron,intron	GRAMD3	NM_001146319.1,NM_001146320.1,NM_001146321.1,NM_001146322.1,NM_023927.2	,,56,,	130,893,1260	AA,AG,GG		25.7385,24.1329,25.2519	,,,,	,,76/441,,	125802027	1153,3413	692	1591	2283	SO:0001627	intron_variant	65983	exon3			GACCAAGAGTAAG	BC008590	CCDS4136.1, CCDS54891.1, CCDS54892.1, CCDS54893.1, CCDS54894.1	5q23.2	2014-02-12	2005-11-03		ENSG00000155324	ENSG00000155324			24911	protein-coding gene	gene with protein product	"""HCV NS3 transactivated protein 2"""					12477932	Standard	NM_023927		Approved	NS3TP2, FLJ21313	uc011cwt.2	Q96HH9	OTTHUMG00000128943	ENST00000285689.3:c.203+790G>A	5.37:g.125802027G>A		Somatic	237	0	0		WXS	Illumina HiSeq	Phase_I	180	87	0.483333	NM_001146321	B7Z1F2|B7Z3R1|B7Z6D8|B7Z8T2|D3DSZ3|Q9H753	Missense_Mutation	SNP	ENST00000285689.3	37	CCDS4136.1	462|462	0.21153846153846154|0.21153846153846154	107|107	0.21747967479674796|0.21747967479674796	81|81	0.22375690607734808|0.22375690607734808	83|83	0.1451048951048951|0.1451048951048951	191|191	0.2519788918205805|0.2519788918205805	G|G	3.980|3.980	-0.006697|-0.006697	0.07773|0.07773	0.241329|0.241329	0.257385|0.257385	ENSG00000155324|ENSG00000155324	ENST00000542322|ENST00000515200;ENST00000543198	T|T;T	0.32272|0.28454	1.46|1.61;1.61	3.42|3.42	2.54|2.54	0.30619|0.30619	.|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.58432|0.58432	P|P	1.999999999946489E-6|1.999999999946489E-6	B|.	0.16166|.	0.016|.	B|.	0.10450|.	0.005|.	T|T	0.36456|0.36456	-0.9747|-0.9747	6|5	.|0.07482	.|T	.|0.82	.|.	6.5573|6.5573	0.22468|0.22468	0.1315:0.0:0.8685:0.0|0.1315:0.0:0.8685:0.0	rs62394179|rs62394179	76|.	B7Z3R1|.	.|.	K|K	76|82	ENSP00000441876:E76K|ENSP00000426143:R82K;ENSP00000442902:R82K	.|ENSP00000421494:R82K	E|R	+|+	1|2	0|0	GRAMD3|GRAMD3	125829926|125829926	0.224000|0.224000	0.23674|0.23674	0.006000|0.006000	0.13384|0.13384	0.588000|0.588000	0.36517|0.36517	0.739000|0.739000	0.26173|0.26173	1.027000|1.027000	0.39758|0.39758	0.609000|0.609000	0.83330|0.83330	GAG|AGA	G|0.787;A|0.213	0.213	strong		0.408	GRAMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250922.2	NM_023927	
PINK1	65018	hgsc.bcm.edu	37	1	20960230	20960230	+	Silent	SNP	C	C	T	rs45540544|rs45630563|rs45530340	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:20960230C>T	ENST00000321556.4	+	1	283	c.189C>T	c.(187-189)ctC>ctT	p.L63L		NM_032409.2	NP_115785.1	Q9BXM7	PINK1_HUMAN	PTEN induced putative kinase 1	63					activation of protein kinase B activity (GO:0032148)|cell death (GO:0008219)|cellular response to hypoxia (GO:0071456)|cellular response to toxic substance (GO:0097237)|intracellular signal transduction (GO:0035556)|mitochondrion degradation (GO:0000422)|mitochondrion organization (GO:0007005)|negative regulation of gene expression (GO:0010629)|negative regulation of hydrogen peroxide-induced neuron intrinsic apoptotic signaling pathway (GO:1903384)|negative regulation of JNK cascade (GO:0046329)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of oxidative stress-induced cell death (GO:1903202)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|negative regulation of oxidative stress-induced neuron death (GO:1903204)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|peptidyl-serine autophosphorylation (GO:0036289)|peptidyl-serine phosphorylation (GO:0018105)|phosphorylation (GO:0016310)|positive regulation of dopamine secretion (GO:0033603)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of mitochondrial electron transport, NADH to ubiquinone (GO:1902958)|positive regulation of peptidase activity (GO:0010952)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of synaptic transmission, dopaminergic (GO:0032226)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of mitochondrion degradation (GO:1903146)|regulation of protein complex assembly (GO:0043254)|regulation of protein ubiquitination (GO:0031396)|regulation of reactive oxygen species metabolic process (GO:2000377)|regulation of synaptic vesicle transport (GO:1902803)|response to oxidative stress (GO:0006979)|response to stress (GO:0006950)|TORC2 signaling (GO:0038203)|ubiquitin-dependent protein catabolic process (GO:0006511)	astrocyte projection (GO:0097449)|axon (GO:0030424)|cell body (GO:0044297)|chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|integral component of mitochondrial outer membrane (GO:0031307)|Lewy body (GO:0097413)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	ATP binding (GO:0005524)|C3HC4-type RING finger domain binding (GO:0055131)|calcium-dependent protein kinase activity (GO:0010857)|kinase activity (GO:0016301)|magnesium ion binding (GO:0000287)|peptidase activator activity (GO:0016504)|protease binding (GO:0002020)|protein kinase B binding (GO:0043422)|protein serine/threonine kinase activity (GO:0004674)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(4)|ovary(2)	14		all_lung(284;2.72e-05)|Lung NSC(340;2.94e-05)|Colorectal(325;3.46e-05)|Renal(390;0.000147)|Breast(348;0.00179)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|COAD - Colon adenocarcinoma(152;1.21e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000146)|Kidney(64;0.000182)|GBM - Glioblastoma multiforme(114;0.000497)|KIRC - Kidney renal clear cell carcinoma(64;0.00269)|STAD - Stomach adenocarcinoma(196;0.00308)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)		GGCTCGGGCTCCCTAACCGTC	0.791													C|||	644	0.128594	0.053	0.1571	5008	,	,		6081	0.127		0.1938	False		,,,				2504	0.1452				p.L63L	Esophageal Squamous(145;853 1803 8146 34412 35011)	Atlas-SNP	.											.	PINK1	37	.	0			c.C189T						PASS	.	C		165,3267		4,157,1555	3.0	4.0	3.0		189	0.4	0.9	1	dbSNP_127	3	1114,5976		93,928,2524	no	coding-synonymous	PINK1	NM_032409.2		97,1085,4079	TT,TC,CC		15.7123,4.8077,12.1555		63/582	20960230	1279,9243	1716	3545	5261	SO:0001819	synonymous_variant	65018	exon1			CGGGCTCCCTAAC	AB053323	CCDS211.1	1p36.12	2011-07-21			ENSG00000158828	ENSG00000158828		"""Parkinson disease"""	14581	protein-coding gene	gene with protein product		608309	"""Parkinson disease (autosomal recessive) 6"""	PARK6		11494141, 15349860	Standard	NM_032409		Approved		uc001bdm.3	Q9BXM7	OTTHUMG00000002841	ENST00000321556.4:c.189C>T	1.37:g.20960230C>T		Somatic	3	0	0		WXS	Illumina HiSeq	Phase_I	4	4	1	NM_032409	Q8N6T9|Q8NBU3|Q96DE4	Silent	SNP	ENST00000321556.4	37	CCDS211.1																																																																																			C|0.869;T|0.131	0.131	strong		0.791	PINK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007954.1	NM_032409	
CD300LG	146894	hgsc.bcm.edu	37	17	41931375	41931375	+	Missense_Mutation	SNP	A	A	G	rs12453522	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:41931375A>G	ENST00000317310.4	+	4	723	c.682A>G	c.(682-684)Acc>Gcc	p.T228A	CD300LG_ENST00000539718.1_Missense_Mutation_p.T228A|CD300LG_ENST00000586233.1_Missense_Mutation_p.T143A|CD300LG_ENST00000377203.4_Missense_Mutation_p.T194A|CD300LG_ENST00000293396.8_Missense_Mutation_p.T143A	NM_145273.3	NP_660316.2	Q6UXG3	CLM9_HUMAN	CD300 molecule-like family member g	228			T -> A (in dbSNP:rs12453522). {ECO:0000269|PubMed:14702039}.		immune system process (GO:0002376)|immunoglobulin transcytosis in epithelial cells (GO:0002414)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(2)|lung(5)|skin(4)	19		Breast(137;0.0199)		BRCA - Breast invasive adenocarcinoma(366;0.115)		AGCAGAGGACACCAGTCCAGC	0.592													a|||	1153	0.230232	0.5688	0.1383	5008	,	,		19761	0.001		0.1988	False		,,,				2504	0.1063				p.T228A		Atlas-SNP	.											.	CD300LG	46	.	0			c.A682G						PASS	.	G	ALA/THR,ALA/THR,ALA/THR,ALA/THR	2214,2192	578.2+/-384.6	552,1110,541	50.0	43.0	45.0		682,580,427,682	-3.0	0.0	17	dbSNP_120	45	1554,7046	286.5+/-297.7	148,1258,2894	yes	missense,missense,missense,missense	CD300LG	NM_001168322.1,NM_001168323.1,NM_001168324.1,NM_145273.3	58,58,58,58	700,2368,3435	GG,GA,AA		18.0698,49.7503,28.9712	benign,benign,benign,benign	228/308,194/274,143/234,228/333	41931375	3768,9238	2203	4300	6503	SO:0001583	missense	146894	exon4			GAGGACACCAGTC	BC025395	CCDS11470.1, CCDS54131.1, CCDS54132.1, CCDS54133.1	17q21.31	2013-01-11	2006-03-29					"""Immunoglobulin superfamily / V-set domain containing"""	30455	protein-coding gene	gene with protein product	"""nepmucin"""	610520	"""CD300 antigen like family member G"""			16876123, 16754720	Standard	NM_001168322		Approved	Trem4, CLM9	uc002iem.3	Q6UXG3		ENST00000317310.4:c.682A>G	17.37:g.41931375A>G	ENSP00000321005:p.Thr228Ala	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	73	49	0.671233	NM_145273	B4DNY5|F5H7P9|F8W9M3|Q8IX38|Q8IX39|Q8TA95	Missense_Mutation	SNP	ENST00000317310.4	37	CCDS11470.1	481	0.22023809523809523	271	0.5508130081300813	65	0.17955801104972377	1	0.0017482517482517483	144	0.18997361477572558	a	4.255	0.046346	0.08243	0.502497	0.180698	ENSG00000161649	ENST00000317310;ENST00000539718;ENST00000377203;ENST00000293396	T;T;T;T	0.06294	3.33;3.32;3.71;3.52	3.8	-2.95	0.05564	.	0.818608	0.10590	N	0.656836	T	0.00012	0.0000	N	0.16903	0.455	0.80722	P	0.0	B;B;B;B;B	0.06786	0.001;0.0;0.001;0.0;0.0	B;B;B;B;B	0.06405	0.002;0.001;0.001;0.0;0.001	T	0.38243	-0.9670	9	0.25751	T	0.34	-20.7088	1.9333	0.03331	0.5251:0.1282:0.2129:0.1338	rs12453522;rs56909914;rs12453522	194;143;228;228;143	F8W9M3;Q6UXG3-3;F5H7P9;Q6UXG3;Q6UXG3-2	.;.;.;CLM9_HUMAN;.	A	228;228;194;143	ENSP00000321005:T228A;ENSP00000442368:T228A;ENSP00000366408:T194A;ENSP00000293396:T143A	ENSP00000293396:T143A	T	+	1	0	CD300LG	39286901	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.508000	0.02266	-1.072000	0.03141	-2.118000	0.00350	ACC	A|0.735;G|0.265	0.265	strong		0.592	CD300LG-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457646.1	NM_145273	
ITGB2	3689	hgsc.bcm.edu	37	21	46313442	46313442	+	Silent	SNP	G	G	T	rs2230529	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:46313442G>T	ENST00000397850.2	-	11	1553	c.1101C>A	c.(1099-1101)gtC>gtA	p.V367V	ITGB2_ENST00000397854.3_Silent_p.V310V|ITGB2_ENST00000397857.1_Silent_p.V367V|ITGB2_ENST00000397852.1_Silent_p.V367V|ITGB2_ENST00000302347.5_Silent_p.V367V|ITGB2_ENST00000355153.4_Silent_p.V367V			P05107	ITB2_HUMAN	integrin, beta 2 (complement component 3 receptor 3 and 4 subunit)	367					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)	GATCCAGGAAGACCCTGGAGG	0.602													G|||	997	0.199081	0.2292	0.1542	5008	,	,		20095	0.0893		0.2505	False		,,,				2504	0.2505				p.V367V		Atlas-SNP	.											.	ITGB2	107	.	0			c.C1101A						PASS	.	G	,	963,3443	362.6+/-316.2	119,725,1359	148.0	131.0	137.0		1101,1101	3.7	1.0	21	dbSNP_98	137	2170,6430	371.4+/-336.2	270,1630,2400	no	coding-synonymous,coding-synonymous	ITGB2	NM_000211.3,NM_001127491.1	,	389,2355,3759	TT,TG,GG		25.2326,21.8566,24.0889	,	367/770,367/770	46313442	3133,9873	2203	4300	6503	SO:0001819	synonymous_variant	3689	exon10			CAGGAAGACCCTG	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.1101C>A	21.37:g.46313442G>T		Somatic	237	0	0		WXS	Illumina HiSeq	Phase_I	303	122	0.40264	NM_000211	B3KTS8|D3DSM1|Q16418|Q53HS5|Q9UD72	Silent	SNP	ENST00000397850.2	37	CCDS13716.1																																																																																			G|0.775;T|0.225	0.225	strong		0.602	ITGB2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206566.2	NM_000211	
PLCL2	23228	hgsc.bcm.edu	37	3	17051450	17051450	+	Silent	SNP	C	C	A	rs28932173	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:17051450C>A	ENST00000418129.2	+	2	699	c.234C>A	c.(232-234)cgC>cgA	p.R78R	PLCL2_ENST00000396755.2_Silent_p.R78R|PLCL2_ENST00000460467.1_3'UTR|PLCL2_ENST00000432376.1_Silent_p.R78R	NM_001144382.1	NP_001137854.1	Q9UPR0	PLCL2_HUMAN	phospholipase C-like 2	204					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						ACATATTCCGCAGCAATGGCA	0.428													C|||	219	0.04373	0.003	0.1254	5008	,	,		20785	0.0506		0.0209	False		,,,				2504	0.0573				p.R78R		Atlas-SNP	.											PLCL2,colon,carcinoma,+1,1	PLCL2	145	1	0			c.C234A						PASS	.	C	,	34,4372	38.4+/-70.7	0,34,2169	117.0	116.0	116.0		616,234	3.1	1.0	3	dbSNP_125	116	257,8343	100.6+/-161.9	9,239,4052	yes	coding-synonymous,coding-synonymous	PLCL2	NM_001144382.1,NM_015184.5	,	9,273,6221	AA,AC,CC		2.9884,0.7717,2.2374	,	204/1128,78/1002	17051450	291,12715	2203	4300	6503	SO:0001819	synonymous_variant	23228	exon2			ATTCCGCAGCAAT	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.234C>A	3.37:g.17051450C>A		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	79	46	0.582278	NM_015184	A8K5V4|Q8N498|Q9H8L0|Q9UFP9	Silent	SNP	ENST00000418129.2	37	CCDS33713.1																																																																																			C|0.974;A|0.026	0.026	strong		0.428	PLCL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340250.3		
NDUFAF1	51103	hgsc.bcm.edu	37	15	41679717	41679717	+	Silent	SNP	C	C	T	rs73407109	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:41679717C>T	ENST00000260361.4	-	5	1290	c.909G>A	c.(907-909)gtG>gtA	p.V303V		NM_016013.3	NP_057097.2	Q9Y375	CIA30_HUMAN	NADH dehydrogenase (ubiquinone) complex I, assembly factor 1	303					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)		GATCAGTAAACACGCCAATAA	0.338													C|||	479	0.095647	0.1694	0.062	5008	,	,		15537	0.1419		0.0537	False		,,,				2504	0.0153				p.V303V		Atlas-SNP	.											.	NDUFAF1	39	.	0			c.G909A						PASS	.	C		702,3704	290.4+/-280.9	54,594,1555	84.0	93.0	90.0		909	-1.4	0.6	15	dbSNP_130	90	415,8185	130.5+/-188.4	9,397,3894	no	coding-synonymous	NDUFAF1	NM_016013.2		63,991,5449	TT,TC,CC		4.8256,15.9328,8.5883		303/328	41679717	1117,11889	2203	4300	6503	SO:0001819	synonymous_variant	51103	exon5			AGTAAACACGCCA	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.909G>A	15.37:g.41679717C>T		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	142	82	0.577465	NM_016013	Q9BVZ5	Silent	SNP	ENST00000260361.4	37	CCDS10075.1																																																																																			C|0.916;T|0.084	0.084	strong		0.338	NDUFAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252692.2	NM_016013	
UTP20	27340	hgsc.bcm.edu	37	12	101674926	101674926	+	Silent	SNP	T	T	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:101674926T>G	ENST00000261637.4	+	2	252	c.78T>G	c.(76-78)gtT>gtG	p.V26V		NM_014503.2	NP_055318.2	O75691	UTP20_HUMAN	UTP20, small subunit (SSU) processome component, homolog (yeast)	26					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						TGGGGAATGTTAATATTGATA	0.303																																					p.V26V		Atlas-SNP	.											.	UTP20	222	.	0			c.T78G						PASS	.						82.0	83.0	82.0					12																	101674926		2203	4299	6502	SO:0001819	synonymous_variant	27340	exon2			GAATGTTAATATT	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.78T>G	12.37:g.101674926T>G		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	111	31	0.279279	NM_014503	Q9H3H4	Silent	SNP	ENST00000261637.4	37	CCDS9081.1																																																																																			.	.	none		0.303	UTP20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408242.1	NM_014503	
FGFR2	2263	hgsc.bcm.edu	37	10	123325034	123325034	+	Silent	SNP	C	C	T	rs1047101	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:123325034C>T	ENST00000358487.5	-	3	566	c.294G>A	c.(292-294)acG>acA	p.T98T	FGFR2_ENST00000369061.4_Silent_p.T98T|FGFR2_ENST00000346997.2_Silent_p.T98T|FGFR2_ENST00000369059.1_Intron|FGFR2_ENST00000490349.1_5'UTR|FGFR2_ENST00000369060.4_Silent_p.T98T|FGFR2_ENST00000360144.3_Intron|FGFR2_ENST00000369056.1_Silent_p.T98T|FGFR2_ENST00000457416.2_Silent_p.T98T|FGFR2_ENST00000356226.4_Intron|FGFR2_ENST00000351936.6_Silent_p.T98T|FGFR2_ENST00000359354.2_Silent_p.T98T|FGFR2_ENST00000357555.5_Intron	NM_000141.4	NP_000132.3	P21802	FGFR2_HUMAN	fibroblast growth factor receptor 2	98	Ig-like C2-type 1.				angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|axonogenesis (GO:0007409)|bone development (GO:0060348)|bone mineralization (GO:0030282)|bone morphogenesis (GO:0060349)|branch elongation involved in salivary gland morphogenesis (GO:0060667)|branching involved in labyrinthine layer morphogenesis (GO:0060670)|branching involved in prostate gland morphogenesis (GO:0060442)|branching involved in salivary gland morphogenesis (GO:0060445)|branching morphogenesis of a nerve (GO:0048755)|bud elongation involved in lung branching (GO:0060449)|cell fate commitment (GO:0045165)|cell-cell signaling (GO:0007267)|coronal suture morphogenesis (GO:0060365)|digestive tract development (GO:0048565)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic organ development (GO:0048568)|embryonic organ morphogenesis (GO:0048562)|embryonic pattern specification (GO:0009880)|endodermal digestive tract morphogenesis (GO:0061031)|epidermal growth factor receptor signaling pathway (GO:0007173)|epidermis morphogenesis (GO:0048730)|epithelial cell differentiation (GO:0030855)|epithelial cell proliferation involved in salivary gland morphogenesis (GO:0060664)|epithelial to mesenchymal transition (GO:0001837)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|fibroblast growth factor receptor signaling pathway involved in hemopoiesis (GO:0035603)|fibroblast growth factor receptor signaling pathway involved in mammary gland specification (GO:0060595)|fibroblast growth factor receptor signaling pathway involved in negative regulation of apoptotic process in bone marrow (GO:0035602)|fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development (GO:0035607)|fibroblast growth factor receptor signaling pathway involved in positive regulation of cell proliferation in bone marrow (GO:0035604)|gland morphogenesis (GO:0022612)|hair follicle morphogenesis (GO:0031069)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|inner ear morphogenesis (GO:0042472)|insulin receptor signaling pathway (GO:0008286)|lacrimal gland development (GO:0032808)|lateral sprouting from an epithelium (GO:0060601)|lens fiber cell development (GO:0070307)|limb bud formation (GO:0060174)|lung alveolus development (GO:0048286)|lung development (GO:0030324)|lung lobe morphogenesis (GO:0060463)|lung-associated mesenchyme development (GO:0060484)|mammary gland bud formation (GO:0060615)|membranous septum morphogenesis (GO:0003149)|mesenchymal cell differentiation (GO:0048762)|mesenchymal cell differentiation involved in lung development (GO:0060915)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesodermal cell differentiation (GO:0048333)|midbrain development (GO:0030901)|morphogenesis of embryonic epithelium (GO:0016331)|multicellular organism growth (GO:0035264)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of mitosis (GO:0045839)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuromuscular junction development (GO:0007528)|neurotrophin TRK receptor signaling pathway (GO:0048011)|odontogenesis (GO:0042476)|orbitofrontal cortex development (GO:0021769)|organ growth (GO:0035265)|organ morphogenesis (GO:0009887)|otic vesicle formation (GO:0030916)|outflow tract septum morphogenesis (GO:0003148)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of epithelial cell proliferation involved in lung morphogenesis (GO:0060501)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of Wnt signaling pathway (GO:0030177)|post-embryonic development (GO:0009791)|prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis (GO:0060527)|prostate epithelial cord elongation (GO:0060523)|prostate gland morphogenesis (GO:0060512)|protein autophosphorylation (GO:0046777)|pyramidal neuron development (GO:0021860)|regulation of branching involved in prostate gland morphogenesis (GO:0060687)|regulation of cell fate commitment (GO:0010453)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)|regulation of morphogenesis of a branching structure (GO:0060688)|regulation of multicellular organism growth (GO:0040014)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoblast proliferation (GO:0033688)|regulation of smooth muscle cell differentiation (GO:0051150)|regulation of smoothened signaling pathway (GO:0008589)|reproductive structure development (GO:0048608)|skeletal system morphogenesis (GO:0048705)|squamous basal epithelial stem cell differentiation involved in prostate gland acinus development (GO:0060529)|synaptic vesicle transport (GO:0048489)|ureteric bud development (GO:0001657)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|ventricular zone neuroblast division (GO:0021847)	cell cortex (GO:0005938)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|excitatory synapse (GO:0060076)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|fibroblast growth factor binding (GO:0017134)|fibroblast growth factor-activated receptor activity (GO:0005007)|heparin binding (GO:0008201)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)			breast(3)|central_nervous_system(3)|cervix(2)|endometrium(98)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(7)|lung(21)|ovary(4)|skin(30)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(2)	181		Lung NSC(174;0.0841)|all_lung(145;0.106)|all_neural(114;0.107)	STAD - Stomach adenocarcinoma(1;7.52e-05)|all cancers(1;0.0722)	all cancers(201;9.73e-05)|GBM - Glioblastoma multiforme(135;0.0845)	Palifermin(DB00039)|Ponatinib(DB08901)|Regorafenib(DB08896)|Thalidomide(DB01041)	AGTCTCTAGGCGTGGCGCCCT	0.537		5	Mis		"""gastric. NSCLC, endometrial"""		"""Crouzon, Pfeiffer, and Apert syndromes"""		Saethre-Chotzen syndrome;Apert syndrome				C|||	17	0.00339457	0.0015	0.0058	5008	,	,		17879	0.0		0.0099	False		,,,				2504	0.001				p.T98T		Atlas-SNP	.		Dom	yes		10	10q26	2263	fibroblast growth factor receptor 2	yes	E	.	FGFR2	758	.	0			c.G294A						PASS	.	C	,,,,,,,,	7,4399	12.9+/-30.5	0,7,2196	175.0	150.0	158.0		294,294,294,,,294,,,294	-0.8	1.0	10	dbSNP_86	158	79,8521	46.3+/-105.2	1,77,4222	no	coding-synonymous,coding-synonymous,coding-synonymous,intron,intron,coding-synonymous,intron,intron,coding-synonymous	FGFR2	NM_000141.4,NM_001144913.1,NM_001144914.1,NM_001144915.1,NM_001144916.1,NM_001144917.1,NM_001144918.1,NM_001144919.1,NM_022970.3	,,,,,,,,	1,84,6418	TT,TC,CC		0.9186,0.1589,0.6612	,,,,,,,,	98/822,98/770,98/710,,,98/706,,,98/823	123325034	86,12920	2203	4300	6503	SO:0001819	synonymous_variant	2263	exon3	Familial Cancer Database	Acrocephalosyndactyly type III;Acrocephalosyndactyly type I and II, ACS1. ACS2, incl Apert-Crouzon s.	TCTAGGCGTGGCG	AK026508	CCDS7620.2, CCDS31298.1, CCDS44485.1, CCDS44486.1, CCDS44487.1, CCDS44488.1, CCDS44489.1, CCDS53584.1, CCDS73210.1	10q25.3-q26	2013-01-11	2008-08-01		ENSG00000066468	ENSG00000066468		"""CD molecules"", ""Immunoglobulin superfamily / I-set domain containing"""	3689	protein-coding gene	gene with protein product	"""Crouzon syndrome"", ""Pfeiffer syndrome"""	176943	"""bacteria-expressed kinase"", ""keratinocyte growth factor receptor"", ""craniofacial dysostosis 1"", ""Jackson-Weiss syndrome"""	KGFR, BEK, CFD1, JWS			Standard	NM_022970		Approved	CEK3, TK14, TK25, ECT1, K-SAM, CD332	uc021pzy.1	P21802	OTTHUMG00000019175	ENST00000358487.5:c.294G>A	10.37:g.123325034C>T		Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	161	87	0.540373	NM_022970	B4DFC2|E7EVR6|E9PCR0|P18443|Q01742|Q12922|Q14300|Q14301|Q14302|Q14303|Q14304|Q14305|Q14672|Q14718|Q14719|Q1KHY5|Q86YI4|Q8IXC7|Q96KL9|Q96KM0|Q96KM1|Q96KM2|Q9NZU2|Q9NZU3|Q9UD01|Q9UD02|Q9UIH3|Q9UIH4|Q9UIH5|Q9UIH6|Q9UIH7|Q9UIH8|Q9UM87|Q9UMC6|Q9UNS7|Q9UQH7|Q9UQH8|Q9UQH9|Q9UQI0	Silent	SNP	ENST00000358487.5	37	CCDS31298.1																																																																																			C|0.993;T|0.007	0.007	strong		0.537	FGFR2-001	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000050715.1	NM_022976, NM_000141	
ALG1	56052	hgsc.bcm.edu	37	16	5132659	5132659	+	Missense_Mutation	SNP	C	C	T	rs74910062	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:5132659C>T	ENST00000262374.5	+	11	1203	c.1172C>T	c.(1171-1173)gCt>gTt	p.A391V	ALG1_ENST00000588623.1_Missense_Mutation_p.A280V|ALG1_ENST00000544428.1_Missense_Mutation_p.A280V	NM_019109.4	NP_061982.3	Q9BT22	ALG1_HUMAN	ALG1, chitobiosyldiphosphodolichol beta-mannosyltransferase	391					cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|lipopolysaccharide biosynthetic process (GO:0009103)|mannosylation (GO:0097502)|post-translational protein modification (GO:0043687)|protein glycosylation (GO:0006486)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	chitobiosyldiphosphodolichol beta-mannosyltransferase activity (GO:0004578)|mannosyltransferase activity (GO:0000030)			breast(1)|cervix(1)|endometrium(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	13		Ovarian(90;0.0164)				CCTGTGTGTGCTGTGAACTTC	0.597													C|||	37	0.00738818	0.0212	0.0029	5008	,	,		20282	0.004		0.001	False		,,,				2504	0.002				p.A391V		Atlas-SNP	.											.	ALG1	35	.	0			c.C1172T						PASS	.						95.0	71.0	79.0					16																	5132659		2087	3975	6062	SO:0001583	missense	56052	exon11			TGTGTGCTGTGAA	AB019038	CCDS10528.1	16p13.3	2013-02-22	2013-02-22		ENSG00000033011	ENSG00000033011	2.4.1.142	"""Glycosyltransferase group 1 domain containing"""	18294	protein-coding gene	gene with protein product		605907	"""asparagine-linked glycosylation 1 homolog (yeast, beta-1,4-mannosyltransferase)"", ""asparagine-linked glycosylation 1, beta-1,4-mannosyltransferase homolog (S. cerevisiae)"""			10704531	Standard	NM_019109		Approved	HMT-1, HMAT1	uc002cym.3	Q9BT22	OTTHUMG00000129529	ENST00000262374.5:c.1172C>T	16.37:g.5132659C>T	ENSP00000262374:p.Ala391Val	Somatic	17	0	0		WXS	Illumina HiSeq	Phase_I	17	7	0.411765	NM_019109	B4DP08|Q6UVZ9|Q8N5Y4|Q9P2Y2	Missense_Mutation	SNP	ENST00000262374.5	37	CCDS10528.1	.	.	.	.	.	.	.	.	.	.	C	21.9	4.214278	0.79352	.	.	ENSG00000033011	ENST00000262374;ENST00000544428	T;T	0.79141	-1.24;-1.24	5.28	5.28	0.74379	Glycosyl transferase, family 1 (1);	0.000000	0.85682	D	0.000000	D	0.90345	0.6979	M	0.90425	3.115	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.92258	0.5814	10	0.87932	D	0	-20.3409	17.5165	0.87775	0.0:1.0:0.0:0.0	.	280;391	B4DP08;Q9BT22	.;ALG1_HUMAN	V	391;280	ENSP00000262374:A391V;ENSP00000440019:A280V	ENSP00000262374:A391V	A	+	2	0	ALG1	5072660	1.000000	0.71417	0.702000	0.30337	0.479000	0.33129	7.176000	0.77643	2.474000	0.83562	0.555000	0.69702	GCT	.	.	weak		0.597	ALG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251716.2	NM_019109	
SP3	6670	hgsc.bcm.edu	37	2	174820721	174820721	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:174820721T>C	ENST00000310015.6	-	4	1049	c.519A>G	c.(517-519)atA>atG	p.I173M	SP3_ENST00000483084.1_5'Flank|SP3_ENST00000455789.2_Missense_Mutation_p.I120M|SP3_ENST00000418194.2_Missense_Mutation_p.I105M	NM_001172712.1|NM_003111.4	NP_001166183.1|NP_003102.1	Q02447	SP3_HUMAN	Sp3 transcription factor	173	Transactivation domain (Gln-rich).				B cell differentiation (GO:0030183)|definitive hemopoiesis (GO:0060216)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic placenta development (GO:0001892)|embryonic process involved in female pregnancy (GO:0060136)|embryonic skeletal system development (GO:0048706)|enucleate erythrocyte differentiation (GO:0043353)|granulocyte differentiation (GO:0030851)|liver development (GO:0001889)|lung development (GO:0030324)|megakaryocyte differentiation (GO:0030219)|monocyte differentiation (GO:0030224)|natural killer cell differentiation (GO:0001779)|negative regulation of transcription, DNA-templated (GO:0045892)|ossification (GO:0001503)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|T cell differentiation (GO:0030217)|trophectodermal cell differentiation (GO:0001829)	nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|double-stranded DNA binding (GO:0003690)|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)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)		EWSR1/SP3(3)	NS(2)|large_intestine(3)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	9			OV - Ovarian serous cystadenocarcinoma(117;0.185)			GGATCTGTGGTATCACTTGAT	0.403																																					p.I173M		Atlas-SNP	.											SP3_ENST00000310015,NS,carcinoma,-1,1	SP3	82	1	0			c.A519G						scavenged	.						245.0	239.0	241.0					2																	174820721		2203	4300	6503	SO:0001583	missense	6670	exon4			CTGTGGTATCACT	M97191	CCDS2254.1, CCDS46452.1	2q31	2013-01-08			ENSG00000172845	ENSG00000172845		"""Specificity protein transcription factors"", ""Zinc fingers, C2H2-type"""	11208	protein-coding gene	gene with protein product		601804				1341900, 1454515	Standard	NM_003111		Approved	SPR-2	uc002uig.3	Q02447	OTTHUMG00000132333	ENST00000310015.6:c.519A>G	2.37:g.174820721T>C	ENSP00000310301:p.Ile173Met	Somatic	248	0	0		WXS	Illumina HiSeq	Phase_I	176	3	0.0170455	NM_003111	A0AVL9|B4E2B7|Q69B26|Q69B27|Q8TD56|Q8WWU4|Q9BQR1	Missense_Mutation	SNP	ENST00000310015.6	37	CCDS2254.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	14.32|14.32	2.499143|2.499143	0.44455|0.44455	.|.	.|.	ENSG00000172845|ENSG00000172845	ENST00000310015;ENST00000455789;ENST00000418194|ENST00000416195	T;T;T|.	0.15718|.	2.42;2.41;2.4|.	5.95|5.95	3.42|3.42	0.39159|0.39159	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.70465|0.70465	0.3227|0.3227	M|M	0.73598|0.73598	2.24|2.24	0.51233|0.51233	D|D	0.999913|0.999913	D;D;D|.	0.76494|.	0.998;0.999;0.999|.	D;D;D|.	0.83275|.	0.991;0.956;0.996|.	T|T	0.70051|0.70051	-0.4978|-0.4978	10|5	0.87932|.	D|.	0|.	.|.	11.0854|11.0854	0.48084|0.48084	0.2467:0.0:0.0:0.7533|0.2467:0.0:0.0:0.7533	.|.	170;173;120|.	B7ZLN9;Q02447;Q02447-6|.	.;SP3_HUMAN;.|.	M|C	173;120;105|130	ENSP00000310301:I173M;ENSP00000388903:I120M;ENSP00000406140:I105M|.	ENSP00000310301:I173M|.	I|Y	-|-	3|2	3|0	SP3|SP3	174528967|174528967	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.995000|0.995000	0.86356|0.86356	3.514000|3.514000	0.53422|0.53422	1.051000|1.051000	0.40369|0.40369	0.460000|0.460000	0.39030|0.39030	ATA|TAC	.	.	none		0.403	SP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255452.1	NM_003111	
TLR6	10333	hgsc.bcm.edu	37	4	38829832	38829832	+	Silent	SNP	T	T	C	rs3775073	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:38829832T>C	ENST00000381950.1	-	1	1328	c.1263A>G	c.(1261-1263)aaA>aaG	p.K421K	TLR6_ENST00000436693.2_Silent_p.K421K			Q9Y2C9	TLR6_HUMAN	toll-like receptor 6	421					activation of NF-kappaB-inducing kinase activity (GO:0007250)|cellular response to diacyl bacterial lipopeptide (GO:0071726)|defense response to bacterium (GO:0042742)|detection of diacyl bacterial lipopeptide (GO:0042496)|immune response (GO:0006955)|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)|nitric oxide metabolic process (GO:0046209)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-6 biosynthetic process (GO:0045410)|positive regulation of JUN kinase activity (GO:0043507)|regulation of cytokine secretion (GO:0050707)|signal transduction (GO:0007165)|T-helper 1 type immune response (GO:0042088)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 6 signaling pathway (GO:0034150)|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)	cytoplasmic vesicle (GO:0031410)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|Toll-like receptor 2-Toll-like receptor 6 protein complex (GO:0035355)	diacyl lipopeptide binding (GO:0042498)|lipopeptide binding (GO:0071723)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(7)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						TGCAGTTTTCTTTATGTCTAC	0.378													C|||	2291	0.457468	0.7398	0.3156	5008	,	,		20740	0.3958		0.3141	False		,,,				2504	0.3875				p.K421K		Atlas-SNP	.											.	TLR6	67	.	0			c.A1263G						PASS	.	C		2910,1496	467.6+/-354.9	953,1004,246	100.0	107.0	105.0		1263	-2.5	0.0	4	dbSNP_107	105	2942,5658	665.9+/-402.3	519,1904,1877	no	coding-synonymous	TLR6	NM_006068.4		1472,2908,2123	CC,CT,TT		34.2093,33.9537,44.9946		421/797	38829832	5852,7154	2203	4300	6503	SO:0001819	synonymous_variant	10333	exon2			GTTTTCTTTATGT		CCDS3446.1	4p16.1	2009-11-23			ENSG00000174130	ENSG00000174130		"""CD molecules"""	16711	protein-coding gene	gene with protein product		605403				10231569	Standard	NM_006068		Approved	CD286	uc010ifg.2	Q9Y2C9	OTTHUMG00000128579	ENST00000381950.1:c.1263A>G	4.37:g.38829832T>C		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	113	46	0.40708	NM_006068	B3Y640|B6CH35|B6RFS4|B6RFS5|Q2NKL3	Silent	SNP	ENST00000381950.1	37	CCDS3446.1																																																																																			T|0.564;C|0.436	0.436	strong		0.378	TLR6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250431.1		
MUC4	4585	hgsc.bcm.edu	37	3	195508416	195508416	+	Silent	SNP	C	C	A	rs529417345	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195508416C>A	ENST00000463781.3	-	2	10494	c.10035G>T	c.(10033-10035)gtG>gtT	p.V3345V	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Silent_p.V3345V	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)		CGGTGACAGGCACAGGGGTGG	0.597													.|||	1317	0.262979	0.3646	0.2075	5008	,	,		12719	0.2976		0.2336	False		,,,				2504	0.1595				p.V3345V		Atlas-SNP	.											MUC4_ENST00000463781,rectum,carcinoma,0,1	MUC4	1505	1	0			c.G10035T						scavenged	.						31.0	24.0	26.0					3																	195508416		663	1575	2238	SO:0001819	synonymous_variant	4585	exon2			GACAGGCACAGGG	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.10035G>T	3.37:g.195508416C>A		Somatic	89	2	0.0224719		WXS	Illumina HiSeq	Phase_I	78	7	0.0897436	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		0.597	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
NUDT10	170685	hgsc.bcm.edu	37	X	51076018	51076018	+	Silent	SNP	C	C	T	rs12846945	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:51076018C>T	ENST00000376006.3	+	2	421	c.201C>T	c.(199-201)taC>taT	p.Y67Y	NUDT10_ENST00000356450.2_Silent_p.Y67Y	NM_153183.2	NP_694853.1	Q9BW91	NUDT9_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 10	232					ADP catabolic process (GO:0046032)|IDP catabolic process (GO:0046709)|nucleobase-containing small molecule catabolic process (GO:0034656)|nucleobase-containing small molecule metabolic process (GO:0055086)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|mitochondrial matrix (GO:0005759)	adenosine-diphosphatase activity (GO:0043262)|ADP-ribose diphosphatase activity (GO:0047631)|ADP-sugar diphosphatase activity (GO:0019144)			cervix(1)|endometrium(8)|kidney(1)|large_intestine(1)|lung(1)|prostate(3)|upper_aerodigestive_tract(1)	16	Ovarian(276;0.236)					GAGAGGTGTACGAAGAGGCGG	0.642													C|||	371	0.0982781	0.0953	0.0576	3775	,	,		9846	0.0119		0.1233	False		,,,				2504	0.0706				p.Y67Y	NSCLC(90;1817 2035 37909 38249)	Atlas-SNP	.											.	NUDT10	28	.	0			c.C201T						PASS	.	C		516,3319		29,384,74,1219,497	47.0	57.0	54.0		201	0.3	1.0	X	dbSNP_121	54	1094,5634		68,651,307,1709,1565	no	coding-synonymous	NUDT10	NM_153183.2		97,1035,381,2928,2062	TT,TC,T,CC,C		16.2604,13.455,15.2419		67/165	51076018	1610,8953	2203	4300	6503	SO:0001819	synonymous_variant	170685	exon2			GGTGTACGAAGAG	AF469196	CCDS35278.1	Xp11.22-p11.1	2014-05-20			ENSG00000122824	ENSG00000122824		"""Nudix motif containing"""	17621	protein-coding gene	gene with protein product		300527				12105228	Standard	NM_153183		Approved	DIPP3a, hDIPP3alpha	uc004dph.3	Q8NFP7	OTTHUMG00000021530	ENST00000376006.3:c.201C>T	X.37:g.51076018C>T		Somatic	234	0	0		WXS	Illumina HiSeq	Phase_I	162	161	0.993827	NM_153183	Q8NBN1|Q8NCB9|Q8NG25	Silent	SNP	ENST00000376006.3	37	CCDS35278.1																																																																																			C|0.864;T|0.136	0.136	strong		0.642	NUDT10-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056578.1	NM_153183	
PASK	23178	hgsc.bcm.edu	37	2	242065944	242065944	+	Missense_Mutation	SNP	C	C	T	rs35129131	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:242065944C>T	ENST00000405260.1	-	10	3084	c.2386G>A	c.(2386-2388)Gag>Aag	p.E796K	PASK_ENST00000403638.3_Missense_Mutation_p.E796K|PASK_ENST00000358649.4_Missense_Mutation_p.E796K|PASK_ENST00000234040.4_Missense_Mutation_p.E796K|PASK_ENST00000544142.1_Missense_Mutation_p.E610K|PASK_ENST00000539818.1_Missense_Mutation_p.E580K	NM_001252120.1	NP_001239049.1	Q96RG2	PASK_HUMAN	PAS domain containing serine/threonine kinase	796			E -> K (in dbSNP:rs35129131). {ECO:0000269|PubMed:17344846}.		negative regulation of glycogen biosynthetic process (GO:0045719)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of energy homeostasis (GO:2000505)|regulation of glucagon secretion (GO:0070092)|regulation of respiratory gaseous exchange (GO:0043576)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	ATP binding (GO:0005524)|phosphatidylinositol binding (GO:0035091)|protein serine/threonine kinase activity (GO:0004674)|signal transducer activity (GO:0004871)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(6)|lung(20)|ovary(4)|prostate(4)|skin(1)|stomach(1)|urinary_tract(2)	53		all_cancers(19;4.46e-39)|all_epithelial(40;1.34e-17)|Breast(86;1.53e-05)|Renal(207;0.00179)|all_lung(227;0.00481)|Lung NSC(271;0.017)|Ovarian(221;0.0228)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;1.34e-31)|all cancers(36;1e-28)|OV - Ovarian serous cystadenocarcinoma(60;3.53e-14)|Kidney(56;4.31e-09)|KIRC - Kidney renal clear cell carcinoma(57;4.35e-08)|BRCA - Breast invasive adenocarcinoma(100;5.64e-06)|Lung(119;0.000596)|LUSC - Lung squamous cell carcinoma(224;0.00481)|Colorectal(34;0.014)|COAD - Colon adenocarcinoma(134;0.0968)		AGTAACAGCTCCCTGTCATCC	0.572													C|||	50	0.00998403	0.0	0.0173	5008	,	,		20550	0.0		0.0239	False		,,,				2504	0.0143				p.E796K		Atlas-SNP	.											.	PASK	230	.	0			c.G2386A						PASS	.	C	LYS/GLU	17,4389	25.3+/-52.1	0,17,2186	114.0	101.0	106.0		2386	4.0	0.4	2	dbSNP_126	106	244,8356	98.4+/-159.9	2,240,4058	yes	missense	PASK	NM_015148.2	56	2,257,6244	TT,TC,CC		2.8372,0.3858,2.0068	possibly-damaging	796/1324	242065944	261,12745	2203	4300	6503	SO:0001583	missense	23178	exon10			ACAGCTCCCTGTC	U79240	CCDS2545.1, CCDS58758.1, CCDS58759.1	2q37.3	2008-05-23			ENSG00000115687	ENSG00000115687			17270	protein-coding gene	gene with protein product		607505				11688972, 11459942, 15148392	Standard	NM_001252119		Approved	PASKIN, KIAA0135, STK37	uc010fzl.2	Q96RG2	OTTHUMG00000133392	ENST00000405260.1:c.2386G>A	2.37:g.242065944C>T	ENSP00000384016:p.Glu796Lys	Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	92	43	0.467391	NM_015148	G5E9F1|Q05BE4|Q68DY3|Q6GSJ5|Q86XH6|Q99763|Q9UFR7	Missense_Mutation	SNP	ENST00000405260.1	37	CCDS2545.1	27	0.012362637362637362	0	0.0	8	0.022099447513812154	0	0.0	19	0.025065963060686015	C	14.51	2.556186	0.45487	0.003858	0.028372	ENSG00000115687	ENST00000234040;ENST00000544142;ENST00000405260;ENST00000358649;ENST00000539818;ENST00000403638	T;T;T;T;T;T	0.69175	-0.38;-0.38;-0.38;-0.33;-0.37;0.59	3.97	3.97	0.46021	.	0.374026	0.22795	N	0.055552	T	0.42517	0.1206	L	0.34521	1.04	0.09310	N	1	P;D;D;D;P	0.59767	0.915;0.986;0.986;0.986;0.915	B;P;P;P;B	0.56278	0.395;0.795;0.795;0.795;0.395	T	0.49835	-0.8897	10	0.72032	D	0.01	.	10.4806	0.44691	0.0:0.8013:0.1987:0.0	rs35129131	761;610;796;796;796	B7Z7R6;F5GYW7;Q96RG2-2;G5E9F1;Q96RG2	.;.;.;.;PASK_HUMAN	K	796;610;796;796;580;796	ENSP00000234040:E796K;ENSP00000441374:E610K;ENSP00000384016:E796K;ENSP00000351475:E796K;ENSP00000443083:E580K;ENSP00000384438:E796K	ENSP00000234040:E796K	E	-	1	0	PASK	241714617	0.013000	0.17824	0.446000	0.26920	0.180000	0.23129	2.515000	0.45512	2.174000	0.68829	0.561000	0.74099	GAG	C|0.981;T|0.019	0.019	strong		0.572	PASK-003	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000323753.1	NM_015148	
MUC4	4585	hgsc.bcm.edu	37	3	195506917	195506917	+	Missense_Mutation	SNP	A	A	C	rs150128295	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195506917A>C	ENST00000463781.3	-	2	11993	c.11534T>G	c.(11533-11535)aTc>aGc	p.I3845S	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_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	83	2	0.0240964		WXS	Illumina HiSeq	Phase_I	22	16	0.727273	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	
SRP72	6731	hgsc.bcm.edu	37	4	57361553	57361553	+	Silent	SNP	A	A	G	rs34419325	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:57361553A>G	ENST00000342756.5	+	17	2392	c.1671A>G	c.(1669-1671)aaA>aaG	p.K557K	SRP72_ENST00000510663.1_Silent_p.K496K	NM_006947.3	NP_008878.3	O76094	SRP72_HUMAN	signal recognition particle 72kDa	557	Poly-Lys.				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)					AGAAAAAGAAAAAGAAGGGTA	0.269													A|||	583	0.116414	0.0598	0.0576	5008	,	,		15029	0.251		0.0954	False		,,,				2504	0.1176				p.K557K		Atlas-SNP	.											.	SRP72	59	.	0			c.A1671G						PASS	.	A		234,4076		6,222,1927	25.0	26.0	25.0		1671	4.7	1.0	4	dbSNP_126	25	597,7929		27,543,3693	no	coding-synonymous	SRP72	NM_006947.3		33,765,5620	GG,GA,AA		7.0021,5.4292,6.474		557/672	57361553	831,12005	2155	4263	6418	SO:0001819	synonymous_variant	6731	exon17			AAAGAAAAAGAAG	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.1671A>G	4.37:g.57361553A>G		Somatic	282	0	0		WXS	Illumina HiSeq	Phase_I	204	100	0.490196	NM_006947	G5E9Z8|Q7Z3C0	Silent	SNP	ENST00000342756.5	37	CCDS3506.1																																																																																			A|0.915;G|0.085	0.085	strong		0.269	SRP72-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250782.7		
KCNA1	3736	hgsc.bcm.edu	37	12	5021984	5021984	+	Silent	SNP	T	T	A	rs4766309	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:5021984T>A	ENST00000382545.3	+	2	2547	c.1440T>A	c.(1438-1440)acT>acA	p.T480T	KCNA1_ENST00000543874.2_Intron	NM_000217.2	NP_000208.2	Q09470	KCNA1_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 1 (episodic ataxia with myokymia)	480					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	apical plasma membrane (GO:0016324)|dendrite (GO:0030425)|juxtaparanode region of axon (GO:0044224)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|potassium channel activity (GO:0005267)|potassium ion transmembrane transporter activity (GO:0015079)			NS(1)|breast(3)|cervix(2)|endometrium(5)|kidney(1)|large_intestine(14)|lung(23)|ovary(3)|pancreas(2)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	63					Amitriptyline(DB00321)|Dalfampridine(DB06637)|Desflurane(DB01189)|Enflurane(DB00228)|Isoflurane(DB00753)|Methoxyflurane(DB01028)|Nifedipine(DB01115)|Sevoflurane(DB01236)	ATTGCACCACTGCTAACCAAA	0.398													A|||	4109	0.820487	0.8903	0.7493	5008	,	,		20478	0.9623		0.6928	False		,,,				2504	0.7618				p.T480T		Atlas-SNP	.											.	KCNA1	112	.	0			c.T1440A						PASS	.	A		3772,634	273.4+/-271.3	1621,530,52	139.0	138.0	139.0		1440	2.9	1.0	12	dbSNP_111	139	5885,2715	434.8+/-357.8	2006,1873,421	no	coding-synonymous	KCNA1	NM_000217.2		3627,2403,473	AA,AT,TT		31.5698,14.3895,25.7497		480/496	5021984	9657,3349	2203	4300	6503	SO:0001819	synonymous_variant	3736	exon2			CACCACTGCTAAC	L02750	CCDS8535.1	12p13	2012-07-05			ENSG00000111262	ENSG00000111262		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6218	protein-coding gene	gene with protein product		176260		AEMK		1349297, 8821794, 16382104	Standard	NM_000217		Approved	Kv1.1, RBK1, HUK1, MBK1	uc001qnh.3	Q09470	OTTHUMG00000044398	ENST00000382545.3:c.1440T>A	12.37:g.5021984T>A		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	69	69	1	NM_000217	A6NM83|Q3MIQ9	Silent	SNP	ENST00000382545.3	37	CCDS8535.1																																																																																			T|0.233;A|0.767	0.767	strong		0.398	KCNA1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103343.2	NM_000217	
RNASE9	390443	hgsc.bcm.edu	37	14	21024786	21024786	+	Missense_Mutation	SNP	A	A	G	rs12590446	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:21024786A>G	ENST00000557068.1	-	4	2168	c.443T>C	c.(442-444)tTt>tCt	p.F148S	RNASE9_ENST00000338904.3_Missense_Mutation_p.F148S|RNASE9_ENST00000429244.2_Missense_Mutation_p.F148S|RNASE9_ENST00000553541.1_Missense_Mutation_p.F148S|RNASE9_ENST00000555230.1_Missense_Mutation_p.F148S|RNASE9_ENST00000553706.1_Missense_Mutation_p.F153S|RNASE9_ENST00000556208.1_Missense_Mutation_p.F153S|RNASE9_ENST00000554964.1_Missense_Mutation_p.F148S|RNASE9_ENST00000557209.1_Missense_Mutation_p.F153S|RNASE9_ENST00000404716.3_Missense_Mutation_p.F153S			P60153	RNAS9_HUMAN	ribonuclease, RNase A family, 9 (non-active)	148			F -> S (in dbSNP:rs12590446). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:18992174, ECO:0000269|Ref.3}.			extracellular region (GO:0005576)	nucleic acid binding (GO:0003676)			haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|ovary(2)|urinary_tract(1)	8	all_cancers(95;0.00238)		Epithelial(56;3.32e-06)|all cancers(55;2.46e-05)	GBM - Glioblastoma multiforme(265;0.0141)		TGGTATTTCAAATGCTTCTGT	0.358													A|||	2892	0.577476	0.1891	0.6527	5008	,	,		22050	0.6607		0.7823	False		,,,				2504	0.7526				p.F153S		Atlas-SNP	.											.	RNASE9	30	.	0			c.T458C						PASS	.	A	SER/PHE,SER/PHE,SER/PHE,SER/PHE,SER/PHE,SER/PHE,SER/PHE	1231,3175	422.3+/-339.7	169,893,1141	90.0	79.0	83.0		443,443,443,458,458,458,458	-7.5	0.0	14	dbSNP_120	83	6710,1890	726.9+/-406.6	2612,1486,202	yes	missense,missense,missense,missense,missense,missense,missense	RNASE9	NM_001001673.3,NM_001110356.1,NM_001110357.1,NM_001110358.1,NM_001110359.1,NM_001110360.1,NM_001110361.1	155,155,155,155,155,155,155	2781,2379,1343	GG,GA,AA		21.9767,27.9392,38.9436	benign,benign,benign,benign,benign,benign,benign	148/206,148/206,148/206,153/211,153/211,153/211,153/211	21024786	7941,5065	2203	4300	6503	SO:0001583	missense	390443	exon5			ATTTCAAATGCTT	AY665804	CCDS32036.1, CCDS53883.1, CCDS55904.1	14q11.2	2006-10-31				ENSG00000188655		"""Ribonucleases, RNase A"""	20673	protein-coding gene	gene with protein product		614014				15676279, 12920233	Standard	NM_001001673		Approved	h461	uc010ahu.3	P60153		ENST00000557068.1:c.443T>C	14.37:g.21024786A>G	ENSP00000451565:p.Phe148Ser	Somatic	218	0	0		WXS	Illumina HiSeq	Phase_I	185	96	0.518919	NM_001110359	A2RQR8|A8QJS1|Q5GAN7|Q6KG53	Missense_Mutation	SNP	ENST00000557068.1	37	CCDS32036.1	1304	0.5970695970695971	95	0.19308943089430894	230	0.6353591160220995	388	0.6783216783216783	591	0.7796833773087071	A	0.658	-0.807018	0.02819	0.279392	0.780233	ENSG00000188655	ENST00000338904;ENST00000554964;ENST00000555230;ENST00000557068;ENST00000404716;ENST00000556208;ENST00000553541;ENST00000429244;ENST00000553706;ENST00000557209	T;T;T;T;T;T;T;T;T;T	0.70164	-0.46;-0.46;-0.46;-0.46;-0.46;-0.46;-0.46;-0.46;-0.46;-0.46	3.73	-7.47	0.01365	Ribonuclease A, domain (3);	.	.	.	.	T	0.00012	0.0000	N	0.16478	0.41	0.80722	P	0.0	B;B	0.11235	0.004;0.002	B;B	0.09377	0.004;0.002	T	0.24119	-1.0169	8	0.02654	T	1	-2.7172	5.9714	0.19355	0.3762:0.0:0.1314:0.4925	rs12590446;rs17308450;rs60981349;rs12590446	148;153	P60153;P60153-2	RNAS9_HUMAN;.	S	148;148;148;148;153;153;148;148;153;153	ENSP00000340162:F148S;ENSP00000450599:F148S;ENSP00000450800:F148S;ENSP00000451565:F148S;ENSP00000384683:F153S;ENSP00000451160:F153S;ENSP00000451285:F148S;ENSP00000409504:F148S;ENSP00000450570:F153S;ENSP00000450987:F153S	ENSP00000340162:F148S	F	-	2	0	RNASE9	20094626	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.912000	0.01582	-2.947000	0.00295	-2.899000	0.00093	TTT	A|0.411;G|0.589	0.589	strong		0.358	RNASE9-004	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000411094.1	NM_001001673	
LCE1C	353133	hgsc.bcm.edu	37	1	152777908	152777908	+	Missense_Mutation	SNP	C	C	T	rs2006940	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:152777908C>T	ENST00000607093.1	-	1	46	c.47G>A	c.(46-48)tGc>tAc	p.C16Y	LCE1C_ENST00000368768.1_Missense_Mutation_p.C16Y			Q5T751	LCE1C_HUMAN	late cornified envelope 1C	16	Pro-rich.		C -> Y (in dbSNP:rs2006940).		keratinization (GO:0031424)					NS(1)|lung(4)|prostate(1)|skin(2)|urinary_tract(1)	9	Lung NSC(65;9.06e-30)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			cttgggggtgcacttgggagg	0.607													C|||	1105	0.220647	0.2163	0.2248	5008	,	,		12954	0.3135		0.1133	False		,,,				2504	0.2382				p.C16Y		Atlas-SNP	.											.	LCE1C	40	.	0			c.G47A						PASS	.	C	TYR/CYS	864,3540	321.8+/-297.3	75,714,1413	40.0	38.0	39.0		47	3.4	1.0	1	dbSNP_92	39	991,7609	209.8+/-250.9	63,865,3372	no	missense	LCE1C	NM_178351.3	194	138,1579,4785	TT,TC,CC		11.5233,19.6185,14.2648	probably-damaging	16/119	152777908	1855,11149	2202	4300	6502	SO:0001583	missense	353133	exon2			GGGGTGCACTTGG		CCDS1026.1	1q21.3	2008-02-05			ENSG00000197084	ENSG00000197084		"""Late cornified envelopes"""	29464	protein-coding gene	gene with protein product		612605				11698679	Standard	NM_001276331		Approved	LEP3	uc001fap.1	Q5T751	OTTHUMG00000012445	ENST00000607093.1:c.47G>A	1.37:g.152777908C>T	ENSP00000475270:p.Cys16Tyr	Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	127	62	0.488189	NM_178351		Missense_Mutation	SNP	ENST00000607093.1	37	CCDS1026.1	448	0.20512820512820512	101	0.20528455284552846	79	0.21823204419889503	187	0.3269230769230769	81	0.10686015831134564	C	9.616	1.132650	0.21041	0.196185	0.115233	ENSG00000197084	ENST00000368768	T	0.09817	2.94	3.39	3.39	0.38822	.	.	.	.	.	T	0.22859	0.0552	M	0.84082	2.675	0.37686	P	0.07632399999999995	D	0.62365	0.991	D	0.78314	0.991	T	0.05920	-1.0856	8	0.87932	D	0	.	10.6123	0.45429	0.0:1.0:0.0:0.0	rs2006940	16	Q5T751	LCE1C_HUMAN	Y	16	ENSP00000357757:C16Y	ENSP00000357757:C16Y	C	-	2	0	LCE1C	151044532	0.984000	0.35163	0.979000	0.43373	0.997000	0.91878	3.529000	0.53532	1.588000	0.49971	0.655000	0.94253	TGC	C|0.847;T|0.153	0.153	strong		0.607	LCE1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034658.2	NM_178351	
GPC5	2262	hgsc.bcm.edu	37	13	92345579	92345579	+	Missense_Mutation	SNP	C	C	T	rs553717	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:92345579C>T	ENST00000377067.3	+	3	836	c.464C>T	c.(463-465)gCg>gTg	p.A155V		NM_004466.4	NP_004457.1	P78333	GPC5_HUMAN	glypican 5	155			A -> V (in dbSNP:rs553717).		carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	anchored component of membrane (GO:0031225)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)				NS(1)|breast(4)|endometrium(6)|kidney(4)|large_intestine(7)|lung(34)|ovary(2)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	69	all_cancers(3;1.43e-07)|all_neural(89;0.0804)|Medulloblastoma(90;0.163)	Lung NSC(4;0.00454)				TTATTTGGTGCGGATGTTAAT	0.443													C|||	986	0.196885	0.1936	0.1513	5008	,	,		18441	0.2897		0.1481	False		,,,				2504	0.1881				p.A155V		Atlas-SNP	.											GPC5,NS,carcinoma,-1,1	GPC5	140	1	0			c.C464T						PASS	.	C	VAL/ALA	822,3584	328.5+/-300.6	67,688,1448	153.0	156.0	155.0		464	4.2	0.8	13	dbSNP_83	155	970,7630	211.4+/-252.0	45,880,3375	yes	missense	GPC5	NM_004466.4	64	112,1568,4823	TT,TC,CC		11.2791,18.6564,13.7783	benign	155/573	92345579	1792,11214	2203	4300	6503	SO:0001583	missense	2262	exon3			TTGGTGCGGATGT	AF001462	CCDS9468.1	13q32	2011-08-01			ENSG00000179399	ENSG00000179399		"""Proteoglycans / Cell Surface : Glypicans"""	4453	protein-coding gene	gene with protein product	"""glypican proteoglycan 5"""	602446				9070915, 20304703, 19556317, 15057823	Standard	NM_004466		Approved		uc010tif.2	P78333	OTTHUMG00000017200	ENST00000377067.3:c.464C>T	13.37:g.92345579C>T	ENSP00000366267:p.Ala155Val	Somatic	234	0	0		WXS	Illumina HiSeq	Phase_I	225	108	0.48	NM_004466	B2R726|O60436|Q9BX27	Missense_Mutation	SNP	ENST00000377067.3	37	CCDS9468.1	379	0.17353479853479853	78	0.15853658536585366	44	0.12154696132596685	165	0.28846153846153844	92	0.12137203166226913	C	14.72	2.620512	0.46736	0.186564	0.112791	ENSG00000179399	ENST00000377067	T	0.54071	0.59	5.07	4.19	0.49359	.	0.330872	0.32518	N	0.005993	T	0.00012	0.0000	L	0.46157	1.445	0.27994	P	0.9355561	B	0.15473	0.013	B	0.15870	0.014	T	0.09862	-1.0655	9	0.59425	D	0.04	.	11.2088	0.48786	0.0:0.9046:0.0:0.0954	rs553717;rs52808980;rs57920264;rs553717	155	P78333	GPC5_HUMAN	V	155	ENSP00000366267:A155V	ENSP00000366267:A155V	A	+	2	0	GPC5	91143580	0.601000	0.26907	0.790000	0.31976	0.620000	0.37586	2.728000	0.47319	1.044000	0.40200	0.467000	0.42956	GCG	C|0.842;T|0.158	0.158	strong		0.443	GPC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045454.1	NM_004466	
GPR112	139378	hgsc.bcm.edu	37	X	135426968	135426968	+	Missense_Mutation	SNP	C	C	A	rs5930931	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:135426968C>A	ENST00000394143.1	+	6	1394	c.1103C>A	c.(1102-1104)cCt>cAt	p.P368H	GPR112_ENST00000412101.1_Missense_Mutation_p.P163H|GPR112_ENST00000370652.1_Missense_Mutation_p.P368H|GPR112_ENST00000287534.4_Missense_Mutation_p.P305H|GPR112_ENST00000394141.1_Missense_Mutation_p.P163H	NM_153834.3	NP_722576.3	Q8IZF6	GP112_HUMAN	G protein-coupled receptor 112	368			P -> H (in dbSNP:rs5930931). {ECO:0000269|Ref.2}.		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)	p.P368L(1)		NS(2)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(33)|lung(97)|ovary(5)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(2)	199	Acute lymphoblastic leukemia(192;0.000127)					TTTCAACCACCTACACCTTCT	0.368													c|||	1700	0.450331	0.4213	0.3545	3775	,	,		16744	0.2024		0.3738	False		,,,				2504	0.3241				p.P368H		Atlas-SNP	.											.	GPR112	459	.	1	Substitution - Missense(1)	prostate(1)	c.C1103A						PASS	.		HIS/PRO	2081,1754		479,816,307,337,264	84.0	78.0	80.0		1103	2.1	0.0	X	dbSNP_114	80	3200,3528		554,1184,908,690,964	yes	missense	GPR112	NM_153834.3	77	1033,2000,1215,1027,1228	AA,AC,A,CC,C		47.5624,45.7366,49.9953	possibly-damaging	368/3081	135426968	5281,5282	2203	4300	6503	SO:0001583	missense	139378	exon6			AACCACCTACACC	AY140954	CCDS35409.1	Xq26.3	2014-08-08			ENSG00000156920	ENSG00000156920		"""-"", ""GPCR / Class B : Orphans"""	18992	protein-coding gene	gene with protein product						12435584	Standard	XM_005262367		Approved	RP1-299I16, PGR17	uc004ezu.1	Q8IZF6	OTTHUMG00000022508	ENST00000394143.1:c.1103C>A	X.37:g.135426968C>A	ENSP00000377699:p.Pro368His	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	57	57	1	NM_153834	A2A2J1|A2A2J2|Q5EGP2|Q86SM6	Missense_Mutation	SNP	ENST00000394143.1	37	CCDS35409.1	706	0.4255575647980711	138	0.3689839572192513	80	0.27972027972027974	76	0.15702479338842976	186	0.3174061433447099	c	2.747	-0.260836	0.05791	0.542634	0.475624	ENSG00000156920	ENST00000394143;ENST00000370652;ENST00000412101;ENST00000287534;ENST00000394141	T;T;T;T;T	0.29397	1.61;1.61;1.57;1.71;1.57	3.95	2.08	0.27032	.	.	.	.	.	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	D;P;P	0.55605	0.972;0.924;0.875	P;P;B	0.49047	0.599;0.46;0.271	T	0.44544	-0.9321	8	0.66056	D	0.02	.	8.6564	0.34066	0.3924:0.6076:0.0:0.0	rs5930931;rs58573078;rs5930931	305;163;368	Q8IZF6-2;Q8IZF6-3;Q8IZF6	.;.;GP112_HUMAN	H	368;368;163;305;163	ENSP00000377699:P368H;ENSP00000359686:P368H;ENSP00000416526:P163H;ENSP00000287534:P305H;ENSP00000377697:P163H	ENSP00000287534:P305H	P	+	2	0	GPR112	135254634	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	0.303000	0.19210	0.238000	0.21222	-0.519000	0.04390	CCT	0|0.025;A|0.455	0.455	strong		0.368	GPR112-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000286639.1		
MGAM	8972	hgsc.bcm.edu	37	7	141705413	141705413	+	Missense_Mutation	SNP	T	T	C	rs201144916	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:141705413T>C	ENST00000549489.2	+	2	178	c.83T>C	c.(82-84)aTt>aCt	p.I28T	MGAM_ENST00000475668.2_Missense_Mutation_p.I28T	NM_004668.2	NP_004659.2	O43451	MGA_HUMAN	maltase-glucoamylase (alpha-glucosidase)	28					carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)|starch catabolic process (GO:0005983)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|amylase activity (GO:0016160)|carbohydrate binding (GO:0030246)|catalytic activity (GO:0003824)|glucan 1,4-alpha-glucosidase activity (GO:0004339)|maltose alpha-glucosidase activity (GO:0032450)			cervix(1)|endometrium(1)|large_intestine(4)|lung(3)|ovary(2)|skin(2)	13	Melanoma(164;0.0272)				Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	ATCATCAGTATTGTTCTAATT	0.358													T|||	3	0.000599042	0.0	0.0	5008	,	,		17122	0.0		0.002	False		,,,				2504	0.001				p.I28T		Atlas-SNP	.											.	MGAM	767	.	0			c.T83C						PASS	.	T	THR/ILE	1,3713		0,1,1856	114.0	107.0	109.0		83	3.4	0.0	7		109	34,8168		0,34,4067	yes	missense	MGAM	NM_004668.2	89	0,35,5923	CC,CT,TT		0.4145,0.0269,0.2937	benign	28/1858	141705413	35,11881	1857	4101	5958	SO:0001583	missense	8972	exon2			TCAGTATTGTTCT	AF016833	CCDS47727.1	7q34	2012-10-03			ENSG00000257335	ENSG00000257335			7043	protein-coding gene	gene with protein product		154360				9446624	Standard	NM_004668		Approved	MGA	uc003vwy.3	O43451	OTTHUMG00000158395	ENST00000549489.2:c.83T>C	7.37:g.141705413T>C	ENSP00000447378:p.Ile28Thr	Somatic	242	0	0		WXS	Illumina HiSeq	Phase_I	163	62	0.380368	NM_004668	Q0VAX6|Q75ME7|Q86UM5	Missense_Mutation	SNP	ENST00000549489.2	37	CCDS47727.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	T	3.485	-0.105005	0.06967	2.69E-4	0.004145	ENSG00000257335	ENST00000465654;ENST00000549489;ENST00000497673;ENST00000475668	T;D;T	0.90069	-1.05;-2.61;0.4	4.52	3.37	0.38596	.	1.029010	0.07737	N	0.946222	D	0.85813	0.5784	L	0.55213	1.73	0.09310	N	1	B	0.27498	0.18	B	0.25405	0.06	T	0.75932	-0.3143	10	0.72032	D	0.01	.	6.8524	0.24022	0.0:0.1028:0.0:0.8972	.	28	O43451	MGA_HUMAN	T	28	ENSP00000419372:I28T;ENSP00000447378:I28T;ENSP00000417103:I28T	ENSP00000373973:I28T	I	+	2	0	MGAM	141351882	0.001000	0.12720	0.001000	0.08648	0.022000	0.10575	0.742000	0.26216	1.055000	0.40461	0.533000	0.62120	ATT	T|0.999;C|0.001	0.001	strong		0.358	MGAM-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000351244.3		
TEKT3	64518	hgsc.bcm.edu	37	17	15234895	15234895	+	Missense_Mutation	SNP	C	C	T	rs7226363	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:15234895C>T	ENST00000395930.1	-	3	194	c.8G>A	c.(7-9)cGt>cAt	p.R3H	TEKT3_ENST00000338696.2_Missense_Mutation_p.R3H	NM_031898.2	NP_114104.1	Q9BXF9	TEKT3_HUMAN	tektin 3	3			R -> H (in dbSNP:rs7226363).		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)		ACAACCTACACGTTCCATGAT	0.403													C|||	977	0.195088	0.1513	0.1686	5008	,	,		15690	0.2212		0.2356	False		,,,				2504	0.2045				p.R3H		Atlas-SNP	.											.	TEKT3	64	.	0			c.G8A						PASS	.	C	HIS/ARG	696,3710	290.1+/-280.8	44,608,1551	71.0	67.0	68.0		8	-11.0	0.0	17	dbSNP_116	68	2077,6523	359.3+/-331.5	269,1539,2492	yes	missense	TEKT3	NM_031898.2	29	313,2147,4043	TT,TC,CC		24.1512,15.7966,21.3209	benign	3/491	15234895	2773,10233	2203	4300	6503	SO:0001583	missense	64518	exon3			CCTACACGTTCCA	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.8G>A	17.37:g.15234895C>T	ENSP00000379263:p.Arg3His	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	38	18	0.473684	NM_031898	B2RAS7|D3DTT0|Q8N5R5|Q96M48	Missense_Mutation	SNP	ENST00000395930.1	37	CCDS11169.1	436	0.19963369963369965	70	0.14227642276422764	66	0.18232044198895028	141	0.2465034965034965	159	0.20976253298153033	C	8.891	0.954112	0.18431	0.157966	0.241512	ENSG00000125409	ENST00000395930;ENST00000338696;ENST00000536146;ENST00000539316;ENST00000543896	T;T;T;T;T	0.42513	4.15;4.15;1.56;1.56;0.97	5.51	-11.0	0.00169	.	0.900938	0.09728	N	0.763471	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.28350	0.208	B	0.13407	0.009	T	0.13255	-1.0516	9	0.38643	T	0.18	0.0046	1.0096	0.01495	0.3388:0.2037:0.2856:0.1719	rs7226363;rs52810686;rs61496150;rs7226363	3	Q9BXF9	TEKT3_HUMAN	H	3	ENSP00000379263:R3H;ENSP00000343995:R3H;ENSP00000446111:R3H;ENSP00000439713:R3H;ENSP00000444180:R3H	ENSP00000343995:R3H	R	-	2	0	TEKT3	15175620	0.006000	0.16342	0.000000	0.03702	0.001000	0.01503	0.810000	0.27183	-2.238000	0.00712	-0.878000	0.02970	CGT	C|0.794;T|0.206	0.206	strong		0.403	TEKT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130385.2	NM_031898	
ADCY10	55811	hgsc.bcm.edu	37	1	167849414	167849414	+	Silent	SNP	A	A	G	rs203849	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:167849414A>G	ENST00000367851.4	-	11	1339	c.1155T>C	c.(1153-1155)ggT>ggC	p.G385G	ADCY10_ENST00000545172.1_Silent_p.G232G|ADCY10_ENST00000367848.1_Silent_p.G293G	NM_018417.4	NP_060887.2	Q96PN6	ADCYA_HUMAN	adenylate cyclase 10 (soluble)	385	Guanylate cyclase 2. {ECO:0000255|PROSITE-ProRule:PRU00099}.				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)	p.G385G(1)		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						CACTGGCAACACCGATGGATA	0.483													G|||	2470	0.493211	0.6687	0.4597	5008	,	,		19729	0.3224		0.504	False		,,,				2504	0.4448				p.G385G		Atlas-SNP	.											ADCY10,NS,carcinoma,0,1	ADCY10	175	1	1	Substitution - coding silent(1)	stomach(1)	c.T1155C						scavenged	.	G	,	2826,1580	492.2+/-362.3	903,1020,280	66.0	59.0	61.0		696,1155	-1.5	0.1	1	dbSNP_79	61	4122,4476	585.4+/-391.9	1002,2118,1179	yes	coding-synonymous,coding-synonymous	ADCY10	NM_001167749.1,NM_018417.4	,	1905,3138,1459	GG,GA,AA		47.9414,35.8602,46.5703	,	232/1458,385/1611	167849414	6948,6056	2203	4299	6502	SO:0001819	synonymous_variant	55811	exon11			GGCAACACCGATG	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.1155T>C	1.37:g.167849414A>G		Somatic	196	3	0.0153061		WXS	Illumina HiSeq	Phase_I	152	68	0.447368	NM_018417	B4DZF0|F5GWS5|O95558|Q5R329|Q5R330|Q8WXV4|Q9NNX0	Silent	SNP	ENST00000367851.4	37	CCDS1265.1																																																																																			G|0.516;N|0.000	0.516	strong		0.483	ADCY10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083663.1	NM_018417	
OBSCN	84033	hgsc.bcm.edu	37	1	228505727	228505727	+	Missense_Mutation	SNP	C	C	T	rs3795800	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:228505727C>T	ENST00000422127.1	+	53	14028	c.13984C>T	c.(13984-13986)Cgc>Tgc	p.R4662C	OBSCN_ENST00000284548.11_Missense_Mutation_p.R4662C|OBSCN_ENST00000570156.2_Missense_Mutation_p.R5619C|OBSCN_ENST00000366709.4_Missense_Mutation_p.R1781C|OBSCN_ENST00000366707.4_Missense_Mutation_p.R2296C	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	4662	Ig-like 47.		R -> C (in dbSNP:rs3795800).		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)				GGGAATGGAGCGCATCCAGCC	0.627													c|||	432	0.086262	0.0166	0.0115	5008	,	,		17760	0.3165		0.0258	False		,,,				2504	0.0583				p.R5619C		Atlas-SNP	.											.	OBSCN	2142	.	0			c.C16855T						PASS	.		CYS/ARG,CYS/ARG	76,4206		2,72,2067	86.0	96.0	93.0		13984,13984	0.2	0.9	1	dbSNP_107	93	158,8324		0,158,4083	yes	missense,missense	OBSCN	NM_001098623.1,NM_052843.2	180,180	2,230,6150	TT,TC,CC		1.8628,1.7749,1.8333	probably-damaging,probably-damaging	4662/7969,4662/6621	228505727	234,12530	2141	4241	6382	SO:0001583	missense	84033	exon64			ATGGAGCGCATCC	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.13984C>T	1.37:g.228505727C>T	ENSP00000409493:p.Arg4662Cys	Somatic	212	0	0		WXS	Illumina HiSeq	Phase_I	176	83	0.471591	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	231	0.10576923076923077	11	0.022357723577235773	5	0.013812154696132596	190	0.3321678321678322	25	0.032981530343007916	c	10.17	1.277083	0.23307	0.017749	0.018628	ENSG00000154358	ENST00000284548;ENST00000422127;ENST00000366707;ENST00000366709	T;T;T;T	0.67865	-0.29;-0.29;-0.29;-0.29	4.51	0.197	0.15164	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	1.111860	0.06822	N	0.792402	T	0.00012	0.0000	M	0.64170	1.965	0.46749	P	8.129999999999526E-4	B;B	0.16166	0.016;0.016	B;B	0.10450	0.005;0.003	T	0.18116	-1.0347	9	0.62326	D	0.03	.	3.6253	0.08111	0.1154:0.4771:0.2488:0.1586	rs3795800;rs3795800	4662;4662	Q5VST9;Q5VST9-3	OBSCN_HUMAN;.	C	4662;4662;2296;1781	ENSP00000284548:R4662C;ENSP00000409493:R4662C;ENSP00000355668:R2296C;ENSP00000355670:R1781C	ENSP00000284548:R4662C	R	+	1	0	OBSCN	226572350	0.000000	0.05858	0.947000	0.38551	0.125000	0.20455	-0.360000	0.07622	0.181000	0.19994	0.479000	0.44913	CGC	C|0.898;T|0.102	0.102	strong		0.627	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
MUC6	4588	hgsc.bcm.edu	37	11	1027995	1027995	+	Missense_Mutation	SNP	G	G	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:1027995G>C	ENST00000421673.2	-	15	1868	c.1818C>G	c.(1816-1818)caC>caG	p.H606Q		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming	606	VWFD 2. {ECO:0000255|PROSITE- ProRule:PRU00580}.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)	extracellular matrix structural constituent (GO:0005201)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(8)|kidney(10)|large_intestine(6)|lung(43)|ovary(4)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	80		all_cancers(49;3.3e-08)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		all cancers(45;1.24e-24)|BRCA - Breast invasive adenocarcinoma(625;0.00031)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		TCACTGTGGCGTGGCACCTCT	0.667																																					p.H606Q		Atlas-SNP	.											.	MUC6	408	.	0			c.C1818G						PASS	.						29.0	34.0	32.0					11																	1027995		2115	4236	6351	SO:0001583	missense	4588	exon15			TGTGGCGTGGCAC	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.1818C>G	11.37:g.1027995G>C	ENSP00000406861:p.His606Gln	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	110	17	0.154545	NM_005961	O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	Missense_Mutation	SNP	ENST00000421673.2	37	CCDS44513.1	.	.	.	.	.	.	.	.	.	.	G	7.821	0.717831	0.15372	.	.	ENSG00000184956	ENST00000421673	T	0.79845	-1.31	4.93	-2.13	0.07144	von Willebrand factor, type D domain (1);Uncharacterised domain, cysteine-rich (2);	0.000000	0.31847	U	0.006963	D	0.85575	0.5728	M	0.86420	2.815	0.18873	N	0.999982	D	0.61080	0.989	D	0.66351	0.943	T	0.76277	-0.3018	10	0.87932	D	0	.	3.0196	0.06071	0.3712:0.1112:0.4057:0.112	.	606	Q6W4X9	MUC6_HUMAN	Q	606	ENSP00000406861:H606Q	ENSP00000406861:H606Q	H	-	3	2	MUC6	1017995	0.000000	0.05858	0.008000	0.14137	0.098000	0.18820	-0.761000	0.04751	-0.607000	0.05738	-1.564000	0.00881	CAC	.	.	none		0.667	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382120.2	XM_290540	
SNX7	51375	hgsc.bcm.edu	37	1	99164434	99164434	+	Silent	SNP	G	G	A	rs6577322	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:99164434G>A	ENST00000306121.3	+	6	1020	c.1011G>A	c.(1009-1011)gaG>gaA	p.E337E	SNX7_ENST00000370189.5_Silent_p.E273E|SNX7_ENST00000529992.1_Silent_p.E282E	NM_015976.4	NP_057060.2	Q9UNH6	SNX7_HUMAN	sorting nexin 7	273					apoptotic process (GO:0006915)|intracellular protein transport (GO:0006886)	cytoplasmic vesicle (GO:0031410)|endosome (GO:0005768)|membrane (GO:0016020)	phosphatidylinositol binding (GO:0035091)			endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(5)|ovary(2)	13		all_epithelial(167;7.64e-07)|all_lung(203;0.0006)|Lung NSC(277;0.00137)		Epithelial(280;0.0521)|all cancers(265;0.0687)|COAD - Colon adenocarcinoma(174;0.15)|Lung(183;0.207)|Colorectal(170;0.234)		TTGTACATGAGTACGTGCTTT	0.418													G|||	1090	0.217652	0.2088	0.2781	5008	,	,		16727	0.0595		0.2654	False		,,,				2504	0.3006				p.E337E		Atlas-SNP	.											.	SNX7	76	.	0			c.G1011A						PASS	.	G	,	964,3442	361.9+/-315.9	100,764,1339	108.0	95.0	99.0		1011,846	1.0	1.0	1	dbSNP_116	99	2519,6081	411.3+/-350.5	362,1795,2143	no	coding-synonymous,coding-synonymous	SNX7	NM_015976.4,NM_152238.3	,	462,2559,3482	AA,AG,GG		29.2907,21.8793,26.7799	,	337/452,282/397	99164434	3483,9523	2203	4300	6503	SO:0001819	synonymous_variant	51375	exon6			ACATGAGTACGTG	AF121857	CCDS755.2, CCDS756.1, CCDS756.2	1p21	2008-05-22			ENSG00000162627	ENSG00000162627		"""Sorting nexins"""	14971	protein-coding gene	gene with protein product		614904					Standard	NM_015976		Approved		uc010ouc.2	Q9UNH6	OTTHUMG00000010723	ENST00000306121.3:c.1011G>A	1.37:g.99164434G>A		Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	174	93	0.534483	NM_015976	A8KAF3|D3DT50|Q53FQ3|Q5VT09|Q5VT10|Q86U82|Q8WVD4|Q96FW9|Q9Y3Z7	Silent	SNP	ENST00000306121.3	37	CCDS755.2																																																																																			G|0.762;A|0.238	0.238	strong		0.418	SNX7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029609.2		
PTCH1	5727	hgsc.bcm.edu	37	9	98244242	98244242	+	Silent	SNP	T	T	C	rs1805154	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:98244242T>C	ENST00000331920.6	-	5	1034	c.735A>G	c.(733-735)acA>acG	p.T245T	PTCH1_ENST00000430669.2_Silent_p.T179T|PTCH1_ENST00000468211.2_Silent_p.T179T|PTCH1_ENST00000375274.2_Silent_p.T244T|PTCH1_ENST00000418258.1_Silent_p.T94T|PTCH1_ENST00000429896.2_Silent_p.T94T|PTCH1_ENST00000437951.1_Silent_p.T179T|PTCH1_ENST00000421141.1_Silent_p.T94T|PTCH1_ENST00000548379.1_5'UTR	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	91	0	0		WXS	Illumina HiSeq	Phase_I	94	42	0.446809	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	
CLCA2	9635	hgsc.bcm.edu	37	1	86891073	86891073	+	Missense_Mutation	SNP	G	G	A	rs11580625	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:86891073G>A	ENST00000370565.4	+	2	400	c.238G>A	c.(238-240)Gta>Ata	p.V80I		NM_006536.5	NP_006527.1	Q9UQC9	CLCA2_HUMAN	chloride channel accessory 2	80	Metalloprotease domain. {ECO:0000250|UniProtKB:A8K7I4}.		V -> I (in dbSNP:rs11580625).		cell adhesion (GO:0007155)|transport (GO:0006810)	cell junction (GO:0030054)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	chloride channel activity (GO:0005254)|ligand-gated ion channel activity (GO:0015276)			NS(2)|breast(1)|endometrium(1)|kidney(3)|large_intestine(9)|lung(18)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|stomach(1)	42		Lung NSC(277;0.238)		all cancers(265;0.0233)|Epithelial(280;0.0452)		CAAGAGAAGAGTATTTTTCAG	0.303													G|||	82	0.0163738	0.0045	0.0216	5008	,	,		15704	0.0		0.0517	False		,,,				2504	0.0092				p.V80I	Melanoma(157;1000 1898 5363 5664 48018)|Ovarian(88;135 1366 2838 28875 34642)	Atlas-SNP	.											.	CLCA2	102	.	0			c.G238A						PASS	.	G	ILE/VAL	37,4367	37.6+/-69.7	1,35,2166	45.0	49.0	48.0		238	3.1	1.0	1	dbSNP_120	48	361,8207	116.3+/-176.0	12,337,3935	yes	missense	CLCA2	NM_006536.5	29	13,372,6101	AA,AG,GG		4.2134,0.8401,3.0681	possibly-damaging	80/944	86891073	398,12574	2202	4284	6486	SO:0001583	missense	9635	exon2			AGAAGAGTATTTT		CCDS708.1	1p22.3	2012-02-26	2009-01-29		ENSG00000137975	ENSG00000137975			2016	protein-coding gene	gene with protein product		604003	"""chloride channel, calcium activated, family member 2"", ""chloride channel regulator 2"""				Standard	NM_006536		Approved	CLCRG2	uc001dlr.4	Q9UQC9	OTTHUMG00000010256	ENST00000370565.4:c.238G>A	1.37:g.86891073G>A	ENSP00000359596:p.Val80Ile	Somatic	193	0	0		WXS	Illumina HiSeq	Phase_I	170	82	0.482353	NM_006536	A8K2T3|Q9Y6N2	Missense_Mutation	SNP	ENST00000370565.4	37	CCDS708.1	48	0.02197802197802198	1	0.0020325203252032522	8	0.022099447513812154	0	0.0	39	0.051451187335092345	G	16.97	3.268510	0.59540	0.008401	0.042134	ENSG00000137975	ENST00000370565;ENST00000439777	T	0.12255	2.7	5.93	3.08	0.35506	Chloride channel calcium-activated (1);	0.438333	0.23265	N	0.050093	T	0.04318	0.0119	M	0.66939	2.045	0.31514	N	0.663187	B	0.13594	0.008	B	0.16289	0.015	T	0.37033	-0.9723	10	0.19147	T	0.46	-4.1577	4.4784	0.11755	0.2942:0.0:0.5286:0.1772	rs11580625;rs11580625	80	Q9UQC9	CLCA2_HUMAN	I	80	ENSP00000359596:V80I	ENSP00000359596:V80I	V	+	1	0	CLCA2	86663661	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	0.651000	0.24873	0.429000	0.26202	-0.136000	0.14681	GTA	G|0.969;A|0.031	0.031	strong		0.303	CLCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028284.1	NM_006536	
AHNAK2	113146	hgsc.bcm.edu	37	14	105415497	105415497	+	Silent	SNP	T	T	C	rs201263008	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:105415497T>C	ENST00000333244.5	-	7	6410	c.6291A>G	c.(6289-6291)aaA>aaG	p.K2097K	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	2097						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)			TTAGGTCCAGTTTGGGGCCCT	0.602																																					p.K2097K		Atlas-SNP	.											AHNAK2_ENST00000333244,NS,carcinoma,0,1	AHNAK2	719	1	0			c.A6291G						PASS	.	C		317,3343		8,301,1521	129.0	88.0	104.0		6291	-7.9	0.0	14	dbSNP_134	104	264,5546		7,250,2648	no	coding-synonymous	AHNAK2	NM_138420.2		15,551,4169	CC,CT,TT		4.5439,8.6612,6.1352		2097/5796	105415497	581,8889	1830	2905	4735	SO:0001819	synonymous_variant	113146	exon7			GTCCAGTTTGGGG	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.6291A>G	14.37:g.105415497T>C		Somatic	0	0	.		WXS	Illumina HiSeq	Phase_I	109	50	0.458716	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Silent	SNP	ENST00000333244.5	37	CCDS45177.1																																																																																			T|0.948;C|0.052	0.052	strong		0.602	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
TGM4	7047	hgsc.bcm.edu	37	3	44943104	44943104	+	Missense_Mutation	SNP	G	G	C	rs937838	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:44943104G>C	ENST00000296125.4	+	7	814	c.746G>C	c.(745-747)aGt>aCt	p.S249T	RP11-272D20.2_ENST00000427258.1_RNA	NM_003241.3	NP_003232.2	P49221	TGM4_HUMAN	transglutaminase 4	249			S -> T (in dbSNP:rs937838).		mating plug formation (GO:0042628)|peptide cross-linking (GO:0018149)	cytoplasm (GO:0005737)|extracellular matrix (GO:0031012)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)	metal ion binding (GO:0046872)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)	p.S249T(1)		NS(1)|breast(1)|endometrium(2)|large_intestine(9)|lung(21)|ovary(2)|stomach(1)|upper_aerodigestive_tract(1)	38				BRCA - Breast invasive adenocarcinoma(193;0.00963)|KIRC - Kidney renal clear cell carcinoma(197;0.0546)|Kidney(197;0.0686)	L-Glutamine(DB00130)	TGGACAGGCAGTGCCCCGATC	0.567													G|||	352	0.0702875	0.0552	0.1225	5008	,	,		20649	0.0268		0.0855	False		,,,				2504	0.0828				p.S249T		Atlas-SNP	.											TGM4,NS,carcinoma,0,1	TGM4	82	1	1	Substitution - Missense(1)	stomach(1)	c.G746C						PASS	.	G	THR/SER	263,4143	149.2+/-183.4	10,243,1950	119.0	108.0	112.0		746	2.8	0.0	3	dbSNP_86	112	781,7819	183.5+/-231.7	33,715,3552	yes	missense	TGM4	NM_003241.3	58	43,958,5502	CC,CG,GG		9.0814,5.9691,8.0271	probably-damaging	249/685	44943104	1044,11962	2203	4300	6503	SO:0001583	missense	7047	exon7			CAGGCAGTGCCCC	BC007003	CCDS2723.1	3p22-p21.33	2013-05-02	2013-05-02		ENSG00000163810	ENSG00000163810	2.3.2.13	"""Transglutaminases"""	11780	protein-coding gene	gene with protein product		600585	"""transglutaminase 4 (prostate)"""			7665178, 7916568	Standard	NM_003241		Approved	TGP	uc003coc.4	P49221	OTTHUMG00000133096	ENST00000296125.4:c.746G>C	3.37:g.44943104G>C	ENSP00000296125:p.Ser249Thr	Somatic	195	0	0		WXS	Illumina HiSeq	Phase_I	177	79	0.446328	NM_003241	Q16707|Q96QN4	Missense_Mutation	SNP	ENST00000296125.4	37	CCDS2723.1	149	0.06822344322344322	26	0.052845528455284556	43	0.11878453038674033	14	0.024475524475524476	66	0.0870712401055409	G	19.07	3.755813	0.69648	0.059691	0.090814	ENSG00000163810	ENST00000296125	T	0.57907	0.37	2.84	2.84	0.33178	.	0.000000	0.52532	U	0.000062	T	0.03651	0.0104	M	0.89904	3.07	0.20307	P	0.9999149955	D	0.76494	0.999	D	0.91635	0.999	T	0.61212	-0.7108	9	0.87932	D	0	.	14.4392	0.67303	0.0:0.0:1.0:0.0	rs937838;rs52797165;rs937838	249	P49221	TGM4_HUMAN	T	249	ENSP00000296125:S249T	ENSP00000296125:S249T	S	+	2	0	TGM4	44918108	1.000000	0.71417	0.002000	0.10522	0.015000	0.08874	8.226000	0.89785	1.523000	0.49018	0.563000	0.77884	AGT	G|0.924;C|0.076	0.076	strong		0.567	TGM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256755.2	NM_003241	
MSANTD1	345222	hgsc.bcm.edu	37	4	3257593	3257593	+	Silent	SNP	C	C	T	rs362287	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:3257593C>T	ENST00000438480.2	+	3	2485	c.738C>T	c.(736-738)cgC>cgT	p.R246R	MSANTD1_ENST00000507492.1_Silent_p.R233R|MSANTD1_ENST00000510580.1_Silent_p.R246R	NM_001042690.1	NP_001036155.1	Q6ZTZ1	MSD1_HUMAN	Myb/SANT-like DNA-binding domain containing 1	246										endometrium(1)|lung(2)	3						AGGTGCGCCGCGTGCTGGACC	0.667													C|||	1288	0.257188	0.0802	0.3069	5008	,	,		14882	0.3343		0.3787	False		,,,				2504	0.2566				p.R246R		Atlas-SNP	.											.	MSANTD1	14	.	0			c.C738T						PASS	.	C		442,3382		40,362,1510	7.0	8.0	8.0		738	-0.3	1.0	4	dbSNP_79	8	2174,5164		319,1536,1814	no	coding-synonymous	C4orf44	NM_001042690.1		359,1898,3324	TT,TC,CC		29.6266,11.5586,23.4367		246/279	3257593	2616,8546	1912	3669	5581	SO:0001819	synonymous_variant	345222	exon3			GCGCCGCGTGCTG		CCDS47003.1	4p16.2	2012-03-02	2012-03-02	2012-03-02	ENSG00000188981	ENSG00000188981			33741	protein-coding gene	gene with protein product			"""chromosome 4 open reading frame 44"""	C4orf44			Standard	NM_001042690		Approved	LOC345222	uc003ggs.3	Q6ZTZ1	OTTHUMG00000159977	ENST00000438480.2:c.738C>T	4.37:g.3257593C>T		Somatic	2	0	0		WXS	Illumina HiSeq	Phase_I	19	10	0.526316	NM_001042690	C9J6V0	Silent	SNP	ENST00000438480.2	37	CCDS47003.1																																																																																			C|0.700;T|0.300	0.300	strong		0.667	MSANTD1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370924.1	NM_001012982	
MYH1	4619	hgsc.bcm.edu	37	17	10401064	10401064	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:10401064C>A	ENST00000226207.5	-	31	4446	c.4352G>T	c.(4351-4353)aGg>aTg	p.R1451M	CTC-297N7.11_ENST00000587182.2_RNA|RP11-799N11.1_ENST00000399342.2_RNA|RP11-799N11.1_ENST00000581304.1_RNA	NM_005963.3	NP_005954.3	P12882	MYH1_HUMAN	myosin, heavy chain 1, skeletal muscle, adult	1451				R -> T (in Ref. 4; CAA27380). {ECO:0000305}.	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						ATCAAAGTTCCTTTGCTTTTT	0.443																																					p.R1451M		Atlas-SNP	.											.	MYH1	403	.	0			c.G4352T						PASS	.						119.0	117.0	118.0					17																	10401064		2203	4300	6503	SO:0001583	missense	4619	exon31			AAGTTCCTTTGCT		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.4352G>T	17.37:g.10401064C>A	ENSP00000226207:p.Arg1451Met	Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	155	40	0.258065	NM_005963	Q14CA4|Q9Y622	Missense_Mutation	SNP	ENST00000226207.5	37	CCDS11155.1	.	.	.	.	.	.	.	.	.	.	C	16.60	3.169376	0.57584	.	.	ENSG00000109061	ENST00000226207;ENST00000379814	T	0.80393	-1.37	5.65	5.65	0.86999	Myosin tail (1);	0.138860	0.32593	U	0.005888	D	0.91686	0.7372	H	0.96748	3.875	0.41280	D	0.986904	D	0.71674	0.998	D	0.70016	0.967	D	0.92699	0.6173	10	0.87932	D	0	.	7.7121	0.28684	0.0:0.8062:0.0:0.1938	.	1451	P12882	MYH1_HUMAN	M	1451;540	ENSP00000226207:R1451M	ENSP00000226207:R1451M	R	-	2	0	MYH1	10341789	0.929000	0.31497	1.000000	0.80357	0.903000	0.53119	1.648000	0.37271	2.811000	0.96726	0.655000	0.94253	AGG	.	.	none		0.443	MYH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252725.1	NM_005963	
KLHL32	114792	hgsc.bcm.edu	37	6	97423931	97423931	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:97423931G>A	ENST00000369261.4	+	3	445	c.82G>A	c.(82-84)Gtc>Atc	p.V28I	KLHL32_ENST00000544166.1_5'UTR|KLHL32_ENST00000539200.1_Missense_Mutation_p.V28I|KLHL32_ENST00000536676.1_Missense_Mutation_p.V28I	NM_052904.3	NP_443136.2	Q96NJ5	KLH32_HUMAN	kelch-like family member 32	28										breast(2)|endometrium(3)|kidney(4)|large_intestine(9)|lung(13)|ovary(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	38		all_cancers(76;1.19e-06)|Acute lymphoblastic leukemia(125;5.83e-10)|all_hematologic(75;3.67e-07)|all_epithelial(107;0.00778)|Colorectal(196;0.122)		BRCA - Breast invasive adenocarcinoma(108;0.0558)		CAATGACAGTGTCCTGGCAGC	0.493																																					p.V28I		Atlas-SNP	.											.	KLHL32	85	.	0			c.G82A						PASS	.						82.0	69.0	73.0					6																	97423931		2203	4300	6503	SO:0001583	missense	114792	exon3			GACAGTGTCCTGG	AB067487	CCDS5038.1, CCDS69154.1, CCDS69155.1, CCDS75495.1	6q16.3	2013-02-22	2013-02-22	2007-01-09	ENSG00000186231	ENSG00000186231		"""Kelch-like"", ""BTB/POZ domain containing"""	21221	protein-coding gene	gene with protein product			"""BTB and kelch domain containing 5"", ""KIAA1900"", ""kelch-like 32 (Drosophila)"""	BKLHD5, KIAA1900			Standard	NM_052904		Approved		uc010kcm.1	Q96NJ5	OTTHUMG00000015247	ENST00000369261.4:c.82G>A	6.37:g.97423931G>A	ENSP00000358265:p.Val28Ile	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	83	23	0.277108	NM_052904	B7Z346|B7Z4E2|E1P528|Q5THT0|Q96PY7	Missense_Mutation	SNP	ENST00000369261.4	37	CCDS5038.1	.	.	.	.	.	.	.	.	.	.	G	21.7	4.181059	0.78677	.	.	ENSG00000186231	ENST00000369261;ENST00000536676;ENST00000539200;ENST00000369254	T;T;T;T	0.70749	-0.51;1.97;1.97;-0.51	5.14	5.14	0.70334	BTB/POZ fold (2);	0.055908	0.64402	N	0.000001	T	0.61438	0.2347	N	0.24115	0.695	0.80722	D	1	P;P;B;P	0.50156	0.517;0.932;0.397;0.9	B;P;B;B	0.61592	0.227;0.891;0.281;0.323	T	0.57740	-0.7759	10	0.07325	T	0.83	.	18.7846	0.91949	0.0:0.0:1.0:0.0	.	28;28;28;28	B7Z4E2;B7Z346;Q96NJ5;Q6IQ08	.;.;KLH32_HUMAN;.	I	28	ENSP00000358265:V28I;ENSP00000440382:V28I;ENSP00000441527:V28I;ENSP00000358258:V28I	ENSP00000358258:V28I	V	+	1	0	KLHL32	97530652	1.000000	0.71417	0.990000	0.47175	0.702000	0.40608	9.263000	0.95617	2.674000	0.91012	0.591000	0.81541	GTC	.	.	none		0.493	KLHL32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041570.1	NM_052904	
VPS53	55275	hgsc.bcm.edu	37	17	526907	526907	+	Missense_Mutation	SNP	G	G	T	rs16954056	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:526907G>T	ENST00000571805.1	-	11	1118	c.982C>A	c.(982-984)Ctt>Att	p.L328I	VPS53_ENST00000446250.2_Missense_Mutation_p.L130I|VPS53_ENST00000574029.1_Intron|VPS53_ENST00000291074.5_Missense_Mutation_p.L299I|VPS53_ENST00000437048.2_Missense_Mutation_p.L328I|VPS53_ENST00000401468.3_Intron|VPS53_ENST00000576149.1_5'UTR			Q5VIR6	VPS53_HUMAN	vacuolar protein sorting 53 homolog (S. cerevisiae)	328			L -> I (in dbSNP:rs16954056).		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)		ATCTTGGCAAGTTCTGCCCTT	0.353													G|||	472	0.0942492	0.0582	0.0821	5008	,	,		17883	0.1855		0.1093	False		,,,				2504	0.0419				p.L328I		Atlas-SNP	.											.	VPS53	109	.	0			c.C982A						PASS	.	G	ILE/LEU,ILE/LEU	291,4115	157.4+/-190.3	11,269,1923	71.0	65.0	67.0		982,895	5.7	1.0	17	dbSNP_123	67	926,7674	205.8+/-248.1	51,824,3425	yes	missense,missense	VPS53	NM_001128159.2,NM_018289.3	5,5	62,1093,5348	TT,TG,GG		10.7674,6.6046,9.3572	probably-damaging,probably-damaging	328/833,299/671	526907	1217,11789	2203	4300	6503	SO:0001583	missense	55275	exon11			TGGCAAGTTCTGC		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.982C>A	17.37:g.526907G>T	ENSP00000459312:p.Leu328Ile	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	82	33	0.402439	NM_001128159	A8K2S8|B3FH42|Q8WYW3|Q9BRR2|Q9BY02|Q9NV25	Missense_Mutation	SNP	ENST00000571805.1	37		295	0.13507326007326007	38	0.07723577235772358	43	0.11878453038674033	133	0.23251748251748253	81	0.10686015831134564	G	29.1	4.978662	0.92982	0.066046	0.107674	ENSG00000141252	ENST00000437048;ENST00000446250;ENST00000291074;ENST00000389040	T;T;T;T	0.50277	1.02;1.02;1.02;0.75	5.7	5.7	0.88788	Vps53-like, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.00073	0.0002	M	0.75777	2.31	0.09310	P	0.999999999760498	D;D;D;D	0.76494	0.999;0.998;0.998;0.998	D;D;D;D	0.71414	0.939;0.953;0.973;0.953	T	0.00069	-1.2138	9	0.72032	D	0.01	-15.2315	18.8293	0.92132	0.0:0.0:1.0:0.0	rs16954056;rs52793939;rs16954056	328;130;328;299	Q5VIR6-4;G3V0H8;Q5VIR6;Q5VIR6-2	.;.;VPS53_HUMAN;.	I	328;130;299;280	ENSP00000401435:L328I;ENSP00000394386:L130I;ENSP00000291074:L299I;ENSP00000373692:L280I	ENSP00000291074:L299I	L	-	1	0	VPS53	473657	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.476000	0.97823	2.683000	0.91414	0.655000	0.94253	CTT	G|0.889;T|0.111	0.111	strong		0.353	VPS53-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000436940.2	NM_018289	
AMPD1	270	hgsc.bcm.edu	37	1	115231254	115231254	+	Missense_Mutation	SNP	G	G	A	rs61752479	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:115231254G>A	ENST00000520113.2	-	3	257	c.242C>T	c.(241-243)cCg>cTg	p.P81L	AMPD1_ENST00000369538.3_Missense_Mutation_p.P77L|AMPD1_ENST00000353928.6_Missense_Mutation_p.P48L			P23109	AMPD1_HUMAN	adenosine monophosphate deaminase 1	81			P -> L (polymorphism; activity comparable to wild-type; dbSNP:rs61752479). {ECO:0000269|PubMed:1631143}.		IMP salvage (GO:0032264)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase metabolic process (GO:0006144)|purine-containing compound salvage (GO:0043101)|response to organic substance (GO:0010033)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	AMP deaminase activity (GO:0003876)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(17)|ovary(3)|pancreas(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	45	all_epithelial(7;7.83e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;4.64e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)	Adenosine monophosphate(DB00131)	ATGAGAAATCGGACAGATCTC	0.473													G|||	195	0.0389377	0.0045	0.0634	5008	,	,		20447	0.001		0.1233	False		,,,				2504	0.0204				p.P81L		Atlas-SNP	.											AMPD1_ENST00000520113,NS,carcinoma,0,2	AMPD1	223	2	0			c.C242T	GRCh37	CM920026	AMPD1	M	rs61752479	PASS	.	G	LEU/PRO,LEU/PRO	103,4303	82.4+/-120.9	2,99,2102	147.0	140.0	142.0		242,230	5.6	1.0	1	dbSNP_129	142	1144,7456	236.7+/-268.8	90,964,3246	yes	missense,missense	AMPD1	NM_000036.2,NM_001172626.1	98,98	92,1063,5348	AA,AG,GG		13.3023,2.3377,9.5879	probably-damaging,probably-damaging	81/781,77/777	115231254	1247,11759	2203	4300	6503	SO:0001583	missense	270	exon3			GAAATCGGACAGA	M60092	CCDS876.1, CCDS876.2, CCDS53349.1	1p13	2010-02-10	2010-02-10		ENSG00000116748	ENSG00000116748	3.5.4.6		468	protein-coding gene	gene with protein product	"""AMPD isoform M"", ""skeletal muscle AMPD"""	102770	"""adenosine monophosphate deaminase 1 (isoform M)"""			1400401	Standard	NM_001172626		Approved	MAD, MADA	uc001efe.2	P23109	OTTHUMG00000011892	ENST00000520113.2:c.242C>T	1.37:g.115231254G>A	ENSP00000430075:p.Pro81Leu	Somatic	222	0	0		WXS	Illumina HiSeq	Phase_I	204	110	0.539216	NM_000036	A8K5N4|B2RAM1|F2Z3B3|Q5TF00|Q5TF02	Missense_Mutation	SNP	ENST00000520113.2	37	CCDS876.2	119	0.05448717948717949	3	0.006097560975609756	31	0.0856353591160221	0	0.0	85	0.11213720316622691	G	19.67	3.871817	0.72180	0.023377	0.133023	ENSG00000116748	ENST00000520113;ENST00000369538;ENST00000353928	T;T;T	0.63744	-0.06;-0.06;-0.06	5.62	5.62	0.85841	.	0.000000	0.85682	D	0.000000	T	0.70859	0.3272	L	0.43152	1.355	0.09310	P	0.9999999999943356	D;D	0.89917	1.0;1.0	D;D	0.97110	0.998;1.0	T	0.72354	-0.4319	9	0.87932	D	0	-11.3019	20.0247	0.97519	0.0:0.0:1.0:0.0	rs61752479	77;48	Q5TF02;P23109	.;AMPD1_HUMAN	L	81;77;48	ENSP00000430075:P81L;ENSP00000358551:P77L;ENSP00000316520:P48L	ENSP00000316520:P48L	P	-	2	0	AMPD1	115032777	1.000000	0.71417	1.000000	0.80357	0.172000	0.22775	9.232000	0.95325	2.804000	0.96469	0.655000	0.94253	CCG	G|0.913;A|0.087	0.087	strong		0.473	AMPD1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000032860.4		
MTERF4	130916	hgsc.bcm.edu	37	2	242035544	242035544	+	Missense_Mutation	SNP	G	G	C	rs2240539	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:242035544G>C	ENST00000391980.2	-	4	1073	c.1015C>G	c.(1015-1017)Ctg>Gtg	p.L339V	MTERFD2_ENST00000495694.1_Intron|MTERFD2_ENST00000464344.2_Intron|MTERFD2_ENST00000406593.1_Missense_Mutation_p.L151V	NM_182501.3	NP_872307.2	Q7Z6M4	MTEF4_HUMAN		339			L -> V (in dbSNP:rs2240539).		rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|mitochondrial large ribosomal subunit (GO:0005762)|mitochondrion (GO:0005739)	rRNA binding (GO:0019843)			endometrium(3)|large_intestine(6)|lung(5)|ovary(1)|skin(2)|urinary_tract(3)	20		all_cancers(19;4.67e-31)|all_epithelial(40;8.67e-13)|Breast(86;0.000141)|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;2.47e-32)|all cancers(36;1.79e-29)|OV - Ovarian serous cystadenocarcinoma(60;2.59e-14)|Kidney(56;3.21e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;2.81e-06)|Lung(119;0.000509)|LUSC - Lung squamous cell carcinoma(224;0.00442)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0886)		tcctcatcCAGACTTGCCCTT	0.498													G|||	523	0.104433	0.1762	0.0951	5008	,	,		21954	0.124		0.0626	False		,,,				2504	0.0368				p.L339V		Atlas-SNP	.											.	MTERFD2	33	.	0			c.C1015G						PASS	.	G	VAL/LEU	813,3593	325.9+/-299.3	83,647,1473	267.0	186.0	213.0		1015	-3.8	0.0	2	dbSNP_98	213	589,8011	156.9+/-210.6	21,547,3732	yes	missense	MTERFD2	NM_182501.3	32	104,1194,5205	CC,CG,GG		6.8488,18.4521,10.7796	benign	339/382	242035544	1402,11604	2203	4300	6503	SO:0001583	missense	130916	exon4			CATCCAGACTTGC																												ENST00000391980.2:c.1015C>G	2.37:g.242035544G>C	ENSP00000375840:p.Leu339Val	Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	138	71	0.514493	NM_182501	A8K6K0|Q9P0E0	Missense_Mutation	SNP	ENST00000391980.2	37	CCDS2544.1	242	0.1108058608058608	90	0.18292682926829268	35	0.09668508287292818	70	0.12237762237762238	47	0.06200527704485488	G	11.69	1.714390	0.30413	0.184521	0.068488	ENSG00000122085	ENST00000391980;ENST00000406593	T;T	0.05649	3.41;3.41	3.71	-3.84	0.04256	.	2.125570	0.02588	N	0.099626	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	0.43814	-0.9368	9	0.42905	T	0.14	-1.5584	1.5814	0.02635	0.1427:0.3269:0.1599:0.3705	rs2240539;rs52817647;rs2240539	339	Q7Z6M4	MTER2_HUMAN	V	339;151	ENSP00000375840:L339V;ENSP00000384998:L151V	ENSP00000241527:L339V	L	-	1	2	MTERFD2	241684217	0.557000	0.26546	0.000000	0.03702	0.075000	0.17131	-0.466000	0.06672	-0.827000	0.04278	0.460000	0.39030	CTG	G|0.889;C|0.111	0.111	strong		0.498	MTERFD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323798.4		
CENPM	79019	hgsc.bcm.edu	37	22	42341934	42341934	+	Silent	SNP	A	A	G	rs35542507	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:42341934A>G	ENST00000215980.5	-	3	300	c.213T>C	c.(211-213)aaT>aaC	p.N71N	CENPM_ENST00000402338.1_Silent_p.N37N|CENPM_ENST00000402420.1_Silent_p.N37N|CENPM_ENST00000407253.3_Silent_p.N71N|CENPM_ENST00000404067.1_Silent_p.N37N	NM_024053.3	NP_076958.1	Q9NSP4	CENPM_HUMAN	centromere protein M	71					mitotic cell cycle (GO:0000278)	cytosol (GO:0005829)|kinetochore (GO:0000776)|nucleus (GO:0005634)		p.N71N(1)		kidney(1)|large_intestine(1)|prostate(1)	3						TGCTGTGAAGATTAACCACAA	0.537													A|||	262	0.0523163	0.0061	0.0605	5008	,	,		20511	0.0635		0.0795	False		,,,				2504	0.0695				p.N71N		Atlas-SNP	.											CENPM,NS,carcinoma,0,1	CENPM	8	1	1	Substitution - coding silent(1)	prostate(1)	c.T213C						PASS	.	A	,	93,4313	75.7+/-113.9	1,91,2111	72.0	63.0	66.0		213,213	0.4	1.0	22	dbSNP_126	66	658,7942	165.8+/-217.9	30,598,3672	no	coding-synonymous,coding-synonymous	CENPM	NM_001002876.1,NM_024053.3	,	31,689,5783	GG,GA,AA		7.6512,2.1108,5.7743	,	71/108,71/181	42341934	751,12255	2203	4300	6503	SO:0001819	synonymous_variant	79019	exon3			GTGAAGATTAACC	BC000705	CCDS14025.1, CCDS46719.1, CCDS46720.1	22q13.2	2013-11-05	2006-06-15	2006-06-15	ENSG00000100162	ENSG00000100162			18352	protein-coding gene	gene with protein product		610152	"""chromosome 22 open reading frame 18"""	C22orf18		16622420, 16622419	Standard	NM_001110215		Approved	Pane1, CENP-M, MGC861	uc003bbn.3	Q9NSP4	OTTHUMG00000151277	ENST00000215980.5:c.213T>C	22.37:g.42341934A>G		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	86	35	0.406977	NM_024053	A7LM22|B1AHQ9|Q6I9W3	Silent	SNP	ENST00000215980.5	37	CCDS14025.1																																																																																			A|0.939;G|0.061	0.061	strong		0.537	CENPM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322058.1	NM_024053	
OR5B3	441608	hgsc.bcm.edu	37	11	58170342	58170342	+	Missense_Mutation	SNP	C	C	T	rs11229411	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:58170342C>T	ENST00000309403.2	-	1	540	c.541G>A	c.(541-543)Gca>Aca	p.A181T		NM_001005469.1	NP_001005469.1	Q8NH48	OR5B3_HUMAN	olfactory receptor, family 5, subfamily B, member 3	181			A -> T (in dbSNP:rs11229411).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.A181T(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(17)|ovary(1)|prostate(1)|skin(2)|stomach(6)|upper_aerodigestive_tract(1)	34	Esophageal squamous(5;0.0027)	Breast(21;0.0778)				ACCATGACTGCTGGAATATCA	0.408													C|||	1453	0.290136	0.3533	0.2695	5008	,	,		23137	0.1448		0.3628	False		,,,				2504	0.2945				p.A181T		Atlas-SNP	.											OR5B3,NS,carcinoma,0,1	OR5B3	65	1	1	Substitution - Missense(1)	stomach(1)	c.G541A						PASS	.	C	THR/ALA	1442,2960	467.6+/-354.9	229,984,988	98.0	91.0	94.0		541	3.0	1.0	11	dbSNP_120	94	3095,5495	473.1+/-368.5	550,1995,1750	yes	missense	OR5B3	NM_001005469.1	58	779,2979,2738	TT,TC,CC		36.0303,32.7578,34.9215	possibly-damaging	181/315	58170342	4537,8455	2201	4295	6496	SO:0001583	missense	441608	exon1			TGACTGCTGGAAT	AB065545	CCDS31549.1	11q12.1	2012-08-09			ENSG00000172769	ENSG00000172769		"""GPCR / Class A : Olfactory receptors"""	8324	protein-coding gene	gene with protein product				OR5B13			Standard	NM_001005469		Approved	OST129	uc010rkf.2	Q8NH48	OTTHUMG00000167516	ENST00000309403.2:c.541G>A	11.37:g.58170342C>T	ENSP00000308270:p.Ala181Thr	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	69	47	0.681159	NM_001005469	Q6IEV6	Missense_Mutation	SNP	ENST00000309403.2	37	CCDS31549.1	656	0.30036630036630035	195	0.39634146341463417	89	0.24585635359116023	95	0.1660839160839161	277	0.3654353562005277	c	13.88	2.369354	0.42003	0.327578	0.360303	ENSG00000172769	ENST00000309403	T	0.00130	8.69	4.05	3.04	0.35103	GPCR, rhodopsin-like superfamily (1);	0.146062	0.31976	N	0.006773	T	0.00012	0.0000	M	0.73962	2.25	0.46564	P	8.979999999999544E-4	D	0.56968	0.978	P	0.59825	0.864	T	0.34976	-0.9807	9	0.87932	D	0	-35.6255	10.4344	0.44426	0.0:0.6318:0.3682:0.0	rs11229411;rs61524907;rs11229411	181	Q8NH48	OR5B3_HUMAN	T	181	ENSP00000308270:A181T	ENSP00000308270:A181T	A	-	1	0	OR5B3	57926918	0.000000	0.05858	0.999000	0.59377	0.105000	0.19272	-0.039000	0.12124	2.264000	0.75181	0.650000	0.86243	GCA	C|0.676;T|0.324	0.324	strong		0.408	OR5B3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394886.1	NM_001005469	
BEND7	222389	hgsc.bcm.edu	37	10	13494594	13494594	+	Silent	SNP	T	T	C	rs2277222	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:13494594T>C	ENST00000396900.2	-	7	1127	c.1128A>G	c.(1126-1128)gtA>gtG	p.V376V	BEND7_ENST00000486542.1_5'UTR|BEND7_ENST00000341083.3_Silent_p.V324V|BEND7_ENST00000396898.2_Silent_p.V389V|BEND7_ENST00000378605.3_Silent_p.V337V			Q8N7W2	BEND7_HUMAN	BEN domain containing 7	376	BEN. {ECO:0000255|PROSITE- ProRule:PRU00784}.					extracellular vesicular exosome (GO:0070062)				breast(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(2)|ovary(2)|prostate(1)|stomach(1)	17						GTAGAATCTGTACCCAATCTC	0.363													T|||	1785	0.35643	0.1218	0.3458	5008	,	,		18852	0.6696		0.3429	False		,,,				2504	0.3722				p.V337V		Atlas-SNP	.											.	BEND7	85	.	0			c.A1011G						PASS	.	T	,	697,3709	291.8+/-281.7	60,577,1566	142.0	143.0	143.0		1011,972	-5.5	0.9	10	dbSNP_100	143	2829,5771	446.0+/-361.1	458,1913,1929	no	coding-synonymous,coding-synonymous	BEND7	NM_001100912.1,NM_152751.2	,	518,2490,3495	CC,CT,TT		32.8953,15.8193,27.1106	,	337/375,324/469	13494594	3526,9480	2203	4300	6503	SO:0001819	synonymous_variant	222389	exon6			AATCTGTACCCAA	BC031618	CCDS7099.1, CCDS41490.1	10p14	2012-11-22	2008-10-03	2008-10-03	ENSG00000165626	ENSG00000165626		"""BEN domain containing"""	23514	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 30"""	C10orf30			Standard	NM_152751		Approved	FLJ40283	uc001imm.2	Q8N7W2	OTTHUMG00000017699	ENST00000396900.2:c.1128A>G	10.37:g.13494594T>C		Somatic	318	0	0		WXS	Illumina HiSeq	Phase_I	255	124	0.486275	NM_001100912	Q5SYY7|Q5SYY8|Q5SYY9|Q8N5T7	Silent	SNP	ENST00000396900.2	37																																																																																				T|0.677;C|0.323	0.323	strong		0.363	BEND7-202	KNOWN	basic	protein_coding	protein_coding		NM_152751	
TMCO4	255104	hgsc.bcm.edu	37	1	20073019	20073019	+	Silent	SNP	C	C	T	rs34281331	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:20073019C>T	ENST00000294543.6	-	9	928	c.687G>A	c.(685-687)gcG>gcA	p.A229A	TMCO4_ENST00000375122.2_Silent_p.A229A|TMCO4_ENST00000375127.1_Silent_p.A229A	NM_181719.4	NP_859070.3	Q5TGY1	TMCO4_HUMAN	transmembrane and coiled-coil domains 4	229						integral component of membrane (GO:0016021)				biliary_tract(1)|breast(2)|endometrium(2)|kidney(1)|lung(11)|skin(1)|upper_aerodigestive_tract(1)	19		Colorectal(325;0.000147)|Renal(390;0.000469)|all_lung(284;0.00519)|Breast(348;0.00526)|Lung NSC(340;0.00544)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0439)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00708)|COAD - Colon adenocarcinoma(152;2.28e-05)|BRCA - Breast invasive adenocarcinoma(304;5.8e-05)|Kidney(64;0.000367)|GBM - Glioblastoma multiforme(114;0.000377)|KIRC - Kidney renal clear cell carcinoma(64;0.00459)|STAD - Stomach adenocarcinoma(196;0.0072)|READ - Rectum adenocarcinoma(331;0.0862)|Lung(427;0.223)		AGCCCAGAGCCGCTGCCCCGG	0.587													C|||	207	0.0413339	0.0242	0.0735	5008	,	,		17314	0.0605		0.0179	False		,,,				2504	0.046				p.A229A		Atlas-SNP	.											.	TMCO4	46	.	0			c.G687A						PASS	.	C		86,4320	68.1+/-105.8	0,86,2117	22.0	22.0	22.0		687	-10.3	0.0	1	dbSNP_126	22	150,8446	66.3+/-128.7	1,148,4149	no	coding-synonymous	TMCO4	NM_181719.4		1,234,6266	TT,TC,CC		1.745,1.9519,1.8151		229/635	20073019	236,12766	2203	4298	6501	SO:0001819	synonymous_variant	255104	exon9			CAGAGCCGCTGCC		CCDS198.1	1p36.13	2008-02-05			ENSG00000162542	ENSG00000162542			27393	protein-coding gene	gene with protein product							Standard	NM_181719		Approved	DKFZp686C23231	uc001bcn.3	Q5TGY1	OTTHUMG00000002697	ENST00000294543.6:c.687G>A	1.37:g.20073019C>T		Somatic	374	1	0.0026738		WXS	Illumina HiSeq	Phase_I	372	185	0.497312	NM_181719	Q5TGY2|Q6MZN5|Q7Z6K6|Q9UQP4|Q9Y3K1	Silent	SNP	ENST00000294543.6	37	CCDS198.1																																																																																			C|0.973;T|0.027	0.027	strong		0.587	TMCO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007658.1	NM_181719	
MLH3	27030	hgsc.bcm.edu	37	14	75513828	75513828	+	Missense_Mutation	SNP	G	G	A	rs175080	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:75513828G>A	ENST00000556740.1	-	1	2566	c.2531C>T	c.(2530-2532)cCt>cTt	p.P844L	MLH3_ENST00000355774.2_Missense_Mutation_p.P844L|MLH3_ENST00000380968.2_5'UTR|MLH3_ENST00000544985.1_5'Flank|MLH3_ENST00000556257.1_Missense_Mutation_p.P844L|MLH3_ENST00000238662.7_Missense_Mutation_p.P844L|MLH3_ENST00000555671.1_5'UTR			Q9UHC1	MLH3_HUMAN	mutL homolog 3	844			P -> L (in dbSNP:rs175080). {ECO:0000269|PubMed:10615123, ECO:0000269|Ref.3}.		ATP catabolic process (GO:0006200)|female meiosis I (GO:0007144)|male meiosis (GO:0007140)|mismatch repair (GO:0006298)|protein localization (GO:0008104)|reciprocal meiotic recombination (GO:0007131)|synaptonemal complex assembly (GO:0007130)	chiasma (GO:0005712)|male germ cell nucleus (GO:0001673)|mismatch repair complex (GO:0032300)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|centromeric DNA binding (GO:0019237)|chromatin binding (GO:0003682)|mismatched DNA binding (GO:0030983)|satellite DNA binding (GO:0003696)|single-stranded DNA binding (GO:0003697)			breast(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(16)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	44				BRCA - Breast invasive adenocarcinoma(234;0.00688)		TCTCAAACTAGGCATCTGTTG	0.388								Mismatch excision repair (MMR)					G|||	1822	0.363818	0.4259	0.3199	5008	,	,		20917	0.1508		0.4563	False		,,,				2504	0.4356				p.P844L		Atlas-SNP	.											.	MLH3	200	.	0			c.C2531T						PASS	.	G	LEU/PRO,LEU/PRO	1776,2630	519.0+/-369.9	353,1070,780	84.0	88.0	87.0		2531,2531	4.1	0.2	14	dbSNP_79	87	3981,4619	549.4+/-385.5	908,2165,1227	yes	missense,missense	MLH3	NM_001040108.1,NM_014381.2	98,98	1261,3235,2007	AA,AG,GG		46.2907,40.3087,44.2642	benign,benign	844/1454,844/1430	75513828	5757,7249	2203	4300	6503	SO:0001583	missense	27030	exon2			AAACTAGGCATCT	AF195657	CCDS9837.1, CCDS32123.1	14q24.3	2014-09-17	2013-09-12			ENSG00000119684			7128	protein-coding gene	gene with protein product		604395	"""mutL (E. coli) homolog 3"", ""mutL homolog 3 (E. coli)"""			10615123	Standard	XR_245681		Approved		uc001xrd.1	Q9UHC1		ENST00000556740.1:c.2531C>T	14.37:g.75513828G>A	ENSP00000452316:p.Pro844Leu	Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	143	69	0.482517	NM_014381	P49751|Q56DK9|Q9P292|Q9UHC0	Missense_Mutation	SNP	ENST00000556740.1	37	CCDS32123.1	784	0.358974358974359	199	0.40447154471544716	132	0.36464088397790057	101	0.17657342657342656	352	0.46437994722955145	G	3.146	-0.175301	0.06421	0.403087	0.462907	ENSG00000119684	ENST00000355774;ENST00000238662;ENST00000556257;ENST00000556740	T;T;T;T	0.81415	-1.43;-1.44;-1.49;-1.43	5.93	4.12	0.48240	.	0.545323	0.19374	N	0.115835	T	0.00012	0.0000	L	0.40543	1.245	0.58432	P	8.000000000008E-6	B;B	0.14438	0.01;0.001	B;B	0.13407	0.009;0.001	T	0.35301	-0.9794	9	0.27785	T	0.31	-1.2119	7.4116	0.27021	0.2991:0.0:0.7009:0.0	rs175080;rs175519;rs52807483;rs175080	844;844	Q9UHC1-2;Q9UHC1	.;MLH3_HUMAN	L	844	ENSP00000348020:P844L;ENSP00000238662:P844L;ENSP00000451540:P844L;ENSP00000452316:P844L	ENSP00000238662:P844L	P	-	2	0	MLH3	74583581	0.017000	0.18338	0.205000	0.23548	0.377000	0.30045	1.590000	0.36654	0.856000	0.35383	0.655000	0.94253	CCT	G|0.586;A|0.414	0.414	strong		0.388	MLH3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415006.1	NM_014381	
MUT	4594	hgsc.bcm.edu	37	6	49412433	49412433	+	Missense_Mutation	SNP	C	C	T	rs1141321	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:49412433C>T	ENST00000274813.3	-	9	1722	c.1595G>A	c.(1594-1596)cGt>cAt	p.R532H		NM_000255.3	NP_000246.2	P22033	MUTA_HUMAN	methylmalonyl CoA mutase	532			R -> H (in dbSNP:rs1141321). {ECO:0000269|PubMed:16281286, ECO:0000269|PubMed:1980486, ECO:0000269|PubMed:2567699, ECO:0000269|PubMed:7912889}.		cellular lipid metabolic process (GO:0044255)|cobalamin metabolic process (GO:0009235)|fatty acid beta-oxidation (GO:0006635)|homocysteine metabolic process (GO:0050667)|post-embryonic development (GO:0009791)|short-chain fatty acid catabolic process (GO:0019626)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	cobalamin binding (GO:0031419)|metal ion binding (GO:0046872)|methylmalonyl-CoA mutase activity (GO:0004494)|modified amino acid binding (GO:0072341)			endometrium(2)|kidney(1)|large_intestine(4)|lung(17)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	30	Lung NSC(77;0.0376)				Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	AGCAAGACAACGTTCAGCCAA	0.428													C|||	1330	0.265575	0.174	0.2104	5008	,	,		16274	0.2063		0.331	False		,,,				2504	0.4223				p.R532H		Atlas-SNP	.											.	MUT	70	.	0			c.G1595A						PASS	.	C	HIS/ARG	929,3477	352.6+/-311.8	88,753,1362	163.0	155.0	158.0		1595	1.4	0.1	6	dbSNP_86	158	3148,5452	479.1+/-370.0	578,1992,1730	yes	missense	MUT	NM_000255.3	29	666,2745,3092	TT,TC,CC		36.6047,21.0849,31.3471	possibly-damaging	532/751	49412433	4077,8929	2203	4300	6503	SO:0001583	missense	4594	exon9			AGACAACGTTCAG		CCDS4924.1	6p21	2012-10-02	2010-04-30		ENSG00000146085	ENSG00000146085	5.4.99.2		7526	protein-coding gene	gene with protein product		609058	"""methylmalonyl Coenzyme A mutase"""			2907507, 9503014	Standard	NM_000255		Approved		uc003ozg.4	P22033	OTTHUMG00000014814	ENST00000274813.3:c.1595G>A	6.37:g.49412433C>T	ENSP00000274813:p.Arg532His	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	78	34	0.435897	NM_000255	A8K953|Q5SYZ3|Q96B11|Q9UD64	Missense_Mutation	SNP	ENST00000274813.3	37	CCDS4924.1	573	0.2623626373626374	94	0.1910569105691057	83	0.2292817679558011	112	0.1958041958041958	284	0.37467018469656993	C	8.081	0.772374	0.16051	0.210849	0.366047	ENSG00000146085	ENST00000274813	D	0.98280	-4.84	5.31	1.44	0.22558	Cobalamin (vitamin B12)-dependent enzyme, catalytic (1);Methylmalonyl-CoA mutase, alpha/beta chain, catalytic (1);Methylmalonyl-CoA mutase, alpha chain, catalytic (1);	0.336740	0.30028	N	0.010596	D	0.95739	0.8614	M	0.78916	2.43	0.80722	P	0.0	B	0.28850	0.225	B	0.35931	0.214	D	0.92245	0.5804	9	0.44086	T	0.13	-7.7706	9.9771	0.41791	0.0:0.5716:0.0:0.4284	rs1141321;rs2229386;rs3205245;rs9473558;rs17246003;rs17405002;rs56630024;rs9473558	532	P22033	MUTA_HUMAN	H	532	ENSP00000274813:R532H	ENSP00000274813:R532H	R	-	2	0	MUT	49520392	0.003000	0.15002	0.070000	0.20053	0.139000	0.21198	-0.018000	0.12568	0.310000	0.22990	-0.237000	0.12165	CGT	T|0.242;G|0.135;C|0.582;A|0.041	0.242	strong		0.428	MUT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040854.1		
RAB11FIP1	80223	hgsc.bcm.edu	37	8	37732509	37732509	+	Silent	SNP	G	G	A	rs369997427		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:37732509G>A	ENST00000330843.4	-	3	1158	c.1146C>T	c.(1144-1146)tcC>tcT	p.S382S	RAB11FIP1_ENST00000522727.1_Silent_p.S234S|RAB11FIP1_ENST00000287263.4_Silent_p.S382S|RAB11FIP1_ENST00000524118.1_Silent_p.S234S|RAB11FIP1_ENST00000523182.1_5'Flank	NM_001002814.2	NP_001002814.2	Q6WKZ4	RFIP1_HUMAN	RAB11 family interacting protein 1 (class I)	382					protein transport (GO:0015031)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|endosome (GO:0005768)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)				NS(1)|breast(1)|central_nervous_system(4)|endometrium(3)|large_intestine(6)|lung(20)|ovary(3)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	49		Lung NSC(58;0.118)|all_lung(54;0.195)	LUSC - Lung squamous cell carcinoma(8;3.62e-11)			TGGAAGATTCGGAGAGCTGCC	0.567																																					p.S382S		Atlas-SNP	.											.	RAB11FIP1	105	.	0			c.C1146T						PASS	.						59.0	60.0	60.0					8																	37732509		2203	4300	6503	SO:0001819	synonymous_variant	80223	exon3			AGATTCGGAGAGC	AK092296	CCDS34881.1, CCDS34882.1	8p11.22	2005-10-04			ENSG00000156675	ENSG00000156675			30265	protein-coding gene	gene with protein product		608737				11786538, 11495908	Standard	NM_001002814		Approved	RCP, FLJ22622, FLJ22524, Rab11-FIP1	uc003xkm.2	Q6WKZ4	OTTHUMG00000164026	ENST00000330843.4:c.1146C>T	8.37:g.37732509G>A		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	87	24	0.275862	NM_025151	J3KNP0|Q307T1|Q6AZK4|Q6WKZ2|Q6WKZ6|Q86YV4|Q8TDL1|Q9H642	Silent	SNP	ENST00000330843.4	37	CCDS34882.1																																																																																			.	.	weak		0.567	RAB11FIP1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000376816.1	NM_025151	
IRGC	56269	hgsc.bcm.edu	37	19	44223412	44223412	+	Silent	SNP	C	C	T	rs34471331	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:44223412C>T	ENST00000244314.5	+	2	901	c.702C>T	c.(700-702)caC>caT	p.H234H		NM_019612.3	NP_062558.1	Q6NXR0	IIGP5_HUMAN	immunity-related GTPase family, cinema	234	IRG-type G.					membrane (GO:0016020)	GTP binding (GO:0005525)|hydrolase activity, acting on acid anhydrides (GO:0016817)			central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(16)|ovary(1)|prostate(1)|skin(2)	25		Prostate(69;0.0435)				CCTGGGAGCACGACCTGCCCT	0.672													C|||	261	0.0521166	0.0242	0.0548	5008	,	,		16982	0.001		0.1292	False		,,,				2504	0.0613				p.H234H	Colon(189;350 2037 11447 13433 38914)	Atlas-SNP	.											.	IRGC	67	.	0			c.C702T						PASS	.	C		184,4218		3,178,2020	22.0	21.0	21.0		702	-9.2	0.0	19	dbSNP_126	21	987,7607		53,881,3363	no	coding-synonymous	IRGC	NM_019612.3		56,1059,5383	TT,TC,CC		11.4848,4.1799,9.0105		234/464	44223412	1171,11825	2201	4297	6498	SO:0001819	synonymous_variant	56269	exon2			GGAGCACGACCTG	BC066939	CCDS12629.1	19q13.32	2008-02-05	2005-10-31	2005-10-31	ENSG00000124449	ENSG00000124449			28835	protein-coding gene	gene with protein product			"""immunity-related GTPase family, cinema 1"""	IRGC1		12477932	Standard	NM_019612		Approved	Iigp5, CINEMA	uc002oxh.3	Q6NXR0	OTTHUMG00000154587	ENST00000244314.5:c.702C>T	19.37:g.44223412C>T		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	48	18	0.375	NM_019612	Q05BR8	Silent	SNP	ENST00000244314.5	37	CCDS12629.1																																																																																			C|0.924;T|0.076	0.076	strong		0.672	IRGC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336191.1	NM_019612	
CMYA5	202333	hgsc.bcm.edu	37	5	79029025	79029025	+	Silent	SNP	T	T	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:79029025T>C	ENST00000446378.2	+	2	4468	c.4437T>C	c.(4435-4437)tcT>tcC	p.S1479S		NM_153610.3	NP_705838.3	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	1479					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)		AAACATCATCTTCTCAGCATT	0.388																																					p.S1479S		Atlas-SNP	.											CMYA5_ENST00000446378,NS,carcinoma,+1,2	CMYA5	643	2	0			c.T4437C						PASS	.						90.0	88.0	88.0					5																	79029025		1853	4095	5948	SO:0001819	synonymous_variant	202333	exon2			ATCATCTTCTCAG	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.4437T>C	5.37:g.79029025T>C		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	74	16	0.216216	NM_153610	A0PJB7|Q05CT4|Q2NKX1|Q2T9G9|Q69YQ8|Q69YQ9|Q6P517|Q6P5U3|Q7Z4I1|Q86T34|Q86T49|Q8N3S4|Q8N3S7|Q8NAG8|Q9UK88	Silent	SNP	ENST00000446378.2	37	CCDS47238.1																																																																																			.	.	none		0.388	CMYA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369497.1	NM_153610	
ZNF608	57507	hgsc.bcm.edu	37	5	123983915	123983915	+	Missense_Mutation	SNP	G	G	T	rs6862252	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:123983915G>T	ENST00000306315.5	-	4	2597	c.2162C>A	c.(2161-2163)aCc>aAc	p.T721N	ZNF608_ENST00000504926.1_Missense_Mutation_p.T294N	NM_020747.2	NP_065798.2	Q9ULD9	ZN608_HUMAN	zinc finger protein 608	721			T -> N (in dbSNP:rs6862252). {ECO:0000269|PubMed:10508479, ECO:0000269|PubMed:10574462, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005}.				metal ion binding (GO:0046872)			breast(4)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(8)|lung(12)|ovary(3)|skin(6)|urinary_tract(1)	46		all_cancers(142;0.186)|Prostate(80;0.081)	KIRC - Kidney renal clear cell carcinoma(527;0.159)|Kidney(363;0.221)	OV - Ovarian serous cystadenocarcinoma(64;0.00126)|Epithelial(69;0.00238)|all cancers(49;0.00783)		TTTGCAGTTGGTAGCTTTTTT	0.493													T|||	3155	0.629992	0.7065	0.451	5008	,	,		13373	0.753		0.5457	False		,,,				2504	0.6135				p.T721N		Atlas-SNP	.											.	ZNF608	117	.	0			c.C2162A						PASS	.	T	ASN/THR	2891,1515	473.7+/-356.8	941,1009,253	41.0	44.0	43.0		2162	-0.8	0.9	5	dbSNP_116	43	4378,4222	559.8+/-387.5	1133,2112,1055	yes	missense	ZNF608	NM_020747.2	65	2074,3121,1308	TT,TG,GG		49.093,34.3849,44.1104	benign	721/1513	123983915	7269,5737	2203	4300	6503	SO:0001583	missense	57507	exon4			CAGTTGGTAGCTT	AB033107	CCDS34219.1	5q23.2	2008-05-02			ENSG00000168916	ENSG00000168916		"""Zinc fingers, C2H2-type"""	29238	protein-coding gene	gene with protein product						10574462, 10508479	Standard	NM_020747		Approved	KIAA1281, DKFZp434M098, NY-REN-36	uc003ktq.1	Q9ULD9	OTTHUMG00000162999	ENST00000306315.5:c.2162C>A	5.37:g.123983915G>T	ENSP00000307746:p.Thr721Asn	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	107	54	0.504673	NM_020747	A7E2W9|Q3SYM6|Q68D12|Q8IY05|Q9Y5A1	Missense_Mutation	SNP	ENST00000306315.5	37	CCDS34219.1	1373	0.6286630036630036	359	0.7296747967479674	169	0.46685082872928174	433	0.756993006993007	412	0.5435356200527705	T	3.774	-0.046942	0.07407	0.656151	0.50907	ENSG00000168916	ENST00000504926;ENST00000306315	T;T	0.42131	0.98;0.98	5.88	-0.826	0.10805	.	0.435018	0.25283	N	0.031797	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	0.27806	-1.0063	9	0.13853	T	0.58	-13.0083	7.4732	0.27361	0.0:0.2465:0.4483:0.3052	rs6862252;rs17318183;rs45631747;rs52829176;rs59496652;rs61726319;rs6862252	721	Q9ULD9	ZN608_HUMAN	N	294;721	ENSP00000427657:T294N;ENSP00000307746:T721N	ENSP00000307746:T721N	T	-	2	0	ZNF608	124011814	0.125000	0.22332	0.870000	0.34147	0.950000	0.60333	-0.204000	0.09425	-0.377000	0.07930	-0.381000	0.06696	ACC	G|0.405;N|0.001	.	strong		0.493	ZNF608-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371300.1	XM_114432	
AMOTL1	154810	hgsc.bcm.edu	37	11	94602414	94602414	+	Missense_Mutation	SNP	C	C	T	rs11020968	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:94602414C>T	ENST00000433060.2	+	12	2681	c.2540C>T	c.(2539-2541)cCa>cTa	p.P847L	AMOTL1_ENST00000317829.8_Missense_Mutation_p.P797L|AMOTL1_ENST00000317837.9_Missense_Mutation_p.P434L	NM_130847.2	NP_570899.1	Q8IY63	AMOL1_HUMAN	angiomotin like 1	847			P -> L (in dbSNP:rs11020968).		establishment of cell polarity involved in ameboidal cell migration (GO:0003365)|hippo signaling (GO:0035329)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|Wnt signaling pathway (GO:0016055)	apical plasma membrane (GO:0016324)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|tight junction (GO:0005923)	identical protein binding (GO:0042802)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(14)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(2)	36		Acute lymphoblastic leukemia(157;2.38e-05)|all_hematologic(158;0.00824)				CCACTGCTGCCACCCCCACCC	0.552													C|||	462	0.0922524	0.0023	0.0533	5008	,	,		15974	0.1548		0.1272	False		,,,				2504	0.1411				p.P847L		Atlas-SNP	.											.	AMOTL1	95	.	0			c.C2540T						PASS	.	C	LEU/PRO	82,4216		0,82,2067	27.0	35.0	32.0		2540	5.0	0.4	11	dbSNP_120	32	930,7582		44,842,3370	yes	missense	AMOTL1	NM_130847.2	98	44,924,5437	TT,TC,CC		10.9258,1.9079,7.9001	benign	847/957	94602414	1012,11798	2149	4256	6405	SO:0001583	missense	154810	exon12			TGCTGCCACCCCC	AF453742	CCDS44712.1, CCDS73368.1	11q21	2008-07-18				ENSG00000166025			17811	protein-coding gene	gene with protein product	"""junction-enriched and associated protein"""	614657				11733531	Standard	XM_005273798		Approved	JEAP	uc001pfb.3	Q8IY63		ENST00000433060.2:c.2540C>T	11.37:g.94602414C>T	ENSP00000387739:p.Pro847Leu	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	98	76	0.77551	NM_130847	Q63HK7|Q8NDN0|Q8TEN8|Q8WXD1|Q96CM5	Missense_Mutation	SNP	ENST00000433060.2	37	CCDS44712.1	204	0.09340659340659341	3	0.006097560975609756	19	0.052486187845303865	79	0.1381118881118881	103	0.1358839050131926	C	5.147	0.212776	0.09757	0.019079	0.109258	ENSG00000166025	ENST00000317829;ENST00000317837;ENST00000433060	T;T;T	0.50813	2.23;0.73;2.23	5.02	5.02	0.67125	.	0.252596	0.34750	N	0.003701	T	0.00524	0.0017	L	0.37507	1.11	0.31810	P	0.627264	D;B	0.71674	0.998;0.014	D;B	0.63703	0.917;0.007	T	0.05257	-1.0896	9	0.19147	T	0.46	-7.4421	11.7978	0.52110	0.0:0.9192:0.0:0.0808	rs11020968;rs11020968	797;847	Q8IY63-2;Q8IY63	.;AMOL1_HUMAN	L	797;434;847	ENSP00000320968:P797L;ENSP00000323474:P434L;ENSP00000387739:P847L	ENSP00000320968:P797L	P	+	2	0	AMOTL1	94242062	0.928000	0.31464	0.391000	0.26233	0.007000	0.05969	2.380000	0.44327	2.340000	0.79590	0.561000	0.74099	CCA	C|0.899;T|0.101	0.101	strong		0.552	AMOTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396474.3	NM_130847	
OGDH	4967	hgsc.bcm.edu	37	7	44747589	44747589	+	Silent	SNP	C	C	T	rs61756584	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:44747589C>T	ENST00000222673.5	+	23	3105	c.3063C>T	c.(3061-3063)aaC>aaT	p.N1021N	OGDH_ENST00000444676.1_Silent_p.N1036N|OGDH_ENST00000449767.1_Silent_p.N1017N|OGDH_ENST00000439616.2_Silent_p.N871N|OGDH_ENST00000543843.1_Silent_p.N972N|OGDH_ENST00000447398.1_Silent_p.N1032N	NM_002541.3	NP_002532.2	Q02218	ODO1_HUMAN	oxoglutarate (alpha-ketoglutarate) dehydrogenase (lipoamide)	1021					2-oxoglutarate metabolic process (GO:0006103)|cellular metabolic process (GO:0044237)|cellular nitrogen compound metabolic process (GO:0034641)|cerebellar cortex development (GO:0021695)|generation of precursor metabolites and energy (GO:0006091)|glycolytic process (GO:0006096)|hippocampus development (GO:0021766)|lysine catabolic process (GO:0006554)|NADH metabolic process (GO:0006734)|olfactory bulb mitral cell layer development (GO:0061034)|pyramidal neuron development (GO:0021860)|small molecule metabolic process (GO:0044281)|striatum development (GO:0021756)|succinyl-CoA metabolic process (GO:0006104)|tangential migration from the subventricular zone to the olfactory bulb (GO:0022028)|thalamus development (GO:0021794)|tricarboxylic acid cycle (GO:0006099)	mitochondrial matrix (GO:0005759)|mitochondrial membrane (GO:0031966)|mitochondrion (GO:0005739)|oxoglutarate dehydrogenase complex (GO:0045252)	metal ion binding (GO:0046872)|oxoglutarate dehydrogenase (NAD+) activity (GO:0034602)|oxoglutarate dehydrogenase (succinyl-transferring) activity (GO:0004591)|thiamine pyrophosphate binding (GO:0030976)			breast(2)|endometrium(5)|kidney(2)|large_intestine(6)|lung(13)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(4)	36					Valproic Acid(DB00313)	TCTTCAAGAACTTCTCGTAGA	0.612													C|||	234	0.0467252	0.0038	0.0504	5008	,	,		20934	0.0823		0.0417	False		,,,				2504	0.0706				p.N1021N		Atlas-SNP	.											.	OGDH	145	.	0			c.C3063T						PASS	.	C	,	51,4355	49.6+/-84.7	1,49,2153	100.0	85.0	90.0		3051,3063	-3.2	0.6	7	dbSNP_129	90	471,8129	138.4+/-195.2	10,451,3839	no	coding-synonymous,coding-synonymous	OGDH	NM_001165036.1,NM_002541.3	,	11,500,5992	TT,TC,CC		5.4767,1.1575,4.0135	,	1017/1020,1021/1024	44747589	522,12484	2203	4300	6503	SO:0001819	synonymous_variant	4967	exon23			CAAGAACTTCTCG	D10523	CCDS34627.1, CCDS47580.1, CCDS55107.1	7p13-p11.2	2010-11-23			ENSG00000105953	ENSG00000105953	1.2.4.2		8124	protein-coding gene	gene with protein product		613022				8020988, 1542694	Standard	NM_002541		Approved	E1k	uc003tln.3	Q02218	OTTHUMG00000155304	ENST00000222673.5:c.3063C>T	7.37:g.44747589C>T		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	62	36	0.580645	NM_002541	B4E2U9|D3DVL0|E9PBM1|Q96DD3|Q9UDX0	Silent	SNP	ENST00000222673.5	37	CCDS34627.1																																																																																			C|0.956;G|0.000;T|0.044	0.044	strong		0.612	OGDH-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000339391.1		
PDE6B	5158	hgsc.bcm.edu	37	4	647931	647931	+	Silent	SNP	G	G	A	rs75695239	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:647931G>A	ENST00000496514.1	+	5	936	c.915G>A	c.(913-915)acG>acA	p.T305T	RP11-1191J2.2_ENST00000598370.1_RNA|RP11-1191J2.2_ENST00000489312.1_RNA|RP11-1191J2.2_ENST00000599030.1_RNA|RP11-1191J2.2_ENST00000468356.1_RNA|PDE6B_ENST00000255622.6_Silent_p.T305T|PDE6B_ENST00000429163.2_Silent_p.T26T			P35913	PDE6B_HUMAN	phosphodiesterase 6B, cGMP-specific, rod, beta	305	GAF 2.				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)			NS(1)|breast(3)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(11)|ovary(2)|prostate(2)|urinary_tract(1)	30					Caffeine(DB00201)	GCCCACGCACGCCTGATGGCC	0.642													.|||	207	0.0413339	0.09	0.0259	5008	,	,		16841	0.003		0.0487	False		,,,				2504	0.0184				p.T305T	GBM(71;463 1194 9848 25922 46834)	Atlas-SNP	.											.	PDE6B	80	.	0			c.G915A						PASS	.	G	,,	323,4083	166.9+/-198.0	15,293,1895	40.0	44.0	43.0		915,915,78	-10.2	0.5	4	dbSNP_131	43	391,8207	123.9+/-182.7	10,371,3918	no	coding-synonymous,coding-synonymous,coding-synonymous	PDE6B	NM_000283.3,NM_001145291.1,NM_001145292.1	,,	25,664,5813	AA,AG,GG		4.5476,7.3309,5.4906	,,	305/855,305/854,26/576	647931	714,12290	2203	4299	6502	SO:0001819	synonymous_variant	5158	exon5			ACGCACGCCTGAT	BC000249	CCDS33932.1, CCDS46993.1, CCDS54703.1	4p16.3	2014-01-28	2008-07-31		ENSG00000133256	ENSG00000133256	3.1.4.17	"""Phosphodiesterases"""	8786	protein-coding gene	gene with protein product	"""congenital stationary night blindness 3, autosomal dominant"""	180072		PDEB		1313787	Standard	NM_001145292		Approved	CSNB3, rd1, RP40, CSNBAD2	uc003gap.3	P35913	OTTHUMG00000159909	ENST00000496514.1:c.915G>A	4.37:g.647931G>A		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	44	27	0.613636	NM_001145291	B7Z9T9|E7ETT3|Q53XN5|Q9BWH5|Q9UD49	Silent	SNP	ENST00000496514.1	37	CCDS33932.1																																																																																			G|0.949;A|0.051	0.051	strong		0.642	PDE6B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000358109.1	NM_000283	
LINGO1	84894	hgsc.bcm.edu	37	15	77907535	77907535	+	Silent	SNP	C	C	G	rs2271396	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	131	0	0		WXS	Illumina HiSeq	Phase_I	166	166	1	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	
PGLYRP3	114771	hgsc.bcm.edu	37	1	153277423	153277423	+	Splice_Site	SNP	C	C	T	rs843971	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:153277423C>T	ENST00000290722.1	-	3	428	c.376G>A	c.(376-378)Ggc>Agc	p.G126S		NM_052891.1	NP_443123.1	Q96LB9	PGRP3_HUMAN	peptidoglycan recognition protein 3	126			G -> S (in dbSNP:rs843971). {ECO:0000269|PubMed:15489334}.		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)|peptidoglycan catabolic process (GO:0009253)	extracellular region (GO:0005576)|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)			breast(3)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(1)|liver(1)|lung(10)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(1)	28	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)			TGACCCTTACCTATCTTATTG	0.512													C|||	2353	0.469848	0.385	0.4553	5008	,	,		20058	0.5833		0.3996	False		,,,				2504	0.5501				p.G126S		Atlas-SNP	.											.	PGLYRP3	55	.	0			c.G376A						PASS	.	C	SER/GLY	1690,2716	509.9+/-367.4	337,1016,850	130.0	113.0	119.0		376	4.5	1.0	1	dbSNP_86	119	3316,5284	494.4+/-373.8	657,2002,1641	yes	missense-near-splice	PGLYRP3	NM_052891.1	56	994,3018,2491	TT,TC,CC		38.5581,38.3568,38.4899	probably-damaging	126/342	153277423	5006,8000	2203	4300	6503	SO:0001630	splice_region_variant	114771	exon3			CCTTACCTATCTT	AY035376	CCDS1035.1	1q21	2008-02-05			ENSG00000159527	ENSG00000159527			30014	protein-coding gene	gene with protein product	"""peptidoglycan recognition protein I alpha precursor"""	608197				11461926	Standard	NM_052891		Approved	PGRPIA, PGLYRPIalpha, PGRP-Ialpha	uc001fbn.1	Q96LB9	OTTHUMG00000014044	ENST00000290722.1:c.376+1G>A	1.37:g.153277423C>T		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	120	44	0.366667	NM_052891	A1A4U8|Q5SY65	Missense_Mutation	SNP	ENST00000290722.1	37	CCDS1035.1	983	0.4500915750915751	215	0.4369918699186992	164	0.4530386740331492	317	0.5541958041958042	287	0.3786279683377309	C	15.97	2.988634	0.53934	0.383568	0.385581	ENSG00000159527	ENST00000290722	T	0.13307	2.6	4.48	4.48	0.54585	Peptidoglycan recognition protein family domain, metazoa/bacteria (1);N-acetylmuramoyl-L-alanine amidase domain (4);	0.000000	0.49916	D	0.000123	T	0.08758	0.0217	L	0.37507	1.11	0.32243	P	0.572436	P	0.48503	0.911	P	0.49085	0.6	T	0.11494	-1.0585	8	.	.	.	-8.6536	12.509	0.55997	0.0:1.0:0.0:0.0	rs843971;rs1655321;rs16835150;rs59808458;rs843971	126	Q96LB9	PGRP3_HUMAN	S	126	ENSP00000290722:G126S	.	G	-	1	0	PGLYRP3	151544047	0.977000	0.34250	0.991000	0.47740	0.269000	0.26545	2.539000	0.45718	2.307000	0.77673	0.557000	0.71058	GGC	C|0.580;T|0.420	0.420	strong		0.512	PGLYRP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039488.1	NM_052891	Missense_Mutation
ADAL	161823	hgsc.bcm.edu	37	15	43632549	43632549	+	Splice_Site	SNP	T	T	C	rs2278857	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:43632549T>C	ENST00000562188.1	+	4	358	c.342T>C	c.(340-342)acT>acC	p.T114T	ADAL_ENST00000422466.2_Splice_Site_p.T114T|ADAL_ENST00000389651.4_Splice_Site_p.T114T|ADAL_ENST00000428046.3_Splice_Site_p.T114T			Q6DHV7	ADAL_HUMAN	adenosine deaminase-like	114					adenosine catabolic process (GO:0006154)|drug metabolic process (GO:0017144)|inosine biosynthetic process (GO:0046103)|nucleobase-containing small molecule metabolic process (GO:0055086)|nucleotide metabolic process (GO:0009117)|purine nucleobase metabolic process (GO:0006144)|purine-containing compound salvage (GO:0043101)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	adenosine deaminase activity (GO:0004000)|metal ion binding (GO:0046872)			endometrium(1)|kidney(2)|lung(2)|prostate(1)|skin(1)	7		all_cancers(109;7.96e-11)|all_epithelial(112;2.96e-09)|Lung NSC(122;8.91e-07)|all_lung(180;8.8e-06)|Melanoma(134;0.0728)		GBM - Glioblastoma multiforme(94;9.31e-07)		AAAATGCTACTGGTAGAATTT	0.378													C|||	2700	0.539137	0.9334	0.3343	5008	,	,		20547	0.4692		0.3221	False		,,,				2504	0.4468				p.T114T		Atlas-SNP	.											.	ADAL	48	.	0			c.T342C						PASS	.	C	,	3560,842	332.8+/-302.6	1435,690,76	72.0	79.0	77.0		342,342	-1.6	1.0	15	dbSNP_100	77	2724,5874	681.2+/-403.7	428,1868,2003	yes	coding-synonymous-near-splice,coding-synonymous-near-splice	ADAL	NM_001012969.2,NM_001159280.1	,	1863,2558,2079	CC,CT,TT		31.6818,19.1277,48.3385	,	114/268,114/329	43632549	6284,6716	2201	4299	6500	SO:0001630	splice_region_variant	161823	exon6			TGCTACTGGTAGA		CCDS32214.1, CCDS53936.1	15q15.3	2014-08-08			ENSG00000168803	ENSG00000168803			31853	protein-coding gene	gene with protein product							Standard	NM_001012969		Approved		uc010udo.2	Q6DHV7	OTTHUMG00000176646	ENST00000562188.1:c.343+1T>C	15.37:g.43632549T>C		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	132	51	0.386364	NM_001012969	A6NHZ3|B4DQM8	Silent	SNP	ENST00000562188.1	37																																																																																				T|0.487;C|0.513	0.513	strong		0.378	ADAL-002	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000432960.1	XM_091156	Silent
SPATA31E1	286234	hgsc.bcm.edu	37	9	90501448	90501448	+	Missense_Mutation	SNP	C	C	A	rs4076795	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:90501448C>A	ENST00000325643.5	+	4	2112	c.2046C>A	c.(2044-2046)gaC>gaA	p.D682E		NM_178828.4	NP_849150.3	Q6ZUB1	S31E1_HUMAN	SPATA31 subfamily E, member 1	682			D -> E (in dbSNP:rs4076795). {ECO:0000269|PubMed:14702039}.		cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											AGCCTTCTGACTTTGCAGGGA	0.612													.|||	3810	0.760783	0.9493	0.719	5008	,	,		18296	0.877		0.5666	False		,,,				2504	0.6155				p.D682E		Atlas-SNP	.											C9orf79,caecum,carcinoma,0,1	.	.	1	0			c.C2046A						PASS	.	A	GLU/ASP	3876,530	229.1+/-243.8	1714,448,41	46.0	60.0	55.0		2046	-4.9	0.0	9	dbSNP_108	55	4640,3958	541.8+/-384.1	1274,2092,933	yes	missense	C9orf79	NM_178828.4	45	2988,2540,974	AA,AC,CC		46.034,12.0291,34.5125	benign	682/1446	90501448	8516,4488	2203	4299	6502	SO:0001583	missense	286234	exon4			TTCTGACTTTGCA	AK093185	CCDS6676.1	9q22.1-q22.2	2012-10-12	2012-10-12	2012-10-12	ENSG00000177992	ENSG00000177992			26672	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 79"", ""family with sequence similarity 75, member E1"""	C9orf79, FAM75E1			Standard	NM_178828		Approved	FLJ35866	uc004app.4	Q6ZUB1	OTTHUMG00000020157	ENST00000325643.5:c.2046C>A	9.37:g.90501448C>A	ENSP00000322640:p.Asp682Glu	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	36	12	0.333333	NM_178828	B2RPB1|Q5SQC9|Q8NA41|Q8ND27	Missense_Mutation	SNP	ENST00000325643.5	37	CCDS6676.1	1642	0.7518315018315018	461	0.9369918699186992	255	0.7044198895027625	499	0.8723776223776224	427	0.5633245382585752	a	0.008	-1.902883	0.00512	0.879709	0.53966	ENSG00000177992	ENST00000325643;ENST00000539327	T	0.05925	3.37	2.43	-4.86	0.03132	.	11.086800	0.00834	N	0.001682	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	0.31251	-0.9950	9	0.02654	T	1	.	5.9254	0.19110	0.4823:0.3453:0.1724:0.0	rs4076795;rs17536349;rs57937710;rs4076795	682;334	Q6ZUB1;Q8NA33	CI079_HUMAN;.	E	682;334	ENSP00000322640:D682E	ENSP00000322640:D682E	D	+	3	2	C9orf79	89691268	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.165000	0.01274	-2.299000	0.00659	-1.398000	0.01145	GAC	C|0.297;N|0.002	.	strong		0.612	SPATA31E1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052954.2	NM_178828	
PFKP	5214	hgsc.bcm.edu	37	10	3178001	3178001	+	Silent	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:3178001G>A	ENST00000381125.4	+	21	2272	c.2196G>A	c.(2194-2196)gtG>gtA	p.V732V	PFKP_ENST00000381075.2_Silent_p.V724V|PITRM1_ENST00000464395.1_5'Flank|PFKP_ENST00000381072.1_Silent_p.V150V	NM_002627.4	NP_002618.1	Q01813	PFKAP_HUMAN	phosphofructokinase, platelet	732	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)		TTCAACCTGTGGCAGAGCTGA	0.403																																					p.V732V		Atlas-SNP	.											.	PFKP	182	.	0			c.G2196A						PASS	.						78.0	78.0	78.0					10																	3178001		2203	4300	6503	SO:0001819	synonymous_variant	5214	exon21			ACCTGTGGCAGAG	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.2196G>A	10.37:g.3178001G>A		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	118	37	0.313559	NM_002627	B3KS15|Q5VSR7|Q5VSR8	Silent	SNP	ENST00000381125.4	37	CCDS7059.1	.	.	.	.	.	.	.	.	.	.	g	2.795	-0.250360	0.05867	.	.	ENSG00000067057	ENST00000433193	.	.	.	4.92	2.06	0.26882	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	4.47	0.11708	0.2166:0.0:0.5125:0.271	.	.	.	.	X	85	.	.	W	+	2	0	PFKP	3168001	0.798000	0.28890	0.791000	0.31998	0.487000	0.33371	0.615000	0.24329	0.506000	0.28125	-0.361000	0.07541	TGG	.	.	none		0.403	PFKP-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046454.1	NM_002627	
LILRA6	79168	hgsc.bcm.edu	37	19	54744722	54744722	+	Missense_Mutation	SNP	T	T	C	rs56257556	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:54744722T>C	ENST00000396365.2	-	5	979	c.940A>G	c.(940-942)Aac>Gac	p.N314D	LILRA6_ENST00000245621.5_Missense_Mutation_p.N314D|LILRA6_ENST00000440558.2_Missense_Mutation_p.N314D|LILRA6_ENST00000270464.5_Intron|LILRB3_ENST00000407860.2_Intron|LILRA6_ENST00000419410.2_Missense_Mutation_p.N314D|LILRA6_ENST00000391735.3_3'UTR	NM_024318.2	NP_077294	Q6PI73	LIRA6_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 6	314	Ig-like C2-type 1.				immune system process (GO:0002376)	integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(20)|ovary(3)|skin(2)|urinary_tract(2)	38	all_cancers(19;0.00723)|all_epithelial(19;0.00389)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		ATCAGGATGTTCAGGGGGTCG	0.682																																					p.N314D		Atlas-SNP	.											LILRA6,NS,carcinoma,+2,1	LILRA6	75	1	0			c.A940G						scavenged	.						22.0	32.0	29.0					19																	54744722		2100	4147	6247	SO:0001583	missense	79168	exon5			GGATGTTCAGGGG	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.940A>G	19.37:g.54744722T>C	ENSP00000379651:p.Asn314Asp	Somatic	225	0	0		WXS	Illumina HiSeq	Phase_I	159	25	0.157233	NM_024318		Missense_Mutation	SNP	ENST00000396365.2	37	CCDS42610.1	207	0.09478021978021978	73	0.1483739837398374	41	0.1132596685082873	19	0.033216783216783216	74	0.09762532981530343	T	0	-2.690915	0.00100	.	.	ENSG00000244482	ENST00000440558;ENST00000419410;ENST00000421123;ENST00000396365;ENST00000245621	T;T;T;T	0.13778	2.56;2.56;2.56;2.56	2.16	1.1	0.20463	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.389073	0.18849	N	0.129445	T	0.00012	0.0000	N	0.00022	-2.725	0.80722	D	1	B;B;B;B	0.17852	0.002;0.024;0.0;0.0	B;B;B;B	0.28385	0.002;0.089;0.0;0.001	T	0.46020	-0.9221	10	0.02654	T	1	.	5.0417	0.14462	0.0:0.8181:0.0:0.1819	rs56257556	314;314;314;314	C9JFH3;Q6PI73;F8WCY4;D3YTC4	.;LIRA6_HUMAN;.;.	D	314	ENSP00000390120:N314D;ENSP00000411227:N314D;ENSP00000379651:N314D;ENSP00000245621:N314D	ENSP00000245621:N314D	N	-	1	0	LILRA6	59436534	0.686000	0.27661	0.905000	0.35620	0.042000	0.13812	1.191000	0.32138	0.467000	0.27218	-1.232000	0.01568	AAC	CATCAGGATGTT|0.500;GATCAGGATGTC|0.500	.	alt		0.682	LILRA6-003	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000313725.1	NM_024318	
HTT	3064	hgsc.bcm.edu	37	4	3213832	3213832	+	Silent	SNP	G	G	A	rs362336	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:3213832G>A	ENST00000355072.5	+	48	6736	c.6591G>A	c.(6589-6591)gaG>gaA	p.E2197E		NM_002111.6	NP_002102	P42858	HD_HUMAN	huntingtin	2197					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)		TGCCTGCAGAGCCGGCGGCCT	0.493													G|||	1200	0.239617	0.0946	0.2939	5008	,	,		17362	0.3542		0.3151	False		,,,				2504	0.2014				p.E2197E		Atlas-SNP	.											.	HTT	221	.	0			c.G6591A						PASS	.	G		582,3214		47,488,1363	39.0	42.0	41.0		6591	1.0	0.0	4	dbSNP_79	41	2461,5771		346,1769,2001	no	coding-synonymous	HTT	NM_002111.6		393,2257,3364	AA,AG,GG		29.8955,15.3319,25.2993		2197/3143	3213832	3043,8985	1898	4116	6014	SO:0001819	synonymous_variant	3064	exon48			TGCAGAGCCGGCG	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.6591G>A	4.37:g.3213832G>A		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	64	25	0.390625	NM_002111	Q9UQB7	Silent	SNP	ENST00000355072.5	37	CCDS43206.1																																																																																			G|0.718;A|0.282	0.282	strong		0.493	HTT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358234.2	NM_002111	
NOD1	10392	hgsc.bcm.edu	37	7	30492237	30492237	+	Missense_Mutation	SNP	C	C	T	rs2075820|rs398087981	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:30492237C>T	ENST00000222823.4	-	6	1321	c.796G>A	c.(796-798)Gag>Aag	p.E266K	NOD1_ENST00000423334.2_Silent_p.P220P	NM_006092.2	NP_006083.1	Q9Y239	NOD1_HUMAN	nucleotide-binding oligomerization domain containing 1	266	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.		E -> K (in dbSNP:rs2075820).		activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of MAPK activity (GO:0000187)|apoptotic process (GO:0006915)|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)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interleukin-8 biosynthetic process (GO:0042228)|intracellular signal transduction (GO:0035556)|JNK cascade (GO:0007254)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of dendritic cell antigen processing and presentation (GO:0002606)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of JNK cascade (GO:0046330)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of tumor necrosis factor production (GO:0032760)|protein oligomerization (GO:0051259)|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)	basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|cytosol (GO:0005829)	ATP binding (GO:0005524)|CARD domain binding (GO:0050700)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|identical protein binding (GO:0042802)|peptidoglycan binding (GO:0042834)|protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(17)|ovary(2)|prostate(1)|skin(2)	39						AACACCTCCTCGGGGTCCCGC	0.617													C|||	1690	0.33746	0.4032	0.1758	5008	,	,		18812	0.3869		0.2326	False		,,,				2504	0.4202				p.E266K		Atlas-SNP	.											.	NOD1	79	.	0			c.G796A	GRCh37	CM076359	NOD1	M	rs2075820	PASS	.	C	LYS/GLU	1670,2736	488.3+/-361.2	321,1028,854	69.0	67.0	68.0		796	5.5	0.8	7	dbSNP_96	68	2110,6490	351.5+/-328.3	282,1546,2472	yes	missense	NOD1	NM_006092.2	56	603,2574,3326	TT,TC,CC		24.5349,37.9029,29.0635	benign	266/954	30492237	3780,9226	2203	4300	6503	SO:0001583	missense	10392	exon6			CCTCCTCGGGGTC	AF126484	CCDS5427.1	7p15-p14	2006-12-08	2006-12-08	2006-12-08	ENSG00000106100	ENSG00000106100		"""Nucleotide-binding domain and leucine rich repeat containing"""	16390	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 1"", ""NLR family, CARD domain containing 1"""	605980	"""caspase recruitment domain family, member 4"""	CARD4		10224040, 10329646	Standard	NM_006092		Approved	NLRC1, CLR7.1	uc003tav.3	Q9Y239	OTTHUMG00000023923	ENST00000222823.4:c.796G>A	7.37:g.30492237C>T	ENSP00000222823:p.Glu266Lys	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	70	18	0.257143	NM_006092	B4DTU3|Q549U4|Q8IWF5	Missense_Mutation	SNP	ENST00000222823.4	37	CCDS5427.1	649	0.29716117216117216	195	0.39634146341463417	76	0.20994475138121546	209	0.36538461538461536	169	0.22295514511873352	C	16.00	2.999294	0.54147	0.379029	0.245349	ENSG00000106100	ENST00000222823	T	0.79033	-1.23	5.54	5.54	0.83059	NACHT nucleoside triphosphatase (1);	0.640387	0.17056	N	0.188744	T	0.00012	0.0000	L	0.54323	1.7	0.09310	P	0.9999999847827	P	0.47545	0.897	B	0.38156	0.266	T	0.36237	-0.9756	9	0.26408	T	0.33	.	11.8004	0.52124	0.0:0.9113:0.0:0.0887	rs2075820;rs60510801;rs2075820	266	Q9Y239	NOD1_HUMAN	K	266	ENSP00000222823:E266K	ENSP00000222823:E266K	E	-	1	0	NOD1	30458762	0.667000	0.27484	0.795000	0.32087	0.978000	0.69477	2.119000	0.41958	2.602000	0.87976	0.563000	0.77884	GAG	T|0.303;G|0.002	0.303	strong		0.617	NOD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250443.2		
ZNF343	79175	hgsc.bcm.edu	37	20	2464112	2464112	+	Missense_Mutation	SNP	T	T	C	rs61740142	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:2464112T>C	ENST00000278772.4	-	6	1982	c.1495A>G	c.(1495-1497)Agg>Ggg	p.R499G	RP4-734P14.4_ENST00000461548.1_Intron	NM_001282495.1|NM_001282496.1|NM_024325.4	NP_001269424.1|NP_001269425.1|NP_077301.4	Q6P1L6	ZN343_HUMAN	zinc finger protein 343	499					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(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(11)|skin(4)|upper_aerodigestive_tract(1)	25						AAACCTCGCCTACACTCCCTG	0.507													T|||	317	0.0632987	0.1528	0.036	5008	,	,		21689	0.0		0.0368	False		,,,				2504	0.0542				p.R499G		Atlas-SNP	.											.	ZNF343	47	.	0			c.A1495G						PASS	.	T	GLY/ARG	602,3804	261.9+/-264.6	48,506,1649	126.0	115.0	119.0		1495	1.3	0.1	20	dbSNP_129	119	341,8259	116.8+/-176.5	4,333,3963	yes	missense	ZNF343	NM_024325.4	125	52,839,5612	CC,CT,TT		3.9651,13.6632,7.2505	benign	499/600	2464112	943,12063	2203	4300	6503	SO:0001583	missense	79175	exon6			CTCGCCTACACTC	AK096911	CCDS13028.1, CCDS74692.1, CCDS74693.1, CCDS74694.1	20p13	2013-01-08			ENSG00000088876	ENSG00000088876		"""Zinc fingers, C2H2-type"", ""-"""	16017	protein-coding gene	gene with protein product							Standard	NM_001282498		Approved	MGC10715	uc002wge.1	Q6P1L6	OTTHUMG00000031701	ENST00000278772.4:c.1495A>G	20.37:g.2464112T>C	ENSP00000278772:p.Arg499Gly	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	77	38	0.493506	NM_024325	Q5JXU8|Q5JXU9|Q8N8F2|Q96EX8|Q96NA5|Q9BQB0	Missense_Mutation	SNP	ENST00000278772.4	37	CCDS13028.1	113	0.051739926739926737	72	0.14634146341463414	11	0.03038674033149171	1	0.0017482517482517483	29	0.03825857519788918	T	2.733	-0.264032	0.05754	0.136632	0.039651	ENSG00000088876	ENST00000278772	T	0.37584	1.19	2.42	1.34	0.21922	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00039	0.0001	N	0.00036	-2.54	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.43410	-0.9393	9	0.02654	T	1	.	6.9415	0.24496	0.0:0.8434:0.0:0.1566	.	499	Q6P1L6	ZN343_HUMAN	G	499	ENSP00000278772:R499G	ENSP00000278772:R499G	R	-	1	2	ZNF343	2412112	0.933000	0.31639	0.074000	0.20217	0.423000	0.31445	3.628000	0.54259	0.331000	0.23511	-0.285000	0.09966	AGG	T|0.932;C|0.068	0.068	strong		0.507	ZNF343-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077617.1	NM_024325	
PGD	5226	hgsc.bcm.edu	37	1	10473196	10473196	+	Silent	SNP	C	C	T	rs2229687	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:10473196C>T	ENST00000270776.8	+	8	770	c.732C>T	c.(730-732)gaC>gaT	p.D244D	PGD_ENST00000538557.1_Silent_p.D231D|PGD_ENST00000541529.1_Silent_p.D222D	NM_002631.2	NP_002622.2	P52209	6PGD_HUMAN	phosphogluconate dehydrogenase	244					carbohydrate metabolic process (GO:0005975)|D-gluconate metabolic process (GO:0019521)|oxidation-reduction process (GO:0055114)|pentose biosynthetic process (GO:0019322)|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)|nucleus (GO:0005634)	NADP binding (GO:0050661)|phosphogluconate dehydrogenase (decarboxylating) activity (GO:0004616)	p.D244D(1)		NS(1)|breast(1)|cervix(1)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)	14	Ovarian(185;0.203)	all_lung(284;1.31e-05)|Lung NSC(185;2.19e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.14e-07)|COAD - Colon adenocarcinoma(227;7.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000294)|Kidney(185;0.000728)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(132;0.00832)|READ - Rectum adenocarcinoma(331;0.0487)	Dacarbazine(DB00851)|Furosemide(DB00695)|Gadopentetate dimeglumine(DB00789)|Ketotifen(DB00920)|Meloxicam(DB00814)|Methotrexate(DB00563)|Ritodrine(DB00867)	AGTTCCAAGACACCGATGGCA	0.532													c|||	1678	0.335064	0.3457	0.3732	5008	,	,		21311	0.3403		0.338	False		,,,				2504	0.2853				p.D244D		Atlas-SNP	.											PGD,NS,carcinoma,0,1	PGD	39	1	1	Substitution - coding silent(1)	stomach(1)	c.C732T						PASS	.	T		1453,2953	682.7+/-404.2	254,945,1004	86.0	82.0	83.0		732	-10.1	0.0	1	dbSNP_98	83	2817,5783	676.6+/-403.3	487,1843,1970	no	coding-synonymous	PGD	NM_002631.2		741,2788,2974	TT,TC,CC		32.7558,32.9778,32.831		244/484	10473196	4270,8736	2203	4300	6503	SO:0001819	synonymous_variant	5226	exon8			CCAAGACACCGAT	BC000368	CCDS113.1	1p36.22	2012-10-02			ENSG00000142657	ENSG00000142657	1.1.1.43		8891	protein-coding gene	gene with protein product		172200					Standard	NM_002631		Approved		uc001arc.3	P52209	OTTHUMG00000001905	ENST00000270776.8:c.732C>T	1.37:g.10473196C>T		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	82	37	0.451219	NM_002631	A8K2Y9|B4DQJ8|Q9BWD8	Silent	SNP	ENST00000270776.8	37	CCDS113.1																																																																																			C|0.656;T|0.344	0.344	strong		0.532	PGD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005398.1	NM_002631	
ENTPD7	57089	hgsc.bcm.edu	37	10	101458487	101458487	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:101458487A>G	ENST00000370489.4	+	10	1385	c.1207A>G	c.(1207-1209)Ata>Gta	p.I403V		NM_020354.3	NP_065087.1	Q9NQZ7	ENTP7_HUMAN	ectonucleoside triphosphate diphosphohydrolase 7	403						cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)	hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|prostate(2)|urinary_tract(1)	18		Colorectal(252;0.234)		Epithelial(162;4.72e-10)|all cancers(201;3.75e-08)		ACTCAATGGCATATATCAATC	0.517																																					p.I403V		Atlas-SNP	.											.	ENTPD7	44	.	0			c.A1207G						PASS	.						88.0	81.0	83.0					10																	101458487		2203	4300	6503	SO:0001583	missense	57089	exon10			AATGGCATATATC	AF269255	CCDS7480.1	10q23-q24	2004-07-01			ENSG00000198018	ENSG00000198018			19745	protein-coding gene	gene with protein product						11278936	Standard	NM_020354		Approved	LALP1, FLJ30978	uc001kqa.4	Q9NQZ7	OTTHUMG00000018888	ENST00000370489.4:c.1207A>G	10.37:g.101458487A>G	ENSP00000359520:p.Ile403Val	Somatic	247	0	0		WXS	Illumina HiSeq	Phase_I	153	76	0.496732	NM_020354	B2RB83|B3KP21|D3DR64	Missense_Mutation	SNP	ENST00000370489.4	37	CCDS7480.1	.	.	.	.	.	.	.	.	.	.	A	2.485	-0.318732	0.05386	.	.	ENSG00000198018	ENST00000370489	T	0.08282	3.11	4.79	4.79	0.61399	.	0.069391	0.64402	D	0.000010	T	0.02807	0.0084	N	0.02697	-0.525	0.32828	D	0.503591	B	0.02656	0.0	B	0.04013	0.001	T	0.25779	-1.0122	10	0.02654	T	1	-0.8043	8.8175	0.35004	0.9146:0.0:0.0854:0.0	.	403	Q9NQZ7	ENTP7_HUMAN	V	403	ENSP00000359520:I403V	ENSP00000359520:I403V	I	+	1	0	ENTPD7	101448477	1.000000	0.71417	1.000000	0.80357	0.816000	0.46133	2.569000	0.45973	2.022000	0.59522	0.533000	0.62120	ATA	.	.	none		0.517	ENTPD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049809.2	NM_020354	
OR10H3	26532	hgsc.bcm.edu	37	19	15853150	15853150	+	Silent	SNP	C	C	T	rs16980824	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:15853150C>T	ENST00000305892.1	+	1	948	c.948C>T	c.(946-948)tcC>tcT	p.S316S		NM_013938.1	NP_039226.1	O60404	O10H3_HUMAN	olfactory receptor, family 10, subfamily H, member 3	316						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)|kidney(2)|large_intestine(1)|liver(1)|lung(6)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	17						CTCTAAGCTCCTAATGGCCAG	0.413													c|||	1309	0.261382	0.4327	0.2752	5008	,	,		21513	0.0119		0.3131	False		,,,				2504	0.2239				p.S316S		Atlas-SNP	.											.	OR10H3	53	.	0			c.C948T						PASS	.	C		1780,2620		371,1038,791	54.0	58.0	56.0		948	-1.8	0.0	19	dbSNP_123	56	2454,6142		373,1708,2217	no	coding-synonymous	OR10H3	NM_013938.1		744,2746,3008	TT,TC,CC		28.5482,40.4545,32.5793		316/317	15853150	4234,8762	2200	4298	6498	SO:0001819	synonymous_variant	26532	exon1			AAGCTCCTAATGG		CCDS12334.1	19p13.1	2012-08-09				ENSG00000171936		"""GPCR / Class A : Olfactory receptors"""	8174	protein-coding gene	gene with protein product							Standard	NM_013938		Approved		uc010xoq.2	O60404		ENST00000305892.1:c.948C>T	19.37:g.15853150C>T		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	57	27	0.473684	NM_013938	Q2HIZ3|Q6IFQ0	Silent	SNP	ENST00000305892.1	37	CCDS12334.1																																																																																			C|0.720;T|0.280	0.280	strong		0.413	OR10H3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460918.1		
SIGLEC14	100049587	hgsc.bcm.edu	37	19	52149165	52149165	+	Silent	SNP	G	G	A	rs71358847	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:52149165G>A	ENST00000360844.6	-	3	611	c.570C>T	c.(568-570)ccC>ccT	p.P190P	SIGLEC5_ENST00000222107.4_Intron|SIGLEC5_ENST00000429354.3_Intron|SIGLEC5_ENST00000534261.2_5'Flank|SIGLEC5_ENST00000599649.1_Intron	NM_001098612.1	NP_001092082.1	Q08ET2	SIG14_HUMAN	sialic acid binding Ig-like lectin 14	190	Ig-like C2-type 1.				cell adhesion (GO:0007155)|innate immune response (GO:0045087)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(3)|lung(15)|ovary(1)|upper_aerodigestive_tract(1)	29		all_neural(266;0.0299)		GBM - Glioblastoma multiforme(134;0.000965)|OV - Ovarian serous cystadenocarcinoma(262;0.0195)		GGGTGGTCTCGGGGTCCAGGG	0.657													G|||	2173	0.433906	0.475	0.3963	5008	,	,		11433	0.4325		0.3429	False		,,,				2504	0.5				p.P190P		Atlas-SNP	.											.	SIGLEC14	46	.	0			c.C570T						PASS	.	G		1657,2399		519,619,890	10.0	11.0	10.0		570	-2.2	0.0	19	dbSNP_130	10	2942,5324		803,1336,1994	no	coding-synonymous	SIGLEC14	NM_001098612.1		1322,1955,2884	AA,AG,GG		35.5916,40.8531,37.3235		190/397	52149165	4599,7723	2028	4133	6161	SO:0001819	synonymous_variant	100049587	exon3			GGTCTCGGGGTCC	AY854038	CCDS42604.1	19q13.41	2013-01-29			ENSG00000254415	ENSG00000254415		"""Sialic acid binding Ig-like lectins"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	32926	protein-coding gene	gene with protein product						17012248	Standard	NM_001098612		Approved		uc002pxf.4	Q08ET2	OTTHUMG00000165511	ENST00000360844.6:c.570C>T	19.37:g.52149165G>A		Somatic	465	1	0.00215054		WXS	Illumina HiSeq	Phase_I	382	328	0.858639	NM_001098612	Q6UXG0	Silent	SNP	ENST00000360844.6	37	CCDS42604.1																																																																																			G|0.621;A|0.379	0.379	strong		0.657	SIGLEC14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466899.2	NM_001098612	
PRRG4	79056	hgsc.bcm.edu	37	11	32852167	32852167	+	Missense_Mutation	SNP	C	C	T	rs61889489	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:32852167C>T	ENST00000257836.3	+	2	345	c.92C>T	c.(91-93)gCg>gTg	p.A31V		NM_024081.5	NP_076986.1	Q9BZD6	TMG4_HUMAN	proline rich Gla (G-carboxyglutamic acid) 4 (transmembrane)	31						extracellular region (GO:0005576)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)			large_intestine(2)|lung(2)|prostate(2)|urinary_tract(1)	7	Breast(20;0.206)					TCTAAGCATGCGGGAGAAGAA	0.498													C|||	213	0.0425319	0.0098	0.036	5008	,	,		14902	0.0109		0.0795	False		,,,				2504	0.0859				p.A31V		Atlas-SNP	.											.	PRRG4	15	.	0			c.C92T						PASS	.	C	VAL/ALA	80,4324	69.2+/-107.0	0,80,2122	93.0	84.0	87.0		92	1.0	0.0	11	dbSNP_129	87	720,7878	176.0+/-226.0	30,660,3609	yes	missense	PRRG4	NM_024081.5	64	30,740,5731	TT,TC,CC		8.374,1.8165,6.1529	benign	31/227	32852167	800,12202	2202	4299	6501	SO:0001583	missense	79056	exon2			AGCATGCGGGAGA	AF326351	CCDS7881.1	11p13	2008-02-05			ENSG00000135378	ENSG00000135378			30799	protein-coding gene	gene with protein product		611690				11171957	Standard	NM_024081		Approved	TMG4	uc001mtx.3	Q9BZD6	OTTHUMG00000166219	ENST00000257836.3:c.92C>T	11.37:g.32852167C>T	ENSP00000257836:p.Ala31Val	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	39	4	0.102564	NM_024081		Missense_Mutation	SNP	ENST00000257836.3	37	CCDS7881.1	95	0.043498168498168496	5	0.01016260162601626	12	0.03314917127071823	10	0.017482517482517484	68	0.08970976253298153	C	3.274	-0.148515	0.06627	0.018165	0.08374	ENSG00000135378	ENST00000257836	D	0.97831	-4.56	5.05	1.03	0.20045	.	0.370813	0.26187	N	0.025836	T	0.47002	0.1422	L	0.46157	1.445	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.68949	-0.5274	10	0.10636	T	0.68	-3.5083	4.6384	0.12536	0.1863:0.5711:0.0:0.2426	rs61889489	31	Q9BZD6	TMG4_HUMAN	V	31	ENSP00000257836:A31V	ENSP00000257836:A31V	A	+	2	0	PRRG4	32808743	0.019000	0.18553	0.019000	0.16419	0.010000	0.07245	0.040000	0.13905	-0.068000	0.12953	-0.812000	0.03155	GCG	C|0.945;T|0.055	0.055	strong		0.498	PRRG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388446.1	NM_024081	
TRIM49B	283116	hgsc.bcm.edu	37	11	49053390	49053390	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:49053390T>C	ENST00000332682.7	+	2	267	c.239T>C	c.(238-240)gTc>gCc	p.V80A		NM_001206626.1	NP_001193555.1	A6NDI0	TR49B_HUMAN	tripartite motif containing 49B	80						intracellular (GO:0005622)	zinc ion binding (GO:0008270)			lung(8)	8						GCTAGAAAAGTCAGTCTCTGG	0.458																																					p.V80A		Atlas-SNP	.											TRIM49B,NS,NS,-1,1	TRIM49B	27	1	0			c.T239C						scavenged	.																																			SO:0001583	missense	283116	exon1			GAAAAGTCAGTCT		CCDS55762.1	11p11.12	2014-02-17			ENSG00000182053	ENSG00000182053		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	42955	protein-coding gene	gene with protein product							Standard	NM_001206626		Approved		uc021qix.1	A6NDI0		ENST00000332682.7:c.239T>C	11.37:g.49053390T>C	ENSP00000330216:p.Val80Ala	Somatic	174	1	0.00574713		WXS	Illumina HiSeq	Phase_I	150	3	0.02	NM_001206626		Missense_Mutation	SNP	ENST00000332682.7	37	CCDS55762.1	.	.	.	.	.	.	.	.	.	.	T	0.001	-2.970469	0.00048	.	.	ENSG00000182053	ENST00000332682	D	0.84516	-1.86	0.49	-0.979	0.10276	.	.	.	.	.	T	0.62258	0.2413	N	0.08118	0	0.09310	N	0.999994	.	.	.	.	.	.	T	0.43327	-0.9398	7	0.09590	T	0.72	.	3.3156	0.07032	0.0:0.4841:0.2642:0.2517	.	.	.	.	A	80	ENSP00000330216:V80A	ENSP00000330216:V80A	V	+	2	0	AC084851.1	49009966	0.001000	0.12720	0.043000	0.18650	0.016000	0.09150	0.032000	0.13732	-1.832000	0.01196	-1.194000	0.01681	GTC	.	.	none		0.458	TRIM49B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
SCTR	6344	hgsc.bcm.edu	37	2	120199139	120199139	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:120199139C>T	ENST00000019103.5	-	12	1444	c.1177G>A	c.(1177-1179)Ggg>Agg	p.G393R		NM_002980.2	NP_002971.2	P47872	SCTR_HUMAN	secretin receptor	393					digestion (GO:0007586)|excretion (GO:0007588)|G-protein coupled receptor signaling pathway (GO:0007186)	cytoplasmic microtubule (GO:0005881)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	secretin receptor activity (GO:0015055)			central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)|prostate(1)|skin(3)	19					Secretin(DB00021)	CTCACCTCCCCATTGAGGAAG	0.602																																					p.G393R		Atlas-SNP	.											.	SCTR	45	.	0			c.G1177A						PASS	.						81.0	67.0	72.0					2																	120199139		2203	4300	6503	SO:0001583	missense	6344	exon12			CCTCCCCATTGAG		CCDS2127.1	2q14.1	2012-08-10			ENSG00000080293	ENSG00000080293		"""GPCR / Class B : Glucagon receptors"""	10608	protein-coding gene	gene with protein product		182098				1646711	Standard	NM_002980		Approved		uc002tma.3	P47872	OTTHUMG00000131407	ENST00000019103.5:c.1177G>A	2.37:g.120199139C>T	ENSP00000019103:p.Gly393Arg	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	48	23	0.479167	NM_002980	Q12961|Q13213|Q53T00	Missense_Mutation	SNP	ENST00000019103.5	37	CCDS2127.1	.	.	.	.	.	.	.	.	.	.	C	17.75	3.466290	0.63625	.	.	ENSG00000080293	ENST00000019103	T	0.79454	-1.27	4.78	2.02	0.26589	GPCR, family 2, secretin-like, conserved site (1);	0.104147	0.42420	N	0.000703	D	0.86818	0.6024	M	0.84511	2.7	0.46654	D	0.999149	D	0.89917	1.0	D	0.83275	0.996	D	0.85446	0.1158	10	0.87932	D	0	.	8.9316	0.35675	0.0:0.7531:0.0:0.2469	.	393	P47872	SCTR_HUMAN	R	393	ENSP00000019103:G393R	ENSP00000019103:G393R	G	-	1	0	SCTR	119915609	0.823000	0.29233	0.748000	0.31131	0.800000	0.45204	1.860000	0.39428	0.237000	0.21200	-0.140000	0.14226	GGG	.	.	none		0.602	SCTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254198.2		
ARHGAP33	115703	hgsc.bcm.edu	37	19	36273534	36273534	+	Silent	SNP	G	G	A	rs2291067	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:36273534G>A	ENST00000007510.4	+	14	1410	c.1266G>A	c.(1264-1266)ctG>ctA	p.L422L	ARHGAP33_ENST00000314737.5_Silent_p.L422L|ARHGAP33_ENST00000378944.5_Silent_p.L286L			O14559	RHG33_HUMAN	Rho GTPase activating protein 33	422	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				protein transport (GO:0015031)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	phosphatidylinositol binding (GO:0035091)|Rac GTPase activator activity (GO:0030675)			endometrium(7)|large_intestine(8)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	37						AGGAGCGTCTGGTGCGGGTGC	0.662													G|||	922	0.184105	0.1089	0.17	5008	,	,		17626	0.128		0.1829	False		,,,				2504	0.3548				p.L422L		Atlas-SNP	.											.	ARHGAP33	102	.	0			c.G1266A						PASS	.	G	,	526,3880	234.2+/-247.1	26,474,1703	38.0	34.0	36.0		858,1266	1.6	1.0	19	dbSNP_100	36	1626,6974	292.8+/-301.0	143,1340,2817	no	coding-synonymous,coding-synonymous	ARHGAP33	NM_001172630.1,NM_052948.3	,	169,1814,4520	AA,AG,GG		18.907,11.9383,16.5462	,	286/1124,422/1127	36273534	2152,10854	2203	4300	6503	SO:0001819	synonymous_variant	115703	exon14			GCGTCTGGTGCGG	AY044864	CCDS12477.1, CCDS54254.1	19q13.13	2011-06-29	2010-02-19	2010-02-19		ENSG00000004777		"""Rho GTPase activating proteins"""	23085	protein-coding gene	gene with protein product		614902	"""sorting nexin 26"""	SNX26		12297274, 12461558	Standard	NM_052948		Approved	FLJ39019, TCGAP	uc002obs.2	O14559		ENST00000007510.4:c.1266G>A	19.37:g.36273534G>A		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	74	74	1	NM_052948	O14552|O14560|Q6ZSP6|Q96CP3|Q9NT23	Silent	SNP	ENST00000007510.4	37																																																																																				G|0.834;A|0.166	0.166	strong		0.662	ARHGAP33-201	KNOWN	basic	protein_coding	protein_coding		NM_052948	
GLO1	2739	hgsc.bcm.edu	37	6	38650631	38650631	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:38650631T>C	ENST00000373365.4	-	4	415	c.329A>G	c.(328-330)gAt>gGt	p.D110G	GLO1_ENST00000470973.1_5'UTR	NM_006708.2	NP_006699.2	Q04760	LGUL_HUMAN	glyoxalase I	110					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)	CTGGGTCTCATCATCTTCAGT	0.368																																					p.D110G		Atlas-SNP	.											.	GLO1	12	.	0			c.A329G						PASS	.						161.0	131.0	141.0					6																	38650631		2203	4300	6503	SO:0001583	missense	2739	exon4			GTCTCATCATCTT	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.329A>G	6.37:g.38650631T>C	ENSP00000362463:p.Asp110Gly	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	95	5	0.0526316	NM_006708	B2R6P7|B4DDV0|P78375|Q59EL0|Q5TZW3|Q96FC0|Q96J41	Missense_Mutation	SNP	ENST00000373365.4	37	CCDS4837.1	.	.	.	.	.	.	.	.	.	.	T	28.9	4.959074	0.92726	.	.	ENSG00000124767	ENST00000373365	T	0.69561	-0.41	5.95	5.95	0.96441	Glyoxalase/fosfomycin resistance/dioxygenase (1);	0.043159	0.85682	D	0.000000	T	0.79969	0.4538	M	0.85462	2.755	0.80722	D	1	D	0.61080	0.989	D	0.65773	0.938	D	0.83766	0.0217	10	0.87932	D	0	-26.0981	16.0971	0.81132	0.0:0.0:0.0:1.0	.	110	Q04760	LGUL_HUMAN	G	110	ENSP00000362463:D110G	ENSP00000362463:D110G	D	-	2	0	GLO1	38758609	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.140000	0.77322	2.279000	0.76181	0.533000	0.62120	GAT	.	.	none		0.368	GLO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040438.2	NM_006708	
C5orf64	285668	hgsc.bcm.edu	37	5	60982841	60982841	+	Missense_Mutation	SNP	G	G	A	rs16893687	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:60982841G>A	ENST00000505642.1	+	3	244	c.169G>A	c.(169-171)Gct>Act	p.A57T	C5orf64_ENST00000313303.7_Missense_Mutation_p.A57T|RP11-2O17.2_ENST00000513386.1_RNA|RP11-2O17.2_ENST00000507264.1_RNA|RP11-2O17.2_ENST00000505623.1_RNA|C5orf64_ENST00000510414.1_Intron	NM_173667.2	NP_775938.1	Q2M2E5	CE064_HUMAN	chromosome 5 open reading frame 64	57			A -> T (in dbSNP:rs16893687). {ECO:0000269|PubMed:15489334}.			extracellular region (GO:0005576)				breast(1)	1						GGATCTGACCGCTGAAGTTTA	0.438													A|||	2482	0.495607	0.4486	0.4914	5008	,	,		19731	0.6458		0.336	False		,,,				2504	0.5716				p.A57T		Atlas-SNP	.											.	C5orf64	9	.	0			c.G169A						PASS	.	A	THR/ALA	1678,2180		378,922,629	152.0	147.0	149.0		169	0.9	0.7	5	dbSNP_123	149	2665,5593		425,1815,1889	yes	missense	C5orf64	NM_173667.2	58	803,2737,2518	AA,AG,GG		32.2717,43.494,35.8452	benign	57/131	60982841	4343,7773	1929	4129	6058	SO:0001583	missense	285668	exon3			CTGACCGCTGAAG		CCDS54860.1	5q12.1	2014-02-12	2011-05-05		ENSG00000178722	ENSG00000178722			26744	protein-coding gene	gene with protein product							Standard	NM_173667		Approved	FLJ37543	uc003jst.1	Q2M2E5	OTTHUMG00000162412	ENST00000505642.1:c.169G>A	5.37:g.60982841G>A	ENSP00000423157:p.Ala57Thr	Somatic	281	0	0		WXS	Illumina HiSeq	Phase_I	294	96	0.326531	NM_173667	Q2M2H1|Q8N1U8	Missense_Mutation	SNP	ENST00000505642.1	37	CCDS54860.1	1015	0.46474358974358976	208	0.42276422764227645	155	0.4281767955801105	398	0.6958041958041958	254	0.33509234828496043	A	7.117	0.577093	0.13686	0.43494	0.322717	ENSG00000178722	ENST00000505642;ENST00000313303	T;T	0.38401	1.14;1.14	4.92	0.845	0.18950	.	0.559392	0.13523	N	0.381575	T	0.00012	0.0000	N	0.03608	-0.345	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.42498	-0.9448	9	0.02654	T	1	-3.1044	3.2402	0.06778	0.3489:0.4296:0.0825:0.1391	rs16893687;rs52816625;rs56445660;rs16893687	57	Q2M2E5	CE064_HUMAN	T	57	ENSP00000423157:A57T;ENSP00000318395:A57T	ENSP00000318395:A57T	A	+	1	0	C5orf64	61018598	0.010000	0.17322	0.713000	0.30519	0.827000	0.46813	0.102000	0.15272	-0.253000	0.09514	-0.254000	0.11334	GCT	G|0.539;A|0.461	0.461	strong		0.438	C5orf64-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368790.1	NM_173667	
USP54	159195	hgsc.bcm.edu	37	10	75258558	75258558	+	Silent	SNP	G	G	A	rs61749235	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:75258558G>A	ENST00000339859.4	-	23	4984	c.4884C>T	c.(4882-4884)acC>acT	p.T1628T	USP54_ENST00000497106.1_5'UTR|PPP3CB_ENST00000342558.3_5'Flank|USP54_ENST00000408019.1_Silent_p.T1628T|RP11-137L10.6_ENST00000596320.1_RNA|RP11-137L10.6_ENST00000597958.1_RNA|USP54_ENST00000428547.1_Silent_p.T1478T|USP54_ENST00000422491.2_Silent_p.T763T|USP54_ENST00000394811.2_Silent_p.T669T|RP11-137L10.6_ENST00000593790.1_RNA|RP11-137L10.6_ENST00000595069.1_RNA|RP11-137L10.6_ENST00000595935.1_RNA|RP11-137L10.6_ENST00000442133.4_RNA|PPP3CB_ENST00000394822.2_5'Flank|PPP3CB_ENST00000360663.5_5'Flank|RP11-137L10.6_ENST00000600887.1_RNA|PPP3CB_ENST00000394829.2_5'Flank|PPP3CB_ENST00000545874.1_5'Flank|PPP3CB_ENST00000394828.2_5'Flank|RP11-137L10.6_ENST00000600607.1_RNA|RP11-137L10.6_ENST00000422977.1_RNA|RP11-137L10.6_ENST00000600206.1_RNA			Q70EL1	UBP54_HUMAN	ubiquitin specific peptidase 54	1628					ubiquitin-dependent protein catabolic process (GO:0006511)		ubiquitinyl hydrolase activity (GO:0036459)			breast(5)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(12)|ovary(1)|prostate(1)	30	Prostate(51;0.0112)					GAGGACCAGGGGTTCGGGACC	0.547													G|||	37	0.00738818	0.0	0.013	5008	,	,		15599	0.0		0.0159	False		,,,				2504	0.0123				p.T1628T	Colon(195;880 2046 8854 25025 38456)	Atlas-SNP	.											.	USP54	178	.	0			c.C4884T						PASS	.	G		22,4384	29.9+/-59.1	0,22,2181	89.0	87.0	88.0		4884	-1.0	0.6	10	dbSNP_129	88	154,8446	74.2+/-136.8	1,152,4147	no	coding-synonymous	USP54	NM_152586.3		1,174,6328	AA,AG,GG		1.7907,0.4993,1.3532		1628/1685	75258558	176,12830	2203	4300	6503	SO:0001819	synonymous_variant	159195	exon22			ACCAGGGGTTCGG	AJ583820	CCDS7329.2	10q22.3	2006-09-26	2005-08-08	2004-01-30	ENSG00000166348	ENSG00000166348		"""Ubiquitin-specific peptidases"""	23513	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 29"", ""ubiquitin specific protease 54"""	C10orf29		14715245	Standard	NM_152586		Approved	FLJ37318, bA137L10.3, bA137L10.4	uc001juo.3	Q70EL1	OTTHUMG00000018469	ENST00000339859.4:c.4884C>T	10.37:g.75258558G>A		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	99	98	0.989899	NM_152586	A1L4Q4|A3KFK3|A3KFK5|A3KFK6|A3KFK7|A6PVS4|A6PVS5|A6PVS6|A6PVS7|B3KVY1|B9ZVM1|Q5F2F4|Q6P1N6|Q6ZSP1|Q6ZSR1|Q6ZTM0|Q8N1X2	Silent	SNP	ENST00000339859.4	37	CCDS7329.2																																																																																			G|0.989;A|0.011	0.011	strong		0.547	USP54-014	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316563.2	NM_152586	
ENGASE	64772	hgsc.bcm.edu	37	17	77073941	77073941	+	Silent	SNP	T	T	C	rs56353542	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:77073941T>C	ENST00000579016.1	+	3	411	c.411T>C	c.(409-411)gaT>gaC	p.D137D	ENGASE_ENST00000539857.2_Start_Codon_SNP_p.M1T	NM_001042573.2	NP_001036038.1	Q8NFI3	ENASE_HUMAN	endo-beta-N-acetylglucosaminidase	137						cytoplasm (GO:0005737)	mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase activity (GO:0033925)			breast(2)|endometrium(4)|large_intestine(1)|lung(15)|prostate(2)|skin(1)	25						GGTACCTGGATGACAGGTGAG	0.587													C|||	187	0.0373403	0.025	0.0677	5008	,	,		13781	0.001		0.0845	False		,,,				2504	0.0215				p.D137D		Atlas-SNP	.											.	ENGASE	55	.	0			c.T411C						PASS	.	C		94,3788		0,94,1847	23.0	24.0	24.0		411	-9.8	0.6	17	dbSNP_129	24	640,7654		22,596,3529	no	coding-synonymous	ENGASE	NM_001042573.1		22,690,5376	CC,CT,TT		7.7164,2.4214,6.0283		137/744	77073941	734,11442	1941	4147	6088	SO:0001819	synonymous_variant	64772	exon3			CCTGGATGACAGG	AF512564	CCDS42394.1	17q25.3	2009-03-03			ENSG00000167280	ENSG00000167280	3.2.1.96		24622	protein-coding gene	gene with protein product	"""Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase"", ""Di-N-acetylchitobiosyl beta-N-acetylglucosaminidase"""	611898				12114544, 18586680	Standard	NM_001042573		Approved	FLJ21865	uc002jwv.4	Q8NFI3	OTTHUMG00000167714	ENST00000579016.1:c.411T>C	17.37:g.77073941T>C		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	29	12	0.413793	NM_001042573	Q659F0|Q8TB86|Q9H6U4	Silent	SNP	ENST00000579016.1	37	CCDS42394.1																																																																																			T|0.945;C|0.055	0.055	strong		0.587	ENGASE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395807.1	NM_022759	
FARP2	9855	hgsc.bcm.edu	37	2	242407746	242407746	+	Silent	SNP	A	A	G	rs10933559	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:242407746A>G	ENST00000264042.3	+	18	2255	c.2085A>G	c.(2083-2085)ctA>ctG	p.L695L		NM_014808.2	NP_055623.1	O94887	FARP2_HUMAN	FERM, RhoGEF and pleckstrin domain protein 2	695	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				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)		TGCGCCGCCTATGCGGACATT	0.622													A|||	677	0.135184	0.2148	0.1614	5008	,	,		18581	0.0		0.2356	False		,,,				2504	0.045				p.L695L		Atlas-SNP	.											.	FARP2	92	.	0			c.A2085G						PASS	.	A		998,3408	368.3+/-318.6	116,766,1321	46.0	40.0	42.0		2085	1.0	0.9	2	dbSNP_120	42	1818,6782	323.0+/-315.8	194,1430,2676	no	coding-synonymous	FARP2	NM_014808.2		310,2196,3997	GG,GA,AA		21.1395,22.6509,21.6515		695/1055	242407746	2816,10190	2203	4300	6503	SO:0001819	synonymous_variant	9855	exon18			CCGCCTATGCGGA	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.2085A>G	2.37:g.242407746A>G		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	85	31	0.364706	NM_014808	B7Z6J8|F5GZ84|Q53QM5|Q8WU27|Q9UFE7	Silent	SNP	ENST00000264042.3	37	CCDS33424.1																																																																																			A|0.804;G|0.196	0.196	strong		0.622	FARP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323153.1		
DENND3	22898	hgsc.bcm.edu	37	8	142170884	142170884	+	Silent	SNP	C	C	T	rs2289001	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:142170884C>T	ENST00000262585.2	+	9	1388	c.1110C>T	c.(1108-1110)ttC>ttT	p.F370F	DENND3_ENST00000424248.1_Intron|DENND3_ENST00000519811.1_Silent_p.F450F	NM_014957.2	NP_055772.2	A2RUS2	DEND3_HUMAN	DENN/MADD domain containing 3	370	dDENN. {ECO:0000255|PROSITE- ProRule:PRU00306}.				cellular protein catabolic process (GO:0044257)|endosome to lysosome transport (GO:0008333)|positive regulation of Rab GTPase activity (GO:0032851)		Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(19)|ovary(1)|prostate(3)|skin(4)|stomach(2)|urinary_tract(1)	55	all_cancers(97;7.36e-15)|all_epithelial(106;2.33e-13)|Lung NSC(106;1.23e-05)|all_lung(105;1.75e-05)|Ovarian(258;0.01)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.105)			TGAGCATCTTCAGGTACGTGA	0.602											OREG0019024	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	1468	0.293131	0.1339	0.3386	5008	,	,		18390	0.3393		0.2724	False		,,,				2504	0.4499				p.F370F		Atlas-SNP	.											DENND3,NS,carcinoma,0,1	DENND3	127	1	0			c.C1110T						PASS	.	C		731,3661		64,603,1529	40.0	34.0	36.0		1110	5.1	1.0	8	dbSNP_100	36	2515,6069		397,1721,2174	no	coding-synonymous	DENND3	NM_014957.2		461,2324,3703	TT,TC,CC		29.2987,16.6439,25.0154		370/1199	142170884	3246,9730	2196	4292	6488	SO:0001819	synonymous_variant	22898	exon9			CATCTTCAGGTAC	AB020677	CCDS34947.1	8q24.3	2013-01-10				ENSG00000105339		"""DENN/MADD domain containing"", ""WD repeat domain containing"""	29134	protein-coding gene	gene with protein product						10048485	Standard	NM_014957		Approved	KIAA0870	uc003yvy.3	A2RUS2		ENST00000262585.2:c.1110C>T	8.37:g.142170884C>T		Somatic	217	0	0	1669	WXS	Illumina HiSeq	Phase_I	200	39	0.195	NM_014957	B7ZM28|O94947|Q2TAM7|Q6ZMS6|Q96DK3	Silent	SNP	ENST00000262585.2	37	CCDS34947.1																																																																																			C|0.724;T|0.276	0.276	strong		0.602	DENND3-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_014957	
BRINP2	57795	hgsc.bcm.edu	37	1	177242695	177242695	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:177242695G>T	ENST00000361539.4	+	5	1053	c.741G>T	c.(739-741)ttG>ttT	p.L247F	BRINP2_ENST00000478325.1_3'UTR	NM_021165.2	NP_066988.1	Q9C0B6	BRNP2_HUMAN	bone morphogenetic protein/retinoic acid inducible neural-specific 2	247	MACPF.				cell cycle arrest (GO:0007050)|cellular response to retinoic acid (GO:0071300)|negative regulation of mitotic cell cycle (GO:0045930)|positive regulation of neuron differentiation (GO:0045666)	extracellular region (GO:0005576)											GTTCTGTCTTGGTACAGAGTC	0.448																																					p.L247F		Atlas-SNP	.											.	FAM5B	191	.	0			c.G741T						PASS	.						85.0	77.0	79.0					1																	177242695		2203	4300	6503	SO:0001583	missense	57795	exon5			TGTCTTGGTACAG		CCDS1320.1	1q24	2013-08-06	2013-08-06	2013-07-31	ENSG00000198797	ENSG00000198797			13746	protein-coding gene	gene with protein product			"""family with sequence similarity 5, member B"""	FAM5B		15193423	Standard	NM_021165		Approved	DBCCR1L2	uc001glf.3	Q9C0B6	OTTHUMG00000034953	ENST00000361539.4:c.741G>T	1.37:g.177242695G>T	ENSP00000354481:p.Leu247Phe	Somatic	209	0	0		WXS	Illumina HiSeq	Phase_I	190	35	0.184211	NM_021165	O95560|Q6ZWC1|Q7LCZ9|Q8N360	Missense_Mutation	SNP	ENST00000361539.4	37	CCDS1320.1	.	.	.	.	.	.	.	.	.	.	G	20.6	4.015662	0.75161	.	.	ENSG00000198797	ENST00000361539	T	0.27402	1.67	5.39	4.44	0.53790	Membrane attack complex component/perforin (MACPF) domain (1);	0.000000	0.64402	D	0.000002	T	0.54647	0.1871	M	0.74647	2.275	0.58432	D	0.999999	D;D	0.71674	0.995;0.998	D;D	0.83275	0.954;0.996	T	0.58940	-0.7547	10	0.87932	D	0	-11.3146	13.6873	0.62524	0.0:0.0:0.7267:0.2733	.	142;247	Q9C0B6-2;Q9C0B6	.;FAM5B_HUMAN	F	247	ENSP00000354481:L247F	ENSP00000354481:L247F	L	+	3	2	FAM5B	175509318	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	2.030000	0.41108	2.537000	0.85549	0.655000	0.94253	TTG	.	.	none		0.448	BRINP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084599.1	NM_021165	
RP1L1	94137	hgsc.bcm.edu	37	8	10467160	10467160	+	Missense_Mutation	SNP	G	G	A	rs62490855	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:10467160G>A	ENST00000382483.3	-	4	4671	c.4448C>T	c.(4447-4449)gCc>gTc	p.A1483V		NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	1563					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)		CATCATGGTGGCTCCGGGCGG	0.667													G|||	883	0.176318	0.0393	0.1686	5008	,	,		15524	0.1597		0.1421	False		,,,				2504	0.4192				p.A1483V		Atlas-SNP	.											.	RP1L1	453	.	0			c.C4448T						PASS	.	G	VAL/ALA	238,3682		10,218,1732	36.0	40.0	39.0		4448	-2.8	0.0	8	dbSNP_129	39	1217,7131		97,1023,3054	yes	missense	RP1L1	NM_178857.5	64	107,1241,4786	AA,AG,GG		14.5783,6.0714,11.8601	possibly-damaging	1483/2401	10467160	1455,10813	1960	4174	6134	SO:0001583	missense	94137	exon4			ATGGTGGCTCCGG	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.4448C>T	8.37:g.10467160G>A	ENSP00000371923:p.Ala1483Val	Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	39	8	0.205128	NM_178857	Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	Missense_Mutation	SNP	ENST00000382483.3	37	CCDS43708.1	306	0.1401098901098901	27	0.054878048780487805	64	0.17679558011049723	100	0.17482517482517482	115	0.1517150395778364	G	12.96	2.093607	0.36952	0.060714	0.145783	ENSG00000183638	ENST00000382483	T	0.04809	3.55	4.78	-2.78	0.05859	.	1.606950	0.04389	N	0.362076	T	0.00012	0.0000	L	0.29908	0.895	0.80722	P	0.0	P	0.48764	0.915	B	0.41946	0.371	T	0.40496	-0.9560	9	0.06625	T	0.88	0.1679	8.9228	0.35621	0.0:0.1989:0.2911:0.51	rs62490855	1483	A6NKC6	.	V	1483	ENSP00000371923:A1483V	ENSP00000371923:A1483V	A	-	2	0	RP1L1	10504570	0.000000	0.05858	0.000000	0.03702	0.013000	0.08279	-0.334000	0.07883	-0.403000	0.07622	0.561000	0.74099	GCC	G|0.853;A|0.147	0.147	strong		0.667	RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375673.1		
MGMT	4255	hgsc.bcm.edu	37	10	131565064	131565064	+	Missense_Mutation	SNP	A	A	G	rs2308321	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	83	0	0		WXS	Illumina HiSeq	Phase_I	78	36	0.461538	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	
SLC6A3	6531	hgsc.bcm.edu	37	5	1411412	1411412	+	Silent	SNP	T	T	C	rs6347	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:1411412T>C	ENST00000270349.9	-	9	1342	c.1215A>G	c.(1213-1215)tcA>tcG	p.S405S	SLC6A3_ENST00000453492.2_Silent_p.S405S	NM_001044.4	NP_001035.1	Q01959	SC6A3_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 3	405					adenohypophysis development (GO:0021984)|aging (GO:0007568)|cation transmembrane transport (GO:0098655)|cell death (GO:0008219)|dopamine biosynthetic process (GO:0042416)|dopamine catabolic process (GO:0042420)|dopamine transport (GO:0015872)|lactation (GO:0007595)|locomotory behavior (GO:0007626)|monoamine transport (GO:0015844)|neurotransmitter biosynthetic process (GO:0042136)|positive regulation of multicellular organism growth (GO:0040018)|prepulse inhibition (GO:0060134)|regulation of dopamine metabolic process (GO:0042053)|response to cAMP (GO:0051591)|response to cocaine (GO:0042220)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to iron ion (GO:0010039)|response to nicotine (GO:0035094)|sensory perception of smell (GO:0007608)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	axon (GO:0030424)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	dopamine binding (GO:0035240)|dopamine transmembrane transporter activity (GO:0005329)|dopamine:sodium symporter activity (GO:0005330)|drug binding (GO:0008144)|monoamine transmembrane transporter activity (GO:0008504)			breast(2)|endometrium(4)|kidney(1)|large_intestine(3)|lung(19)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	38			OV - Ovarian serous cystadenocarcinoma(19;0.00928)|all cancers(22;0.0262)		Amoxapine(DB00543)|Amphetamine(DB00182)|Atomoxetine(DB00289)|Benzatropine(DB00245)|Benzphetamine(DB00865)|Bupropion(DB01156)|Chloroprocaine(DB01161)|Chlorphenamine(DB01114)|Citalopram(DB00215)|Cocaine(DB00907)|Dexmethylphenidate(DB06701)|Dextroamphetamine(DB01576)|Diethylpropion(DB00937)|Diphenylpyraline(DB01146)|Dopamine(DB00988)|Duloxetine(DB00476)|Ephedra(DB01363)|Escitalopram(DB01175)|Fencamfamine(DB01463)|Imipramine(DB00458)|Ioflupane I 123(DB08824)|Lisdexamfetamine(DB01255)|Loxapine(DB00408)|Mazindol(DB00579)|Methamphetamine(DB01577)|Methylphenidate(DB00422)|Mianserin(DB06148)|Mirtazapine(DB00370)|Modafinil(DB00745)|Nefazodone(DB01149)|Pethidine(DB00454)|Phenmetrazine(DB00830)|Phentermine(DB00191)|Procaine(DB00721)|Pseudoephedrine(DB00852)|Sertraline(DB01104)|Sibutramine(DB01105)|Trimipramine(DB00726)|Venlafaxine(DB00285)	CGGCCCAGGCTGAGGACAGAG	0.637													C|||	1495	0.298522	0.59	0.1988	5008	,	,		16998	0.125		0.2932	False		,,,				2504	0.1595				p.S405S		Atlas-SNP	.											.	SLC6A3	102	.	0			c.A1215G	GRCh37	CM004732	SLC6A3	M	rs6347	PASS	.	C		2057,2239		520,1017,611	83.0	64.0	71.0		1215	-9.4	0.0	5	dbSNP_52	71	2193,6259		324,1545,2357	no	coding-synonymous	SLC6A3	NM_001044.4		844,2562,2968	CC,CT,TT		25.9465,47.8818,33.3386		405/621	1411412	4250,8498	2148	4226	6374	SO:0001819	synonymous_variant	6531	exon9			CCAGGCTGAGGAC		CCDS3863.1	5p15.3	2013-07-19	2013-07-19		ENSG00000142319	ENSG00000142319		"""Solute carriers"""	11049	protein-coding gene	gene with protein product	"""dopamine transporter"""	126455	"""solute carrier family 6 (neurotransmitter transporter, dopamine), member 3"", ""dopamine transporter 1"""	DAT1		1406597	Standard	NM_001044		Approved	DAT	uc003jck.3	Q01959	OTTHUMG00000131016	ENST00000270349.9:c.1215A>G	5.37:g.1411412T>C		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	72	30	0.416667	NM_001044	A2RUN4|Q14996	Silent	SNP	ENST00000270349.9	37	CCDS3863.1																																																																																			T|0.671;C|0.329	0.329	strong		0.637	SLC6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253650.3	NM_001044	
MTIF2	4528	hgsc.bcm.edu	37	2	55470662	55470662	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:55470662A>G	ENST00000263629.4	-	12	1769	c.1454T>C	c.(1453-1455)cTg>cCg	p.L485P	MTIF2_ENST00000403721.1_Missense_Mutation_p.L485P|MTIF2_ENST00000394600.3_Missense_Mutation_p.L485P	NM_002453.2	NP_002444.2	P46199	IF2M_HUMAN	mitochondrial translational initiation factor 2	485					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)			breast(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(5)|ovary(1)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	24						CTTCTTCCACAGTAGATGGCC	0.383																																					p.L485P		Atlas-SNP	.											.	MTIF2	64	.	0			c.T1454C						PASS	.						188.0	184.0	185.0					2																	55470662		2203	4300	6503	SO:0001583	missense	4528	exon12			TTCCACAGTAGAT	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.1454T>C	2.37:g.55470662A>G	ENSP00000263629:p.Leu485Pro	Somatic	256	0	0		WXS	Illumina HiSeq	Phase_I	422	328	0.777251	NM_002453	D6W5D0	Missense_Mutation	SNP	ENST00000263629.4	37	CCDS1853.1	.	.	.	.	.	.	.	.	.	.	A	4.188	0.033551	0.08101	.	.	ENSG00000085760	ENST00000403721;ENST00000263629;ENST00000394600;ENST00000418823	T;T;T;T	0.58358	0.34;0.34;0.34;0.87	5.6	1.63	0.23807	.	0.432007	0.27700	N	0.018206	T	0.28267	0.0698	N	0.08118	0	0.38365	D	0.944718	B	0.16802	0.019	B	0.22601	0.04	T	0.05784	-1.0864	10	0.36615	T	0.2	0.6749	7.0519	0.25077	0.2056:0.0:0.2629:0.5315	.	485	P46199	IF2M_HUMAN	P	485;485;485;163	ENSP00000384481:L485P;ENSP00000263629:L485P;ENSP00000378099:L485P;ENSP00000403492:L163P	ENSP00000263629:L485P	L	-	2	0	MTIF2	55324166	1.000000	0.71417	0.995000	0.50966	0.052000	0.14988	0.787000	0.26858	0.381000	0.24851	-0.275000	0.10095	CTG	.	.	none		0.383	MTIF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251486.4	NM_002453	
RP1L1	94137	hgsc.bcm.edu	37	8	10465942	10465942	+	Missense_Mutation	SNP	T	T	A	rs28446662	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	77	0	0		WXS	Illumina HiSeq	Phase_I	56	46	0.821429	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		
ZNF280A	129025	hgsc.bcm.edu	37	22	22868700	22868700	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:22868700T>C	ENST00000302097.3	-	2	1507	c.1255A>G	c.(1255-1257)Aac>Gac	p.N419D		NM_080740.3	NP_542778.1	P59817	Z280A_HUMAN	zinc finger protein 280A	419					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(4)|lung(8)|ovary(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	18	all_hematologic(9;0.0135)|Acute lymphoblastic leukemia(84;0.17)	all_hematologic(6;1.74e-30)|Acute lymphoblastic leukemia(6;7.75e-22)		READ - Rectum adenocarcinoma(21;0.145)		TTCTTTGTGTTTTCATGGCAC	0.433																																					p.N419D		Atlas-SNP	.											ZNF280A,colon,carcinoma,0,1	ZNF280A	67	1	0			c.A1255G						scavenged	.						122.0	109.0	113.0					22																	22868700		2203	4300	6503	SO:0001583	missense	129025	exon2			TTGTGTTTTCATG	D87009	CCDS13800.1	22q11.21	2007-09-20	2007-09-20	2007-09-20	ENSG00000169548	ENSG00000169548			18597	protein-coding gene	gene with protein product			"""zinc finger protein 280"", ""suppressor of hairy wing homolog 1 (Drosophila)"""	ZNF280, SUHW1		9074928	Standard	NM_080740		Approved	3'OY11.1, ZNF636	uc002zwe.3	P59817	OTTHUMG00000030545	ENST00000302097.3:c.1255A>G	22.37:g.22868700T>C	ENSP00000302855:p.Asn419Asp	Somatic	221	0	0		WXS	Illumina HiSeq	Phase_I	219	3	0.0136986	NM_080740		Missense_Mutation	SNP	ENST00000302097.3	37	CCDS13800.1	.	.	.	.	.	.	.	.	.	.	T	10.52	1.373833	0.24857	.	.	ENSG00000169548	ENST00000302097	T	0.59906	0.23	4.09	1.81	0.25067	.	.	.	.	.	T	0.64182	0.2575	L	0.58583	1.82	0.26359	N	0.977077	D	0.71674	0.998	D	0.64237	0.923	T	0.51764	-0.8664	9	0.48119	T	0.1	-7.2601	4.2681	0.10773	0.2192:0.1002:0.0:0.6807	.	419	P59817	Z280A_HUMAN	D	419	ENSP00000302855:N419D	ENSP00000302855:N419D	N	-	1	0	ZNF280A	21198700	1.000000	0.71417	0.353000	0.25747	0.014000	0.08584	2.496000	0.45346	0.271000	0.22005	-0.256000	0.11100	AAC	.	.	none		0.433	ZNF280A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075433.3	NM_080740	
PCDHB13	56123	hgsc.bcm.edu	37	5	140595756	140595756	+	Silent	SNP	C	C	T	rs17844617	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	44	0	0		WXS	Illumina HiSeq	Phase_I	32	17	0.53125	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	
SGK1	6446	hgsc.bcm.edu	37	6	134494426	134494426	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:134494426G>T	ENST00000237305.7	-	5	491	c.403C>A	c.(403-405)Ctg>Atg	p.L135M	SGK1_ENST00000475719.2_Missense_Mutation_p.L135M|SGK1_ENST00000489458.2_5'UTR|SGK1_ENST00000528577.1_Missense_Mutation_p.L163M|SGK1_ENST00000367858.5_Missense_Mutation_p.L230M|SGK1_ENST00000367857.5_Missense_Mutation_p.L125M|SGK1_ENST00000413996.3_Missense_Mutation_p.L149M	NM_005627.3	NP_005618.2	O00141	SGK1_HUMAN	serum/glucocorticoid regulated kinase 1	135	Glu/Lys-rich.|Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|cellular response to DNA damage stimulus (GO:0006974)|ion transmembrane transport (GO:0034220)|long-term memory (GO:0007616)|positive regulation of transporter activity (GO:0032411)|protein phosphorylation (GO:0006468)|regulation of apoptotic process (GO:0042981)|regulation of blood pressure (GO:0008217)|regulation of catalytic activity (GO:0050790)|regulation of cell growth (GO:0001558)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of gastric acid secretion (GO:0060453)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|renal sodium ion absorption (GO:0070294)|response to stress (GO:0006950)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium channel regulator activity (GO:0005246)|chloride channel regulator activity (GO:0017081)|potassium channel regulator activity (GO:0015459)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|sodium channel regulator activity (GO:0017080)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(21)|kidney(3)|large_intestine(3)|lung(10)|ovary(1)|skin(4)|stomach(1)	46	Colorectal(23;0.221)			OV - Ovarian serous cystadenocarcinoma(155;0.00317)|GBM - Glioblastoma multiforme(68;0.00847)		TTCTTTTTCAGGATTGCTTTC	0.378																																					p.L230M		Atlas-SNP	.											.	SGK1	387	.	0			c.C688A						PASS	.						114.0	113.0	113.0					6																	134494426		2203	4300	6503	SO:0001583	missense	6446	exon7			TTTTCAGGATTGC	AJ000512	CCDS5170.1, CCDS47476.1, CCDS47477.1, CCDS47478.1	6q23	2008-02-05	2007-12-05	2007-12-05	ENSG00000118515	ENSG00000118515			10810	protein-coding gene	gene with protein product		602958	"""serum/glucocorticoid regulated kinase"""	SGK		9114008, 9722955	Standard	NM_005627		Approved		uc003qeo.4	O00141	OTTHUMG00000015613	ENST00000237305.7:c.403C>A	6.37:g.134494426G>T	ENSP00000237305:p.Leu135Met	Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	103	31	0.300971	NM_001143676	B7UUP7|B7UUP8|B7UUP9|B7Z5B2|E1P583|Q5TCN2|Q5TCN3|Q5TCN4|Q5VY65|Q9UN56	Missense_Mutation	SNP	ENST00000237305.7	37	CCDS5170.1	.	.	.	.	.	.	.	.	.	.	G	16.53	3.149912	0.57151	.	.	ENSG00000118515	ENST00000367858;ENST00000413996;ENST00000237305;ENST00000367857;ENST00000528577;ENST00000475719	T;T;T;T;T;T	0.66099	-0.19;-0.19;-0.19;-0.19;-0.19;1.88	6.17	5.3	0.74995	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.54481	0.1861	L	0.42686	1.345	0.80722	D	1	B;B;B;B;B;B	0.32918	0.24;0.386;0.389;0.099;0.39;0.121	B;B;P;B;B;B	0.44673	0.179;0.291;0.457;0.111;0.408;0.177	T	0.61262	-0.7098	10	0.54805	T	0.06	.	15.9715	0.80025	0.0648:0.0:0.9352:0.0	.	163;149;135;125;230;135	O00141-5;O00141-3;E9PR89;O00141-4;O00141-2;O00141	.;.;.;.;.;SGK1_HUMAN	M	230;149;135;125;163;135	ENSP00000356832:L230M;ENSP00000396242:L149M;ENSP00000237305:L135M;ENSP00000356831:L125M;ENSP00000434450:L163M;ENSP00000434302:L135M	ENSP00000237305:L135M	L	-	1	2	SGK1	134536119	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.089000	0.57685	1.599000	0.50093	0.655000	0.94253	CTG	.	.	none		0.378	SGK1-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042312.2		
AGTPBP1	23287	hgsc.bcm.edu	37	9	88204462	88204462	+	Silent	SNP	A	A	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:88204462A>G	ENST00000357081.3	-	20	2847	c.2703T>C	c.(2701-2703)taT>taC	p.Y901Y	AGTPBP1_ENST00000337006.4_3'UTR|AGTPBP1_ENST00000376083.3_Silent_p.Y861Y|AGTPBP1_ENST00000432218.1_Intron|AGTPBP1_ENST00000376109.3_Silent_p.Y913Y			Q9UPW5	CBPC1_HUMAN	ATP/GTP binding protein 1	901					adult walking behavior (GO:0007628)|C-terminal protein deglutamylation (GO:0035609)|cerebellar Purkinje cell differentiation (GO:0021702)|eye photoreceptor cell differentiation (GO:0001754)|mitochondrion organization (GO:0007005)|neuromuscular process (GO:0050905)|neurotransmitter metabolic process (GO:0042133)|olfactory bulb development (GO:0021772)|protein side chain deglutamylation (GO:0035610)|retina development in camera-type eye (GO:0060041)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	metallocarboxypeptidase activity (GO:0004181)|tubulin binding (GO:0015631)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(12)|lung(12)|ovary(5)|skin(2)|urinary_tract(3)	44						AGATATGTTCATAATAATTAG	0.378																																					p.Y861Y		Atlas-SNP	.											.	AGTPBP1	128	.	0			c.T2583C						PASS	.						133.0	129.0	130.0					9																	88204462		2203	4300	6503	SO:0001819	synonymous_variant	23287	exon20			ATGTTCATAATAA	AB028958	CCDS6672.1, CCDS75854.1	9q21.33	2014-06-23			ENSG00000135049	ENSG00000135049			17258	protein-coding gene	gene with protein product	"""cytosolic carboxypeptidase 1"", ""tubulinyl-Tyr carboxypeptidase"", ""carboxypeptidase-tubulin"", ""tyrosine carboxypeptidase"", ""soluble carboxypeptidase"""	606830				11083920	Standard	NM_015239		Approved	KIAA1035, Nna1, CCP1	uc010mqc.3	Q9UPW5	OTTHUMG00000020124	ENST00000357081.3:c.2703T>C	9.37:g.88204462A>G		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	119	48	0.403361	NM_015239	B4DIT6|B4DRZ8|Q5VV80|Q63HM7|Q658P5|Q6P9D6|Q9H8U6|Q9H9W8|Q9NVK1	Silent	SNP	ENST00000357081.3	37																																																																																				.	.	none		0.378	AGTPBP1-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000052893.1	NM_015239	
TULP1	7287	hgsc.bcm.edu	37	6	35477032	35477032	+	Missense_Mutation	SNP	A	A	G	rs2064317	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	100	0	0		WXS	Illumina HiSeq	Phase_I	89	42	0.47191	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		
GCKR	2646	hgsc.bcm.edu	37	2	27741665	27741665	+	Missense_Mutation	SNP	G	G	A	rs141361209	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:27741665G>A	ENST00000264717.2	+	17	1496	c.1433G>A	c.(1432-1434)cGt>cAt	p.R478H	GCKR_ENST00000424318.2_Missense_Mutation_p.R288H	NM_001486.3	NP_001477.2	Q14397	GCKR_HUMAN	glucokinase (hexokinase 4) regulator	478	SIS 2. {ECO:0000255|PROSITE- ProRule:PRU00797}.				carbohydrate metabolic process (GO:0005975)|cellular glucose homeostasis (GO:0001678)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|negative regulation of glucokinase activity (GO:0033132)|positive regulation of glucokinase activity (GO:0033133)|protein import into nucleus, translocation (GO:0000060)|regulation of glucose transport (GO:0010827)|response to fructose (GO:0009750)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|triglyceride homeostasis (GO:0070328)|urate metabolic process (GO:0046415)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)	carbohydrate binding (GO:0030246)|enzyme inhibitor activity (GO:0004857)|fructose-6-phosphate binding (GO:0070095)	p.R478L(1)		breast(2)|endometrium(4)|kidney(2)|large_intestine(4)|liver(2)|lung(13)|ovary(2)	29	Acute lymphoblastic leukemia(172;0.155)					AAGTTCCAGCGTGAGCTAAGC	0.473													G|||	4	0.000798722	0.0	0.0029	5008	,	,		19790	0.0		0.002	False		,,,				2504	0.0				p.R478H		Atlas-SNP	.											GCKR,NS,carcinoma,0,1	GCKR	73	1	1	Substitution - Missense(1)	lung(1)	c.G1433A						PASS	.	G	HIS/ARG	1,4405		0,1,2202	105.0	101.0	103.0		1433	1.2	1.0	2	dbSNP_134	103	3,8597	3.7+/-12.6	0,3,4297	yes	missense	GCKR	NM_001486.3	29	0,4,6499	AA,AG,GG		0.0349,0.0227,0.0308	benign	478/626	27741665	4,13002	2203	4300	6503	SO:0001583	missense	2646	exon17			TCCAGCGTGAGCT	Z48475	CCDS1757.1	2p23	2008-05-21	2004-05-20		ENSG00000084734	ENSG00000084734			4196	protein-coding gene	gene with protein product		600842	"""glucokinase (hexokinase 4) regulatory protein"""			9570959, 8662230	Standard	NM_001486		Approved		uc002rky.3	Q14397	OTTHUMG00000128426	ENST00000264717.2:c.1433G>A	2.37:g.27741665G>A	ENSP00000264717:p.Arg478His	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	123	46	0.373984	NM_001486	A1L4C2|B4DPQ2|Q53RY6|Q99522	Missense_Mutation	SNP	ENST00000264717.2	37	CCDS1757.1	3	0.0013736263736263737	0	0.0	2	0.0055248618784530384	0	0.0	1	0.0013192612137203166	G	7.777	0.708592	0.15239	2.27E-4	3.49E-4	ENSG00000084734	ENST00000264717;ENST00000424318	D;D	0.83419	-1.72;-1.72	3.76	1.18	0.20946	Sugar isomerase (SIS) (1);	0.265072	0.33075	N	0.005308	T	0.58793	0.2147	N	0.25144	0.715	0.28844	N	0.896431	B;B;B	0.10296	0.003;0.001;0.001	B;B;B	0.06405	0.002;0.0;0.0	T	0.47045	-0.9147	10	0.11182	T	0.66	0.0223	9.1221	0.36793	0.1699:0.0:0.8301:0.0	.	288;476;478	F5H1P6;A8K731;Q14397	.;.;GCKR_HUMAN	H	478;288	ENSP00000264717:R478H;ENSP00000409109:R288H	ENSP00000264717:R478H	R	+	2	0	GCKR	27595169	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	1.557000	0.36299	0.269000	0.21961	0.561000	0.74099	CGT	G|0.999;A|0.001	0.001	strong		0.473	GCKR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250214.1	NM_001486	
ERLEC1	27248	hgsc.bcm.edu	37	2	54035447	54035447	+	Silent	SNP	A	A	G	rs1127362	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:54035447A>G	ENST00000185150.4	+	9	1022	c.891A>G	c.(889-891)caA>caG	p.Q297Q	ERLEC1_ENST00000378239.5_Intron|ASB3_ENST00000406625.2_Intron|GPR75-ASB3_ENST00000352846.3_Intron|ERLEC1_ENST00000405123.3_Silent_p.Q297Q|ASB3_ENST00000498475.2_Intron	NM_015701.4	NP_056516.2	Q96DZ1	ERLEC_HUMAN	endoplasmic reticulum lectin 1	297					ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)	endoplasmic reticulum lumen (GO:0005788)	glycoprotein binding (GO:0001948)	p.Q297Q(1)		endometrium(2)|large_intestine(4)|lung(8)|ovary(2)|stomach(1)|urinary_tract(1)	18						AAGATTTGCAATCAACTAAAG	0.373													A|||	865	0.172724	0.1044	0.2032	5008	,	,		17434	0.1597		0.1799	False		,,,				2504	0.2495				p.Q297Q		Atlas-SNP	.											ERLEC1,NS,carcinoma,0,1	ERLEC1	32	1	1	Substitution - coding silent(1)	stomach(1)	c.A891G						PASS	.	A	,,,	525,3881	240.3+/-251.1	34,457,1712	83.0	83.0	83.0		891,,,891	-9.9	0.2	2	dbSNP_100	83	1658,6942	304.9+/-307.2	164,1330,2806	no	coding-synonymous,intron,intron,coding-synonymous	ERLEC1,GPR75-ASB3	NM_001127397.2,NM_001127398.2,NM_001164165.1,NM_015701.4	,,,	198,1787,4518	GG,GA,AA		19.2791,11.9156,16.7846	,,,	297/458,,,297/484	54035447	2183,10823	2203	4300	6503	SO:0001819	synonymous_variant	27248	exon9			TTTGCAATCAACT	AF131849	CCDS1848.1, CCDS46283.1, CCDS46284.1	2p16	2010-03-19	2009-08-26	2009-08-26	ENSG00000068912	ENSG00000068912			25222	protein-coding gene	gene with protein product	"""erlectin 1"""	611229	"""chromosome 2 open reading frame 30"""	C2orf30		9110174, 8619474, 16531414, 18264092	Standard	NM_015701		Approved	CL25084, XTP3TPB, XTP3-B, ERLECTIN	uc002rxl.3	Q96DZ1	OTTHUMG00000129281	ENST00000185150.4:c.891A>G	2.37:g.54035447A>G		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	88	69	0.784091	NM_015701	B2RDB4|B5MC72|O95901|Q6UWN7|Q9NUY7|Q9UQL4	Silent	SNP	ENST00000185150.4	37	CCDS1848.1																																																																																			A|0.835;G|0.165	0.165	strong		0.373	ERLEC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251404.1	NM_015701	
FHL5	9457	hgsc.bcm.edu	37	6	97063555	97063555	+	Silent	SNP	A	A	G	rs9398148	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:97063555A>G	ENST00000326771.2	+	7	1142	c.762A>G	c.(760-762)aaA>aaG	p.K254K	FHL5_ENST00000541107.1_Silent_p.K254K	NM_020482.4	NP_065228.4	Q5TD97	FHL5_HUMAN	four and a half LIM domains 5	254	LIM zinc-binding 4. {ECO:0000255|PROSITE- ProRule:PRU00125}.			K -> R (in Ref. 1; AAF85978). {ECO:0000305}.	positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(4)|lung(17)|ovary(2)|urinary_tract(1)	27		all_cancers(76;1.57e-07)|Acute lymphoblastic leukemia(125;4.93e-10)|all_hematologic(75;3.55e-07)|all_epithelial(107;0.00266)|Colorectal(196;0.0341)|Lung NSC(302;0.204)		BRCA - Breast invasive adenocarcinoma(108;0.0948)		ACTGCGGGAAATGCTCTGTCT	0.463													G|||	1926	0.384585	0.5038	0.2997	5008	,	,		19407	0.3522		0.3489	False		,,,				2504	0.3538				p.K254K		Atlas-SNP	.											FHL5,caecum,carcinoma,+2,1	FHL5	73	1	0			c.A762G						PASS	.	G	,	2161,2245	594.3+/-388.2	533,1095,575	115.0	112.0	113.0		762,762	3.6	1.0	6	dbSNP_119	113	2871,5729	673.0+/-403.0	477,1917,1906	no	coding-synonymous,coding-synonymous	FHL5	NM_001170807.1,NM_020482.4	,	1010,3012,2481	GG,GA,AA		33.3837,49.0468,38.6898	,	254/285,254/285	97063555	5032,7974	2203	4300	6503	SO:0001819	synonymous_variant	9457	exon7			CGGGAAATGCTCT	AF278541	CCDS5035.1	6q16.1-q16.3	2008-02-05			ENSG00000112214	ENSG00000112214			17371	protein-coding gene	gene with protein product		605126					Standard	NM_020482		Approved	FLJ33049, ACT, dJ393D12.2	uc003pot.2	Q5TD97	OTTHUMG00000015239	ENST00000326771.2:c.762A>G	6.37:g.97063555A>G		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	108	108	1	NM_020482	B2RBD1|E1P526|Q5TD98|Q8WW21|Q9NQU2	Silent	SNP	ENST00000326771.2	37	CCDS5035.1																																																																																			A|0.613;G|0.387	0.387	strong		0.463	FHL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041559.1	NM_020482	
MEF2D	4209	hgsc.bcm.edu	37	1	156450719	156450719	+	Silent	SNP	G	G	A	rs1185700	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:156450719G>A	ENST00000348159.4	-	4	783	c.303C>T	c.(301-303)ccC>ccT	p.P101P	MEF2D_ENST00000340875.5_Intron|MEF2D_ENST00000360595.3_Silent_p.P101P|MEF2D_ENST00000464356.2_Intron|MEF2D_ENST00000368240.2_Silent_p.P101P|MEF2D_ENST00000353795.3_Intron	NM_005920.2	NP_005911.1	Q14814	MEF2D_HUMAN	myocyte enhancer factor 2D	101					adult heart development (GO:0007512)|apoptotic process (GO:0006915)|chondrocyte differentiation (GO:0002062)|endochondral ossification (GO:0001958)|muscle organ development (GO:0007517)|nervous system development (GO:0007399)|osteoblast differentiation (GO:0001649)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|skeletal muscle cell differentiation (GO:0035914)|transcription from RNA polymerase II promoter (GO:0006366)	intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	activating transcription factor binding (GO:0033613)|histone deacetylase binding (GO:0042826)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(4)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|urinary_tract(1)	15	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					CCTCCCCGTCGGGCTCGGGGC	0.677											OREG0013874	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	1165	0.232628	0.1808	0.2983	5008	,	,		14474	0.245		0.2386	False		,,,				2504	0.2372				p.P101P		Atlas-SNP	.											.	MEF2D	43	.	0			c.C303T						PASS	.	G		932,3472	332.3+/-302.4	90,752,1360	74.0	84.0	81.0		303	-7.7	0.8	1	dbSNP_87	81	1987,6611	330.6+/-319.3	245,1497,2557	no	coding-synonymous	MEF2D	NM_005920.2		335,2249,3917	AA,AG,GG		23.11,21.1626,22.4504		101/522	156450719	2919,10083	2202	4299	6501	SO:0001819	synonymous_variant	4209	exon4			CCCGTCGGGCTCG	BC054520	CCDS1143.1, CCDS60304.1	1q12-q23	2008-02-05	2007-04-24		ENSG00000116604	ENSG00000116604		"""Myocyte enhancer factors"""	6997	protein-coding gene	gene with protein product		600663				8269842	Standard	NM_005920		Approved		uc001fpb.4	Q14814	OTTHUMG00000033095	ENST00000348159.4:c.303C>T	1.37:g.156450719G>A		Somatic	106	0	0	1778	WXS	Illumina HiSeq	Phase_I	136	57	0.419118	NM_005920	D3DVC0|Q14815|Q5T9U5|Q5T9U6	Silent	SNP	ENST00000348159.4	37	CCDS1143.1																																																																																			G|0.766;A|0.234	0.234	strong		0.677	MEF2D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080562.2	NM_005920	
CALML5	51806	hgsc.bcm.edu	37	10	5541181	5541181	+	Missense_Mutation	SNP	T	T	C	rs10904516|rs373657626|rs386740368	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:5541181T>C	ENST00000380332.3	-	1	352	c.221A>G	c.(220-222)aAg>aGg	p.K74R		NM_017422.4	NP_059118.2	Q9NZT1	CALL5_HUMAN	calmodulin-like 5	74	EF-hand 2. {ECO:0000255|PROSITE- ProRule:PRU00448}.		K -> R (polymorphism confirmed at protein level; dbSNP:rs10904516). {ECO:0000269|PubMed:10777582, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17488105}.		epidermis development (GO:0008544)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)	p.K74R(1)		biliary_tract(1)|large_intestine(2)|lung(2)|ovary(1)|skin(1)|stomach(1)	8						CCTGGCCTTCTTCGCCGCCGT	0.657													T|||	1769	0.353235	0.5121	0.2334	5008	,	,		16118	0.3046		0.3221	False		,,,				2504	0.3057				p.K74R	GBM(149;1055 3356 43077)	Atlas-SNP	.											CALML5,rectum,carcinoma,0,2	CALML5	25	2	1	Substitution - Missense(1)	stomach(1)	c.A221G						PASS	.	T	ARG/LYS	530,3876		209,112,1882	42.0	45.0	44.0		221	-1.8	0.0	10	dbSNP_120	44	464,8136		175,114,4011	no	missense	CALML5	NM_017422.4	26	384,226,5893	CC,CT,TT		5.3953,12.0291,7.6426	possibly-damaging	74/147	5541181	994,12012	2203	4300	6503	SO:0001583	missense	51806	exon1			GCCTTCTTCGCCG	AF172852	CCDS7068.1	10p15.1	2013-01-10			ENSG00000178372	ENSG00000178372		"""EF-hand domain containing"""	18180	protein-coding gene	gene with protein product	"""calmodulin-like skin protein"""	605183				10777582	Standard	NM_017422		Approved	CLSP	uc001iic.2	Q9NZT1	OTTHUMG00000017598	ENST00000380332.3:c.221A>G	10.37:g.5541181T>C	ENSP00000369689:p.Lys74Arg	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	57	28	0.491228	NM_017422	Q5SQI3|Q8IXU8	Missense_Mutation	SNP	ENST00000380332.3	37	CCDS7068.1	738	0.33791208791208793	245	0.49796747967479676	89	0.24585635359116023	165	0.28846153846153844	239	0.3153034300791557	T	3.065	-0.192375	0.06259	0.120291	0.053953	ENSG00000178372	ENST00000380332	T	0.37915	1.17	0.893	-1.79	0.07932	EF-hand-like domain (1);	0.809011	0.11132	N	0.596195	T	0.00012	0.0000	N	0.11023	0.085	0.80722	P	0.0	P	0.41710	0.76	B	0.32624	0.149	T	0.45205	-0.9277	9	0.66056	D	0.02	-3.9447	4.0258	0.09687	0.3917:0.0:0.0:0.6083	rs10904516;rs17846249;rs17859268;rs34351495	74	Q9NZT1	CALL5_HUMAN	R	74	ENSP00000369689:K74R	ENSP00000369689:K74R	K	-	2	0	CALML5	5531181	0.033000	0.19621	0.000000	0.03702	0.000000	0.00434	0.459000	0.21908	-1.160000	0.02804	-1.407000	0.01130	AAG	T|0.625;C|0.375	0.375	strong		0.657	CALML5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046556.1	NM_017422	
FAHD1	81889	hgsc.bcm.edu	37	16	1877558	1877558	+	Missense_Mutation	SNP	G	G	A	rs3743853	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:1877558G>A	ENST00000427358.2	+	1	334	c.328G>A	c.(328-330)Gac>Aac	p.D110N	HAGH_ENST00000397356.3_5'Flank|FAHD1_ENST00000382668.4_Missense_Mutation_p.D110N|HAGH_ENST00000566709.1_5'Flank|HAGH_ENST00000455446.2_5'Flank|HAGH_ENST00000397353.2_5'Flank|FAHD1_ENST00000382666.4_Missense_Mutation_p.D110N	NM_031208.3	NP_112485.1	Q6P587	FAHD1_HUMAN	fumarylacetoacetate hydrolase domain containing 1	110			D -> N (in dbSNP:rs3743853).			cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	acetylpyruvate hydrolase activity (GO:0018773)|acylpyruvate hydrolase activity (GO:0047621)|fumarylpyruvate hydrolase activity (GO:0034545)|metal ion binding (GO:0046872)			NS(1)|large_intestine(1)|liver(1)|ovary(2)|urinary_tract(1)	6						GGACGTGCAGGACGAGTGCAA	0.672													G|||	683	0.136382	0.0106	0.2075	5008	,	,		19134	0.1667		0.1769	False		,,,				2504	0.183				p.D110N		Atlas-SNP	.											.	FAHD1	18	.	0			c.G328A						PASS	.	G	ASN/ASP,ASN/ASP,ASN/ASP	134,4264	88.2+/-126.9	1,132,2066	33.0	32.0	32.0		328,328,328	1.5	1.0	16	dbSNP_107	32	1320,7280	243.5+/-273.1	109,1102,3089	yes	missense,missense,missense	FAHD1	NM_001018104.2,NM_001142398.1,NM_031208.3	23,23,23	110,1234,5155	AA,AG,GG		15.3488,3.0468,11.1863	benign,benign,benign	110/249,110/227,110/225	1877558	1454,11544	2199	4300	6499	SO:0001583	missense	81889	exon1			GTGCAGGACGAGT	BC063017	CCDS10448.1, CCDS32367.1, CCDS45380.1	16p13.3	2011-10-21	2004-08-19	2004-08-26	ENSG00000180185	ENSG00000180185			14169	protein-coding gene	gene with protein product			"""chromosome 16 open reading frame 36"""	C16orf36		21878618	Standard	NM_001018104		Approved	DKFZP566J2046	uc002cnd.3	Q6P587	OTTHUMG00000128663	ENST00000427358.2:c.328G>A	16.37:g.1877558G>A	ENSP00000398053:p.Asp110Asn	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	123	102	0.829268	NM_031208	B1AK40|B1AK41|Q6FIC7|Q96RY1|Q9H0N6	Missense_Mutation	SNP	ENST00000427358.2	37	CCDS10448.1	306	0.1401098901098901	8	0.016260162601626018	57	0.1574585635359116	100	0.17482517482517482	141	0.18601583113456466	G	16.09	3.024726	0.54683	0.030468	0.153488	ENSG00000180185	ENST00000382668;ENST00000382666;ENST00000427358	D;D;D	0.94687	-3.49;-3.49;-3.49	4.53	1.46	0.22682	Fumarylacetoacetase, C-terminal-related (2);Fumarylacetoacetase, C-terminal (1);	0.262703	0.36519	N	0.002558	T	0.00608	0.0020	N	0.16790	0.44	0.19300	P	0.9999759796	B;B;B	0.09022	0.001;0.002;0.002	B;B;B	0.10450	0.002;0.005;0.005	T	0.34875	-0.9811	9	0.22706	T	0.39	.	6.3111	0.21164	0.2373:0.1348:0.6279:0.0	rs3743853;rs3743853	110;110;110	Q6P587-2;B1AK40;Q6P587	.;.;FAHD1_HUMAN	N	110	ENSP00000372114:D110N;ENSP00000372112:D110N;ENSP00000398053:D110N	ENSP00000372112:D110N	D	+	1	0	FAHD1	1817559	1.000000	0.71417	0.998000	0.56505	0.993000	0.82548	2.652000	0.46682	0.166000	0.19597	0.655000	0.94253	GAC	G|0.882;A|0.118	0.118	strong		0.672	FAHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250550.2	NM_001018104	
USHBP1	83878	hgsc.bcm.edu	37	19	17361116	17361116	+	Missense_Mutation	SNP	G	G	A	rs1043963	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:17361116G>A	ENST00000252597.3	-	13	2203	c.2030C>T	c.(2029-2031)gCg>gTg	p.A677V	AC010646.3_ENST00000594059.1_Intron|USHBP1_ENST00000431146.2_Missense_Mutation_p.A613V	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						TTCGAGCACCGCCACCTCCTC	0.667													G|||	159	0.0317492	0.0053	0.0403	5008	,	,		15517	0.0069		0.0785	False		,,,				2504	0.0389				p.A677V		Atlas-SNP	.											.	USHBP1	85	.	0			c.C2030T						PASS	.	G	VAL/ALA	79,4327	68.1+/-105.8	0,79,2124	40.0	37.0	38.0		2030	1.7	0.7	19	dbSNP_86	38	740,7860	173.9+/-224.3	26,688,3586	yes	missense	USHBP1	NM_031941.3	64	26,767,5710	AA,AG,GG		8.6047,1.793,6.2971	possibly-damaging	677/704	17361116	819,12187	2203	4300	6503	SO:0001583	missense	83878	exon13			AGCACCGCCACCT	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.2030C>T	19.37:g.17361116G>A	ENSP00000252597:p.Ala677Val	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	103	50	0.485437	NM_031941		Missense_Mutation	SNP	ENST00000252597.3	37	CCDS12353.1	85	0.03891941391941392	2	0.0040650406504065045	18	0.049723756906077346	5	0.008741258741258742	60	0.079155672823219	G	10.71	1.425532	0.25639	0.01793	0.086047	ENSG00000130307	ENST00000252597;ENST00000431146	T;T	0.19532	2.14;2.14	4.27	1.68	0.24146	.	0.537907	0.16240	N	0.223220	T	0.00666	0.0022	L	0.54323	1.7	0.58432	D	0.999995	D;D	0.61080	0.989;0.989	B;B	0.43251	0.413;0.318	T	0.09378	-1.0677	10	0.30854	T	0.27	-4.0756	8.6808	0.34207	0.0:0.0:0.4602:0.5398	rs1043963;rs3183653;rs52811219;rs1043963	613;677	B4DUE8;Q8N6Y0	.;USBP1_HUMAN	V	677;613	ENSP00000252597:A677V;ENSP00000407902:A613V	ENSP00000252597:A677V	A	-	2	0	USHBP1	17222116	0.253000	0.23982	0.732000	0.30844	0.254000	0.26022	0.501000	0.22578	0.884000	0.36064	0.561000	0.74099	GCG	G|0.948;A|0.052	0.052	strong		0.667	USHBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463328.1	NM_031941	
RIOK1	83732	hgsc.bcm.edu	37	6	7393452	7393452	+	Silent	SNP	C	C	T	rs2274212|rs368069269	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:7393452C>T	ENST00000379834.2	+	2	699	c.192C>T	c.(190-192)gaC>gaT	p.D64D		NM_031480.2|NM_153005.1	NP_113668.2|NP_694550.1	Q9BRS2	RIOK1_HUMAN	RIO kinase 1	64							ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	19	Ovarian(93;0.0418)					agggttatgacgatgatgatg	0.433													T|||	2307	0.460663	0.261	0.4798	5008	,	,		15160	0.4554		0.5586	False		,,,				2504	0.6217				p.D64D		Atlas-SNP	.											RIOK1,colon,carcinoma,+1,1	RIOK1	36	1	0			c.C192T						PASS	.	T		1305,3101	697.6+/-406.2	198,909,1096	188.0	158.0	168.0		192	-2.6	0.0	6	dbSNP_100	168	4848,3752	534.7+/-382.7	1358,2132,810	no	coding-synonymous	RIOK1	NM_031480.2		1556,3041,1906	TT,TC,CC		43.6279,29.6187,47.3089		64/569	7393452	6153,6853	2203	4300	6503	SO:0001819	synonymous_variant	83732	exon2			TTATGACGATGAT	BC006104	CCDS4500.1	6p24.3	2012-12-10	2012-12-10		ENSG00000124784	ENSG00000124784			18656	protein-coding gene	gene with protein product			"""RIO kinase 1 (yeast)"""				Standard	NM_031480		Approved	AD034, FLJ30006, bA288G3.1, RRP10	uc003mxn.3	Q9BRS2	OTTHUMG00000014207	ENST00000379834.2:c.192C>T	6.37:g.7393452C>T		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	106	51	0.481132	NM_031480	B2RB28|Q8NDC8|Q96NV9	Silent	SNP	ENST00000379834.2	37	CCDS4500.1																																																																																			C|0.560;T|0.440	0.440	strong		0.433	RIOK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039780.2	NM_031480	
OR10H4	126541	hgsc.bcm.edu	37	19	16060658	16060658	+	Missense_Mutation	SNP	A	A	G	rs11880184	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:16060658A>G	ENST00000322107.1	+	1	841	c.841A>G	c.(841-843)Act>Gct	p.T281A		NM_001004465.1	NP_001004465.1	Q8NGA5	O10H4_HUMAN	olfactory receptor, family 10, subfamily H, member 4	281			T -> A (in dbSNP:rs11880184).			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)|large_intestine(3)|lung(8)|ovary(1)|pancreas(1)|urinary_tract(1)	17						CACCACCTATACTGTCTTCAC	0.458													A|||	1211	0.241813	0.4622	0.1772	5008	,	,		21784	0.0546		0.2644	False		,,,				2504	0.1595				p.T281A		Atlas-SNP	.											.	OR10H4	48	.	0			c.A841G						PASS	.	A	ALA/THR	1849,2557	537.5+/-374.7	383,1083,737	151.0	133.0	139.0		841	1.0	1.0	19	dbSNP_120	139	2048,6552	357.0+/-330.6	235,1578,2487	yes	missense	OR10H4	NM_001004465.1	58	618,2661,3224	GG,GA,AA		23.814,41.9655,29.9631	benign	281/317	16060658	3897,9109	2203	4300	6503	SO:0001583	missense	126541	exon1			ACCTATACTGTCT	AC011517	CCDS32941.1	19p13.12	2013-09-24			ENSG00000176231	ENSG00000176231		"""GPCR / Class A : Olfactory receptors"""	15388	protein-coding gene	gene with protein product							Standard	NM_001004465		Approved		uc010xov.2	Q8NGA5	OTTHUMG00000182268	ENST00000322107.1:c.841A>G	19.37:g.16060658A>G	ENSP00000318834:p.Thr281Ala	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	73	37	0.506849	NM_001004465	Q6IFJ2|Q96R57	Missense_Mutation	SNP	ENST00000322107.1	37	CCDS32941.1	549	0.25137362637362637	237	0.4817073170731707	82	0.2265193370165746	40	0.06993006993006994	190	0.25065963060686014	a	3.362	-0.130215	0.06753	0.419655	0.23814	ENSG00000176231	ENST00000322107	T	0.00235	8.48	0.988	0.988	0.19796	GPCR, rhodopsin-like superfamily (1);	0.168007	0.27710	U	0.018178	T	0.00012	0.0000	M	0.64404	1.975	0.80722	P	0.0	B	0.21071	0.051	B	0.27887	0.084	T	0.45190	-0.9278	9	0.54805	T	0.06	.	2.8548	0.05569	0.7132:0.0:0.2868:0.0	rs11880184;rs59076186	281	Q8NGA5	O10H4_HUMAN	A	281	ENSP00000318834:T281A	ENSP00000318834:T281A	T	+	1	0	OR10H4	15921658	0.005000	0.15991	0.972000	0.41901	0.349000	0.29174	0.803000	0.27083	0.700000	0.31782	0.397000	0.26171	ACT	A|0.722;G|0.278	0.278	strong		0.458	OR10H4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460311.1		
ZNF93	81931	hgsc.bcm.edu	37	19	20026163	20026163	+	Silent	SNP	G	G	C	rs150804499	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:20026163G>C	ENST00000343769.5	+	2	106	c.78G>C	c.(76-78)cgG>cgC	p.R26R	AC007204.2_ENST00000592245.1_lincRNA|ZNF93_ENST00000592160.1_Silent_p.R26R|ZNF93_ENST00000591366.1_Silent_p.R26R	NM_031218.3	NP_112495.2	P35789	ZNF93_HUMAN	zinc finger protein 93	26	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)|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						CTGCACAGCGGAATCTATATA	0.398													g|||	44	0.00878594	0.0008	0.0115	5008	,	,		15681	0.0		0.0119	False		,,,				2504	0.0235				p.R26R		Atlas-SNP	.											.	ZNF93	81	.	0			c.G78C						PASS	.	G		11,4395	17.9+/-39.9	0,11,2192	144.0	147.0	146.0		78	-1.7	0.3	19	dbSNP_134	146	98,8502	55.2+/-116.2	1,96,4203	no	coding-synonymous	ZNF93	NM_031218.3		1,107,6395	CC,CG,GG		1.1395,0.2497,0.8381		26/621	20026163	109,12897	2203	4300	6503	SO:0001819	synonymous_variant	81931	exon2			ACAGCGGAATCTA	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.78G>C	19.37:g.20026163G>C		Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	27	14	0.518519	NM_031218	A6NMY2|B9EGT2|Q8N8Q4|Q9H9X5|Q9Y2N8	Silent	SNP	ENST00000343769.5	37	CCDS32973.1																																																																																			G|0.991;C|0.009	0.009	strong		0.398	ZNF93-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460808.2	NM_031218	
PREP	5550	hgsc.bcm.edu	37	6	105821449	105821449	+	Silent	SNP	A	A	G	rs9486069	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:105821449A>G	ENST00000369110.3	-	5	582	c.390T>C	c.(388-390)taT>taC	p.Y130Y		NM_002726.4	NP_002717.3	P48147	PPCE_HUMAN	prolyl endopeptidase	130					proteolysis (GO:0006508)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	serine-type endopeptidase activity (GO:0004252)|serine-type exopeptidase activity (GO:0070008)|serine-type peptidase activity (GO:0008236)			breast(1)|endometrium(2)|large_intestine(7)|lung(12)|ovary(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	29		all_cancers(87;0.000128)|Acute lymphoblastic leukemia(125;1.9e-08)|all_hematologic(75;9.25e-07)|all_epithelial(87;0.0344)|Lung NSC(302;0.191)|Colorectal(196;0.202)			Oxytocin(DB00107)	CGCTGAACGCATAACCTATGG	0.463													G|||	1743	0.348043	0.8215	0.1988	5008	,	,		22397	0.002		0.2932	False		,,,				2504	0.227				p.Y130Y		Atlas-SNP	.											.	PREP	65	.	0			c.T390C						PASS	.	G		3241,1165	407.8+/-334.4	1209,823,171	71.0	65.0	67.0		390	3.5	1.0	6	dbSNP_119	67	2406,6194	699.6+/-405.1	341,1724,2235	no	coding-synonymous	PREP	NM_002726.4		1550,2547,2406	GG,GA,AA		27.9767,26.4412,43.4184		130/711	105821449	5647,7359	2203	4300	6503	SO:0001819	synonymous_variant	5550	exon5			GAACGCATAACCT		CCDS5053.1	6q22	2008-02-05			ENSG00000085377	ENSG00000085377	3.4.21.26		9358	protein-coding gene	gene with protein product		600400				7959018	Standard	NM_002726		Approved		uc003prc.3	P48147	OTTHUMG00000015297	ENST00000369110.3:c.390T>C	6.37:g.105821449A>G		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	65	65	1	NM_002726	Q8N6D4	Silent	SNP	ENST00000369110.3	37	CCDS5053.1																																																																																			A|0.586;G|0.414	0.414	strong		0.463	PREP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041658.1		
RASA3	22821	hgsc.bcm.edu	37	13	114795333	114795333	+	Missense_Mutation	SNP	C	C	T	rs200024629		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:114795333C>T	ENST00000334062.7	-	5	524	c.403G>A	c.(403-405)Gag>Aag	p.E135K	RASA3_ENST00000542651.1_Missense_Mutation_p.R103Q|RASA3_ENST00000389544.4_Missense_Mutation_p.E103K	NM_007368.2	NP_031394.2	Q14644	RASA3_HUMAN	RAS p21 protein activator 3	135	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				calcium ion transmembrane transport (GO:0070588)|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)	calcium-release channel activity (GO:0015278)|GTPase activator activity (GO:0005096)|metal ion binding (GO:0046872)|Ras GTPase activator activity (GO:0005099)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(20)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	47	Lung NSC(43;0.00814)|all_neural(89;0.0337)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.016)|all_epithelial(44;0.00577)|all_lung(25;0.0173)|Lung NSC(25;0.0634)|Breast(118;0.188)	BRCA - Breast invasive adenocarcinoma(86;0.128)			GTGATGACCTCGCTCAGCCGC	0.647													c|||	1	0.000199681	0.0008	0.0	5008	,	,		18381	0.0		0.0	False		,,,				2504	0.0				p.E135K		Atlas-SNP	.											.	RASA3	83	.	0			c.G403A						PASS	.						110.0	66.0	81.0					13																	114795333		2201	4297	6498	SO:0001583	missense	22821	exon5			TGACCTCGCTCAG		CCDS32016.1	13q34	2013-01-10			ENSG00000185989	ENSG00000185989		"""Pleckstrin homology (PH) domain containing"""	20331	protein-coding gene	gene with protein product		605182				7637787, 9382842	Standard	NM_007368		Approved	GAP1IP4BP, GAPIII	uc001vui.3	Q14644	OTTHUMG00000017399	ENST00000334062.7:c.403G>A	13.37:g.114795333C>T	ENSP00000335029:p.Glu135Lys	Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	48	23	0.479167	NM_007368	A6NL15|F8W6X8|Q8IUY2	Missense_Mutation	SNP	ENST00000334062.7	37	CCDS32016.1	1|1	4.578754578754579E-4|4.578754578754579E-4	1|1	0.0020325203252032522|0.0020325203252032522	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	C|C	21.5|21.5	4.163421|4.163421	0.78226|0.78226	.|.	.|.	ENSG00000185989|ENSG00000185989	ENST00000334062;ENST00000389544|ENST00000542651	D;D|T	0.86164|0.17054	-1.97;-2.08|2.3	4.5|4.5	4.5|4.5	0.54988|0.54988	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.31606|0.31606	0.0802|0.0802	L|L	0.60455|0.60455	1.87|1.87	0.38497|0.38497	D|D	0.948117|0.948117	P|.	0.40660|.	0.726|.	B|.	0.39503|.	0.301|.	T|T	0.07290|0.07290	-1.0780|-1.0780	9|6	.|.	.|.	.|.	.|.	16.3374|16.3374	0.83068|0.83068	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	135|.	Q14644|.	RASA3_HUMAN|.	K|Q	135;103|103	ENSP00000335029:E135K;ENSP00000374195:E103K|ENSP00000439008:R103Q	.|.	E|R	-|-	1|2	0|0	RASA3|RASA3	113813435|113813435	1.000000|1.000000	0.71417|0.71417	0.990000|0.990000	0.47175|0.47175	0.916000|0.916000	0.54674|0.54674	6.028000|6.028000	0.70889|0.70889	2.207000|2.207000	0.71202|0.71202	0.561000|0.561000	0.74099|0.74099	GAG|CGA	C|1.000;T|0.000	0.000	strong		0.647	RASA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045957.2	NM_007368	
JMJD1C	221037	hgsc.bcm.edu	37	10	64974537	64974537	+	Missense_Mutation	SNP	A	A	T	rs10761725	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:64974537A>T	ENST00000399262.2	-	8	1608	c.1390T>A	c.(1390-1392)Tcg>Acg	p.S464T	JMJD1C_ENST00000399251.1_Missense_Mutation_p.S245T|JMJD1C_ENST00000542921.1_Missense_Mutation_p.S282T|JMJD1C_ENST00000402544.1_Missense_Mutation_p.S245T|JMJD1C_ENST00000489372.2_5'Flank	NM_032776.1	NP_116165.1	Q15652	JHD2C_HUMAN	jumonji domain containing 1C	464			S -> T (in dbSNP:rs10761725). {ECO:0000269|PubMed:17974005}.		blood coagulation (GO:0007596)|chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	intracellular (GO:0005622)|nucleoplasm (GO:0005654)	dioxygenase activity (GO:0051213)|metal ion binding (GO:0046872)|thyroid hormone receptor binding (GO:0046966)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(8)|large_intestine(9)|lung(27)|ovary(6)|prostate(4)|skin(4)|stomach(3)|upper_aerodigestive_tract(3)	77	Prostate(12;0.0119)|all_hematologic(501;0.191)					TGTTCTGACGAATGAATAATC	0.388													A|||	2561	0.511382	0.3154	0.4669	5008	,	,		19020	0.377		0.7783	False		,,,				2504	0.6718				p.S464T		Atlas-SNP	.											JMJD1C_ENST00000399262,NS,carcinoma,+2,2	JMJD1C	347	2	0			c.T1390A						PASS	.	A	THR/SER,THR/SER	1527,2181		311,905,638	164.0	148.0	153.0		733,1390	3.2	1.0	10	dbSNP_120	153	6382,1810		2482,1418,196	yes	missense,missense	JMJD1C	NM_004241.2,NM_032776.1	58,58	2793,2323,834	TT,TA,AA		22.0947,41.1812,33.5378	benign,benign	245/2304,464/2541	64974537	7909,3991	1854	4096	5950	SO:0001583	missense	221037	exon8			CTGACGAATGAAT	L40411	CCDS41532.1, CCDS60538.1	10q22.1	2011-05-25	2004-03-31	2004-04-01	ENSG00000171988	ENSG00000171988			12313	protein-coding gene	gene with protein product		604503	"""thyroid hormone receptor interactor 8"""	TRIP8		7776974	Standard	XM_005269624		Approved	DKFZp761F0118, KIAA1380, FLJ14374	uc001jmn.3	Q15652	OTTHUMG00000018311	ENST00000399262.2:c.1390T>A	10.37:g.64974537A>T	ENSP00000382204:p.Ser464Thr	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	117	38	0.324786	NM_032776	A0T124|Q5SQZ8|Q5SQZ9|Q5SR00|Q7Z3E7|Q8N3U0|Q96KB9|Q9P2G7	Missense_Mutation	SNP	ENST00000399262.2	37	CCDS41532.1	1162	0.532051282051282	149	0.30284552845528456	190	0.5248618784530387	231	0.40384615384615385	592	0.7810026385224275	A	7.754	0.703933	0.15172	0.411812	0.779053	ENSG00000171988	ENST00000399262;ENST00000402544;ENST00000399251;ENST00000542921	T;T;T;T	0.14266	2.52;2.52;2.52;2.52	5.71	3.24	0.37175	.	0.365789	0.26967	N	0.021583	T	0.00012	0.0000	L	0.34521	1.04	0.80722	P	0.0	B;B	0.25007	0.116;0.094	B;B	0.21708	0.036;0.026	T	0.05582	-1.0876	9	0.30078	T	0.28	-4.5093	8.7222	0.34447	0.5488:0.3828:0.0684:0.0	rs10761725;rs52823266;rs10761725	464;282	Q15652;A0T124	JHD2C_HUMAN;.	T	464;245;245;282	ENSP00000382204:S464T;ENSP00000384990:S245T;ENSP00000382195:S245T;ENSP00000444682:S282T	ENSP00000382195:S245T	S	-	1	0	JMJD1C	64644543	0.631000	0.27164	0.958000	0.39756	0.721000	0.41392	0.761000	0.26489	0.951000	0.37770	0.459000	0.35465	TCG	A|0.395;T|0.605	0.605	strong		0.388	JMJD1C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048249.2	NM_004241	
RPS6KB2	6199	hgsc.bcm.edu	37	11	67202156	67202156	+	Missense_Mutation	SNP	C	C	T	rs13859	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:67202156C>T	ENST00000312629.5	+	14	1304	c.1259C>T	c.(1258-1260)gCc>gTc	p.A420V	AP003419.16_ENST00000535922.1_RNA	NM_003952.2	NP_003943.2	Q9UBS0	KS6B2_HUMAN	ribosomal protein S6 kinase, 70kDa, polypeptide 2	420	Pro-rich.		A -> V (in dbSNP:rs13859). {ECO:0000269|PubMed:10490847, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:9804755, ECO:0000269|PubMed:9878560}.		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)			AGCCCCCGGGCCCCCGTCAGG	0.657													C|||	2438	0.486821	0.8079	0.5692	5008	,	,		17451	0.3264		0.4225	False		,,,				2504	0.226				p.A420V		Atlas-SNP	.											RPS6KB2_ENST00000312629,NS,carcinoma,0,2	RPS6KB2	92	2	0			c.C1259T						PASS	.	C	VAL/ALA	2835,1023		1045,745,139	12.0	13.0	13.0		1259	4.4	1.0	11	dbSNP_52	13	3510,4694		792,1926,1384	yes	missense	RPS6KB2	NM_003952.2	64	1837,2671,1523	TT,TC,CC		42.784,26.5163,47.3968	benign	420/483	67202156	6345,5717	1929	4102	6031	SO:0001583	missense	6199	exon14			CCCGGGCCCCCGT	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.1259C>T	11.37:g.67202156C>T	ENSP00000308413:p.Ala420Val	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	85	11	0.129412	NM_003952	B2RMZ9|B4DML8|O94809|Q9UEC1	Missense_Mutation	SNP	ENST00000312629.5	37	CCDS41677.1	1093	0.5004578754578755	381	0.774390243902439	195	0.5386740331491713	182	0.3181818181818182	335	0.4419525065963061	C	14.64	2.596768	0.46318	0.734837	0.42784	ENSG00000175634	ENST00000312629	T	0.68331	-0.32	4.45	4.45	0.53987	.	0.068776	0.56097	D	0.000031	T	0.00012	0.0000	N	0.08118	0	0.09310	P	1.0	B	0.10296	0.003	B	0.13407	0.009	T	0.39210	-0.9625	9	0.51188	T	0.08	.	15.058	0.71930	0.0:1.0:0.0:0.0	rs13859;rs1132410;rs1790751;rs3178163;rs3193142;rs11558387;rs17296783	420	Q9UBS0	KS6B2_HUMAN	V	420	ENSP00000308413:A420V	ENSP00000308413:A420V	A	+	2	0	RPS6KB2	66958732	1.000000	0.71417	0.998000	0.56505	0.220000	0.24768	6.850000	0.75420	2.300000	0.77407	0.462000	0.41574	GCC	C|0.515;T|0.485	0.485	strong		0.657	RPS6KB2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395508.1	NM_003952	
ANKRD35	148741	hgsc.bcm.edu	37	1	145562881	145562881	+	Silent	SNP	T	T	C	rs10910824	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:145562881T>C	ENST00000355594.4	+	10	2656	c.2569T>C	c.(2569-2571)Ttg>Ctg	p.L857L		NM_144698.3	NP_653299.4	Q8N283	ANR35_HUMAN	ankyrin repeat domain 35	857										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)					AAAGGCTCTGTTGGAAAAGTA	0.682													C|||	2949	0.588858	0.6059	0.5389	5008	,	,		14224	0.7252		0.4384	False		,,,				2504	0.6155				p.L857L	Melanoma(9;127 754 22988 51047)	Atlas-SNP	.											.	ANKRD35	96	.	0			c.T2569C						PASS	.	C		2392,2006		658,1076,465	17.0	21.0	20.0		2569	5.5	1.0	1	dbSNP_120	20	3528,5064		747,2034,1515	no	coding-synonymous	ANKRD35	NM_144698.3		1405,3110,1980	CC,CT,TT		41.0615,45.6116,45.5735		857/1002	145562881	5920,7070	2199	4296	6495	SO:0001819	synonymous_variant	148741	exon10			GCTCTGTTGGAAA	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.2569T>C	1.37:g.145562881T>C		Somatic	22	0	0		WXS	Illumina HiSeq	Phase_I	31	17	0.548387	NM_144698	A6NEU0|B4DL62|Q3MJ10|Q96LS3	Silent	SNP	ENST00000355594.4	37	CCDS919.1																																																																																			A|0.133;C|0.355	0.355	strong		0.682	ANKRD35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038515.1	NM_144698	
TUBB8	347688	hgsc.bcm.edu	37	10	93816	93816	+	Silent	SNP	C	C	T	rs9329305	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:93816C>T	ENST00000309812.4	-	4	578	c.516G>A	c.(514-516)tcG>tcA	p.S172S	TUBB8_ENST00000413237.3_5'UTR|TUBB8_ENST00000332708.5_3'UTR|TUBB8_ENST00000447903.2_Silent_p.S100S	NM_177987.2	NP_817124.1	Q3ZCM7	TBB8_HUMAN	tubulin, beta 8 class VIII	172					microtubule-based process (GO:0007017)|protein polymerization (GO:0051258)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)	p.S172S(1)		NS(1)|cervix(1)|endometrium(4)|large_intestine(5)|lung(12)|ovary(2)|prostate(3)|skin(3)|stomach(1)	32		all_cancers(4;0.00131)|all_lung(4;0.000777)|Lung NSC(4;0.0043)|all_epithelial(10;0.0154)|Colorectal(49;0.235)		Epithelial(11;0.00341)|all cancers(11;0.00922)|OV - Ovarian serous cystadenocarcinoma(14;0.0508)|Lung(33;0.132)		ACACCTTGGGCGAGGGCAGGA	0.557													c|||	1442	0.287939	0.2973	0.2378	5008	,	,		29261	0.2163		0.3549	False		,,,				2504	0.316				p.S172S	Pancreas(192;2041 3010 9013 18103)	Atlas-SNP	.											TUBB8,NS,carcinoma,0,1	TUBB8	62	1	1	Substitution - coding silent(1)	stomach(1)	c.G516A						PASS	.	C		1120,3284		32,1056,1114	97.0	88.0	91.0		516		0.6	10	dbSNP_119	91	2730,5864		199,2332,1766	no	coding-synonymous	TUBB8	NM_177987.2		231,3388,2880	TT,TC,CC		31.7663,25.4314,29.6199		172/445	93816	3850,9148	2202	4297	6499	SO:0001819	synonymous_variant	347688	exon4			CTTGGGCGAGGGC	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.516G>A	10.37:g.93816C>T		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	133	67	0.503759	NM_177987	Q5SQX9|Q8WZ78	Silent	SNP	ENST00000309812.4	37	CCDS7051.1																																																																																			C|0.751;T|0.249	0.249	strong		0.557	TUBB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467795.1	NM_177987	
MSRB3	253827	hgsc.bcm.edu	37	12	65857078	65857078	+	Silent	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:65857078C>T	ENST00000355192.3	+	6	681	c.555C>T	c.(553-555)gcC>gcT	p.A185A	MSRB3_ENST00000308259.5_Silent_p.A178A|MSRB3_ENST00000535664.1_Silent_p.A178A	NM_198080.3	NP_932346.1	Q8IXL7	MSRB3_HUMAN	methionine sulfoxide reductase B3	185					protein repair (GO:0030091)|response to oxidative stress (GO:0006979)	endoplasmic reticulum (GO:0005783)|mitochondrion (GO:0005739)	peptide-methionine (R)-S-oxide reductase activity (GO:0033743)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(4)|lung(3)|prostate(1)|skin(1)	13			LUAD - Lung adenocarcinoma(6;0.0234)|LUSC - Lung squamous cell carcinoma(43;0.0975)	GBM - Glioblastoma multiforme(28;0.131)		CCAGCCCGGCCCAGGCAGACA	0.473																																					p.A185A		Atlas-SNP	.											.	MSRB3	80	.	0			c.C555T						PASS	.						49.0	47.0	48.0					12																	65857078		2203	4300	6503	SO:0001819	synonymous_variant	253827	exon6			CCCGGCCCAGGCA	BX640871	CCDS8973.1, CCDS31853.1	12q14.3	2011-11-29			ENSG00000174099	ENSG00000174099			27375	protein-coding gene	gene with protein product		613719	"""deafness, autosomal recessive 74"""	DFNB74		21185009	Standard	NM_198080		Approved	FLJ36866, DKFZp686C1178	uc021qzy.1	Q8IXL7	OTTHUMG00000168866	ENST00000355192.3:c.555C>T	12.37:g.65857078C>T		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	75	27	0.36	NM_198080	B4DR19|B7ZAQ0|Q6UXS2	Silent	SNP	ENST00000355192.3	37	CCDS8973.1																																																																																			.	.	none		0.473	MSRB3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000401421.1	NM_198080	
NDST3	9348	hgsc.bcm.edu	37	4	118975146	118975146	+	Silent	SNP	C	C	T	rs13152576	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:118975146C>T	ENST00000296499.5	+	2	484	c.81C>T	c.(79-81)atC>atT	p.I27I	NDST3_ENST00000433996.2_Silent_p.I27I	NM_004784.2	NP_004775.1	O95803	NDST3_HUMAN	N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 3	27					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						TGAGCATTATCATTTCTGCTT	0.428													C|||	919	0.183506	0.2095	0.1556	5008	,	,		17608	0.0833		0.1948	False		,,,				2504	0.2597				p.I27I		Atlas-SNP	.											.	NDST3	107	.	0			c.C81T						PASS	.	C		1026,3380	377.8+/-322.6	116,794,1293	133.0	127.0	129.0		81	-2.9	0.2	4	dbSNP_121	129	1562,7036	292.6+/-300.9	148,1266,2885	no	coding-synonymous	NDST3	NM_004784.2		264,2060,4178	TT,TC,CC		18.167,23.2864,19.9016		27/874	118975146	2588,10416	2203	4299	6502	SO:0001819	synonymous_variant	9348	exon2			CATTATCATTTCT	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.81C>T	4.37:g.118975146C>T		Somatic	211	0	0		WXS	Illumina HiSeq	Phase_I	142	70	0.492958	NM_004784	B4DI67|Q4W5C1|Q4W5D0|Q6UWC5|Q9UP21	Silent	SNP	ENST00000296499.5	37	CCDS3708.1																																																																																			C|0.816;T|0.184	0.184	strong		0.428	NDST3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256517.4	NM_004784	
MFF	56947	hgsc.bcm.edu	37	2	228221725	228221725	+	Silent	SNP	A	A	G	rs4844	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:228221725A>G	ENST00000353339.3	+	11	1362	c.921A>G	c.(919-921)ctA>ctG	p.L307L	MFF_ENST00000409616.1_Silent_p.L203L|MFF_ENST00000476924.1_3'UTR|MFF_ENST00000304593.9_Silent_p.L256L|MFF_ENST00000354503.6_Silent_p.L183L|MFF_ENST00000409565.1_Silent_p.L183L|MFF_ENST00000337110.7_Silent_p.L208L|MFF_ENST00000524634.1_Silent_p.L54L|MFF_ENST00000392059.1_Silent_p.L307L|MFF_ENST00000349901.7_Silent_p.L203L	NM_001277061.1	NP_001263990.1	Q9GZY8	MFF_HUMAN	mitochondrial fission factor	307					mitochondrial fission (GO:0000266)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|mitochondrial fusion (GO:0008053)|mitochondrion morphogenesis (GO:0070584)|peroxisome fission (GO:0016559)|positive regulation of mitochondrial fission (GO:0090141)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|protein homooligomerization (GO:0051260)|protein targeting to mitochondrion (GO:0006626)|regulation of mitochondrion organization (GO:0010821)|regulation of peroxisome organization (GO:1900063)|release of cytochrome c from mitochondria (GO:0001836)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|integral component of mitochondrial membrane (GO:0032592)|mitochondrial outer membrane (GO:0005741)|peroxisome (GO:0005777)|synapse (GO:0045202)	protein homodimerization activity (GO:0042803)	p.L307L(1)		breast(3)|endometrium(2)|kidney(3)|large_intestine(7)|lung(4)|stomach(2)	21						ATAGACGTCTACAACTTCTGG	0.333													A|||	654	0.130591	0.1997	0.1138	5008	,	,		18914	0.0933		0.1461	False		,,,				2504	0.0716				p.L307L		Atlas-SNP	.											MFF,NS,carcinoma,0,1	MFF	48	1	1	Substitution - coding silent(1)	stomach(1)	c.A921G						PASS	.	A		917,3489	349.0+/-310.2	66,785,1352	105.0	102.0	103.0		921	-5.4	1.0	2	dbSNP_131	103	1318,7282	258.7+/-282.2	97,1124,3079	no	coding-synonymous	MFF	NM_020194.4		163,1909,4431	GG,GA,AA		15.3256,20.8125,17.1844		307/343	228221725	2235,10771	2203	4300	6503	SO:0001819	synonymous_variant	56947	exon11			ACGTCTACAACTT	AF258660	CCDS2465.1, CCDS63139.1, CCDS63140.1, CCDS63141.1, CCDS63142.1, CCDS74662.1	2q36	2008-05-29	2008-05-29	2008-05-29	ENSG00000168958	ENSG00000168958			24858	protein-coding gene	gene with protein product		614785	"""chromosome 2 open reading frame 33"""	C2orf33		18353969	Standard	NM_001277061		Approved	GL004	uc002voy.4	Q9GZY8	OTTHUMG00000133180	ENST00000353339.3:c.921A>G	2.37:g.228221725A>G		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	40	17	0.425	NM_020194	Q567U1|Q658R6|Q9BVZ1|Q9H690|Q9NRG8	Silent	SNP	ENST00000353339.3	37	CCDS2465.1																																																																																			A|0.847;G|0.153	0.153	strong		0.333	MFF-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256887.2	NM_020194	
EEA1	8411	hgsc.bcm.edu	37	12	93195435	93195435	+	Missense_Mutation	SNP	T	T	A	rs73362428	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:93195435T>A	ENST00000322349.8	-	20	2977	c.2713A>T	c.(2713-2715)Atg>Ttg	p.M905L		NM_003566.3	NP_003557	Q15075	EEA1_HUMAN	early endosome antigen 1	905					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						GTGTTTTCCATCTGCACTTGA	0.264													T|||	125	0.0249601	0.0363	0.0115	5008	,	,		13831	0.0377		0.0129	False		,,,				2504	0.0184				p.M905L		Atlas-SNP	.											.	EEA1	104	.	0			c.A2713T						PASS	.	T	LEU/MET	142,4260	96.2+/-134.9	6,130,2065	97.0	95.0	95.0		2713	1.8	0.1	12	dbSNP_130	95	84,8502	47.2+/-106.3	0,84,4209	yes	missense	EEA1	NM_003566.3	15	6,214,6274	AA,AT,TT		0.9783,3.2258,1.7401	benign	905/1412	93195435	226,12762	2201	4293	6494	SO:0001583	missense	8411	exon20			TTTCCATCTGCAC	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.2713A>T	12.37:g.93195435T>A	ENSP00000317955:p.Met905Leu	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	40	21	0.525	NM_003566	Q14221	Missense_Mutation	SNP	ENST00000322349.8	37	CCDS31874.1	51	0.023351648351648352	13	0.026422764227642278	3	0.008287292817679558	24	0.04195804195804196	11	0.014511873350923483	T	0.048	-1.260379	0.01445	0.032258	0.009783	ENSG00000102189	ENST00000322349	T	0.63255	-0.03	5.53	1.81	0.25067	.	0.552802	0.16246	N	0.222923	T	0.08582	0.0213	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.10337	-1.0634	10	0.06757	T	0.87	.	4.5979	0.12340	0.1343:0.2916:0.0:0.574	.	905	Q15075	EEA1_HUMAN	L	905	ENSP00000317955:M905L	ENSP00000317955:M905L	M	-	1	0	EEA1	91719566	0.008000	0.16893	0.073000	0.20177	0.041000	0.13682	0.190000	0.17057	0.347000	0.23924	0.454000	0.30748	ATG	T|0.983;A|0.017	0.017	strong		0.264	EEA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407304.1	NM_003566	
HLA-DPA1	3113	hgsc.bcm.edu	37	6	33037061	33037061	+	Silent	SNP	G	G	C	rs1126544	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:33037061G>C	ENST00000419277.1	-	4	492	c.363C>G	c.(361-363)acC>acG	p.T121T	HLA-DPA1_ENST00000428995.1_Silent_p.T121T|HLA-DPA1_ENST00000463066.1_5'UTR	NM_001242524.1|NM_001242525.1	NP_001229453.1|NP_001229454.1	P20036	DPA1_HUMAN	major histocompatibility complex, class II, DP alpha 1	121	Alpha-2.|Ig-like C1-type.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cellular response to interferon-gamma (GO:0071346)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell proliferation (GO:0042102)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			kidney(5)|large_intestine(1)|lung(6)|prostate(1)|skin(2)	15						TGGGAAACACGGTCACCTCAG	0.582													.|||	856	0.170927	0.1815	0.0288	5008	,	,		19270	0.5298		0.0239	False		,,,				2504	0.0389				p.T121T		Atlas-SNP	.											.	HLA-DPA1	20	.	0			c.C363G						PASS	.	G	,,	461,2555		19,423,1066	69.0	88.0	81.0		363,363,363	-1.0	1.0	6	dbSNP_86	81	128,5286		0,128,2579	no	coding-synonymous,coding-synonymous,coding-synonymous	HLA-DPA1	NM_001242524.1,NM_001242525.1,NM_033554.3	,,	19,551,3645	CC,CG,GG		2.3642,15.2851,6.987	,,	121/261,121/261,121/261	33037061	589,7841	1508	2707	4215	SO:0001819	synonymous_variant	3113	exon3			AAACACGGTCACC	X00457	CCDS4764.1	6p21.3	2013-01-11			ENSG00000231389	ENSG00000231389		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4938	protein-coding gene	gene with protein product		142880		HLA-DP1A		6584734	Standard	NM_033554		Approved		uc003ocs.2	P20036	OTTHUMG00000031058	ENST00000419277.1:c.363C>G	6.37:g.33037061G>C		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	41	9	0.219512	NM_033554	A9YWH7|B9UKH4|O19722|O46883|P01905|P79554|Q2Q060|Q2Q061|Q5EY03|Q5STP1|Q6DQK4|Q9BCQ1|Q9TPX3|Q9XS10	Silent	SNP	ENST00000419277.1	37	CCDS4764.1																																																																																			G|0.903;C|0.097	0.097	strong		0.582	HLA-DPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076071.3	NM_033554	
DSCAML1	57453	hgsc.bcm.edu	37	11	117403235	117403235	+	Missense_Mutation	SNP	G	G	T	rs3741280	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:117403235G>T	ENST00000321322.6	-	4	695	c.694C>A	c.(694-696)Cac>Aac	p.H232N	DSCAML1_ENST00000527706.1_Intron	NM_020693.2	NP_065744.2	Q8TD84	DSCL1_HUMAN	Down syndrome cell adhesion molecule like 1	172	Ig-like C2-type 3.				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.H232N(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)		AAAAACCTGTGTTCTGGAGAC	0.498													T|||	2267	0.452676	0.4796	0.3732	5008	,	,		19258	0.5417		0.2654	False		,,,				2504	0.5736				p.H232N		Atlas-SNP	.											DSCAML1,NS,carcinoma,0,1	DSCAML1	286	1	1	Substitution - Missense(1)	stomach(1)	c.C694A						PASS	.	T	ASN/HIS	1928,2474	624.5+/-394.3	425,1078,698	88.0	81.0	84.0		694	4.9	1.0	11	dbSNP_107	84	2265,6327	707.5+/-405.6	309,1647,2340	yes	missense	DSCAML1	NM_020693.2	68	734,2725,3038	TT,TG,GG		26.3617,43.7983,32.2687	benign	232/2114	117403235	4193,8801	2201	4296	6497	SO:0001583	missense	57453	exon4			ACCTGTGTTCTGG		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.694C>A	11.37:g.117403235G>T	ENSP00000315465:p.His232Asn	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	74	14	0.189189	NM_020693	Q76MU9|Q8IZY3|Q8IZY4|Q8WXU7|Q9ULT7	Missense_Mutation	SNP	ENST00000321322.6	37	CCDS8384.1	823	0.3768315018315018	215	0.4369918699186992	118	0.3259668508287293	297	0.5192307692307693	193	0.2546174142480211	T	5.290	0.238934	0.10023	0.437983	0.263617	ENSG00000177103	ENST00000321322	T	0.76316	-1.01	4.88	4.88	0.63580	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00012	0.0000	N	0.02011	-0.69	0.47737	P	4.92000000000048E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.44620	-0.9316	8	0.23302	T	0.38	.	6.9151	0.24355	0.0:0.0752:0.1524:0.7724	rs3741280;rs52818394;rs60670777;rs3741280	172	Q8TD84	DSCL1_HUMAN	N	232	ENSP00000315465:H232N	ENSP00000315465:H232N	H	-	1	0	DSCAML1	116908445	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	3.341000	0.52151	0.993000	0.38866	-0.256000	0.11100	CAC	G|0.640;T|0.360	0.360	strong		0.498	DSCAML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392907.2	NM_020693	
FUCA2	2519	hgsc.bcm.edu	37	6	143823157	143823157	+	Missense_Mutation	SNP	T	T	C	rs3762002	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:143823157T>C	ENST00000002165.6	-	5	1121	c.1066A>G	c.(1066-1068)Atg>Gtg	p.M356V	RP1-20N2.6_ENST00000589563.1_RNA|FUCA2_ENST00000367585.1_5'UTR|RP1-20N2.6_ENST00000593175.1_RNA|FUCA2_ENST00000438118.2_3'UTR|RP1-20N2.6_ENST00000589489.1_RNA|RP1-20N2.6_ENST00000591892.1_RNA|RP1-20N2.6_ENST00000591189.1_RNA|RP1-20N2.6_ENST00000415586.1_RNA|RP1-20N2.6_ENST00000593045.1_RNA|RP1-20N2.6_ENST00000610068.1_RNA|RP1-20N2.6_ENST00000590703.1_RNA	NM_032020.4	NP_114409.2	Q9BTY2	FUCO2_HUMAN	fucosidase, alpha-L- 2, plasma	356			M -> V (in dbSNP:rs3762002). {ECO:0000269|PubMed:12975309, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:16303743}.		fucose metabolic process (GO:0006004)|glycoside catabolic process (GO:0016139)|regulation of entry of bacterium into host cell (GO:2000535)|response to bacterium (GO:0009617)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	alpha-L-fucosidase activity (GO:0004560)|fucose binding (GO:0042806)			endometrium(1)|large_intestine(1)|lung(2)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	9				OV - Ovarian serous cystadenocarcinoma(155;7.45e-06)|GBM - Glioblastoma multiforme(68;0.0142)		CAGGACCCCATTTGCCTCAGT	0.448													T|||	1164	0.232428	0.3396	0.1859	5008	,	,		14611	0.1687		0.2247	False		,,,				2504	0.1943				p.M356V		Atlas-SNP	.											.	FUCA2	28	.	0			c.A1066G						PASS	.	T	VAL/MET	1408,2998	462.4+/-353.2	231,946,1026	96.0	94.0	95.0		1066	6.0	1.0	6	dbSNP_107	95	1945,6655	343.2+/-324.8	216,1513,2571	yes	missense	FUCA2	NM_032020.4	21	447,2459,3597	CC,CT,TT		22.6163,31.9564,25.7804	benign	356/468	143823157	3353,9653	2203	4300	6503	SO:0001583	missense	2519	exon5			ACCCCATTTGCCT	BC003060	CCDS5200.1	6q24	2012-10-02			ENSG00000001036	ENSG00000001036	3.2.1.51		4008	protein-coding gene	gene with protein product		136820				6590153	Standard	NM_032020		Approved	MGC1314, dJ20N2.5	uc003qjm.3	Q9BTY2	OTTHUMG00000015728	ENST00000002165.6:c.1066A>G	6.37:g.143823157T>C	ENSP00000002165:p.Met356Val	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	65	7	0.107692	NM_032020	E9PEB6|Q7Z6V1|Q7Z6Y2|Q8NBK4	Missense_Mutation	SNP	ENST00000002165.6	37	CCDS5200.1	504	0.23076923076923078	164	0.3333333333333333	60	0.16574585635359115	104	0.18181818181818182	176	0.23218997361477572	T	11.97	1.797932	0.31777	0.319564	0.226163	ENSG00000001036	ENST00000002165;ENST00000451668	T;T	0.56941	0.43;0.43	5.98	5.98	0.97165	Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.074659	0.85682	D	0.000000	T	0.23370	0.0565	L	0.31420	0.93	0.09310	P	1.0	B;B	0.23128	0.08;0.044	B;B	0.24006	0.05;0.034	T	0.11227	-1.0596	9	0.20046	T	0.44	-24.5233	12.26	0.54645	0.0:0.0673:0.0:0.9327	rs3762002;rs17849713;rs17854672;rs52821129;rs60454233;rs3762002	35;356	Q7Z6V2;Q9BTY2	.;FUCO2_HUMAN	V	356;35	ENSP00000002165:M356V;ENSP00000398119:M35V	ENSP00000002165:M356V	M	-	1	0	FUCA2	143864850	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	4.814000	0.62627	2.288000	0.76882	0.528000	0.53228	ATG	T|0.749;C|0.251	0.251	strong		0.448	FUCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042521.2	NM_032020	
VWDE	221806	hgsc.bcm.edu	37	7	12419108	12419108	+	Missense_Mutation	SNP	A	A	T	rs6967241	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:12419108A>T	ENST00000275358.3	-	6	1062	c.874T>A	c.(874-876)Ttt>Att	p.F292I		NM_001135924.1	NP_001129396.1	Q8N2E2	VWDE_HUMAN	von Willebrand factor D and EGF domains	292						extracellular region (GO:0005576)		p.F292I(1)		breast(4)|endometrium(2)|kidney(1)|skin(1)	8						CGTACCTTAAAGCCTGCAAAA	0.413													T|||	3054	0.609824	0.5726	0.5288	5008	,	,		6454	0.5923		0.6819	False		,,,				2504	0.6616				p.F292I		Atlas-SNP	.											VWDE_ENST00000275358,NS,carcinoma,0,1	VWDE	123	1	1	Substitution - Missense(1)	kidney(1)	c.T874A						PASS	.	T	ILE/PHE	782,602		218,346,128	78.0	70.0	73.0		874	4.6	1.0	7	dbSNP_116	73	2279,903		823,633,135	yes	missense	VWDE	NM_001135924.1	21	1041,979,263	TT,TA,AA		28.3784,43.4971,32.961	benign	292/1591	12419108	3061,1505	692	1591	2283	SO:0001583	missense	221806	exon6			CCTTAAAGCCTGC		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.874T>A	7.37:g.12419108A>T	ENSP00000275358:p.Phe292Ile	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	97	24	0.247423	NM_001135924	B7ZM77|Q96SQ3	Missense_Mutation	SNP	ENST00000275358.3	37	CCDS47544.1	1346	0.6163003663003663	273	0.5548780487804879	206	0.569060773480663	346	0.6048951048951049	521	0.6873350923482849	T	7.008	0.556131	0.13436	0.565029	0.716216	ENSG00000146530	ENST00000275358	T	0.77358	-1.09	4.61	4.61	0.57282	.	.	.	.	.	T	0.00012	0.0000	N	0.00101	-2.135	0.48341	P	3.6599999999997745E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.45366	-0.9266	8	0.02654	T	1	.	10.7397	0.46145	0.1427:0.0:0.0:0.8573	rs6967241;rs52826182;rs6967241	292	Q8N2E2	VWDE_HUMAN	I	292	ENSP00000275358:F292I	ENSP00000275358:F292I	F	-	1	0	VWDE	12385633	1.000000	0.71417	1.000000	0.80357	0.934000	0.57294	4.088000	0.57678	0.799000	0.34018	-0.257000	0.10917	TTT	A|0.382;T|0.618	0.618	strong		0.413	VWDE-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325870.3	XM_371878	
TMPRSS5	80975	hgsc.bcm.edu	37	11	113561057	113561057	+	Silent	SNP	A	A	G	rs7110738	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:113561057A>G	ENST00000299882.5	-	11	1250	c.1102T>C	c.(1102-1104)Ttg>Ctg	p.L368L	TMPRSS5_ENST00000545265.1_5'UTR|TMPRSS5_ENST00000540540.1_Silent_p.L109L|TMPRSS5_ENST00000538955.1_Silent_p.L324L|TMPRSS5_ENST00000536856.1_Silent_p.L109L|TMPRSS5_ENST00000545579.1_Silent_p.L359L|TMPRSS5_ENST00000544476.1_Silent_p.L255L|TMPRSS5_ENST00000544634.1_Silent_p.L299L	NM_030770.2	NP_110397.2	Q9H3S3	TMPS5_HUMAN	transmembrane protease, serine 5	368	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				proteolysis (GO:0006508)	integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	peptidase activity (GO:0008233)|scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)			endometrium(2)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)	10		all_cancers(61;2.71e-16)|all_epithelial(67;1e-09)|Melanoma(852;1.46e-05)|all_hematologic(158;0.00014)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|all_neural(223;0.0281)|Prostate(24;0.0421)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;2.75e-06)|Epithelial(105;6.34e-05)|all cancers(92;0.000502)		GTGCTGAACAAGGGCACCACC	0.592													G|||	3857	0.770168	0.9637	0.7594	5008	,	,		13941	0.748		0.6362	False		,,,				2504	0.6769				p.L368L		Atlas-SNP	.											.	TMPRSS5	69	.	0			c.T1102C						PASS	.	G		3857,369		1767,323,23	31.0	37.0	35.0		1102	3.3	1.0	11	dbSNP_116	35	5472,2998		1760,1952,523	no	coding-synonymous	TMPRSS5	NM_030770.2		3527,2275,546	GG,GA,AA		35.3955,8.7317,26.5202		368/458	113561057	9329,3367	2113	4235	6348	SO:0001819	synonymous_variant	80975	exon11			TGAACAAGGGCAC	AB028140	CCDS44735.1, CCDS73390.1, CCDS73391.1, CCDS73392.1, CCDS73393.1	11q	2010-04-13	2008-07-31		ENSG00000166682	ENSG00000166682		"""Serine peptidases / Transmembrane"""	14908	protein-coding gene	gene with protein product	"""spinesin"""	606751					Standard	NM_030770		Approved	MGC141886, MGC148044	uc001poc.4	Q9H3S3	OTTHUMG00000168186	ENST00000299882.5:c.1102T>C	11.37:g.113561057A>G		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	137	36	0.262774	NM_030770		Silent	SNP	ENST00000299882.5	37	CCDS44735.1																																																																																			A|0.259;G|0.741	0.741	strong		0.592	TMPRSS5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398652.1	NM_030770	
CTSS	1520	hgsc.bcm.edu	37	1	150720261	150720261	+	Silent	SNP	C	C	A	rs140408537	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:150720261C>A	ENST00000368985.3	-	7	1148	c.888G>T	c.(886-888)gtG>gtT	p.V296V	CTSS_ENST00000480760.1_5'Flank|CTSS_ENST00000448301.2_Silent_p.V246V	NM_001199739.1|NM_004079.4	NP_001186668.1|NP_004070.3	P25774	CATS_HUMAN	cathepsin S	296					adaptive immune response (GO:0002250)|antigen processing and presentation (GO:0019882)|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-independent (GO:0002480)|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)|basement membrane disassembly (GO:0034769)|cellular response to thyroid hormone stimulus (GO:0097067)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|immune response (GO:0006955)|innate immune response (GO:0045087)|positive regulation of inflammatory response (GO:0050729)|proteolysis (GO:0006508)|proteolysis involved in cellular protein catabolic process (GO:0051603)|toll-like receptor signaling pathway (GO:0002224)	endolysosome lumen (GO:0036021)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)|membrane (GO:0016020)	collagen binding (GO:0005518)|cysteine-type endopeptidase activity (GO:0004197)|fibronectin binding (GO:0001968)|laminin binding (GO:0043236)|proteoglycan binding (GO:0043394)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(5)|skin(1)|stomach(1)|urinary_tract(1)	15	all_cancers(9;6.17e-52)|all_epithelial(9;9.7e-43)|all_lung(15;5.74e-35)|Lung NSC(24;2.09e-31)|Breast(34;0.00146)|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;0.0485)|Epithelial(6;5.02e-21)|all cancers(9;1.28e-20)|OV - Ovarian serous cystadenocarcinoma(6;1.09e-14)|BRCA - Breast invasive adenocarcinoma(12;0.00501)|LUSC - Lung squamous cell carcinoma(543;0.171)			ACCTGTTTTTCACAAGCCAGT	0.348													C|||	7	0.00139776	0.0008	0.0	5008	,	,		16564	0.0		0.006	False		,,,				2504	0.0				p.V296V		Atlas-SNP	.											.	CTSS	31	.	0			c.G888T						PASS	.	C	,	7,4399	12.9+/-30.5	0,7,2196	101.0	98.0	99.0		738,888	4.4	1.0	1	dbSNP_134	99	86,8514	49.8+/-109.6	1,84,4215	no	coding-synonymous,coding-synonymous	CTSS	NM_001199739.1,NM_004079.4	,	1,91,6411	AA,AC,CC		1.0,0.1589,0.7151	,	246/282,296/332	150720261	93,12913	2203	4300	6503	SO:0001819	synonymous_variant	1520	exon7			GTTTTTCACAAGC	M90696	CCDS968.1, CCDS55634.1	1q21	2008-02-05			ENSG00000163131	ENSG00000163131	3.4.22.27	"""Cathepsins"""	2545	protein-coding gene	gene with protein product		116845				1373132	Standard	NM_001199739		Approved		uc001evn.3	P25774	OTTHUMG00000035010	ENST00000368985.3:c.888G>T	1.37:g.150720261C>A		Somatic	226	1	0.00442478		WXS	Illumina HiSeq	Phase_I	163	99	0.607362	NM_004079	B4DWC9|D3DV05|Q5T5I0|Q6FHS5|Q9BUG3	Silent	SNP	ENST00000368985.3	37	CCDS968.1																																																																																			C|0.995;A|0.005	0.005	strong		0.348	CTSS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084737.1	NM_004079	
HSPA6	3310	hgsc.bcm.edu	37	1	161495885	161495885	+	Silent	SNP	T	T	C	rs404508	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:161495885T>C	ENST00000309758.4	+	1	1850	c.1437T>C	c.(1435-1437)acT>acC	p.T479T	RP11-25K21.6_ENST00000537821.2_RNA	NM_002155.3	NP_002146.2	P17066	HSP76_HUMAN	heat shock 70kDa protein 6 (HSP70B')	479					ATP catabolic process (GO:0006200)|cellular response to heat (GO:0034605)|protein refolding (GO:0042026)|response to unfolded protein (GO:0006986)	blood microparticle (GO:0072562)|centriole (GO:0005814)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)|enzyme binding (GO:0019899)|heat shock protein binding (GO:0031072)|unfolded protein binding (GO:0051082)			endometrium(3)|large_intestine(5)|lung(9)|prostate(2)|skin(2)	21	all_cancers(52;4.89e-16)|all_hematologic(112;0.0207)		BRCA - Breast invasive adenocarcinoma(70;0.00376)			TAGAGGTGACTTTTGACATTG	0.552													C|||	4012	0.801118	0.7791	0.7233	5008	,	,		20105	0.9117		0.7883	False		,,,				2504	0.7853				p.T479T		Atlas-SNP	.											.	HSPA6	53	.	0			c.T1437C						PASS	.	C		3495,911		1377,741,85	69.0	64.0	66.0		1437	1.6	0.9	1	dbSNP_80	66	6462,2138		2425,1612,263	no	coding-synonymous	HSPA6	NM_002155.3		3802,2353,348	CC,CT,TT		24.8605,20.6764,23.443		479/644	161495885	9957,3049	2203	4300	6503	SO:0001819	synonymous_variant	3310	exon1			GGTGACTTTTGAC		CCDS1231.1	1q23.3	2011-09-02	2002-08-29		ENSG00000173110	ENSG00000173110		"""Heat shock proteins / HSP70"""	5239	protein-coding gene	gene with protein product		140555	"""heat shock 70kD protein 6 (HSP70B')"""			1346391	Standard	NM_002155		Approved		uc001gaq.3	P17066	OTTHUMG00000034461	ENST00000309758.4:c.1437T>C	1.37:g.161495885T>C		Somatic	213	1	0.00469484		WXS	Illumina HiSeq	Phase_I	198	197	0.99495	NM_002155	Q1HBA8|Q8IYK7|Q9BT95	Silent	SNP	ENST00000309758.4	37	CCDS1231.1																																																																																			T|0.229;G|0.001;C|0.770	0.770	strong		0.552	HSPA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083308.1	NM_002155	
ZNF7	7553	hgsc.bcm.edu	37	8	146067054	146067054	+	Missense_Mutation	SNP	G	G	A	rs1735169	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:146067054G>A	ENST00000528372.1	+	5	802	c.562G>A	c.(562-564)Gga>Aga	p.G188R	ZNF7_ENST00000544249.1_Missense_Mutation_p.G92R|ZNF7_ENST00000446747.2_Missense_Mutation_p.G199R|ZNF7_ENST00000532393.1_3'UTR|ZNF7_ENST00000325217.5_Intron|ZNF7_ENST00000529819.1_Intron|ZNF7_ENST00000325241.6_Missense_Mutation_p.G188R|ZNF7_ENST00000525266.1_Intron			P17097	ZNF7_HUMAN	zinc finger protein 7	188			G -> R (in dbSNP:rs1735169). {ECO:0000269|Ref.4}.		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)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|kidney(1)|large_intestine(7)|lung(6)|ovary(5)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25	all_cancers(97;1.03e-11)|all_epithelial(106;6.69e-11)|Lung NSC(106;4.08e-05)|all_lung(105;0.000125)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)	Breast(495;0.0812)|Ovarian(118;0.0822)|Acute lymphoblastic leukemia(644;0.143)	Epithelial(56;8.75e-39)|OV - Ovarian serous cystadenocarcinoma(54;1.13e-38)|all cancers(56;8.48e-34)|BRCA - Breast invasive adenocarcinoma(115;0.0355)|Colorectal(110;0.055)	GBM - Glioblastoma multiforme(99;2.11e-07)		TGAAAGTCAGGGAGAGAGTGC	0.537													A|||	2660	0.53115	0.6906	0.4294	5008	,	,		20626	0.5833		0.3579	False		,,,				2504	0.5123				p.G188R		Atlas-SNP	.											.	ZNF7	62	.	0			c.G562A						PASS	.	A	ARG/GLY	2939,1467	473.1+/-356.6	985,969,249	63.0	64.0	64.0		562	3.6	0.0	8	dbSNP_89	64	3291,5309	647.1+/-400.3	594,2103,1603	yes	missense	ZNF7	NM_003416.2	125	1579,3072,1852	AA,AG,GG		38.2674,33.2955,47.901	benign	188/687	146067054	6230,6776	2203	4300	6503	SO:0001583	missense	7553	exon5			AGTCAGGGAGAGA	AB209619	CCDS6435.1, CCDS64996.1, CCDS64998.1, CCDS64999.1	8q24	2013-01-08	2006-05-09		ENSG00000147789	ENSG00000147789		"""Zinc fingers, C2H2-type"", ""-"""	13139	protein-coding gene	gene with protein product		194531	"""zinc finger protein 7 (KOX 4, clone HF.16)"""			2106481, 1946370	Standard	NM_003416		Approved	KOX4, HF.16	uc003zeg.4	P17097	OTTHUMG00000165200	ENST00000528372.1:c.562G>A	8.37:g.146067054G>A	ENSP00000432724:p.Gly188Arg	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	50	43	0.86	NM_003416	B4DT08|D3DWN6|P17015|Q8N8Y4	Missense_Mutation	SNP	ENST00000528372.1	37	CCDS6435.1	1084	0.49633699633699635	340	0.6910569105691057	161	0.4447513812154696	309	0.5402097902097902	274	0.36147757255936674	A	0.293	-0.979022	0.02197	0.667045	0.382674	ENSG00000147789	ENST00000532777;ENST00000325241;ENST00000446747;ENST00000544249;ENST00000528372	T;T;T;T;T	0.05855	7.32;3.48;3.49;3.38;3.48	4.67	3.6	0.41247	.	0.677726	0.12547	N	0.459388	T	0.00012	0.0000	N	0.01535	-0.81	0.58432	P	1.999999999946489E-6	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.10109	-1.0644	9	0.35671	T	0.21	-1.9115	5.0258	0.14383	0.6855:0.0:0.3145:0.0	rs1735169;rs4083376;rs52811554;rs59813519;rs1735169	199;188	B4DT08;P17097	.;ZNF7_HUMAN	R	188;188;199;92;188	ENSP00000432641:G188R;ENSP00000320627:G188R;ENSP00000393260:G199R;ENSP00000439424:G92R;ENSP00000432724:G188R	ENSP00000320627:G188R	G	+	1	0	ZNF7	146037858	0.000000	0.05858	0.002000	0.10522	0.006000	0.05464	-0.088000	0.11198	0.401000	0.25424	-0.521000	0.04368	GGA	G|0.515;A|0.485	0.485	strong		0.537	ZNF7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382660.1	NM_003416	
BMP2K	55589	hgsc.bcm.edu	37	4	79832870	79832870	+	Missense_Mutation	SNP	A	A	T	rs116710382	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:79832870A>T	ENST00000335016.5	+	16	3335	c.3169A>T	c.(3169-3171)Aat>Tat	p.N1057Y	PAQR3_ENST00000295462.3_Intron	NM_198892.1	NP_942595.1	Q9NSY1	BMP2K_HUMAN	BMP2 inducible kinase	1057					regulation of bone mineralization (GO:0030500)	nucleus (GO:0005634)	ATP binding (GO:0005524)|phosphatase regulator activity (GO:0019208)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|endometrium(4)|large_intestine(2)|lung(3)|prostate(1)|urinary_tract(1)	13						AGATAGGGGGAATGTCTTACA	0.522													A|||	19	0.00379393	0.0	0.0101	5008	,	,		20274	0.0		0.0119	False		,,,				2504	0.0				p.N1057Y		Atlas-SNP	.											.	BMP2K	169	.	0			c.A3169T						PASS	.	A	TYR/ASN	5,3897		0,5,1946	101.0	101.0	101.0		3169	1.3	0.0	4	dbSNP_132	101	61,8203		0,61,4071	yes	missense	BMP2K	NM_198892.1	143	0,66,6017	TT,TA,AA		0.7381,0.1281,0.5425	benign	1057/1162	79832870	66,12100	1951	4132	6083	SO:0001583	missense	55589	exon16			AGGGGGAATGTCT	AB015331	CCDS34019.1, CCDS47083.1	4q21.21	2008-05-15			ENSG00000138756	ENSG00000138756			18041	protein-coding gene	gene with protein product							Standard	NM_017593		Approved	DKFZp434K0614, BIKe	uc003hlk.3	Q9NSY1	OTTHUMG00000160900	ENST00000335016.5:c.3169A>T	4.37:g.79832870A>T	ENSP00000334836:p.Asn1057Tyr	Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	135	70	0.518519	NM_198892	O94791|Q4W5H2|Q8IYF2|Q8N2G7|Q8NHG9|Q9NTG8	Missense_Mutation	SNP	ENST00000335016.5	37	CCDS47083.1	13|13	0.005952380952380952|0.005952380952380952	0|0	0.0|0.0	4|4	0.011049723756906077|0.011049723756906077	0|0	0.0|0.0	9|9	0.011873350923482849|0.011873350923482849	A|A	3.678|3.678	-0.066194|-0.066194	0.07273|0.07273	0.001281|0.001281	0.007381|0.007381	ENSG00000138756|ENSG00000138756	ENST00000502613|ENST00000335016	.|T	.|0.43688	.|0.94	5.41|5.41	1.3|1.3	0.21679|0.21679	.|.	.|1.089200	.|0.07033	.|N	.|0.828802	T|T	0.24198|0.24198	0.0586|0.0586	N|N	0.22421|0.22421	0.69|0.69	0.09310|0.09310	N|N	0.999999|0.999999	.|B	.|0.26400	.|0.148	.|B	.|0.18263	.|0.021	T|T	0.25363|0.25363	-1.0134|-1.0134	5|10	.|0.44086	.|T	.|0.13	-1.0317|-1.0317	13.6768|13.6768	0.62458|0.62458	0.4465:0.5535:0.0:0.0|0.4465:0.5535:0.0:0.0	.|.	.|1057	.|Q9NSY1	.|BMP2K_HUMAN	V|Y	749|1057	.|ENSP00000334836:N1057Y	.|ENSP00000334836:N1057Y	E|N	+|+	2|1	0|0	BMP2K|BMP2K	80051894|80051894	0.407000|0.407000	0.25352|0.25352	0.000000|0.000000	0.03702|0.03702	0.011000|0.011000	0.07611|0.07611	2.601000|2.601000	0.46249|0.46249	0.336000|0.336000	0.23639|0.23639	0.397000|0.397000	0.26171|0.26171	GAA|AAT	A|0.993;T|0.007	0.007	strong		0.522	BMP2K-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_017593	
C17orf59	54785	hgsc.bcm.edu	37	17	8093324	8093324	+	Missense_Mutation	SNP	C	C	G	rs150061068	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:8093324C>G	ENST00000389017.4	-	1	240	c.135G>C	c.(133-135)gaG>gaC	p.E45D	MIR3676_ENST00000579470.1_RNA	NM_017622.2	NP_060092.2	Q96GS4	CQ059_HUMAN	chromosome 17 open reading frame 59	45										large_intestine(2)|lung(3)|urinary_tract(1)	6						CGGTCTCTTCCTCCCCGGACA	0.706													C|||	16	0.00319489	0.0015	0.0029	5008	,	,		11330	0.0		0.0109	False		,,,				2504	0.001				p.E45D		Atlas-SNP	.											.	C17orf59	19	.	0			c.G135C						PASS	.						5.0	7.0	7.0					17																	8093324		676	1568	2244	SO:0001583	missense	54785	exon1			CTCTTCCTCCCCG	BC018880	CCDS11133.2	17p13.1	2005-12-16			ENSG00000196544	ENSG00000196544			25939	protein-coding gene	gene with protein product						12477932	Standard	NM_017622		Approved	FLJ20014	uc010vut.2	Q96GS4	OTTHUMG00000153930	ENST00000389017.4:c.135G>C	17.37:g.8093324C>G	ENSP00000373669:p.Glu45Asp	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	65	31	0.476923	NM_017622	Q53HS4|Q9NXW8	Missense_Mutation	SNP	ENST00000389017.4	37	CCDS11133.2	10	0.004578754578754579	2	0.0040650406504065045	2	0.0055248618784530384	0	0.0	6	0.0079155672823219	C	13.31	2.199387	0.38806	.	.	ENSG00000196544	ENST00000389017	.	.	.	4.97	3.99	0.46301	.	1.011480	0.07938	N	0.978690	T	0.21761	0.0524	N	0.14661	0.345	0.24756	N	0.992954	B	0.06786	0.001	B	0.06405	0.002	T	0.13335	-1.0513	9	0.33940	T	0.23	-5.7399	11.5007	0.50435	0.0:0.819:0.181:0.0	.	45	Q96GS4	CQ059_HUMAN	D	45	.	ENSP00000373669:E45D	E	-	3	2	C17orf59	8034049	0.914000	0.31030	0.993000	0.49108	0.747000	0.42532	2.072000	0.41510	1.449000	0.47699	0.561000	0.74099	GAG	C|0.995;G|0.005	0.005	strong		0.706	C17orf59-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333072.1	NM_017622	
MUC4	4585	hgsc.bcm.edu	37	3	195513474	195513474	+	Silent	SNP	T	T	G	rs77382269	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195513474T>G	ENST00000463781.3	-	2	5436	c.4977A>C	c.(4975-4977)acA>acC	p.T1659T	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Silent_p.T1659T	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.T1659T(3)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		TGGCGTGACCTGTGGATGCTG	0.592																																					p.T1659T		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,5	MUC4	1505	5	3	Substitution - coding silent(3)	stomach(2)|kidney(1)	c.A4977C						scavenged	.						26.0	30.0	29.0					3																	195513474		689	1579	2268	SO:0001819	synonymous_variant	4585	exon2			GTGACCTGTGGAT	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.4977A>C	3.37:g.195513474T>G		Somatic	163	3	0.0184049		WXS	Illumina HiSeq	Phase_I	224	55	0.245536	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																																																																																			T|0.945;G|0.055	0.055	strong		0.592	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
BEND3	57673	hgsc.bcm.edu	37	6	107391396	107391396	+	Silent	SNP	G	G	A	rs3814073	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:107391396G>A	ENST00000369042.1	-	4	1189	c.999C>T	c.(997-999)aaC>aaT	p.N333N	BEND3_ENST00000429433.2_Silent_p.N333N			Q5T5X7	BEND3_HUMAN	BEN domain containing 3	333	BEN 1. {ECO:0000255|PROSITE- ProRule:PRU00784}.									central_nervous_system(1)|cervix(2)|endometrium(3)|large_intestine(7)|lung(10)|ovary(4)|prostate(3)	30						TGAAGAAGTCGTTCAGCTGGG	0.647													g|||	1323	0.264177	0.1104	0.3617	5008	,	,		16213	0.4107		0.2038	False		,,,				2504	0.3139				p.N333N		Atlas-SNP	.											.	BEND3	70	.	0			c.C999T						PASS	.	G		535,3851		36,463,1694	13.0	14.0	13.0		999	0.2	1.0	6	dbSNP_107	13	1555,6997		136,1283,2857	no	coding-synonymous	BEND3	NM_001080450.2		172,1746,4551	AA,AG,GG		18.1829,12.1979,16.154		333/829	107391396	2090,10848	2193	4276	6469	SO:0001819	synonymous_variant	57673	exon5			GAAGTCGTTCAGC	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.999C>T	6.37:g.107391396G>A		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	86	41	0.476744	NM_001080450	A2RRH2|Q9HCL9	Silent	SNP	ENST00000369042.1	37	CCDS34507.1																																																																																			G|0.783;A|0.217	0.217	strong		0.647	BEND3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041686.1	NM_020913	
EHD2	30846	hgsc.bcm.edu	37	19	48229169	48229169	+	Silent	SNP	A	A	G	rs8111184	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:48229169A>G	ENST00000263277.3	+	4	854	c.603A>G	c.(601-603)tcA>tcG	p.S201S	CTD-2571L23.8_ENST00000599924.1_lincRNA|EHD2_ENST00000538399.1_Silent_p.S65S	NM_014601.3	NP_055416.2	Q9NZN4	EHD2_HUMAN	EH-domain containing 2	201	Dynamin-type G.				blood coagulation (GO:0007596)|cortical actin cytoskeleton organization (GO:0030866)|endocytic recycling (GO:0032456)|endocytosis (GO:0006897)|positive regulation of endocytic recycling (GO:2001137)|positive regulation of myoblast fusion (GO:1901741)|protein localization to plasma membrane (GO:0072659)	caveola (GO:0005901)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|recycling endosome membrane (GO:0055038)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|nucleic acid binding (GO:0003676)			endometrium(3)|large_intestine(7)|lung(2)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)	19		all_cancers(25;6.74e-07)|all_lung(116;2.02e-05)|Lung NSC(112;3.77e-05)|all_epithelial(76;4.89e-05)|all_neural(266;0.0332)|Ovarian(192;0.086)		OV - Ovarian serous cystadenocarcinoma(262;0.000336)|all cancers(93;0.000415)|Epithelial(262;0.0132)|GBM - Glioblastoma multiforme(486;0.0537)		ACGAGTTCTCAGAGGCCATCG	0.637													G|||	551	0.110024	0.1899	0.0836	5008	,	,		17763	0.0139		0.1402	False		,,,				2504	0.089				p.S201S		Atlas-SNP	.											.	EHD2	59	.	0			c.A603G						PASS	.	G		873,3533	738.7+/-411.0	89,695,1419	48.0	39.0	42.0		603	-7.3	0.5	19	dbSNP_116	42	1250,7350	758.1+/-407.5	89,1072,3139	no	coding-synonymous	EHD2	NM_014601.3		178,1767,4558	GG,GA,AA		14.5349,19.8139,16.3232		201/544	48229169	2123,10883	2203	4300	6503	SO:0001819	synonymous_variant	30846	exon4			GTTCTCAGAGGCC	AF181263	CCDS12704.1	19q13.3	2014-08-12			ENSG00000024422	ENSG00000024422		"""EF-hand domain containing"""	3243	protein-coding gene	gene with protein product		605890		PAST2		10673336	Standard	NM_014601		Approved		uc002phj.4	Q9NZN4	OTTHUMG00000183266	ENST00000263277.3:c.603A>G	19.37:g.48229169A>G		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	59	29	0.491525	NM_014601	B2RDH9|B4DNU6|Q96CB6	Silent	SNP	ENST00000263277.3	37	CCDS12704.1																																																																																			A|0.861;G|0.139	0.139	strong		0.637	EHD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465851.1		
IL24	11009	hgsc.bcm.edu	37	1	207074905	207074905	+	Missense_Mutation	SNP	T	T	C	rs1150258	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:207074905T>C	ENST00000294984.2	+	5	644	c.370T>C	c.(370-372)Tac>Cac	p.Y124H	IL24_ENST00000491169.1_3'UTR|IL24_ENST00000367093.3_Intron|IL24_ENST00000391929.3_Missense_Mutation_p.Y125H	NM_001185156.1|NM_006850.3	NP_001172085.1|NP_006841.1	Q13007	IL24_HUMAN	interleukin 24	124			Y -> H (in dbSNP:rs1150258). {ECO:0000269|PubMed:11704829, ECO:0000269|Ref.5}.		apoptotic process (GO:0006915)|cellular response to interleukin-4 (GO:0071353)|cellular response to lipopolysaccharide (GO:0071222)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|serine phosphorylation of STAT3 protein (GO:0033136)|wound healing (GO:0042060)	endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)				endometrium(4)|large_intestine(2)|lung(4)|ovary(1)|prostate(1)	12	Breast(84;0.201)					TTTCAAAAACTACCACAATAG	0.478													T|||	1581	0.315695	0.2905	0.438	5008	,	,		22780	0.2123		0.4533	False		,,,				2504	0.228				p.Y125H		Atlas-SNP	.											.	IL24	20	.	0			c.T373C						PASS	.	T	HIS/TYR,,,HIS/TYR	1303,3103	441.6+/-346.4	199,905,1099	129.0	118.0	121.0		373,,,370	2.4	0.9	1	dbSNP_87	121	4055,4545	558.8+/-387.3	975,2105,1220	yes	missense,intron,intron,missense	IL24	NM_001185156.1,NM_001185157.1,NM_001185158.1,NM_006850.3	83,,,83	1174,3010,2319	CC,CT,TT		47.1512,29.5733,41.1964	probably-damaging,,,probably-damaging	125/208,,,124/207	207074905	5358,7648	2203	4300	6503	SO:0001583	missense	11009	exon5			AAAAACTACCACA	U16261	CCDS1471.1, CCDS53465.1, CCDS53466.1, CCDS73021.1	1q32	2011-07-15		2001-06-29	ENSG00000162892	ENSG00000162892		"""Interleukins and interleukin receptors"""	11346	protein-coding gene	gene with protein product	"""melanoma differentiation association protein 7"", ""suppression of tumorigenicity 16 (melanoma differentiation)"", ""IL-4-induced secreted protein"""	604136		ST16		8545104, 8799171	Standard	NM_001185156		Approved	mda-7, IL10B, Mob-5, C49A, FISP, IL-24	uc001heu.2	Q13007	OTTHUMG00000036459	ENST00000294984.2:c.370T>C	1.37:g.207074905T>C	ENSP00000294984:p.Tyr124His	Somatic	256	0	0		WXS	Illumina HiSeq	Phase_I	195	87	0.446154	NM_001185156	Q2YHE5|Q53XZ7|Q5YLN8|Q96DB0|Q96KG4	Missense_Mutation	SNP	ENST00000294984.2	37	CCDS1471.1	796	0.36446886446886445	146	0.2967479674796748	181	0.5	129	0.22552447552447552	340	0.44854881266490765	T	14.19	2.460607	0.43736	0.295733	0.471512	ENSG00000162892	ENST00000391929;ENST00000294984	T;T	0.17854	2.25;2.25	4.72	2.38	0.29361	Four-helical cytokine-like, core (1);Four-helical cytokine, core (1);	0.144833	0.47852	D	0.000203	T	0.00012	0.0000	M	0.70595	2.14	0.09310	P	0.999999999449859	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.47045	-0.9147	9	0.44086	T	0.13	.	3.6967	0.08367	0.1904:0.1012:0.0:0.7084	rs1150258;rs17436290;rs52789945;rs61085050;rs1150258	125;124	Q53XZ7;Q13007	.;IL24_HUMAN	H	125;124	ENSP00000375795:Y125H;ENSP00000294984:Y124H	ENSP00000294984:Y124H	Y	+	1	0	IL24	205141528	0.625000	0.27111	0.897000	0.35233	0.388000	0.30384	1.076000	0.30729	0.322000	0.23283	0.454000	0.30748	TAC	T|0.623;G|0.003	.	strong		0.478	IL24-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000088680.2	NM_006850	
PASK	23178	hgsc.bcm.edu	37	2	242082262	242082262	+	Silent	SNP	T	T	C	rs6709462	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:242082262T>C	ENST00000405260.1	-	2	884	c.186A>G	c.(184-186)acA>acG	p.T62T	PASK_ENST00000403638.3_Silent_p.T62T|PASK_ENST00000358649.4_Silent_p.T62T|PASK_ENST00000234040.4_Silent_p.T62T|PASK_ENST00000544142.1_Missense_Mutation_p.Q11R|PASK_ENST00000539818.1_Intron	NM_001252120.1	NP_001239049.1	Q96RG2	PASK_HUMAN	PAS domain containing serine/threonine kinase	62					negative regulation of glycogen biosynthetic process (GO:0045719)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of energy homeostasis (GO:2000505)|regulation of glucagon secretion (GO:0070092)|regulation of respiratory gaseous exchange (GO:0043576)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	ATP binding (GO:0005524)|phosphatidylinositol binding (GO:0035091)|protein serine/threonine kinase activity (GO:0004674)|signal transducer activity (GO:0004871)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(6)|lung(20)|ovary(4)|prostate(4)|skin(1)|stomach(1)|urinary_tract(2)	53		all_cancers(19;4.46e-39)|all_epithelial(40;1.34e-17)|Breast(86;1.53e-05)|Renal(207;0.00179)|all_lung(227;0.00481)|Lung NSC(271;0.017)|Ovarian(221;0.0228)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;1.34e-31)|all cancers(36;1e-28)|OV - Ovarian serous cystadenocarcinoma(60;3.53e-14)|Kidney(56;4.31e-09)|KIRC - Kidney renal clear cell carcinoma(57;4.35e-08)|BRCA - Breast invasive adenocarcinoma(100;5.64e-06)|Lung(119;0.000596)|LUSC - Lung squamous cell carcinoma(224;0.00481)|Colorectal(34;0.014)|COAD - Colon adenocarcinoma(134;0.0968)		CAGAGAGCGCTGTCCTGCTCT	0.557													C|||	2993	0.597644	0.4508	0.6167	5008	,	,		20296	0.9097		0.4622	False		,,,				2504	0.6002				p.T62T		Atlas-SNP	.											PASK_ENST00000234040,colon,carcinoma,-1,2	PASK	230	2	0			c.A186G						scavenged	.	C		1995,2411	615.0+/-392.5	447,1101,655	82.0	70.0	74.0		186	-6.0	0.0	2	dbSNP_116	74	3947,4653	601.5+/-394.4	870,2207,1223	no	coding-synonymous	PASK	NM_015148.2		1317,3308,1878	CC,CT,TT		45.8953,45.2792,45.6866		62/1324	242082262	5942,7064	2203	4300	6503	SO:0001819	synonymous_variant	23178	exon2			GAGCGCTGTCCTG	U79240	CCDS2545.1, CCDS58758.1, CCDS58759.1	2q37.3	2008-05-23			ENSG00000115687	ENSG00000115687			17270	protein-coding gene	gene with protein product		607505				11688972, 11459942, 15148392	Standard	NM_001252119		Approved	PASKIN, KIAA0135, STK37	uc010fzl.2	Q96RG2	OTTHUMG00000133392	ENST00000405260.1:c.186A>G	2.37:g.242082262T>C		Somatic	84	1	0.0119048		WXS	Illumina HiSeq	Phase_I	76	43	0.565789	NM_001252122	G5E9F1|Q05BE4|Q68DY3|Q6GSJ5|Q86XH6|Q99763|Q9UFR7	Silent	SNP	ENST00000405260.1	37	CCDS2545.1	1303	0.5966117216117216	225	0.4573170731707317	212	0.585635359116022	523	0.9143356643356644	343	0.4525065963060686	C	0.294	-0.978391	0.02197	0.452792	0.458953	ENSG00000115687	ENST00000544142	T	0.66280	-0.2	4.39	-5.98	0.02220	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.35525	-0.9785	7	0.87932	D	0	.	1.5711	0.02615	0.2099:0.2624:0.1035:0.4241	rs6709462;rs17384140;rs58425904;rs6709462	11	F5GYW7	.	R	11	ENSP00000441374:Q11R	ENSP00000441374:Q11R	Q	-	2	0	PASK	241730935	0.000000	0.05858	0.000000	0.03702	0.114000	0.19823	-0.216000	0.09266	-2.056000	0.00898	-0.930000	0.02707	CAG	T|0.480;C|0.520	0.520	strong		0.557	PASK-003	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000323753.1	NM_015148	
SIMC1	375484	hgsc.bcm.edu	37	5	175772208	175772208	+	Silent	SNP	C	C	T	rs17622467	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:175772208C>T	ENST00000443967.1	+	12	2786	c.2379C>T	c.(2377-2379)atC>atT	p.I793I	SIMC1_ENST00000332772.4_Silent_p.I254I|SIMC1_ENST00000341199.6_Silent_p.I378I|RP11-843P14.2_ENST00000508187.1_RNA|KIAA1191_ENST00000393728.2_5'Flank|SIMC1_ENST00000430704.2_Silent_p.I378I			Q8NDZ2	SIMC1_HUMAN	SUMO-interacting motifs containing 1	793							SUMO polymer binding (GO:0032184)										GTTCCGTGATCGACCGAAAGG	0.423													C|||	559	0.111621	0.0514	0.1556	5008	,	,		19676	0.1111		0.1312	False		,,,				2504	0.1421				p.I378I		Atlas-SNP	.											.	.	.	.	0			c.C1134T						PASS	.	C		303,4103	164.7+/-196.3	10,283,1910	106.0	105.0	105.0		1134	-8.2	0.2	5	dbSNP_123	105	1159,7441	237.8+/-269.5	80,999,3221	no	coding-synonymous	C5orf25	NM_198567.4		90,1282,5131	TT,TC,CC		13.4767,6.877,11.241		378/458	175772208	1462,11544	2203	4300	6503	SO:0001819	synonymous_variant	375484	exon9			CGTGATCGACCGA	BC037298	CCDS4398.2	5q35.2	2013-08-14	2012-11-14	2012-11-14	ENSG00000170085	ENSG00000170085			24779	protein-coding gene	gene with protein product	"""oocyte maturation associated 1"", ""platform element for inhibition of autolytic degradation"""		"""chromosome 5 open reading frame 25"""	C5orf25		23086935, 23707407	Standard	NM_198567		Approved	FLJ44216, OOMA1, PLEIAD	uc003mds.4	Q8NDZ2	OTTHUMG00000130663	ENST00000443967.1:c.2379C>T	5.37:g.175772208C>T		Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	173	71	0.410405	NM_198567	J3KQQ8|Q6NXN8|Q6ZTU4|Q8IZ15	Silent	SNP	ENST00000443967.1	37																																																																																				C|0.896;N|0.000	.	strong		0.423	SIMC1-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000253155.2	NM_198567	
SLFNL1	200172	hgsc.bcm.edu	37	1	41486245	41486245	+	Missense_Mutation	SNP	C	C	T	rs1138293	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:41486245C>T	ENST00000359345.1	-	1	2664	c.88G>A	c.(88-90)Gca>Aca	p.A30T	SLFNL1_ENST00000372611.1_Missense_Mutation_p.A30T|SLFNL1_ENST00000372613.2_Missense_Mutation_p.A30T|SLFNL1_ENST00000302946.8_Missense_Mutation_p.A30T|SLFNL1_ENST00000397197.2_Missense_Mutation_p.A30T|SLFNL1_ENST00000439569.2_Missense_Mutation_p.A30T	NM_144990.3	NP_659427.3	Q499Z3	SLNL1_HUMAN	schlafen-like 1	30			A -> T (in dbSNP:rs1138293). {ECO:0000269|PubMed:14702039}.				ATP binding (GO:0005524)			endometrium(3)|large_intestine(3)|lung(2)|prostate(1)|skin(1)	10	Ovarian(52;0.00769)|all_hematologic(146;0.0977)|Breast(333;0.1)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0393)				GACTGCTCTGCGGGTAGCTCC	0.612													C|||	443	0.0884585	0.0076	0.134	5008	,	,		17231	0.0456		0.2028	False		,,,				2504	0.092				p.A30T		Atlas-SNP	.											.	SLFNL1	37	.	0			c.G88A						PASS	.	C	THR/ALA,THR/ALA	201,4203	117.5+/-155.4	8,185,2009	49.0	51.0	51.0		88,88	-10.1	0.0	1	dbSNP_86	51	1686,6914	296.1+/-302.7	166,1354,2780	yes	missense,missense	SLFNL1	NM_001168247.1,NM_144990.3	58,58	174,1539,4789	TT,TC,CC		19.6047,4.564,14.5109	benign,benign	30/408,30/408	41486245	1887,11117	2202	4300	6502	SO:0001583	missense	200172	exon3			GCTCTGCGGGTAG	BC022037	CCDS460.1, CCDS72766.1	1p34.2	2008-02-05			ENSG00000171790	ENSG00000171790			26313	protein-coding gene	gene with protein product							Standard	NM_144990		Approved	FLJ23878	uc001cgm.2	Q499Z3	OTTHUMG00000005719	ENST00000359345.1:c.88G>A	1.37:g.41486245C>T	ENSP00000352299:p.Ala30Thr	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	77	20	0.25974	NM_001168247	A8K8D1|Q49AG8|Q5VW72|Q5VW74|Q8N7V7|Q8TCH6|Q8WVZ8	Missense_Mutation	SNP	ENST00000359345.1	37	CCDS460.1	238	0.10897435897435898	7	0.014227642276422764	63	0.17403314917127072	27	0.0472027972027972	141	0.18601583113456466	C	0.424	-0.906739	0.02434	0.04564	0.196047	ENSG00000171790	ENST00000302946;ENST00000372613;ENST00000372611;ENST00000359345;ENST00000439569;ENST00000397197	T;T;T;T;T;T	0.60424	0.19;0.19;0.19;0.19;0.19;0.19	5.03	-10.1	0.00402	.	1.914250	0.02419	N	0.082386	T	0.00039	0.0001	N	0.14661	0.345	0.80722	P	0.0	B;B;B	0.10296	0.0;0.0;0.003	B;B;B	0.04013	0.0;0.0;0.001	T	0.10019	-1.0648	9	0.30854	T	0.27	6.572	7.6949	0.28590	0.055:0.4136:0.1081:0.4233	rs1138293;rs3202043;rs17362076;rs1138293	30;30;30	Q499Z3-3;Q499Z3-2;Q499Z3	.;.;SLNL1_HUMAN	T	30	ENSP00000304401:A30T;ENSP00000361696:A30T;ENSP00000361694:A30T;ENSP00000352299:A30T;ENSP00000398938:A30T;ENSP00000380381:A30T	ENSP00000304401:A30T	A	-	1	0	SLFNL1	41258832	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.880000	0.00715	-4.903000	0.00027	-3.753000	0.00022	GCA	C|0.874;T|0.126	0.126	strong		0.612	SLFNL1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000015650.1	NM_144990	
CDH5	1003	hgsc.bcm.edu	37	16	66432381	66432381	+	Missense_Mutation	SNP	T	T	C	rs16956504	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	106	0	0		WXS	Illumina HiSeq	Phase_I	90	31	0.344444	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	
TCHH	7062	hgsc.bcm.edu	37	1	152084216	152084216	+	Missense_Mutation	SNP	C	C	G	rs201131683	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:152084216C>G	ENST00000368804.1	-	2	1476	c.1477G>C	c.(1477-1479)Gag>Cag	p.E493Q		NM_007113.2	NP_009044.2	Q07283	TRHY_HUMAN	trichohyalin	493	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)			CTCTCCTCCTCCTCGAGCTTC	0.672																																					p.E493Q		Atlas-SNP	.											TCHH,NS,lymphoid_neoplasm,0,1	TCHH	275	1	0			c.G1477C						PASS	.		GLN/GLU	0,4218		0,0,2109	64.0	71.0	69.0		1477	-1.7	0.0	1		69	17,8419		0,17,4201	no	missense	TCHH	NM_007113.2	29	0,17,6310	GG,GC,CC		0.2015,0.0,0.1343	benign	493/1944	152084216	17,12637	2109	4218	6327	SO:0001583	missense	7062	exon3			CCTCCTCCTCGAG	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.1477G>C	1.37:g.152084216C>G	ENSP00000357794:p.Glu493Gln	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	100	13	0.13	NM_007113	Q5VUI3	Missense_Mutation	SNP	ENST00000368804.1	37	CCDS41396.1	.	.	.	.	.	.	.	.	.	.	c	7.158	0.585028	0.13749	0.0	0.002015	ENSG00000159450	ENST00000368804	T	0.04551	3.6	3.42	-1.67	0.08238	.	.	.	.	.	T	0.00695	0.0023	N	0.08118	0	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.43147	-0.9409	9	0.12103	T	0.63	.	11.5902	0.50941	0.1022:0.7375:0.1603:0.0	.	493	Q07283	TRHY_HUMAN	Q	493	ENSP00000357794:E493Q	ENSP00000357794:E493Q	E	-	1	0	TCHH	150350840	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-0.797000	0.04570	-0.858000	0.04110	-0.574000	0.04147	GAG	C|0.986;G|0.013	0.013	strong		0.672	TCHH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036671.2	NM_007113	
ARHGEF37	389337	hgsc.bcm.edu	37	5	149003626	149003626	+	Missense_Mutation	SNP	G	G	A	rs113997100	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:149003626G>A	ENST00000333677.6	+	10	1550	c.1387G>A	c.(1387-1389)Gca>Aca	p.A463T		NM_001001669.2	NP_001001669.2	A1IGU5	ARH37_HUMAN	Rho guanine nucleotide exchange factor (GEF) 37	463						cytoplasm (GO:0005737)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			large_intestine(5)|lung(6)|ovary(1)|prostate(2)|stomach(3)	17						GGTGGAGGACGCACTGGGCCG	0.587													G|||	82	0.0163738	0.003	0.0274	5008	,	,		17856	0.0		0.0547	False		,,,				2504	0.0041				p.A463T		Atlas-SNP	.											ARHGEF37,NS,carcinoma,-1,1	ARHGEF37	45	1	0			c.G1387A						PASS	.	G	THR/ALA	39,4011		0,39,1986	85.0	92.0	90.0		1387	-11.2	0.0	5	dbSNP_132	90	464,7896		20,424,3736	yes	missense	ARHGEF37	NM_001001669.2	58	20,463,5722	AA,AG,GG		5.5502,0.963,4.0532	benign	463/676	149003626	503,11907	2025	4180	6205	SO:0001583	missense	389337	exon10			GAGGACGCACTGG	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.1387G>A	5.37:g.149003626G>A	ENSP00000328083:p.Ala463Thr	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	57	32	0.561404	NM_001001669	Q6ZW51	Missense_Mutation	SNP	ENST00000333677.6	37	CCDS43385.1	57	0.0260989010989011	2	0.0040650406504065045	10	0.027624309392265192	0	0.0	45	0.059366754617414245	G	0.094	-1.162062	0.01673	0.00963	0.055502	ENSG00000183111	ENST00000333677	T	0.53857	0.6	5.61	-11.2	0.00127	.	1.021810	0.07745	N	0.947542	T	0.01320	0.0043	N	0.02539	-0.55	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.03296	-1.1051	10	0.02654	T	1	-8.0E-4	1.7419	0.02954	0.3536:0.086:0.3049:0.2555	.	463	A1IGU5	ARH37_HUMAN	T	463	ENSP00000328083:A463T	ENSP00000328083:A463T	A	+	1	0	ARHGEF37	148983819	0.000000	0.05858	0.000000	0.03702	0.146000	0.21551	-0.986000	0.03747	-2.630000	0.00435	-1.319000	0.01295	GCA	G|0.967;A|0.033	0.033	strong		0.587	ARHGEF37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373763.1	NM_001001669	
KRT75	9119	hgsc.bcm.edu	37	12	52818377	52818377	+	Missense_Mutation	SNP	C	C	T	rs61730614	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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						PASS	.	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	175	0	0		WXS	Illumina HiSeq	Phase_I	165	82	0.49697	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	
GRK7	131890	hgsc.bcm.edu	37	3	141535608	141535608	+	Missense_Mutation	SNP	C	C	A	rs33928105	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:141535608C>A	ENST00000264952.2	+	4	1515	c.1378C>A	c.(1378-1380)Cct>Act	p.P460T		NM_139209.2	NP_631948.1	Q8WTQ7	GRK7_HUMAN	G protein-coupled receptor kinase 7	460	AGC-kinase C-terminal.		P -> T (in dbSNP:rs33928105). {ECO:0000269|PubMed:17344846}.		protein autophosphorylation (GO:0046777)|signal transduction (GO:0007165)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|visual perception (GO:0007601)	membrane (GO:0016020)	ATP binding (GO:0005524)|G-protein coupled receptor kinase activity (GO:0004703)|rhodopsin kinase activity (GO:0050254)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(14)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	26						GATCAACTTTCCTCGCCTGGA	0.428													C|||	321	0.0640974	0.0817	0.0677	5008	,	,		17376	0.0139		0.1054	False		,,,				2504	0.047				p.P460T		Atlas-SNP	.											.	GRK7	65	.	0			c.C1378A						PASS	.	C	THR/PRO	369,4037	188.8+/-215.1	17,335,1851	112.0	113.0	113.0		1378	2.5	1.0	3	dbSNP_126	113	1105,7495	230.1+/-264.6	66,973,3261	yes	missense	GRK7	NM_139209.2	38	83,1308,5112	AA,AC,CC		12.8488,8.3749,11.3332	benign	460/554	141535608	1474,11532	2203	4300	6503	SO:0001583	missense	131890	exon4			AACTTTCCTCGCC		CCDS3120.1	3q24	2004-02-04	2004-02-04	2004-02-04	ENSG00000114124	ENSG00000114124			17031	protein-coding gene	gene with protein product		606987		GPRK7		11717351, 11754336	Standard	NM_139209		Approved		uc011bnd.2	Q8WTQ7	OTTHUMG00000159068	ENST00000264952.2:c.1378C>A	3.37:g.141535608C>A	ENSP00000264952:p.Pro460Thr	Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	128	71	0.554688	NM_139209		Missense_Mutation	SNP	ENST00000264952.2	37	CCDS3120.1	165	0.07554945054945054	42	0.08536585365853659	33	0.09116022099447514	5	0.008741258741258742	85	0.11213720316622691	C	14.10	2.434647	0.43224	0.083749	0.128488	ENSG00000114124	ENST00000264952	T	0.24723	1.84	5.4	2.52	0.30459	AGC-kinase, C-terminal (2);Protein kinase-like domain (1);	0.279721	0.36444	N	0.002584	T	0.00210	0.0006	L	0.45581	1.43	0.37836	P	0.07110899999999998	B	0.28128	0.201	B	0.25140	0.058	T	0.08207	-1.0733	9	0.46703	T	0.11	-3.9809	7.2857	0.26337	0.124:0.6777:0.1298:0.0685	rs33928105	460	Q8WTQ7	GRK7_HUMAN	T	460	ENSP00000264952:P460T	ENSP00000264952:P460T	P	+	1	0	GRK7	143018298	1.000000	0.71417	0.991000	0.47740	0.898000	0.52572	3.309000	0.51903	0.210000	0.20664	0.467000	0.42956	CCT	C|0.899;A|0.101	0.101	strong		0.428	GRK7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353168.1	NM_139209	
CRIPAK	285464	hgsc.bcm.edu	37	4	1388631	1388631	+	Missense_Mutation	SNP	C	C	G	rs200849975	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:1388631C>G	ENST00000324803.4	+	1	3292	c.332C>G	c.(331-333)cCa>cGa	p.P111R		NM_175918.3	NP_787114.2	Q8N1N5	CRPAK_HUMAN	cysteine-rich PAK1 inhibitor	111					negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of protein kinase activity (GO:0006469)|regulation of cytoskeleton organization (GO:0051493)|response to estrogen (GO:0043627)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.P111R(1)		NS(3)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(11)|ovary(1)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(1)	35			OV - Ovarian serous cystadenocarcinoma(23;0.0106)			CTCACGTGCCCATGTGGAGTG	0.667													N|||	218	0.0435304	0.0287	0.0548	5008	,	,		18151	0.006		0.0487	False		,,,				2504	0.089				p.P111R		Atlas-SNP	.											CRIPAK,rectum,carcinoma,0,2	CRIPAK	185	2	1	Substitution - Missense(1)	skin(1)	c.C332G						PASS	.						193.0	146.0	162.0					4																	1388631		2203	4299	6502	SO:0001583	missense	285464	exon1			CGTGCCCATGTGG	AK096209	CCDS3349.1	4p16.3	2011-02-10	2006-09-04		ENSG00000179979	ENSG00000179979			26619	protein-coding gene	gene with protein product		610203	"""cysteine-rich PAK1inhibitor"""			16278681	Standard	NM_175918		Approved	FLJ34443	uc003gdf.2	Q8N1N5	OTTHUMG00000121131	ENST00000324803.4:c.332C>G	4.37:g.1388631C>G	ENSP00000323978:p.Pro111Arg	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	47	7	0.148936	NM_175918	Q8NB03	Missense_Mutation	SNP	ENST00000324803.4	37	CCDS3349.1	.	.	.	.	.	.	.	.	.	.	-	5.610	0.297336	0.10622	.	.	ENSG00000179979	ENST00000324803	T	0.22336	1.96	0.948	-0.0113	0.13993	Post-SET domain (1);	.	.	.	.	T	0.07548	0.0190	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.39820	-0.9595	9	0.12103	T	0.63	.	2.6024	0.04869	0.0:0.4564:0.3174:0.2262	.	111	Q8N1N5	CRPAK_HUMAN	R	111	ENSP00000323978:P111R	ENSP00000323978:P111R	P	+	2	0	CRIPAK	1378631	0.005000	0.15991	0.001000	0.08648	0.013000	0.08279	-1.037000	0.03557	-0.011000	0.14247	-1.737000	0.00689	CCA	C|0.935;G|0.065	0.065	strong		0.667	CRIPAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241607.2	NM_175918	
DST	667	hgsc.bcm.edu	37	6	56494071	56494071	+	Silent	SNP	A	A	G	rs112640831	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:56494071A>G	ENST00000361203.3	-	28	3826	c.3819T>C	c.(3817-3819)aaT>aaC	p.N1273N	DST_ENST00000370769.4_Silent_p.N1273N|DST_ENST00000244364.6_Silent_p.N947N|DST_ENST00000518935.1_Silent_p.N947N|DST_ENST00000370765.6_Silent_p.N947N|DST_ENST00000312431.6_Silent_p.N1273N|DST_ENST00000446842.2_Silent_p.N947N|DST_ENST00000370754.5_Silent_p.N1451N|DST_ENST00000370788.2_Silent_p.N1273N|DST_ENST00000421834.2_Silent_p.N1273N			Q03001	DYST_HUMAN	dystonin	1273					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)			GCACATGAACATTTTGCCACC	0.338													A|||	53	0.0105831	0.0015	0.0101	5008	,	,		18282	0.0		0.0268	False		,,,				2504	0.0174				p.N947N		Atlas-SNP	.											.	DST	1427	.	0			c.T2841C						PASS	.	A	,	33,4373	37.6+/-69.7	0,33,2170	276.0	228.0	244.0		2841,2841	-1.0	1.0	6	dbSNP_132	244	360,8240	120.2+/-179.5	9,342,3949	no	coding-synonymous,coding-synonymous	DST	NM_001723.5,NM_015548.4	,	9,375,6119	GG,GA,AA		4.186,0.749,3.0217	,	947/2650,947/5172	56494071	393,12613	2203	4300	6503	SO:0001819	synonymous_variant	667	exon18			ATGAACATTTTGC	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.3819T>C	6.37:g.56494071A>G		Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	128	66	0.515625	NM_001723	B7Z3H1|O94833|Q12825|Q13266|Q13267|Q13775|Q5TBT0|Q5TBT2|Q5TF23|Q5TF24|Q8N1T8|Q8N8J3|Q8WXK8|Q8WXK9|Q96AK9|Q96DQ5|Q96J76|Q96QT5|Q9H555|Q9UGD7|Q9UGD8|Q9UN10	Silent	SNP	ENST00000361203.3	37																																																																																				A|0.974;G|0.026;T|0.000	0.026	strong		0.338	DST-004	NOVEL	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000041021.3	NM_001723	
APOC4	346	hgsc.bcm.edu	37	19	45448036	45448036	+	Missense_Mutation	SNP	T	T	C	rs1132899	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:45448036T>C	ENST00000592954.1	+	2	147	c.107T>C	c.(106-108)cTg>cCg	p.L36P	APOC2_ENST00000592257.1_5'Flank|APOC2_ENST00000590360.1_5'Flank|APOC4-APOC2_ENST00000589057.1_Missense_Mutation_p.L36P|APOC2_ENST00000252490.4_5'Flank|APOC4_ENST00000419266.2_Missense_Mutation_p.L36P|APOC2_ENST00000591597.1_5'Flank|APOC4_ENST00000591600.1_Missense_Mutation_p.L36P	NM_001646.2	NP_001637.1	P55056	APOC4_HUMAN	apolipoprotein C-IV	36			L -> P (in dbSNP:rs1132899). {ECO:0000269|PubMed:10996355, ECO:0000269|Ref.2}.		lipid metabolic process (GO:0006629)|positive regulation of sequestering of triglyceride (GO:0010890)|triglyceride homeostasis (GO:0070328)	high-density lipoprotein particle (GO:0034364)|very-low-density lipoprotein particle (GO:0034361)	lipid transporter activity (GO:0005319)			breast(1)|endometrium(1)|lung(2)	4	Lung NSC(12;0.00858)|all_lung(12;0.0197)	Ovarian(192;0.0728)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.00334)|Epithelial(262;0.178)		GAAGGAACCCTGAGCCCCCCA	0.607													C|||	3327	0.664337	0.7307	0.7248	5008	,	,		14986	0.7262		0.498	False		,,,				2504	0.6391				p.L36P		Atlas-SNP	.											.	APOC4	6	.	0			c.T107C						PASS	.	C	PRO/LEU	3152,1252	415.2+/-337.1	1134,884,184	47.0	49.0	49.0		107	-4.9	0.0	19	dbSNP_86	49	4412,4188	547.6+/-385.2	1147,2118,1035	yes	missense	APOC4	NM_001646.2	98	2281,3002,1219	CC,CT,TT		48.6977,28.4287,41.8333	benign	36/128	45448036	7564,5440	2202	4300	6502	SO:0001583	missense	346	exon2			GAACCCTGAGCCC	U32576	CCDS12649.1	19q13.2	2013-09-30			ENSG00000267467	ENSG00000267467		"""Apolipoproteins"""	611	protein-coding gene	gene with protein product		600745				8530039	Standard	NM_001646		Approved			P55056	OTTHUMG00000180845	ENST00000592954.1:c.107T>C	19.37:g.45448036T>C	ENSP00000468236:p.Leu36Pro	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	64	33	0.515625	NM_001646	B3KWY6|Q53YY8	Missense_Mutation	SNP	ENST00000592954.1	37	CCDS12649.1	1435	0.657051282051282	380	0.7723577235772358	250	0.6906077348066298	417	0.7290209790209791	388	0.5118733509234829	C	2.272	-0.366865	0.05069	0.715713	0.513023	ENSG00000224916	ENST00000419266;ENST00000436871	T;T	0.24151	1.87;1.87	2.44	-4.88	0.03113	.	1.295300	0.05865	N	0.623646	T	0.00012	0.0000	N	0.05124	-0.11	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.29912	-0.9996	9	0.36615	T	0.2	-1.3808	6.3134	0.21176	0.1493:0.1684:0.0:0.6823	rs1132899;rs2304180;rs3194191;rs17251065;rs17257866;rs17561696;rs59271342;rs1132899	36	P55056	APOC4_HUMAN	P	36	ENSP00000406381:L36P;ENSP00000412935:L36P	ENSP00000406381:L36P	L	+	2	0	APOC4	50139876	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.990000	0.01479	-1.844000	0.01178	-2.059000	0.00401	CTG	T|0.387;C|0.613	0.613	strong		0.607	APOC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453255.1	NM_001646	
SIPA1	6494	hgsc.bcm.edu	37	11	65417434	65417434	+	Silent	SNP	G	G	A	rs746429	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:65417434G>A	ENST00000394224.3	+	13	3056	c.2760G>A	c.(2758-2760)gcG>gcA	p.A920A	MIR4489_ENST00000578869.1_RNA|SIPA1_ENST00000534313.1_Silent_p.A920A|SIPA1_ENST00000394227.3_Silent_p.A818A|SIPA1_ENST00000527525.1_Silent_p.A818A	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	69	0	0		WXS	Illumina HiSeq	Phase_I	63	14	0.222222	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	
CCL14	6358	hgsc.bcm.edu	37	17	34313612	34313612	+	Missense_Mutation	SNP	G	G	A	rs75238886	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:34313612G>A	ENST00000394509.4	-	1	182	c.74C>T	c.(73-75)tCc>tTc	p.S25F	CTB-186H2.3_ENST00000591669.1_Missense_Mutation_p.E20K|CCL14_ENST00000480944.2_5'UTR|CCL15-CCL14_ENST00000481427.2_3'UTR|CCL14_ENST00000435911.2_Missense_Mutation_p.S25F|CTB-186H2.3_ENST00000593057.1_Intron|CCL14_ENST00000586216.1_Missense_Mutation_p.S25F|CCL14_ENST00000536149.1_Missense_Mutation_p.S25F			Q16627	CCL14_HUMAN	chemokine (C-C motif) ligand 14	25					cell chemotaxis (GO:0060326)|cellular calcium ion homeostasis (GO:0006874)|immune response (GO:0006955)|positive regulation of cell proliferation (GO:0008284)	extracellular space (GO:0005615)				large_intestine(1)|lung(6)	7		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		CTCACGTGAGGAGGATTCAGT	0.562													G|||	128	0.0255591	0.0197	0.0144	5008	,	,		16475	0.0466		0.0368	False		,,,				2504	0.0082				p.S25F		Atlas-SNP	.											.	CCL14	22	.	0			c.C74T						PASS	.	G	PHE/SER,PHE/SER	103,4303	81.9+/-120.4	1,101,2101	203.0	145.0	164.0		74,74	1.5	0.0	17	dbSNP_132	164	253,8347	99.9+/-161.4	0,253,4047	yes	missense,missense	CCL14	NM_032962.4,NM_032963.3	155,155	1,354,6148	AA,AG,GG		2.9419,2.3377,2.7372	probably-damaging,probably-damaging	25/110,25/94	34313612	356,12650	2203	4300	6503	SO:0001583	missense	6358	exon1			CGTGAGGAGGATT	Z49270	CCDS32624.1, CCDS45652.1	17q11.2	2014-04-10	2002-08-22	2002-08-23	ENSG00000213494	ENSG00000276409		"""Chemokine ligands"", ""Endogenous ligands"""	10612	protein-coding gene	gene with protein product		601392	"""small inducible cytokine subfamily A (Cys-Cys), member 14"""	SCYA14		8661057	Standard	NM_032963		Approved	HCC-1, HCC-3, NCC-2, SCYL2, CKb1, MCIF	uc010wcq.1	Q16627	OTTHUMG00000188403	ENST00000394509.4:c.74C>T	17.37:g.34313612G>A	ENSP00000378017:p.Ser25Phe	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	104	54	0.519231	NM_032962	E1P649|E1P650|Q13954	Missense_Mutation	SNP	ENST00000394509.4	37	CCDS32624.1	65	0.02976190476190476	10	0.02032520325203252	6	0.016574585635359115	19	0.033216783216783216	30	0.0395778364116095	G	13.77	2.335048	0.41398	0.023377	0.029419	ENSG00000213494	ENST00000394509;ENST00000536149;ENST00000435911	T;T;T	0.03831	4.14;3.79;3.79	4.74	1.52	0.23074	Chemokine interleukin-8-like domain (1);	0.920382	0.09005	U	0.862372	T	0.02119	0.0066	.	.	.	0.09310	N	1	D;D	0.57571	0.965;0.98	P;P	0.55303	0.598;0.773	T	0.34750	-0.9816	9	0.42905	T	0.14	.	7.2842	0.26328	0.0:0.1675:0.4863:0.3462	.	25;25	Q16627;Q16627-2	CCL14_HUMAN;.	F	25	ENSP00000378017:S25F;ENSP00000441771:S25F;ENSP00000409197:S25F	ENSP00000378017:S25F	S	-	2	0	CCL14	31337725	0.012000	0.17670	0.000000	0.03702	0.004000	0.04260	1.387000	0.34430	0.180000	0.19960	-0.302000	0.09304	TCC	G|0.973;A|0.027	0.027	strong		0.562	CCL14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000272892.2	NM_032962	
THSD4	79875	hgsc.bcm.edu	37	15	71953045	71953045	+	Silent	SNP	G	G	A	rs62024298	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:71953045G>A	ENST00000355327.3	+	8	1463	c.1329G>A	c.(1327-1329)acG>acA	p.T443T	THSD4_ENST00000261862.6_Silent_p.T443T|THSD4_ENST00000357769.4_Silent_p.T83T|THSD4_ENST00000567838.1_3'UTR			Q6ZMP0	THSD4_HUMAN	thrombospondin, type I, domain containing 4	443					elastic fiber assembly (GO:0048251)	extracellular vesicular exosome (GO:0070062)|microfibril (GO:0001527)	metalloendopeptidase activity (GO:0004222)			breast(1)|central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(20)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	42						TCAACATCACGGAGATGTACA	0.512													G|||	1688	0.337061	0.2027	0.2637	5008	,	,		18803	0.6706		0.2565	False		,,,				2504	0.3098				p.T443T		Atlas-SNP	.											.	THSD4	75	.	0			c.G1329A						PASS	.	G		754,3136		71,612,1262	85.0	88.0	87.0		1329	-9.1	0.7	15	dbSNP_129	87	1936,6356		229,1478,2439	no	coding-synonymous	THSD4	NM_024817.2		300,2090,3701	AA,AG,GG		23.3478,19.383,22.0818		443/1019	71953045	2690,9492	1945	4146	6091	SO:0001819	synonymous_variant	79875	exon7			CATCACGGAGATG	AK023772	CCDS10238.2, CCDS66817.1	15q23	2009-11-09			ENSG00000187720	ENSG00000187720			25835	protein-coding gene	gene with protein product		614476				19734141	Standard	NM_001286429		Approved	FVSY9334, PRO34005, FLJ13710, ADAMTSL6	uc002atb.1	Q6ZMP0	OTTHUMG00000133389	ENST00000355327.3:c.1329G>A	15.37:g.71953045G>A		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	97	55	0.56701	NM_024817	B2RTY3|B4DR13|Q6MZI3|Q6UXZ8|Q9H8E4	Silent	SNP	ENST00000355327.3	37	CCDS10238.2																																																																																			G|0.678;A|0.322	0.322	strong		0.512	THSD4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257253.2	NM_024817	
MS4A14	84689	hgsc.bcm.edu	37	11	60182970	60182970	+	Missense_Mutation	SNP	A	A	T	rs7131283	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:60182970A>T	ENST00000300187.6	+	5	806	c.529A>T	c.(529-531)Aat>Tat	p.N177Y	MS4A14_ENST00000395005.2_Missense_Mutation_p.N160Y|MS4A14_ENST00000531783.1_Missense_Mutation_p.N210Y|MS4A14_ENST00000531787.1_Missense_Mutation_p.N65Y|MS4A14_ENST00000395001.1_3'UTR	NM_032597.4	NP_115986.3	Q96JA4	M4A14_HUMAN	membrane-spanning 4-domains, subfamily A, member 14	177			N -> Y (in dbSNP:rs7131283). {ECO:0000269|Ref.1, ECO:0000269|Ref.2}.			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						CCCAGAAGAAAATGATCAATT	0.358													A|||	2894	0.577875	0.5492	0.6902	5008	,	,		18916	0.4097		0.7018	False		,,,				2504	0.5828				p.N210Y		Atlas-SNP	.											.	MS4A14	120	.	0			c.A628T						PASS	.	A	TYR/ASN,TYR/ASN	2352,2054	606.6+/-390.8	623,1106,474	128.0	125.0	126.0		478,529	0.1	0.0	11	dbSNP_116	126	5976,2624	686.5+/-404.1	2071,1834,395	yes	missense,missense	MS4A14	NM_001079692.1,NM_032597.3	143,143	2694,2940,869	TT,TA,AA		30.5116,46.6182,35.968	probably-damaging,probably-damaging	160/663,177/680	60182970	8328,4678	2203	4300	6503	SO:0001583	missense	84689	exon6			GAAGAAAATGATC	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.529A>T	11.37:g.60182970A>T	ENSP00000300187:p.Asn177Tyr	Somatic	224	0	0		WXS	Illumina HiSeq	Phase_I	234	52	0.222222	NM_001261828	E9PJE3|Q2TVT5|Q3B7W3|Q86XH8|Q9NTC2	Missense_Mutation	SNP	ENST00000300187.6	37	CCDS31569.1	1310	0.5998168498168498	272	0.5528455284552846	247	0.6823204419889503	264	0.46153846153846156	527	0.6952506596306068	A	13.06	2.125193	0.37533	0.533818	0.694884	ENSG00000166928	ENST00000531787;ENST00000300187;ENST00000395005;ENST00000531783	T;T;T;T	0.12879	4.33;4.33;4.33;2.64	3.73	0.0768	0.14405	.	.	.	.	.	T	0.00012	0.0000	M	0.64997	1.995	0.58432	P	6.999999999979245E-6	D;D	0.69078	0.996;0.997	D;D	0.68353	0.947;0.957	T	0.41197	-0.9522	8	0.62326	D	0.03	-7.6972	3.2744	0.06893	0.5593:0.2118:0.2289:0.0	rs7131283;rs52794552;rs57607368;rs7131283	160;177	Q96JA4-2;Q96JA4	.;M4A14_HUMAN	Y	65;177;160;210	ENSP00000437222:N65Y;ENSP00000300187:N177Y;ENSP00000378453:N160Y;ENSP00000433761:N210Y	ENSP00000300187:N177Y	N	+	1	0	MS4A14	59939546	0.700000	0.27796	0.022000	0.16811	0.009000	0.06853	0.397000	0.20883	-0.006000	0.14370	-0.263000	0.10527	AAT	A|0.376;T|0.624	0.624	strong		0.358	MS4A14-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000395383.2		
OR10J5	127385	hgsc.bcm.edu	37	1	159505297	159505297	+	Silent	SNP	C	C	T	rs4656837	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:159505297C>T	ENST00000334857.2	-	1	545	c.501G>A	c.(499-501)ccG>ccA	p.P167P		NM_001004469.1	NP_001004469.1	Q8NHC4	O10J5_HUMAN	olfactory receptor, family 10, subfamily J, member 5	167						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.P167P(1)		kidney(1)|large_intestine(4)|lung(9)|ovary(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	22	all_hematologic(112;0.0429)					TGCCACAGAACGGCAAATTGA	0.443													T|||	2769	0.552915	0.2943	0.6614	5008	,	,		23390	0.494		0.6948	False		,,,				2504	0.7403				p.P167P		Atlas-SNP	.											OR10J5,NS,carcinoma,0,1	OR10J5	68	1	1	Substitution - coding silent(1)	stomach(1)	c.G501A						PASS	.	T		1653,2753	658.8+/-400.5	321,1011,871	114.0	92.0	100.0		501	-1.2	0.2	1	dbSNP_111	100	6129,2471	407.5+/-349.2	2195,1739,366	no	coding-synonymous	OR10J5	NM_001004469.1		2516,2750,1237	TT,TC,CC		28.7326,37.517,40.1661		167/310	159505297	7782,5224	2203	4300	6503	SO:0001819	synonymous_variant	127385	exon1			ACAGAACGGCAAA		CCDS30910.1	1q23.2	2012-08-09			ENSG00000184155	ENSG00000184155		"""GPCR / Class A : Olfactory receptors"""	14993	protein-coding gene	gene with protein product							Standard	NM_001004469		Approved		uc010piw.2	Q8NHC4	OTTHUMG00000022738	ENST00000334857.2:c.501G>A	1.37:g.159505297C>T		Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	112	111	0.991071	NM_001004469	B9EH35|Q6IFH2	Silent	SNP	ENST00000334857.2	37	CCDS30910.1																																																																																			C|0.414;T|0.586	0.586	strong		0.443	OR10J5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059021.1	NM_001004469	
PTOV1	53635	hgsc.bcm.edu	37	19	50360989	50360989	+	Missense_Mutation	SNP	A	A	G	rs59595912	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:50360989A>G	ENST00000601675.1	+	7	858	c.754A>G	c.(754-756)Atc>Gtc	p.I252V	PTOV1_ENST00000221557.9_Missense_Mutation_p.I220V|AC018766.5_ENST00000601893.1_RNA|PTOV1_ENST00000598325.1_3'UTR|AC018766.4_ENST00000596624.1_RNA|PTOV1_ENST00000600603.1_Missense_Mutation_p.I220V|AC018766.5_ENST00000593654.1_RNA|PTOV1_ENST00000601638.1_Missense_Mutation_p.I220V|AC018766.6_ENST00000601211.1_RNA|AC018766.5_ENST00000599259.1_RNA|PTOV1_ENST00000391842.1_Missense_Mutation_p.I252V|PTOV1_ENST00000599732.1_Missense_Mutation_p.I252V			Q86YD1	PTOV1_HUMAN	prostate tumor overexpressed 1	252	Interaction with FLOT1.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				endometrium(5)|kidney(3)|large_intestine(2)|lung(5)|ovary(1)	16		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;0.0116)|OV - Ovarian serous cystadenocarcinoma(262;0.0132)		CCCAGTCCAGATCGTCAACAA	0.607													A|||	454	0.090655	0.0151	0.0764	5008	,	,		19226	0.0883		0.0885	False		,,,				2504	0.2076				p.I252V		Atlas-SNP	.											.	PTOV1	41	.	0			c.A754G						PASS	.	A	VAL/ILE	90,4316	74.1+/-112.3	0,90,2113	104.0	86.0	92.0		754	2.9	1.0	19	dbSNP_129	92	791,7809	185.2+/-233.0	44,703,3553	yes	missense	PTOV1	NM_017432.3	29	44,793,5666	GG,GA,AA		9.1977,2.0427,6.7738	benign	252/417	50360989	881,12125	2203	4300	6503	SO:0001583	missense	53635	exon7			GTCCAGATCGTCA	AF238381	CCDS12782.1	19q13.33	2014-08-28	2008-09-12		ENSG00000104960	ENSG00000104960			9632	protein-coding gene	gene with protein product		610195				12598323, 15713644	Standard	XM_005258998		Approved		uc002pqf.1	Q86YD1	OTTHUMG00000183162	ENST00000601675.1:c.754A>G	19.37:g.50360989A>G	ENSP00000472816:p.Ile252Val	Somatic	212	0	0		WXS	Illumina HiSeq	Phase_I	193	92	0.476684	NM_017432	Q6UXX7|Q96BU3|Q9HBN4|Q9NYL1	Missense_Mutation	SNP	ENST00000601675.1	37	CCDS12782.1	158	0.07234432234432235	12	0.024390243902439025	30	0.08287292817679558	46	0.08041958041958042	70	0.09234828496042216	A	12.80	2.045918	0.36085	0.020427	0.091977	ENSG00000104960	ENST00000221557;ENST00000391842	.	.	.	3.96	2.94	0.34122	Mediator complex, subunit Med25, PTOV activation and synapsin 2 (1);	0.494910	0.19340	N	0.116674	T	0.01124	0.0037	N	0.24115	0.695	0.41878	P	0.009696000000000038	B;B	0.09022	0.0;0.002	B;B	0.04013	0.0;0.001	T	0.05115	-1.0905	8	0.46703	T	0.11	-12.5852	6.3498	0.21369	0.8797:0.0:0.1203:0.0	rs59595912;rs61732750	252;220	Q86YD1;Q86YD1-2	PTOV1_HUMAN;.	V	220;252	.	ENSP00000221557:I220V	I	+	1	0	PTOV1	55052801	0.969000	0.33509	0.985000	0.45067	0.927000	0.56198	1.554000	0.36266	0.652000	0.30806	0.460000	0.39030	ATC	A|0.928;G|0.072	0.072	strong		0.607	PTOV1-007	KNOWN	alternative_3_UTR|NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465347.1	NM_017432	
IQGAP2	10788	hgsc.bcm.edu	37	5	75923285	75923285	+	Silent	SNP	C	C	T	rs2431351	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:75923285C>T	ENST00000274364.6	+	14	1869	c.1572C>T	c.(1570-1572)gcC>gcT	p.A524A	IQGAP2_ENST00000502745.1_Silent_p.A77A|IQGAP2_ENST00000396234.3_Silent_p.A77A|IQGAP2_ENST00000379730.3_Silent_p.A83A	NM_006633.2	NP_006624	Q13576	IQGA2_HUMAN	IQ motif containing GTPase activating protein 2	524					negative regulation of catalytic activity (GO:0043086)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|microvillus (GO:0005902)	actin binding (GO:0003779)|GTPase inhibitor activity (GO:0005095)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|Ras GTPase activator activity (GO:0005099)	p.A524A(1)		NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(15)|lung(23)|ovary(6)|prostate(1)|skin(3)|stomach(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	68		all_lung(232;0.000514)|Lung NSC(167;0.00135)|Prostate(461;0.00838)|Ovarian(174;0.0149)		all cancers(79;1.38e-36)		TACAGCAAGCCGTCGATGATG	0.448													C|||	2718	0.542732	0.5386	0.4856	5008	,	,		18082	0.4712		0.5915	False		,,,				2504	0.6125				p.A524A		Atlas-SNP	.											IQGAP2,NS,carcinoma,0,1	IQGAP2	186	1	1	Substitution - coding silent(1)	stomach(1)	c.C1572T						PASS	.	C		2376,2030	611.3+/-391.7	612,1152,439	180.0	166.0	170.0		1572	-4.6	0.0	5	dbSNP_100	170	4956,3644	623.4+/-397.5	1401,2154,745	no	coding-synonymous	IQGAP2	NM_006633.2		2013,3306,1184	TT,TC,CC		42.3721,46.0735,43.626		524/1576	75923285	7332,5674	2203	4300	6503	SO:0001819	synonymous_variant	10788	exon14			GCAAGCCGTCGAT	U51903	CCDS34188.1, CCDS68897.1, CCDS68898.1, CCDS75262.1	5q	2008-07-18			ENSG00000145703	ENSG00000145703			6111	protein-coding gene	gene with protein product		605401				8756646	Standard	XM_005248409		Approved		uc003kek.3	Q13576	OTTHUMG00000162432	ENST00000274364.6:c.1572C>T	5.37:g.75923285C>T		Somatic	540	2	0.0037037		WXS	Illumina HiSeq	Phase_I	527	525	0.996205	NM_006633	A8K4V1|B7Z8A4|J3KR91	Silent	SNP	ENST00000274364.6	37	CCDS34188.1																																																																																			C|0.452;T|0.548	0.548	strong		0.448	IQGAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368877.1	NM_006633	
TRIM65	201292	hgsc.bcm.edu	37	17	73886888	73886888	+	Missense_Mutation	SNP	A	A	G	rs3760128	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:73886888A>G	ENST00000269383.3	-	6	1591	c.1526T>C	c.(1525-1527)cTg>cCg	p.L509P		NM_001256124.1|NM_173547.3	NP_001243053.1|NP_775818.2	Q6PJ69	TRI65_HUMAN	tripartite motif containing 65	509			L -> P (in dbSNP:rs3760128). {ECO:0000269|PubMed:15489334}.			intracellular (GO:0005622)	zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|lung(5)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	12			Epithelial(20;7.53e-06)|all cancers(21;9.11e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00092)|LUSC - Lung squamous cell carcinoma(166;0.154)			CTGGGGCCCCAGAGGGAACAC	0.627													G|||	2328	0.464856	0.9032	0.3141	5008	,	,		17564	0.2222		0.3499	False		,,,				2504	0.3476				p.L509P		Atlas-SNP	.											TRIM65,NS,carcinoma,0,1	TRIM65	23	1	0			c.T1526C						PASS	.	G	PRO/LEU	3605,787		1492,621,83	19.0	19.0	19.0		1526	3.7	0.0	17	dbSNP_107	19	2944,5646		541,1862,1892	yes	missense	TRIM65	NM_173547.2	98	2033,2483,1975	GG,GA,AA		34.2724,17.9189,49.5532	benign	509/518	73886888	6549,6433	2196	4295	6491	SO:0001583	missense	201292	exon6			GGCCCCAGAGGGA	BC006138	CCDS11732.1	17q25.1	2013-01-09	2011-01-25		ENSG00000141569	ENSG00000141569		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	27316	protein-coding gene	gene with protein product			"""tripartite motif-containing 65"""			12477932	Standard	NM_173547		Approved		uc002jpx.4	Q6PJ69	OTTHUMG00000132127	ENST00000269383.3:c.1526T>C	17.37:g.73886888A>G	ENSP00000269383:p.Leu509Pro	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	77	44	0.571429	NM_173547	Q4G0F0|Q6DKJ6|Q9BRP6	Missense_Mutation	SNP	ENST00000269383.3	37	CCDS11732.1	961	0.440018315018315	441	0.8963414634146342	128	0.35359116022099446	147	0.256993006993007	245	0.3232189973614776	G	0	-2.811358	0.00073	0.820811	0.342724	ENSG00000141569	ENST00000269383	T	0.57595	0.39	4.69	3.69	0.42338	Concanavalin A-like lectin/glucanase (1);	0.337845	0.21595	N	0.072024	T	0.00012	0.0000	N	0.00308	-1.67	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.32481	-0.9905	9	0.11182	T	0.66	.	5.6825	0.17784	0.079:0.1377:0.6412:0.1422	rs3760128;rs57250342;rs3760128	509	Q6PJ69	TRI65_HUMAN	P	509	ENSP00000269383:L509P	ENSP00000269383:L509P	L	-	2	0	TRIM65	71398483	0.002000	0.14202	0.001000	0.08648	0.002000	0.02628	1.022000	0.30052	0.395000	0.25257	-0.215000	0.12644	CTG	A|0.500;G|0.500	0.500	strong		0.627	TRIM65-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255170.2	NM_173547	
MYO5C	55930	hgsc.bcm.edu	37	15	52517714	52517714	+	Missense_Mutation	SNP	C	C	T	rs3825801	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:52517714C>T	ENST00000261839.7	-	26	3384	c.3223G>A	c.(3223-3225)Gaa>Aaa	p.E1075K		NM_018728.3	NP_061198.2	Q9NQX4	MYO5C_HUMAN	myosin VC	1075			E -> K (in dbSNP:rs3825801).			extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)	ATP binding (GO:0005524)|motor activity (GO:0003774)	p.E1075K(1)		breast(1)|central_nervous_system(3)|cervix(1)|endometrium(8)|kidney(7)|large_intestine(15)|lung(12)|ovary(7)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	66				all cancers(107;0.0137)		ATCTCTTTTTCGAACTCAGAG	0.363													C|||	521	0.104034	0.0174	0.0749	5008	,	,		23794	0.2649		0.0805	False		,,,				2504	0.1002				p.E1075K		Atlas-SNP	.											MYO5C,NS,carcinoma,0,1	MYO5C	162	1	1	Substitution - Missense(1)	stomach(1)	c.G3223A						PASS	.	C	LYS/GLU	110,3668		1,108,1780	199.0	180.0	186.0		3223	4.4	1.0	15	dbSNP_107	186	830,7416		42,746,3335	yes	missense	MYO5C	NM_018728.3	56	43,854,5115	TT,TC,CC		10.0655,2.9116,7.8177	benign	1075/1743	52517714	940,11084	1889	4123	6012	SO:0001583	missense	55930	exon26			CTTTTTCGAACTC	AF272390	CCDS42036.1	15q21	2011-09-27				ENSG00000128833		"""Myosins / Myosin superfamily : Class V"""	7604	protein-coding gene	gene with protein product	"""myosin 5C"""	610022				11870218	Standard	NM_018728		Approved	MGC74969	uc010bff.3	Q9NQX4		ENST00000261839.7:c.3223G>A	15.37:g.52517714C>T	ENSP00000261839:p.Glu1075Lys	Somatic	193	0	0		WXS	Illumina HiSeq	Phase_I	160	159	0.99375	NM_018728	Q6P1W8	Missense_Mutation	SNP	ENST00000261839.7	37	CCDS42036.1	254	0.1163003663003663	8	0.016260162601626018	22	0.06077348066298342	158	0.2762237762237762	66	0.0870712401055409	C	13.62	2.290361	0.40494	0.029116	0.100655	ENSG00000128833	ENST00000261839	T	0.23754	1.89	5.38	4.4	0.53042	.	0.125602	0.56097	D	0.000032	T	0.00012	0.0000	N	0.14661	0.345	0.09310	P	1.0	B	0.24576	0.106	B	0.17433	0.018	T	0.31503	-0.9941	9	0.45353	T	0.12	.	12.8326	0.57754	0.0:0.6114:0.3886:0.0	rs3825801;rs17650458;rs58498089;rs3825801	1075	Q9NQX4	MYO5C_HUMAN	K	1075	ENSP00000261839:E1075K	ENSP00000261839:E1075K	E	-	1	0	MYO5C	50305006	0.985000	0.35326	1.000000	0.80357	0.662000	0.39071	2.189000	0.42621	2.693000	0.91896	0.655000	0.94253	GAA	C|0.886;T|0.114	0.114	strong		0.363	MYO5C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419562.1	NM_018728	
CEP192	55125	hgsc.bcm.edu	37	18	13001512	13001512	+	5'UTR	SNP	G	G	C	rs4499304	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:13001512G>C	ENST00000325971.8	+	0	301				CEP192_ENST00000506447.1_Missense_Mutation_p.G74A			Q8TEP8	CE192_HUMAN	centrosomal protein 192kDa						centrosome duplication (GO:0051298)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|negative regulation of phosphatase activity (GO:0010923)|spindle assembly (GO:0051225)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)	phosphatase binding (GO:0019902)	p.G74A(1)		NS(1)|breast(4)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(36)|ovary(4)|pancreas(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	71						GTTCCATCCGGGTCATCTCCC	0.383													G|||	2157	0.430711	0.528	0.4798	5008	,	,		17422	0.3552		0.4493	False		,,,				2504	0.3231				p.G74A		Atlas-SNP	.											CEP192_ENST00000506447,NS,carcinoma,0,1	CEP192	340	1	1	Substitution - Missense(1)	stomach(1)	c.G221C						PASS	.						150.0	130.0	136.0					18																	13001512		692	1591	2283	SO:0001623	5_prime_UTR_variant	55125	exon3			CATCCGGGTCATC	AK074074	CCDS32792.1, CCDS32792.2	18p11.21	2014-02-20				ENSG00000101639		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	25515	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 62"""					11230166, 14654843	Standard	NM_032142		Approved	KIAA1569, FLJ10352, PPP1R62	uc010xac.2	Q8TEP8		ENST00000325971.8:c.-1293G>C	18.37:g.13001512G>C		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	45	18	0.4	NM_032142	A0A060A9S4|E9PF99|Q8WYT8|Q9H0F4|Q9NW27	Missense_Mutation	SNP	ENST00000325971.8	37		1013	0.46382783882783885	264	0.5365853658536586	174	0.48066298342541436	237	0.4143356643356643	338	0.44591029023746703	G	0.005	-2.151523	0.00325	.	.	ENSG00000101639	ENST00000506447	T	0.05025	3.51	4.76	-0.604	0.11626	.	.	.	.	.	T	0.00012	0.0000	N	0.03608	-0.345	0.53688	P	2.6999999999999247E-5	B	0.06786	0.001	B	0.04013	0.001	T	0.40421	-0.9564	8	0.02654	T	1	.	5.6865	0.17805	0.2963:0.5058:0.1979:0.0	rs4499304;rs17659973;rs4499304	74	E9PF99	.	A	74	ENSP00000427550:G74A	ENSP00000427550:G74A	G	+	2	0	CEP192	12991512	0.005000	0.15991	0.005000	0.12908	0.258000	0.26162	0.032000	0.13732	-0.105000	0.12132	0.205000	0.17691	GGG	G|0.535;C|0.465	0.465	strong		0.383	CEP192-201	KNOWN	basic	protein_coding	protein_coding		NM_032142	
MYO7A	4647	hgsc.bcm.edu	37	11	76919478	76919478	+	Missense_Mutation	SNP	C	C	A	rs948962	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:76919478C>A	ENST00000409709.3	+	43	6132	c.5860C>A	c.(5860-5862)Ctc>Atc	p.L1954I	MYO7A_ENST00000458637.2_Missense_Mutation_p.L1916I|MYO7A_ENST00000605744.1_3'UTR|MYO7A_ENST00000409619.2_Missense_Mutation_p.L1905I	NM_000260.3	NP_000251.3	Q13402	MYO7A_HUMAN	myosin VIIA	1954	FERM 2. {ECO:0000255|PROSITE- ProRule:PRU00084}.		L -> I (in dbSNP:rs948962). {ECO:0000269|PubMed:8622919, ECO:0000269|PubMed:8884267}.		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						ACCCCAGGTCCTCAGCGTTCC	0.527													A|||	2499	0.499002	0.7572	0.549	5008	,	,		22715	0.3343		0.5	False		,,,				2504	0.2832				p.L1954I		Atlas-SNP	.											.	MYO7A	164	.	0			c.C5860A						PASS	.	A	ILE/LEU,ILE/LEU	2851,1287		1005,841,223	64.0	68.0	67.0		5860,5746	4.3	1.0	11	dbSNP_86	67	4046,4374		989,2068,1153	yes	missense,missense	MYO7A	NM_000260.3,NM_001127180.1	5,5	1994,2909,1376	AA,AC,CC		48.0523,31.102,45.0788	benign,benign	1954/2216,1916/2176	76919478	6897,5661	2069	4210	6279	SO:0001583	missense	4647	exon43			CAGGTCCTCAGCG	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.5860C>A	11.37:g.76919478C>A	ENSP00000386331:p.Leu1954Ile	Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	119	76	0.638655	NM_000260	B9A011|F8VUN5|P78427|Q13321|Q14785|Q92821|Q92822	Missense_Mutation	SNP	ENST00000409709.3	37	CCDS53683.1	1142	0.5228937728937729	376	0.7642276422764228	199	0.5497237569060773	188	0.32867132867132864	379	0.5	A	0.836	-0.743420	0.03088	0.68898	0.480523	ENSG00000137474	ENST00000409709;ENST00000458637;ENST00000409619;ENST00000545136;ENST00000358342;ENST00000343356;ENST00000341717;ENST00000458169;ENST00000544424	T;T;T;T	0.76709	-1.04;-1.04;-1.04;-1.04	4.29	4.29	0.51040	.	0.257857	0.38272	N	0.001753	T	0.00012	0.0000	.	.	.	0.40727	P	0.017290000000000028	B	0.02656	0.0	B	0.04013	0.001	T	0.42481	-0.9449	8	0.02654	T	1	.	11.0982	0.48157	0.8444:0.1556:0.0:0.0	rs948962;rs58377123;rs948962	1916	F8VUN5	.	I	1954;1916;1905;1127;1953;1923;1830;1096;569	ENSP00000386331:L1954I;ENSP00000392185:L1916I;ENSP00000386635:L1905I;ENSP00000417017:L1096I	ENSP00000345075:L1830I	L	+	1	0	MYO7A	76597126	1.000000	0.71417	1.000000	0.80357	0.269000	0.26545	5.790000	0.69038	0.699000	0.31761	-0.512000	0.04463	CTC	C|0.478;A|0.522	0.522	strong		0.527	MYO7A-001	KNOWN	non_canonical_conserved|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000328133.1	NM_000260	
NOTCH2NL	388677	hgsc.bcm.edu	37	1	145273366	145273366	+	Nonsense_Mutation	SNP	C	C	T	rs140871032	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:145273366C>T	ENST00000369340.3	+	4	664	c.220C>T	c.(220-222)Cga>Tga	p.R74*	RP11-458D21.5_ENST00000468030.1_Nonsense_Mutation_p.R74*|NOTCH2NL_ENST00000362074.6_Nonsense_Mutation_p.R74*|NOTCH2NL_ENST00000344859.3_Nonsense_Mutation_p.R74*			Q7Z3S9	NT2NL_HUMAN	notch 2 N-terminal like	74	EGF-like 3. {ECO:0000255|PROSITE- ProRule:PRU00076}.				cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|Notch signaling pathway (GO:0007219)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)	calcium ion binding (GO:0005509)	p.R74*(2)		NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(10)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	27						CTTTGTGTCTCGACCTTGCCT	0.547																																					p.R74X		Atlas-SNP	.											NOTCH2NL_ENST00000362074,NS,haematopoietic_neoplasm,0,2	NOTCH2NL	100	2	2	Substitution - Nonsense(2)	haematopoietic_and_lymphoid_tissue(2)	c.C220T						scavenged	.	C	stop/ARG	30,4376	27.2+/-55.0	0,30,2173	503.0	457.0	473.0		220	2.8	0.8	1	dbSNP_134	473	104,8496	44.9+/-103.4	0,104,4196	no	stop-gained	NOTCH2NL	NM_203458.3		0,134,6369	TT,TC,CC		1.2093,0.6809,1.0303		74/237	145273366	134,12872	2203	4300	6503	SO:0001587	stop_gained	388677	exon3			GTGTCTCGACCTT		CCDS72880.1	1q21.2	2010-06-24	2010-06-24		ENSG00000213240	ENSG00000213240			31862	protein-coding gene	gene with protein product			"""Notch homolog 2 (Drosophila) N-terminal like"""			14673143	Standard	NM_203458		Approved	N2N	uc001emn.4	Q7Z3S9	OTTHUMG00000013754	ENST00000369340.3:c.220C>T	1.37:g.145273366C>T	ENSP00000358346:p.Arg74*	Somatic	1271	2	0.00157356		WXS	Illumina HiSeq	Phase_I	1284	166	0.129283	NM_203458	Q5BKT8|Q5VTG9|Q5XG84|Q6P192|Q8NC23|Q8WUQ9|Q96FY1	Nonsense_Mutation	SNP	ENST00000369340.3	37	CCDS909.1	.	.	.	.	.	.	.	.	.	.	C	23.1	4.373173	0.82573	0.006809	0.012093	ENSG00000213240	ENST00000362074;ENST00000344859;ENST00000369340	.	.	.	2.75	2.75	0.32379	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.20046	T	0.44	.	11.2552	0.49050	0.0:1.0:0.0:0.0	.	.	.	.	X	74	.	ENSP00000344557:R74X	R	+	1	2	NOTCH2NL	143984723	0.982000	0.34865	0.838000	0.33150	0.100000	0.18952	5.568000	0.67385	1.532000	0.49169	0.394000	0.25966	CGA	C|0.964;T|0.036	0.036	strong		0.547	NOTCH2NL-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000038546.1	NM_203458	
TM7SF3	51768	hgsc.bcm.edu	37	12	27143508	27143508	+	Missense_Mutation	SNP	G	G	A	rs10771314	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:27143508G>A	ENST00000343028.4	-	6	968	c.743C>T	c.(742-744)cCg>cTg	p.P248L	TM7SF3_ENST00000542667.1_Intron	NM_016551.2	NP_057635.1	Q9NS93	TM7S3_HUMAN	transmembrane 7 superfamily member 3	248			P -> L (in dbSNP:rs10771314).			extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(6)|prostate(1)|stomach(1)|upper_aerodigestive_tract(2)	18	Colorectal(261;0.0847)					ACCTTGTCCCGGGAGGGAGGA	0.428													G|||	244	0.048722	0.0144	0.0807	5008	,	,		19155	0.0595		0.0775	False		,,,				2504	0.0317				p.P248L		Atlas-SNP	.											.	TM7SF3	41	.	0			c.C743T						PASS	.	G	LEU/PRO	125,4281	93.4+/-132.2	1,123,2079	122.0	110.0	114.0		743	-1.8	0.0	12	dbSNP_120	114	879,7721	198.5+/-242.8	44,791,3465	yes	missense	TM7SF3	NM_016551.2	98	45,914,5544	AA,AG,GG		10.2209,2.837,7.7195	benign	248/571	27143508	1004,12002	2203	4300	6503	SO:0001583	missense	51768	exon6			TGTCCCGGGAGGG	AB032470	CCDS8710.1	12q11-q12	2012-08-10			ENSG00000064115	ENSG00000064115			23049	protein-coding gene	gene with protein product		605181				10828615	Standard	NM_016551		Approved		uc010sjl.2	Q9NS93	OTTHUMG00000169243	ENST00000343028.4:c.743C>T	12.37:g.27143508G>A	ENSP00000342322:p.Pro248Leu	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	80	38	0.475	NM_016551	B3KMZ3|Q9NUS4	Missense_Mutation	SNP	ENST00000343028.4	37	CCDS8710.1	130|130	0.05952380952380952|0.05952380952380952	4|4	0.008130081300813009|0.008130081300813009	27|27	0.07458563535911603|0.07458563535911603	41|41	0.07167832167832168|0.07167832167832168	58|58	0.07651715039577836|0.07651715039577836	G|G	11.88|11.88	1.769765|1.769765	0.31320|0.31320	0.02837|0.02837	0.102209|0.102209	ENSG00000064115|ENSG00000064115	ENST00000343028;ENST00000543655;ENST00000535819|ENST00000545303	T;T;T|.	0.45668|.	1.42;0.89;0.89|.	5.0|5.0	-1.78|-1.78	0.07957|0.07957	.|.	0.288766|.	0.38897|.	N|.	0.001531|.	T|T	0.02047|0.02047	0.0064|0.0064	L|L	0.42245|0.42245	1.32|1.32	0.58432|0.58432	D|D	0.999996|0.999996	B|.	0.32653|.	0.379|.	B|.	0.17979|.	0.02|.	T|T	0.05209|0.05209	-1.0899|-1.0899	10|5	0.35671|.	T|.	0.21|.	7.0E-4|7.0E-4	9.1426|9.1426	0.36912|0.36912	0.0849:0.1585:0.6733:0.0832|0.0849:0.1585:0.6733:0.0832	rs10771314;rs52837696;rs60050366;rs10771314|rs10771314;rs52837696;rs60050366;rs10771314	248|.	Q9NS93|.	TM7S3_HUMAN|.	L|W	248;39;39|29	ENSP00000342322:P248L;ENSP00000441924:P39L;ENSP00000445156:P39L|.	ENSP00000342322:P248L|.	P|R	-|-	2|1	0|2	TM7SF3|TM7SF3	27034775|27034775	0.993000|0.993000	0.37304|0.37304	0.026000|0.026000	0.17262|0.17262	0.878000|0.878000	0.50629|0.50629	1.827000|1.827000	0.39102|0.39102	-0.105000|-0.105000	0.12132|0.12132	-0.237000|-0.237000	0.12165|0.12165	CCG|CGG	G|0.933;A|0.067	0.067	strong		0.428	TM7SF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403033.1	NM_016551	
SLC38A4	55089	hgsc.bcm.edu	37	12	47186770	47186770	+	Missense_Mutation	SNP	C	C	T	rs2429467	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:47186770C>T	ENST00000447411.1	-	2	291	c.85G>A	c.(85-87)Ggg>Agg	p.G29R	SLC38A4_ENST00000266579.4_Missense_Mutation_p.G29R	NM_001143824.1	NP_001137296.1	Q969I6	S38A4_HUMAN	solute carrier family 38, member 4	29			G -> R (in dbSNP:rs2429467).		amino acid transport (GO:0006865)|ion transport (GO:0006811)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	amino acid transmembrane transporter activity (GO:0015171)|symporter activity (GO:0015293)			NS(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(6)|ovary(3)|skin(1)	21	Lung SC(27;0.192)|Renal(347;0.236)					TTTCCTATCCCGATGTAGCTA	0.443													C|||	684	0.136581	0.0129	0.2248	5008	,	,		18413	0.245		0.0417	False		,,,				2504	0.227				p.G29R		Atlas-SNP	.											.	SLC38A4	58	.	0			c.G85A						PASS	.	C	ARG/GLY,ARG/GLY	140,4266	98.9+/-137.6	3,134,2066	242.0	218.0	226.0		85,85	-2.0	0.0	12	dbSNP_100	226	436,8164	132.8+/-190.4	10,416,3874	yes	missense,missense	SLC38A4	NM_001143824.1,NM_018018.4	125,125	13,550,5940	TT,TC,CC		5.0698,3.1775,4.4287	benign,benign	29/548,29/548	47186770	576,12430	2203	4300	6503	SO:0001583	missense	55089	exon2			CTATCCCGATGTA	AF193836	CCDS8750.1	12q13	2013-05-22				ENSG00000139209		"""Solute carriers"""	14679	protein-coding gene	gene with protein product		608065				11414754	Standard	NM_018018		Approved	PAAT, NAT3, ATA3	uc001rpj.2	Q969I6		ENST00000447411.1:c.85G>A	12.37:g.47186770C>T	ENSP00000389843:p.Gly29Arg	Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	173	83	0.479769	NM_001143824	A8K553	Missense_Mutation	SNP	ENST00000447411.1	37	CCDS8750.1	259	0.11858974358974358	7	0.014227642276422764	79	0.21823204419889503	141	0.2465034965034965	32	0.04221635883905013	C	1.062	-0.672454	0.03403	0.031775	0.050698	ENSG00000139209	ENST00000395426;ENST00000447411;ENST00000266579;ENST00000547477;ENST00000546940	T;T;T;T	0.21361	3.81;3.81;2.34;2.01	5.53	-1.99	0.07457	.	2.811630	0.00807	N	0.001477	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	B	0.31893	0.345	B	0.18561	0.022	T	0.28427	-1.0044	9	0.12766	T	0.61	1.5544	8.125	0.30992	0.096:0.554:0.0:0.35	rs2429467;rs52838269;rs2429467	29	Q969I6	S38A4_HUMAN	R	29	ENSP00000389843:G29R;ENSP00000266579:G29R;ENSP00000450071:G29R;ENSP00000448543:G29R	ENSP00000266579:G29R	G	-	1	0	SLC38A4	45473037	0.000000	0.05858	0.000000	0.03702	0.120000	0.20174	0.061000	0.14366	-1.137000	0.02888	-1.094000	0.02160	GGG	C|0.921;T|0.079	0.079	strong		0.443	SLC38A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404574.1		
PPID	5481	hgsc.bcm.edu	37	4	159631991	159631991	+	Missense_Mutation	SNP	G	G	T	rs9410	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	130	0	0		WXS	Illumina HiSeq	Phase_I	112	49	0.4375	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	
CCDC169	728591	hgsc.bcm.edu	37	13	36828237	36828237	+	Missense_Mutation	SNP	T	T	C	rs9546897	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:36828237T>C	ENST00000239859.7	-	5	390	c.359A>G	c.(358-360)aAg>aGg	p.K120R	CCDC169_ENST00000239860.6_Missense_Mutation_p.K20R|CCDC169_ENST00000379862.2_Missense_Mutation_p.K18R|CCDC169_ENST00000491049.2_Missense_Mutation_p.K18R|SOHLH2_ENST00000554962.1_Missense_Mutation_p.K20R|CCDC169_ENST00000503173.1_Missense_Mutation_p.K120R|CCDC169_ENST00000379864.2_Missense_Mutation_p.K18R|CCDC169_ENST00000510088.1_Missense_Mutation_p.K18R|CCDC169-SOHLH2_ENST00000511166.1_Missense_Mutation_p.K20R			A6NNP5	CC169_HUMAN	coiled-coil domain containing 169	120			K -> R (in dbSNP:rs9546897).							breast(1)|endometrium(1)	2						TTCAAGAGTCTTCTTTTCTTC	0.274													C|||	1882	0.375799	0.2231	0.4755	5008	,	,		15496	0.373		0.4712	False		,,,				2504	0.4162				p.K120R		Atlas-SNP	.											.	CCDC169	20	.	0			c.A359G						PASS	.						189.0	156.0	166.0					13																	36828237		692	1588	2280	SO:0001583	missense	728591	exon5			AGAGTCTTCTTTT		CCDS45027.1, CCDS45028.1, CCDS45029.1, CCDS53863.1, CCDS55897.1	13q13.3	2011-08-09	2011-08-09	2011-08-09	ENSG00000242715	ENSG00000242715			34361	protein-coding gene	gene with protein product			"""chromosome 13 open reading frame 38"""	C13orf38			Standard	NM_001144981		Approved	RP11-251J8.1, LOC728591		A6NNP5	OTTHUMG00000016731	ENST00000239859.7:c.359A>G	13.37:g.36828237T>C	ENSP00000239859:p.Lys120Arg	Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	31	29	0.935484	NM_001144981	A6NC13|A6NCT2|B7ZW45|B7ZW49|B9EJF2|Q9H1T4|Q9H1T5	Missense_Mutation	SNP	ENST00000239859.7	37	CCDS45028.1	830	0.38003663003663	110	0.22357723577235772	166	0.4585635359116022	207	0.3618881118881119	347	0.4577836411609499	C	2.085	-0.409739	0.04799	.	.	ENSG00000120669;ENSG00000250709;ENSG00000242715;ENSG00000242715;ENSG00000242715;ENSG00000242715;ENSG00000242715;ENSG00000242715;ENSG00000242715	ENST00000554962;ENST00000511166;ENST00000491049;ENST00000503173;ENST00000239860;ENST00000379864;ENST00000510088;ENST00000379862;ENST00000239859	T;T;T;T;T;T;T;T;T	0.44083	0.93;0.93;0.93;0.93;0.93;0.93;0.93;0.93;0.93	4.78	3.05	0.35203	.	0.212888	0.31884	N	0.006914	T	0.00012	0.0000	N	0.00368	-1.59	0.58432	P	2.9999999999752447E-6	B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0	B;B;B;B;B	0.04013	0.001;0.001;0.001;0.0;0.0	T	0.45454	-0.9260	9	0.07175	T	0.84	-13.7239	6.8623	0.24074	0.0:0.633:0.0:0.367	rs9546897;rs52836889;rs56836767;rs9546897	120;20;18;20;120	A6NNP5-4;B7ZW49;A6NNP5-3;B4DX90;A6NNP5	.;.;.;.;CC169_HUMAN	R	20;20;18;120;20;18;18;18;120	ENSP00000451542:K20R;ENSP00000421868:K20R;ENSP00000425252:K18R;ENSP00000426174:K120R;ENSP00000239860:K20R;ENSP00000369193:K18R;ENSP00000427495:K18R;ENSP00000369191:K18R;ENSP00000239859:K120R	ENSP00000239859:K120R	K	-	2	0	CCDC169-SOHLH2;SOHLH2;CCDC169	35726237	0.999000	0.42202	0.995000	0.50966	0.967000	0.64934	0.877000	0.28106	0.333000	0.23563	-0.119000	0.15052	AAG	T|0.629;C|0.371	0.371	strong		0.274	CCDC169-014	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368255.1	NM_001144981	
PLIN4	729359	hgsc.bcm.edu	37	19	4511365	4511365	+	Silent	SNP	C	C	G	rs116973517	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:4511365C>G	ENST00000301286.3	-	3	2564	c.2565G>C	c.(2563-2565)gtG>gtC	p.V855V		NM_001080400.1	NP_001073869.1	Q96Q06	PLIN4_HUMAN	perilipin 4	855	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						CAGCACCGGTCACCCCACTGC	0.582													C|||	229	0.0457268	0.0522	0.0692	5008	,	,		25279	0.001		0.0954	False		,,,				2504	0.0153				p.V855V		Atlas-SNP	.											.	PLIN4	191	.	0			c.G2565C						PASS	.	C		186,3692		2,182,1755	66.0	77.0	74.0		2565	-6.5	0.0	19	dbSNP_132	74	762,7514		3,756,3379	no	coding-synonymous	PLIN4	NM_001080400.1		5,938,5134	GG,GC,CC		9.2073,4.7963,7.7999		855/1358	4511365	948,11206	1939	4138	6077	SO:0001819	synonymous_variant	729359	exon3			ACCGGTCACCCCA	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.2565G>C	19.37:g.4511365C>G		Somatic	234	1	0.0042735		WXS	Illumina HiSeq	Phase_I	223	99	0.443946	NM_001080400	A6NEI2	Silent	SNP	ENST00000301286.3	37	CCDS45927.1																																																																																			C|0.937;G|0.063	0.063	strong		0.582	PLIN4-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395095.1	XM_170901	
ESPNL	339768	hgsc.bcm.edu	37	2	239010719	239010719	+	Silent	SNP	T	T	C	rs36066915	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:239010719T>C	ENST00000343063.3	+	2	695	c.432T>C	c.(430-432)gcT>gcC	p.A144A	ESPNL_ENST00000409169.1_Silent_p.A144A	NM_194312.2	NP_919288.2	Q6ZVH7	ESPNL_HUMAN	espin-like	144										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)		TGCACCACGCTGCCGTCAGTG	0.706													C|||	3051	0.609225	0.5635	0.5692	5008	,	,		13875	0.5903		0.6988	False		,,,				2504	0.6268				p.A144A		Atlas-SNP	.											.	ESPNL	63	.	0			c.T432C						PASS	.	C		2656,1670		873,910,380	9.0	11.0	10.0		432	-9.2	0.0	2	dbSNP_126	10	5553,2921		1889,1775,573	no	coding-synonymous	ESPNL	NM_194312.2		2762,2685,953	CC,CT,TT		34.4701,38.6038,35.8672		144/1006	239010719	8209,4591	2163	4237	6400	SO:0001819	synonymous_variant	339768	exon2			CCACGCTGCCGTC	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.432T>C	2.37:g.239010719T>C		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	53	53	1	NM_194312	Q66K27|Q6ZVG1|Q8IVU2	Silent	SNP	ENST00000343063.3	37	CCDS2525.1																																																																																			T|0.377;C|0.623	0.623	strong		0.706	ESPNL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257164.2	NM_194312	
ITGB3	3690	hgsc.bcm.edu	37	17	45360730	45360730	+	Missense_Mutation	SNP	T	T	C	rs5918	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:45360730T>C	ENST00000559488.1	+	3	192	c.176T>C	c.(175-177)cTg>cCg	p.L59P	ITGB3_ENST00000571680.1_Missense_Mutation_p.L59P|ITGB3_ENST00000435993.2_Missense_Mutation_p.L12P|ITGB3_ENST00000560629.1_Silent_p.S47S	NM_000212.2	NP_000203.2	P05106	ITB3_HUMAN	integrin, beta 3 (platelet glycoprotein IIIa, antigen CD61)	59			L -> P (in alloantigen HPA-1B; dbSNP:rs5918). {ECO:0000269|PubMed:10391209, ECO:0000269|PubMed:2565345, ECO:0000269|Ref.13}.		activation of protein kinase activity (GO:0032147)|angiogenesis involved in wound healing (GO:0060055)|apolipoprotein A-I-mediated signaling pathway (GO:0038027)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|cell-substrate adhesion (GO:0031589)|cell-substrate junction assembly (GO:0007044)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|mesodermal cell differentiation (GO:0048333)|negative chemotaxis (GO:0050919)|negative regulation of lipid storage (GO:0010888)|negative regulation of lipid transport (GO:0032369)|negative regulation of lipoprotein metabolic process (GO:0050748)|negative regulation of low-density lipoprotein particle receptor biosynthetic process (GO:0045715)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|protein folding (GO:0006457)|regulation of bone resorption (GO:0045124)|smooth muscle cell migration (GO:0014909)|substrate adhesion-dependent cell spreading (GO:0034446)|tube development (GO:0035295)|viral entry into host cell (GO:0046718)|wound healing (GO:0042060)	alphav-beta3 integrin-vitronectin complex (GO:0071062)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|integrin alphav-beta3 complex (GO:0034683)|integrin complex (GO:0008305)|lamellipodium membrane (GO:0031258)|melanosome (GO:0042470)|microvillus membrane (GO:0031528)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|platelet alpha granule membrane (GO:0031092)|receptor complex (GO:0043235)|ruffle membrane (GO:0032587)	cell adhesion molecule binding (GO:0050839)|extracellular matrix binding (GO:0050840)|fibronectin binding (GO:0001968)|identical protein binding (GO:0042802)|platelet-derived growth factor receptor binding (GO:0005161)|protease binding (GO:0002020)|protein disulfide isomerase activity (GO:0003756)|receptor activity (GO:0004872)|vascular endothelial growth factor receptor 2 binding (GO:0043184)			breast(3)|central_nervous_system(5)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(9)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	39					Abciximab(DB00054)|Antithymocyte globulin(DB00098)|Eptifibatide(DB00063)|Tirofiban(DB00775)	GCCCTGCCTCTGGGCTCACCT	0.552													T|||	445	0.0888578	0.0915	0.1023	5008	,	,		19719	0.0089		0.1322	False		,,,				2504	0.1135				p.L59P		Atlas-SNP	.											.	ITGB3	157	.	0			c.T176C	GRCh37	CM890078	ITGB3	M	rs5918	PASS	.	T	PRO/LEU	470,3936	224.6+/-240.7	28,414,1761	61.0	55.0	57.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	176	-11.8	0.0	17	dbSNP_52	57	1305,7295	257.6+/-281.6	89,1127,3084	yes	missense	ITGB3	NM_000212.2	98	117,1541,4845	CC,CT,TT		15.1744,10.6673,13.6475	benign	59/789	45360730	1775,11231	2203	4300	6503	SO:0001583	missense	3690	exon3			TGCCTCTGGGCTC		CCDS11511.1	17q21.32	2014-09-17			ENSG00000259207	ENSG00000259207		"""CD molecules"", ""Integrins"""	6156	protein-coding gene	gene with protein product	"""platelet glycoprotein IIIa"""	173470		GP3A		2454952	Standard	NM_000212		Approved	CD61, GPIIIa	uc002ilj.3	P05106	OTTHUMG00000171956	ENST00000559488.1:c.176T>C	17.37:g.45360730T>C	ENSP00000452786:p.Leu59Pro	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	65	34	0.523077	NM_000212	A0PJW2|D3DXJ8|O15495|Q12806|Q13413|Q14648|Q16499	Missense_Mutation	SNP	ENST00000559488.1	37	CCDS11511.1	200	0.09157509157509157	59	0.11991869918699187	35	0.09668508287292818	5	0.008741258741258742	101	0.13324538258575197	T	6.670	0.492238	0.12702	0.106673	0.151744	ENSG00000178852	ENST00000262017;ENST00000435993	D	0.92446	-3.04	5.88	-11.8	0.00035	Integrin beta subunit, N-terminal (2);	1.063610	0.07337	N	0.880144	T	0.02193	0.0068	L	0.43152	1.355	0.58432	P	1.0000000000287557E-6	B	0.10296	0.003	B	0.10450	0.005	T	0.48490	-0.9031	9	0.20519	T	0.43	.	9.9068	0.41381	0.1749:0.5694:0.1433:0.1124	rs5918;rs5918	59	P05106	ITB3_HUMAN	P	59;12	ENSP00000407801:L12P	ENSP00000262017:L59P	L	+	2	0	C17orf57	42715729	0.000000	0.05858	0.000000	0.03702	0.040000	0.13550	-1.382000	0.02546	-3.995000	0.00083	-1.117000	0.02048	CTG	T|0.884;C|0.116	0.116	strong		0.552	ITGB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416111.3	NM_000212	
HTR1B	3351	hgsc.bcm.edu	37	6	78172992	78172992	+	Silent	SNP	G	G	A	rs6298	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:78172992G>A	ENST00000369947.2	-	1	498	c.129C>T	c.(127-129)tcC>tcT	p.S43S		NM_000863.1	NP_000854.1	P28222	5HT1B_HUMAN	5-hydroxytryptamine (serotonin) receptor 1B, G protein-coupled	43					adenylate cyclase-inhibiting serotonin receptor signaling pathway (GO:0007198)|bone remodeling (GO:0046849)|cellular response to alkaloid (GO:0071312)|cellular response to drug (GO:0035690)|cellular response to temperature stimulus (GO:0071502)|drinking behavior (GO:0042756)|G-protein coupled receptor internalization (GO:0002031)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|negative regulation of cAMP biosynthetic process (GO:0030818)|negative regulation of serotonin secretion (GO:0014063)|negative regulation of synaptic transmission, GABAergic (GO:0032229)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of behavior (GO:0050795)|regulation of dopamine secretion (GO:0014059)|response to cocaine (GO:0042220)|response to ethanol (GO:0045471)|response to mineralocorticoid (GO:0051385)|synaptic transmission (GO:0007268)|vasoconstriction (GO:0042310)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	drug binding (GO:0008144)|serotonin binding (GO:0051378)|serotonin receptor activity (GO:0004993)			NS(1)|breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(9)|prostate(2)|upper_aerodigestive_tract(2)	25		all_cancers(76;0.0867)|Acute lymphoblastic leukemia(125;0.00119)|all_hematologic(105;0.0332)		BRCA - Breast invasive adenocarcinoma(397;0.205)	Almotriptan(DB00918)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Apomorphine(DB00714)|Aripiprazole(DB01238)|Asenapine(DB06216)|Bopindolol(DB08807)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Clozapine(DB00363)|Dihydroergotamine(DB00320)|Eletriptan(DB00216)|Ergoloid mesylate(DB01049)|Ergotamine(DB00696)|Frovatriptan(DB00998)|Ketamine(DB01221)|Lisuride(DB00589)|Loxapine(DB00408)|Methysergide(DB00247)|Naratriptan(DB00952)|Olanzapine(DB00334)|Ondansetron(DB00904)|Penbutolol(DB01359)|Pergolide(DB01186)|Pindolol(DB00960)|Pramipexole(DB00413)|Propranolol(DB00571)|Quetiapine(DB01224)|Rizatriptan(DB00953)|Ropinirole(DB00268)|Sumatriptan(DB00669)|Yohimbine(DB01392)|Ziprasidone(DB00246)|Zolmitriptan(DB00315)	GTAGGGAGATGGAGTCCTGGT	0.572													G|||	1706	0.340655	0.2443	0.4049	5008	,	,		19989	0.5099		0.2644	False		,,,				2504	0.3292				p.S43S		Atlas-SNP	.											.	HTR1B	55	.	0			c.C129T						PASS	.	G		986,3420	368.3+/-318.6	123,740,1340	194.0	174.0	181.0		129	3.0	0.7	6	dbSNP_52	181	2256,6344	382.6+/-340.4	311,1634,2355	yes	coding-synonymous	HTR1B	NM_000863.1		434,2374,3695	AA,AG,GG		26.2326,22.3786,24.927		43/391	78172992	3242,9764	2203	4300	6503	SO:0001819	synonymous_variant	3351	exon1			GGAGATGGAGTCC	BC069065	CCDS4986.1	6q13	2012-08-08	2012-02-03		ENSG00000135312	ENSG00000135312		"""5-HT (serotonin) receptors"", ""GPCR / Class A : 5-HT (serotonin) receptors, GPCR only"""	5287	protein-coding gene	gene with protein product		182131	"""5-hydroxytryptamine (serotonin) receptor 1B"""			1348246, 11247661	Standard	NM_000863		Approved	S12, 5-HT1B, HTR1D2, 5-HT1DB	uc003pil.1	P28222	OTTHUMG00000015066	ENST00000369947.2:c.129C>T	6.37:g.78172992G>A		Somatic	224	0	0		WXS	Illumina HiSeq	Phase_I	235	126	0.53617	NM_000863	Q4VAY7	Silent	SNP	ENST00000369947.2	37	CCDS4986.1																																																																																			G|0.712;A|0.288	0.288	strong		0.572	HTR1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041292.1	NM_000863	
VCL	7414	hgsc.bcm.edu	37	10	75865065	75865065	+	Silent	SNP	G	G	A	rs767809	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:75865065G>A	ENST00000211998.4	+	16	2482	c.2388G>A	c.(2386-2388)ccG>ccA	p.P796P	VCL_ENST00000372755.3_Silent_p.P796P|VCL_ENST00000417648.2_Intron	NM_014000.2	NP_054706.1	P18206	VINC_HUMAN	vinculin	796	N-terminal globular head.				adherens junction assembly (GO:0034333)|apical junction assembly (GO:0043297)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|cellular component movement (GO:0006928)|epithelial cell-cell adhesion (GO:0090136)|lamellipodium assembly (GO:0030032)|morphogenesis of an epithelium (GO:0002009)|muscle contraction (GO:0006936)|negative regulation of cell migration (GO:0030336)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|protein localization to cell surface (GO:0034394)	actin cytoskeleton (GO:0015629)|adherens junction (GO:0005912)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|cell-substrate junction (GO:0030055)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|vesicle (GO:0031982)	actin binding (GO:0003779)|alpha-catenin binding (GO:0045294)|beta-catenin binding (GO:0008013)|cadherin binding (GO:0045296)|dystroglycan binding (GO:0002162)|structural molecule activity (GO:0005198)		VCL/ALK(4)	breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(8)|ovary(2)|upper_aerodigestive_tract(1)	20	Prostate(51;0.0112)					CCATCTCCCCGATGGTGATGG	0.512													G|||	1626	0.324681	0.0598	0.4568	5008	,	,		19604	0.254		0.5915	False		,,,				2504	0.3875				p.P796P		Atlas-SNP	.											.	VCL	77	.	0			c.G2388A						PASS	.	G	,	636,3770	273.1+/-271.2	51,534,1618	90.0	67.0	75.0		2388,2388	-8.4	0.9	10	dbSNP_86	75	5070,3530	632.4+/-398.6	1505,2060,735	no	coding-synonymous,coding-synonymous	VCL	NM_003373.3,NM_014000.2	,	1556,2594,2353	AA,AG,GG		41.0465,14.4349,43.8721	,	796/1067,796/1135	75865065	5706,7300	2203	4300	6503	SO:0001819	synonymous_variant	7414	exon16			CTCCCCGATGGTG	M33308	CCDS7340.1, CCDS7341.1	10q22.1-q23	2014-09-17			ENSG00000035403	ENSG00000035403			12665	protein-coding gene	gene with protein product	"""metavinculin"""	193065				1339348	Standard	NM_014000		Approved		uc001jwd.3	P18206	OTTHUMG00000018498	ENST00000211998.4:c.2388G>A	10.37:g.75865065G>A		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	71	34	0.478873	NM_003373	Q16450|Q5SWX2|Q7Z3B8|Q8IXU7	Silent	SNP	ENST00000211998.4	37	CCDS7341.1																																																																																			G|0.604;A|0.396	0.396	strong		0.512	VCL-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_003373, NM_014000	
CTNND1	1500	hgsc.bcm.edu	37	11	57563991	57563991	+	Silent	SNP	C	C	T	rs10896644	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:57563991C>T	ENST00000399050.4	+	6	1019	c.483C>T	c.(481-483)gaC>gaT	p.D161D	CTNND1_ENST00000529919.1_Silent_p.D161D|CTNND1_ENST00000532649.1_Silent_p.D107D|CTNND1_ENST00000533667.1_Intron|CTNND1_ENST00000524630.1_Silent_p.D161D|CTNND1_ENST00000358694.6_Silent_p.D161D|CTNND1_ENST00000530094.1_Silent_p.D60D|CTNND1_ENST00000528232.1_Silent_p.D60D|CTNND1_ENST00000526938.1_Silent_p.D161D|CTNND1_ENST00000360682.6_Silent_p.D161D|CTNND1_ENST00000428599.2_Silent_p.D161D|CTNND1_ENST00000534579.1_Silent_p.D107D|CTNND1_ENST00000399039.4_Silent_p.D161D|CTNND1_ENST00000361391.6_Silent_p.D161D|CTNND1_ENST00000526357.1_Silent_p.D107D|CTNND1_ENST00000529986.1_Silent_p.D60D|CTNND1_ENST00000361796.4_Silent_p.D161D|CTNND1_ENST00000532245.1_Silent_p.D60D|CTNND1_ENST00000532787.1_Silent_p.D60D|CTNND1_ENST00000528621.1_Silent_p.D107D|CTNND1_ENST00000361332.4_Silent_p.D161D|CTNND1_ENST00000529526.1_Silent_p.D107D|CTNND1_ENST00000530748.1_Silent_p.D107D|CTNND1_ENST00000526772.1_Intron|CTNND1_ENST00000529873.1_Silent_p.D107D|CTNND1_ENST00000525902.1_Intron|CTNND1_ENST00000532463.1_Silent_p.D60D|CTNND1_ENST00000532844.1_Silent_p.D107D|CTNND1_ENST00000415361.2_Silent_p.D60D|CTNND1_ENST00000527467.1_Intron|CTNND1_ENST00000426142.2_Silent_p.D60D|CTNND1_ENST00000531014.1_Intron	NM_001085458.1	NP_001078927.1	O60716	CTND1_HUMAN	catenin (cadherin-associated protein), delta 1	161					adherens junction organization (GO:0034332)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|regulation of transcription, DNA-templated (GO:0006355)|single organismal cell-cell adhesion (GO:0016337)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|midbody (GO:0030496)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|synapse (GO:0045202)|zonula adherens (GO:0005915)	cadherin binding (GO:0045296)|receptor binding (GO:0005102)			breast(5)|endometrium(8)|kidney(4)|large_intestine(7)|liver(2)|lung(16)|ovary(1)|upper_aerodigestive_tract(2)	45		all_epithelial(135;0.155)				TGGGACCAGACGGGTTGCCTG	0.463													C|||	1359	0.271366	0.1762	0.3314	5008	,	,		20175	0.1012		0.4284	False		,,,				2504	0.3712				p.D161D		Atlas-SNP	.											.	CTNND1	203	.	0			c.C483T						PASS	.	C	,,,,,,,,,,,,,,,,,,,,,	893,3063		116,661,1201	82.0	86.0	85.0		483,483,483,483,483,180,180,180,180,180,180,180,321,321,483,321,321,321,321,180,321,483	-5.8	0.8	11	dbSNP_120	85	3413,4933		696,2021,1456	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	CTNND1	NM_001085458.1,NM_001085459.1,NM_001085460.1,NM_001085461.1,NM_001085462.1,NM_001085463.1,NM_001085464.1,NM_001085465.1,NM_001085466.1,NM_001085467.1,NM_001085468.1,NM_001085469.1,NM_001206883.1,NM_001206884.1,NM_001206885.1,NM_001206886.1,NM_001206887.1,NM_001206888.1,NM_001206889.1,NM_001206890.1,NM_001206891.1,NM_001331.2	,,,,,,,,,,,,,,,,,,,,,	812,2682,2657	TT,TC,CC		40.8938,22.5733,35.0024	,,,,,,,,,,,,,,,,,,,,,	161/969,161/963,161/934,161/934,161/934,60/868,60/862,60/841,60/839,60/833,60/833,60/833,107/915,107/886,161/940,107/909,107/888,107/880,107/880,60/833,107/880,161/942	57563991	4306,7996	1978	4173	6151	SO:0001819	synonymous_variant	1500	exon6			ACCAGACGGGTTG	AB002382	CCDS44604.1, CCDS44605.1, CCDS44606.1, CCDS44607.1, CCDS44608.1, CCDS44609.1, CCDS53632.1, CCDS53633.1, CCDS53634.1, CCDS55763.1, CCDS55764.1, CCDS55765.1, CCDS55766.1, CCDS55767.1, CCDS73290.1	11q12.1	2013-02-14				ENSG00000198561		"""Armadillo repeat containing"""	2515	protein-coding gene	gene with protein product		601045		CTNND		8808291	Standard	NM_001085460		Approved	KIAA0384, p120, p120cas, p120ctn	uc001nmc.4	O60716		ENST00000399050.4:c.483C>T	11.37:g.57563991C>T		Somatic	169	1	0.00591716		WXS	Illumina HiSeq	Phase_I	121	94	0.77686	NM_001085461	A8K939|O15088|O60713|O60714|O60715|O60935|Q6DHZ7|Q6RBX8|Q9UP71|Q9UP72|Q9UP73	Silent	SNP	ENST00000399050.4	37	CCDS44604.1																																																																																			C|0.728;T|0.272	0.272	strong		0.463	CTNND1-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000393944.1	NM_001331	
NOMO1	23420	hgsc.bcm.edu	37	16	14969016	14969016	+	Missense_Mutation	SNP	T	T	A	rs62038475		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:14969016T>A	ENST00000287667.7	+	19	2349	c.2178T>A	c.(2176-2178)aaT>aaA	p.N726K		NM_014287.3	NP_055102.3	Q15155	NOMO1_HUMAN	NODAL modulator 1	726						integral component of membrane (GO:0016021)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)			endometrium(6)|kidney(1)|large_intestine(6)|lung(12)|ovary(2)|pancreas(1)|skin(2)	30						AAAACGGCAATGAGGAAGGCG	0.567																																					p.N726K		Atlas-SNP	.											.	NOMO1	60	.	0			c.T2178A						PASS	.						229.0	236.0	234.0					16																	14969016		2197	4299	6496	SO:0001583	missense	23420	exon19			CGGCAATGAGGAA	X57398	CCDS10556.1	16p13.11	2008-02-05			ENSG00000103512	ENSG00000103512			30060	protein-coding gene	gene with protein product		609157				1310294, 15257293	Standard	NM_014287		Approved	PM5	uc002dcv.3	Q15155	OTTHUMG00000090541	ENST00000287667.7:c.2178T>A	16.37:g.14969016T>A	ENSP00000287667:p.Asn726Lys	Somatic	586	1	0.00170648		WXS	Illumina HiSeq	Phase_I	883	330	0.373726	NM_014287	P78421|Q8IW21|Q96DG0	Missense_Mutation	SNP	ENST00000287667.7	37	CCDS10556.1	.	.	.	.	.	.	.	.	.	.	.	0.003	-2.401964	0.00195	.	.	ENSG00000103512	ENST00000287667;ENST00000456867;ENST00000536948	T	0.03607	3.87	2.86	-1.44	0.08856	.	0.796012	0.12016	N	0.507432	T	0.00967	0.0032	N	0.01352	-0.895	0.09310	N	0.999994	B	0.02656	0.0	B	0.01281	0.0	T	0.41378	-0.9512	10	0.05620	T	0.96	1.8419	1.5646	0.02602	0.4027:0.3305:0.1058:0.161	.	726	Q15155	NOMO1_HUMAN	K	726;726;559	ENSP00000287667:N726K	ENSP00000287667:N726K	N	+	3	2	NOMO1	14876517	0.000000	0.05858	0.005000	0.12908	0.071000	0.16799	-0.760000	0.04756	-0.988000	0.03489	-1.489000	0.00976	AAT	.	.	weak		0.567	NOMO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207065.1		
DHX38	9785	hgsc.bcm.edu	37	16	72139184	72139184	+	Silent	SNP	C	C	A	rs2074626	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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						PASS	.	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	107	0	0		WXS	Illumina HiSeq	Phase_I	127	62	0.488189	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	
MUC20	200958	hgsc.bcm.edu	37	3	195452770	195452770	+	Silent	SNP	G	G	A	rs2550231		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195452770G>A	ENST00000447234.2	+	2	1422	c.1296G>A	c.(1294-1296)acG>acA	p.T432T	MUC20_ENST00000436408.1_Silent_p.T432T|MUC20_ENST00000445522.2_Silent_p.T397T|MUC20_ENST00000320736.6_Silent_p.T261T	NM_001282506.1	NP_001269435.1	Q8N307	MUC20_HUMAN	mucin 20, cell surface associated	432					activation of MAPK activity (GO:0000187)|cellular protein metabolic process (GO:0044267)|hepatocyte growth factor receptor signaling pathway (GO:0048012)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein homooligomerization (GO:0051260)	basal plasma membrane (GO:0009925)|cell projection (GO:0042995)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)				NS(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(4)|skin(4)|stomach(3)|upper_aerodigestive_tract(1)	23	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)	Lung NSC(153;0.191)	Epithelial(36;1e-21)|all cancers(36;9.02e-20)|OV - Ovarian serous cystadenocarcinoma(49;1.6e-18)|Lung(62;0.000104)|LUSC - Lung squamous cell carcinoma(58;0.000128)	GBM - Glioblastoma multiforme(46;1.66e-05)		TAGAAACAACGACTTCCAGCA	0.557																																					p.T261T		Atlas-SNP	.											.	MUC20	84	.	0			c.G783A						PASS	.						26.0	22.0	23.0					3																	195452770		1913	4085	5998	SO:0001819	synonymous_variant	200958	exon3			AACAACGACTTCC	AB037780	CCDS63877.1	3q29	2008-08-07	2006-03-14		ENSG00000176945	ENSG00000176945		"""Mucins"""	23282	protein-coding gene	gene with protein product		610360				14565953	Standard	NM_001282506		Approved	FLJ14408, KIAA1359	uc010hzo.3	Q8N307	OTTHUMG00000155823	ENST00000447234.2:c.1296G>A	3.37:g.195452770G>A		Somatic	655	1	0.00152672		WXS	Illumina HiSeq	Phase_I	613	221	0.360522	NM_152673	Q6UX97|Q76I83|Q76I85|Q86ST8|Q8NBY6|Q96KA1|Q9P2I8	Silent	SNP	ENST00000447234.2	37																																																																																				G|0.500;A|0.500	0.500	strong		0.557	MUC20-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000341835.1	NM_152673	
SDC3	9672	hgsc.bcm.edu	37	1	31347399	31347399	+	Missense_Mutation	SNP	C	C	T	rs4949184	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	86	0	0		WXS	Illumina HiSeq	Phase_I	68	46	0.676471	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	
PTPN13	5783	hgsc.bcm.edu	37	4	87696476	87696476	+	Silent	SNP	G	G	A	rs12499471	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:87696476G>A	ENST00000411767.2	+	34	5724	c.5661G>A	c.(5659-5661)acG>acA	p.T1887T	PTPN13_ENST00000316707.6_Silent_p.T1696T|PTPN13_ENST00000436978.1_Silent_p.T1892T|PTPN13_ENST00000511467.1_Silent_p.T1892T|PTPN13_ENST00000427191.2_Silent_p.T1868T			Q12923	PTN13_HUMAN	protein tyrosine phosphatase, non-receptor type 13 (APO-1/CD95 (Fas)-associated phosphatase)	1887	PDZ 5. {ECO:0000255|PROSITE- ProRule:PRU00143}.				peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cell body (GO:0044297)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|lamellipodium (GO:0030027)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein tyrosine phosphatase activity (GO:0004725)			NS(4)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(23)|lung(24)|ovary(4)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	93		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.00082)		TAACACTAACGTGCAACAAAG	0.373													A|||	353	0.0704872	0.1074	0.0677	5008	,	,		19377	0.0079		0.1143	False		,,,				2504	0.0419				p.T1892T		Atlas-SNP	.											.	PTPN13	203	.	0			c.G5676A						PASS	.	A	,,,	373,3357		19,335,1511	81.0	74.0	76.0		5604,5661,5088,5676	-7.1	0.0	4	dbSNP_120	76	999,7205		61,877,3164	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PTPN13	NM_006264.2,NM_080683.2,NM_080684.2,NM_080685.2	,,,	80,1212,4675	AA,AG,GG		12.177,10.0,11.4966	,,,	1868/2467,1887/2486,1696/2295,1892/2491	87696476	1372,10562	1865	4102	5967	SO:0001819	synonymous_variant	5783	exon34			ACTAACGTGCAAC		CCDS47093.1, CCDS47094.1, CCDS47095.1, CCDS47096.1	4q21.3	2011-06-09			ENSG00000163629	ENSG00000163629		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"""	9646	protein-coding gene	gene with protein product		600267				8287977	Standard	NM_006264		Approved	PTP1E, PTP-BAS, PTPL1, PTP-BL	uc003hpy.3	Q12923	OTTHUMG00000160968	ENST00000411767.2:c.5661G>A	4.37:g.87696476G>A		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	128	48	0.375	NM_080685	B2RTR0|Q15159|Q15263|Q15264|Q15265|Q15674|Q16826|Q8IWH7|Q9NYN9|Q9UDA8	Silent	SNP	ENST00000411767.2	37	CCDS47094.1																																																																																			G|0.906;A|0.094	0.094	strong		0.373	PTPN13-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000363191.1		
NCOR2	9612	hgsc.bcm.edu	37	12	124821413	124821413	+	Missense_Mutation	SNP	G	G	A	rs2230944	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:124821413G>A	ENST00000405201.1	-	38	6001	c.6001C>T	c.(6001-6003)Cct>Tct	p.P2001S	NCOR2_ENST00000356219.3_Missense_Mutation_p.P2008S|NCOR2_ENST00000429285.2_Missense_Mutation_p.P1991S|NCOR2_ENST00000404621.1_Missense_Mutation_p.P1991S|NCOR2_ENST00000404121.2_Missense_Mutation_p.P1562S|NCOR2_ENST00000397355.1_Missense_Mutation_p.P1992S			Q9Y618	NCOR2_HUMAN	nuclear receptor corepressor 2	2012					cellular lipid metabolic process (GO:0044255)|gene expression (GO:0010467)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|regulation of cellular ketone metabolic process by negative regulation of transcription from RNA polymerase II promoter (GO:0072365)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	membrane (GO:0016020)|nuclear body (GO:0016604)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone deacetylase binding (GO:0042826)|Notch binding (GO:0005112)|protein N-terminus binding (GO:0047485)|transcription corepressor activity (GO:0003714)			breast(5)|central_nervous_system(2)|endometrium(7)|kidney(5)|large_intestine(7)|lung(28)|ovary(3)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	69	all_neural(191;0.0804)|Medulloblastoma(191;0.163)			Epithelial(86;3.99e-05)|OV - Ovarian serous cystadenocarcinoma(86;9.14e-05)|all cancers(50;0.000402)|BRCA - Breast invasive adenocarcinoma(302;0.0764)		GCGTGGTGAGGTGCGAGGTTC	0.692													g|||	292	0.0583067	0.0378	0.0288	5008	,	,		10661	0.0298		0.0457	False		,,,				2504	0.1493				p.P2001S		Atlas-SNP	.											.	NCOR2	475	.	0			c.C6001T						PASS	.		SER/PRO,SER/PRO,SER/PRO	191,3771		8,175,1798	25.0	30.0	28.0		6001,5971,5971	-2.9	0.2	12	dbSNP_98	28	284,8004		9,266,3869	yes	missense,missense,missense	NCOR2	NM_006312.5,NM_001206654.1,NM_001077261.3	74,74,74	17,441,5667	AA,AG,GG		3.4266,4.8208,3.8776	benign,benign,benign	2001/2515,1991/2505,1991/2459	124821413	475,11775	1981	4144	6125	SO:0001583	missense	9612	exon40			GGTGAGGTGCGAG	U37146	CCDS41857.1, CCDS41858.1, CCDS41857.2, CCDS41858.2, CCDS55892.1	12q24	2010-06-10	2010-06-10		ENSG00000196498	ENSG00000196498			7673	protein-coding gene	gene with protein product		600848	"""nuclear receptor co-repressor 2"""			7566127, 8813722	Standard	NM_001077261		Approved	SMRT, SMRTE, TRAC-1, CTG26, TNRC14	uc010tbb.2	Q9Y618	OTTHUMG00000150455	ENST00000405201.1:c.6001C>T	12.37:g.124821413G>A	ENSP00000384018:p.Pro2001Ser	Somatic	12	0	0		WXS	Illumina HiSeq	Phase_I	33	26	0.787879	NM_006312	O00613|O15416|O15421|Q13354|Q56D06|Q59GM0|Q9Y5U0	Missense_Mutation	SNP	ENST00000405201.1	37	CCDS41858.2	84	0.038461538461538464	27	0.054878048780487805	9	0.024861878453038673	20	0.03496503496503497	28	0.036939313984168866	g	6.603	0.479561	0.12581	0.048208	0.034266	ENSG00000196498	ENST00000405201;ENST00000404621;ENST00000356219;ENST00000397355;ENST00000447011;ENST00000404121;ENST00000447675;ENST00000429285	T;T;T;T;T;T	0.17370	2.28;2.54;2.28;2.54;2.28;2.54	4.78	-2.89	0.05665	.	0.628292	0.15319	N	0.268643	T	0.01029	0.0034	N	0.08118	0	0.09310	N	0.999999	B;B;B	0.26363	0.073;0.147;0.091	B;B;B	0.24848	0.018;0.056;0.025	T	0.33214	-0.9877	10	0.22109	T	0.4	-8.0739	11.8173	0.52218	0.1447:0.5402:0.3152:0.0	rs2230944;rs3741509;rs2230944	1992;2001;2012	C9J239;C9JFD3;Q9Y618	.;.;NCOR2_HUMAN	S	2001;1991;2008;1992;2000;1562;93;1991	ENSP00000384018:P2001S;ENSP00000384202:P1991S;ENSP00000348551:P2008S;ENSP00000380513:P1992S;ENSP00000385618:P1562S;ENSP00000400281:P1991S	ENSP00000348551:P2008S	P	-	1	0	NCOR2	123387366	0.025000	0.19082	0.213000	0.23690	0.447000	0.32167	0.371000	0.20450	-0.575000	0.05982	0.556000	0.70494	CCT	G|0.970;A|0.030	0.030	strong		0.692	NCOR2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318173.2	NM_006312	
CAV3	859	hgsc.bcm.edu	37	3	8787220	8787220	+	Silent	SNP	T	T	C	rs13087941	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:8787220T>C	ENST00000343849.2	+	2	200	c.123T>C	c.(121-123)ttT>ttC	p.F41F	CAV3_ENST00000397368.2_Silent_p.F41F|SSUH2_ENST00000478513.1_5'Flank|CAV3_ENST00000472766.1_Intron	NM_001234.4|NM_033337.2	NP_001225.1|NP_203123.1	P56539	CAV3_HUMAN	caveolin 3	41					actin filament organization (GO:0007015)|cardiac muscle cell development (GO:0055013)|caveola assembly (GO:0070836)|cell differentiation (GO:0030154)|cell growth (GO:0016049)|cholesterol homeostasis (GO:0042632)|cytoplasmic microtubule organization (GO:0031122)|endocytosis (GO:0006897)|establishment of protein localization to plasma membrane (GO:0090002)|glucose homeostasis (GO:0042593)|heart trabecula formation (GO:0060347)|membrane raft organization (GO:0031579)|muscle cell cellular homeostasis (GO:0046716)|muscle organ development (GO:0007517)|myoblast fusion (GO:0007520)|negative regulation of calcium ion transport (GO:0051926)|negative regulation of cardiac muscle hypertrophy (GO:0010614)|negative regulation of cell growth involved in cardiac muscle cell development (GO:0061052)|negative regulation of cell size (GO:0045792)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of nitric-oxide synthase activity (GO:0051001)|negative regulation of potassium ion transmembrane transport (GO:1901380)|negative regulation of potassium ion transmembrane transporter activity (GO:1901017)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein localization to cell surface (GO:2000009)|negative regulation of sarcomere organization (GO:0060299)|nucleus localization (GO:0051647)|plasma membrane organization (GO:0007009)|plasma membrane repair (GO:0001778)|positive regulation of caveolin-mediated endocytosis (GO:2001288)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of myotube differentiation (GO:0010831)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|protein localization (GO:0008104)|protein localization to plasma membrane (GO:0072659)|regulation of branching involved in mammary gland duct morphogenesis (GO:0060762)|regulation of calcium ion import (GO:0090279)|regulation of calcium ion transmembrane transporter activity (GO:1901019)|regulation of cardiac muscle contraction (GO:0055117)|regulation of heart contraction (GO:0008016)|regulation of heart rate (GO:0002027)|regulation of membrane depolarization during cardiac muscle cell action potential (GO:1900825)|regulation of membrane potential (GO:0042391)|regulation of nerve growth factor receptor activity (GO:0051394)|regulation of p38MAPK cascade (GO:1900744)|regulation of protein kinase B signaling (GO:0051896)|regulation of signal transduction by receptor internalization (GO:0038009)|regulation of skeletal muscle contraction (GO:0014819)|regulation of sodium ion transmembrane transporter activity (GO:2000649)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|regulation of ventricular cardiac muscle cell membrane depolarization (GO:0060373)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|T-tubule organization (GO:0033292)|triglyceride metabolic process (GO:0006641)|ventricular cardiac muscle cell action potential (GO:0086005)	caveola (GO:0005901)|cell surface (GO:0009986)|dystrophin-associated glycoprotein complex (GO:0016010)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|membrane raft (GO:0045121)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|vesicle (GO:0031982)	calcium channel regulator activity (GO:0005246)|connexin binding (GO:0071253)|ion channel binding (GO:0044325)|potassium channel inhibitor activity (GO:0019870)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)|protein complex scaffold (GO:0032947)|sodium channel regulator activity (GO:0017080)	p.F41F(1)		breast(1)|kidney(2)|large_intestine(4)|lung(3)|prostate(1)	11						AGGTGGATTTTGAAGACGTGA	0.562													C|||	766	0.152955	0.2837	0.1311	5008	,	,		18630	0.0139		0.2326	False		,,,				2504	0.0532				p.F41F		Atlas-SNP	.											CAV3,NS,carcinoma,0,1	CAV3	20	1	1	Substitution - coding silent(1)	prostate(1)	c.T123C						PASS	.	C	,	1251,3155	704.6+/-407.1	175,901,1127	60.0	53.0	56.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	123,123	-7.3	0.6	3	dbSNP_121	56	2073,6527	716.8+/-406.1	242,1589,2469	no	coding-synonymous,coding-synonymous	CAV3	NM_001234.3,NM_033337.2	,	417,2490,3596	CC,CT,TT		24.1047,28.3931,25.5574	,	41/152,41/152	8787220	3324,9682	2203	4300	6503	SO:0001819	synonymous_variant	859	exon2			GGATTTTGAAGAC	AF043101	CCDS2569.1	3p25	2014-09-17			ENSG00000182533	ENSG00000182533			1529	protein-coding gene	gene with protein product	"""M-caveolin"""	601253				9536092, 9537420	Standard	NM_033337		Approved	VIP-21, LGMD1C, VIP21, LQT9	uc003brb.3	P56539	OTTHUMG00000090519	ENST00000343849.2:c.123T>C	3.37:g.8787220T>C		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	73	38	0.520548	NM_033337	A8K777|Q3T1A4	Silent	SNP	ENST00000343849.2	37	CCDS2569.1																																																																																			T|0.791;C|0.209	0.209	strong		0.562	CAV3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207008.2	NM_033337	
MUC4	4585	hgsc.bcm.edu	37	3	195506914	195506914	+	Missense_Mutation	SNP	G	G	A	rs186560307	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195506914G>A	ENST00000463781.3	-	2	11996	c.11537C>T	c.(11536-11538)cCt>cTt	p.P3846L	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.P3846L	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)		TACTGAGGAAGGGATGGTGAC	0.582													.|||	658	0.13139	0.3699	0.0778	5008	,	,		7843	0.0129		0.0795	False		,,,				2504	0.0225				p.P3846L		Atlas-SNP	.											.	MUC4	1505	.	0			c.C11537T						PASS	.						7.0	7.0	7.0					3																	195506914		367	1249	1616	SO:0001583	missense	4585	exon2			GAGGAAGGGATGG	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.11537C>T	3.37:g.195506914G>A	ENSP00000417498:p.Pro3846Leu	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	21	17	0.809524	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	336	0.15384615384615385	81	0.16463414634146342	50	0.13812154696132597	110	0.19230769230769232	95	0.12532981530343007	g	4.937	0.174064	0.09391	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.32515	1.51;1.45	.	.	.	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.58432	P	1.0000000000287557E-6	B	0.15141	0.012	B	0.01281	0.0	T	0.40136	-0.9579	6	.	.	.	.	5.844	0.18652	9.0E-4:0.0:0.9991:0.0	.	3718	E7ESK3	.	L	3846	ENSP00000417498:P3846L;ENSP00000420243:P3846L	.	P	-	2	0	MUC4	196991693	0.043000	0.20138	0.054000	0.19295	0.054000	0.15201	1.244000	0.32778	0.064000	0.16427	0.064000	0.15345	CCT	A|0.147;C|0.034;G|0.819	0.147	strong		0.582	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
NFASC	23114	hgsc.bcm.edu	37	1	204943947	204943947	+	Silent	SNP	C	C	A	rs2246662	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:204943947C>A	ENST00000401399.1	+	13	1753	c.1554C>A	c.(1552-1554)gtC>gtA	p.V518V	NFASC_ENST00000338515.6_Silent_p.V518V|NFASC_ENST00000367169.4_Silent_p.V518V|NFASC_ENST00000360049.4_Silent_p.V529V|NFASC_ENST00000339876.6_Silent_p.V518V|NFASC_ENST00000338586.6_Silent_p.V518V|NFASC_ENST00000539706.1_Silent_p.V529V|NFASC_ENST00000513543.1_Silent_p.V529V|NFASC_ENST00000367171.4_Silent_p.V518V|NFASC_ENST00000403080.1_Silent_p.V518V|NFASC_ENST00000404076.1_Silent_p.V512V|NFASC_ENST00000367170.4_Silent_p.V518V|NFASC_ENST00000367172.4_Silent_p.V518V|NFASC_ENST00000404907.1_Silent_p.V529V			O94856	NFASC_HUMAN	neurofascin	518					axon guidance (GO:0007411)|clustering of voltage-gated sodium channels (GO:0045162)|heterotypic cell-cell adhesion (GO:0034113)|myelination (GO:0042552)|paranodal junction assembly (GO:0030913)|peripheral nervous system development (GO:0007422)|protein localization to juxtaparanode region of axon (GO:0071205)|protein localization to paranode region of axon (GO:0002175)|synapse organization (GO:0050808)|transmission of nerve impulse (GO:0019226)	axon initial segment (GO:0043194)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|node of Ranvier (GO:0033268)|paranodal junction (GO:0033010)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)				NS(1)|breast(4)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(22)|liver(1)|lung(24)|ovary(3)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)	81	all_cancers(21;0.0375)|Breast(84;0.0437)|all_epithelial(62;0.171)|Prostate(682;0.19)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.158)			GCCTGGAGGTCAAAGGTAAAG	0.507													C|||	2342	0.467652	0.1952	0.5403	5008	,	,		21316	0.6716		0.4125	False		,,,				2504	0.6309				p.V529V		Atlas-SNP	.											.	NFASC	396	.	0			c.C1587A						PASS	.	C	,,,,,	958,3448	362.6+/-316.2	107,744,1352	85.0	80.0	81.0		1554,1554,1587,1587,1536,1587	5.8	1.0	1	dbSNP_100	81	3338,5262	496.4+/-374.3	644,2050,1606	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NFASC	NM_001005388.2,NM_001005389.1,NM_001160331.1,NM_001160332.1,NM_001160333.1,NM_015090.3	,,,,,	751,2794,2958	AA,AC,CC		38.814,21.7431,33.0309	,,,,,	518/1241,518/620,529/1190,529/1175,512/614,529/1170	204943947	4296,8710	2203	4300	6503	SO:0001819	synonymous_variant	23114	exon14			GGAGGTCAAAGGT	AK027553	CCDS30982.1, CCDS53460.1, CCDS53461.1, CCDS53462.1	1q32.1	2013-02-11	2010-06-24		ENSG00000163531	ENSG00000163531		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	29866	protein-coding gene	gene with protein product		609145	"""neurofascin homolog (chicken)"""			1377696, 8672144	Standard	NM_015090		Approved	NRCAML, KIAA0756, FLJ46866, NF	uc001hbj.3	O94856	OTTHUMG00000151697	ENST00000401399.1:c.1554C>A	1.37:g.204943947C>A		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	55	26	0.472727	NM_015090	B2RNN8|B3KQZ1|B5MDP6|B5MDR6|B7ZMD8|Q149P5|Q5T2F0|Q5T2F1|Q5T2F2|Q5T2F3|Q5T2F4|Q5T2F5|Q5T2F6|Q5T2F7|Q5T2F9|Q5T2G0|Q5W9F8|Q68DH3|Q6ZQV6|Q7Z3K1|Q96HT1|Q96K50	Silent	SNP	ENST00000401399.1	37	CCDS53460.1	1018	0.4661172161172161	112	0.22764227642276422	164	0.4530386740331492	414	0.7237762237762237	328	0.43271767810026385	C	10.48	1.362910	0.24684	0.217431	0.38814	ENSG00000163531	ENST00000367173	.	.	.	5.8	5.8	0.92144	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.3475	0.74350	0.1403:0.8597:0.0:0.0	rs2246662;rs17336991;rs58710035;rs2246662	.	.	.	X	488	.	.	S	+	2	0	NFASC	203210570	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	1.261000	0.32980	2.764000	0.94973	0.485000	0.47835	TCA	C|0.611;A|0.389	0.389	strong		0.507	NFASC-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000131237.1	NM_001005388	
CD300E	342510	hgsc.bcm.edu	37	17	72613352	72613352	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:72613352T>C	ENST00000328630.3	-	2	333	c.293A>G	c.(292-294)gAt>gGt	p.D98G	CD300E_ENST00000426295.2_Missense_Mutation_p.D139G|CD300E_ENST00000392619.1_Missense_Mutation_p.D125G			Q496F6	CLM2_HUMAN	CD300e molecule	98	Ig-like V-type.				innate immune response (GO:0045087)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|kidney(3)|large_intestine(4)|lung(4)|ovary(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	19						AGATCCAGCATCATCTTCATT	0.537																																					p.D98G		Atlas-SNP	.											CD300E_ENST00000426295,right_upper_lobe,carcinoma,-1,2	CD300E	70	2	0			c.A293G						scavenged	.						209.0	165.0	180.0					17																	72613352		2203	4300	6503	SO:0001583	missense	342510	exon2			CCAGCATCATCTT	BX648376	CCDS11702.1	17q25.1	2013-01-11	2006-03-28	2006-02-22	ENSG00000186407	ENSG00000186407		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"""	28874	protein-coding gene	gene with protein product		609801	"""CD300 antigen like family member E"", ""CD300e antigen"""	CD300LE		15549731, 15557162	Standard	NM_181449		Approved	IREM2, CLM2	uc002jlb.2	Q496F6	OTTHUMG00000067605	ENST00000328630.3:c.293A>G	17.37:g.72613352T>C	ENSP00000329942:p.Asp98Gly	Somatic	291	1	0.00343643		WXS	Illumina HiSeq	Phase_I	248	5	0.0201613	NM_181449	B4DNS1|Q7Z7I3	Missense_Mutation	SNP	ENST00000328630.3	37	CCDS11702.1	.	.	.	.	.	.	.	.	.	.	T	17.07	3.295028	0.60086	.	.	ENSG00000186407	ENST00000392619;ENST00000426295;ENST00000328630;ENST00000412268	D;D;D;D	0.88046	-2.33;-2.33;-2.33;-2.33	4.89	4.89	0.63831	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.132514	0.33110	N	0.005268	D	0.95287	0.8471	H	0.96805	3.885	0.09310	N	1	D	0.89917	1.0	D	0.97110	1.0	D	0.89542	0.3793	10	0.72032	D	0.01	-11.2985	11.4488	0.50140	0.0:0.0:0.0:1.0	.	98	Q496F6	CLM2_HUMAN	G	125;139;98;100	ENSP00000376395:D125G;ENSP00000416642:D139G;ENSP00000329942:D98G;ENSP00000415488:D100G	ENSP00000329942:D98G	D	-	2	0	CD300E	70124947	0.247000	0.23920	0.022000	0.16811	0.022000	0.10575	4.007000	0.57093	2.135000	0.66039	0.482000	0.46254	GAT	.	.	none		0.537	CD300E-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_181449	
ARHGAP33	115703	hgsc.bcm.edu	37	19	36275074	36275074	+	Splice_Site	SNP	G	G	A	rs62112163	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:36275074G>A	ENST00000007510.4	+	16	1566	c.1422G>A	c.(1420-1422)cgG>cgA	p.R474R	ARHGAP33_ENST00000314737.5_Splice_Site_p.R474R|ARHGAP33_ENST00000378944.5_Splice_Site_p.R338R			O14559	RHG33_HUMAN	Rho GTPase activating protein 33	474	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				protein transport (GO:0015031)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	phosphatidylinositol binding (GO:0035091)|Rac GTPase activator activity (GO:0030675)	p.R474R(1)		endometrium(7)|large_intestine(8)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	37						TCCCACCCAGGTCCATGGAGC	0.652													G|||	918	0.183307	0.0862	0.1715	5008	,	,		12087	0.1518		0.1829	False		,,,				2504	0.3558				p.R474R		Atlas-SNP	.											ARHGAP33,NS,carcinoma,0,1	ARHGAP33	102	1	1	Substitution - coding silent(1)	stomach(1)	c.G1422A						PASS	.	G	,	443,3963	211.8+/-231.9	13,417,1773	122.0	113.0	116.0		1014,1422	3.8	1.0	19	dbSNP_129	116	1631,6967	300.1+/-304.8	146,1339,2814	no	coding-synonymous-near-splice,coding-synonymous-near-splice	ARHGAP33	NM_001172630.1,NM_052948.3	,	159,1756,4587	AA,AG,GG		18.9695,10.0545,15.9489	,	338/1124,474/1127	36275074	2074,10930	2203	4299	6502	SO:0001630	splice_region_variant	115703	exon16			ACCCAGGTCCATG	AY044864	CCDS12477.1, CCDS54254.1	19q13.13	2011-06-29	2010-02-19	2010-02-19		ENSG00000004777		"""Rho GTPase activating proteins"""	23085	protein-coding gene	gene with protein product		614902	"""sorting nexin 26"""	SNX26		12297274, 12461558	Standard	NM_052948		Approved	FLJ39019, TCGAP	uc002obs.2	O14559		ENST00000007510.4:c.1422-1G>A	19.37:g.36275074G>A		Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	197	197	1	NM_052948	O14552|O14560|Q6ZSP6|Q96CP3|Q9NT23	Silent	SNP	ENST00000007510.4	37																																																																																				G|0.833;A|0.167	0.167	strong		0.652	ARHGAP33-201	KNOWN	basic	protein_coding	protein_coding		NM_052948	Silent
TAF4B	6875	hgsc.bcm.edu	37	18	23872235	23872235	+	Missense_Mutation	SNP	A	A	G	rs12963653	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:23872235A>G	ENST00000269142.5	+	8	2614	c.1616A>G	c.(1615-1617)aAt>aGt	p.N539S	TAF4B_ENST00000578121.1_Missense_Mutation_p.N544S|TAF4B_ENST00000400466.2_Missense_Mutation_p.N539S	NM_005640.1	NP_005631.1	Q92750	TAF4B_HUMAN	TAF4b RNA polymerase II, TATA box binding protein (TBP)-associated factor, 105kDa	539	Nuclear export signal.		N -> S (in dbSNP:rs12963653).		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)			TCAGGAGGCAATGAAAAACAA	0.373													A|||	609	0.121605	0.056	0.1268	5008	,	,		19962	0.0546		0.2913	False		,,,				2504	0.1012				p.N539S		Atlas-SNP	.											.	TAF4B	71	.	0			c.A1616G						PASS	.	A	SER/ASN	358,3454		12,334,1560	137.0	123.0	128.0		1616	-1.8	0.0	18	dbSNP_121	128	2383,5883		334,1715,2084	yes	missense	TAF4B	NM_005640.1	46	346,2049,3644	GG,GA,AA		28.8289,9.3914,22.6942	benign	539/863	23872235	2741,9337	1906	4133	6039	SO:0001583	missense	6875	exon8			GAGGCAATGAAAA	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.1616A>G	18.37:g.23872235A>G	ENSP00000269142:p.Asn539Ser	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	101	49	0.485149	NM_005640	Q29YA4|Q29YA5	Missense_Mutation	SNP	ENST00000269142.5	37	CCDS42421.1	326	0.14926739926739926	31	0.06300813008130081	46	0.1270718232044199	25	0.043706293706293704	224	0.2955145118733509	A	9.026	0.986046	0.18889	0.093914	0.288289	ENSG00000141384	ENST00000418698;ENST00000269142;ENST00000400466	T;T	0.21932	2.01;1.98	5.21	-1.79	0.07932	.	1.245340	0.05224	N	0.509084	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.38993	-0.9635	9	0.07482	T	0.82	0.1811	2.7368	0.05242	0.5082:0.0757:0.1221:0.294	rs12963653	539;544	Q92750;A4PBF7	TAF4B_HUMAN;.	S	542;539;539	ENSP00000269142:N539S;ENSP00000383314:N539S	ENSP00000269142:N539S	N	+	2	0	TAF4B	22126233	0.017000	0.18338	0.007000	0.13788	0.860000	0.49131	0.474000	0.22148	-0.301000	0.08882	-0.339000	0.08088	AAT	A|0.796;G|0.204	0.204	strong		0.373	TAF4B-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000446260.3	NM_005640	
OBSCN	84033	hgsc.bcm.edu	37	1	228550426	228550426	+	Missense_Mutation	SNP	C	C	T	rs35155240	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:228550426C>T	ENST00000422127.1	+	80	18855	c.18811C>T	c.(18811-18813)Ccc>Tcc	p.P6271S	OBSCN_ENST00000570156.2_Missense_Mutation_p.P7228S|OBSCN_ENST00000366707.4_Missense_Mutation_p.P3905S	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	6271					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)				CGGCTCCCAGCCCCCAGTCAC	0.677													C|||	736	0.146965	0.0825	0.0764	5008	,	,		14923	0.3264		0.0984	False		,,,				2504	0.1493				p.P7228S		Atlas-SNP	.											.	OBSCN	2142	.	0			c.C21682T						PASS	.	C	SER/PRO	358,3460		17,324,1568	14.0	18.0	17.0		18811	-3.9	0.0	1	dbSNP_126	17	685,7533		24,637,3448	no	missense	OBSCN	NM_001098623.1	74	41,961,5016	TT,TC,CC		8.3354,9.3766,8.6657	benign	6271/7969	228550426	1043,10993	1909	4109	6018	SO:0001583	missense	84033	exon91			TCCCAGCCCCCAG	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.18811C>T	1.37:g.228550426C>T	ENSP00000409493:p.Pro6271Ser	Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	174	88	0.505747	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	345|345	0.15796703296703296|0.15796703296703296	46|46	0.09349593495934959|0.09349593495934959	35|35	0.09668508287292818|0.09668508287292818	189|189	0.3304195804195804|0.3304195804195804	75|75	0.09894459102902374|0.09894459102902374	C|C	14.62|14.62	2.590870|2.590870	0.46214|0.46214	0.093766|0.093766	0.083354|0.083354	ENSG00000154358|ENSG00000154358	ENST00000441106|ENST00000422127;ENST00000366707	.|T;T	.|0.62232	.|0.04;0.17	4.06|4.06	-3.86|-3.86	0.04230|0.04230	.|.	.|.	.|.	.|.	.|.	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	.|0.09022	.|0.002	.|B	.|0.08055	.|0.003	T|T	0.29336|0.29336	-1.0015|-1.0015	4|8	.|0.22109	.|T	.|0.4	.|.	2.7427|2.7427	0.05258|0.05258	0.4663:0.2405:0.2022:0.0911|0.4663:0.2405:0.2022:0.0911	rs35155240;rs61825330|rs35155240;rs61825330	.|6271	.|Q5VST9	.|OBSCN_HUMAN	V|S	887|6271;3905	.|ENSP00000409493:P6271S;ENSP00000355668:P3905S	.|ENSP00000355668:P3905S	A|P	+|+	2|1	0|0	OBSCN|OBSCN	226617049|226617049	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.001000|0.001000	0.01503|0.01503	-0.456000|-0.456000	0.06754|0.06754	-0.453000|-0.453000	0.07076|0.07076	-0.320000|-0.320000	0.08662|0.08662	GCC|CCC	C|0.851;T|0.149	0.149	strong		0.677	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
HBP1	26959	hgsc.bcm.edu	37	7	106826381	106826381	+	Silent	SNP	C	C	T	rs201145168|rs7794598	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:106826381C>T	ENST00000222574.4	+	4	720	c.534C>T	c.(532-534)caC>caT	p.H178H	HBP1_ENST00000485846.1_Silent_p.H178H|HBP1_ENST00000468410.1_Silent_p.H178H	NM_012257.3	NP_036389.2	O60381	HBP1_HUMAN	HMG-box transcription factor 1	178					cell cycle arrest (GO:0007050)|positive regulation of potassium ion transport (GO:0043268)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA binding (GO:0003723)			large_intestine(4)|lung(3)|prostate(1)|skin(2)	10						CAGTAAGACACGAAAGGGTAA	0.413														792	0.158147	0.1483	0.1282	5008	,	,		18826	0.124		0.2018	False		,,,				2504	0.183				p.H188H		Atlas-SNP	.											.	HBP1	31	.	0			c.C564T						PASS	.	T		637,3769	767.1+/-413.5	61,515,1627	96.0	88.0	91.0		534	-0.4	1.0	7	dbSNP_116	91	1850,6750	730.1+/-406.7	206,1438,2656	no	coding-synonymous	HBP1	NM_012257.3		267,1953,4283	TT,TC,CC		21.5116,14.4576,19.1219		178/515	106826381	2487,10519	2203	4300	6503	SO:0001819	synonymous_variant	26959	exon4			AAGACACGAAAGG	BC017069	CCDS5741.1	7q22-q31	2003-10-08			ENSG00000105856	ENSG00000105856			23200	protein-coding gene	gene with protein product						9030690, 11500377	Standard	NM_001244262		Approved		uc011klv.2	O60381	OTTHUMG00000157642	ENST00000222574.4:c.534C>T	7.37:g.106826381C>T		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	73	31	0.424658	NM_001244262	B3KVB7|Q8TBM1|Q8TE93|Q96AJ2	Silent	SNP	ENST00000222574.4	37	CCDS5741.1																																																																																			C|0.818;T|0.182	0.182	strong		0.413	HBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349297.1	NM_012257	
NPHP1	4867	hgsc.bcm.edu	37	2	110922703	110922703	+	Silent	SNP	C	C	T	rs11675767	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:110922703C>T	ENST00000393272.3	-	7	751	c.654G>A	c.(652-654)gaG>gaA	p.E218E	NPHP1_ENST00000445609.2_Silent_p.E218E|NPHP1_ENST00000417665.1_Silent_p.E218E|NPHP1_ENST00000316534.4_Silent_p.E218E|NPHP1_ENST00000355301.4_Silent_p.E156E	NM_000272.3|NM_207181.2	NP_000263.2|NP_997064.2	O15259	NPHP1_HUMAN	nephronophthisis 1 (juvenile)	218	Glu-rich.				actin cytoskeleton organization (GO:0030036)|cell projection organization (GO:0030030)|cellular protein localization (GO:0034613)|excretion (GO:0007588)|photoreceptor cell outer segment organization (GO:0035845)|retina development in camera-type eye (GO:0060041)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|spermatid differentiation (GO:0048515)|visual behavior (GO:0007632)	cell-cell junction (GO:0005911)|ciliary transition zone (GO:0035869)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|membrane (GO:0016020)|motile cilium (GO:0031514)|photoreceptor connecting cilium (GO:0032391)|tight junction (GO:0005923)	structural molecule activity (GO:0005198)			autonomic_ganglia(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(10)|ovary(2)	24						CTTCACTTGACTCTTGGCCTT	0.383													T|||	2376	0.474441	0.5106	0.4193	5008	,	,		13896	0.5863		0.3032	False		,,,				2504	0.5256				p.E218E		Atlas-SNP	.											.	NPHP1	68	.	0			c.G654A						PASS	.	T	,,,	2153,2253	595.0+/-388.3	534,1085,584	191.0	177.0	182.0		654,654,468,654	-6.8	0.0	2	dbSNP_120	182	2774,5826	678.1+/-403.4	459,1856,1985	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NPHP1	NM_000272.3,NM_001128178.1,NM_001128179.1,NM_207181.2	,,,	993,2941,2569	TT,TC,CC		32.2558,48.8652,37.8825	,,,	218/734,218/678,156/615,218/733	110922703	4927,8079	2203	4300	6503	SO:0001819	synonymous_variant	4867	exon7			ACTTGACTCTTGG	AF023674	CCDS2086.1, CCDS46384.1, CCDS46385.1, CCDS46386.1	2q13	2014-01-28			ENSG00000144061	ENSG00000144061			7905	protein-coding gene	gene with protein product	"""nephrocystin-1"""	607100		NPH1			Standard	NM_000272		Approved	JBTS4, SLSN1	uc002tfm.4	O15259	OTTHUMG00000131195	ENST00000393272.3:c.654G>A	2.37:g.110922703C>T		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	98	98	1	NM_207181	O14837	Silent	SNP	ENST00000393272.3	37	CCDS46385.1																																																																																			C|0.575;T|0.425	0.425	strong		0.383	NPHP1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000253919.3	NM_000272	
ZNF646	9726	hgsc.bcm.edu	37	16	31090094	31090094	+	Missense_Mutation	SNP	G	G	A	rs78522165	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	140	0	0		WXS	Illumina HiSeq	Phase_I	138	53	0.384058	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	
MUC4	4585	hgsc.bcm.edu	37	3	195507262	195507262	+	Missense_Mutation	SNP	T	T	G	rs74187968|rs367631576		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195507262T>G	ENST00000463781.3	-	2	11648	c.11189A>C	c.(11188-11190)cAt>cCt	p.H3730P	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_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	83	2	0.0240964		WXS	Illumina HiSeq	Phase_I	96	19	0.197917	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	
NEB	4703	hgsc.bcm.edu	37	2	152382759	152382759	+	Silent	SNP	T	T	C	rs61730765	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:152382759T>C	ENST00000172853.10	-	121	17007	c.16860A>G	c.(16858-16860)aaA>aaG	p.K5620K	NEB_ENST00000427231.2_Silent_p.K7321K|NEB_ENST00000603639.1_Silent_p.K7321K|NEB_ENST00000409198.1_Silent_p.K5620K|NEB_ENST00000397345.3_Silent_p.K7321K|NEB_ENST00000604864.1_Silent_p.K7321K			P20929	NEBU_HUMAN	nebulin	5620					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)		CCTTGACATGTTTCTCTTTGT	0.488													T|||	107	0.0213658	0.0537	0.0072	5008	,	,		16984	0.0		0.0268	False		,,,				2504	0.0041				p.K7356K		Atlas-SNP	.											.	NEB	1697	.	0			c.A22068G						PASS	.	T	,,	176,3694		7,162,1766	64.0	65.0	65.0		21963,21963,16860	-3.7	1.0	2	dbSNP_129	65	159,8093		2,155,3969	no	coding-synonymous,coding-synonymous,coding-synonymous	NEB	NM_001164507.1,NM_001164508.1,NM_004543.4	,,	9,317,5735	CC,CT,TT		1.9268,4.5478,2.7636	,,	7321/8526,7321/8526,5620/6670	152382759	335,11787	1935	4126	6061	SO:0001819	synonymous_variant	4703	exon150			GACATGTTTCTCT	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.16860A>G	2.37:g.152382759T>C		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	103	47	0.456311	NM_001271208	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Silent	SNP	ENST00000172853.10	37																																																																																				T|0.975;C|0.025	0.025	strong		0.488	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543	
MYO9B	4650	hgsc.bcm.edu	37	19	17303774	17303774	+	Missense_Mutation	SNP	T	T	G	rs1545620	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:17303774T>G	ENST00000594824.1	+	21	3178	c.3031T>G	c.(3031-3033)Tca>Gca	p.S1011A	MYO9B_ENST00000595618.1_Missense_Mutation_p.S1011A|MYO9B_ENST00000397274.2_Missense_Mutation_p.S1011A			Q13459	MYO9B_HUMAN	myosin IXB	1011	IQ 3. {ECO:0000255|PROSITE- ProRule:PRU00116}.|Neck or regulatory domain.			S -> A (in Ref. 1; AAC50402). {ECO:0000305}.	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						CCTCCAGGCCTCATGGAGGGG	0.677													G|||	3227	0.644369	0.7905	0.7032	5008	,	,		14650	0.7391		0.3897	False		,,,				2504	0.5695				p.S1011A		Atlas-SNP	.											MYO9B_ENST00000319396,NS,carcinoma,0,2	MYO9B	264	2	0			c.T3031G	GRCh37	CM066145	MYO9B	M	rs1545620	PASS	.	G	ALA/SER,ALA/SER	2939,1003		1112,715,144	12.0	17.0	15.0		3031,3031	-1.5	0.0	19	dbSNP_88	15	3377,4719		787,1803,1458	yes	missense,missense	MYO9B	NM_001130065.1,NM_004145.3	99,99	1899,2518,1602	GG,GT,TT		41.712,25.4439,47.5328	benign,benign	1011/2023,1011/2158	17303774	6316,5722	1971	4048	6019	SO:0001583	missense	4650	exon21			CAGGCCTCATGGA		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.3031T>G	19.37:g.17303774T>G	ENSP00000471367:p.Ser1011Ala	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	51	31	0.607843	NM_001130065	O75314|Q9NUJ2|Q9UHN0	Missense_Mutation	SNP	ENST00000594824.1	37		1361	0.6231684981684982	382	0.7764227642276422	239	0.6602209944751382	440	0.7692307692307693	300	0.39577836411609496	G	0.005	-2.214157	0.00289	0.745561	0.41712	ENSG00000099331	ENST00000397274	T	0.21361	2.01	4.88	-1.46	0.08800	.	1.199970	0.06003	N	0.648098	T	0.00012	0.0000	N	0.00368	-1.59	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;0.0	T	0.43909	-0.9362	9	0.02654	T	1	.	0.9756	0.01425	0.2544:0.1088:0.337:0.2998	rs1545620;rs57113186;rs1545620	1011;1011;1017	Q13459;B0I1T6;Q4LE74	MYO9B_HUMAN;.;.	A	1011	ENSP00000380444:S1011A	ENSP00000380444:S1011A	S	+	1	0	MYO9B	17164774	0.000000	0.05858	0.043000	0.18650	0.020000	0.10135	0.668000	0.25127	0.092000	0.17331	-0.721000	0.03606	TCA	T|0.363;G|0.637	0.637	strong		0.677	MYO9B-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000463236.1		
C14orf37	145407	hgsc.bcm.edu	37	14	58605156	58605156	+	Silent	SNP	G	G	A	rs61748937	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:58605156G>A	ENST00000267485.7	-	2	1115	c.921C>T	c.(919-921)gcC>gcT	p.A307A	C14orf37_ENST00000334342.5_5'UTR	NM_001001872.2	NP_001001872.2	Q86TY3	CN037_HUMAN	chromosome 14 open reading frame 37	307						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						TTAAGGCAGAGGCAGCTGGAA	0.517													G|||	17	0.00339457	0.0015	0.0029	5008	,	,		21146	0.0		0.0109	False		,,,				2504	0.002				p.A307A		Atlas-SNP	.											.	C14orf37	87	.	0			c.C921T						PASS	.	G		8,4398	14.3+/-33.2	0,8,2195	93.0	97.0	96.0		921	0.4	0.0	14	dbSNP_129	96	134,8466	68.0+/-130.5	1,132,4167	no	coding-synonymous	C14orf37	NM_001001872.2		1,140,6362	AA,AG,GG		1.5581,0.1816,1.0918		307/775	58605156	142,12864	2203	4300	6503	SO:0001819	synonymous_variant	145407	exon2			GGCAGAGGCAGCT		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.921C>T	14.37:g.58605156G>A		Somatic	218	0	0		WXS	Illumina HiSeq	Phase_I	175	98	0.56	NM_001001872	A8K8Z8|Q6P5Q1|Q86TY1	Silent	SNP	ENST00000267485.7	37	CCDS32089.1																																																																																			G|0.989;A|0.011	0.011	strong		0.517	C14orf37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412059.1	NM_001001872	
CAND2	23066	hgsc.bcm.edu	37	3	12861608	12861608	+	Missense_Mutation	SNP	G	G	A	rs3817121	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:12861608G>A	ENST00000456430.2	+	11	3009	c.2968G>A	c.(2968-2970)Gtc>Atc	p.V990I	CAND2_ENST00000295989.5_Missense_Mutation_p.V897I	NM_001162499.1	NP_001155971.1	O75155	CAND2_HUMAN	cullin-associated and neddylation-dissociated 2 (putative)	990			V -> I (in dbSNP:rs3817121).		positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	intracellular (GO:0005622)|nucleus (GO:0005634)				breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(8)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	37						CCGGAGCACCGTCATCACAGC	0.597													G|||	689	0.13758	0.0257	0.2911	5008	,	,		18400	0.1151		0.174	False		,,,				2504	0.1656				p.V990I	GBM(43;676 868 1633 6395 37496)	Atlas-SNP	.											CAND2_ENST00000456430,NS,carcinoma,-2,2	CAND2	138	2	0			c.G2968A						PASS	.	G	ILE/VAL,ILE/VAL	146,4178		2,142,2018	134.0	146.0	142.0		2968,2689	5.1	0.9	3	dbSNP_107	142	1485,7001		141,1203,2899	yes	missense,missense	CAND2	NM_001162499.1,NM_012298.2	29,29	143,1345,4917	AA,AG,GG		17.4994,3.3765,12.7322	benign,benign	990/1237,897/1120	12861608	1631,11179	2162	4243	6405	SO:0001583	missense	23066	exon11			AGCACCGTCATCA		CCDS43053.1, CCDS54554.1	3p25.2	2008-02-05			ENSG00000144712	ENSG00000144712			30689	protein-coding gene	gene with protein product	"""TBP interacting protein"""	610403				9734811, 10441524	Standard	NM_012298		Approved	TIP120B, KIAA0667, Tp120b	uc003bxk.2	O75155	OTTHUMG00000155397	ENST00000456430.2:c.2968G>A	3.37:g.12861608G>A	ENSP00000387641:p.Val990Ile	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	74	38	0.513514	NM_001162499	B9EGM9|E9KL24	Missense_Mutation	SNP	ENST00000456430.2	37	CCDS54554.1	311	0.1423992673992674	19	0.03861788617886179	106	0.292817679558011	67	0.11713286713286714	119	0.15699208443271767	G	19.76	3.886690	0.72410	0.033765	0.174994	ENSG00000144712	ENST00000295989;ENST00000456430	T;T	0.25414	1.8;1.8	5.09	5.09	0.68999	Armadillo-like helical (1);Armadillo-type fold (1);	0.234553	0.34460	N	0.003952	T	0.00012	0.0000	L	0.56124	1.755	0.09310	P	1.0	P;P	0.43909	0.468;0.821	B;B	0.39027	0.065;0.288	T	0.40059	-0.9583	9	0.41790	T	0.15	-19.3095	15.9818	0.80116	0.0:0.0:1.0:0.0	rs3817121;rs52799778;rs59821400;rs3817121	990;897	O75155;O75155-2	CAND2_HUMAN;.	I	897;990	ENSP00000295989:V897I;ENSP00000387641:V990I	ENSP00000295989:V897I	V	+	1	0	CAND2	12836608	1.000000	0.71417	0.855000	0.33649	0.985000	0.73830	5.587000	0.67510	2.391000	0.81399	0.561000	0.74099	GTC	A|0.144;G|0.856	0.144	strong		0.597	CAND2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339856.4	XM_371617	
FUCA2	2519	hgsc.bcm.edu	37	6	143823112	143823112	+	Missense_Mutation	SNP	G	G	A	rs3762001	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:143823112G>A	ENST00000002165.6	-	5	1166	c.1111C>T	c.(1111-1113)Cat>Tat	p.H371Y	RP1-20N2.6_ENST00000589563.1_RNA|FUCA2_ENST00000367585.1_5'UTR|RP1-20N2.6_ENST00000593175.1_RNA|FUCA2_ENST00000438118.2_3'UTR|RP1-20N2.6_ENST00000589489.1_RNA|RP1-20N2.6_ENST00000591892.1_RNA|RP1-20N2.6_ENST00000591189.1_RNA|RP1-20N2.6_ENST00000415586.1_RNA|RP1-20N2.6_ENST00000593045.1_RNA|RP1-20N2.6_ENST00000610068.1_RNA|RP1-20N2.6_ENST00000590703.1_RNA	NM_032020.4	NP_114409.2	Q9BTY2	FUCO2_HUMAN	fucosidase, alpha-L- 2, plasma	371			H -> Y (in dbSNP:rs3762001). {ECO:0000269|PubMed:12975309, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:16303743}.		fucose metabolic process (GO:0006004)|glycoside catabolic process (GO:0016139)|regulation of entry of bacterium into host cell (GO:2000535)|response to bacterium (GO:0009617)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	alpha-L-fucosidase activity (GO:0004560)|fucose binding (GO:0042806)			endometrium(1)|large_intestine(1)|lung(2)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	9				OV - Ovarian serous cystadenocarcinoma(155;7.45e-06)|GBM - Glioblastoma multiforme(68;0.0142)		CGCCAGGTATGGGTTTCATAA	0.428													G|||	852	0.170128	0.1233	0.1484	5008	,	,		15192	0.1696		0.2247	False		,,,				2504	0.1933				p.H371Y		Atlas-SNP	.											FUCA2,NS,carcinoma,0,1	FUCA2	28	1	0			c.C1111T						scavenged	.	G	TYR/HIS	676,3730	286.3+/-278.7	52,572,1579	108.0	108.0	108.0		1111	-1.4	0.0	6	dbSNP_107	108	1934,6666	342.2+/-324.4	213,1508,2579	yes	missense	FUCA2	NM_032020.4	83	265,2080,4158	AA,AG,GG		22.4884,15.3427,20.0677	benign	371/468	143823112	2610,10396	2203	4300	6503	SO:0001583	missense	2519	exon5			AGGTATGGGTTTC	BC003060	CCDS5200.1	6q24	2012-10-02			ENSG00000001036	ENSG00000001036	3.2.1.51		4008	protein-coding gene	gene with protein product		136820				6590153	Standard	NM_032020		Approved	MGC1314, dJ20N2.5	uc003qjm.3	Q9BTY2	OTTHUMG00000015728	ENST00000002165.6:c.1111C>T	6.37:g.143823112G>A	ENSP00000002165:p.His371Tyr	Somatic	62	1	0.016129		WXS	Illumina HiSeq	Phase_I	46	8	0.173913	NM_032020	E9PEB6|Q7Z6V1|Q7Z6Y2|Q8NBK4	Missense_Mutation	SNP	ENST00000002165.6	37	CCDS5200.1	398	0.18223443223443223	71	0.1443089430894309	47	0.1298342541436464	104	0.18181818181818182	176	0.23218997361477572	G	9.312	1.055759	0.19907	0.153427	0.224884	ENSG00000001036	ENST00000002165;ENST00000451668	T;T	0.70045	0.56;-0.45	5.98	-1.41	0.08941	.	0.825483	0.11409	N	0.566960	T	0.31451	0.0797	L	0.29908	0.895	0.58432	P	1.0000000000287557E-6	B;B	0.06786	0.001;0.0	B;B	0.06405	0.002;0.0	T	0.12863	-1.0531	9	0.59425	D	0.04	-0.0053	8.8493	0.35190	0.134:0.0:0.3068:0.5592	rs3762001;rs17854673;rs17857722;rs52815197;rs61174998;rs3762001	50;371	Q7Z6V2;Q9BTY2	.;FUCO2_HUMAN	Y	371;50	ENSP00000002165:H371Y;ENSP00000398119:H50Y	ENSP00000002165:H371Y	H	-	1	0	FUCA2	143864805	0.556000	0.26538	0.001000	0.08648	0.726000	0.41606	1.172000	0.31908	-0.144000	0.11314	0.650000	0.86243	CAT	G|0.804;A|0.196	0.196	strong		0.428	FUCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042521.2	NM_032020	
MUC6	4588	hgsc.bcm.edu	37	11	1026084	1026084	+	Silent	SNP	G	G	A	rs12801568	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:1026084G>A	ENST00000421673.2	-	21	2654	c.2604C>T	c.(2602-2604)tgC>tgT	p.C868C		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming	868	VWFD 3. {ECO:0000255|PROSITE- ProRule:PRU00580}.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)	extracellular matrix structural constituent (GO:0005201)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(8)|kidney(10)|large_intestine(6)|lung(43)|ovary(4)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	80		all_cancers(49;3.3e-08)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		all cancers(45;1.24e-24)|BRCA - Breast invasive adenocarcinoma(625;0.00031)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		CGTAGAGGGTGCAGGTGGATG	0.662													g|||	309	0.0617013	0.121	0.0591	5008	,	,		17492	0.001		0.0875	False		,,,				2504	0.0194				p.C868C		Atlas-SNP	.											.	MUC6	408	.	0			c.C2604T						PASS	.	G		428,3892		13,402,1745	36.0	41.0	39.0		2604	0.5	1.0	11	dbSNP_121	39	615,7879		26,563,3658	no	coding-synonymous	MUC6	NM_005961.2		39,965,5403	AA,AG,GG		7.2404,9.9074,8.1395		868/2440	1026084	1043,11771	2160	4247	6407	SO:0001819	synonymous_variant	4588	exon21			GAGGGTGCAGGTG	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.2604C>T	11.37:g.1026084G>A		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	142	112	0.788732	NM_005961	O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	Silent	SNP	ENST00000421673.2	37	CCDS44513.1																																																																																			G|0.937;A|0.063	0.063	strong		0.662	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382120.2	XM_290540	
OR5L1	219437	hgsc.bcm.edu	37	11	55579068	55579068	+	Silent	SNP	C	C	T	rs575553149		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:55579068C>T	ENST00000333973.2	+	1	215	c.126C>T	c.(124-126)aaC>aaT	p.N42N		NM_001004738.1	NP_001004738.1	Q8NGL2	OR5L1_HUMAN	olfactory receptor, family 5, subfamily L, 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)			NS(1)|breast(2)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(4)|liver(4)|lung(36)|ovary(2)|pancreas(1)|prostate(5)|skin(9)|stomach(4)|upper_aerodigestive_tract(3)	78		all_epithelial(135;0.208)				TGTTAGCCAACCTGGGCATGA	0.498																																					p.N42N		Atlas-SNP	.											OR5L1,colon,carcinoma,0,3	OR5L1	145	3	0			c.C126T						scavenged	.						325.0	285.0	299.0					11																	55579068		2200	4296	6496	SO:0001819	synonymous_variant	219437	exon1			AGCCAACCTGGGC	AB065780	CCDS31509.1	11q11	2012-08-09			ENSG00000186117	ENSG00000186117		"""GPCR / Class A : Olfactory receptors"""	8350	protein-coding gene	gene with protein product							Standard	NM_001004738		Approved	OST262	uc001nhw.1	Q8NGL2	OTTHUMG00000166810	ENST00000333973.2:c.126C>T	11.37:g.55579068C>T		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	143	8	0.0559441	NM_001004738	B2RNK6|Q6IFD0	Silent	SNP	ENST00000333973.2	37	CCDS31509.1																																																																																			.	.	none		0.498	OR5L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391514.1	NM_001004738	
KLHL6	89857	hgsc.bcm.edu	37	3	183211906	183211906	+	Silent	SNP	A	A	G	rs1520101	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:183211906A>G	ENST00000341319.3	-	5	1346	c.1311T>C	c.(1309-1311)aaT>aaC	p.N437N		NM_130446.2	NP_569713.2	Q8WZ60	KLHL6_HUMAN	kelch-like family member 6	437					B cell receptor signaling pathway (GO:0050853)|germinal center formation (GO:0002467)					breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(7)|kidney(1)|large_intestine(6)|liver(1)|lung(16)|ovary(2)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	44	all_cancers(143;9.2e-12)|Ovarian(172;0.0172)		all cancers(12;1.29e-44)|Epithelial(37;1.24e-38)|LUSC - Lung squamous cell carcinoma(7;2.58e-24)|Lung(8;1.79e-22)|OV - Ovarian serous cystadenocarcinoma(80;2.32e-22)			AGGTCTCCACATTGTTGATTC	0.443													G|||	3495	0.697883	0.8722	0.5793	5008	,	,		20217	0.8006		0.4771	False		,,,				2504	0.6677				p.N437N		Atlas-SNP	.											.	KLHL6	100	.	0			c.T1311C						PASS	.	G		3539,867	339.7+/-305.9	1433,673,97	253.0	237.0	242.0		1311	-5.9	0.5	3	dbSNP_88	242	4021,4579	597.1+/-393.7	932,2157,1211	no	coding-synonymous	KLHL6	NM_130446.2		2365,2830,1308	GG,GA,AA		46.7558,19.6777,41.873		437/622	183211906	7560,5446	2203	4300	6503	SO:0001819	synonymous_variant	89857	exon5			CTCCACATTGTTG	AF441792	CCDS3245.2	3q27.3	2013-01-30	2013-01-30		ENSG00000172578	ENSG00000172578		"""Kelch-like"", ""BTB/POZ domain containing"""	18653	protein-coding gene	gene with protein product	"""kelch-like protein KLHL6"""	614214	"""kelch-like 6 (Drosophila)"""			11214971, 12617994	Standard	NM_130446		Approved	FLJ00029	uc003flr.3	Q8WZ60	OTTHUMG00000148673	ENST00000341319.3:c.1311T>C	3.37:g.183211906A>G		Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	152	152	1	NM_130446	B2RB31|D3DNS8|Q8N5I1|Q8N892	Silent	SNP	ENST00000341319.3	37	CCDS3245.2																																																																																			A|0.359;G|0.641	0.641	strong		0.443	KLHL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309024.1	NM_130446	
TPCN2	219931	hgsc.bcm.edu	37	11	68840160	68840160	+	Missense_Mutation	SNP	A	A	G	rs3750965	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:68840160A>G	ENST00000294309.3	+	12	1228	c.1127A>G	c.(1126-1128)aAa>aGa	p.K376R	TPCN2_ENST00000542467.1_Missense_Mutation_p.K376R|TPCN2_ENST00000442692.2_Intron	NM_139075.3	NP_620714.2	Q8NHX9	TPC2_HUMAN	two pore segment channel 2	376			K -> R (in dbSNP:rs3750965).		calcium ion transport (GO:0006816)|cellular calcium ion homeostasis (GO:0006874)|ion transmembrane transport (GO:0034220)|membrane depolarization during action potential (GO:0086010)|release of sequestered calcium ion into cytosol (GO:0051209)|smooth muscle contraction (GO:0006939)|transmembrane transport (GO:0055085)	endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)|NAADP-sensitive calcium-release channel activity (GO:0072345)|protein kinase binding (GO:0019901)|voltage-gated calcium channel activity (GO:0005245)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(17)|prostate(2)|skin(1)|urinary_tract(1)	32			STAD - Stomach adenocarcinoma(18;0.0208)|LUAD - Lung adenocarcinoma(13;0.0713)			AGCTCCCACAAACAGGCCATG	0.632													A|||	1456	0.290735	0.2322	0.1945	5008	,	,		15326	0.2063		0.3032	False		,,,				2504	0.5123				p.K376R		Atlas-SNP	.											TPCN2,colon,carcinoma,0,1	TPCN2	63	1	0			c.A1127G						PASS	.	A	ARG/LYS	1078,3322	387.7+/-326.6	133,812,1255	51.0	49.0	50.0	http://www.ncbi.nlm.nih.gov/pubmed?term	1127	2.6	0.0	11	dbSNP_107	50	2710,5878	429.7+/-356.3	408,1894,1992	yes	missense	TPCN2	NM_139075.3	26	541,2706,3247	GG,GA,AA	http://www.ncbi.nlm.nih.gov/pubmed?term	31.5557,24.5,29.1654	benign	376/753	68840160	3788,9200	2200	4294	6494	SO:0001583	missense	219931	exon12			CCCACAAACAGGC	AK023366	CCDS8189.1	11q13.1	2011-07-05			ENSG00000162341	ENSG00000162341		"""Voltage-gated ion channels / Two-pore channels"""	20820	protein-coding gene	gene with protein product		612163				16382101	Standard	NM_139075		Approved	TPC2	uc001oos.2	Q8NHX9	OTTHUMG00000167898	ENST00000294309.3:c.1127A>G	11.37:g.68840160A>G	ENSP00000294309:p.Lys376Arg	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	162	116	0.716049	NM_139075	Q9NT82	Missense_Mutation	SNP	ENST00000294309.3	37	CCDS8189.1	558	0.2554945054945055	104	0.21138211382113822	83	0.2292817679558011	135	0.23601398601398602	236	0.3113456464379947	A	0.628	-0.818239	0.02776	0.245	0.315557	ENSG00000162341	ENST00000294309;ENST00000535009;ENST00000542467	D;D	0.96913	-4.16;-4.17	4.94	2.61	0.31194	.	0.188884	0.44688	N	0.000427	T	0.00039	0.0001	M	0.64997	1.995	0.33812	P	0.37205200000000005	B;B;B	0.33379	0.287;0.287;0.41	B;B;B	0.29524	0.048;0.048;0.103	T	0.00862	-1.1536	9	0.25106	T	0.35	-5.9663	6.5291	0.22316	0.8026:0.0:0.1974:0.0	rs3750965;rs57180849;rs3750965	376;376;291	E7ETX0;Q8NHX9;F5H1G5	.;TPC2_HUMAN;.	R	376;291;376	ENSP00000294309:K376R;ENSP00000445551:K376R	ENSP00000294309:K376R	K	+	2	0	TPCN2	68596736	0.057000	0.20700	0.030000	0.17652	0.117000	0.20001	0.272000	0.18644	0.327000	0.23409	0.459000	0.35465	AAA	A|0.718;G|0.282	0.282	strong		0.632	TPCN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396878.2	NM_139075	
FAM185A	222234	hgsc.bcm.edu	37	7	102389697	102389697	+	Missense_Mutation	SNP	C	C	T	rs141352868	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:102389697C>T	ENST00000413034.2	+	1	43	c.43C>T	c.(43-45)Ctc>Ttc	p.L15F	FAM185A_ENST00000409231.3_Missense_Mutation_p.L15F|FAM185A_ENST00000481697.1_3'UTR	NM_001145268.1	NP_001138740	Q8N0U4	F185A_HUMAN	family with sequence similarity 185, member A	15										kidney(1)	1						CTGCTTCCGTCTCTGTCTCCG	0.667													.|||	391	0.0780751	0.0023	0.0807	5008	,	,		16501	0.0923		0.0815	False		,,,				2504	0.1605				p.L15F		Atlas-SNP	.											.	FAM185A	10	.	0			c.C43T						PASS	.						7.0	11.0	10.0					7																	102389697		686	1583	2269	SO:0001583	missense	222234	exon1			TTCCGTCTCTGTC	BC029175	CCDS47676.1, CCDS47677.1	7q22.1	2009-07-09			ENSG00000222011	ENSG00000222011			22412	protein-coding gene	gene with protein product							Standard	NM_001145268		Approved	MGC35361	uc011klf.2	Q8N0U4	OTTHUMG00000154140	ENST00000413034.2:c.43C>T	7.37:g.102389697C>T	ENSP00000395340:p.Leu15Phe	Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	158	70	0.443038	NM_001145269	A8MUR7|B4DQD3|C9IZ91	Missense_Mutation	SNP	ENST00000413034.2	37	CCDS47676.1	133	0.060897435897435896	2	0.0040650406504065045	29	0.08011049723756906	41	0.07167832167832168	61	0.08047493403693931	C	12.66	2.005235	0.35415	.	.	ENSG00000222011	ENST00000409231;ENST00000418198;ENST00000413034	T;T;T	0.74842	-0.88;-0.88;-0.88	4.01	2.18	0.27775	.	1.424370	0.04976	N	0.464707	T	0.10465	0.0256	L	0.44542	1.39	0.09310	N	1	B;B	0.14012	0.009;0.005	B;B	0.14578	0.011;0.005	T	0.34625	-0.9821	10	0.87932	D	0	4.5167	5.931	0.19138	0.0:0.7537:0.0:0.2463	.	15;15	Q8N0U4-3;Q8N0U4	.;F185A_HUMAN	F	15	ENSP00000387066:L15F;ENSP00000410034:L15F;ENSP00000395340:L15F	ENSP00000387066:L15F	L	+	1	0	FAM185A	102176933	0.001000	0.12720	0.000000	0.03702	0.046000	0.14306	0.401000	0.20948	0.346000	0.23899	0.543000	0.68304	CTC	C|0.937;T|0.063	0.063	strong		0.667	FAM185A-009	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000349482.1	NM_001145268	
OR5P2	120065	hgsc.bcm.edu	37	11	7817959	7817959	+	Silent	SNP	G	G	A	rs73406603	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:7817959G>A	ENST00000329434.2	-	1	561	c.531C>T	c.(529-531)ttC>ttT	p.F177F	RP11-35J10.5_ENST00000527565.1_lincRNA	NM_153444.1	NP_703145.1	Q8WZ92	OR5P2_HUMAN	olfactory receptor, family 5, subfamily P, member 2	177						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(4)	22				Epithelial(150;8.62e-08)|BRCA - Breast invasive adenocarcinoma(625;0.189)		GTAAGGGAGCGAAATCACAGA	0.388													G|||	1185	0.236621	0.3472	0.2911	5008	,	,		20101	0.128		0.2763	False		,,,				2504	0.1196				p.F177F		Atlas-SNP	.											OR5P2,brain,glioma,0,1	OR5P2	68	1	0			c.C531T						scavenged	.	G		1366,2838		399,568,1135	69.0	81.0	77.0		531	3.2	1.0	11	dbSNP_130	77	2424,6160		392,1640,2260	no	coding-synonymous	OR5P2	NM_153444.1		791,2208,3395	AA,AG,GG		28.2386,32.4929,29.6372		177/323	7817959	3790,8998	2102	4292	6394	SO:0001819	synonymous_variant	120065	exon1			GGGAGCGAAATCA	AF173006	CCDS7782.1	11p15.4	2012-08-09			ENSG00000183303	ENSG00000183303		"""GPCR / Class A : Olfactory receptors"""	14783	protein-coding gene	gene with protein product							Standard	NM_153444		Approved	JCG3	uc001mfp.1	Q8WZ92	OTTHUMG00000165668	ENST00000329434.2:c.531C>T	11.37:g.7817959G>A		Somatic	70	1	0.0142857		WXS	Illumina HiSeq	Phase_I	81	69	0.851852	NM_153444	Q3MIS8	Silent	SNP	ENST00000329434.2	37	CCDS7782.1																																																																																			G|0.739;A|0.261	0.261	strong		0.388	OR5P2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385696.1	NM_153444	
NCKAP5L	57701	hgsc.bcm.edu	37	12	50189807	50189807	+	Silent	SNP	C	C	A	rs2720298	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:50189807C>A	ENST00000335999.6	-	8	2037	c.1836G>T	c.(1834-1836)tcG>tcT	p.S612S		NM_001037806.3	NP_001032895.2	Q9HCH0	NCK5L_HUMAN	NCK-associated protein 5-like	608	Pro-rich.									central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(8)|prostate(2)	18						CATAGGGGTACGATTCTGGGA	0.622													C|||	3026	0.604233	0.7277	0.598	5008	,	,		14259	0.6577		0.3638	False		,,,				2504	0.6339				p.S612S		Atlas-SNP	.											.	NCKAP5L	142	.	0			c.G1836T						PASS	.	C		2483,1191		850,783,204	19.0	23.0	22.0		1836	-4.7	0.3	12	dbSNP_100	22	3147,5039		626,1895,1572	no	coding-synonymous	NCKAP5L	NM_001037806.3		1476,2678,1776	AA,AC,CC		38.4437,32.417,47.4705		612/1335	50189807	5630,6230	1837	4093	5930	SO:0001819	synonymous_variant	57701	exon8			GGGGTACGATTCT	AB046822	CCDS41781.2	12q13.12	2009-08-14	2009-08-14	2009-08-14	ENSG00000167566	ENSG00000167566			29321	protein-coding gene	gene with protein product		615104	"""KIAA1602"""	KIAA1602			Standard	NM_001037806		Approved		uc009zlk.2	Q9HCH0	OTTHUMG00000156969	ENST00000335999.6:c.1836G>T	12.37:g.50189807C>A		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	35	20	0.571429	NM_001037806	Q2TB26|Q71RH1|Q8N4W1|Q96HX2	Silent	SNP	ENST00000335999.6	37	CCDS41781.2	1247	0.5709706959706959	369	0.75	207	0.5718232044198895	391	0.6835664335664335	280	0.36939313984168864	C	0.009	-1.815812	0.00595	0.67583	0.384437	ENSG00000167566	ENST00000433948	.	.	.	4.28	-4.74	0.03249	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.58432	P	2.9999999999752447E-6	.	.	.	.	.	.	T	0.37798	-0.9690	3	.	.	.	-9.0909	1.8684	0.03203	0.4356:0.2543:0.1895:0.1206	rs2720298;rs3813527;rs60184917;rs2720298	.	.	.	L	327	.	.	V	-	1	0	NCKAP5L	48476074	0.084000	0.21492	0.283000	0.24790	0.160000	0.22226	-0.757000	0.04772	-0.729000	0.04875	-0.311000	0.09066	GTA	C|0.433;A|0.567	0.567	strong		0.622	NCKAP5L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346884.2	XM_035497	
HLA-DRB1	3123	hgsc.bcm.edu	37	6	32552060	32552060	+	Missense_Mutation	SNP	A	A	T	rs16822820	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:32552060A>T	ENST00000360004.5	-	2	301	c.196T>A	c.(196-198)Tcc>Acc	p.S66T		NM_002124.3	NP_002115.2	Q30167	2B1A_HUMAN	major histocompatibility complex, class II, DR beta 1	66	Beta-1.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)				large_intestine(3)|lung(2)|ovary(1)|prostate(1)|skin(2)|stomach(1)	10						AAGCGCACGGACTCCTCCTGG	0.602										Multiple Myeloma(14;0.17)			A|||	876	0.17492	0.2284	0.1888	5008	,	,		9661	0.0813		0.1938	False		,,,				2504	0.1697				p.S66T		Atlas-SNP	.											.	HLA-DRB1	41	.	0			c.T196A						PASS	.						36.0	35.0	36.0					6																	32552060		2191	4284	6475	SO:0001583	missense	3123	exon2			GCACGGACTCCTC	AJ297583	CCDS47409.1	6p21.3	2013-01-11			ENSG00000196126	ENSG00000196126		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4948	protein-coding gene	gene with protein product		142857		HLA-DR1B			Standard	NM_001243965		Approved		uc011eri.2	P01911	OTTHUMG00000031196	ENST00000360004.5:c.196T>A	6.37:g.32552060A>T	ENSP00000353099:p.Ser66Thr	Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	55	13	0.236364	NM_002124	P01914|Q9MYF5	Missense_Mutation	SNP	ENST00000360004.5	37	CCDS47409.1	.	.	.	.	.	.	.	.	.	.	.	1.398	-0.578994	0.03854	.	.	ENSG00000196126	ENST00000360004	T	0.00249	8.44	3.52	-7.04	0.01578	MHC class II, alpha/beta chain, N-terminal (1);MHC class II, beta chain, N-terminal (2);MHC classes I/II-like antigen recognition protein (1);	3.581920	0.00597	N	0.000377	T	0.00039	0.0001	N	0.13371	0.34	0.80722	P	0.0	B	0.09022	0.002	B	0.10450	0.005	T	0.50074	-0.8870	9	0.49607	T	0.09	.	1.7273	0.02925	0.1198:0.2542:0.2155:0.4106	rs16822820;rs17881836	66	P01911	2B1F_HUMAN	T	66	ENSP00000353099:S66T	ENSP00000353099:S66T	S	-	1	0	HLA-DRB1	32660038	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.680000	0.01939	-5.225000	0.00019	-3.146000	0.00059	TCC	T|0.164;C|0.002;A|0.834	0.164	strong		0.602	HLA-DRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076393.3	NM_002124	
ZNF687	57592	hgsc.bcm.edu	37	1	151259543	151259543	+	Missense_Mutation	SNP	G	G	A	rs3748545	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:151259543G>A	ENST00000368879.2	+	2	874	c.776G>A	c.(775-777)gGg>gAg	p.G259E		NM_020832.1	NP_065883.1	Q8N1G0	ZN687_HUMAN	zinc finger protein 687	259	Pro-rich.		G -> E (in dbSNP:rs3748545).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(3)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(11)|ovary(1)|upper_aerodigestive_tract(2)	32	Lung SC(34;0.00471)|Ovarian(49;0.0147)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.112)|LUSC - Lung squamous cell carcinoma(543;0.181)			CCAGTTGCTGGGGTGCCCTTC	0.627													G|||	545	0.108826	0.1399	0.1441	5008	,	,		18984	0.0615		0.1282	False		,,,				2504	0.0706				p.G259E		Atlas-SNP	.											.	ZNF687	94	.	0			c.G776A						PASS	.	G	GLU/GLY	617,3789	261.0+/-264.0	46,525,1632	62.0	68.0	66.0		776	3.6	0.0	1	dbSNP_107	66	1026,7574	217.3+/-256.0	55,916,3329	yes	missense	ZNF687	NM_020832.1	98	101,1441,4961	AA,AG,GG		11.9302,14.0036,12.6326	benign	259/1238	151259543	1643,11363	2203	4300	6503	SO:0001583	missense	57592	exon2			TTGCTGGGGTGCC		CCDS992.1	1q21.2	2008-05-02			ENSG00000143373	ENSG00000143373			29277	protein-coding gene	gene with protein product		610568				10718198	Standard	NM_020832		Approved	KIAA1441	uc001exq.3	Q8N1G0	OTTHUMG00000012347	ENST00000368879.2:c.776G>A	1.37:g.151259543G>A	ENSP00000357874:p.Gly259Glu	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	77	35	0.454545	NM_020832	D3DV17|Q68DQ8|Q9H937|Q9P2A7	Missense_Mutation	SNP	ENST00000368879.2	37		246	0.11263736263736264	74	0.15040650406504066	47	0.1298342541436464	40	0.06993006993006994	85	0.11213720316622691	G	0.004	-2.282687	0.00251	0.140036	0.119302	ENSG00000143373	ENST00000336715;ENST00000324048;ENST00000368879	T;T;T	0.00730	5.77;5.77;6.11	4.51	3.6	0.41247	.	0.216731	0.23175	N	0.051099	T	0.00271	0.0008	L	0.29908	0.895	0.80722	P	0.0	B;B;B	0.18461	0.028;0.002;0.028	B;B;B	0.25140	0.058;0.005;0.036	T	0.43750	-0.9372	8	.	.	.	.	4.0428	0.09760	0.1928:0.0:0.62:0.1872	rs3748545;rs3748545	259;259;259	Q8N1G0-2;Q8N1G0;F8WCX2	.;ZN687_HUMAN;.	E	259	ENSP00000336620:G259E;ENSP00000319829:G259E;ENSP00000357874:G259E	.	G	+	2	0	ZNF687	149526167	0.479000	0.25925	0.024000	0.17045	0.018000	0.09664	1.272000	0.33109	1.136000	0.42199	0.407000	0.27541	GGG	G|0.880;A|0.120	0.120	strong		0.627	ZNF687-201	KNOWN	basic	protein_coding	protein_coding		NM_020832	
ATP10D	57205	hgsc.bcm.edu	37	4	47560015	47560015	+	Missense_Mutation	SNP	A	A	G	rs34169638	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:47560015A>G	ENST00000273859.3	+	12	2428	c.2159A>G	c.(2158-2160)aAc>aGc	p.N720S	AC092597.3_ENST00000508081.1_RNA	NM_020453.3	NP_065186.3	Q9P241	AT10D_HUMAN	ATPase, class V, type 10D	720			N -> S (in dbSNP:rs34169638).		cation transport (GO:0006812)|ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(2)|endometrium(5)|kidney(5)|large_intestine(14)|liver(2)|lung(26)|ovary(2)|pancreas(1)|prostate(5)|skin(2)|stomach(1)|urinary_tract(1)	66						TTGGCCTGCAACCTGTGTTAT	0.567													A|||	422	0.0842652	0.0038	0.1282	5008	,	,		19215	0.2054		0.0736	False		,,,				2504	0.0481				p.N720S		Atlas-SNP	.											.	ATP10D	168	.	0			c.A2159G						PASS	.	A	SER/ASN	60,4346	58.1+/-94.6	2,56,2145	63.0	57.0	59.0		2159	-6.8	0.0	4	dbSNP_126	59	553,8047	151.0+/-205.8	20,513,3767	yes	missense	ATP10D	NM_020453.3	46	22,569,5912	GG,GA,AA		6.4302,1.3618,4.7132	benign	720/1427	47560015	613,12393	2203	4300	6503	SO:0001583	missense	57205	exon12			CCTGCAACCTGTG	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.2159A>G	4.37:g.47560015A>G	ENSP00000273859:p.Asn720Ser	Somatic	100	1	0.01		WXS	Illumina HiSeq	Phase_I	65	65	1	NM_020453	A2RRC8|D6REN2|Q8NC70|Q96SR3	Missense_Mutation	SNP	ENST00000273859.3	37	CCDS3476.1	198	0.09065934065934066	2	0.0040650406504065045	35	0.09668508287292818	108	0.1888111888111888	53	0.06992084432717678	A	9.922	1.212541	0.22289	0.013618	0.064302	ENSG00000145246	ENST00000273859	T	0.38240	1.15	5.24	-6.8	0.01709	HAD-like domain (1);	1.162770	0.06021	N	0.651321	T	0.00039	0.0001	N	0.04116	-0.275	0.80722	P	0.0	B	0.06786	0.001	B	0.09377	0.004	T	0.25745	-1.0123	9	0.21014	T	0.42	0.4261	7.0818	0.25235	0.4828:0.2037:0.3135:0.0	rs34169638	720	Q9P241	AT10D_HUMAN	S	720	ENSP00000273859:N720S	ENSP00000273859:N720S	N	+	2	0	ATP10D	47254772	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.308000	0.08156	-1.487000	0.01849	-0.441000	0.05720	AAC	A|0.940;G|0.060	0.060	strong		0.567	ATP10D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216900.1	NM_020453	
CLEC16A	23274	hgsc.bcm.edu	37	16	11272482	11272482	+	Missense_Mutation	SNP	G	G	A	rs72650691	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:11272482G>A	ENST00000409790.1	+	24	3327	c.3097G>A	c.(3097-3099)Gcc>Acc	p.A1033T	CLEC16A_ENST00000381822.2_Missense_Mutation_p.A120T	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						GCCGGCTGCCGCCTGCACAGA	0.687													G|||	4	0.000798722	0.0008	0.0029	5008	,	,		15009	0.0		0.001	False		,,,				2504	0.0				p.A1033T		Atlas-SNP	.											CLEC16A,NS,carcinoma,-1,1	CLEC16A	101	1	1	Whole gene deletion(1)	haematopoietic_and_lymphoid_tissue(1)	c.G3097A						PASS	.	G	THR/ALA	2,4080		0,2,2039	10.0	13.0	12.0		3097	1.3	0.0	16	dbSNP_130	12	20,8320		0,20,4150	yes	missense	CLEC16A	NM_015226.2	58	0,22,6189	AA,AG,GG		0.2398,0.049,0.1771	benign	1033/1054	11272482	22,12400	2041	4170	6211	SO:0001583	missense	23274	exon23			GCTGCCGCCTGCA	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.3097G>A	16.37:g.11272482G>A	ENSP00000387122:p.Ala1033Thr	Somatic	12	0	0		WXS	Illumina HiSeq	Phase_I	13	13	1	NM_015226		Missense_Mutation	SNP	ENST00000409790.1	37	CCDS45409.1	.	.	.	.	.	.	.	.	.	.	G	8.999	0.979594	0.18812	4.9E-4	0.002398	ENSG00000038532	ENST00000409790;ENST00000542102;ENST00000381822	T	0.44482	0.92	4.4	1.28	0.21552	.	1.314290	0.04911	N	0.453315	T	0.23846	0.0577	N	0.08118	0	0.09310	N	1	B;B	0.20261	0.043;0.0	B;B	0.10450	0.005;0.0	T	0.19910	-1.0291	10	0.23302	T	0.38	-0.2189	8.3364	0.32217	0.2744:0.0:0.7256:0.0	.	120;1033	Q2KHT3-3;Q2KHT3	.;CL16A_HUMAN	T	1033;1033;120	ENSP00000387122:A1033T	ENSP00000371244:A120T	A	+	1	0	CLEC16A	11179983	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.320000	0.19540	0.440000	0.26502	-0.794000	0.03295	GCC	.	.	weak		0.687	CLEC16A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328540.2	NM_015226	
NDRG4	65009	hgsc.bcm.edu	37	16	58540875	58540875	+	Silent	SNP	G	G	A	rs17821543	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:58540875G>A	ENST00000570248.1	+	8	682	c.576G>A	c.(574-576)gtG>gtA	p.V192V	NDRG4_ENST00000568640.1_Silent_p.V210V|NDRG4_ENST00000394282.4_Silent_p.V244V|NDRG4_ENST00000566192.1_Silent_p.V192V|NDRG4_ENST00000356752.4_Silent_p.V222V|NDRG4_ENST00000394279.2_Silent_p.V224V|NDRG4_ENST00000569923.1_Silent_p.V137V|NDRG4_ENST00000563799.1_Silent_p.V210V|NDRG4_ENST00000562999.1_Silent_p.V192V|NDRG4_ENST00000258187.5_Silent_p.V224V	NM_001242835.1	NP_001229764.1	Q9ULP0	NDRG4_HUMAN	NDRG family member 4	192					cell differentiation (GO:0030154)|cell growth (GO:0016049)|response to stress (GO:0006950)	cytoplasm (GO:0005737)				breast(1)|endometrium(3)|large_intestine(1)|lung(3)|ovary(1)|skin(1)|urinary_tract(1)	11						TTGGGAACGTGGTGAACCAGG	0.612													G|||	187	0.0373403	0.0038	0.0288	5008	,	,		17683	0.0		0.0865	False		,,,				2504	0.0767				p.V244V		Atlas-SNP	.											.	NDRG4	29	.	0			c.G732A						PASS	.	G	,,,,,,	79,4317	67.6+/-105.2	2,75,2121	108.0	86.0	94.0		732,666,630,576,576,672,672	3.2	1.0	16	dbSNP_123	94	612,7988	159.8+/-213.0	28,556,3716	yes	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NDRG4	NM_001130487.1,NM_001242833.1,NM_001242834.1,NM_001242835.1,NM_001242836.1,NM_020465.3,NM_022910.3	,,,,,,	30,631,5837	AA,AG,GG		7.1163,1.7971,5.317	,,,,,,	244/392,222/370,210/358,192/353,192/340,224/372,224/372	58540875	691,12305	2198	4300	6498	SO:0001819	synonymous_variant	65009	exon10			GAACGTGGTGAAC	AB044947	CCDS10797.1, CCDS45500.1, CCDS55999.1, CCDS58465.1, CCDS58466.1, CCDS58467.1	16q21-q22.3	2008-07-04			ENSG00000103034	ENSG00000103034			14466	protein-coding gene	gene with protein product		614463				11352569, 16408304	Standard	NM_020465		Approved	KIAA1180, SMAP-8	uc002enk.3	Q9ULP0	OTTHUMG00000133485	ENST00000570248.1:c.576G>A	16.37:g.58540875G>A		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	61	45	0.737705	NM_001130487	B3KNU2|B4DK66|B4DSW5|H7C600|Q6ZNE7|Q6ZTI7|Q96PL9|Q9GZM1|Q9GZN3|Q9GZX0	Silent	SNP	ENST00000570248.1	37	CCDS58466.1																																																																																			G|0.951;A|0.049	0.049	strong		0.612	NDRG4-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000422671.2		
OR5P2	120065	hgsc.bcm.edu	37	11	7818151	7818151	+	Silent	SNP	G	G	A	rs73406606	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:7818151G>A	ENST00000329434.2	-	1	369	c.339C>T	c.(337-339)gcC>gcT	p.A113A	RP11-35J10.5_ENST00000527565.1_lincRNA	NM_153444.1	NP_703145.1	Q8WZ92	OR5P2_HUMAN	olfactory receptor, family 5, subfamily P, member 2	113						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(4)	22				Epithelial(150;8.62e-08)|BRCA - Breast invasive adenocarcinoma(625;0.189)		CATAGGCCATGGCAGCCAGAA	0.478													G|||	1185	0.236621	0.348	0.2911	5008	,	,		18204	0.128		0.2763	False		,,,				2504	0.1186				p.A113A		Atlas-SNP	.											OR5P2,brain,glioma,0,1	OR5P2	68	1	0			c.C339T						PASS	.	G		1371,2837		401,569,1134	89.0	103.0	99.0		339	2.4	1.0	11	dbSNP_130	99	2425,6159		393,1639,2260	no	coding-synonymous	OR5P2	NM_153444.1		794,2208,3394	AA,AG,GG		28.2502,32.5808,29.6748		113/323	7818151	3796,8996	2104	4292	6396	SO:0001819	synonymous_variant	120065	exon1			GGCCATGGCAGCC	AF173006	CCDS7782.1	11p15.4	2012-08-09			ENSG00000183303	ENSG00000183303		"""GPCR / Class A : Olfactory receptors"""	14783	protein-coding gene	gene with protein product							Standard	NM_153444		Approved	JCG3	uc001mfp.1	Q8WZ92	OTTHUMG00000165668	ENST00000329434.2:c.339C>T	11.37:g.7818151G>A		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	71	59	0.830986	NM_153444	Q3MIS8	Silent	SNP	ENST00000329434.2	37	CCDS7782.1																																																																																			G|0.739;A|0.261	0.261	strong		0.478	OR5P2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385696.1	NM_153444	
OR8H1	219469	hgsc.bcm.edu	37	11	56058197	56058197	+	Silent	SNP	G	G	A	rs1842674	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:56058197G>A	ENST00000313022.2	-	1	369	c.342C>T	c.(340-342)ctC>ctT	p.L114L		NM_001005199.1	NP_001005199.1	Q8NGG4	OR8H1_HUMAN	olfactory receptor, family 8, subfamily H, member 1	114						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(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(18)|ovary(1)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	43	Esophageal squamous(21;0.00448)					CCATTGATGAGAGAAGAAAAC	0.458													g|||	2150	0.429313	0.1861	0.5072	5008	,	,		21350	0.6151		0.3708	False		,,,				2504	0.5716				p.L114L		Atlas-SNP	.											OR8H1,NS,carcinoma,-1,1	OR8H1	89	1	0			c.C342T						PASS	.	G		942,3460	359.4+/-314.8	104,734,1363	162.0	158.0	160.0		342	-2.2	0.2	11	dbSNP_92	160	3194,5398	483.8+/-371.2	611,1972,1713	no	coding-synonymous	OR8H1	NM_001005199.1		715,2706,3076	AA,AG,GG		37.1741,21.3994,31.8301		114/312	56058197	4136,8858	2201	4296	6497	SO:0001819	synonymous_variant	219469	exon1			TGATGAGAGAAGA	AB065836	CCDS31526.1	11q11	2012-08-09			ENSG00000181693	ENSG00000181693		"""GPCR / Class A : Olfactory receptors"""	14824	protein-coding gene	gene with protein product							Standard	NM_001005199		Approved		uc010rje.2	Q8NGG4	OTTHUMG00000162671	ENST00000313022.2:c.342C>T	11.37:g.56058197G>A		Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	152	38	0.25	NM_001005199	B2RNI7|Q6IFC5	Silent	SNP	ENST00000313022.2	37	CCDS31526.1																																																																																			G|0.650;A|0.350	0.350	strong		0.458	OR8H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370019.1	NM_001005199	
HFE	3077	hgsc.bcm.edu	37	6	26091179	26091179	+	Missense_Mutation	SNP	C	C	G	rs1799945	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:26091179C>G	ENST00000357618.5	+	2	309	c.187C>G	c.(187-189)Cat>Gat	p.H63D	HFE_ENST00000488199.1_Intron|HFE_ENST00000353147.5_Intron|HFE_ENST00000461397.1_Missense_Mutation_p.H63D|HFE_ENST00000317896.7_Missense_Mutation_p.H63D|HFE_ENST00000336625.8_Missense_Mutation_p.H63D|HFE_ENST00000352392.4_Intron|HFE_ENST00000397022.3_Missense_Mutation_p.H40D|HFE_ENST00000309234.6_Missense_Mutation_p.H63D|HFE_ENST00000470149.1_Missense_Mutation_p.H63D|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	201	0	0		WXS	Illumina HiSeq	Phase_I	202	93	0.460396	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		
TTC16	158248	hgsc.bcm.edu	37	9	130493513	130493513	+	Silent	SNP	A	A	G	rs482095	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:130493513A>G	ENST00000373289.3	+	14	2531	c.2451A>G	c.(2449-2451)aaA>aaG	p.K817K	TTC16_ENST00000489226.1_3'UTR|TOR2A_ENST00000472723.1_5'Flank	NM_144965.1	NP_659402.1	Q8NEE8	TTC16_HUMAN	tetratricopeptide repeat domain 16	817										central_nervous_system(2)|endometrium(3)|lung(7)|ovary(3)|pancreas(2)|prostate(4)|skin(1)	22						GCCTCAGCAAAACTGAGTATG	0.597													G|||	3106	0.620208	0.7859	0.6081	5008	,	,		20572	0.369		0.6173	False		,,,				2504	0.6667				p.K817K		Atlas-SNP	.											.	TTC16	55	.	0			c.A2451G						PASS	.	G		3267,1137	395.4+/-329.6	1217,833,152	40.0	43.0	42.0		2451	-9.1	0.0	9	dbSNP_83	42	5015,3585	515.0+/-378.5	1463,2089,748	no	coding-synonymous	TTC16	NM_144965.1		2680,2922,900	GG,GA,AA		41.686,25.8174,36.3119		817/874	130493513	8282,4722	2202	4300	6502	SO:0001819	synonymous_variant	158248	exon14			CAGCAAAACTGAG	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.2451A>G	9.37:g.130493513A>G		Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	178	72	0.404494	NM_144965	B4DYG4|B5ME24|Q5JU66|Q96M72	Silent	SNP	ENST00000373289.3	37	CCDS6875.1																																																																																			A|0.372;G|0.628	0.628	strong		0.597	TTC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054224.1	NM_144965	
AHNAK2	113146	hgsc.bcm.edu	37	14	105415469	105415469	+	Missense_Mutation	SNP	T	T	C	rs11846918	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:105415469T>C	ENST00000333244.5	-	7	6438	c.6319A>G	c.(6319-6321)Atg>Gtg	p.M2107V	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	2107			M -> V (in dbSNP:rs11846918).			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)			GGGACTCTCATTTCCACCTTG	0.597													.|||	2244	0.448083	0.6369	0.4323	5008	,	,		14687	0.374		0.2724	False		,,,				2504	0.4611				p.M2107V		Atlas-SNP	.											.	AHNAK2	719	.	0			c.A6319G						PASS	.	C	VAL/MET	2269,1485		794,681,402	138.0	94.0	111.0		6319	-2.2	0.0	14	dbSNP_120	111	720,5004		240,240,2382	yes	missense	AHNAK2	NM_138420.2	21	1034,921,2784	CC,CT,TT		12.5786,39.5578,31.5362	benign	2107/5796	105415469	2989,6489	1877	2862	4739	SO:0001583	missense	113146	exon7			CTCTCATTTCCAC	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.6319A>G	14.37:g.105415469T>C	ENSP00000353114:p.Met2107Val	Somatic	0	0	.		WXS	Illumina HiSeq	Phase_I	116	116	1	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	935	0.4281135531135531	323	0.6565040650406504	180	0.4972375690607735	201	0.3513986013986014	231	0.30474934036939316	N	0.013	-1.627804	0.00813	0.604422	0.125786	ENSG00000185567	ENST00000333244	T	0.01119	5.31	3.75	-2.21	0.06973	.	.	.	.	.	T	0.00012	0.0000	N	0.00119	-2.075	0.80722	P	0.0	B	0.06786	0.001	B	0.01281	0.0	T	0.19647	-1.0299	8	0.02654	T	1	.	5.9469	0.19223	0.0:0.3584:0.3864:0.2551	rs11846918	2107	Q8IVF2	AHNK2_HUMAN	V	2107	ENSP00000353114:M2107V	ENSP00000353114:M2107V	M	-	1	0	AHNAK2	104486514	0.000000	0.05858	0.000000	0.03702	0.062000	0.15995	-3.969000	0.00323	-1.017000	0.03367	-0.665000	0.03846	ATG	T|0.581;C|0.419	0.419	strong		0.597	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
CLEC18A	348174	hgsc.bcm.edu	37	16	69985383	69985383	+	Silent	SNP	G	G	A	rs4985466		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:69985383G>A	ENST00000288040.6	+	1	301	c.114G>A	c.(112-114)ccG>ccA	p.P38P	CLEC18A_ENST00000393701.2_Silent_p.P38P|CLEC18A_ENST00000449317.2_Silent_p.P38P|CLEC18A_ENST00000568461.1_Silent_p.P38P	NM_001136214.2	NP_001129686.1	A5D8T8	CL18A_HUMAN	C-type lectin domain family 18, member A	38						extracellular region (GO:0005576)	carbohydrate binding (GO:0030246)			NS(1)|endometrium(2)|lung(1)|skin(1)	5						AGCAGGCTCCGATGGCCGGAG	0.667																																					p.P38P		Atlas-SNP	.											CLEC18A,NS,carcinoma,0,1	CLEC18A	9	1	0			c.G114A						scavenged	.						49.0	50.0	50.0					16																	69985383		1509	3170	4679	SO:0001819	synonymous_variant	348174	exon2			GGCTCCGATGGCC	AF428259	CCDS10886.1	16q22.1	2010-04-27	2009-03-10	2009-03-10		ENSG00000157322		"""C-type lectin domain containing"""	30388	protein-coding gene	gene with protein product	"""mannose receptor-like"""					12975309	Standard	NM_001136214		Approved	MRCL	uc010vlo.3	A5D8T8		ENST00000288040.6:c.114G>A	16.37:g.69985383G>A		Somatic	300	2	0.00666667		WXS	Illumina HiSeq	Phase_I	379	124	0.327177	NM_001271197	A8K1G9|Q6DCB3|Q7Z5K9|Q96HH2	Silent	SNP	ENST00000288040.6	37	CCDS10886.1																																																																																			G|0.500;A|0.500	0.500	weak		0.667	CLEC18A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000268955.2	NM_182619	
HELZ2	85441	hgsc.bcm.edu	37	20	62194238	62194238	+	Silent	SNP	C	C	T	rs34996572	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:62194238C>T	ENST00000467148.1	-	8	6006	c.5937G>A	c.(5935-5937)ccG>ccA	p.P1979P	HELZ2_ENST00000427522.2_Silent_p.P1410P	NM_001037335.2	NP_001032412.2	Q9BYK8	HELZ2_HUMAN	helicase with zinc finger 2, transcriptional coactivator	1979					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)										GCTGCCCCTGCGGCGTCCGTG	0.657													C|||	71	0.0141773	0.0008	0.0303	5008	,	,		15702	0.001		0.0408	False		,,,				2504	0.0072				p.P1979P		Atlas-SNP	.											.	.	.	.	0			c.G5937A						PASS	.	C	,	23,4271		0,23,2124	10.0	11.0	11.0		5937,4230	-9.2	0.0	20	dbSNP_126	11	243,8151		3,237,3957	no	coding-synonymous,coding-synonymous	PRIC285	NM_001037335.2,NM_033405.3	,	3,260,6081	TT,TC,CC		2.8949,0.5356,2.0965	,	1979/2650,1410/2081	62194238	266,12422	2147	4197	6344	SO:0001819	synonymous_variant	85441	exon9			CCCCTGCGGCGTC	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.5937G>A	20.37:g.62194238C>T		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	99	38	0.383838	NM_001037335	Q3C2G2|Q4VXQ1|Q8TEF3|Q96ND3|Q9C094	Silent	SNP	ENST00000467148.1	37	CCDS33508.1																																																																																			C|0.984;T|0.016	0.016	strong		0.657	HELZ2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354127.1	NM_001037335	
MAGI1	9223	hgsc.bcm.edu	37	3	65464386	65464386	+	Missense_Mutation	SNP	C	C	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:65464386C>G	ENST00000497477.2	-	4	637	c.638G>C	c.(637-639)gGc>gCc	p.G213A	MAGI1_ENST00000483466.1_Missense_Mutation_p.G213A|MAGI1_ENST00000402939.2_Missense_Mutation_p.G213A|MAGI1_ENST00000330909.8_Missense_Mutation_p.G213A|MAGI1_ENST00000470990.1_5'UTR			Q96QZ7	MAGI1_HUMAN	membrane associated guanylate kinase, WW and PDZ domain containing 1	213	Guanylate kinase-like. {ECO:0000255|PROSITE-ProRule:PRU00100}.				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)		CTGCTTAGAGCCAGACTGAAG	0.527																																					p.G213A		Atlas-SNP	.											.	MAGI1	481	.	0			c.G638C						PASS	.						165.0	143.0	151.0					3																	65464386		2203	4300	6503	SO:0001583	missense	9223	exon4			TTAGAGCCAGACT	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.638G>C	3.37:g.65464386C>G	ENSP00000424369:p.Gly213Ala	Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	146	38	0.260274	NM_001033057	A8K188|O00309|O43863|O75085|Q96QZ8|Q96QZ9	Missense_Mutation	SNP	ENST00000497477.2	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	10.85|10.85	1.467724|1.467724	0.26335|0.26335	.|.	.|.	ENSG00000151276|ENSG00000151276	ENST00000460329|ENST00000402939;ENST00000330909;ENST00000422949;ENST00000463103;ENST00000483466;ENST00000497477	.|T;T;T;T;T	.|0.42900	.|0.96;0.96;2.35;0.96;0.96	5.89|5.89	5.89|5.89	0.94794|0.94794	.|Guanylate kinase/L-type calcium channel (1);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.52613|0.52613	0.1745|0.1745	L|L	0.35854|0.35854	1.095|1.095	0.80722|0.80722	D|D	1|1	.|P;P;P;P;P;P	.|0.52692	.|0.944;0.907;0.955;0.893;0.951;0.656	.|P;B;P;B;D;P	.|0.63113	.|0.599;0.395;0.725;0.303;0.911;0.465	T|T	0.25257|0.25257	-1.0137|-1.0137	5|10	.|0.11485	.|T	.|0.65	-22.988|-22.988	20.2576|20.2576	0.98430|0.98430	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|213;213;213;213;213;213	.|Q96QZ7-6;Q96QZ7;Q96QZ7-4;Q96QZ7-3;Q96QZ7-2;Q96QZ7-5	.|.;MAGI1_HUMAN;.;.;.;.	P|A	94|213;213;109;88;213;213	.|ENSP00000385450:G213A;ENSP00000331157:G213A;ENSP00000418177:G88A;ENSP00000420323:G213A;ENSP00000424369:G213A	.|ENSP00000331157:G213A	A|G	-|-	1|2	0|0	MAGI1|MAGI1	65439426|65439426	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	5.770000|5.770000	0.68873|0.68873	2.783000|2.783000	0.95769|0.95769	0.655000|0.655000	0.94253|0.94253	GCT|GGC	.	.	none		0.527	MAGI1-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000349132.2	NM_004742	
DGKH	160851	hgsc.bcm.edu	37	13	42803315	42803315	+	Silent	SNP	G	G	A	rs376522940		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:42803315G>A	ENST00000337343.4	+	30	3675	c.3654G>A	c.(3652-3654)tcG>tcA	p.S1218S	DGKH_ENST00000379274.2_Silent_p.S1098S|DGKH_ENST00000538674.1_3'UTR|DGKH_ENST00000536612.1_Silent_p.S1082S|DGKH_ENST00000261491.5_3'UTR|DGKH_ENST00000498255.2_3'UTR	NM_178009.3	NP_821077.1	Q86XP1	DGKH_HUMAN	diacylglycerol kinase, eta	1218					blood coagulation (GO:0007596)|intracellular signal transduction (GO:0035556)|platelet activation (GO:0030168)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|protein oligomerization (GO:0051259)	cytoplasm (GO:0005737)|endosome (GO:0005768)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|diacylglycerol kinase activity (GO:0004143)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)			breast(2)|endometrium(3)|kidney(5)|large_intestine(11)|lung(9)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	43		Lung NSC(96;1.02e-05)|Prostate(109;0.0168)|Lung SC(185;0.0262)|Breast(139;0.0709)|Hepatocellular(98;0.114)		OV - Ovarian serous cystadenocarcinoma(117;5.88e-05)|GBM - Glioblastoma multiforme(144;0.000935)|BRCA - Breast invasive adenocarcinoma(63;0.109)		CTCCACAGTCGGAGGTGTAAT	0.413																																					p.S1218S		Atlas-SNP	.											.	DGKH	106	.	0			c.G3654A						PASS	.	G	,,,,	1,4405	2.1+/-5.4	0,1,2202	76.0	77.0	77.0		,3294,3246,,3654	-4.6	0.0	13		77	0,8600		0,0,4300	no	utr-3,coding-synonymous,coding-synonymous,utr-3,coding-synonymous	DGKH	NM_001204504.1,NM_001204505.1,NM_001204506.1,NM_152910.4,NM_178009.3	,,,,	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	,,,,	,1098/1101,1082/1085,,1218/1221	42803315	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	160851	exon30			ACAGTCGGAGGTG	AB078967	CCDS9381.1, CCDS9382.1, CCDS55898.1	13q13.3	2013-01-10			ENSG00000102780	ENSG00000102780		"""Sterile alpha motif (SAM) domain containing"", ""Pleckstrin homology (PH) domain containing"""	2854	protein-coding gene	gene with protein product		604071				8702685	Standard	XM_005266271		Approved	DGKeta	uc001uyl.2	Q86XP1	OTTHUMG00000016804	ENST00000337343.4:c.3654G>A	13.37:g.42803315G>A		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	67	10	0.149254	NM_178009	A2A2W7|A6NFX7|B4DZ34|Q5VZW0|Q6PI56|Q86XP2|Q8N3N0|Q8N7J9	Silent	SNP	ENST00000337343.4	37	CCDS9381.1																																																																																			.	.	weak		0.413	DGKH-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044699.2	NM_178009	
OR10H2	26538	hgsc.bcm.edu	37	19	15839174	15839174	+	Silent	SNP	C	C	T	rs2285956	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:15839174C>T	ENST00000305899.3	+	1	341	c.321C>T	c.(319-321)ttC>ttT	p.F107F		NM_013939.2	NP_039227.1	O60403	O10H2_HUMAN	olfactory receptor, family 10, subfamily H, member 2	107						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(2)|skin(3)|stomach(1)	27	all_hematologic(1;0.0517)|Acute lymphoblastic leukemia(2;0.074)					CCTTCAGCTTCGGCTTCACCC	0.642																																					p.F107F		Atlas-SNP	.											.	OR10H2	59	.	0			c.C321T						PASS	.						60.0	56.0	58.0					19																	15839174		2202	4277	6479	SO:0001819	synonymous_variant	26538	exon1			CAGCTTCGGCTTC	AC004597	CCDS12333.1	19p13.1	2012-08-09				ENSG00000171942		"""GPCR / Class A : Olfactory receptors"""	8173	protein-coding gene	gene with protein product							Standard	NM_013939		Approved		uc002nbm.2	O60403		ENST00000305899.3:c.321C>T	19.37:g.15839174C>T		Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	194	66	0.340206	NM_013939	Q6IFQ1|Q96R58	Silent	SNP	ENST00000305899.3	37	CCDS12333.1																																																																																			T|1.000;|0.000	1.000	weak		0.642	OR10H2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460917.1		
BRMS1	25855	hgsc.bcm.edu	37	11	66105194	66105194	+	3'UTR	SNP	G	G	A	rs1052566	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:66105194G>A	ENST00000359957.3	-	0	1060				RP11-867G23.12_ENST00000526655.1_RNA|RIN1_ENST00000424433.2_5'Flank|RIN1_ENST00000530056.1_5'Flank|BRMS1_ENST00000425825.2_Missense_Mutation_p.A273V|RIN1_ENST00000311320.4_5'Flank	NM_015399.3	NP_056214.1	Q9HCU9	BRMS1_HUMAN	breast cancer metastasis suppressor 1						apoptotic process (GO:0006915)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of anoikis (GO:2000210)|positive regulation of protein deacetylation (GO:0090312)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	NF-kappaB binding (GO:0051059)			large_intestine(1)|liver(1)|lung(1)|prostate(1)|skin(1)	5						AGGAGTCCAGGCCAGTGCCAG	0.682													G|||	1336	0.266773	0.034	0.2161	5008	,	,		17840	0.3284		0.2714	False		,,,				2504	0.5491				p.A273V	GBM(7;55 307 2662 20856 28942)	Atlas-SNP	.											.	BRMS1	42	.	0			c.C818T						PASS	.	G	,VAL/ALA	356,4040		20,316,1862	22.0	28.0	26.0		,818	-4.2	0.0	11	dbSNP_86	26	2563,6027		379,1805,2111	yes	utr-3,missense	BRMS1	NM_015399.3,NM_001024957.1	,64	399,2121,3973	AA,AG,GG		29.837,8.0983,22.4781	,benign	,273/291	66105194	2919,10067	2198	4295	6493	SO:0001624	3_prime_UTR_variant	25855	exon10			GTCCAGGCCAGTG	AF147350	CCDS8135.1, CCDS44654.1	11q13-q13.2	2008-02-05				ENSG00000174744			17262	protein-coding gene	gene with protein product		606259				10850410	Standard	XM_005273883		Approved	DKFZP564A063	uc001oho.1	Q9HCU9		ENST00000359957.3:c.*159C>T	11.37:g.66105194G>A		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	43	8	0.186047	NM_001024957	Q6IAI2	Missense_Mutation	SNP	ENST00000359957.3	37	CCDS8135.1	508	0.2326007326007326	20	0.04065040650406504	88	0.2430939226519337	188	0.32867132867132864	212	0.2796833773087071	G	1.743	-0.491122	0.04322	0.080983	0.29837	ENSG00000174744	ENST00000425825	.	.	.	2.79	-4.24	0.03777	.	.	.	.	.	T	0.00012	0.0000	N	0.00926	-1.1	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.44802	-0.9304	7	0.29301	T	0.29	.	4.6989	0.12818	0.4247:0.1659:0.4094:0.0	rs1052566;rs3178148;rs3192977	273	G5E9I4	.	V	273	.	ENSP00000396052:A273V	A	-	2	0	BRMS1	65861770	0.001000	0.12720	0.000000	0.03702	0.317000	0.28152	-0.952000	0.03881	-0.973000	0.03555	0.400000	0.26472	GCC	G|0.765;A|0.235	0.235	strong		0.682	BRMS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392958.2	NM_015399	
DLX3	1747	hgsc.bcm.edu	37	17	48072225	48072225	+	Silent	SNP	G	G	A	rs33937843	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:48072225G>A	ENST00000434704.2	-	1	363	c.138C>T	c.(136-138)ccC>ccT	p.P46P	DLX3_ENST00000512495.2_5'Flank|RP11-1094H24.3_ENST00000511867.1_lincRNA	NM_005220.2	NP_005211.1	O60479	DLX3_HUMAN	distal-less homeobox 3	46					blood vessel development (GO:0001568)|odontoblast differentiation (GO:0071895)|odontogenesis of dentin-containing tooth (GO:0042475)|placenta development (GO:0001890)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	12						AATCGTGCTGGGGAGCGCTGT	0.602													G|||	769	0.153554	0.1861	0.0937	5008	,	,		17090	0.2024		0.0388	False		,,,				2504	0.2198				p.P46P		Atlas-SNP	.											.	DLX3	28	.	0			c.C138T						PASS	.	G		692,3714	293.3+/-282.5	62,568,1573	108.0	106.0	107.0		138	-3.3	0.9	17	dbSNP_126	107	337,8263	115.7+/-175.5	4,329,3967	no	coding-synonymous	DLX3	NM_005220.2		66,897,5540	AA,AG,GG		3.9186,15.7059,7.9117		46/288	48072225	1029,11977	2203	4300	6503	SO:0001819	synonymous_variant	1747	exon1			GTGCTGGGGAGCG		CCDS11556.1	17q21.33	2011-06-20	2005-12-22			ENSG00000064195		"""Homeoboxes / ANTP class : NKL subclass"""	2916	protein-coding gene	gene with protein product		600525	"""distal-less homeo box 3"""			7613049	Standard	NM_005220		Approved		uc002ipy.3	O60479		ENST00000434704.2:c.138C>T	17.37:g.48072225G>A		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	122	70	0.57377	NM_005220	B3KQL6	Silent	SNP	ENST00000434704.2	37	CCDS11556.1																																																																																			G|0.912;A|0.088	0.088	strong		0.602	DLX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366307.1		
MUC4	4585	hgsc.bcm.edu	37	3	195509651	195509651	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195509651G>A	ENST00000463781.3	-	2	9259	c.8800C>T	c.(8800-8802)Ctt>Ttt	p.L2934F	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.L2934F	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.L2934F(1)|p.P2934S(1)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		ACTGAGGAAAGGCTGGTGACA	0.577																																					p.L2934F		Atlas-SNP	.											MUC4_ENST00000463781,trunk,malignant_melanoma,0,2	MUC4	1505	2	2	Substitution - Missense(2)	skin(2)	c.C8800T						scavenged	.						9.0	8.0	8.0					3																	195509651		662	1509	2171	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.8800C>T	3.37:g.195509651G>A	ENSP00000417498:p.Leu2934Phe	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	117	39	0.333333	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	11.55	1.670874	0.29693	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.35236	1.36;1.32	.	.	.	.	.	.	.	.	T	0.26774	0.0655	N	0.14661	0.345	0.09310	N	1	D	0.57257	0.979	P	0.54026	0.74	T	0.11690	-1.0577	7	.	.	.	.	3.7959	0.08738	0.0:0.0:0.5797:0.4203	.	2806	E7ESK3	.	F	2934	ENSP00000417498:L2934F;ENSP00000420243:L2934F	.	L	-	1	0	MUC4	196994430	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.715000	0.00385	-0.000000	0.14550	0.000000	0.15137	CTT	.	.	none		0.577	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
MYLK2	85366	hgsc.bcm.edu	37	20	30414621	30414621	+	Silent	SNP	C	C	T	rs6089088	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:30414621C>T	ENST00000375994.2	+	7	1377	c.1104C>T	c.(1102-1104)ttC>ttT	p.F368F	MYLK2_ENST00000468730.1_3'UTR|MYLK2_ENST00000375985.4_Silent_p.F368F			Q9H1R3	MYLK2_HUMAN	myosin light chain kinase 2	368	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cardiac muscle contraction (GO:0060048)|cardiac muscle tissue morphogenesis (GO:0055008)|neuromuscular synaptic transmission (GO:0007274)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of gene expression (GO:0010628)|protein autophosphorylation (GO:0046777)|regulation of muscle filament sliding (GO:0032971)|skeletal muscle cell differentiation (GO:0035914)|skeletal muscle satellite cell differentiation (GO:0014816)|striated muscle contraction (GO:0006941)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|sarcomere (GO:0030017)	ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|calmodulin-dependent protein kinase activity (GO:0004683)|myosin light chain kinase activity (GO:0004687)			NS(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(17)|ovary(1)|pancreas(1)|prostate(1)|skin(2)	33			Colorectal(19;0.00306)|COAD - Colon adenocarcinoma(19;0.0347)			GAGAGCTCTTCGAGAGGATTG	0.592													C|||	41	0.0081869	0.0008	0.013	5008	,	,		19225	0.0		0.0209	False		,,,				2504	0.0102				p.F368F		Atlas-SNP	.											.	MYLK2	76	.	0			c.C1104T						PASS	.	C		25,4381	32.6+/-62.9	0,25,2178	124.0	99.0	108.0		1104	1.4	1.0	20	dbSNP_114	108	186,8414	84.0+/-146.5	0,186,4114	no	coding-synonymous	MYLK2	NM_033118.3		0,211,6292	TT,TC,CC		2.1628,0.5674,1.6223		368/597	30414621	211,12795	2203	4300	6503	SO:0001819	synonymous_variant	85366	exon8			GCTCTTCGAGAGG	AF325549	CCDS13191.1	20q13.31	2014-09-17	2008-01-23		ENSG00000101306	ENSG00000101306	2.7.11.18		16243	protein-coding gene	gene with protein product	"""skeletal muscle myosin light chain kinase"""	606566	"""myosin light chain kinase 2, skeletal muscle"""				Standard	NM_033118		Approved	skMLCK, KMLC, MLCK2	uc002wwq.2	Q9H1R3	OTTHUMG00000032194	ENST00000375994.2:c.1104C>T	20.37:g.30414621C>T		Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	159	75	0.471698	NM_033118	Q569L1|Q96I84	Silent	SNP	ENST00000375994.2	37	CCDS13191.1																																																																																			C|0.986;T|0.014	0.014	strong		0.592	MYLK2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078583.2	NM_033118	
PTGES2	80142	hgsc.bcm.edu	37	9	130884753	130884753	+	Missense_Mutation	SNP	C	C	T	rs13283456	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:130884753C>T	ENST00000338961.6	-	6	1637	c.893G>A	c.(892-894)cGc>cAc	p.R298H	PTGES2_ENST00000483625.1_5'Flank|PTGES2_ENST00000277462.5_Missense_Mutation_p.R107H	NM_001256335.1|NM_025072.6	NP_001243264.1|NP_079348.1	Q9H7Z7	PGES2_HUMAN	prostaglandin E synthase 2	298	GST C-terminal.		R -> H (in dbSNP:rs13283456).		cell redox homeostasis (GO:0045454)|positive regulation of transcription, DNA-templated (GO:0045893)|prostaglandin biosynthetic process (GO:0001516)|secretion (GO:0046903)	cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	DNA binding (GO:0003677)|electron carrier activity (GO:0009055)|glutathione binding (GO:0043295)|heme binding (GO:0020037)|lyase activity (GO:0016829)|prostaglandin-E synthase activity (GO:0050220)|protein disulfide oxidoreductase activity (GO:0015035)			endometrium(1)|large_intestine(1)|lung(2)	4						GTCCTGGAGGCGGTGCCTGGG	0.672													C|||	341	0.0680911	0.0106	0.1484	5008	,	,		16207	0.001		0.1918	False		,,,				2504	0.0307				p.R298H		Atlas-SNP	.											.	PTGES2	14	.	0			c.G893A	GRCh37	CM073285	PTGES2	M	rs13283456	PASS	.	C	HIS/ARG	193,4213	121.7+/-159.2	3,187,2013	66.0	63.0	64.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	893	2.2	0.9	9	dbSNP_121	64	1690,6910	310.0+/-309.6	165,1360,2775	yes	missense	PTGES2	NM_025072.5	29	168,1547,4788	TT,TC,CC		19.6512,4.3804,14.4779	benign	298/378	130884753	1883,11123	2203	4300	6503	SO:0001583	missense	80142	exon6			TGGAGGCGGTGCC	AK024100	CCDS6891.1	9q34.12	2008-05-06	2002-06-13	2002-06-14	ENSG00000148334	ENSG00000148334			17822	protein-coding gene	gene with protein product		608152	"""chromosome 9 open reading frame 15"""	C9orf15		11866447	Standard	NM_025072		Approved	FLJ14038	uc004bti.4	Q9H7Z7	OTTHUMG00000020730	ENST00000338961.6:c.893G>A	9.37:g.130884753C>T	ENSP00000345341:p.Arg298His	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	41	19	0.463415	NM_025072	Q53EW9|Q5SYV6|Q96GI0|Q96GL2	Missense_Mutation	SNP	ENST00000338961.6	37	CCDS6891.1	206	0.09432234432234432	7	0.014227642276422764	60	0.16574585635359115	0	0.0	139	0.18337730870712401	C	4.566	0.105135	0.08731	0.043804	0.196512	ENSG00000148334	ENST00000338961;ENST00000277462;ENST00000449878	T;T;T	0.43294	0.95;0.95;0.95	4.83	2.22	0.28083	Glutathione S-transferase, C-terminal-like (2);Glutathione S-transferase/chloride channel, C-terminal (1);Glutathione S-transferase, C-terminal (1);	0.156649	0.56097	N	0.000030	T	0.00012	0.0000	N	0.01874	-0.695	0.41685	P	0.010681000000000052	B	0.06786	0.001	B	0.01281	0.0	T	0.27123	-1.0083	9	0.23302	T	0.38	-0.0266	8.6132	0.33815	0.0:0.1639:0.0:0.8361	rs13283456;rs59654434;rs13283456	298	Q9H7Z7	PGES2_HUMAN	H	298;107;263	ENSP00000345341:R298H;ENSP00000277462:R107H;ENSP00000411378:R263H	ENSP00000277462:R107H	R	-	2	0	PTGES2	129924574	1.000000	0.71417	0.948000	0.38648	0.207000	0.24258	4.616000	0.61197	0.189000	0.20188	-0.459000	0.05422	CGC	C|0.879;T|0.121	0.121	strong		0.672	PTGES2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054339.1		
CXCL2	2920	hgsc.bcm.edu	37	4	74964830	74964830	+	Missense_Mutation	SNP	C	C	T	rs186397980	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:74964830C>T	ENST00000508487.2	-	1	180	c.8G>A	c.(7-9)cGc>cAc	p.R3H	CXCL2_ENST00000296031.4_5'UTR	NM_002089.3	NP_002080.1	P19875	CXCL2_HUMAN	chemokine (C-X-C motif) ligand 2	3					cell chemotaxis (GO:0060326)|chemotaxis (GO:0006935)|immune response (GO:0006955)|inflammatory response (GO:0006954)|response to molecule of bacterial origin (GO:0002237)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	chemokine activity (GO:0008009)			lung(1)	1	Breast(15;0.00612)		all cancers(17;0.00317)|Lung(101;0.196)			GAGCGTGGCGCGGGCCATGGG	0.746													C|||	37	0.00738818	0.0	0.0202	5008	,	,		10043	0.001		0.0189	False		,,,				2504	0.0031				p.R3H		Atlas-SNP	.											.	CXCL2	6	.	0			c.G8A						PASS	.	C	HIS/ARG	14,3322		0,14,1654	3.0	5.0	5.0		8	-6.9	0.0	4		5	109,6715		1,107,3304	no	missense	CXCL2	NM_002089.3	29	1,121,4958	TT,TC,CC		1.5973,0.4197,1.2106	benign	3/108	74964830	123,10037	1668	3412	5080	SO:0001583	missense	2920	exon1			GTGGCGCGGGCCA	M36820	CCDS34008.1	4q13.3	2013-02-25	2002-08-22	2002-08-23		ENSG00000081041		"""Endogenous ligands"""	4603	protein-coding gene	gene with protein product		139110	"""GRO2 oncogene"""	GRO2		2217207	Standard	NM_002089		Approved	SCYB2, GROb, MIP-2a, MGSA-b, CINC-2a	uc003hhm.4	P19875		ENST00000508487.2:c.8G>A	4.37:g.74964830C>T	ENSP00000427279:p.Arg3His	Somatic	6	0	0		WXS	Illumina HiSeq	Phase_I	22	13	0.590909	NM_002089	Q6FGD6|Q9UPB8	Missense_Mutation	SNP	ENST00000508487.2	37	CCDS34008.1	41	0.018772893772893772	9	0.018292682926829267	10	0.027624309392265192	0	0.0	22	0.029023746701846966	C	7.789	0.711127	0.15239	0.004197	0.015973	ENSG00000081041	ENST00000508487	T	0.32515	1.45	3.47	-6.95	0.01628	.	4.302020	0.00839	N	0.001734	T	0.10594	0.0259	M	0.72118	2.19	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.10382	-1.0632	10	0.35671	T	0.21	.	3.007	0.06032	0.1848:0.1184:0.4515:0.2452	.	3	P19875	CXCL2_HUMAN	H	3	ENSP00000427279:R3H	ENSP00000427279:R3H	R	-	2	0	CXCL2	75183694	0.001000	0.12720	0.000000	0.03702	0.015000	0.08874	-1.317000	0.02707	-2.985000	0.00281	-3.010000	0.00075	CGC	C|0.981;T|0.019	0.019	strong		0.746	CXCL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362731.2	NM_002089	
MYBPH	4608	hgsc.bcm.edu	37	1	203144833	203144833	+	Silent	SNP	G	G	A	rs12145010	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:203144833G>A	ENST00000255416.4	-	1	108	c.51C>T	c.(49-51)acC>acT	p.T17T		NM_004997.2	NP_004988.2	Q13203	MYBPH_HUMAN	myosin binding protein H	17					cell adhesion (GO:0007155)|regulation of striated muscle contraction (GO:0006942)	myosin filament (GO:0032982)	structural constituent of muscle (GO:0008307)			endometrium(5)|large_intestine(6)|lung(7)|skin(1)|urinary_tract(1)	20			BRCA - Breast invasive adenocarcinoma(75;0.153)	Colorectal(1306;0.0306)		ATTCAGATGCGGTCTCCTCTG	0.627													G|||	657	0.13119	0.0825	0.0951	5008	,	,		16213	0.375		0.0368	False		,,,				2504	0.0685				p.T17T	NSCLC(32;174 1025 14462 23899 42933)	Atlas-SNP	.											.	MYBPH	41	.	0			c.C51T						PASS	.	G		336,4070	176.6+/-205.7	12,312,1879	78.0	90.0	86.0		51	-10.4	0.0	1	dbSNP_120	86	352,8248	118.3+/-177.8	8,336,3956	no	coding-synonymous	MYBPH	NM_004997.2		20,648,5835	AA,AG,GG		4.093,7.626,5.2899		17/478	203144833	688,12318	2203	4300	6503	SO:0001819	synonymous_variant	4608	exon1			AGATGCGGTCTCC	BC044226	CCDS30975.1	1q32.1	2013-02-11	2001-11-28		ENSG00000133055	ENSG00000133055		"""Myosin binding proteins"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	7552	protein-coding gene	gene with protein product		160795	"""myosin-binding protein H"""			8486381	Standard	NM_004997		Approved		uc001gzh.1	Q13203	OTTHUMG00000042121	ENST00000255416.4:c.51C>T	1.37:g.203144833G>A		Somatic	205	0	0		WXS	Illumina HiSeq	Phase_I	149	79	0.530201	NM_004997	Q16886|Q86YC5	Silent	SNP	ENST00000255416.4	37	CCDS30975.1																																																																																			G|0.915;A|0.085	0.085	strong		0.627	MYBPH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000100264.1	NM_004997	
HLA-A	3105	hgsc.bcm.edu	37	6	29912856	29912856	+	Missense_Mutation	SNP	A	A	T	rs2231119	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:29912856A>T	ENST00000396634.1	+	8	1374	c.1033A>T	c.(1033-1035)Act>Tct	p.T345S	HLA-A_ENST00000376802.2_Intron|HLA-A_ENST00000376809.5_Missense_Mutation_p.T345S|HLA-A_ENST00000376806.5_Missense_Mutation_p.T351S			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	345					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						AGGGAGTTACACTCAGGCTGC	0.517									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|||	3438	0.686502	0.73	0.7752	5008	,	,		18918	0.6885		0.6342	False		,,,				2504	0.6166				p.T345S		Atlas-SNP	.											HLA-A,NS,carcinoma,0,1	HLA-A	89	1	0			c.A1033T						PASS	.						88.0	101.0	96.0					6																	29912856		1511	2709	4220	SO:0001583	missense	3105	exon6	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	AGTTACACTCAGG	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.1033A>T	6.37:g.29912856A>T	ENSP00000379873:p.Thr345Ser	Somatic	238	0	0		WXS	Illumina HiSeq	Phase_I	127	49	0.385827	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Missense_Mutation	SNP	ENST00000396634.1	37	CCDS34373.1	.	.	.	.	.	.	.	.	.	.	.	7.208	0.594792	0.13875	.	.	ENSG00000206503	ENST00000396634;ENST00000376806;ENST00000536480;ENST00000376809	T;T;T	0.01369	4.97;4.97;4.97	3.32	-6.63	0.01807	MHC class I, alpha chain, C-terminal (2);	7.388140	0.00839	N	0.001729	T	0.00384	0.0012	.	.	.	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	0.46233	-0.9206	8	0.87932	D	0	.	3.8447	0.08930	0.3337:0.0:0.2813:0.385	rs2231119;rs3179316;rs41546316;rs52831910	345;351;345	P13746;Q5SRN5;P04439	1A11_HUMAN;.;1A03_HUMAN	S	345;351;94;345	ENSP00000379873:T345S;ENSP00000366002:T351S;ENSP00000366005:T345S	ENSP00000366002:T351S	T	+	1	0	HLA-A	30020835	0.000000	0.05858	0.000000	0.03702	0.223000	0.24884	-3.514000	0.00445	-1.927000	0.01060	-1.865000	0.00557	ACT	A|0.345;T|0.655	0.655	strong		0.517	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
PTGIS	5740	hgsc.bcm.edu	37	20	48156249	48156249	+	Silent	SNP	G	G	A	rs61322884	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:48156249G>A	ENST00000244043.4	-	5	560	c.531C>T	c.(529-531)taC>taT	p.Y177Y	PTGIS_ENST00000478971.1_5'UTR	NM_000961.3	NP_000952.1	Q16647	PTGIS_HUMAN	prostaglandin I2 (prostacyclin) synthase	177					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)			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)	AAAGAGTCAGGTAGCCGGCTC	0.602													G|||	56	0.0111821	0.0015	0.0173	5008	,	,		16309	0.0		0.0358	False		,,,				2504	0.0061				p.Y177Y		Atlas-SNP	.											.	PTGIS	60	.	0			c.C531T						PASS	.	G		17,4387	21.2+/-45.6	0,17,2185	34.0	34.0	34.0		531	4.2	1.0	20	dbSNP_129	34	259,8341	98.6+/-160.1	2,255,4043	no	coding-synonymous	PTGIS	NM_000961.3		2,272,6228	AA,AG,GG		3.0116,0.386,2.1224		177/501	48156249	276,12728	2202	4300	6502	SO:0001819	synonymous_variant	5740	exon5			AGTCAGGTAGCCG		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.531C>T	20.37:g.48156249G>A		Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	31	19	0.612903	NM_000961	Q3MII8|Q9HAX2|Q9HAX3|Q9HAX4	Silent	SNP	ENST00000244043.4	37	CCDS13419.1																																																																																			G|0.982;A|0.018	0.018	strong		0.602	PTGIS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080496.2		
DZIP3	9666	hgsc.bcm.edu	37	3	108373022	108373022	+	Silent	SNP	G	G	A	rs2969901	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:108373022G>A	ENST00000361582.3	+	19	2294	c.2064G>A	c.(2062-2064)ttG>ttA	p.L688L	DZIP3_ENST00000463306.1_Silent_p.L688L	NM_014648.3	NP_055463.1	Q86Y13	DZIP3_HUMAN	DAZ interacting zinc finger protein 3	688					protein polyubiquitination (GO:0000209)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|phosphatase binding (GO:0019902)|poly(A) RNA binding (GO:0044822)|polyubiquitin binding (GO:0031593)|RNA binding (GO:0003723)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|endometrium(3)|large_intestine(9)|lung(21)|ovary(1)|pancreas(1)|prostate(5)|skin(1)	45						AAGAGCAGTTGAGGAAAGAAC	0.378													G|||	1135	0.226637	0.1815	0.3084	5008	,	,		21316	0.0159		0.3419	False		,,,				2504	0.3282				p.L688L		Atlas-SNP	.											.	DZIP3	111	.	0			c.G2064A						PASS	.	G		880,3526	340.7+/-306.4	85,710,1408	138.0	121.0	127.0		2064	3.8	0.8	3	dbSNP_101	127	3199,5401	483.8+/-371.2	611,1977,1712	no	coding-synonymous	DZIP3	NM_014648.3		696,2687,3120	AA,AG,GG		37.1977,19.9728,31.3624		688/1209	108373022	4079,8927	2203	4300	6503	SO:0001819	synonymous_variant	9666	exon19			GCAGTTGAGGAAA	AF279370	CCDS2952.1	3q13.13	2013-05-22	2013-05-22		ENSG00000198919	ENSG00000198919		"""RING-type (C3HC4) zinc fingers"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	30938	protein-coding gene	gene with protein product	"""human RNA-binding ubiquitin ligase of 138 kDa"", ""protein phosphatase 1, regulatory subunit 66"""	608672	"""DAZ interacting protein 3, zinc finger"""			9734811, 12538761	Standard	NM_014648		Approved	hRUL138, PPP1R66	uc003dxd.3	Q86Y13	OTTHUMG00000159232	ENST00000361582.3:c.2064G>A	3.37:g.108373022G>A		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	67	33	0.492537	NM_014648	B3KN01|O75162|Q6P3R9|Q6PH82|Q86Y14|Q86Y15|Q86Y16|Q8IWI0|Q96RS9	Silent	SNP	ENST00000361582.3	37	CCDS2952.1																																																																																			G|0.717;A|0.283	0.283	strong		0.378	DZIP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353968.1	NM_014648	
VCX	26609	hgsc.bcm.edu	37	X	7811747	7811747	+	Missense_Mutation	SNP	T	T	C	rs80291436		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:7811747T>C	ENST00000381059.3	+	3	530	c.311T>C	c.(310-312)cTg>cCg	p.L104P	VCX_ENST00000341408.4_Missense_Mutation_p.L104P	NM_013452.2	NP_038480.2	Q9H320	VCX1_HUMAN	variable charge, X-linked	104	10 X 10 AA tandem repeats of L-S-Q-E-S- [EQ]-V-E-E-P.|Glu-rich.				chromatin organization (GO:0006325)|ribosome assembly (GO:0042255)|spermatogenesis (GO:0007283)	nucleolus (GO:0005730)|nucleus (GO:0005634)	chromatin binding (GO:0003682)			NS(1)|endometrium(4)|large_intestine(2)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	10		Colorectal(8;0.0136)|Medulloblastoma(8;0.184)				CACGACCCCCTGAGTCAGGAG	0.677																																					p.L104P		Atlas-SNP	.											.	VCX	28	.	0			c.T311C						PASS	.						68.0	86.0	80.0					X																	7811747		2128	4069	6197	SO:0001583	missense	26609	exon3			ACCCCCTGAGTCA	AF167081	CCDS14128.1	Xp22.31	2008-02-05	2003-09-12		ENSG00000182583	ENSG00000182583			12667	protein-coding gene	gene with protein product		300229	"""variable charge, X chromosome"""			10607842, 10903929	Standard	NM_013452		Approved	VCX1, VCX10R, VCX-10r, VCX-B1	uc004crz.3	Q9H320	OTTHUMG00000028608	ENST00000381059.3:c.311T>C	X.37:g.7811747T>C	ENSP00000370447:p.Leu104Pro	Somatic	126	1	0.00793651		WXS	Illumina HiSeq	Phase_I	76	75	0.986842	NM_013452	A0JNS5|Q4V774|Q9P0H3	Missense_Mutation	SNP	ENST00000381059.3	37	CCDS14128.1	915	0.5515370705244123	155	0.38944723618090454	127	0.4409722222222222	224	0.5358851674641149	274	0.41896024464831805	-	2.557	-0.302800	0.05495	.	.	ENSG00000182583	ENST00000381059;ENST00000341408	T;T	0.34859	1.34;1.34	.	.	.	.	.	.	.	.	T	0.00012	0.0000	L	0.54323	1.7	0.80722	P	0.0	B	0.10296	0.003	B	0.08055	0.003	T	0.44452	-0.9327	6	0.32370	T	0.25	.	.	.	.	.	104	Q9H320	VCX1_HUMAN	P	104	ENSP00000370447:L104P;ENSP00000344144:L104P	ENSP00000344144:L104P	L	+	2	0	VCX	7771747	0.000000	0.05858	0.032000	0.17829	0.032000	0.12392	-1.350000	0.02624	0.138000	0.18790	0.137000	0.15966	CTG	T|0.449;C|0.551	0.551	strong		0.677	VCX-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000071474.1	NM_013452	
OXTR	5021	hgsc.bcm.edu	37	3	8809184	8809184	+	Silent	SNP	G	G	A	rs237902	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	66	0	0		WXS	Illumina HiSeq	Phase_I	53	30	0.566038	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		
PCSK1	5122	hgsc.bcm.edu	37	5	95751785	95751785	+	Missense_Mutation	SNP	T	T	C	rs6232	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:95751785T>C	ENST00000311106.3	-	6	898	c.661A>G	c.(661-663)Aat>Gat	p.N221D	CTD-2337A12.1_ENST00000502645.2_RNA|PCSK1_ENST00000508626.1_Missense_Mutation_p.N174D	NM_000439.4|NM_001177876.1	NP_000430.3|NP_001171347.1	P29120	NEC1_HUMAN	proprotein convertase subtilisin/kexin type 1	221	Peptidase S8.		N -> D (associated with susceptibility to obesity; induces a 10.4% reduction of activity (P = 0.03) when compared to the wild-type enzyme; dbSNP:rs6232). {ECO:0000269|PubMed:10391209, ECO:0000269|PubMed:18604207}.		cell-cell signaling (GO:0007267)|cellular protein metabolic process (GO:0044267)|metabolic process (GO:0008152)|peptide biosynthetic process (GO:0043043)|peptide hormone processing (GO:0016486)|proteolysis (GO:0006508)|regulation of insulin secretion (GO:0050796)	extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|secretory granule lumen (GO:0034774)	serine-type endopeptidase activity (GO:0004252)			NS(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(14)|ovary(2)|prostate(3)|skin(3)|urinary_tract(2)	36		all_cancers(142;2.67e-06)|all_epithelial(76;6.92e-09)|all_lung(232;0.00307)|Lung NSC(167;0.00452)|Ovarian(225;0.0112)|Colorectal(57;0.0341)|Breast(839;0.244)		all cancers(79;3.44e-16)	"""""""Insulin(DB00071)|Insulin Regular(DB00030)"""	TTGTGATTATTTGCTTGCATG	0.373													T|||	105	0.0209665	0.0023	0.0259	5008	,	,		20477	0.002		0.0328	False		,,,				2504	0.0501				p.N221D		Atlas-SNP	.											.	PCSK1	93	.	0			c.A661G	GRCh37	CM083013	PCSK1	M	rs6232	PASS	.	T	ASP/ASN,ASP/ASN	44,4362	45.3+/-79.5	0,44,2159	170.0	161.0	164.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	661,520	6.1	1.0	5	dbSNP_52	164	431,8169	132.5+/-190.1	9,413,3878	yes	missense,missense	PCSK1	NM_000439.4,NM_001177875.1	23,23	9,457,6037	CC,CT,TT		5.0116,0.9986,3.6522	benign,benign	221/754,174/707	95751785	475,12531	2203	4300	6503	SO:0001583	missense	5122	exon6			GATTATTTGCTTG		CCDS4081.1, CCDS54881.1	5q15-q21	2008-07-18			ENSG00000175426	ENSG00000175426			8743	protein-coding gene	gene with protein product	"""prohormone convertase 3"", ""prohormone convertase 1"", ""neuroendocrine convertase 1"", ""proprotein convertase 1"""	162150		NEC1		1765368	Standard	NM_000439		Approved	PC1, PC3, SPC3	uc003kls.2	P29120	OTTHUMG00000122089	ENST00000311106.3:c.661A>G	5.37:g.95751785T>C	ENSP00000308024:p.Asn221Asp	Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	168	80	0.47619	NM_000439	B7Z8T7|E9PHA1|P78478|Q92532	Missense_Mutation	SNP	ENST00000311106.3	37	CCDS4081.1	39	0.017857142857142856	1	0.0020325203252032522	7	0.019337016574585635	2	0.0034965034965034965	29	0.03825857519788918	T	16.91	3.253847	0.59212	0.009986	0.050116	ENSG00000175426	ENST00000311106;ENST00000508626	D;D	0.87650	-2.28;-2.28	6.06	6.06	0.98353	Peptidase S8/S53, subtilisin/kexin/sedolisin (3);	0.041262	0.85682	D	0.000000	T	0.57460	0.2055	M	0.62088	1.915	0.48040	D	0.999572	B	0.19445	0.036	B	0.23852	0.049	T	0.72760	-0.4196	10	0.36615	T	0.2	-28.6369	16.2708	0.82618	0.0:0.0:0.0:1.0	rs6232;rs17470938;rs57975876;rs6232	221	P29120	NEC1_HUMAN	D	221;174	ENSP00000308024:N221D;ENSP00000421600:N174D	ENSP00000308024:N221D	N	-	1	0	PCSK1	95777541	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	5.656000	0.67988	2.324000	0.78689	0.533000	0.62120	AAT	T|0.968;C|0.032	0.032	strong		0.373	PCSK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000242851.1	NM_000439	
MUC5B	727897	hgsc.bcm.edu	37	11	1264965	1264965	+	Silent	SNP	G	G	A	rs4963051	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:1264965G>A	ENST00000529681.1	+	31	6913	c.6855G>A	c.(6853-6855)acG>acA	p.T2285T	MUC5B_ENST00000447027.1_Silent_p.T2288T|RP11-532E4.2_ENST00000532061.2_RNA	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	2285	7 X Cys-rich subdomain repeats.|Thr-rich.				cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to retinoic acid (GO:0071300)|epithelial cell differentiation (GO:0030855)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|response to lipopolysaccharide (GO:0032496)|response to ozone (GO:0010193)|response to sulfur dioxide (GO:0010477)|response to vitamin A (GO:0033189)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)				cervix(2)|endometrium(36)|kidney(9)|lung(89)|urinary_tract(1)	137		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)		CCACAGCCACGGCCACACCCA	0.677													g|||	559	0.111621	0.1467	0.0821	5008	,	,		15513	0.005		0.1918	False		,,,				2504	0.1125				p.T2285T		Atlas-SNP	.											.	MUC5B	473	.	0			c.G6855A						PASS	.	G		578,3668		40,498,1585	79.0	114.0	102.0		6855	-2.8	0.0	11	dbSNP_111	102	1422,7008		145,1132,2938	no	coding-synonymous	MUC5B	NM_002458.2		185,1630,4523	AA,AG,GG		16.8683,13.6128,15.7778		2285/5763	1264965	2000,10676	2123	4215	6338	SO:0001819	synonymous_variant	727897	exon31			AGCCACGGCCACA	U95031, AF086604	CCDS44515.1, CCDS44515.2	11p15.5	2007-01-19	2006-03-14			ENSG00000117983		"""Mucins"""	7516	protein-coding gene	gene with protein product		600770	"""mucin 5, subtype B, tracheobronchial"""	MUC5		9804771	Standard	NM_002458		Approved	MG1	uc001lta.3	Q9HC84		ENST00000529681.1:c.6855G>A	11.37:g.1264965G>A		Somatic	370	1	0.0027027		WXS	Illumina HiSeq	Phase_I	485	330	0.680412	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Silent	SNP	ENST00000529681.1	37	CCDS44515.2																																																																																			G|0.873;A|0.127	0.127	strong		0.677	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
GFAP	2670	hgsc.bcm.edu	37	17	42989088	42989088	+	Silent	SNP	C	C	T	rs2289681	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:42989088C>T	ENST00000253408.5	-	5	923	c.858G>A	c.(856-858)cgG>cgA	p.R286R	GFAP_ENST00000588735.1_Intron|GFAP_ENST00000591327.1_5'Flank|GFAP_ENST00000435360.2_Silent_p.R286R|GFAP_ENST00000586793.1_Silent_p.R286R	NM_002055.4	NP_002046.1	P14136	GFAP_HUMAN	glial fibrillary acidic protein	286	Coil 2B.|Rod.				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)				GCAACTGGCGCCGGTAGTCGT	0.692													C|||	705	0.140775	0.2413	0.0937	5008	,	,		16391	0.1359		0.1014	False		,,,				2504	0.0838				p.R286R		Atlas-SNP	.											.	GFAP	88	.	0			c.G858A						PASS	.	C	,,	1062,3344	379.2+/-323.2	126,810,1267	52.0	48.0	49.0		858,858,858	2.3	1.0	17	dbSNP_100	49	968,7632	208.0+/-249.6	52,864,3384	no	coding-synonymous,coding-synonymous,coding-synonymous	GFAP	NM_001131019.2,NM_001242376.1,NM_002055.4	,,	178,1674,4651	TT,TC,CC		11.2558,24.1035,15.6082	,,	286/432,286/439,286/433	42989088	2030,10976	2203	4300	6503	SO:0001819	synonymous_variant	2670	exon5			CTGGCGCCGGTAG	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.858G>A	17.37:g.42989088C>T		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	125	67	0.536	NM_001131019	B2RD44|D3DX59|E9PAX3|Q53H98|Q5D055|Q6ZQS3|Q7Z5J6|Q7Z5J7|Q96KS4|Q96P18|Q9UFD0	Silent	SNP	ENST00000253408.5	37	CCDS11491.1																																																																																			C|0.850;T|0.150	0.150	strong		0.692	GFAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448701.1	NM_002055	
ACAN	176	hgsc.bcm.edu	37	15	89400023	89400023	+	Missense_Mutation	SNP	A	A	G	rs12899191		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:89400023A>G	ENST00000561243.1	+	11	4207	c.4207A>G	c.(4207-4209)Act>Gct	p.T1403A	ACAN_ENST00000439576.2_Missense_Mutation_p.T1403A|ACAN_ENST00000559004.1_Missense_Mutation_p.T1403A|ACAN_ENST00000352105.7_Missense_Mutation_p.T1403A			P16112	PGCA_HUMAN	aggrecan	1403	29 X 19 AA approximate tandem repeats of E-[IVDG]-[LV]-[EV]-[GTI]-[STA]-[ATV]- [SP]-[GA]-[VIFAD]-[GEDL]-[DE]-[LVI]-[SG]- [GERK]-[LV]-P-S-G.|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.T1289A(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)			TCTAGAGACTACTGCCCCTGG	0.542																																					p.T1403A		Atlas-SNP	.											AGC1,caecum,carcinoma,0,3	ACAN	220	3	1	Substitution - Missense(1)	stomach(1)	c.A4207G						scavenged	.						53.0	47.0	49.0					15																	89400023		1722	3680	5402	SO:0001583	missense	176	exon12			GAGACTACTGCCC	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.4207A>G	15.37:g.89400023A>G	ENSP00000453342:p.Thr1403Ala	Somatic	50	1	0.02		WXS	Illumina HiSeq	Phase_I	39	32	0.820513	NM_001135	Q13650|Q9UCD3|Q9UCP4|Q9UCP5|Q9UDE0	Missense_Mutation	SNP	ENST00000561243.1	37	CCDS53970.1	.	.	.	.	.	.	.	.	.	.	-	8.246	0.808010	0.16467	.	.	ENSG00000157766	ENST00000439576;ENST00000352105;ENST00000268134	D;D	0.94966	-3.57;-3.57	3.4	-5.11	0.02901	.	.	.	.	.	D	0.88887	0.6559	L	0.48260	1.515	0.80722	P	0.0	P;P	0.34462	0.454;0.454	B;B	0.40864	0.254;0.342	T	0.80991	-0.1135	8	0.07325	T	0.83	.	4.7022	0.12832	0.5802:0.1946:0.0:0.2251	rs12899191;rs60555990	1403;1403	E7ENV9;E7EX88	.;.	A	1403;1403;1289	ENSP00000387356:T1403A;ENSP00000341615:T1403A	ENSP00000268134:T1289A	T	+	1	0	ACAN	87201027	0.000000	0.05858	0.000000	0.03702	0.020000	0.10135	-0.326000	0.07965	-0.748000	0.04753	-0.892000	0.02923	ACT	G|1.000;|0.000	1.000	weak		0.542	ACAN-006	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416267.2	NM_001135	
NUP133	55746	hgsc.bcm.edu	37	1	229623338	229623338	+	Missense_Mutation	SNP	T	T	C	rs1065674	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	62	0	0		WXS	Illumina HiSeq	Phase_I	54	28	0.518519	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	
ARL6IP1	23204	hgsc.bcm.edu	37	16	18809333	18809333	+	Silent	SNP	G	G	A	rs138748723	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:18809333G>A	ENST00000304414.7	-	3	415	c.204C>T	c.(202-204)tcC>tcT	p.S68S	ARL6IP1_ENST00000546206.2_Silent_p.S39S|ARL6IP1_ENST00000562819.1_Intron|RP11-1035H13.3_ENST00000567078.2_Silent_p.S68S	NM_015161.1	NP_055976.1	Q15041	AR6P1_HUMAN	ADP-ribosylation factor-like 6 interacting protein 1	68					cell death (GO:0008219)|cotranslational protein targeting to membrane (GO:0006613)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|Sec61 translocon complex (GO:0005784)		p.S68S(1)		breast(1)|large_intestine(2)|lung(6)|pancreas(1)|prostate(1)	11						AGGAAACGCCGGACAGAACAG	0.343													G|||	20	0.00399361	0.0151	0.0	5008	,	,		19062	0.0		0.0	False		,,,				2504	0.0				p.S68S		Atlas-SNP	.											ARL6IP1,colon,carcinoma,0,1	ARL6IP1	23	1	1	Substitution - coding silent(1)	large_intestine(1)	c.C204T						scavenged	.	G		51,4343	51.6+/-87.1	0,51,2146	58.0	58.0	58.0		204	-8.2	0.8	16	dbSNP_134	58	0,8600		0,0,4300	no	coding-synonymous	ARL6IP1	NM_015161.1		0,51,6446	AA,AG,GG		0.0,1.1607,0.3925		68/204	18809333	51,12943	2197	4300	6497	SO:0001819	synonymous_variant	23204	exon3			AACGCCGGACAGA	BC010281	CCDS10572.1	16p12-p11.2	2014-03-12	2006-09-26	2006-09-26	ENSG00000170540	ENSG00000170540			697	protein-coding gene	gene with protein product		607669	"""ADP-ribosylation factor-like 6 interacting protein"""	ARL6IP		24482476	Standard	NM_015161		Approved	AIP1, ARMER, KIAA0069, SPG61	uc002dfl.1	Q15041	OTTHUMG00000131367	ENST00000304414.7:c.204C>T	16.37:g.18809333G>A		Somatic	223	0	0		WXS	Illumina HiSeq	Phase_I	225	3	0.0133333	NM_015161		Silent	SNP	ENST00000304414.7	37	CCDS10572.1																																																																																			G|0.996;A|0.004	0.004	strong		0.343	ARL6IP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254156.2	NM_015161	
SPATA31E1	286234	hgsc.bcm.edu	37	9	90503007	90503007	+	Missense_Mutation	SNP	A	A	G	rs11789780	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:90503007A>G	ENST00000325643.5	+	4	3671	c.3605A>G	c.(3604-3606)gAc>gGc	p.D1202G		NM_178828.4	NP_849150.3	Q6ZUB1	S31E1_HUMAN	SPATA31 subfamily E, member 1	1202			D -> G (in dbSNP:rs11789780). {ECO:0000269|PubMed:14702039}.		cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											GGCTGTGCGGACAAGGGCGAG	0.652													.|||	2303	0.459864	0.5159	0.4049	5008	,	,		17260	0.3363		0.5169	False		,,,				2504	0.4918				p.D1202G		Atlas-SNP	.											C9orf79,NS,carcinoma,0,3	.	.	3	0			c.A3605G						PASS	.	A	GLY/ASP	2103,2275		533,1037,619	11.0	11.0	11.0		3605	1.5	0.0	9	dbSNP_120	11	4092,4468		1053,1986,1241	yes	missense	C9orf79	NM_178828.4	94	1586,3023,1860	GG,GA,AA		47.8037,48.0356,47.8822	probably-damaging	1202/1446	90503007	6195,6743	2189	4280	6469	SO:0001583	missense	286234	exon4			GTGCGGACAAGGG	AK093185	CCDS6676.1	9q22.1-q22.2	2012-10-12	2012-10-12	2012-10-12	ENSG00000177992	ENSG00000177992			26672	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 79"", ""family with sequence similarity 75, member E1"""	C9orf79, FAM75E1			Standard	NM_178828		Approved	FLJ35866	uc004app.4	Q6ZUB1	OTTHUMG00000020157	ENST00000325643.5:c.3605A>G	9.37:g.90503007A>G	ENSP00000322640:p.Asp1202Gly	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	42	20	0.47619	NM_178828	B2RPB1|Q5SQC9|Q8NA41|Q8ND27	Missense_Mutation	SNP	ENST00000325643.5	37	CCDS6676.1	981	0.4491758241758242	245	0.49796747967479676	157	0.43370165745856354	192	0.3356643356643357	387	0.5105540897097626	a	11.24	1.581690	0.28180	0.480356	0.478037	ENSG00000177992	ENST00000325643	T	0.03772	3.81	2.71	1.51	0.23008	.	1.504920	0.04304	N	0.347788	T	0.00012	0.0000	L	0.39898	1.24	0.80722	P	0.0	D	0.60575	0.988	P	0.57960	0.83	T	0.45991	-0.9223	9	0.23891	T	0.37	.	5.7461	0.18120	0.7205:0.2795:0.0:0.0	rs11789780;rs11789780	1202	Q6ZUB1	CI079_HUMAN	G	1202	ENSP00000322640:D1202G	ENSP00000322640:D1202G	D	+	2	0	C9orf79	89692827	0.001000	0.12720	0.002000	0.10522	0.004000	0.04260	1.304000	0.33482	0.429000	0.26202	0.533000	0.62120	GAC	A|0.555;G|0.445	0.445	strong		0.652	SPATA31E1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052954.2	NM_178828	
TTN	7273	hgsc.bcm.edu	37	2	179414318	179414318	+	Missense_Mutation	SNP	C	C	T	rs747122	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:179414318C>T	ENST00000591111.1	-	288	87432	c.87208G>A	c.(87208-87210)Gtg>Atg	p.V29070M	TTN-AS1_ENST00000438095.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.V21771M|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.V28143M|RP11-65L3.2_ENST00000603415.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.V21646M|TTN-AS1_ENST00000591332.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.V30711M|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.V21838M|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590932.1_RNA			Q8WZ42	TITIN_HUMAN	titin	29070	Fibronectin type-III 111. {ECO:0000255|PROSITE-ProRule:PRU00316}.		V -> M. {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)			TGAGCAACCACTGGATCAGAA	0.373													C|||	752	0.15016	0.2731	0.1787	5008	,	,		21696	0.0248		0.0487	False		,,,				2504	0.1973				p.V30711M		Atlas-SNP	.											.	TTN	18412	.	0			c.G92131A						PASS	.	C	MET/VAL,MET/VAL,MET/VAL,MET/VAL	971,2753		131,709,1022	112.0	111.0	111.0		64936,84427,65311,65512	5.7	1.0	2	dbSNP_86	111	252,7938		8,236,3851	yes	missense,missense,missense,missense	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	21,21,21,21	139,945,4873	TT,TC,CC		3.0769,26.0741,10.2652	probably-damaging,probably-damaging,probably-damaging,probably-damaging	21646/26927,28143/33424,21771/27052,21838/27119	179414318	1223,10691	1862	4095	5957	SO:0001583	missense	7273	exon338			CAACCACTGGATC	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.87208G>A	2.37:g.179414318C>T	ENSP00000465570:p.Val29070Met	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	107	46	0.429907	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		246	0.11263736263736264	150	0.3048780487804878	58	0.16022099447513813	5	0.008741258741258742	33	0.04353562005277045	C	15.04	2.715720	0.48622	0.260741	0.030769	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.57752	0.38;0.38;0.38;0.38	5.74	5.74	0.90152	Fibronectin, type III (2);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00012	0.0000	M	0.66378	2.025	0.23773	P	0.99688228	D;D;D;D	0.54397	0.966;0.966;0.966;0.966	P;P;P;P	0.52159	0.618;0.618;0.618;0.691	T	0.01848	-1.1261	8	0.87932	D	0	.	15.8576	0.78994	0.1362:0.8638:0.0:0.0	rs747122;rs61267780;rs747122	21646;21771;21838;29070	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	M	28143;21646;21838;21771;21643	ENSP00000343764:V28143M;ENSP00000434586:V21646M;ENSP00000340554:V21838M;ENSP00000352154:V21771M	ENSP00000340554:V21838M	V	-	1	0	TTN	179122564	0.993000	0.37304	1.000000	0.80357	0.961000	0.63080	1.240000	0.32731	2.873000	0.98535	0.563000	0.77884	GTG	C|0.882;T|0.118	0.118	strong		0.373	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
CSPG4	1464	hgsc.bcm.edu	37	15	75969335	75969335	+	Missense_Mutation	SNP	C	C	T	rs77237106	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:75969335C>T	ENST00000308508.5	-	10	5617	c.5525G>A	c.(5524-5526)cGg>cAg	p.R1842Q	AC105020.1_ENST00000435356.1_5'Flank|CTD-2026K11.1_ENST00000569467.1_RNA	NM_001897.4	NP_001888.2	Q6UVK1	CSPG4_HUMAN	chondroitin sulfate proteoglycan 4	1842	Cysteine-containing.|Neurite growth inhibition. {ECO:0000250}.				activation of MAPK activity (GO:0000187)|angiogenesis (GO:0001525)|carbohydrate metabolic process (GO:0005975)|cell proliferation (GO:0008283)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|intracellular signal transduction (GO:0035556)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|small molecule metabolic process (GO:0044281)|tissue remodeling (GO:0048771)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell projection (GO:0042995)|cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)	protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)			breast(1)|cervix(2)|endometrium(5)|kidney(5)|large_intestine(3)|liver(2)|lung(18)|ovary(2)|pancreas(2)|prostate(4)|skin(4)	48						TCGGGTGAGCCGGAGTGGGAC	0.662													C|||	274	0.0547125	0.0076	0.0821	5008	,	,		17011	0.0		0.1759	False		,,,				2504	0.0307				p.R1842Q		Atlas-SNP	.											.	CSPG4	175	.	0			c.G5525A						PASS	.	C	GLN/ARG	123,4079		2,119,1980	14.0	15.0	15.0		5525	3.2	0.1	15	dbSNP_131	15	1331,7005		123,1085,2960	yes	missense	CSPG4	NM_001897.4	43	125,1204,4940	TT,TC,CC		15.9669,2.9272,11.5967	possibly-damaging	1842/2323	75969335	1454,11084	2101	4168	6269	SO:0001583	missense	1464	exon10			GTGAGCCGGAGTG	X96753, AY359468	CCDS10284.1	15q24.2	2010-04-19	2007-02-16		ENSG00000173546	ENSG00000173546		"""Proteoglycans / Cell surface : Other"""	2466	protein-coding gene	gene with protein product	"""melanoma-associated chondroitin sulfate proteoglycan"""	601172	"""chondroitin sulfate proteoglycan 4 (melanoma-associated)"""			8790396, 16407841	Standard	NM_001897		Approved	MCSPG, MEL-CSPG, MSK16, NG2, MCSP, HMW-MAA	uc002baw.3	Q6UVK1	OTTHUMG00000142836	ENST00000308508.5:c.5525G>A	15.37:g.75969335C>T	ENSP00000312506:p.Arg1842Gln	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	54	29	0.537037	NM_001897	D3DW77|Q92675	Missense_Mutation	SNP	ENST00000308508.5	37	CCDS10284.1	162	0.07417582417582418	4	0.008130081300813009	34	0.09392265193370165	0	0.0	124	0.16358839050131926	C	10.22	1.288895	0.23478	0.029272	0.159669	ENSG00000173546	ENST00000308508	T	0.19250	2.16	5.29	3.16	0.36331	.	0.295925	0.29087	N	0.013188	T	0.00039	0.0001	N	0.25647	0.755	0.31038	P	0.7166239999999999	B	0.15719	0.014	B	0.06405	0.002	T	0.30563	-0.9974	9	0.11182	T	0.66	.	6.6071	0.22731	0.0:0.6128:0.0:0.3872	.	1842	Q6UVK1	CSPG4_HUMAN	Q	1842	ENSP00000312506:R1842Q	ENSP00000312506:R1842Q	R	-	2	0	CSPG4	73756390	0.015000	0.18098	0.125000	0.21846	0.776000	0.43924	-0.059000	0.11731	1.222000	0.43521	0.561000	0.74099	CGG	C|0.919;T|0.081	0.081	strong		0.662	CSPG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286472.1	NM_001897	
OR4C6	219432	hgsc.bcm.edu	37	11	55433040	55433040	+	Missense_Mutation	SNP	T	T	C	rs11230600	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:55433040T>C	ENST00000314259.3	+	1	427	c.398T>C	c.(397-399)aTc>aCc	p.I133T		NM_001004704.1	NP_001004704.1	Q8NH72	OR4C6_HUMAN	olfactory receptor, family 4, subfamily C, member 6	133			I -> T (in dbSNP:rs11230600).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(4)|lung(49)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	71						TACACGATCATCATGAGTCCA	0.512													t|||	1267	0.252995	0.1029	0.3242	5008	,	,		18616	0.3909		0.2843	False		,,,				2504	0.2311				p.I133T		Atlas-SNP	.											.	OR4C6	114	.	0			c.T398C						PASS	.	T	THR/ILE	567,3833	254.0+/-259.7	33,501,1666	104.0	97.0	99.0		398	2.5	0.4	11	dbSNP_120	99	2291,6301	386.9+/-342.0	330,1631,2335	yes	missense	OR4C6	NM_001004704.1	89	363,2132,4001	CC,CT,TT		26.6643,12.8864,21.9982	possibly-damaging	133/310	55433040	2858,10134	2200	4296	6496	SO:0001583	missense	219432	exon1			CGATCATCATGAG	CR593785	CCDS31506.1	11q11	2012-08-09			ENSG00000181903	ENSG00000181903		"""GPCR / Class A : Olfactory receptors"""	14743	protein-coding gene	gene with protein product							Standard	NM_001004704		Approved		uc010rik.2	Q8NH72	OTTHUMG00000166800	ENST00000314259.3:c.398T>C	11.37:g.55433040T>C	ENSP00000324769:p.Ile133Thr	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	90	13	0.144444	NM_001004704	B2RP11|Q6IFD2	Missense_Mutation	SNP	ENST00000314259.3	37	CCDS31506.1	605	0.27701465201465203	47	0.09552845528455285	126	0.34806629834254144	214	0.3741258741258741	218	0.287598944591029	T	11.60	1.687192	0.29962	0.128864	0.266643	ENSG00000181903	ENST00000314259	T	0.21191	2.02	3.77	2.52	0.30459	GPCR, rhodopsin-like superfamily (1);	0.189403	0.25639	N	0.029298	T	0.00012	0.0000	M	0.65320	2	0.44417	P	0.0026610000000000245	B	0.20164	0.042	B	0.27608	0.081	T	0.38972	-0.9636	9	0.59425	D	0.04	.	7.9326	0.29912	0.1838:0.0:0.0:0.8162	rs11230600;rs11230600	133	Q8NH72	OR4C6_HUMAN	T	133	ENSP00000324769:I133T	ENSP00000324769:I133T	I	+	2	0	OR4C6	55189616	0.000000	0.05858	0.449000	0.26957	0.625000	0.37756	0.307000	0.19296	1.383000	0.46405	0.438000	0.28831	ATC	T|0.759;C|0.241	0.241	strong		0.512	OR4C6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391504.1	NM_001004704	
VWF	7450	hgsc.bcm.edu	37	12	6138595	6138595	+	Silent	SNP	C	C	T	rs1800380	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:6138595C>T	ENST00000261405.5	-	22	3134	c.2880G>A	c.(2878-2880)cgG>cgA	p.R960R		NM_000552.3	NP_000543	P04275	VWF_HUMAN	von Willebrand factor	960	VWFD 3. {ECO:0000255|PROSITE- ProRule:PRU00580}.				blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|cell adhesion (GO:0007155)|cell-substrate adhesion (GO:0031589)|extracellular matrix organization (GO:0030198)|hemostasis (GO:0007599)|liver development (GO:0001889)|placenta development (GO:0001890)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|protein homooligomerization (GO:0051260)|response to wounding (GO:0009611)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|proteinaceous extracellular matrix (GO:0005578)|Weibel-Palade body (GO:0033093)	chaperone binding (GO:0051087)|collagen binding (GO:0005518)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|immunoglobulin binding (GO:0019865)|integrin binding (GO:0005178)|protease binding (GO:0002020)|protein homodimerization activity (GO:0042803)|protein N-terminus binding (GO:0047485)			NS(1)|breast(6)|central_nervous_system(5)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(25)|lung(41)|ovary(7)|pancreas(2)|prostate(6)|skin(15)|stomach(1)|upper_aerodigestive_tract(5)	129					Antihemophilic Factor(DB00025)	GAATGATGTACCGGCCAGACT	0.557													C|||	897	0.179113	0.3079	0.1902	5008	,	,		20208	0.004		0.2555	False		,,,				2504	0.0992				p.R960R		Atlas-SNP	.											.	VWF	338	.	0			c.G2880A						PASS	.	C		1373,3033	456.9+/-351.5	210,953,1040	131.0	116.0	121.0		2880	-5.1	0.1	12	dbSNP_89	121	2162,6438	370.9+/-336.0	264,1634,2402	no	coding-synonymous	VWF	NM_000552.3		474,2587,3442	TT,TC,CC		25.1395,31.1621,27.1798		960/2814	6138595	3535,9471	2203	4300	6503	SO:0001819	synonymous_variant	7450	exon22			GATGTACCGGCCA		CCDS8539.1	12p13.3	2014-09-17			ENSG00000110799	ENSG00000110799		"""Endogenous ligands"""	12726	protein-coding gene	gene with protein product		613160		F8VWF		2251280	Standard	NM_000552		Approved		uc001qnn.1	P04275	OTTHUMG00000168265	ENST00000261405.5:c.2880G>A	12.37:g.6138595C>T		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	88	44	0.5	NM_000552	Q8TCE8|Q99806	Silent	SNP	ENST00000261405.5	37	CCDS8539.1																																																																																			C|0.766;T|0.234	0.234	strong		0.557	VWF-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399020.1	NM_000552	
UBR4	23352	hgsc.bcm.edu	37	1	19486689	19486689	+	Silent	SNP	G	G	A	rs139582695	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:19486689G>A	ENST00000375254.3	-	39	5520	c.5493C>T	c.(5491-5493)gcC>gcT	p.A1831A	UBR4_ENST00000375226.2_Silent_p.A1831A|UBR4_ENST00000375267.2_Silent_p.A1831A|UBR4_ENST00000375217.2_Silent_p.A1831A	NM_020765.2	NP_065816.2	Q5T4S7	UBR4_HUMAN	ubiquitin protein ligase E3 component n-recognin 4	1831					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)		TGCTCCCGACGGCTGAAGCTT	0.522													G|||	5	0.000998403	0.0	0.0014	5008	,	,		18321	0.0		0.004	False		,,,				2504	0.0				p.A1831A		Atlas-SNP	.											UBR4,caecum,carcinoma,-1,1	UBR4	415	1	0			c.C5493T						PASS	.	G		1,4405	2.1+/-5.4	0,1,2202	75.0	71.0	72.0		5493	-11.5	0.1	1	dbSNP_134	72	6,8594	5.0+/-18.6	0,6,4294	no	coding-synonymous	UBR4	NM_020765.2		0,7,6496	AA,AG,GG		0.0698,0.0227,0.0538		1831/5184	19486689	7,12999	2203	4300	6503	SO:0001819	synonymous_variant	23352	exon39			CCCGACGGCTGAA	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.5493C>T	1.37:g.19486689G>A		Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	171	88	0.51462	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																																																																																			G|0.999;A|0.001	0.001	strong		0.522	UBR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007085.1	NM_020765	
CDON	50937	hgsc.bcm.edu	37	11	125891162	125891162	+	Silent	SNP	A	A	G	rs35131477	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:125891162A>G	ENST00000392693.3	-	3	457	c.330T>C	c.(328-330)ccT>ccC	p.P110P	CDON_ENST00000263577.7_Silent_p.P110P	NM_001243597.1|NM_016952.4	NP_001230526.1|NP_058648.4	Q4KMG0	CDON_HUMAN	cell adhesion associated, oncogene regulated	110	Ig-like C2-type 1.				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)		ATACTGTCGCAGGGCCACTCA	0.443													A|||	132	0.0263578	0.0144	0.0331	5008	,	,		19853	0.005		0.0368	False		,,,				2504	0.0491				p.P110P		Atlas-SNP	.											.	CDON	137	.	0			c.T330C						PASS	.	A		119,4283	87.3+/-125.9	2,115,2084	47.0	48.0	48.0		330	-0.6	0.9	11	dbSNP_126	48	408,8190	128.5+/-186.7	10,388,3901	no	coding-synonymous	CDON	NM_016952.4		12,503,5985	GG,GA,AA		4.7453,2.7033,4.0538		110/1265	125891162	527,12473	2201	4299	6500	SO:0001819	synonymous_variant	50937	exon3			TGTCGCAGGGCCA	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.330T>C	11.37:g.125891162A>G		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	58	45	0.775862	NM_016952	O14631	Silent	SNP	ENST00000392693.3	37	CCDS58192.1	50	0.022893772893772892	7	0.014227642276422764	13	0.03591160220994475	3	0.005244755244755245	27	0.03562005277044855	A	1.462	-0.562135	0.03939	0.027033	0.047453	ENSG00000064309	ENST00000534661	.	.	.	5.78	-0.615	0.11587	.	.	.	.	.	T	0.10252	0.0251	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.07233	-1.0783	4	.	.	.	-21.6951	3.7706	0.08640	0.6213:0.0992:0.1801:0.0994	rs35131477	.	.	.	R	86	.	.	C	-	1	0	CDON	125396372	0.119000	0.22226	0.944000	0.38274	0.148000	0.21650	-0.611000	0.05622	-0.126000	0.11682	-2.009000	0.00441	TGC	A|0.963;G|0.037	0.037	strong		0.443	CDON-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386749.2	NM_016952	
SAMD4B	55095	hgsc.bcm.edu	37	19	39873858	39873858	+	Silent	SNP	T	T	G	rs140996761	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:39873858T>G	ENST00000314471.6	+	15	3018	c.1983T>G	c.(1981-1983)gtT>gtG	p.V661V	SAMD4B_ENST00000596368.1_Intron|SAMD4B_ENST00000598913.1_Silent_p.V661V	NM_018028.2	NP_060498.2	Q5PRF9	SMAG2_HUMAN	sterile alpha motif domain containing 4B	661					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			autonomic_ganglia(1)|breast(1)|endometrium(5)|large_intestine(1)|lung(4)|skin(1)|urinary_tract(2)	15	all_cancers(60;2.5e-07)|all_lung(34;4.03e-08)|Lung NSC(34;4.66e-08)|all_epithelial(25;6.4e-07)|Ovarian(47;0.0512)		Epithelial(26;9.6e-28)|all cancers(26;9.14e-25)|Lung(45;0.000168)|LUSC - Lung squamous cell carcinoma(53;0.000199)			ACTGCCCGGTTCCTGGGCCTG	0.562													t|||	12	0.00239617	0.0	0.0014	5008	,	,		20343	0.0		0.0109	False		,,,				2504	0.0				p.V661V		Atlas-SNP	.											.	SAMD4B	48	.	0			c.T1983G						PASS	.	T		4,4402	8.1+/-20.4	0,4,2199	150.0	116.0	128.0		1983	0.1	1.0	19	dbSNP_134	128	72,8528	42.6+/-100.3	1,70,4229	no	coding-synonymous	SAMD4B	NM_018028.2		1,74,6428	GG,GT,TT		0.8372,0.0908,0.5843		661/695	39873858	76,12930	2203	4300	6503	SO:0001819	synonymous_variant	55095	exon15			CCCGGTTCCTGGG		CCDS33020.1	19q13.2	2013-01-10				ENSG00000179134		"""Sterile alpha motif (SAM) domain containing"""	25492	protein-coding gene	gene with protein product	"""smaug homolog B (Drosophila)"""					16221671	Standard	XM_005259029		Approved	FLJ10211, MGC99832, SMGB, hSmaug2	uc002olb.3	Q5PRF9		ENST00000314471.6:c.1983T>G	19.37:g.39873858T>G		Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	105	52	0.495238	NM_018028	A5Z0M6|Q6P194	Silent	SNP	ENST00000314471.6	37	CCDS33020.1	6	0.0027472527472527475	0	0.0	0	0.0	0	0.0	6	0.0079155672823219	T	6.377	0.437719	0.12104	9.08E-4	0.008372	ENSG00000179134	ENST00000429637	.	.	.	4.2	0.092	0.14470	.	.	.	.	.	T	0.47820	0.1466	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.54846	-0.8232	5	0.87932	D	0	.	2.9929	0.05989	0.1656:0.441:0.2913:0.1021	.	.	.	.	A	661	.	ENSP00000387732:S661A	S	+	1	0	SAMD4B	44565698	0.999000	0.42202	1.000000	0.80357	0.583000	0.36354	0.404000	0.20999	0.368000	0.24481	-0.805000	0.03199	TCC	T|0.996;G|0.004	0.004	strong		0.562	SAMD4B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464467.1	NM_018028	
KCNH6	81033	hgsc.bcm.edu	37	17	61611423	61611423	+	Silent	SNP	T	T	C	rs7225568	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:61611423T>C	ENST00000583023.1	+	5	863	c.852T>C	c.(850-852)gaT>gaC	p.D284D	KCNH6_ENST00000580652.1_Silent_p.D284D|KCNH6_ENST00000456941.2_Silent_p.D284D|KCNH6_ENST00000581784.1_Silent_p.D284D|KCNH6_ENST00000314672.5_Silent_p.D284D	NM_030779.2	NP_110406.1	Q9H252	KCNH6_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 6	284					potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	signal transducer activity (GO:0004871)|voltage-gated potassium channel activity (GO:0005249)			breast(2)|central_nervous_system(2)|endometrium(9)|kidney(4)|large_intestine(6)|lung(20)|ovary(2)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	54					Doxazosin(DB00590)|Ibutilide(DB00308)|Miconazole(DB01110)|Prazosin(DB00457)|Terazosin(DB01162)	TGCTCAGCGATCAGGACGAAT	0.587													C|||	2241	0.447484	0.5295	0.4251	5008	,	,		18615	0.2599		0.6064	False		,,,				2504	0.3824				p.D284D		Atlas-SNP	.											KCNH6,NS,malignant_melanoma,+2,1	KCNH6	122	1	0			c.T852C						PASS	.	C	,	2341,2065	570.5+/-382.9	637,1067,499	161.0	140.0	147.0		852,852	1.8	1.0	17	dbSNP_116	147	5115,3485	509.5+/-377.3	1559,1997,744	no	coding-synonymous,coding-synonymous	KCNH6	NM_030779.2,NM_173092.1	,	2196,3064,1243	CC,CT,TT		40.5233,46.8679,42.6726	,	284/995,284/906	61611423	7456,5550	2203	4300	6503	SO:0001819	synonymous_variant	81033	exon5			CAGCGATCAGGAC	AF311913	CCDS11638.1, CCDS11639.1, CCDS62290.1	17q23.3	2012-07-05				ENSG00000173826		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	18862	protein-coding gene	gene with protein product		608168				16382104	Standard	NM_030779		Approved	Kv11.2, erg2, HERG2	uc002jay.3	Q9H252		ENST00000583023.1:c.852T>C	17.37:g.61611423T>C		Somatic	197	0	0		WXS	Illumina HiSeq	Phase_I	161	85	0.52795	NM_030779	Q9BRD7	Silent	SNP	ENST00000583023.1	37	CCDS11638.1																																																																																			C|0.529;N|0.000	0.529	strong		0.587	KCNH6-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443853.1	NM_030779	
ADAR	103	hgsc.bcm.edu	37	1	154573967	154573967	+	Missense_Mutation	SNP	T	T	C	rs2229857	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:154573967T>C	ENST00000368474.4	-	2	1350	c.1151A>G	c.(1150-1152)aAa>aGa	p.K384R	ADAR_ENST00000368471.3_Missense_Mutation_p.K89R|ADAR_ENST00000292205.5_Missense_Mutation_p.K427R|ADAR_ENST00000471068.1_5'Flank	NM_001111.4|NM_015840.3|NM_015841.3	NP_001102|NP_056655.2|NP_056656.2	P55265	DSRAD_HUMAN	adenosine deaminase, RNA-specific	384			K -> R (in dbSNP:rs2229857). {ECO:0000269|PubMed:17974005, ECO:0000269|PubMed:7565688, ECO:0000269|PubMed:9020165, ECO:0000269|Ref.4}.		adenosine to inosine editing (GO:0006382)|base conversion or substitution editing (GO:0016553)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|miRNA loading onto RISC involved in gene silencing by miRNA (GO:0035280)|mRNA modification (GO:0016556)|mRNA processing (GO:0006397)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein kinase activity by regulation of protein phosphorylation (GO:0044387)|negative regulation of viral genome replication (GO:0045071)|positive regulation of viral genome replication (GO:0045070)|pre-miRNA processing (GO:0031054)|protein export from nucleus (GO:0006611)|protein import into nucleus (GO:0006606)|response to interferon-alpha (GO:0035455)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|supraspliceosomal complex (GO:0044530)	DNA binding (GO:0003677)|double-stranded RNA adenosine deaminase activity (GO:0003726)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(9)|lung(20)|ovary(4)|prostate(2)|skin(2)	51	all_lung(78;2.22e-29)|Lung NSC(65;3.66e-27)|all_hematologic(923;0.088)|Hepatocellular(266;0.0997)		LUSC - Lung squamous cell carcinoma(543;0.185)	Colorectal(1306;0.115)		TGCGTTTCTTTTGGTCTCAGG	0.448													T|||	3118	0.622604	0.3691	0.7579	5008	,	,		22598	0.6687		0.673	False		,,,				2504	0.7699				p.K384R		Atlas-SNP	.											.	ADAR	113	.	0			c.A1151G						PASS	.	T	ARG/LYS,ARG/LYS,ARG/LYS,ARG/LYS,ARG/LYS	1888,2518	542.0+/-375.9	409,1070,724	232.0	228.0	229.0		266,1151,266,1151,1151	-0.8	0.0	1	dbSNP_98	229	6018,2582	689.7+/-404.4	2125,1768,407	yes	missense,missense,missense,missense,missense	ADAR	NM_001025107.2,NM_001111.4,NM_001193495.1,NM_015840.3,NM_015841.3	26,26,26,26,26	2534,2838,1131	CC,CT,TT		30.0233,42.8507,39.2127	benign,benign,benign,benign,benign	89/932,384/1227,89/932,384/1201,384/1182	154573967	7906,5100	2203	4300	6503	SO:0001583	missense	103	exon2			TTTCTTTTGGTCT	BC038227	CCDS1071.1, CCDS30879.1	1q21.3	2012-03-22			ENSG00000160710	ENSG00000160710	3.5.4.-		225	protein-coding gene	gene with protein product		146920	"""interferon-induced protein 4"""	IFI4, G1P1		7972084	Standard	NM_001111		Approved	ADAR1	uc001ffh.3	P55265	OTTHUMG00000037261	ENST00000368474.4:c.1151A>G	1.37:g.154573967T>C	ENSP00000357459:p.Lys384Arg	Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	145	145	1	NM_015840	B1AQQ9|B1AQR0|D3DV76|O15223|O43859|O43860|Q9BYM3|Q9BYM4	Missense_Mutation	SNP	ENST00000368474.4	37	CCDS1071.1	1354	0.61996336996337	181	0.3678861788617886	273	0.7541436464088398	393	0.6870629370629371	507	0.6688654353562006	T	10.83	1.460707	0.26248	0.428507	0.699767	ENSG00000160710	ENST00000292205;ENST00000368474;ENST00000368471;ENST00000529168	T;T;T;T	0.14391	2.72;2.73;2.51;2.73	4.54	-0.812	0.10853	.	2.573260	0.01562	N	0.020199	T	0.03011	0.0089	L	0.36672	1.1	0.80722	P	0.0	B;B;B	0.06786	0.0;0.001;0.0	B;B;B	0.04013	0.001;0.001;0.0	T	0.36163	-0.9759	9	0.21014	T	0.42	0.0972	4.8985	0.13762	0.0:0.3454:0.1701:0.4845	rs2229857;rs17843863;rs58094036;rs2229857	384;384;384	P55265-3;P55265-2;P55265	.;.;DSRAD_HUMAN	R	427;384;89;379	ENSP00000292205:K427R;ENSP00000357459:K384R;ENSP00000357456:K89R;ENSP00000431794:K379R	ENSP00000292205:K427R	K	-	2	0	ADAR	152840591	0.000000	0.05858	0.000000	0.03702	0.025000	0.11179	-0.342000	0.07801	-0.036000	0.13669	0.459000	0.35465	AAA	T|0.384;C|0.616	0.616	strong		0.448	ADAR-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000090691.2	NM_001111	
C4orf17	84103	hgsc.bcm.edu	37	4	100443720	100443720	+	Missense_Mutation	SNP	G	G	A	rs13143848	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:100443720G>A	ENST00000326581.4	+	3	553	c.191G>A	c.(190-192)gGa>gAa	p.G64E	C4orf17_ENST00000514652.1_Missense_Mutation_p.G64E|C4orf17_ENST00000503257.1_3'UTR	NM_032149.2	NP_115525.2	Q53FE4	CD017_HUMAN	chromosome 4 open reading frame 17	64			G -> E (in dbSNP:rs13143848). {ECO:0000269|PubMed:11230166, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.2}.					p.G64E(1)		central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(9)|prostate(1)|urinary_tract(3)	18				OV - Ovarian serous cystadenocarcinoma(123;2.08e-08)		ACATTGTGGGGAGTTGGCCAG	0.428													G|||	1574	0.314297	0.3449	0.219	5008	,	,		18112	0.2361		0.2992	False		,,,				2504	0.4366				p.G64E		Atlas-SNP	.											C4orf17,NS,carcinoma,0,1	C4orf17	42	1	1	Substitution - Missense(1)	prostate(1)	c.G191A						PASS	.	G	GLU/GLY	1479,2927	475.7+/-357.4	239,1001,963	178.0	155.0	163.0		191	1.2	0.0	4	dbSNP_121	163	2649,5951	425.6+/-355.0	408,1833,2059	yes	missense	C4orf17	NM_032149.2	98	647,2834,3022	AA,AG,GG		30.8023,33.5679,31.7392	probably-damaging	64/360	100443720	4128,8878	2203	4300	6503	SO:0001583	missense	84103	exon3			TGTGGGGAGTTGG	AL136838	CCDS3649.1	4q23	2008-02-05			ENSG00000138813	ENSG00000138813			25274	protein-coding gene	gene with protein product						11230166	Standard	NM_032149		Approved	DKFZP434G072	uc003huw.3	Q53FE4	OTTHUMG00000131027	ENST00000326581.4:c.191G>A	4.37:g.100443720G>A	ENSP00000322582:p.Gly64Glu	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	117	60	0.512821	NM_032149	Q6FI84|Q6IS77|Q8NA78|Q9H0D9	Missense_Mutation	SNP	ENST00000326581.4	37	CCDS3649.1	565	0.2586996336996337	172	0.34959349593495936	84	0.23204419889502761	91	0.1590909090909091	218	0.287598944591029	G	7.485	0.649475	0.14516	0.335679	0.308023	ENSG00000138813	ENST00000326581;ENST00000514652	T;T	0.16743	2.33;2.32	5.18	1.2	0.21068	.	1.209900	0.05571	N	0.571058	T	0.00012	0.0000	L	0.57536	1.79	0.80722	P	0.0	B	0.28850	0.225	B	0.27380	0.079	T	0.44847	-0.9301	9	0.15066	T	0.55	1.6219	3.2821	0.06918	0.3038:0.0:0.5128:0.1834	rs13143848;rs58148455;rs13143848	64	Q53FE4	CD017_HUMAN	E	64	ENSP00000322582:G64E;ENSP00000427663:G64E	ENSP00000322582:G64E	G	+	2	0	C4orf17	100662743	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.097000	0.15168	0.332000	0.23536	0.585000	0.79938	GGA	G|0.699;A|0.301	0.301	strong		0.428	C4orf17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253670.2	NM_032149	
GPATCH1	55094	hgsc.bcm.edu	37	19	33579128	33579128	+	Silent	SNP	T	T	C	rs7259333	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	144	0	0		WXS	Illumina HiSeq	Phase_I	87	33	0.37931	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	
KRTAP10-6	386674	hgsc.bcm.edu	37	21	46011583	46011583	+	Nonsense_Mutation	SNP	G	G	T	rs233303	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:46011583G>T	ENST00000400368.1	-	1	803	c.783C>A	c.(781-783)tgC>tgA	p.C261*	TSPEAR_ENST00000323084.4_Intron	NM_198688.2	NP_941961.2	P60371	KR106_HUMAN	keratin associated protein 10-6	261	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						GGGAGGAGGTGCAGCAAGCTG	0.652													.|||	1083	0.216254	0.1528	0.2248	5008	,	,		23087	0.3214		0.2107	False		,,,				2504	0.1933				p.C261X		Atlas-SNP	.											.	KRTAP10-6	57	.	0			c.C783A						PASS	.	G	,stop/CYS	708,3698	293.0+/-282.3	54,600,1549	112.0	115.0	114.0		,783	-0.3	0.0	21	dbSNP_79	114	2104,6496	357.5+/-330.8	248,1608,2444	no	intron,stop-gained	TSPEAR,KRTAP10-6	NM_144991.2,NM_198688.2	,	302,2208,3993	TT,TG,GG		24.4651,16.069,21.6208	,	,261/366	46011583	2812,10194	2203	4300	6503	SO:0001587	stop_gained	386674	exon1			GGAGGTGCAGCAA	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.783C>A	21.37:g.46011583G>T	ENSP00000383219:p.Cys261*	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	122	68	0.557377	NM_198688		Nonsense_Mutation	SNP	ENST00000400368.1	37	CCDS42959.1	479	0.21932234432234432	69	0.1402439024390244	78	0.2154696132596685	164	0.2867132867132867	168	0.22163588390501318	g	11.11	1.542055	0.27563	0.16069	0.244651	ENSG00000188155	ENST00000400368	.	.	.	2.61	-0.354	0.12591	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	0.99999877584	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	6.1164	0.20130	0.4549:0.0:0.5451:0.0	rs233303;rs858573;rs56713674;rs233303	.	.	.	X	261	.	ENSP00000383219:C261X	C	-	3	2	KRTAP10-6	44836011	0.015000	0.18098	0.039000	0.18376	0.249000	0.25844	-0.199000	0.09491	0.012000	0.14892	0.400000	0.26472	TGC	G|0.788;T|0.212	0.212	strong		0.652	KRTAP10-6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128037.1	NM_198688	
ZFPM1	161882	hgsc.bcm.edu	37	16	88594567	88594567	+	Silent	SNP	C	C	T	rs35121729	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:88594567C>T	ENST00000319555.3	+	6	955	c.633C>T	c.(631-633)tgC>tgT	p.C211C	RP11-21B21.4_ENST00000563243.1_RNA	NM_153813.2	NP_722520.2	Q8IX07	FOG1_HUMAN	zinc finger protein, FOG family member 1	211					atrial septum morphogenesis (GO:0060413)|atrioventricular valve morphogenesis (GO:0003181)|blood coagulation (GO:0007596)|cardiac muscle tissue morphogenesis (GO:0055008)|definitive erythrocyte differentiation (GO:0060318)|embryonic hemopoiesis (GO:0035162)|erythrocyte differentiation (GO:0030218)|granulocyte differentiation (GO:0030851)|megakaryocyte development (GO:0035855)|megakaryocyte differentiation (GO:0030219)|mitral valve formation (GO:0003192)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of interleukin-4 biosynthetic process (GO:0045403)|negative regulation of mast cell differentiation (GO:0060377)|negative regulation of protein binding (GO:0032091)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|outflow tract morphogenesis (GO:0003151)|platelet formation (GO:0030220)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|primitive erythrocyte differentiation (GO:0060319)|regulation of chemokine production (GO:0032642)|regulation of definitive erythrocyte differentiation (GO:0010724)|T-helper cell lineage commitment (GO:0002295)|transcriptional activation by promoter-enhancer looping (GO:0071733)|tricuspid valve formation (GO:0003195)|ventricular septum morphogenesis (GO:0060412)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|transcription factor complex (GO:0005667)|transcriptional repressor complex (GO:0017053)	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)|RNA polymerase II transcription factor binding (GO:0001085)|transcription factor binding (GO:0008134)			central_nervous_system(1)|ovary(2)|urinary_tract(1)	4				BRCA - Breast invasive adenocarcinoma(80;0.0478)		AGCCCACGTGCCCGGCCCCTG	0.697													c|||	633	0.126398	0.0098	0.1326	5008	,	,		14718	0.3591		0.0905	False		,,,				2504	0.0767				p.C211C	Pancreas(49;850 1106 29641 32847 38344)	Atlas-SNP	.											ZFPM1,NS,carcinoma,0,1	ZFPM1	32	1	0			c.C633T						scavenged	.	C		84,4268		1,82,2093	18.0	21.0	20.0		633	4.1	0.0	16	dbSNP_126	20	684,7898		23,638,3630	no	coding-synonymous	ZFPM1	NM_153813.2		24,720,5723	TT,TC,CC		7.9702,1.9301,5.9378		211/1007	88594567	768,12166	2176	4291	6467	SO:0001819	synonymous_variant	161882	exon6			CACGTGCCCGGCC	AF488691	CCDS32502.1	16q24.2	2013-01-10	2012-11-27		ENSG00000179588	ENSG00000179588		"""Zinc fingers, C2H2-type"", ""Zinc fingers, C2HC-type containing"""	19762	protein-coding gene	gene with protein product		601950	"""zinc finger protein, multitype 1"""				Standard	NM_153813		Approved	FOG1, FOG, ZNF89A, ZC2HC11A	uc002fkv.3	Q8IX07	OTTHUMG00000173152	ENST00000319555.3:c.633C>T	16.37:g.88594567C>T		Somatic	85	1	0.0117647		WXS	Illumina HiSeq	Phase_I	120	118	0.983333	NM_153813		Silent	SNP	ENST00000319555.3	37	CCDS32502.1																																																																																			C|0.911;T|0.089	0.089	strong		0.697	ZFPM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422270.2		
IZUMO1	284359	hgsc.bcm.edu	37	19	49247786	49247786	+	Silent	SNP	G	G	A	rs8108468	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:49247786G>A	ENST00000332955.2	-	4	868	c.321C>T	c.(319-321)ttC>ttT	p.F107F		NM_182575.2	NP_872381.2	Q8IYV9	IZUM1_HUMAN	izumo sperm-egg fusion 1	107					cell adhesion (GO:0007155)|fusion of sperm to egg plasma membrane (GO:0007342)|multicellular organism reproduction (GO:0032504)|single fertilization (GO:0007338)|sperm-egg recognition (GO:0035036)	acrosomal membrane (GO:0002080)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)			endometrium(4)|kidney(3)|large_intestine(4)|lung(2)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	17		all_lung(116;0.000156)|Lung NSC(112;0.000251)|all_epithelial(76;0.000761)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000134)|all cancers(93;0.000348)|Epithelial(262;0.019)|GBM - Glioblastoma multiforme(486;0.022)		GCTCCTTCACGAAGAGATCGC	0.502													G|||	2524	0.503994	0.2769	0.5403	5008	,	,		20854	0.8363		0.4493	False		,,,				2504	0.499				p.F107F		Atlas-SNP	.											.	IZUMO1	30	.	0			c.C321T						PASS	.	G		1247,3159	429.9+/-342.4	194,859,1150	97.0	86.0	89.0		321	-2.6	0.0	19	dbSNP_116	89	3745,4855	532.3+/-382.2	787,2171,1342	no	coding-synonymous	IZUMO1	NM_182575.2		981,3030,2492	AA,AG,GG		43.5465,28.3023,38.3823		107/351	49247786	4992,8014	2203	4300	6503	SO:0001819	synonymous_variant	284359	exon4			CTTCACGAAGAGA	BC034769	CCDS12732.1	19q13.33	2014-07-23			ENSG00000182264	ENSG00000182264		"""-"""	28539	protein-coding gene	gene with protein product	"""oocyte binding/fusion factor"""	609278				15759005, 18952059, 19658160, 22957301	Standard	NM_182575		Approved	IZUMO, MGC34799, OBF	uc002pkj.3	Q8IYV9	OTTHUMG00000183324	ENST00000332955.2:c.321C>T	19.37:g.49247786G>A		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	60	25	0.416667	NM_182575	Q6Q8P6|Q6Q8P7	Silent	SNP	ENST00000332955.2	37	CCDS12732.1																																																																																			G|0.551;A|0.449	0.449	strong		0.502	IZUMO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466189.1	NM_182575	
VSIG1	340547	hgsc.bcm.edu	37	X	107315933	107315933	+	Missense_Mutation	SNP	G	G	A	rs17254305	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:107315933G>A	ENST00000217957.5	+	4	556	c.439G>A	c.(439-441)Gtt>Att	p.V147I	VSIG1_ENST00000415430.3_Missense_Mutation_p.V183I|VSIG1_ENST00000485533.1_3'UTR	NM_182607.4	NP_872413.1	Q86XK7	VSIG1_HUMAN	V-set and immunoglobulin domain containing 1	147	Ig-like C2-type 2.		V -> I (in dbSNP:rs17254305).			integral component of membrane (GO:0016021)				breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)	17						CCTTTGTAGCGTTCAAGGAAG	0.443													A|||	24	0.00635762	0.003	0.0115	3775	,	,		13154	0.0		0.0119	False		,,,				2504	0.0				p.V183I		Atlas-SNP	.											.	VSIG1	126	.	0			c.G547A						PASS	.	A	ILE/VAL,ILE/VAL	16,3819		0,15,1,1617,570	218.0	170.0	186.0		547,439	1.2	0.8	X	dbSNP_123	186	149,6579		2,105,40,2321,1832	yes	missense,missense	VSIG1	NM_001170553.1,NM_182607.4	29,29	2,120,41,3938,2402	AA,AG,A,GG,G		2.2146,0.4172,1.5621	benign,benign	183/424,147/388	107315933	165,10398	2203	4300	6503	SO:0001583	missense	340547	exon5			TGTAGCGTTCAAG	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.439G>A	X.37:g.107315933G>A	ENSP00000217957:p.Val147Ile	Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	105	104	0.990476	NM_001170553	C9J4P2|Q6MZS4	Missense_Mutation	SNP	ENST00000217957.5	37	CCDS14535.1	11	0.006630500301386378	1	0.0020325203252032522	3	0.008333333333333333	0	0.0	4	0.005305039787798408	A	1.748	-0.489953	0.04322	0.004172	0.022146	ENSG00000101842	ENST00000415430;ENST00000217957	T;T	0.15256	2.44;2.44	5.01	1.2	0.21068	Immunoglobulin-like (1);	0.161033	0.41823	N	0.000801	T	0.01627	0.0052	N	0.01779	-0.725	0.09310	N	0.999998	B;B	0.18310	0.027;0.012	B;B	0.16722	0.016;0.011	T	0.33369	-0.9871	10	0.02654	T	1	.	0.8947	0.01261	0.4121:0.1585:0.2732:0.1561	rs17254305;rs52798505;rs17254305	183;147	C9J4P2;Q86XK7	.;VSIG1_HUMAN	I	183;147	ENSP00000402219:V183I;ENSP00000217957:V147I	ENSP00000217957:V147I	V	+	1	0	VSIG1	107202589	0.861000	0.29849	0.837000	0.33122	0.774000	0.43823	0.365000	0.20348	-0.231000	0.09825	-0.314000	0.08810	GTT	0|0.004;A|0.013	0.013	strong		0.443	VSIG1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000057858.1	NM_182607	
CENPE	1062	hgsc.bcm.edu	37	4	104082349	104082349	+	Silent	SNP	C	C	T	rs2251634	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	195	0	0		WXS	Illumina HiSeq	Phase_I	140	57	0.407143	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			
FBXO25	26260	hgsc.bcm.edu	37	8	381344	381344	+	Missense_Mutation	SNP	C	C	G	rs28438773	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:381344C>G	ENST00000276326.5	+	3	257	c.138C>G	c.(136-138)atC>atG	p.I46M	FBXO25_ENST00000352684.2_5'UTR|FBXO25_ENST00000350302.3_Missense_Mutation_p.I46M|FBXO25_ENST00000382824.1_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	110	0	0		WXS	Illumina HiSeq	Phase_I	80	54	0.675	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	
PQLC2	54896	hgsc.bcm.edu	37	1	19652874	19652874	+	Missense_Mutation	SNP	G	G	A	rs41264079	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:19652874G>A	ENST00000375153.3	+	5	1158	c.518G>A	c.(517-519)gGc>gAc	p.G173D	PQLC2_ENST00000400548.2_Missense_Mutation_p.G108D|PQLC2_ENST00000375155.3_Missense_Mutation_p.G173D	NM_001040125.1	NP_001035214.1	Q6ZP29	LAAT1_HUMAN	PQ loop repeat containing 2	173				G -> D (in Ref. 1; BAG54217). {ECO:0000305}.	amino acid homeostasis (GO:0080144)|arginine transport (GO:0015809)|lysine transport (GO:0015819)	integral component of organelle membrane (GO:0031301)|lysosomal membrane (GO:0005765)	arginine transmembrane transporter activity (GO:0015181)|basic amino acid transmembrane transporter activity (GO:0015174)|L-lysine transmembrane transporter activity (GO:0015189)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(4)|skin(1)|urinary_tract(1)	10		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000321)|Lung NSC(340;0.000398)|Breast(348;0.00049)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00466)|BRCA - Breast invasive adenocarcinoma(304;1.89e-05)|Kidney(64;0.000177)|GBM - Glioblastoma multiforme(114;0.00124)|KIRC - Kidney renal clear cell carcinoma(64;0.00262)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)		GTGGAGTCGGGCAGCAAGGTG	0.701													G|||	248	0.0495208	0.0061	0.0447	5008	,	,		15617	0.0089		0.1243	False		,,,				2504	0.0767				p.G173D		Atlas-SNP	.											PQLC2,NS,carcinoma,0,2	PQLC2	34	2	0			c.G518A						PASS	.	G	ASP/GLY,ASP/GLY,ASP/GLY	82,4324		3,76,2124	22.0	24.0	23.0		518,323,518	1.0	0.0	1	dbSNP_127	23	954,7644		51,852,3396	yes	missense,missense,missense	PQLC2	NM_001040125.1,NM_001040126.1,NM_017765.2	94,94,94	54,928,5520	AA,AG,GG		11.0956,1.8611,7.9668	possibly-damaging,possibly-damaging,possibly-damaging	173/292,108/227,173/292	19652874	1036,11968	2203	4299	6502	SO:0001583	missense	54896	exon5			AGTCGGGCAGCAA	BC015324	CCDS195.2, CCDS30618.1	1p36.13	2013-10-11			ENSG00000040487	ENSG00000040487			26001	protein-coding gene	gene with protein product		614760				23169667	Standard	XM_005245915		Approved	FLJ20320	uc001bby.3	Q6ZP29	OTTHUMG00000002521	ENST00000375153.3:c.518G>A	1.37:g.19652874G>A	ENSP00000364295:p.Gly173Asp	Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	43	23	0.534884	NM_001040125	B3KWQ5|Q6ZMJ3|Q6ZP27|Q9NXC7	Missense_Mutation	SNP	ENST00000375153.3	37	CCDS195.2	123	0.05631868131868132	6	0.012195121951219513	19	0.052486187845303865	1	0.0017482517482517483	97	0.1279683377308707	G	9.751	1.167406	0.21621	0.018611	0.110956	ENSG00000040487	ENST00000375155;ENST00000375153;ENST00000400548;ENST00000432465	T;T	0.44482	0.92;0.92	5.34	1.03	0.20045	.	0.587200	0.19101	N	0.122716	T	0.00300	0.0009	L	0.46947	1.48	0.09310	N	1	B	0.19445	0.036	B	0.14578	0.011	T	0.08973	-1.0696	10	0.10636	T	0.68	-11.0629	6.7836	0.23662	0.1716:0.2965:0.5319:0.0	rs41264079	173	Q6ZP29	PQLC2_HUMAN	D	173;173;108;78	ENSP00000364297:G173D;ENSP00000364295:G173D	ENSP00000364295:G173D	G	+	2	0	PQLC2	19525461	0.006000	0.16342	0.008000	0.14137	0.252000	0.25951	0.561000	0.23515	0.623000	0.30267	0.462000	0.41574	GGC	G|0.938;A|0.062	0.062	strong		0.701	PQLC2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007255.1	NM_017765	
TNRC6C	57690	hgsc.bcm.edu	37	17	76093866	76093866	+	Intron	SNP	T	T	C	rs2290906	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:76093866T>C	ENST00000588061.1	+	19	5033				TNRC6C_ENST00000541771.1_Intron|TNRC6C_ENST00000335749.4_Silent_p.S1446S|TNRC6C_ENST00000301624.4_Intron|TNRC6C_ENST00000544502.1_Silent_p.S1446S|TNRC6C_ENST00000588847.1_Silent_p.S1446S			Q9HCJ0	TNR6C_HUMAN	trinucleotide repeat containing 6C						embryonic hemopoiesis (GO:0035162)|endoderm formation (GO:0001706)|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)|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 gene silencing by miRNA (GO:0060964)	cytosol (GO:0005829)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(9)|lung(16)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	40			BRCA - Breast invasive adenocarcinoma(99;0.00269)|Lung(188;0.0973)			CGCTGCCTTCTTCGAGTGCCT	0.587													C|||	1470	0.29353	0.4107	0.2666	5008	,	,		19861	0.2976		0.1252	False		,,,				2504	0.3231				p.S1446S		Atlas-SNP	.											.	TNRC6C	173	.	0			c.T4338C						PASS	.	C	,	489,895		86,317,289	43.0	40.0	41.0		4338,	2.6	1.0	17	dbSNP_100	41	468,2714		31,406,1154	no	coding-synonymous,intron	TNRC6C	NM_001142640.1,NM_018996.3	,	117,723,1443	CC,CT,TT		14.7077,35.3324,20.9593	,	1446/1727,	76093866	957,3609	692	1591	2283	SO:0001627	intron_variant	57690	exon18			GCCTTCTTCGAGT	AL834429	CCDS45798.1, CCDS45799.1	17q25.3	2012-10-04			ENSG00000078687	ENSG00000078687		"""Trinucleotide (CAG) repeat containing"""	29318	protein-coding gene	gene with protein product		610741					Standard	NM_018996		Approved	KIAA1582, FLJ20015	uc002juf.2	Q9HCJ0	OTTHUMG00000132642	ENST00000588061.1:c.4307-558T>C	17.37:g.76093866T>C		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	90	46	0.511111	NM_001142640	G3XAB8|Q86UE5|Q8N3D8|Q96MU9	Silent	SNP	ENST00000588061.1	37	CCDS45798.1																																																																																			T|0.737;C|0.263	0.263	strong		0.587	TNRC6C-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000395947.1	NM_018996	
SPATA17	128153	hgsc.bcm.edu	37	1	217915324	217915324	+	Silent	SNP	C	C	T	rs34347452	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:217915324C>T	ENST00000366933.4	+	6	458	c.403C>T	c.(403-405)Ctg>Ttg	p.L135L		NM_138796.2	NP_620151.1	Q96L03	SPT17_HUMAN	spermatogenesis associated 17	135						cytoplasm (GO:0005737)				endometrium(1)|kidney(1)|large_intestine(9)|lung(6)|pancreas(2)|prostate(1)|urinary_tract(1)	21				OV - Ovarian serous cystadenocarcinoma(81;0.0516)|all cancers(67;0.0891)|GBM - Glioblastoma multiforme(131;0.117)		CAGGAAGGCACTGGAGGAGTT	0.383													C|||	632	0.126198	0.0817	0.0951	5008	,	,		21411	0.1419		0.174	False		,,,				2504	0.1431				p.L135L		Atlas-SNP	.											.	SPATA17	59	.	0			c.C403T						PASS	.	C		464,3942	220.4+/-237.8	18,428,1757	99.0	93.0	95.0		403	2.8	0.7	1	dbSNP_126	95	1306,7294	258.1+/-281.9	109,1088,3103	no	coding-synonymous	SPATA17	NM_138796.2		127,1516,4860	TT,TC,CC		15.186,10.5311,13.6091		135/362	217915324	1770,11236	2203	4300	6503	SO:0001819	synonymous_variant	128153	exon6			AAGGCACTGGAGG	AK098591	CCDS1519.1	1q41	2008-02-05			ENSG00000162814	ENSG00000162814			25184	protein-coding gene	gene with protein product	"""IQ motif containing H"""	611032				16395525	Standard	NM_138796		Approved	IQCH	uc001hlh.1	Q96L03	OTTHUMG00000037875	ENST00000366933.4:c.403C>T	1.37:g.217915324C>T		Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	29	29	1	NM_138796	A5D6N2	Silent	SNP	ENST00000366933.4	37	CCDS1519.1																																																																																			C|0.870;T|0.130	0.130	strong		0.383	SPATA17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092433.2	NM_138796	
PRKAG3	53632	hgsc.bcm.edu	37	2	219691801	219691801	+	Missense_Mutation	SNP	G	G	A	rs33985460	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:219691801G>A	ENST00000529249.1	-	10	1333	c.1018C>T	c.(1018-1020)Cgg>Tgg	p.R340W	PRKAG3_ENST00000545803.1_Missense_Mutation_p.R156W|PRKAG3_ENST00000392098.3_Silent_p.P324P|PRKAG3_ENST00000439262.2_Missense_Mutation_p.R315W			Q9UGI9	AAKG3_HUMAN	protein kinase, AMP-activated, gamma 3 non-catalytic subunit	340	CBS 2. {ECO:0000255|PROSITE- ProRule:PRU00703}.		R -> Q. {ECO:0000269|PubMed:17878938}.|R -> W (in dbSNP:rs33985460). {ECO:0000269|PubMed:17878938}.		cell cycle arrest (GO:0007050)|fatty acid biosynthetic process (GO:0006633)|glucose transport (GO:0015758)|glycogen biosynthetic process (GO:0005978)|insulin receptor signaling pathway (GO:0008286)|intracellular signal transduction (GO:0035556)|membrane organization (GO:0061024)|protein phosphorylation (GO:0006468)	AMP-activated protein kinase complex (GO:0031588)|cytosol (GO:0005829)|extracellular space (GO:0005615)	AMP-activated protein kinase activity (GO:0004679)|ATP binding (GO:0005524)|protein kinase binding (GO:0019901)			large_intestine(7)|lung(10)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	20		Renal(207;0.0474)		Epithelial(149;4.35e-07)|all cancers(144;8.96e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)	Acetylsalicylic acid(DB00945)	AAGGAGGGCCGGGGCAGCAGG	0.607													G|||	154	0.0307508	0.0038	0.0432	5008	,	,		18697	0.0		0.0606	False		,,,				2504	0.0593				p.R340W		Atlas-SNP	.											.	PRKAG3	47	.	0			c.C1018T						PASS	.	G	TRP/ARG	53,4353	54.2+/-90.2	0,53,2150	92.0	96.0	95.0		1018	3.8	1.0	2	dbSNP_126	95	493,8107	142.5+/-198.7	10,473,3817	yes	missense	PRKAG3	NM_017431.2	101	10,526,5967	AA,AG,GG		5.7326,1.2029,4.1981	possibly-damaging	340/490	219691801	546,12460	2203	4300	6503	SO:0001583	missense	53632	exon10			AGGGCCGGGGCAG	AF214519	CCDS2424.1	2q35	2012-09-20			ENSG00000115592	ENSG00000115592			9387	protein-coding gene	gene with protein product		604976				10818001	Standard	NM_017431		Approved		uc002vjb.1	Q9UGI9	OTTHUMG00000133078	ENST00000529249.1:c.1018C>T	2.37:g.219691801G>A	ENSP00000436068:p.Arg340Trp	Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	134	64	0.477612	NM_017431	Q4QQG8|Q4V779|Q9NRL1	Missense_Mutation	SNP	ENST00000529249.1	37	CCDS2424.1	60	0.027472527472527472	3	0.006097560975609756	10	0.027624309392265192	0	0.0	47	0.06200527704485488	G	22.0	4.227310	0.79576	0.012029	0.057326	ENSG00000115592	ENST00000439262;ENST00000545803;ENST00000529249	D;D;D	0.88046	-1.64;-2.33;-1.63	5.77	3.79	0.43588	Cystathionine beta-synthase, core (1);	0.342203	0.34046	N	0.004318	T	0.49525	0.1562	L	0.38175	1.15	0.80722	D	1	D	0.64830	0.994	P	0.53360	0.724	T	0.74396	-0.3679	10	0.62326	D	0.03	-7.7995	13.4251	0.61020	0.0:0.0:0.5987:0.4013	rs33985460	340	Q9UGI9	AAKG3_HUMAN	W	315;156;340	ENSP00000397133:R315W;ENSP00000444536:R156W;ENSP00000436068:R340W	ENSP00000233944:R340W	R	-	1	2	PRKAG3	219400045	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.596000	0.61055	1.440000	0.47531	0.655000	0.94253	CGG	G|0.961;A|0.039	0.039	strong		0.607	PRKAG3-006	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385992.1		
MBL2	4153	hgsc.bcm.edu	37	10	54528266	54528266	+	Silent	SNP	G	G	C	rs930507	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:54528266G>C	ENST00000373968.3	-	4	442	c.378C>G	c.(376-378)ctC>ctG	p.L126L		NM_000242.2	NP_000233.1	P11226	MBL2_HUMAN	mannose-binding lectin (protein C) 2, soluble	126					acute-phase response (GO:0006953)|complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|complement activation, lectin pathway (GO:0001867)|defense response to bacterium (GO:0042742)|defense response to Gram-positive bacterium (GO:0050830)|innate immune response (GO:0045087)|killing by host of symbiont cells (GO:0051873)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of viral process (GO:0048525)|opsonization (GO:0008228)|positive regulation of phagocytosis (GO:0050766)|response to oxidative stress (GO:0006979)	cell surface (GO:0009986)|collagen trimer (GO:0005581)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	calcium-dependent protein binding (GO:0048306)|mannose binding (GO:0005537)|receptor binding (GO:0005102)			breast(1)|endometrium(2)|lung(12)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	21						GAGAGAAGGTGAGCCCTAAAA	0.423													C|||	3700	0.738818	0.6399	0.8559	5008	,	,		18473	0.7302		0.8032	False		,,,				2504	0.7321				p.L126L		Atlas-SNP	.											MBL2,colon,carcinoma,0,1	MBL2	55	1	0			c.C378G	GRCh37	CM068190	MBL2	M	rs930507	PASS	.	C		2926,1478	467.4+/-354.8	994,938,270	73.0	78.0	76.0		378	-4.6	0.0	10	dbSNP_86	76	7095,1505	281.8+/-295.3	2935,1225,140	no	coding-synonymous	MBL2	NM_000242.2		3929,2163,410	CC,CG,GG		17.5,33.5604,22.9391		126/249	54528266	10021,2983	2202	4300	6502	SO:0001819	synonymous_variant	4153	exon4			GAAGGTGAGCCCT	AF360991	CCDS7247.1	10q11.2	2014-09-17	2011-02-02		ENSG00000165471	ENSG00000165471		"""Collectins"""	6922	protein-coding gene	gene with protein product		154545	"""mannose-binding lectin (protein C) 2, soluble (opsonic defect)"""	MBL		1675710, 1672848	Standard	NM_000242		Approved	COLEC1	uc001jjt.3	P11226	OTTHUMG00000150270	ENST00000373968.3:c.378C>G	10.37:g.54528266G>C		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	28	8	0.285714	NM_000242	Q4VB12|Q4VB13|Q4VB14|Q5SQS3|Q86SI4|Q96KE4|Q96TF7|Q96TF8|Q96TF9	Silent	SNP	ENST00000373968.3	37	CCDS7247.1																																																																																			G|0.238;C|0.762	0.762	strong		0.423	MBL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048115.1	NM_000242	
AHNAK2	113146	hgsc.bcm.edu	37	14	105411162	105411162	+	Silent	SNP	C	C	T	rs61316883	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:105411162C>T	ENST00000333244.5	-	7	10745	c.10626G>A	c.(10624-10626)ctG>ctA	p.L3542L	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	3542						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)			CGGGGCCCTCCAGGAGTTCCA	0.632													.|||	126	0.0251597	0.0015	0.0187	5008	,	,		16472	0.0218		0.0348	False		,,,				2504	0.0552				p.L3542L		Atlas-SNP	.											.	AHNAK2	719	.	0			c.G10626A						PASS	.	C		21,3777		0,21,1878	90.0	98.0	95.0		10626	-8.2	0.0	14	dbSNP_129	95	256,7956		5,246,3855	no	coding-synonymous	AHNAK2	NM_138420.2		5,267,5733	TT,TC,CC		3.1174,0.5529,2.3064		3542/5796	105411162	277,11733	1899	4106	6005	SO:0001819	synonymous_variant	113146	exon7			GCCCTCCAGGAGT	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.10626G>A	14.37:g.105411162C>T		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	127	68	0.535433	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Silent	SNP	ENST00000333244.5	37	CCDS45177.1																																																																																			C|0.980;T|0.020	0.020	strong		0.632	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
FLCN	201163	hgsc.bcm.edu	37	17	17125868	17125868	+	Silent	SNP	T	T	A	rs113938514	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:17125868T>A	ENST00000285071.4	-	7	1180	c.726A>T	c.(724-726)acA>acT	p.T242T	RP11-45M22.4_ENST00000427497.3_Intron|FLCN_ENST00000389169.5_Silent_p.T242T	NM_144997.5	NP_659434.2	Q8NFG4	FLCN_HUMAN	folliculin	242					cell-cell junction assembly (GO:0007043)|hemopoiesis (GO:0030097)|in utero embryonic development (GO:0001701)|negative regulation of ATP biosynthetic process (GO:2001170)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation involved in kidney development (GO:1901723)|negative regulation of energy homeostasis (GO:2000506)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of gene expression (GO:0010629)|negative regulation of mitochondrion organization (GO:0010823)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein localization to nucleus (GO:1900181)|negative regulation of Rho protein signal transduction (GO:0035024)|negative regulation of TOR signaling (GO:0032007)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of gene expression (GO:0010628)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of TOR signaling (GO:0032008)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of cytokinesis (GO:0032465)|regulation of histone acetylation (GO:0035065)|regulation of pro-B cell differentiation (GO:2000973)|regulation of protein phosphorylation (GO:0001932)|regulation of TOR signaling (GO:0032006)|TOR signaling (GO:0031929)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein complex binding (GO:0032403)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(11)|stomach(1)|thyroid(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	23						TTGTCAGCGATGTCAGCGAGC	0.572									Familial Non-VHL Clear Cell Renal Cancer;Birt-Hogg-Dub syndrome				T|||	139	0.0277556	0.0772	0.0043	5008	,	,		20526	0.0		0.0149	False		,,,				2504	0.0194				p.T242T		Atlas-SNP	.											FLCN_ENST00000389169,NS,carcinoma,-1,2	FLCN	87	2	0			c.A726T						PASS	.	T	,	239,4167	140.8+/-176.2	6,227,1970	139.0	105.0	116.0		726,726	-11.4	0.1	17	dbSNP_132	116	194,8406	85.6+/-148.0	0,194,4106	no	coding-synonymous,coding-synonymous	FLCN	NM_144606.5,NM_144997.5	,	6,421,6076	AA,AT,TT		2.2558,5.4244,3.3292	,	242/343,242/580	17125868	433,12573	2203	4300	6503	SO:0001819	synonymous_variant	201163	exon7	Familial Cancer Database	Familial Clear Cell Renal Cell Cancer, FcRCC, Familial Non-VHL Non-Papillary Clear Cell Renal Cancer;BHD, Fibrofolliculomas with Trichodiscomas and Acrochordons, incl.: Hornstein-Knickenberg syndrome, Perifollicular Fibromatosis	CAGCGATGTCAGC	AF517523	CCDS32579.1, CCDS32580.1	17p11.2	2014-09-17			ENSG00000154803	ENSG00000154803			27310	protein-coding gene	gene with protein product		607273					Standard	NM_144997		Approved	BHD, MGC17998, MGC23445	uc002gra.4	Q8NFG4	OTTHUMG00000059275	ENST00000285071.4:c.726A>T	17.37:g.17125868T>A		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	88	49	0.556818	NM_144997	A6NJJ8|Q6ZRX1|Q96BD2|Q96BE4	Silent	SNP	ENST00000285071.4	37	CCDS32579.1																																																																																			T|0.971;A|0.029	0.029	strong		0.572	FLCN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131577.1	NM_144606	
IL1B	3553	hgsc.bcm.edu	37	2	113590390	113590390	+	Silent	SNP	G	G	A	rs1143634	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:113590390G>A	ENST00000263341.2	-	5	525	c.315C>T	c.(313-315)ttC>ttT	p.F105F	IL1B_ENST00000491056.1_5'UTR	NM_000576.2	NP_000567.1	P01584	IL1B_HUMAN	interleukin 1, beta	105					activation of MAPK activity (GO:0000187)|apoptotic process (GO:0006915)|cell-cell signaling (GO:0007267)|cellular response to drug (GO:0035690)|cellular response to mechanical stimulus (GO:0071260)|cellular response to organic cyclic compound (GO:0071407)|cellular response to organic substance (GO:0071310)|cytokine-mediated signaling pathway (GO:0019221)|ectopic germ cell programmed cell death (GO:0035234)|embryo implantation (GO:0007566)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|fever generation (GO:0001660)|hyaluronan biosynthetic process (GO:0030213)|immune response (GO:0006955)|inflammatory response (GO:0006954)|interleukin-1 beta production (GO:0032611)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|MAPK cascade (GO:0000165)|monocyte aggregation (GO:0070487)|negative regulation of adiponectin secretion (GO:0070164)|negative regulation of cell proliferation (GO:0008285)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of glucose transport (GO:0010829)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of lipid catabolic process (GO:0050995)|negative regulation of lipid metabolic process (GO:0045833)|negative regulation of MAP kinase activity (GO:0043407)|neutrophil chemotaxis (GO:0030593)|positive regulation of angiogenesis (GO:0045766)|positive regulation of calcidiol 1-monooxygenase activity (GO:0060559)|positive regulation of cell adhesion molecule production (GO:0060355)|positive regulation of cell division (GO:0051781)|positive regulation of chemokine biosynthetic process (GO:0045080)|positive regulation of fever generation (GO:0031622)|positive regulation of gene expression (GO:0010628)|positive regulation of granulocyte macrophage colony-stimulating factor production (GO:0032725)|positive regulation of heterotypic cell-cell adhesion (GO:0034116)|positive regulation of histone acetylation (GO:0035066)|positive regulation of histone phosphorylation (GO:0033129)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of interleukin-6 biosynthetic process (GO:0045410)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of JNK cascade (GO:0046330)|positive regulation of lipid catabolic process (GO:0050996)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|positive regulation of mitosis (GO:0045840)|positive regulation of monocyte chemotactic protein-1 production (GO:0071639)|positive regulation of myosin light chain kinase activity (GO:0035505)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of prostaglandin secretion (GO:0032308)|positive regulation of protein export from nucleus (GO:0046827)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of T cell mediated immunity (GO:0002711)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|positive regulation vascular endothelial growth factor production (GO:0010575)|protein kinase B signaling (GO:0043491)|regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043122)|regulation of insulin secretion (GO:0050796)|response to ATP (GO:0033198)|response to carbohydrate (GO:0009743)|sequestering of triglyceride (GO:0030730)|signal transduction (GO:0007165)|smooth muscle adaptation (GO:0014805)	cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|secretory granule (GO:0030141)	cytokine activity (GO:0005125)|interleukin-1 receptor binding (GO:0005149)|protein domain specific binding (GO:0019904)			breast(2)|central_nervous_system(1)|large_intestine(1)|lung(8)	12					Canakinumab(DB06168)|Gallium nitrate(DB05260)|Minocycline(DB01017)|Rilonacept(DB06372)	CCCATGTGTCGAAGAAGATAG	0.488													G|||	665	0.132788	0.1225	0.1254	5008	,	,		23482	0.0228		0.2475	False		,,,				2504	0.1472				p.F105F		Atlas-SNP	.											.	IL1B	35	.	0			c.C315T	GRCh37	CM040228	IL1B	M	rs1143634	PASS	.	G		614,3792	265.9+/-266.9	34,546,1623	155.0	129.0	138.0		315	-4.7	0.0	2	dbSNP_86	138	2042,6558	356.9+/-330.5	229,1584,2487	no	coding-synonymous	IL1B	NM_000576.2		263,2130,4110	AA,AG,GG		23.7442,13.9355,20.4213		105/270	113590390	2656,10350	2203	4300	6503	SO:0001819	synonymous_variant	3553	exon5			TGTGTCGAAGAAG	M15330	CCDS2102.1	2q14	2014-01-30			ENSG00000125538	ENSG00000125538		"""Interleukins and interleukin receptors"", ""Endogenous ligands"""	5992	protein-coding gene	gene with protein product		147720				2954882, 2989698	Standard	NM_000576		Approved	IL1F2, IL-1B, IL1-BETA	uc002tii.1	P01584	OTTHUMG00000131344	ENST00000263341.2:c.315C>T	2.37:g.113590390G>A		Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	158	74	0.468354	NM_000576	Q53X59|Q53XX2|Q7M4S7|Q7RU01|Q96HE5|Q9UCT6	Silent	SNP	ENST00000263341.2	37	CCDS2102.1																																																																																			G|0.828;A|0.172	0.172	strong		0.488	IL1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254125.2	NM_000576	
ASCC3	10973	hgsc.bcm.edu	37	6	100964147	100964147	+	Missense_Mutation	SNP	G	G	C	rs240780	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:100964147G>C	ENST00000369162.2	-	39	6328	c.5984C>G	c.(5983-5985)tCc>tGc	p.S1995C		NM_006828.2	NP_006819.2	Q8N3C0	ASCC3_HUMAN	activating signal cointegrator 1 complex subunit 3	1995	SEC63 2.		S -> C (in dbSNP:rs240780). {ECO:0000269|PubMed:12077347, ECO:0000269|Ref.7}.		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.S1995C(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)		TTCAGGAAGGGACTCGATGGA	0.458													C|||	3845	0.767772	0.9486	0.611	5008	,	,		17929	0.7857		0.5795	False		,,,				2504	0.8098				p.S1995C		Atlas-SNP	.											ASCC3,NS,carcinoma,0,1	ASCC3	205	1	1	Substitution - Missense(1)	prostate(1)	c.C5984G	GRCh37	CM064987	ASCC3	M	rs240780	scavenged	.	C	CYS/SER	3843,563	250.6+/-257.6	1677,489,37	133.0	128.0	130.0		5984	5.0	1.0	6	dbSNP_79	130	5027,3573	518.9+/-379.4	1469,2089,742	yes	missense	ASCC3	NM_006828.2	112	3146,2578,779	CC,CG,GG		41.5465,12.778,31.8007	benign	1995/2203	100964147	8870,4136	2203	4300	6503	SO:0001583	missense	10973	exon39			GGAAGGGACTCGA	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.5984C>G	6.37:g.100964147G>C	ENSP00000358159:p.Ser1995Cys	Somatic	97	1	0.0103093		WXS	Illumina HiSeq	Phase_I	87	84	0.965517	NM_006828	E7EW23|O43738|Q4G1A0|Q5VTN2|Q9H1I9|Q9H5A2|Q9NTR0	Missense_Mutation	SNP	ENST00000369162.2	37	CCDS5046.1	1556	0.7124542124542125	469	0.9532520325203252	232	0.6408839779005525	433	0.756993006993007	422	0.5567282321899736	C	10.40	1.340708	0.24339	0.87222	0.584535	ENSG00000112249	ENST00000369162	T	0.66099	-0.19	4.96	4.96	0.65561	Sec63 domain (3);	0.060161	0.64402	N	0.000002	T	0.25232	0.0613	N	0.08118	0	0.09310	P	1.0	B	0.02656	0.0	B	0.01281	0.0	T	0.03829	-1.1000	9	0.33141	T	0.24	.	14.8991	0.70664	0.0:0.8558:0.1442:0.0	rs240780;rs17303636;rs52801369;rs57462599;rs240780	1995	Q8N3C0	HELC1_HUMAN	C	1995	ENSP00000358159:S1995C	ENSP00000358159:S1995C	S	-	2	0	ASCC3	101070868	1.000000	0.71417	1.000000	0.80357	0.503000	0.33858	3.029000	0.49712	1.244000	0.43870	-0.352000	0.07741	TCC	G|0.308;C|0.692	0.692	strong		0.458	ASCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041632.2	NM_006828	
JAKMIP3	282973	hgsc.bcm.edu	37	10	133966522	133966522	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:133966522G>A	ENST00000298622.4	+	16	2200	c.2062G>A	c.(2062-2064)Gaa>Aaa	p.E688K	JAKMIP3_ENST00000477275.1_3'UTR	NM_001105521.2	NP_001098991.1	Q5VZ66	JKIP3_HUMAN	Janus kinase and microtubule interacting protein 3	688						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)		GACCTTGGCCGAAAAGGTAAC	0.597																																					p.E688K		Atlas-SNP	.											.	JAKMIP3	69	.	0			c.G2062A						PASS	.						116.0	81.0	93.0					10																	133966522		2200	4293	6493	SO:0001583	missense	282973	exon16			TTGGCCGAAAAGG	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.2062G>A	10.37:g.133966522G>A	ENSP00000298622:p.Glu688Lys	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	106	27	0.254717	NM_001105521	A6PW00|Q69YM6|Q6ZT29	Missense_Mutation	SNP	ENST00000298622.4	37	CCDS44494.1	.	.	.	.	.	.	.	.	.	.	G	23.0	4.366941	0.82463	.	.	ENSG00000188385	ENST00000298622	T	0.30714	1.52	4.01	4.01	0.46588	.	.	.	.	.	T	0.49592	0.1566	M	0.68317	2.08	0.49798	D	0.999825	D;D	0.89917	1.0;0.997	D;P	0.64506	0.926;0.715	T	0.46414	-0.9193	9	0.21540	T	0.41	.	16.1506	0.81618	0.0:0.0:1.0:0.0	.	125;688	Q5VZ66-2;Q5VZ66	.;JKIP3_HUMAN	K	688	ENSP00000298622:E688K	ENSP00000298622:E688K	E	+	1	0	JAKMIP3	133816512	1.000000	0.71417	0.876000	0.34364	0.450000	0.32258	9.219000	0.95173	1.780000	0.52325	0.479000	0.44913	GAA	.	.	none		0.597	JAKMIP3-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051049.3	NM_194303	
ANO4	121601	hgsc.bcm.edu	37	12	101520847	101520847	+	Silent	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:101520847G>A	ENST00000392977.3	+	27	3077	c.2867G>A	c.(2866-2868)tGa>tAa	p.*956*	ANO4_ENST00000299222.9_Silent_p.*476*|ANO4_ENST00000550015.1_Silent_p.*476*|ANO4_ENST00000392979.3_Silent_p.*921*			Q32M45	ANO4_HUMAN	anoctamin 4	0					chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	intracellular calcium activated chloride channel activity (GO:0005229)			NS(1)|biliary_tract(1)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(33)|ovary(4)|prostate(5)|skin(7)|stomach(2)|urinary_tract(1)	78						GAGTGGCCGTGACCATGTAGG	0.483										HNSCC(74;0.22)																											p.X921X		Atlas-SNP	.											.	ANO4	183	.	0			c.G2762A						PASS	.						91.0	61.0	71.0					12																	101520847		2203	4300	6503	SO:0001819	synonymous_variant	121601	exon26			GGCCGTGACCATG	AK091540	CCDS31884.1, CCDS66445.1	12q23.3	2014-04-09	2008-08-28	2008-08-28	ENSG00000151572	ENSG00000151572		"""Ion channels / Chloride channels : Calcium activated : Anoctamins"""	23837	protein-coding gene	gene with protein product		610111	"""transmembrane protein 16D"""	TMEM16D		12739008, 15067359, 24692353	Standard	NM_178826		Approved	FLJ34221, FLJ34272, FLJ35277	uc001thw.2	Q32M45		ENST00000392977.3:c.2867G>A	12.37:g.101520847G>A		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	84	22	0.261905	NM_178826	Q8NAJ0|Q8NB39|Q8NB53	Silent	SNP	ENST00000392977.3	37																																																																																				.	.	none		0.483	ANO4-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000409295.1	NM_178826	
ODF4	146852	hgsc.bcm.edu	37	17	8243469	8243469	+	Missense_Mutation	SNP	T	T	C	rs12943505	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:8243469T>C	ENST00000328248.2	+	1	288	c.100T>C	c.(100-102)Tgg>Cgg	p.W34R	ODF4_ENST00000584943.1_Missense_Mutation_p.W34R|RP11-849F2.4_ENST00000585275.1_lincRNA	NM_153007.4	NP_694552.2	Q2M2E3	ODFP4_HUMAN	outer dense fiber of sperm tails 4	34			W -> R (in dbSNP:rs12943505). {ECO:0000269|PubMed:15489334}.		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						GGAGGCAGGATGGGGCACAGG	0.572													T|||	897	0.179113	0.0151	0.3963	5008	,	,		18988	0.0675		0.3469	False		,,,				2504	0.1892				p.W34R		Atlas-SNP	.											.	ODF4	23	.	0			c.T100C						PASS	.	T	ARG/TRP	261,4145	148.4+/-182.8	6,249,1948	85.0	80.0	82.0		100	-2.7	0.0	17	dbSNP_121	82	2589,6011	418.0+/-352.6	410,1769,2121	yes	missense	ODF4	NM_153007.4	101	416,2018,4069	CC,CT,TT		30.1047,5.9237,21.913	benign	34/258	8243469	2850,10156	2203	4300	6503	SO:0001583	missense	146852	exon1			GCAGGATGGGGCA	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.100T>C	17.37:g.8243469T>C	ENSP00000331086:p.Trp34Arg	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	97	54	0.556701	NM_153007	Q8J021	Missense_Mutation	SNP	ENST00000328248.2	37	CCDS11140.1	455	0.20833333333333334	10	0.02032520325203252	136	0.3756906077348066	46	0.08041958041958042	263	0.3469656992084433	T	4.163	0.028769	0.08054	0.059237	0.301047	ENSG00000184650	ENST00000328248	T	0.27557	1.66	3.68	-2.74	0.05932	.	2.012190	0.02669	N	0.108369	T	0.00012	0.0000	L	0.29908	0.895	0.80722	P	0.0	B	0.14438	0.01	B	0.17098	0.017	T	0.36187	-0.9758	9	0.07175	T	0.84	3.2504	5.4871	0.16755	0.0:0.4853:0.1835:0.3312	rs12943505;rs12943505	34	Q2M2E3	ODFP4_HUMAN	R	34	ENSP00000331086:W34R	ENSP00000331086:W34R	W	+	1	0	ODF4	8184194	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-1.952000	0.01528	-0.593000	0.05844	0.533000	0.62120	TGG	T|0.790;C|0.210	0.210	strong		0.572	ODF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226996.1		
EXPH5	23086	hgsc.bcm.edu	37	11	108381247	108381247	+	Missense_Mutation	SNP	C	C	T	rs2640779	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:108381247C>T	ENST00000265843.4	-	6	5097	c.4987G>A	c.(4987-4989)Gga>Aga	p.G1663R	EXPH5_ENST00000428840.1_Missense_Mutation_p.G1587R|EXPH5_ENST00000443411.1_Missense_Mutation_p.G1475R|EXPH5_ENST00000524840.1_5'Flank|EXPH5_ENST00000525344.1_Missense_Mutation_p.G1656R	NM_015065.2	NP_055880	Q8NEV8	EXPH5_HUMAN	exophilin 5	1663			G -> R (in dbSNP:rs2640779). {ECO:0000269|PubMed:12062444, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9734811}.		intracellular protein transport (GO:0006886)|keratinocyte development (GO:0003334)|multivesicular body sorting pathway (GO:0071985)|positive regulation of exocytosis (GO:0045921)|positive regulation of protein secretion (GO:0050714)	endosome (GO:0005768)	Rab GTPase binding (GO:0017137)	p.G1663R(1)		breast(3)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(13)|liver(1)|lung(34)|ovary(3)|pancreas(2)|prostate(2)|skin(11)|stomach(3)|upper_aerodigestive_tract(1)	91		all_cancers(61;3.99e-08)|Acute lymphoblastic leukemia(157;3.97e-05)|Melanoma(852;4.04e-05)|all_epithelial(67;0.000116)|all_hematologic(158;0.000315)|Breast(348;0.104)|all_neural(303;0.16)		Epithelial(105;8.1e-06)|BRCA - Breast invasive adenocarcinoma(274;1.22e-05)|all cancers(92;0.000129)|OV - Ovarian serous cystadenocarcinoma(223;0.11)|Colorectal(284;0.184)		ACATGCTTTCCGTTCTCACTC	0.478													C|||	1434	0.286342	0.028	0.3689	5008	,	,		21940	0.6419		0.2465	False		,,,				2504	0.2515				p.G1663R		Atlas-SNP	.											EXPH5,NS,adenoma,0,2	EXPH5	193	2	1	Substitution - Missense(1)	stomach(1)	c.G4987A						scavenged	.	C	ARG/GLY	276,4126	155.9+/-189.0	4,268,1929	207.0	200.0	202.0		4987	3.4	0.0	11	dbSNP_100	202	2037,6559	355.4+/-329.9	265,1507,2526	yes	missense	EXPH5	NM_015065.2	125	269,1775,4455	TT,TC,CC		23.6971,6.2699,17.795	possibly-damaging	1663/1990	108381247	2313,10685	2201	4298	6499	SO:0001583	missense	23086	exon6			GCTTTCCGTTCTC		CCDS8341.1	11q22.3	2008-02-05			ENSG00000110723	ENSG00000110723			30578	protein-coding gene	gene with protein product	"""synaptotagmin-like homologue lacking C2 domains b"""	612878				9734811, 11773082	Standard	NM_015065		Approved	SLAC2-B	uc001pkk.3	Q8NEV8	OTTHUMG00000166536	ENST00000265843.4:c.4987G>A	11.37:g.108381247C>T	ENSP00000265843:p.Gly1663Arg	Somatic	198	1	0.00505051		WXS	Illumina HiSeq	Phase_I	186	52	0.27957	NM_015065	Q2KHM1|Q9Y4D6	Missense_Mutation	SNP	ENST00000265843.4	37	CCDS8341.1	708	0.3241758241758242	18	0.036585365853658534	115	0.31767955801104975	373	0.6520979020979021	202	0.26649076517150394	C	11.38	1.622865	0.28889	0.062699	0.236971	ENSG00000110723	ENST00000265843;ENST00000428840;ENST00000443411;ENST00000525344;ENST00000526312	T;T;T;T;T	0.02787	4.38;4.31;4.16;4.38;4.23	4.36	3.44	0.39384	.	0.571316	0.16944	N	0.193156	T	0.00012	0.0000	L	0.51422	1.61	0.80722	P	0.0	B	0.20887	0.049	B	0.17098	0.017	T	0.02860	-1.1101	9	0.17369	T	0.5	-0.3997	11.0934	0.48130	0.0:0.9131:0.0:0.0869	rs2640779;rs3802835;rs52819961;rs60165688;rs2640779	1663	Q8NEV8	EXPH5_HUMAN	R	1663;1587;1475;1656;1587	ENSP00000265843:G1663R;ENSP00000391966:G1587R;ENSP00000411390:G1475R;ENSP00000432546:G1656R;ENSP00000432683:G1587R	ENSP00000265843:G1663R	G	-	1	0	EXPH5	107886457	0.005000	0.15991	0.004000	0.12327	0.012000	0.07955	1.616000	0.36933	1.178000	0.42870	0.650000	0.86243	GGA	C|0.760;T|0.240	0.240	strong		0.478	EXPH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390279.1	NM_015065	
SLC15A2	6565	hgsc.bcm.edu	37	3	121646641	121646641	+	Silent	SNP	A	A	G	rs1143670	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:121646641A>G	ENST00000489711.1	+	14	1549	c.1161A>G	c.(1159-1161)gcA>gcG	p.A387A	SLC15A2_ENST00000295605.2_Silent_p.A356A	NM_021082.3	NP_066568.3	Q16348	S15A2_HUMAN	solute carrier family 15 (oligopeptide transporter), member 2	387					drug transport (GO:0015893)|ion transport (GO:0006811)|protein transport (GO:0015031)|proton transport (GO:0015992)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	antibiotic transporter activity (GO:0042895)|dipeptide transporter activity (GO:0042936)|high-affinity oligopeptide transporter activity (GO:0015334)|peptide:proton symporter activity (GO:0015333)			NS(1)|endometrium(1)|kidney(4)|large_intestine(5)|lung(17)|skin(6)|upper_aerodigestive_tract(2)	36				GBM - Glioblastoma multiforme(114;0.0967)	Aminolevulinic acid(DB00855)|Amoxicillin(DB01060)|Ampicillin(DB00415)|Azidocillin(DB08795)|Benazepril(DB00542)|Benzylpenicillin(DB01053)|Cefaclor(DB00833)|Cefadroxil(DB01140)|Cefalotin(DB00456)|Cefdinir(DB00535)|Cefepime(DB01413)|Cefixime(DB00671)|Cefmetazole(DB00274)|Cefotaxime(DB00493)|Cefradine(DB01333)|Ceftazidime(DB00438)|Ceftibuten(DB01415)|Ceftriaxone(DB01212)|Cefuroxime(DB01112)|Cephalexin(DB00567)|Chlorpropamide(DB00672)|Cilazapril(DB01340)|Cloxacillin(DB01147)|Cyclacillin(DB01000)|Dicloxacillin(DB00485)|Fosinopril(DB00492)|Glyburide(DB01016)|Moexipril(DB00691)|Nateglinide(DB00731)|Oxacillin(DB00713)|Perindopril(DB00790)|Quinapril(DB00881)|Ramipril(DB00178)|Spirapril(DB01348)|Tolbutamide(DB01124)|Trandolapril(DB00519)|Tranexamic Acid(DB00302)|Valaciclovir(DB00577)|Valganciclovir(DB01610)	TGATCCTAGCATGCCTGGCAT	0.378													G|||	2192	0.4377	0.4304	0.2925	5008	,	,		20182	0.6984		0.4235	False		,,,				2504	0.2965				p.A387A		Atlas-SNP	.											.	SLC15A2	92	.	0			c.A1161G						PASS	.	G	,	1967,2439	619.5+/-393.4	436,1095,672	99.0	97.0	98.0		1068,1161	-1.9	0.9	3	dbSNP_86	98	3903,4697	606.1+/-395.0	879,2145,1276	no	coding-synonymous,coding-synonymous	SLC15A2	NM_001145998.1,NM_021082.3	,	1315,3240,1948	GG,GA,AA		45.3837,44.6437,45.133	,	356/699,387/730	121646641	5870,7136	2203	4300	6503	SO:0001819	synonymous_variant	6565	exon14			CCTAGCATGCCTG	BC044572	CCDS3007.1, CCDS54631.1	3q21.1	2013-07-18	2013-07-18		ENSG00000163406	ENSG00000163406		"""Solute carriers"""	10921	protein-coding gene	gene with protein product		602339	"""solute carrier family 15 (H+/peptide transporter), member 2"""			7756356	Standard	NM_021082		Approved	PEPT2	uc003eep.2	Q16348	OTTHUMG00000159423	ENST00000489711.1:c.1161A>G	3.37:g.121646641A>G		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	76	37	0.486842	NM_021082	A8K1A5|B4E2A7	Silent	SNP	ENST00000489711.1	37	CCDS3007.1																																																																																			A|0.537;G|0.463	0.463	strong		0.378	SLC15A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355239.1	NM_021082	
AHNAK2	113146	hgsc.bcm.edu	37	14	105420215	105420215	+	Missense_Mutation	SNP	T	T	C	rs2278607	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:105420215T>C	ENST00000333244.5	-	7	1692	c.1573A>G	c.(1573-1575)Act>Gct	p.T525A	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	525			T -> A (in dbSNP:rs2278607).			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)			TTCAGGCCAGTACCCGCTTTT	0.552													T|||	1011	0.201877	0.2882	0.0836	5008	,	,		20330	0.2937		0.0477	False		,,,				2504	0.2331				p.T525A		Atlas-SNP	.											.	AHNAK2	719	.	0			c.A1573G						PASS	.	T	ALA/THR	1011,3025		122,767,1129	108.0	116.0	114.0		1573	-8.2	0.0	14	dbSNP_100	114	356,7958		8,340,3809	yes	missense	AHNAK2	NM_138420.2	58	130,1107,4938	CC,CT,TT		4.2819,25.0496,11.0688	benign	525/5796	105420215	1367,10983	2018	4157	6175	SO:0001583	missense	113146	exon7			GGCCAGTACCCGC	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.1573A>G	14.37:g.105420215T>C	ENSP00000353114:p.Thr525Ala	Somatic	190	0	0		WXS	Illumina HiSeq	Phase_I	155	78	0.503226	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	381	0.17445054945054944	149	0.30284552845528456	39	0.10773480662983426	166	0.2902097902097902	27	0.03562005277044855	t	4.288	0.052681	0.08291	0.250496	0.042819	ENSG00000185567	ENST00000333244	T	0.02236	4.38	4.1	-8.21	0.01041	.	.	.	.	.	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B	0.18741	0.03	B	0.15484	0.013	T	0.49551	-0.8928	8	0.09338	T	0.73	.	1.4322	0.02336	0.3219:0.122:0.1145:0.4416	rs2278607;rs17286503;rs52797214;rs59420103;rs2278607	525	Q8IVF2	AHNK2_HUMAN	A	525	ENSP00000353114:T525A	ENSP00000353114:T525A	T	-	1	0	AHNAK2	104491260	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-5.239000	0.00138	-2.367000	0.00605	-1.275000	0.01399	ACT	T|0.812;C|0.187	0.187	strong		0.552	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
MSH4	4438	hgsc.bcm.edu	37	1	76269460	76269460	+	Missense_Mutation	SNP	G	G	A	rs5745325	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:76269460G>A	ENST00000263187.3	+	2	393	c.289G>A	c.(289-291)Gca>Aca	p.A97T		NM_002440.3	NP_002431.2	O15457	MSH4_HUMAN	mutS homolog 4	97			A -> T (in dbSNP:rs5745325). {ECO:0000269|Ref.3}.		ATP catabolic process (GO:0006200)|chiasma assembly (GO:0051026)|female gamete generation (GO:0007292)|homologous chromosome segregation (GO:0045143)|mismatch repair (GO:0006298)|ovarian follicle development (GO:0001541)|reciprocal meiotic recombination (GO:0007131)|spermatogenesis (GO:0007283)	nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|mismatched DNA binding (GO:0030983)			breast(1)|endometrium(2)|kidney(4)|large_intestine(9)|lung(26)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	47						AAACACAGTTGCATCAAATTT	0.323								Mismatch excision repair (MMR)					G|||	1066	0.212859	0.3026	0.2032	5008	,	,		14851	0.0228		0.3091	False		,,,				2504	0.1953				p.A97T		Atlas-SNP	.											.	MSH4	147	.	0			c.G289A						PASS	.	G	THR/ALA	1324,3082	433.7+/-343.7	176,972,1055	71.0	73.0	72.0		289	0.6	0.2	1	dbSNP_114	72	2572,6028	417.0+/-352.3	382,1808,2110	yes	missense	MSH4	NM_002440.3	58	558,2780,3165	AA,AG,GG		29.907,30.0499,29.9554	benign	97/937	76269460	3896,9110	2203	4300	6503	SO:0001583	missense	4438	exon2			ACAGTTGCATCAA	U89293	CCDS670.1	1p31	2013-09-12	2013-09-12		ENSG00000057468	ENSG00000057468			7327	protein-coding gene	gene with protein product		602105	"""mutS (E. coli) homolog 4"", ""mutS homolog 4 (E. coli)"""			9299235	Standard	NM_002440		Approved		uc001dhd.2	O15457	OTTHUMG00000009788	ENST00000263187.3:c.289G>A	1.37:g.76269460G>A	ENSP00000263187:p.Ala97Thr	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	128	61	0.476562	NM_002440	Q5T4U6|Q8NEB3|Q9UNP8	Missense_Mutation	SNP	ENST00000263187.3	37	CCDS670.1	467	0.21382783882783882	136	0.2764227642276423	75	0.20718232044198895	17	0.02972027972027972	239	0.3153034300791557	G	6.675	0.493057	0.12702	0.300499	0.29907	ENSG00000057468	ENST00000263187	D	0.87256	-2.23	4.73	0.632	0.17705	.	0.895901	0.09711	N	0.765669	T	0.54398	0.1856	L	0.32530	0.975	0.58432	P	8.000000000008E-6	B	0.06786	0.001	B	0.04013	0.001	T	0.14699	-1.0463	9	0.02654	T	1	0.7272	5.9083	0.19014	0.4471:0.132:0.4209:0.0	rs5745325;rs17594581;rs52829653;rs60345283;rs5745325	97	O15457	MSH4_HUMAN	T	97	ENSP00000263187:A97T	ENSP00000263187:A97T	A	+	1	0	MSH4	76042048	0.001000	0.12720	0.190000	0.23270	0.138000	0.21146	0.652000	0.24888	-0.148000	0.11234	-0.315000	0.08773	GCA	G|0.737;A|0.263	0.263	strong		0.323	MSH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026983.1	NM_002440	
CEACAM4	1089	hgsc.bcm.edu	37	19	42132314	42132314	+	Missense_Mutation	SNP	G	G	C	rs1126454	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:42132314G>C	ENST00000221954.2	-	2	195	c.85C>G	c.(85-87)Cac>Gac	p.H29D	CEACAM4_ENST00000600925.1_Missense_Mutation_p.H29D	NM_001817.2	NP_001808.2	O75871	CEAM4_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 4	29			H -> D (in dbSNP:rs1126454). {ECO:0000269|PubMed:2050678}.			integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)				NS(1)|endometrium(1)|large_intestine(3)|lung(4)|prostate(3)|skin(3)|urinary_tract(1)	16						GTGGGCGGGTGCCAGAAGGTT	0.517													C|||	3053	0.609625	0.4599	0.4669	5008	,	,		15995	0.8919		0.5417	False		,,,				2504	0.6922				p.H29D		Atlas-SNP	.											.	CEACAM4	42	.	0			c.C85G						PASS	.	C	ASP/HIS	2085,2321	593.8+/-388.1	492,1101,610	58.0	61.0	60.0		85	0.7	0.0	19	dbSNP_86	60	4402,4198	565.8+/-388.6	1139,2124,1037	yes	missense	CEACAM4	NM_001817.2	81	1631,3225,1647	CC,CG,GG		48.814,47.3218,49.877	benign	29/245	42132314	6487,6519	2203	4300	6503	SO:0001583	missense	1089	exon2			GCGGGTGCCAGAA	D90276	CCDS33033.1	19q13.2	2013-01-11			ENSG00000105352	ENSG00000105352		"""Immunoglobulin superfamily / V-set domain containing"""	1816	protein-coding gene	gene with protein product				CGM7		2050678	Standard	XM_005258434		Approved		uc002orh.1	O75871	OTTHUMG00000151065	ENST00000221954.2:c.85C>G	19.37:g.42132314G>C	ENSP00000221954:p.His29Asp	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	62	32	0.516129	NM_001817	Q03715|Q7LDZ7	Missense_Mutation	SNP	ENST00000221954.2	37	CCDS33033.1	1311	0.6002747252747253	218	0.44308943089430897	169	0.46685082872928174	500	0.8741258741258742	424	0.5593667546174143	C	3.674	-0.066967	0.07273	0.473218	0.51186	ENSG00000105352	ENST00000221954	T	0.01139	5.28	1.76	0.701	0.18104	.	.	.	.	.	T	0.00012	0.0000	N	0.04355	-0.22	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.04203	-1.0969	8	0.44086	T	0.13	.	2.3678	0.04323	0.0:0.2005:0.304:0.4955	rs1126454;rs3815381;rs17266713;rs1126454	29;29	E7EMX3;O75871	.;CEAM4_HUMAN	D	29	ENSP00000221954:H29D	ENSP00000221954:H29D	H	-	1	0	CEACAM4	46824154	0.010000	0.17322	0.023000	0.16930	0.075000	0.17131	-0.344000	0.07780	-0.213000	0.10094	-0.980000	0.02579	CAC	G|0.462;C|0.537	0.537	strong		0.517	CEACAM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321148.1	NM_001817	
CLDN18	51208	hgsc.bcm.edu	37	3	137743508	137743508	+	Missense_Mutation	SNP	A	A	T	rs17204075	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:137743508A>T	ENST00000183605.5	+	3	671	c.445A>T	c.(445-447)Atg>Ttg	p.M149L	CLDN18_ENST00000343735.4_Missense_Mutation_p.M149L	NM_016369.3	NP_057453.1	P56856	CLD18_HUMAN	claudin 18	149			M -> L (in dbSNP:rs17204075).		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)			endometrium(1)|large_intestine(2)|lung(1)|ovary(1)|upper_aerodigestive_tract(1)	6						TAACTTCTGGATGTCCACAGC	0.468													A|||	435	0.086861	0.0741	0.1037	5008	,	,		20645	0.0288		0.1312	False		,,,				2504	0.1063				p.M149L		Atlas-SNP	.											.	CLDN18	33	.	0			c.A445T						PASS	.	A	LEU/MET,LEU/MET	335,4071	176.6+/-205.7	13,309,1881	217.0	190.0	199.0		445,445	5.2	1.0	3	dbSNP_123	199	1063,7537	224.1+/-260.6	82,899,3319	yes	missense,missense	CLDN18	NM_001002026.2,NM_016369.3	15,15	95,1208,5200	TT,TA,AA		12.3605,7.6033,10.7489	possibly-damaging,possibly-damaging	149/262,149/262	137743508	1398,11608	2203	4300	6503	SO:0001583	missense	51208	exon3			TTCTGGATGTCCA	AF221069, AY102073	CCDS3095.1, CCDS33862.1	3q	2008-08-27			ENSG00000066405	ENSG00000066405		"""Claudins"""	2039	protein-coding gene	gene with protein product		609210	"""surfactant associated protein J"""	SFTPJ			Standard	NM_001002026		Approved		uc003ero.1	P56856	OTTHUMG00000159762	ENST00000183605.5:c.445A>T	3.37:g.137743508A>T	ENSP00000183605:p.Met149Leu	Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	144	64	0.444444	NM_016369	A5PL21|Q96PH4	Missense_Mutation	SNP	ENST00000183605.5	37	CCDS3095.1	196	0.08974358974358974	41	0.08333333333333333	39	0.10773480662983426	12	0.02097902097902098	104	0.13720316622691292	A	14.65	2.599308	0.46318	0.076033	0.123605	ENSG00000066405	ENST00000343735;ENST00000183605;ENST00000536138	D;D	0.88354	-2.37;-2.37	5.17	5.17	0.71159	.	0.139586	0.64402	D	0.000007	T	0.03827	0.0108	L	0.48362	1.52	0.18873	P	0.9999891459	P;P	0.44006	0.57;0.824	B;B	0.38880	0.192;0.284	T	0.60021	-0.7344	9	0.87932	D	0	.	15.1756	0.72907	1.0:0.0:0.0:0.0	rs17204075;rs58460905;rs17204075	149;149	P56856;P56856-2	CLD18_HUMAN;.	L	149;149;138	ENSP00000340939:M149L;ENSP00000183605:M149L	ENSP00000183605:M149L	M	+	1	0	CLDN18	139226198	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.791000	0.62460	2.178000	0.69098	0.533000	0.62120	ATG	A|0.903;T|0.097	0.097	strong		0.468	CLDN18-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000357199.2	NM_001002026	
ZNF714	148206	hgsc.bcm.edu	37	19	21300142	21300142	+	Silent	SNP	A	A	C	rs112722125	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:21300142A>C	ENST00000596143.1	+	5	997	c.672A>C	c.(670-672)ggA>ggC	p.G224G	ZNF714_ENST00000601416.1_3'UTR|ZNF714_ENST00000596053.1_Intron|ZNF714_ENST00000291770.7_3'UTR	NM_182515.3	NP_872321	Q96N38	ZN714_HUMAN	zinc finger protein 714	224					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)|urinary_tract(2)	18						TTCATACTGGAGAGAAACCCT	0.403													.|||	272	0.0543131	0.0643	0.0403	5008	,	,		19819	0.001		0.1133	False		,,,				2504	0.045				p.G224G		Atlas-SNP	.											.	ZNF714	121	.	0			c.A672C						PASS	.	A		263,4107		12,239,1934	46.0	48.0	47.0		672	-0.9	0.1	19	dbSNP_132	47	701,7891		25,651,3620	no	coding-synonymous	ZNF714	NM_182515.3		37,890,5554	CC,CA,AA		8.1588,6.0183,7.4371		224/555	21300142	964,11998	2185	4296	6481	SO:0001819	synonymous_variant	148206	exon5			TACTGGAGAGAAA	AK056006	CCDS54239.1	19p12	2013-01-08				ENSG00000160352		"""Zinc fingers, C2H2-type"""	27124	protein-coding gene	gene with protein product						12477932	Standard	NM_182515		Approved		uc002npo.4	Q96N38		ENST00000596143.1:c.672A>C	19.37:g.21300142A>C		Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	25	25	1	NM_182515	Q49AI1|Q86W65|Q8ND40	Silent	SNP	ENST00000596143.1	37	CCDS54239.1																																																																																			A|0.933;C|0.067	0.067	strong		0.403	ZNF714-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463930.1	NM_182515	
OR56A1	120796	hgsc.bcm.edu	37	11	6048408	6048408	+	Missense_Mutation	SNP	C	C	A	rs151331727	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:6048408C>A	ENST00000316650.5	-	1	563	c.527G>T	c.(526-528)tGt>tTt	p.C176F		NM_001001917.2	NP_001001917.2	Q8NGH5	O56A1_HUMAN	olfactory receptor, family 56, subfamily A, member 1	176						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(22)|ovary(2)	33		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)		Epithelial(150;7.01e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		ATTTTCCCCACAGTAATGGAG	0.453													.|||	15	0.00299521	0.0	0.0014	5008	,	,		23480	0.0		0.0139	False		,,,				2504	0.0				p.C176F		Atlas-SNP	.											.	OR56A1	73	.	0			c.G527T						PASS	.	C	PHE/CYS	4,4398	8.1+/-20.4	0,4,2197	107.0	101.0	103.0		527	3.3	0.9	11	dbSNP_134	103	69,8523	41.2+/-98.3	0,69,4227	yes	missense	OR56A1	NM_001001917.2	205	0,73,6424	AA,AC,CC		0.8031,0.0909,0.5618	probably-damaging	176/319	6048408	73,12921	2201	4296	6497	SO:0001583	missense	120796	exon1			TCCCCACAGTAAT	AB065821	CCDS31405.1	11p15.4	2012-08-09			ENSG00000180934	ENSG00000180934		"""GPCR / Class A : Olfactory receptors"""	14781	protein-coding gene	gene with protein product							Standard	NM_001001917		Approved		uc010qzw.2	Q8NGH5	OTTHUMG00000165377	ENST00000316650.5:c.527G>T	11.37:g.6048408C>A	ENSP00000321246:p.Cys176Phe	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	163	36	0.220859	NM_001001917	B2RNI2|Q6IFL0	Missense_Mutation	SNP	ENST00000316650.5	37	CCDS31405.1	7	0.003205128205128205	0	0.0	0	0.0	0	0.0	7	0.009234828496042216	C	8.479	0.859298	0.17178	9.09E-4	0.008031	ENSG00000180934	ENST00000316650	T	0.00211	8.54	4.27	3.34	0.38264	GPCR, rhodopsin-like superfamily (1);	0.000000	0.46758	D	0.000276	T	0.00300	0.0009	M	0.85945	2.785	0.28249	N	0.925365	B	0.31989	0.35	B	0.44163	0.443	T	0.00860	-1.1537	10	0.72032	D	0.01	.	13.1758	0.59626	0.0:0.8382:0.1618:0.0	.	176	Q8NGH5	O56A1_HUMAN	F	176	ENSP00000321246:C176F	ENSP00000321246:C176F	C	-	2	0	OR56A1	6004984	0.990000	0.36364	0.893000	0.35052	0.276000	0.26787	3.002000	0.49496	1.113000	0.41760	0.655000	0.94253	TGT	C|0.996;A|0.004	0.004	strong		0.453	OR56A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383757.1	NM_001001917	
UBR1	197131	hgsc.bcm.edu	37	15	43237572	43237572	+	Silent	SNP	T	T	C	rs16957277	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:43237572T>C	ENST00000290650.4	-	47	5283	c.5205A>G	c.(5203-5205)caA>caG	p.Q1735Q	UBR1_ENST00000382177.2_3'UTR	NM_174916.2	NP_777576.1	Q8IWV7	UBR1_HUMAN	ubiquitin protein ligase E3 component n-recognin 1	1735					cellular response to leucine (GO:0071233)|negative regulation of TOR signaling (GO:0032007)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|proteasome complex (GO:0000502)|ubiquitin ligase complex (GO:0000151)	leucine binding (GO:0070728)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(2)|endometrium(2)|kidney(7)|large_intestine(12)|lung(25)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	58		all_cancers(109;4.32e-15)|all_epithelial(112;4.05e-13)|Lung NSC(122;1.75e-08)|all_lung(180;2e-07)|Melanoma(134;0.0179)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;4.08e-07)|COAD - Colon adenocarcinoma(120;0.185)|Colorectal(105;0.214)		GATTAGTCTCTTGGCTCCTAG	0.453													T|||	452	0.0902556	0.1702	0.0403	5008	,	,		18833	0.0526		0.0497	False		,,,				2504	0.0982				p.Q1735Q		Atlas-SNP	.											.	UBR1	124	.	0			c.A5205G						PASS	.	T		536,3870	241.5+/-251.9	31,474,1698	139.0	125.0	130.0		5205	1.2	1.0	15	dbSNP_123	130	299,8299	109.8+/-170.3	6,287,4006	no	coding-synonymous	UBR1	NM_174916.2		37,761,5704	CC,CT,TT		3.4776,12.1652,6.4211		1735/1750	43237572	835,12169	2203	4299	6502	SO:0001819	synonymous_variant	197131	exon47			AGTCTCTTGGCTC		CCDS10091.1	15q13	2008-06-23			ENSG00000159459	ENSG00000159459		"""Ubiquitin protein ligase E3 component n-recognins"""	16808	protein-coding gene	gene with protein product		605981				9653112	Standard	NM_174916		Approved		uc001zqq.3	Q8IWV7	OTTHUMG00000130702	ENST00000290650.4:c.5205A>G	15.37:g.43237572T>C		Somatic	220	0	0		WXS	Illumina HiSeq	Phase_I	222	98	0.441441	NM_174916	O60708|O75492|Q14D45|Q68DN9|Q8IWY6|Q96JY4	Silent	SNP	ENST00000290650.4	37	CCDS10091.1																																																																																			T|0.928;C|0.072	0.072	strong		0.453	UBR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253202.1	NM_174916	
PRLHR	2834	hgsc.bcm.edu	37	10	120354472	120354472	+	Silent	SNP	C	C	T	rs938700	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:120354472C>T	ENST00000369169.1	-	1	284	c.285G>A	c.(283-285)acG>acA	p.T95T	PRLHR_ENST00000239032.2_Silent_p.T95T			P49683	PRLHR_HUMAN	prolactin releasing hormone receptor	95					feeding behavior (GO:0007631)|female pregnancy (GO:0007565)|G-protein coupled receptor signaling pathway (GO:0007186)|hormone metabolic process (GO:0042445)|neuropeptide signaling pathway (GO:0007218)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|neuropeptide receptor activity (GO:0008188)|neuropeptide Y receptor activity (GO:0004983)			large_intestine(2)|lung(8)|ovary(1)|skin(1)	12		Colorectal(252;0.0429)|Lung NSC(174;0.142)|all_lung(145;0.175)		all cancers(201;0.0166)		TGAGGAAGTTCGTCACGTTGT	0.662													C|||	249	0.0497204	0.0681	0.0735	5008	,	,		17474	0.003		0.0537	False		,,,				2504	0.0521				p.T95T		Atlas-SNP	.											PRLHR,NS,carcinoma,0,2	PRLHR	41	2	0			c.G285A						PASS	.	C		272,4134	148.4+/-182.8	9,254,1940	100.0	80.0	87.0		285	4.0	1.0	10	dbSNP_86	87	385,8213	123.9+/-182.7	10,365,3924	no	coding-synonymous	PRLHR	NM_004248.2		19,619,5864	TT,TC,CC		4.4778,6.1734,5.0523		95/371	120354472	657,12347	2203	4299	6502	SO:0001819	synonymous_variant	2834	exon2			GAAGTTCGTCACG	AB048946	CCDS7606.1	10q25.3-q26	2014-02-21	2005-11-24	2005-11-24	ENSG00000119973	ENSG00000119973		"""GPCR / Class A : RF amide peptide receptors"""	4464	protein-coding gene	gene with protein product		600895	"""G protein-coupled receptor 10"""	GPR10		8666380, 15885496	Standard	NM_004248		Approved	PrRPR	uc001ldp.1	P49683	OTTHUMG00000019136	ENST00000369169.1:c.285G>A	10.37:g.120354472C>T		Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	177	96	0.542373	NM_004248	O75194|Q502U8|Q5VXR9	Silent	SNP	ENST00000369169.1	37	CCDS7606.1																																																																																			C|0.950;T|0.050	0.050	strong		0.662	PRLHR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050610.1	NM_004248	
ZRANB2	9406	hgsc.bcm.edu	37	1	71538191	71538191	+	Silent	SNP	A	A	G	rs11556475	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:71538191A>G	ENST00000370920.3	-	5	643	c.342T>C	c.(340-342)taT>taC	p.Y114Y	ZRANB2_ENST00000254821.6_Silent_p.Y114Y	NM_203350.2	NP_976225.1	O95218	ZRAB2_HUMAN	zinc finger, RAN-binding domain containing 2	114					mRNA processing (GO:0006397)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(4)|lung(4)|ovary(2)|stomach(1)	15						CTCTTTCTATATATTCAACAT	0.284													A|||	355	0.0708866	0.1589	0.0692	5008	,	,		15666	0.0		0.0855	False		,,,				2504	0.0112				p.Y114Y		Atlas-SNP	.											.	ZRANB2	75	.	0			c.T342C						PASS	.	A	,	691,3711	287.5+/-279.3	42,607,1552	65.0	69.0	68.0		342,342	0.3	1.0	1	dbSNP_120	68	725,7857	176.2+/-226.1	36,653,3602	no	coding-synonymous,coding-synonymous	ZRANB2	NM_005455.4,NM_203350.2	,	78,1260,5154	GG,GA,AA		8.4479,15.6974,10.9057	,	114/321,114/331	71538191	1416,11568	2201	4291	6492	SO:0001819	synonymous_variant	9406	exon5			TTCTATATATTCA	AF065391	CCDS659.1, CCDS660.1	1p31	2008-02-05	2006-06-28	2006-06-28	ENSG00000132485	ENSG00000132485		"""Zinc fingers, RAN-binding domain containing"""	13058	protein-coding gene	gene with protein product		604347	"""zinc finger protein 265"""	ZNF265		9931435	Standard	NM_005455		Approved	ZIS, ZIS1, ZIS2	uc001dft.3	O95218	OTTHUMG00000009660	ENST00000370920.3:c.342T>C	1.37:g.71538191A>G		Somatic	341	0	0		WXS	Illumina HiSeq	Phase_I	262	128	0.48855	NM_203350	D3DQ75|Q53GS3|Q59F92|Q5VV33|Q5VV34|Q8IXN6|Q9UP63	Silent	SNP	ENST00000370920.3	37	CCDS659.1																																																																																			A|0.898;G|0.102	0.102	strong		0.284	ZRANB2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000026636.1	NM_203350	
OR5B3	441608	hgsc.bcm.edu	37	11	58170291	58170291	+	Missense_Mutation	SNP	T	T	C	rs11229410	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:58170291T>C	ENST00000309403.2	-	1	591	c.592A>G	c.(592-594)Att>Gtt	p.I198V		NM_001005469.1	NP_001005469.1	Q8NH48	OR5B3_HUMAN	olfactory receptor, family 5, subfamily B, member 3	198			I -> V (in dbSNP:rs11229410).			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(4)|lung(17)|ovary(1)|prostate(1)|skin(2)|stomach(6)|upper_aerodigestive_tract(1)	34	Esophageal squamous(5;0.0027)	Breast(21;0.0778)				ACAACATAAATAAGAACAAGC	0.373													C|||	1453	0.290136	0.3533	0.2695	5008	,	,		23834	0.1448		0.3628	False		,,,				2504	0.2945				p.I198V		Atlas-SNP	.											.	OR5B3	65	.	0			c.A592G						PASS	.	C	VAL/ILE	1442,2960	681.0+/-403.9	229,984,988	74.0	71.0	72.0		592	-8.1	0.0	11	dbSNP_120	72	3095,5495	658.3+/-401.6	550,1995,1750	yes	missense	OR5B3	NM_001005469.1	29	779,2979,2738	CC,CT,TT		36.0303,32.7578,34.9215	benign	198/315	58170291	4537,8455	2201	4295	6496	SO:0001583	missense	441608	exon1			CATAAATAAGAAC	AB065545	CCDS31549.1	11q12.1	2012-08-09			ENSG00000172769	ENSG00000172769		"""GPCR / Class A : Olfactory receptors"""	8324	protein-coding gene	gene with protein product				OR5B13			Standard	NM_001005469		Approved	OST129	uc010rkf.2	Q8NH48	OTTHUMG00000167516	ENST00000309403.2:c.592A>G	11.37:g.58170291T>C	ENSP00000308270:p.Ile198Val	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	69	49	0.710145	NM_001005469	Q6IEV6	Missense_Mutation	SNP	ENST00000309403.2	37	CCDS31549.1	655	0.2999084249084249	195	0.39634146341463417	89	0.24585635359116023	95	0.1660839160839161	276	0.3641160949868074	c	0.009	-1.829691	0.00584	0.327578	0.360303	ENSG00000172769	ENST00000309403	T	0.00091	8.74	4.05	-8.1	0.01086	GPCR, rhodopsin-like superfamily (1);	1.011050	0.07957	N	0.981760	T	0.00012	0.0000	N	0.03071	-0.42	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.06881	-1.0802	9	0.29301	T	0.29	-3.0942	9.5789	0.39475	0.0:0.1083:0.2724:0.6193	rs11229410;rs58700205;rs11229410	198	Q8NH48	OR5B3_HUMAN	V	198	ENSP00000308270:I198V	ENSP00000308270:I198V	I	-	1	0	OR5B3	57926867	0.524000	0.26282	0.001000	0.08648	0.011000	0.07611	0.903000	0.28475	-1.857000	0.01159	-0.147000	0.13772	ATT	C|0.321;T|0.679	0.321	strong		0.373	OR5B3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394886.1	NM_001005469	
ACPT	93650	hgsc.bcm.edu	37	19	51293955	51293955	+	Splice_Site	SNP	G	G	A	rs2162784	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:51293955G>A	ENST00000270593.1	+	2	216	c.216G>A	c.(214-216)acG>acA	p.T72T	CTD-2568A17.8_ENST00000594114.1_RNA|ACPT_ENST00000270594.3_Splice_Site_p.T72T	NM_033068.2	NP_149059.1	Q9BZG2	PPAT_HUMAN	acid phosphatase, testicular	72						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)		AGCTGACCACGGTGAGAAGCG	0.706													G|||	499	0.0996406	0.152	0.0706	5008	,	,		11090	0.126		0.0805	False		,,,				2504	0.0419				p.T72T		Atlas-SNP	.											.	ACPT	43	.	0			c.G216A						PASS	.			450,3752		22,406,1673	7.0	7.0	7.0		216	4.2	0.9	19	dbSNP_96	7	668,7602		23,622,3490	yes	coding-synonymous-near-splice	ACPT	NM_033068.2		45,1028,5163	AA,AG,GG		8.0774,10.7092,8.9641		72/427	51293955	1118,11354	2101	4135	6236	SO:0001630	splice_region_variant	93650	exon2			GACCACGGTGAGA	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.216+1G>A	19.37:g.51293955G>A		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	50	20	0.4	NM_033068	C0H3P7|Q9BZG3|Q9BZG4	Silent	SNP	ENST00000270593.1	37	CCDS12802.1																																																																																			G|0.892;A|0.108	0.108	strong		0.706	ACPT-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464434.1	NM_033068	Silent
ODF3L1	161753	hgsc.bcm.edu	37	15	76017452	76017452	+	Missense_Mutation	SNP	C	C	T	rs55905564	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:76017452C>T	ENST00000332145.2	+	2	345	c.122C>T	c.(121-123)cCg>cTg	p.P41L	DNM1P35_ENST00000501931.1_RNA	NM_175881.3	NP_787077.1	Q8IXM7	OD3L1_HUMAN	outer dense fiber of sperm tails 3-like 1	41			P -> L (in dbSNP:rs55905564).							kidney(1)|lung(1)	2						CTTACAGGTCCGGGGCCCGCC	0.597													C|||	693	0.138379	0.1104	0.1628	5008	,	,		18115	0.1032		0.2386	False		,,,				2504	0.092				p.P41L		Atlas-SNP	.											.	ODF3L1	10	.	0			c.C122T						PASS	.	C	LEU/PRO	560,3834		33,494,1670	56.0	50.0	52.0		122	5.3	0.8	15	dbSNP_129	52	2150,6438		287,1576,2431	yes	missense	ODF3L1	NM_175881.3	98	320,2070,4101	TT,TC,CC		25.0349,12.7447,20.8751	probably-damaging	41/275	76017452	2710,10272	2197	4294	6491	SO:0001583	missense	161753	exon2			CAGGTCCGGGGCC	BC039862	CCDS10285.1	15q23	2008-02-05			ENSG00000182950	ENSG00000182950			28735	protein-coding gene	gene with protein product							Standard	NM_175881		Approved	MGC48986	uc002bax.1	Q8IXM7	OTTHUMG00000142837	ENST00000332145.2:c.122C>T	15.37:g.76017452C>T	ENSP00000329584:p.Pro41Leu	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	73	43	0.589041	NM_175881		Missense_Mutation	SNP	ENST00000332145.2	37	CCDS10285.1	363	0.1662087912087912	56	0.11382113821138211	63	0.17403314917127072	68	0.11888111888111888	176	0.23218997361477572	.	16.95	3.264521	0.59431	0.127447	0.250349	ENSG00000182950	ENST00000332145	T	0.62364	0.03	5.28	5.28	0.74379	.	0.000000	0.50627	D	0.000108	T	0.00073	0.0002	M	0.90814	3.15	0.09310	P	0.99999803192	D	0.89917	1.0	D	0.97110	1.0	T	0.01456	-1.1350	9	0.87932	D	0	-15.6431	14.3961	0.67013	0.0:1.0:0.0:0.0	rs55905564	41	Q8IXM7	OD3L1_HUMAN	L	41	ENSP00000329584:P41L	ENSP00000329584:P41L	P	+	2	0	ODF3L1	73804507	0.944000	0.32072	0.849000	0.33467	0.035000	0.12851	4.735000	0.62051	2.479000	0.83701	0.561000	0.74099	CCG	C|0.806;T|0.194	0.194	strong		0.597	ODF3L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286473.1	NM_175881	
CAMKK2	10645	hgsc.bcm.edu	37	12	121712301	121712301	+	Missense_Mutation	SNP	C	C	T	rs28360477	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:121712301C>T	ENST00000324774.5	-	2	857	c.29G>A	c.(28-30)aGc>aAc	p.S10N	CAMKK2_ENST00000337174.3_Missense_Mutation_p.S10N|CAMKK2_ENST00000535524.1_5'UTR|CAMKK2_ENST00000392473.2_Missense_Mutation_p.S10N|CAMKK2_ENST00000404169.3_Missense_Mutation_p.S10N|CAMKK2_ENST00000412367.2_Missense_Mutation_p.S10N|CAMKK2_ENST00000538733.1_Missense_Mutation_p.S10N|CAMKK2_ENST00000402834.4_Missense_Mutation_p.S10N|CAMKK2_ENST00000392474.2_Missense_Mutation_p.S10N|CAMKK2_ENST00000347034.2_Missense_Mutation_p.S10N|CAMKK2_ENST00000446440.2_Missense_Mutation_p.S10N	NM_006549.3	NP_006540.3	Q96RR4	KKCC2_HUMAN	calcium/calmodulin-dependent protein kinase kinase 2, beta	10			S -> N (in dbSNP:rs28360477). {ECO:0000269|PubMed:17344846}.		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)					CCGGTTGCTGCTGGGCTGGCT	0.657													C|||	88	0.0175719	0.0015	0.0461	5008	,	,		14661	0.0		0.0507	False		,,,				2504	0.0031				p.S10N		Atlas-SNP	.											.	CAMKK2	87	.	0			c.G29A						PASS	.	C	ASN/SER,ASN/SER,ASN/SER,ASN/SER,ASN/SER,ASN/SER,ASN/SER	34,4298		0,34,2132	13.0	16.0	15.0		29,29,29,29,29,29,29	3.3	0.4	12	dbSNP_125	15	400,8052		9,382,3835	yes	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	46,46,46,46,46,46,46	9,416,5967	TT,TC,CC		4.7326,0.7849,3.3949	benign,benign,benign,benign,benign,benign,benign	10/589,10/542,10/499,10/534,10/491,10/546,10/542	121712301	434,12350	2166	4226	6392	SO:0001583	missense	10645	exon2			TTGCTGCTGGGCT	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.29G>A	12.37:g.121712301C>T	ENSP00000312741:p.Ser10Asn	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	83	36	0.433735	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	55	0.025183150183150184	2	0.0040650406504065045	20	0.055248618784530384	0	0.0	33	0.04353562005277045	C	12.25	1.881421	0.33255	0.007849	0.047326	ENSG00000110931	ENST00000392474;ENST00000347034;ENST00000538733;ENST00000337174;ENST00000324774;ENST00000412367;ENST00000404169;ENST00000360452;ENST00000446440;ENST00000392473;ENST00000543477;ENST00000544485;ENST00000398924	T;T;T;T;T;T;T;T;T;T;T	0.75704	-0.94;-0.94;-0.91;-0.92;-0.96;-0.92;-0.96;-0.92;-0.92;1.59;1.24	4.22	3.31	0.37934	.	0.293769	0.27951	N	0.017182	T	0.11965	0.0291	N	0.14661	0.345	0.22213	N	0.999285	B;B;B;B;B;B;B	0.21905	0.027;0.007;0.027;0.027;0.062;0.037;0.027	B;B;B;B;B;B;B	0.24701	0.015;0.015;0.015;0.015;0.055;0.015;0.015	T	0.25152	-1.0140	10	0.66056	D	0.02	-0.6232	6.5087	0.22210	0.0:0.5212:0.3801:0.0986	rs28360477;rs28360477	10;10;10;10;10;10;10	Q96RR4-6;Q96RR4-2;Q96RR4-7;Q96RR4-5;Q96RR4-4;Q96RR4;Q96RR4-3	.;.;.;.;.;KKCC2_HUMAN;.	N	10	ENSP00000376266:S10N;ENSP00000321230:S10N;ENSP00000445944:S10N;ENSP00000336634:S10N;ENSP00000312741:S10N;ENSP00000388368:S10N;ENSP00000384600:S10N;ENSP00000388273:S10N;ENSP00000376265:S10N;ENSP00000444894:S10N;ENSP00000445400:S10N	ENSP00000312741:S10N	S	-	2	0	CAMKK2	120196684	1.000000	0.71417	0.406000	0.26421	0.773000	0.43773	1.703000	0.37846	1.330000	0.45394	0.462000	0.41574	AGC	C|0.971;T|0.029	0.029	strong		0.657	CAMKK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000402563.1	NM_172226	
AHNAK2	113146	hgsc.bcm.edu	37	14	105418504	105418504	+	Missense_Mutation	SNP	G	G	T	rs386781102|rs151013711	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:105418504G>T	ENST00000333244.5	-	7	3403	c.3284C>A	c.(3283-3285)gCc>gAc	p.A1095D	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	1095						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)			GCCCTTGAGGGCCACTTTGGG	0.632													.|||	1021	0.203874	0.3041	0.0821	5008	,	,		18093	0.2887		0.0477	False		,,,				2504	0.228				p.A1095D		Atlas-SNP	.											.	AHNAK2	719	.	0			c.C3284A						PASS	.	T	ASP/ALA	1001,2715		162,677,1019	126.0	148.0	141.0		3284	0.3	0.0	14	dbSNP_134	141	347,7869		9,329,3770	no	missense	AHNAK2	NM_138420.2	126	171,1006,4789	TT,TG,GG		4.2235,26.9376,11.2974	benign	1095/5796	105418504	1348,10584	1858	4108	5966	SO:0001583	missense	113146	exon7			TTGAGGGCCACTT	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.3284C>A	14.37:g.105418504G>T	ENSP00000353114:p.Ala1095Asp	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	153	65	0.424837	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	328	0.15018315018315018	134	0.27235772357723576	34	0.09392265193370165	140	0.24475524475524477	20	0.026385224274406333	t	0	-2.840525	0.00068	0.269376	0.042235	ENSG00000185567	ENST00000333244	T	0.00902	5.56	2.99	0.307	0.15811	.	.	.	.	.	T	0.00012	0.0000	N	0.00008	-3.1	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.34675	-0.9819	8	0.02654	T	1	.	6.7739	0.23609	0.0:0.0916:0.4443:0.464	.	1095	Q8IVF2	AHNK2_HUMAN	D	1095	ENSP00000353114:A1095D	ENSP00000353114:A1095D	A	-	2	0	AHNAK2	104489549	0.000000	0.05858	0.003000	0.11579	0.098000	0.18820	0.548000	0.23314	-0.410000	0.07542	-0.824000	0.03097	GCC	G|0.875;T|0.125	0.125	strong		0.632	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
LGALS9	3965	hgsc.bcm.edu	37	17	25970642	25970642	+	Missense_Mutation	SNP	A	A	T	rs361498	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:25970642A>T	ENST00000395473.2	+	5	2004	c.536A>T	c.(535-537)cAa>cTa	p.Q179L	LGALS9_ENST00000313648.6_Intron|LGALS9_ENST00000310394.5_Intron|LGALS9_ENST00000413914.2_Missense_Mutation_p.Q122L|LGALS9_ENST00000302228.5_Intron	NM_009587.2	NP_033665.1	O00182	LEG9_HUMAN	lectin, galactoside-binding, soluble, 9	179					positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	carbohydrate binding (GO:0030246)|galactose binding (GO:0005534)|signal transducer activity (GO:0004871)			endometrium(3)|large_intestine(2)|lung(12)|skin(1)	18	Lung NSC(42;0.0103)		BRCA - Breast invasive adenocarcinoma(3;0.0141)	UCEC - Uterine corpus endometrioid carcinoma (53;0.155)		GGGCGCAGACAAAAAGTGAGT	0.627													A|||	309	0.0617013	0.0121	0.0965	5008	,	,		17794	0.0		0.1998	False		,,,				2504	0.0256				p.Q179L	Melanoma(106;677 1527 28724 29571 46552)|Ovarian(193;263 2088 2118 29005 43023)	Atlas-SNP	.											.	LGALS9	29	.	0			c.A536T						PASS	.	A	,LEU/GLN	180,4226		2,176,2025	20.0	20.0	20.0		,536	-0.1	0.0	17	dbSNP_79	20	1755,6819		190,1375,2722	no	intron,missense	LGALS9	NM_002308.3,NM_009587.2	,113	192,1551,4747	TT,TA,AA		20.4689,4.0853,14.9076	,benign	,179/356	25970642	1935,11045	2203	4287	6490	SO:0001583	missense	3965	exon5			GCAGACAAAAAGT	AB006782	CCDS11222.1, CCDS32592.1	17q11.2	2013-03-28	2008-07-25		ENSG00000168961	ENSG00000168961		"""Lectins, galactoside-binding"""	6570	protein-coding gene	gene with protein product	"""galectin 9"""	601879				9045665	Standard	NM_009587		Approved	LGALS9A	uc002gzp.3	O00182	OTTHUMG00000179831	ENST00000395473.2:c.536A>T	17.37:g.25970642A>T	ENSP00000378856:p.Gln179Leu	Somatic	316	1	0.00316456		WXS	Illumina HiSeq	Phase_I	278	145	0.521583	NM_009587	A7VJG6|O14532|O75028|Q3B8N1|Q53FQ0|Q9NQ58	Missense_Mutation	SNP	ENST00000395473.2	37	CCDS11222.1	222	0.10164835164835165	14	0.028455284552845527	40	0.11049723756906077	4	0.006993006993006993	164	0.21635883905013192	A	12.31	1.899332	0.33535	0.040853	0.204689	ENSG00000168961	ENST00000395473;ENST00000413914	T;T	0.14893	3.89;2.47	3.53	-0.0973	0.13633	.	0.488214	0.17273	N	0.180295	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B;B	0.21905	0.062;0.017	B;B	0.18871	0.023;0.004	T	0.45963	-0.9225	9	0.10902	T	0.67	.	9.0558	0.36405	0.6141:0.3859:0.0:0.0	rs361498;rs17399029	122;179	B4DWP7;O00182	.;LEG9_HUMAN	L	179;122	ENSP00000378856:Q179L;ENSP00000393695:Q122L	ENSP00000378856:Q179L	Q	+	2	0	LGALS9	22994769	0.000000	0.05858	0.022000	0.16811	0.614000	0.37383	-0.053000	0.11846	-0.054000	0.13266	-0.262000	0.10625	CAA	A|0.874;T|0.126	0.126	strong		0.627	LGALS9-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255583.1	NM_009587	
FIGN	55137	hgsc.bcm.edu	37	2	164467750	164467750	+	Missense_Mutation	SNP	A	A	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:164467750A>T	ENST00000333129.3	-	3	906	c.592T>A	c.(592-594)Tat>Aat	p.Y198N	FIGN_ENST00000482917.1_5'Flank|FIGN_ENST00000409634.1_Intron	NM_018086.2	NP_060556.2	Q5HY92	FIGN_HUMAN	fidgetin	198					mitotic nuclear division (GO:0007067)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nuclear matrix (GO:0016363)	ATP binding (GO:0005524)			breast(2)|endometrium(3)|kidney(2)|large_intestine(13)|lung(23)|ovary(1)|prostate(2)|skin(1)	47						TGGCTACTATAAGTAGAATGC	0.537																																					p.Y198N		Atlas-SNP	.											.	FIGN	106	.	0			c.T592A						PASS	.						70.0	76.0	74.0					2																	164467750		2038	4192	6230	SO:0001583	missense	55137	exon3			TACTATAAGTAGA	AK001267	CCDS2221.2	2q24	2010-04-21			ENSG00000182263	ENSG00000182263		"""ATPases / AAA-type"""	13285	protein-coding gene	gene with protein product		605295				11017077	Standard	XM_005246661		Approved		uc002uck.1	Q5HY92	OTTHUMG00000074059	ENST00000333129.3:c.592T>A	2.37:g.164467750A>T	ENSP00000333836:p.Tyr198Asn	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	105	30	0.285714	NM_018086	B3KWM0|Q9H6M5|Q9NVZ9	Missense_Mutation	SNP	ENST00000333129.3	37	CCDS2221.2	.	.	.	.	.	.	.	.	.	.	A	17.94	3.511293	0.64522	.	.	ENSG00000182263	ENST00000333129	T	0.40225	1.04	6.16	6.16	0.99307	.	0.000000	0.85682	D	0.000000	T	0.60689	0.2288	M	0.66939	2.045	0.80722	D	1	D	0.69078	0.997	P	0.60789	0.879	T	0.60510	-0.7249	10	0.48119	T	0.1	-9.4916	16.8061	0.85666	1.0:0.0:0.0:0.0	.	198	Q5HY92	FIGN_HUMAN	N	198	ENSP00000333836:Y198N	ENSP00000333836:Y198N	Y	-	1	0	FIGN	164175996	1.000000	0.71417	0.972000	0.41901	0.984000	0.73092	9.339000	0.96797	2.367000	0.80283	0.528000	0.53228	TAT	.	.	none		0.537	FIGN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157220.2	NM_018086	
PCP2	126006	hgsc.bcm.edu	37	19	7698320	7698320	+	Silent	SNP	C	C	T	rs1862514	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:7698320C>T	ENST00000311069.5	-	1	314	c.24G>A	c.(22-24)acG>acA	p.T8T	PCP2_ENST00000598935.1_5'Flank|CTD-3214H19.6_ENST00000601797.1_RNA|CTD-3214H19.4_ENST00000595866.1_Intron	NM_174895.1	NP_777555.1	Q8IVA1	PCP2_HUMAN	Purkinje cell protein 2	8					rhodopsin mediated signaling pathway (GO:0016056)	neuronal cell body (GO:0043025)	GTPase regulator activity (GO:0030695)|guanyl-nucleotide exchange factor activity (GO:0005085)			endometrium(1)|urinary_tract(1)	2						AGCCTTCCTCCGTCTTCTCCT	0.602													C|||	1241	0.247804	0.1483	0.2161	5008	,	,		15740	0.2113		0.3827	False		,,,				2504	0.3037				p.T8T		Atlas-SNP	.											.	PCP2	6	.	0			c.G24A						PASS	.	C		719,3679		60,599,1540	95.0	62.0	73.0		24	-3.1	0.0	19	dbSNP_92	73	3163,5425		577,2009,1708	no	coding-synonymous	PCP2	NM_174895.1		637,2608,3248	TT,TC,CC		36.8305,16.3483,29.8937		8/137	7698320	3882,9104	2199	4294	6493	SO:0001819	synonymous_variant	126006	exon1			TTCCTCCGTCTTC	BC025387	CCDS32893.1, CCDS62521.1	19p13.3	2008-02-05				ENSG00000174788			30209	protein-coding gene	gene with protein product						12477932	Standard	NM_174895		Approved	MGC41903, GPSM4	uc031rjd.1	Q8IVA1		ENST00000311069.5:c.24G>A	19.37:g.7698320C>T		Somatic	248	0	0		WXS	Illumina HiSeq	Phase_I	209	106	0.507177	NM_174895	M0R2R7|Q3KRG7	Silent	SNP	ENST00000311069.5	37	CCDS32893.1																																																																																			C|0.738;T|0.262	0.262	strong		0.602	PCP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000461026.2	XM_058956	
HLA-G	3135	hgsc.bcm.edu	37	6	29796451	29796451	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:29796451G>A	ENST00000360323.6	+	3	499	c.475G>A	c.(475-477)Gca>Aca	p.A159T	HLA-G_ENST00000376818.3_Intron|HLA-G_ENST00000376815.3_Intron|HLA-G_ENST00000428701.1_Missense_Mutation_p.A159T|HLA-G_ENST00000376828.2_Missense_Mutation_p.A164T			P17693	HLAG_HUMAN	major histocompatibility complex, class I, G	159	Alpha-2.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular defense response (GO:0006968)|cytokine-mediated signaling pathway (GO:0019221)|immune response-inhibiting cell surface receptor signaling pathway (GO:0002767)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of dendritic cell differentiation (GO:2001199)|negative regulation of T cell proliferation (GO:0042130)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of regulatory T cell differentiation (GO:0045591)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|positive regulation of T cell tolerance induction (GO:0002666)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)	early endosome membrane (GO:0031901)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|membrane (GO:0016020)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	peptide antigen binding (GO:0042605)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)	p.A159T(1)		central_nervous_system(1)|endometrium(1)|large_intestine(5)|lung(4)|ovary(3)|pancreas(1)|prostate(5)|skin(1)	21						CTCCTGGACCGCAGCGGACAC	0.632																																					p.A159T		Atlas-SNP	.											HLA-G,NS,carcinoma,0,1	HLA-G	90	1	1	Substitution - Missense(1)	prostate(1)	c.G475A						scavenged	.						105.0	91.0	96.0					6																	29796451		1511	2709	4220	SO:0001583	missense	3135	exon4			TGGACCGCAGCGG		CCDS4668.1	6p21.3	2013-01-11	2007-12-12		ENSG00000204632	ENSG00000204632		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4964	protein-coding gene	gene with protein product	"""b2 microglobulin"""	142871	"""HLA-G histocompatibility antigen, class I, G"""				Standard	NM_002127		Approved		uc003nnw.2	P17693	OTTHUMG00000031157	ENST00000360323.6:c.475G>A	6.37:g.29796451G>A	ENSP00000353472:p.Ala159Thr	Somatic	200	0	0		WXS	Illumina HiSeq	Phase_I	197	4	0.0203046	NM_002127		Missense_Mutation	SNP	ENST00000360323.6	37	CCDS4668.1	.	.	.	.	.	.	.	.	.	.	.	18.31	3.595535	0.66219	.	.	ENSG00000204632	ENST00000376828;ENST00000428701;ENST00000360323	T;T;T	0.01084	5.36;5.36;5.36	1.72	1.72	0.24424	MHC class I, alpha chain, alpha1/alpha2 (1);MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);	0.000000	0.33772	U	0.004570	T	0.03564	0.0102	H	0.96080	3.765	0.28004	N	0.935162	D;D	0.63880	0.99;0.993	P;P	0.59056	0.851;0.716	T	0.07558	-1.0766	10	0.87932	D	0	.	9.0484	0.36360	0.0:0.0:1.0:0.0	.	164;159	Q5RJ85;P17693	.;HLAG_HUMAN	T	164;159;159	ENSP00000366024:A164T;ENSP00000412927:A159T;ENSP00000353472:A159T	ENSP00000353472:A159T	A	+	1	0	HLA-G	29904430	0.978000	0.34361	0.607000	0.28956	0.016000	0.09150	3.553000	0.53713	0.952000	0.37798	0.298000	0.19748	GCA	.	.	none		0.632	HLA-G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076286.2	NM_002127	
KDM4C	23081	hgsc.bcm.edu	37	9	6981115	6981115	+	Missense_Mutation	SNP	G	G	A	rs35049841	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:6981115G>A	ENST00000381309.3	+	9	1677	c.1112G>A	c.(1111-1113)cGa>cAa	p.R371Q	RP11-403H13.1_ENST00000445708.1_RNA|KDM4C_ENST00000543771.1_Missense_Mutation_p.R371Q|KDM4C_ENST00000428870.2_Missense_Mutation_p.R58Q|KDM4C_ENST00000442236.2_Missense_Mutation_p.R190Q|KDM4C_ENST00000381306.3_Missense_Mutation_p.R371Q|KDM4C_ENST00000535193.1_Missense_Mutation_p.R393Q|KDM4C_ENST00000536108.1_Missense_Mutation_p.R190Q	NM_015061.3	NP_055876.2	Q9H3R0	KDM4C_HUMAN	lysine (K)-specific demethylase 4C	371					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						AAAGCATCCCGAAGGTAATGA	0.453													G|||	2	0.000399361	0.0	0.0014	5008	,	,		19729	0.0		0.001	False		,,,				2504	0.0				p.R393Q		Atlas-SNP	.											.	KDM4C	186	.	0			c.G1178A						PASS	.	G	GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG	0,4406		0,0,2203	70.0	62.0	65.0		1112,1112,1178,1112	-4.8	0.0	9	dbSNP_126	65	37,8563	24.6+/-71.5	0,37,4263	yes	missense,missense,missense,missense	KDM4C	NM_001146694.1,NM_001146695.1,NM_001146696.1,NM_015061.3	43,43,43,43	0,37,6466	AA,AG,GG		0.4302,0.0,0.2845	benign,benign,benign,benign	371/1048,371/814,393/836,371/1057	6981115	37,12969	2203	4300	6503	SO:0001583	missense	23081	exon9			CATCCCGAAGGTA	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.1112G>A	9.37:g.6981115G>A	ENSP00000370710:p.Arg371Gln	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	23	8	0.347826	NM_001146696	B4E1Y4|B7ZL46|F5H347|F5H7P0|O94877|Q2M3M0|Q5JUC9|Q5VYJ2|Q5VYJ3	Missense_Mutation	SNP	ENST00000381309.3	37	CCDS6471.1	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	G	10.47	1.358960	0.24598	0.0	0.004302	ENSG00000107077	ENST00000535193;ENST00000543771;ENST00000381309;ENST00000381306;ENST00000442236;ENST00000536108;ENST00000428870	T;T;T;T;T;T;T	0.19532	2.25;2.26;2.43;2.33;2.64;2.14;3.43	5.47	-4.79	0.03200	.	0.954910	0.08712	N	0.904774	T	0.14657	0.0354	L	0.29908	0.895	0.09310	N	1	B;P;B;B;B	0.47106	0.196;0.89;0.158;0.011;0.045	B;B;B;B;B	0.41466	0.026;0.358;0.039;0.007;0.017	T	0.11275	-1.0594	10	0.13470	T	0.59	-1.4792	15.7963	0.78412	0.7358:0.0:0.2642:0.0	rs35049841;rs61752861	190;371;393;371;371	E7EV17;F5H347;F5H7P0;Q9H3R0;Q9H3R0-2	.;.;.;KDM4C_HUMAN;.	Q	393;371;371;371;190;190;58	ENSP00000442382:R393Q;ENSP00000445427:R371Q;ENSP00000370710:R371Q;ENSP00000370707:R371Q;ENSP00000409353:R190Q;ENSP00000440656:R190Q;ENSP00000405739:R58Q	ENSP00000370707:R371Q	R	+	2	0	KDM4C	6971115	0.001000	0.12720	0.001000	0.08648	0.006000	0.05464	-0.028000	0.12350	-1.432000	0.01979	-0.225000	0.12378	CGA	G|0.998;A|0.002	0.002	strong		0.453	KDM4C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051692.1	NM_015061	
SSPN	8082	hgsc.bcm.edu	37	12	26383834	26383834	+	Missense_Mutation	SNP	G	G	A	rs12313670	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:26383834G>A	ENST00000242729.2	+	3	734	c.557G>A	c.(556-558)aGc>aAc	p.S186N	RP11-283G6.5_ENST00000541940.1_RNA|SSPN_ENST00000422622.2_Missense_Mutation_p.S83N|SSPN_ENST00000535504.1_Intron|RP11-283G6.5_ENST00000537525.1_RNA|SSPN_ENST00000540266.1_Missense_Mutation_p.S83N|RP11-283G6.5_ENST00000540625.1_RNA|RP11-283G6.4_ENST00000540392.1_RNA	NM_005086.4	NP_005077.2	Q14714	SSPN_HUMAN	sarcospan	186			S -> N (in dbSNP:rs12313670).		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)				kidney(1)|large_intestine(2)|lung(5)|skin(1)|stomach(1)	10	Colorectal(261;0.0847)					GACTGTACCAGCGTCACTGGC	0.507													G|||	379	0.0756789	0.2284	0.0504	5008	,	,		18137	0.0		0.0258	False		,,,				2504	0.0164				p.S186N		Atlas-SNP	.											.	SSPN	19	.	0			c.G557A						PASS	.	G	ASN/SER,ASN/SER	789,3617	317.7+/-295.3	72,645,1486	207.0	175.0	186.0		248,557	4.7	1.0	12	dbSNP_120	186	302,8298	109.8+/-170.3	6,290,4004	yes	missense,missense	SSPN	NM_001135823.1,NM_005086.4	46,46	78,935,5490	AA,AG,GG		3.5116,17.9074,8.3884	probably-damaging,probably-damaging	83/141,186/244	26383834	1091,11915	2203	4300	6503	SO:0001583	missense	8082	exon3			GTACCAGCGTCAC	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.557G>A	12.37:g.26383834G>A	ENSP00000242729:p.Ser186Asn	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	41	24	0.585366	NM_005086	B3KS67	Missense_Mutation	SNP	ENST00000242729.2	37	CCDS8707.1	118	0.05402930402930403	81	0.16463414634146342	17	0.04696132596685083	0	0.0	20	0.026385224274406333	G	15.60	2.880269	0.51801	0.179074	0.035116	ENSG00000123096	ENST00000538142;ENST00000540266;ENST00000422622;ENST00000242729;ENST00000441067	T;T;T;T	0.02446	4.29;4.29;4.29;4.29	4.7	4.7	0.59300	.	0.299368	0.38720	N	0.001581	T	0.00012	0.0000	L	0.51422	1.61	0.09310	P	0.999999999305424	D	0.53312	0.959	P	0.52343	0.696	T	0.51903	-0.8646	9	0.30078	T	0.28	-16.3235	8.3888	0.32516	0.0827:0.1567:0.7606:0.0	rs12313670;rs52791948;rs12313670	186	Q14714	SSPN_HUMAN	N	83;83;83;186;160	ENSP00000445360:S83N;ENSP00000442893:S83N;ENSP00000396087:S83N;ENSP00000242729:S186N	ENSP00000242729:S186N	S	+	2	0	SSPN	26275101	0.547000	0.26465	1.000000	0.80357	0.998000	0.95712	0.586000	0.23894	2.336000	0.79503	0.563000	0.77884	AGC	G|0.928;A|0.072	0.072	strong		0.507	SSPN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402654.2	NM_005086	
IGSF9B	22997	hgsc.bcm.edu	37	11	133807819	133807819	+	Silent	SNP	G	G	A	rs329635	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:133807819G>A	ENST00000321016.8	-	4	677	c.447C>T	c.(445-447)atC>atT	p.I149I	IGSF9B_ENST00000533871.2_Silent_p.I149I			Q9UPX0	TUTLB_HUMAN	immunoglobulin superfamily, member 9B	149	Ig-like 2.				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)		CCTTGGCCTCGATGTACTGGG	0.572													G|||	391	0.0780751	0.0719	0.0836	5008	,	,		18828	0.001		0.1332	False		,,,				2504	0.1053				p.I149I		Atlas-SNP	.											.	IGSF9B	290	.	0			c.C447T						PASS	.	G		369,3869		13,343,1763	62.0	67.0	65.0		447	-2.8	1.0	11	dbSNP_79	65	992,7466		58,876,3295	no	coding-synonymous	IGSF9B	NM_014987.1		71,1219,5058	AA,AG,GG		11.7285,8.7069,10.7199		149/1350	133807819	1361,11335	2119	4229	6348	SO:0001819	synonymous_variant	22997	exon4			GGCCTCGATGTAC	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.447C>T	11.37:g.133807819G>A		Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	165	113	0.684848	NM_014987	G5EA26	Silent	SNP	ENST00000321016.8	37																																																																																				G|0.918;A|0.082	0.082	strong		0.572	IGSF9B-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		XM_290502	
IGF1R	3480	hgsc.bcm.edu	37	15	99478225	99478225	+	Silent	SNP	G	G	A	rs2229765	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:99478225G>A	ENST00000268035.6	+	16	3740	c.3129G>A	c.(3127-3129)gaG>gaA	p.E1043E	IGF1R_ENST00000558762.1_Silent_p.E1042E	NM_000875.3	NP_000866.1	P08069	IGF1R_HUMAN	insulin-like growth factor 1 receptor	1043	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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)"""	GCATGCGTGAGAGGATTGAGT	0.468													A|||	1681	0.335663	0.2557	0.3646	5008	,	,		22181	0.3462		0.4294	False		,,,				2504	0.316				p.E1043E		Atlas-SNP	.											.	IGF1R	147	.	0			c.G3129A	GRCh37	CM031698	IGF1R	M	rs2229765	PASS	.	A		1319,3075	695.0+/-405.9	204,911,1082	138.0	122.0	128.0		3129	-9.5	0.0	15	dbSNP_98	128	3911,4683	605.6+/-395.0	908,2095,1294	no	coding-synonymous	IGF1R	NM_000875.3		1112,3006,2376	AA,AG,GG		45.5085,30.0182,40.2679		1043/1368	99478225	5230,7758	2197	4297	6494	SO:0001819	synonymous_variant	3480	exon16			GCGTGAGAGGATT	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.3129G>A	15.37:g.99478225G>A		Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	231	142	0.614719	NM_000875	B1B5Y2|Q14CV2|Q9UCC0	Silent	SNP	ENST00000268035.6	37	CCDS10378.1																																																																																			G|0.625;A|0.375	0.375	strong		0.468	IGF1R-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313537.2	NM_000875	
CYP24A1	1591	hgsc.bcm.edu	37	20	52775528	52775528	+	Silent	SNP	C	C	T	rs2296239	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:52775528C>T	ENST00000216862.3	-	8	1518	c.1125G>A	c.(1123-1125)ccG>ccA	p.P375P	CYP24A1_ENST00000395954.3_Silent_p.P233P|CYP24A1_ENST00000395955.3_Silent_p.P375P|CYP24A1_ENST00000460643.1_5'Flank	NM_000782.4	NP_000773.2	Q07973	CP24A_HUMAN	cytochrome P450, family 24, subfamily A, polypeptide 1	375					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)	CTTTTAAATACGGCATATTCC	0.398													C|||	1981	0.395567	0.4614	0.2695	5008	,	,		18576	0.6052		0.2078	False		,,,				2504	0.3732				p.P375P		Atlas-SNP	.											.	CYP24A1	75	.	0			c.G1125A						PASS	.	C	,	1792,2614	525.2+/-371.5	349,1094,760	127.0	134.0	131.0		1125,1125	-8.8	0.9	20	dbSNP_100	131	1813,6787	325.9+/-317.1	181,1451,2668	no	coding-synonymous,coding-synonymous	CYP24A1	NM_000782.4,NM_001128915.1	,	530,2545,3428	TT,TC,CC		21.0814,40.6718,27.718	,	375/515,375/449	52775528	3605,9401	2203	4300	6503	SO:0001819	synonymous_variant	1591	exon8			TAAATACGGCATA	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.1125G>A	20.37:g.52775528C>T		Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	147	69	0.469388	NM_000782	Q15807|Q32ML3|Q5I2W7	Silent	SNP	ENST00000216862.3	37	CCDS33491.1																																																																																			C|0.677;T|0.323	0.323	strong		0.398	CYP24A1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079769.2		
CYP4F12	66002	hgsc.bcm.edu	37	19	15807830	15807830	+	Silent	SNP	T	T	C	rs593421	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:15807830T>C	ENST00000550308.1	+	13	1890	c.1510T>C	c.(1510-1512)Ttg>Ctg	p.L504L	CYP4F12_ENST00000324632.10_Silent_p.L504L	NM_023944.3	NP_076433	Q9HCS2	CP4FC_HUMAN	cytochrome P450, family 4, subfamily F, polypeptide 12	504					arachidonic acid metabolic process (GO:0019369)|drug metabolic process (GO:0017144)|epoxygenase P450 pathway (GO:0019373)|leukotriene B4 catabolic process (GO:0036101)|long-chain fatty acid metabolic process (GO:0001676)|negative regulation of blood coagulation (GO:0030195)|oxidation-reduction process (GO:0055114)|pressure natriuresis (GO:0003095)|renal water homeostasis (GO:0003091)|small molecule metabolic process (GO:0044281)|sodium ion homeostasis (GO:0055078)|very long-chain fatty acid metabolic process (GO:0000038)|vitamin E metabolic process (GO:0042360)|vitamin K biosynthetic process (GO:0042371)|xenobiotic metabolic process (GO:0006805)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)	alkane 1-monooxygenase activity (GO:0018685)|arachidonic acid epoxygenase activity (GO:0008392)|aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|leukotriene-B4 20-monooxygenase activity (GO:0050051)|vitamin-K-epoxide reductase (warfarin-sensitive) activity (GO:0047057)			NS(1)|central_nervous_system(3)|endometrium(4)|kidney(2)|large_intestine(7)|lung(12)|ovary(3)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	41	Acute lymphoblastic leukemia(2;0.0367)				Fingolimod(DB08868)	GAAGCTGGAATTGATCATGCG	0.587													C|||	1210	0.241613	0.4032	0.2421	5008	,	,		18747	0.0139		0.2763	False		,,,				2504	0.2219				p.L504L		Atlas-SNP	.											.	CYP4F12	89	.	0			c.T1510C						PASS	.	C		1693,2711		329,1035,838	56.0	60.0	59.0		1510	-3.1	0.0	19	dbSNP_83	59	2116,6484		294,1528,2478	no	coding-synonymous	CYP4F12	NM_023944.3		623,2563,3316	CC,CT,TT		24.6047,38.4423,29.291		504/525	15807830	3809,9195	2202	4300	6502	SO:0001819	synonymous_variant	66002	exon13			CTGGAATTGATCA	AB035130	CCDS42517.1	19p13.1	2008-02-05	2003-01-14		ENSG00000186204	ENSG00000186204		"""Cytochrome P450s"""	18857	protein-coding gene	gene with protein product		611485	"""cytochrome P450, subfamily IVF, polypeptide 12"""			11162607	Standard	NM_023944		Approved		uc002nbl.3	Q9HCS2	OTTHUMG00000164477	ENST00000550308.1:c.1510T>C	19.37:g.15807830T>C		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	125	58	0.464	NM_023944	E7ET51|O60389|Q5JPJ7|Q9HCS1	Silent	SNP	ENST00000550308.1	37	CCDS42517.1																																																																																			T|0.770;C|0.230	0.230	strong		0.587	CYP4F12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378938.9		
PDIA2	64714	hgsc.bcm.edu	37	16	335373	335373	+	Missense_Mutation	SNP	C	C	T	rs2685127	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:335373C>T	ENST00000219406.6	+	6	875	c.857C>T	c.(856-858)aCg>aTg	p.T286M	PDIA2_ENST00000404312.1_Missense_Mutation_p.T283M|PDIA2_ENST00000462950.1_3'UTR	NM_006849.2	NP_006840.2	Q13087	PDIA2_HUMAN	protein disulfide isomerase family A, member 2	286			T -> M (in dbSNP:rs2685127).		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)				GTCAACCAGACGCTGGCTGCG	0.662													c|||	406	0.0810703	0.1679	0.0562	5008	,	,		12621	0.0069		0.1183	False		,,,				2504	0.0194				p.T286M		Atlas-SNP	.											.	PDIA2	51	.	0			c.C857T						PASS	.		MET/THR	587,3477		37,513,1482	35.0	40.0	38.0		857	3.9	0.7	16	dbSNP_100	38	995,7375		70,855,3260	yes	missense	PDIA2	NM_006849.2	81	107,1368,4742	TT,TC,CC		11.8877,14.4439,12.7232	probably-damaging	286/526	335373	1582,10852	2032	4185	6217	SO:0001583	missense	64714	exon6			ACCAGACGCTGGC	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.857C>T	16.37:g.335373C>T	ENSP00000219406:p.Thr286Met	Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	115	24	0.208696	NM_006849	A6ZJ64|B4DI27|Q2WGM4|Q4TT67|Q6B010|Q96KJ6|Q9BW95	Missense_Mutation	SNP	ENST00000219406.6	37	CCDS42089.1	202	0.0924908424908425	92	0.18699186991869918	23	0.06353591160220995	3	0.005244755244755245	84	0.11081794195250659	c	11.79	1.742809	0.30865	0.144439	0.118877	ENSG00000185615	ENST00000219406;ENST00000455994;ENST00000404312	T;T	0.14640	2.49;2.49	3.87	3.87	0.44632	Thioredoxin-like fold (1);	0.188317	0.44097	D	0.000499	T	0.00039	0.0001	M	0.61703	1.905	0.24573	P	0.99391392	P	0.51240	0.943	P	0.52386	0.697	T	0.08391	-1.0724	9	0.72032	D	0.01	.	14.7294	0.69368	0.0:1.0:0.0:0.0	rs2685127;rs60535328;rs2685127	286	Q13087	PDIA2_HUMAN	M	286;255;283	ENSP00000219406:T286M;ENSP00000384410:T283M	ENSP00000219406:T286M	T	+	2	0	PDIA2	275374	0.941000	0.31946	0.732000	0.30844	0.062000	0.15995	2.599000	0.46231	2.013000	0.59113	0.486000	0.48141	ACG	C|0.898;T|0.102	0.102	strong		0.662	PDIA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139315.3	NM_006849	
MFHAS1	9258	hgsc.bcm.edu	37	8	8654898	8654898	+	Silent	SNP	C	C	T	rs3827812	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:8654898C>T	ENST00000276282.6	-	2	3688	c.3102G>A	c.(3100-3102)ccG>ccA	p.P1034P	MFHAS1_ENST00000520091.1_5'UTR	NM_004225.2	NP_004216.2	Q9Y4C4	MFHA1_HUMAN	malignant fibrous histiocytoma amplified sequence 1	1034								p.P1034P(1)		endometrium(1)|kidney(3)|large_intestine(7)|lung(6)|ovary(1)|prostate(2)|stomach(1)	21		Hepatocellular(245;0.217)		COAD - Colon adenocarcinoma(149;0.124)		TGATCACAGTCGGCGTGGGTG	0.557													C|||	470	0.0938498	0.0348	0.1023	5008	,	,		16278	0.0466		0.1958	False		,,,				2504	0.1115				p.P1034P	Melanoma(103;1201 2045 17515 28966)	Atlas-SNP	.											MFHAS1,NS,carcinoma,0,1	MFHAS1	58	1	1	Substitution - coding silent(1)	stomach(1)	c.G3102A						PASS	.	C		260,4146	148.0+/-182.4	6,248,1949	118.0	91.0	100.0		3102	-5.8	0.8	8	dbSNP_107	100	1648,6952	304.0+/-306.7	156,1336,2808	no	coding-synonymous	MFHAS1	NM_004225.2		162,1584,4757	TT,TC,CC		19.1628,5.901,14.6702		1034/1053	8654898	1908,11098	2203	4300	6503	SO:0001819	synonymous_variant	9258	exon2			CACAGTCGGCGTG	AB016816	CCDS34844.1	8p23.1	2014-03-07			ENSG00000147324	ENSG00000147324			16982	protein-coding gene	gene with protein product	"""leucine rich repeat containing 65"", ""malignant fibrous histiocytoma-amplified sequences with leucine-rich tandem repeats 1"""	605352				9973190	Standard	NM_004225		Approved	MASL1, LRRC65	uc003wsj.1	Q9Y4C4	OTTHUMG00000163676	ENST00000276282.6:c.3102G>A	8.37:g.8654898C>T		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	115	22	0.191304	NM_004225	Q96CI0	Silent	SNP	ENST00000276282.6	37	CCDS34844.1																																																																																			C|0.876;T|0.124	0.124	strong		0.557	MFHAS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374724.2	NM_004225	
IRS1	3667	hgsc.bcm.edu	37	2	227661043	227661043	+	Silent	SNP	T	T	C	rs1801123	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:227661043T>C	ENST00000305123.5	-	1	3432	c.2412A>G	c.(2410-2412)gcA>gcG	p.A804A	IRS1_ENST00000498335.1_5'Flank	NM_005544.2	NP_005535.1	P35568	IRS1_HUMAN	insulin receptor substrate 1	804					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)		AAGAATCATCTGCTGTTGCAG	0.632													C|||	1402	0.279952	0.4652	0.2594	5008	,	,		17051	0.2649		0.0835	False		,,,				2504	0.2618				p.A804A		Atlas-SNP	.											IRS1,NS,carcinoma,0,1	IRS1	141	1	0			c.A2412G	GRCh37	CM004559	IRS1	M	rs1801123	PASS	.	C		1752,2654	638.3+/-396.9	368,1016,819	71.0	83.0	79.0		2412	-9.4	0.0	2	dbSNP_89	79	834,7766	773.5+/-407.7	48,738,3514	no	coding-synonymous	IRS1	NM_005544.2		416,1754,4333	CC,CT,TT		9.6977,39.764,19.8831		804/1243	227661043	2586,10420	2203	4300	6503	SO:0001819	synonymous_variant	3667	exon1			ATCATCTGCTGTT		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.2412A>G	2.37:g.227661043T>C		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	64	25	0.390625	NM_005544		Silent	SNP	ENST00000305123.5	37	CCDS2463.1																																																																																			T|0.776;C|0.224	0.224	strong		0.632	IRS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256886.3	NM_005544	
ZZEF1	23140	hgsc.bcm.edu	37	17	4015997	4015997	+	Silent	SNP	A	A	G	rs58625333	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:4015997A>G	ENST00000381638.2	-	5	1096	c.972T>C	c.(970-972)aaT>aaC	p.N324N	snoU13_ENST00000459263.1_RNA|ZZEF1_ENST00000574474.1_5'UTR	NM_015113.3	NP_055928.3	O43149	ZZEF1_HUMAN	zinc finger, ZZ-type with EF-hand domain 1	324	DOC. {ECO:0000255|PROSITE- ProRule:PRU00614}.						calcium ion binding (GO:0005509)|zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(17)|lung(19)|ovary(3)|pancreas(1)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(3)	84						GATCGCTGGCATTCCTCCCTA	0.527													A|||	1376	0.27476	0.2716	0.2767	5008	,	,		18402	0.248		0.2634	False		,,,				2504	0.317				p.N324N		Atlas-SNP	.											.	ZZEF1	195	.	0			c.T972C						PASS	.	A		1160,3246	409.5+/-335.0	140,880,1183	111.0	79.0	90.0		972	0.5	0.0	17	dbSNP_129	90	2109,6491	364.5+/-333.5	252,1605,2443	no	coding-synonymous	ZZEF1	NM_015113.3		392,2485,3626	GG,GA,AA		24.5233,26.3277,25.1346		324/2962	4015997	3269,9737	2203	4300	6503	SO:0001819	synonymous_variant	23140	exon5			GCTGGCATTCCTC	BC035319	CCDS11043.1	17p13.3	2013-01-10	2004-11-03		ENSG00000074755	ENSG00000074755		"""Zinc fingers, ZZ-type"", ""EF-hand domain containing"""	29027	protein-coding gene	gene with protein product			"""zinc finger, ZZ-type with EF hand domain 1"""			9455477	Standard	XM_005256560		Approved	KIAA0399, ZZZ4, FLJ10821	uc002fxe.3	O43149	OTTHUMG00000090741	ENST00000381638.2:c.972T>C	17.37:g.4015997A>G		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	129	58	0.449612	NM_015113	A7MBM5|Q6NXG0|Q6ZRA1|Q6ZSF4|Q9NVB9	Silent	SNP	ENST00000381638.2	37	CCDS11043.1																																																																																			A|0.736;G|0.264	0.264	strong		0.527	ZZEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207480.1	NM_015113	
MED24	9862	hgsc.bcm.edu	37	17	38186106	38186106	+	Silent	SNP	C	C	T	rs11555255	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:38186106C>T	ENST00000394128.2	-	13	1242	c.1161G>A	c.(1159-1161)gcG>gcA	p.A387A	MED24_ENST00000394127.2_Silent_p.A374A|SNORD124_ENST00000459577.1_RNA|MED24_ENST00000501516.3_Silent_p.A406A|MED24_ENST00000394126.1_Silent_p.A412A|MED24_ENST00000356271.3_Silent_p.A374A	NM_014815.3	NP_055630.2	O75448	MED24_HUMAN	mediator complex subunit 24	387					androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of transcription, DNA-templated (GO:0045893)|protein heterooligomerization (GO:0051291)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|receptor activity (GO:0004872)|RNA polymerase II transcription cofactor activity (GO:0001104)|thyroid hormone receptor binding (GO:0046966)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			autonomic_ganglia(1)|breast(2)|endometrium(9)|large_intestine(10)|lung(14)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	41	Colorectal(19;0.000442)					GCTCTCGGTCCGCTTTGCTGT	0.557													C|||	528	0.105431	0.1551	0.1182	5008	,	,		20173	0.006		0.164	False		,,,				2504	0.0716				p.A387A		Atlas-SNP	.											.	MED24	89	.	0			c.G1161A						PASS	.	C	,	737,3669	304.1+/-288.3	63,611,1529	221.0	165.0	184.0		1122,1161	-4.2	0.2	17	dbSNP_120	184	1401,7199	270.7+/-289.1	115,1171,3014	no	coding-synonymous,coding-synonymous	MED24	NM_001079518.1,NM_014815.3	,	178,1782,4543	TT,TC,CC		16.2907,16.7272,16.4386	,	374/977,387/990	38186106	2138,10868	2203	4300	6503	SO:0001819	synonymous_variant	9862	exon13			TCGGTCCGCTTTG	AF055995	CCDS11359.1, CCDS42315.1	17q21.2	2007-07-30	2007-07-30	2007-07-30	ENSG00000008838	ENSG00000008838			22963	protein-coding gene	gene with protein product		607000	"""thyroid hormone receptor associated protein 4"", ""cofactor required for Sp1 transcriptional activation, subunit 4, 100kDa"""	THRAP4, CRSP4			Standard	NM_001079518		Approved	TRAP100, KIAA0130, DRIP100, CRSP100	uc002htt.3	O75448	OTTHUMG00000133329	ENST00000394128.2:c.1161G>A	17.37:g.38186106C>T		Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	148	83	0.560811	NM_014815	A8K4S5|B3KMR9|Q14143|Q9NNY5	Silent	SNP	ENST00000394128.2	37	CCDS11359.1																																																																																			T|0.119;G|0.156;C|0.699;A|0.025	0.119	strong		0.557	MED24-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257147.2	NM_014815	
FAM65B	9750	hgsc.bcm.edu	37	6	24818785	24818785	+	Silent	SNP	A	A	G	rs9358802	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:24818785A>G	ENST00000259698.4	-	21	3175	c.3000T>C	c.(2998-3000)gcT>gcC	p.A1000A	FAM65B_ENST00000538035.1_Silent_p.A979A	NM_014722.2	NP_055537.2	Q9Y4F9	FA65B_HUMAN	family with sequence similarity 65, member B	1000					cell differentiation (GO:0030154)|muscle organ development (GO:0007517)	cell projection (GO:0042995)|cytoskeleton (GO:0005856)|mitochondrion (GO:0005739)		p.A1000A(1)		breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(10)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	25						GGATTTTCAGAGCCAGGCAAG	0.493													G|||	1954	0.390176	0.1762	0.4121	5008	,	,		17052	0.6944		0.3002	False		,,,				2504	0.4427				p.A1000A		Atlas-SNP	.											FAM65B_ENST00000259698,NS,carcinoma,0,1	FAM65B	134	1	1	Substitution - coding silent(1)	stomach(1)	c.T3000C						PASS	.	G		274,1110		33,208,451	84.0	73.0	77.0		3000	1.1	0.6	6	dbSNP_119	77	999,2183		158,683,750	no	coding-synonymous	FAM65B	NM_014722.2		191,891,1201	GG,GA,AA		31.3953,19.7977,27.88		1000/1069	24818785	1273,3293	692	1591	2283	SO:0001819	synonymous_variant	9750	exon21			TTTCAGAGCCAGG	U49187	CCDS47383.1, CCDS47384.1, CCDS69057.1, CCDS69058.1, CCDS75410.1	6p22.3-p21.32	2012-11-30	2008-06-13	2008-06-13	ENSG00000111913	ENSG00000111913			13872	protein-coding gene	gene with protein product	"""myogenesis-related and NCAM-associated protein homolog (chicken)"""	611410	"""chromosome 6 open reading frame 32"""	C6orf32		9205841, 17150207, 17825087	Standard	NM_001286447		Approved	KIAA0386, DIFF48, MYONAP	uc003neo.1	Q9Y4F9	OTTHUMG00000014375	ENST00000259698.4:c.3000T>C	6.37:g.24818785A>G		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	130	129	0.992308	NM_014722	A6NHP2|Q13529|Q5VV37|Q5VV38|Q9BQ28	Silent	SNP	ENST00000259698.4	37	CCDS47383.1																																																																																			A|0.664;G|0.336	0.336	strong		0.493	FAM65B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040024.2		
BMPER	168667	hgsc.bcm.edu	37	7	34009946	34009946	+	Silent	SNP	C	C	T	rs10265207	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:34009946C>T	ENST00000297161.2	+	6	782	c.408C>T	c.(406-408)ggC>ggT	p.G136G	BMPER_ENST00000426693.1_Silent_p.G136G	NM_133468.4	NP_597725.1	Q8N8U9	BMPER_HUMAN	BMP binding endothelial regulator	136	VWFC 2. {ECO:0000255|PROSITE- ProRule:PRU00220}.				blood vessel endothelial cell proliferation involved in sprouting angiogenesis (GO:0002043)|endothelial cell activation (GO:0042118)|inner ear development (GO:0048839)|negative regulation of BMP signaling pathway (GO:0030514)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|regulation of endothelial cell migration (GO:0010594)|regulation of pathway-restricted SMAD protein phosphorylation (GO:0060393)|ureteric bud development (GO:0001657)	extracellular space (GO:0005615)				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|lung(24)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	48						TTCAGGAGGGCGTTGTCACAG	0.488													C|||	2144	0.428115	0.3601	0.4121	5008	,	,		19508	0.3929		0.4682	False		,,,				2504	0.5266				p.G136G		Atlas-SNP	.											.	BMPER	131	.	0			c.C408T						PASS	.	C		1703,2703	514.1+/-368.5	332,1039,832	225.0	189.0	201.0		408	-1.5	1.0	7	dbSNP_119	201	4002,4598	554.4+/-386.5	911,2180,1209	no	coding-synonymous	BMPER	NM_133468.3		1243,3219,2041	TT,TC,CC		46.5349,38.6518,43.8644		136/686	34009946	5705,7301	2203	4300	6503	SO:0001819	synonymous_variant	168667	exon6			GGAGGGCGTTGTC		CCDS5442.1	7p14.3	2009-02-18			ENSG00000164619	ENSG00000164619			24154	protein-coding gene	gene with protein product	"""crossveinless-2"""	608699				12897139, 14766204	Standard	NM_133468		Approved	Cv2, CRIM3	uc011kap.2	Q8N8U9	OTTHUMG00000128675	ENST00000297161.2:c.408C>T	7.37:g.34009946C>T		Somatic	168	1	0.00595238		WXS	Illumina HiSeq	Phase_I	119	118	0.991597	NM_133468	A8K1P8|Q8TF36	Silent	SNP	ENST00000297161.2	37	CCDS5442.1	930	0.4258241758241758	166	0.33739837398373984	159	0.43922651933701656	237	0.4143356643356643	368	0.48548812664907653	C	12.48	1.951693	0.34471	0.386518	0.465349	ENSG00000164619	ENST00000436222	.	.	.	5.75	-1.49	0.08718	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.999999999999994	.	.	.	.	.	.	T	0.45279	-0.9272	4	0.87932	D	0	.	5.2999	0.15772	0.2769:0.3448:0.0:0.3784	rs10265207;rs58950274;rs10265207	.	.	.	V	103	.	ENSP00000399843:A103V	A	+	2	0	BMPER	33976471	0.135000	0.22499	0.963000	0.40424	0.864000	0.49448	-1.005000	0.03674	-0.153000	0.11137	0.655000	0.94253	GCG	C|0.570;T|0.430	0.430	strong		0.488	BMPER-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250570.2	NM_133468	
PLCB3	5331	hgsc.bcm.edu	37	11	64023971	64023971	+	Silent	SNP	G	G	A	rs7943988	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:64023971G>A	ENST00000540288.1	+	9	925	c.822G>A	c.(820-822)ctG>ctA	p.L274L	PLCB3_ENST00000325234.5_Silent_p.L207L|PLCB3_ENST00000279230.6_Silent_p.L274L	NM_000932.2	NP_000923.1	Q01970	PLCB3_HUMAN	phospholipase C, beta 3 (phosphatidylinositol-specific)	274					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						AGGCCCGGCTGCTCATCGAAA	0.637													G|||	854	0.170527	0.0227	0.1441	5008	,	,		18463	0.129		0.2982	False		,,,				2504	0.3006				p.L274L		Atlas-SNP	.											.	PLCB3	103	.	0			c.G822A						PASS	.	G	,	267,4135	147.6+/-182.1	8,251,1942	83.0	101.0	95.0		822,621	5.3	1.0	11	dbSNP_116	95	2707,5887	426.2+/-355.2	424,1859,2014	no	coding-synonymous,coding-synonymous	PLCB3	NM_000932.2,NM_001184883.1	,	432,2110,3956	AA,AG,GG		31.4987,6.0654,22.884	,	274/1235,207/1168	64023971	2974,10022	2201	4297	6498	SO:0001819	synonymous_variant	5331	exon9			CCGGCTGCTCATC	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.822G>A	11.37:g.64023971G>A		Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	131	23	0.175573	NM_000932	A5PKZ6|G5E960|Q8N1A4	Silent	SNP	ENST00000540288.1	37	CCDS8064.1																																																																																			G|0.807;A|0.193	0.193	strong		0.637	PLCB3-002	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396405.1		
MEF2A	4205	hgsc.bcm.edu	37	15	100252892	100252892	+	Silent	SNP	A	A	G	rs34851361	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:100252892A>G	ENST00000557785.1	+	11	1759	c.1410A>G	c.(1408-1410)ccA>ccG	p.P470P	MEF2A_ENST00000557942.1_Silent_p.P478P|MEF2A_ENST00000354410.5_Silent_p.P472P|MEF2A_ENST00000558812.1_Silent_p.P410P|MEF2A_ENST00000449277.2_Silent_p.P402P|MEF2A_ENST00000338042.6_Silent_p.P479P|MEF2A_ENST00000453228.2_Silent_p.P470P	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	140	0	0		WXS	Illumina HiSeq	Phase_I	168	55	0.327381	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		
TNS1	7145	hgsc.bcm.edu	37	2	218712606	218712606	+	Silent	SNP	G	G	A	rs1364641	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:218712606G>A	ENST00000171887.4	-	17	2711	c.2259C>T	c.(2257-2259)tcC>tcT	p.S753S	TNS1_ENST00000419504.1_Silent_p.S753S|TNS1_ENST00000480665.1_5'Flank|TNS1_ENST00000430930.1_Silent_p.S753S	NM_022648.4	NP_072174.3	Q9HBL0	TENS1_HUMAN	tensin 1	753					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)		GGGACTGACGGGAGGATCCAG	0.652													G|||	2179	0.435104	0.6218	0.3156	5008	,	,		14719	0.3442		0.3499	False		,,,				2504	0.4489				p.S753S		Atlas-SNP	.											.	TNS1	251	.	0			c.C2259T						PASS	.	G		2473,1933		705,1063,435	17.0	20.0	19.0		2259	3.1	0.8	2	dbSNP_88	19	2685,5915		442,1801,2057	no	coding-synonymous	TNS1	NM_022648.4		1147,2864,2492	AA,AG,GG		31.2209,43.872,39.6586		753/1736	218712606	5158,7848	2203	4300	6503	SO:0001819	synonymous_variant	7145	exon17			CTGACGGGAGGAT	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.2259C>T	2.37:g.218712606G>A		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	67	29	0.432836	NM_022648	Q4ZG71|Q6IPI5	Silent	SNP	ENST00000171887.4	37	CCDS2407.1																																																																																			G|0.592;A|0.408	0.408	strong		0.652	TNS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256672.2	NM_022648	
OR51D1	390038	hgsc.bcm.edu	37	11	4661285	4661285	+	Missense_Mutation	SNP	A	A	G	rs905871	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	272	0	0		WXS	Illumina HiSeq	Phase_I	322	59	0.18323	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	
ROBO1	6091	hgsc.bcm.edu	37	3	78700901	78700901	+	Silent	SNP	G	G	T	rs6795556	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:78700901G>T	ENST00000464233.1	-	19	2906	c.2793C>A	c.(2791-2793)acC>acA	p.T931T	ROBO1_ENST00000436010.2_Silent_p.T892T|ROBO1_ENST00000495273.1_Silent_p.T895T|ROBO1_ENST00000467549.1_Silent_p.T895T	NM_002941.3	NP_002932.1	Q9Y6N7	ROBO1_HUMAN	roundabout, axon guidance receptor, homolog 1 (Drosophila)	931					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|axon guidance (GO:0007411)|axon midline choice point recognition (GO:0016199)|cell adhesion (GO:0007155)|cell migration involved in sprouting angiogenesis (GO:0002042)|chemorepulsion involved in postnatal olfactory bulb interneuron migration (GO:0021836)|homophilic cell adhesion (GO:0007156)|mammary duct terminal end bud growth (GO:0060763)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|negative regulation of negative chemotaxis (GO:0050925)|nervous system development (GO:0007399)|positive regulation of axonogenesis (GO:0050772)|Roundabout signaling pathway (GO:0035385)	axolemma (GO:0030673)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	axon guidance receptor activity (GO:0008046)|identical protein binding (GO:0042802)|LRR domain binding (GO:0030275)			breast(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(2)|lung(25)|urinary_tract(1)	44		Lung SC(41;0.0257)|Lung NSC(201;0.0439)		LUSC - Lung squamous cell carcinoma(21;0.008)|Epithelial(33;0.00999)|Lung(72;0.0177)|BRCA - Breast invasive adenocarcinoma(55;0.0274)		TACCCGCGTAGGTACTAGTAA	0.378													A|||	1085	0.216653	0.1657	0.2161	5008	,	,		16303	0.2222		0.2594	False		,,,				2504	0.2362				p.T931T		Atlas-SNP	.											.	ROBO1	833	.	0			c.C2793A						PASS	.	A	,,	647,3167		46,555,1306	72.0	67.0	68.0		2685,2793,2685	-6.7	0.0	3	dbSNP_116	68	2001,6269		231,1539,2365	no	coding-synonymous,coding-synonymous,coding-synonymous	ROBO1	NM_001145845.1,NM_002941.3,NM_133631.3	,,	277,2094,3671	TT,TG,GG		24.1959,16.9638,21.9133	,,	895/1552,931/1652,895/1607	78700901	2648,9436	1907	4135	6042	SO:0001819	synonymous_variant	6091	exon19			CGCGTAGGTACTA	AF040990	CCDS46872.1, CCDS46872.2, CCDS54610.1, CCDS54611.1	3p12.3	2013-02-11	2001-11-28		ENSG00000169855	ENSG00000169855		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	10249	protein-coding gene	gene with protein product		602430	"""roundabout (axon guidance receptor, Drosophila) homolog 1"""			9458045, 9608531	Standard	NM_002941		Approved	DUTT1, FLJ21882, SAX3	uc003dqe.2	Q9Y6N7	OTTHUMG00000158843	ENST00000464233.1:c.2793C>A	3.37:g.78700901G>T		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	85	43	0.505882	NM_002941	B2RXI1|D3DU36|E9PD49|Q1RMC7|Q7Z300|Q9BUS7	Silent	SNP	ENST00000464233.1	37	CCDS54611.1																																																																																			G|0.764;T|0.236	0.236	strong		0.378	ROBO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352610.1	NM_002941	
TOM1	10043	hgsc.bcm.edu	37	22	35743124	35743124	+	Silent	SNP	G	G	C	rs2071745	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:35743124G>C	ENST00000449058.2	+	15	1526	c.1401G>C	c.(1399-1401)ggG>ggC	p.G467G	TOM1_ENST00000447733.1_Silent_p.G435G|TOM1_ENST00000425375.1_Silent_p.G422G|TOM1_ENST00000382034.5_3'UTR|TOM1_ENST00000436462.2_Silent_p.G429G|TOM1_ENST00000411850.1_Silent_p.G468G	NM_005488.2	NP_005479.1	O60784	TOM1_HUMAN	target of myb1 (chicken)	467					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)			NS(1)|breast(2)|kidney(2)|large_intestine(2)|lung(7)|ovary(3)|prostate(2)	19						CAGCTGAGGGGCCCCCGGGTC	0.607													G|||	1654	0.330272	0.6339	0.3401	5008	,	,		14935	0.1111		0.2237	False		,,,				2504	0.2485				p.G468G		Atlas-SNP	.											.	TOM1	43	.	0			c.G1404C						PASS	.	G	,,,	2405,2001		678,1049,476	47.0	59.0	55.0		1305,1266,1404,1401	-9.0	0.0	22	dbSNP_96	55	2027,6573		234,1559,2507	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TOM1	NM_001135729.1,NM_001135730.1,NM_001135732.1,NM_005488.2	,,,	912,2608,2983	CC,CG,GG		23.5698,45.4153,34.0766	,,,	435/461,422/448,468/494,467/493	35743124	4432,8574	2203	4300	6503	SO:0001819	synonymous_variant	10043	exon15			TGAGGGGCCCCCG	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.1401G>C	22.37:g.35743124G>C		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	41	18	0.439024	NM_001135732	B4DEL9|B4DNA1|Q5TIJ6|Q86X74	Silent	SNP	ENST00000449058.2	37	CCDS13913.1																																																																																			G|0.667;C|0.333	0.333	strong		0.607	TOM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000320641.1	NM_005488	
SEMA6D	80031	hgsc.bcm.edu	37	15	48063374	48063374	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:48063374T>C	ENST00000316364.5	+	19	3053	c.2614T>C	c.(2614-2616)Tct>Cct	p.S872P	SEMA6D_ENST00000536845.2_Missense_Mutation_p.S872P|SEMA6D_ENST00000558816.1_3'UTR|SEMA6D_ENST00000355997.3_3'UTR|SEMA6D_ENST00000389433.2_Missense_Mutation_p.S853P|SEMA6D_ENST00000537942.1_Missense_Mutation_p.S810P|SEMA6D_ENST00000358066.4_Missense_Mutation_p.S810P|SEMA6D_ENST00000354744.4_Missense_Mutation_p.S816P|SEMA6D_ENST00000558014.1_Missense_Mutation_p.S810P|SEMA6D_ENST00000389432.2_Missense_Mutation_p.S829P|SEMA6D_ENST00000389428.3_Missense_Mutation_p.S797P	NM_153618.1	NP_705871.1	Q8NFY4	SEM6D_HUMAN	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D	872					axon guidance (GO:0007411)|negative regulation of smooth muscle cell migration (GO:0014912)|positive regulation of smooth muscle cell migration (GO:0014911)|ventricular system development (GO:0021591)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			biliary_tract(1)|breast(4)|endometrium(4)|kidney(5)|large_intestine(10)|lung(42)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(4)	77		all_lung(180;0.000635)|Myeloproliferative disorder(241;0.116)|Melanoma(134;0.18)		all cancers(107;1.2e-11)|GBM - Glioblastoma multiforme(94;1.2e-06)		TCACCGGCGTTCTGTTGATTC	0.448																																					p.S872P		Atlas-SNP	.											SEMA6D_ENST00000558014,NS,carcinoma,-1,2	SEMA6D	322	2	0			c.T2614C						scavenged	.						88.0	81.0	84.0					15																	48063374		2198	4297	6495	SO:0001583	missense	80031	exon19			CGGCGTTCTGTTG	AF389430	CCDS32224.1, CCDS32225.1, CCDS32226.1, CCDS32227.1, CCDS32228.1, CCDS32229.1	15q21.1	2006-09-18				ENSG00000137872		"""Semaphorins"""	16770	protein-coding gene	gene with protein product		609295				12110693, 14977921	Standard	NM_020858		Approved	KIAA1479, FLJ11598	uc001zvy.3	Q8NFY4		ENST00000316364.5:c.2614T>C	15.37:g.48063374T>C	ENSP00000324857:p.Ser872Pro	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	159	2	0.0125786	NM_153618	A6NF10|A6NM95|A6NNK1|A7E2A0|Q8NFY3|Q8NFY5|Q8NFY6|Q8NFY7|Q9P249	Missense_Mutation	SNP	ENST00000316364.5	37	CCDS32225.1	.	.	.	.	.	.	.	.	.	.	T	15.50	2.850785	0.51270	.	.	ENSG00000137872	ENST00000537942;ENST00000536845;ENST00000316364;ENST00000389433;ENST00000389432;ENST00000354744;ENST00000358066;ENST00000389428	T;T;T;T;T;T;T;T	0.19394	2.15;2.2;2.2;2.18;2.15;2.15;2.15;2.16	5.69	4.5	0.54988	.	1.631400	0.03059	N	0.155593	T	0.33904	0.0879	L	0.36672	1.1	0.80722	D	1	P;P;P;P	0.49090	0.787;0.82;0.919;0.89	P;P;P;P	0.52793	0.544;0.628;0.709;0.628	T	0.01966	-1.1238	10	0.52906	T	0.07	.	12.492	0.55905	0.0:0.0:0.1394:0.8606	.	797;816;872;810	Q8NFY4-3;Q8NFY4-4;Q8NFY4;Q8NFY4-2	.;.;SEM6D_HUMAN;.	P	810;872;872;853;829;816;810;797	ENSP00000442040:S810P;ENSP00000446152:S872P;ENSP00000324857:S872P;ENSP00000374084:S853P;ENSP00000374083:S829P;ENSP00000346786:S816P;ENSP00000350770:S810P;ENSP00000374079:S797P	ENSP00000324857:S872P	S	+	1	0	SEMA6D	45850666	1.000000	0.71417	0.953000	0.39169	0.952000	0.60782	4.700000	0.61803	2.156000	0.67533	0.460000	0.39030	TCT	.	.	none		0.448	SEMA6D-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416868.1	NM_024966	
ITPR2	3709	hgsc.bcm.edu	37	12	26784850	26784850	+	Silent	SNP	G	G	A	rs2230372	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:26784850G>A	ENST00000381340.3	-	22	3299	c.2883C>T	c.(2881-2883)caC>caT	p.H961H	RP11-666F17.1_ENST00000414098.2_RNA|ITPR2_ENST00000545902.1_5'Flank	NM_002223.2	NP_002214.2	Q14571	ITPR2_HUMAN	inositol 1,4,5-trisphosphate receptor, type 2	961					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)	TCACATCCTCGTGCTCGGTGG	0.517													G|||	2468	0.492812	0.5393	0.3285	5008	,	,		18215	0.3839		0.497	False		,,,				2504	0.6544				p.H961H		Atlas-SNP	.											.	ITPR2	270	.	0			c.C2883T						PASS	.	G		2377,1783		685,1007,388	123.0	131.0	128.0		2883	-10.1	0.0	12	dbSNP_98	128	4188,4244		1077,2034,1105	no	coding-synonymous	ITPR2	NM_002223.2		1762,3041,1493	AA,AG,GG		49.6679,42.8606,47.8637		961/2702	26784850	6565,6027	2080	4216	6296	SO:0001819	synonymous_variant	3709	exon22			ATCCTCGTGCTCG	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.2883C>T	12.37:g.26784850G>A		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	112	49	0.4375	NM_002223	O94773	Silent	SNP	ENST00000381340.3	37	CCDS41764.1																																																																																			G|0.527;A|0.473	0.473	strong		0.517	ITPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402732.1	NM_002223	
CLCA2	9635	hgsc.bcm.edu	37	1	86920904	86920904	+	Silent	SNP	A	A	G	rs2390057	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:86920904A>G	ENST00000370565.4	+	14	2688	c.2526A>G	c.(2524-2526)caA>caG	p.Q842Q		NM_006536.5	NP_006527.1	Q9UQC9	CLCA2_HUMAN	chloride channel accessory 2	842					cell adhesion (GO:0007155)|transport (GO:0006810)	cell junction (GO:0030054)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	chloride channel activity (GO:0005254)|ligand-gated ion channel activity (GO:0015276)	p.Q842Q(1)		NS(2)|breast(1)|endometrium(1)|kidney(3)|large_intestine(9)|lung(18)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|stomach(1)	42		Lung NSC(277;0.238)		all cancers(265;0.0233)|Epithelial(280;0.0452)		TCTCACCCCAAATTTCCACGA	0.393													A|||	1647	0.328874	0.2057	0.2435	5008	,	,		17291	0.4405		0.335	False		,,,				2504	0.4346				p.Q842Q	Melanoma(157;1000 1898 5363 5664 48018)|Ovarian(88;135 1366 2838 28875 34642)	Atlas-SNP	.											CLCA2,NS,carcinoma,0,1	CLCA2	102	1	1	Substitution - coding silent(1)	stomach(1)	c.A2526G						PASS	.	A		1085,3321	393.5+/-328.9	142,801,1260	110.0	104.0	106.0		2526	-1.1	0.0	1	dbSNP_100	106	2876,5724	451.3+/-362.6	470,1936,1894	no	coding-synonymous	CLCA2	NM_006536.5		612,2737,3154	GG,GA,AA		33.4419,24.6255,30.4552		842/944	86920904	3961,9045	2203	4300	6503	SO:0001819	synonymous_variant	9635	exon14			ACCCCAAATTTCC		CCDS708.1	1p22.3	2012-02-26	2009-01-29		ENSG00000137975	ENSG00000137975			2016	protein-coding gene	gene with protein product		604003	"""chloride channel, calcium activated, family member 2"", ""chloride channel regulator 2"""				Standard	NM_006536		Approved	CLCRG2	uc001dlr.4	Q9UQC9	OTTHUMG00000010256	ENST00000370565.4:c.2526A>G	1.37:g.86920904A>G		Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	118	63	0.533898	NM_006536	A8K2T3|Q9Y6N2	Silent	SNP	ENST00000370565.4	37	CCDS708.1																																																																																			A|0.686;G|0.314	0.314	strong		0.393	CLCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028284.1	NM_006536	
TERT	7015	hgsc.bcm.edu	37	5	1294086	1294086	+	Silent	SNP	C	C	T	rs2736098	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:1294086C>T	ENST00000310581.5	-	2	972	c.915G>A	c.(913-915)gcG>gcA	p.A305A	TERT_ENST00000522877.1_5'Flank|TERT_ENST00000296820.5_Silent_p.A305A|TERT_ENST00000334602.6_Silent_p.A305A|TERT_ENST00000508104.2_Silent_p.A305A	NM_001193376.1|NM_198253.2	NP_001180305.1|NP_937983.2	O14746	TERT_HUMAN	telomerase reverse transcriptase	305	Linker.|Required for oligomerization.				DNA strand elongation (GO:0022616)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|replicative senescence (GO:0090399)|telomere formation via telomerase (GO:0032203)|telomere maintenance (GO:0000723)|telomere maintenance via telomerase (GO:0007004)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|nuclear telomere cap complex (GO:0000783)|nucleoplasm (GO:0005654)|telomerase holoenzyme complex (GO:0005697)	metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|telomerase activity (GO:0003720)|telomeric DNA binding (GO:0042162)|telomeric RNA binding (GO:0070034)|telomeric template RNA reverse transcriptase activity (GO:0003721)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(2)|kidney(4)|large_intestine(3)|lung(22)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	41	all_cancers(3;3.17e-16)|Lung NSC(6;8.55e-15)|all_lung(6;7.2e-14)|all_epithelial(6;1.87e-10)		Epithelial(17;0.00105)|all cancers(22;0.00178)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|Lung(60;0.185)		Zidovudine(DB00495)	ATGGGGGGCCCGCGTGGTGCT	0.682									TERT Mutation-Associated Haematological Disorders;Pulmonary Fibrosis, Idiopathic;Congenital Dyskeratosis				C|||	1330	0.265575	0.0658	0.2032	5008	,	,		15213	0.371		0.2346	False		,,,				2504	0.5031				p.A305A		Atlas-SNP	.											.	TERT	2594	.	0			c.G915A						PASS	.	C	,	454,3864		27,400,1732	16.0	16.0	16.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	915,915	-4.8	0.0	5	dbSNP_100	16	2202,6278		319,1564,2357	no	coding-synonymous,coding-synonymous	TERT	NM_001193376.1,NM_198253.2	,	346,1964,4089	TT,TC,CC		25.967,10.5141,20.7532	,	305/1070,305/1133	1294086	2656,10142	2159	4240	6399	SO:0001819	synonymous_variant	7015	exon2	Familial Cancer Database	;Hamman-Rich syndrome, Fibrocystic Pulmonary Dysplasia;Zinsser-Engman-Cole syndrome, Dyskeratosis Congenita	GGGGCCCGCGTGG	AF015950	CCDS3861.2, CCDS54831.1	5p15.33	2014-09-17			ENSG00000164362	ENSG00000164362			11730	protein-coding gene	gene with protein product		187270				9252327	Standard	NM_198253		Approved	TRT, TP2, TCS1, hEST2, EST2	uc003jcb.1	O14746	OTTHUMG00000090357	ENST00000310581.5:c.915G>A	5.37:g.1294086C>T		Somatic	16	0	0		WXS	Illumina HiSeq	Phase_I	19	11	0.578947	NM_001193376	O14783|Q2XS35|Q8N6C3|Q8NG38|Q8NG46	Silent	SNP	ENST00000310581.5	37	CCDS3861.2																																																																																			C|0.792;T|0.208	0.208	strong		0.682	TERT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206729.2		
HIST1H3I	8354	hgsc.bcm.edu	37	6	27839746	27839746	+	Silent	SNP	T	T	C	rs200956	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:27839746T>C	ENST00000328488.2	-	1	353	c.348A>G	c.(346-348)aaA>aaG	p.K116K		NM_003533.2	NP_003524.1	P68431	H31_HUMAN	histone cluster 1, H3i	116					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)			endometrium(2)|kidney(1)|lung(4)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	11						TAGTGACGCGTTTGGCGTGAA	0.572													C|||	1273	0.254193	0.4758	0.2305	5008	,	,		18092	0.1389		0.1511	False		,,,				2504	0.1963				p.K116K		Atlas-SNP	.											.	HIST1H3I	28	.	0			c.A348G						PASS	.	C		1856,2550	634.1+/-396.1	405,1046,752	125.0	136.0	133.0		348	2.3	1.0	6	dbSNP_79	133	1396,7204	754.3+/-407.5	114,1168,3018	no	coding-synonymous	HIST1H3I	NM_003533.2		519,2214,3770	CC,CT,TT		16.2326,42.1244,25.0038		116/137	27839746	3252,9754	2203	4300	6503	SO:0001819	synonymous_variant	8354	exon1			GACGCGTTTGGCG	X83550	CCDS4636.1	6p22.1	2011-01-27	2006-10-11	2003-02-14	ENSG00000182572	ENSG00000275379		"""Histones / Replication-dependent"""	4771	protein-coding gene	gene with protein product		602814	"""H3 histone family, member F"", ""histone 1, H3i"""	H3FF		9031620, 9439656, 12408966	Standard	NM_003533		Approved	H3/f, H3.f	uc003njy.3	P68431	OTTHUMG00000016184	ENST00000328488.2:c.348A>G	6.37:g.27839746T>C		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	105	55	0.52381	NM_003533	A0PJT7|A5PLR1|P02295|P02296|P16106|Q6ISV8|Q6NWP8|Q6NWP9|Q6NXU4|Q71DJ3|Q93081	Silent	SNP	ENST00000328488.2	37	CCDS4636.1																																																																																			A|0.004;C|0.245	0.245	strong		0.572	HIST1H3I-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043452.1	NM_003533	
RTN4IP1	84816	hgsc.bcm.edu	37	6	107019974	107019974	+	Missense_Mutation	SNP	C	C	T	rs372866009		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:107019974C>T	ENST00000369063.3	-	9	1553	c.1088G>A	c.(1087-1089)cGg>cAg	p.R363Q	RTN4IP1_ENST00000539449.1_3'UTR|RTN4IP1_ENST00000498091.1_5'UTR	NM_032730.4	NP_116119.2	Q8WWV3	RT4I1_HUMAN	reticulon 4 interacting protein 1	363						mitochondrion (GO:0005739)	oxidoreductase activity (GO:0016491)|zinc ion binding (GO:0008270)	p.R363L(1)		breast(1)|kidney(3)|large_intestine(2)|lung(6)|urinary_tract(1)	13	Breast(9;0.0107)|all_epithelial(6;0.14)	all_cancers(87;9.45e-05)|Acute lymphoblastic leukemia(125;2.13e-07)|all_hematologic(75;5.28e-06)|all_epithelial(87;0.0144)	Epithelial(6;0.000873)|all cancers(7;0.00363)|BRCA - Breast invasive adenocarcinoma(8;0.00721)|OV - Ovarian serous cystadenocarcinoma(5;0.0394)	all cancers(137;0.113)|BRCA - Breast invasive adenocarcinoma(108;0.127)|Epithelial(106;0.144)		AATAACTGGCCGGATCTGTAA	0.418																																					p.R363Q		Atlas-SNP	.											RTN4IP1,NS,carcinoma,0,1	RTN4IP1	31	1	1	Substitution - Missense(1)	lung(1)	c.G1088A						PASS	.	C	GLN/ARG	0,4406		0,0,2203	92.0	95.0	94.0		1088	-2.2	0.9	6		94	2,8598	2.2+/-6.3	0,2,4298	no	missense	RTN4IP1	NM_032730.4	43	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	benign	363/397	107019974	2,13004	2203	4300	6503	SO:0001583	missense	84816	exon9			ACTGGCCGGATCT	AF336861	CCDS5056.1	6q21	2008-02-05			ENSG00000130347	ENSG00000130347			18647	protein-coding gene	gene with protein product		610502					Standard	NM_032730		Approved	NIMP	uc003prj.3	Q8WWV3	OTTHUMG00000015304	ENST00000369063.3:c.1088G>A	6.37:g.107019974C>T	ENSP00000358059:p.Arg363Gln	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	71	26	0.366197	NM_032730	Q8N9B3|Q8WZ66|Q9BRA4	Missense_Mutation	SNP	ENST00000369063.3	37	CCDS5056.1	.	.	.	.	.	.	.	.	.	.	C	10.75	1.439632	0.25900	0.0	2.33E-4	ENSG00000130347	ENST00000369063	T	0.24908	1.83	6.02	-2.25	0.06888	.	0.687056	0.15173	N	0.276506	T	0.06645	0.0170	L	0.33245	0.995	0.30421	N	0.7781	B	0.19583	0.037	B	0.12837	0.008	T	0.35847	-0.9772	10	0.31617	T	0.26	-0.4612	12.1462	0.54024	0.0:0.3328:0.0:0.6672	.	363	Q8WWV3	RT4I1_HUMAN	Q	363	ENSP00000358059:R363Q	ENSP00000358059:R363Q	R	-	2	0	RTN4IP1	107126667	0.011000	0.17503	0.894000	0.35097	0.910000	0.53928	-0.027000	0.12371	-0.270000	0.09285	-0.355000	0.07637	CGG	.	.	weak		0.418	RTN4IP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041673.1		
KMT2C	58508	hgsc.bcm.edu	37	7	151873853	151873853	+	Silent	SNP	C	C	T	rs6464211	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:151873853C>T	ENST00000262189.6	-	38	8903	c.8685G>A	c.(8683-8685)caG>caA	p.Q2895Q	KMT2C_ENST00000355193.2_Silent_p.Q2895Q	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	2895					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)										GAGTGGATGCCTGAATGACAT	0.398													T|||	1917	0.382788	0.7549	0.2392	5008	,	,		20363	0.3016		0.17	False		,,,				2504	0.2843				p.Q2895Q		Atlas-SNP	.											.	MLL3	1564	.	0			c.G8685A						PASS	.	T		3030,1376	455.9+/-351.1	1049,932,222	94.0	93.0	93.0		8685	-3.6	0.0	7	dbSNP_116	93	1408,7192	753.3+/-407.4	126,1156,3018	no	coding-synonymous	MLL3	NM_170606.2		1175,2088,3240	TT,TC,CC		16.3721,31.2301,34.1227		2895/4912	151873853	4438,8568	2203	4300	6503	SO:0001819	synonymous_variant	58508	exon38			GGATGCCTGAATG	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.8685G>A	7.37:g.151873853C>T		Somatic	190	0	0		WXS	Illumina HiSeq	Phase_I	169	80	0.473373	NM_170606	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Silent	SNP	ENST00000262189.6	37	CCDS5931.1	754	0.34523809523809523	358	0.7276422764227642	92	0.2541436464088398	170	0.2972027972027972	134	0.17678100263852242	T	0.007	-1.957464	0.00465	0.687699	0.163721	ENSG00000055609	ENST00000360104	.	.	.	5.12	-3.6	0.04570	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.46798	P	7.970000000000477E-4	.	.	.	.	.	.	T	0.38436	-0.9661	3	.	.	.	.	0.8674	0.01206	0.1496:0.2894:0.2562:0.3048	rs6464211;rs13236845;rs60172642;rs6464211	.	.	.	S	401	.	.	G	-	1	0	MLL3	151504786	0.092000	0.21681	0.000000	0.03702	0.138000	0.21146	0.169000	0.16641	-1.511000	0.01794	-1.256000	0.01477	GGC	C|0.643;T|0.357	0.357	strong		0.398	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3		
DDX31	64794	hgsc.bcm.edu	37	9	135538050	135538050	+	Silent	SNP	C	C	T	rs35918594	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:135538050C>T	ENST00000372159.3	-	2	574	c.423G>A	c.(421-423)gcG>gcA	p.A141A	DDX31_ENST00000544003.1_Silent_p.A45A|DDX31_ENST00000310532.2_Silent_p.A141A|DDX31_ENST00000372153.1_Silent_p.A141A|DDX31_ENST00000480876.1_5'UTR|DDX31_ENST00000438527.3_Silent_p.A12A	NM_022779.7	NP_073616.6	Q9H8H2	DDX31_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 31	141						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)		CCTCACTGGACGCTTGGTATT	0.463													C|||	185	0.0369409	0.0091	0.0504	5008	,	,		18867	0.003		0.0944	False		,,,				2504	0.0409				p.A141A		Atlas-SNP	.											DDX31,caecum,carcinoma,-1,1	DDX31	76	1	0			c.G423A						scavenged	.	C	,	86,4320	71.4+/-109.4	1,84,2118	90.0	80.0	83.0		423,423	-4.7	0.0	9	dbSNP_126	83	909,7691	202.1+/-245.5	41,827,3432	no	coding-synonymous,coding-synonymous	DDX31	NM_022779.7,NM_138620.1	,	42,911,5550	TT,TC,CC		10.5698,1.9519,7.6503	,	141/852,141/586	135538050	995,12011	2203	4300	6503	SO:0001819	synonymous_variant	64794	exon2			ACTGGACGCTTGG	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.423G>A	9.37:g.135538050C>T		Somatic	74	1	0.0135135		WXS	Illumina HiSeq	Phase_I	50	49	0.98	NM_022779	Q5K6N2|Q5K6N3|Q5K6N4|Q5VZJ4|Q5VZJ9|Q96E91|Q96NY2|Q96SX5|Q9H5K6	Silent	SNP	ENST00000372159.3	37	CCDS6951.1																																																																																			C|0.934;T|0.066	0.066	strong		0.463	DDX31-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054794.1	NM_138620	
HLA-C	3107	hgsc.bcm.edu	37	6	31239449	31239449	+	Missense_Mutation	SNP	C	C	G	rs28626310	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:31239449C>G	ENST00000376228.5	-	2	284	c.270G>C	c.(268-270)aaG>aaC	p.K90N	HLA-C_ENST00000383329.3_Missense_Mutation_p.K90N	NM_002117.5	NP_002108.4	Q95604	1C17_HUMAN	major histocompatibility complex, class I, C	90	Alpha-1.		K -> N (in dbSNP:rs28626310).		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						GGCGCTTGTACTTCTGTGTCT	0.701													c|||	710	0.141773	0.1452	0.1282	5008	,	,		12148	0.0516		0.168	False		,,,				2504	0.2127				p.K90N		Atlas-SNP	.											.	HLA-C	92	.	0			c.G270C						PASS	.	C	ASN/LYS	438,2584		26,386,1099	48.0	49.0	48.0		270	-5.5	0.0	6	dbSNP_125	48	999,4419		91,817,1801	no	missense	HLA-C	NM_002117.5	94	117,1203,2900	GG,GC,CC		18.4385,14.4937,17.0261	benign	90/367	31239449	1437,7003	1511	2709	4220	SO:0001583	missense	3107	exon2			CTTGTACTTCTGT	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.270G>C	6.37:g.31239449C>G	ENSP00000365402:p.Lys90Asn	Somatic	188	0	0		WXS	Illumina HiSeq	Phase_I	194	106	0.546392	NM_002117	O02864|O02958|Q29643|Q9MY30	Missense_Mutation	SNP	ENST00000376228.5	37	CCDS34393.1	260|260	0.11904761904761904|0.11904761904761904	60|60	0.12195121951219512|0.12195121951219512	47|47	0.1298342541436464|0.1298342541436464	26|26	0.045454545454545456|0.045454545454545456	127|127	0.16754617414248021|0.16754617414248021	-|-	0.008|0.008	-1.894729|-1.894729	0.00522|0.00522	0.144937|0.144937	0.184385|0.184385	ENSG00000204525|ENSG00000204525	ENST00000376228;ENST00000383329;ENST00000396254;ENST00000539307|ENST00000415537	T;T|.	0.00009|.	9.48;9.48|.	2.75|2.75	-5.49|-5.49	0.02584|0.02584	MHC class I, alpha chain, alpha1/alpha2 (2);MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);|.	2211.810000|.	0.00541|.	N|.	0.000226|.	T|T	0.01489|0.01489	0.0048|0.0048	N|N	0.01751|0.01751	-0.74|-0.74	0.80722|0.80722	P|P	0.0|0.0	B;B;B;B|.	0.10296|.	0.003;0.003;0.001;0.003|.	B;B;B;B|.	0.21151|.	0.033;0.033;0.033;0.022|.	T|T	0.22941|0.22941	-1.0202|-1.0202	9|4	0.36615|.	T|.	0.2|.	.|.	3.7958|3.7958	0.08738|0.08738	0.0845:0.197:0.1701:0.5485|0.0845:0.197:0.1701:0.5485	rs28626310;rs41555912|rs28626310;rs41555912	90;90;90;90|.	A2AEA4;A6H578;A2AEA2;P10321|.	.;.;.;1C07_HUMAN|.	N|L	90;90;90;127|90	ENSP00000365402:K90N;ENSP00000372819:K90N|.	ENSP00000365402:K90N|.	K|V	-|-	3|1	2|0	HLA-C|HLA-C	31347428|31347428	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.000000|0.000000	0.00434|0.00434	-9.984000|-9.984000	0.00008|0.00008	-6.044000|-6.044000	0.00007|0.00007	-3.594000|-3.594000	0.00028|0.00028	AAG|GTA	C|0.840;G|0.160	0.160	strong		0.701	HLA-C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076281.3	NM_002117	
FAT1	2195	hgsc.bcm.edu	37	4	187538942	187538942	+	Missense_Mutation	SNP	T	T	G	rs1280098	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:187538942T>G	ENST00000441802.2	-	10	9007	c.8798A>C	c.(8797-8799)cAa>cCa	p.Q2933P		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	2933	Cadherin 27. {ECO:0000255|PROSITE- ProRule:PRU00043}.				actin filament organization (GO:0007015)|anatomical structure morphogenesis (GO:0009653)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(38)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(33)|lung(88)|ovary(13)|pancreas(2)|prostate(16)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	228						CACCCCACCTTGGGGGTCATC	0.448										HNSCC(5;0.00058)			G|||	2965	0.592053	0.7655	0.6037	5008	,	,		15877	0.631		0.5467	False		,,,				2504	0.3558				p.Q2933P	Colon(197;1040 2055 4143 4984 49344)	Atlas-SNP	.											.	FAT1	500	.	0			c.A8798C						PASS	.	G	PRO/GLN	2928,936		1116,696,120	117.0	115.0	116.0		8798	4.0	0.0	4	dbSNP_87	116	4621,3625		1308,2005,810	yes	missense	FAT1	NM_005245.3	76	2424,2701,930	GG,GT,TT		43.9607,24.2236,37.6631	benign	2933/4589	187538942	7549,4561	1932	4123	6055	SO:0001583	missense	2195	exon10			CCACCTTGGGGGT	X87241	CCDS47177.1	4q35.2	2013-05-31	2013-05-31	2008-10-30	ENSG00000083857	ENSG00000083857		"""Cadherins / Cadherin-related"""	3595	protein-coding gene	gene with protein product	"""cadherin-related family member 8"""	600976	"""FAT tumor suppressor (Drosophila) homolog"", ""FAT tumor suppressor homolog 1 (Drosophila)"""	FAT		8586420	Standard	XM_005262834		Approved	CDHF7, CDHR8	uc003izf.3	Q14517	OTTHUMG00000160320	ENST00000441802.2:c.8798A>C	4.37:g.187538942T>G	ENSP00000406229:p.Gln2933Pro	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	67	31	0.462687	NM_005245		Missense_Mutation	SNP	ENST00000441802.2	37	CCDS47177.1	1444	0.6611721611721612	388	0.7886178861788617	236	0.6519337016574586	401	0.701048951048951	419	0.5527704485488126	G	0.009	-1.827288	0.00584	0.757764	0.560393	ENSG00000083857	ENST00000441802;ENST00000260147	T	0.49139	0.79	4.89	4.04	0.47022	Cadherin (3);Cadherin-like (1);	0.000000	0.85682	N	0.000000	T	0.00012	0.0000	N	0.00022	-2.73	0.45272	P	0.001727000000000034	B	0.02656	0.0	B	0.01281	0.0	T	0.43278	-0.9401	9	0.02654	T	1	.	10.101	0.42504	0.0716:0.0:0.791:0.1374	rs1280098;rs3822061;rs60812614	2933	Q14517	FAT1_HUMAN	P	2933;2935	ENSP00000406229:Q2933P	ENSP00000260147:Q2935P	Q	-	2	0	FAT1	187775936	1.000000	0.71417	0.014000	0.15608	0.074000	0.17049	5.993000	0.70616	0.780000	0.33566	-0.127000	0.14921	CAA	T|0.357;G|0.629;A|0.015	0.629	strong		0.448	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245	
TNXB	7148	hgsc.bcm.edu	37	6	32020512	32020512	+	Missense_Mutation	SNP	T	T	C	rs17207895	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:32020512T>C	ENST00000375244.3	-	26	9251	c.9050A>G	c.(9049-9051)aAg>aGg	p.K3017R	TNXB_ENST00000375247.2_Missense_Mutation_p.K3015R			P22105	TENX_HUMAN	tenascin XB	3062	Fibronectin type-III 22. {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						CAGGTGCATCTTGTATTTGCA	0.662													t|||	33	0.00658946	0.0	0.0144	5008	,	,		14494	0.003		0.0189	False		,,,				2504	0.001				p.K3015R		Atlas-SNP	.											.	TNXB	553	.	0			c.A9044G						PASS	.	T	ARG/LYS	12,2636		0,12,1312	53.0	58.0	56.0		9044	3.2	1.0	6	dbSNP_123	56	123,5023		3,117,2453	no	missense	TNXB	NM_019105.6	26	3,129,3765	CC,CT,TT		2.3902,0.4532,1.7321	probably-damaging	3015/4243	32020512	135,7659	1324	2573	3897	SO:0001583	missense	7148	exon26			TGCATCTTGTATT	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.9050A>G	6.37:g.32020512T>C	ENSP00000364393:p.Lys3017Arg	Somatic	170	1	0.00588235		WXS	Illumina HiSeq	Phase_I	74	50	0.675676	NM_019105	P78530|P78531|Q08424|Q08AM0|Q08AM1|Q59GU7|Q5SQD3|Q5ST74|Q7L8Q4|Q8N4R1|Q9NPK9|Q9UC10|Q9UC11|Q9UC12|Q9UC13|Q9UMG7	Missense_Mutation	SNP	ENST00000375244.3	37		19	0.0086996336996337	0	0.0	3	0.008287292817679558	1	0.0017482517482517483	15	0.01978891820580475	t	15.97	2.988563	0.53934	0.004532	0.023902	ENSG00000168477	ENST00000375244;ENST00000375247	T;T	0.57107	0.42;0.42	4.42	3.16	0.36331	.	0.000000	0.39759	U	0.001278	T	0.45657	0.1353	L	0.52206	1.635	0.23984	N	0.996267	D	0.69078	0.997	D	0.76575	0.988	T	0.19321	-1.0309	10	0.20046	T	0.44	.	8.4385	0.32801	0.0:0.0:0.1973:0.8026	rs17207895	3015	P22105-3	.	R	3017;3015	ENSP00000364393:K3017R;ENSP00000364396:K3015R	ENSP00000364393:K3017R	K	-	2	0	TNXB	32128490	1.000000	0.71417	1.000000	0.80357	0.826000	0.46750	0.787000	0.26858	1.602000	0.50124	0.459000	0.35465	AAG	T|0.981;C|0.019	0.019	strong		0.662	TNXB-001	PUTATIVE	not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000268927.2	NM_019105	
UVSSA	57654	hgsc.bcm.edu	37	4	1369885	1369885	+	Silent	SNP	G	G	A	rs11724369	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:1369885G>A	ENST00000389851.4	+	10	1944	c.1497G>A	c.(1495-1497)gcG>gcA	p.A499A	UVSSA_ENST00000507531.1_Silent_p.A499A|UVSSA_ENST00000512728.1_Silent_p.A50A|UVSSA_ENST00000511216.1_Silent_p.A499A|UVSSA_ENST00000511563.1_Silent_p.A50A	NM_020894.2	NP_065945.2	Q2YD98	UVSSA_HUMAN	UV-stimulated scaffold protein A	499					protein ubiquitination (GO:0016567)|response to UV (GO:0009411)|transcription-coupled nucleotide-excision repair (GO:0006283)	chromosome (GO:0005694)	RNA polymerase II core binding (GO:0000993)										GGGCCCGGGCGCCTGTGGTGC	0.662													G|||	913	0.182308	0.0371	0.2896	5008	,	,		15144	0.0704		0.3827	False		,,,				2504	0.2117				p.A499A		Atlas-SNP	.											.	.	.	.	0			c.G1497A						PASS	.	G		375,3975		23,329,1823	18.0	19.0	19.0		1497	-10.6	0.0	4	dbSNP_120	19	3279,5307		648,1983,1662	no	coding-synonymous	KIAA1530	NM_020894.2		671,2312,3485	AA,AG,GG		38.1901,8.6207,28.2468		499/710	1369885	3654,9282	2175	4293	6468	SO:0001819	synonymous_variant	57654	exon10			CCGGGCGCCTGTG	BC021930	CCDS33938.1	4p16.3	2012-04-27	2012-04-27	2012-04-27		ENSG00000163945			29304	protein-coding gene	gene with protein product		614632	"""KIAA1530"""	KIAA1530		10819331, 22466610, 22466611, 22466612	Standard	NM_020894		Approved		uc003gde.4	Q2YD98		ENST00000389851.4:c.1497G>A	4.37:g.1369885G>A		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	125	56	0.448	NM_020894	A8K9E6|B2RU11|Q8WTX4|Q9P1Z8	Silent	SNP	ENST00000389851.4	37	CCDS33938.1																																																																																			G|0.793;A|0.207	0.207	strong		0.662	UVSSA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359480.1	NM_020894	
MYOM1	8736	hgsc.bcm.edu	37	18	3075746	3075746	+	Silent	SNP	G	G	A	rs1143657	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:3075746G>A	ENST00000356443.4	-	35	4995	c.4662C>T	c.(4660-4662)gcC>gcT	p.A1554A	MYOM1_ENST00000400569.3_Silent_p.A1554A|MYOM1_ENST00000261606.7_Silent_p.A1458A	NM_003803.3|NM_019856.1	NP_003794.3|NP_062830.1	P52179	MYOM1_HUMAN	myomesin 1	1554					muscle contraction (GO:0006936)	M band (GO:0031430)|striated muscle myosin thick filament (GO:0005863)	identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|structural constituent of muscle (GO:0008307)	p.A1554A(3)		NS(2)|autonomic_ganglia(1)|central_nervous_system(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(20)|ovary(4)|pancreas(1)|prostate(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	77						ATTCAGCATAGGCCTCATCGT	0.443													G|||	919	0.183506	0.1747	0.183	5008	,	,		18427	0.1875		0.2008	False		,,,				2504	0.1738				p.A1554A		Atlas-SNP	.											MYOM1,NS,carcinoma,0,2	MYOM1	192	2	3	Substitution - coding silent(3)	prostate(2)|stomach(1)	c.C4662T						PASS	.	G	,	525,3227		38,449,1389	58.0	58.0	58.0		4662,4374	4.2	1.0	18	dbSNP_123	58	1395,6825		108,1179,2823	no	coding-synonymous,coding-synonymous	MYOM1	NM_003803.3,NM_019856.1	,	146,1628,4212	AA,AG,GG		16.9708,13.9925,16.0374	,	1554/1686,1458/1590	3075746	1920,10052	1876	4110	5986	SO:0001819	synonymous_variant	8736	exon35			AGCATAGGCCTCA	AF185573	CCDS45823.1, CCDS45824.1	18p11.31	2014-09-17	2012-10-17		ENSG00000101605	ENSG00000101605		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	7613	protein-coding gene	gene with protein product	"""skelemin"""	603508	"""myomesin 1 (skelemin) (185kD)"", ""myomesin 1 (skelemin) 185kDa"", ""myomesin 1, 185kDa"""			9806852	Standard	NM_019856		Approved		uc002klp.3	P52179	OTTHUMG00000178209	ENST00000356443.4:c.4662C>T	18.37:g.3075746G>A		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	62	30	0.483871	NM_003803	Q14BD6|Q6H969|Q6ZUU0	Silent	SNP	ENST00000356443.4	37	CCDS45824.1																																																																																			G|0.810;A|0.190	0.190	strong		0.443	MYOM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441037.2	NM_003803	
TRIM50	135892	hgsc.bcm.edu	37	7	72738561	72738561	+	Silent	SNP	G	G	T	rs61741334	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:72738561G>T	ENST00000333149.2	-	2	425	c.225C>A	c.(223-225)atC>atA	p.I75I	TRIM50_ENST00000493498.1_5'UTR|TRIM50_ENST00000453152.1_Silent_p.I75I	NM_178125.2	NP_835226.2	Q86XT4	TRI50_HUMAN	tripartite motif containing 50	75						cytoplasm (GO:0005737)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			endometrium(3)|kidney(1)|large_intestine(2)|lung(11)|ovary(1)|skin(2)	20						TCAGGGCTTCGATCACCCTGG	0.687											OREG0018105	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	50	0.00998403	0.0038	0.0173	5008	,	,		16084	0.0		0.0278	False		,,,				2504	0.0051				p.I75I		Atlas-SNP	.											.	TRIM50	78	.	0			c.C225A						PASS	.	G		23,4383	32.6+/-62.9	0,23,2180	61.0	61.0	61.0		225	-1.5	1.0	7	dbSNP_129	61	306,8294	109.4+/-169.9	4,298,3998	no	coding-synonymous	TRIM50	NM_178125.2		4,321,6178	TT,TG,GG		3.5581,0.522,2.5296		75/488	72738561	329,12677	2203	4300	6503	SO:0001819	synonymous_variant	135892	exon2			GGCTTCGATCACC	AY081948	CCDS34654.1	7q11.23	2013-01-09	2011-01-25	2006-03-31	ENSG00000146755	ENSG00000146755		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	19017	protein-coding gene	gene with protein product		612548	"""tripartite motif-containing 50A"", ""tripartite motif-containing 50"""	TRIM50A			Standard	NM_001281450		Approved	FLJ32804	uc003txy.1	Q86XT4	OTTHUMG00000156805	ENST00000333149.2:c.225C>A	7.37:g.72738561G>T		Somatic	241	0	0	1139	WXS	Illumina HiSeq	Phase_I	214	96	0.448598	NM_178125	Q86XT3	Silent	SNP	ENST00000333149.2	37	CCDS34654.1																																																																																			G|0.978;T|0.022	0.022	strong		0.687	TRIM50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345925.1	NM_178125	
OR51L1	119682	hgsc.bcm.edu	37	11	5020509	5020509	+	Silent	SNP	C	C	T	rs11035066	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:5020509C>T	ENST00000321543.1	+	1	297	c.297C>T	c.(295-297)tgC>tgT	p.C99C		NM_001004755.1	NP_001004755.1	Q8NGJ5	O51L1_HUMAN	olfactory receptor, family 51, subfamily L, 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)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(3)|lung(19)|skin(2)|stomach(1)	31		Medulloblastoma(188;0.0061)|all_neural(188;0.0479)|Breast(177;0.086)		Epithelial(150;1.75e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0285)|LUSC - Lung squamous cell carcinoma(625;0.19)		CAAGTGCTTGCTATGCTCAGC	0.512													C|||	1155	0.230631	0.3011	0.1599	5008	,	,		24680	0.0694		0.3131	False		,,,				2504	0.2669				p.C99C		Atlas-SNP	.											.	OR51L1	60	.	0			c.C297T						PASS	.	C		1371,3031	455.5+/-351.0	199,973,1029	267.0	199.0	222.0		297	4.5	1.0	11	dbSNP_120	222	2566,6030	418.5+/-352.8	383,1800,2115	no	coding-synonymous	OR51L1	NM_001004755.1		582,2773,3144	TT,TC,CC		29.8511,31.1449,30.2893		99/316	5020509	3937,9061	2201	4298	6499	SO:0001819	synonymous_variant	119682	exon1			TGCTTGCTATGCT	AB065799	CCDS31369.1	11p15.4	2012-08-09			ENSG00000176798	ENSG00000176798		"""GPCR / Class A : Olfactory receptors"""	14759	protein-coding gene	gene with protein product							Standard	NM_001004755		Approved		uc010qyu.2	Q8NGJ5	OTTHUMG00000066605	ENST00000321543.1:c.297C>T	11.37:g.5020509C>T		Somatic	372	0	0		WXS	Illumina HiSeq	Phase_I	359	354	0.986072	NM_001004755	Q6IFE5	Silent	SNP	ENST00000321543.1	37	CCDS31369.1																																																																																			C|0.718;T|0.282	0.282	strong		0.512	OR51L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142812.1	NM_001004755	
ARL2	402	hgsc.bcm.edu	37	11	64789194	64789194	+	Splice_Site	SNP	T	T	C	rs664226	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:64789194T>C	ENST00000246747.4	+	5	517	c.422T>C	c.(421-423)gTc>gCc	p.V141A	ARL2_ENST00000529384.1_Splice_Site_p.V141A|RP11-399J13.3_ENST00000301886.3_Intron|ARL2_ENST00000533729.1_Splice_Site_p.V114A	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	51	0	0		WXS	Illumina HiSeq	Phase_I	31	9	0.290323	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
FRAS1	80144	hgsc.bcm.edu	37	4	79437155	79437155	+	Silent	SNP	C	C	T	rs3749487	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:79437155C>T	ENST00000264895.6	+	66	10817	c.10377C>T	c.(10375-10377)acC>acT	p.T3459T		NM_025074.6	NP_079350.5	Q86XX4	FRAS1_HUMAN	Fraser extracellular matrix complex subunit 1	3455					cell communication (GO:0007154)|embryonic limb morphogenesis (GO:0030326)|metanephros morphogenesis (GO:0003338)|morphogenesis of an epithelium (GO:0002009)|palate development (GO:0060021)|protein transport (GO:0015031)|skin development (GO:0043588)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sublamina densa (GO:0061618)	metal ion binding (GO:0046872)	p.T3459T(2)|p.T3460T(1)		breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(5)|lung(54)|prostate(7)|skin(2)|urinary_tract(4)	103						GCTCTGTAACCGCTGACTTCC	0.507													C|||	884	0.176518	0.177	0.1398	5008	,	,		18849	0.2242		0.2058	False		,,,				2504	0.1227				p.T3459T		Atlas-SNP	.											FRAS1_ENST00000264895,NS,carcinoma,0,2	FRAS1	779	2	3	Substitution - coding silent(3)	prostate(3)	c.C10377T						PASS	.	C		762,3516		66,630,1443	69.0	74.0	72.0		10377	-4.6	0.7	4	dbSNP_107	72	1551,6979		140,1271,2854	no	coding-synonymous	FRAS1	NM_025074.6		206,1901,4297	TT,TC,CC		18.1829,17.8121,18.059		3459/4013	79437155	2313,10495	2139	4265	6404	SO:0001819	synonymous_variant	80144	exon66			TGTAACCGCTGAC	AB040933	CCDS54772.1	4q21.21	2014-06-25	2014-06-25		ENSG00000138759	ENSG00000138759			19185	protein-coding gene	gene with protein product		607830	"""Fraser syndrome 1"""			12766769, 3118036	Standard	NM_025074		Approved	FLJ22031, FLJ14927, KIAA1500	uc003hlb.2	Q86XX4	OTTHUMG00000160856	ENST00000264895.6:c.10377C>T	4.37:g.79437155C>T		Somatic	212	0	0		WXS	Illumina HiSeq	Phase_I	156	70	0.448718	NM_025074	A2RRR8|Q86UZ4|Q8N3U9|Q8NAU7|Q96JW7|Q9H6N9|Q9P228	Silent	SNP	ENST00000264895.6	37	CCDS54771.1	432	0.1978021978021978	96	0.1951219512195122	58	0.16022099447513813	128	0.22377622377622378	150	0.19788918205804748	C	1.309	-0.602724	0.03744	0.178121	0.181829	ENSG00000138759	ENST00000512123	.	.	.	5.97	-4.61	0.03380	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.33929	-0.9849	3	.	.	.	.	2.7957	0.05400	0.1827:0.3609:0.0961:0.3603	rs3749487;rs57228815	.	.	.	C	1688	.	.	R	+	1	0	FRAS1	79656179	0.002000	0.14202	0.743000	0.31040	0.168000	0.22595	-1.645000	0.02000	-0.358000	0.08162	-0.606000	0.04082	CGC	C|0.803;T|0.197	0.197	strong		0.507	FRAS1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
ZNF235	9310	hgsc.bcm.edu	37	19	44791537	44791537	+	Missense_Mutation	SNP	G	G	A	rs149947768		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:44791537G>A	ENST00000291182.4	-	5	2153	c.2051C>T	c.(2050-2052)aCg>aTg	p.T684M	ZNF235_ENST00000589248.1_Intron|ZNF235_ENST00000589799.1_Intron	NM_004234.4	NP_004225.3	Q14590	ZN235_HUMAN	zinc finger protein 235	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)|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)				CTGCTGACACGTATAGGGTTT	0.493													G|||	1	0.000199681	0.0	0.0	5008	,	,		21663	0.0		0.001	False		,,,				2504	0.0				p.T684M		Atlas-SNP	.											.	ZNF235	60	.	0			c.C2051T						PASS	.	G	MET/THR	0,4406		0,0,2203	127.0	116.0	120.0		2051	1.1	0.1	19	dbSNP_134	120	10,8590	7.1+/-27.0	0,10,4290	yes	missense	ZNF235	NM_004234.4	81	0,10,6493	AA,AG,GG		0.1163,0.0,0.0769	benign	684/739	44791537	10,12996	2203	4300	6503	SO:0001583	missense	9310	exon5			TGACACGTATAGG	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.2051C>T	19.37:g.44791537G>A	ENSP00000291182:p.Thr684Met	Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	86	41	0.476744	NM_004234	B4DTQ7|O14898|O14899|Q17RR8	Missense_Mutation	SNP	ENST00000291182.4	37	CCDS33048.1	.	.	.	.	.	.	.	.	.	.	G	6.572	0.473837	0.12521	0.0	0.001163	ENSG00000159917	ENST00000391957;ENST00000291182;ENST00000359844	T	0.19806	2.12	4.97	1.08	0.20341	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.171331	0.28203	N	0.016214	T	0.14270	0.0345	L	0.37697	1.125	0.09310	N	1	B;B	0.28470	0.086;0.213	B;B	0.24701	0.012;0.055	T	0.18493	-1.0335	10	0.62326	D	0.03	-1.4434	7.5912	0.28023	0.0867:0.0:0.5441:0.3692	.	680;684	Q14590-2;Q14590	.;ZN235_HUMAN	M	684;684;576	ENSP00000291182:T684M	ENSP00000291182:T684M	T	-	2	0	ZNF235	49483377	0.000000	0.05858	0.100000	0.21137	0.510000	0.34073	-0.585000	0.05794	0.616000	0.30141	0.313000	0.20887	ACG	G|0.998;A|0.002	0.002	strong		0.493	ZNF235-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460732.1		
ARSD	414	hgsc.bcm.edu	37	X	2836184	2836184	+	Missense_Mutation	SNP	C	C	T	rs73632976		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:2836184C>T	ENST00000381154.1	-	5	599	c.524G>A	c.(523-525)gGc>gAc	p.G175D	ARSD_ENST00000217890.6_5'UTR	NM_001669.3	NP_001660.2	P51689	ARSD_HUMAN	arylsulfatase D	175					cellular protein metabolic process (GO:0044267)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	arylsulfatase activity (GO:0004065)|metal ion binding (GO:0046872)			large_intestine(3)|lung(3)	6		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				GAAGGGCATGCCGTAGAAATA	0.592																																					p.G175D		Atlas-SNP	.											.	ARSD	47	.	0			c.G524A						PASS	.						36.0	22.0	27.0					X																	2836184		2202	4298	6500	SO:0001583	missense	414	exon5			GGCATGCCGTAGA	X83572	CCDS35196.1	Xp22.3	2013-02-14			ENSG00000006756	ENSG00000006756		"""Arylsulfatase family"""	717	protein-coding gene	gene with protein product		300002				7720070	Standard	NM_001669		Approved		uc004cqy.3	P51689	OTTHUMG00000021077	ENST00000381154.1:c.524G>A	X.37:g.2836184C>T	ENSP00000370546:p.Gly175Asp	Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	132	19	0.143939	NM_001669	Q9UHJ8	Missense_Mutation	SNP	ENST00000381154.1	37	CCDS35196.1	140	0.08438818565400844	34	0.07727272727272727	28	0.08187134502923976	34	0.0625	61	0.08333333333333333	c	23.6	4.432561	0.83776	.	.	ENSG00000006756	ENST00000381154;ENST00000217890	D	0.95622	-3.76	3.47	3.47	0.39725	Alkaline phosphatase-like, alpha/beta/alpha (1);Sulfatase (1);Alkaline-phosphatase-like, core domain (1);	0.000000	0.85682	U	0.000000	D	0.82770	0.5109	H	0.97265	3.97	0.09310	P	0.999999842849	P;D	0.58620	0.931;0.983	P;P	0.61070	0.873;0.883	T	0.80400	-0.1398	9	0.72032	D	0.01	.	14.5312	0.67926	0.0:1.0:0.0:0.0	.	175;175	E9PAW5;P51689	.;ARSD_HUMAN	D	175	ENSP00000370546:G175D	ENSP00000217890:G175D	G	-	2	0	ARSD	2846184	1.000000	0.71417	0.184000	0.23157	0.851000	0.48451	4.701000	0.61810	1.394000	0.46624	0.420000	0.28162	GGC	C|0.915;T|0.085	0.085	strong		0.592	ARSD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055636.1		
HTT	3064	hgsc.bcm.edu	37	4	3107140	3107140	+	Silent	SNP	C	C	T	rs184820567		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:3107140C>T	ENST00000355072.5	+	5	730	c.585C>T	c.(583-585)caC>caT	p.H195H		NM_002111.6	NP_002102	P42858	HD_HUMAN	huntingtin	195					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)		AGCTGGCTCACCTGGTTCGGC	0.527													C|||	1	0.000199681	0.0	0.0014	5008	,	,		18849	0.0		0.0	False		,,,				2504	0.0				p.H195H		Atlas-SNP	.											.	HTT	221	.	0			c.C585T						PASS	.	C		0,4288		0,0,2144	111.0	116.0	114.0		585	3.4	1.0	4		114	3,8537		0,3,4267	no	coding-synonymous	HTT	NM_002111.6		0,3,6411	TT,TC,CC		0.0351,0.0,0.0234		195/3143	3107140	3,12825	2144	4270	6414	SO:0001819	synonymous_variant	3064	exon5			GGCTCACCTGGTT	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.585C>T	4.37:g.3107140C>T		Somatic	182	0	0		WXS	Illumina HiSeq	Phase_I	145	70	0.482759	NM_002111	Q9UQB7	Silent	SNP	ENST00000355072.5	37	CCDS43206.1																																																																																			C|0.999;T|0.001	0.001	strong		0.527	HTT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358234.2	NM_002111	
XAF1	54739	hgsc.bcm.edu	37	17	6663895	6663895	+	Silent	SNP	C	C	G	rs2271231|rs386794960	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:6663895C>G	ENST00000361842.3	+	4	635	c.396C>G	c.(394-396)cgC>cgG	p.R132R	XAF1_ENST00000346752.4_Silent_p.R113R|XAF1_ENST00000438512.1_Silent_p.R132R|XAF1_ENST00000441631.1_Silent_p.R132R	NM_017523.3	NP_059993.2	Q6GPH4	XAF1_HUMAN	XIAP associated factor 1	132			R -> H (in dbSNP:rs2271232).	R -> Q (in Ref. 3; BAF85537). {ECO:0000305}.	apoptotic process (GO:0006915)|cytokine-mediated signaling pathway (GO:0019221)|negative regulation of protein complex assembly (GO:0031333)|response to interferon-beta (GO:0035456)|type I interferon signaling pathway (GO:0060337)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			large_intestine(2)|lung(2)|prostate(1)|urinary_tract(1)	6						ATGTCTGTCGCAGTGAACAGG	0.592													G|||	2629	0.52496	0.7383	0.3934	5008	,	,		17143	0.5813		0.3141	False		,,,				2504	0.4888				p.R132R		Atlas-SNP	.											XAF1,colon,carcinoma,+2,1	XAF1	16	1	0			c.C396G						scavenged	.	G	,	2694,1712		958,778,467	51.0	50.0	50.0		396,339	1.8	0.0	17	dbSNP_100	50	2637,5963		446,1745,2109	no	coding-synonymous,coding-synonymous	XAF1	NM_017523.2,NM_199139.1	,	1404,2523,2576	GG,GC,CC		30.6628,38.8561,40.9888	,	132/302,113/283	6663895	5331,7675	2203	4300	6503	SO:0001819	synonymous_variant	54739	exon4			CTGTCGCAGTGAA	X99699	CCDS11080.1, CCDS11081.1	17p13.2	2010-03-19			ENSG00000132530	ENSG00000132530			30932	protein-coding gene	gene with protein product		606717				12029096, 11175744	Standard	NM_199139		Approved	BIRC4BP, XIAPAF1, HSXIAPAF1	uc002gdn.3	Q6GPH4		ENST00000361842.3:c.396C>G	17.37:g.6663895C>G		Somatic	202	1	0.00495049		WXS	Illumina HiSeq	Phase_I	222	108	0.486486	NM_017523	A2T931|A2T932|A8K2L1|A8K9Y3|D3DTM6|Q6MZE8|Q8N557|Q99982	Silent	SNP	ENST00000361842.3	37	CCDS11080.1																																																																																			C|0.550;G|0.450	0.450	strong		0.592	XAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439643.5	NM_017523	
WDR38	401551	hgsc.bcm.edu	37	9	127616537	127616537	+	Silent	SNP	A	A	G	rs12375547	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:127616537A>G	ENST00000373574.1	+	2	179	c.123A>G	c.(121-123)gaA>gaG	p.E41E		NM_001045476.1|NM_001276374.1	NP_001038941.1|NP_001263303.1	Q5JTN6	WDR38_HUMAN	WD repeat domain 38	41					hematopoietic progenitor cell differentiation (GO:0002244)					breast(1)|large_intestine(1)|lung(4)|prostate(1)|skin(1)	8						CAGGCTCAGAAGATGGCTGCG	0.612													G|||	2267	0.452676	0.4803	0.3573	5008	,	,		18063	0.5804		0.4324	False		,,,				2504	0.3722				p.K10R		Atlas-SNP	.											.	WDR38	21	.	0			c.A29G						PASS	.	G		1968,2132		475,1018,557	125.0	134.0	131.0		123	-6.9	0.2	9	dbSNP_120	131	3636,4778		832,1972,1403	yes	coding-synonymous	WDR38	NM_001045476.1		1307,2990,1960	GG,GA,AA		43.2137,48.0,44.7818		41/315	127616537	5604,6910	2050	4207	6257	SO:0001819	synonymous_variant	401551	exon2			CTCAGAAGATGGC		CCDS43876.1, CCDS75898.1, CCDS75899.1	9q33.3	2013-01-09			ENSG00000136918	ENSG00000136918		"""WD repeat domain containing"""	23745	protein-coding gene	gene with protein product							Standard	NM_001276375		Approved		uc011lzo.3	Q5JTN6	OTTHUMG00000020664	ENST00000373574.1:c.123A>G	9.37:g.127616537A>G		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	81	79	0.975309	NM_001276376	A0PK24	Missense_Mutation	SNP	ENST00000373574.1	37	CCDS43876.1																																																																																			A|0.541;G|0.459	0.459	strong		0.612	WDR38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054048.1	NM_001045476	
RPTN	126638	hgsc.bcm.edu	37	1	152127455	152127455	+	Missense_Mutation	SNP	T	T	C	rs75957773	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:152127455T>C	ENST00000316073.3	-	3	2184	c.2120A>G	c.(2119-2121)gAa>gGa	p.E707G		NM_001122965.1	NP_001116437.1	Q6XPR3	RPTN_HUMAN	repetin	707	Gln-rich.					cornified envelope (GO:0001533)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(1)|endometrium(14)|kidney(2)|large_intestine(1)|lung(32)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	59						GCCCTGCTCTTCCTCTGCCCA	0.562													T|||	281	0.0561102	0.0053	0.0965	5008	,	,		21543	0.001		0.1362	False		,,,				2504	0.0706				p.E707G		Atlas-SNP	.											RPTN,NS,carcinoma,0,1	RPTN	123	1	0			c.A2120G						PASS	.	T	GLY/GLU	79,3057		0,79,1489	306.0	251.0	268.0		2120	2.8	0.0	1	dbSNP_131	268	981,6183		62,857,2663	yes	missense	RPTN	NM_001122965.1	98	62,936,4152	CC,CT,TT		13.6935,2.5191,10.2913	probably-damaging	707/785	152127455	1060,9240	1568	3582	5150	SO:0001583	missense	126638	exon3			TGCTCTTCCTCTG	AK096436	CCDS41397.1	1q21.3	2013-01-10			ENSG00000215853	ENSG00000215853		"""EF-hand domain containing"""	26809	protein-coding gene	gene with protein product		613259				15854042	Standard	NM_001122965		Approved	FLJ39117	uc001ezs.1	Q6XPR3	OTTHUMG00000154095	ENST00000316073.3:c.2120A>G	1.37:g.152127455T>C	ENSP00000317895:p.Glu707Gly	Somatic	318	0	0		WXS	Illumina HiSeq	Phase_I	269	139	0.516729	NM_001122965	B7ZBZ3	Missense_Mutation	SNP	ENST00000316073.3	37	CCDS41397.1	149	0.06822344322344322	3	0.006097560975609756	40	0.11049723756906077	0	0.0	106	0.13984168865435356	T	11.43	1.636369	0.29068	0.025191	0.136935	ENSG00000215853	ENST00000316073;ENST00000541545	T	0.23147	1.92	5.15	2.82	0.32997	.	.	.	.	.	T	0.10035	0.0246	M	0.61703	1.905	0.80722	P	0.0	B	0.32101	0.356	B	0.30855	0.121	T	0.13335	-1.0513	8	0.25751	T	0.34	0.1107	7.9769	0.30159	0.0:0.1718:0.0:0.8282	.	707	Q6XPR3	RPTN_HUMAN	G	707;362	ENSP00000317895:E707G	ENSP00000317895:E707G	E	-	2	0	RPTN	150394079	.	.	0.007000	0.13788	0.104000	0.19210	.	.	0.300000	0.22699	0.523000	0.50628	GAA	T|0.884;C|0.116	0.116	strong		0.562	RPTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333867.1	XM_371312	
RIN3	79890	hgsc.bcm.edu	37	14	93118668	93118668	+	Missense_Mutation	SNP	C	C	T	rs3742717	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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						scavenged	.	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	135	1	0.00740741		WXS	Illumina HiSeq	Phase_I	94	55	0.585106	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		
FAM114A1	92689	hgsc.bcm.edu	37	4	38880046	38880046	+	Splice_Site	SNP	T	T	C	rs11555334	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:38880046T>C	ENST00000358869.2	+	3	523	c.347T>C	c.(346-348)cTg>cCg	p.L116P	FAM114A1_ENST00000515037.1_Intron	NM_138389.2	NP_612398.2	Q8IWE2	NXP20_HUMAN	family with sequence similarity 114, member A1	116			L -> P (in dbSNP:rs11944159). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:20068231}.			cytoplasm (GO:0005737)				haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(8)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	20						CAGAATTATCTGGTAAGAATG	0.468													C|||	1016	0.202875	0.3192	0.2061	5008	,	,		21143	0.0863		0.2475	False		,,,				2504	0.1176				p.L116P		Atlas-SNP	.											.	FAM114A1	42	.	0			c.T347C						PASS	.	C	PRO/LEU	1355,3033		214,927,1053	50.0	48.0	49.0		347	-9.5	0.0	4	dbSNP_120	49	2303,6281		334,1635,2323	yes	missense-near-splice	FAM114A1	NM_138389.2	98	548,2562,3376	CC,CT,TT		26.829,30.8797,28.1992	benign	116/564	38880046	3658,9314	2194	4292	6486	SO:0001630	splice_region_variant	92689	exon3			ATTATCTGGTAAG		CCDS3447.1	4p14	2006-09-21			ENSG00000197712	ENSG00000197712			25087	protein-coding gene	gene with protein product							Standard	NM_138389		Approved	Noxp20	uc003gtn.3	Q8IWE2	OTTHUMG00000128583	ENST00000358869.2:c.348+1T>C	4.37:g.38880046T>C		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	102	50	0.490196	NM_138389	A8K9W6|Q6MZV4|Q9BVL6	Missense_Mutation	SNP	ENST00000358869.2	37	CCDS3447.1	496	0.2271062271062271	170	0.34552845528455284	78	0.2154696132596685	46	0.08041958041958042	202	0.26649076517150394	C	1.123	-0.654738	0.03480	0.308797	0.26829	ENSG00000197712	ENST00000510213;ENST00000358869	T;T	0.22743	1.94;2.96	4.73	-9.46	0.00597	.	1.229040	0.05567	N	0.570410	T	0.00012	0.0000	N	0.00972	-1.085	0.50039	P	1.52000000000041E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.44726	-0.9309	9	0.27785	T	0.31	4.2843	7.5742	0.27926	0.0837:0.1181:0.1658:0.6323	rs11944159;rs17857219;rs52824981;rs60460409;rs11944159	116	Q8IWE2	NXP20_HUMAN	P	116	ENSP00000422965:L116P;ENSP00000351740:L116P	ENSP00000351740:L116P	L	+	2	0	FAM114A1	38556441	0.000000	0.05858	0.000000	0.03702	0.043000	0.13939	-2.405000	0.01045	-2.805000	0.00350	-0.320000	0.08662	CTG	T|0.757;C|0.243	0.243	strong		0.468	FAM114A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250436.1	NM_138389	Missense_Mutation
GSPT1	2935	hgsc.bcm.edu	37	16	11969724	11969724	+	Silent	SNP	G	G	C	rs33657	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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_ENST00000434724.2_Silent_p.V585V|GSPT1_ENST00000420576.2_Silent_p.V447V|GSPT1_ENST00000439887.2_Silent_p.V584V			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	229	0	0		WXS	Illumina HiSeq	Phase_I	241	55	0.228216	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	
YIPF7	285525	hgsc.bcm.edu	37	4	44652030	44652030	+	Missense_Mutation	SNP	C	C	T	rs2348353	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	137	0	0		WXS	Illumina HiSeq	Phase_I	126	56	0.444444	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	
USHBP1	83878	hgsc.bcm.edu	37	19	17366313	17366313	+	Missense_Mutation	SNP	C	C	T	rs12459398	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	56	0	0		WXS	Illumina HiSeq	Phase_I	57	27	0.473684	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	
ABCG2	9429	hgsc.bcm.edu	37	4	89052323	89052323	+	Missense_Mutation	SNP	G	G	T	rs2231142	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:89052323G>T	ENST00000237612.3	-	5	966	c.421C>A	c.(421-423)Cag>Aag	p.Q141K	ABCG2_ENST00000515655.1_Missense_Mutation_p.Q141K	NM_004827.2	NP_004818.2	Q9UNQ0	ABCG2_HUMAN	ATP-binding cassette, sub-family G (WHITE), member 2 (Junior blood group)	141	ABC transporter. {ECO:0000255|PROSITE- ProRule:PRU00434}.		Q -> K (polymorphism associated with high serum levels of uric acid and increased risk of gout; results in lower urate transport rates compared to wild-type; dbSNP:rs2231142). {ECO:0000269|PubMed:12111378, ECO:0000269|PubMed:12544509, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:16702730, ECO:0000269|Ref.11, ECO:0000269|Ref.8}.		cellular iron ion homeostasis (GO:0006879)|drug export (GO:0046618)|drug transmembrane transport (GO:0006855)|embryonic process involved in female pregnancy (GO:0060136)|heme transport (GO:0015886)|response to drug (GO:0042493)|response to folic acid (GO:0051593)|response to glucocorticoid (GO:0051384)|response to iron ion (GO:0010039)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)|urate metabolic process (GO:0046415)	apical plasma membrane (GO:0016324)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|heme transporter activity (GO:0015232)|protein homodimerization activity (GO:0042803)|transporter activity (GO:0005215)|xenobiotic-transporting ATPase activity (GO:0008559)	p.Q141K(1)		breast(5)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(13)|lung(10)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	42		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;7.02e-05)	Afatinib(DB08916)|Apixaban(DB06605)|Buprenorphine(DB00921)|Cabazitaxel(DB06772)|Carboplatin(DB00958)|Cisplatin(DB00515)|Cladribine(DB00242)|Clofarabine(DB00631)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Dabrafenib(DB08912)|Dactinomycin(DB00970)|Dasatinib(DB01254)|Daunorubicin(DB00694)|Dexamethasone(DB01234)|Diethylstilbestrol(DB00255)|Docetaxel(DB01248)|Doxorubicin(DB00997)|Dronabinol(DB00470)|Erlotinib(DB00530)|Estradiol(DB00783)|Estrone(DB00655)|Etoposide(DB00773)|Ezetimibe(DB00973)|Fluorouracil(DB00544)|Folic Acid(DB00158)|Gefitinib(DB00317)|Glyburide(DB01016)|Hesperetin(DB01094)|Hydrocortisone(DB00741)|Imatinib(DB00619)|Irinotecan(DB00762)|Ivermectin(DB00602)|Lamivudine(DB00709)|Lansoprazole(DB00448)|Leflunomide(DB01097)|Methotrexate(DB00563)|Mitoxantrone(DB01204)|Mycophenolate mofetil(DB00688)|Nelfinavir(DB00220)|Nilotinib(DB04868)|Nitrofurantoin(DB00698)|Novobiocin(DB01051)|Omeprazole(DB00338)|Oxaliplatin(DB00526)|Paclitaxel(DB01229)|Pantoprazole(DB00213)|Pazopanib(DB06589)|Pitavastatin(DB08860)|Ponatinib(DB08901)|Pravastatin(DB00175)|Prazosin(DB00457)|Rabeprazole(DB01129)|Regorafenib(DB08896)|Rilpivirine(DB08864)|Riluzole(DB00740)|Ritonavir(DB00503)|Rosuvastatin(DB01098)|Saquinavir(DB01232)|Sorafenib(DB00398)|Sulfasalazine(DB00795)|Sumatriptan(DB00669)|Sunitinib(DB01268)|Tamoxifen(DB00675)|Telmisartan(DB00966)|Teniposide(DB00444)|Teriflunomide(DB08880)|Testosterone(DB00624)|Topotecan(DB01030)|Vandetanib(DB05294)|Vemurafenib(DB08881)|Venlafaxine(DB00285)|Verapamil(DB00661)|Vincristine(DB00541)|Vismodegib(DB08828)|Zafirlukast(DB00549)|Zidovudine(DB00495)	GCTGAGAACTGTAAGTTTTCT	0.398													G|||	598	0.119409	0.0129	0.1412	5008	,	,		22358	0.2907		0.0944	False		,,,				2504	0.0971				p.Q141K		Atlas-SNP	.											ABCG2,NS,carcinoma,0,1	ABCG2	151	1	1	Substitution - Missense(1)	stomach(1)	c.C421A	GRCh37	CM057428	ABCG2	M	rs2231142	PASS	.	G	LYS/GLN	142,4264	100.3+/-138.9	3,136,2064	211.0	190.0	197.0	http://omim.org/entry/612670|http://www.ncbi.nlm.nih.gov/pubmed?term	421	5.4	1.0	4	dbSNP_98	197	957,7643	209.3+/-250.5	47,863,3390	yes	missense	ABCG2	NM_004827.2	53	50,999,5454	TT,TG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	11.1279,3.2229,8.4499	benign	141/656	89052323	1099,11907	2203	4300	6503	SO:0001583	missense	9429	exon5			AGAACTGTAAGTT	AF103796	CCDS3628.1, CCDS58910.1	4q22.1	2014-08-27	2014-08-27		ENSG00000118777	ENSG00000118777		"""CD molecules"", ""ATP binding cassette transporters / subfamily G"""	74	protein-coding gene	gene with protein product		603756	"""ATP-binding cassette, sub-family G (WHITE), member 2"""			8894702, 9861027	Standard	NM_001257386		Approved	EST157481, MXR, BCRP, ABCP, CD338	uc003hrg.3	Q9UNQ0	OTTHUMG00000130601	ENST00000237612.3:c.421C>A	4.37:g.89052323G>T	ENSP00000237612:p.Gln141Lys	Somatic	193	0	0		WXS	Illumina HiSeq	Phase_I	121	64	0.528926	NM_004827	A0A1W3|A8K1T5|O95374|Q4W5I3|Q53ZQ1|Q569L4|Q5YLG4|Q86V64|Q8IX16|Q96LD6|Q96TA8|Q9BY73|Q9NUS0	Missense_Mutation	SNP	ENST00000237612.3	37	CCDS3628.1	304	0.1391941391941392	8	0.016260162601626018	55	0.15193370165745856	167	0.291958041958042	74	0.09762532981530343	G	13.84	2.358265	0.41801	0.032229	0.111279	ENSG00000118777	ENST00000515655;ENST00000237612	T;T	0.38401	1.14;1.14	5.37	5.37	0.77165	ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.166420	0.53938	D	0.000050	T	0.00012	0.0000	N	0.11724	0.165	0.26721	P	0.9707709	B;B;B	0.34214	0.442;0.372;0.257	B;B;B	0.36186	0.219;0.216;0.216	T	0.42949	-0.9421	9	0.26408	T	0.33	-0.0036	19.0867	0.93206	0.0:0.0:1.0:0.0	rs2231142;rs3736117;rs12721641;rs28365035;rs52809243;rs58973676;rs2231142	141;141;141	Q9UNQ0-2;Q9UNQ0;Q4W5I3	.;ABCG2_HUMAN;.	K	141	ENSP00000426917:Q141K;ENSP00000237612:Q141K	ENSP00000237612:Q141K	Q	-	1	0	ABCG2	89271347	0.985000	0.35326	0.996000	0.52242	0.985000	0.73830	1.742000	0.38248	2.677000	0.91161	0.655000	0.94253	CAG	G|0.883;T|0.117	0.117	strong		0.398	ABCG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253051.1	NM_004827	
FRMD5	84978	hgsc.bcm.edu	37	15	44198049	44198049	+	Silent	SNP	A	A	G	rs2306674	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:44198049A>G	ENST00000417257.1	-	6	704	c.528T>C	c.(526-528)gcT>gcC	p.A176A	FRMD5_ENST00000484674.1_Silent_p.A87A|FRMD5_ENST00000402883.1_Silent_p.A176A	NM_032892.3	NP_116281.2	Q7Z6J6	FRMD5_HUMAN	FERM domain containing 5	176	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.					cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extrinsic component of membrane (GO:0019898)|integral component of membrane (GO:0016021)				breast(2)|cervix(1)|endometrium(2)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	14		all_cancers(109;2.29e-15)|all_epithelial(112;9.98e-13)|Lung NSC(122;4.89e-08)|all_lung(180;5.08e-07)|Melanoma(134;0.0275)		all cancers(107;8.63e-20)|GBM - Glioblastoma multiforme(94;3.63e-06)		TGTGAATCTCAGCAATTTTCC	0.512													G|||	1101	0.219848	0.4138	0.1354	5008	,	,		21212	0.2857		0.0567	False		,,,				2504	0.1176				p.A176A		Atlas-SNP	.											.	FRMD5	45	.	0			c.T528C						PASS	.	G		1523,2873	673.3+/-402.8	255,1013,930	167.0	156.0	159.0		528	-1.5	1.0	15	dbSNP_100	159	392,8204	801.4+/-407.4	12,368,3918	no	coding-synonymous	FRMD5	NM_032892.3		267,1381,4848	GG,GA,AA		4.5603,34.6451,14.7398		176/571	44198049	1915,11077	2198	4298	6496	SO:0001819	synonymous_variant	84978	exon6			AATCTCAGCAATT	BC007796	CCDS10107.2, CCDS73715.1, CCDS73716.1	15q15.3	2005-08-09			ENSG00000171877	ENSG00000171877			28214	protein-coding gene	gene with protein product							Standard	XM_005254729		Approved	MGC14161	uc001ztl.3	Q7Z6J6	OTTHUMG00000060475	ENST00000417257.1:c.528T>C	15.37:g.44198049A>G		Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	204	91	0.446078	NM_032892	Q8NBG4	Silent	SNP	ENST00000417257.1	37	CCDS10107.2																																																																																			A|0.815;G|0.185	0.185	strong		0.512	FRMD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133879.1	NM_032892	
NEBL	10529	hgsc.bcm.edu	37	10	21108377	21108377	+	Silent	SNP	C	C	T	rs1006363	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:21108377C>T	ENST00000377122.4	-	20	2427	c.2031G>A	c.(2029-2031)agG>agA	p.R677R	NEBL_ENST00000417816.2_Intron|NEBL_ENST00000377159.4_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	217	0	0		WXS	Illumina HiSeq	Phase_I	135	71	0.525926	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	
MYO1C	4641	hgsc.bcm.edu	37	17	1386314	1386314	+	Silent	SNP	C	C	T	rs112029113	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:1386314C>T	ENST00000575158.1	-	4	458	c.282G>A	c.(280-282)acG>acA	p.T94T	MYO1C_ENST00000545534.2_Silent_p.T105T|MYO1C_ENST00000359786.5_Silent_p.T129T|MYO1C_ENST00000438665.2_Silent_p.T110T|MYO1C_ENST00000361007.2_Silent_p.T94T|MYO1C_ENST00000573198.1_5'Flank			Q12965	MYO1E_HUMAN	myosin IC	101	Myosin motor.				actin filament-based movement (GO:0030048)|ATP catabolic process (GO:0006200)|endocytosis (GO:0006897)|glomerular basement membrane development (GO:0032836)|glomerular filtration (GO:0003094)|glomerular visceral epithelial cell development (GO:0072015)|in utero embryonic development (GO:0001701)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|post-embryonic hemopoiesis (GO:0035166)|vasculogenesis (GO:0001570)	actin cytoskeleton (GO:0015629)|adherens junction (GO:0005912)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|motor activity (GO:0003774)|phosphatidylinositol binding (GO:0035091)			breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|liver(2)|lung(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	17				UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)		CCCGACGCTCCGTGCGCAGTG	0.662													C|||	16	0.00319489	0.0	0.0058	5008	,	,		11981	0.001		0.0109	False		,,,				2504	0.0				p.T129T		Atlas-SNP	.											.	MYO1C	57	.	0			c.G387A						PASS	.	C	,,	18,4384	25.3+/-52.1	0,18,2183	25.0	25.0	25.0		387,330,282	-2.2	1.0	17	dbSNP_132	25	138,8460	67.7+/-130.1	1,136,4162	no	coding-synonymous,coding-synonymous,coding-synonymous	MYO1C	NM_001080779.1,NM_001080950.1,NM_033375.4	,,	1,154,6345	TT,TC,CC		1.605,0.4089,1.2	,,	129/1064,110/1045,94/1029	1386314	156,12844	2201	4299	6500	SO:0001819	synonymous_variant	4641	exon4			ACGCTCCGTGCGC	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.282G>A	17.37:g.1386314C>T		Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	106	45	0.424528	NM_001080779	Q14778	Silent	SNP	ENST00000575158.1	37	CCDS11003.1																																																																																			C|0.989;T|0.011	0.011	strong		0.662	MYO1C-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438694.2		
DNAI1	27019	hgsc.bcm.edu	37	9	34500821	34500821	+	Missense_Mutation	SNP	G	G	A	rs11793196	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:34500821G>A	ENST00000242317.4	+	11	1174	c.1003G>A	c.(1003-1005)Gtc>Atc	p.V335I		NM_001281428.1|NM_012144.2	NP_001268357.1|NP_036276.1	Q9UI46	DNAI1_HUMAN	dynein, axonemal, intermediate chain 1	335			V -> I (in dbSNP:rs11793196).		cell projection organization (GO:0030030)|epithelial cilium movement (GO:0003351)|metabolic process (GO:0008152)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dynein complex (GO:0030286)|microtubule (GO:0005874)	motor activity (GO:0003774)			autonomic_ganglia(1)|endometrium(7)|kidney(1)|large_intestine(8)|lung(13)|prostate(1)|skin(2)|urinary_tract(1)	34	all_epithelial(49;0.244)		LUSC - Lung squamous cell carcinoma(29;0.0107)|STAD - Stomach adenocarcinoma(86;0.212)	GBM - Glioblastoma multiforme(74;0.0222)		GCGCCTGTCCGTCACTGCCCT	0.537									Kartagener syndrome		OREG0019152	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	884	0.176518	0.3601	0.1455	5008	,	,		18776	0.0119		0.1561	False		,,,				2504	0.1411				p.V335I		Atlas-SNP	.											.	DNAI1	72	.	0			c.G1003A						PASS	.	G	ILE/VAL	1420,2986	463.2+/-353.5	229,962,1012	61.0	61.0	61.0		1003	5.0	1.0	9	dbSNP_120	61	1308,7292	258.4+/-282.1	114,1080,3106	yes	missense	DNAI1	NM_012144.2	29	343,2042,4118	AA,AG,GG		15.2093,32.2288,20.9749	probably-damaging	335/700	34500821	2728,10278	2203	4300	6503	SO:0001583	missense	27019	exon11	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	CTGTCCGTCACTG	AF091619	CCDS6557.1, CCDS75829.1	9p13.3	2013-02-19	2006-09-04		ENSG00000122735	ENSG00000122735		"""Axonemal dyneins"", ""WD repeat domain containing"""	2954	protein-coding gene	gene with protein product		604366	"""dynein, axonemal, intermediate polypeptide 1"""			10577904, 21953912	Standard	NM_012144		Approved	DIC1, PCD, CILD1	uc003zum.3	Q9UI46	OTTHUMG00000019825	ENST00000242317.4:c.1003G>A	9.37:g.34500821G>A	ENSP00000242317:p.Val335Ile	Somatic	69	0	0	848	WXS	Illumina HiSeq	Phase_I	51	32	0.627451	NM_012144	B7Z7U1|Q5T8G7|Q8NHQ7|Q9UEZ8	Missense_Mutation	SNP	ENST00000242317.4	37	CCDS6557.1	350	0.16025641025641027	168	0.34146341463414637	53	0.1464088397790055	8	0.013986013986013986	121	0.15963060686015831	G	17.37	3.372643	0.61624	0.322288	0.152093	ENSG00000122735	ENST00000242317	T	0.71579	-0.58	4.99	4.99	0.66335	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.065937	0.64402	D	0.000011	T	0.00012	0.0000	M	0.85710	2.77	0.09310	P	1.0	B	0.27700	0.186	B	0.25405	0.06	T	0.07635	-1.0762	9	0.54805	T	0.06	.	16.1322	0.81449	0.0:0.0:1.0:0.0	rs11793196;rs59607272;rs11793196	335	Q9UI46	DNAI1_HUMAN	I	335	ENSP00000242317:V335I	ENSP00000242317:V335I	V	+	1	0	DNAI1	34490821	1.000000	0.71417	0.979000	0.43373	0.880000	0.50808	7.069000	0.76755	2.470000	0.83445	0.462000	0.41574	GTC	G|0.812;A|0.188	0.188	strong		0.537	DNAI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052192.1		
DSG1	1828	hgsc.bcm.edu	37	18	28919913	28919913	+	Missense_Mutation	SNP	G	G	A	rs34302455|rs200575647|rs386802123	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:28919913G>A	ENST00000257192.4	+	11	1824	c.1612G>A	c.(1612-1614)Gat>Aat	p.D538N		NM_001942.2	NP_001933.2	Q02413	DSG1_HUMAN	desmoglein 1	538			D -> N (in dbSNP:rs34302455).		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)			CGGAGCCAAAGATTTGTTATC	0.413													G|||	746	0.148962	0.2421	0.0994	5008	,	,		16728	0.0665		0.0845	False		,,,				2504	0.2096				p.D538N		Atlas-SNP	.											DSG1,NS,carcinoma,0,1	DSG1	176	1	0			c.G1612A						scavenged	.	G	ASN/ASP	8,4398		1,6,2196	98.0	97.0	97.0		1612	-1.4	0.0	18	dbSNP_126	97	2,8598		1,0,4299	yes	missense	DSG1	NM_001942.2	23	2,6,6495	AA,AG,GG		0.0233,0.1816,0.0769	benign	538/1050	28919913	10,12996	2203	4300	6503	SO:0001583	missense	1828	exon11			GCCAAAGATTTGT	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.1612G>A	18.37:g.28919913G>A	ENSP00000257192:p.Asp538Asn	Somatic	127	1	0.00787402		WXS	Illumina HiSeq	Phase_I	104	48	0.461538	NM_001942	B7Z845	Missense_Mutation	SNP	ENST00000257192.4	37	CCDS11896.1	247	0.1130952380952381	117	0.23780487804878048	40	0.11049723756906077	34	0.05944055944055944	56	0.07387862796833773	G	0.049	-1.257018	0.01457	0.001816	2.33E-4	ENSG00000134760	ENST00000257192	T	0.57107	0.42	1.12	-1.36	0.09085	.	7739.210000	0.00166	N	0.000000	T	0.00012	0.0000	L	0.36672	1.1	0.58432	P	5.000000000032756E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.05037	-1.0910	9	0.12766	T	0.61	.	4.3923	0.11346	0.4926:0.0:0.5074:0.0	rs34302455	538	Q02413	DSG1_HUMAN	N	538	ENSP00000257192:D538N	ENSP00000257192:D538N	D	+	1	0	DSG1	27173911	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.282000	0.08445	-0.601000	0.05783	-0.652000	0.03908	GAT	G|0.894;A|0.106	0.106	strong		0.413	DSG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254947.1	NM_001942	
PCDHB10	56126	hgsc.bcm.edu	37	5	140573442	140573442	+	Silent	SNP	C	C	G	rs622424	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:140573442C>G	ENST00000239446.4	+	1	1501	c.1317C>G	c.(1315-1317)gtC>gtG	p.V439V		NM_018930.3	NP_061753.1	Q9UN67	PCDBA_HUMAN	protocadherin beta 10	439	Cadherin 4. {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)			ACATAACGGTCCTGGTCTCCG	0.592													G|||	2442	0.48762	0.5076	0.5461	5008	,	,		13937	0.5685		0.4076	False		,,,				2504	0.4182				p.V439V		Atlas-SNP	.											.	PCDHB10	177	.	0			c.C1317G						PASS	.						80.0	77.0	78.0					5																	140573442		2203	4299	6502	SO:0001819	synonymous_variant	56126	exon1			AACGGTCCTGGTC	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.1317C>G	5.37:g.140573442C>G		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	140	61	0.435714	NM_018930	Q96T99	Silent	SNP	ENST00000239446.4	37	CCDS4252.1																																																																																			C|0.549;G|0.451	0.451	strong		0.592	PCDHB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251821.1	NM_018930	
DTX4	23220	hgsc.bcm.edu	37	11	58940278	58940278	+	Splice_Site	SNP	G	G	T	rs12796683	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:58940278G>T	ENST00000227451.3	+	1	314	c.210G>T	c.(208-210)acG>acT	p.T70T	DTX4_ENST00000532982.1_Intron	NM_015177.1	NP_055992.1	Q9Y2E6	DTX4_HUMAN	deltex 4, E3 ubiquitin ligase	70	WWE 1. {ECO:0000255|PROSITE- ProRule:PRU00248}.				innate immune response (GO:0045087)|Notch signaling pathway (GO:0007219)|positive regulation of type I interferon production (GO:0032481)|protein ubiquitination (GO:0016567)|regulation of type I interferon production (GO:0032479)	cytosol (GO:0005829)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(3)|large_intestine(3)|lung(11)|prostate(1)|upper_aerodigestive_tract(1)	20		all_epithelial(135;0.125)				GCCAAGACACGGGTGAGCCAG	0.697													G|||	1262	0.251997	0.152	0.3646	5008	,	,		9870	0.2679		0.2147	False		,,,				2504	0.3292				p.T70T		Atlas-SNP	.											.	DTX4	84	.	0			c.G210T						PASS	.	G		683,3671		61,561,1555	12.0	15.0	14.0		210	-2.2	1.0	11	dbSNP_121	14	1861,6707		199,1463,2622	yes	coding-synonymous-near-splice	DTX4	NM_015177.1		260,2024,4177	TT,TG,GG		21.7204,15.6867,19.6874		70/620	58940278	2544,10378	2177	4284	6461	SO:0001630	splice_region_variant	23220	exon1			AGACACGGGTGAG	AB023154	CCDS44612.1	11q12.2	2014-01-28	2014-01-28		ENSG00000110042	ENSG00000110042		"""RING-type (C3HC4) zinc fingers"""	29151	protein-coding gene	gene with protein product			"""deltex 4 homolog (Drosophila)"", ""deltex homolog 4 (Drosophila)"""			10231032, 22388039	Standard	NM_015177		Approved	KIAA0937, RNF155	uc001nns.2	Q9Y2E6	OTTHUMG00000167336	ENST00000227451.3:c.211+1G>T	11.37:g.58940278G>T		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	136	38	0.279412	NM_015177	Q0VF38	Silent	SNP	ENST00000227451.3	37	CCDS44612.1																																																																																			G|0.762;T|0.238	0.238	strong		0.697	DTX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394228.1	XM_166213	Silent
ADAM21	8747	hgsc.bcm.edu	37	14	70924507	70924507	+	Silent	SNP	A	A	C	rs3751524	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:70924507A>C	ENST00000603540.1	+	2	549	c.291A>C	c.(289-291)gcA>gcC	p.A97A	RP11-486O13.4_ENST00000556646.1_lincRNA|ADAM21_ENST00000267499.3_Silent_p.A97A	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	153	2	0.0130719		WXS	Illumina HiSeq	Phase_I	119	69	0.579832	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		
C1orf177	163747	hgsc.bcm.edu	37	1	55307501	55307501	+	Silent	SNP	A	A	G	rs41297871	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:55307501A>G	ENST00000371273.3	+	10	1227	c.1212A>G	c.(1210-1212)ggA>ggG	p.G404G	C1orf177_ENST00000358193.3_3'UTR	NM_001110533.1	NP_001104003	Q3ZCV2	CA177_HUMAN	chromosome 1 open reading frame 177	404										breast(1)|cervix(1)|kidney(1)|large_intestine(6)|lung(6)|prostate(2)	17						ttactaagggaaagtgccctc	0.468													G|||	1154	0.230431	0.1498	0.281	5008	,	,		21304	0.4405		0.2316	False		,,,				2504	0.0859				p.G404G		Atlas-SNP	.											.	C1orf177	36	.	0			c.A1212G						PASS	.	G	,	237,1147		17,203,472	101.0	81.0	87.0		1212,	-3.0	0.3	1	dbSNP_127	87	653,2529		66,521,1004	no	coding-synonymous,utr-3	C1orf177	NM_001110533.1,NM_152607.2	,	83,724,1476	GG,GA,AA		20.5217,17.1243,19.4919	,	404/419,	55307501	890,3676	692	1591	2283	SO:0001819	synonymous_variant	163747	exon10			TAAGGGAAAGTGC	AK097520	CCDS599.1, CCDS44153.1	1p32.3	2012-07-25			ENSG00000162398	ENSG00000162398			26854	protein-coding gene	gene with protein product							Standard	NM_152607		Approved	FLJ40201	uc001cyb.4	Q3ZCV2	OTTHUMG00000009986	ENST00000371273.3:c.1212A>G	1.37:g.55307501A>G		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	58	29	0.5	NM_001110533	B7WPL2|Q8N7Y9	Silent	SNP	ENST00000371273.3	37	CCDS44153.1																																																																																			A|0.737;G|0.263	0.263	strong		0.468	C1orf177-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000027674.1	NM_152607	
NACAD	23148	hgsc.bcm.edu	37	7	45123857	45123857	+	Missense_Mutation	SNP	A	A	G	rs7790844	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:45123857A>G	ENST00000490531.2	-	2	1941	c.1922T>C	c.(1921-1923)gTt>gCt	p.V641A		NM_001146334.1	NP_001139806.1	O15069	NACAD_HUMAN	NAC alpha domain containing	641					protein transport (GO:0015031)	cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.V641A(1)		breast(1)|endometrium(2)|skin(2)	5						CGGTGTCATAACGGAGTCCTG	0.597																																					p.V641A		Atlas-SNP	.											NACAD,NS,carcinoma,0,1	NACAD	44	1	1	Substitution - Missense(1)	endometrium(1)	c.T1922C						scavenged	.						4.0	5.0	5.0					7																	45123857		604	1531	2135	SO:0001583	missense	23148	exon2			GTCATAACGGAGT	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.1922T>C	7.37:g.45123857A>G	ENSP00000420477:p.Val641Ala	Somatic	13	1	0.0769231		WXS	Illumina HiSeq	Phase_I	9	7	0.777778	NM_001146334		Missense_Mutation	SNP	ENST00000490531.2	37	CCDS47582.1	.	.	.	.	.	.	.	.	.	.	a	1.045	-0.677539	0.03378	.	.	ENSG00000136274	ENST00000490531	T	0.12039	2.72	1.41	0.403	0.16350	.	3.406300	0.02110	N	0.054755	T	0.06050	0.0157	N	0.04508	-0.205	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.30327	-0.9982	9	0.07482	T	0.82	.	5.5804	0.17247	0.3401:0.0:0.6599:0.0	rs7790844;rs7790844	641	O15069	NACAD_HUMAN	A	641	ENSP00000420477:V641A	ENSP00000420477:V641A	V	-	2	0	NACAD	45090382	.	.	0.002000	0.10522	0.107000	0.19398	.	.	-0.244000	0.09639	-0.665000	0.03846	GTT	A|0.007;G|0.993	0.993	strong		0.597	NACAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353652.2	NM_001146334	
EXT1	2131	hgsc.bcm.edu	37	8	118847782	118847782	+	Silent	SNP	G	G	A	rs11546829	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	74	0	0		WXS	Illumina HiSeq	Phase_I	75	15	0.2	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	
OR1L8	138881	hgsc.bcm.edu	37	9	125330325	125330325	+	Silent	SNP	C	C	G	rs10985703	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:125330325C>G	ENST00000304865.2	-	1	513	c.432G>C	c.(430-432)ctG>ctC	p.L144L		NM_001004454.1	NP_001004454.1	Q8NGR8	OR1L8_HUMAN	olfactory receptor, family 1, subfamily L, member 8	144						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(5)|lung(6)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	20						AGGCCACCAGCAGGACACAGT	0.547													G|||	2119	0.423123	0.3283	0.389	5008	,	,		21856	0.8006		0.2555	False		,,,				2504	0.3589				p.L144L		Atlas-SNP	.											.	OR1L8	90	.	0			c.G432C						PASS	.	G		1441,2965	683.9+/-404.3	239,963,1001	117.0	87.0	97.0		432	-0.9	0.0	9	dbSNP_120	97	2239,6361	708.8+/-405.7	293,1653,2354	no	coding-synonymous	OR1L8	NM_001004454.1		532,2616,3355	GG,GC,CC		26.0349,32.7054,28.2946		144/310	125330325	3680,9326	2203	4300	6503	SO:0001819	synonymous_variant	138881	exon1			CACCAGCAGGACA		CCDS35124.1	9q33.2	2013-09-20			ENSG00000171496	ENSG00000171496		"""GPCR / Class A : Olfactory receptors"""	15110	protein-coding gene	gene with protein product							Standard	NM_001004454		Approved		uc004bmp.1	Q8NGR8	OTTHUMG00000020609	ENST00000304865.2:c.432G>C	9.37:g.125330325C>G		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	91	48	0.527473	NM_001004454	A3KFM3|B9EIR6|Q6IF15|Q96R79	Silent	SNP	ENST00000304865.2	37	CCDS35124.1																																																																																			C|0.662;G|0.338	0.338	strong		0.547	OR1L8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053939.1		
OR4A15	81328	hgsc.bcm.edu	37	11	55135435	55135435	+	Missense_Mutation	SNP	C	C	T	rs1425193	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:55135435C>T	ENST00000314706.3	+	1	76	c.76C>T	c.(76-78)Cct>Tct	p.P26S		NM_001005275.1	NP_001005275.1	Q8NGL6	O4A15_HUMAN	olfactory receptor, family 4, subfamily A, member 15	26			P -> S (in dbSNP:rs1425193).			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(2)|endometrium(2)|kidney(2)|large_intestine(7)|lung(48)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	71						GAGTCCAACACCTTCAGAAGA	0.398													.|||	1139	0.227436	0.0159	0.3141	5008	,	,		17645	0.3869		0.2823	False		,,,				2504	0.2311				p.P26S		Atlas-SNP	.											.	OR4A15	161	.	0			c.C76T						PASS	.	C	SER/PRO	275,4127	153.7+/-187.2	6,263,1932	62.0	58.0	59.0		76	-2.7	0.0	11	dbSNP_88	59	2281,6311	383.2+/-340.6	325,1631,2340	yes	missense	OR4A15	NM_001005275.1	74	331,1894,4272	TT,TC,CC		26.548,6.2472,19.6706	benign	26/345	55135435	2556,10438	2201	4296	6497	SO:0001583	missense	81328	exon1			CCAACACCTTCAG	AB065776	CCDS31500.1	11q11	2012-08-09			ENSG00000181958	ENSG00000181958		"""GPCR / Class A : Olfactory receptors"""	15152	protein-coding gene	gene with protein product							Standard	NM_001005275		Approved		uc010rif.2	Q8NGL6	OTTHUMG00000166711	ENST00000314706.3:c.76C>T	11.37:g.55135435C>T	ENSP00000325065:p.Pro26Ser	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	111	23	0.207207	NM_001005275	Q6IFL4|Q96R65	Missense_Mutation	SNP	ENST00000314706.3	37	CCDS31500.1	564	0.25824175824175827	13	0.026422764227642278	122	0.3370165745856354	212	0.3706293706293706	217	0.2862796833773087	c	9.493	1.101203	0.20632	0.062472	0.26548	ENSG00000181958	ENST00000314706	T	0.37584	1.19	2.8	-2.65	0.06095	.	.	.	.	.	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	0.41752	-0.9491	8	0.07030	T	0.85	.	0.9311	0.01335	0.3917:0.2726:0.194:0.1417	rs1425193;rs59457328;rs1425193	26	Q8NGL6	O4A15_HUMAN	S	26	ENSP00000325065:P26S	ENSP00000325065:P26S	P	+	1	0	OR4A15	54892011	.	.	0.000000	0.03702	0.043000	0.13939	.	.	-0.268000	0.09312	0.492000	0.49549	CCT	C|0.778;T|0.222	0.222	strong		0.398	OR4A15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391161.1	NM_001005275	
ST3GAL3	6487	hgsc.bcm.edu	37	1	44290530	44290530	+	Intron	SNP	A	A	G	rs37458	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:44290530A>G	ENST00000361392.4	+	4	386				ST3GAL3_ENST00000262915.3_Missense_Mutation_p.T128A|ST3GAL3_ENST00000531451.1_Intron|ST3GAL3_ENST00000353126.3_Intron|ST3GAL3_ENST00000332628.6_Intron|ST3GAL3_ENST00000372372.2_Missense_Mutation_p.T97A|ST3GAL3_ENST00000335430.6_Intron|ST3GAL3_ENST00000372362.2_Intron|ST3GAL3_ENST00000545417.1_Intron|ST3GAL3_ENST00000372368.2_Missense_Mutation_p.T113A|ST3GAL3_ENST00000531993.1_Intron|ST3GAL3_ENST00000461375.1_Intron|ST3GAL3_ENST00000351035.3_Missense_Mutation_p.T97A|ST3GAL3_ENST00000361746.4_Missense_Mutation_p.T128A|ST3GAL3_ENST00000533933.1_Intron|ST3GAL3_ENST00000361400.4_Intron|ST3GAL3_ENST00000347631.2_Intron|ST3GAL3_ENST00000330208.2_Intron|ST3GAL3_ENST00000372366.1_Intron|ST3GAL3_ENST00000372369.1_Intron|ST3GAL3_ENST00000372377.4_Intron|ST3GAL3_ENST00000372374.2_Intron|ST3GAL3_ENST00000372375.2_Missense_Mutation_p.T113A|ST3GAL3_ENST00000531816.1_Intron|ST3GAL3_ENST00000361812.4_Intron|ST3GAL3_ENST00000372365.1_Intron|ST3GAL3_ENST00000528371.1_Intron|ST3GAL3_ENST00000372367.1_Intron	NM_001270459.1|NM_006279.3|NM_174964.2	NP_001257388.1|NP_006270.1|NP_777624.1	Q11203	SIAT6_HUMAN	ST3 beta-galactoside alpha-2,3-sialyltransferase 3						carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|sialylation (GO:0097503)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)	beta-galactoside (CMP) alpha-2,3-sialyltransferase activity (GO:0003836)|N-acetyllactosaminide alpha-2,3-sialyltransferase activity (GO:0008118)			central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(3)|ovary(3)|skin(1)	19	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0518)				gagcgaggacacagcctttgc	0.428													A|||	1184	0.236422	0.3139	0.2378	5008	,	,		19230	0.1429		0.3459	False		,,,				2504	0.1145				p.T128A		Atlas-SNP	.											.	ST3GAL3	56	.	0			c.A382G						PASS	.	A	,ALA/THR,,,,,ALA/THR,,,ALA/THR	1361,3039		214,933,1053	65.0	63.0	64.0		,382,,,,,337,,,289	-0.0	0.0	1	dbSNP_76	64	2985,5577		524,1937,1820	yes	intron,missense,intron,intron,intron,intron,missense,intron,intron,missense	ST3GAL3	NM_006279.2,NM_174963.2,NM_174964.1,NM_174965.1,NM_174966.1,NM_174967.1,NM_174968.2,NM_174969.1,NM_174970.1,NM_174971.2	,58,,,,,58,,,58	738,2870,2873	GG,GA,AA		34.8633,30.9318,33.5288	,benign,,,,,benign,,,benign	,128/445,,,,,113/430,,,97/414	44290530	4346,8616	2200	4281	6481	SO:0001627	intron_variant	6487	exon5			GAGGACACAGCCT	L23768	CCDS492.1, CCDS493.1, CCDS494.1, CCDS495.1, CCDS496.1, CCDS497.1, CCDS498.1, CCDS499.1, CCDS500.1, CCDS53310.1, CCDS57988.1, CCDS57989.1, CCDS57990.1, CCDS57991.1, CCDS57992.1, CCDS57993.1, CCDS57994.1	1p34.1	2014-01-31	2005-02-07	2005-02-07	ENSG00000126091	ENSG00000126091	2.4.99.6	"""Sialyltransferases"""	10866	protein-coding gene	gene with protein product	"""ST3Gal III"""	606494	"""sialyltransferase 6 (N-acetyllacosaminide alpha 2,3-sialyltransferase)"", ""mental retardation, non-syndromic, autosomal recessive, 12"""	SIAT6, MRT12		8333853, 21907012	Standard	NM_174963		Approved		uc001cjz.4	Q11203	OTTHUMG00000007561	ENST00000361392.4:c.209+9925A>G	1.37:g.44290530A>G		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	53	53	1	NM_174963	A9Z1W2|D3DPX8|Q5T4W9|Q5T4X0|Q5T4X7|Q5T4X8|Q5T4X9|Q5T4Y0|Q5T4Y2|Q5T4Y3|Q5T4Y4|Q86UR6|Q86UR7|Q86UR8|Q86UR9|Q86US0|Q86US1|Q86US2|Q8IX41|Q8IX42|Q8IX43|Q8IX44|Q8IX45|Q8IX46|Q8IX47|Q8IX48|Q8IX49|Q8IX50|Q8IX51|Q8IX52|Q8IX53|Q8IX54|Q8IX55|Q8IX56|Q8IX57|Q8IX58	Missense_Mutation	SNP	ENST00000361392.4	37	CCDS492.1	597	0.2733516483516483	154	0.3130081300813008	109	0.3011049723756906	82	0.14335664335664336	252	0.3324538258575198	A	2.667	-0.278401	0.05679	0.309318	0.348633	ENSG00000126091	ENST00000262915;ENST00000372375;ENST00000351035;ENST00000361746;ENST00000372368;ENST00000372372	T;T;T;T;T;T	0.50548	0.74;0.74;0.75;0.74;0.74;0.75	2.01	-0.0277	0.13925	.	.	.	.	.	T	0.00012	0.0000	.	.	.	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	0.40117	-0.9580	7	0.07990	T	0.79	.	4.239	0.10638	0.4076:0.0:0.5924:0.0	rs37458;rs3791070;rs52797725;rs56835574;rs37458	97;113;128	Q11203-19;Q11203-13;Q11203-4	.;.;.	A	128;113;97;128;113;97	ENSP00000262915:T128A;ENSP00000361450:T113A;ENSP00000316999:T97A;ENSP00000354657:T128A;ENSP00000361443:T113A;ENSP00000361447:T97A	ENSP00000262915:T128A	T	+	1	0	ST3GAL3	44063117	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.151000	0.10175	-0.010000	0.14271	-0.456000	0.05471	ACA	A|0.707;G|0.293	0.293	strong		0.428	ST3GAL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019964.1	NM_174963	
CDH11	1009	hgsc.bcm.edu	37	16	65038674	65038674	+	Silent	SNP	G	G	A	rs35182	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:65038674G>A	ENST00000268603.4	-	3	714	c.99C>T	c.(97-99)ccC>ccT	p.P33P	CDH11_ENST00000569624.1_5'UTR|CDH11_ENST00000394156.3_Silent_p.P33P|CDH11_ENST00000566827.1_Intron	NM_001797.2	NP_001788.2	P55287	CAD11_HUMAN	cadherin 11, type 2, OB-cadherin (osteoblast)	33					adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|corticospinal tract morphogenesis (GO:0021957)|homophilic cell adhesion (GO:0007156)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(19)|lung(40)|ovary(3)|prostate(3)|skin(2)|urinary_tract(2)	88		Ovarian(137;0.0973)		OV - Ovarian serous cystadenocarcinoma(108;0.205)		CATGGAAGGAGGGCCGCAGGT	0.607			T	USP6	aneurysmal bone cysts					TSP Lung(24;0.17)			G|||	313	0.0625	0.0061	0.0865	5008	,	,		14916	0.0675		0.1054	False		,,,				2504	0.0726				p.P33P		Atlas-SNP	.		Dom	yes		16	16q22.1	1009	"""cadherin 11, type 2, OB-cadherin (osteoblast)"""		M	.	CDH11	260	.	0			c.C99T						PASS	.	G		87,4317	69.2+/-107.0	2,83,2117	29.0	26.0	27.0		99	2.2	1.0	16	dbSNP_76	27	969,7631	198.5+/-242.8	56,857,3387	no	coding-synonymous	CDH11	NM_001797.2		58,940,5504	AA,AG,GG		11.2674,1.9755,8.1206		33/797	65038674	1056,11948	2202	4300	6502	SO:0001819	synonymous_variant	1009	exon3			GAAGGAGGGCCGC	D21255	CCDS10803.1	16q21	2010-01-26			ENSG00000140937	ENSG00000140937		"""Cadherins / Major cadherins"""	1750	protein-coding gene	gene with protein product	"""OB-Cadherin"""	600023				9615235	Standard	NM_001797		Approved	OB, CAD11	uc002eoi.3	P55287	OTTHUMG00000137494	ENST00000268603.4:c.99C>T	16.37:g.65038674G>A		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	137	46	0.335766	NM_001797	A8K5D6|A8MZC8|B7WP28|Q15065|Q15066|Q9UQ93|Q9UQ94	Silent	SNP	ENST00000268603.4	37	CCDS10803.1																																																																																			G|0.923;A|0.077	0.077	strong		0.607	CDH11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268755.1	NM_033664	
CDH5	1003	hgsc.bcm.edu	37	16	66432423	66432423	+	Missense_Mutation	SNP	T	T	C	rs1049970|rs386791725	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:66432423T>C	ENST00000341529.3	+	10	1698	c.1550T>C	c.(1549-1551)aTc>aCc	p.I517T	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)	p.I517T(1)		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)	TTCAAATTCATCTTGAATACT	0.473													C|||	3728	0.744409	0.7474	0.83	5008	,	,		21203	0.8224		0.6869	False		,,,				2504	0.6585				p.I517T		Atlas-SNP	.											CDH5,NS,carcinoma,0,2	CDH5	111	2	1	Substitution - Missense(1)	prostate(1)	c.T1550C						PASS	.	C	THR/ILE	2722,1680		1096,530,575	150.0	127.0	135.0		1550	4.0	0.9	16	dbSNP_86	135	4823,3777		1885,1053,1362	yes	missense	CDH5	NM_001795.3	89	2981,1583,1937	CC,CT,TT		43.9186,38.1645,41.9705	benign	517/785	66432423	7545,5457	2201	4300	6501	SO:0001583	missense	1003	exon10			AATTCATCTTGAA	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.1550T>C	16.37:g.66432423T>C	ENSP00000344115:p.Ile517Thr	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	107	107	1	NM_001795	Q4VAI5|Q4VAI6	Missense_Mutation	SNP	ENST00000341529.3	37	CCDS10804.1	1542	0.7060439560439561	328	0.6666666666666666	269	0.7430939226519337	453	0.791958041958042	492	0.6490765171503958	C	8.228	0.803910	0.16467	0.618355	0.560814	ENSG00000179776	ENST00000341529;ENST00000379531;ENST00000539262	T	0.59502	0.26	4.95	3.99	0.46301	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.00012	0.0000	N	0.01188	-0.97	0.09310	P	0.9999999999986131	B	0.02656	0.0	B	0.04013	0.001	T	0.31364	-0.9946	8	0.48119	T	0.1	.	7.3952	0.26931	0.1654:0.7492:0.0:0.0854	rs1049970;rs3190184;rs52795742;rs61244397;rs1049970	517	P33151	CADH5_HUMAN	T	517;402;258	ENSP00000344115:I517T	ENSP00000344115:I517T	I	+	2	0	CDH5	64989924	0.998000	0.40836	0.911000	0.35937	0.055000	0.15305	1.933000	0.40153	0.699000	0.31761	-0.215000	0.12644	ATC	T|0.282;C|0.718	0.718	strong		0.473	CDH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268767.1	NM_001795	
NLRP13	126204	hgsc.bcm.edu	37	19	56413532	56413532	+	Silent	SNP	G	G	A	rs7258847	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:56413532G>A	ENST00000342929.3	-	9	2657	c.2658C>T	c.(2656-2658)caC>caT	p.H886H	NLRP13_ENST00000588751.1_Silent_p.H886H	NM_176810.2	NP_789780.2	Q86W25	NAL13_HUMAN	NLR family, pyrin domain containing 13	886							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)		CATCTGACAAGTGCTTGCAAG	0.582													G|||	744	0.148562	0.0287	0.1787	5008	,	,		15155	0.0456		0.2803	False		,,,				2504	0.2597				p.H886H		Atlas-SNP	.											.	NLRP13	220	.	0			c.C2658T						PASS	.	G		289,4117	161.1+/-193.3	8,273,1922	91.0	69.0	77.0		2658	1.5	0.0	19	dbSNP_116	77	2291,6309	386.3+/-341.8	337,1617,2346	no	coding-synonymous	NLRP13	NM_176810.2		345,1890,4268	AA,AG,GG		26.6395,6.5592,19.837		886/1044	56413532	2580,10426	2203	4300	6503	SO:0001819	synonymous_variant	126204	exon9			TGACAAGTGCTTG	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.2658C>T	19.37:g.56413532G>A		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	72	37	0.513889	NM_176810	Q7RTR5	Silent	SNP	ENST00000342929.3	37	CCDS33119.1																																																																																			G|0.824;A|0.176	0.176	strong		0.582	NLRP13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396560.1	NM_176810	
ATP12A	479	hgsc.bcm.edu	37	13	25255705	25255705	+	Silent	SNP	C	C	A	rs41288276	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:25255705C>A	ENST00000381946.3	+	2	182	c.15C>A	c.(13-15)acC>acA	p.T5T	ATP12A_ENST00000218548.6_Silent_p.T5T			P54707	AT12A_HUMAN	ATPase, H+/K+ transporting, nongastric, alpha polypeptide	5					ATP biosynthetic process (GO:0006754)|ion transmembrane transport (GO:0034220)|potassium ion homeostasis (GO:0055075)|regulation of pH (GO:0006885)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|hydrogen:potassium-exchanging ATPase complex (GO:0005889)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|hydrogen:potassium-exchanging ATPase activity (GO:0008900)|metal ion binding (GO:0046872)			breast(6)|central_nervous_system(4)|endometrium(3)|kidney(5)|large_intestine(23)|lung(23)|ovary(2)|pancreas(1)|prostate(2)|skin(5)	74		Lung SC(185;0.0225)|Breast(139;0.077)		all cancers(112;0.0307)|Epithelial(112;0.086)|OV - Ovarian serous cystadenocarcinoma(117;0.228)		TTCAGAAAACCCCAGAAATTT	0.542													C|||	256	0.0511182	0.1044	0.0303	5008	,	,		17355	0.001		0.0477	False		,,,				2504	0.0491				p.T5T	Pancreas(156;1582 1935 18898 22665 26498)	Atlas-SNP	.											.	ATP12A	172	.	0			c.C15A						PASS	.	C	,	401,4005	199.8+/-223.2	18,365,1820	51.0	54.0	53.0		15,15	-6.3	0.0	13	dbSNP_127	53	391,8209	125.5+/-184.1	5,381,3914	no	coding-synonymous,coding-synonymous	ATP12A	NM_001185085.1,NM_001676.5	,	23,746,5734	AA,AC,CC		4.5465,9.1012,6.0895	,	5/1046,5/1040	25255705	792,12214	2203	4300	6503	SO:0001819	synonymous_variant	479	exon2			GAAAACCCCAGAA	L42558	CCDS31948.1, CCDS53858.1	13q11-q12.1	2010-04-20	2002-02-25		ENSG00000075673	ENSG00000075673	3.6.3.10	"""ATPases / P-type"""	13816	protein-coding gene	gene with protein product	"""ATPase, Na+K+ transporting, alpha-1 polypeptide-like"", ""potassium-transporting ATPase alpha chain 2"", ""proton pump"", ""non-gastric H(+)/K(+) ATPase alpha subunit"", ""sodium/potassium ATPase, alpha polypeptide-like"""	182360	"""ATPase, Na+/K+ transporting, alpha polypeptide-like 1"""	ATP1AL1		8838794, 2842249	Standard	NM_001676		Approved		uc010aaa.3	P54707	OTTHUMG00000016588	ENST00000381946.3:c.15C>A	13.37:g.25255705C>A		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	71	36	0.507042	NM_001185085	Q13816|Q13817|Q16734|Q5W035|Q8N5U2	Silent	SNP	ENST00000381946.3	37	CCDS31948.1																																																																																			C|0.942;A|0.058	0.058	strong		0.542	ATP12A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044199.1	NM_001676	
ESYT2	57488	hgsc.bcm.edu	37	7	158534372	158534372	+	Silent	SNP	G	G	A	rs57686648	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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						PASS	.			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	94	0	0		WXS	Illumina HiSeq	Phase_I	83	41	0.493976	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	
CENPE	1062	hgsc.bcm.edu	37	4	104041448	104041448	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:104041448T>C	ENST00000265148.3	-	44	7275	c.7186A>G	c.(7186-7188)Agt>Ggt	p.S2396G	CENPE_ENST00000380026.3_Missense_Mutation_p.S2275G	NM_001813.2	NP_001804.2	Q02224	CENPE_HUMAN	centromere protein E, 312kDa	2396	Kinetochore-binding domain.				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)		TGCATAGCACTTTCTTTAGCT	0.338																																					p.S2396G		Atlas-SNP	.											CENPE,NS,carcinoma,+2,1	CENPE	253	1	0			c.A7186G						scavenged	.						143.0	120.0	128.0					4																	104041448		2202	4299	6501	SO:0001583	missense	1062	exon44			TAGCACTTTCTTT	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.7186A>G	4.37:g.104041448T>C	ENSP00000265148:p.Ser2396Gly	Somatic	196	0	0		WXS	Illumina HiSeq	Phase_I	196	4	0.0204082	NM_001813	A6NKY9|A8K2U7|Q4LE75	Missense_Mutation	SNP	ENST00000265148.3	37	CCDS34042.1	.	.	.	.	.	.	.	.	.	.	T	11.67	1.709281	0.30322	.	.	ENSG00000138778	ENST00000265148;ENST00000380026	T;T	0.68479	-0.33;-0.32	4.62	4.62	0.57501	.	.	.	.	.	T	0.58047	0.2095	L	0.40543	1.245	0.19945	N	0.999946	B;B	0.28971	0.229;0.147	B;B	0.30572	0.117;0.055	T	0.51826	-0.8656	9	0.40728	T	0.16	.	10.7208	0.46040	0.0:0.0:0.0:1.0	.	2275;2396	Q02224-3;Q02224	.;CENPE_HUMAN	G	2396;2275	ENSP00000265148:S2396G;ENSP00000369365:S2275G	ENSP00000265148:S2396G	S	-	1	0	CENPE	104260897	0.995000	0.38212	0.902000	0.35471	0.441000	0.31987	3.505000	0.53356	1.835000	0.53391	0.533000	0.62120	AGT	.	.	none		0.338	CENPE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
COL18A1	80781	hgsc.bcm.edu	37	21	46896303	46896303	+	Silent	SNP	C	C	G	rs2230687	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:46896303C>G	ENST00000359759.4	+	5	2103	c.2082C>G	c.(2080-2082)ccC>ccG	p.P694P	COL18A1_ENST00000400337.2_Silent_p.P279P|COL18A1_ENST00000355480.5_Silent_p.P459P			P39060	COIA1_HUMAN	collagen, type XVIII, alpha 1	694	Nonhelical region 1 (NC1).				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)		CGCCACCCCCCGTCACCACGC	0.642													G|||	1229	0.245407	0.4342	0.1311	5008	,	,		16164	0.2956		0.0984	False		,,,				2504	0.1708				p.P459P		Atlas-SNP	.											.	COL18A1	129	.	0			c.C1377G						PASS	.	G	,	1445,2563		285,875,844	45.0	48.0	47.0		1377,837	-7.7	0.0	21	dbSNP_98	47	778,7534		43,692,3421	no	coding-synonymous,coding-synonymous	COL18A1	NM_030582.3,NM_130445.2	,	328,1567,4265	GG,GC,CC		9.36,36.0529,18.0438	,	459/1520,279/1340	46896303	2223,10097	2004	4156	6160	SO:0001819	synonymous_variant	80781	exon5			ACCCCCCGTCACC		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.2082C>G	21.37:g.46896303C>G		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	96	33	0.34375	NM_030582	A8MVI4|Q58EX6|Q6RZ39|Q6RZ40|Q6RZ41|Q8N4S4|Q8WXI5|Q96T70|Q9UK38|Q9Y6Q7|Q9Y6Q8	Silent	SNP	ENST00000359759.4	37																																																																																				C|0.793;G|0.207	0.207	strong		0.642	COL18A1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000206827.1		
MTMR2	8898	hgsc.bcm.edu	37	11	95569326	95569326	+	Silent	SNP	G	G	T	rs61735577	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:95569326G>T	ENST00000346299.5	-	14	2096	c.1756C>A	c.(1756-1758)Cgg>Agg	p.R586R	MTMR2_ENST00000352297.7_Silent_p.R514R|MTMR2_ENST00000409459.1_Silent_p.R514R|MTMR2_ENST00000393223.3_Silent_p.R514R	NM_016156.5	NP_057240.3	Q13614	MTMR2_HUMAN	myotubularin related protein 2	586					cell death (GO:0008219)|dendritic spine maintenance (GO:0097062)|inositol phosphate dephosphorylation (GO:0046855)|myelin assembly (GO:0032288)|negative regulation of endocytosis (GO:0045806)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of myelination (GO:0031642)|negative regulation of receptor catabolic process (GO:2000645)|negative regulation of receptor internalization (GO:0002091)|neuron development (GO:0048666)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|positive regulation of early endosome to late endosome transport (GO:2000643)|protein dephosphorylation (GO:0006470)|protein tetramerization (GO:0051262)|small molecule metabolic process (GO:0044281)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|endosome (GO:0005768)|neuronal postsynaptic density (GO:0097481)|nucleus (GO:0005634)|synaptic membrane (GO:0097060)|synaptic vesicle (GO:0008021)|vacuolar membrane (GO:0005774)	phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity (GO:0052629)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			autonomic_ganglia(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	19		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)				GGTTTCATCCGTGGATTCCAC	0.438													G|||	211	0.0421326	0.056	0.0202	5008	,	,		19893	0.002		0.0288	False		,,,				2504	0.0941				p.R586R		Atlas-SNP	.											.	MTMR2	79	.	0			c.C1756A						PASS	.	G	,,	246,4156	141.9+/-177.2	8,230,1963	184.0	184.0	184.0		1756,1540,1540	1.9	1.0	11	dbSNP_129	184	182,8414	82.3+/-144.9	0,182,4116	no	coding-synonymous,coding-synonymous,coding-synonymous	MTMR2	NM_016156.5,NM_201278.2,NM_201281.2	,,	8,412,6079	TT,TG,GG		2.1173,5.5884,3.2928	,,	586/644,514/572,514/572	95569326	428,12570	2201	4298	6499	SO:0001819	synonymous_variant	8898	exon14			TCATCCGTGGATT	U58033	CCDS8305.1, CCDS8306.1	11q22	2014-09-17			ENSG00000087053	ENSG00000087053		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"""	7450	protein-coding gene	gene with protein product		603557		CMT4B		8640223, 9736772	Standard	NM_016156		Approved	KIAA1073	uc001pfu.3	Q13614	OTTHUMG00000153837	ENST00000346299.5:c.1756C>A	11.37:g.95569326G>T		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	106	16	0.150943	NM_016156	A6NN98|Q9UPS9	Silent	SNP	ENST00000346299.5	37	CCDS8305.1																																																																																			G|0.969;T|0.031	0.031	strong		0.438	MTMR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332620.1	NM_016156	
KIF17	57576	hgsc.bcm.edu	37	1	21042094	21042094	+	Silent	SNP	G	G	A	rs12046928	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:21042094G>A	ENST00000247986.2	-	2	580	c.270C>T	c.(268-270)taC>taT	p.Y90Y	KIF17_ENST00000400463.3_Silent_p.Y90Y|KIF17_ENST00000375044.1_De_novo_Start_OutOfFrame			Q9P2E2	KIF17_HUMAN	kinesin family member 17	90	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|cell projection organization (GO:0030030)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|neurogenesis (GO:0022008)|protein complex localization (GO:0031503)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|intraciliary transport particle B (GO:0030992)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|plus-end-directed microtubule motor activity (GO:0008574)			NS(2)|endometrium(3)|kidney(3)|large_intestine(9)|liver(1)|lung(23)|ovary(4)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	50		all_lung(284;2.99e-05)|Lung NSC(340;3.26e-05)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00179)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|COAD - Colon adenocarcinoma(152;1.43e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000168)|Kidney(64;0.000221)|GBM - Glioblastoma multiforme(114;0.000651)|KIRC - Kidney renal clear cell carcinoma(64;0.0031)|STAD - Stomach adenocarcinoma(196;0.00336)|READ - Rectum adenocarcinoma(331;0.0686)|Lung(427;0.209)		CTGTCTGGCCGTAGGCAAAGA	0.647													G|||	1404	0.280351	0.0741	0.1614	5008	,	,		19859	0.7232		0.1451	False		,,,				2504	0.3262				p.Y90Y		Atlas-SNP	.											.	KIF17	130	.	0			c.C270T						PASS	.	G	,	369,4037	187.1+/-213.8	14,341,1848	98.0	83.0	88.0		270,270	-5.7	0.9	1	dbSNP_120	88	1106,7494	230.8+/-265.0	82,942,3276	no	coding-synonymous,coding-synonymous	KIF17	NM_001122819.1,NM_020816.2	,	96,1283,5124	AA,AG,GG		12.8605,8.3749,11.3409	,	90/1029,90/1030	21042094	1475,11531	2203	4300	6503	SO:0001819	synonymous_variant	57576	exon2			CTGGCCGTAGGCA	AB037826	CCDS213.1, CCDS44079.1, CCDS72722.1	1p36.13	2012-08-01			ENSG00000117245	ENSG00000117245		"""Kinesins"""	19167	protein-coding gene	gene with protein product	"""kinesin-like protein KIF17"", ""KIF3-related motor protein"", ""KIF17 variant protein"""	605037				10846156	Standard	XR_241202		Approved	KIAA1405, KIF3X, KIF17B, OSM-3, KLP-2	uc001bdr.4	Q9P2E2	OTTHUMG00000002863	ENST00000247986.2:c.270C>T	1.37:g.21042094G>A		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	54	22	0.407407	NM_001122819	A2A3Q7|A2A3Q8|O95077|Q53YS6|Q5VWA9|Q6GSA8|Q8N411	Silent	SNP	ENST00000247986.2	37	CCDS213.1																																																																																			G|0.810;A|0.190	0.190	strong		0.647	KIF17-009	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276995.1	NM_020816	
PPTC7	160760	hgsc.bcm.edu	37	12	110974890	110974890	+	Silent	SNP	T	T	C	rs10849900	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:110974890T>C	ENST00000354300.3	-	6	1155	c.867A>G	c.(865-867)ccA>ccG	p.P289P		NM_139283.1	NP_644812.1	Q8NI37	PPTC7_HUMAN	PTC7 protein phosphatase homolog (S. cerevisiae)	289	PP2C-like.					mitochondrion (GO:0005739)	metal ion binding (GO:0046872)|phosphoprotein phosphatase activity (GO:0004721)	p.P289P(1)		endometrium(1)|large_intestine(2)|lung(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	9						TGATGTCATCTGGCTTTCCAC	0.383													T|||	1625	0.324481	0.1309	0.2781	5008	,	,		20337	0.3889		0.3161	False		,,,				2504	0.5613				p.P289P		Atlas-SNP	.											PPTC7,NS,carcinoma,0,1	PPTC7	30	1	1	Substitution - coding silent(1)	stomach(1)	c.A867G						PASS	.	T		637,3769	273.4+/-271.3	55,527,1621	199.0	169.0	179.0		867	0.4	1.0	12	dbSNP_120	179	2738,5862	436.3+/-358.3	446,1846,2008	no	coding-synonymous	PPTC7	NM_139283.1		501,2373,3629	CC,CT,TT		31.8372,14.4576,25.9496		289/305	110974890	3375,9631	2203	4300	6503	SO:0001819	synonymous_variant	160760	exon6			GTCATCTGGCTTT	AF385435	CCDS9149.1	12q24.11	2009-11-05				ENSG00000196850			30695	protein-coding gene	gene with protein product	"""T cell activation protein phosphatase 2C"""	609668				15177553	Standard	NM_139283		Approved	TA-PP2C	uc001trh.1	Q8NI37	OTTHUMG00000169529	ENST00000354300.3:c.867A>G	12.37:g.110974890T>C		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	73	30	0.410959	NM_139283	B3KWC5|Q68DZ7|Q6UY82	Silent	SNP	ENST00000354300.3	37	CCDS9149.1																																																																																			T|0.725;C|0.275	0.275	strong		0.383	PPTC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404635.1	NM_139283	
MPV17L2	84769	hgsc.bcm.edu	37	19	18304700	18304700	+	Missense_Mutation	SNP	A	A	G	rs874628	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:18304700A>G	ENST00000599612.2	+	2	314	c.214A>G	c.(214-216)Atg>Gtg	p.M72V		NM_032683.2	NP_116072.2	Q567V2	M17L2_HUMAN	MPV17 mitochondrial membrane protein-like 2	72			M -> V (in dbSNP:rs874628). {ECO:0000269|Ref.2}.			integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)				large_intestine(1)|lung(2)|urinary_tract(1)	4						GGGCTGCAGCATGGGTCCCTT	0.602													A|||	875	0.17472	0.1967	0.1974	5008	,	,		17411	0.0655		0.2813	False		,,,				2504	0.1319				p.M72V		Atlas-SNP	.											.	MPV17L2	12	.	0			c.A214G						PASS	.	A	VAL/MET	778,3310		69,640,1335	101.0	103.0	103.0	http://www.ncbi.nlm.nih.gov/pubmed?term	214	4.4	1.0	19	dbSNP_86	103	2318,6088		324,1670,2209	yes	missense	MPV17L2	NM_032683.2	21	393,2310,3544	GG,GA,AA	http://www.ncbi.nlm.nih.gov/pubmed?term	27.5755,19.0313,24.7799	benign	72/207	18304700	3096,9398	2044	4203	6247	SO:0001583	missense	84769	exon2			TGCAGCATGGGTC	AK094091	CCDS42522.1	19p13.11	2011-05-26			ENSG00000254858	ENSG00000254858			28177	protein-coding gene	gene with protein product						12477932	Standard	NM_032683		Approved	FKSG24, MGC12972	uc002nid.3	Q567V2	OTTHUMG00000165628	ENST00000599612.2:c.214A>G	19.37:g.18304700A>G	ENSP00000469836:p.Met72Val	Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	155	66	0.425806	NM_032683	Q96P34|Q96QA0|Q9BSG4	Missense_Mutation	SNP	ENST00000599612.2	37	CCDS42522.1	421	0.19276556776556777	94	0.1910569105691057	80	0.22099447513812154	38	0.06643356643356643	209	0.2757255936675462	A	13.44	2.238933	0.39598	0.190313	0.275755	ENSG00000254858	ENST00000534474;ENST00000247712	T;D	0.88586	0.97;-2.4	4.45	4.45	0.53987	.	0.044008	0.85682	D	0.000000	T	0.00039	0.0001	L	0.28014	0.82	0.27925	P	0.9381094	P;B	0.43094	0.799;0.138	P;B	0.48704	0.587;0.082	T	0.48502	-0.9030	9	0.02654	T	1	-38.605	9.8021	0.40770	0.8273:0.1727:0.0:0.0	rs874628;rs52827712;rs59626732;rs874628	8;72	B3KSQ2;Q567V2	.;M17L2_HUMAN	V	72	ENSP00000435162:M72V;ENSP00000247712:M72V	ENSP00000247712:M72V	M	+	1	0	MPV17L2	18165700	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	2.477000	0.45180	1.758000	0.51981	0.260000	0.18958	ATG	A|0.783;G|0.217	0.217	strong		0.602	MPV17L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466294.2	NM_032683	
LILRA6	79168	hgsc.bcm.edu	37	19	54745665	54745665	+	Missense_Mutation	SNP	C	C	T	rs1052966	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:54745665C>T	ENST00000396365.2	-	4	484	c.445G>A	c.(445-447)Gga>Aga	p.G149R	LILRA6_ENST00000245621.5_Missense_Mutation_p.G149R|LILRA6_ENST00000440558.2_Missense_Mutation_p.G149R|LILRA6_ENST00000270464.5_Missense_Mutation_p.G149R|LILRB3_ENST00000407860.2_Intron|LILRA6_ENST00000419410.2_Missense_Mutation_p.G149R|LILRA6_ENST00000391735.3_Missense_Mutation_p.G149R	NM_024318.2	NP_077294	Q6PI73	LIRA6_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 6	149			G -> R (in dbSNP:rs1052966).		immune system process (GO:0002376)	integral component of membrane (GO:0016021)		p.G149R(2)		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)		TGGTGATATCCCTTCTGTGAG	0.582																																					p.G149R		Atlas-SNP	.											LILRA6,NS,carcinoma,+1,4	LILRA6	75	4	2	Substitution - Missense(2)	large_intestine(2)	c.G445A						scavenged	.						25.0	40.0	35.0					19																	54745665		2106	4268	6374	SO:0001583	missense	79168	exon4			GATATCCCTTCTG	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.445G>A	19.37:g.54745665C>T	ENSP00000379651:p.Gly149Arg	Somatic	604	0	0		WXS	Illumina HiSeq	Phase_I	584	93	0.159247	NM_024318		Missense_Mutation	SNP	ENST00000396365.2	37	CCDS42610.1	.	.	.	.	.	.	.	.	.	.	C	12.06	1.825878	0.32237	.	.	ENSG00000244482	ENST00000440558;ENST00000270464;ENST00000419410;ENST00000391735;ENST00000421123;ENST00000396365;ENST00000245621	T;T;T;T;T;T	0.11604	2.76;2.76;2.76;3.85;2.76;2.76	3.1	-6.21	0.02065	Immunoglobulin-like fold (1);	2.192950	0.01626	N	0.023278	T	0.12050	0.0293	L	0.39326	1.205	0.09310	N	1	P;B;P;P;B;P	0.41978	0.64;0.037;0.767;0.555;0.383;0.716	P;B;B;B;B;B	0.47044	0.535;0.085;0.444;0.211;0.344;0.276	T	0.27773	-1.0064	10	0.44086	T	0.13	.	4.765	0.13128	0.0:0.4155:0.3207:0.2638	rs1052966;rs3193450;rs13346484	149;149;149;149;149;149	C9JFH3;Q6PI73-2;Q6PI73;F8WCY4;D3YTC4;F8W6G6	.;.;LIRA6_HUMAN;.;.;.	R	149	ENSP00000390120:G149R;ENSP00000270464:G149R;ENSP00000411227:G149R;ENSP00000375615:G149R;ENSP00000379651:G149R;ENSP00000245621:G149R	ENSP00000245621:G149R	G	-	1	0	LILRA6	59437477	0.000000	0.05858	0.000000	0.03702	0.046000	0.14306	-2.553000	0.00927	-1.315000	0.02297	0.162000	0.16502	GGA	C|0.972;T|0.028	0.028	strong		0.582	LILRA6-003	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000313725.1	NM_024318	
TYMP	1890	hgsc.bcm.edu	37	22	50964236	50964236	+	Missense_Mutation	SNP	G	G	A	rs11479	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:50964236G>A	ENST00000252029.3	-	10	1574	c.1412C>T	c.(1411-1413)tCg>tTg	p.S471L	SCO2_ENST00000543927.1_Intron|CTA-384D8.36_ENST00000608319.1_RNA|TYMP_ENST00000395678.3_Missense_Mutation_p.S471L|SCO2_ENST00000535425.1_Intron|TYMP_ENST00000395680.1_Missense_Mutation_p.S471L|SCO2_ENST00000395693.3_5'Flank|TYMP_ENST00000395681.1_Missense_Mutation_p.S476L|SCO2_ENST00000252785.3_5'Flank	NM_001113755.2|NM_001113756.2|NM_001257988.1|NM_001257989.1|NM_001953.4	NP_001107227.1|NP_001107228.1|NP_001244917.1|NP_001244918.1|NP_001944.1	P19971	TYPH_HUMAN	thymidine phosphorylase	471			S -> L (in dbSNP:rs11479). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:2467210}.		angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|chemotaxis (GO:0006935)|DNA replication (GO:0006260)|mitochondrial genome maintenance (GO:0000002)|nucleobase-containing small molecule metabolic process (GO:0055086)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside catabolic process (GO:0046135)|pyrimidine nucleoside salvage (GO:0043097)|pyrimidine nucleotide metabolic process (GO:0006220)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	phosphorylase activity (GO:0004645)|platelet-derived growth factor receptor binding (GO:0005161)|pyrimidine-nucleoside phosphorylase activity (GO:0016154)|thymidine phosphorylase activity (GO:0009032)|transferase activity, transferring pentosyl groups (GO:0016763)			large_intestine(1)|lung(2)|ovary(1)|prostate(1)	5		all_cancers(38;4.58e-14)|all_epithelial(38;1.12e-12)|all_lung(38;3.07e-05)|Breast(42;6.27e-05)|Lung NSC(38;0.000813)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.206)|LUAD - Lung adenocarcinoma(64;0.247)	Capecitabine(DB01101)|Cidofovir(DB00369)|Floxuridine(DB00322)|Fluorouracil(DB00544)|Trifluridine(DB00432)	TGCGAAGGGCGAGGGGGCGGC	0.711													g|||	715	0.142772	0.0318	0.17	5008	,	,		10052	0.2937		0.0716	False		,,,				2504	0.1912				p.S476L		Atlas-SNP	.											.	TYMP	25	.	0			c.C1427T	GRCh37	CM073022	TYMP	M	rs11479	PASS	.		LEU/SER,LEU/SER,,,LEU/SER	183,3979		0,183,1898	8.0	10.0	9.0		1412,1412,,,1412	2.2	1.0	22	dbSNP_52	9	663,7551		18,627,3462	yes	missense,missense,intron,intron,missense	TYMP,SCO2	NM_001113755.1,NM_001113756.1,NM_001169109.1,NM_001169110.1,NM_001953.3	145,145,,,145	18,810,5360	AA,AG,GG		8.0716,4.3969,6.8358	probably-damaging,probably-damaging,,,probably-damaging	471/483,471/483,,,471/483	50964236	846,11530	2081	4107	6188	SO:0001583	missense	1890	exon10			AAGGGCGAGGGGG	M63193	CCDS14096.1, CCDS58811.1	22q13	2014-09-17	2008-01-21	2008-01-21	ENSG00000025708	ENSG00000025708	2.4.2.4		3148	protein-coding gene	gene with protein product	"""gliostatin"""	131222	"""endothelial cell growth factor 1 (platelet-derived)"""	MNGIE, ECGF1		1590793, 11733540	Standard	NM_001113755		Approved		uc003bme.5	P19971	OTTHUMG00000150249	ENST00000252029.3:c.1412C>T	22.37:g.50964236G>A	ENSP00000252029:p.Ser471Leu	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	93	41	0.44086	NM_001257989	A8MW15|H9KVA0|Q13390|Q8WVB7	Missense_Mutation	SNP	ENST00000252029.3	37	CCDS14096.1	278	0.12728937728937728	14	0.028455284552845527	58	0.16022099447513813	144	0.2517482517482518	62	0.08179419525065963	g	8.982	0.975673	0.18736	0.043969	0.080716	ENSG00000025708	ENST00000395680;ENST00000395681;ENST00000252029;ENST00000395678;ENST00000425169	D;D;D;D;D	0.97529	-1.57;-1.57;-1.57;-1.57;-4.42	2.19	2.19	0.27852	Pyrimidine nucleoside phosphorylase, C-terminal (1);	1.178860	0.06499	U	0.735987	T	0.00109	0.0003	N	0.08118	0	0.38307	P	0.05685499999999999	D;D;D	0.59767	0.986;0.986;0.986	B;B;B	0.34991	0.193;0.193;0.193	T	0.63466	-0.6631	9	0.02654	T	1	-7.7224	7.9411	0.29959	0.0:0.0:1.0:0.0	rs11479;rs3202233;rs3829983;rs17846490;rs17859554	471;471;471	B2RBL3;E5KRG5;P19971	.;.;TYPH_HUMAN	L	471;476;471;471;438	ENSP00000379037:S471L;ENSP00000379038:S476L;ENSP00000252029:S471L;ENSP00000379036:S471L;ENSP00000395875:S438L	ENSP00000252029:S471L	S	-	2	0	TYMP	49311102	0.000000	0.05858	0.996000	0.52242	0.199000	0.23934	-0.219000	0.09228	1.551000	0.49450	0.298000	0.19748	TCG	G|0.877;A|0.123	0.123	strong		0.711	TYMP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317081.1	NM_001953	
TYW1	55253	hgsc.bcm.edu	37	7	66648199	66648199	+	Silent	SNP	G	G	A	rs55756354	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	111	0	0		WXS	Illumina HiSeq	Phase_I	74	32	0.432432	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	
OR52R1	119695	hgsc.bcm.edu	37	11	4825010	4825010	+	Missense_Mutation	SNP	T	T	A	rs6578533	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:4825010T>A	ENST00000356069.2	-	1	600	c.601A>T	c.(601-603)Aat>Tat	p.N201Y	OR52R1_ENST00000380382.1_Missense_Mutation_p.N280Y|MMP26_ENST00000477339.1_Intron|MMP26_ENST00000380390.1_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	73	0	0		WXS	Illumina HiSeq	Phase_I	92	16	0.173913	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	
STK32C	282974	hgsc.bcm.edu	37	10	134040367	134040367	+	Silent	SNP	C	C	T	rs12413251	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:134040367C>T	ENST00000368622.1	-	4	606	c.225G>A	c.(223-225)acG>acA	p.T75T	STK32C_ENST00000368625.4_Silent_p.T205T					serine/threonine kinase 32C											breast(1)|endometrium(2)|large_intestine(2)|lung(15)|ovary(2)|skin(1)	23		all_cancers(35;2.72e-11)|all_epithelial(44;2.33e-08)|Lung NSC(174;0.000855)|all_lung(145;0.00146)|all_neural(114;0.0299)|Breast(234;0.106)|Colorectal(31;0.112)|Melanoma(40;0.124)|Glioma(114;0.203)		Epithelial(32;3.99e-05)|all cancers(32;5.58e-05)|OV - Ovarian serous cystadenocarcinoma(35;9.96e-05)|BRCA - Breast invasive adenocarcinoma(275;0.222)		ACAGCCTCACCGTGTCCTCGG	0.627													C|||	427	0.0852636	0.0242	0.0706	5008	,	,		22499	0.1825		0.0805	False		,,,				2504	0.0828				p.T192T		Atlas-SNP	.											.	STK32C	61	.	0			c.G576A						PASS	.	C		127,4279	93.4+/-132.2	7,113,2083	163.0	111.0	128.0		576	-7.1	0.6	10	dbSNP_120	128	628,7972	163.3+/-215.9	29,570,3701	no	coding-synonymous	STK32C	NM_173575.2		36,683,5784	TT,TC,CC		7.3023,2.8824,5.805		192/487	134040367	755,12251	2203	4300	6503	SO:0001819	synonymous_variant	282974	exon4			CCTCACCGTGTCC	AK057849	CCDS7666.1	10q26.3	2004-07-22			ENSG00000165752	ENSG00000165752			21332	protein-coding gene	gene with protein product							Standard	NM_173575		Approved	PKE, MGC23665, YANK3	uc001lle.1	Q86UX6	OTTHUMG00000019285	ENST00000368622.1:c.225G>A	10.37:g.134040367C>T		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	104	36	0.346154	NM_173575		Silent	SNP	ENST00000368622.1	37		204	0.09340659340659341	9	0.018292682926829267	27	0.07458563535911603	97	0.16958041958041958	71	0.09366754617414248	C	11.47	1.648300	0.29336	0.028824	0.073023	ENSG00000165752	ENST00000368620	.	.	.	4.75	-7.08	0.01558	.	.	.	.	.	T	0.00073	0.0002	.	.	.	0.09310	P	0.999999999999897	.	.	.	.	.	.	T	0.19451	-1.0305	4	0.87932	D	0	.	2.8052	0.05425	0.0896:0.2575:0.2879:0.365	rs12413251	.	.	.	S	263	.	ENSP00000357609:G263S	G	-	1	0	STK32C	133890357	0.000000	0.05858	0.561000	0.28357	0.901000	0.52897	-4.135000	0.00288	-2.113000	0.00833	-0.460000	0.05396	GGT	C|0.932;T|0.068	0.068	strong		0.627	STK32C-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000051068.2	NM_173575	
COL4A1	1282	hgsc.bcm.edu	37	13	110850842	110850842	+	Silent	SNP	A	A	G	rs995224	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	85	0	0		WXS	Illumina HiSeq	Phase_I	86	37	0.430233	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		
MPI	4351	hgsc.bcm.edu	37	15	75189930	75189930	+	Silent	SNP	A	A	G	rs1130741	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:75189930A>G	ENST00000352410.4	+	8	1198	c.1131A>G	c.(1129-1131)gtA>gtG	p.V377V	MPI_ENST00000323744.6_Silent_p.V316V|CTD-2235H24.2_ENST00000564692.1_RNA|MPI_ENST00000566377.1_3'UTR|MPI_ENST00000563786.1_Silent_p.V357V|MPI_ENST00000535694.1_Silent_p.V327V			P34949	MPI_HUMAN	mannose phosphate isomerase	377					cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|GDP-mannose biosynthetic process (GO:0009298)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	mannose-6-phosphate isomerase activity (GO:0004476)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(1)|large_intestine(1)|lung(2)|ovary(2)|upper_aerodigestive_tract(1)	9						AGGGGACAGTAATAGCCAGCA	0.542													A|||	1696	0.338658	0.289	0.5807	5008	,	,		20503	0.2292		0.5109	False		,,,				2504	0.1697				p.V377V		Atlas-SNP	.											.	MPI	32	.	0			c.A1131G						PASS	.	A		1428,2966	464.9+/-354.0	239,950,1008	174.0	142.0	153.0		1131	2.5	1.0	15	dbSNP_86	153	4694,3896	606.3+/-395.1	1295,2104,896	yes	coding-synonymous	MPI	NM_002435.1		1534,3054,1904	GG,GA,AA		45.3551,32.4989,47.1503		377/424	75189930	6122,6862	2197	4295	6492	SO:0001819	synonymous_variant	4351	exon8			GACAGTAATAGCC		CCDS10272.1, CCDS73756.1, CCDS73757.1, CCDS73758.1	15q24.1	2013-09-19			ENSG00000178802	ENSG00000178802	5.3.1.8		7216	protein-coding gene	gene with protein product	"""mannose-6-phosphate isomerase"""	154550					Standard	NM_002435		Approved		uc002azc.1	P34949	OTTHUMG00000142826	ENST00000352410.4:c.1131A>G	15.37:g.75189930A>G		Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	202	201	0.995049	NM_002435	A8K8K9|Q96AB0	Silent	SNP	ENST00000352410.4	37	CCDS10272.1																																																																																			A|0.574;G|0.426	0.426	strong		0.542	MPI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286418.4		
ITFG2	55846	hgsc.bcm.edu	37	12	2930731	2930731	+	Silent	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:2930731C>T	ENST00000228799.2	+	8	955	c.816C>T	c.(814-816)ggC>ggT	p.G272G	ITFG2_ENST00000542548.1_Silent_p.G160G|ITFG2_ENST00000419778.2_Silent_p.G95G	NM_018463.3	NP_060933.3	Q969R8	ITFG2_HUMAN	integrin alpha FG-GAP repeat containing 2	272					germinal center B cell differentiation (GO:0002314)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)				central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(13)|upper_aerodigestive_tract(2)	19			OV - Ovarian serous cystadenocarcinoma(31;0.000818)			AGAGTAGTGGCTCTGGCCTCT	0.607																																					p.G272G		Atlas-SNP	.											.	ITFG2	38	.	0			c.C816T						PASS	.						89.0	78.0	82.0					12																	2930731		2203	4300	6503	SO:0001819	synonymous_variant	55846	exon8			TAGTGGCTCTGGC	AF220048	CCDS8513.1	12p13.33	2006-11-29		2006-07-25	ENSG00000111203	ENSG00000111203			30879	protein-coding gene	gene with protein product						12477932	Standard	NM_018463		Approved	MDS028	uc001qlb.2	Q969R8	OTTHUMG00000130617	ENST00000228799.2:c.816C>T	12.37:g.2930731C>T		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	97	4	0.0412371	NM_018463	A8K4Z5|D3DUQ2|Q6PKU5|Q96SX6	Silent	SNP	ENST00000228799.2	37	CCDS8513.1																																																																																			.	.	none		0.607	ITFG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253091.1	NM_018463	
ZNF460	10794	hgsc.bcm.edu	37	19	57802116	57802116	+	Silent	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:57802116C>T	ENST00000360338.3	+	3	529	c.207C>T	c.(205-207)gcC>gcT	p.A69A	ZNF460_ENST00000537645.1_Silent_p.A28A	NM_006635.3	NP_006626.3	Q14592	ZN460_HUMAN	zinc finger protein 460	69	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)|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)		CTCATCTGGCCTTGCCTGAGG	0.483																																					p.A69A		Atlas-SNP	.											.	ZNF460	59	.	0			c.C207T						PASS	.						71.0	64.0	66.0					19																	57802116		2203	4300	6503	SO:0001819	synonymous_variant	10794	exon3			TCTGGCCTTGCCT	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.207C>T	19.37:g.57802116C>T		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	140	33	0.235714	NM_006635	A4FU64|B4DNX9|Q2VPC7|Q6VSF8	Silent	SNP	ENST00000360338.3	37	CCDS12949.1																																																																																			.	.	none		0.483	ZNF460-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465727.1	NM_006635	
HLA-G	3135	hgsc.bcm.edu	37	6	29797696	29797696	+	Silent	SNP	A	A	G	rs1130363	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:29797696A>G	ENST00000360323.6	+	5	1023	c.999A>G	c.(997-999)agA>agG	p.R333R	HLA-G_ENST00000376818.3_Silent_p.R241R|HLA-G_ENST00000376815.3_Silent_p.R149R|HLA-G_ENST00000428701.1_Silent_p.R333R|HLA-G_ENST00000376828.2_Silent_p.R338R			P17693	HLAG_HUMAN	major histocompatibility complex, class I, G	333					antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular defense response (GO:0006968)|cytokine-mediated signaling pathway (GO:0019221)|immune response-inhibiting cell surface receptor signaling pathway (GO:0002767)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of dendritic cell differentiation (GO:2001199)|negative regulation of T cell proliferation (GO:0042130)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of regulatory T cell differentiation (GO:0045591)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|positive regulation of T cell tolerance induction (GO:0002666)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)	early endosome membrane (GO:0031901)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|membrane (GO:0016020)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	peptide antigen binding (GO:0042605)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)			central_nervous_system(1)|endometrium(1)|large_intestine(5)|lung(4)|ovary(3)|pancreas(1)|prostate(5)|skin(1)	21						TGCTGTGGAGAAAGAAGAGCT	0.567													N|||	2995	0.598043	0.621	0.5548	5008	,	,		20312	0.6101		0.4592	False		,,,				2504	0.728				p.R333R		Atlas-SNP	.											.	HLA-G	90	.	0			c.A999G						PASS	.	G		2670,1736		804,1062,337	79.0	72.0	74.0		999	1.3	0.0	6	dbSNP_86	74	4364,4236		1111,2142,1047	no	coding-synonymous	HLA-G	NM_002127.5		1915,3204,1384	GG,GA,AA		49.2558,39.4008,45.9173		333/339	29797696	7034,5972	2203	4300	6503	SO:0001819	synonymous_variant	3135	exon6			GTGGAGAAAGAAG		CCDS4668.1	6p21.3	2013-01-11	2007-12-12		ENSG00000204632	ENSG00000204632		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4964	protein-coding gene	gene with protein product	"""b2 microglobulin"""	142871	"""HLA-G histocompatibility antigen, class I, G"""				Standard	NM_002127		Approved		uc003nnw.2	P17693	OTTHUMG00000031157	ENST00000360323.6:c.999A>G	6.37:g.29797696A>G		Somatic	112	1	0.00892857		WXS	Illumina HiSeq	Phase_I	76	76	1	NM_002127		Silent	SNP	ENST00000360323.6	37	CCDS4668.1																																																																																			A|0.442;G|0.558	0.558	strong		0.567	HLA-G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076286.2	NM_002127	
LILRB4	11006	hgsc.bcm.edu	37	19	55175009	55175009	+	Missense_Mutation	SNP	G	G	T	rs11540761	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:55175009G>T	ENST00000391736.1	+	4	369	c.54G>T	c.(52-54)agG>agT	p.R18S	LILRB4_ENST00000391734.3_Missense_Mutation_p.R18S|LILRB4_ENST00000391733.3_Missense_Mutation_p.R18S|LILRB4_ENST00000270452.2_Missense_Mutation_p.R18S|LILRB4_ENST00000430952.2_Missense_Mutation_p.R18S	NM_001278426.2|NM_001278428.2|NM_001278429.2|NM_001278430.2	NP_001265355.1|NP_001265357.1|NP_001265358.1|NP_001265359.1	Q8NHJ6	LIRB4_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 4	18			R -> S (in dbSNP:rs11574570).		immune system process (GO:0002376)|negative regulation of osteoclast differentiation (GO:0045671)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	antigen binding (GO:0003823)|receptor activity (GO:0004872)			breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(20)|ovary(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(3)	39				GBM - Glioblastoma multiforme(193;0.035)		TGGGCCCCAGGACCCACATGC	0.592													G|||	979	0.195487	0.2118	0.2032	5008	,	,		12985	0.124		0.1799	False		,,,				2504	0.2577				p.R18S		Atlas-SNP	.											.	LILRB4	86	.	0			c.G54T						PASS	.	G	SER/ARG,SER/ARG	957,3449	359.4+/-314.8	94,769,1340	53.0	59.0	57.0		54,54	1.3	0.0	19	dbSNP_120	57	1598,7002	297.9+/-303.7	156,1286,2858	no	missense,missense	LILRB4	NM_001081438.1,NM_006847.3	110,110	250,2055,4198	TT,TG,GG		18.5814,21.7204,19.6448	possibly-damaging,possibly-damaging	18/448,18/449	55175009	2555,10451	2203	4300	6503	SO:0001583	missense	11006	exon2			CCCCAGGACCCAC	U82979	CCDS12902.1, CCDS42618.1	19q13.4	2013-01-11				ENSG00000186818		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6608	protein-coding gene	gene with protein product		604821				9151699, 9079806	Standard	XM_005277050		Approved	LIR-5, ILT3, HM18, LIR5, CD85k	uc002qgp.3	Q8NHJ6		ENST00000391736.1:c.54G>T	19.37:g.55175009G>T	ENSP00000375616:p.Arg18Ser	Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	195	114	0.584615	NM_006847	A8MVL8|O15468|O75021|Q6FGQ9|Q8N1C7|Q8NHL5	Missense_Mutation	SNP	ENST00000391736.1	37	CCDS12902.1	382	0.1749084249084249	104	0.21138211382113822	58	0.16022099447513813	77	0.1346153846153846	143	0.18865435356200527	G	9.489	1.100156	0.20552	0.217204	0.185814	ENSG00000186818	ENST00000420271;ENST00000391736;ENST00000270452;ENST00000430952;ENST00000391734;ENST00000391733;ENST00000434286	T;T;T;T;T;T	0.00477	7.2;7.2;7.2;7.17;7.22;7.14	2.4	1.28	0.21552	.	.	.	.	.	T	0.00012	0.0000	M	0.87180	2.865	0.80722	P	0.0	B;D;B;B;D	0.89917	0.404;0.963;0.364;0.431;1.0	B;P;B;B;D	0.87578	0.254;0.885;0.341;0.358;0.998	T	0.49234	-0.8961	8	0.21014	T	0.42	.	6.8653	0.24091	0.0:0.2927:0.7073:0.0	rs11574570;rs11574570	18;18;18;18;59	C9JST2;Q8NHJ6-3;Q8NHJ6-2;Q8NHJ6;C9JHA6	.;.;.;LIRB4_HUMAN;.	S	59;18;18;18;18;18;18	ENSP00000375616:R18S;ENSP00000270452:R18S;ENSP00000408995:R18S;ENSP00000375614:R18S;ENSP00000375613:R18S;ENSP00000401962:R18S	ENSP00000270452:R18S	R	+	3	2	LILRB4	59866821	0.001000	0.12720	0.002000	0.10522	0.145000	0.21501	0.498000	0.22530	0.312000	0.23038	0.407000	0.27541	AGG	G|0.810;T|0.190	0.190	strong		0.592	LILRB4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000141127.3		
UNK	85451	hgsc.bcm.edu	37	17	73819525	73819525	+	Silent	SNP	C	C	T	rs8078208	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:73819525C>T	ENST00000589666.1	+	15	2309	c.2199C>T	c.(2197-2199)tcC>tcT	p.S733S	UNK_ENST00000293218.3_Silent_p.S809S	NM_001080419.2	NP_001073888.2	Q9C0B0	UNK_HUMAN	unkempt family zinc finger	733							poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			cervix(3)|endometrium(8)|kidney(2)|large_intestine(5)|lung(3)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	25			all cancers(21;2.61e-06)|Epithelial(20;7.39e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00194)|LUSC - Lung squamous cell carcinoma(166;0.154)			CCGCCTTCTCCGACCTGGAGG	0.667													C|||	2036	0.40655	0.7579	0.2622	5008	,	,		15101	0.4226		0.2266	False		,,,				2504	0.2025				p.S733S		Atlas-SNP	.											UNK_ENST00000293218,NS,carcinoma,0,4	UNK	87	4	0			c.C2199T						PASS	.	C		2510,1374		837,836,269	10.0	14.0	13.0		2199	-9.2	0.0	17	dbSNP_116	13	1830,6388		229,1372,2508	no	coding-synonymous	UNK	NM_001080419.2		1066,2208,2777	TT,TC,CC		22.2682,35.3759,35.8618		733/811	73819525	4340,7762	1942	4109	6051	SO:0001819	synonymous_variant	85451	exon15			CTTCTCCGACCTG	AB051540	CCDS45778.1, CCDS45778.2	17q25.3	2013-10-17	2013-10-17	2007-02-06		ENSG00000132478		"""Zinc fingers, CCCH-type domain containing"""	29369	protein-coding gene	gene with protein product			"""zinc finger CCCH-type domain containing 5"", ""zinc finger CCCH-type containing 5"", ""unkempt homolog (Drosophila)"""	ZC3HDC5, ZC3H5		11214970	Standard	NM_001080419		Approved	KIAA1753	uc021udd.2	Q9C0B0		ENST00000589666.1:c.2199C>T	17.37:g.73819525C>T		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	101	49	0.485149	NM_001080419		Silent	SNP	ENST00000589666.1	37	CCDS45778.2																																																																																			C|0.528;T|0.472	0.472	strong		0.667	UNK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448835.1	NM_001080419	
PCDHB12	56124	hgsc.bcm.edu	37	5	140590139	140590139	+	Missense_Mutation	SNP	G	G	A	rs145232861	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:140590139G>A	ENST00000239450.2	+	1	1849	c.1660G>A	c.(1660-1662)Gcc>Acc	p.A554T	PCDHB12_ENST00000541609.1_Missense_Mutation_p.A217T	NM_018932.3	NP_061755.1	Q9Y5F1	PCDBC_HUMAN	protocadherin beta 12	554	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(10)|large_intestine(17)|lung(38)|ovary(3)|pancreas(1)|prostate(2)|skin(7)|stomach(1)	83			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			GGTGCTGGACGCCAACGACAA	0.711													G|||	11	0.00219649	0.0	0.0014	5008	,	,		16609	0.0		0.0099	False		,,,				2504	0.0				p.A554T		Atlas-SNP	.											.	PCDHB12	179	.	0			c.G1660A						PASS	.	G	THR/ALA	6,4392		0,6,2193	23.0	27.0	26.0		1660	2.5	1.0	5	dbSNP_134	26	29,8559		0,29,4265	no	missense	PCDHB12	NM_018932.3	58	0,35,6458	AA,AG,GG		0.3377,0.1364,0.2695	benign	554/796	140590139	35,12951	2199	4294	6493	SO:0001583	missense	56124	exon1			CTGGACGCCAACG	AF152491	CCDS4254.1	5q31	2010-01-26			ENSG00000120328	ENSG00000120328		"""Cadherins / Protocadherins : Clustered"""	8683	other	protocadherin		606338				10380929	Standard	NM_018932		Approved	PCDH-BETA12	uc003liz.3	Q9Y5F1	OTTHUMG00000129620	ENST00000239450.2:c.1660G>A	5.37:g.140590139G>A	ENSP00000239450:p.Ala554Thr	Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	126	73	0.579365	NM_018932	B4DDU1	Missense_Mutation	SNP	ENST00000239450.2	37	CCDS4254.1	.	.	.	.	.	.	.	.	.	.	G	8.941	0.965816	0.18583	0.001364	0.003377	ENSG00000120328	ENST00000541609;ENST00000239450;ENST00000507840	T;T	0.03181	4.02;4.02	3.41	2.5	0.30297	Cadherin (4);Cadherin conserved site (1);Cadherin-like (1);	.	.	.	.	T	0.02533	0.0077	N	0.13352	0.335	0.09310	N	0.999998	B	0.34015	0.435	B	0.23716	0.048	T	0.46442	-0.9191	9	0.40728	T	0.16	.	12.3896	0.55350	0.0:0.481:0.519:0.0	.	554	Q9Y5F1	PCDBC_HUMAN	T	217;554;174	ENSP00000440199:A217T;ENSP00000239450:A554T	ENSP00000239450:A554T	A	+	1	0	PCDHB12	140570323	0.000000	0.05858	0.953000	0.39169	0.995000	0.86356	0.135000	0.15952	0.525000	0.28522	0.485000	0.47835	GCC	G|0.875;A|0.125	0.125	strong		0.711	PCDHB12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251815.2	NM_018932	
CLEC18B	497190	hgsc.bcm.edu	37	16	74451960	74451960	+	Silent	SNP	C	C	T	rs201007386	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:74451960C>T	ENST00000339953.5	-	3	574	c.453G>A	c.(451-453)acG>acA	p.T151T		NM_001011880.2	NP_001011880.2	Q6UXF7	CL18B_HUMAN	C-type lectin domain family 18, member B	151	SCP.					extracellular region (GO:0005576)	carbohydrate binding (GO:0030246)			endometrium(3)|kidney(9)|large_intestine(3)|lung(7)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	27						CACTCACCTGCGTGTAGTGGG	0.592																																					p.T151T		Atlas-SNP	.											CLEC18B,NS,carcinoma,-1,4	CLEC18B	45	4	0			c.G453A						scavenged	.						8.0	9.0	8.0					16																	74451960		1773	3617	5390	SO:0001819	synonymous_variant	497190	exon3			CACCTGCGTGTAG	AY358373	CCDS32484.1	16q22.3	2010-04-27	2009-03-10	2009-03-10		ENSG00000140839		"""C-type lectin domain containing"""	33849	protein-coding gene	gene with protein product							Standard	NM_001011880		Approved		uc002fct.3	Q6UXF7		ENST00000339953.5:c.453G>A	16.37:g.74451960C>T		Somatic	262	0	0		WXS	Illumina HiSeq	Phase_I	613	58	0.0946166	NM_001011880	B4DF90	Silent	SNP	ENST00000339953.5	37	CCDS32484.1																																																																																			.	.	weak		0.592	CLEC18B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434697.1	NM_001011880	
MUC4	4585	hgsc.bcm.edu	37	3	195509955	195509955	+	Silent	SNP	A	A	C	rs71635078		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195509955A>C	ENST00000463781.3	-	2	8955	c.8496T>G	c.(8494-8496)tcT>tcG	p.S2832S	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Silent_p.S2832S	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		TGACAGGAAGAGAGGTGGCAT	0.592																																					p.S2832S		Atlas-SNP	.											.	MUC4	1505	.	0			c.T8496G						PASS	.						95.0	61.0	71.0					3																	195509955		685	1545	2230	SO:0001819	synonymous_variant	4585	exon2			AGGAAGAGAGGTG	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.8496T>G	3.37:g.195509955A>C		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	152	117	0.769737	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Silent	SNP	ENST00000463781.3	37	CCDS54700.1																																																																																			C|1.000;|0.000	1.000	weak		0.592	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
ZMAT4	79698	hgsc.bcm.edu	37	8	40438757	40438757	+	Missense_Mutation	SNP	T	T	C	rs17851751	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:40438757T>C	ENST00000297737.6	-	6	747	c.601A>G	c.(601-603)Acc>Gcc	p.T201A	ZMAT4_ENST00000315769.7_Missense_Mutation_p.T125A	NM_024645.2	NP_078921.1	Q9H898	ZMAT4_HUMAN	zinc finger, matrin-type 4	201			T -> A (in dbSNP:rs17851751). {ECO:0000269|PubMed:15489334}.			nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			NS(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(4)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	18	Ovarian(28;0.00724)|Colorectal(14;0.0468)	all_cancers(7;0.00936)|all_epithelial(6;3.53e-06)|all_lung(54;0.0318)|Lung NSC(58;0.0919)|Esophageal squamous(32;0.15)|Hepatocellular(245;0.152)	LUSC - Lung squamous cell carcinoma(45;0.00722)			CTGCAGATGGTACATCTGTAA	0.458													T|||	710	0.141773	0.0688	0.2147	5008	,	,		18996	0.002		0.3121	False		,,,				2504	0.1575				p.T201A		Atlas-SNP	.											ZMAT4,NS,adenoma,0,1	ZMAT4	47	1	0			c.A601G						PASS	.	T	ALA/THR,ALA/THR	447,3959	214.8+/-234.0	23,401,1779	206.0	167.0	180.0		373,601	4.5	1.0	8	dbSNP_123	180	2594,6006	419.9+/-353.2	359,1876,2065	yes	missense,missense	ZMAT4	NM_001135731.1,NM_024645.2	58,58	382,2277,3844	CC,CT,TT		30.1628,10.1453,23.3815	benign,benign	125/154,201/230	40438757	3041,9965	2203	4300	6503	SO:0001583	missense	79698	exon6			AGATGGTACATCT	AK023904	CCDS34885.1, CCDS47848.1	8p11.21	2012-10-05	2010-09-15		ENSG00000165061	ENSG00000165061		"""Zinc fingers, matrin-type"""	25844	protein-coding gene	gene with protein product						12477932	Standard	NM_024645		Approved	FLJ13842	uc003xnr.3	Q9H898	OTTHUMG00000164049	ENST00000297737.6:c.601A>G	8.37:g.40438757T>C	ENSP00000297737:p.Thr201Ala	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	71	10	0.140845	NM_024645	Q8WUT8	Missense_Mutation	SNP	ENST00000297737.6	37	CCDS34885.1	336	0.15384615384615385	37	0.07520325203252033	68	0.1878453038674033	0	0.0	231	0.30474934036939316	T	13.31	2.198852	0.38806	0.101453	0.301628	ENSG00000165061	ENST00000315769;ENST00000297737;ENST00000519406	T;T;T	0.41065	2.01;2.01;1.01	5.65	4.49	0.54785	Zinc finger, C2H2-like (1);Zinc finger, U1-type (1);Zinc finger, C2H2 (1);	0.473547	0.25352	N	0.031295	T	0.00012	0.0000	L	0.27053	0.805	0.38791	P	0.04502099999999998	B;B	0.20671	0.001;0.047	B;B	0.22386	0.001;0.039	T	0.35724	-0.9777	9	0.24483	T	0.36	-27.2282	9.5492	0.39299	0.0:0.0828:0.0:0.9172	rs17851751;rs17851751	125;201	Q9H898-2;Q9H898	.;ZMAT4_HUMAN	A	125;201;201	ENSP00000319785:T125A;ENSP00000297737:T201A;ENSP00000428423:T201A	ENSP00000297737:T201A	T	-	1	0	ZMAT4	40557914	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.601000	0.46249	0.971000	0.38288	0.533000	0.62120	ACC	T|0.790;C|0.210	0.210	strong		0.458	ZMAT4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376950.1	NM_024645	
LAMA5	3911	hgsc.bcm.edu	37	20	60901762	60901762	+	Missense_Mutation	SNP	C	C	T	rs11699758	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:60901762C>T	ENST00000252999.3	-	40	5335	c.5269G>A	c.(5269-5271)Gtt>Att	p.V1757I		NM_005560.3	NP_005551.3	O15230	LAMA5_HUMAN	laminin, alpha 5	1757	Laminin IV type A. {ECO:0000255|PROSITE- ProRule:PRU00458}.				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)			CCACGGTGAACGTGGCCAGGC	0.657													C|||	73	0.0145767	0.0121	0.0231	5008	,	,		18170	0.0		0.0368	False		,,,				2504	0.0041				p.V1757I		Atlas-SNP	.											.	LAMA5	268	.	0			c.G5269A						PASS	.	C	ILE/VAL	99,4307	79.3+/-117.8	2,95,2106	71.0	54.0	60.0		5269	-1.0	0.0	20	dbSNP_120	60	254,8344	99.0+/-160.6	3,248,4048	yes	missense	LAMA5	NM_005560.3	29	5,343,6154	TT,TC,CC		2.9542,2.2469,2.7145	benign	1757/3696	60901762	353,12651	2203	4299	6502	SO:0001583	missense	3911	exon40			GGTGAACGTGGCC	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.5269G>A	20.37:g.60901762C>T	ENSP00000252999:p.Val1757Ile	Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	144	79	0.548611	NM_005560	Q8TDF8|Q8WZA7|Q9H1P1	Missense_Mutation	SNP	ENST00000252999.3	37	CCDS33502.1	42	0.019230769230769232	8	0.016260162601626018	14	0.03867403314917127	0	0.0	20	0.026385224274406333	C	0.464	-0.887824	0.02511	0.022469	0.029542	ENSG00000130702	ENST00000252999	T	0.36157	1.27	5.12	-1.04	0.10068	Laminin B type IV (2);Laminin B, subgroup (1);	0.497398	0.22077	N	0.064941	T	0.03915	0.0110	N	0.17474	0.49	0.09310	N	1	B	0.13145	0.007	B	0.10450	0.005	T	0.13953	-1.0490	10	0.25106	T	0.35	.	7.414	0.27034	0.0:0.4374:0.2158:0.3468	rs11699758	1757	O15230	LAMA5_HUMAN	I	1757	ENSP00000252999:V1757I	ENSP00000252999:V1757I	V	-	1	0	LAMA5	60335157	0.000000	0.05858	0.001000	0.08648	0.003000	0.03518	-0.028000	0.12350	-0.054000	0.13266	-0.355000	0.07637	GTT	C|0.974;T|0.026	0.026	strong		0.657	LAMA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080014.2	NM_005560	
PROSER1	80209	hgsc.bcm.edu	37	13	39587166	39587166	+	Silent	SNP	A	A	G	rs11147745	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:39587166A>G	ENST00000352251.3	-	11	3056	c.2223T>C	c.(2221-2223)ccT>ccC	p.P741P	PROSER1_ENST00000350125.3_Silent_p.P719P|PROSER1_ENST00000484434.3_Intron	NM_025138.4	NP_079414.3	Q86XN7	PRSR1_HUMAN	proline and serine rich 1	741	Ser-rich.																CCGTTGAGCTAGGATGAGGGA	0.527													G|||	1236	0.246805	0.3336	0.1643	5008	,	,		20634	0.2183		0.162	False		,,,				2504	0.3047				p.P741P		Atlas-SNP	.											.	.	.	.	0			c.T2223C						PASS	.	G	,	1472,2934	678.7+/-403.6	230,1012,961	150.0	162.0	158.0		2223,2157	-9.9	0.0	13	dbSNP_120	158	1210,7390	762.9+/-407.6	92,1026,3182	no	coding-synonymous,coding-synonymous	PROSER1	NM_025138.3,NM_170719.2	,	322,2038,4143	GG,GA,AA		14.0698,33.409,20.6213	,	741/945,719/923	39587166	2682,10324	2203	4300	6503	SO:0001819	synonymous_variant	80209	exon11			TGAGCTAGGATGA	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.2223T>C	13.37:g.39587166A>G		Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	141	66	0.468085	NM_025138	A6NJ97|Q6P2S2|Q7Z3X5|Q8N3D2|Q8N3P1|Q9H9M1	Silent	SNP	ENST00000352251.3	37	CCDS9368.2																																																																																			A|0.781;G|0.219	0.219	strong		0.527	PROSER1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044607.5	NM_025138	
HIST1H1D	3007	hgsc.bcm.edu	37	6	26234883	26234883	+	Silent	SNP	A	A	G	rs2050950	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:26234883A>G	ENST00000244534.5	-	1	333	c.279T>C	c.(277-279)acT>acC	p.T93T		NM_005320.2	NP_005311.1	P16402	H13_HUMAN	histone cluster 1, H1d	93	H15. {ECO:0000255|PROSITE- ProRule:PRU00837}.				nucleosome assembly (GO:0006334)|nucleosome positioning (GO:0016584)	nuclear chromatin (GO:0000790)|nuclear euchromatin (GO:0005719)|nucleosome (GO:0000786)	chromatin DNA binding (GO:0031490)|poly(A) RNA binding (GO:0044822)	p.T93fs*35(1)		breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(5)|large_intestine(4)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	23		all_hematologic(11;0.0945)|Acute lymphoblastic leukemia(11;0.167)				TCTGCACCAGAGTACCTTTGC	0.542													G|||	842	0.168131	0.2262	0.111	5008	,	,		17770	0.1012		0.1571	False		,,,				2504	0.2106				p.T93T		Atlas-SNP	.											.	HIST1H1D	40	.	1	Deletion - Frameshift(1)	endometrium(1)	c.T279C						PASS	.	G		851,3555		77,697,1429	100.0	107.0	105.0		279	2.5	0.9	6	dbSNP_94	105	1155,7445		70,1015,3215	no	coding-synonymous	HIST1H1D	NM_005320.2		147,1712,4644	GG,GA,AA		13.4302,19.3146,15.4237		93/222	26234883	2006,11000	2203	4300	6503	SO:0001819	synonymous_variant	3007	exon1			CACCAGAGTACCT	M60747	CCDS4597.1	6p21.3	2012-10-02	2006-10-11	2003-02-21	ENSG00000124575	ENSG00000124575		"""Histones / Replication-dependent"""	4717	protein-coding gene	gene with protein product		142210	"""H1 histone family, member 3"", ""histone 1, H1d"""	H1F3		1916825, 12408966	Standard	NM_005320		Approved	H1.3, H1d, H1s-2	uc003nhd.3	P16402	OTTHUMG00000014432	ENST00000244534.5:c.279T>C	6.37:g.26234883A>G		Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	155	66	0.425806	NM_005320	B2R751|Q2M2I2	Silent	SNP	ENST00000244534.5	37	CCDS4597.1																																																																																			A|0.854;G|0.146	0.146	strong		0.542	HIST1H1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040095.1	NM_005320	
CDHR3	222256	hgsc.bcm.edu	37	7	105636765	105636765	+	Silent	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:105636765C>T	ENST00000317716.9	+	6	758	c.678C>T	c.(676-678)atC>atT	p.I226I	CDHR3_ENST00000478080.1_Silent_p.I138I|CDHR3_ENST00000542731.1_Silent_p.I226I|CDHR3_ENST00000470188.1_Intron|CDHR3_ENST00000541203.1_Intron|CDHR3_ENST00000343407.5_5'UTR	NM_152750.4	NP_689963.2	Q6ZTQ4	CDHR3_HUMAN	cadherin-related family member 3	226	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(1)|cervix(3)|endometrium(1)|kidney(1)|large_intestine(1)|lung(15)|ovary(1)	23						AGGTGAACATCGTGAACCTCA	0.587																																					p.I226I		Atlas-SNP	.											.	CDHR3	153	.	0			c.C678T						PASS	.						41.0	44.0	43.0					7																	105636765		2011	4165	6176	SO:0001819	synonymous_variant	222256	exon6			GAACATCGTGAAC	AK126338	CCDS47684.1, CCDS75651.1	7q22.2	2011-07-01			ENSG00000128536	ENSG00000128536		"""Cadherins / Cadherin-related"""	26308	protein-coding gene	gene with protein product		615610					Standard	NM_152750		Approved	FLJ44366, FLJ23834, CDH28	uc003vdl.4	Q6ZTQ4	OTTHUMG00000157520	ENST00000317716.9:c.678C>T	7.37:g.105636765C>T		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	51	4	0.0784314	NM_152750	Q8TCI7	Silent	SNP	ENST00000317716.9	37	CCDS47684.1																																																																																			.	.	none		0.587	CDHR3-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000349025.2	NM_152750	
TTC39A	22996	hgsc.bcm.edu	37	1	51753904	51753904	+	Silent	SNP	G	G	A	rs17392930	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:51753904G>A	ENST00000447632.2	-	18	1815	c.1767C>T	c.(1765-1767)atC>atT	p.I589I	TTC39A_ENST00000534098.1_5'UTR|TTC39A_ENST00000413473.2_Silent_p.I557I|TTC39A_ENST00000530004.1_Silent_p.I197I|TTC39A_ENST00000371750.5_Silent_p.I554I|TTC39A_ENST00000451380.1_Silent_p.I553I|TTC39A_ENST00000262675.7_Silent_p.I526I			Q5SRH9	TT39A_HUMAN	tetratricopeptide repeat domain 39A	589								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						TGGCTGCCTGGATTCGAAAGT	0.517													G|||	102	0.0203674	0.0008	0.0159	5008	,	,		21285	0.0		0.0567	False		,,,				2504	0.0337				p.I557I		Atlas-SNP	.											.	TTC39A	40	.	2	Whole gene deletion(2)	thyroid(1)|central_nervous_system(1)	c.C1671T						PASS	.	G	,	50,4132		0,50,2041	201.0	209.0	206.0		1662,1671	5.6	1.0	1	dbSNP_123	206	426,8024		14,398,3813	no	coding-synonymous,coding-synonymous	TTC39A	NM_001080494.2,NM_001144832.1	,	14,448,5854	AA,AG,GG		5.0414,1.1956,3.7682	,	554/579,557/582	51753904	476,12156	2091	4225	6316	SO:0001819	synonymous_variant	22996	exon18			TGCCTGGATTCGA	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.1767C>T	1.37:g.51753904G>A		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	79	44	0.556962	NM_001144832	B7Z782|E7EQY9|G3XAF8|O43417|O75040|Q5SRH5|Q5SRH6|Q5SRH7|Q5SRH8|Q5SRI0|Q5SRI1|Q5SRI2|Q5T7S1|Q6PIU8|Q9BT24	Silent	SNP	ENST00000447632.2	37																																																																																				A|0.028;C|0.000;G|0.971	0.028	strong		0.517	TTC39A-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000022434.2		
NUDCD3	23386	hgsc.bcm.edu	37	7	44444122	44444122	+	Missense_Mutation	SNP	G	G	A	rs11550029	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:44444122G>A	ENST00000355451.7	-	4	982	c.703C>T	c.(703-705)Cgc>Tgc	p.R235C	NUDCD3_ENST00000460110.1_5'UTR	NM_015332.3	NP_056147.2	Q8IVD9	NUDC3_HUMAN	NudC domain containing 3	235	CS. {ECO:0000255|PROSITE- ProRule:PRU00547}.		R -> C (in dbSNP:rs11550029). {ECO:0000269|PubMed:15489334}.							endometrium(2)|large_intestine(1)|lung(3)|skin(1)	7						ATGAGGACGCGCTCCCCATTT	0.552													G|||	359	0.0716853	0.0174	0.0807	5008	,	,		19407	0.005		0.165	False		,,,				2504	0.1115				p.R235C		Atlas-SNP	.											NUDCD3,NS,carcinoma,0,1	NUDCD3	20	1	0			c.C703T						PASS	.	G	CYS/ARG	198,4208	123.3+/-160.7	4,190,2009	123.0	114.0	117.0		703	5.4	1.0	7	dbSNP_120	117	1602,6998	299.4+/-304.4	154,1294,2852	yes	missense	NUDCD3	NM_015332.3	180	158,1484,4861	AA,AG,GG		18.6279,4.4939,13.8398	probably-damaging	235/362	44444122	1800,11206	2203	4300	6503	SO:0001583	missense	23386	exon4			GGACGCGCTCCCC	BC003691	CCDS5490.2	7p13-p12	2005-03-18			ENSG00000015676	ENSG00000015676			22208	protein-coding gene	gene with protein product		610296					Standard	NM_015332		Approved	KIAA1068	uc003tkz.3	Q8IVD9	OTTHUMG00000129174	ENST00000355451.7:c.703C>T	7.37:g.44444122G>A	ENSP00000347626:p.Arg235Cys	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	69	52	0.753623	NM_015332	Q9BTI3|Q9H7W9|Q9UPT4	Missense_Mutation	SNP	ENST00000355451.7	37	CCDS5490.2	168	0.07692307692307693	6	0.012195121951219513	38	0.10497237569060773	4	0.006993006993006993	120	0.158311345646438	G	17.86	3.492703	0.64074	0.044939	0.186279	ENSG00000015676	ENST00000355451	T	0.14516	2.5	5.39	5.39	0.77823	CS-like domain (1);CS domain (1);HSP20-like chaperone (1);	0.253930	0.43919	D	0.000502	T	0.00039	0.0001	L	0.42245	1.32	0.18873	P	0.9999869917	B	0.20052	0.041	B	0.31191	0.125	T	0.27020	-1.0086	9	0.56958	D	0.05	-17.9805	18.7517	0.91818	0.0:0.0:1.0:0.0	rs11550029;rs17655076;rs17853368;rs52835525;rs11550029	235	Q8IVD9	NUDC3_HUMAN	C	235	ENSP00000347626:R235C	ENSP00000347626:R235C	R	-	1	0	NUDCD3	44410647	1.000000	0.71417	0.987000	0.45799	0.965000	0.64279	5.089000	0.64492	2.519000	0.84933	0.561000	0.74099	CGC	G|0.890;A|0.110	0.110	strong		0.552	NUDCD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251248.3	NM_015332	
EFCAB14	9813	hgsc.bcm.edu	37	1	47152515	47152515	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:47152515T>C	ENST00000371933.3	-	8	1991	c.1015A>G	c.(1015-1017)Aga>Gga	p.R339G	EFCAB14_ENST00000484461.1_5'UTR|EFCAB14-AS1_ENST00000418985.1_RNA|EFCAB14_ENST00000544071.1_Missense_Mutation_p.R275G|EFCAB14-AS1_ENST00000442839.1_RNA	NM_014774.2	NP_055589.1	O75071	EFC14_HUMAN	EF-hand calcium binding domain 14	339							calcium ion binding (GO:0005509)										AAAGACTGTCTTTTCAGAGTG	0.363																																					p.R339G		Atlas-SNP	.											KIAA0494,colon,carcinoma,+1,1	.	.	1	0			c.A1015G						scavenged	.						217.0	196.0	204.0					1																	47152515		2203	4300	6503	SO:0001583	missense	9813	exon8			ACTGTCTTTTCAG	AB007963	CCDS30706.1	1p33	2013-01-10	2012-11-29	2012-11-29	ENSG00000159658	ENSG00000159658		"""EF-hand domain containing"""	29051	protein-coding gene	gene with protein product			"""KIAA0494"""	KIAA0494		9455484	Standard	NM_014774		Approved		uc001cqk.4	O75071	OTTHUMG00000007992	ENST00000371933.3:c.1015A>G	1.37:g.47152515T>C	ENSP00000361001:p.Arg339Gly	Somatic	249	0	0		WXS	Illumina HiSeq	Phase_I	191	3	0.0157068	NM_014774	D3DQ23|Q5SXB8	Missense_Mutation	SNP	ENST00000371933.3	37	CCDS30706.1	.	.	.	.	.	.	.	.	.	.	T	13.04	2.117969	0.37339	.	.	ENSG00000159658	ENST00000544071;ENST00000371933	D;D	0.94931	-3.56;-3.48	5.65	4.5	0.54988	.	0.445742	0.22708	N	0.056604	D	0.91418	0.7292	L	0.53249	1.67	0.20403	N	0.999906	B;B;B;B	0.10296	0.003;0.002;0.002;0.001	B;B;B;B	0.11329	0.001;0.006;0.006;0.001	T	0.82589	-0.0382	10	0.37606	T	0.19	-5.8736	9.555	0.39332	0.0:0.0:0.1769:0.8231	.	131;275;275;339	B7Z3D1;F5H7K3;B7Z444;O75071	.;.;.;K0494_HUMAN	G	275;339	ENSP00000442465:R275G;ENSP00000361001:R339G	ENSP00000361001:R339G	R	-	1	2	KIAA0494	46925102	0.998000	0.40836	1.000000	0.80357	0.961000	0.63080	0.162000	0.16501	1.120000	0.41904	0.533000	0.62120	AGA	.	.	none		0.363	EFCAB14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021931.1	NM_014774	
POM121L12	285877	hgsc.bcm.edu	37	7	53103382	53103382	+	Silent	SNP	G	G	T	rs72598685	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:53103382G>T	ENST00000408890.4	+	1	34	c.18G>T	c.(16-18)ccG>ccT	p.P6P		NM_182595.3	NP_872401.3	Q8N7R1	P1L12_HUMAN	POM121 transmembrane nucleoporin-like 12	6										endometrium(5)|kidney(1)|large_intestine(5)|lung(44)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	61						CTGCAGCTCCGGCCGAGTCCG	0.701													G|||	1517	0.302915	0.1392	0.2349	5008	,	,		13789	0.4325		0.2853	False		,,,				2504	0.4571				p.P6P		Atlas-SNP	.											.	POM121L12	146	.	0			c.G18T						PASS	.	G		550,3462		41,468,1497	7.0	10.0	9.0		18	-2.9	0.0	7	dbSNP_130	9	2020,6212		248,1524,2344	no	coding-synonymous	POM121L12	NM_182595.3		289,1992,3841	TT,TG,GG		24.5384,13.7089,20.9899		6/297	53103382	2570,9674	2006	4116	6122	SO:0001819	synonymous_variant	285877	exon1			AGCTCCGGCCGAG		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.18G>T	7.37:g.53103382G>T		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	60	27	0.45	NM_182595	Q8NDI9	Silent	SNP	ENST00000408890.4	37	CCDS43584.1																																																																																			G|0.718;T|0.282	0.282	strong		0.701	POM121L12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342656.1	NM_182595	
CCDC88C	440193	hgsc.bcm.edu	37	14	91773568	91773568	+	Silent	SNP	T	T	C	rs1970912	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:91773568T>C	ENST00000389857.6	-	18	3095	c.3009A>G	c.(3007-3009)ctA>ctG	p.L1003L		NM_001080414.3	NP_001073883.2	Q9P219	DAPLE_HUMAN	coiled-coil domain containing 88C	1003					protein destabilization (GO:0031648)|protein homooligomerization (GO:0051260)|regulation of protein phosphorylation (GO:0001932)|Wnt signaling pathway (GO:0016055)		PDZ domain binding (GO:0030165)|protein self-association (GO:0043621)			central_nervous_system(3)|endometrium(2)|kidney(3)|large_intestine(2)|lung(6)|ovary(6)|pancreas(1)|urinary_tract(1)	24		all_cancers(154;0.0468)				ACTCCTTCTTTAGCTACAGGT	0.602													C|||	2406	0.480431	0.5522	0.4914	5008	,	,		18579	0.3552		0.5994	False		,,,				2504	0.3824				p.L1003L		Atlas-SNP	.											.	CCDC88C	192	.	0			c.A3009G						PASS	.	C		2299,1741		642,1015,363	47.0	49.0	48.0		3009	2.1	0.1	14	dbSNP_92	48	4874,3466		1434,2006,730	no	coding-synonymous	CCDC88C	NM_001080414.3		2076,3021,1093	CC,CT,TT		41.5588,43.0941,42.0598		1003/2029	91773568	7173,5207	2020	4170	6190	SO:0001819	synonymous_variant	440193	exon18			CTTCTTTAGCTAC		CCDS45151.1	14q32.12	2014-07-30	2007-05-31	2007-05-31		ENSG00000015133			19967	protein-coding gene	gene with protein product	"""Dvl-associating protein with a high frequency of leucine residues"", ""spinocerebellar ataxia 40"""	611204	"""KIAA1509"""	KIAA1509		17185515, 25062847	Standard	NM_001080414		Approved	DAPLE, HkRP2, SCA40	uc010aty.3	Q9P219		ENST00000389857.6:c.3009A>G	14.37:g.91773568T>C		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	31	16	0.516129	NM_001080414	Q69YK1|Q7L1M2|Q86SX7|Q8IYG8	Silent	SNP	ENST00000389857.6	37	CCDS45151.1																																																																																			C|0.517;N|0.000	0.517	strong		0.602	CCDC88C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411650.1	XM_029353	
SLC13A1	6561	hgsc.bcm.edu	37	7	122809234	122809234	+	Missense_Mutation	SNP	T	T	C	rs2140516	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:122809234T>C	ENST00000194130.2	-	4	560	c.521A>G	c.(520-522)aAc>aGc	p.N174S	SLC13A1_ENST00000539873.1_Missense_Mutation_p.N110S	NM_022444.3	NP_071889.2	Q9BZW2	S13A1_HUMAN	solute carrier family 13 (sodium/sulfate symporter), member 1	174			N -> S (in dbSNP:rs2140516).		transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sodium:sulfate symporter activity (GO:0015382)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|lung(20)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	45					Succinic acid(DB00139)	GGTTGATCCGTTGAAGTAAGT	0.478													T|||	1377	0.27496	0.2375	0.1988	5008	,	,		18537	0.3522		0.337	False		,,,				2504	0.2362				p.N174S		Atlas-SNP	.											SLC13A1,NS,meningioma,0,1	SLC13A1	110	1	0			c.A521G						PASS	.	T	SER/ASN	1220,3186	423.6+/-340.2	178,864,1161	201.0	160.0	174.0		521	-4.7	0.0	7	dbSNP_96	174	2710,5890	433.4+/-357.4	439,1832,2029	yes	missense	SLC13A1	NM_022444.3	46	617,2696,3190	CC,CT,TT		31.5116,27.6895,30.2168	benign	174/596	122809234	3930,9076	2203	4300	6503	SO:0001583	missense	6561	exon4			GATCCGTTGAAGT		CCDS5786.1	7q31.32	2013-07-18	2013-07-18		ENSG00000081800	ENSG00000081800		"""Solute carriers"""	10916	protein-coding gene	gene with protein product		606193	"""solute carrier family 13 (sodium/sulphate symporters), member 1"""			11161786	Standard	NM_022444		Approved	NaSi-1, NAS1	uc003vkm.3	Q9BZW2	OTTHUMG00000157087	ENST00000194130.2:c.521A>G	7.37:g.122809234T>C	ENSP00000194130:p.Asn174Ser	Somatic	230	0	0		WXS	Illumina HiSeq	Phase_I	187	100	0.534759	NM_022444	Q9H5Z0	Missense_Mutation	SNP	ENST00000194130.2	37	CCDS5786.1	670	0.3067765567765568	124	0.25203252032520324	81	0.22375690607734808	219	0.38286713286713286	246	0.3245382585751979	T	2.341	-0.351029	0.05173	0.276895	0.315116	ENSG00000081800	ENST00000194130;ENST00000539873	T;T	0.65732	-0.17;1.92	5.3	-4.68	0.03309	.	0.851968	0.10200	N	0.703502	T	0.00012	0.0000	N	0.17474	0.49	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.12156	0.007	T	0.30357	-0.9981	9	0.08837	T	0.75	-17.0782	7.0619	0.25131	0.0:0.3285:0.2197:0.4518	rs2140516;rs3779265;rs10342943;rs17145433;rs52789363;rs58242429;rs2140516	174	Q9BZW2	S13A1_HUMAN	S	174;110	ENSP00000194130:N174S;ENSP00000441309:N110S	ENSP00000194130:N174S	N	-	2	0	SLC13A1	122596470	0.000000	0.05858	0.001000	0.08648	0.090000	0.18270	-0.434000	0.06939	-0.774000	0.04590	-0.350000	0.07774	AAC	A|0.003;C|0.297	0.297	strong		0.478	SLC13A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347404.1	NM_022444	
CTNNA1	1495	hgsc.bcm.edu	37	5	138266546	138266546	+	Silent	SNP	G	G	A	rs1059110	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:138266546G>A	ENST00000302763.7	+	16	2310	c.2220G>A	c.(2218-2220)tcG>tcA	p.S740S	CTNNA1_ENST00000518825.1_Silent_p.S740S|CTNNA1_ENST00000540387.1_Silent_p.S370S|CTNNA1_ENST00000355078.5_Silent_p.S637S	NM_001903.2	NP_001894.2	P35221	CTNA1_HUMAN	catenin (cadherin-associated protein), alpha 1, 102kDa	740					adherens junction organization (GO:0034332)|aging (GO:0007568)|apical junction assembly (GO:0043297)|axon regeneration (GO:0031103)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|cellular protein localization (GO:0034613)|cellular response to indole-3-methanol (GO:0071681)|epithelial cell-cell adhesion (GO:0090136)|establishment or maintenance of cell polarity (GO:0007163)|gap junction assembly (GO:0016264)|male gonad development (GO:0008584)|muscle cell differentiation (GO:0042692)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell motility (GO:2000146)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of integrin-mediated signaling pathway (GO:2001045)|negative regulation of neuroblast proliferation (GO:0007406)|odontogenesis of dentin-containing tooth (GO:0042475)|ovarian follicle development (GO:0001541)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of smoothened signaling pathway (GO:0045880)|protein heterooligomerization (GO:0051291)|response to estrogen (GO:0043627)	acrosomal vesicle (GO:0001669)|actin cytoskeleton (GO:0015629)|catenin complex (GO:0016342)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|intercalated disc (GO:0014704)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|zonula adherens (GO:0005915)	beta-catenin binding (GO:0008013)|cadherin binding (GO:0045296)|gamma-catenin binding (GO:0045295)|poly(A) RNA binding (GO:0044822)|structural molecule activity (GO:0005198)|vinculin binding (GO:0017166)			NS(1)|breast(7)|cervix(2)|endometrium(4)|kidney(6)|large_intestine(16)|lung(9)|oesophagus(2)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)	52			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			AAAATACATCGGATGTCATCA	0.463													A|||	1247	0.249002	0.4259	0.2695	5008	,	,		20368	0.0079		0.2714	False		,,,				2504	0.2209				p.S740S		Atlas-SNP	.											.	CTNNA1	114	.	0			c.G2220A						PASS	.	A		1797,2609	641.3+/-397.4	345,1107,751	85.0	87.0	86.0		2220	-2.0	1.0	5	dbSNP_86	86	2557,6043	691.9+/-404.5	371,1815,2114	no	coding-synonymous	CTNNA1	NM_001903.2		716,2922,2865	AA,AG,GG		29.7326,40.7853,33.4769		740/907	138266546	4354,8652	2203	4300	6503	SO:0001819	synonymous_variant	1495	exon16			TACATCGGATGTC	D13866	CCDS34243.1, CCDS75315.1	5q31.2	2008-02-05	2002-08-29			ENSG00000044115			2509	protein-coding gene	gene with protein product		116805	"""catenin (cadherin-associated protein), alpha 1 (102kD)"""			1924379	Standard	XM_005271898		Approved	CAP102	uc003ldh.3	P35221		ENST00000302763.7:c.2220G>A	5.37:g.138266546G>A		Somatic	207	1	0.00483092		WXS	Illumina HiSeq	Phase_I	171	84	0.491228	NM_001903	Q12795|Q8N1C0	Silent	SNP	ENST00000302763.7	37	CCDS34243.1																																																																																			G|0.693;A|0.307	0.307	strong		0.463	CTNNA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373868.1	NM_001903	
APOL5	80831	hgsc.bcm.edu	37	22	36122930	36122930	+	Missense_Mutation	SNP	C	C	T	rs2076671	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:36122930C>T	ENST00000249044.2	+	3	815	c.815C>T	c.(814-816)aCg>aTg	p.T272M		NM_030642.1	NP_085145.1	Q9BWW9	APOL5_HUMAN	apolipoprotein L, 5	272			T -> M (in dbSNP:rs2076671).		lipid metabolic process (GO:0006629)|lipid transport (GO:0006869)|lipoprotein metabolic process (GO:0042157)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)	high-density lipoprotein particle binding (GO:0008035)|lipid binding (GO:0008289)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(6)|skin(2)|urinary_tract(1)	19						CCTTTCTGGACGGCTAGAGGG	0.527													G|||	1935	0.386382	0.32	0.2349	5008	,	,		18520	0.5962		0.2903	False		,,,				2504	0.4663				p.T272M		Atlas-SNP	.											.	APOL5	45	.	0			c.C815T						PASS	.	G	MET/THR	1410,2996		245,920,1038	139.0	146.0	144.0		815	-0.3	0.0	22	dbSNP_96	144	2663,5937		437,1789,2074	yes	missense	APOL5	NM_030642.1	81	682,2709,3112	TT,TC,CC		30.9651,32.0018,31.3163	probably-damaging	272/434	36122930	4073,8933	2203	4300	6503	SO:0001583	missense	80831	exon3			TCTGGACGGCTAG	AY014878	CCDS13920.1	22q12.3	2013-01-24			ENSG00000128313	ENSG00000128313		"""Apolipoproteins"""	14869	protein-coding gene	gene with protein product		607255				11374903	Standard	NM_030642		Approved	APOLV	uc003aof.3	Q9BWW9	OTTHUMG00000150588	ENST00000249044.2:c.815C>T	22.37:g.36122930C>T	ENSP00000249044:p.Thr272Met	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	128	62	0.484375	NM_030642	Q5TFL9|Q9UGW5	Missense_Mutation	SNP	ENST00000249044.2	37	CCDS13920.1	796	0.36446886446886445	156	0.3170731707317073	89	0.24585635359116023	335	0.5856643356643356	216	0.2849604221635884	G	18.41	3.617524	0.66787	0.320018	0.309651	ENSG00000128313	ENST00000249044	T	0.03607	3.87	3.8	-0.258	0.12975	.	2.147360	0.02570	U	0.097668	T	0.00012	0.0000	N	0.24115	0.695	0.80722	P	0.0	P	0.45283	0.855	B	0.35770	0.21	T	0.40515	-0.9559	9	0.62326	D	0.03	.	2.6112	0.04891	0.1212:0.2999:0.4272:0.1518	rs2076671;rs52791490;rs57567438;rs2076671	272	Q9BWW9	APOL5_HUMAN	M	272	ENSP00000249044:T272M	ENSP00000249044:T272M	T	+	2	0	APOL5	34452876	0.008000	0.16893	0.000000	0.03702	0.009000	0.06853	0.057000	0.14279	-0.784000	0.04528	-1.137000	0.01932	ACG	C|0.663;T|0.337	0.337	strong		0.527	APOL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318979.1	NM_030642	
PRPF19	27339	hgsc.bcm.edu	37	11	60666341	60666341	+	Silent	SNP	G	G	A	rs3763840	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:60666341G>A	ENST00000227524.4	-	12	1252	c.1047C>T	c.(1045-1047)tcC>tcT	p.S349S		NM_014502.4	NP_055317.1			pre-mRNA processing factor 19											haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(10)|ovary(1)|prostate(1)|urinary_tract(1)	22						TACAGCAGCCGGAGGTCTCAT	0.393											OREG0020994	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	g|||	1545	0.308506	0.1422	0.3905	5008	,	,		19784	0.3194		0.3887	False		,,,				2504	0.3814				p.S349S		Atlas-SNP	.											.	PRPF19	62	.	0			c.C1047T						PASS	.	A		808,3598		68,672,1463	21.0	19.0	20.0		1047	-9.2	0.8	11	dbSNP_107	20	3438,5160		693,2052,1554	no	coding-synonymous	PRPF19	NM_014502.4		761,2724,3017	AA,AG,GG		39.986,18.3386,32.6515		349/505	60666341	4246,8758	2203	4299	6502	SO:0001819	synonymous_variant	27339	exon12			GCAGCCGGAGGTC	BC018698	CCDS7995.1	11q12.2	2014-05-20	2013-06-10	2005-04-01	ENSG00000110107	ENSG00000110107		"""WD repeat domain containing"", ""U-box domain containing"""	17896	protein-coding gene	gene with protein product	"""nuclear matrix protein NMP200 related to splicing factor PRP19"", ""psoralen 4"""	608330	"""PRP19/PSO4 homolog (S. cerevisiae)"", ""PRP19/PSO4 pre-mRNA processing factor 19 homolog (S. cerevisiae)"""	PRP19		12960389	Standard	NM_014502		Approved	UBOX4, NMP200, PSO4, hPSO4	uc001nqf.3	Q9UMS4	OTTHUMG00000167798	ENST00000227524.4:c.1047C>T	11.37:g.60666341G>A		Somatic	193	0	0	1047	WXS	Illumina HiSeq	Phase_I	188	186	0.989362	NM_014502		Silent	SNP	ENST00000227524.4	37	CCDS7995.1																																																																																			G|0.691;A|0.309	0.309	strong		0.393	PRPF19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396334.1	NM_014502	
NBPF15	284565	hgsc.bcm.edu	37	1	148594455	148594455	+	Missense_Mutation	SNP	A	A	G	rs1043751	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:148594455A>G	ENST00000369187.3	+	19	2317	c.1828A>G	c.(1828-1830)Aga>Gga	p.R610G	NBPF15_ENST00000442702.2_Missense_Mutation_p.R610G	NM_173638.3	NP_775909.2	Q8N660	NBPFF_HUMAN	neuroblastoma breakpoint family, member 15	610	NBPF 6. {ECO:0000255|PROSITE- ProRule:PRU00647}.					cytoplasm (GO:0005737)				NS(1)|cervix(1)|endometrium(1)|large_intestine(4)|lung(3)|skin(2)	12	all_hematologic(923;0.032)					CTCACTGGATAGATGTTATTC	0.453																																					p.R610G		Atlas-SNP	.											NBPF15,NS,carcinoma,-1,1	NBPF15	20	1	0			c.A1828G						scavenged	.						193.0	250.0	231.0					1																	148594455		2203	4299	6502	SO:0001583	missense	284565	exon19			CTGGATAGATGTT	BC023087	CCDS72852.1	1q21.1	2014-01-16			ENSG00000243452	ENSG00000266338		"""neuroblastoma breakpoint family"""	28791	protein-coding gene	gene with protein product		610414, 614005	"""neuroblastoma breakpoint family, member 16"""	NBPF16		16079250	Standard	NM_173638		Approved	MGC8902	uc001esc.2	Q8N660	OTTHUMG00000013634	ENST00000369187.3:c.1828A>G	1.37:g.148594455A>G	ENSP00000358188:p.Arg610Gly	Somatic	230	19	0.0826087		WXS	Illumina HiSeq	Phase_I	226	28	0.123894	NM_173638	Q3BBV9|Q8IX77	Missense_Mutation	SNP	ENST00000369187.3	37	CCDS932.1	.	.	.	.	.	.	.	.	.	.	.	3.941	-0.014253	0.07681	.	.	ENSG00000243452	ENST00000442702;ENST00000369187	T;T	0.07908	3.15;3.15	0.502	-0.965	0.10323	DUF1220 (2);	.	.	.	.	T	0.02083	0.0065	L	0.45470	1.425	0.09310	N	1	B	0.06786	0.001	B	0.12156	0.007	T	0.44544	-0.9321	8	0.38643	T	0.18	.	.	.	.	rs1043751;rs3183409	610	Q8N660	NBPFF_HUMAN	G	610	ENSP00000416864:R610G;ENSP00000358188:R610G	ENSP00000358188:R610G	R	+	1	2	NBPF15	146861079	0.958000	0.32768	0.000000	0.03702	0.002000	0.02628	-0.245000	0.08890	-0.355000	0.08199	0.310000	0.20435	AGA	A|0.996;G|0.004	0.004	strong		0.453	NBPF15-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038609.3	NM_173638	
EIF2AK1	27102	hgsc.bcm.edu	37	7	6080686	6080686	+	Missense_Mutation	SNP	A	A	T	rs34909691	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:6080686A>T	ENST00000199389.6	-	9	1102	c.956T>A	c.(955-957)cTt>cAt	p.L319H	EIF2AK1_ENST00000495565.1_5'UTR|EIF2AK1_ENST00000536084.1_Missense_Mutation_p.L195H	NM_001134335.1|NM_014413.3	NP_001127807.1|NP_055228.2	Q9BQI3	E2AK1_HUMAN	eukaryotic translation initiation factor 2-alpha kinase 1	319	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		L -> H (in dbSNP:rs34909691). {ECO:0000269|PubMed:17344846}.		negative regulation of cell proliferation (GO:0008285)|negative regulation of hemoglobin biosynthetic process (GO:0046986)|negative regulation of translational initiation by iron (GO:0045993)|protein autophosphorylation (GO:0046777)|protoporphyrinogen IX metabolic process (GO:0046501)|regulation of eIF2 alpha phosphorylation by heme (GO:0010999)|response to external stimulus (GO:0009605)|response to stress (GO:0006950)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|eukaryotic translation initiation factor 2alpha kinase activity (GO:0004694)|heme binding (GO:0020037)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(10)|prostate(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(2)	27		Ovarian(82;0.0423)		UCEC - Uterine corpus endometrioid carcinoma (126;0.106)|OV - Ovarian serous cystadenocarcinoma(56;5.22e-14)		GGTCGACTCAAGTTCACCAGA	0.458													A|||	45	0.00898562	0.0008	0.0173	5008	,	,		16878	0.0		0.0179	False		,,,				2504	0.0143				p.L319H		Atlas-SNP	.											.	EIF2AK1	76	.	0			c.T956A						PASS	.	A	HIS/LEU,HIS/LEU	15,4391		0,15,2188	164.0	161.0	162.0		953,956	-1.8	0.0	7	dbSNP_126	162	193,8407		2,189,4109	yes	missense,missense	EIF2AK1	NM_001134335.1,NM_014413.3	99,99	2,204,6297	TT,TA,AA		2.2442,0.3404,1.5993	benign,benign	318/630,319/631	6080686	208,12798	2203	4300	6503	SO:0001583	missense	27102	exon9			GACTCAAGTTCAC	BC006524	CCDS5345.1	7p22	2005-01-20			ENSG00000086232	ENSG00000086232			24921	protein-coding gene	gene with protein product	"""heme regulated initiation factor 2 alpha kinase"""	613635				7709427, 10718198	Standard	NM_014413		Approved	HRI, KIAA1369	uc003spp.3	Q9BQI3	OTTHUMG00000090689	ENST00000199389.6:c.956T>A	7.37:g.6080686A>T	ENSP00000199389:p.Leu319His	Somatic	187	0	0		WXS	Illumina HiSeq	Phase_I	178	137	0.769663	NM_014413	A8K2R2|Q549K6|Q8NBW3|Q9HC02|Q9NYE0|Q9P0V6|Q9P1J5|Q9P2H8|Q9UHG4	Missense_Mutation	SNP	ENST00000199389.6	37	CCDS5345.1	21	0.009615384615384616	1	0.0020325203252032522	8	0.022099447513812154	0	0.0	12	0.0158311345646438	.	7.886	0.731364	0.15507	0.003404	0.022442	ENSG00000086232	ENST00000199389;ENST00000536084	T;T	0.68624	-0.27;-0.34	5.36	-1.8	0.07907	Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.737749	0.14214	N	0.333889	T	0.23649	0.0572	N	0.14661	0.345	0.09310	N	1	B;P;B	0.34826	0.003;0.471;0.401	B;B;B	0.33196	0.005;0.159;0.151	T	0.22208	-1.0223	10	0.15499	T	0.54	-0.6525	6.7447	0.23454	0.2399:0.4967:0.0:0.2635	rs34909691;rs61731539	195;318;319	B4DIP4;Q9BQI3-2;Q9BQI3	.;.;E2AK1_HUMAN	H	319;195	ENSP00000199389:L319H;ENSP00000445784:L195H	ENSP00000199389:L319H	L	-	2	0	EIF2AK1	6047212	0.000000	0.05858	0.013000	0.15412	0.024000	0.10985	0.404000	0.20999	0.018000	0.15052	0.533000	0.62120	CTT	A|0.978;T|0.022	0.022	strong		0.458	EIF2AK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207373.2	NM_014413	
RASSF6	166824	hgsc.bcm.edu	37	4	74451073	74451073	+	Missense_Mutation	SNP	A	A	G	rs12507775	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:74451073A>G	ENST00000342081.3	-	6	617	c.487T>C	c.(487-489)Tct>Cct	p.S163P	RASSF6_ENST00000395777.2_Missense_Mutation_p.S131P|RASSF6_ENST00000335049.5_Missense_Mutation_p.S119P|RASSF6_ENST00000307439.5_Missense_Mutation_p.S131P	NM_201431.2	NP_958834.1	Q6ZTQ3	RASF6_HUMAN	Ras association (RalGDS/AF-6) domain family member 6	163			S -> P (in dbSNP:rs12507775). {ECO:0000269|PubMed:15489334}.		apoptotic process (GO:0006915)|positive regulation of apoptotic process (GO:0043065)|signal transduction (GO:0007165)					breast(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(4)|pancreas(2)|skin(2)	17	Breast(15;0.00102)		all cancers(17;0.00104)|Lung(101;0.128)|LUSC - Lung squamous cell carcinoma(112;0.187)			CTGTGATAAGATAAATAGTCT	0.418													A|||	1319	0.263379	0.2761	0.4712	5008	,	,		17888	0.1141		0.2833	False		,,,				2504	0.2321				p.S163P		Atlas-SNP	.											.	RASSF6	68	.	0			c.T487C						PASS	.	A	PRO/SER,PRO/SER	1307,3099	443.1+/-346.9	188,931,1084	102.0	95.0	97.0		391,487	4.7	1.0	4	dbSNP_120	97	2374,6224	394.4+/-344.7	322,1730,2247	yes	missense,missense	RASSF6	NM_177532.3,NM_201431.1	74,74	510,2661,3331	GG,GA,AA		27.6111,29.6641,28.3067	benign,benign	131/338,163/370	74451073	3681,9323	2203	4299	6502	SO:0001583	missense	166824	exon6			GATAAGATAAATA	AY217664	CCDS3558.1, CCDS3559.1, CCDS58904.1, CCDS58905.1	4q21.1	2008-02-22	2008-02-22		ENSG00000169435	ENSG00000169435			20796	protein-coding gene	gene with protein product		612620					Standard	NM_177532		Approved		uc003hhd.2	Q6ZTQ3	OTTHUMG00000130007	ENST00000342081.3:c.487T>C	4.37:g.74451073A>G	ENSP00000340578:p.Ser163Pro	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	122	43	0.352459	NM_201431	Q68DT2|Q6PDA6|Q86WG9|Q86WH0	Missense_Mutation	SNP	ENST00000342081.3	37	CCDS3558.1	549	0.25137362637362637	123	0.25	150	0.4143646408839779	64	0.11188811188811189	212	0.2796833773087071	A	9.003	0.980560	0.18812	0.296641	0.276111	ENSG00000169435	ENST00000307439;ENST00000342081;ENST00000395777;ENST00000335049	T;T;T;T	0.38401	1.14;1.14;1.14;1.14	5.91	4.74	0.60224	.	0.456851	0.26788	N	0.022498	T	0.00012	0.0000	L	0.31664	0.95	0.32144	P	0.5851740000000001	B;B;B	0.19200	0.034;0.006;0.009	B;B;B	0.22152	0.038;0.014;0.012	T	0.43798	-0.9369	9	0.34782	T	0.22	-4.3402	4.8405	0.13487	0.7508:0.0:0.0844:0.1648	rs12507775;rs17854967;rs59189514;rs12507775	119;131;163	Q6ZTQ3-3;Q6ZTQ3-4;Q6ZTQ3	.;.;RASF6_HUMAN	P	131;163;131;119	ENSP00000303877:S131P;ENSP00000340578:S163P;ENSP00000379123:S131P;ENSP00000335582:S119P	ENSP00000303877:S131P	S	-	1	0	RASSF6	74669937	0.988000	0.35896	1.000000	0.80357	0.463000	0.32649	1.490000	0.35573	2.254000	0.74563	0.533000	0.62120	TCT	A|0.733;G|0.267	0.267	strong		0.418	RASSF6-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252279.1	NM_177532	
TTLL1	25809	hgsc.bcm.edu	37	22	43435812	43435812	+	Silent	SNP	C	C	T	rs1052163	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:43435812C>T	ENST00000266254.7	-	11	1482	c.1242G>A	c.(1240-1242)tcG>tcA	p.S414S	AL022476.2_ENST00000443063.1_RNA|TTLL1_ENST00000331018.7_Silent_p.S385S	NM_012263.4	NP_036395.1	O95922	TTLL1_HUMAN	tubulin tyrosine ligase-like family, member 1	414					axoneme assembly (GO:0035082)|epithelial cilium movement (GO:0003351)|protein polyglutamylation (GO:0018095)	cytoplasm (GO:0005737)|microtubule (GO:0005874)	tubulin-glutamic acid ligase activity (GO:0070740)			breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(7)|ovary(1)|skin(2)|stomach(1)	23		Ovarian(80;0.0694)		BRCA - Breast invasive adenocarcinoma(115;0.00461)		CCGCTCTCCCCGAGTCTCTCG	0.587													C|||	2432	0.485623	0.5318	0.4438	5008	,	,		14881	0.8333		0.173	False		,,,				2504	0.4162				p.S414S		Atlas-SNP	.											.	TTLL1	41	.	0			c.G1242A						PASS	.	C		2108,2298	553.7+/-378.8	500,1108,595	59.0	59.0	59.0		1242	-11.1	0.0	22	dbSNP_86	59	1509,7091	274.1+/-291.0	139,1231,2930	no	coding-synonymous	TTLL1	NM_012263.4		639,2339,3525	TT,TC,CC		17.5465,47.8438,27.8102		414/424	43435812	3617,9389	2203	4300	6503	SO:0001819	synonymous_variant	25809	exon11			TCTCCCCGAGTCT	AL096886	CCDS14043.1	22q13.1	2013-02-14			ENSG00000100271	ENSG00000100271		"""Tubulin tyrosine ligase-like family"""	1312	protein-coding gene	gene with protein product		608955	"""tubulin tyrosine ligase-like 1"""	C22orf7		10591208, 11054573	Standard	NM_012263		Approved		uc003bdi.3	O95922	OTTHUMG00000150699	ENST00000266254.7:c.1242G>A	22.37:g.43435812C>T		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	46	21	0.456522	NM_012263	B2RDS7|Q9BR27|Q9NRS9|Q9UMU0	Silent	SNP	ENST00000266254.7	37	CCDS14043.1																																																																																			C|0.665;T|0.335	0.335	strong		0.587	TTLL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319659.1	NM_012263	
KRTAP12-2	353323	hgsc.bcm.edu	37	21	46086719	46086719	+	Missense_Mutation	SNP	A	A	G	rs7276859|rs368303093	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:46086719A>G	ENST00000360770.3	-	1	125	c.85T>C	c.(85-87)Tcc>Ccc	p.S29P	TSPEAR_ENST00000323084.4_Intron	NM_181684.2	NP_859012.1	P59991	KR122_HUMAN	keratin associated protein 12-2	29	23 X 5 AA approximate repeats.		S -> C (in dbSNP:rs7275281).|S -> P (in dbSNP:rs7276859).			keratin filament (GO:0045095)				central_nervous_system(1)|endometrium(1)|lung(3)	5						GCCTGGCAGGAGCTGGGCACA	0.682													G|||	3070	0.613019	0.7262	0.5807	5008	,	,		16573	0.5675		0.5547	False		,,,				2504	0.59				p.S29P		Atlas-SNP	.											.	KRTAP12-2	10	.	0			c.T85C						PASS	.	G	,PRO/SER	1221,3097		486,249,1424	33.0	40.0	38.0		,85	-6.8	0.0	21	dbSNP_129	38	1508,6988		620,268,3360	no	intron,missense	TSPEAR,KRTAP12-2	NM_144991.2,NM_181684.2	,74	1106,517,4784	GG,GA,AA		17.7495,28.277,21.297	,benign	,29/147	46086719	2729,10085	2159	4248	6407	SO:0001583	missense	353323	exon1			GGCAGGAGCTGGG	AJ566389	CCDS42965.1	21q22.3	2006-03-13			ENSG00000221864	ENSG00000221864		"""Keratin associated proteins"""	20530	protein-coding gene	gene with protein product							Standard	NM_181684		Approved	KRTAP12.2, KAP12.2	uc002zfu.3	P59991	OTTHUMG00000057636	ENST00000360770.3:c.85T>C	21.37:g.46086719A>G	ENSP00000354001:p.Ser29Pro	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	106	62	0.584906	NM_181684	A6NIS1|A6NMS9|Q0VAS4	Missense_Mutation	SNP	ENST00000360770.3	37	CCDS42965.1	1167	0.5343406593406593	320	0.6504065040650406	199	0.5497237569060773	279	0.48776223776223776	369	0.4868073878627968	g	1.782	-0.481680	0.04383	0.28277	0.177495	ENSG00000221864	ENST00000360770	T	0.03152	4.03	3.4	-6.8	0.01709	.	.	.	.	.	T	0.00012	0.0000	N	0.13003	0.285	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.42799	-0.9430	8	0.05833	T	0.94	.	1.6096	0.02691	0.3939:0.0934:0.138:0.3746	rs7276859;rs34421715	29	P59991	KR122_HUMAN	P	29	ENSP00000354001:S29P	ENSP00000354001:S29P	S	-	1	0	KRTAP12-2	44911147	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-4.335000	0.00251	-4.007000	0.00082	-2.692000	0.00139	TCC	A|0.470;G|0.530	0.530	strong		0.682	KRTAP12-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128039.1	NM_181684	
TET1	80312	hgsc.bcm.edu	37	10	70405541	70405541	+	Missense_Mutation	SNP	A	A	G	rs72799515|rs71483917	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:70405541A>G	ENST00000373644.4	+	4	3264	c.3055A>G	c.(3055-3057)Aaa>Gaa	p.K1019E		NM_030625.2	NP_085128.2	Q8NFU7	TET1_HUMAN	tet methylcytosine dioxygenase 1	1019					chromatin modification (GO:0016568)|DNA demethylation (GO:0080111)|inner cell mass cell differentiation (GO:0001826)|negative regulation of methylation-dependent chromatin silencing (GO:0090310)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein O-linked glycosylation (GO:0006493)|regulation of DNA methylation (GO:0044030)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	iron ion binding (GO:0005506)|methylcytosine dioxygenase activity (GO:0070579)|structure-specific DNA binding (GO:0043566)|zinc ion binding (GO:0008270)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(2)|ovary(5)|prostate(1)|upper_aerodigestive_tract(2)	21						TGACACCAATAAAAGTATTGC	0.328													A|||	49	0.00978435	0.0015	0.0072	5008	,	,		22481	0.001		0.0378	False		,,,				2504	0.0031				p.K1019E		Atlas-SNP	.											.	TET1	255	.	0			c.A3055G						PASS	.	A	GLU/LYS	21,4385	29.0+/-57.7	0,21,2182	69.0	69.0	69.0		3055	4.3	0.2	10	dbSNP_130	69	271,8329	103.1+/-164.3	8,255,4037	yes	missense	TET1	NM_030625.2	56	8,276,6219	GG,GA,AA		3.1512,0.4766,2.2451	probably-damaging	1019/2137	70405541	292,12714	2203	4300	6503	SO:0001583	missense	80312	exon4			ACCAATAAAAGTA	AF430147	CCDS7281.1	10q21	2014-02-18	2011-09-30	2008-03-12	ENSG00000138336	ENSG00000138336			29484	protein-coding gene	gene with protein product	"""leukemia-associated protein with a CXXC domain"", ""ten-eleven translocation-1"""	607790	"""CXXC zinc finger 6"", ""tet oncogene 1"""	CXXC6		12124344, 12646957	Standard	NM_030625		Approved	LCX, KIAA1676, bA119F7.1	uc001jok.4	Q8NFU7	OTTHUMG00000018359	ENST00000373644.4:c.3055A>G	10.37:g.70405541A>G	ENSP00000362748:p.Lys1019Glu	Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	151	65	0.430464	NM_030625	Q5VUP7|Q7Z6B6|Q8TCR1|Q9C0I7	Missense_Mutation	SNP	ENST00000373644.4	37	CCDS7281.1	31	0.014194139194139194	1	0.0020325203252032522	4	0.011049723756906077	1	0.0017482517482517483	25	0.032981530343007916	A	9.980	1.227751	0.22542	0.004766	0.031512	ENSG00000138336	ENST00000373644	T	0.08720	3.06	5.46	4.33	0.51752	.	4.278170	0.00520	N	0.000180	T	0.03095	0.0091	L	0.29908	0.895	0.23089	N	0.998316	P	0.42692	0.787	B	0.40199	0.322	T	0.34925	-0.9809	10	0.45353	T	0.12	.	9.6735	0.40026	0.9213:0.0:0.0787:0.0	.	1019	Q8NFU7	TET1_HUMAN	E	1019	ENSP00000362748:K1019E	ENSP00000362748:K1019E	K	+	1	0	TET1	70075547	0.997000	0.39634	0.162000	0.22713	0.375000	0.29983	3.686000	0.54685	0.919000	0.36945	0.460000	0.39030	AAA	A|0.980;G|0.020	0.020	strong		0.328	TET1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048354.1	NM_030625	
KRTAP10-9	386676	hgsc.bcm.edu	37	21	46047418	46047418	+	Silent	SNP	C	C	T	rs8126553	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:46047418C>T	ENST00000397911.3	+	1	379	c.330C>T	c.(328-330)tgC>tgT	p.C110C	TSPEAR_ENST00000323084.4_Intron|KRTAP10-9_ENST00000484861.1_Intron	NM_198690.2	NP_941963.2	P60411	KR109_HUMAN	keratin associated protein 10-9	110	25 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				endometrium(1)|kidney(1)|large_intestine(1)|lung(6)	9						ctgtgtgctgcgtgcccgtct	0.667													T|||	3942	0.787141	0.9123	0.745	5008	,	,		20271	0.6746		0.7714	False		,,,				2504	0.7802				p.C110C		Atlas-SNP	.											.	KRTAP10-9	24	.	0			c.C330T						PASS	.	T	,	3913,489	215.8+/-234.7	1747,419,35	100.0	113.0	108.0		,330	-7.1	0.0	21	dbSNP_116	108	6219,2379	388.3+/-342.5	2266,1687,346	no	intron,coding-synonymous	TSPEAR,KRTAP10-9	NM_144991.2,NM_198690.2	,	4013,2106,381	TT,TC,CC		27.6692,11.1086,22.0615	,	,110/293	46047418	10132,2868	2201	4299	6500	SO:0001819	synonymous_variant	386676	exon1			GTGCTGCGTGCCC	AJ566386	CCDS42961.1	21q22.3	2007-10-05			ENSG00000221837	ENSG00000221837		"""Keratin associated proteins"""	22971	protein-coding gene	gene with protein product				KRTAP18-9			Standard	NM_198690		Approved	KAP10.9, KAP18.9	uc002zfp.4	P60411	OTTHUMG00000057637	ENST00000397911.3:c.330C>T	21.37:g.46047418C>T		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	165	165	1	NM_198690	A2RRG1|A6NIR9|Q70LJ1	Silent	SNP	ENST00000397911.3	37	CCDS42961.1																																																																																			C|0.234;T|0.766	0.766	strong		0.667	KRTAP10-9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128040.1		
OR1N2	138882	hgsc.bcm.edu	37	9	125315542	125315542	+	Silent	SNP	C	C	T	rs1831369	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:125315542C>T	ENST00000373688.2	+	1	152	c.94C>T	c.(94-96)Cta>Tta	p.L32L		NM_001004457.1	NP_001004457.1	Q8NGR9	OR1N2_HUMAN	olfactory receptor, family 1, subfamily N, member 2	32						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L32L(1)		breast(2)|large_intestine(6)|lung(10)|ovary(2)|skin(3)|stomach(3)	26						CTTCCTCCTTCTAGGACTCTC	0.512													C|||	1906	0.380591	0.3956	0.3934	5008	,	,		19282	0.5367		0.2376	False		,,,				2504	0.3374				p.L32L		Atlas-SNP	.											OR1N2,NS,carcinoma,0,1	OR1N2	51	1	1	Substitution - coding silent(1)	stomach(1)	c.C94T						PASS	.	C		1673,2733	508.9+/-367.1	322,1029,852	101.0	95.0	97.0		94	1.3	1.0	9	dbSNP_92	97	2026,6574	354.0+/-329.3	241,1544,2515	no	coding-synonymous	OR1N2	NM_001004457.1		563,2573,3367	TT,TC,CC		23.5581,37.9709,28.4407		32/331	125315542	3699,9307	2203	4300	6503	SO:0001819	synonymous_variant	138882	exon1			CTCCTTCTAGGAC		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.94C>T	9.37:g.125315542C>T		Somatic	207	0	0		WXS	Illumina HiSeq	Phase_I	147	76	0.517007	NM_001004457	A3KFM2|B2RNY4|Q6IF17|Q96RA3	Silent	SNP	ENST00000373688.2	37	CCDS35123.1																																																																																			C|0.682;N|0.000	.	strong		0.512	OR1N2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053937.2		
CRACR2A	84766	hgsc.bcm.edu	37	12	3789452	3789452	+	Missense_Mutation	SNP	C	C	T	rs17836273	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	126	0	0		WXS	Illumina HiSeq	Phase_I	132	68	0.515152	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		
KRTAP4-11	653240	hgsc.bcm.edu	37	17	39274157	39274157	+	Silent	SNP	G	G	A	rs145503152		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:39274157G>A	ENST00000391413.2	-	1	449	c.411C>T	c.(409-411)ccC>ccT	p.P137P		NM_033059.3	NP_149048.2	Q9BYQ6	KR411_HUMAN	keratin associated protein 4-11	137	27 X 5 AA repeats of C-C-[GIKRQVHEL]- [SPTR]-[STVQRMC].					keratin filament (GO:0045095)		p.P137P(3)		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)			tgctgcagctggggtggcagc	0.672																																					p.P137P		Atlas-SNP	.											KRTAP4-11,NS,carcinoma,0,8	KRTAP4-11	94	8	3	Substitution - coding silent(3)	prostate(1)|lung(1)|endometrium(1)	c.C411T						PASS	.						8.0	13.0	12.0					17																	39274157		684	1586	2270	SO:0001819	synonymous_variant	653240	exon1			GCAGCTGGGGTGG	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.411C>T	17.37:g.39274157G>A		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	59	9	0.152542	NM_033059	A0AUY2	Silent	SNP	ENST00000391413.2	37	CCDS45675.1																																																																																			G|0.500;A|0.500	0.500	weak		0.672	KRTAP4-11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257690.1		
AP5Z1	9907	hgsc.bcm.edu	37	7	4823971	4823971	+	Silent	SNP	C	C	T	rs17135121	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:4823971C>T	ENST00000348624.4	+	6	853	c.759C>T	c.(757-759)agC>agT	p.S253S	AP5Z1_ENST00000401897.1_Silent_p.S253S	NM_014855.2	NP_055670.1	O43299	AP5Z1_HUMAN	adaptor-related protein complex 5, zeta 1 subunit	253					cell death (GO:0008219)|double-strand break repair via homologous recombination (GO:0000724)|endosomal transport (GO:0016197)|protein transport (GO:0015031)	AP-5 adaptor complex (GO:0044599)|AP-type membrane coat adaptor complex (GO:0030119)|cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.S964S(1)|p.S97S(1)									TGCTGCACAGCGGCCCCGAGG	0.682													C|||	1251	0.2498	0.6112	0.0951	5008	,	,		12021	0.0496		0.0984	False		,,,				2504	0.2331				p.S253S		Atlas-SNP	.											KIAA0415_ENST00000450194,NS,carcinoma,0,2	.	.	2	2	Substitution - coding silent(2)	prostate(2)	c.C759T						PASS	.	C		1840,2170		446,948,611	8.0	10.0	9.0		759	-3.8	0.0	7	dbSNP_123	9	846,7450		55,736,3357	no	coding-synonymous	KIAA0415	NM_014855.2		501,1684,3968	TT,TC,CC		10.1977,45.8853,21.8268		253/808	4823971	2686,9620	2005	4148	6153	SO:0001819	synonymous_variant	9907	exon6			GCACAGCGGCCCC	AB007875	CCDS47528.1	7p22.1	2012-03-20	2012-03-20	2012-03-20	ENSG00000242802	ENSG00000242802			22197	protein-coding gene	gene with protein product		613653	"""KIAA0415"""	KIAA0415		20613862, 22022230	Standard	NM_014855		Approved	SPG48, zeta	uc003sne.3	O43299	OTTHUMG00000151754	ENST00000348624.4:c.759C>T	7.37:g.4823971C>T		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	79	57	0.721519	NM_014855	Q8N3X2|Q96H80	Silent	SNP	ENST00000348624.4	37	CCDS47528.1																																																																																			C|0.761;T|0.239	0.239	strong		0.682	AP5Z1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323771.1		
CCDC154	645811	hgsc.bcm.edu	37	16	1486462	1486462	+	Missense_Mutation	SNP	C	C	T	rs35583599	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:1486462C>T	ENST00000389176.3	-	13	1664	c.1498G>A	c.(1498-1500)Gcc>Acc	p.A500T	CCDC154_ENST00000409671.1_Missense_Mutation_p.A346T	NM_001143980.1	NP_001137452.1	A6NI56	CC154_HUMAN	coiled-coil domain containing 154	500						endosome (GO:0005768)		p.A500T(1)		NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)	5						TTGCCTTCGGCGGAAATCCTG	0.647													C|||	262	0.0523163	0.0265	0.0836	5008	,	,		18142	0.001		0.1123	False		,,,				2504	0.0562				p.A491T		Atlas-SNP	.											CCDC154,NS,lymphoid_neoplasm,0,1	CCDC154	27	1	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.G1471A						PASS	.	C	THR/ALA	55,1329		0,55,637	54.0	54.0	54.0		1471	0.3	0.0	16	dbSNP_126	54	385,2797		21,343,1227	yes	missense	CCDC154	NM_001143980.1	58	21,398,1864	TT,TC,CC		12.0993,3.974,9.6364	possibly-damaging	491/668	1486462	440,4126	692	1591	2283	SO:0001583	missense	645811	exon13			CTTCGGCGGAAAT			16p13.3	2012-12-13			ENSG00000197599	ENSG00000197599			34454	protein-coding gene	gene with protein product			"""chromosome 16 open reading frame 29"""	C16orf29			Standard	NM_001143980		Approved	LOC645811	uc010uve.2	A6NI56	OTTHUMG00000154097	ENST00000389176.3:c.1498G>A	16.37:g.1486462C>T	ENSP00000373828:p.Ala500Thr	Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	48	10	0.208333	NM_001143980	G9JV18	Missense_Mutation	SNP	ENST00000389176.3	37		134	0.06135531135531135	8	0.016260162601626018	34	0.09392265193370165	0	0.0	92	0.12137203166226913	C	7.896	0.733344	0.15574	0.03974	0.120993	ENSG00000197599	ENST00000409671;ENST00000389176	.	.	.	4.61	0.311	0.15831	.	0.705929	0.12364	N	0.475365	T	0.00178	0.0005	N	0.17082	0.46	0.80722	P	0.0	P	0.41420	0.749	B	0.32211	0.142	T	0.19095	-1.0316	8	0.27082	T	0.32	-4.5205	3.4262	0.07412	0.3577:0.4494:0.0:0.1929	rs35583599;rs61734650	500	A6NI56	CC154_HUMAN	T	346;500	.	ENSP00000373828:A500T	A	-	1	0	CCDC154	1426463	0.000000	0.05858	0.000000	0.03702	0.031000	0.12232	-0.754000	0.04787	0.252000	0.21531	0.491000	0.48974	GCC	C|0.928;T|0.072	0.072	strong		0.647	CCDC154-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_001143980	
ARMC5	79798	hgsc.bcm.edu	37	16	31476458	31476458	+	Intron	SNP	C	C	T	rs11150624	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:31476458C>T	ENST00000563544.1	+	5	2410				ARMC5_ENST00000268314.4_Intron|ARMC5_ENST00000412665.2_Intron|ARMC5_ENST00000538189.1_Intron|ARMC5_ENST00000457010.2_Missense_Mutation_p.A705V|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	101	0	0		WXS	Illumina HiSeq	Phase_I	104	104	1	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	
RAD51D	5892	hgsc.bcm.edu	37	17	33433487	33433487	+	Missense_Mutation	SNP	C	C	T	rs4796033	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:33433487C>T	ENST00000345365.6	-	6	749	c.494G>A	c.(493-495)cGg>cAg	p.R165Q	RAD51D_ENST00000394589.4_Missense_Mutation_p.R165Q|RAD51L3-RFFL_ENST00000593039.1_Missense_Mutation_p.R6Q|RAD51D_ENST00000460118.2_Missense_Mutation_p.R46Q|RAD51D_ENST00000590380.1_5'UTR|RAD51D_ENST00000590016.1_Missense_Mutation_p.R185Q|RAD51D_ENST00000335858.7_Missense_Mutation_p.R53Q|RAD51D_ENST00000360276.3_Missense_Mutation_p.R120Q	NM_002878.3	NP_002869.3	O75771	RA51D_HUMAN	RAD51 paralog D	165			R -> Q (in dbSNP:rs4796033). {ECO:0000269|Ref.4}.		ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)|double-strand break repair via homologous recombination (GO:0000724)|reciprocal meiotic recombination (GO:0007131)|strand invasion (GO:0042148)|telomere maintenance (GO:0000723)	centrosome (GO:0005813)|chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|Rad51B-Rad51C-Rad51D-XRCC2 complex (GO:0033063)|replication fork (GO:0005657)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|gamma-tubulin binding (GO:0043015)|single-stranded DNA binding (GO:0003697)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(2)|liver(1)|lung(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	13						CTGGATCCTCCGGAGAGCTTC	0.562								Direct reversal of damage					C|||	476	0.0950479	0.0136	0.2205	5008	,	,		23141	0.0407		0.1292	False		,,,				2504	0.137				p.R185Q		Atlas-SNP	.											.	RAD51D	53	.	0			c.G554A						PASS	.	C	GLN/ARG,GLN/ARG,GLN/ARG	162,4244	107.8+/-146.2	4,154,2045	44.0	40.0	42.0		554,494,158	0.2	1.0	17	dbSNP_111	42	1227,7373	243.5+/-273.1	87,1053,3160	yes	missense,missense,missense	RAD51D	NM_001142571.1,NM_002878.3,NM_133629.2	43,43,43	91,1207,5205	TT,TC,CC		14.2674,3.6768,10.6797	,,	185/349,165/329,53/217	33433487	1389,11617	2203	4300	6503	SO:0001583	missense	5892	exon6			ATCCTCCGGAGAG	AF034956	CCDS11287.1, CCDS11288.1, CCDS45646.1	17q11	2014-09-17	2013-07-02	2011-07-01	ENSG00000185379	ENSG00000185379			9823	protein-coding gene	gene with protein product	"""recombination repair protein"", ""DNA repair protein RAD51 homolog 4"""	602954	"""RAD51 (S. cerevisiae)-like 3"", ""RAD51-like 3 (S. cerevisiae)"", ""RAD51 homolog D (S. cerevisiae)"""	RAD51L3		9570954	Standard	NM_001142571		Approved	R51H3, Trad, HsTRAD	uc010ctj.2	O75771	OTTHUMG00000132930	ENST00000345365.6:c.494G>A	17.37:g.33433487C>T	ENSP00000338790:p.Arg165Gln	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	90	51	0.566667	NM_001142571	B4DJU7|E1P637|O43537|O60355|O75196|O75847|O75848|O76073|O76085|O94908|Q9UFU5	Missense_Mutation	SNP	ENST00000345365.6	37	CCDS11287.1	212	0.09706959706959707	10	0.02032520325203252	73	0.20165745856353592	24	0.04195804195804196	105	0.13852242744063326	C	12.22	1.871652	0.33069	0.036768	0.142674	ENSG00000185379	ENST00000345365;ENST00000394589;ENST00000335858;ENST00000360276;ENST00000345766;ENST00000418935;ENST00000415064	T;T	0.65916	-0.18;-0.18	4.96	0.253	0.15551	DNA recombination/repair protein RecA/RadB, ATP-binding domain (1);ATPase, AAA+ type, core (1);DNA recombination and repair protein Rad51, C-terminal (1);	0.164310	0.56097	N	0.000032	T	0.00039	0.0001	N	0.00652	-1.29	0.09310	P	0.9999999999941145	B;B;B;B	0.16166	0.016;0.008;0.0;0.0	B;B;B;B	0.15484	0.013;0.001;0.001;0.0	T	0.19031	-1.0318	9	0.02654	T	1	-3.6654	8.0109	0.30353	0.0:0.3404:0.0:0.6596	rs4796033;rs52810365;rs59839357;rs4796033	185;53;165;165	B4DJU7;O75771-3;O75771;F8W8E6	.;.;RA51D_HUMAN;.	Q	165;185;165;120;53;165;168	ENSP00000338790:R165Q;ENSP00000353417:R120Q	ENSP00000338408:R165Q	R	-	2	0	RAD51D	30457600	1.000000	0.71417	0.998000	0.56505	0.886000	0.51366	1.326000	0.33735	-0.161000	0.10983	-0.383000	0.06682	CGG	C|0.903;T|0.097	0.097	strong		0.562	RAD51D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256446.1	NM_002878	
CYP4F3	4051	hgsc.bcm.edu	37	19	15760035	15760035	+	Silent	SNP	C	C	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:15760035C>G	ENST00000221307.8	+	6	638	c.591C>G	c.(589-591)ctC>ctG	p.L197L	CYP4F3_ENST00000585846.1_Silent_p.L197L|CYP4F3_ENST00000591058.1_Silent_p.L197L|CYP4F3_ENST00000586182.2_Silent_p.L197L	NM_000896.2	NP_000887.2	Q08477	CP4F3_HUMAN	cytochrome P450, family 4, subfamily F, polypeptide 3	197					arachidonic acid metabolic process (GO:0019369)|icosanoid metabolic process (GO:0006690)|leukotriene metabolic process (GO:0006691)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	alpha-tocopherol omega-hydroxylase activity (GO:0052871)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|leukotriene-B4 20-monooxygenase activity (GO:0050051)|monooxygenase activity (GO:0004497)			endometrium(3)|large_intestine(4)|lung(21)|ovary(3)|prostate(2)|stomach(1)	34						ACATCAGCCTCATGACCTTGG	0.577																																					p.L197L		Atlas-SNP	.											.	CYP4F3	69	.	0			c.C591G						PASS	.						124.0	107.0	113.0					19																	15760035		2203	4300	6503	SO:0001819	synonymous_variant	4051	exon6			CAGCCTCATGACC	AB002454	CCDS12332.1, CCDS59362.1	19p13.12	2013-02-21	2003-01-14		ENSG00000186529	ENSG00000186529		"""Cytochrome P450s"""	2646	protein-coding gene	gene with protein product		601270	"""cytochrome P450, subfamily IVF, polypeptide 3 (leukotriene B4 omega hydroxylase)"""	LTB4H		8486631, 9539102	Standard	NM_000896		Approved	CYP4F	uc010xol.2	Q08477	OTTHUMG00000182374	ENST00000221307.8:c.591C>G	19.37:g.15760035C>G		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	125	36	0.288	NM_001199209	B7Z8Z3|O60634|Q5U740	Silent	SNP	ENST00000221307.8	37	CCDS12332.1																																																																																			.	.	none		0.577	CYP4F3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460819.3	NM_000896	
CTBS	1486	hgsc.bcm.edu	37	1	85029085	85029085	+	Missense_Mutation	SNP	A	A	G	rs143993403	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:85029085A>G	ENST00000370630.5	-	6	860	c.812T>C	c.(811-813)aTt>aCt	p.I271T	CTBS_ENST00000477677.1_5'UTR	NM_004388.2	NP_004379.1	Q01459	DIAC_HUMAN	chitobiase, di-N-acetyl-	271					chitin catabolic process (GO:0006032)|oligosaccharide catabolic process (GO:0009313)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	chitinase activity (GO:0004568)			breast(1)|endometrium(1)|large_intestine(4)|lung(2)|ovary(1)	9				all cancers(265;0.00727)|Epithelial(280;0.0192)|OV - Ovarian serous cystadenocarcinoma(397;0.166)		GACTTTTGCAATGGTACAAAC	0.363													A|||	7	0.00139776	0.0	0.0	5008	,	,		12899	0.0		0.007	False		,,,				2504	0.0				p.I271T		Atlas-SNP	.											.	CTBS	24	.	0			c.T812C						PASS	.	A	THR/ILE	2,4394		0,2,2196	42.0	46.0	44.0		812	0.2	1.0	1	dbSNP_134	44	31,8567		0,31,4268	yes	missense	CTBS	NM_004388.2	89	0,33,6464	GG,GA,AA		0.3605,0.0455,0.254	benign	271/386	85029085	33,12961	2198	4299	6497	SO:0001583	missense	1486	exon6			TTTGCAATGGTAC	M95767	CCDS698.1	1p22	2010-05-04			ENSG00000117151	ENSG00000117151	3.2.1.-		2496	protein-coding gene	gene with protein product		600873		CTB		1549114, 7606925	Standard	NM_004388		Approved		uc001dka.2	Q01459	OTTHUMG00000009922	ENST00000370630.5:c.812T>C	1.37:g.85029085A>G	ENSP00000359664:p.Ile271Thr	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	97	42	0.43299	NM_004388	Q5VX50	Missense_Mutation	SNP	ENST00000370630.5	37	CCDS698.1	7	0.003205128205128205	0	0.0	0	0.0	0	0.0	7	0.009234828496042216	A	15.09	2.730266	0.48939	4.55E-4	0.003605	ENSG00000117151	ENST00000370630	T	0.05081	3.5	5.39	0.206	0.15208	Chitinase II (1);Glycoside hydrolase, family 18, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.218455	0.46758	N	0.000269	T	0.02610	0.0079	L	0.43598	1.365	0.33049	D	0.532445	P	0.38420	0.63	B	0.42625	0.393	T	0.44651	-0.9314	10	0.22109	T	0.4	-10.2359	11.7481	0.51832	0.8713:0.0:0.1287:0.0	.	271	Q01459	DIAC_HUMAN	T	271	ENSP00000359664:I271T	ENSP00000359659:I180T	I	-	2	0	CTBS	84801673	0.997000	0.39634	0.992000	0.48379	0.887000	0.51463	3.142000	0.50601	-0.226000	0.09899	0.528000	0.53228	ATT	A|0.997;G|0.003	0.003	strong		0.363	CTBS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027457.2	NM_004388	
SPINT4	391253	hgsc.bcm.edu	37	20	44352620	44352620	+	Missense_Mutation	SNP	G	G	A	rs6017667	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:44352620G>A	ENST00000279058.3	+	2	234	c.217G>A	c.(217-219)Ggc>Agc	p.G73S		NM_178455.1	NP_848550.1	Q6UDR6	SPIT4_HUMAN	serine peptidase inhibitor, Kunitz type 4	73	BPTI/Kunitz inhibitor. {ECO:0000255|PROSITE-ProRule:PRU00031}.		G -> S (in dbSNP:rs6017667).			extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)			lung(6)|ovary(1)|skin(1)	8		Myeloproliferative disorder(115;0.028)				TGTCTTCTCCGGCTGTAATGG	0.388													G|||	2603	0.519768	0.7231	0.3199	5008	,	,		19332	0.4742		0.3857	False		,,,				2504	0.5716				p.G73S		Atlas-SNP	.											.	SPINT4	17	.	0			c.G217A						PASS	.	G	SER/GLY	2825,1581		963,899,341	92.0	93.0	93.0		217	4.5	1.0	20	dbSNP_114	93	3223,5377		645,1933,1722	yes	missense	SPINT4	NM_178455.1	56	1608,2832,2063	AA,AG,GG		37.4767,35.8829,46.5016	probably-damaging	73/100	44352620	6048,6958	2203	4300	6503	SO:0001583	missense	391253	exon2			TTCTCCGGCTGTA	AY372174	CCDS33477.1	20q13.12	2012-08-20	2005-10-18	2005-10-25	ENSG00000149651	ENSG00000149651			16130	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 137"", ""serine peptidase inhibitor, Kunitz type 4"""	C20orf137		21988899	Standard	NM_178455		Approved	dJ601O1.1	uc002xpe.1	Q6UDR6	OTTHUMG00000130153	ENST00000279058.3:c.217G>A	20.37:g.44352620G>A	ENSP00000279058:p.Gly73Ser	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	63	24	0.380952	NM_178455	Q9BQN3	Missense_Mutation	SNP	ENST00000279058.3	37	CCDS33477.1	1037	0.4748168498168498	365	0.741869918699187	125	0.3453038674033149	277	0.48426573426573427	270	0.3562005277044855	G	15.75	2.926993	0.52759	0.641171	0.374767	ENSG00000149651	ENST00000279058	T	0.68903	-0.36	4.47	4.47	0.54385	Proteinase inhibitor I2, Kunitz metazoa (6);	0.000000	0.52532	D	0.000066	T	0.00012	0.0000	.	.	.	0.31161	P	0.704375	D	0.89917	1.0	D	0.97110	1.0	T	0.50575	-0.8812	8	0.87932	D	0	-19.0015	12.8514	0.57860	0.0:0.0:1.0:0.0	rs6017667;rs52836880;rs60202144;rs6017667	73	Q6UDR6	SPIT4_HUMAN	S	73	ENSP00000279058:G73S	ENSP00000279058:G73S	G	+	1	0	SPINT4	43786034	0.997000	0.39634	0.952000	0.39060	0.055000	0.15305	3.976000	0.56867	2.486000	0.83907	0.650000	0.86243	GGC	G|0.508;A|0.492	0.492	strong		0.388	SPINT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252463.2	XM_372869	
VSTM4	196740	hgsc.bcm.edu	37	10	50315893	50315893	+	Missense_Mutation	SNP	A	A	G	rs13088	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:50315893A>G	ENST00000332853.4	-	2	226	c.203T>C	c.(202-204)tTc>tCc	p.F68S	VSTM4_ENST00000298454.3_Missense_Mutation_p.F68S	NM_001031746.3	NP_001026916.2	Q8IW00	VSTM4_HUMAN	V-set and transmembrane domain containing 4	68	Ig-like.		F -> S (in dbSNP:rs13088). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(3)|kidney(1)|large_intestine(9)|liver(1)|lung(14)|skin(2)	31						CTGGGAGTCGAAGGAGTGTGC	0.607													G|||	2485	0.496206	0.7753	0.4827	5008	,	,		19434	0.2401		0.3907	False		,,,				2504	0.501				p.F68S		Atlas-SNP	.											.	VSTM4	83	.	0			c.T203C						PASS	.	G	SER/PHE,SER/PHE	3121,1285	438.0+/-345.2	1116,889,198	61.0	61.0	61.0		203,203	1.8	0.0	10	dbSNP_52	61	3376,5224	640.7+/-399.6	676,2024,1600	yes	missense,missense	VSTM4	NM_001031746.3,NM_144984.2	155,155	1792,2913,1798	GG,GA,AA		39.2558,29.1648,49.9539	benign,benign	68/321,68/192	50315893	6497,6509	2203	4300	6503	SO:0001583	missense	196740	exon2			GAGTCGAAGGAGT	BC041414	CCDS7228.1, CCDS31198.1	10q11.23	2013-01-11	2011-07-01	2011-07-01	ENSG00000165633	ENSG00000165633		"""Immunoglobulin superfamily / V-set domain containing"""	26470	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 72"""	C10orf72			Standard	XR_246075		Approved	FLJ31737	uc001jhf.2	Q8IW00	OTTHUMG00000018184	ENST00000332853.4:c.203T>C	10.37:g.50315893A>G	ENSP00000331062:p.Phe68Ser	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	87	42	0.482759	NM_144984	B4DNI6|Q96MX7	Missense_Mutation	SNP	ENST00000332853.4	37	CCDS31198.1	954	0.4368131868131868	374	0.7601626016260162	170	0.4696132596685083	121	0.21153846153846154	289	0.3812664907651715	G	0.006	-2.068113	0.00382	0.708352	0.392558	ENSG00000165633	ENST00000332853;ENST00000298454	T;T	0.62941	-0.01;-0.01	1.75	1.75	0.24633	.	0.284997	0.21139	N	0.079509	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	0.46414	-0.9193	9	0.02654	T	1	.	4.4037	0.11399	0.2404:0.0:0.7596:0.0	rs13088;rs1137471;rs3201257;rs17857253;rs52807236;rs61590125;rs13088	68;68	Q8IW00-2;Q8IW00	.;VSTM4_HUMAN	S	68	ENSP00000331062:F68S;ENSP00000298454:F68S	ENSP00000298454:F68S	F	-	2	0	VSTM4	49985899	0.001000	0.12720	0.001000	0.08648	0.046000	0.14306	-0.111000	0.10807	-0.651000	0.05415	-0.642000	0.03964	TTC	A|0.518;G|0.482	0.482	strong		0.607	VSTM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047966.2	NM_144984	
MEP1A	4224	hgsc.bcm.edu	37	6	46787399	46787399	+	Missense_Mutation	SNP	C	C	T	rs376658556		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:46787399C>T	ENST00000230588.4	+	7	523	c.514C>T	c.(514-516)Cgg>Tgg	p.R172W		NM_005588.2	NP_005579.2	Q16819	MEP1A_HUMAN	meprin A, alpha (PABA peptide hydrolase)	172	Metalloprotease.				digestion (GO:0007586)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|meprin A complex (GO:0017090)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(5)|kidney(2)|large_intestine(4)|lung(21)|ovary(1)|pancreas(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	42			Lung(136;0.192)			AAGGACGGACCGGGATGATTA	0.468																																					p.R172W		Atlas-SNP	.											MEP1A,colon,carcinoma,0,1	MEP1A	93	1	0			c.C514T						scavenged	.	C	TRP/ARG	0,4406		0,0,2203	294.0	272.0	279.0		514	5.8	1.0	6		279	1,8599	1.2+/-3.3	0,1,4299	no	missense	MEP1A	NM_005588.2	101	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	172/747	46787399	1,13005	2203	4300	6503	SO:0001583	missense	4224	exon7			ACGGACCGGGATG		CCDS4918.1	6p12-p11	2010-10-18			ENSG00000112818	ENSG00000112818	3.4.24.18		7015	protein-coding gene	gene with protein product		600388				7774936	Standard	NM_005588		Approved	PPHA	uc010jzh.1	Q16819	OTTHUMG00000014790	ENST00000230588.4:c.514C>T	6.37:g.46787399C>T	ENSP00000230588:p.Arg172Trp	Somatic	231	0	0		WXS	Illumina HiSeq	Phase_I	232	5	0.0215517	NM_005588	A2RRM4|B0AZP9|B2RCS2|Q8TDC9|Q9H1R1	Missense_Mutation	SNP	ENST00000230588.4	37	CCDS4918.1	.	.	.	.	.	.	.	.	.	.	C	24.0	4.479963	0.84747	0.0	1.16E-4	ENSG00000112818	ENST00000230588	T	0.73258	-0.73	5.81	5.81	0.92471	Peptidase, metallopeptidase (1);Peptidase M12A, astacin (2);Metallopeptidase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.91260	0.7245	H	0.99197	4.465	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.94321	0.7553	10	0.87932	D	0	-25.2727	20.0795	0.97766	0.0:1.0:0.0:0.0	.	200;172	B7ZL91;Q16819	.;MEP1A_HUMAN	W	172	ENSP00000230588:R172W	ENSP00000230588:R172W	R	+	1	2	MEP1A	46895358	0.992000	0.36948	1.000000	0.80357	0.987000	0.75469	0.380000	0.20602	2.747000	0.94245	0.650000	0.86243	CGG	.	.	weak		0.468	MEP1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040803.1	NM_005588	
ITGA3	3675	hgsc.bcm.edu	37	17	48155425	48155425	+	Missense_Mutation	SNP	G	G	A	rs2230392	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:48155425G>A	ENST00000320031.8	+	17	2485	c.2155G>A	c.(2155-2157)Gcc>Acc	p.A719T	ITGA3_ENST00000007722.7_Missense_Mutation_p.A719T	NM_002204.2|NM_005501.2	NP_002195.1|NP_005492.1	P26006	ITA3_HUMAN	integrin, alpha 3 (antigen CD49C, alpha 3 subunit of VLA-3 receptor)	719			A -> T (in dbSNP:rs2230392).		blood coagulation (GO:0007596)|cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|lung development (GO:0030324)|maternal process involved in female pregnancy (GO:0060135)|memory (GO:0007613)|mesodermal cell differentiation (GO:0048333)|negative regulation of cell projection organization (GO:0031345)|nephron development (GO:0072006)|neuron migration (GO:0001764)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of gene expression (GO:0010628)|positive regulation of neuron projection development (GO:0010976)|regulation of BMP signaling pathway (GO:0030510)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|regulation of Wnt signaling pathway (GO:0030111)|renal filtration (GO:0097205)|response to drug (GO:0042493)|response to gonadotropin (GO:0034698)|skin development (GO:0043588)	basolateral plasma membrane (GO:0016323)|cell periphery (GO:0071944)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|integrin alpha3-beta1 complex (GO:0034667)|integrin complex (GO:0008305)|invadopodium membrane (GO:0071438)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|synapse (GO:0045202)	glycoprotein binding (GO:0001948)|metal ion binding (GO:0046872)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)	p.A719T(1)		endometrium(3)|kidney(2)|large_intestine(7)|lung(11)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(2)	31						GCTGCTCATCGCCTTTGAGGT	0.602													G|||	774	0.154553	0.0076	0.2118	5008	,	,		19318	0.2808		0.0706	False		,,,				2504	0.2689				p.A719T		Atlas-SNP	.											ITGA3,NS,carcinoma,0,1	ITGA3	128	1	1	Substitution - Missense(1)	stomach(1)	c.G2155A						PASS	.	G	THR/ALA,THR/ALA	99,4307	79.3+/-117.8	0,99,2104	100.0	88.0	92.0		2155,2155	3.2	0.9	17	dbSNP_98	92	764,7836	182.3+/-230.8	29,706,3565	yes	missense,missense	ITGA3	NM_002204.2,NM_005501.2	58,58	29,805,5669	AA,AG,GG		8.8837,2.2469,6.6354	benign,benign	719/1052,719/1067	48155425	863,12143	2203	4300	6503	SO:0001583	missense	3675	exon17			CTCATCGCCTTTG	M59911	CCDS11557.1, CCDS11558.1	17q21.33	2010-03-23	2003-10-13		ENSG00000005884	ENSG00000005884		"""CD molecules"", ""Integrins"""	6139	protein-coding gene	gene with protein product		605025	"""antigen identified by monoclonal antibody J143"""	MSK18		1655803, 9704023	Standard	NM_005501		Approved	CD49c, VLA3a, VCA-2, GAP-B3	uc010dbm.3	P26006	OTTHUMG00000161890	ENST00000320031.8:c.2155G>A	17.37:g.48155425G>A	ENSP00000315190:p.Ala719Thr	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	86	38	0.44186	NM_005501	A7E246|B7ZM80|B9EGQ1|D3DTX4|D3DTX5	Missense_Mutation	SNP	ENST00000320031.8	37	CCDS11558.1	287|287	0.13141025641025642|0.13141025641025642	9|9	0.018292682926829267|0.018292682926829267	62|62	0.1712707182320442|0.1712707182320442	168|168	0.2937062937062937|0.2937062937062937	48|48	0.0633245382585752|0.0633245382585752	G|G	12.57|12.57	1.977842|1.977842	0.34942|0.34942	0.022469|0.022469	0.088837|0.088837	ENSG00000005884|ENSG00000005884	ENST00000007722;ENST00000538917;ENST00000320031|ENST00000506827	T;T|.	0.41400|.	1.0;1.0|.	5.44|5.44	3.2|3.2	0.36748|0.36748	Integrin alpha-2 (1);|.	0.466272|.	0.25130|.	N|.	0.032912|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.17082|0.17082	0.46|0.46	0.09310|0.09310	P|P	0.999999693964|0.999999693964	B;B|.	0.32781|.	0.384;0.203|.	B;B|.	0.26693|.	0.072;0.032|.	T|T	0.37079|0.37079	-0.9721|-0.9721	9|4	0.13470|.	T|.	0.59|.	.|.	8.3074|8.3074	0.32051|0.32051	0.2942:0.0:0.7058:0.0|0.2942:0.0:0.7058:0.0	rs2230392;rs2285523;rs11545789;rs16948646;rs41538980;rs41539565;rs41539793;rs45631883;rs52791957;rs60523998;rs2230392|rs2230392;rs2285523;rs11545789;rs16948646;rs41538980;rs41539565;rs41539793;rs45631883;rs52791957;rs60523998;rs2230392	719;719|.	P26006-1;P26006|.	.;ITA3_HUMAN|.	T|H	719;705;719|97	ENSP00000007722:A719T;ENSP00000315190:A719T|.	ENSP00000007722:A719T|.	A|R	+|+	1|2	0|0	ITGA3|ITGA3	45510424|45510424	0.962000|0.962000	0.33011|0.33011	0.867000|0.867000	0.34043|0.34043	0.836000|0.836000	0.47400|0.47400	1.948000|1.948000	0.40303|0.40303	0.495000|0.495000	0.27882|0.27882	0.655000|0.655000	0.94253|0.94253	GCC|CGC	G|0.907;A|0.093	0.093	strong		0.602	ITGA3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000366298.1	NM_005501	
TGM6	343641	hgsc.bcm.edu	37	20	2398017	2398017	+	Silent	SNP	G	G	A	rs2295077	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:2398017G>A	ENST00000202625.2	+	10	1537	c.1476G>A	c.(1474-1476)aaG>aaA	p.K492K	TGM6_ENST00000381423.1_Silent_p.K492K	NM_198994.2	NP_945345.2	O95932	TGM3L_HUMAN	transglutaminase 6	492					cell death (GO:0008219)|peptide cross-linking (GO:0018149)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)			breast(1)|endometrium(6)|kidney(2)|large_intestine(2)|lung(32)|ovary(4)|prostate(1)|skin(4)	52					L-Glutamine(DB00130)	CTGCCACCAAGCCCAGCATCG	0.652													G|||	1625	0.324481	0.5121	0.1931	5008	,	,		18063	0.3333		0.1561	False		,,,				2504	0.3282				p.K492K		Atlas-SNP	.											.	TGM6	126	.	0			c.G1476A						PASS	.	G		2056,2350	552.3+/-378.5	483,1090,630	43.0	38.0	40.0		1476	3.6	1.0	20	dbSNP_100	40	1476,7124	274.3+/-291.2	120,1236,2944	no	coding-synonymous	TGM6	NM_198994.2		603,2326,3574	AA,AG,GG		17.1628,46.6636,27.1567		492/707	2398017	3532,9474	2203	4300	6503	SO:0001819	synonymous_variant	343641	exon10			CACCAAGCCCAGC	AF540970	CCDS13025.1, CCDS58761.1	20p13	2010-12-19	2004-07-05	2004-07-07	ENSG00000166948	ENSG00000166948		"""Transglutaminases"""	16255	protein-coding gene	gene with protein product	"""spinocerebellar ataxia 35"""	613900	"""transglutaminase 3-like"""	TGM3L		11390390, 21106500	Standard	NM_198994		Approved	dJ734P14.3, TGY, SCA35	uc002wfy.1	O95932	OTTHUMG00000031692	ENST00000202625.2:c.1476G>A	20.37:g.2398017G>A		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	48	34	0.708333	NM_198994	Q5JXU4|Q5JXU5|Q719M2|Q719M3|Q9Y4U8	Silent	SNP	ENST00000202625.2	37	CCDS13025.1																																																																																			G|0.719;A|0.281	0.281	strong		0.652	TGM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077581.2	NM_198994	
AHRR	57491	hgsc.bcm.edu	37	5	422955	422955	+	Missense_Mutation	SNP	C	C	G	rs2292596	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:422955C>G	ENST00000505113.1	+	6	609	c.565C>G	c.(565-567)Ccc>Gcc	p.P189A	AHRR_ENST00000506456.1_Missense_Mutation_p.P45A|AHRR_ENST00000316418.5_Missense_Mutation_p.P189A|AHRR_ENST00000512529.1_Missense_Mutation_p.P35A	NM_001242412.1	NP_001229341.1	A9YTQ3	AHRR_HUMAN	aryl-hydrocarbon receptor repressor	189			P -> A (in dbSNP:rs2292596). {ECO:0000269|PubMed:10574462, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.2, ECO:0000269|Ref.5}.		negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of protein sumoylation (GO:0033235)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|signal transducer activity (GO:0004871)			breast(2)|endometrium(4)|large_intestine(1)|lung(12)|prostate(1)	20			Epithelial(17;0.0011)|OV - Ovarian serous cystadenocarcinoma(19;0.00353)|all cancers(22;0.00354)|Lung(60;0.0863)			GTTTGGGCAGCCCCCGCCCTT	0.592																																					p.P189A		Atlas-SNP	.											AHRR,brain,glioma,0,2	AHRR	67	2	0			c.C565G	GRCh37	CM057935	AHRR	M	rs2292596	PASS	.	C	ALA/PRO,ALA/PRO	593,3451		43,507,1472	43.0	50.0	47.0		565,565	3.1	0.3	5	dbSNP_100	47	3154,5190		622,1910,1640	yes	missense,missense	AHRR	NM_001242412.1,NM_020731.4	27,27	665,2417,3112	GG,GC,CC		37.7996,14.6637,30.247	benign,benign	189/702,189/720	422955	3747,8641	2022	4172	6194	SO:0001583	missense	57491	exon6			GGGCAGCCCCCGC	AB033060	CCDS43297.1, CCDS56355.1	5p15.33	2013-05-21	2003-09-11	2003-09-12	ENSG00000063438	ENSG00000063438		"""Basic helix-loop-helix proteins"""	346	protein-coding gene	gene with protein product		606517	"""aryl hydrocarbon receptor regulator"""	AHH, AHHR		1070014, 11423533	Standard	NM_020731		Approved	KIAA1234, bHLHe77	uc003jaw.3	A9YTQ3	OTTHUMG00000162171	ENST00000505113.1:c.565C>G	5.37:g.422955C>G	ENSP00000424601:p.Pro189Ala	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	84	35	0.416667	NM_001242412	A7MBN5|D6RAZ1|Q9HAZ3|Q9ULI6	Missense_Mutation	SNP	ENST00000505113.1	37	CCDS56355.1	672	0.3076923076923077	62	0.12601626016260162	109	0.3011049723756906	229	0.40034965034965037	272	0.35883905013192613	C	4.514	0.095307	0.08681	0.146637	0.377996	ENSG00000063438	ENST00000505113;ENST00000316418;ENST00000512529;ENST00000506456	T;T;T;T	0.22134	2.24;2.24;1.98;1.97	4.9	3.08	0.35506	.	0.186887	0.46442	D	0.000291	T	0.00012	0.0000	M	0.71581	2.175	0.45284	P	0.001715000000000022	P;B;B	0.50156	0.932;0.067;0.036	P;B;B	0.50659	0.647;0.012;0.061	T	0.44757	-0.9307	9	0.22109	T	0.4	.	4.6477	0.12580	0.0:0.614:0.182:0.2039	rs2292596;rs2292596	45;189;189	D6RE68;A9YTQ3;A9YTQ3-2	.;AHRR_HUMAN;.	A	189;189;35;45	ENSP00000424601:P189A;ENSP00000323816:P189A;ENSP00000424880:P35A;ENSP00000426932:P45A	ENSP00000323816:P189A	P	+	1	0	AHRR	475955	0.543000	0.26434	0.279000	0.24732	0.048000	0.14542	1.157000	0.31724	0.450000	0.26774	0.655000	0.94253	CCC	C|0.670;G|0.330	0.330	strong		0.592	AHRR-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000367720.1	NM_020731	
PIGZ	80235	hgsc.bcm.edu	37	3	196674879	196674879	+	Silent	SNP	A	A	G	rs12636891	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:196674879A>G	ENST00000412723.1	-	3	1035	c.889T>C	c.(889-891)Ttg>Ctg	p.L297L		NM_025163.2	NP_079439.2	Q86VD9	PIGZ_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class Z	297					GPI anchor biosynthetic process (GO:0006506)|mannosylation (GO:0097502)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	alpha-1,2-mannosyltransferase activity (GO:0000026)|mannosyltransferase activity (GO:0000030)			breast(1)|endometrium(1)|lung(7)|ovary(3)|prostate(1)|urinary_tract(1)	14	all_cancers(143;1.05e-08)|Ovarian(172;0.0634)|Breast(254;0.0838)		Epithelial(36;4.29e-24)|all cancers(36;2.79e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.03e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00603)		TTGTAGTGCAAGAAGTTGACA	0.597													A|||	2967	0.592452	0.6036	0.6095	5008	,	,		19489	0.755		0.4881	False		,,,				2504	0.5051				p.L297L		Atlas-SNP	.											.	PIGZ	34	.	0			c.T889C						PASS	.	A		2500,1906	611.4+/-391.8	701,1098,404	133.0	138.0	137.0		889	-2.6	0.9	3	dbSNP_120	137	3901,4699	528.0+/-381.3	879,2143,1278	no	coding-synonymous	PIGZ	NM_025163.2		1580,3241,1682	GG,GA,AA		45.3605,43.2592,49.2157		297/580	196674879	6401,6605	2203	4300	6503	SO:0001819	synonymous_variant	80235	exon3			AGTGCAAGAAGTT	BC018804	CCDS3324.1	3q29	2013-02-26	2006-06-28		ENSG00000119227	ENSG00000119227		"""Dolichyl D-mannosyl phosphate dependent mannosyltransferases"", ""Phosphatidylinositol glycan anchor biosynthesis"""	30596	protein-coding gene	gene with protein product	"""GPI mannosyltransferase 4"", ""dol-P-Man dependent GPI mannosyltransferase"""	611671	"""phosphatidylinositol glycan, class Z"""			15208306	Standard	NM_025163		Approved	FLJ12768, MGC52163, SMP3	uc003fxh.3	Q86VD9	OTTHUMG00000155522	ENST00000412723.1:c.889T>C	3.37:g.196674879A>G		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	53	52	0.981132	NM_025163	Q9H9G6	Silent	SNP	ENST00000412723.1	37	CCDS3324.1																																																																																			A|0.453;G|0.547	0.547	strong		0.597	PIGZ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340486.2	NM_025163	
CCDC102A	92922	hgsc.bcm.edu	37	16	57562804	57562804	+	Missense_Mutation	SNP	G	G	A	rs12935069		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:57562804G>A	ENST00000258214.2	-	2	532	c.286C>T	c.(286-288)Cgg>Tgg	p.R96W		NM_033212.3	NP_149989.2	Q96A19	C102A_HUMAN	coiled-coil domain containing 102A	96				R -> W (in Ref. 2; AAH08285/AAH09941). {ECO:0000305}.						endometrium(1)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)	8						TCCGACCACCGGCGCATGGTC	0.731													A|||	5008	1.0	1.0	1.0	5008	,	,		3757	1.0		1.0	False		,,,				2504	1.0				p.R96W		Atlas-SNP	.											.	CCDC102A	22	.	0			c.C286T						PASS	.						8.0	10.0	9.0					16																	57562804		1834	3717	5551	SO:0001583	missense	92922	exon2			ACCACCGGCGCAT	BC008285	CCDS10784.1	16q13	2008-02-05			ENSG00000135736	ENSG00000135736			28097	protein-coding gene	gene with protein product						12477932	Standard	NM_033212		Approved	MGC10992	uc002elw.3	Q96A19	OTTHUMG00000133472	ENST00000258214.2:c.286C>T	16.37:g.57562804G>A	ENSP00000258214:p.Arg96Trp	Somatic	0	0	.		WXS	Illumina HiSeq	Phase_I	4	4	1	NM_033212	Q9BT74	Missense_Mutation	SNP	ENST00000258214.2	37	CCDS10784.1	2180	0.9981684981684982	492	1.0	360	0.994475138121547	570	0.9965034965034965	758	1.0	A	10.17	1.277909	0.23307	.	.	ENSG00000135736	ENST00000258214	T	0.37752	1.18	4.82	4.82	0.62117	.	0.000000	0.64402	N	0.000001	T	0.00012	0.0000	N	0.00049	-2.415	0.40217	P	0.022302999999999962	B	0.02656	0.0	B	0.01281	0.0	T	0.44787	-0.9305	9	0.33141	T	0.24	-23.2491	9.5348	0.39216	0.9152:0.0:0.0848:0.0	rs12935069;rs12935069	96	Q96A19	C102A_HUMAN	W	96	ENSP00000258214:R96W	ENSP00000258214:R96W	R	-	1	2	CCDC102A	56120305	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	6.801000	0.75170	0.698000	0.31739	-0.556000	0.04195	CGG	G|0.001;A|0.999	0.999	strong		0.731	CCDC102A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257348.1	NM_033212	
PDE4A	5141	hgsc.bcm.edu	37	19	10531491	10531491	+	Silent	SNP	C	C	T	rs117495488	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:10531491C>T	ENST00000352831.6	+	1	161	c.51C>T	c.(49-51)ccC>ccT	p.P17P	PDE4A_ENST00000380702.2_Intron|PDE4A_ENST00000592685.1_Intron	NM_001111307.1	NP_001104777.1	P27815	PDE4A_HUMAN	phosphodiesterase 4A, cAMP-specific	17					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)			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)	TGTCACTGCCCGGGCCCCGGG	0.726													C|||	34	0.00678914	0.0	0.0	5008	,	,		8964	0.0278		0.004	False		,,,				2504	0.002				p.P17P		Atlas-SNP	.											.	PDE4A	236	.	0			c.C51T						PASS	.	C		0,2670		0,0,1335	7.0	8.0	8.0		51	-7.6	0.9	19	dbSNP_132	8	6,6434		0,6,3214	no	coding-synonymous	PDE4A	NM_001111307.1		0,6,4549	TT,TC,CC		0.0932,0.0,0.0659		17/887	10531491	6,9104	1335	3220	4555	SO:0001819	synonymous_variant	5141	exon1			ACTGCCCGGGCCC		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.51C>T	19.37:g.10531491C>T		Somatic	2	0	0		WXS	Illumina HiSeq	Phase_I	32	18	0.5625	NM_001111307	O75522|O76092|Q16255|Q16691|Q5DM53|Q6PMT2|Q8IVA7|Q8WUQ3|Q9H3H2	Silent	SNP	ENST00000352831.6	37	CCDS45961.1																																																																																			C|0.987;T|0.013	0.013	strong		0.726	PDE4A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451244.1		
COL4A3	1285	hgsc.bcm.edu	37	2	228128568	228128568	+	Missense_Mutation	SNP	G	G	A	rs34505188	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:228128568G>A	ENST00000396578.3	+	21	1385	c.1223G>A	c.(1222-1224)cGc>cAc	p.R408H	AC097662.2_ENST00000439598.2_RNA|AC097662.2_ENST00000396588.2_RNA|AC097662.2_ENST00000437673.1_RNA	NM_000091.4	NP_000082.2	Q01955	CO4A3_HUMAN	collagen, type IV, alpha 3 (Goodpasture antigen)	408	Triple-helical region.		R -> H (in dbSNP:rs34505188). {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)		GAACGAGGCCGCCCAGGAAAG	0.562													G|||	504	0.100639	0.028	0.1772	5008	,	,		15959	0.1577		0.0686	False		,,,				2504	0.1186				p.R408H		Atlas-SNP	.											COL4A3_ENST00000328380,NS,carcinoma,+1,2	COL4A3	293	2	0			c.G1223A						PASS	.	G	HIS/ARG	123,3603		3,117,1743	40.0	45.0	44.0		1223	2.1	1.0	2	dbSNP_126	44	630,7548		21,588,3480	yes	missense	COL4A3	NM_000091.4	29	24,705,5223	AA,AG,GG		7.7036,3.3011,6.3256	probably-damaging	408/1671	228128568	753,11151	1863	4089	5952	SO:0001583	missense	1285	exon21			GAGGCCGCCCAGG		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.1223G>A	2.37:g.228128568G>A	ENSP00000379823:p.Arg408His	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	101	44	0.435644	NM_000091	Q53QQ1|Q53R14|Q53RW8|Q9BQT2|Q9NYC4|Q9UDJ9|Q9UDK9|Q9UDL0|Q9UDL1	Missense_Mutation	SNP	ENST00000396578.3	37	CCDS42829.1	210	0.09615384615384616	16	0.032520325203252036	58	0.16022099447513813	87	0.1520979020979021	49	0.06464379947229551	G	8.597	0.885960	0.17540	0.033011	0.077036	ENSG00000169031	ENST00000396578;ENST00000328380;ENST00000335583;ENST00000396574;ENST00000315699	D	0.94000	-3.33	6.02	2.07	0.26955	.	0.318892	0.27522	N	0.018999	T	0.03608	0.0103	L	0.33093	0.98	0.44937	P	0.0020459999999999923	D;D;D;D	0.76494	0.998;0.998;0.998;0.999	P;P;P;D	0.63192	0.731;0.731;0.856;0.912	T	0.60662	-0.7219	9	0.28530	T	0.3	.	2.6414	0.04972	0.1368:0.4371:0.2739:0.1523	rs34505188	408;408;408;408	Q01955-5;Q01955-4;Q01955-2;Q01955	.;.;.;CO4A3_HUMAN	H	408	ENSP00000379823:R408H	ENSP00000323334:R408H	R	+	2	0	COL4A3	227836812	0.994000	0.37717	0.989000	0.46669	0.043000	0.13939	0.671000	0.25172	0.456000	0.26937	-0.783000	0.03347	CGC	G|0.907;A|0.093	0.093	strong		0.562	COL4A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331409.2	NM_000091	
AKNA	80709	hgsc.bcm.edu	37	9	117103973	117103973	+	Missense_Mutation	SNP	A	A	G	rs2250242	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:117103973A>G	ENST00000307564.4	-	21	4068	c.3907T>C	c.(3907-3909)Tct>Cct	p.S1303P	AKNA_ENST00000374075.5_Missense_Mutation_p.S1222P|AKNA_ENST00000374088.3_Missense_Mutation_p.S1303P|AKNA_ENST00000223791.3_Missense_Mutation_p.S763P|AKNA_ENST00000374079.4_Missense_Mutation_p.S248P|AKNA_ENST00000492875.1_5'UTR	NM_030767.4	NP_110394.3	Q7Z591	AKNA_HUMAN	AT-hook transcription factor	1303			S -> P (in dbSNP:rs2250242). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		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)			breast(3)|central_nervous_system(4)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(7)|liver(2)|lung(22)|ovary(4)|stomach(2)	51						GGAGTTGAAGATGCTTTTCTC	0.622													G|||	3056	0.610224	0.8828	0.536	5008	,	,		17107	0.6131		0.4841	False		,,,				2504	0.4213				p.S1303P		Atlas-SNP	.											.	AKNA	119	.	0			c.T3907C						PASS	.	G	PRO/SER	3616,790	317.7+/-295.3	1492,632,79	62.0	60.0	60.0		3907	0.6	0.0	9	dbSNP_100	60	4094,4506	592.0+/-392.9	955,2184,1161	yes	missense	AKNA	NM_030767.4	74	2447,2816,1240	GG,GA,AA		47.6047,17.9301,40.7197	benign	1303/1440	117103973	7710,5296	2203	4300	6503	SO:0001583	missense	80709	exon21			TTGAAGATGCTTT	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.3907T>C	9.37:g.117103973A>G	ENSP00000303769:p.Ser1303Pro	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	47	47	1	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	1340	0.6135531135531136	434	0.8821138211382114	187	0.5165745856353591	355	0.6206293706293706	364	0.48021108179419525	G	0.858	-0.736344	0.03111	0.820699	0.476047	ENSG00000106948	ENST00000307564;ENST00000374079;ENST00000374088;ENST00000223791;ENST00000374075	T;T;T;T;T	0.19938	2.52;2.11;2.52;2.27;2.5	5.32	0.646	0.17789	.	0.217040	0.32802	N	0.005639	T	0.00012	0.0000	N	0.01576	-0.805	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.09509	-1.0671	9	0.23302	T	0.38	0.251	4.3501	0.11151	0.4136:0.1632:0.4232:0.0	rs2250242;rs17857447;rs52828574;rs59133154;rs2250242	1303;1222	Q7Z591;Q7Z591-2	AKNA_HUMAN;.	P	1303;248;1303;763;1222	ENSP00000303769:S1303P;ENSP00000363192:S248P;ENSP00000363201:S1303P;ENSP00000223791:S763P;ENSP00000363188:S1222P	ENSP00000223791:S763P	S	-	1	0	AKNA	116143794	0.002000	0.14202	0.000000	0.03702	0.009000	0.06853	-0.029000	0.12329	0.042000	0.15717	-0.119000	0.15052	TCT	A|0.404;G|0.596	0.596	strong		0.622	AKNA-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053767.2	NM_030767	
AGBL1	123624	hgsc.bcm.edu	37	15	86940622	86940622	+	Silent	SNP	T	T	C	rs4362360	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:86940622T>C	ENST00000441037.2	+	17	2357	c.2262T>C	c.(2260-2262)acT>acC	p.T754T	AGBL1_ENST00000389298.3_Silent_p.T485T|AGBL1_ENST00000421325.2_Silent_p.T754T	NM_152336.2	NP_689549.2	Q96MI9	CBPC4_HUMAN	ATP/GTP binding protein-like 1	754					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						AGGTGATCACTGCTCGAGTTC	0.428													C|||	3727	0.744209	0.9735	0.6859	5008	,	,		18211	0.88		0.4284	False		,,,				2504	0.6605				p.T754T		Atlas-SNP	.											.	AGBL1	151	.	0			c.T2262C						PASS	.	C		3501,379		1588,325,27	113.0	108.0	110.0		2262	-11.0	0.5	15	dbSNP_111	110	3879,4395		891,2097,1149	yes	coding-synonymous	AGBL1	NM_152336.2		2479,2422,1176	CC,CT,TT		46.8818,9.768,39.2792		754/1067	86940622	7380,4774	1940	4137	6077	SO:0001819	synonymous_variant	123624	exon17			GATCACTGCTCGA	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.2262T>C	15.37:g.86940622T>C		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	143	143	1	NM_152336	A1A4X5|A6NJH6|C9JHL5	Silent	SNP	ENST00000441037.2	37	CCDS58398.1																																																																																			T|0.292;C|0.708	0.708	strong		0.428	AGBL1-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000314929.5	NM_152336	
OR56B1	387748	hgsc.bcm.edu	37	11	5758386	5758386	+	Missense_Mutation	SNP	C	C	T	rs62621167	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:5758386C>T	ENST00000317121.3	+	1	706	c.640C>T	c.(640-642)Ctt>Ttt	p.L214F	TRIM5_ENST00000380027.1_Intron	NM_001005180.2	NP_001005180.1	Q8NGI3	O56B1_HUMAN	olfactory receptor, family 56, subfamily B, member 1	214						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(7)|prostate(1)|skin(1)	13		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.086)		Epithelial(150;1.74e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)|LUSC - Lung squamous cell carcinoma(625;0.184)		TCTGGCATGGCTTGGAATGGG	0.463													C|||	90	0.0179712	0.0008	0.0216	5008	,	,		21859	0.0		0.0626	False		,,,				2504	0.0112				p.L214F		Atlas-SNP	.											.	OR56B1	38	.	0			c.C640T						PASS	.	C	PHE/LEU	42,4360	45.3+/-79.5	0,42,2159	82.0	74.0	77.0		640	-11.5	0.0	11	dbSNP_129	77	475,8119	139.4+/-196.0	17,441,3839	yes	missense	OR56B1	NM_001005180.2	22	17,483,5998	TT,TC,CC		5.5271,0.9541,3.9781	benign	214/325	5758386	517,12479	2201	4297	6498	SO:0001583	missense	387748	exon1			GCATGGCTTGGAA	BK004386	CCDS31395.1	11p15.4	2012-08-09		2004-03-10	ENSG00000181023	ENSG00000181023		"""GPCR / Class A : Olfactory receptors"""	15245	protein-coding gene	gene with protein product				OR56B1P			Standard	NM_001005180		Approved		uc001mbt.2	Q8NGI3	OTTHUMG00000066891	ENST00000317121.3:c.640C>T	11.37:g.5758386C>T	ENSP00000322939:p.Leu214Phe	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	115	22	0.191304	NM_001005180	B2RNY6|B3KV42|Q6IF76	Missense_Mutation	SNP	ENST00000317121.3	37	CCDS31395.1	58	0.026556776556776556	1	0.0020325203252032522	8	0.022099447513812154	0	0.0	49	0.06464379947229551	C	7.884	0.730758	0.15507	0.009541	0.055271	ENSG00000181023	ENST00000317121	T	0.39056	1.1	5.74	-11.5	0.00074	GPCR, rhodopsin-like superfamily (1);	1.191410	0.06470	N	0.731014	T	0.02119	0.0066	N	0.21617	0.685	0.09310	N	0.999997	B	0.06786	0.001	B	0.15484	0.013	T	0.05649	-1.0872	10	0.23302	T	0.38	-0.0243	7.2229	0.25999	0.2901:0.0937:0.5002:0.116	rs62621167	214	Q8NGI3	O56B1_HUMAN	F	214	ENSP00000322939:L214F	ENSP00000322939:L214F	L	+	1	0	OR56B1	5714962	0.000000	0.05858	0.000000	0.03702	0.987000	0.75469	-7.112000	0.00044	-3.673000	0.00123	0.643000	0.83706	CTT	C|0.962;T|0.038	0.038	strong		0.463	OR56B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143354.1	NM_001005180	
CCKBR	887	hgsc.bcm.edu	37	11	6291466	6291466	+	Silent	SNP	A	A	G	rs77873910	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:6291466A>G	ENST00000334619.2	+	3	745	c.552A>G	c.(550-552)ctA>ctG	p.L184L	CCKBR_ENST00000532715.1_Silent_p.L100L|CCKBR_ENST00000525462.1_Silent_p.L184L|CCKBR_ENST00000525014.1_3'UTR	NM_176875.3	NP_795344.1	P32239	GASR_HUMAN	cholecystokinin B receptor	184					cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|cholecystokinin signaling pathway (GO:0038188)|digestion (GO:0007586)|digestive tract development (GO:0048565)|feeding behavior (GO:0007631)|gastric acid secretion (GO:0001696)|gland development (GO:0048732)|metabolic process (GO:0008152)|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)|regulation of phosphatidylinositol 3-kinase activity (GO:0043551)|sensory perception (GO:0007600)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase regulator activity (GO:0046935)|cholecystokinin receptor activity (GO:0004951)|gastrin receptor activity (GO:0015054)|phosphatidylinositol phospholipase C activity (GO:0004435)|type B gastrin/cholecystokinin receptor binding (GO:0031741)			NS(2)|breast(2)|endometrium(4)|kidney(13)|large_intestine(10)|lung(22)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	61		Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029)		Epithelial(150;2.62e-08)|BRCA - Breast invasive adenocarcinoma(625;0.139)	Pentagastrin(DB00183)	TGTCCGGACTACTCATGGTGC	0.667													A|||	44	0.00878594	0.0045	0.0187	5008	,	,		2100	0.0		0.0159	False		,,,				2504	0.0092				p.L184L		Atlas-SNP	.											CCKBR_ENST00000525462,NS,carcinoma,+2,2	CCKBR	232	2	0			c.A552G						PASS	.	A		32,4370	36.8+/-68.6	0,32,2169	59.0	49.0	53.0		552	3.2	1.0	11	dbSNP_131	53	155,8437	73.5+/-136.2	1,153,4142	no	coding-synonymous	CCKBR	NM_176875.2		1,185,6311	GG,GA,AA		1.804,0.7269,1.4391		184/448	6291466	187,12807	2201	4296	6497	SO:0001819	synonymous_variant	887	exon3			CGGACTACTCATG	D13305	CCDS7761.1	11p15.4	2012-08-10			ENSG00000110148	ENSG00000110148		"""GPCR / Class A : Cholecystokinin receptors"""	1571	protein-coding gene	gene with protein product		118445				1280419	Standard	NM_176875		Approved		uc001mcp.3	P32239	OTTHUMG00000133380	ENST00000334619.2:c.552A>G	11.37:g.6291466A>G		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	77	16	0.207792	NM_176875	A8K7P9|O75824|Q16144|Q92492|Q96LC6|Q9NYK7|Q9UBV1	Silent	SNP	ENST00000334619.2	37	CCDS7761.1																																																																																			A|0.986;G|0.014	0.014	strong		0.667	CCKBR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257230.2	NM_176875	
TGM4	7047	hgsc.bcm.edu	37	3	44929287	44929287	+	Splice_Site	SNP	G	G	C	rs2271087	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:44929287G>C	ENST00000296125.4	+	3	368	c.300G>C	c.(298-300)gaG>gaC	p.E100D		NM_003241.3	NP_003232.2	P49221	TGM4_HUMAN	transglutaminase 4	100			E -> D (in dbSNP:rs2271087).		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)	CTGGCAAAGAGGTGAGCACCC	0.597													G|||	2139	0.427117	0.1566	0.4251	5008	,	,		17450	0.8165		0.2873	False		,,,				2504	0.5368				p.E100D		Atlas-SNP	.											.	TGM4	82	.	0			c.G300C						PASS	.	G	ASP/GLU	777,3629	312.2+/-292.5	60,657,1486	64.0	59.0	60.0		300	1.4	0.1	3	dbSNP_100	60	2531,6069	411.5+/-350.5	361,1809,2130	yes	missense-near-splice	TGM4	NM_003241.3	45	421,2466,3616	CC,CG,GG		29.4302,17.635,25.4344	possibly-damaging	100/685	44929287	3308,9698	2203	4300	6503	SO:0001630	splice_region_variant	7047	exon3			CAAAGAGGTGAGC	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.300+1G>C	3.37:g.44929287G>C		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	52	28	0.538462	NM_003241	Q16707|Q96QN4	Missense_Mutation	SNP	ENST00000296125.4	37	CCDS2723.1	926	0.423992673992674	78	0.15853658536585366	138	0.3812154696132597	488	0.8531468531468531	222	0.2928759894459103	G	11.20	1.567273	0.28003	0.17635	0.294302	ENSG00000163810	ENST00000296125	D	0.82344	-1.6	1.43	1.43	0.22495	Immunoglobulin E-set (1);Transglutaminase, N-terminal (1);Immunoglobulin-like fold (1);	0.424980	0.17583	U	0.169031	T	0.00012	0.0000	L	0.41710	1.295	0.58432	P	1.999999999946489E-6	B;P	0.48589	0.339;0.912	B;P	0.49085	0.179;0.6	T	0.40384	-0.9566	9	0.27785	T	0.31	.	6.2761	0.20981	0.0:0.0:1.0:0.0	rs2271087;rs52829496;rs58605386	100;100	P49221;B4YUQ1	TGM4_HUMAN;.	D	100	ENSP00000296125:E100D	ENSP00000296125:E100D	E	+	3	2	TGM4	44904291	0.935000	0.31712	0.138000	0.22173	0.048000	0.14542	1.822000	0.39052	1.094000	0.41399	0.467000	0.42956	GAG	G|0.677;C|0.322	0.322	strong		0.597	TGM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256755.2	NM_003241	Missense_Mutation
HDLBP	3069	hgsc.bcm.edu	37	2	242192848	242192848	+	Missense_Mutation	SNP	T	T	C	rs7578199	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:242192848T>C	ENST00000391975.1	-	10	1480	c.1253A>G	c.(1252-1254)aAt>aGt	p.N418S	HDLBP_ENST00000476807.1_5'Flank|HDLBP_ENST00000391976.2_Missense_Mutation_p.N418S|HDLBP_ENST00000310931.4_Missense_Mutation_p.N418S|HDLBP_ENST00000427183.2_Missense_Mutation_p.N385S	NM_203346.3	NP_976221	Q00341	VIGLN_HUMAN	high density lipoprotein binding protein	418	KH 4. {ECO:0000255|PROSITE- ProRule:PRU00117}.		N -> S (in dbSNP:rs7578199).		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)		CTGGGCCACATTGACATCCTC	0.498													T|||	690	0.13778	0.1785	0.1916	5008	,	,		20669	0.001		0.2684	False		,,,				2504	0.0511				p.N418S		Atlas-SNP	.											.	HDLBP	118	.	0			c.A1253G						PASS	.	T	SER/ASN,SER/ASN	805,3601	322.9+/-297.8	65,675,1463	228.0	187.0	201.0		1253,1253	-11.9	0.0	2	dbSNP_116	201	2118,6482	364.2+/-333.4	261,1596,2443	yes	missense,missense	HDLBP	NM_005336.4,NM_203346.3	46,46	326,2271,3906	CC,CT,TT		24.6279,18.2705,22.4742	benign,benign	418/1269,418/1269	242192848	2923,10083	2203	4300	6503	SO:0001583	missense	3069	exon10			GCCACATTGACAT		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.1253A>G	2.37:g.242192848T>C	ENSP00000375836:p.Asn418Ser	Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	142	72	0.507042	NM_005336	B4DTQ2|E7EM71|Q53QU2|Q9UCY3	Missense_Mutation	SNP	ENST00000391975.1	37	CCDS2547.1	356|356	0.163003663003663|0.163003663003663	76|76	0.15447154471544716|0.15447154471544716	79|79	0.21823204419889503|0.21823204419889503	1|1	0.0017482517482517483|0.0017482517482517483	200|200	0.2638522427440633|0.2638522427440633	T|T	6.318|6.318	0.426852|0.426852	0.11987|0.11987	0.182705|0.182705	0.246279|0.246279	ENSG00000115677|ENSG00000115677	ENST00000453141|ENST00000391975;ENST00000391976;ENST00000310931;ENST00000427183	.|T;T;T;T	.|0.29655	.|1.56;1.56;1.56;1.56	5.96|5.96	-11.9|-11.9	0.00025|0.00025	.|K Homology (1);K Homology, type 1, subgroup (1);K Homology, type 1 (1);	.|0.573156	.|0.21521	.|N	.|0.073204	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;B	.|0.10296	.|0.0;0.003;0.0	.|B;B;B	.|0.11329	.|0.005;0.006;0.005	T|T	0.15809|0.15809	-1.0424|-1.0424	4|9	.|0.28530	.|T	.|0.3	-18.9169|-18.9169	10.2925|10.2925	0.43605|0.43605	0.0:0.389:0.3221:0.2889|0.0:0.389:0.3221:0.2889	rs7578199;rs60102099;rs7578199|rs7578199;rs60102099;rs7578199	.|418;385;418	.|B2R5V9;E7EM71;Q00341	.|.;.;VIGLN_HUMAN	V|S	296|418;418;418;385	.|ENSP00000375836:N418S;ENSP00000375837:N418S;ENSP00000312042:N418S;ENSP00000399139:N385S	.|ENSP00000312042:N418S	M|N	-|-	1|2	0|0	HDLBP|HDLBP	241841521|241841521	0.029000|0.029000	0.19370|0.19370	0.000000|0.000000	0.03702|0.03702	0.038000|0.038000	0.13279|0.13279	0.019000|0.019000	0.13444|0.13444	-2.653000|-2.653000	0.00423|0.00423	-2.181000|-2.181000	0.00316|0.00316	ATG|AAT	T|0.798;C|0.202	0.202	strong		0.498	HDLBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257245.5	NM_203346	
AATF	26574	hgsc.bcm.edu	37	17	35346641	35346641	+	Silent	SNP	T	T	C	rs1045056	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:35346641T>C	ENST00000225402.5	+	7	1496	c.1245T>C	c.(1243-1245)tcT>tcC	p.S415S		NM_012138.3	NP_036270.1	Q9NY61	AATF_HUMAN	apoptosis antagonizing transcription factor	415	RB1 and SP1 binding.				apoptotic signaling pathway (GO:0097190)|cell adhesion (GO:0007155)|cellular response to DNA damage stimulus (GO:0006974)|embryonic cleavage (GO:0040016)|negative regulation of amyloid precursor protein biosynthetic process (GO:0042985)|negative regulation of apoptotic process (GO:0043066)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of superoxide anion generation (GO:0032929)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of mitotic cell cycle (GO:0007346)|ribosome biogenesis (GO:0042254)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleus (GO:0005634)	leucine zipper domain binding (GO:0043522)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(2)|endometrium(1)|large_intestine(4)|lung(7)|ovary(2)|skin(2)	18		Breast(25;0.00607)				CCAAGCGCTCTGTCTATCGAG	0.493													T|||	785	0.156749	0.0628	0.1542	5008	,	,		18574	0.0357		0.3419	False		,,,				2504	0.2198				p.S415S	NSCLC(49;901 1159 19183 41572 46244)	Atlas-SNP	.											.	AATF	36	.	0			c.T1245C						PASS	.	T		424,3982	204.8+/-226.9	25,374,1804	190.0	189.0	190.0		1245	3.9	1.0	17	dbSNP_86	190	2733,5867	435.9+/-358.1	440,1853,2007	no	coding-synonymous	AATF	NM_012138.3		465,2227,3811	CC,CT,TT		31.7791,9.6232,24.2734		415/561	35346641	3157,9849	2203	4300	6503	SO:0001819	synonymous_variant	26574	exon7			GCGCTCTGTCTAT	AF083208	CCDS32632.1	17q12	2014-05-06			ENSG00000108270	ENSG00000275700			19235	protein-coding gene	gene with protein product		608463				11027528, 10783144	Standard	NM_012138		Approved	DED, CHE-1, CHE1, BFR2	uc002hni.3	Q9NY61	OTTHUMG00000188458	ENST00000225402.5:c.1245T>C	17.37:g.35346641T>C		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	133	61	0.458647	NM_012138	A6NCJ6|B3KQ26|Q9P0A4|Q9UNX5	Silent	SNP	ENST00000225402.5	37	CCDS32632.1																																																																																			T|0.782;C|0.218	0.218	strong		0.493	AATF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451543.1	NM_012138	
CELSR2	1952	hgsc.bcm.edu	37	1	109806834	109806834	+	Silent	SNP	C	C	T	rs6698843	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:109806834C>T	ENST00000271332.3	+	10	5197	c.5136C>T	c.(5134-5136)ccC>ccT	p.P1712P		NM_001408.2	NP_001399.1	Q9HCU4	CELR2_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 2	1712	Laminin G-like 2. {ECO:0000255|PROSITE- ProRule:PRU00122}.				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)		GCGGGGGGCCCGGCCATGCCA	0.657											OREG0013632	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	1770	0.353435	0.0764	0.4654	5008	,	,		12448	0.498		0.4751	False		,,,				2504	0.3742				p.P1712P	NSCLC(158;1285 2011 34800 34852 42084)	Atlas-SNP	.											.	CELSR2	228	.	0			c.C5136T						PASS	.	C		587,3819	247.8+/-255.9	39,509,1655	33.0	48.0	43.0		5136	-9.9	0.7	1	dbSNP_116	43	4016,4584	536.2+/-383.0	938,2140,1222	no	coding-synonymous	CELSR2	NM_001408.2		977,2649,2877	TT,TC,CC		46.6977,13.3227,35.3914		1712/2924	109806834	4603,8403	2203	4300	6503	SO:0001819	synonymous_variant	1952	exon10			GGGGCCCGGCCAT	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.5136C>T	1.37:g.109806834C>T		Somatic	77	0	0	1422	WXS	Illumina HiSeq	Phase_I	53	51	0.962264	NM_001408	Q5T2Y7|Q92566	Silent	SNP	ENST00000271332.3	37	CCDS796.1																																																																																			C|0.633;T|0.367	0.367	strong		0.657	CELSR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033200.1	NM_001408	
NEK11	79858	hgsc.bcm.edu	37	3	130799314	130799314	+	Missense_Mutation	SNP	C	C	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:130799314C>G	ENST00000510769.1	+	3	471	c.218C>G	c.(217-219)aCt>aGt	p.T73S	NEK11_ENST00000356918.4_Missense_Mutation_p.T73S|NEK11_ENST00000383366.4_Missense_Mutation_p.T73S|NEK11_ENST00000507910.1_Missense_Mutation_p.T73S|NEK11_ENST00000412440.2_Intron|NEK11_ENST00000508196.1_Missense_Mutation_p.T73S|NEK11_ENST00000429253.2_Missense_Mutation_p.T73S|NEK11_ENST00000510688.1_Missense_Mutation_p.T73S|NEK11_ENST00000511262.1_Missense_Mutation_p.T73S					NIMA-related kinase 11											breast(2)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(8)|lung(14)|stomach(1)|urinary_tract(2)	33						CCAAATGAAACTGTACAGGCC	0.368																																					p.T73S		Atlas-SNP	.											.	NEK11	76	.	0			c.C218G						PASS	.						76.0	74.0	75.0					3																	130799314		2203	4300	6503	SO:0001583	missense	79858	exon4			ATGAAACTGTACA	AK027148	CCDS3069.1, CCDS46915.1, CCDS54639.1	3q22.1	2012-11-15	2012-11-15		ENSG00000114670	ENSG00000114670			18593	protein-coding gene	gene with protein product		609779	"""NIMA (never in mitosis gene a)- related kinase 11"""				Standard	NM_024800		Approved	FLJ23495	uc003eny.3	Q8NG66	OTTHUMG00000159654	ENST00000510769.1:c.218C>G	3.37:g.130799314C>G	ENSP00000421549:p.Thr73Ser	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	70	18	0.257143	NM_024800		Missense_Mutation	SNP	ENST00000510769.1	37		.	.	.	.	.	.	.	.	.	.	C	12.87	2.067808	0.36470	.	.	ENSG00000114670	ENST00000510769;ENST00000429253;ENST00000356918;ENST00000510688;ENST00000511262;ENST00000383366;ENST00000507910;ENST00000508196	T;T;T;T;T;T;T;T	0.64618	-0.11;-0.11;-0.11;-0.11;-0.11;-0.11;-0.11;-0.11	5.77	4.89	0.63831	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.53938	D	0.000050	T	0.49847	0.1581	N	0.21240	0.645	0.80722	D	1	P;P;P;P;B	0.49635	0.573;0.513;0.698;0.926;0.063	B;B;B;B;B	0.39935	0.138;0.287;0.161;0.314;0.037	T	0.55927	-0.8063	10	0.54805	T	0.06	.	17.0528	0.86524	0.0:0.8732:0.1268:0.0	.	73;73;73;73;73	Q8NG66-3;E9PHI8;Q8NG66-4;Q8NG66;Q8NG66-2	.;.;.;NEK11_HUMAN;.	S	73	ENSP00000421549:T73S;ENSP00000397180:T73S;ENSP00000349389:T73S;ENSP00000423458:T73S;ENSP00000425114:T73S;ENSP00000372857:T73S;ENSP00000426662:T73S;ENSP00000421851:T73S	ENSP00000349389:T73S	T	+	2	0	NEK11	132282004	1.000000	0.71417	0.983000	0.44433	0.330000	0.28571	3.946000	0.56644	1.415000	0.47037	0.655000	0.94253	ACT	.	.	none		0.368	NEK11-005	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000356757.1	NM_024800	
DBH	1621	hgsc.bcm.edu	37	9	136507473	136507473	+	Missense_Mutation	SNP	G	G	A	rs5320	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:136507473G>A	ENST00000393056.2	+	3	643	c.631G>A	c.(631-633)Gcg>Acg	p.A211T		NM_000787.3	NP_000778.3	P09172	DOPO_HUMAN	dopamine beta-hydroxylase (dopamine beta-monooxygenase)	211			A -> T (in dbSNP:rs5320). {ECO:0000269|PubMed:10391210, 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)	GCCCTCAGACGCGTGCACCAT	0.607													G|||	510	0.101837	0.171	0.0447	5008	,	,		19685	0.1121		0.0616	False		,,,				2504	0.0798				p.A211T		Atlas-SNP	.											.	DBH	86	.	0			c.G631A						PASS	.	G	THR/ALA	635,3771	272.2+/-270.6	35,565,1603	69.0	64.0	66.0		631	-4.7	0.0	9	dbSNP_52	66	482,8118	140.1+/-196.7	18,446,3836	yes	missense	DBH	NM_000787.3	58	53,1011,5439	AA,AG,GG		5.6047,14.4122,8.5883	benign	211/618	136507473	1117,11889	2203	4300	6503	SO:0001583	missense	1621	exon3			TCAGACGCGTGCA	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.631G>A	9.37:g.136507473G>A	ENSP00000376776:p.Ala211Thr	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	87	40	0.45977	NM_000787	Q5T381|Q96AG2	Missense_Mutation	SNP	ENST00000393056.2	37	CCDS6977.2	231	0.10576923076923077	87	0.17682926829268292	19	0.052486187845303865	76	0.13286713286713286	49	0.06464379947229551	G	0.079	-1.187984	0.01607	0.144122	0.056047	ENSG00000123454	ENST00000393056;ENST00000371880;ENST00000263611	T;T	0.34072	1.38;1.38	4.67	-4.71	0.03279	Copper type II, ascorbate-dependent monooxygenase, N-terminal (1);PHM/PNGase F domain (1);	1.057760	0.07311	N	0.875897	T	0.00039	0.0001	N	0.01242	-0.935	0.80722	P	0.0	B	0.02656	0.0	B	0.06405	0.002	T	0.29671	-1.0004	9	0.22109	T	0.4	-12.7818	5.3345	0.15949	0.3613:0.1174:0.4357:0.0856	rs5320;rs61440943;rs5320	211	P09172	DOPO_HUMAN	T	211;148;148	ENSP00000376776:A211T;ENSP00000263611:A148T	ENSP00000263611:A148T	A	+	1	0	DBH	135497294	0.000000	0.05858	0.001000	0.08648	0.004000	0.04260	-0.137000	0.10389	-0.677000	0.05231	-0.573000	0.04149	GCG	G|0.905;A|0.095	0.095	strong		0.607	DBH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054929.2	NM_000787	
NT5DC3	51559	hgsc.bcm.edu	37	12	104186946	104186946	+	Silent	SNP	G	G	T	rs1866295	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:104186946G>T	ENST00000392876.3	-	9	1055	c.1015C>A	c.(1015-1017)Cgg>Agg	p.R339R		NM_001031701.2	NP_001026871.1	Q86UY8	NT5D3_HUMAN	5'-nucleotidase domain containing 3	339						cytosol (GO:0005829)|mitochondrion (GO:0005739)|receptor complex (GO:0043235)	hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(1)|kidney(4)|large_intestine(3)|lung(15)|ovary(2)|skin(1)|stomach(2)	30						ACTCACCTCCGCTTATCATTA	0.403													G|||	2051	0.409545	0.2829	0.3199	5008	,	,		20518	0.6319		0.2406	False		,,,				2504	0.589				p.R339R		Atlas-SNP	.											.	NT5DC3	113	.	0			c.C1015A						PASS	.	G		1180,3226	414.4+/-336.8	152,876,1175	142.0	150.0	147.0		1015	5.0	1.0	12	dbSNP_92	147	2078,6522	361.9+/-332.5	254,1570,2476	no	coding-synonymous	NT5DC3	NM_001031701.2		406,2446,3651	TT,TG,GG		24.1628,26.7817,25.05		339/549	104186946	3258,9748	2203	4300	6503	SO:0001819	synonymous_variant	51559	exon9			ACCTCCGCTTATC	AB032786	CCDS41824.1	12q22-q23.1	2006-02-03			ENSG00000111696	ENSG00000111696			30826	protein-coding gene	gene with protein product		611076					Standard	NM_001031701		Approved	TU12B1-TY, FLJ11266	uc010swe.1	Q86UY8	OTTHUMG00000157017	ENST00000392876.3:c.1015C>A	12.37:g.104186946G>T		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	140	71	0.507143	NM_001031701	Q9NUM7|Q9P2T2|Q9P2T3	Silent	SNP	ENST00000392876.3	37	CCDS41824.1																																																																																			G|0.708;T|0.292	0.292	strong		0.403	NT5DC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347118.2	NM_016575	
CD99	4267	hgsc.bcm.edu	37	X	2656258	2656258	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:2656258G>A	ENST00000381192.3	+	9	675	c.493G>A	c.(493-495)Gac>Aac	p.D165N	CD99_ENST00000381187.3_Missense_Mutation_p.D149N	NM_001277710.1|NM_002414.3	NP_001264639.1|NP_002405.1	P14209	CD99_HUMAN	CD99 molecule	165					cell adhesion (GO:0007155)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(6)|skin(1)	11						AGGGGAGGTGGACATGGAGAG	0.502													.|||	99	0.0197684	0.0068	0.0418	5008	,	,		19539	0.0		0.0557	False		,,,				2504	0.0051				p.D165N		Atlas-SNP	.											.	CD99	12	.	0			c.G493A						PASS	.	G	ASN/ASP,ASN/ASP	63,4343		1,61,2141	331.0	314.0	320.0		445,493	-0.3	0.0	X	dbSNP_134	320	500,8092		8,484,3804	no	missense,missense	CD99	NM_001122898.1,NM_002414.3	23,23	9,545,5945	AA,AG,GG		5.8194,1.4299,4.3314	possibly-damaging,possibly-damaging	149/170,165/186	2656258	563,12435	2203	4296	6499	SO:0001583	missense	4267	exon9			GAGGTGGACATGG	M16279	CCDS14119.1, CCDS48071.1, CCDS75947.1	Xp22.32 and Yp11.3	2012-10-02	2006-03-28	2003-02-14	ENSG00000002586	ENSG00000002586		"""Pseudoautosomal regions / PAR1"", ""CD molecules"""	7082	protein-coding gene	gene with protein product		313470, 450000	"""antigen identified by monoclonal antibodies 12E7, F21 and O13"", ""CD99 antigen"""	MIC2			Standard	NM_001122898		Approved		uc004cqm.3	P14209	OTTHUMG00000021073	ENST00000381192.3:c.493G>A	X.37:g.2656258G>A	ENSP00000370588:p.Asp165Asn	Somatic	678	1	0.00147493		WXS	Illumina HiSeq	Phase_I	487	366	0.75154	NM_002414	A6NIW1|O00518|Q6ICV7	Missense_Mutation	SNP	ENST00000381192.3	37	CCDS14119.1	60|60	0.027472527472527472|0.027472527472527472	5|5	0.01016260162601626|0.01016260162601626	17|17	0.04696132596685083|0.04696132596685083	0|0	0.0|0.0	38|38	0.05013192612137203|0.05013192612137203	G|G	7.819|7.819	0.717453|0.717453	0.15372|0.15372	0.014299|0.014299	0.058194|0.058194	ENSG00000002586|ENSG00000002586	ENST00000381192;ENST00000381187|ENST00000381177	T;T|.	0.20881|.	2.04;2.04|.	1.08|1.08	-0.279|-0.279	0.12890|0.12890	.|.	1.142330|.	0.06830|.	U|.	0.793737|.	T|T	0.00936|0.00936	0.0031|0.0031	N|N	0.01576|0.01576	-0.805|-0.805	0.09310|0.09310	N|N	1|1	B;B;B|.	0.09022|.	0.002;0.002;0.002|.	B;B;B|.	0.06405|.	0.002;0.002;0.002|.	T|T	0.20338|0.20338	-1.0278|-1.0278	10|6	0.25751|0.87932	T|D	0.34|0	.|.	3.0243|3.0243	0.06085|0.06085	0.5423:0.0:0.4577:0.0|0.5423:0.0:0.4577:0.0	.|.	149;165;165|.	A6NIW1;B2R932;P14209|.	.;.;CD99_HUMAN|.	N|E	165;149|63	ENSP00000370588:D165N;ENSP00000370582:D149N|.	ENSP00000370582:D149N|ENSP00000370570:G63E	D|G	+|+	1|2	0|0	CD99|CD99	2666258|2666258	0.000000|0.000000	0.05858|0.05858	0.001000|0.001000	0.08648|0.08648	0.235000|0.235000	0.25334|0.25334	-0.011000|-0.011000	0.12721|0.12721	-0.146000|-0.146000	0.11274|0.11274	0.429000|0.429000	0.28392|0.28392	GAC|GGA	G|0.960;A|0.040	0.040	strong		0.502	CD99-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055624.1	NM_001122898	
AVPR1B	553	hgsc.bcm.edu	37	1	206230986	206230986	+	Silent	SNP	G	G	A	rs28676508	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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						PASS	.	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	37	0	0		WXS	Illumina HiSeq	Phase_I	44	22	0.5	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	
ESF1	51575	hgsc.bcm.edu	37	20	13695680	13695680	+	Silent	SNP	C	C	T	rs6110019	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:13695680C>T	ENST00000202816.1	-	14	2504	c.2397G>A	c.(2395-2397)cgG>cgA	p.R799R		NM_001276380.1|NM_016649.3	NP_001263309.1|NP_057733.2	Q9H501	ESF1_HUMAN	ESF1, nucleolar pre-rRNA processing protein, homolog (S. cerevisiae)	799	Lys-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	extracellular space (GO:0005615)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(3)|kidney(5)|large_intestine(8)|lung(11)|ovary(2)|skin(1)|stomach(1)	31						CTTGTTCTTTCCGTTCTCTTT	0.393													C|||	1208	0.241214	0.1362	0.2911	5008	,	,		13550	0.2143		0.3777	False		,,,				2504	0.2352				p.R799R		Atlas-SNP	.											.	ESF1	77	.	0			c.G2397A						PASS	.	C		698,3708	292.1+/-281.9	58,582,1563	200.0	188.0	192.0		2397	-0.2	0.9	20	dbSNP_114	192	3186,5414	483.4+/-371.1	571,2044,1685	no	coding-synonymous	ESF1	NM_016649.3		629,2626,3248	TT,TC,CC		37.0465,15.842,29.8631		799/852	13695680	3884,9122	2203	4300	6503	SO:0001819	synonymous_variant	51575	exon14			TTCTTTCCGTTCT		CCDS13117.1	20p12.1	2007-02-12	2006-11-13	2006-11-13	ENSG00000089048	ENSG00000089048			15898	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 6"""	C20orf6			Standard	NM_016649		Approved	bA526K24.1	uc002wok.2	Q9H501	OTTHUMG00000031906	ENST00000202816.1:c.2397G>A	20.37:g.13695680C>T		Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	113	113	1	NM_001276380	Q86X92|Q9H9Q5|Q9HA35|Q9NX93|Q9P1S6	Silent	SNP	ENST00000202816.1	37	CCDS13117.1																																																																																			C|0.707;T|0.293	0.293	strong		0.393	ESF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078049.1	NM_016649	
TNS1	7145	hgsc.bcm.edu	37	2	218682771	218682771	+	Silent	SNP	A	A	G	rs3796026	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	94	0	0		WXS	Illumina HiSeq	Phase_I	58	19	0.327586	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	
LRP8	7804	hgsc.bcm.edu	37	1	53792651	53792651	+	Missense_Mutation	SNP	A	A	C	rs3820198	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:53792651A>C	ENST00000306052.6	-	2	239	c.138T>G	c.(136-138)gaT>gaG	p.D46E	LRP8_ENST00000347547.2_Missense_Mutation_p.D46E|RP4-784A16.5_ENST00000445039.2_lincRNA|LRP8_ENST00000354412.3_Missense_Mutation_p.D46E|LRP8_ENST00000465675.1_5'UTR|LRP8_ENST00000371454.2_Missense_Mutation_p.D46E	NM_004631.4	NP_004622.2	Q14114	LRP8_HUMAN	low density lipoprotein receptor-related protein 8, apolipoprotein e receptor	46	LDL-receptor class A 1. {ECO:0000255|PROSITE-ProRule:PRU00124}.		D -> E (in dbSNP:rs3820198). {ECO:0000269|PubMed:11152697, ECO:0000269|PubMed:12399018, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:8626535, ECO:0000269|PubMed:9079678}.		ammon gyrus development (GO:0021541)|blood coagulation (GO:0007596)|cellular response to cholesterol (GO:0071397)|cellular response to growth factor stimulus (GO:0071363)|cytokine-mediated signaling pathway (GO:0019221)|endocytosis (GO:0006897)|layer formation in cerebral cortex (GO:0021819)|lipid metabolic process (GO:0006629)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|phototransduction, visible light (GO:0007603)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of dendrite development (GO:1900006)|positive regulation of dendritic spine morphogenesis (GO:0061003)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein tyrosine kinase activity (GO:0061098)|proteolysis (GO:0006508)|receptor-mediated endocytosis (GO:0006898)|reelin-mediated signaling pathway (GO:0038026)|regulation of synaptic transmission (GO:0050804)|response to drug (GO:0042493)|retinoid metabolic process (GO:0001523)|signal transduction (GO:0007165)	caveola (GO:0005901)|dendrite (GO:0030425)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|microtubule associated complex (GO:0005875)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|receptor complex (GO:0043235)	apolipoprotein binding (GO:0034185)|calcium ion binding (GO:0005509)|high-density lipoprotein particle binding (GO:0008035)|reelin receptor activity (GO:0038025)|transmembrane signaling receptor activity (GO:0004888)|very-low-density lipoprotein particle receptor activity (GO:0030229)			endometrium(2)|kidney(1)|large_intestine(6)|lung(9)|prostate(2)|skin(1)	21						CCTTTTCGCAATCCTTGGCCG	0.657													C|||	2756	0.550319	0.9327	0.2997	5008	,	,		16437	0.4841		0.3867	False		,,,				2504	0.4479				p.D46E		Atlas-SNP	.											.	LRP8	58	.	0			c.T138G						PASS	.	C	GLU/ASP,GLU/ASP,GLU/ASP,GLU/ASP	3635,771	310.2+/-291.5	1503,629,71	73.0	70.0	71.0		138,138,138,138	0.8	0.3	1	dbSNP_107	71	3093,5507	659.0+/-401.6	526,2041,1733	yes	missense,missense,missense,missense	LRP8	NM_001018054.2,NM_004631.4,NM_017522.4,NM_033300.3	45,45,45,45	2029,2670,1804	CC,CA,AA		35.9651,17.4989,48.27	benign,benign,benign,benign	46/905,46/964,46/701,46/794	53792651	6728,6278	2203	4300	6503	SO:0001583	missense	7804	exon2			TTCGCAATCCTTG	D50678	CCDS578.1, CCDS579.1, CCDS580.1, CCDS30720.1	1p32.3	2013-05-29			ENSG00000157193	ENSG00000157193		"""Low density lipoprotein receptors"""	6700	protein-coding gene	gene with protein product		602600				8626535, 9079678	Standard	NM_004631		Approved	APOER2, MCI1, LRP-8, HSZ75190	uc001cvi.2	Q14114	OTTHUMG00000008924	ENST00000306052.6:c.138T>G	1.37:g.53792651A>C	ENSP00000303634:p.Asp46Glu	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	73	31	0.424658	NM_004631	B1AMT6|B1AMT7|B1AMT8|O14968|Q86V27|Q99876|Q9BR78	Missense_Mutation	SNP	ENST00000306052.6	37	CCDS578.1	1137	0.5206043956043956	452	0.9186991869918699	115	0.31767955801104975	273	0.4772727272727273	297	0.391820580474934	C	0.069	-1.207045	0.01568	0.825011	0.359651	ENSG00000157193	ENST00000306052;ENST00000371454;ENST00000354412;ENST00000347547	D;D;D;D	0.95103	-3.61;-3.61;-3.61;-3.61	4.0	0.782	0.18567	.	.	.	.	.	T	0.00012	0.0000	N	0.04820	-0.15	0.47698	P	5.079999999999529E-4	B;B;B;B	0.06786	0.0;0.0;0.001;0.0	B;B;B;B	0.04013	0.0;0.0;0.001;0.001	T	0.43343	-0.9397	8	0.02654	T	1	.	1.5348	0.02543	0.1427:0.4549:0.1388:0.2636	rs3820198;rs57022272;rs3820198	46;46;46;46	Q14114-2;Q14114-4;Q14114-3;Q14114	.;.;.;LRP8_HUMAN	E	46	ENSP00000303634:D46E;ENSP00000360509:D46E;ENSP00000346391:D46E;ENSP00000334522:D46E	ENSP00000303634:D46E	D	-	3	2	LRP8	53565239	0.005000	0.15991	0.274000	0.24659	0.166000	0.22503	-0.884000	0.04166	-0.278000	0.09180	-1.219000	0.01604	GAT	C|0.538;N|0.000	0.538	strong		0.657	LRP8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000024699.1	NM_004631	
AXIN1	8312	hgsc.bcm.edu	37	16	396264	396264	+	Silent	SNP	A	A	G	rs1805105	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:396264A>G	ENST00000262320.3	-	2	1133	c.762T>C	c.(760-762)gaT>gaC	p.D254D	AXIN1_ENST00000481769.1_Intron|AXIN1_ENST00000354866.3_Silent_p.D254D	NM_003502.3	NP_003493.1	O15169	AXIN1_HUMAN	axin 1	254	Interaction with TP53. {ECO:0000250}.				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)				CATCGTCCTCATCCATGTCCT	0.582													G|||	3200	0.638978	0.9024	0.5375	5008	,	,		17364	0.2897		0.6173	False		,,,				2504	0.7372				p.D254D		Atlas-SNP	.											.	AXIN1	290	.	0			c.T762C						PASS	.	G	,	3738,668	283.4+/-277.1	1581,576,46	123.0	116.0	119.0		762,762	-9.6	0.0	16	dbSNP_89	119	5550,3050	469.4+/-367.6	1788,1974,538	no	coding-synonymous,coding-synonymous	AXIN1	NM_003502.3,NM_181050.2	,	3369,2550,584	GG,GA,AA		35.4651,15.1611,28.5868	,	254/863,254/827	396264	9288,3718	2203	4300	6503	SO:0001819	synonymous_variant	8312	exon2			GTCCTCATCCATG	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.762T>C	16.37:g.396264A>G		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	58	58	1	NM_181050	Q4TT26|Q4TT27|Q86YA7|Q8WVW6|Q96S28	Silent	SNP	ENST00000262320.3	37	CCDS10405.1																																																																																			A|0.335;G|0.665	0.665	strong		0.582	AXIN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139441.3		
FAT1	2195	hgsc.bcm.edu	37	4	187629137	187629137	+	Silent	SNP	A	A	G	rs4862726	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:187629137A>G	ENST00000441802.2	-	2	2054	c.1845T>C	c.(1843-1845)ttT>ttC	p.F615F		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	615	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				actin filament organization (GO:0007015)|anatomical structure morphogenesis (GO:0009653)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(38)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(33)|lung(88)|ovary(13)|pancreas(2)|prostate(16)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	228						GGTTTAAACTAAAGAAATCCA	0.433										HNSCC(5;0.00058)			A|||	78	0.0155751	0.0	0.0101	5008	,	,		20191	0.0258		0.0368	False		,,,				2504	0.0082				p.F615F	Colon(197;1040 2055 4143 4984 49344)	Atlas-SNP	.											.	FAT1	500	.	0			c.T1845C						PASS	.	A		23,3713		0,23,1845	68.0	63.0	64.0		1845	-1.3	0.6	4	dbSNP_111	64	305,7891		4,297,3797	no	coding-synonymous	FAT1	NM_005245.3		4,320,5642	GG,GA,AA		3.7213,0.6156,2.7489		615/4589	187629137	328,11604	1868	4098	5966	SO:0001819	synonymous_variant	2195	exon2			TAAACTAAAGAAA	X87241	CCDS47177.1	4q35.2	2013-05-31	2013-05-31	2008-10-30	ENSG00000083857	ENSG00000083857		"""Cadherins / Cadherin-related"""	3595	protein-coding gene	gene with protein product	"""cadherin-related family member 8"""	600976	"""FAT tumor suppressor (Drosophila) homolog"", ""FAT tumor suppressor homolog 1 (Drosophila)"""	FAT		8586420	Standard	XM_005262834		Approved	CDHF7, CDHR8	uc003izf.3	Q14517	OTTHUMG00000160320	ENST00000441802.2:c.1845T>C	4.37:g.187629137A>G		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	62	23	0.370968	NM_005245		Silent	SNP	ENST00000441802.2	37	CCDS47177.1																																																																																			A|0.975;G|0.025	0.025	strong		0.433	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245	
LRRFIP1	9208	hgsc.bcm.edu	37	2	238671328	238671328	+	Silent	SNP	A	A	G	rs868119	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:238671328A>G	ENST00000392000.4	+	11	1089	c.972A>G	c.(970-972)gaA>gaG	p.E324E	LRRFIP1_ENST00000308482.9_Intron|LRRFIP1_ENST00000244815.5_Silent_p.E300E|LRRFIP1_ENST00000289175.6_Silent_p.E268E	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	374	0	0		WXS	Illumina HiSeq	Phase_I	294	132	0.44898	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	
ABCC11	85320	hgsc.bcm.edu	37	16	48226479	48226479	+	Silent	SNP	C	C	T	rs12443685	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:48226479C>T	ENST00000394747.1	-	19	3007	c.2658G>A	c.(2656-2658)aaG>aaA	p.K886K	ABCC11_ENST00000356608.2_Silent_p.K886K|ABCC11_ENST00000353782.5_Silent_p.K886K|ABCC11_ENST00000394748.1_Silent_p.K886K|ABCC11_ENST00000537808.1_3'UTR	NM_033151.3	NP_149163.2	Q96J66	ABCCB_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 11	886	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)	TCCTCGTGACCTTGGTGAAAA	0.582													C|||	683	0.136382	0.0998	0.3184	5008	,	,		15331	0.0298		0.162	False		,,,				2504	0.1401				p.K886K		Atlas-SNP	.											.	ABCC11	177	.	0			c.G2658A						PASS	.	C	,,	481,3921	228.5+/-243.3	29,423,1749	113.0	102.0	106.0		2658,2658,2658	2.0	0.4	16	dbSNP_120	106	1446,7154	276.5+/-292.4	124,1198,2978	no	coding-synonymous,coding-synonymous,coding-synonymous	ABCC11	NM_032583.3,NM_033151.3,NM_145186.2	,,	153,1621,4727	TT,TC,CC		16.814,10.9269,14.8208	,,	886/1383,886/1383,886/1345	48226479	1927,11075	2201	4300	6501	SO:0001819	synonymous_variant	85320	exon19			CGTGACCTTGGTG	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.2658G>A	16.37:g.48226479C>T		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	162	83	0.512346	NM_033151	Q8TDJ0|Q96JA6|Q9BX80	Silent	SNP	ENST00000394747.1	37	CCDS10732.1																																																																																			C|0.860;T|0.140	0.140	strong		0.582	ABCC11-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000429984.1	NM_032583	
ADAMDEC1	27299	hgsc.bcm.edu	37	8	24261526	24261526	+	Missense_Mutation	SNP	A	A	G	rs3765124	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:24261526A>G	ENST00000256412.4	+	13	1551	c.1331A>G	c.(1330-1332)aAt>aGt	p.N444S	RP11-624C23.1_ENST00000519689.1_RNA|RP11-624C23.1_ENST00000523578.1_RNA|ADAMDEC1_ENST00000522298.1_Missense_Mutation_p.N365S|ADAMDEC1_ENST00000538205.1_Missense_Mutation_p.N365S	NM_014479.3	NP_055294.1	O15204	ADEC1_HUMAN	ADAM-like, decysin 1	444	Disintegrin. {ECO:0000255|PROSITE- ProRule:PRU00068}.		N -> S (in dbSNP:rs3765124).		immune response (GO:0006955)|negative regulation of cell adhesion (GO:0007162)	extracellular region (GO:0005576)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|large_intestine(4)|skin(2)|stomach(1)	9		Prostate(55;0.0181)		Colorectal(74;0.016)|COAD - Colon adenocarcinoma(73;0.0646)|BRCA - Breast invasive adenocarcinoma(99;0.168)		GAGTGTACCAATCTCTGCTGT	0.438													A|||	1477	0.294928	0.0968	0.4553	5008	,	,		17229	0.2044		0.4284	False		,,,				2504	0.4049				p.N444S	Ovarian(147;687 1849 3699 25981 31337)	Atlas-SNP	.											.	ADAMDEC1	69	.	0			c.A1331G						PASS	.	A	SER/ASN,SER/ASN,SER/ASN	677,3729	287.8+/-279.5	52,573,1578	218.0	186.0	197.0		1094,1094,1331	0.4	0.0	8	dbSNP_107	197	3804,4796	537.9+/-383.3	833,2138,1329	yes	missense,missense,missense	ADAMDEC1	NM_001145271.1,NM_001145272.1,NM_014479.3	46,46,46	885,2711,2907	GG,GA,AA		44.2326,15.3654,34.4533	benign,benign,benign	365/392,365/392,444/471	24261526	4481,8525	2203	4300	6503	SO:0001583	missense	27299	exon13			GTACCAATCTCTG	Y13323	CCDS6044.1, CCDS55212.1	8p12	2008-08-07			ENSG00000134028	ENSG00000134028			16299	protein-coding gene	gene with protein product		606393				9271581, 12037602	Standard	NM_001145271		Approved	M12.219	uc003xdz.2	O15204	OTTHUMG00000097858	ENST00000256412.4:c.1331A>G	8.37:g.24261526A>G	ENSP00000256412:p.Asn444Ser	Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	127	96	0.755906	NM_014479	B7ZAK5	Missense_Mutation	SNP	ENST00000256412.4	37	CCDS6044.1	643	0.2944139194139194	44	0.08943089430894309	152	0.4198895027624309	120	0.2097902097902098	327	0.4313984168865435	A	9.564	1.119311	0.20877	0.153654	0.442326	ENSG00000134028	ENST00000256412;ENST00000538205;ENST00000522298	T;T;T	0.11604	2.76;2.76;2.76	5.6	0.414	0.16406	Blood coagulation inhibitor, Disintegrin (3);	0.558036	0.18286	N	0.145891	T	0.00012	0.0000	L	0.48986	1.54	0.80722	P	0.0	P	0.49862	0.929	P	0.44696	0.458	T	0.48603	-0.9021	9	0.22706	T	0.39	-7.4265	8.0431	0.30534	0.6671:0.0:0.3329:0.0	rs3765124;rs17737352;rs52806941;rs59180631;rs3765124	444	O15204	ADEC1_HUMAN	S	444;365;365	ENSP00000256412:N444S;ENSP00000442592:N365S;ENSP00000428993:N365S	ENSP00000256412:N444S	N	+	2	0	ADAMDEC1	24317471	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.317000	0.19487	-0.144000	0.11314	-0.388000	0.06559	AAT	A|0.687;G|0.313	0.313	strong		0.438	ADAMDEC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215149.2	NM_014479	
VEZF1	7716	hgsc.bcm.edu	37	17	56056550	56056550	+	Silent	SNP	C	C	G	rs1135655	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:56056550C>G	ENST00000581208.1	-	5	1141	c.1101G>C	c.(1099-1101)ctG>ctC	p.L367L	VEZF1_ENST00000584396.1_Silent_p.L358L	NM_007146.2	NP_009077.2	Q14119	VEZF1_HUMAN	vascular endothelial zinc finger 1	367					angiogenesis (GO:0001525)|cellular defense response (GO:0006968)|endothelial cell development (GO:0001885)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(1)|kidney(2)|lung(5)|ovary(1)	10						CCCACAGTCTCAGTGTTTCTA	0.468													C|||	301	0.0601038	0.0817	0.0663	5008	,	,		18612	0.001		0.0974	False		,,,				2504	0.0491				p.L367L		Atlas-SNP	.											.	VEZF1	50	.	0			c.G1101C						PASS	.	C		381,4025	193.6+/-218.7	20,341,1842	324.0	284.0	298.0		1101	5.7	1.0	17	dbSNP_86	298	891,7709	200.0+/-243.9	42,807,3451	no	coding-synonymous	VEZF1	NM_007146.2		62,1148,5293	GG,GC,CC		10.3605,8.6473,9.7801		367/522	56056550	1272,11734	2203	4300	6503	SO:0001819	synonymous_variant	7716	exon5			CAGTCTCAGTGTT	D28118	CCDS32687.1	17q22	2012-10-05	2006-08-16	2006-08-16	ENSG00000136451	ENSG00000136451		"""Zinc fingers, C2H2-type"""	12949	protein-coding gene	gene with protein product		606747	"""zinc finger protein 161"""	ZNF161		8035792	Standard	XM_005257643		Approved	DB1	uc002ivf.1	Q14119	OTTHUMG00000178777	ENST00000581208.1:c.1101G>C	17.37:g.56056550C>G		Somatic	221	0	0		WXS	Illumina HiSeq	Phase_I	209	86	0.411483	NM_007146		Silent	SNP	ENST00000581208.1	37	CCDS32687.1																																																																																			C|0.907;G|0.093	0.093	strong		0.468	VEZF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000443321.1		
FCGR2A	2212	hgsc.bcm.edu	37	1	161479745	161479745	+	Missense_Mutation	SNP	A	A	G	rs1801274	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:161479745A>G	ENST00000271450.6	+	4	538	c.500A>G	c.(499-501)cAt>cGt	p.H167R	FCGR2A_ENST00000367972.4_Missense_Mutation_p.H166R	NM_001136219.1|NM_021642.3	NP_001129691.1|NP_067674.2	P12318	FCG2A_HUMAN	Fc fragment of IgG, low affinity IIa, receptor (CD32)	167	Ig-like C2-type 2.		H -> R (may be associated with susceptibility to lupus nephritis; does not efficiently recognize IgG2; dbSNP:rs1801274). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:2529342, ECO:0000269|PubMed:2824655, ECO:0000269|PubMed:2965389, ECO:0000269|PubMed:3402431, ECO:0000269|PubMed:8636449}.		Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				autonomic_ganglia(1)|breast(2)|endometrium(2)|large_intestine(2)|lung(11)|ovary(1)	19	all_cancers(52;4.89e-16)|all_hematologic(112;0.0207)		BRCA - Breast invasive adenocarcinoma(70;0.00376)		Abciximab(DB00054)|Adalimumab(DB00051)|Alefacept(DB00092)|Alemtuzumab(DB00087)|Basiliximab(DB00074)|Bevacizumab(DB00112)|Cetuximab(DB00002)|Daclizumab(DB00111)|Efalizumab(DB00095)|Etanercept(DB00005)|Gemtuzumab ozogamicin(DB00056)|Ibritumomab(DB00078)|Intravenous Immunoglobulin(DB00028)|Muromonab(DB00075)|Natalizumab(DB00108)|Palivizumab(DB00110)|Rituximab(DB00073)|Tositumomab(DB00081)|Trastuzumab(DB00072)	AAATTCTCCCATTTGGATCCC	0.502													A|||	2212	0.441693	0.5257	0.451	5008	,	,		21081	0.2778		0.5109	False		,,,				2504	0.4192				p.H167R		Atlas-SNP	.											.	FCGR2A	38	.	0			c.A500G	GRCh37	CM960640	FCGR2A	M	rs1801274	PASS	.	A	ARG/HIS,ARG/HIS	2460,1946		689,1082,432	134.0	120.0	125.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	500,497	-4.2	0.0	1	dbSNP_89	125	4446,4154		1164,2118,1018	yes	missense,missense	FCGR2A	NM_001136219.1,NM_021642.3	29,29	1853,3200,1450	GG,GA,AA	http://www.ncbi.nlm.nih.gov/pubmed?term	48.3023,44.167,46.9014	benign,benign	167/318,166/317	161479745	6906,6100	2203	4300	6503	SO:0001583	missense	2212	exon4			TCTCCCATTTGGA	J03619	CCDS30922.1, CCDS44264.1	1q23	2013-01-11	2005-02-02		ENSG00000143226	ENSG00000143226		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	3616	protein-coding gene	gene with protein product	"""Immunoglobulin G Fc receptor II"""	146790	"""Fc fragment of IgG, low affinity IIa, receptor for (CD32)"""	FCG2, FCGR2A1, FCGR2		2139735	Standard	NM_021642		Approved	CD32, CD32A, IGFR2, CDw32	uc001gan.3	P12318	OTTHUMG00000034469	ENST00000271450.6:c.500A>G	1.37:g.161479745A>G	ENSP00000271450:p.His167Arg	Somatic	575	0	0		WXS	Illumina HiSeq	Phase_I	478	476	0.995816	NM_001136219	Q8WUN1|Q8WW64	Missense_Mutation	SNP	ENST00000271450.6	37	CCDS44264.1	940	0.43040293040293043	240	0.4878048780487805	162	0.44751381215469616	159	0.27797202797202797	379	0.5	.	4.117	0.019927	0.08006	0.55833	0.516977	ENSG00000143226	ENST00000367972;ENST00000271450	T;T	0.11385	2.78;2.78	2.65	-4.15	0.03881	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	5.753470	0.00166	N	0.000000	T	0.02494	0.0076	L	0.43152	1.355	0.32643	P	0.520444	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.001	T	0.40175	-0.9577	9	0.30078	T	0.28	.	4.4985	0.11853	0.3095:0.4391:0.2514:0.0	rs1801274;rs16830404;rs17851761;rs52796393;rs58440466;rs1801274	167;166	P12318;P12318-2	FCG2A_HUMAN;.	R	166;167	ENSP00000356949:H166R;ENSP00000271450:H167R	ENSP00000271450:H167R	H	+	2	0	FCGR2A	159746369	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.902000	0.04088	-0.971000	0.03564	-0.421000	0.06004	CAT	G|0.474;N|0.000	0.474	strong		0.502	FCGR2A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000083318.3	NM_021642	
EYS	346007	hgsc.bcm.edu	37	6	66042231	66042231	+	Intron	SNP	T	T	G	rs12207746	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:66042231T>G	ENST00000370621.3	-	11	2293				EYS_ENST00000393380.2_Missense_Mutation_p.I616L|EYS_ENST00000503581.1_Intron|EYS_ENST00000370616.2_Intron			Q5T1H1	EYS_HUMAN	eyes shut homolog (Drosophila)						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						attcttacgataaatcccacc	0.303													t|||	572	0.114217	0.2496	0.0533	5008	,	,		16246	0.0427		0.0785	False		,,,				2504	0.0849				p.I616L		Atlas-SNP	.											.	EYS	527	.	0			c.A1846C						PASS	.	T	,LEU/ILE	324,1060		36,252,404	190.0	170.0	176.0		,1846	1.0	0.0	6	dbSNP_120	176	237,2945		8,221,1362	yes	intron,missense	EYS	NM_001142800.1,NM_001142801.1	,5	44,473,1766	GG,GT,TT		7.4481,23.4104,12.2865	,	,616/620	66042231	561,4005	692	1591	2283	SO:0001627	intron_variant	346007	exon12			TTACGATAAATCC		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.1766+2641A>C	6.37:g.66042231T>G		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	39	19	0.487179	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		230	0.10531135531135531	135	0.27439024390243905	19	0.052486187845303865	14	0.024475524475524476	62	0.08179419525065963	t	8.337	0.827841	0.16749	0.234104	0.074481	ENSG00000188107	ENST00000393380	D	0.90069	-2.61	1.01	1.01	0.19927	.	.	.	.	.	T	0.77458	0.4133	L	0.52011	1.625	0.80722	P	0.0	P	0.41784	0.762	B	0.43386	0.418	T	0.70310	-0.4907	8	0.87932	D	0	.	4.2312	0.10604	0.0:0.0:0.0:1.0	rs12207746;rs12207746	616	Q5SZM4	.	L	616	ENSP00000377042:I616L	ENSP00000377042:I616L	I	-	1	0	EYS	66098952	0.004000	0.15560	0.005000	0.12908	0.013000	0.08279	0.969000	0.29370	0.704000	0.31869	0.247000	0.18012	ATC	T|0.889;G|0.111	0.111	strong		0.303	EYS-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351351.3	XM_294050	
DSPP	1834	hgsc.bcm.edu	37	4	88536919	88536919	+	Silent	SNP	T	T	C	rs369387818		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:88536919T>C	ENST00000282478.7	+	4	3138	c.3105T>C	c.(3103-3105)gaT>gaC	p.D1035D	RP11-742B18.1_ENST00000506480.1_RNA|DSPP_ENST00000399271.1_Silent_p.D1035D			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	1035	Asp/Ser-rich.				biomineral tissue development (GO:0031214)|cellular response to cell-matrix adhesion (GO:0071460)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)	p.D1035D(2)		breast(2)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|skin(3)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Hepatocellular(203;0.114)|all_hematologic(202;0.236)		OV - Ovarian serous cystadenocarcinoma(123;0.000508)		acagcagcgatagcagtgaca	0.517																																					p.D1035D		Atlas-SNP	.											DSPP,NS,carcinoma,0,3	DSPP	174	3	2	Substitution - coding silent(2)	kidney(2)	c.T3105C						scavenged	.						63.0	70.0	67.0					4																	88536919		1560	2747	4307	SO:0001819	synonymous_variant	1834	exon5			CAGCGATAGCAGT	AF163151	CCDS43248.1	4q21.3	2008-02-05			ENSG00000152591	ENSG00000152591			3054	protein-coding gene	gene with protein product		125485		DFNA39, DGI1		8995371, 9533027	Standard	NM_014208		Approved	DMP3	uc003hqu.3	Q9NZW4	OTTHUMG00000161061	ENST00000282478.7:c.3105T>C	4.37:g.88536919T>C		Somatic	91	1	0.010989		WXS	Illumina HiSeq	Phase_I	65	7	0.107692	NM_014208	A8MUI0|O95815	Silent	SNP	ENST00000282478.7	37	CCDS43248.1																																																																																			.	.	weak		0.517	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208	
HSPA8	3312	hgsc.bcm.edu	37	11	122928622	122928622	+	Silent	SNP	A	A	G	rs4802	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:122928622A>G	ENST00000532636.1	-	9	1880	c.1761T>C	c.(1759-1761)gcT>gcC	p.A587A	HSPA8_ENST00000526862.1_5'Flank|HSPA8_ENST00000453788.2_Intron|HSPA8_ENST00000534319.1_Silent_p.A351A|SNORD14E_ENST00000364009.1_RNA|SNORD14D_ENST00000384390.1_RNA|HSPA8_ENST00000533540.1_Silent_p.A441A|HSPA8_ENST00000534624.1_Silent_p.A587A|SNORD14C_ENST00000365382.1_RNA|HSPA8_ENST00000526110.1_Silent_p.A568A|HSPA8_ENST00000227378.3_Silent_p.A587A			P11142	HSP7C_HUMAN	heat shock 70kDa protein 8	587					ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|chaperone mediated protein folding requiring cofactor (GO:0051085)|clathrin coat disassembly (GO:0072318)|gene expression (GO:0010467)|membrane organization (GO:0061024)|mRNA metabolic process (GO:0016071)|mRNA processing (GO:0006397)|negative regulation of fibril organization (GO:1902904)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotransmitter secretion (GO:0007269)|post-Golgi vesicle-mediated transport (GO:0006892)|protein folding (GO:0006457)|protein refolding (GO:0042026)|regulation of cell cycle (GO:0051726)|response to unfolded protein (GO:0006986)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|synaptic transmission (GO:0007268)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	blood microparticle (GO:0072562)|clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane (GO:0061202)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|intracellular (GO:0005622)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|Prp19 complex (GO:0000974)|ribonucleoprotein complex (GO:0030529)|spliceosomal complex (GO:0005681)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled (GO:0042623)|enzyme binding (GO:0019899)|G-protein coupled receptor binding (GO:0001664)|heat shock protein binding (GO:0031072)|MHC class II protein complex binding (GO:0023026)|poly(A) RNA binding (GO:0044822)|ubiquitin protein ligase binding (GO:0031625)|unfolded protein binding (GO:0051082)			breast(1)|central_nervous_system(7)|endometrium(1)|kidney(9)|large_intestine(4)|lung(13)|upper_aerodigestive_tract(1)	36		Breast(109;0.00249)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0279)		CTTCCTTCTCAGCAGTCTGAG	0.433													G|||	2165	0.432308	0.5703	0.3631	5008	,	,		20850	0.5506		0.2227	False		,,,				2504	0.3885				p.A587A	Colon(21;486 594 5900 6733 14272)	Atlas-SNP	.											.	HSPA8	168	.	0			c.T1761C						PASS	.	G	,	2261,2143	572.6+/-383.4	576,1109,517	103.0	112.0	109.0		1761,	-6.5	0.9	11	dbSNP_52	109	2054,6544	717.9+/-406.2	255,1544,2500	no	coding-synonymous,intron	HSPA8	NM_006597.4,NM_153201.2	,	831,2653,3017	GG,GA,AA		23.8893,48.6603,33.1872	,	587/647,	122928622	4315,8687	2202	4299	6501	SO:0001819	synonymous_variant	3312	exon9			CTTCTCAGCAGTC	Y00371	CCDS8440.1, CCDS44754.1	11q24.1	2011-09-02	2002-08-29		ENSG00000109971	ENSG00000109971		"""Heat shock proteins / HSP70"""	5241	protein-coding gene	gene with protein product		600816	"""heat shock 70kD protein 8"""	HSPA10		8530083, 3037489	Standard	NM_006597		Approved	HSC71, HSC70, HSP73	uc001pyo.3	P11142	OTTHUMG00000166030	ENST00000532636.1:c.1761T>C	11.37:g.122928622A>G		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	28	21	0.75	NM_006597	Q9H3R6	Silent	SNP	ENST00000532636.1	37	CCDS8440.1																																																																																			A|0.653;G|0.347	0.347	strong		0.433	HSPA8-004	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000387515.1		
CSNK2A1	1457	hgsc.bcm.edu	37	20	472938	472938	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:472938G>A	ENST00000217244.3	-	9	956	c.581C>T	c.(580-582)tCc>tTc	p.S194F	CSNK2A1_ENST00000400227.3_Missense_Mutation_p.S194F|CSNK2A1_ENST00000400217.2_Missense_Mutation_p.S58F|CSNK2A1_ENST00000349736.5_Missense_Mutation_p.S194F	NM_177559.2	NP_808227.1	P68400	CSK21_HUMAN	casein kinase 2, alpha 1 polypeptide	194	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axon guidance (GO:0007411)|chaperone-mediated protein folding (GO:0061077)|mitotic cell cycle (GO:0000278)|mitotic spindle checkpoint (GO:0071174)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|positive regulation of cell growth (GO:0030307)|positive regulation of cell proliferation (GO:0008284)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of Wnt signaling pathway (GO:0030177)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of transcription, DNA-templated (GO:0006355)|rhythmic process (GO:0048511)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|nucleus (GO:0005634)|NuRD complex (GO:0016581)|plasma membrane (GO:0005886)|Sin3 complex (GO:0016580)	ATP binding (GO:0005524)|Hsp90 protein binding (GO:0051879)|protein N-terminus binding (GO:0047485)|protein phosphatase regulator activity (GO:0019888)|protein serine/threonine kinase activity (GO:0004674)			autonomic_ganglia(1)|central_nervous_system(2)|endometrium(1)|large_intestine(4)|lung(5)|ovary(1)|prostate(2)|urinary_tract(1)	17		Breast(17;0.231)	OV - Ovarian serous cystadenocarcinoma(29;0.0969)			GAAGTATCGGGAAGCAACTCG	0.408																																					p.S194F		Atlas-SNP	.											.	CSNK2A1	36	.	0			c.C581T						PASS	.						87.0	80.0	83.0					20																	472938		2203	4298	6501	SO:0001583	missense	1457	exon8			TATCGGGAAGCAA	M55265	CCDS13003.1, CCDS13004.1	20p13	2013-01-17			ENSG00000101266	ENSG00000101266			2457	protein-coding gene	gene with protein product		115440				2174700, 1766873	Standard	NM_177559		Approved		uc002wdx.1	P68400	OTTHUMG00000031636	ENST00000217244.3:c.581C>T	20.37:g.472938G>A	ENSP00000217244:p.Ser194Phe	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	60	16	0.266667	NM_001895	B4DYS6|D3DVV8|P19138|P20426|Q14013|Q5U065	Missense_Mutation	SNP	ENST00000217244.3	37	CCDS13003.1	.	.	.	.	.	.	.	.	.	.	G	28.2	4.901024	0.92035	.	.	ENSG00000101266	ENST00000400227;ENST00000349736;ENST00000217244;ENST00000381973;ENST00000400217	T;T;T;T	0.54279	3.06;3.06;3.06;0.58	4.84	4.84	0.62591	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.095477	0.85682	D	0.000000	T	0.81083	0.4749	H	0.95574	3.69	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	D	0.86825	0.2007	10	0.87932	D	0	-7.1666	17.471	0.87646	0.0:0.0:1.0:0.0	.	194	P68400	CSK21_HUMAN	F	194;194;194;194;58	ENSP00000383086:S194F;ENSP00000339247:S194F;ENSP00000217244:S194F;ENSP00000383076:S58F	ENSP00000217244:S194F	S	-	2	0	CSNK2A1	420938	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.562000	0.98145	2.679000	0.91253	0.655000	0.94253	TCC	.	.	none		0.408	CSNK2A1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077466.1	NM_001895	
ITGB2	3689	hgsc.bcm.edu	37	21	46330674	46330674	+	Silent	SNP	C	C	A	rs11088969	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:46330674C>A	ENST00000397850.2	-	3	476	c.24G>T	c.(22-24)ctG>ctT	p.L8L	ITGB2_ENST00000397854.3_Silent_p.L8L|ITGB2_ENST00000397857.1_Silent_p.L8L|ITGB2_ENST00000523126.1_5'Flank|ITGB2_ENST00000397852.1_Silent_p.L8L|ITGB2_ENST00000302347.5_Silent_p.L8L|ITGB2_ENST00000397846.3_Silent_p.L8L|ITGB2_ENST00000355153.4_Silent_p.L8L			P05107	ITB2_HUMAN	integrin, beta 2 (complement component 3 receptor 3 and 4 subunit)	8					apoptotic process (GO:0006915)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|cell-matrix adhesion (GO:0007160)|endodermal cell differentiation (GO:0035987)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|neutrophil chemotaxis (GO:0030593)|receptor clustering (GO:0043113)|regulation of cell shape (GO:0008360)|regulation of immune response (GO:0050776)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integrin alphaL-beta2 complex (GO:0034687)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|vesicle (GO:0031982)	cell adhesion molecule binding (GO:0050839)|glycoprotein binding (GO:0001948)|ICAM-3 receptor activity (GO:0030369)|metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)			breast(2)|central_nervous_system(3)|endometrium(2)|kidney(1)|large_intestine(6)|lung(14)|ovary(4)|skin(3)	35				Colorectal(79;0.0669)	Simvastatin(DB00641)	CCAGGGCGAGCAGTGGGGGGC	0.667													C|||	1067	0.213059	0.2383	0.1383	5008	,	,		19421	0.0595		0.2127	False		,,,				2504	0.3906				p.L8L		Atlas-SNP	.											.	ITGB2	107	.	0			c.G24T						PASS	.	C	,	983,3421	360.6+/-315.3	114,755,1333	38.0	42.0	41.0		24,24	-0.6	0.0	21	dbSNP_120	41	1841,6759	321.5+/-315.1	206,1429,2665	no	coding-synonymous,coding-synonymous	ITGB2	NM_000211.3,NM_001127491.1	,	320,2184,3998	AA,AC,CC		21.407,22.3206,21.7164	,	8/770,8/770	46330674	2824,10180	2202	4300	6502	SO:0001819	synonymous_variant	3689	exon2			GGCGAGCAGTGGG	AK222505	CCDS13716.1	21q22.3	2014-09-17	2006-03-02		ENSG00000160255	ENSG00000160255		"""CD molecules"", ""Complement system"", ""Integrins"""	6155	protein-coding gene	gene with protein product		600065	"""integrin, beta 2 (antigen CD18 (p95), lymphocyte function-associated antigen 1; macrophage antigen 1 (mac-1) beta subunit)"""	CD18, MFI7			Standard	NM_000211		Approved	LFA-1, MAC-1	uc002zgf.3	P05107	OTTHUMG00000090257	ENST00000397850.2:c.24G>T	21.37:g.46330674C>A		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	97	37	0.381443	NM_000211	B3KTS8|D3DSM1|Q16418|Q53HS5|Q9UD72	Silent	SNP	ENST00000397850.2	37	CCDS13716.1																																																																																			C|0.796;A|0.204	0.204	strong		0.667	ITGB2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206566.2	NM_000211	
TNS1	7145	hgsc.bcm.edu	37	2	218712918	218712918	+	Silent	SNP	C	C	T	rs3796031	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:218712918C>T	ENST00000171887.4	-	17	2399	c.1947G>A	c.(1945-1947)tcG>tcA	p.S649S	TNS1_ENST00000419504.1_Silent_p.S649S|TNS1_ENST00000480665.1_5'Flank|TNS1_ENST00000430930.1_Silent_p.S649S	NM_022648.4	NP_072174.3	Q9HBL0	TENS1_HUMAN	tensin 1	649					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)		gctgctgcCACGAATTCAGTC	0.642													T|||	3240	0.646965	0.8313	0.5778	5008	,	,		16160	0.6429		0.4463	False		,,,				2504	0.6575				p.S649S		Atlas-SNP	.											TNS1_ENST00000446903,NS,carcinoma,-1,2	TNS1	251	2	0			c.G1947A						PASS	.	T		3319,1069		1272,775,147	15.0	17.0	16.0		1947	-1.5	1.0	2	dbSNP_107	16	3698,4886		822,2054,1416	no	coding-synonymous	TNS1	NM_022648.4		2094,2829,1563	TT,TC,CC		43.0801,24.3619,45.9066		649/1736	218712918	7017,5955	2194	4292	6486	SO:0001819	synonymous_variant	7145	exon17			CTGCCACGAATTC	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.1947G>A	2.37:g.218712918C>T		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	69	32	0.463768	NM_022648	Q4ZG71|Q6IPI5	Silent	SNP	ENST00000171887.4	37	CCDS2407.1																																																																																			C|0.418;T|0.582	0.582	strong		0.642	TNS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256672.2	NM_022648	
PTPRF	5792	hgsc.bcm.edu	37	1	44083507	44083507	+	Silent	SNP	T	T	C	rs641365	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:44083507T>C	ENST00000359947.4	+	25	4636	c.4296T>C	c.(4294-4296)ggT>ggC	p.G1432G	PTPRF_ENST00000372414.3_Silent_p.G1432G|PTPRF_ENST00000372413.3_Silent_p.G1423G|PTPRF_ENST00000496447.1_3'UTR|PTPRF_ENST00000422171.2_Silent_p.G791G|PTPRF_ENST00000438120.1_Silent_p.G1423G	NM_002840.3	NP_002831.2	P10586	PTPRF_HUMAN	protein tyrosine phosphatase, receptor type, F	1432	Tyrosine-protein phosphatase 1. {ECO:0000255|PROSITE-ProRule:PRU00160}.				cell adhesion (GO:0007155)|cell migration (GO:0016477)|negative regulation of receptor binding (GO:1900121)|peptidyl-tyrosine dephosphorylation (GO:0035335)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	heparin binding (GO:0008201)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(2)|breast(4)|central_nervous_system(3)|endometrium(9)|kidney(4)|large_intestine(11)|liver(1)|lung(24)|ovary(4)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)	72	all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)				AGACCATGGGTGATTTCTGGA	0.622													C|||	3692	0.73722	0.9455	0.5764	5008	,	,		20262	0.7649		0.7157	False		,,,				2504	0.5634				p.G1432G		Atlas-SNP	.											.	PTPRF	172	.	0			c.T4296C						PASS	.	C	,	4040,366	186.7+/-213.5	1857,326,20	53.0	52.0	52.0		4296,4269	-7.1	0.6	1	dbSNP_83	52	6432,2168	370.8+/-336.0	2441,1550,309	no	coding-synonymous,coding-synonymous	PTPRF	NM_002840.3,NM_130440.2	,	4298,1876,329	CC,CT,TT		25.2093,8.3069,19.4833	,	1432/1908,1423/1899	44083507	10472,2534	2203	4300	6503	SO:0001819	synonymous_variant	5792	exon25			CATGGGTGATTTC	Y00815	CCDS489.2, CCDS490.2	1p34	2013-02-11			ENSG00000142949	ENSG00000142949		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	9670	protein-coding gene	gene with protein product		179590		LAR		7558042	Standard	NM_130440		Approved		uc001cjr.3	P10586	OTTHUMG00000007501	ENST00000359947.4:c.4296T>C	1.37:g.44083507T>C		Somatic	256	1	0.00390625		WXS	Illumina HiSeq	Phase_I	226	107	0.473451	NM_002840	D3DPX6|D3DPX7|Q5T021|Q5T022|Q5W9G2|Q86WS0	Silent	SNP	ENST00000359947.4	37	CCDS489.2	1671|1671	0.7651098901098901|0.7651098901098901	459|459	0.9329268292682927|0.9329268292682927	238|238	0.6574585635359116|0.6574585635359116	425|425	0.743006993006993|0.743006993006993	549|549	0.7242744063324539|0.7242744063324539	C|C	9.479|9.479	1.097554|1.097554	0.20552|0.20552	0.916931|0.916931	0.747907|0.747907	ENSG00000142949|ENSG00000142949	ENST00000429895|ENST00000412568;ENST00000414879	.|.	.|.	.|.	5.58|5.58	-7.06|-7.06	0.01568|0.01568	.|.	.|.	.|.	.|.	.|.	T|.	0.00012|.	0.0000|.	.|.	.|.	.|.	0.09310|0.09310	P|P	0.9999999999999997|0.9999999999999997	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.04360|.	-1.0957|.	3|.	.|.	.|.	.|.	.|.	13.3978|13.3978	0.60865|0.60865	0.0:0.332:0.0744:0.5935|0.0:0.332:0.0744:0.5935	rs641365;rs1065773;rs17372133;rs56632439;rs58625857;rs641365|rs641365;rs1065773;rs17372133;rs56632439;rs58625857;rs641365	.|.	.|.	.|.	A|R	1078|816;857	.|.	.|.	V|X	+|+	2|1	0|0	PTPRF|PTPRF	43856094|43856094	0.000000|0.000000	0.05858|0.05858	0.565000|0.565000	0.28409|0.28409	0.909000|0.909000	0.53808|0.53808	-4.012000|-4.012000	0.00314|0.00314	-1.781000|-1.781000	0.01277|0.01277	-0.766000|-0.766000	0.03442|0.03442	GTG|TGA	C|0.789;G|0.000;T|0.211	0.789	strong		0.622	PTPRF-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000019710.1		
USP20	10868	hgsc.bcm.edu	37	9	132636920	132636920	+	Silent	SNP	C	C	T	rs35899714	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:132636920C>T	ENST00000315480.4	+	18	1964	c.1806C>T	c.(1804-1806)caC>caT	p.H602H	USP20_ENST00000372429.3_Silent_p.H602H|USP20_ENST00000358355.1_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	142	0	0		WXS	Illumina HiSeq	Phase_I	130	59	0.453846	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		
ADAMTSL3	57188	hgsc.bcm.edu	37	15	84488636	84488636	+	Missense_Mutation	SNP	A	A	G	rs4483821	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:84488636A>G	ENST00000286744.5	+	6	661	c.437A>G	c.(436-438)cAt>cGt	p.H146R	ADAMTSL3_ENST00000567476.1_Missense_Mutation_p.H146R	NM_207517.2	NP_997400.2	P82987	ATL3_HUMAN	ADAMTS-like 3	146			H -> R (in dbSNP:rs4483821). {ECO:0000269|PubMed:15489334}.			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)			TATCAGGGGCATTACTATGAA	0.527													G|||	3402	0.679313	0.8306	0.549	5008	,	,		18661	0.8085		0.4742	False		,,,				2504	0.6452				p.H146R		Atlas-SNP	.											.	ADAMTSL3	290	.	0			c.A437G						PASS	.	G	ARG/HIS	3358,1048	382.5+/-324.5	1291,776,136	95.0	76.0	82.0		437	-3.4	0.0	15	dbSNP_111	82	3958,4642	601.5+/-394.4	947,2064,1289	yes	missense	ADAMTSL3	NM_207517.2	29	2238,2840,1425	GG,GA,AA		46.0233,23.7857,43.749	benign	146/1692	84488636	7316,5690	2203	4300	6503	SO:0001583	missense	57188	exon6			AGGGGCATTACTA	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.437A>G	15.37:g.84488636A>G	ENSP00000286744:p.His146Arg	Somatic	182	0	0		WXS	Illumina HiSeq	Phase_I	194	193	0.994845	NM_207517	A1A566|A1A567|Q9ULI7	Missense_Mutation	SNP	ENST00000286744.5	37	CCDS10326.1	1435	0.657051282051282	412	0.8373983739837398	192	0.5303867403314917	464	0.8111888111888111	367	0.4841688654353562	G	0.192	-1.052018	0.01981	0.762143	0.460233	ENSG00000156218	ENST00000286744	T	0.03212	4.01	5.26	-3.36	0.04913	.	1.142310	0.06302	N	0.701085	T	0.00012	0.0000	N	0.05574	-0.02	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.0	T	0.19647	-1.0299	9	0.15952	T	0.53	.	15.3716	0.74570	0.8582:0.0:0.1418:0.0	rs4483821;rs12914935;rs52797666;rs58219167;rs4483821	146;146	P82987-2;P82987	.;ATL3_HUMAN	R	146	ENSP00000286744:H146R	ENSP00000286744:H146R	H	+	2	0	ADAMTSL3	82279640	0.000000	0.05858	0.000000	0.03702	0.043000	0.13939	0.350000	0.20079	-0.823000	0.04301	-1.663000	0.00750	CAT	A|0.386;G|0.614	0.614	strong		0.527	ADAMTSL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304007.2	NM_207517	
MAPK8IP3	23162	hgsc.bcm.edu	37	16	1814440	1814440	+	Missense_Mutation	SNP	A	A	G	rs2294619	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:1814440A>G	ENST00000250894.4	+	19	2414	c.2257A>G	c.(2257-2259)Acg>Gcg	p.T753A	MAPK8IP3_ENST00000356010.5_Missense_Mutation_p.T747A	NM_015133.3	NP_055948.2	Q9UPT6	JIP3_HUMAN	mitogen-activated protein kinase 8 interacting protein 3	753			T -> A (in dbSNP:rs2294619).		activation of JUN kinase activity (GO:0007257)|axon guidance (GO:0007411)|forebrain development (GO:0030900)|in utero embryonic development (GO:0001701)|lung alveolus development (GO:0048286)|lung morphogenesis (GO:0060425)|positive regulation of neuron differentiation (GO:0045666)|post-embryonic development (GO:0009791)|protein localization (GO:0008104)|regulation of gene expression (GO:0010468)|regulation of JNK cascade (GO:0046328)|respiratory gaseous exchange (GO:0007585)|vesicle-mediated transport (GO:0016192)	axolemma (GO:0030673)|dendrite (GO:0030425)|Golgi membrane (GO:0000139)|smooth endoplasmic reticulum (GO:0005790)	kinesin binding (GO:0019894)|MAP-kinase scaffold activity (GO:0005078)			NS(1)|breast(3)|central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(20)|ovary(1)|prostate(2)|skin(2)|urinary_tract(3)	42						GAGCGCCCACACGTCTCCCGA	0.657													A|||	1482	0.295927	0.382	0.3386	5008	,	,		16930	0.2639		0.1988	False		,,,				2504	0.2822				p.T753A		Atlas-SNP	.											MAPK8IP3_ENST00000250894,NS,carcinoma,0,2	MAPK8IP3	164	2	0			c.A2257G						PASS	.	A	ALA/THR,ALA/THR	1365,2797		237,891,953	20.0	26.0	24.0		2239,2257	-3.8	0.2	16	dbSNP_100	24	1544,6870		144,1256,2807	yes	missense,missense	MAPK8IP3	NM_001040439.1,NM_015133.3	58,58	381,2147,3760	GG,GA,AA		18.3504,32.7967,23.1314	benign,benign	747/1331,753/1337	1814440	2909,9667	2081	4207	6288	SO:0001583	missense	23162	exon19			GCCCACACGTCTC	AB028989	CCDS10442.2, CCDS45379.1	16p13.3	2009-11-23			ENSG00000138834	ENSG00000138834			6884	protein-coding gene	gene with protein product	"""homolog of Drosophila Sunday driver 2"""	605431				10523642, 10629060	Standard	XM_005255187		Approved	KIAA1066, JSAP1, JIP3, syd	uc002cmk.3	Q9UPT6	OTTHUMG00000128637	ENST00000250894.4:c.2257A>G	16.37:g.1814440A>G	ENSP00000250894:p.Thr753Ala	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	87	87	1	NM_015133	A2A2B3|A7E2B3|Q96RY4|Q9H4I4|Q9H7P1|Q9NUG0	Missense_Mutation	SNP	ENST00000250894.4	37	CCDS10442.2	569	0.26053113553113555	167	0.3394308943089431	103	0.2845303867403315	144	0.2517482517482518	155	0.20448548812664907	a	7.199	0.593035	0.13875	0.327967	0.183504	ENSG00000138834	ENST00000250894;ENST00000356010	T;T	0.29917	1.55;1.55	4.99	-3.85	0.04243	.	0.438582	0.25978	N	0.027089	T	0.00012	0.0000	L	0.44542	1.39	0.58432	P	6.999999999979245E-6	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.06405	0.0;0.001;0.002	T	0.43228	-0.9404	9	0.10377	T	0.69	-0.7791	2.6217	0.04918	0.5542:0.1115:0.2229:0.1114	rs2294619;rs58067579;rs2294619	754;747;753	B7ZMF3;E9PFH7;Q9UPT6	.;.;JIP3_HUMAN	A	753;747	ENSP00000250894:T753A;ENSP00000348290:T747A	ENSP00000250894:T753A	T	+	1	0	MAPK8IP3	1754441	0.714000	0.27936	0.175000	0.22980	0.007000	0.05969	0.880000	0.28159	-1.163000	0.02793	-1.345000	0.01243	ACG	A|0.741;G|0.259	0.259	strong		0.657	MAPK8IP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250508.2	NM_001040439	
DGCR6L	85359	hgsc.bcm.edu	37	22	20307256	20307256	+	Silent	SNP	G	G	A	rs7235	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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						PASS	.	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	300	0	0		WXS	Illumina HiSeq	Phase_I	325	136	0.418462	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	
CYP1A2	1544	hgsc.bcm.edu	37	15	75047426	75047426	+	Silent	SNP	C	C	T	rs2470890	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:75047426C>T	ENST00000343932.4	+	7	1611	c.1548C>T	c.(1546-1548)aaC>aaT	p.N516N		NM_000761.3	NP_000752.2	P05177	CP1A2_HUMAN	cytochrome P450, family 1, subfamily A, polypeptide 2	515					alkaloid metabolic process (GO:0009820)|arachidonic acid metabolic process (GO:0019369)|cellular respiration (GO:0045333)|cellular response to cadmium ion (GO:0071276)|dibenzo-p-dioxin metabolic process (GO:0018894)|drug catabolic process (GO:0042737)|drug metabolic process (GO:0017144)|epoxygenase P450 pathway (GO:0019373)|exogenous drug catabolic process (GO:0042738)|heterocycle metabolic process (GO:0046483)|hydrogen peroxide biosynthetic process (GO:0050665)|lung development (GO:0030324)|methylation (GO:0032259)|monocarboxylic acid metabolic process (GO:0032787)|monoterpenoid metabolic process (GO:0016098)|omega-hydroxylase P450 pathway (GO:0097267)|oxidation-reduction process (GO:0055114)|oxidative deethylation (GO:0071615)|oxidative demethylation (GO:0070989)|porphyrin-containing compound metabolic process (GO:0006778)|post-embryonic development (GO:0009791)|regulation of gene expression (GO:0010468)|response to estradiol (GO:0032355)|response to lipopolysaccharide (GO:0032496)|small molecule metabolic process (GO:0044281)|steroid catabolic process (GO:0006706)|toxin biosynthetic process (GO:0009403)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|intracellular membrane-bounded organelle (GO:0043231)	aromatase activity (GO:0070330)|caffeine oxidase activity (GO:0034875)|demethylase activity (GO:0032451)|electron carrier activity (GO:0009055)|enzyme binding (GO:0019899)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity (GO:0016491)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen (GO:0016712)			breast(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(7)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	33					"""""""Insulin(DB00071)|Acenocoumarol(DB01418)|Acetaminophen(DB00316)|Agomelatine(DB06594)|Albendazole(DB00518)|Alitretinoin(DB00523)|Almotriptan(DB00918)|Alosetron(DB00969)|Aminoglutethimide(DB00357)|Aminophenazone(DB01424)|Aminophylline(DB01223)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amlodipine(DB00381)|Anagrelide(DB00261)|Anastrozole(DB01217)|Antipyrine(DB01435)|Apixaban(DB06605)|Aprepitant(DB00673)|Asenapine(DB06216)|Atropine(DB00572)|Axitinib(DB06626)|Azelastine(DB00972)|Azithromycin(DB00207)|Benzyl alcohol(DB06770)|Betaxolol(DB00195)|Bortezomib(DB00188)|Bromazepam(DB01558)|Bromocriptine(DB01200)|Bupivacaine(DB00297)|Buprenorphine(DB00921)|Bupropion(DB01156)|Caffeine(DB00201)|Carbamazepine(DB00564)|Carmustine(DB00262)|Carvedilol(DB01136)|Chlorpromazine(DB00477)|Chlorzoxazone(DB00356)|Cilostazol(DB01166)|Cimetidine(DB00501)|Cinacalcet(DB01012)|Cinnarizine(DB00568)|Ciprofloxacin(DB00537)|Cisapride(DB00604)|Citalopram(DB00215)|Clarithromycin(DB01211)|Clenbuterol(DB01407)|Clevidipine(DB04920)|Clobetasol propionate(DB01013)|Clomifene(DB00882)|Clomipramine(DB01242)|Clonidine(DB00575)|Clopidogrel(DB00758)|Clotrimazole(DB00257)|Clozapine(DB00363)|Conjugated Estrogens(DB00286)|Cyclobenzaprine(DB00924)|Dacarbazine(DB00851)|Dapagliflozin(DB06292)|Dasatinib(DB01254)|Daunorubicin(DB00694)|Delavirdine(DB00705)|Desipramine(DB01151)|Desloratadine(DB00967)|Dexfenfluramine(DB01191)|Dexmedetomidine(DB00633)|Diazepam(DB00829)|Diclofenac(DB00586)|Dinoprostone(DB00917)|Diphenhydramine(DB01075)|Domperidone(DB01184)|Dopamine(DB00988)|Doxepin(DB01142)|Duloxetine(DB00476)|Edetic Acid(DB00974)|Efavirenz(DB00625)|Eltrombopag(DB06210)|Enoxacin(DB00467)|Epinephrine(DB00668)|Ergotamine(DB00696)|Erlotinib(DB00530)|Erythromycin(DB00199)|Estradiol(DB00783)|Estrone(DB00655)|Estropipate(DB04574)|Ethanol(DB00898)|Etoposide(DB00773)|Etoricoxib(DB01628)|Flunarizine(DB04841)|Flunitrazepam(DB01544)|Fluorouracil(DB00544)|Fluoxetine(DB00472)|Fluphenazine(DB00623)|Flutamide(DB00499)|Fluvastatin(DB01095)|Fluvoxamine(DB00176)|Frovatriptan(DB00998)|Gemfibrozil(DB01241)|Griseofulvin(DB00400)|Guanabenz(DB00629)|Haloperidol(DB00502)|Hesperetin(DB01094)|Hexobarbital(DB01355)|Iloperidone(DB04946)|Imatinib(DB00619)|Imipramine(DB00458)|Imiquimod(DB00724)|inhaled insulin(DB05278)|Insulin Aspart(DB01306)|Insulin Detemir(DB01307)|Insulin Glargine(DB00047)|Insulin Glulisine(DB01309)|Insulin Lispro(DB00046)|Insulin Regular(DB00030)|Irbesartan(DB01029)|Isoniazid(DB00951)|Ketoconazole(DB01026)|Lansoprazole(DB00448)|Leflunomide(DB01097)|Levobupivacaine(DB01002)|Levofloxacin(DB01137)|Lidocaine(DB00281)|Lomefloxacin(DB00978)|Lopinavir(DB01601)|Lorcaserin(DB04871)|Losartan(DB00678)|Lumiracoxib(DB01283)|Malathion(DB00772)|Maprotiline(DB00934)|Meclizine(DB00737)|Melatonin(DB01065)|Menadione(DB00170)|Methadone(DB00333)|Methimazole(DB00763)|Methotrimeprazine(DB01403)|Methoxsalen(DB00553)|Methoxyflurane(DB01028)|Mexiletine(DB00379)|Mianserin(DB06148)|Miconazole(DB01110)|Mirtazapine(DB00370)|Moclobemide(DB01171)|Modafinil(DB00745)|Nabumetone(DB00461)|Nafcillin(DB00607)|Naproxen(DB00788)|Nelfinavir(DB00220)|Nevirapine(DB00238)|Niclosamide(DB06803)|Nicotine(DB00184)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nisoldipine(DB00401)|Nitric Oxide(DB00435)|Nitroprusside(DB00325)|Norepinephrine(DB00368)|Norfloxacin(DB01059)|Nortriptyline(DB00540)|Ofloxacin(DB01165)|Olanzapine(DB00334)|Omeprazole(DB00338)|Ondansetron(DB00904)|Oxaliplatin(DB00526)|Oxtriphylline(DB01303)|Palonosetron(DB00377)|Pantoprazole(DB00213)|Pazopanib(DB06589)|Pefloxacin(DB00487)|Pentamidine(DB00738)|Pentoxifylline(DB00806)|Perphenazine(DB00850)|Phenobarbital(DB01174)|Phentermine(DB00191)|Phenylephrine(DB00388)|Phenylpropanolamine(DB00397)|Pimozide(DB01100)|Pipotiazine(DB01621)|Pomalidomide(DB08910)|Praziquantel(DB01058)|Primaquine(DB01087)|Primidone(DB00794)|Progesterone(DB00396)|Proguanil(DB01131)|Promazine(DB00420)|Propafenone(DB01182)|Propofol(DB00818)|Propranolol(DB00571)|Pyrazinamide(DB00339)|Quinidine(DB00908)|Quinine(DB00468)|Rabeprazole(DB01129)|Ramelteon(DB00980)|Ranitidine(DB00863)|Rasagiline(DB01367)|Rifabutin(DB00615)|Rifampicin(DB01045)|Rilpivirine(DB08864)|Riluzole(DB00740)|Ritonavir(DB00503)|Rizatriptan(DB00953)|Ropinirole(DB00268)|Ropivacaine(DB00296)|Rosiglitazone(DB00412)|Rotigotine(DB05271)|Roxithromycin(DB00778)|Secobarbital(DB00418)|Selegiline(DB01037)|Sertraline(DB01104)|SIMEPREVIR(DB06290)|Sorafenib(DB00398)|Streptozocin(DB00428)|Sulindac(DB00605)|Tamoxifen(DB00675)|Telithromycin(DB00976)|Tenofovir(DB00300)|Terbinafine(DB00857)|Thalidomide(DB01041)|Theobromine(DB01412)|Theophylline(DB00277)|Thiabendazole(DB00730)|Thioridazine(DB00679)|Thiothixene(DB01623)|Ticlopidine(DB00208)|Tioconazole(DB01007)|Tizanidine(DB00697)|Tocainide(DB01056)|Toremifene(DB00539)|Tranylcypromine(DB00752)|Triamterene(DB00384)|Trifluoperazine(DB00831)|Valproic Acid(DB00313)|Vemurafenib(DB08881)|Verapamil(DB00661)|Warfarin(DB00682)|Zafirlukast(DB00549)|Zileuton(DB00744)|Ziprasidone(DB00246)|Zolmitriptan(DB00315)|Zolpidem(DB00425)"""	TCTCCATCAACTGAAGAAGAC	0.577													C|||	1183	0.236222	0.028	0.3271	5008	,	,		14798	0.1637		0.5964	False		,,,				2504	0.1575				p.N516N		Atlas-SNP	.											.	CYP1A2	70	.	0			c.C1548T						PASS	.	C		547,3847	238.0+/-249.6	40,467,1690	30.0	28.0	28.0		1548	0.6	0.3	15	dbSNP_100	28	5619,2973	631.2+/-398.5	1863,1893,540	no	coding-synonymous	CYP1A2	NM_000761.3		1903,2360,2230	TT,TC,CC		34.602,12.4488,47.4819		516/517	75047426	6166,6820	2197	4296	6493	SO:0001819	synonymous_variant	1544	exon7			CATCAACTGAAGA	AF182274	CCDS32293.1	15q24.1	2013-11-11	2003-01-14		ENSG00000140505	ENSG00000140505	1.14.14.1	"""Cytochrome P450s"""	2596	protein-coding gene	gene with protein product		124060	"""cytochrome P450, subfamily I (aromatic compound-inducible), polypeptide 2"""			15128046	Standard	NM_000761		Approved	P3-450, CP12	uc002ayr.1	P05177	OTTHUMG00000172901	ENST00000343932.4:c.1548C>T	15.37:g.75047426C>T		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	34	22	0.647059	NM_000761	Q16754|Q6NWU5|Q9BXX7|Q9UK49	Silent	SNP	ENST00000343932.4	37	CCDS32293.1																																																																																			C|0.616;T|0.384	0.384	strong		0.577	CYP1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421263.2	NM_000761	
ZNF624	57547	hgsc.bcm.edu	37	17	16527357	16527357	+	Silent	SNP	G	G	A	rs62072859	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:16527357G>A	ENST00000311331.7	-	6	934	c.843C>T	c.(841-843)tgC>tgT	p.C281C		NM_020787.3	NP_065838.2	Q9P2J8	ZN624_HUMAN	zinc finger protein 624	281					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(4)|endometrium(1)|kidney(1)|large_intestine(8)|lung(9)|ovary(1)|prostate(1)|skin(1)	26				UCEC - Uterine corpus endometrioid carcinoma (92;0.0837)		AGGCCTTTTCGCATGTACTAC	0.363													G|||	151	0.0301518	0.0121	0.0432	5008	,	,		19683	0.0		0.0845	False		,,,				2504	0.0204				p.C281C	NSCLC(186;1023 2134 13330 38202 39800)	Atlas-SNP	.											.	ZNF624	91	.	0			c.C843T						PASS	.	G		86,4314	69.2+/-107.0	0,86,2114	135.0	142.0	140.0		843	2.1	1.0	17	dbSNP_129	140	577,8023	152.2+/-206.8	17,543,3740	no	coding-synonymous	ZNF624	NM_020787.3		17,629,5854	AA,AG,GG		6.7093,1.9545,5.1		281/866	16527357	663,12337	2200	4300	6500	SO:0001819	synonymous_variant	57547	exon6			CTTTTCGCATGTA	AB037770	CCDS11180.1	17p11.2	2013-01-08			ENSG00000197566	ENSG00000197566		"""Zinc fingers, C2H2-type"", ""-"""	29254	protein-coding gene	gene with protein product						10718198	Standard	NM_020787		Approved	KIAA1349	uc010cpi.2	Q9P2J8	OTTHUMG00000058996	ENST00000311331.7:c.843C>T	17.37:g.16527357G>A		Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	120	64	0.533333	NM_020787	Q3SY62|Q3SY63|Q6ZN27	Silent	SNP	ENST00000311331.7	37	CCDS11180.1																																																																																			G|0.948;A|0.052	0.052	strong		0.363	ZNF624-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130512.3	XM_047617	
TSPYL6	388951	hgsc.bcm.edu	37	2	54482989	54482989	+	Silent	SNP	C	C	T	rs6740641	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:54482989C>T	ENST00000317802.7	-	1	420	c.300G>A	c.(298-300)gcG>gcA	p.A100A	ACYP2_ENST00000606865.1_Intron|ACYP2_ENST00000607452.1_Intron|ACYP2_ENST00000394666.3_Intron|ACYP2_ENST00000303536.4_Intron	NM_001003937.2	NP_001003937.2	Q8N831	TSYL6_HUMAN	TSPY-like 6	100					nucleosome assembly (GO:0006334)	nucleus (GO:0005634)		p.A100A(1)		NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(1)|ovary(1)|skin(1)|stomach(2)	20						AGGCAGAGGCCGCTTCTAGGC	0.607													T|||	694	0.138578	0.1263	0.0994	5008	,	,		16663	0.1835		0.1093	False		,,,				2504	0.1667				p.A100A		Atlas-SNP	.											TSPYL6,NS,carcinoma,0,1	TSPYL6	54	1	1	Substitution - coding silent(1)	stomach(1)	c.G300A						PASS	.	T	,	602,3542		69,464,1539	35.0	40.0	38.0		300,	-0.2	0.0	2	dbSNP_116	38	1221,7165		86,1049,3058	no	coding-synonymous,intron	ACYP2,TSPYL6	NM_001003937.2,NM_138448.3	,	155,1513,4597	TT,TC,CC		14.56,14.527,14.5491	,	100/411,	54482989	1823,10707	2072	4193	6265	SO:0001819	synonymous_variant	388951	exon1			AGAGGCCGCTTCT	AK097417	CCDS42682.1	2p16.3	2007-10-22			ENSG00000178021	ENSG00000178021			14521	protein-coding gene	gene with protein product							Standard	NM_001003937		Approved		uc002rxr.2	Q8N831	OTTHUMG00000151823	ENST00000317802.7:c.300G>A	2.37:g.54482989C>T		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	185	146	0.789189	NM_001003937	Q6NUJ3	Silent	SNP	ENST00000317802.7	37	CCDS42682.1																																																																																			C|0.869;G|0.001;T|0.130	0.130	strong		0.607	TSPYL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324069.3	XM_371494	
NIF3L1	60491	hgsc.bcm.edu	37	2	201768238	201768238	+	Missense_Mutation	SNP	C	C	T	rs7917	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:201768238C>T	ENST00000409020.1	+	7	1265	c.971C>T	c.(970-972)aCt>aTt	p.T324I	NIF3L1_ENST00000359683.4_Missense_Mutation_p.T297I|NIF3L1_ENST00000409357.1_Missense_Mutation_p.T324I|NIF3L1_ENST00000416651.1_Missense_Mutation_p.T324I|NIF3L1_ENST00000409588.1_Missense_Mutation_p.L278F			Q9GZT8	GTPC1_HUMAN	NIF3 NGG1 interacting factor 3-like 1 (S. cerevisiae)	324			T -> I (in dbSNP:rs7917).		7,8-dihydroneopterin 3'-triphosphate biosynthetic process (GO:0035998)|positive regulation of transcription, DNA-templated (GO:0045893)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)	GTP binding (GO:0005525)|GTP cyclohydrolase I activity (GO:0003934)|metal ion binding (GO:0046872)|transcription factor binding (GO:0008134)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(5)|skin(1)|urinary_tract(2)	13						CATCATGATACTTTGGATGCT	0.413													T|||	1419	0.283347	0.6694	0.1772	5008	,	,		20225	0.0149		0.2555	False		,,,				2504	0.1421				p.T324I		Atlas-SNP	.											.	NIF3L1	51	.	0			c.C971T						PASS	.	T	ILE/THR,ILE/THR,PHE/LEU,ILE/THR	2196,1598		645,906,346	156.0	150.0	152.0		971,890,832,890	5.3	0.6	2	dbSNP_52	152	1824,6416		184,1456,2480	yes	missense,missense,missense,missense	NIF3L1	NM_001136039.2,NM_001142355.1,NM_001142356.1,NM_021824.3	89,89,22,89	829,2362,2826	TT,TC,CC		22.1359,42.1191,33.4054	benign,benign,benign,benign	324/378,297/351,278/286,297/351	201768238	4020,8014	1897	4120	6017	SO:0001583	missense	60491	exon7			ATGATACTTTGGA	AB038949	CCDS42797.1, CCDS46485.1, CCDS46486.1	2q33	2011-11-10	2011-11-10		ENSG00000196290	ENSG00000196290			13390	protein-coding gene	gene with protein product		605778	"""NIF3 (Ngg1 interacting factor 3, S.pombe homolog)-like 1"", ""NIF3 NGG1 interacting factor 3-like 1 (S. pombe)"""	ALS2CR1		11124544, 11161814, 12522100	Standard	NM_001136039		Approved	CALS-7, MDS015	uc002uwm.2	Q9GZT8	OTTHUMG00000154588	ENST00000409020.1:c.971C>T	2.37:g.201768238C>T	ENSP00000386394:p.Thr324Ile	Somatic	272	0	0		WXS	Illumina HiSeq	Phase_I	217	110	0.506912	NM_001136039	Q53TX4|Q6X735|Q9H2D2|Q9HC18	Missense_Mutation	SNP	ENST00000409020.1	37	CCDS46485.1	577|577	0.2641941391941392|0.2641941391941392	305|305	0.6199186991869918|0.6199186991869918	72|72	0.19889502762430938|0.19889502762430938	3|3	0.005244755244755245|0.005244755244755245	197|197	0.2598944591029024|0.2598944591029024	T|T	7.341|7.341	0.620919|0.620919	0.14193|0.14193	0.578809|0.578809	0.221359|0.221359	ENSG00000196290|ENSG00000196290	ENST00000409588|ENST00000416651;ENST00000409020;ENST00000359683;ENST00000409357	.|T;T;T;T	.|0.39592	.|1.07;1.07;1.07;1.07	5.33|5.33	5.33|5.33	0.75918|0.75918	.|.	.|0.167825	.|0.52532	.|N	.|0.000073	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.54753|0.54753	P|P	1.4999999999987246E-5|1.4999999999987246E-5	B|B	0.02656|0.02656	0.0|0.0	B|B	0.01281|0.01281	0.0|0.0	T|T	0.41448|0.41448	-0.9508|-0.9508	6|8	0.87932|0.23891	D|T	0|0.37	-3.6914|-3.6914	11.5287|11.5287	0.50595|0.50595	0.0:0.0708:0.0:0.9292|0.0:0.0708:0.0:0.9292	rs7917;rs1128563;rs3177342;rs3185643;rs11555980;rs13396213;rs17349459;rs52807793;rs58476980;rs7917|rs7917;rs1128563;rs3177342;rs3185643;rs11555980;rs13396213;rs17349459;rs52807793;rs58476980;rs7917	278|324	Q6X735|Q9GZT8	.|NIF3L_HUMAN	F|I	278|324;324;297;324	.|ENSP00000400787:T324I;ENSP00000386394:T324I;ENSP00000352711:T297I;ENSP00000387315:T324I	ENSP00000387021:L278F|ENSP00000352711:T297I	L|T	+|+	1|2	0|0	NIF3L1|NIF3L1	201476483|201476483	1.000000|1.000000	0.71417|0.71417	0.577000|0.577000	0.28562|0.28562	0.920000|0.920000	0.55202|0.55202	5.883000|5.883000	0.69721|0.69721	0.968000|0.968000	0.38212|0.38212	-0.381000|-0.381000	0.06696|0.06696	CTT|ACT	C|0.715;T|0.285	0.285	strong		0.413	NIF3L1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336201.1	NM_021824	
OR10AD1	121275	hgsc.bcm.edu	37	12	48596254	48596254	+	Silent	SNP	A	A	C	rs11830378	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:48596254A>C	ENST00000310248.2	-	1	916	c.822T>G	c.(820-822)ccT>ccG	p.P274P		NM_001004134.1	NP_001004134.1	Q8NGE0	O10AD_HUMAN	olfactory receptor, family 10, subfamily AD, member 1	274						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(2)|lung(3)|ovary(1)|stomach(1)|urinary_tract(1)	9						GGAGGGAGAAAGGTTTGTCTT	0.483													A|||	212	0.0423323	0.059	0.036	5008	,	,		22069	0.006		0.0924	False		,,,				2504	0.0102				p.P274P		Atlas-SNP	.											OR10AD1,colon,carcinoma,-1,1	OR10AD1	24	1	0			c.T822G						PASS	.	A		275,4131	155.5+/-188.7	8,259,1936	122.0	122.0	122.0		822	0.8	1.0	12	dbSNP_120	122	764,7836	181.9+/-230.5	30,704,3566	no	coding-synonymous	OR10AD1	NM_001004134.1		38,963,5502	CC,CA,AA		8.8837,6.2415,7.9886		274/318	48596254	1039,11967	2203	4300	6503	SO:0001819	synonymous_variant	121275	exon1			GGAGAAAGGTTTG		CCDS31787.1	12q13.11	2013-09-24	2002-11-13	2002-11-15	ENSG00000172640	ENSG00000172640		"""GPCR / Class A : Olfactory receptors"""	14819	protein-coding gene	gene with protein product			"""olfactory receptor, family 10, subfamily AD, member 1 pseudogene"""	OR10AD1P			Standard	NM_001004134		Approved		uc001rrl.1	Q8NGE0	OTTHUMG00000168027	ENST00000310248.2:c.822T>G	12.37:g.48596254A>C		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	95	41	0.431579	NM_001004134	B9EGT9|Q6IFA8	Silent	SNP	ENST00000310248.2	37	CCDS31787.1																																																																																			A|0.938;C|0.062	0.062	strong		0.483	OR10AD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397577.1		
SIGLEC5	8778	hgsc.bcm.edu	37	19	52130830	52130830	+	Silent	SNP	C	C	A	rs8107754	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:52130830C>A	ENST00000534261.2	-	7	1566	c.1167G>T	c.(1165-1167)ggG>ggT	p.G389G	SIGLEC5_ENST00000222107.4_Silent_p.G389G|SIGLEC5_ENST00000429354.3_Silent_p.G389G|SIGLEC5_ENST00000599649.1_Silent_p.G389G|SIGLEC5_ENST00000570106.2_Silent_p.G389G			O15389	SIGL5_HUMAN	sialic acid binding Ig-like lectin 5	389					cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(3)|large_intestine(4)|lung(9)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	27		all_neural(266;0.0726)		GBM - Glioblastoma multiforme(134;0.00124)|OV - Ovarian serous cystadenocarcinoma(262;0.0218)		TGGCCCAGGGCCCAGCTGAGC	0.662													C|||	1646	0.328674	0.382	0.5562	5008	,	,		15906	0.0089		0.4602	False		,,,				2504	0.2894				p.G389G		Atlas-SNP	.											SIGLEC5,NS,carcinoma,-1,1	SIGLEC5	67	1	0			c.G1167T						scavenged	.	C		1864,2542	534.0+/-373.9	378,1108,717	47.0	46.0	46.0		1167	3.0	0.9	19	dbSNP_116	46	4136,4464	559.5+/-387.4	996,2144,1160	no	coding-synonymous	SIGLEC5	NM_003830.2		1374,3252,1877	AA,AC,CC		48.093,42.3059,46.1326		389/552	52130830	6000,7006	2203	4300	6503	SO:0001819	synonymous_variant	8778	exon6			CCAGGGCCCAGCT	U71383	CCDS33088.1	19q13.41	2013-01-29			ENSG00000105501	ENSG00000105501		"""Sialic acid binding Ig-like lectins"", ""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	10874	protein-coding gene	gene with protein product		604200		CD33L2		10343116	Standard	NM_003830		Approved	OB-BP2, SIGLEC-5, CD170	uc002pxe.4	O15389	OTTHUMG00000165510	ENST00000534261.2:c.1167G>T	19.37:g.52130830C>A		Somatic	87	1	0.0114943		WXS	Illumina HiSeq	Phase_I	82	80	0.97561	NM_003830		Silent	SNP	ENST00000534261.2	37	CCDS33088.1																																																																																			C|0.575;A|0.425	0.425	strong		0.662	SIGLEC5-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466897.2	NM_003830	
PDXDC1	23042	hgsc.bcm.edu	37	16	15095675	15095675	+	Silent	SNP	C	C	A	rs9921162	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:15095675C>A	ENST00000396410.4	+	4	301	c.204C>A	c.(202-204)ctC>ctA	p.L68L	PDXDC1_ENST00000450288.2_Intron|PDXDC1_ENST00000447912.2_Intron|PDXDC1_ENST00000325823.7_Silent_p.L53L|PDXDC1_ENST00000563679.1_Silent_p.L86L|PDXDC1_ENST00000535621.2_Silent_p.L68L|PDXDC1_ENST00000455313.2_Silent_p.L68L|PDXDC1_ENST00000569715.1_Intron	NM_015027.2	NP_055842.2	Q6P996	PDXD1_HUMAN	pyridoxal-dependent decarboxylase domain containing 1	68					carboxylic acid metabolic process (GO:0019752)	Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)	carboxy-lyase activity (GO:0016831)|pyridoxal phosphate binding (GO:0030170)			central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(2)|liver(1)|lung(10)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						TTCAGAATCTCATGCATGGAG	0.483																																					p.L68L		Atlas-SNP	.											PDXDC1,NS,carcinoma,0,1	PDXDC1	59	1	0			c.C204A						PASS	.	A		909,3485		55,799,1343	60.0	58.0	58.0		204	-1.9	1.0	16	dbSNP_119	58	1467,7133		37,1393,2870	no	coding-synonymous	PDXDC1	NM_015027.2		92,2192,4213	AA,AC,CC		17.0581,20.6873,18.2854		68/789	15095675	2376,10618	2197	4300	6497	SO:0001819	synonymous_variant	23042	exon4			GAATCTCATGCAT	AK025504, BX647809	CCDS32393.1, CCDS66954.1, CCDS66957.1, CCDS73830.1, CCDS73831.1	16p13.11	2008-02-05							28995	protein-coding gene	gene with protein product		614244					Standard	XM_005255173		Approved	KIAA0251	uc002dda.4	Q6P996	OTTHUMG00000166304	ENST00000396410.4:c.204C>A	16.37:g.15095675C>A		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	173	67	0.387283	NM_015027	B4DR55|B4DSL3|E7EMH5|E7EPL4|H3BNZ1|O00236|Q4F6X7|Q6PID7|Q86YF1|Q8N4Q9|Q8TBS5	Silent	SNP	ENST00000396410.4	37	CCDS32393.1																																																																																			C|0.773;A|0.227	0.227	strong		0.483	PDXDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389065.2	NM_015027	
FAN1	22909	hgsc.bcm.edu	37	15	31229420	31229420	+	Silent	SNP	T	T	C	rs2955795	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:31229420T>C	ENST00000362065.4	+	14	3306	c.3015T>C	c.(3013-3015)caT>caC	p.H1005H		NM_014967.4	NP_055782.3	Q9Y2M0	FAN1_HUMAN	FANCD2/FANCI-associated nuclease 1	1005	VRR-NUC.				DNA catabolic process, endonucleolytic (GO:0000737)|DNA repair (GO:0006281)|double-strand break repair via homologous recombination (GO:0000724)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA incision (GO:0033683)	nucleus (GO:0005634)	5'-3' exonuclease activity (GO:0008409)|5'-flap endonuclease activity (GO:0017108)|DNA binding (GO:0003677)|magnesium ion binding (GO:0000287)|phosphodiesterase I activity (GO:0004528)|ubiquitin binding (GO:0043130)			autonomic_ganglia(2)|breast(2)|cervix(2)|endometrium(7)|kidney(1)|large_intestine(6)|lung(8)|skin(1)	29						AAGTCTGCCATGTGGTTGCAG	0.438								Direct reversal of damage					T|||	2289	0.457069	0.1089	0.4654	5008	,	,		17523	0.8294		0.4473	False		,,,				2504	0.5481				p.H1005H		Atlas-SNP	.											.	FAN1	77	.	0			c.T3015C						PASS	.	T		741,3663	303.5+/-288.0	71,599,1532	110.0	109.0	109.0		3015	-10.6	0.1	15	dbSNP_101	109	3787,4813	536.4+/-383.0	814,2159,1327	no	coding-synonymous	FAN1	NM_014967.4		885,2758,2859	CC,CT,TT		44.0349,16.8256,34.8201		1005/1018	31229420	4528,8476	2202	4300	6502	SO:0001819	synonymous_variant	22909	exon14			CTGCCATGTGGTT		CCDS32186.1, CCDS58344.1	15q13.2-q13.3	2010-08-04	2010-08-04	2010-08-04		ENSG00000198690			29170	protein-coding gene	gene with protein product		613534	"""KIAA1018"", ""myotubularin related protein 15"""	KIAA1018, MTMR15		20603015, 20603016, 20603073	Standard	NM_014967		Approved		uc001zff.3	Q9Y2M0		ENST00000362065.4:c.3015T>C	15.37:g.31229420T>C		Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	107	107	1	NM_014967	A8K4M2|Q86WU8	Silent	SNP	ENST00000362065.4	37	CCDS32186.1																																																																																			T|0.603;C|0.397	0.397	strong		0.438	FAN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430740.1	NM_014967	
DENND5B	160518	hgsc.bcm.edu	37	12	31648826	31648826	+	Missense_Mutation	SNP	C	C	T	rs4930979	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:31648826C>T	ENST00000389082.5	-	2	419	c.155G>A	c.(154-156)aGa>aAa	p.R52K	DENND5B_ENST00000536562.1_Missense_Mutation_p.R87K|DENND5B_ENST00000545147.1_5'UTR|DENND5B_ENST00000354285.4_Missense_Mutation_p.R74K|DENND5B_ENST00000306833.6_Missense_Mutation_p.R87K	NM_144973.3	NP_659410.3	Q6ZUT9	DEN5B_HUMAN	DENN/MADD domain containing 5B	52	UDENN.		R -> K (in dbSNP:rs4930979). {ECO:0000269|PubMed:14702039}.		positive regulation of Rab GTPase activity (GO:0032851)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			NS(2)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(8)|lung(17)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	38						GAATGTTCTTCTCAAAGGACT	0.333													C|||	1986	0.396565	0.084	0.6095	5008	,	,		16127	0.5734		0.4165	False		,,,				2504	0.4652				p.R52K		Atlas-SNP	.											.	DENND5B	114	.	0			c.G155A						PASS	.	C	LYS/ARG	458,3182		32,394,1394	113.0	101.0	105.0		155	3.7	1.0	12	dbSNP_111	105	3279,4887		678,1923,1482	yes	missense	DENND5B	NM_144973.3	26	710,2317,2876	TT,TC,CC		40.1543,12.5824,31.6534	benign	52/1275	31648826	3737,8069	1820	4083	5903	SO:0001583	missense	160518	exon2			GTTCTTCTCAAAG	AF086301	CCDS44857.1	12p11.21	2012-10-03			ENSG00000170456	ENSG00000170456		"""DENN/MADD domain containing"""	28338	protein-coding gene	gene with protein product						12477932	Standard	NM_144973		Approved	MGC24039	uc001rki.1	Q6ZUT9	OTTHUMG00000169034	ENST00000389082.5:c.155G>A	12.37:g.31648826C>T	ENSP00000373734:p.Arg52Lys	Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	114	55	0.482456	NM_144973	B5ME75|Q59FW8|Q68CZ7|Q6NUJ0|Q7Z3F9|Q8N973|Q8WUC8	Missense_Mutation	SNP	ENST00000389082.5	37	CCDS44857.1	908	0.4157509157509158	49	0.09959349593495935	206	0.569060773480663	334	0.583916083916084	319	0.420844327176781	C	13.73	2.323020	0.41096	0.125824	0.401543	ENSG00000170456	ENST00000389082;ENST00000306833;ENST00000536562;ENST00000354285;ENST00000546299	T;T;T;T;T	0.28895	3.82;1.59;1.59;3.35;3.34	4.6	3.71	0.42584	uDENN (3);	0.133121	0.49916	N	0.000128	T	0.00012	0.0000	N	0.25380	0.74	0.21697	P	0.999584744	B;B;B	0.11235	0.004;0.002;0.003	B;B;B	0.20577	0.03;0.008;0.017	T	0.41734	-0.9492	9	0.31617	T	0.26	-3.6645	11.8628	0.52476	0.0:0.9123:0.0:0.0877	rs4930979;rs4930979	74;52;87	Q6ZUT9-4;Q6ZUT9;G3V1S3	.;DEN5B_HUMAN;.	K	52;87;87;74;4	ENSP00000373734:R52K;ENSP00000306482:R87K;ENSP00000444889:R87K;ENSP00000346238:R74K;ENSP00000442938:R4K	ENSP00000306482:R87K	R	-	2	0	DENND5B	31540093	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	1.535000	0.36061	1.277000	0.44412	0.650000	0.86243	AGA	C|0.605;T|0.395	0.395	strong		0.333	DENND5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402040.1	NM_144973	
MAP4K4	9448	hgsc.bcm.edu	37	2	102472459	102472459	+	Silent	SNP	A	A	G	rs1139583	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:102472459A>G	ENST00000347699.4	+	13	1254	c.1254A>G	c.(1252-1254)gaA>gaG	p.E418E	MAP4K4_ENST00000302217.5_Silent_p.E271E|MAP4K4_ENST00000413150.2_Silent_p.E418E|MAP4K4_ENST00000350198.4_Silent_p.E418E|MAP4K4_ENST00000456652.1_Silent_p.E271E|MAP4K4_ENST00000425019.1_Silent_p.E418E|MAP4K4_ENST00000324219.4_Silent_p.E418E|MAP4K4_ENST00000350878.4_Silent_p.E398E	NM_001242559.1|NM_145687.3	NP_001229488.1|NP_663720.1	O95819	M4K4_HUMAN	mitogen-activated protein kinase kinase kinase kinase 4	418					intracellular signal transduction (GO:0035556)|protein phosphorylation (GO:0006468)|regulation of JNK cascade (GO:0046328)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)			breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(15)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	41						gagagcgggaagctagaaggc	0.463													A|||	660	0.131789	0.1051	0.0879	5008	,	,		20227	0.0982		0.1789	False		,,,				2504	0.1851				p.E418E		Atlas-SNP	.											.	MAP4K4	111	.	0			c.A1254G						PASS	.	A	,,,,	260,1932		18,224,854	127.0	169.0	155.0		1254,1254,1254,1254,1254	-2.0	0.3	2	dbSNP_86	155	684,3626		53,578,1524	yes	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	MAP4K4	NM_001242559.1,NM_001242560.1,NM_004834.4,NM_145686.3,NM_145687.3	,,,,	71,802,2378	GG,GA,AA		15.8701,11.8613,14.5186	,,,,	418/1240,418/1236,418/1166,418/1274,418/1213	102472459	944,5558	1096	2155	3251	SO:0001819	synonymous_variant	9448	exon13			GCGGGAAGCTAGA	AF096300	CCDS56130.1, CCDS74546.1	2q11.2-q12	2011-06-09			ENSG00000071054	ENSG00000071054		"""Mitogen-activated protein kinase cascade / Kinase kinase kinase kinases"""	6866	protein-coding gene	gene with protein product	"""HPK/GCK-like kinase"", ""hepatocyte progenitor kinase-like/germinal center kinase-like kinase"""	604666				9890973, 9734811, 9135144	Standard	NM_004834		Approved	HGK, NIK, FLH21957	uc002tbf.3	O95819	OTTHUMG00000155394	ENST00000347699.4:c.1254A>G	2.37:g.102472459A>G		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	56	24	0.428571	NM_004834	O75172|Q9NST7	Silent	SNP	ENST00000347699.4	37	CCDS56130.1	248	0.11355311355311355	40	0.08130081300813008	34	0.09392265193370165	41	0.07167832167832168	133	0.17546174142480211	A	9.181	1.023658	0.19433	0.118613	0.158701	ENSG00000071054	ENST00000421882	.	.	.	4.29	-1.97	0.07503	.	.	.	.	.	T	0.00073	0.0002	.	.	.	0.35830	P	0.17476999999999998	.	.	.	.	.	.	T	0.22382	-1.0218	3	.	.	.	.	8.4533	0.32884	0.5261:0.0:0.4739:0.0	rs1139583;rs2074745;rs11556523;rs17802230;rs57286746;rs1139583	.	.	.	G	158	.	.	S	+	1	0	MAP4K4	101838891	0.999000	0.42202	0.305000	0.25099	0.972000	0.66771	0.324000	0.19610	-0.219000	0.10003	0.377000	0.23210	AGC	A|0.881;G|0.119	0.119	strong		0.463	MAP4K4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000339839.1	NM_004834	
TLR10	81793	hgsc.bcm.edu	37	4	38777173	38777173	+	Silent	SNP	A	A	T	rs10856838	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:38777173A>T	ENST00000308973.4	-	4	644	c.39T>A	c.(37-39)atT>atA	p.I13I	TLR10_ENST00000506111.1_Silent_p.I13I|TLR10_ENST00000361424.2_Silent_p.I13I|TLR10_ENST00000508334.1_Silent_p.I13I|TLR10_ENST00000507953.1_5'Flank	NM_001017388.2|NM_001195107.1|NM_030956.3	NP_001017388.1|NP_001182036.1|NP_112218.2	Q9BXR5	TLR10_HUMAN	toll-like receptor 10	13					immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of inflammatory response (GO:0050729)|regulation of cytokine secretion (GO:0050707)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor signaling pathway (GO:0002224)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	transmembrane signaling receptor activity (GO:0004888)			breast(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(11)|prostate(1)|urinary_tract(2)	25						CTGTCATAACAATACTACAAA	0.403													A|||	1657	0.330871	0.5053	0.2723	5008	,	,		16858	0.2302		0.1909	False		,,,				2504	0.3845				p.I13I		Atlas-SNP	.											.	TLR10	87	.	0			c.T39A						PASS	.	A	,,,,	2028,2378	563.5+/-381.2	466,1096,641	68.0	68.0	68.0		39,39,39,,39	2.6	0.0	4	dbSNP_120	68	1423,7177	273.5+/-290.7	129,1165,3006	no	coding-synonymous,coding-synonymous,coding-synonymous,utr-5,coding-synonymous	TLR10	NM_001017388.2,NM_001195106.1,NM_001195107.1,NM_001195108.1,NM_030956.3	,,,,	595,2261,3647	TT,TA,AA		16.5465,46.0281,26.5339	,,,,	13/812,13/812,13/812,,13/812	38777173	3451,9555	2203	4300	6503	SO:0001819	synonymous_variant	81793	exon2			CATAACAATACTA	AF296673	CCDS3445.1	4p14	2009-11-23			ENSG00000174123	ENSG00000174123		"""CD molecules"""	15634	protein-coding gene	gene with protein product		606270				11267672	Standard	NM_030956		Approved	CD290	uc003gtk.3	Q9BXR5	OTTHUMG00000128578	ENST00000308973.4:c.39T>A	4.37:g.38777173A>T		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	144	68	0.472222	NM_001017388	A8K7L1|B3Y668|D1CS21|D1CS22|Q32MI7|Q32MI8|Q5FWG4|Q6UXL3	Silent	SNP	ENST00000308973.4	37	CCDS3445.1																																																																																			A|0.721;T|0.279	0.279	strong		0.403	TLR10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250430.1		
TMEM225	338661	hgsc.bcm.edu	37	11	123753958	123753958	+	Missense_Mutation	SNP	C	C	T	rs35551906	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:123753958C>T	ENST00000375026.2	-	4	781	c.565G>A	c.(565-567)Gaa>Aaa	p.E189K		NM_001013743.1	NP_001013765.1	Q6GV28	TM225_HUMAN	transmembrane protein 225	189					negative regulation of phosphatase activity (GO:0010923)	integral component of membrane (GO:0016021)				endometrium(2)|kidney(2)|large_intestine(2)|lung(12)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(3)	28						GAAATATCTTCGATAGAATTC	0.428													C|||	204	0.0407348	0.0151	0.0432	5008	,	,		19308	0.0218		0.0964	False		,,,				2504	0.0358				p.E189K		Atlas-SNP	.											.	TMEM225	56	.	0			c.G565A						PASS	.	C	LYS/GLU	104,4300	81.4+/-119.9	2,100,2100	136.0	126.0	129.0		565	-6.9	0.0	11	dbSNP_126	129	645,7953	165.8+/-217.9	24,597,3678	yes	missense	TMEM225	NM_001013743.1	56	26,697,5778	TT,TC,CC		7.5017,2.3615,5.7607	benign	189/226	123753958	749,12253	2202	4299	6501	SO:0001583	missense	338661	exon4			TATCTTCGATAGA	AY634366	CCDS31697.1	11q24.1	2014-06-13			ENSG00000204300	ENSG00000204300			32390	protein-coding gene	gene with protein product	"""PMP22 claudin domain containing"", ""protein phosphatase 1, regulatory subunit 154"""						Standard	XM_006718832		Approved	PMP22CD, PPP1R154	uc001pzi.3	Q6GV28	OTTHUMG00000165959	ENST00000375026.2:c.565G>A	11.37:g.123753958C>T	ENSP00000364166:p.Glu189Lys	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	101	79	0.782178	NM_001013743		Missense_Mutation	SNP	ENST00000375026.2	37	CCDS31697.1	106	0.048534798534798536	10	0.02032520325203252	13	0.03591160220994475	11	0.019230769230769232	72	0.09498680738786279	C	0.320	-0.962284	0.02249	0.023615	0.075017	ENSG00000204300	ENST00000375026;ENST00000528595	T;T	0.30714	1.54;1.52	3.43	-6.87	0.01671	.	1.268580	0.05565	N	0.570093	T	0.00412	0.0013	N	0.04880	-0.145	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.21690	-1.0238	10	0.02654	T	1	-0.7212	8.7768	0.34767	0.0:0.2425:0.5997:0.1578	rs35551906;rs61908535	189	Q6GV28	TM225_HUMAN	K	189;139	ENSP00000364166:E189K;ENSP00000431282:E139K	ENSP00000364166:E189K	E	-	1	0	TMEM225	123259168	0.004000	0.15560	0.000000	0.03702	0.001000	0.01503	-0.228000	0.09114	-2.821000	0.00343	-1.567000	0.00876	GAA	C|0.945;T|0.055	0.055	strong		0.428	TMEM225-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387260.1	NM_001013743	
HLA-DQA1	3117	hgsc.bcm.edu	37	6	32609195	32609195	+	Missense_Mutation	SNP	G	G	A	rs36219699	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:32609195G>A	ENST00000343139.5	+	2	293	c.191G>A	c.(190-192)aGg>aAg	p.R64K	HLA-DQA1_ENST00000395363.1_Missense_Mutation_p.R64K|HLA-DQA1_ENST00000374949.2_Missense_Mutation_p.R64K	NM_002122.3	NP_002113.2	P01909	DQA1_HUMAN	major histocompatibility complex, class II, DQ alpha 1	64	Alpha-1.		R -> K (in allele DQA1*01:03; dbSNP:rs36219699).		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			NS(1)|lung(3)|skin(1)|upper_aerodigestive_tract(1)	6						GACCTGGAGAGGAAGGAGACT	0.512													.|||	574	0.114617	0.0461	0.0764	5008	,	,		13154	0.131		0.0696	False		,,,				2504	0.2638				p.R64K		Atlas-SNP	.											.	HLA-DQA1	52	.	0			c.G191A						PASS	.	G	LYS/ARG	242,4154		58,126,2014	110.0	95.0	101.0		191	1.3	0.4	6	dbSNP_126	101	836,7694		253,330,3682	yes	missense	HLA-DQA1	NM_002122.3	26	311,456,5696	AA,AG,GG		9.8007,5.505,8.3398	benign	64/256	32609195	1078,11848	2198	4265	6463	SO:0001583	missense	3117	exon2			TGGAGAGGAAGGA		CCDS4752.1	6p21.3	2013-01-11			ENSG00000196735	ENSG00000196735		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4942	protein-coding gene	gene with protein product		146880		HLA-DQA			Standard	NM_002122		Approved	CELIAC1	uc003obr.3	P01909	OTTHUMG00000031106	ENST00000343139.5:c.191G>A	6.37:g.32609195G>A	ENSP00000339398:p.Arg64Lys	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	86	54	0.627907	NM_002122	O19630|O19706|P01907|P01908|P04225|P04226|P05536|P79553|Q06751|Q29876|Q29994|Q2Q6Y6|Q2Q6Y7|Q2Q6Y8|Q2WCM3|Q30064|Q30067|Q30068|Q30070|Q30071|Q30072|Q30073|Q30086|Q30101|Q5Y7D5|Q5Y7F5|Q6ICU6|Q6PR46|Q6QDB1|Q860W2|Q860W4|Q9BD37|Q9TPM3|Q9UM31	Missense_Mutation	SNP	ENST00000343139.5	37	CCDS4752.1	197|197	0.0902014652014652|0.0902014652014652	30|30	0.06097560975609756|0.06097560975609756	21|21	0.058011049723756904|0.058011049723756904	95|95	0.1660839160839161|0.1660839160839161	51|51	0.06728232189973615|0.06728232189973615	.|.	0.005|0.005	-2.138877|-2.138877	0.00335|0.00335	0.05505|0.05505	0.098007|0.098007	ENSG00000196735|ENSG00000196735	ENST00000486548|ENST00000343139;ENST00000395364;ENST00000395363;ENST00000496318;ENST00000374949	.|T;T;T;T	.|0.00633	.|6.08;6.08;6.08;6.08	3.84|3.84	1.32|1.32	0.21799|0.21799	.|.	.|0.359807	.|0.27388	.|N	.|0.019586	T|T	0.00109|0.00109	0.0003|0.0003	.|.	.|.	.|.	0.44985|0.44985	P|P	0.0019930000000000225|0.0019930000000000225	.|B;B	.|0.11235	.|0.004;0.0	.|B;B	.|0.17979	.|0.02;0.0	T|T	0.23440|0.23440	-1.0188|-1.0188	3|8	.|0.02654	.|T	.|1	.|.	3.789|3.789	0.08712|0.08712	0.6207:0.1917:0.1877:0.0|0.6207:0.1917:0.1877:0.0	rs36219699;rs41552513;rs62404089|rs36219699;rs41552513;rs62404089	.|70;64	.|Q59F33;G4XQK2	.|.;.	R|K	37|64	.|ENSP00000339398:R64K;ENSP00000378767:R64K;ENSP00000437302:R64K;ENSP00000364087:R64K	.|ENSP00000339398:R64K	G|R	+|+	1|2	0|0	HLA-DQA1|HLA-DQA1	32717173|32717173	1.000000|1.000000	0.71417|0.71417	0.425000|0.425000	0.26659|0.26659	0.003000|0.003000	0.03518|0.03518	1.664000|1.664000	0.37439|0.37439	0.186000|0.186000	0.20125|0.20125	-0.448000|-0.448000	0.05591|0.05591	GGA|AGG	G|0.915;A|0.085	0.085	strong		0.512	HLA-DQA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076176.3	NM_002122	
HR	55806	hgsc.bcm.edu	37	8	21984765	21984765	+	Missense_Mutation	SNP	C	C	T	rs73549523	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:21984765C>T	ENST00000381418.4	-	3	2670	c.1190G>A	c.(1189-1191)tGc>tAc	p.C397Y	HR_ENST00000312841.8_Missense_Mutation_p.C397Y	NM_005144.4	NP_005135.2	O43593	HAIR_HUMAN	hair growth associated	397					negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nuclear body (GO:0016604)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|oxidoreductase activity (GO:0016491)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(12)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	27		Breast(100;0.000162)|Acute lymphoblastic leukemia(644;0.0775)|Prostate(55;0.116)		KIRC - Kidney renal clear cell carcinoma(542;1.19e-05)|BRCA - Breast invasive adenocarcinoma(99;3.56e-05)|Colorectal(74;0.00191)|COAD - Colon adenocarcinoma(73;0.0615)|READ - Rectum adenocarcinoma(644;0.1)		GACCTCAGGGCAGCCGCGTGG	0.672													C|||	193	0.0385383	0.0295	0.0375	5008	,	,		14158	0.0149		0.0915	False		,,,				2504	0.0215				p.C397Y		Atlas-SNP	.											.	HR	71	.	0			c.G1190A						PASS	.	C	TYR/CYS,TYR/CYS	148,4258	99.4+/-138.0	2,144,2057	92.0	104.0	100.0		1190,1190	5.2	0.5	8	dbSNP_130	100	754,7846	176.3+/-226.2	30,694,3576	yes	missense,missense	HR	NM_005144.4,NM_018411.4	194,194	32,838,5633	TT,TC,CC		8.7674,3.3591,6.9353	benign,benign	397/1190,397/1135	21984765	902,12104	2203	4300	6503	SO:0001583	missense	55806	exon3			TCAGGGCAGCCGC	AF039196	CCDS6022.1, CCDS6023.1	8p12	2012-12-07	2012-12-07		ENSG00000168453	ENSG00000168453			5172	protein-coding gene	gene with protein product		602302	"""hairless (mouse) homolog"", ""hairless homolog (mouse)"""	ALUNC		10051399, 9463324	Standard	NM_018411		Approved	AU	uc003xas.3	O43593	OTTHUMG00000097089	ENST00000381418.4:c.1190G>A	8.37:g.21984765C>T	ENSP00000370826:p.Cys397Tyr	Somatic	173	1	0.00578035		WXS	Illumina HiSeq	Phase_I	165	127	0.769697	NM_018411	Q6GS30|Q96H33|Q9NPE1	Missense_Mutation	SNP	ENST00000381418.4	37	CCDS6022.1	110	0.05036630036630037	13	0.026422764227642278	13	0.03591160220994475	7	0.012237762237762238	77	0.10158311345646438	C	13.74	2.327208	0.41197	0.033591	0.087674	ENSG00000168453	ENST00000381418;ENST00000312841	T;T	0.73363	-0.73;-0.74	6.04	5.17	0.71159	.	0.093497	0.47852	D	0.000204	T	0.04634	0.0126	L	0.34521	1.04	0.35503	D	0.799986	P;P	0.38440	0.631;0.498	B;B	0.40534	0.332;0.178	T	0.52426	-0.8577	10	0.48119	T	0.1	-6.8662	12.7418	0.57257	0.1644:0.8356:0.0:0.0	.	397;397	O43593-2;O43593	.;HAIR_HUMAN	Y	397	ENSP00000370826:C397Y;ENSP00000326765:C397Y	ENSP00000326765:C397Y	C	-	2	0	HR	22040710	0.862000	0.29867	0.487000	0.27428	0.749000	0.42624	1.146000	0.31589	1.555000	0.49500	0.563000	0.77884	TGC	C|0.933;T|0.067	0.067	strong		0.672	HR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214213.1		
PNPLA1	285848	hgsc.bcm.edu	37	6	36275458	36275458	+	Missense_Mutation	SNP	T	T	C	rs4713956	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:36275458T>C	ENST00000394571.2	+	8	1564	c.1564T>C	c.(1564-1566)Tcg>Ccg	p.S522P	PNPLA1_ENST00000312917.5_Missense_Mutation_p.S436P|PNPLA1_ENST00000388715.3_Missense_Mutation_p.S427P	NM_001145717.1	NP_001139189.2	Q8N8W4	PLPL1_HUMAN	patatin-like phospholipase domain containing 1	522			S -> P (in dbSNP:rs4713956). {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						CCCAAGACATTCGGGATCCAA	0.473													C|||	3247	0.648363	0.7375	0.6643	5008	,	,		21355	0.6091		0.6352	False		,,,				2504	0.5706				p.S522P		Atlas-SNP	.											PNPLA1_ENST00000394571,NS,carcinoma,-1,6	PNPLA1	92	6	0			c.T1564C						PASS	.	C	PRO/SER,PRO/SER,PRO/SER	3180,1226	424.9+/-340.6	1131,918,154	96.0	87.0	90.0		1306,1564,1279	2.5	0.0	6	dbSNP_111	90	5415,3185	480.7+/-370.5	1731,1953,616	yes	missense,missense,missense	PNPLA1	NM_001145716.1,NM_001145717.1,NM_173676.2	74,74,74	2862,2871,770	CC,CT,TT		37.0349,27.8257,33.9151	benign,benign,benign	436/447,522/533,427/438	36275458	8595,4411	2203	4300	6503	SO:0001583	missense	285848	exon8			AGACATTCGGGAT		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.1564T>C	6.37:g.36275458T>C	ENSP00000378072:p.Ser522Pro	Somatic	182	0	0		WXS	Illumina HiSeq	Phase_I	173	78	0.450867	NM_001145717	A3RMU3|J3JS20|Q2A6N1|Q3SY95|Q3SY96|Q5R3L2	Missense_Mutation	SNP	ENST00000394571.2	37	CCDS54997.1	1392	0.6373626373626373	360	0.7317073170731707	241	0.6657458563535912	318	0.5559440559440559	473	0.6240105540897097	C	0.235	-1.017690	0.02078	0.721743	0.629651	ENSG00000180316	ENST00000388715;ENST00000312917;ENST00000457797;ENST00000394571	T;T;T;T	0.26373	1.97;1.97;1.74;1.74	5.34	2.53	0.30540	.	1.098950	0.07033	N	0.828792	T	0.01523	0.0049	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	0.41858	-0.9485	9	0.02654	T	1	-0.0037	2.7662	0.05321	0.146:0.5497:0.1415:0.1629	rs4713956;rs52811349;rs56418349;rs60329487;rs4713956	522;436	Q8N8W4;Q8N8W4-3	PLPL1_HUMAN;.	P	427;436;523;522	ENSP00000373367:S427P;ENSP00000321116:S436P;ENSP00000391868:S523P;ENSP00000378072:S522P	ENSP00000321116:S436P	S	+	1	0	PNPLA1	36383436	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.419000	0.21247	-0.019000	0.14055	-0.825000	0.03093	TCG	C|0.644;N|0.000	0.644	strong		0.473	PNPLA1-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_173676	
RPTOR	57521	hgsc.bcm.edu	37	17	78820351	78820351	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:78820351G>A	ENST00000306801.3	+	11	1653	c.1291G>A	c.(1291-1293)Gaa>Aaa	p.E431K	RPTOR_ENST00000544334.2_Missense_Mutation_p.E431K|RPTOR_ENST00000537330.1_Missense_Mutation_p.E246K|RPTOR_ENST00000575542.1_3'UTR	NM_020761.2	NP_065812.1	Q8N122	RPTOR_HUMAN	regulatory associated protein of MTOR, complex 1	431					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						AAACCCACCCGAACAGCTGCC	0.627																																					p.E431K		Atlas-SNP	.											.	RPTOR	122	.	0			c.G1291A						PASS	.						145.0	112.0	123.0					17																	78820351		2203	4300	6503	SO:0001583	missense	57521	exon11			CCACCCGAACAGC		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.1291G>A	17.37:g.78820351G>A	ENSP00000307272:p.Glu431Lys	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	88	27	0.306818	NM_001163034	B2RN36|C6KEF2|F5H7J5|Q8N4V9|Q8TB32|Q9P2P3	Missense_Mutation	SNP	ENST00000306801.3	37	CCDS11773.1	.	.	.	.	.	.	.	.	.	.	G	28.4	4.912856	0.92178	.	.	ENSG00000141564	ENST00000537330;ENST00000306801;ENST00000544334	T;T;T	0.34472	1.36;1.36;1.36	4.92	4.92	0.64577	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.68778	0.3038	M	0.92219	3.285	0.80722	D	1	D;D;D	0.89917	0.995;1.0;0.998	D;D;P	0.85130	0.956;0.997;0.843	T	0.74390	-0.3681	10	0.35671	T	0.21	.	17.7008	0.88294	0.0:0.0:1.0:0.0	.	431;246;431	F5H7J5;F5GXV9;Q8N122	.;.;RPTOR_HUMAN	K	246;431;431	ENSP00000440947:E246K;ENSP00000307272:E431K;ENSP00000442479:E431K	ENSP00000307272:E431K	E	+	1	0	RPTOR	76434946	1.000000	0.71417	0.834000	0.33040	0.611000	0.37282	8.736000	0.91554	2.267000	0.75376	0.467000	0.42956	GAA	.	.	none		0.627	RPTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438125.1	NM_020761	
THBS2	7058	hgsc.bcm.edu	37	6	169648767	169648767	+	Silent	SNP	G	G	A	rs12178180	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:169648767G>A	ENST00000366787.3	-	4	603	c.354C>T	c.(352-354)aaC>aaT	p.N118N		NM_003247.2	NP_003238.2	P35442	TSP2_HUMAN	thrombospondin 2	118	Heparin-binding. {ECO:0000255}.|Laminin G-like.				cell adhesion (GO:0007155)|negative regulation of angiogenesis (GO:0016525)|positive regulation of synapse assembly (GO:0051965)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|platelet alpha granule (GO:0031091)	calcium ion binding (GO:0005509)|heparin binding (GO:0008201)			NS(3)|biliary_tract(1)|endometrium(8)|kidney(3)|large_intestine(23)|liver(1)|lung(56)|ovary(6)|prostate(1)|skin(3)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	111		Breast(66;1.78e-05)|Ovarian(120;0.0728)|Esophageal squamous(34;0.247)		OV - Ovarian serous cystadenocarcinoma(33;1.85e-21)|BRCA - Breast invasive adenocarcinoma(81;1.43e-06)|GBM - Glioblastoma multiforme(31;0.000379)		CCGCGGGGCCGTTGGAGACGA	0.657													A|||	726	0.144968	0.1021	0.17	5008	,	,		17580	0.0248		0.2575	False		,,,				2504	0.1933				p.N118N	Esophageal Squamous(91;219 1934 18562 44706)	Atlas-SNP	.											.	THBS2	230	.	0			c.C354T						PASS	.	A		553,3853	774.9+/-414.1	34,485,1684	93.0	87.0	89.0		354	-4.3	0.8	6	dbSNP_120	89	2264,6336	708.6+/-405.7	313,1638,2349	no	coding-synonymous	THBS2	NM_003247.2		347,2123,4033	AA,AG,GG		26.3256,12.5511,21.6592		118/1173	169648767	2817,10189	2203	4300	6503	SO:0001819	synonymous_variant	7058	exon4			GGGGCCGTTGGAG		CCDS34574.1	6q27	2008-07-28			ENSG00000186340	ENSG00000186340			11786	protein-coding gene	gene with protein product		188061				18455130	Standard	NM_003247		Approved	TSP2	uc003qwt.3	P35442	OTTHUMG00000045408	ENST00000366787.3:c.354C>T	6.37:g.169648767G>A		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	60	10	0.166667	NM_003247	A6H8N1|A7E232|Q5RI52	Silent	SNP	ENST00000366787.3	37	CCDS34574.1																																																																																			A|0.184;C|0.000;G|0.816	0.184	strong		0.657	THBS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000105439.1	NM_003247	
KRT83	3889	hgsc.bcm.edu	37	12	52713088	52713088	+	Missense_Mutation	SNP	G	G	A	rs2857663	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:52713088G>A	ENST00000293670.3	-	2	507	c.445C>T	c.(445-447)Cgc>Tgc	p.R149C		NM_002282.3	NP_002273.3	P78385	KRT83_HUMAN	keratin 83	149	Linker 1.|Rod.		R -> C (in dbSNP:rs2857663). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9084137}.		aging (GO:0007568)|epidermis development (GO:0008544)|hair cycle (GO:0042633)	extracellular space (GO:0005615)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			NS(1)|central_nervous_system(1)|endometrium(4)|large_intestine(4)|lung(9)|prostate(1)|skin(4)|stomach(7)|upper_aerodigestive_tract(1)	32	Myeloproliferative disorder(4;0.0484)|all_hematologic(5;0.088)			BRCA - Breast invasive adenocarcinoma(357;0.189)		CAGCACTCGCGGTTTTGGTAG	0.607													g|||	640	0.127796	0.1589	0.0576	5008	,	,		18957	0.0804		0.1034	False		,,,				2504	0.2096				p.R149C	GBM(41;747 834 12702 24089 39393)|Esophageal Squamous(97;805 1414 12559 28198 31861)	Atlas-SNP	.											KRT83,NS,carcinoma,+2,1	KRT83	64	1	0			c.C445T						PASS	.	G	CYS/ARG	644,3762	276.9+/-273.4	48,548,1607	76.0	81.0	80.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	445	4.4	1.0	12	dbSNP_100	80	963,7637	210.4+/-251.3	55,853,3392	yes	missense	KRT83	NM_002282.3	180	103,1401,4999	AA,AG,GG		11.1977,14.6164,12.3558	probably-damaging	149/494	52713088	1607,11399	2203	4300	6503	SO:0001583	missense	3889	exon2			ACTCGCGGTTTTG	X99141	CCDS8823.1	12q13.13	2013-06-20	2006-07-17	2006-07-17	ENSG00000170523	ENSG00000170523		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6460	protein-coding gene	gene with protein product	"""hard keratin type II"""	602765	"""keratin, hair, basic, 3"""	KRTHB3		9084137, 16831889	Standard	NM_002282		Approved	Hb-3	uc001saf.2	P78385	OTTHUMG00000169632	ENST00000293670.3:c.445C>T	12.37:g.52713088G>A	ENSP00000293670:p.Arg149Cys	Somatic	283	1	0.00353357		WXS	Illumina HiSeq	Phase_I	278	126	0.453237	NM_002282	A1A4S9|B2RC21|Q6NT21|Q9NSB3	Missense_Mutation	SNP	ENST00000293670.3	37	CCDS8823.1	226	0.10347985347985347	81	0.16463414634146342	29	0.08011049723756906	42	0.07342657342657342	74	0.09762532981530343	G	17.25	3.342823	0.61073	0.146164	0.111977	ENSG00000170523	ENST00000293670	D	0.89617	-2.54	4.39	4.39	0.52855	Filament (1);	0.221679	0.23420	U	0.048369	T	0.03477	0.0100	M	0.90425	3.115	0.49687	D	0.99981	B	0.22276	0.067	B	0.27170	0.077	T	0.58836	-0.7566	10	0.72032	D	0.01	.	12.453	0.55686	0.0:0.0:0.8325:0.1675	rs2857663;rs3741714;rs17368348;rs56529229;rs59248948;rs2857663	149	P78385	KRT83_HUMAN	C	149	ENSP00000293670:R149C	ENSP00000293670:R149C	R	-	1	0	KRT83	50999355	1.000000	0.71417	0.995000	0.50966	0.912000	0.54170	9.621000	0.98376	2.157000	0.67596	0.563000	0.77884	CGC	G|0.876;A|0.124	0.124	strong		0.607	KRT83-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405182.1	NM_002282	
FOXRED2	80020	hgsc.bcm.edu	37	22	36897427	36897427	+	Silent	SNP	T	T	C	rs5756223	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:36897427T>C	ENST00000397224.4	-	5	1170	c.1077A>G	c.(1075-1077)gcA>gcG	p.A359A	FOXRED2_ENST00000397223.4_Silent_p.A359A|FOXRED2_ENST00000366463.3_5'Flank|FOXRED2_ENST00000216187.6_Silent_p.A359A	NM_001102371.1	NP_001095841.1	Q8IWF2	FXRD2_HUMAN	FAD-dependent oxidoreductase domain containing 2	359					ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)	endoplasmic reticulum lumen (GO:0005788)	flavin adenine dinucleotide binding (GO:0050660)|glycoprotein binding (GO:0001948)|oxidoreductase activity (GO:0016491)			breast(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(2)|lung(5)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	22						TCTTGCCGAATGCATTTCCCG	0.483													T|||	203	0.0405351	0.0091	0.0403	5008	,	,		18922	0.0536		0.0646	False		,,,				2504	0.045				p.A359A		Atlas-SNP	.											.	FOXRED2	48	.	0			c.A1077G						PASS	.	T	,	111,4295	85.8+/-124.5	0,111,2092	76.0	72.0	73.0		1077,1077	-2.3	0.0	22	dbSNP_114	73	566,8034	153.7+/-208.1	27,512,3761	no	coding-synonymous,coding-synonymous	FOXRED2	NM_001102371.1,NM_024955.5	,	27,623,5853	CC,CT,TT		6.5814,2.5193,5.2053	,	359/685,359/685	36897427	677,12329	2203	4300	6503	SO:0001819	synonymous_variant	80020	exon5			GCCGAATGCATTT	BC027716	CCDS13929.1	22q12.3	2006-07-05			ENSG00000100350	ENSG00000100350			26264	protein-coding gene	gene with protein product		613777				12477932	Standard	NM_024955		Approved	FLJ23322	uc003app.4	Q8IWF2	OTTHUMG00000044614	ENST00000397224.4:c.1077A>G	22.37:g.36897427T>C		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	124	53	0.427419	NM_001102371	B2RDI4|Q8N378|Q96BD1|Q9H5L5|Q9H6M8	Silent	SNP	ENST00000397224.4	37	CCDS13929.1																																																																																			T|0.944;C|0.056	0.056	strong		0.483	FOXRED2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000104098.2	NM_024955	
DSPP	1834	hgsc.bcm.edu	37	4	88536460	88536460	+	Silent	SNP	C	C	T	rs199691318		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:88536460C>T	ENST00000282478.7	+	4	2679	c.2646C>T	c.(2644-2646)agC>agT	p.S882S	RP11-742B18.1_ENST00000506480.1_RNA|DSPP_ENST00000399271.1_Silent_p.S882S			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	882	Asp/Ser-rich.				biomineral tissue development (GO:0031214)|cellular response to cell-matrix adhesion (GO:0071460)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|skin(3)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Hepatocellular(203;0.114)|all_hematologic(202;0.236)		OV - Ovarian serous cystadenocarcinoma(123;0.000508)		gcagtgatagcagtgacagca	0.498																																					p.S882S		Atlas-SNP	.											.	DSPP	174	.	0			c.C2646T						PASS	.						73.0	87.0	82.0					4																	88536460		1617	2929	4546	SO:0001819	synonymous_variant	1834	exon5			TGATAGCAGTGAC	AF163151	CCDS43248.1	4q21.3	2008-02-05			ENSG00000152591	ENSG00000152591			3054	protein-coding gene	gene with protein product		125485		DFNA39, DGI1		8995371, 9533027	Standard	NM_014208		Approved	DMP3	uc003hqu.3	Q9NZW4	OTTHUMG00000161061	ENST00000282478.7:c.2646C>T	4.37:g.88536460C>T		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	65	17	0.261538	NM_014208	A8MUI0|O95815	Silent	SNP	ENST00000282478.7	37	CCDS43248.1																																																																																			.	.	weak		0.498	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208	
SPPL2A	84888	hgsc.bcm.edu	37	15	51017488	51017488	+	Silent	SNP	G	G	T	rs140457962	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:51017488G>T	ENST00000261854.5	-	12	1453	c.1179C>A	c.(1177-1179)atC>atA	p.I393I	SPPL2A_ENST00000559293.1_5'UTR	NM_032802.3	NP_116191.2	Q8TCT8	SPP2A_HUMAN	signal peptide peptidase like 2A	393					membrane protein ectodomain proteolysis (GO:0006509)|membrane protein intracellular domain proteolysis (GO:0031293)|regulation of immune response (GO:0050776)	extracellular vesicular exosome (GO:0070062)|Golgi-associated vesicle membrane (GO:0030660)|integral component of cytoplasmic side of endoplasmic reticulum membrane (GO:0071458)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	aspartic-type endopeptidase activity (GO:0004190)|protein homodimerization activity (GO:0042803)			endometrium(1)|kidney(1)|large_intestine(4)|lung(6)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	15				all cancers(107;0.000712)|GBM - Glioblastoma multiforme(94;0.00314)		CTGAGAAATAGATCAGTTTTG	0.338													G|||	8	0.00159744	0.0008	0.0	5008	,	,		17872	0.0		0.007	False		,,,				2504	0.0				p.I393I	Melanoma(50;790 1209 4069 22965 33125)	Atlas-SNP	.											.	SPPL2A	26	.	0			c.C1179A						PASS	.	G		6,4386	11.4+/-27.6	0,6,2190	104.0	101.0	102.0		1179	-2.8	0.8	15	dbSNP_134	102	77,8511	44.9+/-103.4	0,77,4217	no	coding-synonymous	SPPL2A	NM_032802.3		0,83,6407	TT,TG,GG		0.8966,0.1366,0.6394		393/521	51017488	83,12897	2196	4294	6490	SO:0001819	synonymous_variant	84888	exon12			GAAATAGATCAGT		CCDS10138.1	15q21.2	2012-02-21			ENSG00000138600	ENSG00000138600			30227	protein-coding gene	gene with protein product	"""intramembrane protease 3"", ""presenilin-like protein 2"""	608238				12077416, 12139484	Standard	NM_032802		Approved	IMP3, PSL2	uc001zyv.3	Q8TCT8	OTTHUMG00000131647	ENST00000261854.5:c.1179C>A	15.37:g.51017488G>T		Somatic	229	0	0		WXS	Illumina HiSeq	Phase_I	223	127	0.569507	NM_032802	B2RDS0|Q8TAW1|Q96SZ8	Silent	SNP	ENST00000261854.5	37	CCDS10138.1																																																																																			G|0.995;T|0.005	0.005	strong		0.338	SPPL2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254543.3	NM_032802	
DSPP	1834	hgsc.bcm.edu	37	4	88537357	88537357	+	Silent	SNP	T	T	C	rs146317878	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:88537357T>C	ENST00000282478.7	+	4	3576	c.3543T>C	c.(3541-3543)agT>agC	p.S1181S	RP11-742B18.1_ENST00000506480.1_RNA|DSPP_ENST00000399271.1_Silent_p.S1181S			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	1181	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)		gcaatagcagtgatagcagcg	0.567													t|||	285	0.0569089	0.0091	0.0879	5008	,	,		25184	0.003		0.168	False		,,,				2504	0.0409				p.S1181S		Atlas-SNP	.											DSPP,rectum,carcinoma,0,1	DSPP	174	1	0			c.T3543C						scavenged	.	C		80,3200		0,80,1560	55.0	74.0	67.0		3543	1.2	0.0	4	dbSNP_134	67	750,5074		47,656,2209	no	coding-synonymous	DSPP	NM_014208.3		47,736,3769	CC,CT,TT		12.8777,2.439,9.1169		1181/1302	88537357	830,8274	1640	2912	4552	SO:0001819	synonymous_variant	1834	exon5			TAGCAGTGATAGC	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.3543T>C	4.37:g.88537357T>C		Somatic	144	2	0.0138889		WXS	Illumina HiSeq	Phase_I	127	45	0.354331	NM_014208	A8MUI0|O95815	Silent	SNP	ENST00000282478.7	37	CCDS43248.1																																																																																			T|0.922;C|0.078	0.078	strong		0.567	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208	
BRINP1	1620	hgsc.bcm.edu	37	9	121930344	121930344	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:121930344C>T	ENST00000265922.3	-	8	1765	c.1304G>A	c.(1303-1305)aGc>aAc	p.S435N	BRINP1_ENST00000482797.1_Intron	NM_014618.2	NP_055433.2	O60477	BRNP1_HUMAN	bone morphogenetic protein/retinoic acid inducible neural-specific 1	435					cell cycle arrest (GO:0007050)|cell death (GO:0008219)|cellular response to retinoic acid (GO:0071300)|negative regulation of cell cycle (GO:0045786)|negative regulation of mitotic cell cycle (GO:0045930)|positive regulation of neuron differentiation (GO:0045666)	cytoplasm (GO:0005737)											CATGGCGCAGCTGTTGTTCCC	0.632																																					p.S435N		Atlas-SNP	.											.	DBC1	194	.	0			c.G1304A						PASS	.						31.0	31.0	31.0					9																	121930344		2203	4300	6503	SO:0001583	missense	1620	exon8			GCGCAGCTGTTGT	AF027734	CCDS6822.1	9q32-q33	2013-08-06	2013-08-06	2013-07-31	ENSG00000078725	ENSG00000078725			2687	protein-coding gene	gene with protein product		602865	"""deleted in bladder cancer chromosome region candidate 1"", ""deleted in bladder cancer 1"""	DBCCR1, DBC1		9175739, 10444335, 15193422	Standard	NM_014618		Approved	FAM5A	uc004bkc.2	O60477	OTTHUMG00000021020	ENST00000265922.3:c.1304G>A	9.37:g.121930344C>T	ENSP00000265922:p.Ser435Asn	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	115	16	0.13913	NM_014618	Q6IPV6|Q6P1A0|Q8WU22	Missense_Mutation	SNP	ENST00000265922.3	37	CCDS6822.1	.	.	.	.	.	.	.	.	.	.	C	16.86	3.239289	0.58995	.	.	ENSG00000078725	ENST00000373969;ENST00000265922	T	0.54479	0.57	5.69	5.69	0.88448	.	0.000000	0.85682	D	0.000000	T	0.56558	0.1993	L	0.40543	1.245	0.80722	D	1	D	0.53885	0.963	P	0.49853	0.624	T	0.55166	-0.8183	10	0.46703	T	0.11	-29.9476	19.8211	0.96595	0.0:1.0:0.0:0.0	.	435	O60477	DBC1_HUMAN	N	435	ENSP00000265922:S435N	ENSP00000265922:S435N	S	-	2	0	DBC1	120970165	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	3.947000	0.56652	2.687000	0.91594	0.655000	0.94253	AGC	.	.	none		0.632	BRINP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055440.2	NM_014618	
FUS	2521	hgsc.bcm.edu	37	16	31193942	31193942	+	Silent	SNP	C	C	A	rs741810	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:31193942C>A	ENST00000254108.7	+	3	252	c.147C>A	c.(145-147)ggC>ggA	p.G49G	FUS_ENST00000380244.3_Silent_p.G49G|RP11-388M20.6_ENST00000564743.1_RNA|FUS_ENST00000568685.1_Silent_p.G49G	NM_001170634.1|NM_001170937.1|NM_004960.3	NP_001164105.1|NP_001164408.1|NP_004951.1	P35637	FUS_HUMAN	FUS RNA binding protein	49	Gln/Gly/Ser/Tyr-rich.				cell death (GO:0008219)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)		FUS/ERG(167)|FUS/DDIT3(631)|FUS/FEV(2)|FUS/ATF1(4)|FUS/CREB3L1(6)|FUS/CREB3L2(158)	breast(3)|endometrium(5)|kidney(3)|large_intestine(1)|lung(5)|prostate(3)|skin(1)|urinary_tract(1)	22		Renal(780;0.000219)|Breast(268;0.00957)|Hepatocellular(780;0.121)		GBM - Glioblastoma multiforme(240;2.31e-05)|Kidney(780;0.000209)		ACACTTCAGGCTATGGCCAGA	0.532			T	"""DDIT3, ERG, FEV, ATF1, CREB3L2, CREB3L1"""	"""liposarcoma, AML, Ewing sarcoma, angiomatoid fibrous histiocytoma, fibromyxoid sarcoma"""								C|||	1397	0.278954	0.028	0.3617	5008	,	,		19513	0.253		0.3062	False		,,,				2504	0.5583				p.G49G		Atlas-SNP	.		Dom	yes		16	16p11.2	2521	"""fusion, derived from t(12;16) malignant liposarcoma"""		"""M, L"""	FUS,caecum,carcinoma,0,1	FUS	52	1	0			c.C147A						PASS	.	C	,,	321,4073	169.4+/-200.1	16,289,1892	101.0	95.0	97.0		147,147,147	4.1	1.0	16	dbSNP_86	97	2495,6105	410.1+/-350.0	357,1781,2162	no	coding-synonymous,coding-synonymous,coding-synonymous	FUS	NM_001170634.1,NM_001170937.1,NM_004960.3	,,	373,2070,4054	AA,AC,CC		29.0116,7.3054,21.6715	,,	49/526,49/523,49/527	31193942	2816,10178	2197	4300	6497	SO:0001819	synonymous_variant	2521	exon3			TTCAGGCTATGGC	AF071213	CCDS10707.1, CCDS58454.1	16p11.2	2014-09-17	2014-05-09		ENSG00000089280	ENSG00000089280		"""RNA binding motif (RRM) containing"""	4010	protein-coding gene	gene with protein product	"""heterogeneous nuclear ribonucleoprotein P2"", ""translocated in liposarcoma"""	137070	"""fusion, derived from t(12;16) malignant liposarcoma"", ""amyotrophic lateral sclerosis 6"", ""fusion (involved in t(12;16) in malignant liposarcoma)"", ""fused in sarcoma"""	ALS6		2372777, 7503811, 19251628, 19251627	Standard	NM_004960		Approved	TLS, FUS1, hnRNP-P2, HNRNPP2	uc002ebe.2	P35637	OTTHUMG00000132395	ENST00000254108.7:c.147C>A	16.37:g.31193942C>A		Somatic	206	0	0		WXS	Illumina HiSeq	Phase_I	224	96	0.428571	NM_001170634	Q9H4A8	Silent	SNP	ENST00000254108.7	37	CCDS10707.1																																																																																			C|0.783;A|0.217	0.217	strong		0.532	FUS-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255526.2	NM_004960	
APRT	353	hgsc.bcm.edu	37	16	88874632	88874632	+	IGR	SNP	C	C	G	rs572275	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:88874632C>G	ENST00000378364.3	-	0	947				CDT1_ENST00000301019.4_Silent_p.L529L	NM_000485.2	NP_000476.1	P07741	APT_HUMAN	adenine phosphoribosyltransferase						adenine salvage (GO:0006168)|AMP salvage (GO:0044209)|cellular response to insulin stimulus (GO:0032869)|grooming behavior (GO:0007625)|lactation (GO:0007595)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase metabolic process (GO:0006144)|purine-containing compound salvage (GO:0043101)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	adenine binding (GO:0002055)|adenine phosphoribosyltransferase activity (GO:0003999)|AMP binding (GO:0016208)			cervix(1)|endometrium(1)|liver(1)	3				BRCA - Breast invasive adenocarcinoma(80;0.0477)	Adenine(DB00173)|Adenosine monophosphate(DB00131)	CCGCGGACCTCGCCCACATCA	0.667													G|||	2768	0.552716	0.7489	0.4942	5008	,	,		17709	0.6637		0.3767	False		,,,				2504	0.3957				p.L529L		Atlas-SNP	.											.	CDT1	30	.	0			c.C1587G						PASS	.	G		3098,1278	405.1+/-333.4	1101,896,191	46.0	36.0	40.0		1587	1.0	0.0	16	dbSNP_83	40	3170,5426	623.9+/-397.5	577,2016,1705	no	coding-synonymous	CDT1	NM_030928.3		1678,2912,1896	GG,GC,CC		36.8776,29.2048,48.3195		529/547	88874632	6268,6704	2188	4298	6486	SO:0001628	intergenic_variant	81620	exon10			GGACCTCGCCCAC		CCDS32511.1, CCDS45546.1	16q24	2012-10-02				ENSG00000198931	2.4.2.7		626	protein-coding gene	gene with protein product		102600					Standard	NM_000485		Approved		uc002flv.3	P07741			16.37:g.88874632C>G		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	172	112	0.651163	NM_030928	G5E9J2|Q3KP55|Q68DF9	Silent	SNP	ENST00000378364.3	37	CCDS32511.1																																																																																			C|0.482;G|0.518	0.518	strong		0.667	APRT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430000.2	NM_000485	
DCC	1630	hgsc.bcm.edu	37	18	50278563	50278563	+	Silent	SNP	T	T	C	rs112141078	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:50278563T>C	ENST00000442544.2	+	2	847	c.231T>C	c.(229-231)gaT>gaC	p.D77D	DCC_ENST00000412726.1_5'UTR	NM_005215.3	NP_005206.2	P43146	DCC_HUMAN	DCC netrin 1 receptor	77	Ig-like C2-type 1.				anterior/posterior axon guidance (GO:0033564)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|axonogenesis (GO:0007409)|dorsal/ventral axon guidance (GO:0033563)|negative regulation of collateral sprouting (GO:0048671)|negative regulation of dendrite development (GO:2000171)|negative regulation of neuron projection development (GO:0010977)|neuron migration (GO:0001764)|positive regulation of apoptotic process (GO:0043065)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of neuron projection development (GO:0010976)|regulation of apoptotic process (GO:0042981)|response to amphetamine (GO:0001975)|spinal cord ventral commissure morphogenesis (GO:0021965)	axon (GO:0030424)|cytosol (GO:0005829)|growth cone membrane (GO:0032584)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	netrin receptor activity (GO:0005042)|transcription coactivator activity (GO:0003713)|transmembrane signaling receptor activity (GO:0004888)			NS(3)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(23)|liver(1)|lung(56)|ovary(7)|pancreas(3)|prostate(2)|skin(16)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(6)	148		all_cancers(7;0.11)|all_epithelial(6;0.00126)		Colorectal(16;0.0251)|COAD - Colon adenocarcinoma(17;0.0942)		GGAAGAAAGATGGCATTCATC	0.507													T|||	33	0.00658946	0.0015	0.0115	5008	,	,		17210	0.0		0.0209	False		,,,				2504	0.002				p.D77D		Atlas-SNP	.											.	DCC	360	.	0			c.T231C						PASS	.	T		27,4379	35.2+/-66.4	0,27,2176	104.0	98.0	100.0		231	0.1	1.0	18	dbSNP_132	100	215,8385	91.1+/-153.3	2,211,4087	no	coding-synonymous	DCC	NM_005215.3		2,238,6263	CC,CT,TT		2.5,0.6128,1.8607		77/1448	50278563	242,12764	2203	4300	6503	SO:0001819	synonymous_variant	1630	exon2			GAAAGATGGCATT	X76132	CCDS11952.1	18q21.1	2014-06-20	2014-06-20		ENSG00000187323	ENSG00000187323		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	2701	protein-coding gene	gene with protein product	"""immunoglobulin superfamily, DCC subclass, member 1"""	120470	"""deleted in colorectal carcinoma"""			2294591, 24400119	Standard	NM_005215		Approved	IGDCC1, NTN1R1	uc002lfe.2	P43146	OTTHUMG00000132698	ENST00000442544.2:c.231T>C	18.37:g.50278563T>C		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	98	43	0.438776	NM_005215		Silent	SNP	ENST00000442544.2	37	CCDS11952.1																																																																																			T|0.986;C|0.014	0.014	strong		0.507	DCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255996.3	NM_005215	
VPS26A	9559	hgsc.bcm.edu	37	10	70892791	70892791	+	Silent	SNP	C	C	T	rs5030932	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:70892791C>T	ENST00000373382.1	+	3	794	c.141C>T	c.(139-141)tcC>tcT	p.S47S	VPS26A_ENST00000263559.6_Silent_p.S47S|VPS26A_ENST00000490696.1_3'UTR|VPS26A_ENST00000395098.1_Silent_p.S47S|VPS26A_ENST00000541711.1_5'UTR|VPS26A_ENST00000546041.1_Missense_Mutation_p.P5L|VPS26A_ENST00000489794.1_Silent_p.S22S			O75436	VP26A_HUMAN	vacuolar protein sorting 26 homolog A (S. pombe)	47					retrograde transport, endosome to Golgi (GO:0042147)	cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|vesicle (GO:0031982)	protein transporter activity (GO:0008565)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(2)	8						ACGGAGAATCCGTTTCAGGAA	0.333													T|||	839	0.167532	0.2723	0.1297	5008	,	,		17109	0.0367		0.2545	False		,,,				2504	0.0982				p.S47S	Colon(90;545 1358 4729 6702 16773)	Atlas-SNP	.											VPS26A,NS,carcinoma,0,1	VPS26A	24	1	0			c.C141T						PASS	.	T	,	1098,3308	720.1+/-409.0	132,834,1237	90.0	86.0	88.0		141,141	-2.9	1.0	10	dbSNP_113	88	1829,6771	730.1+/-406.7	185,1459,2656	no	coding-synonymous,coding-synonymous	VPS26A	NM_001035260.1,NM_004896.3	,	317,2293,3893	TT,TC,CC		21.2674,24.9206,22.505	,	47/252,47/328	70892791	2927,10079	2203	4300	6503	SO:0001819	synonymous_variant	9559	exon2			AGAATCCGTTTCA	AF054179	CCDS7286.1, CCDS41536.1	10q21.1	2007-01-12	2007-01-12	2005-10-11	ENSG00000122958	ENSG00000122958			12711	protein-coding gene	gene with protein product		605506	"""vacuolar protein sorting 26 (yeast homolog)"", ""vacuolar protein sorting 26 (yeast)"", ""vacuolar protein sorting 26 homolog A (yeast)"""	VPS26		1638986, 9653160	Standard	NM_004896		Approved	Hbeta58, PEP8A	uc001jpb.3	O75436	OTTHUMG00000018376	ENST00000373382.1:c.141C>T	10.37:g.70892791C>T		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	78	40	0.512821	NM_004896	A8MZ56|B2RDD3|Q8TBH4|Q9H982	Silent	SNP	ENST00000373382.1	37	CCDS7286.1	391	0.17902930402930403	128	0.2601626016260163	58	0.16022099447513813	14	0.024475524475524476	191	0.2519788918205805	T	4.419	0.077459	0.08485	0.249206	0.212674	ENSG00000122958	ENST00000546041	.	.	.	5.42	-2.87	0.05700	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	B	0.02656	0.0	B	0.01281	0.0	T	0.36407	-0.9749	6	0.10636	T	0.68	-15.7599	0.9869	0.01448	0.3904:0.2523:0.1098:0.2474	rs5030932;rs56739005;rs5030932	5	F5H4L7	.	L	5	.	ENSP00000446081:P5L	P	+	2	0	VPS26A	70562797	0.015000	0.18098	0.970000	0.41538	0.993000	0.82548	-1.102000	0.03332	-0.793000	0.04475	-0.254000	0.11334	CCG	C|0.795;T|0.205	0.205	strong		0.333	VPS26A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048403.1	NM_004896	
ZNF878	729747	hgsc.bcm.edu	37	19	12157507	12157507	+	Silent	SNP	G	G	C	rs11668160	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:12157507G>C	ENST00000547628.1	-	2	209	c.72C>G	c.(70-72)tcC>tcG	p.S24S	CTD-2006C1.10_ENST00000547473.1_Silent_p.S24S|CTD-2006C1.2_ENST00000591898.1_RNA|ZNF878_ENST00000602107.1_Silent_p.S71S|CTD-2006C1.2_ENST00000476474.1_RNA|CTD-2006C1.2_ENST00000591838.1_RNA	NM_001080404.2	NP_001073873.2	C9JN71	ZN878_HUMAN	zinc finger protein 878	24	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			cervix(1)|endometrium(1)|kidney(1)|lung(4)|urinary_tract(1)	8						GATTTTTCTGGGAAGGATCCA	0.473													G|||	69	0.013778	0.0015	0.0159	5008	,	,		18686	0.0		0.0368	False		,,,				2504	0.0194				p.S24S		Atlas-SNP	.											.	ZNF878	172	.	0			c.C72G						PASS	.	G		46,4360	48.2+/-83.0	4,38,2161	121.0	131.0	128.0		72	-0.5	0.6	19	dbSNP_120	128	380,8220	123.4+/-182.3	11,358,3931	no	coding-synonymous	ZNF878	NM_001080404.2		15,396,6092	CC,CG,GG		4.4186,1.044,3.2754		24/532	12157507	426,12580	2203	4300	6503	SO:0001819	synonymous_variant	729747	exon2			TTTCTGGGAAGGA		CCDS45984.1, CCDS45984.2	19p13.2	2013-01-08				ENSG00000257446		"""Zinc fingers, C2H2-type"", ""-"""	37246	protein-coding gene	gene with protein product							Standard	NM_001080404		Approved		uc021upl.1	C9JN71		ENST00000547628.1:c.72C>G	19.37:g.12157507G>C		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	53	26	0.490566	NM_001080404		Silent	SNP	ENST00000547628.1	37	CCDS45984.2																																																																																			G|0.981;C|0.019	0.019	strong		0.473	ZNF878-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403723.1	NM_001080404	
HIST1H2BI	8346	hgsc.bcm.edu	37	6	26273368	26273368	+	Missense_Mutation	SNP	C	C	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:26273368C>G	ENST00000377733.2	+	1	225	c.165C>G	c.(163-165)atC>atG	p.I55M	HIST1H3G_ENST00000305910.3_5'Flank	NM_003525.2	NP_003516.1	P62807	H2B1C_HUMAN	histone cluster 1, H2bi	55					antibacterial humoral response (GO:0019731)|chromatin organization (GO:0006325)|defense response to Gram-positive bacterium (GO:0050830)|innate immune response in mucosa (GO:0002227)|nucleosome assembly (GO:0006334)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			central_nervous_system(1)|cervix(2)|endometrium(3)|large_intestine(1)|lung(8)|urinary_tract(1)	16						ACACCGGCATCTCGTCCAAGG	0.562																																					p.I55M		Atlas-SNP	.											.	HIST1H2BI	29	.	0			c.C165G						PASS	.						215.0	203.0	207.0					6																	26273368		2203	4300	6503	SO:0001583	missense	8346	exon1			CGGCATCTCGTCC	Z80782	CCDS4603.1	6p22.1	2011-01-27	2006-10-11	2003-02-14	ENSG00000168242	ENSG00000278588		"""Histones / Replication-dependent"""	4756	protein-coding gene	gene with protein product		602807	"""H2B histone family, member K"", ""histone 1, H2bi"""	H2BFK		9119399, 12408966	Standard	NM_003525		Approved	H2B/k	uc003nhk.3	P62807	OTTHUMG00000014448	ENST00000377733.2:c.165C>G	6.37:g.26273368C>G	ENSP00000366962:p.Ile55Met	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	108	22	0.203704	NM_003525	P02278|Q3B872|Q4VB69|Q93078|Q93080	Missense_Mutation	SNP	ENST00000377733.2	37	CCDS4603.1	.	.	.	.	.	.	.	.	.	.	.	16.73	3.205259	0.58234	.	.	ENSG00000168242	ENST00000377733	T	0.73152	-0.72	4.5	2.68	0.31781	.	.	.	.	.	T	0.73401	0.3582	M	0.89904	3.07	0.27866	N	0.940224	.	.	.	.	.	.	T	0.68550	-0.5379	7	0.87932	D	0	.	10.0332	0.42114	0.0:0.8284:0.0:0.1716	.	.	.	.	M	55	ENSP00000366962:I55M	ENSP00000366962:I55M	I	+	3	3	HIST1H2BI	26381347	1.000000	0.71417	1.000000	0.80357	0.677000	0.39632	1.163000	0.31798	0.335000	0.23614	0.563000	0.77884	ATC	.	.	none		0.562	HIST1H2BI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040111.1	NM_003525	
BPIFB4	149954	hgsc.bcm.edu	37	20	31671411	31671411	+	Silent	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:31671411C>T	ENST00000375483.3	+	3	408	c.408C>T	c.(406-408)ctC>ctT	p.L136L		NM_182519.2	NP_872325.2	P59827	BPIB4_HUMAN	BPI fold containing family B, member 4	136	Gly-rich.					cytoplasm (GO:0005737)|extracellular region (GO:0005576)	lipid binding (GO:0008289)										ACAGGGGCCTCGGGCGATACA	0.627																																					p.L136L		Atlas-SNP	.											.	.	.	.	0			c.C408T						PASS	.						59.0	57.0	58.0					20																	31671411		2203	4300	6503	SO:0001819	synonymous_variant	149954	exon3			GGGCCTCGGGCGA	AF549190	CCDS13213.2	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000186191	ENSG00000186191		"""BPI fold containing"""	16179	protein-coding gene	gene with protein product		615718	"""chromosome 20 open reading frame 186"""	C20orf186		11971875, 21787333	Standard	NM_182519		Approved	dJ726C3.5, LPLUNC4	uc010zue.2	P59827	OTTHUMG00000032235	ENST00000375483.3:c.408C>T	20.37:g.31671411C>T		Somatic	215	0	0		WXS	Illumina HiSeq	Phase_I	178	48	0.269663	NM_182519	Q5TDX6	Silent	SNP	ENST00000375483.3	37	CCDS13213.2																																																																																			.	.	none		0.627	BPIFB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078655.5	NM_182519	
SPICE1	152185	hgsc.bcm.edu	37	3	113222054	113222054	+	Silent	SNP	G	G	A	rs75865495	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:113222054G>A	ENST00000295872.4	-	3	379	c.120C>T	c.(118-120)acC>acT	p.T40T		NM_144718.3	NP_653319.1	Q8N0Z3	SPICE_HUMAN	spindle and centriole associated protein 1	40					metaphase plate congression (GO:0051310)|regulation of centriole replication (GO:0046599)|spindle assembly involved in mitosis (GO:0090307)	centriole (GO:0005814)|centrosome (GO:0005813)|spindle (GO:0005819)				NS(1)|autonomic_ganglia(1)|breast(4)|endometrium(3)|large_intestine(9)|lung(10)|ovary(2)|skin(2)|urinary_tract(1)	33						CCCGATGAACGGTTAGATCAG	0.299													g|||	290	0.0579073	0.0575	0.0216	5008	,	,		14237	0.0873		0.0427	False		,,,				2504	0.0695				p.T40T		Atlas-SNP	.											.	SPICE1	130	.	0			c.C120T						PASS	.	G		235,4171	136.1+/-172.1	7,221,1975	55.0	57.0	57.0		120	3.1	1.0	3	dbSNP_131	57	314,8286	111.6+/-171.8	5,304,3991	no	coding-synonymous	SPICE1	NM_144718.3		12,525,5966	AA,AG,GG		3.6512,5.3336,4.2211		40/856	113222054	549,12457	2203	4300	6503	SO:0001819	synonymous_variant	152185	exon3			ATGAACGGTTAGA	AY099107	CCDS2973.1	3q13.2	2010-09-01	2010-09-01	2010-09-01	ENSG00000163611	ENSG00000163611			25083	protein-coding gene	gene with protein product	"""spindle and centriole protein"""	613447	"""coiled-coil domain containing 52"""	CCDC52		20736305	Standard	NM_144718		Approved	SPICE	uc003eag.4	Q8N0Z3	OTTHUMG00000159261	ENST00000295872.4:c.120C>T	3.37:g.113222054G>A		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	98	47	0.479592	NM_144718	D3DN72|Q8WUX6	Silent	SNP	ENST00000295872.4	37	CCDS2973.1																																																																																			G|0.955;A|0.045	0.045	strong		0.299	SPICE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354177.2	NM_144718	
TUBB8	347688	hgsc.bcm.edu	37	10	93714	93714	+	Silent	SNP	A	A	T	rs41288743		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:93714A>T	ENST00000309812.4	-	4	680	c.618T>A	c.(616-618)gcT>gcA	p.A206A	TUBB8_ENST00000413237.3_5'UTR|TUBB8_ENST00000332708.5_3'UTR|TUBB8_ENST00000447903.2_Silent_p.A134A	NM_177987.2	NP_817124.1	Q3ZCM7	TBB8_HUMAN	tubulin, beta 8 class VIII	206					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)		TGTCATACAGAGCTTCGTTAT	0.537																																					p.A206A	Pancreas(192;2041 3010 9013 18103)	Atlas-SNP	.											TUBB8,NS,carcinoma,0,1	TUBB8	62	1	0			c.T618A						scavenged	.						94.0	87.0	90.0					10																	93714		2203	4299	6502	SO:0001819	synonymous_variant	347688	exon4			ATACAGAGCTTCG	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.618T>A	10.37:g.93714A>T		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	48	5	0.104167	NM_177987	Q5SQX9|Q8WZ78	Silent	SNP	ENST00000309812.4	37	CCDS7051.1																																																																																			.	.	alt		0.537	TUBB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467795.1	NM_177987	
GATA5	140628	hgsc.bcm.edu	37	20	61040951	61040951	+	Silent	SNP	C	C	T	rs6587239	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:61040951C>T	ENST00000252997.2	-	5	913	c.852G>A	c.(850-852)aaG>aaA	p.K284K		NM_080473.4	NP_536721.1	Q9BWX5	GATA5_HUMAN	GATA binding protein 5	284					blood coagulation (GO:0007596)|cellular response to BMP stimulus (GO:0071773)|intestinal epithelial cell differentiation (GO:0060575)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	enhancer sequence-specific DNA binding (GO:0001158)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)	p.K284K(1)		kidney(1)|lung(3)|ovary(1)|stomach(1)	6	Breast(26;2.05e-08)		BRCA - Breast invasive adenocarcinoma(19;3.08e-06)			GGATGCTTTCCTTCTTCATAG	0.682													C|||	2652	0.529553	0.7224	0.4769	5008	,	,		16945	0.4315		0.4622	False		,,,				2504	0.4765				p.K284K		Atlas-SNP	.											GATA5,NS,haematopoietic_neoplasm,-2,4	GATA5	22	4	1	Substitution - coding silent(1)	stomach(1)	c.G852A						PASS	.	C		2858,1536		952,954,291	93.0	86.0	88.0		852	1.9	1.0	20	dbSNP_116	88	4106,4492		985,2136,1178	no	coding-synonymous	GATA5	NM_080473.4		1937,3090,1469	TT,TC,CC		47.7553,34.9568,46.3978		284/398	61040951	6964,6028	2197	4299	6496	SO:0001819	synonymous_variant	140628	exon5			GCTTTCCTTCTTC	BC047790, BC117356	CCDS13499.1	20q13.33	2013-07-17	2001-11-28		ENSG00000130700	ENSG00000130700		"""GATA zinc finger domain containing"""	15802	protein-coding gene	gene with protein product		611496	"""GATA-binding protein 5"""			9566909	Standard	NM_080473		Approved	bB379O24.1, GATAS	uc002ycx.1	Q9BWX5	OTTHUMG00000032919	ENST00000252997.2:c.852G>A	20.37:g.61040951C>T		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	60	23	0.383333	NM_080473	D9ZGF7|Q17RE2|Q86VU4	Silent	SNP	ENST00000252997.2	37	CCDS13499.1																																																																																			C|0.469;T|0.531	0.531	strong		0.682	GATA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080038.2	NM_080473	
IL5RA	3568	hgsc.bcm.edu	37	3	3139910	3139910	+	Silent	SNP	T	T	C	rs141948767	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:3139910T>C	ENST00000446632.2	-	6	1006	c.432A>G	c.(430-432)tcA>tcG	p.S144S	IL5RA_ENST00000430514.2_Silent_p.S144S|IL5RA_ENST00000256452.3_Silent_p.S144S|IL5RA_ENST00000438560.1_Silent_p.S144S|IL5RA_ENST00000311981.8_Silent_p.S144S|IL5RA_ENST00000383846.1_Silent_p.S144S|IL5RA_ENST00000445864.2_Intron|IL5RA_ENST00000456302.1_Silent_p.S144S|IL5RA_ENST00000418488.2_Silent_p.S144S	NM_175726.3	NP_783853.1	Q01344	IL5RA_HUMAN	interleukin 5 receptor, alpha	144					cell proliferation (GO:0008283)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-5-mediated signaling pathway (GO:0038043)|regulation of interleukin-5 production (GO:0032674)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	interleukin-5 receptor activity (GO:0004914)			cervix(1)|endometrium(2)|large_intestine(7)|lung(9)|ovary(1)|prostate(2)|skin(2)	24				Epithelial(13;0.00278)|all cancers(10;0.00809)|OV - Ovarian serous cystadenocarcinoma(96;0.00944)		ACCTTAAACGTGAATAATTGT	0.423													T|||	5	0.000998403	0.0	0.0029	5008	,	,		21487	0.0		0.003	False		,,,				2504	0.0				p.S144S	GBM(169;430 2801 24955 28528)	Atlas-SNP	.											.	IL5RA	55	.	0			c.A432G						PASS	.	T	,,,,,	5,4401	9.9+/-24.2	0,5,2198	208.0	215.0	213.0		432,432,432,432,432,432	-8.4	0.0	3	dbSNP_134	213	23,8577	16.6+/-54.9	0,23,4277	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	IL5RA	NM_000564.4,NM_175724.2,NM_175725.2,NM_175726.3,NM_175727.2,NM_175728.2	,,,,,	0,28,6475	CC,CT,TT		0.2674,0.1135,0.2153	,,,,,	144/421,144/334,144/336,144/421,144/334,144/336	3139910	28,12978	2203	4300	6503	SO:0001819	synonymous_variant	3568	exon6			TAAACGTGAATAA	M96652	CCDS2559.1, CCDS2560.1, CCDS46739.1, CCDS58813.1	3p26-p24	2008-01-11			ENSG00000091181	ENSG00000091181		"""Interleukins and interleukin receptors"", ""CD molecules"""	6017	protein-coding gene	gene with protein product		147851		IL5R		1732409	Standard	NM_175727		Approved	CDw125, CD125	uc010hbs.3	Q01344	OTTHUMG00000090245	ENST00000446632.2:c.432A>G	3.37:g.3139910T>C		Somatic	268	0	0		WXS	Illumina HiSeq	Phase_I	244	109	0.446721	NM_001243099	B3IU77|B4E2G0|Q14633|Q15469|Q6ISX9	Silent	SNP	ENST00000446632.2	37	CCDS2559.1																																																																																			T|0.998;C|0.002	0.002	strong		0.423	IL5RA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337537.2		
C22orf23	84645	hgsc.bcm.edu	37	22	38341134	38341134	+	Silent	SNP	T	T	C	rs139859	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:38341134T>C	ENST00000249079.2	-	5	652	c.396A>G	c.(394-396)acA>acG	p.T132T	C22orf23_ENST00000403305.1_Silent_p.T132T|C22orf23_ENST00000403026.1_Silent_p.T132T			Q9BZE7	EVG1_HUMAN	chromosome 22 open reading frame 23	132										endometrium(3)|kidney(2)|large_intestine(7)	12	Melanoma(58;0.045)					TGTCCTTCCCTGTGGCAAAGA	0.507													C|||	3913	0.78135	0.9667	0.67	5008	,	,		17177	0.8353		0.6531	False		,,,				2504	0.6861				p.T132T		Atlas-SNP	.											.	C22orf23	21	.	0			c.A396G						PASS	.	C	,	4088,318	170.1+/-200.6	1899,290,14	157.0	156.0	156.0		333,396	-10.6	0.1	22	dbSNP_78	156	5633,2967	461.1+/-365.4	1838,1957,505	no	coding-synonymous,coding-synonymous	C22orf23	NM_001207062.1,NM_032561.4	,	3737,2247,519	CC,CT,TT		34.5,7.2174,25.2576	,	111/197,132/218	38341134	9721,3285	2203	4300	6503	SO:0001819	synonymous_variant	84645	exon5			CTTCCCTGTGGCA	AF324466	CCDS13962.1, CCDS74860.1	22q13.1	2013-10-11			ENSG00000128346	ENSG00000128346			18589	protein-coding gene	gene with protein product						11237012	Standard	NM_032561		Approved	FLJ32787, EVG1, LOC84645	uc003auj.2	Q9BZE7	OTTHUMG00000150672	ENST00000249079.2:c.396A>G	22.37:g.38341134T>C		Somatic	325	1	0.00307692		WXS	Illumina HiSeq	Phase_I	272	114	0.419118	NM_032561	Q5JYU9|Q96M68	Silent	SNP	ENST00000249079.2	37	CCDS13962.1																																																																																			T|0.238;C|0.762	0.762	strong		0.507	C22orf23-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319564.1	NM_032561	
OR5B3	441608	hgsc.bcm.edu	37	11	58170374	58170374	+	Missense_Mutation	SNP	T	T	C	rs12280114	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:58170374T>C	ENST00000309403.2	-	1	508	c.509A>G	c.(508-510)aAt>aGt	p.N170S		NM_001005469.1	NP_001005469.1	Q8NH48	OR5B3_HUMAN	olfactory receptor, family 5, subfamily B, member 3	170			N -> S (in dbSNP:rs12280114).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.N170S(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(17)|ovary(1)|prostate(1)|skin(2)|stomach(6)|upper_aerodigestive_tract(1)	34	Esophageal squamous(5;0.0027)	Breast(21;0.0778)				ATGGACTTCATTGGACTTACA	0.448													T|||	1453	0.290136	0.3533	0.2695	5008	,	,		22324	0.1448		0.3628	False		,,,				2504	0.2945				p.N170S		Atlas-SNP	.											OR5B3,NS,carcinoma,0,1	OR5B3	65	1	1	Substitution - Missense(1)	stomach(1)	c.A509G						PASS	.	T	SER/ASN	1442,2960	467.9+/-355.0	229,984,988	107.0	99.0	102.0		509	1.7	0.0	11	dbSNP_120	102	3094,5496	473.6+/-368.6	550,1994,1751	yes	missense	OR5B3	NM_001005469.1	46	779,2978,2739	CC,CT,TT		36.0186,32.7578,34.9138	benign	170/315	58170374	4536,8456	2201	4295	6496	SO:0001583	missense	441608	exon1			ACTTCATTGGACT	AB065545	CCDS31549.1	11q12.1	2012-08-09			ENSG00000172769	ENSG00000172769		"""GPCR / Class A : Olfactory receptors"""	8324	protein-coding gene	gene with protein product				OR5B13			Standard	NM_001005469		Approved	OST129	uc010rkf.2	Q8NH48	OTTHUMG00000167516	ENST00000309403.2:c.509A>G	11.37:g.58170374T>C	ENSP00000308270:p.Asn170Ser	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	74	50	0.675676	NM_001005469	Q6IEV6	Missense_Mutation	SNP	ENST00000309403.2	37	CCDS31549.1	655	0.2999084249084249	195	0.39634146341463417	89	0.24585635359116023	95	0.1660839160839161	276	0.3641160949868074	t	10.45	1.352391	0.24512	0.327578	0.360186	ENSG00000172769	ENST00000309403	T	0.00241	8.46	4.05	1.67	0.24075	GPCR, rhodopsin-like superfamily (1);	0.255793	0.27577	N	0.018745	T	0.00012	0.0000	M	0.91196	3.185	0.80722	P	0.0	P	0.44044	0.825	P	0.48524	0.58	T	0.17776	-1.0358	9	0.87932	D	0	-35.2106	7.5725	0.27915	0.0:0.1867:0.0:0.8133	rs12280114;rs52832394;rs57173256;rs12280114	170	Q8NH48	OR5B3_HUMAN	S	170	ENSP00000308270:N170S	ENSP00000308270:N170S	N	-	2	0	OR5B3	57926950	0.114000	0.22134	0.001000	0.08648	0.382000	0.30200	2.299000	0.43611	0.232000	0.21100	0.528000	0.53228	AAT	T|0.668;C|0.332	0.332	strong		0.448	OR5B3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394886.1	NM_001005469	
METTL12	751071	hgsc.bcm.edu	37	11	62434173	62434173	+	Missense_Mutation	SNP	G	G	A	rs11231181	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:62434173G>A	ENST00000532971.1	+	3	630	c.373G>A	c.(373-375)Ggc>Agc	p.G125S	C11orf48_ENST00000525675.1_5'Flank|RP11-831H9.11_ENST00000528405.1_5'Flank|C11orf48_ENST00000431002.2_Intron|SNORA57_ENST00000383870.1_RNA|C11orf48_ENST00000532208.1_Intron|METTL12_ENST00000398922.2_3'UTR|C11orf48_ENST00000354588.3_Intron|C11orf48_ENST00000524958.1_5'Flank	NM_001043229.1	NP_001036694.1	A8MUP2	MET12_HUMAN	methyltransferase like 12	125			G -> S (in dbSNP:rs11231181).			mitochondrion (GO:0005739)	methyltransferase activity (GO:0008168)			endometrium(1)|large_intestine(1)|lung(2)|ovary(1)|urinary_tract(1)	6						GGGTGGCCCAGGCCAAACACC	0.592													G|||	748	0.149361	0.0756	0.2161	5008	,	,		17989	0.0526		0.2604	False		,,,				2504	0.1871				p.G125S		Atlas-SNP	.											.	METTL12	11	.	0			c.G373A						PASS	.	G	SER/GLY,	467,3523		31,405,1559	42.0	46.0	45.0		373,	1.7	0.2	11	dbSNP_120	45	2405,5925		366,1673,2126	yes	missense,intron	C11orf48,METTL12	NM_001043229.1,NM_024099.3	56,	397,2078,3685	AA,AG,GG		28.8715,11.7043,23.3117	benign,	125/241,	62434173	2872,9448	1995	4165	6160	SO:0001583	missense	751071	exon3			GGCCCAGGCCAAA	BC041359	CCDS41657.1	11q12.3	2013-09-30			ENSG00000214756	ENSG00000214756			33113	protein-coding gene	gene with protein product							Standard	NM_001043229		Approved	U99HG	uc001nuh.3	A8MUP2	OTTHUMG00000167545	ENST00000532971.1:c.373G>A	11.37:g.62434173G>A	ENSP00000431287:p.Gly125Ser	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	76	75	0.986842	NM_001043229	B7Z4C1	Missense_Mutation	SNP	ENST00000532971.1	37	CCDS41657.1	371	0.16987179487179488	41	0.08333333333333333	95	0.26243093922651933	36	0.06293706293706294	199	0.262532981530343	G	9.658	1.143349	0.21205	0.117043	0.288715	ENSG00000214756	ENST00000532971	T	0.42513	0.97	4.87	1.72	0.24424	Methyltransferase type 11 (1);	1.077670	0.07388	U	0.888510	T	0.00012	0.0000	N	0.12746	0.255	0.80722	P	0.0	B	0.13145	0.007	B	0.15052	0.012	T	0.34179	-0.9839	9	0.38643	T	0.18	-25.8093	3.6963	0.08365	0.2209:0.0:0.5822:0.1969	rs11231181;rs11231181	125	A8MUP2	MTL12_HUMAN	S	125	ENSP00000431287:G125S	ENSP00000431287:G125S	G	+	1	0	METTL12	62190749	0.001000	0.12720	0.161000	0.22692	0.358000	0.29455	0.978000	0.29488	0.258000	0.21686	-0.355000	0.07637	GGC	G|0.803;A|0.197	0.197	strong		0.592	METTL12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394990.1	NM_001043229	
LILRB3	11025	hgsc.bcm.edu	37	19	54725913	54725913	+	Missense_Mutation	SNP	C	C	T	rs199822090	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:54725913C>T	ENST00000391750.1	-	5	581	c.445G>A	c.(445-447)Gga>Aga	p.G149R	CTB-83J4.1_ENST00000601161.1_lincRNA|LILRB3_ENST00000424807.1_Missense_Mutation_p.G149R|LILRB3_ENST00000346401.6_Missense_Mutation_p.G149R|LILRA6_ENST00000440558.2_Intron|LILRA6_ENST00000270464.5_Intron|LILRB3_ENST00000407860.2_Missense_Mutation_p.G149R|LILRB3_ENST00000469273.1_5'Flank|LILRA6_ENST00000419410.2_Intron|LILRA6_ENST00000391735.3_Intron|LILRB3_ENST00000245620.9_Missense_Mutation_p.G149R			O75022	LIRB3_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 3	149	Ig-like C2-type 2.			G -> R (in Ref. 2; AAB87667). {ECO:0000305}.	cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)|immune system process (GO:0002376)|negative regulation of osteoclast differentiation (GO:0045671)	integral component of plasma membrane (GO:0005887)	receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			endometrium(3)|kidney(13)|large_intestine(1)|lung(6)|ovary(2)|prostate(5)|skin(2)|stomach(1)|urinary_tract(1)	34	all_cancers(19;0.00723)|all_epithelial(19;0.00389)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		TGGTGATATCCCTTCTGTGAG	0.597													.|||	783	0.15635	0.3411	0.1715	5008	,	,		12077	0.002		0.1362	False		,,,				2504	0.0757				p.G149R		Atlas-SNP	.											.	LILRB3	67	.	0			c.G445A						PASS	.						23.0	15.0	18.0					19																	54725913		2079	3867	5946	SO:0001583	missense	11025	exon4			GATATCCCTTCTG	U91928	CCDS33105.1, CCDS46175.1	19q13.4	2013-01-11			ENSG00000204577	ENSG00000204577		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6607	protein-coding gene	gene with protein product		604820				9278324, 9382880	Standard	NM_006864		Approved	LIR-3, HL9, ILT5, LIR3, CD85a	uc002qee.1	O75022	OTTHUMG00000066626	ENST00000391750.1:c.445G>A	19.37:g.54725913C>T	ENSP00000375630:p.Gly149Arg	Somatic	233	0	0		WXS	Illumina HiSeq	Phase_I	213	84	0.394366	NM_006864	C9J1P3|C9JIP1|O15471|Q86U49	Missense_Mutation	SNP	ENST00000391750.1	37	CCDS33105.1	.	.	.	.	.	.	.	.	.	.	C	6.911	0.537697	0.13188	.	.	ENSG00000204577	ENST00000391750;ENST00000424807;ENST00000346401;ENST00000245620;ENST00000407860;ENST00000445347	T;T;T;T;T;T	0.11604	2.76;2.76;2.76;2.76;2.76;5.76	2.87	-5.75	0.02384	Immunoglobulin-like fold (1);	2.192950	0.01626	N	0.023278	T	0.07683	0.0193	L	0.37800	1.135	0.80722	P	0.0	B;B;P;P;P	0.41546	0.218;0.08;0.555;0.754;0.68	B;B;B;B;B	0.39094	0.271;0.132;0.29;0.049;0.209	T	0.17258	-1.0375	9	0.41790	T	0.15	.	1.2731	0.02025	0.1365:0.1909:0.2699:0.4027	.	149;149;149;149;149	B5MCX0;F8WD89;O75022-2;O75022;O75022-3	.;.;.;LIRB3_HUMAN;.	R	149	ENSP00000375630:G149R;ENSP00000412771:G149R;ENSP00000345184:G149R;ENSP00000245620:G149R;ENSP00000384274:G149R;ENSP00000388199:G149R	ENSP00000245620:G149R	G	-	1	0	LILRB3	59417725	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.520000	0.00951	-1.631000	0.01543	-0.510000	0.04470	GGA	C|0.931;T|0.069	0.069	strong		0.597	LILRB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000142844.5	NM_006864	
DYSF	8291	hgsc.bcm.edu	37	2	71780248	71780248	+	Silent	SNP	C	C	T	rs35721373	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:71780248C>T	ENST00000258104.3	+	20	2137	c.1860C>T	c.(1858-1860)taC>taT	p.Y620Y	DYSF_ENST00000413539.2_Silent_p.Y651Y|DYSF_ENST00000394120.2_Silent_p.Y621Y|DYSF_ENST00000409651.1_Silent_p.Y652Y|DYSF_ENST00000409366.1_Silent_p.Y621Y|DYSF_ENST00000409762.1_Silent_p.Y637Y|DYSF_ENST00000429174.2_Silent_p.Y620Y|DYSF_ENST00000409582.3_Silent_p.Y637Y|DYSF_ENST00000410020.3_Silent_p.Y638Y|DYSF_ENST00000410041.1_Silent_p.Y638Y|DYSF_ENST00000409744.1_Silent_p.Y607Y	NM_001130976.1|NM_003494.3	NP_001124448.1|NP_003485.1	O75923	DYSF_HUMAN	dysferlin	620					plasma membrane repair (GO:0001778)|vesicle fusion (GO:0006906)	cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|phospholipid binding (GO:0005543)			autonomic_ganglia(2)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|lung(57)|ovary(3)|pancreas(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(2)	111						TCGGGAACTACGGGAACAAGT	0.587													c|||	179	0.0357428	0.0514	0.0202	5008	,	,		18980	0.0089		0.0258	False		,,,				2504	0.0634				p.Y652Y		Atlas-SNP	.											.	DYSF	536	.	0			c.C1956T						PASS	.	C	,,,,,,,,,,,,,	209,4197	129.0+/-165.8	5,199,1999	132.0	106.0	115.0		1863,1818,1818,1860,1953,1911,1911,1956,1863,1821,1914,1821,1914,1860	-5.2	0.8	2	dbSNP_126	115	261,8339	102.3+/-163.5	5,251,4044	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	DYSF	NM_001130455.1,NM_001130976.1,NM_001130977.1,NM_001130978.1,NM_001130979.1,NM_001130980.1,NM_001130981.1,NM_001130982.1,NM_001130983.1,NM_001130984.1,NM_001130985.1,NM_001130986.1,NM_001130987.1,NM_003494.3	,,,,,,,,,,,,,	10,450,6043	TT,TC,CC		3.0349,4.7435,3.6137	,,,,,,,,,,,,,	621/2082,606/2067,606/2088,620/2102,651/2112,637/2098,637/2119,652/2113,621/2103,607/2089,638/2099,607/2068,638/2120,620/2081	71780248	470,12536	2203	4300	6503	SO:0001819	synonymous_variant	8291	exon21			GAACTACGGGAAC	AF075575	CCDS1918.1, CCDS46323.1, CCDS46324.1, CCDS46325.1, CCDS46326.1, CCDS46327.1, CCDS46328.1, CCDS46329.1, CCDS46330.1, CCDS46331.1, CCDS46332.1	2p13.3	2014-09-17	2013-09-12		ENSG00000135636	ENSG00000135636			3097	protein-coding gene	gene with protein product	"""fer-1-like family member 1"""	603009	"""limb girdle muscular dystrophy 2B (autosomal recessive)"""	LGMD2B		8320700	Standard	NM_003494		Approved	FER1L1	uc010fen.3	O75923	OTTHUMG00000129757	ENST00000258104.3:c.1860C>T	2.37:g.71780248C>T		Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	134	65	0.485075	NM_001130982	A0FK00|B1PZ70|B1PZ71|B1PZ72|B1PZ73|B1PZ74|B1PZ75|B1PZ76|B1PZ77|B1PZ78|B1PZ79|B1PZ80|B1PZ81|B3KQB9|O75696|Q09EX5|Q0H395|Q53QY3|Q53TD2|Q8TEL8|Q9UEN7	Silent	SNP	ENST00000258104.3	37	CCDS1918.1																																																																																			C|0.967;T|0.033	0.033	strong		0.587	DYSF-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251970.3	NM_003494	
ELSPBP1	64100	hgsc.bcm.edu	37	19	48517538	48517538	+	Missense_Mutation	SNP	G	G	A	rs62129078|rs369872763	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:48517538G>A	ENST00000339841.2	+	3	359	c.181G>A	c.(181-183)Ggc>Agc	p.G61S	ELSPBP1_ENST00000597519.1_Intron	NM_022142.4	NP_071425.3	Q96BH3	ESPB1_HUMAN	epididymal sperm binding protein 1	61	Fibronectin type-II 1. {ECO:0000255|PROSITE-ProRule:PRU00479}.				single fertilization (GO:0007338)	extracellular region (GO:0005576)				NS(1)|breast(1)|kidney(1)|large_intestine(1)|lung(6)	10		all_cancers(25;8.7e-09)|all_lung(116;1.15e-06)|all_epithelial(76;1.17e-06)|Lung NSC(112;2.56e-06)|all_neural(266;0.0138)|Ovarian(192;0.0261)|Breast(70;0.203)		OV - Ovarian serous cystadenocarcinoma(262;0.000253)|all cancers(93;0.00129)|Epithelial(262;0.0314)|GBM - Glioblastoma multiforme(486;0.0606)		CGTGTACAACGGCCAGTGGAA	0.488													g|||	750	0.14976	0.1831	0.1225	5008	,	,		16645	0.0724		0.1531	False		,,,				2504	0.2004				p.G61S		Atlas-SNP	.											.	ELSPBP1	29	.	0			c.G181A						PASS	.	G	SER/GLY	794,3612	319.3+/-296.1	74,646,1483	156.0	135.0	142.0		181	1.1	0.0	19	dbSNP_129	142	1284,7316	254.7+/-279.9	87,1110,3103	yes	missense	ELSPBP1	NM_022142.4	56	161,1756,4586	AA,AG,GG		14.9302,18.0209,15.9772	possibly-damaging	61/224	48517538	2078,10928	2203	4300	6503	SO:0001583	missense	64100	exon3			TACAACGGCCAGT	AJ278478	CCDS12708.1	19q13.33	2009-09-17							14417	protein-coding gene	gene with protein product	"""epididymal protein 12"""	607443					Standard	NM_022142		Approved	HE12, E12, EDDM12	uc002pht.3	Q96BH3		ENST00000339841.2:c.181G>A	19.37:g.48517538G>A	ENSP00000340660:p.Gly61Ser	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	122	65	0.532787	NM_022142	Q96RT0|Q9H4C8	Missense_Mutation	SNP	ENST00000339841.2	37	CCDS12708.1	315	0.14423076923076922	98	0.1991869918699187	58	0.16022099447513813	47	0.08216783216783216	112	0.14775725593667546	G	11.26	1.587673	0.28268	0.180209	0.149302	ENSG00000169393	ENST00000339841	T	0.52983	0.64	3.27	1.14	0.20703	Fibronectin, type II, collagen-binding (4);Kringle-like fold (2);	0.734607	0.11192	N	0.589780	T	0.00039	0.0001	M	0.71920	2.185	0.80722	P	0.0	P	0.37864	0.61	B	0.39617	0.305	T	0.07849	-1.0751	9	0.18276	T	0.48	.	5.4873	0.16757	0.2546:0.0:0.7454:0.0	rs62129078	61	Q96BH3	ESPB1_HUMAN	S	61	ENSP00000340660:G61S	ENSP00000340660:G61S	G	+	1	0	ELSPBP1	53209350	0.005000	0.15991	0.001000	0.08648	0.009000	0.06853	0.606000	0.24194	0.397000	0.25310	0.544000	0.68410	GGC	G|0.845;A|0.155	0.155	strong		0.488	ELSPBP1-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465207.1		
MST1L	11223	hgsc.bcm.edu	37	1	17085614	17085614	+	RNA	SNP	G	G	A	rs3891100	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:17085614G>A	ENST00000455405.2	-	0	0							Q2TV78	MST1L_HUMAN	macrophage stimulating 1-like							extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)										CACCCTTGCGGGTCTTGCTGA	0.736																																					p.T369T		Atlas-SNP	.											.	.	.	.	0			c.C1107T						PASS	.																																					11223	exon9			CTTGCGGGTCTTG	U28055, AF083416		1p36.33	2013-03-27	2012-11-09	2012-11-09	ENSG00000186715	ENSG00000186715			7390	other	unknown			"""macrophage stimulating, pseudogene 7"", ""macrophage stimulating, pseudogene 9"", ""macrophage stimulating 1 (hepatocyte growth factor-like) pseudogene 9"""	MSTP7, MSTP9, MST1P9		10728827	Standard	NM_001271733		Approved	D1F15S1A, MSPL7, MSPL-7	uc010ock.3	Q2TV78	OTTHUMG00000002578		1.37:g.17085614G>A		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	66	8	0.121212	NM_001271733	B7WPB1|Q13209	Silent	SNP	ENST00000455405.2	37																																																																																				G|0.990;A|0.010	0.010	strong		0.736	MST1L-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000400328.1	NM_001271733	
OTOP3	347741	hgsc.bcm.edu	37	17	72943126	72943126	+	Silent	SNP	G	G	A	rs8066909	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:72943126G>A	ENST00000328801.4	+	6	1176	c.1176G>A	c.(1174-1176)gcG>gcA	p.A392A		NM_178233.1	NP_839947.1	Q7RTS5	OTOP3_HUMAN	otopetrin 3	392						integral component of membrane (GO:0016021)	metal ion binding (GO:0046872)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(5)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	23	all_lung(278;0.151)|Lung NSC(278;0.185)					CGTGCCTGGCGGGCACAGCCA	0.607													G|||	1456	0.290735	0.1672	0.4885	5008	,	,		18262	0.0655		0.5109	False		,,,				2504	0.3231				p.A392A		Atlas-SNP	.											OTOP3,NS,carcinoma,0,1	OTOP3	64	1	0			c.G1176A						PASS	.						74.0	66.0	69.0					17																	72943126		2203	4300	6503	SO:0001819	synonymous_variant	347741	exon6			CCTGGCGGGCACA	BK000568	CCDS11709.1	17q25	2004-01-19				ENSG00000182938			19658	protein-coding gene	gene with protein product		607828				12651873	Standard	NM_178233		Approved		uc010wrr.3	Q7RTS5		ENST00000328801.4:c.1176G>A	17.37:g.72943126G>A		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	88	40	0.454545	NM_178233		Silent	SNP	ENST00000328801.4	37	CCDS11709.1																																																																																			G|0.683;A|0.317	0.317	strong		0.607	OTOP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445308.1	NM_178233	
GPR112	139378	hgsc.bcm.edu	37	X	135431236	135431236	+	Missense_Mutation	SNP	T	T	C	rs5930932	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:135431236T>C	ENST00000394143.1	+	6	5662	c.5371T>C	c.(5371-5373)Ttt>Ctt	p.F1791L	GPR112_ENST00000412101.1_Missense_Mutation_p.F1586L|GPR112_ENST00000370652.1_Missense_Mutation_p.F1791L|GPR112_ENST00000287534.4_Missense_Mutation_p.F1728L|GPR112_ENST00000394141.1_Missense_Mutation_p.F1586L	NM_153834.3	NP_722576.3	Q8IZF6	GP112_HUMAN	G protein-coupled receptor 112	1791			F -> L (in dbSNP:rs5930932).		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)	p.F1791L(1)		NS(2)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(33)|lung(97)|ovary(5)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(2)	199	Acute lymphoblastic leukemia(192;0.000127)					CACCAATTGCTTTTCTTCTAA	0.383													c|||	1834	0.485828	0.4569	0.3617	3775	,	,		15609	0.2778		0.3797	False		,,,				2504	0.3241				p.F1791L		Atlas-SNP	.											.	GPR112	459	.	1	Substitution - Missense(1)	prostate(1)	c.T5371C						PASS	.		LEU/PHE	2257,1576		567,784,339,280,232	133.0	133.0	133.0		5371	-1.8	0.0	X	dbSNP_114	133	3229,3499		567,1181,914,680,958	yes	missense	GPR112	NM_153834.3	22	1134,1965,1253,960,1190	CC,CT,C,TT,T		47.9935,41.1166,48.0542	benign	1791/3081	135431236	5486,5075	2202	4300	6502	SO:0001583	missense	139378	exon6			AATTGCTTTTCTT	AY140954	CCDS35409.1	Xq26.3	2014-08-08			ENSG00000156920	ENSG00000156920		"""-"", ""GPCR / Class B : Orphans"""	18992	protein-coding gene	gene with protein product						12435584	Standard	XM_005262367		Approved	RP1-299I16, PGR17	uc004ezu.1	Q8IZF6	OTTHUMG00000022508	ENST00000394143.1:c.5371T>C	X.37:g.135431236T>C	ENSP00000377699:p.Phe1791Leu	Somatic	282	1	0.0035461		WXS	Illumina HiSeq	Phase_I	183	182	0.994536	NM_153834	A2A2J1|A2A2J2|Q5EGP2|Q86SM6	Missense_Mutation	SNP	ENST00000394143.1	37	CCDS35409.1	786	0.47377938517179025	152	0.4175824175824176	84	0.29577464788732394	112	0.24669603524229075	190	0.3242320819112628	c	0.020	-1.432654	0.01108	0.588834	0.479935	ENSG00000156920	ENST00000394143;ENST00000370652;ENST00000412101;ENST00000287534;ENST00000394141	T;T;T;T;T	0.20463	2.11;2.11;2.07;2.25;2.07	3.63	-1.78	0.07957	.	.	.	.	.	T	0.00012	0.0000	N	0.01352	-0.895	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.37291	-0.9712	8	0.21014	T	0.42	.	5.3382	0.15969	0.0:0.2802:0.1606:0.5593	rs5930932;rs6635265;rs52832481;rs60264923;rs5930932	1728;1586;1791	Q8IZF6-2;Q8IZF6-3;Q8IZF6	.;.;GP112_HUMAN	L	1791;1791;1586;1728;1586	ENSP00000377699:F1791L;ENSP00000359686:F1791L;ENSP00000416526:F1586L;ENSP00000287534:F1728L;ENSP00000377697:F1586L	ENSP00000287534:F1728L	F	+	1	0	GPR112	135258902	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.934000	0.03955	-1.013000	0.03383	-1.690000	0.00728	TTT	0|0.015;C|0.499	0.499	strong		0.383	GPR112-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000286639.1		
ARSB	411	hgsc.bcm.edu	37	5	78135201	78135201	+	Silent	SNP	C	C	T	rs25413	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:78135201C>T	ENST00000264914.4	-	6	1727	c.1191G>A	c.(1189-1191)ccG>ccA	p.P397P	ARSB_ENST00000396151.3_Silent_p.P397P|ARSB_ENST00000565165.1_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	150	0	0		WXS	Illumina HiSeq	Phase_I	194	70	0.360825	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	
CCR3	1232	hgsc.bcm.edu	37	3	46306700	46306700	+	Silent	SNP	T	T	C	rs4987053	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:46306700T>C	ENST00000357422.2	+	4	594	c.51T>C	c.(49-51)taT>taC	p.Y17Y	CCR3_ENST00000545097.1_Silent_p.Y38Y|CCR3_ENST00000395940.2_Silent_p.Y17Y|CCR3_ENST00000395942.2_Silent_p.Y17Y|CCR3_ENST00000541018.1_Silent_p.Y17Y			P51677	CCR3_HUMAN	chemokine (C-C motif) receptor 3	17					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|cell adhesion (GO:0007155)|cellular defense response (GO:0006968)|chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|inflammatory response (GO:0006954)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of endothelial cell proliferation (GO:0001938)|viral process (GO:0016032)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	C-C chemokine receptor activity (GO:0016493)|chemokine receptor activity (GO:0004950)			breast(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(5)|ovary(3)|urinary_tract(1)	18				BRCA - Breast invasive adenocarcinoma(193;0.00119)|KIRC - Kidney renal clear cell carcinoma(197;0.0183)|Kidney(197;0.0216)		CATCCTACTATGATGACGTGG	0.488													T|||	578	0.115415	0.1573	0.0692	5008	,	,		20484	0.0337		0.0805	False		,,,				2504	0.2117				p.Y38Y		Atlas-SNP	.											.	CCR3	52	.	0			c.T114C						PASS	.	T	,,,	548,3858	249.0+/-256.6	37,474,1692	106.0	101.0	103.0		105,51,114,51	0.7	0.0	3	dbSNP_111	103	613,7987	160.7+/-213.8	22,569,3709	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CCR3	NM_001164680.1,NM_001837.3,NM_178328.1,NM_178329.2	,,,	59,1043,5401	CC,CT,TT		7.1279,12.4376,8.9266	,,,	35/374,17/356,38/377,17/356	46306700	1161,11845	2203	4300	6503	SO:0001819	synonymous_variant	1232	exon3			CTACTATGATGAC	AF247361	CCDS2738.1, CCDS54574.1	3p21.3	2012-08-08			ENSG00000183625	ENSG00000183625		"""GPCR / Class A : Chemokine receptors : C-C motif"", ""CD molecules"""	1604	protein-coding gene	gene with protein product		601268		CMKBR3			Standard	NM_178328		Approved	CC-CKR-3, CKR3, CD193	uc003cpk.2	P51677	OTTHUMG00000133484	ENST00000357422.2:c.51T>C	3.37:g.46306700T>C		Somatic	241	0	0		WXS	Illumina HiSeq	Phase_I	216	98	0.453704	NM_178328	B3KVQ1|F5GWL6|Q15748|Q2YDB9|Q86WD2|Q8TDP6|Q9ULY8	Silent	SNP	ENST00000357422.2	37	CCDS2738.1																																																																																			T|0.903;C|0.097	0.097	strong		0.488	CCR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257380.2		
TTN	7273	hgsc.bcm.edu	37	2	179438866	179438866	+	Missense_Mutation	SNP	C	C	T	rs10164753	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:179438866C>T	ENST00000591111.1	-	276	67294	c.67070G>A	c.(67069-67071)cGt>cAt	p.R22357H	TTN-AS1_ENST00000438095.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.R15058H|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.R21430H|TTN-AS1_ENST00000586452.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.R14933H|TTN-AS1_ENST00000591332.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.R23998H|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.R15125H|TTN-AS1_ENST00000586707.1_RNA|RP11-171I2.5_ENST00000604215.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590932.1_RNA			Q8WZ42	TITIN_HUMAN	titin	22357	Fibronectin type-III 62. {ECO:0000255|PROSITE-ProRule:PRU00316}.		R -> H. {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)			GGCGATCACACGGAATTCATA	0.473													C|||	490	0.0978435	0.0877	0.1542	5008	,	,		20055	0.0258		0.0467	False		,,,				2504	0.1984				p.R23998H		Atlas-SNP	.											.	TTN	18412	.	0			c.G71993A						PASS	.	C	HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG	345,3617		16,313,1652	109.0	102.0	104.0		44798,64289,45173,45374	5.6	1.0	2	dbSNP_119	104	243,8085		8,227,3929	yes	missense,missense,missense,missense	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	29,29,29,29	24,540,5581	TT,TC,CC		2.9179,8.7077,4.7844	probably-damaging,probably-damaging,probably-damaging,probably-damaging	14933/26927,21430/33424,15058/27052,15125/27119	179438866	588,11702	1981	4164	6145	SO:0001583	missense	7273	exon326			ATCACACGGAATT	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.67070G>A	2.37:g.179438866C>T	ENSP00000465570:p.Arg22357His	Somatic	194	1	0.00515464		WXS	Illumina HiSeq	Phase_I	189	98	0.518519	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		122	0.055860805860805864	38	0.07723577235772358	46	0.1270718232044199	5	0.008741258741258742	33	0.04353562005277045	C	15.00	2.703799	0.48412	0.087077	0.029179	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.52295	0.67;0.67;0.67;0.67	5.58	5.58	0.84498	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.03695	0.0105	H	0.97390	3.995	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;0.999;0.999	T	0.63637	-0.6592	9	0.87932	D	0	.	19.546	0.95297	0.0:1.0:0.0:0.0	rs10164753;rs52791736;rs61126566;rs10164753	14933;15058;15125;22357	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	H	21430;14933;15125;15058;14931	ENSP00000343764:R21430H;ENSP00000434586:R14933H;ENSP00000340554:R15125H;ENSP00000352154:R15058H	ENSP00000340554:R15125H	R	-	2	0	TTN	179147112	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.818000	0.86416	2.635000	0.89317	0.561000	0.74099	CGT	C|0.944;T|0.056	0.056	strong		0.473	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
ZMYND10	51364	hgsc.bcm.edu	37	3	50379257	50379257	+	Missense_Mutation	SNP	G	G	A	rs142613783	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:50379257G>A	ENST00000231749.3	-	10	2377	c.1105C>T	c.(1105-1107)Cgg>Tgg	p.R369W	ZMYND10-AS1_ENST00000440013.1_RNA|RASSF1_ENST00000357043.2_5'Flank|RASSF1_ENST00000488024.1_5'Flank|ZMYND10_ENST00000490675.1_5'UTR|ZMYND10_ENST00000360165.3_Missense_Mutation_p.R364W|RASSF1_ENST00000359365.4_5'Flank	NM_015896.2	NP_056980.2	O75800	ZMY10_HUMAN	zinc finger, MYND-type containing 10	369	Interaction with LRRC6.		R -> W (in dbSNP:rs142613783). {ECO:0000269|Ref.1}.		inner dynein arm assembly (GO:0036159)|motile cilium assembly (GO:0044458)|outer dynein arm assembly (GO:0036158)	centriolar satellite (GO:0034451)|cytoplasm (GO:0005737)	metal ion binding (GO:0046872)			endometrium(3)|kidney(2)|large_intestine(1)|lung(5)|ovary(1)|urinary_tract(2)	14				BRCA - Breast invasive adenocarcinoma(193;0.000272)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00607)		GCCTGCAGCCGCAGGTCCTGC	0.627										TSP Lung(30;0.18)			G|||	9	0.00179712	0.0	0.0014	5008	,	,		20400	0.0		0.006	False		,,,				2504	0.002				p.R369W		Atlas-SNP	.											.	ZMYND10	37	.	0			c.C1105T						PASS	.	G	TRP/ARG	7,4399	12.9+/-30.5	0,7,2196	42.0	42.0	42.0		1105	2.2	1.0	3	dbSNP_134	42	67,8533	39.8+/-96.3	0,67,4233	yes	missense	ZMYND10	NM_015896.2	101	0,74,6429	AA,AG,GG		0.7791,0.1589,0.569	probably-damaging	369/441	50379257	74,12932	2203	4300	6503	SO:0001583	missense	51364	exon10			GCAGCCGCAGGTC	U70824	CCDS2825.1	3p21.3	2014-02-03			ENSG00000004838	ENSG00000004838		"""Zinc fingers, MYND-type"""	19412	protein-coding gene	gene with protein product		607070				12629521, 23891469	Standard	NM_015896		Approved	BLU, CILD22	uc003dag.1	O75800	OTTHUMG00000156874	ENST00000231749.3:c.1105C>T	3.37:g.50379257G>A	ENSP00000231749:p.Arg369Trp	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	60	31	0.516667	NM_015896	A6NK41|B3KU54|O14570|O75801|Q53FE6|Q8N4R6|Q8NDN6	Missense_Mutation	SNP	ENST00000231749.3	37	CCDS2825.1	4	0.0018315018315018315	0	0.0	0	0.0	0	0.0	4	0.005277044854881266	G	12.24	1.879643	0.33162	0.001589	0.007791	ENSG00000004838	ENST00000231749;ENST00000360165	.	.	.	5.11	2.16	0.27623	.	0.226724	0.41194	D	0.000924	T	0.57007	0.2024	M	0.72894	2.215	0.23468	N	0.997615	D;D	0.89917	0.992;1.0	P;D	0.67725	0.765;0.953	T	0.60105	-0.7328	9	0.87932	D	0	-31.184	14.5087	0.67769	0.0:0.0:0.3974:0.6026	.	364;369	O75800-2;O75800	.;ZMY10_HUMAN	W	369;364	.	ENSP00000231749:R369W	R	-	1	2	ZMYND10	50354261	0.663000	0.27448	0.964000	0.40570	0.168000	0.22595	1.029000	0.30140	0.131000	0.18576	0.462000	0.41574	CGG	G|0.995;A|0.005	0.005	strong		0.627	ZMYND10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000346376.1	NM_015896	
NRXN1	9378	hgsc.bcm.edu	37	2	50464109	50464109	+	Splice_Site	SNP	C	C	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:50464109C>A	ENST00000406316.2	-	18	4841		c.e18-1		NRXN1_ENST00000331040.5_Splice_Site|NRXN1_ENST00000404971.1_Splice_Site|NRXN1_ENST00000342183.5_Splice_Site|NRXN1_ENST00000405472.3_Splice_Site|NRXN1_ENST00000406859.3_Splice_Site|NRXN1_ENST00000401710.1_Splice_Site|NRXN1_ENST00000401669.2_Splice_Site|NRXN1_ENST00000402717.3_Splice_Site	NM_004801.4	NP_004792.1	Q9ULB1	NRX1A_HUMAN	neurexin 1						adult behavior (GO:0030534)|axon guidance (GO:0007411)|calcium-dependent cell-cell adhesion (GO:0016339)|cerebellar granule cell differentiation (GO:0021707)|establishment of protein localization (GO:0045184)|extracellular matrix organization (GO:0030198)|gamma-aminobutyric acid receptor clustering (GO:0097112)|gephyrin clustering (GO:0097116)|guanylate kinase-associated protein clustering (GO:0097117)|heterophilic cell-cell adhesion (GO:0007157)|learning (GO:0007612)|N-methyl-D-aspartate receptor clustering (GO:0097114)|negative regulation of filopodium assembly (GO:0051490)|neuroligin clustering (GO:0097118)|neuromuscular process controlling balance (GO:0050885)|neuron cell-cell adhesion (GO:0007158)|neuron maturation (GO:0042551)|neurotransmitter secretion (GO:0007269)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|postsynaptic density protein 95 clustering (GO:0097119)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|receptor localization to synapse (GO:0097120)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic vesicle clustering (GO:0097091)|vocal learning (GO:0042297)|vocalization behavior (GO:0071625)	axonal growth cone (GO:0044295)|cell junction (GO:0030054)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	acetylcholine receptor binding (GO:0033130)|calcium channel regulator activity (GO:0005246)|calcium ion binding (GO:0005509)|cell adhesion molecule binding (GO:0050839)|neuroligin family protein binding (GO:0097109)|receptor activity (GO:0004872)			breast(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(33)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	58		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.192)	Lung(47;0.0813)|LUSC - Lung squamous cell carcinoma(58;0.116)			GTCGTCCCAGCTGGAAAACAA	0.413																																					.		Atlas-SNP	.											.	NRXN1	1118	.	0			c.3485-1G>T						PASS	.						79.0	76.0	77.0					2																	50464109		2203	4300	6503	SO:0001630	splice_region_variant	9378	exon20			TCCCAGCTGGAAA	AB011150	CCDS1845.1, CCDS46282.1, CCDS54360.1	2p16.3	2008-05-15			ENSG00000179915	ENSG00000179915			8008	protein-coding gene	gene with protein product		600565					Standard	NM_001135659		Approved	KIAA0578, Hs.22998	uc021vhj.1	P58400	OTTHUMG00000129263	ENST00000406316.2:c.3365-1G>T	2.37:g.50464109C>A		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	160	35	0.21875	NM_001135659	A7KRL9|O60323|Q53TJ9|Q53TQ1|Q9C079|Q9C080|Q9C081|Q9H3M2|Q9UDM6	Splice_Site	SNP	ENST00000406316.2	37	CCDS54360.1	.	.	.	.	.	.	.	.	.	.	C	24.1	4.488228	0.84854	.	.	ENSG00000179915	ENST00000342183;ENST00000536347;ENST00000401710;ENST00000404971;ENST00000406316;ENST00000405472;ENST00000401669;ENST00000536085;ENST00000402717;ENST00000406859	.	.	.	5.68	5.68	0.88126	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.7969	0.96490	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	NRXN1	50317613	1.000000	0.71417	1.000000	0.80357	0.869000	0.49853	7.731000	0.84895	2.679000	0.91253	0.650000	0.86243	.	.	.	none		0.413	NRXN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000325291.2		Intron
TNN	63923	hgsc.bcm.edu	37	1	175087884	175087884	+	Silent	SNP	C	C	T	rs2269654|rs386636935	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:175087884C>T	ENST00000239462.4	+	11	2687	c.2574C>T	c.(2572-2574)ggC>ggT	p.G858G		NM_022093.1	NP_071376.1	Q9UQP3	TENN_HUMAN	tenascin N	858	Fibronectin type-III 7. {ECO:0000255|PROSITE-ProRule:PRU00316}.				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)		p.G858G(1)		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)		TGAGGCCGGGCATGGAGTACA	0.592													C|||	866	0.172923	0.0424	0.17	5008	,	,		18416	0.3452		0.1292	False		,,,				2504	0.2188				p.G858G		Atlas-SNP	.											TNN,NS,carcinoma,0,2	TNN	297	2	1	Substitution - coding silent(1)	stomach(1)	c.C2574T						scavenged	.	C		213,4193		5,203,1995	85.0	71.0	76.0		2574	-10.0	0.0	1	dbSNP_100	76	1011,7589		83,845,3372	no	coding-synonymous	TNN	NM_022093.1		88,1048,5367	TT,TC,CC		11.7558,4.8343,9.411		858/1300	175087884	1224,11782	2203	4300	6503	SO:0001819	synonymous_variant	63923	exon11			GCCGGGCATGGAG	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.2574C>T	1.37:g.175087884C>T		Somatic	159	1	0.00628931		WXS	Illumina HiSeq	Phase_I	156	76	0.487179	NM_022093	B9EGP3|Q5R360	Silent	SNP	ENST00000239462.4	37	CCDS30943.1																																																																																			C|0.865;T|0.135	0.135	strong		0.592	TNN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084422.1	XM_040527	
PHIP	55023	hgsc.bcm.edu	37	6	79688366	79688366	+	Silent	SNP	T	T	C	rs12209235	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:79688366T>C	ENST00000275034.4	-	24	2999	c.2832A>G	c.(2830-2832)acA>acG	p.T944T	PHIP_ENST00000479165.1_5'UTR	NM_017934.5	NP_060404	Q8WWQ0	PHIP_HUMAN	pleckstrin homology domain interacting protein	944	Mediates interaction with IRS1. {ECO:0000250}.				cytoskeleton organization (GO:0007010)|insulin receptor signaling pathway (GO:0008286)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of mitosis (GO:0045840)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein import into nucleus (GO:0006606)|regulation of cell morphogenesis (GO:0022604)|regulation of growth (GO:0040008)|regulation of protein phosphorylation (GO:0001932)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	insulin receptor binding (GO:0005158)|lysine-acetylated histone binding (GO:0070577)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(10)|kidney(4)|large_intestine(20)|lung(20)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	68		all_cancers(76;0.00125)|Acute lymphoblastic leukemia(125;1.1e-05)|all_hematologic(105;0.00117)|all_epithelial(107;0.219)		BRCA - Breast invasive adenocarcinoma(397;0.231)		CTGTAATCCATGTTGATGGCA	0.343													T|||	121	0.0241613	0.0045	0.0418	5008	,	,		15169	0.001		0.0746	False		,,,				2504	0.0102				p.T944T		Atlas-SNP	.											.	PHIP	177	.	0			c.A2832G						PASS	.	T		61,4345	58.1+/-94.6	0,61,2142	104.0	99.0	101.0		2832	-1.8	1.0	6	dbSNP_120	101	627,7973	163.3+/-215.9	31,565,3704	no	coding-synonymous	PHIP	NM_017934.5		31,626,5846	CC,CT,TT		7.2907,1.3845,5.2899		944/1822	79688366	688,12318	2203	4300	6503	SO:0001819	synonymous_variant	55023	exon24			AATCCATGTTGAT	AF310250	CCDS4987.1	6q14	2013-01-09			ENSG00000146247	ENSG00000146247		"""WD repeat domain containing"", ""DDB1 and CUL4 associated factors"""	15673	protein-coding gene	gene with protein product	"""DDB1 and CUL4 associated factor 14"""	612870		WDR11		11018022	Standard	NM_017934		Approved	ndrp, FLJ20705, DCAF14, BRWD2	uc003pir.3	Q8WWQ0	OTTHUMG00000015071	ENST00000275034.4:c.2832A>G	6.37:g.79688366T>C		Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	128	59	0.460938	NM_017934	A7J992|B2RPK4|Q05CQ9|Q5VVH4|Q66I29|Q69YV1|Q8NBZ5|Q96H52|Q96ME2|Q9H261	Silent	SNP	ENST00000275034.4	37	CCDS4987.1																																																																																			T|0.952;C|0.048	0.048	strong		0.343	PHIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041297.2		
SESN1	27244	hgsc.bcm.edu	37	6	109323519	109323519	+	Missense_Mutation	SNP	G	G	T	rs2273668	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:109323519G>T	ENST00000356644.7	-	2	224	c.130C>A	c.(130-132)Cta>Ata	p.L44I	SESN1_ENST00000302071.2_5'UTR|SESN1_ENST00000436639.2_Missense_Mutation_p.L103I	NM_001199933.1	NP_001186862.1	Q9Y6P5	SESN1_HUMAN	sestrin 1	44			L -> I (in dbSNP:rs2273668). {ECO:0000269|PubMed:12607115}.		cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|negative regulation of cell proliferation (GO:0008285)|regulation of protein kinase B signaling (GO:0051896)|regulation of response to reactive oxygen species (GO:1901031)	nucleus (GO:0005634)				cervix(1)|large_intestine(3)|lung(3)|ovary(1)|skin(1)|urinary_tract(1)	10		all_cancers(87;6.45e-05)|Acute lymphoblastic leukemia(125;3.55e-10)|all_hematologic(75;1.68e-07)|all_epithelial(87;0.0106)|Colorectal(196;0.0637)		Epithelial(106;0.0014)|BRCA - Breast invasive adenocarcinoma(108;0.00146)|all cancers(137;0.0031)|OV - Ovarian serous cystadenocarcinoma(136;0.0117)		CCCTGTCCTAGTGGTCGAGGA	0.428													G|||	431	0.0860623	0.0053	0.072	5008	,	,		20704	0.0407		0.1352	False		,,,				2504	0.2014				p.L103I		Atlas-SNP	.											.	SESN1	29	.	0			c.C307A						PASS	.	G	ILE/LEU,,ILE/LEU	106,4300	80.9+/-119.3	3,100,2100	157.0	130.0	139.0		130,,307	5.6	1.0	6	dbSNP_100	139	1004,7596	215.7+/-255.0	72,860,3368	yes	missense,utr-5,missense	SESN1	NM_001199933.1,NM_001199934.1,NM_014454.2	5,,5	75,960,5468	TT,TG,GG		11.6744,2.4058,8.5345	benign,,benign	44/493,,103/552	109323519	1110,11896	2203	4300	6503	SO:0001583	missense	27244	exon2			GTCCTAGTGGTCG	AF033120	CCDS5070.1, CCDS56444.1, CCDS56445.1	6q21	2008-10-23			ENSG00000080546	ENSG00000080546			21595	protein-coding gene	gene with protein product		606103				9926927, 7938006	Standard	NM_014454		Approved	SEST1, PA26	uc003psu.3	Q9Y6P5	OTTHUMG00000015338	ENST00000356644.7:c.130C>A	6.37:g.109323519G>T	ENSP00000349061:p.Leu44Ile	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	83	45	0.542169	NM_014454	Q2M2B7|Q5T316|Q9NV00|Q9UPD5|Q9Y6P6	Missense_Mutation	SNP	ENST00000356644.7	37	CCDS56445.1	153	0.07005494505494506	4	0.008130081300813009	26	0.0718232044198895	23	0.04020979020979021	100	0.13192612137203166	G	14.18	2.458009	0.43634	0.024058	0.116744	ENSG00000080546	ENST00000436639;ENST00000356644	T;T	0.19394	2.18;2.15	5.58	5.58	0.84498	.	0.068247	0.64402	D	0.000011	T	0.06600	0.0169	N	0.08118	0	0.51482	D	0.999924	P;B	0.35348	0.496;0.243	B;B	0.34242	0.178;0.06	T	0.29882	-0.9997	10	0.27082	T	0.32	-8.8817	19.5825	0.95473	0.0:0.0:1.0:0.0	rs2273668;rs52836178;rs60044736;rs2273668	103;44	Q9Y6P5-2;Q9Y6P5	.;SESN1_HUMAN	I	103;44	ENSP00000393762:L103I;ENSP00000349061:L44I	ENSP00000349061:L44I	L	-	1	2	SESN1	109430212	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	4.365000	0.59486	2.624000	0.88883	0.655000	0.94253	CTA	G|0.927;T|0.073	0.073	strong		0.428	SESN1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000041738.4	NM_014454	
SAMSN1	64092	hgsc.bcm.edu	37	21	15873026	15873026	+	Missense_Mutation	SNP	T	T	C	rs62227165	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:15873026T>C	ENST00000400566.1	-	6	673	c.592A>G	c.(592-594)Aca>Gca	p.T198A	SAMSN1_ENST00000285670.2_Missense_Mutation_p.T266A|SAMSN1_ENST00000463807.1_5'Flank|SAMSN1_ENST00000400564.1_Missense_Mutation_p.T30A	NM_022136.4	NP_071419.3	Q9NSI8	SAMN1_HUMAN	SAM domain, SH3 domain and nuclear localization signals 1	198	SH3.				negative regulation of adaptive immune response (GO:0002820)|negative regulation of B cell activation (GO:0050869)|negative regulation of peptidyl-tyrosine phosphorylation (GO:0050732)	cell projection (GO:0042995)|cytosol (GO:0005829)|nucleus (GO:0005634)	phosphotyrosine binding (GO:0001784)|poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(1)|kidney(1)|large_intestine(3)|lung(9)|ovary(3)|pancreas(1)|prostate(3)|urinary_tract(1)	24				Epithelial(23;0.000155)|COAD - Colon adenocarcinoma(22;0.00118)|Colorectal(24;0.00961)|Lung(58;0.164)		CCCATTGGTGTTTTGCAAATA	0.378													T|||	30	0.00599042	0.0008	0.0202	5008	,	,		20252	0.0		0.0149	False		,,,				2504	0.0				p.T266A		Atlas-SNP	.											.	SAMSN1	112	.	0			c.A796G						PASS	.	T	ALA/THR	21,3673		0,21,1826	193.0	170.0	177.0		592	5.8	1.0	21	dbSNP_129	177	203,8003		2,199,3902	yes	missense	SAMSN1	NM_022136.3	58	2,220,5728	CC,CT,TT		2.4738,0.5685,1.8824	probably-damaging	198/374	15873026	224,11676	1847	4103	5950	SO:0001583	missense	64092	exon7			TTGGTGTTTTGCA	AF222927	CCDS42906.1, CCDS58786.1, CCDS74774.1	21q11	2013-01-10	2006-12-13		ENSG00000155307	ENSG00000155307		"""SAM and SH3 domain containing"", ""Sterile alpha motif (SAM) domain containing"""	10528	protein-coding gene	gene with protein product	"""nuclear localization signals, SAM and SH3 domain containing 1"", ""SAM and SH3 domain containing 2"", ""hematopoietic adapter-containing SH3 and sterile &#945;-motif (SAM) domains 1"", ""Src homology domain 3 (SH3)-containing adapter protein SH3 lymphocyte protein 2"""	607978				11536050, 11594764	Standard	NM_022136		Approved	NASH1, SASH2, SH3D6B, HACS1, SLy2	uc002yjv.1	Q9NSI8	OTTHUMG00000074317	ENST00000400566.1:c.592A>G	21.37:g.15873026T>C	ENSP00000383411:p.Thr198Ala	Somatic	188	0	0		WXS	Illumina HiSeq	Phase_I	223	141	0.632287	NM_001256370	B3KWJ3|F8WAA1|Q8NFF7|Q9C041	Missense_Mutation	SNP	ENST00000400566.1	37	CCDS42906.1	21	0.009615384615384616	0	0.0	8	0.022099447513812154	0	0.0	13	0.017150395778364115	T	21.6	4.169451	0.78452	0.005685	0.024738	ENSG00000155307	ENST00000285670;ENST00000400566;ENST00000400564	T;T;T	0.29917	3.22;3.22;1.55	5.77	5.77	0.91146	Src homology-3 domain (2);Variant SH3 (1);	0.046352	0.85682	D	0.000000	T	0.26810	0.0656	N	0.21142	0.635	0.44067	D	0.996815	P;D;D	0.71674	0.954;0.998;0.983	P;D;P	0.80764	0.761;0.994;0.895	T	0.26538	-1.0100	10	0.59425	D	0.04	-17.7917	16.0902	0.81086	0.0:0.0:0.0:1.0	rs62227165	30;266;198	Q9NSI8-2;F8WAA1;Q9NSI8	.;.;SAMN1_HUMAN	A	266;198;30	ENSP00000285670:T266A;ENSP00000383411:T198A;ENSP00000383409:T30A	ENSP00000285670:T266A	T	-	1	0	SAMSN1	14794897	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.226000	0.58606	2.194000	0.70268	0.528000	0.53228	ACA	T|0.985;C|0.015	0.015	strong		0.378	SAMSN1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157914.1		
EIF2AK3	9451	hgsc.bcm.edu	37	2	88879131	88879131	+	Silent	SNP	T	T	C	rs1805164	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:88879131T>C	ENST00000303236.3	-	11	2092	c.1791A>G	c.(1789-1791)caA>caG	p.Q597Q	EIF2AK3_ENST00000419748.1_Silent_p.Q446Q	NM_004836.5	NP_004827.4	Q9NZJ5	E2AK3_HUMAN	eukaryotic translation initiation factor 2-alpha kinase 3	597	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of signaling protein activity involved in unfolded protein response (GO:0006987)|bone mineralization (GO:0030282)|calcium-mediated signaling (GO:0019722)|cellular protein metabolic process (GO:0044267)|chondrocyte development (GO:0002063)|endocrine pancreas development (GO:0031018)|endoplasmic reticulum organization (GO:0007029)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER overload response (GO:0006983)|fat cell differentiation (GO:0045444)|insulin secretion (GO:0030073)|insulin-like growth factor receptor signaling pathway (GO:0048009)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|lactation (GO:0007595)|negative regulation of apoptotic process (GO:0043066)|negative regulation of gene expression (GO:0010629)|negative regulation of myelination (GO:0031642)|negative regulation of translation (GO:0017148)|negative regulation of translational initiation in response to stress (GO:0032057)|ossification (GO:0001503)|positive regulation of protein binding (GO:0032092)|positive regulation of signal transduction (GO:0009967)|protein autophosphorylation (GO:0046777)|protein homooligomerization (GO:0051260)|protein phosphorylation (GO:0006468)|regulation of fatty acid metabolic process (GO:0019217)|response to endoplasmic reticulum stress (GO:0034976)|skeletal system development (GO:0001501)|SREBP signaling pathway (GO:0032933)|translation (GO:0006412)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|eukaryotic translation initiation factor 2alpha kinase activity (GO:0004694)|identical protein binding (GO:0042802)|protein kinase activity (GO:0004672)|protein phosphatase binding (GO:0019903)|protein serine/threonine kinase activity (GO:0004674)			ovary(3)	3						GTCCCAGGCATTGAATTGGCT	0.338													T|||	1293	0.258187	0.1989	0.3617	5008	,	,		17972	0.3115		0.3062	False		,,,				2504	0.1605				p.Q597Q	GBM(138;671 1851 16235 39058 45249)	Atlas-SNP	.											.	EIF2AK3	160	.	0			c.A1791G						PASS	.	T		955,3451	361.1+/-315.5	104,747,1352	84.0	82.0	83.0		1791	3.2	1.0	2	dbSNP_89	83	2597,6003	420.0+/-353.3	404,1789,2107	no	coding-synonymous	EIF2AK3	NM_004836.5		508,2536,3459	CC,CT,TT		30.1977,21.675,27.3105		597/1117	88879131	3552,9454	2203	4300	6503	SO:0001819	synonymous_variant	9451	exon11			CAGGCATTGAATT	AF110146	CCDS33241.1	2p12	2008-05-21			ENSG00000172071	ENSG00000172071			3255	protein-coding gene	gene with protein product		604032				10026192, 10575235	Standard	NM_004836		Approved	PEK, PERK	uc002stc.4	Q9NZJ5	OTTHUMG00000155046	ENST00000303236.3:c.1791A>G	2.37:g.88879131T>C		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	45	15	0.333333	NM_004836	A0AVH1|A0AVH2|B2RCU9|O95846|Q53QY0|Q53SB1	Silent	SNP	ENST00000303236.3	37	CCDS33241.1																																																																																			T|0.725;C|0.275	0.275	strong		0.338	EIF2AK3-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000338233.2	NM_004836	
DSG2	1829	hgsc.bcm.edu	37	18	29125854	29125854	+	Silent	SNP	A	A	G	rs1042769	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:29125854A>G	ENST00000261590.8	+	15	2714	c.2505A>G	c.(2503-2505)acA>acG	p.T835T	RP11-75N4.2_ENST00000583706.1_RNA	NM_001943.3	NP_001934.2	Q14126	DSG2_HUMAN	desmoglein 2	835					apoptotic process (GO:0006915)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cell adhesion (GO:0007155)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|homophilic cell adhesion (GO:0007156)|maternal process involved in female pregnancy (GO:0060135)|regulation of heart rate by cardiac conduction (GO:0086091)|response to progesterone (GO:0032570)|ventricular cardiac muscle cell action potential (GO:0086005)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lateral plasma membrane (GO:0016328)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(6)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(17)|ovary(2)|prostate(4)|skin(2)|urinary_tract(1)	49			OV - Ovarian serous cystadenocarcinoma(10;0.0068)			AATTCAAGACACTAGCTGAAG	0.373													A|||	989	0.197484	0.3661	0.1383	5008	,	,		16684	0.2222		0.1004	False		,,,				2504	0.0859				p.T835T		Atlas-SNP	.											.	DSG2	115	.	0			c.A2505G						PASS	.	A		1254,2414		214,826,794	91.0	87.0	88.0		2505	-4.7	1.0	18	dbSNP_86	88	880,7298		56,768,3265	no	coding-synonymous	DSG2	NM_001943.3		270,1594,4059	GG,GA,AA		10.7606,34.1876,18.0145		835/1119	29125854	2134,9712	1834	4089	5923	SO:0001819	synonymous_variant	1829	exon15			CAAGACACTAGCT	Z26317	CCDS42423.1	18q12.1	2014-09-17				ENSG00000046604		"""Cadherins / Major cadherins"""	3049	protein-coding gene	gene with protein product		125671				1612610	Standard	NM_001943		Approved	CDHF5	uc002kwu.4	Q14126		ENST00000261590.8:c.2505A>G	18.37:g.29125854A>G		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	52	52	1	NM_001943	Q4KKU6	Silent	SNP	ENST00000261590.8	37	CCDS42423.1																																																																																			T|0.014;G|0.185	0.185	strong		0.373	DSG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447506.1	NM_001943	
MLLT1	4298	hgsc.bcm.edu	37	19	6222552	6222552	+	Silent	SNP	C	C	T	rs139655596	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:6222552C>T	ENST00000252674.7	-	6	853	c.690G>A	c.(688-690)tcG>tcA	p.S230S		NM_005934.3	NP_005925.2	Q03111	ENL_HUMAN	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 1	230					negative regulation of protein kinase activity (GO:0006469)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)	DNA binding (GO:0003677)			endometrium(3)|kidney(3)|large_intestine(2)|lung(5)|prostate(2)|skin(2)	17						CCAGCTTCCGCGAGGTGTCCT	0.647			T	MLL	AL								C|||	64	0.0127796	0.0023	0.0173	5008	,	,		11334	0.004		0.0258	False		,,,				2504	0.0194				p.S230S		Atlas-SNP	.		Dom	yes		19	19p13.3	4298	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 1 (ENL)"""		L	.	MLLT1	47	.	0			c.G690A						PASS	.	C		23,4381	29.9+/-59.1	0,23,2179	36.0	35.0	36.0		690	-9.6	0.0	19	dbSNP_134	36	220,8378	90.6+/-152.8	1,218,4080	no	coding-synonymous	MLLT1	NM_005934.3		1,241,6259	TT,TC,CC		2.5587,0.5223,1.8689		230/560	6222552	243,12759	2202	4299	6501	SO:0001819	synonymous_variant	4298	exon6			CTTCCGCGAGGTG		CCDS12160.1	19p13.3	2012-10-04	2001-11-28		ENSG00000130382	ENSG00000130382			7134	protein-coding gene	gene with protein product		159556	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 1"""				Standard	XM_005259561		Approved	ENL, LTG19, YEATS1	uc002mek.3	Q03111	OTTHUMG00000180757	ENST00000252674.7:c.690G>A	19.37:g.6222552C>T		Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	27	15	0.555556	NM_005934	Q14768	Silent	SNP	ENST00000252674.7	37	CCDS12160.1																																																																																			C|0.981;T|0.019	0.019	strong		0.647	MLLT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452909.1	NM_005934	
LPIN1	23175	hgsc.bcm.edu	37	2	11913845	11913845	+	Silent	SNP	G	G	C	rs145180224	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:11913845G>C	ENST00000256720.2	+	5	789	c.696G>C	c.(694-696)tcG>tcC	p.S232S	LPIN1_ENST00000425416.2_Silent_p.S238S|LPIN1_ENST00000396098.1_Silent_p.S238S|LPIN1_ENST00000396099.1_Silent_p.S238S|LPIN1_ENST00000449576.2_Silent_p.S281S	NM_145693.2	NP_663731.1	Q14693	LPIN1_HUMAN	lipin 1	232					cellular lipid metabolic process (GO:0044255)|fatty acid catabolic process (GO:0009062)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phosphatidylethanolamine biosynthetic process (GO:0006646)|phospholipid metabolic process (GO:0006644)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)|triglyceride biosynthetic process (GO:0019432)|triglyceride mobilization (GO:0006642)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	phosphatidate phosphatase activity (GO:0008195)			autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(15)|liver(1)|lung(10)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	45	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.11)|OV - Ovarian serous cystadenocarcinoma(76;0.173)		ACCCTAATTCGGATAGAGAGT	0.478													G|||	18	0.00359425	0.0	0.0014	5008	,	,		14112	0.0		0.0149	False		,,,				2504	0.002				p.S281S		Atlas-SNP	.											.	LPIN1	99	.	0			c.G843C						PASS	.	G		10,4396	16.8+/-37.8	0,10,2193	127.0	125.0	125.0		696	-10.7	0.5	2	dbSNP_134	125	117,8483	61.3+/-123.2	2,113,4185	no	coding-synonymous	LPIN1	NM_145693.1		2,123,6378	CC,CG,GG		1.3605,0.227,0.9765		232/891	11913845	127,12879	2203	4300	6503	SO:0001819	synonymous_variant	23175	exon6			TAATTCGGATAGA	D80010	CCDS1682.1, CCDS58699.1, CCDS58700.1, CCDS58701.1	2p25.1	2008-05-23			ENSG00000134324	ENSG00000134324			13345	protein-coding gene	gene with protein product		605518				11138012, 8724849, 16950137	Standard	NM_145693		Approved	KIAA0188	uc010yjm.3	Q14693	OTTHUMG00000119082	ENST00000256720.2:c.696G>C	2.37:g.11913845G>C		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	121	34	0.280992	NM_001261428	A8MU38|B4DET9|B4DGS4|B4DGZ6|B5MC18|B7Z858|D6W506|E7ESE7|F5GY24|Q53T25	Silent	SNP	ENST00000256720.2	37	CCDS1682.1																																																																																			G|0.991;C|0.009	0.009	strong		0.478	LPIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239296.3	NM_145693	
LAT	27040	hgsc.bcm.edu	37	16	28996225	28996225	+	5'Flank	SNP	T	T	C	rs41301797	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:28996225T>C	ENST00000360872.5	+	0	0				LAT_ENST00000564277.1_5'Flank|RP11-264B17.3_ENST00000569969.1_RNA|LAT_ENST00000395456.2_5'Flank|LAT_ENST00000454369.2_5'Flank|LAT_ENST00000395461.3_Silent_p.L15L|LAT_ENST00000566177.1_5'Flank|LAT_ENST00000354453.4_5'Flank			O43561	LAT_HUMAN	linker for activation of T cells						blood coagulation (GO:0007596)|calcium-mediated signaling (GO:0019722)|Fc-epsilon receptor signaling pathway (GO:0038095)|gene expression (GO:0010467)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|intracellular signal transduction (GO:0035556)|lymphocyte homeostasis (GO:0002260)|mast cell degranulation (GO:0043303)|platelet activation (GO:0030168)|positive regulation of signal transduction (GO:0009967)|Ras protein signal transduction (GO:0007265)|regulation of T cell activation (GO:0050863)|T cell activation (GO:0042110)|T cell receptor signaling pathway (GO:0050852)	cell-cell junction (GO:0005911)|COP9 signalosome (GO:0008180)|immunological synapse (GO:0001772)|integral component of membrane (GO:0016021)|mast cell granule (GO:0042629)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)|SH3/SH2 adaptor activity (GO:0005070)			large_intestine(2)|lung(3)|urinary_tract(1)	6		Hepatocellular(780;0.244)				TGTCCCCGTCTTGGGGGGGGC	0.721													T|||	17	0.00339457	0.0	0.0014	5008	,	,		11049	0.0		0.0159	False		,,,				2504	0.0				p.L15L		Atlas-SNP	.											.	LAT	22	.	0			c.T43C						PASS	.						6.0	8.0	7.0					16																	28996225		689	1585	2274	SO:0001631	upstream_gene_variant	27040	exon1			CCCGTCTTGGGGG	AF036905	CCDS10647.1, CCDS32425.1, CCDS45455.1, CCDS53999.1	16q13	2011-11-01			ENSG00000213658	ENSG00000213658			18874	protein-coding gene	gene with protein product	"""linker for activation of T cells, transmembrane adaptor"""	602354				9489702	Standard	NM_014387		Approved	LAT1	uc010vdj.2	O43561	OTTHUMG00000131761		16.37:g.28996225T>C	Exception_encountered	Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	69	31	0.449275	NM_001014989	B7WPI0|C7C5T6|G5E9K3|O43919	Silent	SNP	ENST00000360872.5	37	CCDS10647.1																																																																																			T|0.500;C|0.500	0.500	weak		0.721	LAT-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254688.2		
GPR78	27201	hgsc.bcm.edu	37	4	8588950	8588950	+	Missense_Mutation	SNP	C	C	T	rs61746144	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:8588950C>T	ENST00000382487.4	+	3	1369	c.952C>T	c.(952-954)Cgc>Tgc	p.R318C	GPR78_ENST00000509216.1_3'UTR	NM_080819.4	NP_543009.2	Q96P69	GPR78_HUMAN	G protein-coupled receptor 78	318					adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(4)|kidney(4)|large_intestine(1)|lung(8)|ovary(3)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)	26						GAGAACCCCGCGCCCAGCATC	0.672													C|||	22	0.00439297	0.0023	0.0029	5008	,	,		16850	0.0		0.0159	False		,,,				2504	0.001				p.R318C		Atlas-SNP	.											.	GPR78	58	.	0			c.C952T						PASS	.	C	CYS/ARG	21,4385	26.2+/-53.5	0,21,2182	42.0	46.0	45.0		952	-2.8	0.0	4	dbSNP_129	45	173,8425	77.8+/-140.4	0,173,4126	yes	missense	GPR78	NM_080819.2	180	0,194,6308	TT,TC,CC		2.0121,0.4766,1.4918	possibly-damaging	318/364	8588950	194,12810	2203	4299	6502	SO:0001583	missense	27201	exon3			ACCCCGCGCCCAG	AF411107	CCDS3403.1	4p16.1	2012-08-21			ENSG00000155269	ENSG00000155269		"""GPCR / Class A : Orphans"""	4528	protein-coding gene	gene with protein product		606921				11574155	Standard	NM_080819		Approved		uc003glk.4	Q96P69	OTTHUMG00000128483	ENST00000382487.4:c.952C>T	4.37:g.8588950C>T	ENSP00000371927:p.Arg318Cys	Somatic	247	0	0		WXS	Illumina HiSeq	Phase_I	193	86	0.445596	NM_080819	Q8NGV3	Missense_Mutation	SNP	ENST00000382487.4	37	CCDS3403.1	17	0.007783882783882784	1	0.0020325203252032522	2	0.0055248618784530384	0	0.0	14	0.018469656992084433	C	5.506	0.278329	0.10403	0.004766	0.020121	ENSG00000155269	ENST00000382487	T	0.38887	1.11	2.09	-2.81	0.05805	.	0.196794	0.33610	U	0.004723	T	0.06781	0.0173	N	0.08118	0	0.26252	N	0.978707	D	0.54207	0.965	B	0.38156	0.266	T	0.36163	-0.9759	10	0.39692	T	0.17	.	3.0938	0.06302	0.2097:0.1443:0.0:0.646	rs61746144	318	Q96P69	GPR78_HUMAN	C	318	ENSP00000371927:R318C	ENSP00000371927:R318C	R	+	1	0	GPR78	8639850	1.000000	0.71417	0.006000	0.13384	0.105000	0.19272	3.454000	0.52986	-1.075000	0.03129	0.205000	0.17691	CGC	C|0.986;T|0.014	0.014	strong		0.672	GPR78-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359201.1		
XRCC6BP1	91419	hgsc.bcm.edu	37	12	58335626	58335626	+	Missense_Mutation	SNP	A	A	T	rs3751325	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	62	0	0		WXS	Illumina HiSeq	Phase_I	56	30	0.535714	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	
C5orf45	51149	hgsc.bcm.edu	37	5	179285752	179285752	+	Silent	SNP	G	G	A	rs10060182	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:179285752G>A	ENST00000292586.6	-	1	135	c.45C>T	c.(43-45)tgC>tgT	p.C15C	C5orf45_ENST00000518235.1_Silent_p.C15C|C5orf45_ENST00000523084.1_5'UTR|C5orf45_ENST00000518219.1_Silent_p.C15C|C5orf45_ENST00000521333.1_Silent_p.C15C|C5orf45_ENST00000403396.2_Missense_Mutation_p.P31S|C5orf45_ENST00000520698.1_Silent_p.C15C|C5orf45_ENST00000376931.2_Silent_p.C15C|CTC-241N9.1_ENST00000499601.2_5'Flank	NM_016175.3	NP_057259.2	Q6NTE8	CE045_HUMAN	chromosome 5 open reading frame 45	15										breast(2)|endometrium(2)|large_intestine(2)|lung(4)|ovary(1)|prostate(1)	12						GGAAGAGGCGGCAGCTGCAGC	0.706													G|||	2240	0.447284	0.1687	0.5706	5008	,	,		14354	0.7589		0.2982	False		,,,				2504	0.5685				p.C15C		Atlas-SNP	.											C5orf45,colon,carcinoma,0,1	C5orf45	23	1	0			c.C45T						PASS	.	G	,	760,3204		108,544,1330	10.0	11.0	11.0		45,45	1.6	1.0	5	dbSNP_119	11	2081,5543		332,1417,2063	no	coding-synonymous,coding-synonymous	C5orf45	NM_001017987.2,NM_016175.3	,	440,1961,3393	AA,AG,GG		27.2954,19.1726,24.5167	,	15/289,15/344	179285752	2841,8747	1982	3812	5794	SO:0001819	synonymous_variant	51149	exon1			GAGGCGGCAGCTG		CCDS34318.1, CCDS34319.1	5q35.3	2008-07-10			ENSG00000161010	ENSG00000161010			30817	protein-coding gene	gene with protein product	"""truncated calcium binding protein"""						Standard	NM_016175		Approved	MGC65027, MGC78537, DKFZp686L2452, LOC51149	uc003mla.3	Q6NTE8	OTTHUMG00000163490	ENST00000292586.6:c.45C>T	5.37:g.179285752G>A		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	75	39	0.52	NM_016175	B5MD09|E9PAK6|Q7Z3D8|Q9BUC1|Q9UN54	Silent	SNP	ENST00000292586.6	37	CCDS34319.1	936	0.42857142857142855	86	0.17479674796747968	182	0.5027624309392266	453	0.791958041958042	215	0.2836411609498681	G	11.87	1.766751	0.31320	0.191726	0.272954	ENSG00000161010	ENST00000403396	T	0.30182	1.54	3.43	1.62	0.23740	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.43172	P	0.005027000000000004	.	.	.	.	.	.	T	0.11717	-1.0576	5	0.87932	D	0	-12.471	8.1787	0.31298	0.1954:0.0:0.8046:0.0	rs10060182;rs56833977;rs10060182	.	.	.	S	31	ENSP00000384599:P31S	ENSP00000384599:P31S	P	-	1	0	C5orf45	179218358	1.000000	0.71417	0.998000	0.56505	0.719000	0.41307	1.018000	0.30002	0.445000	0.26639	0.561000	0.74099	CCG	G|0.579;A|0.421	0.421	strong		0.706	C5orf45-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000373760.2	NM_016175	
LRRC27	80313	hgsc.bcm.edu	37	10	134151131	134151131	+	Silent	SNP	G	G	T	rs116451295	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:134151131G>T	ENST00000368614.3	+	3	378	c.273G>T	c.(271-273)ccG>ccT	p.P91P	LRRC27_ENST00000432555.2_5'UTR|LRRC27_ENST00000368612.1_Silent_p.P29P|LRRC27_ENST00000368610.3_Silent_p.P29P|LRRC27_ENST00000368613.4_Silent_p.P91P|LRRC27_ENST00000344079.5_Silent_p.P91P|LRRC27_ENST00000392638.2_Silent_p.P91P|LRRC27_ENST00000356571.4_Silent_p.P91P|LRRC27_ENST00000368615.3_Silent_p.P91P	NM_030626.2	NP_085129.1	Q9C0I9	LRC27_HUMAN	leucine rich repeat containing 27	91								p.P91P(2)		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)		AGTTGCTTCCGAACCTGACTT	0.408													G|||	85	0.0169728	0.0015	0.0115	5008	,	,		16328	0.001		0.0129	False		,,,				2504	0.0624				p.P91P		Atlas-SNP	.											LRRC27,rectum,carcinoma,0,2	LRRC27	64	2	2	Substitution - coding silent(2)	large_intestine(1)|pancreas(1)	c.G273T						PASS	.	G	,,,	15,4391	23.3+/-48.9	0,15,2188	105.0	99.0	101.0		273,273,273,273	-9.5	0.0	10	dbSNP_132	101	198,8402	86.6+/-149.0	5,188,4107	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	LRRC27	NM_001143757.1,NM_001143758.1,NM_001143759.1,NM_030626.2	,,,	5,203,6295	TT,TG,GG		2.3023,0.3404,1.6377	,,,	91/531,91/384,91/384,91/531	134151131	213,12793	2203	4300	6503	SO:0001819	synonymous_variant	80313	exon3			GCTTCCGAACCTG	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.273G>T	10.37:g.134151131G>T		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	118	56	0.474576	NM_001143757	A6NE72|A6NJB4|A6NKD3|D3DRH0|Q5SZH6|Q5SZH8|Q5SZH9|Q86XT5|Q8N7C8|Q8NA21	Silent	SNP	ENST00000368614.3	37	CCDS31316.1	16	0.007326007326007326	2	0.0040650406504065045	5	0.013812154696132596	0	0.0	9	0.011873350923482849	G	0.061	-1.225056	0.01530	0.003404	0.023023	ENSG00000148814	ENST00000450442	.	.	.	4.73	-9.47	0.00594	.	.	.	.	.	T	0.28599	0.0708	.	.	.	0.53005	D	0.999965	.	.	.	.	.	.	T	0.60398	-0.7271	4	.	.	.	-20.1907	6.1334	0.20217	0.2244:0.4943:0.2025:0.0788	.	.	.	.	L	43	.	.	R	+	2	0	LRRC27	134001121	0.957000	0.32711	0.005000	0.12908	0.040000	0.13550	-0.274000	0.08537	-4.666000	0.00037	-1.623000	0.00790	CGA	G|0.984;T|0.016	0.016	strong		0.408	LRRC27-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051058.2	XM_290462	
SNN	8303	hgsc.bcm.edu	37	16	11769963	11769963	+	Silent	SNP	C	C	T	rs1050069	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:11769963C>T	ENST00000329565.5	+	2	260	c.48C>T	c.(46-48)atC>atT	p.I16I	TXNDC11_ENST00000570917.1_5'Flank	NM_003498.5	NP_003489.1	O75324	SNN_HUMAN	stannin	16					response to abiotic stimulus (GO:0009628)|response to stress (GO:0006950)	integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)				endometrium(1)	1						TCACAGTCATCGTCATCCTCA	0.637													C|||	1281	0.255791	0.0688	0.2032	5008	,	,		18820	0.252		0.4672	False		,,,				2504	0.3323				p.I16I		Atlas-SNP	.											.	SNN	7	.	0			c.C48T						PASS	.	C		567,3827	252.1+/-258.6	42,483,1672	66.0	53.0	57.0		48	-3.7	1.0	16	dbSNP_86	57	4033,4567	556.7+/-386.9	903,2227,1170	no	coding-synonymous	SNN	NM_003498.5		945,2710,2842	TT,TC,CC		46.8953,12.904,35.401		16/89	11769963	4600,8394	2197	4300	6497	SO:0001819	synonymous_variant	8303	exon2			AGTCATCGTCATC	AF030196	CCDS10549.1	16p13	2008-02-05			ENSG00000184602	ENSG00000184602			11149	protein-coding gene	gene with protein product		603032				9657854	Standard	NM_003498		Approved		uc002dbf.3	O75324	OTTHUMG00000090535	ENST00000329565.5:c.48C>T	16.37:g.11769963C>T		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	45	45	1	NM_003498	D3DUG4|Q6FGI0	Silent	SNP	ENST00000329565.5	37	CCDS10549.1																																																																																			C|0.685;T|0.315	0.315	strong		0.637	SNN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207059.1	NM_003498	
LRP1	4035	hgsc.bcm.edu	37	12	57587714	57587714	+	Missense_Mutation	SNP	C	C	T	rs367968116		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:57587714C>T	ENST00000243077.3	+	48	8303	c.7837C>T	c.(7837-7839)Cgg>Tgg	p.R2613W	MIR1228_ENST00000408438.1_RNA	NM_002332.2	NP_002323.2	Q07954	LRP1_HUMAN	low density lipoprotein receptor-related protein 1	2613	LDL-receptor class A 13. {ECO:0000255|PROSITE-ProRule:PRU00124}.				aging (GO:0007568)|aorta morphogenesis (GO:0035909)|apoptotic cell clearance (GO:0043277)|beta-amyloid clearance (GO:0097242)|cell proliferation (GO:0008283)|cholesterol metabolic process (GO:0008203)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of platelet-derived growth factor receptor-beta signaling pathway (GO:2000587)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of Wnt signaling pathway (GO:0030178)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of lipid transport (GO:0032370)|positive regulation of protein transport (GO:0051222)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|receptor-mediated endocytosis (GO:0006898)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cholesterol transport (GO:0032374)|regulation of phospholipase A2 activity (GO:0032429)|retinoid metabolic process (GO:0001523)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	apolipoprotein binding (GO:0034185)|calcium ion binding (GO:0005509)|lipoprotein particle receptor binding (GO:0070325)|lipoprotein transporter activity (GO:0042954)|poly(A) RNA binding (GO:0044822)|protein complex binding (GO:0032403)|receptor activity (GO:0004872)			NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(33)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(26)|lung(58)|ovary(10)|pancreas(2)|prostate(11)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	184				BRCA - Breast invasive adenocarcinoma(357;0.0103)	Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031)	GTTCCGCTGCCGGGACGGGAC	0.607																																					p.R2613W		Atlas-SNP	.											LRP1,NS,lymphoid_neoplasm,-1,1	LRP1	428	1	0			c.C7837T						PASS	.	C	TRP/ARG	0,4406		0,0,2203	97.0	89.0	92.0		7837	4.2	1.0	12		92	1,8599	1.2+/-3.3	0,1,4299	no	missense	LRP1	NM_002332.2	101	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	2613/4545	57587714	1,13005	2203	4300	6503	SO:0001583	missense	4035	exon48			CGCTGCCGGGACG	X13916	CCDS8932.1	12q13.3	2013-05-28	2010-01-26		ENSG00000123384	ENSG00000123384		"""CD molecules"", ""Low density lipoprotein receptors"""	6692	protein-coding gene	gene with protein product		107770	"""alpha-2-macroglobulin receptor"""	APR, A2MR		2548950	Standard	NM_002332		Approved	LRP, CD91, LRP1A, APOER	uc001snd.3	Q07954	OTTHUMG00000044412	ENST00000243077.3:c.7837C>T	12.37:g.57587714C>T	ENSP00000243077:p.Arg2613Trp	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	105	38	0.361905	NM_002332	Q2PP12|Q86SW0|Q8IVG8	Missense_Mutation	SNP	ENST00000243077.3	37	CCDS8932.1	.	.	.	.	.	.	.	.	.	.	C	15.34	2.803636	0.50315	0.0	1.16E-4	ENSG00000123384	ENST00000243077	D	0.95690	-3.78	5.09	4.19	0.49359	.	0.164278	0.37261	N	0.002175	D	0.96617	0.8896	M	0.62088	1.915	0.80722	D	1	D	0.76494	0.999	D	0.63283	0.913	D	0.96868	0.9637	10	0.66056	D	0.02	.	14.7368	0.69422	0.0:0.8543:0.1457:0.0	.	2613	Q07954	LRP1_HUMAN	W	2613	ENSP00000243077:R2613W	ENSP00000243077:R2613W	R	+	1	2	LRP1	55873981	1.000000	0.71417	1.000000	0.80357	0.515000	0.34225	1.355000	0.34068	1.368000	0.46115	0.650000	0.86243	CGG	.	.	weak		0.607	LRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412772.2	NM_002332	
PRR21	643905	hgsc.bcm.edu	37	2	240982389	240982389	+	Missense_Mutation	SNP	C	C	G	rs143417758		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:240982389C>G	ENST00000408934.1	-	1	10	c.11G>C	c.(10-12)tGt>tCt	p.C4S		NM_001080835.1	NP_001074304.1	Q8WXC7	PRR21_HUMAN	proline rich 21	4										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						TGTGGATGAACAGGCATGCAT	0.567																																					p.C4S		Atlas-SNP	.											.	PRR21	53	.	0			c.G11C						PASS	.						73.0	62.0	65.0					2																	240982389		2172	4269	6441	SO:0001583	missense	643905	exon1			GATGAACAGGCAT	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.11G>C	2.37:g.240982389C>G	ENSP00000386166:p.Cys4Ser	Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	12	7	0.583333	NM_001080835		Missense_Mutation	SNP	ENST00000408934.1	37	CCDS33417.1	.	.	.	.	.	.	.	.	.	.	c	5.954	0.359922	0.11296	.	.	ENSG00000221961	ENST00000408934;ENST00000486799	T;T	0.37752	1.18;1.18	0.149	0.149	0.14863	.	.	.	.	.	T	0.18173	0.0436	N	0.08118	0	0.19945	N	0.999941	P	0.37500	0.597	B	0.39119	0.291	T	0.15435	-1.0437	8	0.42905	T	0.14	.	.	.	.	.	4	Q8WXC7	PRR21_HUMAN	S	4	ENSP00000386166:C4S;ENSP00000418240:C4S	ENSP00000386166:C4S	C	-	2	0	PRR21	240631062	0.000000	0.05858	0.009000	0.14445	0.017000	0.09413	-0.776000	0.04674	0.192000	0.20272	0.195000	0.17529	TGT	.	.	weak		0.567	PRR21-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001080835	
ZPLD1	131368	hgsc.bcm.edu	37	3	102157365	102157365	+	Missense_Mutation	SNP	A	A	T	rs6784362	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:102157365A>T	ENST00000491959.1	+	9	916	c.34A>T	c.(34-36)Att>Ttt	p.I12F	ZPLD1_ENST00000306176.1_Missense_Mutation_p.I28F|ZPLD1_ENST00000466937.1_Missense_Mutation_p.I12F			Q8TCW7	ZPLD1_HUMAN	zona pellucida-like domain containing 1	12			I -> F (in dbSNP:rs6784362).			integral component of membrane (GO:0016021)				central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(18)|ovary(2)|skin(3)	35						GCTTCTAACAATTAGAGTGCT	0.438													A|||	484	0.0966454	0.09	0.1585	5008	,	,		18750	0.0357		0.1372	False		,,,				2504	0.0828				p.I28F		Atlas-SNP	.											ZPLD1,NS,carcinoma,-2,1	ZPLD1	82	1	0			c.A82T						PASS	.	A	PHE/ILE	404,4002	201.8+/-224.7	18,368,1817	151.0	134.0	140.0		82	3.8	1.0	3	dbSNP_116	140	1330,7270	260.8+/-283.4	95,1140,3065	yes	missense	ZPLD1	NM_175056.1	21	113,1508,4882	TT,TA,AA		15.4651,9.1693,13.3323	benign	28/432	102157365	1734,11272	2203	4300	6503	SO:0001583	missense	131368	exon2			CTAACAATTAGAG	AY090780	CCDS2947.1	3q12.3	2009-03-25			ENSG00000170044	ENSG00000170044			27022	protein-coding gene	gene with protein product		615915				18632209	Standard	NM_175056		Approved		uc003dvt.1	Q8TCW7	OTTHUMG00000159229	ENST00000491959.1:c.34A>T	3.37:g.102157365A>T	ENSP00000420265:p.Ile12Phe	Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	154	63	0.409091	NM_175056	Q49AS1|Q8WU36	Missense_Mutation	SNP	ENST00000491959.1	37		219	0.10027472527472528	40	0.08130081300813008	58	0.16022099447513813	16	0.027972027972027972	105	0.13852242744063326	A	10.93	1.490772	0.26774	0.091693	0.154651	ENSG00000170044	ENST00000491959;ENST00000306176;ENST00000466937	T;T;T	0.80653	-1.4;-1.4;-1.4	5.0	3.81	0.43845	.	0.357489	0.34484	N	0.003924	T	0.00328	0.0010	N	0.08118	0	0.31825	P	0.625469	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.04128	-1.0975	9	0.10902	T	0.67	-11.2344	6.1708	0.20416	0.7811:0.0:0.0772:0.1417	rs6784362;rs17771116;rs52789307;rs6784362	28;12	Q8TCW7-2;Q8TCW7	.;ZPLD1_HUMAN	F	12;28;12	ENSP00000420265:I12F;ENSP00000307801:I28F;ENSP00000418253:I12F	ENSP00000307801:I28F	I	+	1	0	ZPLD1	103640055	0.003000	0.15002	0.972000	0.41901	0.976000	0.68499	1.147000	0.31602	0.723000	0.32274	0.482000	0.46254	ATT	A|0.881;N|0.000	.	strong		0.438	ZPLD1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000353984.1	NM_175056	
ARNTL	406	hgsc.bcm.edu	37	11	13380068	13380068	+	Silent	SNP	C	C	T	rs138340325	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:13380068C>T	ENST00000403290.1	+	8	664	c.309C>T	c.(307-309)aaC>aaT	p.N103N	ARNTL_ENST00000401424.1_Silent_p.N60N|ARNTL_ENST00000497429.1_3'UTR|ARNTL_ENST00000389708.3_Silent_p.N103N|ARNTL_ENST00000403482.3_Silent_p.N101N|ARNTL_ENST00000361003.4_Silent_p.N103N|ARNTL_ENST00000403510.3_Silent_p.N60N|ARNTL_ENST00000389707.4_Silent_p.N103N|ARNTL_ENST00000396441.3_Silent_p.N103N			O00327	BMAL1_HUMAN	aryl hydrocarbon receptor nuclear translocator-like	103	bHLH. {ECO:0000255|PROSITE- ProRule:PRU00981}.				circadian regulation of gene expression (GO:0032922)|circadian rhythm (GO:0007623)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of glucocorticoid receptor signaling pathway (GO:2000323)|negative regulation of TOR signaling (GO:0032007)|negative regulation of transcription, DNA-templated (GO:0045892)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of circadian rhythm (GO:0042753)|positive regulation of skeletal muscle cell differentiation (GO:2001016)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein import into nucleus, translocation (GO:0000060)|regulation of cell cycle (GO:0051726)|regulation of cellular senescence (GO:2000772)|regulation of hair cycle (GO:0042634)|regulation of insulin secretion (GO:0050796)|regulation of neurogenesis (GO:0050767)|regulation of protein catabolic process (GO:0042176)|regulation of transcription, DNA-templated (GO:0006355)|regulation of type B pancreatic cell development (GO:2000074)|response to redox state (GO:0051775)|spermatogenesis (GO:0007283)	chromatoid body (GO:0033391)|nuclear body (GO:0016604)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	aryl hydrocarbon receptor binding (GO:0017162)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|E-box binding (GO:0070888)|Hsp90 protein binding (GO:0051879)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity (GO:0000982)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding (GO:0043565)|signal transducer activity (GO:0004871)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			breast(1)|endometrium(2)|large_intestine(11)|lung(5)|upper_aerodigestive_tract(1)	20				Epithelial(150;0.0243)		CAACATGCAACGCAATGTCCA	0.413																																					p.N103N		Atlas-SNP	.											ARNTL,NS,carcinoma,0,1	ARNTL	46	1	0			c.C309T						scavenged	.	C	,,	0,4400		0,0,2200	174.0	184.0	181.0		309,180,309	-9.0	0.2	11	dbSNP_134	181	4,8584	3.7+/-12.6	0,4,4290	no	coding-synonymous,coding-synonymous,coding-synonymous	ARNTL	NM_001030272.1,NM_001030273.1,NM_001178.4	,,	0,4,6490	TT,TC,CC		0.0466,0.0,0.0308	,,	103/626,60/583,103/626	13380068	4,12984	2200	4294	6494	SO:0001819	synonymous_variant	406	exon7			ATGCAACGCAATG	D89722	CCDS31430.1, CCDS44543.1, CCDS73259.1	11p15	2013-05-21			ENSG00000133794	ENSG00000133794		"""Basic helix-loop-helix proteins"""	701	protein-coding gene	gene with protein product		602550				9144434, 9079689	Standard	XM_005252930		Approved	MOP3, JAP3, BMAL1, PASD3, bHLHe5	uc001mkp.3	O00327	OTTHUMG00000150623	ENST00000403290.1:c.309C>T	11.37:g.13380068C>T		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	94	3	0.0319149	NM_001030272	A2I2N6|A8K645|B5ME11|B7WPG7|D3DQW6|O00313|O00314|O00315|O00316|O00317|Q4G136|Q8IUT4|Q99631|Q99649	Silent	SNP	ENST00000403290.1	37																																																																																				C|1.000;T|0.000	0.000	strong		0.413	ARNTL-004	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000319173.1	NM_001178	
GAS8	2622	hgsc.bcm.edu	37	16	90095558	90095558	+	Intron	SNP	C	C	T	rs76646627		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:90095558C>T	ENST00000268699.4	+	2	212				GAS8_ENST00000540721.1_Intron|GAS8_ENST00000536122.1_Intron|C16orf3_ENST00000408886.2_Missense_Mutation_p.G65S	NM_001481.2	NP_001472.1	O95995	GAS8_HUMAN	growth arrest-specific 8						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)		p.G65S(1)		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)		acggggcagcctacggggcag	0.672																																					p.G65S		Atlas-SNP	.											C16orf3,NS,carcinoma,0,2	C16orf3	14	2	1	Substitution - Missense(1)	lung(1)	c.G193A						scavenged	.						25.0	20.0	21.0					16																	90095558		2191	4298	6489	SO:0001627	intron_variant	750	exon1			GGCAGCCTACGGG	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.90+1428C>T	16.37:g.90095558C>T		Somatic	92	3	0.0326087		WXS	Illumina HiSeq	Phase_I	127	20	0.15748	NM_001214	B2RCT1|B7Z4U1|G3V1L5|Q2M234	Missense_Mutation	SNP	ENST00000268699.4	37	CCDS10992.1	.	.	.	.	.	.	.	.	.	.	C	9.046	0.990885	0.18966	.	.	ENSG00000221819	ENST00000408886	T	0.57595	0.39	1.2	-1.14	0.09741	.	.	.	.	.	T	0.23492	0.0568	N	0.08118	0	0.09310	N	1	B	0.22604	0.072	B	0.14578	0.011	T	0.14755	-1.0461	8	.	.	.	.	2.4936	0.04616	0.0:0.4385:0.3231:0.2384	.	73	O95177	CP003_HUMAN	S	65	ENSP00000386218:G65S	.	G	-	1	0	C16orf3	88623059	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.145000	0.10265	-0.326000	0.08564	0.407000	0.27541	GGC	C|0.500;T|0.500	0.500	weak		0.672	GAS8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000272877.2		
CDHR1	92211	hgsc.bcm.edu	37	10	85978991	85978991	+	IGR	SNP	C	C	T	rs7895270	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:85978991C>T	ENST00000372117.3	+	0	5428				CDHR1_ENST00000332904.3_Silent_p.L733L	NM_033100.2	NP_149091.1	Q96JP9	CDHR1_HUMAN	cadherin-related family member 1						cellular process (GO:0009987)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)	integral component of plasma membrane (GO:0005887)|photoreceptor outer segment membrane (GO:0042622)	calcium ion binding (GO:0005509)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(21)|ovary(1)|prostate(1)|skin(1)	36						TAATGTGAATCTGTACTCTAG	0.408													C|||	1392	0.277955	0.5227	0.2291	5008	,	,		18558	0.0655		0.2286	False		,,,				2504	0.2515				p.L733L		Atlas-SNP	.											.	CDHR1	122	.	0			c.C2197T						PASS	.																																			SO:0001628	intergenic_variant	92211	exon17			GTGAATCTGTACT	AB053448	CCDS7372.1, CCDS53548.1	10q23.1	2014-01-28	2010-01-25	2010-01-25	ENSG00000148600	ENSG00000148600		"""Cadherins / Cadherin-related"""	14550	protein-coding gene	gene with protein product		609502	"""protocadherin 21"""	PCDH21		11597768	Standard	NM_001171971		Approved	KIAA1775, CORD15, RP65	uc001kcv.3	Q96JP9	OTTHUMG00000018634		10.37:g.85978991C>T		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	93	51	0.548387	NM_001171971	Q69YZ8|Q8IXY5	Silent	SNP	ENST00000372117.3	37	CCDS7372.1																																																																																			C|0.735;T|0.265	0.265	strong		0.408	CDHR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049111.1	NM_033100	
RAB40B	10966	hgsc.bcm.edu	37	17	80616397	80616397	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:80616397C>T	ENST00000571995.1	-	5	666	c.535G>A	c.(535-537)Ggg>Agg	p.G179R	RAB40B_ENST00000571880.1_5'Flank|RAB40B_ENST00000538809.2_Missense_Mutation_p.M128I|RAB40B_ENST00000269347.6_5'UTR	NM_006822.2	NP_006813.1	Q12829	RB40B_HUMAN	RAB40B, member RAS oncogene family	179	SOCS box. {ECO:0000255|PROSITE- ProRule:PRU00194}.				protein transport (GO:0015031)|protein ubiquitination (GO:0016567)|small GTPase mediated signal transduction (GO:0007264)	plasma membrane (GO:0005886)	GTP binding (GO:0005525)			central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|urinary_tract(2)	10	Breast(20;0.00132)|all_neural(118;0.0952)	all_cancers(8;0.072)|all_epithelial(8;0.139)	BRCA - Breast invasive adenocarcinoma(99;0.0262)|OV - Ovarian serous cystadenocarcinoma(97;0.061)			CGGTCCATCCCATGCCGCAGC	0.662																																					p.G179R		Atlas-SNP	.											.	RAB40B	24	.	0			c.G535A						PASS	.						65.0	66.0	66.0					17																	80616397		2203	4300	6503	SO:0001583	missense	10966	exon5			CCATCCCATGCCG	U05227	CCDS11816.1	17q25.3	2014-08-12			ENSG00000141542	ENSG00000141542		"""RAB, member RAS oncogene"""	18284	protein-coding gene	gene with protein product						11697911	Standard	NM_006822		Approved	SEC4L, RAR	uc002kft.3	Q12829	OTTHUMG00000177806	ENST00000571995.1:c.535G>A	17.37:g.80616397C>T	ENSP00000461785:p.Gly179Arg	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	119	31	0.260504	NM_006822	Q8WVG3	Missense_Mutation	SNP	ENST00000571995.1	37	CCDS11816.1	.	.	.	.	.	.	.	.	.	.	C	18.88	3.716630	0.68844	.	.	ENSG00000141542	ENST00000269347;ENST00000538809	.	.	.	4.24	4.24	0.50183	SOCS protein, C-terminal (1);	0.000000	0.64402	D	0.000003	T	0.62600	0.2441	L	0.47716	1.5	0.43412	D	0.995555	B	0.25609	0.13	B	0.36567	0.228	T	0.64702	-0.6345	9	0.51188	T	0.08	.	17.0842	0.86606	0.0:1.0:0.0:0.0	.	179	Q12829	RB40B_HUMAN	R	179;213	.	ENSP00000269347:G179R	G	-	1	0	RAB40B	78209686	1.000000	0.71417	0.998000	0.56505	0.998000	0.95712	7.573000	0.82421	2.283000	0.76528	0.591000	0.81541	GGG	.	.	none		0.662	RAB40B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439007.1		
ZNF587	84914	hgsc.bcm.edu	37	19	58371202	58371202	+	Silent	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:58371202C>T	ENST00000339656.5	+	3	1604	c.1422C>T	c.(1420-1422)ggC>ggT	p.G474G	ZNF814_ENST00000595295.1_Intron|ZNF587_ENST00000423137.1_Silent_p.G473G|ZNF587_ENST00000419854.1_Silent_p.G431G|ZNF814_ENST00000597342.1_Intron|ZNF814_ENST00000597832.1_Intron|ZNF814_ENST00000596604.1_Intron|ZNF814_ENST00000597652.1_5'Flank	NM_001204817.1|NM_032828.3	NP_001191746.1|NP_116217.1	Q96SQ5	ZN587_HUMAN	zinc finger protein 587	474					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(1)|lung(4)|ovary(1)|pancreas(1)|stomach(1)	15		Colorectal(82;0.000256)|all_neural(62;0.0577)|Breast(46;0.147)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0264)		AATTATTTGGCAATAAGCACA	0.433																																					p.G474G	Pancreas(59;641 1233 1885 20055 50741)	Atlas-SNP	.											.	ZNF587	53	.	0			c.C1422T						PASS	.						154.0	150.0	151.0					19																	58371202		2203	4300	6503	SO:0001819	synonymous_variant	84914	exon3			ATTTGGCAATAAG	AF294842	CCDS12964.1, CCDS56110.1	19q13.43	2013-01-08				ENSG00000198466		"""Zinc fingers, C2H2-type"", ""-"""	30955	protein-coding gene	gene with protein product						10520746	Standard	NM_032828		Approved	ZF6, FLJ14710, UBF-fl, FLJ20813	uc002qql.3	Q96SQ5	OTTHUMG00000154901	ENST00000339656.5:c.1422C>T	19.37:g.58371202C>T		Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	224	13	0.0580357	NM_032828	A0AV72|G3V0H5|Q6ZMK8	Silent	SNP	ENST00000339656.5	37	CCDS12964.1																																																																																			.	.	none		0.433	ZNF587-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337594.2	NM_032828	
ATAD5	79915	hgsc.bcm.edu	37	17	29214387	29214387	+	Missense_Mutation	SNP	T	T	C	rs11657270	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:29214387T>C	ENST00000321990.4	+	19	4633	c.4255T>C	c.(4255-4257)Tat>Cat	p.Y1419H		NM_024857.3	NP_079133.3	Q96QE3	ATAD5_HUMAN	ATPase family, AAA domain containing 5	1419			Y -> H (in dbSNP:rs11657270).		cellular response to DNA damage stimulus (GO:0006974)	nucleus (GO:0005634)	ATP binding (GO:0005524)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(3)|large_intestine(18)|lung(13)|ovary(3)|pancreas(1)	51		all_hematologic(16;0.0202)|Acute lymphoblastic leukemia(14;0.0238)|Myeloproliferative disorder(56;0.0393)				ATTAACCCTTTATCGTAAGTT	0.368													T|||	723	0.144369	0.0719	0.1859	5008	,	,		18356	0.1359		0.1074	False		,,,				2504	0.2597				p.Y1419H		Atlas-SNP	.											.	ATAD5	150	.	0			c.T4255C						PASS	.	T	HIS/TYR	323,4083	166.2+/-197.5	14,295,1894	77.0	82.0	80.0		4255	2.0	0.8	17	dbSNP_120	80	898,7702	196.8+/-241.6	37,824,3439	yes	missense	ATAD5	NM_024857.3	83	51,1119,5333	CC,CT,TT		10.4419,7.3309,9.388	benign	1419/1845	29214387	1221,11785	2203	4300	6503	SO:0001583	missense	79915	exon19			ACCCTTTATCGTA		CCDS11260.1	17q11.2	2010-04-21	2007-02-08	2007-02-08	ENSG00000176208	ENSG00000176208		"""ATPases / AAA-type"""	25752	protein-coding gene	gene with protein product	"""enhanced level of genomic instability 1 homolog (S. cerevisiae)"""	609534	"""chromosome 17 open reading frame 41"""	C17orf41		15983387, 11468690, 19755857	Standard	NM_024857		Approved	FLJ12735, FRAG1, ELG1	uc002hfs.1	Q96QE3	OTTHUMG00000132794	ENST00000321990.4:c.4255T>C	17.37:g.29214387T>C	ENSP00000313171:p.Tyr1419His	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	105	48	0.457143	NM_024857	Q05DH0|Q69YR6|Q9H9I1	Missense_Mutation	SNP	ENST00000321990.4	37	CCDS11260.1	274	0.12545787545787546	45	0.09146341463414634	65	0.17955801104972377	92	0.16083916083916083	72	0.09498680738786279	T	2.914	-0.224752	0.06022	0.073309	0.104419	ENSG00000176208	ENST00000321990	T	0.16597	2.33	5.77	1.95	0.26073	.	0.817337	0.12029	N	0.506113	T	0.00012	0.0000	N	0.04508	-0.205	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.44298	-0.9337	9	0.14656	T	0.56	.	8.7899	0.34843	0.0:0.323:0.0:0.677	rs11657270;rs11657270	1419	Q96QE3	ATAD5_HUMAN	H	1419	ENSP00000313171:Y1419H	ENSP00000313171:Y1419H	Y	+	1	0	ATAD5	26238513	0.108000	0.22018	0.774000	0.31636	0.600000	0.36913	0.445000	0.21677	0.425000	0.26087	-1.111000	0.02071	TAT	T|0.887;C|0.113	0.113	strong		0.368	ATAD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256206.2	NM_024857	
AAMDC	28971	hgsc.bcm.edu	37	11	77583266	77583266	+	Missense_Mutation	SNP	G	G	A	rs2186564	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:77583266G>A	ENST00000526415.1	+	5	447	c.274G>A	c.(274-276)Gtg>Atg	p.V92M	AAMDC_ENST00000527134.1_Intron|AAMDC_ENST00000304716.8_Intron|AAMDC_ENST00000533193.1_Missense_Mutation_p.V138M|RP11-91P24.7_ENST00000525594.1_RNA|AAMDC_ENST00000525409.1_Missense_Mutation_p.V60M|AAMDC_ENST00000393427.2_Missense_Mutation_p.V92M|RP11-91P24.6_ENST00000530972.1_RNA|AAMDC_ENST00000525034.1_Missense_Mutation_p.V111M|AAMDC_ENST00000532481.1_Intron			Q9H7C9	AAMDC_HUMAN	adipogenesis associated, Mth938 domain containing	92	MTH138-like domain. {ECO:0000250}.		V -> M (in dbSNP:rs2186564).		negative regulation of apoptotic process (GO:0043066)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	cytoplasm (GO:0005737)		p.V92M(1)									TGGCATTGATGTGCGGGTCCT	0.552													G|||	706	0.140974	0.1286	0.1888	5008	,	,		20307	0.1766		0.1004	False		,,,				2504	0.1288				p.V92M		Atlas-SNP	.											C11orf67,NS,carcinoma,0,1	.	.	1	1	Substitution - Missense(1)	stomach(1)	c.G274A						PASS	.	G	MET/VAL	526,3874	239.9+/-250.9	28,470,1702	114.0	103.0	107.0		274	5.3	1.0	11	dbSNP_96	107	827,7757	191.1+/-237.4	37,753,3502	yes	missense	C11orf67	NM_024684.2	21	65,1223,5204	AA,AG,GG		9.6342,11.9545,10.4205	probably-damaging	92/123	77583266	1353,11631	2200	4292	6492	SO:0001583	missense	28971	exon4			ATTGATGTGCGGG	BC016854	CCDS8254.1	11q14.1	2012-10-08	2012-10-08	2012-10-08	ENSG00000087884	ENSG00000087884			30205	protein-coding gene	gene with protein product			"""chromosome 11 open reading frame 67"""	C11orf67		12477932	Standard	NM_024684		Approved	PTD015, FLJ21035, CK067	uc001oyq.3	Q9H7C9	OTTHUMG00000166651	ENST00000526415.1:c.274G>A	11.37:g.77583266G>A	ENSP00000431808:p.Val92Met	Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	140	108	0.771429	NM_024684	Q96AQ4|Q9Y6B1	Missense_Mutation	SNP	ENST00000526415.1	37	CCDS8254.1	320	0.14652014652014653	76	0.15447154471544716	56	0.15469613259668508	112	0.1958041958041958	76	0.10026385224274406	G	22.1	4.244571	0.79912	0.119545	0.096342	ENSG00000087884	ENST00000526415;ENST00000393427;ENST00000525409;ENST00000533193;ENST00000525034	D;D;D;D;D	0.81579	-1.51;-1.51;-1.51;-1.51;-1.51	5.28	5.28	0.74379	.	0.000000	0.64402	D	0.000001	T	0.00552	0.0018	M	0.74881	2.28	0.20074	P	0.9999344981	D	0.71674	0.998	D	0.67725	0.953	T	0.03887	-1.0995	9	0.54805	T	0.06	-10.6555	14.3405	0.66622	0.0:0.1481:0.8519:0.0	rs2186564;rs52804138;rs57349472;rs2186564	92	Q9H7C9	CK067_HUMAN	M	92;92;60;138;111	ENSP00000431808:V92M;ENSP00000377078:V92M;ENSP00000433956:V60M;ENSP00000436086:V138M;ENSP00000432830:V111M	ENSP00000377078:V92M	V	+	1	0	C11orf67	77260914	1.000000	0.71417	0.998000	0.56505	0.986000	0.74619	6.493000	0.73658	2.746000	0.94184	0.655000	0.94253	GTG	G|0.876;N|0.000	.	strong		0.552	AAMDC-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390976.1	NM_024684	
WDR27	253769	hgsc.bcm.edu	37	6	170070723	170070723	+	Missense_Mutation	SNP	A	A	G	rs4236176	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:170070723A>G	ENST00000448612.1	-	4	507	c.398T>C	c.(397-399)cTg>cCg	p.L133P	WDR27_ENST00000423258.1_Intron|WDR27_ENST00000420344.2_Missense_Mutation_p.L133P|WDR27_ENST00000333572.6_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	67	0	0		WXS	Illumina HiSeq	Phase_I	41	22	0.536585	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	
C10orf120	399814	hgsc.bcm.edu	37	10	124457906	124457906	+	Silent	SNP	C	C	T	rs2901343	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:124457906C>T	ENST00000329446.4	-	3	382	c.351G>A	c.(349-351)ccG>ccA	p.P117P		NM_001010912.1	NP_001010912.1	Q5SQS8	CJ120_HUMAN	chromosome 10 open reading frame 120	117										endometrium(1)|kidney(1)|large_intestine(6)|lung(9)|skin(2)|stomach(1)|urinary_tract(1)	21		all_neural(114;0.169)|Glioma(114;0.222)				GTTTGTAGTCCGGAGACAGCA	0.448													C|||	2208	0.440895	0.4062	0.3343	5008	,	,		21925	0.5179		0.4046	False		,,,				2504	0.5215				p.P117P		Atlas-SNP	.											.	C10orf120	55	.	0			c.G351A						PASS	.	C		1826,2580	533.4+/-373.7	390,1046,767	199.0	207.0	204.0		351	-5.8	0.0	10	dbSNP_101	204	3552,5048	517.2+/-379.0	737,2078,1485	no	coding-synonymous	C10orf120	NM_001010912.1		1127,3124,2252	TT,TC,CC		41.3023,41.4435,41.3501		117/336	124457906	5378,7628	2203	4300	6503	SO:0001819	synonymous_variant	399814	exon3			GTAGTCCGGAGAC		CCDS31302.1	10q26.13	2012-06-12			ENSG00000183559	ENSG00000183559			25707	protein-coding gene	gene with protein product							Standard	NM_001010912		Approved	bA318C4.1	uc001lgn.3	Q5SQS8	OTTHUMG00000019187	ENST00000329446.4:c.351G>A	10.37:g.124457906C>T		Somatic	262	0	0		WXS	Illumina HiSeq	Phase_I	166	73	0.439759	NM_001010912	B2RU17	Silent	SNP	ENST00000329446.4	37	CCDS31302.1	942	0.43131868131868134	220	0.44715447154471544	144	0.39779005524861877	277	0.48426573426573427	301	0.3970976253298153	C	3.300	-0.143157	0.06669	0.414435	0.413023	ENSG00000183559	ENST00000432000	.	.	.	4.82	-5.83	0.02325	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.38329	-0.9666	3	.	.	.	-0.0498	8.0998	0.30850	0.0:0.4681:0.1245:0.4073	rs2901343;rs60009641;rs2901343	.	.	.	Q	110	.	.	R	-	2	0	C10orf120	124447896	0.076000	0.21285	0.000000	0.03702	0.001000	0.01503	-0.598000	0.05706	-1.334000	0.02244	-1.379000	0.01178	CGG	C|0.580;T|0.420	0.420	strong		0.448	C10orf120-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050803.1	NM_001010912	
SRSF9	8683	hgsc.bcm.edu	37	12	120907332	120907332	+	Silent	SNP	C	C	T	rs11548264	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:120907332C>T	ENST00000229390.3	-	1	264	c.81G>A	c.(79-81)gaG>gaA	p.E27E	DYNLL1_ENST00000392509.2_5'Flank|DYNLL1_ENST00000548342.1_5'Flank	NM_003769.2	NP_003760.1	Q13242	SRSF9_HUMAN	serine/arginine-rich splicing factor 9	27	RRM 1. {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 splice site selection (GO:0006376)|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)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			cervix(1)|endometrium(1)|large_intestine(1)|lung(3)|prostate(1)|skin(1)|urinary_tract(1)	9						CCAAGTCCTTCTCGCGCACGT	0.697													C|||	204	0.0407348	0.0008	0.0447	5008	,	,		6453	0.0099		0.0606	False		,,,				2504	0.1033				p.E27E		Atlas-SNP	.											.	SRSF9	14	.	0			c.G81A						PASS	.	C		43,4363	47.5+/-82.1	1,41,2161	44.0	42.0	43.0		81	4.4	1.0	12	dbSNP_120	43	498,8102	139.5+/-196.2	17,464,3819	no	coding-synonymous	SRSF9	NM_003769.2		18,505,5980	TT,TC,CC		5.7907,0.9759,4.1596		27/222	120907332	541,12465	2203	4300	6503	SO:0001819	synonymous_variant	8683	exon1			GTCCTTCTCGCGC	U30825	CCDS9199.1	12q24.31	2013-02-12	2010-06-22	2010-06-22	ENSG00000111786	ENSG00000111786		"""Serine/arginine-rich splicing factors"", ""RNA binding motif (RRM) containing"""	10791	protein-coding gene	gene with protein product	"""SR splicing factor 9"""	601943	"""splicing factor, arginine/serine-rich 9"""	SFRS9		7556075, 20516191	Standard	NM_003769		Approved	SRp30c	uc001tyi.3	Q13242	OTTHUMG00000047790	ENST00000229390.3:c.81G>A	12.37:g.120907332C>T		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	46	18	0.391304	NM_003769	Q52LD1	Silent	SNP	ENST00000229390.3	37	CCDS9199.1	65	0.02976190476190476	1	0.0020325203252032522	21	0.058011049723756904	1	0.0017482517482517483	42	0.055408970976253295	C	12.66	2.003325	0.35320	0.009759	0.057907	ENSG00000111786	ENST00000550458	T	0.21031	2.03	4.45	4.45	0.53987	.	0.138702	0.52532	D	0.000080	T	0.06462	0.0166	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.01102	-1.1451	7	0.62326	D	0.03	.	16.0652	0.80865	0.0:1.0:0.0:0.0	rs11548264;rs11548264	.	.	.	K	15	ENSP00000449030:E15K	ENSP00000449030:E15K	E	-	1	0	SRSF9	119391715	0.051000	0.20477	1.000000	0.80357	0.944000	0.59088	0.367000	0.20382	2.316000	0.78162	0.597000	0.82753	GAA	C|0.961;T|0.039	0.039	strong		0.697	SRSF9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000108983.2	NM_003769	
ELOVL1	64834	hgsc.bcm.edu	37	1	43830438	43830438	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:43830438A>G	ENST00000372458.3	-	5	463	c.346T>C	c.(346-348)Ttc>Ctc	p.F116L	ELOVL1_ENST00000470769.1_5'UTR|ELOVL1_ENST00000413844.2_Missense_Mutation_p.F89L	NM_001256399.1|NM_001256402.1|NM_022821.3	NP_001243328.1|NP_001243331.1|NP_073732.1	Q9BW60	ELOV1_HUMAN	ELOVL fatty acid elongase 1	116					cellular lipid metabolic process (GO:0044255)|fatty acid elongation, monounsaturated fatty acid (GO:0034625)|fatty acid elongation, saturated fatty acid (GO:0019367)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|triglyceride biosynthetic process (GO:0019432)|very long-chain fatty acid biosynthetic process (GO:0042761)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|membrane (GO:0016020)	fatty acid elongase activity (GO:0009922)			endometrium(1)|kidney(1)|large_intestine(1)|prostate(1)	4	all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)				AACTTGGAGAAGAGGAAGAGC	0.498																																					p.F116L		Atlas-SNP	.											.	ELOVL1	18	.	0			c.T346C						PASS	.						112.0	123.0	119.0					1																	43830438		2203	4300	6503	SO:0001583	missense	64834	exon5			TGGAGAAGAGGAA	AK001653	CCDS485.1, CCDS57987.1	1p34	2011-05-25	2011-05-25		ENSG00000066322	ENSG00000066322			14418	protein-coding gene	gene with protein product		611813	"""elongation of very long chain fatty acids (FEN1/Elo2, SUR4/Elo3, yeast)-like 1"""				Standard	NM_022821		Approved	Ssc1	uc031pmf.1	Q9BW60	OTTHUMG00000007422	ENST00000372458.3:c.346T>C	1.37:g.43830438A>G	ENSP00000361536:p.Phe116Leu	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	79	42	0.531646	NM_001256399	B4DP24|Q53HT2|Q5JUY3|Q8WXU3|Q9NVD9|Q9Y396	Missense_Mutation	SNP	ENST00000372458.3	37	CCDS485.1	.	.	.	.	.	.	.	.	.	.	A	15.45	2.837426	0.50951	.	.	ENSG00000066322	ENST00000372458;ENST00000413844	T;T	0.16073	2.37;2.37	5.77	4.65	0.58169	.	0.042915	0.85682	N	0.000000	T	0.18002	0.0432	L	0.45470	1.425	0.80722	D	1	B;B	0.13145	0.001;0.007	B;B	0.28465	0.011;0.09	T	0.02844	-1.1103	10	0.38643	T	0.18	0.4038	10.9623	0.47393	0.9261:0.0:0.0739:0.0	.	89;116	B4DP24;Q9BW60	.;ELOV1_HUMAN	L	116;89	ENSP00000361536:F116L;ENSP00000416024:F89L	ENSP00000361536:F116L	F	-	1	0	ELOVL1	43603025	1.000000	0.71417	0.999000	0.59377	0.997000	0.91878	4.126000	0.57937	1.026000	0.39733	0.533000	0.62120	TTC	.	.	none		0.498	ELOVL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019496.1	NM_022821	
FOXK1	221937	hgsc.bcm.edu	37	7	4802035	4802035	+	Silent	SNP	A	A	G	rs1053753	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:4802035A>G	ENST00000328914.4	+	9	2142	c.2142A>G	c.(2140-2142)gtA>gtG	p.V714V	FOXK1_ENST00000446823.1_Silent_p.V551V	NM_001037165.1	NP_001032242.1			forkhead box K1											breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(7)|ovary(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	29		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.101)|OV - Ovarian serous cystadenocarcinoma(56;7.43e-15)		GTGGTGCTGTAACCACACCGG	0.701													G|||	1465	0.292532	0.6785	0.121	5008	,	,		12597	0.0704		0.1471	False		,,,				2504	0.271				p.V714V		Atlas-SNP	.											.	FOXK1	64	.	0			c.A2142G						PASS	.	G		2104,2054		524,1056,499	12.0	14.0	14.0		2142	-5.3	0.0	7	dbSNP_86	14	1140,7002		97,946,3028	no	coding-synonymous	FOXK1	NM_001037165.1		621,2002,3527	GG,GA,AA		14.0015,49.3987,26.374		714/734	4802035	3244,9056	2079	4071	6150	SO:0001819	synonymous_variant	221937	exon9			TGCTGTAACCACA	BK004104	CCDS34591.1	7p22	2006-12-15			ENSG00000164916	ENSG00000164916		"""Forkhead boxes"""	23480	protein-coding gene	gene with protein product						15202027	Standard	NM_001037165		Approved	IMAGE:5164497	uc003snc.1	P85037	OTTHUMG00000151739	ENST00000328914.4:c.2142A>G	7.37:g.4802035A>G		Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	40	40	1	NM_001037165		Silent	SNP	ENST00000328914.4	37	CCDS34591.1																																																																																			A|0.728;G|0.272	0.272	strong		0.701	FOXK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323729.2		
TATDN1	83940	hgsc.bcm.edu	37	8	125499363	125499363	+	IGR	SNP	G	G	A	rs72713066	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:125499363G>A	ENST00000276692.6	-	0	1018				RP11-158K1.3_ENST00000518639.1_RNA|RNF139_ENST00000303545.3_Silent_p.S491S	NM_032026.3	NP_114415.1	Q6P1N9	TATD1_HUMAN	TatD DNase domain containing 1						DNA catabolic process (GO:0006308)	intracellular organelle (GO:0043229)|nucleus (GO:0005634)	deoxyribonuclease activity (GO:0004536)|endodeoxyribonuclease activity, producing 5'-phosphomonoesters (GO:0016888)|metal ion binding (GO:0046872)			endometrium(1)|kidney(2)|large_intestine(3)|lung(6)|prostate(2)|upper_aerodigestive_tract(1)	15	Ovarian(258;0.00438)|all_neural(195;0.0779)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.00288)			TGTTTGAGTCGGGAAGTAAAA	0.363													G|||	768	0.153355	0.1203	0.0504	5008	,	,		21535	0.1915		0.0338	False		,,,				2504	0.3548				p.S491S		Atlas-SNP	.											.	RNF139	57	.	0			c.G1473A						PASS	.	G		466,3940	205.2+/-227.1	23,420,1760	97.0	103.0	101.0		1473	0.1	1.0	8	dbSNP_130	101	417,8183	127.7+/-186.0	10,397,3893	no	coding-synonymous	RNF139	NM_007218.3		33,817,5653	AA,AG,GG		4.8488,10.5765,6.7892		491/665	125499363	883,12123	2203	4300	6503	SO:0001628	intergenic_variant	11236	exon2			TGAGTCGGGAAGT	AF212250	CCDS6351.1, CCDS55273.1	8q24.13	2004-06-07			ENSG00000147687	ENSG00000147687			24220	protein-coding gene	gene with protein product						12477932	Standard	NM_032026		Approved	CDA11	uc003yrd.2	Q6P1N9	OTTHUMG00000165068		8.37:g.125499363G>A		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	77	17	0.220779	NM_007218	B2R5J0|Q8TD02|Q9BY40	Silent	SNP	ENST00000276692.6	37	CCDS6351.1																																																																																			G|0.919;A|0.081	0.081	strong		0.363	TATDN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381655.1	NM_032026	
TMEM26	219623	hgsc.bcm.edu	37	10	63170292	63170292	+	Silent	SNP	A	A	G	rs7083475	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:63170292A>G	ENST00000399298.3	-	6	1263	c.895T>C	c.(895-897)Ttg>Ctg	p.L299L	TMEM26_ENST00000507507.1_5'UTR	NM_178505.6	NP_848600.2	Q6ZUK4	TMM26_HUMAN	transmembrane protein 26	299						integral component of membrane (GO:0016021)				kidney(1)|large_intestine(2)|lung(11)|prostate(1)|skin(2)|urinary_tract(1)	18	Prostate(12;0.0112)					TAGAGTTGCAACACCACCACG	0.527													A|||	1071	0.213858	0.3767	0.1671	5008	,	,		20549	0.0952		0.2386	False		,,,				2504	0.1237				p.L299L		Atlas-SNP	.											.	TMEM26	47	.	0			c.T895C						PASS	.	A		1329,2883		205,919,982	114.0	118.0	117.0		895	-0.8	0.9	10	dbSNP_116	117	1654,6806		142,1370,2718	no	coding-synonymous	TMEM26	NM_178505.6		347,2289,3700	GG,GA,AA		19.5508,31.5527,23.5401		299/369	63170292	2983,9689	2106	4230	6336	SO:0001819	synonymous_variant	219623	exon6			GTTGCAACACCAC	BC042872	CCDS41530.1	10q21.3	2008-10-20			ENSG00000196932	ENSG00000196932			28550	protein-coding gene	gene with protein product						12477932	Standard	NM_178505		Approved	MGC35010, Em:AC068892.1	uc001jlo.2	Q6ZUK4	OTTHUMG00000018293	ENST00000399298.3:c.895T>C	10.37:g.63170292A>G		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	118	67	0.567797	NM_178505	Q6ZVM0|Q8IVN9	Silent	SNP	ENST00000399298.3	37	CCDS41530.1																																																																																			A|0.802;G|0.198	0.198	strong		0.527	TMEM26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359121.1	NM_178505	
KIAA0368	23392	hgsc.bcm.edu	37	9	114182353	114182353	+	Silent	SNP	C	C	T	rs16916080	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:114182353C>T	ENST00000338205.5	-	15	1722	c.1503G>A	c.(1501-1503)gtG>gtA	p.V501V	KIAA0368_ENST00000259335.4_Silent_p.V679V			Q5VYK3	ECM29_HUMAN	KIAA0368	507					ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)	centrosome (GO:0005813)|cytoplasmic membrane-bounded vesicle (GO:0016023)|early endosome (GO:0005769)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle (GO:0030134)|late endosome (GO:0005770)|membrane (GO:0016020)|multivesicular body (GO:0005771)|nucleus (GO:0005634)|proteasome complex (GO:0000502)		p.V679V(1)		NS(2)|breast(3)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(23)|prostate(3)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	65						CTGAGGGAAACACCGTACTGG	0.398													C|||	479	0.095647	0.1868	0.0187	5008	,	,		13432	0.1627		0.0109	False		,,,				2504	0.045				p.V679V		Atlas-SNP	.											KIAA0368,NS,carcinoma,0,1	KIAA0368	144	1	1	Substitution - coding silent(1)	stomach(1)	c.G2037A						scavenged	.	C		553,3213		43,467,1373	101.0	99.0	99.0		2037	5.4	1.0	9	dbSNP_123	99	114,8106		0,114,3996	no	coding-synonymous	KIAA0368	NM_001080398.1		43,581,5369	TT,TC,CC		1.3869,14.684,5.5648		679/2018	114182353	667,11319	1883	4110	5993	SO:0001819	synonymous_variant	23392	exon17			GGGAAACACCGTA	AK025689	CCDS48006.1	9q32	2012-11-29	2006-11-23	2006-11-23	ENSG00000136813	ENSG00000136813			29020	protein-coding gene	gene with protein product	"""ECM29 homolog (S. cerevisiae)"""					9205841, 15496406, 20682791	Standard	NM_001080398		Approved	FLJ22036, ECM29	uc004bfe.1	Q5VYK3	OTTHUMG00000020489	ENST00000338205.5:c.1503G>A	9.37:g.114182353C>T		Somatic	82	1	0.0121951		WXS	Illumina HiSeq	Phase_I	53	29	0.54717	NM_001080398	O15074|Q8WU82	Silent	SNP	ENST00000338205.5	37																																																																																				C|0.908;T|0.092	0.092	strong		0.398	KIAA0368-001	NOVEL	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000053637.2	NM_014686	
CCDC168	643677	hgsc.bcm.edu	37	13	103388880	103388880	+	Missense_Mutation	SNP	T	T	C	rs17592459	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:103388880T>C	ENST00000322527.2	-	1	279	c.280A>G	c.(280-282)Atg>Gtg	p.M94V		NM_001146197.1	NP_001139669.1	Q8NDH2	CC168_HUMAN	coiled-coil domain containing 168	94			M -> V (in dbSNP:rs17592459).														AGATGTGGCATAAAGCTTCTT	0.413													T|||	122	0.024361	0.003	0.0216	5008	,	,		24116	0.0		0.0408	False		,,,				2504	0.0634				p.M4723V		Atlas-SNP	.											.	.	.	.	0			c.A14167G						PASS	.	T	VAL/MET	6,1378		0,6,686	250.0	192.0	210.0		14167	-2.3	0.0	13	dbSNP_123	210	116,3066		3,110,1478	yes	missense	CCDC168	NM_001146197.1	21	3,116,2164	CC,CT,TT		3.6455,0.4335,2.6719	benign	4723/7082	103388880	122,4444	692	1591	2283	SO:0001583	missense	643677	exon4			GTGGCATAAAGCT		CCDS73596.1	13q33.1	2014-06-17	2011-08-09	2011-08-09	ENSG00000175820	ENSG00000175820			26851	protein-coding gene	gene with protein product			"""chromosome 13 open reading frame 40"""	C13orf40			Standard	NM_001146197		Approved	FLJ40176	uc001vpm.3	Q8NDH2	OTTHUMG00000187287	ENST00000322527.2:c.280A>G	13.37:g.103388880T>C	ENSP00000320232:p.Met94Val	Somatic	197	0	0		WXS	Illumina HiSeq	Phase_I	164	81	0.493902	NM_001146197	Q8N800	Missense_Mutation	SNP	ENST00000322527.2	37		42	0.019230769230769232	4	0.008130081300813009	8	0.022099447513812154	0	0.0	30	0.0395778364116095	T	0.007	-2.011250	0.00422	0.004335	0.036455	ENSG00000175820	ENST00000322527	T	0.02631	4.22	4.0	-2.27	0.06846	.	1.931660	0.02917	N	0.137481	T	0.00384	0.0012	N	0.10874	0.06	0.09310	N	1	B	0.09022	0.002	B	0.08055	0.003	T	0.37384	-0.9708	10	0.02654	T	1	.	3.0766	0.06248	0.3203:0.2667:0.0:0.413	rs17592459;rs52821179;rs17592459	94	Q8NDH2	CC168_HUMAN	V	94	ENSP00000320232:M94V	ENSP00000320232:M94V	M	-	1	0	CCDC168	102186881	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.063000	0.11655	-0.568000	0.06038	-0.464000	0.05259	ATG	T|0.978;C|0.022	0.022	strong		0.413	CCDC168-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001146197	
EAF1	85403	hgsc.bcm.edu	37	3	15477872	15477872	+	Missense_Mutation	SNP	A	A	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:15477872A>C	ENST00000396842.2	+	5	975	c.550A>C	c.(550-552)Att>Ctt	p.I184L	EAF1_ENST00000432764.2_Missense_Mutation_p.I83L|EAF1-AS1_ENST00000593876.1_RNA|EAF1-AS1_ENST00000494875.3_RNA|EAF1-AS1_ENST00000597949.1_RNA|EAF1-AS1_ENST00000608780.1_RNA|EAF1-AS1_ENST00000596371.1_RNA|EAF1-AS1_ENST00000595627.1_RNA|EAF1-AS1_ENST00000594820.1_RNA|EAF1-AS1_ENST00000609310.1_RNA|EAF1-AS1_ENST00000595975.1_RNA	NM_033083.6	NP_149074.3	Q96JC9	EAF1_HUMAN	ELL associated factor 1	184	Necessary for transactivation activity.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|ELL-EAF complex (GO:0032783)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)				central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(1)|prostate(1)|urinary_tract(1)	7						AGTTGACATTATTGAACAAAT	0.483																																					p.I184L		Atlas-SNP	.											.	EAF1	16	.	0			c.A550C						PASS	.						46.0	47.0	47.0					3																	15477872		2203	4300	6503	SO:0001583	missense	85403	exon5			GACATTATTGAAC	AF272973	CCDS2626.1	3p25.1	2011-06-10			ENSG00000144597	ENSG00000144597			20907	protein-coding gene	gene with protein product		608315				11418481	Standard	NM_033083		Approved		uc003bzu.3	Q96JC9	OTTHUMG00000162544	ENST00000396842.2:c.550A>C	3.37:g.15477872A>C	ENSP00000380054:p.Ile184Leu	Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	168	35	0.208333	NM_033083	B4E3F5|Q8IW10	Missense_Mutation	SNP	ENST00000396842.2	37	CCDS2626.1	.	.	.	.	.	.	.	.	.	.	A	28.0	4.885242	0.91814	.	.	ENSG00000144597	ENST00000396842;ENST00000432764	.	.	.	5.67	5.67	0.87782	.	0.091650	0.64402	D	0.000001	T	0.62368	0.2422	M	0.65975	2.015	0.58432	D	0.999999	B;B	0.15473	0.013;0.011	B;B	0.17722	0.019;0.003	T	0.60347	-0.7281	9	0.49607	T	0.09	-10.8435	14.8972	0.70651	1.0:0.0:0.0:0.0	.	83;184	B4E3F5;Q96JC9	.;EAF1_HUMAN	L	184;83	.	ENSP00000380054:I184L	I	+	1	0	EAF1	15452876	1.000000	0.71417	0.966000	0.40874	0.886000	0.51366	8.962000	0.93254	2.159000	0.67721	0.454000	0.30748	ATT	.	.	none		0.483	EAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252100.4	NM_033083	
TAF3	83860	hgsc.bcm.edu	37	10	8006798	8006798	+	Missense_Mutation	SNP	A	A	G	rs4747647	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:8006798A>G	ENST00000344293.5	+	3	1531	c.1325A>G	c.(1324-1326)aAt>aGt	p.N442S		NM_031923.3	NP_114129.1	Q5VWG9	TAF3_HUMAN	TAF3 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 140kDa	442			N -> S (in dbSNP:rs4747647). {ECO:0000269|PubMed:15489334}.		maintenance of protein location in nucleus (GO:0051457)|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)|transcription factor TFIID complex (GO:0005669)	zinc ion binding (GO:0008270)			NS(2)|breast(4)|endometrium(2)|kidney(1)|large_intestine(6)|lung(16)|ovary(3)|prostate(4)|skin(2)	40						TCCGCGAACAATTTCACAAAG	0.468													A|||	2715	0.542133	0.2632	0.7349	5008	,	,		18510	0.7103		0.6203	False		,,,				2504	0.5286				p.N442S		Atlas-SNP	.											TAF3,NS,carcinoma,0,1	TAF3	93	1	0			c.A1325G						PASS	.	A	SER/ASN	1374,2464		255,864,800	82.0	82.0	82.0		1325	1.7	0.1	10	dbSNP_111	82	5028,3232		1511,2006,613	yes	missense	TAF3	NM_031923.2	46	1766,2870,1413	GG,GA,AA		39.1283,35.7999,47.0822	benign	442/930	8006798	6402,5696	1919	4130	6049	SO:0001583	missense	83860	exon3			CGAACAATTTCAC	AJ292190	CCDS41487.1	10p15.1	2013-01-28	2002-08-29		ENSG00000165632	ENSG00000165632		"""Zinc fingers, PHD-type"""	17303	protein-coding gene	gene with protein product		606576	"""TAF3 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 140 kD"""			11438666, 18549481	Standard	NM_031923		Approved	TAF140, TAFII140	uc010qbd.3	Q5VWG9	OTTHUMG00000017643	ENST00000344293.5:c.1325A>G	10.37:g.8006798A>G	ENSP00000340271:p.Asn442Ser	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	68	30	0.441176	NM_031923	Q05DA0|Q6GMS5|Q6P6B5|Q86VY6|Q9BQS9|Q9UFI8	Missense_Mutation	SNP	ENST00000344293.5	37	CCDS41487.1	1254	0.5741758241758241	115	0.23373983739837398	256	0.7071823204419889	413	0.722027972027972	470	0.6200527704485488	A	2.419	-0.333541	0.05278	0.357999	0.608717	ENSG00000165632	ENST00000344293	T	0.17528	2.27	5.47	1.74	0.24563	.	0.355569	0.26979	N	0.021521	T	0.00012	0.0000	L	0.39566	1.225	0.80722	P	0.0	B	0.10296	0.003	B	0.08055	0.003	T	0.34925	-0.9809	9	0.08599	T	0.76	-31.1186	6.7744	0.23611	0.6442:0.1185:0.2372:0.0	rs4747647;rs52821947;rs58942805;rs4747647	442	Q5VWG9	TAF3_HUMAN	S	442	ENSP00000340271:N442S	ENSP00000340271:N442S	N	+	2	0	TAF3	8046804	0.000000	0.05858	0.107000	0.21349	0.438000	0.31896	-0.160000	0.10041	0.358000	0.24211	0.528000	0.53228	AAT	A|0.444;G|0.556	0.556	strong		0.468	TAF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046725.1	NM_031923	
DMBT1	1755	hgsc.bcm.edu	37	10	124358421	124358421	+	Missense_Mutation	SNP	G	G	A	rs368405942		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:124358421G>A	ENST00000338354.3	+	26	3194	c.3088G>A	c.(3088-3090)Gtc>Atc	p.V1030I	DMBT1_ENST00000368909.3_Missense_Mutation_p.V1030I|DMBT1_ENST00000359586.6_Intron|DMBT1_ENST00000344338.3_Missense_Mutation_p.V1020I|DMBT1_ENST00000368955.3_Missense_Mutation_p.V1020I|DMBT1_ENST00000330163.4_Missense_Mutation_p.V531I|DMBT1_ENST00000368956.2_Missense_Mutation_p.V531I			Q9UGM3	DMBT1_HUMAN	deleted in malignant brain tumors 1	1030	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)				TGCCAATGTCGTCTGCAGGCA	0.607													g|||	1	0.000199681	0.0008	0.0	5008	,	,		19742	0.0		0.0	False		,,,				2504	0.0				p.V1030I	Ovarian(182;93 2026 18125 22222 38972)	Atlas-SNP	.											.	DMBT1	677	.	0			c.G3088A						PASS	.	G	ILE/VAL,ILE/VAL,ILE/VAL	0,4072		0,0,2036	260.0	259.0	259.0		1591,3088,3058	2.6	0.9	10		259	2,8420		0,2,4209	no	missense,missense,missense	DMBT1	NM_004406.2,NM_007329.2,NM_017579.2	29,29,29	0,2,6245	AA,AG,GG		0.0237,0.0,0.016	possibly-damaging,possibly-damaging,possibly-damaging	531/1786,1030/2414,1020/2404	124358421	2,12492	2036	4211	6247	SO:0001583	missense	1755	exon26			AATGTCGTCTGCA		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.3088G>A	10.37:g.124358421G>A	ENSP00000342210:p.Val1030Ile	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	43	14	0.325581	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		.	.	.	.	.	.	.	.	.	.	G	16.84	3.233595	0.58886	0.0	2.37E-4	ENSG00000187908	ENST00000338354;ENST00000368915;ENST00000341278;ENST00000368953;ENST00000339871;ENST00000368942;ENST00000327438;ENST00000344338;ENST00000339712;ENST00000330163;ENST00000368909;ENST00000368955;ENST00000368956	T;T;T;T;T;T	0.39229	1.09;1.09;1.09;1.09;1.09;1.09	3.57	2.63	0.31362	Speract/scavenger receptor (3);Speract/scavenger receptor-related (2);	0.725684	0.11251	N	0.583638	T	0.60143	0.2246	M	0.69248	2.105	0.80722	D	1	D;D;P;P	0.76494	0.99;0.999;0.923;0.938	P;D;B;B	0.74674	0.606;0.984;0.154;0.24	T	0.52540	-0.8562	10	0.38643	T	0.18	.	11.4562	0.50183	0.0924:0.0:0.9076:0.0	.	1030;531;1020;1030	Q9UGM3-6;Q9UGM3-2;Q9UGM3-3;Q9UGM3	.;.;.;DMBT1_HUMAN	I	1030;1030;1030;1030;1030;1030;531;1020;531;531;1030;1020;531	ENSP00000342210:V1030I;ENSP00000343175:V1020I;ENSP00000327747:V531I;ENSP00000357905:V1030I;ENSP00000357951:V1020I;ENSP00000357952:V531I	ENSP00000331522:V531I	V	+	1	0	DMBT1	124348411	1.000000	0.71417	0.922000	0.36590	0.566000	0.35808	7.239000	0.78182	0.585000	0.29608	0.558000	0.71614	GTC	.	.	none		0.607	DMBT1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050792.2	NM_004406	
C1orf111	284680	hgsc.bcm.edu	37	1	162344069	162344069	+	Silent	SNP	G	G	A	rs13823	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:162344069G>A	ENST00000367935.5	-	3	634	c.555C>T	c.(553-555)tgC>tgT	p.C185C	RP11-565P22.6_ENST00000431696.1_Intron	NM_182581.3	NP_872387.2	Q5T0L3	CA111_HUMAN	chromosome 1 open reading frame 111	185										central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)	11	all_hematologic(112;0.15)		BRCA - Breast invasive adenocarcinoma(70;0.0938)			AGCAGGCCACGCACTTGTAGC	0.582													G|||	379	0.0756789	0.003	0.1124	5008	,	,		18001	0.0804		0.0596	False		,,,				2504	0.1595				p.C185C		Atlas-SNP	.											.	C1orf111	26	.	0			c.C555T						PASS	.	G		42,4364	45.3+/-79.5	0,42,2161	153.0	148.0	150.0		555	-3.1	0.1	1	dbSNP_52	150	457,8143	137.5+/-194.4	9,439,3852	no	coding-synonymous	C1orf111	NM_182581.3		9,481,6013	AA,AG,GG		5.314,0.9532,3.8367		185/262	162344069	499,12507	2203	4300	6503	SO:0001819	synonymous_variant	284680	exon3			GGCCACGCACTTG	BC032957	CCDS1238.1	1q23.3	2008-02-05			ENSG00000171722	ENSG00000171722			27648	protein-coding gene	gene with protein product						12477932	Standard	NM_182581		Approved		uc001gbx.2	Q5T0L3	OTTHUMG00000031375	ENST00000367935.5:c.555C>T	1.37:g.162344069G>A		Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	117	49	0.418803	NM_182581	Q6X961|Q8NEC3	Silent	SNP	ENST00000367935.5	37	CCDS1238.1																																																																																			G|0.952;A|0.048	0.048	strong		0.582	C1orf111-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076791.2	NM_182581	
AHNAK2	113146	hgsc.bcm.edu	37	14	105418502	105418502	+	Missense_Mutation	SNP	G	G	T	rs386781102|rs201268922	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:105418502G>T	ENST00000333244.5	-	7	3405	c.3286C>A	c.(3286-3288)Ctc>Atc	p.L1096I	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	1096						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)			GGGCCCTTGAGGGCCACTTTG	0.632													.|||	643	0.128395	0.1452	0.0432	5008	,	,		18495	0.2202		0.0308	False		,,,				2504	0.1718				p.L1096I		Atlas-SNP	.											.	AHNAK2	719	.	0			c.C3286A						PASS	.						125.0	148.0	141.0					14																	105418502		1855	4107	5962	SO:0001583	missense	113146	exon7			CCTTGAGGGCCAC	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.3286C>A	14.37:g.105418502G>T	ENSP00000353114:p.Leu1096Ile	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	156	31	0.198718	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	.	.	.	.	.	.	.	.	.	.	g	0.156	-1.086024	0.01873	.	.	ENSG00000185567	ENST00000333244	T	0.00591	6.35	2.99	0.701	0.18104	.	.	.	.	.	T	0.00524	0.0017	L	0.39566	1.225	0.80722	P	0.0	B	0.24576	0.106	B	0.25614	0.062	T	0.24657	-1.0154	8	0.11182	T	0.66	.	6.0501	0.19781	0.0:0.3108:0.4318:0.2574	.	1096	Q8IVF2	AHNK2_HUMAN	I	1096	ENSP00000353114:L1096I	ENSP00000353114:L1096I	L	-	1	0	AHNAK2	104489547	0.000000	0.05858	0.014000	0.15608	0.100000	0.18952	-2.006000	0.01459	0.019000	0.15079	0.313000	0.20887	CTC	.	.	weak		0.632	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
ALAS1	211	hgsc.bcm.edu	37	3	52237970	52237970	+	Silent	SNP	C	C	T	rs352168	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:52237970C>T	ENST00000394965.2	+	5	879	c.519C>T	c.(517-519)atC>atT	p.I173I	ALAS1_ENST00000310271.2_Silent_p.I173I|ALAS1_ENST00000484952.1_Silent_p.I173I|ALAS1_ENST00000469224.1_Silent_p.I173I	NM_000688.5	NP_000679.1	P13196	HEM1_HUMAN	aminolevulinate, delta-, synthase 1	173					cellular lipid metabolic process (GO:0044255)|heme biosynthetic process (GO:0006783)|porphyrin-containing compound metabolic process (GO:0006778)|protoporphyrinogen IX biosynthetic process (GO:0006782)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	5-aminolevulinate synthase activity (GO:0003870)|pyridoxal phosphate binding (GO:0030170)			endometrium(3)|kidney(3)|large_intestine(7)|liver(2)|lung(5)|ovary(2)|upper_aerodigestive_tract(1)	23				BRCA - Breast invasive adenocarcinoma(193;5.13e-05)|Kidney(197;0.000583)|KIRC - Kidney renal clear cell carcinoma(197;0.000751)	Glycine(DB00145)	TCCAGGACATCATGCAAAAGC	0.433													C|||	1995	0.398363	0.2625	0.487	5008	,	,		19357	0.3948		0.5298	False		,,,				2504	0.3875				p.I173I		Atlas-SNP	.											.	ALAS1	56	.	0			c.C519T						PASS	.	C	,	1442,2964	467.0+/-354.7	237,968,998	130.0	116.0	121.0		519,519	1.8	0.9	3	dbSNP_79	121	4705,3895	606.5+/-395.1	1277,2151,872	no	coding-synonymous,coding-synonymous	ALAS1	NM_000688.4,NM_199166.1	,	1514,3119,1870	TT,TC,CC		45.2907,32.7281,47.2628	,	173/641,173/641	52237970	6147,6859	2203	4300	6503	SO:0001819	synonymous_variant	211	exon5			GGACATCATGCAA	X56351	CCDS2847.1	3p21	2004-11-18			ENSG00000023330	ENSG00000023330	2.3.1.37		396	protein-coding gene	gene with protein product		125290		ALAS3, ALAS			Standard	NM_000688		Approved		uc003dcz.2	P13196	OTTHUMG00000158108	ENST00000394965.2:c.519C>T	3.37:g.52237970C>T		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	72	72	1	NM_000688		Silent	SNP	ENST00000394965.2	37	CCDS2847.1																																																																																			C|0.549;T|0.451	0.451	strong		0.433	ALAS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350207.1		
NSMCE4A	54780	hgsc.bcm.edu	37	10	123727280	123727280	+	Silent	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:123727280G>A	ENST00000369023.3	-	4	594	c.543C>T	c.(541-543)ctC>ctT	p.L181L	NSMCE4A_ENST00000538652.1_Silent_p.L22L|NSMCE4A_ENST00000489266.1_5'UTR|NSMCE4A_ENST00000369017.5_Silent_p.L181L	NM_001167865.1|NM_017615.2	NP_001161337.1|NP_060085.2	Q9NXX6	NSE4A_HUMAN	non-SMC element 4 homolog A (S. cerevisiae)	181					DNA recombination (GO:0006310)|DNA repair (GO:0006281)|positive regulation of response to DNA damage stimulus (GO:2001022)	chromosome, telomeric region (GO:0000781)|nucleus (GO:0005634)|Smc5-Smc6 complex (GO:0030915)				breast(2)|endometrium(1)|large_intestine(1)|lung(1)|prostate(1)	6		all_neural(114;0.138)|Glioma(114;0.222)				CATCACGGATGAGTTCTTCAG	0.378																																					p.L181L		Atlas-SNP	.											NSMCE4A,caecum,carcinoma,-2,1	NSMCE4A	12	1	0			c.C543T						scavenged	.						150.0	143.0	145.0					10																	123727280		2203	4300	6503	SO:0001819	synonymous_variant	54780	exon4			ACGGATGAGTTCT	AF258584	CCDS7624.1	10q26.13	2007-05-17	2006-11-24	2006-11-24	ENSG00000107672	ENSG00000107672			25935	protein-coding gene	gene with protein product		612987	"""chromosome 10 open reading frame 86"""	C10orf86		15752197	Standard	NM_017615		Approved	FLJ20003, bA500G22.3, NSE4A	uc001lfs.3	Q9NXX6	OTTHUMG00000019180	ENST00000369023.3:c.543C>T	10.37:g.123727280G>A		Somatic	147	1	0.00680272		WXS	Illumina HiSeq	Phase_I	113	2	0.0176991	NM_001167865	Q5SQQ5|Q6P673|Q8WY66|Q9BS90	Silent	SNP	ENST00000369023.3	37	CCDS7624.1																																																																																			.	.	none		0.378	NSMCE4A-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050749.1	NM_017615	
LMX1A	4009	hgsc.bcm.edu	37	1	165218792	165218792	+	Silent	SNP	G	G	A	rs10753668	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:165218792G>A	ENST00000342310.3	-	4	731	c.349C>T	c.(349-351)Ctg>Ttg	p.L117L	LMX1A_ENST00000294816.2_Silent_p.L117L|LMX1A_ENST00000367893.4_Silent_p.L117L	NM_177398.3	NP_796372.1	Q8TE12	LMX1A_HUMAN	LIM homeobox transcription factor 1, alpha	117	LIM zinc-binding 2. {ECO:0000255|PROSITE- ProRule:PRU00125}.				axon guidance (GO:0007411)|central nervous system neuron differentiation (GO:0021953)|cerebellum development (GO:0021549)|dentate gyrus development (GO:0021542)|dopaminergic neuron differentiation (GO:0071542)|midbrain development (GO:0030901)|negative regulation of neuron differentiation (GO:0045665)|regulation of cell growth (GO:0001558)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)			NS(2)|biliary_tract(1)|central_nervous_system(3)|cervix(2)|endometrium(4)|large_intestine(6)|lung(10)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(4)	35	all_hematologic(923;0.248)					AAGCAGCTCAGGTGGTATACA	0.552													G|||	1626	0.324681	0.1263	0.3545	5008	,	,		19587	0.5605		0.2406	False		,,,				2504	0.4151				p.L117L		Atlas-SNP	.											.	LMX1A	87	.	0			c.C349T						PASS	.	G	,	709,3697	293.0+/-282.3	50,609,1544	52.0	51.0	51.0		349,349	3.7	1.0	1	dbSNP_120	51	2088,6512	361.6+/-332.4	234,1620,2446	no	coding-synonymous,coding-synonymous	LMX1A	NM_001174069.1,NM_177398.3	,	284,2229,3990	AA,AG,GG		24.2791,16.0917,21.5055	,	117/383,117/383	165218792	2797,10209	2203	4300	6503	SO:0001819	synonymous_variant	4009	exon4			AGCTCAGGTGGTA	AY078391	CCDS1247.1	1q24.1	2011-06-20			ENSG00000162761	ENSG00000162761		"""Homeoboxes / LIM class"""	6653	protein-coding gene	gene with protein product		600298		LMX1		7698771	Standard	NM_177398		Approved	LMX1.1	uc001gcz.2	Q8TE12	OTTHUMG00000034575	ENST00000342310.3:c.349C>T	1.37:g.165218792G>A		Somatic	182	0	0		WXS	Illumina HiSeq	Phase_I	143	73	0.51049	NM_001174069	B3KXP6|Q0VDB5|Q5VWG4|Q8TE11	Silent	SNP	ENST00000342310.3	37	CCDS1247.1																																																																																			G|0.743;A|0.257	0.257	strong		0.552	LMX1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083668.2	NM_177398	
MKI67	4288	hgsc.bcm.edu	37	10	129901570	129901570	+	Missense_Mutation	SNP	C	C	T	rs11016072	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:129901570C>T	ENST00000368654.3	-	13	8909	c.8534G>A	c.(8533-8535)cGt>cAt	p.R2845H	MKI67_ENST00000368653.3_Missense_Mutation_p.R2485H	NM_002417.4	NP_002408.3	P46013	KI67_HUMAN	marker of proliferation Ki-67	2845	16 X 122 AA approximate repeats.		R -> H (in dbSNP:rs11016072).		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)				TTTCTGGGCACGTGTCCTGGG	0.502													C|||	393	0.0784744	0.174	0.0303	5008	,	,		19749	0.1052		0.0199	False		,,,				2504	0.0164				p.R2845H		Atlas-SNP	.											.	MKI67	363	.	0			c.G8534A						PASS	.	C	HIS/ARG,HIS/ARG	684,3722	289.2+/-280.3	50,584,1569	177.0	158.0	165.0		7454,8534	-2.3	0.0	10	dbSNP_120	165	239,8361	96.3+/-158.1	4,231,4065	yes	missense,missense	MKI67	NM_001145966.1,NM_002417.4	29,29	54,815,5634	TT,TC,CC		2.7791,15.5243,7.0967	probably-damaging,probably-damaging	2485/2897,2845/3257	129901570	923,12083	2203	4300	6503	SO:0001583	missense	4288	exon13			TGGGCACGTGTCC	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.8534G>A	10.37:g.129901570C>T	ENSP00000357643:p.Arg2845His	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	96	36	0.375	NM_002417	Q5VWH2	Missense_Mutation	SNP	ENST00000368654.3	37	CCDS7659.1	151	0.06913919413919414	63	0.12804878048780488	9	0.024861878453038673	62	0.10839160839160839	17	0.022427440633245383	C	15.02	2.708856	0.48517	0.155243	0.027791	ENSG00000148773	ENST00000368654;ENST00000368653;ENST00000537609	T;T	0.02345	4.33;4.33	4.55	-2.34	0.06704	.	.	.	.	.	T	0.00012	0.0000	L	0.34521	1.04	0.80722	P	0.0	P;P;P	0.50528	0.809;0.914;0.936	B;P;P	0.56278	0.337;0.548;0.795	T	0.43925	-0.9361	8	0.45353	T	0.12	.	0.9621	0.01397	0.2304:0.3759:0.1712:0.2225	rs11016072;rs11016072	2844;2485;2845	F5H4V4;P46013-2;P46013	.;.;KI67_HUMAN	H	2845;2485;2844	ENSP00000357643:R2845H;ENSP00000357642:R2485H	ENSP00000357642:R2485H	R	-	2	0	MKI67	129791560	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.229000	0.09098	-0.119000	0.11830	0.655000	0.94253	CGT	C|0.927;T|0.073	0.073	strong		0.502	MKI67-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050999.1	NM_002417	
RC3H1	149041	hgsc.bcm.edu	37	1	173961985	173961985	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:173961985G>A	ENST00000367696.2	-	2	490	c.139C>T	c.(139-141)Cgc>Tgc	p.R47C	RC3H1_ENST00000258349.4_Missense_Mutation_p.R47C|RC3H1_ENST00000367694.2_Missense_Mutation_p.R47C			Q5TC82	RC3H1_HUMAN	ring finger and CCCH-type domains 1	47					B cell homeostasis (GO:0001782)|cytoplasmic mRNA processing body assembly (GO:0033962)|lymph node development (GO:0048535)|negative regulation of activated T cell proliferation (GO:0046007)|negative regulation of B cell proliferation (GO:0030889)|negative regulation of germinal center formation (GO:0002635)|negative regulation of T-helper cell differentiation (GO:0045623)|nuclear-transcribed mRNA catabolic process (GO:0000956)|positive regulation of NIK/NF-kappaB signaling (GO:1901224)|posttranscriptional regulation of gene expression (GO:0010608)|protein ubiquitination (GO:0016567)|regulation of germinal center formation (GO:0002634)|regulation of mRNA stability (GO:0043488)|regulation of T cell receptor signaling pathway (GO:0050856)|spleen development (GO:0048536)|T cell homeostasis (GO:0043029)|T cell proliferation (GO:0042098)|T follicular helper cell differentiation (GO:0061470)	cytoplasmic mRNA processing body (GO:0000932)|cytoplasmic stress granule (GO:0010494)	mRNA 3'-UTR binding (GO:0003730)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(7)|lung(20)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	50						CAAGCCTTGCGGTGGAGTTTA	0.502																																					p.R47C		Atlas-SNP	.											RC3H1,NS,carcinoma,+1,1	RC3H1	110	1	0			c.C139T						scavenged	.						151.0	130.0	137.0					1																	173961985		2203	4300	6503	SO:0001583	missense	149041	exon1			CCTTGCGGTGGAG	AK093501	CCDS30940.1, CCDS72987.1	1q25.1	2013-01-18	2010-09-15		ENSG00000135870	ENSG00000135870		"""RING-type (C3HC4) zinc fingers"", ""Zinc fingers, CCCH-type domain containing"""	29434	protein-coding gene	gene with protein product	"""KIAA2025 protein"""	609424	"""ring finger and CCCH-type zinc finger domains 1"""			15917799	Standard	XM_005244918		Approved	KIAA2025, roquin, RP5-1198E17.5, RNF198	uc001gju.4	Q5TC82	OTTHUMG00000037275	ENST00000367696.2:c.139C>T	1.37:g.173961985G>A	ENSP00000356669:p.Arg47Cys	Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	148	3	0.0202703	NM_172071	B3KVK1|Q5W180|Q5W181|Q8IVE6|Q8N9V1	Missense_Mutation	SNP	ENST00000367696.2	37	CCDS30940.1	.	.	.	.	.	.	.	.	.	.	G	27.5	4.837794	0.91117	.	.	ENSG00000135870	ENST00000367696;ENST00000258349;ENST00000367694	D;D;D	0.94417	-3.42;-3.42;-3.42	5.68	5.68	0.88126	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (2);Zinc finger, C3HC4 RING-type (1);	0.000000	0.85682	D	0.000000	D	0.96886	0.8983	M	0.63428	1.95	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.998;0.999;0.997;0.994	D	0.97096	0.9794	10	0.87932	D	0	-9.7826	19.7923	0.96464	0.0:0.0:1.0:0.0	.	47;47;47;47	B9EGU6;B7ZMB3;Q5TC82-2;Q5TC82	.;.;.;RC3H1_HUMAN	C	47	ENSP00000356669:R47C;ENSP00000258349:R47C;ENSP00000356667:R47C	ENSP00000258349:R47C	R	-	1	0	RC3H1	172228608	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.349000	0.97066	2.693000	0.91896	0.655000	0.94253	CGC	.	.	none		0.502	RC3H1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090733.2	NM_172071	
SYT8	90019	hgsc.bcm.edu	37	11	1857751	1857751	+	Missense_Mutation	SNP	C	C	G	rs3741231	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:1857751C>G	ENST00000381968.3	+	6	783	c.655C>G	c.(655-657)Cca>Gca	p.P219A	SYT8_ENST00000535046.1_3'UTR|TNNI2_ENST00000381911.1_5'Flank|TNNI2_ENST00000381906.1_5'Flank|SYT8_ENST00000341958.3_Missense_Mutation_p.P205A	NM_138567.3	NP_612634	Q8NBV8	SYT8_HUMAN	synaptotagmin VIII	219					acrosome reaction (GO:0007340)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)	transporter activity (GO:0005215)			breast(1)|large_intestine(1)|lung(2)|ovary(1)|skin(1)	6		all_epithelial(84;0.000138)|Breast(177;0.000962)|Ovarian(85;0.0014)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00136)|Lung(200;0.0681)|LUSC - Lung squamous cell carcinoma(625;0.082)		GCTCCGTCTGCCACTGGGCAC	0.662													C|||	1692	0.337859	0.2398	0.3732	5008	,	,		14859	0.3026		0.3926	False		,,,				2504	0.4254				p.P219A		Atlas-SNP	.											.	SYT8	29	.	0			c.C655G						PASS	.	C	ALA/PRO	1150,3254		163,824,1215	23.0	27.0	26.0		655	2.3	0.0	11	dbSNP_107	26	3269,5323		656,1957,1683	yes	missense	SYT8	NM_138567.3	27	819,2781,2898	GG,GC,CC		38.047,26.1126,34.0028	probably-damaging	219/402	1857751	4419,8577	2202	4296	6498	SO:0001583	missense	90019	exon6			CGTCTGCCACTGG	AL137708	CCDS7726.2	11p15.5	2013-01-21			ENSG00000149043	ENSG00000149043		"""Synaptotagmins"""	19264	protein-coding gene	gene with protein product		607719				7791877	Standard	XM_005253216		Approved	DKFZp434K0322	uc001lue.1	Q8NBV8	OTTHUMG00000009026	ENST00000381968.3:c.655C>G	11.37:g.1857751C>G	ENSP00000371394:p.Pro219Ala	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	153	107	0.699346	NM_138567	A6NFJ4|Q9NSV9	Missense_Mutation	SNP	ENST00000381968.3	37	CCDS7726.2	738|738	0.33791208791208793|0.33791208791208793	115|115	0.23373983739837398|0.23373983739837398	141|141	0.38950276243093923|0.38950276243093923	177|177	0.3094405594405594|0.3094405594405594	305|305	0.4023746701846966|0.4023746701846966	c|c	14.91|14.91	2.675253|2.675253	0.47781|0.47781	0.261126|0.261126	0.38047|0.38047	ENSG00000149043|ENSG00000149043	ENST00000381978|ENST00000381968;ENST00000341958	.|T;T	.|0.09350	.|2.99;2.99	3.28|3.28	2.33|2.33	0.28932|0.28932	.|C2 calcium-dependent membrane targeting (1);C2 calcium/lipid-binding domain, CaLB (1);	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	M|M	0.62266|0.62266	1.93|1.93	0.29145|0.29145	P|P	0.878737|0.878737	.|P;P	.|0.39282	.|0.666;0.666	.|B;B	.|0.33339	.|0.162;0.162	T|T	0.46992|0.46992	-0.9151|-0.9151	4|8	.|0.59425	.|D	.|0.04	.|.	8.09|8.09	0.30795|0.30795	0.0:0.745:0.1598:0.0952|0.0:0.745:0.1598:0.0952	rs3741231;rs57303263|rs3741231;rs57303263	.|219;205	.|Q8NBV8;A6NCR4	.|SYT8_HUMAN;.	G|A	217|219;205	.|ENSP00000371394:P219A;ENSP00000343691:P205A	.|ENSP00000343691:P205A	A|P	+|+	2|1	0|0	SYT8|SYT8	1814327|1814327	0.099000|0.099000	0.21834|0.21834	0.015000|0.015000	0.15790|0.15790	0.505000|0.505000	0.33919|0.33919	1.232000|1.232000	0.32636|0.32636	0.459000|0.459000	0.27016|0.27016	0.313000|0.313000	0.20887|0.20887	GCC|CCA	C|0.667;G|0.333	0.333	strong		0.662	SYT8-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000025013.4		
FBN3	84467	hgsc.bcm.edu	37	19	8168545	8168545	+	Missense_Mutation	SNP	C	C	T	rs33967815	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	131	0	0		WXS	Illumina HiSeq	Phase_I	131	49	0.374046	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	
E2F2	1870	hgsc.bcm.edu	37	1	23845566	23845566	+	Missense_Mutation	SNP	G	G	A	rs139052092	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:23845566G>A	ENST00000361729.2	-	5	1220	c.794C>T	c.(793-795)aCa>aTa	p.T265I	E2F2_ENST00000487237.1_5'UTR	NM_004091.3	NP_004082.1	Q14209	E2F2_HUMAN	E2F transcription factor 2	265	Dimerization. {ECO:0000255}.				intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|lens fiber cell apoptotic process (GO:1990086)|mitotic cell cycle (GO:0000278)|regulation of cell cycle (GO:0051726)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)|transcription factor complex (GO:0005667)	core promoter binding (GO:0001047)|DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			endometrium(4)|large_intestine(2)|lung(1)|ovary(3)|skin(2)|urinary_tract(1)	13		Colorectal(325;3.46e-05)|Lung NSC(340;4.15e-05)|all_lung(284;6.64e-05)|Renal(390;0.000219)|Breast(348;0.00262)|Ovarian(437;0.00539)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;1.52e-24)|Colorectal(126;6.25e-08)|COAD - Colon adenocarcinoma(152;3.42e-06)|GBM - Glioblastoma multiforme(114;8.98e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00102)|KIRC - Kidney renal clear cell carcinoma(1967;0.00366)|STAD - Stomach adenocarcinoma(196;0.0132)|READ - Rectum adenocarcinoma(331;0.0652)|Lung(427;0.0888)|LUSC - Lung squamous cell carcinoma(448;0.19)		GGCAATCACTGTCTGCTCCTT	0.532													G|||	5	0.000998403	0.0	0.0	5008	,	,		20103	0.0		0.005	False		,,,				2504	0.0				p.T265I		Atlas-SNP	.											.	E2F2	31	.	0			c.C794T						PASS	.	G	ILE/THR	2,4404	4.2+/-10.8	0,2,2201	113.0	97.0	103.0		794	6.1	1.0	1	dbSNP_134	103	27,8573	19.2+/-60.6	0,27,4273	yes	missense	E2F2	NM_004091.3	89	0,29,6474	AA,AG,GG		0.314,0.0454,0.223	probably-damaging	265/438	23845566	29,12977	2203	4300	6503	SO:0001583	missense	1870	exon5			ATCACTGTCTGCT	L22846	CCDS236.1	1p36	2008-02-05			ENSG00000007968	ENSG00000007968			3114	protein-coding gene	gene with protein product		600426				8246995, 8246996	Standard	NM_004091		Approved	E2F-2	uc001bhe.2	Q14209	OTTHUMG00000003223	ENST00000361729.2:c.794C>T	1.37:g.23845566G>A	ENSP00000355249:p.Thr265Ile	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	128	64	0.5	NM_004091	B2R9W1|Q7Z6H1	Missense_Mutation	SNP	ENST00000361729.2	37	CCDS236.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	G	35	5.445078	0.96187	4.54E-4	0.00314	ENSG00000007968	ENST00000361729	D	0.87412	-2.25	6.07	6.07	0.98685	.	0.000000	0.85682	D	0.000000	D	0.89234	0.6657	M	0.63428	1.95	0.80722	D	1	P	0.51240	0.943	P	0.48189	0.57	D	0.88744	0.3245	10	0.49607	T	0.09	-19.7296	19.2232	0.93806	0.0:0.0:1.0:0.0	.	265	Q14209	E2F2_HUMAN	I	265	ENSP00000355249:T265I	ENSP00000355249:T265I	T	-	2	0	E2F2	23718153	1.000000	0.71417	0.992000	0.48379	0.988000	0.76386	9.803000	0.99136	2.885000	0.99019	0.650000	0.86243	ACA	G|0.998;A|0.002	0.002	strong		0.532	E2F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008885.1	NM_004091	
WDFY4	57705	hgsc.bcm.edu	37	10	49987998	49987998	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:49987998C>T	ENST00000325239.5	+	18	3437	c.3410C>T	c.(3409-3411)cCt>cTt	p.P1137L	WDFY4_ENST00000413659.2_Intron	NM_020945.1	NP_065996.1	Q6ZS81	WDFY4_HUMAN	WDFY family member 4	1137						integral component of membrane (GO:0016021)				NS(2)|breast(5)|central_nervous_system(4)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|lung(3)|pancreas(2)|prostate(5)|skin(6)|stomach(1)	48						GTCATGGAACCTGAGGATGAC	0.567																																					p.P1137L		Atlas-SNP	.											.	WDFY4	205	.	0			c.C3410T						PASS	.						126.0	112.0	116.0					10																	49987998		692	1591	2283	SO:0001583	missense	57705	exon19			TGGAACCTGAGGA	AK074085	CCDS44385.1	10q11.23	2013-01-10			ENSG00000128815	ENSG00000128815		"""WD repeat domain containing"""	29323	protein-coding gene	gene with protein product		613316	"""chromosome 10 open reading frame 64"""	C10orf64		10997877	Standard	NM_020945		Approved	KIAA1607, Em:AC060234.3, FLJ45748	uc001jha.4	Q6ZS81	OTTHUMG00000018180	ENST00000325239.5:c.3410C>T	10.37:g.49987998C>T	ENSP00000320563:p.Pro1137Leu	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	79	26	0.329114	NM_020945	B9ZVP2|Q86WZ4|Q8N4A3|Q8TEN7|Q96BE1|Q9H7H8|Q9HCG5	Missense_Mutation	SNP	ENST00000325239.5	37	CCDS44385.1	.	.	.	.	.	.	.	.	.	.	C	15.81	2.943757	0.53079	.	.	ENSG00000128815	ENST00000426033;ENST00000325239	T	0.56444	0.46	5.71	4.81	0.61882	.	.	.	.	.	T	0.37320	0.0999	N	0.24115	0.695	0.80722	D	1	B	0.20052	0.041	B	0.20184	0.028	T	0.14062	-1.0486	8	.	.	.	.	12.1701	0.54152	0.0:0.9213:0.0:0.0787	.	1137	Q6ZS81	WDFY4_HUMAN	L	1137	ENSP00000320563:P1137L	.	P	+	2	0	WDFY4	49658004	1.000000	0.71417	0.816000	0.32577	0.917000	0.54804	4.981000	0.63819	1.422000	0.47177	0.561000	0.74099	CCT	.	.	none		0.567	WDFY4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		XM_033379	
ZFP36L1	677	hgsc.bcm.edu	37	14	69259598	69259598	+	Splice_Site	SNP	C	C	T	rs563928424		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:69259598C>T	ENST00000439696.2	-	1	359		c.e1+1		ZFP36L1_ENST00000555997.1_5'Flank|ZFP36L1_ENST00000336440.3_Splice_Site	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)		CCCCCCTTTACCTTGCATAAA	0.517													C|||	1	0.000199681	0.0008	0.0	5008	,	,		14835	0.0		0.0	False		,,,				2504	0.0				.		Atlas-SNP	.											.	ZFP36L1	47	.	0			c.57+1G>A						PASS	.						163.0	168.0	166.0					14																	69259598		2203	4300	6503	SO:0001630	splice_region_variant	677	exon2			CCTTTACCTTGCA	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.57+1G>A	14.37:g.69259598C>T		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	34	6	0.176471	NM_004926	Q13851	Splice_Site	SNP	ENST00000439696.2	37	CCDS9791.1	.	.	.	.	.	.	.	.	.	.	C	19.73	3.882604	0.72410	.	.	ENSG00000185650	ENST00000439696;ENST00000336440;ENST00000435246;ENST00000553375	.	.	.	4.56	4.56	0.56223	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.0951	0.81114	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	ZFP36L1	68329351	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	5.059000	0.64306	2.065000	0.61736	0.561000	0.74099	.	.	.	none		0.517	ZFP36L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413227.1		Intron
CERS3	204219	hgsc.bcm.edu	37	15	101041921	101041921	+	Missense_Mutation	SNP	T	T	C	rs60405735	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:101041921T>C	ENST00000394113.1	-	5	824	c.134A>G	c.(133-135)tAt>tGt	p.Y45C	CERS3_ENST00000284382.4_Missense_Mutation_p.Y45C|CERS3_ENST00000538112.2_Missense_Mutation_p.Y45C|CERS3_ENST00000560944.1_Intron			Q8IU89	CERS3_HUMAN	ceramide synthase 3	45			Y -> C (in dbSNP:rs60405735).		ceramide biosynthetic process (GO:0046513)|keratinocyte differentiation (GO:0030216)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sphingosine N-acyltransferase activity (GO:0050291)										GAGAAAAGCATATGGAATTGT	0.383													T|||	561	0.112021	0.292	0.036	5008	,	,		20588	0.0119		0.0507	False		,,,				2504	0.089				p.Y45C		Atlas-SNP	.											.	.	.	.	0			c.A134G						PASS	.	T	CYS/TYR	1105,3301	397.6+/-330.5	136,833,1234	102.0	89.0	93.0		134	-7.7	0.0	15	dbSNP_129	93	528,8072	147.9+/-203.2	17,494,3789	yes	missense	CERS3	NM_178842.3	194	153,1327,5023	CC,CT,TT		6.1395,25.0794,12.5557	benign	45/384	101041921	1633,11373	2203	4300	6503	SO:0001583	missense	204219	exon4			AAAGCATATGGAA		CCDS10384.1	15q26.3	2012-11-19	2011-07-08	2011-07-08	ENSG00000154227	ENSG00000154227		"""Homeoboxes / CERS class"""	23752	protein-coding gene	gene with protein product		615276	"""LAG1 longevity assurance homolog 3 (S. cerevisiae)"", ""LAG1 homolog, ceramide synthase 3"""	LASS3			Standard	NM_178842		Approved	MGC27091	uc002bwb.3	Q8IU89	OTTHUMG00000172568	ENST00000394113.1:c.134A>G	15.37:g.101041921T>C	ENSP00000377672:p.Tyr45Cys	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	114	73	0.640351	NM_178842	Q8NE64|Q8NEN6	Missense_Mutation	SNP	ENST00000394113.1	37	CCDS10384.1	195	0.08928571428571429	130	0.26422764227642276	15	0.04143646408839779	5	0.008741258741258742	45	0.059366754617414245	T	10.35	1.327124	0.24080	0.250794	0.061395	ENSG00000154227	ENST00000284382;ENST00000394113;ENST00000538112	T;T	0.69926	-0.44;-0.44	5.49	-7.72	0.01250	.	0.617290	0.17774	N	0.162475	T	0.00012	0.0000	M	0.71296	2.17	0.49299	P	2.2999999999995246E-4	B	0.09022	0.002	B	0.06405	0.002	T	0.07888	-1.0749	9	0.56958	D	0.05	-0.038	5.2062	0.15293	0.314:0.3799:0.0:0.3061	rs60405735;rs62619254	45	Q8IU89	CERS3_HUMAN	C	45;56;45	ENSP00000284382:Y45C;ENSP00000437640:Y45C	ENSP00000284382:Y45C	Y	-	2	0	CERS3	98859444	0.992000	0.36948	0.007000	0.13788	0.722000	0.41435	0.336000	0.19823	-1.463000	0.01904	-0.924000	0.02725	TAT	T|0.888;C|0.112	0.112	strong		0.383	CERS3-002	KNOWN	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000313594.4	NM_178842	
RASGRP3	25780	hgsc.bcm.edu	37	2	33759395	33759395	+	Silent	SNP	C	C	T	rs35933402	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:33759395C>T	ENST00000403687.3	+	11	1829	c.1089C>T	c.(1087-1089)tcC>tcT	p.S363S	RASGRP3_ENST00000402538.3_Silent_p.S363S|RASGRP3_ENST00000407811.1_Silent_p.S363S	NM_001139488.1	NP_001132960.1	Q8IV61	GRP3_HUMAN	RAS guanyl releasing protein 3 (calcium and DAG-regulated)	363	Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00168}.				MAPK cascade (GO:0000165)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Rap GTPase activity (GO:0032854)|Ras protein signal transduction (GO:0007265)|small GTPase mediated signal transduction (GO:0007264)	guanyl-nucleotide exchange factor complex (GO:0032045)|integral component of plasma membrane (GO:0005887)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|diacylglycerol binding (GO:0019992)|guanyl-nucleotide exchange factor activity (GO:0005085)|Rap GTPase activator activity (GO:0046582)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)|signal transducer activity (GO:0004871)			large_intestine(3)|lung(3)|ovary(2)|pancreas(1)|stomach(2)	11	all_hematologic(175;0.115)					TGTAGCTTTCCCTGGACCTCT	0.328													C|||	442	0.0882588	0.0484	0.1931	5008	,	,		17421	0.006		0.1501	False		,,,				2504	0.089				p.S363S		Atlas-SNP	.											.	RASGRP3	87	.	0			c.C1089T						PASS	.	C	,,	200,3414		7,186,1614	103.0	88.0	93.0		1089,1089,1089	1.7	1.0	2	dbSNP_126	93	1225,6923		81,1063,2930	no	coding-synonymous,coding-synonymous,coding-synonymous	RASGRP3	NM_001139488.1,NM_015376.2,NM_170672.2	,,	88,1249,4544	TT,TC,CC		15.0344,5.534,12.1153	,,	363/691,363/690,363/691	33759395	1425,10337	1807	4074	5881	SO:0001819	synonymous_variant	25780	exon12			GCTTTCCCTGGAC	AB020653	CCDS46256.1, CCDS54346.1	2p25.1-p24.1	2013-01-10			ENSG00000152689	ENSG00000152689		"""EF-hand domain containing"""	14545	protein-coding gene	gene with protein product		609531				10048485, 10934204	Standard	NM_170672		Approved	KIAA0846, GRP3	uc002roy.3	Q8IV61	OTTHUMG00000152124	ENST00000403687.3:c.1089C>T	2.37:g.33759395C>T		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	87	49	0.563218	NM_170672	D6W583|O94931|Q53SD7	Silent	SNP	ENST00000403687.3	37	CCDS46256.1																																																																																			C|0.890;T|0.110	0.110	strong		0.328	RASGRP3-006	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000325462.2	NM_015376	
TTN	7273	hgsc.bcm.edu	37	2	179416556	179416556	+	Silent	SNP	A	A	C	rs11897366	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:179416556A>C	ENST00000591111.1	-	285	86372	c.86148T>G	c.(86146-86148)acT>acG	p.T28716T	TTN-AS1_ENST00000438095.1_RNA|TTN_ENST00000359218.5_Silent_p.T21417T|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN_ENST00000342992.6_Silent_p.T27789T|RP11-65L3.2_ENST00000603415.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN_ENST00000460472.2_Silent_p.T21292T|TTN-AS1_ENST00000591332.1_RNA|TTN_ENST00000589042.1_Silent_p.T30357T|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN_ENST00000342175.6_Silent_p.T21484T|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590932.1_RNA			Q8WZ42	TITIN_HUMAN	titin	28716	Fibronectin type-III 109. {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)			CATGGAATCCAGTAACTTCTG	0.418													A|||	763	0.152356	0.2738	0.183	5008	,	,		22144	0.0258		0.0527	False		,,,				2504	0.1994				p.T30357T		Atlas-SNP	.											.	TTN	18412	.	0			c.T91071G						PASS	.	A	,,,	980,2812		132,716,1048	162.0	165.0	164.0		63876,83367,64251,64452	-0.1	1.0	2	dbSNP_120	164	270,7962		9,252,3855	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	,,,	141,968,4903	CC,CA,AA		3.2799,25.8439,10.3959	,,,	21292/26927,27789/33424,21417/27052,21484/27119	179416556	1250,10774	1896	4116	6012	SO:0001819	synonymous_variant	7273	exon335			GAATCCAGTAACT	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.86148T>G	2.37:g.179416556A>C		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	108	47	0.435185	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|0.880;C|0.120	0.120	strong		0.418	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
RFPL1	5988	hgsc.bcm.edu	37	22	29837537	29837537	+	Missense_Mutation	SNP	T	T	C	rs3804076	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:29837537T>C	ENST00000354373.2	+	2	589	c.380T>C	c.(379-381)aTg>aCg	p.M127T	RFPL1S_ENST00000461286.3_RNA|RFPL1S_ENST00000539579.1_RNA	NM_021026.2	NP_066306.2	O75677	RFPL1_HUMAN	ret finger protein-like 1	127	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.		M -> T (in dbSNP:rs3804076). {ECO:0000269|PubMed:10508838, ECO:0000269|PubMed:15461802, ECO:0000269|PubMed:15489334}.				zinc ion binding (GO:0008270)			endometrium(3)|large_intestine(1)|lung(6)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	16						ACAGTGGATATGACCTTGGAT	0.488													-|||	1157	0.23103	0.0356	0.4006	5008	,	,		20603	0.1091		0.4384	False		,,,				2504	0.2873				p.M127T		Atlas-SNP	.											RFPL1,colon,carcinoma,0,1	RFPL1	43	1	0			c.T380C						PASS	.	T	THR/MET	403,4003		19,365,1819	105.0	93.0	97.0		380	1.1	0.3	22	dbSNP_107	97	3740,4860		821,2098,1381	no	missense	RFPL1	NM_021026.2	81	840,2463,3200	CC,CT,TT		43.4884,9.1466,31.8545	possibly-damaging	127/318	29837537	4143,8863	2203	4300	6503	SO:0001583	missense	5988	exon2			TGGATATGACCTT	AJ010228	CCDS13857.2	22q12	2006-04-25			ENSG00000128250	ENSG00000128250		"""RING-type (C3HC4) zinc fingers"""	9977	protein-coding gene	gene with protein product		605968				10508838	Standard	NM_021026		Approved	RNF78	uc003afn.3	O75677	OTTHUMG00000150516	ENST00000354373.2:c.380T>C	22.37:g.29837537T>C	ENSP00000346342:p.Met127Thr	Somatic	242	0	0		WXS	Illumina HiSeq	Phase_I	170	78	0.458824	NM_021026	Q6IC06|Q9UJ97	Missense_Mutation	SNP	ENST00000354373.2	37	CCDS13857.2	571	0.26144688644688646	26	0.052845528455284556	141	0.38950276243093923	73	0.12762237762237763	331	0.4366754617414248	-	14.91	2.676780	0.47886	0.091466	0.434884	ENSG00000128250	ENST00000354373	T	0.10477	2.87	1.1	1.1	0.20463	Concanavalin A-like lectin/glucanase (1);SPRY-associated (1);Butyrophylin-like (1);B30.2/SPRY domain (1);	.	.	.	.	T	0.00012	0.0000	M	0.88570	2.965	0.41774	P	0.010213999999999945	D	0.58268	0.982	D	0.87578	0.998	T	0.39981	-0.9587	8	0.59425	D	0.04	.	6.3123	0.21171	0.0:0.0:0.0:1.0	rs3804076;rs3804076	127	O75677	RFPL1_HUMAN	T	127	ENSP00000346342:M127T	ENSP00000346342:M127T	M	+	2	0	RFPL1	28167537	0.939000	0.31865	0.345000	0.25642	0.354000	0.29330	3.478000	0.53158	0.744000	0.32741	0.348000	0.21847	ATG	T|0.702;C|0.298	0.298	strong		0.488	RFPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318719.1	NM_021026	
CCDC185	164127	hgsc.bcm.edu	37	1	223568034	223568034	+	Missense_Mutation	SNP	G	G	A	rs376013077		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:223568034G>A	ENST00000366875.3	+	1	1320	c.1217G>A	c.(1216-1218)cGc>cAc	p.R406H		NM_152610.2	NP_689823.2	Q8N715	CC185_HUMAN		406										breast(4)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(12)|skin(3)	29				GBM - Glioblastoma multiforme(131;0.0704)		GAAGCCTGTCGCAAGAGGCAC	0.632																																					p.R406H		Atlas-SNP	.											C1orf65,trunk,malignant_melanoma,+1,1	C1orf65	71	1	0			c.G1217A						scavenged	.						33.0	30.0	31.0					1																	223568034		2201	4297	6498	SO:0001583	missense	164127	exon1			CCTGTCGCAAGAG																												ENST00000366875.3:c.1217G>A	1.37:g.223568034G>A	ENSP00000355840:p.Arg406His	Somatic	275	0	0		WXS	Illumina HiSeq	Phase_I	242	5	0.0206612	NM_152610	Q8N746|Q8NA93	Missense_Mutation	SNP	ENST00000366875.3	37	CCDS1537.1	.	.	.	.	.	.	.	.	.	.	G	7.043	0.562865	0.13498	.	.	ENSG00000178395	ENST00000366875	T	0.21932	1.98	5.55	-3.75	0.04372	.	.	.	.	.	T	0.06554	0.0168	N	0.08118	0	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.38351	-0.9665	9	0.10902	T	0.67	.	1.0101	0.01495	0.2065:0.36:0.1769:0.2565	.	406	Q8N715	CA065_HUMAN	H	406	ENSP00000355840:R406H	ENSP00000355840:R406H	R	+	2	0	C1orf65	221634657	0.000000	0.05858	0.000000	0.03702	0.770000	0.43624	-0.274000	0.08537	-0.700000	0.05070	-0.345000	0.07892	CGC	.	.	none		0.632	C1orf65-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092718.1		
ZFP64	55734	hgsc.bcm.edu	37	20	50803444	50803444	+	Silent	SNP	C	C	T	rs36027430	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:50803444C>T	ENST00000216923.4	-	2	562	c.213G>A	c.(211-213)tcG>tcA	p.S71S	ZFP64_ENST00000346617.4_Silent_p.S71S|ZFP64_ENST00000371515.4_Silent_p.S69S|ZFP64_ENST00000361387.2_Silent_p.S71S|ZFP64_ENST00000371518.2_Silent_p.S71S	NM_018197.2|NM_199426.1	NP_060667.2|NP_955458.1	Q9NPA5	ZF64A_HUMAN	ZFP64 zinc finger protein	71					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(5)|large_intestine(8)|lung(11)|ovary(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	33						CTGTTTCCTCCGATACAAACT	0.577													C|||	842	0.168131	0.3154	0.1643	5008	,	,		16761	0.1736		0.0706	False		,,,				2504	0.0665				p.S71S		Atlas-SNP	.											.	ZFP64	240	.	0			c.G213A						PASS	.	C	,,,	1206,3200	419.3+/-338.6	170,866,1167	138.0	121.0	127.0		213,213,207,213	-11.2	0.0	20	dbSNP_126	127	493,8107	142.3+/-198.5	8,477,3815	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ZFP64	NM_018197.2,NM_022088.4,NM_199426.1,NM_199427.2	,,,	178,1343,4982	TT,TC,CC		5.7326,27.3718,13.0632	,,,	71/682,71/628,69/680,71/646	50803444	1699,11307	2203	4300	6503	SO:0001819	synonymous_variant	55734	exon2			TTCCTCCGATACA	AK001596	CCDS13439.1, CCDS13440.1, CCDS13441.1, CCDS13442.1	20q13.11-q13.13	2013-01-08	2012-11-27		ENSG00000020256	ENSG00000020256		"""Zinc fingers, C2H2-type"""	15940	protein-coding gene	gene with protein product			"""zinc finger protein 338"", ""zinc finger protein 64 homolog (mouse)"", ""zinc finger protein 64"""	ZNF338		9034307	Standard	NM_199427		Approved	FLJ10734, dJ831D17.1, FLJ12628, dJ548G19.1	uc002xwl.3	Q9NPA5	OTTHUMG00000032756	ENST00000216923.4:c.213G>A	20.37:g.50803444C>T		Somatic	232	1	0.00431034		WXS	Illumina HiSeq	Phase_I	191	88	0.460733	NM_018197	Q9NTS7|Q9NVH4	Silent	SNP	ENST00000216923.4	37	CCDS13440.1																																																																																			C|0.865;T|0.135	0.135	strong		0.577	ZFP64-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000079744.1	NM_018197	
XAB2	56949	hgsc.bcm.edu	37	19	7694393	7694393	+	Silent	SNP	G	G	A	rs4134809	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:7694393G>A	ENST00000358368.4	-	1	58	c.21C>T	c.(19-21)ctC>ctT	p.L7L	PET100_ENST00000456958.3_5'Flank|XAB2_ENST00000534844.1_Silent_p.L4L|CTD-3214H19.4_ENST00000595866.1_5'Flank|PET100_ENST00000601406.1_5'Flank|PET100_ENST00000594797.1_5'Flank	NM_020196.2	NP_064581.2	Q9HCS7	SYF1_HUMAN	XPA binding protein 2	7					blastocyst development (GO:0001824)|DNA repair (GO:0006281)|mRNA splicing, via spliceosome (GO:0000398)|nucleotide-excision repair (GO:0006289)|transcription, DNA-templated (GO:0006351)|transcription-coupled nucleotide-excision repair (GO:0006283)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				breast(1)|central_nervous_system(2)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(2)|lung(11)|prostate(1)|skin(2)|urinary_tract(1)	26						CGGGCCGCGAGAGTCGCGCCA	0.667								Direct reversal of damage;Nucleotide excision repair (NER)					G|||	1320	0.263578	0.2103	0.2219	5008	,	,		14881	0.2083		0.3777	False		,,,				2504	0.3047				p.L7L		Atlas-SNP	.											.	XAB2	69	.	0			c.C21T						PASS	.	G		915,3483		96,723,1380	25.0	27.0	26.0		21	-8.9	0.0	19	dbSNP_108	26	3162,5430		573,2016,1707	no	coding-synonymous	XAB2	NM_020196.2		669,2739,3087	AA,AG,GG		36.8017,20.8049,31.3857		7/856	7694393	4077,8913	2199	4296	6495	SO:0001819	synonymous_variant	56949	exon1			CCGCGAGAGTCGC	AB026111	CCDS32892.1	19p13.3	2013-08-21				ENSG00000076924			14089	protein-coding gene	gene with protein product	"""SYF1 homolog, RNA splicing factor (S. cerevisiae)"", ""SYF1 pre-mRNA-splicing factor"""	610850				10944529	Standard	NM_020196		Approved	HCNP, HCRN, SYF1, NTC90	uc002mgx.3	Q9HCS7		ENST00000358368.4:c.21C>T	19.37:g.7694393G>A		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	135	60	0.444444	NM_020196	Q8TET6|Q96HB0|Q96IW0|Q9NRG6|Q9ULP3	Silent	SNP	ENST00000358368.4	37	CCDS32892.1																																																																																			G|0.720;A|0.280	0.280	strong		0.667	XAB2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000461021.1	NM_020196	
THBS1	7057	hgsc.bcm.edu	37	15	39885301	39885301	+	Silent	SNP	T	T	C	rs2228263	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:39885301T>C	ENST00000260356.5	+	18	3033	c.2868T>C	c.(2866-2868)gaT>gaC	p.D956D	CTD-2033D15.1_ENST00000560769.1_RNA	NM_003246.2	NP_003237.2	P07996	TSP1_HUMAN	thrombospondin 1	956					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)		GTGAGACCGATTTCCGCCGAT	0.502													T|||	574	0.114617	0.2224	0.1037	5008	,	,		20624	0.002		0.159	False		,,,				2504	0.047				p.D956D		Atlas-SNP	.											.	THBS1	106	.	0			c.T2868C						PASS	.	T		920,3480	351.3+/-311.2	108,704,1388	81.0	69.0	73.0		2868	2.2	1.0	15	dbSNP_98	73	1461,7133	277.5+/-292.9	110,1241,2946	no	coding-synonymous	THBS1	NM_003246.2		218,1945,4334	CC,CT,TT		17.0002,20.9091,18.3238		956/1171	39885301	2381,10613	2200	4297	6497	SO:0001819	synonymous_variant	7057	exon18			GACCGATTTCCGC		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.2868T>C	15.37:g.39885301T>C		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	115	57	0.495652	NM_003246	A8K6H4|B4E3J7|B9EGH6|Q15667|Q59E99	Silent	SNP	ENST00000260356.5	37	CCDS32194.1																																																																																			T|0.841;C|0.159	0.159	strong		0.502	THBS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257831.2	NM_003246	
CLDN5	7122	hgsc.bcm.edu	37	22	19511925	19511925	+	Nonsense_Mutation	SNP	G	G	A	rs885985	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:19511925G>A	ENST00000406028.1	-	2	1169	c.109C>T	c.(109-111)Cag>Tag	p.Q37*	CLDN5_ENST00000403084.1_Nonsense_Mutation_p.Q37*|CLDN5_ENST00000413119.2_Nonsense_Mutation_p.Q37*			O00501	CLD5_HUMAN	claudin 5	0					calcium-independent cell-cell adhesion (GO:0016338)|myelination (GO:0042552)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|Schmidt-Lanterman incisure (GO:0043220)|tight junction (GO:0005923)	identical protein binding (GO:0042802)|structural molecule activity (GO:0005198)			liver(1)|lung(2)|prostate(1)	4	Colorectal(54;0.0993)					CGCACCTCCTGGGTCTGCCAG	0.751													A|||	2488	0.496805	0.2073	0.5879	5008	,	,		11791	0.5298		0.5567	False		,,,				2504	0.728				p.Q37X		Atlas-SNP	.											.	CLDN5	22	.	0			c.C109T						PASS	.						3.0	4.0	4.0					22																	19511925		571	1393	1964	SO:0001587	stop_gained	7122	exon1			CCTCCTGGGTCTG	AF000959	CCDS13763.2	22q11.21	2008-08-01	2008-08-01		ENSG00000184113	ENSG00000184113		"""Claudins"""	2047	protein-coding gene	gene with protein product		602101	"""transmembrane protein deleted in velocardiofacial syndrome"""	AWAL, TMVCF		9441748, 9192844	Standard	NM_003277		Approved	CPETRL1, BEC1	uc002zpu.2	O00501	OTTHUMG00000150441	ENST00000406028.1:c.109C>T	22.37:g.19511925G>A	ENSP00000385477:p.Gln37*	Somatic	18	0	0		WXS	Illumina HiSeq	Phase_I	27	20	0.740741	NM_001130861	B3KS11|Q53XW2|Q8WUW3	Nonsense_Mutation	SNP	ENST00000406028.1	37	CCDS13763.2	1017	0.46565934065934067	109	0.22154471544715448	199	0.5497237569060773	287	0.5017482517482518	422	0.5567282321899736	A	23.9	4.466684	0.84425	.	.	ENSG00000184113	ENST00000406028;ENST00000403084;ENST00000413119	.	.	.	5.24	-6.49	0.01890	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	.	3.0235	0.06083	0.3175:0.1814:0.409:0.0921	rs885985;rs17209295;rs885985	.	.	.	X	37	.	ENSP00000384554:Q37X	Q	-	1	0	CLDN5	17891925	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.689000	0.05144	-1.461000	0.01909	-2.530000	0.00182	CAG	G|0.554;A|0.446	0.446	strong		0.751	CLDN5-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318122.3	NM_003277	
RPP38	10557	hgsc.bcm.edu	37	10	15145361	15145361	+	Silent	SNP	G	G	A	rs35539850	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:15145361G>A	ENST00000378197.4	+	3	562	c.48G>A	c.(46-48)acG>acA	p.T16T	RPP38_ENST00000451677.1_Intron|NMT2_ENST00000466201.1_5'UTR|RPP38_ENST00000378202.5_Silent_p.T16T	NM_183005.4	NP_892117.1	P78345	RPP38_HUMAN	ribonuclease P/MRP 38kDa subunit	16					RNA phosphodiester bond hydrolysis (GO:0090501)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|tRNA processing (GO:0008033)	nucleolar ribonuclease P complex (GO:0005655)|nucleus (GO:0005634)	ribonuclease P activity (GO:0004526)			breast(1)|endometrium(3)|large_intestine(1)|lung(2)|ovary(1)	8						TCCGTAAGACGAGACCTCTGG	0.502													G|||	511	0.102037	0.1112	0.0951	5008	,	,		15633	0.0506		0.1392	False		,,,				2504	0.1094				p.T16T	GBM(118;1591 1611 9649 34378 50720)	Atlas-SNP	.											.	RPP38	26	.	0			c.G48A						PASS	.	G	,,	572,3834	251.8+/-258.4	41,490,1672	71.0	75.0	73.0		48,48,48	-11.5	0.1	10	dbSNP_126	73	1320,7280	258.4+/-282.1	107,1106,3087	no	coding-synonymous,coding-synonymous,coding-synonymous	RPP38	NM_001097590.1,NM_006414.3,NM_183005.3	,,	148,1596,4759	AA,AG,GG		15.3488,12.9823,14.5471	,,	16/284,16/284,16/284	15145361	1892,11114	2203	4300	6503	SO:0001819	synonymous_variant	10557	exon2			TAAGACGAGACCT	U77664	CCDS7108.1	10p13	2012-05-21			ENSG00000152464	ENSG00000152464			30329	protein-coding gene	gene with protein product		606116				9037013, 9630247	Standard	NM_183005		Approved		uc001inx.5	P78345	OTTHUMG00000017728	ENST00000378197.4:c.48G>A	10.37:g.15145361G>A		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	75	43	0.573333	NM_001265601	B3KPY0|D3DRT8|Q53F71|Q8NHS8	Silent	SNP	ENST00000378197.4	37	CCDS7108.1																																																																																			T|0.000;G|0.863;C|0.000;A|0.136	0.136	strong		0.502	RPP38-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046976.1	NM_006414	
PHF2	5253	hgsc.bcm.edu	37	9	96407920	96407920	+	Silent	SNP	C	C	T	rs7038310	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:96407920C>T	ENST00000359246.4	+	4	676	c.309C>T	c.(307-309)gaC>gaT	p.D103D	PHF2_ENST00000375376.4_Intron	NM_005392.3	NP_005383.3	O75151	PHF2_HUMAN	PHD finger protein 2	103					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)		GTGCTGAAGACGTGGTGGCCC	0.647													C|||	258	0.0515176	0.0408	0.0461	5008	,	,		20457	0.0694		0.0656	False		,,,				2504	0.0368				p.D103D		Atlas-SNP	.											.	PHF2	113	.	0			c.C309T						PASS	.	C		211,4195	130.6+/-167.2	5,201,1997	80.0	75.0	77.0		309	-9.2	0.3	9	dbSNP_116	77	728,7872	177.5+/-227.1	38,652,3610	no	coding-synonymous	PHF2	NM_005392.3		43,853,5607	TT,TC,CC		8.4651,4.7889,7.2197		103/1097	96407920	939,12067	2203	4300	6503	SO:0001819	synonymous_variant	5253	exon4			TGAAGACGTGGTG	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.309C>T	9.37:g.96407920C>T		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	44	21	0.477273	NM_005392	Q4VXG0|Q8N3K2|Q9Y6N4	Silent	SNP	ENST00000359246.4	37	CCDS35069.1																																																																																			C|0.932;T|0.068	0.068	strong		0.647	PHF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053162.1	NM_005392	
GPRIN1	114787	hgsc.bcm.edu	37	5	176026138	176026138	+	Missense_Mutation	SNP	T	T	A	rs142779818|rs550332435|rs201635586|rs371149640|rs386695335	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:176026138T>A	ENST00000303991.4	-	2	875	c.698A>T	c.(697-699)gAg>gTg	p.E233V		NM_052899.2	NP_443131.2	Q7Z2K8	GRIN1_HUMAN	G protein regulated inducer of neurite outgrowth 1	233				Missing (in Ref. 4; CAD38868). {ECO:0000305}.	neuron projection development (GO:0031175)	cell projection (GO:0042995)|plasma membrane (GO:0005886)				NS(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(3)|liver(1)|lung(15)|ovary(2)|prostate(5)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	35	all_cancers(89;0.00263)|Renal(175;0.000269)|Lung NSC(126;0.00902)|all_lung(126;0.0142)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CCCAGGATCCTCCTTCCTCGG	0.488																																					p.E233V		Atlas-SNP	.											.	GPRIN1	77	.	0			c.A698T						PASS	.						87.0	88.0	88.0					5																	176026138		2153	4218	6371	SO:0001583	missense	114787	exon2			GGATCCTCCTTCC	AB067480	CCDS4405.1	5q35.2	2008-02-05			ENSG00000169258	ENSG00000169258			24835	protein-coding gene	gene with protein product		611239				11572484	Standard	NM_052899		Approved	GRIN1, KIAA1893	uc003meo.1	Q7Z2K8	OTTHUMG00000130659	ENST00000303991.4:c.698A>T	5.37:g.176026138T>A	ENSP00000305839:p.Glu233Val	Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	125	35	0.28	NM_052899	C9JM70|Q8ND74|Q96PZ4	Missense_Mutation	SNP	ENST00000303991.4	37	CCDS4405.1	.	.	.	.	.	.	.	.	.	.	T	12.30	1.897302	0.33535	.	.	ENSG00000169258	ENST00000303991;ENST00000335532	T	0.09163	3.01	4.92	2.48	0.30137	.	0.222228	0.23132	N	0.051562	T	0.12561	0.0305	M	0.77103	2.36	0.09310	N	1	B	0.30146	0.27	B	0.31337	0.128	T	0.18429	-1.0337	10	0.40728	T	0.16	-7.1862	3.6069	0.08046	0.1625:0.1858:0.0:0.6517	.	233	Q7Z2K8	GRIN1_HUMAN	V	233	ENSP00000305839:E233V	ENSP00000305839:E233V	E	-	2	0	GPRIN1	175958744	0.024000	0.19004	0.794000	0.32065	0.466000	0.32739	1.906000	0.39887	0.731000	0.32448	0.260000	0.18958	GAG	T|0.795;A|0.205	0.205	strong		0.488	GPRIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253149.1	NM_052899	
UHRF1BP1	54887	hgsc.bcm.edu	37	6	34831856	34831856	+	Missense_Mutation	SNP	T	T	C	rs13205210	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:34831856T>C	ENST00000192788.5	+	15	3464	c.3293T>C	c.(3292-3294)aTg>aCg	p.M1098T	UHRF1BP1_ENST00000452449.2_Missense_Mutation_p.M1098T	NM_017754.3	NP_060224.3	Q6BDS2	URFB1_HUMAN	UHRF1 binding protein 1	1098			M -> T (in dbSNP:rs13205210).				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						TTTTTCTCCATGAAGAGGACG	0.488													T|||	720	0.14377	0.2133	0.1081	5008	,	,		19013	0.1339		0.1352	False		,,,				2504	0.0941				p.M1098T		Atlas-SNP	.											.	UHRF1BP1	102	.	0			c.T3293C						PASS	.	T	THR/MET	778,3248		73,632,1308	114.0	123.0	120.0		3293	6.0	1.0	6	dbSNP_121	120	924,7386		66,792,3297	yes	missense	UHRF1BP1	NM_017754.3	81	139,1424,4605	CC,CT,TT		11.1191,19.3244,13.797	possibly-damaging	1098/1441	34831856	1702,10634	2013	4155	6168	SO:0001583	missense	54887	exon15			TCTCCATGAAGAG	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.3293T>C	6.37:g.34831856T>C	ENSP00000192788:p.Met1098Thr	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	109	49	0.449541	NM_017754	Q9NXE0	Missense_Mutation	SNP	ENST00000192788.5	37	CCDS43455.1	311	0.1423992673992674	102	0.2073170731707317	42	0.11602209944751381	73	0.12762237762237763	94	0.12401055408970976	T	21.5	4.165605	0.78339	0.193244	0.111191	ENSG00000065060	ENST00000192788;ENST00000452449	T;T	0.18016	2.24;2.24	6.04	6.04	0.98038	.	0.039451	0.85682	D	0.000000	T	0.08403	0.0209	N	0.19112	0.55	0.20196	P	0.9999201035	P	0.44429	0.835	B	0.43445	0.42	T	0.04991	-1.0913	9	0.87932	D	0	-25.5457	15.1474	0.72667	0.0:0.0:0.0:1.0	rs13205210;rs52805012;rs59502513;rs13205210	1098	Q6BDS2	URFB1_HUMAN	T	1098	ENSP00000192788:M1098T;ENSP00000400628:M1098T	ENSP00000192788:M1098T	M	+	2	0	UHRF1BP1	34939834	1.000000	0.71417	1.000000	0.80357	0.796000	0.44982	6.833000	0.75334	2.317000	0.78254	0.459000	0.35465	ATG	T|0.851;C|0.149	0.149	strong		0.488	UHRF1BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040260.1	NM_017754	
NAV3	89795	hgsc.bcm.edu	37	12	78574783	78574783	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:78574783C>A	ENST00000397909.2	+	30	5823	c.5650C>A	c.(5650-5652)Ctt>Att	p.L1884I	NAV3_ENST00000266692.7_Missense_Mutation_p.L1685I|NAV3_ENST00000552300.1_3'UTR|NAV3_ENST00000228327.6_Missense_Mutation_p.L1862I|NAV3_ENST00000536525.2_Missense_Mutation_p.L1862I			Q8IVL0	NAV3_HUMAN	neuron navigator 3	1884	Ser-rich.					membrane (GO:0016020)|nuclear envelope (GO:0005635)				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						GTCATTAGGACTTTCTCTAAA	0.488										HNSCC(70;0.22)																											p.L1862I		Atlas-SNP	.											.	NAV3	506	.	0			c.C5584A						PASS	.						116.0	117.0	117.0					12																	78574783		2000	4164	6164	SO:0001583	missense	89795	exon29			TTAGGACTTTCTC	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.5650C>A	12.37:g.78574783C>A	ENSP00000381007:p.Leu1884Ile	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	103	18	0.174757	NM_014903	Q8NFW7|Q9Y2E7	Missense_Mutation	SNP	ENST00000397909.2	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	27.9|27.9	4.869227|4.869227	0.91587|0.91587	.|.	.|.	ENSG00000067798|ENSG00000067798	ENST00000536525;ENST00000397909;ENST00000228327;ENST00000266692;ENST00000378640;ENST00000550788|ENST00000552895	T;T;T;T;T|.	0.32023|.	1.53;1.51;1.52;1.47;2.32|.	6.02|6.02	6.02|6.02	0.97574|0.97574	.|.	0.000000|.	0.36034|.	U|.	0.002827|.	T|T	0.76285|0.76285	0.3966|0.3966	M|M	0.66939|0.66939	2.045|2.045	0.80722|0.80722	D|D	1|1	D;D;D;D|.	0.76494|.	0.998;0.996;0.999;0.998|.	D;D;D;D|.	0.83275|.	0.949;0.986;0.996;0.99|.	T|T	0.72404|0.72404	-0.4304|-0.4304	10|5	0.59425|.	D|.	0.04|.	-12.5593|-12.5593	20.547|20.547	0.99278|0.99278	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	1862;1685;1884;1862|.	E7EUC6;Q8IVL0-3;Q8IVL0;Q8IVL0-2|.	.;.;NAV3_HUMAN;.|.	I|N	1862;1884;1862;1685;476;484|756	ENSP00000446132:L1862I;ENSP00000381007:L1884I;ENSP00000228327:L1862I;ENSP00000266692:L1685I;ENSP00000448303:L484I|.	ENSP00000228327:L1862I|.	L|T	+|+	1|2	0|0	NAV3|NAV3	77098914|77098914	1.000000|1.000000	0.71417|0.71417	0.417000|0.417000	0.26559|0.26559	0.868000|0.868000	0.49771|0.49771	7.487000|7.487000	0.81328|0.81328	2.850000|2.850000	0.98022|0.98022	0.650000|0.650000	0.86243|0.86243	CTT|ACT	.	.	none		0.488	NAV3-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000406812.1	NM_001024383	
SETX	23064	hgsc.bcm.edu	37	9	135139901	135139901	+	Missense_Mutation	SNP	T	T	C	rs1056899	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:135139901T>C	ENST00000224140.5	-	26	7941	c.7759A>G	c.(7759-7761)Ata>Gta	p.I2587V	SETX_ENST00000393220.1_Missense_Mutation_p.I2554V|SETX_ENST00000372169.2_Missense_Mutation_p.I2616V|SETX_ENST00000477049.1_5'UTR	NM_015046.5	NP_055861.3	Q7Z333	SETX_HUMAN	senataxin	2587			I -> V (in dbSNP:rs1056899). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005}.		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)		GGCTGCTGTATATGGCTCAGG	0.632													C|||	2698	0.538738	0.8094	0.3487	5008	,	,		15929	0.6835		0.2694	False		,,,				2504	0.4356				p.I2587V		Atlas-SNP	.											.	SETX	234	.	0			c.A7759G						PASS	.	C	VAL/ILE	3227,1179	410.0+/-335.2	1199,829,175	65.0	76.0	72.0		7759	-3.8	0.0	9	dbSNP_86	72	2550,6050	690.4+/-404.4	374,1802,2124	yes	missense	SETX	NM_015046.5	29	1573,2631,2299	CC,CT,TT		29.6512,26.759,44.418	benign	2587/2678	135139901	5777,7229	2203	4300	6503	SO:0001583	missense	23064	exon26			GCTGTATATGGCT	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.7759A>G	9.37:g.135139901T>C	ENSP00000224140:p.Ile2587Val	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	48	22	0.458333	NM_015046	A2A396|B2RPB2|B5ME16|C9JQ10|O75120|Q3KQX4|Q5JUJ1|Q68DW5|Q6AZD7|Q7Z3J6|Q8WX33|Q9H9D1|Q9NVP9	Missense_Mutation	SNP	ENST00000224140.5	37	CCDS6947.1	1114	0.51007326007326	380	0.7723577235772358	137	0.3784530386740331	395	0.6905594405594405	202	0.26649076517150394	C	0.692	-0.794242	0.02862	0.73241	0.296512	ENSG00000107290	ENST00000224140;ENST00000436441;ENST00000372169;ENST00000393220	D;D;D;D	0.89681	-1.95;-2.55;-2.03;-1.66	5.0	-3.8	0.04307	.	1.973910	0.02590	N	0.099880	T	0.00012	0.0000	N	0.04880	-0.145	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	0.48581	-0.9023	9	0.02654	T	1	.	0.0833	0.00033	0.3191:0.1632:0.2101:0.3076	rs1056899;rs3197515;rs3739926;rs59785171;rs1056899	2554;2587;2616	Q7Z333-3;Q7Z333;Q7Z333-4	.;SETX_HUMAN;.	V	2587;858;2616;2554	ENSP00000224140:I2587V;ENSP00000409143:I858V;ENSP00000361242:I2616V;ENSP00000376913:I2554V	ENSP00000224140:I2587V	I	-	1	0	SETX	134129722	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.111000	0.03303	-0.616000	0.05671	-1.383000	0.01170	ATA	T|0.505;C|0.495	0.495	strong		0.632	SETX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054774.3	NM_015046	
MCL1	4170	hgsc.bcm.edu	37	1	150550920	150550920	+	Missense_Mutation	SNP	A	A	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:150550920A>C	ENST00000369026.2	-	2	795	c.736T>G	c.(736-738)Ttg>Gtg	p.L246V	MCL1_ENST00000464132.1_5'UTR|MCL1_ENST00000307940.3_Intron	NM_001197320.1|NM_021960.4	NP_001184249.1|NP_068779.1	Q07820	MCL1_HUMAN	myeloid cell leukemia 1	246					apoptotic mitochondrial changes (GO:0008637)|cell fate determination (GO:0001709)|cellular homeostasis (GO:0019725)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|multicellular organismal development (GO:0007275)|negative regulation of anoikis (GO:2000811)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway (GO:1903378)|protein transmembrane transport (GO:0071806)|regulation of response to DNA damage stimulus (GO:2001020)|response to cytokine (GO:0034097)	Bcl-2 family protein complex (GO:0097136)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial matrix (GO:0005759)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	BH3 domain binding (GO:0051434)|protein channel activity (GO:0015266)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			endometrium(2)|large_intestine(1)|lung(4)|prostate(1)	8	all_cancers(9;1.69e-53)|all_epithelial(9;1.95e-43)|all_lung(15;1.09e-34)|Lung NSC(24;4.04e-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)			ACTCGAGACAACGATTTCACA	0.478																																					p.L246V		Atlas-SNP	.											.	MCL1	27	.	0			c.T736G						PASS	.						106.0	108.0	107.0					1																	150550920		2203	4300	6503	SO:0001583	missense	4170	exon2			GAGACAACGATTT	BC017197	CCDS956.1, CCDS957.1, CCDS72909.1	1q21	2014-03-07	2014-03-07		ENSG00000143384	ENSG00000143384			6943	protein-coding gene	gene with protein product		159552	"""myeloid cell leukemia sequence 1 (BCL2-related)"""			7682708, 7835896	Standard	NM_021960		Approved	BCL2L3, Mcl-1	uc001euz.3	Q07820	OTTHUMG00000034867	ENST00000369026.2:c.736T>G	1.37:g.150550920A>C	ENSP00000358022:p.Leu246Val	Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	107	28	0.261682	NM_021960	B2R6B2|D3DV03|D3DV04|Q9HD91|Q9NRQ3|Q9NRQ4|Q9UHR7|Q9UHR8|Q9UHR9|Q9UNJ1	Missense_Mutation	SNP	ENST00000369026.2	37	CCDS957.1	.	.	.	.	.	.	.	.	.	.	A	12.37	1.917467	0.33815	.	.	ENSG00000143384	ENST00000369026;ENST00000439749	T	0.04603	3.59	4.77	1.08	0.20341	Apoptosis regulator, Bcl2-like (1);Apoptosis regulator, Bcl-2, BH (3);	0.298701	0.31601	N	0.007374	T	0.00815	0.0027	N	0.11560	0.145	0.80722	D	1	B	0.06786	0.001	B	0.15484	0.013	T	0.46965	-0.9153	10	0.33141	T	0.24	-5.5956	4.6041	0.12368	0.4735:0.2298:0.2967:0.0	.	246	Q07820	MCL1_HUMAN	V	246;175	ENSP00000358022:L246V	ENSP00000358022:L246V	L	-	1	2	MCL1	148817544	0.087000	0.21565	0.993000	0.49108	0.996000	0.88848	0.574000	0.23714	0.345000	0.23873	0.533000	0.62120	TTG	.	.	none		0.478	MCL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084402.1	NM_021960	
CEP152	22995	hgsc.bcm.edu	37	15	49048705	49048705	+	Missense_Mutation	SNP	G	G	C	rs16961560	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:49048705G>C	ENST00000380950.2	-	20	2927	c.2740C>G	c.(2740-2742)Ctt>Gtt	p.L914V	CEP152_ENST00000399334.3_Missense_Mutation_p.L914V|CEP152_ENST00000325747.5_Missense_Mutation_p.L821V	NM_001194998.1|NM_014985.3	NP_001181927.1|NP_055800.2	O94986	CE152_HUMAN	centrosomal protein 152kDa	914			L -> V (in dbSNP:rs16961560).		cell projection organization (GO:0030030)|centriole replication (GO:0007099)|centrosome duplication (GO:0051298)|de novo centriole assembly (GO:0098535)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytosol (GO:0005829)|deuterosome (GO:0098536)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)			breast(3)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(16)|lung(30)|ovary(1)|prostate(2)|skin(2)	63		all_lung(180;0.0428)		all cancers(107;1.08e-07)|GBM - Glioblastoma multiforme(94;2.32e-06)		ATATTTTCAAGCTCACTCTTC	0.353													G|||	253	0.0505192	0.0053	0.0476	5008	,	,		17356	0.0724		0.0815	False		,,,				2504	0.0593				p.L914V		Atlas-SNP	.											.	CEP152	145	.	0			c.C2740G						PASS	.	G	VAL/LEU,VAL/LEU	50,3578		0,50,1764	42.0	40.0	41.0		2740,2740	0.3	0.9	15	dbSNP_123	41	603,7539		16,571,3484	yes	missense,missense	CEP152	NM_001194998.1,NM_014985.3	32,32	16,621,5248	CC,CG,GG		7.406,1.3782,5.548	benign,benign	914/1711,914/1655	49048705	653,11117	1814	4071	5885	SO:0001583	missense	22995	exon20			TTTCAAGCTCACT	AB020719	CCDS42033.1, CCDS58361.1	15q21.1	2014-02-20							29298	protein-coding gene	gene with protein product	"""asterless"""	613529	"""microcephaly, primary autosomal recessive 4"""	MCPH4		14654843, 21131973	Standard	NM_014985		Approved	KIAA0912, SCKL5	uc001zwz.3	O94986		ENST00000380950.2:c.2740C>G	15.37:g.49048705G>C	ENSP00000370337:p.Leu914Val	Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	50	19	0.38	NM_014985	E7ER66|Q17RV1|Q6NTA0	Missense_Mutation	SNP	ENST00000380950.2	37	CCDS58361.1	130	0.05952380952380952	3	0.006097560975609756	12	0.03314917127071823	47	0.08216783216783216	68	0.08970976253298153	G	7.966	0.748128	0.15710	0.013782	0.07406	ENSG00000103995	ENST00000380950;ENST00000325747;ENST00000399334	T;T;T	0.54866	0.55;0.58;0.57	5.68	0.317	0.15861	.	0.691841	0.14451	N	0.318785	T	0.01287	0.0042	L	0.40543	1.245	0.80722	P	0.0	B;B;B	0.12013	0.001;0.005;0.005	B;B;B	0.12156	0.003;0.007;0.004	T	0.08513	-1.0718	9	0.17369	T	0.5	-0.3226	1.1175	0.01718	0.1777:0.1994:0.2942:0.3287	rs16961560;rs16961560	821;914;914	O94986-1;E7ER66;O94986	.;.;CE152_HUMAN	V	914;821;914	ENSP00000370337:L914V;ENSP00000321000:L821V;ENSP00000382271:L914V	ENSP00000321000:L821V	L	-	1	0	CEP152	46835997	0.606000	0.26949	0.894000	0.35097	0.974000	0.67602	0.785000	0.26830	-0.108000	0.12066	-0.229000	0.12294	CTT	G|0.933;C|0.067	0.067	strong		0.353	CEP152-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417365.1	NM_014985	
PTPRF	5792	hgsc.bcm.edu	37	1	44083519	44083519	+	Silent	SNP	G	G	A	rs641351	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:44083519G>A	ENST00000359947.4	+	25	4648	c.4308G>A	c.(4306-4308)agG>agA	p.R1436R	PTPRF_ENST00000372414.3_Silent_p.R1436R|PTPRF_ENST00000372413.3_Silent_p.R1427R|PTPRF_ENST00000496447.1_3'UTR|PTPRF_ENST00000422171.2_Silent_p.R795R|PTPRF_ENST00000438120.1_Silent_p.R1427R	NM_002840.3	NP_002831.2	P10586	PTPRF_HUMAN	protein tyrosine phosphatase, receptor type, F	1436	Tyrosine-protein phosphatase 1. {ECO:0000255|PROSITE-ProRule:PRU00160}.				cell adhesion (GO:0007155)|cell migration (GO:0016477)|negative regulation of receptor binding (GO:1900121)|peptidyl-tyrosine dephosphorylation (GO:0035335)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	heparin binding (GO:0008201)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(2)|breast(4)|central_nervous_system(3)|endometrium(9)|kidney(4)|large_intestine(11)|liver(1)|lung(24)|ovary(4)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)	72	all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)				ATTTCTGGAGGATGGTGTGGG	0.617													A|||	3692	0.73722	0.9455	0.5764	5008	,	,		19953	0.7649		0.7157	False		,,,				2504	0.5634				p.R1436R		Atlas-SNP	.											.	PTPRF	172	.	0			c.G4308A						PASS	.	A	,	4040,366	186.7+/-213.5	1857,326,20	54.0	53.0	53.0		4308,4281	2.3	1.0	1	dbSNP_83	53	6431,2169	370.0+/-335.7	2440,1551,309	no	coding-synonymous,coding-synonymous	PTPRF	NM_002840.3,NM_130440.2	,	4297,1877,329	AA,AG,GG		25.2209,8.3069,19.491	,	1436/1908,1427/1899	44083519	10471,2535	2203	4300	6503	SO:0001819	synonymous_variant	5792	exon25			CTGGAGGATGGTG	Y00815	CCDS489.2, CCDS490.2	1p34	2013-02-11			ENSG00000142949	ENSG00000142949		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	9670	protein-coding gene	gene with protein product		179590		LAR		7558042	Standard	NM_130440		Approved		uc001cjr.3	P10586	OTTHUMG00000007501	ENST00000359947.4:c.4308G>A	1.37:g.44083519G>A		Somatic	255	0	0		WXS	Illumina HiSeq	Phase_I	228	111	0.486842	NM_002840	D3DPX6|D3DPX7|Q5T021|Q5T022|Q5W9G2|Q86WS0	Silent	SNP	ENST00000359947.4	37	CCDS489.2	1671|1671	0.7651098901098901|0.7651098901098901	459|459	0.9329268292682927|0.9329268292682927	238|238	0.6574585635359116|0.6574585635359116	425|425	0.743006993006993|0.743006993006993	549|549	0.7242744063324539|0.7242744063324539	A|A	10.11|10.11	1.260861|1.260861	0.23051|0.23051	0.916931|0.916931	0.747791|0.747791	ENSG00000142949|ENSG00000142949	ENST00000412568;ENST00000414879|ENST00000429895	.|.	.|.	.|.	5.58|5.58	2.32|2.32	0.28847|0.28847	.|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.09310|0.09310	P|P	1.0|1.0	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.16571|0.16571	-1.0398|-1.0398	3|3	.|.	.|.	.|.	.|.	9.1101|9.1101	0.36723|0.36723	0.1843:0.2027:0.613:0.0|0.1843:0.2027:0.613:0.0	rs641351;rs1065774;rs17380724;rs57918403|rs641351;rs1065774;rs17380724;rs57918403	.|.	.|.	.|.	N|E	820;861|1082	.|.	.|.	D|G	+|+	1|2	0|0	PTPRF|PTPRF	43856106|43856106	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.907000|0.907000	0.53573|0.53573	1.439000|1.439000	0.35013|0.35013	0.384000|0.384000	0.24942|0.24942	-0.834000|-0.834000	0.03071|0.03071	GAT|GGA	A|0.793;G|0.207;T|0.000	0.793	strong		0.617	PTPRF-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000019710.1		
IRX5	10265	hgsc.bcm.edu	37	16	54967096	54967096	+	Missense_Mutation	SNP	C	C	A	rs13336114	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:54967096C>A	ENST00000394636.4	+	3	1100	c.763C>A	c.(763-765)Ccg>Acg	p.P255T	CTD-3032H12.2_ENST00000560487.1_lincRNA|IRX5_ENST00000560154.1_Intron|IRX5_ENST00000558597.1_Missense_Mutation_p.P189T|IRX5_ENST00000320990.5_Missense_Mutation_p.P254T			P78411	IRX5_HUMAN	iroquois homeobox 5	255					embryonic cranial skeleton morphogenesis (GO:0048701)|gonad development (GO:0008406)|neuron maturation (GO:0042551)|regulation of heart rate (GO:0002027)|regulation of transcription, DNA-templated (GO:0006355)|response to stimulus (GO:0050896)|retinal bipolar neuron differentiation (GO:0060040)|transcription, DNA-templated (GO:0006351)|visual perception (GO:0007601)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|vitamin D binding (GO:0005499)			kidney(3)|large_intestine(6)|lung(4)|prostate(1)	14						TTTTAAGGAGCCGCCCTCGGA	0.756													C|||	1820	0.363419	0.236	0.3458	5008	,	,		6748	0.5397		0.3201	False		,,,				2504	0.411				p.P255T		Atlas-SNP	.											.	IRX5	41	.	0			c.C763A						PASS	.	C	THR/PRO	885,3209		99,687,1261	5.0	6.0	5.0		763	-0.9	0.4	16	dbSNP_121	5	2431,5665		389,1653,2006	yes	missense	IRX5	NM_005853.5	38	488,2340,3267	AA,AC,CC		30.0272,21.617,27.2026	benign	255/484	54967096	3316,8874	2047	4048	6095	SO:0001583	missense	10265	exon3			AAGGAGCCGCCCT	U90309	CCDS10751.1, CCDS58462.1	16q12.2	2011-06-20	2007-07-13		ENSG00000176842	ENSG00000176842		"""Homeoboxes / TALE class"""	14361	protein-coding gene	gene with protein product		606195					Standard	NM_005853		Approved	IRX-2a	uc002ehv.3	P78411	OTTHUMG00000133201	ENST00000394636.4:c.763C>A	16.37:g.54967096C>A	ENSP00000378132:p.Pro255Thr	Somatic	1	0	0		WXS	Illumina HiSeq	Phase_I	6	4	0.666667	NM_005853	H0YMS7|P78416|Q7Z2E1	Missense_Mutation	SNP	ENST00000394636.4	37	CCDS10751.1	799	0.3658424908424908	127	0.258130081300813	122	0.3370165745856354	304	0.5314685314685315	246	0.3245382585751979	C	0.036	-1.305222	0.01353	0.21617	0.300272	ENSG00000176842	ENST00000394636;ENST00000320990	T;T	0.59083	0.29;0.3	3.95	-0.895	0.10560	.	1.436920	0.04206	N	0.330834	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	0.44081	-0.9351	9	0.17832	T	0.49	-0.4156	0.4964	0.00572	0.182:0.2712:0.1785:0.3683	rs13336114	255	P78411	IRX5_HUMAN	T	255;254	ENSP00000378132:P255T;ENSP00000316250:P254T	ENSP00000316250:P254T	P	+	1	0	IRX5	53524597	0.410000	0.25376	0.364000	0.25888	0.100000	0.18952	0.924000	0.28777	-0.006000	0.14370	-0.266000	0.10368	CCG	C|0.632;A|0.368	0.368	strong		0.756	IRX5-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256911.2		
SYT6	148281	hgsc.bcm.edu	37	1	114680310	114680310	+	Missense_Mutation	SNP	G	G	A	rs41274114	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:114680310G>A	ENST00000610222.1	-	3	1024	c.878C>T	c.(877-879)aCc>aTc	p.T293I	SYT6_ENST00000369547.1_Missense_Mutation_p.T208I|SYT6_ENST00000609117.1_Missense_Mutation_p.T208I|SYT6_ENST00000607941.1_Missense_Mutation_p.T208I|SYT6_ENST00000393296.1_Missense_Mutation_p.T293I			Q5T7P8	SYT6_HUMAN	synaptotagmin VI	293	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.				acrosomal vesicle exocytosis (GO:0060478)	cell junction (GO:0030054)|cytosol (GO:0005829)|extrinsic component of membrane (GO:0019898)|integral component of membrane (GO:0016021)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)	clathrin binding (GO:0030276)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|syntaxin binding (GO:0019905)|transporter activity (GO:0005215)			central_nervous_system(1)|endometrium(3)|large_intestine(10)|lung(14)|ovary(4)|pancreas(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	37	Lung SC(450;0.184)	all_cancers(81;4.41e-08)|all_epithelial(167;5.18e-08)|all_lung(203;1.58e-05)|Lung NSC(69;2.82e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		CTCATCAAAGGTGGGGTTCAG	0.557													G|||	825	0.164736	0.2042	0.1902	5008	,	,		20755	0.0784		0.175	False		,,,				2504	0.1718				p.T208I		Atlas-SNP	.											.	SYT6	66	.	0			c.C623T						PASS	.	G	ILE/THR	876,3530	343.3+/-307.6	75,726,1402	121.0	114.0	116.0		623	5.4	1.0	1	dbSNP_127	116	1528,7072	287.3+/-298.2	133,1262,2905	yes	missense	SYT6	NM_205848.2	89	208,1988,4307	AA,AG,GG		17.7674,19.882,18.4838	possibly-damaging	208/426	114680310	2404,10602	2203	4300	6503	SO:0001583	missense	148281	exon3			TCAAAGGTGGGGT		CCDS871.1	1p13.1	2013-01-21			ENSG00000134207	ENSG00000134207		"""Synaptotagmins"""	18638	protein-coding gene	gene with protein product		607718				11543631	Standard	NM_205848		Approved		uc021orz.1	Q5T7P8	OTTHUMG00000011755	ENST00000610222.1:c.878C>T	1.37:g.114680310G>A	ENSP00000476396:p.Thr293Ile	Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	167	85	0.508982	NM_205848	B1AMB8|B3KPK1	Missense_Mutation	SNP	ENST00000610222.1	37		371	0.16987179487179488	110	0.22357723577235772	73	0.20165745856353592	54	0.0944055944055944	134	0.17678100263852242	G	15.06	2.721352	0.48728	0.19882	0.177674	ENSG00000134207	ENST00000369547;ENST00000393296;ENST00000369546;ENST00000369545	T;T;T;T	0.68181	-0.31;-0.31;-0.31;-0.31	5.45	5.45	0.79879	C2 membrane targeting protein (1);C2 region (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.050367	0.85682	D	0.000000	T	0.44138	0.1279	N	0.17723	0.515	0.09310	P	0.999999855013	B	0.17465	0.022	B	0.29353	0.101	T	0.36939	-0.9727	9	0.30854	T	0.27	.	19.29	0.94095	0.0:0.0:1.0:0.0	rs41274114;rs61080477;rs61730009	293	Q5T7P8	SYT6_HUMAN	I	208;293;208;293	ENSP00000358560:T208I;ENSP00000376974:T293I;ENSP00000358559:T208I;ENSP00000358558:T293I	ENSP00000358558:T293I	T	-	2	0	SYT6	114481833	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	5.813000	0.69201	2.567000	0.86603	0.650000	0.86243	ACC	G|0.820;A|0.180	0.180	strong		0.557	SYT6-004	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000314819.2	NM_205848	
MARCH10	162333	hgsc.bcm.edu	37	17	60813627	60813627	+	Silent	SNP	G	G	A	rs2041283	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:60813627G>A	ENST00000311269.5	-	6	1876	c.1602C>T	c.(1600-1602)aaC>aaT	p.N534N	RP11-156L14.1_ENST00000582564.1_RNA|RP11-156L14.1_ENST00000584597.1_RNA|MARCH10_ENST00000583600.1_Silent_p.N572N|RP11-156L14.1_ENST00000577270.1_RNA|MARCH10_ENST00000456609.2_Silent_p.N534N|MARCH10_ENST00000544856.2_Silent_p.N533N|RP11-156L14.1_ENST00000579201.1_RNA	NM_152598.2	NP_689811.2	Q8NA82	MARHA_HUMAN	membrane-associated ring finger (C3HC4) 10, E3 ubiquitin protein ligase	534					protein ubiquitination (GO:0016567)		ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(11)|liver(1)|lung(15)	38						CGTGTGCACTGTTTACTGGGA	0.448													G|||	1359	0.271366	0.1309	0.3876	5008	,	,		18880	0.2083		0.4215	False		,,,				2504	0.2894				p.N534N		Atlas-SNP	.											.	MARCH10	102	.	0			c.C1602T						PASS	.	G	,	821,3585	324.2+/-298.5	86,649,1468	91.0	95.0	93.0		1602,1602	0.6	0.0	17	dbSNP_94	93	3387,5213	498.5+/-374.8	714,1959,1627	no	coding-synonymous,coding-synonymous	MARCH10	NM_001100875.1,NM_152598.2	,	800,2608,3095	AA,AG,GG		39.3837,18.6337,32.3543	,	534/809,534/809	60813627	4208,8798	2203	4300	6503	SO:0001819	synonymous_variant	162333	exon6			TGCACTGTTTACT	AK093076	CCDS11635.1, CCDS74122.1, CCDS74123.1	17q23.3	2013-01-09	2012-02-23	2007-08-20		ENSG00000173838		"""RING-type (C3HC4) zinc fingers"", ""MARCH membrane-associated ring fingers"""	26655	protein-coding gene	gene with protein product		613337	"""ring finger protein 190"", ""membrane-associated ring finger (C3HC4) 10"""	RNF190		17604280	Standard	XM_005257103		Approved	FLJ35757, MARCH-X	uc002jag.4	Q8NA82		ENST00000311269.5:c.1602C>T	17.37:g.60813627G>A		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	128	127	0.992188	NM_001100875	D3DU09|Q8IYS7|Q8N7Z7	Silent	SNP	ENST00000311269.5	37	CCDS11635.1																																																																																			G|0.692;A|0.308	0.308	strong		0.448	MARCH10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000445252.1	NM_152598	
SPTBN5	51332	hgsc.bcm.edu	37	15	42145049	42145049	+	Silent	SNP	C	C	T	rs55978013	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	134	0	0		WXS	Illumina HiSeq	Phase_I	204	118	0.578431	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	
SYNE1	23345	hgsc.bcm.edu	37	6	152529260	152529260	+	Silent	SNP	G	G	A	rs3798756	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:152529260G>A	ENST00000367255.5	-	125	23272	c.22671C>T	c.(22669-22671)atC>atT	p.I7557I	SYNE1_ENST00000265368.4_Silent_p.I7557I|SYNE1_ENST00000448038.1_Silent_p.I7486I|SYNE1_ENST00000423061.1_Silent_p.I7486I|SYNE1_ENST00000356820.4_Silent_p.I2081I|SYNE1_ENST00000341594.5_Silent_p.I7169I	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	97	0	0		WXS	Illumina HiSeq	Phase_I	73	26	0.356164	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	
DTNB	1838	hgsc.bcm.edu	37	2	25655772	25655772	+	Silent	SNP	T	T	C	rs7583475	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:25655772T>C	ENST00000406818.3	-	14	1689	c.1440A>G	c.(1438-1440)gcA>gcG	p.A480A	DTNB_ENST00000496972.2_Silent_p.A423A|DTNB_ENST00000407661.3_Silent_p.A480A|DTNB_ENST00000405222.1_Silent_p.A450A|DTNB_ENST00000404103.3_Silent_p.A480A|DTNB_ENST00000545439.1_Silent_p.A276A|DTNB_ENST00000407186.1_Silent_p.A450A|DTNB_ENST00000288642.8_Silent_p.A480A|DTNB_ENST00000407038.3_Silent_p.A450A	NM_001256303.1|NM_021907.4	NP_001243232.1|NP_068707.1	O60941	DTNB_HUMAN	dystrobrevin, beta	480						cytoplasm (GO:0005737)|synapse (GO:0045202)	calcium ion binding (GO:0005509)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(3)|lung(4)|ovary(2)|upper_aerodigestive_tract(1)	11	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GCCGCAGCTCTGCCAGCAGCG	0.567													T|||	1199	0.239417	0.3298	0.2104	5008	,	,		19600	0.005		0.3489	False		,,,				2504	0.2669				p.A480A		Atlas-SNP	.											.	DTNB	43	.	0			c.A1440G						PASS	.	T	,,,,	1405,2935		240,925,1005	23.0	28.0	27.0		1440,1440,1350,1440,1350	-9.0	0.9	2	dbSNP_116	27	2850,5716		493,1864,1926	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	DTNB	NM_021907.3,NM_033147.2,NM_033148.2,NM_183360.1,NM_183361.1	,,,,	733,2789,2931	CC,CT,TT		33.2711,32.3733,32.9692	,,,,	480/628,480/598,450/568,480/610,450/561	25655772	4255,8651	2170	4283	6453	SO:0001819	synonymous_variant	1838	exon14			CAGCTCTGCCAGC	AF022728	CCDS46233.1, CCDS46234.1, CCDS46235.1, CCDS46236.1, CCDS46237.1, CCDS58702.1, CCDS74496.1	2p23.2	2008-05-15			ENSG00000138101	ENSG00000138101			3058	protein-coding gene	gene with protein product		602415				9419360	Standard	NM_021907		Approved		uc002rgh.4	O60941	OTTHUMG00000152129	ENST00000406818.3:c.1440A>G	2.37:g.25655772T>C		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	66	66	1	NM_021907	B7Z733|F5GZG4|G5E9F6|O43782|O60881|O75538|Q86VR4|Q96AW0|Q9UE14|Q9UE15|Q9UE16	Silent	SNP	ENST00000406818.3	37	CCDS46237.1																																																																																			T|0.743;C|0.257	0.257	strong		0.567	DTNB-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000325361.1	NM_033147	
GALC	2581	hgsc.bcm.edu	37	14	88407888	88407888	+	Missense_Mutation	SNP	A	A	G	rs386779713|rs398607	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:88407888A>G	ENST00000261304.2	-	15	1791	c.1685T>C	c.(1684-1686)aTa>aCa	p.I562T	GALC_ENST00000393569.2_Missense_Mutation_p.I536T|GALC_ENST00000544807.2_Missense_Mutation_p.I506T|GALC_ENST00000393568.4_Missense_Mutation_p.I539T	NM_000153.3|NM_001201401.1	NP_000144.2|NP_001188330.1	P54803	GALC_HUMAN	galactosylceramidase	562			I -> T (common polymorphism; dbSNP:rs398607). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:20886637, ECO:0000269|PubMed:7601472, ECO:0000269|PubMed:8940268, ECO:0000269|PubMed:9272171}.		carbohydrate metabolic process (GO:0005975)|galactosylceramide catabolic process (GO:0006683)|glycosphingolipid metabolic process (GO:0006687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)	galactosylceramidase activity (GO:0004336)			endometrium(2)|kidney(2)|large_intestine(1)|lung(10)|ovary(1)|prostate(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	21						ATCACACTTTATAGTCAGATT	0.373													A|||	2241	0.447484	0.6452	0.379	5008	,	,		18575	0.2312		0.4881	False		,,,				2504	0.41				p.I562T		Atlas-SNP	.											.	GALC	48	.	0			c.T1685C						PASS	.	A	THR/ILE,THR/ILE,THR/ILE	2248,1412		701,846,283	126.0	113.0	117.0		1685,1616,1607	5.7	0.0	14	dbSNP_80	117	3934,4240		940,2054,1093	yes	missense,missense,missense	GALC	NM_000153.3,NM_001201401.1,NM_001201402.1	89,89,89	1641,2900,1376	GG,GA,AA		48.1282,38.5792,47.7607	benign,benign,benign	562/686,539/663,536/660	88407888	6182,5652	1830	4087	5917	SO:0001583	missense	2581	exon15			CACTTTATAGTCA	L23116	CCDS9878.2, CCDS55936.1, CCDS55937.1	14q31	2009-01-06	2005-11-29		ENSG00000054983	ENSG00000054983	3.2.1.46		4115	protein-coding gene	gene with protein product	"""Krabbe disease"""	606890	"""galactosylceramidase (Krabbe disease)"""				Standard	NM_000153		Approved		uc001xvt.3	P54803	OTTHUMG00000028646	ENST00000261304.2:c.1685T>C	14.37:g.88407888A>G	ENSP00000261304:p.Ile562Thr	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	106	46	0.433962	NM_000153	B4DKE8|B4DYN1|B4DZJ8|B7Z7Z2|J3KN25|J3KPP8|Q8J030	Missense_Mutation	SNP	ENST00000261304.2	37	CCDS9878.2	934	0.42765567765567764	302	0.6138211382113821	145	0.4005524861878453	127	0.22202797202797203	360	0.47493403693931396	A	20.2	3.950939	0.73787	0.614208	0.481282	ENSG00000054983	ENST00000261304;ENST00000544807;ENST00000393569;ENST00000539620;ENST00000393568	D;D;D;D	0.94000	-3.33;-3.33;-3.33;-3.33	5.73	5.73	0.89815	.	0.254810	0.38959	N	0.001511	T	0.00012	0.0000	M	0.61703	1.905	0.42359	P	0.007595000000000018	P;P;P;P	0.39044	0.515;0.656;0.604;0.459	B;B;B;B	0.40982	0.156;0.345;0.234;0.345	T	0.28364	-1.0046	9	0.62326	D	0.03	-2.3458	16.0255	0.80541	1.0:0.0:0.0:0.0	rs398607;rs1805080;rs11552557;rs17686019;rs17853649;rs52812386;rs59276819;rs398607	506;539;536;562	P54803-5;E7EPA4;P54803-4;P54803	.;.;.;GALC_HUMAN	T	562;506;536;351;539	ENSP00000261304:I562T;ENSP00000437513:I506T;ENSP00000377199:I536T;ENSP00000377198:I539T	ENSP00000261304:I562T	I	-	2	0	GALC	87477641	0.977000	0.34250	0.024000	0.17045	0.281000	0.26958	9.270000	0.95690	2.195000	0.70347	0.477000	0.44152	ATA	A|0.576;G|0.424	0.424	strong		0.373	GALC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071559.2		
SVEP1	79987	hgsc.bcm.edu	37	9	113191533	113191533	+	Silent	SNP	C	C	T	rs75212846	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:113191533C>T	ENST00000401783.2	-	35	6033	c.5697G>A	c.(5695-5697)gtG>gtA	p.V1899V	SVEP1_ENST00000374469.1_Silent_p.V1876V|SVEP1_ENST00000297826.5_5'Flank	NM_153366.3	NP_699197.3	Q4LDE5	SVEP1_HUMAN	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	1899	Sushi 8. {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						CTGGTTCACACACAGGAGGGG	0.383													C|||	166	0.033147	0.0234	0.0259	5008	,	,		16684	0.0476		0.0457	False		,,,				2504	0.0235				p.V1899V		Atlas-SNP	.											.	SVEP1	326	.	0			c.G5697A						PASS	.	C		78,3602		1,76,1763	41.0	40.0	40.0		5697	3.3	1.0	9	dbSNP_132	40	345,7839		9,327,3756	no	coding-synonymous	SVEP1	NM_153366.3		10,403,5519	TT,TC,CC		4.2155,2.1196,3.5654		1899/3572	113191533	423,11441	1840	4092	5932	SO:0001819	synonymous_variant	79987	exon35			TTCACACACAGGA	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.5697G>A	9.37:g.113191533C>T		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	47	24	0.510638	NM_153366	Q0P675|Q5D213|Q5T938|Q5VTE4|Q5VTE5|Q7Z387|Q7Z3G3|Q8NBT9|Q96JU7|Q9H284|Q9H8J9	Silent	SNP	ENST00000401783.2	37	CCDS48004.1																																																																																			C|0.963;T|0.037	0.037	strong		0.383	SVEP1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
GOLGA1	2800	hgsc.bcm.edu	37	9	127661645	127661645	+	Missense_Mutation	SNP	G	G	A	rs634710	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:127661645G>A	ENST00000373555.4	-	14	1607	c.1274C>T	c.(1273-1275)aCg>aTg	p.T425M	AL354928.1_ENST00000580940.1_RNA	NM_002077.3	NP_002068	Q92805	GOGA1_HUMAN	golgin A1	425	Gln-rich.		T -> M (in dbSNP:rs634710). {ECO:0000269|PubMed:15489334}.		protein targeting to Golgi (GO:0000042)	Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|trans-Golgi network (GO:0005802)				NS(1)|endometrium(5)|kidney(2)|large_intestine(3)|lung(7)|ovary(1)|stomach(1)	20						AGCTGCCCGCGTTCTCTCCAG	0.637													G|||	2004	0.40016	0.2965	0.353	5008	,	,		17342	0.5694		0.4254	False		,,,				2504	0.3732				p.T425M		Atlas-SNP	.											.	GOLGA1	60	.	0			c.C1274T						PASS	.	G	MET/THR	1359,2935		238,883,1026	44.0	36.0	39.0		1274	3.5	0.0	9	dbSNP_83	39	3473,4877		832,1809,1534	yes	missense	GOLGA1	NM_002077.3	81	1070,2692,2560	AA,AG,GG		41.5928,31.6488,38.2158	possibly-damaging	425/768	127661645	4832,7812	2147	4175	6322	SO:0001583	missense	2800	exon14			GCCCGCGTTCTCT	U51587	CCDS6860.1	9q34.11	2010-02-12	2010-02-12		ENSG00000136935	ENSG00000136935			4424	protein-coding gene	gene with protein product		602502	"""golgi autoantigen, golgin subfamily a, 1"""			9324025	Standard	NM_002077		Approved	golgin-97, MGC33154	uc004bpc.3	Q92805	OTTHUMG00000020665	ENST00000373555.4:c.1274C>T	9.37:g.127661645G>A	ENSP00000362656:p.Thr425Met	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	51	50	0.980392	NM_002077	Q5T164|Q8IYZ9	Missense_Mutation	SNP	ENST00000373555.4	37	CCDS6860.1	921	0.4217032967032967	150	0.3048780487804878	130	0.35911602209944754	339	0.5926573426573427	302	0.39841688654353563	G	11.28	1.590714	0.28357	0.316488	0.415928	ENSG00000136935	ENST00000373555	T	0.22539	1.95	5.36	3.5	0.40072	.	0.913583	0.09089	U	0.850191	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	D	0.54772	0.968	B	0.35182	0.197	T	0.38693	-0.9649	9	0.51188	T	0.08	-0.0077	7.3442	0.26654	0.0889:0.1684:0.7427:0.0	rs634710;rs3816271;rs16927715;rs17855565;rs52820334;rs56548659;rs58712407;rs634710	425	Q92805	GOGA1_HUMAN	M	425	ENSP00000362656:T425M	ENSP00000362656:T425M	T	-	2	0	GOLGA1	126701466	0.024000	0.19004	0.001000	0.08648	0.002000	0.02628	1.416000	0.34759	0.800000	0.34041	-0.150000	0.13652	ACG	G|0.595;T|0.005	.	strong		0.637	GOLGA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054049.1	NM_002077	
CD82	3732	hgsc.bcm.edu	37	11	44640268	44640268	+	Missense_Mutation	SNP	A	A	G	rs1139971	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:44640268A>G	ENST00000227155.4	+	9	969	c.721A>G	c.(721-723)Atc>Gtc	p.I241V	CD82_ENST00000342935.3_Missense_Mutation_p.I216V|CD82_ENST00000530931.1_3'UTR	NM_002231.3	NP_002222.1	P27701	CD82_HUMAN	CD82 molecule	241			I -> V (in dbSNP:rs1139971). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.4, ECO:0000269|Ref.8}.	II -> MV (in Ref. 2; AAB23825). {ECO:0000305}.		extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				large_intestine(1)|ovary(1)	2						TGTGGCCATCATCGAGGTCTG	0.642													A|||	2940	0.587061	0.388	0.6311	5008	,	,		15095	0.502		0.6571	False		,,,				2504	0.8405				p.I241V		Atlas-SNP	.											.	CD82	27	.	0			c.A721G						PASS	.	A	VAL/ILE,VAL/ILE	1854,2552	537.1+/-374.7	370,1114,719	102.0	83.0	89.0		646,721	0.7	0.7	11	dbSNP_86	89	5759,2839	672.9+/-403.0	1890,1979,430	yes	missense,missense	CD82	NM_001024844.1,NM_002231.3	29,29	2260,3093,1149	GG,GA,AA		33.0193,42.079,41.4565	benign,benign	216/243,241/268	44640268	7613,5391	2203	4299	6502	SO:0001583	missense	3732	exon9			GCCATCATCGAGG	U20770	CCDS7909.1, CCDS31469.1	11p11.2	2013-02-14	2006-03-28	2005-03-03		ENSG00000085117		"""CD molecules"", ""Tetraspanins"""	6210	protein-coding gene	gene with protein product	"""suppression of tumorigenicity 6"", ""R2 leukocyte antigen"""	600623	"""kangai 1 (suppression of tumorigenicity 6, prostate; CD82 antigen (R2 leukocyte antigen, antigen detected by monoclonal and antibody IA4))"", ""CD82 antigen"""	ST6, KAI1			Standard	XM_006718222		Approved	R2, IA4, TSPAN27	uc001myc.3	P27701		ENST00000227155.4:c.721A>G	11.37:g.44640268A>G	ENSP00000227155:p.Ile241Val	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	63	12	0.190476	NM_002231	D3DQN6|E9PC70|Q7Z2D4|Q7Z5N2	Missense_Mutation	SNP	ENST00000227155.4	37	CCDS7909.1	1200	0.5494505494505495	193	0.39227642276422764	230	0.6353591160220995	274	0.479020979020979	503	0.6635883905013192	A	5.992	0.366980	0.11352	0.42079	0.669807	ENSG00000085117	ENST00000227155;ENST00000342935	T;T	0.80214	-1.35;-1.35	4.32	0.664	0.17890	.	0.518909	0.20303	N	0.094998	T	0.00012	0.0000	L	0.37897	1.145	0.09310	P	1.0	B;B	0.19935	0.04;0.016	B;B	0.24974	0.057;0.024	T	0.46345	-0.9198	9	0.17832	T	0.49	.	6.1582	0.20350	0.6605:0.0:0.3395:0.0	rs1139971;rs3204038;rs11541053;rs12790100;rs17404342;rs17844860;rs17857575;rs17857656;rs57026608;rs1139971	216;241	E9PC70;P27701	.;CD82_HUMAN	V	241;216	ENSP00000227155:I241V;ENSP00000339686:I216V	ENSP00000227155:I241V	I	+	1	0	CD82	44596844	0.958000	0.32768	0.691000	0.30163	0.044000	0.14063	0.750000	0.26334	-0.153000	0.11137	0.260000	0.18958	ATC	A|0.450;G|0.550	0.550	strong		0.642	CD82-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389886.1		
CDC42BPG	55561	hgsc.bcm.edu	37	11	64597205	64597205	+	Silent	SNP	G	G	T	rs7936466	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:64597205G>T	ENST00000342711.5	-	30	3704	c.3705C>A	c.(3703-3705)ggC>ggA	p.G1235G	CDC42BPG_ENST00000491280.1_5'Flank	NM_017525.2	NP_059995.2			CDC42 binding protein kinase gamma (DMPK-like)											central_nervous_system(1)|lung(3)	4						ATAGCCGGTCGCCCAGCAGCC	0.716													G|||	1371	0.273762	0.0439	0.2147	5008	,	,		14616	0.4931		0.2555	False		,,,				2504	0.4192				p.G1235G		Atlas-SNP	.											.	CDC42BPG	101	.	0			c.C3705A						PASS	.	G		328,3866		16,296,1785	7.0	9.0	8.0		3705	-0.6	1.0	11	dbSNP_116	8	1926,6434		211,1504,2465	no	coding-synonymous	CDC42BPG	NM_017525.2		227,1800,4250	TT,TG,GG		23.0383,7.8207,17.9544		1235/1552	64597205	2254,10300	2097	4180	6277	SO:0001819	synonymous_variant	55561	exon30			CCGGTCGCCCAGC	AY648038	CCDS31601.1	11q13	2013-01-10			ENSG00000171219	ENSG00000171219		"""Pleckstrin homology (PH) domain containing"""	29829	protein-coding gene	gene with protein product		613991				9341881, 15194684	Standard	NM_017525		Approved	HSMDPKIN, MRCKgamma, DMPK2, kappa-200	uc001obs.4	Q6DT37	OTTHUMG00000045365	ENST00000342711.5:c.3705C>A	11.37:g.64597205G>T		Somatic	7	0	0		WXS	Illumina HiSeq	Phase_I	10	7	0.7	NM_017525		Silent	SNP	ENST00000342711.5	37	CCDS31601.1																																																																																			G|0.734;T|0.266	0.266	strong		0.716	CDC42BPG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000105352.4	XM_290516	
ADAMTS19	171019	hgsc.bcm.edu	37	5	129040056	129040056	+	Missense_Mutation	SNP	A	A	T	rs11749126	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:129040056A>T	ENST00000274487.4	+	21	3411	c.3266A>T	c.(3265-3267)tAt>tTt	p.Y1089F	CTC-575N7.1_ENST00000503616.1_RNA|ADAMTS19_ENST00000509467.1_3'UTR	NM_133638.3	NP_598377.3	Q8TE59	ATS19_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 19	1089	TSP type-1 5. {ECO:0000255|PROSITE- ProRule:PRU00210}.		Y -> F (in dbSNP:rs11749126).			proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|endometrium(10)|kidney(9)|large_intestine(14)|lung(34)|ovary(6)|pancreas(1)|prostate(6)|skin(6)	91		all_cancers(142;0.0148)|Prostate(80;0.0494)|Breast(839;0.238)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	OV - Ovarian serous cystadenocarcinoma(64;0.222)		TCAAAATGCTATGTGTGGCGA	0.448													A|||	355	0.0708866	0.0083	0.1009	5008	,	,		19397	0.002		0.163	False		,,,				2504	0.1104				p.Y1089F		Atlas-SNP	.											.	ADAMTS19	216	.	0			c.A3266T						PASS	.	A	PHE/TYR	176,4230	113.8+/-151.8	6,164,2033	176.0	152.0	160.0		3266	4.3	1.0	5	dbSNP_120	160	1583,7017	296.2+/-302.8	131,1321,2848	yes	missense	ADAMTS19	NM_133638.3	22	137,1485,4881	TT,TA,AA		18.407,3.9946,13.5245	benign	1089/1208	129040056	1759,11247	2203	4300	6503	SO:0001583	missense	171019	exon21			AATGCTATGTGTG	AJ311904	CCDS4146.1	5q23.3	2009-04-27	2005-08-19		ENSG00000145808	ENSG00000145808		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	17111	protein-coding gene	gene with protein product		607513	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 19"""			11867212	Standard	NM_133638		Approved		uc003kvb.1	Q8TE59	OTTHUMG00000128990	ENST00000274487.4:c.3266A>T	5.37:g.129040056A>T	ENSP00000274487:p.Tyr1089Phe	Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	189	101	0.534392	NM_133638		Missense_Mutation	SNP	ENST00000274487.4	37	CCDS4146.1	178	0.0815018315018315	8	0.016260162601626018	45	0.12430939226519337	0	0.0	125	0.16490765171503957	A	13.84	2.356939	0.41801	0.039946	0.18407	ENSG00000145808	ENST00000274487	T	0.60424	0.19	4.29	4.29	0.51040	.	0.000000	0.64402	D	0.000008	T	0.00109	0.0003	L	0.33137	0.985	0.20975	P	0.999813509	B	0.21606	0.058	B	0.18561	0.022	T	0.05451	-1.0884	8	.	.	.	.	14.4892	0.67639	1.0:0.0:0.0:0.0	rs11749126;rs17681638;rs52806550;rs11749126	1089	Q8TE59	ATS19_HUMAN	F	1089	ENSP00000274487:Y1089F	.	Y	+	2	0	ADAMTS19	129067955	0.999000	0.42202	0.996000	0.52242	0.994000	0.84299	4.259000	0.58828	2.166000	0.68216	0.533000	0.62120	TAT	A|0.890;T|0.110	0.110	strong		0.448	ADAMTS19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250979.2	NM_133638	
PTPN13	5783	hgsc.bcm.edu	37	4	87692393	87692393	+	Missense_Mutation	SNP	G	G	A	rs12500797	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:87692393G>A	ENST00000411767.2	+	31	4936	c.4873G>A	c.(4873-4875)Gag>Aag	p.E1625K	PTPN13_ENST00000316707.6_Missense_Mutation_p.E1434K|PTPN13_ENST00000436978.1_Missense_Mutation_p.E1630K|PTPN13_ENST00000511467.1_Missense_Mutation_p.E1630K|PTPN13_ENST00000427191.2_Missense_Mutation_p.E1606K			Q12923	PTN13_HUMAN	protein tyrosine phosphatase, non-receptor type 13 (APO-1/CD95 (Fas)-associated phosphatase)	1625			E -> K (in dbSNP:rs12500797).		peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cell body (GO:0044297)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|lamellipodium (GO:0030027)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein tyrosine phosphatase activity (GO:0004725)			NS(4)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(23)|lung(24)|ovary(4)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	93		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.00082)		ATCATGTGTGGAGCAAAGCAC	0.443													G|||	222	0.0443291	0.0098	0.0663	5008	,	,		18384	0.0079		0.1133	False		,,,				2504	0.0419				p.E1630K		Atlas-SNP	.											PTPN13,NS,carcinoma,-2,1	PTPN13	203	1	0			c.G4888A	GRCh37	CM067710	PTPN13	M	rs12500797	PASS	.	G	LYS/GLU,LYS/GLU,LYS/GLU,LYS/GLU	119,3839		3,113,1863	33.0	32.0	32.0		4816,4873,4300,4888	5.3	1.0	4	dbSNP_120	32	1002,7334		61,880,3227	yes	missense,missense,missense,missense	PTPN13	NM_006264.2,NM_080683.2,NM_080684.2,NM_080685.2	56,56,56,56	64,993,5090	AA,AG,GG		12.0202,3.0066,9.1183	probably-damaging,probably-damaging,probably-damaging,probably-damaging	1606/2467,1625/2486,1434/2295,1630/2491	87692393	1121,11173	1979	4168	6147	SO:0001583	missense	5783	exon31			TGTGTGGAGCAAA		CCDS47093.1, CCDS47094.1, CCDS47095.1, CCDS47096.1	4q21.3	2011-06-09			ENSG00000163629	ENSG00000163629		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"""	9646	protein-coding gene	gene with protein product		600267				8287977	Standard	NM_006264		Approved	PTP1E, PTP-BAS, PTPL1, PTP-BL	uc003hpy.3	Q12923	OTTHUMG00000160968	ENST00000411767.2:c.4873G>A	4.37:g.87692393G>A	ENSP00000407249:p.Glu1625Lys	Somatic	277	1	0.00361011		WXS	Illumina HiSeq	Phase_I	241	122	0.506224	NM_080685	B2RTR0|Q15159|Q15263|Q15264|Q15265|Q15674|Q16826|Q8IWH7|Q9NYN9|Q9UDA8	Missense_Mutation	SNP	ENST00000411767.2	37	CCDS47094.1	122	0.055860805860805864	6	0.012195121951219513	25	0.06906077348066299	4	0.006993006993006993	87	0.11477572559366754	G	10.86	1.469049	0.26335	0.030066	0.120202	ENSG00000163629	ENST00000427191;ENST00000436978;ENST00000316707;ENST00000411767;ENST00000511467;ENST00000357349	T;T;T;T;T	0.52526	0.66;0.68;0.76;0.66;0.68	5.32	5.32	0.75619	.	0.134693	0.33217	N	0.005151	T	0.00784	0.0026	L	0.47716	1.5	0.27061	P	0.9635484	P;B;B;B	0.41848	0.763;0.21;0.215;0.057	B;B;B;B	0.42361	0.385;0.147;0.07;0.131	T	0.01532	-1.1331	9	0.16896	T	0.51	.	19.3643	0.94456	0.0:0.0:1.0:0.0	rs12500797;rs17454863;rs52799273;rs12500797	1434;1606;1625;1630	Q12923-2;Q12923-3;Q12923;Q12923-4	.;.;PTN13_HUMAN;.	K	1606;1630;1434;1625;1630;1574	ENSP00000408368:E1606K;ENSP00000394794:E1630K;ENSP00000322675:E1434K;ENSP00000407249:E1625K;ENSP00000426626:E1630K	ENSP00000322675:E1434K	E	+	1	0	PTPN13	87911417	1.000000	0.71417	0.979000	0.43373	0.828000	0.46876	5.276000	0.65580	2.659000	0.90383	0.655000	0.94253	GAG	G|0.939;A|0.061	0.061	strong		0.443	PTPN13-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000363191.1		
C6orf136	221545	hgsc.bcm.edu	37	6	30615413	30615413	+	Intron	SNP	T	T	C	rs146616682	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:30615413T>C	ENST00000376473.5	+	1	231				C6orf136_ENST00000376471.4_Intron|AL662800.2_ENST00000583820.1_RNA|C6orf136_ENST00000493705.1_3'UTR|C6orf136_ENST00000528347.2_5'Flank|C6orf136_ENST00000293604.6_Silent_p.I135I	NM_001109938.2	NP_001103408.1	Q5SQH8	CF136_HUMAN	chromosome 6 open reading frame 136							mitochondrion (GO:0005739)				endometrium(1)|large_intestine(2)|lung(6)|ovary(1)	10						GCCGAGAGATTCGTAGCCCTG	0.716													T|||	13	0.00259585	0.0	0.0072	5008	,	,		13756	0.001		0.007	False		,,,				2504	0.0				p.I135I		Atlas-SNP	.											.	C6orf136	31	.	0			c.T405C						PASS	.						5.0	7.0	7.0					6																	30615413		669	1552	2221	SO:0001627	intron_variant	221545	exon1			AGAGATTCGTAGC	BC016167	CCDS4684.1, CCDS43443.1, CCDS4684.2, CCDS54979.1	6p21.32	2012-02-06			ENSG00000204564	ENSG00000204564			21301	protein-coding gene	gene with protein product							Standard	NM_001109938		Approved	Em:AB023049.8	uc003nqx.4	Q5SQH8	OTTHUMG00000031221	ENST00000376473.5:c.72+333T>C	6.37:g.30615413T>C		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	67	44	0.656716	NM_001161376	A9R9P9|F8VX15|Q5SU01|Q6ZSB7|Q8TB84	Silent	SNP	ENST00000376473.5	37	CCDS43443.1																																																																																			T|0.994;C|0.006	0.006	strong		0.716	C6orf136-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076457.4	NM_145029	
KRT84	3890	hgsc.bcm.edu	37	12	52777439	52777439	+	Silent	SNP	A	A	G	rs1614888	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	134	0	0		WXS	Illumina HiSeq	Phase_I	109	55	0.504587	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	
CRYBG3	131544	hgsc.bcm.edu	37	3	97607290	97607290	+	Silent	SNP	G	G	A	rs13065340	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:97607290G>A	ENST00000182096.4	+	6	1615	c.1551G>A	c.(1549-1551)ccG>ccA	p.P517P		NM_153605.3	NP_705833.3	Q68DQ2	CRBG3_HUMAN	beta-gamma crystallin domain containing 3	2465							carbohydrate binding (GO:0030246)	p.P517P(1)		breast(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(10)|stomach(1)|upper_aerodigestive_tract(2)	32						CATTACATCCGCTTCAAATGG	0.368													G|||	1024	0.204473	0.112	0.317	5008	,	,		17657	0.1637		0.2833	False		,,,				2504	0.2106				p.P2465P		Atlas-SNP	.											CRYBG3,NS,carcinoma,0,1	CRYBG3	86	1	1	Substitution - coding silent(1)	stomach(1)	c.G7395A						scavenged	.	G		455,3197		26,403,1397	48.0	43.0	45.0		7395	-1.9	1.0	3	dbSNP_121	45	2341,5823		348,1645,2089	no	coding-synonymous	CRYBG3	XM_003118522.2		374,2048,3486	AA,AG,GG		28.6747,12.4589,23.6628		2465/2971	97607290	2796,9020	1826	4082	5908	SO:0001819	synonymous_variant	131544	exon9			ACATCCGCTTCAA			3q11.2	2008-09-30			ENSG00000080200	ENSG00000080200			34427	protein-coding gene	gene with protein product							Standard	NM_153605		Approved	DKFZp667G2110	uc021xbn.2	Q68DQ2	OTTHUMG00000159187	ENST00000182096.4:c.1551G>A	3.37:g.97607290G>A		Somatic	136	1	0.00735294		WXS	Illumina HiSeq	Phase_I	106	42	0.396226	NM_153605	B4DLE8|F6VHI2|Q4G0V8|Q7Z4R9|Q86VD0|Q8N262|Q8N7F1|Q8NDQ8	Silent	SNP	ENST00000182096.4	37																																																																																				G|0.786;A|0.214	0.214	strong		0.368	CRYBG3-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000353751.1	NM_153605	
SERPINI1	5274	hgsc.bcm.edu	37	3	167510472	167510472	+	Silent	SNP	G	G	A	rs2229697	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:167510472G>A	ENST00000295777.5	+	4	1007	c.576G>A	c.(574-576)tcG>tcA	p.S192S	SERPINI1_ENST00000446050.2_Silent_p.S192S	NM_005025.4	NP_005016.1	Q99574	NEUS_HUMAN	serpin peptidase inhibitor, clade I (neuroserpin), member 1	192					cell death (GO:0008219)|central nervous system development (GO:0007417)|negative regulation of endopeptidase activity (GO:0010951)|peripheral nervous system development (GO:0007422)|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(3)|large_intestine(4)|lung(7)|skin(2)	20						ACTGGAAGTCGCAGTTTAGGC	0.383													A|||	576	0.115016	0.2073	0.1542	5008	,	,		14995	0.0526		0.1004	False		,,,				2504	0.0419				p.S192S		Atlas-SNP	.											.	SERPINI1	52	.	0			c.G576A						PASS	.	A	,	875,3531	742.7+/-411.4	79,717,1407	110.0	113.0	112.0		576,576	0.5	1.0	3	dbSNP_98	112	758,7842	784.5+/-407.6	27,704,3569	no	coding-synonymous,coding-synonymous	SERPINI1	NM_001122752.1,NM_005025.4	,	106,1421,4976	AA,AG,GG		8.814,19.8593,12.5557	,	192/411,192/411	167510472	1633,11373	2203	4300	6503	SO:0001819	synonymous_variant	5274	exon4			GAAGTCGCAGTTT	Z81326	CCDS3203.1	3q26.1	2014-02-18	2005-08-18		ENSG00000163536	ENSG00000163536		"""Serine (or cysteine) peptidase inhibitors"""	8943	protein-coding gene	gene with protein product		602445	"""serine (or cysteine) proteinase inhibitor, clade I (neuroserpin), member 1"""	PI12		24172014	Standard	NM_005025		Approved	neuroserpin	uc003ffa.4	Q99574	OTTHUMG00000158450	ENST00000295777.5:c.576G>A	3.37:g.167510472G>A		Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	132	69	0.522727	NM_005025	A8K217|D3DNP1|Q6AHZ4	Silent	SNP	ENST00000295777.5	37	CCDS3203.1																																																																																			G|0.875;A|0.125	0.125	strong		0.383	SERPINI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351056.1		
HRG	3273	hgsc.bcm.edu	37	3	186390627	186390627	+	Missense_Mutation	SNP	C	C	T	rs9898	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:186390627C>T	ENST00000232003.4	+	5	690	c.610C>T	c.(610-612)Ccc>Tcc	p.P204S		NM_000412.2	NP_000403.1	P04196	HRG_HUMAN	histidine-rich glycoprotein	204	Cystatin 2.		P -> S (in dbSNP:rs9898).		angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|chemotaxis (GO:0006935)|defense response to fungus (GO:0050832)|fibrinolysis (GO:0042730)|heme export (GO:0097037)|negative regulation of angiogenesis (GO:0016525)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell adhesion mediated by integrin (GO:0033629)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of endothelial cell chemotaxis (GO:2001027)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of lamellipodium assembly (GO:0010593)|negative regulation of vascular endothelial growth factor signaling pathway (GO:1900747)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of apoptotic process (GO:0043065)|positive regulation of blood vessel remodeling (GO:2000504)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of immune response to tumor cell (GO:0002839)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|regulation of platelet activation (GO:0010543)|regulation of protein complex assembly (GO:0043254)|regulation of transcription from RNA polymerase II promoter in response to iron (GO:0034395)|response to organic cyclic compound (GO:0014070)	blood microparticle (GO:0072562)|endolysosome (GO:0036019)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|phagolysosome membrane (GO:0061474)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	cysteine-type endopeptidase inhibitor activity (GO:0004869)|heme binding (GO:0020037)|heparan sulfate proteoglycan binding (GO:0043395)|heparin binding (GO:0008201)|immunoglobulin binding (GO:0019865)|metal ion binding (GO:0046872)|receptor binding (GO:0005102)|serine-type endopeptidase inhibitor activity (GO:0004867)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(12)|lung(13)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	37	all_cancers(143;6.64e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;5.73e-20)	GBM - Glioblastoma multiforme(93;0.0683)		GCGGAACTGCCCCAGACACCA	0.443													T|||	2461	0.491414	0.6278	0.3977	5008	,	,		17738	0.5724		0.327	False		,,,				2504	0.4591				p.P204S		Atlas-SNP	.											HRG,NS,adenoma,0,1	HRG	81	1	0			c.C610T						PASS	.	T	SER/PRO	2615,1791	528.1+/-372.3	781,1053,369	97.0	94.0	95.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	610	4.3	1.0	3	dbSNP_52	95	2945,5655	668.1+/-402.5	523,1899,1878	yes	missense	HRG	NM_000412.2	74	1304,2952,2247	TT,TC,CC	http://www.ncbi.nlm.nih.gov/pubmed?term	34.2442,40.6491,42.7495	benign	204/526	186390627	5560,7446	2203	4300	6503	SO:0001583	missense	3273	exon5			AACTGCCCCAGAC		CCDS3280.1	3q27	2008-07-18			ENSG00000113905	ENSG00000113905			5181	protein-coding gene	gene with protein product	"""histidine-proline rich glycoprotein"", ""thrombophilia due to elevated HRG"""	142640				1678514	Standard	NM_000412		Approved	HRGP, HPRG	uc003fqq.3	P04196	OTTHUMG00000156578	ENST00000232003.4:c.610C>T	3.37:g.186390627C>T	ENSP00000232003:p.Pro204Ser	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	85	85	1	NM_000412	B9EK35|D3DNU7	Missense_Mutation	SNP	ENST00000232003.4	37	CCDS3280.1	1012	0.4633699633699634	309	0.6280487804878049	153	0.42265193370165743	308	0.5384615384615384	242	0.31926121372031663	T	0.012	-1.670189	0.00758	0.593509	0.342442	ENSG00000113905	ENST00000232003	T	0.12879	2.64	4.35	4.35	0.52113	Proteinase inhibitor I25, cystatin (1);	0.000000	0.42294	N	0.000735	T	0.00012	0.0000	N	0.00170	-1.935	0.54753	P	1.799999999996249E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.41466	-0.9507	9	0.02654	T	1	-16.0271	7.2132	0.25945	0.0:0.1061:0.0:0.8939	rs9898;rs1042439;rs1468076;rs3181917;rs3733013;rs52820836;rs58677142;rs9898	204	P04196	HRG_HUMAN	S	204	ENSP00000232003:P204S	ENSP00000232003:P204S	P	+	1	0	HRG	187873321	0.993000	0.37304	0.977000	0.42913	0.017000	0.09413	2.157000	0.42320	0.779000	0.33543	-0.361000	0.07541	CCC	C|0.544;T|0.456	0.456	strong		0.443	HRG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344655.1	NM_000412	
CFHR2	3080	hgsc.bcm.edu	37	1	196918741	196918741	+	Missense_Mutation	SNP	G	G	A	rs79351096	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:196918741G>A	ENST00000367415.5	+	2	315	c.215G>A	c.(214-216)tGc>tAc	p.C72Y	CFHR2_ENST00000476712.2_Missense_Mutation_p.C72Y|CFHR2_ENST00000496448.1_Intron|CFHR2_ENST00000367421.3_Missense_Mutation_p.C72Y	NM_005666.2	NP_005657.1	P36980	FHR2_HUMAN	complement factor H-related 2	72	Sushi 1. {ECO:0000255|PROSITE- ProRule:PRU00302}.					extracellular region (GO:0005576)				large_intestine(2)|ovary(1)|skin(3)	6						CGCATAACGTGCGCAGAAGAA	0.403													g|||	76	0.0151757	0.0015	0.0288	5008	,	,		18573	0.0		0.0189	False		,,,				2504	0.0358				p.C72Y		Atlas-SNP	.											CFHR2_ENST00000367415,NS,carcinoma,-1,1	CFHR2	73	1	0			c.G215A						PASS	.	G	TYR/CYS	30,4376		0,30,2173	101.0	89.0	93.0		215	3.3	0.0	1	dbSNP_133	93	220,8380		2,216,4082	no	missense	CFHR2	NM_005666.2	194	2,246,6255	AA,AG,GG		2.5581,0.6809,1.9222	probably-damaging	72/271	196918741	250,12756	2203	4300	6503	SO:0001583	missense	3080	exon2			TAACGTGCGCAGA	X64877	CCDS30959.1	1q31.3	2008-02-05	2004-08-09	2006-02-28	ENSG00000080910	ENSG00000080910		"""Complement system"""	4890	protein-coding gene	gene with protein product		600889	"""H factor (complement)-like 3"""	HFL3, CFHL2		1533657, 7672821	Standard	NM_005666		Approved	FHR2	uc001gtq.1	P36980	OTTHUMG00000036518	ENST00000367415.5:c.215G>A	1.37:g.196918741G>A	ENSP00000356385:p.Cys72Tyr	Somatic	247	0	0		WXS	Illumina HiSeq	Phase_I	213	103	0.483568	NM_005666	Q14310|Q5T9T1	Missense_Mutation	SNP	ENST00000367415.5	37	CCDS30959.1	33	0.01510989010989011	1	0.0020325203252032522	14	0.03867403314917127	0	0.0	18	0.023746701846965697	.	13.46	2.242600	0.39598	0.006809	0.025581	ENSG00000080910	ENST00000367421;ENST00000367415	D;D	0.98090	-4.71;-4.71	3.33	3.33	0.38152	Complement control module (2);Sushi/SCR/CCP (2);	0.000000	0.36893	N	0.002344	D	0.94305	0.8170	M	0.84082	2.675	0.09310	N	1	D	0.89917	1.0	D	0.91635	0.999	D	0.86843	0.2018	10	0.87932	D	0	.	10.313	0.43721	0.0:0.0:1.0:0.0	.	72	P36980	FHR2_HUMAN	Y	72	ENSP00000356391:C72Y;ENSP00000356385:C72Y	ENSP00000356385:C72Y	C	+	2	0	CFHR2	195185364	0.417000	0.25432	0.004000	0.12327	0.001000	0.01503	3.949000	0.56668	1.825000	0.53177	0.508000	0.49915	TGC	G|0.983;A|0.017	0.017	strong		0.403	CFHR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088815.2	NM_005666	
VTN	7448	hgsc.bcm.edu	37	17	26694483	26694483	+	Silent	SNP	A	A	G	rs2227728	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:26694483A>G	ENST00000226218.4	-	8	1962	c.1344T>C	c.(1342-1344)aaT>aaC	p.N448N	VTN_ENST00000431468.1_5'Flank|VTN_ENST00000438614.1_Missense_Mutation_p.I32T|CTB-96E2.2_ENST00000555059.2_Silent_p.N106N|TMEM199_ENST00000509083.1_Intron|SARM1_ENST00000379061.4_Intron|CTB-96E2.3_ENST00000591482.1_RNA|VTN_ENST00000536498.1_Missense_Mutation_p.I32T	NM_000638.3	NP_000629.3	P04004	VTNC_HUMAN	vitronectin	448					cell adhesion (GO:0007155)|cell adhesion mediated by integrin (GO:0033627)|cell-matrix adhesion (GO:0007160)|endodermal cell differentiation (GO:0035987)|extracellular matrix organization (GO:0030198)|immune response (GO:0006955)|innate immune response (GO:0045087)|negative regulation of blood coagulation (GO:0030195)|negative regulation of endopeptidase activity (GO:0010951)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein binding (GO:0032092)|positive regulation of receptor-mediated endocytosis (GO:0048260)|positive regulation of smooth muscle cell migration (GO:0014911)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|positive regulation of wound healing (GO:0090303)|regulation of complement activation (GO:0030449)|smooth muscle cell-matrix adhesion (GO:0061302)	alphav-beta3 integrin-vitronectin complex (GO:0071062)|blood microparticle (GO:0072562)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix binding (GO:0050840)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)			kidney(2)|large_intestine(7)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)	13	all_lung(13;0.000533)|Lung NSC(42;0.00171)			UCEC - Uterine corpus endometrioid carcinoma (53;0.153)	Abciximab(DB00054)	GTGTGCGAAGATTGACTCGGT	0.602													G|||	779	0.155551	0.1596	0.0821	5008	,	,		19913	0.245		0.0785	False		,,,				2504	0.1892				p.N448N		Atlas-SNP	.											.	VTN	45	.	0			c.T1344C						PASS	.	G		647,3759	762.5+/-413.1	50,547,1606	128.0	106.0	113.0		1344	3.3	1.0	17	dbSNP_98	113	701,7899	786.9+/-407.6	31,639,3630	no	coding-synonymous	VTN	NM_000638.3		81,1186,5236	GG,GA,AA		8.1512,14.6845,10.3644		448/479	26694483	1348,11658	2203	4300	6503	SO:0001819	synonymous_variant	7448	exon8			GCGAAGATTGACT	BC005046	CCDS11229.1	17q11.2	2014-08-08	2006-02-10		ENSG00000109072	ENSG00000109072		"""Endogenous ligands"""	12724	protein-coding gene	gene with protein product	"""serum spreading factor"", ""somatomedin B"", ""complement S-protein"""	193190	"""vitronectin (serum spreading factor, somatomedin B, complement S-protein)"""			2447940	Standard	NM_000638		Approved	VN	uc002hbc.3	P04004	OTTHUMG00000132500	ENST00000226218.4:c.1344T>C	17.37:g.26694483A>G		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	130	71	0.546154	NM_000638	B2R7G0|P01141|Q9BSH7	Silent	SNP	ENST00000226218.4	37	CCDS11229.1	278	0.12728937728937728	87	0.17682926829268292	36	0.09944751381215469	100	0.17482517482517482	55	0.07255936675461741	G	9.371	1.070412	0.20147	0.146845	0.081512	ENSG00000109072;ENSG00000109072;ENSG00000258852	ENST00000536498;ENST00000438614;ENST00000555059	D;D	0.91351	-2.83;-2.83	5.27	3.28	0.37604	.	.	.	.	.	T	0.00580	0.0019	.	.	.	0.09310	P	1.0	B	0.02656	0.0	B	0.01281	0.0	T	0.21280	-1.0250	7	0.13108	T	0.6	-46.27	8.5936	0.33701	0.2913:0.0:0.7087:0.0	rs2227728;rs57255300;rs2227728	32	C9JDG5	.	T	32;32;58	ENSP00000444503:I32T;ENSP00000395142:I32T	ENSP00000395142:I32T	I	-	2	0	VTN;CTB-96E2.2	23718610	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	1.941000	0.40233	0.381000	0.24851	-0.186000	0.12905	ATC	A|0.881;G|0.119	0.119	strong		0.602	VTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255680.2	NM_000638	
PSG8	440533	hgsc.bcm.edu	37	19	43269699	43269699	+	Missense_Mutation	SNP	C	C	T	rs71337226|rs7260508	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	24	0	0		WXS	Illumina HiSeq	Phase_I	13	9	0.692308	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		
PTPN12	5782	hgsc.bcm.edu	37	7	77256150	77256150	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:77256150A>G	ENST00000248594.6	+	13	1426	c.1154A>G	c.(1153-1155)gAt>gGt	p.D385G	PTPN12_ENST00000435495.2_Missense_Mutation_p.D255G|PTPN12_ENST00000415482.2_Missense_Mutation_p.D266G	NM_002835.3	NP_002826.3	Q05209	PTN12_HUMAN	protein tyrosine phosphatase, non-receptor type 12	385	Interaction with TGFB1I1. {ECO:0000250}.				protein dephosphorylation (GO:0006470)|tissue regeneration (GO:0042246)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)|podosome (GO:0002102)	non-membrane spanning protein tyrosine phosphatase activity (GO:0004726)|SH3 domain binding (GO:0017124)			breast(2)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(12)|lung(7)|ovary(3)|pancreas(1)|prostate(1)|skin(5)|urinary_tract(1)	39						CAGGACAATGATAGATACCAT	0.458																																					p.D385G		Atlas-SNP	.											.	PTPN12	83	.	0			c.A1154G						PASS	.						94.0	83.0	87.0					7																	77256150		2203	4300	6503	SO:0001583	missense	5782	exon13			ACAATGATAGATA		CCDS5592.1, CCDS47619.1, CCDS47620.1	7q11.23	2011-06-09			ENSG00000127947	ENSG00000127947		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"""	9645	protein-coding gene	gene with protein product		600079				7509295	Standard	NM_002835		Approved	PTPG1, PTP-PEST	uc003ugh.2	Q05209	OTTHUMG00000023501	ENST00000248594.6:c.1154A>G	7.37:g.77256150A>G	ENSP00000248594:p.Asp385Gly	Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	178	37	0.207865	NM_002835	A4D1C5|B4DKY2|E9PBR5|E9PEH9|Q16130|Q59FD6|Q75MN8|Q86XU4	Missense_Mutation	SNP	ENST00000248594.6	37	CCDS5592.1	.	.	.	.	.	.	.	.	.	.	A	20.3	3.974843	0.74360	.	.	ENSG00000127947	ENST00000248594;ENST00000415482;ENST00000543073;ENST00000435495	T;T;T	0.51574	0.7;0.7;0.7	6.17	5.02	0.67125	.	0.043790	0.85682	N	0.000000	T	0.64627	0.2615	M	0.72894	2.215	0.58432	D	0.999998	D	0.89917	1.0	D	0.91635	0.999	T	0.62144	-0.6916	10	0.24483	T	0.36	.	12.092	0.53733	0.9337:0.0:0.0663:0.0	.	385	Q05209	PTN12_HUMAN	G	385;266;266;255	ENSP00000248594:D385G;ENSP00000392429:D266G;ENSP00000397991:D255G	ENSP00000248594:D385G	D	+	2	0	PTPN12	77094086	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.871000	0.75531	1.160000	0.42584	0.533000	0.62120	GAT	.	.	none		0.458	PTPN12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253183.3		
CCDC79	283847	hgsc.bcm.edu	37	16	66792714	66792714	+	Missense_Mutation	SNP	T	T	C	rs363156	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:66792714T>C	ENST00000558713.2	-	17	2030	c.1958A>G	c.(1957-1959)cAa>cGa	p.Q653R	CCDC79_ENST00000415744.1_3'UTR|CCDC79_ENST00000433574.1_3'UTR|CCDC79_ENST00000432602.1_Missense_Mutation_p.Q606R|CCDC79_ENST00000433154.1_Missense_Mutation_p.Q653R			Q8NA31	TERB1_HUMAN	coiled-coil domain containing 79	653	Interaction with TERF1. {ECO:0000250}.				meiotic telomere clustering (GO:0045141)|synapsis (GO:0007129)	chromosome, telomeric region (GO:0000781)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			NS(1)|endometrium(2)|kidney(1)|large_intestine(1)|skin(2)	7						ACTGAGTCGTTGTCTTCTACG	0.348													T|||	1722	0.34385	0.0681	0.3963	5008	,	,		17640	0.6161		0.3479	False		,,,				2504	0.3947				p.Q653R		Atlas-SNP	.											.	CCDC79	32	.	0			c.A1958G						PASS	.	T	ARG/GLN	172,1212		16,140,536	213.0	172.0	185.0		1958	-7.6	0.0	16	dbSNP_79	185	1152,2030		210,732,649	yes	missense	CCDC79	NM_001136505.1	43	226,872,1185	CC,CT,TT		36.2036,12.4277,28.9969	benign	653/728	66792714	1324,3242	692	1591	2283	SO:0001583	missense	283847	exon18			AGTCGTTGTCTTC	AK093213		16q22.1	2012-10-03			ENSG00000249961	ENSG00000249961			26675	protein-coding gene	gene with protein product							Standard	NM_001136505		Approved	FLJ35894	uc010viv.2	Q8NA31	OTTHUMG00000133562	ENST00000558713.2:c.1958A>G	16.37:g.66792714T>C	ENSP00000462883:p.Gln653Arg	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	59	21	0.355932	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		
EHD2	30846	hgsc.bcm.edu	37	19	48219893	48219893	+	Silent	SNP	C	C	T	rs11550017	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:48219893C>T	ENST00000263277.3	+	2	275	c.24C>T	c.(22-24)ggC>ggT	p.G8G	CTD-2571L23.8_ENST00000599924.1_lincRNA|EHD2_ENST00000538399.1_Intron	NM_014601.3	NP_055416.2	Q9NZN4	EHD2_HUMAN	EH-domain containing 2	8					blood coagulation (GO:0007596)|cortical actin cytoskeleton organization (GO:0030866)|endocytic recycling (GO:0032456)|endocytosis (GO:0006897)|positive regulation of endocytic recycling (GO:2001137)|positive regulation of myoblast fusion (GO:1901741)|protein localization to plasma membrane (GO:0072659)	caveola (GO:0005901)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|recycling endosome membrane (GO:0055038)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|nucleic acid binding (GO:0003676)			endometrium(3)|large_intestine(7)|lung(2)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)	19		all_cancers(25;6.74e-07)|all_lung(116;2.02e-05)|Lung NSC(112;3.77e-05)|all_epithelial(76;4.89e-05)|all_neural(266;0.0332)|Ovarian(192;0.086)		OV - Ovarian serous cystadenocarcinoma(262;0.000336)|all cancers(93;0.000415)|Epithelial(262;0.0132)|GBM - Glioblastoma multiforme(486;0.0537)		TGAAGCGGGGCGGGGCACGGG	0.682													C|||	172	0.034345	0.0091	0.0533	5008	,	,		16828	0.0		0.0895	False		,,,				2504	0.0337				p.G8G		Atlas-SNP	.											.	EHD2	59	.	0			c.C24T						PASS	.	C		115,4219		3,109,2055	10.0	10.0	10.0		24	-5.4	1.0	19	dbSNP_120	10	850,7620		43,764,3428	no	coding-synonymous	EHD2	NM_014601.3		46,873,5483	TT,TC,CC		10.0354,2.6534,7.5367		8/544	48219893	965,11839	2167	4235	6402	SO:0001819	synonymous_variant	30846	exon2			GCGGGGCGGGGCA	AF181263	CCDS12704.1	19q13.3	2014-08-12			ENSG00000024422	ENSG00000024422		"""EF-hand domain containing"""	3243	protein-coding gene	gene with protein product		605890		PAST2		10673336	Standard	NM_014601		Approved		uc002phj.4	Q9NZN4	OTTHUMG00000183266	ENST00000263277.3:c.24C>T	19.37:g.48219893C>T		Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	34	16	0.470588	NM_014601	B2RDH9|B4DNU6|Q96CB6	Silent	SNP	ENST00000263277.3	37	CCDS12704.1																																																																																			C|0.939;T|0.061	0.061	strong		0.682	EHD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465851.1		
DSG1	1828	hgsc.bcm.edu	37	18	28919794	28919794	+	Missense_Mutation	SNP	C	C	A	rs8091117	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:28919794C>A	ENST00000257192.4	+	11	1705	c.1493C>A	c.(1492-1494)aCt>aAt	p.T498N		NM_001942.2	NP_001933.2	Q02413	DSG1_HUMAN	desmoglein 1	498			T -> N (in dbSNP:rs8091117).		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)			GAGCCGAACACTAAAATTACT	0.348													C|||	1119	0.223442	0.5113	0.1182	5008	,	,		16069	0.0645		0.0905	False		,,,				2504	0.2096				p.T498N		Atlas-SNP	.											.	DSG1	176	.	0			c.C1493A						PASS	.	C	ASN/THR	1872,2534	540.7+/-375.6	391,1090,722	105.0	105.0	105.0		1493	-1.9	0.0	18	dbSNP_116	105	624,7976	162.3+/-215.1	30,564,3706	yes	missense	DSG1	NM_001942.2	65	421,1654,4428	AA,AC,CC		7.2558,42.4875,19.1911	benign	498/1050	28919794	2496,10510	2203	4300	6503	SO:0001583	missense	1828	exon11			CGAACACTAAAAT	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.1493C>A	18.37:g.28919794C>A	ENSP00000257192:p.Thr498Asn	Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	103	53	0.514563	NM_001942	B7Z845	Missense_Mutation	SNP	ENST00000257192.4	37	CCDS11896.1	383	0.17536630036630035	247	0.5020325203252033	44	0.12154696132596685	34	0.05944055944055944	58	0.07651715039577836	C	1.831	-0.469873	0.04445	0.424875	0.072558	ENSG00000134760	ENST00000257192	T	0.57595	0.39	3.29	-1.94	0.07571	Cadherin (1);	0.894418	0.09631	N	0.776187	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	0.48186	-0.9057	9	0.18276	T	0.48	.	7.7511	0.28898	0.1709:0.3254:0.5036:0.0	rs8091117;rs56989750;rs8091117	498	Q02413	DSG1_HUMAN	N	498	ENSP00000257192:T498N	ENSP00000257192:T498N	T	+	2	0	DSG1	27173792	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.296000	0.08287	-0.473000	0.06871	-0.233000	0.12211	ACT	C|0.806;A|0.194	0.194	strong		0.348	DSG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254947.1	NM_001942	
LRRC16B	90668	hgsc.bcm.edu	37	14	24529260	24529260	+	Silent	SNP	C	C	T	rs58283036	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:24529260C>T	ENST00000342740.5	+	23	2104	c.1950C>T	c.(1948-1950)gaC>gaT	p.D650D	LRRC16B_ENST00000334420.7_5'UTR	NM_138360.3	NP_612369.3	Q8ND23	LR16B_HUMAN	leucine rich repeat containing 16B	650						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)		GCACCGAGGACGTCTGGCAGA	0.662													C|||	1594	0.318291	0.382	0.2478	5008	,	,		21073	0.5556		0.0924	False		,,,				2504	0.2699				p.D650D		Atlas-SNP	.											.	LRRC16B	120	.	0			c.C1950T						PASS	.	C		1461,2945	472.0+/-356.2	261,939,1003	120.0	105.0	110.0		1950	-4.8	0.9	14	dbSNP_129	110	777,7823	183.3+/-231.6	39,699,3562	no	coding-synonymous	LRRC16B	NM_138360.3		300,1638,4565	TT,TC,CC		9.0349,33.1593,17.2074		650/1373	24529260	2238,10768	2203	4300	6503	SO:0001819	synonymous_variant	90668	exon23			CGAGGACGTCTGG	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.1950C>T	14.37:g.24529260C>T		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	71	71	1	NM_138360	Q8TEF7|Q96HS9	Silent	SNP	ENST00000342740.5	37	CCDS32054.1																																																																																			C|0.788;T|0.212	0.212	strong		0.662	LRRC16B-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416527.1	NM_138360	
NELFB	25920	hgsc.bcm.edu	37	9	140147273	140147273	+	5'Flank	SNP	C	C	T	rs61759822	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:140147273C>T	ENST00000343053.4	+	0	0				C9orf173_ENST00000388931.3_Missense_Mutation_p.L218F|C9orf173_ENST00000412566.1_Missense_Mutation_p.L218F	NM_015456.3	NP_056271.2	Q8WX92	NELFB_HUMAN	negative elongation factor complex member B						gene expression (GO:0010467)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of viral transcription (GO:0050434)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	cytoplasm (GO:0005737)|NELF complex (GO:0032021)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)											CCAGTCCCTGCTTCAGGCCTC	0.667													C|||	715	0.142772	0.0204	0.1066	5008	,	,		12190	0.3075		0.1243	False		,,,				2504	0.183				p.L218F		Atlas-SNP	.											.	C9orf173	19	.	0			c.C652T						PASS	.	C	PHE/LEU	174,3596		4,166,1715	12.0	14.0	13.0		652	1.6	0.0	9	dbSNP_129	13	866,7272		57,752,3260	yes	missense	C9orf173	NM_001004353.2	22	61,918,4975	TT,TC,CC		10.6414,4.6154,8.7336	benign	218/309	140147273	1040,10868	1885	4069	5954	SO:0001631	upstream_gene_variant	441476	exon5			TCCCTGCTTCAGG	AF464935	CCDS7040.1	9q34	2013-01-31	2013-01-31	2013-01-31	ENSG00000188986	ENSG00000188986			24324	protein-coding gene	gene with protein product		611180	"""cofactor of BRCA1"""	COBRA1		11230166, 10574461, 17910036, 17659869	Standard	NM_015456		Approved	KIAA1182, NELF-B	uc004cmm.4	Q8WX92	OTTHUMG00000131778		9.37:g.140147273C>T	Exception_encountered	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	75	32	0.426667	NM_001004353	A2BFA3|Q96EW5|Q9H9R4|Q9ULN8|Q9Y3W0	Missense_Mutation	SNP	ENST00000343053.4	37	CCDS7040.1	331	0.15155677655677655	13	0.026422764227642278	37	0.10220994475138122	184	0.32167832167832167	97	0.1279683377308707	C	9.287	1.049649	0.19827	0.046154	0.106414	ENSG00000197768	ENST00000388931;ENST00000412566	T;T	0.59502	0.26;0.44	3.65	1.63	0.23807	.	1.740450	0.03652	N	0.241159	T	0.00012	0.0000	L	0.48642	1.525	0.80722	P	0.0	D;D	0.58268	0.982;0.982	P;P	0.54210	0.745;0.745	T	0.04153	-1.0973	9	0.32370	T	0.25	.	8.2084	0.31469	0.4328:0.5672:0.0:0.0	rs61759822	218;218	Q8N7X2-2;Q8N7X2-4	.;.	F	218	ENSP00000373583:L218F;ENSP00000391218:L218F	ENSP00000373583:L218F	L	+	1	0	C9orf173	139267094	0.000000	0.05858	0.003000	0.11579	0.016000	0.09150	-1.225000	0.02956	0.274000	0.22072	-0.310000	0.09108	CTT	C|0.847;T|0.153	0.153	strong		0.667	NELFB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254710.1	NM_015456	
DRAXIN	374946	hgsc.bcm.edu	37	1	11771988	11771988	+	Silent	SNP	A	A	G	rs17037327	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:11771988A>G	ENST00000294485.5	+	4	858	c.723A>G	c.(721-723)ttA>ttG	p.L241L		NM_198545.3	NP_940947.3			dorsal inhibitory axon guidance protein																		ATGAAGACTTAAAACCTGATG	0.582													A|||	484	0.0966454	0.0938	0.0821	5008	,	,		20678	0.0655		0.1262	False		,,,				2504	0.1125				p.L241L		Atlas-SNP	.											.	.	.	.	0			c.A723G						PASS	.	A		423,3983	204.1+/-226.4	19,385,1799	90.0	61.0	71.0		723	-1.9	0.8	1	dbSNP_123	71	1134,7466	232.1+/-265.8	55,1024,3221	no	coding-synonymous	C1orf187	NM_198545.3		74,1409,5020	GG,GA,AA		13.186,9.6005,11.9714		241/350	11771988	1557,11449	2203	4300	6503	SO:0001819	synonymous_variant	374946	exon4			AGACTTAAAACCT	AY358750	CCDS135.1	1p36.22	2012-08-20	2012-08-14	2012-08-14	ENSG00000162490	ENSG00000162490			25054	protein-coding gene	gene with protein product	"""dorsal repulsive axon guidance protein"", ""neural tissue-specific cysteine-rich protein"""	612682	"""chromosome 1 open reading frame 187"""	C1orf187		19150847	Standard	NM_198545		Approved	FLJ34999, Draxin, Neucrin	uc001asr.1	Q8NBI3	OTTHUMG00000002227	ENST00000294485.5:c.723A>G	1.37:g.11771988A>G		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	59	23	0.38983	NM_198545		Silent	SNP	ENST00000294485.5	37	CCDS135.1																																																																																			A|0.885;G|0.115	0.115	strong		0.582	DRAXIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006325.1	NM_198545	
ALMS1	7840	hgsc.bcm.edu	37	2	73679990	73679990	+	Missense_Mutation	SNP	T	T	A	rs6724782	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:73679990T>A	ENST00000264448.6	+	8	6444	c.6333T>A	c.(6331-6333)agT>agA	p.S2111R	ALMS1_ENST00000377715.1_Missense_Mutation_p.S2111R|ALMS1_ENST00000409009.1_Missense_Mutation_p.S2069R	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	2111	34 X 47 AA approximate tandem repeat.		S -> R (in dbSNP:rs6724782). {ECO:0000269|PubMed:11941370}.		endosomal transport (GO:0016197)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of stress fiber assembly (GO:0051492)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)				breast(4)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(31)|lung(68)|ovary(4)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	147						TGCCAGGTAGTCATGTAACTG	0.403													A|||	1822	0.363818	0.8775	0.3919	5008	,	,		20591	0.0089		0.2276	False		,,,				2504	0.1554				p.S2111R		Atlas-SNP	.											.	ALMS1	384	.	0			c.T6333A						PASS	.	A	ARG/SER	2748,966		1032,684,141	37.0	36.0	36.0		6333	-5.1	0.0	2	dbSNP_116	36	1956,6228		226,1504,2362	yes	missense	ALMS1	NM_015120.4	110	1258,2188,2503	AA,AT,TT		23.9003,26.0097,39.5361	benign	2111/4168	73679990	4704,7194	1857	4092	5949	SO:0001583	missense	7840	exon8			AGGTAGTCATGTA	AB002326	CCDS42697.1	2p13.1	2014-09-17			ENSG00000116127	ENSG00000116127			428	protein-coding gene	gene with protein product		606844				9063741	Standard	NM_015120		Approved	KIAA0328	uc002sje.1	Q8TCU4	OTTHUMG00000152812	ENST00000264448.6:c.6333T>A	2.37:g.73679990T>A	ENSP00000264448:p.Ser2111Arg	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	80	79	0.9875	NM_015120	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Missense_Mutation	SNP	ENST00000264448.6	37	CCDS42697.1	737	0.3374542124542125	425	0.8638211382113821	126	0.34806629834254144	8	0.013986013986013986	178	0.23482849604221637	A	0.003	-2.434460	0.00182	0.739903	0.239003	ENSG00000116127	ENST00000409009;ENST00000264448;ENST00000377715	T;T;T	0.12774	3.53;3.53;2.65	3.99	-5.06	0.02946	.	1.049810	0.07584	N	0.920720	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	0.39292	-0.9621	9	0.02654	T	1	.	0.5589	0.00676	0.257:0.124:0.2356:0.3834	rs6724782;rs17349573;rs17848883;rs52820401;rs56921282;rs6724782	2111;2069;2111	Q8TCU4-3;B8ZZJ3;Q8TCU4	.;.;ALMS1_HUMAN	R	2069;2111;2111	ENSP00000386627:S2069R;ENSP00000264448:S2111R;ENSP00000366944:S2111R	ENSP00000264448:S2111R	S	+	3	2	ALMS1	73533498	0.000000	0.05858	0.000000	0.03702	0.124000	0.20399	-0.204000	0.09425	-1.484000	0.01856	-0.375000	0.07067	AGT	T|0.691;A|0.309	0.309	strong		0.403	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120	
MEFV	4210	hgsc.bcm.edu	37	16	3297175	3297175	+	Silent	SNP	T	T	C	rs224207	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:3297175T>C	ENST00000219596.1	-	5	1467	c.1428A>G	c.(1426-1428)caA>caG	p.Q476Q	MEFV_ENST00000339854.4_Silent_p.Q296Q|MEFV_ENST00000541159.1_Silent_p.Q265Q|MEFV_ENST00000536379.1_Silent_p.Q265Q	NM_000243.2	NP_000234.1	O15553	MEFV_HUMAN	Mediterranean fever	476	Required for homotrimerization and induction of pyroptosomes.				inflammatory response (GO:0006954)|innate immune response (GO:0045087)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-1 beta production (GO:0032691)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of macrophage inflammatory protein 1 alpha production (GO:0071641)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of cysteine-type endopeptidase activity (GO:2001056)	cell projection (GO:0042995)|cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|nucleus (GO:0005634)	actin binding (GO:0003779)|zinc ion binding (GO:0008270)			NS(2)|biliary_tract(1)|breast(5)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(6)|lung(19)|ovary(3)|prostate(1)|skin(6)	50						AGAAATGCTCTTGCTGCTCCA	0.582													T|||	3258	0.650559	0.649	0.6239	5008	,	,		21091	0.6528		0.5577	False		,,,				2504	0.7648				p.Q476Q		Atlas-SNP	.											MEFV_ENST00000541159,NS,carcinoma,-2,2	MEFV	170	2	0			c.A1428G						PASS	.	T	,	2810,1584	663.6+/-401.2	888,1034,275	166.0	152.0	157.0		1428,795	-9.1	0.2	16	dbSNP_79	157	4578,4022	596.9+/-393.7	1248,2082,970	no	coding-synonymous,coding-synonymous	MEFV	NM_000243.2,NM_001198536.1	,	2136,3116,1245	CC,CT,TT		46.7674,36.0492,43.143	,	476/782,265/446	3297175	7388,5606	2197	4300	6497	SO:0001819	synonymous_variant	4210	exon5			ATGCTCTTGCTGC	AF018080	CCDS10498.1, CCDS55981.1	16p13.3	2014-09-17			ENSG00000103313	ENSG00000103313		"""Tripartite motif containing / Tripartite motif containing"""	6998	protein-coding gene	gene with protein product	"""pyrin"""	608107		MEF		9288094	Standard	NM_000243		Approved	FMF, TRIM20	uc002cun.1	O15553	OTTHUMG00000129324	ENST00000219596.1:c.1428A>G	16.37:g.3297175T>C		Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	192	27	0.140625	NM_000243	D3DUC0|F5H0Q3|Q3MJ84|Q96PN4|Q96PN5	Silent	SNP	ENST00000219596.1	37	CCDS10498.1																																																																																			T|0.407;C|0.593	0.593	strong		0.582	MEFV-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251464.1	NM_000243	
GJA3	2700	hgsc.bcm.edu	37	13	20716411	20716411	+	Silent	SNP	C	C	T	rs11617415	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:20716411C>T	ENST00000241125.3	-	2	1193	c.1017G>A	c.(1015-1017)gcG>gcA	p.A339A		NM_021954.3	NP_068773.2	Q9Y6H8	CXA3_HUMAN	gap junction protein, alpha 3, 46kDa	339					cell-cell signaling (GO:0007267)|transport (GO:0006810)|visual perception (GO:0007601)	connexon complex (GO:0005922)|integral component of membrane (GO:0016021)	gap junction channel activity (GO:0005243)			NS(1)|endometrium(1)|kidney(1)|lung(1)|pancreas(1)|prostate(1)|skin(1)	7		all_cancers(29;1.4e-21)|all_epithelial(30;8.75e-19)|all_lung(29;1.28e-17)|Lung SC(185;0.0257)|Ovarian(182;0.0822)		all cancers(112;0.000554)|Epithelial(112;0.000872)|OV - Ovarian serous cystadenocarcinoma(117;0.0105)|Lung(94;0.0251)|LUSC - Lung squamous cell carcinoma(192;0.0784)		AAGCCTTGAGCGCCGGGGGCT	0.736													C|||	1274	0.254393	0.1672	0.2032	5008	,	,		10210	0.3363		0.2346	False		,,,				2504	0.3446				p.A339A		Atlas-SNP	.											GJA3,caecum,carcinoma,0,1	GJA3	32	1	0			c.G1017A						PASS	.	C		631,3677		54,523,1577	10.0	14.0	12.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1017	-5.4	0.0	13	dbSNP_120	12	1674,6754		166,1342,2706	no	coding-synonymous	GJA3	NM_021954.3		220,1865,4283	TT,TC,CC		19.8624,14.6472,18.0983		339/436	20716411	2305,10431	2154	4214	6368	SO:0001819	synonymous_variant	2700	exon2			CTTGAGCGCCGGG	AF075290	CCDS9289.1	13q12.11	2008-02-05	2007-01-16		ENSG00000121743	ENSG00000121743		"""Ion channels / Gap junction proteins (connexins)"""	4277	protein-coding gene	gene with protein product	"""connexin 46"""	121015	"""gap junction protein, alpha 3, 46kD (connexin 46)"", ""gap junction protein, alpha 3, 46kDa (connexin 46)"""	CZP3		10205266, 7342922	Standard	NM_021954		Approved	CX46	uc001umx.1	Q9Y6H8	OTTHUMG00000016510	ENST00000241125.3:c.1017G>A	13.37:g.20716411C>T		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	64	43	0.671875	NM_021954	Q0VAB7|Q9H537	Silent	SNP	ENST00000241125.3	37	CCDS9289.1																																																																																			C|0.755;T|0.245	0.245	strong		0.736	GJA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044059.3	NM_021954	
ITIH3	3699	hgsc.bcm.edu	37	3	52833805	52833805	+	Missense_Mutation	SNP	C	C	A	rs3617	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:52833805C>A	ENST00000449956.2	+	9	949	c.943C>A	c.(943-945)Caa>Aaa	p.Q315K	ITIH3_ENST00000465243.2_3'UTR|ITIH3_ENST00000416872.2_Missense_Mutation_p.Q315K	NM_002217.3	NP_002208.3	Q06033	ITIH3_HUMAN	inter-alpha-trypsin inhibitor heavy chain 3	315	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.		Q -> K (in dbSNP:rs3617). {ECO:0000269|PubMed:7681778}.		hyaluronan metabolic process (GO:0030212)|negative regulation of endopeptidase activity (GO:0010951)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(6)|liver(1)|lung(6)|ovary(2)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	25				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)		GGAAGATATGCAAGAGGAAGA	0.537													A|||	2723	0.54373	0.7663	0.6095	5008	,	,		19671	0.4137		0.4841	False		,,,				2504	0.3916				p.Q315K		Atlas-SNP	.											ITIH3_ENST00000449956,NS,carcinoma,0,2	ITIH3	132	2	0			c.C943A						PASS	.	A	LYS/GLN	2690,1098		934,822,138	60.0	64.0	63.0		943	4.2	0.0	3	dbSNP_36	63	3852,4422		917,2018,1202	yes	missense	ITIH3	NM_002217.3	53	1851,2840,1340	AA,AC,CC		46.5555,28.9863,45.7636	benign	315/891	52833805	6542,5520	1894	4137	6031	SO:0001583	missense	3699	exon9			GATATGCAAGAGG		CCDS46845.1	3p21.1	2011-10-26	2011-10-26		ENSG00000162267	ENSG00000162267			6168	protein-coding gene	gene with protein product	"""pre-alpha (globulin) inhibitor, H3 polypeptide"", ""inter-alpha-trypsin inhibitor heavy chain H3"""	146650	"""inter-alpha (globulin) inhibitor, H3 polypeptide"", ""inter-alpha (globulin) inhibitor H3"""			2465147, 10100603	Standard	NM_002217		Approved	H3P	uc003dfv.2	Q06033	OTTHUMG00000158956	ENST00000449956.2:c.943C>A	3.37:g.52833805C>A	ENSP00000415769:p.Gln315Lys	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	34	34	1	NM_002217	Q3B7H5|Q53F06|Q6LAM2|Q99085	Missense_Mutation	SNP	ENST00000449956.2	37	CCDS46845.1	1234	0.565018315018315	366	0.7439024390243902	226	0.6243093922651933	269	0.47027972027972026	373	0.4920844327176781	A	1.453	-0.564539	0.03939	0.710137	0.465555	ENSG00000162267	ENST00000398670;ENST00000536431;ENST00000273291;ENST00000416872;ENST00000449956	D;D	0.82803	-1.65;-1.65	5.33	4.15	0.48705	von Willebrand factor, type A (3);	0.296777	0.41500	N	0.000863	T	0.00012	0.0000	N	0.01091	-1.02	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.46638	-0.9177	9	0.15066	T	0.55	-9.9923	11.8647	0.52486	0.5731:0.4269:0.0:0.0	rs3617;rs52792886;rs59027071;rs3617	315;315	E7ET33;Q06033	.;ITIH3_HUMAN	K	315;303;310;315;315	ENSP00000413922:Q315K;ENSP00000415769:Q315K	ENSP00000273291:Q310K	Q	+	1	0	ITIH3	52808845	0.000000	0.05858	0.004000	0.12327	0.164000	0.22412	0.355000	0.20163	0.453000	0.26858	-0.256000	0.11100	CAA	T|0.010;G|0.001	.	strong		0.537	ITIH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352668.2	NM_002217	
C1orf168	199920	hgsc.bcm.edu	37	1	57257817	57257817	+	Silent	SNP	T	T	C	rs2298130	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:57257817T>C	ENST00000343433.6	-	2	749	c.669A>G	c.(667-669)aaA>aaG	p.K223K	C1orf168_ENST00000484327.1_5'UTR	NM_001004303.4	NP_001004303.3	Q5VWT5	CA168_HUMAN	chromosome 1 open reading frame 168	223										NS(1)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(10)|lung(13)|ovary(3)|skin(6)|stomach(1)|urinary_tract(2)	46						TTTCCCAGCTTTTTCTGATAT	0.522													C|||	1259	0.251398	0.3601	0.1599	5008	,	,		16319	0.3542		0.1431	False		,,,				2504	0.1748				p.K223K		Atlas-SNP	.											.	C1orf168	102	.	0			c.A669G						PASS	.	C		1414,2990	651.2+/-399.2	224,966,1012	69.0	77.0	74.0		669	2.8	0.0	1	dbSNP_100	74	1191,7409	754.7+/-407.5	105,981,3214	no	coding-synonymous	C1orf168	NM_001004303.4		329,1947,4226	CC,CT,TT		13.8488,32.1072,20.0323		223/729	57257817	2605,10399	2202	4300	6502	SO:0001819	synonymous_variant	199920	exon2			CCAGCTTTTTCTG	BX648439	CCDS30729.1	1p32.2	2011-02-22			ENSG00000187889	ENSG00000187889			27295	protein-coding gene	gene with protein product						14702039	Standard	NM_001004303		Approved	RP4-758N20.2, FLJ43208	uc001cym.4	Q5VWT5	OTTHUMG00000008281	ENST00000343433.6:c.669A>G	1.37:g.57257817T>C		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	114	61	0.535088	NM_001004303	Q63HM3|Q6ZUY6	Silent	SNP	ENST00000343433.6	37	CCDS30729.1																																																																																			T|0.778;C|0.222	0.222	strong		0.522	C1orf168-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022751.2	NM_001004303	
KIAA0355	9710	hgsc.bcm.edu	37	19	34842488	34842488	+	Silent	SNP	T	T	C	rs392340	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:34842488T>C	ENST00000299505.6	+	13	3768	c.2895T>C	c.(2893-2895)gaT>gaC	p.D965D	AC010504.2_ENST00000591311.1_RNA	NM_014686.3	NP_055501.2	O15063	K0355_HUMAN	KIAA0355	965										breast(1)|endometrium(7)|kidney(1)|large_intestine(4)|lung(15)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	41	Esophageal squamous(110;0.162)					CGGTGGAGGATGTGAACCAGG	0.547													C|||	3018	0.602636	0.739	0.4049	5008	,	,		16866	0.8155		0.3897	False		,,,				2504	0.5583				p.D965D		Atlas-SNP	.											.	KIAA0355	105	.	0			c.T2895C						PASS	.	C		2819,1587	493.2+/-362.6	904,1011,288	84.0	68.0	73.0		2895	-1.7	0.2	19	dbSNP_80	73	3080,5520	658.6+/-401.6	544,1992,1764	no	coding-synonymous	KIAA0355	NM_014686.3		1448,3003,2052	CC,CT,TT		35.814,36.0191,45.356		965/1071	34842488	5899,7107	2203	4300	6503	SO:0001819	synonymous_variant	9710	exon13			GGAGGATGTGAAC		CCDS12436.1	19q13.12	2012-11-29			ENSG00000166398	ENSG00000166398			29016	protein-coding gene	gene with protein product						9205841	Standard	NM_014686		Approved		uc002nvd.4	O15063	OTTHUMG00000180505	ENST00000299505.6:c.2895T>C	19.37:g.34842488T>C		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	38	21	0.552632	NM_014686	Q2M3W4	Silent	SNP	ENST00000299505.6	37	CCDS12436.1																																																																																			T|0.473;C|0.527	0.527	strong		0.547	KIAA0355-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451678.4	NM_014686	
TRIOBP	11078	hgsc.bcm.edu	37	22	38119213	38119213	+	Missense_Mutation	SNP	G	G	A	rs12628603	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:38119213G>A	ENST00000406386.3	+	7	905	c.650G>A	c.(649-651)aGc>aAc	p.S217N		NM_001039141.2	NP_001034230.1	Q9H2D6	TARA_HUMAN	TRIO and F-actin binding protein	217			S -> N (in dbSNP:rs12628603).		actin modification (GO:0030047)|barbed-end actin filament capping (GO:0051016)|mitotic nuclear division (GO:0007067)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	actin filament binding (GO:0051015)|GTP-Rho binding (GO:0017049)|myosin II binding (GO:0045159)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	12	Melanoma(58;0.0574)					GGGGGCCGGAGCGCAGGACAG	0.612													G|||	2637	0.526558	0.3752	0.611	5008	,	,		16088	0.7073		0.5696	False		,,,				2504	0.4407				p.S217N		Atlas-SNP	.											.	TRIOBP	262	.	0			c.G650A						PASS	.	G	ASN/SER	1614,2338		348,918,710	18.0	21.0	20.0		650	3.2	0.7	22	dbSNP_120	20	5038,3244		1516,2006,619	yes	missense	TRIOBP	NM_001039141.2	46	1864,2924,1329	AA,AG,GG		39.1693,40.8401,45.6269	probably-damaging	217/2366	38119213	6652,5582	1976	4141	6117	SO:0001583	missense	11078	exon7			GCCGGAGCGCAGG	AB051449	CCDS33644.1, CCDS43015.1, CCDS43016.1	22q13.1	2014-06-03			ENSG00000100106	ENSG00000100106		"""Pleckstrin homology (PH) domain containing"""	17009	protein-coding gene	gene with protein product		609761		DFNB28		11148140, 16385457, 16385458	Standard	NM_001039141		Approved	HRIHFB2122, KIAA1662, Tara, TAP68	uc003atr.3	Q9H2D6	OTTHUMG00000150657	ENST00000406386.3:c.650G>A	22.37:g.38119213G>A	ENSP00000384312:p.Ser217Asn	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	92	49	0.532609	NM_001039141	B1AHD4|B1AHD7|F2Z2W0|F8W6V6|O94797|Q2PZW8|Q2Q3Z9|Q2Q400|Q5R3M6|Q96DW1|Q9BT77|Q9BTL7|Q9BY98|Q9Y3L4	Missense_Mutation	SNP	ENST00000406386.3	37	CCDS43015.1	1212	0.554945054945055	192	0.3902439024390244	216	0.5966850828729282	378	0.6608391608391608	426	0.5620052770448549	G	13.36	2.213080	0.39102	0.408401	0.608307	ENSG00000100106	ENST00000406386;ENST00000417174	T	0.26810	1.71	4.18	3.16	0.36331	.	.	.	.	.	T	0.00012	0.0000	L	0.27053	0.805	0.09310	P	0.99999081851	B	0.32781	0.384	B	0.30105	0.111	T	0.34775	-0.9815	8	0.66056	D	0.02	.	6.9728	0.24658	0.126:0.0:0.874:0.0	rs12628603	217	Q9H2D6	TARA_HUMAN	N	217	ENSP00000384312:S217N	ENSP00000384312:S217N	S	+	2	0	TRIOBP	36449159	0.985000	0.35326	0.709000	0.30452	0.656000	0.38851	3.006000	0.49529	1.910000	0.55303	0.456000	0.33151	AGC	G|0.436;A|0.564	0.564	strong		0.612	TRIOBP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319439.2		
HLA-A	3105	hgsc.bcm.edu	37	6	29911228	29911228	+	Missense_Mutation	SNP	A	A	C	rs9256983	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:29911228A>C	ENST00000396634.1	+	5	868	c.527A>C	c.(526-528)gAg>gCg	p.E176A	HLA-A_ENST00000376802.2_Missense_Mutation_p.E176A|HLA-A_ENST00000376809.5_Missense_Mutation_p.E176A|HLA-A_ENST00000376806.5_Missense_Mutation_p.E176A			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	176	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						GCGGCCCATGAGGCGGAGCAG	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)			N|||	949	0.189497	0.0847	0.0879	5008	,	,		12286	0.2817		0.1819	False		,,,				2504	0.316				p.E176A		Atlas-SNP	.											.	HLA-A	89	.	0			c.A527C						PASS	.						36.0	29.0	31.0					6																	29911228		1507	2706	4213	SO:0001583	missense	3105	exon3	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	CCCATGAGGCGGA	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.527A>C	6.37:g.29911228A>C	ENSP00000379873:p.Glu176Ala	Somatic	274	1	0.00364964		WXS	Illumina HiSeq	Phase_I	136	50	0.367647	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Missense_Mutation	SNP	ENST00000396634.1	37	CCDS34373.1	.	.	.	.	.	.	.	.	.	.	.	0.023	-1.395936	0.01175	.	.	ENSG00000206503	ENST00000396634;ENST00000376806;ENST00000376809;ENST00000376802	T;T;T;T	0.00008	9.59;9.59;9.59;9.59	3.78	-7.56	0.01322	MHC class I, alpha chain, alpha1/alpha2 (1);MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);	17.376800	0.00944	N	0.002869	T	0.00012	0.0000	N	0.13043	0.29	0.09310	N	1	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.08055	0.0;0.0;0.002;0.003	T	0.52328	-0.8590	10	0.22706	T	0.39	.	8.3683	0.32399	0.4726:0.382:0.0:0.1454	rs9256983;rs28390090;rs41564221	55;176;176;176	B4DVB9;Q5SRN7;Q5SRN5;P04439	.;.;.;1A03_HUMAN	A	176	ENSP00000379873:E176A;ENSP00000366002:E176A;ENSP00000366005:E176A;ENSP00000365998:E176A	ENSP00000365998:E176A	E	+	2	0	HLA-A	30019207	0.257000	0.24022	0.000000	0.03702	0.000000	0.00434	1.149000	0.31626	-7.540000	0.00001	-7.138000	0.00000	GAG	A|0.277;C|0.043;G|0.004;T|0.676	0.043	strong		0.647	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
SLIT2	9353	hgsc.bcm.edu	37	4	20493415	20493415	+	Missense_Mutation	SNP	T	T	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:20493415T>A	ENST00000504154.1	+	9	1059	c.807T>A	c.(805-807)agT>agA	p.S269R	SLIT2_ENST00000503837.1_Missense_Mutation_p.S273R|SLIT2_ENST00000273739.5_Missense_Mutation_p.S273R|SLIT2_ENST00000503823.1_Missense_Mutation_p.S269R	NM_004787.1	NP_004778.1	O94813	SLIT2_HUMAN	slit homolog 2 (Drosophila)	269	LRRNT 2.				apoptotic process involved in luteolysis (GO:0061364)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|branching morphogenesis of an epithelial tube (GO:0048754)|cell migration involved in sprouting angiogenesis (GO:0002042)|cellular response to heparin (GO:0071504)|cellular response to hormone stimulus (GO:0032870)|chemorepulsion involved in postnatal olfactory bulb interneuron migration (GO:0021836)|corticospinal neuron axon guidance through spinal cord (GO:0021972)|dorsal/ventral axon guidance (GO:0033563)|in utero embryonic development (GO:0001701)|induction of negative chemotaxis (GO:0050929)|mammary duct terminal end bud growth (GO:0060763)|metanephros development (GO:0001656)|motor neuron axon guidance (GO:0008045)|negative chemotaxis (GO:0050919)|negative regulation of actin filament polymerization (GO:0030837)|negative regulation of axon extension (GO:0030517)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cellular response to growth factor stimulus (GO:0090288)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of gene expression (GO:0010629)|negative regulation of lamellipodium assembly (GO:0010593)|negative regulation of leukocyte chemotaxis (GO:0002689)|negative regulation of monocyte chemotaxis (GO:0090027)|negative regulation of mononuclear cell migration (GO:0071676)|negative regulation of neutrophil chemotaxis (GO:0090024)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of retinal ganglion cell axon guidance (GO:0090260)|negative regulation of small GTPase mediated signal transduction (GO:0051058)|negative regulation of smooth muscle cell chemotaxis (GO:0071672)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of vascular permeability (GO:0043116)|positive regulation of apoptotic process (GO:0043065)|positive regulation of axonogenesis (GO:0050772)|response to cortisol (GO:0051414)|retinal ganglion cell axon guidance (GO:0031290)|Roundabout signaling pathway (GO:0035385)|single organismal cell-cell adhesion (GO:0016337)|ureteric bud development (GO:0001657)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|chemorepellent activity (GO:0045499)|GTPase inhibitor activity (GO:0005095)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|laminin-1 binding (GO:0043237)|protein homodimerization activity (GO:0042803)|proteoglycan binding (GO:0043394)|Roundabout binding (GO:0048495)			NS(1)|breast(4)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(7)|large_intestine(17)|lung(60)|ovary(3)|pancreas(1)|prostate(2)|skin(10)|upper_aerodigestive_tract(1)	116						CTTCTTGTAGTGTTTTGCACT	0.408																																					p.S269R		Atlas-SNP	.											.	SLIT2	290	.	0			c.T807A						PASS	.						132.0	132.0	132.0					4																	20493415		2203	4300	6503	SO:0001583	missense	9353	exon9			TTGTAGTGTTTTG	AF055585	CCDS3426.1, CCDS75110.1, CCDS75111.1	4p15.2	2008-08-01	2001-11-28		ENSG00000145147	ENSG00000145147			11086	protein-coding gene	gene with protein product		603746	"""slit (Drosophila) homolog 2"""	SLIL3		9813312, 18269211	Standard	XM_005248211		Approved	Slit-2	uc003gpr.1	O94813	OTTHUMG00000128551	ENST00000504154.1:c.807T>A	4.37:g.20493415T>A	ENSP00000422591:p.Ser269Arg	Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	106	32	0.301887	NM_004787	B7ZLR5|O95710|Q17RU3|Q9Y5Q7	Missense_Mutation	SNP	ENST00000504154.1	37	CCDS3426.1	.	.	.	.	.	.	.	.	.	.	T	19.90	3.912535	0.72983	.	.	ENSG00000145147	ENST00000503823;ENST00000504154;ENST00000273739;ENST00000382173;ENST00000503837	T;T;T;T	0.81247	-1.45;-1.47;-1.38;-1.44	5.63	-10.6	0.00265	.	0.000000	0.85682	D	0.000000	T	0.71719	0.3373	N	0.17764	0.52	0.54753	D	0.999988	P;D	0.55172	0.801;0.97	P;P	0.53912	0.578;0.737	D	0.85392	0.1126	10	0.48119	T	0.1	.	17.9392	0.89022	0.0:0.5825:0.0:0.4175	.	269;269	O94813-3;O94813	.;SLIT2_HUMAN	R	269;269;273;273;273	ENSP00000427548:S269R;ENSP00000422591:S269R;ENSP00000273739:S273R;ENSP00000422261:S273R	ENSP00000273739:S273R	S	+	3	2	SLIT2	20102513	0.076000	0.21285	0.120000	0.21714	0.952000	0.60782	-0.425000	0.07017	-2.280000	0.00675	-0.146000	0.13790	AGT	.	.	none		0.408	SLIT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250396.2		
CCDC110	256309	hgsc.bcm.edu	37	4	186380295	186380295	+	Silent	SNP	A	A	G	rs36007437	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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_ENST00000393540.3_Silent_p.N445N|CCDC110_ENST00000507501.1_5'Flank	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	130	0	0		WXS	Illumina HiSeq	Phase_I	87	42	0.482759	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	
WDR4	10785	hgsc.bcm.edu	37	21	44270229	44270229	+	Missense_Mutation	SNP	C	C	T	rs6586250	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:44270229C>T	ENST00000398208.2	-	11	1228	c.1169G>A	c.(1168-1170)cGg>cAg	p.R390Q	WDR4_ENST00000492742.1_5'UTR|WDR4_ENST00000330317.2_Missense_Mutation_p.R390Q	NM_001260474.1|NM_001260475.1|NM_001260476.1|NM_018669.5	NP_001247403.1|NP_001247404.1|NP_001247405.1|NP_061139.2			WD repeat domain 4											haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(3)|ovary(2)	11				Colorectal(79;0.0165)|Lung(125;0.0484)|STAD - Stomach adenocarcinoma(101;0.0624)|COAD - Colon adenocarcinoma(84;0.128)|LUSC - Lung squamous cell carcinoma(216;0.244)		CGGGGGACTCCGGCGCCGCTG	0.602													C|||	1169	0.233427	0.4811	0.1513	5008	,	,		16852	0.0734		0.1779	False		,,,				2504	0.1789				p.R390Q		Atlas-SNP	.											.	WDR4	35	.	0			c.G1169A						PASS	.	C	GLN/ARG,GLN/ARG	1921,2485	544.3+/-376.5	442,1037,724	77.0	85.0	82.0		1169,1169	-1.8	0.0	21	dbSNP_116	82	1626,6974	299.3+/-304.4	144,1338,2818	yes	missense,missense	WDR4	NM_018669.4,NM_033661.3	43,43	586,2375,3542	TT,TC,CC		18.907,43.5996,27.272	benign,benign	390/413,390/413	44270229	3547,9459	2203	4300	6503	SO:0001583	missense	10785	exon11			GGACTCCGGCGCC	AJ243912	CCDS13691.1	21q22.3	2013-01-09			ENSG00000160193	ENSG00000160193		"""WD repeat domain containing"""	12756	protein-coding gene	gene with protein product	"""TRM82 tRNA methyltransferase 82 homolog (S. cerevisiae)"""	605924				12403464	Standard	NM_018669		Approved	TRM82, TRMT82	uc002zci.4	P57081	OTTHUMG00000086826	ENST00000398208.2:c.1169G>A	21.37:g.44270229C>T	ENSP00000381266:p.Arg390Gln	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	77	40	0.519481	NM_018669		Missense_Mutation	SNP	ENST00000398208.2	37	CCDS13691.1	475	0.2174908424908425	238	0.483739837398374	62	0.1712707182320442	45	0.07867132867132867	130	0.17150395778364116	C	2.150	-0.394655	0.04899	0.435996	0.18907	ENSG00000160193	ENST00000330317;ENST00000398208	T;T	0.62788	-0.0;-0.0	2.7	-1.78	0.07957	.	1.424290	0.04586	N	0.395909	T	0.00012	0.0000	N	0.04018	-0.295	0.80722	P	0.0	B;B	0.17268	0.021;0.012	B;B	0.06405	0.002;0.001	T	0.28996	-1.0026	9	0.09590	T	0.72	-3.2097	6.1533	0.20324	0.0:0.4154:0.0:0.5846	rs6586250;rs58274587;rs6586250	389;390	P57081-2;P57081	.;WDR4_HUMAN	Q	390	ENSP00000328671:R390Q;ENSP00000381266:R390Q	ENSP00000328671:R390Q	R	-	2	0	WDR4	43143298	0.000000	0.05858	0.007000	0.13788	0.022000	0.10575	-0.223000	0.09177	-0.438000	0.07232	-1.012000	0.02466	CGG	C|0.748;T|0.252	0.252	strong		0.602	WDR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195479.1		
MTDH	92140	hgsc.bcm.edu	37	8	98656966	98656966	+	Missense_Mutation	SNP	G	G	T	rs17854373	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:98656966G>T	ENST00000336273.3	+	1	560	c.232G>T	c.(232-234)Gcc>Tcc	p.A78S	MTDH_ENST00000519934.1_Missense_Mutation_p.A55S	NM_178812.3	NP_848927.2	Q86UE4	LYRIC_HUMAN	metadherin	78	Interaction with BCCIP.			A -> S (in Ref. 5; AAH09324/AAH45642). {ECO:0000305}.	lipopolysaccharide-mediated signaling pathway (GO:0031663)|negative regulation of apoptotic process (GO:0043066)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of angiogenesis (GO:0045766)|positive regulation of autophagy (GO:0010508)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein kinase B signaling (GO:0051897)|tight junction assembly (GO:0070830)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intercellular canaliculus (GO:0046581)|nuclear body (GO:0016604)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|tight junction (GO:0005923)	double-stranded RNA binding (GO:0003725)|NF-kappaB binding (GO:0051059)|poly(A) RNA binding (GO:0044822)|RNA polymerase II transcription factor binding (GO:0001085)|transcription coactivator activity (GO:0003713)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(6)|large_intestine(5)|liver(1)|lung(8)|ovary(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	32	Breast(36;2.56e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.178)			TTGCGCCGGCGCCCGCAAAAA	0.736													G|||	124	0.0247604	0.0008	0.0274	5008	,	,		8475	0.0		0.0547	False		,,,				2504	0.0501				p.A78S		Atlas-SNP	.											MTDH,NS,carcinoma,0,1	MTDH	54	1	0			c.G232T						PASS	.	G	SER/ALA	42,4076		0,42,2017	6.0	9.0	8.0		232	5.5	1.0	8	dbSNP_123	8	401,7773		7,387,3693	no	missense	MTDH	NM_178812.3	99	7,429,5710	TT,TG,GG		4.9058,1.0199,3.604	probably-damaging	78/583	98656966	443,11849	2059	4087	6146	SO:0001583	missense	92140	exon1			GCCGGCGCCCGCA	AF411226	CCDS6274.1	8q22.1	2014-07-14			ENSG00000147649	ENSG00000147649			29608	protein-coding gene	gene with protein product	"""astrocyte elevated gene 1"""	610323				15093543	Standard	NM_178812		Approved	LYRIC, 3D3, AEG-1	uc003yhz.3	Q86UE4	OTTHUMG00000164692	ENST00000336273.3:c.232G>T	8.37:g.98656966G>T	ENSP00000338235:p.Ala78Ser	Somatic	2	0	0		WXS	Illumina HiSeq	Phase_I	8	8	1	NM_178812	Q05DH2|Q52QU9|Q6PK07|Q8TCX3	Missense_Mutation	SNP	ENST00000336273.3	37	CCDS6274.1	55	0.025183150183150184	0	0.0	13	0.03591160220994475	0	0.0	42	0.055408970976253295	G	25.7	4.660641	0.88154	0.010199	0.049058	ENSG00000147649	ENST00000336273;ENST00000519934	T;T	0.10382	2.88;2.88	5.48	5.48	0.80851	.	0.401308	0.24100	N	0.041542	T	0.02193	0.0068	L	0.34521	1.04	0.41950	D	0.990659	D	0.65815	0.995	P	0.61397	0.888	T	0.00621	-1.1640	10	0.39692	T	0.17	-4.8235	17.1332	0.86732	0.0:0.0:1.0:0.0	rs17854373	78	Q86UE4	LYRIC_HUMAN	S	78;55	ENSP00000338235:A78S;ENSP00000428168:A55S	ENSP00000338235:A78S	A	+	1	0	MTDH	98726142	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.476000	0.53143	2.567000	0.86603	0.591000	0.81541	GCC	G|0.973;T|0.027	0.027	strong		0.736	MTDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379772.2		
CCDC90B	60492	hgsc.bcm.edu	37	11	82973004	82973004	+	Silent	SNP	C	C	T	rs8789	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:82973004C>T	ENST00000529689.1	-	9	1148	c.714G>A	c.(712-714)tcG>tcA	p.S238S	CCDC90B_ENST00000525504.1_5'UTR|CCDC90B_ENST00000455220.2_Silent_p.S229S|CCDC90B_ENST00000525503.1_Silent_p.S137S|CCDC90B_ENST00000529611.1_Silent_p.S137S|CCDC90B_ENST00000529073.1_3'UTR			Q9GZT6	CC90B_HUMAN	coiled-coil domain containing 90B	238						integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)				kidney(2)|large_intestine(2)|lung(4)|ovary(1)|skin(1)	10		Acute lymphoblastic leukemia(157;0.103)				AAGTAAACACCGAAGCTGTGA	0.363													C|||	2347	0.46865	0.6316	0.3285	5008	,	,		18470	0.3502		0.4056	False		,,,				2504	0.5348				p.S238S		Atlas-SNP	.											.	CCDC90B	20	.	0			c.G714A						PASS	.	C		2589,1817	637.9+/-396.8	770,1049,384	130.0	141.0	137.0		714	-10.4	0.9	11	dbSNP_52	137	3543,5057	514.7+/-378.5	738,2067,1495	no	coding-synonymous	CCDC90B	NM_021825.3		1508,3116,1879	TT,TC,CC		41.1977,41.2392,47.1475		238/255	82973004	6132,6874	2203	4300	6503	SO:0001819	synonymous_variant	60492	exon9			AAACACCGAAGCT	BC048795	CCDS8266.1, CCDS66190.1, CCDS66191.1	11q14.1	2006-10-23			ENSG00000137500	ENSG00000137500			28108	protein-coding gene	gene with protein product						11230166	Standard	XM_005274154		Approved	MDS025, MDS011	uc001pae.3	Q9GZT6	OTTHUMG00000167078	ENST00000529689.1:c.714G>A	11.37:g.82973004C>T		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	110	87	0.790909	NM_021825	A8K8I4|B3KP87|B4E3L2|Q3B781|Q9GZU6	Silent	SNP	ENST00000529689.1	37	CCDS8266.1	949	0.43452380952380953	312	0.6341463414634146	131	0.36187845303867405	196	0.34265734265734266	310	0.40897097625329815	C	14.34	2.507009	0.44558	0.587608	0.411977	ENSG00000137500	ENST00000527495	T	0.44083	0.93	5.19	-10.4	0.00318	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.37126	-0.9719	4	.	.	.	-2.2497	5.2364	0.15448	0.0973:0.4137:0.0907:0.3982	rs8789;rs646348;rs1042954;rs3182397;rs11556843;rs17515843;rs59287609;rs646348	.	.	.	Q	127	ENSP00000436974:R127Q	.	R	-	2	0	CCDC90B	82650652	0.009000	0.17119	0.871000	0.34182	0.717000	0.41224	-2.556000	0.00924	-1.470000	0.01888	-1.090000	0.02178	CGG	C|0.508;A|0.022	.	strong		0.363	CCDC90B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392940.2	NM_021825	
EPHX1	2052	hgsc.bcm.edu	37	1	226026406	226026406	+	Missense_Mutation	SNP	A	A	G	rs2234922	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:226026406A>G	ENST00000366837.4	+	4	612	c.416A>G	c.(415-417)cAt>cGt	p.H139R	RP11-285F7.2_ENST00000424332.1_RNA|EPHX1_ENST00000272167.5_Missense_Mutation_p.H139R	NM_000120.3	NP_000111.1	P07099	HYEP_HUMAN	epoxide hydrolase 1, microsomal (xenobiotic)	139			H -> R (in allele EPHX1*4; 62% of wild type enzyme activity; dbSNP:rs2234922). {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)					CCCGCAGGCCATACCCCGAAG	0.607													G|||	1079	0.215455	0.3533	0.1427	5008	,	,		16264	0.1181		0.164	False		,,,				2504	0.2342				p.H139R		Atlas-SNP	.											.	EPHX1	57	.	0			c.A416G	GRCh37	CM024366	EPHX1	M	rs2234922	PASS	.	G	ARG/HIS,ARG/HIS	1484,2922	677.4+/-403.4	250,984,969	88.0	97.0	94.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	416,416	2.5	0.0	1	dbSNP_98	94	1763,6837	734.5+/-406.9	191,1381,2728	yes	missense,missense	EPHX1	NM_000120.3,NM_001136018.2	29,29	441,2365,3697	GG,GA,AA		20.5,33.6813,24.9654	benign,benign	139/456,139/456	226026406	3247,9759	2203	4300	6503	SO:0001583	missense	2052	exon4			CAGGCCATACCCC	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.416A>G	1.37:g.226026406A>G	ENSP00000355802:p.His139Arg	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	74	35	0.472973	NM_001136018	B2R8N0|Q5VTJ6|Q9NP75|Q9NPE7|Q9NQU6|Q9NQU7|Q9NQU8|Q9NQU9|Q9NQV0|Q9NQV1|Q9NQV2	Missense_Mutation	SNP	ENST00000366837.4	37	CCDS1547.1	404	0.184981684981685	165	0.3353658536585366	50	0.13812154696132597	62	0.10839160839160839	127	0.16754617414248021	G	0.008	-1.918526	0.00498	0.336813	0.205	ENSG00000143819	ENST00000445856;ENST00000272167;ENST00000366837	T;T;T	0.03524	3.9;3.9;3.9	5.83	2.55	0.30701	Epoxide hydrolase, N-terminal (1);	0.550791	0.21311	N	0.076624	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	0.40478	-0.9561	9	0.12430	T	0.62	-11.8523	7.654	0.28365	0.5145:0.0:0.4855:0.0	rs2234922;rs59975602;rs2234922	139	P07099	HYEP_HUMAN	R	139	ENSP00000398491:H139R;ENSP00000272167:H139R;ENSP00000355802:H139R	ENSP00000272167:H139R	H	+	2	0	EPHX1	224093029	0.002000	0.14202	0.004000	0.12327	0.035000	0.12851	0.819000	0.27308	0.379000	0.24794	-0.227000	0.12334	CAT	A|0.779;G|0.221	0.221	strong		0.607	EPHX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092064.1	NM_000120	
SPICE1	152185	hgsc.bcm.edu	37	3	113169205	113169205	+	Silent	SNP	C	C	T	rs11920725	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:113169205C>T	ENST00000295872.4	-	15	2560	c.2301G>A	c.(2299-2301)caG>caA	p.Q767Q		NM_144718.3	NP_653319.1	Q8N0Z3	SPICE_HUMAN	spindle and centriole associated protein 1	767					metaphase plate congression (GO:0051310)|regulation of centriole replication (GO:0046599)|spindle assembly involved in mitosis (GO:0090307)	centriole (GO:0005814)|centrosome (GO:0005813)|spindle (GO:0005819)				NS(1)|autonomic_ganglia(1)|breast(4)|endometrium(3)|large_intestine(9)|lung(10)|ovary(2)|skin(2)|urinary_tract(1)	33						TGAGAGGTAACTGAACAGGTG	0.373													C|||	408	0.0814696	0.1218	0.0303	5008	,	,		17425	0.1071		0.0487	False		,,,				2504	0.0706				p.Q767Q		Atlas-SNP	.											.	SPICE1	130	.	0			c.G2301A						PASS	.	C		513,3893	235.5+/-248.0	29,455,1719	134.0	119.0	124.0		2301	1.2	0.9	3	dbSNP_120	124	351,8249	119.4+/-178.7	5,341,3954	no	coding-synonymous	SPICE1	NM_144718.3		34,796,5673	TT,TC,CC		4.0814,11.6432,6.6431		767/856	113169205	864,12142	2203	4300	6503	SO:0001819	synonymous_variant	152185	exon15			AGGTAACTGAACA	AY099107	CCDS2973.1	3q13.2	2010-09-01	2010-09-01	2010-09-01	ENSG00000163611	ENSG00000163611			25083	protein-coding gene	gene with protein product	"""spindle and centriole protein"""	613447	"""coiled-coil domain containing 52"""	CCDC52		20736305	Standard	NM_144718		Approved	SPICE	uc003eag.4	Q8N0Z3	OTTHUMG00000159261	ENST00000295872.4:c.2301G>A	3.37:g.113169205C>T		Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	111	50	0.45045	NM_144718	D3DN72|Q8WUX6	Silent	SNP	ENST00000295872.4	37	CCDS2973.1																																																																																			C|0.931;T|0.069	0.069	strong		0.373	SPICE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354177.2	NM_144718	
HLA-G	3135	hgsc.bcm.edu	37	6	29795657	29795657	+	Silent	SNP	G	G	A	rs1630185	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:29795657G>A	ENST00000360323.6	+	1	60	c.36G>A	c.(34-36)ctG>ctA	p.L12L	HLA-G_ENST00000376818.3_Silent_p.L12L|HLA-G_ENST00000376815.3_Silent_p.L12L|HLA-G_ENST00000428701.1_Silent_p.L12L|HLA-G_ENST00000376828.2_Silent_p.L17L			P17693	HLAG_HUMAN	major histocompatibility complex, class I, G	12					antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular defense response (GO:0006968)|cytokine-mediated signaling pathway (GO:0019221)|immune response-inhibiting cell surface receptor signaling pathway (GO:0002767)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of dendritic cell differentiation (GO:2001199)|negative regulation of T cell proliferation (GO:0042130)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of regulatory T cell differentiation (GO:0045591)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|positive regulation of T cell tolerance induction (GO:0002666)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)	early endosome membrane (GO:0031901)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|membrane (GO:0016020)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	peptide antigen binding (GO:0042605)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)			central_nervous_system(1)|endometrium(1)|large_intestine(5)|lung(4)|ovary(3)|pancreas(1)|prostate(5)|skin(1)	21						TCTTCCTGCTGCTCTCGGGGG	0.706													g|||	2726	0.544329	0.5083	0.4654	5008	,	,		13560	0.6032		0.4324	False		,,,				2504	0.7035				p.L12L		Atlas-SNP	.											.	HLA-G	90	.	0			c.G36A						PASS	.	G		1538,1484		393,752,366	38.0	43.0	41.0		36	0.6	0.3	6	dbSNP_89	41	2507,2911		597,1313,799	no	coding-synonymous	HLA-G	NM_002127.5		990,2065,1165	AA,AG,GG		46.2717,49.1066,47.9265		12/339	29795657	4045,4395	1511	2709	4220	SO:0001819	synonymous_variant	3135	exon2			CCTGCTGCTCTCG		CCDS4668.1	6p21.3	2013-01-11	2007-12-12		ENSG00000204632	ENSG00000204632		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4964	protein-coding gene	gene with protein product	"""b2 microglobulin"""	142871	"""HLA-G histocompatibility antigen, class I, G"""				Standard	NM_002127		Approved		uc003nnw.2	P17693	OTTHUMG00000031157	ENST00000360323.6:c.36G>A	6.37:g.29795657G>A		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	112	107	0.955357	NM_002127		Silent	SNP	ENST00000360323.6	37	CCDS4668.1																																																																																			G|0.518;A|0.482	0.482	strong		0.706	HLA-G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076286.2	NM_002127	
SRSF4	6429	hgsc.bcm.edu	37	1	29475341	29475341	+	Missense_Mutation	SNP	C	C	T	rs2230678	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:29475341C>T	ENST00000373795.4	-	6	1300	c.1066G>A	c.(1066-1068)Ggc>Agc	p.G356S	SRSF4_ENST00000466448.1_5'UTR|RP11-242O24.3_ENST00000413004.1_lincRNA|SRSF4_ENST00000546138.1_3'UTR	NM_005626.4	NP_005617.2	Q08170	SRSF4_HUMAN	serine/arginine-rich splicing factor 4	356	Arg/Ser-rich (RS domain).		G -> S (in dbSNP:rs2230678). {ECO:0000269|PubMed:8321209}.		gene expression (GO:0010467)|hematopoietic progenitor cell differentiation (GO:0002244)|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)|RNA splicing, via transesterification reactions (GO:0000375)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(8)|liver(1)|lung(8)|ovary(1)|prostate(1)	27						ctcttcctgcccttcctcttg	0.647													C|||	2479	0.495008	0.5598	0.5447	5008	,	,		17387	0.1528		0.7694	False		,,,				2504	0.4427				p.G356S		Atlas-SNP	.											.	SRSF4	44	.	0			c.G1066A						PASS	.	C	SER/GLY	2685,1719	622.7+/-394.0	844,997,361	42.0	37.0	39.0		1066	3.8	1.0	1	dbSNP_98	39	6859,1737	701.7+/-405.2	2740,1379,179	yes	missense	SRSF4	NM_005626.4	56	3584,2376,540	TT,TC,CC		20.2071,39.0327,26.5846	benign	356/495	29475341	9544,3456	2202	4298	6500	SO:0001583	missense	6429	exon6			TCCTGCCCTTCCT	BC002781	CCDS333.1	1p35.3	2013-02-12	2010-06-22	2010-06-22	ENSG00000116350	ENSG00000116350		"""Serine/arginine-rich splicing factors"", ""RNA binding motif (RRM) containing"""	10786	protein-coding gene	gene with protein product	"""SR splicing factor 4"""	601940	"""splicing factor, arginine/serine-rich 4"""	SFRS4		8321209, 20516191	Standard	NM_005626		Approved	SRP75	uc001bro.3	Q08170	OTTHUMG00000003663	ENST00000373795.4:c.1066G>A	1.37:g.29475341C>T	ENSP00000362900:p.Gly356Ser	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	69	69	1	NM_005626	Q5VXP1|Q9BUA4|Q9UEB5	Missense_Mutation	SNP	ENST00000373795.4	37	CCDS333.1	1144	0.5238095238095238	275	0.5589430894308943	204	0.56353591160221	83	0.1451048951048951	582	0.7678100263852242	C	9.148	1.015494	0.19355	0.609673	0.797929	ENSG00000116350	ENST00000373795;ENST00000434636	T	0.03889	3.77	5.62	3.76	0.43208	.	0.985643	0.08329	N	0.962558	T	0.00012	0.0000	N	0.22421	0.69	0.09310	P	0.9999999999989855	B	0.13594	0.008	B	0.08055	0.003	T	0.13019	-1.0525	9	0.11485	T	0.65	.	9.5483	0.39295	0.0:0.7705:0.0:0.2295	rs61726743	356	Q08170	SRSF4_HUMAN	S	356	ENSP00000362900:G356S	ENSP00000362900:G356S	G	-	1	0	SRSF4	29347928	0.964000	0.33143	0.984000	0.44739	0.966000	0.64601	1.246000	0.32803	0.730000	0.32425	-0.140000	0.14226	GGC	C|0.384;T|0.616	0.616	strong		0.647	SRSF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010392.1	NM_005626	
TEX35	84066	hgsc.bcm.edu	37	1	178489978	178489978	+	Missense_Mutation	SNP	T	T	G	rs3813636	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:178489978T>G	ENST00000319416.2	+	7	624	c.512T>G	c.(511-513)cTg>cGg	p.L171R	TEX35_ENST00000258298.2_Missense_Mutation_p.L95R|TEX35_ENST00000367639.1_Missense_Mutation_p.L179R|TEX35_ENST00000367642.3_3'UTR|TEX35_ENST00000367641.3_Missense_Mutation_p.L171R|TEX35_ENST00000367643.3_Missense_Mutation_p.L171R	NM_032126.4	NP_115502.2			testis expressed 35																		CAGGGCTCACTGGATCCCCTT	0.577													T|||	1848	0.36901	0.2247	0.4827	5008	,	,		19228	0.4077		0.4543	False		,,,				2504	0.3558				p.L179R		Atlas-SNP	.											TEX35,NS,carcinoma,0,3	TEX35	15	3	0			c.T536G						PASS	.	T	ARG/LEU,ARG/LEU,ARG/LEU,ARG/LEU	1246,3160	410.0+/-335.2	213,820,1170	69.0	68.0	68.0		536,512,512,512	1.8	0.0	1	dbSNP_107	68	3548,5052	515.1+/-378.5	731,2086,1483	yes	missense,missense,missense,missense	C1orf49	NM_001170722.1,NM_001170723.1,NM_001170724.1,NM_032126.4	102,102,102,102	944,2906,2653	GG,GT,TT		41.2558,28.2796,36.8599	probably-damaging,probably-damaging,probably-damaging,probably-damaging	179/216,171/213,171/208,171/234	178489978	4794,8212	2203	4300	6503	SO:0001583	missense	84066	exon7			GCTCACTGGATCC	AL136694	CCDS1323.1, CCDS53433.1, CCDS53434.1	1q25.2	2014-01-28	2012-06-29	2012-06-29	ENSG00000240021	ENSG00000240021			25366	protein-coding gene	gene with protein product	"""Testis-Specific Conserved gene 24kDa"""		"""chromosome 1 open reading frame 49"""	C1orf49		11230166, 17077512	Standard	NM_032126		Approved	DKFZP564J047, TSC24	uc001glt.2	Q5T0J7	OTTHUMG00000035023	ENST00000319416.2:c.512T>G	1.37:g.178489978T>G	ENSP00000323795:p.Leu171Arg	Somatic	222	0	0		WXS	Illumina HiSeq	Phase_I	159	157	0.987421	NM_001170722		Missense_Mutation	SNP	ENST00000319416.2	37	CCDS1323.1	883	0.4043040293040293	140	0.2845528455284553	168	0.46408839779005523	240	0.4195804195804196	335	0.4419525065963061	T	13.59	2.283107	0.40394	0.282796	0.412558	ENSG00000240021	ENST00000319416;ENST00000258298;ENST00000367643;ENST00000367641;ENST00000367639	T;T;T;T;T	0.26373	1.74;1.74;1.74;1.74;1.74	4.09	1.82	0.25136	.	1.177410	0.06477	N	0.732108	T	0.00012	0.0000	L	0.48642	1.525	0.80722	P	0.0	P;P;P	0.52061	0.95;0.95;0.95	P;P;P	0.52424	0.648;0.698;0.698	T	0.44513	-0.9323	9	0.38643	T	0.18	-2.4585	5.1247	0.14878	0.0:0.2385:0.0:0.7615	rs3813636;rs52829520;rs59954509;rs3813636	179;171;171	Q5T0J7-2;Q5T0J7-3;Q5T0J7	.;.;CA049_HUMAN	R	171;95;171;171;179	ENSP00000323795:L171R;ENSP00000258298:L95R;ENSP00000356615:L171R;ENSP00000356613:L171R;ENSP00000356611:L179R	ENSP00000258298:L95R	L	+	2	0	C1orf49	176756601	0.002000	0.14202	0.041000	0.18516	0.040000	0.13550	0.068000	0.14531	0.743000	0.32719	0.438000	0.28831	CTG	C|0.001;G|0.385;T|0.614	0.385	strong		0.577	TEX35-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000084917.1	NM_032126	
RNF150	57484	hgsc.bcm.edu	37	4	141789457	141789457	+	Silent	SNP	T	T	A	rs61744098	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:141789457T>A	ENST00000515673.2	-	7	1308	c.1275A>T	c.(1273-1275)gtA>gtT	p.V425V	RNF150_ENST00000379512.2_Silent_p.V284V|RNF150_ENST00000306799.3_Silent_p.V383V|RNF150_ENST00000420921.2_Silent_p.V284V			Q9ULK6	RN150_HUMAN	ring finger protein 150	425						integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)			breast(1)|large_intestine(10)|lung(7)|ovary(1)	19	all_hematologic(180;0.162)					TGGAAAGTTCTACATCAGACA	0.468													T|||	119	0.023762	0.0	0.0173	5008	,	,		20123	0.0		0.0368	False		,,,				2504	0.0716				p.V425V		Atlas-SNP	.											.	RNF150	94	.	0			c.A1275T						PASS	.	T		39,4367	43.8+/-77.6	0,39,2164	184.0	144.0	157.0		1275	-1.3	1.0	4	dbSNP_129	157	399,8201	127.2+/-185.5	5,389,3906	no	coding-synonymous	RNF150	NM_020724.1		5,428,6070	AA,AT,TT		4.6395,0.8852,3.3677		425/439	141789457	438,12568	2203	4300	6503	SO:0001819	synonymous_variant	57484	exon7			AAGTTCTACATCA	AB033040	CCDS34065.1	4q31.1	2013-01-09			ENSG00000170153	ENSG00000170153		"""RING-type (C3HC4) zinc fingers"""	23138	protein-coding gene	gene with protein product						10574462	Standard	XM_005263150		Approved	KIAA1214	uc003iio.1	Q9ULK6	OTTHUMG00000161380	ENST00000515673.2:c.1275A>T	4.37:g.141789457T>A		Somatic	203	0	0		WXS	Illumina HiSeq	Phase_I	174	91	0.522988	NM_020724	Q3T1D0|Q6ZNW6	Silent	SNP	ENST00000515673.2	37	CCDS34065.1																																																																																			T|0.961;A|0.039	0.039	strong		0.468	RNF150-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364739.2	XM_291090	
TACC2	10579	hgsc.bcm.edu	37	10	123903133	123903133	+	Missense_Mutation	SNP	G	G	A	rs12765679	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:123903133G>A	ENST00000369005.1	+	7	6086	c.5746G>A	c.(5746-5748)Gaa>Aaa	p.E1916K	TACC2_ENST00000358010.1_Intron|TACC2_ENST00000334433.3_Missense_Mutation_p.E1916K|TACC2_ENST00000493951.1_3'UTR|TACC2_ENST00000515603.1_Intron|TACC2_ENST00000453444.2_Intron|TACC2_ENST00000369000.1_Intron|TACC2_ENST00000513429.1_Intron|TACC2_ENST00000515273.1_Intron|TACC2_ENST00000369001.1_Intron	NM_206862.2	NP_996744.2	O95359	TACC2_HUMAN	transforming, acidic coiled-coil containing protein 2	1916			E -> K (in dbSNP:rs12765679).		astral microtubule organization (GO:0030953)|cerebral cortex development (GO:0021987)|interkinetic nuclear migration (GO:0022027)|neurogenesis (GO:0022008)|regulation of microtubule-based process (GO:0032886)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleus (GO:0005634)	nuclear hormone receptor binding (GO:0035257)			NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(15)|lung(27)|ovary(6)|prostate(3)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	83		all_neural(114;0.0656)|Lung NSC(174;0.136)|all_lung(145;0.17)|Breast(234;0.197)				CTCGGCTGCAGAACACATAGT	0.577											OREG0020589	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	453	0.0904553	0.0688	0.1138	5008	,	,		14875	0.0		0.2286	False		,,,				2504	0.0542				p.E1916K		Atlas-SNP	.											.	TACC2	271	.	0			c.G5746A						PASS	.	G	,LYS/GLU	361,4045	185.7+/-212.7	15,331,1857	103.0	89.0	94.0		,5746	3.5	0.0	10	dbSNP_121	94	1929,6671	341.6+/-324.1	219,1491,2590	yes	intron,missense	TACC2	NM_206861.1,NM_206862.2	,56	234,1822,4447	AA,AG,GG		22.4302,8.1934,17.6073	,probably-damaging	,1916/2949	123903133	2290,10716	2203	4300	6503	SO:0001583	missense	10579	exon7			GCTGCAGAACACA	AF095791	CCDS7625.1, CCDS7626.1, CCDS7627.1, CCDS7628.1	10q26	2008-07-29			ENSG00000138162	ENSG00000138162			11523	protein-coding gene	gene with protein product		605302				14767476	Standard	XM_005269388		Approved	AZU-1	uc001lfv.3	O95359	OTTHUMG00000019181	ENST00000369005.1:c.5746G>A	10.37:g.123903133G>A	ENSP00000358001:p.Glu1916Lys	Somatic	62	0	0	1530	WXS	Illumina HiSeq	Phase_I	59	26	0.440678	NM_206862	Q4VXL0|Q4VXL3|Q4VXL6|Q4VXL7|Q5U5T7|Q86WG6|Q86WG7|Q8TCK9|Q9BVQ1|Q9NZ41|Q9NZR5	Missense_Mutation	SNP	ENST00000369005.1	37	CCDS7626.1	268	0.1227106227106227	31	0.06300813008130081	55	0.15193370165745856	0	0.0	182	0.24010554089709762	G	14.03	2.413032	0.42817	0.081934	0.224302	ENSG00000138162	ENST00000369005;ENST00000334433;ENST00000340076	T;T	0.57907	0.37;0.37	4.45	3.53	0.40419	.	0.443678	0.16781	N	0.199795	T	0.00012	0.0000	L	0.32530	0.975	0.48571	P	3.269999999999662E-4	P	0.37061	0.58	B	0.37601	0.254	T	0.11665	-1.0578	9	0.72032	D	0.01	-4.7039	10.6039	0.45384	0.0:0.1948:0.8052:0.0	rs12765679;rs17551488;rs52820192;rs57234473;rs12765679	1916	O95359	TACC2_HUMAN	K	1916;1916;1906	ENSP00000358001:E1916K;ENSP00000334280:E1916K	ENSP00000334280:E1916K	E	+	1	0	TACC2	123893123	0.032000	0.19561	0.003000	0.11579	0.003000	0.03518	2.480000	0.45206	1.209000	0.43321	-0.304000	0.09214	GAA	G|0.854;A|0.146	0.146	strong		0.577	TACC2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090004.1		
TTC29	83894	hgsc.bcm.edu	37	4	147788728	147788728	+	Silent	SNP	G	G	A	rs35231662	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:147788728G>A	ENST00000325106.4	-	8	1033	c.807C>T	c.(805-807)gaC>gaT	p.D269D	TTC29_ENST00000398886.4_Silent_p.D295D|TTC29_ENST00000513335.1_Silent_p.D295D	NM_031956.2	NP_114162.2	Q8NA56	TTC29_HUMAN	tetratricopeptide repeat domain 29	269										breast(2)|cervix(2)|endometrium(3)|kidney(4)|large_intestine(6)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	26	all_hematologic(180;0.151)					CCATCTTTTTGTCACTTCCTG	0.333													G|||	312	0.0623003	0.0454	0.1643	5008	,	,		14672	0.0506		0.0457	False		,,,				2504	0.0419				p.D269D		Atlas-SNP	.											.	TTC29	63	.	0			c.C807T						PASS	.	G		186,3442		2,182,1630	59.0	56.0	57.0		807	4.6	1.0	4	dbSNP_126	57	372,7782		10,352,3715	no	coding-synonymous	TTC29	NM_031956.2		12,534,5345	AA,AG,GG		4.5622,5.1268,4.736		269/476	147788728	558,11224	1814	4077	5891	SO:0001819	synonymous_variant	83894	exon8			CTTTTTGTCACTT	AF345910	CCDS47141.1, CCDS75200.1	4q31.23	2013-01-11				ENSG00000137473		"""Tetratricopeptide (TTC) repeat domain containing"""	29936	protein-coding gene	gene with protein product						12477932	Standard	NM_031956		Approved	NYD-SP14	uc003ikw.4	Q8NA56		ENST00000325106.4:c.807C>T	4.37:g.147788728G>A		Somatic	220	0	0		WXS	Illumina HiSeq	Phase_I	179	77	0.430168	NM_031956	A4GU95|Q9BXB6	Silent	SNP	ENST00000325106.4	37	CCDS47141.1																																																																																			G|0.938;A|0.062	0.062	strong		0.333	TTC29-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_031956	
TEP1	7011	hgsc.bcm.edu	37	14	20849169	20849169	+	Silent	SNP	G	G	A	rs2228039	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:20849169G>A	ENST00000262715.5	-	33	4723	c.4683C>T	c.(4681-4683)ttC>ttT	p.F1561F	TEP1_ENST00000545983.1_5'UTR|TEP1_ENST00000556935.1_Silent_p.F1453F	NM_007110.4	NP_009041.2	Q99973	TEP1_HUMAN	telomerase-associated protein 1	1561					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)		GGTTGGTAAGGAACTTCGAAA	0.527													A|||	288	0.057508	0.093	0.036	5008	,	,		18921	0.001		0.0676	False		,,,				2504	0.0726				p.F1561F		Atlas-SNP	.											.	TEP1	224	.	0			c.C4683T						PASS	.	A		378,4028	791.5+/-415.1	16,346,1841	69.0	63.0	65.0		4683	-1.8	0.9	14	dbSNP_98	65	565,8035	793.8+/-407.5	20,525,3755	no	coding-synonymous	TEP1	NM_007110.4		36,871,5596	AA,AG,GG		6.5698,8.5792,7.2505		1561/2628	20849169	943,12063	2203	4300	6503	SO:0001819	synonymous_variant	7011	exon33			GGTAAGGAACTTC		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.4683C>T	14.37:g.20849169G>A		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	109	52	0.477064	NM_007110	A0AUV9	Silent	SNP	ENST00000262715.5	37	CCDS9548.1																																																																																			G|0.935;A|0.065	0.065	strong		0.527	TEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073563.2	NM_007110	
NOTCH3	4854	hgsc.bcm.edu	37	19	15295134	15295134	+	Silent	SNP	G	G	A	rs1043996	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:15295134G>A	ENST00000263388.2	-	16	2613	c.2538C>T	c.(2536-2538)tgC>tgT	p.C846C		NM_000435.2	NP_000426.2	Q9UM47	NOTC3_HUMAN	notch 3	846	EGF-like 21; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				forebrain development (GO:0030900)|gene expression (GO:0010467)|glomerular capillary formation (GO:0072104)|negative regulation of neuron differentiation (GO:0045665)|neuron fate commitment (GO:0048663)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|positive regulation of smooth muscle cell proliferation (GO:0048661)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)			breast(4)|central_nervous_system(3)|endometrium(10)|kidney(3)|large_intestine(16)|liver(1)|lung(31)|ovary(8)|prostate(3)|skin(7)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	93			OV - Ovarian serous cystadenocarcinoma(3;2.6e-20)|Epithelial(3;1.34e-16)|all cancers(3;5.13e-15)			TGTCCTGATCGCAGGAAGGGC	0.597													G|||	2604	0.519968	0.1997	0.562	5008	,	,		17319	0.5933		0.6928	False		,,,				2504	0.6697				p.C846C		Atlas-SNP	.											NOTCH3_ENST00000263388,colon,carcinoma,-2,2	NOTCH3	340	2	0			c.C2538T						PASS	.	G		1217,3189	422.5+/-339.8	184,849,1170	75.0	56.0	62.0		2538	-1.0	0.9	19	dbSNP_86	62	6150,2450	695.4+/-404.8	2210,1730,360	yes	coding-synonymous	NOTCH3	NM_000435.2		2394,2579,1530	AA,AG,GG		28.4884,27.6214,43.3569		846/2322	15295134	7367,5639	2203	4300	6503	SO:0001819	synonymous_variant	4854	exon16			CTGATCGCAGGAA	U97669	CCDS12326.1	19p13.2-p13.1	2013-01-10	2010-06-24			ENSG00000074181		"""Ankyrin repeat domain containing"""	7883	protein-coding gene	gene with protein product		600276	"""Notch (Drosophila) homolog 3"", ""Notch homolog 3 (Drosophila)"""	CADASIL		7835890	Standard	NM_000435		Approved	CASIL	uc002nan.3	Q9UM47		ENST00000263388.2:c.2538C>T	19.37:g.15295134G>A		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	128	127	0.992188	NM_000435	Q9UEB3|Q9UPL3|Q9Y6L8	Silent	SNP	ENST00000263388.2	37	CCDS12326.1																																																																																			G|0.460;T|0.004	.	strong		0.597	NOTCH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465714.1	NM_000435	
ZNF573	126231	hgsc.bcm.edu	37	19	38230720	38230720	+	Missense_Mutation	SNP	C	C	G	rs3752365	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:38230720C>G	ENST00000590414.2	-	4	692	c.671G>C	c.(670-672)gGg>gCg	p.G224A	ZNF573_ENST00000536220.1_Missense_Mutation_p.G136A|ZNF573_ENST00000357309.3_Missense_Mutation_p.G136A|ZNF573_ENST00000392138.1_Missense_Mutation_p.G137A|ZNF573_ENST00000339503.4_Missense_Mutation_p.G166A			Q86YE8	ZN573_HUMAN	zinc finger protein 573	224			G -> A (in dbSNP:rs3752365).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|cervix(3)|endometrium(2)|large_intestine(8)|liver(1)|lung(5)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	25			UCEC - Uterine corpus endometrioid carcinoma (49;0.0775)|Lung(45;0.0813)|LUSC - Lung squamous cell carcinoma(53;0.146)			AAAGGCCTTCCCACACTGCCT	0.438													c|||	498	0.0994409	0.0189	0.1254	5008	,	,		20686	0.0694		0.2167	False		,,,				2504	0.1002				p.G224A		Atlas-SNP	.											.	ZNF573	63	.	0			c.G671C						PASS	.	C	ALA/GLY,ALA/GLY,ALA/GLY,ALA/GLY,ALA/GLY	261,4145	147.6+/-182.1	7,247,1949	116.0	107.0	110.0		407,671,665,407,497	2.6	0.7	19	dbSNP_107	110	1808,6792	324.5+/-316.5	217,1374,2709	yes	missense,missense,missense,missense,missense	ZNF573	NM_001172689.1,NM_001172690.1,NM_001172691.1,NM_001172692.1,NM_152360.3	60,60,60,60,60	224,1621,4658	GG,GC,CC		21.0233,5.9237,15.908	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	136/578,224/666,222/664,136/578,166/608	38230720	2069,10937	2203	4300	6503	SO:0001583	missense	126231	exon5			GCCTTCCCACACT	AK074539	CCDS12508.1, CCDS54260.1, CCDS59381.1	19q13.12	2013-09-20			ENSG00000189144	ENSG00000189144		"""Zinc fingers, C2H2-type"", ""-"""	26420	protein-coding gene	gene with protein product						12477932	Standard	NM_152360		Approved	FLJ30921	uc002ohe.3	Q86YE8	OTTHUMG00000048183	ENST00000590414.2:c.671G>C	19.37:g.38230720C>G	ENSP00000465020:p.Gly224Ala	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	46	23	0.5	NM_001172690	B7WPE1|K7EJ45|Q6P1P1|Q7Z7Q3|Q8N2Q1|Q96BM3|Q96NH0	Missense_Mutation	SNP	ENST00000590414.2	37	CCDS59381.1	270	0.12362637362637363	15	0.03048780487804878	57	0.1574585635359116	43	0.07517482517482517	155	0.20448548812664907	c	13.65	2.299980	0.40694	0.059237	0.210233	ENSG00000189144	ENST00000392138;ENST00000536220;ENST00000357309;ENST00000339503;ENST00000427026	T;T;T;T	0.57595	0.39;0.39;0.39;0.39	2.62	2.62	0.31277	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00109	0.0003	M	0.89414	3.03	0.41481	P	0.011831000000000036	D;D;D;D	0.61080	0.987;0.957;0.989;0.987	B;B;P;B	0.47891	0.342;0.342;0.56;0.424	T	0.21143	-1.0254	8	0.72032	D	0.01	.	12.0468	0.53485	0.0:1.0:0.0:0.0	rs3752365;rs17663719;rs3752365	137;166;204;136	Q86YE8-4;Q86YE8-3;Q86YE8;Q86YE8-2	.;.;ZN573_HUMAN;.	A	137;136;136;166;136	ENSP00000375983:G137A;ENSP00000440464:G136A;ENSP00000349861:G136A;ENSP00000340171:G166A	ENSP00000340171:G166A	G	-	2	0	ZNF573	42922560	0.846000	0.29590	0.685000	0.30070	0.396000	0.30629	1.580000	0.36547	1.300000	0.44818	0.645000	0.84053	GGG	C|0.852;G|0.148	0.148	strong		0.438	ZNF573-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459773.2	NM_152360	
TYW1	55253	hgsc.bcm.edu	37	7	66660247	66660247	+	Silent	SNP	T	T	C	rs55673383		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	204	0	0		WXS	Illumina HiSeq	Phase_I	130	31	0.238462	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	
TMEM127	55654	hgsc.bcm.edu	37	2	96919642	96919642	+	Silent	SNP	C	C	T	rs3852673	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:96919642C>T	ENST00000258439.3	-	4	877	c.621G>A	c.(619-621)gcG>gcA	p.A207A	TMEM127_ENST00000432959.1_Silent_p.A207A|TMEM127_ENST00000435268.1_Silent_p.A123A	NM_001193304.2|NM_017849.3	NP_001180233.1|NP_060319.1	O75204	TM127_HUMAN	transmembrane protein 127	207					negative regulation of cell proliferation (GO:0008285)|negative regulation of TOR signaling (GO:0032007)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.A207A(1)		endometrium(1)|large_intestine(1)|lung(1)|prostate(1)|stomach(1)	5						GCAGCTCCAGCGCCTGCTCCT	0.607													C|||	698	0.139377	0.0469	0.1398	5008	,	,		18524	0.0873		0.1779	False		,,,				2504	0.2781				p.A207A		Atlas-SNP	.											TMEM127,NS,carcinoma,-1,2	TMEM127	13	2	1	Substitution - coding silent(1)	stomach(1)	c.G621A						PASS	.	C	,	304,4102	163.6+/-195.4	12,280,1911	72.0	69.0	70.0		621,621	-11.6	0.4	2	dbSNP_108	70	1500,7100	285.0+/-296.9	136,1228,2936	no	coding-synonymous,coding-synonymous	TMEM127	NM_001193304.2,NM_017849.3	,	148,1508,4847	TT,TC,CC		17.4419,6.8997,13.8705	,	207/239,207/239	96919642	1804,11202	2203	4300	6503	SO:0001819	synonymous_variant	55654	exon4			CTCCAGCGCCTGC	AK000514	CCDS2018.1	2q11.2	2014-09-17			ENSG00000135956	ENSG00000135956			26038	protein-coding gene	gene with protein product		613403				10493829	Standard	NM_017849		Approved	FLJ20507, FLJ22257	uc002svr.3	O75204	OTTHUMG00000130454	ENST00000258439.3:c.621G>A	2.37:g.96919642C>T		Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	165	74	0.448485	NM_001193304	D3DXH0	Silent	SNP	ENST00000258439.3	37	CCDS2018.1																																																																																			C|0.874;T|0.126	0.126	strong		0.607	TMEM127-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252845.3	NM_017849	
AGAP1	116987	hgsc.bcm.edu	37	2	236817442	236817442	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:236817442C>T	ENST00000304032.8	+	11	1796	c.1216C>T	c.(1216-1218)Cca>Tca	p.P406S	AGAP1_ENST00000409538.1_Missense_Mutation_p.P671S|AGAP1_ENST00000428334.2_Missense_Mutation_p.P245S|AGAP1_ENST00000336665.5_Missense_Mutation_p.P406S	NM_001037131.2	NP_001032208.1	Q9UPQ3	AGAP1_HUMAN	ArfGAP with GTPase domain, ankyrin repeat and PH domain 1	406	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				protein transport (GO:0015031)|regulation of ARF GTPase activity (GO:0032312)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	ARF GTPase activator activity (GO:0008060)|GTP binding (GO:0005525)|phospholipid binding (GO:0005543)|zinc ion binding (GO:0008270)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(12)|lung(11)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	41						TGTGAAAGTCCCAGGGAAGAG	0.468																																					p.P406S		Atlas-SNP	.											.	AGAP1	95	.	0			c.C1216T						PASS	.						73.0	68.0	70.0					2																	236817442		2203	4300	6503	SO:0001583	missense	116987	exon11			AAAGTCCCAGGGA	AF413078	CCDS2514.1, CCDS33408.1, CCDS58756.1	2q37	2013-01-10	2008-09-22	2008-09-22	ENSG00000157985	ENSG00000157985		"""ADP-ribosylation factor GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"", ""Ankyrin repeat domain containing"""	16922	protein-coding gene	gene with protein product		608651	"""centaurin, gamma 2"""	CENTG2			Standard	NM_001037131		Approved	KIAA1099, GGAP1	uc002vvs.3	Q9UPQ3	OTTHUMG00000133293	ENST00000304032.8:c.1216C>T	2.37:g.236817442C>T	ENSP00000307634:p.Pro406Ser	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	153	20	0.130719	NM_014914	B2RTX7|Q541S5|Q6P9D7|Q9NV93	Missense_Mutation	SNP	ENST00000304032.8	37	CCDS33408.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	32|32	5.116727|5.116727	0.94385|0.94385	.|.	.|.	ENSG00000157985|ENSG00000157985	ENST00000448025|ENST00000304032;ENST00000336665;ENST00000409538;ENST00000428334	.|T;T;T;T	.|0.75367	.|-0.93;-0.93;-0.93;-0.93	4.66|4.66	4.66|4.66	0.58398|0.58398	.|Pleckstrin homology domain (3);	0.000000|0.000000	0.85682|0.85682	D|D	0.000000|0.000000	D|D	0.87350|0.87350	0.6155|0.6155	M|M	0.84082|0.84082	2.675|2.675	0.80722|0.80722	D|D	1|1	.|D;D	.|0.76494	.|0.998;0.999	.|D;D	.|0.91635	.|0.948;0.999	D|D	0.88666|0.88666	0.3192|0.3192	6|10	.|0.56958	.|D	.|0.05	.|.	18.4385|18.4385	0.90654|0.90654	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|406;406	.|Q9UPQ3-2;Q9UPQ3	.|.;AGAP1_HUMAN	L|S	39|406;406;671;245	.|ENSP00000307634:P406S;ENSP00000338378:P406S;ENSP00000386897:P671S;ENSP00000411824:P245S	.|ENSP00000307634:P406S	P|P	+|+	2|1	0|0	AGAP1|AGAP1	236482181|236482181	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	7.610000|7.610000	0.82949|0.82949	2.527000|2.527000	0.85204|0.85204	0.655000|0.655000	0.94253|0.94253	CCC|CCA	.	.	none		0.468	AGAP1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000257076.2	NM_014914	
ERICH6B	220081	hgsc.bcm.edu	37	13	46170609	46170609	+	Missense_Mutation	SNP	C	C	T	rs3014939	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:46170609C>T	ENST00000298738.2	-	3	696	c.532G>A	c.(532-534)Gag>Aag	p.E178K		NM_182542.2	NP_872348.2	Q5W0A0	ERI6B_HUMAN		178	Glu-rich.		E -> K (in dbSNP:rs3014939). {ECO:0000269|PubMed:14702039}.							breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)	5						GCCTTTTCCTCTTCTAGATAT	0.418													c|||	1409	0.28135	0.1422	0.438	5008	,	,		21517	0.1647		0.502	False		,,,				2504	0.2515				p.E178K		Atlas-SNP	.											.	FAM194B	42	.	0			c.G532A						PASS	.	C	LYS/GLU	256,1128		28,200,464	101.0	80.0	86.0		532	1.2	0.0	13	dbSNP_101	86	1599,1583		411,777,403	yes	missense	FAM194B	NM_182542.2	56	439,977,867	TT,TC,CC		49.7486,18.4971,40.6264	possibly-damaging	178/697	46170609	1855,2711	692	1591	2283	SO:0001583	missense	220081	exon3			TTTCCTCTTCTAG																												ENST00000298738.2:c.532G>A	13.37:g.46170609C>T	ENSP00000298738:p.Glu178Lys	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	99	47	0.474747	NM_182542	Q96MB5	Missense_Mutation	SNP	ENST00000298738.2	37	CCDS45045.1	690	0.3159340659340659	68	0.13821138211382114	158	0.43646408839779005	89	0.1555944055944056	375	0.4947229551451187	C	11.85	1.761883	0.31228	0.184971	0.502514	ENSG00000165837	ENST00000298738	T	0.06933	3.24	1.17	1.17	0.20885	.	.	.	.	.	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B;D	0.60575	0.421;0.988	B;D	0.65010	0.101;0.931	T	0.48570	-0.9024	8	0.87932	D	0	.	3.4521	0.07502	0.0:0.7336:0.0:0.2663	rs3014939;rs9526094;rs61535659;rs3014939	178;178	A2VDI6;Q5W0A0	.;F194B_HUMAN	K	178	ENSP00000298738:E178K	ENSP00000298738:E178K	E	-	1	0	FAM194B	45068610	0.000000	0.05858	0.002000	0.10522	0.004000	0.04260	-0.954000	0.03873	0.932000	0.37266	0.511000	0.50034	GAG	C|0.695;T|0.305	0.305	strong		0.418	FAM194B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044781.3		
HIPK2	28996	hgsc.bcm.edu	37	7	139316360	139316360	+	Silent	SNP	C	C	T	rs28579164	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:139316360C>T	ENST00000406875.3	-	3	1309	c.1215G>A	c.(1213-1215)tcG>tcA	p.S405S	HIPK2_ENST00000342645.6_Silent_p.S405S|HIPK2_ENST00000428878.2_Silent_p.S405S	NM_022740.4	NP_073577.3	Q9H2X6	HIPK2_HUMAN	homeodomain interacting protein kinase 2	405	Interaction with DAXX.|Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				adult walking behavior (GO:0007628)|anterior/posterior pattern specification (GO:0009952)|cellular response to hypoxia (GO:0071456)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|erythrocyte differentiation (GO:0030218)|eye development (GO:0001654)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|iris morphogenesis (GO:0061072)|lens induction in camera-type eye (GO:0060235)|modulation by virus of host morphology or physiology (GO:0019048)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron differentiation (GO:0030182)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|PML body organization (GO:0030578)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA binding (GO:0043388)|positive regulation of JNK cascade (GO:0046330)|positive regulation of protein binding (GO:0032092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|protein phosphorylation (GO:0006468)|regulation of cell cycle (GO:0051726)|retina layer formation (GO:0010842)|SMAD protein signal transduction (GO:0060395)|smoothened signaling pathway (GO:0007224)|transforming growth factor beta receptor signaling pathway (GO:0007179)|voluntary musculoskeletal movement (GO:0050882)	cytoplasm (GO:0005737)|nuclear body (GO:0016604)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II transcription coactivator activity (GO:0001105)|SMAD binding (GO:0046332)|transcription corepressor activity (GO:0003714)|virion binding (GO:0046790)			breast(4)|central_nervous_system(4)|endometrium(7)|kidney(2)|large_intestine(5)|lung(11)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	43	Melanoma(164;0.205)					GATCATACTCCGAAGCTCCTG	0.433													T|||	740	0.147764	0.3359	0.0879	5008	,	,		19828	0.005		0.1322	False		,,,				2504	0.0992				p.S405S		Atlas-SNP	.											.	HIPK2	192	.	0			c.G1215A						PASS	.	T	,	1107,2853		156,795,1029	94.0	92.0	92.0		165,165	-10.4	0.0	7	dbSNP_125	92	918,7458		50,818,3320	no	coding-synonymous,coding-synonymous	HIPK2	NM_001113239.2,NM_022740.4	,	206,1613,4349	TT,TC,CC		10.9599,27.9545,16.4154	,	55/822,55/849	139316360	2025,10311	1980	4188	6168	SO:0001819	synonymous_variant	28996	exon3			ATACTCCGAAGCT	AF208291	CCDS75666.1, CCDS75667.1	7q32-q34	2004-01-29	2001-11-29		ENSG00000064393	ENSG00000064393			14402	protein-coding gene	gene with protein product		606868	"""homeodomain-interacting protein kinase 2"""			11120354	Standard	NM_001113239		Approved		uc003vvf.4	Q9H2X6	OTTHUMG00000157704	ENST00000406875.3:c.1215G>A	7.37:g.139316360C>T		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	75	48	0.64	NM_022740	Q75MR7|Q8WWI4|Q9H2Y1	Silent	SNP	ENST00000406875.3	37																																																																																				C|0.834;T|0.166	0.166	strong		0.433	HIPK2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000349430.3	NM_022740	
C11orf86	254439	hgsc.bcm.edu	37	11	66743098	66743098	+	Missense_Mutation	SNP	C	C	T	rs118060724|rs137983778	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:66743098C>T	ENST00000308963.4	+	1	351	c.265C>T	c.(265-267)Cgg>Tgg	p.R89W		NM_001136485.1	NP_001129957.1	A6NJI1	CK086_HUMAN	chromosome 11 open reading frame 86	89										NS(1)|skin(1)	2						GTGGCTGAGGCGGTACCAACA	0.652													C|||	110	0.0219649	0.0015	0.0548	5008	,	,		17871	0.0		0.0507	False		,,,				2504	0.0194				p.R89W		Atlas-SNP	.											.	C11orf86	7	.	0			c.C265T						PASS	.						19.0	30.0	27.0					11																	66743098		692	1591	2283	SO:0001583	missense	254439	exon1			CTGAGGCGGTACC	AK026328, AP003176	CCDS44656.1	11q13.1	2012-08-10			ENSG00000173237	ENSG00000173237			34442	protein-coding gene	gene with protein product							Standard	NM_001136485		Approved	FLJ22675	uc010rpm.2	A6NJI1	OTTHUMG00000153671	ENST00000308963.4:c.265C>T	11.37:g.66743098C>T	ENSP00000311479:p.Arg89Trp	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	44	32	0.727273	NM_001136485		Missense_Mutation	SNP	ENST00000308963.4	37	CCDS44656.1	67	0.030677655677655676	2	0.0040650406504065045	23	0.06353591160220995	1	0.0017482517482517483	41	0.05408970976253298	.	2.776	-0.254606	0.05829	.	.	ENSG00000173237	ENST00000308963	.	.	.	4.95	0.873	0.19118	.	0.748097	0.12110	N	0.498652	T	0.01387	0.0045	N	0.03608	-0.345	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.16276	-1.0408	9	0.42905	T	0.14	-13.8993	4.008	0.09610	0.1637:0.5651:0.0:0.2712	.	89	A6NJI1	CK086_HUMAN	W	89	.	ENSP00000311479:R89W	R	+	1	2	C11orf86	66499674	0.026000	0.19158	0.004000	0.12327	0.069000	0.16628	0.454000	0.21827	-0.025000	0.13918	-1.018000	0.02450	CGG	C|0.969;T|0.031	0.031	strong		0.652	C11orf86-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332022.2	NM_001136485	
SPHKAP	80309	hgsc.bcm.edu	37	2	228883721	228883721	+	Missense_Mutation	SNP	T	T	C	rs3811514	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:228883721T>C	ENST00000392056.3	-	7	1895	c.1849A>G	c.(1849-1851)Aag>Gag	p.K617E	SPHKAP_ENST00000344657.5_Missense_Mutation_p.K617E	NM_001142644.1	NP_001136116.1	Q2M3C7	SPKAP_HUMAN	SPHK1 interactor, AKAP domain containing	617			K -> E (in dbSNP:rs3811514). {ECO:0000269|PubMed:11214970, ECO:0000269|PubMed:17974005}.			extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|Z disc (GO:0030018)	protein kinase A binding (GO:0051018)			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)		AGCAATCCCTTGGCAATGGCT	0.527													C|||	3210	0.640974	0.7693	0.6585	5008	,	,		21336	0.624		0.4891	False		,,,				2504	0.6288				p.K617E		Atlas-SNP	.											.	SPHKAP	750	.	0			c.A1849G						PASS	.	C	GLU/LYS,GLU/LYS	3248,1158	406.0+/-333.7	1196,856,151	46.0	45.0	45.0		1849,1849	4.1	0.1	2	dbSNP_107	45	4291,4309	575.2+/-390.2	1083,2125,1092	yes	missense,missense	SPHKAP	NM_001142644.1,NM_030623.3	56,56	2279,2981,1243	CC,CT,TT		49.8953,26.2823,42.0344	benign,benign	617/1701,617/1672	228883721	7539,5467	2203	4300	6503	SO:0001583	missense	80309	exon7			ATCCCTTGGCAAT		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.1849A>G	2.37:g.228883721T>C	ENSP00000375909:p.Lys617Glu	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	98	98	1	NM_030623	Q68DA3|Q68DR8|Q9C0I5	Missense_Mutation	SNP	ENST00000392056.3	37	CCDS46537.1	1355	0.6204212454212454	380	0.7723577235772358	221	0.6104972375690608	374	0.6538461538461539	380	0.5013192612137203	C	0.203	-1.042950	0.01997	0.737177	0.498953	ENSG00000153820	ENST00000392056;ENST00000344657	T;T	0.36878	1.23;1.23	5.84	4.05	0.47172	.	0.150182	0.64402	N	0.000018	T	0.00012	0.0000	N	0.00347	-1.61	0.58432	P	5.999999999950489E-6	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.41893	-0.9483	9	0.02654	T	1	.	6.1848	0.20491	0.0:0.6428:0.1426:0.2147	rs3811514;rs59048160;rs3811514	617;617	Q2M3C7;Q2M3C7-2	SPKAP_HUMAN;.	E	617	ENSP00000375909:K617E;ENSP00000339886:K617E	ENSP00000339886:K617E	K	-	1	0	SPHKAP	228591965	0.795000	0.28851	0.074000	0.20217	0.330000	0.28571	1.423000	0.34837	0.389000	0.25086	-0.119000	0.15052	AAG	T|0.388;C|0.612	0.612	strong		0.527	SPHKAP-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331750.1	NM_030623	
SACS	26278	hgsc.bcm.edu	37	13	23908034	23908034	+	Silent	SNP	A	A	G	rs2737700	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:23908034A>G	ENST00000382292.3	-	9	10254	c.9981T>C	c.(9979-9981)gcT>gcC	p.A3327A	SACS_ENST00000382298.3_Silent_p.A3327A|SACS_ENST00000402364.1_Silent_p.A2577A			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	90	0	0		WXS	Illumina HiSeq	Phase_I	95	47	0.494737	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	
PRAMEF4	400735	hgsc.bcm.edu	37	1	12942119	12942119	+	Missense_Mutation	SNP	C	C	T	rs61781964	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:12942119C>T	ENST00000235349.5	-	3	501	c.431G>A	c.(430-432)aGa>aAa	p.R144K		NM_001009611.2	NP_001009611.1	O60810	PRAM4_HUMAN	PRAME family member 4	144					negative regulation of apoptotic process (GO:0043066)|negative regulation of cell differentiation (GO:0045596)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)					breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(10)|ovary(2)|prostate(3)|skin(1)	24	Ovarian(185;0.249)	Lung NSC(185;3.67e-05)|all_lung(284;4.03e-05)|Renal(390;0.000147)|Breast(348;0.000278)|Colorectal(325;0.00058)|Ovarian(437;0.00965)|Hepatocellular(190;0.0245)|Myeloproliferative disorder(586;0.0255)		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)		CTGCCGTCCTCTCATCCTTGG	0.502													c|||	1106	0.220847	0.0303	0.3285	5008	,	,		19322	0.2183		0.3201	False		,,,				2504	0.3027				p.R144K		Atlas-SNP	.											.	PRAMEF4	62	.	0			c.G431A						PASS	.	C	LYS/ARG	245,2609		61,123,1243	54.0	67.0	62.0		431	-1.9	0.0	1	dbSNP_131	62	1722,3578		472,778,1400	no	missense	PRAMEF4	NM_001009611.2	26	533,901,2643	TT,TC,CC		32.4906,8.5844,24.1231	probably-damaging	144/479	12942119	1967,6187	1427	2650	4077	SO:0001583	missense	400735	exon3			CGTCCTCTCATCC		CCDS30592.1	1p36.21	2013-01-17			ENSG00000243073	ENSG00000243073		"""-"""	31971	protein-coding gene	gene with protein product							Standard	NM_001009611		Approved	RP5-845O24.6	uc001aun.2	O60810	OTTHUMG00000001987	ENST00000235349.5:c.431G>A	1.37:g.12942119C>T	ENSP00000235349:p.Arg144Lys	Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	41	18	0.439024	NM_001009611	Q5LJB5	Missense_Mutation	SNP	ENST00000235349.5	37	CCDS30592.1	471	0.21565934065934067	17	0.034552845528455285	115	0.31767955801104975	117	0.20454545454545456	222	0.2928759894459103	c	0.877	-0.730109	0.03135	0.085844	0.324906	ENSG00000243073	ENST00000235349	T	0.05258	3.47	1.06	-1.88	0.07713	.	2.960340	0.00963	N	0.003123	T	0.00012	0.0000	N	0.20401	0.57	0.80722	P	0.0	P	0.35551	0.509	B	0.38500	0.275	T	0.40646	-0.9552	9	0.07175	T	0.84	.	2.7787	0.05355	0.3083:0.3848:0.3069:0.0	.	144	O60810	PRAM4_HUMAN	K	144	ENSP00000235349:R144K	ENSP00000235349:R144K	R	-	2	0	PRAMEF4	12864706	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.146000	0.10250	-0.572000	0.06006	0.400000	0.26472	AGA	C|0.785;T|0.215	0.215	strong		0.502	PRAMEF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005518.1	NM_001009611	
CRISPLD2	83716	hgsc.bcm.edu	37	16	84922859	84922859	+	Silent	SNP	C	C	T	rs767050	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:84922859C>T	ENST00000262424.5	+	14	1553	c.1329C>T	c.(1327-1329)gcC>gcT	p.A443A	CRISPLD2_ENST00000567845.1_Silent_p.A442A	NM_031476.3	NP_113664.1	Q9H0B8	CRLD2_HUMAN	cysteine-rich secretory protein LCCL domain containing 2	443	LCCL 2. {ECO:0000255|PROSITE- ProRule:PRU00123}.				extracellular matrix organization (GO:0030198)|face morphogenesis (GO:0060325)|lung development (GO:0030324)	extracellular matrix (GO:0031012)|extracellular vesicular exosome (GO:0070062)|transport vesicle (GO:0030133)	heparin binding (GO:0008201)			endometrium(3)|large_intestine(5)|lung(8)|prostate(1)|stomach(1)	18						GCAAGACAGCCGTGCACGCGG	0.577													C|||	3419	0.682708	0.7171	0.5692	5008	,	,		18663	0.8591		0.5507	False		,,,				2504	0.6708				p.A443A		Atlas-SNP	.											CRISPLD2,NS,carcinoma,0,1	CRISPLD2	36	1	0			c.C1329T						PASS	.	C		2948,1450	680.8+/-403.9	995,958,246	130.0	122.0	125.0		1329	-5.2	0.7	16	dbSNP_86	125	4656,3944	603.0+/-394.6	1258,2140,902	no	coding-synonymous	CRISPLD2	NM_031476.3		2253,3098,1148	TT,TC,CC		45.8605,32.9695,41.4987		443/498	84922859	7604,5394	2199	4300	6499	SO:0001819	synonymous_variant	83716	exon14			GACAGCCGTGCAC	AL136861	CCDS10949.1	16q24.1	2008-02-05	2005-02-16	2005-02-16	ENSG00000103196	ENSG00000103196			25248	protein-coding gene	gene with protein product		612434	"""LCCL domain containing cysteine-rich secretory protein 2"""	LCRISP2		11230166	Standard	NM_031476		Approved	DKFZP434B044	uc010voh.1	Q9H0B8	OTTHUMG00000137644	ENST00000262424.5:c.1329C>T	16.37:g.84922859C>T		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	74	74	1	NM_031476	D3DUM0|Q6P590|Q6UWH0|Q6UXC6|Q96IB1|Q96K61	Silent	SNP	ENST00000262424.5	37	CCDS10949.1																																																																																			T|0.620;G|0.006	0.620	strong		0.577	CRISPLD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269086.2	NM_031476	
XRCC1	7515	hgsc.bcm.edu	37	19	44057574	44057574	+	Missense_Mutation	SNP	G	G	A	rs1799782	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:44057574G>A	ENST00000262887.5	-	6	1127	c.580C>T	c.(580-582)Cgg>Tgg	p.R194W	XRCC1_ENST00000543982.1_Missense_Mutation_p.R163W|L34079.3_ENST00000597119.1_RNA			P18887	XRCC1_HUMAN	X-ray repair complementing defective repair in Chinese hamster cells 1	194			R -> W (in dbSNP:rs1799782). {ECO:0000269|PubMed:9485007, ECO:0000269|Ref.2}.		base-excision repair (GO:0006284)|DNA repair (GO:0006281)|hippocampus development (GO:0021766)|response to drug (GO:0042493)|response to hypoxia (GO:0001666)|response to organic substance (GO:0010033)|single strand break repair (GO:0000012)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	damaged DNA binding (GO:0003684)			breast(2)|endometrium(2)|large_intestine(4)|lung(6)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19		Prostate(69;0.0153)				TTGTTGATCCGGCTGAAGAAG	0.597								Other BER factors					G|||	620	0.123802	0.0719	0.1167	5008	,	,		18638	0.2817		0.0517	False		,,,				2504	0.1104				p.R194W		Atlas-SNP	.											.	XRCC1	47	.	0			c.C580T	GRCh37	CM033678	XRCC1	M	rs1799782	PASS	.	G	TRP/ARG	247,4159	144.2+/-179.2	7,233,1963	81.0	76.0	78.0		580	1.0	1.0	19	dbSNP_89	78	555,8045	151.9+/-206.6	16,523,3761	yes	missense	XRCC1	NM_006297.2	101	23,756,5724	AA,AG,GG		6.4535,5.606,6.1664	probably-damaging	194/634	44057574	802,12204	2203	4300	6503	SO:0001583	missense	7515	exon6			TGATCCGGCTGAA	M36089	CCDS12624.1	19q13.2	2014-09-17				ENSG00000073050			12828	protein-coding gene	gene with protein product		194360		RCC		2247054	Standard	NM_006297		Approved		uc002owt.2	P18887		ENST00000262887.5:c.580C>T	19.37:g.44057574G>A	ENSP00000262887:p.Arg194Trp	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	101	50	0.49505	NM_006297	Q6IBS4|Q9HCB1	Missense_Mutation	SNP	ENST00000262887.5	37	CCDS12624.1	283	0.1295787545787546	36	0.07317073170731707	38	0.10497237569060773	165	0.28846153846153844	44	0.05804749340369393	G	19.83	3.900060	0.72754	0.05606	0.064535	ENSG00000073050	ENST00000458471;ENST00000262887;ENST00000543982;ENST00000538738	T;T	0.03772	3.83;3.81	4.73	1.03	0.20045	.	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	M	0.72894	2.215	0.19575	P	0.9999696885	P;D	0.89917	0.912;1.0	P;P	0.62184	0.574;0.899	T	0.39961	-0.9588	9	0.45353	T	0.12	-6.33	6.6426	0.22917	0.0899:0.0:0.599:0.3111	rs1799782;rs2229674;rs3213359;rs3826914;rs11553655	163;194	F5H8D7;P18887	.;XRCC1_HUMAN	W	208;194;163;194	ENSP00000262887:R194W;ENSP00000443671:R163W	ENSP00000262887:R194W	R	-	1	2	XRCC1	48749414	1.000000	0.71417	0.986000	0.45419	0.972000	0.66771	1.506000	0.35747	0.645000	0.30675	0.655000	0.94253	CGG	G|0.905;A|0.095	0.095	strong		0.597	XRCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463194.1	NM_006297	
CLPSL1	340204	hgsc.bcm.edu	37	6	35755658	35755658	+	Silent	SNP	A	A	G	rs12211728	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:35755658A>G	ENST00000373861.5	+	3	331	c.237A>G	c.(235-237)caA>caG	p.Q79Q	CLPSL1_ENST00000542261.1_Silent_p.Q78Q			A2RUU4	COLL1_HUMAN	colipase-like 1	79					digestion (GO:0007586)|lipid catabolic process (GO:0016042)	extracellular region (GO:0005576)	enzyme activator activity (GO:0008047)										TCTTTGGCCAATATAGAGCGT	0.542													A|||	1827	0.364816	0.3298	0.3847	5008	,	,		26184	0.2649		0.4324	False		,,,				2504	0.4315				p.Q79Q		Atlas-SNP	.											.	.	.	.	0			c.A237G						PASS	.	A		1278,2802		87,1104,849	137.0	133.0	134.0		237	-1.1	0.0	6	dbSNP_120	134	3481,4915		151,3179,868	no	coding-synonymous	C6orf127	NM_001010886.3		238,4283,1717	GG,GA,AA		41.4602,31.3235,38.1452		79/122	35755658	4759,7717	2040	4198	6238	SO:0001819	synonymous_variant	340204	exon3			TGGCCAATATAGA		CCDS43456.1	6p21.31	2014-01-28	2012-02-06	2012-02-06	ENSG00000204140	ENSG00000204140			21251	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 127"""	C6orf127			Standard	NM_001010886		Approved	dJ510O8.6	uc003old.4	A2RUU4	OTTHUMG00000014582	ENST00000373861.5:c.237A>G	6.37:g.35755658A>G		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	92	91	0.98913	NM_001010886	A7E2T6|B2RPE2|B5G4V2|B6ZDM9|Q5T9G1	Silent	SNP	ENST00000373861.5	37	CCDS43456.1																																																																																			A|0.641;G|0.359	0.359	strong		0.542	CLPSL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040317.2	NM_001010886	
CDHR3	222256	hgsc.bcm.edu	37	7	105615426	105615426	+	Missense_Mutation	SNP	G	G	C	rs34426483	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:105615426G>C	ENST00000317716.9	+	2	263	c.183G>C	c.(181-183)caG>caC	p.Q61H	CDHR3_ENST00000478080.1_Intron|CDHR3_ENST00000542731.1_Missense_Mutation_p.Q61H|CDHR3_ENST00000470188.1_3'UTR|CDHR3_ENST00000541203.1_Missense_Mutation_p.Q61H|CDHR3_ENST00000343407.5_5'UTR	NM_152750.4	NP_689963.2	Q6ZTQ4	CDHR3_HUMAN	cadherin-related family member 3	61	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.		Q -> H (in dbSNP:rs34426483).		homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|cervix(3)|endometrium(1)|kidney(1)|large_intestine(1)|lung(15)|ovary(1)	23						GATTTCCCCAGATAGTCAACT	0.463													G|||	806	0.160942	0.062	0.2133	5008	,	,		22218	0.2619		0.1789	False		,,,				2504	0.135				p.Q61H		Atlas-SNP	.											.	CDHR3	153	.	0			c.G183C						PASS	.	G	HIS/GLN	343,3425		17,309,1558	194.0	179.0	184.0		183	2.5	0.3	7	dbSNP_126	184	1634,6600		162,1310,2645	yes	missense	CDHR3	NM_152750.4	24	179,1619,4203	CC,CG,GG		19.8445,9.103,16.4723	benign	61/886	105615426	1977,10025	1884	4117	6001	SO:0001583	missense	222256	exon2			TCCCCAGATAGTC	AK126338	CCDS47684.1, CCDS75651.1	7q22.2	2011-07-01			ENSG00000128536	ENSG00000128536		"""Cadherins / Cadherin-related"""	26308	protein-coding gene	gene with protein product		615610					Standard	NM_152750		Approved	FLJ44366, FLJ23834, CDH28	uc003vdl.4	Q6ZTQ4	OTTHUMG00000157520	ENST00000317716.9:c.183G>C	7.37:g.105615426G>C	ENSP00000325954:p.Gln61His	Somatic	234	0	0		WXS	Illumina HiSeq	Phase_I	212	91	0.429245	NM_152750	Q8TCI7	Missense_Mutation	SNP	ENST00000317716.9	37	CCDS47684.1	383	0.17536630036630035	36	0.07317073170731707	85	0.23480662983425415	126	0.2202797202797203	136	0.17941952506596306	G	5.960	0.361167	0.11296	0.09103	0.198445	ENSG00000128536	ENST00000542731;ENST00000317716;ENST00000541203	T;T;T	0.15256	2.44;2.44;2.44	5.4	2.47	0.30058	Cadherin (2);	1.214480	0.05938	N	0.636408	T	0.00012	0.0000	N	0.22421	0.69	0.43403	P	0.004468999999999945	B;B	0.26845	0.161;0.161	B;B	0.24541	0.054;0.054	T	0.40627	-0.9553	9	0.39692	T	0.17	0.5332	4.229	0.10594	0.076:0.1241:0.4259:0.3741	rs34426483;rs58941570	48;61	B3KYA0;Q6ZTQ4	.;CDHR3_HUMAN	H	61	ENSP00000439766:Q61H;ENSP00000325954:Q61H;ENSP00000443733:Q61H	ENSP00000325954:Q61H	Q	+	3	2	CDHR3	105402662	0.359000	0.24955	0.254000	0.24359	0.314000	0.28054	0.535000	0.23114	0.825000	0.34637	0.655000	0.94253	CAG	G|0.824;C|0.176	0.176	strong		0.463	CDHR3-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000349025.2	NM_152750	
ZNF442	79973	hgsc.bcm.edu	37	19	12461745	12461745	+	Silent	SNP	A	A	G	rs117398535	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:12461745A>G	ENST00000242804.4	-	6	1236	c.654T>C	c.(652-654)ttT>ttC	p.F218F	CTD-3105H18.13_ENST00000563695.2_lincRNA|ZNF442_ENST00000438182.1_Silent_p.F149F	NM_030824.2	NP_110451.1	Q9H7R0	ZN442_HUMAN	zinc finger protein 442	218					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)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(8)|lung(8)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	31						TAGGCCAAAAAAAGGCTTTCC	0.403													A|||	10	0.00199681	0.0015	0.0014	5008	,	,		22597	0.0		0.007	False		,,,				2504	0.0				p.F218F		Atlas-SNP	.											ZNF442,middle_lobe,carcinoma,0,1	ZNF442	102	1	0			c.T654C						PASS	.	A		4,4402	8.1+/-20.4	0,4,2199	138.0	134.0	135.0		654	-1.5	0.0	19	dbSNP_132	135	56,8544	35.9+/-90.5	0,56,4244	no	coding-synonymous	ZNF442	NM_030824.2		0,60,6443	GG,GA,AA		0.6512,0.0908,0.4613		218/628	12461745	60,12946	2203	4300	6503	SO:0001819	synonymous_variant	79973	exon6			CCAAAAAAAGGCT	AK024418	CCDS12271.1	19p13.13	2013-01-08			ENSG00000198342	ENSG00000198342		"""Zinc fingers, C2H2-type"", ""-"""	20877	protein-coding gene	gene with protein product							Standard	NM_030824		Approved	FLJ14356	uc002mtr.1	Q9H7R0	OTTHUMG00000156411	ENST00000242804.4:c.654T>C	19.37:g.12461745A>G		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	46	18	0.391304	NM_030824	B4DJ48	Silent	SNP	ENST00000242804.4	37	CCDS12271.1																																																																																			A|0.995;G|0.005	0.005	strong		0.403	ZNF442-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344109.1	NM_030824	
CDCA2	157313	hgsc.bcm.edu	37	8	25364331	25364331	+	Missense_Mutation	SNP	G	G	A	rs4872318	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	59	0	0		WXS	Illumina HiSeq	Phase_I	52	39	0.75	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	
Unknown	0	hgsc.bcm.edu	37	17	17326605	17326605	+	IGR	SNP	A	A	G	rs370938128|rs7225831	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:17326605A>G								NT5M (75630 upstream) : Y_RNA (37152 downstream)																							ATGATGGGGCAAATGCCAGAG	0.478													G|||	2121	0.423522	0.798	0.268	5008	,	,		23339	0.1915		0.3221	False		,,,				2504	0.3712				p.A140A		Atlas-SNP	.											.	.	.	.	0			c.A420G						PASS	.																																			SO:0001628	intergenic_variant	140776	exon3			TGGGGCAAATGCC																													17.37:g.17326605A>G		Somatic	18	0	0		WXS	Illumina HiSeq	Phase_I	23	10	0.434783	NM_001243312		Silent	SNP		37																																																																																				A|0.600;G|0.400	0.400	strong	0	0.478								
BRD3	8019	hgsc.bcm.edu	37	9	136915508	136915508	+	Silent	SNP	C	C	T	rs2301576	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:136915508C>T	ENST00000303407.7	-	5	887	c.702G>A	c.(700-702)ccG>ccA	p.P234P	BRD3_ENST00000371834.2_Silent_p.P234P|BRD3_ENST00000357885.2_Silent_p.P234P	NM_007371.3	NP_031397.1	Q15059	BRD3_HUMAN	bromodomain containing 3	234					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)		TGACGACAGGCGGCGTAGGAG	0.697			T	C15orf55	lethal midline carcinoma of young people								C|||	452	0.0902556	0.0091	0.1383	5008	,	,		13483	0.1339		0.0775	False		,,,				2504	0.1339				p.P234P		Atlas-SNP	.		Dom	yes		9	9q34	8019	bromodomain containing 3		E	.	BRD3	82	.	0			c.G702A						PASS	.	C		122,4284	89.2+/-127.9	4,114,2085	53.0	54.0	53.0		702	-2.3	0.7	9	dbSNP_100	53	862,7736	193.7+/-239.3	30,802,3467	no	coding-synonymous	BRD3	NM_007371.3		34,916,5552	TT,TC,CC		10.0256,2.769,7.5669		234/727	136915508	984,12020	2203	4299	6502	SO:0001819	synonymous_variant	8019	exon5			GACAGGCGGCGTA		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.702G>A	9.37:g.136915508C>T		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	31	19	0.612903	NM_007371	B1APD9|Q4G5Y3|Q5T1R7|Q8N5M3|Q92645	Silent	SNP	ENST00000303407.7	37	CCDS6980.1																																																																																			C|0.923;T|0.077	0.077	strong		0.697	BRD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055390.4	NM_007371	
PCSK9	255738	hgsc.bcm.edu	37	1	55505679	55505679	+	Missense_Mutation	SNP	G	G	A	rs145886902	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:55505679G>A	ENST00000302118.5	+	1	459	c.169G>A	c.(169-171)Gag>Aag	p.E57K	PCSK9_ENST00000543384.1_5'Flank|PCSK9_ENST00000452118.2_Missense_Mutation_p.E57K	NM_174936.3	NP_777596.2	Q8NBP7	PCSK9_HUMAN	proprotein convertase subtilisin/kexin type 9	57			E -> K. {ECO:0000269|PubMed:16465619}.		apoptotic process (GO:0006915)|cellular response to insulin stimulus (GO:0032869)|cellular response to starvation (GO:0009267)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|kidney development (GO:0001822)|lipoprotein metabolic process (GO:0042157)|liver development (GO:0001889)|low-density lipoprotein particle receptor catabolic process (GO:0032802)|lysosomal transport (GO:0007041)|negative regulation of low-density lipoprotein particle clearance (GO:0010989)|negative regulation of receptor recycling (GO:0001920)|neurogenesis (GO:0022008)|neuron differentiation (GO:0030182)|phospholipid metabolic process (GO:0006644)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of receptor internalization (GO:0002092)|protein autoprocessing (GO:0016540)|proteolysis (GO:0006508)|regulation of low-density lipoprotein particle receptor catabolic process (GO:0032803)|regulation of neuron apoptotic process (GO:0043523)|regulation of receptor activity (GO:0010469)|triglyceride metabolic process (GO:0006641)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle (GO:0030134)|extracellular space (GO:0005615)|extrinsic component of external side of plasma membrane (GO:0031232)|Golgi apparatus (GO:0005794)|late endosome (GO:0005770)|lysosome (GO:0005764)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|rough endoplasmic reticulum (GO:0005791)	apolipoprotein binding (GO:0034185)|apolipoprotein receptor binding (GO:0034190)|low-density lipoprotein particle binding (GO:0030169)|low-density lipoprotein particle receptor binding (GO:0050750)|poly(A) RNA binding (GO:0044822)|protein self-association (GO:0043621)|serine-type endopeptidase activity (GO:0004252)|sodium channel inhibitor activity (GO:0019871)|very-low-density lipoprotein particle binding (GO:0034189)|very-low-density lipoprotein particle receptor binding (GO:0070326)			NS(2)|breast(2)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(1)|liver(2)|lung(4)|ovary(3)|prostate(3)|skin(1)|urinary_tract(1)	32						CGAAGCACCCGAGCACGGAAC	0.716													G|||	5	0.000998403	0.0038	0.0	5008	,	,		14732	0.0		0.0	False		,,,				2504	0.0				p.E57K	Pancreas(137;1454 1827 5886 22361 42375)	Atlas-SNP	.											.	PCSK9	76	.	0			c.G169A	GRCh37	CM060421	PCSK9	M	rs145886902	PASS	.	G	LYS/GLU	11,4359		0,11,2174	29.0	24.0	26.0		169	-4.7	0.0	1	dbSNP_134	26	2,8534		0,2,4266	yes	missense	PCSK9	NM_174936.3	56	0,13,6440	AA,AG,GG		0.0234,0.2517,0.1007	benign	57/693	55505679	13,12893	2185	4268	6453	SO:0001583	missense	255738	exon1			GCACCCGAGCACG	AX207686	CCDS603.1	1p34.1-p32	2014-09-17	2003-05-13		ENSG00000169174	ENSG00000169174			20001	protein-coding gene	gene with protein product		607786	"""hypercholesterolemia, autosomal dominant 3"""	HCHOLA3		12552133, 12730697	Standard	NM_174936		Approved	NARC-1, FH3	uc001cyf.2	Q8NBP7	OTTHUMG00000008136	ENST00000302118.5:c.169G>A	1.37:g.55505679G>A	ENSP00000303208:p.Glu57Lys	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	106	22	0.207547	NM_174936	A8T640|C0JYY9|Q5PSM5|Q5SZQ2	Missense_Mutation	SNP	ENST00000302118.5	37	CCDS603.1	.	.	.	.	.	.	.	.	.	.	G	7.413	0.635044	0.14322	0.002517	2.34E-4	ENSG00000169174	ENST00000302118;ENST00000452118	T;T	0.71461	-0.51;-0.57	3.09	-4.71	0.03279	.	1.506200	0.05619	U	0.579657	T	0.45296	0.1335	N	0.14661	0.345	0.09310	N	0.999991	B	0.02656	0.0	B	0.01281	0.0	T	0.26292	-1.0107	10	0.11794	T	0.64	3.2202	5.4094	0.16341	0.1325:0.2249:0.5426:0.1	.	57	Q8NBP7	PCSK9_HUMAN	K	57	ENSP00000303208:E57K;ENSP00000401598:E57K	ENSP00000303208:E57K	E	+	1	0	PCSK9	55278267	0.000000	0.05858	0.000000	0.03702	0.228000	0.25075	-0.351000	0.07711	-0.725000	0.04901	-0.802000	0.03209	GAG	G|0.999;A|0.001	0.001	strong		0.716	PCSK9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022280.1	NM_174936	
BMP1	649	hgsc.bcm.edu	37	8	22054197	22054197	+	Silent	SNP	T	T	C	rs2229777	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:22054197T>C	ENST00000306385.5	+	14	2440	c.1770T>C	c.(1768-1770)gcT>gcC	p.A590A	BMP1_ENST00000354870.5_3'UTR|BMP1_ENST00000306349.8_Silent_p.A590A|BMP1_ENST00000397816.3_Silent_p.A590A	NM_006129.4	NP_006120.1	P13497	BMP1_HUMAN	bone morphogenetic protein 1	590					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)		CCGCAGCTGCTTGTGGCGGAT	0.637													C|||	651	0.129992	0.118	0.0735	5008	,	,		16170	0.1806		0.1292	False		,,,				2504	0.135				p.A590A		Atlas-SNP	.											.	BMP1	131	.	0			c.T1770C						PASS	.	C	,	495,3911	775.1+/-414.1	26,443,1734	51.0	51.0	51.0		1770,1770	5.7	1.0	8	dbSNP_98	51	906,7694	771.2+/-407.7	53,800,3447	no	coding-synonymous,coding-synonymous	BMP1	NM_001199.3,NM_006129.4	,	79,1243,5181	CC,CT,TT		10.5349,11.2347,10.772	,	590/731,590/987	22054197	1401,11605	2203	4300	6503	SO:0001819	synonymous_variant	649	exon14			AGCTGCTTGTGGC		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	ENST00000306385.5:c.1770T>C	8.37:g.22054197T>C		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	64	15	0.234375	NM_001199	A8K6F5|B2RN46|D3DSR0|Q13292|Q13872|Q14874|Q99421|Q99422|Q99423|Q9UL38	Silent	SNP	ENST00000306385.5	37	CCDS6026.1																																																																																			A|0.000;C|0.125;T|0.875	0.125	strong		0.637	BMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214995.2	NM_006132	
P2RX4	5025	hgsc.bcm.edu	37	12	121660787	121660787	+	Silent	SNP	T	T	C	rs25643	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:121660787T>C	ENST00000337233.4	+	5	773	c.465T>C	c.(463-465)tcT>tcC	p.S155S	P2RX4_ENST00000540930.1_Intron|P2RX4_ENST00000541532.1_Intron|P2RX4_ENST00000543171.1_Silent_p.S54S|P2RX4_ENST00000359949.7_Silent_p.S171S	NM_001261397.1|NM_001261398.1|NM_002560.2	NP_001248326.1|NP_001248327.1|NP_002551.2	Q99571	P2RX4_HUMAN	purinergic receptor P2X, ligand-gated ion channel, 4	155					apoptotic signaling pathway (GO:0097190)|calcium ion transport (GO:0006816)|cation transmembrane transport (GO:0098655)|cellular response to ATP (GO:0071318)|endothelial cell activation (GO:0042118)|ion transmembrane transport (GO:0034220)|membrane depolarization (GO:0051899)|negative regulation of cardiac muscle hypertrophy (GO:0010614)|neuronal action potential (GO:0019228)|nitric oxide biosynthetic process (GO:0006809)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of calcium ion transport into cytosol (GO:0010524)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of prostaglandin secretion (GO:0032308)|protein homooligomerization (GO:0051260)|purinergic nucleotide receptor signaling pathway (GO:0035590)|regulation of blood pressure (GO:0008217)|regulation of cardiac muscle contraction (GO:0055117)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of sodium ion transport (GO:0002028)|relaxation of cardiac muscle (GO:0055119)|response to ATP (GO:0033198)|response to fluid shear stress (GO:0034405)|sensory perception of pain (GO:0019233)|signal transduction (GO:0007165)|tissue homeostasis (GO:0001894)|transport (GO:0006810)|vasodilation (GO:0042311)	apical part of cell (GO:0045177)|cell junction (GO:0030054)|dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|integral component of nuclear inner membrane (GO:0005639)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|terminal bouton (GO:0043195)	ATP binding (GO:0005524)|cadherin binding (GO:0045296)|copper ion binding (GO:0005507)|drug binding (GO:0008144)|extracellular ATP-gated cation channel activity (GO:0004931)|protein homodimerization activity (GO:0042803)|purinergic nucleotide receptor activity (GO:0001614)|receptor binding (GO:0005102)|zinc ion binding (GO:0008270)			breast(1)|kidney(4)|large_intestine(4)|lung(7)|prostate(1)	17	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					TCAACGGGTCTGTCAAGACGT	0.562													C|||	2205	0.440296	0.4312	0.4222	5008	,	,		19659	0.3433		0.4751	False		,,,				2504	0.5297				p.S171S		Atlas-SNP	.											P2RX4,NS,carcinoma,0,1	P2RX4	27	1	0			c.T513C						PASS	.	C		1973,2433	618.3+/-393.1	450,1073,680	141.0	105.0	117.0		465	-10.3	0.0	12	dbSNP_72	117	3906,4694	604.9+/-394.9	910,2086,1304	no	coding-synonymous	P2RX4	NM_002560.2		1360,3159,1984	CC,CT,TT		45.4186,44.7798,45.2022		155/389	121660787	5879,7127	2203	4300	6503	SO:0001819	synonymous_variant	5025	exon6			CGGGTCTGTCAAG	Y07684	CCDS9214.1, CCDS58282.1	12q24.32	2012-01-17			ENSG00000135124	ENSG00000135124		"""Purinergic receptors"", ""Ligand-gated ion channels / Purinergic receptors, ionotropic"""	8535	protein-coding gene	gene with protein product		600846				9016352	Standard	NM_002560		Approved	P2X4	uc031qjt.1	Q99571	OTTHUMG00000169155	ENST00000337233.4:c.465T>C	12.37:g.121660787T>C		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	109	58	0.53211	NM_001256796	E7EPF7|F6RU17|O00450|O14722|Q5U089|Q5U090|Q8N4N1|Q9UBG9	Silent	SNP	ENST00000337233.4	37	CCDS9214.1																																																																																			C|0.421;N|0.000;T|0.579	0.421	strong		0.562	P2RX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402545.1	NM_175567	
GPR112	139378	hgsc.bcm.edu	37	X	135429503	135429503	+	Missense_Mutation	SNP	C	C	A	rs4829830	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:135429503C>A	ENST00000394143.1	+	6	3929	c.3638C>A	c.(3637-3639)aCc>aAc	p.T1213N	GPR112_ENST00000412101.1_Missense_Mutation_p.T1008N|GPR112_ENST00000370652.1_Missense_Mutation_p.T1213N|GPR112_ENST00000287534.4_Missense_Mutation_p.T1150N|GPR112_ENST00000394141.1_Missense_Mutation_p.T1008N	NM_153834.3	NP_722576.3	Q8IZF6	GP112_HUMAN	G protein-coupled receptor 112	1213			T -> N (in dbSNP:rs4829830).		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(13)|central_nervous_system(2)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(33)|lung(97)|ovary(5)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(2)	199	Acute lymphoblastic leukemia(192;0.000127)					GTTGATGAGACCACACCCTCA	0.473													c|||	1760	0.466225	0.4289	0.3573	3775	,	,		15390	0.246		0.3797	False		,,,				2504	0.3221				p.T1213N		Atlas-SNP	.											.	GPR112	459	.	0			c.C3638A						PASS	.		ASN/THR	2122,1713		502,805,313,325,258	214.0	183.0	193.0		3638	-1.5	0.0	X	dbSNP_111	193	3220,3508		566,1176,912,686,960	yes	missense	GPR112	NM_153834.3	65	1068,1981,1225,1011,1218	AA,AC,A,CC,C		47.8597,44.6675,49.4272	benign	1213/3081	135429503	5342,5221	2203	4300	6503	SO:0001583	missense	139378	exon6			ATGAGACCACACC	AY140954	CCDS35409.1	Xq26.3	2014-08-08			ENSG00000156920	ENSG00000156920		"""-"", ""GPCR / Class B : Orphans"""	18992	protein-coding gene	gene with protein product						12435584	Standard	XM_005262367		Approved	RP1-299I16, PGR17	uc004ezu.1	Q8IZF6	OTTHUMG00000022508	ENST00000394143.1:c.3638C>A	X.37:g.135429503C>A	ENSP00000377699:p.Thr1213Asn	Somatic	227	0	0		WXS	Illumina HiSeq	Phase_I	186	186	1	NM_153834	A2A2J1|A2A2J2|Q5EGP2|Q86SM6	Missense_Mutation	SNP	ENST00000394143.1	37	CCDS35409.1	746	0.4496684749849307	138	0.372972972972973	83	0.2902097902097902	99	0.21063829787234042	190	0.3242320819112628	c	6.546	0.469051	0.12461	0.553325	0.478597	ENSG00000156920	ENST00000394143;ENST00000370652;ENST00000412101;ENST00000287534;ENST00000394141	T;T;T;T;T	0.33865	1.43;1.43;1.39;1.52;1.39	2.98	-1.46	0.08800	.	.	.	.	.	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B;B;B	0.15930	0.015;0.001;0.001	B;B;B	0.14578	0.011;0.003;0.001	T	0.46190	-0.9209	8	0.37606	T	0.19	.	0.3457	0.00341	0.2044:0.3206:0.1987:0.2763	rs4829830;rs58174019;rs4829830	1150;1008;1213	Q8IZF6-2;Q8IZF6-3;Q8IZF6	.;.;GP112_HUMAN	N	1213;1213;1008;1150;1008	ENSP00000377699:T1213N;ENSP00000359686:T1213N;ENSP00000416526:T1008N;ENSP00000287534:T1150N;ENSP00000377697:T1008N	ENSP00000287534:T1150N	T	+	2	0	GPR112	135257169	0.000000	0.05858	0.000000	0.03702	0.032000	0.12392	-0.312000	0.08113	-0.347000	0.08299	-0.313000	0.08912	ACC	0|0.015;A|0.479	0.479	strong		0.473	GPR112-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000286639.1		
ABCA4	24	hgsc.bcm.edu	37	1	94467447	94467447	+	Silent	SNP	G	G	A	rs1801359	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:94467447G>A	ENST00000370225.3	-	45	6335	c.6249C>T	c.(6247-6249)atC>atT	p.I2083I	ABCA4_ENST00000535881.1_Silent_p.I202I|ABCA4_ENST00000536513.1_Silent_p.I353I|ABCA4_ENST00000465352.1_5'UTR	NM_000350.2	NP_000341.2	P78363	ABCA4_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 4	2083	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				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)		CAATGAGTGCGATGGCTGTGG	0.587													G|||	671	0.133986	0.3177	0.062	5008	,	,		16862	0.0665		0.0586	False		,,,				2504	0.0838				p.I2083I		Atlas-SNP	.											.	ABCA4	275	.	0			c.C6249T						PASS	.	G		1316,3090	440.8+/-346.1	183,950,1070	75.0	70.0	71.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	6249	-10.2	0.2	1	dbSNP_89	71	583,8017	154.5+/-208.7	25,533,3742	no	coding-synonymous	ABCA4	NM_000350.2		208,1483,4812	AA,AG,GG		6.7791,29.8684,14.601		2083/2274	94467447	1899,11107	2203	4300	6503	SO:0001819	synonymous_variant	24	exon45			GAGTGCGATGGCT	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.6249C>T	1.37:g.94467447G>A		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	92	46	0.5	NM_000350	O15112|O60438|O60915|Q0QD48|Q4LE31	Silent	SNP	ENST00000370225.3	37	CCDS747.1																																																																																			G|0.860;A|0.140	0.140	strong		0.587	ABCA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029320.1	NM_000350	
SLC35G6	643664	hgsc.bcm.edu	37	17	7386234	7386234	+	Missense_Mutation	SNP	G	G	A	rs200251320	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:7386234G>A	ENST00000412468.2	+	2	1046	c.931G>A	c.(931-933)Gtg>Atg	p.V311M	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	311	EamA 2.					integral component of membrane (GO:0016021)		p.V311M(1)									TTCTGACATCGTGGGGGCAGG	0.572																																					p.V311M		Atlas-SNP	.											POLR2A_ENST00000412468,extremity,malignant_melanoma,0,1	.	.	1	1	Substitution - Missense(1)	skin(1)	c.G931A						scavenged	.						119.0	108.0	112.0					17																	7386234		2203	4300	6503	SO:0001583	missense	643664	exon2			GACATCGTGGGGG		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.931G>A	17.37:g.7386234G>A	ENSP00000396523:p.Val311Met	Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	124	21	0.169355	NM_001102614		Missense_Mutation	SNP	ENST00000412468.2	37	CCDS45603.1	.	.	.	.	.	.	.	.	.	.	G	0.036	-1.304956	0.01353	.	.	ENSG00000181222	ENST00000412468	T	0.53857	0.6	4.38	3.29	0.37713	.	.	.	.	.	T	0.31670	0.0804	N	0.14661	0.345	0.23581	N	0.997368	B	0.06786	0.001	B	0.04013	0.001	T	0.19516	-1.0303	9	0.13108	T	0.6	-2.3468	9.3381	0.38062	0.911:0.0:0.089:0.0	.	311	P0C7Q6	S35G6_HUMAN	M	311	ENSP00000396523:V311M	ENSP00000396523:V311M	V	+	1	0	SLC35G6	7326958	1.000000	0.71417	1.000000	0.80357	0.650000	0.38633	1.343000	0.33930	0.645000	0.30675	-0.383000	0.06682	GTG	G|0.793;A|0.207	0.207	strong		0.572	SLC35G6-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001102614	
KMT2D	8085	hgsc.bcm.edu	37	12	49427919	49427919	+	Silent	SNP	T	T	C	rs61942218	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:49427919T>C	ENST00000301067.7	-	38	10670	c.10671A>G	c.(10669-10671)ccA>ccG	p.P3557P	KMT2D_ENST00000549743.1_5'Flank	NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	3557	Gln-rich.				chromatin silencing (GO:0006342)|histone H3-K4 methylation (GO:0051568)|oocyte growth (GO:0001555)|oogenesis (GO:0048477)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to estrogen (GO:0043627)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)										CATCAGCTTCTGGGAACTCAC	0.547													T|||	112	0.0223642	0.003	0.0447	5008	,	,		19627	0.0		0.0646	False		,,,				2504	0.0123				p.P3557P		Atlas-SNP	.											.	MLL2	1173	.	0			c.A10671G						PASS	.	T		53,3943		2,49,1947	69.0	67.0	67.0		10671	-9.5	0.9	12	dbSNP_129	67	564,7810		26,512,3649	no	coding-synonymous	MLL2	NM_003482.3		28,561,5596	CC,CT,TT		6.7351,1.3263,4.9879		3557/5538	49427919	617,11753	1998	4187	6185	SO:0001819	synonymous_variant	8085	exon38			AGCTTCTGGGAAC	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.10671A>G	12.37:g.49427919T>C		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	65	35	0.538462	NM_003482	O14687	Silent	SNP	ENST00000301067.7	37	CCDS44873.1																																																																																			T|0.964;C|0.036	0.036	strong		0.547	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2		
GPAA1	8733	hgsc.bcm.edu	37	8	145139727	145139727	+	Silent	SNP	C	C	T	rs4977165	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:145139727C>T	ENST00000355091.4	+	8	1234	c.1113C>T	c.(1111-1113)atC>atT	p.I371I	GPAA1_ENST00000361036.6_Silent_p.I311I	NM_003801.3	NP_003792.1	O43292	GPAA1_HUMAN	glycosylphosphatidylinositol anchor attachment 1	371					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)			TCGTCTCCATCGGCCTCTACA	0.602													C|||	616	0.123003	0.3404	0.0648	5008	,	,		18028	0.001		0.0885	False		,,,				2504	0.0317				p.I371I		Atlas-SNP	.											.	GPAA1	40	.	0			c.C1113T						PASS	.	C		1208,2792		186,836,978	105.0	115.0	112.0		1113	-2.8	1.0	8	dbSNP_111	112	663,7701		25,613,3544	no	coding-synonymous	GPAA1	NM_003801.3		211,1449,4522	TT,TC,CC		7.9268,30.2,15.1326		371/622	145139727	1871,10493	2000	4182	6182	SO:0001819	synonymous_variant	8733	exon8			CTCCATCGGCCTC	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.1113C>T	8.37:g.145139727C>T		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	85	85	1	NM_003801	Q9NSS0|Q9UQ31	Silent	SNP	ENST00000355091.4	37	CCDS43776.1																																																																																			C|0.892;T|0.108	0.108	strong		0.602	GPAA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384070.1	NM_003801	
KRT6B	3854	hgsc.bcm.edu	37	12	52841179	52841179	+	Missense_Mutation	SNP	T	T	C	rs61746354	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:52841179T>C	ENST00000252252.3	-	9	1537	c.1490A>G	c.(1489-1491)tAt>tGt	p.Y497C		NM_005555.3	NP_005546.2	P04259	K2C6B_HUMAN	keratin 6B	497	Tail.				ectoderm development (GO:0007398)	extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural constituent of cytoskeleton (GO:0005200)			NS(1)|breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(19)|ovary(4)|prostate(2)	40				BRCA - Breast invasive adenocarcinoma(357;0.083)		GGCACCGCCATAGCCACTGGA	0.612													T|||	128	0.0255591	0.003	0.0317	5008	,	,		20137	0.0		0.0427	False		,,,				2504	0.0603				p.Y497C		Atlas-SNP	.											.	KRT6B	90	.	0			c.A1490G						PASS	.	T	CYS/TYR	57,4349	53.6+/-89.4	0,57,2146	44.0	45.0	45.0		1490	2.0	0.4	12	dbSNP_129	45	459,8141	136.2+/-193.3	19,421,3860	no	missense	KRT6B	NM_005555.3	194	19,478,6006	CC,CT,TT		5.3372,1.2937,3.9674	benign	497/565	52841179	516,12490	2203	4300	6503	SO:0001583	missense	3854	exon9			CCGCCATAGCCAC	BC034535	CCDS8828.1	12q13.13	2013-01-16	2004-08-11		ENSG00000185479	ENSG00000185479		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6444	protein-coding gene	gene with protein product		148042	"""keratin-like 1 (a type II keratin sequence)"""	KRTL1		1713141, 16831889	Standard	NM_005555		Approved		uc001sak.3	P04259	OTTHUMG00000169593	ENST00000252252.3:c.1490A>G	12.37:g.52841179T>C	ENSP00000252252:p.Tyr497Cys	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	83	48	0.578313	NM_005555	P48669	Missense_Mutation	SNP	ENST00000252252.3	37	CCDS8828.1	58	0.026556776556776556	1	0.0020325203252032522	16	0.04419889502762431	0	0.0	41	0.05408970976253298	T	4.060	0.008900	0.07912	0.012937	0.053372	ENSG00000185479	ENST00000252252;ENST00000544607	D	0.86030	-2.06	3.2	2.04	0.26737	.	0.000000	0.49916	D	0.000127	T	0.40546	0.1121	L	0.58583	1.82	0.36687	D	0.879362	B	0.22414	0.069	B	0.14578	0.011	T	0.58329	-0.7655	10	0.12430	T	0.62	.	8.1187	0.30959	0.0:0.0998:0.0:0.9002	.	497	P04259	K2C6B_HUMAN	C	497;457	ENSP00000252252:Y497C	ENSP00000252252:Y497C	Y	-	2	0	KRT6B	51127446	0.005000	0.15991	0.400000	0.26346	0.160000	0.22226	0.547000	0.23299	0.451000	0.26802	0.254000	0.18369	TAT	T|0.961;C|0.039	0.039	strong		0.612	KRT6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404969.1	NM_005555	
DOPEY1	23033	hgsc.bcm.edu	37	6	83810482	83810482	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:83810482G>A	ENST00000349129.2	+	4	457	c.197G>A	c.(196-198)cGc>cAc	p.R66H	DOPEY1_ENST00000369739.3_Missense_Mutation_p.R66H|DOPEY1_ENST00000536812.1_Missense_Mutation_p.R66H|DOPEY1_ENST00000237163.5_Missense_Mutation_p.R66H	NM_015018.3	NP_055833.2	Q5JWR5	DOP1_HUMAN	dopey family member 1	66					protein transport (GO:0015031)					breast(4)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(16)|ovary(5)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	67		all_cancers(76;2.29e-06)|Acute lymphoblastic leukemia(125;3.41e-06)|all_hematologic(105;0.000865)|all_epithelial(107;0.00203)		BRCA - Breast invasive adenocarcinoma(397;0.053)		ATAGGCAAACGCCTAGCTCAA	0.363																																					p.R66H		Atlas-SNP	.											DOPEY1,caecum,carcinoma,+1,3	DOPEY1	190	3	0			c.G197A						scavenged	.						165.0	172.0	169.0					6																	83810482		2203	4300	6503	SO:0001583	missense	23033	exon4			GCAAACGCCTAGC	AK027030	CCDS4996.1, CCDS64467.1	6q15	2013-03-05	2006-02-02	2006-02-02	ENSG00000083097	ENSG00000083097			21194	protein-coding gene	gene with protein product			"""KIAA1117"""	KIAA1117		16301316, 16303751, 10931277	Standard	NM_015018		Approved	dJ202D23.2	uc011dyy.2	Q5JWR5	OTTHUMG00000016365	ENST00000349129.2:c.197G>A	6.37:g.83810482G>A	ENSP00000195654:p.Arg66His	Somatic	305	2	0.00655738		WXS	Illumina HiSeq	Phase_I	305	4	0.0131148	NM_015018	Q86XV1|Q9H5J5|Q9NSL4|Q9UPN5|Q9Y414	Missense_Mutation	SNP	ENST00000349129.2	37	CCDS4996.1	.	.	.	.	.	.	.	.	.	.	G	34	5.294928	0.95546	.	.	ENSG00000083097	ENST00000349129;ENST00000237163;ENST00000536812;ENST00000369739	T;T;T	0.41758	1.06;1.0;0.99	5.18	5.18	0.71444	Dopey, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.70971	0.3285	M	0.94101	3.495	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.997;0.998;0.998	T	0.79624	-0.1726	10	0.87932	D	0	.	19.027	0.92935	0.0:0.0:1.0:0.0	.	66;66;66	E1P545;B2RWN9;Q5JWR5	.;.;DOP1_HUMAN	H	66	ENSP00000195654:R66H;ENSP00000237163:R66H;ENSP00000358754:R66H	ENSP00000237163:R66H	R	+	2	0	DOPEY1	83867201	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	9.352000	0.97076	2.563000	0.86464	0.591000	0.81541	CGC	.	.	none		0.363	DOPEY1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043785.2	NM_015018	
B4GALNT1	2583	hgsc.bcm.edu	37	12	58025813	58025813	+	Missense_Mutation	SNP	G	G	C	rs774896	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:58025813G>C	ENST00000341156.4	-	2	687	c.103C>G	c.(103-105)Cta>Gta	p.L35V	B4GALNT1_ENST00000550943.1_5'UTR|B4GALNT1_ENST00000449184.3_Missense_Mutation_p.L35V|B4GALNT1_ENST00000418555.2_Missense_Mutation_p.L35V|B4GALNT1_ENST00000552350.1_Missense_Mutation_p.L35V|B4GALNT1_ENST00000550764.1_Missense_Mutation_p.L35V	NM_001478.3	NP_001469.1	Q00973	B4GN1_HUMAN	beta-1,4-N-acetyl-galactosaminyl transferase 1	35			L -> V (in dbSNP:rs774896).		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)			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)			GCAAGAGGTAGCCGGAGGCCG	0.731													C|||	1262	0.251997	0.382	0.2954	5008	,	,		11009	0.1339		0.2256	False		,,,				2504	0.1943				p.A35A		Atlas-SNP	.											.	B4GALNT1	53	.	0			c.G103G						PASS	.	C	VAL/LEU	1247,2957		200,847,1055	5.0	6.0	6.0		103	1.5	0.2	12	dbSNP_86	6	1620,6572		195,1230,2671	no	missense	B4GALNT1	NM_001478.3	32	395,2077,3726	CC,CG,GG		19.7754,29.6622,23.1284	benign	35/534	58025813	2867,9529	2102	4096	6198	SO:0001583	missense	2583	exon2			GAGGTAGCCGGAG	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.103C>G	12.37:g.58025813G>C	ENSP00000341562:p.Leu35Val	Somatic	15	0	0		WXS	Illumina HiSeq	Phase_I	18	12	0.666667	NM_001478	B4DE26|Q8N636	Silent	SNP	ENST00000341156.4	37	CCDS8950.1	540	0.24725274725274726	179	0.3638211382113821	99	0.27348066298342544	85	0.1486013986013986	177	0.23350923482849603	C	0.416	-0.911008	0.02434	0.296622	0.197754	ENSG00000135454	ENST00000341156;ENST00000418555;ENST00000550764;ENST00000552350;ENST00000548888;ENST00000551220	T;T;T;T;T;T	0.39406	2.37;2.3;1.54;1.54;1.64;1.08	3.84	1.53	0.23141	.	0.422445	0.23293	N	0.049766	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B;B;B	0.15930	0.0;0.003;0.015;0.0	B;B;B;B	0.09377	0.001;0.003;0.004;0.0	T	0.45469	-0.9259	9	0.26408	T	0.33	.	3.2655	0.06864	0.0:0.4617:0.2117:0.3266	rs774896;rs1284090;rs2228450	35;35;35;35	B4DSP5;B4DE26;Q8N636;Q00973	.;.;.;B4GN1_HUMAN	V	35	ENSP00000341562:L35V;ENSP00000401601:L35V;ENSP00000450303:L35V;ENSP00000448500:L35V;ENSP00000447945:L35V;ENSP00000446566:L35V	ENSP00000341562:L35V	L	-	1	2	B4GALNT1	56312080	0.000000	0.05858	0.159000	0.22649	0.151000	0.21798	-0.446000	0.06837	-0.127000	0.11661	-0.322000	0.08575	CTA	G|0.665;C|0.335	0.335	strong		0.731	B4GALNT1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407853.1	NM_001478	
ACAN	176	hgsc.bcm.edu	37	15	89402051	89402051	+	Missense_Mutation	SNP	A	A	G	rs1042630	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:89402051A>G	ENST00000561243.1	+	11	6235	c.6235A>G	c.(6235-6237)Att>Gtt	p.I2079V	ACAN_ENST00000439576.2_Missense_Mutation_p.I2079V|ACAN_ENST00000559004.1_Missense_Mutation_p.I2079V|ACAN_ENST00000352105.7_Missense_Mutation_p.I2079V			P16112	PGCA_HUMAN	aggrecan	2087	CS-2.				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.I1965V(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)			AGCTGGGGACATTAGTGGAGC	0.532													G|||	3235	0.645966	0.6808	0.6182	5008	,	,		18229	0.5605		0.7386	False		,,,				2504	0.6115				p.I2079V		Atlas-SNP	.											ACAN,NS,carcinoma,0,1	ACAN	220	1	1	Substitution - Missense(1)	stomach(1)	c.A6235G						PASS	.	G	VAL/ILE,VAL/ILE	2657,1117		937,783,167	35.0	35.0	35.0		6235,6235	-9.7	0.0	15	dbSNP_86	35	6167,2065		2314,1539,263	yes	missense,missense	ACAN	NM_013227.3,NM_001135.3	29,29	3251,2322,430	GG,GA,AA		25.085,29.5972,26.5034	benign,benign	2079/2531,2079/2432	89402051	8824,3182	1887	4116	6003	SO:0001583	missense	176	exon12			GGGGACATTAGTG	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.6235A>G	15.37:g.89402051A>G	ENSP00000453342:p.Ile2079Val	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	76	76	1	NM_001135	Q13650|Q9UCD3|Q9UCP4|Q9UCP5|Q9UDE0	Missense_Mutation	SNP	ENST00000561243.1	37	CCDS53970.1	1449	0.6634615384615384	333	0.676829268292683	233	0.643646408839779	309	0.5402097902097902	574	0.7572559366754618	G	0.001	-2.960603	0.00049	0.704028	0.74915	ENSG00000157766	ENST00000439576;ENST00000352105;ENST00000268134	T;T	0.02236	4.65;4.38	4.85	-9.69	0.00524	.	2.469360	0.02055	N	0.050297	T	0.00012	0.0000	N	0.21282	0.65	0.80722	P	0.0	B;B	0.17667	0.023;0.007	B;B	0.19666	0.026;0.005	T	0.39418	-0.9615	9	0.15499	T	0.54	1.938	1.9954	0.03455	0.2257:0.3375:0.2694:0.1674	rs1042630;rs3743397;rs58801366;rs1042630	2079;2079	E7ENV9;E7EX88	.;.	V	2079;2079;1965	ENSP00000387356:I2079V;ENSP00000341615:I2079V	ENSP00000268134:I1965V	I	+	1	0	ACAN	87203055	0.000000	0.05858	0.001000	0.08648	0.003000	0.03518	-1.811000	0.01728	-1.308000	0.02318	-1.217000	0.01609	ATT	A|0.343;G|0.657	0.657	strong		0.532	ACAN-006	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416267.2	NM_001135	
SLC5A11	115584	hgsc.bcm.edu	37	16	24888593	24888593	+	Silent	SNP	A	A	G	rs8052587	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:24888593A>G	ENST00000347898.3	+	7	1114	c.492A>G	c.(490-492)gcA>gcG	p.A164A	SLC5A11_ENST00000569071.1_Silent_p.A100A|SLC5A11_ENST00000539472.1_Silent_p.A100A|SLC5A11_ENST00000565769.1_Silent_p.A100A|SLC5A11_ENST00000545376.1_Silent_p.A94A|SLC5A11_ENST00000449109.2_Silent_p.A100A|SLC5A11_ENST00000567758.1_Silent_p.A129A|SLC5A11_ENST00000424767.2_Silent_p.A129A|SLC5A11_ENST00000568579.1_Silent_p.A94A	NM_052944.3	NP_443176.2			solute carrier family 5 (sodium/inositol cotransporter), member 11											endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(30)|ovary(2)|prostate(2)|urinary_tract(1)	49				GBM - Glioblastoma multiforme(48;0.0365)		ACATGTATGCAGGTGCCATCT	0.488													A|||	695	0.138778	0.23	0.0965	5008	,	,		23254	0.0		0.1531	False		,,,				2504	0.1738				p.A164A		Atlas-SNP	.											.	SLC5A11	97	.	0			c.A492G						PASS	.	A		895,3499	347.5+/-309.5	92,711,1394	396.0	330.0	352.0		492	-3.7	0.9	16	dbSNP_116	352	1226,7374	247.4+/-275.4	86,1054,3160	no	coding-synonymous	SLC5A11	NM_052944.2		178,1765,4554	GG,GA,AA		14.2558,20.3687,16.3229		164/676	24888593	2121,10873	2197	4300	6497	SO:0001819	synonymous_variant	115584	exon7			GTATGCAGGTGCC	AF292385	CCDS10625.1, CCDS58437.1, CCDS58438.1, CCDS58439.1, CCDS58440.1	16p12.1	2013-07-19	2013-07-19		ENSG00000158865	ENSG00000158865		"""Solute carriers"""	23091	protein-coding gene	gene with protein product		610238	"""solute carrier family 5 (sodium/glucose cotransporter), member 11"""			12039040, 12133831	Standard	NM_001258414		Approved	KST1, SMIT2, SGLT6	uc002dmu.4	Q8WWX8	OTTHUMG00000097003	ENST00000347898.3:c.492A>G	16.37:g.24888593A>G		Somatic	202	1	0.00495049		WXS	Illumina HiSeq	Phase_I	225	160	0.711111	NM_052944		Silent	SNP	ENST00000347898.3	37	CCDS10625.1																																																																																			A|0.850;G|0.150	0.150	strong		0.488	SLC5A11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214091.3	NM_052944	
RTN2	6253	hgsc.bcm.edu	37	19	45998247	45998247	+	Silent	SNP	A	A	G	rs10401270	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:45998247A>G	ENST00000245923.4	-	3	331	c.96T>C	c.(94-96)tcT>tcC	p.S32S	PPM1N_ENST00000396737.2_5'Flank|RTN2_ENST00000589384.1_5'UTR|PPM1N_ENST00000456399.2_5'Flank|RTN2_ENST00000430715.2_5'Flank|RTN2_ENST00000344680.4_Silent_p.S32S|PPM1N_ENST00000401705.1_Intron|RTN2_ENST00000590526.1_5'UTR	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	59	0	0		WXS	Illumina HiSeq	Phase_I	57	33	0.578947	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	
UNC93A	54346	hgsc.bcm.edu	37	6	167719436	167719436	+	Missense_Mutation	SNP	G	G	A	rs2072767	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:167719436G>A	ENST00000230256.3	+	6	1049	c.874G>A	c.(874-876)Gtc>Atc	p.V292I	UNC93A_ENST00000366829.2_Missense_Mutation_p.V250I	NM_018974.3	NP_061847.2	Q86WB7	UN93A_HUMAN	unc-93 homolog A (C. elegans)	292			V -> I (in dbSNP:rs2072767). {ECO:0000269|PubMed:12381271}.			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(7)|lung(20)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	40		Breast(66;7.62e-05)|Ovarian(120;0.105)		OV - Ovarian serous cystadenocarcinoma(33;2.22e-20)|BRCA - Breast invasive adenocarcinoma(81;6.17e-07)|GBM - Glioblastoma multiforme(31;0.00492)		CATCCAGTTCGTCGGCTACGT	0.612													G|||	1404	0.280351	0.2587	0.2349	5008	,	,		20543	0.2629		0.2753	False		,,,				2504	0.365				p.V292I		Atlas-SNP	.											.	UNC93A	66	.	0			c.G874A						PASS	.	G	ILE/VAL,ILE/VAL	1158,3248	409.7+/-335.1	153,852,1198	285.0	237.0	253.0		748,874	3.9	0.0	6	dbSNP_96	253	2187,6413	373.3+/-337.0	263,1661,2376	yes	missense,missense	UNC93A	NM_001143947.1,NM_018974.3	29,29	416,2513,3574	AA,AG,GG		25.4302,26.2823,25.7189	benign,benign	250/416,292/458	167719436	3345,9661	2203	4300	6503	SO:0001583	missense	54346	exon6			CAGTTCGTCGGCT	AJ508812	CCDS5300.1, CCDS47515.1	6q27	2014-05-16	2001-11-28		ENSG00000112494	ENSG00000112494			12570	protein-coding gene	gene with protein product		607995	"""unc93 (C.elegans) homolog A"""			12381271	Standard	NM_001143947		Approved	dJ366N23.2, dJ366N23.1	uc003qvq.3	Q86WB7	OTTHUMG00000016021	ENST00000230256.3:c.874G>A	6.37:g.167719436G>A	ENSP00000230256:p.Val292Ile	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	60	30	0.5	NM_018974	B3KRP5|Q4QQJ4|Q5JZD6	Missense_Mutation	SNP	ENST00000230256.3	37	CCDS5300.1	590	0.27014652014652013	141	0.2865853658536585	88	0.2430939226519337	157	0.2744755244755245	204	0.2691292875989446	G	10.35	1.326484	0.24080	0.262823	0.254302	ENSG00000112494	ENST00000230256;ENST00000366829	T;T	0.16457	2.34;2.62	4.73	3.87	0.44632	Major facilitator superfamily domain, general substrate transporter (1);	0.131212	0.50627	N	0.000115	T	0.04588	0.0125	L	0.49256	1.55	0.19945	P	0.9999408312	P;P	0.51351	0.944;0.506	B;B	0.35073	0.195;0.078	T	0.19160	-1.0314	9	0.09084	T	0.74	-39.111	12.2369	0.54520	0.083:0.0:0.917:0.0	rs2072767;rs56604367;rs58276443;rs2072767	250;292	Q4QQJ4;Q86WB7	.;UN93A_HUMAN	I	292;250	ENSP00000230256:V292I;ENSP00000355794:V250I	ENSP00000230256:V292I	V	+	1	0	UNC93A	167639426	1.000000	0.71417	0.021000	0.16686	0.154000	0.21943	5.362000	0.66098	1.003000	0.39130	-0.222000	0.12452	GTC	G|0.732;A|0.268	0.268	strong		0.612	UNC93A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043125.2	NM_018974	
TIMP3	7078	hgsc.bcm.edu	37	22	33253292	33253292	+	Silent	SNP	C	C	T	rs11547635	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:33253292C>T	ENST00000266085.6	+	3	562	c.261C>T	c.(259-261)tcC>tcT	p.S87S	SYN3_ENST00000358763.2_Intron|SYN3_ENST00000332840.5_Intron	NM_000362.4	NP_000353.1	P35625	TIMP3_HUMAN	TIMP metallopeptidase inhibitor 3	87	NTR. {ECO:0000255|PROSITE- ProRule:PRU00295}.				cellular response to organic substance (GO:0071310)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of membrane protein ectodomain proteolysis (GO:0051045)|visual perception (GO:0007601)	basement membrane (GO:0005604)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|metalloendopeptidase inhibitor activity (GO:0008191)			endometrium(2)|large_intestine(3)|lung(1)|urinary_tract(1)	7						CGGAAGCTTCCGAGAGTCTCT	0.517													C|||	718	0.143371	0.0461	0.232	5008	,	,		20978	0.3581		0.0616	False		,,,				2504	0.0746				p.S87S		Atlas-SNP	.											.	TIMP3	31	.	0			c.C261T						PASS	.	C	,,,	271,4135	152.5+/-186.2	4,263,1936	161.0	130.0	140.0		261,,,	-8.9	0.7	22	dbSNP_120	140	632,7968	162.9+/-215.5	25,582,3693	no	coding-synonymous,intron,intron,intron	TIMP3,SYN3	NM_000362.4,NM_001135774.1,NM_003490.3,NM_133633.2	,,,	29,845,5629	TT,TC,CC		7.3488,6.1507,6.9429	,,,	87/212,,,	33253292	903,12103	2203	4300	6503	SO:0001819	synonymous_variant	7078	exon3			AGCTTCCGAGAGT		CCDS13911.1	22q12.3	2013-01-08	2008-07-31		ENSG00000100234	ENSG00000100234			11822	protein-coding gene	gene with protein product		188826	"""tissue inhibitor of metalloproteinase 3 (Sorsby fundus dystrophy, pseudoinflammatory)"""	SFD		8188246, 12652295	Standard	NM_000362		Approved		uc003anb.3	P35625	OTTHUMG00000030784	ENST00000266085.6:c.261C>T	22.37:g.33253292C>T		Somatic	200	0	0		WXS	Illumina HiSeq	Phase_I	198	96	0.484848	NM_000362	B2RBY9|Q5THV4|Q9UC74|Q9UGS2	Silent	SNP	ENST00000266085.6	37	CCDS13911.1																																																																																			C|0.870;N|0.000	.	strong		0.517	TIMP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075672.2	NM_000362	
TRIM25	7706	hgsc.bcm.edu	37	17	54978794	54978794	+	Missense_Mutation	SNP	G	G	A	rs205498	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:54978794G>A	ENST00000316881.4	-	4	1122	c.1073C>T	c.(1072-1074)cCc>cTc	p.P358L	TRIM25_ENST00000537230.1_Missense_Mutation_p.P358L	NM_005082.4	NP_005073.2	Q14258	TRI25_HUMAN	tripartite motif containing 25	358	Interaction with influenza A virus NS1.		P -> L (in dbSNP:rs205498). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:21269460, ECO:0000269|PubMed:8248217}.		defense response to virus (GO:0051607)|innate immune response (GO:0045087)|negative regulation of type I interferon production (GO:0032480)|negative regulation of viral entry into host cell (GO:0046597)|negative regulation of viral release from host cell (GO:1902187)|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 ubiquitination (GO:0016567)|regulation of viral entry into host cell (GO:0046596)|regulation of viral release from host cell (GO:1902186)|response to estrogen (GO:0043627)|response to vitamin D (GO:0033280)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	acid-amino acid ligase activity (GO:0016881)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(2)|endometrium(2)|kidney(4)|large_intestine(3)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21	Breast(9;6.15e-08)					ACTGGGGGTGGGCTCCTGGAG	0.582													G|||	3878	0.774361	0.8411	0.7061	5008	,	,		16907	0.8095		0.7535	False		,,,				2504	0.7178				p.P358L		Atlas-SNP	.											.	TRIM25	52	.	0			c.C1073T						PASS	.	G	LEU/PRO	3565,841	747.2+/-411.8	1440,685,78	196.0	183.0	188.0		1073	0.6	1.0	17	dbSNP_79	188	6352,2248	708.8+/-405.7	2367,1618,315	yes	missense	TRIM25	NM_005082.4	98	3807,2303,393	AA,AG,GG		26.1395,19.0876,23.7506	benign	358/631	54978794	9917,3089	2203	4300	6503	SO:0001583	missense	7706	exon4			GGGGTGGGCTCCT	D21205	CCDS11591.1	17q23.1	2013-01-09	2011-01-25	2004-03-30				"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	12932	protein-coding gene	gene with protein product		600453	"""zinc finger protein 147 (estrogen-responsive finger protein)"", ""tripartite motif-containing 25"""	ZNF147		7789997	Standard	NM_005082		Approved	EFP, RNF147	uc002iut.3	Q14258		ENST00000316881.4:c.1073C>T	17.37:g.54978794G>A	ENSP00000323889:p.Pro358Leu	Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	110	56	0.509091	NM_005082		Missense_Mutation	SNP	ENST00000316881.4	37	CCDS11591.1	1694	0.7756410256410257	398	0.8089430894308943	257	0.7099447513812155	473	0.8269230769230769	566	0.7467018469656992	G	11.35	1.614070	0.28712	0.809124	0.738605	ENSG00000121060	ENST00000316881;ENST00000537230	T;T	0.66460	-0.21;-0.21	4.16	0.603	0.17541	.	1.641340	0.02994	N	0.147272	T	0.00012	0.0000	N	0.08118	0	0.24640	P	0.99357564	B	0.20988	0.05	B	0.17722	0.019	T	0.40553	-0.9557	9	0.26408	T	0.33	.	3.9494	0.09363	0.0:0.2067:0.195:0.5983	rs205498;rs17851450;rs17859367;rs60679854;rs205498	358	Q14258	TRI25_HUMAN	L	358	ENSP00000323889:P358L;ENSP00000445961:P358L	ENSP00000323889:P358L	P	-	2	0	TRIM25	52333793	0.352000	0.24895	0.992000	0.48379	0.116000	0.19942	-0.009000	0.12765	0.050000	0.15949	-1.105000	0.02106	CCC	G|0.231;A|0.769	0.769	strong		0.582	TRIM25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440609.1	NM_005082	
FGFBP2	83888	hgsc.bcm.edu	37	4	15964501	15964501	+	Silent	SNP	G	G	A	rs2286459|rs111244757	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:15964501G>A	ENST00000259989.6	-	1	358	c.252C>T	c.(250-252)ttC>ttT	p.F84F	FGFBP2_ENST00000509331.1_Intron	NM_031950.3	NP_114156.1	Q9BYJ0	FGFP2_HUMAN	fibroblast growth factor binding protein 2	84			F -> L (in dbSNP:rs2286459).			extracellular region (GO:0005576)				central_nervous_system(1)|lung(5)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	9						GGTCAGCAGCGAAAGCCTGGC	0.622													G|||	2548	0.508786	0.3116	0.6499	5008	,	,		20205	0.4365		0.5179	False		,,,				2504	0.7403				p.F84F		Atlas-SNP	.											.	FGFBP2	22	.	0			c.C252T						PASS	.	G		1658,2748	505.1+/-366.0	323,1012,868	54.0	53.0	54.0		252	1.2	0.0	4	dbSNP_100	54	4550,4050	595.8+/-393.5	1229,2092,979	no	coding-synonymous	FGFBP2	NM_031950.3		1552,3104,1847	AA,AG,GG		47.093,37.6305,47.7318		84/224	15964501	6208,6798	2203	4300	6503	SO:0001819	synonymous_variant	83888	exon1			AGCAGCGAAAGCC	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.252C>T	4.37:g.15964501G>A		Somatic	16	0	0		WXS	Illumina HiSeq	Phase_I	12	5	0.416667	NM_031950		Silent	SNP	ENST00000259989.6	37	CCDS3419.1																																																																																			G|0.528;A|0.472	0.472	strong		0.622	FGFBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250324.1	NM_031950	
TMEM213	155006	hgsc.bcm.edu	37	7	138486096	138486096	+	Missense_Mutation	SNP	G	G	C	rs61729750	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:138486096G>C	ENST00000442682.2	+	2	260	c.107G>C	c.(106-108)aGc>aCc	p.S36T	TMEM213_ENST00000397602.3_Missense_Mutation_p.S35T|TMEM213_ENST00000413208.1_Missense_Mutation_p.S36T|TMEM213_ENST00000458494.1_Intron|TMEM213_ENST00000422794.2_Missense_Mutation_p.S86T	NM_001085429.1	NP_001078898.1	A2RRL7	TM213_HUMAN	transmembrane protein 213	36						integral component of membrane (GO:0016021)				breast(1)|endometrium(3)|kidney(1)|lung(1)	6						AACAGCTCAAGCTTGACCGCT	0.522													C|||	3361	0.671126	0.7421	0.6643	5008	,	,		19175	0.6925		0.6282	False		,,,				2504	0.6022				p.S36T		Atlas-SNP	.											.	TMEM213	20	.	0			c.G107C						PASS	.	C	THR/SER	2848,1090		1045,758,166	37.0	43.0	41.0		107	2.2	0.0	7	dbSNP_129	41	5228,3088		1640,1948,570	yes	missense	TMEM213	NM_001085429.1	58	2685,2706,736	CC,CG,GG		37.1332,27.679,34.095	benign	36/108	138486096	8076,4178	1969	4158	6127	SO:0001583	missense	155006	exon2			GCTCAAGCTTGAC		CCDS47722.1	7q34	2008-08-08			ENSG00000214128	ENSG00000214128			27220	protein-coding gene	gene with protein product							Standard	NM_001085429		Approved		uc010lna.3	A2RRL7	OTTHUMG00000157182	ENST00000442682.2:c.107G>C	7.37:g.138486096G>C	ENSP00000390407:p.Ser36Thr	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	50	50	1	NM_001085429	A4D1R3|C9JH49|C9JX41|C9K0P0	Missense_Mutation	SNP	ENST00000442682.2	37	CCDS47722.1	1477	0.6762820512820513	370	0.7520325203252033	237	0.6546961325966851	396	0.6923076923076923	474	0.6253298153034301	C	0	-2.686823	0.00101	0.72321	0.628668	ENSG00000214128	ENST00000422794;ENST00000397602;ENST00000442682;ENST00000413208	.	.	.	5.03	2.16	0.27623	.	0.612418	0.12401	N	0.472084	T	0.00012	0.0000	N	0.01352	-0.895	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.40887	-0.9539	8	0.02654	T	1	-19.9994	4.426	0.11503	0.1483:0.4827:0.2871:0.0819	rs61729750	35;36	A2RRL7-3;A2RRL7	.;TM213_HUMAN	T	86;35;36;36	.	ENSP00000380727:S35T	S	+	2	0	TMEM213	138136636	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	0.358000	0.20216	0.075000	0.16796	-2.061000	0.00397	AGC	G|0.334;C|0.666	0.666	strong		0.522	TMEM213-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347800.2	NM_001085429	
PADI2	11240	hgsc.bcm.edu	37	1	17413152	17413152	+	Missense_Mutation	SNP	C	C	T	rs61749340	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:17413152C>T	ENST00000375486.4	-	7	761	c.698G>A	c.(697-699)cGg>cAg	p.R233Q	PADI2_ENST00000375481.1_Missense_Mutation_p.R233Q|PADI2_ENST00000444885.2_Missense_Mutation_p.G152R	NM_007365.2	NP_031391.2	Q9Y2J8	PADI2_HUMAN	peptidyl arginine deiminase, type II	233					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)	GTAGAGCTTCCGCCGGCCCAG	0.612													C|||	16	0.00319489	0.0	0.0014	5008	,	,		17851	0.0		0.0119	False		,,,				2504	0.0031				p.R233Q		Atlas-SNP	.											.	PADI2	72	.	0			c.G698A						PASS	.	C	GLN/ARG	25,4381	31.7+/-61.6	1,23,2179	79.0	84.0	83.0		698	-0.0	1.0	1	dbSNP_129	83	86,8514	49.8+/-109.6	0,86,4214	yes	missense	PADI2	NM_007365.2	43	1,109,6393	TT,TC,CC		1.0,0.5674,0.8535	benign	233/666	17413152	111,12895	2203	4300	6503	SO:0001583	missense	11240	exon7			AGCTTCCGCCGGC	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.698G>A	1.37:g.17413152C>T	ENSP00000364635:p.Arg233Gln	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	117	58	0.495726	NM_007365	Q96DA7|Q9UPN2	Missense_Mutation	SNP	ENST00000375486.4	37	CCDS177.1	10|10	0.004578754578754579|0.004578754578754579	0|0	0.0|0.0	1|1	0.0027624309392265192|0.0027624309392265192	0|0	0.0|0.0	9|9	0.011873350923482849|0.011873350923482849	C|C	6.143|6.143	0.394510|0.394510	0.11638|0.11638	0.005674|0.005674	0.01|0.01	ENSG00000117115|ENSG00000117115	ENST00000444885|ENST00000375486;ENST00000375481	T|T;T	0.06294|0.15834	3.32|2.39;2.39	4.71|4.71	-0.0409|-0.0409	0.13870|0.13870	.|Protein-arginine deiminase (PAD), central domain (2);	.|0.666471	.|0.15848	.|N	.|0.241686	T|T	0.03136|0.03136	0.0092|0.0092	N|N	0.02539|0.02539	-0.55|-0.55	0.22185|0.22185	N|N	0.999304|0.999304	B|B	0.06786|0.02656	0.001|0.0	B|B	0.01281|0.04013	0.0|0.001	T|T	0.42327|0.42327	-0.9458|-0.9458	9|10	0.20519|0.02654	T|T	0.43|1	-11.41|-11.41	8.498|8.498	0.33141|0.33141	0.0:0.3828:0.0:0.6172|0.0:0.3828:0.0:0.6172	rs61749340|rs61749340	152|233	B4DIU3|Q9Y2J8	.|PADI2_HUMAN	R|Q	152|233	ENSP00000405894:G152R|ENSP00000364635:R233Q;ENSP00000364630:R233Q	ENSP00000405894:G152R|ENSP00000364630:R233Q	G|R	-|-	1|2	0|0	PADI2|PADI2	17285739|17285739	0.001000|0.001000	0.12720|0.12720	0.981000|0.981000	0.43875|0.43875	0.988000|0.988000	0.76386|0.76386	-0.161000|-0.161000	0.10026|0.10026	0.067000|0.067000	0.16545|0.16545	0.460000|0.460000	0.39030|0.39030	GGA|CGG	C|0.994;T|0.006	0.006	strong		0.612	PADI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006624.1		
HLA-DPB1	3115	hgsc.bcm.edu	37	6	33052981	33052981	+	Missense_Mutation	SNP	C	C	A	rs14362	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:33052981C>A	ENST00000418931.2	+	3	735	c.619C>A	c.(619-621)Ctg>Atg	p.L207M		NM_002121.5	NP_002112.3	P04440	DPB1_HUMAN	major histocompatibility complex, class II, DP beta 1	207	Beta-2.|Ig-like C1-type.		L -> M (in allele DPB1*04:02; dbSNP:rs14362).		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell proliferation (GO:0042102)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	peptide antigen binding (GO:0042605)			cervix(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(3)|ovary(1)|skin(1)	11						GCACACCAGCCTGGATAGTCC	0.577													.|||	399	0.0796725	0.0076	0.2464	5008	,	,		19666	0.0367		0.1163	False		,,,				2504	0.0654				p.L207M		Atlas-SNP	.											.	HLA-DPB1	28	.	0			c.C619A						PASS	.	C	MET/LEU	87,2933		2,83,1425	78.0	82.0	80.0		619	4.0	1.0	6	dbSNP_52	80	597,4819		39,519,2150	yes	missense	HLA-DPB1	NM_002121.5	15	41,602,3575	AA,AC,CC		11.0229,2.8808,8.1081	probably-damaging	207/259	33052981	684,7752	1510	2708	4218	SO:0001583	missense	3115	exon3			ACCAGCCTGGATA		CCDS4765.1	6p21.3	2013-01-11			ENSG00000223865	ENSG00000223865		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4940	protein-coding gene	gene with protein product		142858		HLA-DP1B			Standard	NM_002121		Approved		uc003ocu.2	P04440	OTTHUMG00000031076	ENST00000418931.2:c.619C>A	6.37:g.33052981C>A	ENSP00000408146:p.Leu207Met	Somatic	190	0	0		WXS	Illumina HiSeq	Phase_I	158	85	0.537975	NM_002121	A0PFJ7|A5I886|A8YPB3|B5U8B4|B7VF80|B7VF87|B8ZX68|B8ZYT0|B9W5S8|B9W6F7|B9W6F9|C0MPP5|C0MPQ2|C0MPQ3|C0MPQ5|C0MPQ6|C0MPQ7|C4R9J5|C5IZL1|O00259|O19698|O19700|O19702|O19749|O46884|O77952|O98215|O98216|O98217|O98218|O98219|O98222|O98223|P01916|P04232|P13763|P79493|P79608|Q0P0L4|Q0ZFN3|Q14279|Q27S71|Q29682|Q29684|Q29698|Q29714|Q29775|Q29776|Q29778|Q29779|Q29781|Q29827|Q29828|Q29879|Q29880|Q29898|Q29977|Q2MGW3|Q30015|Q30031|Q30032|Q30033|Q30034|Q30050|Q30051|Q30052|Q30053|Q30054|Q30055|Q30174|Q4GY31|Q4JHD8|Q5ENE0|Q5ENE1|Q5ENW3|Q5EP46|Q5EP47|Q5EP49|Q5EP51|Q5EP52|Q5EP53|Q5EP56|Q5I4H8|Q5I4H9|Q5ISH4|Q5ISH5|Q5SQ73|Q5STP2|Q5YLA6|Q6IVX1|Q6LBX2|Q6LBX3|Q6LBX4|Q6LBX5|Q6LBX6|Q6LBX7|Q6PWX6|Q6TAS4|Q714U1|Q714U2|Q7YQ10|Q860Z7|Q8HWL7|Q8HWT5|Q8SNC4|Q95HC1|Q95IT7|Q95IT8|Q9BD13|Q9GIM2|Q9GIM4|Q9GIX6|Q9GJ41|Q9MY67|Q9TNT7|Q9TQE2|Q9XS11|Q9XS12	Missense_Mutation	SNP	ENST00000418931.2	37	CCDS4765.1	232	0.10622710622710622	6	0.012195121951219513	101	0.27900552486187846	30	0.05244755244755245	95	0.12532981530343007	C	15.53	2.861071	0.51482	0.028808	0.110229	ENSG00000223865	ENST00000418931;ENST00000411942;ENST00000422592;ENST00000428835	T;T	0.04758	3.56;3.56	4.04	4.04	0.47022	Immunoglobulin-like (1);Immunoglobulin C1-set (2);Immunoglobulin-like fold (1);	0.089667	0.47093	D	0.000258	T	0.12689	0.0308	M	0.91459	3.21	0.09310	P	1.0	P;B;B	0.40398	0.716;0.208;0.208	P;P;B	0.51101	0.659;0.489;0.443	T	0.00525	-1.1689	9	0.49607	T	0.09	.	14.0872	0.64964	0.0:1.0:0.0:0.0	rs14362;rs1042355;rs3176965;rs10947383;rs17358460;rs17398327;rs58897057	173;217;207	A2ALJ6;Q59GY1;P04440	.;.;DPB1_HUMAN	M	207;177;18;184	ENSP00000408146:L207M;ENSP00000412654:L184M	ENSP00000389210:L177M	L	+	1	2	HLA-DPB1	33160959	1.000000	0.71417	0.983000	0.44433	0.982000	0.71751	2.741000	0.47426	2.257000	0.74773	0.544000	0.68410	CTG	C|0.874;A|0.126	0.126	strong		0.577	HLA-DPB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076106.2	NM_002121	
OBSCN	84033	hgsc.bcm.edu	37	1	228494790	228494790	+	Missense_Mutation	SNP	G	G	A	rs435776	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:228494790G>A	ENST00000422127.1	+	45	12159	c.12115G>A	c.(12115-12117)Gga>Aga	p.G4039R	OBSCN_ENST00000284548.11_Missense_Mutation_p.G4039R|OBSCN_ENST00000570156.2_Missense_Mutation_p.G4996R|OBSCN_ENST00000366709.4_Missense_Mutation_p.G1158R|OBSCN_ENST00000366707.4_Missense_Mutation_p.G1673R	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	4039	Ig-like 41.		G -> R (in dbSNP:rs435776).		apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				GCTGGTACGCGGAGTGGAGCA	0.642													G|||	1345	0.26857	0.0605	0.3775	5008	,	,		18993	0.249		0.4841	False		,,,				2504	0.271				p.G4996R		Atlas-SNP	.											OBSCN_ENST00000570156,NS,carcinoma,0,2	OBSCN	2142	2	0			c.G14986A						PASS	.	G	ARG/GLY,ARG/GLY	513,3873		42,429,1722	66.0	79.0	74.0		12115,12115	0.3	0.0	1	dbSNP_80	74	4232,4336		1070,2092,1122	yes	missense,missense	OBSCN	NM_001098623.1,NM_052843.2	125,125	1112,2521,2844	AA,AG,GG		49.3931,11.6963,36.6296	probably-damaging,probably-damaging	4039/7969,4039/6621	228494790	4745,8209	2193	4284	6477	SO:0001583	missense	84033	exon56			GTACGCGGAGTGG	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"""Rho guanine nucleotide exchange factors"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.12115G>A	1.37:g.228494790G>A	ENSP00000409493:p.Gly4039Arg	Somatic	321	0	0		WXS	Illumina HiSeq	Phase_I	303	138	0.455446	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Missense_Mutation	SNP	ENST00000422127.1	37	CCDS58065.1	663	0.30357142857142855	35	0.07113821138211382	136	0.3756906077348066	134	0.23426573426573427	358	0.47229551451187335	G	10.99	1.506355	0.26949	0.116963	0.493931	ENSG00000154358	ENST00000284548;ENST00000422127;ENST00000366707;ENST00000366709	T;T;T;T	0.04654	3.58;3.58;3.58;3.58	5.81	0.336	0.15958	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.527305	0.18679	N	0.134218	T	0.00012	0.0000	L	0.37630	1.12	0.80722	P	0.0	P;B	0.43578	0.811;0.058	B;B	0.34652	0.187;0.012	T	0.34403	-0.9830	9	0.15066	T	0.55	.	7.3643	0.26764	0.325:0.1044:0.5706:0.0	rs435776;rs61021469;rs435776	4039;4039	Q5VST9;Q5VST9-3	OBSCN_HUMAN;.	R	4039;4039;1673;1158	ENSP00000284548:G4039R;ENSP00000409493:G4039R;ENSP00000355668:G1673R;ENSP00000355670:G1158R	ENSP00000284548:G4039R	G	+	1	0	OBSCN	226561413	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.390000	0.07332	-0.169000	0.10834	0.462000	0.41574	GGA	G|0.711;A|0.289	0.289	strong		0.642	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
SMC1B	27127	hgsc.bcm.edu	37	22	45767421	45767421	+	Missense_Mutation	SNP	C	C	T	rs56174639	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:45767421C>T	ENST00000357450.4	-	14	2242	c.2243G>A	c.(2242-2244)tGt>tAt	p.C748Y	SMC1B_ENST00000404354.3_Missense_Mutation_p.C748Y	NM_148674.3	NP_683515.3	Q8NDV3	SMC1B_HUMAN	structural maintenance of chromosomes 1B	748					meiotic nuclear division (GO:0007126)|sister chromatid cohesion (GO:0007062)	chromosome, centromeric region (GO:0000775)|lateral element (GO:0000800)|meiotic cohesin complex (GO:0030893)|nuclear meiotic cohesin complex (GO:0034991)	ATP binding (GO:0005524)|DNA binding (GO:0003677)			breast(2)|endometrium(4)|kidney(3)|large_intestine(6)|lung(15)|ovary(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	37		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0182)		CAACATAATACATTGAGACTC	0.279													C|||	434	0.0866613	0.0908	0.0908	5008	,	,		18743	0.003		0.1889	False		,,,				2504	0.0593				p.C748Y		Atlas-SNP	.											.	SMC1B	215	.	0			c.G2243A						PASS	.	C	TYR/CYS	313,3313		11,291,1511	95.0	85.0	88.0		2243	3.3	0.4	22	dbSNP_129	88	1329,6801		115,1099,2851	yes	missense	SMC1B	NM_148674.3	194	126,1390,4362	TT,TC,CC		16.3469,8.6321,13.9673	benign	748/1236	45767421	1642,10114	1813	4065	5878	SO:0001583	missense	27127	exon14			ATAATACATTGAG	AJ504806	CCDS43027.1, CCDS74876.1	22q13	2006-07-06	2006-07-06	2006-07-06	ENSG00000077935	ENSG00000077935		"""Structural maintenance of chromosomes proteins"""	11112	protein-coding gene	gene with protein product		608685	"""SMC1 (structural maintenance of chromosomes 1, yeast)-like 1"", ""SMC1 structural maintenance of chromosomes 1-like 2 (yeast)"""	SMC1L2		10591208, 11564881	Standard	XM_005261566		Approved	bK268H5	uc003bgc.3	Q8NDV3	OTTHUMG00000151334	ENST00000357450.4:c.2243G>A	22.37:g.45767421C>T	ENSP00000350036:p.Cys748Tyr	Somatic	209	0	0		WXS	Illumina HiSeq	Phase_I	170	76	0.447059	NM_148674	A0AV46|B0QY23|B0QY24|Q5TIC3|Q6ZUF9|Q9Y3G5	Missense_Mutation	SNP	ENST00000357450.4	37	CCDS43027.1	243	0.11126373626373626	49	0.09959349593495935	39	0.10773480662983426	3	0.005244755244755245	152	0.20052770448548812	C	4.996	0.184893	0.09495	0.086321	0.163469	ENSG00000077935	ENST00000357450;ENST00000404354	T;T	0.78003	-1.14;-0.97	5.66	3.35	0.38373	RecF/RecN/SMC (1);	0.372163	0.24518	N	0.037825	T	0.00073	0.0002	N	0.01729	-0.75	0.80722	P	0.0	B;B;B	0.06786	0.0;0.001;0.001	B;B;B	0.08055	0.001;0.001;0.003	T	0.03443	-1.1036	9	0.18710	T	0.47	.	6.1198	0.20148	0.1837:0.6861:0.0:0.1302	rs56174639;rs61748561	748;748;748	Q8NDV3;Q8NDV3-2;Q8NDV3-3	SMC1B_HUMAN;.;.	Y	748	ENSP00000350036:C748Y;ENSP00000385902:C748Y	ENSP00000350036:C748Y	C	-	2	0	SMC1B	44146085	0.022000	0.18835	0.436000	0.26797	0.345000	0.29048	0.560000	0.23500	2.669000	0.90835	0.655000	0.94253	TGT	C|0.874;T|0.126	0.126	strong		0.279	SMC1B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322256.2	NM_148674	
TP53BP1	7158	hgsc.bcm.edu	37	15	43748304	43748304	+	Silent	SNP	A	A	G	rs690367	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:43748304A>G	ENST00000263801.3	-	12	2739	c.2487T>C	c.(2485-2487)gaT>gaC	p.D829D	TP53BP1_ENST00000605155.1_5'UTR|TP53BP1_ENST00000382039.3_Silent_p.D834D|TP53BP1_ENST00000450115.2_Silent_p.D834D|TP53BP1_ENST00000382044.4_Silent_p.D834D	NM_005657.2	NP_005648.1	Q12888	TP53B_HUMAN	tumor protein p53 binding protein 1	829					cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|replication fork (GO:0005657)	damaged DNA binding (GO:0003684)|methylated histone binding (GO:0035064)|p53 binding (GO:0002039)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II transcription cofactor activity (GO:0001104)|telomeric DNA binding (GO:0042162)			breast(4)|endometrium(5)|kidney(7)|large_intestine(22)|lung(13)|ovary(4)|pancreas(2)|prostate(1)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(3)	72		all_cancers(109;6.94e-11)|all_epithelial(112;2.69e-09)|Lung NSC(122;7.86e-07)|all_lung(180;7.84e-06)|Melanoma(134;0.0728)		GBM - Glioblastoma multiforme(94;1.59e-06)		GCTGTGAAGAATCTTGCTCTA	0.423								Other conserved DNA damage response genes					G|||	2635	0.526158	0.9735	0.33	5008	,	,		22112	0.3879		0.3032	False		,,,				2504	0.4325				p.D834D		Atlas-SNP	.											.	TP53BP1	157	.	0			c.T2502C						PASS	.	G	,,	3740,662	282.5+/-276.6	1594,552,55	169.0	164.0	166.0		2502,2502,2487	3.4	0.2	15	dbSNP_83	166	2606,5990	687.7+/-404.2	386,1834,2078	no	coding-synonymous,coding-synonymous,coding-synonymous	TP53BP1	NM_001141979.1,NM_001141980.1,NM_005657.2	,,	1980,2386,2133	GG,GA,AA		30.3164,15.0386,48.8229	,,	834/1976,834/1978,829/1973	43748304	6346,6652	2201	4298	6499	SO:0001819	synonymous_variant	7158	exon12			TGAAGAATCTTGC	U09477	CCDS10096.1, CCDS45250.1, CCDS45251.1	15q15-q21	2007-08-02	2007-08-02		ENSG00000067369	ENSG00000067369			11999	protein-coding gene	gene with protein product		605230	"""tumor protein p53-binding protein, 1"""			8016121, 9748285	Standard	NM_005657		Approved	53BP1, p202	uc001zrr.4	Q12888	OTTHUMG00000059757	ENST00000263801.3:c.2487T>C	15.37:g.43748304A>G		Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	156	54	0.346154	NM_001141980	F8VY86|Q2M1Z7|Q4LE46|Q5FWZ3|Q7Z3U4	Silent	SNP	ENST00000263801.3	37	CCDS10096.1																																																																																			A|0.491;G|0.509	0.509	strong		0.423	TP53BP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000132897.3		
ANK3	288	hgsc.bcm.edu	37	10	61868716	61868716	+	Silent	SNP	C	C	A	rs3750800	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:61868716C>A	ENST00000280772.2	-	27	3236	c.3045G>T	c.(3043-3045)acG>acT	p.T1015T	ANK3_ENST00000373827.2_Silent_p.T1009T|ANK3_ENST00000503366.1_Silent_p.T1016T|ANK3_ENST00000355288.2_Silent_p.T149T	NM_020987.3	NP_066267.2	Q12955	ANK3_HUMAN	ankyrin 3, node of Ranvier (ankyrin G)	1015	ZU5 1. {ECO:0000255|PROSITE- ProRule:PRU00485}.				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						GAGTGGGGGCCGTACACTTGC	0.542													C|||	897	0.179113	0.0272	0.2262	5008	,	,		15374	0.0704		0.3221	False		,,,				2504	0.316				p.T1016T		Atlas-SNP	.											.	ANK3	703	.	0			c.G3048T						PASS	.	C	,,,	309,4097	168.0+/-198.9	12,285,1906	67.0	72.0	70.0		447,3027,3048,3045	-9.9	0.3	10	dbSNP_107	70	2807,5793	443.0+/-360.3	468,1871,1961	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ANK3	NM_001149.3,NM_001204403.1,NM_001204404.1,NM_020987.3	,,,	480,2156,3867	AA,AC,CC		32.6395,7.0132,23.9582	,,,	149/1002,1009/1862,1016/1869,1015/4378	61868716	3116,9890	2203	4300	6503	SO:0001819	synonymous_variant	288	exon28			GGGGGCCGTACAC	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.3045G>T	10.37:g.61868716C>A		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	96	51	0.53125	NM_001204404	B1AQT2|B4DIL1|E9PE32|Q13484|Q5CZH9|Q5VXD5|Q7Z3G4|Q9H0P5	Silent	SNP	ENST00000280772.2	37	CCDS7258.1	392	0.1794871794871795	18	0.036585365853658534	97	0.26795580110497236	40	0.06993006993006994	237	0.31266490765171506	C	5.518	0.280589	0.10458	0.070132	0.326395	ENSG00000151150	ENST00000467420	.	.	.	6.04	-9.89	0.00464	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999998	.	.	.	.	.	.	T	0.08638	-1.0712	3	.	.	.	.	10.7989	0.46476	0.153:0.2378:0.0:0.6092	rs3750800;rs17803381;rs3750800	.	.	.	L	40	.	.	R	-	2	0	ANK3	61538722	0.000000	0.05858	0.333000	0.25482	0.987000	0.75469	-2.374000	0.01072	-2.001000	0.00964	-0.251000	0.11542	CGG	C|0.791;A|0.209	0.209	strong		0.542	ANK3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048201.4	NM_020987	
INSRR	3645	hgsc.bcm.edu	37	1	156814027	156814027	+	Missense_Mutation	SNP	G	G	A	rs56252149	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:156814027G>A	ENST00000368195.3	-	15	3179	c.2783C>T	c.(2782-2784)cCt>cTt	p.P928L	NTRK1_ENST00000392302.2_Intron	NM_014215.2	NP_055030.1	P14616	INSRR_HUMAN	insulin receptor-related receptor	928			P -> L (in dbSNP:rs56252149). {ECO:0000269|PubMed:17344846}.		actin cytoskeleton reorganization (GO:0031532)|cellular response to alkaline pH (GO:0071469)|male sex determination (GO:0030238)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein autophosphorylation (GO:0046777)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.P928L(2)		breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(13)|ovary(7)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)	42	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)					GAGCCCCACAGGGGTGGCAGT	0.582													G|||	921	0.183906	0.2519	0.1816	5008	,	,		17644	0.1171		0.1441	False		,,,				2504	0.2035				p.P928L		Atlas-SNP	.											INSRR_ENST00000368195,NS,carcinoma,0,2	INSRR	309	2	2	Substitution - Missense(2)	stomach(2)	c.C2783T						PASS	.	G	,LEU/PRO	1067,3339	387.5+/-326.5	127,813,1263	82.0	79.0	80.0		,2783	5.2	1.0	1	dbSNP_129	80	1370,7230	266.0+/-286.5	115,1140,3045	no	intron,missense	INSRR,NTRK1	NM_001007792.1,NM_014215.2	,98	242,1953,4308	AA,AG,GG		15.9302,24.217,18.7375	,benign	,928/1298	156814027	2437,10569	2203	4300	6503	SO:0001583	missense	3645	exon15			CCCACAGGGGTGG	J05046	CCDS1160.1	1q21-q23	2013-02-11			ENSG00000027644	ENSG00000027644		"""Fibronectin type III domain containing"""	6093	protein-coding gene	gene with protein product		147671				2768234, 2249481	Standard	NM_014215		Approved	IRR	uc010pht.2	P14616	OTTHUMG00000041291	ENST00000368195.3:c.2783C>T	1.37:g.156814027G>A	ENSP00000357178:p.Pro928Leu	Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	44	25	0.568182	NM_014215	O60724|Q5VZS3	Missense_Mutation	SNP	ENST00000368195.3	37	CCDS1160.1	360	0.16483516483516483	113	0.22967479674796748	54	0.14917127071823205	75	0.13111888111888112	118	0.15567282321899736	G	5.060	0.196703	0.09599	0.24217	0.159302	ENSG00000027644	ENST00000368195	T	0.73258	-0.73	5.18	5.18	0.71444	.	0.000000	0.41938	D	0.000793	T	0.69151	0.3079	.	.	.	0.09310	P	0.999999854839	D	0.55172	0.97	P	0.59761	0.863	T	0.65869	-0.6063	8	0.15952	T	0.53	.	15.4079	0.74893	0.0:0.0:1.0:0.0	rs56252149	928	P14616	INSRR_HUMAN	L	928	ENSP00000357178:P928L	ENSP00000357178:P928L	P	-	2	0	INSRR	155080651	1.000000	0.71417	0.964000	0.40570	0.850000	0.48378	4.949000	0.63596	2.398000	0.81561	0.462000	0.41574	CCT	G|0.826;A|0.174	0.174	strong		0.582	INSRR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098929.1	NM_014215	
USH2A	7399	hgsc.bcm.edu	37	1	215960167	215960167	+	Missense_Mutation	SNP	T	T	G	rs10864198	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:215960167T>G	ENST00000307340.3	-	52	10618	c.10232A>C	c.(10231-10233)gAa>gCa	p.E3411A	USH2A_ENST00000366943.2_Missense_Mutation_p.E3411A	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	3411	Fibronectin type-III 19. {ECO:0000255|PROSITE-ProRule:PRU00316}.		E -> A (in dbSNP:rs10864198). {ECO:0000269|PubMed:17085681, ECO:0000269|PubMed:18273898}.		hair cell differentiation (GO:0035315)|inner ear receptor cell differentiation (GO:0060113)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|stereocilia ankle link complex (GO:0002142)|stereocilium bundle (GO:0032421)|stereocilium membrane (GO:0060171)	collagen binding (GO:0005518)|myosin binding (GO:0017022)			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)		GCCACAATGTTCTGTGGCTTC	0.458										HNSCC(13;0.011)			G|||	2948	0.588658	0.7057	0.4899	5008	,	,		17203	0.6518		0.5358	False		,,,				2504	0.4898				p.E3411A		Atlas-SNP	.											.	USH2A	1168	.	0			c.A10232C						PASS	.	G	ALA/GLU	2959,1447	468.1+/-355.0	1004,951,248	64.0	60.0	61.0		10232	4.9	0.2	1	dbSNP_120	61	4462,4138	563.2+/-388.1	1153,2156,991	yes	missense	USH2A	NM_206933.2	107	2157,3107,1239	GG,GT,TT		48.1163,32.8416,42.9417	benign	3411/5203	215960167	7421,5585	2203	4300	6503	SO:0001583	missense	7399	exon52			CAATGTTCTGTGG	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.10232A>C	1.37:g.215960167T>G	ENSP00000305941:p.Glu3411Ala	Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	112	49	0.4375	NM_206933	Q5VVM9|Q6S362|Q9NS27	Missense_Mutation	SNP	ENST00000307340.3	37	CCDS31025.1	1313	0.6011904761904762	346	0.7032520325203252	182	0.5027624309392266	383	0.6695804195804196	402	0.5303430079155673	G	0.015	-1.570097	0.00895	0.671584	0.518837	ENSG00000042781	ENST00000307340;ENST00000366943	T;T	0.07327	3.21;3.2	4.88	4.88	0.63580	Fibronectin, type III (3);	0.000000	0.44688	N	0.000427	T	0.00012	0.0000	N	0.00077	-2.24	0.58432	P	5.000000000032756E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.37572	-0.9700	9	0.02654	T	1	.	13.0708	0.59059	0.0:0.0:0.8389:0.1611	rs10864198;rs52802661;rs59777001;rs10864198	3411	O75445	USH2A_HUMAN	A	3411	ENSP00000305941:E3411A;ENSP00000355910:E3411A	ENSP00000305941:E3411A	E	-	2	0	USH2A	214026790	0.996000	0.38824	0.163000	0.22734	0.037000	0.13140	2.598000	0.46223	1.040000	0.40099	-0.121000	0.15023	GAA	T|0.409;G|0.591	0.591	strong		0.458	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123	
KIAA1524	57650	hgsc.bcm.edu	37	3	108295135	108295135	+	Missense_Mutation	SNP	G	G	T	rs116097126	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:108295135G>T	ENST00000295746.8	-	8	953	c.877C>A	c.(877-879)Cct>Act	p.P293T	SNORA70_ENST00000365509.1_RNA|KIAA1524_ENST00000487834.1_5'UTR|KIAA1524_ENST00000491772.1_Missense_Mutation_p.P134T	NM_020890.2	NP_065941.2	Q8TCG1	CIP2A_HUMAN	KIAA1524	293					positive regulation of neural precursor cell proliferation (GO:2000179)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(21)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						GAGGAATCAGGATCCTTTCCA	0.274													G|||	21	0.00419329	0.0008	0.0029	5008	,	,		15885	0.0		0.0119	False		,,,				2504	0.0061				p.P293T		Atlas-SNP	.											.	KIAA1524	82	.	0			c.C877A						PASS	.	G	THR/PRO	13,4389	19.1+/-41.9	0,13,2188	75.0	85.0	82.0		877	5.9	1.0	3	dbSNP_132	82	166,8422	76.9+/-139.5	1,164,4129	yes	missense	KIAA1524	NM_020890.2	38	1,177,6317	TT,TG,GG		1.9329,0.2953,1.378	benign	293/906	108295135	179,12811	2201	4294	6495	SO:0001583	missense	57650	exon8			AATCAGGATCCTT	AB040957	CCDS33812.1	3q13.13	2014-01-14			ENSG00000163507	ENSG00000163507			29302	protein-coding gene	gene with protein product	"""cancerous inhibitor of protein phosphatase 2A"""	610643				10819331, 24214971	Standard	NM_020890		Approved	CIP2A	uc003dxb.4	Q8TCG1	OTTHUMG00000159233	ENST00000295746.8:c.877C>A	3.37:g.108295135G>T	ENSP00000295746:p.Pro293Thr	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	105	58	0.552381	NM_020890	A1L4J7|B9EGC3|Q6P4G6|Q8WVP8|Q96PI2|Q9H9C6|Q9P204	Missense_Mutation	SNP	ENST00000295746.8	37	CCDS33812.1	12	0.005494505494505495	0	0.0	1	0.0027624309392265192	0	0.0	11	0.014511873350923483	G	15.43	2.831783	0.50845	0.002953	0.019329	ENSG00000163507	ENST00000491772;ENST00000295746	T;T	0.53423	0.62;1.23	5.91	5.91	0.95273	Armadillo-type fold (1);	0.047597	0.85682	D	0.000000	T	0.30262	0.0759	L	0.45581	1.43	0.80722	D	1	P	0.46327	0.876	B	0.43123	0.409	T	0.19484	-1.0304	10	0.42905	T	0.14	-18.7618	16.5332	0.84366	0.0:0.1304:0.8696:0.0	.	293	Q8TCG1	CIP2A_HUMAN	T	134;293	ENSP00000419487:P134T;ENSP00000295746:P293T	ENSP00000295746:P293T	P	-	1	0	KIAA1524	109777825	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	3.847000	0.55895	2.802000	0.96397	0.655000	0.94253	CCT	G|0.987;T|0.013	0.013	strong		0.274	KIAA1524-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353975.2	NM_020890	
GHR	2690	hgsc.bcm.edu	37	5	42719344	42719344	+	Missense_Mutation	SNP	C	C	A	rs6184	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:42719344C>A	ENST00000230882.4	+	10	1925	c.1735C>A	c.(1735-1737)Cct>Act	p.P579T	GHR_ENST00000537449.1_Missense_Mutation_p.P392T|GHR_ENST00000357703.3_Missense_Mutation_p.P557T	NM_000163.4|NM_001242399.2|NM_001242400.2|NM_001242401.3|NM_001242402.2|NM_001242403.2|NM_001242404.2|NM_001242405.2|NM_001242406.2	NP_000154.1|NP_001229328.1|NP_001229329.1|NP_001229330.1|NP_001229331.1|NP_001229332.1|NP_001229333.1|NP_001229334.1|NP_001229335.1	P10912	GHR_HUMAN	growth hormone receptor	579			P -> T (in dbSNP:rs6184). {ECO:0000269|PubMed:10391209}.		2-oxoglutarate metabolic process (GO:0006103)|activation of JAK2 kinase activity (GO:0042977)|activation of MAPK activity (GO:0000187)|allantoin metabolic process (GO:0000255)|cellular response to hormone stimulus (GO:0032870)|citrate metabolic process (GO:0006101)|creatine metabolic process (GO:0006600)|creatinine metabolic process (GO:0046449)|endocytosis (GO:0006897)|fatty acid metabolic process (GO:0006631)|growth hormone receptor signaling pathway (GO:0060396)|insulin-like growth factor receptor signaling pathway (GO:0048009)|isoleucine metabolic process (GO:0006549)|JAK-STAT cascade (GO:0007259)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|multicellular organismal metabolic process (GO:0044236)|oxaloacetate metabolic process (GO:0006107)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|receptor internalization (GO:0031623)|regulation of multicellular organism growth (GO:0040014)|response to cycloheximide (GO:0046898)|response to estradiol (GO:0032355)|succinate metabolic process (GO:0006105)|taurine metabolic process (GO:0019530)|valine metabolic process (GO:0006573)	cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|growth hormone receptor complex (GO:0070195)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	cytokine receptor activity (GO:0004896)|growth factor binding (GO:0019838)|peptide hormone binding (GO:0017046)|proline-rich region binding (GO:0070064)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)			NS(2)|endometrium(2)|kidney(3)|large_intestine(8)|lung(19)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	39		Myeloproliferative disorder(839;0.00878)			Pegvisomant(DB00082)|Somatropin recombinant(DB00052)	TGCTGGGAGGCCTGGGACAGG	0.498													C|||	377	0.0752796	0.0	0.0245	5008	,	,		22184	0.1518		0.005	False		,,,				2504	0.2065				p.P586T		Atlas-SNP	.											GHR,NS,carcinoma,-2,1	GHR	94	1	0			c.C1756A	GRCh37	CM930317	GHR	M	rs6184	PASS	.	C	THR/PRO,THR/PRO,THR/PRO,THR/PRO,THR/PRO,THR/PRO,THR/PRO,THR/PRO,THR/PRO,THR/PRO,,	21,4385	28.1+/-56.4	0,21,2182	98.0	82.0	88.0		1735,1756,1735,1735,1735,1735,1735,1735,1735,1669,,	2.4	0.1	5	dbSNP_52	88	74,8526	43.6+/-101.6	0,74,4226	yes	missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,utr-3,utr-3	GHR	NM_000163.4,NM_001242399.2,NM_001242400.2,NM_001242401.3,NM_001242402.2,NM_001242403.2,NM_001242404.2,NM_001242405.2,NM_001242406.2,NM_001242460.1,NM_001242461.1,NM_001242462.1	38,38,38,38,38,38,38,38,38,38,,	0,95,6408	AA,AC,CC		0.8605,0.4766,0.7304	benign,benign,benign,benign,benign,benign,benign,benign,benign,benign,,	579/639,586/646,579/639,579/639,579/639,579/639,579/639,579/639,579/639,557/617,,	42719344	95,12911	2203	4300	6503	SO:0001583	missense	2690	exon10			GGGAGGCCTGGGA		CCDS3940.1, CCDS56364.1, CCDS75239.1, CCDS75240.1	5p14-p12	2013-03-25			ENSG00000112964	ENSG00000112964		"""Fibronectin type III domain containing"""	4263	protein-coding gene	gene with protein product	"""growth hormone binding protein"""	600946					Standard	NM_001242460		Approved	GHBP	uc003jmt.3	P10912	OTTHUMG00000094791	ENST00000230882.4:c.1735C>A	5.37:g.42719344C>A	ENSP00000230882:p.Pro579Thr	Somatic	227	1	0.00440529		WXS	Illumina HiSeq	Phase_I	249	155	0.62249	NM_001242399	Q9HCX2	Missense_Mutation	SNP	ENST00000230882.4	37	CCDS3940.1	82	0.037545787545787544	0	0.0	10	0.027624309392265192	70	0.12237762237762238	2	0.002638522427440633	C	7.106	0.575012	0.13623	0.004766	0.008605	ENSG00000112964	ENST00000230882;ENST00000357703;ENST00000537449	T;T;T	0.35048	1.33;1.33;1.33	6.08	2.37	0.29283	.	0.369353	0.35096	N	0.003451	T	0.00384	0.0012	L	0.42245	1.32	0.09310	N	1	B	0.13145	0.007	B	0.26416	0.069	T	0.12502	-1.0545	10	0.62326	D	0.03	-4.7662	4.875	0.13651	0.0:0.347:0.1573:0.4957	rs6184;rs52809181;rs58748130;rs6184	579	P10912	GHR_HUMAN	T	579;557;392	ENSP00000230882:P579T;ENSP00000350335:P557T;ENSP00000442206:P392T	ENSP00000230882:P579T	P	+	1	0	GHR	42755101	0.002000	0.14202	0.081000	0.20488	0.713000	0.41058	-0.169000	0.09911	0.167000	0.19631	-0.469000	0.05056	CCT	C|0.974;A|0.026	0.026	strong		0.498	GHR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211605.2	NM_000163	
CDHR5	53841	hgsc.bcm.edu	37	11	617378	617378	+	Silent	SNP	C	C	T	rs61877856	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:617378C>T	ENST00000358353.3	-	16	2833	c.2511G>A	c.(2509-2511)gcG>gcA	p.A837A	IRF7_ENST00000397562.3_5'Flank|IRF7_ENST00000397574.2_5'Flank|CDHR5_ENST00000397542.2_Silent_p.A837A|IRF7_ENST00000348655.6_5'Flank|IRF7_ENST00000397566.1_5'Flank|IRF7_ENST00000525445.1_5'Flank|IRF7_ENST00000397570.1_5'Flank|CDHR5_ENST00000349570.7_Silent_p.A643A|IRF7_ENST00000330243.5_5'Flank			Q9HBB8	CDHR5_HUMAN	cadherin-related family member 5	837					cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(7)|ovary(1)|skin(2)	23						CACCACCGGGCGCATCGTAGG	0.706													C|||	1388	0.277157	0.5855	0.304	5008	,	,		10933	0.0208		0.2704	False		,,,				2504	0.1125				p.A837A		Atlas-SNP	.											.	CDHR5	77	.	0			c.G2511A						PASS	.	C	,,	2267,2125		589,1089,518	27.0	25.0	26.0		2493,2511,1929	-0.5	0.0	11	dbSNP_129	26	2500,6094		364,1772,2161	no	coding-synonymous,coding-synonymous,coding-synonymous	CDHR5	NM_001171968.1,NM_021924.4,NM_031264.3	,,	953,2861,2679	TT,TC,CC		29.0901,48.3834,36.7088	,,	831/840,837/846,643/652	617378	4767,8219	2196	4297	6493	SO:0001819	synonymous_variant	53841	exon15			ACCGGGCGCATCG	AF258675	CCDS7707.1, CCDS7708.1	11p15.5	2011-07-01	2010-01-25	2010-01-25	ENSG00000099834	ENSG00000099834		"""Cadherins / Cadherin-related"""	7521	protein-coding gene	gene with protein product		606839	"""mucin and cadherin-like"", ""mucin-like protocadherin"""	MUCDHL, MUPCDH		11031102, 10801787	Standard	NM_021924		Approved	FLJ20219, MU-PCDH	uc001lqj.3	Q9HBB8	OTTHUMG00000132018	ENST00000358353.3:c.2511G>A	11.37:g.617378C>T		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	76	52	0.684211	NM_021924	C9J7X1|Q9H746|Q9HAU3|Q9HBB5|Q9HBB6|Q9HBB7|Q9NX86|Q9NXI9	Silent	SNP	ENST00000358353.3	37	CCDS7707.1																																																																																			C|0.680;T|0.320	0.320	strong		0.706	CDHR5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255023.2	NM_021924	
MICA	100507436	hgsc.bcm.edu	37	6	31380153	31380153	+	Missense_Mutation	SNP	T	T	C	rs199843678	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:31380153T>C	ENST00000449934.2	+	5	998	c.944T>C	c.(943-945)gTt>gCt	p.V315A	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)				GTTTCTGCTGTTGCTGCTGGC	0.458																																					p.V315A		Atlas-SNP	.											MICA,uveal_tract,malignant_melanoma,0,1	MICA	21	1	0			c.T944C						scavenged	.						288.0	263.0	270.0					6																	31380153		692	1591	2283	SO:0001583	missense	100507436	exon5			CTGCTGTTGCTGC	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.944T>C	6.37:g.31380153T>C	ENSP00000413079:p.Val315Ala	Somatic	139	3	0.0215827		WXS	Illumina HiSeq	Phase_I	81	7	0.0864198	NM_001177519		Missense_Mutation	SNP	ENST00000449934.2	37	CCDS56412.1	.	.	.	.	.	.	.	.	.	.	-	2.519	-0.311081	0.05458	.	.	ENSG00000204520	ENST00000376222;ENST00000364810;ENST00000399172;ENST00000449934;ENST00000421350	T;T	0.01203	5.61;5.18	1.55	-2.91	0.05631	.	.	.	.	.	T	0.00178	0.0005	N	0.01352	-0.895	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.27226	-1.0080	9	0.38643	T	0.18	.	6.6027	0.22708	0.0:0.3216:0.0:0.6784	.	177;315	Q5SS58;Q96QC4	.;.	A	177;315;272;315;206	ENSP00000413079:V315A;ENSP00000402410:V206A	ENSP00000365394:V315A	V	+	2	0	MICA	31488132	0.000000	0.05858	0.000000	0.03702	0.111000	0.19643	-3.279000	0.00529	-0.980000	0.03524	-0.576000	0.04144	GTT	T|0.973;C|0.027	0.027	strong		0.458	MICA-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076101.7	NM_001177519	
KDELC1	79070	hgsc.bcm.edu	37	13	103450973	103450973	+	Silent	SNP	T	T	C	rs7994595	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:103450973T>C	ENST00000376004.4	-	1	384	c.48A>G	c.(46-48)ccA>ccG	p.P16P	BIVM_ENST00000448849.2_5'Flank|KDELC1_ENST00000460338.1_5'UTR|BIVM_ENST00000257336.1_5'Flank|BIVM_ENST00000419638.1_5'Flank	NM_024089.2	NP_076994.2	Q6UW63	KDEL1_HUMAN	KDEL (Lys-Asp-Glu-Leu) containing 1	16						endoplasmic reticulum lumen (GO:0005788)				central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(9)|ovary(1)|prostate(1)|skin(1)	19	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.211)					CGGCGAGTGCTGGAACTGTCG	0.522													T|||	428	0.0854633	0.1513	0.0231	5008	,	,		16117	0.1121		0.0507	False		,,,				2504	0.0491				p.P16P		Atlas-SNP	.											.	KDELC1	66	.	0			c.A48G						PASS	.	T		587,3819	257.4+/-261.8	41,505,1657	58.0	58.0	58.0		48	-0.4	0.3	13	dbSNP_116	58	337,8263	116.3+/-176.0	9,319,3972	no	coding-synonymous	KDELC1	NM_024089.2		50,824,5629	CC,CT,TT		3.9186,13.3227,7.1044		16/503	103450973	924,12082	2203	4300	6503	SO:0001819	synonymous_variant	79070	exon1			GAGTGCTGGAACT	BC001297	CCDS9504.1	13q33	2010-11-18			ENSG00000134901	ENSG00000134901			19350	protein-coding gene	gene with protein product		611613					Standard	NM_024089		Approved	MGC5302, EP58	uc001vpq.4	Q6UW63	OTTHUMG00000017307	ENST00000376004.4:c.48A>G	13.37:g.103450973T>C		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	45	22	0.488889	NM_024089	Q53HL3|Q9BVD2	Silent	SNP	ENST00000376004.4	37	CCDS9504.1																																																																																			T|0.916;C|0.084	0.084	strong		0.522	KDELC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045699.1		
RELN	5649	hgsc.bcm.edu	37	7	103162607	103162607	+	Silent	SNP	G	G	A	rs2075038	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:103162607G>A	ENST00000428762.1	-	48	7689	c.7530C>T	c.(7528-7530)ccC>ccT	p.P2510P	RELN_ENST00000424685.2_Silent_p.P2510P|RELN_ENST00000343529.5_Silent_p.P2510P	NM_005045.3	NP_005036.2	P78509	RELN_HUMAN	reelin	2510					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)		GAGAGGTCTCGGGGTCATCAC	0.512													G|||	296	0.0591054	0.0348	0.0418	5008	,	,		17150	0.0258		0.0348	False		,,,				2504	0.1636				p.P2510P	NSCLC(146;835 1944 15585 22231 52158)	Atlas-SNP	.											.	RELN	593	.	0			c.C7530T						PASS	.	G	,	132,4274	95.3+/-134.0	2,128,2073	100.0	85.0	90.0		7530,7530	-11.1	0.1	7	dbSNP_96	90	310,8290	111.6+/-171.8	5,300,3995	no	coding-synonymous,coding-synonymous	RELN	NM_005045.3,NM_173054.2	,	7,428,6068	AA,AG,GG		3.6047,2.9959,3.3984	,	2510/3461,2510/3459	103162607	442,12564	2203	4300	6503	SO:0001819	synonymous_variant	5649	exon48			GGTCTCGGGGTCA		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.7530C>T	7.37:g.103162607G>A		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	100	47	0.47	NM_173054	A4D0P9|A4D0Q0|Q86UJ0|Q86UJ8|Q8NDV0|Q9UDQ2	Silent	SNP	ENST00000428762.1	37	CCDS47680.1																																																																																			G|0.964;A|0.036	0.036	strong		0.512	RELN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348148.1	NM_005045	
SYCP2L	221711	hgsc.bcm.edu	37	6	10906256	10906256	+	Silent	SNP	A	A	G	rs4713039	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:10906256A>G	ENST00000283141.6	+	9	941	c.645A>G	c.(643-645)aaA>aaG	p.K215K	RP11-637O19.3_ENST00000480294.1_3'UTR|SYCP2L_ENST00000543878.1_Silent_p.K56K	NM_001040274.2	NP_001035364.2	Q5T4T6	SYC2L_HUMAN	synaptonemal complex protein 2-like	215						nucleus (GO:0005634)				breast(3)|central_nervous_system(1)|kidney(4)|large_intestine(10)|lung(12)|ovary(1)|skin(3)|stomach(1)|urinary_tract(1)	36	Breast(50;0.0838)|Ovarian(93;0.107)	all_hematologic(90;0.135)	Epithelial(50;0.239)			GTTTCAGGAAAGACCTTGCAA	0.313													A|||	982	0.196086	0.034	0.1066	5008	,	,		16888	0.377		0.1879	False		,,,				2504	0.3006				p.K215K		Atlas-SNP	.											.	SYCP2L	101	.	0			c.A645G						PASS	.	A		187,3437		3,181,1628	151.0	152.0	151.0		645	-3.0	0.7	6	dbSNP_111	151	1581,6577		151,1279,2649	no	coding-synonymous	SYCP2L	NM_001040274.2		154,1460,4277	GG,GA,AA		19.3797,5.16,15.0059		215/813	10906256	1768,10014	1812	4079	5891	SO:0001819	synonymous_variant	221711	exon9			CAGGAAAGACCTT	AK128130	CCDS43423.1	6p24.2	2008-11-06	2007-07-02	2007-07-02	ENSG00000153157	ENSG00000153157			21537	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 177"""	C6orf177			Standard	NM_001040274		Approved	dJ62D2.1, NO145	uc003mzo.3	Q5T4T6	OTTHUMG00000014250	ENST00000283141.6:c.645A>G	6.37:g.10906256A>G		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	51	32	0.627451	NM_001040274	A6NDS5|Q08GK5|Q6ZRM2|Q96EJ2	Silent	SNP	ENST00000283141.6	37	CCDS43423.1																																																																																			A|0.797;G|0.202	0.202	strong		0.313	SYCP2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039845.3	NM_194299	
AHNAK2	113146	hgsc.bcm.edu	37	14	105417766	105417766	+	Missense_Mutation	SNP	G	G	A	rs2396457	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:105417766G>A	ENST00000333244.5	-	7	4141	c.4022C>T	c.(4021-4023)tCt>tTt	p.S1341F	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	1341						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)			GCCTGGGGCAGACACCCCGAA	0.607													.|||	1575	0.314497	0.5658	0.1225	5008	,	,		13647	0.2937		0.1004	False		,,,				2504	0.3528				p.S1341F		Atlas-SNP	.											.	AHNAK2	719	.	0			c.C4022T						PASS	.	G	PHE/SER	105,3549		16,73,1738	128.0	119.0	122.0		4022	3.4	0.0	14	dbSNP_100	122	18,6534		1,16,3259	no	missense	AHNAK2	NM_138420.2	155	17,89,4997	AA,AG,GG		0.2747,2.8736,1.2052	probably-damaging	1341/5796	105417766	123,10083	1827	3276	5103	SO:0001583	missense	113146	exon7			GGGGCAGACACCC	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.4022C>T	14.37:g.105417766G>A	ENSP00000353114:p.Ser1341Phe	Somatic	0	0	.		WXS	Illumina HiSeq	Phase_I	63	63	1	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	453	0.20741758241758243	248	0.5040650406504065	43	0.11878453038674033	130	0.22727272727272727	32	0.04221635883905013	-	14.71	2.616236	0.46631	0.028736	0.002747	ENSG00000185567	ENST00000333244	T	0.00753	5.74	4.31	3.4	0.38934	.	.	.	.	.	T	0.00012	0.0000	M	0.92122	3.275	0.80722	P	0.0	D	0.89917	1.0	D	0.76575	0.988	T	0.33471	-0.9867	8	0.48119	T	0.1	-6.8464	12.9494	0.58391	0.0:0.0:0.8363:0.1637	.	1341	Q8IVF2	AHNK2_HUMAN	F	1341	ENSP00000353114:S1341F	ENSP00000353114:S1341F	S	-	2	0	AHNAK2	104488811	0.695000	0.27747	0.002000	0.10522	0.000000	0.00434	3.065000	0.49994	0.791000	0.33826	-0.500000	0.04577	TCT	G|0.824;A|0.176	0.176	strong		0.607	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
THBS1	7057	hgsc.bcm.edu	37	15	39880822	39880822	+	Missense_Mutation	SNP	A	A	G	rs2292305	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:39880822A>G	ENST00000260356.5	+	10	1732	c.1567A>G	c.(1567-1569)Aca>Gca	p.T523A		NM_003246.2	NP_003237.2	P07996	TSP1_HUMAN	thrombospondin 1	523	TSP type-1 3. {ECO:0000255|PROSITE- ProRule:PRU00210}.		T -> A (in dbSNP:rs2292305). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:2918029}.		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)	p.T523A(1)		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)		CAACAACCCCACACCCCAGTT	0.542													A|||	1375	0.274561	0.4644	0.1412	5008	,	,		20016	0.3056		0.1312	False		,,,				2504	0.228				p.T523A		Atlas-SNP	.											THBS1,NS,carcinoma,0,1	THBS1	106	1	1	Substitution - Missense(1)	stomach(1)	c.A1567G						PASS	.	A	ALA/THR	1785,2615	527.1+/-372.1	368,1049,783	91.0	87.0	89.0		1567	-2.5	0.6	15	dbSNP_100	89	1134,7460	232.9+/-266.4	64,1006,3227	yes	missense	THBS1	NM_003246.2	58	432,2055,4010	GG,GA,AA		13.1953,40.5682,22.4642	benign	523/1171	39880822	2919,10075	2200	4297	6497	SO:0001583	missense	7057	exon10			AACCCCACACCCC		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.1567A>G	15.37:g.39880822A>G	ENSP00000260356:p.Thr523Ala	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	72	37	0.513889	NM_003246	A8K6H4|B4E3J7|B9EGH6|Q15667|Q59E99	Missense_Mutation	SNP	ENST00000260356.5	37	CCDS32194.1	553	0.2532051282051282	216	0.43902439024390244	54	0.14917127071823205	190	0.3321678321678322	93	0.12269129287598944	A	8.764	0.924339	0.18056	0.405682	0.131953	ENSG00000137801	ENST00000260356	T	0.60040	0.22	5.87	-2.47	0.06442	.	0.716432	0.11505	N	0.557327	T	0.00012	0.0000	N	0.00436	-1.5	0.43953	P	0.0033800000000000496	B	0.02656	0.0	B	0.01281	0.0	T	0.32428	-0.9907	9	0.06365	T	0.9	4.0151	7.117	0.25423	0.3584:0.2348:0.4067:0.0	rs2292305;rs58566849;rs2292305	523	P07996	TSP1_HUMAN	A	523	ENSP00000260356:T523A	ENSP00000260356:T523A	T	+	1	0	THBS1	37668114	0.000000	0.05858	0.617000	0.29091	0.985000	0.73830	0.374000	0.20501	-0.734000	0.04843	-0.993000	0.02533	ACA	A|0.756;G|0.244	0.244	strong		0.542	THBS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257831.2	NM_003246	
SIX5	147912	hgsc.bcm.edu	37	19	46268902	46268902	+	Missense_Mutation	SNP	C	C	T	rs2341097	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:46268902C>T	ENST00000317578.6	-	3	2458	c.2077G>A	c.(2077-2079)Gtg>Atg	p.V693M	AC074212.6_ENST00000590076.1_RNA|AC074212.5_ENST00000559756.1_RNA|SIX5_ENST00000560168.1_3'UTR|AC074212.5_ENST00000592217.2_RNA	NM_175875.4	NP_787071	Q8N196	SIX5_HUMAN	SIX homeobox 5	693			V -> M (in dbSNP:rs2341097).		lens development in camera-type eye (GO:0002088)|negative regulation of cell proliferation (GO:0008285)|regulation of transcription, DNA-templated (GO:0006355)|spermatid development (GO:0007286)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			endometrium(1)|large_intestine(2)|lung(2)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	8		Ovarian(192;0.0308)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.00783)|GBM - Glioblastoma multiforme(486;0.0802)|Epithelial(262;0.235)		AGCCTCAGCACGGTGTGGGGG	0.682													C|||	1493	0.298123	0.3298	0.2305	5008	,	,		15903	0.2937		0.3231	False		,,,				2504	0.2822				p.V693M		Atlas-SNP	.											SIX5,NS,carcinoma,0,1	SIX5	35	1	0			c.G2077A						PASS	.	C	MET/VAL	1342,3064	415.4+/-337.2	214,914,1075	34.0	40.0	38.0		2077	3.1	0.8	19	dbSNP_100	38	3127,5471	449.9+/-362.2	577,1973,1749	yes	missense	SIX5	NM_175875.4	21	791,2887,2824	TT,TC,CC		36.3689,30.4585,34.3663	possibly-damaging	693/740	46268902	4469,8535	2203	4299	6502	SO:0001583	missense	147912	exon3			TCAGCACGGTGTG	L08835	CCDS12673.1	19q13.32	2011-06-20	2007-07-13			ENSG00000177045		"""Homeoboxes / SINE class"""	10891	protein-coding gene	gene with protein product		600963	"""sine oculis homeobox (Drosophila) homolog 5"", ""sine oculis homeobox homolog 5 (Drosophila)"""	DMAHP		8595416	Standard	NM_175875		Approved		uc002pdb.3	Q8N196		ENST00000317578.6:c.2077G>A	19.37:g.46268902C>T	ENSP00000316842:p.Val693Met	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	123	61	0.495935	NM_175875		Missense_Mutation	SNP	ENST00000317578.6	37	CCDS12673.1	635	0.2907509157509158	148	0.3008130081300813	100	0.27624309392265195	138	0.24125874125874125	249	0.32849604221635886	c	10.08	1.253473	0.22965	0.304585	0.363689	ENSG00000177045	ENST00000317578	D	0.91295	-2.82	4.24	3.14	0.36123	.	1.198060	0.06087	N	0.663052	T	0.00012	0.0000	N	0.08118	0	0.44635	P	0.0023849999999999705	P	0.38420	0.63	B	0.33750	0.169	T	0.04140	-1.0974	9	0.59425	D	0.04	-4.6308	9.0942	0.36629	0.0:0.7536:0.2464:0.0	rs2341097;rs17846041;rs17859030;rs57436149;rs2341097	693	Q8N196	SIX5_HUMAN	M	693	ENSP00000316842:V693M	ENSP00000316842:V693M	V	-	1	0	SIX5	50960742	0.430000	0.25538	0.843000	0.33291	0.480000	0.33159	0.682000	0.25335	2.199000	0.70637	0.561000	0.74099	GTG	C|0.678;T|0.322	0.322	strong		0.682	SIX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417341.3	NM_175875	
DLC1	10395	hgsc.bcm.edu	37	8	12957475	12957475	+	Missense_Mutation	SNP	C	C	T	rs532841	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:12957475C>T	ENST00000276297.4	-	9	2780	c.2371G>A	c.(2371-2373)Gtg>Atg	p.V791M	DLC1_ENST00000358919.2_Missense_Mutation_p.V354M|DLC1_ENST00000512044.2_Missense_Mutation_p.V388M|DLC1_ENST00000520226.1_Missense_Mutation_p.V280M	NM_182643.2	NP_872584.2	Q96QB1	RHG07_HUMAN	DLC1 Rho GTPase activating protein	791	Focal adhesion-targeting (FAT).		V -> M (in dbSNP:rs532841). {ECO:0000269|PubMed:10649492, ECO:0000269|PubMed:11214970, ECO:0000269|PubMed:14702039, ECO:0000269|Ref.2, ECO:0000269|Ref.3}.		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)	p.V791M(1)		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						TTCTGCTCCACCACGTTGTTA	0.527													T|||	2487	0.496605	0.6089	0.3847	5008	,	,		20867	0.3363		0.495	False		,,,				2504	0.591				p.V791M		Atlas-SNP	.											DLC1,NS,carcinoma,0,1	DLC1	411	1	1	Substitution - Missense(1)	stomach(1)	c.G2371A						PASS	.	T	MET/VAL,MET/VAL,MET/VAL	2595,1811	530.8+/-373.0	768,1059,376	96.0	90.0	92.0		838,1060,2371	-6.1	0.0	8	dbSNP_83	92	4236,4364	581.8+/-391.3	1035,2166,1099	yes	missense,missense,missense	DLC1	NM_001164271.1,NM_006094.4,NM_182643.2	21,21,21	1803,3225,1475	TT,TC,CC		49.2558,41.103,47.4781	benign,benign,benign	280/1018,354/1092,791/1529	12957475	6831,6175	2203	4300	6503	SO:0001583	missense	10395	exon9			GCTCCACCACGTT	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.2371G>A	8.37:g.12957475C>T	ENSP00000276297:p.Val791Met	Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	21	21	1	NM_182643	B4DR10|B8PTI0|E9PDZ8|E9PF76|E9PGY9|O14868|O43199|Q7Z5R8|Q86UC6|Q9C0E0|Q9H7A2	Missense_Mutation	SNP	ENST00000276297.4	37	CCDS5989.1	1035	0.4739010989010989	299	0.6077235772357723	157	0.43370165745856354	210	0.36713286713286714	369	0.4868073878627968	T	5.482	0.273981	0.10403	0.58897	0.492558	ENSG00000164741	ENST00000276297;ENST00000358919;ENST00000512044;ENST00000520226	T;T;T;T	0.05649	3.64;3.41;3.41;3.41	4.23	-6.1	0.02138	.	0.850997	0.11061	N	0.604004	T	0.00012	0.0000	N	0.02539	-0.55	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.0;0.001;0.0	T	0.39078	-0.9631	9	0.38643	T	0.18	.	11.1358	0.48373	0.0:0.5335:0.1626:0.3039	rs532841;rs3183774;rs3739299;rs61158109;rs532841	791;388;354	Q96QB1;E9PDZ8;Q96QB1-1	RHG07_HUMAN;.;.	M	791;354;388;280	ENSP00000276297:V791M;ENSP00000351797:V354M;ENSP00000422595:V388M;ENSP00000428028:V280M	ENSP00000276297:V791M	V	-	1	0	DLC1	13001846	0.000000	0.05858	0.001000	0.08648	0.716000	0.41182	-0.575000	0.05861	-1.397000	0.02068	-1.197000	0.01672	GTG	C|0.490;T|0.510	0.510	strong		0.527	DLC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207632.2	NM_182643, NM_006094	
CFAP57	149465	hgsc.bcm.edu	37	1	43675467	43675467	+	Silent	SNP	G	G	A	rs2453412	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:43675467G>A	ENST00000372492.4	+	11	2133	c.1809G>A	c.(1807-1809)tcG>tcA	p.S603S	WDR65_ENST00000528956.1_Silent_p.S603S	NM_001195831.2	NP_001182760.2	Q96MR6	WDR65_HUMAN		603										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)				TTGTCATCTCGCATTCTGGAC	0.552													g|||	3480	0.694888	0.5408	0.6772	5008	,	,		19671	0.6786		0.8877	False		,,,				2504	0.7342				p.S603S		Atlas-SNP	.											.	WDR65	76	.	0			c.G1809A						PASS	.	G	,,	2529,1877	630.7+/-395.5	718,1093,392	163.0	131.0	142.0		1809,1809,1809	-11.5	0.4	1	dbSNP_100	142	7532,1068	769.7+/-407.6	3298,936,66	no	coding-synonymous,coding-synonymous,coding-synonymous	WDR65	NM_001167965.1,NM_001167966.1,NM_152498.3	,,	4016,2029,458	AA,AG,GG		12.4186,42.601,22.6434	,,	603/699,603/699,603/699	43675467	10061,2945	2203	4300	6503	SO:0001819	synonymous_variant	149465	exon11			CATCTCGCATTCT																												ENST00000372492.4:c.1809G>A	1.37:g.43675467G>A		Somatic	208	0	0		WXS	Illumina HiSeq	Phase_I	144	142	0.986111	NM_152498	A6NKQ3|Q17RI9|Q5TAI0	Silent	SNP	ENST00000372492.4	37																																																																																				G|0.250;A|0.750	0.750	strong		0.552	WDR65-002	NOVEL	not_organism_supported|basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000384325.1		
TLN2	83660	hgsc.bcm.edu	37	15	63125804	63125804	+	Silent	SNP	G	G	A	rs142793310	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:63125804G>A	ENST00000561311.1	+	54	7334	c.7104G>A	c.(7102-7104)caG>caA	p.Q2368Q	RP11-1069G10.1_ENST00000558404.1_RNA|RP11-1069G10.1_ENST00000558888.1_RNA|TLN2_ENST00000306829.6_Silent_p.Q2368Q			Q9Y4G6	TLN2_HUMAN	talin 2	2368	I/LWEQ. {ECO:0000255|PROSITE- ProRule:PRU00292}.				cell adhesion (GO:0007155)|cell-cell junction assembly (GO:0007043)|cytoskeletal anchoring at plasma membrane (GO:0007016)	actin cytoskeleton (GO:0015629)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|synapse (GO:0045202)	actin binding (GO:0003779)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			NS(3)|breast(6)|central_nervous_system(3)|endometrium(8)|kidney(8)|large_intestine(20)|lung(34)|ovary(6)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)	99						CAGCAGCCCAGAGGGAGCTGG	0.577																																					p.Q2368Q		Atlas-SNP	.											.	TLN2	253	.	0			c.G7104A						PASS	.	G		0,4406		0,0,2203	77.0	77.0	77.0		7104	5.1	1.0	15	dbSNP_134	77	7,8593	6.4+/-24.3	0,7,4293	no	coding-synonymous	TLN2	NM_015059.2		0,7,6496	AA,AG,GG		0.0814,0.0,0.0538		2368/2543	63125804	7,12999	2203	4300	6503	SO:0001819	synonymous_variant	83660	exon52			AGCCCAGAGGGAG	AB002318	CCDS32261.1	15q15-q21	2008-07-03			ENSG00000171914	ENSG00000171914			15447	protein-coding gene	gene with protein product		607349				9205841, 11527381	Standard	NM_015059		Approved	KIAA0320, ILWEQ	uc002alb.4	Q9Y4G6	OTTHUMG00000133679	ENST00000561311.1:c.7104G>A	15.37:g.63125804G>A		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	84	24	0.285714	NM_015059	A6NLB8	Silent	SNP	ENST00000561311.1	37	CCDS32261.1																																																																																			G|1.000;A|0.000	0.000	strong		0.577	TLN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257878.2		
SGCG	6445	hgsc.bcm.edu	37	13	23808782	23808782	+	Silent	SNP	T	T	C	rs1800350	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:23808782T>C	ENST00000218867.3	+	3	352	c.228T>C	c.(226-228)gaT>gaC	p.D76D	SGCG_ENST00000545013.1_Silent_p.D76D|SGCG_ENST00000537476.1_Silent_p.D76D	NM_000231.2	NP_000222	Q13326	SGCG_HUMAN	sarcoglycan, gamma (35kDa dystrophin-associated glycoprotein)	76					muscle organ development (GO:0007517)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sarcoglycan complex (GO:0016012)|sarcolemma (GO:0042383)				NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	22		all_cancers(29;4.34e-23)|all_epithelial(30;4.4e-19)|all_lung(29;2.45e-18)|Lung SC(185;0.0228)|Breast(139;0.188)		all cancers(112;0.00255)|Epithelial(112;0.0129)|OV - Ovarian serous cystadenocarcinoma(117;0.0365)|Lung(94;0.205)		TAACAAAAGATGGACTGCGCT	0.348													T|||	638	0.127396	0.2617	0.0994	5008	,	,		14528	0.002		0.1074	False		,,,				2504	0.1155				p.D76D		Atlas-SNP	.											.	SGCG	64	.	0			c.T228C						PASS	.	T		1040,3366	383.2+/-324.8	133,774,1296	111.0	115.0	113.0		228	4.4	1.0	13	dbSNP_89	113	1024,7576	219.0+/-257.2	68,888,3344	no	coding-synonymous	SGCG	NM_000231.2		201,1662,4640	CC,CT,TT		11.907,23.6042,15.8696		76/292	23808782	2064,10942	2203	4300	6503	SO:0001819	synonymous_variant	6445	exon3			AAAAGATGGACTG	U34976	CCDS9299.1	13q12-q13	2014-09-17	2002-08-29		ENSG00000102683	ENSG00000102683			10809	protein-coding gene	gene with protein product	"""Maghrebian myopathy (autosomal recessive)"", ""35kD dystrophin-associated glycoprotein"", ""limb girdle muscular dystrophy 2C (Duchenne-like muscular dystrophy, autosomal recessive)"", ""gamma sarcoglycan"""	608896	"""sarcoglycan, gamma (35kD dystrophin-associated glycoprotein)"""	DMDA1, MAM, LGMD2C		8968757	Standard	NM_000231		Approved	SCARMD2, DAGA4, SCG3, DMDA, TYPE, A4, MGC130048	uc001uom.2	Q13326	OTTHUMG00000016563	ENST00000218867.3:c.228T>C	13.37:g.23808782T>C		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	84	43	0.511905	NM_000231	Q32M32|Q5T9J6	Silent	SNP	ENST00000218867.3	37	CCDS9299.1																																																																																			T|0.859;C|0.141	0.141	strong		0.348	SGCG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044151.1	NM_000231	
MUC4	4585	hgsc.bcm.edu	37	3	195509880	195509880	+	Silent	SNP	C	C	T	rs201889850		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195509880C>T	ENST00000463781.3	-	2	9030	c.8571G>A	c.(8569-8571)gtG>gtA	p.V2857V	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Silent_p.V2857V	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)		GACCTGTGGACACTGAGGAAG	0.587																																					p.V2857V		Atlas-SNP	.											.	MUC4	1505	.	0			c.G8571A						PASS	.						43.0	30.0	34.0					3																	195509880		681	1571	2252	SO:0001819	synonymous_variant	4585	exon2			TGTGGACACTGAG	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.8571G>A	3.37:g.195509880C>T		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	132	19	0.143939	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		0.587	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
ST3GAL4	6484	hgsc.bcm.edu	37	11	126277216	126277216	+	Silent	SNP	C	C	T	rs2230278	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:126277216C>T	ENST00000526727.1	+	4	626	c.252C>T	c.(250-252)taC>taT	p.Y84Y	ST3GAL4_ENST00000392669.2_Silent_p.Y84Y|ST3GAL4_ENST00000227495.6_Silent_p.Y80Y|ST3GAL4_ENST00000534457.1_Silent_p.Y79Y|ST3GAL4_ENST00000534083.1_Silent_p.Y84Y|ST3GAL4_ENST00000532243.1_Silent_p.Y83Y|ST3GAL4_ENST00000444328.2_Silent_p.Y84Y|ST3GAL4_ENST00000530591.1_Silent_p.Y80Y|ST3GAL4_ENST00000449406.2_Silent_p.Y73Y|ST3GAL4_ENST00000356132.4_Silent_p.Y90Y|ST3GAL4_ENST00000526756.1_3'UTR			Q11206	SIA4C_HUMAN	ST3 beta-galactoside alpha-2,3-sialyltransferase 4	84					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)			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)		CATCTGCTTACGAGCTGCCCT	0.582													C|||	1734	0.346246	0.3646	0.3242	5008	,	,		15739	0.5099		0.3181	False		,,,				2504	0.1973				p.Y84Y		Atlas-SNP	.											.	ST3GAL4	25	.	0			c.C252T						PASS	.	C		1543,2859	486.0+/-360.5	274,995,932	122.0	116.0	118.0		240	-9.4	0.7	11	dbSNP_98	118	2608,5988	422.9+/-354.2	370,1868,2060	no	coding-synonymous	ST3GAL4	NM_006278.1		644,2863,2992	TT,TC,CC		30.3397,35.0522,31.9357		80/330	126277216	4151,8847	2201	4298	6499	SO:0001819	synonymous_variant	6484	exon5			TGCTTACGAGCTG	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.252C>T	11.37:g.126277216C>T		Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	118	83	0.70339	NM_001254757	A8K6B2|O60497|Q8N6A6|Q8NFG7|Q96QQ9	Silent	SNP	ENST00000526727.1	37	CCDS58193.1																																																																																			C|0.657;T|0.343	0.343	strong		0.582	ST3GAL4-003	PUTATIVE	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386470.1	NM_006278	
WBSCR28	135886	hgsc.bcm.edu	37	7	73279482	73279482	+	Missense_Mutation	SNP	T	T	C	rs13227841	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:73279482T>C	ENST00000320531.2	+	2	268	c.232T>C	c.(232-234)Tgg>Cgg	p.W78R		NM_182504.3	NP_872310.2	Q6UE05	WBS28_HUMAN	Williams-Beuren syndrome chromosome region 28	78			W -> R (in dbSNP:rs13227841). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:18398435}.			integral component of membrane (GO:0016021)				breast(2)|kidney(2)|lung(6)|skin(1)	11		Lung NSC(55;0.159)				CCAGGCTCTCTGGGCTGGGCT	0.697													C|||	2813	0.561701	0.3336	0.5893	5008	,	,		15345	0.6498		0.6769	False		,,,				2504	0.6411				p.W78R		Atlas-SNP	.											.	WBSCR28	24	.	0			c.T232C						PASS	.	C	ARG/TRP	1628,2146		354,920,613	52.0	58.0	56.0		232	-3.0	0.0	7	dbSNP_121	56	5687,2521		1963,1761,380	yes	missense	WBSCR28	NM_182504.3	101	2317,2681,993	CC,CT,TT		30.7139,43.1373,38.9501	benign	78/266	73279482	7315,4667	1887	4104	5991	SO:0001583	missense	135886	exon2			GCTCTCTGGGCTG	BC030643	CCDS43597.1	7q11.23	2006-07-04			ENSG00000175877	ENSG00000175877			23018	protein-coding gene	gene with protein product		612547				8812460	Standard	NM_182504		Approved	MGC26719	uc003tzk.2	Q6UE05	OTTHUMG00000157243	ENST00000320531.2:c.232T>C	7.37:g.73279482T>C	ENSP00000316775:p.Trp78Arg	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	76	74	0.973684	NM_182504	Q6UE04|Q8NHP4	Missense_Mutation	SNP	ENST00000320531.2	37	CCDS43597.1	1251	0.5728021978021978	166	0.33739837398373984	203	0.5607734806629834	359	0.6276223776223776	523	0.6899736147757256	C	0.013	-1.639947	0.00799	0.431373	0.692861	ENSG00000175877	ENST00000320531	T	0.12879	2.64	4.51	-3.02	0.05446	.	0.441724	0.17112	N	0.186572	T	0.00012	0.0000	N	0.02247	-0.625	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.36040	-0.9764	9	0.02654	T	1	-2.7121	0.1465	0.00089	0.2688:0.2285:0.2447:0.258	rs13227841;rs17856876;rs13227841	78	Q6UE05	WBS28_HUMAN	R	78	ENSP00000316775:W78R	ENSP00000316775:W78R	W	+	1	0	WBSCR28	72917418	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.305000	0.19254	-0.665000	0.05317	-2.015000	0.00435	TGG	T|0.403;C|0.597	0.597	strong		0.697	WBSCR28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348130.1	NM_182504	
MAP3K1	4214	hgsc.bcm.edu	37	5	56155672	56155672	+	Missense_Mutation	SNP	A	A	G	rs56069227	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:56155672A>G	ENST00000399503.3	+	3	764	c.764A>G	c.(763-765)aAc>aGc	p.N255S	AC008937.2_ENST00000415589.1_RNA|snoU13_ENST00000459264.1_RNA	NM_005921.1	NP_005912.1	Q13233	M3K1_HUMAN	mitogen-activated protein kinase kinase kinase 1, E3 ubiquitin protein ligase	255					activation of MAPKK activity (GO:0000186)|apoptotic mitochondrial changes (GO:0008637)|cellular response to mechanical stimulus (GO:0071260)|epithelial cell morphogenesis (GO:0003382)|eyelid development in camera-type eye (GO:0061029)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of actin filament polymerization (GO:0030838)|protein phosphorylation (GO:0006468)|regulation of cell migration (GO:0030334)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing (GO:0042060)	cytosol (GO:0005829)	ATP binding (GO:0005524)|JUN kinase kinase activity (GO:0008545)|MAP kinase kinase kinase activity (GO:0004709)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|zinc ion binding (GO:0008270)			NS(1)|breast(19)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(8)|lung(11)|ovary(1)|skin(3)|urinary_tract(1)	57		Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223)		OV - Ovarian serous cystadenocarcinoma(10;6.08e-40)		TCTCCTGGCAACTCCCCATCA	0.488													A|||	83	0.0165735	0.025	0.0216	5008	,	,		15055	0.0		0.0338	False		,,,				2504	0.001				p.N255S		Atlas-SNP	.											.	MAP3K1	355	.	0			c.A764G						PASS	.	A	SER/ASN	79,3755		1,77,1839	42.0	42.0	42.0		764	3.9	0.9	5	dbSNP_129	42	229,8029		5,219,3905	yes	missense	MAP3K1	NM_005921.1	46	6,296,5744	GG,GA,AA		2.7731,2.0605,2.5471	benign	255/1513	56155672	308,11784	1917	4129	6046	SO:0001583	missense	4214	exon3			CTGGCAACTCCCC	U29671, AF042838	CCDS43318.1	5q11.2	2012-02-23	2012-02-23		ENSG00000095015	ENSG00000095015		"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	6848	protein-coding gene	gene with protein product		600982	"""mitogen-activated protein kinase kinase kinase 1"""	MEKK1		8597633	Standard	NM_005921		Approved	MEKK, MAPKKK1	uc003jqw.4	Q13233	OTTHUMG00000059486	ENST00000399503.3:c.764A>G	5.37:g.56155672A>G	ENSP00000382423:p.Asn255Ser	Somatic	225	0	0		WXS	Illumina HiSeq	Phase_I	206	128	0.621359	NM_005921		Missense_Mutation	SNP	ENST00000399503.3	37	CCDS43318.1	40	0.018315018315018316	6	0.012195121951219513	9	0.024861878453038673	0	0.0	25	0.032981530343007916	A	13.57	2.277282	0.40294	0.020605	0.027731	ENSG00000095015	ENST00000399503	T	0.63255	-0.03	5.72	3.93	0.45458	.	0.316826	0.39544	N	0.001335	T	0.10465	0.0256	N	0.01352	-0.895	0.26121	N	0.98055	B	0.02656	0.0	B	0.01281	0.0	T	0.14448	-1.0472	10	0.02654	T	1	.	11.7667	0.51935	0.1441:0.0:0.8559:0.0	rs56069227;rs61736548	255	Q13233	M3K1_HUMAN	S	255	ENSP00000382423:N255S	ENSP00000382423:N255S	N	+	2	0	MAP3K1	56191429	1.000000	0.71417	0.938000	0.37757	0.734000	0.41952	3.001000	0.49488	0.871000	0.35750	-0.242000	0.12053	AAC	A|0.976;G|0.024	0.024	strong		0.488	MAP3K1-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000132309.2	XM_042066	
LRIT1	26103	hgsc.bcm.edu	37	10	85992511	85992511	+	Silent	SNP	T	T	C	rs3814209	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:85992511T>C	ENST00000372105.3	-	4	1065	c.1044A>G	c.(1042-1044)ccA>ccG	p.P348P		NM_015613.2	NP_056428.1	Q9P2V4	LRIT1_HUMAN	leucine-rich repeat, immunoglobulin-like and transmembrane domains 1	348						integral component of endoplasmic reticulum membrane (GO:0030176)				breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(13)|skin(1)	23						TGGAAGTCGGTGGCTCAGTGA	0.567													C|||	2468	0.492812	0.8661	0.4798	5008	,	,		21416	0.2579		0.3976	False		,,,				2504	0.3374				p.P348P		Atlas-SNP	.											LRIT1,right_upper_lobe,carcinoma,-1,1	LRIT1	73	1	0			c.A1044G						PASS	.	C		3428,978	367.8+/-318.4	1342,744,117	57.0	48.0	51.0		1044	-8.9	0.0	10	dbSNP_107	51	3357,5243	640.7+/-399.6	681,1995,1624	no	coding-synonymous	LRIT1	NM_015613.2		2023,2739,1741	CC,CT,TT		39.0349,22.197,47.8318		348/624	85992511	6785,6221	2203	4300	6503	SO:0001819	synonymous_variant	26103	exon4			AGTCGGTGGCTCA	AB031547	CCDS7373.1	10q23	2013-02-11	2007-06-19	2007-06-19	ENSG00000148602	ENSG00000148602		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	23404	protein-coding gene	gene with protein product	"""fibronectin type III, immunoglobulin and leucine rich repeat domains 9"""		"""leucine rich repeat containing 21"""	LRRC21		10777785	Standard	NM_015613		Approved	PAL, DKFZP434K091, FIGLER9	uc001kcz.1	Q9P2V4	OTTHUMG00000018632	ENST00000372105.3:c.1044A>G	10.37:g.85992511T>C		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	73	73	1	NM_015613	Q0QD41|Q9Y4N7	Silent	SNP	ENST00000372105.3	37	CCDS7373.1																																																																																			T|0.496;C|0.503	0.503	strong		0.567	LRIT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049109.1	NM_015613	
PGLYRP2	114770	hgsc.bcm.edu	37	19	15582863	15582863	+	Missense_Mutation	SNP	C	C	T	rs34440547	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:15582863C>T	ENST00000340880.4	-	3	1661	c.1181G>A	c.(1180-1182)cGg>cAg	p.R394Q	PGLYRP2_ENST00000292609.4_Missense_Mutation_p.R394Q	NM_052890.3	NP_443122.3	Q96PD5	PGRP2_HUMAN	peptidoglycan recognition protein 2	394			R -> Q (in dbSNP:rs34440547). {ECO:0000269|PubMed:12975309, ECO:0000269|PubMed:15221005}.		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)			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						CGGGCGGCCCCGATAAGGCGC	0.662													C|||	1125	0.224641	0.1581	0.2406	5008	,	,		11284	0.2966		0.2227	False		,,,				2504	0.2311				p.R394Q		Atlas-SNP	.											.	PGLYRP2	116	.	0			c.G1181A						PASS	.	C	GLN/ARG	678,3726		62,554,1586	28.0	28.0	28.0		1181	1.0	0.2	19	dbSNP_126	28	1768,6826		204,1360,2733	yes	missense	PGLYRP2	NM_052890.3	43	266,1914,4319	TT,TC,CC		20.5725,15.3951,18.8183	benign	394/577	15582863	2446,10552	2202	4297	6499	SO:0001583	missense	114770	exon3			CGGCCCCGATAAG	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.1181G>A	19.37:g.15582863C>T	ENSP00000345968:p.Arg394Gln	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	42	29	0.690476	NM_052890	A8K050|A8K8C7|B2RMZ2|B7ZM33|Q68CK1|Q96N74|Q9UC60	Missense_Mutation	SNP	ENST00000340880.4	37	CCDS12330.2	511	0.23397435897435898	80	0.16260162601626016	85	0.23480662983425415	180	0.3146853146853147	166	0.21899736147757257	C	5.762	0.324924	0.10900	0.153951	0.205725	ENSG00000161031	ENST00000340880;ENST00000292609	T;T	0.17691	2.26;2.26	4.43	0.993	0.19825	Peptidoglycan recognition protein family domain, metazoa/bacteria (1);N-acetylmuramoyl-L-alanine amidase domain (3);	0.641695	0.13873	N	0.356872	T	0.00012	0.0000	L	0.40543	1.245	0.53005	P	3.900000000001125E-5	B;B	0.18013	0.025;0.006	B;B	0.16289	0.009;0.015	T	0.43015	-0.9417	9	0.35671	T	0.21	.	8.9339	0.35688	0.0:0.6245:0.0:0.3755	rs34440547	394;394	Q96PD5-2;Q96PD5	.;PGRP2_HUMAN	Q	394	ENSP00000345968:R394Q;ENSP00000292609:R394Q	ENSP00000292609:R394Q	R	-	2	0	PGLYRP2	15443863	0.000000	0.05858	0.184000	0.23157	0.005000	0.04900	-0.486000	0.06513	-0.149000	0.11215	-1.134000	0.01955	CGG	C|0.808;T|0.192	0.192	strong		0.662	PGLYRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319626.1	NM_052890	
EFHB	151651	hgsc.bcm.edu	37	3	19961331	19961331	+	Silent	SNP	T	T	C	rs2929362|rs386659061	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:19961331T>C	ENST00000295824.9	-	3	1151	c.990A>G	c.(988-990)tcA>tcG	p.S330S	EFHB_ENST00000498089.1_5'UTR|EFHB_ENST00000344838.4_Silent_p.S200S	NM_144715.3	NP_653316.3	Q8N7U6	EFHB_HUMAN	EF-hand domain family, member B	330							calcium ion binding (GO:0005509)			breast(2)|endometrium(4)|kidney(1)|lung(17)|prostate(1)|urinary_tract(1)	26						TTACCAGTACTGAAATTTTAG	0.338													T|||	983	0.196286	0.3177	0.1153	5008	,	,		16733	0.1081		0.1481	False		,,,				2504	0.2301				p.S330S		Atlas-SNP	.											.	EFHB	186	.	0			c.A990G						PASS	.	T		24,4380		4,16,2182	84.0	94.0	90.0		990	1.3	0.0	3	dbSNP_101	90	14,8586		2,10,4288	no	coding-synonymous	EFHB	NM_144715.3		6,26,6470	CC,CT,TT		0.1628,0.545,0.2922		330/834	19961331	38,12966	2202	4300	6502	SO:0001819	synonymous_variant	151651	exon3			CAGTACTGAAATT	AK122616	CCDS33715.2	3p24.3	2014-07-18			ENSG00000163576	ENSG00000163576		"""EF-hand domain containing"""	26330	protein-coding gene	gene with protein product	"""cilia and flagella associated protein 21"""					12477932	Standard	NM_144715		Approved	FLJ25200, CFAP21	uc003cbl.4	Q8N7U6	OTTHUMG00000150505	ENST00000295824.9:c.990A>G	3.37:g.19961331T>C		Somatic	218	0	0		WXS	Illumina HiSeq	Phase_I	191	97	0.507853	NM_144715	A6ND25|A8MPR3|Q6ZWK9|Q8IV58|Q96LQ6	Silent	SNP	ENST00000295824.9	37	CCDS33715.2																																																																																			T|0.652;G|0.040;C|0.133;A|0.175	0.133	strong		0.338	EFHB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318673.2	NM_144715	
SGIP1	84251	hgsc.bcm.edu	37	1	67109335	67109335	+	Missense_Mutation	SNP	A	A	G	rs7526812	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:67109335A>G	ENST00000371037.4	+	7	469	c.392A>G	c.(391-393)aAg>aGg	p.K131R	SGIP1_ENST00000237247.6_Missense_Mutation_p.K135R|SGIP1_ENST00000371039.1_Missense_Mutation_p.K107R|SGIP1_ENST00000371036.3_Missense_Mutation_p.K106R|SGIP1_ENST00000468286.1_3'UTR|SGIP1_ENST00000371035.3_Missense_Mutation_p.K88R	NM_032291.2	NP_115667.2	Q9BQI5	SGIP1_HUMAN	SH3-domain GRB2-like (endophilin) interacting protein 1	131			K -> R (in dbSNP:rs7526812). {ECO:0000269|PubMed:11230166, ECO:0000269|PubMed:17974005, ECO:0000269|Ref.2}.		endocytosis (GO:0006897)|membrane tubulation (GO:0097320)|positive regulation of energy homeostasis (GO:2000507)|positive regulation of feeding behavior (GO:2000253)|positive regulation of receptor-mediated endocytosis (GO:0048260)|response to dietary excess (GO:0002021)	AP-2 adaptor complex (GO:0030122)|clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	microtubule binding (GO:0008017)|phospholipid binding (GO:0005543)|SH3 domain binding (GO:0017124)	p.K131R(1)		breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(6)|lung(43)|ovary(4)|pancreas(1)|prostate(1)|skin(3)|stomach(1)	71						GACATTCTTAAGAATGCTGCA	0.368													A|||	1414	0.282348	0.4312	0.2867	5008	,	,		19950	0.2738		0.1402	False		,,,				2504	0.2331				p.K131R		Atlas-SNP	.											SGIP1,NS,carcinoma,0,1	SGIP1	272	1	1	Substitution - Missense(1)	stomach(1)	c.A392G						PASS	.	A	ARG/LYS	1612,2794	498.9+/-364.3	302,1008,893	149.0	145.0	147.0		392	5.3	1.0	1	dbSNP_116	147	1297,7303	256.3+/-280.9	107,1083,3110	yes	missense	SGIP1	NM_032291.2	26	409,2091,4003	GG,GA,AA		15.0814,36.5865,22.3666	possibly-damaging	131/829	67109335	2909,10097	2203	4300	6503	SO:0001583	missense	84251	exon7			TTCTTAAGAATGC	AL136561	CCDS30744.1	1p31.3	2008-02-05			ENSG00000118473	ENSG00000118473			25412	protein-coding gene	gene with protein product		611540				11230166	Standard	NM_032291		Approved	DKFZp761D221	uc001dcr.3	Q9BQI5	OTTHUMG00000009161	ENST00000371037.4:c.392A>G	1.37:g.67109335A>G	ENSP00000360076:p.Lys131Arg	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	112	55	0.491071	NM_032291	A6NL81|A6NLD1|Q4LE32|Q5VYE2|Q5VYE3|Q5VYE4|Q68D76|Q6MZY6|Q8IWC2	Missense_Mutation	SNP	ENST00000371037.4	37	CCDS30744.1	573	0.2623626373626374	217	0.4410569105691057	71	0.19613259668508287	176	0.3076923076923077	109	0.1437994722955145	A	10.21	1.287897	0.23478	0.365865	0.150814	ENSG00000118473	ENST00000237247;ENST00000371039;ENST00000424320;ENST00000371035;ENST00000371038;ENST00000407289;ENST00000371036;ENST00000371037	T;T;T;T;T;T	0.17691	2.26;2.26;2.26;2.26;2.26;2.26	5.3	5.3	0.74995	.	0.161255	0.56097	D	0.000032	T	0.06416	0.0165	L	0.47716	1.5	0.46416	P	9.649999999999936E-4	B	0.12630	0.006	B	0.08055	0.003	T	0.19418	-1.0306	9	0.18276	T	0.48	-13.2771	11.4888	0.50369	0.9272:0.0:0.0728:0.0	rs7526812;rs52830701;rs57004614;rs7526812	131	Q9BQI5	SGIP1_HUMAN	R	135;107;131;88;134;134;106;131	ENSP00000237247:K135R;ENSP00000360078:K107R;ENSP00000410439:K131R;ENSP00000360074:K88R;ENSP00000360075:K106R;ENSP00000360076:K131R	ENSP00000237247:K135R	K	+	2	0	SGIP1	66881923	1.000000	0.71417	0.998000	0.56505	0.963000	0.63663	3.063000	0.49978	2.126000	0.65437	0.533000	0.62120	AAG	A|0.749;G|0.251	0.251	strong		0.368	SGIP1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000025395.4	NM_032291	
NSD1	64324	hgsc.bcm.edu	37	5	176721151	176721151	+	Missense_Mutation	SNP	T	T	C	rs34165241	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:176721151T>C	ENST00000439151.2	+	23	6827	c.6782T>C	c.(6781-6783)aTg>aCg	p.M2261T	NSD1_ENST00000354179.4_Missense_Mutation_p.M1992T|NSD1_ENST00000361032.4_Missense_Mutation_p.M2158T|NSD1_ENST00000347982.4_Missense_Mutation_p.M1992T	NM_022455.4	NP_071900.2	Q96L73	NSD1_HUMAN	nuclear receptor binding SET domain protein 1	2261	Pro-rich.		M -> T (in dbSNP:rs34165241). {ECO:0000269|PubMed:12464997}.		gastrulation with mouth forming second (GO:0001702)|histone H3-K36 methylation (GO:0010452)|histone H4-K20 methylation (GO:0034770)|histone methylation (GO:0016571)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|estrogen receptor binding (GO:0030331)|histone methyltransferase activity (H3-K36 specific) (GO:0046975)|histone methyltransferase activity (H4-K20 specific) (GO:0042799)|retinoic acid receptor binding (GO:0042974)|retinoid X receptor binding (GO:0046965)|thyroid hormone receptor binding (GO:0046966)|transcription cofactor activity (GO:0003712)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(18)|lung(24)|ovary(2)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(3)	96	all_cancers(89;1.57e-05)|Renal(175;0.000269)|Lung NSC(126;0.00111)|all_lung(126;0.002)	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)|Epithelial(233;0.198)	Kidney(146;0.235)		ACCAACCAGATGCTGTCGCTC	0.537			T	NUP98	AML		Sotos Syndrome		Weaver syndrome;Sotos syndrome;Beckwith-Wiedemann syndrome	HNSCC(47;0.14)			C|||	259	0.0517173	0.0734	0.0274	5008	,	,		19007	0.0179		0.0427	False		,,,				2504	0.0838				p.M2261T		Atlas-SNP	.		Dom	yes		5	5q35	64324	nuclear receptor binding SET domain protein 1	yes	L	.	NSD1	416	.	0			c.T6782C						PASS	.	C	THR/MET,THR/MET	259,4147	802.7+/-415.7	7,245,1951	93.0	95.0	94.0		6782,5975	-2.0	0.0	5	dbSNP_126	94	420,8180	800.7+/-407.4	8,404,3888	yes	missense,missense	NSD1	NM_022455.4,NM_172349.2	81,81	15,649,5839	CC,CT,TT		4.8837,5.8783,5.2207	benign,benign	2261/2697,1992/2428	176721151	679,12327	2203	4300	6503	SO:0001583	missense	64324	exon23	Familial Cancer Database	Weaver-Smith syndrome;Cerebral Gigantism;BWS, Exomphalos-Macroglossia-Gigantism (EMG) syndrome, Wiedemann-Beckwith syndrome, WBS	ACCAGATGCTGTC	AK026066	CCDS4412.1, CCDS4413.1	5q35	2014-09-17	2003-03-12		ENSG00000165671	ENSG00000165671		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	14234	protein-coding gene	gene with protein product		606681	"""Sotos syndrome"""	STO		9628876, 11896389	Standard	NM_022455		Approved	ARA267, FLJ22263, KMT3B	uc003mfr.4	Q96L73	OTTHUMG00000130846	ENST00000439151.2:c.6782T>C	5.37:g.176721151T>C	ENSP00000395929:p.Met2261Thr	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	86	29	0.337209	NM_022455	Q96PD8|Q96RN7	Missense_Mutation	SNP	ENST00000439151.2	37	CCDS4412.1	87	0.03983516483516483	37	0.07520325203252033	10	0.027624309392265192	7	0.012237762237762238	33	0.04353562005277045	C	0.004	-2.266099	0.00259	0.058783	0.048837	ENSG00000165671	ENST00000354179;ENST00000439151;ENST00000347982;ENST00000361032	D;D;D;D	0.92199	-2.88;-2.88;-2.88;-2.99	5.19	-2.03	0.07365	.	0.856328	0.10351	N	0.685128	T	0.13884	0.0336	N	0.03608	-0.345	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.53592	-0.8417	10	0.02654	T	1	.	3.2901	0.06945	0.1118:0.1954:0.1593:0.5335	rs34165241	1992;2261	Q96L73-2;Q96L73	.;NSD1_HUMAN	T	1992;2261;1992;2158	ENSP00000346111:M1992T;ENSP00000395929:M2261T;ENSP00000343209:M1992T;ENSP00000354310:M2158T	ENSP00000343209:M1992T	M	+	2	0	NSD1	176653757	0.000000	0.05858	0.002000	0.10522	0.582000	0.36321	-0.244000	0.08903	-0.520000	0.06435	-1.551000	0.00897	ATG	T|0.952;C|0.048	0.048	strong		0.537	NSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253412.2	NM_172349	
KCNK12	56660	hgsc.bcm.edu	37	2	47748558	47748558	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:47748558C>T	ENST00000327876.4	-	2	1388	c.781G>A	c.(781-783)Gac>Aac	p.D261N	MSH2_ENST00000461394.1_Intron	NM_022055.1	NP_071338.1	Q9HB15	KCNKC_HUMAN	potassium channel, subfamily K, member 12	261						integral component of membrane (GO:0016021)	potassium channel activity (GO:0005267)|voltage-gated ion channel activity (GO:0005244)	p.0?(2)|p.?(2)		NS(1)|endometrium(1)|lung(3)|ovary(1)	6		all_hematologic(82;0.0495)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			CTCACCAGGTCCCCGAAGCCG	0.632																																					p.D261N		Atlas-SNP	.											.	KCNK12	11	.	4	Whole gene deletion(2)|Unknown(2)	haematopoietic_and_lymphoid_tissue(3)|prostate(1)	c.G781A						PASS	.						41.0	39.0	40.0					2																	47748558		2203	4299	6502	SO:0001583	missense	56660	exon2			CCAGGTCCCCGAA	AF287302	CCDS1835.1	2p16.3	2012-03-07			ENSG00000184261	ENSG00000184261		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Two-P"""	6274	protein-coding gene	gene with protein product		607366				11060316	Standard	NM_022055		Approved	THIK-2, THIK2, K2p12.1	uc002rwb.3	Q9HB15	OTTHUMG00000129131	ENST00000327876.4:c.781G>A	2.37:g.47748558C>T	ENSP00000327611:p.Asp261Asn	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	170	43	0.252941	NM_022055		Missense_Mutation	SNP	ENST00000327876.4	37	CCDS1835.1	.	.	.	.	.	.	.	.	.	.	C	21.6	4.172527	0.78452	.	.	ENSG00000184261	ENST00000327876	T	0.41758	0.99	4.1	3.22	0.36961	Ion transport 2 (1);	0.000000	0.85682	D	0.000000	T	0.72391	0.3454	H	0.95004	3.61	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.80885	-0.1182	10	0.87932	D	0	.	13.8032	0.63214	0.0:0.8451:0.1549:0.0	.	261	Q9HB15	KCNKC_HUMAN	N	261	ENSP00000327611:D261N	ENSP00000327611:D261N	D	-	1	0	KCNK12	47602062	1.000000	0.71417	0.991000	0.47740	0.950000	0.60333	5.915000	0.69973	0.922000	0.37019	0.305000	0.20034	GAC	.	.	none		0.632	KCNK12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251182.2	NM_022055	
IL7R	3575	hgsc.bcm.edu	37	5	35871273	35871273	+	Silent	SNP	C	C	T	rs2228141	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:35871273C>T	ENST00000303115.3	+	4	624	c.495C>T	c.(493-495)caC>caT	p.H165H	IL7R_ENST00000506850.1_Silent_p.H165H|IL7R_ENST00000343305.4_Silent_p.H165H	NM_002185.3	NP_002176.2	P16871	IL7RA_HUMAN	interleukin 7 receptor	165	Fibronectin type-III. {ECO:0000255|PROSITE-ProRule:PRU00316}.				B cell proliferation (GO:0042100)|cell growth (GO:0016049)|cell morphogenesis (GO:0000902)|cell surface receptor signaling pathway (GO:0007166)|homeostasis of number of cells (GO:0048872)|immune response (GO:0006955)|immunoglobulin production (GO:0002377)|interleukin-7-mediated signaling pathway (GO:0038111)|lymph node development (GO:0048535)|negative regulation of T cell mediated cytotoxicity (GO:0001915)|positive regulation of gene expression (GO:0010628)|positive regulation of T cell differentiation in thymus (GO:0033089)|regulation of cell size (GO:0008361)|regulation of DNA recombination (GO:0000018)|signal transduction (GO:0007165)|T cell differentiation (GO:0030217)	external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	antigen binding (GO:0003823)|interleukin-7 receptor activity (GO:0004917)			NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(78)|kidney(2)|large_intestine(6)|lung(25)|ovary(3)|pancreas(1)|skin(5)|stomach(3)	126	all_lung(31;0.00015)		Lung(74;0.111)|COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.187)|Colorectal(62;0.202)			TTTTAATGCACGATGTAGCTT	0.348			"""Mis, O"""		"""ALL, ETP ALL"""		Severe combined immune deficiency						C|||	644	0.128594	0.1278	0.1657	5008	,	,		17496	0.1528		0.1441	False		,,,				2504	0.0624				p.H165H		Atlas-SNP	.		Dom	yes		5	5p13	146661	interleukin 7 receptor	yes	L	.	IL7R	200	.	0			c.C495T						PASS	.	C		534,3872	242.5+/-252.5	36,462,1705	73.0	72.0	73.0		495	-2.7	0.4	5	dbSNP_98	73	1223,7377	246.4+/-274.8	92,1039,3169	no	coding-synonymous	IL7R	NM_002185.2		128,1501,4874	TT,TC,CC		14.2209,12.1198,13.5091		165/460	35871273	1757,11249	2203	4300	6503	SO:0001819	synonymous_variant	3575	exon4			AATGCACGATGTA	M29696	CCDS3911.1	5p13	2014-09-17			ENSG00000168685	ENSG00000168685		"""Interleukins and interleukin receptors"", ""CD molecules"", ""Fibronectin type III domain containing"""	6024	protein-coding gene	gene with protein product		146661				2317865	Standard	NM_002185		Approved	CD127	uc003jjs.4	P16871	OTTHUMG00000090791	ENST00000303115.3:c.495C>T	5.37:g.35871273C>T		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	118	47	0.398305	NM_002185	B2RCS6|B4DVT1|Q05CU8|Q6NSP4|Q6NWM0|Q6NWM1|Q6NWM2|Q6NWM3|Q6SV45|Q9UPC1	Silent	SNP	ENST00000303115.3	37	CCDS3911.1																																																																																			C|0.867;G|0.000;T|0.133	0.133	strong		0.348	IL7R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207577.2		
TTC9C	283237	hgsc.bcm.edu	37	11	62496519	62496519	+	Silent	SNP	T	T	C	rs584845	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:62496519T>C	ENST00000316461.4	+	1	509	c.199T>C	c.(199-201)Ttg>Ctg	p.L67L	TTC9C_ENST00000532583.1_Silent_p.L67L|TTC9C_ENST00000513247.2_Silent_p.L200L|HNRNPUL2_ENST00000301785.5_5'Flank|HNRNPUL2-BSCL2_ENST00000403734.2_5'Flank	NM_173810.3	NP_776171.1	Q8N5M4	TTC9C_HUMAN	tetratricopeptide repeat domain 9C	67										breast(1)|endometrium(1)|lung(2)|ovary(1)|pancreas(1)	6						AGAAAACATATTGCATACCAC	0.522													C|||	1466	0.292732	0.4947	0.2061	5008	,	,		15824	0.2391		0.2127	False		,,,				2504	0.2188				p.L67L		Atlas-SNP	.											.	TTC9C	12	.	0			c.T199C						PASS	.	C		2007,2397	613.3+/-392.2	483,1041,678	78.0	74.0	75.0		199	6.0	0.9	11	dbSNP_83	75	2104,6494	716.6+/-406.1	267,1570,2462	no	coding-synonymous	TTC9C	NM_173810.3		750,2611,3140	CC,CT,TT		24.4708,45.5722,31.6182		67/172	62496519	4111,8891	2202	4299	6501	SO:0001819	synonymous_variant	283237	exon1			AACATATTGCATA	BC032123	CCDS8033.1	11q12.3	2013-01-10			ENSG00000162222	ENSG00000162222		"""Tetratricopeptide (TTC) repeat domain containing"""	28432	protein-coding gene	gene with protein product							Standard	NM_173810		Approved	MGC29649	uc001nuy.3	Q8N5M4	OTTHUMG00000167607	ENST00000316461.4:c.199T>C	11.37:g.62496519T>C		Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	144	27	0.1875	NM_173810	Q8WYY7	Silent	SNP	ENST00000316461.4	37	CCDS8033.1																																																																																			T|0.690;C|0.310	0.310	strong		0.522	TTC9C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395338.1	NM_173810	
RALGDS	5900	hgsc.bcm.edu	37	9	135982088	135982088	+	Silent	SNP	A	A	C	rs2073822	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:135982088A>C	ENST00000372050.3	-	8	1482	c.1461T>G	c.(1459-1461)tcT>tcG	p.S487S	RALGDS_ENST00000393160.3_Silent_p.S432S|RALGDS_ENST00000372047.3_Silent_p.S475S|RALGDS_ENST00000393157.3_Silent_p.S486S|RALGDS_ENST00000372062.3_Silent_p.S458S|RALGDS_ENST00000469972.1_5'UTR|RALGDS_ENST00000542690.1_Silent_p.S558S	NM_006266.2	NP_006257.1	Q12967	GNDS_HUMAN	ral guanine nucleotide dissociation stimulator	487	Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00168}.				neurotrophin TRK receptor signaling pathway (GO:0048011)|Ras protein signal transduction (GO:0007265)|regulation of catalytic activity (GO:0050790)|regulation of small GTPase mediated signal transduction (GO:0051056)	cytosol (GO:0005829)	guanyl-nucleotide exchange factor activity (GO:0005085)|small GTPase regulator activity (GO:0005083)			endometrium(1)|large_intestine(4)|lung(2)|ovary(1)|upper_aerodigestive_tract(2)	10				OV - Ovarian serous cystadenocarcinoma(145;3.66e-06)|Epithelial(140;2.77e-05)		TCTGCAGGGCAGAGAGGATGG	0.612			T	CIITA	"""PMBL, Hodgkin Lymphona, """								A|||	974	0.194489	0.1422	0.317	5008	,	,		20075	0.1577		0.2962	False		,,,				2504	0.1115				p.S487S	Melanoma(189;762 2088 15384 21931 52515)	Atlas-SNP	.		Dom	yes		9	9q34.3	5900	ral guanine nucleotide dissociation stimulator		L	.	RALGDS	75	.	0			c.T1461G						PASS	.	A	,	750,3652	301.8+/-287.1	70,610,1521	75.0	66.0	69.0		1296,1461	-9.9	0.2	9	dbSNP_96	69	2595,6001	413.4+/-351.1	387,1821,2090	no	coding-synonymous,coding-synonymous	RALGDS	NM_001042368.1,NM_006266.2	,	457,2431,3611	CC,CA,AA		30.1885,17.0377,25.7347	,	432/860,487/915	135982088	3345,9653	2201	4298	6499	SO:0001819	synonymous_variant	5900	exon8			CAGGGCAGAGAGG	AB037729	CCDS6959.1, CCDS43897.1, CCDS65172.1, CCDS65173.1, CCDS65174.1	9q34.3	2009-04-08			ENSG00000160271	ENSG00000160271			9842	protein-coding gene	gene with protein product		601619				7972015	Standard	NM_006266		Approved	RGF, RalGEF, RGDS	uc004ccr.3	Q12967	OTTHUMG00000020858	ENST00000372050.3:c.1461T>G	9.37:g.135982088A>C		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	130	74	0.569231	NM_006266	B7Z753|E7ER93|E7ERZ0|Q5T7V4|Q6KH11|Q6PCE1|Q6ZSD5|Q9HAX7|Q9HAY1|Q9HCT1|Q9P2N8	Silent	SNP	ENST00000372050.3	37	CCDS6959.1																																																																																			A|0.759;C|0.241	0.241	strong		0.612	RALGDS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054837.1	NM_006266	
ADAMTS7	11173	hgsc.bcm.edu	37	15	79069121	79069121	+	Silent	SNP	A	A	G	rs11854507	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:79069121A>G	ENST00000388820.4	-	10	1740	c.1530T>C	c.(1528-1530)gcT>gcC	p.A510A	ADAMTS7_ENST00000566303.1_Intron	NM_014272.3	NP_055087.2	Q9UKP4	ATS7_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 7	510	Disintegrin.				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						TGCCGTCCACAGCTGCATCCA	0.627													G|||	1269	0.253395	0.2057	0.268	5008	,	,		16760	0.1399		0.4006	False		,,,				2504	0.273				p.A510A		Atlas-SNP	.											.	ADAMTS7	142	.	0			c.T1530C						PASS	.	G		993,3275		131,731,1272	75.0	55.0	62.0		1530	-5.1	0.9	15	dbSNP_120	62	3203,5133		691,1821,1656	no	coding-synonymous	ADAMTS7	NM_014272.3		822,2552,2928	GG,GA,AA		38.4237,23.2662,33.291		510/1687	79069121	4196,8408	2134	4168	6302	SO:0001819	synonymous_variant	11173	exon10			GTCCACAGCTGCA	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.1530T>C	15.37:g.79069121A>G		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	85	45	0.529412	NM_014272	Q14F51|Q6P7J9	Silent	SNP	ENST00000388820.4	37	CCDS32303.1																																																																																			A|0.706;G|0.294	0.294	strong		0.627	ADAMTS7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421331.1	NM_014272	
TMEM140	55281	hgsc.bcm.edu	37	7	134849213	134849213	+	Missense_Mutation	SNP	G	G	A	rs3800592	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:134849213G>A	ENST00000275767.3	+	2	243	c.20G>A	c.(19-21)cGg>cAg	p.R7Q	C7orf49_ENST00000459937.1_Intron	NM_018295.3	NP_060765.4	Q9NV12	TM140_HUMAN	transmembrane protein 140	7			R -> Q (in dbSNP:rs3800592). {ECO:0000269|PubMed:15489334}.			integral component of membrane (GO:0016021)				kidney(1)|large_intestine(2)|lung(2)	5						CCAAGGCCTCGGTGGCGCGAC	0.592													G|||	2283	0.455871	0.4009	0.4798	5008	,	,		19594	0.2589		0.4821	False		,,,				2504	0.6892				p.R7Q		Atlas-SNP	.											.	TMEM140	18	.	0			c.G20A						PASS	.	G	GLN/ARG	1933,2473	550.6+/-378.1	435,1063,705	116.0	103.0	108.0		20	-5.3	0.0	7	dbSNP_107	108	4372,4228	583.5+/-391.6	1125,2122,1053	yes	missense	TMEM140	NM_018295.3	43	1560,3185,1758	AA,AG,GG		49.1628,43.872,48.4776	possibly-damaging	7/186	134849213	6305,6701	2203	4300	6503	SO:0001583	missense	55281	exon2			GGCCTCGGTGGCG	AK001862	CCDS5837.1	7q33	2006-03-17			ENSG00000146859	ENSG00000146859			21870	protein-coding gene	gene with protein product							Standard	NM_018295		Approved	FLJ11000	uc003vsi.3	Q9NV12	OTTHUMG00000155413	ENST00000275767.3:c.20G>A	7.37:g.134849213G>A	ENSP00000275767:p.Arg7Gln	Somatic	179	0	0		WXS	Illumina HiSeq	Phase_I	150	148	0.986667	NM_018295	A4D1P9|Q8WUC3	Missense_Mutation	SNP	ENST00000275767.3	37	CCDS5837.1	908	0.4157509157509158	210	0.4268292682926829	165	0.4558011049723757	153	0.2674825174825175	380	0.5013192612137203	G	13.65	2.299389	0.40694	0.43872	0.508372	ENSG00000146859	ENST00000275767;ENST00000456488	T	0.19806	2.12	5.68	-5.31	0.02730	.	0.964256	0.08571	N	0.926035	T	0.00012	0.0000	L	0.60455	1.87	0.80722	P	0.0	B	0.21381	0.055	B	0.12837	0.008	T	0.44757	-0.9307	9	0.34782	T	0.22	-2.082	9.0454	0.36343	0.5179:0.0:0.3867:0.0955	rs3800592;rs10337077;rs11558287;rs17851848;rs3800592	7	Q9NV12	TM140_HUMAN	Q	7	ENSP00000275767:R7Q	ENSP00000275767:R7Q	R	+	2	0	TMEM140	134499753	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.042000	0.12063	-1.042000	0.03262	-1.326000	0.01283	CGG	G|0.536;A|0.464	0.464	strong		0.592	TMEM140-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340017.2	NM_018295	
STRC	161497	hgsc.bcm.edu	37	15	43897499	43897499	+	Missense_Mutation	SNP	T	T	C	rs2920780	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:43897499T>C	ENST00000450892.2	-	19	3970	c.3893A>G	c.(3892-3894)cAc>cGc	p.H1298R	RNU6-554P_ENST00000410466.1_RNA|STRC_ENST00000541030.1_Missense_Mutation_p.H525R	NM_153700.2	NP_714544.1	Q7RTU9	STRC_HUMAN	stereocilin	1298					auditory receptor cell stereocilium organization (GO:0060088)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)	kinocilium (GO:0060091)|stereocilium bundle tip (GO:0032426)				skin(4)	4		all_cancers(109;3.26e-15)|all_epithelial(112;1.48e-12)|Lung NSC(122;2.76e-08)|all_lung(180;3.1e-07)|Melanoma(134;0.027)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;3.56e-07)		GGCTGCCTGGTGGAGGGGGGT	0.542													T|||	1457	0.290935	0.5446	0.2003	5008	,	,		18193	0.2728		0.1014	False		,,,				2504	0.226				p.H1298R		Atlas-SNP	.											.	STRC	58	.	0			c.A3893G						PASS	.	T	ARG/HIS	1981,2409		455,1071,669	15.0	14.0	14.0		3893	2.9	1.0	15	dbSNP_101	14	836,7712		49,738,3487	no	missense	STRC	NM_153700.2	29	504,1809,4156	CC,CT,TT		9.7801,45.1253,21.7731	benign	1298/1776	43897499	2817,10121	2195	4274	6469	SO:0001583	missense	161497	exon19			GCCTGGTGGAGGG	BK000138	CCDS10098.1	15q15.3	2010-02-26			ENSG00000242866	ENSG00000242866			16035	protein-coding gene	gene with protein product		606440		DFNB16		11687802, 9429146	Standard	NM_153700		Approved		uc001zsf.3	Q7RTU9	OTTHUMG00000059899	ENST00000450892.2:c.3893A>G	15.37:g.43897499T>C	ENSP00000401513:p.His1298Arg	Somatic	373	1	0.00268097		WXS	Illumina HiSeq	Phase_I	408	137	0.335784	NM_153700		Missense_Mutation	SNP	ENST00000450892.2	37	CCDS10098.1	590	0.27014652014652013	266	0.540650406504065	74	0.20441988950276244	180	0.3146853146853147	70	0.09234828496042216	T	12.77	2.038989	0.35989	0.451253	0.097801	ENSG00000242866	ENST00000450892;ENST00000299992;ENST00000541030	T;T	0.76186	-1.0;-1.0	5.46	2.86	0.33363	.	0.509337	0.18353	N	0.143832	T	0.00012	0.0000	N	0.12182	0.205	0.34793	P	0.26405100000000004	B;B	0.18310	0.027;0.0	B;B	0.11329	0.006;0.002	T	0.45101	-0.9284	9	0.12766	T	0.61	-5.1913	6.9989	0.24799	0.0:0.23:0.0:0.77	rs2920780;rs58216659	525;1298	F5GXA4;Q7RTU9	.;STRC_HUMAN	R	1298;1298;525	ENSP00000401513:H1298R;ENSP00000440413:H525R	ENSP00000299992:H1298R	H	-	2	0	STRC	41684791	1.000000	0.71417	0.982000	0.44146	0.621000	0.37620	1.762000	0.38451	1.024000	0.39682	0.454000	0.30748	CAC	.	.	weak		0.542	STRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133140.1	NM_153700	
NELFCD	51497	hgsc.bcm.edu	37	20	57564695	57564695	+	Splice_Site	SNP	C	C	T	rs11542234|rs17851253	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:57564695C>T	ENST00000344018.3	+	6	711	c.684C>T	c.(682-684)gcC>gcT	p.A228A	NELFCD_ENST00000602795.1_Splice_Site_p.A237A			Q8IXH7	NELFD_HUMAN	negative elongation factor complex member C/D	228					gene expression (GO:0010467)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of viral transcription (GO:0050434)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	membrane (GO:0016020)|NELF complex (GO:0032021)|nucleoplasm (GO:0005654)											CTGAGTTTGCCGTAAGTTCTT	0.448													C|||	208	0.0415335	0.0023	0.0461	5008	,	,		20242	0.001		0.1193	False		,,,				2504	0.0532				p.A237A		Atlas-SNP	.											TH1L,colon,carcinoma,+1,2	.	.	2	0			c.C711T						PASS	.	C		92,4314	70.9+/-108.8	1,90,2112	82.0	95.0	90.0		684	-11.5	0.3	20	dbSNP_126	90	864,7736	192.8+/-238.7	38,788,3474	yes	coding-synonymous-near-splice	TH1L	NM_198976.1		39,878,5586	TT,TC,CC		10.0465,2.0881,7.3505		228/591	57564695	956,12050	2203	4300	6503	SO:0001630	splice_region_variant	51497	exon6			GTTTGCCGTAAGT	AF161479	CCDS13473.1, CCDS13473.2	20q13	2013-01-31	2013-01-31	2013-01-31	ENSG00000101158	ENSG00000101158			15934	protein-coding gene	gene with protein product	"""trihydrophobin 1"""	605297	"""TH1-like (Drosophila homolog)"", ""TH1-like (Drosophila)"""	TH1L		11030415, 11042152	Standard	NM_198976		Approved	HSPC130, TH1, NELF-C, NELF-D	uc002yag.4	Q8IXH7	OTTHUMG00000032861	ENST00000344018.3:c.684+1C>T	20.37:g.57564695C>T		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	99	54	0.545455	NM_198976	B4DE06|Q9BYL2|Q9H405|Q9H888|Q9H8T3|Q9NVX5|Q9P029|Q9UGN1|Q9UGN2|Q9UGN3	Silent	SNP	ENST00000344018.3	37																																																																																				C|0.929;T|0.071	0.071	strong		0.448	NELFCD-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_198976	Silent
HLA-A	3105	hgsc.bcm.edu	37	6	29911063	29911063	+	Missense_Mutation	SNP	T	T	G	rs386698553|rs199474484|rs199474485	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:29911063T>G	ENST00000396634.1	+	5	703	c.362T>G	c.(361-363)aTa>aGa	p.I121R	HLA-A_ENST00000376802.2_Missense_Mutation_p.I121R|HLA-A_ENST00000376809.5_Missense_Mutation_p.I121R|HLA-A_ENST00000376806.5_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	191	0	0		WXS	Illumina HiSeq	Phase_I	108	40	0.37037	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	
PTPRZ1	5803	hgsc.bcm.edu	37	7	121616250	121616250	+	Silent	SNP	G	G	A	rs4629793	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	72	0	0		WXS	Illumina HiSeq	Phase_I	72	38	0.527778	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	
SREBF2	6721	hgsc.bcm.edu	37	22	42293140	42293140	+	Missense_Mutation	SNP	G	G	C	rs2228313	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:42293140G>C	ENST00000361204.4	+	14	2746	c.2580G>C	c.(2578-2580)agG>agC	p.R860S	SREBF2_ENST00000491541.1_3'UTR	NM_004599.2	NP_004590.2	Q12772	SRBP2_HUMAN	sterol regulatory element binding transcription factor 2	860			R -> S (in dbSNP:rs2228313).		cellular lipid metabolic process (GO:0044255)|cellular response to laminar fluid shear stress (GO:0071499)|cholesterol metabolic process (GO:0008203)|lipid metabolic process (GO:0006629)|negative regulation of cholesterol efflux (GO:0090370)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cholesterol homeostasis (GO:2000188)|regulation of lipid transport by negative regulation of transcription from RNA polymerase II promoter (GO:0072368)|response to low-density lipoprotein particle (GO:0055098)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi membrane (GO:0000139)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SREBP-SCAP-Insig complex (GO:0032937)	E-box binding (GO:0070888)|protein C-terminus binding (GO:0008022)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(2)|breast(6)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(9)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	38						CACTCTCCAGGAGCTCCGTGC	0.542													C|||	293	0.0585064	0.0265	0.0562	5008	,	,		18915	0.0645		0.0805	False		,,,				2504	0.0746				p.R860S		Atlas-SNP	.											.	SREBF2	99	.	0			c.G2580C						PASS	.	C	SER/ARG	155,4251	810.3+/-416.0	2,151,2050	45.0	45.0	45.0		2580	2.2	1.0	22	dbSNP_98	45	650,7950	788.4+/-407.6	30,590,3680	yes	missense	SREBF2	NM_004599.2	110	32,741,5730	CC,CG,GG		7.5581,3.5179,6.1895	benign	860/1142	42293140	805,12201	2203	4300	6503	SO:0001583	missense	6721	exon14			CTCCAGGAGCTCC	U02031	CCDS14023.1	22q13.2	2013-05-21			ENSG00000198911	ENSG00000198911		"""Basic helix-loop-helix proteins"""	11290	protein-coding gene	gene with protein product		600481				7903453	Standard	NM_004599		Approved	SREBP2, bHLHd2	uc003bbi.3	Q12772	OTTHUMG00000151261	ENST00000361204.4:c.2580G>C	22.37:g.42293140G>C	ENSP00000354476:p.Arg860Ser	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	39	23	0.589744	NM_004599	Q05BD5|Q6GTH7|Q86V36|Q9UH04	Missense_Mutation	SNP	ENST00000361204.4	37	CCDS14023.1	145	0.06639194139194139	17	0.034552845528455285	19	0.052486187845303865	47	0.08216783216783216	62	0.08179419525065963	C	7.926	0.739631	0.15642	0.035179	0.075581	ENSG00000198911	ENST00000361204;ENST00000457567	T	0.07444	3.19	5.41	2.15	0.27550	.	0.402301	0.32608	N	0.005875	T	0.00109	0.0003	N	0.00707	-1.245	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.36212	-0.9757	9	0.07175	T	0.84	-6.2861	2.4575	0.04533	0.1316:0.5273:0.1275:0.2137	rs2228313;rs11547820;rs17848350	860	Q12772	SRBP2_HUMAN	S	860	ENSP00000354476:R860S	ENSP00000354476:R860S	R	+	3	2	SREBF2	40623086	0.998000	0.40836	0.998000	0.56505	0.670000	0.39368	0.338000	0.19858	0.023000	0.15187	-0.736000	0.03550	AGG	G|0.936;C|0.064	0.064	strong		0.542	SREBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321956.1	NM_004599	
CCDC13	152206	hgsc.bcm.edu	37	3	42772038	42772038	+	Missense_Mutation	SNP	A	A	T	rs12495805	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:42772038A>T	ENST00000310232.6	-	13	1722	c.1639T>A	c.(1639-1641)Tca>Aca	p.S547T	CCDC13-AS1_ENST00000446950.1_RNA|CCDC13-AS1_ENST00000418161.1_RNA	NM_144719.3	NP_653320.3	Q8IYE1	CCD13_HUMAN	coiled-coil domain containing 13	547			S -> T (in dbSNP:rs12495805).							endometrium(1)|kidney(1)|large_intestine(5)|liver(1)|lung(11)|ovary(1)|prostate(3)|skin(1)|urinary_tract(1)	25						TTGATCTCTGACACTTGTGCC	0.592													T|||	1022	0.204073	0.2451	0.1844	5008	,	,		18415	0.1081		0.1849	False		,,,				2504	0.2812				p.S547T		Atlas-SNP	.											.	CCDC13	71	.	0			c.T1639A						PASS	.	T	THR/SER	1077,3329	722.4+/-409.3	108,861,1234	87.0	85.0	85.0		1639	-3.3	0.0	3	dbSNP_120	85	1567,7033	744.7+/-407.2	123,1321,2856	yes	missense	CCDC13	NM_144719.3	58	231,2182,4090	TT,TA,AA		18.2209,24.4439,20.3291	benign	547/716	42772038	2644,10362	2203	4300	6503	SO:0001583	missense	152206	exon13			TCTCTGACACTTG	AK058196	CCDS2705.1	3p22.1	2005-01-25			ENSG00000244607	ENSG00000244607			26358	protein-coding gene	gene with protein product						12477932	Standard	NM_144719		Approved	FLJ25467	uc003cly.4	Q8IYE1	OTTHUMG00000133046	ENST00000310232.6:c.1639T>A	3.37:g.42772038A>T	ENSP00000309836:p.Ser547Thr	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	120	57	0.475	NM_144719		Missense_Mutation	SNP	ENST00000310232.6	37	CCDS2705.1	427	0.1955128205128205	139	0.28252032520325204	75	0.20718232044198895	71	0.12412587412587413	142	0.18733509234828497	T	0.599	-0.829686	0.02734	0.244439	0.182209	ENSG00000244607	ENST00000310232	T	0.10573	2.86	5.76	-3.26	0.05064	.	0.453819	0.24400	N	0.038850	T	0.00012	0.0000	N	0.00170	-1.935	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.42327	-0.9458	9	0.12766	T	0.61	.	10.1473	0.42771	0.1103:0.5632:0.0:0.3265	rs12495805;rs52834773;rs12495805	547	Q8IYE1	CCD13_HUMAN	T	547	ENSP00000309836:S547T	ENSP00000309836:S547T	S	-	1	0	CCDC13	42747042	0.002000	0.14202	0.006000	0.13384	0.575000	0.36095	-0.454000	0.06770	-0.933000	0.03737	-1.051000	0.02340	TCA	A|0.792;T|0.208	0.208	strong		0.592	CCDC13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256652.1	NM_144719	
GOLGB1	2804	hgsc.bcm.edu	37	3	121386377	121386377	+	Missense_Mutation	SNP	T	T	A	rs144495540	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:121386377T>A	ENST00000340645.5	-	20	9610	c.9485A>T	c.(9484-9486)gAc>gTc	p.D3162V	GOLGB1_ENST00000393667.3_Missense_Mutation_p.D3172V	NM_001256487.1|NM_001256488.1|NM_004487.4	NP_001243416.1|NP_001243417.1|NP_004478.3	Q14789	GOGB1_HUMAN	golgin B1	3162					Golgi organization (GO:0007030)	cis-Golgi network (GO:0005801)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(2)|cervix(2)|endometrium(12)|kidney(3)|large_intestine(26)|liver(2)|lung(36)|ovary(7)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(13)	119				GBM - Glioblastoma multiforme(114;0.0989)		CACTCTTTGGTCTCGTTCTTC	0.493																																					p.D3172V		Atlas-SNP	.											.	GOLGB1	319	.	0			c.A9515T						PASS	.	T	VAL/ASP	0,4406		0,0,2203	104.0	93.0	97.0		9485	5.5	1.0	3	dbSNP_134	97	7,8593	5.7+/-21.5	0,7,4293	yes	missense	GOLGB1	NM_004487.3	152	0,7,6496	AA,AT,TT		0.0814,0.0,0.0538	probably-damaging	3162/3260	121386377	7,12999	2203	4300	6503	SO:0001583	missense	2804	exon20			CTTTGGTCTCGTT	X75304	CCDS3004.1, CCDS58847.1, CCDS74989.1	3q13	2010-02-12	2010-02-12	2007-07-27	ENSG00000173230	ENSG00000173230			4429	protein-coding gene	gene with protein product	"""macrogolgin"", ""golgi integral membrane protein 1"""	602500	"""golgi autoantigen, golgin subfamily b, macrogolgin (with transmembrane signal), 1"", ""golgin B1, golgi integral membrane protein"""			7691276, 15004235	Standard	NM_001256486		Approved	GCP, GCP372, giantin, GOLIM1	uc010hrc.4	Q14789	OTTHUMG00000159411	ENST00000340645.5:c.9485A>T	3.37:g.121386377T>A	ENSP00000341848:p.Asp3162Val	Somatic	264	1	0.00378788		WXS	Illumina HiSeq	Phase_I	248	115	0.46371	NM_001256486	B2ZZ91|D3DN92|E7EP74|Q14398	Missense_Mutation	SNP	ENST00000340645.5	37	CCDS3004.1	.	.	.	.	.	.	.	.	.	.	T	17.05	3.290072	0.59976	0.0	8.14E-4	ENSG00000173230	ENST00000340645;ENST00000393667	T;T	0.16073	2.37;2.37	5.48	5.48	0.80851	.	0.090168	0.48767	D	0.000177	T	0.23451	0.0567	N	0.24115	0.695	0.54753	D	0.999989	D;D;P	0.55800	0.973;0.973;0.903	P;P;P	0.59546	0.859;0.859;0.65	T	0.01456	-1.1350	10	0.56958	D	0.05	.	11.8745	0.52539	0.0:0.0:0.0:1.0	.	3172;3172;3162	E7EP74;B2ZZ91;Q14789	.;.;GOGB1_HUMAN	V	3162;3172	ENSP00000341848:D3162V;ENSP00000377275:D3172V	ENSP00000341848:D3162V	D	-	2	0	GOLGB1	122869067	1.000000	0.71417	1.000000	0.80357	0.937000	0.57800	4.287000	0.59001	2.302000	0.77476	0.528000	0.53228	GAC	T|0.999;A|0.001	0.001	strong		0.493	GOLGB1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000355159.1	NM_004487	
TCOF1	6949	hgsc.bcm.edu	37	5	149755744	149755744	+	Missense_Mutation	SNP	G	G	C	rs2071240	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:149755744G>C	ENST00000504761.2	+	13	1993	c.1993G>C	c.(1993-1995)Gcc>Ccc	p.A665P	TCOF1_ENST00000445265.2_Missense_Mutation_p.A588P|TCOF1_ENST00000513346.1_Missense_Mutation_p.A665P|TCOF1_ENST00000394269.3_Missense_Mutation_p.A665P|TCOF1_ENST00000323668.7_Missense_Mutation_p.A588P|TCOF1_ENST00000451292.1_Missense_Mutation_p.A665P|TCOF1_ENST00000377797.3_Missense_Mutation_p.A665P|TCOF1_ENST00000439160.2_Missense_Mutation_p.A665P			Q13428	TCOF_HUMAN	Treacher Collins-Franceschetti syndrome 1	665			A -> P (in dbSNP:rs2071240). {ECO:0000269|PubMed:15019983, ECO:0000269|PubMed:8563749, ECO:0000269|PubMed:9074926, ECO:0000269|PubMed:9096354}.		skeletal system development (GO:0001501)|transcription of nuclear large rRNA transcript from RNA polymerase I promoter (GO:0042790)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|transporter activity (GO:0005215)			NS(1)|breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(8)|ovary(2)|pancreas(1)|prostate(2)|skin(1)	35		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			GGGCACCCAAGCCCCCCGGAA	0.587													G|||	303	0.0605032	0.0045	0.0274	5008	,	,		18615	0.122		0.0646	False		,,,				2504	0.092				p.A665P		Atlas-SNP	.											.	TCOF1	154	.	0			c.G1993C						PASS	.	G	PRO/ALA,PRO/ALA,PRO/ALA,PRO/ALA,PRO/ALA,PRO/ALA	61,4345	54.9+/-90.9	0,61,2142	114.0	130.0	125.0		1762,1993,1993,1993,1762,1993	1.9	0.1	5	dbSNP_96	125	692,7906	165.1+/-217.3	27,638,3634	yes	missense,missense,missense,missense,missense,missense	TCOF1	NM_000356.3,NM_001008657.2,NM_001135243.1,NM_001135244.1,NM_001135245.1,NM_001195141.1	27,27,27,27,27,27	27,699,5776	CC,CG,GG		8.0484,1.3845,5.7905	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	588/1412,665/959,665/1489,665/1452,588/1413,665/1451	149755744	753,12251	2203	4299	6502	SO:0001583	missense	6949	exon13			ACCCAAGCCCCCC		CCDS4306.1, CCDS47305.1, CCDS47306.1, CCDS47307.1, CCDS54936.1	5q32	2014-06-18			ENSG00000070814	ENSG00000070814			11654	protein-coding gene	gene with protein product		606847				1765376	Standard	NM_001008657		Approved	treacle, TCS	uc003lry.3	Q13428	OTTHUMG00000130081	ENST00000504761.2:c.1993G>C	5.37:g.149755744G>C	ENSP00000421655:p.Ala665Pro	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	111	56	0.504505	NM_001135243	A0JLU0|B4E111|Q6SC72|Q7Z5W9|Q96A52|Q99408|Q99860	Missense_Mutation	SNP	ENST00000504761.2	37	CCDS54936.1	110	0.05036630036630037	3	0.006097560975609756	10	0.027624309392265192	48	0.08391608391608392	49	0.06464379947229551	G	15.25	2.778545	0.49786	0.013845	0.080484	ENSG00000070814	ENST00000451292;ENST00000377797;ENST00000445265;ENST00000323668;ENST00000439160;ENST00000394269;ENST00000427724;ENST00000504761;ENST00000513346	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	4.73	1.85	0.25348	Treacher Collins syndrome, treacle (1);	0.401967	0.18465	N	0.140410	T	0.13415	0.0325	L	0.46157	1.445	0.52501	P	4.700000000001925E-5	D;D;D;D;D;D;D	0.89917	1.0;0.99;0.99;0.99;1.0;0.99;0.995	D;P;P;P;D;P;P	0.91635	0.986;0.901;0.901;0.901;0.999;0.901;0.901	T	0.56475	-0.7973	9	0.20519	T	0.43	-8.1637	3.9132	0.09211	0.2067:0.0:0.5962:0.1972	rs2071240;rs60165384;rs2071240	174;665;588;665;665;588;665	B4DRA2;Q13428-7;Q13428-2;Q13428-6;Q13428;Q13428-8;Q13428-5	.;.;.;.;TCOF_HUMAN;.;.	P	665;665;588;588;665;665;665;665;665	ENSP00000400939:A665P;ENSP00000367028:A665P;ENSP00000409944:A588P;ENSP00000325223:A588P;ENSP00000406888:A665P;ENSP00000377811:A665P;ENSP00000390717:A665P;ENSP00000421655:A665P;ENSP00000427484:A665P	ENSP00000325223:A588P	A	+	1	0	TCOF1	149735937	0.390000	0.25213	0.063000	0.19743	0.021000	0.10359	0.180000	0.16860	0.125000	0.18397	0.561000	0.74099	GCC	G|0.948;C|0.052	0.052	strong		0.587	TCOF1-014	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000380552.1	NM_001008656	
DNAH8	1769	hgsc.bcm.edu	37	6	38854646	38854646	+	Missense_Mutation	SNP	T	T	C	rs142328376	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:38854646T>C	ENST00000359357.3	+	55	7942	c.7688T>C	c.(7687-7689)aTt>aCt	p.I2563T	DNAH8_ENST00000441566.1_Missense_Mutation_p.I2527T|DNAH8_ENST00000449981.2_Missense_Mutation_p.I2780T			Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy chain 8	2563	AAA 3. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(7)|breast(9)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(16)|large_intestine(44)|liver(4)|lung(101)|ovary(7)|pancreas(2)|prostate(8)|skin(28)|stomach(4)|upper_aerodigestive_tract(6)|urinary_tract(4)	260						TTCACTACTATTGTTGATGTG	0.393													T|||	8	0.00159744	0.0	0.0072	5008	,	,		21243	0.0		0.003	False		,,,				2504	0.0				p.I2780T		Atlas-SNP	.											.	DNAH8	1239	.	0			c.T8339C						PASS	.	T	THR/ILE	3,4403	6.2+/-15.9	0,3,2200	160.0	146.0	151.0		8339	5.8	1.0	6	dbSNP_134	151	56,8544	35.9+/-90.5	0,56,4244	yes	missense	DNAH8	NM_001206927.1	89	0,59,6444	CC,CT,TT		0.6512,0.0681,0.4536	probably-damaging	2780/4708	38854646	59,12947	2203	4300	6503	SO:0001583	missense	1769	exon57			CTACTATTGTTGA	Z83806	CCDS75447.1	6p21.2	2012-04-19	2006-09-04		ENSG00000124721	ENSG00000124721		"""Axonemal dyneins"""	2952	protein-coding gene	gene with protein product		603337	"""dynein, axonemal, heavy polypeptide 8"""			9373155	Standard	NM_001206927		Approved	hdhc9	uc021yzh.1	Q96JB1	OTTHUMG00000016253	ENST00000359357.3:c.7688T>C	6.37:g.38854646T>C	ENSP00000352312:p.Ile2563Thr	Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	122	50	0.409836	NM_001206927	O00438|Q5JYI2|Q5T2M3|Q5T2M4|Q5TG00|Q9UEM4	Missense_Mutation	SNP	ENST00000359357.3	37		5	0.0022893772893772895	0	0.0	2	0.0055248618784530384	0	0.0	3	0.00395778364116095	T	25.7	4.667937	0.88348	6.81E-4	0.006512	ENSG00000124721	ENST00000449981;ENST00000327475;ENST00000359357;ENST00000441566	T;T;T	0.48522	0.81;0.81;0.81	5.79	5.79	0.91817	ATPase, AAA+ type, core (1);	0.175846	0.50627	D	0.000107	T	0.75391	0.3843	H	0.96748	3.875	0.46981	D	0.999276	D	0.67145	0.996	D	0.70487	0.969	D	0.84767	0.0765	10	0.87932	D	0	.	16.1307	0.81436	0.0:0.0:0.0:1.0	.	2563	Q96JB1	DYH8_HUMAN	T	2768;2768;2563;2527	ENSP00000333363:I2768T;ENSP00000352312:I2563T;ENSP00000402294:I2527T	ENSP00000333363:I2768T	I	+	2	0	DNAH8	38962624	1.000000	0.71417	0.998000	0.56505	0.958000	0.62258	6.189000	0.72051	2.209000	0.71365	0.459000	0.35465	ATT	T|0.996;C|0.004	0.004	strong		0.393	DNAH8-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000043574.1	NM_001206927	
LGR5	8549	hgsc.bcm.edu	37	12	71977787	71977787	+	Missense_Mutation	SNP	T	T	C	rs17109924	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:71977787T>C	ENST00000266674.5	+	18	2308	c.1997T>C	c.(1996-1998)gTg>gCg	p.V666A	RP11-186F10.2_ENST00000546601.1_RNA|LGR5_ENST00000540815.2_Missense_Mutation_p.V642A|LGR5_ENST00000536515.1_Missense_Mutation_p.V594A			O75473	LGR5_HUMAN	leucine-rich repeat containing G protein-coupled receptor 5	666			V -> A (in dbSNP:rs17109924). {ECO:0000269|PubMed:15489334}.		G-protein coupled receptor signaling pathway (GO:0007186)|inner ear development (GO:0048839)|positive regulation of canonical Wnt signaling pathway (GO:0090263)	integral component of plasma membrane (GO:0005887)|trans-Golgi network membrane (GO:0032588)	G-protein coupled receptor activity (GO:0004930)|transmembrane signaling receptor activity (GO:0004888)		NUP107/LGR5(2)	endometrium(2)|kidney(3)|large_intestine(2)|lung(24)|ovary(1)|pancreas(2)|prostate(1)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(3)	48						GGGTTCTCTGTGAAATATTCT	0.458													T|||	357	0.0712859	0.1172	0.0648	5008	,	,		22071	0.003		0.0606	False		,,,				2504	0.0951				p.V666A		Atlas-SNP	.											LGR5,bladder,carcinoma,-1,1	LGR5	103	1	0			c.T1997C						scavenged	.	T	ALA/VAL	456,3950	218.1+/-236.3	25,406,1772	136.0	134.0	135.0		1997	4.7	1.0	12	dbSNP_123	135	657,7943	165.9+/-218.0	20,617,3663	yes	missense	LGR5	NM_003667.2	64	45,1023,5435	CC,CT,TT		7.6395,10.3495,8.5576	possibly-damaging	666/908	71977787	1113,11893	2203	4300	6503	SO:0001583	missense	8549	exon18			TCTCTGTGAAATA	AF062006	CCDS9000.1, CCDS61194.1, CCDS61195.1	12q22-q23	2012-08-21	2011-01-25	2004-11-12				"""GPCR / Class A : Orphans"""	4504	protein-coding gene	gene with protein product		606667	"""G protein-coupled receptor 49"", ""leucine-rich repeat-containing G protein-coupled receptor 5"""	GPR67, GPR49		9642114	Standard	NM_003667		Approved	HG38, FEX	uc001swl.4	O75473	OTTHUMG00000169543	ENST00000266674.5:c.1997T>C	12.37:g.71977787T>C	ENSP00000266674:p.Val666Ala	Somatic	178	1	0.00561798		WXS	Illumina HiSeq	Phase_I	157	75	0.477707	NM_003667	D8MCT0|Q4VAM0|Q4VAM2|Q9UP75	Missense_Mutation	SNP	ENST00000266674.5	37	CCDS9000.1	130	0.05952380952380952	56	0.11382113821138211	26	0.0718232044198895	1	0.0017482517482517483	47	0.06200527704485488	T	10.78	1.446347	0.25987	0.103495	0.076395	ENSG00000139292	ENST00000266674;ENST00000451585;ENST00000536515;ENST00000540815	T;T;T	0.77620	-1.11;-1.11;-1.11	5.85	4.71	0.59529	GPCR, rhodopsin-like superfamily (1);	0.250903	0.28504	N	0.015110	T	0.03651	0.0104	L	0.45051	1.395	0.37532	D	0.917956	B;B	0.19331	0.028;0.035	B;B	0.26864	0.044;0.074	T	0.30119	-0.9989	10	0.18276	T	0.48	.	11.8686	0.52507	0.0:0.068:0.0:0.932	rs17109924;rs56488504;rs61507334;rs17109924	642;666	O75473-2;O75473	.;LGR5_HUMAN	A	666;666;594;642	ENSP00000266674:V666A;ENSP00000443033:V594A;ENSP00000441035:V642A	ENSP00000266674:V666A	V	+	2	0	LGR5	70264054	1.000000	0.71417	0.995000	0.50966	0.997000	0.91878	3.325000	0.52030	1.044000	0.40200	0.533000	0.62120	GTG	T|0.922;C|0.078	0.078	strong		0.458	LGR5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404744.1	NM_003667	
SLFN13	146857	hgsc.bcm.edu	37	17	33768383	33768383	+	Missense_Mutation	SNP	T	T	A	rs11657183	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:33768383T>A	ENST00000285013.6	-	6	2200	c.1925A>T	c.(1924-1926)gAt>gTt	p.D642V	SLFN13_ENST00000526861.1_Missense_Mutation_p.D642V|SLFN13_ENST00000533791.1_Missense_Mutation_p.D642V|SLFN13_ENST00000534689.1_Missense_Mutation_p.D324V|SLFN13_ENST00000360502.2_Missense_Mutation_p.D324V|SLFN13_ENST00000542635.1_Missense_Mutation_p.D642V	NM_144682.5	NP_653283.3	Q68D06	SLN13_HUMAN	schlafen family member 13	642			D -> V (in dbSNP:rs11657183).			intracellular (GO:0005622)	ATP binding (GO:0005524)			NS(1)|breast(1)|endometrium(1)|large_intestine(10)|lung(8)|ovary(3)|pancreas(1)|prostate(5)|stomach(1)	31				UCEC - Uterine corpus endometrioid carcinoma (308;0.0185)		GATATTTCTATCACTGTAAAA	0.383													T|||	818	0.163339	0.1286	0.0865	5008	,	,		17186	0.1052		0.1123	False		,,,				2504	0.3773				p.D642V		Atlas-SNP	.											.	SLFN13	79	.	0			c.A1925T						PASS	.	T	VAL/ASP	432,3678		28,376,1651	38.0	44.0	42.0		1925	-2.3	0.0	17	dbSNP_120	42	967,7539		56,855,3342	no	missense	SLFN13	NM_144682.5	152	84,1231,4993	AA,AT,TT		11.3684,10.5109,11.0891	benign	642/898	33768383	1399,11217	2055	4253	6308	SO:0001583	missense	146857	exon6			TTTCTATCACTGT	AL832726	CCDS32620.1	17q12	2006-04-05				ENSG00000154760			26481	protein-coding gene	gene with protein product		614957				9846487	Standard	NM_144682		Approved	FLJ31952	uc002hjl.2	Q68D06		ENST00000285013.6:c.1925A>T	17.37:g.33768383T>A	ENSP00000285013:p.Asp642Val	Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	34	16	0.470588	NM_144682	E1P645|Q658M1|Q6ZS51|Q96A81	Missense_Mutation	SNP	ENST00000285013.6	37	CCDS32620.1	247	0.1130952380952381	83	0.16869918699186992	31	0.0856353591160221	50	0.08741258741258741	83	0.10949868073878628	a	5.074	0.199308	0.09652	0.105109	0.113684	ENSG00000154760	ENST00000285013;ENST00000360502;ENST00000526861;ENST00000542635;ENST00000534689	D;D;D;D;D	0.82984	-1.67;-1.67;-1.67;-1.67;-1.67	3.29	-2.27	0.06846	Domain of unknown function DUF2075 (1);	1.570860	0.03754	N	0.257015	T	0.00412	0.0013	N	0.22421	0.69	0.80722	P	0.0	B;B	0.33413	0.226;0.411	B;B	0.33890	0.076;0.172	T	0.09975	-1.0650	9	0.45353	T	0.12	.	0.4205	0.00455	0.1772:0.2366:0.1973:0.3889	rs11657183;rs52816132;rs59899591;rs11657183	324;642	Q68D06-2;Q68D06	.;SLN13_HUMAN	V	642;324;642;642;324	ENSP00000285013:D642V;ENSP00000353692:D324V;ENSP00000434439:D642V;ENSP00000444016:D642V;ENSP00000435442:D324V	ENSP00000285013:D642V	D	-	2	0	SLFN13	30792496	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.126000	0.10563	-0.669000	0.05289	-2.924000	0.00089	GAT	T|0.891;A|0.109	0.109	strong		0.383	SLFN13-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381883.1	NM_144682	
PRKCQ	5588	hgsc.bcm.edu	37	10	6472891	6472891	+	Silent	SNP	G	G	T	rs11258747	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:6472891G>T	ENST00000263125.5	-	17	1945	c.1846C>A	c.(1846-1848)Cga>Aga	p.R616R	PRKCQ_ENST00000397176.2_Silent_p.R553R|PRKCQ_ENST00000539722.1_Silent_p.R491R	NM_001282644.1|NM_006257.3	NP_001269573.1|NP_006248.1	Q04759	KPCT_HUMAN	protein kinase C, theta	616	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|Fc-epsilon receptor signaling pathway (GO:0038095)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|membrane protein ectodomain proteolysis (GO:0006509)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of T cell apoptotic process (GO:0070233)|phototransduction, visible light (GO:0007603)|platelet activation (GO:0030168)|positive regulation of interleukin-17 production (GO:0032740)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of interleukin-4 production (GO:0032753)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of T-helper 17 type immune response (GO:2000318)|positive regulation of T-helper 2 cell activation (GO:2000570)|protein ubiquitination (GO:0016567)|regulation of cell growth (GO:0001558)|regulation of platelet aggregation (GO:0090330)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|regulation of transcription, DNA-templated (GO:0006355)|rhodopsin mediated signaling pathway (GO:0016056)|T cell receptor signaling pathway (GO:0050852)	cytosol (GO:0005829)|immunological synapse (GO:0001772)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)|ubiquitin-protein transferase activity (GO:0004842)			NS(1)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|liver(1)|lung(13)|ovary(4)|prostate(1)|skin(4)|stomach(2)	45					Tamoxifen(DB00675)	TCAGGTTCTCGCACGAAGAGC	0.587													G|||	614	0.122604	0.1271	0.1124	5008	,	,		19945	0.0308		0.2187	False		,,,				2504	0.1196				p.R616R	Ovarian(50;572 1126 10530 25349 30594)	Atlas-SNP	.											.	PRKCQ	113	.	0			c.C1846A						PASS	.	G	,	624,3782	270.1+/-269.4	44,536,1623	62.0	54.0	57.0	http://www.ncbi.nlm.nih.gov/pubmed?term	1657,1846	1.6	1.0	10	dbSNP_120	57	1908,6692	337.4+/-322.3	204,1500,2596	yes	coding-synonymous,coding-synonymous	PRKCQ	NM_001242413.1,NM_006257.3	,	248,2036,4219	TT,TG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	22.186,14.1625,19.4679	,	553/644,616/707	6472891	2532,10474	2203	4300	6503	SO:0001819	synonymous_variant	5588	exon17			GTTCTCGCACGAA	L07032	CCDS7079.1, CCDS55701.1, CCDS60482.1	10p15	2009-07-10			ENSG00000065675	ENSG00000065675	2.7.11.1		9410	protein-coding gene	gene with protein product		600448				8444877	Standard	NM_001282645		Approved		uc001ijj.2	Q04759	OTTHUMG00000017623	ENST00000263125.5:c.1846C>A	10.37:g.6472891G>T		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	29	11	0.37931	NM_006257	B4DF52|Q14DH6|Q3MJF1|Q64FY5|Q9H508|Q9H549	Silent	SNP	ENST00000263125.5	37	CCDS7079.1	287	0.13141025641025642	56	0.11382113821138211	45	0.12430939226519337	18	0.03146853146853147	168	0.22163588390501318	G	8.847	0.943677	0.18281	0.141625	0.22186	ENSG00000065675	ENST00000397178	.	.	.	5.23	1.63	0.23807	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	7.4448	0.27205	0.1186:0.0:0.3386:0.5427	rs11258747;rs11258747	.	.	.	X	388	.	.	C	-	3	2	PRKCQ	6512897	1.000000	0.71417	0.975000	0.42487	0.846000	0.48090	1.036000	0.30228	0.027000	0.15297	0.650000	0.86243	TGC	G|0.847;T|0.153	0.153	strong		0.587	PRKCQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046665.1	NM_006257	
LAMP3	27074	hgsc.bcm.edu	37	3	182853670	182853670	+	Missense_Mutation	SNP	T	T	C	rs482912	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:182853670T>C	ENST00000265598.3	-	5	1207	c.952A>G	c.(952-954)Att>Gtt	p.I318V	LAMP3_ENST00000466939.1_Missense_Mutation_p.I294V	NM_014398.3	NP_055213.2	Q9UQV4	LAMP3_HUMAN	lysosomal-associated membrane protein 3	318			I -> V (in dbSNP:rs482912). {ECO:0000269|PubMed:9721848, ECO:0000269|Ref.3}.		cell proliferation (GO:0008283)|immune system process (GO:0002376)	alveolar lamellar body membrane (GO:0097233)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(6)|lung(9)|ovary(2)|prostate(2)	28	all_cancers(143;9.14e-14)|Ovarian(172;0.0355)		all cancers(12;2.91e-44)|Epithelial(37;5.52e-38)|LUSC - Lung squamous cell carcinoma(7;7.12e-25)|Lung(8;6.39e-23)|OV - Ovarian serous cystadenocarcinoma(80;4.16e-21)			CCTTGGTAAATTGTCTCTGAA	0.522													T|||	2486	0.496406	0.2224	0.5029	5008	,	,		18728	0.4712		0.7247	False		,,,				2504	0.6534				p.I318V		Atlas-SNP	.											.	LAMP3	48	.	0			c.A952G						PASS	.	T	VAL/ILE	1327,3079	445.1+/-347.6	197,933,1073	201.0	197.0	199.0		952	-1.4	0.0	3	dbSNP_83	199	6366,2234	709.8+/-405.7	2366,1634,300	yes	missense	LAMP3	NM_014398.3	29	2563,2567,1373	CC,CT,TT		25.9767,30.118,40.8504	benign	318/417	182853670	7693,5313	2203	4300	6503	SO:0001583	missense	27074	exon5			GGTAAATTGTCTC	AB013924	CCDS3242.1	3q26.3-q27	2011-11-24			ENSG00000078081	ENSG00000078081		"""CD molecules"""	14582	protein-coding gene	gene with protein product		605883				9721848	Standard	NM_014398		Approved	LAMP, TSC403, DC-LAMP, DCLAMP, CD208	uc003flh.4	Q9UQV4	OTTHUMG00000158387	ENST00000265598.3:c.952A>G	3.37:g.182853670T>C	ENSP00000265598:p.Ile318Val	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	87	86	0.988506	NM_014398	D3DNS4|O94781|Q8NEC8	Missense_Mutation	SNP	ENST00000265598.3	37	CCDS3242.1	1151	0.527014652014652	135	0.27439024390243905	190	0.5248618784530387	285	0.4982517482517482	541	0.7137203166226913	T	0.129	-1.116168	0.01799	0.30118	0.740233	ENSG00000078081	ENST00000265598;ENST00000466939	T;T	0.33438	1.41;1.41	5.47	-1.37	0.09056	.	1.391350	0.04601	N	0.398459	T	0.00012	0.0000	N	0.01410	-0.885	0.29514	P	0.853963	B	0.02656	0.0	B	0.04013	0.001	T	0.38243	-0.9670	9	0.02654	T	1	0.4151	9.4867	0.38933	0.0:0.5767:0.0:0.4233	rs482912;rs3736552;rs17856962;rs57467289;rs482912	318	Q9UQV4	LAMP3_HUMAN	V	318;294	ENSP00000265598:I318V;ENSP00000418912:I294V	ENSP00000265598:I318V	I	-	1	0	LAMP3	184336364	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.439000	0.06897	-0.082000	0.12640	-0.274000	0.10170	ATT	T|0.458;C|0.542	0.542	strong		0.522	LAMP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350863.1		
ZNF594	84622	hgsc.bcm.edu	37	17	5087040	5087040	+	Missense_Mutation	SNP	A	A	G	rs9908414	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:5087040A>G	ENST00000399604.4	-	1	652	c.512T>C	c.(511-513)aTt>aCt	p.I171T	ZNF594_ENST00000575779.1_Missense_Mutation_p.I171T			Q96JF6	ZN594_HUMAN	zinc finger protein 594	171			I -> T (in dbSNP:rs9908414).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(3)|lung(10)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	33						CTGATGTATAATAAGATTTGA	0.338													a|||	1134	0.226438	0.1233	0.4265	5008	,	,		20145	0.0972		0.4354	False		,,,				2504	0.1421				p.I171T		Atlas-SNP	.											ZNF594,caecum,carcinoma,0,1	ZNF594	89	1	0			c.T512C						PASS	.						80.0	83.0	82.0					17																	5087040		1993	4200	6193	SO:0001583	missense	84622	exon2			TGTATAATAAGAT	AB058774	CCDS42241.1	17p13	2013-01-08			ENSG00000180626	ENSG00000180626		"""Zinc fingers, C2H2-type"""	29392	protein-coding gene	gene with protein product						11347906	Standard	NM_032530		Approved	KIAA1871	uc010cla.1	Q96JF6	OTTHUMG00000132059	ENST00000399604.4:c.512T>C	17.37:g.5087040A>G	ENSP00000382513:p.Ile171Thr	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	50	19	0.38	NM_032530	Q6RFS0	Missense_Mutation	SNP	ENST00000399604.4	37	CCDS42241.1	604	0.2765567765567766	69	0.1402439024390244	157	0.43370165745856354	51	0.08916083916083917	327	0.4313984168865435	a	0.001	-4.054948	0.00002	.	.	ENSG00000180626	ENST00000399604	T	0.37584	1.19	2.29	-2.72	0.05968	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	L	0.42245	1.32	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.46871	-0.9160	8	0.08837	T	0.75	.	6.3503	0.21373	0.5162:0.0:0.4838:0.0	rs9908414;rs17178125;rs52818653;rs58970192;rs9908414	171	Q96JF6	ZN594_HUMAN	T	171	ENSP00000382513:I171T	ENSP00000382513:I171T	I	-	2	0	ZNF594	5027764	0.000000	0.05858	0.203000	0.23512	0.000000	0.00434	-1.675000	0.01947	-0.853000	0.04136	-1.319000	0.01295	ATT	A|0.710;G|0.290	0.290	strong		0.338	ZNF594-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438996.1	XM_290737	
OR5L2	26338	hgsc.bcm.edu	37	11	55595115	55595115	+	Missense_Mutation	SNP	C	C	T	rs35214936|rs71490506|rs386753701	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:55595115C>T	ENST00000378397.1	+	1	421	c.421C>T	c.(421-423)Cgt>Tgt	p.R141C		NM_001004739.1	NP_001004739.1	Q8NGL0	OR5L2_HUMAN	olfactory receptor, family 5, subfamily L, member 2	141						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.R141C(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)				TCAGAAGCTGCGTGTGGAGCT	0.517										HNSCC(27;0.073)			N|||	449	0.0896565	0.1309	0.0403	5008	,	,		21374	0.0853		0.0924	False		,,,				2504	0.0706				p.R141C		Atlas-SNP	.											OR5L2,NS,carcinoma,0,1	OR5L2	135	1	1	Substitution - Missense(1)	stomach(1)	c.C421T						PASS	.						211.0	182.0	192.0					11																	55595115		2200	4296	6496	SO:0001583	missense	26338	exon1			AAGCTGCGTGTGG	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.421C>T	11.37:g.55595115C>T	ENSP00000367650:p.Arg141Cys	Somatic	254	0	0		WXS	Illumina HiSeq	Phase_I	205	143	0.697561	NM_001004739	Q6IF66|Q96RB2	Missense_Mutation	SNP	ENST00000378397.1	37	CCDS31511.1	146	0.06684981684981685	47	0.09552845528455285	17	0.04696132596685083	36	0.06293706293706294	46	0.06068601583113457	.	0.003	-2.453880	0.00175	.	.	ENSG00000205030	ENST00000378397	T	0.34275	1.37	5.18	0.994	0.19832	GPCR, rhodopsin-like superfamily (1);	0.359940	0.24334	N	0.039423	T	0.00178	0.0005	N	0.00084	-2.21	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.06405	0.002	T	0.37009	-0.9724	9	0.02654	T	1	-1.0929	8.8173	0.35004	0.0:0.2583:0.0:0.7417	.	141	Q8NGL0	OR5L2_HUMAN	C	141	ENSP00000367650:R141C	ENSP00000367650:R141C	R	+	1	0	OR5L2	55351691	0.010000	0.17322	0.064000	0.19789	0.051000	0.14879	0.390000	0.20768	-0.004000	0.14419	-0.389000	0.06534	CGT	C|0.913;G|0.000;T|0.087	0.087	strong		0.517	OR5L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391516.1	NM_001004739	
CEP57L1	285753	hgsc.bcm.edu	37	6	109480562	109480562	+	Missense_Mutation	SNP	T	T	C	rs61743581	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:109480562T>C	ENST00000517392.1	+	9	1339	c.913T>C	c.(913-915)Tgg>Cgg	p.W305R	CEP57L1_ENST00000336977.4_Missense_Mutation_p.W205R|CEP57L1_ENST00000523787.1_Missense_Mutation_p.W308R|CEP57L1_ENST00000407272.1_Missense_Mutation_p.W305R|CEP57L1_ENST00000368970.2_Missense_Mutation_p.W322R|CEP57L1_ENST00000359793.3_Missense_Mutation_p.W305R|CEP57L1_ENST00000520883.1_Missense_Mutation_p.W205R|CEP57L1_ENST00000521522.1_Missense_Mutation_p.W252R|CEP57L1_ENST00000368968.2_Missense_Mutation_p.W305R	NM_001271852.1|NM_001271853.1	NP_001258781.1|NP_001258782.1	Q8IYX8	CE57L_HUMAN	centrosomal protein 57kDa-like 1	305					microtubule anchoring (GO:0034453)	cytoplasm (GO:0005737)|microtubule (GO:0005874)				endometrium(1)|kidney(1)|large_intestine(1)|lung(7)|ovary(1)	11						AACAACTTCCTGGTGTAAAGC	0.423													T|||	612	0.122204	0.1505	0.0836	5008	,	,		18224	0.0427		0.1262	False		,,,				2504	0.1892				p.W305R		Atlas-SNP	.											.	CEP57L1	24	.	0			c.T913C						PASS	.	T	ARG/TRP,ARG/TRP	635,3771	272.5+/-270.8	32,571,1600	100.0	98.0	99.0		913,913	1.4	0.0	6	dbSNP_129	99	876,7724	197.6+/-242.2	61,754,3485	no	missense,missense	CEP57L1	NM_001083535.1,NM_173830.4	101,101	93,1325,5085	CC,CT,TT		10.186,14.4122,11.6177	benign,benign	305/461,305/461	109480562	1511,11495	2203	4300	6503	SO:0001583	missense	285753	exon9			ACTTCCTGGTGTA	AK092723	CCDS5071.1, CCDS64491.1	6q21	2014-01-28	2010-09-30	2010-09-30	ENSG00000183137	ENSG00000183137			21561	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 182"""	C6orf182			Standard	NM_001083535		Approved	bA487F23.2, MGC21731	uc003psy.4	Q8IYX8	OTTHUMG00000015336	ENST00000517392.1:c.913T>C	6.37:g.109480562T>C	ENSP00000427844:p.Trp305Arg	Somatic	374	0	0		WXS	Illumina HiSeq	Phase_I	330	173	0.524242	NM_001271853	G5E992	Missense_Mutation	SNP	ENST00000517392.1	37	CCDS5071.1	212	0.09706959706959707	66	0.13414634146341464	30	0.08287292817679558	23	0.04020979020979021	93	0.12269129287598944	T	3.884	-0.025451	0.07589	0.144122	0.10186	ENSG00000183137	ENST00000517392;ENST00000407272;ENST00000336977;ENST00000521522;ENST00000368968;ENST00000368970;ENST00000520883;ENST00000523787;ENST00000359793;ENST00000523174	T;T;T;T;T;T;T;T;T	0.39056	1.12;1.12;1.1;1.1;1.11;1.13;1.1;1.12;1.12	4.72	1.43	0.22495	.	1.742820	0.02657	N	0.107075	T	0.06508	0.0167	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	0.11842	-1.0571	9	0.06365	T	0.9	13.0819	7.3854	0.26880	0.0:0.6673:0.0:0.3327	rs61743581	305;305	Q8IYX8;G5E992	CE57L_HUMAN;.	R	305;305;205;252;305;322;205;308;305;86	ENSP00000427844:W305R;ENSP00000383936:W305R;ENSP00000337392:W205R;ENSP00000428344:W252R;ENSP00000357964:W305R;ENSP00000357966:W322R;ENSP00000430011:W205R;ENSP00000430529:W308R;ENSP00000352841:W305R	ENSP00000337392:W205R	W	+	1	0	CEP57L1	109587255	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.051000	0.14141	0.051000	0.15978	-0.417000	0.06048	TGG	T|0.887;C|0.113	0.113	strong		0.423	CEP57L1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000041734.4	NM_173830	
EXD1	161829	hgsc.bcm.edu	37	15	41483682	41483682	+	Silent	SNP	A	A	G	rs1971131	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:41483682A>G	ENST00000314992.5	-	8	838	c.648T>C	c.(646-648)ccT>ccC	p.P216P	RN7SL497P_ENST00000476341.2_RNA|EXD1_ENST00000458580.2_Silent_p.P274P	NM_152596.2	NP_689809.2	Q8NHP7	EXD1_HUMAN	exonuclease 3'-5' domain containing 1	216							3'-5' exonuclease activity (GO:0008408)|nucleic acid binding (GO:0003676)	p.P216P(1)		large_intestine(5)|liver(1)|lung(4)|ovary(2)|prostate(2)|skin(2)	16						AGAGATATTTAGGGGCTACTT	0.383													A|||	1710	0.341454	0.5817	0.2161	5008	,	,		17705	0.2788		0.171	False		,,,				2504	0.3456				p.P216P		Atlas-SNP	.											EXD1,NS,carcinoma,0,2	EXD1	52	2	1	Substitution - coding silent(1)	prostate(1)	c.T648C						PASS	.	A		2261,2145	593.4+/-388.0	570,1121,512	87.0	92.0	90.0		648	-2.2	1.0	15	dbSNP_92	90	1382,7218	268.9+/-288.1	110,1162,3028	no	coding-synonymous	EXD1	NM_152596.2		680,2283,3540	GG,GA,AA		16.0698,48.6836,28.0101		216/515	41483682	3643,9363	2203	4300	6503	SO:0001819	synonymous_variant	161829	exon8			ATATTTAGGGGCT	BC030628	CCDS10072.1, CCDS66738.1	15q15.1	2009-02-24	2009-02-24	2009-02-24	ENSG00000178997	ENSG00000178997			28507	protein-coding gene	gene with protein product			"""exonuclease 3'-5' domain-like 1"""	EXDL1		12477932	Standard	NM_001286441		Approved	MGC33637	uc001znk.3	Q8NHP7	OTTHUMG00000130232	ENST00000314992.5:c.648T>C	15.37:g.41483682A>G		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	91	39	0.428571	NM_152596	A8K909|B7Z839|Q6ZW94	Silent	SNP	ENST00000314992.5	37	CCDS10072.1																																																																																			A|0.702;G|0.298	0.298	strong		0.383	EXD1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252553.2	NM_152596	
TTC3	7267	hgsc.bcm.edu	37	21	38572565	38572565	+	Silent	SNP	C	C	T	rs150750778	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:38572565C>T	ENST00000399017.2	+	45	8630	c.5883C>T	c.(5881-5883)caC>caT	p.H1961H	TTC3_ENST00000479930.1_3'UTR|TTC3_ENST00000354749.2_Silent_p.H1961H|TTC3_ENST00000355666.1_Silent_p.H1961H	NM_003316.3	NP_003307.3	P53804	TTC3_HUMAN	tetratricopeptide repeat domain 3	1961					negative regulation of cell morphogenesis involved in differentiation (GO:0010771)|negative regulation of neuron differentiation (GO:0045665)|protein K48-linked ubiquitination (GO:0070936)|ubiquitin-dependent protein catabolic process (GO:0006511)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|vacuole (GO:0005773)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(5)|endometrium(7)|kidney(5)|large_intestine(17)|liver(1)|lung(18)|ovary(4)|prostate(2)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(5)	75		Myeloproliferative disorder(46;0.0412)				AAATATGCCACGAGGTGTTCA	0.433													C|||	14	0.00279553	0.0083	0.0029	5008	,	,		17732	0.0		0.001	False		,,,				2504	0.0				p.H1961H	Ovarian(38;194 1649 35661)	Atlas-SNP	.											.	TTC3	182	.	0			c.C5883T						PASS	.	C	,	12,4394	19.1+/-41.9	0,12,2191	85.0	74.0	78.0		5883,5883	-11.2	0.0	21	dbSNP_134	78	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	TTC3	NM_001001894.1,NM_003316.3	,	0,12,6491	TT,TC,CC		0.0,0.2724,0.0923	,	1961/2026,1961/2026	38572565	12,12994	2203	4300	6503	SO:0001819	synonymous_variant	7267	exon45			ATGCCACGAGGTG	D84296	CCDS13651.1	21q22.2	2013-01-11			ENSG00000182670	ENSG00000182670		"""RING-type (C3HC4) zinc fingers"", ""Tetratricopeptide (TTC) repeat domain containing"""	12393	protein-coding gene	gene with protein product		602259				8947847	Standard	NM_003316		Approved	TPRD, TPRDI, DCRR1, TPRDII, TPRDIII, RNF105	uc002yvz.3	P53804	OTTHUMG00000086654	ENST00000399017.2:c.5883C>T	21.37:g.38572565C>T		Somatic	240	0	0		WXS	Illumina HiSeq	Phase_I	287	56	0.195122	NM_001001894	A8K7H7|B2RPA7|D3DSG9|D3DSH2|D3DSH3|O60767|P78476|P78477|Q569I2|Q6P578|Q9UEK4	Silent	SNP	ENST00000399017.2	37	CCDS13651.1	8	0.003663003663003663	7	0.014227642276422764	1	0.0027624309392265192	0	0.0	0	0.0	C	5.526	0.282044	0.10458	0.002724	0.0	ENSG00000182670	ENST00000428693	.	.	.	5.58	-11.2	0.00127	.	.	.	.	.	.	.	.	.	.	.	0.22684	N	0.99886	.	.	.	.	.	.	.	.	.	.	.	.	.	-6.0597	9.5757	0.39457	0.2457:0.4773:0.0:0.2771	.	.	.	.	X	253	.	.	R	+	1	2	TTC3	37494435	0.000000	0.05858	0.000000	0.03702	0.741000	0.42261	-3.228000	0.00549	-3.780000	0.00108	-1.090000	0.02178	CGA	C|0.998;T|0.002	0.002	strong		0.433	TTC3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194776.1		
TMPRSS11A	339967	hgsc.bcm.edu	37	4	68810246	68810246	+	Silent	SNP	G	G	A	rs1370840	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:68810246G>A	ENST00000334830.7	-	3	989	c.243C>T	c.(241-243)acC>acT	p.T81T	UBA6-AS1_ENST00000500538.2_RNA|TMPRSS11A_ENST00000508048.1_Silent_p.T80T|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	146	0	0		WXS	Illumina HiSeq	Phase_I	99	51	0.515152	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	
FRG1	2483	hgsc.bcm.edu	37	4	190878658	190878658	+	Splice_Site	SNP	G	G	A	rs76810924		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:190878658G>A	ENST00000226798.4	+	6	759		c.e6+1		FRG1_ENST00000514482.1_Splice_Site	NM_004477.2	NP_004468.1	Q14331	FRG1_HUMAN	FSHD region gene 1						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)		AATGATCAAGGTAATGATGAC	0.348																																					.		Atlas-SNP	.											FRG1,right_upper_lobe,carcinoma,0,1	FRG1	76	1	0			c.537+1G>A						scavenged	.						47.0	43.0	44.0					4																	190878658		2169	4247	6416	SO:0001630	splice_region_variant	2483	exon6			ATCAAGGTAATGA	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.537+1G>A	4.37:g.190878658G>A		Somatic	240	4	0.0166667		WXS	Illumina HiSeq	Phase_I	196	3	0.0153061	NM_004477	A8K775	Splice_Site	SNP	ENST00000226798.4	37	CCDS34121.1	.	.	.	.	.	.	.	.	.	.	N	15.05	2.718286	0.48622	.	.	ENSG00000109536	ENST00000226798;ENST00000524583	.	.	.	3.8	3.8	0.43715	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.6226	0.62146	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	FRG1	191115652	1.000000	0.71417	1.000000	0.80357	0.557000	0.35523	9.554000	0.98121	1.860000	0.53959	0.454000	0.30748	.	G|0.875;A|0.125	0.125	weak		0.348	FRG1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000359622.4	NM_004477	Intron
KRTAP4-11	653240	hgsc.bcm.edu	37	17	39274415	39274415	+	Silent	SNP	C	C	T	rs425487		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:39274415C>T	ENST00000391413.2	-	1	191	c.153G>A	c.(151-153)agG>agA	p.R51R		NM_033059.3	NP_149048.2	Q9BYQ6	KR411_HUMAN	keratin associated protein 4-11	51	27 X 5 AA repeats of C-C-[GIKRQVHEL]- [SPTR]-[STVQRMC].		Missing (in allele KAP4.14). {ECO:0000269|PubMed:15955084}.			keratin filament (GO:0045095)		p.R51R(6)		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)			AGCACTGGGGCCTGCAGCAGC	0.667																																					p.R51R		Atlas-SNP	.											KRTAP4-11,NS,carcinoma,-1,11	KRTAP4-11	94	11	6	Substitution - coding silent(6)	endometrium(3)|kidney(2)|lung(1)	c.G153A						scavenged	.						9.0	15.0	13.0					17																	39274415		682	1579	2261	SO:0001819	synonymous_variant	653240	exon1			CTGGGGCCTGCAG	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.153G>A	17.37:g.39274415C>T		Somatic	78	1	0.0128205		WXS	Illumina HiSeq	Phase_I	71	6	0.084507	NM_033059	A0AUY2	Silent	SNP	ENST00000391413.2	37	CCDS45675.1																																																																																			.	.	weak		0.667	KRTAP4-11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257690.1		
CRIPAK	285464	hgsc.bcm.edu	37	4	1388324	1388324	+	Missense_Mutation	SNP	A	A	C	rs74377230		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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						PASS	.						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	139	0	0		WXS	Illumina HiSeq	Phase_I	111	17	0.153153	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	
FLG2	388698	hgsc.bcm.edu	37	1	152329369	152329369	+	Missense_Mutation	SNP	C	C	G	rs2282302	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	100	0	0		WXS	Illumina HiSeq	Phase_I	103	74	0.718447	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	
OR5P2	120065	hgsc.bcm.edu	37	11	7818313	7818313	+	Silent	SNP	C	C	T	rs73406609	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:7818313C>T	ENST00000329434.2	-	1	207	c.177G>A	c.(175-177)ctG>ctA	p.L59L	RP11-35J10.5_ENST00000527565.1_lincRNA	NM_153444.1	NP_703145.1	Q8WZ92	OR5P2_HUMAN	olfactory receptor, family 5, subfamily P, member 2	59						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(4)	22				Epithelial(150;8.62e-08)|BRCA - Breast invasive adenocarcinoma(625;0.189)		CCAAGTGGCTCAGAAAGAAAT	0.408													C|||	1185	0.236621	0.348	0.2911	5008	,	,		18246	0.128		0.2763	False		,,,				2504	0.1186				p.L59L		Atlas-SNP	.											.	OR5P2	68	.	0			c.G177A						PASS	.	C		1363,2839		399,565,1137	67.0	84.0	79.0		177	1.4	1.0	11	dbSNP_130	79	2421,6163		389,1643,2260	no	coding-synonymous	OR5P2	NM_153444.1		788,2208,3397	TT,TC,CC		28.2036,32.4369,29.5949		59/323	7818313	3784,9002	2101	4292	6393	SO:0001819	synonymous_variant	120065	exon1			GTGGCTCAGAAAG	AF173006	CCDS7782.1	11p15.4	2012-08-09			ENSG00000183303	ENSG00000183303		"""GPCR / Class A : Olfactory receptors"""	14783	protein-coding gene	gene with protein product							Standard	NM_153444		Approved	JCG3	uc001mfp.1	Q8WZ92	OTTHUMG00000165668	ENST00000329434.2:c.177G>A	11.37:g.7818313C>T		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	83	72	0.86747	NM_153444	Q3MIS8	Silent	SNP	ENST00000329434.2	37	CCDS7782.1																																																																																			C|0.741;T|0.259	0.259	strong		0.408	OR5P2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385696.1	NM_153444	
LAMC2	3918	hgsc.bcm.edu	37	1	183187603	183187603	+	Silent	SNP	C	C	T	rs1129723	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:183187603C>T	ENST00000264144.4	+	4	548	c.483C>T	c.(481-483)gtC>gtT	p.V161V	LAMC2_ENST00000493293.1_Silent_p.V161V	NM_005562.2	NP_005553.2	Q13753	LAMC2_HUMAN	laminin, gamma 2	161	Laminin EGF-like 3. {ECO:0000255|PROSITE- ProRule:PRU00460}.				cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	cell cortex (GO:0005938)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|laminin-2 complex (GO:0005607)|laminin-5 complex (GO:0005610)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)	heparin binding (GO:0008201)			breast(2)|endometrium(6)|kidney(8)|large_intestine(11)|lung(18)|ovary(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	55						AGCCAGCTGTCACTGGAGAAC	0.537													C|||	1572	0.313898	0.4024	0.3184	5008	,	,		20576	0.3333		0.1571	False		,,,				2504	0.3323				p.V161V		Atlas-SNP	.											.	LAMC2	113	.	0			c.C483T						PASS	.	C	,	1683,2723	505.4+/-366.1	347,989,867	38.0	36.0	37.0		483,483	4.3	1.0	1	dbSNP_86	37	1518,7082	284.4+/-296.6	129,1260,2911	no	coding-synonymous,coding-synonymous	LAMC2	NM_005562.2,NM_018891.2	,	476,2249,3778	TT,TC,CC		17.6512,38.1979,24.6117	,	161/1194,161/1112	183187603	3201,9805	2203	4300	6503	SO:0001819	synonymous_variant	3918	exon4			AGCTGTCACTGGA	Z15008	CCDS1352.1, CCDS44285.1	1q25-q31	2013-03-01	2002-08-29		ENSG00000058085	ENSG00000058085		"""Laminins"""	6493	protein-coding gene	gene with protein product		150292	"""laminin, gamma 2 (nicein (100kD), kalinin (105kD), BM600 (100kD), Herlitz junctional epidermolysis bullosa))"""	EBR2, LAMB2T, LAMNB2, EBR2A		1383240	Standard	NM_005562		Approved	nicein-100kDa, kalinin-105kDa, BM600-100kDa	uc001gqa.2	Q13753	OTTHUMG00000035520	ENST00000264144.4:c.483C>T	1.37:g.183187603C>T		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	95	49	0.515789	NM_005562	Q02536|Q02537|Q13752|Q14941|Q14DF7|Q2M1N2|Q5VYE8	Silent	SNP	ENST00000264144.4	37	CCDS1352.1																																																																																			C|0.734;T|0.266	0.266	strong		0.537	LAMC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086258.1	NM_005562	
FAM170B	170370	hgsc.bcm.edu	37	10	50339754	50339754	+	Missense_Mutation	SNP	G	G	T	rs73302786	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:50339754G>T	ENST00000311787.5	-	2	845	c.756C>A	c.(754-756)gaC>gaA	p.D252E	FAM170B-AS1_ENST00000443389.1_RNA|FAM170B-AS1_ENST00000435809.1_RNA|FAM170B-AS1_ENST00000442525.1_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	135	0	0		WXS	Illumina HiSeq	Phase_I	130	66	0.507692	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	
ECT2L	345930	hgsc.bcm.edu	37	6	139223635	139223635	+	Splice_Site	SNP	A	A	T	rs200545869		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:139223635A>T	ENST00000423192.1	+	21	2748		c.e21-1		ECT2L_ENST00000367682.2_Splice_Site|ECT2L_ENST00000541398.1_Splice_Site			Q008S8	ECT2L_HUMAN	epithelial cell transforming 2 like								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						ATGCTTTTACAGATGTCAAGA	0.289			"""N, Splice, Mis"""		ETP ALL								A|||	1	0.000199681	0.0	0.0	5008	,	,		18297	0.0		0.001	False		,,,				2504	0.0				.		Atlas-SNP	.		Rec	yes		6	6q24.1	345930	epithelial cell transforming sequence 2 oncogene-like		L	.	ECT2L	75	.	0			c.2588-2A>T						PASS	.	A	,	2,3602		0,2,1800	75.0	71.0	72.0		,	5.6	1.0	6		72	5,8143		0,5,4069	yes	splice-3,splice-3	ECT2L	NM_001077706.2,NM_001195037.2	,	0,7,5869	TT,TA,AA		0.0614,0.0555,0.0596	,	,	139223635	7,11745	1802	4074	5876	SO:0001630	splice_region_variant	345930	exon21			TTTTACAGATGTC		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.2588-1A>T	6.37:g.139223635A>T		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	31	12	0.387097	NM_001195037	B2RUV6|Q5JWK2|Q5JWK3|Q5JWK4	Splice_Site	SNP	ENST00000423192.1	37	CCDS43508.1	.	.	.	.	.	.	.	.	.	.	A	20.8	4.049498	0.75846	5.55E-4	6.14E-4	ENSG00000203734	ENST00000423192;ENST00000367682;ENST00000541398	.	.	.	5.63	5.63	0.86233	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.3602	0.60652	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	ECT2L	139265328	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	5.636000	0.67848	2.145000	0.66743	0.533000	0.62120	.	A|0.999;T|0.001	0.001	weak		0.289	ECT2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042441.3	NM_001077706	Intron
PRG4	10216	hgsc.bcm.edu	37	1	186277989	186277989	+	Silent	SNP	A	A	G	rs3737940	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:186277989A>G	ENST00000445192.2	+	7	3183	c.3138A>G	c.(3136-3138)ccA>ccG	p.P1046P	PRG4_ENST00000367486.3_Silent_p.P1003P|PRG4_ENST00000367485.4_Silent_p.P953P|RNU6-1240P_ENST00000365155.1_RNA|PRG4_ENST00000367483.4_Silent_p.P1005P|PRG4_ENST00000367484.3_Silent_p.P575P	NM_005807.3	NP_005798.2	Q92954	PRG4_HUMAN	proteoglycan 4	1046					cell proliferation (GO:0008283)|hematopoietic stem cell proliferation (GO:0071425)|immune response (GO:0006955)|negative regulation of interleukin-6 biosynthetic process (GO:0045409)|regulation of cell proliferation (GO:0042127)	extracellular space (GO:0005615)	polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(33)|prostate(7)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(1)	102						TGAGAAAACCAAAGACGACAC	0.448													A|||	1108	0.221246	0.1142	0.402	5008	,	,		21201	0.125		0.33	False		,,,				2504	0.2249				p.P1046P		Atlas-SNP	.											.	PRG4	259	.	0			c.A3138G						PASS	.	A	,,,	658,3748	281.4+/-275.9	53,552,1598	164.0	175.0	171.0		3015,2859,2736,3138	-2.0	0.3	1	dbSNP_107	171	3044,5556	467.6+/-367.1	543,1958,1799	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PRG4	NM_001127708.1,NM_001127709.1,NM_001127710.1,NM_005807.3	,,,	596,2510,3397	GG,GA,AA		35.3953,14.9342,28.4638	,,,	1005/1364,953/1312,912/1271,1046/1405	186277989	3702,9304	2203	4300	6503	SO:0001819	synonymous_variant	10216	exon7			AAAACCAAAGACG	U70136	CCDS1369.1, CCDS44287.1, CCDS44288.1	1q25-q31	2008-07-18	2004-11-15		ENSG00000116690	ENSG00000116690			9364	protein-coding gene	gene with protein product	"""lubricin"", ""megakaryocyte stimulating factor"", ""articular superficial zone protein"", ""Jacobs camptodactyly-arthropathy-pericarditis syndrome"", ""camptodactyly, arthropathy, coxa vara, pericarditis syndrome"", ""bG174L6.2 (MSF: megakaryocyte stimulating factor )"""	604283	"""proteoglycan 4, (megakaryocyte stimulating factor, articular superficial zone protein, camptodactyly, arthropathy, coxa vara, pericarditis syndrome)"""	CACP		10545950, 9920774	Standard	NM_005807		Approved	JCAP, SZP, MSF, HAPO, bG174L6.2, FLJ32635	uc001gru.4	Q92954	OTTHUMG00000035574	ENST00000445192.2:c.3138A>G	1.37:g.186277989A>G		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	81	79	0.975309	NM_005807	Q6DNC4|Q6DNC5|Q6ZMZ5|Q9BX49	Silent	SNP	ENST00000445192.2	37	CCDS1369.1																																																																																			A|0.735;G|0.265	0.265	strong		0.448	PRG4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000086346.1	NM_005807	
PSTK	118672	hgsc.bcm.edu	37	10	124742858	124742858	+	Silent	SNP	G	G	A	rs45498396	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:124742858G>A	ENST00000368887.3	+	3	1019	c.579G>A	c.(577-579)agG>agA	p.R193R	PSTK_ENST00000405485.1_Silent_p.R193R|PSTK_ENST00000497219.1_3'UTR	NM_153336.2	NP_699167.2	Q8IV42	PSTK_HUMAN	phosphoseryl-tRNA kinase	193					selenocysteine incorporation (GO:0001514)|selenocysteinyl-tRNA(Sec) biosynthetic process (GO:0097056)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|kinase activity (GO:0016301)|tRNA binding (GO:0000049)			endometrium(1)|kidney(1)|large_intestine(2)|liver(1)|lung(5)|skin(1)|stomach(2)	13		all_neural(114;0.169)|Glioma(114;0.222)		Colorectal(40;0.0686)|COAD - Colon adenocarcinoma(40;0.0725)		ATGGCCAGAGGCCACAGGCAC	0.453													G|||	563	0.11242	0.1785	0.1254	5008	,	,		17620	0.0099		0.1869	False		,,,				2504	0.0429				p.R193R		Atlas-SNP	.											.	PSTK	34	.	0			c.G579A						PASS	.	G		648,3758	277.5+/-273.7	59,530,1614	71.0	71.0	71.0		579	-2.4	0.0	10	dbSNP_127	71	1557,7043	292.6+/-300.9	140,1277,2883	no	coding-synonymous	PSTK	NM_153336.2		199,1807,4497	AA,AG,GG		18.1047,14.7072,16.9537		193/349	124742858	2205,10801	2203	4300	6503	SO:0001819	synonymous_variant	118672	exon3			CCAGAGGCCACAG	AK127173	CCDS7633.1	10q26.13	2007-04-17	2007-04-17	2007-04-17	ENSG00000179988	ENSG00000179988			28578	protein-coding gene	gene with protein product		611310	"""chromosome 10 open reading frame 89"""	C10orf89		15317934	Standard	NM_153336		Approved	MGC35392	uc001lgy.1	Q8IV42	OTTHUMG00000019191	ENST00000368887.3:c.579G>A	10.37:g.124742858G>A		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	91	50	0.549451	NM_153336	Q6ZSS9	Silent	SNP	ENST00000368887.3	37	CCDS7633.1	270	0.12362637362637363	71	0.1443089430894309	54	0.14917127071823205	5	0.008741258741258742	140	0.18469656992084432	G	7.080	0.569992	0.13560	0.147072	0.181047	ENSG00000179988	ENST00000406217	.	.	.	5.86	-2.41	0.06562	.	.	.	.	.	T	0.00210	0.0006	.	.	.	0.09310	P	0.99999999577586	.	.	.	.	.	.	T	0.30736	-0.9968	3	.	.	.	-11.4716	15.141	0.72609	0.3487:0.0:0.6513:0.0	rs45498396;rs61744313	.	.	.	D	194	.	.	G	+	2	0	PSTK	124732848	0.019000	0.18553	0.020000	0.16555	0.948000	0.59901	0.213000	0.17521	-0.708000	0.05015	-0.471000	0.05019	GGC	G|0.842;A|0.158	0.158	strong		0.453	PSTK-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050811.1	NM_153336	
PSPH	5723	hgsc.bcm.edu	37	7	56088786	56088786	+	Silent	SNP	A	A	T	rs202027697	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:56088786A>T	ENST00000395471.3	-	4	925	c.120T>A	c.(118-120)gtT>gtA	p.V40V	PSPH_ENST00000275605.3_Silent_p.V40V|PSPH_ENST00000459834.1_Intron			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	138	0	0		WXS	Illumina HiSeq	Phase_I	162	26	0.160494	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	
LINC00283	100874057	hgsc.bcm.edu	37	13	103397387	103397387	+	RNA	SNP	T	T	G	rs7339187	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:103397387T>G	ENST00000430111.1	+	0	1760									long intergenic non-protein coding RNA 283																		TGTGCCATTTTGGGTCTGGAG	0.393													T|||	329	0.0656949	0.1271	0.0144	5008	,	,		21811	0.1042		0.0268	False		,,,				2504	0.0194				p.Q1887P		Atlas-SNP	.											.	.	.	.	0			c.A5660C						PASS	.	T	PRO/GLN	145,1239		9,127,556	199.0	149.0	164.0		5660	1.1	0.0	13	dbSNP_116	164	68,3112		2,64,1524	yes	missense	CCDC168	NM_001146197.1	76	11,191,2080	GG,GT,TT		2.1384,10.4769,4.667		1887/7082	103397387	213,4351	692	1590	2282			643677	exon4			CCATTTTGGGTCT			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.103397387T>G		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	118	54	0.457627	NM_001146197		Missense_Mutation	SNP	ENST00000430111.1	37																																																																																				T|0.916;G|0.084	0.084	strong		0.393	LINC00283-001	KNOWN	not_organism_supported|basic	antisense	antisense	OTTHUMT00000045714.1		
PSG8	440533	hgsc.bcm.edu	37	19	43269704	43269704	+	Silent	SNP	T	T	C	rs71337226|rs34129574|rs62112127	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	24	0	0		WXS	Illumina HiSeq	Phase_I	14	9	0.642857	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		
BCKDHB	594	hgsc.bcm.edu	37	6	80816415	80816415	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:80816415C>T	ENST00000320393.6	+	1	52	c.5C>T	c.(4-6)gCg>gTg	p.A2V	BCKDHB_ENST00000356489.5_Missense_Mutation_p.A2V|BCKDHB_ENST00000369760.4_Missense_Mutation_p.A2V|BCKDHB_ENST00000545529.1_Missense_Mutation_p.A2V	NM_183050.2	NP_898871.1	P21953	ODBB_HUMAN	branched chain keto acid dehydrogenase E1, beta polypeptide	2					branched-chain amino acid catabolic process (GO:0009083)|cellular nitrogen compound metabolic process (GO:0034641)|response to cAMP (GO:0051591)|response to glucocorticoid (GO:0051384)|response to nutrient (GO:0007584)|small molecule metabolic process (GO:0044281)	mitochondrial alpha-ketoglutarate dehydrogenase complex (GO:0005947)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) activity (GO:0003863)|alpha-ketoacid dehydrogenase activity (GO:0003826)|carboxy-lyase activity (GO:0016831)			central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(10)|upper_aerodigestive_tract(1)	15		all_cancers(76;1.38e-05)|Acute lymphoblastic leukemia(125;1.15e-05)|all_hematologic(105;0.00118)|all_epithelial(107;0.0149)		BRCA - Breast invasive adenocarcinoma(397;0.0291)		GCGGGGATGGCGGTTGTAGCG	0.726																																					p.A2V		Atlas-SNP	.											.	BCKDHB	36	.	0			c.C5T						PASS	.						5.0	6.0	5.0					6																	80816415		2025	3958	5983	SO:0001583	missense	594	exon1			GGATGGCGGTTGT	M55575	CCDS4994.1	6q14.1	2008-07-31	2008-07-31		ENSG00000083123	ENSG00000083123			987	protein-coding gene	gene with protein product	"""maple syrup urine disease"""	248611					Standard	NM_183050		Approved		uc003pje.2	P21953	OTTHUMG00000016430	ENST00000320393.6:c.5C>T	6.37:g.80816415C>T	ENSP00000318351:p.Ala2Val	Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	60	21	0.35	NM_000056	Q5T2J3|Q9BQL0	Missense_Mutation	SNP	ENST00000320393.6	37	CCDS4994.1	.	.	.	.	.	.	.	.	.	.	C	15.45	2.837710	0.50951	.	.	ENSG00000083123	ENST00000369760;ENST00000320393;ENST00000356489;ENST00000545529	D;D;D;D	0.97232	-4.3;-4.22;-4.22;-4.3	5.35	4.46	0.54185	.	0.158692	0.53938	D	0.000046	D	0.87038	0.6078	N	0.08118	0	0.25088	N	0.990873	P	0.50943	0.94	B	0.40636	0.335	D	0.84007	0.0346	10	0.72032	D	0.01	-12.6247	11.7712	0.51960	0.0:0.8233:0.1767:0.0	.	2	P21953	ODBB_HUMAN	V	2	ENSP00000358775:A2V;ENSP00000318351:A2V;ENSP00000348880:A2V;ENSP00000443564:A2V	ENSP00000318351:A2V	A	+	2	0	BCKDHB	80873134	1.000000	0.71417	0.983000	0.44433	0.142000	0.21351	3.221000	0.51215	1.458000	0.47871	0.511000	0.50034	GCG	.	.	none		0.726	BCKDHB-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043911.2	NM_000056	
SLITRK3	22865	hgsc.bcm.edu	37	3	164908529	164908529	+	Silent	SNP	C	C	T	rs76663597	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:164908529C>T	ENST00000475390.1	-	2	533	c.90G>A	c.(88-90)ccG>ccA	p.P30P	SLITRK3_ENST00000241274.3_Silent_p.P30P			O94933	SLIK3_HUMAN	SLIT and NTRK-like family, member 3	30					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						TTAGGGGAATCGGGGTAGTCC	0.423										HNSCC(40;0.11)			C|||	46	0.0091853	0.0	0.0029	5008	,	,		17317	0.0		0.0129	False		,,,				2504	0.0317				p.P30P		Atlas-SNP	.											SLITRK3,caecum,carcinoma,0,1	SLITRK3	263	1	0			c.G90A						PASS	.	C		7,4397	14.3+/-33.2	0,7,2195	101.0	98.0	99.0		90	-12.0	0.3	3	dbSNP_132	99	89,8511	49.8+/-109.6	0,89,4211	no	coding-synonymous	SLITRK3	NM_014926.2		0,96,6406	TT,TC,CC		1.0349,0.1589,0.7382		30/978	164908529	96,12908	2202	4300	6502	SO:0001819	synonymous_variant	22865	exon2			GGGAATCGGGGTA	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.90G>A	3.37:g.164908529C>T		Somatic	200	0	0		WXS	Illumina HiSeq	Phase_I	178	85	0.477528	NM_014926	Q1RMY6	Silent	SNP	ENST00000475390.1	37	CCDS3197.1																																																																																			C|0.994;T|0.006	0.006	strong		0.423	SLITRK3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350126.1	NM_014926	
ARAP3	64411	hgsc.bcm.edu	37	5	141059649	141059649	+	Silent	SNP	A	A	G	rs417503	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:141059649A>G	ENST00000239440.4	-	2	470	c.405T>C	c.(403-405)ccT>ccC	p.P135P	ARAP3_ENST00000508305.1_Silent_p.P57P	NM_022481.5	NP_071926.4	Q8WWN8	ARAP3_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 3	135	Pro-rich.				cytoskeleton organization (GO:0007010)|negative regulation of cell migration (GO:0030336)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of Rho protein signal transduction (GO:0035024)|regulation of ARF GTPase activity (GO:0032312)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	ARF GTPase activator activity (GO:0008060)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|Rho GTPase activator activity (GO:0005100)|zinc ion binding (GO:0008270)			NS(1)|breast(7)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(14)|ovary(1)|prostate(2)|skin(4)|stomach(1)	53						GGAGAGGAGGAGGCCTTGGGC	0.612													G|||	3923	0.783347	0.9856	0.8112	5008	,	,		14421	0.6052		0.7107	False		,,,				2504	0.7485				p.P135P		Atlas-SNP	.											.	ARAP3	139	.	0			c.T405C						PASS	.	G		4130,276	140.0+/-175.5	1938,254,11	100.0	126.0	117.0		405	0.1	0.0	5	dbSNP_80	117	6059,2541	405.0+/-348.4	2153,1753,394	no	coding-synonymous	ARAP3	NM_022481.5		4091,2007,405	GG,GA,AA		29.5465,6.2642,21.6592		135/1545	141059649	10189,2817	2203	4300	6503	SO:0001819	synonymous_variant	64411	exon2			AGGAGGAGGCCTT	AJ310567	CCDS4266.1	5q31.3	2013-01-11	2008-09-22	2008-09-22	ENSG00000120318	ENSG00000120318		"""ADP-ribosylation factor GTPase activating proteins"", ""Sterile alpha motif (SAM) domain containing"", ""Pleckstrin homology (PH) domain containing"", ""Ankyrin repeat domain containing"""	24097	protein-coding gene	gene with protein product		606647	"""centaurin, delta 3"""	CENTD3		11804589, 12015138	Standard	XM_005268497		Approved	FLJ21065, DRAG1	uc003llm.3	Q8WWN8	OTTHUMG00000129610	ENST00000239440.4:c.405T>C	5.37:g.141059649A>G		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	63	62	0.984127	NM_022481	B4DIT1|D3DQE3	Silent	SNP	ENST00000239440.4	37	CCDS4266.1																																																																																			A|0.229;G|0.771	0.771	strong		0.612	ARAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251805.1	NM_022481	
C2CD2	25966	hgsc.bcm.edu	37	21	43327793	43327793	+	Silent	SNP	C	C	T	rs3746904	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	30	0	0		WXS	Illumina HiSeq	Phase_I	86	46	0.534884	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	
ATP6V1H	51606	hgsc.bcm.edu	37	8	54682289	54682289	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:54682289T>C	ENST00000359530.2	-	11	1327	c.1064A>G	c.(1063-1065)tAc>tGc	p.Y355C	ATP6V1H_ENST00000355221.3_Missense_Mutation_p.Y337C|ATP6V1H_ENST00000396774.2_Missense_Mutation_p.Y355C|ATP6V1H_ENST00000523899.1_5'Flank|ATP6V1H_ENST00000520188.1_Missense_Mutation_p.Y315C	NM_015941.3	NP_057025.2	Q9UI12	VATH_HUMAN	ATPase, H+ transporting, lysosomal 50/57kDa, V1 subunit H	355					ATP catabolic process (GO:0006200)|ATP hydrolysis coupled proton transport (GO:0015991)|cellular iron ion homeostasis (GO:0006879)|endocytosis (GO:0006897)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|regulation of catalytic activity (GO:0050790)|regulation of defense response to virus by virus (GO:0050690)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)|vacuolar acidification (GO:0007035)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)|vacuolar proton-transporting V-type ATPase, V1 domain (GO:0000221)	enzyme regulator activity (GO:0030234)|proton-transporting ATPase activity, rotational mechanism (GO:0046961)			endometrium(3)|large_intestine(5)|lung(8)|ovary(1)|urinary_tract(1)	18		all_epithelial(80;0.0487)|Lung NSC(129;0.109)|all_lung(136;0.181)	OV - Ovarian serous cystadenocarcinoma(7;2.79e-06)|Epithelial(17;0.000629)|all cancers(17;0.00359)			TTCTGAACTGTATTCATCAAA	0.308																																					p.Y355C		Atlas-SNP	.											ATP6V1H_ENST00000359530,NS,carcinoma,+1,2	ATP6V1H	66	2	0			c.A1064G						scavenged	.						64.0	63.0	64.0					8																	54682289		2202	4298	6500	SO:0001583	missense	51606	exon11			GAACTGTATTCAT	AF132945	CCDS6153.1, CCDS6154.1	8q11.2	2011-05-24	2002-08-29		ENSG00000047249	ENSG00000047249		"""ATPases / V-type"""	18303	protein-coding gene	gene with protein product	"""vacuolar ATP synthase subunit H"""	608861	"""ATPase, H+ transporting, lysosomal 50/57kD, V1 subunit H"""			9620685, 10810093	Standard	NM_015941		Approved	CGI-11, SFD, VMA13, SFDalpha, SFDbeta	uc003xrm.4	Q9UI12	OTTHUMG00000164231	ENST00000359530.2:c.1064A>G	8.37:g.54682289T>C	ENSP00000352522:p.Tyr355Cys	Somatic	244	0	0		WXS	Illumina HiSeq	Phase_I	189	4	0.021164	NM_015941	B3KMR0|Q6PK44|Q9H3E3|Q9Y300	Missense_Mutation	SNP	ENST00000359530.2	37	CCDS6153.1	.	.	.	.	.	.	.	.	.	.	T	18.58	3.653925	0.67472	.	.	ENSG00000047249	ENST00000355221;ENST00000520188;ENST00000359530;ENST00000396774	.	.	.	5.02	5.02	0.67125	ATPase, V1 complex, subunit H, C-terminal (1);Armadillo-type fold (1);	0.055023	0.85682	D	0.000000	D	0.86356	0.5913	H	0.94582	3.555	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.97110	1.0;0.994	D	0.90325	0.4347	9	0.87932	D	0	-13.9855	14.7277	0.69357	0.0:0.0:0.0:1.0	.	337;355	Q9UI12-2;Q9UI12	.;VATH_HUMAN	C	337;315;355;355	.	ENSP00000347359:Y337C	Y	-	2	0	ATP6V1H	54844842	1.000000	0.71417	1.000000	0.80357	0.785000	0.44390	8.021000	0.88750	1.884000	0.54569	0.164000	0.16699	TAC	.	.	none		0.308	ATP6V1H-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377865.1	NM_015941	
CRISP3	10321	hgsc.bcm.edu	37	6	49701439	49701439	+	Missense_Mutation	SNP	C	C	A	rs1864312	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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_ENST00000263045.4_Missense_Mutation_p.A147S|CRISP3_ENST00000423399.2_Missense_Mutation_p.A44S			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	122	0	0		WXS	Illumina HiSeq	Phase_I	101	99	0.980198	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	
STK36	27148	hgsc.bcm.edu	37	2	219562675	219562675	+	Missense_Mutation	SNP	G	G	A	rs1863704	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:219562675G>A	ENST00000295709.3	+	25	3287	c.3008G>A	c.(3007-3009)gGt>gAt	p.G1003D	STK36_ENST00000440309.1_Missense_Mutation_p.G1003D|STK36_ENST00000392106.2_Missense_Mutation_p.G982D|STK36_ENST00000392105.3_Missense_Mutation_p.G982D	NM_015690.4	NP_056505.2			serine/threonine kinase 36											biliary_tract(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(6)|lung(20)|ovary(4)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	52		Renal(207;0.0915)		Epithelial(149;9.65e-07)|all cancers(144;0.000174)|LUSC - Lung squamous cell carcinoma(224;0.00813)|Lung(261;0.00984)		CTCCTTATAGGTGTCTTGGCC	0.557													G|||	950	0.189696	0.0212	0.3285	5008	,	,		21184	0.0556		0.3757	False		,,,				2504	0.2658				p.G1003D		Atlas-SNP	.											STK36,rectum,carcinoma,0,1	STK36	111	1	0			c.G3008A						scavenged	.	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	166	1	0.0060241		WXS	Illumina HiSeq	Phase_I	146	61	0.417808	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		
GPR87	53836	hgsc.bcm.edu	37	3	151011969	151011969	+	Silent	SNP	G	G	A	rs1048408	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:151011969G>A	ENST00000260843.4	-	3	1529	c.1065C>T	c.(1063-1065)taC>taT	p.Y355Y	MED12L_ENST00000474524.1_Intron|MED12L_ENST00000273432.4_Intron|MED12L_ENST00000491549.1_Intron	NM_023915.3	NP_076404.3	Q9BY21	GPR87_HUMAN	G protein-coupled receptor 87	355					negative regulation of adenylate cyclase activity (GO:0007194)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled purinergic nucleotide receptor activity (GO:0045028)			endometrium(6)|large_intestine(6)|lung(5)|skin(1)|upper_aerodigestive_tract(1)	19			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			ACACATCAGTGTAATCATAAT	0.348													A|||	2482	0.495607	0.4561	0.5692	5008	,	,		19851	0.5139		0.4642	False		,,,				2504	0.5102				p.Y355Y		Atlas-SNP	.											.	GPR87	52	.	0			c.C1065T						PASS	.	A	,	1921,2485	625.9+/-394.6	393,1135,675	136.0	137.0	137.0		1065,	-5.0	0.1	3	dbSNP_86	137	4040,4560	595.3+/-393.4	941,2158,1201	no	coding-synonymous,intron	GPR87,MED12L	NM_023915.3,NM_053002.4	,	1334,3293,1876	AA,AG,GG		46.9767,43.5996,45.8327	,	355/359,	151011969	5961,7045	2203	4300	6503	SO:0001819	synonymous_variant	53836	exon3			ATCAGTGTAATCA	AF237763	CCDS3157.1	3q24	2012-08-21			ENSG00000138271	ENSG00000138271		"""GPCR / Class A : Orphans"""	4538	protein-coding gene	gene with protein product		606379		GPR95		11273702	Standard	NM_023915		Approved		uc003eyt.2	Q9BY21	OTTHUMG00000159858	ENST00000260843.4:c.1065C>T	3.37:g.151011969G>A		Somatic	201	0	0		WXS	Illumina HiSeq	Phase_I	162	67	0.41358	NM_023915	Q5KU35|Q96JZ8|Q9BXC2	Silent	SNP	ENST00000260843.4	37	CCDS3157.1																																																																																			G|0.533;A|0.467	0.467	strong		0.348	GPR87-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357788.1		
PPP1R11	6992	hgsc.bcm.edu	37	6	30036471	30036471	+	Silent	SNP	C	C	A	rs2074482	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:30036471C>A	ENST00000376772.3	+	2	497	c.174C>A	c.(172-174)tcC>tcA	p.S58S	PPP1R11_ENST00000376765.2_Silent_p.S6S|PPP1R11_ENST00000376763.1_Silent_p.S6S|PPP1R11_ENST00000376758.1_Silent_p.S6S|PPP1R11_ENST00000376773.1_Silent_p.S6S|PPP1R11_ENST00000376769.2_Silent_p.S6S	NM_021959.2	NP_068778.1	O60927	PP1RB_HUMAN	protein phosphatase 1, regulatory (inhibitor) subunit 11	58						cytoplasm (GO:0005737)	protein phosphatase inhibitor activity (GO:0004864)			lung(2)|ovary(1)|prostate(1)|skin(2)	6						GCCGCTCATCCAAATGTGAGT	0.507													A|||	958	0.191294	0.2988	0.1744	5008	,	,		18885	0.1905		0.0954	False		,,,				2504	0.1575				p.S58S	Pancreas(185;1767 3918 43793)	Atlas-SNP	.											.	PPP1R11	10	.	0			c.C174A						PASS	.	A		772,2250		93,586,832	78.0	72.0	74.0		174	-0.3	1.0	6	dbSNP_96	74	650,4768		48,554,2107	no	coding-synonymous	PPP1R11	NM_021959.2		141,1140,2939	AA,AC,CC		11.997,25.546,16.8483		58/127	30036471	1422,7018	1511	2709	4220	SO:0001819	synonymous_variant	6992	exon2			CTCATCCAAATGT	X81003	CCDS4671.1	6p21.3	2012-04-17			ENSG00000204619	ENSG00000204619		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	9285	protein-coding gene	gene with protein product		606670		TCTE5		9843442, 8781118	Standard	NM_021959		Approved	HCGV, Tctex5, HCG-V	uc003npb.3	O60927	OTTHUMG00000031260	ENST00000376772.3:c.174C>A	6.37:g.30036471C>A		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	46	24	0.521739	NM_021959		Silent	SNP	ENST00000376772.3	37	CCDS4671.1																																																																																			C|0.809;A|0.191	0.191	strong		0.507	PPP1R11-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076557.3	NM_021959	
MUC4	4585	hgsc.bcm.edu	37	3	195505872	195505872	+	Silent	SNP	A	A	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195505872A>C	ENST00000463781.3	-	2	13038	c.12579T>G	c.(12577-12579)ctT>ctG	p.L4193L	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Silent_p.L4193L	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.L4193L(1)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		CGGTGACAGGAAGAGGGGTGG	0.602																																					p.L4193L		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,-2,2	MUC4	1505	2	1	Substitution - coding silent(1)	kidney(1)	c.T12579G						scavenged	.						21.0	15.0	17.0					3																	195505872		689	1579	2268	SO:0001819	synonymous_variant	4585	exon2			GACAGGAAGAGGG	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.12579T>G	3.37:g.195505872A>C		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	85	5	0.0588235	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		0.602	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
DIP2C	22982	hgsc.bcm.edu	37	10	429977	429977	+	Silent	SNP	G	G	A	rs10904083	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:429977G>A	ENST00000280886.6	-	16	1953	c.1866C>T	c.(1864-1866)ggC>ggT	p.G622G	DIP2C_ENST00000381496.3_Silent_p.G515G	NM_014974.2	NP_055789.1	Q9Y2E4	DIP2C_HUMAN	DIP2 disco-interacting protein 2 homolog C (Drosophila)	622			G -> S (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.			nucleus (GO:0005634)	catalytic activity (GO:0003824)	p.G622G(1)		breast(8)|endometrium(6)|kidney(10)|large_intestine(13)|lung(26)|ovary(3)|prostate(6)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(4)	81		all_cancers(4;0.00336)|all_lung(4;0.00732)|Lung NSC(4;0.00785)|all_epithelial(10;0.0159)|Colorectal(49;0.235)	OV - Ovarian serous cystadenocarcinoma(33;0.136)	Epithelial(11;0.0123)|all cancers(11;0.0467)|Lung(33;0.0864)|OV - Ovarian serous cystadenocarcinoma(14;0.106)		AGGGGTTCGCGCCGTCCGCCA	0.517													G|||	1910	0.38139	0.2776	0.4135	5008	,	,		11114	0.4623		0.332	False		,,,				2504	0.4663				p.G622G		Atlas-SNP	.											DIP2C,NS,carcinoma,0,3	DIP2C	195	3	1	Substitution - coding silent(1)	prostate(1)	c.C1866T						PASS	.	G		1268,3138	433.9+/-343.8	189,890,1124	84.0	68.0	73.0		1866	-10.9	0.0	10	dbSNP_120	73	2905,5695	454.5+/-363.5	488,1929,1883	no	coding-synonymous	DIP2C	NM_014974.2		677,2819,3007	AA,AG,GG		33.7791,28.7789,32.0852		622/1557	429977	4173,8833	2203	4300	6503	SO:0001819	synonymous_variant	22982	exon16			GTTCGCGCCGTCC	BC035216	CCDS7054.1	10p15.3	2006-01-13	2006-01-13	2006-01-13	ENSG00000151240	ENSG00000151240			29150	protein-coding gene	gene with protein product		611380	"""KIAA0934"""	KIAA0934			Standard	NM_014974		Approved		uc001ifp.3	Q9Y2E4	OTTHUMG00000017532	ENST00000280886.6:c.1866C>T	10.37:g.429977G>A		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	110	40	0.363636	NM_014974	B4DPI5|Q5SS78	Silent	SNP	ENST00000280886.6	37	CCDS7054.1	801	0.36675824175824173	120	0.24390243902439024	152	0.4198895027624309	274	0.479020979020979	255	0.33641160949868076	G	0.065	-1.214238	0.01555	0.287789	0.337791	ENSG00000151240	ENST00000421992	.	.	.	5.43	-10.9	0.00192	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999971	.	.	.	.	.	.	T	0.30707	-0.9969	3	.	.	.	-27.5253	3.0353	0.06119	0.3195:0.0591:0.1941:0.4273	rs10904083;rs59901965;rs10904083	.	.	.	V	90	.	.	A	-	2	0	DIP2C	419977	0.001000	0.12720	0.017000	0.16124	0.004000	0.04260	-1.514000	0.02254	-2.431000	0.00556	-1.468000	0.01013	GCG	G|0.663;A|0.337	0.337	strong		0.517	DIP2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046389.1	NM_014974	
SDAD1	55153	hgsc.bcm.edu	37	4	76881233	76881233	+	Missense_Mutation	SNP	G	G	T	rs34627298	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:76881233G>T	ENST00000356260.5	-	17	1587	c.1469C>A	c.(1468-1470)gCt>gAt	p.A490D	SDAD1_ENST00000395711.4_Missense_Mutation_p.A453D|SDAD1_ENST00000513089.1_5'Flank	NM_018115.2	NP_060585.2	Q9NVU7	SDA1_HUMAN	SDA1 domain containing 1	490			A -> D (in dbSNP:rs34627298).		actin cytoskeleton organization (GO:0030036)|protein transport (GO:0015031)|ribosomal large subunit biogenesis (GO:0042273)|ribosomal large subunit export from nucleus (GO:0000055)	nucleolus (GO:0005730)				breast(2)|endometrium(2)|kidney(2)|large_intestine(1)|lung(9)|ovary(1)|prostate(1)|skin(1)	19			Lung(101;0.0809)|LUSC - Lung squamous cell carcinoma(112;0.0934)			ATCATTTTCAGCATTCTCTTC	0.368													G|||	478	0.0954473	0.0159	0.1066	5008	,	,		18860	0.123		0.0885	False		,,,				2504	0.1738				p.A490D		Atlas-SNP	.											.	SDAD1	47	.	0			c.C1469A						PASS	.	G	ASP/ALA	130,4276	95.7+/-134.4	1,128,2074	138.0	126.0	130.0		1469	1.0	0.8	4	dbSNP_126	130	810,7790	188.6+/-235.5	47,716,3537	yes	missense	SDAD1	NM_018115.2	126	48,844,5611	TT,TG,GG		9.4186,2.9505,7.2274	benign	490/688	76881233	940,12066	2203	4300	6503	SO:0001583	missense	55153	exon17			TTTTCAGCATTCT	AF132198	CCDS3573.2, CCDS75147.1	4q21.21	2010-11-24			ENSG00000198301	ENSG00000198301			25537	protein-coding gene	gene with protein product						11483580	Standard	NM_001288984		Approved	FLJ10498	uc003hje.4	Q9NVU7	OTTHUMG00000130111	ENST00000356260.5:c.1469C>A	4.37:g.76881233G>T	ENSP00000348596:p.Ala490Asp	Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	158	81	0.512658	NM_018115	Q32Q11|Q68D52|Q7Z5U4|Q9H831|Q9H9P6	Missense_Mutation	SNP	ENST00000356260.5	37	CCDS3573.2	208	0.09523809523809523	9	0.018292682926829267	44	0.12154696132596685	75	0.13111888111888112	80	0.10554089709762533	G	4.553	0.102708	0.08731	0.029505	0.094186	ENSG00000198301	ENST00000356260;ENST00000395711	T;T	0.10573	2.86;2.86	5.37	0.987	0.19790	SDA1 (1);Armadillo-type fold (1);	0.509402	0.22123	N	0.064301	T	0.00039	0.0001	N	0.13235	0.315	0.80722	P	0.0	B;B	0.06786	0.001;0.0	B;B	0.04013	0.001;0.0	T	0.41324	-0.9515	9	0.12103	T	0.63	-0.0925	3.1396	0.06451	0.0903:0.1305:0.3035:0.4758	rs34627298	453;490	E7EW05;Q9NVU7	.;SDA1_HUMAN	D	490;453	ENSP00000348596:A490D;ENSP00000379061:A453D	ENSP00000348596:A490D	A	-	2	0	SDAD1	77100257	0.008000	0.16893	0.819000	0.32651	0.501000	0.33797	0.199000	0.17237	0.627000	0.30340	0.591000	0.81541	GCT	G|0.922;T|0.078	0.078	strong		0.368	SDAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252418.3	NM_018115	
WDR73	84942	hgsc.bcm.edu	37	15	85188839	85188839	+	Missense_Mutation	SNP	C	C	T	rs11073619	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:85188839C>T	ENST00000434634.2	-	7	806	c.746G>A	c.(745-747)cGt>cAt	p.R249H	WDR73_ENST00000398528.3_5'UTR	NM_032856.2	NP_116245.2	Q6P4I2	WDR73_HUMAN	WD repeat domain 73	249			R -> H (in dbSNP:rs11073619).							cervix(1)|large_intestine(1)|lung(1)	3						AAGACAAAGACGCCCATCTGA	0.627													C|||	408	0.0814696	0.1097	0.1902	5008	,	,		16265	0.002		0.1074	False		,,,				2504	0.0215				p.R249H		Atlas-SNP	.											.	WDR73	15	.	0			c.G746A						PASS	.	C	HIS/ARG	441,3489		29,383,1553	25.0	30.0	29.0		746	2.2	0.9	15	dbSNP_120	29	781,7523		38,705,3409	yes	missense	WDR73	NM_032856.2	29	67,1088,4962	TT,TC,CC		9.4051,11.2214,9.9886	benign	249/379	85188839	1222,11012	1965	4152	6117	SO:0001583	missense	84942	exon7			CAAAGACGCCCAT	AK027200	CCDS45339.1	15q25.2	2013-01-09				ENSG00000177082		"""WD repeat domain containing"""	25928	protein-coding gene	gene with protein product						12477932	Standard	NM_032856		Approved	FLJ14888, HSPC264	uc002bkw.2	Q6P4I2		ENST00000434634.2:c.746G>A	15.37:g.85188839C>T	ENSP00000387982:p.Arg249His	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	54	28	0.518519	NM_032856	Q96JZ1|Q9P0B7	Missense_Mutation	SNP	ENST00000434634.2	37	CCDS45339.1	218	0.09981684981684982	71	0.1443089430894309	58	0.16022099447513813	2	0.0034965034965034965	87	0.11477572559366754	C	2.708	-0.269511	0.05716	0.112214	0.094051	ENSG00000177082	ENST00000398528;ENST00000434634	T	0.29397	1.57	5.8	2.21	0.28008	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.634443	0.17879	N	0.158934	T	0.00039	0.0001	N	0.01352	-0.895	0.47153	P	6.690000000000307E-4	B	0.06786	0.001	B	0.04013	0.001	T	0.32561	-0.9902	9	0.23302	T	0.38	-17.6382	6.6191	0.22792	0.1385:0.0823:0.0:0.7792	rs11073619;rs52820653;rs58160077;rs11073619	249	Q6P4I2	WDR73_HUMAN	H	257;249	ENSP00000387982:R249H	ENSP00000381539:R257H	R	-	2	0	WDR73	82989843	0.891000	0.30450	0.864000	0.33941	0.138000	0.21146	0.344000	0.19962	0.111000	0.17947	-1.110000	0.02074	CGT	C|0.903;T|0.097	0.097	strong		0.627	WDR73-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418195.1	NM_032856	
MUC5B	727897	hgsc.bcm.edu	37	11	1266561	1266561	+	Silent	SNP	G	G	A	rs200970694	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:1266561G>A	ENST00000529681.1	+	31	8509	c.8451G>A	c.(8449-8451)agG>agA	p.R2817R	MUC5B_ENST00000447027.1_Silent_p.R2820R|RP11-532E4.2_ENST00000532061.2_RNA	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	2817	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)		CTAGCAGCAGGACCACCGAGT	0.682																																					p.R2817R		Atlas-SNP	.											MUC5B,NS,carcinoma,0,2	MUC5B	473	2	0			c.G8451A						scavenged	.						27.0	43.0	38.0					11																	1266561		1927	4011	5938	SO:0001819	synonymous_variant	727897	exon31			CAGCAGGACCACC	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.8451G>A	11.37:g.1266561G>A		Somatic	333	1	0.003003		WXS	Illumina HiSeq	Phase_I	384	14	0.0364583	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Silent	SNP	ENST00000529681.1	37	CCDS44515.2																																																																																			G|0.989;A|0.011	0.011	strong		0.682	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
PLEKHA5	54477	hgsc.bcm.edu	37	12	19427764	19427764	+	Missense_Mutation	SNP	T	T	C	rs76626801	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:19427764T>C	ENST00000299275.6	+	10	1148	c.1142T>C	c.(1141-1143)gTt>gCt	p.V381A	PLEKHA5_ENST00000510738.2_3'UTR|PLEKHA5_ENST00000543806.1_Missense_Mutation_p.V273A|PLEKHA5_ENST00000538714.1_Missense_Mutation_p.V381A|PLEKHA5_ENST00000359180.3_Missense_Mutation_p.V381A|PLEKHA5_ENST00000429027.2_Missense_Mutation_p.V387A|PLEKHA5_ENST00000424268.1_Missense_Mutation_p.V273A|PLEKHA5_ENST00000317589.4_Missense_Mutation_p.V381A|PLEKHA5_ENST00000309364.4_Missense_Mutation_p.V381A|PLEKHA5_ENST00000539256.1_Missense_Mutation_p.V139A|PLEKHA5_ENST00000355397.3_Missense_Mutation_p.V381A	NM_019012.5	NP_061885.2	Q9HAU0	PKHA5_HUMAN	pleckstrin homology domain containing, family A member 5	381					reproductive system development (GO:0061458)	cytosol (GO:0005829)|membrane (GO:0016020)	1-phosphatidylinositol binding (GO:0005545)|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)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(14)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	35	Acute lymphoblastic leukemia(4;0.000455)|all_hematologic(4;0.00804)					ATAGTCAATGTTAGCCTGGCA	0.473													T|||	135	0.0269569	0.0015	0.0144	5008	,	,		18058	0.0754		0.0119	False		,,,				2504	0.0358				p.V387A	Pancreas(196;329 2193 11246 14234 19524)	Atlas-SNP	.											.	PLEKHA5	198	.	0			c.T1160C						PASS	.	T	ALA/VAL,ALA/VAL	10,4396	17.9+/-39.9	0,10,2193	64.0	70.0	68.0		1142,1142	5.3	0.9	12	dbSNP_131	68	76,8524	43.6+/-101.6	1,74,4225	yes	missense,missense	PLEKHA5	NM_001143821.2,NM_019012.5	64,64	1,84,6418	CC,CT,TT		0.8837,0.227,0.6612	benign,benign	381/1175,381/1117	19427764	86,12920	2203	4300	6503	SO:0001583	missense	54477	exon11			TCAATGTTAGCCT	AF302150	CCDS8682.1, CCDS44840.1, CCDS44840.2, CCDS55809.1, CCDS58213.1, CCDS58214.1	12p12	2013-01-10			ENSG00000052126	ENSG00000052126		"""Pleckstrin homology (PH) domain containing"""	30036	protein-coding gene	gene with protein product		607770				11214970, 11001876	Standard	NM_001143821		Approved	PEPP2, KIAA1686, FLJ10667	uc031qgo.1	Q9HAU0	OTTHUMG00000167921	ENST00000299275.6:c.1142T>C	12.37:g.19427764T>C	ENSP00000299275:p.Val381Ala	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	56	29	0.517857	NM_001256470	A0JP03|B4DGS1|E9PHQ3|F5H0I0|Q6NSF8|Q86ST7|Q8N3K6|Q96DY9|Q9BVR4|Q9C0H7|Q9H924|Q9NVK8	Missense_Mutation	SNP	ENST00000299275.6	37	CCDS8682.1	37	0.01694139194139194	1	0.0020325203252032522	5	0.013812154696132596	21	0.03671328671328671	10	0.013192612137203167	T	7.587	0.669883	0.14776	0.00227	0.008837	ENSG00000052126	ENST00000317589;ENST00000355397;ENST00000359180;ENST00000542828;ENST00000309364;ENST00000429027;ENST00000299275;ENST00000539256;ENST00000538714;ENST00000424268;ENST00000543806;ENST00000536974	T;T;T;T;T;T;T;T;T;T;T	0.14144	2.96;2.94;2.96;2.92;2.95;2.96;2.53;2.94;2.95;2.96;2.96	5.3	5.3	0.74995	.	0.638417	0.15075	N	0.281984	T	0.02380	0.0073	N	0.22421	0.69	0.09310	N	0.999999	P;B;B;B;B;B;B	0.36086	0.536;0.041;0.004;0.224;0.229;0.047;0.041	B;B;B;B;B;B;B	0.39068	0.289;0.032;0.008;0.05;0.05;0.009;0.047	T	0.26395	-1.0104	10	0.17832	T	0.49	-8.4751	13.977	0.64279	0.0:0.0:0.0:1.0	.	381;273;273;387;387;381;381	Q9HAU0-4;F5H0I0;E7EME8;B4DHK5;E9PHQ3;Q9HAU0;Q9HAU0-2	.;.;.;.;.;PKHA5_HUMAN;.	A	381;381;381;388;381;387;381;139;381;273;273;273	ENSP00000325155:V381A;ENSP00000347560:V381A;ENSP00000352104:V381A;ENSP00000311239:V381A;ENSP00000404296:V387A;ENSP00000299275:V381A;ENSP00000440611:V139A;ENSP00000439673:V381A;ENSP00000400411:V273A;ENSP00000439837:V273A;ENSP00000440371:V273A	ENSP00000299275:V381A	V	+	2	0	PLEKHA5	19319031	0.247000	0.23920	0.911000	0.35937	0.559000	0.35586	2.554000	0.45845	2.227000	0.72691	0.455000	0.32223	GTT	T|0.989;C|0.011	0.011	strong		0.473	PLEKHA5-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000397013.1	NM_019012	
NPC1	4864	hgsc.bcm.edu	37	18	21140367	21140367	+	Missense_Mutation	SNP	G	G	A	rs80358251	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:21140367G>A	ENST00000269228.5	-	6	1263	c.709C>T	c.(709-711)Cca>Tca	p.P237S	NPC1_ENST00000540608.1_5'UTR|NPC1_ENST00000412552.2_5'Flank	NM_000271.4	NP_000262.2	O15118	NPC1_HUMAN	Niemann-Pick disease, type C1	237			P -> S (in NPC1; late infantile form; dbSNP:rs80358251). {ECO:0000269|PubMed:11182931, ECO:0000269|PubMed:11333381, ECO:0000269|PubMed:11349231, ECO:0000269|PubMed:12408188, ECO:0000269|PubMed:12955717}.		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)					CAGCTACATGGTGCTGTGACC	0.547													G|||	23	0.00459265	0.0008	0.0043	5008	,	,		16533	0.0		0.0169	False		,,,				2504	0.002				p.P237S		Atlas-SNP	.											.	NPC1	114	.	0			c.C709T	GRCh37	CM990941	NPC1	M	rs80358251	PASS	.	G	SER/PRO	13,4393	20.2+/-43.8	0,13,2190	70.0	60.0	63.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	709	5.9	0.3	18	dbSNP_132	63	137,8463	68.7+/-131.2	1,135,4164	yes	missense	NPC1	NM_000271.4	74	1,148,6354	AA,AG,GG		1.593,0.2951,1.1533	benign	237/1279	21140367	150,12856	2203	4300	6503	SO:0001583	missense	4864	exon6			TACATGGTGCTGT	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.709C>T	18.37:g.21140367G>A	ENSP00000269228:p.Pro237Ser	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	71	70	0.985915	NM_000271	B4DET3|Q9P130	Missense_Mutation	SNP	ENST00000269228.5	37	CCDS11878.1	14	0.00641025641025641	1	0.0020325203252032522	0	0.0	0	0.0	13	0.017150395778364115	G	11.43	1.635647	0.29068	0.002951	0.01593	ENSG00000141458	ENST00000269228;ENST00000540608	D	0.91011	-2.77	5.87	5.87	0.94306	.	0.052444	0.85682	D	0.000000	T	0.79811	0.4510	L	0.39147	1.195	0.80722	D	1	B;B	0.10296	0.002;0.003	B;B	0.04013	0.001;0.001	T	0.78393	-0.2221	10	0.23891	T	0.37	-22.0744	20.206	0.98277	0.0:0.0:1.0:0.0	.	248;237	Q59GR1;O15118	.;NPC1_HUMAN	S	237;82	ENSP00000269228:P237S	ENSP00000269228:P237S	P	-	1	0	NPC1	19394365	1.000000	0.71417	0.333000	0.25482	0.084000	0.17831	8.061000	0.89467	2.785000	0.95823	0.655000	0.94253	CCA	G|0.991;A|0.009	0.009	strong		0.547	NPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254823.2	NM_000271	
CCL2	6347	hgsc.bcm.edu	37	17	32583269	32583269	+	Silent	SNP	T	T	C	rs4586	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:32583269T>C	ENST00000225831.4	+	2	170	c.105T>C	c.(103-105)tgT>tgC	p.C35C	AC005549.3_ENST00000601918.1_5'Flank|CCL2_ENST00000580907.1_Silent_p.C35C	NM_002982.3	NP_002973.1	P13500	CCL2_HUMAN	chemokine (C-C motif) ligand 2	35					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|aging (GO:0007568)|angiogenesis (GO:0001525)|astrocyte cell migration (GO:0043615)|cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|cellular calcium ion homeostasis (GO:0006874)|cellular homeostasis (GO:0019725)|cellular protein metabolic process (GO:0044267)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cellular response to interferon-gamma (GO:0071346)|cellular response to interleukin-1 (GO:0071347)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to organic cyclic compound (GO:0071407)|cellular response to tumor necrosis factor (GO:0071356)|chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|cytokine-mediated signaling pathway (GO:0019221)|cytoskeleton organization (GO:0007010)|endoplasmic reticulum unfolded protein response (GO:0030968)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|helper T cell extravasation (GO:0035684)|humoral immune response (GO:0006959)|inflammatory response (GO:0006954)|JAK-STAT cascade (GO:0007259)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|lymphocyte chemotaxis (GO:0048247)|macrophage chemotaxis (GO:0048246)|MAPK cascade (GO:0000165)|maternal process involved in parturition (GO:0060137)|monocyte chemotaxis (GO:0002548)|negative regulation of angiogenesis (GO:0016525)|negative regulation of glial cell apoptotic process (GO:0034351)|negative regulation of natural killer cell chemotaxis (GO:2000502)|negative regulation of neuron apoptotic process (GO:0043524)|neutrophil chemotaxis (GO:0030593)|organ morphogenesis (GO:0009887)|organ regeneration (GO:0031100)|positive regulation of apoptotic cell clearance (GO:2000427)|positive regulation of calcium ion import (GO:0090280)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of immune complex clearance by monocytes and macrophages (GO:0090265)|positive regulation of macrophage chemotaxis (GO:0010759)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of synaptic transmission (GO:0050806)|positive regulation of T cell activation (GO:0050870)|protein kinase B signaling (GO:0043491)|protein phosphorylation (GO:0006468)|regulation of cell shape (GO:0008360)|regulation of vascular endothelial growth factor production (GO:0010574)|response to activity (GO:0014823)|response to amino acid (GO:0043200)|response to antibiotic (GO:0046677)|response to bacterium (GO:0009617)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to gamma radiation (GO:0010332)|response to glucocorticoid (GO:0051384)|response to heat (GO:0009408)|response to hypoxia (GO:0001666)|response to mechanical stimulus (GO:0009612)|response to progesterone (GO:0032570)|response to vitamin B3 (GO:0033552)|response to wounding (GO:0009611)|signal transduction (GO:0007165)|transforming growth factor beta receptor signaling pathway (GO:0007179)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|viral genome replication (GO:0019079)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|neuronal cell body (GO:0043025)	CCR2 chemokine receptor binding (GO:0031727)|chemokine activity (GO:0008009)|heparin binding (GO:0008201)|protein kinase activity (GO:0004672)|receptor binding (GO:0005102)			kidney(1)|lung(3)|pancreas(1)|upper_aerodigestive_tract(1)	6	Breast(3;0.00224)	Ovarian(249;0.0694)|Breast(31;0.151)|Lung NSC(157;0.153)		UCEC - Uterine corpus endometrioid carcinoma (308;0.000241)|BRCA - Breast invasive adenocarcinoma(366;0.0103)	Danazol(DB01406)|Mimosine(DB01055)	TCACCTGCTGTTATAACTTCA	0.423													C|||	2716	0.542332	0.711	0.5778	5008	,	,		20697	0.5456		0.3897	False		,,,				2504	0.4427				p.C35C		Atlas-SNP	.											.	CCL2	10	.	0			c.T105C						PASS	.	C		2931,1475	475.3+/-357.3	984,963,256	100.0	101.0	101.0		105	1.5	0.6	17	dbSNP_52	101	3104,5496	658.1+/-401.5	572,1960,1768	no	coding-synonymous	CCL2	NM_002982.3		1556,2923,2024	CC,CT,TT		36.093,33.4771,46.4017		35/100	32583269	6035,6971	2203	4300	6503	SO:0001819	synonymous_variant	6347	exon2			CTGCTGTTATAAC	BC009716	CCDS11277.1	17q11.2-q21.1	2013-02-25	2002-08-22	2002-08-23	ENSG00000108691	ENSG00000108691		"""Chemokine ligands"", ""Endogenous ligands"""	10618	protein-coding gene	gene with protein product	"""monocyte chemotactic protein 1, homologous to mouse Sig-je"", ""monocyte chemoattractant protein-1"", ""monocyte chemotactic and activating factor"", ""monocyte secretory protein JE"", ""small inducible cytokine subfamily A (Cys-Cys), member 2"""	158105	"""small inducible cytokine A2 (monocyte chemotactic protein 1, homologous to mouse Sig-je)"""	SCYA2		2004761	Standard	NM_002982		Approved	MCP1, MCP-1, MCAF, SMC-CF, GDCF-2, HC11, MGC9434	uc002hhy.3	P13500	OTTHUMG00000132887	ENST00000225831.4:c.105T>C	17.37:g.32583269T>C		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	128	55	0.429688	NM_002982	B2R4V3|Q9UDF3	Silent	SNP	ENST00000225831.4	37	CCDS11277.1																																																																																			T|0.496;C|0.504	0.504	strong		0.423	CCL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256384.2	NM_002982	
PANK1	53354	hgsc.bcm.edu	37	10	91359116	91359116	+	Silent	SNP	C	C	T	rs11592870	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:91359116C>T	ENST00000307534.4	-	3	1358	c.1203G>A	c.(1201-1203)ccG>ccA	p.P401P	PANK1_ENST00000371774.2_Silent_p.P203P|PANK1_ENST00000342512.3_Silent_p.P176P|PANK1_ENST00000322191.6_Silent_p.P176P	NM_148977.2	NP_683878.1	Q8TE04	PANK1_HUMAN	pantothenate kinase 1	401					coenzyme A biosynthetic process (GO:0015937)|coenzyme biosynthetic process (GO:0009108)|pantothenate metabolic process (GO:0015939)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cell periphery (GO:0071944)|clathrin coat (GO:0030118)|cytosol (GO:0005829)|nucleus (GO:0005634)|recycling endosome (GO:0055037)	ATP binding (GO:0005524)|pantothenate kinase activity (GO:0004594)			cervix(1)|kidney(1)|large_intestine(3)|lung(4)|prostate(2)	11						CAAGGCAGTACGGCTTTTTTT	0.438													C|||	75	0.014976	0.0	0.013	5008	,	,		19072	0.0		0.0408	False		,,,				2504	0.0256				p.P401P		Atlas-SNP	.											PANK1,colon,carcinoma,0,1	PANK1	35	1	0			c.G1203A						scavenged	.	C	,,	30,4376	36.8+/-68.6	0,30,2173	236.0	213.0	221.0		528,1203,528	-4.7	1.0	10	dbSNP_120	221	250,8350	99.0+/-160.6	1,248,4051	no	coding-synonymous,coding-synonymous,coding-synonymous	PANK1	NM_138316.3,NM_148977.2,NM_148978.2	,,	1,278,6224	TT,TC,CC		2.907,0.6809,2.1529	,,	176/315,401/599,176/374	91359116	280,12726	2203	4300	6503	SO:0001819	synonymous_variant	53354	exon3			GCAGTACGGCTTT	AF355198	CCDS7405.1, CCDS7406.1, CCDS31244.1	10q23.31	2008-05-14	2002-11-13	2002-11-15	ENSG00000152782	ENSG00000152782			8598	protein-coding gene	gene with protein product		606160	"""pantothenate kinase"""	PANK		11809413	Standard	NM_148977		Approved	MGC24596, PANK1a, PANK1b	uc001kgp.2	Q8TE04	OTTHUMG00000018718	ENST00000307534.4:c.1203G>A	10.37:g.91359116C>T		Somatic	177	1	0.00564972		WXS	Illumina HiSeq	Phase_I	149	74	0.496644	NM_148977	A6NIP0|Q7RTX6|Q7Z495|Q8TBQ8	Silent	SNP	ENST00000307534.4	37	CCDS31244.1																																																																																			C|0.981;T|0.019	0.019	strong		0.438	PANK1-201	KNOWN	basic|CCDS	protein_coding	protein_coding			
MUC4	4585	hgsc.bcm.edu	37	3	195509769	195509769	+	Silent	SNP	A	A	G	rs77947599	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195509769A>G	ENST00000463781.3	-	2	9141	c.8682T>C	c.(8680-8682)gcT>gcC	p.A2894A	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Silent_p.A2894A	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.A2894A(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)		GAAGAGGGGTAGCGTGACCTG	0.597													.|||	67	0.0133786	0.0424	0.0014	5008	,	,		6903	0.0069		0.002	False		,,,				2504	0.001				p.A2894A		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	1	Substitution - coding silent(1)	stomach(1)	c.T8682C						scavenged	.						30.0	17.0	21.0					3																	195509769		684	1574	2258	SO:0001819	synonymous_variant	4585	exon2			AGGGGTAGCGTGA	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.8682T>C	3.37:g.195509769A>G		Somatic	65	1	0.0153846		WXS	Illumina HiSeq	Phase_I	103	69	0.669903	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Silent	SNP	ENST00000463781.3	37	CCDS54700.1																																																																																			A|0.250;G|0.750	0.750	weak		0.597	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
ZNF135	7694	hgsc.bcm.edu	37	19	58578578	58578578	+	Silent	SNP	C	C	T	rs2229375	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:58578578C>T	ENST00000313434.5	+	5	827	c.726C>T	c.(724-726)taC>taT	p.Y242Y	RN7SL526P_ENST00000469492.2_RNA|ZNF135_ENST00000359978.6_Silent_p.Y254Y|ZNF135_ENST00000506786.1_Silent_p.Y200Y|ZNF135_ENST00000439855.2_Silent_p.Y242Y|ZNF135_ENST00000511556.1_Silent_p.Y254Y|ZNF135_ENST00000401053.4_Silent_p.Y266Y	NM_003436.3	NP_003427.3	P52742	ZN135_HUMAN	zinc finger protein 135	242					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)		AGAGACCTTACGAATGTCACG	0.478													C|||	1837	0.366813	0.3548	0.4798	5008	,	,		20709	0.2103		0.4105	False		,,,				2504	0.4192				p.Y266Y		Atlas-SNP	.											.	ZNF135	159	.	0			c.C798T						PASS	.	C	,,,	1488,2918	474.8+/-357.1	252,984,967	135.0	127.0	130.0		,762,762,798	-7.1	0.0	19	dbSNP_98	130	3459,5141	505.6+/-376.4	685,2089,1526	no	utr-3,coding-synonymous,coding-synonymous,coding-synonymous	ZNF135	NM_001164529.1,NM_001164530.1,NM_003436.3,NM_007134.1	,,,	937,3073,2493	TT,TC,CC		40.2209,33.7721,38.0363	,,,	,254/391,254/671,266/683	58578578	4947,8059	2203	4300	6503	SO:0001819	synonymous_variant	7694	exon4			ACCTTACGAATGT	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.726C>T	19.37:g.58578578C>T		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	55	19	0.345455	NM_007134	B4DHH9|E9PEV2|F5GYY9|I3L0B3|Q5U5L3|Q8N1I7	Silent	SNP	ENST00000313434.5	37		784	0.358974358974359	178	0.3617886178861789	163	0.45027624309392267	138	0.24125874125874125	305	0.4023746701846966	C	0.011	-1.709594	0.00712	0.337721	0.402209	ENSG00000176293	ENST00000391699	.	.	.	3.52	-7.05	0.01573	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.58432	P	5.000000000032756E-6	.	.	.	.	.	.	T	0.26950	-1.0088	3	.	.	.	.	8.0246	0.30430	0.0:0.3306:0.1105:0.5589	rs2229375;rs3745125;rs17307311;rs60749458;rs2229375	.	.	.	M	260	.	.	T	+	2	0	ZNF135	63270390	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-2.161000	0.01278	-2.190000	0.00757	-1.012000	0.02466	ACG	C|0.659;T|0.341	0.341	strong		0.478	ZNF135-003	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000361899.2	NM_003436	
EFHC2	80258	hgsc.bcm.edu	37	X	44171953	44171953	+	Missense_Mutation	SNP	T	T	C	rs17146914	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:44171953T>C	ENST00000420999.1	-	2	175	c.92A>G	c.(91-93)aAt>aGt	p.N31S		NM_025184.3	NP_079460.2	Q5JST6	EFHC2_HUMAN	EF-hand domain (C-terminal) containing 2	31			N -> S (in dbSNP:rs17146914).				calcium ion binding (GO:0005509)			NS(1)|breast(7)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(6)|ovary(2)|skin(1)|urinary_tract(1)	29						CATCATAACATTGTTGCAAAA	0.388													T|||	148	0.0392053	0.0234	0.111	3775	,	,		13971	0.0		0.0318	False		,,,				2504	0.0082				p.N31S		Atlas-SNP	.											.	EFHC2	81	.	0			c.A92G						PASS	.	T	SER/ASN	105,3017		2,85,16,1189,554	86.0	73.0	77.0		92	2.9	1.0	X	dbSNP_123	77	474,5925		8,330,128,1973,1649	yes	missense	EFHC2	NM_025184.3	46	10,415,144,3162,2203	CC,CT,C,TT,T		7.4074,3.3632,6.0813	benign	31/750	44171953	579,8942	1846	4088	5934	SO:0001583	missense	80258	exon2			ATAACATTGTTGC	AK026254	CCDS55405.1	Xp11	2014-01-31			ENSG00000183690	ENSG00000183690		"""EF-hand domain containing"""	26233	protein-coding gene	gene with protein product		300817	"""mental retardation, X-linked 74"""	MRX74		17221867	Standard	NM_025184		Approved	FLJ22843	uc004dgb.4	Q5JST6	OTTHUMG00000021393	ENST00000420999.1:c.92A>G	X.37:g.44171953T>C	ENSP00000404232:p.Asn31Ser	Somatic	267	0	0		WXS	Illumina HiSeq	Phase_I	164	163	0.993902	NM_025184	Q5JST8|Q68DK4|Q8NEI0|Q9H653	Missense_Mutation	SNP	ENST00000420999.1	37	CCDS55405.1	73	0.044002411091018684	11	0.022727272727272728	25	0.07396449704142012	0	0.0	15	0.020107238605898123	T	8.698	0.909024	0.17833	0.033632	0.074074	ENSG00000183690	ENST00000333807;ENST00000420999	T;T	0.68181	-0.3;-0.31	5.42	2.92	0.33932	.	0.503086	0.21755	N	0.069602	T	0.06872	0.0175	L	0.39397	1.21	0.44579	P	0.00245799999999996	B	0.28258	0.205	B	0.20955	0.032	T	0.41342	-0.9514	9	0.41790	T	0.15	-27.1074	6.9969	0.24786	0.0:0.0807:0.1477:0.7715	rs17146914;rs52816335	31	Q5JST6	EFHC2_HUMAN	S	31;59	ENSP00000333823:N31S;ENSP00000404232:N59S	ENSP00000333823:N31S	N	-	2	0	EFHC2	44056897	0.946000	0.32159	0.974000	0.42286	0.532000	0.34746	1.590000	0.36654	1.817000	0.53016	0.417000	0.27973	AAT	0|0.048;C|0.032	0.032	strong		0.388	EFHC2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056312.2	NM_025184	
SPRY3	10251	hgsc.bcm.edu	37	X	155004280	155004280	+	Silent	SNP	A	A	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:155004280A>G	ENST00000302805.2	+	2	1178	c.747A>G	c.(745-747)caA>caG	p.Q249Q		NM_005840.1	NP_005831.1	O43610	SPY3_HUMAN	sprouty homolog 3 (Drosophila)	249	Cys-rich.|SPR. {ECO:0000255|PROSITE- ProRule:PRU00572}.				multicellular organismal development (GO:0007275)|regulation of signal transduction (GO:0009966)	cytoplasm (GO:0005737)|membrane (GO:0016020)						all_cancers(53;1.86e-17)|all_epithelial(53;2.71e-11)|all_lung(58;1.84e-07)|Lung NSC(58;5.62e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)					ATCTGTGCCAACAGGGCTATG	0.592													A|||	970	0.19369	0.2489	0.1744	5008	,	,		20237	0.0179		0.2992	False		,,,				2504	0.2055				p.Q249Q		Atlas-SNP	.											.	SPRY3	52	.	0			c.A747G						PASS	.	A		1040,3366		132,776,1295	207.0	192.0	197.0		747	2.0	1.0	X	dbSNP_134	197	2390,6202		328,1734,2234	no	coding-synonymous	SPRY3	NM_005840.1		460,2510,3529	GG,GA,AA		27.8166,23.6042,26.3887		249/289	155004280	3430,9568	2203	4296	6499	SO:0001819	synonymous_variant	10251	exon2			GTGCCAACAGGGC	AF041038	CCDS14769.4	Xq28 and Yq12	2008-02-05	2001-11-28		ENSG00000168939	ENSG00000168939		"""Pseudoautosomal regions / PAR2"""	11271	protein-coding gene	gene with protein product	"""antagonist of FGF signaling"""	300531	"""sprouty (Drosophila) homolog 2"""			9458049	Standard	NM_005840		Approved	HSPRY3	uc004fnq.1	O43610	OTTHUMG00000022675	ENST00000302805.2:c.747A>G	X.37:g.155004280A>G		Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	119	25	0.210084	NM_005840	A8K0H8	Silent	SNP	ENST00000302805.2	37	CCDS14769.4																																																																																			A|0.771;G|0.229	0.229	strong		0.592	SPRY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058823.2	NM_005840	
LIMD1	8994	hgsc.bcm.edu	37	3	45637439	45637439	+	Silent	SNP	T	T	C	rs267236	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:45637439T>C	ENST00000273317.4	+	1	1089	c.1068T>C	c.(1066-1068)ggT>ggC	p.G356G	LIMD1_ENST00000465039.1_Intron|LIMD1_ENST00000440097.1_Silent_p.G356G	NM_014240.2	NP_055055.1	Q9UGP4	LIMD1_HUMAN	LIM domains containing 1	356					cell migration (GO:0016477)|cytoplasmic mRNA processing body assembly (GO:0033962)|cytoskeleton organization (GO:0007010)|gene silencing by miRNA (GO:0035195)|multicellular organismal development (GO:0007275)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of hippo signaling (GO:0035331)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of transcription, DNA-templated (GO:0045892)|osteoblast development (GO:0002076)|phosphorylation (GO:0016310)|positive regulation of gene silencing by miRNA (GO:2000637)|regulation of cell shape (GO:0008360)|regulation of transcription, DNA-templated (GO:0006355)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	adherens junction (GO:0005912)|cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|RISC complex (GO:0016442)	transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|skin(1)	10				BRCA - Breast invasive adenocarcinoma(193;0.011)|KIRC - Kidney renal clear cell carcinoma(197;0.0264)|Kidney(197;0.0315)		CGCCAGCTGGTCTGGACGGTT	0.622													C|||	3685	0.735823	0.7194	0.6859	5008	,	,		19051	0.9345		0.5915	False		,,,				2504	0.7372				p.G356G		Atlas-SNP	.											.	LIMD1	34	.	0			c.T1068C						PASS	.	C		3191,1215	423.0+/-339.9	1155,881,167	69.0	68.0	68.0		1068	4.7	0.0	3	dbSNP_79	68	5341,3259	490.2+/-372.8	1678,1985,637	no	coding-synonymous	LIMD1	NM_014240.2		2833,2866,804	CC,CT,TT		37.8953,27.576,34.3995		356/677	45637439	8532,4474	2203	4300	6503	SO:0001819	synonymous_variant	8994	exon1			AGCTGGTCTGGAC	AJ132408	CCDS2729.1	3p21.31	2008-02-01			ENSG00000144791	ENSG00000144791			6612	protein-coding gene	gene with protein product		604543				10647888	Standard	NM_014240		Approved		uc003coq.3	Q9UGP4	OTTHUMG00000133453	ENST00000273317.4:c.1068T>C	3.37:g.45637439T>C		Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	117	57	0.487179	NM_014240	Q17RQ1|Q9BQQ9|Q9NQ47	Silent	SNP	ENST00000273317.4	37	CCDS2729.1																																																																																			T|0.317;C|0.683	0.683	strong		0.622	LIMD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257327.1	NM_014240	
PCDHB8	56128	hgsc.bcm.edu	37	5	140559679	140559679	+	Silent	SNP	C	C	G	rs17844507	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	65	0	0		WXS	Illumina HiSeq	Phase_I	51	27	0.529412	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	
TRAPPC11	60684	hgsc.bcm.edu	37	4	184614874	184614874	+	Silent	SNP	C	C	T	rs4862234	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:184614874C>T	ENST00000334690.6	+	21	2572	c.2370C>T	c.(2368-2370)acC>acT	p.T790T	TRAPPC11_ENST00000512476.1_Silent_p.T396T|TRAPPC11_ENST00000357207.4_Silent_p.T790T	NM_021942.5	NP_068761.4	Q7Z392	TPC11_HUMAN	trafficking protein particle complex 11	790					vesicle-mediated transport (GO:0016192)	Golgi apparatus (GO:0005794)											TGAAGCTCACCGCTGGCTTAA	0.388													C|||	1117	0.223043	0.3268	0.1974	5008	,	,		17881	0.1776		0.2177	False		,,,				2504	0.1534				p.T790T		Atlas-SNP	.											.	.	.	.	0			c.C2370T						PASS	.	C	,	1417,2989	462.3+/-353.2	223,971,1009	112.0	112.0	112.0		2370,2370	-0.9	1.0	4	dbSNP_111	112	1932,6668	341.4+/-324.0	221,1490,2589	no	coding-synonymous,coding-synonymous	C4orf41	NM_021942.4,NM_199053.1	,	444,2461,3598	TT,TC,CC		22.4651,32.1607,25.7497	,	790/1134,790/1087	184614874	3349,9657	2203	4300	6503	SO:0001819	synonymous_variant	60684	exon21			GCTCACCGCTGGC		CCDS34112.1, CCDS47166.1	4q35.1	2011-12-12	2011-12-12	2011-12-12	ENSG00000168538	ENSG00000168538		"""Trafficking protein particle complex"""	25751	protein-coding gene	gene with protein product	"""gryzun homolog (Drosophila)"", ""foie gras homolog (zebrafish)"""	614138	"""chromosome 4 open reading frame 41"""	C4orf41		19942856, 21525244	Standard	NM_021942		Approved	FLJ12716, gry, foigr	uc003ivx.3	Q7Z392	OTTHUMG00000160673	ENST00000334690.6:c.2370C>T	4.37:g.184614874C>T		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	78	38	0.487179	NM_021942	A4QPB8|B2RCD6|Q5U5I7|Q6FI73|Q86T25|Q9H0L1|Q9H5K9|Q9H8Q1|Q9H9I7	Silent	SNP	ENST00000334690.6	37	CCDS34112.1																																																																																			C|0.756;T|0.244	0.244	strong		0.388	TRAPPC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361654.2	NM_021942	
ZHX2	22882	hgsc.bcm.edu	37	8	123964953	123964953	+	Silent	SNP	C	C	T	rs3808600	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:123964953C>T	ENST00000314393.4	+	3	2038	c.1203C>T	c.(1201-1203)acC>acT	p.T401T		NM_014943.3	NP_055758.1	Q9Y6X8	ZHX2_HUMAN	zinc fingers and homeoboxes 2	401	Required for interaction with NFYA.|Required for nuclear localization.|Required for repressor activity.				mRNA catabolic process (GO:0006402)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(10)|lung(15)|ovary(1)|prostate(1)|skin(4)|stomach(3)|urinary_tract(1)	45	Lung NSC(37;2e-09)|Ovarian(258;0.0205)|Hepatocellular(40;0.105)		STAD - Stomach adenocarcinoma(47;0.00527)			CAGGAGTCACCAACCATGGCC	0.632													C|||	1161	0.231829	0.0136	0.3314	5008	,	,		16083	0.131		0.3579	False		,,,				2504	0.4305				p.T401T	Esophageal Squamous(94;1056 1388 11767 13799 49639)	Atlas-SNP	.											.	ZHX2	106	.	0			c.C1203T						PASS	.	C		308,4098	164.7+/-196.3	10,288,1905	50.0	57.0	55.0		1203	4.0	1.0	8	dbSNP_107	55	2985,5615	460.5+/-365.2	509,1967,1824	no	coding-synonymous	ZHX2	NM_014943.3		519,2255,3729	TT,TC,CC		34.7093,6.9905,25.3191		401/838	123964953	3293,9713	2203	4300	6503	SO:0001819	synonymous_variant	22882	exon3			AGTCACCAACCAT	AB020661	CCDS6336.1	8q24.13	2012-03-09	2004-01-23		ENSG00000178764	ENSG00000178764		"""Zinc fingers, C2H2-type"", ""Homeoboxes / ZF class"""	18513	protein-coding gene	gene with protein product		609185	"""zinc-fingers and homeoboxes 2"""			10048485, 12741956	Standard	XM_005250837		Approved	KIAA0854	uc003ypk.1	Q9Y6X8	OTTHUMG00000165077	ENST00000314393.4:c.1203C>T	8.37:g.123964953C>T		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	102	29	0.284314	NM_014943		Silent	SNP	ENST00000314393.4	37	CCDS6336.1																																																																																			C|0.762;T|0.238	0.238	strong		0.632	ZHX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381709.1	NM_014943	
CLSTN3	9746	hgsc.bcm.edu	37	12	7288432	7288432	+	Missense_Mutation	SNP	A	A	G	rs7302230	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:7288432A>G	ENST00000266546.6	+	5	1075	c.625A>G	c.(625-627)Agt>Ggt	p.S209G	CLSTN3_ENST00000537408.1_Missense_Mutation_p.S221G	NM_014718.3	NP_055533.2	Q9BQT9	CSTN3_HUMAN	calsyntenin 3	209	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.		S -> G (in dbSNP:rs7302230).		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						GCTGCAGTACAGTGGTGAGAG	0.542													A|||	92	0.0183706	0.0129	0.0274	5008	,	,		-128	0.0		0.0487	False		,,,				2504	0.0072				p.S209G		Atlas-SNP	.											.	CLSTN3	84	.	0			c.A625G						PASS	.	A	GLY/SER	81,4325	70.9+/-108.8	0,81,2122	127.0	115.0	120.0		625	4.9	1.0	12	dbSNP_116	120	493,8107	142.0+/-198.3	14,465,3821	yes	missense	CLSTN3	NM_014718.3	56	14,546,5943	GG,GA,AA		5.7326,1.8384,4.4133	benign	209/957	7288432	574,12432	2203	4300	6503	SO:0001583	missense	9746	exon5			CAGTACAGTGGTG	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	ENST00000266546.6:c.625A>G	12.37:g.7288432A>G	ENSP00000266546:p.Ser209Gly	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	104	44	0.423077	NM_014718	D3DUT6|O94831|Q2T9J5|Q5UE57	Missense_Mutation	SNP	ENST00000266546.6	37	CCDS8575.1	54	0.024725274725274724	3	0.006097560975609756	12	0.03314917127071823	0	0.0	39	0.051451187335092345	A	9.377	1.071908	0.20147	0.018384	0.057326	ENSG00000139182	ENST00000266546;ENST00000537408	T;T	0.61627	0.09;0.09	4.89	4.89	0.63831	Cadherin (5);Cadherin-like (1);	0.128222	0.64402	D	0.000001	T	0.04048	0.0113	N	0.02802	-0.49	0.47698	D	0.999499	B;B	0.25667	0.131;0.0	B;B	0.19946	0.027;0.004	T	0.03981	-1.0987	10	0.21540	T	0.41	-19.9128	14.68	0.69009	1.0:0.0:0.0:0.0	rs7302230;rs17727152;rs52802010;rs60504550;rs7302230	221;209	Q5UE57;Q9BQT9	.;CSTN3_HUMAN	G	209;221	ENSP00000266546:S209G;ENSP00000440679:S221G	ENSP00000266546:S209G	S	+	1	0	CLSTN3	7179699	1.000000	0.71417	0.998000	0.56505	0.977000	0.68977	4.915000	0.63355	2.053000	0.61076	0.379000	0.24179	AGT	A|0.964;G|0.036	0.036	strong		0.542	CLSTN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398560.2	NM_014718	
FAM186A	121006	hgsc.bcm.edu	37	12	50744283	50744283	+	Missense_Mutation	SNP	G	G	A	rs372753266	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:50744283G>A	ENST00000327337.5	-	4	6331	c.6332C>T	c.(6331-6333)gCt>gTt	p.A2111V	FAM186A_ENST00000543111.1_Missense_Mutation_p.A2111V|FAM186A_ENST00000543096.1_Missense_Mutation_p.A122V	NM_001145475.1	NP_001138947.1	A6NE01	F186A_HUMAN	family with sequence similarity 186, member A	2111																	CTTCTTCTGAGCCTCCACATC	0.403													G|||	7	0.00139776	0.0053	0.0	5008	,	,		20592	0.0		0.0	False		,,,				2504	0.0				p.A2111V	NSCLC(138;1796 1887 12511 19463 37884)	Atlas-SNP	.											.	FAM186A	181	.	0			c.C6332T						PASS	.	G	VAL/ALA	2,1382		0,2,690	215.0	170.0	184.0		6332	1.6	1.0	12		184	0,3182		0,0,1591	no	missense	FAM186A	NM_001145475.1	64	0,2,2281	AA,AG,GG		0.0,0.1445,0.0438	probably-damaging	2111/2352	50744283	2,4564	692	1591	2283	SO:0001583	missense	121006	exon4			TTCTGAGCCTCCA		CCDS44878.1	12q13.13	2009-04-22			ENSG00000185958	ENSG00000185958			26980	protein-coding gene	gene with protein product							Standard	NM_001145475		Approved	LOC121006	uc001rwl.2	A6NE01	OTTHUMG00000167889	ENST00000327337.5:c.6332C>T	12.37:g.50744283G>A	ENSP00000329995:p.Ala2111Val	Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	149	43	0.288591	NM_001145475		Missense_Mutation	SNP	ENST00000327337.5	37	CCDS44878.1	.	.	.	.	.	.	.	.	.	.	G	17.68	3.449357	0.63178	0.001445	0.0	ENSG00000185958	ENST00000543111;ENST00000543096;ENST00000327337	T;T;T	0.54279	0.58;0.58;0.58	3.7	1.56	0.23342	.	.	.	.	.	T	0.64271	0.2583	L	0.60455	1.87	0.25564	N	0.986965	D;D	0.76494	0.999;0.999	D;D	0.68943	0.961;0.961	T	0.52011	-0.8632	9	0.87932	D	0	.	9.1064	0.36701	0.0:0.4454:0.5546:0.0	.	2111;2111	F5GYN0;A6NE01	.;F186A_HUMAN	V	2111;122;2111	ENSP00000441337:A2111V;ENSP00000443703:A122V;ENSP00000329995:A2111V	ENSP00000329995:A2111V	A	-	2	0	FAM186A	49030550	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	2.034000	0.41145	0.848000	0.35191	0.462000	0.41574	GCT	.	.	weak		0.403	FAM186A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396838.1	XM_001718353	
OR12D3	81797	hgsc.bcm.edu	37	6	29342287	29342287	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:29342287G>A	ENST00000396806.3	-	1	781	c.778C>T	c.(778-780)Cgt>Tgt	p.R260C	OR5V1_ENST00000377154.1_Intron	NM_030959.2	NP_112221.1	Q9UGF7	O12D3_HUMAN	olfactory receptor, family 12, subfamily D, member 3	260						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(6)|ovary(2)|skin(1)|upper_aerodigestive_tract(3)	23						GAAGCAGGACGAATATATGTG	0.488																																					p.R260C		Atlas-SNP	.											OR12D3,NS,carcinoma,+1,2	OR12D3	55	2	0			c.C778T						scavenged	.						79.0	73.0	75.0					6																	29342287		1510	2708	4218	SO:0001583	missense	81797	exon1			CAGGACGAATATA		CCDS4658.1	6p22.1	2013-09-24			ENSG00000112462	ENSG00000112462		"""GPCR / Class A : Olfactory receptors"""	13963	protein-coding gene	gene with protein product							Standard	NM_030959		Approved	hs6M1-27	uc003nme.3	Q9UGF7	OTTHUMG00000031051	ENST00000396806.3:c.778C>T	6.37:g.29342287G>A	ENSP00000380023:p.Arg260Cys	Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	142	2	0.0140845	NM_030959	A2BDZ1|Q5SQI8|Q6IF23	Missense_Mutation	SNP	ENST00000396806.3	37	CCDS4658.1	.	.	.	.	.	.	.	.	.	.	G	7.891	0.732234	0.15507	.	.	ENSG00000112462	ENST00000377143;ENST00000396806	T	0.35789	1.29	4.19	-3.6	0.04570	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.15132	0.0365	M	0.78049	2.395	0.09310	N	1	B	0.25441	0.126	B	0.27715	0.082	T	0.35025	-0.9805	9	0.32370	T	0.25	-0.282	5.056	0.14533	0.215:0.0:0.3355:0.4495	.	260	Q9UGF7	O12D3_HUMAN	C	260	ENSP00000380023:R260C	ENSP00000366348:R260C	R	-	1	0	OR12D3	29450266	0.000000	0.05858	0.000000	0.03702	0.235000	0.25334	-0.399000	0.07250	-0.589000	0.05874	0.205000	0.17691	CGT	.	.	none		0.488	OR12D3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076056.3		
LOXL2	4017	hgsc.bcm.edu	37	8	23190941	23190941	+	Silent	SNP	T	T	C	rs1010156	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:23190941T>C	ENST00000389131.3	-	5	1308	c.939A>G	c.(937-939)tcA>tcG	p.S313S	RP11-177H13.2_ENST00000519692.1_RNA|LOXL2_ENST00000518472.1_5'UTR	NM_002318.2	NP_002309.1	Q9Y4K0	LOXL2_HUMAN	lysyl oxidase-like 2	313					aging (GO:0007568)|cell adhesion (GO:0007155)|cellular protein modification process (GO:0006464)|collagen fibril organization (GO:0030199)|endothelial cell migration (GO:0043542)|endothelial cell proliferation (GO:0001935)|epithelial to mesenchymal transition (GO:0001837)|histone modification (GO:0016570)|negative regulation of transcription, DNA-templated (GO:0045892)|oxidation-reduction process (GO:0055114)|positive regulation of chondrocyte differentiation (GO:0032332)|protein deamination (GO:0018277)|response to copper ion (GO:0046688)|response to hypoxia (GO:0001666)|sprouting angiogenesis (GO:0002040)|transcription, DNA-templated (GO:0006351)	basement membrane (GO:0005604)|chromosome (GO:0005694)|extracellular space (GO:0005615)|membrane (GO:0016020)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|electron carrier activity (GO:0009055)|methylated histone binding (GO:0035064)|oligosaccharide binding (GO:0070492)|protein-lysine 6-oxidase activity (GO:0004720)|scavenger receptor activity (GO:0005044)|transcription corepressor activity (GO:0003714)			breast(2)|endometrium(4)|kidney(3)|large_intestine(12)|lung(5)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	35		Prostate(55;0.0453)|Breast(100;0.143)		Colorectal(74;0.0288)|COAD - Colon adenocarcinoma(73;0.096)		TCCGGAATCTTGAGGGTCCGT	0.612													c|||	2064	0.412141	0.3169	0.3948	5008	,	,		20241	0.4742		0.5537	False		,,,				2504	0.3436				p.S313S		Atlas-SNP	.											.	LOXL2	97	.	0			c.A939G	GRCh37	CM071849	LOXL2	M	rs1010156	PASS	.			1508,2898	674.4+/-402.9	275,958,970	100.0	85.0	90.0		939	-11.9	0.3	8	dbSNP_86	90	4890,3710	529.8+/-381.7	1404,2082,814	no	coding-synonymous	LOXL2	NM_002318.2		1679,3040,1784	CC,CT,TT		43.1395,34.2261,49.1927		313/775	23190941	6398,6608	2203	4300	6503	SO:0001819	synonymous_variant	4017	exon5			GAATCTTGAGGGT	U89942	CCDS34864.1	8p21.3	2008-05-15				ENSG00000134013			6666	protein-coding gene	gene with protein product		606663				9722957	Standard	NM_002318		Approved	WS9-14	uc003xdh.1	Q9Y4K0		ENST00000389131.3:c.939A>G	8.37:g.23190941T>C		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	73	73	1	NM_002318	B2R5Q0|Q53HV3|Q9BW70|Q9Y5Y8	Silent	SNP	ENST00000389131.3	37	CCDS34864.1	1004	0.4597069597069597	152	0.3089430894308943	149	0.4116022099447514	280	0.48951048951048953	423	0.558047493403694	c	6.097	0.386253	0.11524	0.342261	0.568605	ENSG00000134013	ENST00000520349	.	.	.	5.93	-11.9	0.00025	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.22787	P	0.99873326	.	.	.	.	.	.	T	0.28235	-1.0050	3	.	.	.	.	6.4863	0.22091	0.0712:0.4283:0.1665:0.334	rs1010156;rs1051140;rs3191523;rs17849345;rs59713559;rs1010156	.	.	.	R	23	.	.	Q	-	2	0	LOXL2	23246886	0.000000	0.05858	0.327000	0.25402	0.419000	0.31324	-5.057000	0.00155	-2.452000	0.00542	-0.763000	0.03452	CAA	T|0.521;C|0.479	0.479	strong		0.612	LOXL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375603.1		
SLC25A23	79085	hgsc.bcm.edu	37	19	6458240	6458240	+	Silent	SNP	G	G	C	rs2289784	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	24	0	0		WXS	Illumina HiSeq	Phase_I	26	15	0.576923	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	
GAREM	64762	hgsc.bcm.edu	37	18	30050356	30050356	+	Silent	SNP	C	C	T	rs11664566	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:30050356C>T	ENST00000269209.6	-	1	39	c.36G>A	c.(34-36)aaG>aaA	p.K12K	GAREM_ENST00000399218.4_Silent_p.K12K			Q9H706	GAREM_HUMAN	GRB2 associated, regulator of MAPK1	12	CABIT.				cellular response to epidermal growth factor stimulus (GO:0071364)|epidermal growth factor receptor signaling pathway (GO:0007173)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)	plasma membrane (GO:0005886)	proline-rich region binding (GO:0070064)										ACTTCACATCCTTGAGGCTGC	0.726													c|||	1280	0.255591	0.298	0.2161	5008	,	,		8443	0.3869		0.162	False		,,,				2504	0.1871				p.K12K		Atlas-SNP	.											.	.	.	.	0			c.G36A						PASS	.		,	1195,3201		164,867,1167	16.0	18.0	17.0		36,36	3.5	1.0	18	dbSNP_120	17	1361,7229		122,1117,3056	no	coding-synonymous,coding-synonymous	FAM59A	NM_001242409.1,NM_022751.2	,	286,1984,4223	TT,TC,CC		15.844,27.1838,19.6827	,	12/877,12/876	30050356	2556,10430	2198	4295	6493	SO:0001819	synonymous_variant	64762	exon1			CACATCCTTGAGG	AK025263	CCDS11905.1, CCDS56057.1	18q12.1	2012-11-30	2012-11-30	2012-11-30	ENSG00000141441	ENSG00000141441			26136	protein-coding gene	gene with protein product	"""Grb2-associated and regulator of Erk/MAPK"""		"""chromosome 18 open reading frame 11"", ""family with sequence similarity 59, member A"""	C18orf11, FAM59A		19509291	Standard	NM_001242409		Approved	FLJ21610	uc002kxl.3	Q9H706	OTTHUMG00000132273	ENST00000269209.6:c.36G>A	18.37:g.30050356C>T		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	81	35	0.432099	NM_022751	Q0VAG3|Q0VAG4|Q8ND03|Q9BSF5	Silent	SNP	ENST00000269209.6	37	CCDS56057.1																																																																																			C|0.784;T|0.216	0.216	strong		0.726	GAREM-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255365.1	NM_022751	
OR5M11	219487	hgsc.bcm.edu	37	11	56310497	56310497	+	Silent	SNP	C	C	T	rs72913727	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:56310497C>T	ENST00000528616.2	-	1	260	c.237G>A	c.(235-237)ccG>ccA	p.P79P		NM_001005245.1	NP_001005245.1	Q96RB7	OR5MB_HUMAN	olfactory receptor, family 5, subfamily M, member 11	79						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(14)	18						TCGACATCTGCGGGGTTGCAT	0.423													C|||	275	0.0549121	0.0265	0.0159	5008	,	,		23045	0.0942		0.0577	False		,,,				2504	0.0777				p.P79P		Atlas-SNP	.											OR5M11,right_upper_lobe,carcinoma,-1,1	OR5M11	60	1	0			c.G237A						scavenged	.	C		121,4191		0,121,2035	119.0	118.0	119.0		237	-1.9	1.0	11	dbSNP_130	119	477,8067		14,449,3809	no	coding-synonymous	OR5M11	NM_001005245.1		14,570,5844	TT,TC,CC		5.5829,2.8061,4.6515		79/306	56310497	598,12258	2156	4272	6428	SO:0001819	synonymous_variant	219487	exon1			CATCTGCGGGGTT	AP002517	CCDS53629.1	11q11	2012-08-09				ENSG00000255223		"""GPCR / Class A : Olfactory receptors"""	15291	protein-coding gene	gene with protein product							Standard	NM_001005245		Approved	OR11-199	uc010rjl.2	Q96RB7		ENST00000528616.2:c.237G>A	11.37:g.56310497C>T		Somatic	71	1	0.0140845		WXS	Illumina HiSeq	Phase_I	64	47	0.734375	NM_001005245	B2RNL5|B2RNL7	Silent	SNP	ENST00000528616.2	37	CCDS53629.1																																																																																			C|0.949;T|0.051	0.051	strong		0.423	OR5M11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391608.1	NM_001005245	
TBX21	30009	hgsc.bcm.edu	37	17	45822579	45822579	+	Silent	SNP	G	G	A	rs12721470	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:45822579G>A	ENST00000177694.1	+	6	1666	c.1455G>A	c.(1453-1455)ccG>ccA	p.P485P		NM_013351.1	NP_037483.1	Q9UL17	TBX21_HUMAN	T-box 21	485					cellular response to organic substance (GO:0071310)|lymphocyte migration (GO:0072676)|multicellular organismal development (GO:0007275)|positive regulation of isotype switching to IgG isotypes (GO:0048304)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|response to virus (GO:0009615)|T cell differentiation (GO:0030217)|transcription, DNA-templated (GO:0006351)	neuronal cell body (GO:0043025)|nucleus (GO:0005634)	sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|endometrium(1)|large_intestine(3)|lung(14)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	22						CCATCCGGCCGGAATCCAGTG	0.652													G|||	441	0.0880591	0.0628	0.0778	5008	,	,		16600	0.0694		0.0427	False		,,,				2504	0.1953				p.P485P		Atlas-SNP	.											.	TBX21	50	.	0			c.G1455A						PASS	.	G		246,4160	140.8+/-176.2	5,236,1962	41.0	43.0	42.0		1455	-6.8	0.7	17	dbSNP_123	42	312,8288	111.6+/-171.8	2,308,3990	no	coding-synonymous	TBX21	NM_013351.1		7,544,5952	AA,AG,GG		3.6279,5.5833,4.2903		485/536	45822579	558,12448	2203	4300	6503	SO:0001819	synonymous_variant	30009	exon6			CCGGCCGGAATCC	AF093098	CCDS11514.1	17q21.2	2008-06-23				ENSG00000073861		"""T-boxes"""	11599	protein-coding gene	gene with protein product		604895					Standard	NM_013351		Approved	TBLYM, T-bet	uc002ilv.1	Q9UL17		ENST00000177694.1:c.1455G>A	17.37:g.45822579G>A		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	76	29	0.381579	NM_013351		Silent	SNP	ENST00000177694.1	37	CCDS11514.1																																																																																			G|0.951;A|0.049	0.049	strong		0.652	TBX21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441365.1	NM_013351	
PNKP	11284	hgsc.bcm.edu	37	19	50370404	50370404	+	Missense_Mutation	SNP	G	G	A	rs3739168	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:50370404G>A	ENST00000322344.3	-	2	167	c.58C>T	c.(58-60)Ccc>Tcc	p.P20S	PNKP_ENST00000600910.1_Missense_Mutation_p.P20S|PNKP_ENST00000600573.1_Missense_Mutation_p.P20S|PNKP_ENST00000595792.1_5'UTR|PNKP_ENST00000596014.1_Missense_Mutation_p.P20S	NM_007254.3	NP_009185.2	Q96T60	PNKP_HUMAN	polynucleotide kinase 3'-phosphatase	20	FHA.		P -> S (in dbSNP:rs3739168). {ECO:0000269|Ref.5}.		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)		AAGATGGGGGGCGCTCCCCCA	0.711								Other BER factors					G|||	33	0.00658946	0.0091	0.0159	5008	,	,		11680	0.0		0.0089	False		,,,				2504	0.001				p.P20S		Atlas-SNP	.											.	PNKP	71	.	0			c.C58T						PASS	.	G	SER/PRO	50,4316		0,50,2133	15.0	18.0	17.0		58	4.5	0.1	19	dbSNP_107	17	66,8450		0,66,4192	no	missense	PNKP	NM_007254.3	74	0,116,6325	AA,AG,GG		0.775,1.1452,0.9005	benign	20/522	50370404	116,12766	2183	4258	6441	SO:0001583	missense	11284	exon2			TGGGGGGCGCTCC	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.58C>T	19.37:g.50370404G>A	ENSP00000323511:p.Pro20Ser	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	64	34	0.53125	NM_007254	Q9BUL2|Q9P1V2|Q9UKU8|Q9UNF8|Q9UNI0	Missense_Mutation	SNP	ENST00000322344.3	37	CCDS12783.1	15	0.006868131868131868	3	0.006097560975609756	5	0.013812154696132596	0	0.0	7	0.009234828496042216	G	10.93	1.490782	0.26774	0.011452	0.00775	ENSG00000039650	ENST00000322344	T	0.22743	1.94	5.58	4.52	0.55395	SMAD/FHA domain (1);	0.266214	0.31199	N	0.008073	T	0.10252	0.0251	L	0.36672	1.1	0.31374	N	0.679772	B	0.34241	0.444	B	0.26614	0.071	T	0.09015	-1.0694	10	0.20046	T	0.44	-23.1154	12.1622	0.54110	0.0:0.1725:0.8275:0.0	rs3739168	20	Q96T60	PNKP_HUMAN	S	20	ENSP00000323511:P20S	ENSP00000323511:P20S	P	-	1	0	PNKP	55062216	0.982000	0.34865	0.101000	0.21167	0.039000	0.13416	2.302000	0.43637	1.296000	0.44742	0.655000	0.94253	CCC	G|0.991;A|0.009	0.009	strong		0.711	PNKP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465830.1	NM_007254	
STK32C	282974	hgsc.bcm.edu	37	10	134038809	134038809	+	Silent	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:134038809G>A	ENST00000368622.1	-	7	834	c.453C>T	c.(451-453)ggC>ggT	p.G151G	STK32C_ENST00000368625.4_Silent_p.G281G					serine/threonine kinase 32C											breast(1)|endometrium(2)|large_intestine(2)|lung(15)|ovary(2)|skin(1)	23		all_cancers(35;2.72e-11)|all_epithelial(44;2.33e-08)|Lung NSC(174;0.000855)|all_lung(145;0.00146)|all_neural(114;0.0299)|Breast(234;0.106)|Colorectal(31;0.112)|Melanoma(40;0.124)|Glioma(114;0.203)		Epithelial(32;3.99e-05)|all cancers(32;5.58e-05)|OV - Ovarian serous cystadenocarcinoma(35;9.96e-05)|BRCA - Breast invasive adenocarcinoma(275;0.222)		AGCCGGTCCCGCCGTTGACAA	0.632																																					p.G268G		Atlas-SNP	.											.	STK32C	61	.	0			c.C804T						PASS	.						27.0	29.0	28.0					10																	134038809		2200	4296	6496	SO:0001819	synonymous_variant	282974	exon7			GGTCCCGCCGTTG	AK057849	CCDS7666.1	10q26.3	2004-07-22			ENSG00000165752	ENSG00000165752			21332	protein-coding gene	gene with protein product							Standard	NM_173575		Approved	PKE, MGC23665, YANK3	uc001lle.1	Q86UX6	OTTHUMG00000019285	ENST00000368622.1:c.453C>T	10.37:g.134038809G>A		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	95	49	0.515789	NM_173575		Silent	SNP	ENST00000368622.1	37																																																																																				.	.	none		0.632	STK32C-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000051068.2	NM_173575	
KATNAL2	83473	hgsc.bcm.edu	37	18	44585955	44585955	+	Missense_Mutation	SNP	G	G	A	rs7233515	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:44585955G>A	ENST00000245121.5	+	5	457	c.263G>A	c.(262-264)aGt>aAt	p.S88N	KATNAL2_ENST00000356157.7_Missense_Mutation_p.S160N|KATNAL2_ENST00000592005.1_Intron	NM_031303.2	NP_112593.2			katanin p60 subunit A-like 2											central_nervous_system(2)|endometrium(3)|large_intestine(8)|lung(8)|ovary(1)|pancreas(1)|skin(1)|stomach(1)|urinary_tract(2)	27						CGCCTGGAAAGTGCCAACTTC	0.478													G|||	2180	0.435304	0.3457	0.562	5008	,	,		18487	0.4752		0.3718	False		,,,				2504	0.4908				p.S88N		Atlas-SNP	.											.	KATNAL2	64	.	0			c.G263A						PASS	.	G	ASN/SER	1529,2877	484.0+/-359.9	257,1015,931	167.0	162.0	164.0		263	-4.8	0.0	18	dbSNP_116	164	3438,5162	507.5+/-376.8	729,1980,1591	yes	missense	KATNAL2	NM_031303.2	46	986,2995,2522	AA,AG,GG		39.9767,34.7027,38.1901	benign	88/467	44585955	4967,8039	2203	4300	6503	SO:0001583	missense	83473	exon5			TGGAAAGTGCCAA	BC034999	CCDS32828.1	18q21.1	2010-04-21			ENSG00000167216	ENSG00000167216		"""ATPases / AAA-type"""	25387	protein-coding gene	gene with protein product		614697				12477932	Standard	NM_031303		Approved	MGC33211, DKFZP667C165	uc002lco.3	Q8IYT4		ENST00000245121.5:c.263G>A	18.37:g.44585955G>A	ENSP00000245121:p.Ser88Asn	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	39	21	0.538462	NM_031303		Missense_Mutation	SNP	ENST00000245121.5	37	CCDS32828.1	900	0.41208791208791207	170	0.34552845528455284	191	0.5276243093922652	257	0.4493006993006993	282	0.3720316622691293	G	10.94	1.492908	0.26774	0.347027	0.399767	ENSG00000167216	ENST00000356157;ENST00000245121	D;D	0.94138	-3.34;-3.36	5.69	-4.83	0.03161	.	0.990923	0.08242	N	0.975947	T	0.00012	0.0000	N	0.16307	0.4	0.80722	P	0.0	B	0.06786	0.001	B	0.08055	0.003	T	0.14035	-1.0487	9	0.23302	T	0.38	-6.3496	6.7422	0.23443	0.5191:0.2294:0.2515:0.0	rs7233515;rs17853358;rs52831506;rs7233515	160	Q8IYT4	KATL2_HUMAN	N	160;88	ENSP00000348478:S160N;ENSP00000245121:S88N	ENSP00000245121:S88N	S	+	2	0	KATNAL2	42839953	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.937000	0.03942	-0.685000	0.05177	-0.150000	0.13652	AGT	G|0.601;A|0.399	0.399	strong		0.478	KATNAL2-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446138.2	NM_031303	
NLRC5	84166	hgsc.bcm.edu	37	16	57111232	57111232	+	Silent	SNP	C	C	T	rs11864231	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:57111232C>T	ENST00000262510.6	+	41	5085	c.4860C>T	c.(4858-4860)gaC>gaT	p.D1620D	NLRC5_ENST00000539144.1_Silent_p.D1591D|NLRC5_ENST00000436936.1_3'UTR|NLRC5_ENST00000308149.7_Silent_p.D1591D	NM_032206.4	NP_115582.4	Q86WI3	NLRC5_HUMAN	NLR family, CARD domain containing 5	1620					defense response to virus (GO:0051607)|innate immune response (GO:0045087)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of type I interferon production (GO:0032480)|negative regulation of type I interferon-mediated signaling pathway (GO:0060339)|positive regulation of interferon-gamma-mediated signaling pathway (GO:0060335)|positive regulation of MHC class I biosynthetic process (GO:0045345)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon-mediated signaling pathway (GO:0060340)|regulation of kinase activity (GO:0043549)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)			NS(2)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(21)|ovary(8)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	75		all_neural(199;0.225)				AGATTGGAGACGCTGGTGTCC	0.567													C|||	864	0.172524	0.1036	0.1816	5008	,	,		19784	0.1468		0.2326	False		,,,				2504	0.2239				p.D1620D		Atlas-SNP	.											.	NLRC5	186	.	0			c.C4860T						PASS	.	C		590,3806	260.4+/-263.7	40,510,1648	82.0	70.0	74.0		4860	-2.4	0.0	16	dbSNP_120	74	1835,6765	327.9+/-318.0	202,1431,2667	no	coding-synonymous	NLRC5	NM_032206.3		242,1941,4315	TT,TC,CC		21.3372,13.4213,18.6596		1620/1867	57111232	2425,10571	2198	4300	6498	SO:0001819	synonymous_variant	84166	exon40			TGGAGACGCTGGT	AF389420	CCDS10773.1	16q13	2008-02-05			ENSG00000140853	ENSG00000140853		"""Nucleotide-binding domain and leucine rich repeat containing"""	29933	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 5"", ""NOD-like receptor C5"""	613537				12615073	Standard	NM_032206		Approved	NOD27, CLR16.1, FLJ21709	uc021tiu.1	Q86WI3	OTTHUMG00000133470	ENST00000262510.6:c.4860C>T	16.37:g.57111232C>T		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	181	69	0.381215	NM_032206	B5MEF1|C9JMD8|Q6P4A6|Q86VM7|Q8NF42|Q8TEE2|Q8TEJ1|Q969L7	Silent	SNP	ENST00000262510.6	37	CCDS10773.1																																																																																			C|0.819;T|0.181	0.181	strong		0.567	NLRC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257346.1	NM_032206	
RYR3	6263	hgsc.bcm.edu	37	15	34130697	34130697	+	Silent	SNP	G	G	C	rs75286462	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:34130697G>C	ENST00000389232.4	+	89	12586	c.12516G>C	c.(12514-12516)gtG>gtC	p.V4172V	RYR3_ENST00000415757.3_Silent_p.V4167V	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	4172					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)		ACAGGAACGTGAAAAAGATGA	0.512													G|||	81	0.0161741	0.0015	0.0216	5008	,	,		20602	0.0		0.0557	False		,,,				2504	0.0082				p.V4172V		Atlas-SNP	.											.	RYR3	760	.	0			c.G12516C						PASS	.	G		34,3884		0,34,1925	82.0	89.0	86.0		12516	1.6	1.0	15	dbSNP_132	86	326,7936		5,316,3810	no	coding-synonymous	RYR3	NM_001036.3		5,350,5735	CC,CG,GG		3.9458,0.8678,2.9557		4172/4871	34130697	360,11820	1959	4131	6090	SO:0001819	synonymous_variant	6263	exon89			GAACGTGAAAAAG		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.12516G>C	15.37:g.34130697G>C		Somatic	196	0	0		WXS	Illumina HiSeq	Phase_I	185	111	0.6	NM_001036	O15175|Q15412	Silent	SNP	ENST00000389232.4	37	CCDS45210.1																																																																																			G|0.975;C|0.025	0.025	strong		0.512	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1		
UNC5C	8633	hgsc.bcm.edu	37	4	96127869	96127869	+	Silent	SNP	T	T	G	rs2276322	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:96127869T>G	ENST00000453304.1	-	11	2160	c.1812A>C	c.(1810-1812)ccA>ccC	p.P604P		NM_003728.3	NP_003719.3	O95185	UNC5C_HUMAN	unc-5 homolog C (C. elegans)	604	ZU5. {ECO:0000255|PROSITE- ProRule:PRU00485}.				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)		TGAGGACGACTGGGCGGGTGA	0.587													G|||	2647	0.528554	0.5514	0.513	5008	,	,		14806	0.3601		0.7068	False		,,,				2504	0.499				p.P604P		Atlas-SNP	.											.	UNC5C	141	.	0			c.A1812C						PASS	.	G		2397,2009	561.4+/-380.7	638,1121,444	74.0	68.0	70.0		1812	-10.6	0.1	4	dbSNP_100	70	5785,2815	441.7+/-359.9	1944,1897,459	no	coding-synonymous	UNC5C	NM_003728.3		2582,3018,903	GG,GT,TT		32.7326,45.5969,37.0906		604/932	96127869	8182,4824	2203	4300	6503	SO:0001819	synonymous_variant	8633	exon11			GACGACTGGGCGG	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.1812A>C	4.37:g.96127869T>G		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	96	43	0.447917	NM_003728	Q8IUT0	Silent	SNP	ENST00000453304.1	37	CCDS3643.1																																																																																			T|0.394;G|0.606	0.606	strong		0.587	UNC5C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253607.1	NM_003728	
EN1	2019	hgsc.bcm.edu	37	2	119600674	119600674	+	Missense_Mutation	SNP	A	A	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:119600674A>C	ENST00000295206.6	-	2	1529	c.1019T>G	c.(1018-1020)cTc>cGc	p.L340R	EN1_ENST00000546667.1_5'Flank	NM_001426.3	NP_001417.3	Q05925	HME1_HUMAN	engrailed homeobox 1	340					anatomical structure morphogenesis (GO:0009653)|dorsal/ventral pattern formation (GO:0009953)|embryonic forelimb morphogenesis (GO:0035115)|hindbrain development (GO:0030902)|midbrain development (GO:0030901)|midbrain-hindbrain boundary development (GO:0030917)|multicellular organism growth (GO:0035264)|neuron development (GO:0048666)|pigmentation (GO:0043473)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|proximal/distal pattern formation (GO:0009954)|response to cocaine (GO:0042220)|skeletal system development (GO:0001501)	membrane (GO:0016020)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			endometrium(1)|large_intestine(2)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	9						GTTGAGGCTGAGTTCCTGGGC	0.612																																					p.L340R		Atlas-SNP	.											.	EN1	33	.	0			c.T1019G						PASS	.						69.0	63.0	65.0					2																	119600674		2203	4300	6503	SO:0001583	missense	2019	exon2			AGGCTGAGTTCCT	L12699	CCDS2123.1	2q14.2	2011-06-20	2007-02-15		ENSG00000163064	ENSG00000163064		"""Homeoboxes / ANTP class : NKL subclass"""	3342	protein-coding gene	gene with protein product		131290				8094370	Standard	NM_001426		Approved		uc002tlm.3	Q05925	OTTHUMG00000131401	ENST00000295206.6:c.1019T>G	2.37:g.119600674A>C	ENSP00000295206:p.Leu340Arg	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	96	33	0.34375	NM_001426	Q4ZG44	Missense_Mutation	SNP	ENST00000295206.6	37	CCDS2123.1	.	.	.	.	.	.	.	.	.	.	A	22.3	4.267128	0.80469	.	.	ENSG00000163064	ENST00000295206	D	0.98280	-4.84	4.89	4.89	0.63831	Homeobox, eukaryotic (1);Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);Homeobox, conserved site (1);	0.000000	0.85682	D	0.000000	D	0.99432	0.9799	H	0.99169	4.455	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98029	1.0375	10	0.87932	D	0	-14.1387	14.1743	0.65529	1.0:0.0:0.0:0.0	.	340	Q05925	HME1_HUMAN	R	340	ENSP00000295206:L340R	ENSP00000295206:L340R	L	-	2	0	EN1	119317144	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.330000	0.96422	1.831000	0.53308	0.454000	0.30748	CTC	.	.	none		0.612	EN1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254191.3		
DMBT1	1755	hgsc.bcm.edu	37	10	124399814	124399814	+	Missense_Mutation	SNP	C	C	T	rs200589297	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:124399814C>T	ENST00000338354.3	+	52	6920	c.6814C>T	c.(6814-6816)Cgc>Tgc	p.R2272C	DMBT1_ENST00000368909.3_Missense_Mutation_p.R2272C|DMBT1_ENST00000359586.6_Missense_Mutation_p.R992C|DMBT1_ENST00000344338.3_Missense_Mutation_p.R2262C|DMBT1_ENST00000368955.3_Missense_Mutation_p.R2262C|DMBT1_ENST00000330163.4_Missense_Mutation_p.R1644C|DMBT1_ENST00000368956.2_Missense_Mutation_p.R1644C			Q9UGM3	DMBT1_HUMAN	deleted in malignant brain tumors 1	2272	ZP. {ECO:0000255|PROSITE- ProRule:PRU00375}.				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)				TGTGACCAGCCGCCCTTACTA	0.473													C|||	2	0.000399361	0.0	0.0014	5008	,	,		23698	0.0		0.001	False		,,,				2504	0.0				p.R2272C	Ovarian(182;93 2026 18125 22222 38972)	Atlas-SNP	.											DMBT1_ENST00000368915,NS,carcinoma,0,3	DMBT1	677	3	0			c.C6814T						scavenged	.	C	CYS/ARG,CYS/ARG,CYS/ARG	1,4011		0,1,2005	178.0	168.0	171.0		4930,6814,6784	-2.2	0.0	10		171	12,8342		0,12,4165	yes	missense,missense,missense	DMBT1	NM_004406.2,NM_007329.2,NM_017579.2	180,180,180	0,13,6170	TT,TC,CC		0.1436,0.0249,0.1051	probably-damaging,probably-damaging,probably-damaging	1644/1786,2272/2414,2262/2404	124399814	13,12353	2006	4177	6183	SO:0001583	missense	1755	exon52			ACCAGCCGCCCTT		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.6814C>T	10.37:g.124399814C>T	ENSP00000342210:p.Arg2272Cys	Somatic	336	0	0		WXS	Illumina HiSeq	Phase_I	273	3	0.010989	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		1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	7.272	0.607406	0.14002	2.49E-4	0.001436	ENSG00000187908	ENST00000338354;ENST00000368915;ENST00000341278;ENST00000368953;ENST00000339871;ENST00000368942;ENST00000327438;ENST00000344338;ENST00000339712;ENST00000330163;ENST00000368909;ENST00000368955;ENST00000368956;ENST00000344467;ENST00000359586	D;D;D;D;D;D;D	0.82619	-1.63;-1.63;-1.63;-1.63;-1.63;-1.63;-1.63	5.29	-2.25	0.06888	Zona pellucida sperm-binding protein (3);	1.249510	0.06222	U	0.686990	T	0.73450	0.3588	N	0.14661	0.345	0.09310	N	1	P;D;P;P;P;P;P	0.71674	0.935;0.998;0.935;0.61;0.61;0.61;0.662	B;P;B;B;B;B;B	0.53649	0.36;0.731;0.255;0.169;0.169;0.169;0.261	T	0.63193	-0.6692	10	0.38643	T	0.18	.	2.2084	0.03942	0.285:0.3111:0.0693:0.3346	.	992;2252;1521;2401;1644;2262;2272	F8WEF7;Q9UGM3-5;Q9UGM3-8;Q9UGM3-6;Q9UGM3-2;Q9UGM3-3;Q9UGM3	.;.;.;.;.;.;DMBT1_HUMAN	C	2272;2401;2272;2272;2272;2271;1644;2262;1644;1644;2272;2262;1644;418;992	ENSP00000342210:R2272C;ENSP00000343175:R2262C;ENSP00000327747:R1644C;ENSP00000357905:R2272C;ENSP00000357951:R2262C;ENSP00000357952:R1644C;ENSP00000352593:R992C	ENSP00000331522:R1644C	R	+	1	0	DMBT1	124389804	0.000000	0.05858	0.001000	0.08648	0.163000	0.22366	0.166000	0.16583	-0.275000	0.09219	-0.266000	0.10368	CGC	C|0.999;T|0.001	0.001	strong		0.473	DMBT1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050792.2	NM_004406	
C19orf45	374877	hgsc.bcm.edu	37	19	7573287	7573287	+	Missense_Mutation	SNP	C	C	T	rs1133378	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:7573287C>T	ENST00000361664.2	+	9	1630	c.1489C>T	c.(1489-1491)Cct>Tct	p.P497S	CTD-2207O23.12_ENST00000599312.1_Intron	NM_198534.2	NP_940936.2	Q8NA69	CS045_HUMAN	chromosome 19 open reading frame 45	497			P -> S (in dbSNP:rs1133378). {ECO:0000269|PubMed:14702039}.							endometrium(1)|kidney(1)|liver(1)|lung(2)|ovary(2)|stomach(1)	8						CCCCCAGCCCCCTATGTACCT	0.602													C|||	1198	0.239217	0.1725	0.3285	5008	,	,		17721	0.1746		0.337	False		,,,				2504	0.2321				p.P497S		Atlas-SNP	.											.	C19orf45	36	.	0			c.C1489T						PASS	.	C	SER/PRO	842,3562	313.0+/-292.9	92,658,1452	29.0	28.0	28.0		1489	3.6	0.0	19	dbSNP_86	28	2849,5751	417.1+/-352.3	471,1907,1922	yes	missense	C19orf45	NM_198534.2	74	563,2565,3374	TT,TC,CC		33.1279,19.119,28.3836	probably-damaging	497/506	7573287	3691,9313	2202	4300	6502	SO:0001583	missense	374877	exon9			CAGCCCCCTATGT	BC029824	CCDS12179.2	19p13.2	2008-02-05			ENSG00000198723	ENSG00000198723			24745	protein-coding gene	gene with protein product						12477932	Standard	NM_198534		Approved	FLJ35784	uc002mgm.2	Q8NA69	OTTHUMG00000157183	ENST00000361664.2:c.1489C>T	19.37:g.7573287C>T	ENSP00000355241:p.Pro497Ser	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	111	43	0.387387	NM_198534	Q8N115	Missense_Mutation	SNP	ENST00000361664.2	37	CCDS12179.2	605	0.27701465201465203	98	0.1991869918699187	133	0.3674033149171271	112	0.1958041958041958	262	0.34564643799472294	C	16.86	3.239811	0.58995	0.19119	0.331279	ENSG00000198723	ENST00000361664	T	0.13901	2.55	3.62	3.62	0.41486	.	0.417387	0.20234	N	0.096427	T	0.00012	0.0000	L	0.56769	1.78	0.80722	P	0.0	D	0.63046	0.992	P	0.60541	0.876	T	0.48246	-0.9052	9	0.41790	T	0.15	-2.9932	11.0656	0.47974	0.0:1.0:0.0:0.0	rs1133378;rs3178370;rs3195126;rs3745354;rs1133378	497	Q8NA69	CS045_HUMAN	S	497	ENSP00000355241:P497S	ENSP00000355241:P497S	P	+	1	0	C19orf45	7479287	0.001000	0.12720	0.008000	0.14137	0.035000	0.12851	1.017000	0.29989	2.325000	0.78763	0.462000	0.41574	CCT	C|0.736;T|0.264	0.264	strong		0.602	C19orf45-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347808.1	NM_198534	
LRIT1	26103	hgsc.bcm.edu	37	10	85992478	85992478	+	Silent	SNP	T	T	C	rs3814210	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:85992478T>C	ENST00000372105.3	-	4	1098	c.1077A>G	c.(1075-1077)ggA>ggG	p.G359G		NM_015613.2	NP_056428.1	Q9P2V4	LRIT1_HUMAN	leucine-rich repeat, immunoglobulin-like and transmembrane domains 1	359						integral component of endoplasmic reticulum membrane (GO:0030176)				breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(13)|skin(1)	23						CCCATAGTGCTCCTGGGCTCC	0.567													C|||	2470	0.493211	0.8669	0.4798	5008	,	,		21612	0.2589		0.3976	False		,,,				2504	0.3374				p.G359G		Atlas-SNP	.											LRIT1,NS,carcinoma,-1,1	LRIT1	73	1	0			c.A1077G						PASS	.	C		3424,982	364.4+/-316.9	1340,744,119	61.0	48.0	52.0		1077	-0.2	0.0	10	dbSNP_107	52	3352,5248	640.2+/-399.6	679,1994,1627	no	coding-synonymous	LRIT1	NM_015613.2		2019,2738,1746	CC,CT,TT		38.9767,22.2878,47.901		359/624	85992478	6776,6230	2203	4300	6503	SO:0001819	synonymous_variant	26103	exon4			TAGTGCTCCTGGG	AB031547	CCDS7373.1	10q23	2013-02-11	2007-06-19	2007-06-19	ENSG00000148602	ENSG00000148602		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	23404	protein-coding gene	gene with protein product	"""fibronectin type III, immunoglobulin and leucine rich repeat domains 9"""		"""leucine rich repeat containing 21"""	LRRC21		10777785	Standard	NM_015613		Approved	PAL, DKFZP434K091, FIGLER9	uc001kcz.1	Q9P2V4	OTTHUMG00000018632	ENST00000372105.3:c.1077A>G	10.37:g.85992478T>C		Somatic	128	1	0.0078125		WXS	Illumina HiSeq	Phase_I	77	76	0.987013	NM_015613	Q0QD41|Q9Y4N7	Silent	SNP	ENST00000372105.3	37	CCDS7373.1																																																																																			T|0.493;C|0.507	0.507	strong		0.567	LRIT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049109.1	NM_015613	
ZHX2	22882	hgsc.bcm.edu	37	8	123964431	123964431	+	Silent	SNP	G	G	A	rs3204141	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:123964431G>A	ENST00000314393.4	+	3	1516	c.681G>A	c.(679-681)tcG>tcA	p.S227S		NM_014943.3	NP_055758.1	Q9Y6X8	ZHX2_HUMAN	zinc fingers and homeoboxes 2	227	Required for homodimerization.				mRNA catabolic process (GO:0006402)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)	p.S227S(1)		breast(1)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(10)|lung(15)|ovary(1)|prostate(1)|skin(4)|stomach(3)|urinary_tract(1)	45	Lung NSC(37;2e-09)|Ovarian(258;0.0205)|Hepatocellular(40;0.105)		STAD - Stomach adenocarcinoma(47;0.00527)			AGATCCTCTCGAGACTCGGCG	0.597													G|||	1162	0.232029	0.0174	0.3256	5008	,	,		17175	0.1319		0.3549	False		,,,				2504	0.4325				p.S227S	Esophageal Squamous(94;1056 1388 11767 13799 49639)	Atlas-SNP	.											ZHX2,NS,carcinoma,0,1	ZHX2	106	1	1	Substitution - coding silent(1)	stomach(1)	c.G681A						PASS	.	G		323,4083	170.5+/-200.9	11,301,1891	112.0	120.0	117.0		681	-6.4	0.5	8	dbSNP_105	117	2984,5616	462.5+/-365.7	510,1964,1826	no	coding-synonymous	ZHX2	NM_014943.3		521,2265,3717	AA,AG,GG		34.6977,7.3309,25.4267		227/838	123964431	3307,9699	2203	4300	6503	SO:0001819	synonymous_variant	22882	exon3			CCTCTCGAGACTC	AB020661	CCDS6336.1	8q24.13	2012-03-09	2004-01-23		ENSG00000178764	ENSG00000178764		"""Zinc fingers, C2H2-type"", ""Homeoboxes / ZF class"""	18513	protein-coding gene	gene with protein product		609185	"""zinc-fingers and homeoboxes 2"""			10048485, 12741956	Standard	XM_005250837		Approved	KIAA0854	uc003ypk.1	Q9Y6X8	OTTHUMG00000165077	ENST00000314393.4:c.681G>A	8.37:g.123964431G>A		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	113	30	0.265487	NM_014943		Silent	SNP	ENST00000314393.4	37	CCDS6336.1																																																																																			G|0.767;A|0.233	0.233	strong		0.597	ZHX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381709.1	NM_014943	
CYP4F12	66002	hgsc.bcm.edu	37	19	15784386	15784386	+	Missense_Mutation	SNP	C	C	T	rs16995378	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:15784386C>T	ENST00000550308.1	+	2	427	c.47C>T	c.(46-48)aCg>aTg	p.T16M	CYP4F12_ENST00000324632.10_Missense_Mutation_p.T16M	NM_023944.3	NP_076433	Q9HCS2	CP4FC_HUMAN	cytochrome P450, family 4, subfamily F, polypeptide 12	16			T -> M (in dbSNP:rs16995378). {ECO:0000269|PubMed:11162607, ECO:0000269|PubMed:11162645, ECO:0000269|PubMed:12975309, ECO:0000269|PubMed:16303743, ECO:0000269|PubMed:17974005, ECO:0000269|Ref.7}.		arachidonic acid metabolic process (GO:0019369)|drug metabolic process (GO:0017144)|epoxygenase P450 pathway (GO:0019373)|leukotriene B4 catabolic process (GO:0036101)|long-chain fatty acid metabolic process (GO:0001676)|negative regulation of blood coagulation (GO:0030195)|oxidation-reduction process (GO:0055114)|pressure natriuresis (GO:0003095)|renal water homeostasis (GO:0003091)|small molecule metabolic process (GO:0044281)|sodium ion homeostasis (GO:0055078)|very long-chain fatty acid metabolic process (GO:0000038)|vitamin E metabolic process (GO:0042360)|vitamin K biosynthetic process (GO:0042371)|xenobiotic metabolic process (GO:0006805)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)	alkane 1-monooxygenase activity (GO:0018685)|arachidonic acid epoxygenase activity (GO:0008392)|aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|leukotriene-B4 20-monooxygenase activity (GO:0050051)|vitamin-K-epoxide reductase (warfarin-sensitive) activity (GO:0047057)			NS(1)|central_nervous_system(3)|endometrium(4)|kidney(2)|large_intestine(7)|lung(12)|ovary(3)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	41	Acute lymphoblastic leukemia(2;0.0367)				Fingolimod(DB08868)	CCGGTGGCAACGTCCCCATGG	0.652													.|||	4356	0.869808	0.7738	0.9265	5008	,	,		6229	0.998		0.8728	False		,,,				2504	0.8241				p.T16M		Atlas-SNP	.											.	CYP4F12	89	.	0			c.C47T						PASS	.	T	MET/THR	3867,533		1707,453,40	60.0	66.0	64.0		47	1.4	0.0	19	dbSNP_123	64	7999,599		3719,561,19	yes	missense	CYP4F12	NM_023944.3	81	5426,1014,59	TT,TC,CC		6.9667,12.1136,8.709	possibly-damaging	16/525	15784386	11866,1132	2200	4299	6499	SO:0001583	missense	66002	exon2			TGGCAACGTCCCC	AB035130	CCDS42517.1	19p13.1	2008-02-05	2003-01-14		ENSG00000186204	ENSG00000186204		"""Cytochrome P450s"""	18857	protein-coding gene	gene with protein product		611485	"""cytochrome P450, subfamily IVF, polypeptide 12"""			11162607	Standard	NM_023944		Approved		uc002nbl.3	Q9HCS2	OTTHUMG00000164477	ENST00000550308.1:c.47C>T	19.37:g.15784386C>T	ENSP00000448998:p.Thr16Met	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	96	96	1	NM_023944	E7ET51|O60389|Q5JPJ7|Q9HCS1	Missense_Mutation	SNP	ENST00000550308.1	37	CCDS42517.1	2036	0.9322344322344323	418	0.8495934959349594	348	0.9613259668508287	572	1.0	698	0.920844327176781	.	10.65	1.408957	0.25378	0.878864	0.930333	ENSG00000186204	ENST00000550308;ENST00000324632	D;D	0.88124	-2.34;-2.34	2.46	1.42	0.22433	.	20.022900	0.00871	U	0.002038	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	P;P	0.51057	0.607;0.941	B;B	0.40782	0.042;0.34	T	0.54091	-0.8345	9	0.51188	T	0.08	.	5.3984	0.16283	0.0:0.8373:0.0:0.1627	rs16995378;rs17857061;rs52831203;rs58245950;rs16995378	16;16	B4E2R2;Q9HCS2	.;CP4FC_HUMAN	M	16	ENSP00000448998:T16M;ENSP00000321821:T16M	ENSP00000321821:T16M	T	+	2	0	CYP4F12	15645386	0.003000	0.15002	0.016000	0.15963	0.000000	0.00434	0.418000	0.21230	0.609000	0.30018	-0.320000	0.08662	ACG	C|0.067;T|0.933	0.933	strong		0.652	CYP4F12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378938.9		
XCR1	2829	hgsc.bcm.edu	37	3	46063329	46063329	+	Silent	SNP	T	T	C	rs2230322	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:46063329T>C	ENST00000309285.3	-	2	467	c.111A>G	c.(109-111)ctA>ctG	p.L37L	XCR1_ENST00000542109.1_Silent_p.L37L	NM_001024644.1	NP_001019815.1	P46094	XCR1_HUMAN	chemokine (C motif) receptor 1	37					chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|inflammatory response (GO:0006954)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|release of sequestered calcium ion into cytosol (GO:0051209)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	chemokine receptor activity (GO:0004950)			NS(2)|endometrium(2)|kidney(2)|large_intestine(1)|lung(3)|ovary(1)|pancreas(1)|prostate(2)	14				BRCA - Breast invasive adenocarcinoma(193;0.00113)|KIRC - Kidney renal clear cell carcinoma(197;0.0172)|Kidney(197;0.0203)		CCAGGCAGTATAGGACAGTGG	0.557													C|||	1166	0.232827	0.4425	0.0908	5008	,	,		17479	0.0466		0.1243	False		,,,				2504	0.3538				p.L37L		Atlas-SNP	.											.	XCR1	51	.	0			c.A111G						PASS	.	C	,	1744,2662	648.0+/-398.6	342,1060,801	113.0	107.0	109.0		111,111	-2.5	0.8	3	dbSNP_98	109	971,7629	774.7+/-407.7	46,879,3375	no	coding-synonymous,coding-synonymous	XCR1	NM_001024644.1,NM_005283.2	,	388,1939,4176	CC,CT,TT		11.2907,39.5824,20.875	,	37/334,37/334	46063329	2715,10291	2203	4300	6503	SO:0001819	synonymous_variant	2829	exon2			GCAGTATAGGACA		CCDS2736.1	3p21.3-p21.1	2012-11-19	2006-01-13	2002-08-23	ENSG00000173578	ENSG00000173578		"""GPCR / Class A : Chemokine receptors : X-C motif"""	1625	protein-coding gene	gene with protein product		600552	"""chemokine (C motif) XC receptor 1"""	GPR5, CCXCR1		7832990, 10400311	Standard	NM_005283		Approved		uc003cpf.3	P46094	OTTHUMG00000133449	ENST00000309285.3:c.111A>G	3.37:g.46063329T>C		Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	148	61	0.412162	NM_001024644		Silent	SNP	ENST00000309285.3	37	CCDS2736.1																																																																																			T|0.794;C|0.206	0.206	strong		0.557	XCR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257322.2		
PKD1L2	114780	hgsc.bcm.edu	37	16	81242198	81242198	+	RNA	SNP	G	G	A	rs7499011	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:81242198G>A	ENST00000525539.1	-	0	657				PKD1L2_ENST00000337114.4_RNA	NM_052892.3	NP_443124.3	Q7Z442	PK1L2_HUMAN	polycystic kidney disease 1-like 2						ion transport (GO:0006811)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(20)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44						TGTAGCTCCTGGCACTGGCCT	0.552													G|||	810	0.161741	0.0923	0.2349	5008	,	,		20582	0.003		0.3837	False		,,,				2504	0.1391				p.Q220X		Atlas-SNP	.											.	PKD1L2	361	.	0			c.C658T						PASS	.	G	stop/GLN,stop/GLN	597,3607		50,497,1555	66.0	63.0	64.0		658,658	4.3	1.0	16	dbSNP_116	64	3074,5372		536,2002,1685	yes	stop-gained,stop-gained	PKD1L2	NM_001076780.1,NM_052892.3	,	586,2499,3240	AA,AG,GG		36.3959,14.2008,29.0198	,	220/992,220/2460	81242198	3671,8979	2102	4223	6325			114780	exon4			GCTCCTGGCACTG	AY164483	CCDS61998.1, CCDS61999.1	16q23.2	2014-09-11			ENSG00000166473	ENSG00000166473			21715	protein-coding gene	gene with protein product		607894				12782129	Standard	NM_052892		Approved	KIAA1879	uc002fgf.1	Q7Z442	OTTHUMG00000166126		16.37:g.81242198G>A		Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	41	41	1	NM_001076780	Q6UEE1|Q6ZN46|Q6ZSP2|Q8N1H9|Q96CL2|Q96Q08	Nonsense_Mutation	SNP	ENST00000525539.1	37		427	0.1955128205128205	39	0.07926829268292683	109	0.3011049723756906	1	0.0017482517482517483	278	0.36675461741424803	G	30	5.056326	0.93793	0.142008	0.363959	ENSG00000166473	ENST00000337114	.	.	.	4.31	4.31	0.51392	.	0.067881	0.64402	D	0.000017	.	.	.	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	.	.	.	.	0.59425	D	0.04	-12.5705	16.402	0.83643	0.0:0.0:1.0:0.0	rs7499011	.	.	.	X	220	.	ENSP00000337397:Q220X	Q	-	1	0	PKD1L2	79799699	1.000000	0.71417	1.000000	0.80357	0.521000	0.34408	7.373000	0.79623	1.957000	0.56846	0.313000	0.20887	CAG	G|0.742;A|0.258	0.258	strong		0.552	PKD1L2-001	KNOWN	non_canonical_polymorphism|basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000387972.2		
PGBD1	84547	hgsc.bcm.edu	37	6	28251890	28251890	+	Silent	SNP	C	C	T	rs527450661		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:28251890C>T	ENST00000405948.2	+	2	720	c.300C>T	c.(298-300)ctC>ctT	p.L100L	PGBD1_ENST00000259883.3_Silent_p.L100L	NM_001184743.1|NM_032507.3	NP_001171672.1|NP_115896.1	Q96JS3	PGBD1_HUMAN	piggyBac transposable element derived 1	100	SCAN box. {ECO:0000255|PROSITE- ProRule:PRU00187}.					membrane (GO:0016020)|nucleus (GO:0005634)	scavenger receptor activity (GO:0005044)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|kidney(2)|large_intestine(7)|lung(16)|ovary(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)	41						CCAAGGAGCTCCAGCCCTGTG	0.532													C|||	1	0.000199681	0.0	0.0	5008	,	,		18052	0.001		0.0	False		,,,				2504	0.0				p.L100L		Atlas-SNP	.											.	PGBD1	106	.	0			c.C300T						PASS	.						101.0	93.0	95.0					6																	28251890		2203	4300	6503	SO:0001819	synonymous_variant	84547	exon2			GGAGCTCCAGCCC	D88259	CCDS4648.1	6p22.1	2013-01-09			ENSG00000137338	ENSG00000137338		"""-"""	19398	protein-coding gene	gene with protein product							Standard	NM_001184743		Approved	HUCEP-4, dJ874C20.4, SCAND4	uc003nkz.3	Q96JS3	OTTHUMG00000014520	ENST00000405948.2:c.300C>T	6.37:g.28251890C>T		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	88	4	0.0454545	NM_001184743	Q53F43|Q6NTF5|Q8WWS4	Silent	SNP	ENST00000405948.2	37	CCDS4648.1																																																																																			.	.	none		0.532	PGBD1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040188.2		
PPP1R3C	5507	hgsc.bcm.edu	37	10	93390158	93390158	+	Silent	SNP	C	C	T	rs35530640	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	70	0	0		WXS	Illumina HiSeq	Phase_I	52	30	0.576923	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	
ZCCHC16	340595	hgsc.bcm.edu	37	X	111698613	111698613	+	Silent	SNP	T	T	C	rs7053563	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:111698613T>C	ENST00000340433.2	+	1	887	c.657T>C	c.(655-657)caT>caC	p.H219H		NM_001004308.2	NP_001004308.2	Q6ZR62	ZCH16_HUMAN	zinc finger, CCHC domain containing 16	219							nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(16)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	27						ACAAGAAACATAGTGACAGGC	0.507													T|||	1275	0.337748	0.3797	0.2205	3775	,	,		15140	0.2619		0.159	False		,,,				2504	0.2004				p.H219H		Atlas-SNP	.											.	ZCCHC16	66	.	0			c.T657C						PASS	.	T		1659,2176		293,821,252,518,319	161.0	140.0	147.0		657	-4.2	0.0	X	dbSNP_116	147	1354,5374		103,776,372,1549,1500	no	coding-synonymous	ZCCHC16	NM_001004308.2		396,1597,624,2067,1819	CC,CT,C,TT,T		20.1249,43.2595,28.5241		219/311	111698613	3013,7550	2203	4300	6503	SO:0001819	synonymous_variant	340595	exon3			GAAACATAGTGAC	AK128465	CCDS35369.1	Xq23	2008-05-02			ENSG00000187823	ENSG00000187823		"""Zinc fingers, CCHC domain containing"""	25214	protein-coding gene	gene with protein product						15716091, 16093683	Standard	NM_001004308		Approved	Mart4, Mar4, FLJ46608	uc004epo.1	Q6ZR62	OTTHUMG00000159706	ENST00000340433.2:c.657T>C	X.37:g.111698613T>C		Somatic	121	1	0.00826446		WXS	Illumina HiSeq	Phase_I	95	95	1	NM_001004308	B2RPG1	Silent	SNP	ENST00000340433.2	37	CCDS35369.1																																																																																			T|0.694;C|0.306	0.306	strong		0.507	ZCCHC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356964.1	NM_001004308	
ABCA12	26154	hgsc.bcm.edu	37	2	215910724	215910724	+	Missense_Mutation	SNP	T	T	G	rs11890512	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:215910724T>G	ENST00000272895.7	-	7	928	c.709A>C	c.(709-711)Aac>Cac	p.N237H		NM_173076.2	NP_775099.2	Q86UK0	ABCAC_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 12	237			N -> H (in dbSNP:rs11890512).		cellular homeostasis (GO:0019725)|ceramide transport (GO:0035627)|establishment of skin barrier (GO:0061436)|keratinization (GO:0031424)|lipid homeostasis (GO:0055088)|lipid transport (GO:0006869)|lung alveolus development (GO:0048286)|phospholipid efflux (GO:0033700)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of protein localization to cell surface (GO:2000010)|protein localization to plasma membrane (GO:0072659)|regulated secretory pathway (GO:0045055)|secretion by cell (GO:0032940)|surfactant homeostasis (GO:0043129)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|epidermal lamellar body (GO:0097209)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)	apolipoprotein A-I receptor binding (GO:0034191)|ATP binding (GO:0005524)|lipid transporter activity (GO:0005319)|lipid-transporting ATPase activity (GO:0034040)|receptor binding (GO:0005102)			NS(3)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(45)|lung(44)|ovary(8)|pancreas(2)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	139		Renal(323;0.127)		Epithelial(149;1.01e-05)|all cancers(144;0.00112)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.011)		TTCTGATTGTTGGGGTCACTG	0.368													T|||	827	0.165136	0.5643	0.0591	5008	,	,		17235	0.0		0.0119	False		,,,				2504	0.0286				p.N237H	Ovarian(66;664 1488 5121 34295)	Atlas-SNP	.											ABCA12,NS,carcinoma,+1,1	ABCA12	368	1	0			c.A709C						PASS	.	T	HIS/ASN	1975,2431	533.1+/-373.6	454,1067,682	78.0	83.0	81.0		709	0.0	0.8	2	dbSNP_120	81	108,8492	53.1+/-113.8	0,108,4192	yes	missense	ABCA12	NM_173076.2	68	454,1175,4874	GG,GT,TT		1.2558,44.8252,16.0157	benign	237/2596	215910724	2083,10923	2203	4300	6503	SO:0001583	missense	26154	exon7			GATTGTTGGGGTC	AF418105	CCDS33372.1, CCDS33373.1	2q34	2012-03-14			ENSG00000144452	ENSG00000144452		"""ATP binding cassette transporters / subfamily A"""	14637	protein-coding gene	gene with protein product		607800	"""ichthyosis congenita II, lamellar ichthyosis B"""	ICR2B		11435397, 12915478, 8845852, 10094194	Standard	NM_015657		Approved	DKFZP434G232, LI2	uc002vew.3	Q86UK0	OTTHUMG00000154801	ENST00000272895.7:c.709A>C	2.37:g.215910724T>G	ENSP00000272895:p.Asn237His	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	114	53	0.464912	NM_173076	Q53QE2|Q53S55|Q8IZW6|Q96JT3|Q9Y4M5	Missense_Mutation	SNP	ENST00000272895.7	37	CCDS33372.1	283	0.1295787545787546	250	0.508130081300813	23	0.06353591160220995	0	0.0	10	0.013192612137203167	T	11.33	1.605673	0.28623	0.448252	0.012558	ENSG00000144452	ENST00000272895	D	0.88509	-2.39	5.62	0.0384	0.14200	.	0.631054	0.16196	N	0.225171	T	0.00012	0.0000	N	0.19112	0.55	0.09310	P	0.99999999354271	B	0.33448	0.412	B	0.27262	0.078	T	0.33523	-0.9865	9	0.62326	D	0.03	.	5.1475	0.14993	0.0:0.1568:0.2866:0.5566	rs11890512;rs52807481;rs59636117;rs11890512	237	Q86UK0	ABCAC_HUMAN	H	237	ENSP00000272895:N237H	ENSP00000272895:N237H	N	-	1	0	ABCA12	215618969	0.959000	0.32827	0.827000	0.32855	0.765000	0.43378	0.440000	0.21592	-0.129000	0.11620	-1.643000	0.00768	AAC	T|0.845;G|0.155	0.155	strong		0.368	ABCA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337111.1	NM_173076	
EIF4A1	1973	hgsc.bcm.edu	37	17	7478498	7478498	+	Silent	SNP	G	G	A	rs7358	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:7478498G>A	ENST00000293831.8	+	4	283	c.267G>A	c.(265-267)tcG>tcA	p.S89S	SENP3-EIF4A1_ENST00000579777.1_RNA|SNORA67_ENST00000384423.1_RNA|EIF4A1_ENST00000582746.1_Silent_p.S89S|EIF4A1_ENST00000380512.5_Silent_p.S73S|EIF4A1_ENST00000577269.1_Silent_p.S89S|SNORD10_ENST00000459579.1_RNA|SNORA48_ENST00000386847.1_RNA	NM_001416.3	NP_001407.1	P60842	IF4A1_HUMAN	eukaryotic translation initiation factor 4A1	89	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				cellular protein metabolic process (GO:0044267)|cytokine-mediated signaling pathway (GO:0019221)|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)|organ regeneration (GO:0031100)|RNA metabolic process (GO:0016070)|translation (GO:0006412)|translational initiation (GO:0006413)|viral process (GO:0016032)	cytosol (GO:0005829)|eukaryotic translation initiation factor 4F complex (GO:0016281)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|double-stranded RNA binding (GO:0003725)|helicase activity (GO:0004386)|mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|RNA cap binding (GO:0000339)|translation factor activity, nucleic acid binding (GO:0008135)|translation initiation factor activity (GO:0003743)			NS(1)|breast(2)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|lung(8)|ovary(2)|prostate(2)|upper_aerodigestive_tract(2)	22						TTGCCATATCGATTCTGCAGC	0.453													G|||	685	0.136781	0.171	0.0576	5008	,	,		22062	0.0913		0.1362	False		,,,				2504	0.1943				p.S89S	Melanoma(120;278 1668 15796 27423 46368)	Atlas-SNP	.											.	EIF4A1	38	.	0			c.G267A						PASS	.	G	,	754,3652	308.8+/-290.8	61,632,1510	110.0	107.0	108.0		267,267	-10.8	0.6	17	dbSNP_131	108	1139,7461	235.8+/-268.3	60,1019,3221	no	coding-synonymous,coding-synonymous	EIF4A1	NM_001204510.1,NM_001416.3	,	121,1651,4731	AA,AG,GG		13.2442,17.113,14.5548	,	89/348,89/407	7478498	1893,11113	2203	4300	6503	SO:0001819	synonymous_variant	1973	exon4			CATATCGATTCTG	D13748	CCDS11113.1, CCDS58511.1	17p13	2012-02-23	2010-02-10		ENSG00000161960	ENSG00000161960		"""DEAD-boxes"""	3282	protein-coding gene	gene with protein product		602641	"""eukaryotic translation initiation factor 4A, isoform 1"""	EIF4A		8493113, 9790779	Standard	NM_001416		Approved	DDX2A, EIF-4A		P60842	OTTHUMG00000108149	ENST00000293831.8:c.267G>A	17.37:g.7478498G>A		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	77	43	0.558442	NM_001416	B2R6L8|D3DTP9|J3QLC4|P04765|Q5U018|Q61516	Silent	SNP	ENST00000293831.8	37	CCDS11113.1																																																																																			G|0.856;A|0.144	0.144	strong		0.453	EIF4A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226952.6	NM_001416	
SLC1A1	6505	hgsc.bcm.edu	37	9	4576680	4576680	+	Silent	SNP	T	T	C	rs301430	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	224	0	0		WXS	Illumina HiSeq	Phase_I	234	81	0.346154	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		
TEP1	7011	hgsc.bcm.edu	37	14	20847202	20847202	+	Silent	SNP	A	A	G	rs938887	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:20847202A>G	ENST00000262715.5	-	36	5230	c.5190T>C	c.(5188-5190)gaT>gaC	p.D1730D	TEP1_ENST00000545983.1_Silent_p.D68D|TEP1_ENST00000556935.1_Silent_p.D1622D	NM_007110.4	NP_009041.2	Q99973	TEP1_HUMAN	telomerase-associated protein 1	1730					RNA-dependent DNA replication (GO:0006278)|telomere maintenance via recombination (GO:0000722)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|nuclear matrix (GO:0016363)|ribonucleoprotein complex (GO:0030529)|telomerase holoenzyme complex (GO:0005697)	ATP binding (GO:0005524)|RNA binding (GO:0003723)			NS(4)|breast(1)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(48)|ovary(7)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	96	all_cancers(95;0.00123)	all_lung(585;0.235)	Epithelial(56;7.42e-08)|all cancers(55;6.46e-07)	GBM - Glioblastoma multiforme(265;0.028)|READ - Rectum adenocarcinoma(17;0.233)		GAAAGAGTGTATCATCGGAGA	0.567													A|||	1528	0.305112	0.4531	0.3559	5008	,	,		20391	0.2718		0.2058	False		,,,				2504	0.2055				p.D1730D		Atlas-SNP	.											.	TEP1	224	.	0			c.T5190C						PASS	.	A		1861,2545	539.6+/-375.3	389,1083,731	108.0	101.0	103.0		5190	-11.9	0.0	14	dbSNP_86	103	1688,6912	310.0+/-309.6	162,1364,2774	no	coding-synonymous	TEP1	NM_007110.4		551,2447,3505	GG,GA,AA		19.6279,42.2379,27.2874		1730/2628	20847202	3549,9457	2203	4300	6503	SO:0001819	synonymous_variant	7011	exon36			GAGTGTATCATCG		CCDS9548.1	14q11.2	2013-01-10			ENSG00000129566	ENSG00000129566		"""WD repeat domain containing"""	11726	protein-coding gene	gene with protein product	"""TROVE domain family, member 1"""	601686				9403057	Standard	NM_007110		Approved	TP1, TLP1, VAULT2, p240, TROVE1	uc001vxe.3	Q99973	OTTHUMG00000029515	ENST00000262715.5:c.5190T>C	14.37:g.20847202A>G		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	120	65	0.541667	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	
CELSR2	1952	hgsc.bcm.edu	37	1	109807099	109807099	+	Silent	SNP	G	G	A	rs6689614	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:109807099G>A	ENST00000271332.3	+	11	5374	c.5313G>A	c.(5311-5313)ccG>ccA	p.P1771P		NM_001408.2	NP_001399.1	Q9HCU4	CELR2_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 2	1771	Laminin G-like 2. {ECO:0000255|PROSITE- ProRule:PRU00122}.				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)		GCGATACGCCGGAGGGGGTTA	0.652													A|||	1768	0.353035	0.0764	0.4654	5008	,	,		14927	0.497		0.4751	False		,,,				2504	0.3732				p.P1771P	NSCLC(158;1285 2011 34800 34852 42084)	Atlas-SNP	.											CELSR2,NS,adenoma,0,1	CELSR2	228	1	0			c.G5313A						PASS	.	A		582,3824	772.6+/-413.9	35,512,1656	115.0	101.0	105.0		5313	-10.0	0.0	1	dbSNP_116	105	4005,4595	598.8+/-394.0	929,2147,1224	no	coding-synonymous	CELSR2	NM_001408.2		964,2659,2880	AA,AG,GG		46.5698,13.2093,35.2683		1771/2924	109807099	4587,8419	2203	4300	6503	SO:0001819	synonymous_variant	1952	exon11			TACGCCGGAGGGG	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.5313G>A	1.37:g.109807099G>A		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	59	59	1	NM_001408	Q5T2Y7|Q92566	Silent	SNP	ENST00000271332.3	37	CCDS796.1																																																																																			G|0.632;A|0.368	0.368	strong		0.652	CELSR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033200.1	NM_001408	
SPICE1	152185	hgsc.bcm.edu	37	3	113176122	113176122	+	Silent	SNP	G	G	A	rs7637618	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:113176122G>A	ENST00000295872.4	-	13	1777	c.1518C>T	c.(1516-1518)ccC>ccT	p.P506P		NM_144718.3	NP_653319.1	Q8N0Z3	SPICE_HUMAN	spindle and centriole associated protein 1	506					metaphase plate congression (GO:0051310)|regulation of centriole replication (GO:0046599)|spindle assembly involved in mitosis (GO:0090307)	centriole (GO:0005814)|centrosome (GO:0005813)|spindle (GO:0005819)				NS(1)|autonomic_ganglia(1)|breast(4)|endometrium(3)|large_intestine(9)|lung(10)|ovary(2)|skin(2)|urinary_tract(1)	33						ACAGTTTAACGGGCAACTCTT	0.468													A|||	1642	0.327875	0.5772	0.1758	5008	,	,		17892	0.2996		0.2455	False		,,,				2504	0.2127				p.P506P		Atlas-SNP	.											.	SPICE1	130	.	0			c.C1518T						PASS	.	A		2340,2066	569.8+/-382.7	626,1088,489	104.0	102.0	103.0		1518	2.0	1.0	3	dbSNP_116	103	2164,6436	713.1+/-405.9	270,1624,2406	no	coding-synonymous	SPICE1	NM_144718.3		896,2712,2895	AA,AG,GG		25.1628,46.8906,34.6302		506/856	113176122	4504,8502	2203	4300	6503	SO:0001819	synonymous_variant	152185	exon13			TTTAACGGGCAAC	AY099107	CCDS2973.1	3q13.2	2010-09-01	2010-09-01	2010-09-01	ENSG00000163611	ENSG00000163611			25083	protein-coding gene	gene with protein product	"""spindle and centriole protein"""	613447	"""coiled-coil domain containing 52"""	CCDC52		20736305	Standard	NM_144718		Approved	SPICE	uc003eag.4	Q8N0Z3	OTTHUMG00000159261	ENST00000295872.4:c.1518C>T	3.37:g.113176122G>A		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	75	45	0.6	NM_144718	D3DN72|Q8WUX6	Silent	SNP	ENST00000295872.4	37	CCDS2973.1																																																																																			G|0.662;A|0.338	0.338	strong		0.468	SPICE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354177.2	NM_144718	
MCPH1	79648	hgsc.bcm.edu	37	8	6302154	6302154	+	Missense_Mutation	SNP	G	G	T	rs2083914	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:6302154G>T	ENST00000344683.5	+	8	987	c.911G>T	c.(910-912)aGa>aTa	p.R304I	MCPH1_ENST00000519480.1_Missense_Mutation_p.R304I|MCPH1_ENST00000522905.1_Missense_Mutation_p.R256I	NM_024596.3	NP_078872	Q8NEM0	MCPH1_HUMAN	microcephalin 1	304			R -> I (in dbSNP:rs2083914).		cerebral cortex development (GO:0021987)|mitotic cell cycle (GO:0000278)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleoplasm (GO:0005654)	identical protein binding (GO:0042802)		AGPAT5/MCPH1(2)	central_nervous_system(1)|large_intestine(4)|skin(1)	6		Hepatocellular(245;0.0663)		Colorectal(4;0.0505)		AACTTGCAAAGAAATATTGCA	0.383													G|||	352	0.0702875	0.0295	0.0908	5008	,	,		20069	0.0298		0.159	False		,,,				2504	0.0613				p.R304I	Colon(95;1448 1467 8277 34473 35819)	Atlas-SNP	.											.	MCPH1	65	.	0			c.G911T						PASS	.	G	ILE/ARG,ILE/ARG,ILE/ARG	147,3555		4,139,1708	50.0	46.0	47.0		911,767,911	-2.2	0.0	8	dbSNP_96	47	1256,6914		78,1100,2907	yes	missense,missense,missense	MCPH1	NM_001172574.1,NM_001172575.1,NM_024596.3	97,97,97	82,1239,4615	TT,TG,GG		15.3733,3.9708,11.8177	probably-damaging,probably-damaging,probably-damaging	304/611,256/563,304/836	6302154	1403,10469	1851	4085	5936	SO:0001583	missense	79648	exon8			TGCAAAGAAATAT	AK022909	CCDS43689.1, CCDS55190.1, CCDS55191.1	8p23.1	2012-11-26	2007-11-26		ENSG00000147316	ENSG00000147316			6954	protein-coding gene	gene with protein product	"""BRCT-repeat inhibitor of TERT expression 1"""	607117	"""microcephaly, primary autosomal recessive 1"""			9683597, 17925396	Standard	NM_024596		Approved	FLJ12847, BRIT1	uc003wqi.3	Q8NEM0	OTTHUMG00000163618	ENST00000344683.5:c.911G>T	8.37:g.6302154G>T	ENSP00000342924:p.Arg304Ile	Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	101	26	0.257426	NM_001172574	B4DWW2|E9PGU5|E9PH63|Q66GU1|Q9H9C7	Missense_Mutation	SNP	ENST00000344683.5	37	CCDS43689.1	179	0.08195970695970696	14	0.028455284552845527	35	0.09668508287292818	18	0.03146853146853147	112	0.14775725593667546	G	17.30	3.353605	0.61293	0.039708	0.153733	ENSG00000147316	ENST00000344683;ENST00000519480;ENST00000522905	T;T;T	0.13089	2.62;2.62;2.62	5.5	-2.24	0.06909	.	1.067020	0.07171	N	0.852328	T	0.00144	0.0004	M	0.69823	2.125	0.80722	P	0.0	D;D;D	0.67145	0.996;0.986;0.991	P;D;P	0.64321	0.852;0.924;0.793	T	0.12293	-1.0553	9	0.72032	D	0.01	-0.03	5.7841	0.18322	0.545:0.1472:0.3078:0.0	rs2083914;rs52808508;rs2083914	256;304;304	E9PH63;Q8NEM0;E9PGU5	.;MCPH1_HUMAN;.	I	304;304;256	ENSP00000342924:R304I;ENSP00000430962:R304I;ENSP00000430768:R256I	ENSP00000342924:R304I	R	+	2	0	MCPH1	6289562	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.590000	0.05760	-0.261000	0.09405	0.655000	0.94253	AGA	G|0.900;T|0.100	0.100	strong		0.383	MCPH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374532.2	NM_024596	
ZC2HC1A	51101	hgsc.bcm.edu	37	8	79609647	79609647	+	Silent	SNP	G	G	A	rs35904168	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:79609647G>A	ENST00000263849.4	+	6	612	c.510G>A	c.(508-510)aaG>aaA	p.K170K	ZC2HC1A_ENST00000521176.1_3'UTR	NM_016010.2	NP_057094.2	Q96GY0	ZC21A_HUMAN	zinc finger, C2HC-type containing 1A	170							metal ion binding (GO:0046872)										TTTAGTATAAGCCACCCGCAC	0.363													G|||	153	0.0305511	0.0242	0.0389	5008	,	,		15369	0.0		0.0736	False		,,,				2504	0.0204				p.K170K		Atlas-SNP	.											.	.	.	.	0			c.G510A						PASS	.	G		128,4278	93.0+/-131.7	2,124,2077	57.0	58.0	58.0		510	-0.5	0.8	8	dbSNP_126	58	578,8022	155.4+/-209.4	23,532,3745	no	coding-synonymous	FAM164A	NM_016010.2		25,656,5822	AA,AG,GG		6.7209,2.9051,5.4283		170/326	79609647	706,12300	2203	4300	6503	SO:0001819	synonymous_variant	51101	exon6			GTATAAGCCACCC		CCDS6223.1	8q21.11	2013-01-10	2012-02-03	2012-02-03	ENSG00000104427	ENSG00000104427		"""Zinc fingers, C2HC-type containing"""	24277	protein-coding gene	gene with protein product			"""chromosome 8 open reading frame 70"", ""family with sequence similarity 164, member A"""	C8orf70, FAM164A		10810093	Standard	NM_016010		Approved	CGI-62	uc003ybd.3	Q96GY0	OTTHUMG00000164619	ENST00000263849.4:c.510G>A	8.37:g.79609647G>A		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	54	14	0.259259	NM_016010	Q9Y372	Silent	SNP	ENST00000263849.4	37	CCDS6223.1	89	0.04075091575091575	17	0.034552845528455285	12	0.03314917127071823	0	0.0	60	0.079155672823219	G	2.794	-0.250565	0.05867	0.029051	0.067209	ENSG00000104427	ENST00000519307	.	.	.	5.48	-0.47	0.12131	.	.	.	.	.	T	0.04407	0.0121	.	.	.	0.09310	P	0.9999999999993069	.	.	.	.	.	.	T	0.39663	-0.9603	3	.	.	.	-15.1026	11.4129	0.49935	0.4266:0.0:0.5734:0.0	rs35904168;rs62518983	.	.	.	T	3	.	.	A	+	1	0	FAM164A	79772202	1.000000	0.71417	0.804000	0.32291	0.364000	0.29643	0.417000	0.21214	-0.318000	0.08665	-0.732000	0.03574	GCC	G|0.946;A|0.054	0.054	strong		0.363	ZC2HC1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379423.2	NM_016010	
LRRIQ1	84125	hgsc.bcm.edu	37	12	85466723	85466723	+	Missense_Mutation	SNP	G	G	A	rs17012533	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:85466723G>A	ENST00000393217.2	+	11	2795	c.2734G>A	c.(2734-2736)Gca>Aca	p.A912T		NM_001079910.1	NP_001073379.1	Q96JM4	LRIQ1_HUMAN	leucine-rich repeats and IQ motif containing 1	912			A -> T (in dbSNP:rs17012533). {ECO:0000269|PubMed:11347906}.					p.A912T(1)		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)		TGTTGACAATGCAGGGTTCTG	0.403													A|||	1036	0.206869	0.0446	0.3127	5008	,	,		14597	0.2222		0.2604	False		,,,				2504	0.2802				p.A912T		Atlas-SNP	.											LRRIQ1_ENST00000393217,NS,carcinoma,-1,3	LRRIQ1	512	3	1	Substitution - Missense(1)	stomach(1)	c.G2734A						PASS	.	A	THR/ALA	348,4058	793.9+/-415.2	16,316,1871	85.0	73.0	77.0		2734	1.2	0.0	12	dbSNP_123	77	2369,6231	701.4+/-405.2	331,1707,2262	yes	missense	LRRIQ1	NM_001079910.1	58	347,2023,4133	AA,AG,GG		27.5465,7.8983,20.8904	benign	912/1723	85466723	2717,10289	2203	4300	6503	SO:0001583	missense	84125	exon11			GACAATGCAGGGT	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.2734G>A	12.37:g.85466723G>A	ENSP00000376910:p.Ala912Thr	Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	145	73	0.503448	NM_001079910	Q567P4|Q9BS17|Q9HA36	Missense_Mutation	SNP	ENST00000393217.2	37	CCDS41816.1	462	0.21153846153846154	23	0.046747967479674794	111	0.30662983425414364	128	0.22377622377622378	200	0.2638522427440633	A	0.172	-1.070835	0.01918	0.078983	0.275465	ENSG00000133640	ENST00000256007;ENST00000378580;ENST00000393217	T	0.51325	0.71	2.43	1.19	0.21007	.	2.602770	0.02040	N	0.049237	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	0.25710	-1.0124	9	0.15952	T	0.53	.	2.0682	0.03607	0.5653:0.0:0.161:0.2737	rs17012533;rs52795685;rs17012533	912;887	Q96JM4;C9JI57	LRIQ1_HUMAN;.	T	912;887;912	ENSP00000376910:A912T	ENSP00000256007:A912T	A	+	1	0	LRRIQ1	83990854	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.035000	0.13797	-0.038000	0.13624	-0.550000	0.04213	GCA	G|0.793;A|0.207	0.207	strong		0.403	LRRIQ1-004	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388249.2	NM_032165	
NEU2	4759	hgsc.bcm.edu	37	2	233899126	233899126	+	Missense_Mutation	SNP	C	C	A	rs2233391	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:233899126C>A	ENST00000233840.3	+	2	502	c.502C>A	c.(502-504)Cac>Aac	p.H168N		NM_005383.2	NP_005374.2	Q9Y3R4	NEUR2_HUMAN	sialidase 2 (cytosolic sialidase)	168			H -> N (in dbSNP:rs2233391). {ECO:0000269|PubMed:10191093, ECO:0000269|PubMed:15489334}.		ganglioside catabolic process (GO:0006689)|glycosphingolipid metabolic process (GO:0006687)|oligosaccharide catabolic process (GO:0009313)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	exo-alpha-(2->3)-sialidase activity (GO:0052794)|exo-alpha-(2->6)-sialidase activity (GO:0052795)|exo-alpha-(2->8)-sialidase activity (GO:0052796)			endometrium(3)|large_intestine(2)|lung(10)|skin(2)|urinary_tract(1)	18		Breast(86;0.00279)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0271)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0839)		Epithelial(121;7.17e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000311)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.00942)|GBM - Glioblastoma multiforme(43;0.0488)	Oseltamivir(DB00198)|Zanamivir(DB00558)	TTTGCAGCTTCACGACAGGGC	0.647													C|||	1162	0.232029	0.1626	0.3026	5008	,	,		16182	0.0298		0.502	False		,,,				2504	0.2065				p.H168N		Atlas-SNP	.											.	NEU2	42	.	0			c.C502A						PASS	.	C	ASN/HIS	941,3465	354.1+/-312.5	111,719,1373	53.0	57.0	56.0		502	0.7	0.0	2	dbSNP_98	56	4110,4490	560.1+/-387.5	960,2190,1150	yes	missense	NEU2	NM_005383.2	68	1071,2909,2523	AA,AC,CC		47.7907,21.3572,38.8359	benign	168/381	233899126	5051,7955	2203	4300	6503	SO:0001583	missense	4759	exon2			CAGCTTCACGACA	Y16535	CCDS2501.1	2q37	2008-05-27			ENSG00000115488	ENSG00000115488			7759	protein-coding gene	gene with protein product	"""N-acetyl-alpha-neuraminidase 2"""	605528				10191093, 14613940	Standard	NM_005383		Approved	SIAL2	uc010zmn.2	Q9Y3R4	OTTHUMG00000133274	ENST00000233840.3:c.502C>A	2.37:g.233899126C>A	ENSP00000233840:p.His168Asn	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	77	77	1	NM_005383	Q3KNW4|Q6NTB4	Missense_Mutation	SNP	ENST00000233840.3	37	CCDS2501.1	605	0.27701465201465203	79	0.16056910569105692	128	0.35359116022099446	10	0.017482517482517484	388	0.5118733509234829	C	4.530	0.098352	0.08681	0.213572	0.477907	ENSG00000115488	ENST00000233840	D	0.87334	-2.24	4.88	0.688	0.18027	Neuraminidase (2);	1.629240	0.03019	N	0.150453	T	0.00012	0.0000	M	0.62723	1.935	0.80722	P	0.0	B	0.19583	0.037	B	0.29440	0.102	T	0.26018	-1.0115	9	0.42905	T	0.14	-4.7507	4.0599	0.09834	0.3565:0.3407:0.2323:0.0705	rs2233391;rs57824073;rs2233391	168	Q9Y3R4	NEUR2_HUMAN	N	168	ENSP00000233840:H168N	ENSP00000233840:H168N	H	+	1	0	NEU2	233607370	0.001000	0.12720	0.014000	0.15608	0.019000	0.09904	0.044000	0.13992	0.097000	0.17492	0.561000	0.74099	CAC	C|0.668;A|0.332	0.332	strong		0.647	NEU2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257053.2	NM_005383	
ANO2	57101	hgsc.bcm.edu	37	12	5674754	5674754	+	Silent	SNP	G	G	A	rs2277398	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:5674754G>A	ENST00000356134.5	-	26	2771	c.2700C>T	c.(2698-2700)tcC>tcT	p.S900S	ANO2_ENST00000546188.1_Silent_p.S900S|ANO2_ENST00000327087.8_Silent_p.S899S	NM_001278596.1	NP_001265525.1	Q9NQ90	ANO2_HUMAN	anoctamin 2, calcium activated chloride channel	904					chloride transmembrane transport (GO:1902476)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	chloride channel complex (GO:0034707)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	intracellular calcium activated chloride channel activity (GO:0005229)			central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(11)|lung(23)|ovary(4)|pancreas(1)|prostate(1)|skin(5)|stomach(3)|upper_aerodigestive_tract(1)	58						CCAGACGGGCGGACAGAATAA	0.502													g|||	1714	0.342252	0.211	0.3646	5008	,	,		18034	0.3284		0.4553	False		,,,				2504	0.4018				p.S899S		Atlas-SNP	.											.	ANO2	309	.	0			c.C2697T						PASS	.	A		894,2850		123,648,1101	43.0	42.0	42.0		2697	-0.5	1.0	12	dbSNP_100	42	3835,4387		877,2081,1153	no	coding-synonymous	ANO2	NM_020373.2		1000,2729,2254	AA,AG,GG		46.6432,23.8782,39.5203		899/999	5674754	4729,7237	1872	4111	5983	SO:0001819	synonymous_variant	57101	exon25			ACGGGCGGACAGA	AJ272204	CCDS44807.1, CCDS44807.2	12p13.3	2014-04-09	2014-04-09	2008-08-28		ENSG00000047617		"""Ion channels / Chloride channels : Calcium activated : Anoctamins"""	1183	protein-coding gene	gene with protein product	"""transmembrane protein 16B (eight membrane-spanning domains)"""	610109	"""chromosome 12 open reading frame 3"", ""transmembrane protein 16B"", ""anoctamin 2"""	C12orf3, TMEM16B		12739008, 15067359, 24692353	Standard	NM_001278596		Approved		uc001qnm.2	Q9NQ90		ENST00000356134.5:c.2700C>T	12.37:g.5674754G>A		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	62	62	1	NM_020373	C4N787|Q9H847	Silent	SNP	ENST00000356134.5	37																																																																																				G|0.645;A|0.355	0.355	strong		0.502	ANO2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000399019.4	NM_020373	
TTC27	55622	hgsc.bcm.edu	37	2	32983526	32983526	+	Silent	SNP	C	C	T	rs2273665	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:32983526C>T	ENST00000317907.4	+	13	1851	c.1620C>T	c.(1618-1620)aaC>aaT	p.N540N		NM_001193509.1|NM_017735.4	NP_001180438.1|NP_060205.3	Q6P3X3	TTC27_HUMAN	tetratricopeptide repeat domain 27	540								p.N540N(1)		breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(9)|lung(14)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	38						ATCTTCGGAACAAGGAGTTTC	0.527													C|||	1467	0.292931	0.1536	0.3718	5008	,	,		17491	0.3671		0.4125	False		,,,				2504	0.226				p.N540N		Atlas-SNP	.											TTC27,NS,carcinoma,0,1	TTC27	71	1	1	Substitution - coding silent(1)	stomach(1)	c.C1620T						PASS	.	C	,	923,3483	351.3+/-311.2	88,747,1368	100.0	92.0	94.0		1470,1620	5.9	0.7	2	dbSNP_100	94	3528,5072	514.7+/-378.4	732,2064,1504	no	coding-synonymous,coding-synonymous	TTC27	NM_001193509.1,NM_017735.4	,	820,2811,2872	TT,TC,CC		41.0233,20.9487,34.2227	,	490/794,540/844	32983526	4451,8555	2203	4300	6503	SO:0001819	synonymous_variant	55622	exon13			TCGGAACAAGGAG	BC063791, AK000279	CCDS33176.1	2p22.3	2013-01-10			ENSG00000018699	ENSG00000018699		"""Tetratricopeptide (TTC) repeat domain containing"""	25986	protein-coding gene	gene with protein product							Standard	NM_001193509		Approved	FLJ20272	uc002rom.3	Q6P3X3	OTTHUMG00000152134	ENST00000317907.4:c.1620C>T	2.37:g.32983526C>T		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	109	45	0.412844	NM_017735	A6NKJ0|Q96SS5|Q9BVF1|Q9NWR4|Q9NXG4	Silent	SNP	ENST00000317907.4	37	CCDS33176.1																																																																																			C|0.676;N|0.000	.	strong		0.527	TTC27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325395.1	NM_017735	
FAM120B	84498	hgsc.bcm.edu	37	6	170627266	170627266	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:170627266T>C	ENST00000476287.1	+	2	896	c.788T>C	c.(787-789)aTc>aCc	p.I263T	FAM120B_ENST00000537664.1_Missense_Mutation_p.I286T|FAM120B_ENST00000540480.1_Missense_Mutation_p.I275T|FAM120B_ENST00000252510.9_Intron	NM_032448.1	NP_115824.1	Q96EK7	F120B_HUMAN	family with sequence similarity 120B	263					cell differentiation (GO:0030154)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(11)|liver(1)|lung(15)|ovary(1)|prostate(2)|skin(2)	44		Breast(66;0.000338)|Esophageal squamous(34;0.241)		OV - Ovarian serous cystadenocarcinoma(33;3.94e-22)|BRCA - Breast invasive adenocarcinoma(81;6.47e-06)|GBM - Glioblastoma multiforme(31;0.0899)		AAAGGTAACATCATATTAGCT	0.373																																					p.I263T		Atlas-SNP	.											.	FAM120B	108	.	0			c.T788C						PASS	.						76.0	82.0	80.0					6																	170627266		2203	4300	6503	SO:0001583	missense	84498	exon2			GTAACATCATATT	AB058741	CCDS5314.1, CCDS75555.1	6q27	2011-04-13	2006-07-04	2006-07-04	ENSG00000112584	ENSG00000112584			21109	protein-coding gene	gene with protein product	"""PPARgamma constitutive coactivator 1"", ""constitutive coactivator of PPAR-gamma"""	612266	"""KIAA1838"""	KIAA1838		14585507	Standard	NM_032448		Approved	PGCC1, CCPG	uc003qxp.3	Q96EK7	OTTHUMG00000016080	ENST00000476287.1:c.788T>C	6.37:g.170627266T>C	ENSP00000417970:p.Ile263Thr	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	39	15	0.384615	NM_032448	B4DL34|Q86V68|Q96JI9	Missense_Mutation	SNP	ENST00000476287.1	37	CCDS5314.1	.	.	.	.	.	.	.	.	.	.	t	4.546	0.101307	0.08731	.	.	ENSG00000112584	ENST00000540480;ENST00000537664;ENST00000476287	T;T;T	0.08896	3.05;3.04;3.05	5.36	1.33	0.21861	.	1.307360	0.04590	N	0.396515	T	0.02610	0.0079	L	0.41236	1.265	0.09310	N	0.999999	B;B	0.06786	0.0;0.001	B;B	0.06405	0.001;0.002	T	0.44967	-0.9293	10	0.28530	T	0.3	-0.9253	9.4172	0.38528	0.0:0.263:0.0:0.737	.	263;263	Q96EK7;F2Z2E1	F120B_HUMAN;.	T	275;286;263	ENSP00000444125:I275T;ENSP00000440125:I286T;ENSP00000417970:I263T	ENSP00000436640:I263T	I	+	2	0	FAM120B	170469191	0.001000	0.12720	0.002000	0.10522	0.470000	0.32858	0.928000	0.28831	0.426000	0.26116	-0.266000	0.10368	ATC	.	.	none		0.373	FAM120B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000043259.2	NM_032448	
MGMT	4255	hgsc.bcm.edu	37	10	131565170	131565170	+	Missense_Mutation	SNP	A	A	G	rs2308327	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:131565170A>G	ENST00000306010.7	+	5	658	c.626A>G	c.(625-627)aAg>aGg	p.K209R	RP11-109A6.3_ENST00000428273.1_lincRNA	NM_002412.3	NP_002403.2	P16455	MGMT_HUMAN	O-6-methylguanine-DNA methyltransferase	178					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)	CGGTTGGGGAAGCCAGGCTTG	0.657								Direct reversal of damage					A|||	257	0.0513179	0.0061	0.0519	5008	,	,		17958	0.0139		0.1362	False		,,,				2504	0.0634				p.K209R		Atlas-SNP	.											.	MGMT	32	.	0			c.A626G	GRCh37	CM071862	MGMT	M	rs2308327	PASS	.	A	ARG/LYS	98,4308	75.2+/-113.4	0,98,2105	30.0	33.0	32.0		626	-3.6	0.0	10	dbSNP_100	32	1105,7495	219.7+/-257.6	74,957,3269	yes	missense	MGMT	NM_002412.3	26	74,1055,5374	GG,GA,AA		12.8488,2.2242,9.2496	benign	209/239	131565170	1203,11803	2203	4300	6503	SO:0001583	missense	4255	exon5			TGGGGAAGCCAGG	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.626A>G	10.37:g.131565170A>G	ENSP00000302111:p.Lys209Arg	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	100	46	0.46	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	14.67	2.603562	0.46423	0.022242	0.128488	ENSG00000170430	ENST00000306010	T	0.05786	3.39	5.06	-3.61	0.04556	.	0.492896	0.15478	N	0.260234	T	0.00039	0.0001	N	0.19112	0.55	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.41233	-0.9520	10	0.59425	D	0.04	.	6.5475	0.22414	0.5484:0.1226:0.329:0.0	rs2308327;rs2308327	209	B4DEE8	.	R	209	ENSP00000302111:K209R	ENSP00000302111:K209R	K	+	2	0	MGMT	131455160	0.019000	0.18553	0.000000	0.03702	0.110000	0.19582	1.461000	0.35255	-0.993000	0.03467	0.460000	0.39030	AAG	A|0.923;G|0.077	0.077	strong		0.657	MGMT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051009.3	NM_002412	
OR4F15	390649	hgsc.bcm.edu	37	15	102359203	102359203	+	Missense_Mutation	SNP	G	G	A	rs79724132	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:102359203G>A	ENST00000332238.4	+	1	838	c.814G>A	c.(814-816)Gct>Act	p.A272T		NM_001001674.1	NP_001001674.1	Q8NGB8	O4F15_HUMAN	olfactory receptor, family 4, subfamily F, member 15	272						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(2)|large_intestine(5)|lung(10)	19	Lung NSC(78;0.000991)|all_lung(78;0.00128)|Melanoma(26;0.00505)		OV - Ovarian serous cystadenocarcinoma(32;0.00039)|Lung(145;0.17)|LUSC - Lung squamous cell carcinoma(107;0.187)			TAAATATCTTGCTATTTTTGA	0.418													G|||	264	0.0527157	0.1407	0.0447	5008	,	,		22455	0.0		0.0258	False		,,,				2504	0.0215				p.A272T		Atlas-SNP	.											.	OR4F15	42	.	0			c.G814A						PASS	.	G	THR/ALA	537,3869		30,477,1696	194.0	163.0	174.0		814	5.5	1.0	15	dbSNP_132	174	203,8397		7,189,4104	yes	missense	OR4F15	NM_001001674.1	58	37,666,5800	AA,AG,GG		2.3605,12.1879,5.6897	probably-damaging	272/313	102359203	740,12266	2203	4300	6503	SO:0001583	missense	390649	exon1			TATCTTGCTATTT	BK004405	CCDS32342.1	15q26.3	2012-08-09				ENSG00000182854		"""GPCR / Class A : Olfactory receptors"""	15078	protein-coding gene	gene with protein product							Standard	NM_001001674		Approved		uc010uts.2	Q8NGB8		ENST00000332238.4:c.814G>A	15.37:g.102359203G>A	ENSP00000333184:p.Ala272Thr	Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	137	54	0.394161	NM_001001674	B2RNQ5|Q6IF57|Q96R70	Missense_Mutation	SNP	ENST00000332238.4	37	CCDS32342.1	114	0.0521978021978022	75	0.1524390243902439	18	0.049723756906077346	0	0.0	21	0.027704485488126648	.	21.0	4.076469	0.76415	0.121879	0.023605	ENSG00000182854	ENST00000332238	T	0.00152	8.66	5.46	5.46	0.80206	GPCR, rhodopsin-like superfamily (1);	0.294793	0.24354	N	0.039251	T	0.00012	0.0000	M	0.65677	2.01	0.33322	P	0.432507	P	0.49185	0.92	P	0.48524	0.58	T	0.67734	-0.5594	8	.	.	.	.	10.0884	0.42432	0.0883:0.0:0.9117:0.0	.	272	Q8NGB8	O4F15_HUMAN	T	272	ENSP00000333184:A272T	.	A	+	1	0	OR4F15	100176726	0.021000	0.18746	1.000000	0.80357	0.986000	0.74619	0.850000	0.27737	2.843000	0.97960	0.650000	0.86243	GCT	G|0.944;A|0.056	0.056	strong		0.418	OR4F15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417594.1	NM_001001674	
TNC	3371	hgsc.bcm.edu	37	9	117846570	117846570	+	Silent	SNP	C	C	T	rs2274836	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:117846570C>T	ENST00000350763.4	-	4	2460	c.2049G>A	c.(2047-2049)gaG>gaA	p.E683E	TNC_ENST00000340094.3_Silent_p.E683E|TNC_ENST00000423613.2_Silent_p.E683E|TNC_ENST00000542877.1_Silent_p.E683E|TNC_ENST00000537320.1_Silent_p.E683E|TNC_ENST00000346706.3_Silent_p.E683E|TNC_ENST00000345230.3_Silent_p.E683E|TNC_ENST00000341037.4_Silent_p.E683E|TNC_ENST00000535648.1_Silent_p.E683E	NM_002160.3	NP_002151.2	P24821	TENA_HUMAN	tenascin C	683	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				bud outgrowth involved in lung branching (GO:0060447)|cell adhesion (GO:0007155)|cellular response to prostaglandin D stimulus (GO:0071799)|cellular response to retinoic acid (GO:0071300)|cellular response to vitamin D (GO:0071305)|extracellular matrix organization (GO:0030198)|mesenchymal-epithelial cell signaling involved in prostate gland development (GO:0060739)|negative regulation of cell adhesion (GO:0007162)|neuromuscular junction development (GO:0007528)|odontogenesis of dentin-containing tooth (GO:0042475)|osteoblast differentiation (GO:0001649)|peripheral nervous system axon regeneration (GO:0014012)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|prostate gland epithelium morphogenesis (GO:0060740)|response to ethanol (GO:0045471)|response to fibroblast growth factor (GO:0071774)|response to mechanical stimulus (GO:0009612)|response to wounding (GO:0009611)|wound healing (GO:0042060)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|interstitial matrix (GO:0005614)|membrane (GO:0016020)	syndecan binding (GO:0045545)			NS(3)|breast(5)|central_nervous_system(4)|endometrium(8)|kidney(6)|large_intestine(32)|liver(1)|lung(39)|ovary(1)|pancreas(2)|prostate(5)|skin(5)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	120						CCACACCAGGCTCCAGCTCCT	0.567													C|||	2324	0.464058	0.3933	0.3573	5008	,	,		18928	0.5942		0.4354	False		,,,				2504	0.5307				p.E683E		Atlas-SNP	.											TNC,NS,malignant_melanoma,-2,1	TNC	282	1	0			c.G2049A						PASS	.	C		1815,2591	533.1+/-373.6	373,1069,761	97.0	92.0	94.0		2049	3.9	1.0	9	dbSNP_100	94	3901,4699	545.6+/-384.8	898,2105,1297	no	coding-synonymous	TNC	NM_002160.3		1271,3174,2058	TT,TC,CC		45.3605,41.1938,43.9489		683/2202	117846570	5716,7290	2203	4300	6503	SO:0001819	synonymous_variant	3371	exon4			ACCAGGCTCCAGC		CCDS6811.1	9q33.1	2014-01-28	2008-07-31	2002-06-07	ENSG00000041982	ENSG00000041982		"""Fibrinogen C domain containing"", ""Fibronectin type III domain containing"""	5318	protein-coding gene	gene with protein product	"""hexabrachion (tenascin)"""	187380	"""hexabrachion (tenascin C, cytotactin)"", ""deafness, autosomal dominant 56"""	HXB, DFNA56		1704365, 1707164, 23936043	Standard	NM_002160		Approved	TN, MGC167029	uc004bjj.4	P24821	OTTHUMG00000021010	ENST00000350763.4:c.2049G>A	9.37:g.117846570C>T		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	82	39	0.47561	NM_002160	C9IYT7|C9J575|C9J6D9|C9J848|Q14583|Q15567|Q5T7S3	Silent	SNP	ENST00000350763.4	37	CCDS6811.1																																																																																			C|0.552;T|0.448	0.448	strong		0.567	TNC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055418.2	NM_002160	
RBBP6	5930	hgsc.bcm.edu	37	16	24570844	24570844	+	Silent	SNP	G	G	A	rs45591839	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:24570844G>A	ENST00000319715.4	+	8	1125	c.693G>A	c.(691-693)ggG>ggA	p.G231G	RBBP6_ENST00000381039.3_Silent_p.G231G|RBBP6_ENST00000348022.2_Silent_p.G231G	NM_006910.4	NP_008841.2	Q7Z6E9	RBBP6_HUMAN	retinoblastoma binding protein 6	231					embryonic organ development (GO:0048568)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|somite development (GO:0061053)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(17)|ovary(4)|pancreas(1)|prostate(2)|urinary_tract(1)	46				GBM - Glioblastoma multiforme(48;0.0518)		ATGCAATTGGGAAGAAAGAGA	0.388													G|||	109	0.0217652	0.0045	0.0447	5008	,	,		19662	0.0		0.0606	False		,,,				2504	0.0112				p.G231G		Atlas-SNP	.											.	RBBP6	158	.	0			c.G693A						PASS	.	G	,	41,4353	44.6+/-78.6	1,39,2157	90.0	81.0	84.0		693,693	4.0	1.0	16	dbSNP_127	84	461,8139	135.7+/-192.9	10,441,3849	no	coding-synonymous,coding-synonymous	RBBP6	NM_006910.4,NM_018703.3	,	11,480,6006	AA,AG,GG		5.3605,0.9331,3.8633	,	231/1793,231/1759	24570844	502,12492	2197	4300	6497	SO:0001819	synonymous_variant	5930	exon8			AATTGGGAAGAAA		CCDS10621.1, CCDS10622.1, CCDS45444.1	16p12.2	2008-08-04	2001-11-28		ENSG00000122257	ENSG00000122257			9889	protein-coding gene	gene with protein product	"""proliferation potential-related protein"""	600938	"""retinoblastoma-binding protein 6"""			8595913, 16396680	Standard	NM_006910		Approved	P2P-R, PACT, SNAMA	uc002dmh.3	Q7Z6E9	OTTHUMG00000096991	ENST00000319715.4:c.693G>A	16.37:g.24570844G>A		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	58	37	0.637931	NM_018703	Q147T5|Q15290|Q6DKH4|Q6P4C2|Q6YNC9|Q7Z6E8|Q8N0V2|Q96PH3|Q9H3I8|Q9H5M5|Q9NPX4	Silent	SNP	ENST00000319715.4	37	CCDS10621.1																																																																																			G|0.962;A|0.038	0.038	strong		0.388	RBBP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214067.2	NM_006910	
CFAP44	55779	hgsc.bcm.edu	37	3	113127991	113127991	+	Missense_Mutation	SNP	C	C	A	rs16845107	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:113127991C>A	ENST00000295868.2	-	7	1014	c.852G>T	c.(850-852)aaG>aaT	p.K284N	WDR52-AS1_ENST00000498480.1_RNA|WDR52_ENST00000393845.2_Missense_Mutation_p.K284N|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						GCTGCTCTTCCTTATCAGGAT	0.408													A|||	470	0.0938498	0.0877	0.0461	5008	,	,		15369	0.1647		0.0616	False		,,,				2504	0.0961				p.K284N		Atlas-SNP	.											.	WDR52	151	.	0			c.G852T						PASS	.	A	ASN/LYS,ASN/LYS	446,3960	785.4+/-414.7	26,394,1783	109.0	109.0	109.0		852,852	-1.9	0.2	3	dbSNP_123	109	524,8076	795.7+/-407.5	11,502,3787	yes	missense,missense	WDR52	NM_001164496.1,NM_018338.3	94,94	37,896,5570	AA,AC,CC		6.093,10.1226,7.4581	benign,benign	284/1855,284/983	113127991	970,12036	2203	4300	6503	SO:0001583	missense	55779	exon7			CTCTTCCTTATCA																												ENST00000295868.2:c.852G>T	3.37:g.113127991C>A	ENSP00000295868:p.Lys284Asn	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	106	50	0.471698	NM_001164496		Missense_Mutation	SNP	ENST00000295868.2	37	CCDS2972.1	194	0.08882783882783883	40	0.08130081300813008	16	0.04419889502762431	92	0.16083916083916083	46	0.06068601583113457	A	4.037	0.004376	0.07866	0.101226	0.06093	ENSG00000206530	ENST00000393845;ENST00000295868	T;T	0.64618	-0.11;3.36	5.78	-1.87	0.07737	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	.	.	.	.	T	0.00073	0.0002	N	0.00044	-2.455	0.48452	P	3.4999999999996145E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.21999	-1.0229	8	0.02654	T	1	.	8.7621	0.34680	0.4178:0.1227:0.4595:0.0	rs16845107;rs52834730;rs57634918;rs16845107	284	Q96MT7	WDR52_HUMAN	N	284	ENSP00000377428:K284N;ENSP00000295868:K284N	ENSP00000295868:K284N	K	-	3	2	WDR52	114610681	0.989000	0.36119	0.209000	0.23619	0.733000	0.41908	0.237000	0.17985	-0.622000	0.05626	-1.221000	0.01599	AAG	C|0.916;A|0.084	0.084	strong		0.408	WDR52-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000354128.3		
SLC12A7	10723	hgsc.bcm.edu	37	5	1074696	1074696	+	Silent	SNP	G	G	A	rs12515358	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:1074696G>A	ENST00000264930.5	-	16	2101	c.2058C>T	c.(2056-2058)caC>caT	p.H686H		NM_006598.2	NP_006589.2	Q9Y666	S12A7_HUMAN	solute carrier family 12 (potassium/chloride transporter), member 7	686					cell volume homeostasis (GO:0006884)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transport (GO:0006811)|potassium ion transport (GO:0006813)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	potassium:chloride symporter activity (GO:0015379)|protein kinase binding (GO:0019901)			breast(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(14)|ovary(2)|prostate(1)|skin(4)|urinary_tract(2)	32	Lung NSC(6;2.47e-13)|all_lung(6;1.67e-12)|all_epithelial(6;5.44e-09)		Epithelial(17;0.000497)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|all cancers(22;0.00241)|Lung(60;0.165)		Potassium Chloride(DB00761)	AGTTCTTGGTGTGGGGGGGAC	0.647													G|||	68	0.0135783	0.0015	0.0173	5008	,	,		14593	0.0		0.0457	False		,,,				2504	0.0082				p.H686H		Atlas-SNP	.											.	SLC12A7	97	.	0			c.C2058T						PASS	.	G		24,4378	29.0+/-57.7	0,24,2177	54.0	52.0	53.0		2058	0.8	1.0	5	dbSNP_120	53	320,8278	111.0+/-171.3	10,300,3989	no	coding-synonymous	SLC12A7	NM_006598.2		10,324,6166	AA,AG,GG		3.7218,0.5452,2.6462		686/1084	1074696	344,12656	2201	4299	6500	SO:0001819	synonymous_variant	10723	exon16			CTTGGTGTGGGGG	AF105365	CCDS34129.1	5p15	2013-07-18	2013-07-18		ENSG00000113504	ENSG00000113504		"""Solute carriers"""	10915	protein-coding gene	gene with protein product		604879				10347194	Standard	NM_006598		Approved	KCC4, DKFZP434F076	uc003jbu.3	Q9Y666	OTTHUMG00000161931	ENST00000264930.5:c.2058C>T	5.37:g.1074696G>A		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	102	48	0.470588	NM_006598	A6NDS8|Q4G0F3|Q96I81|Q9H7I3|Q9H7I7|Q9UFW2	Silent	SNP	ENST00000264930.5	37	CCDS34129.1	39	0.017857142857142856	1	0.0020325203252032522	7	0.019337016574585635	0	0.0	31	0.040897097625329816	g	3.220	-0.159816	0.06502	0.005452	0.037218	ENSG00000113504	ENST00000513223	T	0.80393	-1.37	3.81	0.789	0.18607	.	0.000000	0.85682	D	0.000000	T	0.55465	0.1922	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.69978	-0.4998	7	0.87932	D	0	.	6.7556	0.23512	0.3609:0.0:0.6391:0.0	rs12515358	.	.	.	Y	44	ENSP00000428854:H44Y	ENSP00000428854:H44Y	H	-	1	0	SLC12A7	1127696	1.000000	0.71417	0.984000	0.44739	0.262000	0.26303	3.200000	0.51051	0.191000	0.20236	0.313000	0.20887	CAC	G|0.976;A|0.024	0.024	strong		0.647	SLC12A7-001	KNOWN	non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366446.2	NM_006598	
CHRD	8646	hgsc.bcm.edu	37	3	184102814	184102814	+	Missense_Mutation	SNP	G	G	A	rs138882380		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:184102814G>A	ENST00000204604.1	+	14	1852	c.1606G>A	c.(1606-1608)Gtg>Atg	p.V536M	CHRD_ENST00000348986.3_Missense_Mutation_p.V496M|EIF2B5_ENST00000444495.1_Intron|CHRD_ENST00000450923.1_Missense_Mutation_p.V536M|CHRD_ENST00000545352.1_Missense_Mutation_p.V166M	NM_003741.2	NP_003732.2	Q9H2X0	CHRD_HUMAN	chordin	536	CHRD 4. {ECO:0000255|PROSITE- ProRule:PRU00230}.				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)			AGCGCTGCCCGTGCCCCTAGC	0.607													G|||	1	0.000199681	0.0	0.0	5008	,	,		16943	0.0		0.001	False		,,,				2504	0.0				p.V536M		Atlas-SNP	.											.	CHRD	149	.	0			c.G1606A						PASS	.	G	MET/VAL	0,4406		0,0,2203	106.0	112.0	110.0		1606	3.6	1.0	3	dbSNP_134	110	2,8598	2.2+/-6.3	0,2,4298	no	missense	CHRD	NM_003741.2	21	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	probably-damaging	536/956	184102814	2,13004	2203	4300	6503	SO:0001583	missense	8646	exon14			CTGCCCGTGCCCC	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.1606G>A	3.37:g.184102814G>A	ENSP00000204604:p.Val536Met	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	71	40	0.56338	NM_003741	O95254|Q2M1I8|Q6UW83|Q9H2D3|Q9H2W8|Q9H2W9|Q9P0Z2|Q9P0Z3|Q9P0Z4|Q9P0Z5	Missense_Mutation	SNP	ENST00000204604.1	37	CCDS3266.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	16.85	3.236050	0.58886	0.0	2.33E-4	ENSG00000090539	ENST00000204604;ENST00000450923;ENST00000348986;ENST00000545352;ENST00000342610	T;T;T;T	0.46451	0.87;0.87;0.87;0.87	5.38	3.59	0.41128	CHRD (3);	0.125547	0.52532	D	0.000071	T	0.58250	0.2109	M	0.66939	2.045	0.47183	D	0.99934	D;D;D;D	0.89917	0.999;1.0;0.989;1.0	D;D;P;D	0.76071	0.982;0.987;0.906;0.98	T	0.56153	-0.8026	10	0.45353	T	0.12	-20.6515	9.8593	0.41105	0.1666:0.0:0.8334:0.0	.	166;496;536;536	B7Z6F4;Q9H2X0-5;E7ESX1;Q9H2X0	.;.;.;CHRD_HUMAN	M	536;536;496;166;249	ENSP00000204604:V536M;ENSP00000408972:V536M;ENSP00000334036:V496M;ENSP00000442948:V166M	ENSP00000204604:V536M	V	+	1	0	CHRD	185585508	0.810000	0.29049	0.978000	0.43139	0.744000	0.42396	1.230000	0.32612	0.781000	0.33589	0.655000	0.94253	GTG	G|1.000;A|0.000	0.000	strong		0.607	CHRD-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000280432.1	NM_003741	
SLFN12	55106	hgsc.bcm.edu	37	17	33749919	33749919	+	Missense_Mutation	SNP	A	A	C	rs1849733	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:33749919A>C	ENST00000394562.1	-	4	652	c.129T>G	c.(127-129)agT>agG	p.S43R	SLFN12_ENST00000304905.5_Missense_Mutation_p.S43R|SLFN12_ENST00000460530.1_5'Flank|SLFN12_ENST00000452764.3_Missense_Mutation_p.S43R			Q8IYM2	SLN12_HUMAN	schlafen family member 12	43			S -> R (in dbSNP:rs1849733). {ECO:0000269|PubMed:15489334}.				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)		CTCGTGAGACACTTTCATTCT	0.403													A|||	1884	0.376198	0.2685	0.5375	5008	,	,		18787	0.3462		0.4881	False		,,,				2504	0.3231				p.S43R		Atlas-SNP	.											SLFN12,NS,adenoma,0,1	SLFN12	56	1	0			c.T129G						PASS	.	A	ARG/SER	1433,2973	466.2+/-354.4	241,951,1011	142.0	121.0	128.0		129	-6.4	0.0	17	dbSNP_92	128	4207,4393	569.1+/-389.1	1014,2179,1107	yes	missense	SLFN12	NM_018042.3	110	1255,3130,2118	CC,CA,AA		48.9186,32.5238,43.3646	benign	43/579	33749919	5640,7366	2203	4300	6503	SO:0001583	missense	55106	exon2			TGAGACACTTTCA	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.129T>G	17.37:g.33749919A>C	ENSP00000378063:p.Ser43Arg	Somatic	240	1	0.00416667		WXS	Illumina HiSeq	Phase_I	195	88	0.451282	NM_018042	A8K711|Q9NP47	Missense_Mutation	SNP	ENST00000394562.1	37	CCDS11295.1	910	0.4166666666666667	134	0.27235772357723576	182	0.5027624309392266	201	0.3513986013986014	393	0.5184696569920845	a	2.100	-0.406307	0.04832	0.325238	0.489186	ENSG00000172123	ENST00000394562;ENST00000304905;ENST00000452764;ENST00000447040;ENST00000445092	T;T;T;T;T	0.28666	3.93;3.93;3.93;2.02;1.6	3.2	-6.41	0.01938	.	.	.	.	.	T	0.00012	0.0000	N	0.11313	0.125	0.80722	P	0.0	B	0.19331	0.035	B	0.08055	0.003	T	0.47341	-0.9125	8	0.09338	T	0.73	.	3.679	0.08304	0.1948:0.0:0.3113:0.4939	rs1849733;rs17548986;rs17846141;rs17859149;rs52813912;rs56957697;rs1849733	43	Q8IYM2	SLN12_HUMAN	R	43	ENSP00000378063:S43R;ENSP00000302077:S43R;ENSP00000394903:S43R;ENSP00000398315:S43R;ENSP00000404175:S43R	ENSP00000302077:S43R	S	-	3	2	SLFN12	30774032	0.000000	0.05858	0.000000	0.03702	0.155000	0.21991	-2.082000	0.01365	-0.829000	0.04268	0.358000	0.22013	AGT	A|0.586;C|0.414	0.414	strong		0.403	SLFN12-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256491.1	NM_018042	
FAM166B	730112	hgsc.bcm.edu	37	9	35563361	35563361	+	Missense_Mutation	SNP	G	G	A	rs75679360	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:35563361G>A	ENST00000399742.2	-	2	158	c.88C>T	c.(88-90)Cgg>Tgg	p.R30W	FAM166B_ENST00000492890.1_Intron	NM_001099951.2|NM_001164310.1	NP_001093421.1|NP_001157782.1	A8MTA8	F166B_HUMAN	family with sequence similarity 166, member B	30										kidney(3)|large_intestine(1)|lung(4)|ovary(1)	9						ACGCTGAACCGAAGTAGTGGG	0.637													G|||	167	0.0333466	0.0424	0.0144	5008	,	,		17983	0.003		0.0616	False		,,,				2504	0.0368				p.R30W		Atlas-SNP	.											.	FAM166B	19	.	0			c.C88T						PASS	.	G	TRP/ARG,TRP/ARG	145,4119		2,141,1989	28.0	34.0	32.0		88,88	3.8	1.0	9	dbSNP_131	32	416,8064		7,402,3831	yes	missense,missense	FAM166B	NM_001099951.2,NM_001164310.1	101,101	9,543,5820	AA,AG,GG		4.9057,3.4006,4.4021	possibly-damaging,possibly-damaging	30/217,30/276	35563361	561,12183	2132	4240	6372	SO:0001583	missense	730112	exon2			TGAACCGAAGTAG	BC129999	CCDS47963.1, CCDS56572.1	9p13.3	2008-06-10			ENSG00000215187	ENSG00000215187			34242	protein-coding gene	gene with protein product							Standard	NM_001099951		Approved		uc010mkr.3	A8MTA8	OTTHUMG00000019858	ENST00000399742.2:c.88C>T	9.37:g.35563361G>A	ENSP00000382646:p.Arg30Trp	Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	26	9	0.346154	NM_001099951	A1L3B2|B7ZBJ0	Missense_Mutation	SNP	ENST00000399742.2	37	CCDS56572.1	75	0.034340659340659344	16	0.032520325203252036	3	0.008287292817679558	3	0.005244755244755245	53	0.06992084432717678	G	19.57	3.852417	0.71719	0.034006	0.049057	ENSG00000215187	ENST00000399742;ENST00000537504	T	0.48201	0.82	5.76	3.77	0.43336	.	0.238348	0.18353	U	0.143808	T	0.10809	0.0264	M	0.71036	2.16	0.35253	D	0.778862	D;D;D;D	0.76494	0.999;0.999;0.998;0.999	P;P;P;P	0.60886	0.88;0.88;0.861;0.862	T	0.53788	-0.8389	9	.	.	.	-16.4912	9.9346	0.41543	0.0:0.16:0.6944:0.1455	.	30;30;30;30	B7ZW33;B7ZW26;A8MTA8;A8MTA8-2	.;.;F166B_HUMAN;.	W	30	ENSP00000382646:R30W	.	R	-	1	2	FAM166B	35553361	0.999000	0.42202	1.000000	0.80357	0.969000	0.65631	1.531000	0.36018	1.393000	0.46605	0.561000	0.74099	CGG	G|0.963;A|0.037	0.037	strong		0.637	FAM166B-005	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336563.1	NM_001099951	
VPREB1	7441	hgsc.bcm.edu	37	22	22599537	22599537	+	Missense_Mutation	SNP	G	G	A	rs1320	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:22599537G>A	ENST00000403807.3	+	2	365	c.226G>A	c.(226-228)Gac>Aac	p.D76N	VPREB1_ENST00000302273.2_Missense_Mutation_p.D75N			P12018	VPREB_HUMAN	pre-B lymphocyte 1	76	Complementarity-determining-2.|Ig-like V-type.		D -> N (in dbSNP:rs1320).							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)		CTCACAATCAGACAAGAGCCA	0.582													g|||	87	0.0173722	0.0023	0.0317	5008	,	,		16793	0.0		0.0567	False		,,,				2504	0.0051				p.D76N		Atlas-SNP	.											.	VPREB1	20	.	0			c.G226A						PASS	.	G	ASN/ASP	40,4366	44.6+/-78.6	1,38,2164	70.0	79.0	76.0		226	-3.7	0.0	22	dbSNP_36	76	467,8133	138.1+/-194.9	15,437,3848	yes	missense	VPREB1	NM_007128.2	23	16,475,6012	AA,AG,GG		5.4302,0.9079,3.8982	benign	76/146	22599537	507,12499	2203	4300	6503	SO:0001583	missense	7441	exon2			CAATCAGACAAGA	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.226G>A	22.37:g.22599537G>A	ENSP00000385361:p.Asp76Asn	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	68	34	0.5	NM_007128	B5MCG2	Missense_Mutation	SNP	ENST00000403807.3	37	CCDS13798.1	65	0.02976190476190476	4	0.008130081300813009	15	0.04143646408839779	0	0.0	46	0.06068601583113457	g	9.683	1.149914	0.21371	0.009079	0.054302	ENSG00000169575	ENST00000403807;ENST00000302273	T;T	0.64438	-0.1;-0.1	3.91	-3.69	0.04450	Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin V-set, subgroup (1);Immunoglobulin-like fold (1);	0.437965	0.19495	N	0.112877	T	0.07324	0.0185	N	0.25789	0.76	0.09310	N	1	B	0.16802	0.019	B	0.28139	0.086	T	0.14671	-1.0464	10	0.34782	T	0.22	.	10.5029	0.44817	0.7803:0.0:0.2197:0.0	rs1320;rs17570113;rs60335961;rs1320	76	P12018	VPREB_HUMAN	N	76;75	ENSP00000385361:D76N;ENSP00000304590:D75N	ENSP00000304590:D75N	D	+	1	0	VPREB1	20929537	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.623000	0.05546	-0.615000	0.05679	-0.156000	0.13503	GAC	G|0.965;A|0.035	0.035	strong		0.582	VPREB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321101.1		
HLA-DPB1	3115	hgsc.bcm.edu	37	6	33048602	33048602	+	Missense_Mutation	SNP	C	C	A	rs1042131	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:33048602C>A	ENST00000418931.2	+	2	370	c.254C>A	c.(253-255)gCg>gAg	p.A85E	HLA-DPA1_ENST00000419277.1_5'Flank|HLA-DPB1_ENST00000471184.1_3'UTR|HLA-DPB1_ENST00000535465.1_Missense_Mutation_p.A85E	NM_002121.5	NP_002112.3	P04440	DPB1_HUMAN	major histocompatibility complex, class II, DP beta 1	85	Beta-1.		A -> E (in allele DPB1*02:01, allele DPB1*03:01, allele DPB1*04:02, allele DPB1*05:02, allele DPB1*06:01, allele DPB1*06:02, allele DPB1*08:01, allele DPB1*09:01, allele DPB1*10:01, allele DPB1*10:02, allele DPB1*11:02, allele DPB1*14:01, allele DPB1*14:02, allele DPB1*16:01, allele DPB1*16:02, allele DPB1*17:01, allele DPB1*18:01, allele DPB1*18:02, allele DPB1*19:02, allele DPB1*20:01, allele DPB1*22:02, allele DPB1*25:01, allele DPB1*25:02, allele DPB1*26:02, allele DPB1*28:01, allele DPB1*29:01, allele DPB1*32:01, allele DPB1*35:01, allele DPB1*37:01, allele DPB1*41:01, allele DPB1*44:01, allele DPB1*45:01, allele DPB1*46:01, allele DPB1*48:01, allele DPB1*49:01, allele DPB1*50:01, allele DPB1*51:01, allele DPB1*53:01, allele DPB1*57:01, allele DPB1*59:01, allele DPB1*60:01, allele DPB1*68:01, allele DPB1*69:01, allele DPB1*70:01, allele DPB1*73:01, allele DPB1*75:01, allele DPB1*76:01, allele DPB1*77:01, allele DPB1*78:01, allele DPB1*79:01, allele DPB1*80:01, allele DPB1*81:01, allele DPB1*82:01, allele DPB1*83:01, allele DPB1*84:01, allele DPB1*86:01, allele DPB1*88:01, allele DPB1*91:01, allele DPB1*92:01, allele DPB1*93:01, allele DPB1*94:01 and allele DPB1*98:01; dbSNP:rs1042131).		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell proliferation (GO:0042102)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	peptide antigen binding (GO:0042605)			cervix(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(3)|ovary(1)|skin(1)	11						CGGCCTGCTGCGGAGTACTGG	0.647													.|||	2324	0.464058	0.4849	0.598	5008	,	,		13984	0.3452		0.4533	False		,,,				2504	0.4744				p.A85E		Atlas-SNP	.											HLA-DPB1,colon,carcinoma,-1,2	HLA-DPB1	28	2	0			c.C254A						PASS	.	C	GLU/ALA	1466,1556		324,818,369	55.0	56.0	56.0		254	4.0	0.0	6	dbSNP_86	56	2364,3054		484,1396,829	no	missense	HLA-DPB1	NM_002121.5	107	808,2214,1198	AA,AC,CC		43.6323,48.5109,45.3791	benign	85/259	33048602	3830,4610	1511	2709	4220	SO:0001583	missense	3115	exon2			CTGCTGCGGAGTA		CCDS4765.1	6p21.3	2013-01-11			ENSG00000223865	ENSG00000223865		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4940	protein-coding gene	gene with protein product		142858		HLA-DP1B			Standard	NM_002121		Approved		uc003ocu.2	P04440	OTTHUMG00000031076	ENST00000418931.2:c.254C>A	6.37:g.33048602C>A	ENSP00000408146:p.Ala85Glu	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	51	24	0.470588	NM_002121	A0PFJ7|A5I886|A8YPB3|B5U8B4|B7VF80|B7VF87|B8ZX68|B8ZYT0|B9W5S8|B9W6F7|B9W6F9|C0MPP5|C0MPQ2|C0MPQ3|C0MPQ5|C0MPQ6|C0MPQ7|C4R9J5|C5IZL1|O00259|O19698|O19700|O19702|O19749|O46884|O77952|O98215|O98216|O98217|O98218|O98219|O98222|O98223|P01916|P04232|P13763|P79493|P79608|Q0P0L4|Q0ZFN3|Q14279|Q27S71|Q29682|Q29684|Q29698|Q29714|Q29775|Q29776|Q29778|Q29779|Q29781|Q29827|Q29828|Q29879|Q29880|Q29898|Q29977|Q2MGW3|Q30015|Q30031|Q30032|Q30033|Q30034|Q30050|Q30051|Q30052|Q30053|Q30054|Q30055|Q30174|Q4GY31|Q4JHD8|Q5ENE0|Q5ENE1|Q5ENW3|Q5EP46|Q5EP47|Q5EP49|Q5EP51|Q5EP52|Q5EP53|Q5EP56|Q5I4H8|Q5I4H9|Q5ISH4|Q5ISH5|Q5SQ73|Q5STP2|Q5YLA6|Q6IVX1|Q6LBX2|Q6LBX3|Q6LBX4|Q6LBX5|Q6LBX6|Q6LBX7|Q6PWX6|Q6TAS4|Q714U1|Q714U2|Q7YQ10|Q860Z7|Q8HWL7|Q8HWT5|Q8SNC4|Q95HC1|Q95IT7|Q95IT8|Q9BD13|Q9GIM2|Q9GIM4|Q9GIX6|Q9GJ41|Q9MY67|Q9TNT7|Q9TQE2|Q9XS11|Q9XS12	Missense_Mutation	SNP	ENST00000418931.2	37	CCDS4765.1	1010	0.4624542124542125	237	0.4817073170731707	203	0.5607734806629834	238	0.4160839160839161	332	0.43799472295514513	C	14.61	2.587123	0.46110	0.485109	0.436323	ENSG00000223865	ENST00000418931;ENST00000535465;ENST00000411942;ENST00000428835	T;T;T	0.00416	7.51;7.51;7.51	4.02	4.02	0.46733	MHC class II, alpha/beta chain, N-terminal (1);MHC class II, beta chain, N-terminal (3);MHC classes I/II-like antigen recognition protein (1);	0.156019	0.40640	U	0.001054	T	0.00300	0.0009	M	0.80332	2.49	0.58432	P	1.0000000000287557E-6	B	0.19073	0.033	B	0.32677	0.15	T	0.44697	-0.9311	9	0.52906	T	0.07	.	14.0283	0.64599	0.0:1.0:0.0:0.0	rs1042131;rs3173295;rs9277352;rs17214734	85	P04440	DPB1_HUMAN	E	85;85;85;62	ENSP00000408146:A85E;ENSP00000439674:A85E;ENSP00000412654:A62E	ENSP00000389210:A85E	A	+	2	0	HLA-DPB1	33156580	0.919000	0.31177	0.017000	0.16124	0.002000	0.02628	2.057000	0.41365	2.248000	0.74166	0.643000	0.83706	GCG	C|0.544;A|0.456	0.456	strong		0.647	HLA-DPB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076106.2	NM_002121	
PCDH1	5097	hgsc.bcm.edu	37	5	141243646	141243646	+	Silent	SNP	A	A	G	rs3797054	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:141243646A>G	ENST00000394536.3	-	3	2389	c.2250T>C	c.(2248-2250)gcT>gcC	p.A750A	PCDH1_ENST00000456271.1_Silent_p.A738A|PCDH1_ENST00000503492.1_Intron|PCDH1_ENST00000511044.1_5'UTR|PCDH1_ENST00000287008.3_Silent_p.A750A|PCDH1_ENST00000536585.1_Silent_p.A728A	NM_001278613.1|NM_001278615.1	NP_001265542.1|NP_001265544.1	Q08174	PCDH1_HUMAN	protocadherin 1	750	Cadherin 7. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell-cell signaling (GO:0007267)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	cell-cell junction (GO:0005911)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(4)|lung(20)|ovary(5)|skin(3)|upper_aerodigestive_tract(1)	51		Lung NSC(810;0.027)|all_lung(500;0.0321)|all_hematologic(541;0.0433)|Prostate(461;0.0453)|Breast(839;0.128)|Lung SC(612;0.238)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)	GBM - Glioblastoma multiforme(465;1.06e-05)		AGATCAGCTCAGCATTGACAC	0.567													A|||	2107	0.420727	0.2935	0.3357	5008	,	,		21673	0.5784		0.3469	False		,,,				2504	0.5665				p.A750A	Ovarian(132;1609 1739 4190 14731 45037)	Atlas-SNP	.											.	PCDH1	119	.	0			c.T2250C						PASS	.	A	,	1376,3030	454.2+/-350.6	207,962,1034	62.0	59.0	60.0		2250,2250	-8.3	1.0	5	dbSNP_107	60	3019,5581	463.9+/-366.1	551,1917,1832	no	coding-synonymous,coding-synonymous	PCDH1	NM_002587.3,NM_032420.2	,	758,2879,2866	GG,GA,AA		35.1047,31.2301,33.7921	,	750/1061,750/1238	141243646	4395,8611	2203	4300	6503	SO:0001819	synonymous_variant	5097	exon3			CAGCTCAGCATTG	AK075233	CCDS4267.1, CCDS43375.1	5q31.3	2010-01-26	2007-02-12		ENSG00000156453	ENSG00000156453		"""Cadherins / Protocadherins : Non-clustered"""	8655	protein-coding gene	gene with protein product		603626	"""protocadherin 1 (cadherin-like 1)"""			8508762	Standard	NM_032420		Approved	pc42	uc003llp.3	Q08174	OTTHUMG00000129661	ENST00000394536.3:c.2250T>C	5.37:g.141243646A>G		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	82	45	0.548781	NM_032420	Q8IUP2	Silent	SNP	ENST00000394536.3	37	CCDS43375.1																																																																																			A|0.640;G|0.360	0.360	strong		0.567	PCDH1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251862.1	NM_032420	
PRG2	5553	hgsc.bcm.edu	37	11	57157405	57157405	+	Silent	SNP	A	A	G	rs490358	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:57157405A>G	ENST00000311862.5	-	2	86	c.13T>C	c.(13-15)Tta>Cta	p.L5L	PRG2_ENST00000525955.1_Silent_p.L5L|RP11-872D17.8_ENST00000529411.1_Silent_p.L110L|PRG2_ENST00000533605.1_Silent_p.L5L	NM_001243245.1|NM_002728.4	NP_001230174.1|NP_002719.3	P13727	PRG2_HUMAN	proteoglycan 2, bone marrow (natural killer cell activator, eosinophil granule major basic protein)	5					defense response to bacterium (GO:0042742)|defense response to nematode (GO:0002215)|immune response (GO:0006955)|negative regulation of interleukin-10 production (GO:0032693)|positive regulation of interleukin-4 production (GO:0032753)	cytoplasmic vesicle (GO:0031410)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	carbohydrate binding (GO:0030246)|heparin binding (GO:0008201)			central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(4)	10				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)	Sargramostim(DB00020)	GCCAGAAGTAAGGGGAGTTTC	0.423													G|||	3767	0.752196	0.6241	0.8343	5008	,	,		21396	0.7718		0.7406	False		,,,				2504	0.8589				p.L5L		Atlas-SNP	.											.	PRG2	65	.	0			c.T13C						PASS	.	G		2764,1638	498.8+/-364.2	869,1026,306	184.0	171.0	175.0		13	2.8	0.9	11	dbSNP_83	175	6281,2311	384.9+/-341.3	2283,1715,298	no	coding-synonymous	PRG2	NM_002728.4		3152,2741,604	GG,GA,AA		26.8971,37.2104,30.3909		5/223	57157405	9045,3949	2201	4296	6497	SO:0001819	synonymous_variant	5553	exon2			GAAGTAAGGGGAG	BC005929	CCDS7955.1, CCDS58133.1	11q12	2005-11-25				ENSG00000186652			9362	protein-coding gene	gene with protein product		605601				1565101	Standard	NM_001243245		Approved	MBP, BMPG		P13727		ENST00000311862.5:c.13T>C	11.37:g.57157405A>G		Somatic	113	1	0.00884956		WXS	Illumina HiSeq	Phase_I	73	73	1	NM_001243245	A6XMW0|B2R5I1|P81448|Q14227|Q6ICT2	Silent	SNP	ENST00000311862.5	37	CCDS7955.1																																																																																			A|0.292;G|0.708	0.708	strong		0.423	PRG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392468.1	NM_002728	
ANK3	288	hgsc.bcm.edu	37	10	61941147	61941147	+	Silent	SNP	A	A	G	rs34552044	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:61941147A>G	ENST00000280772.2	-	18	2315	c.2124T>C	c.(2122-2124)gaT>gaC	p.D708D	ANK3_ENST00000373827.2_Silent_p.D702D|ANK3_ENST00000503366.1_Silent_p.D691D	NM_020987.3	NP_066267.2	Q12955	ANK3_HUMAN	ankyrin 3, node of Ranvier (ankyrin G)	708					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						CATTCACTCGATCTTCTTGAG	0.522													A|||	57	0.0113818	0.0015	0.0173	5008	,	,		17853	0.0		0.0378	False		,,,				2504	0.0051				p.D708D		Atlas-SNP	.											.	ANK3	703	.	0			c.T2124C						PASS	.	A	,,	52,4354	50.9+/-86.3	0,52,2151	162.0	141.0	148.0		2106,2073,2124	5.1	1.0	10	dbSNP_126	148	361,8239	121.0+/-180.1	6,349,3945	no	coding-synonymous,coding-synonymous,coding-synonymous	ANK3	NM_001204403.1,NM_001204404.1,NM_020987.3	,,	6,401,6096	GG,GA,AA		4.1977,1.1802,3.1755	,,	702/1862,691/1869,708/4378	61941147	413,12593	2203	4300	6503	SO:0001819	synonymous_variant	288	exon18			CACTCGATCTTCT	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.2124T>C	10.37:g.61941147A>G		Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	158	85	0.537975	NM_020987	B1AQT2|B4DIL1|E9PE32|Q13484|Q5CZH9|Q5VXD5|Q7Z3G4|Q9H0P5	Silent	SNP	ENST00000280772.2	37	CCDS7258.1																																																																																			A|0.971;G|0.029	0.029	strong		0.522	ANK3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048201.4	NM_020987	
AHNAK2	113146	hgsc.bcm.edu	37	14	105415352	105415352	+	Missense_Mutation	SNP	G	G	C	rs12890949	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:105415352G>C	ENST00000333244.5	-	7	6555	c.6436C>G	c.(6436-6438)Ctg>Gtg	p.L2146V	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	2146			L -> V (in dbSNP:rs12890949).			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)			TTGGTAGTCAGGTCCTTGTTG	0.592													.|||	26	0.00519169	0.0053	0.0014	5008	,	,		14396	0.003		0.0	False		,,,				2504	0.0153				p.L2146V		Atlas-SNP	.											.	AHNAK2	719	.	0			c.C6436G						PASS	.	C	VAL/LEU	3534,464		1624,286,89	211.0	139.0	166.0		6436	-2.7	0.0	14	dbSNP_121	166	6623,165		3281,61,52	yes	missense	AHNAK2	NM_138420.2	32	4905,347,141	CC,CG,GG		2.4308,11.6058,5.8316	benign	2146/5796	105415352	10157,629	1999	3394	5393	SO:0001583	missense	113146	exon7			TAGTCAGGTCCTT	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.6436C>G	14.37:g.105415352G>C	ENSP00000353114:p.Leu2146Val	Somatic	0	0	.		WXS	Illumina HiSeq	Phase_I	98	98	1	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	1668	0.7637362637362637	422	0.8577235772357723	241	0.6657458563535912	276	0.4825174825174825	729	0.9617414248021108	N	2.407	-0.336164	0.05278	0.883942	0.975692	ENSG00000185567	ENST00000333244	T	0.00840	5.63	4.08	-2.68	0.06041	.	.	.	.	.	T	0.00012	0.0000	N	0.00677	-1.265	0.80722	P	0.0	B	0.06786	0.001	B	0.06405	0.002	T	0.13469	-1.0508	8	0.11794	T	0.64	.	5.2208	0.15368	0.1488:0.226:0.5293:0.0959	rs57710661	2146	Q8IVF2	AHNK2_HUMAN	V	2146	ENSP00000353114:L2146V	ENSP00000353114:L2146V	L	-	1	2	AHNAK2	104486397	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.298000	0.02756	-0.930000	0.03752	-1.813000	0.00610	CTG	C|0.756;G|0.244	0.756	strong		0.592	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
HLA-DQB1	3119	hgsc.bcm.edu	37	6	32632831	32632831	+	Missense_Mutation	SNP	G	G	C	rs111588946		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:32632831G>C	ENST00000399084.1	-	3	301	c.123C>G	c.(121-123)ttC>ttG	p.F41L	HLA-DQB1_ENST00000434651.2_Missense_Mutation_p.F41L|HLA-DQB1_ENST00000399079.3_Missense_Mutation_p.F41L|HLA-DQB1_ENST00000374943.4_Missense_Mutation_p.F41L|HLA-DQB1_ENST00000399082.3_Intron|XXbac-BPG254F23.6_ENST00000443574.1_RNA			P01920	DQB1_HUMAN	major histocompatibility complex, class II, DQ beta 1	41	Beta-1.		Y -> F (in allele DQB1*04:01, allele DQB1*04:02, allele DQB1*04:03, allele DQB1*06:02, allele DQB1*06:10, allele DQB1*06:13, allele DQB1*06:14, allele DQB1*06:15, allele DQB1*06:16, allele DQB1*06:19, allele DQB1*06:20, allele DQB1*06:22, allele DQB1*06:23, allele DQB1*06:24, allele DQB1*06:29, allele DQB1*06:33 and allele DQB1*06:37; dbSNP:rs9274407).|Y -> L (in allele DQB1*06:01 and allele DQB1*06:35; requires 2 nucleotide substitutions).		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|humoral immune response mediated by circulating immunoglobulin (GO:0002455)|immune response (GO:0006955)|immunoglobulin production involved in immunoglobulin mediated immune response (GO:0002381)|interferon-gamma-mediated signaling pathway (GO:0060333)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			breast(1)|large_intestine(1)|lung(1)|pancreas(1)	4					"""""""Insulin(DB00071)"""	CCTTAAACTGGAACACGAAAT	0.647									T-cell Lymphoma, (Cutaneous) , Familial Clustering of;Sjgren syndrome;Melanoma, Familial Clustering of;ACTH-independent macronodular adrenal hyperplasia																												p.F41L	Esophageal Squamous(151;720 1825 15000 40336 43415)	Atlas-SNP	.											.	HLA-DQB1	15	.	0			c.C123G						PASS	.						20.0	21.0	21.0					6																	32632831		2088	4185	6273	SO:0001583	missense	3119	exon2	Familial Cancer Database	incl.: Mycosis Fungoides, Sezary syndrome, Adult T-cell Lymphoma;Sjogren syndrome; ;AIMAH, Cushing disease, Adrenal, Familial	AAACTGGAACACG		CCDS43451.1, CCDS59006.1	6p21.3	2013-01-11			ENSG00000179344	ENSG00000179344		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4944	protein-coding gene	gene with protein product		604305		HLA-DQB			Standard	NM_001243962		Approved	IDDM1, CELIAC1	uc031snw.1	P01920	OTTHUMG00000031124	ENST00000399084.1:c.123C>G	6.37:g.32632831G>C	ENSP00000382034:p.Phe41Leu	Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	65	24	0.369231	NM_002123	A1KR27|A2RPH3|A4Q9R4|A4USG2|A4USG5|A6N8I7|A9YQA0|B0S7Y7|B1A0K6|B1GXI3|B3VLT3|B5BLN7|B7VU69|C0MQ34|C0MQ35|C8ZL52|C8ZLJ8|C8ZLJ9|C9DRQ3|O19708|O19713|O19724|O62861|O78046|O78221|O78223|O98034|O98201|P01917|P01918|P01919|P03992|P05537|P79482|P79526|P79544|P79551|Q08GC8|Q09035|Q0E4V9|Q1M312|Q29731|Q29877|Q29884|Q29915|Q29966|Q2P9N3|Q2QK85|Q30061|Q30075|Q30076|Q30080|Q30081|Q30082|Q30083|Q30084|Q30089|Q30095|Q31633|Q38I47|Q45UE3|Q4QZB5|Q53I44|Q564J6|Q5G841|Q5ISH1|Q5ISH3|Q5W1E1|Q5Y7G8|Q643R4|Q6B9X1|Q70VH8|Q7YP69|Q8HWH0|Q8MH58|Q8SNB4|Q8SND1|Q8SP70|Q8WMA3|Q9BD17|Q9MYH2|Q9TPA9|Q9XRY6|Q9XRY7|Q9XRZ2	Missense_Mutation	SNP	ENST00000399084.1	37	CCDS43451.1	.	.	.	.	.	.	.	.	.	.	.	6.750	0.507124	0.12883	.	.	ENSG00000179344	ENST00000399079;ENST00000374943;ENST00000434651;ENST00000399084	T;T;T;T	0.04758	3.56;3.56;3.56;3.56	4.13	3.23	0.37069	.	0.154608	0.26359	U	0.024831	T	0.01800	0.0057	L	0.52905	1.665	0.35375	D	0.789428	B;B;B	0.16166	0.016;0.0;0.0	B;B;B	0.04013	0.001;0.0;0.0	T	0.35773	-0.9775	10	0.19147	T	0.46	.	6.6967	0.23203	0.2157:0.0:0.7843:0.0	.	51;41;41	Q59F80;A2AAZ0;Q5Y7D6	.;.;.	L	41	ENSP00000382029:F41L;ENSP00000364080:F41L;ENSP00000407332:F41L;ENSP00000382034:F41L	ENSP00000364080:F41L	F	-	3	2	HLA-DQB1	32740809	0.000000	0.05858	0.071000	0.20095	0.019000	0.09904	0.055000	0.14229	2.161000	0.67846	0.305000	0.20034	TTC	T|1.000;|0.000	.	alt		0.647	HLA-DQB1-003	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276127.1	NM_002123	
PTPRF	5792	hgsc.bcm.edu	37	1	44086831	44086831	+	Silent	SNP	C	C	T	rs1143702	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:44086831C>T	ENST00000359947.4	+	33	5923	c.5583C>T	c.(5581-5583)taC>taT	p.Y1861Y	PTPRF_ENST00000372414.3_Silent_p.Y1861Y|PTPRF_ENST00000372413.3_Silent_p.Y1852Y|PTPRF_ENST00000496447.1_3'UTR|PTPRF_ENST00000422171.2_Silent_p.Y1220Y|PTPRF_ENST00000438120.1_Silent_p.Y1852Y	NM_002840.3	NP_002831.2	P10586	PTPRF_HUMAN	protein tyrosine phosphatase, receptor type, F	1861	Tyrosine-protein phosphatase 2. {ECO:0000255|PROSITE-ProRule:PRU00160}.				cell adhesion (GO:0007155)|cell migration (GO:0016477)|negative regulation of receptor binding (GO:1900121)|peptidyl-tyrosine dephosphorylation (GO:0035335)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	heparin binding (GO:0008201)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(2)|breast(4)|central_nervous_system(3)|endometrium(9)|kidney(4)|large_intestine(11)|liver(1)|lung(24)|ovary(4)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)	72	all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)				GCATGCGCTACGAGGGCGTGG	0.617													c|||	2857	0.570487	0.5507	0.5014	5008	,	,		22363	0.6855		0.6441	False		,,,				2504	0.4519				p.Y1861Y		Atlas-SNP	.											.	PTPRF	172	.	0			c.C5583T						PASS	.	T	,	2561,1845	634.9+/-396.3	749,1063,391	85.0	67.0	73.0		5583,5556	-9.5	0.2	1	dbSNP_86	73	5727,2873	672.1+/-402.9	1938,1851,511	no	coding-synonymous,coding-synonymous	PTPRF	NM_002840.3,NM_130440.2	,	2687,2914,902	TT,TC,CC		33.407,41.8747,36.2756	,	1861/1908,1852/1899	44086831	8288,4718	2203	4300	6503	SO:0001819	synonymous_variant	5792	exon33			GCGCTACGAGGGC	Y00815	CCDS489.2, CCDS490.2	1p34	2013-02-11			ENSG00000142949	ENSG00000142949		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	9670	protein-coding gene	gene with protein product		179590		LAR		7558042	Standard	NM_130440		Approved		uc001cjr.3	P10586	OTTHUMG00000007501	ENST00000359947.4:c.5583C>T	1.37:g.44086831C>T		Somatic	294	0	0		WXS	Illumina HiSeq	Phase_I	245	122	0.497959	NM_002840	D3DPX6|D3DPX7|Q5T021|Q5T022|Q5W9G2|Q86WS0	Silent	SNP	ENST00000359947.4	37	CCDS489.2	1276|1276	0.5842490842490843|0.5842490842490843	270|270	0.5487804878048781|0.5487804878048781	199|199	0.5497237569060773|0.5497237569060773	357|357	0.6241258741258742|0.6241258741258742	450|450	0.5936675461741425|0.5936675461741425	c|c	7.649|7.649	0.682443|0.682443	0.14907|0.14907	0.581253|0.581253	0.66593|0.66593	ENSG00000142949|ENSG00000142949	ENST00000412568;ENST00000414879|ENST00000429895	.|.	.|.	.|.	4.76|4.76	-9.52|-9.52	0.00578|0.00578	.|.	.|.	.|.	.|.	.|.	.|T	.|0.00012	.|0.0000	.|.	.|.	.|.	0.09310|0.09310	P|P	1.0|1.0	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.01202	.|-1.1420	.|3	.|.	.|.	.|.	.|.	15.3071|15.3071	0.74001|0.74001	0.0:0.3821:0.0:0.6179|0.0:0.3821:0.0:0.6179	rs1143702;rs7517450;rs17849120;rs1143702|rs1143702;rs7517450;rs17849120;rs1143702	.|.	.|.	.|.	X|M	1245;1286|1507	.|.	.|.	R|T	+|+	1|2	2|0	PTPRF|PTPRF	43859418|43859418	0.000000|0.000000	0.05858|0.05858	0.150000|0.150000	0.22450|0.22450	0.932000|0.932000	0.56968|0.56968	-2.838000|-2.838000	0.00739|0.00739	-2.452000|-2.452000	0.00542|0.00542	-2.203000|-2.203000	0.00303|0.00303	CGA|ACG	A|0.000;C|0.380;T|0.620	0.620	strong		0.617	PTPRF-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000019710.1		
GLRA3	8001	hgsc.bcm.edu	37	4	175598280	175598280	+	Silent	SNP	A	A	G	rs12648678	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:175598280A>G	ENST00000274093.3	-	7	1378	c.876T>C	c.(874-876)acT>acC	p.T292T	GLRA3_ENST00000340217.5_Silent_p.T292T	NM_006529.2	NP_006520.2	O75311	GLRA3_HUMAN	glycine receptor, alpha 3	292					ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	extracellular-glycine-gated chloride channel activity (GO:0016934)|glycine binding (GO:0016594)|transmitter-gated ion channel activity (GO:0022824)	p.T292T(1)		endometrium(2)|kidney(1)|large_intestine(12)|lung(11)|ovary(3)|prostate(1)|skin(3)|stomach(1)|urinary_tract(1)	35		Prostate(90;0.00601)|Breast(14;0.0091)|Melanoma(52;0.00959)|Renal(120;0.0183)|all_neural(102;0.0891)|all_hematologic(60;0.107)		all cancers(43;4.99e-18)|Epithelial(43;1.18e-16)|OV - Ovarian serous cystadenocarcinoma(60;5.88e-09)|STAD - Stomach adenocarcinoma(60;0.00442)|GBM - Glioblastoma multiforme(59;0.0102)|LUSC - Lung squamous cell carcinoma(193;0.0421)	Glycine(DB00145)|Ivermectin(DB00602)|Lindane(DB00431)	TCGTTAGCACAGTGGTTATCC	0.458													A|||	1084	0.216454	0.1589	0.2305	5008	,	,		17324	0.3651		0.1769	False		,,,				2504	0.1718				p.T292T		Atlas-SNP	.											GLRA3,NS,carcinoma,0,1	GLRA3	76	1	1	Substitution - coding silent(1)	stomach(1)	c.T876C						PASS	.	A	,	723,3683	297.3+/-284.7	60,603,1540	113.0	91.0	98.0		876,876	-8.1	0.9	4	dbSNP_120	98	1487,7113	282.8+/-295.8	117,1253,2930	no	coding-synonymous,coding-synonymous	GLRA3	NM_001042543.1,NM_006529.2	,	177,1856,4470	GG,GA,AA		17.2907,16.4094,16.9922	,	292/450,292/465	175598280	2210,10796	2203	4300	6503	SO:0001819	synonymous_variant	8001	exon7			TAGCACAGTGGTT	AF017724	CCDS3822.1, CCDS43283.1	4q34.1	2012-02-07			ENSG00000145451	ENSG00000145451		"""Ligand-gated ion channels / Glycine receptors"""	4328	protein-coding gene	gene with protein product		600421				9677400	Standard	NM_001042543		Approved		uc003ity.1	O75311	OTTHUMG00000149816	ENST00000274093.3:c.876T>C	4.37:g.175598280A>G		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	157	94	0.598726	NM_001042543	D3DP44|O75816|Q5D0E3	Silent	SNP	ENST00000274093.3	37	CCDS3822.1																																																																																			A|0.807;G|0.193	0.193	strong		0.458	GLRA3-001	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000313427.1		
CALCR	799	hgsc.bcm.edu	37	7	93116299	93116299	+	Missense_Mutation	SNP	A	A	G	rs2301680	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:93116299A>G	ENST00000359558.2	-	4	348	c.49T>C	c.(49-51)Tca>Cca	p.S17P	CALCR_ENST00000394441.1_5'UTR|MIR489_ENST00000384923.1_RNA|CALCR_ENST00000421592.1_5'UTR|CALCR_ENST00000426151.1_5'UTR|CALCR_ENST00000360249.4_5'UTR	NM_001164737.1	NP_001158209.1	P30988	CALCR_HUMAN	calcitonin receptor	17					adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|protein localization to plasma membrane (GO:0072659)|protein transport (GO:0015031)|receptor internalization (GO:0031623)|response to glucocorticoid (GO:0051384)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcitonin binding (GO:0032841)|calcitonin receptor activity (GO:0004948)|protein transporter activity (GO:0008565)|receptor activity (GO:0004872)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(27)|ovary(3)|pancreas(1)|skin(3)	45	all_cancers(62;3.18e-12)|all_epithelial(64;1.34e-11)|Breast(17;0.000675)|Lung NSC(181;0.207)		STAD - Stomach adenocarcinoma(171;0.000244)		Pramlintide(DB01278)|Salmon Calcitonin(DB00017)	CTCATTTTTGATTTTTGAAGA	0.299													G|||	2883	0.575679	0.643	0.3934	5008	,	,		17003	0.7103		0.4791	False		,,,				2504	0.5746				p.S17P		Atlas-SNP	.											CALCR_ENST00000359558,NS,malignant_melanoma,+1,3	CALCR	200	3	0			c.T49C						PASS	.	G	PRO/SER,,	2677,1727	507.3+/-366.6	834,1009,359	81.0	87.0	85.0		49,,	0.1	0.0	7	dbSNP_100	85	4341,4257	570.2+/-389.3	1119,2103,1077	yes	missense,utr-5,utr-5	CALCR	NM_001164737.1,NM_001164738.1,NM_001742.3	74,,	1953,3112,1436	GG,GA,AA		49.5115,39.2144,46.0237	,,	17/509,,	93116299	7018,5984	2202	4299	6501	SO:0001583	missense	799	exon4			TTTTTGATTTTTG	L00587	CCDS5631.1, CCDS55125.1	7q21.3	2012-08-10			ENSG00000004948	ENSG00000004948		"""GPCR / Class B : Calcitonin receptors"""	1440	protein-coding gene	gene with protein product		114131				1331173	Standard	NM_001742		Approved	CTR	uc003umw.2	P30988	OTTHUMG00000023599	ENST00000359558.2:c.49T>C	7.37:g.93116299A>G	ENSP00000352561:p.Ser17Pro	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	36	36	1	NM_001164737	A4D1G6|F5H605|O14585|Q13941|Q5ZGL8|Q659U6|Q6DJU8|Q6T712	Missense_Mutation	SNP	ENST00000359558.2	37	CCDS55125.1	1206	0.5521978021978022	304	0.6178861788617886	144	0.39779005524861877	401	0.701048951048951	357	0.470976253298153	G	0.013	-1.627601	0.00813	0.607856	0.504885	ENSG00000004948	ENST00000359558	T	0.48836	0.8	3.92	0.0933	0.14476	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.46954	P	7.399999999999629E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.43766	-0.9371	8	0.02654	T	1	.	4.1206	0.10104	0.4019:0.1716:0.4266:0.0	rs2301680;rs3181599;rs17788498;rs58492476;rs2301680	17	F5H605	.	P	17	ENSP00000352561:S17P	ENSP00000352561:S17P	S	-	1	0	CALCR	92954235	0.005000	0.15991	0.010000	0.14722	0.112000	0.19704	-0.320000	0.08028	-0.202000	0.10268	-1.758000	0.00672	TCA	A|0.450;G|0.550	0.550	strong		0.299	CALCR-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_001742	
NLRP7	199713	hgsc.bcm.edu	37	19	55451050	55451050	+	Silent	SNP	C	C	T	rs10418277	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:55451050C>T	ENST00000590030.1	-	3	1177	c.1137G>A	c.(1135-1137)aaG>aaA	p.K379K	NLRP7_ENST00000340844.2_Silent_p.K379K|NLRP7_ENST00000448121.2_Silent_p.K379K|NLRP7_ENST00000588756.1_Silent_p.K379K|NLRP7_ENST00000592784.1_Silent_p.K379K|NLRP7_ENST00000328092.5_Silent_p.K379K|NLRP7_ENST00000446217.1_Silent_p.K407K			Q8WX94	NALP7_HUMAN	NLR family, pyrin domain containing 7	379	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.						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)		GGTCCTCCCCCTTCTCCATCT	0.682													.|||	905	0.180711	0.0946	0.2507	5008	,	,		15597	0.1786		0.2217	False		,,,				2504	0.2076				p.K379K		Atlas-SNP	.											.	NLRP7	411	.	0			c.G1137A						PASS	.	C	,,	528,3872		38,452,1710	21.0	23.0	22.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1137,1137,1137	-2.5	0.0	19	dbSNP_119	22	1718,6880		196,1326,2777	no	coding-synonymous,coding-synonymous,coding-synonymous	NLRP7	NM_001127255.1,NM_139176.3,NM_206828.3	,,	234,1778,4487	TT,TC,CC		19.9814,12.0,17.2796	,,	379/1038,379/1010,379/981	55451050	2246,10752	2200	4299	6499	SO:0001819	synonymous_variant	199713	exon4			CTCCCCCTTCTCC	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.1137G>A	19.37:g.55451050C>T		Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	116	49	0.422414	NM_001127255	E9PE16|Q32MH8|Q7RTR1	Silent	SNP	ENST00000590030.1	37	CCDS33109.1																																																																																			.	.	weak		0.682	NLRP7-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000451396.1	NM_139176	
LY6K	54742	hgsc.bcm.edu	37	8	143783109	143783109	+	Silent	SNP	A	A	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:143783109A>G	ENST00000292430.6	+	2	612	c.195A>G	c.(193-195)ccA>ccG	p.P65P	LY6K_ENST00000518841.1_Silent_p.P65P|LY6K_ENST00000561179.1_Silent_p.P123P|LY6K_ENST00000519390.1_3'UTR|LY6K_ENST00000522591.1_Silent_p.P65P|LY6K_ENST00000519387.1_Silent_p.P65P|CTD-2292P10.4_ENST00000520572.1_RNA			Q17RY6	LY6K_HUMAN	lymphocyte antigen 6 complex, locus K	65	UPAR/Ly6.					anchored component of membrane (GO:0031225)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(2)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(4)	10	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)					GGACAGAGCCATACTGCGTTA	0.502																																					p.P65P		Atlas-SNP	.											.	LY6K	23	.	0			c.A195G						PASS	.						139.0	130.0	133.0					8																	143783109		2203	4300	6503	SO:0001819	synonymous_variant	54742	exon2			AGAGCCATACTGC	AK092545	CCDS6385.1, CCDS6385.2, CCDS59114.1	8q24.3	2009-08-06				ENSG00000160886			24225	protein-coding gene	gene with protein product	"""cancer/testis antigen 97"""	615093				12516096	Standard	NM_017527		Approved	HSJ001348, FLJ35226, CT97	uc011ljv.2	Q17RY6		ENST00000292430.6:c.195A>G	8.37:g.143783109A>G		Somatic	193	0	0		WXS	Illumina HiSeq	Phase_I	179	32	0.178771	NM_001160354	G3V116|O15227|Q9BVD7	Silent	SNP	ENST00000292430.6	37	CCDS6385.2	.	.	.	.	.	.	.	.	.	.	A	2.177	-0.388411	0.04932	.	.	ENSG00000160886	ENST00000522591	.	.	.	1.96	-3.92	0.04155	.	.	.	.	.	T	0.19406	0.0466	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.04029	-1.0983	4	.	.	.	.	2.3733	0.04336	0.2347:0.2455:0.4048:0.1149	.	.	.	.	R	84	.	.	H	+	2	0	LY6K	143780111	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.285000	0.00526	-4.514000	0.00045	-2.025000	0.00428	CAT	.	.	none		0.502	LY6K-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379893.2	NM_017527	
VPS53	55275	hgsc.bcm.edu	37	17	617869	617869	+	Silent	SNP	G	G	A	rs11558129	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:617869G>A	ENST00000571805.1	-	1	217	c.81C>T	c.(79-81)atC>atT	p.I27I	VPS53_ENST00000446250.2_5'UTR|VPS53_ENST00000574029.1_Silent_p.I27I|VPS53_ENST00000291074.5_Silent_p.I27I|VPS53_ENST00000437048.2_Silent_p.I27I|VPS53_ENST00000401468.3_Silent_p.I27I			Q5VIR6	VPS53_HUMAN	vacuolar protein sorting 53 homolog (S. cerevisiae)	27				I -> V (in Ref. 3; ABW03005). {ECO:0000305}.	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)		TTACCTGCTCGATGGCCAGCT	0.711													G|||	728	0.145367	0.0265	0.2435	5008	,	,		11887	0.0248		0.2356	False		,,,				2504	0.2679				p.I27I		Atlas-SNP	.											.	VPS53	109	.	0			c.C81T						PASS	.	G	,	240,4166	139.2+/-174.8	5,230,1968	56.0	57.0	57.0		81,81	0.7	1.0	17	dbSNP_120	57	2133,6467	361.9+/-332.5	268,1597,2435	no	coding-synonymous,coding-synonymous	VPS53	NM_001128159.2,NM_018289.3	,	273,1827,4403	AA,AG,GG		24.8023,5.4471,18.2454	,	27/833,27/671	617869	2373,10633	2203	4300	6503	SO:0001819	synonymous_variant	55275	exon1			CTGCTCGATGGCC		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.81C>T	17.37:g.617869G>A		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	92	45	0.48913	NM_001128159	A8K2S8|B3FH42|Q8WYW3|Q9BRR2|Q9BY02|Q9NV25	Silent	SNP	ENST00000571805.1	37																																																																																				G|0.785;T|0.003	.	strong		0.711	VPS53-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000436940.2	NM_018289	
MROH7	374977	hgsc.bcm.edu	37	1	55119144	55119144	+	Missense_Mutation	SNP	A	A	G	rs11206407	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:55119144A>G	ENST00000421030.2	+	3	830	c.545A>G	c.(544-546)cAt>cGt	p.H182R	MROH7_ENST00000395690.2_Missense_Mutation_p.H182R|MROH7_ENST00000409996.1_Intron|MROH7_ENST00000545244.1_Intron|MROH7_ENST00000339553.5_Missense_Mutation_p.H182R|MROH7-TTC4_ENST00000414150.2_Missense_Mutation_p.H182R|MROH7_ENST00000454855.2_Intron|MROH7_ENST00000472987.1_3'UTR	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	147	0	0		WXS	Illumina HiSeq	Phase_I	128	53	0.414062	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	
TMPRSS2	7113	hgsc.bcm.edu	37	21	42845374	42845374	+	Silent	SNP	G	G	A	rs2298659	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:42845374G>A	ENST00000332149.5	-	9	911	c.777C>T	c.(775-777)ggC>ggT	p.G259G	TMPRSS2_ENST00000458356.1_Silent_p.G259G|TMPRSS2_ENST00000398585.3_Silent_p.G296G	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	143	0	0		WXS	Illumina HiSeq	Phase_I	173	73	0.421965	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		
FBXO39	162517	hgsc.bcm.edu	37	17	6690161	6690161	+	Silent	SNP	C	C	T	rs17853331	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:6690161C>T	ENST00000321535.4	+	3	1216	c.1086C>T	c.(1084-1086)atC>atT	p.I362I		NM_153230.2	NP_694962.1	Q8N4B4	FBX39_HUMAN	F-box protein 39	362										NS(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(5)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	26						ACCTCCTCATCATATCCTGCA	0.463													C|||	1544	0.308307	0.1944	0.3026	5008	,	,		18317	0.5823		0.2038	False		,,,				2504	0.2914				p.I362I		Atlas-SNP	.											.	FBXO39	50	.	0			c.C1086T						PASS	.	C		844,3562	333.1+/-302.8	95,654,1454	110.0	97.0	102.0		1086	3.5	1.0	17	dbSNP_123	102	1817,6783	326.6+/-317.4	195,1427,2678	no	coding-synonymous	FBXO39	NM_153230.2		290,2081,4132	TT,TC,CC		21.1279,19.1557,20.4598		362/443	6690161	2661,10345	2203	4300	6503	SO:0001819	synonymous_variant	162517	exon3			CCTCATCATATCC	BC034782	CCDS11082.1	17p13.2	2014-01-21			ENSG00000177294	ENSG00000177294		"""F-boxes /  ""other"""""	28565	protein-coding gene	gene with protein product		609106				12477932	Standard	NM_153230		Approved	MGC35179, Fbx39, CT144	uc010vtg.2	Q8N4B4	OTTHUMG00000102062	ENST00000321535.4:c.1086C>T	17.37:g.6690161C>T		Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	151	81	0.536424	NM_153230		Silent	SNP	ENST00000321535.4	37	CCDS11082.1																																																																																			C|0.771;T|0.229	0.229	strong		0.463	FBXO39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219866.2	NM_153230	
NPBWR2	2832	hgsc.bcm.edu	37	20	62737888	62737888	+	Silent	SNP	G	G	A	rs41278242	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:62737888G>A	ENST00000369768.1	-	1	636	c.297C>T	c.(295-297)ccC>ccT	p.P99P		NM_005286.2	NP_005277.2	P48146	NPBW2_HUMAN	neuropeptides B/W receptor 2	99					G-protein coupled receptor signaling pathway (GO:0007186)|opioid receptor signaling pathway (GO:0038003)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	neuropeptide receptor activity (GO:0008188)|opioid receptor activity (GO:0004985)			haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(12)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18	all_cancers(38;2.58e-11)|all_epithelial(29;6.4e-13)|Lung NSC(23;1.25e-09)|all_lung(23;4.21e-09)					CGATGTTGACGGGCAGTACCA	0.592													g|||	73	0.0145767	0.0008	0.0288	5008	,	,		21006	0.001		0.0447	False		,,,				2504	0.0061				p.P99P		Atlas-SNP	.											NPBWR2,colon,carcinoma,0,1	NPBWR2	36	1	0			c.C297T						PASS	.	G		27,4375	32.6+/-62.9	0,27,2174	48.0	40.0	43.0		297	-7.8	0.0	20	dbSNP_127	43	313,8285	111.2+/-171.5	8,297,3994	no	coding-synonymous	NPBWR2	NM_005286.2		8,324,6168	AA,AG,GG		3.6404,0.6134,2.6154		99/334	62737888	340,12660	2201	4299	6500	SO:0001819	synonymous_variant	2832	exon1			GTTGACGGGCAGT	U22492	CCDS13557.1	20q13.3	2012-08-08	2006-02-15	2006-02-15	ENSG00000125522	ENSG00000125522		"""GPCR / Class A : Neuropeptide receptors : W/B"""	4530	protein-coding gene	gene with protein product		600731	"""G protein-coupled receptor 8"""	GPR8		12401809	Standard	NM_005286		Approved		uc011abt.2	P48146	OTTHUMG00000033032	ENST00000369768.1:c.297C>T	20.37:g.62737888G>A		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	48	24	0.5	NM_005286	Q6NWQ6|Q9H4K3	Silent	SNP	ENST00000369768.1	37	CCDS13557.1																																																																																			G|0.975;A|0.025	0.025	strong		0.592	NPBWR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080300.1	NM_005286	
UBXN2B	137886	hgsc.bcm.edu	37	8	59329496	59329496	+	Missense_Mutation	SNP	C	C	T	rs373559127	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:59329496C>T	ENST00000399598.2	+	2	294	c.172C>T	c.(172-174)Cgg>Tgg	p.R58W	UBXN2B_ENST00000522978.1_3'UTR	NM_001077619.1	NP_001071087.1	Q14CS0	UBX2B_HUMAN	UBX domain protein 2B	58						endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)				endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	13						CAAGAGCCCACGGACACCACC	0.333													C|||	2	0.000399361	0.0	0.0	5008	,	,		15290	0.0		0.0	False		,,,				2504	0.002				p.R58W		Atlas-SNP	.											UBXN2B,NS,carcinoma,-1,1	UBXN2B	36	1	0			c.C172T						PASS	.	C	TRP/ARG	0,3690		0,0,1845	87.0	75.0	79.0		172	2.4	1.0	8		79	1,8187		0,1,4093	no	missense	UBXN2B	NM_001077619.1	101	0,1,5938	TT,TC,CC		0.0122,0.0,0.0084	probably-damaging	58/332	59329496	1,11877	1845	4094	5939	SO:0001583	missense	137886	exon2			AGCCCACGGACAC	AK054658	CCDS43741.1	8q12.1	2008-08-08			ENSG00000215114	ENSG00000215114		"""UBX domain containing"""	27035	protein-coding gene	gene with protein product		610686				8619474, 9110174	Standard	NM_001077619		Approved	p37	uc003xtl.3	Q14CS0	OTTHUMG00000164300	ENST00000399598.2:c.172C>T	8.37:g.59329496C>T	ENSP00000382507:p.Arg58Trp	Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	41	14	0.341463	NM_001077619	B3KWZ3	Missense_Mutation	SNP	ENST00000399598.2	37	CCDS43741.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	18.49|18.49	3.635959|3.635959	0.67130|0.67130	0.0|0.0	1.22E-4|1.22E-4	ENSG00000215114|ENSG00000215114	ENST00000399598|ENST00000521796	T|.	0.48522|.	0.81|.	5.62|5.62	2.44|2.44	0.29823|0.29823	.|.	0.547615|.	0.14599|.	U|.	0.309721|.	T|T	0.49525|0.49525	0.1562|0.1562	L|L	0.54323|0.54323	1.7|1.7	0.29724|0.29724	N|N	0.838446|0.838446	D|.	0.71674|.	0.998|.	P|.	0.53185|.	0.72|.	T|T	0.47774|0.47774	-0.9091|-0.9091	10|5	0.72032|.	D|.	0.01|.	-12.2333|-12.2333	11.203|11.203	0.48751|0.48751	0.6042:0.3958:0.0:0.0|0.6042:0.3958:0.0:0.0	.|.	58|.	Q14CS0|.	UBX2B_HUMAN|.	W|M	58|3	ENSP00000382507:R58W|.	ENSP00000382507:R58W|.	R|T	+|+	1|2	2|0	UBXN2B|UBXN2B	59492050|59492050	1.000000|1.000000	0.71417|0.71417	0.995000|0.995000	0.50966|0.50966	0.995000|0.995000	0.86356|0.86356	0.723000|0.723000	0.25939|0.25939	0.670000|0.670000	0.31165|0.31165	0.563000|0.563000	0.77884|0.77884	CGG|ACG	.	.	weak		0.333	UBXN2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378184.1	NM_001077619	
DOCK8	81704	hgsc.bcm.edu	37	9	286593	286593	+	Missense_Mutation	SNP	C	C	A	rs529208	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:286593C>A	ENST00000453981.1	+	3	401	c.289C>A	c.(289-291)Cca>Aca	p.P97T	DOCK8_ENST00000469391.1_Missense_Mutation_p.P29T|DOCK8_ENST00000432829.2_Missense_Mutation_p.P29T			Q8NF50	DOCK8_HUMAN	dedicator of cytokinesis 8	97			P -> T (in dbSNP:rs529208). {ECO:0000269|Ref.1}.		blood coagulation (GO:0007596)|dendritic cell migration (GO:0036336)|immunological synapse formation (GO:0001771)|memory T cell proliferation (GO:0061485)|negative regulation of T cell apoptotic process (GO:0070233)|small GTPase mediated signal transduction (GO:0007264)	cell leading edge (GO:0031252)|cytosol (GO:0005829)|membrane (GO:0016020)	guanyl-nucleotide exchange factor activity (GO:0005085)			breast(1)|central_nervous_system(5)|endometrium(2)|kidney(6)|large_intestine(13)|lung(22)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	65		all_cancers(5;2.13e-17)|all_epithelial(5;2.15e-12)|all_lung(10;6.69e-11)|Lung NSC(10;1.08e-10)|Acute lymphoblastic leukemia(5;0.000242)|all_hematologic(5;0.00317)|Breast(48;0.0151)|Prostate(43;0.128)		all cancers(5;9.3e-07)|GBM - Glioblastoma multiforme(5;2.41e-06)|Epithelial(6;0.00557)|Lung(218;0.00942)		GGTGTTCACGCCAAAGGAATG	0.468													C|||	2653	0.529752	0.3918	0.5231	5008	,	,		18502	0.7212		0.4841	False		,,,				2504	0.5706				p.P97T		Atlas-SNP	.											.	DOCK8	401	.	0			c.C289A						PASS	.	C	THR/PRO,THR/PRO,THR/PRO	1825,2581	534.8+/-374.1	374,1077,752	142.0	124.0	130.0		85,85,289	4.6	0.4	9	dbSNP_83	130	4213,4387	570.7+/-389.4	1040,2133,1127	yes	missense,missense,missense	DOCK8	NM_001190458.1,NM_001193536.1,NM_203447.3	38,38,38	1414,3210,1879	AA,AC,CC		48.9884,41.4208,46.4247	benign,benign,benign	29/2000,29/2032,97/2100	286593	6038,6968	2203	4300	6503	SO:0001583	missense	81704	exon3			TTCACGCCAAAGG	AK090429	CCDS6440.1, CCDS6440.2, CCDS55283.1, CCDS55284.1	9p24.3	2014-09-17			ENSG00000107099	ENSG00000107099			19191	protein-coding gene	gene with protein product		611432				11214971	Standard	NM_203447		Approved	FLJ00026, FLJ00152, ZIR8, FLJ00346	uc003zgf.2	Q8NF50	OTTHUMG00000078789	ENST00000453981.1:c.289C>A	9.37:g.286593C>A	ENSP00000408464:p.Pro97Thr	Somatic	228	1	0.00438596		WXS	Illumina HiSeq	Phase_I	269	266	0.988848	NM_203447	A2A350|A2BDF2|A4FU78|B7ZLP0|E9PH09|Q3MV16|Q5JPJ1|Q8TEP1|Q8WUY2|Q9BYJ5|Q9H1Q2|Q9H1Q3|Q9H308|Q9H7P2	Missense_Mutation	SNP	ENST00000453981.1	37	CCDS6440.2	1145	0.5242673992673993	194	0.3943089430894309	184	0.5082872928176796	414	0.7237762237762237	353	0.4656992084432718	C	18.96	3.734202	0.69189	0.414208	0.489884	ENSG00000107099	ENST00000453981;ENST00000287364;ENST00000432829;ENST00000479404;ENST00000487230;ENST00000469391	T;T;T;T;T	0.51071	0.72;0.72;0.72;0.72;0.72	5.47	4.57	0.56435	.	0.139415	0.49916	D	0.000133	T	0.00012	0.0000	M	0.68593	2.085	0.25048	P	0.99115663	D;D;P	0.67145	0.996;0.964;0.576	D;P;P	0.72625	0.978;0.767;0.457	T	0.39502	-0.9611	9	0.56958	D	0.05	.	9.9931	0.41883	0.0:0.7899:0.1375:0.0726	rs529208;rs3209442;rs17407817;rs17664433;rs52797832;rs59297779;rs529208	29;97;97	E9PH09;A2A349;Q8NF50	.;.;DOCK8_HUMAN	T	97;97;29;29;29;29	ENSP00000408464:P97T;ENSP00000394888:P29T;ENSP00000417082:P29T;ENSP00000418318:P29T;ENSP00000419438:P29T	ENSP00000287364:P97T	P	+	1	0	DOCK8	276593	0.975000	0.34042	0.435000	0.26784	0.990000	0.78478	3.149000	0.50655	1.315000	0.45114	0.563000	0.77884	CCA	C|0.497;A|0.503	0.503	strong		0.468	DOCK8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171792.5	XM_036307	
PLG	5340	hgsc.bcm.edu	37	6	161139480	161139480	+	Silent	SNP	C	C	T	rs1130656	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:161139480C>T	ENST00000308192.9	+	8	1005	c.942C>T	c.(940-942)ttC>ttT	p.F314F		NM_000301.3	NP_000292.1	P00747	PLMN_HUMAN	plasminogen	314	Kringle 3. {ECO:0000255|PROSITE- ProRule:PRU00121}.				blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|fibrinolysis (GO:0042730)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-cell adhesion mediated by cadherin (GO:2000048)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of fibrinolysis (GO:0051918)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of fibrinolysis (GO:0051919)|tissue remodeling (GO:0048771)	blood microparticle (GO:0072562)|cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	apolipoprotein binding (GO:0034185)|protein domain specific binding (GO:0019904)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)	p.F314F(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(19)|ovary(1)|prostate(3)|skin(9)|upper_aerodigestive_tract(1)	59				OV - Ovarian serous cystadenocarcinoma(65;5.24e-17)|BRCA - Breast invasive adenocarcinoma(81;7.08e-06)	Alteplase(DB00009)|Aminocaproic Acid(DB00513)|Anistreplase(DB00029)|Aprotinin(DB06692)|Reteplase(DB00015)|Streptokinase(DB00086)|Tenecteplase(DB00031)|Tranexamic Acid(DB00302)|Urokinase(DB00013)	CAGAAAACTTCCCCTGCAAGT	0.493													T|||	1752	0.34984	0.2368	0.2824	5008	,	,		17527	0.4554		0.3897	False		,,,				2504	0.4008				p.F314F		Atlas-SNP	.											PLG,NS,carcinoma,0,1	PLG	150	1	1	Substitution - coding silent(1)	prostate(1)	c.C942T						PASS	.	T		1176,3230	711.8+/-408.0	161,854,1188	115.0	121.0	119.0		942	-7.0	0.9	6	dbSNP_86	119	3466,5134	634.2+/-398.8	711,2044,1545	no	coding-synonymous	PLG	NM_000301.3		872,2898,2733	TT,TC,CC		40.3023,26.6909,35.6912		314/811	161139480	4642,8364	2203	4300	6503	SO:0001819	synonymous_variant	5340	exon8			AAACTTCCCCTGC	M74220	CCDS5279.1, CCDS55074.1	6q26	2012-10-02			ENSG00000122194	ENSG00000122194			9071	protein-coding gene	gene with protein product		173350					Standard	NM_000301		Approved		uc003qtm.4	P00747	OTTHUMG00000015957	ENST00000308192.9:c.942C>T	6.37:g.161139480C>T		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	36	25	0.694444	NM_000301	Q15146|Q5TEH4|Q6PA00	Silent	SNP	ENST00000308192.9	37	CCDS5279.1																																																																																			C|0.636;T|0.364	0.364	strong		0.493	PLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042959.2	NM_000301	
GUCY2D	3000	hgsc.bcm.edu	37	17	7906519	7906519	+	Missense_Mutation	SNP	G	G	T	rs61749665	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	10	0	0		WXS	Illumina HiSeq	Phase_I	15	7	0.466667	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		
TRAF4	9618	hgsc.bcm.edu	37	17	27075423	27075423	+	Silent	SNP	C	C	T	rs2070265	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:27075423C>T	ENST00000262395.5	+	5	735	c.606C>T	c.(604-606)ttC>ttT	p.F202F	TRAF4_ENST00000262396.6_Intron|AC010761.10_ENST00000579468.1_RNA|AC010761.9_ENST00000577325.1_RNA|TRAF4_ENST00000444415.3_Silent_p.F202F	NM_004295.3	NP_004286.2	Q9BUZ4	TRAF4_HUMAN	TNF receptor-associated factor 4	202					activation of NF-kappaB-inducing kinase activity (GO:0007250)|apoptotic process (GO:0006915)|positive regulation of JNK cascade (GO:0046330)|positive regulation of protein homodimerization activity (GO:0090073)|positive regulation of protein kinase activity (GO:0045860)|regulation of apoptotic process (GO:0042981)|respiratory gaseous exchange (GO:0007585)|respiratory tube development (GO:0030323)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	DNA binding (GO:0003677)|thioesterase binding (GO:0031996)|tumor necrosis factor receptor binding (GO:0005164)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|WW domain binding (GO:0050699)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(2)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)	10	Lung NSC(42;0.01)		Epithelial(11;3.26e-05)|all cancers(11;0.000272)|OV - Ovarian serous cystadenocarcinoma(11;0.235)			CTAAGGAGTTCGTCTTTGACA	0.582													C|||	1049	0.209465	0.1415	0.2363	5008	,	,		21283	0.1786		0.1938	False		,,,				2504	0.3303				p.F202F		Atlas-SNP	.											.	TRAF4	20	.	0			c.C606T						PASS	.	C		662,3744	277.2+/-273.6	63,536,1604	78.0	60.0	66.0		606	-5.5	0.9	17	dbSNP_96	66	1695,6905	304.9+/-307.2	167,1361,2772	no	coding-synonymous	TRAF4	NM_004295.3		230,1897,4376	TT,TC,CC		19.7093,15.025,18.1224		202/471	27075423	2357,10649	2203	4300	6503	SO:0001819	synonymous_variant	9618	exon5			GGAGTTCGTCTTT	X80200	CCDS11243.1	17q11-q21.3	2013-01-09			ENSG00000076604	ENSG00000076604		"""RING-type (C3HC4) zinc fingers"""	12034	protein-coding gene	gene with protein product		602464				7592751, 7490069	Standard	NM_004295		Approved	CART1, MLN62, RNF83	uc002hcs.3	Q9BUZ4	OTTHUMG00000132677	ENST00000262395.5:c.606C>T	17.37:g.27075423C>T		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	89	88	0.988764	NM_004295	O75615|Q14848|Q2KJU4|Q2PJN8	Silent	SNP	ENST00000262395.5	37	CCDS11243.1																																																																																			C|0.813;T|0.187	0.187	strong		0.582	TRAF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255944.2	NM_145751	
ALPP	250	hgsc.bcm.edu	37	2	233243586	233243586	+	Missense_Mutation	SNP	C	C	T	rs1130335	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:233243586C>T	ENST00000392027.2	+	1	343	c.74C>T	c.(73-75)cCa>cTa	p.P25L	AC068134.8_ENST00000439072.1_RNA|AC068134.8_ENST00000441266.1_RNA	NM_001632.3	NP_001623.3	P05187	PPB1_HUMAN	alkaline phosphatase, placental	25			P -> L (in dbSNP:rs1130335). {ECO:0000269|PubMed:3001717, ECO:0000269|PubMed:3461452}.		dephosphorylation (GO:0016311)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alkaline phosphatase activity (GO:0004035)|magnesium ion binding (GO:0000287)|zinc ion binding (GO:0008270)			NS(1)|biliary_tract(1)|endometrium(1)|kidney(4)|large_intestine(2)|liver(1)|lung(10)|ovary(2)	22		all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0449)|Lung NSC(271;0.132)		Epithelial(121;4.45e-22)|Kidney(3;4.42e-11)|KIRC - Kidney renal clear cell carcinoma(3;1.9e-09)|BRCA - Breast invasive adenocarcinoma(100;0.000767)|Lung(119;0.00566)|LUSC - Lung squamous cell carcinoma(224;0.00746)|STAD - Stomach adenocarcinoma(3;0.0181)|GBM - Glioblastoma multiforme(43;0.196)		GGCATCATCCCAGGTAATGAG	0.642													C|||	423	0.0844649	0.025	0.0533	5008	,	,		16904	0.2153		0.0726	False		,,,				2504	0.0644				p.P25L		Atlas-SNP	.											.	ALPP	53	.	0			c.C74T						PASS	.	C	LEU/PRO	183,4223		4,175,2024	71.0	79.0	76.0		74	1.8	0.9	2	dbSNP_86	76	698,7902		32,634,3634	yes	missense	ALPP	NM_001632.3	98	36,809,5658	TT,TC,CC		8.1163,4.1534,6.7738	probably-damaging	25/536	233243586	881,12125	2203	4300	6503	SO:0001583	missense	250	exon1			TCATCCCAGGTAA	M14169	CCDS2490.1	2q37.1	2010-06-24	2010-06-24		ENSG00000163283	ENSG00000163283	3.1.3.1		439	protein-coding gene	gene with protein product	"""Regan isozyme"""	171800	"""alkaline phosphatase, placental (Regan isozyme)"""			3001717, 3461452	Standard	XM_005246439		Approved		uc002vsq.3	P05187	OTTHUMG00000133255	ENST00000392027.2:c.74C>T	2.37:g.233243586C>T	ENSP00000375881:p.Pro25Leu	Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	143	53	0.370629	NM_001632	P05188|P06861|Q53S78|Q96DB7	Missense_Mutation	SNP	ENST00000392027.2	37	CCDS2490.1	208	0.09523809523809523	14	0.028455284552845527	16	0.04419889502762431	121	0.21153846153846154	57	0.07519788918205805	.	14.18	2.459635	0.43736	0.041534	0.081163	ENSG00000163283	ENST00000392027	D	0.83673	-1.75	1.8	1.8	0.24995	Alkaline-phosphatase-like, core domain (1);	0.185016	0.47093	D	0.000260	T	0.00496	0.0016	M	0.86420	2.815	0.29546	P	0.8517250000000001	D	0.89917	1.0	D	0.80764	0.994	T	0.18713	-1.0328	9	0.62326	D	0.03	.	7.5124	0.27581	0.2567:0.7433:0.0:0.0	rs1130335;rs3189045;rs3748968;rs1130335	25	P05187	PPB1_HUMAN	L	25	ENSP00000375881:P25L	ENSP00000375881:P25L	P	+	2	0	ALPP	232951830	0.007000	0.16637	0.863000	0.33907	0.082000	0.17680	-0.094000	0.11094	1.299000	0.44798	0.313000	0.20887	CCA	C|1.000;|0.000	.	weak		0.642	ALPP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257032.3	NM_001632	
ARSD	414	hgsc.bcm.edu	37	X	2833638	2833638	+	Missense_Mutation	SNP	C	C	T	rs370769167		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:2833638C>T	ENST00000381154.1	-	6	1034	c.959G>A	c.(958-960)gGc>gAc	p.G320D	ARSD_ENST00000217890.6_5'UTR	NM_001669.3	NP_001660.2	P51689	ARSD_HUMAN	arylsulfatase D	320					cellular protein metabolic process (GO:0044267)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	arylsulfatase activity (GO:0004065)|metal ion binding (GO:0046872)			large_intestine(3)|lung(3)	6		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				ACCATATAAGCCATGCTGACT	0.507																																					p.G320D		Atlas-SNP	.											.	ARSD	47	.	0			c.G959A						PASS	.						231.0	156.0	181.0					X																	2833638		2203	4300	6503	SO:0001583	missense	414	exon6			TATAAGCCATGCT	X83572	CCDS35196.1	Xp22.3	2013-02-14			ENSG00000006756	ENSG00000006756		"""Arylsulfatase family"""	717	protein-coding gene	gene with protein product		300002				7720070	Standard	NM_001669		Approved		uc004cqy.3	P51689	OTTHUMG00000021077	ENST00000381154.1:c.959G>A	X.37:g.2833638C>T	ENSP00000370546:p.Gly320Asp	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	108	13	0.12037	NM_001669	Q9UHJ8	Missense_Mutation	SNP	ENST00000381154.1	37	CCDS35196.1	.	.	.	.	.	.	.	.	.	.	C	19.13	3.767977	0.69878	.	.	ENSG00000006756	ENST00000381154;ENST00000217890	D	0.93859	-3.3	3.68	3.68	0.42216	Alkaline phosphatase-like, alpha/beta/alpha (1);Sulfatase (1);Alkaline-phosphatase-like, core domain (1);	0.062472	0.64402	U	0.000005	D	0.96390	0.8822	M	0.81497	2.545	0.19775	P	0.9999576602	D;D	0.89917	1.0;0.999	D;D	0.80764	0.994;0.986	D	0.97757	1.0218	9	0.87932	D	0	.	14.8467	0.70264	0.0:1.0:0.0:0.0	.	320;320	E9PAW5;P51689	.;ARSD_HUMAN	D	320	ENSP00000370546:G320D	ENSP00000217890:G320D	G	-	2	0	ARSD	2843638	1.000000	0.71417	0.011000	0.14972	0.003000	0.03518	6.334000	0.72944	1.478000	0.48253	0.508000	0.49915	GGC	.	.	weak		0.507	ARSD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055636.1		
SNN	8303	hgsc.bcm.edu	37	16	11769948	11769948	+	Silent	SNP	C	C	T	rs1050068	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:11769948C>T	ENST00000329565.5	+	2	245	c.33C>T	c.(31-33)ggC>ggT	p.G11G	TXNDC11_ENST00000570917.1_5'Flank	NM_003498.5	NP_003489.1	O75324	SNN_HUMAN	stannin	11					response to abiotic stimulus (GO:0009628)|response to stress (GO:0006950)	integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)				endometrium(1)	1						CCACCACGGGCGTGGTCACAG	0.632													C|||	1235	0.246605	0.0363	0.2017	5008	,	,		17973	0.254		0.4672	False		,,,				2504	0.3282				p.G11G		Atlas-SNP	.											.	SNN	7	.	0			c.C33T						PASS	.	C		473,3921	221.7+/-238.7	30,413,1754	54.0	46.0	49.0		33	-11.0	0.1	16	dbSNP_86	49	4027,4573	553.9+/-386.4	903,2221,1176	yes	coding-synonymous	SNN	NM_003498.5		933,2634,2930	TT,TC,CC		46.8256,10.7647,34.6314		11/89	11769948	4500,8494	2197	4300	6497	SO:0001819	synonymous_variant	8303	exon2			CACGGGCGTGGTC	AF030196	CCDS10549.1	16p13	2008-02-05			ENSG00000184602	ENSG00000184602			11149	protein-coding gene	gene with protein product		603032				9657854	Standard	NM_003498		Approved		uc002dbf.3	O75324	OTTHUMG00000090535	ENST00000329565.5:c.33C>T	16.37:g.11769948C>T		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	37	36	0.972973	NM_003498	D3DUG4|Q6FGI0	Silent	SNP	ENST00000329565.5	37	CCDS10549.1																																																																																			C|0.695;T|0.305	0.305	strong		0.632	SNN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207059.1	NM_003498	
C9orf129	445577	hgsc.bcm.edu	37	9	96097669	96097669	+	Missense_Mutation	SNP	C	C	T	rs62572859	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:96097669C>T	ENST00000375419.1	-	3	715	c.352G>A	c.(352-354)Gga>Aga	p.G118R		NM_001098808.1	NP_001092278.1	Q5T035	CI129_HUMAN	chromosome 9 open reading frame 129	118										endometrium(2)|large_intestine(1)|lung(1)|ovary(2)	6						GTCGCCCCTCCGCTGCCCTCG	0.637													C|||	826	0.164936	0.3298	0.2205	5008	,	,		18223	0.0407		0.1402	False		,,,				2504	0.0562				p.G118R		Atlas-SNP	.											.	C9orf129	18	.	0			c.G352A						PASS	.						15.0	16.0	15.0					9																	96097669		2197	4266	6463	SO:0001583	missense	445577	exon3			CCCCTCCGCTGCC		CCDS43850.1	9q22.31	2012-04-02			ENSG00000204352	ENSG00000204352			31116	protein-coding gene	gene with protein product							Standard	NM_001098808		Approved	bA165J3.3	uc010mre.3	Q5T035	OTTHUMG00000020248	ENST00000375419.1:c.352G>A	9.37:g.96097669C>T	ENSP00000364568:p.Gly118Arg	Somatic	288	0	0		WXS	Illumina HiSeq	Phase_I	272	125	0.459559	NM_001098808		Missense_Mutation	SNP	ENST00000375419.1	37	CCDS43850.1	368	0.1684981684981685	161	0.32723577235772355	73	0.20165745856353592	33	0.057692307692307696	101	0.13324538258575197	C	15.21	2.766972	0.49574	.	.	ENSG00000204352	ENST00000375419	T	0.55760	0.5	2.56	2.56	0.30785	.	.	.	.	.	T	0.00012	0.0000	L	0.32530	0.975	0.29965	P	0.819016	D	0.89917	1.0	D	0.70716	0.97	T	0.31138	-0.9954	8	0.87932	D	0	.	13.5524	0.61740	0.0:1.0:0.0:0.0	rs62572859	118	Q5T035	CI129_HUMAN	R	118	ENSP00000364568:G118R	ENSP00000364568:G118R	G	-	1	0	C9orf129	95137490	1.000000	0.71417	0.991000	0.47740	0.388000	0.30384	5.833000	0.69349	1.438000	0.47492	0.298000	0.19748	GGA	C|0.500;T|0.500	0.500	weak		0.637	C9orf129-001	KNOWN	mRNA_end_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053147.1	NM_001098808	
Unknown	0	hgsc.bcm.edu	37	17	17326604	17326604	+	IGR	SNP	C	C	T	rs370938128|rs7225976	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:17326604C>T								NT5M (75629 upstream) : Y_RNA (37153 downstream)																							CATGATGGGGCAAATGCCAGA	0.473													T|||	2100	0.419329	0.7912	0.2651	5008	,	,		23244	0.1875		0.3201	False		,,,				2504	0.3671				p.A140V		Atlas-SNP	.											.	.	.	.	0			c.C419T						PASS	.																																			SO:0001628	intergenic_variant	140776	exon3			ATGGGGCAAATGC																													17.37:g.17326604C>T		Somatic	20	0	0		WXS	Illumina HiSeq	Phase_I	23	10	0.434783	NM_001243312		Missense_Mutation	SNP		37																																																																																				C|0.662;T|0.338	0.338	strong	0	0.473								
TBC1D29	26083	hgsc.bcm.edu	37	17	28890301	28890301	+	Missense_Mutation	SNP	G	G	A	rs80145926	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:28890301G>A	ENST00000580161.1	+	6	2808	c.311G>A	c.(310-312)aGc>aAc	p.S104N	TBC1D29_ENST00000579181.1_Missense_Mutation_p.S104N|RP11-218M11.1_ENST00000563063.1_lincRNA|TBC1D29_ENST00000584297.1_3'UTR			Q9UFV1	TBC29_HUMAN	TBC1 domain family, member 29	104							Rab GTPase activator activity (GO:0005097)	p.S104N(1)		breast(1)|kidney(1)|lung(3)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	9		Myeloproliferative disorder(56;0.0255)				TCAGAGAGCAGCAGAGGCCCC	0.587																																					p.S104N		Atlas-SNP	.											TBC1D29,NS,carcinoma,0,1	TBC1D29	19	1	1	Substitution - Missense(1)	prostate(1)	c.G311A						scavenged	.						48.0	45.0	46.0					17																	28890301		2203	4300	6503	SO:0001583	missense	26083	exon5			AGAGCAGCAGAGG	BC096718	CCDS32606.1	17q11.2	2014-09-04			ENSG00000266733	ENSG00000266733			24509	protein-coding gene	gene with protein product						12618308	Standard	XM_006721805		Approved	DKFZP434O047	uc002hfh.3	Q9UFV1	OTTHUMG00000178857	ENST00000580161.1:c.311G>A	17.37:g.28890301G>A	ENSP00000462799:p.Ser104Asn	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	116	10	0.0862069	NM_015594		Missense_Mutation	SNP	ENST00000580161.1	37	CCDS32606.1	.	.	.	.	.	.	.	.	.	.	.	9.179	1.023040	0.19433	.	.	ENSG00000197689	ENST00000329040	.	.	.	.	.	.	.	.	.	.	.	T	0.22820	0.0551	N	0.08118	0	0.18873	N	0.999983	B	0.33000	0.393	B	0.42319	0.383	T	0.34850	-0.9812	7	0.72032	D	0.01	.	5.89	0.18904	8.0E-4:0.0:0.9992:0.0	.	104	Q9UFV1	TBC29_HUMAN	N	104	.	ENSP00000330052:S104N	S	+	2	0	TBC1D29	25914427	0.966000	0.33281	0.071000	0.20095	0.071000	0.16799	-0.367000	0.07553	0.107000	0.17824	0.109000	0.15622	AGC	G|0.928;A|0.072	0.072	strong		0.587	TBC1D29-004	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000443632.1	NM_015594	
RUNDC3A	10900	hgsc.bcm.edu	37	17	42392622	42392622	+	Silent	SNP	T	T	C	rs708386	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:42392622T>C	ENST00000426726.3	+	7	1003	c.729T>C	c.(727-729)gaT>gaC	p.D243D	AC003102.3_ENST00000588097.1_RNA|RUNDC3A_ENST00000225441.7_Silent_p.D243D|RUNDC3A_ENST00000590941.1_Silent_p.D238D	NM_001144825.1	NP_001138297.1	Q59EK9	RUN3A_HUMAN	RUN domain containing 3A	243	Interaction with RAP2A. {ECO:0000250}.				positive regulation of cGMP biosynthetic process (GO:0030828)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	guanylate cyclase activator activity (GO:0030250)|small GTPase regulator activity (GO:0005083)			large_intestine(1)|lung(1)|ovary(2)	4		Prostate(33;0.0233)		BRCA - Breast invasive adenocarcinoma(366;0.189)		TCGTCACCGATGAGGACAGCT	0.682													C|||	3162	0.63139	0.711	0.5634	5008	,	,		10721	0.9097		0.3877	False		,,,				2504	0.5358				p.D243D	Pancreas(82;1061 1416 11136 20771 23901)	Atlas-SNP	.											.	RUNDC3A	30	.	0			c.T729C						PASS	.	C	,,	2366,1526		763,840,343	8.0	13.0	11.0		729,714,729	1.1	1.0	17	dbSNP_86	11	2711,5087		530,1651,1718	no	coding-synonymous,coding-synonymous,coding-synonymous	RUNDC3A	NM_001144825.1,NM_001144826.1,NM_006695.4	,,	1293,2491,2061	CC,CT,TT		34.7653,39.2086,43.4303	,,	243/447,238/401,243/406	42392622	5077,6613	1946	3899	5845	SO:0001819	synonymous_variant	10900	exon7			CACCGATGAGGAC	AF055026	CCDS45698.1, CCDS45699.1, CCDS59294.1	17q21.31	2008-02-05			ENSG00000108309	ENSG00000108309			16984	protein-coding gene	gene with protein product		605448				9523700	Standard	NM_006695		Approved	RPIP8, RAP2IP	uc002igl.4	Q59EK9	OTTHUMG00000169259	ENST00000426726.3:c.729T>C	17.37:g.42392622T>C		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	76	34	0.447368	NM_001144825	B2R974|O15483|O60651|Q7Z3S2|Q9UF50	Silent	SNP	ENST00000426726.3	37	CCDS45698.1																																																																																			T|0.367;C|0.633	0.633	strong		0.682	RUNDC3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403173.2	NM_006695	
LRRC56	115399	hgsc.bcm.edu	37	11	554047	554047	+	Missense_Mutation	SNP	G	G	A	rs12793222	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:554047G>A	ENST00000270115.7	+	14	1900	c.1400G>A	c.(1399-1401)cGg>cAg	p.R467Q		NM_198075.3	NP_932341.1	Q8IYG6	LRC56_HUMAN	leucine rich repeat containing 56	467			R -> Q (in dbSNP:rs12793222).							kidney(1)|lung(4)|skin(1)	6		all_cancers(49;2.16e-06)|all_epithelial(84;0.000256)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;7.63e-28)|Epithelial(43;7.29e-27)|OV - Ovarian serous cystadenocarcinoma(40;7.15e-21)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0375)|LUSC - Lung squamous cell carcinoma(625;0.0703)		AGCTCCCCGCGGTGGTCGACA	0.672													G|||	804	0.160543	0.2345	0.2522	5008	,	,		15719	0.0476		0.1918	False		,,,				2504	0.0798				p.R467Q		Atlas-SNP	.											.	LRRC56	23	.	0			c.G1400A						PASS	.	G	GLN/ARG	1047,3359	366.6+/-317.9	127,793,1283	68.0	72.0	71.0		1400	2.2	0.0	11	dbSNP_121	71	1871,6727	326.2+/-317.3	188,1495,2616	yes	missense	LRRC56	NM_198075.3	43	315,2288,3899	AA,AG,GG		21.7609,23.7631,22.4392	possibly-damaging	467/543	554047	2918,10086	2203	4299	6502	SO:0001583	missense	115399	exon14			CCCCGCGGTGGTC		CCDS7700.1	11p15.5	2005-10-18			ENSG00000161328	ENSG00000161328			25430	protein-coding gene	gene with protein product						12477932	Standard	NM_198075		Approved	FLJ00101, DKFZp761L1518	uc010qvz.2	Q8IYG6	OTTHUMG00000132003	ENST00000270115.7:c.1400G>A	11.37:g.554047G>A	ENSP00000270115:p.Arg467Gln	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	145	113	0.77931	NM_198075	Q8N3Q4	Missense_Mutation	SNP	ENST00000270115.7	37	CCDS7700.1	395	0.18086080586080586	124	0.25203252032520324	96	0.26519337016574585	35	0.06118881118881119	140	0.18469656992084432	G	10.68	1.419586	0.25552	0.237631	0.217609	ENSG00000161328	ENST00000270115	T	0.09163	3.01	3.14	2.23	0.28157	.	.	.	.	.	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	P	0.42871	0.792	B	0.31946	0.138	T	0.48433	-0.9036	8	0.20046	T	0.44	-29.9114	6.2194	0.20673	0.1395:0.0:0.8605:0.0	rs12793222;rs60751468	467	Q8IYG6	LRC56_HUMAN	Q	467	ENSP00000270115:R467Q	ENSP00000270115:R467Q	R	+	2	0	LRRC56	544047	0.101000	0.21875	0.008000	0.14137	0.004000	0.04260	0.300000	0.19156	0.897000	0.36392	0.561000	0.74099	CGG	G|0.781;A|0.219	0.219	strong		0.672	LRRC56-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254969.1	NM_198075	
PIK3AP1	118788	hgsc.bcm.edu	37	10	98469693	98469693	+	Missense_Mutation	SNP	C	C	T	rs17112076	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:98469693C>T	ENST00000339364.5	-	2	180	c.61G>A	c.(61-63)Gag>Aag	p.E21K		NM_152309.2	NP_689522.2	Q6ZUJ8	BCAP_HUMAN	phosphoinositide-3-kinase adaptor protein 1	21	Necessary and sufficent to mediate inhibition of NF-kappa-B downstream of activated TLRs; may mediate interaction with MYD88 and TIRAP. {ECO:0000250}.		E -> K (in dbSNP:rs17112076). {ECO:0000269|PubMed:14702039}.		negative regulation of toll-like receptor signaling pathway (GO:0034122)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of toll-like receptor signaling pathway (GO:0034123)|regulation of inflammatory response (GO:0050727)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 7 signaling pathway (GO:0034154)|toll-like receptor 9 signaling pathway (GO:0034162)	cytosol (GO:0005829)|membrane (GO:0016020)|plasma membrane (GO:0005886)	phosphatidylinositol 3-kinase regulatory subunit binding (GO:0036312)			NS(1)|autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(27)|ovary(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(4)	52		Colorectal(252;0.0442)		Epithelial(162;6.29e-08)|all cancers(201;3.18e-06)		CACCATTCCTCGGCATCCGGG	0.602													C|||	628	0.125399	0.0159	0.1037	5008	,	,		18392	0.2292		0.1799	False		,,,				2504	0.1258				p.E21K		Atlas-SNP	.											PIK3AP1,NS,carcinoma,0,1	PIK3AP1	111	1	0			c.G61A						PASS	.	C	LYS/GLU	198,4200		3,192,2004	58.0	50.0	53.0		61	-1.7	0.1	10	dbSNP_123	53	1477,7119		146,1185,2967	yes	missense	PIK3AP1	NM_152309.2	56	149,1377,4971	TT,TC,CC		17.1824,4.502,12.8906	benign	21/806	98469693	1675,11319	2199	4298	6497	SO:0001583	missense	118788	exon2			ATTCCTCGGCATC	AK092883	CCDS31259.1	10q24.2	2008-10-23			ENSG00000155629	ENSG00000155629			30034	protein-coding gene	gene with protein product		607942				1251844, 11163197	Standard	NM_152309		Approved	BCAP, FLJ35564	uc001kmq.3	Q6ZUJ8	OTTHUMG00000018838	ENST00000339364.5:c.61G>A	10.37:g.98469693C>T	ENSP00000339826:p.Glu21Lys	Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	137	72	0.525547	NM_152309	Q5TB56|Q5VXJ9|Q8N6J6|Q8NAC8	Missense_Mutation	SNP	ENST00000339364.5	37	CCDS31259.1	349	0.15979853479853479	18	0.036585365853658534	39	0.10773480662983426	164	0.2867132867132867	128	0.16886543535620052	C	7.774	0.708104	0.15239	0.04502	0.171824	ENSG00000155629	ENST00000339364	T	0.21031	2.03	5.15	-1.72	0.08107	.	0.946473	0.08917	N	0.875016	T	0.00012	0.0000	L	0.47190	1.495	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.43245	-0.9403	9	0.35671	T	0.21	-5.3405	5.7782	0.18292	0.0:0.4428:0.2566:0.3007	rs17112076;rs56647724;rs61136215;rs17112076	21	Q6ZUJ8	BCAP_HUMAN	K	21	ENSP00000339826:E21K	ENSP00000339826:E21K	E	-	1	0	PIK3AP1	98459683	0.000000	0.05858	0.135000	0.22099	0.907000	0.53573	-1.428000	0.02439	0.001000	0.14605	-1.114000	0.02060	GAG	C|0.852;T|0.148	0.148	strong		0.602	PIK3AP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049619.2	NM_152309	
DOCK10	55619	hgsc.bcm.edu	37	2	225670845	225670845	+	Missense_Mutation	SNP	G	G	T	rs375740801		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:225670845G>T	ENST00000258390.7	-	34	3879	c.3812C>A	c.(3811-3813)gCa>gAa	p.A1271E	DOCK10_ENST00000409592.3_Missense_Mutation_p.A1265E	NM_014689.2	NP_055504.2	Q96BY6	DOC10_HUMAN	dedicator of cytokinesis 10	1271					regulation of cell migration (GO:0030334)|small GTPase mediated signal transduction (GO:0007264)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(3)|cervix(1)|endometrium(6)|kidney(10)|large_intestine(16)|lung(40)|ovary(2)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	87		Renal(207;0.0113)|all_lung(227;0.0486)|Lung NSC(271;0.0653)|all_hematologic(139;0.14)		Epithelial(121;2.37e-10)|all cancers(144;2.26e-07)|Lung(261;0.0143)|LUSC - Lung squamous cell carcinoma(224;0.0178)		TCAAGTACCTGCTATGGAATT	0.343																																					p.A1271E		Atlas-SNP	.											.	DOCK10	308	.	0			c.C3812A						PASS	.	G	GLU/ALA	0,3708		0,0,1854	104.0	103.0	103.0		3812	6.0	1.0	2		103	3,8181		0,3,4089	no	missense	DOCK10	NM_014689.2	107	0,3,5943	TT,TG,GG		0.0367,0.0,0.0252	benign	1271/2187	225670845	3,11889	1854	4092	5946	SO:0001583	missense	55619	exon34			GTACCTGCTATGG	AB014594	CCDS46528.1, CCDS74661.1	2q36.3	2013-01-10			ENSG00000135905	ENSG00000135905		"""Pleckstrin homology (PH) domain containing"""	23479	protein-coding gene	gene with protein product	"""zizimin3"""	611518				12432077	Standard	NM_014689		Approved	ZIZ3, KIAA0694	uc010fwz.1	Q96BY6	OTTHUMG00000153428	ENST00000258390.7:c.3812C>A	2.37:g.225670845G>T	ENSP00000258390:p.Ala1271Glu	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	99	46	0.464646	NM_014689	B3FL70|O75178|Q9NW06|Q9NXI8	Missense_Mutation	SNP	ENST00000258390.7	37	CCDS46528.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	25.3|25.3	4.622605|4.622605	0.87460|0.87460	0.0|0.0	3.67E-4|3.67E-4	ENSG00000135905|ENSG00000135905	ENST00000409592;ENST00000258390|ENST00000422684	T;T|.	0.21361|.	3.53;2.01|.	5.96|5.96	5.96|5.96	0.96718|0.96718	.|.	0.049031|.	0.85682|.	D|.	0.000000|.	T|T	0.72653|0.72653	0.3487|0.3487	L|L	0.53249|0.53249	1.67|1.67	0.58432|0.58432	D|D	0.999996|0.999996	D;P;P|.	0.59767|.	0.986;0.799;0.745|.	P;B;B|.	0.55455|.	0.776;0.343;0.276|.	T|T	0.67051|0.67051	-0.5768|-0.5768	10|5	0.45353|.	T|.	0.12|.	.|.	20.4008|20.4008	0.98991|0.98991	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	1271;134;1265|.	Q96BY6;B4DF07;B3FL70|.	DOC10_HUMAN;.;.|.	E|K	1265;1271|162	ENSP00000386694:A1265E;ENSP00000258390:A1271E|.	ENSP00000258390:A1271E|.	A|Q	-|-	2|1	0|0	DOCK10|DOCK10	225379089|225379089	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	8.442000|8.442000	0.90317|0.90317	2.826000|2.826000	0.97356|0.97356	0.655000|0.655000	0.94253|0.94253	GCA|CAG	.	.	weak		0.343	DOCK10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331246.1		
LRP3	4037	hgsc.bcm.edu	37	19	33696647	33696647	+	Missense_Mutation	SNP	C	C	T	rs368108554		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:33696647C>T	ENST00000253193.7	+	5	1173	c.971C>T	c.(970-972)aCg>aTg	p.T324M	CTD-2540B15.13_ENST00000609744.1_RNA	NM_002333.3	NP_002324.2	O75074	LRP3_HUMAN	low density lipoprotein receptor-related protein 3	324	CUB 2. {ECO:0000255|PROSITE- ProRule:PRU00059}.				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)					CTGCTGCAGACGCTGTCCTAC	0.736																																					p.T324M		Atlas-SNP	.											.	LRP3	46	.	0			c.C971T						PASS	.	C	MET/THR	0,4284		0,0,2142	8.0	12.0	10.0		971	5.0	1.0	19		10	1,8407		0,1,4203	no	missense	LRP3	NM_002333.3	81	0,1,6345	TT,TC,CC		0.0119,0.0,0.0079	probably-damaging	324/771	33696647	1,12691	2142	4204	6346	SO:0001583	missense	4037	exon5			TGCAGACGCTGTC	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.971C>T	19.37:g.33696647C>T	ENSP00000253193:p.Thr324Met	Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	36	15	0.416667	NM_002333	B3KQD6|B4DKF2	Missense_Mutation	SNP	ENST00000253193.7	37	CCDS12430.1	.	.	.	.	.	.	.	.	.	.	C	15.91	2.972764	0.53614	0.0	1.19E-4	ENSG00000130881	ENST00000431491;ENST00000253193	D	0.87334	-2.24	5.02	5.02	0.67125	CUB (5);	0.218511	0.42548	D	0.000688	D	0.92113	0.7500	M	0.63843	1.955	0.40643	D	0.981969	D;D;D	0.89917	0.999;1.0;0.999	D;D;D	0.70935	0.96;0.971;0.96	D	0.92597	0.6088	10	0.51188	T	0.08	-22.6449	17.3303	0.87261	0.0:1.0:0.0:0.0	.	198;324;242	C9J8W0;O75074;B7ZAJ9	.;LRP3_HUMAN;.	M	198;324	ENSP00000253193:T324M	ENSP00000253193:T324M	T	+	2	0	LRP3	38388487	0.906000	0.30813	0.994000	0.49952	0.732000	0.41865	2.288000	0.43514	2.341000	0.79615	0.313000	0.20887	ACG	.	.	weak		0.736	LRP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450842.4		
CACNA1C	775	hgsc.bcm.edu	37	12	2224511	2224511	+	Silent	SNP	C	C	T	rs34419050	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:2224511C>T	ENST00000347598.4	+	2	171	c.171C>T	c.(169-171)gaC>gaT	p.D57D	CACNA1C_ENST00000335762.5_Silent_p.D57D|CACNA1C_ENST00000399621.1_Silent_p.D57D|CACNA1C_ENST00000399617.1_Silent_p.D57D|CACNA1C_ENST00000399644.1_Silent_p.D57D|CACNA1C_ENST00000399634.1_Silent_p.D57D|CACNA1C_ENST00000399603.1_Silent_p.D57D|CACNA1C_ENST00000399649.1_Silent_p.D57D|CACNA1C_ENST00000327702.7_Silent_p.D57D|CACNA1C_ENST00000399655.1_Silent_p.D57D|CACNA1C_ENST00000406454.3_Silent_p.D57D|CACNA1C_ENST00000399637.1_Silent_p.D57D|CACNA1C_ENST00000399591.1_Silent_p.D57D|CACNA1C_ENST00000399641.1_Silent_p.D57D|CACNA1C_ENST00000399606.1_Silent_p.D57D|CACNA1C_ENST00000480911.1_Silent_p.D57D|CACNA1C_ENST00000399601.1_Silent_p.D57D|CACNA1C_ENST00000399629.1_Silent_p.D57D|CACNA1C_ENST00000402845.3_Silent_p.D57D|CACNA1C_ENST00000344100.3_Silent_p.D57D|CACNA1C_ENST00000399638.1_Silent_p.D57D|CACNA1C_ENST00000399595.1_Silent_p.D57D|CACNA1C_ENST00000399597.1_Silent_p.D57D	NM_001129827.1|NM_199460.2	NP_001123299.1|NP_955630.2	Q13936	CAC1C_HUMAN	calcium channel, voltage-dependent, L type, alpha 1C subunit	57					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)	CGGCCATCGACGCAGCCCGGC	0.672													C|||	59	0.0117812	0.0	0.0072	5008	,	,		13235	0.001		0.0229	False		,,,				2504	0.0307				p.D57D		Atlas-SNP	.											.	CACNA1C	1023	.	0			c.C171T						PASS	.	C	,,,,,,,,,,,,,,,,,,,,,,	19,4129		0,19,2055	8.0	11.0	10.0		171,171,171,171,171,171,171,171,171,171,171,171,171,171,171,171,171,171,171,171,171,171,171	-4.4	1.0	12	dbSNP_126	10	196,8134		0,196,3969	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	,,,,,,,,,,,,,,,,,,,,,,	0,215,6024	TT,TC,CC		2.3529,0.4581,1.723	,,,,,,,,,,,,,,,,,,,,,,	57/2139,57/2187,57/2180,57/2174,57/2167,57/2159,57/2158,57/2158,57/2158,57/2156,57/2147,57/2147,57/2145,57/2139,57/2139,57/2139,57/2139,57/2136,57/2128,57/2139,57/2174,57/2199,57/2222	2224511	215,12263	2074	4165	6239	SO:0001819	synonymous_variant	775	exon2			CATCGACGCAGCC	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.171C>T	12.37:g.2224511C>T		Somatic	20	0	0		WXS	Illumina HiSeq	Phase_I	19	9	0.473684	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|0.990;T|0.010	0.010	strong		0.672	CACNA1C-017	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317035.1	NM_000719	
CUL9	23113	hgsc.bcm.edu	37	6	43188940	43188940	+	Silent	SNP	C	C	T	rs6917902	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:43188940C>T	ENST00000252050.4	+	34	6717	c.6633C>T	c.(6631-6633)gaC>gaT	p.D2211D	CUL9_ENST00000354495.3_Silent_p.D2101D|RP3-330M21.5_ENST00000500590.1_RNA|CUL9_ENST00000372647.2_Silent_p.D2183D	NM_015089.2	NP_055904.1	Q8IWT3	CUL9_HUMAN	cullin 9	2211					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						AGTGGGTCGACGACGGTGGCT	0.617													T|||	1038	0.207268	0.4947	0.1686	5008	,	,		19497	0.0179		0.1342	False		,,,				2504	0.1166				p.D2211D		Atlas-SNP	.											.	CUL9	248	.	0			c.C6633T						PASS	.	T		2014,2392	613.0+/-392.1	464,1086,653	110.0	76.0	87.0		6633	-7.4	0.0	6	dbSNP_116	87	1463,7137	750.1+/-407.4	108,1247,2945	no	coding-synonymous	CUL9	NM_015089.2		572,2333,3598	TT,TC,CC		17.0116,45.7104,26.7338		2211/2518	43188940	3477,9529	2203	4300	6503	SO:0001819	synonymous_variant	23113	exon34			GGTCGACGACGGT	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.6633C>T	6.37:g.43188940C>T		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	151	70	0.463576	NM_015089	O75188|Q5TCY3|Q68CP2|Q68D92|Q8N3W9|Q9BU56	Silent	SNP	ENST00000252050.4	37	CCDS4890.1																																																																																			C|0.767;T|0.233	0.233	strong		0.617	CUL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040582.2	NM_015089	
CNOT1	23019	hgsc.bcm.edu	37	16	58575489	58575489	+	Silent	SNP	G	G	A	rs11540994	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:58575489G>A	ENST00000317147.5	-	34	5048	c.4716C>T	c.(4714-4716)taC>taT	p.Y1572Y	CNOT1_ENST00000569240.1_Silent_p.Y1567Y|CNOT1_ENST00000245138.4_Silent_p.Y423Y	NM_001265612.1|NM_016284.4	NP_001252541.1|NP_057368.3	A5YKK6	CNOT1_HUMAN	CCR4-NOT transcription complex, subunit 1	1572	Interaction with CNOT6, CNOT6L, CNOT7 and CNOT8.				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)		CAAACTCTTCGTAAACAGCCA	0.398													G|||	2430	0.485224	0.6687	0.2983	5008	,	,		18050	0.5704		0.3211	False		,,,				2504	0.4509				p.Y1572Y		Atlas-SNP	.											.	CNOT1	359	.	0			c.C4716T						PASS	.	G		2658,1738	646.7+/-398.4	835,988,375	106.0	101.0	103.0		4716	3.7	1.0	16	dbSNP_120	103	2516,6084	411.9+/-350.6	380,1756,2164	no	coding-synonymous	CNOT1	NM_016284.3		1215,2744,2539	AA,AG,GG		29.2558,39.5359,39.8122		1572/2377	58575489	5174,7822	2198	4300	6498	SO:0001819	synonymous_variant	23019	exon34			CTCTTCGTAAACA	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.4716C>T	16.37:g.58575489G>A		Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	168	168	1	NM_016284	Q68DX7|Q7Z3K2|Q8IWB8|Q8TB53|Q9BVZ6|Q9UFR8|Q9UI27|Q9Y2L0	Silent	SNP	ENST00000317147.5	37	CCDS10799.1																																																																																			G|0.584;A|0.416	0.416	strong		0.398	CNOT1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257385.3	NM_016284	
CNTN6	27255	hgsc.bcm.edu	37	3	1424745	1424745	+	Silent	SNP	C	C	T	rs4684146	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:1424745C>T	ENST00000446702.2	+	18	2913	c.2286C>T	c.(2284-2286)gtC>gtT	p.V762V	CNTN6_ENST00000539053.1_Silent_p.V690V|CNTN6_ENST00000350110.2_Silent_p.V762V			Q9UQ52	CNTN6_HUMAN	contactin 6	762	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|central nervous system development (GO:0007417)|Notch signaling pathway (GO:0007219)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)				breast(6)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(25)|lung(34)|ovary(1)|pancreas(1)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	90		all_cancers(2;0.000164)|all_epithelial(2;0.107)		Epithelial(13;0.000233)|all cancers(10;0.0013)|OV - Ovarian serous cystadenocarcinoma(96;0.0139)		CAAGGTTTGTCTACAGAAATG	0.453													T|||	767	0.153155	0.2284	0.1744	5008	,	,		18026	0.0645		0.1571	False		,,,				2504	0.1237				p.V762V		Atlas-SNP	.											.	CNTN6	245	.	0			c.C2286T						PASS	.	T		1017,3389	728.8+/-410.0	124,769,1310	163.0	150.0	154.0		2286	-9.5	0.0	3	dbSNP_111	154	1606,6994	743.2+/-407.2	171,1264,2865	no	coding-synonymous	CNTN6	NM_014461.2		295,2033,4175	TT,TC,CC		18.6744,23.0822,20.1676		762/1029	1424745	2623,10383	2203	4300	6503	SO:0001819	synonymous_variant	27255	exon18			GTTTGTCTACAGA	AB003592	CCDS2557.1	3p26-p25	2013-02-11			ENSG00000134115	ENSG00000134115		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	2176	protein-coding gene	gene with protein product	"""neural adhesion molecule"""	607220				9486763	Standard	NM_014461		Approved	NB-3	uc003bpa.3	Q9UQ52	OTTHUMG00000119030	ENST00000446702.2:c.2286C>T	3.37:g.1424745C>T		Somatic	245	0	0		WXS	Illumina HiSeq	Phase_I	195	69	0.353846	NM_014461	Q2KHM2	Silent	SNP	ENST00000446702.2	37	CCDS2557.1																																																																																			C|0.816;T|0.184	0.184	strong		0.453	CNTN6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239235.2	NM_014461	
DDX53	168400	hgsc.bcm.edu	37	X	23019346	23019346	+	Missense_Mutation	SNP	G	G	T	rs5926203	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:23019346G>T	ENST00000327968.5	+	1	1260	c.1172G>T	c.(1171-1173)aGg>aTg	p.R391M	RP11-40F8.2_ENST00000455399.1_lincRNA	NM_182699.3	NP_874358.2	Q86TM3	DDX53_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 53	391	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.		R -> M (in dbSNP:rs5926203).			nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|RNA binding (GO:0003723)			breast(2)|endometrium(5)|kidney(4)|large_intestine(3)|lung(15)|ovary(1)|prostate(1)|skin(2)|urinary_tract(2)	35						CCCCAGATAAGGAAGATTTTA	0.393													T|||	1286	0.340662	0.4902	0.0793	3775	,	,		15013	0.2073		0.0915	False		,,,				2504	0.2883				p.R391M		Atlas-SNP	.											.	DDX53	76	.	0			c.G1172T						PASS	.	T	MET/ARG	2088,1747		490,813,295,329,276	140.0	140.0	140.0		1172	-2.1	0.0	X	dbSNP_114	140	818,5910		30,511,247,1887,1625	yes	missense	DDX53	NM_182699.3	91	520,1324,542,2216,1901	TT,TG,T,GG,G		12.1581,45.5541,27.5111	benign	391/632	23019346	2906,7657	2203	4300	6503	SO:0001583	missense	168400	exon1			AGATAAGGAAGAT	AY039237	CCDS35214.1	Xp22.13	2009-03-25			ENSG00000184735	ENSG00000184735		"""DEAD-boxes"""	20083	protein-coding gene	gene with protein product	"""cancer associated gene"", ""cancer/testis antigen 26"""						Standard	NM_182699		Approved	CAGE, CT26	uc004daj.3	Q86TM3	OTTHUMG00000021248	ENST00000327968.5:c.1172G>T	X.37:g.23019346G>T	ENSP00000368667:p.Arg391Met	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	59	59	1	NM_182699	Q0D2N2|Q6NVV4	Missense_Mutation	SNP	ENST00000327968.5	37	CCDS35214.1	444	0.26763110307414106	164	0.4823529411764706	22	0.06321839080459771	69	0.13745019920318724	52	0.07222222222222222	T	0.455	-0.892045	0.02491	0.544459	0.121581	ENSG00000184735	ENST00000327968	T	0.16196	2.36	4.03	-2.07	0.07276	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.081576	0.85682	N	0.000000	T	0.00012	0.0000	M	0.77313	2.365	0.39580	P	0.030571000000000015	B	0.02656	0.0	B	0.06405	0.002	T	0.48536	-0.9027	9	0.19590	T	0.45	-18.4477	1.365	0.02200	0.2516:0.0862:0.2724:0.3898	rs5926203;rs7065007;rs52811818;rs59571064;rs5926203	391	Q86TM3	DDX53_HUMAN	M	391	ENSP00000368667:R391M	ENSP00000368667:R391M	R	+	2	0	DDX53	22929267	1.000000	0.71417	0.002000	0.10522	0.397000	0.30659	0.907000	0.28531	-1.338000	0.02233	-1.228000	0.01579	AGG	G|0.686;0|0.012	.	strong		0.393	DDX53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056043.1	NM_182699	
ARHGEF28	64283	hgsc.bcm.edu	37	5	73181913	73181913	+	Silent	SNP	T	T	C	rs61734875	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:73181913T>C	ENST00000426542.2	+	24	3314	c.3294T>C	c.(3292-3294)gcT>gcC	p.A1098A	ARHGEF28_ENST00000512883.1_Silent_p.A62A|ARHGEF28_ENST00000296794.6_Silent_p.A1098A|ARHGEF28_ENST00000287898.5_Silent_p.A1098A|ARHGEF28_ENST00000513042.2_Silent_p.A1098A|ARHGEF28_ENST00000296799.4_Silent_p.A785A|ARHGEF28_ENST00000545377.1_Silent_p.A1098A|ARHGEF28_ENST00000437974.1_Silent_p.A1098A			Q8N1W1	ARG28_HUMAN	Rho guanine nucleotide exchange factor (GEF) 28	1098	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				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)										GGAAAACTGCTACAGGTCGTT	0.393													T|||	82	0.0163738	0.0	0.0187	5008	,	,		18831	0.001		0.0586	False		,,,				2504	0.0092				p.A1098A		Atlas-SNP	.											.	.	.	.	0			c.T3294C						PASS	.	T	,	23,3789		0,23,1883	94.0	95.0	95.0		3294,3294	-11.8	0.0	5	dbSNP_129	95	440,7812		9,422,3695	no	coding-synonymous,coding-synonymous	RGNEF	NM_001080479.2,NM_001177693.1	,	9,445,5578	CC,CT,TT		5.332,0.6034,3.8379	,	1098/1732,1098/1706	73181913	463,11601	1906	4126	6032	SO:0001819	synonymous_variant	64283	exon25			AACTGCTACAGGT		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.3294T>C	5.37:g.73181913T>C		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	121	78	0.644628	NM_001080479	B2RXG7|B4E3K4|B5MDA3|B7ZW32|E9PC75|Q8NCM7|Q96E37|Q9H6L3|Q9H6W0	Silent	SNP	ENST00000426542.2	37	CCDS54870.1																																																																																			T|0.967;C|0.033	0.033	strong		0.393	ARHGEF28-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000368975.1		
KDM4D	55693	hgsc.bcm.edu	37	11	94731905	94731905	+	Missense_Mutation	SNP	C	C	G	rs144086807	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:94731905C>G	ENST00000335080.5	+	3	2201	c.1369C>G	c.(1369-1371)Cct>Gct	p.P457A	KDM4D_ENST00000536741.1_Missense_Mutation_p.P457A	NM_018039.2	NP_060509.2	Q6B0I6	KDM4D_HUMAN	lysine (K)-specific demethylase 4D	457					chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	blood microparticle (GO:0072562)|nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|metal ion binding (GO:0046872)			endometrium(4)|kidney(2)|large_intestine(2)|liver(2)|lung(16)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	30						TGGTCGCCCTCCTCAGAAACT	0.597													.|||	5	0.000998403	0.0	0.0	5008	,	,		19936	0.0		0.003	False		,,,				2504	0.002				p.P457A		Atlas-SNP	.											.	KDM4D	58	.	0			c.C1369G						PASS	.	C	ALA/PRO	4,4398	8.1+/-20.4	0,4,2197	52.0	54.0	53.0		1369	1.6	0.0	11	dbSNP_134	53	46,8550	29.0+/-79.6	0,46,4252	yes	missense	KDM4D	NM_018039.2	27	0,50,6449	GG,GC,CC		0.5351,0.0909,0.3847	possibly-damaging	457/524	94731905	50,12948	2201	4298	6499	SO:0001583	missense	55693	exon3			CGCCCTCCTCAGA	AK001113	CCDS8302.1	11q21	2012-03-28	2009-04-06	2009-04-06	ENSG00000186280	ENSG00000186280		"""Chromatin-modifying enzymes / K-demethylases"""	25498	protein-coding gene	gene with protein product		609766	"""jumonji domain containing 2D"""	JMJD2D		15138608	Standard	NM_018039		Approved	FLJ10251	uc001pfe.3	Q6B0I6	OTTHUMG00000167838	ENST00000335080.5:c.1369C>G	11.37:g.94731905C>G	ENSP00000334181:p.Pro457Ala	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	59	48	0.813559	NM_018039	B3KPC4|Q0VF39|Q9NT41|Q9NW76	Missense_Mutation	SNP	ENST00000335080.5	37	CCDS8302.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	C	10.19	1.281211	0.23392	9.09E-4	0.005351	ENSG00000186280	ENST00000335080	T	0.28666	1.6	3.52	1.58	0.23477	.	0.179179	0.35555	U	0.003127	T	0.11281	0.0275	L	0.32530	0.975	0.09310	N	1	P	0.48407	0.91	B	0.38106	0.265	T	0.13335	-1.0513	10	0.22109	T	0.4	-5.8535	4.7061	0.12849	0.0:0.6512:0.2251:0.1236	.	457	Q6B0I6	KDM4D_HUMAN	A	457	ENSP00000334181:P457A	ENSP00000334181:P457A	P	+	1	0	KDM4D	94371553	0.023000	0.18921	0.001000	0.08648	0.002000	0.02628	0.744000	0.26245	0.462000	0.27095	0.655000	0.94253	CCT	C|0.997;G|0.003	0.003	strong		0.597	KDM4D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396558.2	NM_018039	
OR2W5	441932	hgsc.bcm.edu	37	1	247654498	247654498	+	RNA	SNP	G	G	A	rs61070846	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:247654498G>A	ENST00000522351.1	+	0	129							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)			GGCCTGGACTGGAGAAAATTC	0.488													g|||	647	0.129193	0.1483	0.2176	5008	,	,		18871	0.0288		0.1909	False		,,,				2504	0.0808				p.L23L		Atlas-SNP	.											.	OR2W5	97	.	0			c.G69A						PASS	.	A		647,3759	277.5+/-273.7	41,565,1597	164.0	149.0	154.0		69	-3.0	0.0	1	dbSNP_129	154	1810,6790	326.0+/-317.2	186,1438,2676	no	coding-synonymous	OR2W5	NM_001004698.2		227,2003,4273	AA,AG,GG		21.0465,14.6845,18.8913		23/321	247654498	2457,10549	2203	4300	6503			441932	exon1			TGGACTGGAGAAA			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.247654498G>A		Somatic	214	0	0		WXS	Illumina HiSeq	Phase_I	208	81	0.389423	NM_001004698	B9EH85	Silent	SNP	ENST00000522351.1	37																																																																																				G|0.820;A|0.180	0.180	strong		0.488	OR2W5-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000375789.1	NM_001004698	
BPIFB4	149954	hgsc.bcm.edu	37	20	31680334	31680334	+	Missense_Mutation	SNP	C	C	T	rs17122711	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:31680334C>T	ENST00000375483.3	+	9	1214	c.1214C>T	c.(1213-1215)cCg>cTg	p.P405L		NM_182519.2	NP_872325.2	P59827	BPIB4_HUMAN	BPI fold containing family B, member 4	405						cytoplasm (GO:0005737)|extracellular region (GO:0005576)	lipid binding (GO:0008289)										TCTCCCAAGCCGATGCCAGAG	0.597													C|||	161	0.0321486	0.0961	0.0216	5008	,	,		21163	0.0		0.0189	False		,,,				2504	0.0				p.P405L		Atlas-SNP	.											.	.	.	.	0			c.C1214T						PASS	.	C	LEU/PRO	349,4057	181.9+/-209.8	11,327,1865	71.0	64.0	67.0		1214	-1.9	0.0	20	dbSNP_123	67	162,8438	75.4+/-138.0	2,158,4140	yes	missense	BPIFB4	NM_182519.2	98	13,485,6005	TT,TC,CC		1.8837,7.921,3.929	benign	405/615	31680334	511,12495	2203	4300	6503	SO:0001583	missense	149954	exon9			CCAAGCCGATGCC	AF549190	CCDS13213.2	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000186191	ENSG00000186191		"""BPI fold containing"""	16179	protein-coding gene	gene with protein product		615718	"""chromosome 20 open reading frame 186"""	C20orf186		11971875, 21787333	Standard	NM_182519		Approved	dJ726C3.5, LPLUNC4	uc010zue.2	P59827	OTTHUMG00000032235	ENST00000375483.3:c.1214C>T	20.37:g.31680334C>T	ENSP00000364632:p.Pro405Leu	Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	27	19	0.703704	NM_182519	Q5TDX6	Missense_Mutation	SNP	ENST00000375483.3	37	CCDS13213.2	73	0.033424908424908424	54	0.10975609756097561	5	0.013812154696132596	0	0.0	14	0.018469656992084433	C	7.618	0.676280	0.14841	0.07921	0.018837	ENSG00000186191	ENST00000375483	T	0.06608	3.28	5.25	-1.89	0.07689	.	1.301950	0.05005	N	0.469943	T	0.00178	0.0005	L	0.57536	1.79	0.20703	N	0.999864	B	0.16603	0.018	B	0.14023	0.01	T	0.45145	-0.9281	9	.	.	.	-0.1506	13.7686	0.63010	0.4693:0.5307:0.0:0.0	rs17122711;rs52819586;rs17122711	405	P59827	BPIB4_HUMAN	L	405	ENSP00000364632:P405L	.	P	+	2	0	BPIFB4	31143995	0.000000	0.05858	0.003000	0.11579	0.029000	0.11900	-0.355000	0.07671	-0.070000	0.12908	-0.346000	0.07831	CCG	C|0.960;T|0.040	0.040	strong		0.597	BPIFB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078655.5	NM_182519	
CALD1	800	hgsc.bcm.edu	37	7	134618496	134618496	+	Missense_Mutation	SNP	G	G	A	rs61757650	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:134618496G>A	ENST00000361675.2	+	5	1205	c.976G>A	c.(976-978)Gag>Aag	p.E326K	CALD1_ENST00000417172.1_Intron|CALD1_ENST00000495522.1_Intron|CALD1_ENST00000393118.2_Intron|CALD1_ENST00000424922.1_Intron|CALD1_ENST00000361901.2_Intron|CALD1_ENST00000422748.1_Intron|CALD1_ENST00000361388.2_Intron|CALD1_ENST00000543443.1_Intron			Q05682	CALD1_HUMAN	caldesmon 1	326	3 X 14 AA tandem repeats of E-E-E-K-R-A- A-E-E-R-Q-R-I-K.				cellular component movement (GO:0006928)|muscle contraction (GO:0006936)	actin cap (GO:0030478)|actin cytoskeleton (GO:0015629)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|calmodulin binding (GO:0005516)|tropomyosin binding (GO:0005523)			NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(15)|lung(10)	43						aagggcagcagaggagaggca	0.507													g|||	59	0.0117812	0.0008	0.0245	5008	,	,		19892	0.001		0.0288	False		,,,				2504	0.0112				p.E326K		Atlas-SNP	.											.	CALD1	150	.	0			c.G976A						PASS	.	G	,,,,LYS/GLU	33,4345		0,33,2156	86.0	98.0	94.0		,,,,976	2.4	0.9	7	dbSNP_129	94	305,8261		6,293,3984	yes	intron,intron,intron,intron,missense	CALD1	NM_004342.6,NM_033139.3,NM_033140.3,NM_033157.3,NM_033138.3	,,,,56	6,326,6140	AA,AG,GG		3.5606,0.7538,2.6112	,,,,benign	,,,,326/794	134618496	338,12606	2189	4283	6472	SO:0001583	missense	800	exon5			GCAGCAGAGGAGA	M64110	CCDS5834.1, CCDS5835.1, CCDS5836.1, CCDS47716.1, CCDS47717.1, CCDS5836.2	7q33	2007-04-23			ENSG00000122786	ENSG00000122786			1441	protein-coding gene	gene with protein product		114213				1885618	Standard	NM_004342		Approved	CDM, H-CAD, L-CAD	uc003vrz.3	Q05682	OTTHUMG00000155407	ENST00000361675.2:c.976G>A	7.37:g.134618496G>A	ENSP00000354826:p.Glu326Lys	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	49	21	0.428571	NM_033138	A8K0X1|Q13978|Q13979|Q14741|Q14742|Q9UD91	Missense_Mutation	SNP	ENST00000361675.2	37	CCDS5835.1	30	0.013736263736263736	2	0.0040650406504065045	6	0.016574585635359115	1	0.0017482517482517483	21	0.027704485488126648	G	14.24	2.474957	0.43942	0.007538	0.035606	ENSG00000122786	ENST00000361675	T	0.56444	0.46	3.28	2.39	0.29439	.	0.762388	0.10511	U	0.666211	T	0.14056	0.0340	L	0.43152	1.355	0.80722	D	1	B	0.16603	0.018	B	0.20767	0.031	T	0.04467	-1.0949	9	.	.	.	.	8.5163	0.33248	0.1145:0.0:0.8855:0.0	rs61757650	326	Q05682	CALD1_HUMAN	K	326	ENSP00000354826:E326K	.	E	+	1	0	CALD1	134269036	1.000000	0.71417	0.856000	0.33681	0.882000	0.50991	4.459000	0.60102	0.572000	0.29383	0.563000	0.77884	GAG	G|0.979;A|0.021	0.021	strong		0.507	CALD1-005	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339939.1	NM_033138	
ITGA3	3675	hgsc.bcm.edu	37	17	48151353	48151353	+	Silent	SNP	T	T	C	rs2285524	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:48151353T>C	ENST00000320031.8	+	8	1560	c.1230T>C	c.(1228-1230)ctT>ctC	p.L410L	ITGA3_ENST00000007722.7_Silent_p.L410L|ITGA3_ENST00000544892.1_Silent_p.L185L	NM_002204.2|NM_005501.2	NP_002195.1|NP_005492.1	P26006	ITA3_HUMAN	integrin, alpha 3 (antigen CD49C, alpha 3 subunit of VLA-3 receptor)	410					blood coagulation (GO:0007596)|cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|lung development (GO:0030324)|maternal process involved in female pregnancy (GO:0060135)|memory (GO:0007613)|mesodermal cell differentiation (GO:0048333)|negative regulation of cell projection organization (GO:0031345)|nephron development (GO:0072006)|neuron migration (GO:0001764)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of gene expression (GO:0010628)|positive regulation of neuron projection development (GO:0010976)|regulation of BMP signaling pathway (GO:0030510)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|regulation of Wnt signaling pathway (GO:0030111)|renal filtration (GO:0097205)|response to drug (GO:0042493)|response to gonadotropin (GO:0034698)|skin development (GO:0043588)	basolateral plasma membrane (GO:0016323)|cell periphery (GO:0071944)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|integrin alpha3-beta1 complex (GO:0034667)|integrin complex (GO:0008305)|invadopodium membrane (GO:0071438)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|synapse (GO:0045202)	glycoprotein binding (GO:0001948)|metal ion binding (GO:0046872)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)			endometrium(3)|kidney(2)|large_intestine(7)|lung(11)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(2)	31						AGGGGCTCCTTAGACAGCCCC	0.557													C|||	1529	0.305312	0.4402	0.33	5008	,	,		16810	0.3085		0.0954	False		,,,				2504	0.318				p.L410L		Atlas-SNP	.											.	ITGA3	128	.	0			c.T1230C						PASS	.	C	,	1797,2609	641.1+/-397.4	338,1121,744	71.0	75.0	73.0		1230,1230	3.8	0.6	17	dbSNP_100	73	1034,7566	771.7+/-407.7	61,912,3327	no	coding-synonymous,coding-synonymous	ITGA3	NM_002204.2,NM_005501.2	,	399,2033,4071	CC,CT,TT		12.0233,40.7853,21.7669	,	410/1052,410/1067	48151353	2831,10175	2203	4300	6503	SO:0001819	synonymous_variant	3675	exon8			GCTCCTTAGACAG	M59911	CCDS11557.1, CCDS11558.1	17q21.33	2010-03-23	2003-10-13		ENSG00000005884	ENSG00000005884		"""CD molecules"", ""Integrins"""	6139	protein-coding gene	gene with protein product		605025	"""antigen identified by monoclonal antibody J143"""	MSK18		1655803, 9704023	Standard	NM_005501		Approved	CD49c, VLA3a, VCA-2, GAP-B3	uc010dbm.3	P26006	OTTHUMG00000161890	ENST00000320031.8:c.1230T>C	17.37:g.48151353T>C		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	72	45	0.625	NM_005501	A7E246|B7ZM80|B9EGQ1|D3DTX4|D3DTX5	Silent	SNP	ENST00000320031.8	37	CCDS11558.1																																																																																			T|0.775;C|0.225	0.225	strong		0.557	ITGA3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000366298.1	NM_005501	
SLC25A26	115286	hgsc.bcm.edu	37	3	66419956	66419956	+	Missense_Mutation	SNP	C	C	T	rs13874	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:66419956C>T	ENST00000413054.1	+	6	433	c.359C>T	c.(358-360)aCg>aTg	p.T120M	SLC25A26_ENST00000336733.6_Missense_Mutation_p.T120M|SLC25A26_ENST00000354883.6_Missense_Mutation_p.T208M|SLC25A26_ENST00000536651.1_3'UTR|SLC25A26_ENST00000484768.1_3'UTR			Q70HW3	SAMC_HUMAN	solute carrier family 25 (S-adenosylmethionine carrier), member 26	208					S-adenosyl-L-methionine transmembrane transport (GO:1901962)|S-adenosyl-L-methionine transport (GO:0015805)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	S-adenosyl-L-methionine transmembrane transporter activity (GO:0000095)			endometrium(1)|large_intestine(1)|lung(2)|pancreas(1)|stomach(2)|urinary_tract(1)	8		Lung NSC(201;0.00774)		BRCA - Breast invasive adenocarcinoma(55;0.00046)|KIRC - Kidney renal clear cell carcinoma(15;0.0515)|Kidney(15;0.0648)		ACAAGAATTACGCTGGCAAAG	0.433													T|||	3405	0.679912	0.8396	0.621	5008	,	,		21912	0.7659		0.4761	False		,,,				2504	0.6268				p.T208M		Atlas-SNP	.											.	SLC25A26	12	.	0			c.C623T						PASS	.	T	MET/THR,MET/THR	3442,964	352.1+/-311.5	1348,746,109	93.0	84.0	87.0		359,623	5.5	1.0	3	dbSNP_52	87	3801,4799	584.2+/-391.7	861,2079,1360	yes	missense,missense	SLC25A26	NM_001164796.1,NM_173471.3	81,81	2209,2825,1469	TT,TC,CC		44.1977,21.8793,44.3103	benign,benign	120/187,208/275	66419956	7243,5763	2203	4300	6503	SO:0001583	missense	115286	exon9			GAATTACGCTGGC	AJ580932	CCDS54604.1, CCDS2905.2	3p14.2	2013-05-22	2012-03-29		ENSG00000144741	ENSG00000144741		"""Solute carriers"""	20661	protein-coding gene	gene with protein product		611037	"""solute carrier family 25 (mitochondrial carrier; phosphate carrier), member 26"""			14674884	Standard	NM_173471		Approved		uc011bfq.2	Q70HW3	OTTHUMG00000149917	ENST00000413054.1:c.359C>T	3.37:g.66419956C>T	ENSP00000415304:p.Thr120Met	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	74	43	0.581081	NM_173471	A8K758|B3KRZ7|Q7Z786|Q96E68	Missense_Mutation	SNP	ENST00000413054.1	37		1413|1413	0.646978021978022|0.646978021978022	405|405	0.823170731707317|0.823170731707317	226|226	0.6243093922651933|0.6243093922651933	421|421	0.736013986013986|0.736013986013986	361|361	0.4762532981530343|0.4762532981530343	T|T	0.369|0.369	-0.935221|-0.935221	0.02340|0.02340	0.781207|0.781207	0.441977|0.441977	ENSG00000144741|ENSG00000144741	ENST00000413054|ENST00000354883;ENST00000336733	.|T;T	.|0.78595	.|-1.19;-1.19	5.49|5.49	5.49|5.49	0.81192|0.81192	.|Mitochondrial carrier domain (2);	.|0.077986	.|0.85682	.|N	.|0.000000	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.00007|0.00007	-3.15|-3.15	0.48087|0.48087	P|P	4.150000000000542E-4|4.150000000000542E-4	.|B;B	.|0.02656	.|0.0;0.0	.|B;B	.|0.01281	.|0.0;0.0	T|T	0.46400|0.46400	-0.9194|-0.9194	4|9	.|0.02654	.|T	.|1	-23.2708|-23.2708	11.4812|11.4812	0.50326|0.50326	0.0:0.0704:0.0:0.9296|0.0:0.0704:0.0:0.9296	rs13874;rs332380;rs1129181;rs1678130;rs3186777;rs11549728;rs11566372;rs17825759;rs59760960;rs13874|rs13874;rs332380;rs1129181;rs1678130;rs3186777;rs11549728;rs11566372;rs17825759;rs59760960;rs13874	.|208;208	.|F8WAB8;Q70HW3	.|.;SAMC_HUMAN	C|M	145|208;120	.|ENSP00000346955:T208M;ENSP00000336801:T120M	.|ENSP00000336801:T120M	R|T	+|+	1|2	0|0	SLC25A26|SLC25A26	66502646|66502646	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.043000|0.043000	0.13939|0.13939	5.324000|5.324000	0.65863|0.65863	0.922000|0.922000	0.37019|0.37019	-0.254000|-0.254000	0.11334|0.11334	CGC|ACG	C|0.342;T|0.658	0.658	strong		0.433	SLC25A26-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000313895.2	NM_173471	
TANC1	85461	hgsc.bcm.edu	37	2	160086654	160086654	+	Missense_Mutation	SNP	A	A	G	rs67270488|rs55738533|rs4664277	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:160086654A>G	ENST00000263635.6	+	27	4954	c.4717A>G	c.(4717-4719)Act>Gct	p.T1573A	TANC1_ENST00000454300.1_Missense_Mutation_p.T1467A	NM_001145909.1|NM_033394.2	NP_001139381.1|NP_203752.2	Q9C0D5	TANC1_HUMAN	tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 1	1573			T -> A (in dbSNP:rs4664277). {ECO:0000269|PubMed:11214970}.		dendritic spine maintenance (GO:0097062)|myoblast fusion (GO:0007520)|visual learning (GO:0008542)	axon terminus (GO:0043679)|cell junction (GO:0030054)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)|postsynaptic membrane (GO:0045211)				breast(3)|central_nervous_system(4)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(9)|lung(25)|ovary(7)|pancreas(1)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(2)	77						AATCGCTGCCACTCCTGCTGG	0.562													G|||	2553	0.509784	0.4607	0.6095	5008	,	,		20467	0.6181		0.3728	False		,,,				2504	0.5348				p.T1573A		Atlas-SNP	.											.	TANC1	157	.	0			c.A4717G						PASS	.	G	,ALA/THR	1667,2225		388,891,667	54.0	60.0	58.0		,4717	-3.1	0.0	2	dbSNP_129	58	2739,5545		524,1691,1927	yes	utr-3,missense	TANC1	NM_001145909.1,NM_033394.2	,58	912,2582,2594	GG,GA,AA		33.0637,42.8314,36.1859	,benign	,1573/1862	160086654	4406,7770	1946	4142	6088	SO:0001583	missense	85461	exon27			GCTGCCACTCCTG	AB051515	CCDS42766.1	2q24.2	2013-01-11			ENSG00000115183	ENSG00000115183		"""Ankyrin repeat domain containing"", ""Tetratricopeptide (TTC) repeat domain containing"""	29364	protein-coding gene	gene with protein product	"""rolling pebbles homolog B (Drosophila)"""	611397				15673434	Standard	NM_033394		Approved	KIAA1728, ROLSB	uc002uag.3	Q9C0D5	OTTHUMG00000153945	ENST00000263635.6:c.4717A>G	2.37:g.160086654A>G	ENSP00000263635:p.Thr1573Ala	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	102	41	0.401961	NM_033394	C9JD88|Q49AI8	Missense_Mutation	SNP	ENST00000263635.6	37	CCDS42766.1	900	0.41208791208791207	193	0.39227642276422764	178	0.49171270718232046	306	0.534965034965035	223	0.2941952506596306	G	0.003	-2.544700	0.00142	0.428314	0.330637	ENSG00000115183	ENST00000454300;ENST00000263635	T;T	0.68331	-0.32;-0.31	5.86	-3.12	0.05282	.	0.971917	0.08544	N	0.930072	T	0.00012	0.0000	N	0.00926	-1.1	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.37934	-0.9684	8	.	.	.	.	6.0992	0.20037	0.4496:0.0797:0.3902:0.0805	rs55738533;rs59149467;rs62172669	1573	Q9C0D5	TANC1_HUMAN	A	1467;1573	ENSP00000396339:T1467A;ENSP00000263635:T1573A	.	T	+	1	0	TANC1	159794900	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.704000	0.25661	-1.161000	0.02800	-1.736000	0.00690	ACT	A|0.509;CA|0.001	.	alt		0.562	TANC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333135.1		
DMGDH	29958	hgsc.bcm.edu	37	5	78326767	78326767	+	Silent	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:78326767C>T	ENST00000255189.3	-	10	1600	c.1572G>A	c.(1570-1572)caG>caA	p.Q524Q	DMGDH_ENST00000540686.1_Silent_p.Q144Q|DMGDH_ENST00000380311.4_Silent_p.Q323Q	NM_013391.2	NP_037523.2	Q9UI17	M2GD_HUMAN	dimethylglycine dehydrogenase	524					amino-acid betaine catabolic process (GO:0006579)|choline metabolic process (GO:0019695)|glycine catabolic process (GO:0006546)|glycine metabolic process (GO:0006544)	mitochondrial matrix (GO:0005759)	aminomethyltransferase activity (GO:0004047)|dimethylglycine dehydrogenase activity (GO:0047865)|electron carrier activity (GO:0009055)|poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(2)|kidney(2)|large_intestine(10)|liver(1)|lung(10)|ovary(2)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)	34		all_lung(232;0.000638)|Lung NSC(167;0.00173)|Ovarian(174;0.0262)|Prostate(461;0.192)		OV - Ovarian serous cystadenocarcinoma(54;6.52e-45)|Epithelial(54;5.96e-40)|all cancers(79;3.56e-35)		TTTGCATAACCTGTTTATACT	0.423																																					p.Q524Q		Atlas-SNP	.											.	DMGDH	88	.	0			c.G1572A						PASS	.						115.0	109.0	111.0					5																	78326767		2203	4300	6503	SO:0001819	synonymous_variant	29958	exon10			CATAACCTGTTTA	AF111858	CCDS4044.1	5q14.1	2008-02-05			ENSG00000132837	ENSG00000132837	1.5.99.2		24475	protein-coding gene	gene with protein product		605849				10767172, 11231903	Standard	NM_013391		Approved		uc003kfs.3	Q9UI17	OTTHUMG00000108159	ENST00000255189.3:c.1572G>A	5.37:g.78326767C>T		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	133	85	0.639098	NM_013391	B2RBN0|B4E1J9	Silent	SNP	ENST00000255189.3	37	CCDS4044.1																																																																																			.	.	none		0.423	DMGDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226963.3	NM_013391	
PSMD3	5709	hgsc.bcm.edu	37	17	38146154	38146154	+	Silent	SNP	T	T	C	rs9916279	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:38146154T>C	ENST00000264639.4	+	5	1023	c.849T>C	c.(847-849)aaT>aaC	p.N283N	PSMD3_ENST00000541736.1_Silent_p.N145N	NM_002809.3	NP_002800.2	O43242	PSMD3_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 3	283					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 protein catabolic process (GO:0042176)|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)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)|proteasome regulatory particle (GO:0005838)	enzyme regulator activity (GO:0030234)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|pancreas(1)|prostate(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	26	Colorectal(19;0.000442)					CCAACAACAATGAGTGGGCCA	0.537													T|||	844	0.16853	0.3805	0.1398	5008	,	,		18840	0.0069		0.165	False		,,,				2504	0.0726				p.N283N	Ovarian(186;531 2051 6385 19668 48409)	Atlas-SNP	.											.	PSMD3	56	.	0			c.T849C						PASS	.	T		1483,2923	476.4+/-357.6	248,987,968	71.0	57.0	62.0		849	-8.4	0.5	17	dbSNP_119	62	1416,7184	272.8+/-290.3	116,1184,3000	no	coding-synonymous	PSMD3	NM_002809.2		364,2171,3968	CC,CT,TT		16.4651,33.6586,22.2897		283/535	38146154	2899,10107	2203	4300	6503	SO:0001819	synonymous_variant	5709	exon5			CAACAATGAGTGG	D67025	CCDS11356.1	17q21.2	2010-07-23			ENSG00000108344	ENSG00000108344		"""Proteasome (prosome, macropain) subunits"""	9560	protein-coding gene	gene with protein product			"""tissue specific transplantation antigen 2"""	TSTA2		9017604	Standard	NM_002809		Approved	S3, P58, Rpn3	uc002htn.2	O43242	OTTHUMG00000133251	ENST00000264639.4:c.849T>C	17.37:g.38146154T>C		Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	37	16	0.432432	NM_002809	B3KMW9|B4DT72|Q96EI2|Q9BQA4	Silent	SNP	ENST00000264639.4	37	CCDS11356.1																																																																																			T|0.798;C|0.202	0.202	strong		0.537	PSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257018.1	NM_002809	
CRIPAK	285464	hgsc.bcm.edu	37	4	1388693	1388693	+	Missense_Mutation	SNP	C	C	G	rs78906219	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	43	2	0.0465116		WXS	Illumina HiSeq	Phase_I	25	8	0.32	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	
OTUD7B	56957	hgsc.bcm.edu	37	1	149916820	149916820	+	Nonsense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:149916820G>A	ENST00000369135.4	-	12	1762	c.1468C>T	c.(1468-1470)Cga>Tga	p.R490*		NM_020205.2	NP_064590.2	Q6GQQ9	OTU7B_HUMAN	OTU deubiquitinase 7B	490					mucosal immune response (GO:0002385)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of interleukin-8 production (GO:0032717)|negative regulation of protein localization to nucleus (GO:1900181)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|protein K11-linked deubiquitination (GO:0035871)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	cysteine-type peptidase activity (GO:0008234)|DNA binding (GO:0003677)|Lys48-specific deubiquitinase activity (GO:1990380)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			breast(1)|endometrium(6)|kidney(2)|large_intestine(5)|lung(18)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	39	Breast(34;0.0009)|Ovarian(49;0.0265)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.171)|STAD - Stomach adenocarcinoma(528;0.247)			TCCCGATCTCGCTTTGACTTC	0.567																																					p.R490X		Atlas-SNP	.											OTUD7B,caecum,carcinoma,+2,1	OTUD7B	76	1	0			c.C1468T						scavenged	.						191.0	191.0	191.0					1																	149916820		2094	4220	6314	SO:0001587	stop_gained	56957	exon12			GATCTCGCTTTGA	AJ293573	CCDS72903.1	1q21.2	2014-02-24	2014-02-24	2006-07-07	ENSG00000163113	ENSG00000264522		"""OTU domain containing"""	16683	protein-coding gene	gene with protein product		611748	"""zinc finger, A20 domain containing 1"", ""OTU domain containing 7B"""	ZA20D1		11463333, 23827681	Standard	NM_020205		Approved	CEZANNE	uc001etn.3	Q6GQQ9	OTTHUMG00000012291	ENST00000369135.4:c.1468C>T	1.37:g.149916820G>A	ENSP00000358131:p.Arg490*	Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	146	2	0.0136986	NM_020205	B7Z643|D3DUZ8|Q5SZ60|Q8WWA7|Q9NQ53|Q9UFF4	Nonsense_Mutation	SNP	ENST00000369135.4	37	CCDS41389.1	.	.	.	.	.	.	.	.	.	.	G	38	6.883340	0.97908	.	.	ENSG00000163113	ENST00000369135;ENST00000543330	.	.	.	4.99	4.07	0.47477	.	0.271263	0.33772	N	0.004572	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-17.7859	11.3493	0.49579	0.0:0.0:0.5413:0.4587	.	.	.	.	X	490	.	.	R	-	1	2	OTUD7B	148183444	0.999000	0.42202	0.999000	0.59377	0.992000	0.81027	1.398000	0.34554	1.317000	0.45149	0.557000	0.71058	CGA	.	.	none		0.567	OTUD7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034146.3	NM_020205	
ENPP1	5167	hgsc.bcm.edu	37	6	132172368	132172368	+	Missense_Mutation	SNP	A	A	C	rs1044498	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	81	0	0		WXS	Illumina HiSeq	Phase_I	64	41	0.640625	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		
GIMAP2	26157	hgsc.bcm.edu	37	7	150389677	150389677	+	Silent	SNP	G	G	C	rs6952002	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:150389677G>C	ENST00000223293.5	+	3	397	c.303G>C	c.(301-303)ctG>ctC	p.L101L		NM_015660.2	NP_056475.1	Q9UG22	GIMA2_HUMAN	GTPase, IMAP family member 2	101	AIG1-type G.					cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|lipid particle (GO:0005811)	GTP binding (GO:0005525)			kidney(1)|large_intestine(1)|lung(8)|skin(2)|urinary_tract(1)	13			OV - Ovarian serous cystadenocarcinoma(82;0.0145)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		gctacttgctGTCTGCACCAG	0.522													C|||	2455	0.490216	0.8661	0.304	5008	,	,		21424	0.2907		0.337	False		,,,				2504	0.4775				p.L101L		Atlas-SNP	.											GIMAP2,colon,carcinoma,0,1	GIMAP2	39	1	0			c.G303C						PASS	.	C		3470,936	357.4+/-313.9	1380,710,113	59.0	56.0	57.0		303	-0.3	0.2	7	dbSNP_116	57	2841,5759	674.3+/-403.1	477,1887,1936	no	coding-synonymous	GIMAP2	NM_015660.2		1857,2597,2049	CC,CG,GG		33.0349,21.2438,48.5238		101/338	150389677	6311,6695	2203	4300	6503	SO:0001819	synonymous_variant	26157	exon3			CTTGCTGTCTGCA	AL110151	CCDS5905.1	7q36.1	2014-04-04			ENSG00000106560	ENSG00000106560		"""GTPases, IMAP"""	21789	protein-coding gene	gene with protein product	"""immune-associated nucleotide-binding protein 12"""	608085				15474311	Standard	NM_015660		Approved	DKFZp586D0824, HIMAP2, IMAP2, IAN12	uc003who.3	Q9UG22	OTTHUMG00000157488	ENST00000223293.5:c.303G>C	7.37:g.150389677G>C		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	86	85	0.988372	NM_015660	Q96L25	Silent	SNP	ENST00000223293.5	37	CCDS5905.1																																																																																			G|0.525;C|0.475	0.475	strong		0.522	GIMAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348948.1	NM_015660	
CDON	50937	hgsc.bcm.edu	37	11	125871735	125871735	+	Silent	SNP	C	C	T	rs516664	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:125871735C>T	ENST00000392693.3	-	11	2164	c.2037G>A	c.(2035-2037)gcG>gcA	p.A679A	CDON_ENST00000531738.1_Silent_p.A56A|CDON_ENST00000263577.7_Silent_p.A679A	NM_001243597.1|NM_016952.4	NP_001230526.1|NP_058648.4	Q4KMG0	CDON_HUMAN	cell adhesion associated, oncogene regulated	679					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.A679A(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)		TTTTTGATGACGCTGTTTTTT	0.388													T|||	1515	0.302516	0.4017	0.3415	5008	,	,		16262	0.1617		0.337	False		,,,				2504	0.2505				p.A679A		Atlas-SNP	.											CDON,NS,carcinoma,0,2	CDON	137	2	1	Substitution - coding silent(1)	stomach(1)	c.G2037A						PASS	.	T		1697,2705	652.5+/-399.4	318,1061,822	112.0	112.0	112.0		2037	-7.2	0.4	11	dbSNP_83	112	2793,5805	676.8+/-403.3	473,1847,1979	no	coding-synonymous	CDON	NM_016952.4		791,2908,2801	TT,TC,CC		32.4843,38.5507,34.5385		679/1265	125871735	4490,8510	2201	4299	6500	SO:0001819	synonymous_variant	50937	exon11			TGATGACGCTGTT	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.2037G>A	11.37:g.125871735C>T		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	93	23	0.247312	NM_016952	O14631	Silent	SNP	ENST00000392693.3	37	CCDS58192.1																																																																																			C|0.667;T|0.333	0.333	strong		0.388	CDON-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386749.2	NM_016952	
PCSK1	5122	hgsc.bcm.edu	37	5	95728974	95728974	+	Missense_Mutation	SNP	G	G	C	rs6234	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:95728974G>C	ENST00000311106.3	-	14	2230	c.1993C>G	c.(1993-1995)Cag>Gag	p.Q665E	PCSK1_ENST00000513085.1_5'UTR|CTD-2337A12.1_ENST00000502645.2_RNA|PCSK1_ENST00000508626.1_Missense_Mutation_p.Q618E	NM_000439.4|NM_001177876.1	NP_000430.3|NP_001171347.1	P29120	NEC1_HUMAN	proprotein convertase subtilisin/kexin type 1	665			Q -> E (in dbSNP:rs6234). {ECO:0000269|PubMed:10391209, ECO:0000269|PubMed:17595246, ECO:0000269|PubMed:8666140}.		cell-cell signaling (GO:0007267)|cellular protein metabolic process (GO:0044267)|metabolic process (GO:0008152)|peptide biosynthetic process (GO:0043043)|peptide hormone processing (GO:0016486)|proteolysis (GO:0006508)|regulation of insulin secretion (GO:0050796)	extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|secretory granule lumen (GO:0034774)	serine-type endopeptidase activity (GO:0004252)			NS(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(14)|ovary(2)|prostate(3)|skin(3)|urinary_tract(2)	36		all_cancers(142;2.67e-06)|all_epithelial(76;6.92e-09)|all_lung(232;0.00307)|Lung NSC(167;0.00452)|Ovarian(225;0.0112)|Colorectal(57;0.0341)|Breast(839;0.244)		all cancers(79;3.44e-16)	"""""""Insulin(DB00071)|Insulin Regular(DB00030)"""	AGCATGGCCTGGGAAGGGGCT	0.552													C|||	1298	0.259185	0.1808	0.2349	5008	,	,		17556	0.3591		0.2604	False		,,,				2504	0.2781				p.Q665E		Atlas-SNP	.											.	PCSK1	93	.	0			c.C1993G						PASS	.	C	GLU/GLN,GLU/GLN,GLU/GLN	849,3557	745.1+/-411.6	76,697,1430	90.0	93.0	92.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1993,1852,1063	-0.3	0.0	5	dbSNP_52	92	2397,6203	700.2+/-405.1	304,1789,2207	yes	missense,missense,missense	PCSK1	NM_000439.4,NM_001177875.1,NM_001177876.1	29,29,29	380,2486,3637	CC,CG,GG		27.8721,19.2692,24.9577	benign,benign,benign	665/754,618/707,355/444	95728974	3246,9760	2203	4300	6503	SO:0001583	missense	5122	exon14			TGGCCTGGGAAGG		CCDS4081.1, CCDS54881.1	5q15-q21	2008-07-18			ENSG00000175426	ENSG00000175426			8743	protein-coding gene	gene with protein product	"""prohormone convertase 3"", ""prohormone convertase 1"", ""neuroendocrine convertase 1"", ""proprotein convertase 1"""	162150		NEC1		1765368	Standard	NM_000439		Approved	PC1, PC3, SPC3	uc003kls.2	P29120	OTTHUMG00000122089	ENST00000311106.3:c.1993C>G	5.37:g.95728974G>C	ENSP00000308024:p.Gln665Glu	Somatic	281	1	0.00355872		WXS	Illumina HiSeq	Phase_I	239	121	0.506276	NM_000439	B7Z8T7|E9PHA1|P78478|Q92532	Missense_Mutation	SNP	ENST00000311106.3	37	CCDS4081.1	564	0.25824175824175827	74	0.15040650406504066	85	0.23480662983425415	196	0.34265734265734266	209	0.2757255936675462	C	0.226	-1.024627	0.02061	0.192692	0.278721	ENSG00000175426	ENST00000311106;ENST00000508626	T;T	0.64618	0.05;-0.11	5.62	-0.272	0.12919	.	0.788543	0.12504	N	0.463051	T	0.00012	0.0000	N	0.02011	-0.69	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.29274	-1.0017	9	0.02654	T	1	-11.0777	11.1807	0.48627	0.0:0.3751:0.4891:0.1358	rs6234;rs17847297;rs52799711;rs6234	618;665	E9PHA1;P29120	.;NEC1_HUMAN	E	665;618	ENSP00000308024:Q665E;ENSP00000421600:Q618E	ENSP00000308024:Q665E	Q	-	1	0	PCSK1	95754730	0.013000	0.17824	0.045000	0.18777	0.016000	0.09150	0.132000	0.15891	-0.210000	0.10140	-0.815000	0.03128	CAG	G|0.744;C|0.254	0.254	strong		0.552	PCSK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000242851.1	NM_000439	
FOLH1B	219595	hgsc.bcm.edu	37	11	89413824	89413824	+	RNA	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:89413824G>A	ENST00000532352.1	+	0	1309							Q9HBA9	FOH1B_HUMAN	folate hydrolase 1B							cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	dipeptidase activity (GO:0016805)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(26)|ovary(4)|skin(4)|urinary_tract(2)	48						GTACAGCTTGGTATACAACCT	0.284																																					p.V166I		Atlas-SNP	.											FOLH1B,right_lower_lobe,carcinoma,-2,1	FOLH1B	93	1	0			c.G496A						scavenged	.						40.0	41.0	41.0					11																	89413824		2201	4294	6495			219595	exon8			AGCTTGGTATACA	AF261715		11q14.3	2014-03-18			ENSG00000134612	ENSG00000134612			13636	protein-coding gene	gene with protein product	"""prostate specific membrane antigen like protein"", ""Cell growth-inhibiting gene 26 protein"", ""glutamate carboxypeptidase III"""	609020	"""folate hydrolase 2"""	FOLH2, FOLHP		9838072, 14716746	Standard	NM_153696		Approved	PSMAL, GCPIII	uc001pda.3	Q9HBA9	OTTHUMG00000167376		11.37:g.89413824G>A		Somatic	204	0	0		WXS	Illumina HiSeq	Phase_I	313	4	0.0127796	NM_153696		Missense_Mutation	SNP	ENST00000532352.1	37																																																																																				.	.	none		0.284	FOLH1B-004	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000395421.1	NM_153696	
RAVER1	125950	hgsc.bcm.edu	37	19	10439540	10439540	+	Silent	SNP	A	A	G	rs3745262	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:10439540A>G	ENST00000293677.6	-	3	666	c.585T>C	c.(583-585)gcT>gcC	p.A195A		NM_133452.2	NP_597709.2	Q8IY67	RAVR1_HUMAN	ribonucleoprotein, PTB-binding 1	178	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.					cytoplasm (GO:0005737)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(3)|large_intestine(1)|lung(8)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)	18			OV - Ovarian serous cystadenocarcinoma(20;1.81e-09)|Epithelial(33;3.65e-06)|all cancers(31;8.35e-06)			TCATGTACTCAGCAAAGCCAT	0.642													G|||	135	0.0269569	0.0234	0.0058	5008	,	,		16733	0.0397		0.0328	False		,,,				2504	0.0276				p.A195A		Atlas-SNP	.											RAVER1_ENST00000293677,caecum,carcinoma,0,2	RAVER1	67	2	0			c.T585C						PASS	.	G		97,4143		0,97,2023	34.0	40.0	38.0		585	-10.1	0.4	19	dbSNP_107	38	274,8204		6,262,3971	yes	coding-synonymous	RAVER1	NM_133452.2		6,359,5994	GG,GA,AA		3.2319,2.2877,2.9171		195/757	10439540	371,12347	2120	4239	6359	SO:0001819	synonymous_variant	125950	exon3			GTACTCAGCAAAG		CCDS45960.1	19p13.2	2013-02-12				ENSG00000161847		"""RNA binding motif (RRM) containing"""	30296	protein-coding gene	gene with protein product		609950				11853319, 11724819	Standard	NM_133452		Approved	KIAA1978	uc002moa.3	Q8IY67		ENST00000293677.6:c.585T>C	19.37:g.10439540A>G		Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	131	50	0.381679	NM_133452	A6NMU4|Q8IY60|Q8TF24	Silent	SNP	ENST00000293677.6	37	CCDS45960.1																																																																																			A|0.972;G|0.028	0.028	strong		0.642	RAVER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451227.1	NM_133452	
CAPRIN2	65981	hgsc.bcm.edu	37	12	30888001	30888001	+	Missense_Mutation	SNP	T	T	C	rs12146709	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:30888001T>C	ENST00000395805.2	-	4	1257	c.710A>G	c.(709-711)aAa>aGa	p.K237R	CAPRIN2_ENST00000308433.5_5'UTR|CAPRIN2_ENST00000298892.5_Missense_Mutation_p.K237R|CAPRIN2_ENST00000251071.5_Missense_Mutation_p.K237R|CAPRIN2_ENST00000417045.1_Missense_Mutation_p.K237R|CAPRIN2_ENST00000538387.1_5'UTR	NM_001206856.1	NP_001193785.1			caprin family member 2											breast(1)|central_nervous_system(1)|endometrium(8)|kidney(4)|large_intestine(13)|lung(16)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	48	all_lung(12;1.13e-09)|Lung NSC(12;7.98e-08)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0355)|Lung SC(12;0.0905)|Esophageal squamous(101;0.233)					CAAACCCCCTTTGAAGTCTTT	0.393													T|||	810	0.161741	0.0348	0.121	5008	,	,		18804	0.2788		0.2376	False		,,,				2504	0.1636				p.K237R		Atlas-SNP	.											.	CAPRIN2	109	.	0			c.A710G						PASS	.	T	ARG/LYS,ARG/LYS,ARG/LYS,ARG/LYS	296,4110	163.3+/-195.1	11,274,1918	191.0	186.0	188.0		710,710,710,710	-9.2	0.3	12	dbSNP_120	188	2217,6383	378.3+/-338.9	275,1667,2358	yes	missense,missense,missense,missense	CAPRIN2	NM_001002259.1,NM_001206856.1,NM_023925.3,NM_032156.3	26,26,26,26	286,1941,4276	CC,CT,TT		25.7791,6.7181,19.3219	benign,benign,benign,benign	237/1128,237/906,237/1078,237/961	30888001	2513,10493	2203	4300	6503	SO:0001583	missense	65981	exon4			CCCCCTTTGAAGT	AY074491	CCDS8720.1, CCDS41766.1, CCDS41766.2, CCDS55816.1	12p11	2010-08-03	2007-03-27	2007-03-27	ENSG00000110888	ENSG00000110888			21259	protein-coding gene	gene with protein product		610375	"""C1q domain containing 1"""	C1QDC1		11347906, 14764709	Standard	NM_001002259		Approved	EEG1, FLJ22569, FLJ11391, caprin-2, RNG140	uc001rji.1	Q6IMN6	OTTHUMG00000169185	ENST00000395805.2:c.710A>G	12.37:g.30888001T>C	ENSP00000379150:p.Lys237Arg	Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	150	149	0.993333	NM_023925		Missense_Mutation	SNP	ENST00000395805.2	37	CCDS55816.1	421	0.19276556776556777	21	0.042682926829268296	51	0.1408839779005525	165	0.28846153846153844	184	0.24274406332453827	T	10.57	1.387208	0.25031	0.067181	0.257791	ENSG00000110888	ENST00000298892;ENST00000395805;ENST00000251071;ENST00000417045;ENST00000537108;ENST00000541765;ENST00000543380;ENST00000542550	T;T;T;T;T;T;T;T	0.25250	1.81;1.81;1.81;1.81;1.81;1.81;1.81;1.81	4.61	-9.22	0.00675	.	0.756956	0.12957	N	0.425359	T	0.00012	0.0000	L	0.28115	0.83	0.22389	P	0.999147257	B;B;B;B;B	0.09022	0.001;0.001;0.001;0.002;0.0	B;B;B;B;B	0.11329	0.001;0.006;0.003;0.004;0.002	T	0.29822	-0.9999	9	0.27785	T	0.31	-0.1784	7.666	0.28432	0.0949:0.5174:0.097:0.2907	rs12146709;rs52793954;rs58167356;rs12146709	237;237;237;237;237	Q149P6;Q6IMN6-3;Q6IMN6;Q6IMN6-2;E4NKG2	.;.;CAPR2_HUMAN;.;.	R	237;237;237;237;156;34;34;156	ENSP00000298892:K237R;ENSP00000379150:K237R;ENSP00000251071:K237R;ENSP00000391479:K237R;ENSP00000438010:K156R;ENSP00000444137:K34R;ENSP00000440785:K34R;ENSP00000443353:K156R	ENSP00000251071:K237R	K	-	2	0	CAPRIN2	30779268	0.015000	0.18098	0.291000	0.24904	0.966000	0.64601	-1.560000	0.02160	-2.139000	0.00807	-1.512000	0.00943	AAA	T|0.805;C|0.195	0.195	strong		0.393	CAPRIN2-004	PUTATIVE	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000403322.2	NM_023925	
INCENP	3619	hgsc.bcm.edu	37	11	61897359	61897359	+	Silent	SNP	C	C	T	rs1675133	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:61897359C>T	ENST00000394818.3	+	4	562	c.360C>T	c.(358-360)gtC>gtT	p.V120V	INCENP_ENST00000278849.4_Silent_p.V120V	NM_001040694.1	NP_001035784.1	Q9NQS7	INCE_HUMAN	inner centromere protein antigens 135/155kDa	120					chromosome segregation (GO:0007059)|cytokinesis (GO:0000910)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	central element (GO:0000801)|chromocenter (GO:0010369)|chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lateral element (GO:0000800)|microtubule (GO:0005874)|midbody (GO:0030496)|pericentric heterochromatin (GO:0005721)|protein complex (GO:0043234)|spindle (GO:0005819)				breast(1)|endometrium(1)|kidney(6)|large_intestine(2)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	19						ACGGCTCCGTCCTGCGGCGTG	0.647													C|||	1731	0.345647	0.32	0.379	5008	,	,		15888	0.1181		0.6859	False		,,,				2504	0.2413				p.V120V		Atlas-SNP	.											INCENP_ENST00000394818,NS,carcinoma,0,3	INCENP	122	3	0			c.C360T						PASS	.	C	,	1583,2819	474.8+/-357.1	304,975,922	49.0	51.0	50.0		360,360	2.2	0.1	11	dbSNP_89	50	5875,2723	660.2+/-401.7	2026,1823,450	no	coding-synonymous,coding-synonymous	INCENP	NM_001040694.1,NM_020238.2	,	2330,2798,1372	TT,TC,CC		31.6702,35.9609,42.6308	,	120/919,120/915	61897359	7458,5542	2201	4299	6500	SO:0001819	synonymous_variant	3619	exon4			CTCCGTCCTGCGG	AF282265	CCDS31582.1, CCDS44624.1	11q12.3	2013-01-17	2002-08-29		ENSG00000149503	ENSG00000149503			6058	protein-coding gene	gene with protein product		604411	"""inner centromere protein antigens (135kD, 155kD)"""			1860899, 11453556	Standard	NM_001040694		Approved	FLJ31633	uc001nsw.1	Q9NQS7	OTTHUMG00000167470	ENST00000394818.3:c.360C>T	11.37:g.61897359C>T		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	71	58	0.816901	NM_001040694	A8MQD2|Q5Y192	Silent	SNP	ENST00000394818.3	37	CCDS44624.1																																																																																			C|0.500;T|0.500	0.500	strong		0.647	INCENP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000394723.2	NM_020238	
MYO5B	4645	hgsc.bcm.edu	37	18	47455923	47455923	+	Silent	SNP	C	C	T	rs2298628	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:47455923C>T	ENST00000285039.7	-	17	2348	c.2049G>A	c.(2047-2049)gtG>gtA	p.V683V		NM_001080467.2	NP_001073936.1	Q9ULV0	MYO5B_HUMAN	myosin VB	683	Myosin motor.				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)		TCGTCTCCAACACCCCGCAGG	0.527													C|||	2060	0.411342	0.3782	0.3948	5008	,	,		15159	0.2688		0.5507	False		,,,				2504	0.4714				p.V683V		Atlas-SNP	.											.	MYO5B	178	.	0			c.G2049A						PASS	.	C		1662,2190		356,950,620	29.0	30.0	30.0		2049	2.5	0.9	18	dbSNP_100	30	4564,3704		1267,2030,837	no	coding-synonymous	MYO5B	NM_001080467.2		1623,2980,1457	TT,TC,CC		44.7992,43.1464,48.6304		683/1849	47455923	6226,5894	1926	4134	6060	SO:0001819	synonymous_variant	4645	exon17			CTCCAACACCCCG	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.2049G>A	18.37:g.47455923C>T		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	44	43	0.977273	NM_001080467	B0I1R3|Q0P656|Q9H6Y6	Silent	SNP	ENST00000285039.7	37	CCDS42436.1																																																																																			C|0.563;T|0.437	0.437	strong		0.527	MYO5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448515.2		
RPGRIP1	57096	hgsc.bcm.edu	37	14	21796784	21796784	+	Missense_Mutation	SNP	G	G	C	rs3748361	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:21796784G>C	ENST00000400017.2	+	18	3097	c.3097G>C	c.(3097-3099)Gag>Cag	p.E1033Q	RPGRIP1_ENST00000307974.4_Missense_Mutation_p.E392Q|RPGRIP1_ENST00000206660.6_Missense_Mutation_p.E1033Q|RPGRIP1_ENST00000382933.4_Missense_Mutation_p.E359Q|RPGRIP1_ENST00000556336.1_Missense_Mutation_p.E690Q|RPGRIP1_ENST00000557771.1_Missense_Mutation_p.E995Q	NM_020366.3	NP_065099.3	Q96KN7	RPGR1_HUMAN	retinitis pigmentosa GTPase regulator interacting protein 1	1033			E -> Q (in dbSNP:rs3748361). {ECO:0000269|PubMed:10958647, ECO:0000269|PubMed:11528500, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:18682808}.		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)		p.E649Q(1)		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)		AAATACACCAGAGGTAAGACC	0.388													G|||	1479	0.295327	0.0219	0.2291	5008	,	,		20609	0.4246		0.3419	False		,,,				2504	0.5307				p.E1033Q		Atlas-SNP	.											RPGRIP1,NS,carcinoma,0,1	RPGRIP1	213	1	1	Substitution - Missense(1)	stomach(1)	c.G3097C						PASS	.	G	GLN/GLU	265,3473		12,241,1616	72.0	66.0	68.0		3097	1.8	0.4	14	dbSNP_107	68	2888,5328		523,1842,1743	yes	missense	RPGRIP1	NM_020366.3	29	535,2083,3359	CC,CG,GG		35.1509,7.0894,26.3761	benign	1033/1287	21796784	3153,8801	1869	4108	5977	SO:0001583	missense	57096	exon18			ACACCAGAGGTAA	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.3097G>C	14.37:g.21796784G>C	ENSP00000382895:p.Glu1033Gln	Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	45	21	0.466667	NM_020366	Q7Z2W6|Q8IXV5|Q96QA8|Q9HB94|Q9HB95|Q9HBK6|Q9NR40	Missense_Mutation	SNP	ENST00000400017.2	37	CCDS45080.1	587|587	0.26877289377289376|0.26877289377289376	13|13	0.026422764227642278|0.026422764227642278	83|83	0.2292817679558011|0.2292817679558011	227|227	0.3968531468531469|0.3968531468531469	264|264	0.3482849604221636|0.3482849604221636	G|G	0.025|0.025	-1.379822|-1.379822	0.01204|0.01204	0.070894|0.070894	0.351509|0.351509	ENSG00000092200|ENSG00000092200	ENST00000556336;ENST00000557771;ENST00000400017;ENST00000206660;ENST00000382933;ENST00000555587;ENST00000307974|ENST00000557606	T;T;T;T;T;T;T|.	0.77489|.	-0.01;-0.79;-0.83;-0.83;-0.34;-1.1;-1.1|.	4.74|4.74	1.79|1.79	0.24919|0.24919	.|.	0.810519|.	0.11028|.	N|.	0.607627|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.00162|0.00162	-1.95|-1.95	0.80722|0.80722	P|P	0.0|0.0	B;B;B;B;B;B|.	0.06786|.	0.0;0.0;0.0;0.001;0.0;0.0|.	B;B;B;B;B;B|.	0.04013|.	0.001;0.001;0.001;0.001;0.001;0.0|.	T|T	0.47598|0.47598	-0.9105|-0.9105	9|4	0.06365|.	T|.	0.9|.	-9.6351|-9.6351	7.5361|7.5361	0.27710|0.27710	0.1741:0.4739:0.352:0.0|0.1741:0.4739:0.352:0.0	rs3748361;rs17254729;rs52805987;rs3748361|rs3748361;rs17254729;rs52805987;rs3748361	416;392;508;359;649;1033|.	Q96KN7-2;Q96KN7-3;G3V3I7;Q96KN7-4;Q96KN7-5;Q96KN7|.	.;.;.;.;.;RPGR1_HUMAN|.	Q|H	690;995;1033;1033;359;508;392|9	ENSP00000450445:E690Q;ENSP00000451219:E995Q;ENSP00000382895:E1033Q;ENSP00000206660:E1033Q;ENSP00000372391:E359Q;ENSP00000451262:E508Q;ENSP00000309721:E392Q|.	ENSP00000206660:E1033Q|.	E|Q	+|+	1|3	0|2	RPGRIP1|RPGRIP1	20866624|20866624	0.892000|0.892000	0.30473|0.30473	0.418000|0.418000	0.26571|0.26571	0.022000|0.022000	0.10575|0.10575	1.269000|1.269000	0.33074|0.33074	1.233000|1.233000	0.43693|0.43693	-0.153000|-0.153000	0.13522|0.13522	GAG|CAG	G|0.722;C|0.277	0.277	strong		0.388	RPGRIP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410258.1	NM_020366	
VIPR2	7434	hgsc.bcm.edu	37	7	158896517	158896517	+	Silent	SNP	G	G	A	rs2270313	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:158896517G>A	ENST00000262178.2	-	4	473	c.288C>T	c.(286-288)gaC>gaT	p.D96D	VIPR2_ENST00000402066.1_Silent_p.D237D	NM_003382.4	NP_003373.2	P41587	VIPR2_HUMAN	vasoactive intestinal peptide receptor 2	96					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)		CTGACCATCCGTCACTCGTAC	0.507													G|||	1206	0.240815	0.3185	0.1873	5008	,	,		20770	0.1974		0.2485	False		,,,				2504	0.2106				p.D96D	Pancreas(154;1876 1931 2329 17914 20079)	Atlas-SNP	.											.	VIPR2	53	.	0			c.C288T						PASS	.	G		1334,3072	447.9+/-348.5	214,906,1083	235.0	192.0	206.0		288	-7.6	0.2	7	dbSNP_100	206	1995,6605	350.5+/-327.9	225,1545,2530	no	coding-synonymous	VIPR2	NM_003382.4		439,2451,3613	AA,AG,GG		23.1977,30.2769,25.5959		96/439	158896517	3329,9677	2203	4300	6503	SO:0001819	synonymous_variant	7434	exon4			CCATCCGTCACTC	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.288C>T	7.37:g.158896517G>A		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	115	56	0.486957	NM_003382	Q13053|Q15870|Q53Y09|Q6ZN22|Q9UCW0	Silent	SNP	ENST00000262178.2	37	CCDS5950.1	560	0.2564102564102564	169	0.3434959349593496	76	0.20994475138121546	127	0.22202797202797203	188	0.24802110817941952	G	0.289	-0.981342	0.02197	0.302769	0.231977	ENSG00000106018	ENST00000418475	.	.	.	5.0	-7.55	0.01327	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.21841	P	0.999511805	.	.	.	.	.	.	T	0.24621	-1.0155	3	.	.	.	.	9.5043	0.39037	0.7778:0.0:0.1167:0.1054	rs2270313;rs2270313	.	.	.	W	92	.	.	R	-	1	2	VIPR2	158589278	0.647000	0.27304	0.188000	0.23233	0.014000	0.08584	-0.332000	0.07904	-1.063000	0.03177	-1.012000	0.02466	CGG	G|0.750;A|0.250	0.250	strong		0.507	VIPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322675.1	NM_003382	
PTPRF	5792	hgsc.bcm.edu	37	1	44084739	44084739	+	Silent	SNP	C	C	T	rs1143701	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:44084739C>T	ENST00000359947.4	+	27	4852	c.4512C>T	c.(4510-4512)cgC>cgT	p.R1504R	PTPRF_ENST00000372414.3_Silent_p.R1504R|PTPRF_ENST00000372413.3_Silent_p.R1495R|PTPRF_ENST00000496447.1_3'UTR|PTPRF_ENST00000422171.2_Silent_p.R863R|PTPRF_ENST00000438120.1_Silent_p.R1495R	NM_002840.3	NP_002831.2	P10586	PTPRF_HUMAN	protein tyrosine phosphatase, receptor type, F	1504	Tyrosine-protein phosphatase 1. {ECO:0000255|PROSITE-ProRule:PRU00160}.				cell adhesion (GO:0007155)|cell migration (GO:0016477)|negative regulation of receptor binding (GO:1900121)|peptidyl-tyrosine dephosphorylation (GO:0035335)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	heparin binding (GO:0008201)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(2)|breast(4)|central_nervous_system(3)|endometrium(9)|kidney(4)|large_intestine(11)|liver(1)|lung(24)|ovary(4)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)	72	all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)				GTGAGAAGCGCGAGCTGCGTC	0.582													T|||	3693	0.73742	0.9455	0.5764	5008	,	,		16146	0.7649		0.7167	False		,,,				2504	0.5634				p.R1504R		Atlas-SNP	.											.	PTPRF	172	.	0			c.C4512T						PASS	.	T	,	4040,366	186.7+/-213.5	1857,326,20	75.0	69.0	71.0		4512,4485	0.9	1.0	1	dbSNP_86	71	6431,2169	370.9+/-336.0	2440,1551,309	no	coding-synonymous,coding-synonymous	PTPRF	NM_002840.3,NM_130440.2	,	4297,1877,329	TT,TC,CC		25.2209,8.3069,19.491	,	1504/1908,1495/1899	44084739	10471,2535	2203	4300	6503	SO:0001819	synonymous_variant	5792	exon27			GAAGCGCGAGCTG	Y00815	CCDS489.2, CCDS490.2	1p34	2013-02-11			ENSG00000142949	ENSG00000142949		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	9670	protein-coding gene	gene with protein product		179590		LAR		7558042	Standard	NM_130440		Approved		uc001cjr.3	P10586	OTTHUMG00000007501	ENST00000359947.4:c.4512C>T	1.37:g.44084739C>T		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	60	26	0.433333	NM_002840	D3DPX6|D3DPX7|Q5T021|Q5T022|Q5W9G2|Q86WS0	Silent	SNP	ENST00000359947.4	37	CCDS489.2	1672|1672	0.7655677655677655|0.7655677655677655	459|459	0.9329268292682927|0.9329268292682927	238|238	0.6574585635359116|0.6574585635359116	425|425	0.743006993006993|0.743006993006993	550|550	0.7255936675461742|0.7255936675461742	T|T	7.282|7.282	0.609324|0.609324	0.14066|0.14066	0.916931|0.916931	0.747791|0.747791	ENSG00000142949|ENSG00000142949	ENST00000429895|ENST00000412568;ENST00000414879	.|.	.|.	.|.	5.34|5.34	0.888|0.888	0.19206|0.19206	.|.	.|0.000000	.|0.33023	.|N	.|0.005372	T|.	0.00012|.	0.0000|.	.|.	.|.	.|.	0.09310|0.09310	P|P	1.0|1.0	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.40136|.	-0.9579|.	3|.	.|0.02654	.|T	.|1	.|.	3.3878|3.3878	0.07278|0.07278	0.0853:0.1957:0.3769:0.3421|0.0853:0.1957:0.3769:0.3421	rs1143701;rs1274775;rs17849117|rs1143701;rs1274775;rs17849117	.|.	.|.	.|.	V|X	1150|888;929	.|.	.|ENSP00000361484:R838X	A|R	+|+	2|1	0|2	PTPRF|PTPRF	43857326|43857326	1.000000|1.000000	0.71417|0.71417	0.994000|0.994000	0.49952|0.49952	0.942000|0.942000	0.58702|0.58702	0.863000|0.863000	0.27913|0.27913	-0.265000|-0.265000	0.09352|0.09352	-1.214000|-1.214000	0.01621|0.01621	GCG|CGA	A|0.000;C|0.209;T|0.790	0.790	strong		0.582	PTPRF-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000019710.1		
TMCO3	55002	hgsc.bcm.edu	37	13	114175032	114175032	+	Missense_Mutation	SNP	G	G	A	rs2260335	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:114175032G>A	ENST00000434316.2	+	8	1686	c.1327G>A	c.(1327-1329)Gcc>Acc	p.A443T	TMCO3_ENST00000375391.1_Intron|TMCO3_ENST00000474393.1_3'UTR	NM_017905.4	NP_060375.4	Q6UWJ1	TMCO3_HUMAN	transmembrane and coiled-coil domains 3	443			A -> T (in dbSNP:rs2260335).			integral component of membrane (GO:0016021)	solute:proton antiporter activity (GO:0015299)			NS(1)|endometrium(4)|large_intestine(9)|liver(1)|lung(8)|prostate(1)|stomach(1)	25	Lung NSC(43;0.0161)|all_neural(89;0.0337)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0145)|all_epithelial(44;0.00286)|all_lung(25;0.0273)|Breast(118;0.0411)|Lung NSC(25;0.0983)	all cancers(43;0.0317)			ACAGGCGGGCGCCAGTGCATC	0.478													G|||	1020	0.203674	0.41	0.1369	5008	,	,		16153	0.1498		0.1282	False		,,,				2504	0.1053				p.A443T		Atlas-SNP	.											.	TMCO3	77	.	0			c.G1327A						PASS	.	G	THR/ALA	1517,2889	483.0+/-359.6	258,1001,944	79.0	72.0	74.0		1327	4.1	0.0	13	dbSNP_100	74	1079,7521	225.2+/-261.4	60,959,3281	yes	missense	TMCO3	NM_017905.4	58	318,1960,4225	AA,AG,GG		12.5465,34.4303,19.96	benign	443/678	114175032	2596,10410	2203	4300	6503	SO:0001583	missense	55002	exon8			GCGGGCGCCAGTG	BC012564	CCDS9537.1	13q34	2008-02-05	2005-07-22	2005-07-22	ENSG00000150403	ENSG00000150403			20329	protein-coding gene	gene with protein product			"""chromosome 13 open reading frame 11"""	C13orf11			Standard	NM_017905		Approved	FLJ20623	uc001vtu.4	Q6UWJ1	OTTHUMG00000017389	ENST00000434316.2:c.1327G>A	13.37:g.114175032G>A	ENSP00000389399:p.Ala443Thr	Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	99	39	0.393939	NM_017905	Q5JSB1|Q6NUN1|Q8NG29|Q8TCI6|Q96EA6|Q9NWT2	Missense_Mutation	SNP	ENST00000434316.2	37	CCDS9537.1	430	0.19688644688644688	195	0.39634146341463417	51	0.1408839779005525	92	0.16083916083916083	92	0.12137203166226913	G	3.243	-0.154835	0.06544	0.344303	0.125465	ENSG00000150403	ENST00000434316	T	0.15834	2.39	4.94	4.09	0.47781	Cation/H+ exchanger (1);	0.309976	0.34110	N	0.004248	T	0.00012	0.0000	L	0.28274	0.84	0.18873	P	0.9999847456	B;B	0.24092	0.015;0.097	B;B	0.21151	0.021;0.033	T	0.48969	-0.8987	9	0.19590	T	0.45	-19.3477	13.1084	0.59259	0.0789:0.0:0.9211:0.0	rs2260335;rs57107498	443;443	Q6UWJ1;Q6UWJ1-2	TMCO3_HUMAN;.	T	443	ENSP00000389399:A443T	ENSP00000389399:A443T	A	+	1	0	TMCO3	113223033	0.972000	0.33761	0.012000	0.15200	0.017000	0.09413	2.740000	0.47418	1.083000	0.41159	0.495000	0.49567	GCC	G|0.805;A|0.195	0.195	strong		0.478	TMCO3-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045931.3	NM_017905	
USP22	23326	hgsc.bcm.edu	37	17	20911204	20911204	+	Silent	SNP	G	G	T	rs11541311	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:20911204G>T	ENST00000261497.4	-	9	1412	c.1209C>A	c.(1207-1209)atC>atA	p.I403I	USP22_ENST00000537526.2_Silent_p.I391I|USP22_ENST00000455117.2_Intron	NM_015276.1	NP_056091.1	Q9UPT9	UBP22_HUMAN	ubiquitin specific peptidase 22	403	USP.				cell cycle (GO:0007049)|chromatin organization (GO:0006325)|embryo development (GO:0009790)|histone deubiquitination (GO:0016578)|histone H4 acetylation (GO:0043967)|histone ubiquitination (GO:0016574)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of transcription, DNA-templated (GO:0045893)|protein deubiquitination (GO:0016579)|transcription, DNA-templated (GO:0006351)|ubiquitin-dependent protein catabolic process (GO:0006511)	SAGA complex (GO:0000124)	enzyme binding (GO:0019899)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|transcription coactivator activity (GO:0003713)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(3)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)	15						AACAGGCTACGATGGGCAGTT	0.488													G|||	780	0.155751	0.0159	0.1326	5008	,	,		17819	0.1667		0.2465	False		,,,				2504	0.2566				p.I403I		Atlas-SNP	.											.	USP22	45	.	0			c.C1209A						PASS	.	G		176,3664		9,158,1753	136.0	124.0	128.0		1209	-7.8	0.3	17	dbSNP_120	128	1813,6489		201,1411,2539	no	coding-synonymous	USP22	NM_015276.1		210,1569,4292	TT,TG,GG		21.8381,4.5833,16.3812		403/526	20911204	1989,10153	1920	4151	6071	SO:0001819	synonymous_variant	23326	exon9			GGCTACGATGGGC	AB028986	CCDS42285.1	17p11.2	2006-11-24	2005-08-08		ENSG00000124422	ENSG00000124422		"""Ubiquitin-specific peptidases"""	12621	protein-coding gene	gene with protein product		612116	"""ubiquitin specific protease 22"", ""ubiquitin specific peptidase 3-like"""	USP3L		12838346	Standard	NM_015276		Approved	KIAA1063	uc002gym.4	Q9UPT9	OTTHUMG00000133621	ENST00000261497.4:c.1209C>A	17.37:g.20911204G>T		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	89	41	0.460674	NM_015276	A0JNS3|Q2NLE2|Q6MZY4|Q8TBS8|Q96IW5	Silent	SNP	ENST00000261497.4	37	CCDS42285.1																																																																																			G|0.838;T|0.162	0.162	strong		0.488	USP22-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444169.1		
NBPF3	84224	hgsc.bcm.edu	37	1	21797221	21797221	+	Missense_Mutation	SNP	A	A	G	rs145790279	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:21797221A>G	ENST00000318249.5	+	4	790	c.440A>G	c.(439-441)gAg>gGg	p.E147G	NBPF3_ENST00000342104.5_Missense_Mutation_p.E147G|NBPF3_ENST00000454000.2_Missense_Mutation_p.E77G|NBPF3_ENST00000318220.6_Missense_Mutation_p.E91G	NM_032264.3	NP_115640.1	Q9H094	NBPF3_HUMAN	neuroblastoma breakpoint family, member 3	147						cytoplasm (GO:0005737)				breast(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(4)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	20		all_lung(284;2.16e-05)|Lung NSC(340;2.19e-05)|Colorectal(325;3.46e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00432)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0181)|OV - Ovarian serous cystadenocarcinoma(117;7.53e-27)|COAD - Colon adenocarcinoma(152;1.18e-05)|GBM - Glioblastoma multiforme(114;3.47e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000143)|STAD - Stomach adenocarcinoma(196;0.00306)|KIRC - Kidney renal clear cell carcinoma(1967;0.00645)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)		CAAGCTGAGGAGCTCAGGTGA	0.552													.|||	22	0.00439297	0.0	0.0058	5008	,	,		17610	0.0		0.0129	False		,,,				2504	0.0051				p.T147R		Atlas-SNP	.											.	NBPF3	55	.	0			c.C440G						PASS	.	A	GLY/GLU	6,4400		0,6,2197	42.0	47.0	46.0		440	-2.5	0.0	1	dbSNP_134	46	108,8492		0,108,4192	yes	missense	NBPF3	NM_032264.2	98	0,114,6389	GG,GA,AA		1.2558,0.1362,0.8765	probably-damaging	147/634	21797221	114,12892	2203	4300	6503	SO:0001583	missense	84224	exon4			CTGAGGAGCTCAG	BC024011	CCDS216.1, CCDS57976.1, CCDS57977.1	1p36.12	2013-01-17			ENSG00000142794	ENSG00000142794		"""neuroblastoma breakpoint family"""	25076	protein-coding gene	gene with protein product		612992				11230166, 16079250	Standard	NM_032264		Approved	AE2	uc001ber.4	Q9H094	OTTHUMG00000002944	ENST00000318249.5:c.440A>G	1.37:g.21797221A>G	ENSP00000316782:p.Glu147Gly	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	115	63	0.547826	NM_001256416	A8K965|B4DSP2|I3L0I8|Q3BBW1|Q5VTG2|Q5VTG3|Q5VTG4|Q8IX78|Q8ND86|Q8TC96	Missense_Mutation	SNP	ENST00000318249.5	37	CCDS216.1	11	0.005036630036630037	0	0.0	2	0.0055248618784530384	0	0.0	9	0.011873350923482849	.	9.834	1.189143	0.21954	0.001362	0.012558	ENSG00000142794	ENST00000454000;ENST00000318220;ENST00000318249;ENST00000417552;ENST00000342104;ENST00000434838	T;T;T;T;T	0.03860	3.78;4.03;4.03;4.03;4.03	1.23	-2.46	0.06461	.	.	.	.	.	T	0.07188	0.0182	L	0.47716	1.5	0.09310	N	1	P;D;D	0.64830	0.862;0.994;0.976	B;D;P	0.64877	0.405;0.93;0.696	T	0.10917	-1.0609	9	0.56958	D	0.05	.	5.9408	0.19192	0.3793:0.0:0.6207:0.0	.	77;147;147	B4DSP2;Q9H094-3;Q9H094	.;.;NBPF3_HUMAN	G	77;91;147;91;147;91	ENSP00000415711:E77G;ENSP00000316739:E91G;ENSP00000316782:E147G;ENSP00000340336:E147G;ENSP00000391865:E91G	ENSP00000316739:E91G	E	+	2	0	NBPF3	21669808	0.096000	0.21769	0.001000	0.08648	0.076000	0.17211	-0.001000	0.12947	-0.972000	0.03559	0.327000	0.21459	GAG	A|0.992;G|0.008	0.008	strong		0.552	NBPF3-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_032264	
GUCA2B	2981	hgsc.bcm.edu	37	1	42619152	42619152	+	Missense_Mutation	SNP	C	C	A	rs2297567	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:42619152C>A	ENST00000372581.1	+	1	61	c.31C>A	c.(31-33)Cca>Aca	p.P11T		NM_007102.2	NP_009033.1	Q16661	GUC2B_HUMAN	guanylate cyclase activator 2B (uroguanylin)	11			P -> T (in dbSNP:rs2297567).		body fluid secretion (GO:0007589)|cGMP biosynthetic process (GO:0006182)|excretion (GO:0007588)|negative regulation of blood pressure (GO:0045776)|positive regulation of guanylate cyclase activity (GO:0031284)	extracellular vesicular exosome (GO:0070062)	calcium sensitive guanylate cyclase activator activity (GO:0008048)			breast(1)|large_intestine(2)	3	Ovarian(52;0.01)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)				AGGGCTCCTGCCAGGAGTGGC	0.647													C|||	897	0.179113	0.1445	0.0937	5008	,	,		16915	0.1597		0.1869	False		,,,				2504	0.2986				p.P11T		Atlas-SNP	.											.	GUCA2B	9	.	0			c.C31A						PASS	.	C	THR/PRO	731,3675	298.1+/-285.1	59,613,1531	67.0	55.0	59.0		31	-5.2	0.0	1	dbSNP_100	59	1624,6976	297.9+/-303.7	164,1296,2840	no	missense	GUCA2B	NM_007102.2	38	223,1909,4371	AA,AC,CC		18.8837,16.591,18.107	benign	11/113	42619152	2355,10651	2203	4300	6503	SO:0001583	missense	2981	exon1			CTCCTGCCAGGAG	BC069301	CCDS464.1	1p34-p33	2014-01-30			ENSG00000044012	ENSG00000044012		"""Endogenous ligands"""	4683	protein-coding gene	gene with protein product	"""prepro-uroguanylin"""	601271				8605041, 9268639	Standard	NM_007102		Approved		uc001chc.1	Q16661	OTTHUMG00000007024	ENST00000372581.1:c.31C>A	1.37:g.42619152C>A	ENSP00000361662:p.Pro11Thr	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	41	19	0.463415	NM_007102	Q52LV0	Missense_Mutation	SNP	ENST00000372581.1	37	CCDS464.1	308	0.14102564102564102	70	0.14227642276422764	27	0.07458563535911603	75	0.13111888111888112	136	0.17941952506596306	C	8.033	0.762148	0.15914	0.16591	0.188837	ENSG00000044012	ENST00000372581	T	0.41065	1.01	3.85	-5.17	0.02849	.	23.993800	0.00166	N	0.000003	T	0.00039	0.0001	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.07233	-1.0783	9	0.26408	T	0.33	1.1147	1.9	0.03265	0.1614:0.4137:0.2344:0.1904	rs2297567;rs2297567	11	Q16661	GUC2B_HUMAN	T	11	ENSP00000361662:P11T	ENSP00000361662:P11T	P	+	1	0	GUCA2B	42391739	0.000000	0.05858	0.000000	0.03702	0.060000	0.15804	-1.500000	0.02283	-0.978000	0.03533	0.491000	0.48974	CCA	C|0.831;A|0.169	0.169	strong		0.647	GUCA2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000018307.1	NM_007102	
SCN10A	6336	hgsc.bcm.edu	37	3	38766701	38766701	+	Silent	SNP	C	C	T	rs6791171	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	153	0	0		WXS	Illumina HiSeq	Phase_I	137	55	0.40146	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	
PPP1R3D	5509	hgsc.bcm.edu	37	20	58514312	58514312	+	Silent	SNP	C	C	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:58514312C>A	ENST00000370996.3	-	1	1040	c.675G>T	c.(673-675)ggG>ggT	p.G225G	FAM217B_ENST00000360816.3_5'Flank|FAM217B_ENST00000358293.3_Intron	NM_006242.3	NP_006233.1	O95685	PPR3D_HUMAN	protein phosphatase 1, regulatory subunit 3D	225	CBM21. {ECO:0000255|PROSITE- ProRule:PRU00491}.				dephosphorylation (GO:0016311)|glycogen metabolic process (GO:0005977)|regulation of glycogen biosynthetic process (GO:0005979)|regulation of glycogen catabolic process (GO:0005981)	glycogen granule (GO:0042587)|intracellular membrane-bounded organelle (GO:0043231)	protein serine/threonine phosphatase activity (GO:0004722)			endometrium(1)|kidney(1)|large_intestine(1)|lung(8)|prostate(1)|urinary_tract(1)	13	all_lung(29;0.00391)		BRCA - Breast invasive adenocarcinoma(7;5.12e-09)			GGCCTGCGGGCCCGCGCCACC	0.697																																					p.G225G		Atlas-SNP	.											.	PPP1R3D	23	.	0			c.G675T						PASS	.						32.0	34.0	33.0					20																	58514312		2201	4299	6500	SO:0001819	synonymous_variant	5509	exon1			TGCGGGCCCGCGC	Y18206	CCDS13483.1	20q13.3	2012-04-17	2011-10-04	2001-08-01	ENSG00000132825	ENSG00000132825		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	9294	protein-coding gene	gene with protein product		603326	"""protein phosphatase 1, regulatory (inhibitor) subunit 3D"""	PPP1R6		9414128, 9275233	Standard	NM_006242		Approved		uc002ybb.3	O95685	OTTHUMG00000032876	ENST00000370996.3:c.675G>T	20.37:g.58514312C>A		Somatic	4	0	0		WXS	Illumina HiSeq	Phase_I	17	12	0.705882	NM_006242	Q6DK02	Silent	SNP	ENST00000370996.3	37	CCDS13483.1																																																																																			.	.	none		0.697	PPP1R3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079940.2	NM_006242	
FBXO6	26270	hgsc.bcm.edu	37	1	11728952	11728952	+	Silent	SNP	C	C	T	rs7514198	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:11728952C>T	ENST00000376753.4	+	2	372	c.237C>T	c.(235-237)taC>taT	p.Y79Y		NM_018438.5	NP_060908.1	Q9NRD1	FBX6_HUMAN	F-box protein 6	79	FBA. {ECO:0000255|PROSITE- ProRule:PRU00482}.				DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|glycoprotein catabolic process (GO:0006516)|proteolysis (GO:0006508)|response to unfolded protein (GO:0006986)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)	cytoplasm (GO:0005737)|SCF ubiquitin ligase complex (GO:0019005)	carbohydrate binding (GO:0030246)|glycoprotein binding (GO:0001948)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|large_intestine(1)|lung(1)|ovary(1)|upper_aerodigestive_tract(2)	6	Ovarian(185;0.249)	Lung NSC(185;4.15e-05)|all_lung(284;4.76e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.25e-06)|COAD - Colon adenocarcinoma(227;0.000251)|BRCA - Breast invasive adenocarcinoma(304;0.000297)|Kidney(185;0.000747)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.00727)|READ - Rectum adenocarcinoma(331;0.0649)		AAATCTTCTACTTCCTACGGA	0.602													C|||	433	0.0864617	0.1589	0.0735	5008	,	,		18362	0.0129		0.0616	False		,,,				2504	0.0992				p.Y79Y	NSCLC(54;506 1562 46490 51389)	Atlas-SNP	.											FBXO6,NS,carcinoma,+1,1	FBXO6	17	1	0			c.C237T						PASS	.	C		596,3810	261.3+/-264.2	31,534,1638	56.0	61.0	59.0		237	3.2	1.0	1	dbSNP_116	59	662,7938	166.5+/-218.5	25,612,3663	no	coding-synonymous	FBXO6	NM_018438.5		56,1146,5301	TT,TC,CC		7.6977,13.527,9.6725		79/294	11728952	1258,11748	2203	4300	6503	SO:0001819	synonymous_variant	26270	exon2			CTTCTACTTCCTA	AF129536	CCDS133.1	1p36.22	2008-05-14	2004-06-15		ENSG00000116663	ENSG00000116663		"""F-boxes /  ""other"""""	13585	protein-coding gene	gene with protein product		605647	"""F-box only protein 6"""			10531035, 10945468	Standard	NM_018438		Approved	FBX6, FBG2, FBS2, Fbx6b	uc001aso.3	Q9NRD1	OTTHUMG00000002229	ENST00000376753.4:c.237C>T	1.37:g.11728952C>T		Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	118	49	0.415254	NM_018438	B1AK42|B2RC88|Q9UKT3	Silent	SNP	ENST00000376753.4	37	CCDS133.1	142	0.06501831501831502	66	0.13414634146341464	26	0.0718232044198895	3	0.005244755244755245	47	0.06200527704485488	C	0.710	-0.787346	0.02907	0.13527	0.076977	ENSG00000116663	ENST00000449067	.	.	.	5.06	3.16	0.36331	.	.	.	.	.	T	0.00384	0.0012	.	.	.	0.09310	P	0.9999999950805	.	.	.	.	.	.	T	0.09465	-1.0673	3	.	.	.	.	7.5757	0.27935	0.0:0.7273:0.0:0.2727	rs7514198	.	.	.	I	67	.	.	T	+	2	0	FBXO6	11651539	0.915000	0.31059	0.988000	0.46212	0.089000	0.18198	-0.016000	0.12613	0.636000	0.30508	-0.225000	0.12378	ACT	C|0.913;T|0.087	0.087	strong		0.602	FBXO6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006332.1	NM_018438	
PEAR1	375033	hgsc.bcm.edu	37	1	156883493	156883493	+	Missense_Mutation	SNP	G	G	A	rs11264581	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:156883493G>A	ENST00000338302.3	+	22	2879	c.2654G>A	c.(2653-2655)cGc>cAc	p.R885H	PEAR1_ENST00000292357.7_Missense_Mutation_p.R885H			Q5VY43	PEAR1_HUMAN	platelet endothelial aggregation receptor 1	885	Pro-rich.		R -> H (in dbSNP:rs11264581).		recognition of apoptotic cell (GO:0043654)	integral component of membrane (GO:0016021)|phagocytic cup (GO:0001891)				breast(1)|central_nervous_system(2)|endometrium(4)|large_intestine(6)|lung(22)|ovary(4)|skin(3)|upper_aerodigestive_tract(1)	43	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)					GGGAGCAGCCGCCTGGACCGA	0.612													G|||	1161	0.231829	0.0469	0.2954	5008	,	,		16121	0.4732		0.1759	False		,,,				2504	0.2454				p.R885H		Atlas-SNP	.											.	PEAR1	118	.	0			c.G2654A						PASS	.	G	HIS/ARG	293,4113	159.6+/-192.1	7,279,1917	37.0	38.0	38.0		2654	-3.7	0.7	1	dbSNP_120	38	1577,7023	291.1+/-300.1	149,1279,2872	yes	missense	PEAR1	NM_001080471.1	29	156,1558,4789	AA,AG,GG		18.3372,6.65,14.378	benign	885/1038	156883493	1870,11136	2203	4300	6503	SO:0001583	missense	375033	exon21			GCAGCCGCCTGGA	AK098809	CCDS30892.1	1q23.1	2008-02-05	2007-10-25	2007-10-25	ENSG00000187800	ENSG00000187800			33631	protein-coding gene	gene with protein product		610278	"""multiple EGF-like-domains 12"""	MEGF12		15851471	Standard	NM_001080471		Approved	JEDI, FLJ00193	uc001fqj.1	Q5VY43	OTTHUMG00000041293	ENST00000338302.3:c.2654G>A	1.37:g.156883493G>A	ENSP00000344465:p.Arg885His	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	71	45	0.633803	NM_001080471	Q8TEK2	Missense_Mutation	SNP	ENST00000338302.3	37	CCDS30892.1	488	0.22344322344322345	26	0.052845528455284556	79	0.21823204419889503	251	0.4388111888111888	132	0.1741424802110818	G	13.25	2.182510	0.38511	0.0665	0.183372	ENSG00000187800	ENST00000338302;ENST00000292357	D;D	0.88975	-2.45;-2.45	5.78	-3.72	0.04411	.	0.543959	0.15501	N	0.259052	T	0.45975	0.1369	N	0.03608	-0.345	0.80722	P	0.0	B	0.11235	0.004	B	0.04013	0.001	T	0.28396	-1.0045	9	0.15066	T	0.55	.	5.0929	0.14718	0.2315:0.0:0.3078:0.4608	rs11264581;rs59112747;rs11264581	885	Q5VY43	PEAR1_HUMAN	H	885	ENSP00000344465:R885H;ENSP00000292357:R885H	ENSP00000292357:R885H	R	+	2	0	PEAR1	155150117	0.000000	0.05858	0.737000	0.30932	0.740000	0.42216	-0.451000	0.06795	-0.439000	0.07222	0.563000	0.77884	CGC	G|0.832;A|0.168	0.168	strong		0.612	PEAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098937.2	NM_001080471	
RBBP8NL	140893	hgsc.bcm.edu	37	20	60987737	60987737	+	Missense_Mutation	SNP	C	C	T	rs6089366	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:60987737C>T	ENST00000252998.1	-	13	1975	c.1819G>A	c.(1819-1821)Gag>Aag	p.E607K		NM_080833.2	NP_543023.2	Q8NC74	RB8NL_HUMAN	RBBP8 N-terminal like	607			E -> K (in dbSNP:rs6089366).			extracellular space (GO:0005615)											TGCCCGTGCTCCTGGGTGCAG	0.697													C|||	293	0.0585064	0.0356	0.1196	5008	,	,		17782	0.0		0.1421	False		,,,				2504	0.0204				p.E607K		Atlas-SNP	.											.	.	.	.	0			c.G1819A						PASS	.	C	LYS/GLU	274,4128	150.7+/-184.7	8,258,1935	62.0	63.0	63.0		1819	2.3	0.0	20	dbSNP_114	63	1328,7272	259.5+/-282.7	101,1126,3073	no	missense	C20orf151	NM_080833.2	56	109,1384,5008	TT,TC,CC		15.4419,6.2244,12.3212	possibly-damaging	607/665	60987737	1602,11400	2201	4300	6501	SO:0001583	missense	140893	exon13			CGTGCTCCTGGGT	AL121832	CCDS13498.1	20q13.33	2012-10-30	2012-10-30	2012-10-30	ENSG00000130701	ENSG00000130701			16144	protein-coding gene	gene with protein product	"""hypothetical protein LOC140893"""		"""chromosome 20 open reading frame 151"""	C20orf151		11780052	Standard	NM_080833		Approved	dJ908M14.3	uc002ycw.2	Q8NC74	OTTHUMG00000032913	ENST00000252998.1:c.1819G>A	20.37:g.60987737C>T	ENSP00000252998:p.Glu607Lys	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	27	13	0.481481	NM_080833	B2RP98|Q8N4Z9|Q9BR75|Q9H0Y9	Missense_Mutation	SNP	ENST00000252998.1	37	CCDS13498.1	174	0.07967032967032966	20	0.04065040650406504	51	0.1408839779005525	0	0.0	103	0.1358839050131926	C	11.90	1.778096	0.31502	0.062244	0.154419	ENSG00000130701	ENST00000252998	T	0.21361	2.01	3.31	2.3	0.28687	.	0.749692	0.11067	N	0.603324	T	0.00109	0.0003	L	0.46157	1.445	0.80722	P	0.0	B	0.21452	0.056	B	0.15484	0.013	T	0.16988	-1.0384	9	0.26408	T	0.33	-11.2853	8.7343	0.34519	0.0:0.7644:0.2356:0.0	rs6089366;rs6089366	607	Q8NC74	CT151_HUMAN	K	607	ENSP00000252998:E607K	ENSP00000252998:E607K	E	-	1	0	C20orf151	60421132	0.001000	0.12720	0.004000	0.12327	0.006000	0.05464	0.226000	0.17776	0.645000	0.30675	0.491000	0.48974	GAG	C|0.890;T|0.110	0.110	strong		0.697	RBBP8NL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080029.1	NM_080833	
OR5W2	390148	hgsc.bcm.edu	37	11	55681566	55681566	+	Missense_Mutation	SNP	G	G	A	rs61749302	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:55681566G>A	ENST00000344514.1	-	1	492	c.493C>T	c.(493-495)Cgc>Tgc	p.R165C		NM_001001960.1	NP_001001960.1	Q8NH69	OR5W2_HUMAN	olfactory receptor, family 5, subfamily W, member 2	165						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.R165C(1)		breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(28)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49						AAGCATAGGCGGAAGGCCAGT	0.428													G|||	469	0.0936502	0.1392	0.0403	5008	,	,		21011	0.0903		0.0944	False		,,,				2504	0.0726				p.R165C	Melanoma(48;171 1190 15239 43886 49348)	Atlas-SNP	.											OR5W2,NS,carcinoma,+1,5	OR5W2	112	5	1	Substitution - Missense(1)	large_intestine(1)	c.C493T						PASS	.	G	CYS/ARG	556,3846	246.5+/-255.1	41,474,1686	87.0	77.0	80.0		493	1.5	0.0	11	dbSNP_129	80	722,7870	174.6+/-224.8	31,660,3605	yes	missense	OR5W2	NM_001001960.1	180	72,1134,5291	AA,AG,GG		8.4032,12.6306,9.8353	benign	165/311	55681566	1278,11716	2201	4296	6497	SO:0001583	missense	390148	exon1			ATAGGCGGAAGGC	BK004398	CCDS31513.1	11q11	2012-08-09		2004-03-10	ENSG00000187612	ENSG00000187612		"""GPCR / Class A : Olfactory receptors"""	15299	protein-coding gene	gene with protein product				OR5W2P, OR5W3P			Standard	NM_001001960		Approved		uc010rir.2	Q8NH69	OTTHUMG00000166818	ENST00000344514.1:c.493C>T	11.37:g.55681566G>A	ENSP00000342448:p.Arg165Cys	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	67	46	0.686567	NM_001001960		Missense_Mutation	SNP	ENST00000344514.1	37	CCDS31513.1	210	0.09615384615384616	81	0.16463414634146342	18	0.049723756906077346	44	0.07692307692307693	67	0.08839050131926121	G	4.463	0.085831	0.08583	0.126306	0.084032	ENSG00000187612	ENST00000344514	T	0.00188	8.59	4.77	1.45	0.22620	GPCR, rhodopsin-like superfamily (1);	0.602095	0.13398	N	0.390838	T	0.00012	0.0000	L	0.58510	1.815	0.80722	P	0.0	B	0.19583	0.037	B	0.24848	0.056	T	0.15492	-1.0435	9	0.59425	D	0.04	.	5.7223	0.17995	0.1028:0.0:0.3813:0.5159	.	165	Q8NH69	OR5W2_HUMAN	C	165	ENSP00000342448:R165C	ENSP00000342448:R165C	R	-	1	0	OR5W2	55438142	0.000000	0.05858	0.033000	0.17914	0.046000	0.14306	-1.143000	0.03200	0.425000	0.26087	0.549000	0.68633	CGC	G|0.903;A|0.097	0.097	strong		0.428	OR5W2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391523.1	NM_001001960	
UBASH3A	53347	hgsc.bcm.edu	37	21	43852232	43852232	+	Silent	SNP	C	C	T	rs13052676	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:43852232C>T	ENST00000319294.6	+	9	1222	c.1191C>T	c.(1189-1191)agC>agT	p.S397S	UBASH3A_ENST00000291535.6_Silent_p.S359S|UBASH3A_ENST00000398367.1_Silent_p.S359S	NM_018961.3	NP_061834.1	P57075	UBS3A_HUMAN	ubiquitin associated and SH3 domain containing A	397	Phosphatase-like.				negative regulation of T cell receptor signaling pathway (GO:0050860)|regulation of cytokine production (GO:0001817)	cytosol (GO:0005829)|nucleus (GO:0005634)	catalytic activity (GO:0003824)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(9)|lung(12)|ovary(3)	28						CAAGGAAGAGCGTGCTGGTGG	0.587													C|||	1283	0.25619	0.1921	0.2608	5008	,	,		19823	0.2232		0.331	False		,,,				2504	0.2965				p.S397S		Atlas-SNP	.											.	UBASH3A	72	.	0			c.C1191T						PASS	.	C	,	974,3432	359.4+/-314.8	109,756,1338	132.0	89.0	103.0		1077,1191	-0.1	0.1	21	dbSNP_121	103	2809,5791	436.2+/-358.2	456,1897,1947	no	coding-synonymous,coding-synonymous	UBASH3A	NM_001001895.2,NM_018961.3	,	565,2653,3285	TT,TC,CC		32.6628,22.1062,29.0866	,	359/624,397/662	43852232	3783,9223	2203	4300	6503	SO:0001819	synonymous_variant	53347	exon9			GAAGAGCGTGCTG	AJ277750	CCDS13687.1, CCDS33566.1, CCDS58791.1	21q22.3	2010-04-28	2010-04-28		ENSG00000160185	ENSG00000160185			12462	protein-coding gene	gene with protein product		605736				11281453	Standard	NM_018961		Approved	STS-2, TULA, CLIP4	uc002zbf.3	P57075	OTTHUMG00000086805	ENST00000319294.6:c.1191C>T	21.37:g.43852232C>T		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	99	35	0.353535	NM_018961	G5E9E4|Q6HA34|Q6HA35|Q6ISI6|Q6ISK3|Q6ISS9	Silent	SNP	ENST00000319294.6	37	CCDS13687.1																																																																																			C|0.722;T|0.278	0.278	strong		0.587	UBASH3A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000195382.1	NM_001001895	
BIRC6	57448	hgsc.bcm.edu	37	2	32822957	32822957	+	Silent	SNP	G	G	A	rs2710625	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:32822957G>A	ENST00000421745.2	+	69	13886	c.13752G>A	c.(13750-13752)acG>acA	p.T4584T		NM_016252.3	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat containing 6	4584	Ubiquitin-conjugating.				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.T4584T(1)|p.T4556T(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)					AAGCTGTGACGCTTTCAACCT	0.438													A|||	1667	0.332867	0.3207	0.3674	5008	,	,		15901	0.2956		0.4344	False		,,,				2504	0.2587				p.T4584T	Pancreas(94;175 1509 16028 18060 45422)	Atlas-SNP	.											BIRC6_ENST00000421745,NS,carcinoma,0,2	BIRC6	838	2	2	Substitution - coding silent(2)	stomach(2)	c.G13752A						PASS	.	A		1392,3014	688.7+/-405.0	208,976,1019	122.0	100.0	108.0		13752	-9.8	0.0	2	dbSNP_100	108	3646,4954	623.3+/-397.4	773,2100,1427	no	coding-synonymous	BIRC6	NM_016252.3		981,3076,2446	AA,AG,GG		42.3953,31.5933,38.736		4584/4858	32822957	5038,7968	2203	4300	6503	SO:0001819	synonymous_variant	57448	exon69			TGTGACGCTTTCA	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.13752G>A	2.37:g.32822957G>A		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	47	46	0.978723	NM_016252	Q9ULD1	Silent	SNP	ENST00000421745.2	37	CCDS33175.2																																																																																			G|0.624;A|0.376	0.376	strong		0.438	BIRC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318769.3	NM_016252	
AKR1C3	8644	hgsc.bcm.edu	37	10	5138607	5138607	+	Silent	SNP	G	G	A	rs7741	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:5138607G>A	ENST00000380554.3	+	2	742	c.90G>A	c.(88-90)ccG>ccA	p.P30P	U8_ENST00000459536.1_RNA|AKR1C3_ENST00000470862.2_3'UTR|AKR1C3_ENST00000605149.1_Silent_p.P7P|AKR1C3_ENST00000439082.2_5'UTR	NM_001253908.1|NM_003739.5	NP_001240837.1|NP_003730.4	P42330	AK1C3_HUMAN	aldo-keto reductase family 1, member C3	30					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)	TCCAGGTTCCGAGAAGTAAAG	0.438													G|||	1083	0.216254	0.3381	0.196	5008	,	,		20326	0.0		0.3648	False		,,,				2504	0.136				p.P30P		Atlas-SNP	.											.	AKR1C3	21	.	0			c.G90A						PASS	.	G		1485,2921	475.7+/-357.4	246,993,964	72.0	68.0	69.0		90	-3.2	0.0	10	dbSNP_52	69	3041,5557	468.9+/-367.4	544,1953,1802	no	coding-synonymous	AKR1C3	NM_003739.4		790,2946,2766	AA,AG,GG		35.3687,33.704,34.8047		30/324	5138607	4526,8478	2203	4299	6502	SO:0001819	synonymous_variant	8644	exon2			GGTTCCGAGAAGT	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.90G>A	10.37:g.5138607G>A		Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	170	67	0.394118	NM_001253908	A8K2V0|B4DL37|Q5T2L1|Q96DJ1|Q96KI8|Q99530|Q9UCX1|Q9UII3|Q9UKL9	Silent	SNP	ENST00000380554.3	37	CCDS7063.1																																																																																			G|0.710;A|0.290	0.290	strong		0.438	AKR1C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046533.2	NM_003739	
NUP133	55746	hgsc.bcm.edu	37	1	229635521	229635521	+	Silent	SNP	A	A	G	rs10916495	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:229635521A>G	ENST00000261396.3	-	5	649	c.558T>C	c.(556-558)taT>taC	p.Y186Y	NUP133_ENST00000537506.1_Silent_p.Y170Y|NUP133_ENST00000366678.3_Silent_p.Y186Y	NM_018230.2	NP_060700.2	Q8WUM0	NU133_HUMAN	nucleoporin 133kDa	186					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.Y186Y(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)				GGCTTGGCCAATAGCGGATAG	0.453													A|||	883	0.176318	0.1369	0.2896	5008	,	,		17612	0.1577		0.2028	False		,,,				2504	0.1411				p.Y186Y		Atlas-SNP	.											NUP133,NS,carcinoma,0,1	NUP133	111	1	1	Substitution - coding silent(1)	stomach(1)	c.T558C						PASS	.	A		650,3756	276.0+/-272.9	50,550,1603	94.0	91.0	92.0		558	-2.6	1.0	1	dbSNP_120	92	1811,6789	325.4+/-316.9	190,1431,2679	no	coding-synonymous	NUP133	NM_018230.2		240,1981,4282	GG,GA,AA		21.0581,14.7526,18.922		186/1157	229635521	2461,10545	2203	4300	6503	SO:0001819	synonymous_variant	55746	exon5			TGGCCAATAGCGG		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.558T>C	1.37:g.229635521A>G		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	111	42	0.378378	NM_018230	B2RAZ8|Q5T8N0|Q9H9W2|Q9NV71|Q9NVC4	Silent	SNP	ENST00000261396.3	37	CCDS1579.1																																																																																			A|0.813;G|0.187	0.187	strong		0.453	NUP133-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095224.1	NM_018230	
AP5Z1	9907	hgsc.bcm.edu	37	7	4827330	4827330	+	Silent	SNP	C	C	T	rs17135128	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:4827330C>T	ENST00000348624.4	+	11	1471	c.1377C>T	c.(1375-1377)gaC>gaT	p.D459D	AP5Z1_ENST00000401897.1_Silent_p.D459D|MIR4656_ENST00000579503.1_RNA	NM_014855.2	NP_055670.1	O43299	AP5Z1_HUMAN	adaptor-related protein complex 5, zeta 1 subunit	459					cell death (GO:0008219)|double-strand break repair via homologous recombination (GO:0000724)|endosomal transport (GO:0016197)|protein transport (GO:0015031)	AP-5 adaptor complex (GO:0044599)|AP-type membrane coat adaptor complex (GO:0030119)|cytoplasm (GO:0005737)|nucleus (GO:0005634)											CCCTGGTGGACGCTGGCACAG	0.692													C|||	408	0.0814696	0.0401	0.036	5008	,	,		15883	0.0496		0.0736	False		,,,				2504	0.2106				p.D459D		Atlas-SNP	.											KIAA0415_ENST00000450194,rectum,carcinoma,0,2	.	.	2	0			c.C1377T						PASS	.	C		189,3981		5,179,1901	25.0	31.0	29.0		1377	-3.7	0.0	7	dbSNP_123	29	532,7742		19,494,3624	no	coding-synonymous	KIAA0415	NM_014855.2		24,673,5525	TT,TC,CC		6.4298,4.5324,5.794		459/808	4827330	721,11723	2085	4137	6222	SO:0001819	synonymous_variant	9907	exon11			GGTGGACGCTGGC	AB007875	CCDS47528.1	7p22.1	2012-03-20	2012-03-20	2012-03-20	ENSG00000242802	ENSG00000242802			22197	protein-coding gene	gene with protein product		613653	"""KIAA0415"""	KIAA0415		20613862, 22022230	Standard	NM_014855		Approved	SPG48, zeta	uc003sne.3	O43299	OTTHUMG00000151754	ENST00000348624.4:c.1377C>T	7.37:g.4827330C>T		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	95	77	0.810526	NM_014855	Q8N3X2|Q96H80	Silent	SNP	ENST00000348624.4	37	CCDS47528.1																																																																																			C|0.943;T|0.057	0.057	strong		0.692	AP5Z1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323771.1		
CHMP4C	92421	hgsc.bcm.edu	37	8	82670412	82670412	+	Silent	SNP	G	G	A	rs62514262	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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						PASS	.	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	104	0	0		WXS	Illumina HiSeq	Phase_I	107	23	0.214953	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	
DHRS7C	201140	hgsc.bcm.edu	37	17	9676134	9676134	+	Missense_Mutation	SNP	G	G	A	rs2280490	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:9676134G>A	ENST00000330255.5	-	5	692	c.680C>T	c.(679-681)tCg>tTg	p.S227L	DHRS7C_ENST00000571134.1_Missense_Mutation_p.S226L	NM_001105571.2|NM_001220493.1	NP_001099041.1|NP_001207422.1	A6NNS2	DRS7C_HUMAN	dehydrogenase/reductase (SDR family) member 7C	227			S -> L (in dbSNP:rs2280490).		regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)	extracellular region (GO:0005576)|longitudinal sarcoplasmic reticulum (GO:0014801)|sarcoplasmic reticulum membrane (GO:0033017)	retinol dehydrogenase activity (GO:0004745)			NS(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(9)	15						CACGTGGTACGACCGGATGAA	0.582													G|||	447	0.0892572	0.0741	0.062	5008	,	,		18957	0.0992		0.1054	False		,,,				2504	0.1022				p.S227L		Atlas-SNP	.											.	DHRS7C	34	.	0			c.C680T						PASS	.	G	LEU/SER,LEU/SER	399,3997	174.1+/-203.8	24,351,1823	73.0	81.0	78.0		680,677	4.7	0.3	17	dbSNP_100	78	909,7683	196.8+/-241.6	49,811,3436	yes	missense,missense	DHRS7C	NM_001220493.1,NM_001105571.2	145,145	73,1162,5259	AA,AG,GG		10.5796,9.0764,10.0708	benign,benign	227/313,226/312	9676134	1308,11680	2198	4296	6494	SO:0001583	missense	201140	exon5			TGGTACGACCGGA		CCDS56020.1, CCDS58517.1	17p13.1	2011-09-20				ENSG00000184544		"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 3"""	32423	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 32C, member 2"""					19027726	Standard	NM_001105571		Approved	SDR32C2	uc010vvb.2	A6NNS2		ENST00000330255.5:c.680C>T	17.37:g.9676134G>A	ENSP00000327975:p.Ser227Leu	Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	40	15	0.375	NM_001220493	B7ZW74|B9EJH3	Missense_Mutation	SNP	ENST00000330255.5	37	CCDS56020.1	212	0.09706959706959707	50	0.1016260162601626	19	0.052486187845303865	60	0.1048951048951049	83	0.10949868073878628	G	10.84	1.462937	0.26248	0.090764	0.105796	ENSG00000184544	ENST00000330255	T	0.54866	0.55	4.68	4.68	0.58851	NAD(P)-binding domain (1);	0.490245	0.21837	N	0.068386	T	0.00875	0.0029	L	0.40543	1.245	0.27351	P	0.956257	B;P	0.38110	0.226;0.618	B;B	0.20184	0.028;0.023	T	0.35400	-0.9790	9	0.87932	D	0	.	16.5323	0.84364	0.0:0.0:1.0:0.0	rs2280490;rs17207682;rs56923642;rs2280490	227;223	A6NNS2;B9EJH3	DRS7C_HUMAN;.	L	227	ENSP00000327975:S227L	ENSP00000327975:S227L	S	-	2	0	DHRS7C	9616859	1.000000	0.71417	0.317000	0.25265	0.045000	0.14185	7.355000	0.79434	2.429000	0.82318	0.655000	0.94253	TCG	G|0.907;A|0.093	0.093	strong		0.582	DHRS7C-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439863.1	XM_113912	
EXPH5	23086	hgsc.bcm.edu	37	11	108383676	108383676	+	Missense_Mutation	SNP	A	A	G	rs10749920	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:108383676A>G	ENST00000265843.4	-	6	2668	c.2558T>C	c.(2557-2559)cTg>cCg	p.L853P	EXPH5_ENST00000428840.1_Missense_Mutation_p.L777P|EXPH5_ENST00000443411.1_Missense_Mutation_p.L665P|EXPH5_ENST00000524840.1_5'Flank|EXPH5_ENST00000525344.1_Missense_Mutation_p.L846P	NM_015065.2	NP_055880	Q8NEV8	EXPH5_HUMAN	exophilin 5	853			L -> P (in dbSNP:rs10749920).		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)		AGTATCAGTCAGTGCAGAGCT	0.403													G|||	1795	0.358427	0.6876	0.1844	5008	,	,		19778	0.2093		0.1909	False		,,,				2504	0.363				p.L853P		Atlas-SNP	.											.	EXPH5	193	.	0			c.T2558C						PASS	.	G	PRO/LEU	2667,1735	518.5+/-369.7	837,993,371	235.0	228.0	231.0		2558	1.3	0.0	11	dbSNP_120	231	1594,7002	743.4+/-407.2	166,1262,2870	yes	missense	EXPH5	NM_015065.2	98	1003,2255,3241	GG,GA,AA		18.5435,39.4139,32.782	benign	853/1990	108383676	4261,8737	2201	4298	6499	SO:0001583	missense	23086	exon6			TCAGTCAGTGCAG		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.2558T>C	11.37:g.108383676A>G	ENSP00000265843:p.Leu853Pro	Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	119	88	0.739496	NM_015065	Q2KHM1|Q9Y4D6	Missense_Mutation	SNP	ENST00000265843.4	37	CCDS8341.1	650	0.2976190476190476	324	0.6585365853658537	61	0.1685082872928177	132	0.23076923076923078	133	0.17546174142480211	G	0.483	-0.879129	0.02550	0.605861	0.185435	ENSG00000110723	ENST00000265843;ENST00000428840;ENST00000443411;ENST00000525344;ENST00000526312;ENST00000533052	T;T;T;T;T;T	0.03801	4.39;4.32;4.16;4.39;4.25;3.8	5.4	1.31	0.21738	.	0.983285	0.08319	N	0.964210	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	0.35525	-0.9785	9	0.05620	T	0.96	0.8463	2.5384	0.04720	0.1563:0.2705:0.4337:0.1395	rs10749920;rs12786084;rs17108124;rs52803067;rs58088271;rs10749920	853	Q8NEV8	EXPH5_HUMAN	P	853;777;665;846;777;665	ENSP00000265843:L853P;ENSP00000391966:L777P;ENSP00000411390:L665P;ENSP00000432546:L846P;ENSP00000432683:L777P;ENSP00000446434:L665P	ENSP00000265843:L853P	L	-	2	0	EXPH5	107888886	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-0.200000	0.09478	-0.133000	0.11537	-0.213000	0.12676	CTG	A|0.676;G|0.324	0.324	strong		0.403	EXPH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390279.1	NM_015065	
TCEB3B	51224	hgsc.bcm.edu	37	18	44560429	44560429	+	Missense_Mutation	SNP	C	C	A	rs892586	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:44560429C>A	ENST00000332567.4	-	1	1559	c.1207G>T	c.(1207-1209)Gcc>Tcc	p.A403S	KATNAL2_ENST00000356157.7_Intron|KATNAL2_ENST00000245121.5_Intron|KATNAL2_ENST00000592005.1_Intron	NM_016427.2	NP_057511.2	Q8IYF1	ELOA2_HUMAN	transcription elongation factor B polypeptide 3B (elongin A2)	403			A -> S (in dbSNP:rs892586). {ECO:0000269|PubMed:10692460}.		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						GCAGTGGTGGCAGATTTTCCA	0.473													A|||	2989	0.596845	0.5726	0.6772	5008	,	,		19683	0.6518		0.5268	False		,,,				2504	0.5879				p.A403S		Atlas-SNP	.											.	TCEB3B	141	.	0			c.G1207T						PASS	.	A	SER/ALA,	2578,1828	533.7+/-373.8	746,1086,371	117.0	104.0	109.0		1207,	-0.2	0.0	18	dbSNP_86	109	4543,4057	557.6+/-387.1	1215,2113,972	yes	missense,intron	TCEB3B,KATNAL2	NM_016427.2,NM_031303.2	99,	1961,3199,1343	AA,AC,CC		47.1744,41.4889,45.2483	benign,	403/754,	44560429	7121,5885	2203	4300	6503	SO:0001583	missense	51224	exon1			TGGTGGCAGATTT	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.1207G>T	18.37:g.44560429C>A	ENSP00000331302:p.Ala403Ser	Somatic	237	0	0		WXS	Illumina HiSeq	Phase_I	210	89	0.42381	NM_016427	Q9P2V9	Missense_Mutation	SNP	ENST00000332567.4	37	CCDS11932.1	1270	0.5815018315018315	275	0.5589430894308943	227	0.6270718232044199	368	0.6433566433566433	400	0.5277044854881267	A	0.008	-1.916769	0.00503	0.585111	0.528256	ENSG00000206181	ENST00000332567	T	0.05925	3.37	2.19	-0.254	0.12992	.	1.017410	0.07938	N	0.978715	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	0.39781	-0.9597	9	0.02654	T	1	.	2.9058	0.05720	0.4423:0.2487:0.309:0.0	rs892586;rs3826587;rs52815201;rs57988853;rs892586	403	Q8IYF1	ELOA2_HUMAN	S	403	ENSP00000331302:A403S	ENSP00000331302:A403S	A	-	1	0	TCEB3B	42814427	0.007000	0.16637	0.001000	0.08648	0.000000	0.00434	-0.515000	0.06290	-0.396000	0.07703	-1.221000	0.01599	GCC	C|0.431;A|0.569	0.569	strong		0.473	TCEB3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255900.1	NM_016427	
GGT1	2678	hgsc.bcm.edu	37	22	25016442	25016442	+	Missense_Mutation	SNP	C	C	T	rs3895576		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:25016442C>T	ENST00000400382.1	+	8	1285	c.530C>T	c.(529-531)gCc>gTc	p.A177V	GGT1_ENST00000466310.1_3'UTR|GGT1_ENST00000406383.2_Missense_Mutation_p.A177V|GGT1_ENST00000400383.1_Missense_Mutation_p.A177V|GGT1_ENST00000248923.4_Missense_Mutation_p.A177V|GGT1_ENST00000400380.1_Missense_Mutation_p.A177V			P19440	GGT1_HUMAN	gamma-glutamyltransferase 1	177			A -> V (in dbSNP:rs3895576).		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.A177V(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)	TTGGCGGCAGCCCTGGAAAAC	0.687																																					p.A177V		Atlas-SNP	.											GGT1,NS,carcinoma,0,1	GGT1	68	1	1	Substitution - Missense(1)	prostate(1)	c.C530T						scavenged	.						25.0	28.0	27.0					22																	25016442		1906	4095	6001	SO:0001583	missense	2678	exon8			CGGCAGCCCTGGA	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.530C>T	22.37:g.25016442C>T	ENSP00000383232:p.Ala177Val	Somatic	451	16	0.0354767		WXS	Illumina HiSeq	Phase_I	469	7	0.0149254	NM_013430	Q08247|Q14404|Q8TBS1|Q9UMK1	Missense_Mutation	SNP	ENST00000400382.1	37	CCDS42992.1	.	.	.	.	.	.	.	.	.	.	.	14.08	2.430183	0.43122	.	.	ENSG00000100031	ENST00000248923;ENST00000412658;ENST00000400382;ENST00000400383;ENST00000400380;ENST00000406383	T;T;T;T;T;T	0.07021	3.23;3.23;3.23;3.23;3.23;3.23	3.35	3.35	0.38373	.	0.067565	0.64402	U	0.000018	T	0.09730	0.0239	L	0.56340	1.77	0.09310	N	1	B	0.12013	0.005	B	0.20577	0.03	T	0.15065	-1.0450	10	0.46703	T	0.11	-6.9103	10.3241	0.43783	0.0:0.7987:0.2013:0.0	rs3895576;rs4049845	177	P19440	GGT1_HUMAN	V	177	ENSP00000248923:A177V;ENSP00000393537:A177V;ENSP00000383232:A177V;ENSP00000383233:A177V;ENSP00000383231:A177V;ENSP00000385975:A177V	ENSP00000248923:A177V	A	+	2	0	GGT1	23346442	0.997000	0.39634	0.256000	0.24389	0.047000	0.14425	3.457000	0.53007	1.588000	0.49971	0.455000	0.32223	GCC	.	.	weak		0.687	GGT1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250797.1	NM_013430	
CHMP6	79643	hgsc.bcm.edu	37	17	78972192	78972192	+	Silent	SNP	C	C	T	rs61752553	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:78972192C>T	ENST00000325167.5	+	7	600	c.522C>T	c.(520-522)ccC>ccT	p.P174P	CTD-2561B21.7_ENST00000576215.1_RNA|CTD-2561B21.7_ENST00000577061.2_RNA	NM_024591.4	NP_078867.2	Q96FZ7	CHMP6_HUMAN	charged multivesicular body protein 6	174	Interaction with VPS4A.				endosomal transport (GO:0016197)|membrane organization (GO:0061024)|protein transport (GO:0015031)|viral life cycle (GO:0019058)|viral process (GO:0016032)	cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	protein N-terminus binding (GO:0047485)			lung(2)|ovary(1)	3	all_neural(118;0.101)		BRCA - Breast invasive adenocarcinoma(99;0.0175)|OV - Ovarian serous cystadenocarcinoma(97;0.0524)			CAGAGGTTCCCTCCGAGCCCC	0.522																																					p.P174P		Atlas-SNP	.											.	CHMP6	16	.	0			c.C522T						PASS	.	C		2,4404	4.2+/-10.8	0,2,2201	108.0	110.0	109.0		522	-7.9	0.0	17	dbSNP_129	109	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	CHMP6	NM_024591.4		0,3,6500	TT,TC,CC		0.0116,0.0454,0.0231		174/202	78972192	3,13003	2203	4300	6503	SO:0001819	synonymous_variant	79643	exon7			GGTTCCCTCCGAG	BC010108	CCDS11774.1	17q25.3	2014-08-13	2011-09-21		ENSG00000176108	ENSG00000176108		"""Charged multivesicular body proteins"""	25675	protein-coding gene	gene with protein product		610901	"""chromatin modifying protein 6"""			11559748, 15511219	Standard	NM_024591		Approved	FLJ11749, VPS20	uc002jyw.4	Q96FZ7	OTTHUMG00000177645	ENST00000325167.5:c.522C>T	17.37:g.78972192C>T		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	125	5	0.04	NM_024591	A8K7U0|Q53FU4|Q9HAE8	Silent	SNP	ENST00000325167.5	37	CCDS11774.1																																																																																			C|0.999;T|0.001	0.001	strong		0.522	CHMP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438215.1	NM_024591	
DSE	29940	hgsc.bcm.edu	37	6	116756773	116756773	+	Missense_Mutation	SNP	T	T	C	rs41313440	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:116756773T>C	ENST00000331677.3	+	7	1586	c.1142T>C	c.(1141-1143)gTt>gCt	p.V381A	DSE_ENST00000537543.1_Missense_Mutation_p.V400A|DSE_ENST00000359564.2_Missense_Mutation_p.V381A|DSE_ENST00000452085.3_Missense_Mutation_p.V381A			Q9UL01	DSE_HUMAN	dermatan sulfate epimerase	381					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	chondroitin-glucuronate 5-epimerase activity (GO:0047757)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|liver(2)|lung(12)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	35		all_cancers(87;0.00019)|all_epithelial(87;0.000416)|Ovarian(999;0.133)|Colorectal(196;0.234)		Epithelial(106;0.00915)|OV - Ovarian serous cystadenocarcinoma(136;0.0149)|GBM - Glioblastoma multiforme(226;0.0189)|all cancers(137;0.0262)		TTGAAATCGGTTCCTCCTCCA	0.393													T|||	102	0.0203674	0.003	0.0187	5008	,	,		19616	0.0		0.0765	False		,,,				2504	0.0082				p.V381A		Atlas-SNP	.											.	DSE	98	.	0			c.T1142C						PASS	.	T	ALA/VAL,ALA/VAL	55,4351	54.2+/-90.2	0,55,2148	86.0	85.0	86.0		1142,1142	4.8	1.0	6	dbSNP_127	86	576,8024	153.4+/-207.8	23,530,3747	yes	missense,missense	DSE	NM_001080976.1,NM_013352.2	64,64	23,585,5895	CC,CT,TT		6.6977,1.2483,4.8516	benign,benign	381/959,381/959	116756773	631,12375	2203	4300	6503	SO:0001583	missense	29940	exon6			AATCGGTTCCTCC	AF098066	CCDS5107.1	6q22	2008-02-05	2007-01-29	2007-01-29	ENSG00000111817	ENSG00000111817	5.1.3.19		21144	protein-coding gene	gene with protein product		605942	"""squamous cell carcinoma antigen recognized by T cells 2"""	SART2		11920522, 16505484	Standard	NM_001080976		Approved	DSEPI	uc003pws.3	Q9UL01	OTTHUMG00000015434	ENST00000331677.3:c.1142T>C	6.37:g.116756773T>C	ENSP00000332151:p.Val381Ala	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	80	79	0.9875	NM_001080976	Q5R3K6	Missense_Mutation	SNP	ENST00000331677.3	37	CCDS5107.1	70	0.03205128205128205	1	0.0020325203252032522	10	0.027624309392265192	0	0.0	59	0.07783641160949868	T	1.278	-0.611203	0.03690	0.012483	0.066977	ENSG00000111817	ENST00000452085;ENST00000537543;ENST00000331677;ENST00000359564	T;T;T;T	0.16743	2.33;2.32;2.33;2.33	5.99	4.82	0.62117	.	0.275088	0.38164	N	0.001796	T	0.02119	0.0066	N	0.08118	0	0.09310	N	1	B;B	0.15930	0.015;0.015	B;B	0.19391	0.025;0.025	T	0.45614	-0.9249	10	0.08179	T	0.78	-13.794	9.4051	0.38457	0.0:0.1367:0.0:0.8633	rs41313440	400;381	B7Z765;Q9UL01	.;DSE_HUMAN	A	381;400;381;381	ENSP00000404049:V381A;ENSP00000441152:V400A;ENSP00000332151:V381A;ENSP00000352567:V381A	ENSP00000332151:V381A	V	+	2	0	DSE	116863466	0.604000	0.26932	0.993000	0.49108	0.998000	0.95712	2.367000	0.44213	1.076000	0.40961	0.533000	0.62120	GTT	T|0.955;C|0.045	0.045	strong		0.393	DSE-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041940.2	NM_013352	
SUGP1	57794	hgsc.bcm.edu	37	19	19427402	19427402	+	Splice_Site	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:19427402C>T	ENST00000247001.5	-	2	382	c.35G>A	c.(34-36)gGa>gAa	p.G12E	SUGP1_ENST00000585763.1_5'UTR|SUGP1_ENST00000334782.5_Splice_Site_p.G12E	NM_172231.3	NP_757386.2	Q8IWZ8	SUGP1_HUMAN	SURP and G patch domain containing 1	12					gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	nucleoplasm (GO:0005654)|spliceosomal complex (GO:0005681)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(7)|ovary(1)|prostate(1)|stomach(2)|urinary_tract(2)	22						GTTAGCCTTTCCTGGGGAGGG	0.483																																					p.G12E		Atlas-SNP	.											.	SUGP1	63	.	0			c.G35A						PASS	.						61.0	55.0	57.0					19																	19427402		2203	4300	6503	SO:0001630	splice_region_variant	57794	exon2			GCCTTTCCTGGGG	AF521128	CCDS12399.1	19p13	2013-01-28	2010-08-10	2010-08-10		ENSG00000105705		"""G patch domain containing"""	18643	protein-coding gene	gene with protein product		607992	"""splicing factor 4"""	SF4		12594045	Standard	NM_172231		Approved	F23858, DKFZp434E2216, RBP	uc002nmh.3	Q8IWZ8		ENST00000247001.5:c.35-1G>A	19.37:g.19427402C>T		Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	91	4	0.043956	NM_172231	O60378|Q6P3X9|Q8TCQ4|Q8WWT4|Q8WWT5|Q9NTG3	Missense_Mutation	SNP	ENST00000247001.5	37	CCDS12399.1	.	.	.	.	.	.	.	.	.	.	C	19.80	3.894791	0.72639	.	.	ENSG00000105705	ENST00000247001;ENST00000535070;ENST00000334782	T	0.35048	1.33	4.88	4.88	0.63580	.	0.000000	0.85682	D	0.000000	T	0.58581	0.2132	M	0.63843	1.955	0.51767	D	0.999935	D	0.89917	1.0	D	0.91635	0.999	T	0.62397	-0.6863	10	0.87932	D	0	.	16.9497	0.86242	0.0:1.0:0.0:0.0	.	12	Q8IWZ8	SUGP1_HUMAN	E	12	ENSP00000247001:G12E	ENSP00000247001:G12E	G	-	2	0	SUGP1	19288402	1.000000	0.71417	0.998000	0.56505	0.695000	0.40330	4.890000	0.63178	2.425000	0.82216	0.561000	0.74099	GGA	.	.	none		0.483	SUGP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460128.4	NM_021164	Missense_Mutation
CDK5RAP2	55755	hgsc.bcm.edu	37	9	123301346	123301346	+	Silent	SNP	T	T	G	rs3750494	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:123301346T>G	ENST00000349780.4	-	6	659	c.480A>C	c.(478-480)ctA>ctC	p.L160L	CDK5RAP2_ENST00000359309.3_Silent_p.L160L|CDK5RAP2_ENST00000360822.3_Silent_p.L160L|CDK5RAP2_ENST00000360190.4_Silent_p.L160L	NM_018249.4	NP_060719.4	Q96SN8	CK5P2_HUMAN	CDK5 regulatory subunit associated protein 2	160					brain development (GO:0007420)|centrosome organization (GO:0051297)|chromosome segregation (GO:0007059)|establishment of mitotic spindle orientation (GO:0000132)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule bundle formation (GO:0001578)|microtubule cytoskeleton organization (GO:0000226)|mitotic cell cycle (GO:0000278)|negative regulation of centriole replication (GO:0046600)|negative regulation of neuron differentiation (GO:0045665)|neurogenesis (GO:0022008)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of neuron differentiation (GO:0045664)|regulation of spindle checkpoint (GO:0090231)	cell junction (GO:0030054)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|pericentriolar material (GO:0000242)|perinuclear region of cytoplasm (GO:0048471)|spindle pole (GO:0000922)	calmodulin binding (GO:0005516)|microtubule binding (GO:0008017)|protein kinase binding (GO:0019901)|transcription regulatory region DNA binding (GO:0044212)|tubulin binding (GO:0015631)			breast(6)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(12)|lung(21)|ovary(2)|prostate(2)|skin(6)|urinary_tract(1)	58						TTCTTTTAGTTAGGAGATCTT	0.448													T|||	584	0.116613	0.0204	0.1009	5008	,	,		18471	0.2907		0.0626	False		,,,				2504	0.1339				p.L160L		Atlas-SNP	.											.	CDK5RAP2	157	.	0			c.A480C						PASS	.	T	,	176,4230	115.0+/-153.0	3,170,2030	186.0	185.0	185.0		480,480	-11.1	0.0	9	dbSNP_107	185	608,7992	159.8+/-213.0	19,570,3711	no	coding-synonymous,coding-synonymous	CDK5RAP2	NM_001011649.1,NM_018249.4	,	22,740,5741	GG,GT,TT		7.0698,3.9946,6.028	,	160/1815,160/1894	123301346	784,12222	2203	4300	6503	SO:0001819	synonymous_variant	55755	exon6			TTTAGTTAGGAGA	BK005504	CCDS6823.1, CCDS43871.1, CCDS75888.1	9q33.3	2014-02-21			ENSG00000136861	ENSG00000136861			18672	protein-coding gene	gene with protein product	"""centrosomin"""	608201	"""microcephaly, primary autosomal recessive 3"""	MCPH3		10721722, 17764569, 24466316	Standard	NM_018249		Approved	C48, FLJ10867, CEP215	uc004bkf.4	Q96SN8	OTTHUMG00000021043	ENST00000349780.4:c.480A>C	9.37:g.123301346T>G		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	85	38	0.447059	NM_018249	Q5JV18|Q7Z3L4|Q7Z3U1|Q7Z7I6|Q9BSW0|Q9H6J6|Q9HCD9|Q9NV90|Q9UIW9	Silent	SNP	ENST00000349780.4	37	CCDS6823.1																																																																																			T|0.918;G|0.082	0.082	strong		0.448	CDK5RAP2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055535.1	NM_018249	
SVOPL	136306	hgsc.bcm.edu	37	7	138305806	138305806	+	Silent	SNP	T	T	C	rs3734944	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:138305806T>C	ENST00000419765.3	-	13	1371	c.1338A>G	c.(1336-1338)gcA>gcG	p.A446A	SVOPL_ENST00000288513.5_Silent_p.A294A|SVOPL_ENST00000463557.1_Intron|SVOPL_ENST00000421622.1_Silent_p.A326A|SVOPL_ENST00000436657.1_Silent_p.A294A	NM_001139456.1	NP_001132928.1	Q8N434	SVOPL_HUMAN	SVOP-like	446						integral component of membrane (GO:0016021)	transmembrane transporter activity (GO:0022857)			NS(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(4)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	19						ATATAAATGGTGCCACCATTG	0.577													C|||	1319	0.263379	0.0915	0.3444	5008	,	,		16962	0.3919		0.3141	False		,,,				2504	0.2536				p.A446A		Atlas-SNP	.											.	SVOPL	111	.	0			c.A1338G						PASS	.	C	,	544,3862	774.8+/-414.1	34,476,1693	65.0	55.0	58.0		1338,882	-10.7	0.0	7	dbSNP_107	58	2739,5861	680.3+/-403.6	441,1857,2002	no	coding-synonymous,coding-synonymous	SVOPL	NM_001139456.1,NM_174959.2	,	475,2333,3695	CC,CT,TT		31.8488,12.3468,25.2422	,	446/493,294/341	138305806	3283,9723	2203	4300	6503	SO:0001819	synonymous_variant	136306	exon13			AAATGGTGCCACC	BC036796	CCDS5848.1, CCDS47721.1	7q34	2011-07-12	2007-04-04		ENSG00000157703	ENSG00000157703			27034	protein-coding gene	gene with protein product		611700	"""SV2 related protein homolog (rat)-like"""				Standard	NM_001139456		Approved	MGC46715	uc011kqh.2	Q8N434	OTTHUMG00000155870	ENST00000419765.3:c.1338A>G	7.37:g.138305806T>C		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	75	45	0.6	NM_001139456		Silent	SNP	ENST00000419765.3	37	CCDS47721.1																																																																																			T|0.741;C|0.259	0.259	strong		0.577	SVOPL-005	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342092.4	NM_174959	
ZNF568	374900	hgsc.bcm.edu	37	19	37441365	37441365	+	Missense_Mutation	SNP	T	T	C	rs547483	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:37441365T>C	ENST00000333987.7	+	7	1816	c.1310T>C	c.(1309-1311)aTg>aCg	p.M437T	ZNF568_ENST00000427117.1_Intron|ZNF568_ENST00000455427.2_Intron|ZNF568_ENST00000415168.1_Missense_Mutation_p.M373T	NM_001204835.1|NM_198539.3	NP_001191764.1|NP_940941.2	Q3ZCX4	ZN568_HUMAN	zinc finger protein 568	437			M -> T (in dbSNP:rs547483).		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)			ACCGTACATATGCGAAATCAT	0.388													T|||	1519	0.303315	0.3911	0.3718	5008	,	,		20049	0.0913		0.3618	False		,,,				2504	0.2945				p.M437T		Atlas-SNP	.											.	ZNF568	106	.	0			c.T1310C						PASS	.	T	THR/MET,THR/MET,THR/MET,,,THR/MET	1788,2618	480.6+/-358.9	367,1054,782	72.0	80.0	77.0		1307,1118,1118,,,1310	0.4	0.1	19	dbSNP_83	77	3108,5488	458.6+/-364.7	560,1988,1750	yes	missense,missense,missense,intron,intron,missense	ZNF568	NM_001204835.1,NM_001204836.1,NM_001204837.1,NM_001204838.1,NM_001204839.1,NM_198539.3	81,81,81,,,81	927,3042,2532	CC,CT,TT		36.1564,40.581,37.6557	possibly-damaging,possibly-damaging,possibly-damaging,,,possibly-damaging	436/644,373/581,373/581,,,437/645	37441365	4896,8106	2203	4298	6501	SO:0001583	missense	374900	exon7			TACATATGCGAAA	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	ENST00000333987.7:c.1310T>C	19.37:g.37441365T>C	ENSP00000334685:p.Met437Thr	Somatic	23	0	0		WXS	Illumina HiSeq	Phase_I	18	9	0.5	NM_198539	B4DS92|E7ER33|Q6N060|Q8NA64	Missense_Mutation	SNP	ENST00000333987.7	37	CCDS42558.1	645	0.29532967032967034	185	0.37601626016260165	124	0.3425414364640884	47	0.08216783216783216	289	0.3812664907651715	T	6.400	0.442011	0.12164	0.40581	0.361564	ENSG00000198453	ENST00000333987;ENST00000415168	T;T	0.19669	2.13;2.13	4.09	0.406	0.16366	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.173251	0.27966	N	0.017136	T	0.00012	0.0000	L	0.47078	1.49	0.80722	P	0.0	B	0.06786	0.001	B	0.10450	0.005	T	0.44832	-0.9302	9	0.72032	D	0.01	.	8.2689	0.31831	0.6252:0.0:0.0:0.3748	rs547483;rs826302;rs1080456;rs16971821;rs56512048;rs60790821;rs547483	437	Q3ZCX4	ZN568_HUMAN	T	437;373	ENSP00000334685:M437T;ENSP00000394514:M373T	ENSP00000334685:M437T	M	+	2	0	ZNF568	42133205	0.000000	0.05858	0.073000	0.20177	0.791000	0.44710	-1.420000	0.02457	0.203000	0.20529	0.460000	0.39030	ATG	T|0.698;C|0.302	0.302	strong		0.388	ZNF568-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109572.2	NM_198539	
CTSC	1075	hgsc.bcm.edu	37	11	88027393	88027393	+	Silent	SNP	A	A	C	rs17594	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:88027393A>C	ENST00000227266.5	-	7	1287	c.1173T>G	c.(1171-1173)acT>acG	p.T391T		NM_001814.4	NP_001805	P53634	CATC_HUMAN	cathepsin C	391					aging (GO:0007568)|immune response (GO:0006955)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of proteolysis involved in cellular protein catabolic process (GO:1903052)|proteolysis (GO:0006508)|response to organic substance (GO:0010033)|T cell mediated cytotoxicity (GO:0001913)	endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|lysosome (GO:0005764)|membrane (GO:0016020)	chaperone binding (GO:0051087)|chloride ion binding (GO:0031404)|cysteine-type peptidase activity (GO:0008234)|peptidase activator activity involved in apoptotic process (GO:0016505)|phosphatase binding (GO:0019902)|serine-type endopeptidase activity (GO:0004252)			large_intestine(7)|lung(8)|ovary(2)|prostate(3)|skin(2)	22		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)				CTCTTAGACCAGTGTGGTGGT	0.488													A|||	429	0.0856629	0.0802	0.1023	5008	,	,		19653	0.1151		0.0507	False		,,,				2504	0.0869				p.T391T		Atlas-SNP	.											.	CTSC	46	.	0			c.T1173G						PASS	.	A		302,4100	163.6+/-195.4	11,280,1910	140.0	113.0	122.0		1173	-5.8	1.0	11	dbSNP_63	122	326,8272	114.6+/-174.5	5,316,3978	no	coding-synonymous	CTSC	NM_001814.4		16,596,5888	CC,CA,AA		3.7916,6.8605,4.8308		391/464	88027393	628,12372	2201	4299	6500	SO:0001819	synonymous_variant	1075	exon7			TAGACCAGTGTGG	AK223038	CCDS8282.1, CCDS31654.1, CCDS44693.1	11q14.2	2014-09-17			ENSG00000109861	ENSG00000109861	3.4.14.1	"""Cathepsins"""	2528	protein-coding gene	gene with protein product	"""dipeptidyl peptidase 1"""	602365		PLS, PALS		7649281, 9092576	Standard	NM_148170		Approved	DPP1	uc001pck.4	P53634	OTTHUMG00000167290	ENST00000227266.5:c.1173T>G	11.37:g.88027393A>C		Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	173	30	0.17341	NM_001814	A8K7V2|B5MDD5|Q2HIY8|Q53G93|Q71E75|Q71E76|Q7M4N9|Q7Z3G7|Q7Z5U7|Q8WY99|Q8WYA7|Q8WYA8	Silent	SNP	ENST00000227266.5	37	CCDS8282.1																																																																																			A|0.942;C|0.058	0.058	strong		0.488	CTSC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394019.2	NM_001814	
PCDHB10	56126	hgsc.bcm.edu	37	5	140573508	140573508	+	Silent	SNP	C	C	G	rs112214830	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	88	0	0		WXS	Illumina HiSeq	Phase_I	83	22	0.26506	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	
SVEP1	79987	hgsc.bcm.edu	37	9	113244732	113244732	+	Missense_Mutation	SNP	G	G	T	rs41296069	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:113244732G>T	ENST00000401783.2	-	11	2415	c.2079C>A	c.(2077-2079)gaC>gaA	p.D693E	SVEP1_ENST00000374469.1_Missense_Mutation_p.D670E|SVEP1_ENST00000374461.1_Missense_Mutation_p.D670E|SVEP1_ENST00000302728.8_Missense_Mutation_p.D693E|SVEP1_ENST00000467821.1_5'UTR	NM_153366.3	NP_699197.3	Q4LDE5	SVEP1_HUMAN	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	693	HYR 2. {ECO:0000255|PROSITE- ProRule:PRU00113}.				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						GAGGGAAAAGGTCTCCTTGTG	0.403													G|||	314	0.0626997	0.0234	0.1599	5008	,	,		19766	0.0476		0.0855	False		,,,				2504	0.0389				p.D693E		Atlas-SNP	.											.	SVEP1	326	.	0			c.C2079A						PASS	.	G	GLU/ASP	95,3699		2,91,1804	100.0	91.0	94.0		2079	-1.2	0.9	9	dbSNP_127	94	626,7632		21,584,3524	yes	missense	SVEP1	NM_153366.3	45	23,675,5328	TT,TG,GG		7.5805,2.504,5.9824	benign	693/3572	113244732	721,11331	1897	4129	6026	SO:0001583	missense	79987	exon11			GAAAAGGTCTCCT	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.2079C>A	9.37:g.113244732G>T	ENSP00000384917:p.Asp693Glu	Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	160	56	0.35	NM_153366	Q0P675|Q5D213|Q5T938|Q5VTE4|Q5VTE5|Q7Z387|Q7Z3G3|Q8NBT9|Q96JU7|Q9H284|Q9H8J9	Missense_Mutation	SNP	ENST00000401783.2	37	CCDS48004.1	152	0.0695970695970696	11	0.022357723577235773	52	0.143646408839779	23	0.04020979020979021	66	0.0870712401055409	G	12.32	1.901768	0.33535	0.02504	0.075805	ENSG00000165124	ENST00000401783;ENST00000374469;ENST00000302728;ENST00000374461	T;T;T;T	0.25579	1.79;1.79;1.79;1.79	5.83	-1.17	0.09648	Hyalin (2);	0.211440	0.47093	N	0.000257	T	0.00144	0.0004	M	0.61703	1.905	0.39883	P	0.02634000000000003	B;B;B	0.15719	0.008;0.014;0.006	B;B;B	0.20184	0.011;0.028;0.011	T	0.23048	-1.0199	9	0.10902	T	0.67	.	2.9062	0.05721	0.372:0.1129:0.4011:0.114	rs41296069;rs61747760	693;693;693	E9PBN8;Q4LDE5;Q4LDE5-2	.;SVEP1_HUMAN;.	E	693;670;693;670	ENSP00000384917:D693E;ENSP00000363593:D670E;ENSP00000304118:D693E;ENSP00000363585:D670E	ENSP00000304118:D693E	D	-	3	2	SVEP1	112284553	1.000000	0.71417	0.911000	0.35937	0.785000	0.44390	1.022000	0.30052	-0.091000	0.12440	-0.894000	0.02916	GAC	G|0.934;T|0.066	0.066	strong		0.403	SVEP1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
HRG	3273	hgsc.bcm.edu	37	3	186395113	186395113	+	Missense_Mutation	SNP	A	A	G	rs2228243	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:186395113A>G	ENST00000232003.4	+	7	1099	c.1019A>G	c.(1018-1020)cAt>cGt	p.H340R		NM_000412.2	NP_000403.1	P04196	HRG_HUMAN	histidine-rich glycoprotein	340			H -> R (in dbSNP:rs2228243).		angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|chemotaxis (GO:0006935)|defense response to fungus (GO:0050832)|fibrinolysis (GO:0042730)|heme export (GO:0097037)|negative regulation of angiogenesis (GO:0016525)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell adhesion mediated by integrin (GO:0033629)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of endothelial cell chemotaxis (GO:2001027)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of lamellipodium assembly (GO:0010593)|negative regulation of vascular endothelial growth factor signaling pathway (GO:1900747)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of apoptotic process (GO:0043065)|positive regulation of blood vessel remodeling (GO:2000504)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of immune response to tumor cell (GO:0002839)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|regulation of platelet activation (GO:0010543)|regulation of protein complex assembly (GO:0043254)|regulation of transcription from RNA polymerase II promoter in response to iron (GO:0034395)|response to organic cyclic compound (GO:0014070)	blood microparticle (GO:0072562)|endolysosome (GO:0036019)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|phagolysosome membrane (GO:0061474)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	cysteine-type endopeptidase inhibitor activity (GO:0004869)|heme binding (GO:0020037)|heparan sulfate proteoglycan binding (GO:0043395)|heparin binding (GO:0008201)|immunoglobulin binding (GO:0019865)|metal ion binding (GO:0046872)|receptor binding (GO:0005102)|serine-type endopeptidase inhibitor activity (GO:0004867)|zinc ion binding (GO:0008270)	p.H340R(1)		breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(12)|lung(13)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	37	all_cancers(143;6.64e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;5.73e-20)	GBM - Glioblastoma multiforme(93;0.0683)		GCCCAAAGACATTCTCATAAT	0.498													A|||	1026	0.204872	0.0303	0.2147	5008	,	,		20524	0.4137		0.1819	False		,,,				2504	0.2423				p.H340R		Atlas-SNP	.											HRG,NS,adenoma,0,2	HRG	81	2	1	Substitution - Missense(1)	stomach(1)	c.A1019G						PASS	.	A	ARG/HIS	280,4126	153.3+/-186.9	15,250,1938	144.0	138.0	140.0		1019	-1.9	0.0	3	dbSNP_98	140	1752,6848	317.6+/-313.3	191,1370,2739	yes	missense	HRG	NM_000412.2	29	206,1620,4677	GG,GA,AA		20.3721,6.355,15.6236	benign	340/526	186395113	2032,10974	2203	4300	6503	SO:0001583	missense	3273	exon7			AAAGACATTCTCA		CCDS3280.1	3q27	2008-07-18			ENSG00000113905	ENSG00000113905			5181	protein-coding gene	gene with protein product	"""histidine-proline rich glycoprotein"", ""thrombophilia due to elevated HRG"""	142640				1678514	Standard	NM_000412		Approved	HRGP, HPRG	uc003fqq.3	P04196	OTTHUMG00000156578	ENST00000232003.4:c.1019A>G	3.37:g.186395113A>G	ENSP00000232003:p.His340Arg	Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	124	124	1	NM_000412	B9EK35|D3DNU7	Missense_Mutation	SNP	ENST00000232003.4	37	CCDS3280.1	458	0.2097069597069597	12	0.024390243902439025	80	0.22099447513812154	224	0.3916083916083916	142	0.18733509234828497	A	9.261	1.043188	0.19748	0.06355	0.203721	ENSG00000113905	ENST00000232003	T	0.14640	2.49	4.55	-1.9	0.07665	.	0.903725	0.09359	N	0.812968	T	0.00012	0.0000	L	0.43152	1.355	0.80722	P	0.0	P	0.38978	0.652	B	0.31614	0.133	T	0.48175	-0.9058	9	0.20046	T	0.44	0.0549	7.2636	0.26217	0.6619:0.2388:0.0:0.0994	rs2228243;rs3733014;rs16860998;rs58808959;rs2228243	340	P04196	HRG_HUMAN	R	340	ENSP00000232003:H340R	ENSP00000232003:H340R	H	+	2	0	HRG	187877807	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-1.010000	0.03656	-0.477000	0.06832	0.374000	0.22700	CAT	A|0.768;G|0.232	0.232	strong		0.498	HRG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344655.1	NM_000412	
ICAM1	3383	hgsc.bcm.edu	37	19	10385540	10385540	+	Missense_Mutation	SNP	A	A	T	rs5491	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:10385540A>T	ENST00000264832.3	+	2	492	c.167A>T	c.(166-168)aAg>aTg	p.K56M	ICAM1_ENST00000423829.2_Intron|CTD-2369P2.5_ENST00000592893.1_RNA	NM_000201.2	NP_000192.2	P05362	ICAM1_HUMAN	intercellular adhesion molecule 1	56	Ig-like C2-type 1.		K -> M (in Kilifi; at homozygosity it is associated with increased susceptibility to cerebral malaria; dbSNP:rs5491). {ECO:0000269|PubMed:10391210, ECO:0000269|PubMed:9259284, ECO:0000269|Ref.6}.		adhesion of symbiont to host (GO:0044406)|cell adhesion (GO:0007155)|cell adhesion mediated by integrin (GO:0033627)|cell aging (GO:0007569)|cellular response to alkaloid (GO:0071312)|cellular response to glucose stimulus (GO:0071333)|cellular response to hypoxia (GO:0071456)|cellular response to interleukin-1 (GO:0071347)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to nutrient levels (GO:0031669)|cellular response to tumor necrosis factor (GO:0071356)|cytokine-mediated signaling pathway (GO:0019221)|establishment of endothelial barrier (GO:0061028)|extracellular matrix organization (GO:0030198)|heterophilic cell-cell adhesion (GO:0007157)|interferon-gamma-mediated signaling pathway (GO:0060333)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|membrane to membrane docking (GO:0022614)|negative regulation of calcium ion transport (GO:0051926)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|ovarian follicle development (GO:0001541)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cellular extravasation (GO:0002693)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of vasoconstriction (GO:0045907)|receptor-mediated virion attachment to host cell (GO:0046813)|regulation of cell adhesion (GO:0030155)|regulation of cell shape (GO:0008360)|regulation of immune response (GO:0050776)|regulation of leukocyte mediated cytotoxicity (GO:0001910)|regulation of ruffle assembly (GO:1900027)|response to amino acid (GO:0043200)|response to amphetamine (GO:0001975)|response to copper ion (GO:0046688)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to gonadotropin (GO:0034698)|response to ionizing radiation (GO:0010212)|response to organic cyclic compound (GO:0014070)|response to sulfur dioxide (GO:0010477)|T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell (GO:0002291)|T cell antigen processing and presentation (GO:0002457)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|immunological synapse (GO:0001772)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	integrin binding (GO:0005178)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)|virus receptor activity (GO:0001618)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(4)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	14			OV - Ovarian serous cystadenocarcinoma(20;1.39e-09)|Epithelial(33;2.81e-06)|all cancers(31;6.56e-06)		Hyaluronan(DB08818)|Natalizumab(DB00108)	GACCAGCCCAAGTTGTTGGGC	0.562													a|||	423	0.0844649	0.2504	0.0173	5008	,	,		19414	0.0526		0.007	False		,,,				2504	0.0204				p.K56M		Atlas-SNP	.											.	ICAM1	32	.	0			c.A167T	GRCh37	CM970747	ICAM1	M	rs5491	PASS	.	A	MET/LYS	934,3472	357.6+/-314.0	103,728,1372	99.0	95.0	96.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	167	-5.4	0.0	19	dbSNP_52	96	26,8574	16.6+/-54.9	0,26,4274	yes	missense	ICAM1	NM_000201.2	95	103,754,5646	TT,TA,AA		0.3023,21.1984,7.3812	benign	56/533	10385540	960,12046	2203	4300	6503	SO:0001583	missense	3383	exon2			AGCCCAAGTTGTT		CCDS12231.1	19p13.3-p13.2	2014-01-30	2008-07-18			ENSG00000090339		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Endogenous ligands"""	5344	protein-coding gene	gene with protein product	"""human rhinovirus receptor"""	147840				2453850, 3871395	Standard	NM_000201		Approved	BB2, CD54	uc002mnq.2	P05362		ENST00000264832.3:c.167A>T	19.37:g.10385540A>T	ENSP00000264832:p.Lys56Met	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	88	52	0.590909	NM_000201	B2R6M3|Q5NKV7|Q96B50	Missense_Mutation	SNP	ENST00000264832.3	37	CCDS12231.1	164	0.07509157509157509	114	0.23170731707317074	7	0.019337016574585635	36	0.06293706293706294	7	0.009234828496042216	a	10.23	1.293021	0.23564	0.211984	0.003023	ENSG00000090339	ENST00000264832	T	0.15487	2.42	4.45	-5.4	0.02656	Intercellular adhesion molecule, N-terminal (1);Immunoglobulin-like fold (1);	8.976480	0.00166	N	0.000000	T	0.00012	0.0000	N	0.24115	0.695	0.58432	P	5.000000000032756E-6	B	0.22146	0.065	B	0.31442	0.13	T	0.30794	-0.9966	9	0.48119	T	0.1	1.2014	2.5057	0.04645	0.109:0.3535:0.3044:0.2331	rs5491;rs52822152;rs57463344;rs5491	56	P05362	ICAM1_HUMAN	M	56	ENSP00000264832:K56M	ENSP00000264832:K56M	K	+	2	0	ICAM1	10246540	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.205000	0.00559	-1.363000	0.02164	-1.831000	0.00592	AAG	A|0.924;T|0.076	0.076	strong		0.562	ICAM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451207.1		
MAVS	57506	hgsc.bcm.edu	37	20	3838441	3838441	+	Missense_Mutation	SNP	C	C	G	rs17857295	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:3838441C>G	ENST00000428216.2	+	3	405	c.277C>G	c.(277-279)Cag>Gag	p.Q93E	MAVS_ENST00000358134.6_Missense_Mutation_p.Q93E|MAVS_ENST00000416600.2_Intron	NM_020746.4	NP_065797.2	Q7Z434	MAVS_HUMAN	mitochondrial antiviral signaling protein	93			Q -> E (in dbSNP:rs17857295). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:16127453, ECO:0000269|PubMed:16153868}.		activation of innate immune response (GO:0002218)|cellular response to exogenous dsRNA (GO:0071360)|defense response to bacterium (GO:0042742)|defense response to virus (GO:0051607)|innate immune response (GO:0045087)|negative regulation of type I interferon production (GO:0032480)|negative regulation of viral genome replication (GO:0045071)|positive regulation of chemokine (C-C motif) ligand 5 production (GO:0071651)|positive regulation of defense response to virus by host (GO:0002230)|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 interleukin-8 production (GO:0032757)|positive regulation of IP-10 production (GO:0071660)|positive regulation of protein import into nucleus, translocation (GO:0033160)|positive regulation of protein phosphorylation (GO:0001934)|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)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of type I interferon-mediated signaling pathway (GO:0060340)|regulation of peroxisome organization (GO:1900063)|RIG-I signaling pathway (GO:0039529)|signal transduction (GO:0007165)|viral process (GO:0016032)	integral component of membrane (GO:0016021)|mitochondrial membrane (GO:0031966)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|peroxisomal membrane (GO:0005778)	CARD domain binding (GO:0050700)|protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)			autonomic_ganglia(1)|breast(3)|endometrium(1)|large_intestine(3)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	14						CTCTGTCTACCAGAGCTACCA	0.632													C|||	1457	0.290935	0.0779	0.2882	5008	,	,		15267	0.5605		0.2833	False		,,,				2504	0.3108				p.Q93E		Atlas-SNP	.											.	MAVS	34	.	0			c.C277G						PASS	.	C	,GLU/GLN	452,3954	217.8+/-236.0	27,398,1778	113.0	87.0	96.0		,277	2.5	0.4	20	dbSNP_123	96	2136,6464	368.6+/-335.1	250,1636,2414	yes	intron,missense	MAVS	NM_001206491.1,NM_020746.4	,29	277,2034,4192	GG,GC,CC		24.8372,10.2587,19.8985	,possibly-damaging	,93/541	3838441	2588,10418	2203	4300	6503	SO:0001583	missense	57506	exon3			GTCTACCAGAGCT	DQ174270	CCDS33437.1, CCDS56176.1	20p13	2009-04-02			ENSG00000088888	ENSG00000088888			29233	protein-coding gene	gene with protein product	"""virus-induced signaling adaptor"", ""IFN-B promoter stimulator 1"", ""CARD adaptor inducing IFN-beta"""	609676				16125763, 16153868	Standard	NM_020746		Approved	VISA, KIAA1271, IPS-1, Cardif	uc002wjw.4	Q7Z434	OTTHUMG00000031765	ENST00000428216.2:c.277C>G	20.37:g.3838441C>G	ENSP00000401980:p.Gln93Glu	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	93	57	0.612903	NM_020746	A8K6X0|B2BD33|B2BD34|F5H6C8|Q2HWT5|Q3I0Y2|Q5T7I6|Q86VY7|Q9H1H3|Q9H4Y1|Q9H8D3|Q9ULE9	Missense_Mutation	SNP	ENST00000428216.2	37	CCDS33437.1	663	0.30357142857142855	38	0.07723577235772358	96	0.26519337016574585	323	0.5646853146853147	206	0.2717678100263852	C	10.82	1.458798	0.26248	0.102587	0.248372	ENSG00000088888	ENST00000428216;ENST00000358134	T;T	0.12039	2.88;2.72	4.67	2.53	0.30540	.	0.520418	0.17532	N	0.170837	T	0.00012	0.0000	L	0.60455	1.87	0.80722	P	0.0	P;P;P	0.46784	0.571;0.884;0.759	B;B;B	0.42851	0.37;0.4;0.4	T	0.39583	-0.9607	9	0.31617	T	0.26	-4.6837	6.7646	0.23560	0.2075:0.5973:0.1952:0.0	rs17857295;rs59161240	93;93;93	B2BD34;Q7Z434;Q7Z434-2	.;MAVS_HUMAN;.	E	93	ENSP00000401980:Q93E;ENSP00000350852:Q93E	ENSP00000350852:Q93E	Q	+	1	0	MAVS	3786441	0.000000	0.05858	0.401000	0.26359	0.936000	0.57629	-0.228000	0.09114	1.093000	0.41377	0.609000	0.83330	CAG	C|0.764;G|0.236	0.236	strong		0.632	MAVS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077784.3	NM_020746	
LRRC32	2615	hgsc.bcm.edu	37	11	76372052	76372052	+	Silent	SNP	A	A	G	rs3740779	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:76372052A>G	ENST00000407242.2	-	3	827	c.585T>C	c.(583-585)ggT>ggC	p.G195G	LRRC32_ENST00000464145.1_Intron|AP001189.4_ENST00000447519.1_RNA|LRRC32_ENST00000404995.1_Silent_p.G195G|LRRC32_ENST00000260061.5_Silent_p.G195G	NM_005512.2	NP_005503.1	Q14392	LRC32_HUMAN	leucine rich repeat containing 32	195					negative regulation of activated T cell proliferation (GO:0046007)|negative regulation of cytokine secretion (GO:0050710)|positive regulation of gene expression (GO:0010628)	integral component of plasma membrane (GO:0005887)				endometrium(1)|large_intestine(3)|lung(26)|upper_aerodigestive_tract(1)	31						GGCGGGGCAGACCCTCGAAGG	0.622													G|||	3132	0.625399	0.6316	0.5692	5008	,	,		19682	0.6349		0.6064	False		,,,				2504	0.6667				p.G195G		Atlas-SNP	.											.	LRRC32	74	.	0			c.T585C						PASS	.	G	,	2773,1627	500.3+/-364.7	876,1021,303	86.0	78.0	81.0		585,585	0.3	1.0	11	dbSNP_107	81	5337,3247	487.2+/-372.1	1645,2047,600	no	coding-synonymous,coding-synonymous	LRRC32	NM_001128922.1,NM_005512.2	,	2521,3068,903	GG,GA,AA		37.8262,36.9773,37.5385	,	195/663,195/663	76372052	8110,4874	2200	4292	6492	SO:0001819	synonymous_variant	2615	exon3			GGGCAGACCCTCG	Z24680	CCDS8245.1	11q13.5-q14	2008-02-05	2005-02-25	2005-02-25	ENSG00000137507	ENSG00000137507			4161	protein-coding gene	gene with protein product		137207	"""glycoprotein A repetitions predominant"""	D11S833E, GARP		8180135, 1543912	Standard	NM_005512		Approved		uc001oxq.4	Q14392	OTTHUMG00000133687	ENST00000407242.2:c.585T>C	11.37:g.76372052A>G		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	75	64	0.853333	NM_005512	Q86V06	Silent	SNP	ENST00000407242.2	37	CCDS8245.1																																																																																			G|0.616;N|0.000	0.616	strong		0.622	LRRC32-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257926.2	NM_005512	
LMF2	91289	hgsc.bcm.edu	37	22	50944163	50944163	+	Silent	SNP	G	G	A	rs128941	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:50944163G>A	ENST00000474879.2	-	6	871	c.856C>T	c.(856-858)Ctg>Ttg	p.L286L	LMF2_ENST00000216080.5_Silent_p.L261L|NCAPH2_ENST00000420993.2_5'Flank|NCAPH2_ENST00000299821.11_5'Flank|LMF2_ENST00000505981.1_5'UTR|LMF2_ENST00000380796.3_Silent_p.L286L|NCAPH2_ENST00000395698.3_5'Flank|NCAPH2_ENST00000395701.3_5'Flank	NM_033200.2	NP_149977.2	Q9BU23	LMF2_HUMAN	lipase maturation factor 2	286						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				breast(1)|cervix(1)|kidney(1)|lung(4)|prostate(1)|skin(2)	10		all_cancers(38;1.31e-09)|all_epithelial(38;1.81e-08)|all_lung(38;0.000817)|Breast(42;0.00387)|Lung NSC(38;0.0124)|Ovarian(80;0.104)|Lung SC(80;0.162)|Hepatocellular(38;0.178)		BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)		TGGTCGTCCAGCAGCGCAGTG	0.637													g|||	2782	0.555511	0.3124	0.6513	5008	,	,		17733	0.7361		0.6342	False		,,,				2504	0.5491				p.L286L		Atlas-SNP	.											.	LMF2	40	.	0			c.C856T						PASS	.	G		1635,2771	493.8+/-362.8	314,1007,882	66.0	66.0	66.0		856	3.8	0.4	22	dbSNP_78	66	5174,3426	635.7+/-399.0	1521,2132,647	no	coding-synonymous	LMF2	NM_033200.2		1835,3139,1529	AA,AG,GG		39.8372,37.1085,47.6472		286/708	50944163	6809,6197	2203	4300	6503	SO:0001819	synonymous_variant	91289	exon6			CGTCCAGCAGCGC	BC002942	CCDS14093.1, CCDS14093.2	22q13.33	2008-02-04	2007-11-29	2007-11-29	ENSG00000100258	ENSG00000100258			25096	protein-coding gene	gene with protein product			"""transmembrane protein 153"", ""transmembrane protein 112B"""	TMEM153, TMEM112B		12477932	Standard	NM_033200		Approved		uc003blp.2	Q9BU23	OTTHUMG00000150206	ENST00000474879.2:c.856C>T	22.37:g.50944163G>A		Somatic	218	0	0		WXS	Illumina HiSeq	Phase_I	210	102	0.485714	NM_033200	A6NEZ0|Q13392|Q6ZNR2|Q8WU74|Q96C62	Silent	SNP	ENST00000474879.2	37	CCDS14093.2	1284	0.5879120879120879	147	0.29878048780487804	227	0.6270718232044199	441	0.7709790209790209	469	0.6187335092348285	G	0.730	-0.780313	0.02929	0.371085	0.601628	ENSG00000100258	ENST00000487499	.	.	.	4.79	3.77	0.43336	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.26503	-1.0101	3	.	.	.	-1.3933	9.5013	0.39019	0.0995:0.0:0.9005:0.0	rs128941;rs17851222;rs17851865;rs17857715;rs58823072;rs128941	.	.	.	V	292	.	.	A	-	2	0	LMF2	49291029	1.000000	0.71417	0.417000	0.26559	0.004000	0.04260	8.738000	0.91569	1.139000	0.42245	0.655000	0.94253	GCT	G|0.462;A|0.538	0.538	strong		0.637	LMF2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316833.2	NM_033200	
GUCA2B	2981	hgsc.bcm.edu	37	1	42619139	42619139	+	Silent	SNP	A	A	G	rs1047047	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:42619139A>G	ENST00000372581.1	+	1	48	c.18A>G	c.(16-18)gcA>gcG	p.A6A		NM_007102.2	NP_009033.1	Q16661	GUC2B_HUMAN	guanylate cyclase activator 2B (uroguanylin)	6					body fluid secretion (GO:0007589)|cGMP biosynthetic process (GO:0006182)|excretion (GO:0007588)|negative regulation of blood pressure (GO:0045776)|positive regulation of guanylate cyclase activity (GO:0031284)	extracellular vesicular exosome (GO:0070062)	calcium sensitive guanylate cyclase activator activity (GO:0008048)			breast(1)|large_intestine(2)	3	Ovarian(52;0.01)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)				GCAGGGCTGCATCAGGGCTCC	0.637													G|||	1580	0.315495	0.4614	0.2896	5008	,	,		16480	0.4038		0.165	False		,,,				2504	0.2004				p.A6A		Atlas-SNP	.											.	GUCA2B	9	.	0			c.A18G						PASS	.	G		1701,2705	646.7+/-398.4	320,1061,822	67.0	56.0	60.0		18	2.3	0.0	1	dbSNP_86	60	1298,7302	754.4+/-407.5	81,1136,3083	no	coding-synonymous	GUCA2B	NM_007102.2		401,2197,3905	GG,GA,AA		15.093,38.6064,23.0586		6/113	42619139	2999,10007	2203	4300	6503	SO:0001819	synonymous_variant	2981	exon1			GGCTGCATCAGGG	BC069301	CCDS464.1	1p34-p33	2014-01-30			ENSG00000044012	ENSG00000044012		"""Endogenous ligands"""	4683	protein-coding gene	gene with protein product	"""prepro-uroguanylin"""	601271				8605041, 9268639	Standard	NM_007102		Approved		uc001chc.1	Q16661	OTTHUMG00000007024	ENST00000372581.1:c.18A>G	1.37:g.42619139A>G		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	38	19	0.5	NM_007102	Q52LV0	Silent	SNP	ENST00000372581.1	37	CCDS464.1																																																																																			A|0.756;G|0.244	0.244	strong		0.637	GUCA2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000018307.1	NM_007102	
OR6N1	128372	hgsc.bcm.edu	37	1	158736445	158736445	+	Missense_Mutation	SNP	C	C	T	rs1864346	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:158736445C>T	ENST00000335094.2	-	1	47	c.28G>A	c.(28-30)Gca>Aca	p.A10T		NM_001005185.1	NP_001005185.1	Q8NGY5	OR6N1_HUMAN	olfactory receptor, family 6, subfamily N, member 1	10			A -> T (in dbSNP:rs1864346).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|lung(22)|ovary(1)|pancreas(1)|prostate(6)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	54	all_hematologic(112;0.0378)					ATGAATTCTGCTACCTGGCTC	0.458													T|||	1233	0.246206	0.0182	0.3314	5008	,	,		20003	0.4246		0.334	False		,,,				2504	0.2198				p.A10T		Atlas-SNP	.											.	OR6N1	96	.	0			c.G28A						PASS	.	T	THR/ALA	280,4126	783.8+/-414.6	9,262,1932	47.0	43.0	44.0		28	2.5	0.8	1	dbSNP_92	44	2756,5844	662.9+/-402.0	455,1846,1999	yes	missense	OR6N1	NM_001005185.1	58	464,2108,3931	TT,TC,CC		32.0465,6.355,23.3431	benign	10/313	158736445	3036,9970	2203	4300	6503	SO:0001583	missense	128372	exon1			ATTCTGCTACCTG	BK004199	CCDS30905.1	1q23.1	2012-08-09			ENSG00000197403	ENSG00000197403		"""GPCR / Class A : Olfactory receptors"""	15034	protein-coding gene	gene with protein product							Standard	NM_001005185		Approved		uc010piq.2	Q8NGY5	OTTHUMG00000022774	ENST00000335094.2:c.28G>A	1.37:g.158736445C>T	ENSP00000335535:p.Ala10Thr	Somatic	23	0	0		WXS	Illumina HiSeq	Phase_I	33	33	1	NM_001005185	Q5VUU8|Q96R35	Missense_Mutation	SNP	ENST00000335094.2	37	CCDS30905.1	620	0.2838827838827839	14	0.028455284552845527	115	0.31767955801104975	243	0.42482517482517484	248	0.32717678100263853	T	1.784	-0.481159	0.04383	0.06355	0.320465	ENSG00000197403	ENST00000335094	T	0.00606	6.26	4.83	2.52	0.30459	.	0.302038	0.23821	N	0.044234	T	0.00039	0.0001	N	0.00132	-2.035	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.04946	-1.0916	9	0.02654	T	1	0.1271	3.4356	0.07445	0.1622:0.2701:0.0:0.5677	rs1864346;rs56643362;rs59875632;rs1864346	10	Q8NGY5	OR6N1_HUMAN	T	10	ENSP00000335535:A10T	ENSP00000335535:A10T	A	-	1	0	OR6N1	157003069	0.000000	0.05858	0.816000	0.32577	0.965000	0.64279	-0.296000	0.08287	0.040000	0.15660	-0.254000	0.11334	GCA	C|0.753;N|0.000	.	strong		0.458	OR6N1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059067.1	NM_001005185	
GPR142	350383	hgsc.bcm.edu	37	17	72367973	72367973	+	Missense_Mutation	SNP	T	T	C	rs148514779	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:72367973T>C	ENST00000335666.4	+	4	671	c.623T>C	c.(622-624)gTg>gCg	p.V208A		NM_181790.1	NP_861455.1	Q7Z601	GP142_HUMAN	G protein-coupled receptor 142	208						cell junction (GO:0030054)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(1)|endometrium(3)|large_intestine(3)|lung(21)|ovary(2)|prostate(1)|skin(4)	35						ATCATCCAGGTGGTCATCGTG	0.657													T|||	8	0.00159744	0.0008	0.0029	5008	,	,		18903	0.0		0.005	False		,,,				2504	0.0				p.V208A		Atlas-SNP	.											.	GPR142	74	.	0			c.T623C						PASS	.	T	ALA/VAL	5,4401	9.9+/-24.2	0,5,2198	84.0	68.0	74.0		623	5.0	1.0	17	dbSNP_134	74	46,8554	30.1+/-81.4	0,46,4254	yes	missense	GPR142	NM_181790.1	64	0,51,6452	CC,CT,TT		0.5349,0.1135,0.3921	probably-damaging	208/463	72367973	51,12955	2203	4300	6503	SO:0001583	missense	350383	exon4			TCCAGGTGGTCAT	AY255622	CCDS11698.1	17q25.2	2012-08-21				ENSG00000257008		"""GPCR / Class A : Orphans"""	20088	protein-coding gene	gene with protein product		609046				14623098	Standard	NM_181790		Approved	PGR2	uc010wqy.2	Q7Z601		ENST00000335666.4:c.623T>C	17.37:g.72367973T>C	ENSP00000335158:p.Val208Ala	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	65	39	0.6	NM_181790	A4CYJ8|Q86SL3	Missense_Mutation	SNP	ENST00000335666.4	37	CCDS11698.1	6	0.0027472527472527475	0	0.0	2	0.0055248618784530384	0	0.0	4	0.005277044854881266	T	25.2	4.615913	0.87359	0.001135	0.005349	ENSG00000257008	ENST00000335666	T	0.38240	1.15	4.99	4.99	0.66335	GPCR, rhodopsin-like superfamily (1);	0.065348	0.64402	D	0.000007	T	0.43188	0.1236	L	0.47716	1.5	0.43007	D	0.994535	D;D	0.58620	0.977;0.983	P;D	0.65233	0.814;0.933	T	0.50734	-0.8793	10	0.72032	D	0.01	-25.2533	14.4349	0.67274	0.0:0.0:0.0:1.0	.	208;1170	Q7Z601;Q8NGB0	GP142_HUMAN;.	A	208	ENSP00000335158:V208A	ENSP00000335158:V208A	V	+	2	0	GPR142	69879568	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	5.848000	0.69458	2.188000	0.69820	0.529000	0.55759	GTG	T|0.997;C|0.003	0.003	strong		0.657	GPR142-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442545.1	NM_181790	
HID1	283987	hgsc.bcm.edu	37	17	72956124	72956124	+	Silent	SNP	G	G	A	rs3744198	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:72956124G>A	ENST00000425042.2	-	7	1025	c.948C>T	c.(946-948)gcC>gcT	p.A316A	HID1_ENST00000532900.1_5'Flank	NM_030630.2	NP_085133.1	Q8IV36	HID1_HUMAN	HID1 domain containing	316					intracellular protein transport (GO:0006886)|response to brefeldin A (GO:0031001)	cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|extracellular vesicular exosome (GO:0070062)|extrinsic component of Golgi membrane (GO:0090498)|Golgi apparatus (GO:0005794)|Golgi medial cisterna (GO:0005797)|Golgi trans cisterna (GO:0000138)											TCCTTACATCGGCATCATCCA	0.647													G|||	1223	0.244209	0.1815	0.2997	5008	,	,		20873	0.0615		0.4523	False		,,,				2504	0.2638				p.A316A		Atlas-SNP	.											.	.	.	.	0			c.C948T						PASS	.	G		990,3416	368.1+/-318.5	119,752,1332	55.0	50.0	52.0		948	-8.4	0.0	17	dbSNP_107	52	4139,4461	563.6+/-388.2	1014,2111,1175	no	coding-synonymous	C17orf28	NM_030630.2		1133,2863,2507	AA,AG,GG		48.1279,22.4694,39.4356		316/789	72956124	5129,7877	2203	4300	6503	SO:0001819	synonymous_variant	283987	exon7			TACATCGGCATCA		CCDS32726.1	17q25.1	2012-10-10	2012-10-10	2012-10-10	ENSG00000167861	ENSG00000167861			15736	protein-coding gene	gene with protein product	"""downregulated in multiple cancer 1"""	605752	"""chromosome 17 open reading frame 28"""	C17orf28		11281419, 21337012	Standard	NM_030630		Approved	DMC1, HID-1	uc002jmj.4	Q8IV36	OTTHUMG00000166490	ENST00000425042.2:c.948C>T	17.37:g.72956124G>A		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	68	44	0.647059	NM_030630	Q8N5L6|Q8TE83|Q9NT34	Silent	SNP	ENST00000425042.2	37	CCDS32726.1																																																																																			G|0.667;A|0.333	0.333	strong		0.647	HID1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390011.2	NM_030630	
AHNAK	79026	hgsc.bcm.edu	37	11	62293948	62293948	+	Silent	SNP	G	G	A	rs486903	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:62293948G>A	ENST00000378024.4	-	5	8215	c.7941C>T	c.(7939-7941)agC>agT	p.S2647S	AHNAK_ENST00000257247.7_Intron|AHNAK_ENST00000530124.1_Intron	NM_001620.1	NP_001611.1	Q09666	AHNK_HUMAN	AHNAK nucleoprotein	2647					protein oligomerization (GO:0051259)|regulation of RNA splicing (GO:0043484)|regulation of voltage-gated calcium channel activity (GO:1901385)	actin cytoskeleton (GO:0015629)|cell-cell contact zone (GO:0044291)|costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|vesicle (GO:0031982)	poly(A) RNA binding (GO:0044822)|S100 protein binding (GO:0044548)|structural molecule activity conferring elasticity (GO:0097493)	p.S2647S(1)		NS(3)|autonomic_ganglia(1)|breast(10)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(33)|large_intestine(40)|liver(1)|lung(108)|ovary(13)|pancreas(4)|prostate(5)|skin(16)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	268		Melanoma(852;0.155)				AGCCAGGCATGCTGAACTTTG	0.532													G|||	2369	0.473043	0.0779	0.6715	5008	,	,		20347	0.3046		0.7366	False		,,,				2504	0.7689				p.S2647S		Atlas-SNP	.											AHNAK,NS,carcinoma,0,1	AHNAK	532	1	1	Substitution - coding silent(1)	stomach(1)	c.C7941T						PASS	.	G	,	854,3550	334.4+/-303.4	102,650,1450	188.0	190.0	189.0		7941,	3.6	1.0	11	dbSNP_83	189	6405,2193	711.8+/-405.9	2384,1637,278	no	coding-synonymous,intron	AHNAK	NM_001620.1,NM_024060.2	,	2486,2287,1728	AA,AG,GG		25.5059,19.3915,44.1701	,	2647/5891,	62293948	7259,5743	2202	4299	6501	SO:0001819	synonymous_variant	79026	exon5			AGGCATGCTGAAC	M80899	CCDS31584.1, CCDS44625.1	11q12-q13	2008-02-05	2007-03-30		ENSG00000124942	ENSG00000124942			347	protein-coding gene	gene with protein product	"""desmoyokin"""	103390	"""AHNAK nucleoprotein (desmoyokin)"""			7987395, 12153988	Standard	NM_024060		Approved	MGC5395	uc001ntl.3	Q09666	OTTHUMG00000167558	ENST00000378024.4:c.7941C>T	11.37:g.62293948G>A		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	116	96	0.827586	NM_001620	A1A586	Silent	SNP	ENST00000378024.4	37	CCDS31584.1																																																																																			G|0.462;A|0.538	0.538	strong		0.532	AHNAK-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395572.1	NM_024060	
BARD1	580	hgsc.bcm.edu	37	2	215657089	215657089	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:215657089C>T	ENST00000260947.4	-	3	430	c.296G>A	c.(295-297)aGa>aAa	p.R99K	BARD1_ENST00000471787.1_Intron|BARD1_ENST00000449967.2_Intron	NM_000465.2|NM_001282543.1|NM_001282545.1|NM_001282548.1	NP_000456.2|NP_001269472.1|NP_001269474.1|NP_001269477.1	Q99728	BARD1_HUMAN	BRCA1 associated RING domain 1	99	Interaction with BRCA1.				cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|negative regulation of apoptotic process (GO:0043066)|negative regulation of mRNA 3'-end processing (GO:0031441)|negative regulation of protein export from nucleus (GO:0046826)|positive regulation of apoptotic process (GO:0043065)|positive regulation of protein catabolic process (GO:0045732)|protein K6-linked ubiquitination (GO:0085020)|protein ubiquitination (GO:0016567)|regulation of phosphorylation (GO:0042325)|tissue homeostasis (GO:0001894)	BRCA1-A complex (GO:0070531)|BRCA1-BARD1 complex (GO:0031436)|cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	kinase binding (GO:0019900)|ligase activity (GO:0016874)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|RNA binding (GO:0003723)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(2)|breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(1)|lung(14)|prostate(4)|upper_aerodigestive_tract(1)	35		Renal(323;0.0243)		Epithelial(149;3.2e-06)|all cancers(144;0.000461)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.011)		GTCCAGTTGTCTATTTATCTT	0.363									Neuroblastoma, Familial Clustering of;Congenital Central Hypoventilation Syndrome																												p.R99K		Atlas-SNP	.											.	BARD1	138	.	0			c.G296A						PASS	.						139.0	137.0	138.0					2																	215657089		2203	4300	6503	SO:0001583	missense	580	exon3	Familial Cancer Database	Familial Neuroblastoma;CCHS, Ondine Curse, incl. Ondine-Hirschsprung Disease	AGTTGTCTATTTA		CCDS2397.1, CCDS74645.1, CCDS74646.1, CCDS74647.1, CCDS74648.1	2q34-q35	2013-01-10			ENSG00000138376	ENSG00000138376		"""Ankyrin repeat domain containing"""	952	protein-coding gene	gene with protein product		601593				8944023, 9425226, 15159397	Standard	NM_001282548		Approved		uc002veu.2	Q99728	OTTHUMG00000133016	ENST00000260947.4:c.296G>A	2.37:g.215657089C>T	ENSP00000260947:p.Arg99Lys	Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	109	5	0.0458716	NM_000465	F6MDH7|F6MDH8|F6MDH9|O43574|Q53SS5	Missense_Mutation	SNP	ENST00000260947.4	37	CCDS2397.1	.	.	.	.	.	.	.	.	.	.	C	17.13	3.312107	0.60414	.	.	ENSG00000138376	ENST00000260947	T	0.75938	-0.98	5.29	4.42	0.53409	Zinc finger, RING/FYVE/PHD-type (1);	0.047598	0.85682	N	0.000000	T	0.70133	0.3189	L	0.53249	1.67	0.80722	D	1	B	0.25390	0.125	B	0.22152	0.038	T	0.70400	-0.4882	10	0.87932	D	0	-23.2173	14.0072	0.64470	0.0:0.9269:0.0:0.0731	.	99	Q99728	BARD1_HUMAN	K	99	ENSP00000260947:R99K	ENSP00000260947:R99K	R	-	2	0	BARD1	215365334	1.000000	0.71417	0.962000	0.40283	0.949000	0.60115	2.583000	0.46094	1.368000	0.46115	0.557000	0.71058	AGA	.	.	none		0.363	BARD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256602.1	NM_000465	
ZNF749	388567	hgsc.bcm.edu	37	19	57956706	57956706	+	Silent	SNP	G	G	A	rs61745342	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:57956706G>A	ENST00000334181.4	+	3	2440	c.2190G>A	c.(2188-2190)ggG>ggA	p.G730G	AC004076.9_ENST00000596831.1_Intron	NM_001023561.2	NP_001018855.2	O43361	ZN749_HUMAN	zinc finger protein 749	730					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(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)		GGGAATGTGGGAAAGACTTCA	0.388													g|||	119	0.023762	0.0144	0.0058	5008	,	,		19612	0.0218		0.0169	False		,,,				2504	0.0583				p.G730G		Atlas-SNP	.											.	ZNF749	75	.	0			c.G2190A						PASS	.	-		67,4339	61.7+/-98.7	0,67,2136	108.0	109.0	109.0		2190	-2.8	0.0	19	dbSNP_129	109	197,8403	85.8+/-148.2	2,193,4105	no	coding-synonymous	ZNF749	NM_001023561.2		2,260,6241	AA,AG,GG		2.2907,1.5207,2.0298		730/779	57956706	264,12742	2203	4300	6503	SO:0001819	synonymous_variant	388567	exon3			ATGTGGGAAAGAC	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.2190G>A	19.37:g.57956706G>A		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	103	36	0.349515	NM_001023561		Silent	SNP	ENST00000334181.4	37	CCDS33132.2																																																																																			G|0.982;A|0.018	0.018	strong		0.388	ZNF749-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317879.1	NM_001023561	
WIPF3	644150	hgsc.bcm.edu	37	7	29923572	29923572	+	Silent	SNP	T	T	C	rs28439342	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:29923572T>C	ENST00000409290.1	+	4	462	c.462T>C	c.(460-462)aaT>aaC	p.N154N	WIPF3_ENST00000409123.1_Silent_p.N154N|WIPF3_ENST00000242140.5_Silent_p.N154N	NM_001080529.2	NP_001073998.2	A6NGB9	WIPF3_HUMAN	WAS/WASL interacting protein family, member 3	154					cell differentiation (GO:0030154)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytosol (GO:0005829)				breast(2)|large_intestine(3)|lung(6)|ovary(1)	12						GGCTAGGCAATACCTCCGAGG	0.721													T|||	805	0.160743	0.2859	0.1081	5008	,	,		5568	0.0308		0.1769	False		,,,				2504	0.1462				p.N154N		Atlas-SNP	.											.	WIPF3	46	.	0			c.T462C						PASS	.	T		655,2473		59,537,968	3.0	4.0	4.0		462	-0.9	0.0	7	dbSNP_125	4	938,6434		63,812,2811	no	coding-synonymous	WIPF3	NM_001080529.2		122,1349,3779	CC,CT,TT		12.7238,20.9399,15.1714		154/484	29923572	1593,8907	1564	3686	5250	SO:0001819	synonymous_variant	644150	exon5			AGGCAATACCTCC	AK094250	CCDS56472.1	7p15.1	2006-10-12			ENSG00000122574	ENSG00000122574			22004	protein-coding gene	gene with protein product		612432					Standard	NM_001080529		Approved	CR16, FLJ36931	uc022aaz.1	A6NGB9	OTTHUMG00000152761	ENST00000409290.1:c.462T>C	7.37:g.29923572T>C		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	48	10	0.208333	NM_001080529	B8ZZV2	Silent	SNP	ENST00000409290.1	37	CCDS56472.1																																																																																			T|0.850;C|0.150	0.150	strong		0.721	WIPF3-002	NOVEL	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000327705.1		
IDUA	3425	hgsc.bcm.edu	37	4	995919	995919	+	Silent	SNP	G	G	C	rs6830825	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	21	0	0		WXS	Illumina HiSeq	Phase_I	25	10	0.4	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	
HELZ2	85441	hgsc.bcm.edu	37	20	62194128	62194128	+	Missense_Mutation	SNP	G	G	A	rs3810485	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:62194128G>A	ENST00000467148.1	-	8	6116	c.6047C>T	c.(6046-6048)cCg>cTg	p.P2016L	HELZ2_ENST00000427522.2_Missense_Mutation_p.P1447L	NM_001037335.2	NP_001032412.2	Q9BYK8	HELZ2_HUMAN	helicase with zinc finger 2, transcriptional coactivator	2016			P -> L (in dbSNP:rs3810485). {ECO:0000269|PubMed:11214970, ECO:0000269|PubMed:12189208, ECO:0000269|PubMed:16239304}.		cellular lipid metabolic process (GO:0044255)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	membrane (GO:0016020)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)										CGTGGGAGCCGGCAGCCCCTC	0.697													G|||	1375	0.274561	0.2163	0.3833	5008	,	,		12463	0.2659		0.2336	False		,,,				2504	0.3272				p.P2016L		Atlas-SNP	.											.	.	.	.	0			c.C6047T						PASS	.	G	LEU/PRO,LEU/PRO	896,3400		107,682,1359	10.0	12.0	12.0		6047,4340	-8.6	0.0	20	dbSNP_107	12	2189,6271		320,1549,2361	yes	missense,missense	PRIC285	NM_001037335.2,NM_033405.3	98,98	427,2231,3720	AA,AG,GG		25.8747,20.8566,24.1847	benign,benign	2016/2650,1447/2081	62194128	3085,9671	2148	4230	6378	SO:0001583	missense	85441	exon9			GGAGCCGGCAGCC	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.6047C>T	20.37:g.62194128G>A	ENSP00000417401:p.Pro2016Leu	Somatic	17	0	0		WXS	Illumina HiSeq	Phase_I	27	20	0.740741	NM_001037335	Q3C2G2|Q4VXQ1|Q8TEF3|Q96ND3|Q9C094	Missense_Mutation	SNP	ENST00000467148.1	37	CCDS33508.1	572	0.2619047619047619	120	0.24390243902439024	129	0.356353591160221	140	0.24475524475524477	183	0.24142480211081793	G	7.368	0.626191	0.14257	0.208566	0.258747	ENSG00000130589	ENST00000427522;ENST00000467148	T;T	0.79940	-1.32;-1.21	4.32	-8.56	0.00904	.	1.245660	0.06001	N	0.647856	T	0.00012	0.0000	L	0.31294	0.92	0.49389	P	2.1999999999999797E-4	B;B	0.22211	0.022;0.066	B;B	0.11329	0.003;0.006	T	0.08411	-1.0723	9	0.32370	T	0.25	-9.7697	0.534	0.00633	0.2582:0.2606:0.1268:0.3544	rs3810485;rs60386207	2016;1447	Q9BYK8;Q9BYK8-2	PR285_HUMAN;.	L	1447;2016	ENSP00000393257:P1447L;ENSP00000417401:P2016L	ENSP00000393257:P1447L	P	-	2	0	RP4-697K14.7	61664572	0.000000	0.05858	0.008000	0.14137	0.225000	0.24961	-0.362000	0.07602	-1.196000	0.02676	-0.802000	0.03209	CCG	G|0.740;A|0.260	0.260	strong		0.697	HELZ2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354127.1	NM_001037335	
ATXN1	6310	hgsc.bcm.edu	37	6	16327903	16327903	+	Missense_Mutation	SNP	C	C	A	rs3817753		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:16327903C>A	ENST00000244769.4	-	8	1575	c.639G>T	c.(637-639)caG>caT	p.Q213H	ATXN1_ENST00000436367.1_Missense_Mutation_p.Q213H	NM_000332.3	NP_000323.2	P54253	ATX1_HUMAN	ataxin 1	213	Poly-Gln.				adult locomotory behavior (GO:0008344)|cell death (GO:0008219)|negative regulation of insulin-like growth factor receptor signaling pathway (GO:0043569)|negative regulation of phosphorylation (GO:0042326)|negative regulation of transcription, DNA-templated (GO:0045892)|nuclear export (GO:0051168)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|RNA processing (GO:0006396)|transcription, DNA-templated (GO:0006351)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nuclear inclusion body (GO:0042405)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|poly(G) binding (GO:0034046)|poly(U) RNA binding (GO:0008266)|protein C-terminus binding (GO:0008022)|protein self-association (GO:0043621)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(11)|lung(12)|prostate(2)|skin(7)|upper_aerodigestive_tract(2)	44	Breast(50;0.063)|Ovarian(93;0.0733)	all_hematologic(90;0.000682)|Ovarian(999;0.00973)				gctgctgctgctgctgatgct	0.667																																					p.Q213H		Atlas-SNP	.											ATXN1,rectum,carcinoma,0,1	ATXN1	117	1	0			c.G639T						PASS	.						5.0	8.0	7.0					6																	16327903		1624	3504	5128	SO:0001583	missense	6310	exon7			CTGCTGCTGCTGA	X79204	CCDS34342.1	6p23	2014-09-17	2004-08-12	2004-08-13	ENSG00000124788	ENSG00000124788		"""Ataxins"""	10548	protein-coding gene	gene with protein product		601556	"""spinocerebellar ataxia 1 (olivopontocerebellar ataxia 1, autosomal dominant, ataxin 1)"""	SCA1		1582256	Standard	NM_000332		Approved	D6S504E, ATX1	uc010jpi.3	P54253	OTTHUMG00000014303	ENST00000244769.4:c.639G>T	6.37:g.16327903C>A	ENSP00000244769:p.Gln213His	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	44	15	0.340909	NM_001128164	Q17S02|Q9UJG2|Q9Y4J1	Missense_Mutation	SNP	ENST00000244769.4	37	CCDS34342.1	221	0.10119047619047619	38	0.07723577235772358	47	0.1298342541436464	89	0.1555944055944056	47	0.06200527704485488	C	4.787	0.146322	0.09134	.	.	ENSG00000124788	ENST00000244769;ENST00000450222;ENST00000436367	T;T	0.62941	-0.01;-0.01	.	.	.	.	.	.	.	.	T	0.18676	0.0448	N	0.08118	0	0.09310	N	1	.	.	.	.	.	.	T	0.19582	-1.0301	5	0.45353	T	0.12	.	.	.	.	rs3817753	213	P54253	ATX1_HUMAN	H	213	ENSP00000244769:Q213H;ENSP00000416360:Q213H	ENSP00000244769:Q213H	Q	-	3	2	ATXN1	16435882	0.034000	0.19679	0.018000	0.16275	0.072000	0.16883	0.306000	0.19279	0.000000	0.14550	0.000000	0.15137	CAG	C|0.899;A|0.101	0.101	strong		0.667	ATXN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039943.3	NM_000332	
NOC3L	64318	hgsc.bcm.edu	37	10	96106240	96106240	+	Missense_Mutation	SNP	G	G	C	rs11187895	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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_ENST00000371350.1_Missense_Mutation_p.P444R|NOC3L_ENST00000463649.1_5'UTR	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	135	0	0		WXS	Illumina HiSeq	Phase_I	102	43	0.421569	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	
CATSPER2	117155	hgsc.bcm.edu	37	15	43939642	43939642	+	Missense_Mutation	SNP	C	C	T	rs8042868	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:43939642C>T	ENST00000321596.5	-	3	368	c.169G>A	c.(169-171)Gta>Ata	p.V57I	STRC_ENST00000541030.1_Intron|CATSPER2_ENST00000355438.2_Missense_Mutation_p.V57I|CATSPER2_ENST00000354127.4_Missense_Mutation_p.V57I|CATSPER2_ENST00000381761.1_Missense_Mutation_p.V63I|CATSPER2_ENST00000464721.1_5'UTR|CATSPER2_ENST00000396879.1_Missense_Mutation_p.V57I			Q96P56	CTSR2_HUMAN	cation channel, sperm associated 2	57			V -> I (in dbSNP:rs8042868).		calcium ion import (GO:0070509)|cell differentiation (GO:0030154)|membrane depolarization during action potential (GO:0086010)|multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|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)|cervix(1)|endometrium(1)|large_intestine(3)|lung(8)|ovary(1)|prostate(1)|skin(1)|urinary_tract(2)	22		all_cancers(109;3.26e-15)|all_epithelial(112;1.48e-12)|Lung NSC(122;2.76e-08)|all_lung(180;3.1e-07)|Melanoma(134;0.027)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;3.56e-07)		TCTCCCAATACAAGTTTCTTC	0.448													c|||	1019	0.203474	0.2753	0.1787	5008	,	,		20391	0.2718		0.0984	False		,,,				2504	0.1616				p.V57I		Atlas-SNP	.											.	CATSPER2	49	.	0			c.G169A						PASS	.	C	ILE/VAL,ILE/VAL,ILE/VAL	1019,3379	354.9+/-312.8	124,771,1304	76.0	87.0	84.0		169,169,169	2.2	1.0	15	dbSNP_116	84	842,7750	190.4+/-236.9	50,742,3504	yes	missense,missense,missense	CATSPER2	NM_054020.2,NM_172095.1,NM_172097.1	29,29,29	174,1513,4808	TT,TC,CC		9.7998,23.1696,14.3264	benign,benign,benign	57/529,57/531,57/200	43939642	1861,11129	2199	4296	6495	SO:0001583	missense	117155	exon3			CCAATACAAGTTT	AF411817	CCDS10099.1, CCDS32216.1, CCDS73714.1	15q15.3	2011-07-05			ENSG00000166762	ENSG00000166762		"""Voltage-gated ion channels / Cation channels, sperm associated"""	18810	protein-coding gene	gene with protein product		607249				11675491, 16382101	Standard	NM_172095		Approved		uc001zsh.3	Q96P56	OTTHUMG00000059902	ENST00000321596.5:c.169G>A	15.37:g.43939642C>T	ENSP00000321463:p.Val57Ile	Somatic	179	0	0		WXS	Illumina HiSeq	Phase_I	224	78	0.348214	NM_172097	Q8NHT9|Q96P54|Q96P55	Missense_Mutation	SNP	ENST00000321596.5	37	CCDS10099.1	454	0.2078754578754579	139	0.28252032520325204	68	0.1878453038674033	181	0.31643356643356646	66	0.0870712401055409	C	11.49	1.654624	0.29425	0.231696	0.097998	ENSG00000166762	ENST00000396879;ENST00000299989;ENST00000381761;ENST00000321596;ENST00000354127;ENST00000355438;ENST00000432420;ENST00000409481	T;T;T;T;T;T;T	0.29655	1.56;1.56;1.56;1.56;1.56;1.56;1.56	3.38	2.23	0.28157	.	4.205360	0.01036	N	0.004222	T	0.00012	0.0000	N	0.08118	0	0.58432	P	8.000000000008E-6	B;B;B	0.09022	0.002;0.0;0.0	B;B;B	0.04013	0.001;0.0;0.0	T	0.33803	-0.9854	9	0.41790	T	0.15	.	5.663	0.17680	0.0:0.1323:0.0:0.8677	rs8042868;rs52821871;rs61246113;rs8042868	57;63;57	Q96P56-4;F8W9H2;Q96P56	.;.;CTSR2_HUMAN	I	57;57;63;57;57;57;57;57	ENSP00000380088:V57I;ENSP00000371180:V63I;ENSP00000321463:V57I;ENSP00000339137:V57I;ENSP00000347613:V57I;ENSP00000407694:V57I;ENSP00000386595:V57I	ENSP00000299989:V57I	V	-	1	0	CATSPER2	41726934	0.996000	0.38824	0.972000	0.41901	0.031000	0.12232	0.759000	0.26461	0.469000	0.27268	-1.499000	0.00960	GTA	C|0.822;T|0.178	0.178	strong		0.448	CATSPER2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000133151.2	NM_054020	
ARSD	414	hgsc.bcm.edu	37	X	2836138	2836138	+	Silent	SNP	G	G	A	rs73632974		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:2836138G>A	ENST00000381154.1	-	5	645	c.570C>T	c.(568-570)ccC>ccT	p.P190P	ARSD_ENST00000217890.6_5'UTR	NM_001669.3	NP_001660.2	P51689	ARSD_HUMAN	arylsulfatase D	190					cellular protein metabolic process (GO:0044267)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	arylsulfatase activity (GO:0004065)|metal ion binding (GO:0046872)			large_intestine(3)|lung(3)	6		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				CGTCCACTTCGGGGGGCCTGC	0.642																																					p.P190P		Atlas-SNP	.											.	ARSD	47	.	0			c.C570T						PASS	.						23.0	20.0	21.0					X																	2836138		2201	4297	6498	SO:0001819	synonymous_variant	414	exon5			CACTTCGGGGGGC	X83572	CCDS35196.1	Xp22.3	2013-02-14			ENSG00000006756	ENSG00000006756		"""Arylsulfatase family"""	717	protein-coding gene	gene with protein product		300002				7720070	Standard	NM_001669		Approved		uc004cqy.3	P51689	OTTHUMG00000021077	ENST00000381154.1:c.570C>T	X.37:g.2836138G>A		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	111	16	0.144144	NM_001669	Q9UHJ8	Silent	SNP	ENST00000381154.1	37	CCDS35196.1																																																																																			G|0.925;A|0.075	0.075	strong		0.642	ARSD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055636.1		
DNAL4	10126	hgsc.bcm.edu	37	22	39178701	39178701	+	Silent	SNP	A	A	G	rs760482	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:39178701A>G	ENST00000216068.4	-	2	280	c.36T>C	c.(34-36)gaT>gaC	p.D12D	DNAL4_ENST00000406199.3_Silent_p.D12D|SUN2_ENST00000406622.1_Intron|DNAL4_ENST00000486019.1_Intron	NM_005740.2	NP_005731.1	O96015	DNAL4_HUMAN	dynein, axonemal, light chain 4	12					microtubule-based process (GO:0007017)|neurotrophin TRK receptor signaling pathway (GO:0048011)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)|plasma membrane (GO:0005886)	motor activity (GO:0003774)			lung(1)|skin(1)	2	Melanoma(58;0.04)					GTCGCTTATAATCAGCCTCAT	0.587													A|||	2066	0.41254	0.4206	0.245	5008	,	,		18303	0.6925		0.2734	False		,,,				2504	0.3753				p.D12D		Atlas-SNP	.											.	DNAL4	5	.	0			c.T36C						PASS	.	A		1658,2748	505.9+/-366.3	328,1002,873	230.0	170.0	191.0		36	-2.4	1.0	22	dbSNP_86	191	2591,6009	419.8+/-353.2	381,1829,2090	yes	coding-synonymous	DNAL4	NM_005740.2		709,2831,2963	GG,GA,AA		30.1279,37.6305,32.6695		12/106	39178701	4249,8757	2203	4300	6503	SO:0001819	synonymous_variant	10126	exon2			CTTATAATCAGCC	AL035366	CCDS13979.1	22q13.1	2008-06-10	2006-09-04		ENSG00000100246	ENSG00000100246		"""Axonemal dyneins"""	2955	protein-coding gene	gene with protein product		610565	"""dynein, axonemal, light polypeptide 4"", ""dynein, axonemal, light 4"""			10591208	Standard	NM_005740		Approved	dJ327J16, PIG27	uc003awj.3	O96015	OTTHUMG00000151025	ENST00000216068.4:c.36T>C	22.37:g.39178701A>G		Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	159	83	0.522013	NM_005740	Q6FGB2|Q6FGD0	Silent	SNP	ENST00000216068.4	37	CCDS13979.1																																																																																			A|0.627;G|0.373	0.373	strong		0.587	DNAL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321032.1	NM_005740	
BAD	572	hgsc.bcm.edu	37	11	64051823	64051823	+	Silent	SNP	C	C	T	rs34882006	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:64051823C>T	ENST00000394532.3	-	1	288	c.18G>A	c.(16-18)gaG>gaA	p.E6E	GPR137_ENST00000377702.4_5'Flank|GPR137_ENST00000411458.1_5'UTR|GPR137_ENST00000539851.1_5'Flank|BAD_ENST00000544785.1_Silent_p.E6E|GPR137_ENST00000313074.3_5'Flank|BAD_ENST00000394531.3_Silent_p.E6E|GPR137_ENST00000438980.2_5'Flank|BAD_ENST00000309032.3_Silent_p.E6E	NM_004322.3	NP_004313.1	Q92934	BAD_HUMAN	BCL2-associated agonist of cell death	6					activation of cysteine-type endopeptidase activity (GO:0097202)|activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|ADP metabolic process (GO:0046031)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|ATP metabolic process (GO:0046034)|cellular process regulating host cell cycle in response to virus (GO:0060154)|cellular response to chromate (GO:0071247)|cellular response to hypoxia (GO:0071456)|cellular response to lipid (GO:0071396)|cellular response to mechanical stimulus (GO:0071260)|cellular response to nicotine (GO:0071316)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|extrinsic apoptotic signaling pathway (GO:0097191)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose catabolic process (GO:0006007)|glucose homeostasis (GO:0042593)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|pore complex assembly (GO:0046931)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic process by virus (GO:0060139)|positive regulation of autophagy (GO:0010508)|positive regulation of B cell differentiation (GO:0045579)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of glucokinase activity (GO:0033133)|positive regulation of insulin secretion (GO:0032024)|positive regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0035774)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane potential (GO:0010918)|positive regulation of neuron death (GO:1901216)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of proteolysis (GO:0045862)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of T cell differentiation (GO:0045582)|positive regulation of type B pancreatic cell development (GO:2000078)|regulation of mitochondrial membrane permeability (GO:0046902)|release of cytochrome c from mitochondria (GO:0001836)|response to amino acid (GO:0043200)|response to calcium ion (GO:0051592)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to glucocorticoid (GO:0051384)|response to glucose (GO:0009749)|response to hydrogen peroxide (GO:0042542)|response to oleic acid (GO:0034201)|response to progesterone (GO:0032570)|response to testosterone (GO:0033574)|suppression by virus of host apoptotic process (GO:0019050)|type B pancreatic cell proliferation (GO:0044342)	cytosol (GO:0005829)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|lipid binding (GO:0008289)|phospholipid binding (GO:0005543)|protein kinase binding (GO:0019901)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(1)	4						TCGGCTCAAACTCTGGGATCT	0.642													C|||	48	0.00958466	0.0015	0.0187	5008	,	,		18513	0.0		0.0308	False		,,,				2504	0.002				p.E6E		Atlas-SNP	.											.	BAD	8	.	0			c.G18A						PASS	.	C	,,	38,4364	43.1+/-76.7	0,38,2163	71.0	76.0	75.0		,18,18	4.8	1.0	11	dbSNP_126	75	350,8242	117.2+/-176.8	7,336,3953	no	utr-5,coding-synonymous,coding-synonymous	BAD,GPR137	NM_001170726.1,NM_004322.3,NM_032989.2	,,	7,374,6116	TT,TC,CC		4.0736,0.8632,2.986	,,	,6/169,6/169	64051823	388,12606	2201	4296	6497	SO:0001819	synonymous_variant	572	exon2			CTCAAACTCTGGG	AF021792	CCDS8065.1	11q13.1	2014-03-07	2008-08-19		ENSG00000002330	ENSG00000002330			936	protein-coding gene	gene with protein product		603167				8929532	Standard	NM_004322		Approved	BCL2L8, BBC2	uc001nzd.3	Q92934	OTTHUMG00000134302	ENST00000394532.3:c.18G>A	11.37:g.64051823C>T		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	70	50	0.714286	NM_032989	O14803|Q6FH21	Silent	SNP	ENST00000394532.3	37	CCDS8065.1																																																																																			C|0.978;T|0.022	0.022	strong		0.642	BAD-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259180.2	NM_032989	
SYNE1	23345	hgsc.bcm.edu	37	6	152777095	152777095	+	Missense_Mutation	SNP	A	A	C	rs17082709	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:152777095A>C	ENST00000367255.5	-	23	3254	c.2653T>G	c.(2653-2655)Ttg>Gtg	p.L885V	SYNE1_ENST00000367253.4_Missense_Mutation_p.L885V|SYNE1_ENST00000367248.3_Missense_Mutation_p.L875V|SYNE1_ENST00000265368.4_Missense_Mutation_p.L885V|SYNE1_ENST00000413186.2_Missense_Mutation_p.L885V|SYNE1_ENST00000448038.1_Missense_Mutation_p.L892V|SYNE1_ENST00000423061.1_Missense_Mutation_p.L892V|SYNE1_ENST00000495090.2_Missense_Mutation_p.L452V|SYNE1_ENST00000341594.5_Missense_Mutation_p.L937V	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	885			L -> V (in dbSNP:rs17082709).		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)		ACGTTGCTCAAGGTCACAAAC	0.378										HNSCC(10;0.0054)			A|||	217	0.0433307	0.0507	0.0375	5008	,	,		19393	0.002		0.0736	False		,,,				2504	0.0491				p.L892V		Atlas-SNP	.											.	SYNE1	3227	.	0			c.T2674G						PASS	.	A	VAL/LEU,VAL/LEU	240,4166	141.1+/-176.5	6,228,1969	156.0	139.0	145.0		2674,2653	1.5	1.0	6	dbSNP_123	145	584,8016	155.5+/-209.5	29,526,3745	yes	missense,missense	SYNE1	NM_033071.3,NM_182961.3	32,32	35,754,5714	CC,CA,AA		6.7907,5.4471,6.3355	benign,benign	892/8750,885/8798	152777095	824,12182	2203	4300	6503	SO:0001583	missense	23345	exon23			TGCTCAAGGTCAC	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.2653T>G	6.37:g.152777095A>C	ENSP00000356224:p.Leu885Val	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	75	56	0.746667	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	100	0.045787545787545784	29	0.05894308943089431	14	0.03867403314917127	2	0.0034965034965034965	55	0.07255936675461741	A	10.76	1.440627	0.25900	0.054471	0.067907	ENSG00000131018	ENST00000367255;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594;ENST00000367253;ENST00000367248;ENST00000413186;ENST00000495090	T;T;T;T;T;T;T;T;T	0.49432	1.23;1.23;1.23;1.23;0.78;1.23;1.23;1.23;1.23	5.25	1.49	0.22878	.	0.384445	0.19275	N	0.118304	T	0.15219	0.0367	L	0.47716	1.5	0.53688	D	0.999972	B;B;B;B;B;B;B	0.32188	0.055;0.055;0.058;0.052;0.359;0.055;0.023	B;B;B;B;B;B;B	0.26202	0.022;0.03;0.046;0.067;0.067;0.03;0.028	T	0.05801	-1.0863	10	0.26408	T	0.33	.	3.6723	0.08279	0.5774:0.0:0.1491:0.2735	rs17082709;rs52812999;rs17082709	868;885;452;875;885;885;892	B3W695;Q8NF91;F5H422;F5GXQ8;Q8NF91-6;E7EQI5;Q8NF91-4	.;SYNE1_HUMAN;.;.;.;.;.	V	885;892;885;892;937;885;875;885;452	ENSP00000356224:L885V;ENSP00000396024:L892V;ENSP00000265368:L885V;ENSP00000390975:L892V;ENSP00000341887:L937V;ENSP00000356222:L885V;ENSP00000356217:L875V;ENSP00000414510:L885V;ENSP00000438508:L452V	ENSP00000265368:L885V	L	-	1	2	SYNE1	152818788	0.942000	0.31987	0.991000	0.47740	0.887000	0.51463	2.063000	0.41423	0.287000	0.22375	-0.256000	0.11100	TTG	A|0.938;C|0.062	0.062	strong		0.378	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961	
OR5F1	338674	hgsc.bcm.edu	37	11	55761528	55761528	+	Missense_Mutation	SNP	T	T	C	rs35607186	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:55761528T>C	ENST00000278409.1	-	1	573	c.574A>G	c.(574-576)Aca>Gca	p.T192A		NM_003697.1	NP_003688.1	O95221	OR5F1_HUMAN	olfactory receptor, family 5, subfamily F, member 1	192			T -> A (in dbSNP:rs35607186).		detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(6)|kidney(1)|large_intestine(11)|liver(1)|lung(33)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	58	Esophageal squamous(21;0.00448)					TTCAGGATTGTGTCAGAACAA	0.453													T|||	457	0.091254	0.1293	0.0403	5008	,	,		19955	0.0913		0.0944	False		,,,				2504	0.0726				p.T192A		Atlas-SNP	.											OR5F1,NS,carcinoma,+1,1	OR5F1	116	1	0			c.A574G						PASS	.	T	ALA/THR	514,3888	235.5+/-248.0	35,444,1722	90.0	84.0	86.0		574	3.0	0.6	11	dbSNP_126	86	725,7867	176.3+/-226.2	31,663,3602	yes	missense	OR5F1	NM_003697.1	58	66,1107,5324	CC,CT,TT		8.4381,11.6765,9.5352	benign	192/315	55761528	1239,11755	2201	4296	6497	SO:0001583	missense	338674	exon1			GGATTGTGTCAGA	AF065863	CCDS31515.1	11q11	2012-08-09			ENSG00000149133	ENSG00000149133		"""GPCR / Class A : Olfactory receptors"""	8343	protein-coding gene	gene with protein product		608492				9787077	Standard	NM_003697		Approved	OR11-10	uc010riv.2	O95221	OTTHUMG00000166825	ENST00000278409.1:c.574A>G	11.37:g.55761528T>C	ENSP00000278409:p.Thr192Ala	Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	93	68	0.731183	NM_003697	Q495D1|Q6IFB9	Missense_Mutation	SNP	ENST00000278409.1	37	CCDS31515.1	203	0.09294871794871795	74	0.15040650406504066	18	0.049723756906077346	45	0.07867132867132867	66	0.0870712401055409	T	14.83	2.653859	0.47362	0.116765	0.084381	ENSG00000149133	ENST00000278409	T	0.00235	8.48	3.03	3.03	0.35002	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00012	0.0000	M	0.81341	2.54	0.33552	P	0.40374	P	0.34997	0.479	B	0.40066	0.318	T	0.05616	-1.0874	8	0.66056	D	0.02	.	6.9603	0.24593	0.2046:0.0:0.0:0.7954	rs35607186	192	O95221	OR5F1_HUMAN	A	192	ENSP00000278409:T192A	ENSP00000278409:T192A	T	-	1	0	OR5F1	55518104	0.001000	0.12720	0.605000	0.28930	0.483000	0.33249	0.499000	0.22546	1.167000	0.42706	0.247000	0.18012	ACA	T|0.905;C|0.095	0.095	strong		0.453	OR5F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391532.1	NM_003697	
DSCAML1	57453	hgsc.bcm.edu	37	11	117310022	117310022	+	Silent	SNP	A	A	G	rs11216387	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:117310022A>G	ENST00000321322.6	-	23	4285	c.4284T>C	c.(4282-4284)acT>acC	p.T1428T	DSCAML1_ENST00000527706.1_Silent_p.T1158T	NM_020693.2	NP_065744.2	Q8TD84	DSCL1_HUMAN	Down syndrome cell adhesion molecule like 1	1368	Fibronectin type-III 5. {ECO:0000255|PROSITE-ProRule:PRU00316}.				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.T1428T(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)		CAAAGCCACCAGTGTTGGTGG	0.592													G|||	1523	0.304113	0.3116	0.3012	5008	,	,		19567	0.5605		0.1233	False		,,,				2504	0.2178				p.T1428T		Atlas-SNP	.											DSCAML1,NS,carcinoma,0,1	DSCAML1	286	1	1	Substitution - coding silent(1)	stomach(1)	c.T4284C						PASS	.	G		1242,3160	703.8+/-407.0	173,896,1132	121.0	107.0	112.0		4284	-7.4	0.1	11	dbSNP_120	112	916,7676	776.9+/-407.7	50,816,3430	no	coding-synonymous	DSCAML1	NM_020693.2		223,1712,4562	GG,GA,AA		10.6611,28.2144,16.6077		1428/2114	117310022	2158,10836	2201	4296	6497	SO:0001819	synonymous_variant	57453	exon23			GCCACCAGTGTTG		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.4284T>C	11.37:g.117310022A>G		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	100	21	0.21	NM_020693	Q76MU9|Q8IZY3|Q8IZY4|Q8WXU7|Q9ULT7	Silent	SNP	ENST00000321322.6	37	CCDS8384.1																																																																																			A|0.769;G|0.231	0.231	strong		0.592	DSCAML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392907.2	NM_020693	
MIPEP	4285	hgsc.bcm.edu	37	13	24436475	24436475	+	Missense_Mutation	SNP	C	C	T	rs11551114	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:24436475C>T	ENST00000382172.3	-	9	1117	c.1019G>A	c.(1018-1020)cGa>cAa	p.R340Q		NM_005932.3	NP_005923	Q99797	MIPEP_HUMAN	mitochondrial intermediate peptidase	340			R -> Q (in dbSNP:rs11551114).		protein processing involved in protein targeting to mitochondrion (GO:0006627)	mitochondrion (GO:0005739)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			breast(2)|central_nervous_system(1)|endometrium(3)|large_intestine(5)|liver(1)|lung(12)|prostate(2)|skin(1)	27		all_cancers(29;1.83e-22)|all_epithelial(30;8.75e-19)|all_lung(29;9.17e-18)|Lung SC(185;0.0225)|Breast(139;0.14)		all cancers(112;0.00389)|Epithelial(112;0.0266)|OV - Ovarian serous cystadenocarcinoma(117;0.0717)|Lung(94;0.207)|GBM - Glioblastoma multiforme(144;0.232)		TTTCATCCCTCGTATCATCTC	0.279													C|||	328	0.0654952	0.0582	0.072	5008	,	,		18310	0.001		0.1312	False		,,,				2504	0.0695				p.R340Q		Atlas-SNP	.											MIPEP,colon,carcinoma,-1,1	MIPEP	53	1	0			c.G1019A						PASS	.	C	GLN/ARG	272,4120		10,252,1934	50.0	47.0	48.0		1019	1.5	0.0	13	dbSNP_120	48	1126,7454		73,980,3237	yes	missense	MIPEP	NM_005932.3	43	83,1232,5171	TT,TC,CC		13.1235,6.1931,10.7771	benign	340/714	24436475	1398,11574	2196	4290	6486	SO:0001583	missense	4285	exon9			ATCCCTCGTATCA		CCDS9303.1	13q12	2011-01-17			ENSG00000027001	ENSG00000027001	3.4.24.59		7104	protein-coding gene	gene with protein product		602241				9073519	Standard	NM_005932		Approved	MIP	uc001uox.4	Q99797	OTTHUMG00000016573	ENST00000382172.3:c.1019G>A	13.37:g.24436475C>T	ENSP00000371607:p.Arg340Gln	Somatic	248	0	0		WXS	Illumina HiSeq	Phase_I	165	80	0.484848	NM_005932	Q5JV15|Q5T9Q9|Q96G65	Missense_Mutation	SNP	ENST00000382172.3	37	CCDS9303.1	147	0.0673076923076923	32	0.06504065040650407	19	0.052486187845303865	1	0.0017482517482517483	95	0.12532981530343007	C	6.085	0.383896	0.11524	0.061931	0.131235	ENSG00000027001	ENST00000382172	T	0.07114	3.22	4.79	1.51	0.23008	Neurolysin/Thimet oligopeptidase, domain 2 (1);	0.374324	0.28583	N	0.014834	T	0.00073	0.0002	L	0.31664	0.95	0.80722	P	0.0	B	0.19200	0.034	B	0.13407	0.009	T	0.38045	-0.9679	9	0.27785	T	0.31	.	4.5291	0.11995	0.0:0.3188:0.2723:0.4089	rs11551114;rs17424158;rs56587494;rs11551114	340	Q99797	MIPEP_HUMAN	Q	340	ENSP00000371607:R340Q	ENSP00000371607:R340Q	R	-	2	0	MIPEP	23334475	0.010000	0.17322	0.028000	0.17463	0.696000	0.40369	0.276000	0.18716	0.473000	0.27368	-0.150000	0.13652	CGA	C|0.909;T|0.091	0.091	strong		0.279	MIPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044169.1		
HERC4	26091	hgsc.bcm.edu	37	10	69695973	69695973	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:69695973C>T	ENST00000395198.3	-	23	2862	c.2615G>A	c.(2614-2616)gGt>gAt	p.G872D	HERC4_ENST00000277817.6_Missense_Mutation_p.G762D|HERC4_ENST00000412272.2_Missense_Mutation_p.G794D|HERC4_ENST00000373700.4_Missense_Mutation_p.G864D|HERC4_ENST00000395187.2_3'UTR	NM_022079.2	NP_071362.1	Q5GLZ8	HERC4_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase 4	872	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				cell differentiation (GO:0030154)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			NS(1)|breast(1)|cervix(1)|endometrium(1)|large_intestine(6)|lung(13)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	27						TTCTGTTGCACCAAAGTTTTC	0.313																																					p.G872D		Atlas-SNP	.											.	HERC4	78	.	0			c.G2615A						PASS	.						141.0	131.0	135.0					10																	69695973		2203	4300	6503	SO:0001583	missense	26091	exon23			GTTGCACCAAAGT	AY221963	CCDS7274.1, CCDS41533.1, CCDS60541.1, CCDS60542.1	10q21.3	2013-09-20	2012-02-23		ENSG00000148634	ENSG00000148634			24521	protein-coding gene	gene with protein product		609248	"""hect domain and RLD 4"""			10997877	Standard	NM_022079		Approved	DKFZP564G092, KIAA1593	uc001jng.4	Q5GLZ8	OTTHUMG00000018343	ENST00000395198.3:c.2615G>A	10.37:g.69695973C>T	ENSP00000378624:p.Gly872Asp	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	65	17	0.261538	NM_022079	Q5GC98|Q5GC99|Q5GCA0|Q8IXP9|Q9HCH9	Missense_Mutation	SNP	ENST00000395198.3	37	CCDS41533.1	.	.	.	.	.	.	.	.	.	.	C	27.4	4.831789	0.91036	.	.	ENSG00000148634	ENST00000277817;ENST00000412272;ENST00000395198;ENST00000373700	T;T;T;T	0.57107	0.42;0.42;0.42;0.42	5.2	5.2	0.72013	HECT (4);	0.000000	0.85682	D	0.000000	T	0.75391	0.3843	M	0.82323	2.585	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;0.999	D;D;D;D;D	0.91635	0.999;0.999;0.999;0.999;0.992	T	0.75204	-0.3400	10	0.37606	T	0.19	.	19.1052	0.93291	0.0:1.0:0.0:0.0	.	794;762;722;864;872	Q5GLZ8-3;Q5GLZ8-6;Q5VXS9;Q5GLZ8-2;Q5GLZ8	.;.;.;.;HERC4_HUMAN	D	762;794;872;864	ENSP00000277817:G762D;ENSP00000416504:G794D;ENSP00000378624:G872D;ENSP00000362804:G864D	ENSP00000277817:G762D	G	-	2	0	HERC4	69365979	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.364000	0.79526	2.568000	0.86640	0.460000	0.39030	GGT	.	.	none		0.313	HERC4-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359262.1	NM_015601	
PRDM9	56979	hgsc.bcm.edu	37	5	23527387	23527387	+	Missense_Mutation	SNP	C	C	A	rs56256550		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:23527387C>A	ENST00000296682.3	+	11	2372	c.2190C>A	c.(2188-2190)agC>agA	p.S730R		NM_020227.2	NP_064612.2	Q9NQV7	PRDM9_HUMAN	PR domain containing 9	730					meiotic gene conversion (GO:0006311)|positive regulation of meiosis I (GO:0060903)|positive regulation of reciprocal meiotic recombination (GO:0010845)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)	histone methyltransferase activity (H3-K4 specific) (GO:0042800)|metal ion binding (GO:0046872)|recombination hotspot binding (GO:0010844)|sequence-specific DNA binding (GO:0043565)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(15)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(27)|lung(87)|ovary(6)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(11)	172						GGGGCTTTAGCAATAAGTCAC	0.597										HNSCC(3;0.000094)																											p.S730R		Atlas-SNP	.											PRDM9,rectum,carcinoma,0,1	PRDM9	344	1	0			c.C2190A						scavenged	.						23.0	25.0	24.0					5																	23527387		2067	4181	6248	SO:0001583	missense	56979	exon11			CTTTAGCAATAAG	AF275816	CCDS43307.1	5p14.2	2014-06-03			ENSG00000164256	ENSG00000164256		"""-"", ""Zinc fingers, C2H2-type"""	13994	protein-coding gene	gene with protein product	"""PR-domain containing protein 9"""	609760	"""minisatellite binding protein 3, 115kDa"", ""minisatellite binding protein 3 (115kD)"""	MSBP3		10668202, 2062643, 24634223	Standard	NM_020227		Approved	PFM6, ZNF899	uc003jgo.3	Q9NQV7	OTTHUMG00000161918	ENST00000296682.3:c.2190C>A	5.37:g.23527387C>A	ENSP00000296682:p.Ser730Arg	Somatic	88	2	0.0227273		WXS	Illumina HiSeq	Phase_I	116	10	0.0862069	NM_020227	B4DX22|Q27Q50	Missense_Mutation	SNP	ENST00000296682.3	37	CCDS43307.1	.	.	.	.	.	.	.	.	.	.	C	0.029	-1.348632	0.01266	.	.	ENSG00000164256	ENST00000296682	T	0.19669	2.13	2.79	-5.57	0.02521	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.10165	0.0249	L	0.27944	0.81	0.09310	N	1	P	0.47350	0.894	B	0.38880	0.284	T	0.03818	-1.1001	9	0.44086	T	0.13	.	3.9896	0.09532	0.4241:0.2776:0.0:0.2983	.	730	Q9NQV7	PRDM9_HUMAN	R	730	ENSP00000296682:S730R	ENSP00000296682:S730R	S	+	3	2	PRDM9	23563144	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-5.778000	0.00099	-2.704000	0.00397	-0.350000	0.07774	AGC	.	.	weak		0.597	PRDM9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366375.1	NM_020227	
ARID4B	51742	hgsc.bcm.edu	37	1	235383188	235383188	+	Silent	SNP	A	A	G	rs4659654	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:235383188A>G	ENST00000264183.3	-	16	2000	c.1503T>C	c.(1501-1503)gaT>gaC	p.D501D	ARID4B_ENST00000366603.2_Silent_p.D501D|ARID4B_ENST00000349213.3_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						PASS	.	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	284	1	0.00352113		WXS	Illumina HiSeq	Phase_I	198	195	0.984848	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	
DHX33	56919	hgsc.bcm.edu	37	17	5354204	5354204	+	Missense_Mutation	SNP	G	G	C	rs11653658	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:5354204G>C	ENST00000225296.3	-	9	1647	c.1447C>G	c.(1447-1449)Cat>Gat	p.H483D	DHX33_ENST00000433302.3_Missense_Mutation_p.H259D	NM_001199699.1|NM_020162.3	NP_001186628.1|NP_064547.2	Q9H6R0	DHX33_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 33	483			H -> D (in dbSNP:rs11653658).		positive regulation of transcription from RNA polymerase I promoter (GO:0045943)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)|rDNA binding (GO:0000182)			breast(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(2)|lung(2)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17						TCATCCTTATGTTCAAGAGCA	0.428													G|||	234	0.0467252	0.0711	0.0389	5008	,	,		19648	0.002		0.0875	False		,,,				2504	0.0235				p.H483D		Atlas-SNP	.											.	DHX33	41	.	0			c.C1447G						PASS	.	G	ASP/HIS,ASP/HIS	356,4050	184.7+/-212.0	12,332,1859	174.0	163.0	167.0		928,1447	4.9	0.8	17	dbSNP_120	167	617,7983	162.2+/-214.9	26,565,3709	yes	missense,missense	DHX33	NM_001199699.1,NM_020162.3	81,81	38,897,5568	CC,CG,GG		7.1744,8.0799,7.4812	benign,benign	310/535,483/708	5354204	973,12033	2203	4300	6503	SO:0001583	missense	56919	exon9			CCTTATGTTCAAG	AL359945	CCDS11072.1	17p13	2003-06-13	2003-06-13	2003-06-13	ENSG00000005100	ENSG00000005100		"""DEAH-boxes"""	16718	protein-coding gene	gene with protein product		614405	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 33"""	DDX33			Standard	NM_020162		Approved	FLJ21972, DKFZp762F2011	uc002gca.3	Q9H6R0	OTTHUMG00000102041	ENST00000225296.3:c.1447C>G	17.37:g.5354204G>C	ENSP00000225296:p.His483Asp	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	111	54	0.486486	NM_020162	B4DHF9|Q4G149|Q5CZ73|Q9H5M9	Missense_Mutation	SNP	ENST00000225296.3	37	CCDS11072.1	107	0.04899267399267399	24	0.04878048780487805	18	0.049723756906077346	2	0.0034965034965034965	63	0.08311345646437995	G	12.89	2.072280	0.36566	0.080799	0.071744	ENSG00000005100	ENST00000225296;ENST00000433302	T;T	0.01947	4.54;4.54	5.85	4.87	0.63330	Helicase-associated domain (2);	0.559496	0.19884	N	0.103892	T	0.00073	0.0002	N	0.00135	-2.02	0.22156	N	0.999328	B;B	0.29378	0.243;0.001	B;B	0.34489	0.184;0.0	T	0.49781	-0.8903	10	0.87932	D	0	.	13.2079	0.59807	0.0:0.0:0.7104:0.2896	rs11653658;rs11653658	259;483	Q05BE5;Q9H6R0	.;DHX33_HUMAN	D	483;259	ENSP00000225296:H483D;ENSP00000413779:H259D	ENSP00000225296:H483D	H	-	1	0	DHX33	5294928	0.943000	0.32029	0.797000	0.32132	0.964000	0.63967	3.676000	0.54612	1.461000	0.47929	-0.182000	0.12963	CAT	G|0.935;C|0.065	0.065	strong		0.428	DHX33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219826.2	NM_020162	
SYNE1	23345	hgsc.bcm.edu	37	6	152469188	152469188	+	Missense_Mutation	SNP	C	C	G	rs2252755	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:152469188C>G	ENST00000367255.5	-	137	25569	c.24968G>C	c.(24967-24969)gGc>gCc	p.G8323A	SYNE1_ENST00000265368.4_Missense_Mutation_p.G8323A|SYNE1_ENST00000448038.1_Missense_Mutation_p.G8252A|SYNE1_ENST00000539504.1_Missense_Mutation_p.G478A|SYNE1_ENST00000423061.1_Missense_Mutation_p.G8252A|SYNE1_ENST00000356820.4_Missense_Mutation_p.G2847A|SYNE1_ENST00000354674.4_Missense_Mutation_p.G478A|SYNE1_ENST00000341594.5_Missense_Mutation_p.G7935A|SYNE1_ENST00000347037.5_5'UTR	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	8323			G -> A (in dbSNP:rs2252755). {ECO:0000269|PubMed:11792814, ECO:0000269|PubMed:11801724, ECO:0000269|PubMed:12408964, ECO:0000269|PubMed:9872452, ECO:0000269|Ref.4}.		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)		ACCTGATAAGCCAACAGCTCC	0.488										HNSCC(10;0.0054)			C|||	2000	0.399361	0.4576	0.5115	5008	,	,		19254	0.2986		0.333	False		,,,				2504	0.4131				p.G8323A		Atlas-SNP	.											.	SYNE1	3227	.	0			c.G24968C						PASS	.	C	ALA/GLY,ALA/GLY	1958,2448	550.6+/-378.1	446,1066,691	50.0	53.0	52.0		24755,24968	5.3	1.0	6	dbSNP_100	52	2901,5699	452.1+/-362.9	485,1931,1884	yes	missense,missense	SYNE1	NM_033071.3,NM_182961.3	60,60	931,2997,2575	GG,GC,CC		33.7326,44.4394,37.3597	benign,benign	8252/8750,8323/8798	152469188	4859,8147	2203	4300	6503	SO:0001583	missense	23345	exon137			GATAAGCCAACAG	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.24968G>C	6.37:g.152469188C>G	ENSP00000356224:p.Gly8323Ala	Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	25	15	0.6	NM_182961	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Missense_Mutation	SNP	ENST00000367255.5	37	CCDS5236.2	801	0.36675824175824173	218	0.44308943089430897	189	0.5220994475138122	157	0.2744755244755245	237	0.31266490765171506	C	0.218	-1.031183	0.02029	0.444394	0.337326	ENSG00000131018	ENST00000367255;ENST00000539504;ENST00000367257;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594;ENST00000356820;ENST00000313630;ENST00000367247;ENST00000367251;ENST00000354674	T;T;T;T;T;T;T;T;T;T	0.50001	0.85;4.9;1.68;0.9;0.76;0.9;0.95;2.85;2.04;5.02	5.34	5.34	0.76211	.	0.107870	0.41001	D	0.000975	T	0.21347	0.0514	N	0.11284	0.12	0.37104	P	0.09995900000000002	P;P;B;B;B	0.39940	0.696;0.696;0.012;0.007;0.001	B;B;B;B;B	0.40702	0.338;0.338;0.041;0.018;0.002	T	0.07102	-1.0790	9	0.26408	T	0.33	.	19.0332	0.92967	0.0:1.0:0.0:0.0	rs2252755;rs2252755	8323;8323;8252;8252;525	Q8NF91;E7EQI5;Q8NF91-4;E9PEL9;B7Z9Y6	SYNE1_HUMAN;.;.;.;.	A	8323;478;969;8252;8323;8252;7935;2847;485;480;1245;478	ENSP00000356224:G8323A;ENSP00000441052:G478A;ENSP00000356226:G969A;ENSP00000396024:G8252A;ENSP00000265368:G8323A;ENSP00000390975:G8252A;ENSP00000341887:G7935A;ENSP00000349276:G2847A;ENSP00000356220:G1245A;ENSP00000346701:G478A	ENSP00000265368:G8323A	G	-	2	0	SYNE1	152510881	0.877000	0.30153	0.994000	0.49952	0.147000	0.21601	2.665000	0.46791	2.516000	0.84829	0.655000	0.94253	GGC	C|0.627;G|0.373	0.373	strong		0.488	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961	
EXD1	161829	hgsc.bcm.edu	37	15	41476465	41476465	+	Silent	SNP	G	G	A	rs690733	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:41476465G>A	ENST00000314992.5	-	10	1399	c.1209C>T	c.(1207-1209)acC>acT	p.T403T	EXD1_ENST00000458580.2_Silent_p.T461T	NM_152596.2	NP_689809.2	Q8NHP7	EXD1_HUMAN	exonuclease 3'-5' domain containing 1	403							3'-5' exonuclease activity (GO:0008408)|nucleic acid binding (GO:0003676)			large_intestine(5)|liver(1)|lung(4)|ovary(2)|prostate(2)|skin(2)	16						AATCCTCACTGGTTTCCCCTT	0.413													G|||	2624	0.523962	0.8064	0.3833	5008	,	,		21173	0.2907		0.4423	False		,,,				2504	0.5665				p.T403T		Atlas-SNP	.											.	EXD1	52	.	0			c.C1209T						PASS	.	G		3341,1065	723.1+/-409.4	1288,765,150	158.0	160.0	160.0		1209	2.1	0.0	15	dbSNP_83	160	3693,4907	527.8+/-381.2	792,2109,1399	no	coding-synonymous	EXD1	NM_152596.2		2080,2874,1549	AA,AG,GG		42.9419,24.1716,45.9173		403/515	41476465	7034,5972	2203	4300	6503	SO:0001819	synonymous_variant	161829	exon10			CTCACTGGTTTCC	BC030628	CCDS10072.1, CCDS66738.1	15q15.1	2009-02-24	2009-02-24	2009-02-24	ENSG00000178997	ENSG00000178997			28507	protein-coding gene	gene with protein product			"""exonuclease 3'-5' domain-like 1"""	EXDL1		12477932	Standard	NM_001286441		Approved	MGC33637	uc001znk.3	Q8NHP7	OTTHUMG00000130232	ENST00000314992.5:c.1209C>T	15.37:g.41476465G>A		Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	157	83	0.528662	NM_152596	A8K909|B7Z839|Q6ZW94	Silent	SNP	ENST00000314992.5	37	CCDS10072.1																																																																																			G|0.476;A|0.524	0.524	strong		0.413	EXD1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252553.2	NM_152596	
WDR38	401551	hgsc.bcm.edu	37	9	127618775	127618775	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:127618775C>T	ENST00000373574.1	+	6	570	c.514C>T	c.(514-516)Cac>Tac	p.H172Y		NM_001045476.1|NM_001276374.1	NP_001038941.1|NP_001263303.1	Q5JTN6	WDR38_HUMAN	WD repeat domain 38	172			H -> R (in dbSNP:rs2274970). {ECO:0000269|PubMed:15489334}.		hematopoietic progenitor cell differentiation (GO:0002244)					breast(1)|large_intestine(1)|lung(4)|prostate(1)|skin(1)	8						CTCCACCGTACACATCTGGGA	0.637																																					p.H172Y		Atlas-SNP	.											.	WDR38	21	.	0			c.C514T						PASS	.						22.0	26.0	25.0					9																	127618775		2030	4179	6209	SO:0001583	missense	401551	exon6			ACCGTACACATCT		CCDS43876.1, CCDS75898.1, CCDS75899.1	9q33.3	2013-01-09			ENSG00000136918	ENSG00000136918		"""WD repeat domain containing"""	23745	protein-coding gene	gene with protein product							Standard	NM_001276375		Approved		uc011lzo.3	Q5JTN6	OTTHUMG00000020664	ENST00000373574.1:c.514C>T	9.37:g.127618775C>T	ENSP00000362677:p.His172Tyr	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	61	11	0.180328	NM_001045476	A0PK24	Missense_Mutation	SNP	ENST00000373574.1	37	CCDS43876.1	.	.	.	.	.	.	.	.	.	.	C	9.880	1.201340	0.22121	.	.	ENSG00000136918	ENST00000373574	T	0.59906	0.23	4.68	1.78	0.24846	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40 repeat, conserved site (1);WD40-repeat-containing domain (1);	0.349118	0.25127	N	0.032940	T	0.34337	0.0894	N	0.12887	0.27	0.09310	N	1	B	0.25521	0.128	B	0.26310	0.068	T	0.25152	-1.0140	10	0.87932	D	0	.	5.2255	0.15391	0.165:0.6532:0.0:0.1818	.	172	Q5JTN6	WDR38_HUMAN	Y	172	ENSP00000362677:H172Y	ENSP00000362677:H172Y	H	+	1	0	WDR38	126658596	0.006000	0.16342	0.173000	0.22940	0.446000	0.32137	-0.009000	0.12765	0.193000	0.20303	0.561000	0.74099	CAC	.	.	none		0.637	WDR38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054048.1	NM_001045476	
KMT2B	9757	hgsc.bcm.edu	37	19	36224705	36224705	+	Missense_Mutation	SNP	A	A	G	rs231591	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:36224705A>G	ENST00000222270.7	+	30	7091	c.7091A>G	c.(7090-7092)gAt>gGt	p.D2364G	KMT2B_ENST00000607650.1_RNA|KMT2B_ENST00000420124.1_Missense_Mutation_p.D2364G	NM_014727.1	NP_055542.1	Q9UMN6	KMT2B_HUMAN	lysine (K)-specific methyltransferase 2B	2364			D -> G (in dbSNP:rs231591).		chromatin-mediated maintenance of transcription (GO:0048096)|gene silencing (GO:0016458)|histone H3-K4 methylation (GO:0051568)|histone H3-K4 trimethylation (GO:0080182)|oocyte differentiation (GO:0009994)|ovarian follicle development (GO:0001541)|ovulation (GO:0030728)|regulation of histone H3-K4 methylation (GO:0051569)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)										CTTCCGGAAGATGGTCCTCCC	0.637													G|||	3107	0.620407	0.848	0.428	5008	,	,		16478	0.505		0.4811	False		,,,				2504	0.7117				p.D2364G		Atlas-SNP	.											.	MLL4	229	.	0			c.A7091G						PASS	.	G	GLY/ASP	3099,773		1233,633,70	60.0	66.0	64.0		7091	1.7	0.3	19	dbSNP_79	64	3932,4336		924,2084,1126	yes	missense	MLL4	NM_014727.1	94	2157,2717,1196	GG,GA,AA		47.5568,19.9638,42.084	benign	2364/2716	36224705	7031,5109	1936	4134	6070	SO:0001583	missense	8085	exon30			CGGAAGATGGTCC	AJ007041	CCDS46055.1	19q13.1	2014-02-18			ENSG00000105663	ENSG00000272333		"""Chromatin-modifying enzymes / K-methyltransferases"""	15840	protein-coding gene	gene with protein product	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila) 4"""	606834				10409430, 10637508	Standard	XM_006723513		Approved	KIAA0304, MLL2, TRX2, HRX2, WBP7, MLL1B, MLL4		Q9UMN6	OTTHUMG00000048119	ENST00000222270.7:c.7091A>G	19.37:g.36224705A>G	ENSP00000222270:p.Asp2364Gly	Somatic	134	1	0.00746269		WXS	Illumina HiSeq	Phase_I	116	116	1	NM_014727	O15022|O95836|Q96GP2|Q96IP3|Q9UK25|Q9Y668|Q9Y669	Missense_Mutation	SNP	ENST00000222270.7	37	CCDS46055.1	1231	0.5636446886446886	402	0.8170731707317073	164	0.4530386740331492	298	0.5209790209790209	367	0.4841688654353562	G	0.154	-1.088329	0.01873	0.800362	0.475568	ENSG00000105663	ENST00000222270;ENST00000420124	D;D	0.82711	-1.64;-1.64	5.24	1.66	0.24008	.	0.496643	0.17023	N	0.190057	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	9	0.09338	T	0.73	.	3.7383	0.08520	0.0871:0.3105:0.4424:0.16	rs231591;rs661098;rs58885664;rs231591	2364	Q9UMN6	MLL4_HUMAN	G	2364	ENSP00000222270:D2364G;ENSP00000398837:D2364G	ENSP00000222270:D2364G	D	+	2	0	AD000671.1	40916545	0.826000	0.29277	0.293000	0.24932	0.148000	0.21650	0.097000	0.15168	0.219000	0.20840	-0.215000	0.12644	GAT	A|0.441;G|0.559	0.559	strong		0.637	KMT2B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_014727	
TTBK2	146057	hgsc.bcm.edu	37	15	43170793	43170793	+	Missense_Mutation	SNP	A	A	G	rs6493068	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:43170793A>G	ENST00000267890.6	-	2	131	c.23T>C	c.(22-24)cTg>cCg	p.L8P	TTBK2_ENST00000567485.1_5'UTR|TTBK2_ENST00000567840.1_Missense_Mutation_p.L8P|TTBK2_ENST00000567274.1_Missense_Mutation_p.L8P	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	135	0	0		WXS	Illumina HiSeq	Phase_I	126	48	0.380952	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	
PCDHB13	56123	hgsc.bcm.edu	37	5	140595802	140595802	+	Missense_Mutation	SNP	T	T	C	rs17844618	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	60	0	0		WXS	Illumina HiSeq	Phase_I	53	23	0.433962	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	
DIP2C	22982	hgsc.bcm.edu	37	10	459940	459940	+	Silent	SNP	G	G	A	rs4881274	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:459940G>A	ENST00000280886.6	-	8	1057	c.970C>T	c.(970-972)Ctg>Ttg	p.L324L	DIP2C_ENST00000381496.3_Silent_p.L217L	NM_014974.2	NP_055789.1	Q9Y2E4	DIP2C_HUMAN	DIP2 disco-interacting protein 2 homolog C (Drosophila)	324						nucleus (GO:0005634)	catalytic activity (GO:0003824)			breast(8)|endometrium(6)|kidney(10)|large_intestine(13)|lung(26)|ovary(3)|prostate(6)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(4)	81		all_cancers(4;0.00336)|all_lung(4;0.00732)|Lung NSC(4;0.00785)|all_epithelial(10;0.0159)|Colorectal(49;0.235)	OV - Ovarian serous cystadenocarcinoma(33;0.136)	Epithelial(11;0.0123)|all cancers(11;0.0467)|Lung(33;0.0864)|OV - Ovarian serous cystadenocarcinoma(14;0.106)		CACCTCTGCAGTGCGGCCTCC	0.667													G|||	3139	0.626797	0.5772	0.6268	5008	,	,		15834	0.6915		0.5417	False		,,,				2504	0.7147				p.L324L		Atlas-SNP	.											.	DIP2C	195	.	0			c.C970T						PASS	.	G		2460,1946	622.4+/-393.9	691,1078,434	59.0	59.0	59.0		970	1.7	0.1	10	dbSNP_111	59	4653,3947	604.0+/-394.7	1260,2133,907	no	coding-synonymous	DIP2C	NM_014974.2		1951,3211,1341	AA,AG,GG		45.8953,44.167,45.3099		324/1557	459940	7113,5893	2203	4300	6503	SO:0001819	synonymous_variant	22982	exon8			TCTGCAGTGCGGC	BC035216	CCDS7054.1	10p15.3	2006-01-13	2006-01-13	2006-01-13	ENSG00000151240	ENSG00000151240			29150	protein-coding gene	gene with protein product		611380	"""KIAA0934"""	KIAA0934			Standard	NM_014974		Approved		uc001ifp.3	Q9Y2E4	OTTHUMG00000017532	ENST00000280886.6:c.970C>T	10.37:g.459940G>A		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	67	37	0.552239	NM_014974	B4DPI5|Q5SS78	Silent	SNP	ENST00000280886.6	37	CCDS7054.1																																																																																			G|0.440;A|0.560	0.560	strong		0.667	DIP2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046389.1	NM_014974	
BTG1	694	hgsc.bcm.edu	37	12	92538171	92538171	+	Nonsense_Mutation	SNP	G	G	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:92538171G>C	ENST00000256015.3	-	2	562	c.201C>G	c.(199-201)taC>taG	p.Y67*	C12orf79_ENST00000546975.1_5'Flank|RP11-796E2.4_ENST00000501008.2_RNA|C12orf79_ENST00000551563.2_5'Flank|C12orf79_ENST00000551843.1_5'Flank|C12orf79_ENST00000549802.1_5'Flank|RP11-796E2.4_ENST00000499685.2_RNA	NM_001731.2	NP_001722.1	P62324	BTG1_HUMAN	B-cell translocation gene 1, anti-proliferative	67					cell migration (GO:0016477)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of fibroblast apoptotic process (GO:2000271)|positive regulation of myoblast differentiation (GO:0045663)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|kinase binding (GO:0019900)|transcription cofactor activity (GO:0003712)	p.Y67Y(1)		haematopoietic_and_lymphoid_tissue(12)|kidney(1)|large_intestine(1)|lung(2)	16		Acute lymphoblastic leukemia(6;3.02e-13)|all_hematologic(6;4.32e-09)				GAATACAACGGTAACCCGATC	0.458			T	MYC	BCLL						OREG0022024	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.Y67X		Atlas-SNP	.		Dom	yes		12	12q22	694	"""B-cell translocation gene 1, anti-proliferative"""		L	BTG1,NS,lymphoid_neoplasm,0,1	BTG1	30	1	1	Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(1)	c.C201G						PASS	.						131.0	131.0	131.0					12																	92538171		2203	4300	6503	SO:0001587	stop_gained	694	exon2			ACAACGGTAACCC		CCDS9043.1	12q21.33	2012-10-02			ENSG00000133639	ENSG00000133639			1130	protein-coding gene	gene with protein product		109580				15033446	Standard	NM_001731		Approved		uc001tby.3	P62324	OTTHUMG00000170092	ENST00000256015.3:c.201C>G	12.37:g.92538171G>C	ENSP00000256015:p.Tyr67*	Somatic	125	0	0	1291	WXS	Illumina HiSeq	Phase_I	109	20	0.183486	NM_001731	P31607	Nonsense_Mutation	SNP	ENST00000256015.3	37	CCDS9043.1	.	.	.	.	.	.	.	.	.	.	G	37	6.239268	0.97403	.	.	ENSG00000133639	ENST00000256015	.	.	.	5.81	5.81	0.92471	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-9.0719	13.2979	0.60307	0.072:0.0:0.928:0.0	.	.	.	.	X	67	.	ENSP00000256015:Y67X	Y	-	3	2	BTG1	91062302	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.401000	0.66326	2.738000	0.93877	0.655000	0.94253	TAC	.	.	none		0.458	BTG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407227.1		
MTDH	92140	hgsc.bcm.edu	37	8	98703317	98703317	+	Missense_Mutation	SNP	A	A	G	rs17854374	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:98703317A>G	ENST00000336273.3	+	6	1277	c.949A>G	c.(949-951)Act>Gct	p.T317A	MTDH_ENST00000519934.1_Missense_Mutation_p.T294A	NM_178812.3	NP_848927.2	Q86UE4	LYRIC_HUMAN	metadherin	317			T -> A (in dbSNP:rs17854374). {ECO:0000269|PubMed:15489334}.		lipopolysaccharide-mediated signaling pathway (GO:0031663)|negative regulation of apoptotic process (GO:0043066)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of angiogenesis (GO:0045766)|positive regulation of autophagy (GO:0010508)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein kinase B signaling (GO:0051897)|tight junction assembly (GO:0070830)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intercellular canaliculus (GO:0046581)|nuclear body (GO:0016604)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|tight junction (GO:0005923)	double-stranded RNA binding (GO:0003725)|NF-kappaB binding (GO:0051059)|poly(A) RNA binding (GO:0044822)|RNA polymerase II transcription factor binding (GO:0001085)|transcription coactivator activity (GO:0003713)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(6)|large_intestine(5)|liver(1)|lung(8)|ovary(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	32	Breast(36;2.56e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.178)			AAAGAGGAAAACTGAGCCATC	0.473													A|||	127	0.0253594	0.0008	0.0303	5008	,	,		14891	0.0		0.0616	False		,,,				2504	0.044				p.T317A		Atlas-SNP	.											.	MTDH	54	.	0			c.A949G						PASS	.	A	ALA/THR	62,4344	59.3+/-96.0	0,62,2141	117.0	122.0	120.0		949	0.9	0.7	8	dbSNP_123	120	529,8071	149.1+/-204.2	14,501,3785	yes	missense	MTDH	NM_178812.3	58	14,563,5926	GG,GA,AA		6.1512,1.4072,4.5441	possibly-damaging	317/583	98703317	591,12415	2203	4300	6503	SO:0001583	missense	92140	exon6			AGGAAAACTGAGC	AF411226	CCDS6274.1	8q22.1	2014-07-14			ENSG00000147649	ENSG00000147649			29608	protein-coding gene	gene with protein product	"""astrocyte elevated gene 1"""	610323				15093543	Standard	NM_178812		Approved	LYRIC, 3D3, AEG-1	uc003yhz.3	Q86UE4	OTTHUMG00000164692	ENST00000336273.3:c.949A>G	8.37:g.98703317A>G	ENSP00000338235:p.Thr317Ala	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	58	45	0.775862	NM_178812	Q05DH2|Q52QU9|Q6PK07|Q8TCX3	Missense_Mutation	SNP	ENST00000336273.3	37	CCDS6274.1	59	0.027014652014652016	0	0.0	14	0.03867403314917127	0	0.0	45	0.059366754617414245	A	11.53	1.666828	0.29604	0.014072	0.061512	ENSG00000147649	ENST00000336273;ENST00000519934	T;T	0.42900	0.96;0.97	5.91	0.932	0.19466	.	0.979332	0.08421	N	0.948300	T	0.02767	0.0083	N	0.14661	0.345	0.23113	N	0.998277	B	0.02656	0.0	B	0.04013	0.001	T	0.13629	-1.0502	10	0.30854	T	0.27	0.0907	8.5825	0.33637	0.7157:0.0:0.2843:0.0	rs17854374	317	Q86UE4	LYRIC_HUMAN	A	317;294	ENSP00000338235:T317A;ENSP00000428168:T294A	ENSP00000338235:T317A	T	+	1	0	MTDH	98772493	0.116000	0.22171	0.731000	0.30826	0.978000	0.69477	0.084000	0.14891	-0.054000	0.13266	-0.263000	0.10527	ACT	A|0.958;G|0.042	0.042	strong		0.473	MTDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379772.2		
TG	7038	hgsc.bcm.edu	37	8	134144113	134144113	+	Silent	SNP	C	C	T	rs2294024	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:134144113C>T	ENST00000220616.4	+	46	7960	c.7920C>T	c.(7918-7920)taC>taT	p.Y2640Y	TG_ENST00000542445.1_Silent_p.Y1010Y|TG_ENST00000519543.1_Silent_p.Y773Y|TG_ENST00000377869.1_Silent_p.Y2583Y	NM_003235.4	NP_003226.4	P01266	THYG_HUMAN	thyroglobulin	2640					hormone biosynthetic process (GO:0042446)|iodide transport (GO:0015705)|regulation of myelination (GO:0031641)|signal transduction (GO:0007165)|thyroid gland development (GO:0030878)|thyroid hormone generation (GO:0006590)	extracellular region (GO:0005576)|extracellular space (GO:0005615)		p.Y2640Y(1)		NS(1)|breast(11)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(34)|liver(2)|lung(59)|ovary(9)|pancreas(2)|prostate(6)|skin(7)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(8)	168	Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)	Myeloproliferative disorder(644;0.00878)|Acute lymphoblastic leukemia(644;0.0559)|Breast(495;0.0735)	BRCA - Breast invasive adenocarcinoma(115;0.000701)	KIRC - Kidney renal clear cell carcinoma(542;0.0546)		ACCCAGCCTACGAGGGGCAGT	0.498													C|||	2030	0.405351	0.5885	0.4928	5008	,	,		17458	0.1657		0.4841	False		,,,				2504	0.2618				p.Y2640Y		Atlas-SNP	.											TG,NS,carcinoma,0,1	TG	416	1	1	Substitution - coding silent(1)	stomach(1)	c.C7920T						PASS	.	C		2536,1870	631.6+/-395.7	737,1062,404	94.0	94.0	94.0		7920	0.1	0.0	8	dbSNP_100	94	4238,4362	571.7+/-389.6	1070,2098,1132	no	coding-synonymous	TG	NM_003235.4		1807,3160,1536	TT,TC,CC		49.2791,42.4421,47.9163		2640/2769	134144113	6774,6232	2203	4300	6503	SO:0001819	synonymous_variant	7038	exon46			AGCCTACGAGGGG	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.7920C>T	8.37:g.134144113C>T		Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	129	38	0.294574	NM_003235	O15274|O43899|Q15593|Q15948|Q9NYR1|Q9NYR2|Q9UMZ0|Q9UNY3	Silent	SNP	ENST00000220616.4	37	CCDS34944.1	926	0.423992673992674	276	0.5609756097560976	191	0.5276243093922652	97	0.16958041958041958	362	0.47757255936675463	C	6.383	0.438787	0.12104	0.575579	0.492791	ENSG00000042832	ENST00000519178	.	.	.	5.32	0.0514	0.14297	.	.	.	.	.	.	.	.	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	4.8924	0.13733	0.0:0.4075:0.1533:0.4392	rs2294024;rs2294024	.	.	.	X	1096	.	.	R	+	1	2	TG	134213295	0.002000	0.14202	0.013000	0.15412	0.986000	0.74619	-0.075000	0.11431	0.254000	0.21573	0.491000	0.48974	CGA	C|0.522;T|0.478	0.478	strong		0.498	TG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379606.1	NM_003235	
ZNF529	57711	hgsc.bcm.edu	37	19	37038092	37038092	+	Silent	SNP	T	T	C	rs2278168	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:37038092T>C	ENST00000591340.1	-	5	1526	c.1368A>G	c.(1366-1368)ggA>ggG	p.G456G	ZNF529_ENST00000334116.7_Silent_p.G351G	NM_020951.4	NP_066002.3	Q6P280	ZN529_HUMAN	zinc finger protein 529	456					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)	1	Esophageal squamous(110;0.198)					TAAAGAACTTTCCACACTCCT	0.368													T|||	1127	0.22504	0.2791	0.1916	5008	,	,		21349	0.1756		0.2425	False		,,,				2504	0.2086				p.G456G		Atlas-SNP	.											.	ZNF529	82	.	0			c.A1368G						PASS	.	T	,,	1090,3220		133,824,1198	83.0	89.0	87.0		1368,1314,1368	-4.7	0.6	19	dbSNP_100	87	1854,6712		206,1442,2635	no	coding-synonymous,coding-synonymous,coding-synonymous	ZNF529	NM_001145649.1,NM_001145650.1,NM_020951.4	,,	339,2266,3833	CC,CT,TT		21.6437,25.29,22.8642	,,	456/564,438/546,456/564	37038092	2944,9932	2155	4283	6438	SO:0001819	synonymous_variant	57711	exon6			GAACTTTCCACAC	AK025110	CCDS54256.1	19q13.13	2014-08-22			ENSG00000186020	ENSG00000186020		"""Zinc fingers, C2H2-type"", ""-"""	29328	protein-coding gene	gene with protein product						10997877	Standard	NM_020951		Approved	KIAA1615	uc002oeh.4	Q6P280	OTTHUMG00000180714	ENST00000591340.1:c.1368A>G	19.37:g.37038092T>C		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	73	41	0.561644	NM_001145649	K7EKE1|Q9H731|Q9HCF7	Silent	SNP	ENST00000591340.1	37	CCDS54256.1																																																																																			T|0.774;C|0.226	0.226	strong		0.368	ZNF529-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452730.1	NM_020951	
GOLGB1	2804	hgsc.bcm.edu	37	3	121413637	121413637	+	Silent	SNP	G	G	A	rs34833153	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:121413637G>A	ENST00000340645.5	-	13	5843	c.5718C>T	c.(5716-5718)tcC>tcT	p.S1906S	GOLGB1_ENST00000393667.3_Silent_p.S1911S	NM_001256487.1|NM_001256488.1|NM_004487.4	NP_001243416.1|NP_001243417.1|NP_004478.3	Q14789	GOGB1_HUMAN	golgin B1	1906					Golgi organization (GO:0007030)	cis-Golgi network (GO:0005801)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(2)|cervix(2)|endometrium(12)|kidney(3)|large_intestine(26)|liver(2)|lung(36)|ovary(7)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(13)	119				GBM - Glioblastoma multiforme(114;0.0989)		TGGTAACTCTGGAGAGTTCTT	0.373													G|||	199	0.0397364	0.0045	0.0576	5008	,	,		21040	0.001		0.0845	False		,,,				2504	0.0685				p.S1911S		Atlas-SNP	.											.	GOLGB1	319	.	0			c.C5733T						PASS	.	G		73,4333	65.3+/-102.7	2,69,2132	184.0	191.0	188.0		5718	1.8	1.0	3	dbSNP_126	188	664,7936	167.7+/-219.4	16,632,3652	no	coding-synonymous	GOLGB1	NM_004487.3		18,701,5784	AA,AG,GG		7.7209,1.6568,5.6666		1906/3260	121413637	737,12269	2203	4300	6503	SO:0001819	synonymous_variant	2804	exon13			AACTCTGGAGAGT	X75304	CCDS3004.1, CCDS58847.1, CCDS74989.1	3q13	2010-02-12	2010-02-12	2007-07-27	ENSG00000173230	ENSG00000173230			4429	protein-coding gene	gene with protein product	"""macrogolgin"", ""golgi integral membrane protein 1"""	602500	"""golgi autoantigen, golgin subfamily b, macrogolgin (with transmembrane signal), 1"", ""golgin B1, golgi integral membrane protein"""			7691276, 15004235	Standard	NM_001256486		Approved	GCP, GCP372, giantin, GOLIM1	uc010hrc.4	Q14789	OTTHUMG00000159411	ENST00000340645.5:c.5718C>T	3.37:g.121413637G>A		Somatic	272	1	0.00367647		WXS	Illumina HiSeq	Phase_I	238	126	0.529412	NM_001256486	B2ZZ91|D3DN92|E7EP74|Q14398	Silent	SNP	ENST00000340645.5	37	CCDS3004.1																																																																																			G|0.948;A|0.052	0.052	strong		0.373	GOLGB1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000355159.1	NM_004487	
MIA3	375056	hgsc.bcm.edu	37	1	222833538	222833538	+	Silent	SNP	C	C	G	rs2291835	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:222833538C>G	ENST00000344922.5	+	24	5020	c.4995C>G	c.(4993-4995)ggC>ggG	p.G1665G	MIA3_ENST00000344507.1_Intron|RP11-378J18.8_ENST00000608771.1_RNA|MIA3_ENST00000340535.7_Silent_p.G543G|MIA3_ENST00000344441.6_Silent_p.G1665G	NM_198551.2	NP_940953.2	Q5JRA6	MIA3_HUMAN	melanoma inhibitory activity family, member 3	1665	Pro-rich.				chondrocyte development (GO:0002063)|collagen fibril organization (GO:0030199)|exocytosis (GO:0006887)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell migration (GO:0030336)|positive regulation of bone mineralization (GO:0030501)|positive regulation of leukocyte migration (GO:0002687)|protein transport (GO:0015031)|wound healing (GO:0042060)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)		p.G1665G(1)		breast(5)|central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(15)|lung(37)|ovary(5)|pancreas(2)|prostate(2)|skin(2)|stomach(4)|urinary_tract(1)	80				GBM - Glioblastoma multiforme(131;0.0199)		GCCAGAATGGCTCTTTTGGCC	0.468													C|||	635	0.126797	0.087	0.1311	5008	,	,		17069	0.1607		0.1988	False		,,,				2504	0.0685				p.G1665G		Atlas-SNP	.											MIA3,NS,carcinoma,0,1	MIA3	167	1	1	Substitution - coding silent(1)	stomach(1)	c.C4995G						scavenged	.	C		330,3474		14,302,1586	92.0	95.0	94.0		4995	4.1	1.0	1	dbSNP_100	94	1579,6659		147,1285,2687	no	coding-synonymous	MIA3	NM_198551.2		161,1587,4273	GG,GC,CC		19.1673,8.6751,15.8528		1665/1908	222833538	1909,10133	1902	4119	6021	SO:0001819	synonymous_variant	375056	exon24			GAATGGCTCTTTT		CCDS41470.1, CCDS73035.1	1p36.33	2012-12-13		2006-07-25	ENSG00000154305	ENSG00000154305			24008	protein-coding gene	gene with protein product	"""C219 reactive peptide"", ""transport and golgi organization"""	613455				15183315	Standard	XM_005273121		Approved	UNQ6077, FLJ39207, KIAA0268, TANGO	uc001hnl.3	Q5JRA6	OTTHUMG00000037543	ENST00000344922.5:c.4995C>G	1.37:g.222833538C>G		Somatic	131	1	0.00763359		WXS	Illumina HiSeq	Phase_I	124	57	0.459677	NM_198551	A8K2S0|A8MT05|A8MT13|B7Z430|Q14083|Q3S4X3|Q5JRA5|Q5JRB0|Q5JRB1|Q5JRB2|Q6UVY8|Q86Y60|Q8N8M5|Q92580	Silent	SNP	ENST00000344922.5	37	CCDS41470.1																																																																																			C|0.832;G|0.168	0.168	strong		0.468	MIA3-001	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000091489.4	NM_198551	
EFCAB5	374786	hgsc.bcm.edu	37	17	28381141	28381141	+	Silent	SNP	C	C	G	rs4074170	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:28381141C>G	ENST00000394835.3	+	10	2361	c.2169C>G	c.(2167-2169)acC>acG	p.T723T	EFCAB5_ENST00000541045.1_Silent_p.T380T|EFCAB5_ENST00000378738.3_Silent_p.T723T|EFCAB5_ENST00000394832.2_Silent_p.T723T|EFCAB5_ENST00000536908.2_Silent_p.T667T|EFCAB5_ENST00000320856.5_Silent_p.T723T	NM_198529.3	NP_940931	A4FU69	EFCB5_HUMAN	EF-hand calcium binding domain 5	723							calcium ion binding (GO:0005509)			breast(7)|endometrium(2)|kidney(4)|large_intestine(11)|lung(14)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	43						AAGTTCCAACCTTAAGCAGAA	0.388													G|||	2859	0.570887	0.9327	0.4669	5008	,	,		20652	0.2917		0.5656	False		,,,				2504	0.4489				p.T723T		Atlas-SNP	.											.	EFCAB5	122	.	0			c.C2169G						PASS	.	G	,	3203,509		1383,437,36	21.0	20.0	21.0		2001,2169	3.0	0.0	17	dbSNP_108	21	4436,3744		1218,2000,872	no	coding-synonymous,coding-synonymous	EFCAB5	NM_001145053.1,NM_198529.3	,	2601,2437,908	GG,GC,CC		45.7702,13.7123,35.7635	,	667/857,723/1504	28381141	7639,4253	1856	4090	5946	SO:0001819	synonymous_variant	374786	exon10			TCCAACCTTAAGC	AL833911	CCDS11254.2, CCDS54103.1	17q11.2	2013-01-10			ENSG00000176927	ENSG00000176927		"""EF-hand domain containing"""	24801	protein-coding gene	gene with protein product							Standard	NM_198529		Approved	FLJ46247	uc002het.3	A4FU69	OTTHUMG00000132753	ENST00000394835.3:c.2169C>G	17.37:g.28381141C>G		Somatic	280	1	0.00357143		WXS	Illumina HiSeq	Phase_I	245	120	0.489796	NM_198529	B2RPN0|B4DS75|B4DZR5|F5GYL2|Q0VD68|Q6ZRM6|Q8NDG9	Silent	SNP	ENST00000394835.3	37	CCDS11254.2																																																																																			C|0.514;G|0.486	0.486	strong		0.388	EFCAB5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256120.4	NM_198529	
ENPP7	339221	hgsc.bcm.edu	37	17	77705045	77705045	+	Silent	SNP	T	T	C	rs8074728	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:77705045T>C	ENST00000328313.5	+	1	365	c.144T>C	c.(142-144)gaT>gaC	p.D48D		NM_178543.3	NP_848638.3			ectonucleotide pyrophosphatase/phosphodiesterase 7											breast(1)|central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(3)|lung(12)|ovary(2)|prostate(6)|skin(3)	34			OV - Ovarian serous cystadenocarcinoma(97;0.016)|BRCA - Breast invasive adenocarcinoma(99;0.0224)			ACGACCAGGATGTGGACACCC	0.647													C|||	2579	0.514976	0.7005	0.3372	5008	,	,		17202	0.5129		0.3777	False		,,,				2504	0.5337				p.D48D		Atlas-SNP	.											.	ENPP7	63	.	0			c.T144C						PASS	.	C		2836,1570	481.5+/-359.1	922,992,289	52.0	46.0	48.0		144	-2.5	1.0	17	dbSNP_116	48	3292,5308	633.2+/-398.7	623,2046,1631	no	coding-synonymous	ENPP7	NM_178543.3		1545,3038,1920	CC,CT,TT		38.2791,35.6332,47.1167		48/459	77705045	6128,6878	2203	4300	6503	SO:0001819	synonymous_variant	339221	exon1			CCAGGATGTGGAC	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.144T>C	17.37:g.77705045T>C		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	47	20	0.425532	NM_178543		Silent	SNP	ENST00000328313.5	37	CCDS11763.1																																																																																			T|0.527;C|0.473	0.473	strong		0.647	ENPP7-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437038.1	NM_178543	
LRRK2	120892	hgsc.bcm.edu	37	12	40671989	40671989	+	Missense_Mutation	SNP	A	A	G	rs10878307	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:40671989A>G	ENST00000298910.7	+	18	2225	c.2167A>G	c.(2167-2169)Atc>Gtc	p.I723V	LRRK2_ENST00000343742.2_Missense_Mutation_p.I723V	NM_198578.3	NP_940980	Q5S007	LRRK2_HUMAN	leucine-rich repeat kinase 2	723			I -> V (in dbSNP:rs10878307). {ECO:0000269|PubMed:16172858, ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:22415848}.		activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|autophagy (GO:0006914)|cellular protein localization (GO:0034613)|cellular response to dopamine (GO:1903351)|cellular response to manganese ion (GO:0071287)|cellular response to oxidative stress (GO:0034599)|determination of adult lifespan (GO:0008340)|endocytosis (GO:0006897)|exploration behavior (GO:0035640)|GTP catabolic process (GO:0006184)|intracellular distribution of mitochondria (GO:0048312)|intracellular signal transduction (GO:0035556)|locomotory exploration behavior (GO:0035641)|MAPK cascade (GO:0000165)|negative regulation of GTPase activity (GO:0034260)|negative regulation of hydrogen peroxide-induced cell death (GO:1903206)|negative regulation of late endosome to lysosome transport (GO:1902823)|negative regulation of peroxidase activity (GO:2000469)|negative regulation of protein binding (GO:0032091)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein processing (GO:0010955)|negative regulation of protein processing involved in protein targeting to mitochondrion (GO:1903217)|negative regulation of protein targeting to mitochondrion (GO:1903215)|negative regulation of thioredoxin peroxidase activity by peptidyl-threonine phosphorylation (GO:1903125)|neuromuscular junction development (GO:0007528)|neuron death (GO:0070997)|neuron projection morphogenesis (GO:0048812)|olfactory bulb development (GO:0021772)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of autophagy (GO:0010508)|positive regulation of dopamine receptor signaling pathway (GO:0060161)|positive regulation of GTPase activity (GO:0043547)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of programmed cell death (GO:0043068)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein autoubiquitination (GO:1902499)|positive regulation of protein binding (GO:0032092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reactive oxygen species metabolic process (GO:0072593)|regulation of branching morphogenesis of a nerve (GO:2000172)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of dopamine receptor signaling pathway (GO:0060159)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of kidney size (GO:0035564)|regulation of locomotion (GO:0040012)|regulation of membrane potential (GO:0042391)|regulation of mitochondrial depolarization (GO:0051900)|regulation of neuroblast proliferation (GO:1902692)|regulation of neuron death (GO:1901214)|regulation of neuron maturation (GO:0014041)|regulation of protein kinase A signaling (GO:0010738)|regulation of synaptic transmission, glutamatergic (GO:0051966)|regulation of synaptic vesicle exocytosis (GO:2000300)|regulation of synaptic vesicle transport (GO:1902803)|response to oxidative stress (GO:0006979)|small GTPase mediated signal transduction (GO:0007264)|tangential migration from the subventricular zone to the olfactory bulb (GO:0022028)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytoplasmic side of mitochondrial outer membrane (GO:0032473)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendrite (GO:0030425)|dendrite cytoplasm (GO:0032839)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|inclusion body (GO:0016234)|lysosome (GO:0005764)|membrane raft (GO:0045121)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial membrane (GO:0031966)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)|terminal bouton (GO:0043195)|trans-Golgi network (GO:0005802)	actin binding (GO:0003779)|ATP binding (GO:0005524)|clathrin binding (GO:0030276)|glycoprotein binding (GO:0001948)|GTP binding (GO:0005525)|GTP-dependent protein kinase activity (GO:0034211)|GTPase activator activity (GO:0005096)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|kinase activity (GO:0016301)|MAP kinase kinase activity (GO:0004708)|peroxidase inhibitor activity (GO:0036479)|protein homodimerization activity (GO:0042803)|protein kinase A binding (GO:0051018)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|Rho GTPase binding (GO:0017048)|SNARE binding (GO:0000149)|syntaxin-1 binding (GO:0017075)|tubulin binding (GO:0015631)			NS(3)|biliary_tract(1)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(23)|large_intestine(31)|lung(55)|ovary(15)|pancreas(2)|prostate(4)|skin(4)|stomach(9)|upper_aerodigestive_tract(7)|urinary_tract(2)	181	all_cancers(12;0.00108)|Breast(8;0.218)	Lung NSC(34;0.0942)|all_lung(34;0.11)				GAATAACAGCATCATGGTTGA	0.378													A|||	202	0.0403355	0.0015	0.036	5008	,	,		19174	0.0069		0.0825	False		,,,				2504	0.0869				p.I723V		Atlas-SNP	.											LRRK2_ENST00000298910,NS,NS,-2,2	LRRK2	763	2	0			c.A2167G						PASS	.	A	VAL/ILE	60,4346	56.2+/-92.4	2,56,2145	156.0	153.0	154.0		2167	-0.9	0.8	12	dbSNP_120	154	614,7986	161.0+/-214.0	20,574,3706	yes	missense	LRRK2	NM_198578.3	29	22,630,5851	GG,GA,AA		7.1395,1.3618,5.1822	benign	723/2528	40671989	674,12332	2203	4300	6503	SO:0001583	missense	120892	exon18			AACAGCATCATGG	AK026776	CCDS31774.1	12q12	2011-07-21			ENSG00000188906	ENSG00000188906		"""Parkinson disease"""	18618	protein-coding gene	gene with protein product		609007	"""Parkinson disease (autosomal dominant) 8"""	PARK8		15541308	Standard	NM_198578		Approved	ROCO2, DKFZp434H2111, FLJ45829, RIPK7	uc001rmg.4	Q5S007	OTTHUMG00000059742	ENST00000298910.7:c.2167A>G	12.37:g.40671989A>G	ENSP00000298910:p.Ile723Val	Somatic	201	0	0		WXS	Illumina HiSeq	Phase_I	168	168	1	NM_198578	A6NJU2|Q6ZS50|Q8NCX9	Missense_Mutation	SNP	ENST00000298910.7	37	CCDS31774.1	89	0.04075091575091575	3	0.006097560975609756	16	0.04419889502762431	7	0.012237762237762238	63	0.08311345646437995	A	5.736	0.320222	0.10845	0.013618	0.071395	ENSG00000188906	ENST00000416796;ENST00000343742;ENST00000298910	T;T;T	0.53857	0.6;0.6;0.6	5.94	-0.905	0.10527	Ankyrin repeat-containing domain (1);	0.590841	0.18874	N	0.128751	T	0.01092	0.0036	N	0.11560	0.145	0.46499	P	9.299999999999864E-4	B;B	0.06786	0.001;0.0	B;B	0.04013	0.001;0.001	T	0.21314	-1.0249	9	0.02654	T	1	.	5.7556	0.18170	0.5627:0.0:0.3218:0.1155	rs10878307;rs17443691;rs17510615;rs36223901;rs52827030;rs59445435;rs10878307	723;723	E9PC85;Q5S007	.;LRRK2_HUMAN	V	471;723;723	ENSP00000398726:I471V;ENSP00000341930:I723V;ENSP00000298910:I723V	ENSP00000298910:I723V	I	+	1	0	LRRK2	38958256	0.757000	0.28394	0.829000	0.32907	0.988000	0.76386	0.614000	0.24314	-0.073000	0.12842	0.482000	0.46254	ATC	A|0.947;G|0.053	0.053	strong		0.378	LRRK2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277179.1	XM_058513	
IL5RA	3568	hgsc.bcm.edu	37	3	3146610	3146610	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:3146610G>A	ENST00000446632.2	-	3	633	c.59C>T	c.(58-60)gCt>gTt	p.A20V	IL5RA_ENST00000383846.1_Missense_Mutation_p.A20V|IL5RA_ENST00000418488.2_Missense_Mutation_p.A20V|IL5RA_ENST00000438560.1_Missense_Mutation_p.A20V|IL5RA_ENST00000445864.2_Missense_Mutation_p.A20V|IL5RA_ENST00000311981.8_Missense_Mutation_p.A20V|IL5RA_ENST00000256452.3_Missense_Mutation_p.A20V|IL5RA_ENST00000430514.2_Missense_Mutation_p.A20V|SNORA43_ENST00000517240.1_RNA|IL5RA_ENST00000456302.1_Missense_Mutation_p.A20V	NM_175726.3	NP_783853.1	Q01344	IL5RA_HUMAN	interleukin 5 receptor, alpha	20					cell proliferation (GO:0008283)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-5-mediated signaling pathway (GO:0038043)|regulation of interleukin-5 production (GO:0032674)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	interleukin-5 receptor activity (GO:0004914)			cervix(1)|endometrium(2)|large_intestine(7)|lung(9)|ovary(1)|prostate(2)|skin(2)	24				Epithelial(13;0.00278)|all cancers(10;0.00809)|OV - Ovarian serous cystadenocarcinoma(96;0.00944)		AAGTAAGTCAGCTTGCAGTAT	0.348																																					p.A20V	GBM(169;430 2801 24955 28528)	Atlas-SNP	.											IL5RA,caecum,carcinoma,0,1	IL5RA	55	1	0			c.C59T						PASS	.						102.0	100.0	101.0					3																	3146610		2203	4300	6503	SO:0001583	missense	3568	exon3			AAGTCAGCTTGCA	M96652	CCDS2559.1, CCDS2560.1, CCDS46739.1, CCDS58813.1	3p26-p24	2008-01-11			ENSG00000091181	ENSG00000091181		"""Interleukins and interleukin receptors"", ""CD molecules"""	6017	protein-coding gene	gene with protein product		147851		IL5R		1732409	Standard	NM_175727		Approved	CDw125, CD125	uc010hbs.3	Q01344	OTTHUMG00000090245	ENST00000446632.2:c.59C>T	3.37:g.3146610G>A	ENSP00000412209:p.Ala20Val	Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	178	44	0.247191	NM_001243099	B3IU77|B4E2G0|Q14633|Q15469|Q6ISX9	Missense_Mutation	SNP	ENST00000446632.2	37	CCDS2559.1	.	.	.	.	.	.	.	.	.	.	G	12.16	1.853768	0.32791	.	.	ENSG00000091181	ENST00000446632;ENST00000438560;ENST00000256452;ENST00000418488;ENST00000445864;ENST00000383846;ENST00000311981;ENST00000430514;ENST00000456302;ENST00000445701;ENST00000427088	D;D;D;T;T;T;T;T;T;T	0.88664	-2.41;-2.31;-2.41;1.08;1.37;1.14;1.14;1.15;1.15;1.41	5.6	0.812	0.18744	.	0.640598	0.15081	N	0.281648	T	0.79695	0.4490	L	0.31926	0.97	0.09310	N	1	B;B;B;B;B;B	0.33637	0.028;0.047;0.047;0.028;0.42;0.084	B;B;B;B;B;B	0.28465	0.024;0.022;0.032;0.01;0.09;0.028	T	0.66594	-0.5884	10	0.44086	T	0.13	-6.1116	8.1152	0.30940	0.4066:0.0:0.5934:0.0	.	20;20;20;20;20;20	B4E2G0;Q01344-3;Q01344-2;Q01344;B3IU77;E7ERY4	.;.;.;IL5RA_HUMAN;.;.	V	20	ENSP00000412209:A20V;ENSP00000390753:A20V;ENSP00000256452:A20V;ENSP00000388858:A20V;ENSP00000402598:A20V;ENSP00000373358:A20V;ENSP00000309196:A20V;ENSP00000400400:A20V;ENSP00000392059:A20V;ENSP00000398117:A20V	ENSP00000256452:A20V	A	-	2	0	IL5RA	3121610	0.016000	0.18221	0.000000	0.03702	0.030000	0.12068	0.998000	0.29744	-0.062000	0.13088	0.650000	0.86243	GCT	.	.	none		0.348	IL5RA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337537.2		
TYROBP	7305	hgsc.bcm.edu	37	19	36398454	36398454	+	Silent	SNP	G	G	C	rs111477177	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:36398454G>C	ENST00000262629.4	-	3	189	c.123C>G	c.(121-123)ggC>ggG	p.G41G	TYROBP_ENST00000589517.1_Silent_p.G41G|TYROBP_ENST00000585901.2_Silent_p.G41G|TYROBP_ENST00000544690.2_Silent_p.G30G|TYROBP_ENST00000424586.3_Silent_p.G30G	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						PASS	.	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	76	0	0		WXS	Illumina HiSeq	Phase_I	68	39	0.573529	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		
ZNF585B	92285	hgsc.bcm.edu	37	19	37676528	37676528	+	Silent	SNP	G	G	A	rs75662394	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:37676528G>A	ENST00000532828.2	-	5	2162	c.1911C>T	c.(1909-1911)gcC>gcT	p.A637A	CTC-454I21.3_ENST00000585860.2_Intron|ZNF585B_ENST00000527838.1_3'UTR|ZNF585B_ENST00000531805.1_Silent_p.A582A|ZNF585B_ENST00000312908.5_Silent_p.A225A	NM_152279.3	NP_689492.3	Q52M93	Z585B_HUMAN	zinc finger protein 585B	637					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)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(3)|endometrium(1)|large_intestine(9)|lung(13)|ovary(1)|prostate(1)	29			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			TCCCACACTCGGCACACACAT	0.488													G|||	1390	0.277556	0.329	0.3862	5008	,	,		19333	0.0883		0.3579	False		,,,				2504	0.2434				p.A637A	Melanoma(93;882 1454 18863 28917 48427)	Atlas-SNP	.											.	ZNF585B	91	.	0			c.C1911T						PASS	.	G		1584,2822	491.7+/-362.2	283,1018,902	62.0	58.0	60.0		1911	-2.6	0.0	19	dbSNP_131	60	3083,5517	472.7+/-368.4	550,1983,1767	no	coding-synonymous	ZNF585B	NM_152279.3		833,3001,2669	AA,AG,GG		35.8488,35.951,35.8834		637/770	37676528	4667,8339	2203	4300	6503	SO:0001819	synonymous_variant	92285	exon5			ACACTCGGCACAC	AK027834	CCDS12500.1	19q13.13	2013-01-08				ENSG00000245680		"""Zinc fingers, C2H2-type"", ""-"""	30948	protein-coding gene	gene with protein product						12477932	Standard	NM_152279		Approved	FLJ14928, SZFP41	uc002ofq.3	Q52M93		ENST00000532828.2:c.1911C>T	19.37:g.37676528G>A		Somatic	250	1	0.004		WXS	Illumina HiSeq	Phase_I	191	109	0.570681	NM_152279	Q8IZD3|Q96JW6	Silent	SNP	ENST00000532828.2	37	CCDS12500.1																																																																																			G|0.500;A|0.500	0.500	weak		0.488	ZNF585B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388272.2	NM_152279	
MUC4	4585	hgsc.bcm.edu	37	3	195509078	195509078	+	Missense_Mutation	SNP	C	C	T	rs371017154|rs35479616		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195509078C>T	ENST00000463781.3	-	2	9832	c.9373G>A	c.(9373-9375)Gac>Aac	p.D3125N	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.D3125N	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)		GAGGAAGTGTCGGTGACAGGA	0.587																																					p.D3125N		Atlas-SNP	.											.	MUC4	1505	.	0			c.G9373A						PASS	.						12.0	7.0	9.0					3																	195509078		654	1507	2161	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.9373G>A	3.37:g.195509078C>T	ENSP00000417498:p.Asp3125Asn	Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	34	5	0.147059	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	N	9.849	1.193221	0.22037	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.30714	1.53;1.52	.	.	.	.	.	.	.	.	T	0.14700	0.0355	N	0.19112	0.55	0.20403	N	0.9999	B	0.12013	0.005	B	0.01281	0.0	T	0.27938	-1.0059	7	.	.	.	.	2.6652	0.05046	0.0:0.5:0.0:0.5	.	2997	E7ESK3	.	N	3125	ENSP00000417498:D3125N;ENSP00000420243:D3125N	.	D	-	1	0	MUC4	196993857	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.521000	0.06245	-0.000000	0.14550	0.000000	0.15137	GAC	.	.	weak		0.587	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
CNTN2	6900	hgsc.bcm.edu	37	1	205027737	205027737	+	Missense_Mutation	SNP	G	G	A	rs2275697	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:205027737G>A	ENST00000331830.4	+	5	717	c.433G>A	c.(433-435)Gct>Act	p.A145T		NM_005076.3	NP_005067.1	Q02246	CNTN2_HUMAN	contactin 2 (axonal)	145	Ig-like C2-type 2.		A -> T (in dbSNP:rs2275697).		adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|cell adhesion (GO:0007155)|cellular protein localization (GO:0034613)|central nervous system myelination (GO:0022010)|cerebral cortex GABAergic interneuron migration (GO:0021853)|clustering of voltage-gated potassium channels (GO:0045163)|establishment of protein localization to juxtaparanode region of axon (GO:0071206)|learning (GO:0007612)|microtubule cytoskeleton organization (GO:0000226)|negative regulation of neuron differentiation (GO:0045665)|positive regulation of adenosine receptor signaling pathway (GO:0060168)|positive regulation of protein processing (GO:0010954)|presynaptic membrane organization (GO:0097090)|receptor internalization (GO:0031623)|regulation of astrocyte differentiation (GO:0048710)|regulation of axon diameter (GO:0031133)|regulation of neuronal synaptic plasticity (GO:0048168)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|juxtaparanode region of axon (GO:0044224)|myelin sheath (GO:0043209)|neuronal cell body (GO:0043025)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|synapse (GO:0045202)|voltage-gated potassium channel complex (GO:0008076)	carbohydrate binding (GO:0030246)|identical protein binding (GO:0042802)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(11)|lung(23)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	54	all_cancers(21;0.144)|Breast(84;0.0437)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.158)			CCCAGTGAAAGCTCATGAAGG	0.632													A|||	1469	0.293331	0.1369	0.2781	5008	,	,		16061	0.4831		0.1511	False		,,,				2504	0.4663				p.A145T	Melanoma(183;2548 2817 37099 41192)	Atlas-SNP	.											.	CNTN2	116	.	0			c.G433A						PASS	.	A	THR/ALA	657,3749	764.0+/-413.3	52,553,1598	49.0	47.0	48.0		433	2.5	0.9	1	dbSNP_100	48	1349,7251	755.2+/-407.5	121,1107,3072	yes	missense	CNTN2	NM_005076.3	58	173,1660,4670	AA,AG,GG		15.686,14.9115,15.4237	benign	145/1041	205027737	2006,11000	2203	4300	6503	SO:0001583	missense	6900	exon5			GTGAAAGCTCATG	X67734	CCDS1449.1	1q32.1	2013-02-11			ENSG00000184144	ENSG00000184144		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	2172	protein-coding gene	gene with protein product		190197		TAX, AXT		8307567, 8586965	Standard	NM_005076		Approved	TAG-1, TAX1	uc001hbr.3	Q02246	OTTHUMG00000037105	ENST00000331830.4:c.433G>A	1.37:g.205027737G>A	ENSP00000330633:p.Ala145Thr	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	37	12	0.324324	NM_005076	P78432|Q5T054	Missense_Mutation	SNP	ENST00000331830.4	37	CCDS1449.1	505	0.23122710622710624	56	0.11382113821138211	78	0.2154696132596685	266	0.46503496503496505	105	0.13852242744063326	A	12.15	1.852187	0.32699	0.149115	0.15686	ENSG00000184144	ENST00000331830	T	0.78126	-1.15	4.8	2.46	0.29980	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.280267	0.26586	N	0.023559	T	0.00012	0.0000	M	0.62088	1.915	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.11329	0.002;0.002;0.006	T	0.29181	-1.0020	9	0.54805	T	0.06	.	8.8588	0.35245	0.5923:0.0:0.4077:0.0	rs2275697;rs58470387;rs2275697	145;145;36	A1L3A3;Q02246;Q68DA2	.;CNTN2_HUMAN;.	T	145	ENSP00000330633:A145T	ENSP00000330633:A145T	A	+	1	0	CNTN2	203294360	0.754000	0.28360	0.865000	0.33974	0.652000	0.38707	2.103000	0.41806	-0.047000	0.13423	-0.381000	0.06696	GCT	G|0.790;N|0.000	.	strong		0.632	CNTN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090080.3	NM_005076	
RAD21	5885	hgsc.bcm.edu	37	8	117864217	117864217	+	Silent	SNP	A	A	G	rs1050838	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:117864217A>G	ENST00000297338.2	-	11	1727	c.1440T>C	c.(1438-1440)gcT>gcC	p.A480A	RAD21_ENST00000523986.1_5'UTR|RAD21_ENST00000517749.1_5'Flank|RAD21_ENST00000518055.1_Silent_p.A25A	NM_006265.2	NP_006256.1	O60216	RAD21_HUMAN	RAD21 homolog (S. pombe)	480	Pro-rich.				apoptotic process (GO:0006915)|chromosome segregation (GO:0007059)|DNA recombination (GO:0006310)|double-strand break repair (GO:0006302)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|protein localization to chromatin (GO:0071168)|reciprocal meiotic recombination (GO:0007131)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cohesin complex (GO:0008278)|cytosol (GO:0005829)|membrane (GO:0016020)|nuclear meiotic cohesin complex (GO:0034991)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)		p.A480A(1)		endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(16)|ovary(1)|prostate(1)|skin(1)|stomach(1)	32	all_cancers(13;1.21e-21)|Lung NSC(37;0.000134)|Ovarian(258;0.0172)					CAATTTGTCCAGCTTTTCGCT	0.473													A|||	667	0.133187	0.0076	0.2536	5008	,	,		18166	0.1696		0.1501	False		,,,				2504	0.1626				p.A480A		Atlas-SNP	.											RAD21,NS,carcinoma,0,1	RAD21	95	1	1	Substitution - coding silent(1)	stomach(1)	c.T1440C						PASS	.	A		150,4256	104.7+/-143.2	3,144,2056	140.0	125.0	130.0		1440	-11.4	0.0	8	dbSNP_86	130	1464,7136	279.8+/-294.2	128,1208,2964	yes	coding-synonymous	RAD21	NM_006265.2		131,1352,5020	GG,GA,AA		17.0233,3.4044,12.4097		480/632	117864217	1614,11392	2203	4300	6503	SO:0001819	synonymous_variant	5885	exon11			TTGTCCAGCTTTT	BC050381	CCDS6321.1	8q24.11	2014-09-17	2001-11-28		ENSG00000164754	ENSG00000164754			9811	protein-coding gene	gene with protein product	"""sister chromatid cohesion 1"""	606462	"""RAD21 (S. pombe) homolog"""			8812457	Standard	NM_006265		Approved	KIAA0078, hHR21, SCC1	uc003yod.3	O60216	OTTHUMG00000164959	ENST00000297338.2:c.1440T>C	8.37:g.117864217A>G		Somatic	166	1	0.0060241		WXS	Illumina HiSeq	Phase_I	153	118	0.771242	NM_006265	A8K0E0|Q15001|Q99568	Silent	SNP	ENST00000297338.2	37	CCDS6321.1																																																																																			A|0.871;G|0.129	0.129	strong		0.473	RAD21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381184.1	NM_006265	
NMT1	4836	hgsc.bcm.edu	37	17	43171154	43171154	+	Silent	SNP	C	C	T	rs1132898	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:43171154C>T	ENST00000592782.1	+	5	618	c.487C>T	c.(487-489)Ctg>Ttg	p.L163L	NMT1_ENST00000258960.2_Silent_p.L163L|NMT1_ENST00000590114.1_3'UTR			P30419	NMT1_HUMAN	N-myristoyltransferase 1	163					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)				TGCTTTGGACCTGGGCGATCG	0.592													C|||	997	0.199081	0.3616	0.134	5008	,	,		16891	0.0367		0.1769	False		,,,				2504	0.2157				p.L163L		Atlas-SNP	.											.	NMT1	31	.	0			c.C487T						PASS	.	C		1432,2974	464.5+/-353.9	247,938,1018	79.0	65.0	70.0		487	4.1	1.0	17	dbSNP_86	70	1747,6853	316.3+/-312.7	170,1407,2723	no	coding-synonymous	NMT1	NM_021079.3		417,2345,3741	TT,TC,CC		20.314,32.5011,24.4426		163/497	43171154	3179,9827	2203	4300	6503	SO:0001819	synonymous_variant	4836	exon4			TTGGACCTGGGCG		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.487C>T	17.37:g.43171154C>T		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	81	37	0.45679	NM_021079	A8K7C1|Q9UE09	Silent	SNP	ENST00000592782.1	37	CCDS11494.1																																																																																			C|0.785;G|0.000;T|0.215	0.215	strong		0.592	NMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449239.1	NM_021079	
LPIN1	23175	hgsc.bcm.edu	37	2	11943082	11943082	+	Missense_Mutation	SNP	C	C	T	rs4669781	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:11943082C>T	ENST00000256720.2	+	14	1921	c.1828C>T	c.(1828-1830)Cca>Tca	p.P610S	LPIN1_ENST00000425416.2_Missense_Mutation_p.P616S|LPIN1_ENST00000396097.1_Missense_Mutation_p.P340S|LPIN1_ENST00000396099.1_Missense_Mutation_p.P652S|LPIN1_ENST00000449576.2_Missense_Mutation_p.P695S|LPIN1_ENST00000404113.2_Missense_Mutation_p.P111S	NM_145693.2	NP_663731.1	Q14693	LPIN1_HUMAN	lipin 1	610			P -> S (in dbSNP:rs4669781). {ECO:0000269|PubMed:12111372}.		cellular lipid metabolic process (GO:0044255)|fatty acid catabolic process (GO:0009062)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phosphatidylethanolamine biosynthetic process (GO:0006646)|phospholipid metabolic process (GO:0006644)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)|triglyceride biosynthetic process (GO:0019432)|triglyceride mobilization (GO:0006642)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	phosphatidate phosphatase activity (GO:0008195)			autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(15)|liver(1)|lung(10)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	45	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.11)|OV - Ovarian serous cystadenocarcinoma(76;0.173)		AGCTGCCAAGCCATCAAACGC	0.537													C|||	140	0.0279553	0.0008	0.0476	5008	,	,		20971	0.0		0.0378	False		,,,				2504	0.0695				p.P695S		Atlas-SNP	.											LPIN1_ENST00000404113,NS,carcinoma,-2,3	LPIN1	99	3	0			c.C2083T						PASS	.	C	SER/PRO	53,4353	51.6+/-87.1	0,53,2150	182.0	160.0	167.0		1828	4.6	1.0	2	dbSNP_111	167	460,8140	137.5+/-194.4	15,430,3855	yes	missense	LPIN1	NM_145693.1	74	15,483,6005	TT,TC,CC		5.3488,1.2029,3.9443	benign	610/891	11943082	513,12493	2203	4300	6503	SO:0001583	missense	23175	exon16			GCCAAGCCATCAA	D80010	CCDS1682.1, CCDS58699.1, CCDS58700.1, CCDS58701.1	2p25.1	2008-05-23			ENSG00000134324	ENSG00000134324			13345	protein-coding gene	gene with protein product		605518				11138012, 8724849, 16950137	Standard	NM_145693		Approved	KIAA0188	uc010yjm.3	Q14693	OTTHUMG00000119082	ENST00000256720.2:c.1828C>T	2.37:g.11943082C>T	ENSP00000256720:p.Pro610Ser	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	44	17	0.386364	NM_001261428	A8MU38|B4DET9|B4DGS4|B4DGZ6|B5MC18|B7Z858|D6W506|E7ESE7|F5GY24|Q53T25	Missense_Mutation	SNP	ENST00000256720.2	37	CCDS1682.1	49	0.022435897435897436	1	0.0020325203252032522	19	0.052486187845303865	0	0.0	29	0.03825857519788918	C	7.475	0.647393	0.14516	0.012029	0.053488	ENSG00000134324	ENST00000449576;ENST00000396099;ENST00000425416;ENST00000256720;ENST00000396097;ENST00000404113;ENST00000454151	T;T;T;T;T;T;T	0.80480	-1.38;-1.37;-1.36;-1.35;-1.19;-0.35;0.53	4.56	4.56	0.56223	.	0.053133	0.85682	D	0.000000	T	0.24736	0.0600	N	0.17312	0.475	0.36110	D	0.844742	B;B;B	0.31705	0.0;0.336;0.002	B;B;B	0.33454	0.003;0.164;0.008	T	0.57100	-0.7869	10	0.07175	T	0.84	-19.8574	13.5335	0.61635	0.1567:0.8433:0.0:0.0	rs4669781;rs4669781	111;695;610	B4DET9;F5GY24;Q14693	.;.;LPIN1_HUMAN	S	695;652;616;610;340;111;137	ENSP00000397908:P695S;ENSP00000379406:P652S;ENSP00000401522:P616S;ENSP00000256720:P610S;ENSP00000379404:P340S;ENSP00000386120:P111S;ENSP00000413714:P137S	ENSP00000256720:P610S	P	+	1	0	LPIN1	11860533	1.000000	0.71417	0.984000	0.44739	0.046000	0.14306	2.155000	0.42301	2.240000	0.73641	0.462000	0.41574	CCA	C|0.968;T|0.032	0.032	strong		0.537	LPIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239296.3	NM_145693	
SLIT3	6586	hgsc.bcm.edu	37	5	168233474	168233474	+	Silent	SNP	G	G	A	rs3797715	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:168233474G>A	ENST00000519560.1	-	9	1331	c.912C>T	c.(910-912)aaC>aaT	p.N304N	SLIT3_ENST00000332966.8_Silent_p.N304N|SLIT3_ENST00000404867.3_Silent_p.N304N	NM_001271946.1|NM_003062.2	NP_001258875.1|NP_003053	O75094	SLIT3_HUMAN	slit homolog 3 (Drosophila)	304	LRRNT 2.				apoptotic process involved in luteolysis (GO:0061364)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|cellular response to hormone stimulus (GO:0032870)|negative chemotaxis (GO:0050919)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of gene expression (GO:0010629)|organ morphogenesis (GO:0009887)|response to cortisol (GO:0051414)|Roundabout signaling pathway (GO:0035385)	extracellular space (GO:0005615)|mitochondrion (GO:0005739)	calcium ion binding (GO:0005509)|Roundabout binding (GO:0048495)			endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(15)|liver(2)|lung(48)|ovary(4)|prostate(7)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	100	Renal(175;0.000159)|Lung NSC(126;0.0174)|all_lung(126;0.0392)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			CCTCCGGCAAGTTGGCAGGAA	0.567													G|||	779	0.155551	0.0348	0.2032	5008	,	,		20482	0.2927		0.173	False		,,,				2504	0.1258				p.N304N	Ovarian(29;311 847 10864 17279 24903)	Atlas-SNP	.											.	SLIT3	224	.	0			c.C912T						PASS	.	G		283,4123	156.3+/-189.4	12,259,1932	87.0	79.0	82.0		912	3.6	0.9	5	dbSNP_107	82	1324,7276	258.7+/-282.2	107,1110,3083	no	coding-synonymous	SLIT3	NM_003062.2		119,1369,5015	AA,AG,GG		15.3953,6.4231,12.3558		304/1524	168233474	1607,11399	2203	4300	6503	SO:0001819	synonymous_variant	6586	exon9			CGGCAAGTTGGCA	AB011538	CCDS4369.1, CCDS64311.1	5q35	2008-07-18	2001-11-28		ENSG00000184347	ENSG00000184347			11087	protein-coding gene	gene with protein product		603745	"""slit (Drosophila) homolog 3"""	SLIL2		9693030, 9813312	Standard	NM_001271946		Approved	slit2, MEGF5, SLIT1, Slit-3	uc010jjg.4	O75094	OTTHUMG00000130409	ENST00000519560.1:c.912C>T	5.37:g.168233474G>A		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	136	76	0.558824	NM_001271946	A6H8U9|J3KNP3|O95804|Q9UFH5	Silent	SNP	ENST00000519560.1	37	CCDS4369.1																																																																																			G|0.859;A|0.141	0.141	strong		0.567	SLIT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252792.4	NM_003062	
MYBPC2	4606	hgsc.bcm.edu	37	19	50957600	50957600	+	Missense_Mutation	SNP	T	T	C	rs150466277	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:50957600T>C	ENST00000357701.5	+	18	2039	c.1988T>C	c.(1987-1989)aTg>aCg	p.M663T		NM_004533.3	NP_004524.3	Q14324	MYPC2_HUMAN	myosin binding protein C, fast type	663	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				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)		GAGCCACCAATGTACGATGGG	0.542													N|||	28	0.00559105	0.0	0.013	5008	,	,		15828	0.0		0.0179	False		,,,				2504	0.001				p.M663T		Atlas-SNP	.											.	MYBPC2	103	.	0			c.T1988C						PASS	.	T	THR/MET	5,4085		0,5,2040	36.0	40.0	39.0		1988	2.4	1.0	19	dbSNP_134	39	86,8296		1,84,4106	yes	missense	MYBPC2	NM_004533.3	81	1,89,6146	CC,CT,TT		1.026,0.1222,0.7296	benign	663/1142	50957600	91,12381	2045	4191	6236	SO:0001583	missense	4606	exon18			CACCAATGTACGA		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.1988T>C	19.37:g.50957600T>C	ENSP00000350332:p.Met663Thr	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	88	53	0.602273	NM_004533	A1L4G9	Missense_Mutation	SNP	ENST00000357701.5	37	CCDS46152.1	13	0.005952380952380952	0	0.0	3	0.008287292817679558	0	0.0	10	0.013192612137203167	t	0.899	-0.722949	0.03158	0.001222	0.01026	ENSG00000086967	ENST00000357701	T	0.54866	0.55	3.47	2.44	0.29823	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.916880	0.08797	N	0.892359	T	0.13756	0.0333	N	0.00811	-1.165	0.20307	N	0.999916	B	0.06786	0.001	B	0.04013	0.001	T	0.22626	-1.0211	10	0.14656	T	0.56	.	5.0359	0.14434	0.6269:0.1905:0.0:0.1826	.	663	Q14324	MYPC2_HUMAN	T	663	ENSP00000350332:M663T	ENSP00000350332:M663T	M	+	2	0	MYBPC2	55649412	0.997000	0.39634	0.998000	0.56505	0.019000	0.09904	1.684000	0.37649	0.103000	0.17682	-2.001000	0.00444	ATG	T|0.994;C|0.006	0.006	strong		0.542	MYBPC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464751.1	NM_004533	
CDC6	990	hgsc.bcm.edu	37	17	38450248	38450248	+	Missense_Mutation	SNP	G	G	A	rs4135012	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:38450248G>A	ENST00000209728.4	+	6	1354	c.883G>A	c.(883-885)Gat>Aat	p.D295N		NM_001254.3	NP_001245.1	Q99741	CDC6_HUMAN	cell division cycle 6	295			D -> N (in dbSNP:rs4135012). {ECO:0000269|Ref.3}.		DNA replication (GO:0006260)|DNA replication checkpoint (GO:0000076)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|positive regulation of chromosome segregation (GO:0051984)|positive regulation of cytokinesis (GO:0032467)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of mitotic metaphase/anaphase transition (GO:0030071)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|traversing start control point of mitotic cell cycle (GO:0007089)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle midzone (GO:0051233)|spindle pole (GO:0000922)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|kinase binding (GO:0019900)|nucleotide binding (GO:0000166)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(7)|ovary(2)|prostate(1)|stomach(2)|urinary_tract(1)	21						CAAAGGCCAGGATGTATTGTA	0.398													G|||	28	0.00559105	0.0008	0.0086	5008	,	,		19688	0.0		0.0159	False		,,,				2504	0.0051				p.D295N		Atlas-SNP	.											.	CDC6	53	.	0			c.G883A						PASS	.	G	ASN/ASP	21,4385	30.8+/-60.4	0,21,2182	323.0	284.0	297.0		883	5.9	1.0	17	dbSNP_108	297	182,8418	82.3+/-144.9	2,178,4120	yes	missense	CDC6	NM_001254.3	23	2,199,6302	AA,AG,GG		2.1163,0.4766,1.5608	possibly-damaging	295/561	38450248	203,12803	2203	4300	6503	SO:0001583	missense	990	exon6			GGCCAGGATGTAT	U77949	CCDS11365.1	17q21.3	2013-01-17	2013-01-17		ENSG00000094804	ENSG00000094804			1744	protein-coding gene	gene with protein product		602627	"""CDC6 (cell division cycle 6, S. cerevisiae) homolog"", ""CDC6 cell division cycle 6 homolog (S. cerevisiae)"", ""cell division cycle 6 homolog (S. cerevisiae)"""	CDC18L		8990175, 9566895	Standard	NM_001254		Approved		uc002huj.1	Q99741	OTTHUMG00000133324	ENST00000209728.4:c.883G>A	17.37:g.38450248G>A	ENSP00000209728:p.Asp295Asn	Somatic	222	0	0		WXS	Illumina HiSeq	Phase_I	211	101	0.478673	NM_001254	Q8TB30	Missense_Mutation	SNP	ENST00000209728.4	37	CCDS11365.1	17	0.007783882783882784	1	0.0020325203252032522	4	0.011049723756906077	0	0.0	12	0.0158311345646438	G	31	5.059101	0.93846	0.004766	0.021163	ENSG00000094804	ENST00000209728	T	0.59638	0.25	5.95	5.95	0.96441	ATPase, AAA-type, core (1);ATPase, AAA+ type, core (1);	0.046090	0.85682	D	0.000000	T	0.55705	0.1937	L	0.52905	1.665	0.58432	D	0.999993	P	0.47191	0.891	P	0.58013	0.831	T	0.62320	-0.6879	10	0.48119	T	0.1	-6.0538	19.1646	0.93551	0.0:0.0:1.0:0.0	rs4135012;rs17617390;rs52797967;rs4135012	295	Q99741	CDC6_HUMAN	N	295	ENSP00000209728:D295N	ENSP00000209728:D295N	D	+	1	0	CDC6	35703774	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.109000	0.89561	2.824000	0.97209	0.655000	0.94253	GAT	G|0.986;A|0.014	0.014	strong		0.398	CDC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257129.1		
ARHGEF10	9639	hgsc.bcm.edu	37	8	1873540	1873540	+	Silent	SNP	C	C	T	rs2272613	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:1873540C>T	ENST00000398564.1	+	22	2655	c.2655C>T	c.(2653-2655)ccC>ccT	p.P885P	ARHGEF10_ENST00000518288.1_Silent_p.P884P|ARHGEF10_ENST00000349830.3_Silent_p.P860P|ARHGEF10_ENST00000520359.1_Silent_p.P822P|ARHGEF10_ENST00000262112.6_Silent_p.P885P			O15013	ARHGA_HUMAN	Rho guanine nucleotide exchange factor (GEF) 10	885					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)	p.P637P(1)|p.P885P(1)		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)		GACACATGCCCGTGATGGTGG	0.582													C|||	533	0.10643	0.0053	0.0346	5008	,	,		17837	0.3145		0.0706	False		,,,				2504	0.1166				p.P860P		Atlas-SNP	.											ARHGEF10_ENST00000398564,NS,carcinoma,0,2	ARHGEF10	255	2	2	Substitution - coding silent(2)	stomach(2)	c.C2580T						PASS	.	C		81,4325	68.7+/-106.4	0,81,2122	72.0	61.0	65.0		2580	-9.6	0.9	8	dbSNP_100	65	508,8092	145.1+/-200.9	11,486,3803	yes	coding-synonymous	ARHGEF10	NM_014629.2		11,567,5925	TT,TC,CC		5.907,1.8384,4.5287		860/1345	1873540	589,12417	2203	4300	6503	SO:0001819	synonymous_variant	9639	exon22			CATGCCCGTGATG	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.2655C>T	8.37:g.1873540C>T		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	83	64	0.771084	NM_014629	O14665|Q2KHR8|Q68D55|Q8IWD9|Q8IY77	Silent	SNP	ENST00000398564.1	37																																																																																				C|0.925;T|0.075	0.075	strong		0.582	ARHGEF10-203	KNOWN	basic	protein_coding	protein_coding			
MIA3	375056	hgsc.bcm.edu	37	1	222823669	222823669	+	Missense_Mutation	SNP	A	A	G	rs201134844		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:222823669A>G	ENST00000344922.5	+	9	3692	c.3667A>G	c.(3667-3669)Atc>Gtc	p.I1223V	MIA3_ENST00000344507.1_Intron|MIA3_ENST00000340535.7_Missense_Mutation_p.I101V|MIA3_ENST00000344441.6_Missense_Mutation_p.I1223V	NM_198551.2	NP_940953.2	Q5JRA6	MIA3_HUMAN	melanoma inhibitory activity family, member 3	1223					chondrocyte development (GO:0002063)|collagen fibril organization (GO:0030199)|exocytosis (GO:0006887)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell migration (GO:0030336)|positive regulation of bone mineralization (GO:0030501)|positive regulation of leukocyte migration (GO:0002687)|protein transport (GO:0015031)|wound healing (GO:0042060)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				breast(5)|central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(15)|lung(37)|ovary(5)|pancreas(2)|prostate(2)|skin(2)|stomach(4)|urinary_tract(1)	80				GBM - Glioblastoma multiforme(131;0.0199)		GTTGAAGACTATCATGAAAGA	0.274																																					p.I1223V		Atlas-SNP	.											.	MIA3	167	.	0			c.A3667G						PASS	.	A	VAL/ILE	0,3618		0,0,1809	33.0	34.0	34.0		3667	-6.1	0.0	1		34	7,8113		0,7,4053	yes	missense	MIA3	NM_198551.2	29	0,7,5862	GG,GA,AA		0.0862,0.0,0.0596	possibly-damaging	1223/1908	222823669	7,11731	1809	4060	5869	SO:0001583	missense	375056	exon9			AAGACTATCATGA		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.3667A>G	1.37:g.222823669A>G	ENSP00000340900:p.Ile1223Val	Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	102	48	0.470588	NM_198551	A8K2S0|A8MT05|A8MT13|B7Z430|Q14083|Q3S4X3|Q5JRA5|Q5JRB0|Q5JRB1|Q5JRB2|Q6UVY8|Q86Y60|Q8N8M5|Q92580	Missense_Mutation	SNP	ENST00000344922.5	37	CCDS41470.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	8.974|8.974	0.973738|0.973738	0.18736|0.18736	0.0|0.0	8.62E-4|8.62E-4	ENSG00000154305|ENSG00000154305	ENST00000344922;ENST00000344441;ENST00000320831;ENST00000340535;ENST00000284471|ENST00000354906	T;T;T|.	0.28666|.	1.6;1.6;1.6|.	5.75|5.75	-6.14|-6.14	0.02111|0.02111	.|.	.|.	.|.	.|.	.|.	T|T	0.27524|0.27524	0.0676|0.0676	L|L	0.31294|0.31294	0.92|0.92	0.09310|0.09310	N|N	1|1	P;B;B|.	0.39022|.	0.655;0.012;0.081|.	B;B;B|.	0.35039|.	0.194;0.015;0.017|.	T|T	0.36311|0.36311	-0.9753|-0.9753	9|5	0.49607|.	T|.	0.09|.	.|.	7.868|7.868	0.29549|0.29549	0.1682:0.4854:0.0:0.3464|0.1682:0.4854:0.0:0.3464	.|.	1223;101;1223|.	Q5JRA6-2;Q5JRA6-4;Q5JRA6|.	.;.;MIA3_HUMAN|.	V|C	1223;1223;1223;101;101|805	ENSP00000340900:I1223V;ENSP00000340587:I1223V;ENSP00000345866:I101V|.	ENSP00000284471:I101V|.	I|Y	+|+	1|2	0|0	MIA3|MIA3	220890292|220890292	0.177000|0.177000	0.23109|0.23109	0.000000|0.000000	0.03702|0.03702	0.048000|0.048000	0.14542|0.14542	1.442000|1.442000	0.35046|0.35046	-0.870000|-0.870000	0.04047|0.04047	0.482000|0.482000	0.46254|0.46254	ATC|TAT	A|0.999;G|0.001	0.001	weak		0.274	MIA3-001	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000091489.4	NM_198551	
COL6A3	1293	hgsc.bcm.edu	37	2	238258814	238258814	+	Silent	SNP	C	C	G	rs3790993	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:238258814C>G	ENST00000295550.4	-	28	7307	c.6855G>C	c.(6853-6855)ggG>ggC	p.G2285G	COL6A3_ENST00000346358.4_Silent_p.G2085G|COL6A3_ENST00000347401.3_Silent_p.G2084G|COL6A3_ENST00000472056.1_Silent_p.G1678G|COL6A3_ENST00000353578.4_Silent_p.G2079G|COL6A3_ENST00000409809.1_Silent_p.G2079G	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	2285	Collagen-like 4.|Triple-helical 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)		GGCCCCGGTTCCCGATTCCTC	0.612													C|||	2776	0.554313	0.5862	0.4683	5008	,	,		16482	0.6746		0.5278	False		,,,				2504	0.4755				p.G2285G		Atlas-SNP	.											COL6A3,colon,carcinoma,-2,1	COL6A3	608	1	0			c.G6855C						scavenged	.	C	,,	2543,1863	633.0+/-395.9	745,1053,405	92.0	82.0	85.0		6855,5034,6237	-2.8	0.0	2	dbSNP_107	85	4726,3874	608.2+/-395.3	1328,2070,902	no	coding-synonymous,coding-synonymous,coding-synonymous	COL6A3	NM_004369.3,NM_057166.4,NM_057167.3	,,	2073,3123,1307	GG,GC,CC		45.0465,42.2833,44.1104	,,	2285/3178,1678/2571,2079/2972	238258814	7269,5737	2203	4300	6503	SO:0001819	synonymous_variant	1293	exon28			CCGGTTCCCGATT	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.6855G>C	2.37:g.238258814C>G		Somatic	61	1	0.0163934		WXS	Illumina HiSeq	Phase_I	61	29	0.47541	NM_004369	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Silent	SNP	ENST00000295550.4	37	CCDS33412.1																																																																																			C|0.434;G|0.566	0.566	strong		0.612	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369	
PHLPP1	23239	hgsc.bcm.edu	37	18	60645509	60645509	+	Silent	SNP	C	C	T	rs34061095	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	59	0	0		WXS	Illumina HiSeq	Phase_I	68	34	0.5	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	
HMGXB3	22993	hgsc.bcm.edu	37	5	149421502	149421502	+	Silent	SNP	A	A	G	rs2276982	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:149421502A>G	ENST00000502717.1	+	15	3164	c.2700A>G	c.(2698-2700)gaA>gaG	p.E900E	HMGXB3_ENST00000503427.1_Silent_p.E868E	NM_014983.2	NP_055798	Q12766	HMGX3_HUMAN	HMG box domain containing 3	1146					phosphorylation (GO:0016310)	nucleus (GO:0005634)	DNA binding (GO:0003677)|kinase activity (GO:0016301)			central_nervous_system(1)|endometrium(3)|kidney(3)|skin(2)	9						AGAGGAGTGAAGAGAATGTGC	0.517													A|||	1333	0.266174	0.6346	0.3012	5008	,	,		20075	0.1032		0.1302	False		,,,				2504	0.0511				p.E900E		Atlas-SNP	.											.	HMGXB3	31	.	0			c.A2700G						PASS	.	A		803,581		233,337,122	104.0	80.0	87.0		2700	0.9	1.0	5	dbSNP_100	87	384,2798		28,328,1235	no	coding-synonymous	HMGXB3	NM_014983.2		261,665,1357	GG,GA,AA		12.0679,41.9798,25.9965		900/1293	149421502	1187,3379	692	1591	2283	SO:0001819	synonymous_variant	22993	exon15			GAGTGAAGAGAAT	D83778	CCDS54935.1	5q33.1	2011-07-01		2009-01-05	ENSG00000113716	ENSG00000113716		"""High mobility group / Non-canonical"""	28982	protein-coding gene	gene with protein product				HMGX3		8724849	Standard	NM_014983		Approved	SMF, KIAA0194	uc003lrk.4	Q12766	OTTHUMG00000163493	ENST00000502717.1:c.2700A>G	5.37:g.149421502A>G		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	129	70	0.542636	NM_014983	G5E9Y4|Q86UG3|Q9UMF4	Silent	SNP	ENST00000502717.1	37	CCDS54935.1																																																																																			A|0.728;G|0.272	0.272	strong		0.517	HMGXB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373771.1	XM_001717202	
TPO	7173	hgsc.bcm.edu	37	2	1491723	1491723	+	Silent	SNP	G	G	A	rs78406347	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:1491723G>A	ENST00000345913.4	+	10	1819	c.1728G>A	c.(1726-1728)gcG>gcA	p.A576A	TPO_ENST00000382198.1_Silent_p.A403A|TPO_ENST00000349624.3_Silent_p.A403A|TPO_ENST00000346956.3_Silent_p.A576A|TPO_ENST00000329066.4_Silent_p.A576A|TPO_ENST00000382201.3_Intron|TPO_ENST00000497517.2_Intron|TPO_ENST00000337415.3_Silent_p.A576A	NM_000547.5	NP_000538.3	P07202	PERT_HUMAN	thyroid peroxidase	576					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.A576A(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)	TGGATCTGGCGTCCATCAACC	0.592													G|||	214	0.0427316	0.0008	0.0014	5008	,	,		15945	0.0903		0.008	False		,,,				2504	0.1155				p.A576A		Atlas-SNP	.											TPO,NS,carcinoma,+1,2	TPO	224	2	1	Substitution - coding silent(1)	stomach(1)	c.G1728A						PASS	.	G	,,,,,	7,4399	12.9+/-30.5	0,7,2196	112.0	101.0	105.0		1728,1728,,,1728,1209	-9.6	0.3	2	dbSNP_131	105	57,8543	35.9+/-90.5	0,57,4243	no	coding-synonymous,coding-synonymous,intron,intron,coding-synonymous,coding-synonymous	TPO	NM_000547.5,NM_001206744.1,NM_001206745.1,NM_175719.3,NM_175721.3,NM_175722.3	,,,,,	0,64,6439	AA,AG,GG		0.6628,0.1589,0.4921	,,,,,	576/934,576/934,,,576/890,403/761	1491723	64,12942	2203	4300	6503	SO:0001819	synonymous_variant	7173	exon10			TCTGGCGTCCATC		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.1728G>A	2.37:g.1491723G>A		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	110	64	0.581818	NM_001206744	P09934|P09935|Q8IUL0|Q8NF94|Q8NF95|Q8NF96|Q8NF97|Q8TCI9	Silent	SNP	ENST00000345913.4	37	CCDS1643.1																																																																																			G|0.987;A|0.013	0.013	strong		0.592	TPO-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206594.2	NM_000547	
PKHD1	5314	hgsc.bcm.edu	37	6	51890823	51890823	+	Missense_Mutation	SNP	G	G	A	rs9296669	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:51890823G>A	ENST00000371117.3	-	32	4060	c.3785C>T	c.(3784-3786)gCt>gTt	p.A1262V	PKHD1_ENST00000340994.4_Missense_Mutation_p.A1262V	NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	1262	IPT/TIG 7.		A -> V (in dbSNP:rs9296669). {ECO:0000269|PubMed:11919560, ECO:0000269|PubMed:12846734}.		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)					AACAGTGGGAGCGCCCGCATC	0.587													G|||	1776	0.354633	0.1051	0.5879	5008	,	,		16509	0.381		0.502	False		,,,				2504	0.3476				p.A1262V		Atlas-SNP	.											.	PKHD1	927	.	0			c.C3785T						PASS	.	G	VAL/ALA,VAL/ALA	660,3746	279.6+/-274.9	52,556,1595	43.0	44.0	44.0		3785,3785	-1.4	0.0	6	dbSNP_119	44	4443,4157	586.8+/-392.1	1162,2119,1019	yes	missense,missense	PKHD1	NM_138694.3,NM_170724.2	64,64	1214,2675,2614	AA,AG,GG		48.3372,14.9796,39.2357	benign,benign	1262/4075,1262/3397	51890823	5103,7903	2203	4300	6503	SO:0001583	missense	5314	exon32			GTGGGAGCGCCCG	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.3785C>T	6.37:g.51890823G>A	ENSP00000360158:p.Ala1262Val	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	70	68	0.971429	NM_170724	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Missense_Mutation	SNP	ENST00000371117.3	37	CCDS4935.1	869	0.39789377289377287	59	0.11991869918699187	210	0.580110497237569	210	0.36713286713286714	390	0.5145118733509235	G	10.33	1.320491	0.23994	0.149796	0.516628	ENSG00000170927	ENST00000371117;ENST00000340994;ENST00000393616	D;D	0.86956	-2.01;-2.19	5.52	-1.36	0.09085	Cell surface receptor IPT/TIG (1);Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	2.034180	0.01843	N	0.035426	T	0.34658	0.0905	N	0.00707	-1.245	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.40515	-0.9559	9	0.21014	T	0.42	.	0.7485	0.00986	0.2421:0.1289:0.3645:0.2645	rs9296669;rs17747827;rs57134467;rs9296669	1262;1262	P08F94-2;P08F94	.;PKHD1_HUMAN	V	1262	ENSP00000360158:A1262V;ENSP00000341097:A1262V	ENSP00000341097:A1262V	A	-	2	0	PKHD1	51998782	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.265000	0.18515	-0.700000	0.05070	0.655000	0.94253	GCT	G|0.638;A|0.362	0.362	strong		0.587	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694	
MUC4	4585	hgsc.bcm.edu	37	3	195510786	195510786	+	Silent	SNP	T	T	G	rs2948677	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195510786T>G	ENST00000463781.3	-	2	8124	c.7665A>C	c.(7663-7665)acA>acC	p.T2555T	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Silent_p.T2555T	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.T2555T(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)		TGGCGTGACCTGTGGATGCTG	0.582													.|||	2649	0.528954	0.4289	0.4524	5008	,	,		13813	0.754		0.5219	False		,,,				2504	0.4939				p.T2555T		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	2	Substitution - coding silent(2)	stomach(2)	c.A7665C						scavenged	.						78.0	65.0	69.0					3																	195510786		678	1591	2269	SO:0001819	synonymous_variant	4585	exon2			GTGACCTGTGGAT	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.7665A>C	3.37:g.195510786T>G		Somatic	167	1	0.00598802		WXS	Illumina HiSeq	Phase_I	213	67	0.314554	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																																																																																			T|0.500;G|0.500	0.500	strong		0.582	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
HDC	3067	hgsc.bcm.edu	37	15	50555544	50555544	+	Missense_Mutation	SNP	G	G	A	rs17740607	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:50555544G>A	ENST00000267845.3	-	2	494	c.92C>T	c.(91-93)aCg>aTg	p.T31M	HDC_ENST00000543581.1_Missense_Mutation_p.T31M	NM_002112.3	NP_002103.2	Q9UBI9	HDC_HUMAN	histidine decarboxylase	0	Ala/Gly-rich.				respiratory tube development (GO:0030323)	membrane (GO:0016020)				breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(13)|lung(25)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	50		all_lung(180;0.0138)		all cancers(107;1.12e-06)|GBM - Glioblastoma multiforme(94;9.95e-05)		CACGTCTGGCGTCACACGTCT	0.567													G|||	238	0.047524	0.0053	0.085	5008	,	,		20228	0.0466		0.0974	False		,,,				2504	0.0276				p.T31M	GBM(95;1627 1936 6910 9570)	Atlas-SNP	.											.	HDC	86	.	0			c.C92T						PASS	.	G	MET/THR	113,4279	86.8+/-125.4	2,109,2085	96.0	85.0	89.0		92	3.0	0.9	15	dbSNP_123	89	972,7618	212.1+/-252.5	62,848,3385	yes	missense	HDC	NM_002112.3	81	64,957,5470	AA,AG,GG		11.3155,2.5729,8.3577	possibly-damaging	31/663	50555544	1085,11897	2196	4295	6491	SO:0001583	missense	3067	exon2			TCTGGCGTCACAC		CCDS10134.1	15q21.2	2013-09-20			ENSG00000140287	ENSG00000140287	4.1.1.22		4855	protein-coding gene	gene with protein product		142704				1487235	Standard	NM_002112		Approved		uc001zxz.3	P19113	OTTHUMG00000131644	ENST00000267845.3:c.92C>T	15.37:g.50555544G>A	ENSP00000267845:p.Thr31Met	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	111	54	0.486486	NM_002112		Missense_Mutation	SNP	ENST00000267845.3	37	CCDS10134.1	132	0.06043956043956044	5	0.01016260162601626	29	0.08011049723756906	24	0.04195804195804196	74	0.09762532981530343	G	11.65	1.701572	0.30142	0.025729	0.113155	ENSG00000140287	ENST00000267845;ENST00000543581	T;T	0.37915	1.17;1.17	6.05	3.03	0.35002	Pyridoxal phosphate-dependent transferase, major domain (1);	0.429863	0.26836	N	0.022249	T	0.00384	0.0012	L	0.32530	0.975	0.50467	P	1.2299999999998423E-4	D;D	0.54397	0.966;0.966	B;B	0.38562	0.276;0.276	T	0.08330	-1.0727	9	0.36615	T	0.2	-9.5804	6.2745	0.20973	0.1366:0.0:0.6087:0.2548	rs17740607;rs34750797;rs52799745;rs17740607	31;31	B7ZM01;P19113	.;DCHS_HUMAN	M	31	ENSP00000267845:T31M;ENSP00000440252:T31M	ENSP00000267845:T31M	T	-	2	0	HDC	48342836	0.781000	0.28676	0.893000	0.35052	0.476000	0.33039	1.241000	0.32743	0.896000	0.36366	0.650000	0.86243	ACG	G|0.928;A|0.072	0.072	strong		0.567	HDC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254540.1		
SH2D7	646892	hgsc.bcm.edu	37	15	78390909	78390909	+	Missense_Mutation	SNP	C	C	T	rs12593575	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:78390909C>T	ENST00000328828.5	+	4	616	c.616C>T	c.(616-618)Cgg>Tgg	p.R206W	SH2D7_ENST00000409568.2_Missense_Mutation_p.R70W	NM_001101404.1	NP_001094874.1	A6NKC9	SH2D7_HUMAN	SH2 domain containing 7	206			R -> W (in dbSNP:rs12593575).							endometrium(2)|kidney(2)|lung(3)	7						TGTGAGTCCCCGGAACCTCTC	0.602													C|||	1132	0.226038	0.2769	0.17	5008	,	,		20245	0.122		0.2008	False		,,,				2504	0.3303				p.R206W		Atlas-SNP	.											.	SH2D7	26	.	0			c.C616T						PASS	.	C	TRP/ARG	1022,3006		134,754,1126	31.0	37.0	35.0		616	-8.2	0.0	15	dbSNP_120	35	1576,6780		151,1274,2753	yes	missense	SH2D7	NM_001101404.1	101	285,2028,3879	TT,TC,CC		18.8607,25.3724,20.9787	benign	206/452	78390909	2598,9786	2014	4178	6192	SO:0001583	missense	646892	exon4			AGTCCCCGGAACC		CCDS45315.1	15q25.1	2013-02-14			ENSG00000183476	ENSG00000183476		"""SH2 domain containing"""	34549	protein-coding gene	gene with protein product							Standard	NM_001101404		Approved	LOC646892	uc010blb.1	A6NKC9	OTTHUMG00000154271	ENST00000328828.5:c.616C>T	15.37:g.78390909C>T	ENSP00000327846:p.Arg206Trp	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	87	35	0.402299	NM_001101404		Missense_Mutation	SNP	ENST00000328828.5	37	CCDS45315.1	450	0.20604395604395603	145	0.29471544715447157	84	0.23204419889502761	75	0.13111888111888112	146	0.19261213720316622	C	10.26	1.300006	0.23650	0.253724	0.188607	ENSG00000183476	ENST00000409568;ENST00000328828	T;T	0.27720	1.65;1.76	4.09	-8.17	0.01057	.	3.067170	0.01424	N	0.014470	T	0.00012	0.0000	N	0.04880	-0.145	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.15809	-1.0424	9	0.35671	T	0.21	0.4473	1.6216	0.02714	0.2353:0.4398:0.1339:0.1911	rs12593575;rs57849151;rs12593575	206	A6NKC9	SH2D7_HUMAN	W	70;206	ENSP00000386676:R70W;ENSP00000327846:R206W	ENSP00000327846:R206W	R	+	1	2	SH2D7	76177964	0.000000	0.05858	0.000000	0.03702	0.095000	0.18619	-5.350000	0.00129	-2.516000	0.00500	-0.378000	0.06908	CGG	C|0.785;T|0.215	0.215	strong		0.602	SH2D7-002	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000334660.2	NM_001101404	
APCDD1	147495	hgsc.bcm.edu	37	18	10471773	10471773	+	Silent	SNP	C	C	G	rs3748413	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:10471773C>G	ENST00000355285.5	+	3	843	c.489C>G	c.(487-489)ctC>ctG	p.L163L	APCDD1_ENST00000578882.1_Intron	NM_153000.4	NP_694545.1			adenomatosis polyposis coli down-regulated 1											NS(1)|breast(1)|endometrium(3)|large_intestine(5)|lung(7)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22				READ - Rectum adenocarcinoma(15;0.08)		CCGAGAAGCTCGGCCAGCAGG	0.667													c|||	521	0.104034	0.0318	0.0778	5008	,	,		14318	0.1528		0.1123	False		,,,				2504	0.1616				p.L163L		Atlas-SNP	.											.	APCDD1	57	.	0			c.C489G						PASS	.	T		241,4165	137.3+/-173.1	5,231,1967	44.0	52.0	49.0		489	0.9	1.0	18	dbSNP_107	49	1036,7564	217.0+/-255.8	61,914,3325	no	coding-synonymous	APCDD1	NM_153000.4		66,1145,5292	GG,GC,CC		12.0465,5.4698,9.8185		163/515	10471773	1277,11729	2203	4300	6503	SO:0001819	synonymous_variant	147495	exon3			GAAGCTCGGCCAG	AB056722	CCDS11849.1	18p11.21	2006-07-07			ENSG00000154856	ENSG00000154856			15718	protein-coding gene	gene with protein product		607479				12384519	Standard	NM_153000		Approved	B7323	uc002kom.4	Q8J025	OTTHUMG00000131635	ENST00000355285.5:c.489C>G	18.37:g.10471773C>G		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	51	27	0.529412	NM_153000		Silent	SNP	ENST00000355285.5	37	CCDS11849.1																																																																																			C|0.897;G|0.103	0.103	strong		0.667	APCDD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254529.2	NM_153000	
ABCB9	23457	hgsc.bcm.edu	37	12	123444265	123444265	+	Missense_Mutation	SNP	G	G	A	rs114398803	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:123444265G>A	ENST00000542678.1	-	2	3356	c.518C>T	c.(517-519)aCg>aTg	p.T173M	ABCB9_ENST00000540285.1_Missense_Mutation_p.T173M|ABCB9_ENST00000392439.3_Missense_Mutation_p.T173M|ABCB9_ENST00000344275.7_Missense_Mutation_p.T173M|ABCB9_ENST00000280560.8_Missense_Mutation_p.T173M|ABCB9_ENST00000442028.2_Missense_Mutation_p.T173M|ABCB9_ENST00000442833.2_Missense_Mutation_p.T173M|ABCB9_ENST00000346530.5_Missense_Mutation_p.T173M			Q9NP78	ABCB9_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 9	173					peptide transport (GO:0015833)|protein transport (GO:0015031)|transmembrane transport (GO:0055085)	integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)	ATP binding (GO:0005524)|peptide-transporting ATPase activity (GO:0015440)|protein homodimerization activity (GO:0042803)|substrate-specific transmembrane transporter activity (GO:0022891)			central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(9)|ovary(2)|prostate(1)|skin(1)	18	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;6.84e-05)|Epithelial(86;0.000152)|BRCA - Breast invasive adenocarcinoma(302;0.111)		CTTCTGCAGCGTGGCCCCAGA	0.706													G|||	2	0.000399361	0.0008	0.0	5008	,	,		11470	0.0		0.001	False		,,,				2504	0.0				p.T173M	Ovarian(49;786 1333 9175 38236)	Atlas-SNP	.											.	ABCB9	50	.	0			c.C518T						PASS	.	G	MET/THR,MET/THR,MET/THR	0,4406		0,0,2203	37.0	37.0	37.0		518,518,518	5.3	1.0	12	dbSNP_132	37	1,8595	1.2+/-3.3	0,1,4297	no	missense,missense,missense	ABCB9	NM_019624.3,NM_019625.3,NM_203444.3	81,81,81	0,1,6500	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging	173/724,173/767,173/767	123444265	1,13001	2203	4298	6501	SO:0001583	missense	23457	exon2			TGCAGCGTGGCCC	U66676	CCDS9241.1, CCDS58286.1, CCDS58287.1, CCDS58288.1	12q24	2012-03-14			ENSG00000150967	ENSG00000150967		"""ATP binding cassette transporters / subfamily B"""	50	protein-coding gene	gene with protein product		605453				8894702	Standard	NM_019625		Approved	EST122234	uc001udm.4	Q9NP78		ENST00000542678.1:c.518C>T	12.37:g.123444265G>A	ENSP00000440288:p.Thr173Met	Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	26	10	0.384615	NM_019625	B4E2J0|Q5W9G7|Q769F3|Q769F4|Q96AB1|Q9P208	Missense_Mutation	SNP	ENST00000542678.1	37	CCDS9241.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	16.27	3.076558	0.55753	0.0	1.16E-4	ENSG00000150967	ENST00000280560;ENST00000540285;ENST00000346530;ENST00000392439;ENST00000542678;ENST00000442028	D;D;D;D;D;D	0.90732	-2.39;-2.72;-2.61;-2.39;-2.39;-2.37	5.3	5.3	0.74995	ABC transporter, transmembrane domain, type 1 (1);	0.000000	0.85682	D	0.000000	D	0.93177	0.7827	L	0.55481	1.735	0.50467	D	0.999878	P;D;B;D	0.76494	0.48;0.999;0.287;0.999	B;D;B;P	0.68039	0.079;0.955;0.109;0.875	D	0.92663	0.6143	10	0.48119	T	0.1	-32.5478	14.1825	0.65583	0.0:0.0:0.8504:0.1496	.	173;173;173;173	B4E2J0;Q9NP78-3;Q9NP78-2;Q9NP78	.;.;.;ABCB9_HUMAN	M	173	ENSP00000280560:T173M;ENSP00000441734:T173M;ENSP00000280559:T173M;ENSP00000376234:T173M;ENSP00000440288:T173M;ENSP00000394898:T173M	ENSP00000280560:T173M	T	-	2	0	ABCB9	122010218	1.000000	0.71417	0.999000	0.59377	0.886000	0.51366	6.425000	0.73370	2.653000	0.90120	0.561000	0.74099	ACG	G|0.999;A|0.001	0.001	strong		0.706	ABCB9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400956.1	NM_019624	
ATXN1	6310	hgsc.bcm.edu	37	6	16327915	16327915	+	Missense_Mutation	SNP	A	A	C	rs11969612|rs369629396	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:16327915A>C	ENST00000244769.4	-	8	1563	c.627T>G	c.(625-627)caT>caG	p.H209Q	ATXN1_ENST00000436367.1_Missense_Mutation_p.H209Q	NM_000332.3	NP_000323.2	P54253	ATX1_HUMAN	ataxin 1	209	Poly-Gln.		H -> Q (in dbSNP:rs11969612).		adult locomotory behavior (GO:0008344)|cell death (GO:0008219)|negative regulation of insulin-like growth factor receptor signaling pathway (GO:0043569)|negative regulation of phosphorylation (GO:0042326)|negative regulation of transcription, DNA-templated (GO:0045892)|nuclear export (GO:0051168)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|RNA processing (GO:0006396)|transcription, DNA-templated (GO:0006351)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nuclear inclusion body (GO:0042405)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|poly(G) binding (GO:0034046)|poly(U) RNA binding (GO:0008266)|protein C-terminus binding (GO:0008022)|protein self-association (GO:0043621)	p.H209delH(2)|p.H209_H211delHQH(1)		NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(11)|lung(12)|prostate(2)|skin(7)|upper_aerodigestive_tract(2)	44	Breast(50;0.063)|Ovarian(93;0.0733)	all_hematologic(90;0.000682)|Ovarian(999;0.00973)				gctgatgctgatgctgctgct	0.667																																					p.H209Q		Atlas-SNP	.											ATXN1,colon,carcinoma,0,1	ATXN1	117	1	3	Deletion - In frame(3)	upper_aerodigestive_tract(1)|large_intestine(1)|prostate(1)	c.T627G						PASS	.						4.0	8.0	7.0					6																	16327915		1573	3520	5093	SO:0001583	missense	6310	exon7			ATGCTGATGCTGC	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.627T>G	6.37:g.16327915A>C	ENSP00000244769:p.His209Gln	Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	44	17	0.386364	NM_001128164	Q17S02|Q9UJG2|Q9Y4J1	Missense_Mutation	SNP	ENST00000244769.4	37	CCDS34342.1	.	.	.	.	.	.	.	.	.	.	A	0.432	-0.902695	0.02453	.	.	ENSG00000124788	ENST00000244769;ENST00000450222;ENST00000436367	T;T	0.31510	1.49;1.49	0.0465	-0.093	0.13652	.	.	.	.	.	T	0.03178	0.0093	N	0.08118	0	0.09310	N	1	P	0.34662	0.462	B	0.36534	0.227	T	0.35724	-0.9777	8	0.19147	T	0.46	.	.	.	.	rs11969612	209	P54253	ATX1_HUMAN	Q	209	ENSP00000244769:H209Q;ENSP00000416360:H209Q	ENSP00000244769:H209Q	H	-	3	2	ATXN1	16435894	0.098000	0.21812	0.014000	0.15608	0.050000	0.14768	-1.578000	0.02125	-1.642000	0.01521	-1.674000	0.00743	CAT	A|0.571;C|0.429	0.429	strong		0.667	ATXN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039943.3	NM_000332	
TSSK2	23617	hgsc.bcm.edu	37	22	19119686	19119686	+	Silent	SNP	C	C	T	rs1052756	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	84	0	0		WXS	Illumina HiSeq	Phase_I	59	28	0.474576	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		
OR51B5	282763	hgsc.bcm.edu	37	11	5364640	5364640	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:5364640C>T	ENST00000300773.2	-	1	169	c.115G>A	c.(115-117)Ggc>Agc	p.G39S	HBG2_ENST00000380252.1_Intron|HBG2_ENST00000380259.2_Intron|HBE1_ENST00000380237.1_Intron|AC104389.28_ENST00000415970.1_RNA	NM_001005567.2	NP_001005567.2	Q9H339	O51B5_HUMAN	olfactory receptor, family 51, subfamily B, member 5	39					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)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(13)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	28		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;3.05e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		GTGCCATTGCCAAAAAGGATG	0.478																																					p.G39S		Atlas-SNP	.											.	OR51B5	60	.	0			c.G115A						PASS	.						62.0	66.0	65.0					11																	5364640		2201	4297	6498	SO:0001583	missense	282763	exon5			CATTGCCAAAAAG	BK004430	CCDS31378.1	11p15.4	2012-08-09			ENSG00000242180	ENSG00000242180		"""GPCR / Class A : Olfactory receptors"""	19599	protein-coding gene	gene with protein product							Standard	NM_001005567		Approved		uc001maq.2	Q9H339	OTTHUMG00000066676	ENST00000300773.2:c.115G>A	11.37:g.5364640C>T	ENSP00000300773:p.Gly39Ser	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	67	52	0.776119	NM_001005567	B2RN59	Missense_Mutation	SNP	ENST00000300773.2	37	CCDS31378.1	.	.	.	.	.	.	.	.	.	.	C	16.52	3.145360	0.57044	.	.	ENSG00000242180	ENST00000300773	T	0.00530	6.77	4.78	4.78	0.61160	GPCR, rhodopsin-like superfamily (1);	0.000000	0.40064	N	0.001186	T	0.01156	0.0038	M	0.90870	3.155	0.38694	D	0.952823	P	0.37398	0.593	B	0.37550	0.253	T	0.50118	-0.8865	10	0.72032	D	0.01	.	16.5938	0.84789	0.0:1.0:0.0:0.0	.	39	Q9H339	O51B5_HUMAN	S	39	ENSP00000300773:G39S	ENSP00000300773:G39S	G	-	1	0	OR51B5	5321216	0.190000	0.23276	0.966000	0.40874	0.675000	0.39556	2.218000	0.42889	2.482000	0.83794	0.650000	0.86243	GGC	.	.	none		0.478	OR51B5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142975.1	NM_001005567	
RRP1	8568	hgsc.bcm.edu	37	21	45217929	45217929	+	Silent	SNP	T	T	C	rs2838379	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:45217929T>C	ENST00000497547.1	+	8	876	c.759T>C	c.(757-759)ggT>ggC	p.G253G	RRP1_ENST00000471909.1_3'UTR	NM_003683.5	NP_003674.1	P05386	RLA1_HUMAN	ribosomal RNA processing 1	0					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)	RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			central_nervous_system(1)|kidney(1)|lung(4)|stomach(2)	8				COAD - Colon adenocarcinoma(84;0.00753)|Colorectal(79;0.0157)|STAD - Stomach adenocarcinoma(101;0.171)		CCTCTGAGGGTGGTGAGCGTG	0.632													C|||	2017	0.402756	0.6104	0.3631	5008	,	,		17517	0.3204		0.2087	False		,,,				2504	0.4346				p.G253G		Atlas-SNP	.											.	RRP1	23	.	0			c.T759C						PASS	.	C		2325,1931		671,983,474	62.0	73.0	69.0		759	-8.1	0.0	21	dbSNP_100	69	2038,6424		267,1504,2460	no	coding-synonymous	RRP1	NM_003683.5		938,2487,2934	CC,CT,TT		24.0841,45.3712,34.3057		253/462	45217929	4363,8355	2128	4231	6359	SO:0001819	synonymous_variant	8568	exon8			TGAGGGTGGTGAG	U79775	CCDS42951.1	21q22.3	2013-07-02	2013-07-02		ENSG00000160214	ENSG00000160214			18785	protein-coding gene	gene with protein product	"""DNA segment on chromosome 21 (unique) 2056 expressed sequence"", ""Nnp1 homolog, nucleolar protein (Drosophila)"""	610653	"""ribosomal RNA processing 1 homolog (S. cerevisiae)"""			10830953, 10341208	Standard	NM_003683		Approved	NNP-1, Nop52, NOP52, RRP1A, D21S2056E	uc002zds.2	P56182	OTTHUMG00000086884	ENST00000497547.1:c.759T>C	21.37:g.45217929T>C		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	179	77	0.430168	NM_003683	A6NIB2	Silent	SNP	ENST00000497547.1	37	CCDS42951.1																																																																																			T|0.670;C|0.330	0.330	strong		0.632	RRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195680.1	NM_003683	
KNG1	3827	hgsc.bcm.edu	37	3	186437944	186437944	+	Silent	SNP	T	T	C	rs5029980	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:186437944T>C	ENST00000265023.4	+	2	458	c.246T>C	c.(244-246)gaT>gaC	p.D82D	KNG1_ENST00000287611.2_Silent_p.D82D|RP11-573D15.8_ENST00000599314.1_RNA|KNG1_ENST00000447445.1_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	157	0	0		WXS	Illumina HiSeq	Phase_I	145	78	0.537931	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	
PLEKHG4B	153478	hgsc.bcm.edu	37	5	163266	163266	+	Missense_Mutation	SNP	C	C	G	rs3810867	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:163266C>G	ENST00000283426.6	+	11	2061	c.2011C>G	c.(2011-2013)Cgc>Ggc	p.R671G		NM_052909.3	NP_443141.3	Q96PX9	PKH4B_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 4B	671				R -> G (in Ref. 1; BAB67802). {ECO:0000305}.			Rho guanyl-nucleotide exchange factor activity (GO:0005089)			endometrium(1)|large_intestine(2)|lung(2)|prostate(3)|skin(3)	11			all cancers(22;0.0253)|Lung(60;0.113)	Kidney(1;0.119)		GGAGACCCTGCGCCCAGGGCT	0.697													G|||	1920	0.383387	0.4584	0.3184	5008	,	,		13760	0.1944		0.3817	False		,,,				2504	0.5245				p.R671G		Atlas-SNP	.											.	PLEKHG4B	167	.	0			c.C2011G						PASS	.	G	GLY/ARG	1908,2468		436,1036,716	12.0	14.0	13.0		2011	-4.4	0.0	5	dbSNP_107	13	3376,5192		688,2000,1596	yes	missense	PLEKHG4B	NM_052909.3	125	1124,3036,2312	GG,GC,CC		39.4024,43.6015,40.822	benign	671/1272	163266	5284,7660	2188	4284	6472	SO:0001583	missense	153478	exon11			ACCCTGCGCCCAG	BC008352	CCDS34124.1	5p15.33	2013-01-11			ENSG00000153404	ENSG00000153404		"""Pleckstrin homology (PH) domain containing"""	29399	protein-coding gene	gene with protein product						11572484	Standard	NM_052909		Approved	KIAA1909	uc003jak.2	Q96PX9	OTTHUMG00000161570	ENST00000283426.6:c.2011C>G	5.37:g.163266C>G	ENSP00000283426:p.Arg671Gly	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	122	53	0.434426	NM_052909		Missense_Mutation	SNP	ENST00000283426.6	37	CCDS34124.1	677	0.309981684981685	200	0.4065040650406504	112	0.30939226519337015	103	0.18006993006993008	262	0.34564643799472294	G	0.008	-1.917018	0.00503	0.436015	0.394024	ENSG00000153404	ENST00000283426	T	0.28255	1.62	2.91	-4.41	0.03590	.	.	.	.	.	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	0.46596	-0.9180	8	0.22109	T	0.4	.	5.3271	0.15913	0.4358:0.2652:0.2991:0.0	rs3810867;rs59972694	671	Q96PX9	PKH4B_HUMAN	G	671	ENSP00000283426:R671G	ENSP00000283426:R671G	R	+	1	0	PLEKHG4B	216266	0.000000	0.05858	0.004000	0.12327	0.022000	0.10575	-1.042000	0.03539	-1.821000	0.01213	-1.407000	0.01130	CGC	C|0.689;G|0.311	0.311	strong		0.697	PLEKHG4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365359.1	NM_052909	
RAB5B	5869	hgsc.bcm.edu	37	12	56383858	56383858	+	Silent	SNP	C	C	T	rs141101772	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:56383858C>T	ENST00000360299.5	+	3	512	c.291C>T	c.(289-291)atC>atT	p.I97I	RAB5B_ENST00000553116.1_Silent_p.I97I|RAB5B_ENST00000448789.2_Silent_p.I97I	NM_002868.3	NP_002859.1	P61020	RAB5B_HUMAN	RAB5B, member RAS oncogene family	97					antigen processing and presentation (GO:0019882)|endosome organization (GO:0007032)|GTP catabolic process (GO:0006184)|plasma membrane to endosome transport (GO:0048227)|protein transport (GO:0015031)|regulation of endocytosis (GO:0030100)|small GTPase mediated signal transduction (GO:0007264)	endocytic vesicle (GO:0030139)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|membrane (GO:0016020)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTP-dependent protein binding (GO:0030742)|GTPase activity (GO:0003924)			endometrium(1)|large_intestine(1)|liver(2)|lung(4)|upper_aerodigestive_tract(1)	9			UCEC - Uterine corpus endometrioid carcinoma (6;0.0471)|OV - Ovarian serous cystadenocarcinoma(18;0.235)			AAGCTGCAATCGTGGTTTACG	0.488													C|||	2	0.000399361	0.0	0.0014	5008	,	,		23495	0.0		0.001	False		,,,				2504	0.0				p.I97I		Atlas-SNP	.											RAB5B,NS,lymphoid_neoplasm,+2,1	RAB5B	22	1	0			c.C291T						PASS	.	C		3,4403	6.2+/-15.9	0,3,2200	100.0	79.0	86.0		291	-4.7	0.9	12	dbSNP_134	86	9,8591	7.1+/-27.0	0,9,4291	no	coding-synonymous	RAB5B	NM_002868.2		0,12,6491	TT,TC,CC		0.1047,0.0681,0.0923		97/216	56383858	12,12994	2203	4300	6503	SO:0001819	synonymous_variant	5869	exon3			TGCAATCGTGGTT		CCDS8900.1, CCDS58244.1	12q13	2008-07-30						"""RAB, member RAS oncogene"""	9784	protein-coding gene	gene with protein product		179514				1541686, 10403367	Standard	NM_001252037		Approved		uc001siw.3	P61020		ENST00000360299.5:c.291C>T	12.37:g.56383858C>T		Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	150	67	0.446667	NM_002868	A8K982|B4DKD7|P35239|P35277|Q6PIK9|Q86TH0|Q8IXL2	Silent	SNP	ENST00000360299.5	37	CCDS8900.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	10.22	1.290646	0.23564	6.81E-4	0.001047	ENSG00000111540	ENST00000549218	.	.	.	4.81	-4.69	0.03299	.	.	.	.	.	T	0.50000	0.1590	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.48692	-0.9013	4	.	.	.	-8.259	7.6574	0.28383	0.0:0.2762:0.1073:0.6166	.	.	.	.	C	17	.	.	R	+	1	0	RAB5B	54670125	0.398000	0.25279	0.865000	0.33974	0.959000	0.62525	-0.395000	0.07287	-0.990000	0.03481	-1.329000	0.01275	CGT	C|0.999;T|0.001	0.001	strong		0.488	RAB5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405396.1		
OR5K2	402135	hgsc.bcm.edu	37	3	98216586	98216586	+	Missense_Mutation	SNP	C	C	G	rs143260385	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:98216586C>G	ENST00000427338.1	+	1	139	c.62C>G	c.(61-63)cCt>cGt	p.P21R		NM_001004737.1	NP_001004737.1	Q8NHB8	OR5K2_HUMAN	olfactory receptor, family 5, subfamily K, member 2	21						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.P21L(1)		endometrium(2)|large_intestine(1)|lung(10)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	18						ACAGATCACCCTGAGCTGAAG	0.413													C|||	16	0.00319489	0.0008	0.0	5008	,	,		20316	0.0		0.0149	False		,,,				2504	0.0				p.P21R		Atlas-SNP	.											OR5K2,bladder,carcinoma,0,1	OR5K2	56	1	1	Substitution - Missense(1)	urinary_tract(1)	c.C62G						PASS	.	C	ARG/PRO	15,4391	22.3+/-47.3	0,15,2188	94.0	95.0	95.0		62	2.9	0.9	3	dbSNP_134	95	60,8534	36.9+/-92.0	0,60,4237	no	missense	OR5K2	NM_001004737.1	103	0,75,6425	GG,GC,CC		0.6982,0.3404,0.5769	probably-damaging	21/317	98216586	75,12925	2203	4297	6500	SO:0001583	missense	402135	exon1			ATCACCCTGAGCT	AC021660	CCDS33804.1	3q11.2	2013-09-23			ENSG00000231861	ENSG00000231861		"""GPCR / Class A : Olfactory receptors"""	14774	protein-coding gene	gene with protein product							Standard	NM_001004737		Approved		uc011bgx.2	Q8NHB8	OTTHUMG00000160049	ENST00000427338.1:c.62C>G	3.37:g.98216586C>G	ENSP00000393889:p.Pro21Arg	Somatic	349	0	0		WXS	Illumina HiSeq	Phase_I	361	170	0.470914	NM_001004737	B2RN70|Q6IF47	Missense_Mutation	SNP	ENST00000427338.1	37	CCDS33804.1	16	0.007326007326007326	0	0.0	0	0.0	0	0.0	16	0.021108179419525065	C	11.04	1.521543	0.27211	0.003404	0.006982	ENSG00000231861	ENST00000427338	T	0.20332	2.08	2.91	2.91	0.33838	.	0.000000	0.41294	D	0.000912	T	0.18257	0.0438	M	0.69523	2.12	0.23896	N	0.99653	P	0.45396	0.857	P	0.49637	0.617	T	0.04360	-1.0957	10	0.66056	D	0.02	-9.1222	12.101	0.53783	0.0:1.0:0.0:0.0	.	21	Q8NHB8	OR5K2_HUMAN	R	21	ENSP00000393889:P21R	ENSP00000393889:P21R	P	+	2	0	OR5K2	99699276	0.000000	0.05858	0.913000	0.36048	0.263000	0.26337	0.179000	0.16840	1.940000	0.56252	0.298000	0.19748	CCT	C|0.994;G|0.006	0.006	strong		0.413	OR5K2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359020.2		
AHNAK2	113146	hgsc.bcm.edu	37	14	105417581	105417581	+	Missense_Mutation	SNP	C	C	T	rs141283979	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:105417581C>T	ENST00000333244.5	-	7	4326	c.4207G>A	c.(4207-4209)Gag>Aag	p.E1403K	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	1403						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)			CCGGCTCCCTCGGGCACGGGG	0.617													.|||	109	0.0217652	0.0023	0.0331	5008	,	,		12168	0.0		0.0527	False		,,,				2504	0.0307				p.E1403K		Atlas-SNP	.											.	AHNAK2	719	.	0			c.G4207A						PASS	.	C	LYS/GLU	30,3432		7,16,1708	72.0	58.0	63.0		4207	4.2	0.0	14	dbSNP_134	63	418,5144		154,110,2517	no	missense	AHNAK2	NM_138420.2	56	161,126,4225	TT,TC,CC		7.5153,0.8666,4.9645	probably-damaging	1403/5796	105417581	448,8576	1731	2781	4512	SO:0001583	missense	113146	exon7			CTCCCTCGGGCAC	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.4207G>A	14.37:g.105417581C>T	ENSP00000353114:p.Glu1403Lys	Somatic	0	0	.		WXS	Illumina HiSeq	Phase_I	97	96	0.989691	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	36	0.016483516483516484	1	0.0020325203252032522	11	0.03038674033149171	0	0.0	24	0.0316622691292876	-	17.44	3.391204	0.62066	0.008666	0.075153	ENSG00000185567	ENST00000333244	T	0.00518	6.86	4.18	4.18	0.49190	.	.	.	.	.	T	0.00073	0.0002	M	0.78801	2.425	0.24548	N	0.994032	D	0.56287	0.975	P	0.50192	0.634	T	0.27872	-1.0061	9	0.06236	T	0.91	.	9.2716	0.37675	0.0:0.8965:0.0:0.1035	.	1403	Q8IVF2	AHNK2_HUMAN	K	1403	ENSP00000353114:E1403K	ENSP00000353114:E1403K	E	-	1	0	AHNAK2	104488626	0.001000	0.12720	0.030000	0.17652	0.233000	0.25261	-0.449000	0.06812	1.909000	0.55274	0.485000	0.47835	GAG	C|0.984;T|0.016	0.016	strong		0.617	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
SAMD7	344658	hgsc.bcm.edu	37	3	169644710	169644710	+	Missense_Mutation	SNP	G	G	C	rs10513680	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:169644710G>C	ENST00000428432.2	+	6	1049	c.660G>C	c.(658-660)gaG>gaC	p.E220D	SAMD7_ENST00000335556.3_Missense_Mutation_p.E220D	NM_182610.2	NP_872416.1	Q7Z3H4	SAMD7_HUMAN	sterile alpha motif domain containing 7	220			E -> D (in dbSNP:rs10513680).							NS(1)|biliary_tract(1)|breast(1)|kidney(1)|large_intestine(4)|lung(15)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	31	all_cancers(22;1.55e-22)|all_epithelial(15;2.41e-27)|all_lung(20;3.52e-17)|Lung NSC(18;1.44e-16)|Ovarian(172;0.000337)|Breast(254;0.169)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.0106)			CCTATGAAGAGGATCATTATG	0.443													G|||	733	0.146366	0.1377	0.1744	5008	,	,		20196	0.1687		0.1223	False		,,,				2504	0.1401				p.E220D		Atlas-SNP	.											.	SAMD7	69	.	0			c.G660C						PASS	.	G	ASP/GLU	560,3846	251.2+/-258.0	39,482,1682	97.0	96.0	96.0		660	2.7	0.7	3	dbSNP_119	96	1034,7566	220.4+/-258.1	62,910,3328	yes	missense	SAMD7	NM_182610.2	45	101,1392,5010	CC,CG,GG		12.0233,12.7099,12.2559	possibly-damaging	220/447	169644710	1594,11412	2203	4300	6503	SO:0001583	missense	344658	exon6			TGAAGAGGATCAT	BX537903	CCDS3209.1	3q26.31	2013-01-10			ENSG00000187033	ENSG00000187033		"""Sterile alpha motif (SAM) domain containing"""	25394	protein-coding gene	gene with protein product							Standard	NM_182610		Approved	DKFZp686E1583	uc003fgd.3	Q7Z3H4	OTTHUMG00000158730	ENST00000428432.2:c.660G>C	3.37:g.169644710G>C	ENSP00000391299:p.Glu220Asp	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	76	40	0.526316	NM_182610		Missense_Mutation	SNP	ENST00000428432.2	37	CCDS3209.1	313	0.1433150183150183	67	0.13617886178861788	54	0.14917127071823205	102	0.17832167832167833	90	0.11873350923482849	G	18.88	3.717056	0.68844	0.127099	0.120233	ENSG00000187033	ENST00000428432;ENST00000335556	T;T	0.64438	-0.1;-0.1	6.16	2.72	0.32119	.	0.045570	0.85682	D	0.000000	T	0.00356	0.0011	M	0.66939	2.045	0.27516	P	0.9515344	D	0.67145	0.996	P	0.59948	0.866	T	0.20472	-1.0274	9	0.56958	D	0.05	-18.0646	12.5792	0.56381	0.2235:0.0:0.7765:0.0	rs10513680;rs17289453;rs10513680	220	Q7Z3H4	SAMD7_HUMAN	D	220	ENSP00000391299:E220D;ENSP00000334668:E220D	ENSP00000334668:E220D	E	+	3	2	SAMD7	171127404	0.996000	0.38824	0.695000	0.30226	0.009000	0.06853	1.485000	0.35519	0.810000	0.34279	0.650000	0.86243	GAG	G|0.864;C|0.136	0.136	strong		0.443	SAMD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351959.1	NM_182610	
TAS2R31	259290	hgsc.bcm.edu	37	12	11183512	11183512	+	Silent	SNP	A	A	G	rs12370363	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:11183512A>G	ENST00000390675.2	-	1	494	c.423T>C	c.(421-423)gcT>gcC	p.A141A	PRR4_ENST00000536668.1_Intron|TAS2R14_ENST00000381852.4_Intron	NM_176885.2	NP_795366.2	P59538	T2R31_HUMAN	taste receptor, type 2, member 31	141					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)			kidney(1)|lung(6)	7						AAAGTTGACAAGCCAAAAATA	0.368													.|||	1065	0.21266	0.2375	0.2406	5008	,	,		20162	0.1944		0.2068	False		,,,				2504	0.184				p.A141A		Atlas-SNP	.											.	TAS2R31	24	.	0			c.T423C						PASS	.	A		865,3205		79,707,1249	80.0	83.0	82.0		423	1.1	0.0	12	dbSNP_120	82	1835,6611		159,1517,2547	no	coding-synonymous	TAS2R31	NM_176885.2		238,2224,3796	GG,GA,AA		21.7263,21.2531,21.5724		141/310	11183512	2700,9816	2035	4223	6258	SO:0001819	synonymous_variant	259290	exon1			TTGACAAGCCAAA	AX097748, AF494228	CCDS53747.1	12p13.2	2012-08-22				ENSG00000256436		"""Taste receptors / Type 2"", ""GPCR / Unclassified : Taste receptors"""	19113	protein-coding gene	gene with protein product		612669	"""taste receptor, type 2, member 44"""	TAS2R44			Standard	NM_176885		Approved	T2R31, T2R53	uc001qzo.1	P59538		ENST00000390675.2:c.423T>C	12.37:g.11183512A>G		Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	127	59	0.464567	NM_176885	P59547|Q17R84|Q645X5	Silent	SNP	ENST00000390675.2	37	CCDS53747.1																																																																																			A|0.785;G|0.215	0.215	strong		0.368	TAS2R31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400233.1	NM_176885	
PKD1L1	168507	hgsc.bcm.edu	37	7	47917087	47917087	+	Splice_Site	SNP	C	C	T	rs72601626	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	101	0	0		WXS	Illumina HiSeq	Phase_I	57	39	0.684211	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
TRPC4	7223	hgsc.bcm.edu	37	13	38357384	38357384	+	Silent	SNP	G	G	A	rs12875527	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:38357384G>A	ENST00000379705.3	-	2	944	c.87C>T	c.(85-87)ctC>ctT	p.L29L	TRPC4_ENST00000338947.5_Silent_p.L29L|TRPC4_ENST00000358477.2_Silent_p.L29L|TRPC4_ENST00000355779.2_Silent_p.L29L|TRPC4_ENST00000447043.1_Silent_p.L29L|TRPC4_ENST00000426868.2_Silent_p.L29L|TRPC4_ENST00000379679.1_Silent_p.L29L|TRPC4_ENST00000379673.2_Silent_p.L29L|TRPC4_ENST00000379681.3_Silent_p.L29L			Q9UBN4	TRPC4_HUMAN	transient receptor potential cation channel, subfamily C, member 4	29					axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|gamma-aminobutyric acid secretion (GO:0014051)|ion transmembrane transport (GO:0034220)|oligodendrocyte differentiation (GO:0048709)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|calcium channel complex (GO:0034704)|caveola (GO:0005901)|cell surface (GO:0009986)|cortical cytoskeleton (GO:0030863)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|cadherin binding (GO:0045296)|inositol 1,4,5 trisphosphate binding (GO:0070679)|store-operated calcium channel activity (GO:0015279)			NS(2)|breast(4)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(26)|lung(30)|ovary(4)|prostate(1)|skin(4)|urinary_tract(2)	83				all cancers(112;1.92e-08)|Epithelial(112;5.04e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000677)|GBM - Glioblastoma multiforme(144;0.00623)|BRCA - Breast invasive adenocarcinoma(63;0.0126)		CTGATGGCGAGAGTTCTGATT	0.393													G|||	213	0.0425319	0.0068	0.0677	5008	,	,		15525	0.0288		0.0954	False		,,,				2504	0.0327				p.L29L		Atlas-SNP	.											.	TRPC4	389	.	0			c.C87T						PASS	.	G	,,,,,	50,4356	50.9+/-86.3	0,50,2153	162.0	154.0	156.0		87,87,87,87,87,87	2.4	1.0	13	dbSNP_121	156	796,7804	186.7+/-234.1	32,732,3536	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TRPC4	NM_001135955.1,NM_001135956.1,NM_001135957.1,NM_001135958.1,NM_003306.1,NM_016179.2	,,,,,	32,782,5689	AA,AG,GG		9.2558,1.1348,6.5047	,,,,,	29/894,29/829,29/837,29/805,29/983,29/978	38357384	846,12160	2203	4300	6503	SO:0001819	synonymous_variant	7223	exon2			TGGCGAGAGTTCT	U40983	CCDS9365.1, CCDS45035.1, CCDS45036.1, CCDS45038.1, CCDS45039.1	13q13.3	2013-01-10			ENSG00000133107	ENSG00000133107		"""Voltage-gated ion channels / Transient receptor potential cation channels"", ""Ankyrin repeat domain containing"""	12336	protein-coding gene	gene with protein product		603651				8646775, 16382100	Standard	NM_016179		Approved	HTRP4, TRP4	uc010abx.3	Q9UBN4	OTTHUMG00000016752	ENST00000379705.3:c.87C>T	13.37:g.38357384G>A		Somatic	218	0	0		WXS	Illumina HiSeq	Phase_I	172	76	0.44186	NM_001135958	B1ALE0|B1ALE1|B1ALE2|Q15721|Q3SWS6|Q96P03|Q96P04|Q96P05|Q9UIB0|Q9UIB1|Q9UIB2	Silent	SNP	ENST00000379705.3	37	CCDS9365.1																																																																																			G|0.938;A|0.062	0.062	strong		0.393	TRPC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044574.2	NM_003306	
STAB1	23166	hgsc.bcm.edu	37	3	52556890	52556890	+	Missense_Mutation	SNP	A	A	G	rs4434138	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:52556890A>G	ENST00000321725.6	+	62	6920	c.6844A>G	c.(6844-6846)Ata>Gta	p.I2282V		NM_015136.2	NP_055951.2	Q9NY15	STAB1_HUMAN	stabilin 1	2282	Link. {ECO:0000255|PROSITE- ProRule:PRU00323, ECO:0000305}.		I -> V (in dbSNP:rs4434138). {ECO:0000269|PubMed:11829752}.		cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|defense response to bacterium (GO:0042742)|inflammatory response (GO:0006954)|negative regulation of angiogenesis (GO:0016525)|oxidation-reduction process (GO:0055114)|receptor-mediated endocytosis (GO:0006898)	endocytic vesicle membrane (GO:0030666)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	hyaluronic acid binding (GO:0005540)|low-density lipoprotein particle binding (GO:0030169)|low-density lipoprotein receptor activity (GO:0005041)|protein disulfide oxidoreductase activity (GO:0015035)|scavenger receptor activity (GO:0005044)			breast(4)|central_nervous_system(3)|endometrium(7)|kidney(2)|large_intestine(13)|liver(1)|lung(27)|ovary(1)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(3)	76				BRCA - Breast invasive adenocarcinoma(193;1.73e-05)|Kidney(197;0.00182)|KIRC - Kidney renal clear cell carcinoma(197;0.00205)|OV - Ovarian serous cystadenocarcinoma(275;0.0482)		TCGGGTGGGCATAGTCAGCCT	0.627													A|||	1709	0.341254	0.1528	0.4957	5008	,	,		16846	0.4385		0.4732	False		,,,				2504	0.2505				p.I2282V		Atlas-SNP	.											.	STAB1	178	.	0			c.A6844G						PASS	.	A	VAL/ILE	827,3579	328.3+/-300.5	76,675,1452	88.0	91.0	90.0		6844	-0.5	0.2	3	dbSNP_111	90	4070,4530	557.6+/-387.1	1002,2066,1232	yes	missense	STAB1	NM_015136.2	29	1078,2741,2684	GG,GA,AA		47.3256,18.7699,37.6519	benign	2282/2571	52556890	4897,8109	2203	4300	6503	SO:0001583	missense	23166	exon62			GTGGGCATAGTCA	AJ275213	CCDS33768.1	3p21.31	2008-07-18			ENSG00000010327	ENSG00000010327			18628	protein-coding gene	gene with protein product	"""MS-1 antigen"", ""fasciclin egf-like, laminin-type egf-like, and link domain-containing scavenger receptor-1"", ""common lymphatic endothelial and vascular endothelial receptor-1"""	608560				11829752, 12077138	Standard	XM_005264973		Approved	KIAA0246, STAB-1, FEEL-1, CLEVER-1, FELE-1, FEX1	uc003dej.3	Q9NY15	OTTHUMG00000158574	ENST00000321725.6:c.6844A>G	3.37:g.52556890A>G	ENSP00000312946:p.Ile2282Val	Somatic	236	1	0.00423729		WXS	Illumina HiSeq	Phase_I	243	241	0.99177	NM_015136	A7E297|Q8IUH0|Q8IUH1|Q93072	Missense_Mutation	SNP	ENST00000321725.6	37	CCDS33768.1	916	0.4194139194139194	87	0.17682926829268292	182	0.5027624309392266	288	0.5034965034965035	359	0.4736147757255937	a	11.31	1.602172	0.28534	0.187699	0.473256	ENSG00000010327	ENST00000321725	T	0.04275	3.66	5.73	-0.467	0.12150	C-type lectin fold (1);Link (3);C-type lectin-like (1);	0.477047	0.20847	N	0.084583	T	0.00012	0.0000	N	0.05510	-0.035	0.45554	P	0.001495000000000024	B	0.10296	0.003	B	0.13407	0.009	T	0.32929	-0.9888	9	0.22109	T	0.4	.	9.8647	0.41136	0.7551:0.0:0.2449:0.0	rs4434138	2282	Q9NY15	STAB1_HUMAN	V	2282	ENSP00000312946:I2282V	ENSP00000312946:I2282V	I	+	1	0	STAB1	52531930	0.993000	0.37304	0.151000	0.22473	0.838000	0.47535	1.215000	0.32431	-0.043000	0.13513	0.454000	0.30748	ATA	A|0.608;G|0.392	0.392	strong		0.627	STAB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351380.2	NM_015136	
PITRM1	10531	hgsc.bcm.edu	37	10	3181126	3181126	+	Missense_Mutation	SNP	C	C	T	rs17849904	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:3181126C>T	ENST00000224949.4	-	25	2921	c.2887G>A	c.(2887-2889)Gta>Ata	p.V963I	PITRM1-AS1_ENST00000601046.1_RNA|PITRM1_ENST00000380994.1_Missense_Mutation_p.V521I|PITRM1_ENST00000380989.2_Missense_Mutation_p.V964I|PITRM1_ENST00000451104.2_Missense_Mutation_p.V865I|PITRM1-AS1_ENST00000598280.1_RNA|PITRM1_ENST00000464395.1_5'UTR|PITRM1-AS1_ENST00000441377.1_RNA			Q5JRX3	PREP_HUMAN	pitrilysin metallopeptidase 1	963			V -> I (in dbSNP:rs17849904). {ECO:0000269|PubMed:15489334}.		positive regulation of catalytic activity (GO:0043085)|proteolysis (GO:0006508)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	enzyme activator activity (GO:0008047)|metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			breast(2)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(5)|liver(1)|lung(5)|ovary(1)|pancreas(1)|prostate(4)|skin(1)|stomach(2)|urinary_tract(3)	33						GGAGCATCTACGGTTGAGAAG	0.473													C|||	176	0.0351438	0.0038	0.0576	5008	,	,		21710	0.0		0.0944	False		,,,				2504	0.0368				p.V964I		Atlas-SNP	.											.	PITRM1	109	.	0			c.G2890A						PASS	.	C	ILE/VAL,ILE/VAL,ILE/VAL	44,3950		0,44,1953	188.0	188.0	188.0		2890,2593,2887	5.5	0.5	10	dbSNP_123	188	687,7663		19,649,3507	yes	missense,missense,missense	PITRM1	NM_001242307.1,NM_001242309.1,NM_014889.3	29,29,29	19,693,5460	TT,TC,CC		8.2275,1.1017,5.9219	benign,benign,benign	964/1039,865/940,963/1038	3181126	731,11613	1997	4175	6172	SO:0001583	missense	10531	exon25			CATCTACGGTTGA	AB029027	CCDS55699.1, CCDS55700.1, CCDS59208.1	10p15.2	2008-07-30	2005-08-17		ENSG00000107959	ENSG00000107959			17663	protein-coding gene	gene with protein product	"""PreP peptidasome"""		"""pitrilysin metalloproteinase 1"""			1036083, 10470851, 16849325	Standard	NM_014889		Approved	MP1, KIAA1104, hMP1, PreP	uc009xhv.2	Q5JRX3	OTTHUMG00000017557	ENST00000224949.4:c.2887G>A	10.37:g.3181126C>T	ENSP00000224949:p.Val963Ile	Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	160	85	0.53125	NM_001242307	B3KMJ6|B4E0J8|C9JSL2|E7ES23|O95204|Q2M2G6|Q4VBR1|Q5JRW7|Q7L5Z7|Q9BSI6|Q9BVJ5|Q9UPP8	Missense_Mutation	SNP	ENST00000224949.4	37	CCDS59208.1	100	0.045787545787545784	1	0.0020325203252032522	26	0.0718232044198895	0	0.0	73	0.09630606860158311	c	10.97	1.502821	0.26949	0.011017	0.082275	ENSG00000107959	ENST00000224949;ENST00000380980;ENST00000380989;ENST00000380994;ENST00000451104;ENST00000455371	T;T;T;T;T	0.08984	3.03;3.03;3.03;3.03;3.03	5.54	5.54	0.83059	Metalloenzyme, LuxS/M16 peptidase-like, metal-binding (1);	0.054483	0.64402	D	0.000001	T	0.00241	0.0007	L	0.39085	1.19	0.53688	D	0.999977	B;B;B;B;B;B	0.29270	0.061;0.24;0.073;0.073;0.185;0.073	B;B;B;B;B;B	0.21708	0.008;0.036;0.017;0.026;0.026;0.017	T	0.50154	-0.8861	10	0.15952	T	0.53	-27.7539	19.4783	0.94998	0.0:1.0:0.0:0.0	rs17849904;rs17849904	956;865;964;963;898;956	E9PDX6;E7ES23;C9JSL2;Q5JRX3;E9PDX7;B4DH07	.;.;.;PREP_HUMAN;.;.	I	963;956;964;521;865;144	ENSP00000224949:V963I;ENSP00000370377:V964I;ENSP00000370382:V521I;ENSP00000401201:V865I;ENSP00000399307:V144I	ENSP00000224949:V963I	V	-	1	0	PITRM1	3171126	1.000000	0.71417	0.497000	0.27552	0.022000	0.10575	5.252000	0.65445	2.598000	0.87819	0.462000	0.41574	GTA	C|0.954;T|0.046	0.046	strong		0.473	PITRM1-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000046469.2		
ASAP3	55616	hgsc.bcm.edu	37	1	23761028	23761028	+	Silent	SNP	G	G	A	rs11542556|rs74415268	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:23761028G>A	ENST00000336689.3	-	18	1877	c.1833C>T	c.(1831-1833)aaC>aaT	p.N611N	ASAP3_ENST00000437606.2_Silent_p.N602N|ASAP3_ENST00000495646.1_Silent_p.N115N	NM_017707.3	NP_060177.2	Q8TDY4	ASAP3_HUMAN	ArfGAP with SH3 domain, ankyrin repeat and PH domain 3	611					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						GCTCTCACCCGTTCTGGATGA	0.537													g|||	106	0.0211661	0.0061	0.0403	5008	,	,		17715	0.0		0.0437	False		,,,				2504	0.0266				p.N611N		Atlas-SNP	.											.	ASAP3	65	.	0			c.C1833T						PASS	.	A	,	67,4339	61.7+/-98.7	2,63,2138	89.0	90.0	90.0		1806,1833	-1.3	1.0	1	dbSNP_131	90	420,8180	131.2+/-189.0	5,410,3885	no	coding-synonymous,coding-synonymous	ASAP3	NM_001143778.1,NM_017707.3	,	7,473,6023	AA,AG,GG		4.8837,1.5207,3.7444	,	602/895,611/904	23761028	487,12519	2203	4300	6503	SO:0001819	synonymous_variant	55616	exon18			TCACCCGTTCTGG	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.1833C>T	1.37:g.23761028G>A		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	104	45	0.432692	NM_017707	B3KRW0|B4DHH4|Q6P9F4|Q86UY1|Q9NXK2	Silent	SNP	ENST00000336689.3	37	CCDS235.1																																																																																			G|0.969;A|0.031	0.031	strong		0.537	ASAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008916.2	NM_017707	
CFAP44	55779	hgsc.bcm.edu	37	3	113098217	113098217	+	Missense_Mutation	SNP	G	G	A	rs58988763	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:113098217G>A	ENST00000295868.2	-	17	2396	c.2234C>T	c.(2233-2235)cCg>cTg	p.P745L	WDR52_ENST00000393845.2_Missense_Mutation_p.P745L|WDR52_ENST00000475568.1_5'Flank	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						GGGGGTTGACGGAATAAATAT	0.428													.|||	227	0.0453275	0.0023	0.0159	5008	,	,		13431	0.1062		0.0398	False		,,,				2504	0.0675				p.P745L		Atlas-SNP	.											.	WDR52	151	.	0			c.C2234T						PASS	.	G	LEU/PRO,LEU/PRO	29,4377	35.2+/-66.4	0,29,2174	81.0	80.0	80.0		2234,2234	5.4	0.3	3	dbSNP_129	80	313,8287	112.3+/-172.5	6,301,3993	yes	missense,missense	WDR52	NM_001164496.1,NM_018338.3	98,98	6,330,6167	AA,AG,GG		3.6395,0.6582,2.6296	probably-damaging,probably-damaging	745/1855,745/983	113098217	342,12664	2203	4300	6503	SO:0001583	missense	55779	exon17			GTTGACGGAATAA																												ENST00000295868.2:c.2234C>T	3.37:g.113098217G>A	ENSP00000295868:p.Pro745Leu	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	37	19	0.513514	NM_001164496		Missense_Mutation	SNP	ENST00000295868.2	37	CCDS2972.1	91	0.041666666666666664	1	0.0020325203252032522	7	0.019337016574585635	53	0.09265734265734266	30	0.0395778364116095	G	16.74	3.207429	0.58343	0.006582	0.036395	ENSG00000206530	ENST00000393845;ENST00000295868	T;T	0.18174	2.23;2.23	5.42	5.42	0.78866	WD40 repeat-like-containing domain (1);	.	.	.	.	T	0.02380	0.0073	M	0.77313	2.365	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.00180	-1.1949	9	0.87932	D	0	.	19.0063	0.92852	0.0:0.0:1.0:0.0	rs58988763	745	Q96MT7	WDR52_HUMAN	L	745	ENSP00000377428:P745L;ENSP00000295868:P745L	ENSP00000295868:P745L	P	-	2	0	WDR52	114580907	1.000000	0.71417	0.291000	0.24904	0.112000	0.19704	6.997000	0.76270	2.826000	0.97356	0.563000	0.77884	CCG	G|0.969;A|0.031	0.031	strong		0.428	WDR52-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000354128.3		
DNA2	1763	hgsc.bcm.edu	37	10	70218913	70218913	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:70218913C>T	ENST00000358410.3	-	5	717	c.667G>A	c.(667-669)Gat>Aat	p.D223N	DNA2_ENST00000399179.2_Missense_Mutation_p.D223N|DNA2_ENST00000399180.2_Missense_Mutation_p.D309N|RNA5SP319_ENST00000362768.1_RNA	NM_001080449.2	NP_001073918.2	P51530	DNA2_HUMAN	DNA replication helicase/nuclease 2	223	Nuclease 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)	p.D223Y(1)|p.D309Y(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(7)|prostate(1)	20						TGCATGAAATCTCCTGCCCAT	0.338																																					p.D223N		Atlas-SNP	.											DNA2L,colon,carcinoma,0,2	DNA2	76	2	2	Substitution - Missense(2)	large_intestine(2)	c.G667A						scavenged	.						92.0	83.0	86.0					10																	70218913		1844	4099	5943	SO:0001583	missense	1763	exon5			TGAAATCTCCTGC	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.667G>A	10.37:g.70218913C>T	ENSP00000351185:p.Asp223Asn	Somatic	133	1	0.0075188		WXS	Illumina HiSeq	Phase_I	101	3	0.029703	NM_001080449	Q2NKM1|Q5TC49|Q5TC50|Q6P455|Q6PI80|Q7Z6H9|Q8N346	Missense_Mutation	SNP	ENST00000358410.3	37		.	.	.	.	.	.	.	.	.	.	C	13.63	2.294356	0.40594	.	.	ENSG00000138346	ENST00000551118;ENST00000399180;ENST00000399179;ENST00000358410	D;D;D	0.93712	-2.77;-3.27;-2.75	5.46	4.55	0.56014	DNA replication factor Dna2 (1);	0.554792	0.15548	N	0.256583	D	0.87779	0.6263	N	0.25380	0.74	0.41145	D	0.985983	B;P	0.36330	0.047;0.548	B;B	0.35727	0.021;0.209	D	0.85076	0.0943	10	0.22706	T	0.39	.	13.3218	0.60436	0.0:0.9229:0.0:0.077	.	223;223	F8VR31;P51530	.;DNA2L_HUMAN	N	223;309;223;223	ENSP00000382133:D309N;ENSP00000382132:D223N;ENSP00000351185:D223N	ENSP00000351185:D223N	D	-	1	0	DNA2	69888919	1.000000	0.71417	0.998000	0.56505	0.901000	0.52897	2.173000	0.42472	2.564000	0.86499	0.591000	0.81541	GAT	.	.	none		0.338	DNA2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000048334.2		
ZNF587	84914	hgsc.bcm.edu	37	19	58371274	58371274	+	Silent	SNP	G	G	T	rs10405892	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:58371274G>T	ENST00000339656.5	+	3	1676	c.1494G>T	c.(1492-1494)ggG>ggT	p.G498G	ZNF814_ENST00000595295.1_Intron|ZNF587_ENST00000423137.1_Silent_p.G497G|ZNF587_ENST00000419854.1_Silent_p.G455G|ZNF814_ENST00000597342.1_Intron|ZNF814_ENST00000597832.1_Intron|ZNF814_ENST00000596604.1_Intron|ZNF814_ENST00000597652.1_5'Flank	NM_001204817.1|NM_032828.3	NP_001191746.1|NP_116217.1	Q96SQ5	ZN587_HUMAN	zinc finger protein 587	498					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(1)|lung(4)|ovary(1)|pancreas(1)|stomach(1)	15		Colorectal(82;0.000256)|all_neural(62;0.0577)|Breast(46;0.147)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0264)		GTGAATGTGGGAAATCATTTC	0.408																																					p.G498G	Pancreas(59;641 1233 1885 20055 50741)	Atlas-SNP	.											ZNF587,NS,carcinoma,+2,1	ZNF587	53	1	0			c.G1494T						PASS	.						132.0	136.0	134.0					19																	58371274		2203	4300	6503	SO:0001819	synonymous_variant	84914	exon3			ATGTGGGAAATCA	AF294842	CCDS12964.1, CCDS56110.1	19q13.43	2013-01-08				ENSG00000198466		"""Zinc fingers, C2H2-type"", ""-"""	30955	protein-coding gene	gene with protein product						10520746	Standard	NM_032828		Approved	ZF6, FLJ14710, UBF-fl, FLJ20813	uc002qql.3	Q96SQ5	OTTHUMG00000154901	ENST00000339656.5:c.1494G>T	19.37:g.58371274G>T		Somatic	245	0	0		WXS	Illumina HiSeq	Phase_I	357	61	0.170868	NM_032828	A0AV72|G3V0H5|Q6ZMK8	Silent	SNP	ENST00000339656.5	37	CCDS12964.1																																																																																			G|0.822;T|0.178	0.178	strong		0.408	ZNF587-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337594.2	NM_032828	
MTX2	10651	hgsc.bcm.edu	37	2	177194090	177194090	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:177194090A>G	ENST00000249442.6	+	8	690	c.479A>G	c.(478-480)cAa>cGa	p.Q160R	MTX2_ENST00000392529.2_Missense_Mutation_p.Q150R|MTX2_ENST00000443241.1_Missense_Mutation_p.Q104R	NM_006554.4	NP_006545.1	O75431	MTX2_HUMAN	metaxin 2	160					cellular protein metabolic process (GO:0044267)|mitochondrial transport (GO:0006839)|protein targeting to mitochondrion (GO:0006626)	mitochondrial outer membrane (GO:0005741)				breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	12			OV - Ovarian serous cystadenocarcinoma(117;0.00365)|Epithelial(96;0.0654)|all cancers(119;0.181)			TTGGCCTATCAAAAACAGTGG	0.403																																					p.Q160R		Atlas-SNP	.											.	MTX2	25	.	0			c.A479G						PASS	.						110.0	109.0	110.0					2																	177194090		2203	4300	6503	SO:0001583	missense	10651	exon8			CCTATCAAAAACA	AF053551	CCDS2272.1	2q31.1	2012-02-07			ENSG00000128654	ENSG00000128654			7506	protein-coding gene	gene with protein product		608555				10381257, 17624330	Standard	NM_006554		Approved		uc002ukx.3	O75431	OTTHUMG00000132514	ENST00000249442.6:c.479A>G	2.37:g.177194090A>G	ENSP00000249442:p.Gln160Arg	Somatic	219	0	0		WXS	Illumina HiSeq	Phase_I	222	111	0.5	NM_006554	A8JZZ4|Q53S50|Q53SQ2|Q5M7Z6|Q8IZ68	Missense_Mutation	SNP	ENST00000249442.6	37	CCDS2272.1	.	.	.	.	.	.	.	.	.	.	A	10.81	1.456513	0.26161	.	.	ENSG00000128654	ENST00000249442;ENST00000392529;ENST00000443241	T;T;T	0.41758	0.99;0.99;0.99	5.19	5.19	0.71726	Glutathione S-transferase, C-terminal-like (1);	0.059658	0.64402	D	0.000001	T	0.26376	0.0644	N	0.17594	0.5	0.58432	D	0.999999	B;B	0.14012	0.002;0.009	B;B	0.09377	0.004;0.003	T	0.08700	-1.0709	10	0.09843	T	0.71	-0.1211	15.031	0.71708	1.0:0.0:0.0:0.0	.	160;150	O75431;Q8IZ68	MTX2_HUMAN;.	R	160;150;104	ENSP00000249442:Q160R;ENSP00000376314:Q150R;ENSP00000414176:Q104R	ENSP00000249442:Q160R	Q	+	2	0	MTX2	176902336	1.000000	0.71417	1.000000	0.80357	0.905000	0.53344	9.172000	0.94808	1.948000	0.56530	0.455000	0.32223	CAA	.	.	none		0.403	MTX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255695.4	NM_006554	
LGR4	55366	hgsc.bcm.edu	37	11	27390144	27390144	+	Missense_Mutation	SNP	G	G	A	rs34717439	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:27390144G>A	ENST00000379214.4	-	18	2569	c.2126C>T	c.(2125-2127)aCg>aTg	p.T709M	LGR4_ENST00000389858.4_Missense_Mutation_p.T685M	NM_018490.2	NP_060960.2	Q9BXB1	LGR4_HUMAN	leucine-rich repeat containing G protein-coupled receptor 4	709			T -> M (in dbSNP:rs34717439).		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						TAGCACTAACGTTACAGTGAA	0.403													G|||	157	0.0313498	0.0522	0.0375	5008	,	,		17626	0.003		0.0298	False		,,,				2504	0.0297				p.T709M		Atlas-SNP	.											LGR4,NS,carcinoma,+1,1	LGR4	87	1	0			c.C2126T						PASS	.	G	MET/THR	236,4168	139.2+/-174.8	7,222,1973	104.0	100.0	101.0		2126	5.6	0.7	11	dbSNP_126	101	284,8314	106.0+/-166.9	3,278,4018	yes	missense	LGR4	NM_018490.2	81	10,500,5991	AA,AG,GG		3.3031,5.3588,3.9994	probably-damaging	709/952	27390144	520,12482	2202	4299	6501	SO:0001583	missense	55366	exon18			ACTAACGTTACAG	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.2126C>T	11.37:g.27390144G>A	ENSP00000368516:p.Thr709Met	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	91	73	0.802198	NM_018490	A6NCH3|G5E9B3|Q8N537|Q9NYD1	Missense_Mutation	SNP	ENST00000379214.4	37	CCDS31449.1	57	0.0260989010989011	16	0.032520325203252036	20	0.055248618784530384	1	0.0017482517482517483	20	0.026385224274406333	G	15.27	2.784721	0.49997	0.053588	0.033031	ENSG00000205213	ENST00000379214;ENST00000389858	T;T	0.72615	1.18;-0.67	5.64	5.64	0.86602	GPCR, rhodopsin-like superfamily (1);	0.269864	0.42172	D	0.000757	T	0.35128	0.0921	L	0.42245	1.32	0.80722	D	1	D;D	0.71674	0.996;0.998	D;P	0.63192	0.912;0.862	T	0.66408	-0.5931	10	0.62326	D	0.03	.	19.6922	0.96007	0.0:0.0:1.0:0.0	rs34717439	685;709	G5E9B3;Q9BXB1	.;LGR4_HUMAN	M	709;685	ENSP00000368516:T709M;ENSP00000374508:T685M	ENSP00000368516:T709M	T	-	2	0	LGR4	27346720	0.997000	0.39634	0.686000	0.30086	0.683000	0.39861	6.294000	0.72738	2.658000	0.90341	0.555000	0.69702	ACG	G|0.965;A|0.035	0.035	strong		0.403	LGR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257467.1	NM_018490	
MFAP3	4238	hgsc.bcm.edu	37	5	153432733	153432733	+	Silent	SNP	T	T	C	rs2578386	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:153432733T>C	ENST00000436816.1	+	3	768	c.549T>C	c.(547-549)gcT>gcC	p.A183A	MFAP3_ENST00000322602.5_Silent_p.A183A|MFAP3_ENST00000439768.2_Silent_p.A37A	NM_001242336.1|NM_005927.4	NP_001229265.1|NP_005918.1	P55082	MFAP3_HUMAN	microfibrillar-associated protein 3	183					extracellular matrix organization (GO:0030198)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|kidney(2)|large_intestine(1)|lung(2)|pancreas(1)	7	Renal(175;0.00488)	Lung NSC(249;0.00145)|all_lung(500;0.00226)|all_neural(177;0.122)|Breast(839;0.14)	Kidney(363;0.000173)|KIRC - Kidney renal clear cell carcinoma(527;0.000785)	OV - Ovarian serous cystadenocarcinoma(192;9.69e-06)|GBM - Glioblastoma multiforme(465;0.0201)		CTGAGAAGGCTATCAATGAGT	0.443													C|||	3582	0.715256	0.6218	0.7161	5008	,	,		20321	0.8581		0.6252	False		,,,				2504	0.7863				p.A183A		Atlas-SNP	.											.	MFAP3	20	.	0			c.T549C						PASS	.	C	,,	2856,1550	489.2+/-361.4	930,996,277	75.0	70.0	72.0		111,549,549	0.9	1.0	5	dbSNP_100	72	5349,3251	488.5+/-372.4	1663,2023,614	no	coding-synonymous,coding-synonymous,coding-synonymous	MFAP3	NM_001135037.1,NM_001242336.1,NM_005927.4	,,	2593,3019,891	CC,CT,TT		37.8023,35.1793,36.9137	,,	37/217,183/363,183/363	153432733	8205,4801	2203	4300	6503	SO:0001819	synonymous_variant	4238	exon3			GAAGGCTATCAAT		CCDS4324.1, CCDS47319.1	5q32-q33.2	2013-01-11			ENSG00000037749	ENSG00000037749		"""Immunoglobulin superfamily / I-set domain containing"""	7034	protein-coding gene	gene with protein product		600491				7782085	Standard	NM_005927		Approved		uc010jib.2	P55082	OTTHUMG00000130149	ENST00000436816.1:c.549T>C	5.37:g.153432733T>C		Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	134	70	0.522388	NM_005927	B2RDK0|B4DKA1|Q9NXA7	Silent	SNP	ENST00000436816.1	37	CCDS4324.1																																																																																			T|0.347;C|0.653	0.653	strong		0.443	MFAP3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252457.2	NM_005927	
SULT2B1	6820	hgsc.bcm.edu	37	19	49102599	49102599	+	Missense_Mutation	SNP	C	C	T	rs17842463	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:49102599C>T	ENST00000201586.2	+	7	1212	c.1034C>T	c.(1033-1035)cCc>cTc	p.P345L	SULT2B1_ENST00000323090.4_Missense_Mutation_p.P330L	NM_177973.1	NP_814444.1	O00204	ST2B1_HUMAN	sulfotransferase family, cytosolic, 2B, member 1	345	Pro/Ser-rich.		P -> L (in dbSNP:rs17842463).		3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|sulfate assimilation (GO:0000103)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	alcohol sulfotransferase activity (GO:0004027)|steroid sulfotransferase activity (GO:0050294)			central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(2)|skin(2)|urinary_tract(1)	11		all_epithelial(76;2.38e-06)|all_lung(116;4.89e-06)|Lung NSC(112;9.34e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000115)|all cancers(93;0.000147)|GBM - Glioblastoma multiforme(486;0.00707)|Epithelial(262;0.0178)		GAGcccagacccaactccagc	0.662													C|||	43	0.00858626	0.0	0.0187	5008	,	,		10930	0.0		0.0278	False		,,,				2504	0.002				p.P345L		Atlas-SNP	.											.	SULT2B1	72	.	0			c.C1034T						PASS	.	C	LEU/PRO,LEU/PRO	10,4364		0,10,2177	28.0	20.0	23.0		989,1034	1.8	0.0	19	dbSNP_126	23	160,8420		0,160,4130	yes	missense,missense	SULT2B1	NM_004605.2,NM_177973.1	98,98	0,170,6307	TT,TC,CC		1.8648,0.2286,1.3123	probably-damaging,probably-damaging	330/351,345/366	49102599	170,12784	2187	4290	6477	SO:0001583	missense	6820	exon7			CCAGACCCAACTC	U92314	CCDS12723.1, CCDS12724.1	19q13.3	2008-02-05				ENSG00000088002		"""Sulfotransferases, cytosolic"""	11459	protein-coding gene	gene with protein product		604125				9799594	Standard	NM_177973		Approved	HSST2	uc002pjl.3	O00204		ENST00000201586.2:c.1034C>T	19.37:g.49102599C>T	ENSP00000201586:p.Pro345Leu	Somatic	207	0	0		WXS	Illumina HiSeq	Phase_I	204	83	0.406863	NM_177973	O00205|O75814	Missense_Mutation	SNP	ENST00000201586.2	37	CCDS12723.1	30	0.013736263736263736	0	0.0	8	0.022099447513812154	0	0.0	22	0.029023746701846966	C	13.73	2.323169	0.41096	0.002286	0.018648	ENSG00000088002	ENST00000201586;ENST00000323090	T;T	0.58060	0.36;0.36	1.83	1.83	0.25207	.	.	.	.	.	T	0.29223	0.0727	N	0.19112	0.55	0.09310	N	0.999999	D;D	0.76494	0.999;0.999	D;D	0.76575	0.988;0.972	T	0.18304	-1.0341	9	0.87932	D	0	.	7.3051	0.26443	0.0:1.0:0.0:0.0	rs17842463;rs45514997;rs58865188	330;345	O00204-2;O00204	.;ST2B1_HUMAN	L	345;330	ENSP00000201586:P345L;ENSP00000312880:P330L	ENSP00000201586:P345L	P	+	2	0	SULT2B1	53794411	0.000000	0.05858	0.020000	0.16555	0.052000	0.14988	-0.366000	0.07563	0.702000	0.31825	0.454000	0.30748	CCC	C|0.989;T|0.011	0.011	strong		0.662	SULT2B1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466140.1	NM_004605	
SERPINA6	866	hgsc.bcm.edu	37	14	94780608	94780608	+	Silent	SNP	G	G	A	rs3748320	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:94780608G>A	ENST00000341584.3	-	2	524	c.378C>T	c.(376-378)acC>acT	p.T126T		NM_001756.3	NP_001747	P08185	CBG_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 6	126					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)	CATTGCCCATGGTCATTTCTA	0.488													G|||	718	0.143371	0.1021	0.1254	5008	,	,		22183	0.0804		0.2416	False		,,,				2504	0.1759				p.T126T		Atlas-SNP	.											.	SERPINA6	102	.	0			c.C378T						PASS	.	G		580,3826	256.7+/-261.4	34,512,1657	79.0	76.0	77.0		378	2.1	0.0	14	dbSNP_107	77	1806,6794	325.4+/-316.9	212,1382,2706	no	coding-synonymous	SERPINA6	NM_001756.3		246,1894,4363	AA,AG,GG		21.0,13.1639,18.3454		126/406	94780608	2386,10620	2203	4300	6503	SO:0001819	synonymous_variant	866	exon2			GCCCATGGTCATT	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.378C>T	14.37:g.94780608G>A		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	122	44	0.360656	NM_001756	A8K456|Q7Z2Q9	Silent	SNP	ENST00000341584.3	37	CCDS9924.1																																																																																			G|0.833;A|0.167	0.167	strong		0.488	SERPINA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413065.1	NM_001756	
RBBP8NL	140893	hgsc.bcm.edu	37	20	60987921	60987921	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:60987921C>T	ENST00000252998.1	-	12	1867	c.1711G>A	c.(1711-1713)Gac>Aac	p.D571N		NM_080833.2	NP_543023.2	Q8NC74	RB8NL_HUMAN	RBBP8 N-terminal like	571						extracellular space (GO:0005615)											TCCAGTTCGTCGGACTCTGGT	0.657																																					p.D571N		Atlas-SNP	.											.	.	.	.	0			c.G1711A						PASS	.						129.0	106.0	114.0					20																	60987921		2203	4300	6503	SO:0001583	missense	140893	exon12			GTTCGTCGGACTC	AL121832	CCDS13498.1	20q13.33	2012-10-30	2012-10-30	2012-10-30	ENSG00000130701	ENSG00000130701			16144	protein-coding gene	gene with protein product	"""hypothetical protein LOC140893"""		"""chromosome 20 open reading frame 151"""	C20orf151		11780052	Standard	NM_080833		Approved	dJ908M14.3	uc002ycw.2	Q8NC74	OTTHUMG00000032913	ENST00000252998.1:c.1711G>A	20.37:g.60987921C>T	ENSP00000252998:p.Asp571Asn	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	81	31	0.382716	NM_080833	B2RP98|Q8N4Z9|Q9BR75|Q9H0Y9	Missense_Mutation	SNP	ENST00000252998.1	37	CCDS13498.1	.	.	.	.	.	.	.	.	.	.	C	15.48	2.846159	0.51164	.	.	ENSG00000130701	ENST00000252998	T	0.20598	2.06	3.52	2.56	0.30785	.	0.908502	0.09136	N	0.843633	T	0.19765	0.0475	L	0.46157	1.445	0.09310	N	1	D	0.61080	0.989	P	0.44447	0.45	T	0.12218	-1.0556	10	0.18276	T	0.48	-0.964	8.456	0.32899	0.0:0.8818:0.0:0.1182	.	571	Q8NC74	CT151_HUMAN	N	571	ENSP00000252998:D571N	ENSP00000252998:D571N	D	-	1	0	C20orf151	60421316	0.001000	0.12720	0.001000	0.08648	0.005000	0.04900	1.089000	0.30890	0.783000	0.33636	-0.339000	0.08088	GAC	.	.	none		0.657	RBBP8NL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080029.1	NM_080833	
STAC	6769	hgsc.bcm.edu	37	3	36422216	36422216	+	Silent	SNP	T	T	C	rs73052248	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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						scavenged	.	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	64	1	0.015625		WXS	Illumina HiSeq	Phase_I	81	51	0.62963	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	
PRSS33	260429	hgsc.bcm.edu	37	16	2834711	2834711	+	Silent	SNP	G	G	A	rs45570838	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:2834711G>A	ENST00000293851.5	-	6	936	c.777C>T	c.(775-777)aaC>aaT	p.N259N	PRSS33_ENST00000570702.1_Silent_p.N259N|PRSS33_ENST00000576886.1_3'UTR	NM_152891.2	NP_690851.2	Q8NF86	PRS33_HUMAN	protease, serine, 33	259	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular space (GO:0005615)	serine-type endopeptidase activity (GO:0004252)			prostate(1)	1						CCCCTGGACGGTTGGGCAGGG	0.637													G|||	190	0.0379393	0.003	0.0562	5008	,	,		16160	0.001		0.1302	False		,,,				2504	0.0153				p.N259N	NSCLC(194;489 2153 16702 19171 27758)	Atlas-SNP	.											PRSS33,NS,carcinoma,0,1	PRSS33	7	1	0			c.C777T						PASS	.			96,4036		0,96,1970	25.0	30.0	29.0		777	4.7	1.0	16	dbSNP_127	29	1099,7329		70,959,3185	no	coding-synonymous	PRSS33	NM_152891.2		70,1055,5155	AA,AG,GG		13.0399,2.3233,9.5143		259/281	2834711	1195,11365	2066	4214	6280	SO:0001819	synonymous_variant	260429	exon6			TGGACGGTTGGGC	AF536382	CCDS42110.1	16p13.3	2014-09-04			ENSG00000103355	ENSG00000103355		"""Serine peptidases / Serine peptidases"""	30405	protein-coding gene	gene with protein product		613797				12795636	Standard	NM_152891		Approved	EOS	uc002cro.1	Q8NF86	OTTHUMG00000177360	ENST00000293851.5:c.777C>T	16.37:g.2834711G>A		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	109	73	0.669725	NM_152891	A6NNQ3|Q8N171	Silent	SNP	ENST00000293851.5	37	CCDS42110.1																																																																																			G|0.934;A|0.066	0.066	strong		0.637	PRSS33-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436446.1	NM_152891	
GAS8	2622	hgsc.bcm.edu	37	16	90095573	90095573	+	Intron	SNP	C	C	T	rs77382359		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:90095573C>T	ENST00000268699.4	+	2	212				GAS8_ENST00000540721.1_Intron|GAS8_ENST00000536122.1_Intron|C16orf3_ENST00000408886.2_Missense_Mutation_p.V60I	NM_001481.2	NP_001472.1	O95995	GAS8_HUMAN	growth arrest-specific 8						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)		gggcaggctacggggcagctt	0.672																																					p.V60I		Atlas-SNP	.											C16orf3,rectum,carcinoma,0,1	C16orf3	14	1	0			c.G178A						scavenged	.						22.0	20.0	21.0					16																	90095573		2194	4299	6493	SO:0001627	intron_variant	750	exon1			AGGCTACGGGGCA	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.90+1443C>T	16.37:g.90095573C>T		Somatic	88	4	0.0454545		WXS	Illumina HiSeq	Phase_I	115	27	0.234783	NM_001214	B2RCT1|B7Z4U1|G3V1L5|Q2M234	Missense_Mutation	SNP	ENST00000268699.4	37	CCDS10992.1	.	.	.	.	.	.	.	.	.	.	c	0.708	-0.788068	0.02884	.	.	ENSG00000221819	ENST00000408886	T	0.47177	0.85	.	.	.	.	.	.	.	.	T	0.22244	0.0536	N	0.08118	0	0.09310	N	1	.	.	.	.	.	.	T	0.22208	-1.0223	4	.	.	.	.	.	.	.	.	68	O95177	CP003_HUMAN	I	60	ENSP00000386218:V60I	.	V	-	1	0	C16orf3	88623074	0.031000	0.19500	0.015000	0.15790	0.017000	0.09413	0.000000	0.12993	0.000000	0.14550	0.000000	0.15137	GTA	C|0.500;T|0.500	0.500	weak		0.672	GAS8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000272877.2		
SLC45A4	57210	hgsc.bcm.edu	37	8	142225990	142225990	+	Silent	SNP	G	G	A	rs2288998	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:142225990G>A	ENST00000024061.3	-	6	1963	c.1656C>T	c.(1654-1656)gtC>gtT	p.V552V	SLC45A4_ENST00000433583.2_Silent_p.V545V|SLC45A4_ENST00000517878.1_Silent_p.V603V|SLC45A4_ENST00000519067.1_Silent_p.V552V	NM_001080431.1	NP_001073900.1	Q5BKX6	S45A4_HUMAN	solute carrier family 45, member 4						transport (GO:0006810)	integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(6)|lung(9)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	31	all_cancers(97;1.52e-15)|all_epithelial(106;2.92e-14)|Lung NSC(106;1.23e-05)|all_lung(105;1.75e-05)|Ovarian(258;0.01)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0493)			CGGCTGTGCCGACAGAGAAGC	0.587													G|||	1486	0.296725	0.3464	0.1801	5008	,	,		17140	0.4355		0.2604	False		,,,				2504	0.2065				p.V552V		Atlas-SNP	.											.	SLC45A4	71	.	0			c.C1656T						PASS	.	G		1523,2883	484.2+/-360.0	260,1003,940	168.0	114.0	132.0		1656	-7.1	0.0	8	dbSNP_100	132	2136,6464	367.3+/-334.7	264,1608,2428	no	coding-synonymous	SLC45A4	NM_001080431.1		524,2611,3368	AA,AG,GG		24.8372,34.5665,28.1332		552/799	142225990	3659,9347	2203	4300	6503	SO:0001819	synonymous_variant	57210	exon6			TGTGCCGACAGAG	AB032952	CCDS34948.1, CCDS69550.1, CCDS75795.1	8q24.3	2013-05-22						"""Solute carriers"""	29196	protein-coding gene	gene with protein product							Standard	NM_001080431		Approved	KIAA1126	uc003ywd.1	Q5BKX6		ENST00000024061.3:c.1656C>T	8.37:g.142225990G>A		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	83	10	0.120482	NM_001080431	Q6ZRI2|Q9ULU3	Silent	SNP	ENST00000024061.3	37	CCDS34948.1																																																																																			G|0.706;A|0.294	0.294	strong		0.587	SLC45A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378571.3	XM_050325	
ATP13A5	344905	hgsc.bcm.edu	37	3	193081122	193081122	+	Missense_Mutation	SNP	G	G	T	rs12637558	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:193081122G>T	ENST00000342358.4	-	3	404	c.287C>A	c.(286-288)tCc>tAc	p.S96Y		NM_198505.2	NP_940907.2	Q4VNC0	AT135_HUMAN	ATPase type 13A5	96			S -> Y (in dbSNP:rs12637558). {ECO:0000269|PubMed:14702039}.			integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|metal ion binding (GO:0046872)	p.S96F(1)|p.S96Y(1)		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)		CTTCAGTGTGGATAAGTAGAG	0.398													G|||	2083	0.415935	0.2133	0.4337	5008	,	,		18153	0.5764		0.4125	False		,,,				2504	0.5153				p.S96Y		Atlas-SNP	.											ATP13A5,NS,carcinoma,0,2	ATP13A5	171	2	2	Substitution - Missense(2)	ovary(1)|NS(1)	c.C287A						PASS	.	G	TYR/SER	1146,3260	409.1+/-334.9	155,836,1212	98.0	96.0	97.0		287	4.2	1.0	3	dbSNP_120	97	3666,4934	527.1+/-381.1	807,2052,1441	yes	missense	ATP13A5	NM_198505.2	144	962,2888,2653	TT,TG,GG		42.6279,26.01,36.9983	probably-damaging	96/1219	193081122	4812,8194	2203	4300	6503	SO:0001583	missense	344905	exon3			AGTGTGGATAAGT	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.287C>A	3.37:g.193081122G>T	ENSP00000341942:p.Ser96Tyr	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	70	70	1	NM_198505	Q6UWS4|Q6ZWL0	Missense_Mutation	SNP	ENST00000342358.4	37	CCDS33914.1	893	0.4088827838827839	119	0.241869918699187	143	0.39502762430939226	323	0.5646853146853147	308	0.40633245382585753	G	16.92	3.255259	0.59321	0.2601	0.426279	ENSG00000187527	ENST00000342358;ENST00000446087	T;T	0.44881	0.91;0.91	5.06	4.17	0.49024	.	0.195010	0.36893	N	0.002353	T	0.00012	0.0000	M	0.73962	2.25	0.29320	P	0.867429	P	0.36733	0.567	B	0.41764	0.366	T	0.48980	-0.8986	9	0.59425	D	0.04	-6.0887	13.2983	0.60311	0.0:0.0:0.84:0.16	rs12637558;rs59613984	96	Q4VNC0	AT135_HUMAN	Y	96;118	ENSP00000341942:S96Y;ENSP00000389416:S118Y	ENSP00000341942:S96Y	S	-	2	0	ATP13A5	194563816	1.000000	0.71417	0.987000	0.45799	0.953000	0.61014	3.546000	0.53656	1.428000	0.47296	0.655000	0.94253	TCC	G|0.618;T|0.382	0.382	strong		0.398	ATP13A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343012.1	NM_198505	
TEK	7010	hgsc.bcm.edu	37	9	27197486	27197486	+	Missense_Mutation	SNP	G	G	T	rs35030851	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:27197486G>T	ENST00000380036.4	+	12	2240	c.1798G>T	c.(1798-1800)Gtg>Ttg	p.V600L	RNA5SP280_ENST00000411230.1_RNA|TEK_ENST00000406359.4_Missense_Mutation_p.V557L|TEK_ENST00000519097.1_Missense_Mutation_p.V453L	NM_000459.3	NP_000450	Q02763	TIE2_HUMAN	TEK tyrosine kinase, endothelial	600	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.		V -> L (in dbSNP:rs35030851). {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)	CTTGACTTCGGTGCTACTTAA	0.468													G|||	169	0.033746	0.0038	0.0317	5008	,	,		8955	0.0456		0.0477	False		,,,				2504	0.0491				p.V600L		Atlas-SNP	.											.	TEK	250	.	0			c.G1798T						PASS	.	G	LEU/VAL	49,4357	49.6+/-84.7	0,49,2154	101.0	90.0	94.0		1798	4.6	0.4	9	dbSNP_126	94	415,8185	129.7+/-187.7	11,393,3896	yes	missense	TEK	NM_000459.3	32	11,442,6050	TT,TG,GG		4.8256,1.1121,3.5676	benign	600/1125	27197486	464,12542	2203	4300	6503	SO:0001583	missense	7010	exon12			ACTTCGGTGCTAC	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.1798G>T	9.37:g.27197486G>T	ENSP00000369375:p.Val600Leu	Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	152	70	0.460526	NM_000459	A8K6W0|B4DH20|B4DHD3|D3DRK5|E7EWI2|Q5TCU2|Q8IV34	Missense_Mutation	SNP	ENST00000380036.4	37	CCDS6519.1	89	0.04075091575091575	4	0.008130081300813009	16	0.04419889502762431	32	0.055944055944055944	37	0.048812664907651716	G	9.302	1.053453	0.19907	0.011121	0.048256	ENSG00000120156	ENST00000519097;ENST00000380036;ENST00000406359;ENST00000519080	T;T;T;T	0.58940	0.3;0.3;0.3;0.3	5.54	4.64	0.57946	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.154769	0.30177	N	0.010223	T	0.04092	0.0114	N	0.08118	0	0.09310	N	1	B;B;B;B	0.06786	0.001;0.0;0.0;0.001	B;B;B;B	0.12156	0.007;0.006;0.001;0.005	T	0.02766	-1.1113	10	0.32370	T	0.25	.	5.5366	0.17016	0.0735:0.3449:0.4516:0.13	rs35030851	453;633;557;600	E7EWI2;Q59HG2;B4DHD3;Q02763	.;.;.;TIE2_HUMAN	L	453;600;557;410	ENSP00000430686:V453L;ENSP00000369375:V600L;ENSP00000383977:V557L;ENSP00000428337:V410L	ENSP00000369375:V600L	V	+	1	0	TEK	27187486	0.946000	0.32159	0.395000	0.26283	0.964000	0.63967	1.541000	0.36126	1.340000	0.45581	0.655000	0.94253	GTG	G|0.961;T|0.039	0.039	strong		0.468	TEK-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051965.3		
LINC00283	100874057	hgsc.bcm.edu	37	13	103399837	103399837	+	RNA	SNP	C	C	A	rs58265842	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:103399837C>A	ENST00000430111.1	+	0	3894									long intergenic non-protein coding RNA 283																		TAATTTCCTGCCTTTTAAAAT	0.323													C|||	695	0.138778	0.2678	0.0807	5008	,	,		18615	0.0139		0.1252	False		,,,				2504	0.1483				p.R1070S		Atlas-SNP	.											.	.	.	.	0			c.G3210T						PASS	.	C	SER/ARG	286,1098		35,216,441	49.0	41.0	44.0		3210	0.6	0.0	13	dbSNP_129	44	383,2797		22,339,1229	yes	missense	CCDC168	NM_001146197.1	110	57,555,1670	AA,AC,CC		12.044,20.6647,14.6582		1070/7082	103399837	669,3895	692	1590	2282			643677	exon4			TTCCTGCCTTTTA			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.103399837C>A		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	82	37	0.451219	NM_001146197		Missense_Mutation	SNP	ENST00000430111.1	37																																																																																				C|0.875;A|0.125	0.125	strong		0.323	LINC00283-001	KNOWN	not_organism_supported|basic	antisense	antisense	OTTHUMT00000045714.1		
MKI67	4288	hgsc.bcm.edu	37	10	129906980	129906980	+	Missense_Mutation	SNP	C	C	T	rs2152143	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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						PASS	.	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	297	0	0		WXS	Illumina HiSeq	Phase_I	247	120	0.48583	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	
MDN1	23195	hgsc.bcm.edu	37	6	90368380	90368380	+	Silent	SNP	G	G	A	rs34732313	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	191	0	0		WXS	Illumina HiSeq	Phase_I	132	74	0.560606	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		
TENC1	23371	hgsc.bcm.edu	37	12	53457618	53457618	+	Silent	SNP	C	C	T	rs12816417	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:53457618C>T	ENST00000314250.6	+	29	4472	c.4182C>T	c.(4180-4182)ggC>ggT	p.G1394G	TENC1_ENST00000546602.1_Silent_p.G1297G|TENC1_ENST00000552570.1_Silent_p.G1392G|TENC1_ENST00000451358.1_Silent_p.G1384G|TENC1_ENST00000379902.3_Silent_p.G1270G|TENC1_ENST00000549700.1_Silent_p.G1329G|TENC1_ENST00000314276.3_Silent_p.G1404G	NM_170754.2	NP_736610.2	Q63HR2	TENC1_HUMAN	tensin like C1 domain containing phosphatase (tensin 2)	1394					cellular homeostasis (GO:0019725)|collagen metabolic process (GO:0032963)|intracellular signal transduction (GO:0035556)|kidney development (GO:0001822)|multicellular organism growth (GO:0035264)|multicellular organismal homeostasis (GO:0048871)|negative regulation of cell proliferation (GO:0008285)|response to muscle activity (GO:0014850)	focal adhesion (GO:0005925)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|phosphoprotein phosphatase activity (GO:0004721)	p.G1394G(1)		central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(2)|lung(19)|ovary(1)|pancreas(1)|stomach(3)	34						AGCCTGCTGGCGCCATTGTCA	0.562													C|||	322	0.0642971	0.0053	0.0519	5008	,	,		15217	0.1935		0.0636	False		,,,				2504	0.0204				p.G1404G		Atlas-SNP	.											TENC1,NS,carcinoma,0,1	TENC1	148	1	1	Substitution - coding silent(1)	stomach(1)	c.C4212T						PASS	.	C	,,	50,4356	50.9+/-86.3	0,50,2153	111.0	113.0	112.0		4212,4182,3810	-6.6	0.7	12	dbSNP_121	112	564,8036	153.3+/-207.7	14,536,3750	no	coding-synonymous,coding-synonymous,coding-synonymous	TENC1	NM_015319.2,NM_170754.2,NM_198316.1	,,	14,586,5903	TT,TC,CC		6.5581,1.1348,4.7209	,,	1404/1420,1394/1410,1270/1286	53457618	614,12392	2203	4300	6503	SO:0001819	synonymous_variant	23371	exon29			TGCTGGCGCCATT	AF518729	CCDS8842.1, CCDS8843.1, CCDS8844.1	12q13.13	2013-02-14	2004-03-05			ENSG00000111077		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"", ""SH2 domain containing"""	19737	protein-coding gene	gene with protein product	"""tensin 2"""	607717	"""tensin like C1 domain-containing phosphatase"""				Standard	NM_015319		Approved	KIAA1075, C1-TEN, TNS2	uc001sbp.3	Q63HR2	OTTHUMG00000169730	ENST00000314250.6:c.4182C>T	12.37:g.53457618C>T		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	70	35	0.5	NM_015319	A2VDF2|A2VDF3|A2VDI8|A5PKY4|Q2NL80|Q76MW6|Q7Z5T9|Q8NFF9|Q8NFG0|Q96P25|Q9NT29|Q9UPS7	Silent	SNP	ENST00000314250.6	37	CCDS8843.1																																																																																			C|0.938;T|0.062	0.062	strong		0.562	TENC1-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405779.1	NM_170754	
PCDHB10	56126	hgsc.bcm.edu	37	5	140573439	140573439	+	Silent	SNP	G	G	C	rs610836	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:140573439G>C	ENST00000239446.4	+	1	1498	c.1314G>C	c.(1312-1314)acG>acC	p.T438T		NM_018930.3	NP_061753.1	Q9UN67	PCDBA_HUMAN	protocadherin beta 10	438	Cadherin 4. {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)			ACAACATAACGGTCCTGGTCT	0.587													C|||	2442	0.48762	0.5076	0.5461	5008	,	,		14303	0.5685		0.4076	False		,,,				2504	0.4182				p.T438T		Atlas-SNP	.											.	PCDHB10	177	.	0			c.G1314C						PASS	.						82.0	79.0	80.0					5																	140573439		2203	4298	6501	SO:0001819	synonymous_variant	56126	exon1			CATAACGGTCCTG	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.1314G>C	5.37:g.140573439G>C		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	149	69	0.463087	NM_018930	Q96T99	Silent	SNP	ENST00000239446.4	37	CCDS4252.1																																																																																			G|0.551;C|0.449	0.449	strong		0.587	PCDHB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251821.1	NM_018930	
C5orf60	285679	hgsc.bcm.edu	37	5	179071892	179071892	+	Missense_Mutation	SNP	C	C	T	rs4990389	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:179071892C>T	ENST00000448248.2	-	1	155	c.130G>A	c.(130-132)Gtt>Att	p.V44I	C5orf60_ENST00000506142.1_Intron	NM_001142306.1	NP_001135778.1	A6NFR6	CE060_HUMAN	chromosome 5 open reading frame 60	44						integral component of membrane (GO:0016021)		p.V44I(2)		NS(1)|breast(1)|kidney(5)	7						CTGAACACAACAAAGAGGACG	0.517													-|||	83	0.0165735	0.0575	0.0058	5008	,	,		23834	0.0		0.002	False		,,,				2504	0.001				p.V44I		Atlas-SNP	.											C5orf60,NS,carcinoma,0,2	C5orf60	24	2	2	Substitution - Missense(2)	kidney(2)	c.G130A						scavenged	.						91.0	85.0	87.0					5																	179071892		692	1591	2283	SO:0001583	missense	285679	exon1			ACACAACAAAGAG	BC043435	CCDS47353.1	5q35.3	2010-08-19			ENSG00000204661	ENSG00000204661			27753	protein-coding gene	gene with protein product						12477932	Standard	NM_001142306		Approved		uc003mki.3	A6NFR6	OTTHUMG00000163221	ENST00000448248.2:c.130G>A	5.37:g.179071892C>T	ENSP00000404583:p.Val44Ile	Somatic	329	1	0.00303951		WXS	Illumina HiSeq	Phase_I	232	10	0.0431034	NM_001142306	A1L488|B7ZM52|B7ZM53	Missense_Mutation	SNP	ENST00000448248.2	37	CCDS47353.1	14	0.00641025641025641	10	0.02032520325203252	1	0.0027624309392265192	0	0.0	3	0.00395778364116095	N	0.001	-2.963530	0.00049	.	.	ENSG00000204661	ENST00000448248	T	0.23552	1.9	0.526	-1.05	0.10036	.	.	.	.	.	T	0.03827	0.0108	N	0.08118	0	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.27262	-1.0079	8	0.10902	T	0.67	.	.	.	.	rs4990389;rs7731272	44;44	A6NFR6-2;A6NFR6-4	.;.	I	44	ENSP00000404583:V44I	ENSP00000404583:V44I	V	-	1	0	C5orf60	179004498	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.627000	0.02033	-2.544000	0.00483	-2.140000	0.00339	GTT	C|0.994;T|0.006	0.006	strong		0.517	C5orf60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372148.2	NM_001142306	
SPATA31E1	286234	hgsc.bcm.edu	37	9	90500405	90500405	+	Missense_Mutation	SNP	A	A	C	rs7850542	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:90500405A>C	ENST00000325643.5	+	4	1069	c.1003A>C	c.(1003-1005)Acc>Ccc	p.T335P		NM_178828.4	NP_849150.3	Q6ZUB1	S31E1_HUMAN	SPATA31 subfamily E, member 1	335			T -> P (in dbSNP:rs7850542). {ECO:0000269|PubMed:14702039}.		cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											TCCCGACCACACCTCAGAGGC	0.607													.|||	3815	0.761781	0.9493	0.7205	5008	,	,		17626	0.878		0.5686	False		,,,				2504	0.6166				p.T335P		Atlas-SNP	.											.	.	.	.	0			c.A1003C						PASS	.	C	PRO/THR	3880,526		1715,450,38	51.0	54.0	53.0		1003	0.5	0.0	9	dbSNP_116	53	4657,3943		1278,2101,921	yes	missense	C9orf79	NM_178828.4	38	2993,2551,959	CC,CA,AA		45.8488,11.9383,34.3611	benign	335/1446	90500405	8537,4469	2203	4300	6503	SO:0001583	missense	286234	exon4			GACCACACCTCAG	AK093185	CCDS6676.1	9q22.1-q22.2	2012-10-12	2012-10-12	2012-10-12	ENSG00000177992	ENSG00000177992			26672	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 79"", ""family with sequence similarity 75, member E1"""	C9orf79, FAM75E1			Standard	NM_178828		Approved	FLJ35866	uc004app.4	Q6ZUB1	OTTHUMG00000020157	ENST00000325643.5:c.1003A>C	9.37:g.90500405A>C	ENSP00000322640:p.Thr335Pro	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	71	40	0.56338	NM_178828	B2RPB1|Q5SQC9|Q8NA41|Q8ND27	Missense_Mutation	SNP	ENST00000325643.5	37	CCDS6676.1	1645	0.7532051282051282	461	0.9369918699186992	256	0.7071823204419889	499	0.8723776223776224	429	0.5659630606860159	.	0.010	-1.795530	0.00617	0.880617	0.541512	ENSG00000177992	ENST00000325643	T	0.02944	4.1	2.72	0.534	0.17127	.	1.049360	0.07604	N	0.924180	T	0.00012	0.0000	N	0.00086	-2.195	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.27020	-1.0086	9	0.02654	T	1	.	3.2309	0.06747	0.4565:0.3991:0.0:0.1444	rs7850542;rs17536335;rs58031507;rs7850542	335	Q6ZUB1	CI079_HUMAN	P	335	ENSP00000322640:T335P	ENSP00000322640:T335P	T	+	1	0	C9orf79	89690225	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	-0.432000	0.06956	0.071000	0.16664	-0.224000	0.12420	ACC	A|0.303;C|0.697	0.697	strong		0.607	SPATA31E1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052954.2	NM_178828	
CRAMP1L	57585	hgsc.bcm.edu	37	16	1664931	1664931	+	Silent	SNP	T	T	C	rs11539468|rs7201813	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:1664931T>C	ENST00000397412.3	+	2	390	c.291T>C	c.(289-291)gaT>gaC	p.D97D	CRAMP1L_ENST00000293925.5_Silent_p.D97D|CRAMP1L_ENST00000436138.3_Silent_p.D97D|IFT140_ENST00000426508.2_5'Flank			Q96RY5	CRML_HUMAN	Crm, cramped-like (Drosophila)	97						nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(3)|lung(6)|pancreas(1)	22						CCAGGAAGGATCCTCCGAGCG	0.761													C|||	3511	0.701078	0.9092	0.6383	5008	,	,		9970	0.7371		0.4016	False		,,,				2504	0.7352				p.D97D		Atlas-SNP	.											.	CRAMP1L	60	.	0			c.T291C						PASS	.						5.0	9.0	8.0					16																	1664931		639	1533	2172	SO:0001819	synonymous_variant	57585	exon1			GAAGGATCCTCCG	AB037847	CCDS10440.2	16p13.3	2008-07-30	2001-11-28		ENSG00000007545	ENSG00000007545			14122	protein-coding gene	gene with protein product			"""Crm (Cramped Drosophila)-like"""				Standard	NM_020825		Approved	KIAA1426	uc010uvh.2	Q96RY5	OTTHUMG00000074087	ENST00000397412.3:c.291T>C	16.37:g.1664931T>C		Somatic	8	0	0		WXS	Illumina HiSeq	Phase_I	7	7	1	NM_020825	A8MZL1|B1AJY1|Q8NDN1|Q9P2C1	Silent	SNP	ENST00000397412.3	37	CCDS10440.2																																																																																			T|0.365;C|0.635	0.635	strong		0.761	CRAMP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157297.4		
HIST1H2AC	8334	hgsc.bcm.edu	37	6	26124805	26124805	+	Silent	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:26124805G>A	ENST00000602637.1	+	1	375	c.345G>A	c.(343-345)gtG>gtA	p.V115V	HIST1H2BC_ENST00000396984.1_5'Flank|HIST1H2BC_ENST00000314332.5_5'Flank|HIST1H2AC_ENST00000377791.2_Silent_p.V115V			Q93077	H2A1C_HUMAN	histone cluster 1, H2ac	115						extracellular vesicular exosome (GO:0070062)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(4)|lung(5)	12						TCCAGGCCGTGCTTCTGCCTA	0.562																																					p.V115V		Atlas-SNP	.											.	HIST1H2AC	29	.	0			c.G345A						PASS	.						82.0	82.0	82.0					6																	26124805		2203	4300	6503	SO:0001819	synonymous_variant	8334	exon1			GGCCGTGCTTCTG	Z80778	CCDS4585.1	6p22.1	2011-01-27	2006-10-11	2003-02-21	ENSG00000180573	ENSG00000180573		"""Histones / Replication-dependent"""	4733	protein-coding gene	gene with protein product		602794	"""H2A histone family, member L"", ""histone 1, H2ac"""	H2AFL		9119399, 12408966	Standard	NM_003512		Approved		uc003ngm.3	Q93077	OTTHUMG00000014428	ENST00000602637.1:c.345G>A	6.37:g.26124805G>A		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	128	40	0.3125	NM_003512	B2R4F7|O00775|O00776|O00777|O00778|Q540R1	Silent	SNP	ENST00000602637.1	37	CCDS4585.1																																																																																			.	.	none		0.562	HIST1H2AC-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000468023.1	NM_003512	
ESYT2	57488	hgsc.bcm.edu	37	7	158534381	158534381	+	Silent	SNP	G	G	C	rs59980573	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	104	0	0		WXS	Illumina HiSeq	Phase_I	78	39	0.5	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	
PFN4	375189	hgsc.bcm.edu	37	2	24342505	24342505	+	Silent	SNP	T	T	C	rs1056122	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:24342505T>C	ENST00000313213.4	-	4	674	c.303A>G	c.(301-303)gtA>gtG	p.V101V	PFN4_ENST00000465360.1_5'UTR	NM_199346.1	NP_955378.1	Q8NHR9	PROF4_HUMAN	profilin family, member 4	101					actin cytoskeleton organization (GO:0030036)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	lipid binding (GO:0008289)			breast(1)|kidney(1)|large_intestine(1)|lung(1)|ovary(1)|pancreas(1)	6	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TGTAAGTTGCTACCAGAAGAT	0.453													C|||	1387	0.276957	0.2133	0.2075	5008	,	,		18510	0.1528		0.3738	False		,,,				2504	0.4407				p.V101V		Atlas-SNP	.											.	PFN4	16	.	0			c.A303G						PASS	.	C		1091,3315	721.9+/-409.2	129,833,1241	137.0	124.0	129.0		303	5.4	1.0	2	dbSNP_86	129	3051,5549	661.9+/-401.9	537,1977,1786	no	coding-synonymous	PFN4	NM_199346.1		666,2810,3027	CC,CT,TT		35.4767,24.7617,31.8468		101/130	24342505	4142,8864	2203	4300	6503	SO:0001819	synonymous_variant	375189	exon4			AGTTGCTACCAGA	BC029523	CCDS1709.1	2p24.1	2008-02-05			ENSG00000176732	ENSG00000176732			31103	protein-coding gene	gene with protein product							Standard	NM_199346		Approved		uc002rfa.1	Q8NHR9	OTTHUMG00000090816	ENST00000313213.4:c.303A>G	2.37:g.24342505T>C		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	42	19	0.452381	NM_199346	Q53TL9	Silent	SNP	ENST00000313213.4	37	CCDS1709.1																																																																																			T|0.709;C|0.291	0.291	strong		0.453	PFN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207617.2	NM_199346	
ASGR1	432	hgsc.bcm.edu	37	17	7080316	7080316	+	Silent	SNP	C	C	T	rs55714927	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:7080316C>T	ENST00000269299.3	-	4	666	c.267G>A	c.(265-267)aaG>aaA	p.K89K	ASGR1_ENST00000574388.1_Silent_p.K50K|ASGR1_ENST00000380920.4_5'UTR|ASGR1_ENST00000572879.1_5'UTR	NM_001197216.2|NM_001671.4	NP_001184145.1|NP_001662.1	P07306	ASGR1_HUMAN	asialoglycoprotein receptor 1	89					cellular response to extracellular stimulus (GO:0031668)|receptor-mediated endocytosis (GO:0006898)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	asialoglycoprotein receptor activity (GO:0004873)|carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(3)|skin(1)|urinary_tract(1)	10						TGCTCAAGCCCTTGACCTGGG	0.706													C|||	866	0.172923	0.0469	0.2839	5008	,	,		6394	0.3165		0.1839	False		,,,				2504	0.1053				p.K89K		Atlas-SNP	.											.	ASGR1	20	.	0			c.G267A						PASS	.	C	,	314,4092		8,298,1897	30.0	29.0	29.0		150,267	3.9	0.7	17	dbSNP_129	29	1525,7075		139,1247,2914	no	coding-synonymous,coding-synonymous	ASGR1	NM_001197216.2,NM_001671.4	,	147,1545,4811	TT,TC,CC		17.7326,7.1266,14.1396	,	50/253,89/292	7080316	1839,11167	2203	4300	6503	SO:0001819	synonymous_variant	432	exon4			CAAGCCCTTGACC		CCDS11089.1, CCDS56017.1	17p13-p11	2011-08-30			ENSG00000141505	ENSG00000141505		"""C-type lectin domain containing"""	742	protein-coding gene	gene with protein product		108360					Standard	NM_001671		Approved	CLEC4H1	uc002ges.4	P07306	OTTHUMG00000102159	ENST00000269299.3:c.267G>A	17.37:g.7080316C>T		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	97	54	0.556701	NM_001671	I3L1X1	Silent	SNP	ENST00000269299.3	37	CCDS11089.1																																																																																			C|0.844;T|0.156	0.156	strong		0.706	ASGR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000220004.3	NM_001671	
SCN3B	55800	hgsc.bcm.edu	37	11	123513161	123513161	+	Silent	SNP	G	G	A	rs1275085	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:123513161G>A	ENST00000392770.2	-	3	1240	c.438C>T	c.(436-438)acC>acT	p.T146T	SCN3B_ENST00000530277.1_Silent_p.T146T|SCN3B_ENST00000299333.3_Silent_p.T146T	NM_018400.3	NP_060870.1	Q9NY72	SCN3B_HUMAN	sodium channel, voltage-gated, type III, beta subunit	146	Ig-like C2-type.				atrial cardiac muscle cell action potential (GO:0086014)|axon guidance (GO:0007411)|cardiac muscle cell action potential involved in contraction (GO:0086002)|cardiac muscle contraction (GO:0060048)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|positive regulation of heart rate (GO:0010460)|positive regulation of sodium ion transport (GO:0010765)|protein localization to plasma membrane (GO:0072659)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of sodium ion transmembrane transporter activity (GO:2000649)|regulation of ventricular cardiac muscle cell membrane depolarization (GO:0060373)|SA node cell to atrial cardiac muscle cell communication (GO:0086070)|sensory perception of pain (GO:0019233)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|ventricular cardiac muscle cell action potential (GO:0086005)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)|Z disc (GO:0030018)	ion channel binding (GO:0044325)|sodium channel regulator activity (GO:0017080)|voltage-gated sodium channel activity (GO:0005248)|voltage-gated sodium channel activity involved in cardiac muscle cell action potential (GO:0086006)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(16)|ovary(2)|skin(2)	26		Breast(109;0.00204)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;5.37e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0227)	Valproic Acid(DB00313)|Zonisamide(DB00909)	CACCCTCCTCGGTGACTCTTA	0.587													G|||	411	0.0820687	0.0953	0.0634	5008	,	,		18757	0.004		0.0984	False		,,,				2504	0.1411				p.T146T		Atlas-SNP	.											.	SCN3B	53	.	0			c.C438T						PASS	.	G	,	403,4001	200.1+/-223.5	15,373,1814	54.0	53.0	53.0		438,438	-9.2	0.8	11	dbSNP_87	53	770,7828	182.2+/-230.7	35,700,3564	no	coding-synonymous,coding-synonymous	SCN3B	NM_001040151.1,NM_018400.3	,	50,1073,5378	AA,AG,GG		8.9556,9.1508,9.0217	,	146/216,146/216	123513161	1173,11829	2202	4299	6501	SO:0001819	synonymous_variant	55800	exon3			CTCCTCGGTGACT	AJ243396	CCDS8442.1	11q24.1	2014-09-17	2012-02-28		ENSG00000166257	ENSG00000166257		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"", ""Immunoglobulin superfamily / V-set domain containing"""	20665	protein-coding gene	gene with protein product		608214	"""sodium channel, voltage-gated, type III, beta"""			10688874	Standard	XR_428980		Approved	HSA243396	uc001pzb.1	Q9NY72	OTTHUMG00000166006	ENST00000392770.2:c.438C>T	11.37:g.123513161G>A		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	66	55	0.833333	NM_018400	A5H1I5|Q17RL3|Q9ULR2	Silent	SNP	ENST00000392770.2	37	CCDS8442.1																																																																																			G|0.914;A|0.086	0.086	strong		0.587	SCN3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387412.1	NM_018400	
SLC41A3	54946	hgsc.bcm.edu	37	3	125726062	125726062	+	Missense_Mutation	SNP	T	T	C	rs79696429	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:125726062T>C	ENST00000315891.6	-	11	1499	c.1261A>G	c.(1261-1263)Atc>Gtc	p.I421V	SLC41A3_ENST00000383598.2_Missense_Mutation_p.I395V|SLC41A3_ENST00000360370.4_Missense_Mutation_p.I421V|SLC41A3_ENST00000346785.5_Missense_Mutation_p.I385V|SLC41A3_ENST00000508835.1_Missense_Mutation_p.I304V	NM_001008485.1|NM_017836.3	NP_001008485|NP_060306.3	Q96GZ6	S41A3_HUMAN	solute carrier family 41, member 3	421						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)		TACAGCAGGATTGTCACCTGT	0.537													T|||	99	0.0197684	0.056	0.0072	5008	,	,		21514	0.0		0.007	False		,,,				2504	0.0133				p.I421V		Atlas-SNP	.											.	SLC41A3	80	.	0			c.A1261G						PASS	.	T	VAL/ILE,VAL/ILE,VAL/ILE,VAL/ILE,VAL/ILE	242,4164	140.0+/-175.5	8,226,1969	56.0	52.0	53.0		1261,1153,1183,910,1261	4.4	0.8	3	dbSNP_132	53	63,8537	39.3+/-95.6	1,61,4238	yes	missense,missense,missense,missense,missense	SLC41A3	NM_001008485.1,NM_001008486.1,NM_001008487.1,NM_001164475.1,NM_017836.3	29,29,29,29,29	9,287,6207	CC,CT,TT		0.7326,5.4925,2.3451	benign,benign,benign,benign,benign	421/508,385/472,395/462,304/371,421/488	125726062	305,12701	2203	4300	6503	SO:0001583	missense	54946	exon11			GCAGGATTGTCAC		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.1261A>G	3.37:g.125726062T>C	ENSP00000326070:p.Ile421Val	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	70	27	0.385714	NM_017836	A6ND60|B3KSD9|B7Z4Y2|C9JE96|E7ENY4|Q8N342|Q8NB27|Q9H9I6|Q9HAB1|Q9NX30	Missense_Mutation	SNP	ENST00000315891.6	37	CCDS33843.1	37	0.01694139194139194	27	0.054878048780487805	5	0.013812154696132596	0	0.0	5	0.006596306068601583	T	10.45	1.353842	0.24512	0.054925	0.007326	ENSG00000114544	ENST00000360370;ENST00000346785;ENST00000383598;ENST00000458524;ENST00000315891;ENST00000508835	T;T;T;T;T	0.30182	1.54;1.54;1.54;1.54;1.54	5.52	4.37	0.52481	MgtE magnesium transporter, integral membrane (1);	0.088897	0.85682	N	0.000000	T	0.04272	0.0118	L	0.35249	1.045	0.45150	D	0.998169	B;B;B;B;B	0.30439	0.031;0.279;0.236;0.279;0.144	B;B;B;B;B	0.36092	0.058;0.217;0.138;0.217;0.084	T	0.02574	-1.1139	10	0.38643	T	0.18	0.3499	9.4473	0.38706	0.0:0.0848:0.0:0.9152	.	304;421;385;421;395	B7Z4Y2;E7ENY4;Q96GZ6-3;Q96GZ6;Q96GZ6-7	.;.;.;S41A3_HUMAN;.	V	421;385;395;412;421;304	ENSP00000353533:I421V;ENSP00000264471:I385V;ENSP00000373092:I395V;ENSP00000326070:I421V;ENSP00000427409:I304V	ENSP00000326070:I421V	I	-	1	0	SLC41A3	127208752	0.388000	0.25197	0.794000	0.32065	0.903000	0.53119	0.596000	0.24044	0.939000	0.37446	0.482000	0.46254	ATC	T|0.980;C|0.020	0.020	strong		0.537	SLC41A3-024	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000370886.1	NM_017836	
PWP1	11137	hgsc.bcm.edu	37	12	108096769	108096769	+	Missense_Mutation	SNP	G	G	C	rs11547907	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:108096769G>C	ENST00000412830.3	+	9	1032	c.864G>C	c.(862-864)ttG>ttC	p.L288F	PWP1_ENST00000541166.1_Missense_Mutation_p.L226F	NM_007062.1	NP_008993.1	Q13610	PWP1_HUMAN	PWP1 homolog (S. cerevisiae)	288			L -> F (in dbSNP:rs11547907).		transcription, DNA-templated (GO:0006351)	Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleus (GO:0005634)				breast(3)|endometrium(4)|kidney(1)|large_intestine(8)|lung(6)|urinary_tract(1)	23						ATATGTCCTTGGGGAAACCAG	0.403													G|||	226	0.0451278	0.0098	0.0245	5008	,	,		17751	0.0774		0.0348	False		,,,				2504	0.0849				p.L288F		Atlas-SNP	.											.	PWP1	43	.	0			c.G864C						PASS	.	G	PHE/LEU	84,4322	72.0+/-110.0	2,80,2121	121.0	111.0	114.0		864	4.8	1.0	12	dbSNP_120	114	340,8260	117.6+/-177.1	5,330,3965	yes	missense	PWP1	NM_007062.1	22	7,410,6086	CC,CG,GG		3.9535,1.9065,3.26	benign	288/502	108096769	424,12582	2203	4300	6503	SO:0001583	missense	11137	exon9			GTCCTTGGGGAAA	BC000067	CCDS9114.1	12q23.3	2013-06-10				ENSG00000136045		"""WD repeat domain containing"""	17015	protein-coding gene	gene with protein product	"""endonuclein"""					7828893, 11850830	Standard	NM_007062		Approved	IEF-SSP-9502	uc001tmo.1	Q13610	OTTHUMG00000169913	ENST00000412830.3:c.864G>C	12.37:g.108096769G>C	ENSP00000387365:p.Leu288Phe	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	79	36	0.455696	NM_007062	A8K3R6|Q7Z3X9	Missense_Mutation	SNP	ENST00000412830.3	37	CCDS9114.1	87	0.03983516483516483	11	0.022357723577235773	11	0.03038674033149171	37	0.06468531468531469	28	0.036939313984168866	G	14.02	2.410319	0.42715	0.019065	0.039535	ENSG00000136045	ENST00000412830;ENST00000258531;ENST00000541166	T;T	0.29142	1.58;2.23	5.71	4.82	0.62117	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.543212	0.20171	N	0.097733	T	0.02418	0.0074	L	0.27053	0.805	0.29613	N	0.846797	B	0.17667	0.023	B	0.25140	0.058	T	0.04767	-1.0928	10	0.56958	D	0.05	.	8.9358	0.35700	0.2248:0.0:0.7752:0.0	rs11547907;rs52791867;rs11547907	288	Q13610	PWP1_HUMAN	F	288;288;226	ENSP00000387365:L288F;ENSP00000445249:L226F	ENSP00000258531:L288F	L	+	3	2	PWP1	106620899	1.000000	0.71417	0.991000	0.47740	0.961000	0.63080	2.422000	0.44696	1.422000	0.47177	-0.140000	0.14226	TTG	G|0.964;C|0.036	0.036	strong		0.403	PWP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406539.1	NM_007062	
ITGA9	3680	hgsc.bcm.edu	37	3	37695260	37695260	+	Missense_Mutation	SNP	A	A	G	rs57547208	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:37695260A>G	ENST00000264741.5	+	17	2151	c.1895A>G	c.(1894-1896)cAg>cGg	p.Q632R		NM_002207.2	NP_002198.2	Q13797	ITA9_HUMAN	integrin, alpha 9	632					axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|neutrophil chemotaxis (GO:0030593)|wound healing (GO:0042060)	basal plasma membrane (GO:0009925)|integrin alpha9-beta1 complex (GO:0034679)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)			breast(3)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(17)|pancreas(1)|prostate(2)|skin(6)|stomach(1)|urinary_tract(1)	44				KIRC - Kidney renal clear cell carcinoma(284;0.165)|Kidney(284;0.197)		CTGCAGCTTCAGGGTAAACTG	0.507													G|||	141	0.028155	0.0424	0.0432	5008	,	,		18863	0.0		0.0427	False		,,,				2504	0.0123				p.Q632R		Atlas-SNP	.											.	ITGA9	98	.	0			c.A1895G						PASS	.	G	ARG/GLN	267,4139	802.0+/-415.6	9,249,1945	119.0	123.0	122.0		1895	-3.7	0.0	3	dbSNP_129	122	379,8221	802.3+/-407.3	12,355,3933	yes	missense	ITGA9	NM_002207.2	43	21,604,5878	GG,GA,AA		4.407,6.0599,4.9669	benign	632/1036	37695260	646,12360	2203	4300	6503	SO:0001583	missense	3680	exon17			AGCTTCAGGGTAA	L24158	CCDS2669.1	3p21.3	2010-03-23			ENSG00000144668	ENSG00000144668		"""Integrins"""	6145	protein-coding gene	gene with protein product	"""integrin, alpha 4-like"""	603963				8245132, 8290272	Standard	NM_002207		Approved	RLC, ITGA4L, ALPHA-RLC	uc003chd.3	Q13797	OTTHUMG00000130815	ENST00000264741.5:c.1895A>G	3.37:g.37695260A>G	ENSP00000264741:p.Gln632Arg	Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	160	77	0.48125	NM_002207	Q14638	Missense_Mutation	SNP	ENST00000264741.5	37	CCDS2669.1	80	0.03663003663003663	28	0.056910569105691054	20	0.055248618784530384	0	0.0	32	0.04221635883905013	G	11.59	1.683475	0.29872	0.060599	0.04407	ENSG00000144668	ENST00000264741	T	0.46451	0.87	5.75	-3.67	0.04476	Integrin alpha-2 (1);	0.502707	0.23217	N	0.050616	T	0.02970	0.0088	L	0.33485	1.01	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.09164	-1.0687	10	0.19147	T	0.46	.	14.0419	0.64681	0.7894:0.0:0.2106:0.0	rs57547208;rs61762996	632	Q13797	ITA9_HUMAN	R	632	ENSP00000264741:Q632R	ENSP00000264741:Q632R	Q	+	2	0	ITGA9	37670264	0.080000	0.21391	0.015000	0.15790	0.883000	0.51084	-0.415000	0.07106	-0.929000	0.03757	-0.757000	0.03467	CAG	A|0.953;G|0.047	0.047	strong		0.507	ITGA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253361.1	NM_002207	
CTNNA2	1496	hgsc.bcm.edu	37	2	80101372	80101372	+	Silent	SNP	C	C	T	rs76801084	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:80101372C>T	ENST00000402739.4	+	5	761	c.756C>T	c.(754-756)gcC>gcT	p.A252A	CTNNA2_ENST00000541047.1_Silent_p.A252A|CTNNA2_ENST00000540488.1_Silent_p.A252A|CTNNA2_ENST00000466387.1_Silent_p.A252A|CTNNA2_ENST00000361291.4_Silent_p.A286A|CTNNA2_ENST00000496558.1_Silent_p.A252A	NM_001282597.1	NP_001269526.1	P26232	CTNA2_HUMAN	catenin (cadherin-associated protein), alpha 2	252					axonogenesis (GO:0007409)|brain morphogenesis (GO:0048854)|dendrite morphogenesis (GO:0048813)|muscle cell differentiation (GO:0042692)|positive regulation of muscle cell differentiation (GO:0051149)|prepulse inhibition (GO:0060134)|radial glia guided migration of Purkinje cell (GO:0021942)|regulation of synapse structural plasticity (GO:0051823)|single organismal cell-cell adhesion (GO:0016337)	actin cytoskeleton (GO:0015629)|adherens junction (GO:0005912)|axon (GO:0030424)|basolateral plasma membrane (GO:0016323)|cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|lamellipodium (GO:0030027)	structural constituent of cytoskeleton (GO:0005200)			breast(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(49)|pancreas(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	78						AGGCCATCGCCGGCATCTCCA	0.577													C|||	276	0.0551118	0.0499	0.013	5008	,	,		16050	0.1746		0.003	False		,,,				2504	0.0225				p.A252A		Atlas-SNP	.											CTNNA2_ENST00000466387,colon,carcinoma,+2,2	CTNNA2	462	2	0			c.C756T						PASS	.	C	,	179,3973		4,171,1901	46.0	50.0	49.0		756,756	-1.4	1.0	2	dbSNP_131	49	27,8401		0,27,4187	yes	coding-synonymous,coding-synonymous	CTNNA2	NM_001164883.1,NM_004389.3	,	4,198,6088	TT,TC,CC		0.3204,4.3112,1.6375	,	252/861,252/906	80101372	206,12374	2076	4214	6290	SO:0001819	synonymous_variant	1496	exon6			CATCGCCGGCATC		CCDS42703.2, CCDS62944.1, CCDS62945.1, CCDS74531.1	2p12-p11.1	2010-05-04			ENSG00000066032	ENSG00000066032			2510	protein-coding gene	gene with protein product	"""cadherin-associated protein, related"", ""cancer/testis antigen 114"""	114025				8432524	Standard	NM_004389		Approved	CAP-R, CT114	uc010ysf.2	P26232	OTTHUMG00000152903	ENST00000402739.4:c.756C>T	2.37:g.80101372C>T		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	72	39	0.541667	NM_001164883	B3KXE5|B7Z2W7|B7Z352|B7Z898|Q4ZFW1|Q53R26|Q53R33|Q53T67|Q53T71|Q53TM8|Q7Z3L1|Q7Z3Y0	Silent	SNP	ENST00000402739.4	37																																																																																				C|0.964;T|0.036	0.036	strong		0.577	CTNNA2-003	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000328511.4	NM_004389	
EXO5	64789	hgsc.bcm.edu	37	1	40981230	40981230	+	Silent	SNP	G	G	A	rs3795344	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:40981230G>A	ENST00000372703.1	+	2	2088	c.1014G>A	c.(1012-1014)gaG>gaA	p.E338E	EXO5_ENST00000358527.2_Silent_p.E338E|RP11-656D10.6_ENST00000437060.1_RNA|RP11-656D10.5_ENST00000453437.1_RNA|EXO5_ENST00000296380.4_Silent_p.E338E			Q9H790	EXO5_HUMAN	exonuclease 5	338					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)										TTGACGTGGAGGAGGCTTGGA	0.547													G|||	216	0.043131	0.0598	0.0331	5008	,	,		19359	0.0208		0.0328	False		,,,				2504	0.0613				p.E338E		Atlas-SNP	.											.	.	.	.	0			c.G1014A						PASS	.	G		245,4161	140.8+/-176.2	9,227,1967	61.0	50.0	54.0		1014	-2.1	1.0	1	dbSNP_107	54	300,8300	107.4+/-168.2	5,290,4005	no	coding-synonymous	DEM1	NM_022774.1		14,517,5972	AA,AG,GG		3.4884,5.5606,4.1904		338/374	40981230	545,12461	2203	4300	6503	SO:0001819	synonymous_variant	64789	exon3			CGTGGAGGAGGCT	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.1014G>A	1.37:g.40981230G>A		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	93	45	0.483871	NM_022774	D3DPV4|Q5SWM7|Q5SWM8|Q5SWM9|Q5SWN0|Q5SWN1|Q8WTW9	Silent	SNP	ENST00000372703.1	37	CCDS453.1																																																																																			G|0.958;A|0.042	0.042	strong		0.547	EXO5-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019087.1	NM_022774	
SOX6	55553	hgsc.bcm.edu	37	11	16133413	16133413	+	Silent	SNP	A	A	G	rs4617548	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:16133413A>G	ENST00000352083.6	-	7	911	c.834T>C	c.(832-834)acT>acC	p.T278T	SOX6_ENST00000396356.3_Silent_p.T278T|SOX6_ENST00000528429.1_Silent_p.T278T|SOX6_ENST00000528252.1_Silent_p.T278T|SOX6_ENST00000527619.1_Silent_p.T281T|SOX6_ENST00000316399.6_Silent_p.T278T			P35712	SOX6_HUMAN	SRY (sex determining region Y)-box 6	278					astrocyte differentiation (GO:0048708)|cardiac muscle cell differentiation (GO:0055007)|cartilage development (GO:0051216)|cell morphogenesis (GO:0000902)|cellular response to transforming growth factor beta stimulus (GO:0071560)|erythrocyte development (GO:0048821)|gene silencing (GO:0016458)|in utero embryonic development (GO:0001701)|muscle organ development (GO:0007517)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|oligodendrocyte cell fate specification (GO:0021778)|positive regulation of cartilage development (GO:0061036)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of mesenchymal stem cell differentiation (GO:2000741)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	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)			NS(1)|breast(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(23)|ovary(3)|pancreas(1)|prostate(2)	43						CTGCTGCCAGAGTCCGCTGGT	0.488													G|||	2533	0.505791	0.4569	0.647	5008	,	,		17597	0.6121		0.5119	False		,,,				2504	0.3558				p.T291T		Atlas-SNP	.											.	SOX6	149	.	0			c.T873C						PASS	.	G	,,,	2209,2191	586.9+/-386.6	548,1113,539	83.0	83.0	83.0		834,873,843,834	4.0	1.0	11	dbSNP_111	83	4421,4167	566.7+/-388.7	1147,2127,1020	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SOX6	NM_001145811.1,NM_001145819.1,NM_017508.2,NM_033326.3	,,,	1695,3240,1559	GG,GA,AA		48.5212,49.7955,48.9529	,,,	278/802,291/842,281/805,278/809	16133413	6630,6358	2200	4294	6494	SO:0001819	synonymous_variant	55553	exon7			TGCCAGAGTCCGC	AF309034	CCDS7821.1, CCDS53604.1, CCDS53605.1	11p15.3	2008-02-05						"""SRY (sex determining region Y)-boxes"""	16421	protein-coding gene	gene with protein product		607257				11255018	Standard	NM_033326		Approved		uc001mme.3	P35712		ENST00000352083.6:c.834T>C	11.37:g.16133413A>G		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	114	114	1	NM_001145819	Q86VX7|Q9BXQ3|Q9BXQ4|Q9BXQ5|Q9H0I8	Silent	SNP	ENST00000352083.6	37																																																																																				A|0.493;G|0.507	0.507	strong		0.488	SOX6-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000386811.1	NM_033326	
NWD2	57495	hgsc.bcm.edu	37	4	37445315	37445315	+	Missense_Mutation	SNP	C	C	A	rs4634233	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:37445315C>A	ENST00000309447.5	+	7	2553	c.1705C>A	c.(1705-1707)Ctg>Atg	p.L569M		NM_001144990.1	NP_001138462.1	Q9ULI1	NWD2_HUMAN		569	NACHT.		L -> M (in dbSNP:rs4634233).							breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(1)|prostate(2)|skin(2)	16						CTACATCGAGCTGATTCCCCG	0.512													C|||	757	0.151158	0.1218	0.1715	5008	,	,		22977	0.0625		0.2773	False		,,,				2504	0.138				p.L569M		Atlas-SNP	.											.	KIAA1239	79	.	0			c.C1705A						PASS	.	C	MET/LEU	182,1202		7,168,517	94.0	75.0	81.0		1705	4.4	1.0	4	dbSNP_111	81	854,2328		105,644,842	yes	missense	KIAA1239	NM_001144990.1	15	112,812,1359	AA,AC,CC		26.8385,13.1503,22.6894	probably-damaging	569/1743	37445315	1036,3530	692	1591	2283	SO:0001583	missense	57495	exon7			ATCGAGCTGATTC																												ENST00000309447.5:c.1705C>A	4.37:g.37445315C>A	ENSP00000309501:p.Leu569Met	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	65	38	0.584615	NM_001144990	A8MRU1	Missense_Mutation	SNP	ENST00000309447.5	37	CCDS47040.1	389	0.17811355311355312	70	0.14227642276422764	67	0.1850828729281768	44	0.07692307692307693	208	0.27440633245382584	C	14.30	2.494469	0.44352	0.131503	0.268385	ENSG00000174145	ENST00000309447	D	0.84146	-1.81	6.07	4.36	0.52297	.	.	.	.	.	T	0.00073	0.0002	L	0.58101	1.795	0.22489	P	0.999053227	D	0.76494	0.999	D	0.87578	0.998	T	0.01048	-1.1469	8	0.87932	D	0	.	9.2091	0.37306	0.0:0.732:0.0:0.268	rs4634233;rs52808878;rs4634233	569	Q9ULI1	K1239_HUMAN	M	569	ENSP00000309501:L569M	ENSP00000309501:L569M	L	+	1	2	KIAA1239	37121710	0.998000	0.40836	1.000000	0.80357	0.996000	0.88848	0.952000	0.29149	0.911000	0.36747	0.650000	0.86243	CTG	C|0.819;A|0.181	0.181	strong		0.512	KIAA1239-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347551.2		
ZFP42	132625	hgsc.bcm.edu	37	4	188924230	188924230	+	Missense_Mutation	SNP	C	C	T	rs149675060		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:188924230C>T	ENST00000326866.4	+	4	677	c.269C>T	c.(268-270)tCa>tTa	p.S90L	ZFP42_ENST00000509524.1_Missense_Mutation_p.S90L	NM_174900.3	NP_777560.2	Q96MM3	ZFP42_HUMAN	ZFP42 zinc finger protein	90					female gonad development (GO:0008585)|in utero embryonic development (GO:0001701)|male gonad development (GO:0008584)|meiotic nuclear division (GO:0007126)|regulation of genetic imprinting (GO:2000653)|spermatid development (GO:0007286)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|protein complex (GO:0043234)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(15)|ovary(1)|skin(2)|stomach(1)	27		all_cancers(14;6.2e-52)|all_epithelial(14;7.36e-37)|all_lung(41;2.29e-15)|Lung NSC(41;6.7e-15)|Breast(6;1.53e-05)|Melanoma(20;3.01e-05)|Hepatocellular(41;0.00335)|all_hematologic(60;0.014)|Renal(120;0.0183)|Prostate(90;0.0421)|Colorectal(36;0.227)		OV - Ovarian serous cystadenocarcinoma(60;1.54e-11)|BRCA - Breast invasive adenocarcinoma(30;4.21e-06)|GBM - Glioblastoma multiforme(59;8.93e-05)|STAD - Stomach adenocarcinoma(60;0.000279)|LUSC - Lung squamous cell carcinoma(40;0.00902)|READ - Rectum adenocarcinoma(43;0.157)		GAAGAGGACTCACTTTTTGAG	0.453													C|||	1	0.000199681	0.0	0.0	5008	,	,		20567	0.0		0.001	False		,,,				2504	0.0				p.S90L		Atlas-SNP	.											.	ZFP42	87	.	0			c.C269T						PASS	.	C	LEU/SER	2,4404	4.2+/-10.8	0,2,2201	83.0	85.0	85.0		269	-1.7	0.0	4	dbSNP_134	85	6,8594	5.0+/-18.6	0,6,4294	yes	missense	ZFP42	NM_174900.3	145	0,8,6495	TT,TC,CC		0.0698,0.0454,0.0615	benign	90/311	188924230	8,12998	2203	4300	6503	SO:0001583	missense	132625	exon4			AGGACTCACTTTT	AK056719	CCDS3849.1	4q35.2	2014-09-04	2012-11-27		ENSG00000179059	ENSG00000179059		"""Zinc fingers, C2H2-type"""	30949	protein-coding gene	gene with protein product		614572	"""zinc finger protein 42 homolog (mouse)"", ""zinc finger protein 42"""			12110702	Standard	NM_174900		Approved	REX1, ZNF754	uc003izh.1	Q96MM3	OTTHUMG00000160235	ENST00000326866.4:c.269C>T	4.37:g.188924230C>T	ENSP00000317686:p.Ser90Leu	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	89	44	0.494382	NM_174900	D3DP65|Q8WXE2	Missense_Mutation	SNP	ENST00000326866.4	37	CCDS3849.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	0.005	-2.129602	0.00338	4.54E-4	6.98E-4	ENSG00000179059	ENST00000326866;ENST00000509524	T;T	0.62788	0.0;0.0	4.49	-1.68	0.08212	.	0.950524	0.08730	N	0.902147	T	0.42314	0.1197	N	0.14661	0.345	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.27806	-1.0063	10	0.39692	T	0.17	.	10.2546	0.43390	0.0:0.717:0.0:0.283	.	90	Q96MM3	ZFP42_HUMAN	L	90	ENSP00000317686:S90L;ENSP00000424662:S90L	ENSP00000317686:S90L	S	+	2	0	ZFP42	189161224	0.000000	0.05858	0.000000	0.03702	0.019000	0.09904	-0.552000	0.06020	-0.188000	0.10499	0.655000	0.94253	TCA	C|0.999;T|0.001	0.001	strong		0.453	ZFP42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359794.1	NM_174900	
ZNF474	133923	hgsc.bcm.edu	37	5	121487969	121487969	+	Missense_Mutation	SNP	G	G	A	rs72786994	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:121487969G>A	ENST00000296600.4	+	2	667	c.284G>A	c.(283-285)cGg>cAg	p.R95Q	ZNF474_ENST00000514925.1_Intron|CTC-441N14.2_ENST00000504829.1_RNA|CTC-441N14.1_ENST00000505209.1_RNA	NM_207317.1	NP_997200.1	Q6S9Z5	ZN474_HUMAN	zinc finger protein 474	95							metal ion binding (GO:0046872)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(10)|stomach(1)	21		all_cancers(142;0.229)|Prostate(80;0.0387)	KIRC - Kidney renal clear cell carcinoma(527;0.206)	OV - Ovarian serous cystadenocarcinoma(64;0.000197)|Epithelial(69;0.00029)|all cancers(49;0.00415)		CCTGGATTCCGGGTATGCTAT	0.502													G|||	52	0.0103834	0.0008	0.0086	5008	,	,		17148	0.0		0.0179	False		,,,				2504	0.0276				p.R95Q		Atlas-SNP	.											.	ZNF474	43	.	0			c.G284A						PASS	.	G	GLN/ARG	15,4391	23.3+/-48.9	0,15,2188	74.0	81.0	79.0		284	-1.7	0.1	5	dbSNP_130	79	171,8429	78.6+/-141.3	1,169,4130	yes	missense	ZNF474	NM_207317.1	43	1,184,6318	AA,AG,GG		1.9884,0.3404,1.4301	probably-damaging	95/365	121487969	186,12820	2203	4300	6503	SO:0001583	missense	133923	exon2			GATTCCGGGTATG	AK057483	CCDS4130.1	5q23.2	2008-02-05			ENSG00000164185	ENSG00000164185		"""Zinc fingers, C2H2-type"""	23245	protein-coding gene	gene with protein product							Standard	NM_207317		Approved	4933409D10Rik, FLJ32921	uc003ksv.3	Q6S9Z5	OTTHUMG00000128911	ENST00000296600.4:c.284G>A	5.37:g.121487969G>A	ENSP00000296600:p.Arg95Gln	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	91	43	0.472527	NM_207317	A8K4M0|Q96M07	Missense_Mutation	SNP	ENST00000296600.4	37	CCDS4130.1	16	0.007326007326007326	0	0.0	3	0.008287292817679558	0	0.0	13	0.017150395778364115	G	10.15	1.271155	0.23221	0.003404	0.019884	ENSG00000164185	ENST00000296600	T	0.51325	0.71	5.58	-1.72	0.08107	.	3.416030	0.00792	N	0.001340	T	0.30230	0.0758	L	0.52011	1.625	0.19775	N	0.999959	P	0.51147	0.942	P	0.47470	0.548	T	0.34551	-0.9824	10	0.27082	T	0.32	1.9702	6.2544	0.20865	0.5859:0.0:0.2818:0.1323	.	95	Q6S9Z5	ZN474_HUMAN	Q	95	ENSP00000296600:R95Q	ENSP00000296600:R95Q	R	+	2	0	ZNF474	121515868	0.019000	0.18553	0.146000	0.22360	0.062000	0.15995	-0.172000	0.09868	-0.163000	0.10946	-0.123000	0.14984	CGG	G|0.988;A|0.012	0.012	strong		0.502	ZNF474-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250883.2	NM_207317	
ESPL1	9700	hgsc.bcm.edu	37	12	53671005	53671005	+	Missense_Mutation	SNP	G	G	A	rs17125266	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:53671005G>A	ENST00000257934.4	+	9	2170	c.2079G>A	c.(2077-2079)atG>atA	p.M693I	ESPL1_ENST00000552462.1_Missense_Mutation_p.M693I	NM_012291.4	NP_036423.4	Q14674	ESPL1_HUMAN	extra spindle pole bodies homolog 1 (S. cerevisiae)	693				M -> I (in Ref. 1; AAR18247 and 2; BAA11482). {ECO:0000305}.	apoptotic process (GO:0006915)|cytokinesis (GO:0000910)|establishment of mitotic spindle localization (GO:0040001)|homologous chromosome segregation (GO:0045143)|meiotic spindle organization (GO:0000212)|mitotic cell cycle (GO:0000278)|mitotic sister chromatid segregation (GO:0000070)|negative regulation of sister chromatid cohesion (GO:0045875)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)	centrosome (GO:0005813)|cytosol (GO:0005829)|nucleus (GO:0005634)	catalytic activity (GO:0003824)|cysteine-type peptidase activity (GO:0008234)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(10)|large_intestine(12)|lung(21)|ovary(2)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(8)	70						AAGCCAAAATGCAGGAAGTGA	0.532													G|||	452	0.0902556	0.0968	0.1556	5008	,	,		20426	0.1319		0.0149	False		,,,				2504	0.0695				p.M693I	Colon(53;1069 1201 2587 5382)	Atlas-SNP	.											.	ESPL1	158	.	0			c.G2079A						PASS	.	G	ILE/MET	399,4007	199.4+/-223.0	17,365,1821	57.0	60.0	59.0		2079	4.3	1.0	12	dbSNP_123	59	158,8442	74.8+/-137.4	0,158,4142	yes	missense	ESPL1	NM_012291.4	10	17,523,5963	AA,AG,GG		1.8372,9.0558,4.2826	benign	693/2121	53671005	557,12449	2203	4300	6503	SO:0001583	missense	9700	exon9			CAAAATGCAGGAA	D79987	CCDS8852.1	12q13.13	2014-08-04	2013-05-03		ENSG00000135476	ENSG00000135476	3.4.22.49		16856	protein-coding gene	gene with protein product	"""separin"", ""separase"", ""separin, cysteine protease"""	604143	"""extra spindle poles like 1 (S. cerevisiae)"""			8724849, 16258266	Standard	NM_012291		Approved	KIAA0165, ESP1, SEPA	uc001sck.2	Q14674	OTTHUMG00000169674	ENST00000257934.4:c.2079G>A	12.37:g.53671005G>A	ENSP00000257934:p.Met693Ile	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	89	35	0.393258	NM_012291		Missense_Mutation	SNP	ENST00000257934.4	37	CCDS8852.1	197	0.0902014652014652	44	0.08943089430894309	45	0.12430939226519337	100	0.17482517482517482	8	0.010554089709762533	G	13.72	2.321436	0.41096	0.090558	0.018372	ENSG00000135476	ENST00000257934;ENST00000552671;ENST00000552462	T;T	0.12984	2.63;2.63	5.19	4.3	0.51218	.	0.143965	0.64402	D	0.000005	T	0.00039	0.0001	M	0.67953	2.075	0.30290	P	0.790505	B	0.02656	0.0	B	0.04013	0.001	T	0.07102	-1.0790	9	0.51188	T	0.08	.	12.9785	0.58549	0.0791:0.0:0.9209:0.0	rs17125266;rs52837590;rs17125266	693	Q14674	ESPL1_HUMAN	I	693;368;693	ENSP00000257934:M693I;ENSP00000449831:M693I	ENSP00000257934:M693I	M	+	3	0	ESPL1	51957272	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.160000	0.42348	1.435000	0.47434	-0.137000	0.14449	ATG	G|0.939;A|0.061	0.061	strong		0.532	ESPL1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406899.2	NM_012291	
NUDT12	83594	hgsc.bcm.edu	37	5	102895169	102895169	+	Splice_Site	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:102895169C>T	ENST00000230792.2	-	3	303	c.207G>A	c.(205-207)ggG>ggA	p.G69G	NUDT12_ENST00000507423.1_Splice_Site_p.M51I	NM_031438.2	NP_113626.1	Q9BQG2	NUD12_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 12	69					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)		ATCTGTCACACCTATAGATGG	0.323																																					p.G69G		Atlas-SNP	.											.	NUDT12	27	.	0			c.G207A						PASS	.						34.0	34.0	34.0					5																	102895169		2037	4218	6255	SO:0001630	splice_region_variant	83594	exon3			GTCACACCTATAG	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.207-1G>A	5.37:g.102895169C>T		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	74	18	0.243243	NM_031438	B3KUW2|Q8TAL7	Silent	SNP	ENST00000230792.2	37	CCDS4096.1	.	.	.	.	.	.	.	.	.	.	C	10.38	1.333868	0.24253	.	.	ENSG00000112874	ENST00000507423	T	0.34072	1.38	5.9	3.17	0.36434	.	.	.	.	.	T	0.29749	0.0743	.	.	.	0.19945	N	0.999946	B	0.09022	0.002	B	0.12837	0.008	T	0.24190	-1.0167	8	0.62326	D	0.03	.	10.3521	0.43943	0.0:0.7281:0.0:0.2719	.	51	E7EM93	.	I	51	ENSP00000424521:M51I	ENSP00000424521:M51I	M	-	3	0	NUDT12	102923068	1.000000	0.71417	0.998000	0.56505	0.533000	0.34776	1.488000	0.35551	0.399000	0.25367	-0.142000	0.14014	ATG	.	.	none		0.323	NUDT12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250650.1	NM_031438	Silent
TAS2R42	353164	hgsc.bcm.edu	37	12	11338669	11338669	+	Missense_Mutation	SNP	C	C	T	rs1669412	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:11338669C>T	ENST00000334266.1	-	1	874	c.875G>A	c.(874-876)cGa>cAa	p.R292Q		NM_181429.1	NP_852094.1	Q7RTR8	T2R42_HUMAN	taste receptor, type 2, member 42	292			R -> Q (in dbSNP:rs1669412).		sensory perception of taste (GO:0050909)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(1)|kidney(2)|lung(4)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	11			OV - Ovarian serous cystadenocarcinoma(49;0.0455)			AGCTGTCTGTCGCAGCTTGCT	0.408													C|||	1102	0.220048	0.2474	0.2305	5008	,	,		18104	0.1944		0.2167	False		,,,				2504	0.2055				p.R292Q	Melanoma(15;352 722 10077 19546 48810)	Atlas-SNP	.											.	TAS2R42	30	.	0			c.G875A						PASS	.	C	GLN/ARG	1067,3339	386.3+/-326.1	137,793,1273	76.0	71.0	73.0		875	2.2	0.0	12	dbSNP_89	73	2041,6559	356.6+/-330.4	248,1545,2507	yes	missense	TAS2R42	NM_181429.1	43	385,2338,3780	TT,TC,CC		23.7326,24.217,23.8967	probably-damaging	292/315	11338669	3108,9898	2203	4300	6503	SO:0001583	missense	353164	exon1			GTCTGTCGCAGCT	AX097739, AB199241	CCDS31747.1	12p13	2012-08-22			ENSG00000186136	ENSG00000186136		"""Taste receptors / Type 2"", ""GPCR / Unclassified : Taste receptors"""	18888	protein-coding gene	gene with protein product		613966				12679530	Standard	NM_181429		Approved	T2R24, T2R55, hT2R55, TAS2R55	uc001qzr.1	Q7RTR8	OTTHUMG00000168567	ENST00000334266.1:c.875G>A	12.37:g.11338669C>T	ENSP00000334050:p.Arg292Gln	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	79	35	0.443038	NM_181429	A2RRP4|Q645X0	Missense_Mutation	SNP	ENST00000334266.1	37	CCDS31747.1	491	0.22481684981684982	114	0.23170731707317074	77	0.212707182320442	126	0.2202797202797203	174	0.22955145118733508	C	15.20	2.763624	0.49574	0.24217	0.237326	ENSG00000186136	ENST00000334266	T	0.01025	5.43	4.02	2.17	0.27698	.	0.165147	0.40064	N	0.001188	T	0.00012	0.0000	M	0.80028	2.48	0.80722	P	0.0	D	0.89917	1.0	D	0.80764	0.994	T	0.43814	-0.9368	9	0.72032	D	0.01	.	6.581	0.22594	0.0:0.7685:0.0:0.2315	rs1669412	292	Q7RTR8	T2R42_HUMAN	Q	292	ENSP00000334050:R292Q	ENSP00000334050:R292Q	R	-	2	0	TAS2R42	11229936	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.018000	0.13422	0.318000	0.23185	-0.145000	0.13849	CGA	C|0.762;T|0.238	0.238	strong		0.408	TAS2R42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400243.1	NM_181429	
ZBP1	81030	hgsc.bcm.edu	37	20	56189956	56189956	+	Silent	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:56189956C>T	ENST00000371173.3	-	4	666	c.489G>A	c.(487-489)acG>acA	p.T163T	ZBP1_ENST00000343535.4_Silent_p.T163T|ZBP1_ENST00000538947.1_5'Flank|ZBP1_ENST00000541799.1_Silent_p.T163T|ZBP1_ENST00000340462.4_Silent_p.T140T|ZBP1_ENST00000395822.3_Silent_p.T88T	NM_001160417.1|NM_030776.2	NP_001153889.1|NP_110403.2	Q9H171	ZBP1_HUMAN	Z-DNA binding protein 1	163					innate immune response (GO:0045087)|positive regulation of type I interferon production (GO:0032481)|positive regulation of type I interferon-mediated signaling pathway (GO:0060340)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	DNA binding (GO:0003677)|double-stranded RNA adenosine deaminase activity (GO:0003726)|left-handed Z-DNA binding (GO:0003692)|RNA binding (GO:0003723)			large_intestine(11)|lung(8)|ovary(4)|prostate(1)|skin(2)|urinary_tract(1)	27	Lung NSC(12;0.000545)|all_lung(29;0.00195)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(13;7.87e-13)|Epithelial(14;3.26e-09)|all cancers(14;3.62e-08)			GGCGGTAAATCGTCCATGCTT	0.552																																					p.T163T		Atlas-SNP	.											ZBP1,NS,carcinoma,0,1	ZBP1	65	1	0			c.G489A						PASS	.						161.0	127.0	139.0					20																	56189956		2203	4300	6503	SO:0001819	synonymous_variant	81030	exon4			GTAAATCGTCCAT	AJ300575	CCDS13461.1, CCDS54477.1, CCDS54478.1	20q13.31	2009-08-21	2002-07-25	2002-07-26	ENSG00000124256	ENSG00000124256			16176	protein-coding gene	gene with protein product	"""DNA-dependent activator of IRFs"""	606750	"""chromosome 20 open reading frame 183"""	C20orf183		11842111	Standard	NM_030776		Approved	dJ718J7.3, DLM1, DLM-1, DAI	uc002xyo.3	Q9H171	OTTHUMG00000032824	ENST00000371173.3:c.489G>A	20.37:g.56189956C>T		Somatic	187	0	0		WXS	Illumina HiSeq	Phase_I	135	28	0.207407	NM_001160419	A2A2F7|B3KVA1|F5GYT1|Q5JY39|Q9BYW4	Silent	SNP	ENST00000371173.3	37	CCDS13461.1																																																																																			.	.	none		0.552	ZBP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079849.1	NM_030776	
TRIOBP	11078	hgsc.bcm.edu	37	22	38119902	38119902	+	Missense_Mutation	SNP	A	A	G	rs537300122	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:38119902A>G	ENST00000406386.3	+	7	1594	c.1339A>G	c.(1339-1341)Aca>Gca	p.T447A		NM_001039141.2	NP_001034230.1	Q9H2D6	TARA_HUMAN	TRIO and F-actin binding protein	447					actin modification (GO:0030047)|barbed-end actin filament capping (GO:0051016)|mitotic nuclear division (GO:0007067)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	actin filament binding (GO:0051015)|GTP-Rho binding (GO:0017049)|myosin II binding (GO:0045159)|ubiquitin protein ligase binding (GO:0031625)	p.T447A(3)		central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	12	Melanoma(58;0.0574)					CAGTAGAGCTACACGAGACAA	0.587													A|||	50	0.00998403	0.0	0.0029	5008	,	,		19561	0.0337		0.0119	False		,,,				2504	0.002				p.T447A		Atlas-SNP	.											TRIOBP_ENST00000344404,NS,carcinoma,0,4	TRIOBP	262	4	3	Substitution - Missense(3)	prostate(2)|skin(1)	c.A1339G						scavenged	.						60.0	64.0	63.0					22																	38119902		1870	4095	5965	SO:0001583	missense	11078	exon7			AGAGCTACACGAG	AB051449	CCDS33644.1, CCDS43015.1, CCDS43016.1	22q13.1	2014-06-03			ENSG00000100106	ENSG00000100106		"""Pleckstrin homology (PH) domain containing"""	17009	protein-coding gene	gene with protein product		609761		DFNB28		11148140, 16385457, 16385458	Standard	NM_001039141		Approved	HRIHFB2122, KIAA1662, Tara, TAP68	uc003atr.3	Q9H2D6	OTTHUMG00000150657	ENST00000406386.3:c.1339A>G	22.37:g.38119902A>G	ENSP00000384312:p.Thr447Ala	Somatic	167	4	0.0239521		WXS	Illumina HiSeq	Phase_I	170	5	0.0294118	NM_001039141	B1AHD4|B1AHD7|F2Z2W0|F8W6V6|O94797|Q2PZW8|Q2Q3Z9|Q2Q400|Q5R3M6|Q96DW1|Q9BT77|Q9BTL7|Q9BY98|Q9Y3L4	Missense_Mutation	SNP	ENST00000406386.3	37	CCDS43015.1	.	.	.	.	.	.	.	.	.	.	A	5.040	0.193024	0.09599	.	.	ENSG00000100106	ENST00000406386;ENST00000417174	T	0.19806	2.12	2.54	2.54	0.30619	.	.	.	.	.	T	0.23727	0.0574	L	0.36672	1.1	0.19945	N	0.999945	P	0.52463	0.953	P	0.53988	0.739	T	0.07558	-1.0766	9	0.30854	T	0.27	.	6.7436	0.23449	1.0:0.0:0.0:0.0	.	447	Q9H2D6	TARA_HUMAN	A	447	ENSP00000384312:T447A	ENSP00000384312:T447A	T	+	1	0	TRIOBP	36449848	0.000000	0.05858	0.003000	0.11579	0.005000	0.04900	-0.062000	0.11674	1.059000	0.40554	0.113000	0.15668	ACA	.	.	none		0.587	TRIOBP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319439.2		
ZNF358	140467	hgsc.bcm.edu	37	19	7584223	7584223	+	Missense_Mutation	SNP	A	A	G	rs11555037	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:7584223A>G	ENST00000597229.1	+	2	265	c.95A>G	c.(94-96)aAt>aGt	p.N32S	CTD-2207O23.11_ENST00000602083.1_RNA|ZNF358_ENST00000394341.2_Missense_Mutation_p.N32S|CTD-2207O23.12_ENST00000599312.1_3'UTR	NM_018083.4	NP_060553.4	Q9NW07	ZN358_HUMAN	zinc finger protein 358	32			N -> S (in dbSNP:rs11555037).		embryonic forelimb morphogenesis (GO:0035115)|neural tube development (GO:0021915)|regulation of transcription, DNA-templated (GO:0006355)|stem cell maintenance (GO:0019827)|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)|cervix(1)|kidney(1)|lung(1)|skin(2)	8						CTAGACCCCAATCCTGAAGAT	0.567													A|||	979	0.195487	0.1044	0.1772	5008	,	,		12926	0.1042		0.326	False		,,,				2504	0.2914				p.N32S		Atlas-SNP	.											.	ZNF358	41	.	0			c.A95G						PASS	.	A	SER/ASN	523,3855		36,451,1702	52.0	60.0	58.0		95	0.3	0.0	19	dbSNP_120	58	2575,6005		375,1825,2090	yes	missense	ZNF358	NM_018083.4	46	411,2276,3792	GG,GA,AA		30.0117,11.9461,23.908	benign	32/569	7584223	3098,9860	2189	4290	6479	SO:0001583	missense	140467	exon2			ACCCCAATCCTGA	AK001252	CCDS32890.2	19p13.2	2013-01-08			ENSG00000198816	ENSG00000198816		"""Zinc fingers, C2H2-type"""	16838	protein-coding gene	gene with protein product							Standard	NM_018083		Approved	FLJ10390, ZFEND	uc002mgn.2	Q9NW07		ENST00000597229.1:c.95A>G	19.37:g.7584223A>G	ENSP00000472305:p.Asn32Ser	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	52	28	0.538462	NM_018083	Q9BTM7	Missense_Mutation	SNP	ENST00000597229.1	37	CCDS32890.2	434	0.1987179487179487	64	0.13008130081300814	72	0.19889502762430938	51	0.08916083916083917	247	0.3258575197889182	A	0.007	-1.982298	0.00448	0.119461	0.300117	ENSG00000198816	ENST00000361576;ENST00000394341	T	0.05649	3.41	4.73	0.314	0.15847	.	.	.	.	.	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	0.46289	-0.9202	8	0.09590	T	0.72	-0.2651	7.971	0.30127	0.612:0.0:0.388:0.0	rs11555037	32	Q9NW07	ZN358_HUMAN	S	32	ENSP00000377873:N32S	ENSP00000354703:N32S	N	+	2	0	ZNF358	7490223	0.000000	0.05858	0.003000	0.11579	0.186000	0.23388	0.385000	0.20685	0.078000	0.16900	0.456000	0.33151	AAT	A|0.768;G|0.231;T|0.000	0.231	strong		0.567	ZNF358-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316747.1		
KRTAP10-2	386679	hgsc.bcm.edu	37	21	45971081	45971081	+	Silent	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:45971081C>T	ENST00000391621.1	-	1	307	c.261G>A	c.(259-261)ccG>ccA	p.P87P	TSPEAR_ENST00000397916.1_Intron|TSPEAR_ENST00000323084.4_Intron|KRTAP10-2_ENST00000498210.1_Intron	NM_198693.2	NP_941966.1	P60368	KR102_HUMAN	keratin associated protein 10-2	87	22 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				large_intestine(1)|lung(4)|skin(1)	6						TGCAGCAAGCCGGCTGGCAGC	0.687																																					p.P87P		Atlas-SNP	.											KRTAP10-2,trunk,malignant_melanoma,-1,1	KRTAP10-2	21	1	0			c.G261A						scavenged	.						57.0	61.0	60.0					21																	45971081		2202	4292	6494	SO:0001819	synonymous_variant	386679	exon1			GCAAGCCGGCTGG	AJ566381	CCDS42955.1	21q22.3	2007-10-05			ENSG00000205445	ENSG00000205445		"""Keratin associated proteins"""	22967	protein-coding gene	gene with protein product				KRTAP18-2			Standard	NM_198693		Approved	KAP10.2, KAP18.2	uc002zfi.1	P60368	OTTHUMG00000057625	ENST00000391621.1:c.261G>A	21.37:g.45971081C>T		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	124	19	0.153226	NM_198693	Q70LJ5	Silent	SNP	ENST00000391621.1	37	CCDS42955.1																																																																																			.	.	weak		0.687	KRTAP10-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128027.1		
SYT3	84258	hgsc.bcm.edu	37	19	51140654	51140654	+	Silent	SNP	G	G	A	rs3815749	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:51140654G>A	ENST00000338916.4	-	1	648	c.15C>T	c.(13-15)taC>taT	p.Y5Y	SYT3_ENST00000600079.1_Silent_p.Y5Y|SYT3_ENST00000593901.1_Silent_p.Y5Y|SYT3_ENST00000544769.1_Silent_p.Y5Y	NM_032298.2	NP_115674.1	Q9BQG1	SYT3_HUMAN	synaptotagmin III	5					calcium ion-dependent exocytosis (GO:0017156)|positive regulation of vesicle fusion (GO:0031340)|response to calcium ion (GO:0051592)	cell junction (GO:0030054)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|synaptic vesicle (GO:0008021)	calcium-dependent phospholipid binding (GO:0005544)|metal ion binding (GO:0046872)|phosphatidylserine binding (GO:0001786)|transporter activity (GO:0005215)			breast(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(16)|ovary(2)|prostate(2)|skin(3)|urinary_tract(2)	35		all_neural(266;0.131)		OV - Ovarian serous cystadenocarcinoma(262;0.00462)|GBM - Glioblastoma multiforme(134;0.0188)		GGTCATCCTCGTAGTCTCCTG	0.622													G|||	511	0.102037	0.0514	0.0403	5008	,	,		19077	0.0982		0.1501	False		,,,				2504	0.1687				p.Y5Y		Atlas-SNP	.											.	SYT3	85	.	0			c.C15T						PASS	.	G	,,	334,4072	168.7+/-199.5	14,306,1883	43.0	38.0	40.0		15,15,15	-4.6	1.0	19	dbSNP_107	40	1460,7140	268.3+/-287.8	133,1194,2973	no	coding-synonymous,coding-synonymous,coding-synonymous	SYT3	NM_001160328.1,NM_001160329.1,NM_032298.2	,,	147,1500,4856	AA,AG,GG		16.9767,7.5806,13.7936	,,	5/591,5/591,5/591	51140654	1794,11212	2203	4300	6503	SO:0001819	synonymous_variant	84258	exon1			ATCCTCGTAGTCT	AL136594	CCDS12798.1	19q13.33	2014-07-02			ENSG00000213023	ENSG00000213023		"""Synaptotagmins"""	11511	protein-coding gene	gene with protein product		600327				7749232	Standard	NM_032298		Approved		uc002psv.3	Q9BQG1	OTTHUMG00000183064	ENST00000338916.4:c.15C>T	19.37:g.51140654G>A		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	33	19	0.575758	NM_032298	Q8N5Z1|Q8N640	Silent	SNP	ENST00000338916.4	37	CCDS12798.1																																																																																			G|0.881;A|0.119	0.119	strong		0.622	SYT3-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464910.1	NM_032298	
ZNF774	342132	hgsc.bcm.edu	37	15	90903502	90903502	+	Missense_Mutation	SNP	G	G	A	rs11854320	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:90903502G>A	ENST00000354377.3	+	4	625	c.439G>A	c.(439-441)Gta>Ata	p.V147I	ZNF774_ENST00000379090.5_Intron|ZNF774_ENST00000558115.1_3'UTR	NM_001004309.2	NP_001004309.2	Q6NX45	ZN774_HUMAN	zinc finger protein 774	147			V -> I (in dbSNP:rs11854320).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.V147I(1)		breast(1)|cervix(1)|endometrium(2)|large_intestine(4)|lung(4)|prostate(1)|stomach(1)	14	Melanoma(11;0.00551)|Lung NSC(78;0.0158)|all_lung(78;0.0331)		BRCA - Breast invasive adenocarcinoma(143;0.0224)|KIRC - Kidney renal clear cell carcinoma(17;0.138)|Kidney(142;0.194)			GGATGGATATGTAGGAGAGAA	0.493													G|||	482	0.096246	0.1694	0.1066	5008	,	,		19912	0.0427		0.1163	False		,,,				2504	0.0245				p.V147I		Atlas-SNP	.											ZNF774,NS,carcinoma,0,1	ZNF774	35	1	1	Substitution - Missense(1)	stomach(1)	c.G439A						scavenged	.	G	ILE/VAL	772,3626	310.8+/-291.8	74,624,1501	74.0	76.0	75.0		439	1.5	0.0	15	dbSNP_120	75	953,7643	207.9+/-249.5	60,833,3405	yes	missense	ZNF774	NM_001004309.2	29	134,1457,4906	AA,AG,GG		11.0866,17.5534,13.2754	benign	147/484	90903502	1725,11269	2199	4298	6497	SO:0001583	missense	342132	exon4			GGATATGTAGGAG	BC067279	CCDS32330.1	15q26.1	2013-01-08				ENSG00000196391		"""Zinc fingers, C2H2-type"""	33108	protein-coding gene	gene with protein product							Standard	NM_001004309		Approved	MGC75360	uc002bpk.4	Q6NX45		ENST00000354377.3:c.439G>A	15.37:g.90903502G>A	ENSP00000346348:p.Val147Ile	Somatic	83	2	0.0240964		WXS	Illumina HiSeq	Phase_I	88	36	0.409091	NM_001004309	A8K020	Missense_Mutation	SNP	ENST00000354377.3	37	CCDS32330.1	245	0.11217948717948718	79	0.16056910569105692	38	0.10497237569060773	35	0.06118881118881119	93	0.12269129287598944	G	9.491	1.100722	0.20552	0.175534	0.110866	ENSG00000196391	ENST00000354377	T	0.05925	3.37	5.51	1.5	0.22942	.	0.528567	0.14024	N	0.346624	T	0.00012	0.0000	N	0.22421	0.69	0.09310	P	0.9999999999047681	B	0.06786	0.001	B	0.04013	0.001	T	0.38067	-0.9678	9	0.66056	D	0.02	.	6.8497	0.24008	0.4968:0.0:0.5032:0.0	rs11854320;rs52813081;rs11854320	147	Q6NX45	ZN774_HUMAN	I	147	ENSP00000346348:V147I	ENSP00000346348:V147I	V	+	1	0	ZNF774	88704506	0.000000	0.05858	0.014000	0.15608	0.205000	0.24178	-0.425000	0.07017	0.270000	0.21984	0.655000	0.94253	GTA	G|0.879;A|0.121	0.121	strong		0.493	ZNF774-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418048.1	NM_001004309	
AP5Z1	9907	hgsc.bcm.edu	37	7	4821352	4821352	+	Missense_Mutation	SNP	G	G	C	rs11549840	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:4821352G>C	ENST00000348624.4	+	3	427	c.333G>C	c.(331-333)caG>caC	p.Q111H	AP5Z1_ENST00000401897.1_Missense_Mutation_p.Q111H	NM_014855.2	NP_055670.1	O43299	AP5Z1_HUMAN	adaptor-related protein complex 5, zeta 1 subunit	111					cell death (GO:0008219)|double-strand break repair via homologous recombination (GO:0000724)|endosomal transport (GO:0016197)|protein transport (GO:0015031)	AP-5 adaptor complex (GO:0044599)|AP-type membrane coat adaptor complex (GO:0030119)|cytoplasm (GO:0005737)|nucleus (GO:0005634)											ACAGCCGGCAGCTGAGCCTGG	0.662													G|||	63	0.0125799	0.0015	0.0187	5008	,	,		17920	0.0		0.0249	False		,,,				2504	0.0235				p.Q111H		Atlas-SNP	.											.	.	.	.	0			c.G333C						PASS	.	G	HIS/GLN	13,4247		0,13,2117	21.0	26.0	24.0		333	2.1	0.8	7	dbSNP_120	24	205,8303		4,197,4053	yes	missense	KIAA0415	NM_014855.2	24	4,210,6170	CC,CG,GG		2.4095,0.3052,1.7074	possibly-damaging	111/808	4821352	218,12550	2130	4254	6384	SO:0001583	missense	9907	exon3			CCGGCAGCTGAGC	AB007875	CCDS47528.1	7p22.1	2012-03-20	2012-03-20	2012-03-20	ENSG00000242802	ENSG00000242802			22197	protein-coding gene	gene with protein product		613653	"""KIAA0415"""	KIAA0415		20613862, 22022230	Standard	NM_014855		Approved	SPG48, zeta	uc003sne.3	O43299	OTTHUMG00000151754	ENST00000348624.4:c.333G>C	7.37:g.4821352G>C	ENSP00000297562:p.Gln111His	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	124	27	0.217742	NM_014855	Q8N3X2|Q96H80	Missense_Mutation	SNP	ENST00000348624.4	37	CCDS47528.1	33	0.01510989010989011	2	0.0040650406504065045	12	0.03314917127071823	0	0.0	19	0.025065963060686015	G	10.63	1.404230	0.25378	0.003052	0.024095	ENSG00000242802	ENST00000348624;ENST00000401897	T;T	0.44482	0.92;0.92	5.08	2.13	0.27403	.	0.485095	0.20242	N	0.096270	T	0.13970	0.0338	M	0.63428	1.95	0.24747	N	0.993007	B	0.23316	0.083	B	0.20184	0.028	T	0.12941	-1.0528	10	0.27785	T	0.31	.	5.8299	0.18574	0.1763:0.2946:0.5291:0.0	rs11549840	111	O43299	K0415_HUMAN	H	111	ENSP00000297562:Q111H;ENSP00000384980:Q111H	ENSP00000297562:Q111H	Q	+	3	2	KIAA0415	4787878	0.601000	0.26907	0.815000	0.32552	0.847000	0.48162	-0.102000	0.10956	0.256000	0.21614	0.655000	0.94253	CAG	G|0.986;C|0.014	0.014	strong		0.662	AP5Z1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323771.1		
MRGPRX3	117195	hgsc.bcm.edu	37	11	18158958	18158958	+	Missense_Mutation	SNP	C	C	T	rs61733595	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:18158958C>T	ENST00000396275.2	+	3	570	c.209C>T	c.(208-210)gCg>gTg	p.A70V		NM_054031.3	NP_473372.3	Q96LB0	MRGX3_HUMAN	MAS-related GPR, member X3	70						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(5)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	27						AACCTGGTCGCGGCCGACTTC	0.567													c|||	38	0.00758786	0.0015	0.0144	5008	,	,		20868	0.0		0.0249	False		,,,				2504	0.001				p.A70V		Atlas-SNP	.											MRGPRX3,colon,carcinoma,-1,1	MRGPRX3	59	1	0			c.C209T						PASS	.	C	VAL/ALA	16,4384	24.3+/-50.5	0,16,2184	97.0	93.0	94.0		209	-2.9	0.0	11	dbSNP_129	94	205,8381	88.9+/-151.2	6,193,4094	yes	missense	MRGPRX3	NM_054031.3	64	6,209,6278	TT,TC,CC		2.3876,0.3636,1.7018	benign	70/323	18158958	221,12765	2200	4293	6493	SO:0001583	missense	117195	exon3			TGGTCGCGGCCGA		CCDS7830.1	11p15.1	2013-10-10			ENSG00000179826	ENSG00000179826		"""GPCR / Class A : Orphans"""	17980	protein-coding gene	gene with protein product		607229				11551509	Standard	NM_054031		Approved	MRGX3	uc001mnu.3	Q96LB0	OTTHUMG00000166435	ENST00000396275.2:c.209C>T	11.37:g.18158958C>T	ENSP00000379571:p.Ala70Val	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	74	57	0.77027	NM_054031	B0M0L1|Q8TDE0|Q8TDE1	Missense_Mutation	SNP	ENST00000396275.2	37	CCDS7830.1	24	0.01098901098901099	1	0.0020325203252032522	4	0.011049723756906077	0	0.0	19	0.025065963060686015	C	6.482	0.457078	0.12283	0.003636	0.023876	ENSG00000179826	ENST00000396275;ENST00000531264	T;T	0.17691	2.26;2.26	1.46	-2.93	0.05598	GPCR, rhodopsin-like superfamily (1);	1.571520	0.03654	N	0.241532	T	0.02970	0.0088	L	0.29908	0.895	0.09310	N	1	B	0.14805	0.011	B	0.15870	0.014	T	0.25398	-1.0133	10	0.06236	T	0.91	.	4.2118	0.10515	0.0:0.3809:0.2485:0.3706	rs61733595	70	Q96LB0	MRGX3_HUMAN	V	70	ENSP00000379571:A70V;ENSP00000436242:A70V	ENSP00000379571:A70V	A	+	2	0	MRGPRX3	18115534	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.038000	0.12144	-1.289000	0.02375	-0.687000	0.03738	GCG	C|0.987;T|0.013	0.013	strong		0.567	MRGPRX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389767.1	NM_054031	
RAP1GAP	5909	hgsc.bcm.edu	37	1	21940555	21940555	+	Missense_Mutation	SNP	C	C	T	rs2275363	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:21940555C>T	ENST00000374765.4	-	8	519	c.319G>A	c.(319-321)Gct>Act	p.A107T	RAP1GAP_ENST00000374761.2_Missense_Mutation_p.A138T|RAP1GAP_ENST00000374757.3_5'UTR|RAP1GAP_ENST00000542643.2_Missense_Mutation_p.A107T|RAP1GAP_ENST00000290101.4_Missense_Mutation_p.A171T|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	106	0	0		WXS	Illumina HiSeq	Phase_I	87	24	0.275862	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	
TNFRSF10C	8794	hgsc.bcm.edu	37	8	22974315	22974315	+	Missense_Mutation	SNP	A	A	C	rs61736405		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:22974315A>C	ENST00000356864.3	+	5	1083	c.551A>C	c.(550-552)aAc>aCc	p.N184T	TNFRSF10C_ENST00000540813.1_Missense_Mutation_p.N82T	NM_003841.3	NP_003832	O14798	TR10C_HUMAN	tumor necrosis factor receptor superfamily, member 10c, decoy without an intracellular domain	184					apoptotic process (GO:0006915)|signal transduction (GO:0007165)	anchored component of membrane (GO:0031225)|integral component of plasma membrane (GO:0005887)	transmembrane signaling receptor activity (GO:0004888)	p.N184T(1)		endometrium(1)|large_intestine(6)|lung(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	15		Prostate(55;0.0421)|Breast(100;0.067)		Colorectal(74;0.0147)|COAD - Colon adenocarcinoma(73;0.0612)		GAGACAATGAACACCAGCCCG	0.602																																					p.N184T		Atlas-SNP	.											TNFRSF10C,trunk,malignant_melanoma,0,1	TNFRSF10C	30	1	1	Substitution - Missense(1)	skin(1)	c.A551C						scavenged	.						68.0	80.0	76.0					8																	22974315		2203	4297	6500	SO:0001583	missense	8794	exon5			CAATGAACACCAG	AF012536	CCDS6037.1	8p22-p21	2006-02-22			ENSG00000173535	ENSG00000173535		"""Tumor necrosis factor receptor superfamily"", ""CD molecules"""	11906	protein-coding gene	gene with protein product		603613				9314565, 9325248	Standard	NM_003841		Approved	DcR1, TRAILR3, LIT, TRID, CD263	uc003xcy.3	O14798	OTTHUMG00000097844	ENST00000356864.3:c.551A>C	8.37:g.22974315A>C	ENSP00000349324:p.Asn184Thr	Somatic	120	9	0.075		WXS	Illumina HiSeq	Phase_I	118	11	0.0932203	NM_003841	O14755|Q08AS6|Q6FH98|Q6UXM5	Missense_Mutation	SNP	ENST00000356864.3	37	CCDS6037.1	.	.	.	.	.	.	.	.	.	.	A	1.881	-0.457883	0.04508	.	.	ENSG00000173535	ENST00000356864;ENST00000540813;ENST00000544885	T;T	0.62788	0.0;1.25	.	.	.	.	0.568776	0.17737	U	0.163718	T	0.28400	0.0702	N	0.03608	-0.345	0.22213	N	0.999289	P	0.38110	0.618	B	0.33690	0.168	T	0.14924	-1.0455	9	0.37606	T	0.19	.	2.8413	0.05530	0.5024:0.497:2.0E-4:3.0E-4	rs61736405	184	O14798	TR10C_HUMAN	T	184;82;184	ENSP00000349324:N184T;ENSP00000437612:N82T	ENSP00000349324:N184T	N	+	2	0	TNFRSF10C	23030260	0.001000	0.12720	0.054000	0.19295	0.104000	0.19210	0.918000	0.28678	0.077000	0.16863	0.076000	0.15429	AAC	A|0.013;C|0.987	0.987	weak		0.602	TNFRSF10C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215134.3		
APOBEC3F	200316	hgsc.bcm.edu	37	22	39440149	39440149	+	Intron	SNP	C	C	T	rs5750728	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:39440149C>T	ENST00000308521.5	+	3	528				APOBEC3F_ENST00000381565.2_Missense_Mutation_p.A78V|APOBEC3F_ENST00000491387.1_Intron|APOBEC3G_ENST00000452957.2_Intron	NM_145298.5	NP_660341.2	Q8IUX4	ABC3F_HUMAN	apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3F						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)					ggccagtgcgccccaccacat	0.582													C|||	2504	0.5	0.202	0.6239	5008	,	,		18242	0.7093		0.4911	False		,,,				2504	0.6084				p.A78V		Atlas-SNP	.											.	APOBEC3F	37	.	0			c.C233T						PASS	.	C	VAL/ALA,	1141,3239		159,823,1208	48.0	42.0	44.0		233,	0.2	0.0	22	dbSNP_114	44	4530,4050		1198,2134,958	no	missense,intron	APOBEC3F	NM_001006666.1,NM_145298.5	64,	1357,2957,2166	TT,TC,CC		47.2028,26.0502,43.7577	,	78/102,	39440149	5671,7289	2190	4290	6480	SO:0001627	intron_variant	200316	exon3			AGTGCGCCCCACC	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.172-797C>T	22.37:g.39440149C>T		Somatic	232	0	0		WXS	Illumina HiSeq	Phase_I	222	117	0.527027	NM_001006666	B0QYD4|Q45F03|Q6ICH3|Q7Z2N2|Q7Z2N5	Missense_Mutation	SNP	ENST00000308521.5	37	CCDS33648.1	1108	0.5073260073260073	110	0.22357723577235772	236	0.6519337016574586	405	0.708041958041958	357	0.470976253298153	.	6.374	0.437123	0.12104	0.260502	0.527972	ENSG00000128394	ENST00000381565	T	0.17370	2.28	0.235	0.235	0.15431	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.17667	0.023	B	0.11329	0.006	T	0.20907	-1.0261	6	0.48119	T	0.1	.	.	.	.	rs5750728;rs8141017;rs52830498;rs59723377;rs5750728	78	Q6ICH3	.	V	78	ENSP00000370977:A78V	ENSP00000370977:A78V	A	+	2	0	APOBEC3F	37770095	0.001000	0.12720	0.033000	0.17914	0.034000	0.12701	-0.356000	0.07661	0.308000	0.22923	0.313000	0.20887	GCC	C|0.534;T|0.466	0.466	strong		0.582	APOBEC3F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321216.1	NM_145298	
C19orf53	28974	hgsc.bcm.edu	37	19	13885484	13885484	+	Missense_Mutation	SNP	A	A	G	rs10104	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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_ENST00000591826.1_RNA|CTB-5E10.3_ENST00000586297.1_RNA|CTB-5E10.3_ENST00000586894.1_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	265	0	0		WXS	Illumina HiSeq	Phase_I	224	108	0.482143	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	
GRK4	2868	hgsc.bcm.edu	37	4	3015553	3015553	+	Missense_Mutation	SNP	G	G	A	rs1140085	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:3015553G>A	ENST00000398052.4	+	8	1082	c.739G>A	c.(739-741)Gta>Ata	p.V247I	GRK4_ENST00000345167.6_Missense_Mutation_p.V215I|GRK4_ENST00000504933.1_Missense_Mutation_p.V247I|GRK4_ENST00000398051.4_Missense_Mutation_p.V215I	NM_182982.2	NP_892027.2	P32298	GRK4_HUMAN	G protein-coupled receptor kinase 4	247	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		V -> I (in dbSNP:rs35605687). {ECO:0000269|PubMed:17344846}.		G-protein coupled receptor internalization (GO:0002031)|receptor internalization (GO:0031623)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|signal transduction (GO:0007165)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytosol (GO:0005829)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)	ATP binding (GO:0005524)|G-protein coupled receptor kinase activity (GO:0004703)|rhodopsin kinase activity (GO:0050254)			lung(1)|upper_aerodigestive_tract(1)	2				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)		AAGTAGATTCGTAGTAAGTGT	0.418													G|||	217	0.0433307	0.0053	0.0576	5008	,	,		20854	0.001		0.1541	False		,,,				2504	0.0143				p.V247I		Atlas-SNP	.											GRK4_ENST00000398052,NS,carcinoma,0,1	GRK4	72	1	0			c.G739A						PASS	.	G	ILE/VAL,ILE/VAL,ILE/VAL	130,4276	94.4+/-133.1	6,118,2079	114.0	97.0	103.0		643,739,739	4.8	1.0	4	dbSNP_86	103	1131,7469	233.9+/-267.0	73,985,3242	yes	missense,missense,missense	GRK4	NM_001004056.1,NM_001004057.1,NM_182982.2	29,29,29	79,1103,5321	AA,AG,GG		13.1512,2.9505,9.6955	possibly-damaging,possibly-damaging,possibly-damaging	215/547,247/533,247/579	3015553	1261,11745	2203	4300	6503	SO:0001583	missense	2868	exon8			AGATTCGTAGTAA		CCDS33946.1, CCDS33947.1, CCDS47002.1, CCDS68656.1	4p16.3	2008-02-05	2004-02-04	2004-02-06	ENSG00000125388	ENSG00000125388			4543	protein-coding gene	gene with protein product		137026	"""G protein-coupled receptor kinase 2-like (Drosophila)"""	GPRK2L		1338872	Standard	NM_182982		Approved	GPRK4	uc003ggn.1	P32298	OTTHUMG00000159914	ENST00000398052.4:c.739G>A	4.37:g.3015553G>A	ENSP00000381129:p.Val247Ile	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	61	28	0.459016	NM_182982	O00641|O00642|Q13293|Q13294|Q13295|Q14453|Q14725|Q15313|Q15314|Q15315|Q15316|Q17RH6|Q53EQ8	Missense_Mutation	SNP	ENST00000398052.4	37	CCDS33946.1	149	0.06822344322344322	3	0.006097560975609756	25	0.06906077348066299	0	0.0	121	0.15963060686015831	G	12.40	1.925259	0.34002	0.029505	0.131512	ENSG00000125388	ENST00000398051;ENST00000398052;ENST00000345167;ENST00000504933	T;T;T;T	0.17528	2.27;2.27;2.27;2.27	4.76	4.76	0.60689	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.64402	U	0.000001	T	0.00039	0.0001	N	0.04090	-0.28	0.09310	P	1.0	P;B;P;P	0.48998	0.918;0.069;0.644;0.868	P;B;B;P	0.46825	0.448;0.081;0.26;0.528	T	0.48514	-0.9029	9	0.14656	T	0.56	-9.527	16.8263	0.85933	0.0:0.0:1.0:0.0	rs35605687	215;215;247;247	P32298-3;P32298-2;P32298-4;P32298	.;.;.;GRK4_HUMAN	I	215;247;215;247	ENSP00000381128:V215I;ENSP00000381129:V247I;ENSP00000264764:V215I;ENSP00000427445:V247I	ENSP00000264764:V215I	V	+	1	0	GRK4	2985351	1.000000	0.71417	0.998000	0.56505	0.019000	0.09904	7.688000	0.84153	2.199000	0.70637	0.650000	0.86243	GTA	G|0.914;A|0.086	0.086	strong		0.418	GRK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358176.2	NM_005307	
GTF2IRD2	84163	hgsc.bcm.edu	37	7	74212036	74212036	+	Missense_Mutation	SNP	C	C	G	rs707394	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:74212036C>G	ENST00000405086.2	-	16	2004	c.1815G>C	c.(1813-1815)aaG>aaC	p.K605N	GTF2IRD2_ENST00000451013.2_Missense_Mutation_p.K152N	NM_173537.2	NP_775808	Q86UP8	GTD2A_HUMAN	GTF2I repeat domain containing 2	605					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)	p.K605K(1)		breast(1)|endometrium(3)|large_intestine(2)|lung(2)|ovary(2)|skin(1)	11						cgatacagaactttttcaggc	0.502													C|||	427	0.0852636	0.0507	0.072	5008	,	,		20449	0.0169		0.1441	False		,,,				2504	0.1513				p.K605N	NSCLC(40;560 1096 7501 40315 49546)	Atlas-SNP	.											GTF2IRD2,colon,carcinoma,0,1	GTF2IRD2	38	1	1	Substitution - coding silent(1)	large_intestine(1)	c.G1815C						PASS	.	C	ASN/LYS	277,4129	152.9+/-186.6	13,251,1939	39.0	38.0	38.0		1815	1.7	0.8	7	dbSNP_86	38	1273,7325	247.1+/-275.3	98,1077,3124	no	missense	GTF2IRD2	NM_173537.2	94	111,1328,5063	GG,GC,CC		14.8058,6.2869,11.9194	benign	605/950	74212036	1550,11454	2203	4299	6502	SO:0001583	missense	84163	exon16			ACAGAACTTTTTC	BC047706	CCDS5576.1, CCDS64682.1	7q11.23	2014-05-06			ENSG00000196275	ENSG00000196275			30775	protein-coding gene	gene with protein product	"""transcription factor GTF2IRD2"""	608899				15243160	Standard	NM_173537		Approved	FLJ37938, GTF2IRD2A	uc003ubd.1	Q86UP8	OTTHUMG00000181527	ENST00000405086.2:c.1815G>C	7.37:g.74212036C>G	ENSP00000385491:p.Lys605Asn	Somatic	650	1	0.00153846		WXS	Illumina HiSeq	Phase_I	566	233	0.411661	NM_173537	A8K5W6|B3KUZ2|Q69G40|Q6EKI8|Q6EKI9|Q6NVW2|Q6P7N8|Q86WX4|Q8ND85|Q8NDE5	Missense_Mutation	SNP	ENST00000405086.2	37	CCDS5576.1	.	.	.	.	.	.	.	.	.	.	c	4.974	0.180974	0.09443	0.062869	0.148058	ENSG00000196275	ENST00000405086;ENST00000451013	D;D	0.85861	-2.04;-2.04	1.74	1.74	0.24563	Ribonuclease H-like (1);	.	.	.	.	T	0.00936	0.0031	L	0.28556	0.865	0.09310	P	0.9999999968134	P	0.36065	0.535	B	0.34301	0.179	T	0.20240	-1.0281	8	0.25751	T	0.34	-13.8646	7.1297	0.25493	0.0:1.0:0.0:0.0	rs707394	605	Q86UP8	GTD2A_HUMAN	N	605;152	ENSP00000385491:K605N;ENSP00000406723:K152N	ENSP00000385491:K605N	K	-	3	2	GTF2IRD2	73849972	0.915000	0.31059	0.828000	0.32881	0.705000	0.40729	0.705000	0.25675	1.317000	0.45149	0.442000	0.29010	AAG	C|0.885;G|0.115	0.115	strong		0.502	GTF2IRD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252712.3	NM_173537	
KPRP	448834	hgsc.bcm.edu	37	1	152733301	152733301	+	Missense_Mutation	SNP	T	T	A	rs4329520	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:152733301T>A	ENST00000606109.1	+	1	1265	c.1237T>A	c.(1237-1239)Tgc>Agc	p.C413S	KPRP_ENST00000368773.1_Missense_Mutation_p.C413S			Q5T749	KPRP_HUMAN	keratinocyte proline-rich protein	413	Pro-rich.		C -> S (in dbSNP:rs4329520).			cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)				NS(1)|breast(1)|endometrium(9)|kidney(1)|large_intestine(10)|lung(21)|ovary(6)|pancreas(1)|prostate(6)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	60	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)			CCCAGAACCATGCATAAGTCT	0.577													T|||	2455	0.490216	0.5787	0.4914	5008	,	,		19481	0.4177		0.5159	False		,,,				2504	0.4182				p.C413S		Atlas-SNP	.											.	KPRP	152	.	0			c.T1237A						PASS	.	T	SER/CYS	2439,1967	620.2+/-393.5	676,1087,440	166.0	170.0	168.0		1237	-0.3	0.0	1	dbSNP_111	168	4323,4277	579.2+/-390.9	1097,2129,1074	yes	missense	KPRP	NM_001025231.1	112	1773,3216,1514	AA,AT,TT		49.7326,44.6437,48.0086	benign	413/580	152733301	6762,6244	2203	4300	6503	SO:0001583	missense	448834	exon2			GAACCATGCATAA	AY960854	CCDS30862.1	1q21.3	2008-02-05	2007-02-02	2006-12-07	ENSG00000203786	ENSG00000203786			31823	protein-coding gene	gene with protein product		613260	"""chromosome 1 open reading frame 45"""	C1orf45		16297201	Standard	NM_001025231		Approved		uc001fal.1	Q5T749	OTTHUMG00000012402	ENST00000606109.1:c.1237T>A	1.37:g.152733301T>A	ENSP00000475216:p.Cys413Ser	Somatic	209	0	0		WXS	Illumina HiSeq	Phase_I	195	101	0.517949	NM_001025231		Missense_Mutation	SNP	ENST00000606109.1	37	CCDS30862.1	1120	0.5128205128205128	294	0.5975609756097561	196	0.5414364640883977	248	0.43356643356643354	382	0.503957783641161	T	13.38	2.220864	0.39201	0.553563	0.502674	ENSG00000203786	ENST00000368773	T	0.24908	1.83	4.88	-0.312	0.12758	.	0.277746	0.26359	N	0.024827	T	0.04452	0.0122	L	0.52573	1.65	0.80722	P	0.0	B	0.16396	0.017	B	0.15484	0.013	T	0.38023	-0.9680	9	0.09590	T	0.72	-8.4552	0.3401	0.00332	0.2846:0.1651:0.1471:0.4032	rs4329520;rs60534699;rs4329520	413	Q5T749	KPRP_HUMAN	S	413	ENSP00000357762:C413S	ENSP00000357762:C413S	C	+	1	0	KPRP	150999925	0.000000	0.05858	0.000000	0.03702	0.092000	0.18411	-0.196000	0.09532	-0.142000	0.11354	0.379000	0.24179	TGC	T|0.489;A|0.511	0.511	strong		0.577	KPRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034522.2	NM_001025231	
OR6B3	150681	hgsc.bcm.edu	37	2	240984833	240984833	+	Silent	SNP	C	C	G	rs13389099	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:240984833C>G	ENST00000319423.4	-	1	656	c.657G>C	c.(655-657)gcG>gcC	p.A219A	PRR21_ENST00000408934.1_5'Flank	NM_173351.1	NP_775486.1	Q8NGW1	OR6B3_HUMAN	olfactory receptor, family 6, subfamily B, member 3	219						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(10)|lung(4)|ovary(2)|prostate(1)	18		all_epithelial(40;1.64e-11)|Breast(86;0.000327)|Renal(207;0.00571)|Ovarian(221;0.104)|all_hematologic(139;0.182)|all_lung(227;0.229)|Melanoma(123;0.238)		Epithelial(121;1.05e-29)|all cancers(36;3.52e-28)|OV - Ovarian serous cystadenocarcinoma(60;4.63e-14)|Kidney(56;2.99e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.56e-05)|Lung(119;0.00344)|LUSC - Lung squamous cell carcinoma(224;0.0148)|Colorectal(34;0.019)|COAD - Colon adenocarcinoma(134;0.141)		GGGTGATGTGCGCATATGACA	0.592													t|||	1218	0.243211	0.2912	0.1744	5008	,	,		20769	0.2054		0.2614	False		,,,				2504	0.2474				p.A219A		Atlas-SNP	.											.	OR6B3	37	.	0			c.G657C						PASS	.	T		1287,3011		197,893,1059	62.0	67.0	65.0		657	-8.2	0.0	2	dbSNP_121	65	2297,6203		310,1677,2263	no	coding-synonymous	OR6B3	NM_173351.1		507,2570,3322	GG,GC,CC		27.0235,29.9442,28.0044		219/332	240984833	3584,9214	2149	4250	6399	SO:0001819	synonymous_variant	150681	exon1			GATGTGCGCATAT		CCDS42837.1	2q37.3	2013-09-23	2002-11-13	2002-11-15	ENSG00000178586	ENSG00000178586		"""GPCR / Class A : Olfactory receptors"""	15042	protein-coding gene	gene with protein product			"""olfactory receptor, family 6, subfamily B, member 3 pseudogene"""	OR6B3P			Standard	NM_173351		Approved	OR6B3Q	uc010zoe.2	Q8NGW1	OTTHUMG00000152399	ENST00000319423.4:c.657G>C	2.37:g.240984833C>G		Somatic	251	1	0.00398406		WXS	Illumina HiSeq	Phase_I	229	100	0.436681	NM_173351	Q6IFH3	Silent	SNP	ENST00000319423.4	37	CCDS42837.1																																																																																			C|0.751;G|0.249	0.249	strong		0.592	OR6B3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326078.1		
OR7A5	26659	hgsc.bcm.edu	37	19	14938616	14938616	+	Silent	SNP	T	T	C	rs2190686	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	106	0	0		WXS	Illumina HiSeq	Phase_I	79	37	0.468354	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	
ATP10D	57205	hgsc.bcm.edu	37	4	47560163	47560163	+	Silent	SNP	C	C	A	rs11729411	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	180	0	0		WXS	Illumina HiSeq	Phase_I	171	165	0.964912	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	
MUC20	200958	hgsc.bcm.edu	37	3	195452799	195452799	+	Missense_Mutation	SNP	C	C	T	rs2550232		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195452799C>T	ENST00000447234.2	+	2	1451	c.1325C>T	c.(1324-1326)aCa>aTa	p.T442I	MUC20_ENST00000436408.1_Missense_Mutation_p.T442I|MUC20_ENST00000445522.2_Missense_Mutation_p.T407I|MUC20_ENST00000320736.6_Missense_Mutation_p.T271I	NM_001282506.1	NP_001269435.1	Q8N307	MUC20_HUMAN	mucin 20, cell surface associated	442			T -> I (in dbSNP:rs2550232). {ECO:0000269|PubMed:12975309, ECO:0000269|PubMed:14565953, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		activation of MAPK activity (GO:0000187)|cellular protein metabolic process (GO:0044267)|hepatocyte growth factor receptor signaling pathway (GO:0048012)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein homooligomerization (GO:0051260)	basal plasma membrane (GO:0009925)|cell projection (GO:0042995)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)		p.T442I(1)		NS(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(4)|skin(4)|stomach(3)|upper_aerodigestive_tract(1)	23	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)	Lung NSC(153;0.191)	Epithelial(36;1e-21)|all cancers(36;9.02e-20)|OV - Ovarian serous cystadenocarcinoma(49;1.6e-18)|Lung(62;0.000104)|LUSC - Lung squamous cell carcinoma(58;0.000128)	GBM - Glioblastoma multiforme(46;1.66e-05)		GCCTCAGACACAGATCTCATC	0.532																																					p.T271I		Atlas-SNP	.											MUC20,NS,carcinoma,0,1	MUC20	84	1	1	Substitution - Missense(1)	stomach(1)	c.C812T						PASS	.						32.0	28.0	29.0					3																	195452799		2010	4148	6158	SO:0001583	missense	200958	exon3			CAGACACAGATCT	AB037780	CCDS63877.1	3q29	2008-08-07	2006-03-14		ENSG00000176945	ENSG00000176945		"""Mucins"""	23282	protein-coding gene	gene with protein product		610360				14565953	Standard	NM_001282506		Approved	FLJ14408, KIAA1359	uc010hzo.3	Q8N307	OTTHUMG00000155823	ENST00000447234.2:c.1325C>T	3.37:g.195452799C>T	ENSP00000414350:p.Thr442Ile	Somatic	483	0	0		WXS	Illumina HiSeq	Phase_I	488	215	0.440574	NM_152673	Q6UX97|Q76I83|Q76I85|Q86ST8|Q8NBY6|Q96KA1|Q9P2I8	Missense_Mutation	SNP	ENST00000447234.2	37		.	.	.	.	.	.	.	.	.	.	C	5.403	0.259635	0.10239	.	.	ENSG00000176945	ENST00000447234;ENST00000320736;ENST00000436408;ENST00000445522	T;T;T;T	0.13657	2.99;2.99;3.16;2.57	4.27	-2.63	0.06133	.	1.775520	0.02976	N	0.144951	T	0.06690	0.0171	N	0.11201	0.11	0.80722	P	0.0	B	0.09022	0.002	B	0.13407	0.009	T	0.31280	-0.9949	9	0.12430	T	0.62	5.5294	5.5723	0.17204	0.0:0.4472:0.1347:0.4182	rs2550232;rs3906442	271	E9PH32	.	I	442;271;442;407	ENSP00000414350:T442I;ENSP00000325431:T271I;ENSP00000396774:T442I;ENSP00000405629:T407I	ENSP00000325431:T271I	T	+	2	0	MUC20	196938470	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.576000	0.05854	-0.731000	0.04862	-0.291000	0.09656	ACA	C|0.500;T|0.500	0.500	weak		0.532	MUC20-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000341835.1	NM_152673	
MUC2	4583	hgsc.bcm.edu	37	11	1092920	1092920	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:1092920C>A	ENST00000441003.2	+	30	4766	c.4739C>A	c.(4738-4740)aCc>aAc	p.T1580N	MUC2_ENST00000359061.5_Missense_Mutation_p.T1581N|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)				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)	ggcacacagaccccaacatcg	0.632																																					p.T1580N		Atlas-SNP	.											.	MUC2	614	.	0			c.C4739A						PASS	.						74.0	113.0	100.0					11																	1092920		1924	3573	5497	SO:0001583	missense	4583	exon30			CACAGACCCCAAC	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.4739C>A	11.37:g.1092920C>A	ENSP00000415183:p.Thr1580Asn	Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	72	4	0.0555556	NM_002457	Q14878	Missense_Mutation	SNP	ENST00000441003.2	37		.	.	.	.	.	.	.	.	.	.	C	2.897	-0.228278	0.06022	.	.	ENSG00000198788	ENST00000441003;ENST00000359061	T;T	0.15952	2.38;2.53	1.75	-3.51	0.04696	.	7739.210000	0.00597	U	0.000365	T	0.08492	0.0211	.	.	.	0.09310	N	1	B	0.28026	0.198	B	0.17098	0.017	T	0.10776	-1.0615	9	0.27082	T	0.32	.	2.0197	0.03506	0.1703:0.3607:0.3305:0.1386	.	1580	E7EUV1	.	N	1580;1581	ENSP00000415183:T1580N;ENSP00000351956:T1581N	ENSP00000351956:T1581N	T	+	2	0	MUC2	1082920	0.001000	0.12720	0.000000	0.03702	0.071000	0.16799	1.304000	0.33482	-1.223000	0.02584	0.121000	0.15741	ACC	.	.	none		0.632	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
MUC5B	727897	hgsc.bcm.edu	37	11	1262907	1262907	+	Silent	SNP	T	T	C	rs2037089	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:1262907T>C	ENST00000529681.1	+	31	4855	c.4797T>C	c.(4795-4797)agT>agC	p.S1599S	MUC5B_ENST00000447027.1_Silent_p.S1602S|RP11-532E4.2_ENST00000532061.2_RNA	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	1599	7 X Cys-rich subdomain repeats.				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)		TCTGCTGCAGTGACGACCACT	0.637													t|||	1025	0.204673	0.2685	0.2709	5008	,	,		15649	0.0615		0.2078	False		,,,				2504	0.2157				p.S1599S		Atlas-SNP	.											.	MUC5B	473	.	0			c.T4797C						PASS	.			1122,3124		151,820,1152	21.0	28.0	26.0		4797	-2.8	0.0	11	dbSNP_94	26	1595,6851		162,1271,2790	no	coding-synonymous	MUC5B	NM_002458.2		313,2091,3942	CC,CT,TT		18.8847,26.4249,21.4072		1599/5763	1262907	2717,9975	2123	4223	6346	SO:0001819	synonymous_variant	727897	exon31			CTGCAGTGACGAC	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.4797T>C	11.37:g.1262907T>C		Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	126	21	0.166667	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Silent	SNP	ENST00000529681.1	37	CCDS44515.2																																																																																			T|0.797;C|0.203	0.203	strong		0.637	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
TICRR	90381	hgsc.bcm.edu	37	15	90170237	90170237	+	Missense_Mutation	SNP	C	C	T	rs3743372	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:90170237C>T	ENST00000268138.7	+	22	5758	c.5653C>T	c.(5653-5655)Cgc>Tgc	p.R1885C	TICRR_ENST00000560985.1_Missense_Mutation_p.R1884C|KIF7_ENST00000558928.1_Intron			Q7Z2Z1	TICRR_HUMAN	TOPBP1-interacting checkpoint and replication regulator	1885			R -> C (in dbSNP:rs3743372). {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)										TCCTTTCAGTCGCGCTTTCTC	0.512													C|||	1339	0.267372	0.0514	0.2839	5008	,	,		18146	0.3958		0.33	False		,,,				2504	0.3507				p.R1885C		Atlas-SNP	.											.	.	.	.	0			c.C5653T						PASS	.	C	CYS/ARG	380,4020	189.5+/-215.6	19,342,1839	155.0	167.0	162.0		5653	3.5	0.8	15	dbSNP_107	162	2873,5725	450.8+/-362.5	476,1921,1902	yes	missense	C15orf42	NM_152259.3	180	495,2263,3741	TT,TC,CC		33.4147,8.6364,25.0269	probably-damaging	1885/1911	90170237	3253,9745	2200	4299	6499	SO:0001583	missense	90381	exon22			TTCAGTCGCGCTT	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.5653C>T	15.37:g.90170237C>T	ENSP00000268138:p.Arg1885Cys	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	75	27	0.36	NM_152259	B2RE07|B3KVV9|D3IUT4|Q8N4X8|Q8NCH6|Q9BU55	Missense_Mutation	SNP	ENST00000268138.7	37	CCDS10352.2	572	0.2619047619047619	28	0.056910569105691054	89	0.24585635359116023	200	0.34965034965034963	255	0.33641160949868076	C	15.60	2.881889	0.51908	0.086364	0.334147	ENSG00000140534	ENST00000268138	T	0.09073	3.02	5.55	3.49	0.39957	.	0.543177	0.13398	N	0.390899	T	0.00012	0.0000	L	0.60455	1.87	0.20926	P	0.999826096	D	0.71674	0.998	P	0.56700	0.804	T	0.48422	-0.9037	9	0.62326	D	0.03	-0.6141	8.4641	0.32944	0.5226:0.3609:0.1166:0.0	rs3743372;rs58716305;rs3743372	1885	Q7Z2Z1	TICRR_HUMAN	C	1885	ENSP00000268138:R1885C	ENSP00000268138:R1885C	R	+	1	0	C15orf42	87971241	0.396000	0.25262	0.816000	0.32577	0.334000	0.28698	0.993000	0.29680	1.328000	0.45358	0.563000	0.77884	CGC	C|0.746;T|0.254	0.254	strong		0.512	TICRR-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000312856.1	NM_152259	
WIPF2	147179	hgsc.bcm.edu	37	17	38416827	38416827	+	Missense_Mutation	SNP	G	G	A	rs142659099	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:38416827G>A	ENST00000323571.4	+	3	344	c.104G>A	c.(103-105)cGg>cAg	p.R35Q	WIPF2_ENST00000494757.1_3'UTR|WIPF2_ENST00000394103.3_Missense_Mutation_p.R35Q|WIPF2_ENST00000583130.1_Missense_Mutation_p.R35Q|WIPF2_ENST00000536600.1_Missense_Mutation_p.R35Q|WIPF2_ENST00000585043.1_Missense_Mutation_p.R35Q	NM_133264.4	NP_573571.1	Q8TF74	WIPF2_HUMAN	WAS/WASL interacting protein family, member 2	35					Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)				NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(6)|ovary(1)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	30						GATGAGCAGCGGGGTCGAGGC	0.527										HNSCC(43;0.11)			G|||	10	0.00199681	0.0	0.0029	5008	,	,		18945	0.0		0.005	False		,,,				2504	0.0031				p.R35Q		Atlas-SNP	.											.	WIPF2	55	.	0			c.G104A						PASS	.	G	GLN/ARG	5,4401	9.9+/-24.2	0,5,2198	105.0	91.0	96.0		104	5.7	1.0	17	dbSNP_134	96	55,8545	34.3+/-88.2	0,55,4245	yes	missense	WIPF2	NM_133264.4	43	0,60,6443	AA,AG,GG		0.6395,0.1135,0.4613	possibly-damaging	35/441	38416827	60,12946	2203	4300	6503	SO:0001583	missense	147179	exon3			AGCAGCGGGGTCG	BC025965	CCDS11364.1	17q21.2	2006-10-12			ENSG00000171475	ENSG00000171475			30923	protein-coding gene	gene with protein product		609692				12213210, 11829459	Standard	XM_005257083		Approved	WICH, WIRE	uc002hug.1	Q8TF74	OTTHUMG00000133331	ENST00000323571.4:c.104G>A	17.37:g.38416827G>A	ENSP00000320924:p.Arg35Gln	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	78	37	0.474359	NM_133264	A8K0L3|Q658J8|Q71RE1|Q8TE44	Missense_Mutation	SNP	ENST00000323571.4	37	CCDS11364.1	7	0.003205128205128205	0	0.0	2	0.0055248618784530384	0	0.0	5	0.006596306068601583	G	23.0	4.362796	0.82353	0.001135	0.006395	ENSG00000171475	ENST00000323571;ENST00000394103;ENST00000536600	T;T;T	0.42131	1.6;0.98;0.98	5.74	5.74	0.90152	.	0.065269	0.64402	D	0.000005	T	0.20170	0.0485	N	0.17082	0.46	0.36982	D	0.894329	P;D	0.59357	0.898;0.985	B;B	0.41299	0.147;0.353	T	0.12502	-1.0545	10	0.30078	T	0.28	-8.5645	13.1603	0.59540	0.0727:0.0:0.9273:0.0	.	35;35	A8MWR2;Q8TF74	.;WIPF2_HUMAN	Q	35	ENSP00000320924:R35Q;ENSP00000377663:R35Q;ENSP00000439175:R35Q	ENSP00000320924:R35Q	R	+	2	0	WIPF2	35670353	1.000000	0.71417	0.993000	0.49108	0.998000	0.95712	6.376000	0.73141	2.709000	0.92574	0.555000	0.69702	CGG	G|0.997;A|0.003	0.003	strong		0.527	WIPF2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257157.2	NM_133264	
PEX14	5195	hgsc.bcm.edu	37	1	10689942	10689942	+	Silent	SNP	G	G	T	rs11539794	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:10689942G>T	ENST00000356607.4	+	9	1112	c.1032G>T	c.(1030-1032)ggG>ggT	p.G344G	PEX14_ENST00000538836.1_Silent_p.G280G	NM_004565.2	NP_004556.1	O75381	PEX14_HUMAN	peroxisomal biogenesis factor 14	344					microtubule anchoring (GO:0034453)|negative regulation of protein binding (GO:0032091)|negative regulation of protein homotetramerization (GO:1901094)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription, DNA-templated (GO:0045892)|peroxisome organization (GO:0007031)|peroxisome transport along microtubule (GO:0036250)|protein complex assembly (GO:0006461)|protein homooligomerization (GO:0051260)|protein import into peroxisome matrix (GO:0016558)|protein import into peroxisome matrix, substrate release (GO:0044721)|protein import into peroxisome matrix, translocation (GO:0016561)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)|protein complex (GO:0043234)	beta-tubulin binding (GO:0048487)|microtubule binding (GO:0008017)|protein N-terminus binding (GO:0047485)|receptor binding (GO:0005102)|transcription corepressor activity (GO:0003714)			breast(3)|endometrium(1)|large_intestine(3)|lung(5)|prostate(1)	13	Ovarian(185;0.203)	all_lung(284;6.02e-06)|Lung NSC(185;9.62e-06)|Renal(390;0.000147)|Breast(348;0.000932)|Colorectal(325;0.00215)|Hepatocellular(190;0.00913)|Ovarian(437;0.023)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0292)|Colorectal(212;9.13e-08)|COAD - Colon adenocarcinoma(227;2.07e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000482)|Kidney(185;0.00174)|KIRC - Kidney renal clear cell carcinoma(229;0.00457)|STAD - Stomach adenocarcinoma(132;0.0249)|READ - Rectum adenocarcinoma(331;0.0419)		ACTGCCTGGGGGTGCAGAGGG	0.657													G|||	519	0.103634	0.0197	0.1326	5008	,	,		16747	0.0228		0.1948	False		,,,				2504	0.1861				p.G344G		Atlas-SNP	.											PEX14,NS,carcinoma,0,1	PEX14	40	1	0			c.G1032T						PASS	.	G		200,4202	123.7+/-161.0	3,194,2004	183.0	190.0	188.0		1032	0.2	1.0	1	dbSNP_120	188	1631,6969	298.5+/-303.9	148,1335,2817	no	coding-synonymous	PEX14	NM_004565.2		151,1529,4821	TT,TG,GG		18.9651,4.5434,14.0824		344/378	10689942	1831,11171	2201	4300	6501	SO:0001819	synonymous_variant	5195	exon9			CCTGGGGGTGCAG	AF045186	CCDS30582.1	1p36.22	2008-05-14			ENSG00000142655	ENSG00000142655			8856	protein-coding gene	gene with protein product		601791				9653144	Standard	NM_004565		Approved		uc001arn.3	O75381	OTTHUMG00000001908	ENST00000356607.4:c.1032G>T	1.37:g.10689942G>T		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	71	39	0.549296	NM_004565	B2R7N1|B3KML6|B7Z1N2|Q8WX51	Silent	SNP	ENST00000356607.4	37	CCDS30582.1																																																																																			G|0.875;T|0.125	0.125	strong		0.657	PEX14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005414.1		
MUC4	4585	hgsc.bcm.edu	37	3	195509817	195509817	+	Silent	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195509817G>A	ENST00000463781.3	-	2	9093	c.8634C>T	c.(8632-8634)gcC>gcT	p.A2878A	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Silent_p.A2878A	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)		GAAGAGGGGTGGCATGACCTG	0.597																																					p.A2878A		Atlas-SNP	.											.	MUC4	1505	.	0			c.C8634T						PASS	.						11.0	14.0	13.0					3																	195509817		644	1518	2162	SO:0001819	synonymous_variant	4585	exon2			AGGGGTGGCATGA	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.8634C>T	3.37:g.195509817G>A		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	114	29	0.254386	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		0.597	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
PRAMEF10	343071	hgsc.bcm.edu	37	1	12954921	12954921	+	Missense_Mutation	SNP	A	A	G	rs199792484	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:12954921A>G	ENST00000235347.4	-	3	441	c.362T>C	c.(361-363)gTc>gCc	p.V121A		NM_001039361.3	NP_001034450.2	O60809	PRA10_HUMAN	PRAME family member 10	121					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)					NS(2)|breast(1)|large_intestine(2)|lung(5)|ovary(1)|upper_aerodigestive_tract(1)	12	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00143)|all_lung(284;0.00181)|Colorectal(325;0.00215)|Breast(348;0.00224)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Colorectal(212;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)		GCAGGAGAGGACCCTGGCTCC	0.532																																					p.V121A		Atlas-SNP	.											PRAMEF10,NS,carcinoma,0,1	PRAMEF10	35	1	0			c.T362C						scavenged	.						16.0	16.0	16.0					1																	12954921		1209	2747	3956	SO:0001583	missense	343071	exon3			GAGAGGACCCTGG	AL049682	CCDS41255.1	1p36.21	2013-01-17			ENSG00000187545	ENSG00000187545		"""-"""	27997	protein-coding gene	gene with protein product							Standard	NM_001039361		Approved		uc001auo.3	O60809	OTTHUMG00000001981	ENST00000235347.4:c.362T>C	1.37:g.12954921A>G	ENSP00000235347:p.Val121Ala	Somatic	148	2	0.0135135		WXS	Illumina HiSeq	Phase_I	37	18	0.486486	NM_001039361	Q2M1V2	Missense_Mutation	SNP	ENST00000235347.4	37	CCDS41255.1	.	.	.	.	.	.	.	.	.	.	.	0.001	-2.989193	0.00046	.	.	ENSG00000187545	ENST00000235347	T	0.04706	3.57	1.65	-3.3	0.05003	.	2.600110	0.01694	N	0.026836	T	0.01287	0.0042	N	0.00642	-1.3	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.35101	-0.9802	10	0.02654	T	1	.	2.8919	0.05679	0.4191:0.0:0.2344:0.3465	.	121	O60809	PRA10_HUMAN	A	121	ENSP00000235347:V121A	ENSP00000235347:V121A	V	-	2	0	PRAMEF10	12877508	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-3.380000	0.00491	-2.367000	0.00605	-1.140000	0.01884	GTC	A|0.930;G|0.070	0.070	strong		0.532	PRAMEF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005512.2	XM_496342	
ARSD	414	hgsc.bcm.edu	37	X	2835863	2835863	+	Missense_Mutation	SNP	G	G	T	rs78034736	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:2835863G>T	ENST00000381154.1	-	5	920	c.845C>A	c.(844-846)gCt>gAt	p.A282D	ARSD_ENST00000217890.6_5'UTR	NM_001669.3	NP_001660.2	P51689	ARSD_HUMAN	arylsulfatase D	282					cellular protein metabolic process (GO:0044267)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	arylsulfatase activity (GO:0004065)|metal ion binding (GO:0046872)			large_intestine(3)|lung(3)	6		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				ATAGGAAACAGCTTCCTTTAG	0.512																																					p.A282D		Atlas-SNP	.											.	ARSD	47	.	0			c.C845A						PASS	.						47.0	40.0	42.0					X																	2835863		2203	4300	6503	SO:0001583	missense	414	exon5			GAAACAGCTTCCT	X83572	CCDS35196.1	Xp22.3	2013-02-14			ENSG00000006756	ENSG00000006756		"""Arylsulfatase family"""	717	protein-coding gene	gene with protein product		300002				7720070	Standard	NM_001669		Approved		uc004cqy.3	P51689	OTTHUMG00000021077	ENST00000381154.1:c.845C>A	X.37:g.2835863G>T	ENSP00000370546:p.Ala282Asp	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	89	18	0.202247	NM_001669	Q9UHJ8	Missense_Mutation	SNP	ENST00000381154.1	37	CCDS35196.1	131	0.07896323086196504	63	0.13577586206896552	45	0.1271186440677966	28	0.0498220640569395	68	0.0913978494623656	g	15.63	2.889517	0.52014	.	.	ENSG00000006756	ENST00000381154;ENST00000217890	D	0.95949	-3.86	3.36	3.36	0.38483	Alkaline phosphatase-like, alpha/beta/alpha (1);Sulfatase (1);Alkaline-phosphatase-like, core domain (1);	0.199306	0.41294	U	0.000909	T	0.50633	0.1627	H	0.99712	4.72	0.09310	P	0.999999469392	D;D	0.89917	1.0;0.999	D;D	0.79784	0.993;0.971	T	0.55522	-0.8128	9	0.87932	D	0	.	14.3198	0.66479	0.0:0.0:1.0:0.0	.	282;282	E9PAW5;P51689	.;ARSD_HUMAN	D	282	ENSP00000370546:A282D	ENSP00000217890:A282D	A	-	2	0	ARSD	2845863	1.000000	0.71417	0.008000	0.14137	0.274000	0.26718	6.148000	0.71788	1.338000	0.45544	0.281000	0.19383	GCT	G|0.920;T|0.080	0.080	strong		0.512	ARSD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055636.1		
COL6A5	256076	hgsc.bcm.edu	37	3	130104206	130104206	+	Splice_Site	SNP	A	A	G	rs10212372	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:130104206A>G	ENST00000432398.2	+	5	2354	c.1860A>G	c.(1858-1860)aaA>aaG	p.K620K	COL6A5_ENST00000265379.6_Splice_Site_p.K620K	NM_153264.5	NP_694996.5	A8TX70	CO6A5_HUMAN	collagen, type VI, alpha 5	620	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						GCGCTGAAAAAGGTAAGCAAC	0.408													A|||	2012	0.401757	0.4871	0.4597	5008	,	,		22209	0.5198		0.2028	False		,,,				2504	0.3282				p.K620K		Atlas-SNP	.											.	COL6A5	205	.	0			c.A1860G						PASS	.						16.0	14.0	14.0					3																	130104206		692	1590	2282	SO:0001630	splice_region_variant	256076	exon5			TGAAAAAGGTAAG	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.1861+1A>G	3.37:g.130104206A>G		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	74	33	0.445946	NM_153264	A9J6L2|A9J6L4|A9J6L6|A9J6L7|A9J6M0|A9J6M1|A9J6M2|B5MEA7|Q6ZW26|Q8NA36	Silent	SNP	ENST00000432398.2	37																																																																																				A|0.613;G|0.387	0.387	strong		0.408	COL6A5-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_153264	Silent
LRP1	4035	hgsc.bcm.edu	37	12	57587437	57587437	+	Silent	SNP	T	T	C	rs34456957	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:57587437T>C	ENST00000243077.3	+	47	8239	c.7773T>C	c.(7771-7773)tgT>tgC	p.C2591C	MIR1228_ENST00000408438.1_RNA	NM_002332.2	NP_002323.2	Q07954	LRP1_HUMAN	low density lipoprotein receptor-related protein 1	2591	LDL-receptor class A 12. {ECO:0000255|PROSITE-ProRule:PRU00124}.				aging (GO:0007568)|aorta morphogenesis (GO:0035909)|apoptotic cell clearance (GO:0043277)|beta-amyloid clearance (GO:0097242)|cell proliferation (GO:0008283)|cholesterol metabolic process (GO:0008203)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of platelet-derived growth factor receptor-beta signaling pathway (GO:2000587)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of Wnt signaling pathway (GO:0030178)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of lipid transport (GO:0032370)|positive regulation of protein transport (GO:0051222)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|receptor-mediated endocytosis (GO:0006898)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cholesterol transport (GO:0032374)|regulation of phospholipase A2 activity (GO:0032429)|retinoid metabolic process (GO:0001523)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	apolipoprotein binding (GO:0034185)|calcium ion binding (GO:0005509)|lipoprotein particle receptor binding (GO:0070325)|lipoprotein transporter activity (GO:0042954)|poly(A) RNA binding (GO:0044822)|protein complex binding (GO:0032403)|receptor activity (GO:0004872)			NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(33)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(26)|lung(58)|ovary(10)|pancreas(2)|prostate(11)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	184				BRCA - Breast invasive adenocarcinoma(357;0.0103)	Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031)	CCGACGACTGTGGGGATGGCT	0.602													T|||	7	0.00139776	0.0	0.0029	5008	,	,		21660	0.0		0.005	False		,,,				2504	0.0				p.C2591C		Atlas-SNP	.											.	LRP1	428	.	0			c.T7773C						PASS	.	T		6,4400	11.4+/-27.6	0,6,2197	94.0	84.0	87.0		7773	-8.4	0.8	12	dbSNP_126	87	63,8537	39.3+/-95.6	0,63,4237	no	coding-synonymous	LRP1	NM_002332.2		0,69,6434	CC,CT,TT		0.7326,0.1362,0.5305		2591/4545	57587437	69,12937	2203	4300	6503	SO:0001819	synonymous_variant	4035	exon47			CGACTGTGGGGAT	X13916	CCDS8932.1	12q13.3	2013-05-28	2010-01-26		ENSG00000123384	ENSG00000123384		"""CD molecules"", ""Low density lipoprotein receptors"""	6692	protein-coding gene	gene with protein product		107770	"""alpha-2-macroglobulin receptor"""	APR, A2MR		2548950	Standard	NM_002332		Approved	LRP, CD91, LRP1A, APOER	uc001snd.3	Q07954	OTTHUMG00000044412	ENST00000243077.3:c.7773T>C	12.37:g.57587437T>C		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	64	29	0.453125	NM_002332	Q2PP12|Q86SW0|Q8IVG8	Silent	SNP	ENST00000243077.3	37	CCDS8932.1																																																																																			T|0.996;C|0.004	0.004	strong		0.602	LRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412772.2	NM_002332	
TWF2	11344	hgsc.bcm.edu	37	3	52264907	52264907	+	Silent	SNP	T	T	C	rs352143	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:52264907T>C	ENST00000305533.5	-	6	831	c.588A>G	c.(586-588)aaA>aaG	p.K196K	TWF2_ENST00000499914.2_Silent_p.K196K|TLR9_ENST00000597542.1_5'UTR|TLR9_ENST00000494383.1_Missense_Mutation_p.N57D	NM_007284.3	NP_009215.1	Q6IBS0	TWF2_HUMAN	twinfilin actin-binding protein 2	196	ADF-H 2. {ECO:0000255|PROSITE- ProRule:PRU00599}.				barbed-end actin filament capping (GO:0051016)|cell projection organization (GO:0030030)|cellular response to growth factor stimulus (GO:0071363)|cellular response to retinoic acid (GO:0071300)|negative regulation of actin filament polymerization (GO:0030837)|positive regulation of axon extension (GO:0045773)|positive regulation of lamellipodium assembly (GO:0010592)|positive regulation of neuron projection development (GO:0010976)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of microvillus length (GO:0032532)|sequestering of actin monomers (GO:0042989)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|myofibril (GO:0030016)|perinuclear region of cytoplasm (GO:0048471)|stereocilium (GO:0032420)	actin monomer binding (GO:0003785)|ATP binding (GO:0005524)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|poly(A) RNA binding (GO:0044822)|protein kinase C binding (GO:0005080)			breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|stomach(1)|urinary_tract(1)	15				BRCA - Breast invasive adenocarcinoma(193;2.43e-05)|Kidney(197;0.000539)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)		AGTTGACCATTTTCTGCTTGA	0.597													C|||	1016	0.202875	0.4244	0.1671	5008	,	,		21314	0.0357		0.1909	False		,,,				2504	0.1135				p.K196K		Atlas-SNP	.											.	TWF2	33	.	0			c.A588G						PASS	.	C		1514,2890	657.1+/-400.2	261,992,949	87.0	84.0	85.0		588	3.9	0.4	3	dbSNP_79	85	1736,6864	721.9+/-406.4	174,1388,2738	no	coding-synonymous	TWF2	NM_007284.3		435,2380,3687	CC,CT,TT		20.186,34.3778,24.9923		196/350	52264907	3250,9754	2202	4300	6502	SO:0001819	synonymous_variant	11344	exon6			GACCATTTTCTGC	Y17169	CCDS2849.1	3p21.1	2013-04-25	2013-04-25	2006-11-13	ENSG00000247596	ENSG00000247596			9621	protein-coding gene	gene with protein product		607433	"""protein tyrosine kinase 9-like (A6-related protein)"", ""PTK9L protein tyrosine kinase 9-like (A6-related protein)"", ""twinfilin, actin-binding protein, homolog 2 (Drosophila)"""	PTK9L		10406962, 12807912	Standard	NM_007284		Approved	A6RP, A6r		Q6IBS0	OTTHUMG00000158105	ENST00000305533.5:c.588A>G	3.37:g.52264907T>C		Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	108	49	0.453704	NM_007284	Q9Y3F5	Silent	SNP	ENST00000305533.5	37	CCDS2849.1	419	0.19184981684981686	192	0.3902439024390244	67	0.1850828729281768	21	0.03671328671328671	139	0.18337730870712401	C	3.859	-0.030265	0.07543	0.343778	0.20186	ENSG00000173366	ENST00000494383	.	.	.	4.74	3.86	0.44501	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.999999168762	.	.	.	.	.	.	T	0.38650	-0.9651	3	.	.	.	.	10.7667	0.46297	0.0:0.8434:0.0:0.1566	rs352143;rs17844842;rs17857554;rs17858381;rs57276328;rs352143	.	.	.	D	57	.	.	N	-	1	0	RP11-330H6.5	52239947	0.071000	0.21146	0.409000	0.26459	0.360000	0.29518	0.533000	0.23082	0.431000	0.26258	-0.374000	0.07098	AAT	T|0.768;G|0.002	.	strong		0.597	TWF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350199.2		
NAPB	63908	hgsc.bcm.edu	37	20	23377815	23377815	+	Silent	SNP	G	G	A	rs17750862	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:23377815G>A	ENST00000377026.4	-	3	274	c.189C>T	c.(187-189)aaC>aaT	p.N63N	NAPB_ENST00000432543.2_Intron|NAPB_ENST00000398425.3_De_novo_Start_InFrame|NAPB_ENST00000472855.1_Intron	NM_001283018.1|NM_001283020.1|NM_022080.2	NP_001269947.1|NP_001269949.1|NP_071363.1	Q9H115	SNAB_HUMAN	N-ethylmaleimide-sensitive factor attachment protein, beta	63					intracellular protein transport (GO:0006886)|regulation of synaptic vesicle priming (GO:0010807)|SNARE complex disassembly (GO:0035494)|synaptic transmission, glutamatergic (GO:0035249)	extracellular vesicular exosome (GO:0070062)|synaptobrevin 2-SNAP-25-syntaxin-1a complex (GO:0070044)				endometrium(1)|kidney(2)|large_intestine(2)|lung(5)|ovary(1)|skin(1)	12	Lung NSC(19;0.0646)|Colorectal(13;0.0993)|all_lung(19;0.143)					GACAAAATGCGTTTCCTGCAG	0.478													G|||	110	0.0219649	0.0015	0.0231	5008	,	,		17642	0.001		0.0537	False		,,,				2504	0.0378				p.N63N		Atlas-SNP	.											.	NAPB	22	.	0			c.C189T						PASS	.	G		47,4359	48.2+/-83.0	0,47,2156	71.0	59.0	63.0		189	-2.1	1.0	20	dbSNP_123	63	440,8160	134.7+/-192.1	18,404,3878	no	coding-synonymous	NAPB	NM_022080.2		18,451,6034	AA,AG,GG		5.1163,1.0667,3.7444		63/299	23377815	487,12519	2203	4300	6503	SO:0001819	synonymous_variant	63908	exon3			AAATGCGTTTCCT	AK022817	CCDS13152.1, CCDS63241.1, CCDS63242.1, CCDS74710.1	20p12.3-p11.21	2008-08-01			ENSG00000125814	ENSG00000125814			15751	protein-coding gene	gene with protein product		611270				8455721	Standard	NM_022080		Approved	SNAP-BETA, SNAPB	uc002wta.3	Q9H115	OTTHUMG00000032062	ENST00000377026.4:c.189C>T	20.37:g.23377815G>A		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	62	24	0.387097	NM_022080	B4DK44|Q4G0M0|Q4G187|Q5JXF9|Q8N3C4	Silent	SNP	ENST00000377026.4	37	CCDS13152.1																																																																																			G|0.966;A|0.034	0.034	strong		0.478	NAPB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078317.2	NM_022080	
SALL4	57167	hgsc.bcm.edu	37	20	50407966	50407966	+	Silent	SNP	C	C	T	rs13038893	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:50407966C>T	ENST00000217086.4	-	2	1167	c.1056G>A	c.(1054-1056)gcG>gcA	p.A352A	SALL4_ENST00000395997.3_Silent_p.A352A|SALL4_ENST00000371539.3_Intron|SALL4_ENST00000483130.1_5'Flank	NM_020436.3	NP_065169.1	Q9UJQ4	SALL4_HUMAN	spalt-like transcription factor 4	352					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						ATGTGTCTAGCGCCACAGTGG	0.612													C|||	1048	0.209265	0.3071	0.2046	5008	,	,		17598	0.0278		0.328	False		,,,				2504	0.1452				p.A352A		Atlas-SNP	.											SALL4,NS,carcinoma,-1,2	SALL4	168	2	0			c.G1056A						PASS	.	C		1466,2940	464.0+/-353.7	232,1002,969	44.0	46.0	45.0		1056	-3.9	0.0	20	dbSNP_121	45	2894,5706	447.8+/-361.6	488,1918,1894	no	coding-synonymous	SALL4	NM_020436.3		720,2920,2863	TT,TC,CC		33.6512,33.2728,33.523		352/1054	50407966	4360,8646	2203	4300	6503	SO:0001819	synonymous_variant	57167	exon2			GTCTAGCGCCACA	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.1056G>A	20.37:g.50407966C>T		Somatic	24	0	0		WXS	Illumina HiSeq	Phase_I	31	30	0.967742	NM_020436	A2A2D8|Q540H3|Q6Y8G6	Silent	SNP	ENST00000217086.4	37	CCDS13438.1																																																																																			C|0.725;T|0.275	0.275	strong		0.612	SALL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079738.3		
ALPK3	57538	hgsc.bcm.edu	37	15	85383145	85383145	+	Missense_Mutation	SNP	C	C	G	rs3803403	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:85383145C>G	ENST00000258888.5	+	5	1408	c.1241C>G	c.(1240-1242)aCt>aGt	p.T414S		NM_020778.4	NP_065829.3	Q96L96	ALPK3_HUMAN	alpha-kinase 3	414			T -> S (in dbSNP:rs3803403). {ECO:0000269|PubMed:17344846}.		heart development (GO:0007507)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(3)|breast(2)|central_nervous_system(2)|endometrium(12)|kidney(4)|large_intestine(9)|lung(27)|ovary(3)|prostate(5)|skin(8)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	81			BRCA - Breast invasive adenocarcinoma(143;0.0587)			GAGGTCGACACTCTGCGCAAG	0.677													C|||	683	0.136382	0.0159	0.1628	5008	,	,		16453	0.1329		0.2575	False		,,,				2504	0.1595				p.T414S		Atlas-SNP	.											.	ALPK3	289	.	0			c.C1241G						PASS	.	C	SER/THR	247,4159	141.1+/-176.5	10,227,1966	38.0	40.0	40.0		1241	3.0	0.0	15	dbSNP_107	40	2334,6264	387.5+/-342.2	314,1706,2279	yes	missense	ALPK3	NM_020778.4	58	324,1933,4245	GG,GC,CC		27.1458,5.606,19.8477	benign	414/1908	85383145	2581,10423	2203	4299	6502	SO:0001583	missense	57538	exon5			TCGACACTCTGCG	AY044449	CCDS10333.1	15q25.2	2013-01-29			ENSG00000136383	ENSG00000136383		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	17574	protein-coding gene	gene with protein product	"""myocyte induction differentiation originator"", ""muscle alpha-kinase"""					10021370	Standard	NM_020778		Approved	MAK, KIAA1330, Midori	uc002ble.3	Q96L96	OTTHUMG00000148667	ENST00000258888.5:c.1241C>G	15.37:g.85383145C>G	ENSP00000258888:p.Thr414Ser	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	117	69	0.589744	NM_020778	Q9P2L6	Missense_Mutation	SNP	ENST00000258888.5	37	CCDS10333.1	359	0.16437728937728938	7	0.014227642276422764	72	0.19889502762430938	81	0.14160839160839161	199	0.262532981530343	C	2.744	-0.261585	0.05791	0.05606	0.271458	ENSG00000136383	ENST00000258888	T	0.59502	0.26	4.95	2.95	0.34219	.	0.880280	0.09710	N	0.765881	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	B	0.26318	0.146	B	0.24974	0.057	T	0.21042	-1.0257	9	0.22109	T	0.4	-2.83	4.2817	0.10836	0.1755:0.6128:0.0:0.2117	rs3803403;rs60827617;rs3803403	414	Q96L96	ALPK3_HUMAN	S	414	ENSP00000258888:T414S	ENSP00000258888:T414S	T	+	2	0	ALPK3	83184149	0.001000	0.12720	0.003000	0.11579	0.126000	0.20510	0.517000	0.22832	0.981000	0.38548	0.563000	0.77884	ACT	C|0.808;G|0.192	0.192	strong		0.677	ALPK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000308997.1	NM_020778	
CABLES1	91768	hgsc.bcm.edu	37	18	20815908	20815908	+	Missense_Mutation	SNP	G	G	A	rs373572190		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:20815908G>A	ENST00000256925.7	+	6	1235	c.1235G>A	c.(1234-1236)cGg>cAg	p.R412Q	CABLES1_ENST00000585061.1_Intron|CABLES1_ENST00000400473.2_Missense_Mutation_p.R85Q|TMEM241_ENST00000450466.2_Intron|CABLES1_ENST00000420687.2_Missense_Mutation_p.R147Q	NM_001100619.2	NP_001094089.1	Q8TDN4	CABL1_HUMAN	Cdk5 and Abl enzyme substrate 1	412	Interacts with CDK3. {ECO:0000250}.			R -> W (in Ref. 4; AAL83906). {ECO:0000305}.	blood coagulation (GO:0007596)|cell cycle (GO:0007049)|cell division (GO:0051301)|nervous system development (GO:0007399)|regulation of cell cycle (GO:0051726)|regulation of cell division (GO:0051302)	cytosol (GO:0005829)|nucleus (GO:0005634)	cyclin-dependent protein serine/threonine kinase regulator activity (GO:0016538)			breast(1)|kidney(2)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)|stomach(1)	11	all_cancers(21;0.000102)|all_epithelial(16;2.48e-06)|Lung NSC(20;0.00696)|all_lung(20;0.0197)|Colorectal(14;0.0202)|Ovarian(20;0.127)					TTTGGAGCCCGGAGAAATACC	0.527																																					p.R412Q		Atlas-SNP	.											CABLES1,NS,carcinoma,+1,1	CABLES1	32	1	0			c.G1235A						scavenged	.	G	GLN/ARG,GLN/ARG	1,3773		0,1,1886	175.0	170.0	172.0		1235,440	5.5	1.0	18		172	0,8204		0,0,4102	no	missense,missense	CABLES1	NM_001100619.2,NM_138375.2	43,43	0,1,5988	AA,AG,GG		0.0,0.0265,0.0083	possibly-damaging,possibly-damaging	412/634,147/369	20815908	1,11977	1887	4102	5989	SO:0001583	missense	91768	exon6			GAGCCCGGAGAAA	BC037218	CCDS42417.1, CCDS42418.1, CCDS58615.1	18q11.2	2005-08-16				ENSG00000134508			25097	protein-coding gene	gene with protein product		609194				12477932	Standard	NM_138375		Approved	HsT2563, FLJ35924	uc002kuc.2	Q8TDN4		ENST00000256925.7:c.1235G>A	18.37:g.20815908G>A	ENSP00000256925:p.Arg412Gln	Somatic	191	1	0.0052356		WXS	Illumina HiSeq	Phase_I	182	3	0.0164835	NM_001100619	B4DK60|Q8N3Y8|Q8NA22|Q9BTG1	Missense_Mutation	SNP	ENST00000256925.7	37	CCDS42417.1	.	.	.	.	.	.	.	.	.	.	G	33	5.285654	0.95517	2.65E-4	0.0	ENSG00000134508	ENST00000400473;ENST00000256925;ENST00000420687	T;T;T	0.46819	0.95;0.86;0.92	5.47	5.47	0.80525	.	0.000000	0.85682	D	0.000000	T	0.64450	0.2599	L	0.47716	1.5	0.80722	D	1	D;D	0.89917	0.998;1.0	D;D	0.79108	0.986;0.992	T	0.64202	-0.6463	10	0.54805	T	0.06	-13.7876	19.3324	0.94297	0.0:0.0:1.0:0.0	.	147;412	Q8TDN4-2;Q8TDN4	.;CABL1_HUMAN	Q	85;412;147	ENSP00000383321:R85Q;ENSP00000256925:R412Q;ENSP00000413851:R147Q	ENSP00000256925:R412Q	R	+	2	0	CABLES1	19069906	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.386000	0.97228	2.571000	0.86741	0.655000	0.94253	CGG	.	.	weak		0.527	CABLES1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000445198.2	NM_138375	
DMTF1	9988	hgsc.bcm.edu	37	7	86800364	86800364	+	Missense_Mutation	SNP	G	G	C	rs117360089	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:86800364G>C	ENST00000394703.5	+	7	849	c.286G>C	c.(286-288)Gca>Cca	p.A96P	DMTF1_ENST00000331242.7_Missense_Mutation_p.A96P|DMTF1_ENST00000414194.2_5'UTR|DMTF1_ENST00000432937.2_Missense_Mutation_p.A8P|DMTF1_ENST00000413276.2_Missense_Mutation_p.A96P|DMTF1_ENST00000411766.2_Missense_Mutation_p.A55P|DMTF1_ENST00000394702.3_Missense_Mutation_p.A96P	NM_021145.3	NP_066968.3	Q9Y222	DMTF1_HUMAN	cyclin D binding myb-like transcription factor 1	96	Interaction with CCND2. {ECO:0000250}.|Required for DNA-binding. {ECO:0000250}.|Required for transcriptional activation. {ECO:0000250}.				cell cycle (GO:0007049)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.A96P(1)		central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(4)|ovary(1)	16	Esophageal squamous(14;0.0058)					CACAGAAGTAGCAGATGATGA	0.413													G|||	65	0.0129792	0.0008	0.0058	5008	,	,		18079	0.0		0.0209	False		,,,				2504	0.0399				p.A96P		Atlas-SNP	.											DMTF1,NS,carcinoma,0,1	DMTF1	48	1	1	Substitution - Missense(1)	endometrium(1)	c.G286C						PASS	.	G	PRO/ALA,PRO/ALA,PRO/ALA	16,4390	24.3+/-50.5	0,16,2187	120.0	107.0	112.0		22,286,286	4.5	1.0	7	dbSNP_132	112	134,8466	67.7+/-130.1	1,132,4167	yes	missense,missense,missense	DMTF1	NM_001142326.1,NM_001142327.1,NM_021145.3	27,27,27	1,148,6354	CC,CG,GG		1.5581,0.3631,1.1533	benign,benign,benign	8/673,96/761,96/761	86800364	150,12856	2203	4300	6503	SO:0001583	missense	9988	exon5			GAAGTAGCAGATG	AF084530	CCDS5601.1, CCDS47633.1	7q21	2014-06-25			ENSG00000135164	ENSG00000135164			14603	protein-coding gene	gene with protein product	"""cyclin D-binding Myb-like protein"""	608491				10095122, 24958102	Standard	NR_024549		Approved	DMP1, DMTF, hDMP1, MRUL	uc003uih.3	Q9Y222	OTTHUMG00000154135	ENST00000394703.5:c.286G>C	7.37:g.86800364G>C	ENSP00000378193:p.Ala96Pro	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	92	44	0.478261	NM_001142327	B2RBE1|B4DJS5|Q05C48|Q59G79|Q6IS13|Q969T2|Q9H2Z2|Q9H2Z3	Missense_Mutation	SNP	ENST00000394703.5	37	CCDS5601.1	20	0.009157509157509158	1	0.0020325203252032522	2	0.0055248618784530384	0	0.0	17	0.022427440633245383	G	24.6	4.554574	0.86231	0.003631	0.015581	ENSG00000135164	ENST00000331242;ENST00000394702;ENST00000413276;ENST00000447863;ENST00000425406;ENST00000411766;ENST00000420131;ENST00000449088;ENST00000430405;ENST00000432937;ENST00000394703;ENST00000434534;ENST00000412139;ENST00000425705	T;T;T;T	0.53640	0.71;0.76;0.61;0.71	5.39	4.51	0.55191	.	0.247775	0.39909	N	0.001226	T	0.21062	0.0507	L	0.29908	0.895	0.80722	D	1	B	0.09022	0.002	B	0.09377	0.004	T	0.05550	-1.0878	10	0.36615	T	0.2	-9.3253	13.3078	0.60363	0.076:0.0:0.9239:0.0	.	96	Q9Y222	DMTF1_HUMAN	P	96;96;96;96;55;55;8;96;96;8;96;96;96;96	ENSP00000332171:A96P;ENSP00000402627:A96P;ENSP00000412532:A8P;ENSP00000378193:A96P	ENSP00000332171:A96P	A	+	1	0	DMTF1	86638300	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.782000	0.55401	1.415000	0.47037	0.655000	0.94253	GCA	G|0.989;C|0.011	0.011	strong		0.413	DMTF1-002	KNOWN	alternative_5_UTR|non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334025.5	NM_021145	
OR8H2	390151	hgsc.bcm.edu	37	11	55872657	55872657	+	Missense_Mutation	SNP	A	A	C	rs28681529	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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						scavenged	.	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	277	2	0.00722022		WXS	Illumina HiSeq	Phase_I	171	122	0.71345	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	
CEL	1056	hgsc.bcm.edu	37	9	135946599	135946599	+	Silent	SNP	C	C	T	rs488087	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:135946599C>T	ENST00000372080.4	+	11	1735	c.1719C>T	c.(1717-1719)ccC>ccT	p.P573P	CEL_ENST00000351304.7_Silent_p.P504P	NM_001807.3	NP_001798.2	P19835	CEL_HUMAN	carboxyl ester lipase	570	17 X 11 AA tandem repeats, glycodomain, O-linked (mucin type).				cholesterol catabolic process (GO:0006707)|fatty acid catabolic process (GO:0009062)|intestinal cholesterol absorption (GO:0030299)|intestinal lipid catabolic process (GO:0044258)|lipid digestion (GO:0044241)|lipid metabolic process (GO:0006629)|pancreatic juice secretion (GO:0030157)|protein esterification (GO:0018350)|small molecule metabolic process (GO:0044281)|triglyceride metabolic process (GO:0006641)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	acylglycerol lipase activity (GO:0047372)|catalytic activity (GO:0003824)|heparin binding (GO:0008201)|hydrolase activity (GO:0016787)|sterol esterase activity (GO:0004771)|triglyceride lipase activity (GO:0004806)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(9)|pancreas(2)|skin(1)	20				OV - Ovarian serous cystadenocarcinoma(145;1.03e-40)|Epithelial(140;3.58e-37)|GBM - Glioblastoma multiforme(294;0.00164)|READ - Rectum adenocarcinoma(205;0.196)		AGGCCACTCCCGTGCCCCCCA	0.756													C|||	959	0.191494	0.1399	0.3012	5008	,	,		9320	0.1925		0.3091	False		,,,				2504	0.0613				p.P573P		Atlas-SNP	.											.	CEL	71	.	0			c.C1719T						PASS	.	C		558,3128		47,464,1332	16.0	19.0	18.0		1719	-4.1	0.0	9	dbSNP_83	18	2422,5714		353,1716,1999	no	coding-synonymous	CEL	NM_001807.3		400,2180,3331	TT,TC,CC		29.7689,15.1384,25.2072		573/757	135946599	2980,8842	1843	4068	5911	SO:0001819	synonymous_variant	1056	exon11			CACTCCCGTGCCC	M54994	CCDS43896.1	9q34.3	2013-03-13	2013-03-13		ENSG00000170835	ENSG00000170835	3.1.1.3, 3.1.1.13		1848	protein-coding gene	gene with protein product	"""bile salt-stimulated lipase"""	114840				1676983	Standard	NM_001807		Approved	BSSL, MODY8	uc010naa.2	P19835	OTTHUMG00000020855	ENST00000372080.4:c.1719C>T	9.37:g.135946599C>T		Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	82	33	0.402439	NM_001807	Q16398|Q5T7U7|Q9UCH1|Q9UP41	Silent	SNP	ENST00000372080.4	37	CCDS43896.1																																																																																			C|0.760;T|0.240	0.240	strong		0.756	CEL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054823.1		
FGD6	55785	hgsc.bcm.edu	37	12	95602780	95602780	+	Silent	SNP	G	G	A	rs766404	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:95602780G>A	ENST00000343958.4	-	2	2503	c.2280C>T	c.(2278-2280)taC>taT	p.Y760Y	FGD6_ENST00000550368.1_5'Flank|FGD6_ENST00000549499.1_Silent_p.Y760Y|FGD6_ENST00000546711.1_Silent_p.Y760Y	NM_018351.3	NP_060821.3	Q6ZV73	FGD6_HUMAN	FYVE, RhoGEF and PH domain containing 6	760					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)			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						GCAAGTTCTCGTACTCTGGTA	0.453													G|||	41	0.0081869	0.0015	0.0115	5008	,	,		21616	0.0		0.0239	False		,,,				2504	0.0072				p.Y760Y		Atlas-SNP	.											.	FGD6	127	.	0			c.C2280T						PASS	.	G		19,4387	26.2+/-53.5	0,19,2184	148.0	133.0	138.0		2280	-0.4	1.0	12	dbSNP_86	138	169,8431	78.4+/-141.0	3,163,4134	no	coding-synonymous	FGD6	NM_018351.3		3,182,6318	AA,AG,GG		1.9651,0.4312,1.4455		760/1431	95602780	188,12818	2203	4300	6503	SO:0001819	synonymous_variant	55785	exon2			GTTCTCGTACTCT	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.2280C>T	12.37:g.95602780G>A		Somatic	282	0	0		WXS	Illumina HiSeq	Phase_I	213	88	0.413146	NM_018351	Q6ZR53|Q7Z2Z7|Q96D44|Q9NUR8|Q9P2I5	Silent	SNP	ENST00000343958.4	37	CCDS31878.1																																																																																			G|0.986;A|0.014	0.014	strong		0.453	FGD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407600.1	NM_018351	
EAF2	55840	hgsc.bcm.edu	37	3	121563355	121563355	+	Silent	SNP	T	T	C	rs9884018	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:121563355T>C	ENST00000273668.2	+	2	233	c.162T>C	c.(160-162)ggT>ggC	p.G54G	EAF2_ENST00000451944.2_Silent_p.G54G	NM_018456.4	NP_060926.2	Q96CJ1	EAF2_HUMAN	ELL associated factor 2	54	Necessary for interaction with ELL.				apoptotic process (GO:0006915)|negative regulation of cell growth (GO:0030308)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	ELL-EAF complex (GO:0032783)|transcription elongation factor complex (GO:0008023)	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)	p.G54G(1)		endometrium(1)|kidney(2)|large_intestine(1)|lung(4)|prostate(1)	9				GBM - Glioblastoma multiforme(114;0.0972)		TTGAGGTTGGTGAAGGTGAAC	0.323													T|||	1233	0.246206	0.1339	0.1455	5008	,	,		16668	0.6161		0.1382	False		,,,				2504	0.1994				p.G54G	Esophageal Squamous(194;1942 2097 24663 29345 31866)	Atlas-SNP	.											EAF2,NS,carcinoma,0,1	EAF2	26	1	1	Substitution - coding silent(1)	prostate(1)	c.T162C						PASS	.	T		715,3691	299.3+/-285.7	70,575,1558	125.0	129.0	128.0		162	3.3	1.0	3	dbSNP_119	128	1184,7416	241.5+/-271.8	85,1014,3201	no	coding-synonymous	EAF2	NM_018456.4		155,1589,4759	CC,CT,TT		13.7674,16.2279,14.601		54/261	121563355	1899,11107	2203	4300	6503	SO:0001819	synonymous_variant	55840	exon2			GGTTGGTGAAGGT	AF517829	CCDS3006.1	3q21.1	2007-08-01			ENSG00000145088	ENSG00000145088			23115	protein-coding gene	gene with protein product		607659				12446457, 12907652	Standard	NM_018456		Approved	BM040, TRAITS, U19	uc003een.3	Q96CJ1	OTTHUMG00000159424	ENST00000273668.2:c.162T>C	3.37:g.121563355T>C		Somatic	222	0	0		WXS	Illumina HiSeq	Phase_I	168	81	0.482143	NM_018456	Q9NZ82	Silent	SNP	ENST00000273668.2	37	CCDS3006.1																																																																																			T|0.799;C|0.201	0.201	strong		0.323	EAF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355247.1	NM_018456	
PHLDB3	653583	hgsc.bcm.edu	37	19	43979589	43979589	+	Silent	SNP	G	G	T	rs1055099	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:43979589G>T	ENST00000292140.5	-	16	2256	c.1896C>A	c.(1894-1896)acC>acA	p.T632T		NM_198850.3	NP_942147.3	Q6NSJ2	PHLB3_HUMAN	pleckstrin homology-like domain, family B, member 3	632	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.						enzyme binding (GO:0019899)			breast(1)|central_nervous_system(1)|lung(5)	7		Prostate(69;0.0153)				CGTCAGCGGCGGTCACGATGA	0.672													T|||	2800	0.559105	0.6316	0.5086	5008	,	,		15307	0.6944		0.4165	False		,,,				2504	0.5041				p.T632T		Atlas-SNP	.											.	PHLDB3	30	.	0			c.C1896A						PASS	.	T		2074,1704		585,904,400	34.0	41.0	39.0		1896	-8.7	0.0	19	dbSNP_86	39	3402,4826		703,1996,1415	no	coding-synonymous	PHLDB3	NM_198850.3		1288,2900,1815	TT,TG,GG		41.3466,45.1032,45.6105		632/641	43979589	5476,6530	1889	4114	6003	SO:0001819	synonymous_variant	653583	exon16			AGCGGCGGTCACG		CCDS12621.2	19q13.31	2013-01-10			ENSG00000176531	ENSG00000176531		"""Pleckstrin homology (PH) domain containing"""	30499	protein-coding gene	gene with protein product							Standard	NM_198850		Approved	FLJ40193	uc002own.4	Q6NSJ2	OTTHUMG00000150693	ENST00000292140.5:c.1896C>A	19.37:g.43979589G>T		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	89	88	0.988764	NM_198850	Q8N7Z4	Silent	SNP	ENST00000292140.5	37	CCDS12621.2																																																																																			G|0.453;T|0.547	0.547	strong		0.672	PHLDB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319643.2		
SAAL1	113174	hgsc.bcm.edu	37	11	18108492	18108492	+	Silent	SNP	T	T	C	rs12363226	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:18108492T>C	ENST00000524803.1	-	9	1012	c.963A>G	c.(961-963)acA>acG	p.T321T	SAAL1_ENST00000533851.1_5'Flank|SAAL1_ENST00000300013.4_Silent_p.T321T|SAAL1_ENST00000529318.1_Silent_p.T321T			Q96ER3	SAAL1_HUMAN	serum amyloid A-like 1	321										breast(2)|large_intestine(5)|lung(8)	15						AGGCTAGCACTGTTTTCTGTT	0.423													T|||	719	0.14357	0.0182	0.1556	5008	,	,		14756	0.1349		0.2604	False		,,,				2504	0.1933				p.T321T		Atlas-SNP	.											.	SAAL1	34	.	0			c.A963G						PASS	.	T		234,4166	138.0+/-173.8	9,216,1975	105.0	99.0	101.0		963	-2.8	1.0	11	dbSNP_120	101	2156,6430	370.4+/-335.9	252,1652,2389	no	coding-synonymous	SAAL1	NM_138421.2		261,1868,4364	CC,CT,TT		25.1106,5.3182,18.4044		321/475	18108492	2390,10596	2200	4293	6493	SO:0001819	synonymous_variant	113174	exon9			TAGCACTGTTTTC	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.963A>G	11.37:g.18108492T>C		Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	134	25	0.186567	NM_138421	A6NH05	Silent	SNP	ENST00000524803.1	37	CCDS31439.1																																																																																			T|0.823;C|0.177	0.177	strong		0.423	SAAL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000389728.1	NM_138421	
MUC4	4585	hgsc.bcm.edu	37	3	195509964	195509964	+	Silent	SNP	A	A	G	rs71635079	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195509964A>G	ENST00000463781.3	-	2	8946	c.8487T>C	c.(8485-8487)caT>caC	p.H2829H	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Silent_p.H2829H	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)		GAGAGGTGGCATGACCTGTGA	0.592													.|||	220	0.0439297	0.1422	0.0029	5008	,	,		6953	0.001		0.0119	False		,,,				2504	0.0174				p.H2829H		Atlas-SNP	.											.	MUC4	1505	.	0			c.T8487C						PASS	.	G	,,	1080,288		494,92,98	82.0	55.0	63.0		,8487,		0.0	3	dbSNP_130	63	2335,737		1012,311,213	no	intron,coding-synonymous,intron	MUC4	NM_004532.5,NM_018406.6,NM_138297.4	,,	1506,403,311	GG,GA,AA		23.9909,21.0526,23.0856	,,	,2829/5413,	195509964	3415,1025	684	1536	2220	SO:0001819	synonymous_variant	4585	exon2			GGTGGCATGACCT	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.8487T>C	3.37:g.195509964A>G		Somatic	112	1	0.00892857		WXS	Illumina HiSeq	Phase_I	143	142	0.993007	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|1.000;|0.000	1.000	weak		0.592	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
LILRA1	11024	hgsc.bcm.edu	37	19	55106288	55106288	+	Missense_Mutation	SNP	A	A	C	rs147848714	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:55106288A>C	ENST00000251372.3	+	4	411	c.229A>C	c.(229-231)Att>Ctt	p.I77L	LILRB1_ENST00000448689.1_Intron|LILRB1_ENST00000396321.2_Intron|LILRA1_ENST00000473156.1_3'UTR|LILRB1_ENST00000418536.2_Intron|LILRA1_ENST00000453777.1_Missense_Mutation_p.I77L	NM_006863.2	NP_006854.1	O75019	LIRA1_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 1	77	Ig-like C2-type 1.				cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)|immune system process (GO:0002376)|regulation of immune response (GO:0050776)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	antigen binding (GO:0003823)|transmembrane signaling receptor activity (GO:0004888)	p.I77L(1)		breast(2)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(5)|liver(1)|lung(23)|ovary(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)	47				GBM - Glioblastoma multiforme(193;0.0348)		CCCACAGGAGATTGTGAAGAA	0.562																																					p.I77L		Atlas-SNP	.											LILRA1,colon,carcinoma,0,1	LILRA1	105	1	1	Substitution - Missense(1)	large_intestine(1)	c.A229C						PASS	.						162.0	152.0	155.0					19																	55106288		2203	4300	6503	SO:0001583	missense	11024	exon4			CAGGAGATTGTGA	AF025530	CCDS12901.1, CCDS62802.1	19q13.4	2013-01-11			ENSG00000104974	ENSG00000104974		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6602	protein-coding gene	gene with protein product		604810				9548455	Standard	NM_006863		Approved	LIR-6, CD85i, LIR6	uc002qgh.2	O75019	OTTHUMG00000065701	ENST00000251372.3:c.229A>C	19.37:g.55106288A>C	ENSP00000251372:p.Ile77Leu	Somatic	255	0	0		WXS	Illumina HiSeq	Phase_I	210	41	0.195238	NM_006863	O75018|Q3MJA6	Missense_Mutation	SNP	ENST00000251372.3	37	CCDS12901.1	.	.	.	.	.	.	.	.	.	.	C	4.547	0.101544	0.08731	.	.	ENSG00000104974	ENST00000251372;ENST00000453777	T;T	0.00695	5.83;5.83	1.62	-1.94	0.07571	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	1.576540	0.03526	N	0.221733	T	0.00300	0.0009	N	0.00224	-1.81	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.06405	0.0;0.002	T	0.46693	-0.9173	10	0.25106	T	0.35	.	4.3965	0.11365	0.55:0.2547:0.1953:0.0	.	77;77	O75019-2;O75019	.;LIRA1_HUMAN	L	77	ENSP00000251372:I77L;ENSP00000413715:I77L	ENSP00000251372:I77L	I	+	1	0	LILRA1	59798100	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-4.742000	0.00191	-0.999000	0.03442	-0.982000	0.02568	ATT	A|0.996;C|0.004	0.004	strong		0.562	LILRA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140807.2	NM_006863	
HIST1H2BF	8343	hgsc.bcm.edu	37	6	26199903	26199903	+	Silent	SNP	C	C	T	rs34961555	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:26199903C>T	ENST00000359985.1	+	1	156	c.117C>T	c.(115-117)tcC>tcT	p.S39S	HIST1H3D_ENST00000356476.2_5'Flank|HIST1H2AD_ENST00000341023.1_5'Flank|HIST1H3D_ENST00000377831.5_5'Flank	NM_003522.3	NP_003513.1	P62807	H2B1C_HUMAN	histone cluster 1, H2bf	39					antibacterial humoral response (GO:0019731)|chromatin organization (GO:0006325)|defense response to Gram-positive bacterium (GO:0050830)|innate immune response in mucosa (GO:0002227)|nucleosome assembly (GO:0006334)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|liver(2)|lung(7)|upper_aerodigestive_tract(3)	17		all_hematologic(11;0.196)				AGAGCTATTCCGTGTACGTGT	0.547													C|||	88	0.0175719	0.0038	0.0259	5008	,	,		20850	0.0		0.0646	False		,,,				2504	0.0				p.S39S		Atlas-SNP	.											.	HIST1H2BF	25	.	0			c.C117T						PASS	.	C		83,4323		1,81,2121	219.0	201.0	207.0		117	-7.8	0.1	6	dbSNP_126	207	653,7947		26,601,3673	no	coding-synonymous	HIST1H2BF	NM_003522.3		27,682,5794	TT,TC,CC		7.593,1.8838,5.6589		39/127	26199903	736,12270	2203	4300	6503	SO:0001819	synonymous_variant	8343	exon1			CTATTCCGTGTAC	Z80779	CCDS4592.1	6p22.1	2011-01-27	2006-10-11	2003-02-14	ENSG00000197846	ENSG00000277224		"""Histones / Replication-dependent"""	4752	protein-coding gene	gene with protein product		602804	"""H2B histone family, member G"", ""histone 1, H2bf"""	H2BFG		9119399, 12408966	Standard	NM_003522		Approved	H2B/g	uc003ngx.3	P62807	OTTHUMG00000014445	ENST00000359985.1:c.117C>T	6.37:g.26199903C>T		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	108	38	0.351852	NM_003522	P02278|Q3B872|Q4VB69|Q93078|Q93080	Silent	SNP	ENST00000359985.1	37	CCDS4592.1																																																																																			C|0.953;T|0.047	0.047	strong		0.547	HIST1H2BF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040108.1	NM_003522	
RNF39	80352	hgsc.bcm.edu	37	6	30041009	30041009	+	Missense_Mutation	SNP	A	A	G	rs2074479	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	145	0	0		WXS	Illumina HiSeq	Phase_I	123	67	0.544715	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	
CATSPERB	79820	hgsc.bcm.edu	37	14	92102819	92102819	+	Silent	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:92102819G>A	ENST00000256343.3	-	17	1848	c.1692C>T	c.(1690-1692)atC>atT	p.I564I		NM_024764.2	NP_079040.2	Q9H7T0	CTSRB_HUMAN	catsper channel auxiliary subunit beta	564					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)				TCTTGCTGTAGATCGTTTCCT	0.408																																					p.I564I		Atlas-SNP	.											.	CATSPERB	114	.	0			c.C1692T						PASS	.						174.0	157.0	163.0					14																	92102819		2203	4300	6503	SO:0001819	synonymous_variant	79820	exon17			GCTGTAGATCGTT	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.1692C>T	14.37:g.92102819G>A		Somatic	212	0	0		WXS	Illumina HiSeq	Phase_I	180	39	0.216667	NM_024764	A0AV51	Silent	SNP	ENST00000256343.3	37	CCDS32142.1																																																																																			.	.	none		0.408	CATSPERB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411769.1	NM_024764	
LACTB	114294	hgsc.bcm.edu	37	15	63419223	63419223	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:63419223C>T	ENST00000261893.4	+	3	662	c.590C>T	c.(589-591)cCa>cTa	p.P197L	LACTB_ENST00000413507.2_Missense_Mutation_p.P197L|RPS27L_ENST00000559763.1_Intron	NM_032857.3	NP_116246.2	P83111	LACTB_HUMAN	lactamase, beta	197						cytoplasm (GO:0005737)|mitochondrion (GO:0005739)	hydrolase activity (GO:0016787)			NS(1)|breast(1)|kidney(1)|large_intestine(3)|lung(3)|prostate(1)|skin(1)|stomach(1)	12						CCCGAATTCCCAGAAAAAGAA	0.363																																					p.P197L	Melanoma(85;443 1381 6215 27308 35583)	Atlas-SNP	.											.	LACTB	29	.	0			c.C590T						PASS	.						67.0	58.0	61.0					15																	63419223		2203	4300	6503	SO:0001583	missense	114294	exon3			AATTCCCAGAAAA	AK027808	CCDS10182.1, CCDS45275.1	15q22.1	2012-11-14	2001-12-12	2001-12-14	ENSG00000103642	ENSG00000103642		"""Mitochondrial ribosomal proteins / large subunits"""	16468	protein-coding gene	gene with protein product		608440	"""mitochondrial ribosomal protein L56"""	MRPL56		11707067	Standard	NM_032857		Approved	FLJ14902	uc002alw.3	P83111	OTTHUMG00000132807	ENST00000261893.4:c.590C>T	15.37:g.63419223C>T	ENSP00000261893:p.Pro197Leu	Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	155	28	0.180645	NM_171846	P83096	Missense_Mutation	SNP	ENST00000261893.4	37	CCDS10182.1	.	.	.	.	.	.	.	.	.	.	C	25.0	4.588482	0.86851	.	.	ENSG00000103642	ENST00000261893;ENST00000413507	T;T	0.47177	0.85;0.85	5.5	5.5	0.81552	Beta-lactamase/transpeptidase-like (2);Beta-lactamase-related (1);	0.000000	0.85682	D	0.000000	T	0.69160	0.3080	M	0.70108	2.13	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	T	0.71059	-0.4702	10	0.62326	D	0.03	-9.8513	18.3852	0.90464	0.0:1.0:0.0:0.0	.	197	P83111	LACTB_HUMAN	L	197	ENSP00000261893:P197L;ENSP00000392956:P197L	ENSP00000261893:P197L	P	+	2	0	LACTB	61206276	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.616000	0.83018	2.585000	0.87301	0.563000	0.77884	CCA	.	.	none		0.363	LACTB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256224.1	NM_032857	
NLRP8	126205	hgsc.bcm.edu	37	19	56473460	56473460	+	Silent	SNP	T	T	C	rs6509975	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:56473460T>C	ENST00000291971.3	+	4	2141	c.2070T>C	c.(2068-2070)cgT>cgC	p.R690R	NLRP8_ENST00000590542.1_Silent_p.R690R	NM_176811.2	NP_789781.2	Q86W28	NALP8_HUMAN	NLR family, pyrin domain containing 8	690					neuron death (GO:0070997)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)			breast(4)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(14)|ovary(5)|skin(2)|stomach(3)|upper_aerodigestive_tract(2)	35		Colorectal(82;0.000147)|Ovarian(87;0.17)		GBM - Glioblastoma multiforme(193;0.0695)		GGCTGCATCGTTGGTGGCAAG	0.483													C|||	1724	0.344249	0.4092	0.3646	5008	,	,		19927	0.2827		0.2972	False		,,,				2504	0.3538				p.R690R		Atlas-SNP	.											NLRP8_ENST00000291971,rectum,carcinoma,+1,2	NLRP8	225	2	0			c.T2070C						PASS	.	C		1776,2630	638.5+/-396.9	357,1062,784	198.0	171.0	180.0		2070	-0.6	0.0	19	dbSNP_116	180	2593,6007	688.2+/-404.3	407,1779,2114	no	coding-synonymous	NLRP8	NM_176811.2		764,2841,2898	CC,CT,TT		30.1512,40.3087,33.5922		690/1049	56473460	4369,8637	2203	4300	6503	SO:0001819	synonymous_variant	126205	exon4			GCATCGTTGGTGG	AY154463	CCDS12937.1	19q13.43	2008-02-05	2006-12-08	2006-12-08		ENSG00000179709		"""Nucleotide-binding domain and leucine rich repeat containing"""	22940	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 8"""	609659	"""NACHT, leucine rich repeat and PYD containing 8"""	NALP8		12563287	Standard	NM_176811		Approved	NOD16, PAN4, CLR19.2	uc002qmh.3	Q86W28		ENST00000291971.3:c.2070T>C	19.37:g.56473460T>C		Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	125	50	0.4	NM_176811	Q7RTR4	Silent	SNP	ENST00000291971.3	37	CCDS12937.1																																																																																			C|0.330;N|0.000	0.330	strong		0.483	NLRP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457462.1	NM_176811	
PDGFRB	5159	hgsc.bcm.edu	37	5	149509446	149509446	+	Missense_Mutation	SNP	C	C	T	rs41287110	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:149509446C>T	ENST00000261799.4	-	10	1922	c.1453G>A	c.(1453-1455)Gag>Aag	p.E485K		NM_002609.3	NP_002600.1	P09619	PGFRB_HUMAN	platelet-derived growth factor receptor, beta polypeptide	485	Ig-like C2-type 5.		E -> K (in dbSNP:rs41287110). {ECO:0000269|PubMed:17344846}.		adrenal gland development (GO:0030325)|aorta morphogenesis (GO:0035909)|cardiac myofibril assembly (GO:0055003)|cell chemotaxis (GO:0060326)|cell migration (GO:0016477)|cell migration involved in coronary angiogenesis (GO:0060981)|cell migration involved in vasculogenesis (GO:0035441)|cellular response to platelet-derived growth factor stimulus (GO:0036120)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|glycosaminoglycan biosynthetic process (GO:0006024)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|inner ear development (GO:0048839)|metanephric comma-shaped body morphogenesis (GO:0072278)|metanephric glomerular capillary formation (GO:0072277)|metanephric glomerular mesangial cell proliferation involved in metanephros development (GO:0072262)|metanephric mesenchymal cell migration (GO:0035789)|metanephric mesenchyme development (GO:0072075)|metanephric S-shaped body morphogenesis (GO:0072284)|negative regulation of apoptotic process (GO:0043066)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol metabolic process (GO:0046488)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|platelet-derived growth factor receptor-beta signaling pathway (GO:0035791)|positive regulation of calcium ion import (GO:0090280)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signaling pathway (GO:0038091)|positive regulation of chemotaxis (GO:0050921)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of metanephric mesenchymal cell migration by platelet-derived growth factor receptor-beta signaling pathway (GO:0035793)|positive regulation of mitosis (GO:0045840)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of smooth muscle cell migration (GO:0014911)|positive regulation of smooth muscle cell proliferation (GO:0048661)|protein autophosphorylation (GO:0046777)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|response to estradiol (GO:0032355)|response to fluid shear stress (GO:0034405)|response to hydrogen peroxide (GO:0042542)|response to hyperoxia (GO:0055093)|response to retinoic acid (GO:0032526)|response to toxic substance (GO:0009636)|retina vasculature development in camera-type eye (GO:0061298)|signal transduction (GO:0007165)|skeletal system morphogenesis (GO:0048705)|smooth muscle cell chemotaxis (GO:0071670)|smooth muscle tissue development (GO:0048745)|tissue homeostasis (GO:0001894)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intrinsic component of plasma membrane (GO:0031226)|lysosome (GO:0005764)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|platelet activating factor receptor activity (GO:0004992)|platelet-derived growth factor beta-receptor activity (GO:0005019)|platelet-derived growth factor binding (GO:0048407)|platelet-derived growth factor receptor binding (GO:0005161)|platelet-derived growth factor-activated receptor activity (GO:0005017)|protein kinase binding (GO:0019901)|protein tyrosine kinase activity (GO:0004713)|receptor binding (GO:0005102)|vascular endothelial growth factor binding (GO:0038085)			breast(3)|central_nervous_system(5)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(9)|kidney(3)|large_intestine(12)|lung(20)|ovary(3)|prostate(3)|skin(3)|stomach(6)|urinary_tract(1)	75		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		Becaplermin(DB00102)|Dasatinib(DB01254)|Imatinib(DB00619)|Pazopanib(DB06589)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	TCCTGCTCCTCCTCCCAGTAC	0.647			T	"""ETV6, TRIP11, HIP1, RAB5EP, H4, NIN, HCMOGT-1, PDE4DIP"""	"""MPD, AML, CMML, CML"""						OREG0016927	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	54	0.0107827	0.0015	0.0216	5008	,	,		23425	0.0		0.0328	False		,,,				2504	0.0041				p.E485K		Atlas-SNP	.		Dom	yes		5	5q31-q32	5159	"""platelet-derived growth factor receptor, beta polypeptide"""		L	.	PDGFRB	142	.	0			c.G1453A						PASS	.	C	LYS/GLU	21,4385	29.0+/-57.7	0,21,2182	186.0	118.0	141.0		1453	3.7	1.0	5	dbSNP_127	141	224,8376	93.3+/-155.3	4,216,4080	yes	missense	PDGFRB	NM_002609.3	56	4,237,6262	TT,TC,CC		2.6047,0.4766,1.8837	benign	485/1107	149509446	245,12761	2203	4300	6503	SO:0001583	missense	5159	exon10			GCTCCTCCTCCCA	M21616	CCDS4303.1	5q33.1	2013-01-29			ENSG00000113721	ENSG00000113721		"""CD molecules"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	8804	protein-coding gene	gene with protein product		173410		PDGFR			Standard	XM_005268464		Approved	JTK12, CD140b, PDGFR1	uc003lro.3	P09619	OTTHUMG00000130053	ENST00000261799.4:c.1453G>A	5.37:g.149509446C>T	ENSP00000261799:p.Glu485Lys	Somatic	175	0	0	1725	WXS	Illumina HiSeq	Phase_I	123	62	0.504065	NM_002609	B5A957|Q8N5L4	Missense_Mutation	SNP	ENST00000261799.4	37	CCDS4303.1	39	0.017857142857142856	2	0.0040650406504065045	10	0.027624309392265192	0	0.0	27	0.03562005277044855	C	13.36	2.214386	0.39102	0.004766	0.026047	ENSG00000113721	ENST00000261799;ENST00000544453	T	0.75938	-0.98	4.64	3.73	0.42828	.	0.108236	0.40554	N	0.001077	T	0.25754	0.0627	N	0.22421	0.69	0.38651	D	0.951848	B;B	0.25441	0.126;0.126	B;B	0.21360	0.034;0.034	T	0.46219	-0.9207	10	0.23302	T	0.38	.	12.5115	0.56007	0.0:0.8166:0.1834:0.0	rs41287110;rs62620662	485;485	A8KAM8;P09619	.;PGFRB_HUMAN	K	485;155	ENSP00000261799:E485K	ENSP00000261799:E485K	E	-	1	0	PDGFRB	149489639	0.920000	0.31207	0.958000	0.39756	0.940000	0.58332	1.826000	0.39092	2.409000	0.81822	0.462000	0.41574	GAG	C|0.980;T|0.020	0.020	strong		0.647	PDGFRB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252332.1	NM_002609	
MUC20	200958	hgsc.bcm.edu	37	3	195453417	195453417	+	Missense_Mutation	SNP	C	C	T	rs73203948	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195453417C>T	ENST00000447234.2	+	2	2069	c.1943C>T	c.(1942-1944)aCg>aTg	p.T648M	MUC20_ENST00000436408.1_Missense_Mutation_p.T648M|MUC20_ENST00000445522.2_Missense_Mutation_p.T613M|MUC20_ENST00000320736.6_Missense_Mutation_p.T477M	NM_001282506.1	NP_001269435.1	Q8N307	MUC20_HUMAN	mucin 20, cell surface associated	648	Involved in oligomerization.|Thr-rich.				activation of MAPK activity (GO:0000187)|cellular protein metabolic process (GO:0044267)|hepatocyte growth factor receptor signaling pathway (GO:0048012)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein homooligomerization (GO:0051260)	basal plasma membrane (GO:0009925)|cell projection (GO:0042995)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)				NS(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(4)|skin(4)|stomach(3)|upper_aerodigestive_tract(1)	23	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)	Lung NSC(153;0.191)	Epithelial(36;1e-21)|all cancers(36;9.02e-20)|OV - Ovarian serous cystadenocarcinoma(49;1.6e-18)|Lung(62;0.000104)|LUSC - Lung squamous cell carcinoma(58;0.000128)	GBM - Glioblastoma multiforme(46;1.66e-05)		ACTGCCCGGACGAGGCCGACC	0.602													c|||	153	0.0305511	0.0219	0.0461	5008	,	,		27461	0.0		0.0696	False		,,,				2504	0.0225				p.T477M		Atlas-SNP	.											.	MUC20	84	.	0			c.C1430T						PASS	.	C	MET/THR,MET/THR	103,4059		0,103,1978	96.0	103.0	100.0		1325,1430	0.8	0.0	3	dbSNP_130	100	457,7959		0,457,3751	no	missense,missense	MUC20	NM_001098516.1,NM_152673.2	81,81	0,560,5729	TT,TC,CC		5.4301,2.4748,4.4522	probably-damaging,probably-damaging	442/504,477/539	195453417	560,12018	2081	4208	6289	SO:0001583	missense	200958	exon3			CCCGGACGAGGCC	AB037780	CCDS63877.1	3q29	2008-08-07	2006-03-14		ENSG00000176945	ENSG00000176945		"""Mucins"""	23282	protein-coding gene	gene with protein product		610360				14565953	Standard	NM_001282506		Approved	FLJ14408, KIAA1359	uc010hzo.3	Q8N307	OTTHUMG00000155823	ENST00000447234.2:c.1943C>T	3.37:g.195453417C>T	ENSP00000414350:p.Thr648Met	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	71	30	0.422535	NM_152673	Q6UX97|Q76I83|Q76I85|Q86ST8|Q8NBY6|Q96KA1|Q9P2I8	Missense_Mutation	SNP	ENST00000447234.2	37		72	0.03296703296703297	14	0.028455284552845527	11	0.03038674033149171	0	0.0	47	0.06200527704485488	C	13.78	2.338533	0.41398	0.024748	0.054301	ENSG00000176945	ENST00000381954;ENST00000447234;ENST00000320736;ENST00000436408;ENST00000445522	T;T;T;T	0.16196	2.79;2.82;2.94;2.36	4.8	0.798	0.18660	.	0.839202	0.10084	N	0.718050	T	0.00967	0.0032	L	0.27053	0.805	0.09310	N	1	P	0.50710	0.938	B	0.38921	0.285	T	0.24119	-1.0169	10	0.56958	D	0.05	2.6174	5.0028	0.14273	0.0:0.4789:0.3342:0.1869	.	477	E9PH32	.	M	459;648;477;648;613	ENSP00000414350:T648M;ENSP00000325431:T477M;ENSP00000396774:T648M;ENSP00000405629:T613M	ENSP00000325431:T477M	T	+	2	0	MUC20	196939088	0.001000	0.12720	0.001000	0.08648	0.001000	0.01503	-0.292000	0.08332	0.272000	0.22027	-0.122000	0.15005	ACG	C|0.965;T|0.035	0.035	strong		0.602	MUC20-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000341835.1	NM_152673	
SLC22A24	283238	hgsc.bcm.edu	37	11	62886800	62886800	+	Missense_Mutation	SNP	G	G	C	rs4963245	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:62886800G>C	ENST00000417740.1	-	3	955	c.514C>G	c.(514-516)Cgg>Ggg	p.R172G	SLC22A24_ENST00000326192.5_Missense_Mutation_p.R172G	NM_001136506.2	NP_001129978.2	Q8N4F4	S22AO_HUMAN	solute carrier family 22, member 24	172					ion transport (GO:0006811)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)				kidney(1)|stomach(1)	2						ATGATCTTCCGTCCAACCCTA	0.418													G|||	820	0.163738	0.0522	0.3415	5008	,	,		20519	0.0317		0.3002	False		,,,				2504	0.184				p.R172G		Atlas-SNP	.											.	SLC22A24	31	.	0			c.C514G						PASS	.	G	GLY/ARG	145,1239		10,125,557	132.0	116.0	121.0		514	-3.7	0.0	11	dbSNP_111	121	1023,2159		172,679,740	yes	missense	SLC22A24	NM_001136506.2	125	182,804,1297	CC,CG,GG		32.1496,10.4769,25.5804	probably-damaging	172/553	62886800	1168,3398	692	1591	2283	SO:0001583	missense	283238	exon3			TCTTCCGTCCAAC		CCDS73308.1	11q12.3	2013-05-22			ENSG00000197658	ENSG00000197658		"""Solute carriers"""	28542	protein-coding gene	gene with protein product		611698				17714910	Standard	NM_001136506		Approved	MGC34821, NET46	uc021qkp.1	Q8N4F4	OTTHUMG00000165372	ENST00000417740.1:c.514C>G	11.37:g.62886800G>C	ENSP00000396586:p.Arg172Gly	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	72	19	0.263889	NM_001136506		Missense_Mutation	SNP	ENST00000417740.1	37		369	0.16895604395604397	28	0.056910569105691054	102	0.281767955801105	23	0.04020979020979021	216	0.2849604221635884	G	13.83	2.352998	0.41700	0.104769	0.321496	ENSG00000197658	ENST00000417740;ENST00000531535;ENST00000326192	D;T	0.84370	-1.84;-0.25	3.86	-3.71	0.04424	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.85682	U	0.000000	T	0.00039	0.0001	H	0.98446	4.235	0.80722	P	0.0	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.48559	-0.9025	9	0.87932	D	0	.	5.6254	0.17480	0.1821:0.0:0.2292:0.5887	rs4963245;rs52815620;rs4963245	172;172	Q8N4F4;C9JC66	S22AO_HUMAN;.	G	172	ENSP00000396586:R172G;ENSP00000321549:R172G	ENSP00000321549:R172G	R	-	1	2	SLC22A24	62643376	0.000000	0.05858	0.000000	0.03702	0.083000	0.17756	-3.203000	0.00559	-0.444000	0.07170	-0.403000	0.06358	CGG	G|0.827;C|0.173	0.173	strong		0.418	SLC22A24-003	PUTATIVE	non_canonical_polymorphism|basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000383747.1	NM_173586	
AGL	178	hgsc.bcm.edu	37	1	100340286	100340286	+	Silent	SNP	G	G	A	rs369218410		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:100340286G>A	ENST00000294724.4	+	8	1480	c.1002G>A	c.(1000-1002)acG>acA	p.T334T	AGL_ENST00000477753.1_3'UTR|AGL_ENST00000361915.3_Silent_p.T334T|AGL_ENST00000361522.4_Silent_p.T317T|AGL_ENST00000370163.3_Silent_p.T334T|AGL_ENST00000361302.3_Silent_p.T318T|AGL_ENST00000370161.2_Silent_p.T318T|AGL_ENST00000370165.3_Silent_p.T334T	NM_000028.2	NP_000019.2	P35573	GDE_HUMAN	amylo-alpha-1, 6-glucosidase, 4-alpha-glucanotransferase	334					carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|glycogen catabolic process (GO:0005980)|response to glucocorticoid (GO:0051384)|response to nutrient (GO:0007584)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|inclusion body (GO:0016234)|isoamylase complex (GO:0043033)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)	4-alpha-glucanotransferase activity (GO:0004134)|amylo-alpha-1,6-glucosidase activity (GO:0004135)|glycogen debranching enzyme activity (GO:0004133)|polysaccharide binding (GO:0030247)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(9)|lung(35)|ovary(1)|prostate(4)|skin(3)|urinary_tract(1)	69		all_epithelial(167;2.2e-06)|all_lung(203;0.000295)|Lung NSC(277;0.00131)		Epithelial(280;0.15)|COAD - Colon adenocarcinoma(174;0.151)|Lung(183;0.209)|all cancers(265;0.237)		AACACCTTACGATTATTCAAG	0.343																																					p.T334T		Atlas-SNP	.											.	AGL	137	.	0			c.G1002A						PASS	.	G	,,,,,	1,4405	2.1+/-5.4	0,1,2202	127.0	111.0	116.0		1002,1002,1002,1002,951,954	1.8	1.0	1		116	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	AGL	NM_000028.2,NM_000642.2,NM_000643.2,NM_000644.2,NM_000645.2,NM_000646.2	,,,,,	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	,,,,,	334/1533,334/1533,334/1533,334/1533,317/1516,318/1517	100340286	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	178	exon8			CCTTACGATTATT	BC078663	CCDS759.1, CCDS760.1, CCDS761.1	1p21	2010-04-27	2010-04-27		ENSG00000162688	ENSG00000162688	2.4.1.25, 3.2.1.33		321	protein-coding gene	gene with protein product	"""glycogen debranching enzyme"", ""glycogen storage disease type III"""	610860	"""amylo-1, 6-glucosidase, 4-alpha-glucanotransferase"""			1505983	Standard	NM_000028		Approved		uc001dsi.1	P35573	OTTHUMG00000010803	ENST00000294724.4:c.1002G>A	1.37:g.100340286G>A		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	75	4	0.0533333	NM_000644	A6NCX7|A6NEK2|D3DT51|P78354|P78544|Q59H92|Q6AZ90|Q9UF08	Silent	SNP	ENST00000294724.4	37	CCDS759.1																																																																																			.	.	none		0.343	AGL-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029778.1	NM_000028	
OVCH1	341350	hgsc.bcm.edu	37	12	29639186	29639186	+	Missense_Mutation	SNP	T	T	C	rs3847680	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:29639186T>C	ENST00000318184.5	-	8	987	c.988A>G	c.(988-990)Aag>Gag	p.K330E	OVCH1-AS1_ENST00000551108.1_Intron|OVCH1-AS1_ENST00000549411.1_Intron	NM_183378.2	NP_899234.2	Q7RTY7	OVCH1_HUMAN	ovochymase 1	330	CUB 1. {ECO:0000255|PROSITE- ProRule:PRU00059}.		K -> E (in dbSNP:rs3847680).			extracellular region (GO:0005576)	metal ion binding (GO:0046872)|serine-type endopeptidase activity (GO:0004252)			NS(2)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(15)|lung(43)|ovary(5)|pancreas(3)|prostate(2)|skin(1)|soft_tissue(1)|stomach(3)	92	Lung NSC(12;1.84e-09)|Acute lymphoblastic leukemia(23;0.00885)|all_hematologic(23;0.0155)					CACATACCCTTTCCTCTCTGG	0.443													C|||	3082	0.615415	0.6778	0.4813	5008	,	,		12142	0.7331		0.6044	False		,,,				2504	0.5164				p.K330E		Atlas-SNP	.											.	OVCH1	195	.	0			c.A988G						PASS	.	C	GLU/LYS	2425,1253		803,819,217	98.0	92.0	94.0		988	1.0	0.0	12	dbSNP_108	94	4787,3405		1390,2007,699	yes	missense	OVCH1	NM_183378.2	56	2193,2826,916	CC,CT,TT		41.5649,34.0674,39.2418	benign	330/1135	29639186	7212,4658	1839	4096	5935	SO:0001583	missense	341350	exon8			TACCCTTTCCTCT	BN000128		12p11.23	2012-11-08			ENSG00000187950	ENSG00000187950			23080	protein-coding gene	gene with protein product						12838346	Standard	NM_183378		Approved	OVCH	uc001rix.1	Q7RTY7	OTTHUMG00000167741	ENST00000318184.5:c.988A>G	12.37:g.29639186T>C	ENSP00000326708:p.Lys330Glu	Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	115	64	0.556522	NM_183378		Missense_Mutation	SNP	ENST00000318184.5	37		1383	0.6332417582417582	334	0.6788617886178862	170	0.4696132596685083	431	0.7534965034965035	448	0.5910290237467019	C	0.006	-2.069785	0.00382	0.659326	0.584351	ENSG00000187950	ENST00000318184	D	0.86097	-2.07	1.94	1.03	0.20045	.	.	.	.	.	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	0.42275	-0.9461	8	0.13853	T	0.58	.	4.3278	0.11048	0.0:0.6333:0.0:0.3667	rs3847680;rs52790299;rs60032983;rs3847680	330	Q7RTY7	OVCH1_HUMAN	E	330	ENSP00000326708:K330E	ENSP00000326708:K330E	K	-	1	0	OVCH1	29530453	0.000000	0.05858	0.000000	0.03702	0.024000	0.10985	-0.432000	0.06956	-0.006000	0.14370	-0.971000	0.02607	AAG	T|0.367;C|0.633	0.633	strong		0.443	OVCH1-001	KNOWN	non_canonical_TEC|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000395997.2	NM_183378	
SENP7	57337	hgsc.bcm.edu	37	3	101080694	101080694	+	Silent	SNP	T	T	C	rs7616677	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:101080694T>C	ENST00000394095.2	-	11	1541	c.1488A>G	c.(1486-1488)gaA>gaG	p.E496E	SENP7_ENST00000314261.7_Silent_p.E430E|SENP7_ENST00000394094.2_Silent_p.E431E|SENP7_ENST00000358203.3_Silent_p.E332E|SENP7_ENST00000394091.1_Silent_p.E332E|SENP7_ENST00000348610.3_Silent_p.E463E	NM_001282802.1|NM_020654.3	NP_001269731.1|NP_065705.3	Q9BQF6	SENP7_HUMAN	SUMO1/sentrin specific peptidase 7	496						intracellular (GO:0005622)|nucleus (GO:0005634)	cysteine-type peptidase activity (GO:0008234)			breast(2)|endometrium(1)|kidney(1)|large_intestine(16)|lung(15)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44						ATGGGCATAATTCAGATGACA	0.284													T|||	2142	0.427716	0.348	0.5533	5008	,	,		15942	0.4901		0.4115	False		,,,				2504	0.3988				p.E496E		Atlas-SNP	.											.	SENP7	170	.	0			c.A1488G						PASS	.	T	,	1400,3002	434.1+/-343.8	229,942,1030	56.0	57.0	57.0		1293,1488	1.8	1.0	3	dbSNP_116	57	3450,5104	498.2+/-374.7	701,2048,1528	no	coding-synonymous,coding-synonymous	SENP7	NM_001077203.1,NM_020654.3	,	930,2990,2558	CC,CT,TT		40.332,31.8037,37.4344	,	431/986,496/1051	101080694	4850,8106	2201	4277	6478	SO:0001819	synonymous_variant	57337	exon11			GCATAATTCAGAT		CCDS2941.2, CCDS43121.1, CCDS63704.1, CCDS63705.1, CCDS63706.1	3q12	2008-02-05	2005-08-17		ENSG00000138468	ENSG00000138468			30402	protein-coding gene	gene with protein product		612846	"""SUMO1/sentrin specific protease 7"""			11214970, 11230166	Standard	NM_001282802		Approved		uc003dut.3	Q9BQF6	OTTHUMG00000149927	ENST00000394095.2:c.1488A>G	3.37:g.101080694T>C		Somatic	239	0	0		WXS	Illumina HiSeq	Phase_I	185	183	0.989189	NM_020654	A1L3A5|A8MW39|B7WNW8|Q7Z3F4|Q96PS5|Q9C0F6|Q9HBT5	Silent	SNP	ENST00000394095.2	37	CCDS2941.2																																																																																			T|0.604;C|0.396	0.396	strong		0.284	SENP7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313957.2	NM_020654	
MUC4	4585	hgsc.bcm.edu	37	3	195512480	195512480	+	Missense_Mutation	SNP	A	A	G	rs200533337	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195512480A>G	ENST00000463781.3	-	2	6430	c.5971T>C	c.(5971-5973)Tcc>Ccc	p.S1991P	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.S1991P	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)		GACACTGAGGAAGCGTCGGTG	0.602													.|||	91	0.0181709	0.0068	0.0418	5008	,	,		25743	0.0		0.0507	False		,,,				2504	0.002				p.S1991P		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	0			c.T5971C						PASS	.						43.0	40.0	41.0					3																	195512480		691	1590	2281	SO:0001583	missense	4585	exon2			CTGAGGAAGCGTC	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.5971T>C	3.37:g.195512480A>G	ENSP00000417498:p.Ser1991Pro	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	129	31	0.24031	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	A	3.721	-0.057533	0.07317	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.32515	1.45;1.46	.	.	.	.	.	.	.	.	T	0.14399	0.0348	N	0.19112	0.55	0.09310	N	0.999997	B	0.10296	0.003	B	0.06405	0.002	T	0.27400	-1.0075	7	.	.	.	.	3.355	0.07165	0.649:0.0:1.0E-4:0.3509	.	1991	E7ESK3	.	P	1991	ENSP00000417498:S1991P;ENSP00000420243:S1991P	.	S	-	1	0	MUC4	196996875	0.997000	0.39634	0.003000	0.11579	0.158000	0.22134	0.513000	0.22770	-0.876000	0.04017	0.055000	0.15244	TCC	A|0.973;G|0.027	0.027	strong		0.602	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
SPATA13	221178	hgsc.bcm.edu	37	13	24797786	24797786	+	Intron	SNP	G	G	A	rs9511156	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:24797786G>A	ENST00000382095.4	+	2	185				SPATA13_ENST00000382108.3_Missense_Mutation_p.R240K|SPATA13_ENST00000424834.2_Missense_Mutation_p.R240K|RP11-307N16.6_ENST00000382141.4_Missense_Mutation_p.R240K	NM_153023.2	NP_694568.1	Q96N96	SPT13_HUMAN	spermatogenesis associated 13						cell migration (GO:0016477)|filopodium assembly (GO:0046847)|lamellipodium assembly (GO:0030032)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Rac GTPase activity (GO:0032855)|regulation of cell migration (GO:0030334)	cytoplasm (GO:0005737)|filopodium (GO:0030175)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|ruffle membrane (GO:0032587)	guanyl-nucleotide exchange factor activity (GO:0005085)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)			breast(4)|endometrium(2)|large_intestine(9)|lung(4)|ovary(1)|prostate(1)|skin(2)	23		all_cancers(29;4.05e-15)|all_lung(29;2.77e-14)|all_epithelial(30;7.77e-13)|Lung SC(185;0.0279)		all cancers(112;0.00616)|Epithelial(112;0.0195)|OV - Ovarian serous cystadenocarcinoma(117;0.0705)|Lung(94;0.231)		ATTCTCGTGAGGGACCCTGAA	0.582													G|||	125	0.0249601	0.0038	0.0375	5008	,	,		19046	0.002		0.0835	False		,,,				2504	0.0082				p.R240K		Atlas-SNP	.											.	SPATA13	92	.	0			c.G719A						PASS	.	G	LYS/ARG,	21,1363		0,21,671	66.0	62.0	63.0		719,	-0.9	0.0	13	dbSNP_119	63	273,2909		7,259,1325	yes	missense,intron	SPATA13	NM_001166271.1,NM_153023.2	26,	7,280,1996	AA,AG,GG		8.5795,1.5173,6.4389	,	240/1278,	24797786	294,4272	692	1591	2283	SO:0001627	intron_variant	221178	exon2			TCGTGAGGGACCC	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.-222-25829G>A	13.37:g.24797786G>A		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	29	15	0.517241	NM_001166271	A2VEA9|A6NF85|B4DQB1|B4DSZ0|B4DVM8|J3KPJ7|J3KQH2|Q5VX68|Q6ZML1|Q8N873|Q8TEK6	Missense_Mutation	SNP	ENST00000382095.4	37	CCDS9305.1	67	0.030677655677655676	3	0.006097560975609756	13	0.03591160220994475	1	0.0017482517482517483	50	0.06596306068601583	G	1.388	-0.581698	0.03854	0.015173	0.085795	ENSG00000182957	ENST00000382108	T	0.70164	-0.46	4.5	-0.89	0.10577	.	0.707747	0.10080	N	0.718534	T	0.01254	0.0041	N	0.02539	-0.55	0.09310	N	1	.	.	.	.	.	.	T	0.04242	-1.0966	8	0.02654	T	1	.	8.4744	0.33005	0.535:0.0:0.465:0.0	rs9511156;rs17365633;rs9511156	.	.	.	K	240	ENSP00000371542:R240K	ENSP00000371542:R240K	R	+	2	0	SPATA13	23695786	0.185000	0.23213	0.000000	0.03702	0.076000	0.17211	1.607000	0.36836	-0.160000	0.11002	-0.361000	0.07541	AGG	G|0.962;A|0.038	0.038	strong		0.582	SPATA13-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000044180.2	NM_153023	
GALNT8	26290	hgsc.bcm.edu	37	12	4873163	4873163	+	Missense_Mutation	SNP	G	G	T	rs1468556	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:4873163G>T	ENST00000252318.2	+	9	1880	c.1543G>T	c.(1543-1545)Gtt>Ttt	p.V515F		NM_017417.1	NP_059113.1	Q9NY28	GALT8_HUMAN	polypeptide N-acetylgalactosaminyltransferase 8	515	Ricin B-type lectin. {ECO:0000255|PROSITE-ProRule:PRU00174}.		V -> F (in dbSNP:rs1468556). {ECO:0000269|PubMed:10767557}.		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)			central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(13)|ovary(2)|pancreas(1)|prostate(4)|skin(2)|urinary_tract(1)	35						TCAGGGACCCGTTCCAGGCAA	0.502													G|||	1651	0.329673	0.2466	0.4251	5008	,	,		19640	0.3611		0.4225	False		,,,				2504	0.2464				p.V515F	Colon(108;631 1558 7270 20097 39846)	Atlas-SNP	.											GALNT8,NS,adenoma,0,1	GALNT8	89	1	0			c.G1543T						PASS	.	G	PHE/VAL	1305,3101	442.3+/-346.6	207,891,1105	196.0	174.0	182.0		1543	-7.6	0.0	12	dbSNP_88	182	3609,4991	521.6+/-379.9	761,2087,1452	yes	missense	GALNT8	NM_017417.1	50	968,2978,2557	TT,TG,GG		41.9651,29.6187,37.7826	possibly-damaging	515/638	4873163	4914,8092	2203	4300	6503	SO:0001583	missense	26290	exon9			GGACCCGTTCCAG	AJ271385	CCDS8533.1	12p13.32	2014-03-13	2014-03-13		ENSG00000130035	ENSG00000130035	2.4.1.41	"""Glycosyltransferase family 2 domain containing"""	4130	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase 8"""	606250	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 8 (GalNAc-T8)"""			10767557	Standard	NM_017417		Approved	GALNAC-T8	uc001qne.1	Q9NY28	OTTHUMG00000166188	ENST00000252318.2:c.1543G>T	12.37:g.4873163G>T	ENSP00000252318:p.Val515Phe	Somatic	242	0	0		WXS	Illumina HiSeq	Phase_I	223	115	0.515695	NM_017417	B2RU02	Missense_Mutation	SNP	ENST00000252318.2	37	CCDS8533.1	814	0.3727106227106227	124	0.25203252032520324	150	0.4143646408839779	223	0.38986013986013984	317	0.4182058047493404	G	8.342	0.828853	0.16749	0.296187	0.419651	ENSG00000130035	ENST00000252318	T	0.26957	1.7	4.43	-7.55	0.01327	Ricin B-related lectin (1);Ricin B lectin (3);	1.667950	0.02954	N	0.142084	T	0.00012	0.0000	L	0.31926	0.97	0.80722	P	0.0	B	0.31383	0.321	B	0.29716	0.106	T	0.18935	-1.0321	9	0.56958	D	0.05	.	8.9706	0.35903	0.596:0.0:0.3027:0.1014	rs1468556;rs17783619;rs59456221;rs1468556	515	Q9NY28	GALT8_HUMAN	F	515	ENSP00000252318:V515F	ENSP00000252318:V515F	V	+	1	0	GALNT8	4743424	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.158000	0.10070	-1.811000	0.01229	-0.751000	0.03497	GTT	G|0.627;T|0.373	0.373	strong		0.502	GALNT8-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388277.2	NM_017417	
CHD5	26038	hgsc.bcm.edu	37	1	6209363	6209363	+	Silent	SNP	T	T	C	rs12565328	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:6209363T>C	ENST00000262450.3	-	8	1203	c.1104A>G	c.(1102-1104)gtA>gtG	p.V368V	CHD5_ENST00000378021.1_5'UTR	NM_015557.2	NP_056372.1	O00258	WRB_HUMAN	chromodomain helicase DNA binding protein 5	0					tail-anchored membrane protein insertion into ER membrane (GO:0071816)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)				breast(3)|central_nervous_system(3)|liver(1)|lung(1)|ovary(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)	16	Ovarian(185;0.0634)	all_cancers(23;5.36e-32)|all_epithelial(116;2.32e-17)|all_neural(13;3.68e-06)|all_lung(118;3.94e-06)|all_hematologic(16;2.39e-05)|Lung NSC(185;5.33e-05)|Acute lymphoblastic leukemia(12;0.000372)|Glioma(11;0.00127)|Renal(390;0.00188)|Colorectal(325;0.00342)|Breast(487;0.00373)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.15)		Epithelial(90;3.08e-37)|GBM - Glioblastoma multiforme(13;1.36e-31)|OV - Ovarian serous cystadenocarcinoma(86;7.7e-19)|Colorectal(212;9.97e-08)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(185;6.16e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.00109)|BRCA - Breast invasive adenocarcinoma(365;0.0012)|STAD - Stomach adenocarcinoma(132;0.00346)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.193)		GGTCCAGGCATACGAGATGGT	0.652													C|||	2623	0.523762	0.7216	0.2147	5008	,	,		17436	0.6538		0.3082	False		,,,				2504	0.5634				p.V368V		Atlas-SNP	.											.	CHD5	267	.	0			c.A1104G						PASS	.	C		2866,1540	481.9+/-359.3	938,990,275	66.0	54.0	58.0		1104	-0.9	1.0	1	dbSNP_120	58	2466,6134	693.8+/-404.7	362,1742,2196	no	coding-synonymous	CHD5	NM_015557.2		1300,2732,2471	CC,CT,TT		28.6744,34.9523,40.9965		368/1955	6209363	5332,7674	2203	4300	6503	SO:0001819	synonymous_variant	26038	exon8			CAGGCATACGAGA	AF425231	CCDS57.1	1p36.3	2013-01-28			ENSG00000116254	ENSG00000116254		"""Zinc fingers, PHD-type"""	16816	protein-coding gene	gene with protein product		610771				11889561, 12592387	Standard	NM_015557		Approved		uc001amb.2	Q8TDI0	OTTHUMG00000000952	ENST00000262450.3:c.1104A>G	1.37:g.6209363T>C		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	68	20	0.294118	NM_015557	A8KAP8|A8MQ44|D3DSH9|O60740	Silent	SNP	ENST00000262450.3	37	CCDS57.1																																																																																			T|0.543;C|0.457	0.457	strong		0.652	CHD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002823.2	NM_015557	
CES1	1066	hgsc.bcm.edu	37	16	55862691	55862691	+	Missense_Mutation	SNP	G	G	A	rs62028647	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:55862691G>A	ENST00000361503.4	-	2	375	c.245C>T	c.(244-246)tCg>tTg	p.S82L	CES1_ENST00000360526.3_Missense_Mutation_p.S83L|CES1_ENST00000422046.2_Missense_Mutation_p.S82L|CES1_ENST00000566555.1_5'Flank			P23141	EST1_HUMAN	carboxylesterase 1	82					epithelial cell differentiation (GO:0030855)|metabolic process (GO:0008152)|response to toxic substance (GO:0009636)	endoplasmic reticulum (GO:0005783)	carboxylic ester hydrolase activity (GO:0052689)|methylumbelliferyl-acetate deacetylase activity (GO:0047374)								all cancers(182;0.13)|Epithelial(162;0.137)	Benzocaine(DB01086)|Capecitabine(DB01101)|Ciclesonide(DB01410)|Clopidogrel(DB00758)|Cyclandelate(DB04838)|Dabigatran etexilate(DB06695)|Indomethacin(DB00328)|Irinotecan(DB00762)|L-Carnitine(DB00583)|Mycophenolate mofetil(DB00688)|Oseltamivir(DB00198)|Probucol(DB01599)|Rufinamide(DB06201)|Tamoxifen(DB00675)|Trandolapril(DB00519)	AGGAGGGTACGAGGTGGCATT	0.542																																					p.S83L	NSCLC(162;1801 2756 42904 52896)	Atlas-SNP	.											.	CES1	78	.	0			c.C248T						PASS	.						106.0	104.0	105.0					16																	55862691		2198	4300	6498	SO:0001583	missense	1066	exon2			GGGTACGAGGTGG	BC012418	CCDS32450.1, CCDS45488.1, CCDS45489.1	16q22.2	2010-10-12	2010-10-12		ENSG00000198848	ENSG00000198848	3.1.1.1	"""Carboxylesterases"""	1863	protein-coding gene	gene with protein product	"""human monocyte/macrophage serine esterase 1"""	114835	"""carboxylesterase 1 (monocyte/macrophage serine esterase 1)"""			2070086, 20931200	Standard	XM_005255774		Approved	HMSE, CES2, HMSE1, SES1, CEH, CES1A1, CES1A2	uc002eil.3	P23141		ENST00000361503.4:c.245C>T	16.37:g.55862691G>A	ENSP00000355193:p.Ser82Leu	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	109	32	0.293578	NM_001025195	A6NIM1|A8K3K8|A8K844|E9PAU8|P82127|Q00015|Q13657|Q14062|Q16737|Q16788|Q549X7|Q549X8|Q86UK2|Q96EE8|Q9UC52|Q9UDG8|Q9UK77|Q9ULY2	Missense_Mutation	SNP	ENST00000361503.4	37	CCDS45488.1	824	0.3772893772893773	224	0.45528455284552843	145	0.4005524861878453	117	0.20454545454545456	338	0.44591029023746703	.	12.07	1.827253	0.32329	.	.	ENSG00000198848	ENST00000360526;ENST00000361503;ENST00000422046	T;T;T	0.68765	-0.35;-0.35;-0.35	4.48	4.48	0.54585	Carboxylesterase, type B (1);	0.146929	0.31472	N	0.007582	T	0.00012	0.0000	M	0.82823	2.61	0.36044	D	0.840328	D;D;P	0.53312	0.959;0.959;0.949	P;P;B	0.46253	0.509;0.509;0.375	T	0.34900	-0.9810	10	0.87932	D	0	.	14.6933	0.69101	0.0:0.0:1.0:0.0	rs62028647	82;82;83	E9PAU8;P23141;P23141-2	.;EST1_HUMAN;.	L	83;82;82	ENSP00000353720:S83L;ENSP00000355193:S82L;ENSP00000390492:S82L	ENSP00000353720:S83L	S	-	2	0	CES1	54420192	0.941000	0.31946	0.984000	0.44739	0.053000	0.15095	3.676000	0.54612	2.051000	0.60960	0.393000	0.25936	TCG	G|0.622;A|0.378	0.378	strong		0.542	CES1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000433285.1	NM_001266	
SBSN	374897	hgsc.bcm.edu	37	19	36015652	36015652	+	Silent	SNP	C	C	T	rs17705633	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	97	0	0		WXS	Illumina HiSeq	Phase_I	63	25	0.396825	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	
PRX	57716	hgsc.bcm.edu	37	19	40901496	40901496	+	Missense_Mutation	SNP	T	T	C	rs268673	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:40901496T>C	ENST00000324001.7	-	7	3033	c.2763A>G	c.(2761-2763)atA>atG	p.I921M	PRX_ENST00000291825.7_3'UTR	NM_181882.2	NP_870998.2	Q9BXM0	PRAX_HUMAN	periaxin	921			I -> M (in dbSNP:rs268673). {ECO:0000269|PubMed:11133365}.		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)			CTTTTGTCTCTATCATCTCCA	0.577													C|||	1486	0.296725	0.3071	0.3833	5008	,	,		18355	0.1885		0.3767	False		,,,				2504	0.2505				p.I921M		Atlas-SNP	.											.	PRX	151	.	0			c.A2763G						PASS	.	C	,MET/ILE	1428,2978	683.5+/-404.3	254,920,1029	75.0	86.0	82.0		,2763	-5.4	0.0	19	dbSNP_79	82	3336,5264	642.8+/-399.9	633,2070,1597	yes	utr-3,missense	PRX	NM_020956.2,NM_181882.2	,10	887,2990,2626	CC,CT,TT		38.7907,32.4103,36.6292	,benign	,921/1462	40901496	4764,8242	2203	4300	6503	SO:0001583	missense	57716	exon7			TGTCTCTATCATC	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.2763A>G	19.37:g.40901496T>C	ENSP00000326018:p.Ile921Met	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	83	44	0.53012	NM_181882	Q9BXL9|Q9HCF2	Missense_Mutation	SNP	ENST00000324001.7	37	CCDS33028.1	683	0.31272893772893773	153	0.31097560975609756	158	0.43646408839779005	93	0.16258741258741258	279	0.36807387862796836	C	1.471	-0.559849	0.03967	0.324103	0.387907	ENSG00000105227	ENST00000324001;ENST00000341562	T	0.03094	4.05	5.2	-5.36	0.02689	.	2.289120	0.01899	N	0.039096	T	0.00012	0.0000	N	0.03608	-0.345	0.09310	P	0.9999999999480482	B	0.02656	0.0	B	0.01281	0.0	T	0.46428	-0.9192	9	0.29301	T	0.29	7.6947	8.8913	0.35434	0.1258:0.2674:0.0:0.6068	rs268673;rs60675249;rs268673	921	Q9BXM0	PRAX_HUMAN	M	921	ENSP00000326018:I921M	ENSP00000326018:I921M	I	-	3	3	PRX	45593336	0.000000	0.05858	0.003000	0.11579	0.076000	0.17211	-2.763000	0.00784	-0.939000	0.03709	-0.215000	0.12644	ATA	T|0.669;C|0.331	0.331	strong		0.577	PRX-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000462582.1	NM_020956	
TEX26	122046	hgsc.bcm.edu	37	13	31543095	31543095	+	Silent	SNP	C	C	T	rs2274869	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:31543095C>T	ENST00000380473.3	+	6	733	c.720C>T	c.(718-720)taC>taT	p.Y240Y	TEX26_ENST00000530916.1_Intron	NM_152325.1	NP_689538.1	Q8N6G2	TEX26_HUMAN	testis expressed 26	240																	AAAGTGACTACGACAAAACCT	0.428													C|||	965	0.192692	0.0726	0.317	5008	,	,		20151	0.126		0.2445	False		,,,				2504	0.2822				p.Y240Y		Atlas-SNP	.											.	.	.	.	0			c.C720T						PASS	.	C		458,3948	220.7+/-238.1	27,404,1772	177.0	173.0	174.0		720	-4.5	0.2	13	dbSNP_100	174	2265,6335	382.8+/-340.5	322,1621,2357	no	coding-synonymous	C13orf26	NM_152325.1		349,2025,4129	TT,TC,CC		26.3372,10.3949,20.9365		240/290	31543095	2723,10283	2203	4300	6503	SO:0001819	synonymous_variant	122046	exon6			TGACTACGACAAA	BC030277	CCDS9339.1	13q12.3	2012-02-06	2012-02-06	2012-02-06	ENSG00000175664	ENSG00000175664			28622	protein-coding gene	gene with protein product			"""chromosome 13 open reading frame 26"""	C13orf26		12477932	Standard	NM_152325		Approved	MGC40178	uc001uti.3	Q8N6G2	OTTHUMG00000016682	ENST00000380473.3:c.720C>T	13.37:g.31543095C>T		Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	142	70	0.492958	NM_152325		Silent	SNP	ENST00000380473.3	37	CCDS9339.1																																																																																			C|0.784;T|0.216	0.216	strong		0.428	TEX26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044380.2	NM_152325	
NEUROD4	58158	hgsc.bcm.edu	37	12	55420891	55420891	+	Missense_Mutation	SNP	A	A	G	rs118105704	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:55420891A>G	ENST00000242994.3	+	2	1046	c.668A>G	c.(667-669)cAt>cGt	p.H223R		NM_021191.2	NP_067014.2	Q9HD90	NDF4_HUMAN	neuronal differentiation 4	223					amacrine cell differentiation (GO:0035881)|cell fate commitment (GO:0045165)|glial cell differentiation (GO:0010001)|neuroblast proliferation (GO:0007405)|neuron development (GO:0048666)|neuron migration (GO:0001764)|Notch signaling pathway (GO:0007219)|positive regulation of cell differentiation (GO:0045597)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(14)|ovary(3)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)	41						CATCTCCTTCATCTCAAGCCC	0.512													A|||	27	0.00539137	0.0	0.0058	5008	,	,		20029	0.0		0.0189	False		,,,				2504	0.0041				p.H223R		Atlas-SNP	.											.	NEUROD4	87	.	0			c.A668G						PASS	.	A	ARG/HIS	22,4384	29.9+/-59.1	0,22,2181	100.0	102.0	102.0		668	5.7	1.0	12	dbSNP_132	102	187,8413	84.0+/-146.5	4,179,4117	yes	missense	NEUROD4	NM_021191.2	29	4,201,6298	GG,GA,AA		2.1744,0.4993,1.607	benign	223/332	55420891	209,12797	2203	4300	6503	SO:0001583	missense	58158	exon2			TCCTTCATCTCAA	AF203901	CCDS8886.1	12q13.13	2013-05-21	2012-02-22			ENSG00000123307		"""Basic helix-loop-helix proteins"""	13802	protein-coding gene	gene with protein product		611635	"""neurogenic differentiation 4"""				Standard	NM_021191		Approved	Atoh3, ATH-3, MATH-3, bHLHa4	uc001sgp.4	Q9HD90		ENST00000242994.3:c.668A>G	12.37:g.55420891A>G	ENSP00000242994:p.His223Arg	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	97	46	0.474227	NM_021191	B2RAC9	Missense_Mutation	SNP	ENST00000242994.3	37	CCDS8886.1	18	0.008241758241758242	1	0.0020325203252032522	4	0.011049723756906077	0	0.0	13	0.017150395778364115	A	16.42	3.117738	0.56505	0.004993	0.021744	ENSG00000123307	ENST00000242994	T	0.62364	0.03	5.71	5.71	0.89125	Neurogenic differentiation factor, domain of unknown function (1);	0.093571	0.64402	D	0.000001	T	0.46288	0.1385	L	0.55834	1.745	0.50813	D	0.999896	B	0.20780	0.048	B	0.32289	0.143	T	0.56902	-0.7902	10	0.56958	D	0.05	-0.0463	14.2377	0.65937	1.0:0.0:0.0:0.0	.	223	Q9HD90	NDF4_HUMAN	R	223	ENSP00000242994:H223R	ENSP00000242994:H223R	H	+	2	0	NEUROD4	53707158	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.150000	0.77403	2.302000	0.77476	0.533000	0.62120	CAT	A|0.987;G|0.013	0.013	strong		0.512	NEUROD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406104.1		
LIMK2	3985	hgsc.bcm.edu	37	22	31663842	31663842	+	Silent	SNP	C	C	G	rs2228619	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:31663842C>G	ENST00000331728.4	+	10	1323	c.1209C>G	c.(1207-1209)ctC>ctG	p.L403L	LIMK2_ENST00000406516.1_Silent_p.L325L|LIMK2_ENST00000340552.4_Silent_p.L382L|LIMK2_ENST00000333611.4_Silent_p.L382L|LIMK2_ENST00000444929.2_Silent_p.L157L	NM_005569.3	NP_005560.1	P53671	LIMK2_HUMAN	LIM domain kinase 2	403	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				phosphorylation (GO:0016310)|spermatogenesis (GO:0007283)	cis-Golgi network (GO:0005801)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|zinc ion binding (GO:0008270)			endometrium(7)|kidney(3)|large_intestine(6)|lung(6)|ovary(2)|prostate(4)|skin(1)	29						AGCTGAACCTCCTGACAGAGT	0.552													G|||	4232	0.845048	0.9856	0.7478	5008	,	,		20970	0.876		0.7266	False		,,,				2504	0.8139				p.L403L		Atlas-SNP	.											.	LIMK2	101	.	0			c.C1209G						PASS	.	G	,,	4165,241		1971,223,9	88.0	78.0	82.0		1146,1209,1146	3.6	1.0	22	dbSNP_98	82	6233,2367		2258,1717,325	no	coding-synonymous,coding-synonymous,coding-synonymous	LIMK2	NM_001031801.1,NM_005569.3,NM_016733.2	,,	4229,1940,334	GG,GC,CC		27.5233,5.4698,20.0523	,,	382/687,403/639,382/618	31663842	10398,2608	2203	4300	6503	SO:0001819	synonymous_variant	3985	exon10			GAACCTCCTGACA	D45906	CCDS13891.1, CCDS13892.1, CCDS33637.1	22q12	2005-01-21			ENSG00000182541	ENSG00000182541			6614	protein-coding gene	gene with protein product		601988				8537403, 10591208	Standard	NM_005569		Approved		uc003akh.3	P53671	OTTHUMG00000151251	ENST00000331728.4:c.1209C>G	22.37:g.31663842C>G		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	60	21	0.35	NM_005569	A8K6H5|Q7KZ80|Q7L3H5|Q96E10|Q99464|Q9UFU0	Silent	SNP	ENST00000331728.4	37	CCDS13891.1																																																																																			C|0.189;G|0.811	0.811	strong		0.552	LIMK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321911.1	NM_016733	
SLC22A3	6581	hgsc.bcm.edu	37	6	160858188	160858188	+	Silent	SNP	G	G	A	rs2292334	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:160858188G>A	ENST00000275300.2	+	7	1385	c.1233G>A	c.(1231-1233)gcG>gcA	p.A411A	SLC22A3_ENST00000392145.1_Silent_p.A411A	NM_021977.3	NP_068812.1	O75751	S22A3_HUMAN	solute carrier family 22 (organic cation transporter), member 3	411					dopamine transport (GO:0015872)|drug transmembrane transport (GO:0006855)|histamine uptake (GO:0051615)|organic cation transport (GO:0015695)|quaternary ammonium group transport (GO:0015697)|regulation of appetite (GO:0032098)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	dopamine transmembrane transporter activity (GO:0005329)|organic cation transmembrane transporter activity (GO:0015101)|quaternary ammonium group transmembrane transporter activity (GO:0015651)|toxin transporter activity (GO:0019534)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(5)|ovary(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	27		Breast(66;0.00028)|Ovarian(120;0.0308)|Prostate(117;0.218)		OV - Ovarian serous cystadenocarcinoma(65;9.47e-17)|BRCA - Breast invasive adenocarcinoma(81;9.75e-06)	Adefovir Dipivoxil(DB00718)|Amphetamine(DB00182)|Choline(DB00122)|Cimetidine(DB00501)|Clonidine(DB00575)|Colchicine(DB01394)|Desipramine(DB01151)|Dopamine(DB00988)|Estradiol(DB00783)|Guanidine(DB00536)|Histamine Phosphate(DB00667)|Imipramine(DB00458)|Irinotecan(DB00762)|Lamivudine(DB00709)|Melphalan(DB01042)|Metformin(DB00331)|Methamphetamine(DB01577)|Nicotine(DB00184)|Norepinephrine(DB00368)|Oxaliplatin(DB00526)|Phenoxybenzamine(DB00925)|Prazosin(DB00457)|Procainamide(DB01035)|Progesterone(DB00396)|Testosterone(DB00624)|Vincristine(DB00541)	TCCCCTTTGCGGCAAGCAATA	0.507													G|||	1557	0.310903	0.1006	0.4625	5008	,	,		15509	0.4603		0.3529	False		,,,				2504	0.2904				p.A411A		Atlas-SNP	.											.	SLC22A3	58	.	0			c.G1233A						PASS	.	G		601,3805	263.4+/-265.5	50,501,1652	138.0	142.0	141.0		1233	-11.7	0.0	6	dbSNP_100	141	3126,5474	476.2+/-369.3	570,1986,1744	no	coding-synonymous	SLC22A3	NM_021977.2		620,2487,3396	AA,AG,GG		36.3488,13.6405,28.656		411/557	160858188	3727,9279	2203	4300	6503	SO:0001819	synonymous_variant	6581	exon7			CTTTGCGGCAAGC	AF078749	CCDS5277.1	6q25.3	2013-07-18	2013-07-18		ENSG00000146477	ENSG00000146477		"""Solute carriers"""	10967	protein-coding gene	gene with protein product		604842	"""solute carrier family 22 (extraneuronal monoamine transporter), member 3"""			9632645, 9933568	Standard	NM_021977		Approved	OCT3, EMT	uc003qti.4	O75751	OTTHUMG00000015953	ENST00000275300.2:c.1233G>A	6.37:g.160858188G>A		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	91	35	0.384615	NM_021977	Q5SYN6|Q9UP02	Silent	SNP	ENST00000275300.2	37	CCDS5277.1																																																																																			G|0.697;A|0.303	0.303	strong		0.507	SLC22A3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000042953.1	NM_021977	
ALPPL2	251	hgsc.bcm.edu	37	2	233274475	233274475	+	Missense_Mutation	SNP	C	C	A	rs56080708	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:233274475C>A	ENST00000295453.3	+	11	1544	c.1492C>A	c.(1492-1494)Cgc>Agc	p.R498S		NM_031313.2	NP_112603.2	P10696	PPBN_HUMAN	alkaline phosphatase, placental-like 2	498				R -> P (in Ref. 1; AAA98616 and 4; CAA39425). {ECO:0000305}.|R -> S (in Ref. 3; CAA37374). {ECO:0000305}.	dephosphorylation (GO:0016311)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)	alkaline phosphatase activity (GO:0004035)|metal ion binding (GO:0046872)			breast(2)|kidney(1)|large_intestine(1)|liver(2)|lung(6)|skin(1)	13		all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0449)|Lung NSC(271;0.132)		Epithelial(121;4.45e-22)|Kidney(3;4.42e-11)|KIRC - Kidney renal clear cell carcinoma(3;1.9e-09)|BRCA - Breast invasive adenocarcinoma(100;0.000767)|Lung(119;0.00566)|LUSC - Lung squamous cell carcinoma(224;0.00746)|STAD - Stomach adenocarcinoma(3;0.0181)|GBM - Glioblastoma multiforme(43;0.196)	Amifostine(DB01143)	CCTGGCGCCCCGCGCCGGCAC	0.731													c|||	477	0.0952476	0.0514	0.062	5008	,	,		10169	0.2133		0.0785	False		,,,				2504	0.0736				p.R498S		Atlas-SNP	.											.	ALPPL2	36	.	0			c.C1492A						PASS	.	C	SER/ARG	328,4022		17,294,1864	12.0	16.0	15.0		1492	1.2	0.0	2	dbSNP_129	15	716,7764		55,606,3579	no	missense	ALPPL2	NM_031313.2	110	72,900,5443	AA,AC,CC		8.4434,7.5402,8.1372	benign	498/533	233274475	1044,11786	2175	4240	6415	SO:0001583	missense	251	exon11			GCGCCCCGCGCCG	J04948	CCDS2491.1	2q37	2008-05-20			ENSG00000163286	ENSG00000163286			441	protein-coding gene	gene with protein product		171810					Standard	NM_031313		Approved		uc002vss.4	P10696	OTTHUMG00000133257	ENST00000295453.3:c.1492C>A	2.37:g.233274475C>A	ENSP00000295453:p.Arg498Ser	Somatic	0	0	.		WXS	Illumina HiSeq	Phase_I	4	4	1	NM_031313	A8KAF2|Q16727|Q53S81|Q96CM1	Missense_Mutation	SNP	ENST00000295453.3	37	CCDS2491.1	231	0.10576923076923077	28	0.056910569105691054	21	0.058011049723756904	120	0.2097902097902098	62	0.08179419525065963	c	0.762	-0.768825	0.02974	0.075402	0.084434	ENSG00000163286	ENST00000295453	D	0.95412	-3.7	2.17	1.24	0.21308	Alkaline-phosphatase-like, core domain (1);	0.504996	0.18426	N	0.141584	T	0.00271	0.0008	N	0.08118	0	0.80722	P	0.0	B	0.06786	0.001	B	0.06405	0.002	T	0.42327	-0.9458	9	0.06236	T	0.91	.	4.2075	0.10495	0.3616:0.5075:0.0:0.1308	rs56080708;rs61730276	498	P10696	PPBN_HUMAN	S	498	ENSP00000295453:R498S	ENSP00000295453:R498S	R	+	1	0	ALPPL2	232982719	0.000000	0.05858	0.020000	0.16555	0.076000	0.17211	-0.511000	0.06321	0.233000	0.21120	0.205000	0.17691	CGC	C|0.900;A|0.100	0.100	strong		0.731	ALPPL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257034.2	NM_031313	
AOC2	314	hgsc.bcm.edu	37	17	40997461	40997461	+	Missense_Mutation	SNP	G	G	A	rs35508987	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:40997461G>A	ENST00000253799.3	+	1	845	c.818G>A	c.(817-819)cGg>cAg	p.R273Q	AOC2_ENST00000452774.2_Missense_Mutation_p.R273Q	NM_009590.2	NP_033720.2	O75106	AOC2_HUMAN	amine oxidase, copper containing 2 (retina-specific)	273			R -> Q (in dbSNP:rs35508987). {ECO:0000269|Ref.4}.		amine metabolic process (GO:0009308)|catecholamine metabolic process (GO:0006584)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	aliphatic-amine oxidase activity (GO:0052595)|aminoacetone:oxygen oxidoreductase(deaminating) activity (GO:0052594)|copper ion binding (GO:0005507)|electron carrier activity (GO:0009055)|phenethylamine:oxygen oxidoreductase (deaminating) activity (GO:0052596)|primary amine oxidase activity (GO:0008131)|quinone binding (GO:0048038)|tryptamine:oxygen oxidoreductase (deaminating) activity (GO:0052593)			NS(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(14)|ovary(4)|skin(2)	30		Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.156)		CAGTTGGAACGGGAGTTTAAG	0.572													G|||	14	0.00279553	0.0	0.0029	5008	,	,		18840	0.0		0.0099	False		,,,				2504	0.002				p.R273Q		Atlas-SNP	.											.	AOC2	61	.	0			c.G818A						PASS	.	G	GLN/ARG,GLN/ARG	13,4393	20.2+/-43.8	0,13,2190	81.0	80.0	81.0		818,818	1.0	0.8	17	dbSNP_126	81	79,8521	47.2+/-106.3	0,79,4221	yes	missense,missense	AOC2	NM_001158.3,NM_009590.2	43,43	0,92,6411	AA,AG,GG		0.9186,0.2951,0.7074	benign,benign	273/730,273/757	40997461	92,12914	2203	4300	6503	SO:0001583	missense	314	exon1			TGGAACGGGAGTT	AF081363	CCDS11443.1, CCDS45690.1	17q21	2012-07-13				ENSG00000131480	1.4.3.21		549	protein-coding gene	gene with protein product		602268				9119395, 9722954	Standard	NM_001158		Approved	RAO, DAO2	uc002ibu.3	O75106		ENST00000253799.3:c.818G>A	17.37:g.40997461G>A	ENSP00000253799:p.Arg273Gln	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	116	60	0.517241	NM_009590	A5PKW2|O00120|O75105|Q4TTW5|Q9UNY0	Missense_Mutation	SNP	ENST00000253799.3	37	CCDS11443.1	10	0.004578754578754579	0	0.0	1	0.0027624309392265192	0	0.0	9	0.011873350923482849	G	5.383	0.255861	0.10185	0.002951	0.009186	ENSG00000131480	ENST00000253799;ENST00000452774	T;T	0.15603	2.41;2.41	5.75	1.03	0.20045	Copper amine oxidase, N2/N3-terminal (1);Copper amine oxidase, N-terminal (1);	1.003210	0.08026	N	0.992717	T	0.05181	0.0138	N	0.08118	0	0.09310	N	1	B;B	0.15141	0.007;0.012	B;B	0.10450	0.002;0.005	T	0.42275	-0.9461	10	0.12766	T	0.61	-24.7701	6.4476	0.21885	0.3468:0.0:0.5339:0.1193	rs35508987	273;273	O75106;O75106-2	AOC2_HUMAN;.	Q	273	ENSP00000253799:R273Q;ENSP00000406134:R273Q	ENSP00000253799:R273Q	R	+	2	0	AOC2	38250987	0.000000	0.05858	0.837000	0.33122	0.916000	0.54674	0.563000	0.23547	0.366000	0.24427	-0.254000	0.11334	CGG	G|0.993;A|0.007	0.007	strong		0.572	AOC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452442.1	NM_009590, NM_001158	
OBSCN	84033	hgsc.bcm.edu	37	1	228476367	228476367	+	Missense_Mutation	SNP	A	A	T	rs386640016|rs3795790	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:228476367A>T	ENST00000422127.1	+	38	10161	c.10117A>T	c.(10117-10119)Agc>Tgc	p.S3373C	OBSCN_ENST00000284548.11_Missense_Mutation_p.S3373C|OBSCN_ENST00000359599.6_Missense_Mutation_p.S2220C|OBSCN_ENST00000570156.2_Missense_Mutation_p.S3802C|OBSCN_ENST00000366709.4_Missense_Mutation_p.S492C|OBSCN_ENST00000366707.4_Missense_Mutation_p.S492C	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	3373	Ig-like 34.		S -> C (in dbSNP:rs3795790).		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)				ACACCAAGAGAGCATAGAAGG	0.602													A|||	480	0.0958466	0.0514	0.0144	5008	,	,		20986	0.3165		0.0258	False		,,,				2504	0.0583				p.S3802C		Atlas-SNP	.											.	OBSCN	2142	.	0			c.A11404T						PASS	.	A	CYS/SER,CYS/SER	182,3930		8,166,1882	72.0	77.0	75.0		10117,10117	-1.3	0.1	1	dbSNP_107	75	119,8285		0,119,4083	no	missense,missense	OBSCN	NM_001098623.1,NM_052843.2	112,112	8,285,5965	TT,TA,AA		1.416,4.4261,2.4049	benign,benign	3373/7969,3373/6621	228476367	301,12215	2056	4202	6258	SO:0001583	missense	84033	exon43			CAAGAGAGCATAG	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.10117A>T	1.37:g.228476367A>T	ENSP00000409493:p.Ser3373Cys	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	57	30	0.526316	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	208	0.09523809523809523	17	0.034552845528455285	3	0.008287292817679558	167	0.291958041958042	21	0.027704485488126648	A	9.448	1.089846	0.20390	0.044261	0.01416	ENSG00000154358	ENST00000284548;ENST00000422127;ENST00000366707;ENST00000366709;ENST00000359599	T;T;T;T;T	0.66815	-0.23;-0.23;-0.23;-0.23;-0.23	0.666	-1.33	0.09172	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.536026	0.14449	U	0.318939	T	0.00012	0.0000	N	0.20483	0.58	0.49483	P	2.0699999999995722E-4	P;B	0.52170	0.951;0.002	P;B	0.59115	0.852;0.008	T	0.15009	-1.0452	8	0.34782	T	0.22	.	.	.	.	rs3795790;rs60799870;rs3795790	3373;3373	Q5VST9;Q5VST9-3	OBSCN_HUMAN;.	C	3373;3373;492;492;2220	ENSP00000284548:S3373C;ENSP00000409493:S3373C;ENSP00000355668:S492C;ENSP00000355670:S492C;ENSP00000352613:S2220C	ENSP00000284548:S3373C	S	+	1	0	OBSCN	226542990	0.124000	0.22315	0.095000	0.20976	0.198000	0.23893	0.791000	0.26915	-1.387000	0.02095	-0.608000	0.04076	AGC	A|0.887;T|0.113	0.113	strong		0.602	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
OAS3	4940	hgsc.bcm.edu	37	12	113398919	113398919	+	Silent	SNP	G	G	A	rs2072136	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:113398919G>A	ENST00000228928.7	+	8	1880	c.1701G>A	c.(1699-1701)tcG>tcA	p.S567S	RP1-71H24.1_ENST00000552784.1_RNA	NM_006187.2	NP_006178.2	Q9Y6K5	OAS3_HUMAN	2'-5'-oligoadenylate synthetase 3, 100kDa	567	OAS domain 2.				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						AGGTCTACTCGAGGCTCCTCA	0.537													G|||	1580	0.315495	0.0862	0.2752	5008	,	,		18330	0.6577		0.2346	False		,,,				2504	0.3845				p.S567S		Atlas-SNP	.											.	OAS3	63	.	0			c.G1701A						PASS	.	G		430,3478		30,370,1554	45.0	46.0	46.0		1701	-8.9	0.0	12	dbSNP_96	46	1909,6421		221,1467,2477	no	coding-synonymous	OAS3	NM_006187.2		251,1837,4031	AA,AG,GG		22.9172,11.0031,19.1126		567/1088	113398919	2339,9899	1954	4165	6119	SO:0001819	synonymous_variant	4940	exon8			CTACTCGAGGCTC	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.1701G>A	12.37:g.113398919G>A		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	81	35	0.432099	NM_006187	Q2HJ14|Q9H3P5	Silent	SNP	ENST00000228928.7	37	CCDS44981.1																																																																																			G|0.696;N|0.000	.	strong		0.537	OAS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405920.1		
GJA8	2703	hgsc.bcm.edu	37	1	147380886	147380886	+	Silent	SNP	C	C	T	rs3766503	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:147380886C>T	ENST00000369235.1	+	1	804	c.804C>T	c.(802-804)ctC>ctT	p.L268L	GJA8_ENST00000240986.4_Silent_p.L268L			P48165	CXA8_HUMAN	gap junction protein, alpha 8, 50kDa	268					cell-cell signaling (GO:0007267)|lens development in camera-type eye (GO:0002088)|protein homooligomerization (GO:0051260)|transmembrane transport (GO:0055085)|transport (GO:0006810)|visual perception (GO:0007601)	connexon complex (GO:0005922)|integral component of plasma membrane (GO:0005887)	channel activity (GO:0015267)	p.L268L(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(12)|ovary(2)|pancreas(1)|prostate(3)|skin(1)|stomach(1)	37	all_hematologic(923;0.0276)					GCTATCAGCTCCTAGAAGAAG	0.542													.|||	246	0.0491214	0.0628	0.013	5008	,	,		18214	0.0476		0.0358	False		,,,				2504	0.0716				p.L268L	Melanoma(76;1255 1795 8195 52096)	Atlas-SNP	.											GJA8,NS,carcinoma,0,1	GJA8	108	1	1	Substitution - coding silent(1)	stomach(1)	c.C804T						PASS	.	C		341,4065	174.8+/-204.3	20,301,1882	54.0	56.0	55.0		804	-1.7	0.9	1	dbSNP_107	55	360,8240	118.5+/-177.9	7,346,3947	no	coding-synonymous	GJA8	NM_005267.4		27,647,5829	TT,TC,CC		4.186,7.7394,5.3898		268/434	147380886	701,12305	2203	4300	6503	SO:0001819	synonymous_variant	2703	exon2			TCAGCTCCTAGAA	U34802	CCDS30834.1	1q21.1	2008-02-05	2007-01-16		ENSG00000121634	ENSG00000121634		"""Ion channels / Gap junction proteins (connexins)"""	4281	protein-coding gene	gene with protein product	"""connexin 50"""	600897	"""gap junction protein, alpha 8, 50kD (connexin 50)"", ""gap junction protein, alpha 8, 50kDa (connexin 50)"""	CAE1, CZP1, CAE		9497259, 7796604	Standard	NM_005267		Approved	CX50	uc001epu.2	P48165	OTTHUMG00000024085	ENST00000369235.1:c.804C>T	1.37:g.147380886C>T		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	55	25	0.454545	NM_005267	A7L5M5|Q5VVN9|Q9NP25	Silent	SNP	ENST00000369235.1	37	CCDS30834.1																																																																																			C|0.948;T|0.052	0.052	strong		0.542	GJA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060647.1	NM_005267	
CCDC180	100499483	hgsc.bcm.edu	37	9	100122384	100122384	+	Splice_Site	SNP	G	G	A	rs376419121		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:100122384G>A	ENST00000357054.1	+	37	4463		c.e37+1		CCDC180_ENST00000375202.2_Splice_Site|RP11-23J9.4_ENST00000534123.1_RNA|CCDC180_ENST00000529487.1_Splice_Site|CCDC180_ENST00000395220.1_Splice_Site			Q9P1Z9	CC180_HUMAN	coiled-coil domain containing 180							extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)		p.?(1)									GGTCTTTACCGTAAGGAATGG	0.547																																					.		Atlas-SNP	.											KIAA1529,mouth,carcinoma,0,1	.	.	1	1	Unknown(1)	upper_aerodigestive_tract(1)	c.3615+1G>A						PASS	.	G		0,4406		0,0,2203	100.0	95.0	97.0			3.5	0.9	9		97	1,8599	1.2+/-3.3	0,1,4299	no	splice-5	C9orf174	NM_020893.2		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077			100122384	1,13005	2203	4300	6503	SO:0001630	splice_region_variant	0	exon26			TTTACCGTAAGGA	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.3528+1G>A	9.37:g.100122384G>A		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	67	17	0.253731	NM_020893	Q2KHR6|Q5VV25|Q68DP5|Q69YV9|Q6AHY0	Splice_Site	SNP	ENST00000357054.1	37		.	.	.	.	.	.	.	.	.	.	G	12.90	2.075193	0.36662	0.0	1.16E-4	ENSG00000197816	ENST00000357054;ENST00000375202;ENST00000529487	.	.	.	5.31	3.47	0.39725	.	.	.	.	.	.	.	.	.	.	.	0.58432	D	0.999998	.	.	.	.	.	.	.	.	.	.	.	.	.	.	7.3386	0.26623	0.1896:0.0:0.8104:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	C9orf174	99162205	0.974000	0.33945	0.889000	0.34880	0.044000	0.14063	1.890000	0.39728	1.571000	0.49722	0.561000	0.74099	.	.	.	weak		0.547	CCDC180-201	KNOWN	basic	protein_coding	protein_coding		NM_020893	Intron
TPTE	7179	hgsc.bcm.edu	37	21	10942923	10942923	+	Missense_Mutation	SNP	G	G	A	rs76723236	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:10942923G>A	ENST00000361285.4	-	12	993	c.664C>T	c.(664-666)Cgg>Tgg	p.R222W	TPTE_ENST00000415664.2_5'UTR|TPTE_ENST00000298232.7_Missense_Mutation_p.R204W|TPTE_ENST00000342420.5_Missense_Mutation_p.R184W	NM_199261.2	NP_954870	P56180	TPTE_HUMAN	transmembrane phosphatase with tensin homology	222					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)		CCACTTACCCGCCTTCTTATC	0.318																																					p.R222W		Atlas-SNP	.											.	TPTE	513	.	0			c.C664T						PASS	.						104.0	94.0	98.0					21																	10942923		2203	4299	6502	SO:0001583	missense	7179	exon12			TTACCCGCCTTCT	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.664C>T	21.37:g.10942923G>A	ENSP00000355208:p.Arg222Trp	Somatic	414	0	0		WXS	Illumina HiSeq	Phase_I	293	63	0.215017	NM_199261	B2RAP7|C9J6D6|C9JKK8|Q6XPS4|Q6XPS5|Q71JA8|Q8NCS8	Missense_Mutation	SNP	ENST00000361285.4	37	CCDS13560.2	.	.	.	.	.	.	.	.	.	.	.	9.529	1.110372	0.20714	.	.	ENSG00000166157	ENST00000298232;ENST00000361285;ENST00000342420	D;D;D	0.97455	-4.39;-4.39;-4.39	2.07	-0.258	0.12975	.	0.147653	0.64402	U	0.000017	D	0.92890	0.7738	N	0.14661	0.345	0.20196	N	0.999925	D;D;B	0.56521	0.976;0.976;0.042	B;P;B	0.52710	0.279;0.707;0.008	D	0.87285	0.2295	10	0.72032	D	0.01	-5.1188	4.2955	0.10899	0.1714:0.0:0.5546:0.2741	.	184;204;222	P56180-3;P56180-2;P56180	.;.;TPTE_HUMAN	W	204;222;184	ENSP00000298232:R204W;ENSP00000355208:R222W;ENSP00000344441:R184W	ENSP00000298232:R204W	R	-	1	2	TPTE	9964794	0.985000	0.35326	0.103000	0.21229	0.018000	0.09664	0.502000	0.22594	-0.070000	0.12908	0.194000	0.17425	CGG	G|0.949;A|0.051	0.051	strong		0.318	TPTE-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000157413.1		
OXGR1	27199	hgsc.bcm.edu	37	13	97639021	97639021	+	Silent	SNP	A	A	G	rs9584456	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:97639021A>G	ENST00000298440.1	-	4	1236	c.993T>C	c.(991-993)atT>atC	p.I331I	OXGR1_ENST00000543457.1_Silent_p.I331I	NM_080818.3	NP_543008.3	Q96P68	OXGR1_HUMAN	oxoglutarate (alpha-ketoglutarate) receptor 1	331					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)			NS(1)|large_intestine(1)|lung(9)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	15	all_neural(89;0.0982)|Medulloblastoma(90;0.163)		BRCA - Breast invasive adenocarcinoma(86;0.186)			TTGAGTAACTAATTTTCTTTG	0.398													G|||	319	0.0636981	0.2118	0.0288	5008	,	,		21899	0.0		0.0179	False		,,,				2504	0.001				p.I331I		Atlas-SNP	.											.	OXGR1	46	.	0			c.T993C						PASS	.	G		814,3592	740.9+/-411.2	74,666,1463	104.0	107.0	106.0		993	2.4	0.0	13	dbSNP_119	106	83,8517	814.3+/-407.0	0,83,4217	no	coding-synonymous	OXGR1	NM_080818.3		74,749,5680	GG,GA,AA		0.9651,18.4748,6.8968		331/338	97639021	897,12109	2203	4300	6503	SO:0001819	synonymous_variant	27199	exon4			GTAACTAATTTTC	AF411109	CCDS9482.1	13q32.2	2014-04-09	2004-07-08	2004-07-09	ENSG00000165621	ENSG00000165621		"""GPCR / Class A : Orphans"""	4531	protein-coding gene	gene with protein product	"""2-oxoglutarate receptor 1"", ""alpha-ketoglutarate receptor 1"""	606922	"""G protein-coupled receptor 80"""	GPR99, GPR80		15141213, 12098360	Standard	NM_080818		Approved	P2RY15, P2Y15, aKGR	uc001vmx.1	Q96P68	OTTHUMG00000017236	ENST00000298440.1:c.993T>C	13.37:g.97639021A>G		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	34	13	0.382353	NM_080818	Q5T5A7|Q86TL1	Silent	SNP	ENST00000298440.1	37	CCDS9482.1																																																																																			A|0.933;G|0.067	0.067	strong		0.398	OXGR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045521.3	NM_080818	
RIMKLA	284716	hgsc.bcm.edu	37	1	42880516	42880516	+	Silent	SNP	T	T	C	rs1055055	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:42880516T>C	ENST00000431473.3	+	5	1176	c.1047T>C	c.(1045-1047)agT>agC	p.S349S		NM_173642.3	NP_775913.2	Q8IXN7	RIMKA_HUMAN	ribosomal modification protein rimK-like family member A	349					cellular protein modification process (GO:0006464)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|N-acetyl-L-aspartate-L-glutamate ligase activity (GO:0072590)	p.S308S(1)		NS(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	13						CTACCTCTAGTGAAAGTGAGC	0.552													C|||	2451	0.489417	0.5197	0.5173	5008	,	,		20089	0.3433		0.6441	False		,,,				2504	0.4202				p.S349S		Atlas-SNP	.											RIMKLA,NS,carcinoma,0,1	RIMKLA	32	1	1	Substitution - coding silent(1)	stomach(1)	c.T1047C						PASS	.	C		2364,2042	566.4+/-381.9	644,1076,483	73.0	72.0	73.0		1047	-3.2	0.9	1	dbSNP_86	73	5474,3126	476.6+/-369.4	1759,1956,585	yes	coding-synonymous	RIMKLA	NM_173642.3		2403,3032,1068	CC,CT,TT		36.3488,46.3459,39.7355		349/392	42880516	7838,5168	2203	4300	6503	SO:0001819	synonymous_variant	284716	exon5			CTCTAGTGAAAGT	BC039737	CCDS466.2	1p34.2	2011-09-21	2008-10-13	2008-10-13	ENSG00000177181	ENSG00000177181	6.3.2.N6		28725	protein-coding gene	gene with protein product	"""N-acetylaspartylglutamate synthetase II"""		"""family with sequence similarity 80, member A"""	FAM80A		20657015, 21454531	Standard	NM_173642		Approved	MGC47816, RP11-157D18.1, NAAGS-II	uc001chi.2	Q8IXN7	OTTHUMG00000007335	ENST00000431473.3:c.1047T>C	1.37:g.42880516T>C		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	94	47	0.5	NM_173642	Q5VUS5	Silent	SNP	ENST00000431473.3	37	CCDS466.2																																																																																			T|0.444;C|0.556	0.556	strong		0.552	RIMKLA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019174.3	NM_173642	
CHD6	84181	hgsc.bcm.edu	37	20	40049579	40049579	+	Missense_Mutation	SNP	T	T	A	rs55864139	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:40049579T>A	ENST00000373233.3	-	31	5873	c.5696A>T	c.(5695-5697)aAc>aTc	p.N1899I		NM_032221.3	NP_115597.3	Q8TD26	CHD6_HUMAN	chromodomain helicase DNA binding protein 6	1899					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)				CCTTGAGATGTTAGTAGTGGG	0.517													T|||	32	0.00638978	0.0008	0.0216	5008	,	,		18821	0.0		0.0159	False		,,,				2504	0.0				p.N1899I		Atlas-SNP	.											.	CHD6	312	.	0			c.A5696T						PASS	.	T	ILE/ASN	18,4388	24.3+/-50.5	0,18,2185	140.0	139.0	139.0		5696	-6.9	0.0	20	dbSNP_129	139	125,8475	63.9+/-126.0	1,123,4176	yes	missense	CHD6	NM_032221.3	149	1,141,6361	AA,AT,TT		1.4535,0.4085,1.0995	benign	1899/2716	40049579	143,12863	2203	4300	6503	SO:0001583	missense	84181	exon31			GAGATGTTAGTAG	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.5696A>T	20.37:g.40049579T>A	ENSP00000362330:p.Asn1899Ile	Somatic	281	0	0		WXS	Illumina HiSeq	Phase_I	252	125	0.496032	NM_032221	Q5JYQ0|Q5TGZ9|Q5TH00|Q5TH01|Q8IZR2|Q8WTY0|Q9H4H6|Q9H6D4|Q9NTT7|Q9P2L1	Missense_Mutation	SNP	ENST00000373233.3	37	CCDS13317.1	13	0.005952380952380952	0	0.0	4	0.011049723756906077	0	0.0	9	0.011873350923482849	T	3.272	-0.148971	0.06585	0.004085	0.014535	ENSG00000124177	ENST00000373233	D	0.85702	-2.02	5.86	-6.91	0.01649	.	1.661450	0.02896	N	0.134718	T	0.58221	0.2107	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.52895	-0.8514	10	0.34782	T	0.22	-0.042	4.3803	0.11290	0.0875:0.369:0.3003:0.2432	rs55864139;rs61752059	1899	Q8TD26	CHD6_HUMAN	I	1899	ENSP00000362330:N1899I	ENSP00000362330:N1899I	N	-	2	0	CHD6	39482993	0.000000	0.05858	0.000000	0.03702	0.038000	0.13279	-0.483000	0.06536	-0.683000	0.05190	0.533000	0.62120	AAC	T|0.991;A|0.009	0.009	strong		0.517	CHD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079270.1		
KCNN1	3780	hgsc.bcm.edu	37	19	18096220	18096220	+	Silent	SNP	C	C	T	rs76273600		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:18096220C>T	ENST00000222249.9	+	6	1336	c.1017C>T	c.(1015-1017)caC>caT	p.H339H		NM_002248.3	NP_002239.2	Q92952	KCNN1_HUMAN	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 1	339					potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	calcium-activated potassium channel activity (GO:0015269)|calmodulin binding (GO:0005516)|small conductance calcium-activated potassium channel activity (GO:0016286)			endometrium(1)|kidney(1)|lung(5)|urinary_tract(1)	8					Miconazole(DB01110)|Procaine(DB00721)	TGGTGCCCCACACCTACTGCG	0.597													C|||	1	0.000199681	0.0	0.0	5008	,	,		21197	0.0		0.001	False		,,,				2504	0.0				p.H339H		Atlas-SNP	.											.	KCNN1	74	.	0			c.C1017T						PASS	.	C		0,4346		0,0,2173	91.0	98.0	96.0		1017	2.7	1.0	19	dbSNP_131	96	5,8567	4.3+/-15.6	0,5,4281	no	coding-synonymous	KCNN1	NM_002248.3		0,5,6454	TT,TC,CC		0.0583,0.0,0.0387		339/544	18096220	5,12913	2173	4286	6459	SO:0001819	synonymous_variant	3780	exon6			GCCCCACACCTAC	U69883	CCDS67611.1	19p13.1	2012-07-05				ENSG00000105642		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, calcium-activated"""	6290	protein-coding gene	gene with protein product		602982				8781233, 10516439, 16382103	Standard	NM_002248		Approved	KCa2.1, hSK1	uc002nht.3	Q92952		ENST00000222249.9:c.1017C>T	19.37:g.18096220C>T		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	187	104	0.55615	NM_002248	Q5KR10|Q6DJU4	Silent	SNP	ENST00000222249.9	37																																																																																				C|0.998;T|0.002	0.002	weak		0.597	KCNN1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000471896.2	NM_002248	
TNS1	7145	hgsc.bcm.edu	37	2	218712936	218712936	+	Silent	SNP	C	C	T	rs3796032	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:218712936C>T	ENST00000171887.4	-	17	2381	c.1929G>A	c.(1927-1929)gtG>gtA	p.V643V	TNS1_ENST00000419504.1_Silent_p.V643V|TNS1_ENST00000480665.1_5'Flank|TNS1_ENST00000430930.1_Silent_p.V643V	NM_022648.4	NP_072174.3	Q9HBL0	TENS1_HUMAN	tensin 1	643					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)		GTCCCCTTTGCACAGCCTCCC	0.632													C|||	2178	0.434904	0.6218	0.3156	5008	,	,		17092	0.3442		0.3499	False		,,,				2504	0.4479				p.V643V		Atlas-SNP	.											.	TNS1	251	.	0			c.G1929A						PASS	.	C		2445,1955		691,1063,446	20.0	20.0	20.0		1929	3.7	1.0	2	dbSNP_107	20	2685,5907		448,1789,2059	no	coding-synonymous	TNS1	NM_022648.4		1139,2852,2505	TT,TC,CC		31.25,44.4318,39.4858		643/1736	218712936	5130,7862	2200	4296	6496	SO:0001819	synonymous_variant	7145	exon17			CCTTTGCACAGCC	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.1929G>A	2.37:g.218712936C>T		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	65	31	0.476923	NM_022648	Q4ZG71|Q6IPI5	Silent	SNP	ENST00000171887.4	37	CCDS2407.1																																																																																			C|0.600;T|0.400	0.400	strong		0.632	TNS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256672.2	NM_022648	
ODF2L	57489	hgsc.bcm.edu	37	1	86822231	86822231	+	Silent	SNP	A	A	G	rs385437	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:86822231A>G	ENST00000359242.3	-	14	1695	c.1414T>C	c.(1414-1416)Ttg>Ctg	p.L472L	ODF2L_ENST00000524695.1_5'UTR|ODF2L_ENST00000370566.3_Intron|ODF2L_ENST00000394731.1_Silent_p.L312L|ODF2L_ENST00000294678.2_Silent_p.L443L|ODF2L_ENST00000370567.1_Silent_p.L443L|ODF2L_ENST00000317336.7_Silent_p.L472L	NM_001007022.2	NP_001007023.2	Q9ULJ1	ODF2L_HUMAN	outer dense fiber of sperm tails 2-like	472						centrosome (GO:0005813)				endometrium(2)|kidney(2)|large_intestine(10)|lung(6)|ovary(1)|pancreas(1)|skin(1)|stomach(1)	24				all cancers(265;0.0313)|Epithelial(280;0.0611)		GCCGCCGTCAAGGAATCGCAG	0.542													A|||	612	0.122204	0.1104	0.1167	5008	,	,		16079	0.0327		0.171	False		,,,				2504	0.184				p.L472L		Atlas-SNP	.											.	ODF2L	53	.	0			c.T1414C						PASS	.	A	,,,	455,3951	216.1+/-234.9	27,401,1775	77.0	69.0	72.0		1414,,,1327	-2.1	0.9	1	dbSNP_80	72	1295,7305	253.3+/-279.0	105,1085,3110	no	coding-synonymous,intron,intron,coding-synonymous	ODF2L	NM_001007022.2,NM_001184765.1,NM_001184766.1,NM_020729.2	,,,	132,1486,4885	GG,GA,AA		15.0581,10.3268,13.4553	,,,	472/637,,,443/621	86822231	1750,11256	2203	4300	6503	SO:0001819	synonymous_variant	57489	exon14			CCGTCAAGGAATC		CCDS30763.1, CCDS41354.1, CCDS30763.2, CCDS41354.2, CCDS53339.1	1p22.3	2008-02-05			ENSG00000122417	ENSG00000122417			29225	protein-coding gene	gene with protein product						10574462	Standard	NM_020729		Approved	KIAA1229	uc001dll.2	Q9ULJ1	OTTHUMG00000010080	ENST00000359242.3:c.1414T>C	1.37:g.86822231A>G		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	57	30	0.526316	NM_001007022	A8MU56|B4E037|Q05C40|Q5BJG5|Q5TBX3|Q5TBX4|Q86X31	Silent	SNP	ENST00000359242.3	37	CCDS41354.2																																																																																			A|0.872;G|0.128	0.128	strong		0.542	ODF2L-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000027873.2		
ZFAT	57623	hgsc.bcm.edu	37	8	135602581	135602581	+	Silent	SNP	A	A	G	rs3739425	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:135602581A>G	ENST00000377838.3	-	8	2667	c.2493T>C	c.(2491-2493)tcT>tcC	p.S831S	ZFAT_ENST00000520214.1_Silent_p.S819S|ZFAT_ENST00000517307.1_5'UTR|ZFAT_ENST00000523399.1_Silent_p.S769S|ZFAT_ENST00000520356.1_Silent_p.S819S|ZFAT_ENST00000520727.1_Silent_p.S819S|ZFAT_ENST00000429442.2_Silent_p.S819S	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	71	0	0		WXS	Illumina HiSeq	Phase_I	48	40	0.833333	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	
ESD	2098	hgsc.bcm.edu	37	13	47354101	47354101	+	Missense_Mutation	SNP	C	C	T	rs9778	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:47354101C>T	ENST00000378720.3	-	8	751	c.569G>A	c.(568-570)gGa>gAa	p.G190E	ESD_ENST00000378697.1_Missense_Mutation_p.G161E|ESD_ENST00000495654.1_5'UTR	NM_001984.1	NP_001975.1	P10768	ESTD_HUMAN	esterase D	190			G -> E (in allele ESD*2; dbSNP:rs9778). {ECO:0000269|PubMed:12721789, ECO:0000269|PubMed:7907313}.		formaldehyde catabolic process (GO:0046294)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	carboxylic ester hydrolase activity (GO:0052689)|hydrolase activity, acting on ester bonds (GO:0016788)|methylumbelliferyl-acetate deacetylase activity (GO:0047374)|S-formylglutathione hydrolase activity (GO:0018738)			endometrium(1)|kidney(2)|large_intestine(1)|lung(4)|ovary(1)	9		all_lung(13;3.54e-08)|Lung NSC(96;9.1e-06)|Breast(56;0.000148)|Prostate(109;0.0029)|Lung SC(185;0.0367)|Myeloproliferative disorder(33;0.0505)|Hepatocellular(98;0.0556)		GBM - Glioblastoma multiforme(144;2.66e-05)	Glutathione(DB00143)	TCCCAAATATCCACTAAAGGC	0.358													C|||	962	0.192093	0.0855	0.1383	5008	,	,		10141	0.4206		0.0775	False		,,,				2504	0.2566				p.G190E		Atlas-SNP	.											.	ESD	23	.	0			c.G569A						PASS	.	C	GLU/GLY	350,4056	181.5+/-209.5	10,330,1863	106.0	104.0	105.0		569	4.4	1.0	13	dbSNP_52	105	914,7686	202.1+/-245.5	42,830,3428	yes	missense	ESD	NM_001984.1	98	52,1160,5291	TT,TC,CC		10.6279,7.9437,9.7186	benign	190/283	47354101	1264,11742	2203	4300	6503	SO:0001583	missense	2098	exon8			AAATATCCACTAA	M13450	CCDS9404.1	13q14.1-q14.2	2014-05-13	2010-05-07		ENSG00000139684	ENSG00000139684	3.1.2.12		3465	protein-coding gene	gene with protein product	"""S-formylglutathione hydrolase"""	133280	"""esterase D/formylglutathione hydrolase"""				Standard	NM_001984		Approved		uc001vbn.3	P10768	OTTHUMG00000016878	ENST00000378720.3:c.569G>A	13.37:g.47354101C>T	ENSP00000367992:p.Gly190Glu	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	44	25	0.568182	NM_001984	Q5TBU8|Q5TBV0|Q5TBV2|Q9BVJ2	Missense_Mutation	SNP	ENST00000378720.3	37	CCDS9404.1	380|380	0.17399267399267399|0.17399267399267399	51|51	0.10365853658536585|0.10365853658536585	54|54	0.14917127071823205|0.14917127071823205	226|226	0.3951048951048951|0.3951048951048951	49|49	0.06464379947229551|0.06464379947229551	C|C	20.9|20.9	4.071880|4.071880	0.76301|0.76301	0.079437|0.079437	0.106279|0.106279	ENSG00000139684|ENSG00000139684	ENST00000412582|ENST00000378720;ENST00000378697	.|T;T	.|0.31510	.|1.49;1.49	6.16|6.16	4.42|4.42	0.53409|0.53409	.|.	.|0.155857	.|0.56097	.|N	.|0.000026	T|T	0.00012|0.00012	0.0000|0.0000	M|M	0.82517|0.82517	2.595|2.595	0.09310|0.09310	P|P	0.9999999635137|0.9999999635137	.|P	.|0.39737	.|0.685	.|B	.|0.39503	.|0.301	T|T	0.39502|0.39502	-0.9611|-0.9611	4|9	.|0.46703	.|T	.|0.11	-6.916|-6.916	10.9038|10.9038	0.47067|0.47067	0.0:0.7987:0.1311:0.0702|0.0:0.7987:0.1311:0.0702	rs9778;rs1051064;rs3191448;rs8192894;rs17342262;rs17353977;rs52797294;rs57577491;rs8192894|rs9778;rs1051064;rs3191448;rs8192894;rs17342262;rs17353977;rs52797294;rs57577491;rs8192894	.|190	.|P10768	.|ESTD_HUMAN	N|E	138|190;161	.|ENSP00000367992:G190E;ENSP00000367969:G161E	.|ENSP00000367969:G161E	D|G	-|-	1|2	0|0	ESD|ESD	46252102|46252102	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.997000|0.997000	0.91878|0.91878	4.842000|4.842000	0.62831|0.62831	0.912000|0.912000	0.36772|0.36772	0.650000|0.650000	0.86243|0.86243	GAT|GGA	T|0.140;G|0.000;C|0.859	0.140	strong		0.358	ESD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044826.1		
KLHL31	401265	hgsc.bcm.edu	37	6	53519857	53519857	+	Silent	SNP	G	G	A	rs12210809	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	184	0	0		WXS	Illumina HiSeq	Phase_I	162	159	0.981481	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	
CACNA1C	775	hgsc.bcm.edu	37	12	2791130	2791130	+	Missense_Mutation	SNP	C	C	T	rs10848683|rs71441836	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:2791130C>T	ENST00000399617.1	+	43	5459	c.5459C>T	c.(5458-5460)cCg>cTg	p.P1820L	CACNA1C_ENST00000335762.5_Intron|CACNA1C_ENST00000399621.1_Intron|CACNA1C_ENST00000399644.1_Intron|CACNA1C_ENST00000347598.4_Intron|CACNA1C_ENST00000399634.1_Intron|CACNA1C_ENST00000399603.1_Intron|CACNA1C_ENST00000399649.1_Intron|CACNA1C_ENST00000327702.7_Missense_Mutation_p.P1820L|CACNA1C_ENST00000399655.1_Intron|CACNA1C_ENST00000406454.3_Intron|CACNA1C_ENST00000399637.1_Intron|CACNA1C_ENST00000399591.1_Intron|CACNA1C_ENST00000399641.1_Intron|CACNA1C_ENST00000399606.1_Intron|CACNA1C-AS1_ENST00000501371.1_RNA|CACNA1C_ENST00000399601.1_Intron|CACNA1C_ENST00000399629.1_Intron|CACNA1C_ENST00000402845.3_Intron|CACNA1C_ENST00000344100.3_Intron|CACNA1C_ENST00000399638.1_Intron|CACNA1C_ENST00000399595.1_Intron|CACNA1C_ENST00000399597.1_Intron	NM_001167624.1	NP_001161096.1	Q13936	CAC1C_HUMAN	calcium channel, voltage-dependent, L type, alpha 1C subunit	1868					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)	AGGCACGTTCCGATGTGTGAG	0.567													T|||	3351	0.669129	0.4622	0.7248	5008	,	,		21231	0.5744		0.8191	False		,,,				2504	0.8528				p.P1868L		Atlas-SNP	.											CACNA1C_ENST00000399617,NS,meningioma,0,2	CACNA1C	1023	2	0			c.C5603T						PASS	.	T	,,,LEU/PRO,,,,,,,,,,,,,,,,,LEU/PRO,,LEU/PRO	1581,1555		411,759,398	125.0	105.0	111.0		,,,5459,,,,,,,,,,,,,,,,,5459,,5603	1.6	0.0	12	dbSNP_120	111	5884,1280		2431,1022,129	yes	intron,intron,intron,missense,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,missense,intron,missense	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	,,,98,,,,,,,,,,,,,,,,,98,,98	2842,1781,527	TT,TC,CC		17.8671,49.5855,27.5243	,,,,,,,,,,,,,,,,,,,,,,	,,,1820/2174,,,,,,,,,,,,,,,,,1820/2174,,1868/2222	2791130	7465,2835	1568	3582	5150	SO:0001583	missense	775	exon45			ACGTTCCGATGTG	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	ENST00000399617.1:c.5459C>T	12.37:g.2791130C>T	ENSP00000382526:p.Pro1820Leu	Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	40	40	1	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	ENST00000399617.1	37	CCDS53733.1	1452	0.6648351648351648	207	0.42073170731707316	271	0.7486187845303868	349	0.6101398601398601	625	0.8245382585751979	T	6.045	0.376619	0.11466	0.504145	0.821329	ENSG00000151067	ENST00000327702;ENST00000399617	D;D	0.95205	-3.54;-3.64	2.85	1.64	0.23874	.	.	.	.	.	T	0.00012	0.0000	L	0.60455	1.87	0.80722	P	0.0	B;B;B	0.09022	0.002;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.42413	-0.9453	8	0.34782	T	0.22	.	2.4217	0.04449	0.2365:0.1391:0.0:0.6245	rs10848683;rs58264517;rs10848683	1868;1820;1820	Q13936;Q13936-33;E9PDJ0	CAC1C_HUMAN;.;.	L	1820	ENSP00000329877:P1820L;ENSP00000382526:P1820L	ENSP00000329877:P1820L	P	+	2	0	CACNA1C	2661391	0.000000	0.05858	0.007000	0.13788	0.004000	0.04260	-1.323000	0.02692	0.051000	0.15978	-0.352000	0.07741	CCG	TGG|0.500;CGA|0.500	.	alt		0.567	CACNA1C-013	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317031.1	NM_000719	
FAM46C	54855	hgsc.bcm.edu	37	1	118165577	118165577	+	Silent	SNP	C	C	G	rs865443	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:118165577C>G	ENST00000369448.3	+	2	334	c.87C>G	c.(85-87)ctC>ctG	p.L29L		NM_017709.3	NP_060179.2	Q5VWP2	FA46C_HUMAN	family with sequence similarity 46, member C	29										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)		ATGAGGTCCTCACTGAAGTTG	0.557			"""Mis, F, O"""		MM					Multiple Myeloma(3;1.13e-06)			G|||	635	0.126797	0.2617	0.085	5008	,	,		21909	0.122		0.0626	False		,,,				2504	0.045				p.L29L		Atlas-SNP	.		Rec	yes		1	1p12	54855	"""family with sequence similarity 46, member C"""		L	.	FAM46C	25	.	0			c.C87G						PASS	.	G		948,3458	735.6+/-410.7	109,730,1364	102.0	87.0	92.0		87	4.1	1.0	1	dbSNP_86	92	501,8099	796.8+/-407.5	12,477,3811	no	coding-synonymous	FAM46C	NM_017709.3		121,1207,5175	GG,GC,CC		5.8256,21.5161,11.141		29/392	118165577	1449,11557	2203	4300	6503	SO:0001819	synonymous_variant	54855	exon2			GGTCCTCACTGAA	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.87C>G	1.37:g.118165577C>G		Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	133	70	0.526316	NM_017709	A3KMG2|Q8NE25|Q9NXK0	Silent	SNP	ENST00000369448.3	37	CCDS896.1																																																																																			C|0.882;G|0.118	0.118	strong		0.557	FAM46C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038424.1	NM_017709	
PCDHB11	56125	hgsc.bcm.edu	37	5	140580931	140580931	+	Missense_Mutation	SNP	C	C	G	rs34415020|rs799834	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:140580931C>G	ENST00000354757.3	+	1	1584	c.1584C>G	c.(1582-1584)gaC>gaG	p.D528E	PCDHB11_ENST00000536699.1_Missense_Mutation_p.D163E	NM_018931.2	NP_061754.1	Q9Y5F2	PCDBB_HUMAN	protocadherin beta 11	528	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.		D -> E (in dbSNP:rs799834).		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)			AGGCTTTCGACTTCCGCGTGG	0.677													G|||	2793	0.557708	0.7648	0.5576	5008	,	,		16257	0.5694		0.4105	False		,,,				2504	0.4172				p.D528E		Atlas-SNP	.											PCDHB11,NS,carcinoma,+2,1	PCDHB11	162	1	0			c.C1584G						PASS	.	G	GLU/ASP	3038,1366		1027,984,191	58.0	76.0	70.0		1584	1.6	0.0	5	dbSNP_86	70	3520,5080		757,2006,1537	no	missense	PCDHB11	NM_018931.2	45	1784,2990,1728	GG,GC,CC		40.9302,31.0173,49.5694	benign	528/798	140580931	6558,6446	2202	4300	6502	SO:0001583	missense	56125	exon1			TTTCGACTTCCGC	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.1584C>G	5.37:g.140580931C>G	ENSP00000346802:p.Asp528Glu	Somatic	235	0	0		WXS	Illumina HiSeq	Phase_I	248	142	0.572581	NM_018931	B4DSF7|Q2M223	Missense_Mutation	SNP	ENST00000354757.3	37	CCDS4253.1	1096	0.5018315018315018	329	0.6686991869918699	165	0.4558011049723757	320	0.5594405594405595	282	0.3720316622691293	N	0.046	-1.265433	0.01433	0.689827	0.409302	ENSG00000197479	ENST00000536699;ENST00000354757	T;T	0.01705	4.68;4.68	2.51	1.61	0.23674	Cadherin (5);Cadherin-like (1);	.	.	.	.	T	0.00012	0.0000	N	0.00926	-1.1	0.80722	P	0.0	B	0.02656	0.0	B	0.08055	0.003	T	0.18461	-1.0336	8	0.02654	T	1	.	3.8674	0.09022	0.3311:0.1861:0.4828:0.0	rs799834;rs61497114	528	Q9Y5F2	PCDBB_HUMAN	E	163;528	ENSP00000440344:D163E;ENSP00000346802:D528E	ENSP00000346802:D528E	D	+	3	2	PCDHB11	140561115	0.001000	0.12720	0.010000	0.14722	0.076000	0.17211	0.179000	0.16840	0.005000	0.14708	-0.702000	0.03669	GAC	C|0.497;G|0.503	0.503	strong		0.677	PCDHB11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251813.1	NM_018931	
FAM185A	222234	hgsc.bcm.edu	37	7	102427889	102427889	+	Missense_Mutation	SNP	C	C	T	rs116082009	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:102427889C>T	ENST00000413034.2	+	7	1039	c.1039C>T	c.(1039-1041)Cgt>Tgt	p.R347C	FAM185A_ENST00000409231.3_Missense_Mutation_p.R230C	NM_001145268.1	NP_001138740	Q8N0U4	F185A_HUMAN	family with sequence similarity 185, member A	347										kidney(1)	1						GGCTGAAGTTCGTAAAGATGA	0.403													C|||	590	0.117812	0.1407	0.1542	5008	,	,		19248	0.0119		0.1948	False		,,,				2504	0.091				p.R347C		Atlas-SNP	.											.	FAM185A	10	.	0			c.C1039T						PASS	.						191.0	152.0	164.0					7																	102427889		692	1591	2283	SO:0001583	missense	222234	exon7			GAAGTTCGTAAAG	BC029175	CCDS47676.1, CCDS47677.1	7q22.1	2009-07-09			ENSG00000222011	ENSG00000222011			22412	protein-coding gene	gene with protein product							Standard	NM_001145268		Approved	MGC35361	uc011klf.2	Q8N0U4	OTTHUMG00000154140	ENST00000413034.2:c.1039C>T	7.37:g.102427889C>T	ENSP00000395340:p.Arg347Cys	Somatic	629	1	0.00158983		WXS	Illumina HiSeq	Phase_I	536	261	0.48694	NM_001145268	A8MUR7|B4DQD3|C9IZ91	Missense_Mutation	SNP	ENST00000413034.2	37	CCDS47676.1	292	0.1336996336996337	64	0.13008130081300814	66	0.18232044198895028	5	0.008741258741258742	157	0.20712401055408972	C	12.82	2.052152	0.36181	.	.	ENSG00000222011	ENST00000432852;ENST00000409231;ENST00000413034	T;T	0.45668	0.89;0.93	4.09	2.16	0.27623	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B;B	0.06786	0.001;0.001;0.0	B;B;B	0.04013	0.001;0.001;0.0	T	0.13710	-1.0499	8	0.52906	T	0.07	0.6665	6.9447	0.24512	0.0:0.771:0.0:0.229	rs17842496;rs17842496	247;230;347	B4DMG7;Q8N0U4-3;Q8N0U4	.;.;F185A_HUMAN	C	247;230;347	ENSP00000387066:R230C;ENSP00000395340:R347C	ENSP00000387066:R230C	R	+	1	0	FAM185A	102215125	0.000000	0.05858	0.001000	0.08648	0.863000	0.49368	0.422000	0.21296	0.883000	0.36040	0.536000	0.68110	CGT	C|0.859;T|0.141	0.141	strong		0.403	FAM185A-009	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000349482.1	NM_001145268	
DENND5B	160518	hgsc.bcm.edu	37	12	31604928	31604928	+	Silent	SNP	G	G	C	rs3205175	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:31604928G>C	ENST00000389082.5	-	5	1839	c.1575C>G	c.(1573-1575)gcC>gcG	p.A525A	DENND5B_ENST00000536562.1_Silent_p.A560A|DENND5B_ENST00000354285.4_Silent_p.A547A|snoU13_ENST00000458765.1_RNA|DENND5B_ENST00000306833.6_Silent_p.A560A	NM_144973.3	NP_659410.3	Q6ZUT9	DEN5B_HUMAN	DENN/MADD domain containing 5B	525	dDENN. {ECO:0000255|PROSITE- ProRule:PRU00306}.				positive regulation of Rab GTPase activity (GO:0032851)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			NS(2)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(8)|lung(17)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	38						CCATGTCCTGGGCAGTCTGAA	0.428													G|||	883	0.176318	0.2247	0.1052	5008	,	,		18455	0.247		0.1233	False		,,,				2504	0.1431				p.A525A		Atlas-SNP	.											.	DENND5B	114	.	0			c.C1575G						PASS	.	G		758,3032		75,608,1212	99.0	96.0	97.0		1575	-0.6	1.0	12	dbSNP_105	97	870,7388		54,762,3313	no	coding-synonymous	DENND5B	NM_144973.3		129,1370,4525	CC,CG,GG		10.5352,20.0,13.5126		525/1275	31604928	1628,10420	1895	4129	6024	SO:0001819	synonymous_variant	160518	exon5			GTCCTGGGCAGTC	AF086301	CCDS44857.1	12p11.21	2012-10-03			ENSG00000170456	ENSG00000170456		"""DENN/MADD domain containing"""	28338	protein-coding gene	gene with protein product						12477932	Standard	NM_144973		Approved	MGC24039	uc001rki.1	Q6ZUT9	OTTHUMG00000169034	ENST00000389082.5:c.1575C>G	12.37:g.31604928G>C		Somatic	202	0	0		WXS	Illumina HiSeq	Phase_I	175	81	0.462857	NM_144973	B5ME75|Q59FW8|Q68CZ7|Q6NUJ0|Q7Z3F9|Q8N973|Q8WUC8	Silent	SNP	ENST00000389082.5	37	CCDS44857.1																																																																																			G|0.814;C|0.186	0.186	strong		0.428	DENND5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402040.1	NM_144973	
USP43	124739	hgsc.bcm.edu	37	17	9604775	9604775	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:9604775A>G	ENST00000285199.7	+	12	1865	c.1769A>G	c.(1768-1770)aAa>aGa	p.K590R	USP43_ENST00000570827.2_3'UTR|USP43_ENST00000570475.1_Missense_Mutation_p.K590R	NM_001267576.1|NM_153210.4	NP_001254505.1|NP_694942.3	Q70EL4	UBP43_HUMAN	ubiquitin specific peptidase 43	590	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						ATCCACCTCAAAAGGTTCTGC	0.567																																					p.K590R		Atlas-SNP	.											.	USP43	65	.	0			c.A1769G						PASS	.						34.0	36.0	36.0					17																	9604775		2123	4249	6372	SO:0001583	missense	124739	exon12			ACCTCAAAAGGTT	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.1769A>G	17.37:g.9604775A>G	ENSP00000285199:p.Lys590Arg	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	44	7	0.159091	NM_001267576	A6NDT9|B7ZLT9|B7ZVX5|Q8N2C5|Q96DQ6	Missense_Mutation	SNP	ENST00000285199.7	37	CCDS45610.1	.	.	.	.	.	.	.	.	.	.	A	22.4	4.284577	0.80803	.	.	ENSG00000154914	ENST00000285199	T	0.39229	1.09	5.12	5.12	0.69794	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.000000	0.85682	D	0.000000	T	0.72867	0.3514	H	0.94964	3.605	0.58432	D	0.999999	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.999;0.999;1.0;1.0	T	0.81026	-0.1119	10	0.87932	D	0	-15.7098	13.1508	0.59488	1.0:0.0:0.0:0.0	.	590;279;590;102	B7ZVX5;Q70EL4-3;Q70EL4;Q70EL4-2	.;.;UBP43_HUMAN;.	R	590	ENSP00000285199:K590R	ENSP00000285199:K590R	K	+	2	0	USP43	9545500	1.000000	0.71417	0.691000	0.30163	0.845000	0.48019	8.748000	0.91615	2.040000	0.60383	0.460000	0.39030	AAA	.	.	none		0.567	USP43-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439855.3	NM_153210	
NUP133	55746	hgsc.bcm.edu	37	1	229631734	229631734	+	Missense_Mutation	SNP	T	T	C	rs11805194	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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						PASS	.	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	156	0	0		WXS	Illumina HiSeq	Phase_I	115	51	0.443478	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	
SRRM5	100170229	hgsc.bcm.edu	37	19	44118188	44118188	+	Missense_Mutation	SNP	A	A	C	rs3815422	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:44118188A>C	ENST00000607544.1	+	3	2237	c.1915A>C	c.(1915-1917)Agc>Cgc	p.S639R	SRRM5_ENST00000417606.1_Missense_Mutation_p.S639R|SRRM5_ENST00000526798.1_Missense_Mutation_p.S654R|ZNF428_ENST00000300811.3_Intron			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	34	0	0		WXS	Illumina HiSeq	Phase_I	31	13	0.419355	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	
FSCB	84075	hgsc.bcm.edu	37	14	44975052	44975052	+	Missense_Mutation	SNP	A	A	G	rs3825630	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:44975052A>G	ENST00000340446.4	-	1	1430	c.1139T>C	c.(1138-1140)cTt>cCt	p.L380P	RP11-163M18.1_ENST00000557465.1_RNA|RP11-163M18.1_ENST00000555433.1_RNA	NM_032135.3	NP_115511.3	Q5H9T9	FSCB_HUMAN	fibrous sheath CABYR binding protein	380	Pro-rich.		L -> P (in dbSNP:rs3825630). {ECO:0000269|PubMed:15489334}.			sperm fibrous sheath (GO:0035686)|sperm principal piece (GO:0097228)	calcium ion binding (GO:0005509)	p.L380P(1)		breast(4)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(10)|lung(47)|ovary(2)|pancreas(1)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(1)	89				GBM - Glioblastoma multiforme(112;0.128)		TTCACCAAGAAGCTCTACTGA	0.522													A|||	1358	0.271166	0.2859	0.3055	5008	,	,		18322	0.3968		0.1193	False		,,,				2504	0.2536				p.L380P		Atlas-SNP	.											FSCB,NS,carcinoma,0,1	FSCB	173	1	1	Substitution - Missense(1)	stomach(1)	c.T1139C						PASS	.	A	PRO/LEU	1168,3238	363.6+/-316.6	160,848,1195	88.0	101.0	97.0		1139	-0.2	0.0	14	dbSNP_107	97	938,7662	196.9+/-241.7	50,838,3412	yes	missense	FSCB	NM_032135.3	98	210,1686,4607	GG,GA,AA		10.907,26.5093,16.1925	probably-damaging	380/826	44975052	2106,10900	2203	4300	6503	SO:0001583	missense	84075	exon1			CCAAGAAGCTCTA	AK124110	CCDS9679.1	14q21.3	2007-11-22	2007-11-22	2007-11-22	ENSG00000189139	ENSG00000189139			20494	protein-coding gene	gene with protein product		611779	"""chromosome 14 open reading frame 155"""	C14orf155		17855365	Standard	NM_032135		Approved	DKFZP434F1017	uc001wvn.3	Q5H9T9	OTTHUMG00000140262	ENST00000340446.4:c.1139T>C	14.37:g.44975052A>G	ENSP00000344579:p.Leu380Pro	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	95	37	0.389474	NM_032135	Q5H9U7|Q86YI2|Q9H0J3	Missense_Mutation	SNP	ENST00000340446.4	37	CCDS9679.1	542	0.24816849816849818	138	0.2804878048780488	97	0.26795580110497236	223	0.38986013986013984	84	0.11081794195250659	a	4.879	0.163307	0.09287	0.265093	0.10907	ENSG00000189139	ENST00000340446;ENST00000537803	T	0.17528	2.27	3.87	-0.16	0.13375	.	.	.	.	.	T	0.00012	0.0000	N	0.17474	0.49	0.80722	P	0.0	B	0.11235	0.004	B	0.08055	0.003	T	0.48502	-0.9030	8	0.30078	T	0.28	.	6.2119	0.20633	0.5846:0.0:0.4154:0.0	rs3825630;rs17855636;rs58475266;rs3825630	380	Q5H9T9	FSCB_HUMAN	P	380	ENSP00000344579:L380P	ENSP00000344579:L380P	L	-	2	0	FSCB	44044802	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-0.903000	0.04084	-0.139000	0.11414	-0.479000	0.04858	CTT	A|0.796;G|0.204	0.204	strong		0.522	FSCB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276788.1	NM_032135	
HIF3A	64344	hgsc.bcm.edu	37	19	46823803	46823803	+	Missense_Mutation	SNP	C	C	T	rs61755707	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:46823803C>T	ENST00000377670.4	+	9	1160	c.1129C>T	c.(1129-1131)Cct>Tct	p.P377S	AC007193.10_ENST00000596807.1_RNA|HIF3A_ENST00000244303.6_Missense_Mutation_p.P308S|HIF3A_ENST00000339613.2_Missense_Mutation_p.P321S|HIF3A_ENST00000472815.1_Missense_Mutation_p.P308S|HIF3A_ENST00000600383.1_Missense_Mutation_p.P308S|HIF3A_ENST00000420102.2_Missense_Mutation_p.P326S|HIF3A_ENST00000300862.3_Missense_Mutation_p.P375S	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	38	0	0		WXS	Illumina HiSeq	Phase_I	32	16	0.5	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		
LILRA6	79168	hgsc.bcm.edu	37	19	54742900	54742900	+	Missense_Mutation	SNP	C	C	G	rs117376661	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:54742900C>G	ENST00000396365.2	-	8	1414	c.1375G>C	c.(1375-1377)Gtg>Ctg	p.V459L	LILRA6_ENST00000245621.5_Missense_Mutation_p.V442L|LILRA6_ENST00000440558.2_Intron|LILRA6_ENST00000270464.5_Intron|LILRB3_ENST00000407860.2_Intron|LILRA6_ENST00000419410.2_Intron|LILRA6_ENST00000391735.3_Intron	NM_024318.2	NP_077294	Q6PI73	LIRA6_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 6	459					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)		CCGAGGAACACCAGGACCAAG	0.577													.|||	108	0.0215655	0.0045	0.0274	5008	,	,		21162	0.0		0.0815	False		,,,				2504	0.001				p.V459L		Atlas-SNP	.											LILRA6,NS,carcinoma,0,1	LILRA6	75	1	0			c.G1375C						PASS	.	C	LEU/VAL	75,4277	64.1+/-101.4	7,61,2108	116.0	105.0	109.0		1375	-4.1	0.0	19	dbSNP_132	109	674,7924	167.8+/-219.5	42,590,3667	no	missense	LILRA6	NM_024318.2	32	49,651,5775	GG,GC,CC		7.839,1.7233,5.7838		459/482	54742900	749,12201	2176	4299	6475	SO:0001583	missense	79168	exon8			GGAACACCAGGAC	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.1375G>C	19.37:g.54742900C>G	ENSP00000379651:p.Val459Leu	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	136	76	0.558824	NM_024318		Missense_Mutation	SNP	ENST00000396365.2	37	CCDS42610.1	80	0.03663003663003663	1	0.0020325203252032522	12	0.03314917127071823	0	0.0	67	0.08839050131926121	C	11.91	1.779274	0.31502	0.017233	0.07839	ENSG00000244482	ENST00000396365;ENST00000245621	T;T	0.00526	6.93;6.8	2.59	-4.11	0.03928	.	387.339000	0.00166	N	0.000003	T	0.00012	0.0000	L	0.31157	0.91	0.09310	N	0.999999	B	0.06786	0.001	B	0.09377	0.004	T	0.44636	-0.9315	10	0.02654	T	1	.	0.8427	0.01154	0.1461:0.201:0.2625:0.3904	.	459	Q6PI73	LIRA6_HUMAN	L	459;442	ENSP00000379651:V459L;ENSP00000245621:V442L	ENSP00000245621:V442L	V	-	1	0	LILRA6	59434712	0.000000	0.05858	0.020000	0.16555	0.085000	0.17905	-3.862000	0.00348	-0.470000	0.06901	0.174000	0.16983	GTG	C|0.953;G|0.047	0.047	strong		0.577	LILRA6-003	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000313725.1	NM_024318	
HCAR3	8843	hgsc.bcm.edu	37	12	123200768	123200768	+	Missense_Mutation	SNP	T	T	G	rs386767126|rs1798192	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:123200768T>G	ENST00000528880.2	-	1	671	c.517A>C	c.(517-519)Act>Cct	p.T173P	RP11-324E6.6_ENST00000543611.1_lincRNA|HCAR1_ENST00000356987.2_Intron	NM_006018.2	NP_006009.2	P49019	HCAR3_HUMAN	hydroxycarboxylic acid receptor 3	173			T -> P (in dbSNP:rs1798192). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:7505609, ECO:0000269|Ref.2}.		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)	p.T173P(1)		endometrium(1)|large_intestine(1)|lung(5)|ovary(1)|skin(1)	9					Niacin(DB00627)	ACATTTGCAGTGCCATTCTGG	0.527													t|||	2324	0.464058	0.5008	0.4409	5008	,	,		21393	0.495		0.5716	False		,,,				2504	0.2883				p.T173P		Atlas-SNP	.											HCAR3_ENST00000528880,NS,carcinoma,0,1	HCAR3	49	1	1	Substitution - Missense(1)	stomach(1)	c.A517C						PASS	.	T	PRO/THR	2231,2175	591.4+/-387.6	583,1065,555	99.0	95.0	96.0		517	-4.7	0.0	12	dbSNP_89	96	4921,3679	621.2+/-397.2	1410,2101,789	yes	missense	HCAR3	NM_006018.2	38	1993,3166,1344	GG,GT,TT		42.7791,49.3645,45.01	benign	173/388	123200768	7152,5854	2203	4300	6503	SO:0001583	missense	8843	exon1			TTGCAGTGCCATT	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.517A>C	12.37:g.123200768T>G	ENSP00000436714:p.Thr173Pro	Somatic	132	1	0.00757576		WXS	Illumina HiSeq	Phase_I	120	120	1	NM_006018	A8K4G5|B2R830|E9PI97|Q8NGE4	Missense_Mutation	SNP	ENST00000528880.2	37	CCDS53842.1	1139	0.5215201465201466	251	0.5101626016260162	169	0.46685082872928174	304	0.5314685314685315	415	0.5474934036939314	T	0.572	-0.840675	0.02692	0.506355	0.572209	ENSG00000255398	ENST00000528880	T	0.37058	1.22	2.99	-4.69	0.03299	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.06786	0.001	B	0.10450	0.005	T	0.45963	-0.9225	7	0.49607	T	0.09	.	5.7314	0.18042	0.0:0.6545:0.1482:0.1973	rs1798192;rs3741539;rs17883771;rs60927003;rs1798192	173	E9PI97	.	P	173	ENSP00000436714:T173P	ENSP00000436714:T173P	T	-	1	0	HCAR3	121766721	0.000000	0.05858	0.000000	0.03702	0.138000	0.21146	-0.594000	0.05733	-1.206000	0.02641	0.155000	0.16302	ACT	T|0.481;G|0.519	0.519	strong		0.527	HCAR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387549.2	NM_006018	
TMF1	7110	hgsc.bcm.edu	37	3	69082708	69082708	+	Missense_Mutation	SNP	C	C	G	rs1532918	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:69082708C>G	ENST00000398559.2	-	10	2608	c.2392G>C	c.(2392-2394)Gat>Cat	p.D798H	CTD-2013N24.2_ENST00000598783.1_RNA|CTD-2013N24.2_ENST00000597366.1_RNA|CTD-2013N24.2_ENST00000596732.1_RNA|CTD-2013N24.2_ENST00000595925.1_RNA|CTD-2013N24.2_ENST00000599467.1_RNA|CTD-2013N24.2_ENST00000596523.1_RNA|CTD-2013N24.2_ENST00000601735.1_RNA|CTD-2013N24.2_ENST00000597950.1_RNA|TMF1_ENST00000543976.1_Missense_Mutation_p.D801H|CTD-2013N24.2_ENST00000601511.1_RNA|CTD-2013N24.2_ENST00000596274.1_RNA|CTD-2013N24.2_ENST00000482368.2_RNA			P82094	TMF1_HUMAN	TATA element modulatory factor 1	798			D -> H (in dbSNP:rs1532918).		acrosome assembly (GO:0001675)|cellular response to organic cyclic compound (GO:0071407)|defense response to bacterium (GO:0042742)|Leydig cell differentiation (GO:0033327)|luteinizing hormone secretion (GO:0032275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of gene expression (GO:0010629)|positive regulation of cytokine production (GO:0001819)|positive regulation of testosterone secretion (GO:2000845)|regulation of proteasomal protein catabolic process (GO:0061136)|regulation of transcription, DNA-templated (GO:0006355)|sperm motility (GO:0030317)|spermatid nucleus differentiation (GO:0007289)|transcription from RNA polymerase II promoter (GO:0006366)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|transcription cofactor activity (GO:0003712)			cervix(1)|kidney(1)|large_intestine(4)|lung(13)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	22		Lung NSC(201;0.0193)|Prostate(884;0.174)		BRCA - Breast invasive adenocarcinoma(55;4.48e-05)|Epithelial(33;0.000274)|LUSC - Lung squamous cell carcinoma(21;0.0123)|KIRC - Kidney renal clear cell carcinoma(39;0.211)|Kidney(39;0.247)		CCAAGCCTATCAGAAAGATTC	0.363													C|||	285	0.0569089	0.0113	0.0764	5008	,	,		15443	0.001		0.1521	False		,,,				2504	0.0644				p.D798H		Atlas-SNP	.											.	TMF1	77	.	0			c.G2392C						PASS	.	C	HIS/ASP	86,3560		1,84,1738	118.0	112.0	114.0		2392	5.8	1.0	3	dbSNP_88	114	1213,6943		97,1019,2962	yes	missense	TMF1	NM_007114.2	81	98,1103,4700	GG,GC,CC		14.8725,2.3587,11.0066	probably-damaging	798/1094	69082708	1299,10503	1823	4078	5901	SO:0001583	missense	7110	exon10			GCCTATCAGAAAG		CCDS43105.1	3p21-p12	2009-02-11			ENSG00000144747	ENSG00000144747			11870	protein-coding gene	gene with protein product		601126				1409643	Standard	NM_007114		Approved	ARA160, TMF	uc003dnn.3	P82094	OTTHUMG00000158771	ENST00000398559.2:c.2392G>C	3.37:g.69082708C>G	ENSP00000381567:p.Asp798His	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	88	42	0.477273	NM_007114	B7ZLJ2|Q17R87|Q59GK0	Missense_Mutation	SNP	ENST00000398559.2	37	CCDS43105.1	156	0.07142857142857142	6	0.012195121951219513	30	0.08287292817679558	0	0.0	120	0.158311345646438	C	27.0	4.790972	0.90367	0.023587	0.148725	ENSG00000144747	ENST00000398559;ENST00000543976;ENST00000356248	T;T	0.19394	2.15;2.15	5.83	5.83	0.93111	.	0.134289	0.64402	D	0.000003	T	0.00241	0.0007	L	0.60455	1.87	0.09310	P	0.999999999219925	D;D	0.89917	1.0;1.0	D;D	0.81914	0.995;0.979	T	0.00002	-1.2649	9	0.72032	D	0.01	-14.6947	20.1338	0.98010	0.0:1.0:0.0:0.0	rs1532918;rs11557641;rs17330362;rs52791053;rs56563580;rs1532918	801;798	P82094-2;P82094	.;TMF1_HUMAN	H	798;801;714	ENSP00000381567:D798H;ENSP00000438706:D801H	ENSP00000348582:D714H	D	-	1	0	TMF1	69165398	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.786000	0.85741	2.770000	0.95276	0.655000	0.94253	GAT	C|0.912;G|0.088	0.088	strong		0.363	TMF1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000352106.1	NM_007114	
DSG1	1828	hgsc.bcm.edu	37	18	28919884	28919884	+	Missense_Mutation	SNP	A	A	C	rs16961689	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:28919884A>C	ENST00000257192.4	+	11	1795	c.1583A>C	c.(1582-1584)tAt>tCt	p.Y528S		NM_001942.2	NP_001933.2	Q02413	DSG1_HUMAN	desmoglein 1	528			Y -> S (in dbSNP:rs16961689).		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)			AGCCAAGTATATTCTTCTGAA	0.418													T|||	745	0.148762	0.2428	0.0994	5008	,	,		16518	0.0645		0.0845	False		,,,				2504	0.2096				p.Y528S		Atlas-SNP	.											.	DSG1	176	.	0			c.A1583C						PASS	.	T	SER/TYR	790,3616		73,644,1486	112.0	112.0	112.0		1583	-7.3	0.0	18	dbSNP_123	112	613,7987		29,555,3716	yes	missense	DSG1	NM_001942.2	144	102,1199,5202	CC,CA,AA		7.1279,17.9301,10.7873	benign	528/1050	28919884	1403,11603	2203	4300	6503	SO:0001583	missense	1828	exon11			AAGTATATTCTTC	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.1583A>C	18.37:g.28919884A>C	ENSP00000257192:p.Tyr528Ser	Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	88	42	0.477273	NM_001942	B7Z845	Missense_Mutation	SNP	ENST00000257192.4	37	CCDS11896.1	252	0.11538461538461539	120	0.24390243902439024	40	0.11049723756906077	34	0.05944055944055944	58	0.07651715039577836	T	0	-2.792046	0.00077	0.179301	0.071279	ENSG00000134760	ENST00000257192	T	0.56103	0.48	3.66	-7.33	0.01431	.	64.773800	0.00166	N	0.000000	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	0.14868	-1.0457	9	0.45353	T	0.12	.	0.6084	0.00757	0.3335:0.2049:0.266:0.1956	rs16961689;rs52817095;rs16961689	528	Q02413	DSG1_HUMAN	S	528	ENSP00000257192:Y528S	ENSP00000257192:Y528S	Y	+	2	0	DSG1	27173882	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.182000	0.01256	-4.536000	0.00043	-5.634000	0.00000	TAT	A|0.885;C|0.115	0.115	strong		0.418	DSG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254947.1	NM_001942	
CPA4	51200	hgsc.bcm.edu	37	7	129950740	129950740	+	Missense_Mutation	SNP	G	G	T	rs2171492	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:129950740G>T	ENST00000222482.4	+	9	935	c.907G>T	c.(907-909)Ggc>Tgc	p.G303C	CPA4_ENST00000445470.2_Missense_Mutation_p.G270C|CPA4_ENST00000493259.1_Missense_Mutation_p.G199C	NM_016352.3	NP_057436.2	Q9UI42	CBPA4_HUMAN	carboxypeptidase A4	303			G -> C (in dbSNP:rs2171492).		histone acetylation (GO:0016573)	extracellular region (GO:0005576)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	21	Melanoma(18;0.0435)					GAATTTCAAGGGCTTCATCGA	0.512													T|||	1586	0.316693	0.2065	0.3156	5008	,	,		20193	0.374		0.3638	False		,,,				2504	0.3589				p.G303C		Atlas-SNP	.											.	CPA4	47	.	0			c.G907T						PASS	.	T	CYS/GLY,CYS/GLY	1003,3403	730.5+/-410.2	123,757,1323	148.0	142.0	144.0		808,907	0.5	1.0	7	dbSNP_96	144	3310,5290	645.2+/-400.1	644,2022,1634	yes	missense,missense	CPA4	NM_001163446.1,NM_016352.3	159,159	767,2779,2957	TT,TG,GG		38.4884,22.7644,33.1616	benign,benign	270/389,303/422	129950740	4313,8693	2203	4300	6503	SO:0001583	missense	51200	exon9			TTCAAGGGCTTCA	AF095719	CCDS5818.1, CCDS55163.1	7q32	2008-07-18			ENSG00000128510	ENSG00000128510			15740	protein-coding gene	gene with protein product	"""carboxypeptidase A3"""	607635				10383164, 10860668	Standard	NM_016352		Approved	CPA3	uc003vpr.3	Q9UI42	OTTHUMG00000157825	ENST00000222482.4:c.907G>T	7.37:g.129950740G>T	ENSP00000222482:p.Gly303Cys	Somatic	101	1	0.00990099		WXS	Illumina HiSeq	Phase_I	51	51	1	NM_016352	B7Z576|Q86UY9	Missense_Mutation	SNP	ENST00000222482.4	37	CCDS5818.1	719	0.3292124542124542	108	0.21951219512195122	122	0.3370165745856354	227	0.3968531468531469	262	0.34564643799472294	T	12.75	2.032247	0.35893	0.227644	0.384884	ENSG00000128510	ENST00000445470;ENST00000222482;ENST00000538687;ENST00000493259	T;T;T	0.11063	2.81;2.81;2.81	6.17	0.479	0.16796	Peptidase M14, carboxypeptidase A (2);	0.437819	0.26746	N	0.022720	T	0.00012	0.0000	N	0.16130	0.375	0.52099	P	5.100000000002325E-5	B;B	0.15141	0.012;0.004	B;B	0.28849	0.095;0.021	T	0.49031	-0.8981	9	0.51188	T	0.08	.	11.7939	0.52088	0.1397:0.0:0.6312:0.2291	rs2171492;rs17327657;rs52837974;rs58222478;rs2171492	270;303	B7Z576;Q9UI42	.;CBPA4_HUMAN	C	270;303;108;199	ENSP00000412947:G270C;ENSP00000222482:G303C;ENSP00000419660:G199C	ENSP00000222482:G303C	G	+	1	0	CPA4	129737976	0.998000	0.40836	0.992000	0.48379	0.691000	0.40173	0.552000	0.23376	-0.068000	0.12953	-1.131000	0.01979	GGC	G|0.677;T|0.323	0.323	strong		0.512	CPA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349725.1	NM_016352	
TRPV5	56302	hgsc.bcm.edu	37	7	142609714	142609714	+	Silent	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:142609714G>A	ENST00000265310.1	-	13	2070	c.1722C>T	c.(1720-1722)ttC>ttT	p.F574F		NM_019841.4	NP_062815.2	Q9NQA5	TRPV5_HUMAN	transient receptor potential cation channel, subfamily V, member 5	574					calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|ion transmembrane transport (GO:0034220)|protein tetramerization (GO:0051262)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)			NS(1)|breast(2)|central_nervous_system(3)|endometrium(2)|kidney(1)|large_intestine(14)|lung(32)|ovary(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	67	Melanoma(164;0.059)					TCATGGCGATGAACAAGTTGA	0.532																																					p.F574F		Atlas-SNP	.											TRPV5,NS,malignant_melanoma,-2,1	TRPV5	164	1	0			c.C1722T						scavenged	.						145.0	125.0	132.0					7																	142609714		2203	4300	6503	SO:0001819	synonymous_variant	56302	exon13			GGCGATGAACAAG	AJ271207	CCDS5875.1	7q34	2013-01-10	2002-01-29	2002-02-01	ENSG00000127412	ENSG00000127412		"""Voltage-gated ion channels / Transient receptor potential cation channels"", ""Ankyrin repeat domain containing"""	3145	protein-coding gene	gene with protein product		606679	"""epithelial calcium channel 1"""	ECAC1		10944439, 10945469, 16382100	Standard	NM_019841		Approved	CaT2	uc003wby.1	Q9NQA5	OTTHUMG00000157157	ENST00000265310.1:c.1722C>T	7.37:g.142609714G>A		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	108	2	0.0185185	NM_019841	A4D2H7|E9PBZ6|Q8N4C1|Q8NDW5|Q8NDX7|Q8NDX8|Q96PM6	Silent	SNP	ENST00000265310.1	37	CCDS5875.1																																																																																			.	.	none		0.532	TRPV5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347660.1	NM_019841	
FNIP2	57600	hgsc.bcm.edu	37	4	159780274	159780274	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:159780274G>A	ENST00000264433.6	+	9	998	c.923G>A	c.(922-924)aGg>aAg	p.R308K	FNIP2_ENST00000379346.3_Missense_Mutation_p.R331K	NM_020840.1	NP_065891.1	Q9P278	FNIP2_HUMAN	folliculin interacting protein 2	308					intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein phosphorylation (GO:0006468)|regulation of protein phosphorylation (GO:0001932)	cytoplasm (GO:0005737)|microtubule organizing center (GO:0005815)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(3)|prostate(1)	9	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.00936)		ATGGTTAGGAGGAAGAAAATT	0.403																																					p.R308K		Atlas-SNP	.											.	FNIP2	90	.	0			c.G923A						PASS	.						80.0	78.0	78.0					4																	159780274		1843	4097	5940	SO:0001583	missense	57600	exon9			TTAGGAGGAAGAA	AB040883	CCDS47155.1	4q32.1	2012-10-31			ENSG00000052795	ENSG00000052795			29280	protein-coding gene	gene with protein product	"""O6-methylguanine-induced apoptosis 1"""	612768				18403135	Standard	NM_020840		Approved	KIAA1450, FNIPL, MAPO1	uc003iqe.4	Q9P278	OTTHUMG00000161983	ENST00000264433.6:c.923G>A	4.37:g.159780274G>A	ENSP00000264433:p.Arg308Lys	Somatic	345	0	0		WXS	Illumina HiSeq	Phase_I	339	77	0.227139	NM_020840	Q05DC3|Q96I31|Q9H994	Missense_Mutation	SNP	ENST00000264433.6	37	CCDS47155.1	.	.	.	.	.	.	.	.	.	.	G	15.24	2.774472	0.49786	.	.	ENSG00000052795	ENST00000264433;ENST00000512986;ENST00000379346;ENST00000504715	T;T;T;T	0.26373	1.74;1.74;1.74;1.74	5.51	5.51	0.81932	.	.	.	.	.	T	0.25382	0.0617	L	0.34521	1.04	0.53688	D	0.999978	B	0.29162	0.235	B	0.33890	0.172	T	0.03443	-1.1036	8	.	.	.	.	19.4099	0.94667	0.0:0.0:1.0:0.0	.	308	Q9P278	FNIP2_HUMAN	K	308;331;331;173	ENSP00000264433:R308K;ENSP00000421488:R331K;ENSP00000368651:R331K;ENSP00000420841:R173K	.	R	+	2	0	FNIP2	159999724	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	4.620000	0.61226	2.582000	0.87167	0.655000	0.94253	AGG	.	.	none		0.403	FNIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366602.1	NM_020840	
AHNAK2	113146	hgsc.bcm.edu	37	14	105418481	105418481	+	Missense_Mutation	SNP	C	C	T	rs200172350		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:105418481C>T	ENST00000333244.5	-	7	3426	c.3307G>A	c.(3307-3309)Gtc>Atc	p.V1103I	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	1103						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)			GGGCCCTTGACGTCCACCTGG	0.642																																					p.V1103I		Atlas-SNP	.											.	AHNAK2	719	.	0			c.G3307A						PASS	.						116.0	142.0	134.0					14																	105418481		1860	4112	5972	SO:0001583	missense	113146	exon7			CCTTGACGTCCAC	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.3307G>A	14.37:g.105418481C>T	ENSP00000353114:p.Val1103Ile	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	152	24	0.157895	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	.	.	.	.	.	.	.	.	.	.	c	1.053	-0.675202	0.03378	.	.	ENSG00000185567	ENST00000333244	T	0.01159	5.25	4.03	-8.07	0.01098	.	.	.	.	.	T	0.00815	0.0027	N	0.25789	0.76	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.47182	-0.9137	9	0.10636	T	0.68	.	8.8812	0.35376	0.0:0.4198:0.3366:0.2436	.	1103	Q8IVF2	AHNK2_HUMAN	I	1103	ENSP00000353114:V1103I	ENSP00000353114:V1103I	V	-	1	0	AHNAK2	104489526	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-3.504000	0.00449	-2.752000	0.00374	-1.564000	0.00881	GTC	.	.	weak		0.642	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
HIST1H2AL	8332	hgsc.bcm.edu	37	6	27833174	27833174	+	Silent	SNP	A	A	G	rs200981	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:27833174A>G	ENST00000357320.2	+	1	141	c.42A>G	c.(40-42)aaA>aaG	p.K14K		NM_003511.2	NP_003502.1	P0C0S8	H2A1_HUMAN	histone cluster 1, H2al	14						extracellular vesicular exosome (GO:0070062)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)			breast(1)|endometrium(1)|large_intestine(2)|lung(3)|urinary_tract(2)	9						CTCGCGCCAAAGCCAAGACCC	0.627													G|||	614	0.122604	0.2005	0.1398	5008	,	,		15027	0.0655		0.0895	False		,,,				2504	0.0982				p.K14K		Atlas-SNP	.											.	HIST1H2AL	14	.	0			c.A42G						PASS	.	G		829,3577		78,673,1452	82.0	93.0	89.0		42	2.8	1.0	6	dbSNP_79	89	951,7649		53,845,3402	no	coding-synonymous	HIST1H2AL	NM_003511.2		131,1518,4854	GG,GA,AA		11.0581,18.8153,13.686		14/131	27833174	1780,11226	2203	4300	6503	SO:0001819	synonymous_variant	8332	exon1			CGCCAAAGCCAAG	X83549	CCDS4634.1	6p22.1	2011-01-27	2006-10-11	2003-02-14	ENSG00000198374	ENSG00000276903		"""Histones / Replication-dependent"""	4730	protein-coding gene	gene with protein product		602793	"""H2A histone family, member I"", ""histone 1, H2al"""	H2AFI		9439656, 9031620, 12408966	Standard	NM_003511		Approved	H2A/i, dJ193B12.9	uc003njw.3	P0C0S8	OTTHUMG00000014492	ENST00000357320.2:c.42A>G	6.37:g.27833174A>G		Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	167	94	0.562874	NM_003511	P02261|Q2M1R2|Q76PA6	Silent	SNP	ENST00000357320.2	37	CCDS4634.1																																																																																			.	.	weak		0.627	HIST1H2AL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040160.1	NM_003511	
KLB	152831	hgsc.bcm.edu	37	4	39436192	39436192	+	Missense_Mutation	SNP	A	A	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:39436192A>C	ENST00000257408.4	+	2	1285	c.1188A>C	c.(1186-1188)ttA>ttC	p.L396F		NM_175737.3	NP_783864.1	Q86Z14	KLOTB_HUMAN	klotho beta	396	Glycosyl hydrolase-1 1.				carbohydrate metabolic process (GO:0005975)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell proliferation (GO:0008284)|positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway (GO:0090080)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	fibroblast growth factor binding (GO:0017134)|hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(11)|skin(6)	29						CACTTAATTTAAGAGAAGCGC	0.418																																					p.L396F		Atlas-SNP	.											.	KLB	95	.	0			c.A1188C						PASS	.						105.0	105.0	105.0					4																	39436192		2203	4300	6503	SO:0001583	missense	152831	exon2			TAATTTAAGAGAA	AB079373	CCDS3451.1	4p14	2008-02-05			ENSG00000134962	ENSG00000134962			15527	protein-coding gene	gene with protein product		611135					Standard	NM_175737		Approved		uc003gua.3	Q86Z14	OTTHUMG00000128577	ENST00000257408.4:c.1188A>C	4.37:g.39436192A>C	ENSP00000257408:p.Leu396Phe	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	43	12	0.27907	NM_175737	Q2M3K8	Missense_Mutation	SNP	ENST00000257408.4	37	CCDS3451.1	.	.	.	.	.	.	.	.	.	.	A	13.59	2.283680	0.40394	.	.	ENSG00000134962	ENST00000257408	T	0.44482	0.92	6.06	-0.216	0.13153	Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.000000	0.64402	D	0.000001	T	0.52581	0.1743	L	0.49699	1.58	0.42547	D	0.993094	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.50030	-0.8875	10	0.56958	D	0.05	-15.1023	10.3696	0.44046	0.412:0.0:0.588:0.0	.	396;396	B7ZL50;Q86Z14	.;KLOTB_HUMAN	F	396	ENSP00000257408:L396F	ENSP00000257408:L396F	L	+	3	2	KLB	39112587	1.000000	0.71417	0.945000	0.38365	0.055000	0.15305	1.488000	0.35551	-0.025000	0.13918	-0.250000	0.11733	TTA	.	.	none		0.418	KLB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250429.1	NM_175737	
HLA-DOB	3112	hgsc.bcm.edu	37	6	32782149	32782149	+	Silent	SNP	G	G	A	rs17501267	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:32782149G>A	ENST00000438763.2	-	3	687	c.591C>T	c.(589-591)taC>taT	p.Y197Y	TAP2_ENST00000452392.2_Silent_p.Y804Y	NM_002120.3	NP_002111.1	P13765	DOB_HUMAN	major histocompatibility complex, class II, DO beta	197	Beta-2.|Ig-like C1-type.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|immune response (GO:0006955)|negative regulation of antigen processing and presentation of peptide antigen via MHC class II (GO:0002587)|signal transduction (GO:0007165)	endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|MHC class II protein complex (GO:0042613)	MHC class II protein complex binding (GO:0023026)|MHC class II receptor activity (GO:0032395)			endometrium(2)|large_intestine(1)|lung(2)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	9						CAAGGCAGGTGTAGACATGTC	0.507													G|||	176	0.0351438	0.0151	0.0231	5008	,	,		21326	0.0556		0.0507	False		,,,				2504	0.0337				p.Y197Y		Atlas-SNP	.											.	HLA-DOB	17	.	0			c.C591T						PASS	.	G		45,2977		1,43,1467	187.0	157.0	167.0		591	2.1	1.0	6	dbSNP_123	167	274,5144		9,256,2444	no	coding-synonymous	HLA-DOB	NM_002120.3		10,299,3911	AA,AG,GG		5.0572,1.4891,3.7796		197/274	32782149	319,8121	1511	2709	4220	SO:0001819	synonymous_variant	3112	exon3			GCAGGTGTAGACA		CCDS4754.1	6p21.3	2013-01-11			ENSG00000241106	ENSG00000241106		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4937	protein-coding gene	gene with protein product		600629					Standard	NM_002120		Approved			P13765	OTTHUMG00000031213	ENST00000438763.2:c.591C>T	6.37:g.32782149G>A		Somatic	225	0	0		WXS	Illumina HiSeq	Phase_I	143	47	0.328671	NM_002120	B0V0Y0|Q29746|Q29825|Q6FHC2	Silent	SNP	ENST00000438763.2	37	CCDS4754.1	85	0.03891941391941392	8	0.016260162601626018	10	0.027624309392265192	29	0.050699300699300696	38	0.05013192612137203	G	7.248	0.602670	0.13939	0.014891	0.050572	ENSG00000241106	ENST00000447394	.	.	.	3.96	2.07	0.26955	.	.	.	.	.	T	0.41465	0.1160	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.28681	-1.0036	4	.	.	.	.	7.7352	0.28810	0.227:0.0:0.773:0.0	rs17501267;rs17882057;rs17501267	.	.	.	Y	181	.	.	H	-	1	0	HLA-DOB	32890127	1.000000	0.71417	0.998000	0.56505	0.957000	0.61999	1.566000	0.36396	0.569000	0.29329	-0.366000	0.07423	CAC	.	.	weak		0.507	HLA-DOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076439.1	NM_002120	
ZNF749	388567	hgsc.bcm.edu	37	19	57955729	57955729	+	Missense_Mutation	SNP	G	G	A	rs2240038	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:57955729G>A	ENST00000334181.4	+	3	1463	c.1213G>A	c.(1213-1215)Gct>Act	p.A405T	AC004076.9_ENST00000596831.1_Intron	NM_001023561.2	NP_001018855.2	O43361	ZN749_HUMAN	zinc finger protein 749	405			A -> T (in dbSNP:rs2240038).		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(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)		GAGAGTTCATGCTGGCAAAAG	0.418													A|||	225	0.0449281	0.0915	0.0115	5008	,	,		22279	0.0218		0.0169	False		,,,				2504	0.0583				p.A405T		Atlas-SNP	.											.	ZNF749	75	.	0			c.G1213A						PASS	.	A	THR/ALA	332,4074	796.0+/-415.3	16,300,1887	98.0	98.0	98.0		1213	0.6	0.0	19	dbSNP_98	98	199,8401	810.5+/-407.1	2,195,4103	yes	missense	ZNF749	NM_001023561.2	58	18,495,5990	AA,AG,GG		2.314,7.5352,4.0827	benign	405/779	57955729	531,12475	2203	4300	6503	SO:0001583	missense	388567	exon3			GTTCATGCTGGCA	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.1213G>A	19.37:g.57955729G>A	ENSP00000333980:p.Ala405Thr	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	123	49	0.398374	NM_001023561		Missense_Mutation	SNP	ENST00000334181.4	37	CCDS33132.2	71	0.03250915750915751	43	0.08739837398373984	6	0.016574585635359115	8	0.013986013986013986	14	0.018469656992084433	A	0.885	-0.727487	0.03158	0.075352	0.02314	ENSG00000186230	ENST00000334181	T	0.11277	2.79	1.64	0.575	0.17374	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00144	0.0004	N	0.02985	-0.445	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.41484	-0.9506	9	0.02654	T	1	.	6.0837	0.19954	0.7206:0.0:0.2794:0.0	rs2240038;rs2240038	405	O43361	ZN749_HUMAN	T	405	ENSP00000333980:A405T	ENSP00000333980:A405T	A	+	1	0	ZNF749	62647541	0.000000	0.05858	0.001000	0.08648	0.449000	0.32228	0.943000	0.29030	-0.287000	0.09064	-0.893000	0.02921	GCT	G|0.957;A|0.043	0.043	strong		0.418	ZNF749-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317879.1	NM_001023561	
MRPL10	124995	hgsc.bcm.edu	37	17	45904420	45904420	+	Missense_Mutation	SNP	C	C	T	rs11538868	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:45904420C>T	ENST00000351111.2	-	3	378	c.373G>A	c.(373-375)Gtc>Atc	p.V125I	MRPL10_ENST00000290208.7_Missense_Mutation_p.V135I|MRPL10_ENST00000414011.1_Missense_Mutation_p.V135I	NM_145255.3	NP_660298.2	Q7Z7H8	RM10_HUMAN	mitochondrial ribosomal protein L10	125			V -> I (in dbSNP:rs16948568). {ECO:0000269|PubMed:15489334}.		ribosome biogenesis (GO:0042254)|translation (GO:0006412)	mitochondrial large ribosomal subunit (GO:0005762)|mitochondrion (GO:0005739)|ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			endometrium(3)|large_intestine(1)|lung(3)|ovary(1)	8						TTGGGGAAGACCTTCATCAGG	0.577													C|||	795	0.158746	0.0696	0.2161	5008	,	,		20754	0.0139		0.3549	False		,,,				2504	0.1861				p.V135I		Atlas-SNP	.											.	MRPL10	24	.	0			c.G403A						PASS	.	C	ILE/VAL,ILE/VAL	493,3913	228.8+/-243.5	22,449,1732	83.0	71.0	76.0		373,403	-0.1	1.0	17	dbSNP_120	76	3273,5327	491.8+/-373.2	642,1989,1669	yes	missense,missense	MRPL10	NM_145255.3,NM_148887.2	29,29	664,2438,3401	TT,TC,CC		38.0581,11.1893,28.9559	benign,benign	125/262,135/272	45904420	3766,9240	2203	4300	6503	SO:0001583	missense	124995	exon4			GGAAGACCTTCAT	AB051618	CCDS11516.1, CCDS11517.1	17q21.3	2012-09-13			ENSG00000159111	ENSG00000159111		"""Mitochondrial ribosomal proteins / large subunits"""	14055	protein-coding gene	gene with protein product	"""39S ribosomal protein L10, mitochondrial"""	611825				11551941	Standard	NM_148887		Approved	RPML8, MRP-L8, L10MT, MRP-L10, MRPL8, MGC17973	uc002ily.3	Q7Z7H8	OTTHUMG00000156302	ENST00000351111.2:c.373G>A	17.37:g.45904420C>T	ENSP00000324100:p.Val125Ile	Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	125	62	0.496	NM_148887	A6NGJ4|Q96B80|Q96Q55	Missense_Mutation	SNP	ENST00000351111.2	37	CCDS11516.1	425	0.1945970695970696	45	0.09146341463414634	95	0.26243093922651933	7	0.012237762237762238	278	0.36675461741424803	C	10.70	1.425026	0.25639	0.111893	0.380581	ENSG00000159111	ENST00000351111;ENST00000290208;ENST00000414011	T;T;T	0.53857	0.6;0.6;0.6	5.62	-0.131	0.13494	.	0.482175	0.23941	N	0.043052	T	0.00012	0.0000	N	0.21448	0.665	0.48511	P	3.3799999999994945E-4	B;B	0.15930	0.002;0.015	B;B	0.18561	0.015;0.022	T	0.37820	-0.9689	9	0.42905	T	0.14	-2.0015	1.9376	0.03340	0.127:0.3325:0.1243:0.4161	rs16948568;rs17700922;rs17851354;rs52817339;rs16948568	125;135	Q7Z7H8;A6NGJ4	RM10_HUMAN;.	I	125;135;135	ENSP00000324100:V125I;ENSP00000290208:V135I;ENSP00000395870:V135I	ENSP00000290208:V135I	V	-	1	0	MRPL10	43259419	0.779000	0.28652	0.971000	0.41717	0.804000	0.45430	0.048000	0.14078	-0.216000	0.10048	-0.367000	0.07326	GTC	C|0.761;T|0.239	0.239	strong		0.577	MRPL10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343764.1	NM_145255	
ZNF879	345462	hgsc.bcm.edu	37	5	178459426	178459426	+	Missense_Mutation	SNP	A	A	C	rs17078991	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	162	0	0		WXS	Illumina HiSeq	Phase_I	166	100	0.60241	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	
TBATA	219793	hgsc.bcm.edu	37	10	72534090	72534090	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:72534090G>T	ENST00000299290.1	-	9	1185	c.796C>A	c.(796-798)Ctg>Atg	p.L266M	TBATA_ENST00000394982.2_5'Flank|TBATA_ENST00000456372.2_Silent_p.S238S	NM_152710.2	NP_689923	Q96M53	TBATA_HUMAN	thymus, brain and testes associated	266					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytosol (GO:0005829)|nucleus (GO:0005634)											GCTGTCTGCAGGAGTCCCAGA	0.612																																					p.L266M		Atlas-SNP	.											.	.	.	.	0			c.C796A						PASS	.						47.0	46.0	46.0					10																	72534090		2203	4300	6503	SO:0001583	missense	219793	exon9			TCTGCAGGAGTCC	AK057382	CCDS7308.1	10q22.2	2012-05-23	2012-05-23	2012-05-23	ENSG00000166220	ENSG00000166220			23511	protein-coding gene	gene with protein product		612640	"""chromosome 10 open reading frame 27"""	C10orf27		20937703	Standard	NM_152710		Approved	FLJ32820, spatial	uc001jrj.1	Q96M53	OTTHUMG00000018413	ENST00000299290.1:c.796C>A	10.37:g.72534090G>T	ENSP00000299290:p.Leu266Met	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	77	16	0.207792	NM_152710	A4QPA8|B2RPQ2|Q5T4G2	Missense_Mutation	SNP	ENST00000299290.1	37	CCDS7308.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	14.85|14.85	2.659135|2.659135	0.47467|0.47467	.|.	.|.	ENSG00000166220|ENSG00000166220	ENST00000299290|ENST00000536955	T|.	0.24151|.	1.87|.	4.94|4.94	4.94|4.94	0.65067|0.65067	.|.	0.000000|.	0.52532|.	D|.	0.000080|.	T|T	0.74635|0.74635	0.3742|0.3742	M|M	0.75447|0.75447	2.3|2.3	0.80722|0.80722	D|D	1|1	D;D;D|.	0.89917|.	1.0;1.0;1.0|.	D;D;D|.	0.91635|.	0.999;0.999;0.999|.	T|T	0.78290|0.78290	-0.2261|-0.2261	10|6	0.72032|0.87932	D|D	0.01|0	-13.863|-13.863	13.674|13.674	0.62443|0.62443	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	265;267;266|.	B7ZMN4;B7ZMN5;Q96M53|.	.;.;SPATL_HUMAN|.	M|H	266|288	ENSP00000299290:L266M|.	ENSP00000299290:L266M|ENSP00000438618:P288H	L|P	-|-	1|2	2|0	C10orf27|C10orf27	72204096|72204096	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.193000|0.193000	0.23685|0.23685	3.298000|3.298000	0.51818|0.51818	2.298000|2.298000	0.77334|0.77334	0.655000|0.655000	0.94253|0.94253	CTG|CCT	.	.	none		0.612	TBATA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048519.1	NM_152710	
ICAM3	3385	hgsc.bcm.edu	37	19	10446568	10446568	+	Missense_Mutation	SNP	T	T	C	rs2304237	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:10446568T>C	ENST00000160262.5	-	3	636	c.428A>G	c.(427-429)gAt>gGt	p.D143G	ICAM3_ENST00000589261.1_Missense_Mutation_p.D66G|RAVER1_ENST00000293677.6_5'Flank	NM_002162.3	NP_002153.2	P32942	ICAM3_HUMAN	intercellular adhesion molecule 3	143	Ig-like C2-type 2.		D -> G (in dbSNP:rs2304237). {ECO:0000269|PubMed:1448173, ECO:0000269|PubMed:1448174, ECO:0000269|PubMed:8459213}.		extracellular matrix organization (GO:0030198)|regulation of immune response (GO:0050776)|single organismal cell-cell adhesion (GO:0016337)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	integrin binding (GO:0005178)|receptor binding (GO:0005102)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(7)|ovary(1)|upper_aerodigestive_tract(2)	13			OV - Ovarian serous cystadenocarcinoma(20;6.13e-09)|Epithelial(33;9.69e-06)|all cancers(31;2.05e-05)			GGGCGACCCATCCTCCACTTG	0.697													C|||	899	0.179513	0.1407	0.1744	5008	,	,		15342	0.1131		0.2336	False		,,,				2504	0.2485				p.D143G		Atlas-SNP	.											.	ICAM3	29	.	0			c.A428G						PASS	.	C	GLY/ASP	721,3681		55,611,1535	15.0	16.0	15.0		428	5.0	0.0	19	dbSNP_100	15	1901,6689		230,1441,2624	yes	missense	ICAM3	NM_002162.3	94	285,2052,4159	CC,CT,TT		22.1304,16.3789,20.1817	benign	143/548	10446568	2622,10370	2201	4295	6496	SO:0001583	missense	3385	exon3			GACCCATCCTCCA		CCDS12235.1	19p13.3-p13.2	2013-01-11				ENSG00000076662		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5346	protein-coding gene	gene with protein product		146631				1448174	Standard	NM_002162		Approved	CDW50, ICAM-R, CD50	uc002mob.2	P32942		ENST00000160262.5:c.428A>G	19.37:g.10446568T>C	ENSP00000160262:p.Asp143Gly	Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	38	21	0.552632	NM_002162	Q6PD68	Missense_Mutation	SNP	ENST00000160262.5	37	CCDS12235.1	383	0.17536630036630035	61	0.12398373983739837	70	0.19337016574585636	68	0.11888111888111888	184	0.24274406332453827	C	3.139	-0.176746	0.06380	0.163789	0.221304	ENSG00000076662	ENST00000160262	T	0.04083	3.71	4.98	4.98	0.66077	Intercellular adhesion molecule/vascular cell adhesion molecule, N-terminal (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.240354	0.35739	N	0.003008	T	0.00012	0.0000	N	0.00023	-2.72	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.35847	-0.9772	9	0.02654	T	1	-18.3636	9.9304	0.41519	0.0:0.9044:0.0:0.0956	rs2304237;rs59711512;rs2304237	66;143	B7Z6W6;P32942	.;ICAM3_HUMAN	G	143	ENSP00000160262:D143G	ENSP00000160262:D143G	D	-	2	0	ICAM3	10307568	0.005000	0.15991	0.026000	0.17262	0.003000	0.03518	0.596000	0.24044	1.249000	0.43950	-0.227000	0.12334	GAT	T|0.817;C|0.183	0.183	strong		0.697	ICAM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451234.1		
FAM66D	100132923	hgsc.bcm.edu	37	8	11991210	11991210	+	RNA	SNP	C	C	T	rs117041743	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:11991210C>T	ENST00000434078.2	+	0	608					NR_027425.1				family with sequence similarity 66, member D																		AGTTGGAAAGCGGCAGTGTGT	0.532													G|||	227	0.0453275	0.0378	0.0389	5008	,	,		24919	0.0		0.0746	False		,,,				2504	0.0767				p.P103P		Atlas-SNP	.											.	.	.	.	0			c.G309A						PASS	.																																					392197	exon1			GGAAAGCGGCAGT			8p23.1	2013-07-05			ENSG00000255052	ENSG00000255052		"""Long non-coding RNAs"""	24159	non-coding RNA	RNA, long non-coding							Standard	NR_027425		Approved				OTTHUMG00000165269		8.37:g.11991210C>T		Somatic	22	0	0		WXS	Illumina HiSeq	Phase_I	20	17	0.85	NM_001256869		Silent	SNP	ENST00000434078.2	37																																																																																				C|0.961;T|0.039	0.039	strong		0.532	FAM66D-201	KNOWN	basic	antisense	antisense		NR_027425	
KRT37	8688	hgsc.bcm.edu	37	17	39580739	39580739	+	Missense_Mutation	SNP	C	C	A	rs9910204	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:39580739C>A	ENST00000225550.3	-	1	36	c.37G>T	c.(37-39)Ggt>Tgt	p.G13C	AC003958.2_ENST00000432258.1_RNA	NM_003770.4	NP_003761.3	O76014	KRT37_HUMAN	keratin 37	13	Head.		G -> C (in dbSNP:rs9910204).			extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(9)|lung(6)|skin(3)	25		Breast(137;0.000496)				ATGGTGCAACCCAGAGGGCAT	0.567													C|||	1097	0.21905	0.1505	0.2147	5008	,	,		21078	0.0843		0.2833	False		,,,				2504	0.3875				p.G13C		Atlas-SNP	.											KRT37,NS,carcinoma,0,1	KRT37	61	1	0			c.G37T						PASS	.	C	CYS/GLY	737,3669		57,623,1523	68.0	71.0	70.0		37	4.0	0.1	17	dbSNP_119	70	2652,5948		399,1854,2047	yes	missense	KRT37	NM_003770.4	159	456,2477,3570	AA,AC,CC		30.8372,16.7272,26.0572	possibly-damaging	13/450	39580739	3389,9617	2203	4300	6503	SO:0001583	missense	8688	exon1			TGCAACCCAGAGG	Y16793	CCDS32653.1	17q21.2	2013-06-20	2006-07-17	2006-07-17	ENSG00000108417	ENSG00000108417		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6455	protein-coding gene	gene with protein product		604541	"""keratin, hair, acidic, 7"""	KRTHA7		9756910, 16831889	Standard	NM_003770		Approved		uc002hwp.1	O76014	OTTHUMG00000133606	ENST00000225550.3:c.37G>T	17.37:g.39580739C>A	ENSP00000225550:p.Gly13Cys	Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	175	86	0.491429	NM_003770		Missense_Mutation	SNP	ENST00000225550.3	37	CCDS32653.1	433	0.19826007326007325	82	0.16666666666666666	97	0.26795580110497236	49	0.08566433566433566	205	0.2704485488126649	.	12.85	2.061581	0.36373	0.167272	0.308372	ENSG00000108417	ENST00000225550	D	0.83673	-1.75	4.0	4.0	0.46444	.	0.273779	0.26153	N	0.026036	T	0.00012	0.0000	N	0.24115	0.695	0.80722	P	0.0	D	0.56287	0.975	B	0.43536	0.423	T	0.02226	-1.1192	9	0.41790	T	0.15	.	12.269	0.54695	0.1701:0.8299:0.0:0.0	rs9910204;rs61147575	13	O76014	KRT37_HUMAN	C	13	ENSP00000225550:G13C	ENSP00000225550:G13C	G	-	1	0	KRT37	36834265	0.122000	0.22280	0.052000	0.19188	0.019000	0.09904	1.771000	0.38542	1.955000	0.56771	0.655000	0.94253	GGT	C|0.764;A|0.236	0.236	strong		0.567	KRT37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257714.2	NM_003770	
SLC12A6	9990	hgsc.bcm.edu	37	15	34544468	34544468	+	Silent	SNP	C	C	T	rs2290940	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:34544468C>T	ENST00000354181.3	-	10	1728	c.1236G>A	c.(1234-1236)tcG>tcA	p.S412S	SLC12A6_ENST00000290209.5_Silent_p.S361S|SLC12A6_ENST00000560164.1_Silent_p.S224S|SLC12A6_ENST00000397707.2_Silent_p.S397S|SLC12A6_ENST00000458406.2_Silent_p.S353S|SLC12A6_ENST00000397702.2_Silent_p.S353S|SLC12A6_ENST00000451844.2_Silent_p.S224S|SLC12A6_ENST00000558667.1_Silent_p.S412S|SLC12A6_ENST00000560611.1_Silent_p.S412S|SLC12A6_ENST00000558589.1_Silent_p.S403S			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	196	0	0		WXS	Illumina HiSeq	Phase_I	188	99	0.526596	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	
ATG4C	84938	hgsc.bcm.edu	37	1	63284834	63284834	+	Missense_Mutation	SNP	T	T	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:63284834T>A	ENST00000317868.4	+	5	760	c.553T>A	c.(553-555)Tat>Aat	p.Y185N	ATG4C_ENST00000371120.3_Missense_Mutation_p.Y185N	NM_032852.3	NP_116241.2	Q96DT6	ATG4C_HUMAN	autophagy related 4C, cysteine peptidase	185					autophagic vacuole assembly (GO:0000045)|autophagy (GO:0006914)|protein targeting to membrane (GO:0006612)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)	cysteine-type endopeptidase activity (GO:0004197)|peptidase activity (GO:0008233)		ATG4C/FBXO38(2)	NS(1)|breast(1)|endometrium(2)|kidney(3)|large_intestine(6)|lung(3)|ovary(1)|prostate(2)	19						AATTGGGAAATATTCTGATGA	0.363																																					p.Y185N		Atlas-SNP	.											.	ATG4C	96	.	0			c.T553A						PASS	.						106.0	113.0	111.0					1																	63284834		2203	4300	6503	SO:0001583	missense	84938	exon5			GGGAAATATTCTG	AK027773	CCDS623.1	1p31.3	2014-02-12	2012-06-06	2005-09-11	ENSG00000125703	ENSG00000125703			16040	protein-coding gene	gene with protein product		611339	"""AUT (S. cerevisiae)-like 1, cysteine endopeptidase; AUT-like 1, cysteine endopeptidase (S. cerevisiae)"", ""APG4 autophagy 4 homolog C (S. cerevisiae)"", ""ATG4 autophagy related 4 homolog C (S. cerevisiae)"""	AUTL1, APG4C		12446702	Standard	NM_032852		Approved	FLJ14867, AUTL3	uc001dau.3	Q96DT6	OTTHUMG00000009142	ENST00000317868.4:c.553T>A	1.37:g.63284834T>A	ENSP00000322159:p.Tyr185Asn	Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	114	26	0.22807	NM_178221	A6NLR8|D3DQ58|Q96K04	Missense_Mutation	SNP	ENST00000317868.4	37	CCDS623.1	.	.	.	.	.	.	.	.	.	.	T	10.07	1.249108	0.22880	.	.	ENSG00000125703	ENST00000317868;ENST00000371120;ENST00000540025;ENST00000371118	.	.	.	5.92	-1.03	0.10102	.	1.091040	0.06854	N	0.797869	T	0.09862	0.0242	L	0.34521	1.04	0.09310	N	1	B	0.02656	0.0	B	0.09377	0.004	T	0.26121	-1.0112	9	0.28530	T	0.3	-1.3461	1.7001	0.02870	0.1081:0.2507:0.2521:0.3891	.	185	Q96DT6	ATG4C_HUMAN	N	185	.	ENSP00000322159:Y185N	Y	+	1	0	ATG4C	63057422	0.000000	0.05858	0.003000	0.11579	0.952000	0.60782	0.067000	0.14510	0.136000	0.18733	0.528000	0.53228	TAT	.	.	none		0.363	ATG4C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025332.2	NM_032852	
PLB1	151056	hgsc.bcm.edu	37	2	28761981	28761981	+	Missense_Mutation	SNP	G	G	C	rs6753929	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	171	0	0		WXS	Illumina HiSeq	Phase_I	160	46	0.2875	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		
OR52J3	119679	hgsc.bcm.edu	37	11	5068177	5068177	+	Missense_Mutation	SNP	A	A	T	rs2500018	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:5068177A>T	ENST00000380370.1	+	1	422	c.422A>T	c.(421-423)cAa>cTa	p.Q141L		NM_001001916.2	NP_001001916.2	Q8NH60	O52J3_HUMAN	olfactory receptor, family 52, subfamily J, member 3	141			Q -> L (in dbSNP:rs2500018). {ECO:0000269|PubMed:14983052, ECO:0000269|Ref.1, 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)			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)		TTGACATCCCAAGTGTTGGTG	0.493													A|||	2442	0.48762	0.5915	0.4971	5008	,	,		21422	0.2619		0.508	False		,,,				2504	0.5521				p.Q141L		Atlas-SNP	.											OR52J3,NS,carcinoma,-1,1	OR52J3	77	1	0			c.A422T						PASS	.	A	LEU/GLN	2444,1958	621.1+/-393.7	688,1068,445	182.0	118.0	139.0		422	-5.2	0.0	11	dbSNP_100	139	4304,4292	578.0+/-390.6	1067,2170,1061	yes	missense	OR52J3	NM_001001916.2	113	1755,3238,1506	TT,TA,AA		49.9302,44.4798,48.0843	benign	141/312	5068177	6748,6250	2201	4298	6499	SO:0001583	missense	119679	exon1			CATCCCAAGTGTT	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.422A>T	11.37:g.5068177A>T	ENSP00000369728:p.Gln141Leu	Somatic	251	0	0		WXS	Illumina HiSeq	Phase_I	322	321	0.996894	NM_001001916	Q6IFE4	Missense_Mutation	SNP	ENST00000380370.1	37	CCDS31370.1	995	0.4555860805860806	290	0.5894308943089431	170	0.4696132596685083	149	0.26048951048951047	386	0.5092348284960422	A	1.867	-0.461166	0.04508	0.555202	0.500698	ENSG00000205495	ENST00000380370	T	0.11277	2.79	4.19	-5.19	0.02832	GPCR, rhodopsin-like superfamily (1);	1.059250	0.07502	N	0.907470	T	0.00012	0.0000	L	0.33293	1	0.80722	P	0.0	B	0.02656	0.0	B	0.06405	0.002	T	0.43621	-0.9380	9	0.46703	T	0.11	.	7.2722	0.26262	0.4249:0.2007:0.3744:0.0	rs2500018;rs17259473;rs52831001;rs60936519;rs2500018	141	Q8NH60	O52J3_HUMAN	L	141	ENSP00000369728:Q141L	ENSP00000369728:Q141L	Q	+	2	0	OR52J3	5024753	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.528000	0.02225	-0.989000	0.03485	-2.338000	0.00246	CAA	A|0.494;T|0.506	0.506	strong		0.493	OR52J3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142807.1	NM_001001916	
KRTAP10-2	386679	hgsc.bcm.edu	37	21	45971109	45971109	+	Missense_Mutation	SNP	G	G	A	rs200984587	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:45971109G>A	ENST00000391621.1	-	1	279	c.233C>T	c.(232-234)tCg>tTg	p.S78L	TSPEAR_ENST00000397916.1_Intron|TSPEAR_ENST00000323084.4_Intron|KRTAP10-2_ENST00000498210.1_Intron	NM_198693.2	NP_941966.1	P60368	KR102_HUMAN	keratin associated protein 10-2	78	22 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				large_intestine(1)|lung(4)|skin(1)	6						CTGGCAGCACGAGGGCGTGCA	0.687																																					p.S78L		Atlas-SNP	.											KRTAP10-2,caecum,carcinoma,0,1	KRTAP10-2	21	1	0			c.C233T						scavenged	.																																			SO:0001583	missense	386679	exon1			CAGCACGAGGGCG	AJ566381	CCDS42955.1	21q22.3	2007-10-05			ENSG00000205445	ENSG00000205445		"""Keratin associated proteins"""	22967	protein-coding gene	gene with protein product				KRTAP18-2			Standard	NM_198693		Approved	KAP10.2, KAP18.2	uc002zfi.1	P60368	OTTHUMG00000057625	ENST00000391621.1:c.233C>T	21.37:g.45971109G>A	ENSP00000375479:p.Ser78Leu	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	123	33	0.268293	NM_198693	Q70LJ5	Missense_Mutation	SNP	ENST00000391621.1	37	CCDS42955.1	.	.	.	.	.	.	.	.	.	.	g	5.987	0.366047	0.11352	.	.	ENSG00000205445	ENST00000391621	T	0.01572	4.76	3.44	1.48	0.22813	.	.	.	.	.	T	0.03305	0.0096	M	0.87682	2.9	0.09310	N	1	B	0.22683	0.073	B	0.16289	0.015	T	0.40384	-0.9566	9	0.51188	T	0.08	.	2.1189	0.03721	0.1176:0.1948:0.4883:0.1993	.	78	P60368	KR102_HUMAN	L	78	ENSP00000375479:S78L	ENSP00000375479:S78L	S	-	2	0	KRTAP10-2	44795537	0.060000	0.20803	0.001000	0.08648	0.073000	0.16967	1.997000	0.40786	0.133000	0.18654	0.456000	0.33151	TCG	.	.	weak		0.687	KRTAP10-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128027.1		
GOLGA4	2803	hgsc.bcm.edu	37	3	37368710	37368710	+	Missense_Mutation	SNP	T	T	A	rs144205536	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:37368710T>A	ENST00000361924.2	+	14	5707	c.5333T>A	c.(5332-5334)aTa>aAa	p.I1778K	GOLGA4_ENST00000356847.4_Missense_Mutation_p.I1800K|GOLGA4_ENST00000444882.1_Intron	NM_002078.4	NP_002069.2	Q13439	GOGA4_HUMAN	golgin A4	1778	Glu-rich.				Golgi to plasma membrane protein transport (GO:0043001)|protein targeting to Golgi (GO:0000042)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)|trans-Golgi network (GO:0005802)	GTPase binding (GO:0051020)			NS(2)|breast(3)|central_nervous_system(3)|endometrium(6)|kidney(2)|large_intestine(17)|liver(2)|lung(16)|ovary(4)|prostate(2)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	65						GAGCGCTTAATAAAGCTAGAA	0.373													T|||	2	0.000399361	0.0	0.0	5008	,	,		20680	0.0		0.002	False		,,,				2504	0.0				p.I1800K		Atlas-SNP	.											.	GOLGA4	173	.	0			c.T5399A						PASS	.	T	LYS/ILE,LYS/ILE	1,4405	2.1+/-5.4	0,1,2202	98.0	100.0	99.0		5399,5333	-4.5	0.0	3	dbSNP_134	99	3,8597	3.0+/-9.4	0,3,4297	yes	missense,missense	GOLGA4	NM_001172713.1,NM_002078.4	102,102	0,4,6499	AA,AT,TT		0.0349,0.0227,0.0308	benign,benign	1800/2244,1778/2231	37368710	4,13002	2203	4300	6503	SO:0001583	missense	2803	exon15			GCTTAATAAAGCT	U31906	CCDS2666.1, CCDS54564.1	3p22-p21.3	2010-02-12	2010-02-12		ENSG00000144674	ENSG00000144674			4427	protein-coding gene	gene with protein product	"""golgin 245"""	602509	"""golgi autoantigen, golgin subfamily a, 4"""			8626529	Standard	NM_002078		Approved	GOLG, GCP2, p230, golgin-240	uc003cgw.3	Q13439	OTTHUMG00000130799	ENST00000361924.2:c.5333T>A	3.37:g.37368710T>A	ENSP00000354486:p.Ile1778Lys	Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	106	52	0.490566	NM_001172713	F8W8Q7|Q13270|Q13654|Q14436|Q59EW8	Missense_Mutation	SNP	ENST00000361924.2	37	CCDS2666.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	T	4.803	0.149256	0.09185	2.27E-4	3.49E-4	ENSG00000144674	ENST00000361924;ENST00000356847;ENST00000437131	T;T;T	0.20332	2.08;2.08;2.08	4.59	-4.53	0.03462	.	0.710473	0.11563	N	0.551556	T	0.06917	0.0176	N	0.17474	0.49	0.09310	N	1	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.04013	0.001;0.001;0.001;0.0	T	0.39840	-0.9594	10	0.06099	T	0.92	.	1.6064	0.02684	0.1664:0.2826:0.3456:0.2054	.	1778;1778;1800;1778	Q13439-3;Q13439-4;F8W8Q7;Q13439	.;.;.;GOGA4_HUMAN	K	1778;1800;1649	ENSP00000354486:I1778K;ENSP00000349305:I1800K;ENSP00000405842:I1649K	ENSP00000349305:I1800K	I	+	2	0	GOLGA4	37343714	0.000000	0.05858	0.000000	0.03702	0.156000	0.22039	-0.047000	0.11963	-0.318000	0.08665	0.459000	0.35465	ATA	T|0.999;A|0.001	0.001	strong		0.373	GOLGA4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253339.2	NM_002078	
NUP133	55746	hgsc.bcm.edu	37	1	229622162	229622162	+	Silent	SNP	A	A	G	rs1065675	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	150	0	0		WXS	Illumina HiSeq	Phase_I	113	43	0.380531	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	
PPP1R12A	4659	hgsc.bcm.edu	37	12	80199958	80199958	+	Missense_Mutation	SNP	C	C	G	rs61756418	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:80199958C>G	ENST00000450142.2	-	13	2077	c.1811G>C	c.(1810-1812)gGc>gCc	p.G604A	AC073569.1_ENST00000598624.1_Intron|PPP1R12A_ENST00000550107.1_Intron|PPP1R12A_ENST00000261207.5_Missense_Mutation_p.G604A|PPP1R12A_ENST00000437004.2_Missense_Mutation_p.G604A|PPP1R12A_ENST00000546369.1_Missense_Mutation_p.G517A	NM_002480.2	NP_002471.1	O14974	MYPT1_HUMAN	protein phosphatase 1, regulatory subunit 12A	604	Ser/Thr-rich.				centrosome organization (GO:0051297)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of catalytic activity (GO:0043086)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein dephosphorylation (GO:0006470)|regulation of cell adhesion (GO:0030155)|regulation of myosin-light-chain-phosphatase activity (GO:0035507)|regulation of nucleocytoplasmic transport (GO:0046822)|signal transduction (GO:0007165)	actin cytoskeleton (GO:0015629)|centrosome (GO:0005813)|contractile fiber (GO:0043292)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)|PTW/PP1 phosphatase complex (GO:0072357)	14-3-3 protein binding (GO:0071889)|enzyme inhibitor activity (GO:0004857)|phosphatase regulator activity (GO:0019208)|protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)			breast(5)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(7)|liver(1)|lung(4)|ovary(2)|skin(1)	29						GCTTTGTGTGCCTGCTGAGGA	0.458													C|||	12	0.00239617	0.0008	0.0058	5008	,	,		18491	0.0		0.007	False		,,,				2504	0.0				p.G604A		Atlas-SNP	.											.	PPP1R12A	76	.	0			c.G1811C						PASS	.	C	ALA/GLY,ALA/GLY,ALA/GLY	3,3917		0,3,1957	290.0	274.0	279.0		1811,1550,1811	5.6	1.0	12	dbSNP_129	279	61,8257		0,61,4098	yes	missense,missense,missense	PPP1R12A	NM_001143885.1,NM_001143886.1,NM_002480.2	60,60,60	0,64,6055	GG,GC,CC		0.7333,0.0765,0.523	possibly-damaging,possibly-damaging,possibly-damaging	604/1031,517/944,604/1031	80199958	64,12174	1960	4159	6119	SO:0001583	missense	4659	exon13			TGTGTGCCTGCTG	D87930	CCDS44947.1, CCDS44948.1, CCDS58259.1, CCDS58260.1	12q15-q21	2013-01-18	2011-10-04	2001-08-10	ENSG00000058272	ENSG00000058272		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Ankyrin repeat domain containing"""	7618	protein-coding gene	gene with protein product	"""myosin phosphatase-targeting subunit 1"", ""myosin binding subunit"""	602021	"""protein phosphatase 1, regulatory (inhibitor) subunit 12A"""	MYPT1		9286714	Standard	NM_002480		Approved	MBS, M130	uc001syz.3	O14974	OTTHUMG00000170100	ENST00000450142.2:c.1811G>C	12.37:g.80199958C>G	ENSP00000389168:p.Gly604Ala	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	118	51	0.432203	NM_002480	B4DZ09|F8VWB4|Q2NKL4|Q569H0|Q86WU3|Q8NFR6|Q9BYH0	Missense_Mutation	SNP	ENST00000450142.2	37	CCDS44947.1	6|6	0.0027472527472527475|0.0027472527472527475	0|0	0.0|0.0	2|2	0.0055248618784530384|0.0055248618784530384	0|0	0.0|0.0	4|4	0.005277044854881266|0.005277044854881266	C|C	15.42|15.42	2.827657|2.827657	0.50845|0.50845	7.65E-4|7.65E-4	0.007333|0.007333	ENSG00000058272|ENSG00000058272	ENST00000553081|ENST00000261207;ENST00000546189;ENST00000360825;ENST00000312727;ENST00000450142;ENST00000437004;ENST00000546369;ENST00000547330	.|T;T;T;T;T	.|0.36340	.|1.33;1.33;1.37;1.36;1.26	5.62|5.62	5.62|5.62	0.85841|0.85841	.|.	.|0.151958	.|0.64402	.|D	.|0.000009	T|T	0.33585|0.33585	0.0868|0.0868	L|L	0.31065|0.31065	0.9|0.9	0.44871|0.44871	D|D	0.997885|0.997885	.|P;D;P	.|0.56035	.|0.93;0.974;0.956	.|P;P;P	.|0.54499	.|0.459;0.754;0.572	T|T	0.03112|0.03112	-1.1071|-1.1071	5|10	.|0.20046	.|T	.|0.44	.|.	19.6432|19.6432	0.95764|0.95764	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	rs61756418|rs61756418	.|604;604;604	.|F8W8Q6;O14974-2;O14974	.|.;.;MYPT1_HUMAN	P|A	196|604;604;604;604;604;604;517;604	.|ENSP00000261207:G604A;ENSP00000389168:G604A;ENSP00000416769:G604A;ENSP00000449514:G517A;ENSP00000446816:G604A	.|ENSP00000261207:G604A	A|G	-|-	1|2	0|0	PPP1R12A|PPP1R12A	78724089|78724089	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	3.058000|3.058000	0.49939|0.49939	2.641000|2.641000	0.89580|0.89580	0.591000|0.591000	0.81541|0.81541	GCA|GGC	C|0.996;G|0.004	0.004	strong		0.458	PPP1R12A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407254.2	NM_002480	
HLA-DQB1	3119	hgsc.bcm.edu	37	6	32632777	32632777	+	Silent	SNP	C	C	T	rs1049068	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:32632777C>T	ENST00000399084.1	-	3	355	c.177G>A	c.(175-177)gtG>gtA	p.V59V	HLA-DQB1_ENST00000434651.2_Silent_p.V59V|HLA-DQB1_ENST00000399079.3_Silent_p.V59V|HLA-DQB1_ENST00000374943.4_Silent_p.V59V|HLA-DQB1_ENST00000399082.3_Intron|XXbac-BPG254F23.6_ENST00000443574.1_RNA			P01920	DQB1_HUMAN	major histocompatibility complex, class II, DQ beta 1	59	Beta-1.		V -> L (in allele DQB1*03:18; dbSNP:rs41563539).		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|humoral immune response mediated by circulating immunoglobulin (GO:0002455)|immune response (GO:0006955)|immunoglobulin production involved in immunoglobulin mediated immune response (GO:0002381)|interferon-gamma-mediated signaling pathway (GO:0060333)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			breast(1)|large_intestine(1)|lung(1)|pancreas(1)	4					"""""""Insulin(DB00071)"""	TGTATCTGGTCACAAGACGCA	0.622									T-cell Lymphoma, (Cutaneous) , Familial Clustering of;Sjgren syndrome;Melanoma, Familial Clustering of;ACTH-independent macronodular adrenal hyperplasia				C|||	474	0.0946486	0.1044	0.0908	5008	,	,		7780	0.0427		0.1233	False		,,,				2504	0.1084				p.V59V	Esophageal Squamous(151;720 1825 15000 40336 43415)	Atlas-SNP	.											.	HLA-DQB1	15	.	0			c.G177A						PASS	.	C		473,3789		100,273,1758	30.0	32.0	32.0		177	3.0	0.1	6	dbSNP_86	32	1130,7308		260,610,3349	no	coding-synonymous	HLA-DQB1	NM_002123.4		360,883,5107	TT,TC,CC		13.3918,11.0981,12.622		59/262	32632777	1603,11097	2131	4219	6350	SO:0001819	synonymous_variant	3119	exon2	Familial Cancer Database	incl.: Mycosis Fungoides, Sezary syndrome, Adult T-cell Lymphoma;Sjogren syndrome; ;AIMAH, Cushing disease, Adrenal, Familial	TCTGGTCACAAGA		CCDS43451.1, CCDS59006.1	6p21.3	2013-01-11			ENSG00000179344	ENSG00000179344		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4944	protein-coding gene	gene with protein product		604305		HLA-DQB			Standard	NM_001243962		Approved	IDDM1, CELIAC1	uc031snw.1	P01920	OTTHUMG00000031124	ENST00000399084.1:c.177G>A	6.37:g.32632777C>T		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	102	66	0.647059	NM_002123	A1KR27|A2RPH3|A4Q9R4|A4USG2|A4USG5|A6N8I7|A9YQA0|B0S7Y7|B1A0K6|B1GXI3|B3VLT3|B5BLN7|B7VU69|C0MQ34|C0MQ35|C8ZL52|C8ZLJ8|C8ZLJ9|C9DRQ3|O19708|O19713|O19724|O62861|O78046|O78221|O78223|O98034|O98201|P01917|P01918|P01919|P03992|P05537|P79482|P79526|P79544|P79551|Q08GC8|Q09035|Q0E4V9|Q1M312|Q29731|Q29877|Q29884|Q29915|Q29966|Q2P9N3|Q2QK85|Q30061|Q30075|Q30076|Q30080|Q30081|Q30082|Q30083|Q30084|Q30089|Q30095|Q31633|Q38I47|Q45UE3|Q4QZB5|Q53I44|Q564J6|Q5G841|Q5ISH1|Q5ISH3|Q5W1E1|Q5Y7G8|Q643R4|Q6B9X1|Q70VH8|Q7YP69|Q8HWH0|Q8MH58|Q8SNB4|Q8SND1|Q8SP70|Q8WMA3|Q9BD17|Q9MYH2|Q9TPA9|Q9XRY6|Q9XRY7|Q9XRZ2	Silent	SNP	ENST00000399084.1	37	CCDS43451.1																																																																																			C|0.901;T|0.099	0.099	strong		0.622	HLA-DQB1-003	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276127.1	NM_002123	
LINC00283	100874057	hgsc.bcm.edu	37	13	103392709	103392709	+	RNA	SNP	A	A	T	rs79592880	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:103392709A>T	ENST00000430111.1	+	0	0									long intergenic non-protein coding RNA 283																		TGCTTAGCTGATCTGCAGAAA	0.408													A|||	442	0.0882588	0.0817	0.0706	5008	,	,		20545	0.0139		0.1252	False		,,,				2504	0.1483				p.D3446E		Atlas-SNP	.											.	.	.	.	0			c.T10338A						PASS	.	A	GLU/ASP	114,1270		6,102,584	78.0	60.0	66.0		10338	-2.2	0.0	13	dbSNP_132	66	380,2800		22,336,1232	yes	missense	CCDC168	NM_001146197.1	45	28,438,1816	TT,TA,AA		11.9497,8.237,10.8238		3446/7082	103392709	494,4070	692	1590	2282			643677	exon4			TAGCTGATCTGCA			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.103392709A>T		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	95	50	0.526316	NM_001146197		Missense_Mutation	SNP	ENST00000430111.1	37																																																																																				A|0.922;T|0.078	0.078	strong		0.408	LINC00283-001	KNOWN	not_organism_supported|basic	antisense	antisense	OTTHUMT00000045714.1		
SCRIB	23513	hgsc.bcm.edu	37	8	144875168	144875168	+	Missense_Mutation	SNP	G	G	A	rs202137464	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:144875168G>A	ENST00000320476.3	-	29	4001	c.3995C>T	c.(3994-3996)cCg>cTg	p.P1332L	SCRIB_ENST00000377533.3_Missense_Mutation_p.P1251L|SCRIB_ENST00000356994.2_Missense_Mutation_p.P1332L|RP11-429J17.8_ENST00000527139.1_RNA|RP11-429J17.8_ENST00000534089.1_RNA|RP11-429J17.8_ENST00000532625.1_RNA|SCRIB_ENST00000546337.1_5'UTR	NM_015356.4	NP_056171	Q14160	SCRIB_HUMAN	scribbled planar cell polarity protein	1332	Pro-rich.				activation of Rac GTPase activity (GO:0032863)|apoptotic process involved in morphogenesis (GO:0060561)|astrocyte cell migration (GO:0043615)|asymmetric protein localization (GO:0008105)|auditory receptor cell stereocilium organization (GO:0060088)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cochlear nucleus development (GO:0021747)|establishment of apical/basal cell polarity (GO:0035089)|mammary gland duct morphogenesis (GO:0060603)|negative regulation of mitotic cell cycle (GO:0045930)|neural tube closure (GO:0001843)|positive chemotaxis (GO:0050918)|positive regulation of apoptotic process (GO:0043065)|positive regulation of receptor recycling (GO:0001921)|protein localization to adherens junction (GO:0071896)|single organismal cell-cell adhesion (GO:0016337)|synaptic vesicle endocytosis (GO:0048488)|synaptic vesicle targeting (GO:0016080)|viral process (GO:0016032)|wound healing (GO:0042060)	basolateral plasma membrane (GO:0016323)|cell projection (GO:0042995)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|myelin sheath abaxonal region (GO:0035748)|plasma membrane (GO:0005886)|Scrib-APC-beta-catenin complex (GO:0034750)				NS(1)|autonomic_ganglia(1)|central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(3)|lung(20)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	42	all_cancers(97;2.31e-11)|all_epithelial(106;1.58e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;1.23e-39)|all cancers(56;1.12e-34)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.18)			ATCCTCAGGCGGGTGAGAAGT	0.716													G|||	10	0.00199681	0.0	0.0	5008	,	,		12252	0.0		0.008	False		,,,				2504	0.002				p.P1332L	Pancreas(51;966 1133 10533 14576 29674)	Atlas-SNP	.											.	SCRIB	192	.	0			c.C3995T						PASS	.	G	LEU/PRO,LEU/PRO	9,4275		0,9,2133	15.0	16.0	15.0		3995,3995	2.2	0.0	8		15	62,8392		0,62,4165	yes	missense,missense	SCRIB	NM_015356.3,NM_182706.3	98,98	0,71,6298	AA,AG,GG		0.7334,0.2101,0.5574	possibly-damaging,possibly-damaging	1332/1631,1332/1656	144875168	71,12667	2142	4227	6369	SO:0001583	missense	23513	exon29			TCAGGCGGGTGAG	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.3995C>T	8.37:g.144875168G>A	ENSP00000322938:p.Pro1332Leu	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	110	83	0.754545	NM_015356	Q6P496|Q7Z5D1|Q8WWV8|Q96C69|Q96GG1	Missense_Mutation	SNP	ENST00000320476.3	37	CCDS6411.1	5	0.0022893772893772895	0	0.0	0	0.0	0	0.0	5	0.006596306068601583	G	14.28	2.488712	0.44249	0.002101	0.007334	ENSG00000180900	ENST00000356994;ENST00000320476;ENST00000377533;ENST00000377539	T;T;T	0.37411	1.41;1.36;1.2	4.17	2.25	0.28309	.	.	.	.	.	T	0.41442	0.1159	L	0.56769	1.78	0.09310	N	1	D;D;D	0.89917	0.998;0.999;1.0	P;P;D	0.91635	0.688;0.904;0.999	T	0.16719	-1.0393	9	0.42905	T	0.14	.	5.165	0.15081	0.1014:0.0:0.5328:0.3658	.	1332;1332;1251	Q14160;Q14160-3;Q14160-2	SCRIB_HUMAN;.;.	L	1332;1332;1251;701	ENSP00000349486:P1332L;ENSP00000322938:P1332L;ENSP00000366756:P1251L	ENSP00000322938:P1332L	P	-	2	0	SCRIB	144947156	0.955000	0.32602	0.040000	0.18447	0.028000	0.11728	1.498000	0.35660	0.693000	0.31634	0.195000	0.17529	CCG	G|0.998;A|0.002	0.002	strong		0.716	SCRIB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000382215.1	NM_015356	
CPEB4	80315	hgsc.bcm.edu	37	5	173372015	173372015	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:173372015G>A	ENST00000265085.5	+	5	2782	c.1328G>A	c.(1327-1329)gGc>gAc	p.G443D	CPEB4_ENST00000519467.1_3'UTR|CPEB4_ENST00000522336.1_Missense_Mutation_p.G53D|CPEB4_ENST00000334035.5_Missense_Mutation_p.G426D|CPEB4_ENST00000517880.1_Missense_Mutation_p.G36D|CPEB4_ENST00000520867.1_Missense_Mutation_p.G418D|CPEB4_ENST00000519835.1_Missense_Mutation_p.G418D	NM_030627.2	NP_085130.2	Q17RY0	CPEB4_HUMAN	cytoplasmic polyadenylation element binding protein 4	443					cellular response to amino acid stimulus (GO:0071230)|cellular response to decreased oxygen levels (GO:0036294)|cellular response to glucose starvation (GO:0042149)|ionotropic glutamate receptor signaling pathway (GO:0035235)|negative regulation of neuron apoptotic process (GO:0043524)|response to ischemia (GO:0002931)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|postsynaptic density (GO:0014069)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(5)|prostate(1)|stomach(1)|upper_aerodigestive_tract(2)	20	Renal(175;0.000159)|Lung NSC(126;0.0128)|all_lung(126;0.0202)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)			TTGGATGATGGCCGTGGGGAT	0.463																																					p.G443D		Atlas-SNP	.											CPEB4,NS,carcinoma,-1,1	CPEB4	54	1	0			c.G1328A						scavenged	.						194.0	176.0	182.0					5																	173372015		2203	4300	6503	SO:0001583	missense	80315	exon5			ATGATGGCCGTGG	BX538213	CCDS4390.1	5q21	2013-02-12			ENSG00000113742	ENSG00000113742		"""RNA binding motif (RRM) containing"""	21747	protein-coding gene	gene with protein product		610607				11214970, 12672660	Standard	NM_030627		Approved	KIAA1673	uc003mcs.4	Q17RY0	OTTHUMG00000130541	ENST00000265085.5:c.1328G>A	5.37:g.173372015G>A	ENSP00000265085:p.Gly443Asp	Somatic	297	1	0.003367		WXS	Illumina HiSeq	Phase_I	362	6	0.0165746	NM_030627	B7ZLQ7|Q7Z310|Q8N405|Q9C0J0	Missense_Mutation	SNP	ENST00000265085.5	37	CCDS4390.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	16.30|16.30	3.084057|3.084057	0.55861|0.55861	.|.	.|.	ENSG00000113742|ENSG00000113742	ENST00000519152|ENST00000265085;ENST00000520867;ENST00000334035;ENST00000519835;ENST00000522336;ENST00000517880	.|T;T;T;T	.|0.46451	.|0.9;0.88;0.89;0.87	5.37|5.37	5.37|5.37	0.77165|0.77165	.|Nucleotide-binding, alpha-beta plait (1);	.|0.095649	.|0.64402	.|D	.|0.000001	T|T	0.37073|0.37073	0.0990|0.0990	L|L	0.29908|0.29908	0.895|0.895	0.53005|0.53005	D|D	0.999965|0.999965	.|B;B;B;B;B	.|0.13594	.|0.002;0.008;0.002;0.001;0.002	.|B;B;B;B;B	.|0.17433	.|0.008;0.018;0.008;0.002;0.011	T|T	0.11966|0.11966	-1.0566|-1.0566	5|10	.|0.52906	.|T	.|0.07	-11.9199|-11.9199	19.4739|19.4739	0.94976|0.94976	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|418;426;418;53;443	.|B7ZLQ8;Q17RY0-2;E5RJM0;E5RFP2;Q17RY0	.|.;.;.;.;CPEB4_HUMAN	T|D	121|443;418;426;418;53;36	.|ENSP00000265085:G443D;ENSP00000429092:G418D;ENSP00000334533:G426D;ENSP00000429048:G418D	.|ENSP00000265085:G443D	A|G	+|+	1|2	0|0	CPEB4|CPEB4	173304621|173304621	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	6.061000|6.061000	0.71148|0.71148	2.697000|2.697000	0.92050|0.92050	0.655000|0.655000	0.94253|0.94253	GCC|GGC	.	.	none		0.463	CPEB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252964.2	NM_030627	
RBBP8NL	140893	hgsc.bcm.edu	37	20	60989185	60989185	+	Missense_Mutation	SNP	C	C	T	rs10888228	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:60989185C>T	ENST00000252998.1	-	10	1378	c.1222G>A	c.(1222-1224)Gca>Aca	p.A408T		NM_080833.2	NP_543023.2	Q8NC74	RB8NL_HUMAN	RBBP8 N-terminal like	408			A -> T (in dbSNP:rs10888228).			extracellular space (GO:0005615)											AGGCCTGCTGCGGCCAGAGCT	0.701													T|||	622	0.124201	0.2685	0.1412	5008	,	,		12780	0.0		0.1352	False		,,,				2504	0.0337				p.A408T		Atlas-SNP	.											.	.	.	.	0			c.G1222A						PASS	.	T	THR/ALA	1056,3252		110,836,1208	8.0	10.0	9.0		1222	-1.6	0.0	20	dbSNP_120	9	1136,7320		84,968,3176	no	missense	C20orf151	NM_080833.2	58	194,1804,4384	TT,TC,CC		13.4342,24.5125,17.1733	benign	408/665	60989185	2192,10572	2154	4228	6382	SO:0001583	missense	140893	exon10			CTGCTGCGGCCAG	AL121832	CCDS13498.1	20q13.33	2012-10-30	2012-10-30	2012-10-30	ENSG00000130701	ENSG00000130701			16144	protein-coding gene	gene with protein product	"""hypothetical protein LOC140893"""		"""chromosome 20 open reading frame 151"""	C20orf151		11780052	Standard	NM_080833		Approved	dJ908M14.3	uc002ycw.2	Q8NC74	OTTHUMG00000032913	ENST00000252998.1:c.1222G>A	20.37:g.60989185C>T	ENSP00000252998:p.Ala408Thr	Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	47	33	0.702128	NM_080833	B2RP98|Q8N4Z9|Q9BR75|Q9H0Y9	Missense_Mutation	SNP	ENST00000252998.1	37	CCDS13498.1	275	0.1259157509157509	125	0.2540650406504065	56	0.15469613259668508	2	0.0034965034965034965	92	0.12137203166226913	T	12.25	1.880138	0.33162	0.245125	0.134342	ENSG00000130701	ENST00000252998	T	0.17054	2.3	4.65	-1.63	0.08345	.	1.468830	0.04019	N	0.299475	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	0.40308	-0.9570	9	0.11485	T	0.65	-0.8276	1.2388	0.01958	0.1491:0.3211:0.1523:0.3775	rs10888228;rs10888228	408	Q8NC74	CT151_HUMAN	T	408	ENSP00000252998:A408T	ENSP00000252998:A408T	A	-	1	0	C20orf151	60422580	0.000000	0.05858	0.000000	0.03702	0.140000	0.21249	-0.494000	0.06451	-0.228000	0.09869	-0.490000	0.04691	GCA	C|0.851;T|0.149	0.149	strong		0.701	RBBP8NL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080029.1	NM_080833	
TUBG2	27175	hgsc.bcm.edu	37	17	40818451	40818451	+	Silent	SNP	G	G	A	rs1554227	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:40818451G>A	ENST00000251412.7	+	10	1306	c.1107G>A	c.(1105-1107)tcG>tcA	p.S369S	PLEKHH3_ENST00000456950.2_5'Flank	NM_016437.2	NP_057521.1	Q9NRH3	TBG2_HUMAN	tubulin, gamma 2	369					cytoplasmic microtubule organization (GO:0031122)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule nucleation (GO:0007020)|mitotic cell cycle (GO:0000278)	cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|gamma-tubulin complex (GO:0000930)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|pericentriolar material (GO:0000242)|spindle microtubule (GO:0005876)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)	15		Breast(137;0.00116)		BRCA - Breast invasive adenocarcinoma(366;0.141)		ACCTGCCCTCGGCCCACCGGG	0.612													G|||	2523	0.503794	0.4365	0.4726	5008	,	,		18996	0.4633		0.5189	False		,,,				2504	0.6431				p.S369S		Atlas-SNP	.											TUBG2,bladder,carcinoma,+1,1	TUBG2	43	1	0			c.G1107A						PASS	.						71.0	74.0	73.0					17																	40818451		2203	4297	6500	SO:0001819	synonymous_variant	27175	exon10			GCCCTCGGCCCAC	AF225971	CCDS32658.1	17q21.2	2014-09-04			ENSG00000037042	ENSG00000037042		"""Tubulins"""	12419	protein-coding gene	gene with protein product		605785					Standard	NM_016437		Approved		uc010wgr.2	Q9NRH3	OTTHUMG00000180640	ENST00000251412.7:c.1107G>A	17.37:g.40818451G>A		Somatic	302	0	0		WXS	Illumina HiSeq	Phase_I	295	127	0.430508	NM_016437	A6NDI4|Q32NB2	Silent	SNP	ENST00000251412.7	37	CCDS32658.1																																																																																			.	.	weak		0.612	TUBG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452326.1	NM_016437	
ARHGAP25	9938	hgsc.bcm.edu	37	2	69040500	69040500	+	Silent	SNP	G	G	A	rs2280310	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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_ENST00000544262.1_Silent_p.Q226Q|ARHGAP25_ENST00000409202.3_Silent_p.Q252Q|ARHGAP25_ENST00000409030.3_Silent_p.Q244Q	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	75	0	0		WXS	Illumina HiSeq	Phase_I	76	76	1	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	
TDG	6996	hgsc.bcm.edu	37	12	104373829	104373829	+	Silent	SNP	C	C	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:104373829C>A	ENST00000392872.3	+	3	621	c.387C>A	c.(385-387)acC>acA	p.T129T	TDG_ENST00000544861.1_5'UTR|TDG_ENST00000542036.1_5'UTR|TDG_ENST00000266775.9_Silent_p.T125T	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	247	1	0.00404858		WXS	Illumina HiSeq	Phase_I	251	14	0.0557769	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		
XIRP1	165904	hgsc.bcm.edu	37	3	39227664	39227664	+	Silent	SNP	G	G	A	rs61736155	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:39227664G>A	ENST00000340369.3	-	2	3501	c.3273C>T	c.(3271-3273)gaC>gaT	p.D1091D	XIRP1_ENST00000396251.1_Silent_p.D1091D|XIRP1_ENST00000421646.1_Intron	NM_194293.2	NP_919269.2	Q702N8	XIRP1_HUMAN	xin actin-binding repeat containing 1	1091					cardiac muscle cell development (GO:0055013)|negative regulation of cell proliferation (GO:0008285)|regulation of membrane potential (GO:0042391)|sarcomere organization (GO:0045214)	fascia adherens (GO:0005916)	poly(A) RNA binding (GO:0044822)			breast(4)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(14)|lung(22)|ovary(4)|pancreas(1)|prostate(2)|skin(6)	71				KIRC - Kidney renal clear cell carcinoma(284;0.0517)|Kidney(284;0.065)		TCCGAAGACCGTCCTGGATGG	0.602													G|||	505	0.100839	0.0091	0.1023	5008	,	,		17430	0.0615		0.1988	False		,,,				2504	0.1636				p.D1091D		Atlas-SNP	.											.	XIRP1	173	.	0			c.C3273T						PASS	.	G	,	187,4219		4,179,2020	58.0	57.0	57.0		3273,3273	-5.2	0.0	3	dbSNP_129	57	1755,6843		176,1403,2720	no	coding-synonymous,coding-synonymous	XIRP1	NM_001198621.1,NM_194293.2	,	180,1582,4740	AA,AG,GG		20.4117,4.2442,14.9339	,	1091/1122,1091/1844	39227664	1942,11062	2203	4299	6502	SO:0001819	synonymous_variant	165904	exon2			AAGACCGTCCTGG	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.3273C>T	3.37:g.39227664G>A		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	62	30	0.483871	NM_001198621	A0JP25|A4QPE2|Q68DF2|Q6ZTR3|Q702N9|Q8IVN7|Q8N1N3|Q8N904|Q8TCG7	Silent	SNP	ENST00000340369.3	37	CCDS2683.1																																																																																			G|0.862;A|0.138	0.138	strong		0.602	XIRP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254065.1	XM_093522	
OR4N2	390429	hgsc.bcm.edu	37	14	20295627	20295627	+	Missense_Mutation	SNP	C	C	G	rs72663752	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:20295627C>G	ENST00000315947.1	+	1	20	c.20C>G	c.(19-21)aCa>aGa	p.T7R	OR4N2_ENST00000568211.1_Missense_Mutation_p.T7R	NM_001004723.1	NP_001004723.1	Q8NGD1	OR4N2_HUMAN	olfactory receptor, family 4, subfamily N, member 2	7						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)		GAGAACAGAACAGTGATAAGA	0.388													.|||	364	0.0726837	0.0174	0.1023	5008	,	,		27982	0.1002		0.1093	False		,,,				2504	0.0603				p.T7R		Atlas-SNP	.											.	OR4N2	125	.	0			c.C20G						PASS	.	C	ARG/THR	195,4211		2,191,2010	119.0	129.0	125.0		20	4.4	0.3	14	dbSNP_131	125	987,7613		10,967,3323	yes	missense	OR4N2	NM_001004723.1	71	12,1158,5333	GG,GC,CC		11.4767,4.4258,9.0881	possibly-damaging	7/308	20295627	1182,11824	2203	4300	6503	SO:0001583	missense	390429	exon1			ACAGAACAGTGAT		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.20C>G	14.37:g.20295627C>G	ENSP00000319601:p.Thr7Arg	Somatic	299	0	0		WXS	Illumina HiSeq	Phase_I	342	106	0.309942	NM_001004723	Q6IEY9|Q6IFA2	Missense_Mutation	SNP	ENST00000315947.1	37	CCDS32022.1	181	0.08287545787545787	6	0.012195121951219513	36	0.09944751381215469	53	0.09265734265734266	86	0.11345646437994723	.	10.85	1.467128	0.26335	0.044258	0.114767	ENSG00000176294	ENST00000557414;ENST00000557677;ENST00000315947	T;T;T	0.54279	5.72;0.58;0.58	4.41	4.41	0.53225	.	0.000000	0.49916	D	0.000123	T	0.02083	0.0065	M	0.73962	2.25	0.18873	N	0.999982	P	0.45396	0.857	P	0.46452	0.517	T	0.01039	-1.1472	10	0.49607	T	0.09	-7.0137	14.8767	0.70498	0.0:1.0:0.0:0.0	.	7	Q8NGD1	OR4N2_HUMAN	R	7	ENSP00000451462:T7R;ENSP00000452022:T7R;ENSP00000319601:T7R	ENSP00000319601:T7R	T	+	2	0	OR4N2	19365467	0.058000	0.20735	0.339000	0.25562	0.050000	0.14768	2.603000	0.46266	2.431000	0.82371	0.591000	0.81541	ACA	C|0.916;G|0.084	0.084	strong		0.388	OR4N2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409821.2		
GAA	2548	hgsc.bcm.edu	37	17	78081661	78081661	+	Silent	SNP	A	A	T	rs1800303	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:78081661A>T	ENST00000302262.3	+	5	1140	c.921A>T	c.(919-921)gcA>gcT	p.A307A	GAA_ENST00000390015.3_Silent_p.A307A	NM_000152.3	NP_000143.2	P10253	LYAG_HUMAN	glucosidase, alpha; acid	307					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)			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)	GCGGGTCGGCACACGGGGTGT	0.682													A|||	552	0.110224	0.2716	0.0576	5008	,	,		12980	0.0		0.0736	False		,,,				2504	0.0808				p.A307A		Atlas-SNP	.											GAA,NS,NS,+1,1	GAA	66	1	0			c.A921T						PASS	.	A	,,	959,3443		118,723,1360	31.0	33.0	32.0		921,921,921	-10.6	0.0	17	dbSNP_89	32	618,7980		28,562,3709	no	coding-synonymous,coding-synonymous,coding-synonymous	GAA	NM_000152.3,NM_001079803.1,NM_001079804.1	,,	146,1285,5069	TT,TA,AA		7.1877,21.7856,12.1308	,,	307/953,307/953,307/953	78081661	1577,11423	2201	4299	6500	SO:0001819	synonymous_variant	2548	exon6			GTCGGCACACGGG		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.921A>T	17.37:g.78081661A>T		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	79	38	0.481013	NM_001079803	Q09GN4|Q14351|Q16302|Q8IWE7	Silent	SNP	ENST00000302262.3	37	CCDS32760.1																																																																																			A|0.890;T|0.110	0.110	strong		0.682	GAA-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437441.1		
PRICKLE1	144165	hgsc.bcm.edu	37	12	42854205	42854205	+	Silent	SNP	A	A	G	rs3747562	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:42854205A>G	ENST00000455697.1	-	8	2187	c.1902T>C	c.(1900-1902)tcT>tcC	p.S634S	PRICKLE1_ENST00000552240.1_Silent_p.S634S|PRICKLE1_ENST00000345127.3_Silent_p.S634S|RP11-328C8.4_ENST00000547824.1_RNA|PRICKLE1_ENST00000548696.1_Silent_p.S634S|PRICKLE1_ENST00000445766.2_Silent_p.S634S	NM_001144882.1|NM_001144883.1	NP_001138354.1|NP_001138355.1	Q96MT3	PRIC1_HUMAN	prickle homolog 1 (Drosophila)	634					negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cardiac muscle cell myoblast differentiation (GO:2000691)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube closure (GO:0001843)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein ubiquitination (GO:0031398)|protein import into nucleus (GO:0006606)	cytosol (GO:0005829)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(4)|kidney(2)|large_intestine(12)|liver(1)|lung(13)|ovary(3)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	47	all_cancers(12;4.25e-05)|Breast(8;0.176)			GBM - Glioblastoma multiforme(48;0.2)		TGACATCATCAGAAAACTTGA	0.483													G|||	2150	0.429313	0.472	0.4841	5008	,	,		18126	0.4137		0.4284	False		,,,				2504	0.3497				p.S634S		Atlas-SNP	.											.	PRICKLE1	105	.	0			c.T1902C						PASS	.	G	,,,	2021,2385		487,1047,669	98.0	93.0	95.0		1902,1902,1902,1902	-11.1	0.0	12	dbSNP_107	95	3640,4960		824,1992,1484	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PRICKLE1	NM_001144881.1,NM_001144882.1,NM_001144883.1,NM_153026.2	,,,	1311,3039,2153	GG,GA,AA		42.3256,45.8693,43.5261	,,,	634/832,634/832,634/832,634/832	42854205	5661,7345	2203	4300	6503	SO:0001819	synonymous_variant	144165	exon8			ATCATCAGAAAAC	AK056499	CCDS8742.1	12p11-q12	2010-08-13	2006-09-12			ENSG00000139174			17019	protein-coding gene	gene with protein product		608500	"""prickle-like 1 (Drosophila)"""			12525887, 18976727	Standard	NM_153026		Approved	FLJ31937, EPM1B	uc010skv.2	Q96MT3		ENST00000455697.1:c.1902T>C	12.37:g.42854205A>G		Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	139	62	0.446043	NM_001144882	Q14C83|Q71QF8|Q96N00	Silent	SNP	ENST00000455697.1	37	CCDS8742.1																																																																																			A|0.550;G|0.450	0.450	strong		0.483	PRICKLE1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404069.1		
TET1	80312	hgsc.bcm.edu	37	10	70332862	70332862	+	Missense_Mutation	SNP	C	C	T	rs12221107	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:70332862C>T	ENST00000373644.4	+	2	976	c.767C>T	c.(766-768)gCa>gTa	p.A256V		NM_030625.2	NP_085128.2	Q8NFU7	TET1_HUMAN	tet methylcytosine dioxygenase 1	256			A -> V (in dbSNP:rs12221107).		chromatin modification (GO:0016568)|DNA demethylation (GO:0080111)|inner cell mass cell differentiation (GO:0001826)|negative regulation of methylation-dependent chromatin silencing (GO:0090310)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein O-linked glycosylation (GO:0006493)|regulation of DNA methylation (GO:0044030)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	iron ion binding (GO:0005506)|methylcytosine dioxygenase activity (GO:0070579)|structure-specific DNA binding (GO:0043566)|zinc ion binding (GO:0008270)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(2)|ovary(5)|prostate(1)|upper_aerodigestive_tract(2)	21						CCCCAAAGAGCAACCCCCAAA	0.448													C|||	548	0.109425	0.0038	0.0807	5008	,	,		20588	0.1498		0.1024	False		,,,				2504	0.2382				p.A256V		Atlas-SNP	.											.	TET1	255	.	0			c.C767T						PASS	.	C	VAL/ALA	77,4329	68.7+/-106.4	1,75,2127	65.0	65.0	65.0		767	4.6	0.2	10	dbSNP_120	65	660,7940	167.4+/-219.2	27,606,3667	yes	missense	TET1	NM_030625.2	64	28,681,5794	TT,TC,CC		7.6744,1.7476,5.6666	benign	256/2137	70332862	737,12269	2203	4300	6503	SO:0001583	missense	80312	exon2			AAAGAGCAACCCC	AF430147	CCDS7281.1	10q21	2014-02-18	2011-09-30	2008-03-12	ENSG00000138336	ENSG00000138336			29484	protein-coding gene	gene with protein product	"""leukemia-associated protein with a CXXC domain"", ""ten-eleven translocation-1"""	607790	"""CXXC zinc finger 6"", ""tet oncogene 1"""	CXXC6		12124344, 12646957	Standard	NM_030625		Approved	LCX, KIAA1676, bA119F7.1	uc001jok.4	Q8NFU7	OTTHUMG00000018359	ENST00000373644.4:c.767C>T	10.37:g.70332862C>T	ENSP00000362748:p.Ala256Val	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	52	23	0.442308	NM_030625	Q5VUP7|Q7Z6B6|Q8TCR1|Q9C0I7	Missense_Mutation	SNP	ENST00000373644.4	37	CCDS7281.1	213	0.09752747252747253	4	0.008130081300813009	33	0.09116022099447514	98	0.17132867132867133	78	0.10290237467018469	C	12.95	2.090658	0.36855	0.017476	0.076744	ENSG00000138336	ENST00000373644	T	0.08546	3.08	5.53	4.63	0.57726	.	1.023250	0.07810	N	0.957964	T	0.00039	0.0001	L	0.27053	0.805	0.80722	P	0.0	B	0.17465	0.022	B	0.14578	0.011	T	0.29181	-1.0020	9	0.51188	T	0.08	.	10.1526	0.42803	0.0:0.908:0.0:0.092	rs12221107;rs52822436;rs57641106;rs12221107	256	Q8NFU7	TET1_HUMAN	V	256	ENSP00000362748:A256V	ENSP00000362748:A256V	A	+	2	0	TET1	70002868	0.000000	0.05858	0.246000	0.24233	0.966000	0.64601	0.335000	0.19806	1.329000	0.45376	0.563000	0.77884	GCA	C|0.925;T|0.075	0.075	strong		0.448	TET1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048354.1	NM_030625	
MUC17	140453	hgsc.bcm.edu	37	7	100681453	100681453	+	Silent	SNP	C	C	T	rs77440980	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:100681453C>T	ENST00000306151.4	+	3	6820	c.6756C>T	c.(6754-6756)acC>acT	p.T2252T		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	2252	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)					CACCTGTGACCACTTCTACTG	0.483													C|||	164	0.0327476	0.084	0.0072	5008	,	,		26690	0.0278		0.0159	False		,,,				2504	0.0041				p.T2252T		Atlas-SNP	.											MUC17,NS,carcinoma,+2,1	MUC17	804	1	0			c.C6756T						PASS	.	C		373,4033	187.4+/-214.1	13,347,1843	288.0	290.0	289.0		6756	-1.0	0.0	7	dbSNP_131	289	93,8501	52.3+/-112.8	0,93,4204	no	coding-synonymous	MUC17	NM_001040105.1		13,440,6047	TT,TC,CC		1.0822,8.4657,3.5846		2252/4494	100681453	466,12534	2203	4297	6500	SO:0001819	synonymous_variant	140453	exon3			TGTGACCACTTCT	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.6756C>T	7.37:g.100681453C>T		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	72	39	0.541667	NM_001040105	O14761|Q685J2|Q8TDH7	Silent	SNP	ENST00000306151.4	37	CCDS34711.1																																																																																			C|0.963;T|0.037	0.037	strong		0.483	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
MUC4	4585	hgsc.bcm.edu	37	3	195510827	195510827	+	Missense_Mutation	SNP	C	C	T	rs413807	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195510827C>T	ENST00000463781.3	-	2	8083	c.7624G>A	c.(7624-7626)Gcc>Acc	p.A2542T	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.A2542T	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		AGAGAGGTGGCGTGACGTGTG	0.582													.|||	177	0.0353435	0.1293	0.0058	5008	,	,		17991	0.001		0.0	False		,,,				2504	0.001				p.A2542T		Atlas-SNP	.											.	MUC4	1505	.	0			c.G7624A						PASS	.						179.0	144.0	154.0					3																	195510827		652	1591	2243	SO:0001583	missense	4585	exon2			AGGTGGCGTGACG	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.7624G>A	3.37:g.195510827C>T	ENSP00000417498:p.Ala2542Thr	Somatic	245	0	0		WXS	Illumina HiSeq	Phase_I	339	221	0.651917	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	-	9.405	1.079094	0.20227	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.33216	1.43;1.42	.	.	.	.	.	.	.	.	T	0.09113	0.0225	N	0.08118	0	0.52099	P	5.999999999994898E-5	P	0.52463	0.953	B	0.28991	0.097	T	0.23404	-1.0189	6	.	.	.	.	4.4363	0.11552	0.0:0.666:0.0:0.334	rs413807	2542	E7ESK3	.	T	2542	ENSP00000417498:A2542T;ENSP00000420243:A2542T	.	A	-	1	0	MUC4	196995222	0.040000	0.19996	0.000000	0.03702	0.000000	0.00434	-1.533000	0.02215	-0.000000	0.14550	0.000000	0.15137	GCC	C|0.500;T|0.500	0.500	weak		0.582	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
CNGA3	1261	hgsc.bcm.edu	37	2	99013274	99013274	+	Silent	SNP	C	C	T	rs104893617	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:99013274C>T	ENST00000272602.2	+	7	1680	c.1641C>T	c.(1639-1641)ttC>ttT	p.F547F	CNGA3_ENST00000393504.1_Silent_p.F547F|CNGA3_ENST00000436404.2_Silent_p.F529F|CNGA3_ENST00000409937.1_Silent_p.F551F			Q16281	CNGA3_HUMAN	cyclic nucleotide gated channel alpha 3	547			F -> L (in ACHM2; does not reveal any detectable calcium influx upon agonist application at 37 degrees Celsius; the channel function could be restored by incubating the transfected cells at 27 degrees Celsius; the dose-response relationship for cGMP-activation is shifted toward a lower cGMP concentration; a substantial reduction of macroscopic cGMP maximum current to only one-third of the mean value for wild-type CNGA3 + CNGB3 is observed for the mutant CNGA3 + CNGB3; is in large part located in the cell membrane at 37 and 27 degrees Celsius). {ECO:0000269|PubMed:11536077, ECO:0000269|PubMed:14757870, ECO:0000269|PubMed:18521937, ECO:0000269|PubMed:9662398}.		cation transport (GO:0006812)|phototransduction, visible light (GO:0007603)|potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|response to cAMP (GO:0051591)|response to corticosteroid (GO:0031960)|response to magnesium ion (GO:0032026)|retinal cone cell development (GO:0046549)|signal transduction (GO:0007165)|transport (GO:0006810)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|perikaryon (GO:0043204)|photoreceptor outer segment membrane (GO:0042622)|transmembrane transporter complex (GO:1902495)	cGMP binding (GO:0030553)|intracellular cAMP activated cation channel activity (GO:0005222)|intracellular cGMP activated cation channel activity (GO:0005223)|ligand-gated ion channel activity (GO:0015276)|voltage-gated potassium channel activity (GO:0005249)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(10)|lung(17)|ovary(5)|prostate(3)|skin(4)|upper_aerodigestive_tract(3)	49						GCAGCTACTTCGGGGAGATCA	0.562													C|||	2	0.000399361	0.0008	0.0	5008	,	,		20469	0.0		0.001	False		,,,				2504	0.0				p.F547F		Atlas-SNP	.											CNGA3,NS,carcinoma,0,1	CNGA3	118	1	0			c.C1641T	GRCh37	CM980380	CNGA3	M	rs104893617	scavenged	.	C	,	2,4404	4.2+/-10.8	0,2,2201	136.0	132.0	133.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1587,1641	1.9	1.0	2	dbSNP_132	133	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	CNGA3	NM_001079878.1,NM_001298.2	,	0,2,6501	TT,TC,CC		0.0,0.0454,0.0154	,	529/677,547/695	99013274	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	1261	exon8			CTACTTCGGGGAG	S76069	CCDS2034.1, CCDS42719.1	2q11.2	2013-01-08			ENSG00000144191	ENSG00000144191		"""Voltage-gated ion channels / Cyclic nucleotide-regulated channels"""	2150	protein-coding gene	gene with protein product		600053		CNCG3, ACHM2		7532814, 9517456, 16382102	Standard	NM_001298		Approved	CCNC1, CCNCa, CNG3	uc002syt.3	Q16281	OTTHUMG00000130561	ENST00000272602.2:c.1641C>T	2.37:g.99013274C>T		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	87	2	0.0229885	NM_001298	E9PF93|Q4VAP7|Q53RD2|Q6ZNA7|Q9UP64	Silent	SNP	ENST00000272602.2	37	CCDS2034.1																																																																																			A|0.000;C|0.999;T|0.000	0.000	strong		0.562	CNGA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252986.1	NM_001298	
PSORS1C1	170679	hgsc.bcm.edu	37	6	31084170	31084170	+	Intron	SNP	A	A	C	rs1042127	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:31084170A>C	ENST00000259881.9	+	1	61				PSORS1C1_ENST00000467107.1_3'UTR|CDSN_ENST00000376288.2_Missense_Mutation_p.S408A	NM_014068.2	NP_054787.2	Q9UIG5	PS1C1_HUMAN	psoriasis susceptibility 1 candidate 1											kidney(1)|ovary(2)|prostate(1)|skin(1)	5						GGTAAACCGGAGCTGCTGGAA	0.642													A|||	981	0.195887	0.0893	0.2104	5008	,	,		16545	0.2054		0.1968	False		,,,				2504	0.319				p.S408A		Atlas-SNP	.											.	CDSN	48	.	0			c.T1222G						PASS	.	A	ALA/SER,	505,3901		22,461,1720	39.0	45.0	43.0		1222,	2.8	0.3	6	dbSNP_86	43	1566,7034		146,1274,2880	yes	missense,intron	CDSN,PSORS1C1	NM_001264.4,NM_014068.2	99,	168,1735,4600	CC,CA,AA		18.2093,11.4616,15.9234	possibly-damaging,	408/530,	31084170	2071,10935	2203	4300	6503	SO:0001627	intron_variant	1041	exon2			AACCGGAGCTGCT	AB031479	CCDS34390.1	6p21.3	2014-01-28	2003-06-12		ENSG00000204540	ENSG00000204540			17202	protein-coding gene	gene with protein product		613525	"""chromosome 6 open reading frame 16"""	C6orf16			Standard	NM_014068		Approved	SEEK1	uc003nsl.2	Q9UIG5	OTTHUMG00000031077	ENST00000259881.9:c.-229+1502A>C	6.37:g.31084170A>C		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	34	13	0.382353	NM_001264	B0V083|Q5ST21|Q86WJ8|Q86WJ9|Q96QC3	Missense_Mutation	SNP	ENST00000259881.9	37	CCDS34390.1	349	0.15979853479853479	44	0.08943089430894309	79	0.21823204419889503	90	0.15734265734265734	136	0.17941952506596306	A	14.96	2.692342	0.48202	0.114616	0.182093	ENSG00000204539	ENST00000376288	T	0.07444	3.19	3.92	2.75	0.32379	.	0.370638	0.19960	N	0.102238	T	0.03564	0.0102	L	0.34521	1.04	0.80722	P	0.0	P	0.49783	0.928	P	0.50049	0.629	T	0.43245	-0.9403	9	0.33940	T	0.23	.	5.8931	0.18925	0.8765:0.0:0.1235:0.0	rs1042127;rs3181593;rs9263655;rs17840015;rs60353924;rs1042127	408	Q15517	CDSN_HUMAN	A	408	ENSP00000365465:S408A	ENSP00000365465:S408A	S	-	1	0	CDSN	31192149	0.090000	0.21635	0.258000	0.24420	0.822000	0.46500	1.327000	0.33746	0.667000	0.31107	0.386000	0.25728	TCC	A|0.846;C|0.154	0.154	strong		0.642	PSORS1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076110.3	NM_014068	
CHORDC1	26973	hgsc.bcm.edu	37	11	89935586	89935586	+	Missense_Mutation	SNP	G	G	T	rs1045861	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:89935586G>T	ENST00000320585.6	-	11	1395	c.986C>A	c.(985-987)gCc>gAc	p.A329D	CHORDC1_ENST00000457199.2_Missense_Mutation_p.A310D|CHORDC1_ENST00000529987.1_Missense_Mutation_p.A141D|CHORDC1_ENST00000529726.1_Missense_Mutation_p.A141D	NM_012124.2	NP_036256.2	Q9UHD1	CHRD1_HUMAN	cysteine and histidine-rich domain (CHORD) containing 1	329			A -> D (in dbSNP:rs1045861). {ECO:0000269|PubMed:10571178, ECO:0000269|PubMed:14702039, ECO:0000269|Ref.2, ECO:0000269|Ref.5}.		chaperone-mediated protein folding (GO:0061077)|negative regulation of Rho-dependent protein serine/threonine kinase activity (GO:2000299)|regulation of cellular response to heat (GO:1900034)|regulation of centrosome duplication (GO:0010824)|response to stress (GO:0006950)		Hsp90 protein binding (GO:0051879)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(2)|liver(1)|lung(6)	11		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.00915)				ATCTGTTGTGGCATCTTTTTG	0.403													T|||	3057	0.610423	0.3714	0.6542	5008	,	,		19227	0.6756		0.6958	False		,,,				2504	0.7474				p.A329D		Atlas-SNP	.											.	CHORDC1	34	.	0			c.C986A						PASS	.	T	ASP/ALA,ASP/ALA	1817,2583	637.6+/-396.8	384,1049,767	126.0	105.0	112.0		929,986	4.1	0.7	11	dbSNP_86	112	5977,2619	422.7+/-354.1	2062,1853,383	yes	missense,missense	CHORDC1	NM_001144073.1,NM_012124.2	126,126	2446,2902,1150	TT,TG,GG		30.4677,41.2955,40.0277	benign,benign	310/314,329/333	89935586	7794,5202	2200	4298	6498	SO:0001583	missense	26973	exon11			GTTGTGGCATCTT	AF192466	CCDS8289.1, CCDS44705.1	11q14.3	2011-01-25	2011-01-25		ENSG00000110172	ENSG00000110172			14525	protein-coding gene	gene with protein product		604353	"""cysteine and histidine-rich domain (CHORD)-containing, zinc-binding protein 1"", ""cysteine and histidine-rich domain (CHORD)-containing 1"""			10571178	Standard	NM_012124		Approved	CHP1	uc001pdg.2	Q9UHD1	OTTHUMG00000167305	ENST00000320585.6:c.986C>A	11.37:g.89935586G>T	ENSP00000319255:p.Ala329Asp	Somatic	210	1	0.0047619		WXS	Illumina HiSeq	Phase_I	154	152	0.987013	NM_012124	B2R6P8|Q6IN49|Q8WVL9|Q9H3D6	Missense_Mutation	SNP	ENST00000320585.6	37	CCDS8289.1	1385	0.6341575091575091	203	0.41260162601626016	247	0.6823204419889503	411	0.7185314685314685	524	0.6912928759894459	T	0.115	-1.133751	0.01756	0.412955	0.695323	ENSG00000110172	ENST00000320585;ENST00000529987;ENST00000457199;ENST00000529726	T;T;T;T	0.43294	0.96;0.95;0.95;0.95	5.24	4.08	0.47627	HSP20-like chaperone (1);	1.095060	0.06902	N	0.806057	T	0.00012	0.0000	N	0.02011	-0.69	0.09310	P	0.99999999876564	B;B	0.13145	0.007;0.0	B;B	0.06405	0.002;0.0	T	0.44907	-0.9297	8	.	.	.	0.1129	11.064	0.47964	0.0:0.0:0.2982:0.7018	rs1045861;rs3185831;rs52803502;rs1045861	310;329	Q9UHD1-2;Q9UHD1	.;CHRD1_HUMAN	D	329;141;310;141	ENSP00000319255:A329D;ENSP00000433719:A141D;ENSP00000401080:A310D;ENSP00000436632:A141D	.	A	-	2	0	CHORDC1	89575234	0.036000	0.19791	0.718000	0.30602	0.172000	0.22775	1.500000	0.35682	0.292000	0.22492	-0.262000	0.10625	GCC	G|0.384;T|0.616	0.616	strong		0.403	CHORDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394111.1	NM_012124	
TTLL11	158135	hgsc.bcm.edu	37	9	124855211	124855211	+	Missense_Mutation	SNP	C	C	T	rs61742319	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:124855211C>T	ENST00000373776.3	-	1	674	c.487G>A	c.(487-489)Gct>Act	p.A163T	TTLL11_ENST00000321582.5_Missense_Mutation_p.A163T|TTLL11_ENST00000474723.1_5'UTR	NM_194252.2	NP_919228.2	Q8NHH1	TTL11_HUMAN	tubulin tyrosine ligase-like family, member 11	163					cellular protein modification process (GO:0006464)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	ligase activity (GO:0016874)			breast(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(5)|prostate(3)|skin(1)	18						CCCTCCTCAGCCGCACTGGGC	0.766													C|||	1236	0.246805	0.3691	0.3271	5008	,	,		11025	0.0645		0.3012	False		,,,				2504	0.1564				p.A163T		Atlas-SNP	.											.	TTLL11	67	.	0			c.G487A						PASS	.	C	THR/ALA,THR/ALA	1219,2527		207,805,861	5.0	6.0	6.0		487,487	-3.5	0.8	9	dbSNP_129	6	1866,5634		260,1346,2144	no	missense,missense	TTLL11	NM_001139442.1,NM_194252.2	58,58	467,2151,3005	TT,TC,CC		24.88,32.5414,27.432	benign,benign	163/801,163/539	124855211	3085,8161	1873	3750	5623	SO:0001583	missense	158135	exon1			CCTCAGCCGCACT	AF521886	CCDS6834.2, CCDS48012.1	9q34.11	2013-02-14	2005-07-28	2005-07-28	ENSG00000175764	ENSG00000175764		"""Tubulin tyrosine ligase-like family"""	18113	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 20"""	C9orf20		15890843	Standard	NM_001139442		Approved	bA244O19.1	uc011lyl.2	Q8NHH1	OTTHUMG00000020597	ENST00000373776.3:c.487G>A	9.37:g.124855211C>T	ENSP00000362881:p.Ala163Thr	Somatic	7	0	0		WXS	Illumina HiSeq	Phase_I	13	12	0.923077	NM_001139442		Missense_Mutation	SNP	ENST00000373776.3	37	CCDS6834.2	551	0.2522893772893773	184	0.37398373983739835	110	0.30386740331491713	29	0.050699300699300696	228	0.3007915567282322	C	7.277	0.608368	0.14002	0.325414	0.2488	ENSG00000175764	ENST00000321582;ENST00000373776	T;T	0.06294	3.47;3.32	4.73	-3.49	0.04724	.	2587.460000	0.00357	U	0.000031	T	0.00012	0.0000	N	0.14661	0.345	0.58432	P	1.0000000000287557E-6	B;B	0.11235	0.004;0.001	B;B	0.10450	0.005;0.002	T	0.48747	-0.9008	8	.	.	.	.	5.0877	0.14691	0.0941:0.3934:0.3609:0.1515	.	163;163	F8W6M1;Q8NHH1	.;TTL11_HUMAN	T	163	ENSP00000321346:A163T;ENSP00000362881:A163T	.	A	-	1	0	TTLL11	123895032	0.133000	0.22466	0.781000	0.31783	0.146000	0.21551	0.583000	0.23849	-0.487000	0.06735	-0.502000	0.04539	GCT	C|0.742;T|0.258	0.258	strong		0.766	TTLL11-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000053907.1	XM_088486	
FUK	197258	hgsc.bcm.edu	37	16	70506907	70506907	+	Silent	SNP	T	T	C	rs7192865	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:70506907T>C	ENST00000288078.6	+	15	1660	c.1428T>C	c.(1426-1428)ccT>ccC	p.P476P	FUK_ENST00000378912.2_Silent_p.P508P|FUK_ENST00000571514.1_5'UTR	NM_145059.2	NP_659496.2	Q8N0W3	FUK_HUMAN	fucokinase	476						cytoplasm (GO:0005737)	ATP binding (GO:0005524)|fucokinase activity (GO:0050201)	p.P476P(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(11)|ovary(2)|prostate(2)	23		Ovarian(137;0.0694)				TGTGGGACCCTGAGACGCTGC	0.647													C|||	2895	0.578075	0.7821	0.5764	5008	,	,		15962	0.6607		0.498	False		,,,				2504	0.3006				p.P476P		Atlas-SNP	.											FUK,NS,carcinoma,0,1	FUK	72	1	1	Substitution - coding silent(1)	prostate(1)	c.T1428C						PASS	.	C		3008,986		1159,690,148	11.0	16.0	15.0		1428	-2.7	0.9	16	dbSNP_116	15	4055,4293		1019,2017,1138	no	coding-synonymous	FUK	NM_145059.2		2178,2707,1286	CC,CT,TT		48.5745,24.687,42.7726		476/1085	70506907	7063,5279	1997	4174	6171	SO:0001819	synonymous_variant	197258	exon15			GGACCCTGAGACG		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.1428T>C	16.37:g.70506907T>C		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	122	78	0.639344	NM_145059	Q5PSM3|Q5XKL6|Q6ZRA0|Q96MT9	Silent	SNP	ENST00000288078.6	37	CCDS10891.2																																																																																			T|0.402;C|0.598	0.598	strong		0.647	FUK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157291.2	NM_145059	
MYH4	4622	hgsc.bcm.edu	37	17	10363410	10363410	+	Silent	SNP	A	A	G	rs3744561	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:10363410A>G	ENST00000255381.2	-	14	1385	c.1275T>C	c.(1273-1275)aaT>aaC	p.N425N	CTC-297N7.11_ENST00000587182.2_RNA|RP11-799N11.1_ENST00000399342.2_RNA|RP11-799N11.1_ENST00000581304.1_RNA	NM_017533.2	NP_060003.2	Q9Y623	MYH4_HUMAN	myosin, heavy chain 4, skeletal muscle	425	Myosin motor.				actin filament-based movement (GO:0030048)|ATP catabolic process (GO:0006200)|membrane organization (GO:0061024)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|response to activity (GO:0014823)	muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin filament (GO:0032982)|sarcomere (GO:0030017)	ATP binding (GO:0005524)|double-stranded RNA binding (GO:0003725)|microfilament motor activity (GO:0000146)			NS(4)|breast(8)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(13)|lung(72)|ovary(10)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	149						CACCCACTGCATTGTACACCT	0.448													A|||	2682	0.535543	0.3442	0.5245	5008	,	,		19217	0.8601		0.3708	False		,,,				2504	0.637				p.N425N		Atlas-SNP	.											.	MYH4	349	.	0			c.T1275C						PASS	.	A		1585,2821	494.3+/-362.9	281,1023,899	182.0	169.0	174.0		1275	-2.7	0.0	17	dbSNP_107	174	3590,5010	520.1+/-379.6	761,2068,1471	no	coding-synonymous	MYH4	NM_017533.2		1042,3091,2370	GG,GA,AA		41.7442,35.9737,39.7893		425/1940	10363410	5175,7831	2203	4300	6503	SO:0001819	synonymous_variant	4622	exon14			CACTGCATTGTAC		CCDS11154.1	17p13.1	2013-09-19	2006-09-29		ENSG00000264424	ENSG00000264424		"""Myosins / Myosin superfamily : Class II"""	7574	protein-coding gene	gene with protein product		160742	"""myosin, heavy polypeptide 4, skeletal muscle"""			8518795	Standard	NM_017533		Approved	MYH2B, MyHC-2B, MyHC-IIb	uc002gmn.3	Q9Y623	OTTHUMG00000130365	ENST00000255381.2:c.1275T>C	17.37:g.10363410A>G		Somatic	205	1	0.00487805		WXS	Illumina HiSeq	Phase_I	159	79	0.496855	NM_017533		Silent	SNP	ENST00000255381.2	37	CCDS11154.1																																																																																			A|0.575;G|0.425	0.425	strong		0.448	MYH4-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252731.1	NM_017533	
MAG	4099	hgsc.bcm.edu	37	19	35786868	35786868	+	Silent	SNP	C	C	T	rs2301600	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:35786868C>T	ENST00000392213.3	+	4	558	c.399C>T	c.(397-399)agC>agT	p.S133S	MAG_ENST00000537831.2_Silent_p.S108S|MAG_ENST00000361922.4_Silent_p.S133S|MAG_ENST00000597035.1_Intron	NM_002361.3	NP_002352.1	P20916	MAG_HUMAN	myelin associated glycoprotein	133					blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|leukocyte migration (GO:0050900)|negative regulation of axonogenesis (GO:0050771)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of axonogenesis (GO:0050770)|substantia nigra development (GO:0021762)	integral component of membrane (GO:0016021)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|Schmidt-Lanterman incisure (GO:0043220)	carbohydrate binding (GO:0030246)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(3)|large_intestine(10)|lung(11)|skin(2)|upper_aerodigestive_tract(2)	34	all_lung(56;2.37e-08)|Lung NSC(56;3.66e-08)|Esophageal squamous(110;0.162)	Renal(1328;0.242)	Epithelial(14;3.14e-19)|OV - Ovarian serous cystadenocarcinoma(14;1.5e-18)|all cancers(14;1.5e-16)|LUSC - Lung squamous cell carcinoma(66;0.0417)			CAGAGCACAGCGTCCTGGATA	0.662													C|||	1450	0.289537	0.0998	0.3746	5008	,	,		17137	0.4226		0.2416	False		,,,				2504	0.3978				p.S133S		Atlas-SNP	.											.	MAG	172	.	0			c.C399T						PASS	.	C	,,	519,3887		28,463,1712	88.0	86.0	87.0		324,399,399	2.8	1.0	19	dbSNP_100	87	1857,6739		199,1459,2640	no	coding-synonymous,coding-synonymous,coding-synonymous	MAG	NM_001199216.1,NM_002361.3,NM_080600.2	,,	227,1922,4352	TT,TC,CC		21.6031,11.7794,18.2741	,,	108/602,133/627,133/583	35786868	2376,10626	2203	4298	6501	SO:0001819	synonymous_variant	4099	exon4			GCACAGCGTCCTG	M29273	CCDS12455.1, CCDS12456.1, CCDS56090.1	19q13.1	2013-01-29			ENSG00000105695	ENSG00000105695		"""Sialic acid binding Ig-like lectins"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6783	protein-coding gene	gene with protein product	"""sialic acid binding Ig-like lectin 4A"""	159460		GMA		2476987, 8432525	Standard	NM_080600		Approved	SIGLEC4A, SIGLEC-4A, S-MAG	uc002nyy.2	P20916		ENST00000392213.3:c.399C>T	19.37:g.35786868C>T		Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	39	24	0.615385	NM_080600	B7Z2E5|F5GYC0|Q567S4	Silent	SNP	ENST00000392213.3	37	CCDS12455.1																																																																																			C|0.780;T|0.220	0.220	strong		0.662	MAG-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000466071.1	NM_080600	
ZFP36L1	677	hgsc.bcm.edu	37	14	69256848	69256848	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:69256848C>A	ENST00000439696.2	-	2	720	c.419G>T	c.(418-420)gGc>gTc	p.G140V	ZFP36L1_ENST00000555997.1_3'UTR|ZFP36L1_ENST00000336440.3_Missense_Mutation_p.G140V	NM_001244701.1|NM_004926.3	NP_001231630.1|NP_004917.2	Q07352	TISB_HUMAN	ZFP36 ring finger protein-like 1	140					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)		CTCGTGGATGCCGTGTGCGAA	0.647											OREG0022753	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.G209V		Atlas-SNP	.											.	ZFP36L1	47	.	0			c.G626T						PASS	.						96.0	91.0	93.0					14																	69256848		2203	4300	6503	SO:0001583	missense	677	exon3			TGGATGCCGTGTG	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.419G>T	14.37:g.69256848C>A	ENSP00000388402:p.Gly140Val	Somatic	158	0	0	1113	WXS	Illumina HiSeq	Phase_I	155	27	0.174194	NM_001244701	Q13851	Missense_Mutation	SNP	ENST00000439696.2	37	CCDS9791.1	.	.	.	.	.	.	.	.	.	.	C	21.1	4.090153	0.76756	.	.	ENSG00000185650	ENST00000439696;ENST00000336440;ENST00000435246;ENST00000557086;ENST00000557022	T;T;T;T	0.51071	0.72;0.72;0.72;0.72	4.69	4.69	0.59074	Zinc finger, CCCH-type (3);	0.000000	0.85682	D	0.000000	T	0.79209	0.4407	H	0.96460	3.825	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.86683	0.1918	10	0.87932	D	0	0.0068	17.8126	0.88620	0.0:1.0:0.0:0.0	.	140	Q07352	TISB_HUMAN	V	140;140;123;146;118	ENSP00000388402:G140V;ENSP00000337386:G140V;ENSP00000450784:G146V;ENSP00000450600:G118V	ENSP00000337386:G140V	G	-	2	0	ZFP36L1	68326601	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.563000	0.82314	2.423000	0.82170	0.585000	0.79938	GGC	.	.	none		0.647	ZFP36L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413227.1		
PKHD1L1	93035	hgsc.bcm.edu	37	8	110420429	110420429	+	Silent	SNP	A	A	G	rs13252234	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:110420429A>G	ENST00000378402.5	+	18	2069	c.1965A>G	c.(1963-1965)gaA>gaG	p.E655E		NM_177531.4	NP_803875.2	Q86WI1	PKHL1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1	655					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)			GGTCATCAGAAGCTGAAGTAC	0.443										HNSCC(38;0.096)			G|||	1573	0.314097	0.1551	0.4741	5008	,	,		15357	0.3929		0.3111	False		,,,				2504	0.3374				p.E655E		Atlas-SNP	.											.	PKHD1L1	522	.	0			c.A1965G						PASS	.	G		736,3176		76,584,1296	107.0	105.0	105.0		1965	4.8	1.0	8	dbSNP_121	105	2644,5672		428,1788,1942	no	coding-synonymous	PKHD1L1	NM_177531.4		504,2372,3238	GG,GA,AA		31.7941,18.8139,27.6415		655/4244	110420429	3380,8848	1956	4158	6114	SO:0001819	synonymous_variant	93035	exon18			ATCAGAAGCTGAA	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.1965A>G	8.37:g.110420429A>G		Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	88	70	0.795455	NM_177531	Q567P2|Q9UF27	Silent	SNP	ENST00000378402.5	37	CCDS47911.1																																																																																			A|0.689;G|0.311	0.311	strong		0.443	PKHD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381017.1	NM_177531	
NPY4R	5540	hgsc.bcm.edu	37	10	47087371	47087371	+	Silent	SNP	G	G	A	rs1048156	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:47087371G>A	ENST00000395716.1	+	2	673	c.588G>A	c.(586-588)gcG>gcA	p.A196A	NPY4R_ENST00000374312.1_Silent_p.A196A			P50391	NPY4R_HUMAN	neuropeptide Y receptor Y4	196					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)	p.A196A(1)									AGTTCCTGGCGGATAAGGTGG	0.582													g|||	639	0.127596	0.0318	0.1671	5008	,	,		42287	0.0109		0.2833	False		,,,				2504	0.1892				p.A196A		Atlas-SNP	.											PPYR1,mouth,carcinoma,0,1	PPYR1	54	1	1	Substitution - coding silent(1)	upper_aerodigestive_tract(1)	c.G588A						PASS	.			267,4139		0,267,1936	190.0	159.0	169.0		588	-9.9	0.0	10	dbSNP_86	169	2052,6548		0,2052,2248	no	coding-synonymous	PPYR1	NM_005972.4		0,2319,4184	AA,AG,GG		23.8605,6.0599,17.8302		196/376	47087371	2319,10687	2203	4300	6503	SO:0001819	synonymous_variant	5540	exon3			CCTGGCGGATAAG		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.588G>A	10.37:g.47087371G>A		Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	133	34	0.255639	NM_005972	Q13456|Q5ISU3|Q5T2X9|Q6FH06	Silent	SNP	ENST00000395716.1	37	CCDS31193.1																																																																																			G|0.870;A|0.130	0.130	strong		0.582	NPY4R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047837.1		
UPK3A	7380	hgsc.bcm.edu	37	22	45691594	45691594	+	Silent	SNP	A	A	G	rs1057356	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:45691594A>G	ENST00000216211.4	+	6	890	c.858A>G	c.(856-858)caA>caG	p.Q286Q	UPK3A_ENST00000396082.2_Silent_p.Q165Q	NM_006953.3	NP_008884.1	O75631	UPK3A_HUMAN	uroplakin 3A	286					cell morphogenesis (GO:0000902)|epithelial cell differentiation (GO:0030855)|kidney development (GO:0001822)|potassium ion homeostasis (GO:0055075)|sodium ion homeostasis (GO:0055078)|urea transport (GO:0015840)|urinary bladder development (GO:0060157)|water transport (GO:0006833)	apical plasma membrane (GO:0016324)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				kidney(1)|large_intestine(1)|lung(2)|skin(1)	5		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0178)		GCAAGCTCCAAGACTGAGCCC	0.647													G|||	3146	0.628195	0.8843	0.4841	5008	,	,		17593	0.6508		0.3598	False		,,,				2504	0.637				p.Q286Q		Atlas-SNP	.											.	UPK3A	14	.	0			c.A858G						PASS	.	G	,	3524,882	328.3+/-300.5	1414,696,93	35.0	33.0	34.0		495,858	3.0	1.0	22	dbSNP_86	34	2982,5618	641.4+/-399.7	519,1944,1837	no	coding-synonymous,coding-synonymous	UPK3A	NM_001167574.1,NM_006953.3	,	1933,2640,1930	GG,GA,AA		34.6744,20.0182,49.9769	,	165/167,286/288	45691594	6506,6500	2203	4300	6503	SO:0001819	synonymous_variant	7380	exon6			GCTCCAAGACTGA	AB010637	CCDS14064.1, CCDS54539.1	22q13.31	2005-11-14	2003-07-29	2003-07-30	ENSG00000100373	ENSG00000100373			12580	protein-coding gene	gene with protein product		611559	"""uroplakin 3"""	UPK3		9818021	Standard	NM_006953		Approved		uc003bfy.3	O75631	OTTHUMG00000151339	ENST00000216211.4:c.858A>G	22.37:g.45691594A>G		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	44	16	0.363636	NM_006953	B0QY25|O60261|Q32N05|Q5TII6	Silent	SNP	ENST00000216211.4	37	CCDS14064.1																																																																																			A|0.474;G|0.526	0.526	strong		0.647	UPK3A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000322276.1	NM_006953	
MUC13	56667	hgsc.bcm.edu	37	3	124646594	124646594	+	Missense_Mutation	SNP	A	A	G	rs4679392	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:124646594A>G	ENST00000311075.3	-	2	334	c.296T>C	c.(295-297)aTa>aCa	p.I99T	MUC13_ENST00000497378.1_5'Flank	NM_033049.3	NP_149038	Q9H3R2	MUC13_HUMAN	mucin 13, cell surface associated	100	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)	apical plasma membrane (GO:0016324)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)	protein homodimerization activity (GO:0042803)	p.I99T(1)		breast(1)|central_nervous_system(1)|cervix(1)|kidney(1)|large_intestine(6)|lung(5)|prostate(1)|skin(1)|stomach(1)	18						AGCAGTAGGTATAGGAATTGT	0.423													G|||	1972	0.39377	0.4251	0.4496	5008	,	,		21391	0.2212		0.4294	False		,,,				2504	0.453				p.I99T		Atlas-SNP	.											MUC13,NS,carcinoma,0,1	MUC13	57	1	1	Substitution - Missense(1)	stomach(1)	c.T296C						scavenged	.	-	THR/ILE	1998,2408	617.4+/-393.0	452,1094,657	230.0	228.0	228.0		296	1.9	0.0	3	dbSNP_111	228	3636,4964	624.6+/-397.6	761,2114,1425	yes	missense	MUC13	NM_033049.3	89	1213,3208,2082	GG,GA,AA		42.2791,45.3473,43.3185	benign	99/512	124646594	5634,7372	2203	4300	6503	SO:0001583	missense	56667	exon2			GTAGGTATAGGAA	AF286113		3q21.2	2007-01-17	2006-03-14		ENSG00000173702	ENSG00000173702		"""Mucins"""	7511	protein-coding gene	gene with protein product		612181	"""down-regulated in colon cancer 1"", ""mucin 13, epithelial transmembrane"""	DRCC1		11278439	Standard	NM_033049		Approved		uc003ehq.2	Q9H3R2	OTTHUMG00000159484	ENST00000311075.3:c.296T>C	3.37:g.124646594A>G	ENSP00000312235:p.Ile99Thr	Somatic	243	2	0.00823045		WXS	Illumina HiSeq	Phase_I	187	92	0.491979	NM_033049	Q6UWD9|Q9NXT5	Missense_Mutation	SNP	ENST00000311075.3	37		823	0.3768315018315018	203	0.41260162601626016	170	0.4696132596685083	127	0.22202797202797203	323	0.4261213720316623	G	2.109	-0.404188	0.04832	0.453473	0.422791	ENSG00000173702	ENST00000311075	T	0.13089	2.62	2.84	1.89	0.25635	.	.	.	.	.	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	0.44050	-0.9353	8	0.16420	T	0.52	.	4.1598	0.10278	0.1411:0.2396:0.6193:0.0	rs4679392;rs16836253;rs60405159;rs4679392	99	Q9H3R2	MUC13_HUMAN	T	99	ENSP00000312235:I99T	ENSP00000312235:I99T	I	-	2	0	MUC13	126129284	0.001000	0.12720	0.000000	0.03702	0.007000	0.05969	0.394000	0.20834	0.230000	0.21059	-0.156000	0.13503	ATA	A|0.600;G|0.400	0.400	strong		0.423	MUC13-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000355714.1	NM_033049	
ME3	10873	hgsc.bcm.edu	37	11	86267633	86267633	+	Silent	SNP	C	C	T	rs17211115	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:86267633C>T	ENST00000393324.3	-	3	682	c.429G>A	c.(427-429)ctG>ctA	p.L143L	ME3_ENST00000323418.6_Silent_p.L81L|ME3_ENST00000359636.2_Silent_p.L143L|RP11-317J19.1_ENST00000524610.1_RNA|ME3_ENST00000543262.1_Silent_p.L143L	NM_001014811.1	NP_001014811.1	Q16798	MAON_HUMAN	malic enzyme 3, NADP(+)-dependent, mitochondrial	143					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)				GCTGACAGGCCAGCCCCACGG	0.582													C|||	1380	0.275559	0.1921	0.3487	5008	,	,		18963	0.5317		0.1799	False		,,,				2504	0.1708				p.L143L		Atlas-SNP	.											.	ME3	70	.	0			c.G429A						PASS	.	C	,,	819,3585	325.6+/-299.2	67,685,1450	75.0	60.0	65.0		429,429,429	5.1	1.0	11	dbSNP_123	65	1448,7150	276.9+/-292.6	110,1228,2961	no	coding-synonymous,coding-synonymous,coding-synonymous	ME3	NM_001014811.1,NM_001161586.1,NM_006680.2	,,	177,1913,4411	TT,TC,CC		16.8411,18.5967,17.4358	,,	143/605,143/605,143/605	86267633	2267,10735	2202	4299	6501	SO:0001819	synonymous_variant	10873	exon4			ACAGGCCAGCCCC	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.429G>A	11.37:g.86267633C>T		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	78	20	0.25641	NM_006680	B7Z6V0|Q8TBJ0	Silent	SNP	ENST00000393324.3	37	CCDS8277.1																																																																																			C|0.784;T|0.216	0.216	strong		0.582	ME3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393767.2		
AOAH	313	hgsc.bcm.edu	37	7	36763688	36763688	+	Silent	SNP	C	C	T	rs2228411	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:36763688C>T	ENST00000258749.5	-	1	465	c.66G>A	c.(64-66)tcG>tcA	p.S22S	AOAH_ENST00000431169.1_Silent_p.S22S|AOAH_ENST00000535891.1_Silent_p.S22S	NM_001637.3	NP_001628.1	P28039	AOAH_HUMAN	acyloxyacyl hydrolase (neutrophil)	22					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)	p.S22S(1)		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						CTGGAGAGGCCGAGGACTGAA	0.512													C|||	1894	0.378195	0.553	0.2867	5008	,	,		16715	0.4177		0.325	False		,,,				2504	0.2209				p.S22S		Atlas-SNP	.											AOAH,NS,carcinoma,0,2	AOAH	79	2	1	Substitution - coding silent(1)	stomach(1)	c.G66A						PASS	.	C	,,	2299,2107	602.4+/-389.9	610,1079,514	57.0	63.0	61.0		66,66,66	-2.8	0.0	7	dbSNP_98	61	3052,5548	469.0+/-367.5	554,1944,1802	no	coding-synonymous,coding-synonymous,coding-synonymous	AOAH	NM_001177506.1,NM_001177507.1,NM_001637.3	,,	1164,3023,2316	TT,TC,CC		35.4884,47.8212,41.1425	,,	22/689,22/544,22/576	36763688	5351,7655	2203	4300	6503	SO:0001819	synonymous_variant	313	exon1			AGAGGCCGAGGAC	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.66G>A	7.37:g.36763688C>T		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	33	31	0.939394	NM_001177507	A4D1Y5|B7Z490|Q53F13	Silent	SNP	ENST00000258749.5	37	CCDS5448.1																																																																																			C|0.590;T|0.410	0.410	strong		0.512	AOAH-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000219829.2	NM_001637	
IGSF9	57549	hgsc.bcm.edu	37	1	159904270	159904270	+	Silent	SNP	C	C	T	rs34790966	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:159904270C>T	ENST00000368094.1	-	8	1103	c.906G>A	c.(904-906)gtG>gtA	p.V302V	IGSF9_ENST00000361509.3_Silent_p.V302V|IGSF9_ENST00000493195.1_5'Flank	NM_001135050.1	NP_001128522.1	Q9P2J2	TUTLA_HUMAN	immunoglobulin superfamily, member 9	302	Ig-like 3.				dendrite development (GO:0016358)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synapse (GO:0045202)				central_nervous_system(2)|endometrium(8)|kidney(3)|large_intestine(13)|lung(17)|ovary(3)|prostate(4)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	56	all_hematologic(112;0.0597)	Breast(1374;0.000126)	BRCA - Breast invasive adenocarcinoma(70;0.111)			CATTGCTGGGCACACAGGTGT	0.662													C|||	161	0.0321486	0.0015	0.013	5008	,	,		16341	0.0139		0.0149	False		,,,				2504	0.1237				p.V302V		Atlas-SNP	.											.	IGSF9	123	.	0			c.G906A						PASS	.	C	,	18,4382		0,18,2182	46.0	39.0	41.0		906,906	0.4	1.0	1	dbSNP_126	41	161,8437		1,159,4139	no	coding-synonymous,coding-synonymous	IGSF9	NM_001135050.1,NM_020789.3	,	1,177,6321	TT,TC,CC		1.8725,0.4091,1.3771	,	302/1180,302/1164	159904270	179,12819	2200	4299	6499	SO:0001819	synonymous_variant	57549	exon8			GCTGGGCACACAG	AB037776	CCDS1190.1, CCDS44254.1	1q22-q23	2013-02-11			ENSG00000085552	ENSG00000085552		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	18132	protein-coding gene	gene with protein product		609738				11991715	Standard	NM_020789		Approved	KIAA1355, Nrt1, IGSF9A	uc001fur.2	Q9P2J2	OTTHUMG00000022794	ENST00000368094.1:c.906G>A	1.37:g.159904270C>T		Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	135	63	0.466667	NM_001135050		Silent	SNP	ENST00000368094.1	37	CCDS44254.1																																																																																			C|0.990;T|0.010	0.010	strong		0.662	IGSF9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059115.1	NM_020789	
FAM205A	259308	hgsc.bcm.edu	37	9	34726155	34726155	+	Missense_Mutation	SNP	C	C	T	rs76045500	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:34726155C>T	ENST00000378788.3	-	4	1121	c.1082G>A	c.(1081-1083)tGt>tAt	p.C361Y		NM_001141917.1	NP_001135389.1	Q6ZU69	F205A_HUMAN	family with sequence similarity 205, member A	361						integral component of membrane (GO:0016021)|nucleus (GO:0005634)				breast(1)|endometrium(2)|kidney(1)	4						CACACATGAACACCAGGTCTG	0.478													c|||	596	0.11901	0.2965	0.0735	5008	,	,		14160	0.0367		0.0328	False		,,,				2504	0.0849				p.C361Y		Atlas-SNP	.											.	FAM205A	45	.	0			c.G1082A						PASS	.						27.0	22.0	24.0					9																	34726155		681	1369	2050	SO:0001583	missense	259308	exon4			CATGAACACCAGG		CCDS55305.1	9p13.3	2014-05-16			ENSG00000205108	ENSG00000205108			41911	protein-coding gene	gene with protein product							Standard	NM_001141917		Approved	C9orf144B	uc011lor.2	Q6ZU69	OTTHUMG00000000448	ENST00000378788.3:c.1082G>A	9.37:g.34726155C>T	ENSP00000417711:p.Cys361Tyr	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	478	198	0.414226	NM_001141917	A8MVW7	Missense_Mutation	SNP	ENST00000378788.3	37	CCDS55305.1	147	0.0673076923076923	81	0.16463414634146342	24	0.06629834254143646	20	0.03496503496503497	22	0.029023746701846966	c	14.81	2.646414	0.47258	.	.	ENSG00000205108	ENST00000378788	T	0.21361	2.01	4.11	-0.233	0.13078	.	.	.	.	.	T	0.00039	0.0001	N	0.03608	-0.345	0.80722	P	0.0	P	0.45176	0.852	B	0.38378	0.272	T	0.10706	-1.0618	8	0.02654	T	1	.	4.4897	0.11808	0.0:0.4317:0.3575:0.2108	.	361	Q6ZU69	F205A_HUMAN	Y	361	ENSP00000417711:C361Y	ENSP00000417711:C361Y	C	-	2	0	RP11-195F19.10	34716155	0.000000	0.05858	0.000000	0.03702	0.641000	0.38312	-0.146000	0.10250	0.143000	0.18926	-0.226000	0.12346	TGT	C|0.937;T|0.063	0.063	strong		0.478	FAM205A-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001150.2	NM_001141917	
BTBD16	118663	hgsc.bcm.edu	37	10	124096035	124096035	+	Silent	SNP	T	T	C	rs3817281	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:124096035T>C	ENST00000260723.4	+	15	1541	c.1290T>C	c.(1288-1290)tcT>tcC	p.S430S	BTBD16_ENST00000495370.2_3'UTR|BTBD16_ENST00000368994.2_Silent_p.S431S	NM_144587.2	NP_653188.2	Q32M84	BTBDG_HUMAN	BTB (POZ) domain containing 16	430										breast(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(5)|lung(3)|skin(2)|stomach(1)|urinary_tract(1)	15		all_neural(114;0.107)|Lung NSC(174;0.175)|all_lung(145;0.222)|Breast(234;0.238)				ACCTGGAATCTCCCTCTGCGG	0.572													C|||	2300	0.459265	0.3956	0.4856	5008	,	,		17882	0.6935		0.326	False		,,,				2504	0.4223				p.S430S		Atlas-SNP	.											.	BTBD16	44	.	0			c.T1290C						PASS	.	C		1571,2835	654.3+/-399.7	293,985,925	67.0	57.0	60.0		1290	-6.6	0.0	10	dbSNP_107	60	2746,5854	670.0+/-402.7	445,1856,1999	no	coding-synonymous	BTBD16	NM_144587.2		738,2841,2924	CC,CT,TT		31.9302,35.6559,33.1924		430/507	124096035	4317,8689	2203	4300	6503	SO:0001819	synonymous_variant	118663	exon15			GGAATCTCCCTCT	AK058088	CCDS31301.1	10q26.13	2013-01-24	2006-07-04	2006-07-04	ENSG00000138152	ENSG00000138152		"""BTB/POZ domain containing"""	26340	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 87"""	C10orf87			Standard	NM_144587		Approved	FLJ25359, Em:AC061711.1	uc001lgc.1	Q32M84	OTTHUMG00000019182	ENST00000260723.4:c.1290T>C	10.37:g.124096035T>C		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	78	31	0.397436	NM_144587	A6NM63|Q4VXL1|Q96LN0	Silent	SNP	ENST00000260723.4	37	CCDS31301.1																																																																																			T|0.613;C|0.387	0.387	strong		0.572	BTBD16-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000050780.3	NM_144587	
HEATR1	55127	hgsc.bcm.edu	37	1	236729956	236729956	+	Missense_Mutation	SNP	T	T	C	rs653737	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:236729956T>C	ENST00000366582.3	-	30	4412	c.4298A>G	c.(4297-4299)tAt>tGt	p.Y1433C	HEATR1_ENST00000366581.2_Missense_Mutation_p.Y1352C	NM_018072.5	NP_060542.4	Q9H583	HEAT1_HUMAN	HEAT repeat containing 1	1433			Y -> C (in dbSNP:rs653737).		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)			CTTTTCGCCATAGGCAGCCGC	0.428													T|||	447	0.0892572	0.0061	0.1023	5008	,	,		16717	0.0397		0.1869	False		,,,				2504	0.1431				p.Y1433C		Atlas-SNP	.											.	HEATR1	197	.	0			c.A4298G						PASS	.	T	CYS/TYR	142,4264	100.3+/-138.9	2,138,2063	29.0	29.0	29.0		4298	-11.2	0.0	1	dbSNP_83	29	1458,7142	274.5+/-291.2	122,1214,2964	yes	missense	HEATR1	NM_018072.5	194	124,1352,5027	CC,CT,TT		16.9535,3.2229,12.302	benign	1433/2145	236729956	1600,11406	2203	4300	6503	SO:0001583	missense	55127	exon30			TCGCCATAGGCAG	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.4298A>G	1.37:g.236729956T>C	ENSP00000355541:p.Tyr1433Cys	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	82	40	0.487805	NM_018072	Q5T3Q8|Q6P197|Q9NW23	Missense_Mutation	SNP	ENST00000366582.3	37	CCDS31066.1	209	0.09569597069597069	5	0.01016260162601626	40	0.11049723756906077	16	0.027972027972027972	148	0.19525065963060687	T	9.755	1.168397	0.21621	0.032229	0.169535	ENSG00000119285	ENST00000366582;ENST00000366581	T;T	0.29142	1.58;1.58	5.6	-11.2	0.00127	Armadillo-like helical (1);Armadillo-type fold (1);	0.841096	0.10696	N	0.644610	T	0.00012	0.0000	L	0.44542	1.39	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.09662	-1.0664	9	0.37606	T	0.19	.	10.4002	0.44225	0.0883:0.576:0.0899:0.2459	rs653737;rs61339276;rs653737	1352;1433	Q5T3Q7;Q9H583	.;HEAT1_HUMAN	C	1433;1352	ENSP00000355541:Y1433C;ENSP00000355540:Y1352C	ENSP00000355540:Y1352C	Y	-	2	0	HEATR1	234796579	0.001000	0.12720	0.005000	0.12908	0.819000	0.46315	-1.428000	0.02439	-2.264000	0.00689	-0.993000	0.02533	TAT	T|0.891;C|0.109	0.109	strong		0.428	HEATR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096635.1	XM_375853	
ELL3	80237	hgsc.bcm.edu	37	15	44069069	44069069	+	Missense_Mutation	SNP	G	G	C	rs2277531	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:44069069G>C	ENST00000319359.3	-	1	672	c.31C>G	c.(31-33)Cag>Gag	p.Q11E	SERF2_ENST00000381359.1_5'Flank|RP11-296A16.1_ENST00000417761.2_Intron|ELL3_ENST00000497465.1_5'Flank	NM_025165.2	NP_079441.1	Q9HB65	ELL3_HUMAN	elongation factor RNA polymerase II-like 3	11			Q -> E (in dbSNP:rs2277531).		DNA-templated transcription, elongation (GO:0006354)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:1902166)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|positive regulation of neural precursor cell proliferation (GO:2000179)|positive regulation of neurogenesis (GO:0050769)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of epithelial to mesenchymal transition (GO:0010717)|snRNA transcription from RNA polymerase II promoter (GO:0042795)|spermatogenesis (GO:0007283)|stem cell differentiation (GO:0048863)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)	nucleolus (GO:0005730)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)	enhancer binding (GO:0035326)			cervix(1)|kidney(1)|large_intestine(5)|lung(4)|ovary(1)|skin(1)	13		all_cancers(109;7.57e-15)|all_epithelial(112;3.51e-12)|Lung NSC(122;4.72e-08)|all_lung(180;4.9e-07)|Melanoma(134;0.027)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;7.81e-07)		AGCCGGAGCTGTCCTCTCAGA	0.652											OREG0003946	type=REGULATORY REGION|Gene=NM_005770|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	G|||	1061	0.211861	0.32	0.1758	5008	,	,		12505	0.2609		0.0964	False		,,,				2504	0.1595				p.Q11E		Atlas-SNP	.											.	ELL3	38	.	0			c.C31G						PASS	.	G	GLU/GLN	1206,3190	394.2+/-329.2	157,892,1149	34.0	37.0	36.0		31	1.5	0.5	15	dbSNP_100	36	819,7777	182.3+/-230.8	37,745,3516	yes	missense	ELL3	NM_025165.2	29	194,1637,4665	CC,CG,GG		9.5277,27.434,15.5865	benign	11/398	44069069	2025,10967	2198	4298	6496	SO:0001583	missense	80237	exon1			GGAGCTGTCCTCT	AF276512	CCDS10102.1	15q15.1	2008-02-05			ENSG00000128886	ENSG00000128886			23113	protein-coding gene	gene with protein product		609885				10882741	Standard	NM_025165		Approved	FLJ22637	uc001zsw.1	Q9HB65	OTTHUMG00000059936	ENST00000319359.3:c.31C>G	15.37:g.44069069G>C	ENSP00000320346:p.Gln11Glu	Somatic	58	0	0	921	WXS	Illumina HiSeq	Phase_I	59	18	0.305085	NM_025165	B3KQ66|B3KX08|Q6I9Z7|Q9H634	Missense_Mutation	SNP	ENST00000319359.3	37	CCDS10102.1	498	0.22802197802197802	166	0.33739837398373984	71	0.19613259668508287	178	0.3111888111888112	83	0.10949868073878628	G	8.314	0.822681	0.16678	0.27434	0.095277	ENSG00000128886	ENST00000319359;ENST00000433927	T;T	0.28666	1.6;1.6	5.39	1.53	0.23141	.	0.332281	0.24904	N	0.034667	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	B	0.19073	0.033	B	0.17433	0.018	T	0.42732	-0.9434	9	0.51188	T	0.08	-42.4331	11.2871	0.49228	0.0:0.0:0.4793:0.5206	rs2277531;rs2277531	11	Q9HB65	ELL3_HUMAN	E	11;41	ENSP00000320346:Q11E;ENSP00000404209:Q41E	ENSP00000320346:Q11E	Q	-	1	0	ELL3	41856361	0.592000	0.26832	0.546000	0.28166	0.022000	0.10575	0.725000	0.25970	0.348000	0.23949	-0.457000	0.05445	CAG	G|0.819;C|0.181	0.181	strong		0.652	ELL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133236.2	NM_025165	
TRPM8	79054	hgsc.bcm.edu	37	2	234854540	234854540	+	Missense_Mutation	SNP	G	G	C	rs13004520	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:234854540G>C	ENST00000324695.4	+	7	780	c.740G>C	c.(739-741)aGa>aCa	p.R247T	TRPM8_ENST00000433712.2_5'UTR|AC005538.5_ENST00000455991.1_RNA	NM_024080.4	NP_076985.4	Q7Z2W7	TRPM8_HUMAN	transient receptor potential cation channel, subfamily M, member 8	247			R -> T (in dbSNP:rs13004520).		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)	GACTTCACAAGAGATCCACTG	0.433													G|||	232	0.0463259	0.0182	0.0836	5008	,	,		21891	0.0744		0.0368	False		,,,				2504	0.0389				p.R247T		Atlas-SNP	.											.	TRPM8	146	.	0			c.G740C						PASS	.	G	THR/ARG	107,4299	82.9+/-121.4	4,99,2100	133.0	122.0	126.0		740	5.7	0.8	2	dbSNP_121	126	440,8160	134.6+/-191.9	10,420,3870	yes	missense	TRPM8	NM_024080.4	71	14,519,5970	CC,CG,GG		5.1163,2.4285,4.2058	possibly-damaging	247/1105	234854540	547,12459	2203	4300	6503	SO:0001583	missense	79054	exon7			TCACAAGAGATCC	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.740G>C	2.37:g.234854540G>C	ENSP00000323926:p.Arg247Thr	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	63	35	0.555556	NM_024080	A0AVG2|Q3YFM7|Q6QNH9|Q8TAC3|Q8TDX8|Q9BVK1	Missense_Mutation	SNP	ENST00000324695.4	37	CCDS33407.1	126	0.057692307692307696	10	0.02032520325203252	45	0.12430939226519337	39	0.06818181818181818	32	0.04221635883905013	G	17.73	3.461501	0.63513	0.024285	0.051163	ENSG00000144481	ENST00000324695	T	0.03065	4.06	5.72	5.72	0.89469	.	0.139997	0.50627	D	0.000109	T	0.00109	0.0003	M	0.68593	2.085	0.09310	P	1.0	P	0.34462	0.454	B	0.32677	0.15	T	0.13202	-1.0518	9	0.72032	D	0.01	-15.9163	11.8613	0.52467	0.0797:0.0:0.9203:0.0	rs13004520;rs17868386;rs52815062;rs13004520	247	Q7Z2W7	TRPM8_HUMAN	T	247	ENSP00000323926:R247T	ENSP00000323926:R247T	R	+	2	0	TRPM8	234519279	1.000000	0.71417	0.830000	0.32933	0.914000	0.54420	7.098000	0.76974	2.717000	0.92951	0.655000	0.94253	AGA	G|0.955;C|0.045	0.045	strong		0.433	TRPM8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131005.4	NM_024080	
MUC17	140453	hgsc.bcm.edu	37	7	100681221	100681221	+	Missense_Mutation	SNP	G	G	C	rs147785825	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:100681221G>C	ENST00000306151.4	+	3	6588	c.6524G>C	c.(6523-6525)aGt>aCt	p.S2175T		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	2175	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)					GTGGTGGCCAGTTCTGCAATC	0.473													G|||	132	0.0263578	0.0038	0.0504	5008	,	,		27143	0.001		0.0706	False		,,,				2504	0.0204				p.S2175T		Atlas-SNP	.											.	MUC17	804	.	0			c.G6524C						PASS	.	G	THR/SER	30,4376	29.9+/-59.1	0,30,2173	254.0	248.0	250.0		6524	-1.4	0.0	7	dbSNP_134	250	338,8262	108.0+/-168.7	5,328,3967	no	missense	MUC17	NM_001040105.1	58	5,358,6140	CC,CG,GG		3.9302,0.6809,2.8295	benign	2175/4494	100681221	368,12638	2203	4300	6503	SO:0001583	missense	140453	exon3			TGGCCAGTTCTGC	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.6524G>C	7.37:g.100681221G>C	ENSP00000302716:p.Ser2175Thr	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	65	34	0.523077	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	64	0.029304029304029304	2	0.0040650406504065045	17	0.04696132596685083	2	0.0034965034965034965	43	0.05672823218997362	g	0.572	-0.840600	0.02692	0.006809	0.039302	ENSG00000169876	ENST00000306151	T	0.02498	4.27	0.683	-1.37	0.09056	.	.	.	.	.	T	0.00178	0.0005	N	0.03608	-0.345	0.09310	N	1	B	0.20459	0.045	B	0.13407	0.009	T	0.46162	-0.9211	9	0.07482	T	0.82	.	6.329	0.21259	0.0:0.3983:0.6017:0.0	.	2175	Q685J3	MUC17_HUMAN	T	2175	ENSP00000302716:S2175T	ENSP00000302716:S2175T	S	+	2	0	MUC17	100467941	0.002000	0.14202	0.002000	0.10522	0.019000	0.09904	-0.282000	0.08445	-0.468000	0.06922	0.134000	0.15878	AGT	G|0.973;C|0.027	0.027	strong		0.473	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
SRRM5	100170229	hgsc.bcm.edu	37	19	44117582	44117582	+	Missense_Mutation	SNP	T	T	C	rs10410000	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:44117582T>C	ENST00000607544.1	+	3	1631	c.1309T>C	c.(1309-1311)Tgc>Cgc	p.C437R	SRRM5_ENST00000417606.1_Missense_Mutation_p.C437R|SRRM5_ENST00000526798.1_Missense_Mutation_p.C452R|ZNF428_ENST00000300811.3_Intron			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	50	2	0.04		WXS	Illumina HiSeq	Phase_I	65	33	0.507692	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	
DNAH17	8632	hgsc.bcm.edu	37	17	76490894	76490894	+	Silent	SNP	G	G	A	rs372912923		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:76490894G>A	ENST00000585328.1	-	40	6160	c.6036C>T	c.(6034-6036)taC>taT	p.Y2012Y	DNAH17_ENST00000389840.5_Silent_p.Y2003Y|RP11-559N14.5_ENST00000591373.1_RNA|RP11-559N14.5_ENST00000585969.1_RNA	NM_173628.3	NP_775899.3	Q9UFH2	DYH17_HUMAN	dynein, axonemal, heavy chain 17	2003	AAA 1. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(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)			GGCCCCAGTCGTAATGATCCT	0.672																																					p.Y2017Y		Atlas-SNP	.											.	DNAH17	347	.	0			c.C6051T						PASS	.	G		0,4330		0,0,2165	18.0	21.0	20.0		6051	-2.0	0.9	17		20	9,8557		0,9,4274	no	coding-synonymous	DNAH17	NM_173628.3		0,9,6439	AA,AG,GG		0.1051,0.0,0.0698		2017/4463	76490894	9,12887	2165	4283	6448	SO:0001819	synonymous_variant	8632	exon40			CCAGTCGTAATGA	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.6036C>T	17.37:g.76490894G>A		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	85	42	0.494118	NM_173628	O00431|O15206|Q2M2Y1|Q6ZRQ2|Q8N7Q7	Silent	SNP	ENST00000585328.1	37																																																																																				.	.	weak		0.672	DNAH17-001	PUTATIVE	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000318962.2	NM_173628	
RRP7A	27341	hgsc.bcm.edu	37	22	42910769	42910769	+	Silent	SNP	G	G	A	rs4822146	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:42910769G>A	ENST00000323013.6	-	5	492	c.477C>T	c.(475-477)taC>taT	p.Y159Y	SERHL_ENST00000359906.2_RNA	NM_015703.4	NP_056518.2	Q9Y3A4	RRP7A_HUMAN	ribosomal RNA processing 7 homolog A (S. cerevisiae)	159							nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.Y159Y(1)		central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|liver(2)|lung(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	10						CAGAGTCTGCGTAGTCACTGA	0.622													G|||	383	0.0764776	0.0582	0.1772	5008	,	,		20886	0.004		0.1461	False		,,,				2504	0.0327				p.Y159Y		Atlas-SNP	.											RRP7A,NS,carcinoma,0,1	RRP7A	25	1	1	Substitution - coding silent(1)	prostate(1)	c.C477T						scavenged	.	G		362,4036	158.9+/-191.5	33,296,1870	44.0	47.0	46.0		477	1.5	0.6	22	dbSNP_111	46	1171,7427	220.5+/-258.2	85,1001,3213	no	coding-synonymous	RRP7A	NM_015703.4		118,1297,5083	AA,AG,GG		13.6194,8.231,11.7959		159/281	42910769	1533,11463	2199	4299	6498	SO:0001819	synonymous_variant	27341	exon5			GTCTGCGTAGTCA	BC035992	CCDS14036.1	22q13.2	2008-08-08			ENSG00000189306	ENSG00000189306			24286	protein-coding gene	gene with protein product						10810093, 12087473	Standard	NM_015703		Approved	CGI-96	uc003bcq.3	Q9Y3A4	OTTHUMG00000150891	ENST00000323013.6:c.477C>T	22.37:g.42910769G>A		Somatic	252	2	0.00793651		WXS	Illumina HiSeq	Phase_I	236	88	0.372881	NM_015703	A4FTX2|B2RBG4|Q0VAD0|Q5JZ94|Q6P4B5|Q8IVR9|Q8IVY0|Q8N5Q3|Q8NEY6|Q9Y3H5	Silent	SNP	ENST00000323013.6	37	CCDS14036.1																																																																																			G|0.898;A|0.102	0.102	strong		0.622	RRP7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320451.1	NM_015703	
GALNTL6	442117	hgsc.bcm.edu	37	4	173232805	173232805	+	Silent	SNP	G	G	A	rs9312524	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:173232805G>A	ENST00000506823.1	+	4	945	c.288G>A	c.(286-288)gaG>gaA	p.E96E	GALNTL6_ENST00000457021.1_3'UTR|GALNTL6_ENST00000508122.1_Silent_p.E79E	NM_001034845.2	NP_001030017.2	Q49A17	GLTL6_HUMAN	polypeptide N-acetylgalactosaminyltransferase-like 6	96					protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			breast(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|liver(2)|lung(21)|ovary(1)|pancreas(1)|prostate(1)|skin(2)	45						TTACTGAAGAGGACCATGATG	0.388													G|||	522	0.104233	0.1558	0.0879	5008	,	,		15998	0.0089		0.1859	False		,,,				2504	0.0603				p.E96E		Atlas-SNP	.											.	GALNTL6	102	.	0			c.G288A						PASS	.	G		666,3740	283.1+/-276.9	50,566,1587	131.0	131.0	131.0		288	0.1	1.0	4	dbSNP_119	131	1609,6991	297.8+/-303.6	160,1289,2851	no	coding-synonymous	GALNTL6	NM_001034845.2		210,1855,4438	AA,AG,GG		18.7093,15.1158,17.4919		96/602	173232805	2275,10731	2203	4300	6503	SO:0001819	synonymous_variant	442117	exon4			TGAAGAGGACCAT		CCDS34104.1	4q34.1	2014-03-13	2014-03-13		ENSG00000174473	ENSG00000174473		"""Glycosyltransferase family 2 domain containing"""	33844	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase-like 6"""	615138	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase-like 6"""				Standard	NM_001034845		Approved	GALNT17, GalNAc-T6L	uc003isv.3	Q49A17	OTTHUMG00000160807	ENST00000506823.1:c.288G>A	4.37:g.173232805G>A		Somatic	236	0	0		WXS	Illumina HiSeq	Phase_I	187	187	1	NM_001034845	Q2L4S6	Silent	SNP	ENST00000506823.1	37	CCDS34104.1																																																																																			G|0.852;A|0.148	0.148	strong		0.388	GALNTL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362395.1	NM_001034845	
ITSN1	6453	hgsc.bcm.edu	37	21	35147359	35147359	+	Missense_Mutation	SNP	A	A	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:35147359A>C	ENST00000381318.3	+	14	1831	c.1543A>C	c.(1543-1545)Aaa>Caa	p.K515Q	ITSN1_ENST00000379960.5_Missense_Mutation_p.K515Q|ITSN1_ENST00000399349.1_Missense_Mutation_p.K515Q|ITSN1_ENST00000381291.4_Missense_Mutation_p.K515Q|ITSN1_ENST00000399326.3_Missense_Mutation_p.K515Q|ITSN1_ENST00000437442.2_Missense_Mutation_p.K515Q|ITSN1_ENST00000399367.3_Missense_Mutation_p.K515Q|ITSN1_ENST00000381285.4_Missense_Mutation_p.K515Q|AP000304.12_ENST00000429238.1_Intron|ITSN1_ENST00000399355.2_Missense_Mutation_p.K515Q|ITSN1_ENST00000399338.4_Missense_Mutation_p.K515Q|ITSN1_ENST00000399352.1_Missense_Mutation_p.K515Q|ITSN1_ENST00000399353.1_Missense_Mutation_p.K478Q	NM_003024.2	NP_003015.2	Q15811	ITSN1_HUMAN	intersectin 1 (SH3 domain protein)	515	KLERQ.				apoptotic signaling pathway (GO:0097190)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|positive regulation of protein kinase B signaling (GO:0051897)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|synaptic vesicle endocytosis (GO:0048488)	cell junction (GO:0030054)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|lamellipodium (GO:0030027)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|synapse (GO:0045202)	calcium ion binding (GO:0005509)|guanyl-nucleotide exchange factor activity (GO:0005085)|kinase activator activity (GO:0019209)|proline-rich region binding (GO:0070064)|protein complex scaffold (GO:0032947)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(16)|lung(26)|ovary(4)|prostate(1)|skin(4)|stomach(1)|urinary_tract(2)	67						GAGCACAAACAAATCTAGAGA	0.368																																					p.K515Q		Atlas-SNP	.											.	ITSN1	166	.	0			c.A1543C						PASS	.						100.0	103.0	102.0					21																	35147359		2203	4300	6503	SO:0001583	missense	6453	exon14			ACAAACAAATCTA	AF064244	CCDS33545.1, CCDS33546.1	21q22.1-q22.2	2013-01-10			ENSG00000205726	ENSG00000205726		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"", ""EF-hand domain containing"""	6183	protein-coding gene	gene with protein product	"""SH3 domain protein-1A"", ""human intersectin-SH3 domain-containing protein SH3P17"", ""Src homology 3 domain-containing protein"", ""intersectin 1 short form variant, 11"", ""intersectin 1 short form variant 3"", ""intersectin short variant 12"""	602442		SH3D1A, ITSN		9799604, 9813051	Standard	NM_003024		Approved	SH3P17, MGC134948, MGC134949	uc002yta.1	Q15811	OTTHUMG00000065284	ENST00000381318.3:c.1543A>C	21.37:g.35147359A>C	ENSP00000370719:p.Lys515Gln	Somatic	214	0	0		WXS	Illumina HiSeq	Phase_I	198	106	0.535354	NM_001001132	A7Y322|A8CTX8|A8CTY3|A8CTY7|A8D7D0|A8DCP3|B4DTM2|E7ERJ1|E9PE44|E9PG01|E9PHV2|O95216|Q0PW94|Q0PW95|Q0PW97|Q14BD3|Q1ED40|Q20BK3|Q9UET5|Q9UK60|Q9UNK1|Q9UNK2|Q9UQ92	Missense_Mutation	SNP	ENST00000381318.3	37	CCDS33545.1	.	.	.	.	.	.	.	.	.	.	A	14.52	2.560779	0.45590	.	.	ENSG00000205726	ENST00000399353;ENST00000381318;ENST00000381291;ENST00000381285;ENST00000381288;ENST00000381289;ENST00000399367;ENST00000399352;ENST00000399355;ENST00000399349;ENST00000399338;ENST00000437442;ENST00000399326;ENST00000379960	T;T;T;T;T;T;T;T;T;T;T;T	0.44881	1.53;0.93;1.0;0.93;1.53;1.53;1.0;1.53;1.53;1.53;1.53;0.91	5.07	5.07	0.68467	.	0.114374	0.56097	D	0.000026	T	0.38825	0.1055	L	0.27053	0.805	0.43936	D	0.996595	P;B;B;B;P;B;B;B;P;B	0.39352	0.539;0.397;0.068;0.264;0.669;0.296;0.245;0.245;0.542;0.397	B;B;B;B;B;B;B;B;P;B	0.45794	0.281;0.209;0.019;0.17;0.19;0.046;0.077;0.077;0.493;0.209	T	0.16660	-1.0395	10	0.31617	T	0.26	.	14.8326	0.70159	1.0:0.0:0.0:0.0	.	478;478;478;515;515;515;515;515;515;478	A8D7D0;A7XZY7;A8CTY7;A8CTY3;F8W7U0;E7ERJ1;A8CTX8;Q15811;Q15811-3;E7ERJ0	.;.;.;.;.;.;.;ITSN1_HUMAN;.;.	Q	478;515;515;515;515;515;515;515;515;515;515;515;515;515	ENSP00000382290:K478Q;ENSP00000370719:K515Q;ENSP00000370691:K515Q;ENSP00000370685:K515Q;ENSP00000382301:K515Q;ENSP00000382289:K515Q;ENSP00000382292:K515Q;ENSP00000382286:K515Q;ENSP00000382275:K515Q;ENSP00000387377:K515Q;ENSP00000382265:K515Q;ENSP00000369294:K515Q	ENSP00000369294:K515Q	K	+	1	0	ITSN1	34069229	1.000000	0.71417	0.999000	0.59377	0.997000	0.91878	6.956000	0.76013	1.910000	0.55303	0.482000	0.46254	AAA	.	.	none		0.368	ITSN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000140070.4	NM_003024	
KRTAP4-8	728224	hgsc.bcm.edu	37	17	39253835	39253835	+	Missense_Mutation	SNP	C	C	T	rs72625995	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:39253835C>T	ENST00000333822.4	-	1	558	c.502G>A	c.(502-504)Gcc>Acc	p.A168T		NM_031960.2	NP_114166.1	Q9BYQ9	KRA48_HUMAN	keratin associated protein 4-8	168				A -> T (in Ref. 2; CAC27579). {ECO:0000305}.	aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)		p.A168T(1)		endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(1)|prostate(1)	11						ATGACACAGGCTGGGCGATAG	0.662													T|||	3187	0.636382	0.9168	0.6326	5008	,	,		15964	0.4147		0.6183	False		,,,				2504	0.5072				p.A168T		Atlas-SNP	.											KRTAP4-8,NS,carcinoma,0,1	KRTAP4-8	57	1	1	Substitution - Missense(1)	prostate(1)	c.G502A						PASS	.						49.0	57.0	54.0					17																	39253835		692	1591	2283	SO:0001583	missense	728224	exon1			CACAGGCTGGGCG	AJ406940	CCDS45674.1	17q21.2	2013-06-25			ENSG00000204880	ENSG00000204880		"""Keratin associated proteins"""	17230	protein-coding gene	gene with protein product						11279113	Standard	NM_031960		Approved	KAP4.8	uc010wfo.2	Q9BYQ9	OTTHUMG00000133580	ENST00000333822.4:c.502G>A	17.37:g.39253835C>T	ENSP00000328444:p.Ala168Thr	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	96	45	0.46875	NM_031960	A8MSH3	Missense_Mutation	SNP	ENST00000333822.4	37	CCDS45674.1	.	.	.	.	.	.	.	.	.	.	.	3.713	-0.059042	0.07317	.	.	ENSG00000204880	ENST00000333822;ENST00000332991	T	0.00570	6.51	3.73	2.63	0.31362	.	0.219558	0.22220	N	0.062972	T	0.00144	0.0004	N	0.00178	-1.915	0.58432	P	8.000000000008E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.10474	-1.0628	9	0.07990	T	0.79	.	5.1348	0.14928	0.0:0.2562:0.0:0.7438	.	168	Q9BYQ9	KRA48_HUMAN	T	168;138	ENSP00000328444:A168T	ENSP00000414561:A138T	A	-	1	0	KRTAP4-8	36507361	0.706000	0.27856	0.999000	0.59377	0.662000	0.39071	0.104000	0.15313	0.434000	0.26340	-0.572000	0.04151	GCC	C|0.980;T|0.020	0.020	strong		0.662	KRTAP4-8-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257684.1	NM_031960	
MUC5B	727897	hgsc.bcm.edu	37	11	1269707	1269707	+	Missense_Mutation	SNP	C	C	T	rs187569173	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:1269707C>T	ENST00000529681.1	+	31	11655	c.11597C>T	c.(11596-11598)cCg>cTg	p.P3866L	MUC5B_ENST00000447027.1_Missense_Mutation_p.P3869L|RP11-532E4.2_ENST00000532061.2_RNA	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	3866	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)		ACCAAAGTGCCGACTACCACA	0.637													T|||	226	0.0451278	0.0272	0.111	5008	,	,		15811	0.003		0.0636	False		,,,				2504	0.047				p.P3866L		Atlas-SNP	.											MUC5B,NS,carcinoma,0,2	MUC5B	473	2	0			c.C11597T						scavenged	.	T	LEU/PRO	42,4128		3,36,2046	114.0	135.0	128.0		11597	0.1	0.0	11		128	343,8057		28,287,3885	no	missense	MUC5B	NM_002458.2	98	31,323,5931	TT,TC,CC		4.0833,1.0072,3.0628	benign	3866/5763	1269707	385,12185	2085	4200	6285	SO:0001583	missense	727897	exon31			AAGTGCCGACTAC	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.11597C>T	11.37:g.1269707C>T	ENSP00000436812:p.Pro3866Leu	Somatic	228	1	0.00438596		WXS	Illumina HiSeq	Phase_I	242	36	0.14876	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Missense_Mutation	SNP	ENST00000529681.1	37	CCDS44515.2	83	0.038003663003663	10	0.02032520325203252	24	0.06629834254143646	0	0.0	49	0.06464379947229551	T	1.195	-0.634140	0.03584	0.010072	0.040833	ENSG00000117983	ENST00000529681;ENST00000447027;ENST00000349637;ENST00000406844	T;T	0.39997	1.05;1.21	0.118	0.118	0.14667	.	.	.	.	.	T	0.01222	0.0040	N	0.02802	-0.49	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.12760	-1.0535	9	0.87932	D	0	.	4.6773	0.12719	0.0:0.6499:0.0:0.3501	.	4394;3869	A7Y9J9;E9PBJ0	.;.	L	3866;3869;3810;3771	ENSP00000436812:P3866L;ENSP00000415793:P3869L	ENSP00000343037:P3810L	P	+	2	0	MUC5B	1226283	0.000000	0.05858	0.005000	0.12908	0.024000	0.10985	-2.617000	0.00881	-1.195000	0.02680	-1.220000	0.01600	CCG	C|0.967;T|0.033	0.033	strong		0.637	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
TMEM123	114908	hgsc.bcm.edu	37	11	102272884	102272884	+	Missense_Mutation	SNP	C	C	T	rs2155587	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:102272884C>T	ENST00000398136.2	-	3	631	c.211G>A	c.(211-213)Gtg>Atg	p.V71M	TMEM123_ENST00000361236.3_Missense_Mutation_p.V52M|TMEM123_ENST00000532161.1_De_novo_Start_InFrame|TMEM123_ENST00000525577.1_5'UTR	NM_052932.2	NP_443164.2	Q8N131	PORIM_HUMAN	transmembrane protein 123	71	Thr-rich.		V -> M (in dbSNP:rs2155587).		oncosis (GO:0070267)	external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			breast(3)|kidney(1)|large_intestine(1)|lung(3)|urinary_tract(1)	9	all_cancers(8;0.00027)|all_epithelial(12;0.0021)|Lung NSC(15;0.227)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0033)	Epithelial(9;0.0314)|Lung(13;0.109)|all cancers(10;0.12)|LUSC - Lung squamous cell carcinoma(19;0.151)	BRCA - Breast invasive adenocarcinoma(274;0.0149)		GGTGGTTTCACAGTACTGTTG	0.428													C|||	283	0.0565096	0.003	0.1527	5008	,	,		17030	0.0635		0.0865	False		,,,				2504	0.0225				p.V71M		Atlas-SNP	.											.	TMEM123	16	.	0			c.G211A						PASS	.	C	MET/VAL	107,3919		2,103,1908	270.0	251.0	257.0		211	-0.6	0.0	11	dbSNP_96	257	786,7546		39,708,3419	yes	missense	TMEM123	NM_052932.2	21	41,811,5327	TT,TC,CC		9.4335,2.6577,7.2261	possibly-damaging	71/209	102272884	893,11465	2013	4166	6179	SO:0001583	missense	114908	exon3			GTTTCACAGTACT	AL050161	CCDS41702.1	11q22.1	2014-01-02			ENSG00000152558	ENSG00000152558			30138	protein-coding gene	gene with protein product	"""pro oncosis receptor inducing membrane injury gene"""	606356				11481458, 24318988	Standard	NM_052932		Approved	PORIMIN, KCT3	uc001pha.3	Q8N131	OTTHUMG00000167326	ENST00000398136.2:c.211G>A	11.37:g.102272884C>T	ENSP00000381204:p.Val71Met	Somatic	332	0	0		WXS	Illumina HiSeq	Phase_I	317	246	0.776025	NM_052932	Q8IWS2|Q96QV2	Missense_Mutation	SNP	ENST00000398136.2	37	CCDS41702.1	156	0.07142857142857142	1	0.0020325203252032522	46	0.1270718232044199	43	0.07517482517482517	66	0.0870712401055409	C	11.51	1.659731	0.29515	0.026577	0.094335	ENSG00000152558	ENST00000361236;ENST00000398136;ENST00000526676	T;T;T	0.53640	1.84;1.78;0.61	5.36	-0.649	0.11461	.	4.242690	0.00639	N	0.000519	T	0.00356	0.0011	N	0.22421	0.69	0.58432	P	1.0000000000287557E-6	B;B	0.13594	0.008;0.008	B;B	0.18561	0.022;0.022	T	0.09596	-1.0667	9	0.45353	T	0.12	2.6989	3.637	0.08153	0.1716:0.3951:0.0:0.4334	rs2155587;rs17258581;rs52821242;rs60976972;rs2155587	52;71	Q8N131-2;Q8N131	.;PORIM_HUMAN	M	52;71;29	ENSP00000355285:V52M;ENSP00000381204:V71M;ENSP00000435842:V29M	ENSP00000355285:V52M	V	-	1	0	TMEM123	101778094	0.000000	0.05858	0.000000	0.03702	0.014000	0.08584	-2.339000	0.01102	0.039000	0.15632	0.563000	0.77884	GTG	C|0.929;T|0.071	0.071	strong		0.428	TMEM123-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394178.1	NM_052932	
EBP	10682	hgsc.bcm.edu	37	X	48382174	48382174	+	Silent	SNP	G	G	T	rs3048	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:48382174G>T	ENST00000495186.1	+	2	838	c.15G>T	c.(13-15)gcG>gcT	p.A5A	EBP_ENST00000276096.6_Intron	NM_006579.2	NP_006570.1	Q15125	EBP_HUMAN	emopamil binding protein (sterol isomerase)	5					cholesterol biosynthetic process (GO:0006695)|cholesterol metabolic process (GO:0008203)|drug transmembrane transport (GO:0006855)|hemopoiesis (GO:0030097)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)	C-8 sterol isomerase activity (GO:0000247)|cholestenol delta-isomerase activity (GO:0047750)|drug transmembrane transporter activity (GO:0015238)|steroid delta-isomerase activity (GO:0004769)|transmembrane signaling receptor activity (GO:0004888)	p.A5A(1)		NS(1)|endometrium(2)|large_intestine(3)|lung(2)|ovary(1)|prostate(1)|stomach(1)	11					Tamoxifen(DB00675)	CTACCAACGCGGGCCCCTTGC	0.478													g|||	1190	0.315232	0.1467	0.2305	3775	,	,		10105	0.3155		0.2724	False		,,,				2504	0.2495				p.A5A	Ovarian(41;550 1000 33077 33474 52335)	Atlas-SNP	.											.	EBP	30	.	1	Substitution - coding silent(1)	stomach(1)	c.G15T						PASS	.			786,3049		78,526,104,1028,467	58.0	42.0	47.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	15	-2.7	0.0	X	dbSNP_36	47	2306,4422		326,1040,614,1062,1258	no	coding-synonymous	EBP	NM_006579.2		404,1566,718,2090,1725	TT,TG,T,GG,G		34.2747,20.4954,29.272		5/231	48382174	3092,7471	2203	4300	6503	SO:0001819	synonymous_variant	10682	exon2			CAACGCGGGCCCC	Z37986	CCDS14300.1	Xp11.23-p11.22	2013-05-22	2001-11-28		ENSG00000147155	ENSG00000147155			3133	protein-coding gene	gene with protein product	"""3-beta-hydroxysteroid-delta-8,delta-7-isomerase"", ""Chondrodysplasia punctata-2, X-linked dominant (Happle syndrome)"", ""sterol 8-isomerase"""	300205	"""emopamil-binding protein (sterol isomerase)"""	CDPX2		7706302, 8938429	Standard	NM_006579		Approved	CPX, CPXD, CHO2	uc004djx.4	Q15125	OTTHUMG00000034482	ENST00000495186.1:c.15G>T	X.37:g.48382174G>T		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	55	54	0.981818	NM_006579	Q6FGL3|Q6IBI9	Silent	SNP	ENST00000495186.1	37	CCDS14300.1																																																																																			G|0.693;T|0.307	0.307	strong		0.478	EBP-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083372.1	NM_006579	
C7orf31	136895	hgsc.bcm.edu	37	7	25194665	25194665	+	Missense_Mutation	SNP	G	G	C	rs2523072	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:25194665G>C	ENST00000409280.1	-	6	868	c.560C>G	c.(559-561)aCc>aGc	p.T187S	C7orf31_ENST00000283905.3_Missense_Mutation_p.T187S			Q8N865	CG031_HUMAN	chromosome 7 open reading frame 31	187			T -> S (in dbSNP:rs2523072). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005, ECO:0000269|Ref.3}.							autonomic_ganglia(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(6)|skin(2)|stomach(1)	14						ATAAGCCTTGGTTGGCACCGT	0.463													G|||	2696	0.538339	0.5855	0.5029	5008	,	,		18115	0.4206		0.6093	False		,,,				2504	0.5481				p.T187S		Atlas-SNP	.											.	C7orf31	53	.	0			c.C560G						PASS	.	G	SER/THR	2605,1801	640.7+/-397.3	767,1071,365	67.0	69.0	69.0		560	5.4	0.9	7	dbSNP_100	69	5221,3379	641.1+/-399.7	1546,2129,625	yes	missense	C7orf31	NM_138811.3	58	2313,3200,990	CC,CG,GG		39.2907,40.8761,39.8278	benign	187/591	25194665	7826,5180	2203	4300	6503	SO:0001583	missense	136895	exon6			GCCTTGGTTGGCA	AK097248	CCDS5394.1	7p15.2	2011-11-24			ENSG00000153790	ENSG00000153790			21722	protein-coding gene	gene with protein product							Standard	NM_138811		Approved		uc003sxn.1	Q8N865	OTTHUMG00000128497	ENST00000409280.1:c.560C>G	7.37:g.25194665G>C	ENSP00000386604:p.Thr187Ser	Somatic	156	1	0.00641026		WXS	Illumina HiSeq	Phase_I	131	130	0.992366	NM_138811	A4D165|Q6MZV8|Q6P989|Q7LE28|Q86XK1|Q8N1H5|Q96BN4	Missense_Mutation	SNP	ENST00000409280.1	37	CCDS5394.1	1146	0.5247252747252747	282	0.573170731707317	190	0.5248618784530387	219	0.38286713286713286	455	0.600263852242744	g	14.26	2.481050	0.44147	0.591239	0.607093	ENSG00000153790	ENST00000409280;ENST00000283905	T;T	0.10477	2.87;2.87	5.36	5.36	0.76844	.	0.212591	0.33199	N	0.005170	T	0.00012	0.0000	L	0.55103	1.725	0.34400	P	0.30483000000000005	D	0.64830	0.994	D	0.64144	0.922	T	0.06285	-1.0835	9	0.08381	T	0.77	-3.4082	14.5892	0.68351	0.0:0.0:1.0:0.0	rs2523072;rs17857285;rs17857514;rs52792533;rs56736187;rs2523072	187	Q8N865	CG031_HUMAN	S	187	ENSP00000386604:T187S;ENSP00000283905:T187S	ENSP00000283905:T187S	T	-	2	0	C7orf31	25161190	0.982000	0.34865	0.893000	0.35052	0.262000	0.26303	2.267000	0.43329	2.523000	0.85059	0.563000	0.77884	ACC	G|0.428;C|0.572	0.572	strong		0.463	C7orf31-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326929.1	NM_138811	
ACAN	176	hgsc.bcm.edu	37	15	89401109	89401109	+	Missense_Mutation	SNP	A	A	G	rs4932439	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:89401109A>G	ENST00000561243.1	+	11	5293	c.5293A>G	c.(5293-5295)Att>Gtt	p.I1765V	ACAN_ENST00000439576.2_Missense_Mutation_p.I1765V|ACAN_ENST00000559004.1_Missense_Mutation_p.I1765V|ACAN_ENST00000352105.7_Missense_Mutation_p.I1765V			P16112	PGCA_HUMAN	aggrecan	1789	CS-2.				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|proteolysis (GO:0006508)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)	carbohydrate binding (GO:0030246)|extracellular matrix structural constituent (GO:0005201)|hyaluronic acid binding (GO:0005540)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(4)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(15)|liver(2)|lung(40)|ovary(2)|prostate(5)|skin(5)|stomach(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	93	Lung NSC(78;0.0392)|all_lung(78;0.077)		BRCA - Breast invasive adenocarcinoma(143;0.146)			ACAACCAGGTATTAGTGGAGA	0.507													G|||	3808	0.760383	0.9909	0.6527	5008	,	,		20228	0.494		0.8101	False		,,,				2504	0.7485				p.I1765V		Atlas-SNP	.											.	ACAN	220	.	0			c.A5293G						PASS	.	G	VAL/ILE,VAL/ILE	3662,150		1762,138,6	61.0	63.0	62.0		5293,5293	1.8	0.5	15	dbSNP_111	62	6791,1443		2801,1189,127	yes	missense,missense	ACAN	NM_013227.3,NM_001135.3	29,29	4563,1327,133	GG,GA,AA		17.5249,3.9349,13.2243	benign,benign	1765/2531,1765/2432	89401109	10453,1593	1906	4117	6023	SO:0001583	missense	176	exon12			CCAGGTATTAGTG	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.5293A>G	15.37:g.89401109A>G	ENSP00000453342:p.Ile1765Val	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	183	182	0.994536	NM_001135	Q13650|Q9UCD3|Q9UCP4|Q9UCP5|Q9UDE0	Missense_Mutation	SNP	ENST00000561243.1	37	CCDS53970.1	1604	0.7344322344322345	485	0.9857723577235772	245	0.6767955801104972	256	0.44755244755244755	618	0.8153034300791556	G	0.021	-1.432403	0.01108	0.960651	0.824751	ENSG00000157766	ENST00000439576;ENST00000352105;ENST00000268134	T;T	0.01933	4.76;4.55	5.86	1.82	0.25136	.	0.938409	0.08642	N	0.915321	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B;B	0.16166	0.007;0.016	B;B	0.14023	0.007;0.01	T	0.26744	-1.0094	8	0.02654	T	1	-6.7047	6.0572	0.19819	0.3:0.3461:0.354:0.0	rs4932439;rs57208465;rs4932439	1765;1765	E7ENV9;E7EX88	.;.	V	1765;1765;1651	ENSP00000387356:I1765V;ENSP00000341615:I1765V	ENSP00000268134:I1651V	I	+	1	0	ACAN	87202113	0.005000	0.15991	0.482000	0.27366	0.926000	0.56050	-0.059000	0.11731	-0.103000	0.12175	-0.119000	0.15052	ATT	A|0.243;G|0.757	0.757	strong		0.507	ACAN-006	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416267.2	NM_001135	
FAM160A2	84067	hgsc.bcm.edu	37	11	6245256	6245256	+	Missense_Mutation	SNP	C	C	T	rs200289464		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:6245256C>T	ENST00000449352.2	-	3	624	c.361G>A	c.(361-363)Gat>Aat	p.D121N	FAM160A2_ENST00000524416.1_Missense_Mutation_p.D121N|FAM160A2_ENST00000265978.4_Missense_Mutation_p.D121N			Q8N612	F16A2_HUMAN	family with sequence similarity 160, member A2	121					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						TCGACCCCATCCCCAAGCTCA	0.607																																					p.D121N		Atlas-SNP	.											.	FAM160A2	100	.	0			c.G361A						PASS	.	C	ASN/ASP,ASN/ASP	0,4402		0,0,2201	54.0	46.0	48.0		361,361	4.1	1.0	11		48	3,8589	3.0+/-9.4	0,3,4293	yes	missense,missense	FAM160A2	NM_001098794.1,NM_032127.3	23,23	0,3,6494	TT,TC,CC		0.0349,0.0,0.0231	probably-damaging,probably-damaging	121/973,121/987	6245256	3,12991	2201	4296	6497	SO:0001583	missense	84067	exon3			CCCCATCCCCAAG		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.361G>A	11.37:g.6245256C>T	ENSP00000416918:p.Asp121Asn	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	97	17	0.175258	NM_032127	Q9C0A4|Q9H0N3|Q9H624	Missense_Mutation	SNP	ENST00000449352.2	37	CCDS44530.1	.	.	.	.	.	.	.	.	.	.	C	17.45	3.392996	0.62066	0.0	3.49E-4	ENSG00000051009	ENST00000449352;ENST00000442917;ENST00000265978;ENST00000524416	T;T;T	0.34472	1.36;1.36;1.36	5.05	4.14	0.48551	.	0.244954	0.28914	N	0.013721	T	0.35508	0.0934	N	0.14661	0.345	0.36163	D	0.84822	D;P;P	0.67145	0.996;0.611;0.557	D;B;B	0.66716	0.946;0.257;0.167	T	0.43877	-0.9364	10	0.48119	T	0.1	-17.8004	6.1565	0.20340	0.1851:0.7216:0.0:0.0933	.	121;121;121	E9PJK5;Q8N612;Q8N612-2	.;F16A2_HUMAN;.	N	121;46;121;121	ENSP00000416918:D121N;ENSP00000265978:D121N;ENSP00000431773:D121N	ENSP00000265978:D121N	D	-	1	0	FAM160A2	6201832	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.975000	0.49281	1.364000	0.46038	0.655000	0.94253	GAT	C|0.999;T|0.001	0.001	weak		0.607	FAM160A2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000383759.1	NM_032127	
RABEP1	9135	hgsc.bcm.edu	37	17	5280440	5280440	+	Silent	SNP	T	T	C	rs3026101	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:5280440T>C	ENST00000546142.2	+	14	2242	c.2055T>C	c.(2053-2055)cgT>cgC	p.R685R	RABEP1_ENST00000537505.1_Silent_p.R642R|RABEP1_ENST00000408982.2_Silent_p.R685R|RABEP1_ENST00000341923.6_Silent_p.R685R|NUP88_ENST00000573169.1_Intron|RABEP1_ENST00000262477.6_Silent_p.R685R			Q15276	RABE1_HUMAN	rabaptin, RAB GTPase binding effector protein 1	685					apoptotic process (GO:0006915)|endocytosis (GO:0006897)|membrane fusion (GO:0061025)|protein transport (GO:0015031)	early endosome (GO:0005769)|endocytic vesicle (GO:0030139)|endosome (GO:0005768)|intracellular membrane-bounded organelle (GO:0043231)	GTPase activator activity (GO:0005096)|protein homodimerization activity (GO:0042803)			NS(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|ovary(2)|stomach(1)|upper_aerodigestive_tract(1)	8						TAAAATACCGTGAGGACATCA	0.408													T|||	1963	0.391973	0.2315	0.3573	5008	,	,		18412	0.6012		0.3479	False		,,,				2504	0.4632				p.R685R		Atlas-SNP	.											RABEP1,NS,haematopoietic_neoplasm,+1,1	RABEP1	59	1	0			c.T2055C						PASS	.	T	,	907,2861		102,703,1079	141.0	135.0	137.0		2055,2055	-10.0	0.2	17	dbSNP_102	137	2497,5717		364,1769,1974	no	coding-synonymous,coding-synonymous	RABEP1	NM_001083585.1,NM_004703.4	,	466,2472,3053	CC,CT,TT		30.3993,24.0711,28.4093	,	685/830,685/863	5280440	3404,8578	1884	4107	5991	SO:0001819	synonymous_variant	9135	exon14			ATACCGTGAGGAC	AF098638	CCDS42243.1, CCDS45592.1	17p13.2	2008-02-05				ENSG00000029725			17677	protein-coding gene	gene with protein product		603616				8521472	Standard	NM_001291582		Approved	neurocrescin, RAB5EP, RABPT5, rabaptin-5	uc002gbm.4	Q15276		ENST00000546142.2:c.2055T>C	17.37:g.5280440T>C		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	61	28	0.459016	NM_004703	B2RAG7|O95369|Q8IVX3	Silent	SNP	ENST00000546142.2	37	CCDS45592.1																																																																																			T|0.635;C|0.365	0.365	strong		0.408	RABEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439349.1	NM_004703	
DNAH1	25981	hgsc.bcm.edu	37	3	52409421	52409421	+	Missense_Mutation	SNP	A	A	G	rs56002041	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	33	0	0		WXS	Illumina HiSeq	Phase_I	26	18	0.692308	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	
ORAI1	84876	hgsc.bcm.edu	37	12	122079429	122079429	+	Silent	SNP	T	T	C	rs3825174	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:122079429T>C	ENST00000330079.7	+	2	985	c.792T>C	c.(790-792)gtT>gtC	p.V264V		NM_032790.3	NP_116179	Q96D31	CRCM1_HUMAN	ORAI calcium release-activated calcium modulator 1	262					blood coagulation (GO:0007596)|immune system process (GO:0002376)|positive regulation of calcium ion transport (GO:0051928)|regulation of calcium ion transport (GO:0051924)|store-operated calcium entry (GO:0002115)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|protein complex (GO:0043234)	identical protein binding (GO:0042802)|store-operated calcium channel activity (GO:0015279)			breast(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(3)|upper_aerodigestive_tract(1)	11	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)			OV - Ovarian serous cystadenocarcinoma(86;0.000415)|Epithelial(86;0.00148)		GCTCACTGGTTAGCCATAAGA	0.617													C|||	239	0.0477236	0.0802	0.0043	5008	,	,		19718	0.1131		0.0089	False		,,,				2504	0.0072				p.V264V		Atlas-SNP	.											.	ORAI1	66	.	0			c.T792C						PASS	.	C		308,3960		6,296,1832	70.0	82.0	78.0		792	5.5	1.0	12	dbSNP_107	78	53,8439		0,53,4193	no	coding-synonymous	ORAI1	NM_032790.3		6,349,6025	CC,CT,TT		0.6241,7.2165,2.8292		264/304	122079429	361,12399	2134	4246	6380	SO:0001819	synonymous_variant	84876	exon2			ACTGGTTAGCCAT	AK027372		12q24.31	2014-09-17	2007-08-14	2007-08-14	ENSG00000182500	ENSG00000276045		"""ORAI calcium release-activated calcium modulators"""	25896	protein-coding gene	gene with protein product	"""calcium release-activated calcium modulator 1"""	610277	"""transmembrane protein 142A"""	TMEM142A		16582901	Standard	NM_032790		Approved	FLJ14466, CRACM1	uc021rff.1	Q96D31		ENST00000330079.7:c.792T>C	12.37:g.122079429T>C		Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	149	58	0.389262	NM_032790	Q3MHV3|Q6DHX2|Q96BP7|Q96K71	Silent	SNP	ENST00000330079.7	37	CCDS41851.1																																																																																			T|0.962;C|0.038	0.038	strong		0.617	ORAI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402151.1	NM_032790	
PRDM9	56979	hgsc.bcm.edu	37	5	23527385	23527385	+	Missense_Mutation	SNP	A	A	C	rs572984210	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:23527385A>C	ENST00000296682.3	+	11	2370	c.2188A>C	c.(2188-2190)Agc>Cgc	p.S730R		NM_020227.2	NP_064612.2	Q9NQV7	PRDM9_HUMAN	PR domain containing 9	730					meiotic gene conversion (GO:0006311)|positive regulation of meiosis I (GO:0060903)|positive regulation of reciprocal meiotic recombination (GO:0010845)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)	histone methyltransferase activity (H3-K4 specific) (GO:0042800)|metal ion binding (GO:0046872)|recombination hotspot binding (GO:0010844)|sequence-specific DNA binding (GO:0043565)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(15)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(27)|lung(87)|ovary(6)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(11)	172						GCGGGGCTTTAGCAATAAGTC	0.592										HNSCC(3;0.000094)			A|||	2	0.000399361	0.0	0.0	5008	,	,		18107	0.0		0.001	False		,,,				2504	0.001				p.S730R		Atlas-SNP	.											PRDM9,rectum,carcinoma,-2,1	PRDM9	344	1	0			c.A2188C						scavenged	.						23.0	25.0	24.0					5																	23527385		2061	4175	6236	SO:0001583	missense	56979	exon11			GGCTTTAGCAATA	AF275816	CCDS43307.1	5p14.2	2014-06-03			ENSG00000164256	ENSG00000164256		"""-"", ""Zinc fingers, C2H2-type"""	13994	protein-coding gene	gene with protein product	"""PR-domain containing protein 9"""	609760	"""minisatellite binding protein 3, 115kDa"", ""minisatellite binding protein 3 (115kD)"""	MSBP3		10668202, 2062643, 24634223	Standard	NM_020227		Approved	PFM6, ZNF899	uc003jgo.3	Q9NQV7	OTTHUMG00000161918	ENST00000296682.3:c.2188A>C	5.37:g.23527385A>C	ENSP00000296682:p.Ser730Arg	Somatic	89	1	0.011236		WXS	Illumina HiSeq	Phase_I	128	31	0.242188	NM_020227	B4DX22|Q27Q50	Missense_Mutation	SNP	ENST00000296682.3	37	CCDS43307.1	.	.	.	.	.	.	.	.	.	.	A	1.456	-0.563682	0.03939	.	.	ENSG00000164256	ENST00000296682	T	0.19669	2.13	2.88	2.88	0.33553	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.12390	0.0301	L	0.27944	0.81	0.09310	N	1	P	0.47350	0.894	B	0.38880	0.284	T	0.11324	-1.0592	9	0.44086	T	0.13	.	5.3589	0.16077	0.7466:0.0:0.0:0.2534	.	730	Q9NQV7	PRDM9_HUMAN	R	730	ENSP00000296682:S730R	ENSP00000296682:S730R	S	+	1	0	PRDM9	23563142	0.001000	0.12720	0.030000	0.17652	0.002000	0.02628	0.832000	0.27490	1.549000	0.49425	0.454000	0.30748	AGC	.	.	none		0.592	PRDM9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366375.1	NM_020227	
SVEP1	79987	hgsc.bcm.edu	37	9	113191597	113191597	+	Missense_Mutation	SNP	G	G	A	rs76469101	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:113191597G>A	ENST00000401783.2	-	35	5969	c.5633C>T	c.(5632-5634)aCt>aTt	p.T1878I	SVEP1_ENST00000374469.1_Missense_Mutation_p.T1855I|SVEP1_ENST00000297826.5_5'Flank	NM_153366.3	NP_699197.3	Q4LDE5	SVEP1_HUMAN	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	1878	Sushi 8. {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						ACCGGCCAGAGTATATCCTTT	0.373													G|||	51	0.0101837	0.0	0.0144	5008	,	,		16574	0.0		0.0368	False		,,,				2504	0.0041				p.T1878I		Atlas-SNP	.											SVEP1,NS,carcinoma,0,1	SVEP1	326	1	0			c.C5633T						PASS	.	G	ILE/THR	15,3637		0,15,1811	31.0	29.0	30.0		5633	0.5	0.2	9	dbSNP_132	30	249,7915		6,237,3839	no	missense	SVEP1	NM_153366.3	89	6,252,5650	AA,AG,GG		3.05,0.4107,2.2343	possibly-damaging	1878/3572	113191597	264,11552	1826	4082	5908	SO:0001583	missense	79987	exon35			GCCAGAGTATATC	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.5633C>T	9.37:g.113191597G>A	ENSP00000384917:p.Thr1878Ile	Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	29	14	0.482759	NM_153366	Q0P675|Q5D213|Q5T938|Q5VTE4|Q5VTE5|Q7Z387|Q7Z3G3|Q8NBT9|Q96JU7|Q9H284|Q9H8J9	Missense_Mutation	SNP	ENST00000401783.2	37	CCDS48004.1	39	0.017857142857142856	0	0.0	8	0.022099447513812154	0	0.0	31	0.040897097625329816	G	8.910	0.958458	0.18507	0.004107	0.0305	ENSG00000165124	ENST00000401783;ENST00000374469	T;T	0.65549	-0.16;-0.16	5.17	0.493	0.16878	Complement control module (2);Sushi/SCR/CCP (3);	0.564203	0.19954	N	0.102353	T	0.13243	0.0321	L	0.33293	1	0.09310	N	0.99999	B	0.17667	0.023	B	0.15052	0.012	T	0.06092	-1.0846	10	0.37606	T	0.19	.	1.835	0.03138	0.1462:0.1919:0.3544:0.3075	.	1878	Q4LDE5	SVEP1_HUMAN	I	1878;1855	ENSP00000384917:T1878I;ENSP00000363593:T1855I	ENSP00000363593:T1855I	T	-	2	0	SVEP1	112231418	0.001000	0.12720	0.220000	0.23810	0.893000	0.52053	-0.099000	0.11007	0.282000	0.22254	0.650000	0.86243	ACT	G|0.980;A|0.020	0.020	strong		0.373	SVEP1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
HYDIN	54768	hgsc.bcm.edu	37	16	70972595	70972595	+	Missense_Mutation	SNP	T	T	C	rs2502726	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:70972595T>C	ENST00000393567.2	-	44	7067	c.6917A>G	c.(6916-6918)gAa>gGa	p.E2306G		NM_001270974.1	NP_001257903.1	Q4G0P3	HYDIN_HUMAN	HYDIN, axonemal central pair apparatus protein	2306			E -> G (in dbSNP:rs2502726).		cilium assembly (GO:0042384)|cilium movement (GO:0003341)|epithelial cell development (GO:0002064)|trachea development (GO:0060438)|ventricular system development (GO:0021591)	cell projection (GO:0042995)				breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(12)|ovary(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	43		Ovarian(137;0.0654)				GGCATCATATTCTTCCTCATC	0.552													T|||	2273	0.453874	0.205	0.4597	5008	,	,		19914	0.4365		0.7445	False		,,,				2504	0.5051				p.E2306G		Atlas-SNP	.											.	HYDIN	788	.	0			c.A6917G						PASS	.						88.0	79.0	82.0					16																	70972595		1905	4129	6034	SO:0001583	missense	54768	exon44			TCATATTCTTCCT	AK074472	CCDS10897.1, CCDS56004.1, CCDS56005.1, CCDS59269.1	16q22.2	2014-02-05	2012-01-06		ENSG00000157423	ENSG00000157423		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	19368	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 31"""	610812	"""hydrocephalus inducing"", ""hydrocephalus inducing homolog (mouse)"""			12719380, 23022101	Standard	NM_001198542		Approved	DKFZp434D0513, KIAA1864, PPP1R31, CILD5	uc031qwy.1	Q4G0P3	OTTHUMG00000137584	ENST00000393567.2:c.6917A>G	16.37:g.70972595T>C	ENSP00000377197:p.Glu2306Gly	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	132	128	0.969697	NM_001270974	A6NC70|A6NLZ0|B4DQY4|B4DRN4|F5H6V3|Q8N3H8|Q8N3P6|Q8TC08|Q96JG3|Q96SS4|Q9H5U3|Q9H9B8|Q9NTI0|Q9UBE5	Missense_Mutation	SNP	ENST00000393567.2	37	CCDS59269.1	1116	0.510989010989011	100	0.2032520325203252	184	0.5082872928176796	258	0.45104895104895104	574	0.7572559366754618	T	28.1	4.886630	0.91814	.	.	ENSG00000157423	ENST00000393567;ENST00000316490	T	0.01887	4.58	5.6	5.6	0.85130	.	0.000000	0.33040	U	0.005343	T	0.00012	0.0000	L	0.36672	1.1	0.09310	P	1.0	D	0.89917	1.0	D	0.87578	0.998	T	0.00277	-1.1854	9	0.72032	D	0.01	.	15.4913	0.75607	0.0:0.0:0.0:1.0	rs2502726;rs4451953;rs59602564	2305	F8WD23	.	G	2306;2305	ENSP00000377197:E2306G	ENSP00000313052:E2305G	E	-	2	0	HYDIN	69530096	1.000000	0.71417	0.998000	0.56505	0.958000	0.62258	6.226000	0.72277	2.148000	0.66965	0.491000	0.48974	GAA	T|0.489;C|0.511	0.511	strong		0.552	HYDIN-001	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000398624.3		
NAGK	55577	hgsc.bcm.edu	37	2	71297695	71297695	+	Silent	SNP	T	T	C	rs2287328	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:71297695T>C	ENST00000244204.6	+	2	155	c.93T>C	c.(91-93)gaT>gaC	p.D31D	RP11-467P9.1_ENST00000608897.1_lincRNA|NAGK_ENST00000443938.2_Silent_p.D31D|NAGK_ENST00000443872.2_Intron|NAGK_ENST00000455662.2_Silent_p.D77D|NAGK_ENST00000418807.3_Intron|NAGK_ENST00000428360.2_3'UTR			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	100	0	0	1128	WXS	Illumina HiSeq	Phase_I	81	37	0.45679	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		
MYO7B	4648	hgsc.bcm.edu	37	2	128321770	128321770	+	Missense_Mutation	SNP	G	G	A	rs2404991	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:128321770G>A	ENST00000409816.2	+	2	93	c.61G>A	c.(61-63)Ggc>Agc	p.G21S	MYO7B_ENST00000389524.4_Missense_Mutation_p.G21S|MYO7B_ENST00000428314.1_Missense_Mutation_p.G21S			Q6PIF6	MYO7B_HUMAN	myosin VIIB	21			G -> S (in dbSNP:rs2404991).			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)		CCACAAGACCGGCGTGGCCAT	0.612													G|||	1980	0.395367	0.1392	0.5807	5008	,	,		20314	0.5526		0.4801	False		,,,				2504	0.3609				p.G21S		Atlas-SNP	.											.	MYO7B	359	.	0			c.G61A						PASS	.	G	SER/GLY	773,3267		85,603,1332	53.0	66.0	62.0		61	-0.3	0.0	2	dbSNP_100	62	4180,4166		1054,2072,1047	yes	missense	MYO7B	NM_001080527.1	56	1139,2675,2379	AA,AG,GG		49.9161,19.1337,39.9887	benign	21/2117	128321770	4953,7433	2020	4173	6193	SO:0001583	missense	4648	exon3			AAGACCGGCGTGG		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.61G>A	2.37:g.128321770G>A	ENSP00000386461:p.Gly21Ser	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	109	53	0.486239	NM_001080527	Q14786|Q8TEE1	Missense_Mutation	SNP	ENST00000409816.2	37	CCDS46405.1	989	0.45283882783882784	82	0.16666666666666666	206	0.569060773480663	316	0.5524475524475524	385	0.5079155672823219	G	6.991	0.552909	0.13374	0.191337	0.500839	ENSG00000169994	ENST00000389524;ENST00000428314;ENST00000409816	D;D;D	0.86956	-2.19;-2.19;-2.19	5.48	-0.284	0.12870	.	1.356880	0.04746	N	0.423624	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.18310	0.027	B	0.12156	0.007	T	0.19614	-1.0300	9	0.07030	T	0.85	.	10.5274	0.44957	0.7558:0.0:0.2442:0.0	rs2404991;rs17261901;rs57174242	21	Q6PIF6	MYO7B_HUMAN	S	21	ENSP00000374175:G21S;ENSP00000415090:G21S;ENSP00000386461:G21S	ENSP00000374175:G21S	G	+	1	0	MYO7B	128038240	0.000000	0.05858	0.000000	0.03702	0.078000	0.17371	0.446000	0.21694	0.001000	0.14605	0.563000	0.77884	GGC	G|0.541;A|0.458	0.458	strong		0.612	MYO7B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000331124.3	XM_291001	
RNF213	57674	hgsc.bcm.edu	37	17	78237572	78237572	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:78237572T>C	ENST00000582970.1	+	2	235	c.92T>C	c.(91-93)aTa>aCa	p.I31T	RNF213_ENST00000456466.1_Missense_Mutation_p.I31T|RNF213_ENST00000508628.2_Missense_Mutation_p.I31T|RNF213_ENST00000319921.4_Missense_Mutation_p.I31T	NM_001256071.1	NP_001243000.1	Q63HN8	RN213_HUMAN	ring finger protein 213	31					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)			GCAGCCCCCATAGCAGGTGAG	0.642																																					p.I31T		Atlas-SNP	.											.	RNF213	766	.	0			c.T92C						PASS	.						39.0	41.0	40.0					17																	78237572		2203	4300	6503	SO:0001583	missense	57674	exon2			CCCCCATAGCAGG	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.92T>C	17.37:g.78237572T>C	ENSP00000464087:p.Ile31Thr	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	90	4	0.0444444	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	.	.	.	.	.	.	.	.	.	.	T	8.002	0.755608	0.15846	.	.	ENSG00000173821	ENST00000508628;ENST00000411702;ENST00000456466;ENST00000319921	T	0.22743	1.94	3.71	-6.01	0.02199	.	.	.	.	.	T	0.07188	0.0182	N	0.08118	0	0.09310	N	0.999995	B	0.21452	0.056	B	0.18263	0.021	T	0.28202	-1.0051	9	0.46703	T	0.11	.	0.4433	0.00489	0.2848:0.2872:0.1455:0.2825	.	31	Q9HCF4-2	.	T	31	ENSP00000425956:I31T	ENSP00000324392:I31T	I	+	2	0	RNF213	75852167	0.000000	0.05858	0.000000	0.03702	0.060000	0.15804	-3.408000	0.00481	-1.514000	0.01786	0.460000	0.39030	ATA	.	.	none		0.642	RNF213-020	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443298.1	NM_020914	
CAND2	23066	hgsc.bcm.edu	37	3	12857493	12857493	+	Missense_Mutation	SNP	C	C	T	rs2305397	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:12857493C>T	ENST00000456430.2	+	9	1468	c.1427C>T	c.(1426-1428)cCt>cTt	p.P476L	CAND2_ENST00000295989.5_Missense_Mutation_p.P383L	NM_001162499.1	NP_001155971.1	O75155	CAND2_HUMAN	cullin-associated and neddylation-dissociated 2 (putative)	476			P -> L (in dbSNP:rs2305397).		positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	intracellular (GO:0005622)|nucleus (GO:0005634)				breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(8)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	37						GAGCATATGCCTGTGCTGGTA	0.627													C|||	1617	0.322883	0.3154	0.366	5008	,	,		19330	0.1766		0.5775	False		,,,				2504	0.1912				p.P476L	GBM(43;676 868 1633 6395 37496)	Atlas-SNP	.											CAND2_ENST00000456430,caecum,carcinoma,0,2	CAND2	138	2	0			c.C1427T						PASS	.	C	LEU/PRO,LEU/PRO	1410,2662		251,908,877	57.0	63.0	61.0		1427,1148	5.1	0.8	3	dbSNP_100	61	4400,3966		1144,2112,927	yes	missense,missense	CAND2	NM_001162499.1,NM_012298.2	98,98	1395,3020,1804	TT,TC,CC		47.4062,34.6267,46.7117	benign,benign	476/1237,383/1120	12857493	5810,6628	2036	4183	6219	SO:0001583	missense	23066	exon9			ATATGCCTGTGCT		CCDS43053.1, CCDS54554.1	3p25.2	2008-02-05			ENSG00000144712	ENSG00000144712			30689	protein-coding gene	gene with protein product	"""TBP interacting protein"""	610403				9734811, 10441524	Standard	NM_012298		Approved	TIP120B, KIAA0667, Tp120b	uc003bxk.2	O75155	OTTHUMG00000155397	ENST00000456430.2:c.1427C>T	3.37:g.12857493C>T	ENSP00000387641:p.Pro476Leu	Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	151	77	0.509934	NM_001162499	B9EGM9|E9KL24	Missense_Mutation	SNP	ENST00000456430.2	37	CCDS54554.1	803	0.3676739926739927	162	0.32926829268292684	122	0.3370165745856354	88	0.15384615384615385	431	0.5686015831134564	C	12.11	1.841013	0.32513	0.346267	0.525938	ENSG00000144712	ENST00000295989;ENST00000456430	T;T	0.11277	2.79;2.79	5.12	5.12	0.69794	Armadillo-like helical (1);Armadillo-type fold (1);	0.126888	0.53938	D	0.000055	T	0.00012	0.0000	M	0.69248	2.105	0.09310	P	1.0	B;B	0.25904	0.005;0.137	B;B	0.32533	0.009;0.147	T	0.45175	-0.9279	9	0.46703	T	0.11	-10.0664	16.0847	0.81038	0.0:1.0:0.0:0.0	rs2305397;rs17825005;rs52819689;rs59943117;rs2305397	476;383	O75155;O75155-2	CAND2_HUMAN;.	L	383;476	ENSP00000295989:P383L;ENSP00000387641:P476L	ENSP00000295989:P383L	P	+	2	0	CAND2	12832493	1.000000	0.71417	0.846000	0.33378	0.346000	0.29079	5.984000	0.70548	2.395000	0.81488	0.561000	0.74099	CCT	C|0.612;T|0.386	0.386	strong		0.627	CAND2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339856.4	XM_371617	
KRTAP10-9	386676	hgsc.bcm.edu	37	21	46047925	46047925	+	Silent	SNP	G	G	T	rs9979457	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:46047925G>T	ENST00000397911.3	+	1	886	c.837G>T	c.(835-837)ccG>ccT	p.P279P	TSPEAR_ENST00000323084.4_Intron|KRTAP10-9_ENST00000484861.1_Intron	NM_198690.2	NP_941963.2	P60411	KR109_HUMAN	keratin associated protein 10-9	279						keratin filament (GO:0045095)				endometrium(1)|kidney(1)|large_intestine(1)|lung(6)	9						GCTCCCGCCCGGCCTGCTACA	0.692													G|||	3169	0.632788	0.5212	0.6715	5008	,	,		17780	0.6627		0.7107	False		,,,				2504	0.6452				p.P279P		Atlas-SNP	.											.	KRTAP10-9	24	.	0			c.G837T						PASS	.	G	,	2373,1995		667,1039,478	60.0	74.0	70.0		,837	-5.6	0.0	21	dbSNP_119	70	5797,2777		1967,1863,457	no	intron,coding-synonymous	TSPEAR,KRTAP10-9	NM_144991.2,NM_198690.2	,	2634,2902,935	TT,TG,GG		32.3886,45.6731,36.8722	,	,279/293	46047925	8170,4772	2184	4287	6471	SO:0001819	synonymous_variant	386676	exon1			CCGCCCGGCCTGC	AJ566386	CCDS42961.1	21q22.3	2007-10-05			ENSG00000221837	ENSG00000221837		"""Keratin associated proteins"""	22971	protein-coding gene	gene with protein product				KRTAP18-9			Standard	NM_198690		Approved	KAP10.9, KAP18.9	uc002zfp.4	P60411	OTTHUMG00000057637	ENST00000397911.3:c.837G>T	21.37:g.46047925G>T		Somatic	116	1	0.00862069		WXS	Illumina HiSeq	Phase_I	151	150	0.993378	NM_198690	A2RRG1|A6NIR9|Q70LJ1	Silent	SNP	ENST00000397911.3	37	CCDS42961.1																																																																																			G|0.347;T|0.653	0.653	strong		0.692	KRTAP10-9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128040.1		
GIMAP6	474344	hgsc.bcm.edu	37	7	150324825	150324825	+	Silent	SNP	C	C	T	rs3735084	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:150324825C>T	ENST00000328902.5	-	3	1077	c.861G>A	c.(859-861)ctG>ctA	p.L287L	GIMAP6_ENST00000493969.1_3'UTR	NM_001244072.1|NM_024711.5	NP_001231001.1|NP_078987.3	Q6P9H5	GIMA6_HUMAN	GTPase, IMAP family member 6	287						cytosol (GO:0005829)	GTP binding (GO:0005525)	p.L287L(1)		endometrium(4)|kidney(1)|large_intestine(6)|lung(11)|ovary(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	29			OV - Ovarian serous cystadenocarcinoma(82;0.0145)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		CAGCCTTCCCCAGCAGGCATC	0.587													C|||	1424	0.284345	0.2829	0.2507	5008	,	,		19513	0.2956		0.3091	False		,,,				2504	0.273				p.L357L		Atlas-SNP	.											GIMAP6,NS,carcinoma,0,1	GIMAP6	60	1	1	Substitution - coding silent(1)	stomach(1)	c.G1071A						PASS	.	C		1263,3143	427.8+/-341.7	197,869,1137	77.0	68.0	72.0		861	1.8	0.0	7	dbSNP_107	72	2636,5964	419.2+/-353.0	412,1812,2076	no	coding-synonymous	GIMAP6	NM_024711.5		609,2681,3213	TT,TC,CC		30.6512,28.6655,29.9785		287/293	150324825	3899,9107	2203	4300	6503	SO:0001819	synonymous_variant	474344	exon3			CTTCCCCAGCAGG	AK026343	CCDS34778.1, CCDS59087.1, CCDS75676.1	7q36.1	2014-04-04			ENSG00000133561	ENSG00000133561		"""GTPases, IMAP"""	21918	protein-coding gene	gene with protein product	"""immune-associated nucleotide-binding protein 6"""					15474311	Standard	NM_001244072		Approved	FLJ22690, IAN6	uc022apv.1	Q6P9H5	OTTHUMG00000159137	ENST00000328902.5:c.861G>A	7.37:g.150324825C>T		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	86	86	1	NM_001244072	C9J7B6|D3DWZ4|Q5ZPR6|Q9H612	Silent	SNP	ENST00000328902.5	37	CCDS34778.1																																																																																			C|0.705;T|0.295	0.295	strong		0.587	GIMAP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353457.1	NM_024711	
NSUN4	387338	hgsc.bcm.edu	37	1	46810530	46810530	+	Missense_Mutation	SNP	A	A	G	rs3737744	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:46810530A>G	ENST00000474844.1	+	2	801	c.151A>G	c.(151-153)Act>Gct	p.T51A	NSUN4_ENST00000536062.1_Missense_Mutation_p.T2A|NSUN4_ENST00000537428.1_Missense_Mutation_p.T2A|NSUN4_ENST00000498008.1_3'UTR	NM_199044.3	NP_950245.2	Q96CB9	NSUN4_HUMAN	NOP2/Sun domain family, member 4	51			T -> A (in dbSNP:rs3737744). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		rRNA methylation (GO:0031167)	mitochondrial large ribosomal subunit (GO:0005762)	methyltransferase activity (GO:0008168)|rRNA binding (GO:0019843)			endometrium(2)|kidney(1)|large_intestine(2)|lung(2)|prostate(1)	8	Acute lymphoblastic leukemia(166;0.155)					TTTTGACATGACTTACAGTGT	0.483													A|||	1525	0.304513	0.1415	0.3559	5008	,	,		23393	0.5169		0.3419	False		,,,				2504	0.2311				p.T51A		Atlas-SNP	.											.	NSUN4	26	.	0			c.A151G						PASS	.	A	ALA/THR	801,3605	321.5+/-297.2	77,647,1479	177.0	173.0	175.0		151	5.4	1.0	1	dbSNP_107	175	2849,5751	449.1+/-362.0	466,1917,1917	yes	missense	NSUN4	NM_199044.2	58	543,2564,3396	GG,GA,AA		33.1279,18.1798,28.064	benign	51/385	46810530	3650,9356	2203	4300	6503	SO:0001583	missense	387338	exon2			GACATGACTTACA	AK021577	CCDS534.1, CCDS57996.1	1p34	2012-02-24	2009-11-23		ENSG00000117481	ENSG00000117481		"""NOP2/Sun domain containing"""	31802	protein-coding gene	gene with protein product	"""sperm head and tail associated protein"""	615394	"""NOL1/NOP2/Sun domain family 4"", ""NOL1/NOP2/Sun domain family, member 4"""				Standard	NM_199044		Approved	MGC22960, SHTAP	uc001cpr.2	Q96CB9	OTTHUMG00000007808	ENST00000474844.1:c.151A>G	1.37:g.46810530A>G	ENSP00000419740:p.Thr51Ala	Somatic	258	0	0		WXS	Illumina HiSeq	Phase_I	193	91	0.471503	NM_199044	A8K6S6|B3KQ50|B4DHA4|Q5TDF7|Q96AN8|Q9HAJ8	Missense_Mutation	SNP	ENST00000474844.1	37	CCDS534.1	775	0.35485347985347987	81	0.16463414634146342	143	0.39502762430939226	282	0.493006993006993	269	0.3548812664907652	A	16.01	3.001459	0.54254	0.181798	0.331279	ENSG00000117481	ENST00000474844;ENST00000536062;ENST00000537428	T;T;T	0.14516	2.54;2.5;2.5	5.45	5.45	0.79879	.	0.207467	0.49916	D	0.000140	T	0.00012	0.0000	L	0.46157	1.445	0.24446	P	0.99450097	B	0.11235	0.004	B	0.10450	0.005	T	0.47381	-0.9122	9	0.17369	T	0.5	-15.6344	15.1862	0.73002	1.0:0.0:0.0:0.0	rs3737744;rs3895370;rs17845416;rs17858282;rs52835213;rs61120032;rs3737744	51	Q96CB9	NSUN4_HUMAN	A	51;2;2	ENSP00000419740:T51A;ENSP00000438912:T2A;ENSP00000437758:T2A	ENSP00000419740:T51A	T	+	1	0	NSUN4	46583117	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	5.480000	0.66820	2.080000	0.62538	0.460000	0.39030	ACT	G|0.311;N|0.000	0.311	strong		0.483	NSUN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021427.1	NM_199044	
MRGPRX4	117196	hgsc.bcm.edu	37	11	18194944	18194944	+	Silent	SNP	T	T	A	rs11024531	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:18194944T>A	ENST00000314254.3	+	1	561	c.141T>A	c.(139-141)gtT>gtA	p.V47V	RP11-113D6.6_ENST00000527671.1_Intron	NM_054032.3	NP_473373.2	Q96LA9	MRGX4_HUMAN	MAS-related GPR, member X4	47						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						GAAACGCGGTTGTGCTCTGGC	0.557													T|||	1374	0.274361	0.0862	0.3617	5008	,	,		21062	0.504		0.2734	False		,,,				2504	0.2311				p.V47V		Atlas-SNP	.											.	MRGPRX4	68	.	0			c.T141A						PASS	.	T		534,3864	243.4+/-253.1	29,476,1694	145.0	129.0	134.0		141	-1.1	0.0	11	dbSNP_120	134	2251,6335	380.7+/-339.8	310,1631,2352	no	coding-synonymous	MRGPRX4	NM_054032.3		339,2107,4046	AA,AT,TT		26.2171,12.1419,21.4495		47/323	18194944	2785,10199	2199	4293	6492	SO:0001819	synonymous_variant	117196	exon1			CGCGGTTGTGCTC	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.141T>A	11.37:g.18194944T>A		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	123	96	0.780488	NM_054032	Q3KNU3|Q3KNU4|Q502W0|Q8TDD6|Q8TDD7	Silent	SNP	ENST00000314254.3	37	CCDS7831.1																																																																																			T|0.760;A|0.240	0.240	strong		0.557	MRGPRX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389788.1	NM_054032	
ZNF732	654254	hgsc.bcm.edu	37	4	289272	289272	+	Missense_Mutation	SNP	C	C	T	rs112132883	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:289272C>T	ENST00000419098.1	-	3	191	c.181G>A	c.(181-183)Gag>Aag	p.E61K		NM_001137608.1	NP_001131080.1	B4DXR9	ZN732_HUMAN	zinc finger protein 732	61	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						TTGTAGGGCTCCTTTCTTTGC	0.448													.|||	80	0.0159744	0.0023	0.0245	5008	,	,		16257	0.001		0.0537	False		,,,				2504	0.0051				p.E60K		Atlas-SNP	.											.	ZNF732	117	.	0			c.G178A						PASS	.	C	LYS/GLU	16,1368		0,16,676	191.0	151.0	163.0		181	1.2	0.2	4	dbSNP_132	163	180,3002		2,176,1413	yes	missense	ZNF732	NM_001137608.1	56	2,192,2089	TT,TC,CC		5.6568,1.1561,4.2926	probably-damaging	61/586	289272	196,4370	692	1591	2283	SO:0001583	missense	654254	exon2			AGGGCTCCTTTCT	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.181G>A	4.37:g.289272C>T	ENSP00000415774:p.Glu61Lys	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	95	46	0.484211	NM_001137608		Missense_Mutation	SNP	ENST00000419098.1	37	CCDS46990.1	54	0.024725274725274724	1	0.0020325203252032522	12	0.03314917127071823	1	0.0017482517482517483	40	0.052770448548812667	C	10.55	1.382271	0.24944	0.011561	0.056568	ENSG00000186777	ENST00000419098	T	0.06687	3.27	1.22	1.22	0.21188	Krueppel-associated box (2);	.	.	.	.	T	0.01870	0.0059	L	0.56199	1.76	0.09310	N	1	D	0.89917	1.0	D	0.83275	0.996	T	0.08889	-1.0700	9	0.42905	T	0.14	.	5.3307	0.15930	0.0:1.0:0.0:0.0	.	61	B4DXR9	ZN732_HUMAN	K	61	ENSP00000415774:E61K	ENSP00000415774:E61K	E	-	1	0	ZNF732	279272	0.689000	0.27690	0.176000	0.23000	0.179000	0.23085	0.965000	0.29319	0.300000	0.22699	0.305000	0.20034	GAG	C|0.975;T|0.025	0.025	strong		0.448	ZNF732-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000357937.2	NM_001137608	
ANKRD18B	441459	hgsc.bcm.edu	37	9	33572347	33572347	+	Missense_Mutation	SNP	T	T	C	rs7853994	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:33572347T>C	ENST00000290943.6	+	16	3121	c.3025T>C	c.(3025-3027)Ttt>Ctt	p.F1009L		NM_001244752.1	NP_001231681.1	A2A2Z9	AN18B_HUMAN	ankyrin repeat domain 18B	1009										NS(1)|breast(1)|endometrium(2)|lung(1)|prostate(1)|stomach(1)	7						TCCTATCTACTTTCTTCTCTA	0.323													.|||	972	0.194089	0.1679	0.2104	5008	,	,		16850	0.2103		0.2048	False		,,,				2504	0.1902				p.F1008L		Atlas-SNP	.											ANKRD18B,NS,carcinoma,0,1	ANKRD18B	46	1	0			c.T3022C						PASS	.																																			SO:0001583	missense	441459	exon16			ATCTACTTTCTTC			9p13.3	2013-01-10			ENSG00000230453	ENSG00000230453		"""Ankyrin repeat domain containing"""	23644	protein-coding gene	gene with protein product							Standard	NM_001244752		Approved	bA255A11.3	uc010mjw.2	A2A2Z9	OTTHUMG00000019776	ENST00000290943.6:c.3025T>C	9.37:g.33572347T>C	ENSP00000290943:p.Phe1009Leu	Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	167	85	0.508982	NM_001244752		Missense_Mutation	SNP	ENST00000290943.6	37		467	0.21382783882783882	102	0.2073170731707317	84	0.23204419889502761	125	0.21853146853146854	156	0.20580474934036938	T	11.80	1.746056	0.30955	.	.	ENSG00000230453	ENST00000290943	T	0.26223	1.75	1.46	-2.27	0.06846	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.30974	P	0.7227589999999999	.	.	.	.	.	.	T	0.40850	-0.9541	5	0.08837	T	0.75	.	5.3397	0.15976	0.0:0.3931:0.0:0.6069	rs7853994;rs17503365;rs52813410;rs7853994	.	.	.	L	1009	ENSP00000290943:F1009L	ENSP00000290943:F1009L	F	+	1	0	ANKRD18B	33562347	0.000000	0.05858	0.000000	0.03702	0.013000	0.08279	-0.197000	0.09518	-0.749000	0.04747	0.248000	0.18094	TTT	T|0.791;C|0.209	0.209	strong		0.323	ANKRD18B-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000313729.2	XM_001718334	
TNFRSF14	8764	hgsc.bcm.edu	37	1	2488153	2488153	+	Missense_Mutation	SNP	A	A	G	rs4870	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:2488153A>G	ENST00000355716.4	+	1	349	c.50A>G	c.(49-51)aAa>aGa	p.K17R	TNFRSF14_ENST00000409119.1_Missense_Mutation_p.K17R|RP3-395M20.8_ENST00000452793.1_RNA|TNFRSF14_ENST00000442392.2_3'UTR|RP3-395M20.8_ENST00000416860.2_RNA	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	77	0	0		WXS	Illumina HiSeq	Phase_I	45	17	0.377778	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		
ESPL1	9700	hgsc.bcm.edu	37	12	53682457	53682457	+	Missense_Mutation	SNP	G	G	A	rs56358776	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:53682457G>A	ENST00000257934.4	+	20	4773	c.4682G>A	c.(4681-4683)cGg>cAg	p.R1561Q	ESPL1_ENST00000552462.1_Missense_Mutation_p.R1561Q	NM_012291.4	NP_036423.4	Q14674	ESPL1_HUMAN	extra spindle pole bodies homolog 1 (S. cerevisiae)	1561				R -> Q (in Ref. 1; AAR18247 and 2; BAA11482). {ECO:0000305}.	apoptotic process (GO:0006915)|cytokinesis (GO:0000910)|establishment of mitotic spindle localization (GO:0040001)|homologous chromosome segregation (GO:0045143)|meiotic spindle organization (GO:0000212)|mitotic cell cycle (GO:0000278)|mitotic sister chromatid segregation (GO:0000070)|negative regulation of sister chromatid cohesion (GO:0045875)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)	centrosome (GO:0005813)|cytosol (GO:0005829)|nucleus (GO:0005634)	catalytic activity (GO:0003824)|cysteine-type peptidase activity (GO:0008234)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(10)|large_intestine(12)|lung(21)|ovary(2)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(8)	70						CCTCGGCTCCGGCTCCCCTCA	0.592													g|||	1190	0.23762	0.2632	0.3386	5008	,	,		17662	0.1319		0.341	False		,,,				2504	0.1339				p.R1561Q	Colon(53;1069 1201 2587 5382)	Atlas-SNP	.											.	ESPL1	158	.	0			c.G4682A						PASS	.	G	GLN/ARG	1263,3143		181,901,1121	47.0	47.0	47.0		4682	-7.1	0.0	12	dbSNP_129	47	2904,5694		498,1908,1893	yes	missense	ESPL1	NM_012291.4	43	679,2809,3014	AA,AG,GG		33.7753,28.6655,32.044	benign	1561/2121	53682457	4167,8837	2203	4299	6502	SO:0001583	missense	9700	exon20			GGCTCCGGCTCCC	D79987	CCDS8852.1	12q13.13	2014-08-04	2013-05-03		ENSG00000135476	ENSG00000135476	3.4.22.49		16856	protein-coding gene	gene with protein product	"""separin"", ""separase"", ""separin, cysteine protease"""	604143	"""extra spindle poles like 1 (S. cerevisiae)"""			8724849, 16258266	Standard	NM_012291		Approved	KIAA0165, ESP1, SEPA	uc001sck.2	Q14674	OTTHUMG00000169674	ENST00000257934.4:c.4682G>A	12.37:g.53682457G>A	ENSP00000257934:p.Arg1561Gln	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	164	85	0.518293	NM_012291		Missense_Mutation	SNP	ENST00000257934.4	37	CCDS8852.1	634	0.2902930402930403	139	0.28252032520325204	123	0.3397790055248619	100	0.17482517482517482	272	0.35883905013192613	g	6.020	0.372128	0.11409	0.286655	0.337753	ENSG00000135476	ENST00000257934;ENST00000552671;ENST00000552462	T;T	0.11604	2.76;2.76	5.34	-7.11	0.01542	.	1.494160	0.03591	N	0.231873	T	0.00012	0.0000	M	0.63428	1.95	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.43048	-0.9415	9	0.14656	T	0.56	.	9.7156	0.40272	0.6513:0.1114:0.2373:0.0	rs56358776;rs57423655;rs61741333	1561	Q14674	ESPL1_HUMAN	Q	1561;1236;1561	ENSP00000257934:R1561Q;ENSP00000449831:R1561Q	ENSP00000257934:R1561Q	R	+	2	0	ESPL1	51968724	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-2.550000	0.00929	-1.910000	0.01083	-1.723000	0.00705	CGG	G|0.698;A|0.302	0.302	strong		0.592	ESPL1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406899.2	NM_012291	
MCPH1	79648	hgsc.bcm.edu	37	8	6500544	6500544	+	Missense_Mutation	SNP	C	C	T	rs1057091	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:6500544C>T	ENST00000344683.5	+	14	2558	c.2482C>T	c.(2482-2484)Cct>Tct	p.P828S	MCPH1_ENST00000521175.1_3'UTR|CTD-2541M15.1_ENST00000522897.1_RNA|CTD-2541M15.1_ENST00000515608.1_RNA|CTD-2541M15.1_ENST00000527490.1_RNA|CTD-2541M15.1_ENST00000525186.1_RNA	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	131	0	0		WXS	Illumina HiSeq	Phase_I	82	64	0.780488	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	
ZC3HAV1	56829	hgsc.bcm.edu	37	7	138732457	138732457	+	Silent	SNP	G	G	A	rs3735008	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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						PASS	.	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	128	1	0.0078125		WXS	Illumina HiSeq	Phase_I	106	106	1	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	
PRPH	5630	hgsc.bcm.edu	37	12	49691250	49691250	+	Silent	SNP	A	A	G	rs73112143	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:49691250A>G	ENST00000257860.4	+	6	2606	c.1107A>G	c.(1105-1107)aaA>aaG	p.K369K	RP11-161H23.9_ENST00000553259.1_RNA	NM_006262.3	NP_006253.2	P23942	PRPH2_HUMAN	peripherin	0					cell adhesion (GO:0007155)|retina development in camera-type eye (GO:0060041)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)				kidney(1)|large_intestine(2)|lung(8)|skin(1)	12						GACAGCTAAAAGAGGAGATGG	0.657											OREG0021790	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	1028	0.205272	0.3979	0.1484	5008	,	,		11296	0.0367		0.2048	False		,,,				2504	0.1595				p.K369K		Atlas-SNP	.											.	PRPH	26	.	0			c.A1107G						PASS	.	G		1549,2857		284,981,938	23.0	25.0	24.0		1107	3.7	1.0	12	dbSNP_130	24	1722,6876		201,1320,2778	no	coding-synonymous	PRPH	NM_006262.3		485,2301,3716	GG,GA,AA		20.0279,35.1566,25.1538		369/471	49691250	3271,9733	2203	4299	6502	SO:0001819	synonymous_variant	5630	exon6			GCTAAAAGAGGAG		CCDS8783.1	12q12-q13	2013-01-16						"""Intermediate filaments type III"""	9461	protein-coding gene	gene with protein product		170710		NEF4		1378416	Standard	XM_005269025		Approved	PRPH1	uc001rtu.3	P41219		ENST00000257860.4:c.1107A>G	12.37:g.49691250A>G		Somatic	42	0	0	964	WXS	Illumina HiSeq	Phase_I	30	17	0.566667	NM_006262	Q5TFH5|Q6DK65	Silent	SNP	ENST00000257860.4	37	CCDS8783.1	437	0.2000915750915751	189	0.38414634146341464	62	0.1712707182320442	27	0.0472027972027972	159	0.20976253298153033	G	18.31	3.596407	0.66332	0.351566	0.200279	ENSG00000135406	ENST00000532332	.	.	.	5.48	3.65	0.41850	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.38950	-0.9637	3	.	.	.	.	9.7563	0.40504	0.2302:0.0:0.7698:0.0	.	.	.	.	G	98	.	.	R	+	1	2	PRPH	47977517	1.000000	0.71417	0.993000	0.49108	0.968000	0.65278	4.851000	0.62896	0.690000	0.31570	-0.119000	0.15052	AGA	A|0.778;G|0.222	0.222	strong		0.657	PRPH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393381.1	NM_006262	
MYBL2	4605	hgsc.bcm.edu	37	20	42338621	42338621	+	Missense_Mutation	SNP	G	G	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:42338621G>C	ENST00000217026.4	+	10	1651	c.1524G>C	c.(1522-1524)caG>caC	p.Q508H	MYBL2_ENST00000396863.4_Missense_Mutation_p.Q484H	NM_002466.2	NP_002457.1	P10244	MYBB_HUMAN	v-myb avian myeloblastosis viral oncogene homolog-like 2	508					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)			CCCCAGATCAGAAGTACTCCA	0.622																																					p.Q508H		Atlas-SNP	.											.	MYBL2	82	.	0			c.G1524C						PASS	.						211.0	213.0	212.0					20																	42338621		2203	4300	6503	SO:0001583	missense	4605	exon10			AGATCAGAAGTAC		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.1524G>C	20.37:g.42338621G>C	ENSP00000217026:p.Gln508His	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	63	25	0.396825	NM_002466	B2RBS5|B7Z8D9|F8W6N6|Q53F07	Missense_Mutation	SNP	ENST00000217026.4	37	CCDS13322.1	.	.	.	.	.	.	.	.	.	.	G	13.61	2.289002	0.40494	.	.	ENSG00000101057	ENST00000396863;ENST00000217026	T;T	0.28069	1.63;1.63	4.86	4.86	0.63082	C-myb, C-terminal (1);	0.198115	0.46442	D	0.000282	T	0.09774	0.0240	N	0.00926	-1.1	0.40656	D	0.982083	B;B	0.33637	0.287;0.42	B;B	0.31686	0.078;0.134	T	0.30707	-0.9969	10	0.11794	T	0.64	-30.2082	12.2911	0.54819	0.0:0.0:0.8302:0.1697	.	484;508	F8W6N6;P10244	.;MYBB_HUMAN	H	484;508	ENSP00000380072:Q484H;ENSP00000217026:Q508H	ENSP00000217026:Q508H	Q	+	3	2	MYBL2	41772035	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	4.551000	0.60740	2.427000	0.82271	0.467000	0.42956	CAG	.	.	none		0.622	MYBL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080408.1	NM_002466	
KRIT1	889	hgsc.bcm.edu	37	7	91842554	91842554	+	Silent	SNP	T	T	C	rs11542682	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:91842554T>C	ENST00000340022.2	-	17	2998	c.1980A>G	c.(1978-1980)gtA>gtG	p.V660V	KRIT1_ENST00000394503.2_Silent_p.V612V|KRIT1_ENST00000394507.1_Silent_p.V660V|KRIT1_ENST00000394505.2_Silent_p.V660V|KRIT1_ENST00000412043.2_Silent_p.V660V	NM_004912.3|NM_194455.1	NP_004903.2|NP_919437.1	O00522	KRIT1_HUMAN	KRIT1, ankyrin repeat containing	660	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				angiogenesis (GO:0001525)|cell redox homeostasis (GO:0045454)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|positive regulation of protein binding (GO:0032092)|regulation of catalytic activity (GO:0050790)|regulation of establishment of cell polarity (GO:2000114)|small GTPase mediated signal transduction (GO:0007264)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|microtubule (GO:0005874)|plasma membrane (GO:0005886)	microtubule binding (GO:0008017)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|protein complex binding (GO:0032403)|small GTPase regulator activity (GO:0005083)	p.V660V(1)		autonomic_ganglia(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(9)|ovary(2)|stomach(1)	22	all_cancers(62;1.04e-09)|all_epithelial(64;5.75e-09)|Breast(17;0.00206)|all_lung(186;0.0509)|Lung NSC(181;0.0692)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)			TATTCACTCCTACATACACAG	0.363													t|||	904	0.180511	0.1589	0.1239	5008	,	,		18715	0.3403		0.0825	False		,,,				2504	0.1861				p.V660V		Atlas-SNP	.											KRIT1,NS,carcinoma,0,1	KRIT1	66	1	1	Substitution - coding silent(1)	stomach(1)	c.A1980G						PASS	.	G	,,,,	536,3870	243.4+/-253.1	40,456,1707	159.0	149.0	152.0		1836,1980,1980,1980,1980	-0.2	1.0	7	dbSNP_120	152	795,7805	186.0+/-233.6	39,717,3544	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	KRIT1	NM_001013406.1,NM_004912.3,NM_194454.1,NM_194455.1,NM_194456.1	,,,,	79,1173,5251	CC,CT,TT		9.2442,12.1652,10.2337	,,,,	612/689,660/737,660/737,660/737,660/737	91842554	1331,11675	2203	4300	6503	SO:0001819	synonymous_variant	889	exon18			CACTCCTACATAC	AJ294850	CCDS5624.1, CCDS34679.1	7q21.2	2014-09-17	2005-03-15	2005-03-17	ENSG00000001631	ENSG00000001631		"""Ankyrin repeat domain containing"""	1573	protein-coding gene	gene with protein product		604214	"""cerebral cavernous malformations 1"""	CCM1		7604043, 11342228	Standard	NM_194455		Approved	CAM	uc003ulu.1	O00522	OTTHUMG00000131187	ENST00000340022.2:c.1980A>G	7.37:g.91842554T>C		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	82	43	0.52439	NM_194456	A6NNU0|O43894|Q506L6|Q6U276|Q75N19|Q9H180|Q9H264|Q9HAX5	Silent	SNP	ENST00000340022.2	37	CCDS5624.1																																																																																			T|0.867;C|0.133	0.133	strong		0.363	KRIT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253910.1		
UFC1	51506	hgsc.bcm.edu	37	1	161123901	161123901	+	Silent	SNP	C	C	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:161123901C>G	ENST00000368003.5	+	1	360	c.114C>G	c.(112-114)tcC>tcG	p.S38S	UFC1_ENST00000473766.1_3'UTR|RP11-297K8.2_ENST00000420498.1_RNA	NM_016406.3	NP_057490.2	Q9Y3C8	UFC1_HUMAN	ubiquitin-fold modifier conjugating enzyme 1	38					protein ufmylation (GO:0071569)|response to endoplasmic reticulum stress (GO:0034976)	extracellular vesicular exosome (GO:0070062)	UFM1 conjugating enzyme activity (GO:0071568)			endometrium(1)|lung(9)	10	all_cancers(52;3.73e-19)|Breast(13;0.000577)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00275)			AATATCAGTCCCTTATCCGGG	0.537																																					p.S38S		Atlas-SNP	.											.	UFC1	16	.	0			c.C114G						PASS	.						179.0	157.0	165.0					1																	161123901		2203	4300	6503	SO:0001819	synonymous_variant	51506	exon1			TCAGTCCCTTATC	AF161504	CCDS1220.1	1q23.3	2008-02-05			ENSG00000143222	ENSG00000143222			26941	protein-coding gene	gene with protein product		610554				15071506, 11042152	Standard	NM_016406		Approved	HSPC155	uc001fyd.4	Q9Y3C8	OTTHUMG00000033155	ENST00000368003.5:c.114C>G	1.37:g.161123901C>G		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	96	11	0.114583	NM_016406	A8K9R1|D3DVF9|Q549X0|Q5VTX1|Q9BS96|Q9P009	Silent	SNP	ENST00000368003.5	37	CCDS1220.1																																																																																			.	.	none		0.537	UFC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080810.1	NM_016406	
OR2M2	391194	hgsc.bcm.edu	37	1	248343721	248343721	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:248343721C>T	ENST00000359682.2	+	1	434	c.434C>T	c.(433-435)gCt>gTt	p.A145V		NM_001004688.1	NP_001004688.1	Q96R28	OR2M2_HUMAN	olfactory receptor, family 2, subfamily M, member 2	145						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.A145D(2)		NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(45)|ovary(3)|prostate(1)|skin(3)	70	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0245)			GGACTTATGGCTACCTTCTCC	0.428																																					p.A145V		Atlas-SNP	.											OR2M2,NS,carcinoma,0,2	OR2M2	149	2	2	Substitution - Missense(2)	lung(1)|endometrium(1)	c.C434T						scavenged	.						200.0	207.0	205.0					1																	248343721		2203	4300	6503	SO:0001583	missense	391194	exon1			TTATGGCTACCTT	AF399616	CCDS31106.1	1q44	2012-08-09			ENSG00000198601	ENSG00000198601		"""GPCR / Class A : Olfactory receptors"""	8268	protein-coding gene	gene with protein product						12213199	Standard	NM_001004688		Approved	OST423, OR2M2Q	uc010pzf.2	Q96R28	OTTHUMG00000040460	ENST00000359682.2:c.434C>T	1.37:g.248343721C>T	ENSP00000352710:p.Ala145Val	Somatic	258	0	0		WXS	Illumina HiSeq	Phase_I	235	4	0.0170213	NM_001004688	A3KFT4	Missense_Mutation	SNP	ENST00000359682.2	37	CCDS31106.1	.	.	.	.	.	.	.	.	.	.	c	0.054	-1.241058	0.01493	.	.	ENSG00000198601	ENST00000359682	T	0.34472	1.36	1.7	-3.39	0.04868	GPCR, rhodopsin-like superfamily (1);	0.986151	0.08198	N	0.982665	T	0.12220	0.0297	N	0.04245	-0.25	0.09310	N	1	B	0.14805	0.011	B	0.22880	0.042	T	0.29427	-1.0012	10	0.05351	T	0.99	.	4.6546	0.12611	0.0:0.3745:0.2983:0.3271	.	145	Q96R28	OR2M2_HUMAN	V	145	ENSP00000352710:A145V	ENSP00000352710:A145V	A	+	2	0	OR2M2	246410344	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.691000	0.05133	-1.004000	0.03421	-1.301000	0.01330	GCT	.	.	none		0.428	OR2M2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097356.2	NM_001004688	
ARSF	416	hgsc.bcm.edu	37	X	3021870	3021870	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:3021870G>T	ENST00000381127.1	+	9	1391	c.1170G>T	c.(1168-1170)aaG>aaT	p.K390N	ARSF_ENST00000537104.1_Missense_Mutation_p.K390N|ARSF_ENST00000359361.2_Missense_Mutation_p.K390N	NM_001201538.1|NM_001201539.1	NP_001188467.1|NP_001188468.1	P54793	ARSF_HUMAN	arylsulfatase F	390					cellular protein metabolic process (GO:0044267)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)	arylsulfatase activity (GO:0004065)|metal ion binding (GO:0046872)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(15)|ovary(2)|prostate(3)|skin(3)|urinary_tract(2)	38		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				GGCCTGGAAAGGTACCAGCTG	0.473																																					p.K390N		Atlas-SNP	.											.	ARSF	97	.	0			c.G1170T						PASS	.						101.0	92.0	95.0					X																	3021870		2203	4300	6503	SO:0001583	missense	416	exon9			TGGAAAGGTACCA	X97868	CCDS14123.1	Xp22.3	2013-02-14			ENSG00000062096	ENSG00000062096		"""Arylsulfatase family"""	721	protein-coding gene	gene with protein product		300003				7720070	Standard	NM_004042		Approved		uc022brz.1	P54793	OTTHUMG00000021081	ENST00000381127.1:c.1170G>T	X.37:g.3021870G>T	ENSP00000370519:p.Lys390Asn	Somatic	248	0	0		WXS	Illumina HiSeq	Phase_I	152	152	1	NM_004042	Q8TCC5	Missense_Mutation	SNP	ENST00000381127.1	37	CCDS14123.1	.	.	.	.	.	.	.	.	.	.	G	10.14	1.268921	0.23221	.	.	ENSG00000062096	ENST00000381127;ENST00000537104;ENST00000359361	D;D;D	0.98684	-5.07;-5.07;-5.07	3.4	-1.61	0.08399	Alkaline phosphatase-like, alpha/beta/alpha (1);Sulfatase (1);Alkaline-phosphatase-like, core domain (1);	0.484707	0.19510	U	0.112538	D	0.96414	0.8830	L	0.61387	1.9	0.09310	N	1	B	0.20671	0.047	B	0.32090	0.14	D	0.89916	0.4055	10	0.16896	T	0.51	.	6.4355	0.21821	0.2735:0.1278:0.5988:0.0	.	390	P54793	ARSF_HUMAN	N	390	ENSP00000370519:K390N;ENSP00000445594:K390N;ENSP00000352319:K390N	ENSP00000352319:K390N	K	+	3	2	ARSF	3031870	0.000000	0.05858	0.000000	0.03702	0.115000	0.19883	-1.019000	0.03622	-0.569000	0.06030	0.279000	0.19357	AAG	.	.	none		0.473	ARSF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055652.1		
BOC	91653	hgsc.bcm.edu	37	3	113004240	113004240	+	Silent	SNP	C	C	T	rs34600669	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:113004240C>T	ENST00000495514.1	+	19	3689	c.2985C>T	c.(2983-2985)gaC>gaT	p.D995D	BOC_ENST00000355385.3_Silent_p.D995D|BOC_ENST00000273395.4_Silent_p.D996D			Q9BWV1	BOC_HUMAN	BOC cell adhesion associated, oncogene regulated	995					axon guidance (GO:0007411)|cell adhesion (GO:0007155)|muscle cell differentiation (GO:0042692)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of myoblast differentiation (GO:0045663)|smoothened signaling pathway (GO:0007224)	axonal growth cone (GO:0044295)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)				NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(17)|lung(18)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	68			Epithelial(53;0.227)			CTAGCCCGGACGAGGGCTCTT	0.662													C|||	219	0.04373	0.0023	0.0115	5008	,	,		18585	0.1081		0.0507	False		,,,				2504	0.0491				p.D995D		Atlas-SNP	.											.	BOC	139	.	0			c.C2985T						PASS	.	C		27,4379	33.5+/-64.1	0,27,2176	53.0	54.0	54.0		2985	-6.9	0.1	3	dbSNP_126	54	324,8276	114.2+/-174.2	5,314,3981	no	coding-synonymous	BOC	NM_033254.2		5,341,6157	TT,TC,CC		3.7674,0.6128,2.6988		995/1115	113004240	351,12655	2203	4300	6503	SO:0001819	synonymous_variant	91653	exon19			CCCGGACGAGGGC	AY027658	CCDS2971.1	3q13.2	2013-02-11	2012-12-07		ENSG00000144857	ENSG00000144857		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	17173	protein-coding gene	gene with protein product	"""brother of CDO"", ""brother of CDON"", ""cell adhesion associated, oncogene regulated 2"""	608708	"""Boc homolog (mouse)"""			11782431	Standard	NM_033254		Approved	CDON2	uc003dzy.3	Q9BWV1	OTTHUMG00000159305	ENST00000495514.1:c.2985C>T	3.37:g.113004240C>T		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	104	48	0.461538	NM_033254	A6NJ30|B2RMS8|D3DN70|Q6UXJ5|Q8N2P7|Q8NF26	Silent	SNP	ENST00000495514.1	37	CCDS2971.1																																																																																			C|0.967;T|0.033	0.033	strong		0.662	BOC-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000354485.3	NM_033254	
KLHL30	377007	hgsc.bcm.edu	37	2	239049540	239049540	+	Missense_Mutation	SNP	G	G	A	rs2241985	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:239049540G>A	ENST00000409223.1	+	2	252	c.145G>A	c.(145-147)Ggc>Agc	p.G49S	KLHL30_ENST00000305959.4_Missense_Mutation_p.G31S			Q0D2K2	KLH30_HUMAN	kelch-like family member 30	49	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.			G -> S (in Ref. 4; AAI05697). {ECO:0000305}.						lung(4)	4		Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0481)|all_hematologic(139;0.158)|all_lung(227;0.198)|Melanoma(123;0.203)|Hepatocellular(293;0.244)		Epithelial(121;4.71e-24)|OV - Ovarian serous cystadenocarcinoma(60;3.02e-12)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;5.63e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000109)|Lung(119;0.0108)|LUSC - Lung squamous cell carcinoma(224;0.0253)		ATGCCACCGCGGCCTCCTGGC	0.697													G|||	1935	0.386382	0.3812	0.4006	5008	,	,		17698	0.3938		0.3847	False		,,,				2504	0.3773				p.G49S		Atlas-SNP	.											.	KLHL30	79	.	0			c.G145A						PASS	.	G	SER/GLY	1662,2602		333,996,803	40.0	48.0	46.0		145	1.3	1.0	2	dbSNP_98	46	3261,5177		633,1995,1591	yes	missense	KLHL30	NM_198582.3	56	966,2991,2394	AA,AG,GG		38.6466,38.9775,38.7577	benign	49/579	239049540	4923,7779	2132	4219	6351	SO:0001583	missense	377007	exon2			CACCGCGGCCTCC		CCDS46555.1, CCDS46555.2	2q37.3	2013-02-22	2013-02-22		ENSG00000168427	ENSG00000168427		"""Kelch-like"", ""BTB/POZ domain containing"""	24770	protein-coding gene	gene with protein product			"""kelch-like 30 (Drosophila)"""				Standard	NM_198582		Approved	FLJ43374	uc002vxr.2	Q0D2K2	OTTHUMG00000152905	ENST00000409223.1:c.145G>A	2.37:g.239049540G>A	ENSP00000386389:p.Gly49Ser	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	100	57	0.57	NM_198582	Q6ZUS1	Missense_Mutation	SNP	ENST00000409223.1	37	CCDS46555.2	848	0.3882783882783883	194	0.3943089430894309	150	0.4143646408839779	213	0.3723776223776224	291	0.3839050131926121	G	6.300	0.423477	0.11928	0.389775	0.386466	ENSG00000168427	ENST00000409223;ENST00000305959	T;T	0.66280	-0.2;-0.2	5.66	1.26	0.21427	BTB/POZ-like (2);BTB/POZ (1);BTB/POZ fold (2);	0.378699	0.28958	N	0.013586	T	0.00012	0.0000	N	0.01529	-0.815	0.80722	P	0.0	B	0.23937	0.094	B	0.23018	0.043	T	0.42682	-0.9437	9	0.46703	T	0.11	.	7.8189	0.29276	0.485:0.0:0.515:0.0	rs2241985;rs2241985	49	Q0D2K2	KLH30_HUMAN	S	49;31	ENSP00000386389:G49S;ENSP00000302386:G31S	ENSP00000302386:G31S	G	+	1	0	KLHL30	238714279	0.319000	0.24607	0.963000	0.40424	0.927000	0.56198	0.962000	0.29280	0.329000	0.23460	-0.218000	0.12543	GGC	G|0.618;A|0.382	0.382	strong		0.697	KLHL30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328518.1	NM_198582	
KIAA1211	57482	hgsc.bcm.edu	37	4	57176832	57176832	+	Splice_Site	SNP	T	T	C	rs79868722	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:57176832T>C	ENST00000504228.1	+	4	391	c.286T>C	c.(286-288)Tcc>Ccc	p.S96P	KIAA1211_ENST00000541073.1_Splice_Site_p.S89P|KIAA1211_ENST00000264229.6_Splice_Site_p.S96P|KIAA1211_ENST00000505410.1_3'UTR			Q6ZU35	K1211_HUMAN	KIAA1211	96										endometrium(7)|large_intestine(10)|lung(39)|ovary(2)|prostate(3)|skin(3)|stomach(1)	65	Glioma(25;0.08)|all_neural(26;0.101)					ACTGTTCCAGTCCAGTGATAC	0.468													T|||	323	0.0644968	0.0038	0.0259	5008	,	,		20277	0.1875		0.0169	False		,,,				2504	0.0961				p.S96P		Atlas-SNP	.											.	KIAA1211	178	.	0			c.T286C						PASS	.	T	PRO/SER	20,3806		0,20,1893	138.0	136.0	136.0		286	-2.3	1.0	4	dbSNP_131	136	162,8112		1,160,3976	yes	missense-near-splice	KIAA1211	NM_020722.1	74	1,180,5869	CC,CT,TT		1.9579,0.5227,1.5041	benign	96/1234	57176832	182,11918	1913	4137	6050	SO:0001630	splice_region_variant	57482	exon6			TTCCAGTCCAGTG	AB033037	CCDS43230.1	4q12	2012-08-03			ENSG00000109265	ENSG00000109265			29219	protein-coding gene	gene with protein product						10574462, 11230166	Standard	NM_020722		Approved		uc003hbk.2	Q6ZU35	OTTHUMG00000160749	ENST00000504228.1:c.286-1T>C	4.37:g.57176832T>C		Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	141	70	0.496454	NM_020722	Q9NTE2|Q9NTP8|Q9ULK9	Missense_Mutation	SNP	ENST00000504228.1	37	CCDS43230.1	149	0.06822344322344322	3	0.006097560975609756	15	0.04143646408839779	119	0.20804195804195805	12	0.0158311345646438	T	9.606	1.129904	0.21041	0.005227	0.019579	ENSG00000109265	ENST00000264229;ENST00000504228;ENST00000541073;ENST00000546221	T;T;T	0.13901	2.58;2.58;2.55	4.74	-2.32	0.06745	.	.	.	.	.	T	0.00012	0.0000	L	0.31664	0.95	0.31151	P	0.705522	B;B;B	0.13594	0.008;0.008;0.008	B;B;B	0.13407	0.009;0.009;0.009	T	0.45804	-0.9236	7	.	.	.	-4.3071	6.2278	0.20718	0.0:0.2771:0.4589:0.2641	.	89;89;96	B7ZVZ4;F5H1N7;Q6ZU35	.;.;K1211_HUMAN	P	96;96;89;6	ENSP00000264229:S96P;ENSP00000423366:S96P;ENSP00000444006:S89P	.	S	+	1	0	KIAA1211	56871589	0.901000	0.30685	0.986000	0.45419	0.932000	0.56968	-0.371000	0.07513	-0.560000	0.06102	-1.271000	0.01417	TCC	T|0.952;C|0.048	0.048	strong		0.468	KIAA1211-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362097.2	NM_020722	Missense_Mutation
DNAH6	1768	hgsc.bcm.edu	37	2	85024731	85024731	+	Silent	SNP	C	C	T	rs1192395	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:85024731C>T	ENST00000237449.6	+	69	11438	c.11430C>T	c.(11428-11430)atC>atT	p.I3810I	DNAH6_ENST00000389394.3_Silent_p.I3810I			Q9C0G6	DYH6_HUMAN	dynein, axonemal, heavy chain 6	3810					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						TGCCTTTGATCGATGACCCAG	0.353													C|||	522	0.104233	0.1044	0.1628	5008	,	,		20546	0.0883		0.1093	False		,,,				2504	0.0736				p.I3810I		Atlas-SNP	.											.	DNAH6	194	.	0			c.C11430T						PASS	.	C		161,1223		7,147,538	196.0	172.0	179.0		11430	-1.7	1.0	2	dbSNP_87	179	382,2800		15,352,1224	no	coding-synonymous	DNAH6	NM_001370.1		22,499,1762	TT,TC,CC		12.005,11.6329,11.8922		3810/4159	85024731	543,4023	692	1591	2283	SO:0001819	synonymous_variant	1768	exon70			TTTGATCGATGAC	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.11430C>T	2.37:g.85024731C>T		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	81	43	0.530864	NM_001370	A0PJN9|B5MEE0|B7ZL99|O95493|Q53QZ1|Q53TE5|Q8N1W6|Q92861|Q96BL6|Q9H030|Q9H5E1	Silent	SNP	ENST00000237449.6	37	CCDS46348.1																																																																																			C|0.902;T|0.098	0.098	strong		0.353	DNAH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328537.2	NM_001370	
CPAMD8	27151	hgsc.bcm.edu	37	19	17088319	17088319	+	Missense_Mutation	SNP	G	G	T	rs3745335	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	34	0	0		WXS	Illumina HiSeq	Phase_I	23	23	1	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	
GDF15	9518	hgsc.bcm.edu	37	19	18497137	18497137	+	Silent	SNP	G	G	A	rs6413435	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:18497137G>A	ENST00000252809.3	+	1	170	c.138G>A	c.(136-138)ttG>ttA	p.L46L	MIR3189_ENST00000578735.1_RNA	NM_004864.2	NP_004855.2	Q99988	GDF15_HUMAN	growth differentiation factor 15	46					cell-cell signaling (GO:0007267)|signal transduction (GO:0007165)|transforming growth factor beta receptor signaling pathway (GO:0007179)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	cytokine activity (GO:0005125)			kidney(2)|large_intestine(1)|liver(1)|lung(5)|prostate(2)|skin(1)	12						CCTCAGAGTTGCACTCCGAAG	0.632													G|||	516	0.103035	0.0983	0.1383	5008	,	,		13585	0.0069		0.1829	False		,,,				2504	0.1012				p.L46L		Atlas-SNP	.											.	GDF15	31	.	0			c.G138A						PASS	.	G		456,3950	217.1+/-235.6	15,426,1762	40.0	41.0	41.0		138	-4.7	0.0	19	dbSNP_116	41	1597,7003	294.8+/-302.1	149,1299,2852	no	coding-synonymous	GDF15	NM_004864.2		164,1725,4614	AA,AG,GG		18.5698,10.3495,15.785		46/309	18497137	2053,10953	2203	4300	6503	SO:0001819	synonymous_variant	9518	exon1			AGAGTTGCACTCC	BC008962	CCDS12376.1	19p13.11	2008-05-14				ENSG00000130513			30142	protein-coding gene	gene with protein product	"""prostate differentiation factor"""	605312				11895857, 9593718	Standard	NM_004864		Approved	PLAB, MIC-1, PDF, MIC1, NAG-1, PTGFB	uc002niv.2	Q99988		ENST00000252809.3:c.138G>A	19.37:g.18497137G>A		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	85	43	0.505882	NM_004864	O14629|P78360|Q9BWA0|Q9NRT0	Silent	SNP	ENST00000252809.3	37	CCDS12376.1																																																																																			G|0.857;A|0.143	0.143	strong		0.632	GDF15-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466340.2	NM_004864	
CBLC	23624	hgsc.bcm.edu	37	19	45296767	45296767	+	Missense_Mutation	SNP	G	G	A	rs35457630	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:45296767G>A	ENST00000270279.3	+	8	1237	c.1174G>A	c.(1174-1176)Gag>Aag	p.E392K	CBLC_ENST00000341505.4_Missense_Mutation_p.E346K	NM_012116.3	NP_036248.3	Q9ULV8	CBLC_HUMAN	Cbl proto-oncogene C, E3 ubiquitin protein ligase	392	Interaction with RET.				cell surface receptor signaling pathway (GO:0007166)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of epidermal growth factor-activated receptor activity (GO:0007175)|negative regulation of MAP kinase activity (GO:0043407)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|epidermal growth factor receptor binding (GO:0005154)|ligase activity (GO:0016874)|phosphotyrosine binding (GO:0001784)|SH3 domain binding (GO:0017124)|signal transducer activity (GO:0004871)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|kidney(1)|lung(6)|ovary(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	17	Lung NSC(12;0.00136)|all_lung(12;0.00371)	Ovarian(192;0.231)				CTGCCGCTGCGAGATCAAGGG	0.627			M		AML								G|||	16	0.00319489	0.0	0.0086	5008	,	,		17152	0.0		0.008	False		,,,				2504	0.002				p.E392K		Atlas-SNP	.		Rec	yes		19	19q13.2	23624	Cas-Br-M (murine) ecotropic retroviral transforming sequence c		L	CBLC,bladder,carcinoma,-2,1	CBLC	41	1	0			c.G1174A						PASS	.	G	LYS/GLU,LYS/GLU	3,4403		0,3,2200	43.0	38.0	40.0		1036,1174	-5.7	0.0	19	dbSNP_126	40	59,8541		0,59,4241	yes	missense,missense	CBLC	NM_001130852.1,NM_012116.3	56,56	0,62,6441	AA,AG,GG		0.686,0.0681,0.4767	benign,benign	346/429,392/475	45296767	62,12944	2203	4300	6503	SO:0001583	missense	23624	exon8			CGCTGCGAGATCA	AB028645	CCDS12643.1, CCDS46109.1	19q13.2	2013-07-09	2013-07-09		ENSG00000142273	ENSG00000142273		"""RING-type (C3HC4) zinc fingers"""	15961	protein-coding gene	gene with protein product		608453	"""Cas-Br-M (murine) ectropic retroviral transforming sequence c"", ""Cas-Br-M (murine) ecotropic retroviral transforming sequence c"""			10362357, 10571044	Standard	NM_012116		Approved	CBL-3, CBL-SL, RNF57	uc002ozs.3	Q9ULV8	OTTHUMG00000150715	ENST00000270279.3:c.1174G>A	19.37:g.45296767G>A	ENSP00000270279:p.Glu392Lys	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	52	32	0.615385	NM_012116	Q8N1E5|Q9Y5Z2|Q9Y5Z3	Missense_Mutation	SNP	ENST00000270279.3	37	CCDS12643.1	11	0.005036630036630037	0	0.0	4	0.011049723756906077	0	0.0	7	0.009234828496042216	.	10.17	1.276699	0.23307	6.81E-4	0.00686	ENSG00000142273	ENST00000270279;ENST00000341505	D;D	0.95412	-3.7;-3.7	4.52	-5.69	0.02428	Zinc finger, RING/FYVE/PHD-type (1);	1.068980	0.07326	N	0.878397	D	0.85630	0.5741	N	0.17631	0.505	0.29287	N	0.869621	B;B	0.09022	0.002;0.001	B;B	0.06405	0.002;0.001	T	0.74844	-0.3526	10	0.59425	D	0.04	-4.2053	8.6979	0.34307	0.1979:0.3979:0.4042:0.0	rs35457630	346;392	Q9ULV8-2;Q9ULV8	.;CBLC_HUMAN	K	392;346	ENSP00000270279:E392K;ENSP00000340250:E346K	ENSP00000270279:E392K	E	+	1	0	CBLC	49988607	0.638000	0.27225	0.015000	0.15790	0.191000	0.23601	0.834000	0.27518	-1.423000	0.02002	-2.785000	0.00117	GAG	G|0.995;A|0.005	0.005	strong		0.627	CBLC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319732.2	NM_012116	
SVEP1	79987	hgsc.bcm.edu	37	9	113189954	113189954	+	Silent	SNP	T	T	G	rs41279045	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:113189954T>G	ENST00000401783.2	-	36	6228	c.5892A>C	c.(5890-5892)ggA>ggC	p.G1964G	SVEP1_ENST00000374469.1_Silent_p.G1941G|SVEP1_ENST00000297826.5_5'UTR	NM_153366.3	NP_699197.3	Q4LDE5	SVEP1_HUMAN	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	1964	Sushi 10. {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						CAGGTGGTTCTCCACAGAAGA	0.517											OREG0019389	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	T|||	166	0.033147	0.0234	0.0259	5008	,	,		17532	0.0476		0.0457	False		,,,				2504	0.0235				p.G1964G		Atlas-SNP	.											.	SVEP1	326	.	0			c.A5892C						PASS	.	T		83,4071		0,83,1994	107.0	112.0	110.0		5892	0.9	1.0	9	dbSNP_127	110	357,8087		8,341,3873	no	coding-synonymous	SVEP1	NM_153366.3		8,424,5867	GG,GT,TT		4.2279,1.9981,3.4926		1964/3572	113189954	440,12158	2077	4222	6299	SO:0001819	synonymous_variant	79987	exon36			TGGTTCTCCACAG	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.5892A>C	9.37:g.113189954T>G		Somatic	160	0	0	1448	WXS	Illumina HiSeq	Phase_I	135	55	0.407407	NM_153366	Q0P675|Q5D213|Q5T938|Q5VTE4|Q5VTE5|Q7Z387|Q7Z3G3|Q8NBT9|Q96JU7|Q9H284|Q9H8J9	Silent	SNP	ENST00000401783.2	37	CCDS48004.1																																																																																			T|0.963;G|0.037	0.037	strong		0.517	SVEP1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
CCDC183	84960	hgsc.bcm.edu	37	9	139701108	139701108	+	Missense_Mutation	SNP	A	A	C	rs2254143	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:139701108A>C	ENST00000338005.6	+	11	1297	c.1262A>C	c.(1261-1263)aAc>aCc	p.N421T	RP11-216L13.19_ENST00000415992.1_RNA|KIAA1984-AS1_ENST00000414656.1_RNA|RABL6_ENST00000371671.4_5'Flank|RABL6_ENST00000357466.2_5'Flank|RP11-216L13.18_ENST00000471502.1_RNA|RABL6_ENST00000311502.7_5'Flank|RABL6_ENST00000371663.4_5'Flank	NM_001039374.4	NP_001034463.4	Q5T5S1	CC183_HUMAN		421			N -> T (in dbSNP:rs2254143). {ECO:0000269|PubMed:15164053, ECO:0000269|PubMed:15489334}.							biliary_tract(1)|breast(1)|endometrium(1)|kidney(2)|lung(4)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(1)	13	all_cancers(76;0.0882)|all_epithelial(76;0.228)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;9.33e-06)|Epithelial(140;0.000124)		ATGGGCATTAACTTGCCTGCG	0.632													C|||	4039	0.80651	0.8177	0.7032	5008	,	,		19133	0.8581		0.8032	False		,,,				2504	0.8149				p.N421T		Atlas-SNP	.											.	KIAA1984	39	.	0			c.A1262C						PASS	.	C	THR/ASN	3424,738		1401,622,58	33.0	38.0	36.0		1262	5.1	0.0	9	dbSNP_100	36	6678,1708		2666,1346,181	yes	missense	KIAA1984	NM_001039374.4	65	4067,1968,239	CC,CA,AA		20.3673,17.7319,19.4931	benign	421/535	139701108	10102,2446	2081	4193	6274	SO:0001583	missense	84960	exon11			GCATTAACTTGCC																												ENST00000338005.6:c.1262A>C	9.37:g.139701108A>C	ENSP00000338013:p.Asn421Thr	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	59	39	0.661017	NM_001039374	B2RP89|C9JD38|Q6P2D9|Q8NAI4|Q8TF18	Missense_Mutation	SNP	ENST00000338005.6	37	CCDS43906.1	1758	0.804945054945055	397	0.806910569105691	263	0.7265193370165746	485	0.8479020979020979	613	0.8087071240105541	C	0.692	-0.794278	0.02862	0.822681	0.796327	ENSG00000213213	ENST00000423962;ENST00000338005	T	0.10763	2.84	5.07	5.07	0.68467	.	.	.	.	.	T	0.00012	0.0000	N	0.00926	-1.1	0.41256	P	0.01325900000000002	B	0.02656	0.0	B	0.01281	0.0	T	0.12502	-1.0545	8	0.15499	T	0.54	-0.7687	11.0894	0.48106	0.1855:0.8145:0.0:0.0	rs2254143;rs61409775;rs2254143	421	Q5T5S1	K1984_HUMAN	T	421	ENSP00000338013:N421T	ENSP00000338013:N421T	N	+	2	0	KIAA1984	138820929	0.000000	0.05858	0.003000	0.11579	0.001000	0.01503	0.816000	0.27267	1.134000	0.42165	-0.217000	0.12591	AAC	A|0.176;C|0.824	0.824	strong		0.632	KIAA1984-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354899.1		
AHNAK2	113146	hgsc.bcm.edu	37	14	105416255	105416255	+	Missense_Mutation	SNP	A	A	T	rs386781100|rs544344402	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:105416255A>T	ENST00000333244.5	-	7	5652	c.5533T>A	c.(5533-5535)Tcg>Acg	p.S1845T	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	1845						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)			ACATCCACCGAGGCCTCGATG	0.607													.|||	12	0.00239617	0.0076	0.0014	5008	,	,		19055	0.0		0.001	False		,,,				2504	0.0				p.S1845T		Atlas-SNP	.											AHNAK2_ENST00000333244,colon,carcinoma,+2,1	AHNAK2	719	1	0			c.T5533A						scavenged	.						178.0	216.0	204.0					14																	105416255		1933	4101	6034	SO:0001583	missense	113146	exon7			CCACCGAGGCCTC	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.5533T>A	14.37:g.105416255A>T	ENSP00000353114:p.Ser1845Thr	Somatic	196	1	0.00510204		WXS	Illumina HiSeq	Phase_I	182	9	0.0494506	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	.	.	.	.	.	.	.	.	.	.	a	9.486	1.099439	0.20552	.	.	ENSG00000185567	ENST00000333244	T	0.00932	5.53	4.12	0.296	0.15757	.	.	.	.	.	T	0.01421	0.0046	M	0.82630	2.6	0.09310	N	1	B	0.12013	0.005	B	0.16289	0.015	T	0.48364	-0.9042	9	0.21540	T	0.41	-10.2489	1.8701	0.03207	0.3818:0.3625:0.0953:0.1604	.	1845	Q8IVF2	AHNK2_HUMAN	T	1845	ENSP00000353114:S1845T	ENSP00000353114:S1845T	S	-	1	0	AHNAK2	104487300	0.000000	0.05858	0.001000	0.08648	0.010000	0.07245	-0.342000	0.07801	-0.096000	0.12329	-0.375000	0.07067	TCG	.	.	none		0.607	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
PRDM15	63977	hgsc.bcm.edu	37	21	43221555	43221555	+	Silent	SNP	G	G	A	rs2236694	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:43221555G>A	ENST00000269844.3	-	31	4479	c.4369C>T	c.(4369-4371)Ctg>Ttg	p.L1457L	PRDM15_ENST00000398548.1_Silent_p.L1128L|PRDM15_ENST00000422911.1_Silent_p.L1148L|PRDM15_ENST00000447207.2_Silent_p.L1091L|PRDM15_ENST00000470586.1_5'UTR|PRDM15_ENST00000538201.1_Silent_p.L1111L	NM_022115.3	NP_071398.3	P57071	PRD15_HUMAN	PR domain containing 15	1457					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.L1457L(1)		NS(2)|breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(11)|ovary(3)|skin(2)|stomach(2)|urinary_tract(1)	43						TGGCTCCCCAGGGGCGTGATG	0.647													g|||	499	0.0996406	0.0265	0.062	5008	,	,		16209	0.1558		0.1054	False		,,,				2504	0.1616				p.L1457L		Atlas-SNP	.											PRDM15,NS,carcinoma,0,1	PRDM15	110	1	1	Substitution - coding silent(1)	stomach(1)	c.C4369T						PASS	.		,	156,4250	106.5+/-144.9	3,150,2050	84.0	74.0	78.0		3382,4369	2.5	1.0	21	dbSNP_98	78	808,7792	188.9+/-235.7	38,732,3530	no	coding-synonymous,coding-synonymous	PRDM15	NM_001040424.1,NM_022115.3	,	41,882,5580	AA,AG,GG		9.3953,3.5406,7.412	,	1128/1179,1457/1508	43221555	964,12042	2203	4300	6503	SO:0001819	synonymous_variant	63977	exon31			TCCCCAGGGGCGT	AF276513	CCDS13676.1, CCDS42932.1, CCDS63370.1	21q22.3	2013-01-08	2002-07-31		ENSG00000141956	ENSG00000141956		"""Zinc fingers, C2H2-type"""	13999	protein-coding gene	gene with protein product			"""chromosome 21 open reading frame 83"""	ZNF298, C21orf83		12036297, 12036298	Standard	NM_022115		Approved		uc002yzq.1	P57071	OTTHUMG00000086781	ENST00000269844.3:c.4369C>T	21.37:g.43221555G>A		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	117	80	0.683761	NM_022115	E9PDJ6|E9PF37|E9PGL3|Q4W8S0|Q4W8S3|Q4W8S4|Q4W8S5|Q8N0X3|Q8NEX0|Q9NQV3	Silent	SNP	ENST00000269844.3	37	CCDS13676.1																																																																																			G|0.915;A|0.085	0.085	strong		0.647	PRDM15-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_022115	
CEP128	145508	hgsc.bcm.edu	37	14	80971261	80971261	+	Missense_Mutation	SNP	C	C	T	rs61744330	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:80971261C>T	ENST00000555265.1	-	24	3550	c.3175G>A	c.(3175-3177)Gtg>Atg	p.V1059M	CEP128_ENST00000281129.3_Missense_Mutation_p.V1059M|CEP128_ENST00000553717.1_5'UTR			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	59	0	0		WXS	Illumina HiSeq	Phase_I	41	16	0.390244	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	
SMCHD1	23347	hgsc.bcm.edu	37	18	2763697	2763697	+	Silent	SNP	C	C	T	rs483547	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:2763697C>T	ENST00000320876.6	+	37	4967	c.4629C>T	c.(4627-4629)ggC>ggT	p.G1543G	SMCHD1_ENST00000261598.8_Silent_p.G1543G|RP11-703M24.5_ENST00000583546.1_RNA	NM_015295.2	NP_056110.2	A6NHR9	SMHD1_HUMAN	structural maintenance of chromosomes flexible hinge domain containing 1	1543					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						CCATTAAAGGCTCTAATGAGG	0.358													C|||	1381	0.275759	0.264	0.317	5008	,	,		18800	0.1895		0.4612	False		,,,				2504	0.1605				p.G1543G		Atlas-SNP	.											SMCHD1,colon,carcinoma,0,3	SMCHD1	88	3	0			c.C4629T						scavenged	.	C		1096,2578		176,744,917	86.0	83.0	84.0		4629	-2.0	1.0	18	dbSNP_83	84	3607,4579		805,1997,1291	no	coding-synonymous	SMCHD1	NM_015295.2		981,2741,2208	TT,TC,CC		44.063,29.8312,39.6543		1543/2006	2763697	4703,7157	1837	4093	5930	SO:0001819	synonymous_variant	23347	exon37			TAAAGGCTCTAAT	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.4629C>T	18.37:g.2763697C>T		Somatic	156	1	0.00641026		WXS	Illumina HiSeq	Phase_I	129	71	0.550388	NM_015295	O75141|Q6AHX6|Q6ZTQ8|Q9H6Q2|Q9UG39	Silent	SNP	ENST00000320876.6	37	CCDS45822.1																																																																																			C|0.685;T|0.315	0.315	strong		0.358	SMCHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441082.2		
KCNIP4	80333	hgsc.bcm.edu	37	4	20852166	20852166	+	Splice_Site	SNP	A	A	G	rs3765121	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:20852166A>G	ENST00000382152.2	-	3	455	c.288T>C	c.(286-288)aaT>aaC	p.N96N	KCNIP4_ENST00000447367.2_Splice_Site_p.N62N|KCNIP4_ENST00000359001.5_Splice_Site_p.N34N|KCNIP4_ENST00000509207.1_Splice_Site_p.N34N|KCNIP4_ENST00000382149.4_5'UTR|KCNIP4_ENST00000382148.3_Splice_Site_p.N71N|KCNIP4_ENST00000382150.4_Splice_Site_p.N75N	NM_025221.5	NP_079497.2	Q6PIL6	KCIP4_HUMAN	Kv channel interacting protein 4	96	EF-hand 1; degenerate. {ECO:0000255|PROSITE-ProRule:PRU00448}.					dendrite (GO:0030425)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|potassium channel activity (GO:0005267)|voltage-gated ion channel activity (GO:0005244)			NS(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)	13		Breast(46;0.134)				AAGTTCTTACATTCTTAAATC	0.448													G|||	1749	0.349241	0.121	0.4755	5008	,	,		19126	0.4335		0.4274	False		,,,				2504	0.4008				p.N76N		Atlas-SNP	.											KCNIP4_ENST00000447367,colon,carcinoma,0,4	KCNIP4	85	4	0			c.T228C						PASS	.	G	,,,,,	749,3657	753.7+/-412.4	69,611,1523	97.0	104.0	102.0		213,102,288,186,102,225	-0.4	1.0	4	dbSNP_107	102	3484,5116	634.3+/-398.8	705,2074,1521	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	KCNIP4	NM_001035003.1,NM_001035004.1,NM_025221.5,NM_147181.3,NM_147182.3,NM_147183.3	,,,,,	774,2685,3044	GG,GA,AA		40.5116,16.9995,32.5465	,,,,,	71/226,34/189,96/251,62/217,34/189,75/230	20852166	4233,8773	2203	4300	6503	SO:0001630	splice_region_variant	80333	exon2			TCTTACATTCTTA	AF453244	CCDS3428.1, CCDS43215.1, CCDS43216.1, CCDS43217.1, CCDS47035.1	4p15.32	2013-01-10			ENSG00000185774	ENSG00000185774		"""EF-hand domain containing"""	30083	protein-coding gene	gene with protein product		608182				11805342, 11847232	Standard	XM_005248190		Approved	CALP, KCHIP4, MGC44947	uc003gqh.1	Q6PIL6	OTTHUMG00000128557	ENST00000382152.2:c.288+1T>C	4.37:g.20852166A>G		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	45	17	0.377778	NM_025221	Q3YAB8|Q3YAB9|Q3YAC0|Q3YAC1|Q3YAC2|Q4W5G8|Q8NEU0|Q9BWT2|Q9H294|Q9H2A4	Silent	SNP	ENST00000382152.2	37	CCDS43216.1																																																																																			A|0.672;G|0.328	0.328	strong		0.448	KCNIP4-004	KNOWN	non_canonical_conserved|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000360407.3	NM_025221	Silent
C2orf16	84226	hgsc.bcm.edu	37	2	27804547	27804547	+	Missense_Mutation	SNP	G	G	A	rs201164610	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:27804547G>A	ENST00000408964.2	+	1	5159	c.5108G>A	c.(5107-5109)cGt>cAt	p.R1703H	ZNF512_ENST00000416005.2_5'Flank|ZNF512_ENST00000413371.2_5'Flank|RP11-158I13.2_ENST00000505973.1_RNA|ZNF512_ENST00000556601.1_5'Flank|ZNF512_ENST00000355467.4_5'Flank|AC074091.1_ENST00000408604.1_RNA|ZNF512_ENST00000379717.1_5'Flank	NM_032266.3	NP_115642.3	Q68DN1	CB016_HUMAN	chromosome 2 open reading frame 16	1703	27 X 8 AA approximative tandem repeat of P-S-E-R-S-H-H-S.|Arg-rich.					extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(33)|urinary_tract(1)	47	Acute lymphoblastic leukemia(172;0.155)					AGGAGCCATCGTGGTCCCTCT	0.587													g|||	16	0.00319489	0.0	0.0	5008	,	,		20437	0.0		0.0	False		,,,				2504	0.0164				p.R1703H		Atlas-SNP	.											.	C2orf16	357	.	0			c.G5108A						PASS	.						156.0	159.0	158.0					2																	27804547		1929	4134	6063	SO:0001583	missense	84226	exon1			GCCATCGTGGTCC	AL136898	CCDS42666.1	2p23.3	2013-09-20			ENSG00000221843	ENSG00000221843			25275	protein-coding gene	gene with protein product	"""P-S-E-R-S-H-H-S repeats containing"""						Standard	NM_032266		Approved	DKFZp434G118	uc002rkz.4	Q68DN1	OTTHUMG00000159099	ENST00000408964.2:c.5108G>A	2.37:g.27804547G>A	ENSP00000386190:p.Arg1703His	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	72	24	0.333333	NM_032266	B9EIQ4|Q53S01|Q8ND64|Q9H088	Missense_Mutation	SNP	ENST00000408964.2	37	CCDS42666.1	.	.	.	.	.	.	.	.	.	.	g	8.649	0.897869	0.17686	.	.	ENSG00000221843	ENST00000408964	T	0.05447	3.44	3.34	-4.16	0.03869	.	.	.	.	.	T	0.02533	0.0077	N	0.19112	0.55	0.09310	N	1	B	0.32800	0.385	B	0.21708	0.036	T	0.39921	-0.9590	9	0.33940	T	0.23	.	0.1461	0.00088	0.2733:0.2564:0.2106:0.2596	.	1703	Q68DN1	CB016_HUMAN	H	1703	ENSP00000386190:R1703H	ENSP00000386190:R1703H	R	+	2	0	C2orf16	27658051	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.454000	0.01004	-1.009000	0.03400	-1.402000	0.01139	CGT	G|0.999;A|0.001	0.001	weak		0.587	C2orf16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353292.1	NM_032266	
ZNF189	7743	hgsc.bcm.edu	37	9	104170796	104170796	+	Missense_Mutation	SNP	A	A	T	rs370077009		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:104170796A>T	ENST00000339664.2	+	3	875	c.746A>T	c.(745-747)aAa>aTa	p.K249I	ZNF189_ENST00000374861.3_Missense_Mutation_p.K235I|ZNF189_ENST00000259395.4_Missense_Mutation_p.K207I	NM_001278240.1	NP_001265169.1	O75820	ZN189_HUMAN	zinc finger protein 189	249					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(10)|ovary(2)|prostate(3)|skin(2)|urinary_tract(1)	26		Acute lymphoblastic leukemia(62;0.0559)				AGCCTTGTTAAACATCAAAGG	0.423																																					p.K249I		Atlas-SNP	.											.	ZNF189	79	.	0			c.A746T						PASS	.	A	ILE/LYS,ILE/LYS	0,4406		0,0,2203	183.0	188.0	186.0		746,620	4.7	1.0	9		186	2,8598	2.2+/-6.3	0,2,4298	no	missense,missense	ZNF189	NM_003452.2,NM_197977.1	102,102	0,2,6501	TT,TA,AA		0.0233,0.0,0.0154	benign,benign	249/627,207/585	104170796	2,13004	2203	4300	6503	SO:0001583	missense	7743	exon3			TTGTTAAACATCA	AF025770	CCDS6754.1, CCDS6755.1, CCDS65096.1, CCDS75867.1	9q22-q31	2013-01-08			ENSG00000136870	ENSG00000136870		"""Zinc fingers, C2H2-type"", ""-"""	12980	protein-coding gene	gene with protein product		603132				9653648	Standard	NM_003452		Approved		uc004bbh.2	O75820	OTTHUMG00000020383	ENST00000339664.2:c.746A>T	9.37:g.104170796A>T	ENSP00000342019:p.Lys249Ile	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	46	27	0.586957	NM_003452	O75802|Q5T7D7|Q5T7D8|Q5T7D9|Q9UBL4|Q9UPE9|Q9UPF0|Q9UPF1	Missense_Mutation	SNP	ENST00000339664.2	37	CCDS6754.1	.	.	.	.	.	.	.	.	.	.	A	8.404	0.842724	0.16963	0.0	2.33E-4	ENSG00000136870	ENST00000374861;ENST00000339664;ENST00000259395	T;T;T	0.20598	2.06;2.06;2.06	4.67	4.67	0.58626	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.52532	D	0.000079	T	0.12689	0.0308	L	0.28649	0.875	0.31428	N	0.67353	P;B;P	0.43314	0.803;0.136;0.507	B;B;B	0.37304	0.246;0.032;0.205	T	0.06917	-1.0800	10	0.30078	T	0.28	.	7.1431	0.25566	0.9035:0.0:0.0965:0.0	.	234;235;249	B7ZLK9;Q5T7D8;O75820	.;.;ZN189_HUMAN	I	235;249;207	ENSP00000363995:K235I;ENSP00000342019:K249I;ENSP00000259395:K207I	ENSP00000259395:K207I	K	+	2	0	ZNF189	103210617	0.000000	0.05858	1.000000	0.80357	0.998000	0.95712	-2.494000	0.00972	2.324000	0.78689	0.533000	0.62120	AAA	.	.	weak		0.423	ZNF189-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053447.1	NM_003452	
HIP1	3092	hgsc.bcm.edu	37	7	75211414	75211414	+	Silent	SNP	A	A	G	rs237238	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:75211414A>G	ENST00000336926.6	-	6	545	c.519T>C	c.(517-519)gcT>gcC	p.A173A	RN7SL642P_ENST00000581382.1_RNA|HIP1_ENST00000434438.2_Silent_p.A173A	NM_005338.5	NP_005329.3	O00291	HIP1_HUMAN	huntingtin interacting protein 1	173					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						CACTTTCTCCAGCCTCGTCCA	0.552			T	PDGFRB	CMML								A|||	488	0.0974441	0.1074	0.0793	5008	,	,		19934	0.0754		0.0795	False		,,,				2504	0.138				p.A173A		Atlas-SNP	.		Dom	yes		7	7q11.23	3092	huntingtin interacting protein 1		L	HIP1,NS,carcinoma,-1,1	HIP1	91	1	0			c.T519C						PASS	.	A		411,3995	203.5+/-225.9	24,363,1816	92.0	69.0	77.0	http://www.ncbi.nlm.nih.gov/pubmed?term	519	-10.8	0.7	7	dbSNP_79	77	621,7979	161.4+/-214.4	26,569,3705	no	coding-synonymous	HIP1	NM_005338.5		50,932,5521	GG,GA,AA	http://www.ncbi.nlm.nih.gov/pubmed?term	7.2209,9.3282,7.9348		173/1038	75211414	1032,11974	2203	4300	6503	SO:0001819	synonymous_variant	3092	exon6			TTCTCCAGCCTCG	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.519T>C	7.37:g.75211414A>G		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	69	36	0.521739	NM_005338	B4E3I7|E7ES17|O00328|Q2TB58|Q8TDL4	Silent	SNP	ENST00000336926.6	37	CCDS34669.1																																																																																			A|0.912;G|0.088	0.088	strong		0.552	HIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342863.2	NM_005338	
AHNAK2	113146	hgsc.bcm.edu	37	14	105407327	105407327	+	Missense_Mutation	SNP	G	G	A	rs77215854	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:105407327G>A	ENST00000333244.5	-	7	14580	c.14461C>T	c.(14461-14463)Cct>Tct	p.P4821S	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	4821						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)			TTGGGAAGAGGAATATCAGCC	0.517													g|||	127	0.0253594	0.0015	0.0187	5008	,	,		19000	0.0218		0.0358	False		,,,				2504	0.0552				p.P4821S		Atlas-SNP	.											.	AHNAK2	719	.	0			c.C14461T						PASS	.	A	SER/PRO	20,3886		0,20,1933	41.0	41.0	41.0		14461	-6.0	0.0	14	dbSNP_132	41	255,8057		4,247,3905	yes	missense	AHNAK2	NM_138420.2	74	4,267,5838	AA,AG,GG		3.0679,0.512,2.2508	benign	4821/5796	105407327	275,11943	1953	4156	6109	SO:0001583	missense	113146	exon7			GAAGAGGAATATC	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.14461C>T	14.37:g.105407327G>A	ENSP00000353114:p.Pro4821Ser	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	62	32	0.516129	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	43	0.019688644688644688	1	0.0020325203252032522	6	0.016574585635359115	17	0.02972027972027972	19	0.025065963060686015	G	2.089	-0.408857	0.04799	0.00512	0.030679	ENSG00000185567	ENST00000333244	T	0.00700	5.82	4.03	-6.0	0.02206	.	.	.	.	.	T	0.00178	0.0005	N	0.08118	0	0.09310	N	1	B	0.17268	0.021	B	0.16289	0.015	T	0.43523	-0.9386	9	0.14656	T	0.56	.	6.0796	0.19935	0.3322:0.3411:0.3267:0.0	.	4821	Q8IVF2	AHNK2_HUMAN	S	4821	ENSP00000353114:P4821S	ENSP00000353114:P4821S	P	-	1	0	AHNAK2	104478372	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.673000	0.05239	-1.294000	0.02360	-1.094000	0.02160	CCT	G|0.980;A|0.020	0.020	strong		0.517	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
MUC4	4585	hgsc.bcm.edu	37	3	195509795	195509795	+	Missense_Mutation	SNP	C	C	T	rs201497773		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195509795C>T	ENST00000463781.3	-	2	9115	c.8656G>A	c.(8656-8658)Gct>Act	p.A2886T	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.A2886T	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)		ACTGAGGAAGCGTCGGTGACA	0.592																																					p.A2886T		Atlas-SNP	.											.	MUC4	1505	.	0			c.G8656A						PASS	.						22.0	15.0	17.0					3																	195509795		682	1576	2258	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.8656G>A	3.37:g.195509795C>T	ENSP00000417498:p.Ala2886Thr	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	101	47	0.465347	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	14.42	2.529251	0.44969	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.34275	1.37;1.37	.	.	.	.	.	.	.	.	T	0.13586	0.0329	N	0.08118	0	0.09310	N	1	B	0.28350	0.208	B	0.09377	0.004	T	0.22138	-1.0225	7	.	.	.	.	4.4363	0.11552	0.0:0.666:0.0:0.334	.	2758	E7ESK3	.	T	2886	ENSP00000417498:A2886T;ENSP00000420243:A2886T	.	A	-	1	0	MUC4	196994574	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.261000	0.00536	-0.000000	0.14550	0.000000	0.15137	GCT	.	.	weak		0.592	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
ZMIZ1	57178	hgsc.bcm.edu	37	10	81053248	81053248	+	Silent	SNP	G	G	A	rs146995829	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:81053248G>A	ENST00000334512.5	+	12	1640	c.1068G>A	c.(1066-1068)acG>acA	p.T356T	ZMIZ1_ENST00000478357.1_3'UTR	NM_020338.3	NP_065071.1	Q9ULJ6	ZMIZ1_HUMAN	zinc finger, MIZ-type containing 1	356	Pro-rich.				artery morphogenesis (GO:0048844)|cell aging (GO:0007569)|developmental growth (GO:0048589)|heart morphogenesis (GO:0003007)|in utero embryonic development (GO:0001701)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)|vasculogenesis (GO:0001570)|vitellogenesis (GO:0007296)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(14)|ovary(2)|prostate(3)|skin(1)	30	all_cancers(46;0.0292)|Breast(12;8.52e-05)|all_epithelial(25;0.000854)|Prostate(51;0.00985)		Epithelial(14;0.00256)|all cancers(16;0.00726)|Colorectal(32;0.229)			CTGGCATGACGCCCTCGGGGA	0.701													G|||	26	0.00519169	0.0	0.0029	5008	,	,		10851	0.0		0.0129	False		,,,				2504	0.0112				p.T356T		Atlas-SNP	.											ZMIZ1,NS,carcinoma,+1,1	ZMIZ1	101	1	0			c.G1068A						PASS	.	G		9,4379		0,9,2185	31.0	41.0	38.0		1068	-9.8	0.9	10	dbSNP_134	38	88,8482		0,88,4197	no	coding-synonymous	ZMIZ1	NM_020338.3		0,97,6382	AA,AG,GG		1.0268,0.2051,0.7486		356/1068	81053248	97,12861	2194	4285	6479	SO:0001819	synonymous_variant	57178	exon12			CATGACGCCCTCG	AB033050	CCDS7357.1	10q22.3	2012-11-30	2006-10-24	2006-10-24	ENSG00000108175	ENSG00000108175		"""Zinc fingers, MIZ-type"""	16493	protein-coding gene	gene with protein product		607159	"""retinoic acid induced 17"""	RAI17		15626329	Standard	NM_020338		Approved	RP11-519K18.1, KIAA1224, FLJ13541, hZIMP10, Zimp10, MIZ	uc001kaf.2	Q9ULJ6	OTTHUMG00000018560	ENST00000334512.5:c.1068G>A	10.37:g.81053248G>A		Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	32	13	0.40625	NM_020338	Q5JSH9|Q7Z7E6	Silent	SNP	ENST00000334512.5	37	CCDS7357.1																																																																																			G|0.995;A|0.005	0.005	strong		0.701	ZMIZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048944.2	NM_020338	
CACNA1G	8913	hgsc.bcm.edu	37	17	48703752	48703752	+	Silent	SNP	T	T	C	rs739925	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:48703752T>C	ENST00000359106.5	+	38	6774	c.6774T>C	c.(6772-6774)ccT>ccC	p.P2258P	CACNA1G_ENST00000514717.1_Silent_p.P2108P|CACNA1G_ENST00000515411.1_Silent_p.P2195P|CACNA1G_ENST00000513964.1_Silent_p.P2120P|CACNA1G_ENST00000510366.1_Silent_p.P2113P|CACNA1G_ENST00000505165.1_Silent_p.P2086P|CACNA1G_ENST00000503485.1_Silent_p.P2131P|CACNA1G_ENST00000515165.1_Silent_p.P2165P|CACNA1G_ENST00000514181.1_Silent_p.P2140P|CACNA1G_ENST00000442258.2_Silent_p.P2124P|CACNA1G_ENST00000510115.1_Silent_p.P2179P|CACNA1G_ENST00000513689.2_Silent_p.P2168P|CACNA1G_ENST00000507336.1_Silent_p.P2247P|CACNA1G_ENST00000507609.1_Silent_p.P2158P|CACNA1G_ENST00000358244.5_Silent_p.P2052P|CACNA1G_ENST00000514079.1_Silent_p.P2172P|CACNA1G_ENST00000515765.1_Silent_p.P2202P|CACNA1G_ENST00000507896.1_Silent_p.P2075P|CACNA1G_ENST00000360761.4_Silent_p.P2142P|CACNA1G_ENST00000352832.5_Silent_p.P2131P|CACNA1G_ENST00000429973.2_Silent_p.P2147P|CACNA1G_ENST00000354983.4_Silent_p.P2224P|CTB-22K21.2_ENST00000502435.1_RNA|CACNA1G_ENST00000507510.2_Silent_p.P2213P|CACNA1G_ENST00000512389.1_Silent_p.P2154P|CACNA1G_ENST00000502264.1_Silent_p.P2187P	NM_018896.4	NP_061496.2	O43497	CAC1G_HUMAN	calcium channel, voltage-dependent, T type, alpha 1G subunit	2258					axon guidance (GO:0007411)|calcium ion import (GO:0070509)|membrane depolarization during action potential (GO:0086010)|positive regulation of calcium ion-dependent exocytosis (GO:0045956)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of heart rate (GO:0002027)|regulation of membrane potential (GO:0042391)|response to nickel cation (GO:0010045)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	low voltage-gated calcium channel activity (GO:0008332)|scaffold protein binding (GO:0097110)			breast(5)|cervix(1)|endometrium(13)|kidney(5)|lung(23)	47	Breast(11;6.7e-17)		BRCA - Breast invasive adenocarcinoma(22;7.52e-09)		Cinnarizine(DB00568)|Ethosuximide(DB00593)|Flunarizine(DB04841)|Methsuximide(DB05246)|Spironolactone(DB00421)|Trimethadione(DB00347)|Verapamil(DB00661)|Zonisamide(DB00909)	AGCGCCGGCCTACGTCCTGGC	0.677											OREG0024569	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	1839	0.367212	0.5393	0.2651	5008	,	,		14167	0.1786		0.4433	False		,,,				2504	0.3231				p.P2258P		Atlas-SNP	.											.	CACNA1G	659	.	0			c.T6774C						PASS	.	C	,,,,,,,,,,,,,	2057,2001		538,981,510	16.0	21.0	19.0		6774,6156,6705,6462,6537,6606,6426,6561,6495,6639,6441,6393,6372,6672	-10.9	0.0	17	dbSNP_86	19	3608,4724		780,2048,1338	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	CACNA1G	NM_018896.3,NM_198376.1,NM_198377.1,NM_198378.1,NM_198379.1,NM_198380.1,NM_198382.1,NM_198383.1,NM_198384.1,NM_198385.1,NM_198386.1,NM_198387.1,NM_198388.1,NM_198396.1	,,,,,,,,,,,,,	1318,3029,1848	CC,CT,TT		43.3029,49.31,45.7224	,,,,,,,,,,,,,	2258/2378,2052/2172,2235/2355,2154/2274,2179/2299,2202/2322,2142/2262,2187/2307,2165/2285,2213/2333,2147/2267,2131/2251,2124/2244,2224/2344	48703752	5665,6725	2029	4166	6195	SO:0001819	synonymous_variant	8913	exon38			CCGGCCTACGTCC	AC004590	CCDS45730.1, CCDS45731.1, CCDS45732.1, CCDS45733.1, CCDS45734.1, CCDS45735.1, CCDS45736.1, CCDS45737.1, CCDS54142.1, CCDS54143.1, CCDS54144.1, CCDS54145.1, CCDS54146.1, CCDS58565.1, CCDS58566.1, CCDS58567.1, CCDS58568.1, CCDS58569.1, CCDS58570.1, CCDS58571.1, CCDS58572.1, CCDS58573.1, CCDS58574.1, CCDS58575.1, CCDS58576.1	17q22	2012-03-07	2007-02-16		ENSG00000006283	ENSG00000006283		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1394	protein-coding gene	gene with protein product		604065				9495342, 16382099	Standard	NM_001256334		Approved	Cav3.1, NBR13	uc002irk.2	O43497	OTTHUMG00000162180	ENST00000359106.5:c.6774T>C	17.37:g.48703752T>C		Somatic	129	0	0	956	WXS	Illumina HiSeq	Phase_I	136	73	0.536765	NM_018896	D6RA64|E7EPR0|O43498|O94770|Q19QY8|Q19QY9|Q19QZ0|Q19QZ1|Q19QZ2|Q19QZ3|Q19QZ4|Q19QZ5|Q19QZ6|Q19QZ7|Q19QZ8|Q19QZ9|Q19R00|Q19R01|Q19R02|Q19R03|Q19R04|Q19R05|Q19R06|Q19R07|Q19R08|Q19R09|Q19R10|Q19R11|Q19R12|Q19R13|Q19R15|Q19R16|Q19R17|Q19R18|Q2TAC4|Q9NYU4|Q9NYU5|Q9NYU6|Q9NYU7|Q9NYU8|Q9NYU9|Q9NYV0|Q9NYV1|Q9UHN9|Q9UHP0|Q9ULU6|Q9UNG7|Q9Y5T2|Q9Y5T3	Silent	SNP	ENST00000359106.5	37	CCDS45730.1																																																																																			T|0.603;G|0.006	.	strong		0.677	CACNA1G-013	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367895.1	NM_018896	
EP300	2033	hgsc.bcm.edu	37	22	41548008	41548008	+	Missense_Mutation	SNP	A	A	G	rs20551	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:41548008A>G	ENST00000263253.7	+	15	4208	c.2989A>G	c.(2989-2991)Att>Gtt	p.I997V		NM_001429.3	NP_001420.2	Q09472	EP300_HUMAN	E1A binding protein p300	997			I -> V (in dbSNP:rs20551).		apoptotic process (GO:0006915)|cellular response to hypoxia (GO:0071456)|chromatin organization (GO:0006325)|circadian rhythm (GO:0007623)|G2/M transition of mitotic cell cycle (GO:0000086)|heart development (GO:0007507)|histone H2B acetylation (GO:0043969)|histone H4 acetylation (GO:0043967)|innate immune response (GO:0045087)|internal peptidyl-lysine acetylation (GO:0018393)|internal protein amino acid acetylation (GO:0006475)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|lung development (GO:0030324)|mitotic cell cycle (GO:0000278)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of protein binding (GO:0032092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|regulation of androgen receptor signaling pathway (GO:0060765)|regulation of cell cycle (GO:0051726)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)|regulation of tubulin deacetylation (GO:0090043)|response to estrogen (GO:0043627)|response to hypoxia (GO:0001666)|skeletal muscle tissue development (GO:0007519)|somitogenesis (GO:0001756)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	acetyltransferase activity (GO:0016407)|activating transcription factor binding (GO:0033613)|androgen receptor binding (GO:0050681)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|lysine N-acetyltransferase activity, acting on acetyl phosphate as donor (GO:0004468)|nuclear hormone receptor binding (GO:0035257)|pre-mRNA intronic binding (GO:0097157)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transferase activity, transferring acyl groups (GO:0016746)|zinc ion binding (GO:0008270)			NS(2)|breast(11)|central_nervous_system(7)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(31)|kidney(5)|large_intestine(31)|liver(2)|lung(33)|ovary(2)|pancreas(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(16)	171						GCCGGAGGATATTTCAGAGGT	0.418			"""T,  N, F, Mis, O"""	"""MLL, RUNXBP2"""	"""colorectal, breast, pancreatic, AML, ALL, DLBCL"""				Rubinstein-Taybi syndrome				A|||	1119	0.223442	0.0227	0.513	5008	,	,		17915	0.0536		0.3032	False		,,,				2504	0.3824				p.I997V		Atlas-SNP	.		Rec	yes		22	22q13	2033	300 kd E1A-Binding protein gene		"""L, E"""	.	EP300	367	.	0			c.A2989G						PASS	.	A	VAL/ILE	266,4140	151.0+/-185.0	8,250,1945	100.0	105.0	103.0		2989	3.6	0.2	22	dbSNP_67	103	2411,6189	399.6+/-346.5	341,1729,2230	yes	missense	EP300	NM_001429.3	29	349,1979,4175	GG,GA,AA		28.0349,6.0372,20.5828	benign	997/2415	41548008	2677,10329	2203	4300	6503	SO:0001583	missense	2033	exon15	Familial Cancer Database	Broad Thumb-Hallux syndrome	GAGGATATTTCAG	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.2989A>G	22.37:g.41548008A>G	ENSP00000263253:p.Ile997Val	Somatic	216	0	0		WXS	Illumina HiSeq	Phase_I	225	101	0.448889	NM_001429	B1AKC2	Missense_Mutation	SNP	ENST00000263253.7	37	CCDS14010.1	460	0.21062271062271062	15	0.03048780487804878	181	0.5	32	0.055944055944055944	232	0.30606860158311344	A	7.139	0.581359	0.13686	0.060372	0.280349	ENSG00000100393	ENST00000263253	D	0.81996	-1.56	5.77	3.62	0.41486	.	0.552881	0.14785	N	0.298584	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	0.42649	-0.9439	9	0.27082	T	0.32	-4.794	10.2891	0.43586	0.8649:0.0:0.1351:0.0	rs20551;rs2413638;rs17349228;rs17398623;rs20551	997	Q09472	EP300_HUMAN	V	997	ENSP00000263253:I997V	ENSP00000263253:I997V	I	+	1	0	EP300	39877954	0.717000	0.27966	0.250000	0.24296	0.132000	0.20833	2.165000	0.42396	0.432000	0.26286	0.460000	0.39030	ATT	A|0.802;G|0.198	0.198	strong		0.418	EP300-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320600.1	NM_001429	
C6orf15	29113	hgsc.bcm.edu	37	6	31079440	31079440	+	Missense_Mutation	SNP	C	C	T	rs2233982	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:31079440C>T	ENST00000259870.3	-	2	699	c.696G>A	c.(694-696)atG>atA	p.M232I		NM_014070.2	NP_054789.2	Q6UXA7	CF015_HUMAN	chromosome 6 open reading frame 15	232	Gly-rich.		M -> I (in dbSNP:rs2233982).		extracellular matrix organization (GO:0030198)	interstitial matrix (GO:0005614)	heparin binding (GO:0008201)|hyaluronic acid binding (GO:0005540)			endometrium(3)|large_intestine(2)|lung(9)|prostate(1)|skin(1)|stomach(1)	17						CAGGGTGTGGCATGGGCCTCG	0.562													C|||	255	0.0509185	0.0227	0.0447	5008	,	,		15627	0.0466		0.0497	False		,,,				2504	0.0992				p.M232I		Atlas-SNP	.											.	C6orf15	29	.	0			c.G696A						PASS	.	C	ILE/MET	110,3358		1,108,1625	40.0	41.0	41.0		696	2.4	0.9	6	dbSNP_98	41	303,6383		12,279,3052	yes	missense	C6orf15	NM_014070.2	10	13,387,4677	TT,TC,CC		4.5319,3.1719,4.0674	possibly-damaging	232/326	31079440	413,9741	1734	3343	5077	SO:0001583	missense	29113	exon2			GTGTGGCATGGGC	AB031481	CCDS4693.1	6p21	2011-12-12			ENSG00000204542	ENSG00000204542			13927	protein-coding gene	gene with protein product		611401					Standard	NM_014070		Approved	STG	uc003nsk.1	Q6UXA7	OTTHUMG00000031111	ENST00000259870.3:c.696G>A	6.37:g.31079440C>T	ENSP00000259870:p.Met232Ile	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	109	50	0.458716	NM_014070	B0S7V8|Q0EFA6|Q2L6G7|Q5SQ81|Q86Z05|Q9UIG3	Missense_Mutation	SNP	ENST00000259870.3	37	CCDS4693.1	88	0.040293040293040296	11	0.022357723577235773	20	0.055248618784530384	19	0.033216783216783216	38	0.05013192612137203	C	13.45	2.241861	0.39598	0.031719	0.045319	ENSG00000204542	ENST00000259870	T	0.09538	2.97	4.4	2.4	0.29515	.	0.246295	0.29814	N	0.011137	T	0.04048	0.0113	M	0.65975	2.015	0.20403	N	0.999905	P	0.38677	0.642	B	0.28385	0.089	T	0.21724	-1.0237	10	0.87932	D	0	-0.1295	8.8562	0.35229	0.4343:0.5657:0.0:0.0	rs2233982;rs52789401;rs2233982	232	Q6UXA7	CF015_HUMAN	I	232	ENSP00000259870:M232I	ENSP00000259870:M232I	M	-	3	0	C6orf15	31187419	0.826000	0.29277	0.903000	0.35520	0.320000	0.28249	0.664000	0.25068	1.046000	0.40249	0.643000	0.83706	ATG	C|0.950;T|0.050	0.050	strong		0.562	C6orf15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076184.2	NM_014070	
TTF1	7270	hgsc.bcm.edu	37	9	135277341	135277341	+	Missense_Mutation	SNP	C	C	A	rs8999	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:135277341C>A	ENST00000334270.2	-	2	907	c.868G>T	c.(868-870)Gca>Tca	p.A290S		NM_001205296.1|NM_007344.3	NP_001192225.1|NP_031370.2	Q15361	TTF1_HUMAN	transcription termination factor, RNA polymerase I	290			A -> S (in dbSNP:rs8999).		chromatin remodeling (GO:0006338)|DNA-templated transcription, termination (GO:0006353)|gene expression (GO:0010467)|negative regulation of DNA replication (GO:0008156)|regulation of transcription, DNA-templated (GO:0006355)|termination of RNA polymerase I transcription (GO:0006363)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			endometrium(3)|kidney(1)|large_intestine(5)|lung(13)|ovary(2)|pancreas(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	30		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;4.25e-06)|Epithelial(140;9.09e-05)		ATGGCCAATGCCTCAAATTCC	0.473													C|||	760	0.151757	0.1316	0.1066	5008	,	,		18978	0.252		0.0825	False		,,,				2504	0.1789				p.A290S		Atlas-SNP	.											.	TTF1	82	.	0			c.G868T						PASS	.	C	,SER/ALA	557,3849	248.1+/-256.1	33,491,1679	151.0	147.0	148.0		,868	-0.6	0.0	9	dbSNP_52	148	592,8008	157.3+/-211.0	24,544,3732	yes	intron,missense	TTF1	NM_001205296.1,NM_007344.3	,99	57,1035,5411	AA,AC,CC		6.8837,12.6419,8.8344	,possibly-damaging	,290/906	135277341	1149,11857	2203	4300	6503	SO:0001583	missense	7270	exon2			CCAATGCCTCAAA	BC050734	CCDS6948.1, CCDS75925.1	9q34.3	2008-02-05			ENSG00000125482	ENSG00000125482			12397	protein-coding gene	gene with protein product		600777				7597036	Standard	NM_007344		Approved		uc004cbl.3	Q15361	OTTHUMG00000020836	ENST00000334270.2:c.868G>T	9.37:g.135277341C>A	ENSP00000333920:p.Ala290Ser	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	66	29	0.439394	NM_007344	A1L160|Q4VXF3|Q58EY2|Q6P5T5	Missense_Mutation	SNP	ENST00000334270.2	37	CCDS6948.1	324	0.14835164835164835	77	0.1565040650406504	36	0.09944751381215469	152	0.26573426573426573	59	0.07783641160949868	C	4.220	0.039741	0.08148	0.126419	0.068837	ENSG00000125482	ENST00000334270;ENST00000245588	T	0.09255	3.0	2.52	-0.643	0.11482	.	.	.	.	.	T	0.00012	0.0000	L	0.36672	1.1	0.80722	P	0.0	B	0.24576	0.106	B	0.10450	0.005	T	0.42816	-0.9429	8	0.02654	T	1	.	2.3524	0.04287	0.3905:0.4102:0.0:0.1993	rs8999;rs3188185;rs3739913;rs52817153;rs61483795;rs8999	290	Q15361	TTF1_HUMAN	S	290	ENSP00000333920:A290S	ENSP00000245588:A290S	A	-	1	0	TTF1	134267162	0.000000	0.05858	0.010000	0.14722	0.017000	0.09413	0.141000	0.16076	0.153000	0.19213	0.467000	0.42956	GCA	C|0.878;A|0.122	0.122	strong		0.473	TTF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054784.2	NM_007344	
DNAH14	127602	hgsc.bcm.edu	37	1	225565073	225565073	+	Silent	SNP	C	C	T	rs3856155	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:225565073C>T	ENST00000445597.2	+	54	9321	c.9321C>T	c.(9319-9321)ggC>ggT	p.G3107G	DNAH14_ENST00000439375.2_Silent_p.G4115G|DNAH14_ENST00000430092.1_Silent_p.G4115G			Q0VDD8	DYH14_HUMAN	dynein, axonemal, heavy chain 14	3107					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						AGACCCAGGGCGAAAAGTTTA	0.453													c|||	2463	0.491813	0.171	0.7118	5008	,	,		17842	0.7411		0.6123	False		,,,				2504	0.3885				p.G4115G		Atlas-SNP	.											.	DNAH14	300	.	0			c.C12345T						PASS	.	T		315,1069		38,239,415	85.0	81.0	82.0		12345	4.3	0.0	1	dbSNP_108	82	1923,1259		574,775,242	no	coding-synonymous	DNAH14	NM_001373.1		612,1014,657	TT,TC,CC		39.5663,22.7601,49.0145		4115/4516	225565073	2238,2328	692	1591	2283	SO:0001819	synonymous_variant	127602	exon77			CCAGGGCGAAAAG	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.9321C>T	1.37:g.225565073C>T		Somatic	353	0	0		WXS	Illumina HiSeq	Phase_I	316	307	0.971519	NM_001373	A6NG62|A6NNL2|Q0VDD9|Q4VXC7|Q4VXG4|Q4VXG5|Q5VU33|Q5VU34	Silent	SNP	ENST00000445597.2	37																																																																																				C|0.457;T|0.543	0.543	strong		0.453	DNAH14-007	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000331217.3	XM_059166	
REV3L	5980	hgsc.bcm.edu	37	6	111631254	111631254	+	Silent	SNP	T	T	C	rs150392515		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:111631254T>C	ENST00000358835.3	-	31	9298	c.8844A>G	c.(8842-8844)cgA>cgG	p.R2948R	RP5-1112D6.8_ENST00000607434.1_RNA|REV3L_ENST00000462119.1_5'UTR|REV3L_ENST00000368802.3_Silent_p.R2948R|REV3L_ENST00000435970.1_Silent_p.R2870R|REV3L_ENST00000368805.1_Silent_p.R2948R			O60673	DPOLZ_HUMAN	REV3-like, polymerase (DNA directed), zeta, catalytic subunit	2948					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)		CGTATGGCACTCGCTCCCCAA	0.498								DNA polymerases (catalytic subunits)																													p.R2948R		Atlas-SNP	.											REV3L,NS,carcinoma,-2,1	REV3L	386	1	0			c.A8844G						PASS	.	T		0,4406		0,0,2203	74.0	76.0	75.0		8844	0.2	1.0	6	dbSNP_134	75	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	REV3L	NM_002912.3		0,2,6501	CC,CT,TT		0.0233,0.0,0.0154		2948/3131	111631254	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	5980	exon30			TGGCACTCGCTCC	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.8844A>G	6.37:g.111631254T>C		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	31	15	0.483871	NM_002912	O43214|Q5TC33	Silent	SNP	ENST00000358835.3	37	CCDS5091.2																																																																																			T|1.000;C|0.000	0.000	weak		0.498	REV3L-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043695.1	NM_002912	
HHIPL2	79802	hgsc.bcm.edu	37	1	222713503	222713503	+	Silent	SNP	C	C	G	rs3748664	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:222713503C>G	ENST00000343410.6	-	4	1357	c.1299G>C	c.(1297-1299)acG>acC	p.T433T		NM_024746.3	NP_079022.2	Q6UWX4	HIPL2_HUMAN	HHIP-like 2	433					carbohydrate metabolic process (GO:0005975)	extracellular region (GO:0005576)	oxidoreductase activity, acting on the CH-OH group of donors, quinone or similar compound as acceptor (GO:0016901)|quinone binding (GO:0048038)			NS(2)|endometrium(8)|kidney(4)|large_intestine(7)|lung(28)|ovary(1)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	59				GBM - Glioblastoma multiforme(131;0.0185)		GGCCCTGGCGCGTGATGGGGT	0.567													C|||	1881	0.375599	0.3434	0.5058	5008	,	,		17111	0.5089		0.2604	False		,,,				2504	0.3078				p.T433T		Atlas-SNP	.											HHIPL2,colon,carcinoma,0,1	HHIPL2	122	1	0			c.G1299C						scavenged	.	C		1446,2960	466.2+/-354.4	222,1002,979	70.0	70.0	70.0		1299	-11.0	0.0	1	dbSNP_107	70	2505,6095	408.3+/-349.4	366,1773,2161	no	coding-synonymous	HHIPL2	NM_024746.3		588,2775,3140	GG,GC,CC		29.1279,32.8189,30.3783		433/725	222713503	3951,9055	2203	4300	6503	SO:0001819	synonymous_variant	79802	exon4			CTGGCGCGTGATG	BC007638	CCDS1530.2	1q41	2008-02-05	2008-01-16	2008-01-16	ENSG00000143512	ENSG00000143512			25842	protein-coding gene	gene with protein product			"""KIAA1822-like"""	KIAA1822L		12975309	Standard	NM_024746		Approved	FLJ13840	uc001hnh.1	Q6UWX4	OTTHUMG00000037545	ENST00000343410.6:c.1299G>C	1.37:g.222713503C>G		Somatic	99	1	0.010101		WXS	Illumina HiSeq	Phase_I	75	30	0.4	NM_024746	Q6GU65|Q96BT4|Q96BU5|Q9H8A0	Silent	SNP	ENST00000343410.6	37	CCDS1530.2																																																																																			C|0.679;G|0.321	0.321	strong		0.567	HHIPL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091499.2	NM_024746	
RYR3	6263	hgsc.bcm.edu	37	15	34015013	34015013	+	Silent	SNP	G	G	A	rs2293027	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:34015013G>A	ENST00000389232.4	+	44	6787	c.6717G>A	c.(6715-6717)ggG>ggA	p.G2239G	Y_RNA_ENST00000363138.1_RNA|RYR3_ENST00000415757.3_Silent_p.G2239G	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	90	0	0		WXS	Illumina HiSeq	Phase_I	83	82	0.987952	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		
CFHR2	3080	hgsc.bcm.edu	37	1	196884258	196884258	+	Intron	SNP	A	A	T	rs150845796		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:196884258A>T	ENST00000367421.3	+	2	135				CFHR4_ENST00000608469.1_Silent_p.P133P|CFHR4_ENST00000367416.2_Silent_p.P509P|CFHR4_ENST00000367418.2_Silent_p.P263P|CFHR4_ENST00000251424.4_Silent_p.P263P			P36980	FHR2_HUMAN	complement factor H-related 2							extracellular region (GO:0005576)				large_intestine(2)|ovary(1)|skin(3)	6						CGGAACCACCAAGATGCATAC	0.358																																					p.P510P		Atlas-SNP	.											CFHR4_ENST00000367416,right_lower_lobe,carcinoma,+1,2	CFHR4	141	2	0			c.A1530T						scavenged	.						67.0	69.0	68.0					1																	196884258		2199	4295	6494	SO:0001627	intron_variant	10877	exon9			ACCACCAAGATGC	X64877	CCDS30959.1	1q31.3	2008-02-05	2004-08-09	2006-02-28	ENSG00000080910	ENSG00000080910		"""Complement system"""	4890	protein-coding gene	gene with protein product		600889	"""H factor (complement)-like 3"""	HFL3, CFHL2		1533657, 7672821	Standard	NM_005666		Approved	FHR2	uc001gtq.1	P36980	OTTHUMG00000036518	ENST00000367421.3:c.59-34327A>T	1.37:g.196884258A>T		Somatic	454	0	0		WXS	Illumina HiSeq	Phase_I	543	174	0.320442	NM_001201550	Q14310|Q5T9T1	Silent	SNP	ENST00000367421.3	37																																																																																				.	.	weak		0.358	CFHR2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_005666	
TAAR2	9287	hgsc.bcm.edu	37	6	132938817	132938817	+	Silent	SNP	G	G	A	rs61745666	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:132938817G>A	ENST00000367931.1	-	2	527	c.528C>T	c.(526-528)ttC>ttT	p.F176F	TAAR2_ENST00000275191.2_Silent_p.F131F|TAAR2_ENST00000537809.1_Silent_p.F131F			Q9P1P5	TAAR2_HUMAN	trace amine associated receptor 2	176					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)|trace-amine receptor activity (GO:0001594)			breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(15)|ovary(1)|skin(1)	23	Breast(56;0.135)			OV - Ovarian serous cystadenocarcinoma(155;0.00608)|GBM - Glioblastoma multiforme(226;0.0151)		AGACCACCCCGAAGGCAAATG	0.443													G|||	971	0.19389	0.5287	0.1196	5008	,	,		19402	0.0893		0.0239	False		,,,				2504	0.0767				p.F176F		Atlas-SNP	.											TAAR2,colon,carcinoma,0,1	TAAR2	45	1	0			c.C528T						scavenged	.	G	,	2102,2304	575.0+/-383.9	515,1072,616	61.0	57.0	59.0		528,393	-1.5	0.3	6	dbSNP_129	59	166,8434	76.3+/-139.0	2,162,4136	yes	coding-synonymous,coding-synonymous	TAAR2	NM_001033080.1,NM_014626.3	,	517,1234,4752	AA,AG,GG		1.9302,47.7077,17.4381	,	176/352,131/307	132938817	2268,10738	2203	4300	6503	SO:0001819	synonymous_variant	9287	exon2			CACCCCGAAGGCA	AF112460	CCDS34541.1, CCDS5157.1	6q24	2012-08-08	2005-02-23	2005-02-24	ENSG00000146378	ENSG00000146378		"""GPCR / Class A : Trace amine associated receptors"""	4514	protein-coding gene	gene with protein product		604849	"""G protein-coupled receptor 58"""	GPR58		10684976, 15718104	Standard	NM_014626		Approved		uc003qdl.1	Q9P1P5	OTTHUMG00000015585	ENST00000367931.1:c.528C>T	6.37:g.132938817G>A		Somatic	93	1	0.0107527		WXS	Illumina HiSeq	Phase_I	51	12	0.235294	NM_001033080	Q5QD02|Q6NWS1|Q6NWS2|Q6NWS3	Silent	SNP	ENST00000367931.1	37	CCDS34541.1																																																																																			A|0.164;G|0.836;T|0.000	0.164	strong		0.443	TAAR2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000390735.1	NM_014626	
KRT84	3890	hgsc.bcm.edu	37	12	52774305	52774305	+	Silent	SNP	A	A	G	rs1732293	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	98	0	0	987	WXS	Illumina HiSeq	Phase_I	70	27	0.385714	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	
UNC45A	55898	hgsc.bcm.edu	37	15	91496233	91496233	+	Missense_Mutation	SNP	G	G	A	rs149872991		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:91496233G>A	ENST00000418476.2	+	18	2418	c.2378G>A	c.(2377-2379)cGg>cAg	p.R793Q	RCCD1_ENST00000556618.1_5'Flank|UNC45A_ENST00000394275.2_Missense_Mutation_p.R778Q|RCCD1_ENST00000555155.1_5'Flank|RCCD1_ENST00000394258.2_5'Flank|AC068831.6_ENST00000553321.1_RNA	NM_018671.3	NP_061141.2	Q9H3U1	UN45A_HUMAN	unc-45 homolog A (C. elegans)	793					cell differentiation (GO:0030154)|chaperone-mediated protein folding (GO:0061077)|muscle organ development (GO:0007517)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)				breast(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(7)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25	Lung NSC(78;0.0771)|all_lung(78;0.137)		Lung(145;0.189)			ATGATCCGCCGGGCAGCCACG	0.582													g|||	1	0.000199681	0.0	0.0	5008	,	,		22008	0.0		0.001	False		,,,				2504	0.0				p.R793Q		Atlas-SNP	.											.	UNC45A	57	.	0			c.G2378A						PASS	.		GLN/ARG,GLN/ARG	1,4395	2.1+/-5.4	0,1,2197	83.0	62.0	69.0		2333,2378	4.9	1.0	15	dbSNP_134	69	7,8589	5.7+/-21.5	0,7,4291	yes	missense,missense	UNC45A	NM_001039675.1,NM_018671.3	43,43	0,8,6488	AA,AG,GG		0.0814,0.0227,0.0616	benign,benign	778/930,793/945	91496233	8,12984	2198	4298	6496	SO:0001583	missense	55898	exon18			TCCGCCGGGCAGC		CCDS10367.1, CCDS42082.1	15q26.1	2008-02-05			ENSG00000140553	ENSG00000140553			30594	protein-coding gene	gene with protein product	"""smooth muscle cell associated protein-1"""	611219				12356907	Standard	XM_005254963		Approved	SMAP-1, GC-UNC45	uc002bqg.3	Q9H3U1	OTTHUMG00000141261	ENST00000418476.2:c.2378G>A	15.37:g.91496233G>A	ENSP00000407487:p.Arg793Gln	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	74	48	0.648649	NM_018671	A8K6F7|Q7L3Y6|Q9H3U8|Q9NSE8|Q9NSE9	Missense_Mutation	SNP	ENST00000418476.2	37	CCDS10367.1	.	.	.	.	.	.	.	.	.	.	g	15.13	2.742516	0.49151	2.27E-4	8.14E-4	ENSG00000140553	ENST00000394275;ENST00000418476	T;T	0.49720	0.77;0.77	4.88	4.88	0.63580	Armadillo-like helical (1);Armadillo-type fold (1);	0.457993	0.23413	N	0.048457	T	0.28830	0.0715	N	0.25992	0.78	0.37116	D	0.900608	P;P	0.48640	0.913;0.913	B;B	0.33799	0.17;0.17	T	0.30909	-0.9962	10	0.40728	T	0.16	-27.8398	10.8602	0.46823	0.0:0.0:0.7065:0.2935	.	793;778	Q9H3U1;A8K6F7	UN45A_HUMAN;.	Q	778;793	ENSP00000377816:R778Q;ENSP00000407487:R793Q	ENSP00000377816:R778Q	R	+	2	0	UNC45A	89297237	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.880000	0.39628	2.549000	0.85964	0.645000	0.84053	CGG	G|1.000;A|0.000	0.000	strong		0.582	UNC45A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000280406.2	NM_018671	
NOSTRIN	115677	hgsc.bcm.edu	37	2	169721377	169721377	+	Missense_Mutation	SNP	G	G	A	rs479661	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:169721377G>A	ENST00000317647.7	+	16	1647	c.1418G>A	c.(1417-1419)gGa>gAa	p.G473E	NOSTRIN_ENST00000421711.2_Missense_Mutation_p.G445E|NOSTRIN_ENST00000445023.2_Missense_Mutation_p.G395E|NOSTRIN_ENST00000397209.2_Missense_Mutation_p.G445E|NOSTRIN_ENST00000397206.2_Missense_Mutation_p.G395E|NOSTRIN_ENST00000458381.2_Missense_Mutation_p.G530E|NOSTRIN_ENST00000444448.2_Missense_Mutation_p.G530E	NM_001039724.3	NP_001034813.2	Q8IVI9	NOSTN_HUMAN	nitric oxide synthase trafficking	473	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.		G -> E (in dbSNP:rs479661). {ECO:0000269|PubMed:12446846, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.2}.		endocytosis (GO:0006897)|negative regulation of transcription, DNA-templated (GO:0045892)|nitric oxide metabolic process (GO:0046209)|regulation of nitric-oxide synthase activity (GO:0050999)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytoskeleton (GO:0005856)|endocytic vesicle membrane (GO:0030666)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)			kidney(1)|large_intestine(1)|lung(4)|prostate(1)|skin(1)|urinary_tract(1)	9						AAAAAAGAAGGAGGATGGTGG	0.433													A|||	4543	0.907149	0.9629	0.8098	5008	,	,		20528	0.9395		0.832	False		,,,				2504	0.9448				p.G530E		Atlas-SNP	.											.	NOSTRIN	68	.	0			c.G1589A						PASS	.	A	GLU/GLY,GLU/GLY,GLU/GLY,GLU/GLY	3529,205		1668,193,6	148.0	134.0	138.0		1418,1589,1334,1184	5.0	1.0	2	dbSNP_83	138	6827,1387		2831,1165,111	yes	missense,missense,missense,missense	NOSTRIN	NM_001039724.3,NM_001171631.1,NM_001171632.1,NM_052946.3	98,98,98,98	4499,1358,117	AA,AG,GG		16.8858,5.4901,13.3244	benign,benign,benign,benign	473/507,530/564,445/479,395/429	169721377	10356,1592	1867	4107	5974	SO:0001583	missense	115677	exon21			AAGAAGGAGGATG	AJ532842	CCDS42771.1, CCDS42772.1, CCDS54415.1, CCDS54416.1	2q31.1	2013-08-05	2013-08-05		ENSG00000163072	ENSG00000163072			20203	protein-coding gene	gene with protein product		607496	"""nitric oxide synthase trafficker"""			12446846	Standard	NM_001171631		Approved	MGC20702	uc002ueg.3	Q8IVI9	OTTHUMG00000153990	ENST00000317647.7:c.1418G>A	2.37:g.169721377G>A	ENSP00000318921:p.Gly473Glu	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	68	68	1	NM_001171631	A8K2I9|B3KSF5|E7EPT9|Q27HG3|Q53S62|Q96CJ9	Missense_Mutation	SNP	ENST00000317647.7	37	CCDS42771.1	1939	0.8878205128205128	475	0.9654471544715447	296	0.8176795580110497	531	0.9283216783216783	637	0.8403693931398417	A	5.378	0.255043	0.10185	0.945099	0.831142	ENSG00000163072	ENST00000458381;ENST00000444448;ENST00000317647;ENST00000445023;ENST00000397206;ENST00000397209;ENST00000421711	T;T;T;T;T;T;T	0.27890	1.64;1.64;1.64;1.64;1.64;1.64;1.64	4.96	4.96	0.65561	Src homology-3 domain (5);	0.402041	0.27023	N	0.021320	T	0.00012	0.0000	N	0.12746	0.255	0.09310	P	0.9999999999999981	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	0.38693	-0.9649	9	0.08381	T	0.77	-8.8781	8.8432	0.35155	0.9116:0.0:0.0884:0.0	rs479661;rs1044339;rs3184075;rs17404542;rs17855448;rs56931979;rs479661	445;395;473;530	Q8IVI9-2;Q8IVI9-3;Q8IVI9;E7EPT9	.;.;NOSTN_HUMAN;.	E	530;530;473;395;395;445;445	ENSP00000402140:G530E;ENSP00000394051:G530E;ENSP00000318921:G473E;ENSP00000404413:G395E;ENSP00000380390:G395E;ENSP00000380392:G445E;ENSP00000401316:G445E	ENSP00000318921:G473E	G	+	2	0	NOSTRIN	169429623	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	2.153000	0.42282	0.834000	0.34852	-0.381000	0.06696	GGA	G|0.133;A|0.867	0.867	strong		0.433	NOSTRIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333356.4	NM_052946	
SYMPK	8189	hgsc.bcm.edu	37	19	46319415	46319415	+	Silent	SNP	G	G	C	rs1132645	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:46319415G>C	ENST00000245934.7	-	26	3625	c.3381C>G	c.(3379-3381)gcC>gcG	p.A1127A	RSPH6A_ENST00000597055.1_5'Flank|SYMPK_ENST00000598155.1_5'UTR|RSPH6A_ENST00000221538.3_5'Flank	NM_004819.2	NP_004810.2	Q92797	SYMPK_HUMAN	symplekin	1127					cell adhesion (GO:0007155)|mRNA polyadenylation (GO:0006378)|positive regulation of protein dephosphorylation (GO:0035307)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|tight junction (GO:0005923)				breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(7)|liver(1)|lung(25)|ovary(1)|urinary_tract(1)	45		all_neural(266;0.0299)|Ovarian(192;0.0308)		OV - Ovarian serous cystadenocarcinoma(262;0.00509)|GBM - Glioblastoma multiforme(486;0.0593)		CTGGGGCCGGGGCCAAGGTCA	0.652													G|||	1793	0.358027	0.2905	0.232	5008	,	,		11505	0.6409		0.3181	False		,,,				2504	0.2883				p.A1127A		Atlas-SNP	.											.	SYMPK	104	.	0			c.C3381G						PASS	.						3.0	3.0	3.0					19																	46319415		1528	3134	4662	SO:0001819	synonymous_variant	8189	exon26			GGCCGGGGCCAAG	U49240	CCDS12676.2	19q13.3	2008-02-05			ENSG00000125755	ENSG00000125755			22935	protein-coding gene	gene with protein product		602388				9330635	Standard	NM_004819		Approved	SYM, SPK	uc002pdn.3	Q92797	OTTHUMG00000150151	ENST00000245934.7:c.3381C>G	19.37:g.46319415G>C		Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	45	19	0.422222	NM_004819	O00521|O00689|O00733|Q59GT5|Q8N2U5	Silent	SNP	ENST00000245934.7	37	CCDS12676.2																																																																																			G|0.613;C|0.387	0.387	strong		0.652	SYMPK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316581.1	NM_004819	
HLA-A	3105	hgsc.bcm.edu	37	6	29910551	29910551	+	Missense_Mutation	SNP	T	T	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:29910551T>G	ENST00000396634.1	+	4	432	c.91T>G	c.(91-93)Tat>Gat	p.Y31D	HLA-A_ENST00000376802.2_Missense_Mutation_p.Y31D|HLA-A_ENST00000376809.5_Missense_Mutation_p.Y31D|HLA-A_ENST00000376806.5_Missense_Mutation_p.Y31D			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	31	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						CTCCATGAGGTATTTCTTCAC	0.726									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.Y31D		Atlas-SNP	.											.	HLA-A	89	.	0			c.T91G						PASS	.						15.0	14.0	15.0					6																	29910551		2179	4262	6441	SO:0001583	missense	3105	exon2	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	ATGAGGTATTTCT	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.91T>G	6.37:g.29910551T>G	ENSP00000379873:p.Tyr31Asp	Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	33	15	0.454545	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Missense_Mutation	SNP	ENST00000396634.1	37	CCDS34373.1	.	.	.	.	.	.	.	.	.	.	.	9.530	1.110553	0.20714	.	.	ENSG00000206503	ENST00000396634;ENST00000376806;ENST00000376809;ENST00000355767;ENST00000376802	T;T;T;T	0.01854	4.6;4.6;4.6;4.6	3.72	2.49	0.30216	MHC class I, alpha chain, alpha1/alpha2 (3);MHC classes I/II-like antigen recognition protein (3);MHC class I-like antigen recognition (3);	0.275088	0.19018	U	0.124883	T	0.19087	0.0458	H	0.99999	5.785	0.09310	N	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0	T	0.48115	-0.9063	10	0.87932	D	0	.	6.2298	0.20728	0.2235:0.0:0.0:0.7765	.	31;31;31;31;31	P13746;Q5SRN7;P16188;Q5SRN5;P04439	1A11_HUMAN;.;1A30_HUMAN;.;1A03_HUMAN	D	31	ENSP00000379873:Y31D;ENSP00000366002:Y31D;ENSP00000366005:Y31D;ENSP00000365998:Y31D	ENSP00000348012:Y31D	Y	+	1	0	HLA-A	30018530	0.000000	0.05858	0.020000	0.16555	0.261000	0.26267	0.438000	0.21559	0.583000	0.29574	0.391000	0.25812	TAT	.	.	none		0.726	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
WDR4	10785	hgsc.bcm.edu	37	21	44273858	44273858	+	Missense_Mutation	SNP	G	G	A	rs15736	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:44273858G>A	ENST00000398208.2	-	9	855	c.796C>T	c.(796-798)Cct>Tct	p.P266S	WDR4_ENST00000492742.1_5'UTR|WDR4_ENST00000330317.2_Missense_Mutation_p.P266S	NM_001260474.1|NM_001260475.1|NM_001260476.1|NM_018669.5	NP_001247403.1|NP_001247404.1|NP_001247405.1|NP_061139.2			WD repeat domain 4											haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(3)|ovary(2)	11				Colorectal(79;0.0165)|Lung(125;0.0484)|STAD - Stomach adenocarcinoma(101;0.0624)|COAD - Colon adenocarcinoma(84;0.128)|LUSC - Lung squamous cell carcinoma(216;0.244)		TAGACCACAGGAGTGCTTGCC	0.622													G|||	1720	0.34345	0.6543	0.232	5008	,	,		18571	0.0744		0.3767	False		,,,				2504	0.2454				p.P266S		Atlas-SNP	.											.	WDR4	35	.	0			c.C796T						PASS	.	G	SER/PRO,SER/PRO	2681,1675		865,951,362	20.0	17.0	18.0		796,796	4.5	0.1	21	dbSNP_52	18	3341,5193		705,1931,1631	yes	missense,missense	WDR4	NM_018669.4,NM_033661.3	74,74	1570,2882,1993	AA,AG,GG		39.1493,38.4527,46.7184	benign,benign	266/413,266/413	44273858	6022,6868	2178	4267	6445	SO:0001583	missense	10785	exon9			CCACAGGAGTGCT	AJ243912	CCDS13691.1	21q22.3	2013-01-09			ENSG00000160193	ENSG00000160193		"""WD repeat domain containing"""	12756	protein-coding gene	gene with protein product	"""TRM82 tRNA methyltransferase 82 homolog (S. cerevisiae)"""	605924				12403464	Standard	NM_018669		Approved	TRM82, TRMT82	uc002zci.4	P57081	OTTHUMG00000086826	ENST00000398208.2:c.796C>T	21.37:g.44273858G>A	ENSP00000381266:p.Pro266Ser	Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	27	6	0.222222	NM_018669		Missense_Mutation	SNP	ENST00000398208.2	37	CCDS13691.1	760	0.34798534798534797	329	0.6686991869918699	92	0.2541436464088398	46	0.08041958041958042	293	0.3865435356200528	G	11.05	1.525330	0.27299	0.615473	0.391493	ENSG00000160193	ENST00000330317;ENST00000398208	T;T	0.26957	1.7;1.7	4.52	4.52	0.55395	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.230781	0.36234	N	0.002702	T	0.00012	0.0000	M	0.71581	2.175	0.23351	P	0.99785247	P;B	0.40431	0.717;0.314	B;B	0.41271	0.352;0.106	T	0.25328	-1.0135	9	0.18710	T	0.47	-17.5226	14.5336	0.67944	0.0:0.0:1.0:0.0	rs15736;rs7282594;rs16994761;rs17344018;rs17844881;rs17857598;rs52837379;rs57453345;rs15736	265;266	P57081-2;P57081	.;WDR4_HUMAN	S	266	ENSP00000328671:P266S;ENSP00000381266:P266S	ENSP00000328671:P266S	P	-	1	0	WDR4	43146927	1.000000	0.71417	0.134000	0.22075	0.274000	0.26718	4.410000	0.59774	2.227000	0.72691	0.609000	0.83330	CCT	G|0.581;A|0.419	0.419	strong		0.622	WDR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195479.1		
SLC41A2	84102	hgsc.bcm.edu	37	12	105199038	105199038	+	Silent	SNP	G	G	A	rs11112201	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	125	0	0		WXS	Illumina HiSeq	Phase_I	94	38	0.404255	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	
SFTA2	389376	hgsc.bcm.edu	37	6	30899524	30899524	+	Missense_Mutation	SNP	T	T	C	rs3131787	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:30899524T>C	ENST00000359086.3	-	2	188	c.110A>G	c.(109-111)aAt>aGt	p.N37S	Y_RNA_ENST00000516952.1_RNA	NM_205854.2	NP_995326.1	Q6UW10	SFTA2_HUMAN	surfactant associated 2	37			N -> S (in dbSNP:rs3131787).			extracellular region (GO:0005576)				lung(2)	2						ATAGGAGGAATTTGTCAGAAA	0.507													T|||	412	0.0822684	0.0968	0.0663	5008	,	,		19669	0.0218		0.1551	False		,,,				2504	0.0613				p.N37S		Atlas-SNP	.											.	SFTA2	6	.	0			c.A110G						PASS	.	T	SER/ASN	367,2655		15,337,1159	89.0	104.0	98.0		110	3.0	0.0	6	dbSNP_103	98	1047,4371		94,859,1756	yes	missense	SFTA2	NM_205854.2	46	109,1196,2915	CC,CT,TT		19.3245,12.1443,16.7536	possibly-damaging	37/79	30899524	1414,7026	1511	2709	4220	SO:0001583	missense	389376	exon2			GAGGAATTTGTCA	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.110A>G	6.37:g.30899524T>C	ENSP00000351989:p.Asn37Ser	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	78	25	0.320513	NM_205854	A2ABK7|A2ACH1|B7ZCJ7	Missense_Mutation	SNP	ENST00000359086.3	37	CCDS4691.1	246	0.11263736263736264	71	0.1443089430894309	27	0.07458563535911603	20	0.03496503496503497	128	0.16886543535620052	T	13.67	2.305613	0.40795	0.121443	0.193245	ENSG00000196260	ENST00000359086	T	0.47869	0.83	4.12	2.96	0.34315	.	.	.	.	.	T	0.14313	0.0346	.	.	.	0.80722	P	0.0	B	0.33318	0.408	B	0.25987	0.065	T	0.05115	-1.0905	7	0.40728	T	0.16	.	5.9551	0.19269	0.0:0.1188:0.0:0.8812	rs3131787;rs17196060;rs52836965;rs3131787	37	Q6UW10	SFTA2_HUMAN	S	37	ENSP00000351989:N37S	ENSP00000351989:N37S	N	-	2	0	SFTA2	31007503	0.012000	0.17670	0.002000	0.10522	0.310000	0.27922	1.306000	0.33505	0.649000	0.30751	0.383000	0.25322	AAT	T|0.854;C|0.146	0.146	strong		0.507	SFTA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076360.2	NM_205854	
LRPAP1	4043	hgsc.bcm.edu	37	4	3526645	3526645	+	Missense_Mutation	SNP	C	C	T	rs11549516	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:3526645C>T	ENST00000500728.2	-	2	484	c.338G>A	c.(337-339)cGc>cAc	p.R113H	LRPAP1_ENST00000296325.5_5'UTR	NM_002337.3	NP_002328.1	P30533	AMRP_HUMAN	low density lipoprotein receptor-related protein associated protein 1	113					extracellular negative regulation of signal transduction (GO:1900116)|negative regulation of beta-amyloid clearance (GO:1900222)|negative regulation of protein binding (GO:0032091)|negative regulation of very-low-density lipoprotein particle clearance (GO:0010916)|protein folding (GO:0006457)|receptor-mediated endocytosis (GO:0006898)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|rough endoplasmic reticulum lumen (GO:0048237)|vesicle (GO:0031982)	asialoglycoprotein receptor activity (GO:0004873)|heparin binding (GO:0008201)|low-density lipoprotein particle receptor binding (GO:0050750)|receptor antagonist activity (GO:0048019)|unfolded protein binding (GO:0051082)|very-low-density lipoprotein particle receptor binding (GO:0070326)			breast(1)|endometrium(2)|large_intestine(2)|lung(5)|ovary(1)|prostate(1)|skin(2)	14				UCEC - Uterine corpus endometrioid carcinoma (64;0.165)		ATTGAGGTTGCGTATGAGTCT	0.478													.|||	248	0.0495208	0.0461	0.0793	5008	,	,		21715	0.0337		0.0358	False		,,,				2504	0.0634				p.R113H		Atlas-SNP	.											LRPAP1,NS,carcinoma,-1,1	LRPAP1	29	1	0			c.G338A						PASS	.	C	HIS/ARG	161,4245	109.1+/-147.4	4,153,2046	331.0	333.0	332.0		338	1.8	0.0	4	dbSNP_120	332	299,8301	109.4+/-169.9	4,291,4005	yes	missense	LRPAP1	NM_002337.3	29	8,444,6051	TT,TC,CC		3.4767,3.6541,3.5368	benign	113/358	3526645	460,12546	2203	4300	6503	SO:0001583	missense	4043	exon2			AGGTTGCGTATGA		CCDS3371.1	4p16.3	2008-05-02	2003-03-17		ENSG00000163956	ENSG00000163956			6701	protein-coding gene	gene with protein product		104225	"""low density lipoprotein-related protein-associated protein 1 (alpha-2-macroglobulin receptor-associated protein 1)"""	A2MRAP		1712782	Standard	NM_002337		Approved	HBP44	uc003ghh.4	P30533	OTTHUMG00000090299	ENST00000500728.2:c.338G>A	4.37:g.3526645C>T	ENSP00000421922:p.Arg113His	Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	161	74	0.459627	NM_002337	D3DVR9|Q2M310|Q53HQ3|Q53HS6	Missense_Mutation	SNP	ENST00000500728.2	37	CCDS3371.1	86	0.039377289377289376	21	0.042682926829268296	23	0.06353591160220995	16	0.027972027972027972	26	0.03430079155672823	C	13.32	2.201919	0.38905	0.036541	0.034767	ENSG00000163956	ENST00000500728	T	0.51574	0.7	4.08	1.82	0.25136	Alpha-2-macroglobulin receptor-associated protein, domain 1 (3);	0.112824	0.64402	N	0.000007	T	0.05364	0.0142	L	0.51422	1.61	0.54753	D	0.999985	B	0.28713	0.22	B	0.30716	0.119	T	0.01899	-1.1251	10	0.38643	T	0.18	-26.787	6.8256	0.23880	0.0:0.7121:0.0:0.2879	rs11549516;rs17848283	113	P30533	AMRP_HUMAN	H	113	ENSP00000421922:R113H	ENSP00000421922:R113H	R	-	2	0	LRPAP1	3496443	1.000000	0.71417	0.011000	0.14972	0.026000	0.11368	2.865000	0.48412	0.268000	0.21939	0.655000	0.94253	CGC	C|0.964;T|0.036	0.036	strong		0.478	LRPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206659.4		
CDON	50937	hgsc.bcm.edu	37	11	125851181	125851181	+	Silent	SNP	G	G	A	rs684805	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:125851181G>A	ENST00000392693.3	-	17	3166	c.3039C>T	c.(3037-3039)aaC>aaT	p.N1013N	CDON_ENST00000531738.1_Silent_p.N390N|CDON_ENST00000263577.7_Silent_p.N1013N	NM_001243597.1|NM_016952.4	NP_001230526.1|NP_058648.4	Q4KMG0	CDON_HUMAN	cell adhesion associated, oncogene regulated	1013					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)		CCATCTGCCCGTTCATATCTG	0.473													A|||	1340	0.267572	0.4955	0.2161	5008	,	,		18332	0.0655		0.2604	False		,,,				2504	0.2117				p.N1013N		Atlas-SNP	.											.	CDON	137	.	0			c.C3039T						PASS	.	A		2015,2387	613.7+/-392.2	465,1085,651	121.0	113.0	116.0		3039	-7.0	0.0	11	dbSNP_83	116	2327,6271	703.8+/-405.4	318,1691,2290	no	coding-synonymous	CDON	NM_016952.4		783,2776,2941	AA,AG,GG		27.0644,45.7746,33.4		1013/1265	125851181	4342,8658	2201	4299	6500	SO:0001819	synonymous_variant	50937	exon17			CTGCCCGTTCATA	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.3039C>T	11.37:g.125851181G>A		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	75	19	0.253333	NM_016952	O14631	Silent	SNP	ENST00000392693.3	37	CCDS58192.1																																																																																			G|0.695;A|0.305	0.305	strong		0.473	CDON-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386749.2	NM_016952	
OR2C1	4993	hgsc.bcm.edu	37	16	3406516	3406516	+	Silent	SNP	A	A	G	rs11643487	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	76	0	0		WXS	Illumina HiSeq	Phase_I	79	62	0.78481	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		
RP1L1	94137	hgsc.bcm.edu	37	8	10464755	10464755	+	Missense_Mutation	SNP	C	C	T	rs55642448	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:10464755C>T	ENST00000382483.3	-	4	7076	c.6853G>A	c.(6853-6855)Gga>Aga	p.G2285R		NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	2365	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)		p.G2285R(1)		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)		GGAGTGTCTCCACCTGGGGAA	0.597													C|||	2364	0.472045	0.3464	0.5317	5008	,	,		17514	0.5516		0.3976	False		,,,				2504	0.5941				p.G2285R		Atlas-SNP	.											RP1L1,NS,carcinoma,0,2	RP1L1	453	2	1	Substitution - Missense(1)	prostate(1)	c.G6853A						PASS	.	C	ARG/GLY	1376,2534		259,858,838	130.0	135.0	134.0		6853	3.3	0.0	8	dbSNP_129	134	3221,5071		630,1961,1555	yes	missense	RP1L1	NM_178857.5	125	889,2819,2393	TT,TC,CC		38.8447,35.1918,37.6742	possibly-damaging	2285/2401	10464755	4597,7605	1955	4146	6101	SO:0001583	missense	94137	exon4			TGTCTCCACCTGG	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.6853G>A	8.37:g.10464755C>T	ENSP00000371923:p.Gly2285Arg	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	86	85	0.988372	NM_178857	Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	Missense_Mutation	SNP	ENST00000382483.3	37	CCDS43708.1	974	0.445970695970696	161	0.32723577235772355	172	0.47513812154696133	331	0.5786713286713286	310	0.40897097625329815	C	12.65	2.000991	0.35320	0.351918	0.388447	ENSG00000183638	ENST00000382483	T	0.07327	3.2	4.23	3.35	0.38373	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	P	0.36010	0.532	B	0.32342	0.144	T	0.06698	-1.0812	8	0.39692	T	0.17	-4.8465	7.615	0.28152	0.0:0.7443:0.1654:0.0904	rs55642448;rs62490853	2285	A6NKC6	.	R	2285	ENSP00000371923:G2285R	ENSP00000371923:G2285R	G	-	1	0	RP1L1	10502165	0.000000	0.05858	0.001000	0.08648	0.105000	0.19272	0.102000	0.15272	1.141000	0.42275	0.505000	0.49811	GGA	C|0.574;T|0.426	0.426	strong		0.597	RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375673.1		
LY75	4065	hgsc.bcm.edu	37	2	160738677	160738677	+	Silent	SNP	G	G	A	rs16822581	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:160738677G>A	ENST00000263636.4	-	7	1231	c.1204C>T	c.(1204-1206)Cta>Tta	p.L402L	LY75_ENST00000554112.1_Silent_p.L402L|LY75_ENST00000553424.1_Silent_p.L402L|LY75-CD302_ENST00000504764.1_Silent_p.L402L|LY75-CD302_ENST00000505052.1_Silent_p.L402L	NM_002349.3	NP_002340.2	O60449	LY75_HUMAN	lymphocyte antigen 75	402	C-type lectin 2. {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)		ACATCTGCTAGAGAATGAATG	0.388													G|||	1070	0.213658	0.1112	0.3703	5008	,	,		22695	0.3185		0.16	False		,,,				2504	0.1881				p.L402L		Atlas-SNP	.											.	LY75	151	.	0			c.C1204T						PASS	.	G	,,	574,3832	256.7+/-261.4	42,490,1671	134.0	130.0	131.0		1204,1204,1204	1.7	0.9	2	dbSNP_123	131	1511,7089	286.3+/-297.7	121,1269,2910	no	coding-synonymous,coding-synonymous,coding-synonymous	LY75,LY75-CD302	NM_001198759.1,NM_001198760.1,NM_002349.3	,,	163,1759,4581	AA,AG,GG		17.5698,13.0277,16.0311	,,	402/1874,402/1818,402/1723	160738677	2085,10921	2203	4300	6503	SO:0001819	synonymous_variant	4065	exon7			CTGCTAGAGAATG	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.1204C>T	2.37:g.160738677G>A		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	136	69	0.507353	NM_002349	O75913|Q53R46|Q53TF5|Q7Z575|Q7Z577	Silent	SNP	ENST00000263636.4	37	CCDS2211.1																																																																																			G|0.816;A|0.184	0.184	strong		0.388	LY75-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255035.1		
OTOP1	133060	hgsc.bcm.edu	37	4	4228424	4228424	+	Silent	SNP	T	T	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:4228424T>C	ENST00000296358.4	-	1	192	c.168A>G	c.(166-168)aaA>aaG	p.K56K		NM_177998.1	NP_819056.1	Q7RTM1	OTOP1_HUMAN	otopetrin 1	56					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)		TCTCGGCCAGTTTCTGTGGGA	0.741																																					p.K56K		Atlas-SNP	.											OTOP1,caecum,carcinoma,-1,2	OTOP1	118	2	0			c.A168G						scavenged	.						7.0	7.0	7.0					4																	4228424		2122	4154	6276	SO:0001819	synonymous_variant	133060	exon1			GGCCAGTTTCTGT	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.168A>G	4.37:g.4228424T>C		Somatic	34	6	0.176471		WXS	Illumina HiSeq	Phase_I	37	9	0.243243	NM_177998	A1L476	Silent	SNP	ENST00000296358.4	37	CCDS3372.1																																																																																			.	.	weak		0.741	OTOP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206661.2	NM_177998	
SLC25A13	10165	hgsc.bcm.edu	37	7	95761057	95761057	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:95761057G>A	ENST00000265631.5	-	15	1725	c.1589C>T	c.(1588-1590)gCt>gTt	p.A530V	SLC25A13_ENST00000542654.1_Missense_Mutation_p.A422V|SLC25A13_ENST00000416240.2_Missense_Mutation_p.A531V			Q9UJS0	CMC2_HUMAN	solute carrier family 25 (aspartate/glutamate carrier), member 13	530					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)	ACACTCACCAGCTATGGCACC	0.507																																					p.A531V		Atlas-SNP	.											.	SLC25A13	131	.	0			c.C1592T						PASS	.						76.0	68.0	70.0					7																	95761057		2203	4300	6503	SO:0001583	missense	10165	exon15			TCACCAGCTATGG	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.1589C>T	7.37:g.95761057G>A	ENSP00000265631:p.Ala530Val	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	104	49	0.471154	NM_001160210	O14566|O14575|Q546F9|Q9NZW1|Q9UNI7	Missense_Mutation	SNP	ENST00000265631.5	37	CCDS5645.1	.	.	.	.	.	.	.	.	.	.	G	32	5.127249	0.94473	.	.	ENSG00000004864	ENST00000265631;ENST00000416240;ENST00000542654	D;D;D	0.87256	-2.23;-2.23;-2.23	4.65	4.65	0.58169	Mitochondrial carrier domain (2);	0.000000	0.85682	D	0.000000	D	0.94719	0.8296	M	0.90252	3.1	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.998;0.999;0.999	D	0.95624	0.8683	10	0.87932	D	0	-12.4191	18.1095	0.89530	0.0:0.0:1.0:0.0	.	422;531;530	F5GX33;Q546F9;Q9UJS0	.;.;CMC2_HUMAN	V	530;531;422	ENSP00000265631:A530V;ENSP00000400101:A531V;ENSP00000440484:A422V	ENSP00000265631:A530V	A	-	2	0	SLC25A13	95598993	1.000000	0.71417	1.000000	0.80357	0.940000	0.58332	9.657000	0.98554	2.599000	0.87857	0.655000	0.94253	GCT	.	.	none		0.507	SLC25A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059395.2	NM_014251	
WWC1	23286	hgsc.bcm.edu	37	5	167835539	167835539	+	Missense_Mutation	SNP	C	C	T	rs17551608	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:167835539C>T	ENST00000265293.4	+	7	1250	c.748C>T	c.(748-750)Cgc>Tgc	p.R250C	WWC1_ENST00000521089.1_Missense_Mutation_p.R250C	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	250			R -> C (in dbSNP:rs17551608).		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)		GGACGGCTTCCGCACTGACAG	0.602													C|||	350	0.0698882	0.0287	0.0908	5008	,	,		20282	0.001		0.1581	False		,,,				2504	0.091				p.R250C		Atlas-SNP	.											.	WWC1	98	.	0			c.C748T						PASS	.	C	CYS/ARG,CYS/ARG,CYS/ARG	195,4211	122.9+/-160.3	3,189,2011	114.0	107.0	110.0		748,748,748	4.3	0.8	5	dbSNP_123	110	1339,7261	262.8+/-284.6	111,1117,3072	yes	missense,missense,missense	WWC1	NM_001161661.1,NM_001161662.1,NM_015238.2	180,180,180	114,1306,5083	TT,TC,CC		15.5698,4.4258,11.7946	possibly-damaging,possibly-damaging,possibly-damaging	250/1120,250/1119,250/1114	167835539	1534,11472	2203	4300	6503	SO:0001583	missense	23286	exon7			GGCTTCCGCACTG	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.748C>T	5.37:g.167835539C>T	ENSP00000265293:p.Arg250Cys	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	112	80	0.714286	NM_015238	B4DK05|O94946|Q6MZX4|Q6Y2F8|Q7Z4G8|Q8WVM4|Q9BT29	Missense_Mutation	SNP	ENST00000265293.4	37	CCDS4366.1	175|175	0.08012820512820513|0.08012820512820513	16|16	0.032520325203252036|0.032520325203252036	38|38	0.10497237569060773|0.10497237569060773	0|0	0.0|0.0	121|121	0.15963060686015831|0.15963060686015831	C|C	18.69|18.69	3.678888|3.678888	0.68042|0.68042	0.044258|0.044258	0.155698|0.155698	ENSG00000113645|ENSG00000113645	ENST00000393895;ENST00000524228|ENST00000265293;ENST00000521089	.|T;T	.|0.05319	.|3.46;3.46	5.22|5.22	4.35|4.35	0.52113|0.52113	.|.	.|0.643175	.|0.15673	.|N	.|0.250300	T|T	0.00039|0.00039	0.0001|0.0001	L|L	0.29908|0.29908	0.895|0.895	0.24609|0.24609	P|P	0.99373963|0.99373963	.|P;P;P;P	.|0.52577	.|0.851;0.954;0.939;0.941	.|B;B;B;B	.|0.41723	.|0.292;0.292;0.365;0.288	T|T	0.43180|0.43180	-0.9407|-0.9407	4|9	.|0.72032	.|D	.|0.01	.|.	9.9187|9.9187	0.41450|0.41450	0.0:0.7404:0.1792:0.0804|0.0:0.7404:0.1792:0.0804	rs17551608;rs60117665;rs17551608|rs17551608;rs60117665;rs17551608	.|250;156;156;250	.|Q8IX03-2;F5H498;B3KX05;Q8IX03	.|.;.;.;KIBRA_HUMAN	L|C	211;26|250	.|ENSP00000265293:R250C;ENSP00000427772:R250C	.|ENSP00000265293:R250C	P|R	+|+	2|1	0|0	WWC1|WWC1	167768117|167768117	0.369000|0.369000	0.25039|0.25039	0.821000|0.821000	0.32701|0.32701	0.675000|0.675000	0.39556|0.39556	0.999000|0.999000	0.29757|0.29757	1.199000|1.199000	0.43173|0.43173	0.655000|0.655000	0.94253|0.94253	CCG|CGC	C|0.895;T|0.105	0.105	strong		0.602	WWC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252791.2	NM_015238	
SLC29A4	222962	hgsc.bcm.edu	37	7	5339049	5339049	+	Silent	SNP	C	C	T	rs142638970	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:5339049C>T	ENST00000396872.3	+	9	1361	c.1200C>T	c.(1198-1200)ttC>ttT	p.F400F	SLC29A4_ENST00000406453.3_Silent_p.F386F|SLC29A4_ENST00000439491.2_3'UTR|SLC29A4_ENST00000297195.4_Silent_p.F400F			Q7RTT9	S29A4_HUMAN	solute carrier family 29 (equilibrative nucleoside transporter), member 4	400					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	nucleoside transmembrane transporter activity (GO:0005337)			breast(1)|cervix(2)|kidney(7)|large_intestine(1)|liver(1)|lung(7)|urinary_tract(1)	20		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0903)|OV - Ovarian serous cystadenocarcinoma(56;2.65e-15)	Metformin(DB00331)	TGTCAGACTTCGTGGGCAAGG	0.657													C|||	3	0.000599042	0.0015	0.0	5008	,	,		18164	0.0		0.001	False		,,,				2504	0.0				p.F400F		Atlas-SNP	.											.	SLC29A4	52	.	0			c.C1200T						PASS	.	C	,	4,4402		0,4,2199	49.0	37.0	41.0		1200,1200	0.2	1.0	7	dbSNP_134	41	53,8543		0,53,4245	no	coding-synonymous,coding-synonymous	SLC29A4	NM_001040661.1,NM_153247.2	,	0,57,6444	TT,TC,CC		0.6166,0.0908,0.4384	,	400/531,400/531	5339049	57,12945	2203	4298	6501	SO:0001819	synonymous_variant	222962	exon9			AGACTTCGTGGGC	AK075422	CCDS5340.1, CCDS75561.1	7p22.2	2013-07-17	2013-07-17		ENSG00000164638	ENSG00000164638		"""Solute carriers"""	23097	protein-coding gene	gene with protein product		609149	"""solute carrier family 29 (nucleoside transporters), member 4"""			12838422	Standard	NM_153247		Approved	FLJ34923, ENT4	uc003soc.3	Q7RTT9	OTTHUMG00000023797	ENST00000396872.3:c.1200C>T	7.37:g.5339049C>T		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	124	99	0.798387	NM_153247	Q6PJ08|Q86WY8|Q8NAR3|Q8NBM2	Silent	SNP	ENST00000396872.3	37	CCDS5340.1																																																																																			C|0.997;T|0.003	0.003	strong		0.657	SLC29A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060118.6	NM_153247	
EPHX2	2053	hgsc.bcm.edu	37	8	27396208	27396208	+	Splice_Site	SNP	G	G	A	rs4149253	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:27396208G>A	ENST00000521400.1	+	14	1705	c.1275G>A	c.(1273-1275)gcG>gcA	p.A425A	EPHX2_ENST00000517536.1_Splice_Site_p.A242A|EPHX2_ENST00000518379.1_Splice_Site_p.A393A|EPHX2_ENST00000521780.1_Splice_Site_p.A359A|EPHX2_ENST00000380476.3_Splice_Site_p.A372A	NM_001979.5	NP_001970.2	P34913	HYES_HUMAN	epoxide hydrolase 2, cytoplasmic	425	Epoxide hydrolase.				arachidonic acid metabolic process (GO:0019369)|cellular calcium ion homeostasis (GO:0006874)|cholesterol homeostasis (GO:0042632)|dephosphorylation (GO:0016311)|drug metabolic process (GO:0017144)|epoxygenase P450 pathway (GO:0019373)|inflammatory response (GO:0006954)|phospholipid dephosphorylation (GO:0046839)|positive regulation of gene expression (GO:0010628)|positive regulation of vasodilation (GO:0045909)|reactive oxygen species metabolic process (GO:0072593)|regulation of blood pressure (GO:0008217)|regulation of cholesterol metabolic process (GO:0090181)|response to toxic substance (GO:0009636)|small molecule metabolic process (GO:0044281)|stilbene catabolic process (GO:0046272)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|peroxisome (GO:0005777)	10-hydroxy-9-(phosphonooxy)octadecanoate phosphatase activity (GO:0033885)|epoxide hydrolase activity (GO:0004301)|lipid phosphatase activity (GO:0042577)|magnesium ion binding (GO:0000287)|phosphatase activity (GO:0016791)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|toxic substance binding (GO:0015643)			cervix(1)|endometrium(8)|kidney(1)|large_intestine(1)|lung(8)|ovary(1)|skin(5)|stomach(1)|urinary_tract(1)	27		Ovarian(32;2.61e-05)|all_epithelial(46;0.207)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0226)|Epithelial(17;1.12e-09)|Colorectal(74;0.157)		TCTGTGAAGCGGGTAAGAGAC	0.433													G|||	569	0.113618	0.115	0.0648	5008	,	,		21023	0.1746		0.0596	False		,,,				2504	0.1391				p.A425A		Atlas-SNP	.											.	EPHX2	57	.	0			c.G1275A						PASS	.	G		446,3960	213.1+/-232.8	19,408,1776	126.0	120.0	122.0		1275	2.8	0.8	8	dbSNP_110	122	507,8093	144.0+/-200.0	15,477,3808	yes	coding-synonymous-near-splice	EPHX2	NM_001979.4		34,885,5584	AA,AG,GG		5.8953,10.1226,7.3274		425/556	27396208	953,12053	2203	4300	6503	SO:0001630	splice_region_variant	2053	exon14			TGAAGCGGGTAAG	L05779	CCDS6060.1, CCDS59097.1, CCDS59098.1	8p21	2010-04-23			ENSG00000120915	ENSG00000120915	3.3.2.10		3402	protein-coding gene	gene with protein product		132811					Standard	NM_001979		Approved		uc003xfu.4	P34913	OTTHUMG00000102115	ENST00000521400.1:c.1276+1G>A	8.37:g.27396208G>A		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	80	14	0.175	NM_001979	B2Z3B1|B3KTU8|B3KUA0|G3V134|J3KPH7|Q16764|Q9HBJ1|Q9HBJ2	Silent	SNP	ENST00000521400.1	37	CCDS6060.1																																																																																			G|0.907;A|0.093	0.093	strong		0.433	EPHX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219954.4		Silent
CEP78	84131	hgsc.bcm.edu	37	9	80879149	80879149	+	Silent	SNP	C	C	T	rs1057650	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:80879149C>T	ENST00000424347.2	+	13	1831	c.1542C>T	c.(1540-1542)atC>atT	p.I514I	CEP78_ENST00000415759.2_Silent_p.I515I|CEP78_ENST00000376598.2_Silent_p.I514I|CEP78_ENST00000376597.4_Silent_p.I515I|CEP78_ENST00000277082.5_Silent_p.I514I			Q5JTW2	CEP78_HUMAN	centrosomal protein 78kDa	514					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytosol (GO:0005829)		p.I514I(1)		breast(1)|cervix(1)|endometrium(5)|large_intestine(7)|lung(4)|ovary(1)|stomach(1)|urinary_tract(1)	21						CAAATATGATCCTGGATGATG	0.373													C|||	424	0.0846645	0.1399	0.0778	5008	,	,		15567	0.0109		0.0835	False		,,,				2504	0.092				p.I515I		Atlas-SNP	.											CEP78,NS,carcinoma,0,1	CEP78	79	1	1	Substitution - coding silent(1)	stomach(1)	c.C1545T						scavenged	.	C	,	482,3220		27,428,1396	107.0	100.0	102.0		1545,1545	2.3	1.0	9	dbSNP_86	102	693,7485		26,641,3422	no	coding-synonymous,coding-synonymous	CEP78	NM_001098802.1,NM_032171.1	,	53,1069,4818	TT,TC,CC		8.474,13.02,9.8906	,	515/723,515/707	80879149	1175,10705	1851	4089	5940	SO:0001819	synonymous_variant	84131	exon13			TATGATCCTGGAT	BC058931	CCDS47984.1, CCDS47985.1	9q21.2	2014-02-20	2005-12-01	2005-12-01	ENSG00000148019	ENSG00000148019			25740	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 81"""	C9orf81		14654843	Standard	NM_001098802		Approved	FLJ12643	uc004aky.4	Q5JTW2	OTTHUMG00000020062	ENST00000424347.2:c.1542C>T	9.37:g.80879149C>T		Somatic	154	1	0.00649351		WXS	Illumina HiSeq	Phase_I	146	76	0.520548	NM_001098802	A1A4S8|E9PHX5|Q5BJE3|Q5JTW0|Q5JTW1|Q9H9N3	Silent	SNP	ENST00000424347.2	37																																																																																				C|0.921;T|0.079	0.079	strong		0.373	CEP78-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000052766.2	XM_095991	
FCGBP	8857	hgsc.bcm.edu	37	19	40420087	40420087	+	Silent	SNP	G	G	A	rs12460562	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:40420087G>A	ENST00000221347.6	-	6	2914	c.2907C>T	c.(2905-2907)gcC>gcT	p.A969A		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	969	VWFD 2. {ECO:0000255|PROSITE- ProRule:PRU00580}.					extracellular vesicular exosome (GO:0070062)				NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(5)|endometrium(13)|kidney(9)|large_intestine(27)|lung(49)|ovary(8)|pancreas(3)|prostate(13)|skin(9)|stomach(9)|upper_aerodigestive_tract(6)|urinary_tract(3)	165	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			TGCGCACGACGGCATCCCTGC	0.597													G|||	694	0.138578	0.0129	0.3329	5008	,	,		20473	0.0417		0.1998	False		,,,				2504	0.2076				p.A969A		Atlas-SNP	.											FCGBP,rectum,carcinoma,0,1	FCGBP	416	1	0			c.C2907T						PASS	.	G		208,4198	126.6+/-163.6	7,194,2002	62.0	58.0	60.0		2907	-9.7	0.0	19	dbSNP_120	60	1795,6805	321.8+/-315.3	192,1411,2697	no	coding-synonymous	FCGBP	NM_003890.2		199,1605,4699	AA,AG,GG		20.8721,4.7208,15.4006		969/5406	40420087	2003,11003	2203	4300	6503	SO:0001819	synonymous_variant	8857	exon6			CACGACGGCATCC	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.2907C>T	19.37:g.40420087G>A		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	56	33	0.589286	NM_003890	O95784	Silent	SNP	ENST00000221347.6	37	CCDS12546.1																																																																																			G|0.862;A|0.138	0.138	strong		0.597	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890	
DOCK7	85440	hgsc.bcm.edu	37	1	62960101	62960101	+	Silent	SNP	A	A	G	rs10889335	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:62960101A>G	ENST00000340370.5	-	39	4986	c.4969T>C	c.(4969-4971)Ttg>Ctg	p.L1657L	DOCK7_ENST00000251157.5_Silent_p.L1679L	NM_033407.2	NP_212132.2	Q96N67	DOCK7_HUMAN	dedicator of cytokinesis 7	1688					activation of Rac GTPase activity (GO:0032863)|axonogenesis (GO:0007409)|establishment of neuroblast polarity (GO:0045200)|hematopoietic progenitor cell differentiation (GO:0002244)|interkinetic nuclear migration (GO:0022027)|microtubule cytoskeleton organization (GO:0000226)|neuron projection development (GO:0031175)|pigmentation (GO:0043473)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|regulation of neurogenesis (GO:0050767)|small GTPase mediated signal transduction (GO:0007264)	axon (GO:0030424)|basal part of cell (GO:0045178)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|neuron projection (GO:0043005)	guanyl-nucleotide exchange factor activity (GO:0005085)|Rac GTPase binding (GO:0048365)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(8)|kidney(6)|large_intestine(19)|lung(42)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	92						AACCAGGTCAATCGCAGATCT	0.468													A|||	1751	0.349641	0.4228	0.3573	5008	,	,		18621	0.1815		0.3171	False		,,,				2504	0.4519				p.L1679L		Atlas-SNP	.											.	DOCK7	184	.	0			c.T5035C						PASS	.	A		1726,2680	518.5+/-369.7	350,1026,827	102.0	79.0	87.0		4969	-8.7	0.0	1	dbSNP_120	87	2870,5730	451.3+/-362.6	508,1854,1938	no	coding-synonymous	DOCK7	NM_033407.2		858,2880,2765	GG,GA,AA		33.3721,39.1739,35.3375		1657/2110	62960101	4596,8410	2203	4300	6503	SO:0001819	synonymous_variant	85440	exon40			AGGTCAATCGCAG		CCDS30734.1, CCDS60156.1, CCDS60157.1	1p32.1	2008-02-05			ENSG00000116641	ENSG00000116641			19190	protein-coding gene	gene with protein product		615730				12432077	Standard	NM_033407		Approved	KIAA1771, ZIR2	uc001daq.4	Q96N67	OTTHUMG00000013131	ENST00000340370.5:c.4969T>C	1.37:g.62960101A>G		Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	94	47	0.5	NM_001271999	Q00M63|Q2PPY7|Q45RE8|Q45RE9|Q5T1B9|Q5T1C0|Q6ZV32|Q8TB82|Q96NG6|Q96NI0|Q9C092	Silent	SNP	ENST00000340370.5	37	CCDS30734.1	667	0.30540293040293043	204	0.4146341463414634	116	0.32044198895027626	100	0.17482517482517482	247	0.3258575197889182	A	8.164	0.790280	0.16258	0.391739	0.333721	ENSG00000116641	ENST00000454575	.	.	.	5.9	-8.68	0.00859	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999740427	.	.	.	.	.	.	T	0.27365	-1.0076	3	.	.	.	.	22.854	0.99977	0.2653:0.0:0.7347:0.0	rs10889335;rs59629051;rs10889335	.	.	.	T	850	.	.	I	-	2	0	DOCK7	62732689	0.003000	0.15002	0.003000	0.11579	0.990000	0.78478	-0.049000	0.11924	-1.661000	0.01484	-0.353000	0.07706	ATT	A|0.670;G|0.330	0.330	strong		0.468	DOCK7-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036806.1	NM_033407	
FAT2	2196	hgsc.bcm.edu	37	5	150901597	150901597	+	Silent	SNP	G	G	C	rs3734047	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:150901597G>C	ENST00000261800.5	-	18	10569	c.10557C>G	c.(10555-10557)gtC>gtG	p.V3519V		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	3519	Cadherin 31. {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)			CTGTGACATGGACACGGACAG	0.542													G|||	488	0.0974441	0.0083	0.1585	5008	,	,		20790	0.126		0.1948	False		,,,				2504	0.045				p.V3519V		Atlas-SNP	.											.	FAT2	465	.	0			c.C10557G						PASS	.	G		164,4242	107.8+/-146.2	6,152,2045	57.0	51.0	53.0		10557	2.3	0.1	5	dbSNP_107	53	1829,6771	328.1+/-318.2	206,1417,2677	no	coding-synonymous	FAT2	NM_001447.2		212,1569,4722	CC,CG,GG		21.2674,3.7222,15.3237		3519/4350	150901597	1993,11013	2203	4300	6503	SO:0001819	synonymous_variant	2196	exon18			GACATGGACACGG	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.10557C>G	5.37:g.150901597G>C		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	44	14	0.318182	NM_001447	O75091|Q9NSR7	Silent	SNP	ENST00000261800.5	37	CCDS4317.1	290	0.13278388278388278	6	0.012195121951219513	65	0.17955801104972377	82	0.14335664335664336	137	0.18073878627968337	G	0.017	-1.494745	0.01009	0.037222	0.212674	ENSG00000086570	ENST00000520200	.	.	.	5.14	2.3	0.28687	.	.	.	.	.	T	0.00039	0.0001	.	.	.	0.09310	P	0.9999999999996599	.	.	.	.	.	.	T	0.14531	-1.0469	3	.	.	.	.	4.8548	0.13554	0.0715:0.1279:0.5208:0.2799	rs3734047;rs3734047	.	.	.	A	378	.	.	P	-	1	0	FAT2	150881790	0.998000	0.40836	0.059000	0.19551	0.012000	0.07955	0.818000	0.27295	0.246000	0.21394	-0.261000	0.10672	CCA	G|0.858;C|0.142	0.142	strong		0.542	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447	
THNSL1	79896	hgsc.bcm.edu	37	10	25313818	25313818	+	Silent	SNP	C	C	T	rs7086282	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:25313818C>T	ENST00000524413.1	+	3	2013	c.1666C>T	c.(1666-1668)Cta>Tta	p.L556L	THNSL1_ENST00000376356.4_Silent_p.L556L			Q8IYQ7	THNS1_HUMAN	threonine synthase-like 1 (S. cerevisiae)	556						cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)		p.L556L(1)		NS(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|lung(5)|pancreas(1)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	28					L-Threonine(DB00156)	GGAAAGAAAACTAGCACAAAC	0.353													T|||	2549	0.508986	0.6936	0.5389	5008	,	,		19211	0.4861		0.3459	False		,,,				2504	0.4294				p.L556L		Atlas-SNP	.											THNSL1,NS,carcinoma,0,1	THNSL1	70	1	1	Substitution - coding silent(1)	stomach(1)	c.C1666T						PASS	.	T		2813,1593	481.0+/-359.0	899,1015,289	50.0	54.0	53.0		1666	-0.9	0.5	10	dbSNP_116	53	3044,5556	655.5+/-401.3	507,2030,1763	no	coding-synonymous	THNSL1	NM_024838.4		1406,3045,2052	TT,TC,CC		35.3953,36.1552,45.0331		556/744	25313818	5857,7149	2203	4300	6503	SO:0001819	synonymous_variant	79896	exon3			AGAAAACTAGCAC	AK025655	CCDS7147.1	10p12.31	2008-02-05	2007-06-20		ENSG00000185875	ENSG00000185875			26160	protein-coding gene	gene with protein product		611260	"""threonine synthase-like 1 (bacterial)"""			12477932	Standard	NM_024838		Approved	FLJ22002	uc001isi.4	Q8IYQ7	OTTHUMG00000017828	ENST00000524413.1:c.1666C>T	10.37:g.25313818C>T		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	33	33	1	NM_024838	B3KWL1|D3DRV3|Q5VV21	Silent	SNP	ENST00000524413.1	37	CCDS7147.1																																																																																			C|0.530;T|0.470	0.470	strong		0.353	THNSL1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394913.1	NM_024838	
TPTE2	93492	hgsc.bcm.edu	37	13	20066994	20066994	+	Missense_Mutation	SNP	T	T	C	rs78472618	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:20066994T>C	ENST00000400230.2	-	3	159	c.115A>G	c.(115-117)Aaa>Gaa	p.K39E	TPTE2_ENST00000382977.4_Missense_Mutation_p.K39E|TPTE2_ENST00000382978.1_Missense_Mutation_p.K39E|TPTE2_ENST00000457266.2_Missense_Mutation_p.K39E|TPTE2_ENST00000400103.2_Missense_Mutation_p.K39E|TPTE2_ENST00000255310.6_Missense_Mutation_p.K39E|TPTE2_ENST00000382975.4_Missense_Mutation_p.K39E|TPTE2_ENST00000390680.2_Missense_Mutation_p.K39E			Q6XPS3	TPTE2_HUMAN	transmembrane phosphoinositide 3-phosphatase and tensin homolog 2	39					phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	ion channel activity (GO:0005216)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.K39E(3)		NS(2)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(8)|lung(21)|pancreas(1)|prostate(8)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	65		all_cancers(29;1.23e-20)|all_lung(29;1.97e-20)|all_epithelial(30;5.86e-20)|Lung NSC(5;3.36e-17)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;1.73e-05)|Epithelial(112;7.42e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000785)|Lung(94;0.0176)|LUSC - Lung squamous cell carcinoma(192;0.089)		ACTCACCTTTTACTGATAGGT	0.388																																					p.K39E		Atlas-SNP	.											TPTE2_ENST00000400230,NS,carcinoma,0,3	TPTE2	225	3	3	Substitution - Missense(3)	prostate(2)|NS(1)	c.A115G						scavenged	.						103.0	91.0	95.0					13																	20066994		2203	4300	6503	SO:0001583	missense	93492	exon4			ACCTTTTACTGAT	AJ421032	CCDS9285.1, CCDS45013.1, CCDS45014.1	13q12.11	2012-12-10			ENSG00000132958	ENSG00000132958		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"""	17299	protein-coding gene	gene with protein product		606791				11716755, 12717346, 15057823	Standard	NM_130785		Approved	TPIP	uc001umd.3	Q6XPS3	OTTHUMG00000016493	ENST00000400230.2:c.115A>G	13.37:g.20066994T>C	ENSP00000383089:p.Lys39Glu	Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	170	13	0.0764706	NM_199254	A1A4X0|A1A4X1|A8MX64|B1AQ16|B4DWZ2|Q5VUH2|Q8WWL4|Q8WWL5	Missense_Mutation	SNP	ENST00000400230.2	37	CCDS45014.1	.	.	.	.	.	.	.	.	.	.	T	0.931	-0.712684	0.03206	.	.	ENSG00000132958	ENST00000382978;ENST00000400103;ENST00000400230;ENST00000255310;ENST00000390680;ENST00000382977;ENST00000382975;ENST00000457266;ENST00000343548;ENST00000419256	D;D;D;D;D;D;D;D	0.95205	-3.64;-3.51;-3.47;-3.49;-3.49;-3.47;-3.64;-3.51	1.03	-1.53	0.08611	.	0.321368	0.27539	N	0.018903	D	0.84915	0.5578	N	0.21448	0.665	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	0.71059	-0.4702	9	.	.	.	.	4.2942	0.10894	0.0:0.5094:0.0:0.4906	.	39;39;39	A8MX64;Q6XPS3-3;Q6XPS3	.;.;TPTE2_HUMAN	E	39	ENSP00000372438:K39E;ENSP00000382974:K39E;ENSP00000383089:K39E;ENSP00000255310:K39E;ENSP00000375098:K39E;ENSP00000372437:K39E;ENSP00000372435:K39E;ENSP00000442218:K39E	.	K	-	1	0	TPTE2	18964994	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.444000	0.02403	-0.630000	0.05567	-0.464000	0.05259	AAA	T|0.820;C|0.180	0.180	strong		0.388	TPTE2-205	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_199254	
PLA2G7	7941	hgsc.bcm.edu	37	6	46684222	46684222	+	Missense_Mutation	SNP	C	C	T	rs1805017	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:46684222C>T	ENST00000274793.7	-	4	471	c.275G>A	c.(274-276)cGc>cAc	p.R92H	PLA2G7_ENST00000537365.1_Missense_Mutation_p.R92H|PLA2G7_ENST00000538237.1_Missense_Mutation_p.R47H|PLA2G7_ENST00000541026.1_Intron	NM_005084.3	NP_005075.3	Q13093	PAFA_HUMAN	phospholipase A2, group VII (platelet-activating factor acetylhydrolase, plasma)	92			R -> H (common polymorphism; dbSNP:rs1805017). {ECO:0000269|PubMed:10733466, ECO:0000269|Ref.3}.		cellular protein metabolic process (GO:0044267)|lipid catabolic process (GO:0016042)|lipid oxidation (GO:0034440)|low-density lipoprotein particle remodeling (GO:0034374)|plasma lipoprotein particle oxidation (GO:0034441)|positive regulation of inflammatory response (GO:0050729)|positive regulation of monocyte chemotaxis (GO:0090026)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|low-density lipoprotein particle (GO:0034362)	1-alkyl-2-acetylglycerophosphocholine esterase activity (GO:0003847)|calcium-independent phospholipase A2 activity (GO:0047499)|phospholipid binding (GO:0005543)			endometrium(1)|kidney(1)|large_intestine(5)|lung(5)|skin(1)|soft_tissue(1)	14			Lung(136;0.192)			GGTGTCAAGGCGATCATTATC	0.373													C|||	1590	0.317492	0.2572	0.3746	5008	,	,		18617	0.2192		0.2555	False		,,,				2504	0.5235				p.R92H		Atlas-SNP	.											PLA2G7,NS,carcinoma,0,1	PLA2G7	49	1	0			c.G275A	GRCh37	CM081751	PLA2G7	M	rs1805017	scavenged	.	C	HIS/ARG,HIS/ARG	1216,3190	421.3+/-339.3	159,898,1146	108.0	108.0	108.0	http://www.ncbi.nlm.nih.gov/pubmed?term	275,275	-10.0	0.0	6	dbSNP_89	108	2250,6350	380.3+/-339.6	322,1606,2372	yes	missense,missense	PLA2G7	NM_001168357.1,NM_005084.3	29,29	481,2504,3518	TT,TC,CC	http://www.ncbi.nlm.nih.gov/pubmed?term	26.1628,27.5987,26.6492	benign,benign	92/442,92/442	46684222	3466,9540	2203	4300	6503	SO:0001583	missense	7941	exon4			TCAAGGCGATCAT	U20157	CCDS4917.1	6p21.2-p12	2008-09-19			ENSG00000146070	ENSG00000146070	3.1.1.4		9040	protein-coding gene	gene with protein product		601690				7700381, 8624782	Standard	NM_005084		Approved	PAFAH, LDL-PLA2	uc021zae.1	Q13093	OTTHUMG00000014789	ENST00000274793.7:c.275G>A	6.37:g.46684222C>T	ENSP00000274793:p.Arg92His	Somatic	109	1	0.00917431		WXS	Illumina HiSeq	Phase_I	75	33	0.44	NM_005084	A5HTT5|Q15692|Q5VTT1|Q8IVA2	Missense_Mutation	SNP	ENST00000274793.7	37	CCDS4917.1	552	0.25274725274725274	115	0.23373983739837398	127	0.35082872928176795	115	0.20104895104895104	195	0.25725593667546176	C	6.523	0.464769	0.12402	0.275987	0.261628	ENSG00000146070	ENST00000274793;ENST00000537365;ENST00000538237	T;T;T	0.54071	0.59;0.59;0.59	5.29	-10.0	0.00425	.	1.092260	0.06797	N	0.788055	T	0.08179	0.0204	N	0.04746	-0.17	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.21314	-1.0249	9	0.37606	T	0.19	.	5.6226	0.17465	0.0969:0.4775:0.1969:0.2287	rs1805017;rs17288912;rs52794316;rs1805017	47;92	F5GYY6;Q13093	.;PAFA_HUMAN	H	92;92;47	ENSP00000274793:R92H;ENSP00000445666:R92H;ENSP00000441416:R47H	ENSP00000274793:R92H	R	-	2	0	PLA2G7	46792181	0.000000	0.05858	0.000000	0.03702	0.109000	0.19521	-2.392000	0.01056	-1.652000	0.01502	-0.251000	0.11542	CGC	C|0.737;T|0.263	0.263	strong		0.373	PLA2G7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040802.1		
GPR137C	283554	hgsc.bcm.edu	37	14	53098902	53098902	+	Missense_Mutation	SNP	G	G	A	rs762063	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:53098902G>A	ENST00000321662.6	+	4	742	c.742G>A	c.(742-744)Gtc>Atc	p.V248I		NM_001099652.1	NP_001093122.1	Q8N3F9	G137C_HUMAN	G protein-coupled receptor 137C	248			V -> I (in dbSNP:rs762063). {ECO:0000269|PubMed:17974005}.			integral component of membrane (GO:0016021)				NS(1)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)	8	Breast(41;0.0716)					CCAGACTGTCGTCGTGGGCTC	0.368													G|||	2065	0.41234	0.2458	0.5288	5008	,	,		20036	0.4157		0.5626	False		,,,				2504	0.3967				p.V248I		Atlas-SNP	.											.	GPR137C	24	.	0			c.G742A						PASS	.	G	ILE/VAL	1081,2705		148,785,960	160.0	160.0	160.0		742	3.3	0.6	14	dbSNP_86	160	4383,3859		1145,2093,883	yes	missense	GPR137C	NM_001099652.1	29	1293,2878,1843	AA,AG,GG		46.8212,28.5526,45.4273	benign	248/430	53098902	5464,6564	1893	4121	6014	SO:0001583	missense	283554	exon4			ACTGTCGTCGTGG	BX647179	CCDS45106.1	14q22.1	2012-08-10				ENSG00000180998			25445	protein-coding gene	gene with protein product							Standard	NM_001099652		Approved	DKFZp762F0713, TM7SF1L2	uc001wzu.4	Q8N3F9		ENST00000321662.6:c.742G>A	14.37:g.53098902G>A	ENSP00000315106:p.Val248Ile	Somatic	287	0	0		WXS	Illumina HiSeq	Phase_I	224	109	0.486607	NM_001099652	Q86SM2	Missense_Mutation	SNP	ENST00000321662.6	37	CCDS45106.1	1005|1005	0.46016483516483514|0.46016483516483514	121|121	0.2459349593495935|0.2459349593495935	196|196	0.5414364640883977|0.5414364640883977	253|253	0.4423076923076923|0.4423076923076923	435|435	0.5738786279683378|0.5738786279683378	G|G	11.91|11.91	1.778467|1.778467	0.31502|0.31502	0.285526|0.285526	0.531788|0.531788	ENSG00000180998|ENSG00000180998	ENST00000542169|ENST00000321662	.|T	.|0.43294	.|0.95	5.58|5.58	3.32|3.32	0.38043|0.38043	.|.	.|0.275088	.|0.40222	.|N	.|0.001147	T|T	0.00012|0.00012	0.0000|0.0000	L|L	0.31926|0.31926	0.97|0.97	0.80722|0.80722	P|P	0.0|0.0	.|B;B	.|0.16396	.|0.007;0.017	.|B;B	.|0.08055	.|0.003;0.003	T|T	0.44667|0.44667	-0.9313|-0.9313	4|9	.|0.34782	.|T	.|0.22	-22.2491|-22.2491	7.5544|7.5544	0.27817|0.27817	0.2054:0.1674:0.6272:0.0|0.2054:0.1674:0.6272:0.0	rs762063;rs17725449;rs52793350;rs56718140;rs762063|rs762063;rs17725449;rs52793350;rs56718140;rs762063	.|248;77	.|Q8N3F9;B3KW22	.|G137C_HUMAN;.	H|I	217|248	.|ENSP00000315106:V248I	.|ENSP00000315106:V248I	R|V	+|+	2|1	0|0	GPR137C|GPR137C	52168652|52168652	0.980000|0.980000	0.34600|0.34600	0.592000|0.592000	0.28758|0.28758	0.976000|0.976000	0.68499|0.68499	3.034000|3.034000	0.49751|0.49751	1.149000|1.149000	0.42402|0.42402	0.591000|0.591000	0.81541|0.81541	CGT|GTC	G|0.569;A|0.431	0.431	strong		0.368	GPR137C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411685.1	XM_290615	
IGSF22	283284	hgsc.bcm.edu	37	11	18729819	18729819	+	Missense_Mutation	SNP	C	C	T	rs78892734	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:18729819C>T	ENST00000513874.1	-	19	3161	c.3022G>A	c.(3022-3024)Gcc>Acc	p.A1008T	RP11-1081L13.4_ENST00000527285.1_RNA|IGSF22_ENST00000510673.1_5'Flank	NM_173588.3	NP_775859	Q8N9C0	IGS22_HUMAN	immunoglobulin superfamily, member 22	611										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						TTCAGCCGGGCACTGAGGTCA	0.547													C|||	96	0.0191693	0.003	0.0346	5008	,	,		20943	0.0		0.0616	False		,,,				2504	0.0061				p.A1008T		Atlas-SNP	.											.	IGSF22	211	.	0			c.G3022A						PASS	.	C	THR/ALA	10,1374		1,8,683	114.0	116.0	115.0		3022	3.3	0.8	11	dbSNP_132	115	220,2962		7,206,1378	yes	missense	IGSF22	NM_173588.3	58	8,214,2061	TT,TC,CC		6.9139,0.7225,5.0372	benign	1008/1327	18729819	230,4336	692	1591	2283	SO:0001583	missense	283284	exon19			GCCGGGCACTGAG	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.3022G>A	11.37:g.18729819C>T	ENSP00000421191:p.Ala1008Thr	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	68	42	0.617647	NM_173588	A6NNA0|D6RGV7	Missense_Mutation	SNP	ENST00000513874.1	37	CCDS41625.2	60	0.027472527472527472	2	0.0040650406504065045	17	0.04696132596685083	0	0.0	41	0.05408970976253298	C	14.01	2.406900	0.42715	0.007225	0.069139	ENSG00000179057	ENST00000513874	T	0.53206	0.63	4.26	3.33	0.38152	.	.	.	.	.	T	0.04998	0.0134	L	0.33485	1.01	0.19300	N	0.99998	P	0.52170	0.951	P	0.52646	0.705	T	0.02009	-1.1230	9	0.14656	T	0.56	.	11.1304	0.48343	0.0:0.9114:0.0:0.0886	.	1008	D6RGV7	.	T	1008	ENSP00000421191:A1008T	ENSP00000421191:A1008T	A	-	1	0	IGSF22	18686395	0.093000	0.21703	0.761000	0.31378	0.988000	0.76386	0.578000	0.23773	1.107000	0.41642	0.650000	0.86243	GCC	C|0.972;T|0.028	0.028	strong		0.547	IGSF22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360850.2	NM_173588	
NEK3	4752	hgsc.bcm.edu	37	13	52710320	52710320	+	Missense_Mutation	SNP	T	T	C	rs371075629		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:52710320T>C	ENST00000400357.2	-	11	2348	c.1055A>G	c.(1054-1056)aAt>aGt	p.N352S	NEK3_ENST00000378101.2_Missense_Mutation_p.N369S|NEK3_ENST00000452082.2_Missense_Mutation_p.N373S|NEK3_ENST00000339406.3_Missense_Mutation_p.N369S			P51956	NEK3_HUMAN	NIMA-related kinase 3	369					mitotic nuclear division (GO:0007067)|protein phosphorylation (GO:0006468)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(3)|ovary(1)|prostate(1)|stomach(2)	18		Breast(56;0.000207)|Lung NSC(96;0.00145)|Prostate(109;0.034)|Hepatocellular(98;0.065)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;2.81e-08)		AAGAGCTGTATTGGGTACATT	0.378																																					p.N369S		Atlas-SNP	.											.	NEK3	41	.	0			c.A1106G						PASS	.	T	SER/ASN,SER/ASN	0,3738		0,0,1869	160.0	153.0	156.0		1055,1105	-11.1	0.0	13		156	1,8193		0,1,4096	no	missense,missense	NEK3	NM_001146099.1,NM_152720.2	46,46	0,1,5965	CC,CT,TT		0.0122,0.0,0.0084	benign,benign	352/490,369/507	52710320	1,11931	1869	4097	5966	SO:0001583	missense	4752	exon13			GCTGTATTGGGTA	AK290259, BC019916	CCDS73576.1	13q14.2-q21.1	2014-07-17	2012-11-15		ENSG00000136098	ENSG00000136098	2.7.11.1		7746	protein-coding gene	gene with protein product	"""serine/threonine-protein kinase NEK3"", ""phosphorylase B kinase kinase"", ""glycogen synthase A kinase"", ""hydroxyalkyl-protein kinase"""	604044	"""NIMA (never in mitosis gene a)-related kinase 3"""			8274451, 7522034	Standard	NM_002498		Approved	HSPK36, MGC29949	uc010tgy.2	P51956	OTTHUMG00000016958	ENST00000400357.2:c.1055A>G	13.37:g.52710320T>C	ENSP00000383210:p.Asn352Ser	Somatic	232	0	0		WXS	Illumina HiSeq	Phase_I	230	97	0.421739	NM_002498	A8K2J4|Q5TAP2|Q8J023|Q8WUN5	Missense_Mutation	SNP	ENST00000400357.2	37	CCDS53871.1	.	.	.	.	.	.	.	.	.	.	T	2.579	-0.297749	0.05532	0.0	1.22E-4	ENSG00000136098	ENST00000339406;ENST00000378101;ENST00000400357;ENST00000452082;ENST00000547422	T;T;T;T;T	0.70631	-0.34;-0.34;-0.5;-0.36;-0.34	5.57	-11.1	0.00147	.	0.832180	0.11642	N	0.543642	T	0.32882	0.0844	N	0.03608	-0.345	0.09310	N	1	B;B;B	0.06786	0.001;0.001;0.0	B;B;B	0.06405	0.001;0.001;0.002	T	0.31110	-0.9955	10	0.07175	T	0.84	.	9.6098	0.39657	0.0:0.2182:0.255:0.5268	.	369;373;346	P51956;Q6ZN64;F8VS47	NEK3_HUMAN;.;.	S	369;369;352;373;346	ENSP00000339429:N369S;ENSP00000367341:N369S;ENSP00000383210:N352S;ENSP00000404197:N373S;ENSP00000448716:N346S	ENSP00000339429:N369S	N	-	2	0	NEK3	51608321	0.000000	0.05858	0.000000	0.03702	0.020000	0.10135	-2.293000	0.01145	-2.658000	0.00420	-0.290000	0.09829	AAT	.	.	weak		0.378	NEK3-002	KNOWN	upstream_ATG|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000045047.3		
HEG1	57493	hgsc.bcm.edu	37	3	124746182	124746182	+	Silent	SNP	C	C	A	rs2333041	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	206	1	0.00485437		WXS	Illumina HiSeq	Phase_I	195	89	0.45641	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	
SEMA4B	10509	hgsc.bcm.edu	37	15	90768959	90768959	+	Silent	SNP	A	A	C	rs908044	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:90768959A>C	ENST00000411539.2	+	12	1848	c.1588A>C	c.(1588-1590)Agg>Cgg	p.R530R	SEMA4B_ENST00000332496.6_Silent_p.R530R|SEMA4B_ENST00000379122.3_Silent_p.R525R	NM_198925.2	NP_945119.1	Q9NPR2	SEM4B_HUMAN	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4B	525	PSI.				cell differentiation (GO:0030154)|nervous system development (GO:0007399)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synapse (GO:0045202)	receptor activity (GO:0004872)			NS(1)|breast(2)|endometrium(1)|kidney(2)|large_intestine(2)|lung(2)|ovary(1)|stomach(1)	12	Melanoma(11;0.00551)|Lung NSC(78;0.0125)|all_lung(78;0.0272)		BRCA - Breast invasive adenocarcinoma(143;0.0107)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.217)			CAGCCTGTACAGGAGCTGTGG	0.662													C|||	1794	0.358227	0.6997	0.3026	5008	,	,		17449	0.1002		0.3628	False		,,,				2504	0.1973				p.R530R		Atlas-SNP	.											.	SEMA4B	51	.	0			c.A1588C						PASS	.	C	,	2591,1563		836,919,322	14.0	18.0	17.0		1588,1588	4.7	1.0	15	dbSNP_86	17	2856,5524		517,1822,1851	no	coding-synonymous,coding-synonymous	SEMA4B	NM_020210.3,NM_198925.2	,	1353,2741,2173	CC,CA,AA		34.0811,37.6264,43.4578	,	530/838,530/838	90768959	5447,7087	2077	4190	6267	SO:0001819	synonymous_variant	10509	exon13			CTGTACAGGAGCT	AB051532	CCDS45347.1	15q25	2008-07-18						"""Semaphorins"""	10730	protein-coding gene	gene with protein product				SEMAC		7748561	Standard	NM_020210		Approved	SemC, KIAA1745, MGC131831	uc002boz.3	Q9NPR2		ENST00000411539.2:c.1588A>C	15.37:g.90768959A>C		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	90	89	0.988889	NM_020210	Q6UXE3|Q8WVP9|Q96FK5|Q9C0B8|Q9H691|Q9NPM8|Q9NPN0	Silent	SNP	ENST00000411539.2	37	CCDS45347.1																																																																																			A|0.634;C|0.366	0.366	strong		0.662	SEMA4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416810.1	NM_198925	
LAMB1	3912	hgsc.bcm.edu	37	7	107626770	107626770	+	Silent	SNP	G	G	A	rs25659	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:107626770G>A	ENST00000222399.6	-	6	692	c.462C>T	c.(460-462)tcC>tcT	p.S154S	LAMB1_ENST00000393561.1_Silent_p.S178S|LAMB1_ENST00000393560.1_Silent_p.S154S	NM_002291.2	NP_002282.2	P07942	LAMB1_HUMAN	laminin, beta 1	154	Laminin N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00466}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|embryo implantation (GO:0007566)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of cell adhesion (GO:0007162)|neuron projection development (GO:0031175)|neuronal-glial interaction involved in cerebral cortex radial glia guided migration (GO:0021812)|odontogenesis (GO:0042476)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell proliferation (GO:0050679)|substrate adhesion-dependent cell spreading (GO:0034446)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-2 complex (GO:0005607)|laminin-8 complex (GO:0043257)|perinuclear region of cytoplasm (GO:0048471)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)|structural molecule activity (GO:0005198)			NS(3)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(4)|large_intestine(11)|lung(37)|ovary(6)|prostate(5)|skin(5)|upper_aerodigestive_tract(3)	82						TCCCAAAGTCGGACGATCGTT	0.428													G|||	457	0.091254	0.059	0.134	5008	,	,		19024	0.0675		0.1203	False		,,,				2504	0.0992				p.S154S		Atlas-SNP	.											.	LAMB1	185	.	0			c.C462T						PASS	.	G		322,4084	173.7+/-203.5	14,294,1895	83.0	83.0	83.0		462	-7.5	0.3	7	dbSNP_72	83	1073,7527	226.4+/-262.1	67,939,3294	no	coding-synonymous	LAMB1	NM_002291.2		81,1233,5189	AA,AG,GG		12.4767,7.3082,10.7258		154/1787	107626770	1395,11611	2203	4300	6503	SO:0001819	synonymous_variant	3912	exon6			AAAGTCGGACGAT	M61916	CCDS5750.1	7q22	2013-03-01			ENSG00000091136	ENSG00000091136		"""Laminins"""	6486	protein-coding gene	gene with protein product		150240	"""cutis laxa with marfanoid phenotype"""	CLM		2563160, 2704655, 1864606	Standard	NM_002291		Approved		uc003vew.2	P07942	OTTHUMG00000149966	ENST00000222399.6:c.462C>T	7.37:g.107626770G>A		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	104	42	0.403846	NM_002291	Q14D91	Silent	SNP	ENST00000222399.6	37	CCDS5750.1																																																																																			G|0.898;A|0.102	0.102	strong		0.428	LAMB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314584.1	NM_002291	
TOR1AIP1	26092	hgsc.bcm.edu	37	1	179876988	179876988	+	Missense_Mutation	SNP	C	C	G	rs609521	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:179876988C>G	ENST00000606911.2	+	7	1018	c.827C>G	c.(826-828)cCt>cGt	p.P276R	TOR1AIP1_ENST00000474875.1_3'UTR|TOR1AIP1_ENST00000435319.4_Missense_Mutation_p.P155R|TOR1AIP1_ENST00000528443.2_Missense_Mutation_p.P277R|TOR1AIP1_ENST00000271583.3_Missense_Mutation_p.P277R			Q5JTV8	TOIP1_HUMAN	torsin A interacting protein 1	276			P -> R (in dbSNP:rs609521). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		positive regulation of ATPase activity (GO:0032781)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)	ATPase activator activity (GO:0001671)|ATPase binding (GO:0051117)|cytoskeletal protein binding (GO:0008092)			breast(4)|central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(4)|ovary(2)|skin(1)|urinary_tract(1)	18						GATAAGCAACCTTCAGTGCTA	0.338													C|||	2925	0.584065	0.3041	0.6715	5008	,	,		11847	0.7778		0.6093	False		,,,				2504	0.6748				p.P277R		Atlas-SNP	.											.	TOR1AIP1	58	.	0			c.C830G						PASS	.	C	ARG/PRO	1613,2793	495.5+/-363.3	292,1029,882	130.0	118.0	122.0		827	3.8	0.0	1	dbSNP_83	122	5413,3187	652.5+/-400.9	1700,2013,587	yes	missense	TOR1AIP1	NM_015602.2	103	1992,3042,1469	GG,GC,CC		37.0581,36.6092,45.9788	benign	276/584	179876988	7026,5980	2203	4300	6503	SO:0001583	missense	26092	exon7			AGCAACCTTCAGT		CCDS1335.1, CCDS65737.1	1q24.2	2008-02-05			ENSG00000143337	ENSG00000143337			29456	protein-coding gene	gene with protein product	"""lamina associated polypeptide 1B"""	614512				12061773, 15767459	Standard	NM_015602		Approved	LAP1B, FLJ13142	uc001gnp.2	Q5JTV8	OTTHUMG00000035257	ENST00000606911.2:c.827C>G	1.37:g.179876988C>G	ENSP00000476687:p.Pro276Arg	Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	132	66	0.5	NM_001267578	A8K630|B0QZ57|Q5JTV6|Q8IZ65|Q9H8Y6|Q9HAJ1|Q9NV52|Q9Y3X5	Missense_Mutation	SNP	ENST00000606911.2	37	CCDS1335.1	1296|1296	0.5934065934065934|0.5934065934065934	150|150	0.3048780487804878|0.3048780487804878	234|234	0.6464088397790055|0.6464088397790055	451|451	0.7884615384615384|0.7884615384615384	461|461	0.6081794195250659|0.6081794195250659	c|c	10.85|10.85	1.466776|1.466776	0.26335|0.26335	0.366092|0.366092	0.629419|0.629419	ENSG00000143337|ENSG00000143337	ENST00000447964|ENST00000528443;ENST00000325993;ENST00000271583;ENST00000435319	.|T;T;T	.|0.42900	.|0.96;0.96;0.96	4.74|4.74	3.81|3.81	0.43845|0.43845	.|.	.|1.063160	.|0.07290	.|N	.|0.872300	T|T	0.00012|0.00012	0.0000|0.0000	L|L	0.54323|0.54323	1.7|1.7	0.80722|0.80722	P|P	0.0|0.0	.|B;P	.|0.43542	.|0.175;0.81	.|B;B	.|0.40375	.|0.104;0.327	T|T	0.34950|0.34950	-0.9808|-0.9808	4|8	.|.	.|.	.|.	-1.1775|-1.1775	10.0678|10.0678	0.42315|0.42315	0.2007:0.7993:0.0:0.0|0.2007:0.7993:0.0:0.0	rs609521;rs1281381;rs2482472;rs11551052;rs16854942;rs17852134;rs52832171;rs609521|rs609521;rs1281381;rs2482472;rs11551052;rs16854942;rs17852134;rs52832171;rs609521	.|276;277	.|Q5JTV8;E9PKD1	.|TOIP1_HUMAN;.	V|R	30|277;276;277;276	.|ENSP00000435365:P277R;ENSP00000271583:P277R;ENSP00000393292:P276R	.|.	L|P	+|+	1|2	0|0	TOR1AIP1|TOR1AIP1	178143611|178143611	0.003000|0.003000	0.15002|0.15002	0.002000|0.002000	0.10522|0.10522	0.042000|0.042000	0.13812|0.13812	1.705000|1.705000	0.37867|0.37867	1.187000|1.187000	0.43000|0.43000	0.650000|0.650000	0.86243|0.86243	CTT|CCT	C|0.442;G|0.557	0.557	strong		0.338	TOR1AIP1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000100313.4	NM_015602	
PYGB	5834	hgsc.bcm.edu	37	20	25262769	25262769	+	Missense_Mutation	SNP	G	G	A	rs2227891	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:25262769G>A	ENST00000216962.4	+	12	1614	c.1504G>A	c.(1504-1506)Gat>Aat	p.D502N		NM_002862.3	NP_002853.2	P11216	PYGB_HUMAN	phosphorylase, glycogen; brain	502			D -> N (in dbSNP:rs2227891).		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						GGGGCTGGCCGATACCATCGT	0.612													G|||	812	0.162141	0.0514	0.1297	5008	,	,		16098	0.3502		0.1849	False		,,,				2504	0.1176				p.D502N		Atlas-SNP	.											.	PYGB	84	.	0			c.G1504A						PASS	.	G	ASN/ASP	349,4051	176.6+/-205.7	10,329,1861	33.0	40.0	38.0		1504	3.9	0.1	20	dbSNP_98	38	1593,7005	290.5+/-299.9	155,1283,2861	yes	missense	PYGB	NM_002862.3	23	165,1612,4722	AA,AG,GG		18.5276,7.9318,14.9408	benign	502/844	25262769	1942,11056	2200	4299	6499	SO:0001583	missense	5834	exon12			CTGGCCGATACCA		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.1504G>A	20.37:g.25262769G>A	ENSP00000216962:p.Asp502Asn	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	56	32	0.571429	NM_002862	Q96AK1|Q9NPX8	Missense_Mutation	SNP	ENST00000216962.4	37	CCDS13171.1	424	0.19413919413919414	27	0.054878048780487805	58	0.16022099447513813	197	0.34440559440559443	142	0.18733509234828497	G	14.15	2.448638	0.43531	0.079318	0.185276	ENSG00000100994	ENST00000216962	D	0.93189	-3.18	3.93	3.93	0.45458	.	0.197780	0.51477	D	0.000095	T	0.00012	0.0000	L	0.39245	1.2	0.09310	P	0.99999999854778	B	0.14012	0.009	B	0.15052	0.012	T	0.01977	-1.1236	9	0.36615	T	0.2	-19.3115	16.1009	0.81169	0.0:0.0:1.0:0.0	rs2227891;rs2261789;rs13044002;rs16987631;rs2227891	502	P11216	PYGB_HUMAN	N	502	ENSP00000216962:D502N	ENSP00000216962:D502N	D	+	1	0	PYGB	25210769	1.000000	0.71417	0.069000	0.20011	0.430000	0.31655	7.572000	0.82409	2.182000	0.69389	0.462000	0.41574	GAT	G|0.839;A|0.161	0.161	strong		0.612	PYGB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078415.2	NM_002862	
CENPE	1062	hgsc.bcm.edu	37	4	104062223	104062223	+	Silent	SNP	C	C	T	rs1381658	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:104062223C>T	ENST00000265148.3	-	36	5591	c.5502G>A	c.(5500-5502)acG>acA	p.T1834T	CENPE_ENST00000380026.3_Silent_p.T1809T	NM_001813.2	NP_001804.2	Q02224	CENPE_HUMAN	centromere protein E, 312kDa	1834					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)		CTTTTTTTAACGTAATAAGTT	0.284													C|||	847	0.169129	0.0431	0.1916	5008	,	,		19051	0.1548		0.1779	False		,,,				2504	0.3292				p.T1834T		Atlas-SNP	.											.	CENPE	253	.	0			c.G5502A						PASS	.	C		277,4125	140.0+/-175.5	8,261,1932	64.0	64.0	64.0		5502	2.9	1.0	4	dbSNP_88	64	1538,7052	281.3+/-295.0	141,1256,2898	no	coding-synonymous	CENPE	NM_001813.2		149,1517,4830	TT,TC,CC		17.9045,6.2926,13.9701		1834/2702	104062223	1815,11177	2201	4295	6496	SO:0001819	synonymous_variant	1062	exon36			TTTTAACGTAATA	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.5502G>A	4.37:g.104062223C>T		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	86	30	0.348837	NM_001813	A6NKY9|A8K2U7|Q4LE75	Silent	SNP	ENST00000265148.3	37	CCDS34042.1																																																																																			C|0.861;T|0.139	0.139	strong		0.284	CENPE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
HR	55806	hgsc.bcm.edu	37	8	21982991	21982991	+	Missense_Mutation	SNP	T	T	C	rs74596676	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:21982991T>C	ENST00000381418.4	-	5	3063	c.1583A>G	c.(1582-1584)cAg>cGg	p.Q528R	HR_ENST00000312841.8_Missense_Mutation_p.Q528R	NM_005144.4	NP_005135.2	O43593	HAIR_HUMAN	hair growth associated	528					negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nuclear body (GO:0016604)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|oxidoreductase activity (GO:0016491)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(12)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	27		Breast(100;0.000162)|Acute lymphoblastic leukemia(644;0.0775)|Prostate(55;0.116)		KIRC - Kidney renal clear cell carcinoma(542;1.19e-05)|BRCA - Breast invasive adenocarcinoma(99;3.56e-05)|Colorectal(74;0.00191)|COAD - Colon adenocarcinoma(73;0.0615)|READ - Rectum adenocarcinoma(644;0.1)		GTCTTCCTCCTGCTGCAGCTC	0.677													T|||	224	0.0447284	0.0378	0.0389	5008	,	,		15804	0.0149		0.0994	False		,,,				2504	0.0327				p.Q528R		Atlas-SNP	.											.	HR	71	.	0			c.A1583G						PASS	.	T	ARG/GLN,ARG/GLN	195,4211	118.8+/-156.5	3,189,2011	37.0	39.0	38.0		1583,1583	-5.6	0.0	8	dbSNP_131	38	801,7799	182.3+/-230.8	34,733,3533	yes	missense,missense	HR	NM_005144.4,NM_018411.4	43,43	37,922,5544	CC,CT,TT		9.314,4.4258,7.658	benign,benign	528/1190,528/1135	21982991	996,12010	2203	4300	6503	SO:0001583	missense	55806	exon5			TCCTCCTGCTGCA	AF039196	CCDS6022.1, CCDS6023.1	8p12	2012-12-07	2012-12-07		ENSG00000168453	ENSG00000168453			5172	protein-coding gene	gene with protein product		602302	"""hairless (mouse) homolog"", ""hairless homolog (mouse)"""	ALUNC		10051399, 9463324	Standard	NM_018411		Approved	AU	uc003xas.3	O43593	OTTHUMG00000097089	ENST00000381418.4:c.1583A>G	8.37:g.21982991T>C	ENSP00000370826:p.Gln528Arg	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	51	42	0.823529	NM_018411	Q6GS30|Q96H33|Q9NPE1	Missense_Mutation	SNP	ENST00000381418.4	37	CCDS6022.1	122	0.055860805860805864	19	0.03861788617886179	15	0.04143646408839779	7	0.012237762237762238	81	0.10686015831134564	T	9.997	1.232545	0.22626	0.044258	0.09314	ENSG00000168453	ENST00000381418;ENST00000312841	T;T	0.71341	-0.56;-0.56	4.85	-5.56	0.02529	.	1.835560	0.02834	N	0.127104	T	0.02380	0.0073	L	0.54323	1.7	0.09310	N	1	B;B	0.12630	0.006;0.003	B;B	0.10450	0.005;0.002	T	0.25537	-1.0129	10	0.36615	T	0.2	-0.7724	7.682	0.28520	0.2402:0.0:0.5246:0.2353	.	528;528	O43593-2;O43593	.;HAIR_HUMAN	R	528	ENSP00000370826:Q528R;ENSP00000326765:Q528R	ENSP00000326765:Q528R	Q	-	2	0	HR	22038936	0.000000	0.05858	0.000000	0.03702	0.018000	0.09664	-0.466000	0.06672	-0.673000	0.05259	-0.689000	0.03729	CAG	T|0.930;C|0.070	0.070	strong		0.677	HR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214213.1		
UBR4	23352	hgsc.bcm.edu	37	1	19447882	19447882	+	Silent	SNP	G	G	A	rs34710232	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:19447882G>A	ENST00000375254.3	-	68	9969	c.9942C>T	c.(9940-9942)ggC>ggT	p.G3314G	UBR4_ENST00000375226.2_Silent_p.G3290G|UBR4_ENST00000375267.2_Silent_p.G3314G|UBR4_ENST00000375218.3_5'Flank|UBR4_ENST00000375217.2_Silent_p.G3307G	NM_020765.2	NP_065816.2	Q5T4S7	UBR4_HUMAN	ubiquitin protein ligase E3 component n-recognin 4	3314					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)		CTGGGGACACGCCCTCATCCA	0.592													G|||	23	0.00459265	0.0008	0.0043	5008	,	,		15686	0.0		0.0159	False		,,,				2504	0.0031				p.G3314G		Atlas-SNP	.											UBR4,right_upper_lobe,carcinoma,-1,1	UBR4	415	1	0			c.C9942T						PASS	.	G		7,4399	12.9+/-30.5	0,7,2196	73.0	66.0	68.0		9942	-6.2	0.9	1	dbSNP_126	68	64,8536	38.8+/-94.9	0,64,4236	no	coding-synonymous	UBR4	NM_020765.2		0,71,6432	AA,AG,GG		0.7442,0.1589,0.5459		3314/5184	19447882	71,12935	2203	4300	6503	SO:0001819	synonymous_variant	23352	exon68			GGACACGCCCTCA	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.9942C>T	1.37:g.19447882G>A		Somatic	360	1	0.00277778		WXS	Illumina HiSeq	Phase_I	329	175	0.531915	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																																																																																			G|0.996;A|0.004	0.004	strong		0.592	UBR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007085.1	NM_020765	
ENG	2022	hgsc.bcm.edu	37	9	130586661	130586661	+	Silent	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:130586661C>T	ENST00000373203.4	-	8	1456	c.1056G>A	c.(1054-1056)ccG>ccA	p.P352P	RP11-228B15.4_ENST00000425991.1_RNA|ENG_ENST00000480266.1_5'UTR|ENG_ENST00000344849.3_Silent_p.P352P|RP11-228B15.4_ENST00000439298.1_RNA	NM_000118.2|NM_001114753.1|NM_001278138.1	NP_000109.1|NP_001108225.1|NP_001265067.1	P17813	EGLN_HUMAN	endoglin	352	Ser/Thr-rich.				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)	p.P352P(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)	17						TGAGCAGCTCCGGGCTACAAG	0.597									Juvenile Polyposis;Hereditary Hemorrhagic Telangiectasia																												p.P352P		Atlas-SNP	.											ENG,NS,carcinoma,0,1	ENG	44	1	1	Substitution - coding silent(1)	lung(1)	c.G1056A						scavenged	.						142.0	116.0	125.0					9																	130586661		2203	4300	6503	SO:0001819	synonymous_variant	2022	exon8	Familial Cancer Database	incl.: Juvenile Polyposis of the Stomach;HHT, Rendu-Osler-Weber disease, incl.: Pulmonary arteriovenous malformations, hypertrophic osteoarthropathy and juvenile polyposis,	CAGCTCCGGGCTA	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.1056G>A	9.37:g.130586661C>T		Somatic	154	1	0.00649351		WXS	Illumina HiSeq	Phase_I	116	56	0.482759	NM_001114753	Q14248|Q14926|Q5T9C0	Silent	SNP	ENST00000373203.4	37	CCDS48029.1																																																																																			.	.	none		0.597	ENG-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054313.1		
AKAP3	10566	hgsc.bcm.edu	37	12	4735970	4735970	+	Missense_Mutation	SNP	A	A	G	rs527978551|rs370203105|rs71441828|rs67512580|rs2041290	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:4735970A>G	ENST00000545990.2	-	5	2622	c.2098T>C	c.(2098-2100)Tct>Cct	p.S700P	AKAP3_ENST00000228850.1_Missense_Mutation_p.S700P|RP11-500M8.7_ENST00000536588.1_Intron	NM_001278309.1	NP_001265238.1	O75969	AKAP3_HUMAN	A kinase (PRKA) anchor protein 3	700			S -> F (in dbSNP:rs2041291).|S -> P (in dbSNP:rs2041290).	S -> L (in Ref. 2; AAC35854). {ECO:0000305}.	acrosome reaction (GO:0007340)|cellular component movement (GO:0006928)|protein localization (GO:0008104)|single fertilization (GO:0007338)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	acrosomal vesicle (GO:0001669)|nucleus (GO:0005634)|sperm fibrous sheath (GO:0035686)|sperm principal piece (GO:0097228)	protein kinase A binding (GO:0051018)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(13)|liver(1)|lung(17)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	51						GCATCTCCAGACTTGTCATCT	0.502														793	0.158347	0.1248	0.1225	5008	,	,		22621	0.1647		0.1143	False		,,,				2504	0.2679				p.S700P		Atlas-SNP	.											.	AKAP3	212	.	0			c.T2098C						PASS	.						76.0	65.0	69.0					12																	4735970		2203	4300	6503	SO:0001583	missense	10566	exon4			CTCCAGACTTGTC	U85715	CCDS8531.1	12p13.3	2009-03-12				ENSG00000111254		"""A-kinase anchor proteins"""	373	protein-coding gene	gene with protein product	"""Fibrous Sheath Protein of 95 kDa"", ""cancer/testis antigen 82"""	604689				10334916, 10319321	Standard	NM_001278309		Approved	FSP95, SOB1, AKAP110, CT82	uc001qnb.4	O75969		ENST00000545990.2:c.2098T>C	12.37:g.4735970A>G	ENSP00000440994:p.Ser700Pro	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	79	22	0.278481	NM_006422	O75945|Q86X01|Q9UM61	Missense_Mutation	SNP	ENST00000545990.2	37	CCDS8531.1	.	.	.	.	.	.	.	.	.	.	A	10.66	1.413702	0.25465	.	.	ENSG00000111254	ENST00000228850;ENST00000545990	T;T	0.09630	2.96;2.96	4.91	3.74	0.42951	A-kinase anchor 110kDa, C-terminal (1);	0.689588	0.13317	N	0.396989	T	0.20251	0.0487	M	0.65975	2.015	0.18873	N	0.999986	D	0.59767	0.986	P	0.54815	0.761	T	0.10989	-1.0606	10	0.46703	T	0.11	-2.5718	5.5631	0.17154	0.6459:0.1808:0.0:0.1733	rs2041290;rs34696134	700	O75969	AKAP3_HUMAN	P	700	ENSP00000228850:S700P;ENSP00000440994:S700P	ENSP00000228850:S700P	S	-	1	0	AKAP3	4606231	0.991000	0.36638	0.794000	0.32065	0.117000	0.20001	1.631000	0.37092	0.869000	0.35703	0.533000	0.62120	TCT	A|0.881;G|0.119	0.119	strong		0.502	AKAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398911.2	NM_006422	
TRIOBP	11078	hgsc.bcm.edu	37	22	38122448	38122448	+	Silent	SNP	C	C	T	rs739137	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:38122448C>T	ENST00000406386.3	+	7	4140	c.3885C>T	c.(3883-3885)agC>agT	p.S1295S		NM_001039141.2	NP_001034230.1	Q9H2D6	TARA_HUMAN	TRIO and F-actin binding protein	1295					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)					AGTGCAGCAGCGGGGGCCGCA	0.726													C|||	1686	0.336661	0.1543	0.2867	5008	,	,		13163	0.5863		0.3877	False		,,,				2504	0.3088				p.S1295S		Atlas-SNP	.											.	TRIOBP	262	.	0			c.C3885T						PASS	.	C		648,3004		99,450,1277	5.0	7.0	6.0		3885	3.6	1.0	22	dbSNP_86	6	3246,4490		767,1712,1389	no	coding-synonymous	TRIOBP	NM_001039141.2		866,2162,2666	TT,TC,CC		41.9597,17.7437,34.1939		1295/2366	38122448	3894,7494	1826	3868	5694	SO:0001819	synonymous_variant	11078	exon7			CAGCAGCGGGGGC	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.3885C>T	22.37:g.38122448C>T		Somatic	4	0	0		WXS	Illumina HiSeq	Phase_I	8	5	0.625	NM_001039141	B1AHD4|B1AHD7|F2Z2W0|F8W6V6|O94797|Q2PZW8|Q2Q3Z9|Q2Q400|Q5R3M6|Q96DW1|Q9BT77|Q9BTL7|Q9BY98|Q9Y3L4	Silent	SNP	ENST00000406386.3	37	CCDS43015.1																																																																																			C|0.621;T|0.379	0.379	strong		0.726	TRIOBP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319439.2		
OR8B8	26493	hgsc.bcm.edu	37	11	124310622	124310622	+	Silent	SNP	A	A	G	rs4296049	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:124310622A>G	ENST00000328064.2	-	1	432	c.360T>C	c.(358-360)taT>taC	p.Y120Y		NM_012378.1	NP_036510.1	Q15620	OR8B8_HUMAN	olfactory receptor, family 8, subfamily B, member 8	120					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(15)|ovary(1)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(1)	39		Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0277)		CATAGCGGTCATACGCCATTG	0.473													A|||	1244	0.248403	0.0303	0.33	5008	,	,		23587	0.5317		0.2644	False		,,,				2504	0.1769				p.Y120Y		Atlas-SNP	.											.	OR8B8	76	.	0			c.T360C						PASS	.	A		300,4102	164.0+/-195.7	8,284,1909	93.0	86.0	88.0		360	1.2	0.9	11	dbSNP_111	88	2499,6099	410.5+/-350.2	360,1779,2160	no	coding-synonymous	OR8B8	NM_012378.1		368,2063,4069	GG,GA,AA		29.0649,6.8151,21.5308		120/312	124310622	2799,10201	2201	4299	6500	SO:0001819	synonymous_variant	26493	exon1			GCGGTCATACGCC	AF238488	CCDS8446.1	11q24.2	2012-08-09			ENSG00000197125	ENSG00000197125		"""GPCR / Class A : Olfactory receptors"""	8477	protein-coding gene	gene with protein product						9119360	Standard	NM_012378		Approved	TPCR85	uc010sal.2	Q15620	OTTHUMG00000165917	ENST00000328064.2:c.360T>C	11.37:g.124310622A>G		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	39	12	0.307692	NM_012378	A1L446|Q96RC8	Silent	SNP	ENST00000328064.2	37	CCDS8446.1																																																																																			A|0.756;G|0.244	0.244	strong		0.473	OR8B8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387056.1	NM_012378	
DHX9	1660	hgsc.bcm.edu	37	1	182844020	182844020	+	Silent	SNP	C	C	T	rs11332	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:182844020C>T	ENST00000367549.3	+	16	1856	c.1746C>T	c.(1744-1746)acC>acT	p.T582T		NM_001357.4	NP_001348.2	Q08211	DHX9_HUMAN	DEAH (Asp-Glu-Ala-His) box helicase 9	582					ATP catabolic process (GO:0006200)|cellular response to heat (GO:0034605)|circadian rhythm (GO:0007623)|CRD-mediated mRNA stabilization (GO:0070934)|DNA duplex unwinding (GO:0032508)|gene expression (GO:0010467)|innate immune response (GO:0045087)|mRNA splicing, via spliceosome (GO:0000398)|osteoblast differentiation (GO:0001649)|positive regulation of type I interferon production (GO:0032481)|RNA splicing (GO:0008380)	centrosome (GO:0005813)|CRD-mediated mRNA stability complex (GO:0070937)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|ATP-dependent RNA helicase activity (GO:0004004)|DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|RNA helicase activity (GO:0003724)|RNA polymerase II transcription factor binding (GO:0001085)			NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(10)|kidney(3)|large_intestine(7)|liver(1)|lung(19)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	49						TTCAGATGACCCACTTTGTTC	0.383													C|||	900	0.179712	0.3449	0.1254	5008	,	,		19735	0.1181		0.0746	False		,,,				2504	0.1667				p.T582T	Colon(69;210 1162 3697 13559 39565)	Atlas-SNP	.											.	DHX9	114	.	0			c.C1746T						PASS	.	C		1131,2635		160,811,912	129.0	134.0	132.0		1746	3.5	1.0	1	dbSNP_52	132	652,7578		23,606,3486	no	coding-synonymous	DHX9	NM_001357.4		183,1417,4398	TT,TC,CC		7.9222,30.0319,14.8633		582/1271	182844020	1783,10213	1883	4115	5998	SO:0001819	synonymous_variant	1660	exon16			GATGACCCACTTT	L13848	CCDS41444.1	1q25	2013-05-13	2013-05-13	2003-06-20	ENSG00000135829	ENSG00000135829		"""DEAH-boxes"""	2750	protein-coding gene	gene with protein product	"""NDH II"", ""RNA helicase A"""	603115	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 9 (RNA helicase A, nuclear DNA helicase II; leukophysin)"", ""DEAH (Asp-Glu-Ala-His) box polypeptide 9"""	LKP, DDX9		8344961, 9111062	Standard	NM_001357		Approved	RHA	uc001gpr.3	Q08211	OTTHUMG00000035337	ENST00000367549.3:c.1746C>T	1.37:g.182844020C>T		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	52	32	0.615385	NM_001357	B2RNV4|Q05CI5|Q12803|Q32Q22|Q5VY62|Q6PD69|Q99556	Silent	SNP	ENST00000367549.3	37	CCDS41444.1																																																																																			C|0.865;T|0.135	0.135	strong		0.383	DHX9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085522.2	NM_030588	
BFSP2	8419	hgsc.bcm.edu	37	3	133167363	133167363	+	Silent	SNP	G	G	A	rs2276737	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:133167363G>A	ENST00000302334.2	+	3	692	c.603G>A	c.(601-603)gcG>gcA	p.A201A	BFSP2-AS1_ENST00000515542.1_RNA	NM_003571.2	NP_003562.1	Q13515	BFSP2_HUMAN	beaded filament structural protein 2, phakinin	201	Rod.				cell maturation (GO:0048469)|intermediate filament cytoskeleton organization (GO:0045104)|lens fiber cell development (GO:0070307)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|intermediate filament (GO:0005882)|plasma membrane (GO:0005886)	structural constituent of cytoskeleton (GO:0005200)|structural constituent of eye lens (GO:0005212)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(4)|pancreas(1)|urinary_tract(1)	13						TTCGAAAGGCGGCAGAAGAGG	0.348													G|||	2186	0.436502	0.0968	0.3833	5008	,	,		21426	0.5853		0.5746	False		,,,				2504	0.638				p.A201A		Atlas-SNP	.											.	BFSP2	48	.	0			c.G603A						PASS	.	G		753,3653	302.7+/-287.5	69,615,1519	59.0	62.0	61.0		603	-2.0	0.9	3	dbSNP_100	61	5282,3318	643.3+/-399.9	1629,2024,647	no	coding-synonymous	BFSP2	NM_003571.2		1698,2639,2166	AA,AG,GG		38.5814,17.0903,46.4017		201/416	133167363	6035,6971	2203	4300	6503	SO:0001819	synonymous_variant	8419	exon3			AAAGGCGGCAGAA	U48224	CCDS33859.1	3q22.1	2013-01-16			ENSG00000170819	ENSG00000170819		"""Intermediate filaments type VI, eye lens intermediate filaments"""	1041	protein-coding gene	gene with protein product		603212					Standard	NM_003571		Approved	CP47, CP49, LIFL-L, phakinin	uc003epn.1	Q13515	OTTHUMG00000159719	ENST00000302334.2:c.603G>A	3.37:g.133167363G>A		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	102	44	0.431373	NM_003571	Q14D32|Q9HBW5	Silent	SNP	ENST00000302334.2	37	CCDS33859.1																																																																																			G|0.551;A|0.449	0.449	strong		0.348	BFSP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357031.1		
PCDHA9	9752	hgsc.bcm.edu	37	5	140238124	140238124	+	Intron	SNP	T	T	A	rs62384480	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:140238124T>A	ENST00000532602.1	+	1	3427				PCDHA4_ENST00000512229.2_Intron|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|PCDHA5_ENST00000529619.1_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA1_ENST00000504120.2_Intron	NM_031857.1	NP_114063.1	Q9Y5H5	PCDA9_HUMAN	protocadherin alpha 9						homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|lung(18)|ovary(4)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	59			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TTTGTCTACATTCCATTTATG	0.279													.|||	116	0.0231629	0.003	0.0331	5008	,	,		15415	0.001		0.0815	False		,,,				2504	0.0061				p.F831I	Melanoma(55;1800 1972 14909)	Atlas-SNP	.											.	PCDHA10	358	.	0			c.T2491A						PASS	.	T	,,,,,,,,,,,,ILE/PHE,	27,1875		3,21,927	67.0	61.0	63.0		,,,,,,,,,,,,2491,	-3.6	0.0	5	dbSNP_129	63	251,3919		24,203,1858	yes	intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,missense,intron	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,	27,224,2785	AA,AT,TT		6.0192,1.4196,4.5784	,,,,,,,,,,,,,	,,,,,,,,,,,,831/845,	140238124	278,5794	951	2085	3036	SO:0001627	intron_variant	56139	exon1			TCTACATTCCATT	AF152487	CCDS54920.1	5q31	2010-11-26				ENSG00000204961		"""Cadherins / Protocadherins : Clustered"""	8675	other	complex locus constituent	"""KIAA0345-like 5"""	606315				10380929	Standard	NM_031857		Approved	KIAA0345, PCDH-ALPHA9		Q9Y5H5		ENST00000532602.1:c.2394+7650T>A	5.37:g.140238124T>A		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	51	51	1	NM_031859	O15053|Q2M3S5	Missense_Mutation	SNP	ENST00000532602.1	37	CCDS54920.1																																																																																			T|0.967;A|0.033	0.033	strong		0.279	PCDHA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372896.2	NM_031857	
METTL3	56339	hgsc.bcm.edu	37	14	21967685	21967685	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:21967685C>T	ENST00000298717.4	-	8	1554	c.1403G>A	c.(1402-1404)cGg>cAg	p.R468Q		NM_019852.3	NP_062826.2	Q86U44	MTA70_HUMAN	methyltransferase like 3	468					circadian rhythm (GO:0007623)|gene expression (GO:0010467)|mRNA destabilization (GO:0061157)|mRNA methylation (GO:0080009)|mRNA processing (GO:0006397)|RNA methylation (GO:0001510)|stem cell maintenance (GO:0019827)	MIS complex (GO:0036396)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	mRNA (2'-O-methyladenosine-N6-)-methyltransferase activity (GO:0016422)|RNA binding (GO:0003723)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(5)|pancreas(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)	20	all_cancers(95;0.000628)		Epithelial(56;6.61e-06)	GBM - Glioblastoma multiforme(265;0.0146)		ACGGCCTGTCCGAATGATGCG	0.448																																					p.R468Q		Atlas-SNP	.											METTL3,NS,adenocarcinoma,0,1	METTL3	48	1	0			c.G1403A						scavenged	.						166.0	156.0	160.0					14																	21967685		2203	4300	6503	SO:0001583	missense	56339	exon8			CCTGTCCGAATGA	AF014837	CCDS32044.1	14q11.1	2012-06-12			ENSG00000165819	ENSG00000165819	2.1.1.62		17563	protein-coding gene	gene with protein product	"""N6-adenosine-methyltransferase 70 kDa subunit"""	612472					Standard	XM_006720206		Approved	Spo8, M6A, MT-A70	uc001wbc.3	Q86U44	OTTHUMG00000168825	ENST00000298717.4:c.1403G>A	14.37:g.21967685C>T	ENSP00000298717:p.Arg468Gln	Somatic	351	1	0.002849		WXS	Illumina HiSeq	Phase_I	366	6	0.0163934	NM_019852	O14736|Q86V05|Q9HB32	Missense_Mutation	SNP	ENST00000298717.4	37	CCDS32044.1	.	.	.	.	.	.	.	.	.	.	C	27.5	4.837382	0.91117	.	.	ENSG00000165819	ENST00000298717	T	0.43294	0.95	4.9	4.02	0.46733	.	0.000000	0.85682	D	0.000000	T	0.65450	0.2692	M	0.82630	2.6	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.70475	-0.4861	10	0.66056	D	0.02	-11.8337	12.3983	0.55397	0.0:0.9167:0.0:0.0833	.	468	Q86U44	MTA70_HUMAN	Q	468	ENSP00000298717:R468Q	ENSP00000298717:R468Q	R	-	2	0	METTL3	21037525	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.059000	0.76684	1.300000	0.44818	0.460000	0.39030	CGG	.	.	none		0.448	METTL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401227.1	NM_019852	
TOR1AIP1	26092	hgsc.bcm.edu	37	1	179852074	179852074	+	Missense_Mutation	SNP	T	T	C	rs1281378	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:179852074T>C	ENST00000606911.2	+	1	628	c.437T>C	c.(436-438)aTg>aCg	p.M146T	TOR1AIP1_ENST00000435319.4_Missense_Mutation_p.M25T|TOR1AIP1_ENST00000528443.2_Missense_Mutation_p.M146T|TOR1AIP1_ENST00000271583.3_Missense_Mutation_p.M146T|RP11-533E19.7_ENST00000610272.1_lincRNA			Q5JTV8	TOIP1_HUMAN	torsin A interacting protein 1	146			M -> T (in dbSNP:rs1281378). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:20068231, ECO:0000269|PubMed:21406692}.		positive regulation of ATPase activity (GO:0032781)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)	ATPase activator activity (GO:0001671)|ATPase binding (GO:0051117)|cytoskeletal protein binding (GO:0008092)			breast(4)|central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(4)|ovary(2)|skin(1)|urinary_tract(1)	18						TCTCCTGTTATGACCAGGAGA	0.657													T|||	3049	0.608826	0.3812	0.6758	5008	,	,		15312	0.7778		0.6133	False		,,,				2504	0.6902				p.M146T		Atlas-SNP	.											.	TOR1AIP1	58	.	0			c.T437C						PASS	.	T	THR/MET	1953,2443		455,1043,700	16.0	19.0	18.0		437	-1.5	0.0	1	dbSNP_87	18	5433,3147		1737,1959,594	yes	missense	TOR1AIP1	NM_015602.2	81	2192,3002,1294	CC,CT,TT		36.6783,44.4268,43.0795	benign	146/584	179852074	7386,5590	2198	4290	6488	SO:0001583	missense	26092	exon1			CTGTTATGACCAG		CCDS1335.1, CCDS65737.1	1q24.2	2008-02-05			ENSG00000143337	ENSG00000143337			29456	protein-coding gene	gene with protein product	"""lamina associated polypeptide 1B"""	614512				12061773, 15767459	Standard	NM_015602		Approved	LAP1B, FLJ13142	uc001gnp.2	Q5JTV8	OTTHUMG00000035257	ENST00000606911.2:c.437T>C	1.37:g.179852074T>C	ENSP00000476687:p.Met146Thr	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	98	43	0.438776	NM_001267578	A8K630|B0QZ57|Q5JTV6|Q8IZ65|Q9H8Y6|Q9HAJ1|Q9NV52|Q9Y3X5	Missense_Mutation	SNP	ENST00000606911.2	37	CCDS1335.1	1338	0.6126373626373627	189	0.38414634146341464	234	0.6464088397790055	451	0.7884615384615384	464	0.6121372031662269	T	0.020	-1.444634	0.01089	0.444268	0.633217	ENSG00000143337	ENST00000528443;ENST00000325993;ENST00000271583;ENST00000435319	T;T;T	0.20738	2.05;2.05;2.05	4.2	-1.54	0.08584	.	0.677608	0.12768	N	0.440772	T	0.00012	0.0000	N	0.00182	-1.905	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.29181	-1.0020	9	0.02654	T	1	0.019	3.6348	0.08145	0.1718:0.3958:0.0:0.4323	rs1281378;rs1758150;rs3889647;rs17370693;rs17845719;rs17858667;rs57247449;rs1281378	146;146	Q5JTV8;E9PKD1	TOIP1_HUMAN;.	T	146	ENSP00000435365:M146T;ENSP00000271583:M146T;ENSP00000393292:M146T	ENSP00000271583:M146T	M	+	2	0	TOR1AIP1	178118697	0.014000	0.17966	0.000000	0.03702	0.010000	0.07245	0.473000	0.22132	-0.363000	0.08101	-0.230000	0.12252	ATG	T|0.410;C|0.590	0.590	strong		0.657	TOR1AIP1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000100313.4	NM_015602	
RNF32	140545	hgsc.bcm.edu	37	7	156469190	156469190	+	Silent	SNP	A	A	G	rs2302145	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:156469190A>G	ENST00000405335.1	+	10	1339	c.930A>G	c.(928-930)gcA>gcG	p.A310A	RNF32_ENST00000317955.5_Silent_p.A310A|LMBR1_ENST00000430825.2_5'UTR|RNF32_ENST00000392743.2_Silent_p.A310A|RNF32_ENST00000311822.8_3'UTR|RNF32_ENST00000432459.2_Silent_p.A310A|RNF32_ENST00000343665.4_Silent_p.A286A			Q9H0A6	RNF32_HUMAN	ring finger protein 32	310						aggresome (GO:0016235)|endosome (GO:0005768)	zinc ion binding (GO:0008270)			cervix(2)|endometrium(3)|kidney(1)|large_intestine(2)|lung(5)|upper_aerodigestive_tract(2)	15	Ovarian(565;0.218)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.00291)	UCEC - Uterine corpus endometrioid carcinoma (81;0.169)		GCGTGGGTGCAGGCAGGCGTT	0.657													G|||	2666	0.532348	0.8646	0.4597	5008	,	,		12418	0.5248		0.4006	False		,,,				2504	0.2781				p.A310A		Atlas-SNP	.											.	RNF32	77	.	0			c.A930G						PASS	.	G	,,	3413,993	369.5+/-319.1	1336,741,126	56.0	47.0	50.0		930,930,930	-2.9	0.0	7	dbSNP_100	50	3246,5354	647.9+/-400.4	615,2016,1669	no	coding-synonymous,coding-synonymous,coding-synonymous	RNF32	NM_001184996.1,NM_001184997.1,NM_030936.3	,,	1951,2757,1795	GG,GA,AA		37.7442,22.5374,48.8006	,,	310/363,310/363,310/363	156469190	6659,6347	2203	4300	6503	SO:0001819	synonymous_variant	140545	exon9			GGGTGCAGGCAGG		CCDS5944.1	7q36	2013-08-05			ENSG00000105982	ENSG00000105982		"""RING-type (C3HC4) zinc fingers"""	17118	protein-coding gene	gene with protein product		610241				11890671	Standard	NM_001184996		Approved	FKSG33, HSD15, LMBR2	uc003wmr.3	Q9H0A6	OTTHUMG00000151440	ENST00000405335.1:c.930A>G	7.37:g.156469190A>G		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	69	40	0.57971	NM_001184996	Q6FIB3|Q6X7T4|Q8N6V8|Q8TDG0|Q96BM5|Q9Y6U1	Silent	SNP	ENST00000405335.1	37	CCDS5944.1																																																																																			A|0.477;G|0.523	0.523	strong		0.657	RNF32-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322660.2	NM_030936	
ZIM3	114026	hgsc.bcm.edu	37	19	57649962	57649962	+	Missense_Mutation	SNP	C	C	T	rs10407445	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:57649962C>T	ENST00000269834.1	-	3	405	c.20G>A	c.(19-21)aGa>aAa	p.R7K		NM_052882.1	NP_443114.1	Q96PE6	ZIM3_HUMAN	zinc finger, imprinted 3	7			R -> K (in dbSNP:rs10407445).		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)		GAAGGTCACTCTTCCCTGTAA	0.473													C|||	712	0.142173	0.2534	0.1167	5008	,	,		19803	0.1597		0.0835	False		,,,				2504	0.0521				p.R7K		Atlas-SNP	.											.	ZIM3	107	.	0			c.G20A						PASS	.	C	LYS/ARG	962,3444	361.1+/-315.5	106,750,1347	93.0	85.0	88.0		20	-3.1	0.1	19	dbSNP_119	88	706,7894	173.3+/-223.8	27,652,3621	yes	missense	ZIM3	NM_052882.1	26	133,1402,4968	TT,TC,CC		8.2093,21.8339,12.8249	benign	7/473	57649962	1668,11338	2203	4300	6503	SO:0001583	missense	114026	exon3			GTCACTCTTCCCT	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.20G>A	19.37:g.57649962C>T	ENSP00000269834:p.Arg7Lys	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	62	20	0.322581	NM_052882	Q14CA6	Missense_Mutation	SNP	ENST00000269834.1	37	CCDS33125.1	322	0.14743589743589744	121	0.2459349593495935	45	0.12430939226519337	87	0.1520979020979021	69	0.09102902374670185	C	1.921	-0.448315	0.04572	0.218339	0.082093	ENSG00000141946	ENST00000269834	T	0.00792	5.69	2.87	-3.11	0.05299	Krueppel-associated box (1);	.	.	.	.	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B	0.09022	0.002	B	0.04013	0.001	T	0.30937	-0.9961	8	0.15952	T	0.53	.	2.7852	0.05372	0.1629:0.2351:0.4713:0.1307	rs10407445;rs17305570;rs10407445	7	Q96PE6	ZIM3_HUMAN	K	7	ENSP00000269834:R7K	ENSP00000269834:R7K	R	-	2	0	ZIM3	62341774	0.000000	0.05858	0.128000	0.21923	0.305000	0.27757	-0.785000	0.04628	-0.038000	0.13624	0.205000	0.17691	AGA	C|0.866;T|0.134	0.134	strong		0.473	ZIM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465078.1		
IKZF3	22806	hgsc.bcm.edu	37	17	37922259	37922259	+	Silent	SNP	G	G	A	rs907092	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:37922259G>A	ENST00000346872.3	-	8	1375	c.1314C>T	c.(1312-1314)tcC>tcT	p.S438S	IKZF3_ENST00000467757.1_Silent_p.S382S|IKZF3_ENST00000351680.3_Silent_p.S399S|IKZF3_ENST00000439167.2_Silent_p.S365S|IKZF3_ENST00000394189.2_Silent_p.S256S|IKZF3_ENST00000350532.3_Silent_p.S399S|IKZF3_ENST00000377952.2_Silent_p.S217S|IKZF3_ENST00000377958.2_Silent_p.S351S|IKZF3_ENST00000439016.2_Silent_p.S343S|IKZF3_ENST00000535189.1_Silent_p.S404S|RP11-94L15.2_ENST00000488188.2_lincRNA|IKZF3_ENST00000346243.3_Silent_p.S360S|IKZF3_ENST00000583368.1_Silent_p.S191S|IKZF3_ENST00000377945.3_Silent_p.S304S|IKZF3_ENST00000377944.3_Silent_p.S295S	NM_012481.4	NP_036613.2	Q9UKT9	IKZF3_HUMAN	IKAROS family zinc finger 3 (Aiolos)	438					B cell activation (GO:0042113)|mesoderm development (GO:0007498)|regulation of apoptotic process (GO:0042981)|regulation of B cell differentiation (GO:0045577)|regulation of B cell proliferation (GO:0030888)|regulation of lymphocyte differentiation (GO:0045619)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.S438S(1)		NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(5)|kidney(6)|large_intestine(4)|liver(1)|lung(13)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	42	Breast(7;4.5e-103)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052)		UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|Colorectal(5;6.23e-08)|COAD - Colon adenocarcinoma(5;8.58e-06)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|LUSC - Lung squamous cell carcinoma(15;0.171)			TCACTTTGACGGAGTCTCTTG	0.562													G|||	1496	0.298722	0.1384	0.3401	5008	,	,		20021	0.2937		0.4732	False		,,,				2504	0.3119				p.S438S		Atlas-SNP	.											IKZF3,NS,carcinoma,0,1	IKZF3	79	1	1	Substitution - coding silent(1)	stomach(1)	c.C1314T						PASS	.	G	,,,,,	736,3670	303.0+/-287.7	70,596,1537	133.0	134.0	133.0	http://www.ncbi.nlm.nih.gov/pubmed?term	1314,1146,1197,1197,1029,1080	4.7	1.0	17	dbSNP_86	133	3899,4701	545.6+/-384.8	869,2161,1270	yes	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	IKZF3	NM_012481.3,NM_183228.1,NM_183229.1,NM_183230.1,NM_183231.1,NM_183232.1	,,,,,	939,2757,2807	AA,AG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	45.3372,16.7045,35.6374	,,,,,	438/510,382/454,399/471,399/471,343/415,360/432	37922259	4635,8371	2203	4300	6503	SO:0001819	synonymous_variant	22806	exon8			TTTGACGGAGTCT	AF129512	CCDS11346.1, CCDS11347.1, CCDS11348.1, CCDS11349.1, CCDS11350.1, CCDS11351.1, CCDS58539.1, CCDS58540.1, CCDS58541.1, CCDS58542.1, CCDS58543.1, CCDS58544.1, CCDS58545.1, CCDS74055.1	17q11.2	2013-01-08	2006-08-25	2006-08-25	ENSG00000161405	ENSG00000161405		"""Zinc fingers, C2H2-type"", ""IKAROS zinc fingers"""	13178	protein-coding gene	gene with protein product		606221	"""zinc finger protein, subfamily 1A, 3 (Aiolos)"""	ZNFN1A3		9155026, 10552935	Standard	NM_012481		Approved	Aiolos	uc002hsu.4	Q9UKT9	OTTHUMG00000133250	ENST00000346872.3:c.1314C>T	17.37:g.37922259G>A		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	119	50	0.420168	NM_012481	B4DVV5|Q69BL6|Q69BL7|Q69BL8|Q69BL9|Q69BM0|Q69BM1|Q69BM2|Q69BM3|Q69BM5|Q8N574|Q8WWQ9|Q8WWR0|Q8WWR1|Q8WWR2|Q8WWR3	Silent	SNP	ENST00000346872.3	37	CCDS11346.1	757	0.3466117216117216	64	0.13008130081300814	131	0.36187845303867405	198	0.34615384615384615	364	0.48021108179419525	G	8.414	0.844787	0.16963	0.167045	0.453372	ENSG00000161405	ENST00000439167;ENST00000439016	.	.	.	5.72	4.73	0.59995	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999982	.	.	.	.	.	.	T	0.51236	-0.8731	3	.	.	.	-8.8222	9.9806	0.41811	0.0716:0.1395:0.7888:0.0	rs907092;rs3751904;rs17607446;rs56570169;rs58485549;rs907092	.	.	.	L	353;392	.	.	P	-	2	0	IKZF3	35175785	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	2.032000	0.41127	1.382000	0.46385	0.655000	0.94253	CCG	G|0.660;A|0.340	0.340	strong		0.562	IKZF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257004.2	NM_012481	
ZNF699	374879	hgsc.bcm.edu	37	19	9408658	9408658	+	Silent	SNP	G	G	A	rs73920733	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:9408658G>A	ENST00000591998.1	-	4	412	c.184C>T	c.(184-186)Cta>Tta	p.L62L	ZNF699_ENST00000308650.3_Silent_p.L62L			Q32M78	ZN699_HUMAN	zinc finger protein 699	62	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)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(7)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	24						GGTGTGTGTAGCGGATACCCT	0.453													G|||	559	0.111621	0.2201	0.072	5008	,	,		13896	0.0228		0.0865	False		,,,				2504	0.1104				p.L62L		Atlas-SNP	.											.	ZNF699	67	.	0			c.C184T						PASS	.	G		845,2951		89,667,1142	100.0	95.0	96.0		184	-2.7	0.0	19	dbSNP_130	96	717,7515		21,675,3420	no	coding-synonymous	ZNF699	NM_198535.1		110,1342,4562	AA,AG,GG		8.7099,22.2603,12.9864		62/643	9408658	1562,10466	1898	4116	6014	SO:0001819	synonymous_variant	374879	exon3			TGTGTAGCGGATA	BC109268	CCDS42495.1	19p13.2	2013-01-08				ENSG00000196110		"""Zinc fingers, C2H2-type"", ""-"""	24750	protein-coding gene	gene with protein product	hangover homolog (Drosophila)	609571				16940975	Standard	NM_198535		Approved	FLJ38144, hang	uc002mlc.1	Q32M78		ENST00000591998.1:c.184C>T	19.37:g.9408658G>A		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	77	35	0.454545	NM_198535	Q8N9A1	Silent	SNP	ENST00000591998.1	37	CCDS42495.1																																																																																			G|0.892;A|0.108	0.108	strong		0.453	ZNF699-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449010.1	NM_198535	
HERC2	8924	hgsc.bcm.edu	37	15	28386626	28386626	+	Silent	SNP	C	C	T	rs11636232	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:28386626C>T	ENST00000261609.7	-	78	12075	c.11967G>A	c.(11965-11967)caG>caA	p.Q3989Q		NM_004667.5	NP_004658.3			HECT and RLD domain containing E3 ubiquitin protein ligase 2											NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(3)|cervix(3)|endometrium(20)|kidney(11)|large_intestine(33)|lung(95)|ovary(7)|prostate(8)|skin(7)|upper_aerodigestive_tract(8)|urinary_tract(4)	204		all_lung(180;1.3e-11)|Breast(32;0.000194)|Colorectal(260;0.227)		all cancers(64;3.93e-09)|Epithelial(43;9.99e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0271)|GBM - Glioblastoma multiforme(186;0.0497)|Lung(196;0.199)		CTCCGATTAACTGCACGGGTC	0.537													c|||	429	0.0856629	0.0151	0.0908	5008	,	,		16725	0.0		0.3221	False		,,,				2504	0.0225				p.Q3989Q		Atlas-SNP	.											.	HERC2	501	.	0			c.G11967A						PASS	.	C		343,4063	176.6+/-205.7	11,321,1871	85.0	78.0	81.0		11967	1.9	0.6	15	dbSNP_120	81	3289,5311	493.0+/-373.5	636,2017,1647	no	coding-synonymous	HERC2	NM_004667.4		647,2338,3518	TT,TC,CC		38.2442,7.7848,27.9256		3989/4835	28386626	3632,9374	2203	4300	6503	SO:0001819	synonymous_variant	8924	exon78			GATTAACTGCACG	AF071172	CCDS10021.1	15q13	2012-02-23	2012-02-23		ENSG00000128731	ENSG00000128731			4868	protein-coding gene	gene with protein product		605837	"""hect domain and RLD 2"""			9949213	Standard	NM_004667		Approved	jdf2, p528, D15F37S1	uc001zbj.4	O95714	OTTHUMG00000129251	ENST00000261609.7:c.11967G>A	15.37:g.28386626C>T		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	121	58	0.479339	NM_004667		Silent	SNP	ENST00000261609.7	37	CCDS10021.1																																																																																			C|0.783;T|0.217	0.217	strong		0.537	HERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251358.2	NM_004667	
TBC1D26	353149	hgsc.bcm.edu	37	17	15645289	15645289	+	Missense_Mutation	SNP	G	G	A	rs17855672	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:15645289G>A	ENST00000437605.2	+	11	950	c.700G>A	c.(700-702)Ggc>Agc	p.G234S	ZNF286A_ENST00000413242.2_3'UTR|AC005324.6_ENST00000580194.1_RNA|AC005324.6_ENST00000434017.1_RNA|AC005324.6_ENST00000433873.1_RNA	NM_178571.4	NP_848666	Q86UD7	TBC26_HUMAN	TBC1 domain family, member 26	234	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.		G -> S (in dbSNP:rs17855672). {ECO:0000269|PubMed:15489334}.				Rab GTPase activator activity (GO:0005097)			endometrium(1)|large_intestine(1)|lung(4)|skin(1)	7				UCEC - Uterine corpus endometrioid carcinoma (92;0.0822)|READ - Rectum adenocarcinoma(1115;0.0222)|BRCA - Breast invasive adenocarcinoma(8;0.078)		TGGCTCGAGAGGCTCCTATCG	0.572													.|||	1233	0.246206	0.0809	0.2651	5008	,	,		18897	0.254		0.3946	False		,,,				2504	0.2955				p.G234S		Atlas-SNP	.											.	TBC1D26	16	.	0			c.G700A						PASS	.	G	SER/GLY	516,3532		35,446,1543	57.0	57.0	57.0		700	-0.5	0.0	17	dbSNP_123	57	3324,5042		636,2052,1495	yes	missense	TBC1D26	NM_178571.4	56	671,2498,3038	AA,AG,GG		39.7322,12.747,30.9328	probably-damaging	234/251	15645289	3840,8574	2024	4183	6207	SO:0001583	missense	353149	exon11			TCGAGAGGCTCCT		CCDS42265.1	17p11.2	2008-11-04			ENSG00000214946	ENSG00000214946			28745	protein-coding gene	gene with protein product						11347906	Standard	NM_178571		Approved	MGC51025	uc010cov.3	Q86UD7	OTTHUMG00000059071	ENST00000437605.2:c.700G>A	17.37:g.15645289G>A	ENSP00000410111:p.Gly234Ser	Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	57	25	0.438596	NM_178571	A8K929|Q4G172	Missense_Mutation	SNP	ENST00000437605.2	37	CCDS42265.1																																																																																			G|0.722;A|0.278	0.278	strong		0.572	TBC1D26-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_178571	
ALMS1	7840	hgsc.bcm.edu	37	2	73717567	73717567	+	Missense_Mutation	SNP	G	G	T	rs2056486	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:73717567G>T	ENST00000264448.6	+	10	8589	c.8478G>T	c.(8476-8478)agG>agT	p.R2826S	AC096546.1_ENST00000408160.1_RNA|ALMS1_ENST00000409009.1_Missense_Mutation_p.R2784S	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	2826					endosomal transport (GO:0016197)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of stress fiber assembly (GO:0051492)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)				breast(4)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(31)|lung(68)|ovary(4)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	147						CCAGTACCAGGGCAAATTGTA	0.393													T|||	1794	0.358227	0.8578	0.3905	5008	,	,		19374	0.0089		0.2266	False		,,,				2504	0.1554				p.R2826S		Atlas-SNP	.											.	ALMS1	384	.	0			c.G8478T						PASS	.	T	SER/ARG	2699,1011		994,711,150	60.0	57.0	58.0		8478	0.3	0.0	2	dbSNP_94	58	1935,6237		218,1499,2369	yes	missense	ALMS1	NM_015120.4	110	1212,2210,2519	TT,TG,GG		23.6784,27.2507,39.0002	benign	2826/4168	73717567	4634,7248	1855	4086	5941	SO:0001583	missense	7840	exon10			TACCAGGGCAAAT	AB002326	CCDS42697.1	2p13.1	2014-09-17			ENSG00000116127	ENSG00000116127			428	protein-coding gene	gene with protein product		606844				9063741	Standard	NM_015120		Approved	KIAA0328	uc002sje.1	Q8TCU4	OTTHUMG00000152812	ENST00000264448.6:c.8478G>T	2.37:g.73717567G>T	ENSP00000264448:p.Arg2826Ser	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	71	70	0.985915	NM_015120	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Missense_Mutation	SNP	ENST00000264448.6	37	CCDS42697.1	730	0.3342490842490842	418	0.8495934959349594	126	0.34806629834254144	8	0.013986013986013986	178	0.23482849604221637	T	0.011	-1.709383	0.00712	0.727493	0.236784	ENSG00000116127	ENST00000409009;ENST00000264448	T;T	0.04654	3.58;3.58	4.33	0.258	0.15578	.	0.517985	0.18103	N	0.151608	T	0.00012	0.0000	N	0.00729	-1.24	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	0.16070	-1.0415	9	0.02654	T	1	.	6.6891	0.23161	0.1571:0.0:0.4864:0.3565	rs2056486;rs17349629;rs17848863;rs52800268;rs60591669;rs2056486	2826;2784;2826	Q8TCU4-3;B8ZZJ3;Q8TCU4	.;.;ALMS1_HUMAN	S	2784;2826	ENSP00000386627:R2784S;ENSP00000264448:R2826S	ENSP00000264448:R2826S	R	+	3	2	ALMS1	73571075	0.000000	0.05858	0.000000	0.03702	0.746000	0.42486	-0.037000	0.12164	-0.189000	0.10482	-0.264000	0.10439	AGG	G|0.663;T|0.337	0.337	strong		0.393	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120	
BMPR2	659	hgsc.bcm.edu	37	2	203421199	203421199	+	Silent	SNP	G	G	A	rs1061157	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	55	0	0		WXS	Illumina HiSeq	Phase_I	38	18	0.473684	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	
CYP19A1	1588	hgsc.bcm.edu	37	15	51529112	51529112	+	Silent	SNP	T	T	C	rs700518	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:51529112T>C	ENST00000396402.1	-	3	393	c.240A>G	c.(238-240)gtA>gtG	p.V80V	CYP19A1_ENST00000260433.2_Silent_p.V80V|CYP19A1_ENST00000396404.4_Silent_p.V80V|RP11-108K3.1_ENST00000559909.1_lincRNA|CYP19A1_ENST00000559878.1_Silent_p.V80V|CYP19A1_ENST00000557858.1_Silent_p.V80V|CYP19A1_ENST00000405913.3_Silent_p.V80V	NM_000103.3	NP_000094.2	P11511	CP19A_HUMAN	cytochrome P450, family 19, subfamily A, polypeptide 1	80					androgen metabolic process (GO:0008209)|estrogen biosynthetic process (GO:0006703)|prostate gland growth (GO:0060736)|small molecule metabolic process (GO:0044281)|steroid biosynthetic process (GO:0006694)|steroid metabolic process (GO:0008202)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|membrane (GO:0016020)	aromatase activity (GO:0070330)|electron carrier activity (GO:0009055)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen (GO:0016712)|oxygen binding (GO:0019825)	p.V80V(1)		endometrium(1)|kidney(4)|large_intestine(9)|lung(11)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	33				all cancers(107;0.000372)|GBM - Glioblastoma multiforme(94;0.0128)	Aminoglutethimide(DB00357)|Anastrozole(DB01217)|Betamethasone(DB00443)|Bifonazole(DB04794)|Buserelin(DB06719)|Carbimazole(DB00389)|Chlorphenesin(DB00856)|Clomifene(DB00882)|Clotrimazole(DB00257)|Cyproterone acetate(DB04839)|Danazol(DB01406)|Dexamethasone(DB01234)|Diethylstilbestrol(DB00255)|Dinoprostone(DB00917)|Drostanolone(DB00858)|Econazole(DB01127)|Edetic Acid(DB00974)|Etomidate(DB00292)|Exemestane(DB00990)|Ketoconazole(DB01026)|Letrozole(DB01006)|Levomethadyl Acetate(DB01227)|Levonorgestrel(DB00367)|Mefloquine(DB00358)|Melatonin(DB01065)|Methadone(DB00333)|Methyltestosterone(DB06710)|Miconazole(DB01110)|Nandrolone decanoate(DB08804)|Nandrolone phenpropionate(DB00984)|Nicotine(DB00184)|Paclitaxel(DB01229)|Raloxifene(DB00481)|Sulfathiazole(DB06147)|Tamoxifen(DB00675)|Terbinafine(DB00857)|Testolactone(DB00894)|Testosterone(DB00624)|Tioconazole(DB01007)|Trastuzumab(DB00072)	ATTCTCCATATACCCGGTTGT	0.488													C|||	1632	0.325879	0.1619	0.3156	5008	,	,		18329	0.4385		0.4692	False		,,,				2504	0.2914				p.V80V	Melanoma(142;1016 1807 39614 48966 51721)	Atlas-SNP	.											CYP19A1,NS,adenoma,0,2	CYP19A1	75	2	1	Substitution - coding silent(1)	stomach(1)	c.A240G						scavenged	.	C	,	941,3451	735.8+/-410.7	111,719,1366	130.0	125.0	126.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	240,240	4.1	1.0	15	dbSNP_86	126	4310,4276	575.0+/-390.2	1068,2174,1051	no	coding-synonymous,coding-synonymous	CYP19A1	NM_000103.3,NM_031226.2	,	1179,2893,2417	CC,CT,TT		49.802,21.4253,40.4608	,	80/504,80/504	51529112	5251,7727	2196	4293	6489	SO:0001819	synonymous_variant	1588	exon4			TCCATATACCCGG	D14473	CCDS10139.1	15q21	2009-01-26	2003-02-14	2003-02-28	ENSG00000137869	ENSG00000137869		"""Cytochrome P450s"""	2594	protein-coding gene	gene with protein product		107910	"""cytochrome P450, subfamily XIX (aromatization of androgens)"""	CYP19		8477708	Standard	NM_031226		Approved	ARO, P-450AROM, CPV1, ARO1, CYAR, aromatase	uc001zza.4	P11511	OTTHUMG00000131747	ENST00000396402.1:c.240A>G	15.37:g.51529112T>C		Somatic	176	2	0.0113636		WXS	Illumina HiSeq	Phase_I	134	134	1	NM_031226	Q16731|Q3B764|Q58FA0|Q8IYJ7	Silent	SNP	ENST00000396402.1	37	CCDS10139.1																																																																																			T|0.612;C|0.388	0.388	strong		0.488	CYP19A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254669.1		
OBSCN	84033	hgsc.bcm.edu	37	1	228492044	228492044	+	Intron	SNP	G	G	A	rs1150910	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:228492044G>A	ENST00000422127.1	+	44	11703				OBSCN_ENST00000284548.11_Intron|RP5-1139B12.4_ENST00000602778.1_RNA|OBSCN_ENST00000359599.6_3'UTR|OBSCN_ENST00000570156.2_Silent_p.E4681E|OBSCN_ENST00000366709.4_Intron|OBSCN_ENST00000366707.4_Silent_p.E1371E	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	60	0	0		WXS	Illumina HiSeq	Phase_I	48	15	0.3125	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	
COL7A1	1294	hgsc.bcm.edu	37	3	48623124	48623124	+	Splice_Site	SNP	G	G	A	rs2229819|rs35761247	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:48623124G>A	ENST00000328333.8	-	30	3937	c.3830C>T	c.(3829-3831)cCg>cTg	p.P1277L	COL7A1_ENST00000454817.1_Splice_Site_p.P1277L	NM_000094.3	NP_000085.1	Q02388	CO7A1_HUMAN	collagen, type VII, alpha 1	1277	Interrupted collagenous region.|Triple-helical region.		P -> L (in RDEB; dbSNP:rs35761247).		cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|collagen type VII trimer (GO:0005590)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	serine-type endopeptidase inhibitor activity (GO:0004867)			NS(3)|breast(8)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(57)|ovary(7)|prostate(5)|skin(9)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(5)	137				BRCA - Breast invasive adenocarcinoma(193;0.000293)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		GACACTCACCGGGAGGCCAGG	0.627													G|||	114	0.0227636	0.0038	0.0173	5008	,	,		16456	0.001		0.0517	False		,,,				2504	0.045				p.P1277L		Atlas-SNP	.											.	COL7A1	320	.	0			c.C3830T						PASS	.	G	LEU/PRO	44,4362	46.7+/-81.2	0,44,2159	115.0	132.0	126.0		3830	5.8	1.0	3	dbSNP_126	126	477,8123	139.5+/-196.2	10,457,3833	yes	missense-near-splice	COL7A1	NM_000094.3	98	10,501,5992	AA,AG,GG		5.5465,0.9986,4.0058	probably-damaging	1277/2945	48623124	521,12485	2203	4300	6503	SO:0001630	splice_region_variant	1294	exon30			CTCACCGGGAGGC	L02870	CCDS2773.1	3p21.1	2014-09-17	2008-08-01		ENSG00000114270	ENSG00000114270		"""Collagens"", ""Fibronectin type III domain containing"""	2214	protein-coding gene	gene with protein product	"""collagen VII, alpha-1 polypeptide"", ""LC collagen"""	120120	"""epidermolysis bullosa, dystrophic, dominant and recessive"""	EBDCT, EBD1, EBR1		1871109	Standard	NM_000094		Approved		uc003ctz.2	Q02388	OTTHUMG00000133541	ENST00000328333.8:c.3831+1C>T	3.37:g.48623124G>A		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	87	52	0.597701	NM_000094	Q14054|Q16507	Missense_Mutation	SNP	ENST00000328333.8	37	CCDS2773.1	56	0.02564102564102564	5	0.01016260162601626	9	0.024861878453038673	0	0.0	42	0.055408970976253295	G	13.72	2.322726	0.41096	0.009986	0.055465	ENSG00000114270	ENST00000328333;ENST00000454817	D;D	0.93859	-3.3;-3.3	5.81	5.81	0.92471	.	0.000000	0.45126	D	0.000385	D	0.82953	0.5149	M	0.78801	2.425	0.58432	D	0.999996	D	0.89917	1.0	D	0.91635	0.999	D	0.85280	0.1061	10	0.72032	D	0.01	.	18.2466	0.89988	0.0:0.0:1.0:0.0	rs35761247	1277	Q02388	CO7A1_HUMAN	L	1277	ENSP00000332371:P1277L;ENSP00000412569:P1277L	ENSP00000332371:P1277L	P	-	2	0	COL7A1	48598128	1.000000	0.71417	1.000000	0.80357	0.923000	0.55619	4.068000	0.57534	2.739000	0.93911	0.563000	0.77884	CCG	G|0.962;A|0.038	0.038	strong		0.627	COL7A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257519.1	NM_000094	Missense_Mutation
PUM1	9698	hgsc.bcm.edu	37	1	31426815	31426815	+	Silent	SNP	A	A	G	rs2275741	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:31426815A>G	ENST00000257075.5	-	15	2430	c.2337T>C	c.(2335-2337)aaT>aaC	p.N779N	PUM1_ENST00000373747.3_Silent_p.N780N|PUM1_ENST00000423018.2_Silent_p.N635N|PUM1_ENST00000424085.2_Silent_p.N537N|PUM1_ENST00000373741.4_Silent_p.N815N|PUM1_ENST00000373742.2_Silent_p.N720N|PUM1_ENST00000426105.2_Silent_p.N779N|PUM1_ENST00000440538.2_Silent_p.N753N	NM_014676.2	NP_055491.1	Q14671	PUM1_HUMAN	pumilio RNA-binding family member 1	779	Ser-rich.				membrane organization (GO:0061024)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of translation (GO:0006417)	cytosol (GO:0005829)	poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(2)|endometrium(8)|kidney(4)|large_intestine(8)|lung(17)|ovary(2)|pancreas(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	48		Colorectal(325;0.0211)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0308)|all_neural(195;0.0381)|Breast(348;0.0848)|Medulloblastoma(700;0.123)		STAD - Stomach adenocarcinoma(196;0.0232)|READ - Rectum adenocarcinoma(331;0.0681)		TTCCACTGCCATTCGTGAGTC	0.512													G|||	1790	0.357428	0.2859	0.4726	5008	,	,		19157	0.3462		0.3767	False		,,,				2504	0.364				p.N779N		Atlas-SNP	.											.	PUM1	107	.	0			c.T2337C						PASS	.	G	,	1356,3050	690.7+/-405.3	226,904,1073	80.0	83.0	82.0		2337,2337	-4.6	0.8	1	dbSNP_100	82	3437,5163	637.2+/-399.2	680,2077,1543	no	coding-synonymous,coding-synonymous	PUM1	NM_001020658.1,NM_014676.2	,	906,2981,2616	GG,GA,AA		39.9651,30.7762,36.8522	,	779/1189,779/1187	31426815	4793,8213	2203	4300	6503	SO:0001819	synonymous_variant	9698	exon15			ACTGCCATTCGTG	AF315592	CCDS338.1, CCDS44099.1	1p35.2	2013-09-02	2013-09-02		ENSG00000134644	ENSG00000134644			14957	protein-coding gene	gene with protein product		607204	"""pumilio (Drosophila) homolog 1"", ""pumilio homolog 1 (Drosophila)"""				Standard	NM_001020658		Approved	PUMH1, KIAA0099	uc001bsh.1	Q14671	OTTHUMG00000003795	ENST00000257075.5:c.2337T>C	1.37:g.31426815A>G		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	94	50	0.531915	NM_014676	A8K6W4|B4DG92|D3DPN3|E9PCJ0|Q53HH5|Q5VXY7|Q9HAN1	Silent	SNP	ENST00000257075.5	37	CCDS338.1	791	0.36217948717948717	144	0.2926829268292683	162	0.44751381215469616	197	0.34440559440559443	288	0.37994722955145116	G	8.399	0.841585	0.16963	0.307762	0.399651	ENSG00000134644	ENST00000525843;ENST00000498419	.	.	.	6.02	-4.63	0.03359	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.14924	-1.0455	3	.	.	.	-8.7022	16.103	0.81201	0.8127:0.0:0.1873:0.0	rs2275741;rs17851037;rs59426957;rs2275741	.	.	.	R	718;491	.	.	W	-	1	0	PUM1	31199402	0.053000	0.20554	0.831000	0.32960	0.925000	0.55904	-0.433000	0.06948	-1.276000	0.02414	-1.551000	0.00897	TGG	A|0.647;G|0.353	0.353	strong		0.512	PUM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000010671.1		
NUTM1	256646	hgsc.bcm.edu	37	15	34649336	34649336	+	Missense_Mutation	SNP	G	G	A	rs149177074	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:34649336G>A	ENST00000333756.4	+	7	3198	c.3043G>A	c.(3043-3045)Gag>Aag	p.E1015K	NUTM1_ENST00000537011.1_Missense_Mutation_p.E1043K|NUTM1_ENST00000438749.3_Missense_Mutation_p.E1033K	NM_175741.1	NP_786883	Q86Y26	NUTM1_HUMAN	NUT midline carcinoma, family member 1	1015						cytoplasm (GO:0005737)|nucleus (GO:0005634)											GGAAGAGGATGAGGAACTCTC	0.498													G|||	8	0.00159744	0.0	0.0029	5008	,	,		20984	0.0		0.006	False		,,,				2504	0.0				p.E1015K		Atlas-SNP	.											C15orf55_ENST00000333756,NS,lymphoid_neoplasm,0,1	C15orf55	110	1	0			c.G3043A						PASS	.	G	LYS/GLU	4,4398	9.9+/-24.2	0,4,2197	76.0	61.0	66.0		3043	4.3	1.0	15	dbSNP_134	66	31,8565	22.8+/-68.1	0,31,4267	yes	missense	C15orf55	NM_175741.1	56	0,35,6464	AA,AG,GG		0.3606,0.0909,0.2693	benign	1015/1133	34649336	35,12963	2201	4298	6499	SO:0001583	missense	256646	exon7			GAGGATGAGGAAC	AF482429	CCDS32190.1, CCDS61584.1, CCDS61585.1	15q14	2014-01-28	2013-03-14	2013-03-14	ENSG00000184507	ENSG00000184507			29919	protein-coding gene	gene with protein product	"""nuclear protein in testis"""	608963	"""chromosome 15 open reading frame 55"""	C15orf55		12543779	Standard	NM_175741		Approved	NUT, DKFZp434O192, FAM22H	uc001zif.3	Q86Y26	OTTHUMG00000172348	ENST00000333756.4:c.3043G>A	15.37:g.34649336G>A	ENSP00000329448:p.Glu1015Lys	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	52	27	0.519231	NM_175741	B4DZ00|B7Z7Y4|E7EVE8|F5H4I6|Q86YS8|Q8N7F2|Q9NTB3	Missense_Mutation	SNP	ENST00000333756.4	37	CCDS32190.1	5	0.0022893772893772895	0	0.0	2	0.0055248618784530384	0	0.0	3	0.00395778364116095	G	15.74	2.923315	0.52653	9.09E-4	0.003606	ENSG00000184507	ENST00000537011;ENST00000438749;ENST00000333756	T;T;T	0.13307	2.62;2.6;2.61	5.2	4.28	0.50868	.	0.557345	0.16563	N	0.208980	T	0.11324	0.0276	L	0.61387	1.9	0.33479	D	0.58722	B;B;B	0.29085	0.232;0.154;0.192	B;B;B	0.27076	0.059;0.076;0.031	T	0.10222	-1.0639	10	0.66056	D	0.02	.	9.6167	0.39696	0.0944:0.0:0.9056:0.0	.	1033;1043;1015	E7EVE8;F5H4I6;Q86Y26	.;.;NUT_HUMAN	K	1043;1033;1015	ENSP00000444896:E1043K;ENSP00000407031:E1033K;ENSP00000329448:E1015K	ENSP00000329448:E1015K	E	+	1	0	C15orf55	32436628	0.965000	0.33210	0.991000	0.47740	0.842000	0.47809	1.928000	0.40104	1.422000	0.47177	0.655000	0.94253	GAG	G|0.998;A|0.002	0.002	strong		0.498	NUTM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418026.1	NM_175741	
FAM83A	84985	hgsc.bcm.edu	37	8	124206324	124206324	+	Missense_Mutation	SNP	G	G	A	rs7813708	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:124206324G>A	ENST00000518448.1	+	4	2723	c.709G>A	c.(709-711)Gct>Act	p.A237T	FAM83A_ENST00000536633.1_Missense_Mutation_p.A237T|FAM83A_ENST00000546351.1_Missense_Mutation_p.A181T|FAM83A_ENST00000276699.6_Missense_Mutation_p.A237T|FAM83A_ENST00000522648.1_Missense_Mutation_p.A181T|FAM83A_ENST00000318462.6_Missense_Mutation_p.A237T			Q86UY5	FA83A_HUMAN	family with sequence similarity 83, member A	237			A -> T (in dbSNP:rs7813708). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.2}.							breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(3)|ovary(3)|prostate(2)|skin(1)	17	Lung NSC(37;1.55e-09)|Ovarian(258;0.0205)		STAD - Stomach adenocarcinoma(47;0.00527)			CAGGAAATTCGCTGGCCAAAT	0.478													G|||	784	0.15655	0.0219	0.1988	5008	,	,		21893	0.2133		0.2008	False		,,,				2504	0.2045				p.A237T		Atlas-SNP	.											.	FAM83A	64	.	0			c.G709A						PASS	.	G	THR/ALA,THR/ALA	254,4152	148.0+/-182.4	7,240,1956	139.0	117.0	125.0		709,709	1.2	0.3	8	dbSNP_116	125	1791,6809	324.7+/-316.6	191,1409,2700	yes	missense,missense	FAM83A	NM_032899.4,NM_207006.1	58,58	198,1649,4656	AA,AG,GG		20.8256,5.7649,15.7235	benign,benign	237/435,237/368	124206324	2045,10961	2203	4300	6503	SO:0001583	missense	84985	exon3			AAATTCGCTGGCC	BC052300	CCDS6339.1, CCDS6340.1, CCDS75784.1	8q24.13	2014-03-13			ENSG00000147689	ENSG00000147689			28210	protein-coding gene	gene with protein product						22886303	Standard	XM_005251087		Approved	MGC14128, BJ-TSA-9	uc003ypx.3	Q86UY5	OTTHUMG00000165083	ENST00000518448.1:c.709G>A	8.37:g.124206324G>A	ENSP00000428876:p.Ala237Thr	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	86	16	0.186047	NM_032899	Q71HL2|Q8N7I1|Q96I47	Missense_Mutation	SNP	ENST00000518448.1	37	CCDS6340.1	389	0.17811355311355312	14	0.028455284552845527	70	0.19337016574585636	150	0.26223776223776224	155	0.20448548812664907	G	7.351	0.622953	0.14193	0.057649	0.208256	ENSG00000147689	ENST00000518448;ENST00000546351;ENST00000536633;ENST00000318462;ENST00000522648;ENST00000276699	T;T;T;T;T;T	0.10860	2.83;2.83;2.83;2.83;2.83;2.83	5.62	1.17	0.20885	.	0.346115	0.30455	N	0.009597	T	0.00012	0.0000	N	0.17082	0.46	0.48632	P	3.1800000000004047E-4	B;B;B	0.31209	0.313;0.066;0.048	B;B;B	0.22601	0.03;0.009;0.04	T	0.41215	-0.9521	9	0.02654	T	1	-15.2663	14.8562	0.70338	0.0:0.0:0.4168:0.5832	rs7813708;rs13279798;rs17377444;rs17845132;rs17857935;rs52838187;rs59588076;rs7813708	181;237;237	Q86UY5-2;Q86UY5-3;Q86UY5	.;.;FA83A_HUMAN	T	237;181;237;237;181;237	ENSP00000428876:A237T;ENSP00000440565:A181T;ENSP00000445218:A237T;ENSP00000323034:A237T;ENSP00000427979:A181T;ENSP00000276699:A237T	ENSP00000276699:A237T	A	+	1	0	FAM83A	124275505	0.211000	0.23529	0.302000	0.25058	0.914000	0.54420	1.323000	0.33701	0.273000	0.22049	0.555000	0.69702	GCT	G|0.835;A|0.165	0.165	strong		0.478	FAM83A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381737.1	NM_032899	
FREM1	158326	hgsc.bcm.edu	37	9	14846036	14846036	+	Missense_Mutation	SNP	C	C	G	rs2779500	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:14846036C>G	ENST00000380880.3	-	8	2098	c.1315G>C	c.(1315-1317)Gtt>Ctt	p.V439L	FREM1_ENST00000380881.4_Missense_Mutation_p.V440L|FREM1_ENST00000422223.2_Missense_Mutation_p.V439L			Q5H8C1	FREM1_HUMAN	FRAS1 related extracellular matrix 1	439			V -> L (in dbSNP:rs2779500). {ECO:0000269|PubMed:15878328}.		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)	p.V440L(1)		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)		TTGTCGACAACCTGAAACTGT	0.488													C|||	2508	0.500799	0.4576	0.5	5008	,	,		19643	0.2708		0.6233	False		,,,				2504	0.6708				p.V439L		Atlas-SNP	.											FREM1,NS,carcinoma,0,1	FREM1	261	1	1	Substitution - Missense(1)	stomach(1)	c.G1315C						PASS	.	C	LEU/VAL	2038,2146		517,1004,571	60.0	65.0	63.0		1315	1.0	1.0	9	dbSNP_100	63	5134,3328		1564,2006,661	yes	missense	FREM1	NM_144966.5	32	2081,3010,1232	GG,GC,CC		39.3288,48.7094,43.2864	benign	439/2180	14846036	7172,5474	2092	4231	6323	SO:0001583	missense	158326	exon9			CGACAACCTGAAA	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.1315G>C	9.37:g.14846036C>G	ENSP00000370262:p.Val439Leu	Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	197	86	0.436548	NM_144966	B7ZBX4|Q5VV00|Q5VV01|Q6MZI4|Q8NEG9|Q96LI3	Missense_Mutation	SNP	ENST00000380880.3	37	CCDS47952.1	1053	0.48214285714285715	219	0.4451219512195122	187	0.5165745856353591	175	0.30594405594405594	472	0.6226912928759895	C	8.581	0.882357	0.17467	0.487094	0.606712	ENSG00000164946	ENST00000380881;ENST00000422223;ENST00000380880	T;T;T	0.42131	0.98;0.98;0.98	4.65	0.988	0.19796	.	0.353172	0.31221	N	0.008034	T	0.00012	0.0000	N	0.25201	0.72	0.32668	P	0.5171399999999999	B	0.15141	0.012	B	0.19391	0.025	T	0.42982	-0.9419	9	0.41790	T	0.15	-6.7469	10.5066	0.44836	0.0:0.2214:0.0:0.7786	rs2779500;rs2779500	439	Q5H8C1	FREM1_HUMAN	L	440;439;439	ENSP00000370263:V440L;ENSP00000412940:V439L;ENSP00000370262:V439L	ENSP00000370257:V442L	V	-	1	0	FREM1	14836036	1.000000	0.71417	0.994000	0.49952	0.112000	0.19704	1.299000	0.33424	-0.017000	0.14103	-1.214000	0.01621	GTT	C|0.496;G|0.504	0.504	strong		0.488	FREM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339474.2	NM_144966	
FAM13A	10144	hgsc.bcm.edu	37	4	89653257	89653257	+	Silent	SNP	G	G	A	rs1801915	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:89653257G>A	ENST00000264344.5	-	22	2946	c.2739C>T	c.(2737-2739)gaC>gaT	p.D913D	FAM13A-AS1_ENST00000500765.1_RNA|FAM13A_ENST00000513837.1_Silent_p.D559D|FAM13A_ENST00000508369.1_Silent_p.D587D|FAM13A_ENST00000395002.2_Silent_p.D559D|FAM13A_ENST00000511976.1_Silent_p.D499D|FAM13A_ENST00000503556.1_Silent_p.D573D	NM_014883.3	NP_055698.2	O94988	FA13A_HUMAN	family with sequence similarity 13, member A	913					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						CTTCGAATTGGTCCAGAAAGC	0.458													G|||	987	0.197085	0.2042	0.1931	5008	,	,		1847	0.2321		0.1561	False		,,,				2504	0.1963				p.D913D		Atlas-SNP	.											.	FAM13A	181	.	0			c.C2739T						PASS	.	G	,	833,3573	329.3+/-301.0	77,679,1447	166.0	141.0	149.0		1761,2739	4.5	1.0	4	dbSNP_89	149	1261,7339	251.8+/-278.1	96,1069,3135	no	coding-synonymous,coding-synonymous	FAM13A	NM_001015045.1,NM_014883.2	,	173,1748,4582	AA,AG,GG		14.6628,18.906,16.1003	,	587/698,913/1024	89653257	2094,10912	2203	4300	6503	SO:0001819	synonymous_variant	10144	exon22			GAATTGGTCCAGA	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.2739C>T	4.37:g.89653257G>A		Somatic	243	0	0		WXS	Illumina HiSeq	Phase_I	210	102	0.485714	NM_014883	B4DLC1|Q24JP0|Q5PR21|Q8NBA3	Silent	SNP	ENST00000264344.5	37	CCDS34029.1																																																																																			G|0.831;A|0.169	0.169	strong		0.458	FAM13A-022	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363371.1		
COL22A1	169044	hgsc.bcm.edu	37	8	139749799	139749799	+	Missense_Mutation	SNP	G	G	T	rs10111520	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:139749799G>T	ENST00000303045.6	-	23	2553	c.2107C>A	c.(2107-2109)Cca>Aca	p.P703T	COL22A1_ENST00000435777.1_Missense_Mutation_p.P703T	NM_152888.1	NP_690848.1	Q8NFW1	COMA1_HUMAN	collagen, type XXII, alpha 1	703	Collagen-like 4.|Gly-rich.|Pro-rich.		P -> T (in dbSNP:rs10111520).		extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(14)|large_intestine(29)|lung(107)|ovary(13)|pancreas(1)|prostate(3)|skin(12)|upper_aerodigestive_tract(15)|urinary_tract(4)	211	all_epithelial(106;1.55e-12)|Lung NSC(106;1.67e-05)|all_lung(105;3.39e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0517)			ATTCCAGGTGGTCCCATGTCA	0.448										HNSCC(7;0.00092)			G|||	240	0.0479233	0.0083	0.1066	5008	,	,		19565	0.0526		0.0507	False		,,,				2504	0.0521				p.P703T		Atlas-SNP	.											.	COL22A1	390	.	0			c.C2107A						PASS	.	G	THR/PRO	107,4299	85.3+/-124.0	0,107,2096	95.0	93.0	93.0		2107	-1.2	0.0	8	dbSNP_119	93	576,8024	155.1+/-209.2	25,526,3749	yes	missense	COL22A1	NM_152888.1	38	25,633,5845	TT,TG,GG		6.6977,2.4285,5.2514	benign	703/1627	139749799	683,12323	2203	4300	6503	SO:0001583	missense	169044	exon23			CAGGTGGTCCCAT	AF406780	CCDS6376.1	8q24.3	2013-01-16			ENSG00000169436	ENSG00000169436		"""Collagens"""	22989	protein-coding gene	gene with protein product		610026					Standard	NM_152888		Approved		uc003yvd.3	Q8NFW1	OTTHUMG00000150035	ENST00000303045.6:c.2107C>A	8.37:g.139749799G>T	ENSP00000303153:p.Pro703Thr	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	95	26	0.273684	NM_152888	B7ZMH0|C9K0G4|Q8IVT9	Missense_Mutation	SNP	ENST00000303045.6	37	CCDS6376.1	108	0.04945054945054945	9	0.018292682926829267	35	0.09668508287292818	27	0.0472027972027972	37	0.048812664907651716	G	7.365	0.625676	0.14257	0.024285	0.066977	ENSG00000169436	ENST00000303045;ENST00000435777;ENST00000545577	D;D	0.97710	-4.5;-4.5	3.16	-1.25	0.09405	.	0.628214	0.12886	U	0.431056	T	0.43233	0.1238	L	0.54863	1.705	0.09310	N	1	B;B	0.23650	0.073;0.089	B;B	0.22880	0.025;0.042	T	0.70992	-0.4721	10	0.14252	T	0.57	.	7.1842	0.25791	0.1183:0.5885:0.2932:0.0	rs10111520;rs52810650;rs10111520	703;703	Q8NFW1-2;Q8NFW1	.;COMA1_HUMAN	T	703;703;416	ENSP00000303153:P703T;ENSP00000387655:P703T	ENSP00000303153:P703T	P	-	1	0	COL22A1	139818981	0.004000	0.15560	0.001000	0.08648	0.715000	0.41141	-0.750000	0.04808	-0.287000	0.09064	0.561000	0.74099	CCA	G|0.948;T|0.052	0.052	strong		0.448	COL22A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000315905.2	XM_291257	
GABRG3	2567	hgsc.bcm.edu	37	15	27765249	27765249	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:27765249A>G	ENST00000333743.6	+	7	1098	c.844A>G	c.(844-846)Acg>Gcg	p.T282A	RP11-100M12.3_ENST00000556642.1_RNA	NM_033223.4	NP_150092.2	Q99928	GBRG3_HUMAN	gamma-aminobutyric acid (GABA) A receptor, gamma 3	282					gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|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)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(23)|skin(1)|upper_aerodigestive_tract(4)	42		all_lung(180;4.58e-12)|Breast(32;0.000625)|Colorectal(260;0.235)		all cancers(64;3.15e-07)|Epithelial(43;1.17e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0261)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|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)	AAAAGATGCTACGCCAGCAAG	0.348																																					p.T282A	NSCLC(114;800 1656 7410 37729 45293)	Atlas-SNP	.											.	GABRG3	115	.	0			c.A844G						PASS	.						63.0	59.0	60.0					15																	27765249		1840	4106	5946	SO:0001583	missense	2567	exon7			GATGCTACGCCAG		CCDS45195.1, CCDS59251.1	15q12	2012-06-22			ENSG00000182256	ENSG00000182256		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	4088	protein-coding gene	gene with protein product	"""GABA(G) receptor, gamma 3"""	600233				7601451	Standard	NM_033223		Approved		uc001zbg.2	Q99928	OTTHUMG00000044462	ENST00000333743.6:c.844A>G	15.37:g.27765249A>G	ENSP00000331912:p.Thr282Ala	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	99	4	0.040404	NM_033223	G3V594|Q9HD46|Q9NYT2	Missense_Mutation	SNP	ENST00000333743.6	37	CCDS45195.1	.	.	.	.	.	.	.	.	.	.	A	13.53	2.264631	0.40095	.	.	ENSG00000182256	ENST00000333743;ENST00000554696	D;D	0.86097	-2.07;-2.07	5.39	5.39	0.77823	Neurotransmitter-gated ion-channel transmembrane domain (2);	0.101026	0.64402	D	0.000002	T	0.72946	0.3524	N	0.13168	0.305	0.80722	D	1	B	0.20780	0.048	B	0.28305	0.088	T	0.67448	-0.5668	10	0.25751	T	0.34	.	9.2407	0.37495	0.9204:0.0:0.0795:0.0	.	282	Q99928	GBRG3_HUMAN	A	282;224	ENSP00000331912:T282A;ENSP00000451862:T224A	ENSP00000331912:T282A	T	+	1	0	GABRG3	25438844	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	4.888000	0.63164	2.260000	0.74910	0.528000	0.53228	ACG	.	.	none		0.348	GABRG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103584.2		
BSN	8927	hgsc.bcm.edu	37	3	49693972	49693972	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:49693972C>T	ENST00000296452.4	+	5	7097	c.6983C>T	c.(6982-6984)cCt>cTt	p.P2328L		NM_003458.3	NP_003449.2	Q9UPA5	BSN_HUMAN	bassoon presynaptic cytomatrix protein	2328					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)		GCCCCAGCTCCTGCCCCACTA	0.652																																					p.P2328L		Atlas-SNP	.											.	BSN	272	.	0			c.C6983T						PASS	.						8.0	9.0	9.0					3																	49693972		2177	4270	6447	SO:0001583	missense	8927	exon5			CAGCTCCTGCCCC	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.6983C>T	3.37:g.49693972C>T	ENSP00000296452:p.Pro2328Leu	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	45	18	0.4	NM_003458	O43161|Q7LGH3	Missense_Mutation	SNP	ENST00000296452.4	37	CCDS2800.1	.	.	.	.	.	.	.	.	.	.	C	3.630	-0.075656	0.07184	.	.	ENSG00000164061	ENST00000296452	T	0.17370	2.28	5.38	5.38	0.77491	.	0.902375	0.09734	N	0.762721	T	0.14013	0.0339	N	0.24115	0.695	0.53688	D	0.999974	B	0.27559	0.181	B	0.21708	0.036	T	0.11348	-1.0591	10	0.30854	T	0.27	-0.369	14.5099	0.67776	0.0:1.0:0.0:0.0	.	2328	Q9UPA5	BSN_HUMAN	L	2328	ENSP00000296452:P2328L	ENSP00000296452:P2328L	P	+	2	0	BSN	49668976	0.002000	0.14202	0.055000	0.19348	0.331000	0.28603	1.786000	0.38694	2.813000	0.96785	0.655000	0.94253	CCT	.	.	none		0.652	BSN-001	KNOWN	NMD_exception|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000258164.1	NM_003458	
FAN1	22909	hgsc.bcm.edu	37	15	31197564	31197564	+	Missense_Mutation	SNP	G	G	A	rs4779794	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:31197564G>A	ENST00000362065.4	+	2	989	c.698G>A	c.(697-699)gGa>gAa	p.G233E	FAN1_ENST00000561594.1_Missense_Mutation_p.G233E|FAN1_ENST00000565466.1_Missense_Mutation_p.G233E|FAN1_ENST00000561607.1_Missense_Mutation_p.G233E	NM_014967.4	NP_055782.3	Q9Y2M0	FAN1_HUMAN	FANCD2/FANCI-associated nuclease 1	233			G -> E (in dbSNP:rs4779794). {ECO:0000269|PubMed:15489334}.		DNA catabolic process, endonucleolytic (GO:0000737)|DNA repair (GO:0006281)|double-strand break repair via homologous recombination (GO:0000724)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA incision (GO:0033683)	nucleus (GO:0005634)	5'-3' exonuclease activity (GO:0008409)|5'-flap endonuclease activity (GO:0017108)|DNA binding (GO:0003677)|magnesium ion binding (GO:0000287)|phosphodiesterase I activity (GO:0004528)|ubiquitin binding (GO:0043130)			autonomic_ganglia(2)|breast(2)|cervix(2)|endometrium(7)|kidney(1)|large_intestine(6)|lung(8)|skin(1)	29						ATGGTAAGAGGAAGTAAAATA	0.408								Direct reversal of damage					G|||	2116	0.422524	0.0401	0.4539	5008	,	,		21085	0.7679		0.4374	False		,,,				2504	0.546				p.G233E		Atlas-SNP	.											FAN1,NS,carcinoma,+1,1	FAN1	77	1	0			c.G698A						PASS	.	G	GLU/GLY,GLU/GLY,GLU/GLY,GLU/GLY	494,3910	225.6+/-241.4	34,426,1742	53.0	52.0	52.0		698,698,698,698	-2.2	0.0	15	dbSNP_111	52	3661,4939	522.8+/-380.2	760,2141,1399	yes	missense,missense,missense,missense	FAN1	NM_001146094.1,NM_001146095.1,NM_001146096.1,NM_014967.4	98,98,98,98	794,2567,3141	AA,AG,GG		42.5698,11.2171,31.9517	benign,benign,benign,benign	233/534,233/534,233/534,233/1018	31197564	4155,8849	2202	4300	6502	SO:0001583	missense	22909	exon2			TAAGAGGAAGTAA		CCDS32186.1, CCDS58344.1	15q13.2-q13.3	2010-08-04	2010-08-04	2010-08-04		ENSG00000198690			29170	protein-coding gene	gene with protein product		613534	"""KIAA1018"", ""myotubularin related protein 15"""	KIAA1018, MTMR15		20603015, 20603016, 20603073	Standard	NM_014967		Approved		uc001zff.3	Q9Y2M0		ENST00000362065.4:c.698G>A	15.37:g.31197564G>A	ENSP00000354497:p.Gly233Glu	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	61	61	1	NM_001146095	A8K4M2|Q86WU8	Missense_Mutation	SNP	ENST00000362065.4	37	CCDS32186.1	985	0.451007326007326	28	0.056910569105691054	157	0.43370165745856354	456	0.7972027972027972	344	0.45382585751978893	G	1.907	-0.451723	0.04572	0.112171	0.425698	ENSG00000198690	ENST00000362065	T	0.41065	1.01	5.18	-2.16	0.07080	.	1.092420	0.06802	N	0.788905	T	0.00012	0.0000	L	0.60455	1.87	0.80722	P	0.0	B;B	0.33583	0.146;0.418	B;B	0.30855	0.026;0.121	T	0.48547	-0.9026	9	0.02654	T	1	-2.2897	6.1061	0.20073	0.5001:0.0:0.3751:0.1248	rs4779794;rs17227870;rs57472252;rs4779794	233;233	Q9Y2M0;Q9Y2M0-2	FAN1_HUMAN;.	E	233	ENSP00000354497:G233E	ENSP00000354497:G233E	G	+	2	0	FAN1	28984856	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.063000	0.11655	-0.319000	0.08652	-0.126000	0.14955	GGA	G|0.626;A|0.374	0.374	strong		0.408	FAN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430740.1	NM_014967	
TRIM16	10626	hgsc.bcm.edu	37	17	15554504	15554504	+	Silent	SNP	G	G	A	rs4792642	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:15554504G>A	ENST00000578237.1	-	6	1275	c.420C>T	c.(418-420)gcC>gcT	p.A140A	TRIM16_ENST00000336708.7_Silent_p.A140A|TRIM16_ENST00000416464.2_Intron|RP11-640I15.1_ENST00000584540.1_RNA|RP11-385D13.1_ENST00000455584.2_Silent_p.A140A|TRIM16_ENST00000581224.1_Intron			O95361	TRI16_HUMAN	tripartite motif containing 16	140					histone H3 acetylation (GO:0043966)|histone H4 acetylation (GO:0043967)|positive regulation of interleukin-1 beta secretion (GO:0050718)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of retinoic acid receptor signaling pathway (GO:0048386)|positive regulation of transcription, DNA-templated (GO:0045893)|response to growth hormone (GO:0060416)|response to organophosphorus (GO:0046683)|response to retinoic acid (GO:0032526)	cytoplasm (GO:0005737)|PML body (GO:0016605)	DNA binding (GO:0003677)|interleukin-1 binding (GO:0019966)|NACHT domain binding (GO:0032089)|zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(4)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(1)	19				UCEC - Uterine corpus endometrioid carcinoma (92;0.0839)|Epithelial(1;8.4e-29)|all cancers(1;3.06e-28)|Colorectal(1;1.57e-19)|OV - Ovarian serous cystadenocarcinoma(1;6.1e-17)|COAD - Colon adenocarcinoma(1;3.38e-12)|READ - Rectum adenocarcinoma(2;1.46e-05)|BRCA - Breast invasive adenocarcinoma(8;0.0559)		GGCAGCAGAAGGCAGACAGTG	0.602													G|||	1384	0.276358	0.2829	0.281	5008	,	,		21480	0.3125		0.2107	False		,,,				2504	0.2945				p.A140A		Atlas-SNP	.											.	TRIM16	45	.	0			c.C420T						PASS	.	G		1318,3088	443.3+/-347.0	205,908,1090	147.0	137.0	140.0		420	4.4	1.0	17	dbSNP_111	140	1949,6651	343.2+/-324.8	214,1521,2565	no	coding-synonymous	TRIM16	NM_006470.3		419,2429,3655	AA,AG,GG		22.6628,29.9138,25.1192		140/565	15554504	3267,9739	2203	4300	6503	SO:0001819	synonymous_variant	10626	exon4			GCAGAAGGCAGAC	AF096870	CCDS11171.1	17p11.2	2011-04-20	2011-01-25		ENSG00000221926	ENSG00000221926		"""Tripartite motif containing / Tripartite motif containing"""	17241	protein-coding gene	gene with protein product	"""estrogen-responsive B box protein"""	609505	"""tripartite motif-containing 16"""			11331580	Standard	NM_006470		Approved	EBBP	uc002gor.1	O95361	OTTHUMG00000059067	ENST00000578237.1:c.420C>T	17.37:g.15554504G>A		Somatic	118	1	0.00847458		WXS	Illumina HiSeq	Phase_I	78	77	0.987179	NM_006470	Q6IAL8|Q7Z6I2|Q96BE8|Q96J43	Silent	SNP	ENST00000578237.1	37	CCDS11171.1	541	0.24771062271062272	134	0.27235772357723576	90	0.24861878453038674	159	0.27797202797202797	158	0.20844327176781002	g	10.27	1.304808	0.23736	0.299138	0.226628	ENSG00000251537	ENST00000455584	.	.	.	5.47	4.44	0.53790	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999375809	.	.	.	.	.	.	T	0.07462	-1.0771	3	.	.	.	.	13.5372	0.61653	0.0:0.2408:0.7592:0.0	rs4792642;rs4792642	.	.	.	L	155	.	.	P	-	2	0	RP11-385D13.1	15495229	0.844000	0.29557	0.998000	0.56505	0.842000	0.47809	0.296000	0.19083	2.563000	0.86464	0.563000	0.77884	CCT	G|0.746;A|0.254	0.254	strong		0.602	TRIM16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130700.2	NM_006470	
PRR21	643905	hgsc.bcm.edu	37	2	240982379	240982379	+	Silent	SNP	T	T	C	rs138056768		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:240982379T>C	ENST00000408934.1	-	1	20	c.21A>G	c.(19-21)acA>acG	p.T7T		NM_001080835.1	NP_001074304.1	Q8WXC7	PRR21_HUMAN	proline rich 21	7										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						GATGAAGAGCTGTGGATGAAC	0.572																																					p.T7T		Atlas-SNP	.											.	PRR21	53	.	0			c.A21G						PASS	.						78.0	66.0	70.0					2																	240982379		2185	4279	6464	SO:0001819	synonymous_variant	643905	exon1			AAGAGCTGTGGAT	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.21A>G	2.37:g.240982379T>C		Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	18	9	0.5	NM_001080835		Silent	SNP	ENST00000408934.1	37	CCDS33417.1																																																																																			T|0.989;C|0.011	0.011	strong		0.572	PRR21-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001080835	
SYNE1	23345	hgsc.bcm.edu	37	6	152469331	152469331	+	Silent	SNP	C	C	T	rs2252748	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:152469331C>T	ENST00000367255.5	-	137	25426	c.24825G>A	c.(24823-24825)ccG>ccA	p.P8275P	SYNE1_ENST00000265368.4_Silent_p.P8275P|SYNE1_ENST00000448038.1_Silent_p.P8204P|SYNE1_ENST00000539504.1_Silent_p.P430P|SYNE1_ENST00000423061.1_Silent_p.P8204P|SYNE1_ENST00000356820.4_Silent_p.P2799P|SYNE1_ENST00000354674.4_Silent_p.P430P|SYNE1_ENST00000341594.5_Silent_p.P7887P|SYNE1_ENST00000347037.5_5'UTR	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	8275					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)		CCACACTAGCCGGGGTGTCTC	0.617										HNSCC(10;0.0054)			C|||	1700	0.339457	0.3079	0.4597	5008	,	,		18551	0.2976		0.2833	False		,,,				2504	0.3978				p.P8275P		Atlas-SNP	.											.	SYNE1	3227	.	0			c.G24825A						PASS	.	C	,	1382,3024	455.9+/-351.1	216,950,1037	60.0	59.0	59.0		24612,24825	-10.5	0.2	6	dbSNP_100	59	2532,6068	413.6+/-351.2	376,1780,2144	no	coding-synonymous,coding-synonymous	SYNE1	NM_033071.3,NM_182961.3	,	592,2730,3181	TT,TC,CC		29.4419,31.3663,30.0938	,	8204/8750,8275/8798	152469331	3914,9092	2203	4300	6503	SO:0001819	synonymous_variant	23345	exon137			ACTAGCCGGGGTG	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.24825G>A	6.37:g.152469331C>T		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	40	31	0.775	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																																																																																			C|0.691;T|0.309	0.309	strong		0.617	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961	
PLEKHM2	23207	hgsc.bcm.edu	37	1	16056364	16056364	+	Silent	SNP	G	G	A	rs3817269	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:16056364G>A	ENST00000375799.3	+	14	2375	c.2148G>A	c.(2146-2148)acG>acA	p.T716T	RP11-288I21.1_ENST00000453804.1_RNA|PLEKHM2_ENST00000375793.2_Silent_p.T696T|PLEKHM2_ENST00000477849.1_3'UTR	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	52	0	0		WXS	Illumina HiSeq	Phase_I	63	36	0.571429	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	
CEP170	9859	hgsc.bcm.edu	37	1	243333027	243333027	+	Silent	SNP	A	A	G	rs200644784		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:243333027A>G	ENST00000366542.1	-	12	1797	c.1746T>C	c.(1744-1746)cgT>cgC	p.R582R	RP11-261C10.4_ENST00000422938.1_RNA|CEP170_ENST00000366543.1_Silent_p.R484R|CEP170_ENST00000366544.1_Silent_p.R484R|RP11-261C10.4_ENST00000437499.1_RNA	NM_014812.2	NP_055627.2	Q5SW79	CE170_HUMAN	centrosomal protein 170kDa	582						centriole (GO:0005814)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|nuclear membrane (GO:0031965)		p.R582R(3)		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)			GTGAAACCCAACGTTTGCTTC	0.398																																					p.R582R		Atlas-SNP	.											CEP170_ENST00000366543,NS,carcinoma,0,6	CEP170	153	6	3	Substitution - coding silent(3)	kidney(3)	c.T1746C						scavenged	.						103.0	92.0	95.0					1																	243333027		1878	4106	5984	SO:0001819	synonymous_variant	9859	exon12			AACCCAACGTTTG	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.1746T>C	1.37:g.243333027A>G		Somatic	511	5	0.00978474		WXS	Illumina HiSeq	Phase_I	432	6	0.0138889	NM_014812	O75058|Q5SW77|Q5SW78|Q7LGA9|Q86W31|Q9UQ08|Q9UQ09	Silent	SNP	ENST00000366542.1	37	CCDS44339.1	.	.	.	.	.	.	.	.	.	.	A	9.754	1.168273	0.21621	.	.	ENSG00000143702	ENST00000336415	.	.	.	4.66	-6.75	0.01738	.	.	.	.	.	T	0.46833	0.1413	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.51576	-0.8688	4	.	.	.	-8.1159	6.5973	0.22681	0.3246:0.0:0.4436:0.2317	.	.	.	.	A	546	.	.	V	-	2	0	CEP170	241399650	0.846000	0.29590	0.974000	0.42286	0.957000	0.61999	-0.087000	0.11215	-0.781000	0.04548	-0.555000	0.04198	GTT	.	.	weak		0.398	CEP170-003	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096178.2	NM_014812	
C9orf43	257169	hgsc.bcm.edu	37	9	116191205	116191205	+	Missense_Mutation	SNP	A	A	C	rs111841972	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:116191205A>C	ENST00000288462.4	+	13	1579	c.1133A>C	c.(1132-1134)aAc>aCc	p.N378T	C9orf43_ENST00000374165.1_Missense_Mutation_p.N378T	NM_152786.1	NP_689999.1	Q8TAL5	CI043_HUMAN	chromosome 9 open reading frame 43	378										breast(2)|large_intestine(6)|lung(2)|ovary(1)|pancreas(1)|prostate(3)	15						CCAAAGATGAACTACTATGAC	0.383													A|||	198	0.0395367	0.0091	0.0231	5008	,	,		21567	0.0139		0.0517	False		,,,				2504	0.1063				p.N378T		Atlas-SNP	.											.	C9orf43	49	.	0			c.A1133C						PASS	.	A	THR/ASN	58,4348	56.8+/-93.2	0,58,2145	108.0	99.0	102.0		1133	0.4	0.0	9	dbSNP_132	102	492,8108	141.6+/-197.9	10,472,3818	yes	missense	C9orf43	NM_152786.1	65	10,530,5963	CC,CA,AA		5.7209,1.3164,4.2288	benign	378/462	116191205	550,12456	2203	4300	6503	SO:0001583	missense	257169	exon13			AGATGAACTACTA	BC026884	CCDS6796.1	9q33.1	2012-03-15			ENSG00000157653	ENSG00000157653			23570	protein-coding gene	gene with protein product						12477932	Standard	NM_152786		Approved	MGC17358	uc004bhp.3	Q8TAL5	OTTHUMG00000020526	ENST00000288462.4:c.1133A>C	9.37:g.116191205A>C	ENSP00000288462:p.Asn378Thr	Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	108	62	0.574074	NM_152786		Missense_Mutation	SNP	ENST00000288462.4	37	CCDS6796.1	59	0.027014652014652016	3	0.006097560975609756	9	0.024861878453038673	6	0.01048951048951049	41	0.05408970976253298	A	5.082	0.200850	0.09652	0.013164	0.057209	ENSG00000157653	ENST00000374165;ENST00000288462	T;T	0.42513	0.97;0.97	4.02	0.443	0.16587	.	1.458660	0.04555	N	0.390634	T	0.02929	0.0087	N	0.14661	0.345	0.09310	N	1	B	0.16166	0.016	B	0.18561	0.022	T	0.12477	-1.0546	10	0.34782	T	0.22	0.1584	5.9019	0.18972	0.6626:0.0:0.3374:0.0	.	378	Q8TAL5	CI043_HUMAN	T	378	ENSP00000363280:N378T;ENSP00000288462:N378T	ENSP00000288462:N378T	N	+	2	0	C9orf43	115231026	0.000000	0.05858	0.000000	0.03702	0.101000	0.19017	0.044000	0.13992	0.061000	0.16311	0.383000	0.25322	AAC	A|0.957;C|0.043	0.043	strong		0.383	C9orf43-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053739.1	NM_152786	
HLA-A	3105	hgsc.bcm.edu	37	6	29911261	29911261	+	Missense_Mutation	SNP	C	C	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:29911261C>G	ENST00000396634.1	+	5	901	c.560C>G	c.(559-561)aCg>aGg	p.T187R	HLA-A_ENST00000376802.2_Missense_Mutation_p.T187R|HLA-A_ENST00000376809.5_Missense_Mutation_p.T187R|HLA-A_ENST00000376806.5_Missense_Mutation_p.T187R			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	187	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						CTGGATGGCACGTGCGTGGAG	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)			g|||	1039	0.207468	0.0809	0.1037	5008	,	,		12986	0.3185		0.2018	False		,,,				2504	0.3436				p.T187R		Atlas-SNP	.											.	HLA-A	89	.	0			c.C560G						PASS	.						45.0	35.0	39.0					6																	29911261		1508	2702	4210	SO:0001583	missense	3105	exon3	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	ATGGCACGTGCGT	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.560C>G	6.37:g.29911261C>G	ENSP00000379873:p.Thr187Arg	Somatic	218	0	0		WXS	Illumina HiSeq	Phase_I	136	100	0.735294	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Missense_Mutation	SNP	ENST00000396634.1	37	CCDS34373.1	360	0.16483516483516483	26	0.052845528455284556	33	0.09116022099447514	149	0.26048951048951047	152	0.20052770448548812	.	0.003	-2.554518	0.00138	.	.	ENSG00000206503	ENST00000396634;ENST00000376806;ENST00000376809;ENST00000376802	T;T;T;T	0.00768	5.72;5.72;5.72;5.72	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);	80.137900	0.00166	N	0.000017	T	0.00109	0.0003	L	0.33668	1.02	0.80722	P	0.0	B;B;B;B;B;B	0.16396	0.017;0.003;0.003;0.001;0.003;0.003	B;B;B;B;B;B	0.22386	0.017;0.039;0.02;0.009;0.02;0.02	T	0.50980	-0.8763	9	0.05620	T	0.96	.	2.6157	0.04902	0.4361:0.0993:0.2856:0.1791	rs3129017;rs9260159;rs41555617	66;187;187;187;187;187	B4DVB9;Q5SRN7;P16188;Q5SRN5;P30455;P04439	.;.;1A30_HUMAN;.;1A36_HUMAN;1A03_HUMAN	R	187	ENSP00000379873:T187R;ENSP00000366002:T187R;ENSP00000366005:T187R;ENSP00000365998:T187R	ENSP00000365998:T187R	T	+	2	0	HLA-A	30019240	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-13.082000	0.00001	-8.487000	0.00000	-3.856000	0.00018	ACG	G|0.132;C|0.681;A|0.188	0.132	strong		0.667	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
CEP170B	283638	hgsc.bcm.edu	37	14	105346632	105346632	+	Silent	SNP	G	G	A	rs72700176	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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_ENST00000418279.1_Silent_p.K44K|CEP170B_ENST00000556508.1_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	73	31	0.424658	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	
SULT1A1	6817	hgsc.bcm.edu	37	16	28617472	28617472	+	Missense_Mutation	SNP	G	G	A	rs150459557	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:28617472G>A	ENST00000395607.1	-	7	953	c.680C>T	c.(679-681)aCg>aTg	p.T227M	SULT1A1_ENST00000395609.1_Missense_Mutation_p.T227M|SULT1A1_ENST00000314752.7_Missense_Mutation_p.T227M|SULT1A1_ENST00000569554.1_Missense_Mutation_p.T227M|SULT1A1_ENST00000350842.4_Missense_Mutation_p.T149M	NM_177530.2|NM_177534.2	NP_803566.1|NP_803878.1	P50225	ST1A1_HUMAN	sulfotransferase family, cytosolic, 1A, phenol-preferring, member 1	227					3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|amine metabolic process (GO:0009308)|catecholamine metabolic process (GO:0006584)|estrogen metabolic process (GO:0008210)|flavonoid metabolic process (GO:0009812)|small molecule metabolic process (GO:0044281)|sulfation (GO:0051923)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	aryl sulfotransferase activity (GO:0004062)|flavonol 3-sulfotransferase activity (GO:0047894)|steroid sulfotransferase activity (GO:0050294)|sulfotransferase activity (GO:0008146)	p.T149M(1)|p.T227M(1)		endometrium(2)|kidney(7)|large_intestine(2)|lung(2)|ovary(1)|stomach(2)	16					Acetaminophen(DB00316)|Tamoxifen(DB00675)	CTTGAACGACGTGTGCTGAAC	0.557													.|||	6	0.00119808	0.0	0.0014	5008	,	,		16587	0.0		0.005	False		,,,				2504	0.0				p.T227M		Atlas-SNP	.											SULT1A1,NS,carcinoma,0,1	SULT1A1	53	1	2	Substitution - Missense(2)	endometrium(2)	c.C680T						scavenged	.	G	MET/THR,MET/THR,MET/THR,MET/THR,MET/THR	3,4391	4.2+/-10.8	0,3,2194	119.0	64.0	82.0		680,680,680,680,446	2.2	0.1	16	dbSNP_134	82	35,8559	21.6+/-65.8	0,35,4262	no	missense,missense,missense,missense,missense	SULT1A1	NM_001055.3,NM_177529.2,NM_177530.2,NM_177534.2,NM_177536.3	81,81,81,81,81	0,38,6456	AA,AG,GG		0.4073,0.0683,0.2926	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	227/296,227/296,227/296,227/296,149/218	28617472	38,12950	2197	4297	6494	SO:0001583	missense	6817	exon6			AACGACGTGTGCT	U52852	CCDS10637.1, CCDS32420.1	16p12.1	2008-02-05			ENSG00000196502	ENSG00000196502	2.8.2.1	"""Sulfotransferases, cytosolic"""	11453	protein-coding gene	gene with protein product		171150		STP, STP1		8288252, 8912648	Standard	NM_177534		Approved	P-PST	uc002dqj.3	P50225	OTTHUMG00000131765	ENST00000395607.1:c.680C>T	16.37:g.28617472G>A	ENSP00000378971:p.Thr227Met	Somatic	277	2	0.00722022		WXS	Illumina HiSeq	Phase_I	456	114	0.25	NM_177534	Q2NL71|Q86U58|Q92818|Q9BVU6|Q9UGG7	Missense_Mutation	SNP	ENST00000395607.1	37	CCDS32420.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	g	9.434	1.086340	0.20390	6.83E-4	0.004073	ENSG00000196502	ENST00000314752;ENST00000350842;ENST00000395609;ENST00000395607	D;D;D;D	0.82711	-1.64;-1.64;-1.64;-1.64	2.18	2.18	0.27775	Sulfotransferase domain (1);	0.080875	0.51477	D	0.000090	D	0.91355	0.7273	M	0.91920	3.255	0.24615	N	0.993706	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.997;0.999;0.999	T	0.82684	-0.0335	10	0.87932	D	0	.	10.4847	0.44715	0.0:0.0:1.0:0.0	.	179;149;227	Q59GG0;P50225-2;P50225	.;.;ST1A1_HUMAN	M	227;149;227;227	ENSP00000321988:T227M;ENSP00000329399:T149M;ENSP00000378972:T227M;ENSP00000378971:T227M	ENSP00000321988:T227M	T	-	2	0	SULT1A1	28524973	0.991000	0.36638	0.060000	0.19600	0.064000	0.16182	2.688000	0.46984	1.559000	0.49555	0.306000	0.20318	ACG	G|0.998;A|0.002	0.002	strong		0.557	SULT1A1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254694.2	NM_001055	
STK25	10494	hgsc.bcm.edu	37	2	242441080	242441080	+	Missense_Mutation	SNP	C	C	T	rs200593123		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:242441080C>T	ENST00000316586.4	-	3	423	c.74G>A	c.(73-75)cGc>cAc	p.R25H	STK25_ENST00000478403.1_5'Flank|STK25_ENST00000405585.1_Intron|STK25_ENST00000535007.1_5'UTR|STK25_ENST00000405883.3_Intron|STK25_ENST00000403346.3_Missense_Mutation_p.R25H|STK25_ENST00000543554.1_5'UTR|STK25_ENST00000401869.1_Missense_Mutation_p.R25H	NM_001271977.1|NM_001271978.1|NM_001282308.1	NP_001258906.1|NP_001258907.1|NP_001269237.1	O00506	STK25_HUMAN	serine/threonine kinase 25	25	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				establishment or maintenance of cell polarity (GO:0007163)|Golgi localization (GO:0051645)|positive regulation of axonogenesis (GO:0050772)|response to oxidative stress (GO:0006979)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|kidney(1)|large_intestine(2)|lung(5)|upper_aerodigestive_tract(1)	10		all_cancers(19;2.09e-34)|all_epithelial(40;2.09e-14)|Breast(86;0.000141)|Renal(207;0.0143)|all_lung(227;0.0344)|Ovarian(221;0.069)|Lung NSC(271;0.0886)|Esophageal squamous(248;0.131)|all_hematologic(139;0.182)|Melanoma(123;0.2)		Epithelial(32;8.24e-34)|all cancers(36;3.46e-31)|OV - Ovarian serous cystadenocarcinoma(60;3.6e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.1e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0839)		CTTGCCAATGCGGTCGAGCTT	0.622																																					p.R25H	NSCLC(99;1100 1566 7679 28647 48345)	Atlas-SNP	.											STK25,caecum,carcinoma,0,1	STK25	32	1	0			c.G74A						scavenged	.						152.0	120.0	131.0					2																	242441080		2203	4300	6503	SO:0001583	missense	10494	exon3			CCAATGCGGTCGA	D63780	CCDS2549.1, CCDS63199.1, CCDS63200.1	2q37.3	2010-06-25	2010-06-25		ENSG00000115694	ENSG00000115694			11404	protein-coding gene	gene with protein product		602255	"""serine/threonine kinase 25 (Ste20, yeast homolog)"""			8887545, 9160885, 15037601	Standard	NM_001271977		Approved	SOK1, YSK1	uc002wbp.4	O00506	OTTHUMG00000133408	ENST00000316586.4:c.74G>A	2.37:g.242441080C>T	ENSP00000325748:p.Arg25His	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	82	2	0.0243902	NM_006374	A8K6Z3|A8K7D2|B7Z9K1|Q15522|Q5BJF1	Missense_Mutation	SNP	ENST00000316586.4	37	CCDS2549.1	.	.	.	.	.	.	.	.	.	.	C	11.21	1.570453	0.28003	.	.	ENSG00000115694	ENST00000316586;ENST00000403346;ENST00000401869;ENST00000436402;ENST00000426941;ENST00000420551	T;T;T;T;T;T	0.39997	1.81;1.81;1.81;1.05;1.05;1.05	3.78	1.95	0.26073	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.067963	0.64402	D	0.000014	T	0.31513	0.0799	L	0.45698	1.435	0.80722	D	1	P;P	0.37573	0.6;0.563	B;B	0.32149	0.141;0.048	T	0.10800	-1.0614	10	0.62326	D	0.03	.	9.9645	0.41717	0.0:0.8268:0.0:0.1732	.	25;25	B4DZ52;O00506	.;STK25_HUMAN	H	25;25;25;25;25;40	ENSP00000325748:R25H;ENSP00000384162:R25H;ENSP00000385687:R25H;ENSP00000412617:R25H;ENSP00000414191:R25H;ENSP00000404552:R40H	ENSP00000325748:R25H	R	-	2	0	STK25	242089753	1.000000	0.71417	0.573000	0.28510	0.003000	0.03518	7.541000	0.82084	0.341000	0.23771	-0.253000	0.11424	CGC	C|0.999;T|0.001	0.001	weak		0.622	STK25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257265.4	NM_006374	
MAP3K5	4217	hgsc.bcm.edu	37	6	137026266	137026266	+	Silent	SNP	T	T	G	rs9321567	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:137026266T>G	ENST00000359015.4	-	3	954	c.594A>C	c.(592-594)atA>atC	p.I198I		NM_005923.3	NP_005914.1	Q99683	M3K5_HUMAN	mitogen-activated protein kinase kinase kinase 5	198					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of JUN kinase activity (GO:0007257)|activation of MAPKK activity (GO:0000186)|apoptotic signaling pathway (GO:0097190)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to reactive nitrogen species (GO:1902170)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|JNK cascade (GO:0007254)|MAPK cascade (GO:0000165)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of neuron death (GO:1901216)|programmed necrotic cell death (GO:0097300)|protein phosphorylation (GO:0006468)|response to ischemia (GO:0002931)|viral process (GO:0016032)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|protein kinase complex (GO:1902911)	ATP binding (GO:0005524)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|magnesium ion binding (GO:0000287)|MAP kinase kinase kinase activity (GO:0004709)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein phosphatase binding (GO:0019903)			NS(1)|breast(1)|cervix(1)|endometrium(8)|kidney(6)|large_intestine(6)|lung(24)|ovary(2)|prostate(1)|skin(4)|urinary_tract(4)	58	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00137)|OV - Ovarian serous cystadenocarcinoma(155;0.00569)		TCTGGCAAATTATTTCCTGAA	0.244													G|||	3212	0.641374	0.798	0.647	5008	,	,		14936	0.5823		0.4652	False		,,,				2504	0.6677				p.I198I		Atlas-SNP	.											.	MAP3K5	136	.	0			c.A594C						PASS	.	G		3181,1073		1218,745,164	21.0	24.0	23.0		594	1.5	1.0	6	dbSNP_119	23	4117,4319		1035,2047,1136	no	coding-synonymous	MAP3K5	NM_005923.3		2253,2792,1300	GG,GT,TT		48.8028,25.2233,42.4901		198/1375	137026266	7298,5392	2127	4218	6345	SO:0001819	synonymous_variant	4217	exon3			GCAAATTATTTCC	U67156	CCDS5179.1	6q22.33	2011-06-09			ENSG00000197442	ENSG00000197442		"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	6857	protein-coding gene	gene with protein product	"""apoptosis signal regulating kinase 1"""	602448		MEKK5		9465908	Standard	NM_005923		Approved	MAPKKK5, ASK1	uc003qhc.3	Q99683	OTTHUMG00000015647	ENST00000359015.4:c.594A>C	6.37:g.137026266T>G		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	88	11	0.125	NM_005923	A6NIA0|B4DGB2|Q5THN3|Q99461	Silent	SNP	ENST00000359015.4	37	CCDS5179.1																																																																																			T|0.413;G|0.587	0.587	strong		0.244	MAP3K5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042383.1		
BGN	633	hgsc.bcm.edu	37	X	152770230	152770230	+	Silent	SNP	G	G	A	rs4833	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:152770230G>A	ENST00000331595.4	+	2	327	c.141G>A	c.(139-141)tcG>tcA	p.S47S	BGN_ENST00000480756.1_3'UTR	NM_001711.4	NP_001702.1	P21810	PGS1_HUMAN	biglycan	47					blood vessel remodeling (GO:0001974)|carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|peptide cross-linking via chondroitin 4-sulfate glycosaminoglycan (GO:0019800)|small molecule metabolic process (GO:0044281)	cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|transport vesicle (GO:0030133)	extracellular matrix binding (GO:0050840)|extracellular matrix structural constituent (GO:0005201)|glycosaminoglycan binding (GO:0005539)			breast(2)|endometrium(3)|large_intestine(1)|lung(9)|ovary(1)	16	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					CTGACACCTCGGGCGTCCTGG	0.627													G|||	1467	0.388609	0.1914	0.4092	3775	,	,		13825	0.3601		0.2913	False		,,,				2504	0.2802				p.S47S		Atlas-SNP	.											.	BGN	44	.	0			c.G141A						PASS	.	G		1026,2809		122,637,145,873,426	105.0	88.0	93.0		141	-9.5	0.0	X	dbSNP_52	93	2751,3977		419,1184,729,825,1143	no	coding-synonymous	BGN	NM_001711.4		541,1821,874,1698,1569	AA,AG,A,GG,G		40.8888,26.7536,35.7569		47/369	152770230	3777,6786	2203	4300	6503	SO:0001819	synonymous_variant	633	exon2			CACCTCGGGCGTC	AK092954	CCDS14721.1	Xq28	2008-02-05			ENSG00000182492	ENSG00000182492		"""Proteoglycans / Extracellular Matrix : Small leucine-rich repeats"""	1044	protein-coding gene	gene with protein product	"""biglycan proteoglycan"""	301870				1612609	Standard	NM_001711		Approved	DSPG1, SLRR1A	uc004fhr.2	P21810	OTTHUMG00000024205	ENST00000331595.4:c.141G>A	X.37:g.152770230G>A		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	43	42	0.976744	NM_001711	D3DWU3|P13247	Silent	SNP	ENST00000331595.4	37	CCDS14721.1																																																																																			G|0.631;A|0.369	0.369	strong		0.627	BGN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060981.1	NM_001711	
NID2	22795	hgsc.bcm.edu	37	14	52520746	52520746	+	Missense_Mutation	SNP	G	G	T	rs35657569	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:52520746G>T	ENST00000216286.5	-	4	1060	c.1061C>A	c.(1060-1062)cCt>cAt	p.P354H	NID2_ENST00000541773.1_Missense_Mutation_p.P301H	NM_007361.3	NP_031387.3	Q14112	NID2_HUMAN	nidogen 2 (osteonidogen)	354			P -> H (in dbSNP:rs35657569).		basement membrane organization (GO:0071711)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|cell surface (GO:0009986)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)			NS(1)|breast(5)|endometrium(9)|kidney(4)|large_intestine(11)|liver(1)|lung(40)|ovary(2)|pancreas(2)|prostate(2)|skin(3)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	87	Breast(41;0.0639)|all_epithelial(31;0.123)					ACCCTCTAAAGGCTTTGTATC	0.483													G|||	139	0.0277556	0.0038	0.0519	5008	,	,		20528	0.0		0.0895	False		,,,				2504	0.0082				p.P354H		Atlas-SNP	.											.	NID2	201	.	0			c.C1061A						PASS	.	G	HIS/PRO	71,4335	63.5+/-100.7	0,71,2132	92.0	91.0	92.0		1061	1.3	0.0	14	dbSNP_126	92	787,7813	185.3+/-233.1	34,719,3547	yes	missense	NID2	NM_007361.3	77	34,790,5679	TT,TG,GG		9.1512,1.6114,6.597	possibly-damaging	354/1376	52520746	858,12148	2203	4300	6503	SO:0001583	missense	22795	exon4			TCTAAAGGCTTTG	AB009799	CCDS9706.1	14q22.1	2008-05-14			ENSG00000087303	ENSG00000087303			13389	protein-coding gene	gene with protein product		605399				9733643	Standard	NM_007361		Approved		uc001wzo.3	Q14112	OTTHUMG00000140298	ENST00000216286.5:c.1061C>A	14.37:g.52520746G>T	ENSP00000216286:p.Pro354His	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	96	96	1	NM_007361	A8K6I7|B4DU19|O43710	Missense_Mutation	SNP	ENST00000216286.5	37	CCDS9706.1	91	0.041666666666666664	5	0.01016260162601626	26	0.0718232044198895	0	0.0	60	0.079155672823219	G	14.90	2.674903	0.47781	0.016114	0.091512	ENSG00000087303	ENST00000216286;ENST00000541773;ENST00000395707	D;D	0.83992	-1.79;-1.69	5.48	1.27	0.21489	.	0.804485	0.10712	N	0.642768	T	0.15825	0.0381	L	0.29908	0.895	0.09310	N	1	D;P	0.65815	0.995;0.761	P;B	0.60473	0.875;0.338	T	0.46679	-0.9174	10	0.59425	D	0.04	.	2.5868	0.04832	0.0946:0.153:0.4015:0.3509	rs35657569	301;354	Q14112-2;Q14112	.;NID2_HUMAN	H	354;301;356	ENSP00000216286:P354H;ENSP00000443730:P301H	ENSP00000216286:P354H	P	-	2	0	NID2	51590496	0.000000	0.05858	0.001000	0.08648	0.025000	0.11179	0.286000	0.18902	0.664000	0.31047	0.563000	0.77884	CCT	G|0.939;T|0.061	0.061	strong		0.483	NID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276888.1		
MBOAT1	154141	hgsc.bcm.edu	37	6	20109956	20109956	+	Missense_Mutation	SNP	A	A	G	rs45596536	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:20109956A>G	ENST00000324607.7	-	12	1398	c.1234T>C	c.(1234-1236)Ttc>Ctc	p.F412L	MBOAT1_ENST00000541730.1_Missense_Mutation_p.F263L	NM_001080480.1	NP_001073949.1	Q6ZNC8	MBOA1_HUMAN	membrane bound O-acyltransferase domain containing 1	412					glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	transferase activity, transferring acyl groups other than amino-acyl groups (GO:0016747)			breast(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(5)	20	all_cancers(95;0.244)|Breast(50;0.0379)|Ovarian(93;0.0473)|all_epithelial(95;0.109)		OV - Ovarian serous cystadenocarcinoma(7;0.00392)|all cancers(50;0.0117)|Epithelial(50;0.0454)			GAAGAAAGGAAGTAATGTCTG	0.493													A|||	26	0.00519169	0.0008	0.0086	5008	,	,		17690	0.0		0.0189	False		,,,				2504	0.0				p.F412L		Atlas-SNP	.											.	MBOAT1	48	.	0			c.T1234C						PASS	.	A	LEU/PHE	18,4388	24.3+/-50.5	0,18,2185	135.0	118.0	124.0		1234	5.4	1.0	6	dbSNP_127	124	179,8421	81.2+/-143.8	1,177,4122	yes	missense	MBOAT1	NM_001080480.1	22	1,195,6307	GG,GA,AA		2.0814,0.4085,1.5147	probably-damaging	412/496	20109956	197,12809	2203	4300	6503	SO:0001583	missense	154141	exon12			AAAGGAAGTAATG	AK093994	CCDS34346.1	6p22.3	2013-10-11	2006-06-29	2006-06-29	ENSG00000172197	ENSG00000172197			21579	protein-coding gene	gene with protein product	"""lysophosphatidylethanolamine acyltransferase 1"""	611732	"""O-acyltransferase (membrane bound) domain containing 1"""	OACT1		18287005	Standard	NM_001080480		Approved	MGC44669, dJ434O11.1, LPEAT1	uc003ncx.2	Q6ZNC8	OTTHUMG00000014334	ENST00000324607.7:c.1234T>C	6.37:g.20109956A>G	ENSP00000324944:p.Phe412Leu	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	98	62	0.632653	NM_001080480	A9EDQ5|B4DL59|B4E3J4|Q86XC2|Q8N9R5	Missense_Mutation	SNP	ENST00000324607.7	37	CCDS34346.1	15	0.006868131868131868	0	0.0	4	0.011049723756906077	0	0.0	11	0.014511873350923483	A	32	5.135821	0.94517	0.004085	0.020814	ENSG00000172197	ENST00000541730;ENST00000324607	T;T	0.73363	-0.74;-0.74	5.38	5.38	0.77491	.	0.000000	0.85682	D	0.000000	D	0.85366	0.5680	M	0.89904	3.07	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.83275	0.996;0.996	D	0.85930	0.1451	10	0.34782	T	0.22	-10.9253	14.6643	0.68896	1.0:0.0:0.0:0.0	rs45596536	263;412	Q6ZNC8-2;Q6ZNC8	.;MBOA1_HUMAN	L	263;412	ENSP00000441568:F263L;ENSP00000324944:F412L	ENSP00000324944:F412L	F	-	1	0	MBOAT1	20217935	1.000000	0.71417	1.000000	0.80357	0.810000	0.45777	9.012000	0.93624	2.140000	0.66376	0.533000	0.62120	TTC	A|0.986;G|0.014	0.014	strong		0.493	MBOAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039980.1		
NME8	51314	hgsc.bcm.edu	37	7	37934147	37934147	+	Silent	SNP	A	A	T	rs41276027|rs386712272	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:37934147A>T	ENST00000199447.4	+	16	1851	c.1479A>T	c.(1477-1479)atA>atT	p.I493I	EPDR1_ENST00000476620.1_Intron|NME8_ENST00000440017.1_Silent_p.I493I	NM_016616.4	NP_057700.3	Q8N427	TXND3_HUMAN	NME/NM23 family member 8	493	NDK 3.		I -> T (in dbSNP:rs56128139). {ECO:0000269|PubMed:15489334}.		cell differentiation (GO:0030154)|cell redox homeostasis (GO:0045454)|CTP biosynthetic process (GO:0006241)|GTP biosynthetic process (GO:0006183)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)|UTP biosynthetic process (GO:0006228)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|nucleoside diphosphate kinase activity (GO:0004550)										CTGAGCAAATAGAGAAAATTT	0.303													A|||	790	0.157748	0.0151	0.2291	5008	,	,		17450	0.1359		0.3419	False		,,,				2504	0.1329				p.I493I		Atlas-SNP	.											.	.	.	.	0			c.A1479T						PASS	.	A		2,4404		0,2,2201	59.0	61.0	61.0		1479	-3.0	0.0	7	dbSNP_127	61	47,8551		6,35,4258	no	coding-synonymous	TXNDC3	NM_016616.4		6,37,6459	TT,TA,AA		0.5466,0.0454,0.3768		493/589	37934147	49,12955	2203	4299	6502	SO:0001819	synonymous_variant	51314	exon16			GCAAATAGAGAAA	AF202051	CCDS5452.1	7p15.2	2012-05-18	2012-05-18	2012-05-18	ENSG00000086288	ENSG00000086288			16473	protein-coding gene	gene with protein product	"""sperm-specific thioredoxin 2"""	607421	"""thioredoxin domain containing 3 (spermatozoa)"""	TXNDC3		11737268, 11768308, 19852809	Standard	NM_016616		Approved	CILD6, SPTRX2, NM23-H8	uc003tfn.3	Q8N427	OTTHUMG00000023716	ENST00000199447.4:c.1479A>T	7.37:g.37934147A>T		Somatic	269	0	0		WXS	Illumina HiSeq	Phase_I	242	189	0.780992	NM_016616	Q9NZH1	Silent	SNP	ENST00000199447.4	37	CCDS5452.1																																																																																			A|0.761;T|0.239	0.239	strong		0.303	NME8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219946.1	NM_016616	
TMPRSS5	80975	hgsc.bcm.edu	37	11	113570405	113570405	+	Silent	SNP	T	T	C	rs4936280	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:113570405T>C	ENST00000299882.5	-	3	265	c.117A>G	c.(115-117)gcA>gcG	p.A39A	TMPRSS5_ENST00000540540.1_Intron|TMPRSS5_ENST00000538955.1_5'UTR|TMPRSS5_ENST00000536856.1_Intron|TMPRSS5_ENST00000545579.1_Silent_p.A30A|TMPRSS5_ENST00000544476.1_5'UTR|TMPRSS5_ENST00000544634.1_Silent_p.A39A	NM_030770.2	NP_110397.2	Q9H3S3	TMPS5_HUMAN	transmembrane protease, serine 5	39					proteolysis (GO:0006508)	integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	peptidase activity (GO:0008233)|scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)			endometrium(2)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)	10		all_cancers(61;2.71e-16)|all_epithelial(67;1e-09)|Melanoma(852;1.46e-05)|all_hematologic(158;0.00014)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|all_neural(223;0.0281)|Prostate(24;0.0421)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;2.75e-06)|Epithelial(105;6.34e-05)|all cancers(92;0.000502)		GCCAGCACACTGCCTGAGAAA	0.632													N|||	3860	0.770767	0.9675	0.7565	5008	,	,		17135	0.749		0.6352	False		,,,				2504	0.6769				p.A39A		Atlas-SNP	.											TMPRSS5_ENST00000299882,NS,carcinoma,-1,2	TMPRSS5	69	2	0			c.A117G						scavenged	.			3913,343		1805,303,20	17.0	23.0	21.0		117	-8.1	0.0	11	dbSNP_111	21	5521,2935		1793,1935,500	no	coding-synonymous	TMPRSS5	NM_030770.2		3598,2238,520	CC,CT,TT		34.7091,8.0592,25.7867		39/458	113570405	9434,3278	2128	4228	6356	SO:0001819	synonymous_variant	80975	exon3			GCACACTGCCTGA	AB028140	CCDS44735.1, CCDS73390.1, CCDS73391.1, CCDS73392.1, CCDS73393.1	11q	2010-04-13	2008-07-31		ENSG00000166682	ENSG00000166682		"""Serine peptidases / Transmembrane"""	14908	protein-coding gene	gene with protein product	"""spinesin"""	606751					Standard	NM_030770		Approved	MGC141886, MGC148044	uc001poc.4	Q9H3S3	OTTHUMG00000168186	ENST00000299882.5:c.117A>G	11.37:g.113570405T>C		Somatic	238	1	0.00420168		WXS	Illumina HiSeq	Phase_I	209	47	0.22488	NM_030770		Silent	SNP	ENST00000299882.5	37	CCDS44735.1																																																																																			T|0.231;C|0.769	0.769	strong		0.632	TMPRSS5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398652.1	NM_030770	
TPTE2	93492	hgsc.bcm.edu	37	13	20006680	20006680	+	Silent	SNP	G	G	C	rs201767816		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:20006680G>C	ENST00000400230.2	-	16	1199	c.1155C>G	c.(1153-1155)ctC>ctG	p.L385L	TPTE2_ENST00000382977.4_Silent_p.L385L|TPTE2_ENST00000382978.1_Silent_p.L345L|TPTE2_ENST00000457266.2_Silent_p.L274L|TPTE2_ENST00000400103.2_Silent_p.L274L|TPTE2_ENST00000255310.6_Silent_p.L308L|TPTE2_ENST00000382975.4_Silent_p.L345L|TPTE2_ENST00000390680.2_Silent_p.L308L			Q6XPS3	TPTE2_HUMAN	transmembrane phosphoinositide 3-phosphatase and tensin homolog 2	385	Phosphatase tensin-type. {ECO:0000255|PROSITE-ProRule:PRU00590}.				phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	ion channel activity (GO:0005216)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.L308L(1)		NS(2)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(8)|lung(21)|pancreas(1)|prostate(8)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	65		all_cancers(29;1.23e-20)|all_lung(29;1.97e-20)|all_epithelial(30;5.86e-20)|Lung NSC(5;3.36e-17)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;1.73e-05)|Epithelial(112;7.42e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000785)|Lung(94;0.0176)|LUSC - Lung squamous cell carcinoma(192;0.089)		TCCAGTTGTAGAGATGTTTCA	0.343																																					p.L385L		Atlas-SNP	.											TPTE2,mouth,carcinoma,0,1	TPTE2	225	1	1	Substitution - coding silent(1)	upper_aerodigestive_tract(1)	c.C1155G						scavenged	.						34.0	33.0	34.0					13																	20006680		2202	4291	6493	SO:0001819	synonymous_variant	93492	exon17			GTTGTAGAGATGT	AJ421032	CCDS9285.1, CCDS45013.1, CCDS45014.1	13q12.11	2012-12-10			ENSG00000132958	ENSG00000132958		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"""	17299	protein-coding gene	gene with protein product		606791				11716755, 12717346, 15057823	Standard	NM_130785		Approved	TPIP	uc001umd.3	Q6XPS3	OTTHUMG00000016493	ENST00000400230.2:c.1155C>G	13.37:g.20006680G>C		Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	170	20	0.117647	NM_199254	A1A4X0|A1A4X1|A8MX64|B1AQ16|B4DWZ2|Q5VUH2|Q8WWL4|Q8WWL5	Silent	SNP	ENST00000400230.2	37	CCDS45014.1																																																																																			G|0.999;C|0.001	0.001	weak		0.343	TPTE2-205	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_199254	
DLG1	1739	hgsc.bcm.edu	37	3	196771554	196771554	+	Silent	SNP	T	T	C	rs35370245	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:196771554T>C	ENST00000419354.1	-	26	2941	c.2655A>G	c.(2653-2655)aaA>aaG	p.K885K	DLG1_ENST00000448528.2_Silent_p.K885K|DLG1_ENST00000443183.1_Silent_p.K781K|DLG1_ENST00000314062.3_Silent_p.K834K|DLG1_ENST00000357674.4_Silent_p.K874K|DLG1_ENST00000450955.1_Silent_p.K874K|DLG1_ENST00000452595.1_Silent_p.K769K|DLG1_ENST00000392382.2_Silent_p.K852K|DLG1_ENST00000422288.1_Silent_p.K834K|DLG1_ENST00000346964.2_Silent_p.K907K			Q12959	DLG1_HUMAN	discs, large homolog 1 (Drosophila)	885	Guanylate kinase-like. {ECO:0000255|PROSITE-ProRule:PRU00100}.				actin filament organization (GO:0007015)|activation of protein kinase activity (GO:0032147)|amyloid precursor protein metabolic process (GO:0042982)|axon guidance (GO:0007411)|branching involved in ureteric bud morphogenesis (GO:0001658)|cortical actin cytoskeleton organization (GO:0030866)|dephosphorylation (GO:0016311)|embryonic skeletal system morphogenesis (GO:0048704)|endothelial cell proliferation (GO:0001935)|establishment or maintenance of cell polarity (GO:0007163)|hard palate development (GO:0060022)|immunological synapse formation (GO:0001771)|lens development in camera-type eye (GO:0002088)|membrane raft organization (GO:0031579)|mitotic cell cycle checkpoint (GO:0007093)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of T cell proliferation (GO:0042130)|nucleotide phosphorylation (GO:0046939)|peristalsis (GO:0030432)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cell proliferation (GO:0008284)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of potassium ion transport (GO:0043268)|protein localization to plasma membrane (GO:0072659)|regulation of membrane potential (GO:0042391)|regulation of myelination (GO:0031641)|regulation of sodium ion transmembrane transport (GO:1902305)|reproductive structure development (GO:0048608)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle tissue development (GO:0048745)|synaptic transmission (GO:0007268)|T cell activation (GO:0042110)|T cell cytokine production (GO:0002369)|tight junction assembly (GO:0070830)|viral process (GO:0016032)	basal lamina (GO:0005605)|basolateral plasma membrane (GO:0016323)|cell junction (GO:0030054)|cell projection membrane (GO:0031253)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|immunological synapse (GO:0001772)|intercalated disc (GO:0014704)|lateral loop (GO:0043219)|lateral plasma membrane (GO:0016328)|membrane raft (GO:0045121)|microtubule (GO:0005874)|MPP7-DLG1-LIN7 complex (GO:0097025)|myelin sheath abaxonal region (GO:0035748)|neuromuscular junction (GO:0031594)|node of Ranvier (GO:0033268)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|tight junction (GO:0005923)	cytoskeletal protein binding (GO:0008092)|guanylate kinase activity (GO:0004385)|ion channel binding (GO:0044325)|L27 domain binding (GO:0097016)|mitogen-activated protein kinase kinase binding (GO:0031434)|phosphatase binding (GO:0019902)|phosphoprotein phosphatase activity (GO:0004721)|potassium channel regulator activity (GO:0015459)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)			breast(2)|endometrium(1)|kidney(3)|large_intestine(4)|liver(1)|lung(9)|ovary(3)|prostate(1)|skin(1)|urinary_tract(1)	26	all_cancers(143;6.22e-10)|Ovarian(172;0.0418)|Breast(254;0.0589)	Lung NSC(153;0.133)	Epithelial(36;3.23e-24)|all cancers(36;2.15e-22)|OV - Ovarian serous cystadenocarcinoma(49;3.88e-19)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.0148)		CTATGATCTGTTTCACTTGGT	0.358													T|||	127	0.0253594	0.003	0.0303	5008	,	,		17651	0.001		0.0577	False		,,,				2504	0.044				p.K907K		Atlas-SNP	.											.	DLG1	120	.	0			c.A2721G						PASS	.	T	,,,,	57,4349	56.2+/-92.4	0,57,2146	164.0	154.0	158.0		2655,2619,2343,2307,2721	0.2	1.0	3	dbSNP_126	158	404,8196	129.0+/-187.1	9,386,3905	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	DLG1	NM_001098424.1,NM_001204386.1,NM_001204387.1,NM_001204388.1,NM_004087.2	,,,,	9,443,6051	CC,CT,TT		4.6977,1.2937,3.5445	,,,,	885/905,873/893,781/801,769/789,907/927	196771554	461,12545	2203	4300	6503	SO:0001819	synonymous_variant	1739	exon26			GATCTGTTTCACT	U13897	CCDS3327.1, CCDS43194.1, CCDS56300.1, CCDS56301.1, CCDS75072.1	3q29	2008-12-15	2001-11-28		ENSG00000075711	ENSG00000075711			2900	protein-coding gene	gene with protein product	"""discs large homolog 1"", ""presynaptic protein SAP97"", ""synapse-associated protein 97"""	601014	"""discs, large (Drosophila) homolog 1"""			7937897, 8825652	Standard	NM_004087		Approved	SAP97, SAP-97, hdlg, DLGH1, dJ1061C18.1.1	uc003fxn.4	Q12959	OTTHUMG00000047972	ENST00000419354.1:c.2655A>G	3.37:g.196771554T>C		Somatic	182	0	0		WXS	Illumina HiSeq	Phase_I	119	54	0.453782	NM_004087	A5YKK7|B4DGU1|B4DGZ8|B7ZMM0|B9EIQ5|D3DXB8|D3DXB9|E7EWL7|E9PG21|Q12958	Silent	SNP	ENST00000419354.1	37	CCDS43194.1																																																																																			T|0.966;C|0.034	0.034	strong		0.358	DLG1-008	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000258170.2	NM_004087	
PYCRL	65263	hgsc.bcm.edu	37	8	144689146	144689146	+	Missense_Mutation	SNP	C	C	T	rs2242089	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:144689146C>T	ENST00000220966.6	-	3	378	c.349G>A	c.(349-351)Gtg>Atg	p.V117M	PYCRL_ENST00000495276.1_5'UTR|PYCRL_ENST00000377579.3_De_novo_Start_InFrame	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	155	0	0		WXS	Illumina HiSeq	Phase_I	157	124	0.789809	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	
C11orf1	64776	hgsc.bcm.edu	37	11	111754574	111754574	+	Silent	SNP	A	A	C	rs1045282	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:111754574A>C	ENST00000260276.3	+	4	760	c.423A>C	c.(421-423)tcA>tcC	p.S141S	C11orf1_ENST00000530214.1_Missense_Mutation_p.Q119P|C11orf1_ENST00000529270.1_Silent_p.S181S|C11orf1_ENST00000528125.1_Silent_p.S95S	NM_022761.2	NP_073598.1	Q9H5F2	CK001_HUMAN	chromosome 11 open reading frame 1	141						nucleus (GO:0005634)				kidney(2)|lung(3)	5		all_cancers(61;1.26e-15)|all_epithelial(67;9.52e-10)|Melanoma(852;1.91e-06)|all_hematologic(158;0.000405)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0112)|Medulloblastoma(222;0.0228)|all_neural(223;0.0281)		all cancers(92;6.28e-09)|Epithelial(105;4.11e-08)|OV - Ovarian serous cystadenocarcinoma(223;1.52e-07)|BRCA - Breast invasive adenocarcinoma(274;1.1e-06)		CAGAAAAGTCAACTTACATGA	0.398													A|||	1200	0.239617	0.1952	0.3069	5008	,	,		18184	0.1905		0.3231	False		,,,				2504	0.2168				p.S141S		Atlas-SNP	.											.	C11orf1	15	.	0			c.A423C						PASS	.	A		963,3439	363.1+/-316.4	106,751,1344	114.0	108.0	110.0		423	4.2	1.0	11	dbSNP_86	110	2579,6015	419.8+/-353.2	394,1791,2112	no	coding-synonymous	C11orf1	NM_022761.2		500,2542,3456	CC,CA,AA		30.0093,21.8764,27.2545		141/151	111754574	3542,9454	2201	4297	6498	SO:0001819	synonymous_variant	64776	exon4			AAAGTCAACTTAC	AJ250229	CCDS8350.1	11q23.1	2012-05-30			ENSG00000137720	ENSG00000137720			1163	protein-coding gene	gene with protein product						10873569	Standard	NM_022761		Approved	FLJ23499	uc001pmd.3	Q9H5F2	OTTHUMG00000166884	ENST00000260276.3:c.423A>C	11.37:g.111754574A>C		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	53	13	0.245283	NM_022761	Q6I9X7|Q9NQC6	Silent	SNP	ENST00000260276.3	37	CCDS8350.1	583	0.26694139194139194	114	0.23170731707317074	126	0.34806629834254144	101	0.17657342657342656	242	0.31926121372031663	A	10.58	1.389114	0.25118	0.218764	0.300093	ENSG00000137720	ENST00000530214	T	0.25085	1.82	5.37	4.22	0.49857	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.999999999994803	.	.	.	.	.	.	T	0.43196	-0.9406	5	0.62326	D	0.03	-22.8715	5.7886	0.18347	0.5843:0.3324:0.0833:0.0	rs1045282;rs3168261;rs17489575;rs59543330;rs1045282	.	.	.	P	119	ENSP00000435864:Q119P	ENSP00000435864:Q119P	Q	+	2	0	C11orf1	111259784	0.960000	0.32886	0.982000	0.44146	0.994000	0.84299	1.708000	0.37899	1.017000	0.39495	0.528000	0.53228	CAA	A|0.734;C|0.266	0.266	strong		0.398	C11orf1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391650.1	NM_022761	
CST4	1472	hgsc.bcm.edu	37	20	23667738	23667738	+	Missense_Mutation	SNP	G	G	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:23667738G>C	ENST00000217423.3	-	2	399	c.329C>G	c.(328-330)cCa>cGa	p.P110R		NM_001899.2	NP_001890.1	P01036	CYTS_HUMAN	cystatin S	110					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of proteolysis (GO:0045861)|retina homeostasis (GO:0001895)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	cysteine-type endopeptidase inhibitor activity (GO:0004869)			breast(1)|endometrium(1)|large_intestine(2)|lung(10)|skin(1)|upper_aerodigestive_tract(1)	16	Lung NSC(19;0.0789)|Colorectal(13;0.0993)|all_lung(19;0.169)					CTGCAGTTCTGGCTGTTCATG	0.572																																					p.P110R		Atlas-SNP	.											.	CST4	37	.	0			c.C329G						PASS	.						207.0	168.0	181.0					20																	23667738		2203	4300	6503	SO:0001583	missense	1472	exon2			AGTTCTGGCTGTT		CCDS13159.1	20p11.2	2008-04-15			ENSG00000101441	ENSG00000101441			2476	protein-coding gene	gene with protein product		123857				1801729	Standard	NM_001899		Approved		uc002wto.1	P01036	OTTHUMG00000032083	ENST00000217423.3:c.329C>G	20.37:g.23667738G>C	ENSP00000217423:p.Pro110Arg	Somatic	242	0	0		WXS	Illumina HiSeq	Phase_I	194	37	0.190722	NM_001899	Q9UBI5|Q9UCS9	Missense_Mutation	SNP	ENST00000217423.3	37	CCDS13159.1	.	.	.	.	.	.	.	.	.	.	G	13.20	2.165362	0.38217	.	.	ENSG00000101441	ENST00000217423	T	0.14516	2.5	1.51	0.516	0.17019	Proteinase inhibitor I25, cystatin (2);	0.298786	0.30959	U	0.008521	T	0.33118	0.0852	M	0.87682	2.9	0.09310	N	0.999999	D	0.69078	0.997	D	0.80764	0.994	T	0.08617	-1.0713	10	0.87932	D	0	.	3.9044	0.09176	0.2423:0.0:0.7577:0.0	.	110	P01036	CYTS_HUMAN	R	110	ENSP00000217423:P110R	ENSP00000217423:P110R	P	-	2	0	CST4	23615738	0.017000	0.18338	0.006000	0.13384	0.644000	0.38419	-0.007000	0.12810	0.190000	0.20209	0.205000	0.17691	CCA	.	.	none		0.572	CST4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078349.2	NM_001899	
NLRP7	199713	hgsc.bcm.edu	37	19	55451232	55451232	+	Missense_Mutation	SNP	C	C	T	rs775882	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:55451232C>T	ENST00000590030.1	-	3	995	c.955G>A	c.(955-957)Gta>Ata	p.V319I	NLRP7_ENST00000340844.2_Missense_Mutation_p.V319I|NLRP7_ENST00000448121.2_Missense_Mutation_p.V319I|NLRP7_ENST00000588756.1_Missense_Mutation_p.V319I|NLRP7_ENST00000592784.1_Missense_Mutation_p.V319I|NLRP7_ENST00000328092.5_Missense_Mutation_p.V319I|NLRP7_ENST00000446217.1_Missense_Mutation_p.V347I			Q8WX94	NALP7_HUMAN	NLR family, pyrin domain containing 7	319	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.		V -> I (in dbSNP:rs775882).				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)		TCCACCCTTACGTAGATCGGC	0.597													.|||	1447	0.288938	0.4652	0.2954	5008	,	,		17793	0.1835		0.2276	False		,,,				2504	0.2178				p.V319I		Atlas-SNP	.											.	NLRP7	411	.	0			c.G955A						PASS	.	C	ILE/VAL,ILE/VAL,ILE/VAL	2034,2372	553.9+/-378.9	451,1132,620	38.0	41.0	40.0		955,955,955	-3.1	0.0	19	dbSNP_86	40	1808,6792	319.7+/-314.3	196,1416,2688	yes	missense,missense,missense	NLRP7	NM_001127255.1,NM_139176.3,NM_206828.3	29,29,29	647,2548,3308	TT,TC,CC		21.0233,46.1643,29.5402	benign,benign,benign	319/1038,319/1010,319/981	55451232	3842,9164	2203	4300	6503	SO:0001583	missense	199713	exon4			CCCTTACGTAGAT	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.955G>A	19.37:g.55451232C>T	ENSP00000465520:p.Val319Ile	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	93	38	0.408602	NM_001127255	E9PE16|Q32MH8|Q7RTR1	Missense_Mutation	SNP	ENST00000590030.1	37	CCDS33109.1	608	0.2783882783882784	230	0.46747967479674796	107	0.2955801104972376	98	0.17132867132867133	173	0.22823218997361477	c	0.001	-3.214710	0.00024	0.461643	0.210233	ENSG00000167634	ENST00000328092;ENST00000448121;ENST00000340844;ENST00000446217	T;T;T;T	0.79554	-1.28;-1.28;-1.28;-1.28	1.56	-3.12	0.05282	NACHT nucleoside triphosphatase (1);	.	.	.	.	T	0.00012	0.0000	N	0.13198	0.31	0.80722	P	0.0	B;B;B;B	0.14438	0.01;0.005;0.004;0.003	B;B;B;B	0.13407	0.009;0.009;0.006;0.003	T	0.22382	-1.0218	8	0.13108	T	0.6	.	8.7467	0.34591	0.0:0.5737:0.2729:0.1534	rs775882;rs52796909;rs775882	347;319;319;319	E7EPM2;Q32MH9;Q8WX94;Q8WX94-2	.;.;NALP7_HUMAN;.	I	319;319;319;347	ENSP00000329568:V319I;ENSP00000409137:V319I;ENSP00000339491:V319I;ENSP00000414273:V347I	ENSP00000329568:V319I	V	-	1	0	NLRP7	60143044	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.175000	0.03102	-3.374000	0.00176	-1.957000	0.00481	GTA	C|0.705;A|0.001	.	strong		0.597	NLRP7-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000451396.1	NM_139176	
OTOP1	133060	hgsc.bcm.edu	37	4	4228425	4228425	+	Missense_Mutation	SNP	T	T	C	rs78657691		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:4228425T>C	ENST00000296358.4	-	1	191	c.167A>G	c.(166-168)aAa>aGa	p.K56R		NM_177998.1	NP_819056.1	Q7RTM1	OTOP1_HUMAN	otopetrin 1	56					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)		CTCGGCCAGTTTCTGTGGGAC	0.741																																					p.K56R		Atlas-SNP	.											OTOP1,caecum,carcinoma,0,2	OTOP1	118	2	0			c.A167G						scavenged	.																																			SO:0001583	missense	133060	exon1			GCCAGTTTCTGTG	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.167A>G	4.37:g.4228425T>C	ENSP00000296358:p.Lys56Arg	Somatic	34	6	0.176471		WXS	Illumina HiSeq	Phase_I	37	10	0.27027	NM_177998	A1L476	Missense_Mutation	SNP	ENST00000296358.4	37	CCDS3372.1	.	.	.	.	.	.	.	.	.	.	T	15.92	2.976461	0.53720	.	.	ENSG00000163982	ENST00000296358	T	0.13420	2.59	4.08	2.78	0.32641	.	0.000000	0.85682	U	0.000000	T	0.24812	0.0602	L	0.39898	1.24	0.53005	D	0.99996	D	0.89917	1.0	D	0.80764	0.994	T	0.01561	-1.1324	10	0.87932	D	0	.	10.0264	0.42074	0.0:0.0:0.1696:0.8304	.	56	Q7RTM1	OTOP1_HUMAN	R	56	ENSP00000296358:K56R	ENSP00000296358:K56R	K	-	2	0	OTOP1	4279326	1.000000	0.71417	1.000000	0.80357	0.133000	0.20885	4.318000	0.59190	1.490000	0.48466	0.352000	0.21897	AAA	.	.	weak		0.741	OTOP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206661.2	NM_177998	
ZYG11B	79699	hgsc.bcm.edu	37	1	53250650	53250650	+	Silent	SNP	G	G	A	rs6588443	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:53250650G>A	ENST00000294353.6	+	5	1339	c.1194G>A	c.(1192-1194)ggG>ggA	p.G398G	ZYG11B_ENST00000545132.1_Silent_p.G398G|ZYG11B_ENST00000443756.2_Silent_p.G398G	NM_024646.2	NP_078922.1	Q9C0D3	ZY11B_HUMAN	zyg-11 family member B, cell cycle regulator	398										breast(1)|endometrium(1)|kidney(6)|large_intestine(5)|lung(10)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	30						TTGCTGCAGGGATGCCTGTCC	0.478													A|||	3580	0.714856	0.9077	0.6729	5008	,	,		19255	0.9792		0.4284	False		,,,				2504	0.5061				p.G398G		Atlas-SNP	.											.	ZYG11B	61	.	0			c.G1194A						PASS	.	A		3635,771	314.4+/-293.6	1509,617,77	119.0	115.0	117.0		1194	2.6	1.0	1	dbSNP_116	117	3826,4774	611.1+/-395.8	841,2144,1315	no	coding-synonymous	ZYG11B	NM_024646.2		2350,2761,1392	AA,AG,GG		44.4884,17.4989,42.6342		398/745	53250650	7461,5545	2203	4300	6503	SO:0001819	synonymous_variant	79699	exon5			TGCAGGGATGCCT	AB051517	CCDS30717.1	1p32.3	2013-01-17	2012-12-10	2005-07-11	ENSG00000162378	ENSG00000162378		"""ZYG11 cell cycle regulator family"""	25820	protein-coding gene	gene with protein product			"""zyg-11 homolog (C. elegans)"", ""zyg-11 homolog B (C. elegans)"""	ZYG11		11214970	Standard	NM_024646		Approved	FLJ13456	uc001cuj.3	Q9C0D3	OTTHUMG00000008938	ENST00000294353.6:c.1194G>A	1.37:g.53250650G>A		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	93	44	0.473118	NM_024646	Q8N2X3|Q9H8L8	Silent	SNP	ENST00000294353.6	37	CCDS30717.1																																																																																			G|0.397;A|0.603	0.603	strong		0.478	ZYG11B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024749.1	NM_024646	
SLC5A9	200010	hgsc.bcm.edu	37	1	48705066	48705066	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:48705066G>A	ENST00000438567.2	+	12	1586	c.1534G>A	c.(1534-1536)Gcg>Acg	p.A512T	SLC5A9_ENST00000533824.1_Missense_Mutation_p.A533T|SLC5A9_ENST00000236495.5_Missense_Mutation_p.A537T	NM_001011547.2	NP_001011547.2	Q2M3M2	SC5A9_HUMAN	solute carrier family 5 (sodium/sugar cotransporter), member 9	512					sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			breast(1)|endometrium(3)|large_intestine(4)|liver(2)|lung(11)|ovary(3)|prostate(1)|urinary_tract(1)	26						CTCATACCCAGCGCCAGCCTG	0.597																																					p.A537T		Atlas-SNP	.											.	SLC5A9	82	.	0			c.G1609A						PASS	.						172.0	163.0	166.0					1																	48705066		2203	4300	6503	SO:0001583	missense	200010	exon13			TACCCAGCGCCAG	BX648549	CCDS30709.2, CCDS44136.1	1p33	2013-07-19	2013-07-19		ENSG00000117834	ENSG00000117834		"""Solute carriers"""	22146	protein-coding gene	gene with protein product			"""solute carrier family 5 (sodium/glucose cotransporter), member 9"""				Standard	NM_001011547		Approved	SGLT4	uc001crn.2	Q2M3M2	OTTHUMG00000007959	ENST00000438567.2:c.1534G>A	1.37:g.48705066G>A	ENSP00000401730:p.Ala512Thr	Somatic	230	1	0.00434783		WXS	Illumina HiSeq	Phase_I	194	87	0.448454	NM_001135181	B3KY87|B7ZL45|B7ZL47|E9PAK4|E9PJ08|Q5TET3	Missense_Mutation	SNP	ENST00000438567.2	37	CCDS30709.2	.	.	.	.	.	.	.	.	.	.	G	10.33	1.320633	0.23994	.	.	ENSG00000117834	ENST00000533824;ENST00000438567;ENST00000236495	T;T;T	0.63096	-0.02;-0.02;-0.02	5.18	5.18	0.71444	.	0.458166	0.26086	N	0.026430	T	0.41488	0.1161	N	0.11673	0.155	0.29064	N	0.883691	B;B;B	0.19445	0.036;0.005;0.009	B;B;B	0.13407	0.007;0.009;0.009	T	0.07520	-1.0768	10	0.06757	T	0.87	.	17.85	0.88744	0.0:0.0:1.0:0.0	.	533;512;537	E9PJ08;Q2M3M2;E9PAK4	.;SC5A9_HUMAN;.	T	533;512;537	ENSP00000431900:A533T;ENSP00000401730:A512T;ENSP00000236495:A537T	ENSP00000236495:A537T	A	+	1	0	SLC5A9	48477653	0.000000	0.05858	0.855000	0.33649	0.575000	0.36095	0.380000	0.20602	2.682000	0.91365	0.650000	0.86243	GCG	.	.	none		0.597	SLC5A9-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022061.3	XM_117174	
CR1	1378	hgsc.bcm.edu	37	1	207782931	207782931	+	Missense_Mutation	SNP	A	A	G	rs6691117	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:207782931A>G	ENST00000367049.4	+	37	6193	c.6193A>G	c.(6193-6195)Atc>Gtc	p.I2065V	CR1_ENST00000367053.1_Missense_Mutation_p.I1615V|CR1_ENST00000367052.1_Missense_Mutation_p.I1615V|CR1_ENST00000367051.1_Missense_Mutation_p.I1615V|CR1_ENST00000400960.2_Missense_Mutation_p.I1615V	NM_000651.4	NP_000642.3	P17927	CR1_HUMAN	complement component (3b/4b) receptor 1 (Knops blood group)	1615					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						CACTGAGATCATCAGATTTAG	0.498													G|||	2471	0.493411	0.8722	0.3761	5008	,	,		19776	0.3433		0.2256	False		,,,				2504	0.4949				p.I2065V		Atlas-SNP	.											.	CR1	354	.	0			c.A6193G						PASS	.	G	VAL/ILE,VAL/ILE	2892,958		1089,714,122	36.0	37.0	37.0		4843,6193	2.5	0.0	1	dbSNP_116	37	1761,6497		162,1437,2530	yes	missense,missense	CR1	NM_000573.3,NM_000651.4	29,29	1251,2151,2652	GG,GA,AA		21.3248,24.8831,38.4291	benign,benign	1615/2040,2065/2490	207782931	4653,7455	1925	4129	6054	SO:0001583	missense	1378	exon37			GAGATCATCAGAT	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.6193A>G	1.37:g.207782931A>G	ENSP00000356016:p.Ile2065Val	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	87	45	0.517241	NM_000651	Q16744|Q16745|Q5SR43|Q5SR45|Q9UQV2	Missense_Mutation	SNP	ENST00000367049.4	37	CCDS44308.1	850	0.3891941391941392	408	0.8292682926829268	135	0.3729281767955801	143	0.25	164	0.21635883905013192	G	0.017	-1.509804	0.00984	0.751169	0.213248	ENSG00000203710	ENST00000367052;ENST00000367051;ENST00000367053;ENST00000400960;ENST00000367049	T;T;T;T;T	0.60672	0.17;0.17;0.17;0.17;0.17	2.54	2.54	0.30619	Complement control module (2);Sushi/SCR/CCP (3);	.	.	.	.	T	0.00012	0.0000	N	0.00246	-1.78	0.80722	P	0.0	B;B;B	0.06786	0.0;0.0;0.001	B;B;B	0.10450	0.0;0.0;0.005	T	0.38866	-0.9641	8	0.02654	T	1	.	5.5311	0.16985	0.1589:0.0:0.8411:0.0	rs6691117;rs59510794;rs6691117	1615;1615;2065	Q5SR44;P17927;E9PDY4	.;CR1_HUMAN;.	V	1615;1615;1615;1615;2065	ENSP00000356019:I1615V;ENSP00000356018:I1615V;ENSP00000356020:I1615V;ENSP00000383744:I1615V;ENSP00000356016:I2065V	ENSP00000356016:I2065V	I	+	1	0	CR1	205849554	0.801000	0.28930	0.004000	0.12327	0.078000	0.17371	2.671000	0.46842	0.637000	0.30526	-0.355000	0.07637	ATC	A|0.601;G|0.399	0.399	strong		0.498	CR1-012	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382527.1	NM_000573	
ANKRD30A	91074	hgsc.bcm.edu	37	10	37486216	37486216	+	Silent	SNP	C	C	T	rs574286090	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:37486216C>T	ENST00000602533.1	+	28	2553	c.2454C>T	c.(2452-2454)ccC>ccT	p.P818P	ANKRD30A_ENST00000361713.1_Silent_p.P818P|ANKRD30A_ENST00000374660.1_Silent_p.P937P			Q9BXX3	AN30A_HUMAN	ankyrin repeat domain 30A	874					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.P818P(4)		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						TAGAGCCTCCCGAGAAGCCAT	0.323																																					p.P818P		Atlas-SNP	.											ANKRD30A,colon,carcinoma,0,16	ANKRD30A	448	16	4	Substitution - coding silent(4)	lung(1)|ovary(1)|prostate(1)|kidney(1)	c.C2454T						scavenged	.						201.0	165.0	176.0					10																	37486216		1812	4087	5899	SO:0001819	synonymous_variant	91074	exon28			GCCTCCCGAGAAG	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.2454C>T	10.37:g.37486216C>T		Somatic	343	0	0		WXS	Illumina HiSeq	Phase_I	296	8	0.027027	NM_052997	Q5W025	Silent	SNP	ENST00000602533.1	37																																																																																				.	.	none		0.323	ANKRD30A-001	KNOWN	NMD_exception|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000047588.2	NM_052997	
FAM86B1	85002	hgsc.bcm.edu	37	8	12044262	12044262	+	Silent	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:12044262G>A	ENST00000448228.2	-	4	370	c.321C>T	c.(319-321)gcC>gcT	p.A107A	FAM86B1_ENST00000533513.1_Silent_p.A141A|FAM86B1_ENST00000534520.1_Silent_p.A107A|FAM86B1_ENST00000321602.8_Missense_Mutation_p.P2L|FAM86B1_ENST00000533852.2_Silent_p.A141A	NM_001083537.1	NP_001077006.1	Q8N7N1	F86B1_HUMAN	family with sequence similarity 86, member B1	107										kidney(1)|prostate(1)|stomach(1)	3			STAD - Stomach adenocarcinoma(15;0.033)	COAD - Colon adenocarcinoma(149;0.0965)		GGTAGAGGGCGGCATCCCATG	0.612																																					p.A107A		Atlas-SNP	.											FAM86B1_ENST00000321602,NS,carcinoma,0,2	FAM86B1	7	2	0			c.C321T						scavenged	.						1.0	1.0	1.0					8																	12044262		473	1093	1566	SO:0001819	synonymous_variant	85002	exon4			GAGGGCGGCATCC	BC007983	CCDS59512.1	8p23.1	2014-02-12	2005-08-19		ENSG00000186523	ENSG00000186523			28268	protein-coding gene	gene with protein product						12477932	Standard	NM_001083537		Approved	MGC16279	uc010lse.3	Q8N7N1	OTTHUMG00000165298	ENST00000448228.2:c.321C>T	8.37:g.12044262G>A		Somatic	260	0	0		WXS	Illumina HiSeq	Phase_I	324	134	0.41358	NM_001083537		Silent	SNP	ENST00000448228.2	37	CCDS59512.1	.	.	.	.	.	.	.	.	.	.	-	0.003	-2.469420	0.00169	.	.	ENSG00000186523	ENST00000321602;ENST00000526802	T	0.30714	1.52	1.17	-0.949	0.10376	.	.	.	.	.	T	0.19604	0.0471	.	.	.	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.08166	-1.0735	8	0.87932	D	0	.	2.4515	0.04519	0.3509:0.0:0.425:0.2241	.	2;39	F6QN85;Q4KMP3	.;.	L	2;103	ENSP00000439686:P2L	ENSP00000439686:P2L	P	-	2	0	FAM86B1	12081671	0.000000	0.05858	0.092000	0.20876	0.049000	0.14656	-3.087000	0.00610	-0.554000	0.06150	-1.169000	0.01745	CCG	.	.	none		0.612	FAM86B1-016	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000383317.1	NM_032916	
CAND2	23066	hgsc.bcm.edu	37	3	12861586	12861586	+	Splice_Site	SNP	T	T	C	rs4684883	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:12861586T>C	ENST00000456430.2	+	11	2987	c.2946T>C	c.(2944-2946)ggT>ggC	p.G982G	CAND2_ENST00000295989.5_Splice_Site_p.G889G	NM_001162499.1	NP_001155971.1	O75155	CAND2_HUMAN	cullin-associated and neddylation-dissociated 2 (putative)	982					positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	intracellular (GO:0005622)|nucleus (GO:0005634)				breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(8)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	37						GTCCTGCAGGTCGGCCACACA	0.597													T|||	743	0.148363	0.0454	0.304	5008	,	,		18115	0.1171		0.1799	False		,,,				2504	0.1769				p.G982G	GBM(43;676 868 1633 6395 37496)	Atlas-SNP	.											.	CAND2	138	.	0			c.T2946C						PASS	.	T	,	251,4061		4,243,1909	107.0	116.0	113.0		2946,2667	-0.2	0.9	3	dbSNP_111	113	1537,6939		153,1231,2854	yes	coding-synonymous-near-splice,coding-synonymous-near-splice	CAND2	NM_001162499.1,NM_012298.2	,	157,1474,4763	CC,CT,TT		18.1336,5.821,13.9819	,	982/1237,889/1120	12861586	1788,11000	2156	4238	6394	SO:0001630	splice_region_variant	23066	exon11			TGCAGGTCGGCCA		CCDS43053.1, CCDS54554.1	3p25.2	2008-02-05			ENSG00000144712	ENSG00000144712			30689	protein-coding gene	gene with protein product	"""TBP interacting protein"""	610403				9734811, 10441524	Standard	NM_012298		Approved	TIP120B, KIAA0667, Tp120b	uc003bxk.2	O75155	OTTHUMG00000155397	ENST00000456430.2:c.2945-1T>C	3.37:g.12861586T>C		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	63	35	0.555556	NM_001162499	B9EGM9|E9KL24	Silent	SNP	ENST00000456430.2	37	CCDS54554.1																																																																																			T|0.852;C|0.148	0.148	strong		0.597	CAND2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339856.4	XM_371617	Silent
ITSN2	50618	hgsc.bcm.edu	37	2	24524958	24524958	+	Missense_Mutation	SNP	C	C	T	rs7603997	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:24524958C>T	ENST00000355123.4	-	10	1314	c.871G>A	c.(871-873)Gtt>Att	p.V291I	ITSN2_ENST00000406921.3_Missense_Mutation_p.V291I|ITSN2_ENST00000361999.3_Missense_Mutation_p.V291I	NM_006277.2	NP_006268.2	Q9NZM3	ITSN2_HUMAN	intersectin 2	291	EH 2. {ECO:0000255|PROSITE- ProRule:PRU00077}.		V -> I (in dbSNP:rs7603997). {ECO:0000269|PubMed:14702039}.		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)					TCACCATCAACGTCAGCCAGA	0.353													T|||	1463	0.292133	0.388	0.2075	5008	,	,		15878	0.1915		0.3509	False		,,,				2504	0.2658				p.V291I		Atlas-SNP	.											.	ITSN2	224	.	0			c.G871A						PASS	.	T	ILE/VAL,ILE/VAL,ILE/VAL	1863,2543	632.7+/-395.9	407,1049,747	87.0	80.0	83.0		871,871,871	2.1	1.0	2	dbSNP_116	83	2841,5759	673.9+/-403.1	462,1917,1921	yes	missense,missense,missense	ITSN2	NM_006277.2,NM_019595.3,NM_147152.2	29,29,29	869,2966,2668	TT,TC,CC		33.0349,42.2833,36.1679	benign,benign,benign	291/1698,291/1671,291/1250	24524958	4704,8302	2203	4300	6503	SO:0001583	missense	50618	exon10			CATCAACGTCAGC	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.871G>A	2.37:g.24524958C>T	ENSP00000347244:p.Val291Ile	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	83	24	0.289157	NM_147152	O95062|Q15812|Q9HAK4|Q9NXE6|Q9NYG0|Q9NZM2|Q9ULG4	Missense_Mutation	SNP	ENST00000355123.4	37	CCDS1710.2	664	0.304029304029304	200	0.4065040650406504	84	0.23204419889502761	111	0.19405594405594406	269	0.3548812664907652	T	3.130	-0.178539	0.06380	0.422833	0.330349	ENSG00000198399	ENST00000361999;ENST00000355123;ENST00000380868;ENST00000445614;ENST00000406921;ENST00000412011	T;T;T;T;T	0.26810	1.71;1.71;1.71;1.71;1.71	4.44	2.11	0.27256	EPS15 homology (EH) (2);EF-hand-like domain (1);	0.000000	0.37483	N	0.002070	T	0.00012	0.0000	N	0.04508	-0.205	0.52501	P	4.899999999996574E-5	P;P;P;P	0.51791	0.911;0.911;0.948;0.622	P;P;P;B	0.48952	0.496;0.496;0.596;0.275	T	0.11867	-1.0570	9	0.02654	T	1	.	9.1297	0.36837	0.0:0.2282:0.0:0.7718	rs7603997;rs17845626;rs17858557;rs52793399;rs59754072;rs7603997	291;291;291;291	Q9NZM3-4;Q9NZM3-3;Q9NZM3-2;Q9NZM3	.;.;.;ITSN2_HUMAN	I	291;291;291;315;291;316	ENSP00000354561:V291I;ENSP00000347244:V291I;ENSP00000370250:V291I;ENSP00000384499:V291I;ENSP00000391224:V316I	ENSP00000347244:V291I	V	-	1	0	ITSN2	24378462	0.991000	0.36638	0.999000	0.59377	0.973000	0.67179	0.343000	0.19944	0.338000	0.23692	-0.524000	0.04348	GTT	C|0.652;N|0.000	.	strong		0.353	ITSN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207620.2	NM_006277	
ZBP1	81030	hgsc.bcm.edu	37	20	56189985	56189985	+	Missense_Mutation	SNP	C	C	G	rs16981187	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:56189985C>G	ENST00000371173.3	-	4	637	c.460G>C	c.(460-462)Gac>Cac	p.D154H	ZBP1_ENST00000343535.4_Missense_Mutation_p.D154H|ZBP1_ENST00000538947.1_5'Flank|ZBP1_ENST00000541799.1_Missense_Mutation_p.D154H|ZBP1_ENST00000340462.4_Missense_Mutation_p.D131H|ZBP1_ENST00000395822.3_Missense_Mutation_p.D79H	NM_001160417.1|NM_030776.2	NP_001153889.1|NP_110403.2	Q9H171	ZBP1_HUMAN	Z-DNA binding protein 1	154			D -> H (in dbSNP:rs16981187).		innate immune response (GO:0045087)|positive regulation of type I interferon production (GO:0032481)|positive regulation of type I interferon-mediated signaling pathway (GO:0060340)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	DNA binding (GO:0003677)|double-stranded RNA adenosine deaminase activity (GO:0003726)|left-handed Z-DNA binding (GO:0003692)|RNA binding (GO:0003723)			large_intestine(11)|lung(8)|ovary(4)|prostate(1)|skin(2)|urinary_tract(1)	27	Lung NSC(12;0.000545)|all_lung(29;0.00195)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(13;7.87e-13)|Epithelial(14;3.26e-09)|all cancers(14;3.62e-08)			TCATCCATGTCCAGAAGGTGC	0.572													C|||	268	0.0535144	0.0719	0.0432	5008	,	,		21012	0.0079		0.0487	False		,,,				2504	0.0879				p.D154H		Atlas-SNP	.											.	ZBP1	65	.	0			c.G460C						PASS	.	C	HIS/ASP,HIS/ASP,HIS/ASP,HIS/ASP	317,4089	169.4+/-200.1	15,287,1901	222.0	174.0	191.0		460,235,460,460	-5.4	0.0	20	dbSNP_123	191	408,8192	128.7+/-186.9	13,382,3905	yes	missense,missense,missense,missense	ZBP1	NM_001160417.1,NM_001160418.1,NM_001160419.1,NM_030776.2	81,81,81,81	28,669,5806	GG,GC,CC		4.7442,7.1947,5.5744	probably-damaging,probably-damaging,probably-damaging,probably-damaging	154/429,79/355,154/249,154/430	56189985	725,12281	2203	4300	6503	SO:0001583	missense	81030	exon4			CCATGTCCAGAAG	AJ300575	CCDS13461.1, CCDS54477.1, CCDS54478.1	20q13.31	2009-08-21	2002-07-25	2002-07-26	ENSG00000124256	ENSG00000124256			16176	protein-coding gene	gene with protein product	"""DNA-dependent activator of IRFs"""	606750	"""chromosome 20 open reading frame 183"""	C20orf183		11842111	Standard	NM_030776		Approved	dJ718J7.3, DLM1, DLM-1, DAI	uc002xyo.3	Q9H171	OTTHUMG00000032824	ENST00000371173.3:c.460G>C	20.37:g.56189985C>G	ENSP00000360215:p.Asp154His	Somatic	247	0	0		WXS	Illumina HiSeq	Phase_I	183	99	0.540984	NM_001160419	A2A2F7|B3KVA1|F5GYT1|Q5JY39|Q9BYW4	Missense_Mutation	SNP	ENST00000371173.3	37	CCDS13461.1	95	0.043498168498168496	38	0.07723577235772358	18	0.049723756906077346	1	0.0017482517482517483	38	0.05013192612137203	C	9.503	1.103680	0.20632	0.071947	0.047442	ENSG00000124256	ENST00000371173;ENST00000395822;ENST00000340462;ENST00000357677;ENST00000343535;ENST00000541799	T;T;T;T;T	0.30182	1.54;1.54;1.54;1.54;1.54	3.39	-5.43	0.02632	Winged helix-turn-helix transcription repressor DNA-binding (1);	1.755500	0.02862	N	0.130409	T	0.00875	0.0029	N	0.17082	0.46	0.09310	N	1	B;B;B;B	0.32543	0.324;0.375;0.375;0.375	B;B;B;B	0.34301	0.077;0.126;0.179;0.126	T	0.08493	-1.0719	10	0.42905	T	0.14	-2.5151	5.7903	0.18357	0.0:0.1813:0.4126:0.406	rs16981187;rs16981187	154;154;79;154	F5GYT1;A2RRL9;A2A2F7;Q9H171	.;.;.;ZBP1_HUMAN	H	154;79;131;154;154;154	ENSP00000360215:D154H;ENSP00000379167:D79H;ENSP00000344954:D131H;ENSP00000340584:D154H;ENSP00000440552:D154H	ENSP00000344954:D131H	D	-	1	0	ZBP1	55623391	0.000000	0.05858	0.000000	0.03702	0.024000	0.10985	-1.232000	0.02936	-1.257000	0.02475	-0.175000	0.13238	GAC	C|0.946;G|0.054	0.054	strong		0.572	ZBP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079849.1	NM_030776	
CD200R1	131450	hgsc.bcm.edu	37	3	112648107	112648107	+	Silent	SNP	G	G	A	rs373257099		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:112648107G>A	ENST00000471858.1	-	3	613	c.381C>T	c.(379-381)gaC>gaT	p.D127D	CD200R1_ENST00000295863.4_Silent_p.D105D|CD200R1_ENST00000308611.3_Silent_p.D150D|CD200R1_ENST00000490004.1_Silent_p.D127D|CD200R1_ENST00000440122.2_Silent_p.D150D	NM_170780.2	NP_740750.1	Q8TD46	MO2R1_HUMAN	CD200 receptor 1	127	Ig-like V-type.				regulation of immune response (GO:0050776)|viral process (GO:0016032)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)				cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(9)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(1)	26						TGTAATACCCGTCATGAGTGA	0.443													g|||	1	0.000199681	0.0	0.0	5008	,	,		20605	0.0		0.0	False		,,,				2504	0.001				p.D150D		Atlas-SNP	.											CD200R1_ENST00000440122,NS,carcinoma,0,2	CD200R1	91	2	0			c.C450T						PASS	.	A	,,,	0,4406		0,0,2203	164.0	156.0	159.0		450,450,381,381	-10.9	0.2	3		159	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CD200R1	NM_138806.3,NM_138939.2,NM_138940.2,NM_170780.2	,,,	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,,,	150/349,150/189,127/166,127/326	112648107	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	131450	exon4			ATACCCGTCATGA	AK126349	CCDS2969.1, CCDS2970.1, CCDS46889.1, CCDS54623.1	3q13	2014-05-15	2004-08-31	2004-09-01	ENSG00000163606	ENSG00000163606		"""Immunoglobulin superfamily / C2-set domain containing"""	24235	protein-coding gene	gene with protein product		607546	"""MOX2 receptor"""	MOX2R		10981966, 11133863	Standard	NM_138806		Approved	OX2R, HCRTR2, CD200R	uc003dzj.1	Q8TD46	OTTHUMG00000159298	ENST00000471858.1:c.381C>T	3.37:g.112648107G>A		Somatic	302	0	0		WXS	Illumina HiSeq	Phase_I	244	108	0.442623	NM_138806	B3KWZ9|E9PCM9|Q52LJ7|Q6IS95|Q6UW94|Q6WHB8|Q8TD44|Q8TD45|Q8TD52	Silent	SNP	ENST00000471858.1	37	CCDS2970.1																																																																																			.	.	weak		0.443	CD200R1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354467.1	NM_138806	
MUC4	4585	hgsc.bcm.edu	37	3	195507385	195507385	+	Missense_Mutation	SNP	G	G	A	rs199842409		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195507385G>A	ENST00000463781.3	-	2	11525	c.11066C>T	c.(11065-11067)gCa>gTa	p.A3689V	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.A3689V	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.A3689V(1)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		ACCTGTGGATGCTGAGGAAGT	0.572																																					p.A3689V		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	1	Substitution - Missense(1)	stomach(1)	c.C11066T						scavenged	.						15.0	15.0	15.0					3																	195507385		598	1552	2150	SO:0001583	missense	4585	exon2			GTGGATGCTGAGG	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.11066C>T	3.37:g.195507385G>A	ENSP00000417498:p.Ala3689Val	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	37	20	0.540541	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	N	8.097	0.775840	0.16051	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.27104	1.69;1.8	0.743	-0.753	0.11068	.	.	.	.	.	T	0.10165	0.0249	N	0.08118	0	0.80722	P	0.0	B	0.06786	0.001	B	0.01281	0.0	T	0.36335	-0.9752	7	.	.	.	.	4.7378	0.12997	0.3389:0.0:0.6611:0.0	.	3561	E7ESK3	.	V	3689	ENSP00000417498:A3689V;ENSP00000420243:A3689V	.	A	-	2	0	MUC4	196992164	0.004000	0.15560	0.010000	0.14722	0.010000	0.07245	0.039000	0.13884	-2.027000	0.00932	-2.047000	0.00414	GCA	.	.	weak		0.572	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
POM121L12	285877	hgsc.bcm.edu	37	7	53103554	53103554	+	Missense_Mutation	SNP	C	C	G	rs11238247	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:53103554C>G	ENST00000408890.4	+	1	206	c.190C>G	c.(190-192)Cag>Gag	p.Q64E		NM_182595.3	NP_872401.3	Q8N7R1	P1L12_HUMAN	POM121 transmembrane nucleoporin-like 12	64			Q -> E (in dbSNP:rs11238247). {ECO:0000269|PubMed:14702039}.							endometrium(5)|kidney(1)|large_intestine(5)|lung(44)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	61						GAGCCATATTCAGTACTTCCA	0.697													C|||	1680	0.335463	0.1921	0.4323	5008	,	,		12258	0.3095		0.4861	False		,,,				2504	0.3323				p.Q64E		Atlas-SNP	.											.	POM121L12	146	.	0			c.C190G						PASS	.	C	GLU/GLN	852,3038		105,642,1198	29.0	33.0	32.0		190	1.1	0.0	7	dbSNP_120	32	4217,4067		1064,2089,989	yes	missense	POM121L12	NM_182595.3	29	1169,2731,2187	GG,GC,CC		49.0946,21.9023,41.6379	possibly-damaging	64/297	53103554	5069,7105	1945	4142	6087	SO:0001583	missense	285877	exon1			CATATTCAGTACT		CCDS43584.1	7p12.1	2012-03-13	2012-03-13		ENSG00000221900	ENSG00000221900			25369	protein-coding gene	gene with protein product			"""POM121 membrane glycoprotein-like 12"""				Standard	NM_182595		Approved	DKFZp564N2472	uc003tpz.3	Q8N7R1	OTTHUMG00000155995	ENST00000408890.4:c.190C>G	7.37:g.53103554C>G	ENSP00000386133:p.Gln64Glu	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	53	28	0.528302	NM_182595	Q8NDI9	Missense_Mutation	SNP	ENST00000408890.4	37	CCDS43584.1	806	0.36904761904761907	102	0.2073170731707317	154	0.425414364640884	175	0.30594405594405594	375	0.4947229551451187	C	6.806	0.517760	0.13005	0.219023	0.509054	ENSG00000221900	ENST00000408890	T	0.23348	1.91	1.11	1.11	0.20524	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	P	0.43701	0.815	B	0.33690	0.168	T	0.43065	-0.9414	8	0.66056	D	0.02	.	5.5761	0.17225	0.0:1.0:0.0:0.0	rs11238247;rs52794294;rs11238247	64	Q8N7R1	P1L12_HUMAN	E	64	ENSP00000386133:Q64E	ENSP00000386133:Q64E	Q	+	1	0	POM121L12	53071048	0.000000	0.05858	0.002000	0.10522	0.006000	0.05464	0.130000	0.15850	0.903000	0.36546	0.313000	0.20887	CAG	C|0.588;G|0.412	0.412	strong		0.697	POM121L12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342656.1	NM_182595	
TRIP6	7205	hgsc.bcm.edu	37	7	100465824	100465824	+	Missense_Mutation	SNP	G	G	A	rs2437100	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	55	0	0		WXS	Illumina HiSeq	Phase_I	50	22	0.44	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	
MUC4	4585	hgsc.bcm.edu	37	3	195505827	195505827	+	Silent	SNP	A	A	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195505827A>G	ENST00000463781.3	-	2	13083	c.12624T>C	c.(12622-12624)ccT>ccC	p.P4208P	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Silent_p.P4208P	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.P4208P(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)		TGACAGGAAGAGGGGTGGCGT	0.597																																					p.P4208P		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,-2,3	MUC4	1505	3	1	Substitution - coding silent(1)	kidney(1)	c.T12624C						scavenged	.						17.0	16.0	16.0					3																	195505827		688	1570	2258	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.12624T>C	3.37:g.195505827A>G		Somatic	72	4	0.0555556		WXS	Illumina HiSeq	Phase_I	117	4	0.034188	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		0.597	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
LHB	3972	hgsc.bcm.edu	37	19	49519905	49519905	+	Missense_Mutation	SNP	A	A	G	rs1800447|rs35296413	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:49519905A>G	ENST00000221421.2	-	2	81	c.82T>C	c.(82-84)Tgg>Cgg	p.W28R	CTB-60B18.10_ENST00000600007.1_lincRNA	NM_000894.2	NP_000885.1	P01229	LSHB_HUMAN	luteinizing hormone beta polypeptide	28			W -> R (in dbSNP:rs1800447). {ECO:0000269|PubMed:9886510}.		cell-cell signaling (GO:0007267)|cellular protein metabolic process (GO:0044267)|male gonad development (GO:0008584)|peptide hormone processing (GO:0016486)|progesterone biosynthetic process (GO:0006701)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	receptor binding (GO:0005102)			cervix(1)|endometrium(1)|large_intestine(1)|lung(4)|prostate(1)	8		all_epithelial(76;9.62e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		all cancers(93;0.000371)|OV - Ovarian serous cystadenocarcinoma(262;0.000503)|GBM - Glioblastoma multiforme(486;0.00518)|Epithelial(262;0.0427)		GGGTGGCACCATGGCCGAAGC	0.637													a|||	290	0.0579073	0.0552	0.0519	5008	,	,		17127	0.0585		0.0954	False		,,,				2504	0.0266				p.W28R		Atlas-SNP	.											LHB,NS,carcinoma,0,1	LHB	20	1	0			c.T82C	GRCh37	CM993948	LHB	M	rs1800447	PASS	.	A	ARG/TRP	190,4216	106.5+/-144.9	8,174,2021	101.0	81.0	88.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	82	0.3	0.6	19	dbSNP_89	88	642,7958	151.9+/-206.6	26,590,3684	no	missense	LHB	NM_000894.2	101	34,764,5705	GG,GA,AA		7.4651,4.3123,6.397	benign	28/142	49519905	832,12174	2203	4300	6503	SO:0001583	missense	3972	exon2			GGCACCATGGCCG		CCDS12748.1	19q13.3	2013-02-26				ENSG00000104826		"""Endogenous ligands"""	6584	protein-coding gene	gene with protein product	"""lutropin, beta chain"", ""interstitial cell stimulating hormone, beta chain"", ""luteinizing hormone beta subunit"""	152780				1191677	Standard	NM_000894		Approved	LSH-B, CGB4, hLHB	uc002plt.3	P01229		ENST00000221421.2:c.82T>C	19.37:g.49519905A>G	ENSP00000221421:p.Trp28Arg	Somatic	360	0	0		WXS	Illumina HiSeq	Phase_I	253	50	0.197628	NM_000894	Q9UDI0	Missense_Mutation	SNP	ENST00000221421.2	37	CCDS12748.1	134	0.06135531135531135	24	0.04878048780487805	21	0.058011049723756904	24	0.04195804195804196	65	0.08575197889182058	a	0.280	-0.987219	0.02180	0.043123	0.074651	ENSG00000104826	ENST00000221421;ENST00000391870	D	0.90197	-2.63	4.18	0.272	0.15645	Cystine knot (1);	0.243672	0.26963	N	0.021601	T	0.06690	0.0171	N	0.00483	-1.445	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.47114	-0.9142	9	0.23302	T	0.38	-16.6805	7.0569	0.25104	0.3174:0.0:0.6826:0.0	rs1800447;rs1800447	28	P01229	LSHB_HUMAN	R	28;44	ENSP00000221421:W28R	ENSP00000221421:W28R	W	-	1	0	LHB	54211717	0.021000	0.18746	0.563000	0.28383	0.006000	0.05464	0.412000	0.21131	0.015000	0.14971	-0.400000	0.06385	TGG	A|0.005;T|0.995	.	alt		0.637	LHB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466246.1	NM_000894	
DDIAS	220042	hgsc.bcm.edu	37	11	82644904	82644904	+	Missense_Mutation	SNP	G	G	A	rs7130899	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:82644904G>A	ENST00000533655.1	+	6	2736	c.2524G>A	c.(2524-2526)Gtt>Att	p.V842I	C11orf82_ENST00000528759.1_3'UTR|C11orf82_ENST00000329143.3_Missense_Mutation_p.V541I|C11orf82_ENST00000430323.2_Missense_Mutation_p.V842I|C11orf82_ENST00000525361.1_Intron	NM_145018.3	NP_659455.3	Q8IXT1	DDIAS_HUMAN		842			V -> I (in dbSNP:rs7130899). {ECO:0000269|PubMed:15489334}.		apoptotic process (GO:0006915)|cellular response to cytokine stimulus (GO:0071345)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|cellular response to hydroperoxide (GO:0071447)|cellular response to UV (GO:0034644)|hemopoiesis (GO:0030097)|mitotic cell cycle arrest (GO:0071850)|negative regulation of fibroblast apoptotic process (GO:2000270)|spermatid development (GO:0007286)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(17)|ovary(3)|prostate(1)|skin(1)|urinary_tract(1)	33						TGTATCTGGTGTTTCACAACC	0.408													A|||	2772	0.553514	0.7678	0.6369	5008	,	,		18048	0.3442		0.498	False		,,,				2504	0.4775				p.V842I		Atlas-SNP	.											.	C11orf82	71	.	0			c.G2524A						PASS	.	A	ILE/VAL	3205,1201	416.7+/-337.7	1179,847,177	53.0	53.0	53.0		2524	-8.0	0.0	11	dbSNP_116	53	4310,4290	570.3+/-389.3	1085,2140,1075	yes	missense	C11orf82	NM_145018.3	29	2264,2987,1252	AA,AG,GG		49.8837,27.2583,42.219	benign	842/999	82644904	7515,5491	2203	4300	6503	SO:0001583	missense	220042	exon6			TCTGGTGTTTCAC																												ENST00000533655.1:c.2524G>A	11.37:g.82644904G>A	ENSP00000435421:p.Val842Ile	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	82	14	0.170732	NM_145018	Q96LK6|Q9H856	Missense_Mutation	SNP	ENST00000533655.1	37	CCDS8263.1	1150	0.5265567765567766	373	0.758130081300813	220	0.6077348066298343	177	0.3094405594405594	380	0.5013192612137203	A	2.376	-0.343140	0.05243	0.727417	0.501163	ENSG00000165490	ENST00000430323;ENST00000533655;ENST00000329143	T;T;T	0.17054	2.56;2.56;2.3	5.45	-8.02	0.01118	.	1.828400	0.02661	N	0.107500	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	0.35798	-0.9774	8	.	.	.	.	2.7784	0.05354	0.1081:0.2063:0.3774:0.3082	rs7130899;rs17650919;rs17846253;rs17859275;rs56943641;rs7130899	842	Q8IXT1	NOXIN_HUMAN	I	842;842;541	ENSP00000414687:V842I;ENSP00000435421:V842I;ENSP00000329930:V541I	.	V	+	1	0	C11orf82	82322552	0.000000	0.05858	0.000000	0.03702	0.033000	0.12548	-0.653000	0.05360	-1.988000	0.00980	-0.352000	0.07741	GTT	G|0.454;A|0.546	0.546	strong		0.408	C11orf82-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391936.1		
LEPR	3953	hgsc.bcm.edu	37	1	66075952	66075952	+	Missense_Mutation	SNP	G	G	C	rs1805094	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:66075952G>C	ENST00000349533.6	+	14	2153	c.1968G>C	c.(1966-1968)aaG>aaC	p.K656N	LEPR_ENST00000371059.3_Missense_Mutation_p.K656N|LEPR_ENST00000371060.3_Missense_Mutation_p.K656N|LEPR_ENST00000344610.8_Missense_Mutation_p.K656N|LEPR_ENST00000371058.1_Missense_Mutation_p.K656N|LEPR_ENST00000406510.3_Intron	NM_002303.5	NP_002294.2	O15243	OBRG_HUMAN	leptin receptor	0					negative regulation of growth hormone receptor signaling pathway (GO:0060400)|negative regulation of JAK-STAT cascade (GO:0046426)|negative regulation of protein localization to cell surface (GO:2000009)	endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	receptor binding (GO:0005102)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(22)|skin(2)	36				OV - Ovarian serous cystadenocarcinoma(397;0.00722)|KIRC - Kidney renal clear cell carcinoma(1967;0.094)		CTATGAAAAAGGAGAAAAATG	0.269													G|||	713	0.142372	0.1997	0.1888	5008	,	,		18092	0.0585		0.1511	False		,,,				2504	0.1094				p.K656N		Atlas-SNP	.											.	LEPR	284	.	0			c.G1968C	GRCh37	CM025915	LEPR	M	rs8179183	PASS	.	G	ASN/LYS,ASN/LYS,ASN/LYS,ASN/LYS,ASN/LYS,ASN/LYS	828,3574	303.5+/-288.0	71,686,1444	53.0	55.0	54.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1968,1968,1968,1968,1968,1968	-2.9	0.0	1	dbSNP_117	54	1467,7121	271.3+/-289.5	134,1199,2961	yes	missense,missense,missense,missense,missense,missense	LEPR	NM_001003679.3,NM_001003680.3,NM_001198687.1,NM_001198688.1,NM_001198689.1,NM_002303.5	94,94,94,94,94,94	205,1885,4405	CC,CG,GG		17.082,18.8096,17.6674	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	656/897,656/959,656/959,656/907,656/897,656/1166	66075952	2295,10695	2201	4294	6495	SO:0001583	missense	3953	exon14			GAAAAAGGAGAAA	U43168	CCDS631.1, CCDS30740.1, CCDS30741.1, CCDS55604.1	1p31	2014-09-17			ENSG00000116678	ENSG00000116678		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6554	protein-coding gene	gene with protein product		601007				8548812, 8812446	Standard	NM_001003680		Approved	OBR, CD295	uc001dci.3	P48357	OTTHUMG00000009115	ENST00000349533.6:c.1968G>C	1.37:g.66075952G>C	ENSP00000330393:p.Lys656Asn	Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	138	53	0.384058	NM_001003680	Q6FHL5	Missense_Mutation	SNP	ENST00000349533.6	37	CCDS631.1	317	0.14514652014652016	87	0.17682926829268292	68	0.1878453038674033	38	0.06643356643356643	124	0.16358839050131926	G	8.525	0.869742	0.17322	0.188096	0.17082	ENSG00000116678	ENST00000344610;ENST00000349533;ENST00000371060;ENST00000371059;ENST00000371058	T;T;T;T;T	0.57273	0.43;0.42;0.43;0.41;0.43	5.33	-2.91	0.05631	Fibronectin, type III (2);	0.254500	0.43260	D	0.000596	T	0.27313	0.0670	L	0.47190	1.495	0.25609	P	0.9865115	P;P;P	0.51351	0.696;0.798;0.944	B;B;P	0.48552	0.232;0.409;0.581	T	0.28427	-1.0044	9	0.23891	T	0.37	-8.3309	9.1333	0.36859	0.3785:0.0:0.5107:0.1108	rs8179183;rs17127774;rs52811589;rs8179183	656;656;656	P48357;P48357-2;P48357-3	LEPR_HUMAN;.;.	N	656	ENSP00000340884:K656N;ENSP00000330393:K656N;ENSP00000360099:K656N;ENSP00000360098:K656N;ENSP00000360097:K656N	ENSP00000340884:K656N	K	+	3	2	LEPR	65848540	0.102000	0.21896	0.045000	0.18777	0.677000	0.39632	-0.497000	0.06428	-0.833000	0.04245	-1.000000	0.02509	AAG	G|0.841;C|0.159	0.159	strong		0.269	LEPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025275.1	NM_002303	
FAM71F1	84691	hgsc.bcm.edu	37	7	128358891	128358891	+	Silent	SNP	C	C	A	rs745229|rs397954408	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:128358891C>A	ENST00000315184.5	+	3	494	c.441C>A	c.(439-441)ctC>ctA	p.L147L	FAM71F1_ENST00000469348.1_Intron|FAM71F1_ENST00000485070.1_Intron	NM_001282788.1|NM_032599.2	NP_001269717.1|NP_115988.1	Q96KD3	F71F1_HUMAN	family with sequence similarity 71, member F1	147										NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(6)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	18						TCAGGATTCTCCCATTGAGGT	0.473													C|||	1008	0.201278	0.2209	0.1571	5008	,	,		21880	0.1042		0.2366	False		,,,				2504	0.2699				p.L147L		Atlas-SNP	.											.	FAM71F1	42	.	0			c.C441A						PASS	.	C		877,3529	342.0+/-307.0	85,707,1411	263.0	240.0	248.0		441	2.8	1.0	7	dbSNP_86	248	1989,6611	349.1+/-327.3	209,1571,2520	no	coding-synonymous	FAM71F1	NM_032599.2		294,2278,3931	AA,AC,CC		23.1279,19.9047,22.036		147/345	128358891	2866,10140	2203	4300	6503	SO:0001819	synonymous_variant	84691	exon3			GATTCTCCCATTG	AF367470	CCDS5804.1, CCDS64763.1	7q32.1	2007-11-20	2007-11-20	2007-11-20	ENSG00000135248	ENSG00000135248			30704	protein-coding gene	gene with protein product			"""family with sequence similarity 137, member A"""	FAM137A		12477932	Standard	XM_005250645		Approved	NYD-SP18	uc003vno.1	Q96KD3	OTTHUMG00000158276	ENST00000315184.5:c.441C>A	7.37:g.128358891C>A		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	58	31	0.534483	NM_032599	Q8IY75|Q8NA48	Silent	SNP	ENST00000315184.5	37	CCDS5804.1																																																																																			C|0.797;A|0.203	0.203	strong		0.473	FAM71F1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350544.2	NM_032599	
CCDC81	60494	hgsc.bcm.edu	37	11	86123556	86123556	+	Missense_Mutation	SNP	A	A	G	rs3741005	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:86123556A>G	ENST00000445632.2	+	11	1618	c.1346A>G	c.(1345-1347)tAc>tGc	p.Y449C	CCDC81_ENST00000278487.3_Missense_Mutation_p.Y184C|CCDC81_ENST00000528728.1_Missense_Mutation_p.Y184C|CCDC81_ENST00000354755.1_Missense_Mutation_p.Y359C	NM_001156474.1	NP_001149946.1	Q6ZN84	CCD81_HUMAN	coiled-coil domain containing 81	449			Y -> C (in dbSNP:rs3741005).							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)				CAAAGACAATACAGAGAGTTG	0.438													A|||	241	0.048123	0.0053	0.0274	5008	,	,		20777	0.0496		0.1143	False		,,,				2504	0.0511				p.Y449C		Atlas-SNP	.											.	CCDC81	89	.	0			c.A1346G						PASS	.	A	CYS/TYR,CYS/TYR	88,4316	74.1+/-112.3	2,84,2116	108.0	98.0	102.0		1346,1076	5.5	1.0	11	dbSNP_107	102	859,7739	196.9+/-241.7	34,791,3474	yes	missense,missense	CCDC81	NM_001156474.1,NM_021827.4	194,194	36,875,5590	GG,GA,AA		9.9907,1.9982,7.2835	possibly-damaging,possibly-damaging	449/653,359/563	86123556	947,12055	2202	4299	6501	SO:0001583	missense	60494	exon11			GACAATACAGAGA	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.1346A>G	11.37:g.86123556A>G	ENSP00000415528:p.Tyr449Cys	Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	160	28	0.175	NM_001156474	A0AVL7|Q53FW3|Q9H5E5	Missense_Mutation	SNP	ENST00000445632.2	37	CCDS53691.1	141	0.06456043956043957	5	0.01016260162601626	13	0.03591160220994475	27	0.0472027972027972	96	0.1266490765171504	A	12.88	2.070782	0.36566	0.019982	0.099907	ENSG00000149201	ENST00000354755;ENST00000278487;ENST00000445632;ENST00000528728	T;T;T;T	0.40756	1.02;1.02;1.02;1.02	5.51	5.51	0.81932	.	0.314770	0.32719	N	0.005739	T	0.00300	0.0009	N	0.08118	0	0.35953	P	0.16596999999999995	B;P;P	0.40931	0.049;0.733;0.683	B;B;B	0.43575	0.009;0.424;0.326	T	0.13737	-1.0498	8	.	.	.	-7.3214	14.6291	0.68643	1.0:0.0:0.0:0.0	rs3741005;rs52830324;rs56601221;rs61016688;rs3741005	184;449;359	Q6ZN84-3;Q6ZN84;Q6ZN84-2	.;CCD81_HUMAN;.	C	359;184;449;184	ENSP00000346800:Y359C;ENSP00000278487:Y184C;ENSP00000415528:Y449C;ENSP00000437165:Y184C	.	Y	+	2	0	CCDC81	85801204	1.000000	0.71417	0.995000	0.50966	0.407000	0.30961	5.373000	0.66162	2.088000	0.63022	0.533000	0.62120	TAC	A|0.936;G|0.064	0.064	strong		0.438	CCDC81-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393756.1	NM_021827	
SNED1	25992	hgsc.bcm.edu	37	2	242021742	242021742	+	Missense_Mutation	SNP	G	G	T	rs2108485	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:242021742G>T	ENST00000310397.8	+	29	4084	c.4084G>T	c.(4084-4086)Gcc>Tcc	p.A1362S	SNED1_ENST00000342631.6_Missense_Mutation_p.A1329S|MTERFD2_ENST00000464344.2_Intron|SNED1_ENST00000405547.3_Missense_Mutation_p.A1329S	NM_001080437.1	NP_001073906.1	Q8TER0	SNED1_HUMAN	sushi, nidogen and EGF-like domains 1	1362			A -> S (in dbSNP:rs2108485). {ECO:0000269|PubMed:15489334}.		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)		CGAGACAAAGGCCTTTCCAGT	0.572													T|||	2132	0.425719	0.7511	0.3545	5008	,	,		18972	0.5546		0.168	False		,,,				2504	0.1687				p.A1362S		Atlas-SNP	.											.	SNED1	76	.	0			c.G4084T						PASS	.	T	SER/ALA	2626,1462		858,910,276	203.0	220.0	215.0		4084	3.3	0.8	2	dbSNP_96	215	1345,7043		100,1145,2949	yes	missense	SNED1	NM_001080437.1	99	958,2055,3225	TT,TG,GG		16.0348,35.7632,31.8291	benign	1362/1414	242021742	3971,8505	2044	4194	6238	SO:0001583	missense	25992	exon29			ACAAAGGCCTTTC	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.4084G>T	2.37:g.242021742G>T	ENSP00000308893:p.Ala1362Ser	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	104	47	0.451923	NM_001080437	B5MDC3|B7WNK6|B7WPM0|Q336F4|Q336F5|Q8N369|Q8TEP7	Missense_Mutation	SNP	ENST00000310397.8	37	CCDS46562.1	919	0.4207875457875458	357	0.725609756097561	118	0.3259668508287293	321	0.5611888111888111	123	0.16226912928759896	T	1.878	-0.458563	0.04508	0.642368	0.160348	ENSG00000162804	ENST00000405547;ENST00000310397;ENST00000342631	T;D;T	0.81739	-1.41;-1.53;-1.4	4.48	3.31	0.37934	.	0.172481	0.27768	N	0.017929	T	0.00012	0.0000	N	0.01493	-0.835	0.58432	P	1.0000000000287557E-6	B;B	0.06786	0.0;0.001	B;B	0.04013	0.0;0.001	T	0.46162	-0.9211	9	0.02654	T	1	.	9.5049	0.39040	0.0:0.0:0.3742:0.6258	rs2108485;rs17856779;rs52791508;rs57854954;rs2108485	1329;1362	B5MEF5;Q8TER0	.;SNED1_HUMAN	S	1329;1362;1329	ENSP00000386007:A1329S;ENSP00000308893:A1362S;ENSP00000342992:A1329S	ENSP00000308893:A1362S	A	+	1	0	SNED1	241670415	0.999000	0.42202	0.796000	0.32109	0.768000	0.43524	1.115000	0.31209	0.137000	0.18759	-0.525000	0.04345	GCC	G|0.576;T|0.424	0.424	strong		0.572	SNED1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323935.2	XM_059482	
APBA3	9546	hgsc.bcm.edu	37	19	3753874	3753874	+	Silent	SNP	G	G	A	rs34868972	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	26	0	0		WXS	Illumina HiSeq	Phase_I	41	18	0.439024	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		
DKK2	27123	hgsc.bcm.edu	37	4	107845794	107845794	+	Missense_Mutation	SNP	C	C	T	rs17037102	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:107845794C>T	ENST00000285311.3	-	3	1142	c.437G>A	c.(436-438)cGg>cAg	p.R146Q	DKK2_ENST00000513208.1_Missense_Mutation_p.R46Q|DKK2_ENST00000510463.1_Missense_Mutation_p.R100Q	NM_014421.2	NP_055236.1	Q9UBU2	DKK2_HUMAN	dickkopf WNT signaling pathway inhibitor 2	146			R -> Q (in dbSNP:rs17037102). {ECO:0000269|PubMed:15489334}.		multicellular organismal development (GO:0007275)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|Wnt signaling pathway (GO:0016055)	extracellular space (GO:0005615)		p.R146Q(2)		autonomic_ganglia(1)|breast(1)|endometrium(2)|large_intestine(7)|lung(10)|ovary(3)|pancreas(1)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	32		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;6.34e-06)		ATCTCTGTGCCGAGTACCATC	0.438													C|||	829	0.165535	0.0053	0.3069	5008	,	,		15707	0.3859		0.1083	False		,,,				2504	0.1135				p.R146Q		Atlas-SNP	.											DKK2,NS,carcinoma,0,3	DKK2	96	3	2	Substitution - Missense(2)	prostate(1)|stomach(1)	c.G437A						PASS	.	C	GLN/ARG	141,4265	98.5+/-137.1	3,135,2065	232.0	211.0	218.0		437	5.8	1.0	4	dbSNP_123	218	881,7719	198.9+/-243.1	45,791,3464	yes	missense	DKK2	NM_014421.2	43	48,926,5529	TT,TC,CC		10.2442,3.2002,7.8579	possibly-damaging	146/260	107845794	1022,11984	2203	4300	6503	SO:0001583	missense	27123	exon3			CTGTGCCGAGTAC	AB033208	CCDS3675.1	4q25	2013-05-15	2013-05-15		ENSG00000155011	ENSG00000155011			2892	protein-coding gene	gene with protein product		605415	"""dickkopf (Xenopus laevis) homolog 2"", ""dickkopf 2 homolog (Xenopus laevis)"""			10570958	Standard	NM_014421		Approved		uc003hyi.3	Q9UBU2	OTTHUMG00000131216	ENST00000285311.3:c.437G>A	4.37:g.107845794C>T	ENSP00000285311:p.Arg146Gln	Somatic	273	0	0		WXS	Illumina HiSeq	Phase_I	254	251	0.988189	NM_014421	A0AVE9|B2R6S7|Q9UIU3	Missense_Mutation	SNP	ENST00000285311.3	37	CCDS3675.1	380	0.17399267399267399	3	0.006097560975609756	86	0.23756906077348067	194	0.33916083916083917	97	0.1279683377308707	C	16.95	3.263558	0.59431	0.032002	0.102442	ENSG00000155011	ENST00000285311;ENST00000513208;ENST00000510463	T;T;T	0.44482	0.92;0.94;0.93	5.75	5.75	0.90469	.	0.069405	0.64402	D	0.000020	T	0.00012	0.0000	L	0.29908	0.895	0.27606	P	0.9488256	D;D	0.89917	1.0;0.99	D;D	0.79108	0.992;0.953	T	0.16305	-1.0407	9	0.48119	T	0.1	-20.6321	19.9462	0.97183	0.0:1.0:0.0:0.0	rs17037102;rs17584606;rs52807260;rs58306699;rs17037102	146;146	Q9H3R7;Q9UBU2	.;DKK2_HUMAN	Q	146;46;100	ENSP00000285311:R146Q;ENSP00000421255:R46Q;ENSP00000423797:R100Q	ENSP00000285311:R146Q	R	-	2	0	DKK2	108065243	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.645000	0.46621	2.717000	0.92951	0.585000	0.79938	CGG	C|0.879;T|0.121	0.121	strong		0.438	DKK2-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253959.4		
CACNA1I	8911	hgsc.bcm.edu	37	22	40054948	40054948	+	Silent	SNP	T	T	C	rs5757761	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:40054948T>C	ENST00000402142.3	+	12	2157	c.2157T>C	c.(2155-2157)atT>atC	p.I719I	CACNA1I_ENST00000407673.1_Silent_p.I684I|CACNA1I_ENST00000401624.1_Silent_p.I719I|CACNA1I_ENST00000336649.4_Silent_p.I725I|CACNA1I_ENST00000404898.1_Silent_p.I684I|CACNA1I_ENST00000400164.3_Silent_p.I684I	NM_021096.3	NP_066919.2	Q9P0X4	CAC1I_HUMAN	calcium channel, voltage-dependent, T type, alpha 1I subunit	719					axon guidance (GO:0007411)|calcium ion import (GO:0070509)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|signal transduction (GO:0007165)|sleep (GO:0030431)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	voltage-gated calcium channel activity (GO:0005245)	p.I684I(1)		breast(2)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|liver(2)|lung(27)|ovary(1)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	60	Melanoma(58;0.0749)				Cinnarizine(DB00568)|Flunarizine(DB04841)|Paramethadione(DB00617)|Spironolactone(DB00421)|Verapamil(DB00661)|Zonisamide(DB00909)	TCTGGGAGATTGTGGGGCAGG	0.672													C|||	3748	0.748403	0.8328	0.7392	5008	,	,		18304	0.994		0.5567	False		,,,				2504	0.5849				p.I719I		Atlas-SNP	.											CACNA1I,NS,carcinoma,0,1	CACNA1I	264	1	1	Substitution - coding silent(1)	prostate(1)	c.T2157C						PASS	.	C	,	3391,899		1349,693,103	17.0	21.0	20.0		2052,2157	-2.8	0.8	22	dbSNP_114	20	4616,3876		1278,2060,908	no	coding-synonymous,coding-synonymous	CACNA1I	NM_001003406.1,NM_021096.3	,	2627,2753,1011	CC,CT,TT		45.643,20.9557,37.3572	,	684/2189,719/2224	40054948	8007,4775	2145	4246	6391	SO:0001819	synonymous_variant	8911	exon12			GGAGATTGTGGGG	AF129133	CCDS46710.1, CCDS46711.1	22q13.1	2012-03-07	2007-02-16		ENSG00000100346	ENSG00000100346		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1396	protein-coding gene	gene with protein product		608230				10454147, 16382099	Standard	NM_021096		Approved	Cav3.3	uc003ayd.3	Q9P0X4	OTTHUMG00000151096	ENST00000402142.3:c.2157T>C	22.37:g.40054948T>C		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	92	48	0.521739	NM_021096	B0QY12|B0QY13|B0QY14|O95504|Q5JZ88|Q7Z6S9|Q8NFX6|Q9NZC8|Q9UH15|Q9UH30|Q9ULU9|Q9UNE6	Silent	SNP	ENST00000402142.3	37	CCDS46710.1																																																																																			T|0.245;C|0.755	0.755	strong		0.672	CACNA1I-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000321290.1	NM_001003406	
WDR78	79819	hgsc.bcm.edu	37	1	67390416	67390416	+	Missense_Mutation	SNP	G	G	C	rs3008858	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:67390416G>C	ENST00000371026.3	-	1	154	c.99C>G	c.(97-99)tgC>tgG	p.C33W	MIER1_ENST00000401041.1_5'Flank|MIER1_ENST00000371018.3_5'Flank|WDR78_ENST00000431318.1_5'UTR|MIER1_ENST00000371014.1_5'Flank|WDR78_ENST00000371023.3_Missense_Mutation_p.C33W|MIER1_ENST00000371012.2_5'Flank|WDR78_ENST00000371022.3_Missense_Mutation_p.C33W|MIER1_ENST00000371016.1_5'Flank|MIER1_ENST00000357692.2_5'Flank|MIER1_ENST00000355977.6_5'Flank	NM_024763.4	NP_079039.4	Q5VTH9	WDR78_HUMAN	WD repeat domain 78	33			C -> W (in dbSNP:rs3008858).		hematopoietic progenitor cell differentiation (GO:0002244)					NS(1)|endometrium(3)|kidney(6)|large_intestine(6)|lung(10)|ovary(3)|skin(3)	32						GGGGAGTGGTGCACCACCCCT	0.617													C|||	4196	0.837859	0.8449	0.8343	5008	,	,		13072	0.8829		0.7326	False		,,,				2504	0.8926				p.C33W		Atlas-SNP	.											.	WDR78	102	.	0			c.C99G						PASS	.	C	TRP/CYS,TRP/CYS	3699,707	296.1+/-284.1	1565,569,69	97.0	96.0	96.0		99,99	-3.5	0.0	1	dbSNP_101	96	6295,2305	387.3+/-342.2	2322,1651,327	yes	missense,missense	WDR78	NM_024763.4,NM_207014.2	215,215	3887,2220,396	CC,CG,GG		26.8023,16.0463,23.1585	benign,benign	33/849,33/546	67390416	9994,3012	2203	4300	6503	SO:0001583	missense	79819	exon1			AGTGGTGCACCAC	BX648840	CCDS635.1, CCDS44157.1	1p31.2	2014-02-21	2013-02-19	2013-02-19	ENSG00000152763	ENSG00000152763		"""WD repeat domain containing"""	26252	protein-coding gene	gene with protein product						21953912	Standard	NM_207014		Approved	DIC4, FLJ23129	uc001dcx.3	Q5VTH9	OTTHUMG00000009165	ENST00000371026.3:c.99C>G	1.37:g.67390416G>C	ENSP00000360065:p.Cys33Trp	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	102	101	0.990196	NM_207014	A8K9W5|B5MDT3|H7BY80|Q5VTI0|Q8N5G5|Q9H5R9|Q9UF44	Missense_Mutation	SNP	ENST00000371026.3	37	CCDS635.1	1776	0.8131868131868132	414	0.8414634146341463	312	0.861878453038674	506	0.8846153846153846	544	0.7176781002638523	C	5.337	0.247501	0.10130	0.839537	0.731977	ENSG00000152763	ENST00000371026;ENST00000371023;ENST00000371022	T;T;T	0.59083	0.29;1.94;1.14	3.71	-3.46	0.04767	.	2.488790	0.01888	N	0.038354	T	0.11324	0.0276	N	0.08118	0	0.50632	P	1.2000000000000899E-4	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.03344	-1.1046	9	0.26408	T	0.33	8.4958	1.9025	0.03270	0.1302:0.2164:0.3851:0.2683	rs3008858;rs52815963;rs3008858	33;33	Q5TAD8;Q5VTH9	.;WDR78_HUMAN	W	33	ENSP00000360065:C33W;ENSP00000360062:C33W;ENSP00000360061:C33W	ENSP00000360061:C33W	C	-	3	2	WDR78	67163004	0.000000	0.05858	0.000000	0.03702	0.015000	0.08874	-2.345000	0.01097	-1.103000	0.03019	-0.216000	0.12614	TGC	G|0.211;C|0.789	0.789	strong		0.617	WDR78-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025404.1	NM_024763	
ZNF710	374655	hgsc.bcm.edu	37	15	90611521	90611521	+	Silent	SNP	C	C	T	rs147080007	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:90611521C>T	ENST00000268154.4	+	2	1403	c.1152C>T	c.(1150-1152)tgC>tgT	p.C384C		NM_198526.2	NP_940928.2	Q8N1W2	ZN710_HUMAN	zinc finger protein 710	384					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(2)|kidney(2)|large_intestine(4)|lung(1)|ovary(2)|prostate(1)|stomach(1)|urinary_tract(3)	19	Melanoma(11;0.00551)|Lung NSC(78;0.0196)|all_lung(78;0.04)		BRCA - Breast invasive adenocarcinoma(143;0.00769)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.129)			GCCACTTCTGCGGCCGCGGCT	0.632													C|||	35	0.00698882	0.0023	0.0058	5008	,	,		18638	0.0		0.0129	False		,,,				2504	0.0153				p.C384C		Atlas-SNP	.											.	ZNF710	50	.	0			c.C1152T						PASS	.	C		12,4382		0,12,2185	35.0	40.0	39.0		1152	-0.9	1.0	15	dbSNP_134	39	118,8452		0,118,4167	no	coding-synonymous	ZNF710	NM_198526.2		0,130,6352	TT,TC,CC		1.3769,0.2731,1.0028		384/665	90611521	130,12834	2197	4285	6482	SO:0001819	synonymous_variant	374655	exon2			CTTCTGCGGCCGC	AK094712	CCDS10358.1	15q26.1	2013-01-08			ENSG00000140548	ENSG00000140548		"""Zinc fingers, C2H2-type"""	25352	protein-coding gene	gene with protein product							Standard	XM_005254905		Approved	DKFZp547K1113, FLJ37393, FLJ00306	uc002bov.2	Q8N1W2	OTTHUMG00000149812	ENST00000268154.4:c.1152C>T	15.37:g.90611521C>T		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	85	40	0.470588	NM_198526	A0AVS3|Q6ZMK9|Q8NDU0	Silent	SNP	ENST00000268154.4	37	CCDS10358.1																																																																																			C|0.989;T|0.011	0.011	strong		0.632	ZNF710-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313423.1	NM_198526	
GPR161	23432	hgsc.bcm.edu	37	1	168059866	168059866	+	Silent	SNP	A	A	G	rs275149	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:168059866A>G	ENST00000367838.1	-	6	1453	c.1140T>C	c.(1138-1140)ggT>ggC	p.G380G	GPR161_ENST00000361697.2_Silent_p.G380G|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_ENST00000539777.1_Silent_p.G302G|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						PASS	.	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	95	0	0		WXS	Illumina HiSeq	Phase_I	52	35	0.673077	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	
HNRNPA1L2	144983	hgsc.bcm.edu	37	13	53216666	53216666	+	Silent	SNP	G	G	A	rs113869751	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:53216666G>A	ENST00000357495.2	+	1	99	c.39G>A	c.(37-39)ctG>ctA	p.L13L	HNRNPA1L2_ENST00000342657.3_Silent_p.L13L|HNRNPA1L2_ENST00000398039.1_Silent_p.L13L			Q32P51	RA1L2_HUMAN	heterogeneous nuclear ribonucleoprotein A1-like 2	13	Globular A domain.				alternative mRNA splicing, via spliceosome (GO:0000380)|mRNA transport (GO:0051028)	cytoplasm (GO:0005737)|spliceosomal complex (GO:0005681)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			cervix(1)|large_intestine(1)|lung(5)	7						CCGAACAGCTGAGGAAGCTCT	0.502													-|||	54	0.0107827	0.0015	0.0144	5008	,	,		19278	0.0		0.0348	False		,,,				2504	0.0072				p.L13L		Atlas-SNP	.											.	HNRNPA1L2	20	.	0			c.G39A						PASS	.	G	,	19,4387	25.3+/-52.1	0,19,2184	68.0	71.0	70.0		39,39	0.3	0.9	13	dbSNP_132	70	266,8334	101.2+/-162.5	5,256,4039	no	coding-synonymous,coding-synonymous	HNRNPA1L2	NM_001011724.1,NM_001011725.1	,	5,275,6223	AA,AG,GG		3.093,0.4312,2.1913	,	13/321,13/321	53216666	285,12721	2203	4300	6503	SO:0001819	synonymous_variant	144983	exon7			ACAGCTGAGGAAG		CCDS31980.1	13q14.3	2013-02-12			ENSG00000139675	ENSG00000139675		"""RNA binding motif (RRM) containing"""	27067	protein-coding gene	gene with protein product						12477932	Standard	NM_001011724		Approved	LOC144983	uc001vgy.1	Q32P51	OTTHUMG00000016972	ENST00000357495.2:c.39G>A	13.37:g.53216666G>A		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	54	26	0.481481	NM_001011724	Q5TBS2	Silent	SNP	ENST00000357495.2	37	CCDS31980.1																																																																																			G|0.980;A|0.020	0.020	strong		0.502	HNRNPA1L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045098.1	NM_001011724	
PTGER3	5733	hgsc.bcm.edu	37	1	71512643	71512643	+	Silent	SNP	C	C	A	rs5671	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:71512643C>A	ENST00000306666.5	-	1	828	c.618G>T	c.(616-618)acG>acT	p.T206T	PTGER3_ENST00000370931.3_Silent_p.T206T|PTGER3_ENST00000414819.1_Silent_p.T206T|ZRANB2-AS1_ENST00000450461.1_RNA|PTGER3_ENST00000370924.4_Silent_p.T206T|PTGER3_ENST00000351052.5_Silent_p.T206T|PTGER3_ENST00000356595.4_Silent_p.T206T|PTGER3_ENST00000354608.5_Silent_p.T206T|PTGER3_ENST00000370932.2_Silent_p.T206T|PTGER3_ENST00000460330.1_Silent_p.T206T	NM_198719.1	NP_942012.1	P43115	PE2R3_HUMAN	prostaglandin E receptor 3 (subtype EP3)	206					cell death (GO:0008219)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular receptor signaling pathway (GO:0030522)|positive regulation of fever generation (GO:0031622)|transcription, DNA-templated (GO:0006351)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)	ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|prostaglandin E receptor activity (GO:0004957)			endometrium(2)|large_intestine(5)|lung(14)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	25					Bimatoprost(DB00905)|Dinoprostone(DB00917)|Misoprostol(DB00929)	TGAAGCACCACGTCCCGGGCC	0.677													C|||	355	0.0708866	0.1589	0.0706	5008	,	,		15416	0.0		0.0845	False		,,,				2504	0.0112				p.T206T		Atlas-SNP	.											PTGER3_ENST00000460330,NS,carcinoma,0,5	PTGER3	246	5	0			c.G618T						scavenged	.	C	,,,,,,	692,3712	279.9+/-275.1	44,604,1554	55.0	57.0	57.0		618,618,618,618,618,618,618	-1.9	1.0	1	dbSNP_52	57	731,7869	174.5+/-224.7	37,657,3606	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PTGER3	NM_001126044.1,NM_198714.1,NM_198715.2,NM_198716.1,NM_198717.1,NM_198718.1,NM_198719.1	,,,,,,	81,1261,5160	AA,AC,CC		8.5,15.713,10.9428	,,,,,,	206/391,206/391,206/389,206/375,206/366,206/419,206/391	71512643	1423,11581	2202	4300	6502	SO:0001819	synonymous_variant	5733	exon1			GCACCACGTCCCG	X83863	CCDS652.1, CCDS655.1, CCDS656.1, CCDS657.1, CCDS658.1	1p31.2	2012-08-08			ENSG00000050628	ENSG00000050628		"""GPCR / Class A : Prostanoid receptors"""	9595	protein-coding gene	gene with protein product		176806				7759114, 9073510	Standard	NM_001126044		Approved	EP3	uc001dfo.3	P43115	OTTHUMG00000009399	ENST00000306666.5:c.618G>T	1.37:g.71512643C>A		Somatic	57	1	0.0175439		WXS	Illumina HiSeq	Phase_I	68	32	0.470588	NM_001126044	B0AZN4|B1AK19|B5BUP5|O00326|Q12943|Q12944|Q12945|Q16546|Q5CZ59|Q5CZ61|Q5CZ62|Q5CZ63|Q5CZ64	Silent	SNP	ENST00000306666.5	37	CCDS657.1																																																																																			C|0.893;A|0.107	0.107	strong		0.677	PTGER3-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000026076.1	NM_000957	
NOM1	64434	hgsc.bcm.edu	37	7	156762248	156762248	+	Missense_Mutation	SNP	G	G	A	rs12919	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:156762248G>A	ENST00000275820.3	+	11	2449	c.2434G>A	c.(2434-2436)Gtg>Atg	p.V812M		NM_138400.1	NP_612409.1	Q5C9Z4	NOM1_HUMAN	nucleolar protein with MIF4G domain 1	812			V -> M (in dbSNP:rs12919).			nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(5)|kidney(4)|large_intestine(9)|lung(7)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	31	Ovarian(565;0.218)	all_hematologic(28;0.0749)	OV - Ovarian serous cystadenocarcinoma(82;0.00301)	UCEC - Uterine corpus endometrioid carcinoma (81;0.169)		AAAGCTGGGGGTGTTACGTGA	0.512													A|||	2411	0.48143	0.556	0.536	5008	,	,		16487	0.2778		0.5706	False		,,,				2504	0.4601				p.V812M		Atlas-SNP	.											NOM1,rectum,carcinoma,0,1	NOM1	73	1	0			c.G2434A						PASS	.	A	MET/VAL	2437,1969	555.5+/-379.3	672,1093,438	107.0	109.0	108.0		2434	-3.1	0.0	7	dbSNP_52	108	4907,3693	529.1+/-381.5	1388,2131,781	yes	missense	NOM1	NM_138400.1	21	2060,3224,1219	AA,AG,GG		42.9419,44.6891,43.5338	benign	812/861	156762248	7344,5662	2203	4300	6503	SO:0001583	missense	64434	exon11			CTGGGGGTGTTAC	AF107455	CCDS34787.1	7q36.3	2014-06-13	2005-03-30	2005-03-30	ENSG00000146909	ENSG00000146909			13244	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 113"""	611269	"""chromosome 7 open reading frame 3"""	C7orf3		10329000	Standard	XM_005249560		Approved	SGD1, PPP1R113	uc003wmy.3	Q5C9Z4	OTTHUMG00000152639	ENST00000275820.3:c.2434G>A	7.37:g.156762248G>A	ENSP00000275820:p.Val812Met	Somatic	24	0	0		WXS	Illumina HiSeq	Phase_I	21	21	1	NM_138400	Q96I08	Missense_Mutation	SNP	ENST00000275820.3	37	CCDS34787.1	1047	0.4793956043956044	274	0.556910569105691	199	0.5497237569060773	154	0.2692307692307692	420	0.554089709762533	A	0.021	-1.421065	0.01126	0.553109	0.570581	ENSG00000146909	ENST00000275820	T	0.11169	2.8	5.41	-3.13	0.05266	.	0.201867	0.64402	N	0.000012	T	0.00012	0.0000	N	0.00138	-2.015	0.80722	P	0.0	B	0.09022	0.002	B	0.08055	0.003	T	0.20009	-1.0288	9	0.15066	T	0.55	-9.8241	3.0886	0.06286	0.4413:0.1173:0.3376:0.1038	rs12919;rs17354962;rs56648938;rs61096186;rs12919	812	Q5C9Z4	NOM1_HUMAN	M	812	ENSP00000275820:V812M	ENSP00000275820:V812M	V	+	1	0	NOM1	156455009	0.011000	0.17503	0.001000	0.08648	0.280000	0.26924	-0.199000	0.09491	-1.325000	0.02269	-0.516000	0.04426	GTG	G|0.474;A|0.526	0.526	strong		0.512	NOM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327098.1	NM_138400	
CKM	1158	hgsc.bcm.edu	37	19	45815033	45815033	+	Silent	SNP	G	G	T	rs17875616	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:45815033G>T	ENST00000221476.3	-	5	801	c.627C>A	c.(625-627)cgC>cgA	p.R209R		NM_001824.4	NP_001815.2	P06732	KCRM_HUMAN	creatine kinase, muscle	209	Phosphagen kinase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00843}.				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)	CGGGCCAGTCGCGGGCCATGC	0.672													G|||	353	0.0704872	0.1256	0.0476	5008	,	,		11665	0.0		0.0736	False		,,,				2504	0.0818				p.R209R		Atlas-SNP	.											CKM,rectum,carcinoma,0,2	CKM	40	2	0			c.C627A						PASS	.	G		455,3949		21,413,1768	30.0	24.0	26.0		627	-10.4	0.1	19	dbSNP_124	26	579,8019		21,537,3741	no	coding-synonymous	CKM	NM_001824.3		42,950,5509	TT,TG,GG		6.7341,10.3315,7.9526		209/382	45815033	1034,11968	2202	4299	6501	SO:0001819	synonymous_variant	1158	exon5			CCAGTCGCGGGCC	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.627C>A	19.37:g.45815033G>T		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	68	41	0.602941	NM_001824	Q96QL9	Silent	SNP	ENST00000221476.3	37	CCDS12659.1																																																																																			G|0.928;T|0.072	0.072	strong		0.672	CKM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457569.1		
C16orf45	89927	hgsc.bcm.edu	37	16	15661871	15661871	+	Missense_Mutation	SNP	A	A	G	rs149928639	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:15661871A>G	ENST00000300006.4	+	3	621	c.262A>G	c.(262-264)Atg>Gtg	p.M88V	C16orf45_ENST00000452191.2_Missense_Mutation_p.M71V|C16orf45_ENST00000561692.1_Missense_Mutation_p.M40V|C16orf45_ENST00000566490.1_Missense_Mutation_p.M88V	NM_033201.2	NP_149978.1	Q96MC5	CP045_HUMAN	chromosome 16 open reading frame 45	88										endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(3)|ovary(1)	11						CAAGGACATCATGGACTTGAA	0.552													A|||	2	0.000399361	0.0008	0.0	5008	,	,		20396	0.0		0.001	False		,,,				2504	0.0				p.M88V		Atlas-SNP	.											.	C16orf45	24	.	0			c.A262G						PASS	.	A	VAL/MET,VAL/MET	4,4390	8.1+/-20.4	0,4,2193	112.0	89.0	97.0		211,262	5.1	1.0	16	dbSNP_134	97	28,8572	21.0+/-64.5	0,28,4272	yes	missense,missense	C16orf45	NM_001142469.1,NM_033201.2	21,21	0,32,6465	GG,GA,AA		0.3256,0.091,0.2463	benign,benign	71/188,88/205	15661871	32,12962	2197	4300	6497	SO:0001583	missense	89927	exon3			GACATCATGGACT	AK057180	CCDS10561.1, CCDS45422.1	16p13.2	2012-10-09			ENSG00000166780	ENSG00000166780			19213	protein-coding gene	gene with protein product							Standard	NM_033201		Approved	FLJ32618	uc002ddo.3	Q96MC5	OTTHUMG00000129883	ENST00000300006.4:c.262A>G	16.37:g.15661871A>G	ENSP00000300006:p.Met88Val	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	109	74	0.678899	NM_033201	O00223|O75769|Q8IZ36|Q96H25	Missense_Mutation	SNP	ENST00000300006.4	37	CCDS10561.1	.	.	.	.	.	.	.	.	.	.	A	14.23	2.474202	0.43942	9.1E-4	0.003256	ENSG00000166780	ENST00000300006;ENST00000452191	T;T	0.41065	1.01;1.01	5.1	5.1	0.69264	Domain of unknown function DUF3585 (1);	0.037124	0.85682	D	0.000000	T	0.44808	0.1311	L	0.38838	1.175	0.45930	D	0.99876	P;B	0.35542	0.508;0.025	P;B	0.51945	0.685;0.013	T	0.28364	-1.0046	10	0.09084	T	0.74	-11.5179	11.286	0.49222	1.0:0.0:0.0:0.0	.	32;88	B4DE25;Q96MC5	.;CP045_HUMAN	V	88;71	ENSP00000300006:M88V;ENSP00000408976:M71V	ENSP00000300006:M88V	M	+	1	0	C16orf45	15569372	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.924000	0.70054	1.911000	0.55334	0.533000	0.62120	ATG	A|0.996;G|0.004	0.004	strong		0.552	C16orf45-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252130.2	NM_033201	
TOR1AIP1	26092	hgsc.bcm.edu	37	1	179877780	179877780	+	Missense_Mutation	SNP	A	A	C	rs17279712	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:179877780A>C	ENST00000606911.2	+	8	1070	c.879A>C	c.(877-879)caA>caC	p.Q293H	TOR1AIP1_ENST00000474875.1_3'UTR|TOR1AIP1_ENST00000435319.4_Missense_Mutation_p.Q172H|TOR1AIP1_ENST00000528443.2_Missense_Mutation_p.Q294H|TOR1AIP1_ENST00000271583.3_Missense_Mutation_p.Q294H			Q5JTV8	TOIP1_HUMAN	torsin A interacting protein 1	293			Q -> H (in dbSNP:rs17279712).		positive regulation of ATPase activity (GO:0032781)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)	ATPase activator activity (GO:0001671)|ATPase binding (GO:0051117)|cytoskeletal protein binding (GO:0008092)			breast(4)|central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(4)|ovary(2)|skin(1)|urinary_tract(1)	18						GGGCCCCACAAACTGCAAGAA	0.323													A|||	189	0.0377396	0.0151	0.0576	5008	,	,		16998	0.002		0.0845	False		,,,				2504	0.0429				p.Q294H		Atlas-SNP	.											.	TOR1AIP1	58	.	0			c.A882C						PASS	.	A	HIS/GLN	91,4315	74.1+/-112.3	0,91,2112	73.0	80.0	78.0		879	-2.5	0.0	1	dbSNP_123	78	536,8064	146.9+/-202.4	19,498,3783	yes	missense	TOR1AIP1	NM_015602.2	24	19,589,5895	CC,CA,AA		6.2326,2.0654,4.8209	benign	293/584	179877780	627,12379	2203	4300	6503	SO:0001583	missense	26092	exon8			CCCACAAACTGCA		CCDS1335.1, CCDS65737.1	1q24.2	2008-02-05			ENSG00000143337	ENSG00000143337			29456	protein-coding gene	gene with protein product	"""lamina associated polypeptide 1B"""	614512				12061773, 15767459	Standard	NM_015602		Approved	LAP1B, FLJ13142	uc001gnp.2	Q5JTV8	OTTHUMG00000035257	ENST00000606911.2:c.879A>C	1.37:g.179877780A>C	ENSP00000476687:p.Gln293His	Somatic	269	0	0		WXS	Illumina HiSeq	Phase_I	203	98	0.482759	NM_001267578	A8K630|B0QZ57|Q5JTV6|Q8IZ65|Q9H8Y6|Q9HAJ1|Q9NV52|Q9Y3X5	Missense_Mutation	SNP	ENST00000606911.2	37	CCDS1335.1	100|100|100	0.045787545787545784|0.045787545787545784|0.045787545787545784	14|14|14	0.028455284552845527|0.028455284552845527|0.028455284552845527	18|18|18	0.049723756906077346|0.049723756906077346|0.049723756906077346	1|1|1	0.0017482517482517483|0.0017482517482517483|0.0017482517482517483	67|67|67	0.08839050131926121|0.08839050131926121|0.08839050131926121	A|A|A	8.824|8.824|8.824	0.938178|0.938178|0.938178	0.18206|0.18206|0.18206	0.020654|0.020654|0.020654	0.062326|0.062326|0.062326	ENSG00000143337|ENSG00000143337|ENSG00000143337	ENST00000447964|ENST00000527391|ENST00000528443;ENST00000271583;ENST00000435319	.|.|T;T;T	.|.|0.25912	.|.|1.77;1.77;1.77	5.39|5.39|5.39	-2.45|-2.45|-2.45	0.06481|0.06481|0.06481	.|.|.	.|.|0.735393	.|.|0.12522	.|.|N	.|.|0.461581	T|T|T	0.00580|0.00580|0.00580	0.0019|0.0019|0.0019	L|L|L	0.50333|0.50333|0.50333	1.59|1.59|1.59	0.80722|0.80722|0.80722	P|P|P	0.0|0.0|0.0	.|.|B	.|.|0.09022	.|.|0.002	.|.|B	.|.|0.12156	.|.|0.007	T|T|T	0.22977|0.22977|0.22977	-1.0201|-1.0201|-1.0201	4|4|8	.|.|.	.|.|.	.|.|.	-0.095|-0.095|-0.095	2.2348|2.2348|2.2348	0.04005|0.04005|0.04005	0.472:0.1223:0.2863:0.1193|0.472:0.1223:0.2863:0.1193|0.472:0.1223:0.2863:0.1193	rs17279712;rs52792036;rs17279712|rs17279712;rs52792036;rs17279712|rs17279712;rs52792036;rs17279712	.|.|293	.|.|Q5JTV8	.|.|TOIP1_HUMAN	T|H|H	47|170|294;294;293	.|.|ENSP00000435365:Q294H;ENSP00000271583:Q294H;ENSP00000393292:Q293H	.|.|.	K|N|Q	+|+|+	2|1|3	0|0|2	TOR1AIP1|TOR1AIP1|TOR1AIP1	178144403|178144403|178144403	0.000000|0.000000|0.000000	0.05858|0.05858|0.05858	0.000000|0.000000|0.000000	0.03702|0.03702|0.03702	0.000000|0.000000|0.000000	0.00434|0.00434|0.00434	-0.023000|-0.023000|-0.023000	0.12456|0.12456|0.12456	-0.482000|-0.482000|-0.482000	0.06782|0.06782|0.06782	-2.720000|-2.720000|-2.720000	0.00132|0.00132|0.00132	AAA|AAC|CAA	A|0.955;C|0.045	0.045	strong		0.323	TOR1AIP1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000100313.4	NM_015602	
AHNAK2	113146	hgsc.bcm.edu	37	14	105419234	105419234	+	Missense_Mutation	SNP	T	T	C	rs74090129	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:105419234T>C	ENST00000333244.5	-	7	2673	c.2554A>G	c.(2554-2556)Atg>Gtg	p.M852V	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	852						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)			GAGTCCTCCATGGACTTGCCT	0.602													.|||	1035	0.206669	0.3048	0.0793	5008	,	,		18647	0.2966		0.0477	False		,,,				2504	0.2352				p.M852V		Atlas-SNP	.											.	AHNAK2	719	.	0			c.A2554G						PASS	.	T	VAL/MET	1057,2883		165,727,1078	213.0	236.0	228.0		2554	-8.0	0.0	14	dbSNP_130	228	352,7932		8,336,3798	no	missense	AHNAK2	NM_138420.2	21	173,1063,4876	CC,CT,TT		4.2492,26.8274,11.5265	benign	852/5796	105419234	1409,10815	1970	4142	6112	SO:0001583	missense	113146	exon7			CCTCCATGGACTT	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.2554A>G	14.37:g.105419234T>C	ENSP00000353114:p.Met852Val	Somatic	203	0	0		WXS	Illumina HiSeq	Phase_I	250	67	0.268	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	390	0.17857142857142858	160	0.3252032520325203	38	0.10497237569060773	165	0.28846153846153844	27	0.03562005277044855	t	6.701	0.498028	0.12762	0.268274	0.042492	ENSG00000185567	ENST00000333244	T	0.01745	4.66	4.02	-8.03	0.01114	.	.	.	.	.	T	0.00012	0.0000	L	0.31804	0.96	0.80722	P	0.0	B	0.15141	0.012	B	0.16722	0.016	T	0.47535	-0.9110	8	0.24483	T	0.36	-3.3492	1.3185	0.02112	0.2028:0.3496:0.1682:0.2794	.	852	Q8IVF2	AHNK2_HUMAN	V	852	ENSP00000353114:M852V	ENSP00000353114:M852V	M	-	1	0	AHNAK2	104490279	0.000000	0.05858	0.000000	0.03702	0.258000	0.26162	-0.118000	0.10692	-2.094000	0.00854	0.402000	0.26972	ATG	T|0.852;C|0.148	0.148	strong		0.602	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
TMPRSS11F	389208	hgsc.bcm.edu	37	4	68930465	68930465	+	Missense_Mutation	SNP	G	G	A	rs143544573	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:68930465G>A	ENST00000356291.2	-	8	1012	c.953C>T	c.(952-954)tCt>tTt	p.S318F	UBA6-AS1_ENST00000500538.2_RNA|RP11-35D5.1_ENST00000600441.1_RNA|UBA6-AS1_ENST00000511571.1_RNA|UBA6-AS1_ENST00000499180.2_RNA	NM_207407.2	NP_997290.2	Q6ZWK6	TM11F_HUMAN	transmembrane protease, serine 11F	318	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	serine-type endopeptidase activity (GO:0004252)	p.S318F(1)		NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(7)|liver(1)|lung(18)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(4)	39						CAACTTTATAGATGAGTCTGG	0.388													G|||	13	0.00259585	0.0	0.0029	5008	,	,		16858	0.0		0.0109	False		,,,				2504	0.0				p.S318F		Atlas-SNP	.											TMPRSS11F,NS,carcinoma,0,1	TMPRSS11F	79	1	1	Substitution - Missense(1)	prostate(1)	c.C953T						PASS	.	G	PHE/SER	6,4400	12.9+/-30.5	0,6,2197	68.0	68.0	68.0		953	4.0	1.0	4	dbSNP_134	68	101,8499	55.6+/-116.7	1,99,4200	yes	missense	TMPRSS11F	NM_207407.2	155	1,105,6397	AA,AG,GG		1.1744,0.1362,0.8227	possibly-damaging	318/439	68930465	107,12899	2203	4300	6503	SO:0001583	missense	389208	exon8			TTTATAGATGAGT	AK122625	CCDS3520.1	4q13.2	2010-04-13			ENSG00000198092	ENSG00000198092		"""Serine peptidases / Transmembrane"""	29994	protein-coding gene	gene with protein product							Standard	NM_207407		Approved	FLJ16046	uc003hdt.1	Q6ZWK6	OTTHUMG00000129307	ENST00000356291.2:c.953C>T	4.37:g.68930465G>A	ENSP00000348639:p.Ser318Phe	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	87	51	0.586207	NM_207407	A8MXX2	Missense_Mutation	SNP	ENST00000356291.2	37	CCDS3520.1	11	0.005036630036630037	0	0.0	1	0.0027624309392265192	0	0.0	10	0.013192612137203167	G	14.79	2.641763	0.47153	0.001362	0.011744	ENSG00000198092	ENST00000356291	D	0.89681	-2.55	5.92	4.0	0.46444	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.207319	0.34652	N	0.003800	T	0.78457	0.4286	L	0.28192	0.835	0.42271	D	0.992056	P	0.49090	0.919	B	0.43082	0.407	T	0.83214	-0.0072	10	0.72032	D	0.01	.	12.357	0.55182	0.0:0.0:0.6819:0.3181	.	318	Q6ZWK6	TM11F_HUMAN	F	318	ENSP00000348639:S318F	ENSP00000348639:S318F	S	-	2	0	TMPRSS11F	68613060	0.983000	0.35010	1.000000	0.80357	0.595000	0.36748	1.369000	0.34227	1.488000	0.48433	0.650000	0.86243	TCT	G|0.994;A|0.006	0.006	strong		0.388	TMPRSS11F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251439.1	NM_207407	
MYO3B	140469	hgsc.bcm.edu	37	2	171260797	171260797	+	Missense_Mutation	SNP	A	A	G	rs33962844	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:171260797A>G	ENST00000408978.4	+	20	2461	c.2318A>G	c.(2317-2319)gAa>gGa	p.E773G	MYO3B_ENST00000602629.1_3'UTR|MYO3B_ENST00000409044.3_Missense_Mutation_p.E773G|MYO3B_ENST00000334231.6_Missense_Mutation_p.E782G	NM_138995.4	NP_620482.3	Q8WXR4	MYO3B_HUMAN	myosin IIIB	773	Myosin motor.		E -> G (in dbSNP:rs33962844). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:17344846}.		peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of filopodium assembly (GO:0051491)|protein autophosphorylation (GO:0046777)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|stereocilium bundle tip (GO:0032426)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(25)|ovary(6)|pancreas(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	59						GTACCCGTGGAATATGAGGAC	0.507													A|||	1244	0.248403	0.0189	0.4251	5008	,	,		18184	0.2718		0.3509	False		,,,				2504	0.3037				p.E773G		Atlas-SNP	.											MYO3B,neck,malignant_melanoma,+1,1	MYO3B	320	1	0			c.A2318G						PASS	.	A	GLY/GLU,GLY/GLU,GLY/GLU	310,3512		14,282,1615	149.0	140.0	143.0		2318,2318,2318	-0.1	0.1	2	dbSNP_126	143	2876,5386		502,1872,1757	yes	missense,missense,missense	MYO3B	NM_001083615.2,NM_001171642.1,NM_138995.3	98,98,98	516,2154,3372	GG,GA,AA		34.81,8.1109,26.3654	benign,benign,benign	773/1315,773/1276,773/1342	171260797	3186,8898	1911	4131	6042	SO:0001583	missense	140469	exon20			CCGTGGAATATGA		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.2318A>G	2.37:g.171260797A>G	ENSP00000386213:p.Glu773Gly	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	78	31	0.397436	NM_001083615	B8ZZR2|Q53QE1|Q53T08|Q8IX64|Q8IX65|Q8IX66|Q8IX67|Q8IX68|Q96N94	Missense_Mutation	SNP	ENST00000408978.4	37	CCDS42773.1	549	0.25137362637362637	12	0.024390243902439025	130	0.35911602209944754	144	0.2517482517482518	263	0.3469656992084433	A	9.337	1.061972	0.19987	0.081109	0.3481	ENSG00000071909	ENST00000409044;ENST00000408978;ENST00000317915;ENST00000484338;ENST00000334231	T;T;T;T	0.72942	-0.7;-0.7;-0.7;-0.7	5.47	-0.0558	0.13808	Myosin head, motor domain (3);	0.464608	0.26432	N	0.024413	T	0.00012	0.0000	M	0.89287	3.02	0.35242	P	0.22210700000000005	B;B;B	0.12013	0.005;0.001;0.002	B;B;B	0.18263	0.018;0.002;0.021	T	0.13764	-1.0497	9	0.36615	T	0.2	.	3.7409	0.08530	0.5646:0.2428:0.0663:0.1263	rs33962844	773;773;773	Q8WXR4-5;Q8WXR4-4;Q8WXR4	.;.;MYO3B_HUMAN	G	773;773;772;782;782	ENSP00000386497:E773G;ENSP00000386213:E773G;ENSP00000446237:E782G;ENSP00000335100:E782G	ENSP00000314213:E772G	E	+	2	0	MYO3B	170969043	0.996000	0.38824	0.068000	0.19968	0.262000	0.26303	2.485000	0.45250	-0.159000	0.11021	0.533000	0.62120	GAA	A|0.726;G|0.274	0.274	strong		0.507	MYO3B-004	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333410.1		
A2ML1	144568	hgsc.bcm.edu	37	12	9009820	9009820	+	Missense_Mutation	SNP	G	G	A	rs1558526	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:9009820G>A	ENST00000299698.7	+	24	3089	c.2909G>A	c.(2908-2910)tGt>tAt	p.C970Y	A2ML1_ENST00000539547.1_Missense_Mutation_p.C479Y	NM_001282424.1|NM_144670.4	NP_001269353.1|NP_653271			alpha-2-macroglobulin-like 1											NS(2)|breast(5)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|liver(2)|lung(36)|ovary(2)|skin(4)|stomach(1)|urinary_tract(1)	80						CCCAGTGGCTGTGGCGAGCAG	0.562													G|||	557	0.111222	0.0159	0.1888	5008	,	,		-128	0.0		0.2684	False		,,,				2504	0.138				p.C970Y		Atlas-SNP	.											.	A2ML1	199	.	0			c.G2909A						PASS	.	G	TYR/CYS	189,3851		7,175,1838	132.0	139.0	137.0		2909	1.8	1.0	12	dbSNP_88	137	2167,6215		298,1571,2322	yes	missense	A2ML1	NM_144670.3	194	305,1746,4160	AA,AG,GG		25.853,4.6782,18.9664	probably-damaging	970/1455	9009820	2356,10066	2020	4191	6211	SO:0001583	missense	144568	exon24			GTGGCTGTGGCGA	AK057908	CCDS8596.2, CCDS73439.1	12p13	2010-12-14	2005-09-01	2005-09-01	ENSG00000166535	ENSG00000166535			23336	protein-coding gene	gene with protein product		610627	"""C3 and PZP-like, alpha-2-macroglobulin domain containing 9"""	CPAMD9		16298998	Standard	NM_144670		Approved	FLJ25179	uc001quz.5	A8K2U0	OTTHUMG00000128499	ENST00000299698.7:c.2909G>A	12.37:g.9009820G>A	ENSP00000299698:p.Cys970Tyr	Somatic	194	0	0		WXS	Illumina HiSeq	Phase_I	176	79	0.448864	NM_144670		Missense_Mutation	SNP	ENST00000299698.7	37	CCDS8596.2	300	0.13736263736263737	13	0.026422764227642278	83	0.2292817679558011	0	0.0	204	0.2691292875989446	G	17.04	3.286741	0.59867	0.046782	0.25853	ENSG00000166535	ENST00000299698;ENST00000539161;ENST00000541459;ENST00000539547	D;D;D	0.81739	-1.53;-1.53;-1.53	3.73	1.81	0.25067	Terpenoid cylases/protein prenyltransferase alpha-alpha toroid (1);Alpha-2-macroglobulin, thiol-ester bond-forming (1);Alpha-2-macroglobulin, conserved site (1);	0.000000	0.64402	D	0.000017	T	0.00073	0.0002	H	0.95917	3.74	0.24571	P	0.99392864	D	0.89917	1.0	D	0.91635	0.999	T	0.02852	-1.1102	9	0.87932	D	0	.	7.8364	0.29371	0.0958:0.1631:0.741:0.0	rs1558526;rs52832831;rs60455871;rs1558526	970	A8K2U0	A2ML1_HUMAN	Y	970;970;520;479	ENSP00000299698:C970Y;ENSP00000443174:C520Y;ENSP00000438292:C479Y	ENSP00000299698:C970Y	C	+	2	0	A2ML1	8901087	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	5.380000	0.66202	0.333000	0.23563	0.462000	0.41574	TGT	G|0.843;A|0.157	0.157	strong		0.562	A2ML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250304.3	NM_144670	
AHNAK2	113146	hgsc.bcm.edu	37	14	105417774	105417774	+	Silent	SNP	G	G	A	rs2013228	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:105417774G>A	ENST00000333244.5	-	7	4133	c.4014C>T	c.(4012-4014)ttC>ttT	p.F1338F	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	1338						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)			CAGACACCCCGAACGACGGCA	0.612													.|||	1956	0.390575	0.5726	0.3213	5008	,	,		14015	0.2986		0.2505	False		,,,				2504	0.4325				p.F1338F		Atlas-SNP	.											.	AHNAK2	719	.	0			c.C4014T						PASS	.	G		1920,1726		696,528,599	143.0	125.0	132.0		4014	-8.2	0.0	14	dbSNP_92	132	1647,4939		654,339,2300	no	coding-synonymous	AHNAK2	NM_138420.2		1350,867,2899	AA,AG,GG		25.0076,47.3396,34.8612		1338/5796	105417774	3567,6665	1823	3293	5116	SO:0001819	synonymous_variant	113146	exon7			CACCCCGAACGAC	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.4014C>T	14.37:g.105417774G>A		Somatic	0	0	.		WXS	Illumina HiSeq	Phase_I	67	66	0.985075	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Silent	SNP	ENST00000333244.5	37	CCDS45177.1																																																																																			G|0.700;A|0.300	0.300	strong		0.612	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
ELFN2	114794	hgsc.bcm.edu	37	22	37770066	37770066	+	Silent	SNP	G	G	T	rs8142615	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:37770066G>T	ENST00000402918.2	-	3	2294	c.1509C>A	c.(1507-1509)atC>atA	p.I503I	RP1-63G5.5_ENST00000430883.1_RNA|ELFN2_ENST00000435824.1_5'Flank|RP1-63G5.8_ENST00000609322.1_RNA	NM_052906.3	NP_443138.2	Q5R3F8	PPR29_HUMAN	extracellular leucine-rich repeat and fibronectin type III domain containing 2	503					negative regulation of phosphatase activity (GO:0010923)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	phosphatase binding (GO:0019902)|protein phosphatase inhibitor activity (GO:0004864)			NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(13)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	35	Melanoma(58;0.0574)					TGCGCACCTCGATATAGTTGC	0.672													G|||	1998	0.398962	0.4924	0.5403	5008	,	,		17217	0.3502		0.3608	False		,,,				2504	0.2618				p.I503I		Atlas-SNP	.											ELFN2,colon,carcinoma,0,1	ELFN2	89	1	0			c.C1509A						scavenged	.	G		2242,2164	558.0+/-379.9	561,1120,522	47.0	49.0	48.0		1509	-4.5	0.9	22	dbSNP_116	48	3169,5429	454.9+/-363.6	595,1979,1725	no	coding-synonymous	ELFN2	NM_052906.3		1156,3099,2247	TT,TG,GG		36.8574,49.1148,41.6103		503/821	37770066	5411,7593	2203	4299	6502	SO:0001819	synonymous_variant	114794	exon3			CACCTCGATATAG	BC041596	CCDS33642.1	22q13.1	2013-02-11	2011-10-27	2011-10-27	ENSG00000166897	ENSG00000166897		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Fibronectin type III domain containing"""	29396	protein-coding gene	gene with protein product			"""leucine rich repeat containing 62"", ""extracellular leucine-rich repeat and fibronectin type III containing 2"", ""extracellular leucine-rich repeat and fibronectin type III domain containing 2"", ""protein phosphatase 1, regulatory subunit 29"""	LRRC62, PPP1R29		17868438	Standard	XR_244427		Approved	dJ63G5.3, KIAA1904	uc003asq.4	Q5R3F8	OTTHUMG00000150558	ENST00000402918.2:c.1509C>A	22.37:g.37770066G>T		Somatic	73	1	0.0136986		WXS	Illumina HiSeq	Phase_I	66	41	0.621212	NM_052906	Q96PY3	Silent	SNP	ENST00000402918.2	37	CCDS33642.1																																																																																			G|0.597;T|0.403	0.403	strong		0.672	ELFN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318900.2	NM_052906	
MMP3	4314	hgsc.bcm.edu	37	11	102713620	102713620	+	Missense_Mutation	SNP	T	T	C	rs679620	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:102713620T>C	ENST00000299855.5	-	2	389	c.133A>G	c.(133-135)Aaa>Gaa	p.K45E		NM_002422.3	NP_002413.1	P08254	MMP3_HUMAN	matrix metallopeptidase 3 (stromelysin 1, progelatinase)	45			K -> E (in dbSNP:rs679620). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.6, ECO:0000269|Ref.7}.		cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of hydrogen peroxide metabolic process (GO:0010727)|positive regulation of oxidative stress-induced cell death (GO:1903209)|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)|endopeptidase activity (GO:0004175)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(3)|large_intestine(3)|liver(1)|lung(7)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	22		all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)		BRCA - Breast invasive adenocarcinoma(274;0.0142)	Marimastat(DB00786)	ACATCTTTTTTGAGGTCGTAG	0.333													C|||	3266	0.652157	0.671	0.6787	5008	,	,		18508	0.6657		0.5278	False		,,,				2504	0.7219				p.K45E		Atlas-SNP	.											MMP3,NS,carcinoma,0,1	MMP3	60	1	0			c.A133G						PASS	.	C	GLU/LYS	2815,1591	483.9+/-359.9	907,1001,295	30.0	30.0	30.0		133	-0.2	0.0	11	dbSNP_83	30	4301,4297	567.7+/-388.9	1067,2167,1065	yes	missense	MMP3	NM_002422.3	56	1974,3168,1360	CC,CT,TT		49.9767,36.1099,45.2784	benign	45/478	102713620	7116,5888	2203	4299	6502	SO:0001583	missense	4314	exon2			CTTTTTTGAGGTC	X05232	CCDS8323.1	11q22.3	2012-10-02	2005-08-08		ENSG00000149968	ENSG00000149968	3.4.24.17		7173	protein-coding gene	gene with protein product		185250	"""matrix metalloproteinase 3 (stromelysin 1, progelatinase)"""	STMY1, STMY			Standard	NM_002422		Approved		uc001phj.1	P08254	OTTHUMG00000048254	ENST00000299855.5:c.133A>G	11.37:g.102713620T>C	ENSP00000299855:p.Lys45Glu	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	58	58	1	NM_002422	B2R8B8|Q3B7S0|Q6GRF8	Missense_Mutation	SNP	ENST00000299855.5	37	CCDS8323.1	1373	0.6286630036630036	348	0.7073170731707317	231	0.638121546961326	384	0.6713286713286714	410	0.5408970976253298	C	1.799	-0.477598	0.04414	0.638901	0.500233	ENSG00000149968	ENST00000299855	T	0.34859	1.34	6.16	-0.221	0.13126	Peptidoglycan binding-like (2);Metallopeptidase, catalytic domain (1);	2.486670	0.02224	N	0.064238	T	0.00012	0.0000	N	0.10733	0.035	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.39502	-0.9611	9	0.02654	T	1	.	6.9869	0.24733	0.0:0.2794:0.318:0.4026	rs679620;rs1051161;rs3168234;rs56822421;rs679620	45	P08254	MMP3_HUMAN	E	45	ENSP00000299855:K45E	ENSP00000299855:K45E	K	-	1	0	MMP3	102218830	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.578000	0.02125	-0.250000	0.09555	-2.364000	0.00238	AAA	T|0.428;C|0.572	0.572	strong		0.333	MMP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109758.2	NM_002422	
AOC1	26	hgsc.bcm.edu	37	7	150553605	150553605	+	Missense_Mutation	SNP	C	C	T	rs10156191	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:150553605C>T	ENST00000493429.1	+	4	631	c.47C>T	c.(46-48)aCg>aTg	p.T16M	AOC1_ENST00000360937.4_Missense_Mutation_p.T16M|AOC1_ENST00000416793.2_Missense_Mutation_p.T16M|AOC1_ENST00000467291.1_Missense_Mutation_p.T16M			P19801	AOC1_HUMAN	amine oxidase, copper containing 1	16			T -> M (in dbSNP:rs10156191). {ECO:0000269|Ref.4}.		amine metabolic process (GO:0009308)|cellular response to azide (GO:0097185)|cellular response to copper ion (GO:0071280)|cellular response to copper ion starvation (GO:0035874)|cellular response to heparin (GO:0071504)|cellular response to histamine (GO:0071420)|oxidation-reduction process (GO:0055114)|response to antibiotic (GO:0046677)|response to drug (GO:0042493)|sodium ion transmembrane transport (GO:0035725)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|peroxisome (GO:0005777)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	calcium ion binding (GO:0005509)|cation channel activity (GO:0005261)|copper ion binding (GO:0005507)|diamine oxidase activity (GO:0052597)|drug binding (GO:0008144)|heparin binding (GO:0008201)|histamine oxidase activity (GO:0052598)|methylputrescine oxidase activity (GO:0052599)|primary amine oxidase activity (GO:0008131)|propane-1,3-diamine oxidase activity (GO:0052600)|protein complex binding (GO:0032403)|protein homodimerization activity (GO:0042803)|quinone binding (GO:0048038)|receptor activity (GO:0004872)|sodium channel activity (GO:0005272)|zinc ion binding (GO:0008270)									Amiloride(DB00594)	ATGCTGCAGACGGCCATGGCG	0.602													T|||	1567	0.312899	0.5613	0.2464	5008	,	,		18928	0.122		0.2654	False		,,,				2504	0.2699				p.T16M		Atlas-SNP	.											.	ABP1	92	.	0			c.C47T						PASS	.	T	MET/THR	1966,1902		502,962,470	31.0	33.0	32.0		47	-0.6	0.0	7	dbSNP_119	32	2203,6057		270,1663,2197	yes	missense	ABP1	NM_001091.2	81	772,2625,2667	TT,TC,CC		26.6707,49.1727,34.375	benign	16/752	150553605	4169,7959	1934	4130	6064	SO:0001583	missense	26	exon2			TGCAGACGGCCAT	AK092514	CCDS43679.1, CCDS64797.1	7q36.1	2013-06-19	2013-06-19	2013-06-19	ENSG00000002726	ENSG00000002726	1.4.3.22		80	protein-coding gene	gene with protein product	"""diamine oxidase"""	104610	"""amiloride binding protein 1 (amine oxidase (copper-containing))"""	ABP1		8182053	Standard	NM_001091		Approved	DAO	uc003wia.2	P19801	OTTHUMG00000158306	ENST00000493429.1:c.47C>T	7.37:g.150553605C>T	ENSP00000418614:p.Thr16Met	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	54	31	0.574074	NM_001091	C9J690|Q16683|Q16684|Q56II4|Q6GU42	Missense_Mutation	SNP	ENST00000493429.1	37	CCDS43679.1	627	0.28708791208791207	274	0.556910569105691	91	0.2513812154696133	67	0.11713286713286714	195	0.25725593667546176	T	9.043	0.990180	0.18966	0.508273	0.266707	ENSG00000002726	ENST00000493429;ENST00000467291;ENST00000460213;ENST00000360937;ENST00000416793;ENST00000483043	T;T;T;T;T;T	0.11821	4.4;4.4;2.74;4.4;4.4;3.39	4.84	-0.636	0.11508	Copper amine oxidase, N2/N3-terminal (1);	1.880150	0.03074	N	0.157613	T	0.00012	0.0000	N	0.01352	-0.895	0.80722	P	0.0	B;B	0.06786	0.0;0.001	B;B	0.04013	0.0;0.001	T	0.47114	-0.9142	9	0.32370	T	0.25	1.8438	10.1427	0.42744	0.0:0.501:0.0:0.499	rs10156191;rs10278856;rs10156191	16;16	C9J690;P19801	.;ABP1_HUMAN	M	16	ENSP00000418614:T16M;ENSP00000418328:T16M;ENSP00000418557:T16M;ENSP00000354193:T16M;ENSP00000411613:T16M;ENSP00000417392:T16M	ENSP00000354193:T16M	T	+	2	0	ABP1	150184538	0.007000	0.16637	0.000000	0.03702	0.019000	0.09904	0.182000	0.16900	-0.572000	0.06006	-1.062000	0.02293	ACG	C|0.708;T|0.292	0.292	strong		0.602	AOC1-009	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350628.1	NM_001091	
XAB2	56949	hgsc.bcm.edu	37	19	7685843	7685843	+	Silent	SNP	G	G	A	rs794078	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:7685843G>A	ENST00000358368.4	-	14	1897	c.1860C>T	c.(1858-1860)acC>acT	p.T620T	XAB2_ENST00000534844.1_Silent_p.T617T	NM_020196.2	NP_064581.2	Q9HCS7	SYF1_HUMAN	XPA binding protein 2	620					blastocyst development (GO:0001824)|DNA repair (GO:0006281)|mRNA splicing, via spliceosome (GO:0000398)|nucleotide-excision repair (GO:0006289)|transcription, DNA-templated (GO:0006351)|transcription-coupled nucleotide-excision repair (GO:0006283)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				breast(1)|central_nervous_system(2)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(2)|lung(11)|prostate(1)|skin(2)|urinary_tract(1)	26						CCACGGCCCTGGTGGCACGCT	0.657								Direct reversal of damage;Nucleotide excision repair (NER)					G|||	738	0.147364	0.1135	0.183	5008	,	,		10661	0.1062		0.2376	False		,,,				2504	0.1176				p.T620T		Atlas-SNP	.											XAB2,NS,carcinoma,0,1	XAB2	69	1	0			c.C1860T						PASS	.	G		618,3776		46,526,1625	17.0	17.0	17.0		1860	2.0	0.8	19	dbSNP_86	17	1708,6878		138,1432,2723	no	coding-synonymous	XAB2	NM_020196.2		184,1958,4348	AA,AG,GG		19.8928,14.0646,17.9199		620/856	7685843	2326,10654	2197	4293	6490	SO:0001819	synonymous_variant	56949	exon14			GGCCCTGGTGGCA	AB026111	CCDS32892.1	19p13.3	2013-08-21				ENSG00000076924			14089	protein-coding gene	gene with protein product	"""SYF1 homolog, RNA splicing factor (S. cerevisiae)"", ""SYF1 pre-mRNA-splicing factor"""	610850				10944529	Standard	NM_020196		Approved	HCNP, HCRN, SYF1, NTC90	uc002mgx.3	Q9HCS7		ENST00000358368.4:c.1860C>T	19.37:g.7685843G>A		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	51	26	0.509804	NM_020196	Q8TET6|Q96HB0|Q96IW0|Q9NRG6|Q9ULP3	Silent	SNP	ENST00000358368.4	37	CCDS32892.1																																																																																			A|0.158;C|0.007	0.158	strong		0.657	XAB2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000461021.1	NM_020196	
OR2C1	4993	hgsc.bcm.edu	37	16	3405986	3405986	+	Missense_Mutation	SNP	G	G	A	rs1218762	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:3405986G>A	ENST00000304936.2	+	1	98	c.46G>A	c.(46-48)Ggc>Agc	p.G16S		NM_012368.2	NP_036500.2	O95371	OR2C1_HUMAN	olfactory receptor, family 2, subfamily C, member 1	16			G -> S (in dbSNP:rs1218762). {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						TGTTCTGATGGGCATATCAGA	0.463													G|||	1265	0.252596	0.3389	0.2435	5008	,	,		19587	0.1429		0.2614	False		,,,				2504	0.2464				p.G16S		Atlas-SNP	.											.	OR2C1	38	.	0			c.G46A						PASS	.		SER/GLY	1520,2874	481.4+/-359.1	249,1022,926	90.0	83.0	85.0		46	4.3	1.0	16	dbSNP_87	85	2364,6236	395.4+/-345.0	330,1704,2266	yes	missense	OR2C1	NM_012368.2	56	579,2726,3192	AA,AG,GG		27.4884,34.5926,29.8907	probably-damaging	16/313	3405986	3884,9110	2197	4300	6497	SO:0001583	missense	4993	exon1			CTGATGGGCATAT	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.46G>A	16.37:g.3405986G>A	ENSP00000307726:p.Gly16Ser	Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	147	118	0.802721	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	15.47	2.841769	0.51057	0.345926	0.274884	ENSG00000168158	ENST00000304936	T	0.00653	5.96	4.35	4.35	0.52113	.	0.000000	0.41294	D	0.000912	T	0.00012	0.0000	H	0.95780	3.72	0.24446	P	0.99450032	D	0.71674	0.998	D	0.64144	0.922	T	0.39121	-0.9629	9	0.66056	D	0.02	.	14.4129	0.67128	0.0:0.0:1.0:0.0	rs1218762;rs1690437;rs11647420;rs17650668;rs17841234;rs52799351;rs58577150;rs1218762	16	O95371	OR2C1_HUMAN	S	16	ENSP00000307726:G16S	ENSP00000307726:G16S	G	+	1	0	OR2C1	3345987	1.000000	0.71417	0.979000	0.43373	0.583000	0.36354	7.449000	0.80643	2.241000	0.73720	0.401000	0.26515	GGC	G|0.723;A|0.277	0.277	strong		0.463	OR2C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206993.3		
CANT1	124583	hgsc.bcm.edu	37	17	76993546	76993546	+	Silent	SNP	A	A	G	rs8077024	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:76993546A>G	ENST00000302345.2	-	2	653	c.159T>C	c.(157-159)gcT>gcC	p.A53A	CANT1_ENST00000591773.1_Silent_p.A53A|CANT1_ENST00000591732.1_5'Flank|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	90	0	0		WXS	Illumina HiSeq	Phase_I	91	37	0.406593	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	
NRCAM	4897	hgsc.bcm.edu	37	7	107872816	107872816	+	Silent	SNP	G	G	A	rs2072546	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:107872816G>A	ENST00000425651.2	-	4	380	c.381C>T	c.(379-381)aaC>aaT	p.N127N	NRCAM_ENST00000351718.4_Silent_p.N121N|NRCAM_ENST00000413765.2_Silent_p.N127N|NRCAM_ENST00000379022.4_Silent_p.N127N|NRCAM_ENST00000379024.4_Silent_p.N127N|NRCAM_ENST00000379028.3_Silent_p.N127N	NM_001037132.2	NP_001032209.1	Q92823	NRCAM_HUMAN	neuronal cell adhesion molecule	127	Ig-like 1.				angiogenesis (GO:0001525)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|axonogenesis (GO:0007409)|central nervous system development (GO:0007417)|clustering of voltage-gated sodium channels (GO:0045162)|heterotypic cell-cell adhesion (GO:0034113)|neuron migration (GO:0001764)|neuronal action potential propagation (GO:0019227)|positive regulation of neuron differentiation (GO:0045666)|protein localization (GO:0008104)|regulation of axon extension (GO:0030516)|retinal ganglion cell axon guidance (GO:0031290)|single organismal cell-cell adhesion (GO:0016337)|synapse assembly (GO:0007416)	axon initial segment (GO:0043194)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|synapse (GO:0045202)	ankyrin binding (GO:0030506)			breast(4)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(8)|liver(1)|lung(36)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(4)	65						CTCCGCGTTCGTTCCTTGCTG	0.458													G|||	1067	0.213059	0.0061	0.2723	5008	,	,		18947	0.5466		0.1243	False		,,,				2504	0.1984				p.N127N		Atlas-SNP	.											NRCAM_ENST00000379028,colon,carcinoma,0,2	NRCAM	267	2	0			c.C381T						PASS	.	G	,,,,	144,4262	101.6+/-140.2	1,142,2060	193.0	174.0	181.0		381,381,381,381,363	-9.8	0.4	7	dbSNP_96	181	1168,7432	239.4+/-270.5	87,994,3219	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NRCAM	NM_001037132.2,NM_001193582.1,NM_001193583.1,NM_001193584.1,NM_005010.4	,,,,	88,1136,5279	AA,AG,GG		13.5814,3.2683,10.0877	,,,,	127/1305,127/1212,127/1193,127/1181,121/1184	107872816	1312,11694	2203	4300	6503	SO:0001819	synonymous_variant	4897	exon4			GCGTTCGTTCCTT		CCDS5751.1, CCDS47686.1, CCDS55153.1, CCDS75652.1	7q31	2013-02-11			ENSG00000091129	ENSG00000091129		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	7994	protein-coding gene	gene with protein product	"""NgCAM-related cell adhesion molecule"""	601581				8812479	Standard	NM_001037132		Approved	KIAA0343, Bravo	uc022aka.1	Q92823	OTTHUMG00000154973	ENST00000425651.2:c.381C>T	7.37:g.107872816G>A		Somatic	196	0	0		WXS	Illumina HiSeq	Phase_I	187	102	0.545455	NM_001037132	A4D0S3|E9PDA4|O15051|O15179|Q14BM2|Q9UHI3|Q9UHI4	Silent	SNP	ENST00000425651.2	37	CCDS47686.1																																																																																			G|0.834;A|0.166	0.166	strong		0.458	NRCAM-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337942.2	NM_001037132	
AADACL3	126767	hgsc.bcm.edu	37	1	12785749	12785749	+	Missense_Mutation	SNP	C	C	T	rs11121969	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:12785749C>T	ENST00000359318.5	+	4	1044	c.839C>T	c.(838-840)cCg>cTg	p.P280L	AADACL3_ENST00000332530.3_Missense_Mutation_p.P210L	NM_001103170.1	NP_001096640.1	Q5VUY0	ADCL3_HUMAN	arylacetamide deacetylase-like 3	280			P -> L (in dbSNP:rs11121969).				hydrolase activity (GO:0016787)			breast(1)|kidney(1)|large_intestine(2)|lung(8)|ovary(1)|prostate(1)|skin(1)	15	Ovarian(185;0.249)	Lung NSC(185;8.27e-05)|all_lung(284;9.47e-05)|Renal(390;0.000147)|Colorectal(325;0.000583)|Breast(348;0.000596)|Ovarian(437;0.00965)|Hepatocellular(190;0.0245)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.13e-06)|COAD - Colon adenocarcinoma(227;0.000274)|BRCA - Breast invasive adenocarcinoma(304;0.000311)|Kidney(185;0.00217)|KIRC - Kidney renal clear cell carcinoma(229;0.00579)|STAD - Stomach adenocarcinoma(313;0.00743)|READ - Rectum adenocarcinoma(331;0.0649)		TCTCAGCTCCCGGAAACCTGC	0.517													C|||	365	0.0728834	0.174	0.0548	5008	,	,		20313	0.002		0.0676	False		,,,				2504	0.0276				p.P280L		Atlas-SNP	.											.	AADACL3	84	.	0			c.C839T						PASS	.	C	LEU/PRO,LEU/PRO	623,3487		43,537,1475	94.0	94.0	94.0		629,839	4.7	0.1	1	dbSNP_120	94	499,7919		11,477,3721	yes	missense,missense	AADACL3	NM_001103169.1,NM_001103170.1	98,98	54,1014,5196	TT,TC,CC		5.9278,15.1582,8.9559	probably-damaging,probably-damaging	210/281,280/351	12785749	1122,11406	2055	4209	6264	SO:0001583	missense	126767	exon4			AGCTCCCGGAAAC		CCDS41253.1	1p36.21	2014-07-17			ENSG00000188984	ENSG00000188984			32037	protein-coding gene	gene with protein product							Standard	XM_006710337		Approved	OTTHUMG00000001887	uc009vnn.1	Q5VUY0	OTTHUMG00000001887	ENST00000359318.5:c.839C>T	1.37:g.12785749C>T	ENSP00000352268:p.Pro280Leu	Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	162	87	0.537037	NM_001103170	B3KXR9|Q5VUY1	Missense_Mutation	SNP	ENST00000359318.5	37	CCDS41253.1	159	0.07280219780219781	85	0.17276422764227642	22	0.06077348066298342	2	0.0034965034965034965	50	0.06596306068601583	C	15.38	2.816627	0.50633	0.151582	0.059278	ENSG00000188984	ENST00000332530;ENST00000359318	T;T	0.14516	2.5;2.5	5.56	4.65	0.58169	Alpha/beta hydrolase fold-3 (1);	0.000000	0.85682	D	0.000000	T	0.00241	0.0007	H	0.98701	4.305	0.09310	P	0.999999999504842	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.47849	-0.9085	9	0.87932	D	0	-17.3038	15.758	0.78051	0.0:0.8637:0.1363:0.0	rs11121969;rs52809400;rs11121969	280;210	Q5VUY0;Q5VUY0-2	ADCL3_HUMAN;.	L	210;280	ENSP00000333352:P210L;ENSP00000352268:P280L	ENSP00000333352:P210L	P	+	2	0	AADACL3	12708336	1.000000	0.71417	0.109000	0.21407	0.042000	0.13812	4.756000	0.62205	1.339000	0.45563	0.484000	0.47621	CCG	C|0.922;T|0.078	0.078	strong		0.517	AADACL3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005324.2	NM_001103170	
GFRA2	2675	hgsc.bcm.edu	37	8	21550800	21550800	+	Missense_Mutation	SNP	A	A	T	rs1128397	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:21550800A>T	ENST00000524240.1	-	9	2035	c.1385T>A	c.(1384-1386)cTg>cAg	p.L462Q	GFRA2_ENST00000400782.4_Missense_Mutation_p.L357Q|GFRA2_ENST00000517328.1_Missense_Mutation_p.L462Q|GFRA2_ENST00000518077.1_Missense_Mutation_p.L329Q	NM_001495.4	NP_001486.4	O00451	GFRA2_HUMAN	GDNF family receptor alpha 2	462			L -> Q (in dbSNP:rs1128397). {ECO:0000269|PubMed:9182803, ECO:0000269|PubMed:9259272, ECO:0000269|Ref.4}.		negative regulation of protein autophosphorylation (GO:0031953)|nervous system development (GO:0007399)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	anchored component of membrane (GO:0031225)|extrinsic component of membrane (GO:0019898)|plasma membrane (GO:0005886)	glial cell-derived neurotrophic factor receptor activity (GO:0016167)			NS(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|prostate(1)|skin(1)	7				Colorectal(74;0.0189)|COAD - Colon adenocarcinoma(73;0.0727)		CTACAAGGCCAGTTTCAGCAT	0.522													A|||	1863	0.372005	0.3396	0.3228	5008	,	,		16700	0.4296		0.4026	False		,,,				2504	0.3599				p.L462Q		Atlas-SNP	.											.	GFRA2	23	.	0			c.T1385A						PASS	.	A	GLN/LEU,GLN/LEU,GLN/LEU	1321,2641		231,859,891	84.0	79.0	81.0		1070,986,1385	2.8	0.5	8	dbSNP_86	81	3335,5019		655,2025,1497	yes	missense,missense,missense	GFRA2	NM_001165038.1,NM_001165039.1,NM_001495.4	113,113,113	886,2884,2388	TT,TA,AA		39.921,33.3417,37.8045	probably-damaging,probably-damaging,probably-damaging	357/360,329/332,462/465	21550800	4656,7660	1981	4177	6158	SO:0001583	missense	2675	exon9			AAGGCCAGTTTCA	AF002700	CCDS47816.1, CCDS55207.1	8p21.3	2008-05-02			ENSG00000168546	ENSG00000168546			4244	protein-coding gene	gene with protein product		601956				9177201	Standard	NM_001165038		Approved	RETL2, GDNFRB, NTNRA, TRNR2	uc003wzu.1	O00451	OTTHUMG00000163897	ENST00000524240.1:c.1385T>A	8.37:g.21550800A>T	ENSP00000428518:p.Leu462Gln	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	78	60	0.769231	NM_001495	E9PD47|O15316|O15328|Q58J92|Q6GTR9|Q7Z5C2	Missense_Mutation	SNP	ENST00000524240.1	37	CCDS47816.1	840	0.38461538461538464	168	0.34146341463414637	113	0.31215469613259667	249	0.4353146853146853	310	0.40897097625329815	A	17.73	3.462459	0.63513	0.333417	0.39921	ENSG00000168546	ENST00000524240;ENST00000400782;ENST00000517328;ENST00000518077;ENST00000517892	T;T;T;T;T	0.38401	1.61;1.19;1.61;1.14;1.19	5.34	2.85	0.33270	.	0.113536	0.36409	N	0.002616	T	0.00012	0.0000	L	0.60455	1.87	0.27066	P	0.9634426	D;D;D	0.69078	0.994;0.994;0.997	P;P;P	0.60789	0.804;0.855;0.879	T	0.44682	-0.9312	9	0.54805	T	0.06	-3.6087	9.6789	0.40059	0.6625:0.3375:0.0:0.0	rs1128397;rs2229905;rs3087672;rs3185307;rs52833017;rs1128397	329;357;462	O00451-2;E9PD47;O00451	.;.;GFRA2_HUMAN	Q	462;357;462;329;357	ENSP00000428518:L462Q;ENSP00000383592:L357Q;ENSP00000429445:L462Q;ENSP00000429206:L329Q;ENSP00000429979:L357Q	ENSP00000383592:L357Q	L	-	2	0	GFRA2	21595080	0.999000	0.42202	0.516000	0.27786	0.739000	0.42172	2.372000	0.44257	0.299000	0.22661	0.528000	0.53228	CTG	A|0.607;T|0.393	0.393	strong		0.522	GFRA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376254.3	NM_001495	
RECK	8434	hgsc.bcm.edu	37	9	36110063	36110063	+	Silent	SNP	T	T	A	rs10972727	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:36110063T>A	ENST00000377966.3	+	15	2441	c.1875T>A	c.(1873-1875)cgT>cgA	p.R625R		NM_021111.2	NP_066934.1	O95980	RECK_HUMAN	reversion-inducing-cysteine-rich protein with kazal motifs	625					blood vessel maturation (GO:0001955)|embryo implantation (GO:0007566)|extracellular matrix organization (GO:0030198)|negative regulation of endopeptidase activity (GO:0010951)	anchored component of membrane (GO:0031225)|membrane (GO:0016020)|plasma membrane (GO:0005886)	endopeptidase inhibitor activity (GO:0004866)|metalloendopeptidase inhibitor activity (GO:0008191)|serine-type endopeptidase inhibitor activity (GO:0004867)			cervix(1)|endometrium(7)|kidney(3)|large_intestine(6)|lung(10)|ovary(1)|pancreas(1)|skin(2)|stomach(1)	32			LUSC - Lung squamous cell carcinoma(32;0.112)|STAD - Stomach adenocarcinoma(86;0.228)			AAGATGACCGTCGTACCTTCA	0.483													T|||	1232	0.246006	0.0469	0.2378	5008	,	,		18159	0.3056		0.3638	False		,,,				2504	0.3384				p.R625R		Atlas-SNP	.											.	RECK	73	.	0			c.T1875A						PASS	.	T		426,3980	207.2+/-228.6	26,374,1803	195.0	151.0	166.0		1875	-5.2	0.9	9	dbSNP_120	166	3241,5359	487.6+/-372.2	645,1951,1704	no	coding-synonymous	RECK	NM_021111.2		671,2325,3507	AA,AT,TT		37.686,9.6686,28.1947		625/972	36110063	3667,9339	2203	4300	6503	SO:0001819	synonymous_variant	8434	exon15			TGACCGTCGTACC	E13833	CCDS6597.1	9p13.3	2008-05-15			ENSG00000122707	ENSG00000122707			11345	protein-coding gene	gene with protein product		605227		ST15		9789069	Standard	NM_021111		Approved	hRECK	uc003zyv.3	O95980	OTTHUMG00000019898	ENST00000377966.3:c.1875T>A	9.37:g.36110063T>A		Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	142	84	0.591549	NM_021111	B2RNS1|Q5W0K6|Q8WX37	Silent	SNP	ENST00000377966.3	37	CCDS6597.1																																																																																			T|0.719;A|0.281	0.281	strong		0.483	RECK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052409.1		
FHL5	9457	hgsc.bcm.edu	37	6	97058553	97058553	+	Missense_Mutation	SNP	A	A	G	rs2273621	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:97058553A>G	ENST00000326771.2	+	6	990	c.610A>G	c.(610-612)Aga>Gga	p.R204G	FHL5_ENST00000541107.1_Missense_Mutation_p.R204G	NM_020482.4	NP_065228.4	Q5TD97	FHL5_HUMAN	four and a half LIM domains 5	204	LIM zinc-binding 3. {ECO:0000255|PROSITE- ProRule:PRU00125}.		R -> G (in dbSNP:rs2273621).		positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(4)|lung(17)|ovary(2)|urinary_tract(1)	27		all_cancers(76;1.57e-07)|Acute lymphoblastic leukemia(125;4.93e-10)|all_hematologic(75;3.55e-07)|all_epithelial(107;0.00266)|Colorectal(196;0.0341)|Lung NSC(302;0.204)		BRCA - Breast invasive adenocarcinoma(108;0.0948)		GTTCATGTCCAGAGACGACTA	0.433													A|||	1994	0.398163	0.5499	0.3026	5008	,	,		17809	0.3522		0.3519	False		,,,				2504	0.3558				p.R204G		Atlas-SNP	.											.	FHL5	73	.	0			c.A610G						PASS	.	A	GLY/ARG,GLY/ARG	2230,2176	592.3+/-387.8	559,1112,532	259.0	236.0	244.0		610,610	4.7	1.0	6	dbSNP_100	244	2876,5724	451.4+/-362.6	483,1910,1907	yes	missense,missense	FHL5	NM_001170807.1,NM_020482.4	125,125	1042,3022,2439	GG,GA,AA		33.4419,49.3872,39.2588	possibly-damaging,possibly-damaging	204/285,204/285	97058553	5106,7900	2203	4300	6503	SO:0001583	missense	9457	exon6			ATGTCCAGAGACG	AF278541	CCDS5035.1	6q16.1-q16.3	2008-02-05			ENSG00000112214	ENSG00000112214			17371	protein-coding gene	gene with protein product		605126					Standard	NM_020482		Approved	FLJ33049, ACT, dJ393D12.2	uc003pot.2	Q5TD97	OTTHUMG00000015239	ENST00000326771.2:c.610A>G	6.37:g.97058553A>G	ENSP00000326022:p.Arg204Gly	Somatic	271	0	0		WXS	Illumina HiSeq	Phase_I	217	217	1	NM_020482	B2RBD1|E1P526|Q5TD98|Q8WW21|Q9NQU2	Missense_Mutation	SNP	ENST00000326771.2	37	CCDS5035.1	857	0.3923992673992674	275	0.5589430894308943	126	0.34806629834254144	201	0.3513986013986014	255	0.33641160949868076	A	15.86	2.958370	0.53400	0.506128	0.334419	ENSG00000112214	ENST00000541107;ENST00000326771;ENST00000450218	D;D;D	0.88046	-2.32;-2.32;-2.33	5.88	4.7	0.59300	Zinc finger, LIM-type (4);	0.148657	0.32015	N	0.006702	D	0.85592	0.5732	M	0.88450	2.955	0.29237	P	0.872905	B	0.21071	0.051	B	0.30782	0.12	D	0.84571	0.0655	9	0.66056	D	0.02	.	13.1274	0.59363	0.8662:0.1338:0.0:0.0	rs2273621;rs2273621	204	Q5TD97	FHL5_HUMAN	G	204	ENSP00000442357:R204G;ENSP00000326022:R204G;ENSP00000396390:R204G	ENSP00000326022:R204G	R	+	1	2	FHL5	97165274	1.000000	0.71417	0.998000	0.56505	0.896000	0.52359	4.670000	0.61583	1.019000	0.39547	0.528000	0.53228	AGA	A|0.603;G|0.397	0.397	strong		0.433	FHL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041559.1	NM_020482	
SEZ6	124925	hgsc.bcm.edu	37	17	27284443	27284443	+	Missense_Mutation	SNP	A	A	G	rs12941884	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:27284443A>G	ENST00000317338.12	-	12	2845	c.2417T>C	c.(2416-2418)aTg>aCg	p.M806T	SEZ6_ENST00000360295.9_Missense_Mutation_p.M806T|PIPOX_ENST00000583215.1_Intron|SEZ6_ENST00000335960.6_Intron|SEZ6_ENST00000442608.3_Missense_Mutation_p.M806T			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	130	0	0		WXS	Illumina HiSeq	Phase_I	89	89	1	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		
EFHB	151651	hgsc.bcm.edu	37	3	19975215	19975215	+	Missense_Mutation	SNP	C	C	A	rs17795400	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:19975215C>A	ENST00000295824.9	-	1	457	c.296G>T	c.(295-297)gGa>gTa	p.G99V	EFHB_ENST00000498089.1_5'UTR|EFHB_ENST00000344838.4_Intron	NM_144715.3	NP_653316.3	Q8N7U6	EFHB_HUMAN	EF-hand domain family, member B	99			G -> V (in dbSNP:rs17795400).				calcium ion binding (GO:0005509)			breast(2)|endometrium(4)|kidney(1)|lung(17)|prostate(1)|urinary_tract(1)	26						AGGTTTTGTTCCCTGTGAAGC	0.458													C|||	950	0.189696	0.0809	0.1686	5008	,	,		21397	0.2192		0.2376	False		,,,				2504	0.272				p.G99V		Atlas-SNP	.											.	EFHB	186	.	0			c.G296T						PASS	.	C	VAL/GLY	400,3646		22,356,1645	147.0	146.0	146.0		296	-1.2	0.0	3	dbSNP_123	146	2188,6190		279,1630,2280	yes	missense	EFHB	NM_144715.3	109	301,1986,3925	AA,AC,CC		26.116,9.8863,20.8307	possibly-damaging	99/834	19975215	2588,9836	2023	4189	6212	SO:0001583	missense	151651	exon1			TTTGTTCCCTGTG	AK122616	CCDS33715.2	3p24.3	2014-07-18			ENSG00000163576	ENSG00000163576		"""EF-hand domain containing"""	26330	protein-coding gene	gene with protein product	"""cilia and flagella associated protein 21"""					12477932	Standard	NM_144715		Approved	FLJ25200, CFAP21	uc003cbl.4	Q8N7U6	OTTHUMG00000150505	ENST00000295824.9:c.296G>T	3.37:g.19975215C>A	ENSP00000295824:p.Gly99Val	Somatic	331	0	0		WXS	Illumina HiSeq	Phase_I	266	133	0.5	NM_144715	A6ND25|A8MPR3|Q6ZWK9|Q8IV58|Q96LQ6	Missense_Mutation	SNP	ENST00000295824.9	37	CCDS33715.2	436	0.19963369963369965	53	0.10772357723577236	67	0.1850828729281768	127	0.22202797202797203	189	0.24934036939313983	C	9.672	1.146992	0.21288	0.098863	0.26116	ENSG00000163576	ENST00000295824;ENST00000389256	T;T	0.25579	1.79;2.04	3.6	-1.22	0.09494	.	.	.	.	.	T	0.00012	0.0000	L	0.34521	1.04	0.80722	P	0.0	B	0.15141	0.012	B	0.09377	0.004	T	0.42999	-0.9418	7	.	.	.	-3.0822	7.0131	0.24873	0.0:0.3945:0.0:0.6055	rs17795400;rs52807659;rs17795400	99	Q8N7U6	EFHB_HUMAN	V	99	ENSP00000295824:G99V;ENSP00000373908:G99V	.	G	-	2	0	EFHB	19950219	0.001000	0.12720	0.000000	0.03702	0.154000	0.21943	-0.159000	0.10056	-0.238000	0.09724	0.555000	0.69702	GGA	C|0.797;A|0.202	0.202	strong		0.458	EFHB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318673.2	NM_144715	
TUBB1	81027	hgsc.bcm.edu	37	20	57599402	57599402	+	Missense_Mutation	SNP	G	G	A	rs6070697	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	65	0	0		WXS	Illumina HiSeq	Phase_I	50	24	0.48	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	
GALNS	2588	hgsc.bcm.edu	37	16	88902183	88902183	+	Silent	SNP	G	G	A	rs1064315	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:88902183G>A	ENST00000268695.5	-	7	796	c.708C>T	c.(706-708)caC>caT	p.H236H	GALNS_ENST00000542788.1_Silent_p.H161H	NM_000512.4	NP_000503.1	P34059	GALNS_HUMAN	galactosamine (N-acetyl)-6-sulfatase	236	Catalytic domain.				carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)	metal ion binding (GO:0046872)|N-acetylgalactosamine-4-sulfatase activity (GO:0003943)|N-acetylgalactosamine-6-sulfatase activity (GO:0043890)|sulfuric ester hydrolase activity (GO:0008484)			breast(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(8)	22				BRCA - Breast invasive adenocarcinoma(80;0.0496)		AGACGGGTGCGTGCGTGGCGT	0.617													G|||	1586	0.316693	0.211	0.2767	5008	,	,		17738	0.5486		0.2724	False		,,,				2504	0.2945				p.H236H	GBM(129;1929 2344 25209 33204)	Atlas-SNP	.											.	GALNS	37	.	0			c.C708T						PASS	.	G		920,3476	351.6+/-311.3	84,752,1362	135.0	112.0	119.0		708	-4.9	0.2	16	dbSNP_86	119	2205,6395	375.8+/-337.9	257,1691,2352	no	coding-synonymous	GALNS	NM_000512.4		341,2443,3714	AA,AG,GG		25.6395,20.9281,24.0459		236/523	88902183	3125,9871	2198	4300	6498	SO:0001819	synonymous_variant	2588	exon7			GGGTGCGTGCGTG	D17629	CCDS10970.1	16q24.3	2014-07-03	2014-07-03		ENSG00000141012	ENSG00000141012	3.1.6.4	"""Arylsulfatase family"""	4122	protein-coding gene	gene with protein product	"""Morquio syndrome"", ""mucopolysaccharidosis type IVA"""	612222	"""galactosamine (N-acetyl)-6-sulfate sulfatase"""			1755850	Standard	NM_000512		Approved	GAS, GALNAC6S	uc002fly.4	P34059	OTTHUMG00000137862	ENST00000268695.5:c.708C>T	16.37:g.88902183G>A		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	147	90	0.612245	NM_000512	Q86VK3	Silent	SNP	ENST00000268695.5	37	CCDS10970.1																																																																																			G|0.715;A|0.285	0.285	strong		0.617	GALNS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269543.1		
PTDSS2	81490	hgsc.bcm.edu	37	11	490035	490035	+	Missense_Mutation	SNP	C	C	T	rs61742833	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:490035C>T	ENST00000308020.5	+	11	1444	c.1268C>T	c.(1267-1269)gCg>gTg	p.A423V		NM_030783.1	NP_110410.1	Q9BVG9	PTSS2_HUMAN	phosphatidylserine synthase 2	423					glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylserine biosynthetic process (GO:0006659)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	CDP-diacylglycerol-serine O-phosphatidyltransferase activity (GO:0003882)			autonomic_ganglia(1)|breast(1)|cervix(2)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|skin(1)	9		all_cancers(49;1.59e-06)|all_epithelial(84;0.000256)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;2.76e-26)|Epithelial(43;2.56e-25)|OV - Ovarian serous cystadenocarcinoma(40;7.54e-20)|BRCA - Breast invasive adenocarcinoma(625;8.76e-05)|Lung(200;0.0407)|LUSC - Lung squamous cell carcinoma(625;0.0735)	Phosphatidylserine(DB00144)	TCCGTCCTGGCGCTCACCTGG	0.657													T|||	238	0.047524	0.0053	0.1974	5008	,	,		15849	0.001		0.0726	False		,,,				2504	0.0204				p.A423V		Atlas-SNP	.											PTDSS2,caecum,carcinoma,-1,3	PTDSS2	27	3	0			c.C1268T						PASS	.	T	VAL/ALA	91,4315	809.3+/-416.0	1,89,2113	90.0	60.0	70.0		1268	2.6	1.0	11	dbSNP_129	70	876,7724	776.3+/-407.7	45,786,3469	yes	missense	PTDSS2	NM_030783.1	64	46,875,5582	TT,TC,CC		10.186,2.0654,7.435	benign	423/488	490035	967,12039	2203	4300	6503	SO:0001583	missense	81490	exon11			TCCTGGCGCTCAC	BC001210	CCDS7696.1	11p15	2008-05-02			ENSG00000174915	ENSG00000174915			15463	protein-coding gene	gene with protein product		612793				14984733	Standard	NM_030783		Approved	PSS2	uc001lpj.3	Q9BVG9	OTTHUMG00000119087	ENST00000308020.5:c.1268C>T	11.37:g.490035C>T	ENSP00000308258:p.Ala423Val	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	45	33	0.733333	NM_030783		Missense_Mutation	SNP	ENST00000308020.5	37	CCDS7696.1	132	0.06043956043956044	7	0.014227642276422764	70	0.19337016574585636	1	0.0017482517482517483	54	0.0712401055408971	T	6.945	0.544199	0.13312	0.020654	0.10186	ENSG00000174915	ENST00000308020	.	.	.	3.74	2.6	0.31112	.	0.151894	0.44688	N	0.000433	T	0.00039	0.0001	N	0.02539	-0.55	0.54753	P	1.3000000000040757E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.27739	-1.0065	8	0.12430	T	0.62	-7.4345	8.089	0.30790	0.0:0.1704:0.0:0.8296	rs61742833	423	Q9BVG9	PTSS2_HUMAN	V	423	.	ENSP00000308258:A423V	A	+	2	0	PTDSS2	480035	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	3.134000	0.50538	0.177000	0.19895	-0.361000	0.07541	GCG	C|0.925;T|0.075	0.075	strong		0.657	PTDSS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239301.2		
GPR18	2841	hgsc.bcm.edu	37	13	99907341	99907341	+	Silent	SNP	G	G	A	rs3742130	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:99907341G>A	ENST00000340807.3	-	3	1342	c.786C>T	c.(784-786)aaC>aaT	p.N262N	UBAC2_ENST00000376440.2_Intron|GPR18_ENST00000397470.2_Silent_p.N262N|GPR18_ENST00000397473.2_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	149	0	0		WXS	Illumina HiSeq	Phase_I	156	155	0.99359	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		
PSPH	5723	hgsc.bcm.edu	37	7	56087423	56087423	+	Missense_Mutation	SNP	G	G	A	rs79451216		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:56087423G>A	ENST00000395471.3	-	5	950	c.145C>T	c.(145-147)Cgg>Tgg	p.R49W	PSPH_ENST00000275605.3_Missense_Mutation_p.R49W|PSPH_ENST00000459834.1_Intron			P78330	SERB_HUMAN	phosphoserine phosphatase	49					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)	p.R49W(1)		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)			ATGGCTCGCCGTGTCCTAGGA	0.602													G|||	1	0.000199681	0.0	0.0	5008	,	,		13539	0.0		0.001	False		,,,				2504	0.0				p.R49W		Atlas-SNP	.											PSPH,NS,lymphoid_neoplasm,0,1	PSPH	23	1	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.C145T						scavenged	.						48.0	34.0	39.0					7																	56087423		2203	4300	6503	SO:0001583	missense	5723	exon5			CTCGCCGTGTCCT	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.145C>T	7.37:g.56087423G>A	ENSP00000378854:p.Arg49Trp	Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	28	4	0.142857	NM_004577	B2RCR5|Q7Z3S5	Missense_Mutation	SNP	ENST00000395471.3	37	CCDS5522.1	.	.	.	.	.	.	.	.	.	.	G	13.02	2.112152	0.37242	.	.	ENSG00000146733	ENST00000275605;ENST00000395471;ENST00000421626	D;D;D	0.82526	-1.62;-1.62;-1.62	4.5	3.6	0.41247	Haloacid dehalogenase-like hydrolase (1);HAD-like domain (1);Phosphoserine phosphatase, domain 2 (1);	0.186825	0.48767	D	0.000180	D	0.82346	0.5017	M	0.77486	2.375	0.80722	D	1	B;B	0.25235	0.106;0.121	B;B	0.21546	0.034;0.035	T	0.81686	-0.0820	10	0.87932	D	0	-7.1074	12.8694	0.57957	0.0:0.0:0.8358:0.1642	.	49;49	Q53EY1;P78330	.;SERB_HUMAN	W	49	ENSP00000275605:R49W;ENSP00000378854:R49W;ENSP00000398653:R49W	ENSP00000275605:R49W	R	-	1	2	PSPH	56054917	0.999000	0.42202	0.920000	0.36463	0.415000	0.31203	3.353000	0.52247	1.076000	0.40961	0.591000	0.81541	CGG	G|0.913;A|0.086	0.086	strong		0.602	PSPH-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343304.1	NM_004577	
PPP1R1A	5502	hgsc.bcm.edu	37	12	54974803	54974803	+	Silent	SNP	C	C	T	rs8407	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:54974803C>T	ENST00000257905.8	-	6	605	c.435G>A	c.(433-435)gaG>gaA	p.E145E	PPP1R1A_ENST00000547431.1_Missense_Mutation_p.R72K	NM_006741.3	NP_006732	Q13522	PPR1A_HUMAN	protein phosphatase 1, regulatory (inhibitor) subunit 1A	145	Interaction with PPP1R15A.				glycogen metabolic process (GO:0005977)|negative regulation of catalytic activity (GO:0043086)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	protein serine/threonine phosphatase inhibitor activity (GO:0004865)			lung(2)	2						TACTGCCTCTCTCGTGAGTTT	0.542													C|||	829	0.165535	0.0348	0.2666	5008	,	,		17061	0.0595		0.3012	False		,,,				2504	0.2403				p.E145E		Atlas-SNP	.											PPP1R1A_ENST00000257905,NS,carcinoma,-2,2	PPP1R1A	18	2	0			c.G435A						PASS	.	C		284,3490		5,274,1608	203.0	190.0	194.0		435	4.9	1.0	12	dbSNP_52	194	2522,5724		381,1760,1982	no	coding-synonymous	PPP1R1A	NM_006741.3		386,2034,3590	TT,TC,CC		30.5845,7.5252,23.3444		145/172	54974803	2806,9214	1887	4123	6010	SO:0001819	synonymous_variant	5502	exon6			GCCTCTCTCGTGA	U48707	CCDS44912.1	12q13.2	2012-04-17			ENSG00000135447	ENSG00000135447	3.1.3.16	"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	9286	protein-coding gene	gene with protein product		613246				8611507	Standard	NM_006741		Approved		uc001sgg.2	Q13522	OTTHUMG00000169934	ENST00000257905.8:c.435G>A	12.37:g.54974803C>T		Somatic	295	0	0		WXS	Illumina HiSeq	Phase_I	310	137	0.441935	NM_006741	Q6IB01|Q8TBJ2|Q8WWV2	Silent	SNP	ENST00000257905.8	37	CCDS44912.1	381	0.17445054945054944	20	0.04065040650406504	94	0.2596685082872928	39	0.06818181818181818	228	0.3007915567282322	C	5.450	0.268099	0.10349	0.075252	0.305845	ENSG00000135447	ENST00000379690;ENST00000553113	.	.	.	4.95	4.95	0.65309	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.04053	-1.0981	4	0.02654	T	1	.	14.0661	0.64831	0.0:1.0:0.0:0.0	rs8407;rs867623;rs1050103;rs3190383;rs17795135;rs17845698;rs17858640;rs8407	.	.	.	K	72;64	.	ENSP00000369012:R72K	R	-	2	0	PPP1R1A	53261070	0.985000	0.35326	0.963000	0.40424	0.460000	0.32559	3.445000	0.52921	2.458000	0.83093	0.655000	0.94253	AGA	C|0.825;T|0.175	0.175	strong		0.542	PPP1R1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406604.1	NM_006741	
MLX	6945	hgsc.bcm.edu	37	17	40722162	40722162	+	Silent	SNP	G	G	A	rs1474040	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:40722162G>A	ENST00000246912.4	+	7	854	c.801G>A	c.(799-801)gcG>gcA	p.A267A	MLX_ENST00000346833.4_Silent_p.A183A|MLX_ENST00000435881.2_Silent_p.A213A	NM_170607.2	NP_733752.1	Q9UH92	MLX_HUMAN	MLX, MAX dimerization protein	267					energy reserve metabolic process (GO:0006112)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleocytoplasmic transport (GO:0006913)|positive regulation of cellular metabolic process (GO:0031325)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			kidney(3)|large_intestine(4)|lung(1)|ovary(1)|urinary_tract(1)	10		all_cancers(22;4.26e-05)|Breast(137;0.000153)|all_epithelial(22;0.00148)		BRCA - Breast invasive adenocarcinoma(366;0.129)		AGCTGTCAGCGTGTGTCTTCA	0.532													G|||	484	0.0966454	0.0113	0.1816	5008	,	,		21738	0.0		0.2783	False		,,,				2504	0.0644				p.A267A	GBM(121;657 1601 4665 24731 34640)	Atlas-SNP	.											MLX,colon,carcinoma,+1,1	MLX	17	1	0			c.G801A						PASS	.	G	,,	207,4199	127.8+/-164.7	6,195,2002	109.0	91.0	97.0		801,639,549	-4.0	0.9	17	dbSNP_88	97	2264,6336	384.5+/-341.1	295,1674,2331	no	coding-synonymous,coding-synonymous,coding-synonymous	MLX	NM_170607.2,NM_198204.1,NM_198205.1	,,	301,1869,4333	AA,AG,GG		26.3256,4.6981,18.9989	,,	267/299,213/245,183/215	40722162	2471,10535	2203	4300	6503	SO:0001819	synonymous_variant	6945	exon7			GTCAGCGTGTGTC	AF213668	CCDS11430.1, CCDS42341.1, CCDS45687.1	17q21.1	2013-05-21	2012-11-15	2005-02-11		ENSG00000108788		"""MAX dimerization proteins"", ""Basic helix-loop-helix proteins"""	11645	protein-coding gene	gene with protein product		602976	"""transcription factor-like 4"", ""MAX-like protein X"""	TCFL4		8973301	Standard	NM_170607		Approved	MAD7, MXD7, bHLHd13	uc002iag.3	Q9UH92		ENST00000246912.4:c.801G>A	17.37:g.40722162G>A		Somatic	201	0	0		WXS	Illumina HiSeq	Phase_I	152	75	0.493421	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	
GIPR	2696	hgsc.bcm.edu	37	19	46181392	46181392	+	Missense_Mutation	SNP	G	G	C	rs1800437	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:46181392G>C	ENST00000590918.1	+	12	1159	c.1060G>C	c.(1060-1062)Gag>Cag	p.E354Q	GIPR_ENST00000263281.3_Missense_Mutation_p.E354Q|GIPR_ENST00000304207.8_Missense_Mutation_p.E318Q	NM_000164.2	NP_000155.1	P48546	GIPR_HUMAN	gastric inhibitory polypeptide receptor	354			E -> Q (in dbSNP:rs1800437).		activation of adenylate cyclase activity (GO:0007190)|cell surface receptor signaling pathway (GO:0007166)|desensitization of G-protein coupled receptor protein signaling pathway (GO:0002029)|endocrine pancreas development (GO:0031018)|generation of precursor metabolites and energy (GO:0006091)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of insulin secretion (GO:0032024)|response to axon injury (GO:0048678)|response to calcium ion (GO:0051592)|response to fatty acid (GO:0070542)|response to glucose (GO:0009749)|response to nutrient (GO:0007584)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	gastric inhibitory peptide receptor activity (GO:0016519)|peptide hormone binding (GO:0017046)|transmembrane signaling receptor activity (GO:0004888)			endometrium(1)|kidney(2)|lung(5)|prostate(1)|skin(2)|urinary_tract(1)	12		Ovarian(192;0.051)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.0056)|GBM - Glioblastoma multiforme(486;0.0832)|Epithelial(262;0.199)		GGGTGTCCACGAGGTGGTGTT	0.667													G|||	807	0.161142	0.1233	0.1268	5008	,	,		14796	0.2073		0.2137	False		,,,				2504	0.135				p.E354Q		Atlas-SNP	.											.	GIPR	36	.	0			c.G1060C	GRCh37	CM960738	GIPR	M	rs1800437	PASS	.		GLN/GLU	500,3906		29,442,1732	23.0	22.0	22.0		1060	3.1	1.0	19	dbSNP_89	22	1750,6850		195,1360,2745	yes	missense	GIPR	NM_000164.2	29	224,1802,4477	CC,CG,GG		20.3488,11.3482,17.2997	probably-damaging	354/467	46181392	2250,10756	2203	4300	6503	SO:0001583	missense	2696	exon12			GTCCACGAGGTGG		CCDS12671.1	19q13.2-q13.3	2012-08-10				ENSG00000010310		"""GPCR / Class B : Glucagon receptors"""	4271	protein-coding gene	gene with protein product		137241				7490109	Standard	NM_000164		Approved		uc002pcu.1	P48546		ENST00000590918.1:c.1060G>C	19.37:g.46181392G>C	ENSP00000467494:p.Glu354Gln	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	110	58	0.527273	NM_000164	B7WP14|B7ZKQ0|Q14401|Q16400|Q52M04|Q9UPI1	Missense_Mutation	SNP	ENST00000590918.1	37	CCDS12671.1	396	0.1813186813186813	62	0.12601626016260162	49	0.13535911602209943	127	0.22202797202797203	158	0.20844327176781002	G	23.9	4.467820	0.84533	0.113482	0.203488	ENSG00000010310	ENST00000263281;ENST00000304207	T;T	0.45276	0.9;0.9	4.19	3.14	0.36123	GPCR, family 2-like (1);	0.000000	0.46758	D	0.000263	T	0.00073	0.0002	M	0.81497	2.545	0.26226	P	0.9790859	D;D;D	0.89917	0.993;1.0;0.995	P;D;D	0.91635	0.904;0.999;0.958	T	0.04255	-1.0965	9	0.52906	T	0.07	.	11.0623	0.47955	0.0:0.0:0.8131:0.1869	rs1800437;rs3745801;rs52793261;rs57928589;rs1800437	318;354;354	B7WP14;P48546;P48546-2	.;GIPR_HUMAN;.	Q	354;318	ENSP00000263281:E354Q;ENSP00000305321:E318Q	ENSP00000263281:E354Q	E	+	1	0	GIPR	50873232	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	3.265000	0.51561	0.954000	0.37851	0.313000	0.20887	GAG	G|0.836;C|0.164	0.164	strong		0.667	GIPR-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000459640.1		
PDXDC1	23042	hgsc.bcm.edu	37	16	15129970	15129970	+	Silent	SNP	A	A	G	rs7200543	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:15129970A>G	ENST00000396410.4	+	23	2302	c.2205A>G	c.(2203-2205)ctA>ctG	p.L735L	PDXDC1_ENST00000450288.2_Silent_p.L707L|PDXDC1_ENST00000447912.2_Silent_p.L644L|PDXDC1_ENST00000325823.7_Silent_p.L720L|PDXDC1_ENST00000563679.1_Silent_p.L753L|PDXDC1_ENST00000535621.2_Intron|PDXDC1_ENST00000569715.1_Silent_p.L708L	NM_015027.2	NP_055842.2	Q6P996	PDXD1_HUMAN	pyridoxal-dependent decarboxylase domain containing 1	735					carboxylic acid metabolic process (GO:0019752)	Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)	carboxy-lyase activity (GO:0016831)|pyridoxal phosphate binding (GO:0030170)			central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(2)|liver(1)|lung(10)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						TGGAGCGCCTATCCAGTGGGC	0.582													G|||	1728	0.345048	0.1846	0.5331	5008	,	,		18589	0.371		0.3062	False		,,,				2504	0.4417				p.L735L		Atlas-SNP	.											.	PDXDC1	59	.	0			c.A2205G						PASS	.	G		989,3405	730.4+/-410.2	119,751,1327	120.0	120.0	120.0	http://www.ncbi.nlm.nih.gov/pubmed?term	2205	4.7	0.1	16	dbSNP_116	120	2587,6013	689.7+/-404.4	359,1869,2072	yes	coding-synonymous	PDXDC1	NM_015027.2		478,2620,3399	GG,GA,AA	http://www.ncbi.nlm.nih.gov/pubmed?term	30.0814,22.508,27.5204		735/789	15129970	3576,9418	2197	4300	6497	SO:0001819	synonymous_variant	23042	exon23			GCGCCTATCCAGT	AK025504, BX647809	CCDS32393.1, CCDS66954.1, CCDS66957.1, CCDS73830.1, CCDS73831.1	16p13.11	2008-02-05							28995	protein-coding gene	gene with protein product		614244					Standard	XM_005255173		Approved	KIAA0251	uc002dda.4	Q6P996	OTTHUMG00000166304	ENST00000396410.4:c.2205A>G	16.37:g.15129970A>G		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	43	35	0.813953	NM_015027	B4DR55|B4DSL3|E7EMH5|E7EPL4|H3BNZ1|O00236|Q4F6X7|Q6PID7|Q86YF1|Q8N4Q9|Q8TBS5	Silent	SNP	ENST00000396410.4	37	CCDS32393.1																																																																																			A|0.706;G|0.294	0.294	strong		0.582	PDXDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389065.2	NM_015027	
LBP	3929	hgsc.bcm.edu	37	20	36979265	36979265	+	Silent	SNP	T	T	C	rs2232582	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:36979265T>C	ENST00000217407.2	+	3	452	c.291T>C	c.(289-291)ccT>ccC	p.P97P		NM_004139.3	NP_004130.2	P18428	LBP_HUMAN	lipopolysaccharide binding protein	97					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)				GGCCTGTCCCTGGCCAGGGCC	0.617													C|||	1068	0.213259	0.4221	0.1023	5008	,	,		21538	0.0734		0.1322	False		,,,				2504	0.2372				p.P97P		Atlas-SNP	.											.	LBP	60	.	0			c.T291C						PASS	.	C		1635,2771	658.5+/-400.4	306,1023,874	88.0	80.0	83.0		291	-9.4	0.0	20	dbSNP_98	83	1364,7236	755.0+/-407.5	111,1142,3047	no	coding-synonymous	LBP	NM_004139.2		417,2165,3921	CC,CT,TT		15.8605,37.1085,23.0586		97/482	36979265	2999,10007	2203	4300	6503	SO:0001819	synonymous_variant	3929	exon3			TGTCCCTGGCCAG		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.291T>C	20.37:g.36979265T>C		Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	51	28	0.54902	NM_004139	B2R938|O43438|Q92672|Q9H403|Q9UD66	Silent	SNP	ENST00000217407.2	37	CCDS13304.1																																																																																			T|0.792;C|0.208	0.208	strong		0.617	LBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079174.2	NM_004139	
DGKH	160851	hgsc.bcm.edu	37	13	42729463	42729463	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:42729463G>A	ENST00000337343.4	+	4	442	c.421G>A	c.(421-423)Gag>Aag	p.E141K	DGKH_ENST00000379274.2_Missense_Mutation_p.E5K|DGKH_ENST00000540693.1_Missense_Mutation_p.E141K|DGKH_ENST00000538674.1_5'UTR|DGKH_ENST00000536612.1_Missense_Mutation_p.E5K|DGKH_ENST00000261491.5_Missense_Mutation_p.E141K|DGKH_ENST00000498255.2_3'UTR	NM_178009.3	NP_821077.1	Q86XP1	DGKH_HUMAN	diacylglycerol kinase, eta	141	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				blood coagulation (GO:0007596)|intracellular signal transduction (GO:0035556)|platelet activation (GO:0030168)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|protein oligomerization (GO:0051259)	cytoplasm (GO:0005737)|endosome (GO:0005768)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|diacylglycerol kinase activity (GO:0004143)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)			breast(2)|endometrium(3)|kidney(5)|large_intestine(11)|lung(9)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	43		Lung NSC(96;1.02e-05)|Prostate(109;0.0168)|Lung SC(185;0.0262)|Breast(139;0.0709)|Hepatocellular(98;0.114)		OV - Ovarian serous cystadenocarcinoma(117;5.88e-05)|GBM - Glioblastoma multiforme(144;0.000935)|BRCA - Breast invasive adenocarcinoma(63;0.109)		GCTGTGTGCTGAGAACAGAAA	0.398																																					p.E141K		Atlas-SNP	.											.	DGKH	106	.	0			c.G421A						PASS	.						157.0	152.0	154.0					13																	42729463		2203	4300	6503	SO:0001583	missense	160851	exon5			TGTGCTGAGAACA	AB078967	CCDS9381.1, CCDS9382.1, CCDS55898.1	13q13.3	2013-01-10			ENSG00000102780	ENSG00000102780		"""Sterile alpha motif (SAM) domain containing"", ""Pleckstrin homology (PH) domain containing"""	2854	protein-coding gene	gene with protein product		604071				8702685	Standard	XM_005266271		Approved	DGKeta	uc001uyl.2	Q86XP1	OTTHUMG00000016804	ENST00000337343.4:c.421G>A	13.37:g.42729463G>A	ENSP00000337572:p.Glu141Lys	Somatic	205	0	0		WXS	Illumina HiSeq	Phase_I	206	42	0.203883	NM_001204504	A2A2W7|A6NFX7|B4DZ34|Q5VZW0|Q6PI56|Q86XP2|Q8N3N0|Q8N7J9	Missense_Mutation	SNP	ENST00000337343.4	37	CCDS9381.1	.	.	.	.	.	.	.	.	.	.	G	21.8	4.196603	0.79015	.	.	ENSG00000102780	ENST00000540693;ENST00000337343;ENST00000261491;ENST00000379274;ENST00000536612	T;T;T;T;T	0.35605	1.3;1.3;1.3;1.3;1.3	6.04	5.2	0.72013	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.454524	0.24815	N	0.035363	T	0.42720	0.1215	L	0.59967	1.855	0.80722	D	1	B;B	0.26845	0.161;0.065	B;B	0.35607	0.079;0.206	T	0.36040	-0.9764	10	0.52906	T	0.07	.	15.3721	0.74573	0.0664:0.0:0.9336:0.0	.	141;141	Q86XP1-2;Q86XP1	.;DGKH_HUMAN	K	141;141;141;5;5	ENSP00000440823:E141K;ENSP00000337572:E141K;ENSP00000261491:E141K;ENSP00000368576:E5K;ENSP00000445114:E5K	ENSP00000261491:E141K	E	+	1	0	DGKH	41627463	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	9.837000	0.99465	1.591000	0.50007	-0.236000	0.12185	GAG	.	.	none		0.398	DGKH-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044699.2	NM_178009	
COL6A5	256076	hgsc.bcm.edu	37	3	130104062	130104062	+	Silent	SNP	T	T	C	rs10212241	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:130104062T>C	ENST00000432398.2	+	5	2210	c.1716T>C	c.(1714-1716)acT>acC	p.T572T	COL6A5_ENST00000265379.6_Silent_p.T572T	NM_153264.5	NP_694996.5	A8TX70	CO6A5_HUMAN	collagen, type VI, alpha 5	572	Nonhelical region.|VWFA 3. {ECO:0000255|PROSITE- ProRule:PRU00219}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				endometrium(6)|kidney(4)|large_intestine(8)|lung(19)|pancreas(2)|prostate(3)|stomach(1)|urinary_tract(1)	44						AGCAAATCACTGTTCATGCAG	0.453													T|||	2102	0.419728	0.4834	0.4597	5008	,	,		18666	0.6022		0.2087	False		,,,				2504	0.3344				p.T572T		Atlas-SNP	.											.	COL6A5	205	.	0			c.T1716C						PASS	.	T		589,795		118,353,221	72.0	59.0	63.0		1716	1.9	0.0	3	dbSNP_119	63	696,2484		87,522,981	no	coding-synonymous	COL6A5	NM_153264.5		205,875,1202	CC,CT,TT		21.8868,42.5578,28.1551		572/2527	130104062	1285,3279	692	1590	2282	SO:0001819	synonymous_variant	256076	exon5			AATCACTGTTCAT	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.1716T>C	3.37:g.130104062T>C		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	89	44	0.494382	NM_153264	A9J6L2|A9J6L4|A9J6L6|A9J6L7|A9J6M0|A9J6M1|A9J6M2|B5MEA7|Q6ZW26|Q8NA36	Silent	SNP	ENST00000432398.2	37																																																																																				T|0.605;C|0.395	0.395	strong		0.453	COL6A5-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_153264	
BBS1	582	hgsc.bcm.edu	37	11	66297363	66297363	+	Silent	SNP	C	C	T	rs3816492	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:66297363C>T	ENST00000318312.7	+	14	1464	c.1413C>T	c.(1411-1413)ctC>ctT	p.L471L	BBS1_ENST00000455748.2_Silent_p.L374L|CTD-3074O7.11_ENST00000419755.3_Silent_p.L508L|BBS1_ENST00000393994.2_Silent_p.L342L|ZDHHC24_ENST00000526986.1_Intron	NM_024649.4	NP_078925.3	Q8NFJ9	BBS1_HUMAN	Bardet-Biedl syndrome 1	471					cilium assembly (GO:0042384)|Golgi to plasma membrane protein transport (GO:0043001)|nonmotile primary cilium assembly (GO:0035058)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|retina homeostasis (GO:0001895)|visual perception (GO:0007601)	BBSome (GO:0034464)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)	patched binding (GO:0005113)|RNA polymerase II repressing transcription factor binding (GO:0001103)|smoothened binding (GO:0005119)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|kidney(5)|large_intestine(5)|lung(5)|ovary(1)|prostate(2)|skin(2)|stomach(2)|urinary_tract(1)	28						TGCAGGCCCTCGAGTCCAGCC	0.672									Bardet-Biedl syndrome				C|||	718	0.143371	0.0136	0.1441	5008	,	,		16469	0.1548		0.2396	False		,,,				2504	0.2076				p.L471L	GBM(152;173 2612 9770 10137)	Atlas-SNP	.											.	BBS1	58	.	0			c.C1413T						PASS	.	C		211,4189	128.2+/-165.1	3,205,1992	64.0	44.0	51.0		1413	-8.9	0.7	11	dbSNP_107	51	1978,6612	342.7+/-324.6	221,1536,2538	yes	coding-synonymous	BBS1	NM_024649.4		224,1741,4530	TT,TC,CC		23.0268,4.7955,16.8514		471/594	66297363	2189,10801	2200	4295	6495	SO:0001819	synonymous_variant	582	exon14	Familial Cancer Database	BBS, Bardet-Biedl syndrome, type 1-12: BBS1-12,Laurence-Moon-Biedl syndrome	GGCCCTCGAGTCC	AF503941	CCDS8142.1	11q13	2013-01-08			ENSG00000174483	ENSG00000174483			966	protein-coding gene	gene with protein product		209901				9039982, 12567324	Standard	NM_024649		Approved	FLJ23590	uc001oij.1	Q8NFJ9	OTTHUMG00000167110	ENST00000318312.7:c.1413C>T	11.37:g.66297363C>T		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	48	37	0.770833	NM_024649	Q32MM9|Q32MN0|Q96SN4	Silent	SNP	ENST00000318312.7	37	CCDS8142.1																																																																																			C|0.843;T|0.157	0.157	strong		0.672	BBS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393235.2		
ZNF676	163223	hgsc.bcm.edu	37	19	22363448	22363448	+	Silent	SNP	A	A	T	rs200452805		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:22363448A>T	ENST00000397121.2	-	3	1388	c.1071T>A	c.(1069-1071)atT>atA	p.I357I		NM_001001411.2	NP_001001411.2	Q8N7Q3	ZN676_HUMAN	zinc finger protein 676	357					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)				CAGTATGAATAATCTTATGTT	0.383																																					p.I357I		Atlas-SNP	.											ZNF676,rectum,carcinoma,0,2	ZNF676	146	2	0			c.T1071A						scavenged	.						68.0	74.0	72.0					19																	22363448		2162	4271	6433	SO:0001819	synonymous_variant	163223	exon3			ATGAATAATCTTA	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.1071T>A	19.37:g.22363448A>T		Somatic	25	2	0.08		WXS	Illumina HiSeq	Phase_I	18	3	0.166667	NM_001001411	A8MVX5	Silent	SNP	ENST00000397121.2	37	CCDS42539.1																																																																																			.	.	weak		0.383	ZNF676-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464392.1	NM_001001411	
ADAM21	8747	hgsc.bcm.edu	37	14	70924696	70924696	+	Silent	SNP	G	G	A	rs77892318|rs386778613	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:70924696G>A	ENST00000603540.1	+	2	738	c.480G>A	c.(478-480)aaG>aaA	p.K160K	RP11-486O13.4_ENST00000556646.1_lincRNA|ADAM21_ENST00000267499.3_Silent_p.K160K	NM_003813.3	NP_003804.2	Q9UKJ8	ADA21_HUMAN	ADAM metallopeptidase domain 21	160					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.K160K(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)		TGGTTTATAAGATAAACAGTA	0.423													G|||	1254	0.250399	0.3026	0.1297	5008	,	,		18930	0.496		0.1173	False		,,,				2504	0.1493				p.K160K		Atlas-SNP	.											ADAM21_ENST00000267499,NS,carcinoma,0,1	ADAM21	181	1	1	Substitution - coding silent(1)	stomach(1)	c.G480A						scavenged	.						39.0	48.0	45.0					14																	70924696		2133	4291	6424	SO:0001819	synonymous_variant	8747	exon2			TTATAAGATAAAC	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.480G>A	14.37:g.70924696G>A		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	64	13	0.203125	NM_003813	O43507|Q2VPC6|Q32MR0	Silent	SNP	ENST00000603540.1	37	CCDS9804.1																																																																																			G|0.946;A|0.054	0.054	strong		0.423	ADAM21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413008.3		
CLDN15	24146	hgsc.bcm.edu	37	7	100875772	100875772	+	Silent	SNP	T	T	G	rs1047319	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:100875772T>G	ENST00000401528.1	-	6	1731	c.606A>C	c.(604-606)ccA>ccC	p.P202P	CLDN15_ENST00000433422.1_5'Flank|CLDN15_ENST00000308344.5_Silent_p.P202P	NM_001185080.1	NP_001172009.1	P56746	CLD15_HUMAN	claudin 15	202					calcium-independent cell-cell adhesion (GO:0016338)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|ion transport (GO:0006811)|tight junction assembly (GO:0070830)	integral component of membrane (GO:0016021)|lateral plasma membrane (GO:0016328)|tight junction (GO:0005923)	identical protein binding (GO:0042802)|structural molecule activity (GO:0005198)	p.P202P(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(1)|lung(3)|ovary(1)|skin(1)	10	Lung NSC(181;0.168)|all_lung(186;0.215)					TCACGGACACTGGAGCCTGGT	0.716													T|||	1127	0.22504	0.1846	0.2061	5008	,	,		11952	0.1677		0.2435	False		,,,				2504	0.3333				p.P202P		Atlas-SNP	.											CLDN15,NS,lymphoid_neoplasm,0,1	CLDN15	20	1	1	Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(1)	c.A606C						PASS	.	T	,	837,3567		88,661,1453	38.0	35.0	36.0		606,606	-1.3	0.0	7	dbSNP_86	36	1950,6648		247,1456,2596	no	coding-synonymous,coding-synonymous	CLDN15	NM_001185080.1,NM_014343.2	,	335,2117,4049	GG,GT,TT		22.6797,19.0054,21.4352	,	202/229,202/229	100875772	2787,10215	2202	4299	6501	SO:0001819	synonymous_variant	24146	exon5			GGACACTGGAGCC	AJ245738	CCDS5717.1	7q22	2008-07-18			ENSG00000106404	ENSG00000106404		"""Claudins"""	2036	protein-coding gene	gene with protein product		615778					Standard	NM_014343		Approved		uc003uyg.2	P56746	OTTHUMG00000150512	ENST00000401528.1:c.606A>C	7.37:g.100875772T>G		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	52	21	0.403846	NM_014343	B3KPB5	Silent	SNP	ENST00000401528.1	37	CCDS5717.1																																																																																			T|0.787;G|0.213	0.213	strong		0.716	CLDN15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318698.1	NM_014343	
PTPN13	5783	hgsc.bcm.edu	37	4	87685796	87685796	+	Missense_Mutation	SNP	T	T	G	rs10033029	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:87685796T>G	ENST00000411767.2	+	25	4131	c.4068T>G	c.(4066-4068)ttT>ttG	p.F1356L	PTPN13_ENST00000316707.6_Missense_Mutation_p.F1165L|PTPN13_ENST00000436978.1_Missense_Mutation_p.F1356L|PTPN13_ENST00000511467.1_Missense_Mutation_p.F1356L|PTPN13_ENST00000427191.2_Missense_Mutation_p.F1337L			Q12923	PTN13_HUMAN	protein tyrosine phosphatase, non-receptor type 13 (APO-1/CD95 (Fas)-associated phosphatase)	1356			F -> L (in dbSNP:rs10033029).		peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cell body (GO:0044297)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|lamellipodium (GO:0030027)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein tyrosine phosphatase activity (GO:0004725)			NS(4)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(23)|lung(24)|ovary(4)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	93		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.00082)		TTAAAACTTTTTCTTCATCAC	0.343													T|||	261	0.0521166	0.0318	0.072	5008	,	,		14756	0.0089		0.1203	False		,,,				2504	0.0399				p.F1356L		Atlas-SNP	.											.	PTPN13	203	.	0			c.T4068G						PASS	.	T	LEU/PHE,LEU/PHE,LEU/PHE,LEU/PHE	192,3402		7,178,1612	80.0	75.0	76.0		4011,4068,3495,4068	1.2	0.9	4	dbSNP_119	76	974,7170		67,840,3165	yes	missense,missense,missense,missense	PTPN13	NM_006264.2,NM_080683.2,NM_080684.2,NM_080685.2	22,22,22,22	74,1018,4777	GG,GT,TT		11.9597,5.3422,9.9335	benign,benign,benign,benign	1337/2467,1356/2486,1165/2295,1356/2491	87685796	1166,10572	1797	4072	5869	SO:0001583	missense	5783	exon25			AACTTTTTCTTCA		CCDS47093.1, CCDS47094.1, CCDS47095.1, CCDS47096.1	4q21.3	2011-06-09			ENSG00000163629	ENSG00000163629		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"""	9646	protein-coding gene	gene with protein product		600267				8287977	Standard	NM_006264		Approved	PTP1E, PTP-BAS, PTPL1, PTP-BL	uc003hpy.3	Q12923	OTTHUMG00000160968	ENST00000411767.2:c.4068T>G	4.37:g.87685796T>G	ENSP00000407249:p.Phe1356Leu	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	101	53	0.524752	NM_080683	B2RTR0|Q15159|Q15263|Q15264|Q15265|Q15674|Q16826|Q8IWH7|Q9NYN9|Q9UDA8	Missense_Mutation	SNP	ENST00000411767.2	37	CCDS47094.1	139	0.06364468864468864	21	0.042682926829268296	27	0.07458563535911603	4	0.006993006993006993	87	0.11477572559366754	T	8.444	0.851464	0.17034	0.053422	0.119597	ENSG00000163629	ENST00000427191;ENST00000436978;ENST00000316707;ENST00000411767;ENST00000511467;ENST00000357349	T;T;T;T;T	0.37752	1.18;1.18;1.18;1.18;1.18	5.04	1.19	0.21007	PDZ/DHR/GLGF (1);	0.771215	0.11048	N	0.605413	T	0.00271	0.0008	N	0.19112	0.55	0.41615	P	0.011063999999999963	B;B;B;B	0.06786	0.001;0.001;0.001;0.001	B;B;B;B	0.10450	0.003;0.005;0.002;0.005	T	0.30880	-0.9963	9	0.10902	T	0.67	.	6.1894	0.20516	0.0:0.1444:0.1361:0.7194	rs10033029;rs52835693;rs59145610;rs10033029	1165;1337;1356;1356	Q12923-2;Q12923-3;Q12923;Q12923-4	.;.;PTN13_HUMAN;.	L	1337;1356;1165;1356;1356;1305	ENSP00000408368:F1337L;ENSP00000394794:F1356L;ENSP00000322675:F1165L;ENSP00000407249:F1356L;ENSP00000426626:F1356L	ENSP00000322675:F1165L	F	+	3	2	PTPN13	87904820	0.990000	0.36364	0.876000	0.34364	0.859000	0.49053	2.666000	0.46799	0.042000	0.15717	0.528000	0.53228	TTT	T|0.934;G|0.066	0.066	strong		0.343	PTPN13-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000363191.1		
DYNC2H1	79659	hgsc.bcm.edu	37	11	103158278	103158278	+	Missense_Mutation	SNP	C	C	T	rs10895391	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:103158278C>T	ENST00000375735.2	+	75	11183	c.11039C>T	c.(11038-11040)gCg>gTg	p.A3680V	DYNC2H1_ENST00000398093.3_Missense_Mutation_p.A3687V|DYNC2H1_ENST00000334267.7_Intron	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	234	1	0.0042735		WXS	Illumina HiSeq	Phase_I	137	134	0.978102	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	
FBXO40	51725	hgsc.bcm.edu	37	3	121341019	121341019	+	Missense_Mutation	SNP	A	A	T	rs142436040	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:121341019A>T	ENST00000338040.4	+	3	1157	c.743A>T	c.(742-744)aAa>aTa	p.K248I		NM_016298.3	NP_057382.2	Q9UH90	FBX40_HUMAN	F-box protein 40	248					muscle cell differentiation (GO:0042692)	cytoplasm (GO:0005737)	ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|kidney(1)|large_intestine(11)|lung(19)|ovary(2)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	46				GBM - Glioblastoma multiforme(114;0.189)		GACTCCGAGAAAGAACAGATT	0.468													A|||	10	0.00199681	0.0	0.0043	5008	,	,		22737	0.0		0.007	False		,,,				2504	0.0				p.K248I		Atlas-SNP	.											.	FBXO40	108	.	0			c.A743T						PASS	.	A	ILE/LYS	4,4402	8.1+/-20.4	1,2,2200	64.0	69.0	67.0		743	0.2	0.0	3	dbSNP_134	67	34,8566	23.4+/-69.3	0,34,4266	yes	missense	FBXO40	NM_016298.3	102	1,36,6466	TT,TA,AA		0.3953,0.0908,0.2922	possibly-damaging	248/710	121341019	38,12968	2203	4300	6503	SO:0001583	missense	51725	exon3			CCGAGAAAGAACA	AF204674	CCDS33835.1	3q21.1	2004-08-24			ENSG00000163833	ENSG00000163833		"""F-boxes /  ""other"""""	29816	protein-coding gene	gene with protein product		609107				10574462	Standard	NM_016298		Approved	KIAA1195, Fbx40	uc003eeg.2	Q9UH90	OTTHUMG00000159410	ENST00000338040.4:c.743A>T	3.37:g.121341019A>T	ENSP00000337510:p.Lys248Ile	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	47	28	0.595745	NM_016298	B2RAX7|Q32M70|Q9ULM5	Missense_Mutation	SNP	ENST00000338040.4	37	CCDS33835.1	5	0.0022893772893772895	0	0.0	0	0.0	0	0.0	5	0.006596306068601583	A	8.429	0.848116	0.17034	9.08E-4	0.003953	ENSG00000163833	ENST00000338040	T	0.49139	0.79	5.51	0.213	0.15244	.	0.880954	0.10192	N	0.704471	T	0.29716	0.0742	L	0.47716	1.5	0.23036	N	0.998398	P	0.42620	0.785	B	0.40940	0.344	T	0.15983	-1.0418	10	0.44086	T	0.13	-7.038	5.3399	0.15979	0.6143:0.1385:0.2472:0.0	.	248	Q9UH90	FBX40_HUMAN	I	248	ENSP00000337510:K248I	ENSP00000337510:K248I	K	+	2	0	FBXO40	122823709	0.008000	0.16893	0.009000	0.14445	0.009000	0.06853	0.391000	0.20784	0.058000	0.16222	0.402000	0.26972	AAA	A|0.997;T|0.003	0.003	strong		0.468	FBXO40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355158.1	NM_016298	
C9orf66	157983	hgsc.bcm.edu	37	9	214804	214804	+	Missense_Mutation	SNP	A	A	G	rs76707254	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:214804A>G	ENST00000382387.2	-	1	1089	c.593T>C	c.(592-594)gTc>gCc	p.V198A	DOCK8_ENST00000453981.1_5'Flank|DOCK8_ENST00000432829.2_5'Flank	NM_152569.2	NP_689782.2	Q5T8R8	CI066_HUMAN	chromosome 9 open reading frame 66	198	Arg-rich.									central_nervous_system(1)|cervix(1)|kidney(1)|skin(1)	4	all_lung(41;0.218)	all_cancers(5;2.09e-12)|all_epithelial(5;6.16e-09)|all_lung(10;1.15e-08)|Lung NSC(10;1.91e-08)|Acute lymphoblastic leukemia(5;0.00457)|all_hematologic(5;0.0332)|Breast(48;0.0646)|Prostate(43;0.137)	Kidney(42;0.112)|KIRC - Kidney renal clear cell carcinoma(5;0.157)	all cancers(5;0.000704)|Lung(218;0.00755)|GBM - Glioblastoma multiforme(5;0.0149)|Epithelial(6;0.0154)		CCGAGCTCGGACCCTCCCCCG	0.716													G|||	964	0.192492	0.0514	0.2334	5008	,	,		11646	0.3829		0.1103	False		,,,				2504	0.2423				p.V198A		Atlas-SNP	.											C9orf66,colon,carcinoma,0,1	C9orf66	16	1	0			c.T593C						PASS	.	G	ALA/VAL	169,3369		4,161,1604	8.0	8.0	8.0		593	2.4	0.8	9	dbSNP_131	8	592,6276		23,546,2865	yes	missense	C9orf66	NM_152569.2	64	27,707,4469	GG,GA,AA		8.6197,4.7767,7.3131	benign	198/296	214804	761,9645	1769	3434	5203	SO:0001583	missense	157983	exon1			GCTCGGACCCTCC	AK055720	CCDS6439.1	9p24.3	2008-02-05			ENSG00000183784	ENSG00000183784			26436	protein-coding gene	gene with protein product							Standard	NM_152569		Approved	FLJ31158	uc003zge.4	Q5T8R8	OTTHUMG00000021017	ENST00000382387.2:c.593T>C	9.37:g.214804A>G	ENSP00000371824:p.Val198Ala	Somatic	24	0	0		WXS	Illumina HiSeq	Phase_I	40	13	0.325	NM_152569	Q96NB0	Missense_Mutation	SNP	ENST00000382387.2	37	CCDS6439.1	382	0.1749084249084249	25	0.0508130081300813	70	0.19337016574585636	198	0.34615384615384615	89	0.11741424802110818	.	8.016	0.758590	0.15846	0.047767	0.086197	ENSG00000183784	ENST00000382387	T	0.20332	2.08	4.42	2.41	0.29592	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.52099	P	5.999999999994898E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.45131	-0.9282	8	0.87932	D	0	.	3.1036	0.06334	0.0997:0.1737:0.5476:0.179	.	198	Q5T8R8	CI066_HUMAN	A	198	ENSP00000371824:V198A	ENSP00000371824:V198A	V	-	2	0	C9orf66	204804	0.985000	0.35326	0.833000	0.33012	0.019000	0.09904	0.157000	0.16402	0.475000	0.27415	-0.338000	0.08134	GTC	A|0.831;G|0.169	0.169	strong		0.716	C9orf66-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055436.1	NM_152569	
TFEB	7942	hgsc.bcm.edu	37	6	41652514	41652514	+	Silent	SNP	C	C	T	rs2073158	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:41652514C>T	ENST00000230323.4	-	10	1555	c.1254G>A	c.(1252-1254)gcG>gcA	p.A418A	TFEB_ENST00000403298.4_Silent_p.A418A|TFEB_ENST00000358871.2_Silent_p.A432A|TFEB_ENST00000373033.1_Silent_p.A418A|AL035588.1_ENST00000597468.1_5'Flank|TFEB_ENST00000420312.1_Silent_p.A333A	NM_001271945.1|NM_007162.2	NP_001258874.1|NP_009093.1	P19484	TFEB_HUMAN	transcription factor EB	418					autophagy (GO:0006914)|embryonic placenta development (GO:0001892)|humoral immune response (GO:0006959)|lysosome organization (GO:0007040)|positive regulation of autophagy (GO:0010508)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|prostate(1)	11	Ovarian(28;0.0355)|Colorectal(47;0.121)		Epithelial(12;7.61e-05)|STAD - Stomach adenocarcinoma(11;0.000204)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00507)			CATGCCCCGGCGCCAGGGGTT	0.647			T	ALPHA	renal (childhood epithelioid)								C|||	989	0.197484	0.0749	0.183	5008	,	,		14273	0.3194		0.1998	False		,,,				2504	0.2454				p.A432A		Atlas-SNP	.		Dom	yes		6	6p21	7942	transcription factor EB		"""E,M"""	TFEB,NS,carcinoma,-1,1	TFEB	37	1	0			c.G1296A						PASS	.	C	,	385,4019	183.6+/-211.2	14,357,1831	34.0	36.0	35.0		1254,1254	4.3	1.0	6	dbSNP_96	35	1681,6919	294.2+/-301.7	175,1331,2794	no	coding-synonymous,coding-synonymous	TFEB	NM_001167827.1,NM_007162.2	,	189,1688,4625	TT,TC,CC		19.5465,8.7421,15.8874	,	418/477,418/477	41652514	2066,10938	2202	4300	6502	SO:0001819	synonymous_variant	7942	exon9			CCCCGGCGCCAGG	M33782	CCDS4858.1, CCDS64424.1, CCDS64425.1	6p21	2013-05-21			ENSG00000112561	ENSG00000112561		"""Basic helix-loop-helix proteins"""	11753	protein-coding gene	gene with protein product		600744				2115126	Standard	NM_007162		Approved	TCFEB, bHLHe35	uc003oqu.2	P19484	OTTHUMG00000014684	ENST00000230323.4:c.1254G>A	6.37:g.41652514C>T		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	126	55	0.436508	NM_001167827	Q709B3|Q7Z6P9|Q9BRJ5|Q9UJD8	Silent	SNP	ENST00000230323.4	37	CCDS4858.1																																																																																			C|0.832;T|0.168	0.168	strong		0.647	TFEB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040522.3		
ABCA7	10347	hgsc.bcm.edu	37	19	1045173	1045173	+	Missense_Mutation	SNP	G	G	A	rs3752233	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:1045173G>A	ENST00000263094.6	+	12	1619	c.1388G>A	c.(1387-1389)cGc>cAc	p.R463H	ABCA7_ENST00000435683.2_Missense_Mutation_p.R325H|ABCA7_ENST00000433129.1_Missense_Mutation_p.R463H	NM_019112.3	NP_061985.2	Q8IZY2	ABCA7_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 7	463			R -> H (in dbSNP:rs3752233). {ECO:0000269|PubMed:12111378}.		apolipoprotein A-I-mediated signaling pathway (GO:0038027)|ATP catabolic process (GO:0006200)|cholesterol efflux (GO:0033344)|high-density lipoprotein particle assembly (GO:0034380)|memory (GO:0007613)|negative regulation of amyloid precursor protein biosynthetic process (GO:0042985)|negative regulation of ATPase activity (GO:0032780)|negative regulation of beta-amyloid formation (GO:1902430)|peptide cross-linking (GO:0018149)|phagocytosis (GO:0006909)|phospholipid efflux (GO:0033700)|phospholipid scrambling (GO:0017121)|positive regulation of ATPase activity (GO:0032781)|positive regulation of beta-amyloid clearance (GO:1900223)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of engulfment of apoptotic cell (GO:1901076)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of phagocytosis (GO:0050766)|positive regulation of phospholipid efflux (GO:1902995)|protein localization to nucleus (GO:0034504)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|ATP-binding cassette (ABC) transporter complex (GO:0043190)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|phagocytic cup (GO:0001891)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	apolipoprotein A-I receptor activity (GO:0034188)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|phospholipid transporter activity (GO:0005548)|transporter activity (GO:0005215)			NS(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(7)|lung(22)|ovary(1)|pancreas(7)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	65		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GGCCACGTGCGCATCAAAATC	0.642													G|||	304	0.0607029	0.003	0.0086	5008	,	,		11646	0.1915		0.0408	False		,,,				2504	0.0613				p.R463H		Atlas-SNP	.											ABCA7,NS,carcinoma,0,1	ABCA7	174	1	0			c.G1388A						PASS	.	G	HIS/ARG	35,4369	37.6+/-69.7	0,35,2167	46.0	47.0	46.0		1388	1.2	0.9	19	dbSNP_107	46	353,8247	116.5+/-176.2	5,343,3952	yes	missense	ABCA7	NM_019112.3	29	5,378,6119	AA,AG,GG		4.1047,0.7947,2.9837	probably-damaging	463/2147	1045173	388,12616	2202	4300	6502	SO:0001583	missense	10347	exon12			ACGTGCGCATCAA	AF328787	CCDS12055.1	19p13.3	2012-03-14			ENSG00000064687	ENSG00000064687		"""ATP binding cassette transporters / subfamily A"""	37	protein-coding gene	gene with protein product		605414					Standard	NM_019112		Approved	ABCX	uc002lqw.4	Q8IZY2	OTTHUMG00000167547	ENST00000263094.6:c.1388G>A	19.37:g.1045173G>A	ENSP00000263094:p.Arg463His	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	58	24	0.413793	NM_019112	Q96S58|Q9BZC4|Q9NR73|Q9UKP8	Missense_Mutation	SNP	ENST00000263094.6	37	CCDS12055.1	129	0.059065934065934064	2	0.0040650406504065045	3	0.008287292817679558	93	0.16258741258741258	31	0.040897097625329816	G	26.3	4.720067	0.89205	0.007947	0.041047	ENSG00000064687	ENST00000263094;ENST00000433129	D;D	0.96073	-3.9;-3.9	4.66	1.22	0.21188	.	.	.	.	.	T	0.07728	0.0194	L	0.56769	1.78	0.80722	P	0.0	D;D	0.69078	0.989;0.997	P;P	0.58266	0.796;0.836	T	0.61148	-0.7121	8	0.36615	T	0.2	.	2.9423	0.05834	0.3017:0.0:0.5006:0.1977	rs3752233;rs3752233	325;463	Q8IZY2-2;Q8IZY2	.;ABCA7_HUMAN	H	463	ENSP00000263094:R463H;ENSP00000414062:R463H	ENSP00000263094:R463H	R	+	2	0	ABCA7	996173	0.000000	0.05858	0.852000	0.33557	0.856000	0.48823	-0.365000	0.07573	0.356000	0.24157	0.462000	0.41574	CGC	A|0.041;C|0.000;G|0.959	0.041	strong		0.642	ABCA7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000394993.1	NM_019112	
USHBP1	83878	hgsc.bcm.edu	37	19	17361064	17361064	+	Silent	SNP	C	C	T	rs10415471	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:17361064C>T	ENST00000252597.3	-	13	2255	c.2082G>A	c.(2080-2082)ccG>ccA	p.P694P	AC010646.3_ENST00000594059.1_Intron|USHBP1_ENST00000431146.2_Silent_p.P630P	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						GCTGGGGAGGCGGGAGGGGAG	0.627													C|||	623	0.124401	0.1868	0.0994	5008	,	,		17027	0.002		0.1759	False		,,,				2504	0.1309				p.P694P		Atlas-SNP	.											.	USHBP1	85	.	0			c.G2082A						PASS	.	C		908,3498	324.8+/-298.8	86,736,1381	26.0	25.0	25.0		2082	-6.7	0.0	19	dbSNP_119	25	1669,6931	287.5+/-298.3	174,1321,2805	no	coding-synonymous	USHBP1	NM_031941.3		260,2057,4186	TT,TC,CC		19.407,20.6083,19.8139		694/704	17361064	2577,10429	2203	4300	6503	SO:0001819	synonymous_variant	83878	exon13			GGGAGGCGGGAGG	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.2082G>A	19.37:g.17361064C>T		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	80	41	0.5125	NM_031941		Silent	SNP	ENST00000252597.3	37	CCDS12353.1																																																																																			C|0.828;T|0.172	0.172	strong		0.627	USHBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463328.1	NM_031941	
MRGPRX2	117194	hgsc.bcm.edu	37	11	19077765	19077765	+	Missense_Mutation	SNP	T	T	C	rs10833049	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	63	0	0		WXS	Illumina HiSeq	Phase_I	68	15	0.220588	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	
VILL	50853	hgsc.bcm.edu	37	3	38043904	38043904	+	Silent	SNP	T	T	C	rs9843296	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	47	0	0		WXS	Illumina HiSeq	Phase_I	50	27	0.54	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	
MUC4	4585	hgsc.bcm.edu	37	3	195506597	195506597	+	Missense_Mutation	SNP	G	G	A	rs200685331	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195506597G>A	ENST00000463781.3	-	2	12313	c.11854C>T	c.(11854-11856)Cct>Tct	p.P3952S	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_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	128	1	0.0078125		WXS	Illumina HiSeq	Phase_I	39	22	0.564103	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	
WDR46	9277	hgsc.bcm.edu	37	6	33254665	33254665	+	Missense_Mutation	SNP	A	A	G	rs14398	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:33254665A>G	ENST00000374617.4	-	10	1378	c.1022T>C	c.(1021-1023)gTg>gCg	p.V341A	PFDN6_ENST00000395131.1_5'Flank|PFDN6_ENST00000374606.5_5'Flank|PFDN6_ENST00000374607.1_5'Flank|PFDN6_ENST00000374610.2_5'Flank|PFDN6_ENST00000463584.1_5'Flank|WDR46_ENST00000477718.1_5'Flank	NM_001164267.1|NM_005452.5	NP_001157739.1|NP_005443.3	O15213	WDR46_HUMAN	WD repeat domain 46	341			V -> A (in dbSNP:rs14398). {ECO:0000269|PubMed:14574404}.				poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|kidney(1)|large_intestine(6)|lung(9)|prostate(1)	20						CCATAAAGACACAGTACCTGG	0.473													A|||	492	0.0982428	0.0061	0.1081	5008	,	,		21134	0.0754		0.1233	False		,,,				2504	0.2137				p.V341A		Atlas-SNP	.											.	WDR46	43	.	0			c.T1022C						PASS	.	A	ALA/VAL,ALA/VAL	130,4276	93.4+/-132.2	3,124,2076	117.0	112.0	113.0		860,1022	4.8	1.0	6	dbSNP_52	113	1237,7363	249.3+/-276.6	88,1061,3151	yes	missense,missense	WDR46	NM_001164267.1,NM_005452.5	64,64	91,1185,5227	GG,GA,AA		14.3837,2.9505,10.5105	probably-damaging,probably-damaging	287/557,341/611	33254665	1367,11639	2203	4300	6503	SO:0001583	missense	9277	exon10			AAAGACACAGTAC	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.1022T>C	6.37:g.33254665A>G	ENSP00000363746:p.Val341Ala	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	90	41	0.455556	NM_005452	A6NDP5|Q5HYZ0|Q5STK5|Q5STR3	Missense_Mutation	SNP	ENST00000374617.4	37	CCDS4772.1	176	0.08058608058608059	2	0.0040650406504065045	36	0.09944751381215469	52	0.09090909090909091	86	0.11345646437994723	A	21.0	4.083439	0.76642	0.029505	0.143837	ENSG00000227057	ENST00000374617;ENST00000444176	T;T	0.23950	4.64;1.88	4.79	4.79	0.61399	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.49423	0.1556	M	0.92833	3.35	0.09310	P	0.999999880934	D;D	0.89917	1.0;0.999	D;D	0.71414	0.973;0.973	T	0.64592	-0.6371	9	0.66056	D	0.02	-22.0617	12.3349	0.55060	1.0:0.0:0.0:0.0	rs14398;rs466384;rs1128307;rs3177285;rs11539345;rs17343705;rs17358516;rs17359296;rs17439302;rs57185605;rs14398	287;341	B4DP15;O15213	.;WDR46_HUMAN	A	341;268	ENSP00000363746:V341A;ENSP00000405568:V268A	ENSP00000363746:V341A	V	-	2	0	WDR46	33362643	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	6.393000	0.73217	2.003000	0.58678	0.448000	0.29417	GTG	A|0.903;G|0.097	0.097	strong		0.473	WDR46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076382.2	NM_005452	
MUC4	4585	hgsc.bcm.edu	37	3	195510149	195510149	+	Missense_Mutation	SNP	G	G	A	rs542186658	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195510149G>A	ENST00000463781.3	-	2	8761	c.8302C>T	c.(8302-8304)Cct>Tct	p.P2768S	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.P2768S	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.P2768S(1)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		ACAGGAAGAGGGGTGGCGTGA	0.577													.|||	2	0.000399361	0.0015	0.0	5008	,	,		5215	0.0		0.0	False		,,,				2504	0.0				p.P2768S		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	1	Substitution - Missense(1)	endometrium(1)	c.C8302T						scavenged	.																																			SO:0001583	missense	4585	exon2			GAAGAGGGGTGGC	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.8302C>T	3.37:g.195510149G>A	ENSP00000417498:p.Pro2768Ser	Somatic	42	2	0.047619		WXS	Illumina HiSeq	Phase_I	79	11	0.139241	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	-	5.381	0.255488	0.10185	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.27256	1.68;1.68	1.02	-2.03	0.07365	.	.	.	.	.	T	0.09158	0.0226	N	0.08118	0	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.33523	-0.9865	8	.	.	.	.	2.0272	0.03521	0.2702:0.0:0.2738:0.456	.	2640	E7ESK3	.	S	2768	ENSP00000417498:P2768S;ENSP00000420243:P2768S	.	P	-	1	0	MUC4	196994928	0.000000	0.05858	0.010000	0.14722	0.113000	0.19764	-2.060000	0.01392	-0.413000	0.07507	0.074000	0.15403	CCT	.	.	none		0.577	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
GABBR2	9568	hgsc.bcm.edu	37	9	101340316	101340316	+	Silent	SNP	T	T	C	rs3750344	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:101340316T>C	ENST00000259455.2	-	2	819	c.360A>G	c.(358-360)gcA>gcG	p.A120A		NM_005458.7	NP_005449.5	O75899	GABR2_HUMAN	gamma-aminobutyric acid (GABA) B receptor, 2	120					G-protein coupled receptor signaling pathway (GO:0007186)|gamma-aminobutyric acid signaling pathway (GO:0007214)|negative regulation of adenylate cyclase activity (GO:0007194)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|G-protein coupled receptor heterodimeric complex (GO:0038039)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	G-protein coupled GABA receptor activity (GO:0004965)		NOTCH1_ENST00000277541/GABBR2(2)	breast(4)|endometrium(4)|large_intestine(12)|lung(21)|ovary(2)|skin(4)|stomach(1)|urinary_tract(1)	49		Acute lymphoblastic leukemia(62;0.0527)			Baclofen(DB00181)	CGTATTTTATTGCATCGTAGA	0.493													t|||	807	0.161142	0.236	0.0908	5008	,	,		21374	0.1508		0.1799	False		,,,				2504	0.1012				p.A120A		Atlas-SNP	.											.	GABBR2	126	.	0			c.A360G						PASS	.			996,3410	373.0+/-320.6	113,770,1320	181.0	165.0	171.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	360	2.2	1.0	9	dbSNP_107	171	1435,7165	274.9+/-291.5	123,1189,2988	no	coding-synonymous	GABBR2	NM_005458.7		236,1959,4308	CC,CT,TT		16.686,22.6055,18.6914		120/942	101340316	2431,10575	2203	4300	6503	SO:0001819	synonymous_variant	9568	exon2			TTTTATTGCATCG	AF069755	CCDS6736.1	9q22.1-q22.3	2012-08-29	2006-02-16	2006-02-16	ENSG00000136928	ENSG00000136928		"""GABA receptors"", ""GPCR / Class C : GABA(B) receptors"""	4507	protein-coding gene	gene with protein product		607340	"""G protein-coupled receptor 51"""	GPR51		10087195	Standard	NM_005458		Approved	HG20, GABABR2, GPRC3B	uc004ays.3	O75899	OTTHUMG00000020345	ENST00000259455.2:c.360A>G	9.37:g.101340316T>C		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	105	52	0.495238	NM_005458	O75974|O75975|Q5VXZ2|Q8WX04|Q9P1R2|Q9UNR1|Q9UNS9	Silent	SNP	ENST00000259455.2	37	CCDS6736.1																																																																																			T|0.809;C|0.191	0.191	strong		0.493	GABBR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053373.1		
ESPL1	9700	hgsc.bcm.edu	37	12	53682986	53682986	+	Silent	SNP	C	C	T	rs3214023	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:53682986C>T	ENST00000257934.4	+	21	4912	c.4821C>T	c.(4819-4821)tgC>tgT	p.C1607C	ESPL1_ENST00000552462.1_Silent_p.C1607C	NM_012291.4	NP_036423.4	Q14674	ESPL1_HUMAN	extra spindle pole bodies homolog 1 (S. cerevisiae)	1607					apoptotic process (GO:0006915)|cytokinesis (GO:0000910)|establishment of mitotic spindle localization (GO:0040001)|homologous chromosome segregation (GO:0045143)|meiotic spindle organization (GO:0000212)|mitotic cell cycle (GO:0000278)|mitotic sister chromatid segregation (GO:0000070)|negative regulation of sister chromatid cohesion (GO:0045875)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)	centrosome (GO:0005813)|cytosol (GO:0005829)|nucleus (GO:0005634)	catalytic activity (GO:0003824)|cysteine-type peptidase activity (GO:0008234)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(10)|large_intestine(12)|lung(21)|ovary(2)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(8)	70						TGGCCTTGTGCCTGGGCCACC	0.592													C|||	2267	0.452676	0.3449	0.5764	5008	,	,		17522	0.3899		0.6064	False		,,,				2504	0.4172				p.C1607C	Colon(53;1069 1201 2587 5382)	Atlas-SNP	.											.	ESPL1	158	.	0			c.C4821T						PASS	.	C		1666,2740	509.6+/-367.3	311,1044,848	131.0	125.0	127.0		4821	1.6	1.0	12	dbSNP_106	127	5251,3349	644.0+/-400.0	1601,2049,650	no	coding-synonymous	ESPL1	NM_012291.4		1912,3093,1498	TT,TC,CC		38.9419,37.8121,46.8169		1607/2121	53682986	6917,6089	2203	4300	6503	SO:0001819	synonymous_variant	9700	exon21			CTTGTGCCTGGGC	D79987	CCDS8852.1	12q13.13	2014-08-04	2013-05-03		ENSG00000135476	ENSG00000135476	3.4.22.49		16856	protein-coding gene	gene with protein product	"""separin"", ""separase"", ""separin, cysteine protease"""	604143	"""extra spindle poles like 1 (S. cerevisiae)"""			8724849, 16258266	Standard	NM_012291		Approved	KIAA0165, ESP1, SEPA	uc001sck.2	Q14674	OTTHUMG00000169674	ENST00000257934.4:c.4821C>T	12.37:g.53682986C>T		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	120	56	0.466667	NM_012291		Silent	SNP	ENST00000257934.4	37	CCDS8852.1																																																																																			C|0.499;T|0.501	0.501	strong		0.592	ESPL1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406899.2	NM_012291	
HLA-A	3105	hgsc.bcm.edu	37	6	29911319	29911319	+	Splice_Site	SNP	G	G	T	rs41554520	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:29911319G>T	ENST00000396634.1	+	5	959	c.618G>T	c.(616-618)acG>acT	p.T206T	HLA-A_ENST00000376802.2_Splice_Site_p.T206T|HLA-A_ENST00000376809.5_Splice_Site_p.T206T|HLA-A_ENST00000376806.5_Splice_Site_p.T206T			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						TGCAGCGCACGGGTACCAGGG	0.637									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.T206T		Atlas-SNP	.											.	HLA-A	89	.	0			c.G618T						PASS	.						45.0	41.0	42.0					6																	29911319		1505	2707	4212	SO:0001630	splice_region_variant	3105	exon3	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	GCGCACGGGTACC	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.619+1G>T	6.37:g.29911319G>T		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	125	51	0.408	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Silent	SNP	ENST00000396634.1	37	CCDS34373.1																																																																																			G|0.885;T|0.115	0.115	strong		0.637	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	Silent
TAS2R42	353164	hgsc.bcm.edu	37	12	11338750	11338750	+	Missense_Mutation	SNP	T	T	C	rs1451772	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:11338750T>C	ENST00000334266.1	-	1	793	c.794A>G	c.(793-795)tAc>tGc	p.Y265C		NM_181429.1	NP_852094.1	Q7RTR8	T2R42_HUMAN	taste receptor, type 2, member 42	265			Y -> C (in dbSNP:rs1451772).		sensory perception of taste (GO:0050909)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(1)|kidney(2)|lung(4)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	11			OV - Ovarian serous cystadenocarcinoma(49;0.0455)			AAACTTTATGTACTTGTTGTT	0.398													T|||	1102	0.220048	0.2474	0.2305	5008	,	,		19207	0.1944		0.2167	False		,,,				2504	0.2055				p.Y265C	Melanoma(15;352 722 10077 19546 48810)	Atlas-SNP	.											.	TAS2R42	30	.	0			c.A794G						PASS	.	T	CYS/TYR	1067,3339	387.5+/-326.5	137,793,1273	90.0	82.0	84.0		794	-0.4	0.0	12	dbSNP_92	84	2040,6560	356.5+/-330.3	248,1544,2508	yes	missense	TAS2R42	NM_181429.1	194	385,2337,3781	CC,CT,TT		23.7209,24.217,23.889	possibly-damaging	265/315	11338750	3107,9899	2203	4300	6503	SO:0001583	missense	353164	exon1			TTTATGTACTTGT	AX097739, AB199241	CCDS31747.1	12p13	2012-08-22			ENSG00000186136	ENSG00000186136		"""Taste receptors / Type 2"", ""GPCR / Unclassified : Taste receptors"""	18888	protein-coding gene	gene with protein product		613966				12679530	Standard	NM_181429		Approved	T2R24, T2R55, hT2R55, TAS2R55	uc001qzr.1	Q7RTR8	OTTHUMG00000168567	ENST00000334266.1:c.794A>G	12.37:g.11338750T>C	ENSP00000334050:p.Tyr265Cys	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	78	34	0.435897	NM_181429	A2RRP4|Q645X0	Missense_Mutation	SNP	ENST00000334266.1	37	CCDS31747.1	491	0.22481684981684982	114	0.23170731707317074	77	0.212707182320442	126	0.2202797202797203	174	0.22955145118733508	T	7.012	0.557044	0.13436	0.24217	0.237209	ENSG00000186136	ENST00000334266	T	0.00737	5.76	3.59	-0.391	0.12446	GPCR, rhodopsin-like superfamily (1);	4.835580	0.00857	N	0.001895	T	0.00012	0.0000	L	0.43152	1.355	0.80722	P	0.0	P	0.47841	0.901	B	0.40066	0.318	T	0.43278	-0.9401	9	0.45353	T	0.12	.	2.6081	0.04883	0.4343:0.0:0.2782:0.2874	rs1451772;rs1650018;rs17817145	265	Q7RTR8	T2R42_HUMAN	C	265	ENSP00000334050:Y265C	ENSP00000334050:Y265C	Y	-	2	0	TAS2R42	11230017	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-0.540000	0.06106	0.078000	0.16900	0.528000	0.53228	TAC	C|0.238;N|0.001	0.238	strong		0.398	TAS2R42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400243.1	NM_181429	
ARMS2	387715	hgsc.bcm.edu	37	10	124214448	124214448	+	Missense_Mutation	SNP	G	G	T	rs10490924	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:124214448G>T	ENST00000528446.1	+	1	280	c.205G>T	c.(205-207)Gct>Tct	p.A69S		NM_001099667.1	NP_001093137.1	P0C7Q2	ARMS2_HUMAN	age-related maculopathy susceptibility 2	69			A -> S (in dbSNP:rs10490924). {ECO:0000269|PubMed:16174643, ECO:0000269|PubMed:16642439, ECO:0000269|PubMed:16936732, ECO:0000269|PubMed:17000705, ECO:0000269|PubMed:17053108, ECO:0000269|PubMed:17210852, ECO:0000269|PubMed:17675241, ECO:0000269|PubMed:17884985, ECO:0000269|PubMed:18423869, ECO:0000269|PubMed:18436811, ECO:0000269|PubMed:18452766}.		retina homeostasis (GO:0001895)	mitochondrion (GO:0005739)|photoreceptor inner segment (GO:0001917)				ovary(1)	1		all_neural(114;0.0765)|Lung NSC(174;0.132)|all_lung(145;0.163)|Breast(234;0.238)				GATCCCAGCTGCTAAAATCCA	0.537													G|||	1435	0.286542	0.2458	0.2478	5008	,	,		19203	0.4038		0.1948	False		,,,				2504	0.3425				p.A69S		Atlas-SNP	.											.	ARMS2	7	.	0			c.G205T	GRCh37	CM066533	ARMS2	M	rs10490924	PASS	.	G	SER/ALA	824,3200		89,646,1277	95.0	94.0	94.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	205	1.0	0.0	10	dbSNP_119	94	1724,6652		182,1360,2646	yes	missense	ARMS2	NM_001099667.1	99	271,2006,3923	TT,TG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	20.5826,20.4771,20.5484	benign	69/108	124214448	2548,9852	2012	4188	6200	SO:0001583	missense	387715	exon1			CCAGCTGCTAAAA	BC066349	CCDS53585.1	10q26.13	2013-01-23			ENSG00000254636	ENSG00000254636			32685	protein-coding gene	gene with protein product		611313				16080115, 16174643	Standard	NM_001099667		Approved	LOC387715, ARMD8	uc001lgi.3	P0C7Q2	OTTHUMG00000048232	ENST00000528446.1:c.205G>T	10.37:g.124214448G>T	ENSP00000436682:p.Ala69Ser	Somatic	197	0	0		WXS	Illumina HiSeq	Phase_I	214	106	0.495327	NM_001099667	B2Y7I5	Missense_Mutation	SNP	ENST00000528446.1	37	CCDS53585.1	597	0.2733516483516483	126	0.25609756097560976	90	0.24861878453038674	230	0.4020979020979021	151	0.19920844327176782	G	8.897	0.955517	0.18507	0.204771	0.205826	ENSG00000254636	ENST00000528446	T	0.38401	1.14	1.97	0.998	0.19857	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	D	0.64830	0.994	D	0.68353	0.957	T	0.41822	-0.9487	8	0.87932	D	0	.	6.1676	0.20398	0.0:0.3219:0.6781:0.0	rs10490924;rs10490924	69	P0C7Q2	ARMS2_HUMAN	S	69	ENSP00000436682:A69S	ENSP00000436682:A69S	A	+	1	0	ARMS2	124204438	0.006000	0.16342	0.005000	0.12908	0.078000	0.17371	0.208000	0.17415	0.370000	0.24538	0.491000	0.48974	GCT	G|0.712;T|0.288	0.288	strong		0.537	ARMS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109727.2		
KIAA1549	57670	hgsc.bcm.edu	37	7	138596064	138596064	+	Silent	SNP	G	G	A	rs6969074	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:138596064G>A	ENST00000422774.1	-	4	3021	c.2973C>T	c.(2971-2973)taC>taT	p.Y991Y	KIAA1549_ENST00000440172.1_Silent_p.Y991Y|KIAA1549_ENST00000242365.4_Silent_p.Y941Y			Q9HCM3	K1549_HUMAN	KIAA1549	991						integral component of membrane (GO:0016021)			KIAA1549/BRAF(703)	large_intestine(4)|pancreas(1)|upper_aerodigestive_tract(2)	7						TAAATAGTTCGTAAACCTAGG	0.323			O	BRAF	pilocytic astrocytoma								A|||	2446	0.488419	0.8714	0.3055	5008	,	,		16340	0.1885		0.4712	False		,,,				2504	0.4274				p.Y991Y	NSCLC(119;1534 1718 44213 46230 50068)	Atlas-SNP	.		Dom	yes		7	7q34	57670	KIAA1549		O	.	KIAA1549	314	.	0			c.C2973T						PASS	.	A	,	2935,727		1167,601,63	45.0	46.0	46.0		2973,2973	4.1	1.0	7	dbSNP_116	46	3666,4500		852,1962,1269	no	coding-synonymous,coding-synonymous	KIAA1549	NM_001164665.1,NM_020910.2	,	2019,2563,1332	AA,AG,GG		44.8935,19.8525,44.1917	,	991/1951,991/1935	138596064	6601,5227	1831	4083	5914	SO:0001819	synonymous_variant	57670	exon4			TAGTTCGTAAACC		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.2973C>T	7.37:g.138596064G>A		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	50	27	0.54	NM_020910	B6HY55|B6HY56|B6HY58|B6HY60|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q5BJD6|Q8IY15|Q9H0M3	Silent	SNP	ENST00000422774.1	37	CCDS56513.1																																																																																			G|0.513;A|0.486	0.486	strong		0.323	KIAA1549-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348092.1		
CTSH	1512	hgsc.bcm.edu	37	15	79237247	79237247	+	Missense_Mutation	SNP	C	C	G	rs1036938	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:79237247C>G	ENST00000220166.5	-	1	186	c.77G>C	c.(76-78)tGc>tCc	p.C26S		NM_004390.3	NP_004381.2	P09668	CATH_HUMAN	cathepsin H	26			C -> S (in dbSNP:rs1036938). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:2587265}.		activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|adaptive immune response (GO:0002250)|antigen processing and presentation (GO:0019882)|bradykinin catabolic process (GO:0010815)|cellular response to thyroid hormone stimulus (GO:0097067)|dichotomous subdivision of terminal units involved in lung branching (GO:0060448)|ERK1 and ERK2 cascade (GO:0070371)|immune response-regulating signaling pathway (GO:0002764)|membrane protein proteolysis (GO:0033619)|metanephros development (GO:0001656)|negative regulation of apoptotic process (GO:0043066)|neuropeptide catabolic process (GO:0010813)|positive regulation of angiogenesis (GO:0045766)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of gene expression (GO:0010628)|positive regulation of peptidase activity (GO:0010952)|protein destabilization (GO:0031648)|proteolysis (GO:0006508)|response to retinoic acid (GO:0032526)|spermatogenesis (GO:0007283)|surfactant homeostasis (GO:0043129)|T cell mediated cytotoxicity (GO:0001913)|zymogen activation (GO:0031638)	acrosomal vesicle (GO:0001669)|alveolar lamellar body (GO:0097208)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|outer dense fiber (GO:0001520)	aminopeptidase activity (GO:0004177)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|cysteine-type endopeptidase activity (GO:0004197)|cysteine-type peptidase activity (GO:0008234)|endopeptidase activity (GO:0004175)|HLA-A specific activating MHC class I receptor activity (GO:0030108)|peptidase activity (GO:0008233)|serine-type endopeptidase activity (GO:0004252)|thyroid hormone binding (GO:0070324)			central_nervous_system(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(1)	10						GGAGTTCACGCACAGTTCGGC	0.706													G|||	1940	0.38738	0.211	0.4179	5008	,	,		12407	0.0952		0.6839	False		,,,				2504	0.6002				p.C26S		Atlas-SNP	.											.	CTSH	23	.	0			c.G77C						PASS	.	G	SER/CYS	1162,2626		219,724,951	12.0	12.0	12.0		77	2.2	0.0	15	dbSNP_86	12	5510,2156		2046,1418,369	yes	missense	CTSH	NM_004390.3	112	2265,2142,1320	GG,GC,CC		28.1242,30.6758,41.7496	benign	26/336	79237247	6672,4782	1894	3833	5727	SO:0001583	missense	1512	exon1			TTCACGCACAGTT	X07549	CCDS10308.1	15q25.1	2014-01-28			ENSG00000103811	ENSG00000103811	3.4.22.16	"""Cathepsins"""	2535	protein-coding gene	gene with protein product		116820		CPSB		2849458	Standard	NM_004390		Approved	ACC-4, ACC-5	uc021srk.1	P09668	OTTHUMG00000144171	ENST00000220166.5:c.77G>C	15.37:g.79237247C>G	ENSP00000220166:p.Cys26Ser	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	159	159	1	NM_004390	B2RBK0|Q96NY6|Q9BUM7	Missense_Mutation	SNP	ENST00000220166.5	37	CCDS10308.1	848	0.3882783882783883	118	0.23983739837398374	174	0.48066298342541436	50	0.08741258741258741	506	0.6675461741424802	G	7.933	0.741161	0.15642	0.306758	0.718758	ENSG00000103811	ENST00000220166;ENST00000394758;ENST00000444399	T	0.70516	-0.49	3.12	2.16	0.27623	.	9.562280	0.00567	N	0.000297	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B	0.12630	0.006;0.0	B;B	0.01281	0.0;0.0	T	0.40720	-0.9548	9	0.06365	T	0.9	.	5.6349	0.17532	0.0:0.222:0.5491:0.2289	rs1036938;rs1130855;rs3177820;rs17856064;rs1036938	26;14	E9PF73;E9PBP2	.;.	S	26;14;26	ENSP00000220166:C26S	ENSP00000220166:C26S	C	-	2	0	CTSH	77024302	0.004000	0.15560	0.000000	0.03702	0.001000	0.01503	0.797000	0.26999	0.317000	0.23160	-0.322000	0.08575	TGC	C|0.624;G|0.376	0.376	strong		0.706	CTSH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000291370.1	NM_004390	
ZNF804A	91752	hgsc.bcm.edu	37	2	185800768	185800768	+	Silent	SNP	T	T	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:185800768T>C	ENST00000302277.6	+	4	1239	c.645T>C	c.(643-645)tcT>tcC	p.S215S		NM_194250.1	NP_919226.1	Q7Z570	Z804A_HUMAN	zinc finger protein 804A	215							metal ion binding (GO:0046872)	p.S215S(1)		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						TCGGCTTTTCTTTTGCATTTC	0.433																																					p.S215S		Atlas-SNP	.											ZNF804A,colon,carcinoma,0,1	ZNF804A	322	1	1	Substitution - coding silent(1)	large_intestine(1)	c.T645C						PASS	.						66.0	67.0	66.0					2																	185800768		2203	4300	6503	SO:0001819	synonymous_variant	91752	exon4			CTTTTCTTTTGCA	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.645T>C	2.37:g.185800768T>C		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	71	20	0.28169	NM_194250	A7E253|Q6ZN26	Silent	SNP	ENST00000302277.6	37	CCDS2291.1																																																																																			.	.	none		0.433	ZNF804A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255871.1	NM_194250	
COQ5	84274	hgsc.bcm.edu	37	12	120966921	120966921	+	Silent	SNP	A	A	G	rs3742052	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:120966921A>G	ENST00000288532.6	-	1	64	c.24T>C	c.(22-24)gcT>gcC	p.A8A	COQ5_ENST00000445328.2_Silent_p.A8A	NM_032314.3	NP_115690.3	Q5HYK3	COQ5_HUMAN	coenzyme Q5 homolog, methyltransferase (S. cerevisiae)	8					small molecule metabolic process (GO:0044281)|ubiquinone biosynthetic process (GO:0006744)	mitochondrion (GO:0005739)	methyltransferase activity (GO:0008168)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(8)|ovary(1)|prostate(1)|urinary_tract(3)	20	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					AGCTCCATAGAGCACAGCTCC	0.667													A|||	1325	0.264577	0.0809	0.2579	5008	,	,		14695	0.4921		0.2783	False		,,,				2504	0.2689				p.A8A		Atlas-SNP	.											.	COQ5	26	.	0			c.T24C						PASS	.	A		466,3938		24,418,1760	18.0	21.0	20.0		24	-1.4	0.0	12	dbSNP_107	20	2678,5920		424,1830,2045	no	coding-synonymous	COQ5	NM_032314.3		448,2248,3805	GG,GA,AA		31.1468,10.5813,24.1809		8/328	120966921	3144,9858	2202	4299	6501	SO:0001819	synonymous_variant	84274	exon1			CCATAGAGCACAG	AK057777	CCDS31912.1	12q24.31	2011-09-16	2006-04-04		ENSG00000110871	ENSG00000110871	2.1.1.201		28722	protein-coding gene	gene with protein product	"""2-methoxy-6-polyprenyl-1,4-benzoquinol methylase"""		"""coenzyme Q5 homolog, methyltransferase (yeast)"""				Standard	NM_032314		Approved	MGC4767	uc001tyn.3	Q5HYK3	OTTHUMG00000169375	ENST00000288532.6:c.24T>C	12.37:g.120966921A>G		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	79	37	0.468354	NM_032314	B4DEJ4|Q32Q28|Q53HH0|Q96LV1|Q9BSP8	Silent	SNP	ENST00000288532.6	37	CCDS31912.1																																																																																			A|0.748;G|0.252	0.252	strong		0.667	COQ5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403767.2	NM_032314	
ATP8A2	51761	hgsc.bcm.edu	37	13	26043182	26043182	+	Silent	SNP	A	A	C	rs7317185	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:26043182A>C	ENST00000381655.2	+	2	286	c.144A>C	c.(142-144)ggA>ggC	p.G48G	ATP8A2_ENST00000255283.8_Silent_p.G8G	NM_016529.4	NP_057613.4	Q9NTI2	AT8A2_HUMAN	ATPase, aminophospholipid transporter, class I, type 8A, member 2	8					aging (GO:0007568)|axonogenesis (GO:0007409)|detection of light stimulus involved in visual perception (GO:0050908)|eating behavior (GO:0042755)|inner ear morphogenesis (GO:0042472)|involuntary skeletal muscle contraction (GO:0003011)|negative regulation of cell proliferation (GO:0008285)|neurofilament cytoskeleton organization (GO:0060052)|neuromuscular process controlling posture (GO:0050884)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of neuron projection development (GO:0010976)|positive regulation of phospholipid translocation (GO:0061092)|response to auditory stimulus (GO:0010996)|retina layer formation (GO:0010842)|skin development (GO:0043588)	cell projection (GO:0042995)|endosome (GO:0005768)|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)			breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(17)|lung(31)|ovary(4)|skin(3)|stomach(1)|urinary_tract(1)	72		Breast(139;0.0201)|Lung SC(185;0.0225)		all cancers(112;0.043)|OV - Ovarian serous cystadenocarcinoma(117;0.0748)|Epithelial(112;0.079)		CGTCTGTTGGAGACCAGCTGG	0.582													A|||	1022	0.204073	0.354	0.1484	5008	,	,		9431	0.119		0.1998	False		,,,				2504	0.1329				p.G48G		Atlas-SNP	.											ATP8A2,colon,carcinoma,0,1	ATP8A2	181	1	0			c.A144C						PASS	.	A		1226,2880		185,856,1012	77.0	86.0	83.0		144	0.1	1.0	13	dbSNP_116	83	1789,6605		191,1407,2599	no	coding-synonymous	ATP8A2	NM_016529.4		376,2263,3611	CC,CA,AA		21.3128,29.8587,24.12		48/1189	26043182	3015,9485	2053	4197	6250	SO:0001819	synonymous_variant	51761	exon2			TGTTGGAGACCAG	AL137256	CCDS41873.1	13q12	2010-04-20	2010-03-31		ENSG00000132932	ENSG00000132932	3.6.3.1	"""ATPases / P-type"""	13533	protein-coding gene	gene with protein product		605870	"""ATPase, aminophospholipid transporter-like, Class I, type 8A, member 2"", ""ATPase, aminophospholipid transporter-like, class I, type 8A, member 2"""			11015572, 19778899	Standard	NM_016529		Approved	ATPIB, ML-1	uc001uqk.3	Q9NTI2	OTTHUMG00000016611	ENST00000381655.2:c.144A>C	13.37:g.26043182A>C		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	115	51	0.443478	NM_016529	Q9H527|Q9NPU6|Q9NTL2|Q9NYM3	Silent	SNP	ENST00000381655.2	37	CCDS41873.1	455	0.20833333333333334	166	0.33739837398373984	68	0.1878453038674033	75	0.13111888111888112	146	0.19261213720316622	A	12.71	2.020365	0.35606	0.298587	0.213128	ENSG00000132932	ENST00000544544	.	.	.	4.16	0.119	0.14685	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.42310	-0.9459	4	0.11485	T	0.65	.	0.3655	0.00371	0.3332:0.1995:0.2735:0.1938	rs7317185;rs7317185	.	.	.	A	10	.	ENSP00000444329:E10A	E	+	2	0	ATP8A2	24941182	1.000000	0.71417	0.999000	0.59377	0.994000	0.84299	1.074000	0.30703	0.144000	0.18951	0.329000	0.21502	GAG	A|0.790;C|0.210	0.210	strong		0.582	ATP8A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044236.2	NM_016529	
OR10G3	26533	hgsc.bcm.edu	37	14	22038450	22038450	+	Silent	SNP	G	G	A	rs11626669	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	107	0	0		WXS	Illumina HiSeq	Phase_I	71	32	0.450704	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		
RNF144A	9781	hgsc.bcm.edu	37	2	7164578	7164578	+	Silent	SNP	A	A	G	rs376219	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:7164578A>G	ENST00000320892.6	+	7	1030	c.588A>G	c.(586-588)gaA>gaG	p.E196E	RNF144A_ENST00000467276.1_3'UTR	NM_014746.3	NP_055561.2	P50876	R144A_HUMAN	ring finger protein 144A	196					protein ubiquitination (GO:0016567)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(15)|ovary(1)|prostate(1)	25	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)	all_cancers(51;0.226)		OV - Ovarian serous cystadenocarcinoma(76;0.195)		AGCGAGACGAAGGCTGCGCGC	0.572													A|||	1324	0.264377	0.1097	0.3905	5008	,	,		19524	0.1696		0.3459	False		,,,				2504	0.3978				p.E196E		Atlas-SNP	.											.	RNF144A	38	.	0			c.A588G						PASS	.	A		675,3731	283.1+/-276.9	58,559,1586	109.0	92.0	98.0		588	0.5	1.0	2	dbSNP_80	98	3261,5339	487.7+/-372.2	628,2005,1667	no	coding-synonymous	RNF144A	NM_014746.3		686,2564,3253	GG,GA,AA		37.9186,15.32,30.263		196/293	7164578	3936,9070	2203	4300	6503	SO:0001819	synonymous_variant	9781	exon7			AGACGAAGGCTGC	D79983	CCDS1657.1	2p25.2	2008-02-05	2007-08-20	2007-08-20	ENSG00000151692	ENSG00000151692		"""RING-type (C3HC4) zinc fingers"""	20457	protein-coding gene	gene with protein product			"""ring finger protein 144"""	RNF144		8724849, 10431818	Standard	NM_014746		Approved	UBCE7IP4, KIAA0161	uc002qys.3	P50876	OTTHUMG00000090353	ENST00000320892.6:c.588A>G	2.37:g.7164578A>G		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	94	94	1	NM_014746	D6W4Y6|Q585H5	Silent	SNP	ENST00000320892.6	37	CCDS1657.1	536	0.2454212454212454	42	0.08536585365853659	132	0.36464088397790057	98	0.17132867132867133	264	0.3482849604221636	A	1.539	-0.542170	0.04053	0.1532	0.379186	ENSG00000151692	ENST00000432850	.	.	.	5.87	0.485	0.16830	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.39881	-0.9592	3	.	.	.	.	10.6812	0.45815	0.5408:0.0:0.4592:0.0	rs376219;rs17661911;rs376219	.	.	.	R	192	.	.	K	+	2	0	RNF144A	7082029	0.983000	0.35010	0.985000	0.45067	0.056000	0.15407	0.309000	0.19332	-0.138000	0.11434	-0.256000	0.11100	AAG	A|0.727;G|0.273	0.273	strong		0.572	RNF144A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206725.2	NM_014746	
ALPPL2	251	hgsc.bcm.edu	37	2	233271669	233271669	+	Missense_Mutation	SNP	C	C	T	rs16836187|rs139018608	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:233271669C>T	ENST00000295453.3	+	1	117	c.65C>T	c.(64-66)cCa>cTa	p.P22L		NM_031313.2	NP_112603.2	P10696	PPBN_HUMAN	alkaline phosphatase, placental-like 2	22					dephosphorylation (GO:0016311)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)	alkaline phosphatase activity (GO:0004035)|metal ion binding (GO:0046872)			breast(2)|kidney(1)|large_intestine(1)|liver(2)|lung(6)|skin(1)	13		all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0449)|Lung NSC(271;0.132)		Epithelial(121;4.45e-22)|Kidney(3;4.42e-11)|KIRC - Kidney renal clear cell carcinoma(3;1.9e-09)|BRCA - Breast invasive adenocarcinoma(100;0.000767)|Lung(119;0.00566)|LUSC - Lung squamous cell carcinoma(224;0.00746)|STAD - Stomach adenocarcinoma(3;0.0181)|GBM - Glioblastoma multiforme(43;0.196)	Amifostine(DB01143)	GGCATCATCCCAGGTAATGAG	0.647																																					p.P22L		Atlas-SNP	.											.	ALPPL2	36	.	0			c.C65T						PASS	.						72.0	75.0	74.0					2																	233271669		2203	4300	6503	SO:0001583	missense	251	exon1			TCATCCCAGGTAA	J04948	CCDS2491.1	2q37	2008-05-20			ENSG00000163286	ENSG00000163286			441	protein-coding gene	gene with protein product		171810					Standard	NM_031313		Approved		uc002vss.4	P10696	OTTHUMG00000133257	ENST00000295453.3:c.65C>T	2.37:g.233271669C>T	ENSP00000295453:p.Pro22Leu	Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	166	19	0.114458	NM_031313	A8KAF2|Q16727|Q53S81|Q96CM1	Missense_Mutation	SNP	ENST00000295453.3	37	CCDS2491.1	.	.	.	.	.	.	.	.	.	.	C	14.92	2.679525	0.47886	.	.	ENSG00000163286	ENST00000295453	D	0.83673	-1.75	2.19	2.19	0.27852	Alkaline-phosphatase-like, core domain (1);	0.185016	0.47093	D	0.000260	T	0.81187	0.4770	M	0.87097	2.86	0.58432	D	0.999995	P	0.44139	0.827	B	0.37304	0.246	T	0.82715	-0.0320	10	0.66056	D	0.02	.	7.8156	0.29258	0.2487:0.7513:0.0:0.0	rs16836187	22	P10696	PPBN_HUMAN	L	22	ENSP00000295453:P22L	ENSP00000295453:P22L	P	+	2	0	ALPPL2	232979913	0.080000	0.21391	0.999000	0.59377	0.074000	0.17049	0.145000	0.16157	1.528000	0.49103	0.205000	0.17691	CCA	C|1.000;|0.000	.	weak		0.647	ALPPL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257034.2	NM_031313	
BTN3A2	11118	hgsc.bcm.edu	37	6	26373150	26373150	+	Silent	SNP	C	C	T	rs12174631	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:26373150C>T	ENST00000356386.2	+	6	929	c.741C>T	c.(739-741)ccC>ccT	p.P247P	BTN3A2_ENST00000396948.1_Silent_p.P247P|BTN3A2_ENST00000396934.3_Silent_p.P224P|BTN3A2_ENST00000532994.1_3'UTR|BTN3A2_ENST00000527422.1_Silent_p.P247P|BTN3A2_ENST00000508906.2_Silent_p.P205P|BTN3A2_ENST00000377708.2_Silent_p.P247P	NM_001197246.2|NM_001197247.1|NM_007047.3	NP_001184175.1|NP_001184176.1|NP_008978.2	P78410	BT3A2_HUMAN	butyrophilin, subfamily 3, member A2	247					interferon-gamma secretion (GO:0072643)|T cell mediated immunity (GO:0002456)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(5)	10						GCGCCCAGCCCTGGATCGCAG	0.607													C|||	406	0.0810703	0.0287	0.0389	5008	,	,		16332	0.0992		0.1103	False		,,,				2504	0.1329				p.P247P		Atlas-SNP	.											.	BTN3A2	44	.	0			c.C741T						PASS	.	C	,,,,	165,4241	108.2+/-146.6	2,161,2040	61.0	62.0	62.0		741,741,672,615,741	0.6	0.0	6	dbSNP_120	62	929,7671	200.9+/-244.5	50,829,3421	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	BTN3A2	NM_001197246.1,NM_001197247.1,NM_001197248.1,NM_001197249.1,NM_007047.3	,,,,	52,990,5461	TT,TC,CC		10.8023,3.7449,8.4115	,,,,	247/335,247/335,224/312,205/293,247/335	26373150	1094,11912	2203	4300	6503	SO:0001819	synonymous_variant	11118	exon4			CCAGCCCTGGATC	U90546	CCDS4605.1, CCDS56399.1, CCDS56400.1	6p22.1	2014-01-14			ENSG00000186470	ENSG00000186470		"""Immunoglobulin superfamily / V-set domain containing"", ""Butyrophilins"""	1139	protein-coding gene	gene with protein product		613594				9149941	Standard	NM_007047		Approved	BTN3.2	uc010jqi.2	P78410	OTTHUMG00000014450	ENST00000356386.2:c.741C>T	6.37:g.26373150C>T		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	74	73	0.986486	NM_001197246	B4DRT7|B4E103|F5H791|F8W6E0|O00477|O15338|O75658|Q76PA0|Q9BU81|Q9NR44	Silent	SNP	ENST00000356386.2	37	CCDS4605.1																																																																																			C|0.924;T|0.076	0.076	strong		0.607	BTN3A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040113.2		
CEACAM20	125931	hgsc.bcm.edu	37	19	45021252	45021252	+	RNA	SNP	G	G	A	rs16959164	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:45021252G>A	ENST00000454753.1	-	0	1342							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)				CTCAGATGCCGACTCCCTGGT	0.572													G|||	235	0.0469249	0.056	0.0576	5008	,	,		18446	0.0585		0.0219	False		,,,				2504	0.0409				p.S355L		Atlas-SNP	.											.	CEACAM20	31	.	0			c.C1064T						PASS	.	G	LEU/SER,,,LEU/SER	178,4080		4,170,1955	80.0	75.0	77.0		1064,,,1064	0.9	0.0	19	dbSNP_123	77	174,8332		3,168,4082	yes	missense,intron,intron,missense	CEACAM20	NM_001102597.1,NM_001102598.1,NM_001102599.1,NM_001102600.1	145,,,145	7,338,6037	AA,AG,GG		2.0456,4.1804,2.7578	benign,,,benign	355/597,,,355/585	45021252	352,12412	2129	4253	6382			125931	exon6			GATGCCGACTCCC	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.45021252G>A		Somatic	26	0	0		WXS	Illumina HiSeq	Phase_I	21	21	1	NM_001102600		Missense_Mutation	SNP	ENST00000454753.1	37																																																																																				G|0.956;A|0.044	0.044	strong		0.572	CEACAM20-001	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000323032.1	NM_198444	
ZNF415	55786	hgsc.bcm.edu	37	19	53612055	53612055	+	Missense_Mutation	SNP	T	T	C	rs10410030	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:53612055T>C	ENST00000500065.4	-	4	1576	c.1243A>G	c.(1243-1245)Aat>Gat	p.N415D	ZNF415_ENST00000440291.1_Missense_Mutation_p.N402D|ZNF415_ENST00000601493.1_Missense_Mutation_p.N185D|ZNF415_ENST00000455735.2_Missense_Mutation_p.N463D|ZNF415_ENST00000448501.1_Missense_Mutation_p.N463D|ZNF415_ENST00000243643.4_Missense_Mutation_p.N415D|ZNF415_ENST00000597748.1_3'UTR|ZNF415_ENST00000421033.1_Missense_Mutation_p.N427D|ZNF415_ENST00000594011.1_3'UTR|ZNF415_ENST00000597503.1_3'UTR|ZNF415_ENST00000595193.1_3'UTR	NM_001136038.2	NP_001129510.2	Q09FC8	ZN415_HUMAN	zinc finger protein 415	463					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|kidney(3)|large_intestine(8)|lung(11)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31				GBM - Glioblastoma multiforme(134;0.0191)		CCACATTCATTGCATTTGTAA	0.408													T|||	609	0.121605	0.2292	0.1412	5008	,	,		24059	0.002		0.1322	False		,,,				2504	0.0746				p.N415D		Atlas-SNP	.											.	ZNF415	68	.	0			c.A1243G						PASS	.	T	ASP/ASN,ASP/ASN,ASP/ASN	870,3536	339.1+/-305.6	93,684,1426	87.0	86.0	86.0		1243,1243,1243	-2.3	0.0	19	dbSNP_119	86	1352,7248	264.5+/-285.6	116,1120,3064	yes	missense,missense,missense	ZNF415	NM_001136038.2,NM_001164309.1,NM_018355.2	23,23,23	209,1804,4490	CC,CT,TT		15.7209,19.7458,17.0844	benign,benign,benign	415/556,415/556,415/556	53612055	2222,10784	2203	4300	6503	SO:0001583	missense	55786	exon4			ATTCATTGCATTT	AK002053	CCDS12860.1, CCDS54313.1	19q13.42	2014-03-18			ENSG00000170954	ENSG00000170954		"""Zinc fingers, C2H2-type"", ""-"""	20636	protein-coding gene	gene with protein product						14702039	Standard	NM_001136038		Approved		uc002qaw.3	Q09FC8	OTTHUMG00000182865	ENST00000500065.4:c.1243A>G	19.37:g.53612055T>C	ENSP00000439435:p.Asn415Asp	Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	43	19	0.44186	NM_018355	F5H287|Q09FC7|Q09FC9|Q09FD0|Q6NSZ2|Q6P3S0|Q9NUR2	Missense_Mutation	SNP	ENST00000500065.4	37	CCDS54313.1	249	0.11401098901098901	90	0.18292682926829268	59	0.16298342541436464	1	0.0017482517482517483	99	0.13060686015831136	T	12.29	1.892683	0.33442	0.197458	0.157209	ENSG00000170954	ENST00000243643;ENST00000500065;ENST00000448501;ENST00000421033;ENST00000455735;ENST00000440291	T;T;T;T;T;T	0.07327	3.2;3.2;3.2;3.2;3.2;3.2	2.77	-2.29	0.06805	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	N	0.00521	-1.4	0.80722	P	0.0	B;B;B;B;B;B	0.22414	0.002;0.043;0.005;0.002;0.005;0.069	B;B;B;B;B;B	0.29440	0.003;0.102;0.01;0.003;0.005;0.062	T	0.46176	-0.9210	8	0.37606	T	0.19	.	4.8591	0.13573	0.1501:0.4097:0.0:0.4402	rs10410030;rs17846658;rs17859755;rs52797631;rs10410030	415;463;463;415;402;427	F5H287;B3KTG1;Q09FC8;Q09FC8-5;Q09FC8-4;Q09FC8-2	.;.;ZN415_HUMAN;.;.;.	D	415;415;463;427;463;402	ENSP00000243643:N415D;ENSP00000439435:N415D;ENSP00000396492:N463D;ENSP00000395055:N427D;ENSP00000388787:N463D;ENSP00000414601:N402D	ENSP00000243643:N415D	N	-	1	0	ZNF415	58303867	0.000000	0.05858	0.000000	0.03702	0.030000	0.12068	-4.986000	0.00163	-0.870000	0.04047	-0.425000	0.05940	AAT	T|0.842;C|0.158	0.158	strong		0.408	ZNF415-025	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464043.1	NM_018355	
AARS	16	hgsc.bcm.edu	37	16	70303580	70303580	+	Silent	SNP	G	G	A	rs2070203	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:70303580G>A	ENST00000261772.8	-	7	1046	c.903C>T	c.(901-903)caC>caT	p.H301H		NM_001605.2	NP_001596.2			alanyl-tRNA synthetase											breast(3)|cervix(2)|endometrium(5)|large_intestine(7)|lung(7)|ovary(1)|pancreas(1)|prostate(1)	27		Ovarian(137;0.0365)		BRCA - Breast invasive adenocarcinoma(221;0.161)		TGGTCCGAGCGTGGTCAGCCA	0.587													G|||	2130	0.425319	0.438	0.4078	5008	,	,		18233	0.4256		0.5338	False		,,,				2504	0.3088				p.H301H		Atlas-SNP	.											.	AARS	62	.	0			c.C903T	GRCh37	CM995271	AARS	M	rs2070203	PASS	.	G		2071,2325	570.7+/-382.9	465,1141,592	200.0	167.0	178.0		903	-11.3	0.1	16	dbSNP_96	178	4307,4293	578.3+/-390.7	1084,2139,1077	yes	coding-synonymous	AARS	NM_001605.2		1549,3280,1669	AA,AG,GG		49.9186,47.111,49.0766		301/969	70303580	6378,6618	2198	4300	6498	SO:0001819	synonymous_variant	16	exon7			CCGAGCGTGGTCA	D32050	CCDS32474.1	16q22.1	2014-09-17			ENSG00000090861	ENSG00000090861	6.1.1.7	"""Aminoacyl tRNA synthetases / Class II"""	20	protein-coding gene	gene with protein product	"""alanine tRNA ligase 1, cytoplasmic"""	601065				8595897	Standard	NM_001605		Approved		uc002eyn.1	P49588	OTTHUMG00000177042	ENST00000261772.8:c.903C>T	16.37:g.70303580G>A		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	77	45	0.584416	NM_001605		Silent	SNP	ENST00000261772.8	37	CCDS32474.1																																																																																			G|0.526;A|0.474	0.474	strong		0.587	AARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435021.2	NM_001605	
GAREM	64762	hgsc.bcm.edu	37	18	29972964	29972964	+	Silent	SNP	A	A	G	rs3786308	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:29972964A>G	ENST00000269209.6	-	2	159	c.156T>C	c.(154-156)taT>taC	p.Y52Y	GAREM_ENST00000399218.4_Silent_p.Y52Y			Q9H706	GAREM_HUMAN	GRB2 associated, regulator of MAPK1	52	CABIT.				cellular response to epidermal growth factor stimulus (GO:0071364)|epidermal growth factor receptor signaling pathway (GO:0007173)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)	plasma membrane (GO:0005886)	proline-rich region binding (GO:0070064)										GAATCAGCAGATAGTCATTTT	0.443													G|||	771	0.153954	0.23	0.0937	5008	,	,		15768	0.1657		0.1074	False		,,,				2504	0.1299				p.Y52Y		Atlas-SNP	.											.	.	.	.	0			c.T156C						PASS	.	G	,	903,3503	740.8+/-411.2	107,689,1407	139.0	117.0	125.0		156,156	3.2	1.0	18	dbSNP_107	125	806,7794	782.6+/-407.6	44,718,3538	no	coding-synonymous,coding-synonymous	FAM59A	NM_001242409.1,NM_022751.2	,	151,1407,4945	GG,GA,AA		9.3721,20.4948,13.1401	,	52/877,52/876	29972964	1709,11297	2203	4300	6503	SO:0001819	synonymous_variant	64762	exon2			CAGCAGATAGTCA	AK025263	CCDS11905.1, CCDS56057.1	18q12.1	2012-11-30	2012-11-30	2012-11-30	ENSG00000141441	ENSG00000141441			26136	protein-coding gene	gene with protein product	"""Grb2-associated and regulator of Erk/MAPK"""		"""chromosome 18 open reading frame 11"", ""family with sequence similarity 59, member A"""	C18orf11, FAM59A		19509291	Standard	NM_001242409		Approved	FLJ21610	uc002kxl.3	Q9H706	OTTHUMG00000132273	ENST00000269209.6:c.156T>C	18.37:g.29972964A>G		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	136	65	0.477941	NM_022751	Q0VAG3|Q0VAG4|Q8ND03|Q9BSF5	Silent	SNP	ENST00000269209.6	37	CCDS56057.1																																																																																			A|0.855;G|0.145	0.145	strong		0.443	GAREM-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255365.1	NM_022751	
KRTAP19-6	337973	hgsc.bcm.edu	37	21	31914000	31914000	+	Silent	SNP	T	T	A	rs1023364	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:31914000T>A	ENST00000334046.5	-	1	183	c.153A>T	c.(151-153)ggA>ggT	p.G51G		NM_181612.2	NP_853643.1	Q3LI70	KR196_HUMAN	keratin associated protein 19-6	51						intermediate filament (GO:0005882)				breast(1)|large_intestine(2)|lung(5)|upper_aerodigestive_tract(1)	9						AGAATCCATATCCTTCACGGC	0.483													t|||	3745	0.747804	0.8033	0.7277	5008	,	,		16063	0.7024		0.7117	False		,,,				2504	0.771				p.G51G		Atlas-SNP	.											.	KRTAP19-6	16	.	0			c.A153T						PASS	.	T		3448,958	729.0+/-410.0	1350,748,105	109.0	120.0	116.0		153	-1.5	0.0	21	dbSNP_86	116	6103,2497	688.9+/-404.3	2167,1769,364	no	coding-synonymous	KRTAP19-6	NM_181612.2		3517,2517,469	AA,AT,TT		29.0349,21.7431,26.5647		51/59	31914000	9551,3455	2203	4300	6503	SO:0001819	synonymous_variant	337973	exon1			TCCATATCCTTCA	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.153A>T	21.37:g.31914000T>A		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	78	29	0.371795	NM_181612	Q3LI71	Silent	SNP	ENST00000334046.5	37	CCDS13598.1																																																																																			T|0.271;A|0.729	0.729	strong		0.483	KRTAP19-6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128231.4		
TPRX1	284355	hgsc.bcm.edu	37	19	48305586	48305586	+	Missense_Mutation	SNP	G	G	A	rs145255760		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:48305586G>A	ENST00000322175.3	-	2	837	c.682C>T	c.(682-684)Cca>Tca	p.P228S	TPRX1_ENST00000535759.1_Missense_Mutation_p.P325S|TPRX1_ENST00000543508.1_Missense_Mutation_p.P218S	NM_198479.2	NP_940881.2	Q8N7U7	TPRX1_HUMAN	tetra-peptide repeat homeobox 1	228	Gly-rich.					nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(5)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|prostate(2)|skin(1)	18		all_cancers(25;3.02e-09)|all_epithelial(76;7e-07)|all_lung(116;2.48e-06)|Lung NSC(112;5.15e-06)|Ovarian(192;0.0139)|all_neural(266;0.0146)|Breast(70;0.133)		OV - Ovarian serous cystadenocarcinoma(262;0.000241)|all cancers(93;0.00036)|Epithelial(262;0.0127)|GBM - Glioblastoma multiforme(486;0.048)		attgggcctgggattgggcct	0.662																																					p.P228S	Esophageal Squamous(123;175 2281 3051 32395)	Atlas-SNP	.											.	TPRX1	46	.	0			c.C682T						PASS	.						11.0	9.0	9.0					19																	48305586		1986	3954	5940	SO:0001583	missense	284355	exon2			GGCCTGGGATTGG		CCDS33066.1	19q13.33	2011-07-08			ENSG00000178928	ENSG00000178928		"""Homeoboxes / PRD class"""	32174	protein-coding gene	gene with protein product		611166					Standard	XM_005258788		Approved	FLJ40321	uc002php.2	Q8N7U7		ENST00000322175.3:c.682C>T	19.37:g.48305586G>A	ENSP00000323455:p.Pro228Ser	Somatic	19	0	0		WXS	Illumina HiSeq	Phase_I	24	5	0.208333	NM_198479	A5D8Y3|B2RPL5	Missense_Mutation	SNP	ENST00000322175.3	37	CCDS33066.1	93	0.042582417582417584	4	0.008130081300813009	13	0.03591160220994475	1	0.0017482517482517483	75	0.09894459102902374	g	5.125	0.208615	0.09757	.	.	ENSG00000178928	ENST00000322175;ENST00000535759;ENST00000543508	D;D;T	0.93763	-2.04;-3.28;-0.16	0.401	-0.802	0.10889	.	.	.	.	.	T	0.11067	0.0270	N	0.03608	-0.345	0.09310	N	1	B	0.17268	0.021	B	0.11329	0.006	T	0.51748	-0.8666	8	0.40728	T	0.16	.	.	.	.	.	228	Q8N7U7	TPRX1_HUMAN	S	228;325;218	ENSP00000323455:P228S;ENSP00000438832:P325S;ENSP00000438712:P218S	ENSP00000323455:P228S	P	-	1	0	TPRX1	52997398	0.002000	0.14202	0.001000	0.08648	0.001000	0.01503	0.328000	0.19681	-0.453000	0.07076	-0.462000	0.05337	CCA	G|0.957;A|0.043	0.043	strong		0.662	TPRX1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000409868.1	NM_198479	
SRSF4	6429	hgsc.bcm.edu	37	1	29475394	29475394	+	Missense_Mutation	SNP	C	C	G	rs2230677	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:29475394C>G	ENST00000373795.4	-	6	1247	c.1013G>C	c.(1012-1014)gGg>gCg	p.G338A	SRSF4_ENST00000466448.1_5'UTR|RP11-242O24.3_ENST00000413004.1_lincRNA|SRSF4_ENST00000546138.1_3'UTR	NM_005626.4	NP_005617.2	Q08170	SRSF4_HUMAN	serine/arginine-rich splicing factor 4	338	Arg/Ser-rich (RS domain).		G -> A (in dbSNP:rs2230677). {ECO:0000269|PubMed:8321209}.		gene expression (GO:0010467)|hematopoietic progenitor cell differentiation (GO:0002244)|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)|RNA splicing, via transesterification reactions (GO:0000375)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(8)|liver(1)|lung(8)|ovary(1)|prostate(1)	27						cctgctgccccctttgctcct	0.657													C|||	2480	0.495208	0.5598	0.5447	5008	,	,		15719	0.1528		0.7694	False		,,,				2504	0.4438				p.G338A		Atlas-SNP	.											.	SRSF4	44	.	0			c.G1013C						PASS	.	C	ALA/GLY	2683,1721		843,997,362	32.0	31.0	31.0		1013	-0.7	0.3	1	dbSNP_98	31	6860,1738		2743,1374,182	yes	missense	SRSF4	NM_005626.4	60	3586,2371,544	GG,GC,CC		20.214,39.0781,26.6036	benign	338/495	29475394	9543,3459	2202	4299	6501	SO:0001583	missense	6429	exon6			CTGCCCCCTTTGC	BC002781	CCDS333.1	1p35.3	2013-02-12	2010-06-22	2010-06-22	ENSG00000116350	ENSG00000116350		"""Serine/arginine-rich splicing factors"", ""RNA binding motif (RRM) containing"""	10786	protein-coding gene	gene with protein product	"""SR splicing factor 4"""	601940	"""splicing factor, arginine/serine-rich 4"""	SFRS4		8321209, 20516191	Standard	NM_005626		Approved	SRP75	uc001bro.3	Q08170	OTTHUMG00000003663	ENST00000373795.4:c.1013G>C	1.37:g.29475394C>G	ENSP00000362900:p.Gly338Ala	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	66	66	1	NM_005626	Q5VXP1|Q9BUA4|Q9UEB5	Missense_Mutation	SNP	ENST00000373795.4	37	CCDS333.1	1144	0.5238095238095238	275	0.5589430894308943	204	0.56353591160221	83	0.1451048951048951	582	0.7678100263852242	C	1.034	-0.680963	0.03353	0.609219	0.79786	ENSG00000116350	ENST00000373795;ENST00000434636	T	0.12879	2.64	4.96	-0.673	0.11373	.	0.829014	0.10443	N	0.674083	T	0.00012	0.0000	N	0.08118	0	0.53005	P	3.6999999999953737E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.37731	-0.9693	9	0.02654	T	1	.	2.4665	0.04554	0.2754:0.219:0.3836:0.1219	rs2230677;rs2230677	338	Q08170	SRSF4_HUMAN	A	338	ENSP00000362900:G338A	ENSP00000362900:G338A	G	-	2	0	SRSF4	29347981	0.064000	0.20934	0.333000	0.25482	0.163000	0.22366	0.426000	0.21363	-0.178000	0.10672	-0.122000	0.15005	GGG	C|0.377;G|0.623	0.623	strong		0.657	SRSF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010392.1	NM_005626	
MUC4	4585	hgsc.bcm.edu	37	3	195495916	195495916	+	Missense_Mutation	SNP	G	G	C	rs2550240	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195495916G>C	ENST00000346145.4	-	6	837	c.798C>G	c.(796-798)aaC>aaG	p.N266K	MUC4_ENST00000349607.4_Missense_Mutation_p.N215K|MUC4_ENST00000463781.3_Missense_Mutation_p.N4502K|MUC4_ENST00000475231.1_Missense_Mutation_p.N4450K	NM_004532.5	NP_004523.3	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	1259					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)		TGAGCACCGGGTTGCCTGAGC	0.622													.|||	2147	0.428714	0.1581	0.438	5008	,	,		19055	0.7659		0.4423	False		,,,				2504	0.4264				p.N4502K		Atlas-SNP	.											.	MUC4	1505	.	0			c.C13506G						PASS	.	G	LYS/ASN,LYS/ASN,LYS/ASN	922,3484		91,740,1372	67.0	54.0	59.0		798,13506,645	3.4	0.1	3	dbSNP_100	59	3745,4855		840,2065,1395	no	missense,missense,missense	MUC4	NM_004532.5,NM_018406.6,NM_138297.4	94,94,94	931,2805,2767	CC,CG,GG		43.5465,20.926,35.8834	possibly-damaging,possibly-damaging,possibly-damaging	266/1177,4502/5413,215/1126	195495916	4667,8339	2203	4300	6503	SO:0001583	missense	4585	exon7			CACCGGGTTGCCT	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000346145.4:c.798C>G	3.37:g.195495916G>C	ENSP00000304207:p.Asn266Lys	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	57	24	0.421053	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000346145.4	37	CCDS3310.1	977	0.44734432234432236	78	0.15853658536585366	152	0.4198895027624309	412	0.7202797202797203	335	0.4419525065963061	.	6.319	0.426881	0.11987	0.20926	0.435465	ENSG00000145113	ENST00000349607;ENST00000346145;ENST00000463781;ENST00000475231;ENST00000392409	T;T;T;T	0.72051	-0.62;-0.62;-0.62;-0.62	5.5	3.37	0.38596	Nidogen, extracellular domain (3);	0.550562	0.17475	N	0.172932	T	0.00012	0.0000	M	0.73598	2.24	0.80722	P	0.0	P;B;B;B	0.51791	0.948;0.082;0.079;0.037	P;B;B;B	0.57911	0.829;0.081;0.033;0.033	T	0.48151	-0.9060	9	0.12430	T	0.62	-29.412	9.3513	0.38140	0.1583:0.1257:0.716:0.0	rs2550240;rs3749332;rs60021717;rs2550240	4374;1259;215;266	E7ESK3;Q99102;Q99102-12;Q99102-13	.;MUC4_HUMAN;.;.	K	215;266;4502;4450;1228	ENSP00000338109:N215K;ENSP00000304207:N266K;ENSP00000417498:N4502K;ENSP00000420243:N4450K	ENSP00000304207:N266K	N	-	3	2	MUC4	196981550	0.001000	0.12720	0.130000	0.21974	0.019000	0.09904	0.759000	0.26461	1.349000	0.45751	0.540000	0.68198	AAC	G|0.607;C|0.393	0.393	strong		0.622	MUC4-015	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341862.1	NM_018406	
CPT1B	1375	hgsc.bcm.edu	37	22	51015838	51015838	+	Missense_Mutation	SNP	T	T	C	rs3213445	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:51015838T>C	ENST00000360719.2	-	3	333	c.196A>G	c.(196-198)Atc>Gtc	p.I66V	CPT1B_ENST00000312108.7_Missense_Mutation_p.I66V|CPT1B_ENST00000457250.1_Missense_Mutation_p.I66V|CPT1B_ENST00000440709.1_Missense_Mutation_p.I66V|CPT1B_ENST00000405237.3_Missense_Mutation_p.I66V|CPT1B_ENST00000395650.2_Missense_Mutation_p.I66V|CHKB-CPT1B_ENST00000452668.1_5'Flank|CPT1B_ENST00000434492.2_5'UTR|CHKB-CPT1B_ENST00000453634.1_3'UTR|CHKB_ENST00000463053.1_5'Flank	NM_001145135.1|NM_152245.2	NP_001138607.1|NP_689451.1	Q92523	CPT1B_HUMAN	carnitine palmitoyltransferase 1B (muscle)	66			I -> V (in dbSNP:rs3213445).		carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	carnitine O-palmitoyltransferase activity (GO:0004095)			central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(7)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	22		all_cancers(38;8.8e-15)|all_epithelial(38;1.12e-12)|all_lung(38;3.07e-05)|Breast(42;6.27e-05)|Lung NSC(38;0.000813)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		all cancers(3;3.56e-77)|OV - Ovarian serous cystadenocarcinoma(4;5.39e-74)|Epithelial(4;5.58e-70)|GBM - Glioblastoma multiforme(4;5.59e-08)|LUAD - Lung adenocarcinoma(64;0.0016)|Lung(4;0.00942)|BRCA - Breast invasive adenocarcinoma(115;0.207)		GTTGCCATGATGACGACCAGC	0.602													T|||	896	0.178914	0.1218	0.1556	5008	,	,		20942	0.3948		0.0427	False		,,,				2504	0.1902				p.I66V	Esophageal Squamous(170;988 1933 25577 30295 48163)	Atlas-SNP	.											.	CPT1B	61	.	0			c.A196G						PASS	.	T	VAL/ILE,VAL/ILE,VAL/ILE,VAL/ILE,VAL/ILE,VAL/ILE,VAL/ILE	494,3912	230.1+/-244.4	26,442,1735	77.0	72.0	74.0		196,196,196,196,196,196,196	0.9	0.3	22	dbSNP_106	74	480,8120	139.8+/-196.4	12,456,3832	yes	missense,missense,missense,missense,missense,missense,missense	CPT1B	NM_001145134.1,NM_001145135.1,NM_001145136.1,NM_001145137.1,NM_004377.3,NM_152245.2,NM_152246.2	29,29,29,29,29,29,29	38,898,5567	CC,CT,TT		5.5814,11.212,7.4889	benign,benign,benign,benign,benign,benign,benign	66/739,66/773,66/692,66/773,66/773,66/773,66/773	51015838	974,12032	2203	4300	6503	SO:0001583	missense	1375	exon3			CCATGATGACGAC	U62733	CCDS14098.1, CCDS46734.1	22q13.33	2007-07-26			ENSG00000205560	ENSG00000205560			2329	protein-coding gene	gene with protein product		601987				9070950	Standard	NM_152245		Approved	M-CPT1, CPT1-M	uc003bmm.3	Q92523	OTTHUMG00000137390	ENST00000360719.2:c.196A>G	22.37:g.51015838T>C	ENSP00000353945:p.Ile66Val	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	123	56	0.455285	NM_001145135	B7Z4U4|B7Z5T8|E9PCP2|Q13389|Q99655|Q9BY90	Missense_Mutation	SNP	ENST00000360719.2	37	CCDS14098.1	377	0.17261904761904762	64	0.13008130081300814	56	0.15469613259668508	220	0.38461538461538464	37	0.048812664907651716	T	1.689	-0.504435	0.04261	0.11212	0.055814	ENSG00000205560	ENST00000405237;ENST00000312108;ENST00000360719;ENST00000457250;ENST00000440709;ENST00000395650;ENST00000417176	D;D;D;D;D;D;T	0.83250	-1.66;-1.66;-1.66;-1.56;-1.7;-1.66;0.21	5.25	0.879	0.19155	.	0.274240	0.34484	N	0.003934	T	0.00012	0.0000	N	0.00325	-1.645	0.09310	P	0.9999999999994522	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.27606	-1.0069	9	0.02654	T	1	-18.7341	10.8662	0.46856	0.0:0.7627:0.0:0.2373	rs3213445;rs17848477;rs59972630;rs3213445	66;66;66	E9PCP2;B7Z4U4;Q92523	.;.;CPT1B_HUMAN	V	66	ENSP00000385486:I66V;ENSP00000312189:I66V;ENSP00000353945:I66V;ENSP00000409342:I66V;ENSP00000414713:I66V;ENSP00000379011:I66V;ENSP00000406316:I66V	ENSP00000312189:I66V	I	-	1	0	CPT1B	49362704	0.874000	0.30092	0.305000	0.25099	0.973000	0.67179	2.530000	0.45641	0.008000	0.14787	-0.929000	0.02709	ATC	T|0.882;C|0.118	0.118	strong		0.602	CPT1B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317264.5	NM_152246	
FAHD1	81889	hgsc.bcm.edu	37	16	1877494	1877494	+	Silent	SNP	T	T	C	rs3743854	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:1877494T>C	ENST00000427358.2	+	1	270	c.264T>C	c.(262-264)gcT>gcC	p.A88A	HAGH_ENST00000397356.3_5'Flank|FAHD1_ENST00000382668.4_Silent_p.A88A|HAGH_ENST00000566709.1_5'Flank|HAGH_ENST00000455446.2_5'Flank|HAGH_ENST00000397353.2_5'Flank|FAHD1_ENST00000382666.4_Silent_p.A88A	NM_031208.3	NP_112485.1	Q6P587	FAHD1_HUMAN	fumarylacetoacetate hydrolase domain containing 1	88						cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	acetylpyruvate hydrolase activity (GO:0018773)|acylpyruvate hydrolase activity (GO:0047621)|fumarylpyruvate hydrolase activity (GO:0034545)|metal ion binding (GO:0046872)			NS(1)|large_intestine(1)|liver(1)|ovary(2)|urinary_tract(1)	6						TCCCCGAGGCTGCGGCCATGG	0.677													C|||	1007	0.201078	0.1831	0.2262	5008	,	,		18027	0.1746		0.1809	False		,,,				2504	0.2556				p.A88A		Atlas-SNP	.											.	FAHD1	18	.	0			c.T264C						PASS	.	C	,,	775,3617		82,611,1503	33.0	36.0	35.0		264,264,264	1.3	1.0	16	dbSNP_107	35	1312,7276		110,1092,3092	no	coding-synonymous,coding-synonymous,coding-synonymous	FAHD1	NM_001018104.2,NM_001142398.1,NM_031208.3	,,	192,1703,4595	CC,CT,TT		15.2771,17.6457,16.0786	,,	88/249,88/227,88/225	1877494	2087,10893	2196	4294	6490	SO:0001819	synonymous_variant	81889	exon1			CGAGGCTGCGGCC	BC063017	CCDS10448.1, CCDS32367.1, CCDS45380.1	16p13.3	2011-10-21	2004-08-19	2004-08-26	ENSG00000180185	ENSG00000180185			14169	protein-coding gene	gene with protein product			"""chromosome 16 open reading frame 36"""	C16orf36		21878618	Standard	NM_001018104		Approved	DKFZP566J2046	uc002cnd.3	Q6P587	OTTHUMG00000128663	ENST00000427358.2:c.264T>C	16.37:g.1877494T>C		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	91	70	0.769231	NM_031208	B1AK40|B1AK41|Q6FIC7|Q96RY1|Q9H0N6	Silent	SNP	ENST00000427358.2	37	CCDS10448.1																																																																																			T|0.840;C|0.160	0.160	strong		0.677	FAHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250550.2	NM_001018104	
CRTAP	10491	hgsc.bcm.edu	37	3	33161898	33161898	+	Silent	SNP	C	C	T	rs4076086	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:33161898C>T	ENST00000320954.6	+	2	633	c.534C>T	c.(532-534)gaC>gaT	p.D178D	CRTAP_ENST00000449224.1_Silent_p.D178D|CRTAP_ENST00000485310.1_3'UTR	NM_006371.4	NP_006362.1	O75718	CRTAP_HUMAN	cartilage associated protein	178					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)			breast(1)|kidney(1)|large_intestine(1)|lung(3)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	9						ATCCTGATGACGAAATGATGa	0.433													C|||	1414	0.282348	0.3275	0.1369	5008	,	,		19729	0.5843		0.1044	False		,,,				2504	0.1963				p.D178D		Atlas-SNP	.											.	CRTAP	16	.	0			c.C534T						PASS	.	C		1423,2983	464.9+/-354.0	231,961,1011	130.0	116.0	121.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	534	-7.1	0.5	3	dbSNP_108	121	732,7868	177.8+/-227.3	29,674,3597	no	coding-synonymous	CRTAP	NM_006371.4		260,1635,4608	TT,TC,CC		8.5116,32.2969,16.5693		178/402	33161898	2155,10851	2203	4300	6503	SO:0001819	synonymous_variant	10491	exon2			TGATGACGAAATG	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.534C>T	3.37:g.33161898C>T		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	104	53	0.509615	NM_006371	B2RBL6	Silent	SNP	ENST00000320954.6	37	CCDS2657.1																																																																																			C|0.764;T|0.236	0.236	strong		0.433	CRTAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253246.3		
HLA-A	3105	hgsc.bcm.edu	37	6	29912368	29912368	+	Silent	SNP	C	C	T	rs1141891	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:29912368C>T	ENST00000396634.1	+	7	1328	c.987C>T	c.(985-987)gcC>gcT	p.A329A	HLA-A_ENST00000376802.2_Intron|HLA-A_ENST00000376809.5_Silent_p.A329A|HLA-A_ENST00000376806.5_Silent_p.A329A			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	329					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						TGGTCGCTGCCGTGATGTGGA	0.572									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|||	3421	0.683107	0.7216	0.7723	5008	,	,		18786	0.6885		0.6322	False		,,,				2504	0.6145				p.A329A		Atlas-SNP	.											.	HLA-A	89	.	0			c.C987T						PASS	.	C		2022,998		692,638,180	106.0	103.0	104.0		987	-3.0	0.0	6	dbSNP_86	104	3142,2270		984,1174,548	no	coding-synonymous	HLA-A	NM_002116.7		1676,1812,728	TT,TC,CC		41.9438,33.0464,38.7571		329/366	29912368	5164,3268	1510	2706	4216	SO:0001819	synonymous_variant	3105	exon5	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	CGCTGCCGTGATG	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.987C>T	6.37:g.29912368C>T		Somatic	208	0	0		WXS	Illumina HiSeq	Phase_I	155	52	0.335484	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Silent	SNP	ENST00000396634.1	37	CCDS34373.1																																																																																			C|0.359;T|0.641	0.641	strong		0.572	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
ITPR3	3710	hgsc.bcm.edu	37	6	33658780	33658780	+	Silent	SNP	C	C	T	rs35506178	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:33658780C>T	ENST00000374316.5	+	53	8179	c.7119C>T	c.(7117-7119)gcC>gcT	p.A2373A	ITPR3_ENST00000605930.1_Silent_p.A2373A			Q14573	ITPR3_HUMAN	inositol 1,4,5-trisphosphate receptor, type 3	2373					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|calcium ion transport into cytosol (GO:0060402)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|long-term synaptic potentiation (GO:0060291)|memory (GO:0007613)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|regulation of insulin secretion (GO:0050796)|response to calcium ion (GO:0051592)|sensory perception of bitter taste (GO:0050913)|sensory perception of sweet taste (GO:0050916)|sensory perception of umami taste (GO:0050917)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	apical part of cell (GO:0045177)|brush border (GO:0005903)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|myelin sheath (GO:0043209)|neuronal cell body (GO:0043025)|nuclear outer membrane (GO:0005640)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|platelet dense tubular network membrane (GO:0031095)|receptor complex (GO:0043235)	inositol 1,3,4,5 tetrakisphosphate binding (GO:0043533)|inositol 1,4,5 trisphosphate binding (GO:0070679)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|inositol hexakisphosphate binding (GO:0000822)|intracellular ligand-gated calcium channel activity (GO:0005218)|phosphatidylinositol binding (GO:0035091)			NS(1)|breast(6)|central_nervous_system(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|liver(1)|lung(24)|ovary(8)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	85					Caffeine(DB00201)	TGCTGACAGCCCTGCTGGCCC	0.577													C|||	89	0.0177716	0.003	0.013	5008	,	,		21516	0.0119		0.0517	False		,,,				2504	0.0123				p.A2373A		Atlas-SNP	.											.	ITPR3	409	.	0			c.C7119T						PASS	.	C		58,4348	55.5+/-91.7	1,56,2146	150.0	122.0	131.0		7119	1.8	1.0	6	dbSNP_126	131	431,8169	132.8+/-190.4	10,411,3879	no	coding-synonymous	ITPR3	NM_002224.3		11,467,6025	TT,TC,CC		5.0116,1.3164,3.7598		2373/2672	33658780	489,12517	2203	4300	6503	SO:0001819	synonymous_variant	3710	exon52			GACAGCCCTGCTG	D26351	CCDS4783.1	6p21.31	2011-11-24	2011-04-28		ENSG00000096433	ENSG00000096433		"""Ion channels / Inositol triphosphate receptors"""	6182	protein-coding gene	gene with protein product		147267	"""inositol 1,4,5-triphosphate receptor, type 3"""			8081734, 8288584	Standard	NM_002224		Approved	IP3R3	uc021ywr.1	Q14573	OTTHUMG00000014532	ENST00000374316.5:c.7119C>T	6.37:g.33658780C>T		Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	162	81	0.5	NM_002224	Q14649|Q5TAQ2	Silent	SNP	ENST00000374316.5	37	CCDS4783.1																																																																																			C|0.966;T|0.034	0.034	strong		0.577	ITPR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040204.2	NM_002224	
ADAMTSL1	92949	hgsc.bcm.edu	37	9	18829952	18829952	+	Missense_Mutation	SNP	A	A	G	rs41304755	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:18829952A>G	ENST00000380548.4	+	23	4565	c.4226A>G	c.(4225-4227)gAt>gGt	p.D1409G	ADAMTSL1_ENST00000380545.5_Missense_Mutation_p.D110G	NM_001040272.5	NP_001035362.3	Q8N6G6	ATL1_HUMAN	ADAMTS-like 1	1409	Ig-like C2-type 4.			D -> G (in Ref. 3; BAC03925). {ECO:0000305}.		proteinaceous extracellular matrix (GO:0005578)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|liver(2)|lung(17)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	42				GBM - Glioblastoma multiforme(50;1.29e-17)		CTGGTCCTGGATCCTGGGAAT	0.552													A|||	548	0.109425	0.0129	0.2003	5008	,	,		19684	0.0139		0.2465	False		,,,				2504	0.1329				p.D1409G		Atlas-SNP	.											.	ADAMTSL1	306	.	0			c.A4226G						PASS	.	A	GLY/ASP	175,3935		4,167,1884	64.0	64.0	64.0		4226	4.5	1.0	9	dbSNP_127	64	2038,6368		257,1524,2422	yes	missense	ADAMTSL1	NM_001040272.5	94	261,1691,4306	GG,GA,AA		24.2446,4.2579,17.6814	benign	1409/1763	18829952	2213,10303	2055	4203	6258	SO:0001583	missense	92949	exon23			TCCTGGATCCTGG	AF176313	CCDS6485.1, CCDS47954.1	9p21.3	2013-01-11			ENSG00000178031	ENSG00000178031		"""Immunoglobulin superfamily / I-set domain containing"""	14632	protein-coding gene	gene with protein product	"""punctin"""	609198	"""chromosome 9 open reading frame 94"""	C9orf94		9628581, 11805097	Standard	NM_001040272		Approved	ADAMTSR1, FLJ35283	uc003zne.4	Q8N6G6	OTTHUMG00000019604	ENST00000380548.4:c.4226A>G	9.37:g.18829952A>G	ENSP00000369921:p.Asp1409Gly	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	98	39	0.397959	NM_001040272	A6PVN1|A8K7E1|Q496M6|Q496M8|Q5T708|Q5VZT8|Q8NAI9|Q96RW4|Q9BXY3	Missense_Mutation	SNP	ENST00000380548.4	37	CCDS47954.1	276	0.12637362637362637	6	0.012195121951219513	73	0.20165745856353592	6	0.01048951048951049	191	0.2519788918205805	A	12.05	1.822179	0.32237	0.042579	0.242446	ENSG00000178031	ENST00000380548;ENST00000380545;ENST00000316239;ENST00000380541;ENST00000380538	T;T;T	0.66995	-0.24;-0.24;-0.24	5.81	4.48	0.54585	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.472937	0.24393	N	0.038912	T	0.00012	0.0000	L	0.39898	1.24	0.36876	P	0.11082199999999998	B;B	0.28128	0.137;0.201	B;B	0.28385	0.085;0.089	T	0.07673	-1.0760	9	0.29301	T	0.29	.	6.0982	0.20033	0.8341:0.0:0.1659:0.0	rs41304755	110;1409	Q8N6G6-6;Q8N6G6	.;ATL1_HUMAN	G	1409;110;113;113;11	ENSP00000369921:D1409G;ENSP00000369918:D110G;ENSP00000369911:D11G	ENSP00000325584:D113G	D	+	2	0	ADAMTSL1	18819952	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.508000	0.45450	2.225000	0.72522	0.533000	0.62120	GAT	A|0.852;G|0.148	0.148	strong		0.552	ADAMTSL1-012	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401206.1		
MYO7A	4647	hgsc.bcm.edu	37	11	76917220	76917220	+	Silent	SNP	A	A	G	rs2276293	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:76917220A>G	ENST00000409709.3	+	41	5987	c.5715A>G	c.(5713-5715)aaA>aaG	p.K1905K	MYO7A_ENST00000458637.2_Silent_p.K1867K|MYO7A_ENST00000605744.1_3'UTR|MYO7A_ENST00000409619.2_Silent_p.K1856K	NM_000260.3	NP_000251.3	Q13402	MYO7A_HUMAN	myosin VIIA	1905	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						TTTTCCACAAAGTCTACTTCC	0.607													g|||	2779	0.554912	0.7708	0.5994	5008	,	,		18276	0.4683		0.505	False		,,,				2504	0.3722				p.K1905K		Atlas-SNP	.											.	MYO7A	164	.	0			c.A5715G						PASS	.		,	2825,1195		1007,811,192	79.0	90.0	87.0		5715,5601	1.1	1.0	11	dbSNP_100	87	4008,4312		969,2070,1121	no	coding-synonymous,coding-synonymous	MYO7A	NM_000260.3,NM_001127180.1	,	1976,2881,1313	GG,GA,AA		48.1731,29.7264,44.6272	,	1905/2216,1867/2176	76917220	6833,5507	2010	4160	6170	SO:0001819	synonymous_variant	4647	exon41			CCACAAAGTCTAC	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.5715A>G	11.37:g.76917220A>G		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	91	70	0.769231	NM_000260	B9A011|F8VUN5|P78427|Q13321|Q14785|Q92821|Q92822	Silent	SNP	ENST00000409709.3	37	CCDS53683.1																																																																																			A|0.427;G|0.573	0.573	strong		0.607	MYO7A-001	KNOWN	non_canonical_conserved|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000328133.1	NM_000260	
OR10H5	284433	hgsc.bcm.edu	37	19	15905661	15905661	+	Missense_Mutation	SNP	C	C	A	rs67455341	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:15905661C>A	ENST00000308940.8	+	1	901	c.803C>A	c.(802-804)tCt>tAt	p.S268Y		NM_001004466.1	NP_001004466.1	Q8NGA6	O10H5_HUMAN	olfactory receptor, family 10, subfamily H, member 5	268						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(1)|lung(9)|ovary(1)	20						GGTCCCCAGTCTCCGGAAGGA	0.577													.|||	1121	0.223842	0.3812	0.2565	5008	,	,		16995	0.002		0.2952	False		,,,				2504	0.1431				p.S268Y		Atlas-SNP	.											.	OR10H5	49	.	0			c.C803A						PASS	.	C	TYR/SER	1626,2780		303,1020,880	114.0	93.0	100.0		803	2.7	0.0	19	dbSNP_130	100	2161,6439		294,1573,2433	no	missense	OR10H5	NM_001004466.1	144	597,2593,3313	AA,AC,CC		25.1279,36.9042,29.1173	possibly-damaging	268/316	15905661	3787,9219	2203	4300	6503	SO:0001583	missense	284433	exon1			CCCAGTCTCCGGA	AC011537	CCDS32940.1	19p13.12	2013-09-24			ENSG00000172519	ENSG00000172519		"""GPCR / Class A : Olfactory receptors"""	15389	protein-coding gene	gene with protein product							Standard	NM_001004466		Approved		uc010xos.2	Q8NGA6	OTTHUMG00000182284	ENST00000308940.8:c.803C>A	19.37:g.15905661C>A	ENSP00000310704:p.Ser268Tyr	Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	150	88	0.586667	NM_001004466	Q6IFJ0|Q96R60	Missense_Mutation	SNP	ENST00000308940.8	37	CCDS32940.1	515	0.2358058608058608	177	0.3597560975609756	114	0.3149171270718232	1	0.0017482517482517483	223	0.2941952506596306	.	8.445	0.851648	0.17034	0.369042	0.251279	ENSG00000172519	ENST00000308940	T	0.00277	8.34	3.88	2.73	0.32206	GPCR, rhodopsin-like superfamily (1);	0.449535	0.18991	N	0.125583	T	0.00012	0.0000	M	0.85859	2.78	0.80722	P	0.0	D	0.53312	0.959	P	0.62649	0.905	T	0.36261	-0.9755	9	0.72032	D	0.01	.	9.6663	0.39986	0.0:0.6307:0.3693:0.0	.	268	Q8NGA6	O10H5_HUMAN	Y	268	ENSP00000310704:S268Y	ENSP00000310704:S268Y	S	+	2	0	OR10H5	15766661	0.000000	0.05858	0.019000	0.16419	0.035000	0.12851	0.184000	0.16939	1.878000	0.54408	0.585000	0.79938	TCT	C|0.733;A|0.267	0.267	strong		0.577	OR10H5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460363.1		
ZNF831	128611	hgsc.bcm.edu	37	20	57768743	57768743	+	Missense_Mutation	SNP	C	C	T	rs56057707	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	76	0	0		WXS	Illumina HiSeq	Phase_I	91	42	0.461538	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	
ZC3HAV1	56829	hgsc.bcm.edu	37	7	138732497	138732497	+	Missense_Mutation	SNP	G	G	A	rs3735007	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	103	0	0		WXS	Illumina HiSeq	Phase_I	88	88	1	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	
POLR2B	5431	hgsc.bcm.edu	37	4	57889677	57889677	+	Silent	SNP	C	C	T	rs1056364	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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_ENST00000431623.2_Silent_p.S824S|POLR2B_ENST00000314595.5_Silent_p.S899S			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	127	1	0.00787402		WXS	Illumina HiSeq	Phase_I	98	97	0.989796	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	
ABCC5	10057	hgsc.bcm.edu	37	3	183685534	183685534	+	Silent	SNP	A	A	G	rs939336	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:183685534A>G	ENST00000334444.6	-	12	2022	c.1782T>C	c.(1780-1782)tgT>tgC	p.C594C	ABCC5_ENST00000265586.6_Silent_p.C594C	NM_005688.2	NP_005679.2	O15440	MRP5_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 5	594	ABC transporter 1. {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)	CCACACTGCCACAGATTCCAA	0.438													G|||	3464	0.691693	0.7897	0.5951	5008	,	,		19289	0.8621		0.5746	False		,,,				2504	0.5726				p.C594C		Atlas-SNP	.											.	ABCC5	142	.	0			c.T1782C						PASS	.	G		2946,902		1138,670,116	174.0	178.0	177.0		1782	-3.0	0.9	3	dbSNP_86	177	4670,3600		1313,2044,778	no	coding-synonymous	ABCC5	NM_005688.2		2451,2714,894	GG,GA,AA		43.5308,23.4407,37.1513		594/1438	183685534	7616,4502	1924	4135	6059	SO:0001819	synonymous_variant	10057	exon12			ACTGCCACAGATT	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.1782T>C	3.37:g.183685534A>G		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	92	38	0.413043	NM_005688	B9EIQ2|O14517|Q29ZA9|Q29ZB1|Q86UX3|Q86W30|Q9UN85|Q9UNP5|Q9UQC3	Silent	SNP	ENST00000334444.6	37	CCDS43176.1																																																																																			A|0.320;G|0.680	0.680	strong		0.438	ABCC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346350.1	NM_005688	
HIST1H1E	3008	hgsc.bcm.edu	37	6	26157219	26157219	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:26157219C>T	ENST00000304218.3	+	1	661	c.601C>T	c.(601-603)Cca>Tca	p.P201S	HIST1H2BD_ENST00000289316.2_5'Flank|HIST1H2BD_ENST00000377777.4_5'Flank	NM_005321.2	NP_005312.1	P10412	H14_HUMAN	histone cluster 1, H1e	201					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						GGCGGCTAAACCAAAGACCGC	0.527																																					p.P201S		Atlas-SNP	.											.	HIST1H1E	69	.	0			c.C601T						PASS	.						32.0	34.0	33.0					6																	26157219		2202	4299	6501	SO:0001583	missense	3008	exon1			GCTAAACCAAAGA	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.601C>T	6.37:g.26157219C>T	ENSP00000307705:p.Pro201Ser	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	71	10	0.140845	NM_005321	Q4VB25	Missense_Mutation	SNP	ENST00000304218.3	37	CCDS4586.1	.	.	.	.	.	.	.	.	.	.	.	11.35	1.612147	0.28712	.	.	ENSG00000168298	ENST00000304218	T	0.12672	2.66	5.48	4.56	0.56223	.	0.130977	0.52532	D	0.000076	T	0.07007	0.0178	L	0.59912	1.85	0.37467	D	0.915446	B	0.20261	0.043	B	0.14578	0.011	T	0.06427	-1.0827	10	0.31617	T	0.26	-1.4746	11.1455	0.48428	0.1401:0.7241:0.1358:0.0	.	201	P10412	H14_HUMAN	S	201	ENSP00000307705:P201S	ENSP00000307705:P201S	P	+	1	0	HIST1H1E	26265198	1.000000	0.71417	0.284000	0.24805	0.975000	0.68041	2.111000	0.41883	2.717000	0.92951	0.655000	0.94253	CCA	.	.	none		0.527	HIST1H1E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040084.1	NM_005321	
SLC25A13	10165	hgsc.bcm.edu	37	7	95800820	95800820	+	Silent	SNP	T	T	C	rs2301629	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:95800820T>C	ENST00000265631.5	-	12	1330	c.1194A>G	c.(1192-1194)ttA>ttG	p.L398L	SLC25A13_ENST00000542654.1_Silent_p.L290L|SLC25A13_ENST00000416240.2_Silent_p.L399L			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	176	0	0		WXS	Illumina HiSeq	Phase_I	136	74	0.544118	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	
MUC4	4585	hgsc.bcm.edu	37	3	195509784	195509784	+	Silent	SNP	C	C	T	rs61099195		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195509784C>T	ENST00000463781.3	-	2	9126	c.8667G>A	c.(8665-8667)gtG>gtA	p.V2889V	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Silent_p.V2889V	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.V2889V(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)		GACCTGTGGACACTGAGGAAG	0.587																																					p.V2889V		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	1	Substitution - coding silent(1)	stomach(1)	c.G8667A						scavenged	.						27.0	16.0	19.0					3																	195509784		685	1577	2262	SO:0001819	synonymous_variant	4585	exon2			TGTGGACACTGAG	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.8667G>A	3.37:g.195509784C>T		Somatic	65	1	0.0153846		WXS	Illumina HiSeq	Phase_I	93	53	0.569892	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Silent	SNP	ENST00000463781.3	37	CCDS54700.1																																																																																			C|0.250;T|0.750	0.750	weak		0.587	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
CSN3	1448	hgsc.bcm.edu	37	4	71115053	71115053	+	Silent	SNP	T	T	A	rs3775740	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:71115053T>A	ENST00000304954.3	+	4	512	c.426T>A	c.(424-426)ccT>ccA	p.P142P		NM_005212.2	NP_005203.2	Q9UNS2	CSN3_HUMAN	casein kappa	0					cullin deneddylation (GO:0010388)|in utero embryonic development (GO:0001701)|response to light stimulus (GO:0009416)|signal transduction (GO:0007165)	COP9 signalosome (GO:0008180)|cytoplasm (GO:0005737)				central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(5)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	18						CTGTTGAACCTACACCAGCTC	0.473													T|||	359	0.0716853	0.0862	0.0793	5008	,	,		16995	0.0308		0.1233	False		,,,				2504	0.0358				p.P142P		Atlas-SNP	.											.	CSN3	43	.	0			c.T426A						PASS	.	T		412,3994	204.5+/-226.7	19,374,1810	74.0	71.0	72.0		426	-3.1	0.0	4	dbSNP_107	72	1115,7485	231.9+/-265.7	61,993,3246	no	coding-synonymous	CSN3	NM_005212.2		80,1367,5056	AA,AT,TT		12.9651,9.3509,11.7407		142/183	71115053	1527,11479	2203	4300	6503	SO:0001819	synonymous_variant	1448	exon4			TGAACCTACACCA	U51899	CCDS3538.1	4q21.1	2014-02-19	2003-01-24	2003-01-31	ENSG00000171209	ENSG00000171209			2446	protein-coding gene	gene with protein product		601695	"""casein, kappa"""	CSN10		8863730, 9050925	Standard	NM_005212		Approved		uc003hfe.4	P07498	OTTHUMG00000129399	ENST00000304954.3:c.426T>A	4.37:g.71115053T>A		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	75	35	0.466667	NM_005212	B2R683|B4DY81|O43191|Q7LDR6	Silent	SNP	ENST00000304954.3	37	CCDS3538.1																																																																																			T|0.896;A|0.104	0.104	strong		0.473	CSN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251555.1	NM_005212	
PLCB2	5330	hgsc.bcm.edu	37	15	40589002	40589002	+	Silent	SNP	A	A	G	rs2229691	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:40589002A>G	ENST00000260402.3	-	14	1680	c.1431T>C	c.(1429-1431)acT>acC	p.T477T	PLCB2_ENST00000456256.2_Silent_p.T477T|PLCB2_ENST00000557821.1_Silent_p.T477T	NM_001284297.1|NM_004573.2	NP_001271226.1|NP_004564.2	Q00722	PLCB2_HUMAN	phospholipase C, beta 2	477					activation of phospholipase C activity (GO:0007202)|inositol phosphate metabolic process (GO:0043647)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|phospholipid metabolic process (GO:0006644)|sensory perception of bitter taste (GO:0050913)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)	calcium ion binding (GO:0005509)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|signal transducer activity (GO:0004871)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(13)|ovary(4)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(3)	39		all_cancers(109;9.35e-19)|all_epithelial(112;1.18e-15)|Lung NSC(122;2.45e-11)|all_lung(180;6.47e-10)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;9.38e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0508)		CCTCCCCACCAGTATCCTTAC	0.607													A|||	1779	0.355232	0.1293	0.4755	5008	,	,		19466	0.6736		0.2167	False		,,,				2504	0.3896				p.T477T		Atlas-SNP	.											.	PLCB2	177	.	0			c.T1431C						PASS	.	A		635,3191		58,519,1336	54.0	54.0	54.0		1431	-0.3	0.0	15	dbSNP_98	54	1913,6327		223,1467,2430	no	coding-synonymous	PLCB2	NM_004573.2		281,1986,3766	GG,GA,AA		23.216,16.597,21.1172		477/1186	40589002	2548,9518	1913	4120	6033	SO:0001819	synonymous_variant	5330	exon14			CCCACCAGTATCC		CCDS42020.1, CCDS61591.1, CCDS61592.1, CCDS73704.1	15q15.1	2012-01-23			ENSG00000137841	ENSG00000137841	3.1.4.11		9055	protein-coding gene	gene with protein product		604114				1644792, 9925923	Standard	XM_005254448		Approved	FLJ38135	uc001zld.3	Q00722	OTTHUMG00000172412	ENST00000260402.3:c.1431T>C	15.37:g.40589002A>G		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	46	20	0.434783	NM_004573	A8K6J2|B9EGH5	Silent	SNP	ENST00000260402.3	37	CCDS42020.1																																																																																			A|0.697;G|0.303	0.303	strong		0.607	PLCB2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000418430.1		
LETMD1	25875	hgsc.bcm.edu	37	12	51449729	51449729	+	Silent	SNP	T	T	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:51449729T>C	ENST00000262055.4	+	5	624	c.585T>C	c.(583-585)atT>atC	p.I195I	LETMD1_ENST00000547008.1_Intron|LETMD1_ENST00000418425.2_Silent_p.I208I|LETMD1_ENST00000550929.1_Silent_p.I139I|LETMD1_ENST00000552739.1_Silent_p.I78I|LETMD1_ENST00000548516.1_Intron|LETMD1_ENST00000380123.2_3'UTR	NM_015416.4	NP_056231.3	Q6P1Q0	LTMD1_HUMAN	LETM1 domain containing 1	195	LETM1.					integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)				central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(2)|lung(4)|skin(1)|urinary_tract(3)	16						CAGAAATTATTAGTTATTTAG	0.448																																					p.I208I		Atlas-SNP	.											LETMD1,brain,glioma,+2,1	LETMD1	33	1	0			c.T624C						scavenged	.						88.0	90.0	89.0					12																	51449729		2203	4300	6503	SO:0001819	synonymous_variant	25875	exon5			AATTATTAGTTAT	AF195651	CCDS8806.1, CCDS58231.1, CCDS73469.1	12q13.13	2006-04-12				ENSG00000050426			24241	protein-coding gene	gene with protein product	"""cervical cancer 1 protooncogene"""					12879013, 12061725	Standard	NM_015416		Approved	HCCR1	uc009zlw.3	Q6P1Q0	OTTHUMG00000169538	ENST00000262055.4:c.585T>C	12.37:g.51449729T>C		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	78	2	0.025641	NM_001243689	A6NER7|B3KXK7|Q6X2E4|Q6X2E5|Q7L2G9|Q7L690|Q8WXW6|Q96PK7|Q9BY59|Q9Y3X3	Silent	SNP	ENST00000262055.4	37	CCDS8806.1	.	.	.	.	.	.	.	.	.	.	T	1.344	-0.593333	0.03771	.	.	ENSG00000050426	ENST00000551931	.	.	.	5.08	1.53	0.23141	.	.	.	.	.	T	0.30541	0.0768	.	.	.	0.27776	N	0.943321	.	.	.	.	.	.	T	0.23797	-1.0178	4	.	.	.	-0.141	5.0243	0.14376	0.0:0.1675:0.2966:0.5359	.	.	.	.	S	13	.	.	L	+	2	0	LETMD1	49735996	0.009000	0.17119	0.018000	0.16275	0.387000	0.30353	-0.058000	0.11750	0.505000	0.28104	-0.313000	0.08912	TTA	.	.	none		0.448	LETMD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404710.1	NM_015416	
AIM1	202	hgsc.bcm.edu	37	6	106999822	106999822	+	Missense_Mutation	SNP	G	G	A	rs2297970	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	171	0	0		WXS	Illumina HiSeq	Phase_I	141	59	0.41844	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		
RRP7A	27341	hgsc.bcm.edu	37	22	42912097	42912097	+	Missense_Mutation	SNP	C	C	T	rs11553441	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:42912097C>T	ENST00000323013.6	-	3	277	c.262G>A	c.(262-264)Gta>Ata	p.V88I		NM_015703.4	NP_056518.2	Q9Y3A4	RRP7A_HUMAN	ribosomal RNA processing 7 homolog A (S. cerevisiae)	88	RRM.		V -> I (in dbSNP:rs11553441).				nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|liver(2)|lung(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	10						TGCAACTCTACAGACTGGACG	0.627													C|||	381	0.0760783	0.0567	0.1772	5008	,	,		19105	0.003		0.1461	False		,,,				2504	0.0337				p.V88I		Atlas-SNP	.											.	RRP7A	25	.	0			c.G262A						PASS	.	C	ILE/VAL	342,4064	174.1+/-203.8	13,316,1874	53.0	50.0	51.0		262	2.9	0.1	22	dbSNP_120	51	1182,7418	238.1+/-269.7	92,998,3210	yes	missense	RRP7A	NM_015703.4	29	105,1314,5084	TT,TC,CC		13.7442,7.7621,11.7177	benign	88/281	42912097	1524,11482	2203	4300	6503	SO:0001583	missense	27341	exon3			ACTCTACAGACTG	BC035992	CCDS14036.1	22q13.2	2008-08-08			ENSG00000189306	ENSG00000189306			24286	protein-coding gene	gene with protein product						10810093, 12087473	Standard	NM_015703		Approved	CGI-96	uc003bcq.3	Q9Y3A4	OTTHUMG00000150891	ENST00000323013.6:c.262G>A	22.37:g.42912097C>T	ENSP00000321449:p.Val88Ile	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	68	32	0.470588	NM_015703	A4FTX2|B2RBG4|Q0VAD0|Q5JZ94|Q6P4B5|Q8IVR9|Q8IVY0|Q8N5Q3|Q8NEY6|Q9Y3H5	Missense_Mutation	SNP	ENST00000323013.6	37	CCDS14036.1	204	0.09340659340659341	25	0.0508130081300813	71	0.19613259668508287	1	0.0017482517482517483	107	0.14116094986807387	C	9.919	1.211667	0.22289	0.077621	0.137442	ENSG00000189306	ENST00000323013	T	0.18502	2.21	3.93	2.9	0.33743	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (1);	0.000000	0.85682	D	0.000000	T	0.00039	0.0001	M	0.65320	2	0.09310	P	0.9999962723	P	0.51057	0.941	B	0.42030	0.373	T	0.28618	-1.0038	9	0.45353	T	0.12	-21.505	12.1146	0.53858	0.0:0.9124:0.0:0.0876	rs11553441;rs11553441	88	Q9Y3A4	RRP7A_HUMAN	I	88	ENSP00000321449:V88I	ENSP00000321449:V88I	V	-	1	0	RRP7A	41242041	0.994000	0.37717	0.050000	0.19076	0.004000	0.04260	3.845000	0.55880	0.946000	0.37632	-0.346000	0.07831	GTA	C|0.893;T|0.107	0.107	strong		0.627	RRP7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320451.1	NM_015703	
CCAR2	57805	hgsc.bcm.edu	37	8	22471824	22471824	+	Silent	SNP	G	G	A	rs3736147	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:22471824G>A	ENST00000308511.4	+	9	1173	c.924G>A	c.(922-924)tcG>tcA	p.S308S	CCAR2_ENST00000520861.1_5'UTR|RP11-582J16.5_ENST00000521025.1_RNA|CCAR2_ENST00000389279.3_Silent_p.S308S			Q8N163	CCAR2_HUMAN	cell cycle and apoptosis regulator 2	308					cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|mRNA processing (GO:0006397)|negative regulation of catalytic activity (GO:0043086)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902230)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA damage checkpoint (GO:2000003)|regulation of circadian rhythm (GO:0042752)|regulation of DNA-templated transcription, elongation (GO:0032784)|regulation of protein stability (GO:0031647)|response to UV (GO:0009411)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|DBIRD complex (GO:0044609)|mitochondrial matrix (GO:0005759)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)|poly(A) RNA binding (GO:0044822)|RNA polymerase II core binding (GO:0000993)										CTTATAGTTCGAAGGTAAGCT	0.557													C|||	1349	0.269369	0.1135	0.3026	5008	,	,		20178	0.256		0.335	False		,,,				2504	0.4029				p.S308S		Atlas-SNP	.											.	KIAA1967	72	.	0			c.G924A						PASS	.	C		635,3771		44,547,1612	62.0	57.0	59.0		924	2.1	1.0	8	dbSNP_107	59	2782,5818		449,1884,1967	no	coding-synonymous	KIAA1967	NM_021174.5		493,2431,3579	AA,AG,GG		32.3488,14.4122,26.2725		308/924	22471824	3417,9589	2203	4300	6503	SO:0001819	synonymous_variant	57805	exon9			TAGTTCGAAGGTA	AL834351	CCDS34863.1	8p22	2013-08-22	2013-08-22	2013-08-22		ENSG00000158941			23360	protein-coding gene	gene with protein product	"""deleted in breast cancer"""	607359	"""KIAA1967"""	KIAA1967		12370419	Standard	NM_021174		Approved	DBC-1, DBC1, NET35	uc003xci.3	Q8N163		ENST00000308511.4:c.924G>A	8.37:g.22471824G>A		Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	151	115	0.761589	NM_021174	A6NL03|B2RB79|D3DSR6|Q6P0Q9|Q8N3G7|Q8N8M1|Q8TF34|Q9H9Q9|Q9HD12|Q9NT55	Silent	SNP	ENST00000308511.4	37	CCDS34863.1																																																																																			G|0.741;A|0.259	0.259	strong		0.557	CCAR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375865.1	NM_021174	
ADAMTSL3	57188	hgsc.bcm.edu	37	15	84706461	84706461	+	Missense_Mutation	SNP	C	C	T	rs950169	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:84706461C>T	ENST00000286744.5	+	30	5203	c.4979C>T	c.(4978-4980)aCa>aTa	p.T1660I	ADAMTSL3_ENST00000567476.1_Intron	NM_207517.2	NP_997400.2	P82987	ATL3_HUMAN	ADAMTS-like 3	1660	PLAC. {ECO:0000255|PROSITE- ProRule:PRU00233}.		T -> I (in dbSNP:rs950169).			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)			GGAGACTGCACAGACACAACT	0.338													C|||	646	0.128994	0.0113	0.1787	5008	,	,		19381	0.0536		0.2734	False		,,,				2504	0.182				p.T1660I		Atlas-SNP	.											.	ADAMTSL3	290	.	0			c.C4979T						PASS	.	C	ILE/THR	210,4196	129.0+/-165.8	6,198,1999	118.0	112.0	114.0		4979	-0.0	0.7	15	dbSNP_86	114	2323,6275	390.3+/-343.2	313,1697,2289	yes	missense	ADAMTSL3	NM_207517.2	89	319,1895,4288	TT,TC,CC		27.0179,4.7662,19.4786	benign	1660/1692	84706461	2533,10471	2203	4299	6502	SO:0001583	missense	57188	exon30			ACTGCACAGACAC	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.4979C>T	15.37:g.84706461C>T	ENSP00000286744:p.Thr1660Ile	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	81	81	1	NM_207517	A1A566|A1A567|Q9ULI7	Missense_Mutation	SNP	ENST00000286744.5	37	CCDS10326.1	326	0.14926739926739926	8	0.016260162601626018	72	0.19889502762430938	31	0.05419580419580419	215	0.2836411609498681	C	12.18	1.861131	0.32884	0.047662	0.270179	ENSG00000156218	ENST00000286744	T	0.44083	0.93	4.92	-0.0221	0.13948	PLAC (2);	1.471100	0.04514	N	0.383369	T	0.00012	0.0000	L	0.29908	0.895	0.09310	P	0.999999831154	B	0.02656	0.0	B	0.04013	0.001	T	0.27157	-1.0082	9	0.45353	T	0.12	.	3.8634	0.09005	0.3118:0.3571:0.0:0.3311	rs950169;rs17371948;rs52790868;rs58129969;rs950169	1660	P82987	ATL3_HUMAN	I	1660	ENSP00000286744:T1660I	ENSP00000286744:T1660I	T	+	2	0	ADAMTSL3	82497465	1.000000	0.71417	0.731000	0.30826	0.988000	0.76386	2.507000	0.45442	0.071000	0.16664	0.591000	0.81541	ACA	T|0.150;G|0.006	0.150	strong		0.338	ADAMTSL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304007.2	NM_207517	
GYG1	2992	hgsc.bcm.edu	37	3	148727133	148727133	+	Silent	SNP	G	G	A	rs4938	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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_ENST00000479119.1_3'UTR|GYG1_ENST00000296048.6_Silent_p.P184P|GYG1_ENST00000483267.1_Intron	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	89	0	0		WXS	Illumina HiSeq	Phase_I	65	23	0.353846	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	
KCNT1	57582	hgsc.bcm.edu	37	9	138669261	138669261	+	Silent	SNP	G	G	A	rs914428	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:138669261G>A	ENST00000263604.3	+	21	2370	c.2370G>A	c.(2368-2370)acG>acA	p.T790T	KCNT1_ENST00000298480.5_Silent_p.T809T|KCNT1_ENST00000371757.2_Silent_p.T809T|KCNT1_ENST00000486577.2_Silent_p.T768T|KCNT1_ENST00000490355.2_Silent_p.T788T|KCNT1_ENST00000491806.2_Silent_p.T776T|KCNT1_ENST00000488444.2_Silent_p.T790T|KCNT1_ENST00000487664.1_Silent_p.T764T			Q5JUK3	KCNT1_HUMAN	potassium channel, subfamily T, member 1	790					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)		CGGCAGAGACGGCCGGCAATG	0.582													G|||	3266	0.652157	0.5461	0.6916	5008	,	,		16278	0.5744		0.6779	False		,,,				2504	0.8211				p.T809T		Atlas-SNP	.											.	KCNT1	139	.	0			c.G2427A						PASS	.	G		2509,1897	628.7+/-395.1	703,1103,397	105.0	91.0	96.0		2427	-2.5	1.0	9	dbSNP_86	96	5749,2851	673.3+/-403.0	1937,1875,488	no	coding-synonymous	KCNT1	NM_020822.2		2640,2978,885	AA,AG,GG		33.1512,43.0549,36.5062		809/1236	138669261	8258,4748	2203	4300	6503	SO:0001819	synonymous_variant	57582	exon21			AGAGACGGCCGGC	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.2370G>A	9.37:g.138669261G>A		Somatic	190	0	0		WXS	Illumina HiSeq	Phase_I	153	79	0.51634	NM_020822	B3KXF7|B7ZVY4|B9EGP2|G5E9V0|Q9P2C5	Silent	SNP	ENST00000263604.3	37																																																																																				G|0.379;A|0.621	0.621	strong		0.582	KCNT1-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_020822	
HEG1	57493	hgsc.bcm.edu	37	3	124732618	124732618	+	Missense_Mutation	SNP	A	A	G	rs6790837	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	190	0	0		WXS	Illumina HiSeq	Phase_I	148	64	0.432432	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	
TYW1	55253	hgsc.bcm.edu	37	7	66648157	66648157	+	Silent	SNP	C	C	T	rs4145350	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	113	0	0		WXS	Illumina HiSeq	Phase_I	81	33	0.407407	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	
IGLL5	100423062	hgsc.bcm.edu	37	22	23230407	23230407	+	Missense_Mutation	SNP	C	C	G	rs538609996	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:23230407C>G	ENST00000526893.1	+	1	448	c.174C>G	c.(172-174)agC>agG	p.S58R	IGLL5_ENST00000531372.1_Missense_Mutation_p.S58R|IGLL5_ENST00000532223.2_Missense_Mutation_p.S58R|hsa-mir-5571_ENST00000577998.1_RNA	NM_001178126.1	NP_001171597.1	B9A064	IGLL5_HUMAN	immunoglobulin lambda-like polypeptide 5	58						extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|urinary_tract(1)	7						CAGTTGGAAGCAGCCGATCCA	0.662																																					p.S58R		Atlas-SNP	.											.	IGLL5	26	.	0			c.C174G						PASS	.																																			SO:0001583	missense	100423062	exon1			TGGAAGCAGCCGA	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.174C>G	22.37:g.23230407C>G	ENSP00000431254:p.Ser58Arg	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	110	22	0.2	NM_001178126		Missense_Mutation	SNP	ENST00000526893.1	37	CCDS54506.1	.	.	.	.	.	.	.	.	.	.	C	10.98	1.505085	0.26949	.	.	ENSG00000254709	ENST00000532223;ENST00000526893;ENST00000531372	T;T	0.00585	6.4;6.39	3.92	0.621	0.17643	.	.	.	.	.	T	0.00524	0.0017	L	0.32530	0.975	0.09310	N	1	B	0.21225	0.053	B	0.19148	0.024	T	0.46555	-0.9183	9	0.72032	D	0.01	.	4.068	0.09869	0.0:0.5528:0.224:0.2232	.	58	B9A064	IGLL5_HUMAN	R	58	ENSP00000436353:S58R;ENSP00000431254:S58R	ENSP00000431254:S58R	S	+	3	2	IGLL5	21560407	0.001000	0.12720	0.001000	0.08648	0.013000	0.08279	0.487000	0.22356	0.228000	0.21019	-0.152000	0.13540	AGC	.	.	none		0.662	IGLL5-002	KNOWN	basic|appris_candidate|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000385699.1	NM_001178126	
ANXA13	312	hgsc.bcm.edu	37	8	124710664	124710664	+	Missense_Mutation	SNP	C	C	T	rs6995099	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:124710664C>T	ENST00000419625.1	-	4	394	c.322G>A	c.(322-324)Gtc>Atc	p.V108I	ANXA13_ENST00000262219.6_Missense_Mutation_p.V149I	NM_004306.2	NP_004297.2	P27216	ANX13_HUMAN	annexin A13	108			V -> I (in dbSNP:rs6995099).		cell differentiation (GO:0030154)|negative regulation of Golgi to plasma membrane protein transport (GO:0042997)|positive regulation of Golgi to plasma membrane protein transport (GO:0042998)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|exocytic vesicle (GO:0070382)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|phosphatidylglycerol binding (GO:1901611)|phosphatidylserine binding (GO:0001786)			breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|liver(1)|lung(11)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(2)	25	Lung NSC(37;2.06e-11)|Ovarian(258;0.00579)|all_neural(195;0.0741)		STAD - Stomach adenocarcinoma(47;0.00288)			TCAATGAGGACGGACTCATCT	0.597													C|||	257	0.0513179	0.0643	0.062	5008	,	,		19912	0.005		0.0845	False		,,,				2504	0.0399				p.V149I		Atlas-SNP	.											.	ANXA13	38	.	0			c.G445A						PASS	.	C	ILE/VAL,ILE/VAL	313,4093	170.1+/-200.6	14,285,1904	108.0	98.0	102.0		445,322	-2.2	0.0	8	dbSNP_116	102	640,7960	163.6+/-216.1	20,600,3680	yes	missense,missense	ANXA13	NM_001003954.1,NM_004306.2	29,29	34,885,5584	TT,TC,CC		7.4419,7.1039,7.3274	benign,benign	149/358,108/317	124710664	953,12053	2203	4300	6503	SO:0001583	missense	312	exon5			TGAGGACGGACTC	Z11502	CCDS34939.1, CCDS47917.1	8q24.13	2005-11-09			ENSG00000104537	ENSG00000104537		"""Annexins"""	536	protein-coding gene	gene with protein product		602573		ANX13		9503022	Standard	NM_004306		Approved		uc003yqt.3	P27216	OTTHUMG00000164987	ENST00000419625.1:c.322G>A	8.37:g.124710664C>T	ENSP00000390809:p.Val108Ile	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	117	102	0.871795	NM_001003954	Q9BQR5	Missense_Mutation	SNP	ENST00000419625.1	37	CCDS47917.1	129	0.059065934065934064	39	0.07926829268292683	24	0.06629834254143646	1	0.0017482517482517483	65	0.08575197889182058	C	13.11	2.138053	0.37728	0.071039	0.074419	ENSG00000104537	ENST00000262219;ENST00000419625;ENST00000520519	T;T;T	0.03635	3.86;3.86;3.86	5.67	-2.2	0.06994	Annexin repeat, conserved site (1);	0.422095	0.27956	N	0.017164	T	0.00144	0.0004	M	0.63208	1.945	0.53005	P	3.100000000000325E-5	P;P	0.37731	0.607;0.553	B;B	0.33690	0.168;0.105	T	0.34625	-0.9821	9	0.48119	T	0.1	.	0.8559	0.01182	0.2909:0.2147:0.2937:0.2007	rs6995099;rs52822457;rs59748842;rs6995099	108;149	P27216;P27216-2	ANX13_HUMAN;.	I	149;108;79	ENSP00000262219:V149I;ENSP00000390809:V108I;ENSP00000429358:V79I	ENSP00000262219:V149I	V	-	1	0	ANXA13	124779845	0.021000	0.18746	0.014000	0.15608	0.633000	0.38033	0.327000	0.19663	-0.417000	0.07461	-0.291000	0.09656	GTC	C|0.936;T|0.064	0.064	strong		0.597	ANXA13-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381308.1	NM_004306	
ESRRB	2103	hgsc.bcm.edu	37	14	76964655	76964655	+	Missense_Mutation	SNP	C	C	T	rs35774316|rs61742642	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:76964655C>T	ENST00000509242.1	+	8	1254	c.1156C>T	c.(1156-1158)Ccc>Tcc	p.P386S	ESRRB_ENST00000380887.2_Missense_Mutation_p.P386S|RP11-187O7.3_ENST00000554926.1_lincRNA|ESRRB_ENST00000261532.7_Missense_Mutation_p.P386S|ESRRB_ENST00000556177.1_Missense_Mutation_p.P386S	NM_004452.3	NP_004443.3	O95718	ERR2_HUMAN	estrogen-related receptor beta	386			P -> S (in dbSNP:rs61742642). {ECO:0000269|PubMed:18179891}.		gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)|trophectodermal cell proliferation (GO:0001834)|trophectodermal cellular morphogenesis (GO:0001831)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|sequence-specific DNA binding (GO:0043565)|steroid binding (GO:0005496)|steroid hormone receptor activity (GO:0003707)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(4)|lung(14)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	24				BRCA - Breast invasive adenocarcinoma(234;0.0213)		CCATGAGGAGCCCTGGAGGAC	0.612													C|||	351	0.0700879	0.0166	0.1182	5008	,	,		14192	0.1161		0.0567	False		,,,				2504	0.0746				p.P386S		Atlas-SNP	.											ESRRB_ENST00000380887,NS,carcinoma,0,3	ESRRB	114	3	0			c.C1156T						PASS	.	C	SER/PRO	111,4295	78.8+/-117.2	2,107,2094	27.0	27.0	27.0		1156	5.6	1.0	14	dbSNP_129	27	585,8015	145.6+/-201.3	23,539,3738	yes	missense	ESRRB	NM_004452.3	74	25,646,5832	TT,TC,CC		6.8023,2.5193,5.3514	benign	386/509	76964655	696,12310	2203	4300	6503	SO:0001583	missense	2103	exon9			GAGGAGCCCTGGA	X51417	CCDS9850.1, CCDS9850.2	14q24.3	2013-01-16				ENSG00000119715		"""Nuclear hormone receptors"""	3473	protein-coding gene	gene with protein product		602167	"""deafness, autosomal recessive 35"""	ESRL2, DFNB35		3267207, 9344655, 18179891	Standard	NM_004452		Approved	ERR2, ERRbeta, NR3B2, ERRb	uc001xsr.3	O95718		ENST00000509242.1:c.1156C>T	14.37:g.76964655C>T	ENSP00000422488:p.Pro386Ser	Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	101	54	0.534653	NM_004452	A2VDJ2|B6ZGU4|Q5F0P7|Q5F0P8|Q9HCB4	Missense_Mutation	SNP	ENST00000509242.1	37	CCDS9850.2	155	0.07097069597069597	8	0.016260162601626018	37	0.10220994475138122	62	0.10839160839160839	48	0.0633245382585752	C	17.45	3.393905	0.62066	0.025193	0.068023	ENSG00000119715	ENST00000512784;ENST00000509242;ENST00000556177;ENST00000380887;ENST00000261532	D;D;D;D;D	0.95980	-3.87;-3.87;-3.87;-3.87;-3.87	5.57	5.57	0.84162	.	0.000000	0.85682	D	0.000000	T	0.30792	0.0776	L	0.39085	1.19	0.09310	P	0.99999999763753	P;P	0.37548	0.599;0.599	B;B	0.39419	0.299;0.202	T	0.70208	-0.4935	9	0.33141	T	0.24	.	19.5447	0.95287	0.0:1.0:0.0:0.0	rs61742642	386;391	Q5F0P7;E7EWD9	.;.	S	391;386;386;386;386	ENSP00000424992:P391S;ENSP00000422488:P386S;ENSP00000451658:P386S;ENSP00000370270:P386S;ENSP00000261532:P386S	ENSP00000261532:P386S	P	+	1	0	ESRRB	76034408	1.000000	0.71417	0.999000	0.59377	0.988000	0.76386	7.818000	0.86416	2.611000	0.88343	0.561000	0.74099	CCC	C|0.945;T|0.055	0.055	strong		0.612	ESRRB-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000360663.1		
C5	727	hgsc.bcm.edu	37	9	123776220	123776220	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:123776220C>T	ENST00000223642.1	-	17	2217	c.2188G>A	c.(2188-2190)Gaa>Aaa	p.E730K		NM_001735.2	NP_001726.2	P01031	CO5_HUMAN	complement component 5	730	Anaphylatoxin-like. {ECO:0000255|PROSITE- ProRule:PRU00022}.				activation of MAPK activity (GO:0000187)|cell chemotaxis (GO:0060326)|cell surface receptor signaling pathway (GO:0007166)|cellular calcium ion homeostasis (GO:0006874)|chemotaxis (GO:0006935)|complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|complement activation, classical pathway (GO:0006958)|cytolysis (GO:0019835)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|in utero embryonic development (GO:0001701)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|leukocyte migration involved in inflammatory response (GO:0002523)|negative regulation of dopamine secretion (GO:0033602)|negative regulation of macrophage chemotaxis (GO:0010760)|negative regulation of norepinephrine secretion (GO:0010700)|positive regulation of angiogenesis (GO:0045766)|positive regulation of chemokine secretion (GO:0090197)|positive regulation of chemotaxis (GO:0050921)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of complement activation (GO:0030449)|response to stress (GO:0006950)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane attack complex (GO:0005579)	chemokine activity (GO:0008009)|endopeptidase inhibitor activity (GO:0004866)|receptor binding (GO:0005102)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(14)|lung(5)|ovary(2)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	46				OV - Ovarian serous cystadenocarcinoma(323;4.98e-53)|GBM - Glioblastoma multiforme(294;0.0242)	Eculizumab(DB01257)|Intravenous Immunoglobulin(DB00028)	ACACAACATTCAGTGAAAGCT	0.438																																					p.E730K		Atlas-SNP	.											.	C5	124	.	0			c.G2188A						PASS	.						170.0	145.0	154.0					9																	123776220		2203	4300	6503	SO:0001583	missense	727	exon17			AACATTCAGTGAA	M57729	CCDS6826.1	9q33-q34	2014-09-17			ENSG00000106804	ENSG00000106804		"""Complement system"", ""Endogenous ligands"""	1331	protein-coding gene	gene with protein product	"""prepro-C5"", ""C5a anaphylatoxin"""	120900					Standard	NM_001735		Approved	CPAMD4, C5a, C5b	uc004bkv.3	P01031	OTTHUMG00000020579	ENST00000223642.1:c.2188G>A	9.37:g.123776220C>T	ENSP00000223642:p.Glu730Lys	Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	131	42	0.320611	NM_001735	Q14CJ0|Q27I61	Missense_Mutation	SNP	ENST00000223642.1	37	CCDS6826.1	.	.	.	.	.	.	.	.	.	.	C	12.08	1.829145	0.32329	.	.	ENSG00000106804	ENST00000223642;ENST00000430906	T	0.24151	1.87	6.06	0.0997	0.14504	Complement C3a/C4a/C5a anaphylatoxin (1);Anaphylatoxin (2);Anaphylatoxin/fibulin (4);	1.861730	0.01962	N	0.043417	T	0.17662	0.0424	L	0.35593	1.075	0.09310	N	1	B	0.30563	0.285	B	0.28916	0.096	T	0.10291	-1.0636	10	0.15952	T	0.53	.	3.2397	0.06777	0.1112:0.4786:0.1091:0.3011	.	730	P01031	CO5_HUMAN	K	730;801	ENSP00000223642:E730K	ENSP00000223642:E730K	E	-	1	0	C5	122816041	0.000000	0.05858	0.000000	0.03702	0.051000	0.14879	-0.178000	0.09782	0.088000	0.17205	0.650000	0.86243	GAA	.	.	none		0.438	C5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053844.1	NM_001735	
TMEM209	84928	hgsc.bcm.edu	37	7	129813738	129813738	+	Silent	SNP	T	T	C	rs3823482	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:129813738T>C	ENST00000397622.2	-	12	1508	c.1386A>G	c.(1384-1386)ttA>ttG	p.L462L	RP11-775D22.3_ENST00000483283.1_RNA|TMEM209_ENST00000336804.8_Silent_p.L419L|TMEM209_ENST00000462753.1_Silent_p.L461L|TMEM209_ENST00000473456.1_Silent_p.L420L	NM_032842.3	NP_116231.2	Q96SK2	TM209_HUMAN	transmembrane protein 209	462						integral component of membrane (GO:0016021)				NS(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(6)|ovary(2)|skin(1)	12	Melanoma(18;0.0435)					GATGTGGAGGTAATCTGGAAT	0.368													T|||	1520	0.303514	0.1346	0.2651	5008	,	,		17490	0.5546		0.2604	False		,,,				2504	0.3446				p.L462L		Atlas-SNP	.											.	TMEM209	31	.	0			c.A1386G						PASS	.	T		542,3150		46,450,1350	201.0	194.0	196.0		1386	-1.6	1.0	7	dbSNP_107	196	1903,6295		225,1453,2421	no	coding-synonymous	TMEM209	NM_032842.3		271,1903,3771	CC,CT,TT		23.213,14.6804,20.5635		462/562	129813738	2445,9445	1846	4099	5945	SO:0001819	synonymous_variant	84928	exon12			TGGAGGTAATCTG		CCDS47712.1, CCDS75661.1	7q32.2	2008-02-26			ENSG00000146842	ENSG00000146842			21898	protein-coding gene	gene with protein product						12958361	Standard	NM_032842		Approved	FLJ14803, NET31	uc003vpn.2	Q96SK2	OTTHUMG00000157653	ENST00000397622.2:c.1386A>G	7.37:g.129813738T>C		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	87	44	0.505747	NM_032842	A4D1L1|Q49A50|Q6PF00|Q8NCH3|Q96SL6	Silent	SNP	ENST00000397622.2	37	CCDS47712.1																																																																																			T|0.703;C|0.297	0.297	strong		0.368	TMEM209-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000349339.1	NM_032842	
GIMAP5	55340	hgsc.bcm.edu	37	7	150440043	150440043	+	Silent	SNP	C	C	T	rs1046355	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:150440043C>T	ENST00000358647.3	+	3	1183	c.816C>T	c.(814-816)ctC>ctT	p.L272L	GIMAP5_ENST00000479556.1_3'UTR	NM_018384.4	NP_060854.2	Q96F15	GIMA5_HUMAN	GTPase, IMAP family member 5	272					myeloid dendritic cell differentiation (GO:0043011)|negative regulation of apoptotic process (GO:0043066)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of lipid catabolic process (GO:0050995)|negative regulation of nitric oxide biosynthetic process (GO:0045019)|negative regulation of T cell activation (GO:0050868)|positive regulation of calcium ion transport into cytosol (GO:0010524)|positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation (GO:0032831)|positive regulation of gamma-delta T cell differentiation (GO:0045588)|positive regulation of humoral immune response mediated by circulating immunoglobulin (GO:0002925)|positive regulation of membrane potential (GO:0045838)|positive regulation of natural killer cell cytokine production (GO:0002729)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|regulation of mitochondrial membrane permeability (GO:0046902)|T cell differentiation (GO:0030217)|T cell homeostasis (GO:0043029)|temperature homeostasis (GO:0001659)	integral component of membrane (GO:0016021)|lysosome (GO:0005764)|mitochondrial outer membrane (GO:0005741)	GTP binding (GO:0005525)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|urinary_tract(2)	19			OV - Ovarian serous cystadenocarcinoma(82;0.0145)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		ACAAGGCGCTCCTCAGAGTCA	0.418													C|||	1754	0.35024	0.5363	0.2565	5008	,	,		22097	0.3006		0.3082	False		,,,				2504	0.2597				p.L476L		Atlas-SNP	.											.	.	.	.	0			c.C1428T						PASS	.	C	,	2334,2072	605.8+/-390.6	633,1068,502	98.0	73.0	81.0		1428,816	-2.6	0.0	7	dbSNP_86	81	2638,5962	425.0+/-354.8	388,1862,2050	no	coding-synonymous,coding-synonymous	GIMAP5,GIMAP1-GIMAP5	NM_001199577.1,NM_018384.4	,	1021,2930,2552	TT,TC,CC		30.6744,47.0268,38.2285	,	476/512,272/308	150440043	4972,8034	2203	4300	6503	SO:0001819	synonymous_variant	0	exon6			GGCGCTCCTCAGA	AK002158	CCDS5907.1	7q36.1	2014-04-04	2004-10-29	2004-10-30	ENSG00000196329	ENSG00000196329		"""GTPases, IMAP"""	18005	protein-coding gene	gene with protein product	"""immune-associated nucleotide-binding protein 5"""	608086	"""immune associated nucleotide 4 like 1 (mouse)"""	IAN4L1			Standard	NM_018384		Approved	HIMAP3, IAN5		Q96F15	OTTHUMG00000157542	ENST00000358647.3:c.816C>T	7.37:g.150440043C>T		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	121	121	1	NM_001199577	D3DWZ5|Q6IA75|Q96NE4|Q9NUK9	Silent	SNP	ENST00000358647.3	37	CCDS5907.1																																																																																			C|0.620;T|0.380	0.380	strong		0.418	GIMAP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349108.2	NM_018384	
NRG3	10718	hgsc.bcm.edu	37	10	84745256	84745256	+	Silent	SNP	C	C	T	rs2295933	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:84745256C>T	ENST00000404547.1	+	10	2058	c.2058C>T	c.(2056-2058)agC>agT	p.S686S	NRG3_ENST00000372141.2_Silent_p.S662S|NRG3_ENST00000404576.2_Silent_p.S466S|NRG3_ENST00000537893.1_Silent_p.S312S|NRG3_ENST00000545131.1_Silent_p.S312S|NRG3_ENST00000372142.2_Silent_p.S465S|NRG3_ENST00000556918.1_Silent_p.S492S			P56975	NRG3_HUMAN	neuregulin 3	686					activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|intracellular signal transduction (GO:0035556)|mammary placode formation (GO:0060596)|pattern specification process (GO:0007389)|regulation of cell growth (GO:0001558)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	growth factor activity (GO:0008083)|receptor tyrosine kinase binding (GO:0030971)|transmembrane receptor protein tyrosine kinase activator activity (GO:0030297)			breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(41)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	69				GBM - Glioblastoma multiforme(1;2.5e-18)|all cancers(1;2.85e-09)		ACAGTGCAAGCGAAAACACAG	0.483													C|||	2352	0.469649	0.4236	0.4438	5008	,	,		17216	0.6637		0.3439	False		,,,				2504	0.4796				p.S662S		Atlas-SNP	.											.	NRG3	301	.	0			c.C1986T						PASS	.	C	,,	1867,2539	538.7+/-375.1	389,1089,725	80.0	73.0	75.0		1986,1983,1395	0.6	1.0	10	dbSNP_100	75	2565,6035	418.3+/-352.7	386,1793,2121	no	coding-synonymous,coding-synonymous,coding-synonymous	NRG3	NM_001010848.3,NM_001165972.1,NM_001165973.1	,,	775,2882,2846	TT,TC,CC		29.8256,42.374,34.0766	,,	662/697,661/696,465/500	84745256	4432,8574	2203	4300	6503	SO:0001819	synonymous_variant	10718	exon9			TGCAAGCGAAAAC	AK098823	CCDS31233.1, CCDS53547.1	10q22-q23	2003-09-09			ENSG00000185737	ENSG00000185737			7999	protein-coding gene	gene with protein product		605533				9275162	Standard	NM_001010848		Approved		uc001kco.2	P56975	OTTHUMG00000018626	ENST00000404547.1:c.2058C>T	10.37:g.84745256C>T		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	38	38	1	NM_001010848	A4D7U1|Q0PEH2|Q5VYH3	Silent	SNP	ENST00000404547.1	37	CCDS31233.1																																																																																			C|0.606;T|0.394	0.394	strong		0.483	NRG3-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000412262.1	XM_166086	
ST14	6768	hgsc.bcm.edu	37	11	130068491	130068491	+	Silent	SNP	G	G	C	rs11827924	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:130068491G>C	ENST00000278742.5	+	14	2077	c.1659G>C	c.(1657-1659)ggG>ggC	p.G553G		NM_021978.3	NP_068813.1	Q9Y5Y6	ST14_HUMAN	suppression of tumorigenicity 14 (colon carcinoma)	553	LDL-receptor class A 3. {ECO:0000255|PROSITE-ProRule:PRU00124}.				keratinocyte differentiation (GO:0030216)|proteolysis (GO:0006508)	basolateral plasma membrane (GO:0016323)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of plasma membrane (GO:0019897)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(12)|ovary(3)|pancreas(2)|prostate(1)|skin(3)	32	all_hematologic(175;0.0429)	Lung NSC(97;0.000602)|Breast(109;0.000962)|all_lung(97;0.00126)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)		OV - Ovarian serous cystadenocarcinoma(99;0.0183)|Lung(977;0.228)	Urokinase(DB00013)	GTGGGGACGGGTCCGACGAGG	0.657													g|||	589	0.117612	0.1029	0.0749	5008	,	,		13855	0.1974		0.1133	False		,,,				2504	0.09				p.G553G		Atlas-SNP	.											ST14,NS,malignant_melanoma,+1,1	ST14	82	1	0			c.G1659C						scavenged	.			480,3922	222.0+/-238.9	26,428,1747	46.0	47.0	47.0		1659	-3.3	0.6	11	dbSNP_120	47	1206,7388	241.7+/-271.9	85,1036,3176	no	coding-synonymous	ST14	NM_021978.3		111,1464,4923	CC,CG,GG		14.033,10.9041,12.9732		553/856	130068491	1686,11310	2201	4297	6498	SO:0001819	synonymous_variant	6768	exon14			GGACGGGTCCGAC	AF118224	CCDS8487.1	11q24-q25	2011-08-31	2005-11-19		ENSG00000149418	ENSG00000149418		"""Serine peptidases / Transmembrane"""	11344	protein-coding gene	gene with protein product	"""epithin"", ""matriptase"""	606797		PRSS14		9925927, 10373424	Standard	NM_021978		Approved	SNC19, HAI, MT-SP1, TMPRSS14	uc001qfw.3	Q9Y5Y6	OTTHUMG00000165768	ENST00000278742.5:c.1659G>C	11.37:g.130068491G>C		Somatic	174	1	0.00574713		WXS	Illumina HiSeq	Phase_I	171	26	0.152047	NM_021978	Q9BS01|Q9H3S0|Q9HB36|Q9HCA3	Silent	SNP	ENST00000278742.5	37	CCDS8487.1																																																																																			G|0.868;C|0.132	0.132	strong		0.657	ST14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386119.1		
DSC1	1823	hgsc.bcm.edu	37	18	28722039	28722039	+	Silent	SNP	G	G	A	rs2577075	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:28722039G>A	ENST00000257198.5	-	9	1444	c.1183C>T	c.(1183-1185)Cta>Tta	p.L395L	DSC1_ENST00000257197.3_Silent_p.L395L|RP11-408H20.2_ENST00000581836.1_RNA	NM_024421.2	NP_077739.1	Q08554	DSC1_HUMAN	desmocollin 1	395	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|gap junction (GO:0005921)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(20)|ovary(3)|skin(10)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	53			OV - Ovarian serous cystadenocarcinoma(10;0.00778)			TTTCCTTGTAGGATTTTGTAT	0.363													G|||	1726	0.344649	0.4085	0.3746	5008	,	,		16726	0.5655		0.2127	False		,,,				2504	0.1452				p.L395L		Atlas-SNP	.											.	DSC1	240	.	0			c.C1183T						PASS	.	G	,	1770,2636	524.7+/-371.4	357,1056,790	169.0	169.0	169.0		1183,1183	3.7	1.0	18	dbSNP_100	169	1610,6990	299.8+/-304.6	161,1288,2851	no	coding-synonymous,coding-synonymous	DSC1	NM_004948.3,NM_024421.2	,	518,2344,3641	AA,AG,GG		18.7209,40.1725,25.988	,	395/841,395/895	28722039	3380,9626	2203	4300	6503	SO:0001819	synonymous_variant	1823	exon9			CTTGTAGGATTTT	AF293358	CCDS11894.1, CCDS11895.1	18q12.1	2010-01-26			ENSG00000134765	ENSG00000134765		"""Cadherins / Major cadherins"""	3035	protein-coding gene	gene with protein product		125643				8486729	Standard	NM_024421		Approved	CDHF1	uc002kwn.3	Q08554	OTTHUMG00000131982	ENST00000257198.5:c.1183C>T	18.37:g.28722039G>A		Somatic	248	0	0		WXS	Illumina HiSeq	Phase_I	225	107	0.475556	NM_004948	Q9HB01	Silent	SNP	ENST00000257198.5	37	CCDS11894.1																																																																																			G|0.696;A|0.304	0.304	strong		0.363	DSC1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254946.1	NM_004948, NM_024421	
IGLL5	100423062	hgsc.bcm.edu	37	22	23230317	23230317	+	Silent	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:23230317G>A	ENST00000526893.1	+	1	358	c.84G>A	c.(82-84)ctG>ctA	p.L28L	IGLL5_ENST00000531372.1_Silent_p.L28L|IGLL5_ENST00000532223.2_Silent_p.L28L|hsa-mir-5571_ENST00000577998.1_RNA	NM_001178126.1	NP_001171597.1	B9A064	IGLL5_HUMAN	immunoglobulin lambda-like polypeptide 5	28						extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|urinary_tract(1)	7						CCCTGCTGCTGCTGGGTCTGG	0.657																																					p.L28L		Atlas-SNP	.											.	IGLL5	26	.	0			c.G84A						PASS	.																																			SO:0001819	synonymous_variant	100423062	exon1			GCTGCTGCTGGGT	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.84G>A	22.37:g.23230317G>A		Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	158	33	0.208861	NM_001178126		Silent	SNP	ENST00000526893.1	37	CCDS54506.1																																																																																			.	.	none		0.657	IGLL5-002	KNOWN	basic|appris_candidate|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000385699.1	NM_001178126	
OR1F1	4992	hgsc.bcm.edu	37	16	3254470	3254470	+	Missense_Mutation	SNP	T	T	C	rs371443638|rs372744779|rs1834026	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:3254470T>C	ENST00000304646.2	+	1	224	c.224T>C	c.(223-225)tTc>tCc	p.F75S	AJ003147.9_ENST00000576468.1_RNA	NM_012360.1	NP_036492.1	O43749	OR1F1_HUMAN	olfactory receptor, family 1, subfamily F, member 1	75			F -> S (in dbSNP:rs1834026).		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						TGCTTCTCCTTCACCACCGTC	0.502													C|||	2163	0.431909	0.2738	0.5202	5008	,	,		23279	0.5655		0.4314	False		,,,				2504	0.4458				p.F75S		Atlas-SNP	.											.	OR1F1	36	.	0			c.T224C						PASS	.	C	SER/PHE	1368,3026	689.6+/-405.1	196,976,1025	250.0	211.0	224.0		224	4.3	1.0	16	dbSNP_92	224	3775,4825	614.7+/-396.3	837,2101,1362	no	missense	OR1F1	NM_012360.1	155	1033,3077,2387	CC,CT,TT		43.8953,31.1334,39.5798	benign	75/313	3254470	5143,7851	2197	4300	6497	SO:0001583	missense	4992	exon1			TCTCCTTCACCAC	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.224T>C	16.37:g.3254470T>C	ENSP00000305424:p.Phe75Ser	Somatic	318	1	0.00314465		WXS	Illumina HiSeq	Phase_I	246	193	0.784553	NM_012360	O15246|Q6IFL5	Missense_Mutation	SNP	ENST00000304646.2	37	CCDS10496.1	974	0.445970695970696	146	0.2967479674796748	177	0.4889502762430939	314	0.548951048951049	337	0.4445910290237467	C	0.414	-0.911763	0.02434	0.311334	0.438953	ENSG00000168124	ENST00000304646	T	0.00382	7.62	5.26	4.3	0.51218	GPCR, rhodopsin-like superfamily (1);	0.114286	0.39985	N	0.001220	T	0.00012	0.0000	N	0.00013	-2.935	0.47374	P	5.990000000000162E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.15235	-1.0444	9	0.02654	T	1	.	9.205	0.37285	0.0:0.7718:0.1461:0.0821	rs1834026;rs52825102;rs57080263;rs1834026	75	O43749	OR1F1_HUMAN	S	75	ENSP00000305424:F75S	ENSP00000305424:F75S	F	+	2	0	OR1F1	3194471	0.000000	0.05858	1.000000	0.80357	0.820000	0.46376	0.779000	0.26746	0.582000	0.29556	-0.665000	0.03846	TTC	T|0.581;G|0.003	.	strong		0.502	OR1F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206985.1		
SLC2A11	66035	hgsc.bcm.edu	37	22	24224659	24224659	+	Silent	SNP	C	C	A	rs9612499	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:24224659C>A	ENST00000345044.6	+	7	967	c.699C>A	c.(697-699)ctC>ctA	p.L233L	SLC2A11_ENST00000316185.8_Silent_p.L236L|SLC2A11_ENST00000398356.2_Silent_p.L240L|AP000350.10_ENST00000433835.3_Intron|SLC2A11_ENST00000467660.1_3'UTR|RN7SL268P_ENST00000491172.2_RNA			Q9BYW1	GTR11_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 11	233					carbohydrate transport (GO:0008643)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	substrate-specific transmembrane transporter activity (GO:0022891)			endometrium(2)|kidney(1)|large_intestine(2)|lung(3)|ovary(1)|prostate(1)|skin(2)	12						TACGGCGGCTCCGGGGCTCCG	0.711													a|||	1721	0.34365	0.1899	0.3689	5008	,	,		13300	0.3194		0.4076	False		,,,				2504	0.4928				p.L240L		Atlas-SNP	.											.	SLC2A11	32	.	0			c.C720A						PASS	.		,,	723,2953		132,459,1247	3.0	4.0	3.0		699,708,720	1.7	1.0	22	dbSNP_119	3	2732,4606		630,1472,1567	no	coding-synonymous,coding-synonymous,coding-synonymous	SLC2A11	NM_001024938.2,NM_001024939.2,NM_030807.3	,,	762,1931,2814	AA,AC,CC		37.2309,19.6681,31.3692	,,	233/497,236/500,240/504	24224659	3455,7559	1838	3669	5507	SO:0001819	synonymous_variant	66035	exon8			GCGGCTCCGGGGC	AJ271290	CCDS13818.1, CCDS33616.1, CCDS46673.1, CCDS74828.1	22q11.23	2013-05-22			ENSG00000133460	ENSG00000133460		"""Solute carriers"""	14239	protein-coding gene	gene with protein product		610367					Standard	NM_001024938		Approved	GLUT11, GLUT10	uc002zyp.4	Q9BYW1	OTTHUMG00000166469	ENST00000345044.6:c.699C>A	22.37:g.24224659C>A		Somatic	14	0	0		WXS	Illumina HiSeq	Phase_I	20	18	0.9	NM_030807	E9PH55|Q542Y4|Q6ICJ5|Q8WXF9|Q8WYM4	Silent	SNP	ENST00000345044.6	37	CCDS46673.1	712|712	0.326007326007326|0.326007326007326	102|102	0.2073170731707317|0.2073170731707317	114|114	0.3149171270718232|0.3149171270718232	183|183	0.31993006993006995|0.31993006993006995	313|313	0.4129287598944591|0.4129287598944591	a|a	3.415|3.415	-0.119334|-0.119334	0.06838|0.06838	0.196681|0.196681	0.372309|0.372309	ENSG00000133460|ENSG00000251357	ENST00000398363|ENST00000502845	.|.	.|.	.|.	3.92|3.92	1.69|1.69	0.24217|0.24217	.|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.09310|0.09310	P|P	0.999999999999996|0.999999999999996	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.44802|0.44802	-0.9304|-0.9304	4|3	0.44086|.	T|.	0.13|.	.|.	1.5873|1.5873	0.02647|0.02647	0.1956:0.1662:0.4674:0.1708|0.1956:0.1662:0.4674:0.1708	rs9612499|rs9612499	.|.	.|.	.|.	T|Y	184|5	.|.	ENSP00000381404:P184T|.	P|S	+|+	1|2	0|0	SLC2A11|AP000350.10	22554659|22554659	0.903000|0.903000	0.30736|0.30736	0.970000|0.970000	0.41538|0.41538	0.002000|0.002000	0.02628|0.02628	-0.016000|-0.016000	0.12613|0.12613	0.069000|0.069000	0.16605|0.16605	-0.938000|-0.938000	0.02693|0.02693	CCG|TCC	C|0.674;A|0.326	0.326	strong		0.711	SLC2A11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319889.3	NM_030807	
JARID2	3720	hgsc.bcm.edu	37	6	15512616	15512616	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:15512616G>A	ENST00000341776.2	+	14	3374	c.3130G>A	c.(3130-3132)Gcc>Acc	p.A1044T	JARID2_ENST00000397311.3_Missense_Mutation_p.A872T	NM_004973.3	NP_004964.2	Q92833	JARD2_HUMAN	jumonji, AT rich interactive domain 2	1044	JmjC. {ECO:0000255|PROSITE- ProRule:PRU00538}.				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)				CTTTGAGACCGCCAAGGTGAG	0.607																																					p.A1044T		Atlas-SNP	.											.	JARID2	135	.	0			c.G3130A						PASS	.						139.0	133.0	135.0					6																	15512616		2203	4300	6503	SO:0001583	missense	3720	exon14			GAGACCGCCAAGG	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.3130G>A	6.37:g.15512616G>A	ENSP00000341280:p.Ala1044Thr	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	44	13	0.295455	NM_004973	A8K9Z6|B7Z5S5|B7Z8L0|Q5U5L5|Q86X63	Missense_Mutation	SNP	ENST00000341776.2	37	CCDS4533.1	.	.	.	.	.	.	.	.	.	.	G	24.3	4.520516	0.85495	.	.	ENSG00000008083	ENST00000341776;ENST00000397311	T;T	0.70282	-0.47;-0.47	5.02	4.15	0.48705	Transcription factor jumonji/aspartyl beta-hydroxylase (2);	0.000000	0.85682	D	0.000000	T	0.56366	0.1980	L	0.35542	1.07	0.80722	D	1	D	0.67145	0.996	P	0.50136	0.632	T	0.60632	-0.7225	10	0.46703	T	0.11	-15.1615	13.6151	0.62103	0.0757:0.0:0.9243:0.0	.	1044	Q92833	JARD2_HUMAN	T	1044;872	ENSP00000341280:A1044T;ENSP00000380478:A872T	ENSP00000341280:A1044T	A	+	1	0	JARID2	15620595	1.000000	0.71417	0.991000	0.47740	0.956000	0.61745	9.796000	0.99103	1.238000	0.43771	0.609000	0.83330	GCC	.	.	none		0.607	JARID2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000039926.1	NM_004973	
C3	718	hgsc.bcm.edu	37	19	6702157	6702157	+	Silent	SNP	C	C	G	rs428453	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	61	0	0		WXS	Illumina HiSeq	Phase_I	33	33	1	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	
RYR3	6263	hgsc.bcm.edu	37	15	34151901	34151901	+	Silent	SNP	C	C	T	rs79305633	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:34151901C>T	ENST00000389232.4	+	100	14338	c.14268C>T	c.(14266-14268)ttC>ttT	p.F4756F	RYR3_ENST00000415757.3_Silent_p.F4751F|RP11-3D4.3_ENST00000560404.1_RNA|RP11-3D4.2_ENST00000560268.1_RNA	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	4756					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)		TTTTCTTCTTCGTCATTGTCA	0.403													T|||	81	0.0161741	0.0015	0.0216	5008	,	,		22499	0.0		0.0557	False		,,,				2504	0.0082				p.F4756F		Atlas-SNP	.											.	RYR3	760	.	0			c.C14268T						PASS	.	T		36,4004		0,36,1984	239.0	233.0	235.0		14268	-5.1	0.8	15	dbSNP_132	235	327,8059		7,313,3873	no	coding-synonymous	RYR3	NM_001036.3		7,349,5857	TT,TC,CC		3.8994,0.8911,2.9213		4756/4871	34151901	363,12063	2020	4193	6213	SO:0001819	synonymous_variant	6263	exon100			CTTCTTCGTCATT		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.14268C>T	15.37:g.34151901C>T		Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	149	79	0.530201	NM_001036	O15175|Q15412	Silent	SNP	ENST00000389232.4	37	CCDS45210.1																																																																																			C|0.975;T|0.025	0.025	strong		0.403	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1		
CCDC170	80129	hgsc.bcm.edu	37	6	151914265	151914265	+	Silent	SNP	T	T	C	rs17081470	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:151914265T>C	ENST00000239374.7	+	8	1416	c.1317T>C	c.(1315-1317)ctT>ctC	p.L439L	CCDC170_ENST00000367290.5_Silent_p.L439L	NM_025059.3	NP_079335.2	Q8IYT3	CC170_HUMAN	coiled-coil domain containing 170	439																	TGGATCAGCTTTCTCAGAAAA	0.428													T|||	482	0.096246	0.1581	0.0447	5008	,	,		19213	0.0794		0.0527	False		,,,				2504	0.1115				p.L439L		Atlas-SNP	.											.	.	.	.	0			c.T1317C						PASS	.	T		594,3146		56,482,1332	104.0	94.0	97.0		1317	-3.7	1.0	6	dbSNP_123	97	579,7651		19,541,3555	no	coding-synonymous	C6orf97	NM_025059.3		75,1023,4887	CC,CT,TT		7.0352,15.8824,9.7995		439/716	151914265	1173,10797	1870	4115	5985	SO:0001819	synonymous_variant	80129	exon8			TCAGCTTTCTCAG	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.1317T>C	6.37:g.151914265T>C		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	70	50	0.714286	NM_025059	Q5VXB7|Q6P9E4|Q96KA9|Q9H5M3	Silent	SNP	ENST00000239374.7	37	CCDS43515.1																																																																																			T|0.914;C|0.086	0.086	strong		0.428	CCDC170-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000042727.2	NM_025059	
MAN2A2	4122	hgsc.bcm.edu	37	15	91452595	91452595	+	Missense_Mutation	SNP	A	A	G	rs2106673	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:91452595A>G	ENST00000559717.1	+	9	1694	c.1235A>G	c.(1234-1236)cAg>cGg	p.Q412R	MAN2A2_ENST00000430376.2_5'Flank|MAN2A2_ENST00000431652.2_5'UTR|MAN2A2_ENST00000360468.3_Missense_Mutation_p.Q412R			P49641	MA2A2_HUMAN	mannosidase, alpha, class 2A, member 2	412			Q -> R (in dbSNP:rs2106673).		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)			AAGAAGTCCCAGCTGTTCCGA	0.552													G|||	2562	0.511581	0.3275	0.6066	5008	,	,		17237	0.9673		0.2833	False		,,,				2504	0.4581				p.Q412R		Atlas-SNP	.											.	MAN2A2	99	.	0			c.A1235G						PASS	.	G	ARG/GLN	1401,2995	685.4+/-404.6	218,965,1015	72.0	67.0	69.0		1235	2.4	1.0	15	dbSNP_96	69	2592,6004	689.0+/-404.3	380,1832,2086	yes	missense	MAN2A2	NM_006122.2	43	598,2797,3101	GG,GA,AA		30.1536,31.8699,30.7343	benign	412/1151	91452595	3993,8999	2198	4298	6496	SO:0001583	missense	4122	exon8			AGTCCCAGCTGTT	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.1235A>G	15.37:g.91452595A>G	ENSP00000452948:p.Gln412Arg	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	117	116	0.991453	NM_006122	A6NH12|A8K1E8|Q13754	Missense_Mutation	SNP	ENST00000559717.1	37	CCDS32332.1	1119	0.5123626373626373	155	0.3150406504065041	200	0.5524861878453039	556	0.972027972027972	208	0.27440633245382584	G	11.69	1.713975	0.30413	0.318699	0.301536	ENSG00000196547	ENST00000360468	T	0.74002	-0.8	5.74	2.42	0.29668	Glycoside hydrolase/deacetylase, beta/alpha-barrel (1);Glycoside hydrolase, family 38, core (2);	0.273076	0.38959	N	0.001506	T	0.00012	0.0000	N	0.08118	0	0.09310	P	0.9999999999949408	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.001;0.001	T	0.33445	-0.9868	9	0.15499	T	0.54	-25.785	8.1177	0.30953	0.5043:0.0:0.4957:0.0	rs2106673;rs52827682;rs56746832;rs2106673	82;412;412	B4DIK4;P49641-1;P49641	.;.;MA2A2_HUMAN	R	412	ENSP00000353655:Q412R	ENSP00000353655:Q412R	Q	+	2	0	MAN2A2	89253599	1.000000	0.71417	0.998000	0.56505	0.955000	0.61496	3.686000	0.54685	0.394000	0.25230	-0.222000	0.12452	CAG	A|0.596;G|0.404	0.404	strong		0.552	MAN2A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418246.5	NM_006122	
PAK2	5062	hgsc.bcm.edu	37	3	196529982	196529982	+	Missense_Mutation	SNP	A	A	G	rs78043821	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:196529982A>G	ENST00000327134.3	+	4	705	c.383A>G	c.(382-384)aAg>aGg	p.K128R		NM_002577.4	NP_002568.2	Q13177	PAK2_HUMAN	p21 protein (Cdc42/Rac)-activated kinase 2	128	Autoregulatory region. {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)		GATGTCCTAAAGTTCTACGAC	0.463																																					p.K128R		Atlas-SNP	.											PAK2_ENST00000327134,NS,lymphoid_neoplasm,0,2	PAK2	113	2	0			c.A383G						scavenged	.						107.0	95.0	99.0					3																	196529982		2203	4300	6503	SO:0001583	missense	5062	exon4			TCCTAAAGTTCTA	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.383A>G	3.37:g.196529982A>G	ENSP00000314067:p.Lys128Arg	Somatic	109	1	0.00917431		WXS	Illumina HiSeq	Phase_I	110	8	0.0727273	NM_002577	Q13154|Q6ISC3	Missense_Mutation	SNP	ENST00000327134.3	37	CCDS3321.1	.	.	.	.	.	.	.	.	.	.	A	21.6	4.176399	0.78564	.	.	ENSG00000180370	ENST00000327134	D	0.86230	-2.09	5.27	5.27	0.74061	PAK-box/P21-Rho-binding (1);	0.000000	0.85682	D	0.000000	D	0.86990	0.6066	L	0.55743	1.74	0.80722	D	1	P	0.37015	0.578	B	0.43155	0.41	D	0.86926	0.2070	10	0.48119	T	0.1	.	14.3609	0.66771	1.0:0.0:0.0:0.0	.	128	Q13177	PAK2_HUMAN	R	128	ENSP00000314067:K128R	ENSP00000314067:K128R	K	+	2	0	PAK2	198014379	1.000000	0.71417	0.990000	0.47175	0.859000	0.49053	6.986000	0.76200	2.002000	0.58637	0.460000	0.39030	AAG	A|0.915;G|0.084	0.084	strong		0.463	PAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340548.1	NM_002577	
CDC14A	8556	hgsc.bcm.edu	37	1	100949860	100949860	+	Silent	SNP	G	G	A	rs2270694	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:100949860G>A	ENST00000336454.3	+	11	1345	c.990G>A	c.(988-990)tcG>tcA	p.S330S	CDC14A_ENST00000361544.6_Silent_p.S330S|CDC14A_ENST00000542213.1_Silent_p.S272S|CDC14A_ENST00000544534.1_Silent_p.S330S|CDC14A_ENST00000370124.3_Silent_p.S330S|CDC14A_ENST00000370125.2_3'UTR|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	70	0	0		WXS	Illumina HiSeq	Phase_I	29	29	1	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	
DST	667	hgsc.bcm.edu	37	6	56505063	56505063	+	Silent	SNP	A	A	G	rs2144407	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:56505063A>G	ENST00000361203.3	-	14	1742	c.1735T>C	c.(1735-1737)Ttg>Ctg	p.L579L	DST_ENST00000370769.4_Silent_p.L579L|DST_ENST00000244364.6_Silent_p.L253L|DST_ENST00000518935.1_Silent_p.L253L|DST_ENST00000370765.6_Silent_p.L253L|DST_ENST00000312431.6_Silent_p.L579L|DST_ENST00000446842.2_Silent_p.L253L|DST_ENST00000370754.5_Silent_p.L757L|DST_ENST00000370788.2_Silent_p.L579L|DST_ENST00000421834.2_Silent_p.L579L			Q03001	DYST_HUMAN	dystonin	579					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)			ATCAACTTCAAAGTTTGCAAT	0.388													G|||	660	0.131789	0.4281	0.0418	5008	,	,		19856	0.0179		0.0288	False		,,,				2504	0.0184				p.L253L		Atlas-SNP	.											.	DST	1427	.	0			c.T757C						PASS	.	G	,	1704,2702	651.3+/-399.2	335,1034,834	76.0	79.0	78.0		757,757	4.9	0.9	6	dbSNP_96	78	381,8219	801.6+/-407.4	10,361,3929	no	coding-synonymous,coding-synonymous	DST	NM_001723.5,NM_015548.4	,	345,1395,4763	GG,GA,AA		4.4302,38.6745,16.0311	,	253/2650,253/5172	56505063	2085,10921	2203	4300	6503	SO:0001819	synonymous_variant	667	exon4			ACTTCAAAGTTTG	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.1735T>C	6.37:g.56505063A>G		Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	136	68	0.5	NM_001723	B7Z3H1|O94833|Q12825|Q13266|Q13267|Q13775|Q5TBT0|Q5TBT2|Q5TF23|Q5TF24|Q8N1T8|Q8N8J3|Q8WXK8|Q8WXK9|Q96AK9|Q96DQ5|Q96J76|Q96QT5|Q9H555|Q9UGD7|Q9UGD8|Q9UN10	Silent	SNP	ENST00000361203.3	37																																																																																				A|0.854;C|0.000;G|0.146	0.146	strong		0.388	DST-004	NOVEL	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000041021.3	NM_001723	
INTS3	65123	hgsc.bcm.edu	37	1	153701188	153701188	+	Silent	SNP	G	G	A	rs150819290	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:153701188G>A	ENST00000318967.2	+	1	646	c.78G>A	c.(76-78)gcG>gcA	p.A26A	INTS3_ENST00000456435.1_5'UTR|Y_RNA_ENST00000362695.1_RNA|INTS3_ENST00000435409.2_Silent_p.A26A	NM_023015.3	NP_075391.3	Q68E01	INT3_HUMAN	integrator complex subunit 3	0	Ala/Gly-rich.				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)			gaggaggagcgggagcaggag	0.627													G|||	17	0.00339457	0.0	0.0043	5008	,	,		11478	0.0		0.0139	False		,,,				2504	0.0				p.A26A		Atlas-SNP	.											.	INTS3	83	.	0			c.G78A						PASS	.	G		7,4393		0,7,2193	34.0	45.0	41.0		78	4.1	1.0	1	dbSNP_134	41	106,8494		0,106,4194	no	coding-synonymous	INTS3	NM_023015.3		0,113,6387	AA,AG,GG		1.2326,0.1591,0.8692		26/1043	153701188	113,12887	2200	4300	6500	SO:0001819	synonymous_variant	65123	exon1			AGGAGCGGGAGCA	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.78G>A	1.37:g.153701188G>A		Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	137	70	0.510949	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																																																																																			G|0.994;A|0.006	0.006	strong		0.627	INTS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090045.2	NM_023015	
IRF7	3665	hgsc.bcm.edu	37	11	614318	614318	+	Missense_Mutation	SNP	T	T	C	rs1061502	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:614318T>C	ENST00000397574.2	-	6	904	c.535A>G	c.(535-537)Aag>Gag	p.K179E	IRF7_ENST00000397562.3_Intron|IRF7_ENST00000348655.6_Missense_Mutation_p.K179E|IRF7_ENST00000397566.1_Missense_Mutation_p.K192E|IRF7_ENST00000525445.1_Missense_Mutation_p.K73E|IRF7_ENST00000397570.1_Missense_Mutation_p.K179E|IRF7_ENST00000330243.5_Missense_Mutation_p.K192E	NM_001572.3	NP_001563.2	Q92985	IRF7_HUMAN	interferon regulatory factor 7	179			K -> E (in dbSNP:rs1061502). {ECO:0000269|PubMed:9786932, ECO:0000269|Ref.1}.		cellular response to DNA damage stimulus (GO:0006974)|cytokine-mediated signaling pathway (GO:0019221)|establishment of viral latency (GO:0019043)|immunoglobulin mediated immune response (GO:0016064)|innate immune response (GO:0045087)|interferon-alpha production (GO:0032607)|interferon-beta production (GO:0032608)|interferon-gamma-mediated signaling pathway (GO:0060333)|MDA-5 signaling pathway (GO:0039530)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of macrophage apoptotic process (GO:2000110)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta production (GO:0032728)|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)|positive regulation of type I interferon-mediated signaling pathway (GO:0060340)|regulation of adaptive immune response (GO:0002819)|regulation of immune response (GO:0050776)|regulation of monocyte differentiation (GO:0045655)|regulation of MyD88-dependent toll-like receptor signaling pathway (GO:0034124)|regulation of MyD88-independent toll-like receptor signaling pathway (GO:0034127)|regulation of type I interferon production (GO:0032479)|response to virus (GO:0009615)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|transcription from RNA polymerase II promoter (GO:0006366)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|type I interferon biosynthetic process (GO:0045351)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome membrane (GO:0010008)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity (GO:0000982)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)			endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	8		all_cancers(49;1.69e-08)|all_epithelial(84;1.65e-05)|Breast(177;0.000231)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.106)|all_lung(207;0.136)		all cancers(45;7.68e-28)|Epithelial(43;7.44e-27)|OV - Ovarian serous cystadenocarcinoma(40;3.53e-21)|BRCA - Breast invasive adenocarcinoma(625;6.96e-05)|Lung(200;0.0375)|LUSC - Lung squamous cell carcinoma(625;0.0703)		AGGTCCCCCTTGTCACCAGCT	0.657													t|||	1380	0.275559	0.5847	0.3026	5008	,	,		14524	0.0208		0.2674	False		,,,				2504	0.1094				p.K192E		Atlas-SNP	.											.	IRF7	23	.	0			c.A574G						PASS	.		GLU/LYS,GLU/LYS,GLU/LYS	2304,2092	568.5+/-382.4	597,1110,491	28.0	28.0	28.0		535,535,574	-5.2	0.0	11	dbSNP_86	28	2507,6089	386.1+/-341.7	359,1789,2150	yes	missense,missense,missense	IRF7	NM_001572.3,NM_004029.2,NM_004031.2	56,56,56	956,2899,2641	CC,CT,TT		29.1647,47.5887,37.0305	benign,benign,benign	179/504,179/475,192/517	614318	4811,8181	2198	4298	6496	SO:0001583	missense	3665	exon4			CCCCCTTGTCACC	U53830	CCDS7703.1, CCDS7704.1, CCDS7705.1	11p15.5	2005-10-10			ENSG00000185507	ENSG00000185507			6122	protein-coding gene	gene with protein product		605047					Standard	XM_005252906		Approved		uc001lqh.3	Q92985	OTTHUMG00000132019	ENST00000397574.2:c.535A>G	11.37:g.614318T>C	ENSP00000380704:p.Lys179Glu	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	70	55	0.785714	NM_004031	B9EGL3|O00331|O00332|O00333|O75924|Q9UE79	Missense_Mutation	SNP	ENST00000397574.2	37	CCDS7703.1	610	0.2793040293040293	281	0.5711382113821138	124	0.3425414364640884	8	0.013986013986013986	197	0.2598944591029024	t	0.008	-1.918807	0.00498	0.524113	0.291647	ENSG00000185507	ENST00000525445;ENST00000348655;ENST00000397570;ENST00000397566;ENST00000397574;ENST00000330243	D;D;D;D;D;D	0.95756	-2.89;-3.8;-3.8;-3.75;-3.8;-3.75	2.6	-5.21	0.02815	.	.	.	.	.	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	0.19160	-1.0314	8	0.02654	T	1	2.1239	3.7732	0.08650	0.1231:0.1436:0.1225:0.6108	rs1061502;rs3168193	73;179;179;192	E9PSE3;Q92985-2;Q92985;Q92985-4	.;.;IRF7_HUMAN;.	E	73;179;179;192;179;192	ENSP00000434009:K73E;ENSP00000331803:K179E;ENSP00000380700:K179E;ENSP00000380697:K192E;ENSP00000380704:K179E;ENSP00000329411:K192E	ENSP00000329411:K192E	K	-	1	0	IRF7	604318	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.728000	0.01858	-2.239000	0.00711	-1.524000	0.00929	AAG	T|0.664;C|0.336	0.336	strong		0.657	IRF7-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255026.1	NM_001572	
TRAK1	22906	hgsc.bcm.edu	37	3	42251329	42251329	+	Silent	SNP	C	C	T	rs2290133	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:42251329C>T	ENST00000327628.5	+	14	2215	c.1815C>T	c.(1813-1815)ccC>ccT	p.P605P	TRAK1_ENST00000487159.1_3'UTR|TRAK1_ENST00000341421.3_Silent_p.P547P|TRAK1_ENST00000396175.1_Silent_p.P547P	NM_001042646.2	NP_001036111.1	Q9UPV9	TRAK1_HUMAN	trafficking protein, kinesin binding 1	605					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						ACCCCCGGCCCGGTGTGGTCA	0.582													C|||	1811	0.361621	0.2428	0.5346	5008	,	,		17180	0.4663		0.2793	False		,,,				2504	0.3763				p.P605P	GBM(44;195 884 22595 31865 41850)	Atlas-SNP	.											.	TRAK1	188	.	0			c.C1815T						PASS	.	C	,	1134,3272	404.4+/-333.1	152,830,1221	79.0	79.0	79.0		1815,1641	-8.8	0.4	3	dbSNP_100	79	2611,5989	423.1+/-354.3	405,1801,2094	no	coding-synonymous,coding-synonymous	TRAK1	NM_001042646.1,NM_014965.3	,	557,2631,3315	TT,TC,CC		30.3605,25.7376,28.7944	,	605/954,547/687	42251329	3745,9261	2203	4300	6503	SO:0001819	synonymous_variant	22906	exon14			CCGGCCCGGTGTG		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.1815C>T	3.37:g.42251329C>T		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	73	29	0.39726	NM_001265608	E9PDS2|J3KNT7|Q63HR0|Q659B5|Q96B69	Silent	SNP	ENST00000327628.5	37	CCDS43072.1																																																																																			C|0.681;T|0.319	0.319	strong		0.582	TRAK1-004	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343413.1	NM_014965	
PTOV1	53635	hgsc.bcm.edu	37	19	50361353	50361353	+	Silent	SNP	C	C	T	rs2290286	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:50361353C>T	ENST00000601675.1	+	9	1022	c.918C>T	c.(916-918)ctC>ctT	p.L306L	PTOV1_ENST00000221557.9_Silent_p.L274L|AC018766.5_ENST00000601893.1_RNA|PTOV1_ENST00000598325.1_3'UTR|AC018766.4_ENST00000596624.1_RNA|PTOV1_ENST00000600603.1_Silent_p.L274L|AC018766.5_ENST00000593654.1_RNA|PTOV1_ENST00000601638.1_Silent_p.L274L|AC018766.5_ENST00000599259.1_RNA|PTOV1_ENST00000391842.1_Silent_p.L306L|PTOV1_ENST00000599732.1_Silent_p.L306L			Q86YD1	PTOV1_HUMAN	prostate tumor overexpressed 1	306	Interaction with FLOT1.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				endometrium(5)|kidney(3)|large_intestine(2)|lung(5)|ovary(1)	16		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;0.0116)|OV - Ovarian serous cystadenocarcinoma(262;0.0132)		ACATGCAGCTCATCCCGCAGC	0.682													C|||	180	0.0359425	0.0068	0.0216	5008	,	,		16493	0.0139		0.0189	False		,,,				2504	0.1258				p.L306L		Atlas-SNP	.											.	PTOV1	41	.	0			c.C918T						PASS	.	C		60,4346	56.8+/-93.2	0,60,2143	34.0	38.0	37.0		918	1.8	1.0	19	dbSNP_100	37	253,8347	96.6+/-158.3	2,249,4049	no	coding-synonymous	PTOV1	NM_017432.3		2,309,6192	TT,TC,CC		2.9419,1.3618,2.4066		306/417	50361353	313,12693	2203	4300	6503	SO:0001819	synonymous_variant	53635	exon9			GCAGCTCATCCCG	AF238381	CCDS12782.1	19q13.33	2014-08-28	2008-09-12		ENSG00000104960	ENSG00000104960			9632	protein-coding gene	gene with protein product		610195				12598323, 15713644	Standard	XM_005258998		Approved		uc002pqf.1	Q86YD1	OTTHUMG00000183162	ENST00000601675.1:c.918C>T	19.37:g.50361353C>T		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	54	20	0.37037	NM_017432	Q6UXX7|Q96BU3|Q9HBN4|Q9NYL1	Silent	SNP	ENST00000601675.1	37	CCDS12782.1																																																																																			C|0.981;T|0.019	0.019	strong		0.682	PTOV1-007	KNOWN	alternative_3_UTR|NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465347.1	NM_017432	
HLA-A	3105	hgsc.bcm.edu	37	6	29910693	29910693	+	Missense_Mutation	SNP	A	A	G	rs41559716	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:29910693A>G	ENST00000396634.1	+	4	574	c.233A>G	c.(232-234)cAg>cGg	p.Q78R	HLA-A_ENST00000376802.2_Missense_Mutation_p.Q78R|HLA-A_ENST00000376809.5_Missense_Mutation_p.Q78R|HLA-A_ENST00000376806.5_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						scavenged	.						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	223	1	0.00448431		WXS	Illumina HiSeq	Phase_I	207	18	0.0869565	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	
LPL	4023	hgsc.bcm.edu	37	8	19810826	19810826	+	Silent	SNP	G	G	A	rs248	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	87	0	0		WXS	Illumina HiSeq	Phase_I	69	15	0.217391	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		
ITGB8	3696	hgsc.bcm.edu	37	7	20421490	20421490	+	Silent	SNP	T	T	C	rs2230398	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:20421490T>C	ENST00000222573.4	+	6	1626	c.942T>C	c.(940-942)taT>taC	p.Y314Y	ITGB8_ENST00000537992.1_Silent_p.Y179Y	NM_002214.2	NP_002205.1	P26012	ITB8_HUMAN	integrin, beta 8	314	VWFA.				cartilage development (GO:0051216)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|ganglioside metabolic process (GO:0001573)|integrin-mediated signaling pathway (GO:0007229)|negative regulation of gene expression (GO:0010629)|placenta blood vessel development (GO:0060674)|positive regulation of gene expression (GO:0010628)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integrin alphav-beta8 complex (GO:0034686)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)	extracellular matrix protein binding (GO:1990430)|receptor activity (GO:0004872)	p.Y314Y(1)		NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(17)|prostate(2)|skin(4)|stomach(2)|urinary_tract(1)	37						ACAACGTCTATGTCAAATCGA	0.398													C|||	1687	0.336861	0.3336	0.2579	5008	,	,		17840	0.4097		0.4493	False		,,,				2504	0.2065				p.Y314Y		Atlas-SNP	.											ITGB8_ENST00000222573,NS,carcinoma,0,1	ITGB8	159	1	1	Substitution - coding silent(1)	stomach(1)	c.T942C						PASS	.	C		1589,2817	666.0+/-401.6	289,1011,903	133.0	115.0	121.0		942	-0.4	0.9	7	dbSNP_116	121	3733,4867	618.2+/-396.8	804,2125,1371	no	coding-synonymous	ITGB8	NM_002214.2		1093,3136,2274	CC,CT,TT		43.407,36.0645,40.9196		314/770	20421490	5322,7684	2203	4300	6503	SO:0001819	synonymous_variant	3696	exon6			CGTCTATGTCAAA		CCDS5370.1	7p15.3	2010-03-23			ENSG00000105855	ENSG00000105855		"""Integrins"""	6163	protein-coding gene	gene with protein product		604160					Standard	XM_005249751		Approved		uc003suu.3	P26012	OTTHUMG00000023594	ENST00000222573.4:c.942T>C	7.37:g.20421490T>C		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	52	9	0.173077	NM_002214	A4D133|B4DHD4	Silent	SNP	ENST00000222573.4	37	CCDS5370.1																																																																																			A|0.000;C|0.395;G|0.000;T|0.605	0.395	strong		0.398	ITGB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059915.3	NM_002214	
TAX1BP1	8887	hgsc.bcm.edu	37	7	27827103	27827103	+	Missense_Mutation	SNP	T	T	A	rs11540483	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:27827103T>A	ENST00000396319.2	+	8	1007	c.919T>A	c.(919-921)Tta>Ata	p.L307I	TAX1BP1_ENST00000543117.1_Missense_Mutation_p.L307I|TAX1BP1_ENST00000265393.6_Missense_Mutation_p.L307I|TAX1BP1_ENST00000433216.2_Missense_Mutation_p.L150I|TAX1BP1_ENST00000409980.1_Missense_Mutation_p.L307I	NM_006024.6	NP_006015.4	Q86VP1	TAXB1_HUMAN	Tax1 (human T-cell leukemia virus type I) binding protein 1	307			L -> I (in dbSNP:rs11540483). {ECO:0000269|PubMed:15489334}.		apoptotic process (GO:0006915)|innate immune response (GO:0045087)|negative regulation of apoptotic process (GO:0043066)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of type I interferon production (GO:0032480)	cytosol (GO:0005829)	kinase binding (GO:0019900)			breast(1)|endometrium(5)|kidney(3)|large_intestine(10)|lung(8)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	31			GBM - Glioblastoma multiforme(3;0.0823)			TTTAAAAAATTTAGATGGGAA	0.343													T|||	190	0.0379393	0.0061	0.0663	5008	,	,		16596	0.001		0.1173	False		,,,				2504	0.0174				p.L307I		Atlas-SNP	.											TAX1BP1,NS,carcinoma,-1,1	TAX1BP1	71	1	0			c.T919A						PASS	.	T	ILE/LEU,ILE/LEU,ILE/LEU,ILE/LEU	106,4300	83.4+/-121.9	1,104,2098	73.0	78.0	76.0		919,919,448,919	2.3	1.0	7	dbSNP_120	76	1011,7589	215.3+/-254.7	58,895,3347	yes	missense,missense,missense,missense	TAX1BP1	NM_001079864.2,NM_001206901.1,NM_001206902.1,NM_006024.6	5,5,5,5	59,999,5445	AA,AT,TT		11.7558,2.4058,8.5883	benign,benign,benign,benign	307/748,307/748,150/591,307/790	27827103	1117,11889	2203	4300	6503	SO:0001583	missense	8887	exon8			AAAAATTTAGATG	U33821	CCDS5415.1, CCDS43561.1, CCDS56471.1	7p15	2010-08-05			ENSG00000106052	ENSG00000106052			11575	protein-coding gene	gene with protein product		605326				10435631	Standard	NM_006024		Approved	TXBP151, CALCOCO3	uc003szl.3	Q86VP1	OTTHUMG00000023377	ENST00000396319.2:c.919T>A	7.37:g.27827103T>A	ENSP00000379612:p.Leu307Ile	Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	127	28	0.220472	NM_006024	B4DKU7|E7ENV2|O60398|O95770|Q13311|Q9BQG5|Q9UI88	Missense_Mutation	SNP	ENST00000396319.2	37	CCDS5415.1	119	0.05448717948717949	4	0.008130081300813009	30	0.08287292817679558	0	0.0	85	0.11213720316622691	T	15.47	2.843571	0.51057	0.024058	0.117558	ENSG00000106052	ENST00000543117;ENST00000265393;ENST00000409980;ENST00000433216;ENST00000396319	T;T;T;T;T	0.32988	2.83;2.83;2.79;1.43;2.8	5.98	2.28	0.28536	.	0.170216	0.27500	N	0.019093	T	0.00412	0.0013	L	0.47716	1.5	0.26996	P	0.9650325	P;B;B	0.40431	0.717;0.122;0.112	P;B;B	0.48089	0.566;0.2;0.167	T	0.05566	-1.0877	9	0.32370	T	0.25	-1.4847	2.9897	0.05979	0.1204:0.1207:0.1255:0.6334	rs11540483;rs17854622	150;307;307	E7ENV2;Q86VP1;Q86VP1-2	.;TAXB1_HUMAN;.	I	307;307;307;150;307	ENSP00000444811:L307I;ENSP00000265393:L307I;ENSP00000386515:L307I;ENSP00000391907:L150I;ENSP00000379612:L307I	ENSP00000265393:L307I	L	+	1	2	TAX1BP1	27793628	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.318000	0.43779	0.460000	0.27045	0.528000	0.53228	TTA	A|0.078;T|0.922	0.078	strong		0.343	TAX1BP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000214142.1	NM_006024	
ADAT1	23536	hgsc.bcm.edu	37	16	75646576	75646576	+	Missense_Mutation	SNP	G	G	T	rs3743599	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:75646576G>T	ENST00000307921.3	-	7	753	c.608C>A	c.(607-609)aCt>aAt	p.T203N		NM_012091.3	NP_036223.2	Q9BUB4	ADAT1_HUMAN	adenosine deaminase, tRNA-specific 1	203	A to I editase. {ECO:0000255|PROSITE- ProRule:PRU00240}.		T -> N (in dbSNP:rs3743599).		tRNA processing (GO:0008033)		metal ion binding (GO:0046872)|RNA binding (GO:0003723)|tRNA-specific adenosine deaminase activity (GO:0008251)			breast(1)|endometrium(4)|large_intestine(3)|lung(7)|ovary(1)|prostate(1)|skin(1)|stomach(1)	19						CCTGGCTGCAGTCCCAGGCTC	0.507													G|||	1333	0.266174	0.0068	0.3444	5008	,	,		18555	0.6935		0.0427	False		,,,				2504	0.3507				p.T203N		Atlas-SNP	.											.	ADAT1	45	.	0			c.C608A						PASS	.	G	ASN/THR	88,4308	74.7+/-112.8	1,86,2111	167.0	159.0	162.0		608	0.8	0.0	16	dbSNP_107	162	448,8152	135.6+/-192.8	12,424,3864	yes	missense	ADAT1	NM_012091.3	65	13,510,5975	TT,TG,GG		5.2093,2.0018,4.1243	benign	203/503	75646576	536,12460	2198	4300	6498	SO:0001583	missense	23536	exon7			GCTGCAGTCCCAG	AF125188	CCDS10922.1	16q23	2008-02-05			ENSG00000065457	ENSG00000065457			228	protein-coding gene	gene with protein product		604230				10430867	Standard	NM_012091		Approved		uc002feo.2	Q9BUB4	OTTHUMG00000137611	ENST00000307921.3:c.608C>A	16.37:g.75646576G>T	ENSP00000310015:p.Thr203Asn	Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	139	53	0.381295	NM_012091	Q9NVB7|Q9UNG3	Missense_Mutation	SNP	ENST00000307921.3	37	CCDS10922.1	568	0.2600732600732601	7	0.014227642276422764	111	0.30662983425414364	418	0.7307692307692307	32	0.04221635883905013	G	4.141	0.024573	0.08054	0.020018	0.052093	ENSG00000065457	ENST00000307921;ENST00000542252	T	0.13538	2.58	5.75	0.828	0.18841	Adenosine deaminase/editase (3);	159.522000	0.00424	U	0.000070	T	0.00012	0.0000	L	0.59436	1.845	0.80722	P	0.0	B	0.31503	0.326	B	0.28553	0.091	T	0.42032	-0.9475	9	0.17832	T	0.49	0.1318	3.3179	0.07040	0.1606:0.3004:0.4212:0.1177	rs3743599;rs17697114;rs52831138;rs60688501;rs3743599	203	Q9BUB4	ADAT1_HUMAN	N	203;174	ENSP00000310015:T203N	ENSP00000310015:T203N	T	-	2	0	ADAT1	74204077	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	0.070000	0.14573	0.292000	0.22492	0.655000	0.94253	ACT	G|0.860;T|0.140	0.140	strong		0.507	ADAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269027.1	NM_012091	
PBX1	5087	hgsc.bcm.edu	37	1	164529120	164529120	+	Missense_Mutation	SNP	G	G	A	rs2275558	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:164529120G>A	ENST00000420696.2	+	1	249	c.61G>A	c.(61-63)Ggc>Agc	p.G21S	PBX1_ENST00000485769.1_Missense_Mutation_p.G21S|PBX1_ENST00000401534.1_Missense_Mutation_p.G21S|PBX1_ENST00000367897.1_Missense_Mutation_p.G21S|PBX1_ENST00000540236.1_Missense_Mutation_p.G21S|PBX1_ENST00000559240.1_Missense_Mutation_p.G21S	NM_001204961.1|NM_001204963.1|NM_002585.3	NP_001191890.1|NP_001191892.1|NP_002576.1	P40424	PBX1_HUMAN	pre-B-cell leukemia homeobox 1	21					adrenal gland development (GO:0030325)|anterior/posterior pattern specification (GO:0009952)|branching involved in ureteric bud morphogenesis (GO:0001658)|embryonic hemopoiesis (GO:0035162)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal system development (GO:0048706)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|organ morphogenesis (GO:0009887)|positive regulation of cell proliferation (GO:0008284)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|proximal/distal pattern formation (GO:0009954)|regulation of ossification (GO:0030278)|sex differentiation (GO:0007548)|spleen development (GO:0048536)|steroid biosynthetic process (GO:0006694)|thymus development (GO:0048538)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	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)|transcription factor binding (GO:0008134)		EWSR1/PBX1(3)	large_intestine(1)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	4						CGGACACCCCGGCCTGTCCCA	0.627			T	"""TCF3, EWSR1"""	"""pre B-ALL, myoepithelioma"""								G|||	1539	0.307308	0.0159	0.4308	5008	,	,		6892	0.6101		0.1968	False		,,,				2504	0.4151				p.G21S		Atlas-SNP	.		Dom	yes		1	1q23	5087	pre-B-cell leukemia transcription factor 1		"""L, M"""	PBX1_ENST00000420696,colon,carcinoma,0,1	PBX1	60	1	0			c.G61A						PASS	.	G	SER/GLY,SER/GLY,SER/GLY	168,3946		3,162,1892	10.0	11.0	11.0		61,61,61	5.2	1.0	1	dbSNP_100	11	1503,6483		141,1221,2631	yes	missense,missense,missense	PBX1	NM_001204961.1,NM_001204963.1,NM_002585.3	56,56,56	144,1383,4523	AA,AG,GG		18.8204,4.0836,13.8099	benign,benign,benign	21/348,21/421,21/431	164529120	1671,10429	2057	3993	6050	SO:0001583	missense	5087	exon1			CACCCCGGCCTGT	M86546	CCDS1246.1, CCDS55654.1	1q23.3	2011-06-20	2007-01-30		ENSG00000185630	ENSG00000185630		"""Homeoboxes / TALE class"""	8632	protein-coding gene	gene with protein product		176310	"""pre-B-cell leukemia transcription factor 1"""				Standard	NM_002585		Approved		uc001gct.3	P40424	OTTHUMG00000034307	ENST00000420696.2:c.61G>A	1.37:g.164529120G>A	ENSP00000405890:p.Gly21Ser	Somatic	194	0	0		WXS	Illumina HiSeq	Phase_I	140	137	0.978571	NM_001204963	B4DSC1|F5H4U9|Q5T488	Missense_Mutation	SNP	ENST00000420696.2	37	CCDS1246.1	666	0.30494505494505497	21	0.042682926829268296	130	0.35911602209944754	372	0.6503496503496503	143	0.18865435356200527	G	12.17	1.858419	0.32791	0.040836	0.188204	ENSG00000185630	ENST00000340699;ENST00000420696;ENST00000367897;ENST00000540236;ENST00000401534	T;D;D;D;D	0.89681	0.79;-2.51;-2.43;-2.55;-2.43	5.18	5.18	0.71444	.	0.063231	0.64402	D	0.000005	T	0.71005	0.3289	L	0.45137	1.4	0.09310	N	1.0	B;P;B	0.35226	0.054;0.491;0.066	B;B;B	0.19391	0.006;0.025;0.004	T	0.69884	-0.5024	9	0.20519	T	0.43	-8.1196	11.0309	0.47772	0.0866:0.0:0.9134:0.0	rs2275558;rs59646304	21;21;21	F5H4U9;P40424;Q53YC7	.;PBX1_HUMAN;.	S	21	ENSP00000341455:G21S;ENSP00000405890:G21S;ENSP00000356872:G21S;ENSP00000439943:G21S;ENSP00000384856:G21S	ENSP00000341455:G21S	G	+	1	0	PBX1	162795744	1.000000	0.71417	1.000000	0.80357	0.200000	0.23975	7.826000	0.86716	2.409000	0.81822	0.561000	0.74099	GGC	G|0.695;A|0.305	0.305	strong		0.627	PBX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000082864.4	NM_002585	
DHX9	1660	hgsc.bcm.edu	37	1	182850520	182850520	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:182850520G>A	ENST00000367549.3	+	23	2856	c.2746G>A	c.(2746-2748)Gta>Ata	p.V916I	DHX9_ENST00000485081.1_3'UTR	NM_001357.4	NP_001348.2	Q08211	DHX9_HUMAN	DEAH (Asp-Glu-Ala-His) box helicase 9	916					ATP catabolic process (GO:0006200)|cellular response to heat (GO:0034605)|circadian rhythm (GO:0007623)|CRD-mediated mRNA stabilization (GO:0070934)|DNA duplex unwinding (GO:0032508)|gene expression (GO:0010467)|innate immune response (GO:0045087)|mRNA splicing, via spliceosome (GO:0000398)|osteoblast differentiation (GO:0001649)|positive regulation of type I interferon production (GO:0032481)|RNA splicing (GO:0008380)	centrosome (GO:0005813)|CRD-mediated mRNA stability complex (GO:0070937)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|ATP-dependent RNA helicase activity (GO:0004004)|DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|RNA helicase activity (GO:0003724)|RNA polymerase II transcription factor binding (GO:0001085)			NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(10)|kidney(3)|large_intestine(7)|liver(1)|lung(19)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	49						TTCTGATCACGTAGCCCTTTT	0.433																																					p.V916I	Colon(69;210 1162 3697 13559 39565)	Atlas-SNP	.											.	DHX9	114	.	0			c.G2746A						PASS	.						149.0	140.0	143.0					1																	182850520		1865	4107	5972	SO:0001583	missense	1660	exon23			GATCACGTAGCCC	L13848	CCDS41444.1	1q25	2013-05-13	2013-05-13	2003-06-20	ENSG00000135829	ENSG00000135829		"""DEAH-boxes"""	2750	protein-coding gene	gene with protein product	"""NDH II"", ""RNA helicase A"""	603115	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 9 (RNA helicase A, nuclear DNA helicase II; leukophysin)"", ""DEAH (Asp-Glu-Ala-His) box polypeptide 9"""	LKP, DDX9		8344961, 9111062	Standard	NM_001357		Approved	RHA	uc001gpr.3	Q08211	OTTHUMG00000035337	ENST00000367549.3:c.2746G>A	1.37:g.182850520G>A	ENSP00000356520:p.Val916Ile	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	117	62	0.529915	NM_001357	B2RNV4|Q05CI5|Q12803|Q32Q22|Q5VY62|Q6PD69|Q99556	Missense_Mutation	SNP	ENST00000367549.3	37	CCDS41444.1	.	.	.	.	.	.	.	.	.	.	G	31	5.082905	0.94050	.	.	ENSG00000135829	ENST00000367549	T	0.27557	1.66	5.76	5.76	0.90799	Helicase-associated domain (2);	0.000000	0.85682	D	0.000000	T	0.36580	0.0972	N	0.17379	0.485	0.80722	D	1	D;D	0.60575	0.969;0.988	P;P	0.58077	0.572;0.832	T	0.07028	-1.0794	10	0.30854	T	0.27	.	19.5961	0.95538	0.0:0.0:1.0:0.0	.	195;916	B3KU66;Q08211	.;DHX9_HUMAN	I	916	ENSP00000356520:V916I	ENSP00000356520:V916I	V	+	1	0	DHX9	181117143	1.000000	0.71417	0.999000	0.59377	0.931000	0.56810	7.251000	0.78297	2.706000	0.92434	0.655000	0.94253	GTA	.	.	none		0.433	DHX9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085522.2	NM_030588	
OR2T4	127074	hgsc.bcm.edu	37	1	248525640	248525640	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:248525640T>C	ENST00000366475.1	+	1	758	c.758T>C	c.(757-759)aTc>aCc	p.I253T		NM_001004696.1	NP_001004696.1	Q8NH00	OR2T4_HUMAN	olfactory receptor, family 2, subfamily T, member 4	253						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|liver(2)|lung(47)	56	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			TATTTACTCATCCTCCTCACC	0.517																																					p.I253T		Atlas-SNP	.											OR2T4,brain,glioma,+1,1	OR2T4	126	1	0			c.T758C						scavenged	.						135.0	130.0	132.0					1																	248525640		2203	4300	6503	SO:0001583	missense	127074	exon1			TACTCATCCTCCT	BK004464	CCDS31113.1	1q44	2012-08-09			ENSG00000196944	ENSG00000196944		"""GPCR / Class A : Olfactory receptors"""	15016	protein-coding gene	gene with protein product							Standard	NM_001004696		Approved	OR2T4Q	uc001ieh.1	Q8NH00	OTTHUMG00000040453	ENST00000366475.1:c.758T>C	1.37:g.248525640T>C	ENSP00000355431:p.Ile253Thr	Somatic	357	9	0.0252101		WXS	Illumina HiSeq	Phase_I	296	12	0.0405405	NM_001004696	Q6IEZ8	Missense_Mutation	SNP	ENST00000366475.1	37	CCDS31113.1	.	.	.	.	.	.	.	.	.	.	T	10.31	1.315398	0.23908	.	.	ENSG00000196944	ENST00000366475	T	0.00402	7.56	3.09	1.94	0.25998	GPCR, rhodopsin-like superfamily (1);	0.000000	0.47852	D	0.000219	T	0.01523	0.0049	H	0.95151	3.63	0.33277	D	0.561816	D	0.89917	1.0	D	0.85130	0.997	T	0.11299	-1.0593	10	0.87932	D	0	.	7.6506	0.28346	0.0:0.1075:0.0:0.8925	.	253	Q8NH00	OR2T4_HUMAN	T	253	ENSP00000355431:I253T	ENSP00000355431:I253T	I	+	2	0	OR2T4	246592263	1.000000	0.71417	0.061000	0.19648	0.014000	0.08584	4.666000	0.61554	0.295000	0.22570	-0.361000	0.07541	ATC	.	.	none		0.517	OR2T4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097349.2	NM_001004696	
VILL	50853	hgsc.bcm.edu	37	3	38047954	38047954	+	Missense_Mutation	SNP	G	G	C	rs9816693	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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						PASS	.	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	192	0	0		WXS	Illumina HiSeq	Phase_I	108	107	0.990741	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	
TMEM119	338773	hgsc.bcm.edu	37	12	108986031	108986031	+	Silent	SNP	C	C	T	rs74504010	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:108986031C>T	ENST00000392806.3	-	2	297	c.129G>A	c.(127-129)gaG>gaA	p.E43E		NM_181724.2	NP_859075.2	Q4V9L6	TM119_HUMAN	transmembrane protein 119	43					osteoblast differentiation (GO:0001649)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				large_intestine(2)|lung(3)|ovary(1)|skin(1)	7						AGCCCTCGGCCTCCCCACTAC	0.706													C|||	832	0.166134	0.0053	0.1297	5008	,	,		11135	0.3145		0.164	False		,,,				2504	0.2587				p.E43E		Atlas-SNP	.											TMEM119,NS,carcinoma,0,1	TMEM119	31	1	0			c.G129A						scavenged	.	C		156,4214		6,144,2035	8.0	11.0	10.0		129	0.4	1.0	12	dbSNP_131	10	1399,7135		129,1141,2997	no	coding-synonymous	TMEM119	NM_181724.2		135,1285,5032	TT,TC,CC		16.3933,3.5698,12.0505		43/284	108986031	1555,11349	2185	4267	6452	SO:0001819	synonymous_variant	338773	exon2			CTCGGCCTCCCCA	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.129G>A	12.37:g.108986031C>T		Somatic	9	0	0		WXS	Illumina HiSeq	Phase_I	24	11	0.458333	NM_181724	Q6UXE5|Q8N2F5	Silent	SNP	ENST00000392806.3	37	CCDS9119.1																																																																																			C|0.827;T|0.173	0.173	strong		0.706	TMEM119-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403900.1	NM_181724	
CCDC168	643677	hgsc.bcm.edu	37	13	103390386	103390386	+	5'Flank	SNP	C	C	A	rs74471135	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:103390386C>A	ENST00000322527.2	-	0	0					NM_001146197.1	NP_001139669.1	Q8NDH2	CC168_HUMAN	coiled-coil domain containing 168																		tcttgtcctgcacctcttctg	0.458													C|||	390	0.0778754	0.0439	0.0677	5008	,	,		21248	0.0139		0.1252	False		,,,				2504	0.1483				p.A4221S		Atlas-SNP	.											.	.	.	.	0			c.G12661T						PASS	.	C	SER/ALA	57,1327		4,49,639	203.0	160.0	173.0		12661	-2.0	0.0	13	dbSNP_132	173	377,2805		22,333,1236	yes	missense	CCDC168	NM_001146197.1	99	26,382,1875	AA,AC,CC		11.8479,4.1185,9.505		4221/7082	103390386	434,4132	692	1591	2283	SO:0001631	upstream_gene_variant	643677	exon4			GTCCTGCACCTCT		CCDS73596.1	13q33.1	2014-06-17	2011-08-09	2011-08-09	ENSG00000175820	ENSG00000175820			26851	protein-coding gene	gene with protein product			"""chromosome 13 open reading frame 40"""	C13orf40			Standard	NM_001146197		Approved	FLJ40176	uc001vpm.3	Q8NDH2	OTTHUMG00000187287		13.37:g.103390386C>A	Exception_encountered	Somatic	344	1	0.00290698		WXS	Illumina HiSeq	Phase_I	296	138	0.466216	NM_001146197	Q8N800	Missense_Mutation	SNP	ENST00000322527.2	37																																																																																				C|0.931;A|0.069	0.069	strong		0.458	CCDC168-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001146197	
CSMD1	64478	hgsc.bcm.edu	37	8	3200877	3200877	+	Silent	SNP	C	C	T	rs2161752	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:3200877C>T	ENST00000520002.1	-	24	4128	c.3573G>A	c.(3571-3573)ctG>ctA	p.L1191L	CSMD1_ENST00000542608.1_Silent_p.L1190L|CSMD1_ENST00000602557.1_Silent_p.L1191L|CSMD1_ENST00000539096.1_Silent_p.L1190L|CSMD1_ENST00000537824.1_Silent_p.L1190L|CSMD1_ENST00000400186.3_Silent_p.L1191L|CSMD1_ENST00000602723.1_Silent_p.L1191L			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	1191	CUB 7. {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)		ACTCTAGCCACAGGTGATTGG	0.423													C|||	628	0.125399	0.1256	0.1182	5008	,	,		17006	0.1081		0.172	False		,,,				2504	0.1002				p.L1190L		Atlas-SNP	.											CSMD1_ENST00000537824,colon,carcinoma,0,4	CSMD1	1469	4	0			c.G3570A						PASS	.	C		508,3368		43,422,1473	167.0	170.0	169.0		3570	5.0	1.0	8	dbSNP_96	169	1458,6816		130,1198,2809	no	coding-synonymous	CSMD1	NM_033225.5		173,1620,4282	TT,TC,CC		17.6215,13.1063,16.1811		1190/3565	3200877	1966,10184	1938	4137	6075	SO:0001819	synonymous_variant	64478	exon23			TAGCCACAGGTGA			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.3573G>A	8.37:g.3200877C>T		Somatic	244	0	0		WXS	Illumina HiSeq	Phase_I	208	59	0.283654	NM_033225	Q0H0J5|Q96QU9|Q96RM4	Silent	SNP	ENST00000520002.1	37		317	0.14514652014652016	79	0.16056910569105692	48	0.13259668508287292	66	0.11538461538461539	124	0.16358839050131926	C	8.521	0.868721	0.17322	0.131063	0.176215	ENSG00000183117	ENST00000335551	.	.	.	5.86	4.99	0.66335	.	.	.	.	.	T	0.00178	0.0005	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.14504	-1.0470	3	.	.	.	.	9.3779	0.38295	0.0:0.7882:0.0:0.2118	rs2161752;rs59686879;rs2161752	.	.	.	M	671	.	.	V	-	1	0	CSMD1	3188284	0.996000	0.38824	1.000000	0.80357	0.751000	0.42716	0.482000	0.22276	1.626000	0.50381	0.650000	0.86243	GTG	C|0.853;T|0.147	0.147	strong		0.423	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225	
HSPG2	3339	hgsc.bcm.edu	37	1	22150118	22150118	+	Missense_Mutation	SNP	C	C	T	rs1138469	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:22150118C>T	ENST00000374695.3	-	96	13073	c.12994G>A	c.(12994-12996)Gtc>Atc	p.V4332I	LDLRAD2_ENST00000543870.1_Intron|LDLRAD2_ENST00000344642.2_3'UTR|HSPG2_ENST00000486901.1_5'UTR	NM_005529.5	NP_005520.4	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2	4332	Laminin G-like 3. {ECO:0000255|PROSITE- ProRule:PRU00122}.			V -> I (in Ref. 2; CAA44373). {ECO:0000305}.	angiogenesis (GO:0001525)|brain development (GO:0007420)|carbohydrate metabolic process (GO:0005975)|cardiac muscle tissue development (GO:0048738)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|chondrocyte differentiation (GO:0002062)|chondroitin sulfate metabolic process (GO:0030204)|embryonic skeletal system morphogenesis (GO:0048704)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|lipoprotein metabolic process (GO:0042157)|phototransduction, visible light (GO:0007603)|protein localization (GO:0008104)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	basal lamina (GO:0005605)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)			breast(6)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(15)|liver(1)|lung(44)|ovary(10)|pancreas(1)|prostate(10)|skin(9)|upper_aerodigestive_tract(3)|urinary_tract(3)	127		Colorectal(325;3.46e-05)|all_lung(284;7.93e-05)|Lung NSC(340;8.71e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0498)|OV - Ovarian serous cystadenocarcinoma(117;1.14e-26)|Colorectal(126;4.18e-07)|COAD - Colon adenocarcinoma(152;1.82e-05)|GBM - Glioblastoma multiforme(114;3.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000756)|STAD - Stomach adenocarcinoma(196;0.00656)|KIRC - Kidney renal clear cell carcinoma(1967;0.00942)|READ - Rectum adenocarcinoma(331;0.0721)|Lung(427;0.223)	Palifermin(DB00039)	CCGATGTAGACGCTGCCCTTG	0.662													C|||	227	0.0453275	0.0318	0.0317	5008	,	,		14894	0.0		0.0616	False		,,,				2504	0.1033				p.V4332I		Atlas-SNP	.											.	HSPG2	311	.	0			c.G12994A						PASS	.	C	,ILE/VAL	167,4239	111.6+/-149.8	6,155,2042	107.0	104.0	105.0		,12994	-8.6	0.5	1	dbSNP_86	105	529,8071	148.6+/-203.8	15,499,3786	yes	utr-3,missense	HSPG2,LDLRAD2	NM_001013693.2,NM_005529.5	,29	21,654,5828	TT,TC,CC		6.1512,3.7903,5.3514	,benign	,4332/4392	22150118	696,12310	2203	4300	6503	SO:0001583	missense	3339	exon96			TGTAGACGCTGCC	M85289	CCDS30625.1	1p36.1-p35	2013-01-29	2007-02-16	2007-02-16	ENSG00000142798	ENSG00000142798		"""Proteoglycans / Extracellular Matrix : Other"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5273	protein-coding gene	gene with protein product	"""perlecan proteoglycan"""	142461	"""Schwartz-Jampel syndrome 1 (chondrodystrophic myotonia)"""	SJS1		1685141, 11941538	Standard	XM_005245863		Approved	perlecan, PRCAN	uc001bfj.3	P98160	OTTHUMG00000002674	ENST00000374695.3:c.12994G>A	1.37:g.22150118C>T	ENSP00000363827:p.Val4332Ile	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	93	42	0.451613	NM_005529	Q16287|Q5SZI3|Q9H3V5	Missense_Mutation	SNP	ENST00000374695.3	37	CCDS30625.1	75	0.034340659340659344	15	0.03048780487804878	13	0.03591160220994475	0	0.0	47	0.06200527704485488	C	3.049	-0.195888	0.06259	0.037903	0.061512	ENSG00000142798	ENST00000374695	T	0.74842	-0.88	5.03	-8.58	0.00897	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 1 (1);	0.416632	0.17446	N	0.173944	T	0.06962	0.0177	N	0.05467	-0.045	0.28075	N	0.932414	B;B	0.10296	0.001;0.003	B;B	0.06405	0.002;0.002	T	0.27434	-1.0074	10	0.02654	T	1	.	15.0118	0.71555	0.0:0.549:0.0:0.451	rs1138469	2272;4332	Q59EG0;P98160	.;PGBM_HUMAN	I	4332	ENSP00000363827:V4332I	ENSP00000363827:V4332I	V	-	1	0	HSPG2	22022705	0.000000	0.05858	0.542000	0.28115	0.545000	0.35147	-1.412000	0.02476	-2.102000	0.00845	-1.910000	0.00522	GTC	C|0.949;T|0.051	0.051	strong		0.662	HSPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007598.1	NM_005529	
CLCA2	9635	hgsc.bcm.edu	37	1	86909582	86909582	+	Missense_Mutation	SNP	G	G	A	rs1413426	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	86	0	0		WXS	Illumina HiSeq	Phase_I	81	41	0.506173	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	
TRIM39	56658	hgsc.bcm.edu	37	6	30309508	30309508	+	Silent	SNP	T	T	C	rs2074474	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:30309508T>C	ENST00000396547.1	+	8	1189	c.1029T>C	c.(1027-1029)ccT>ccC	p.P343P	TRIM39_ENST00000376656.4_Silent_p.P343P|TRIM39-RPP21_ENST00000513556.1_Silent_p.P225P|TRIM39_ENST00000396548.1_Silent_p.P313P|TRIM39_ENST00000396551.3_Silent_p.P313P|TRIM39_ENST00000540416.1_Silent_p.P313P|TRIM39_ENST00000376659.5_Silent_p.P313P			Q9HCM9	TRI39_HUMAN	tripartite motif containing 39	343	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				apoptotic process (GO:0006915)|negative regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000059)|positive regulation of apoptotic signaling pathway (GO:2001235)|protein ubiquitination (GO:0016567)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	identical protein binding (GO:0042802)|ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			ovary(3)	3						CCCTGGACCCTGAGACAGCTC	0.562													T|||	1887	0.376797	0.3109	0.451	5008	,	,		20955	0.5119		0.2435	False		,,,				2504	0.411				p.P343P		Atlas-SNP	.											TRIM39_ENST00000376656,NS,malignant_melanoma,+2,1	TRIM39	56	1	0			c.T1029C						PASS	.	T	,,	852,2170		114,624,773	59.0	44.0	49.0		939,1029,939	-7.9	1.0	6	dbSNP_96	49	1327,4089		157,1013,1538	yes	coding-synonymous,coding-synonymous,coding-synonymous	TRIM39,TRIM39-RPP21	NM_001199119.1,NM_021253.3,NM_172016.2	,,	271,1637,2311	CC,CT,TT		24.5015,28.1932,25.8237	,,	313/504,343/519,313/489	30309508	2179,6259	1511	2708	4219	SO:0001819	synonymous_variant	56658	exon9			GGACCCTGAGACA	BC034985	CCDS34377.1, CCDS34378.1	6p22.1	2013-01-09	2011-01-25	2002-06-07	ENSG00000204599	ENSG00000204599		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	10065	protein-coding gene	gene with protein product		605700	"""ring finger protein 23"", ""tripartite motif-containing 39"""	RNF23		11006080	Standard	NM_021253		Approved			Q9HCM9	OTTHUMG00000031066	ENST00000396547.1:c.1029T>C	6.37:g.30309508T>C		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	50	29	0.58	NM_021253	Q5STG3|Q5STG4|Q76BL3|Q8IYT9|Q96IB6	Silent	SNP	ENST00000396547.1	37	CCDS34377.1																																																																																			T|0.701;C|0.299	0.299	strong		0.562	TRIM39-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000076086.2	NM_172016	
PDE4DIP	9659	hgsc.bcm.edu	37	1	144856852	144856852	+	Silent	SNP	C	C	T	rs377520030		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:144856852C>T	ENST00000369354.3	-	40	6822	c.6633G>A	c.(6631-6633)gcG>gcA	p.A2211A	PDE4DIP_ENST00000369359.4_Silent_p.A2347A|PDE4DIP_ENST00000313382.9_Silent_p.A2105A|PDE4DIP_ENST00000369356.4_Silent_p.A2211A|RP4-791M13.4_ENST00000532137.1_RNA|PDE4DIP_ENST00000530740.1_Silent_p.A2296A|PDE4DIP_ENST00000524974.1_5'UTR			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	2211					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.A2211A(1)		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)		GGAAGCTGCACGCTGATCTCA	0.502			T	PDGFRB	MPD																																p.A2211A		Atlas-SNP	.		Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	PDE4DIP_ENST00000369356,NS,carcinoma,-1,3	PDE4DIP	817	3	1	Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(1)	c.G6633A						PASS	.						39.0	31.0	34.0					1																	144856852		2199	4286	6485	SO:0001819	synonymous_variant	9659	exon40			GCTGCACGCTGAT	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.6633G>A	1.37:g.144856852C>T		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	128	24	0.1875	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	.	.	.	.	.	.	.	.	.	.	.	5.637	0.302253	0.10678	.	.	ENSG00000178104	ENST00000530130	.	.	.	4.52	-1.01	0.10169	.	.	.	.	.	T	0.12263	0.0298	.	.	.	0.32646	N	0.519982	.	.	.	.	.	.	T	0.19745	-1.0296	4	.	.	.	.	1.5392	0.02551	0.1278:0.2204:0.3685:0.2833	.	.	.	.	H	288	.	.	R	-	2	0	PDE4DIP	143568209	0.000000	0.05858	0.052000	0.19188	0.068000	0.16541	-1.120000	0.03273	0.239000	0.21243	-0.693000	0.03709	CGT	.	.	none		0.502	PDE4DIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000038858.2	NM_022359	
SLC8A1	6546	hgsc.bcm.edu	37	2	40656756	40656756	+	Nonsense_Mutation	SNP	A	A	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:40656756A>T	ENST00000403092.1	-	2	698	c.665T>A	c.(664-666)tTg>tAg	p.L222*	SLC8A1_ENST00000402441.1_Nonsense_Mutation_p.L222*|SLC8A1_ENST00000542756.1_Nonsense_Mutation_p.L222*|SLC8A1_ENST00000542024.1_Nonsense_Mutation_p.L222*|SLC8A1_ENST00000406785.2_Nonsense_Mutation_p.L222*|SLC8A1_ENST00000408028.2_Nonsense_Mutation_p.L222*|SLC8A1_ENST00000332839.4_Nonsense_Mutation_p.L222*|SLC8A1_ENST00000406391.2_Nonsense_Mutation_p.L222*|SLC8A1_ENST00000405901.3_Nonsense_Mutation_p.L222*|SLC8A1_ENST00000405269.1_Nonsense_Mutation_p.L222*			P32418	NAC1_HUMAN	solute carrier family 8 (sodium/calcium exchanger), member 1	222					blood coagulation (GO:0007596)|calcium ion export (GO:1901660)|calcium ion homeostasis (GO:0055074)|calcium ion import (GO:0070509)|calcium ion transport into cytosol (GO:0060402)|cardiac muscle cell development (GO:0055013)|cardiac muscle contraction (GO:0060048)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular response to caffeine (GO:0071313)|cellular response to reactive oxygen species (GO:0034614)|cellular sodium ion homeostasis (GO:0006883)|cytosolic calcium ion transport (GO:0060401)|embryonic heart tube development (GO:0035050)|embryonic placenta development (GO:0001892)|heart morphogenesis (GO:0003007)|ion transport (GO:0006811)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|muscle contraction (GO:0006936)|muscle fiber development (GO:0048747)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|post-embryonic development (GO:0009791)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|regulation of the force of heart contraction (GO:0002026)|relaxation of cardiac muscle (GO:0055119)|relaxation of smooth muscle (GO:0044557)|sodium ion export (GO:0071436)|sodium ion import (GO:0097369)|transmembrane transport (GO:0055085)|vascular smooth muscle contraction (GO:0014829)	basolateral plasma membrane (GO:0016323)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|calcium:sodium antiporter activity (GO:0005432)|cytoskeletal protein binding (GO:0008092)|ion channel binding (GO:0044325)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(1)|endometrium(7)|kidney(5)|large_intestine(14)|liver(1)|lung(57)|ovary(2)|pancreas(1)|skin(7)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(2)	100					Alpha-Linolenic Acid(DB00132)|Icosapent(DB00159)	TATGACAGACAAAATAATGTA	0.473																																					p.L222X		Atlas-SNP	.											.	SLC8A1	221	.	0			c.T665A						PASS	.						52.0	56.0	55.0					2																	40656756		2203	4300	6503	SO:0001587	stop_gained	6546	exon1			ACAGACAAAATAA		CCDS1806.1, CCDS46264.1, CCDS46265.1, CCDS59430.1	2p22.1	2013-07-15			ENSG00000183023	ENSG00000183023		"""Solute carriers"""	11068	protein-coding gene	gene with protein product	"""Na+/Ca++ exchanger"""	182305		NCX1		1559714	Standard	NM_021097		Approved		uc002rrx.3	P32418	OTTHUMG00000102183	ENST00000403092.1:c.665T>A	2.37:g.40656756A>T	ENSP00000384763:p.Leu222*	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	100	15	0.15	NM_001252624	A8K6N1|D6W595|O95849|Q4QQG6|Q587I6|Q59GN4|Q9UBL8|Q9UD55|Q9UDN1|Q9UDN2|Q9UKX6	Nonsense_Mutation	SNP	ENST00000403092.1	37	CCDS1806.1	.	.	.	.	.	.	.	.	.	.	A	25.4	4.631169	0.87660	.	.	ENSG00000183023	ENST00000406785;ENST00000378715;ENST00000542756;ENST00000403092;ENST00000405901;ENST00000402441;ENST00000405269;ENST00000332839;ENST00000408028;ENST00000535962;ENST00000406391;ENST00000542024	.	.	.	5.45	5.45	0.79879	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	13.4743	0.61299	1.0:0.0:0.0:0.0	.	.	.	.	X	222	.	ENSP00000332931:L222X	L	-	2	0	SLC8A1	40510260	1.000000	0.71417	0.954000	0.39281	0.928000	0.56348	9.151000	0.94674	2.076000	0.62316	0.460000	0.39030	TTG	.	.	none		0.473	SLC8A1-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326065.1	NM_021097	
OR5D14	219436	hgsc.bcm.edu	37	11	55563738	55563738	+	Missense_Mutation	SNP	G	G	A	rs67863827	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:55563738G>A	ENST00000335605.1	+	1	707	c.707G>A	c.(706-708)cGc>cAc	p.R236H		NM_001004735.1	NP_001004735.1	Q8NGL3	OR5DE_HUMAN	olfactory receptor, family 5, subfamily D, member 14	236						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.R236H(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(30)|ovary(2)|prostate(1)|skin(2)|stomach(3)|urinary_tract(1)	48		all_epithelial(135;0.196)				GTTAGTGGGCGCCACAAAGCC	0.458													g|||	447	0.0892572	0.1301	0.0432	5008	,	,		18674	0.0823		0.0924	False		,,,				2504	0.0706				p.R236H		Atlas-SNP	.											OR5D14,rectum,carcinoma,+1,4	OR5D14	116	4	1	Substitution - Missense(1)	stomach(1)	c.G707A						PASS	.	G	HIS/ARG	526,3874	239.6+/-250.7	35,456,1709	129.0	120.0	123.0		707	2.1	0.0	11	dbSNP_130	123	722,7870	176.0+/-226.0	31,660,3605	yes	missense	OR5D14	NM_001004735.1	29	66,1116,5314	AA,AG,GG		8.4032,11.9545,9.6059	benign	236/315	55563738	1248,11744	2200	4296	6496	SO:0001583	missense	219436	exon1			GTGGGCGCCACAA	AB065779	CCDS31508.1	11q11	2012-08-09			ENSG00000186113	ENSG00000186113		"""GPCR / Class A : Olfactory receptors"""	15281	protein-coding gene	gene with protein product							Standard	NM_001004735		Approved		uc010rim.2	Q8NGL3	OTTHUMG00000166809	ENST00000335605.1:c.707G>A	11.37:g.55563738G>A	ENSP00000334456:p.Arg236His	Somatic	196	0	0		WXS	Illumina HiSeq	Phase_I	175	125	0.714286	NM_001004735	Q6IF69|Q6IFD4|Q96RB5	Missense_Mutation	SNP	ENST00000335605.1	37	CCDS31508.1	196	0.08974358974358974	76	0.15447154471544716	20	0.055248618784530384	35	0.06118881118881119	65	0.08575197889182058	g	6.197	0.404439	0.11754	0.119545	0.084032	ENSG00000186113	ENST00000335605	T	0.00333	8.07	5.08	2.13	0.27403	GPCR, rhodopsin-like superfamily (1);	0.172823	0.25774	N	0.028382	T	0.00012	0.0000	M	0.79805	2.47	0.80722	P	0.0	B	0.26512	0.151	B	0.29524	0.103	T	0.36696	-0.9737	9	0.54805	T	0.06	-3.9031	5.4947	0.16795	0.2359:0.0:0.6227:0.1413	.	236	Q8NGL3	OR5DE_HUMAN	H	236	ENSP00000334456:R236H	ENSP00000334456:R236H	R	+	2	0	OR5D14	55320314	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-1.512000	0.02258	0.164000	0.19529	0.643000	0.83706	CGC	G|0.907;A|0.093	0.093	strong		0.458	OR5D14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391513.1	NM_001004735	
TMEM199	147007	hgsc.bcm.edu	37	17	26691916	26691916	+	IGR	SNP	T	T	C	rs2277667	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:26691916T>C	ENST00000292114.3	+	0	3148				VTN_ENST00000431468.1_Silent_p.L57L|VTN_ENST00000438614.1_Silent_p.L56L|CTB-96E2.2_ENST00000555059.2_Missense_Mutation_p.T131A|TMEM199_ENST00000509083.1_Intron|SARM1_ENST00000379061.4_Intron|CTB-96E2.3_ENST00000591482.1_RNA|CTB-96E2.7_ENST00000577850.1_RNA|VTN_ENST00000536498.1_Silent_p.L56L	NM_152464.1	NP_689677.1	Q8N511	TM199_HUMAN	transmembrane protein 199							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)		CCAGCTCCAGTAGCTGCCCTT	0.632													C|||	812	0.162141	0.1853	0.0821	5008	,	,		18306	0.244		0.0785	False		,,,				2504	0.1892				p.L57L		Atlas-SNP	.											.	SEBOX	20	.	0			c.A171G						PASS	.	C		721,3659		65,591,1534	58.0	68.0	64.0		171	3.2	1.0	17	dbSNP_100	64	696,7868		33,630,3619	no	coding-synonymous	SEBOX	NM_001080837.2		98,1221,5153	CC,CT,TT		8.127,16.4612,10.9472		57/217	26691916	1417,11527	2190	4282	6472	SO:0001628	intergenic_variant	645832	exon2			CTCCAGTAGCTGC	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		17.37:g.26691916T>C		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	106	46	0.433962	NM_001080837		Silent	SNP	ENST00000292114.3	37	CCDS11228.1																																																																																			T|0.855;C|0.145	0.145	strong		0.632	TMEM199-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255676.2	NM_152464	
RILPL1	353116	hgsc.bcm.edu	37	12	124017850	124017850	+	Silent	SNP	G	G	C	rs28492040	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:124017850G>C	ENST00000376874.4	-	1	415	c.180C>G	c.(178-180)gtC>gtG	p.V60V		NM_178314.3	NP_847884.2	Q5EBL4	RIPL1_HUMAN	Rab interacting lysosomal protein-like 1	60					epithelial cell morphogenesis (GO:0003382)|intracellular protein transport (GO:0006886)|regulation of neuron death (GO:1901214)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|primary cilium (GO:0072372)				endometrium(1)|kidney(2)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(1)	7	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000224)|Epithelial(86;0.00067)|all cancers(50;0.00836)|BRCA - Breast invasive adenocarcinoma(302;0.197)		GGATCTCCAGGACGCGCACGA	0.687													G|||	590	0.117812	0.1225	0.121	5008	,	,		11260	0.0109		0.1909	False		,,,				2504	0.1442				p.V60V		Atlas-SNP	.											RILPL1,NS,carcinoma,0,1	RILPL1	23	1	0			c.C180G						PASS	.	G		592,3648		49,494,1577	10.0	15.0	13.0		180	0.9	1.0	12	dbSNP_125	13	1561,6859		151,1259,2800	no	coding-synonymous	RILPL1	NM_178314.3		200,1753,4377	CC,CG,GG		18.5392,13.9623,17.0063		60/404	124017850	2153,10507	2120	4210	6330	SO:0001819	synonymous_variant	353116	exon1			CTCCAGGACGCGC	AK097550	CCDS45006.1	12q24.31	2007-11-27			ENSG00000188026	ENSG00000188026			26814	protein-coding gene	gene with protein product		614092				14668488	Standard	NM_178314		Approved	FLJ39378	uc001ufe.2	Q5EBL4	OTTHUMG00000168686	ENST00000376874.4:c.180C>G	12.37:g.124017850G>C		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	47	46	0.978723	NM_178314	Q66K36|Q8N1M0	Silent	SNP	ENST00000376874.4	37	CCDS45006.1																																																																																			G|0.882;C|0.118	0.118	strong		0.687	RILPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400595.1	NM_178314	
HIST1H1B	3009	hgsc.bcm.edu	37	6	27835218	27835218	+	Silent	SNP	G	G	A	rs17763089	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:27835218G>A	ENST00000331442.3	-	1	141	c.90C>T	c.(88-90)ggC>ggT	p.G30G		NM_005322.2	NP_005313.1	P16401	H15_HUMAN	histone cluster 1, H1b	30					chromatin organization (GO:0006325)|establishment of protein localization to chromatin (GO:0071169)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nucleosome assembly (GO:0006334)|positive regulation of cell growth (GO:0030307)|positive regulation of histone H3-K9 methylation (GO:0051574)|protein stabilization (GO:0050821)	extracellular vesicular exosome (GO:0070062)|nuclear chromatin (GO:0000790)|nuclear heterochromatin (GO:0005720)|nucleosome (GO:0000786)	chromatin DNA binding (GO:0031490)|histone deacetylase binding (GO:0042826)|poly(A) RNA binding (GO:0044822)			endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(5)|lung(12)|prostate(2)|upper_aerodigestive_tract(2)	24						CAGCGCCGGCGCCGGCAGCCT	0.617													G|||	103	0.0205671	0.0023	0.0389	5008	,	,		13957	0.0		0.0726	False		,,,				2504	0.0				p.G30G		Atlas-SNP	.											.	HIST1H1B	54	.	0			c.C90T						PASS	.	G		90,4302		2,86,2108	31.0	38.0	36.0		90	-5.1	0.0	6	dbSNP_123	36	768,7824		35,698,3563	no	coding-synonymous	HIST1H1B	NM_005322.2		37,784,5671	AA,AG,GG		8.9385,2.0492,6.6081		30/227	27835218	858,12126	2196	4296	6492	SO:0001819	synonymous_variant	3009	exon1			GCCGGCGCCGGCA	AF531304	CCDS4635.1	6p22.1	2012-05-04	2006-10-11	2003-02-14	ENSG00000184357	ENSG00000184357		"""Histones / Replication-dependent"""	4719	protein-coding gene	gene with protein product		142711	"""H1 histone family, member 5"", ""histone 1, H1b"""	H1F5		9031620, 9119399, 12408966	Standard	NM_005322		Approved	H1.5, H1b, H1s-3	uc003njx.3	P16401	OTTHUMG00000016139	ENST00000331442.3:c.90C>T	6.37:g.27835218G>A		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	109	51	0.46789	NM_005322	Q14529|Q3MJ42	Silent	SNP	ENST00000331442.3	37	CCDS4635.1																																																																																			G|0.945;A|0.055	0.055	strong		0.617	HIST1H1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043371.1	NM_005322	
FBXL13	222235	hgsc.bcm.edu	37	7	102462636	102462636	+	Silent	SNP	T	T	C	rs10279449	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:102462636T>C	ENST00000313221.4	-	19	2295	c.1869A>G	c.(1867-1869)gcA>gcG	p.A623A	FBXL13_ENST00000455112.2_Silent_p.A578A|FBXL13_ENST00000379308.3_Silent_p.A578A|FBXL13_ENST00000456695.1_Silent_p.A341A|FBXL13_ENST00000379305.3_Silent_p.A595A|FBXL13_ENST00000436908.1_Silent_p.A623A|FBXL13_ENST00000393772.2_Silent_p.A595A|FBXL13_ENST00000379306.3_Silent_p.A341A	NM_145032.3	NP_659469.3	Q8NEE6	FXL13_HUMAN	F-box and leucine-rich repeat protein 13	623										NS(1)|breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(9)|skin(3)|stomach(1)	27						ACATCTCCATTGCTGAGTCAG	0.418													C|||	2621	0.523363	0.7451	0.3602	5008	,	,		21922	0.5744		0.3181	False		,,,				2504	0.498				p.A623A		Atlas-SNP	.											.	FBXL13	65	.	0			c.A1869G						PASS	.	C	,	3005,1401	461.1+/-352.8	1018,969,216	142.0	126.0	132.0		1734,1869	-7.6	0.0	7	dbSNP_119	132	3058,5542	661.9+/-401.9	542,1974,1784	no	coding-synonymous,coding-synonymous	FBXL13	NM_001111038.1,NM_145032.3	,	1560,2943,2000	CC,CT,TT		35.5581,31.7975,46.6169	,	578/691,623/736	102462636	6063,6943	2203	4300	6503	SO:0001819	synonymous_variant	222235	exon19			CTCCATTGCTGAG	BC031285	CCDS5726.1, CCDS47678.1, CCDS75649.1	7q22.1	2014-07-18			ENSG00000161040	ENSG00000161040		"""F-boxes / Leucine-rich repeats"""	21658	protein-coding gene	gene with protein product		609080					Standard	NM_145032		Approved	MGC21636, Fbl13	uc003vaq.2	Q8NEE6	OTTHUMG00000157224	ENST00000313221.4:c.1869A>G	7.37:g.102462636T>C		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	55	28	0.509091	NM_145032	C9J565|C9J566|Q6UVW7|Q6UVW8|Q75MN5|Q86UJ5|Q8N7Y4|Q8TCL2|Q8WUF9|Q8WUG0	Silent	SNP	ENST00000313221.4	37	CCDS5726.1																																																																																			T|0.517;C|0.483	0.483	strong		0.418	FBXL13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348001.1	NM_145032	
SLC19A1	6573	hgsc.bcm.edu	37	21	46957794	46957794	+	Missense_Mutation	SNP	T	T	C	rs1051266	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:46957794T>C	ENST00000311124.4	-	2	232	c.80A>G	c.(79-81)cAc>cGc	p.H27R	SLC19A1_ENST00000380010.4_Missense_Mutation_p.H27R|SLC19A1_ENST00000567670.1_Missense_Mutation_p.H27R	NM_194255.2	NP_919231.1	P41440	S19A1_HUMAN	solute carrier family 19 (folate transporter), member 1	27			H -> R (in dbSNP:rs1051266). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:7615551, ECO:0000269|PubMed:7641195, ECO:0000269|PubMed:7826387, ECO:0000269|Ref.6}.		folic acid metabolic process (GO:0046655)|folic acid transport (GO:0015884)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	folic acid binding (GO:0005542)|folic acid transporter activity (GO:0008517)|methotrexate transporter activity (GO:0015350)			endometrium(4)|kidney(1)|large_intestine(1)|lung(1)|prostate(1)|skin(1)|urinary_tract(1)	10				Colorectal(79;0.0569)|READ - Rectum adenocarcinoma(84;0.172)	Methotrexate(DB00563)|Pralatrexate(DB06813)	GCACACGAGGTGCCGCCAGGA	0.657													C|||	2447	0.488618	0.3268	0.5821	5008	,	,		11906	0.4742		0.5487	False		,,,				2504	0.5941				p.H27R		Atlas-SNP	.											.	SLC19A1	53	.	0			c.A80G	GRCh37	CM004369	SLC19A1	M	rs1051266	PASS	.	C	ARG/HIS,ARG/HIS	1717,2669		358,1001,834	47.0	36.0	40.0		80,80	2.8	0.2	21	dbSNP_86	40	4894,3700		1416,2062,819	yes	missense,missense	SLC19A1	NM_001205206.1,NM_194255.2	29,29	1774,3063,1653	CC,CT,TT		43.0533,39.1473,49.0678	benign,benign	27/490,27/592	46957794	6611,6369	2193	4297	6490	SO:0001583	missense	6573	exon2			ACGAGGTGCCGCC	U15939	CCDS13725.1, CCDS56217.1, CCDS56218.1	21q22.3	2013-05-22			ENSG00000173638	ENSG00000173638		"""Solute carriers"""	10937	protein-coding gene	gene with protein product		600424				9570943	Standard	NM_194255		Approved	FOLT	uc002zhl.2	P41440	OTTHUMG00000090397	ENST00000311124.4:c.80A>G	21.37:g.46957794T>C	ENSP00000308895:p.His27Arg	Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	28	28	1	NM_001205206	B2R7U8|B7Z8C3|E9PFY4|O00553|O60227|Q13026|Q9BTX8	Missense_Mutation	SNP	ENST00000311124.4	37	CCDS13725.1	1073	0.4913003663003663	171	0.3475609756097561	205	0.5662983425414365	269	0.47027972027972026	428	0.5646437994722955	C	4.113	0.019156	0.08006	0.391473	0.569467	ENSG00000173638	ENST00000311124;ENST00000380010;ENST00000427839;ENST00000443742;ENST00000528477	T;T;T;T;D	0.85171	-1.39;-1.39;0.36;0.36;-1.95	3.85	2.77	0.32553	Major facilitator superfamily domain, general substrate transporter (1);	1.430790	0.04629	N	0.403225	T	0.00012	0.0000	N	0.00841	-1.15	0.24554	P	0.99400732	B;B;B	0.06786	0.0;0.001;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.34079	-0.9843	9	0.23891	T	0.37	-11.6327	4.7202	0.12915	0.4069:0.4723:0.0:0.1207	rs1051266;rs3171496;rs17844977;rs17857726;rs61510559;rs1051266	49;27;27	D3DSM6;E9PFY4;P41440	.;.;S19A1_HUMAN	R	27	ENSP00000308895:H27R;ENSP00000369347:H27R;ENSP00000401850:H27R;ENSP00000411345:H27R;ENSP00000435780:H27R	ENSP00000308895:H27R	H	-	2	0	SLC19A1	45782222	0.827000	0.29292	0.164000	0.22755	0.036000	0.12997	1.608000	0.36847	0.766000	0.33244	-0.197000	0.12766	CAC	T|0.518;C|0.482	0.482	strong		0.657	SLC19A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206796.1		
PGLYRP2	114770	hgsc.bcm.edu	37	19	15587345	15587345	+	Missense_Mutation	SNP	T	T	C	rs3813135	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:15587345T>C	ENST00000340880.4	-	2	616	c.136A>G	c.(136-138)Acc>Gcc	p.T46A	PGLYRP2_ENST00000292609.4_Missense_Mutation_p.T46A	NM_052890.3	NP_443122.3	Q96PD5	PGRP2_HUMAN	peptidoglycan recognition protein 2	46			T -> A (in dbSNP:rs3813135). {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.T46A(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						GTGTGTCTGGTCTTGGCAGCT	0.592													C|||	1762	0.351837	0.3457	0.3429	5008	,	,		19540	0.3651		0.4046	False		,,,				2504	0.2986				p.T46A		Atlas-SNP	.											PGLYRP2_ENST00000292609,NS,carcinoma,0,2	PGLYRP2	116	2	2	Substitution - Missense(2)	stomach(2)	c.A136G						scavenged	.	C	ALA/THR	1512,2894	673.1+/-402.7	258,996,949	49.0	46.0	47.0		136	2.0	0.0	19	dbSNP_107	47	3310,5290	645.4+/-400.2	669,1972,1659	yes	missense	PGLYRP2	NM_052890.3	58	927,2968,2608	CC,CT,TT		38.4884,34.3168,37.0752	benign	46/577	15587345	4822,8184	2203	4300	6503	SO:0001583	missense	114770	exon2			GTCTGGTCTTGGC	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.136A>G	19.37:g.15587345T>C	ENSP00000345968:p.Thr46Ala	Somatic	77	1	0.012987		WXS	Illumina HiSeq	Phase_I	63	25	0.396825	NM_052890	A8K050|A8K8C7|B2RMZ2|B7ZM33|Q68CK1|Q96N74|Q9UC60	Missense_Mutation	SNP	ENST00000340880.4	37	CCDS12330.2	790	0.3617216117216117	162	0.32926829268292684	114	0.3149171270718232	211	0.3688811188811189	303	0.3997361477572559	C	0.130	-1.115003	0.01799	0.343168	0.384884	ENSG00000161031	ENST00000340880;ENST00000292609	T;T	0.03524	3.94;3.9	4.44	2.05	0.26809	.	0.922902	0.09041	N	0.857270	T	0.00012	0.0000	N	0.00085	-2.2	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.45629	-0.9248	9	0.02654	T	1	-1.8112	6.1412	0.20261	0.0:0.5276:0.369:0.1034	rs3813135;rs57916293;rs3813135	46;46	Q96PD5-2;Q96PD5	.;PGRP2_HUMAN	A	46	ENSP00000345968:T46A;ENSP00000292609:T46A	ENSP00000292609:T46A	T	-	1	0	PGLYRP2	15448345	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.075000	0.11431	0.570000	0.29347	-1.096000	0.02151	ACC	T|0.639;C|0.361	0.361	strong		0.592	PGLYRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319626.1	NM_052890	
TMEM204	79652	hgsc.bcm.edu	37	16	1591962	1591962	+	Silent	SNP	G	G	A	rs2076443	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:1591962G>A	ENST00000566264.1	+	2	1024	c.321G>A	c.(319-321)acG>acA	p.T107T	IFT140_ENST00000426508.2_Intron|TMEM204_ENST00000253934.5_Silent_p.T107T	NM_024600.5	NP_078876.2	Q9BSN7	TM204_HUMAN	transmembrane protein 204	107					lymph vessel development (GO:0001945)|regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030947)|response to stress (GO:0006950)|smooth muscle cell differentiation (GO:0051145)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|breast(1)|cervix(1)|endometrium(1)|lung(3)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	11		Hepatocellular(780;0.219)				TGGTGGCCACGGCCGCGCTCA	0.701													G|||	1534	0.30631	0.4228	0.1599	5008	,	,		18178	0.3423		0.1918	False		,,,				2504	0.3333				p.T107T		Atlas-SNP	.											TMEM204,NS,carcinoma,0,1	TMEM204	29	1	0			c.G321A						PASS	.	G	,	1554,2760		288,978,891	30.0	37.0	35.0		,321	-11.5	0.2	16	dbSNP_96	35	1649,6841		166,1317,2762	no	intron,coding-synonymous	IFT140,TMEM204	NM_014714.3,NM_024600.4	,	454,2295,3653	AA,AG,GG		19.4229,36.0223,25.0156	,	,107/227	1591962	3203,9601	2157	4245	6402	SO:0001819	synonymous_variant	79652	exon2			GGCCACGGCCGCG		CCDS42098.1	16p13.3	2008-02-05	2008-01-08	2008-01-08		ENSG00000131634			14158	protein-coding gene	gene with protein product		611002	"""chromosome 16 open reading frame 30"""	C16orf30			Standard	NM_024600		Approved	FLJ20898	uc002cmc.3	Q9BSN7		ENST00000566264.1:c.321G>A	16.37:g.1591962G>A		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	82	29	0.353659	NM_024600	D3DU76|Q3KRC1|Q9H7G5	Silent	SNP	ENST00000566264.1	37	CCDS42098.1																																																																																			G|0.746;A|0.254	0.254	strong		0.701	TMEM204-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432610.1	NM_024600	
RAPGEF1	2889	hgsc.bcm.edu	37	9	134503415	134503415	+	Silent	SNP	C	C	T	rs371503343		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:134503415C>T	ENST00000372189.3	-	9	1158	c.1035G>A	c.(1033-1035)tcG>tcA	p.S345S	RAPGEF1_ENST00000372190.3_Silent_p.S363S|RAPGEF1_ENST00000481260.1_5'UTR|RAPGEF1_ENST00000372195.1_Silent_p.S362S	NM_005312.2	NP_005303.2	Q13905	RPGF1_HUMAN	Rap guanine nucleotide exchange factor (GEF) 1	345					activation of MAPKK activity (GO:0000186)|blood vessel development (GO:0001568)|cellular response to cAMP (GO:0071320)|cellular response to nerve growth factor stimulus (GO:1990090)|establishment of endothelial barrier (GO:0061028)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of neural precursor cell proliferation (GO:2000178)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of Ras protein signal transduction (GO:0046580)|nerve growth factor signaling pathway (GO:0038180)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of neuron projection development (GO:0010976)|positive regulation of Rap GTPase activity (GO:0032854)|Rap protein signal transduction (GO:0032486)|regulation of cell junction assembly (GO:1901888)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytosol (GO:0005829)|early endosome (GO:0005769)|endosome (GO:0005768)	Rap guanyl-nucleotide exchange factor activity (GO:0017034)			NS(2)|breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(8)|lung(9)|ovary(2)|prostate(4)|skin(1)|urinary_tract(1)	39		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;2.19e-05)|Epithelial(140;0.000364)		AGAGGCGGGGCGACTCTCCAC	0.547																																					p.S363S		Atlas-SNP	.											.	RAPGEF1	126	.	0			c.G1089A						PASS	.	C	,	0,4264		0,0,2132	28.0	31.0	30.0		1035,1089	-3.3	0.9	9		30	2,8484		0,2,4241	no	coding-synonymous,coding-synonymous	RAPGEF1	NM_005312.2,NM_198679.1	,	0,2,6373	TT,TC,CC		0.0236,0.0,0.0157	,	345/1078,363/1096	134503415	2,12748	2132	4243	6375	SO:0001819	synonymous_variant	2889	exon9			GCGGGGCGACTCT	BC041710	CCDS48047.1	9q34.3	2008-02-05	2004-03-01	2004-03-02	ENSG00000107263	ENSG00000107263			4568	protein-coding gene	gene with protein product		600303	"""guanine nucleotide-releasing factor 2 (specific for crk proto-oncogene)"""	GRF2		7959692, 7512734	Standard	NM_005312		Approved	C3G	uc022bos.1	Q13905	OTTHUMG00000020829	ENST00000372189.3:c.1035G>A	9.37:g.134503415C>T		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	45	23	0.511111	NM_198679	Q5JUE4|Q8IV73	Silent	SNP	ENST00000372189.3	37	CCDS48047.1																																																																																			.	.	weak		0.547	RAPGEF1-001	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054759.2	NM_005312	
SHROOM3	57619	hgsc.bcm.edu	37	4	77675925	77675925	+	Missense_Mutation	SNP	G	G	A	rs61741104	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:77675925G>A	ENST00000296043.6	+	7	5242	c.4289G>A	c.(4288-4290)cGa>cAa	p.R1430Q	RP11-359D14.2_ENST00000452412.1_RNA	NM_020859.3	NP_065910.3	Q8TF72	SHRM3_HUMAN	shroom family member 3	1430					actin cytoskeleton organization (GO:0030036)|apical protein localization (GO:0045176)|cell morphogenesis (GO:0000902)|cellular pigment accumulation (GO:0043482)|columnar/cuboidal epithelial cell development (GO:0002066)|neural tube closure (GO:0001843)|pattern specification process (GO:0007389)|regulation of cell shape (GO:0008360)	adherens junction (GO:0005912)|apical junction complex (GO:0043296)|apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|microtubule (GO:0005874)				NS(3)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(10)|kidney(2)|large_intestine(6)|lung(29)|ovary(1)|skin(5)|upper_aerodigestive_tract(1)	60			Lung(101;0.0903)			CCTCCTTCTCGAGCAAAGTGG	0.582													G|||	184	0.0367412	0.0045	0.1095	5008	,	,		18804	0.002		0.0487	False		,,,				2504	0.0521				p.R1430Q		Atlas-SNP	.											.	SHROOM3	134	.	0			c.G4289A						PASS	.	G	GLN/ARG	46,4360	47.5+/-82.1	1,44,2158	52.0	45.0	47.0		4289	2.0	0.0	4	dbSNP_129	47	386,8214	124.3+/-183.0	7,372,3921	yes	missense	SHROOM3	NM_020859.3	43	8,416,6079	AA,AG,GG		4.4884,1.044,3.3215	benign	1430/1997	77675925	432,12574	2203	4300	6503	SO:0001583	missense	57619	exon7			CTTCTCGAGCAAA	AB055660	CCDS3579.2	4q21.1	2009-11-25			ENSG00000138771	ENSG00000138771			30422	protein-coding gene	gene with protein product		604570				10589677, 16615870	Standard	NM_020859		Approved	ShrmL, SHRM, KIAA1481, APXL3	uc011cbx.2	Q8TF72	OTTHUMG00000157075	ENST00000296043.6:c.4289G>A	4.37:g.77675925G>A	ENSP00000296043:p.Arg1430Gln	Somatic	224	1	0.00446429		WXS	Illumina HiSeq	Phase_I	184	92	0.5	NM_020859	Q5QTQ3|Q6ZRW3|Q96IR9|Q9P247	Missense_Mutation	SNP	ENST00000296043.6	37	CCDS3579.2	83	0.038003663003663	1	0.0020325203252032522	45	0.12430939226519337	2	0.0034965034965034965	35	0.04617414248021108	G	11.03	1.518941	0.27211	0.01044	0.044884	ENSG00000138771	ENST00000296043	T	0.20598	2.06	5.49	1.95	0.26073	.	1.065700	0.07246	N	0.865024	T	0.00210	0.0006	N	0.19112	0.55	0.80722	P	0.0	B	0.11235	0.004	B	0.08055	0.003	T	0.34477	-0.9827	9	0.23891	T	0.37	0.049	9.3519	0.38142	0.4182:0.0:0.5818:0.0	rs61741104	1430	Q8TF72	SHRM3_HUMAN	Q	1430	ENSP00000296043:R1430Q	ENSP00000296043:R1430Q	R	+	2	0	SHROOM3	77894949	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.774000	0.26675	0.160000	0.19432	-0.880000	0.02959	CGA	G|0.965;A|0.035	0.035	strong		0.582	SHROOM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252408.2	NM_020859	
ZNF417	147687	hgsc.bcm.edu	37	19	58420167	58420167	+	Silent	SNP	T	T	C	rs17852300	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:58420167T>C	ENST00000312026.5	-	3	1643	c.1479A>G	c.(1477-1479)gaA>gaG	p.E493E	ZNF417_ENST00000536263.1_Silent_p.E294E|ZNF417_ENST00000595559.1_Silent_p.E492E|CTD-2583A14.9_ENST00000602124.1_Intron	NM_152475.2	NP_689688.2	Q8TAU3	ZN417_HUMAN	zinc finger protein 417	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)	p.E493E(1)		central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|stomach(3)|upper_aerodigestive_tract(1)	18		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0151)		ATTCATTGCATTCATACGGCC	0.408													T|||	1233	0.246206	0.1543	0.219	5008	,	,		21542	0.2847		0.2972	False		,,,				2504	0.2975				p.E493E		Atlas-SNP	.											ZNF417,NS,carcinoma,0,1	ZNF417	44	1	1	Substitution - coding silent(1)	stomach(1)	c.A1479G						PASS	.	T		525,3881		63,399,1741	112.0	93.0	100.0		1479	-4.8	0.0	19	dbSNP_123	100	2020,6578		348,1324,2627	no	coding-synonymous	ZNF417	NM_152475.2		411,1723,4368	CC,CT,TT		23.4938,11.9156,19.5709		493/576	58420167	2545,10459	2203	4299	6502	SO:0001819	synonymous_variant	147687	exon3			ATTGCATTCATAC	BC025783	CCDS12965.1, CCDS74469.1	19q13.43	2013-01-08				ENSG00000173480		"""Zinc fingers, C2H2-type"", ""-"""	20646	protein-coding gene	gene with protein product							Standard	NM_152475		Approved	MGC34079	uc002qqq.3	Q8TAU3		ENST00000312026.5:c.1479A>G	19.37:g.58420167T>C		Somatic	235	0	0		WXS	Illumina HiSeq	Phase_I	219	101	0.461187	NM_152475	B4DEU1	Silent	SNP	ENST00000312026.5	37	CCDS12965.1																																																																																			T|0.773;C|0.227	0.227	strong		0.408	ZNF417-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466860.1	NM_152475	
VPS18	57617	hgsc.bcm.edu	37	15	41191184	41191184	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:41191184C>T	ENST00000220509.5	+	3	652	c.313C>T	c.(313-315)Ctt>Ttt	p.L105F	VPS18_ENST00000558474.1_Missense_Mutation_p.L105F	NM_020857.2	NP_065908.1	Q9P253	VPS18_HUMAN	vacuolar protein sorting 18 homolog (S. cerevisiae)	105					endosome organization (GO:0007032)|intracellular protein transport (GO:0006886)|lysosome organization (GO:0007040)|vesicle-mediated transport (GO:0016192)|viral entry into host cell (GO:0046718)	actin filament (GO:0005884)|early endosome (GO:0005769)|HOPS complex (GO:0030897)|lysosomal membrane (GO:0005765)	metal ion binding (GO:0046872)			autonomic_ganglia(1)|endometrium(5)|kidney(4)|large_intestine(4)|lung(6)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	28		all_cancers(109;1.35e-17)|all_epithelial(112;3.78e-15)|Lung NSC(122;9.68e-11)|all_lung(180;2.25e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946)		GBM - Glioblastoma multiforme(113;1.07e-05)|COAD - Colon adenocarcinoma(120;0.15)|BRCA - Breast invasive adenocarcinoma(123;0.164)		CAAGATGTTCCTTGACCATAC	0.567																																					p.L105F		Atlas-SNP	.											.	VPS18	67	.	0			c.C313T						PASS	.						117.0	97.0	104.0					15																	41191184		2203	4300	6503	SO:0001583	missense	57617	exon3			ATGTTCCTTGACC	AF308802	CCDS10069.1	15q14-q15	2006-12-19	2006-12-19		ENSG00000104142	ENSG00000104142			15972	protein-coding gene	gene with protein product		608551	"""vacuolar protein sorting protein 18"""			11250079, 16203730	Standard	NM_020857		Approved	KIAA1475, PEP3	uc001zne.3	Q9P253	OTTHUMG00000130135	ENST00000220509.5:c.313C>T	15.37:g.41191184C>T	ENSP00000220509:p.Leu105Phe	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	46	24	0.521739	NM_020857	Q8TCG0|Q96DI3|Q9H268	Missense_Mutation	SNP	ENST00000220509.5	37	CCDS10069.1	.	.	.	.	.	.	.	.	.	.	C	15.41	2.824795	0.50739	.	.	ENSG00000104142	ENST00000220509	T	0.55234	0.53	4.77	3.73	0.42828	.	0.000000	0.64402	D	0.000001	T	0.67832	0.2935	M	0.81682	2.555	0.54753	D	0.999982	D	0.71674	0.998	D	0.72338	0.977	T	0.67925	-0.5544	10	0.56958	D	0.05	-14.8434	5.7082	0.17921	0.0:0.6252:0.0:0.3748	.	105	Q9P253	VPS18_HUMAN	F	105	ENSP00000220509:L105F	ENSP00000220509:L105F	L	+	1	0	VPS18	38978476	1.000000	0.71417	1.000000	0.80357	0.589000	0.36550	1.289000	0.33307	1.063000	0.40649	0.455000	0.32223	CTT	.	.	none		0.567	VPS18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252443.2		
MACF1	23499	hgsc.bcm.edu	37	1	39816626	39816626	+	Missense_Mutation	SNP	C	C	A	rs116162513	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:39816626C>A	ENST00000372915.3	+	42	11237	c.11150C>A	c.(11149-11151)aCa>aAa	p.T3717K	MACF1_ENST00000567887.1_Missense_Mutation_p.T3749K|MACF1_ENST00000564288.1_Missense_Mutation_p.T3712K|MACF1_ENST00000289893.4_Missense_Mutation_p.T2152K|MACF1_ENST00000361689.2_Missense_Mutation_p.T1650K|MACF1_ENST00000545844.1_Missense_Mutation_p.T1650K|MACF1_ENST00000539005.1_Missense_Mutation_p.T1650K|MACF1_ENST00000476350.1_3'UTR|MACF1_ENST00000317713.7_Missense_Mutation_p.T1650K			Q9UPN3	MACF1_HUMAN	microtubule-actin crosslinking factor 1	3717					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)			CAGGAAGAGACACGTGTGGCC	0.493																																					p.T1650K		Atlas-SNP	.											.	MACF1	909	.	0			c.C4949A						PASS	.						72.0	70.0	71.0					1																	39816626		2203	4300	6503	SO:0001583	missense	23499	exon39			AAGAGACACGTGT	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.11150C>A	1.37:g.39816626C>A	ENSP00000362006:p.Thr3717Lys	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	57	14	0.245614	NM_012090	B1ALC5|E9PJT0|O75053|Q5VW20|Q8WXY1|Q8WXY2|Q96PK2|Q9H540|Q9UKP0|Q9ULG9	Missense_Mutation	SNP	ENST00000372915.3	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	18.97|18.97	3.735836|3.735836	0.69189|0.69189	.|.	.|.	ENSG00000127603|ENSG00000127603	ENST00000372925|ENST00000545844;ENST00000372915;ENST00000361689;ENST00000317713;ENST00000539005;ENST00000530262;ENST00000289893	.|T;T;T;T;T;T;T	.|0.62232	.|1.27;0.04;1.27;1.27;1.27;1.27;1.07	6.06|6.06	5.15|5.15	0.70609|0.70609	.|.	.|0.190098	.|0.37012	.|N	.|0.002284	T|T	0.70150|0.70150	0.3191|0.3191	L|L	0.60455|0.60455	1.87|1.87	0.44843|0.44843	D|D	0.997855|0.997855	.|B;P;D;B	.|0.54772	.|0.433;0.864;0.968;0.225	.|B;P;P;B	.|0.56343	.|0.375;0.669;0.796;0.155	T|T	0.73075|0.73075	-0.4097|-0.4097	5|10	.|0.66056	.|D	.|0.02	.|.	12.0779|12.0779	0.53655|0.53655	0.0:0.8611:0.0:0.1389|0.0:0.8611:0.0:0.1389	.|.	.|3717;1650;1650;1615	.|Q9UPN3;F8W8Q1;Q9UPN3-2;Q9UPN3-3	.|MACF1_HUMAN;.;.;.	E|K	783|1650;3717;1650;1650;1650;1799;2152	.|ENSP00000439537:T1650K;ENSP00000362006:T3717K;ENSP00000354573:T1650K;ENSP00000313438:T1650K;ENSP00000444364:T1650K;ENSP00000437059:T1799K;ENSP00000289893:T2152K	.|ENSP00000289893:T2152K	D|T	+|+	3|2	2|0	MACF1|MACF1	39589213|39589213	0.985000|0.985000	0.35326|0.35326	0.012000|0.012000	0.15200|0.15200	0.872000|0.872000	0.50106|0.50106	3.723000|3.723000	0.54955|0.54955	1.584000|1.584000	0.49913|0.49913	0.650000|0.650000	0.86243|0.86243	GAC|ACA	C|0.999;T|0.001	.	alt		0.493	MACF1-028	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000392096.1	NM_033044	
ZNF880	400713	hgsc.bcm.edu	37	19	52887427	52887427	+	Missense_Mutation	SNP	A	A	C	rs8104808	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:52887427A>C	ENST00000422689.2	+	4	609	c.594A>C	c.(592-594)agA>agC	p.R198S		NM_001145434.1	NP_001138906.1	Q6PDB4	ZN880_HUMAN	zinc finger protein 880	198					regulation of transcription, DNA-templated (GO:0006355)	intracellular (GO:0005622)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(2)|skin(1)	10						TGTCTTCAAGACTTGCTAACA	0.373													C|||	1900	0.379393	0.2428	0.379	5008	,	,		20891	0.3462		0.4205	False		,,,				2504	0.5562				p.R198S		Atlas-SNP	.											.	ZNF880	45	.	0			c.A594C						PASS	.	C	SER/ARG	394,990		53,288,351	51.0	50.0	50.0		594	-2.1	0.0	19	dbSNP_116	50	1214,1968		222,770,599	yes	missense	ZNF880	NM_001145434.1	110	275,1058,950	CC,CA,AA		38.1521,28.4682,35.2168	benign	198/578	52887427	1608,2958	692	1591	2283	SO:0001583	missense	400713	exon4			TTCAAGACTTGCT	BC058819	CCDS46164.1	19q13.41	2013-01-08			ENSG00000221923	ENSG00000221923		"""Zinc fingers, C2H2-type"", ""-"""	37249	protein-coding gene	gene with protein product							Standard	NM_001145434		Approved		uc002pzc.3	Q6PDB4	OTTHUMG00000167972	ENST00000422689.2:c.594A>C	19.37:g.52887427A>C	ENSP00000406318:p.Arg198Ser	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	66	66	1	NM_001145434	B4DNA6	Missense_Mutation	SNP	ENST00000422689.2	37	CCDS46164.1	746	0.3415750915750916	120	0.24390243902439024	138	0.3812154696132597	177	0.3094405594405594	311	0.4102902374670185	C	1.585	-0.530539	0.04112	0.284682	0.381521	ENSG00000221923	ENST00000422689	T	0.26660	1.72	1.84	-2.1	0.07210	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	N	0.00408	-1.53	0.80722	P	0.0	B	0.18741	0.03	B	0.04013	0.001	T	0.42932	-0.9422	7	.	.	.	.	3.0674	0.06219	0.3498:0.3892:0.0:0.261	rs8104808;rs17736357;rs52798557;rs8104808	198	Q6PDB4	ZN880_HUMAN	S	198	ENSP00000406318:R198S	.	R	+	3	2	ZNF880	57579239	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.885000	0.01620	-0.814000	0.04352	-1.140000	0.01884	AGA	A|0.652;C|0.348	0.348	strong		0.373	ZNF880-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397374.1	NM_001145434	
TEK	7010	hgsc.bcm.edu	37	9	27206669	27206669	+	Silent	SNP	G	G	C	rs55789591	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:27206669G>C	ENST00000380036.4	+	15	2896	c.2454G>C	c.(2452-2454)gtG>gtC	p.V818V	TEK_ENST00000406359.4_Silent_p.V775V|TEK_ENST00000519097.1_Silent_p.V670V	NM_000459.3	NP_000450	Q02763	TIE2_HUMAN	TEK tyrosine kinase, endothelial	818					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)	TTTATCCAGTGCTTGACTGGA	0.458													G|||	38	0.00758786	0.0008	0.0058	5008	,	,		20271	0.001		0.0119	False		,,,				2504	0.0204				p.V818V		Atlas-SNP	.											.	TEK	250	.	0			c.G2454C						PASS	.	G		13,4393	19.1+/-41.9	0,13,2190	82.0	77.0	79.0		2454	4.0	1.0	9	dbSNP_129	79	134,8466	67.3+/-129.8	1,132,4167	no	coding-synonymous	TEK	NM_000459.3		1,145,6357	CC,CG,GG		1.5581,0.2951,1.1302		818/1125	27206669	147,12859	2203	4300	6503	SO:0001819	synonymous_variant	7010	exon15			TCCAGTGCTTGAC	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.2454G>C	9.37:g.27206669G>C		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	65	30	0.461538	NM_000459	A8K6W0|B4DH20|B4DHD3|D3DRK5|E7EWI2|Q5TCU2|Q8IV34	Silent	SNP	ENST00000380036.4	37	CCDS6519.1																																																																																			G|0.989;C|0.011	0.011	strong		0.458	TEK-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051965.3		
MUC4	4585	hgsc.bcm.edu	37	3	195512597	195512597	+	Missense_Mutation	SNP	G	G	A	rs6799339	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195512597G>A	ENST00000463781.3	-	2	6313	c.5854C>T	c.(5854-5856)Cct>Tct	p.P1952S	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.P1952S	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.P1952_T1967delPLPVTDASSVPTGHAT(4)|p.P1952S(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)		ACAGGAAGAGGGGTGGTGTGA	0.597																																					p.P1952S		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	5	Deletion - In frame(4)|Substitution - Missense(1)	stomach(4)|endometrium(1)	c.C5854T						PASS	.						50.0	44.0	46.0					3																	195512597		691	1588	2279	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.5854C>T	3.37:g.195512597G>A	ENSP00000417498:p.Pro1952Ser	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	112	25	0.223214	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	-	6.807	0.518012	0.13005	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.28895	1.6;1.59	.	.	.	.	.	.	.	.	T	0.13798	0.0334	N	0.19112	0.55	0.09310	N	1	P	0.47604	0.898	B	0.37550	0.253	T	0.12451	-1.0547	7	.	.	.	.	2.8356	0.05513	3.0E-4:2.0E-4:0.5012:0.4983	.	1952	E7ESK3	.	S	1952	ENSP00000417498:P1952S;ENSP00000420243:P1952S	.	P	-	1	0	MUC4	196996992	0.003000	0.15002	0.071000	0.20095	0.056000	0.15407	-2.897000	0.00706	0.064000	0.16427	0.064000	0.15345	CCT	G|0.975;A|0.025	0.025	strong		0.597	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
HLA-A	3105	hgsc.bcm.edu	37	6	29913037	29913037	+	Missense_Mutation	SNP	G	G	A	rs1137631	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:29913037G>A	ENST00000396634.1	+	9	1413	c.1072G>A	c.(1072-1074)Gtg>Atg	p.V358M	HLA-A_ENST00000376802.2_Intron|HLA-A_ENST00000376809.5_Missense_Mutation_p.V358M|HLA-A_ENST00000376806.5_Missense_Mutation_p.V364M			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	215	0	0		WXS	Illumina HiSeq	Phase_I	127	43	0.338583	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	
OR6S1	341799	hgsc.bcm.edu	37	14	21109726	21109726	+	Missense_Mutation	SNP	G	G	A	rs11622794	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:21109726G>A	ENST00000320704.3	-	1	124	c.125C>T	c.(124-126)aCa>aTa	p.T42I		NM_001001968.1	NP_001001968.1	Q8NH40	OR6S1_HUMAN	olfactory receptor, family 6, subfamily S, member 1	42			T -> I (in dbSNP:rs11622794).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			kidney(1)|large_intestine(3)|lung(13)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	23	all_cancers(95;0.00304)		Epithelial(56;1.23e-06)|all cancers(55;1.01e-05)	GBM - Glioblastoma multiforme(265;0.0135)		CACATTGCCTGTCAGATTCAG	0.478													G|||	2305	0.460264	0.4902	0.5461	5008	,	,		21279	0.2897		0.5338	False		,,,				2504	0.4591				p.T42I		Atlas-SNP	.											.	OR6S1	49	.	0			c.C125T						PASS	.	G	ILE/THR	2257,2149	595.7+/-388.5	560,1137,506	97.0	94.0	95.0		125	1.5	0.5	14	dbSNP_120	95	4782,3818	611.6+/-395.8	1333,2116,851	yes	missense	OR6S1	NM_001001968.1	89	1893,3253,1357	AA,AG,GG		44.3953,48.7744,45.8788	benign	42/332	21109726	7039,5967	2203	4300	6503	SO:0001583	missense	341799	exon1			TTGCCTGTCAGAT	AL163636	CCDS32038.1	14q11.2	2013-09-24			ENSG00000181803	ENSG00000181803		"""GPCR / Class A : Olfactory receptors"""	15363	protein-coding gene	gene with protein product							Standard	NM_001001968		Approved	OR6S1Q	uc001vxv.1	Q8NH40	OTTHUMG00000171010	ENST00000320704.3:c.125C>T	14.37:g.21109726G>A	ENSP00000313110:p.Thr42Ile	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	87	52	0.597701	NM_001001968	Q6IFJ9	Missense_Mutation	SNP	ENST00000320704.3	37	CCDS32038.1	1030	0.4716117216117216	229	0.4654471544715447	213	0.5883977900552486	183	0.31993006993006995	405	0.5343007915567283	G	3.081	-0.189020	0.06299	0.512256	0.556047	ENSG00000181803	ENST00000320704	T	0.00420	7.47	5.84	1.53	0.23141	.	0.311322	0.23836	N	0.044083	T	0.00012	0.0000	N	0.13235	0.315	0.80722	P	0.0	B	0.17268	0.021	B	0.16722	0.016	T	0.02358	-1.1171	9	0.40728	T	0.16	-3.8757	8.4026	0.32594	0.4216:0.0:0.5784:0.0	rs11622794;rs17277529;rs56602434;rs57777215;rs11622794	42	Q8NH40	OR6S1_HUMAN	I	42	ENSP00000313110:T42I	ENSP00000313110:T42I	T	-	2	0	OR6S1	20179566	0.000000	0.05858	0.498000	0.27564	0.691000	0.40173	1.178000	0.31981	0.403000	0.25479	-0.126000	0.14955	ACA	G|0.491;A|0.508	0.508	strong		0.478	OR6S1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411227.1		
FOXK2	3607	hgsc.bcm.edu	37	17	80529614	80529614	+	Silent	SNP	G	G	T	rs117692271	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:80529614G>T	ENST00000335255.5	+	4	951	c.777G>T	c.(775-777)ccG>ccT	p.P259P		NM_004514.3	NP_004505.2	Q01167	FOXK2_HUMAN	forkhead box K2	259					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)	intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	magnesium ion binding (GO:0000287)|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)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(5)|prostate(1)|urinary_tract(1)	17	Breast(20;0.00106)|all_neural(118;0.0952)		OV - Ovarian serous cystadenocarcinoma(97;0.0371)|BRCA - Breast invasive adenocarcinoma(99;0.0415)			ATTCAAAGCCGCCTTACTCCT	0.368													G|||	24	0.00479233	0.0	0.0115	5008	,	,		19357	0.0		0.008	False		,,,				2504	0.0082				p.P259P		Atlas-SNP	.											.	FOXK2	46	.	0			c.G777T						PASS	.	G		4,4402	8.1+/-20.4	0,4,2199	64.0	58.0	60.0		777	-4.6	1.0	17	dbSNP_132	60	48,8552	31.7+/-84.0	0,48,4252	no	coding-synonymous	FOXK2	NM_004514.3		0,52,6451	TT,TG,GG		0.5581,0.0908,0.3998		259/661	80529614	52,12954	2203	4300	6503	SO:0001819	synonymous_variant	3607	exon4			AAAGCCGCCTTAC	U58196	CCDS11813.1	17q25	2006-12-15	2004-03-09	2004-03-10	ENSG00000141568	ENSG00000141568		"""Forkhead boxes"""	6036	protein-coding gene	gene with protein product		147685	"""interleukin enhancer binding factor 1"""	ILF, ILF1		3260003	Standard	NM_004514		Approved		uc002kfn.3	Q01167	OTTHUMG00000140374	ENST00000335255.5:c.777G>T	17.37:g.80529614G>T		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	65	35	0.538462	NM_004514	A6NEP5|Q13622|Q13623|Q13624	Silent	SNP	ENST00000335255.5	37	CCDS11813.1																																																																																			G|0.996;T|0.004	0.004	strong		0.368	FOXK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277099.2	NM_181430	
ALMS1	7840	hgsc.bcm.edu	37	2	73677833	73677833	+	Silent	SNP	A	A	G	rs6546836	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:73677833A>G	ENST00000264448.6	+	8	4287	c.4176A>G	c.(4174-4176)caA>caG	p.Q1392Q	ALMS1_ENST00000377715.1_Silent_p.Q1392Q|ALMS1_ENST00000409009.1_Silent_p.Q1350Q	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	1392	34 X 47 AA approximate tandem repeat.				endosomal transport (GO:0016197)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of stress fiber assembly (GO:0051492)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)				breast(4)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(31)|lung(68)|ovary(4)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	147						TTTTCTACCAACAGTCGTTGC	0.473													A|||	1694	0.338259	0.7859	0.3847	5008	,	,		21223	0.0089		0.2256	False		,,,				2504	0.1554				p.Q1392Q		Atlas-SNP	.											ALMS1,colon,carcinoma,0,1	ALMS1	384	1	0			c.A4176G						PASS	.	A		2499,1227		847,805,211	91.0	93.0	92.0		4176	-6.8	0.0	2	dbSNP_116	92	1942,6272		217,1508,2382	no	coding-synonymous	ALMS1	NM_015120.4		1064,2313,2593	GG,GA,AA		23.6426,32.9308,37.1943		1392/4168	73677833	4441,7499	1863	4107	5970	SO:0001819	synonymous_variant	7840	exon8			CTACCAACAGTCG	AB002326	CCDS42697.1	2p13.1	2014-09-17			ENSG00000116127	ENSG00000116127			428	protein-coding gene	gene with protein product		606844				9063741	Standard	NM_015120		Approved	KIAA0328	uc002sje.1	Q8TCU4	OTTHUMG00000152812	ENST00000264448.6:c.4176A>G	2.37:g.73677833A>G		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	84	84	1	NM_015120	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Silent	SNP	ENST00000264448.6	37	CCDS42697.1																																																																																			A|0.737;G|0.263	0.263	strong		0.473	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120	
UPK1A	11045	hgsc.bcm.edu	37	19	36168914	36168914	+	Missense_Mutation	SNP	T	T	C	rs2285421	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:36168914T>C	ENST00000222275.2	+	7	770	c.770T>C	c.(769-771)aTg>aCg	p.M257T	UPK1A_ENST00000379013.2_3'UTR	NM_007000.2	NP_008931.1	O00322	UPK1A_HUMAN	uroplakin 1A	257			M -> T (in dbSNP:rs2285421). {ECO:0000269|PubMed:15489334}.		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)			TTCTACACCATGCTCTGAGGG	0.647													C|||	3299	0.658746	0.8359	0.5029	5008	,	,		14729	0.6161		0.5	False		,,,				2504	0.7372				p.M257T		Atlas-SNP	.											.	UPK1A	23	.	0			c.T770C						PASS	.	C	THR/MET	3461,943	337.3+/-304.8	1355,751,96	47.0	49.0	48.0		770	0.5	0.1	19	dbSNP_100	48	4165,4435	555.1+/-386.6	982,2201,1117	yes	missense	UPK1A	NM_007000.2	81	2337,2952,1213	CC,CT,TT		48.4302,21.4124,41.3565	benign	257/259	36168914	7626,5378	2202	4300	6502	SO:0001583	missense	11045	exon7			ACACCATGCTCTG	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.770T>C	19.37:g.36168914T>C	ENSP00000222275:p.Met257Thr	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	82	82	1	NM_007000	Q3KNU5|Q3KNU6	Missense_Mutation	SNP	ENST00000222275.2	37	CCDS12470.1	1339	0.6130952380952381	401	0.8150406504065041	188	0.5193370165745856	361	0.6311188811188811	389	0.5131926121372031	C	7.118	0.577334	0.13686	0.785876	0.484302	ENSG00000105668	ENST00000222275	T	0.05025	3.51	5.22	0.485	0.16830	.	.	.	.	.	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	0.11470	-1.0586	8	0.09843	T	0.71	.	4.7632	0.13118	0.1406:0.4845:0.0:0.3749	rs2285421;rs17652127;rs52810906;rs58866560;rs2285421	257	O00322	UPK1A_HUMAN	T	257	ENSP00000222275:M257T	ENSP00000222275:M257T	M	+	2	0	UPK1A	40860754	0.015000	0.18098	0.101000	0.21167	0.255000	0.26057	-0.031000	0.12287	0.085000	0.17107	-0.929000	0.02709	ATG	T|0.391;C|0.609	0.609	strong		0.647	UPK1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109486.3		
C7	730	hgsc.bcm.edu	37	5	40934471	40934471	+	Silent	SNP	G	G	A	rs34196526	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:40934471G>A	ENST00000313164.9	+	4	542	c.183G>A	c.(181-183)caG>caA	p.Q61Q		NM_000587.2	NP_000578.2	P10643	CO7_HUMAN	complement component 7	61	TSP type-1 1. {ECO:0000255|PROSITE- ProRule:PRU00210}.				cellular sodium ion homeostasis (GO:0006883)|complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|complement activation, classical pathway (GO:0006958)|cytolysis (GO:0019835)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane attack complex (GO:0005579)							Ovarian(839;0.0112)				ATGGAGGCCAGCCTTGTGTTG	0.458													G|||	35	0.00698882	0.0008	0.0058	5008	,	,		16468	0.0		0.008	False		,,,				2504	0.0225				p.Q61Q		Atlas-SNP	.											.	C7	136	.	0			c.G183A						PASS	.	G		9,3901		0,9,1946	160.0	165.0	163.0		183	-11.8	0.0	5	dbSNP_126	163	197,8095		3,191,3952	no	coding-synonymous	C7	NM_000587.2		3,200,5898	AA,AG,GG		2.3758,0.2302,1.6882		61/844	40934471	206,11996	1955	4146	6101	SO:0001819	synonymous_variant	730	exon4			AGGCCAGCCTTGT	J03507	CCDS47201.1	5p13.1	2014-09-17			ENSG00000112936	ENSG00000112936		"""Complement system"""	1346	protein-coding gene	gene with protein product		217070					Standard	NM_000587		Approved		uc003jmh.3	P10643	OTTHUMG00000150340	ENST00000313164.9:c.183G>A	5.37:g.40934471G>A		Somatic	266	0	0		WXS	Illumina HiSeq	Phase_I	268	162	0.604478	NM_000587	Q6P3T5|Q92489	Silent	SNP	ENST00000313164.9	37	CCDS47201.1																																																																																			G|0.992;A|0.008	0.008	strong		0.458	C7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317680.1		
ACAN	176	hgsc.bcm.edu	37	15	89398330	89398330	+	Silent	SNP	G	G	A	rs3743399	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:89398330G>A	ENST00000561243.1	+	11	2514	c.2514G>A	c.(2512-2514)tcG>tcA	p.S838S	ACAN_ENST00000439576.2_Silent_p.S838S|ACAN_ENST00000559004.1_Silent_p.S838S|ACAN_ENST00000352105.7_Silent_p.S838S			P16112	PGCA_HUMAN	aggrecan	837	12 X 6 AA approximate tandem repeats of E-[GVE]-P-[SFY]-[APT]-[TSP].|KS.				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|proteolysis (GO:0006508)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)	carbohydrate binding (GO:0030246)|extracellular matrix structural constituent (GO:0005201)|hyaluronic acid binding (GO:0005540)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(4)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(15)|liver(2)|lung(40)|ovary(2)|prostate(5)|skin(5)|stomach(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	93	Lung NSC(78;0.0392)|all_lung(78;0.077)		BRCA - Breast invasive adenocarcinoma(143;0.146)			CATCAGCCTCGGAAGAGCCGT	0.617													A|||	3801	0.758986	0.9909	0.6527	5008	,	,		19031	0.4911		0.8101	False		,,,				2504	0.7444				p.S838S		Atlas-SNP	.											.	ACAN	220	.	0			c.G2514A						PASS	.	A	,	3781,155		1819,143,6	34.0	39.0	37.0		2514,2514	-3.9	0.0	15	dbSNP_107	37	6833,1465		2812,1209,128	no	coding-synonymous,coding-synonymous	ACAN	NM_001135.3,NM_013227.3	,	4631,1352,134	AA,AG,GG		17.6549,3.938,13.2418	,	838/2432,838/2531	89398330	10614,1620	1968	4149	6117	SO:0001819	synonymous_variant	176	exon12			AGCCTCGGAAGAG	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.2514G>A	15.37:g.89398330G>A		Somatic	105	1	0.00952381		WXS	Illumina HiSeq	Phase_I	156	155	0.99359	NM_001135	Q13650|Q9UCD3|Q9UCP4|Q9UCP5|Q9UDE0	Silent	SNP	ENST00000561243.1	37	CCDS53970.1																																																																																			G|0.244;A|0.756	0.756	strong		0.617	ACAN-006	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416267.2	NM_001135	
ZC3HAV1L	92092	hgsc.bcm.edu	37	7	138713476	138713476	+	Missense_Mutation	SNP	C	C	T	rs17856272	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:138713476C>T	ENST00000275766.1	-	3	743	c.732G>A	c.(730-732)atG>atA	p.M244I		NM_080660.3	NP_542391.2	Q96H79	ZCCHL_HUMAN	zinc finger CCCH-type, antiviral 1-like	244				M -> I (in Ref. 2; AAH08842). {ECO:0000305}.						NS(2)|endometrium(2)|large_intestine(1)|lung(4)|skin(1)	10						TGTGCAGCTTCATATGCTTGT	0.403													C|||	246	0.0491214	0.0408	0.0576	5008	,	,		22428	0.0		0.0964	False		,,,				2504	0.0562				p.M244I		Atlas-SNP	.											.	ZC3HAV1L	15	.	0			c.G732A						PASS	.	C	ILE/MET	253,4153	145.4+/-180.2	13,227,1963	104.0	101.0	102.0		732	1.4	0.6	7	dbSNP_123	102	831,7769	192.3+/-238.3	38,755,3507	yes	missense	ZC3HAV1L	NM_080660.3	10	51,982,5470	TT,TC,CC		9.6628,5.7422,8.3346	benign	244/301	138713476	1084,11922	2203	4300	6503	SO:0001583	missense	92092	exon3			CAGCTTCATATGC	BC008842	CCDS5850.1	7q34	2006-07-03	2006-07-03	2006-07-03	ENSG00000146858	ENSG00000146858			22423	protein-coding gene	gene with protein product			"""chromosome 7 open reading frame 39"""	C7orf39			Standard	NM_080660		Approved	MGC14289	uc003vum.1	Q96H79	OTTHUMG00000157229	ENST00000275766.1:c.732G>A	7.37:g.138713476C>T	ENSP00000275766:p.Met244Ile	Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	95	95	1	NM_080660	Q8WUD9	Missense_Mutation	SNP	ENST00000275766.1	37	CCDS5850.1	115	0.052655677655677656	20	0.04065040650406504	22	0.06077348066298342	0	0.0	73	0.09630606860158311	C	11.45	1.643554	0.29246	0.057422	0.096628	ENSG00000146858	ENST00000275766	T	0.29917	1.55	5.62	1.42	0.22433	.	0.783556	0.11653	N	0.542628	T	0.00468	0.0015	N	0.24115	0.695	0.09310	N	1	B	0.17038	0.02	B	0.19391	0.025	T	0.16719	-1.0393	10	0.37606	T	0.19	.	5.4478	0.16546	0.0:0.4135:0.4018:0.1847	rs17856272	244	Q96H79	ZCCHL_HUMAN	I	244	ENSP00000275766:M244I	ENSP00000275766:M244I	M	-	3	0	ZC3HAV1L	138364016	0.002000	0.14202	0.558000	0.28319	0.995000	0.86356	-0.187000	0.09656	0.762000	0.33152	0.650000	0.86243	ATG	C|0.925;T|0.075	0.075	strong		0.403	ZC3HAV1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348090.1	NM_080660	
SMG8	55181	hgsc.bcm.edu	37	17	57290383	57290383	+	Silent	SNP	G	G	A	rs3744383	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:57290383G>A	ENST00000543872.2	+	4	2463	c.2199G>A	c.(2197-2199)agG>agA	p.R733R	CTD-2510F5.6_ENST00000577660.1_Intron|SMG8_ENST00000580498.1_3'UTR|SMG8_ENST00000300917.5_Silent_p.R733R			Q8ND04	SMG8_HUMAN	SMG8 nonsense mediated mRNA decay factor	733					gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of protein kinase activity (GO:0045859)|RNA metabolic process (GO:0016070)	cytosol (GO:0005829)				NS(1)|breast(5)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(8)|lung(9)|ovary(3)|prostate(1)|skin(1)	33						CTGAGAAGAGGCCAAACTTCG	0.468													A|||	2445	0.488219	0.7375	0.3646	5008	,	,		19687	0.4415		0.2942	False		,,,				2504	0.4867				p.R733R		Atlas-SNP	.											.	SMG8	79	.	0			c.G2199A						PASS	.	A		2915,1491	474.6+/-357.0	962,991,250	111.0	111.0	111.0		2199	1.0	1.0	17	dbSNP_107	111	2683,5917	684.6+/-404.0	413,1857,2030	no	coding-synonymous	SMG8	NM_018149.6		1375,2848,2280	AA,AG,GG		31.1977,33.8402,43.0417		733/992	57290383	5598,7408	2203	4300	6503	SO:0001819	synonymous_variant	55181	exon3			GAAGAGGCCAAAC	AL834490	CCDS11615.1	17q23.2	2013-07-02	2013-07-02	2011-06-21					25551	protein-coding gene	gene with protein product		613175	"""chromosome 17 open reading frame 71"", ""smg-8 homolog, nonsense mediated mRNA decay factor (C. elegans)"""	C17orf71		19417104	Standard	NM_018149		Approved	FLJ10587, FLJ23205	uc002ixi.3	Q8ND04		ENST00000543872.2:c.2199G>A	17.37:g.57290383G>A		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	109	108	0.990826	NM_018149	Q8N5U5|Q8TDN0|Q9H5P5|Q9NVQ1	Silent	SNP	ENST00000543872.2	37	CCDS11615.1																																																																																			G|0.551;A|0.449	0.449	strong		0.468	SMG8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445960.2	NM_018149	
FER	2241	hgsc.bcm.edu	37	5	108133967	108133967	+	Silent	SNP	A	A	G	rs2229085	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	252	0	0		WXS	Illumina HiSeq	Phase_I	190	94	0.494737	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	
P2RY11	5032	hgsc.bcm.edu	37	19	10224637	10224637	+	Silent	SNP	C	C	T	rs79800334	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:10224637C>T	ENST00000321826.4	+	2	532	c.348C>T	c.(346-348)agC>agT	p.S116S	PPAN_ENST00000556468.1_Silent_p.S536S|PPAN-P2RY11_ENST00000428358.1_3'UTR|PPAN-P2RY11_ENST00000393796.4_Silent_p.S536S	NM_002566.4	NP_002557.2	Q96G91	P2Y11_HUMAN	purinergic receptor P2Y, G-protein coupled, 11	116					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)			TGCTGGGCAGCGTCATCTTCA	0.667											OREG0025230	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	83	0.0165735	0.0	0.0	5008	,	,		17990	0.0228		0.001	False		,,,				2504	0.0603				p.S536S		Atlas-SNP	.											.	PPAN-P2RY11	81	.	0			c.C1608T						PASS	.	C	,,	5,4401	8.1+/-20.4	0,5,2198	82.0	71.0	75.0		1608,,348	0.1	0.0	19	dbSNP_131	75	0,8600		0,0,4300	no	coding-synonymous,utr-3,coding-synonymous	P2RY11,PPAN-P2RY11	NM_001040664.2,NM_001198690.1,NM_002566.4	,,	0,5,6498	TT,TC,CC		0.0,0.1135,0.0384	,,	536/795,,116/375	10224637	5,13001	2203	4300	6503	SO:0001819	synonymous_variant	692312	exon13			GGGCAGCGTCATC	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.348C>T	19.37:g.10224637C>T		Somatic	32	0	0	663	WXS	Illumina HiSeq	Phase_I	30	20	0.666667	NM_001040664	B2R8X9|O43190|Q9BYU4|Q9H170	Silent	SNP	ENST00000321826.4	37	CCDS12226.1																																																																																			C|0.997;T|0.003	0.003	strong		0.667	P2RY11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316664.2	NM_002566	
MUC4	4585	hgsc.bcm.edu	37	3	195515038	195515038	+	Missense_Mutation	SNP	G	G	A	rs201206859		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195515038G>A	ENST00000463781.3	-	2	3872	c.3413C>T	c.(3412-3414)cCt>cTt	p.P1138L	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.P1138L	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	605					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.P1138L(1)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GTCGGTGACAGGAAGAGAGGT	0.567																																					p.P1138L		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	1	Substitution - Missense(1)	endometrium(1)	c.C3413T						scavenged	.																																			SO:0001583	missense	4585	exon2			GTGACAGGAAGAG	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.3413C>T	3.37:g.195515038G>A	ENSP00000417498:p.Pro1138Leu	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	39	3	0.0769231	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	-	5.066	0.197826	0.09652	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.33865	1.39;1.39	0.814	0.814	0.18756	.	.	.	.	.	T	0.38108	0.1028	N	0.19112	0.55	0.09310	N	1	D	0.69078	0.997	D	0.74674	0.984	T	0.21280	-1.0250	8	.	.	.	.	7.6132	0.28142	0.0:0.0:1.0:0.0	.	1138	E7ESK3	.	L	1138	ENSP00000417498:P1138L;ENSP00000420243:P1138L	.	P	-	2	0	MUC4	196999433	0.002000	0.14202	0.001000	0.08648	0.065000	0.16274	1.050000	0.30404	0.776000	0.33473	0.064000	0.15345	CCT	.	.	weak		0.567	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
PDE4A	5141	hgsc.bcm.edu	37	19	10572271	10572271	+	Missense_Mutation	SNP	A	A	G	rs141379029		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:10572271A>G	ENST00000352831.6	+	12	1645	c.1535A>G	c.(1534-1536)aAg>aGg	p.K512R	PDE4A_ENST00000293683.5_Missense_Mutation_p.K486R|PDE4A_ENST00000440014.2_Missense_Mutation_p.K451R|PDE4A_ENST00000380702.2_Missense_Mutation_p.K490R|PDE4A_ENST00000344979.3_Missense_Mutation_p.K273R|PDE4A_ENST00000592685.1_Missense_Mutation_p.K490R	NM_001111307.1	NP_001104777.1	P27815	PDE4A_HUMAN	phosphodiesterase 4A, cAMP-specific	512	Catalytic.				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)			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)	GTGGGCTTCAAGCTGCTGCAG	0.632													A|||	1	0.000199681	0.0	0.0	5008	,	,		10749	0.0		0.001	False		,,,				2504	0.0				p.K512R		Atlas-SNP	.											.	PDE4A	236	.	0			c.A1535G						PASS	.	A	ARG/LYS,ARG/LYS,ARG/LYS,ARG/LYS	0,4406		0,0,2203	77.0	69.0	72.0		1535,1457,1352,818	3.9	1.0	19	dbSNP_134	72	3,8597	2.2+/-6.3	0,3,4297	yes	missense,missense,missense,missense	PDE4A	NM_001111307.1,NM_001111308.1,NM_001111309.1,NM_006202.2	26,26,26,26	0,3,6500	GG,GA,AA		0.0349,0.0,0.0231	benign,benign,benign,benign	512/887,486/861,451/826,273/648	10572271	3,13003	2203	4300	6503	SO:0001583	missense	5141	exon12			GCTTCAAGCTGCT		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.1535A>G	19.37:g.10572271A>G	ENSP00000270474:p.Lys512Arg	Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	105	52	0.495238	NM_001111307	O75522|O76092|Q16255|Q16691|Q5DM53|Q6PMT2|Q8IVA7|Q8WUQ3|Q9H3H2	Missense_Mutation	SNP	ENST00000352831.6	37	CCDS45961.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	A	18.40	3.614645	0.66672	0.0	3.49E-4	ENSG00000065989	ENST00000380702;ENST00000352831;ENST00000293683;ENST00000440014;ENST00000344979;ENST00000380686	D;D;D;D;D	0.81821	-1.54;-1.54;-1.54;-1.54;-1.54	3.92	3.92	0.45320	Metal-dependent phosphohydrolase, HD domain (1);5&apos (2);-cyclic nucleotide phosphodiesterase, catalytic domain (2);3&apos (2);	0.053169	0.64402	D	0.000001	D	0.84433	0.5471	L	0.43701	1.375	0.58432	D	0.999995	B;D;D;D;D	0.64830	0.081;0.994;0.992;0.971;0.989	B;D;D;P;D	0.83275	0.073;0.996;0.988;0.906;0.943	D	0.85413	0.1138	10	0.87932	D	0	.	10.7358	0.46124	1.0:0.0:0.0:0.0	.	178;273;451;486;512	P27815-5;P27815-4;P27815-6;P27815-2;P27815	.;.;.;.;PDE4A_HUMAN	R	490;512;486;451;273;178	ENSP00000370078:K490R;ENSP00000270474:K512R;ENSP00000293683:K486R;ENSP00000394754:K451R;ENSP00000341007:K273R	ENSP00000293683:K486R	K	+	2	0	PDE4A	10433271	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.022000	0.93678	1.652000	0.50683	0.477000	0.44152	AAG	A|1.000;G|0.000	0.000	strong		0.632	PDE4A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451244.1		
VDR	7421	hgsc.bcm.edu	37	12	48238757	48238757	+	Silent	SNP	A	A	G	rs731236	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:48238757A>G	ENST00000395324.2	-	10	1324	c.1056T>C	c.(1054-1056)atT>atC	p.I352I	VDR_ENST00000549336.1_Silent_p.I352I|VDR_ENST00000229022.3_Silent_p.I352I|VDR_ENST00000550325.1_Silent_p.I402I|VDR_ENST00000535672.1_Silent_p.I320I			P11473	VDR_HUMAN	vitamin D (1,25- dihydroxyvitamin D3) receptor	352	Ligand-binding.				bile acid signaling pathway (GO:0038183)|calcium ion transport (GO:0006816)|cell morphogenesis (GO:0000902)|cellular calcium ion homeostasis (GO:0006874)|decidualization (GO:0046697)|gene expression (GO:0010467)|intestinal absorption (GO:0050892)|lactation (GO:0007595)|mammary gland branching involved in pregnancy (GO:0060745)|negative regulation of cell proliferation (GO:0008285)|negative regulation of keratinocyte proliferation (GO:0010839)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|organ morphogenesis (GO:0009887)|positive regulation of apoptotic process involved in mammary gland involution (GO:0060058)|positive regulation of gene expression (GO:0010628)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of vitamin D 24-hydroxylase activity (GO:0010980)|regulation of calcidiol 1-monooxygenase activity (GO:0060558)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)|transcription initiation from RNA polymerase II promoter (GO:0006367)|vitamin D receptor signaling pathway (GO:0070561)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	calcitriol binding (GO:1902098)|calcitriol receptor activity (GO:0008434)|DNA binding (GO:0003677)|lithocholic acid binding (GO:1902121)|lithocholic acid receptor activity (GO:0038186)|retinoid X receptor binding (GO:0046965)|sequence-specific DNA binding (GO:0043565)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(10)|ovary(3)|skin(2)	22		Acute lymphoblastic leukemia(13;0.109)|all_hematologic(14;0.214)		GBM - Glioblastoma multiforme(48;0.17)	Alfacalcidol(DB01436)|Calcidiol(DB00146)|Calcipotriol(DB02300)|Calcitriol(DB00136)|Cholecalciferol(DB00169)|Dihydrotachysterol(DB01070)|Ergocalciferol(DB00153)|Paricalcitol(DB00910)	GGATGGCCTCAATCAGCGCGG	0.642													A|||	1385	0.276558	0.2852	0.255	5008	,	,		16737	0.0675		0.3996	False		,,,				2504	0.3691				p.I402I		Atlas-SNP	.											VDR,NS,carcinoma,0,1	VDR	47	1	0			c.T1206C						scavenged	.	A	,,	1230,3176	427.2+/-341.4	190,850,1163	106.0	111.0	109.0		1056,1056,1206	-7.9	0.0	12	dbSNP_86	109	3392,5208	501.9+/-375.6	679,2034,1587	no	coding-synonymous,coding-synonymous,coding-synonymous	VDR	NM_000376.2,NM_001017535.1,NM_001017536.1	,,	869,2884,2750	GG,GA,AA		39.4419,27.9165,35.5374	,,	352/428,352/428,402/478	48238757	4622,8384	2203	4300	6503	SO:0001819	synonymous_variant	7421	exon10			GGCCTCAATCAGC	J03258	CCDS8757.1, CCDS55820.1	12q12-q14	2014-06-13				ENSG00000111424		"""Nuclear hormone receptors"""	12679	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 163"""	601769				1662663	Standard	NM_001017536		Approved	NR1I1, PPP1R163	uc001rql.3	P11473		ENST00000395324.2:c.1056T>C	12.37:g.48238757A>G		Somatic	169	1	0.00591716		WXS	Illumina HiSeq	Phase_I	129	54	0.418605	NM_001017536	B2R5Q1|G3V1V9|Q5PSV3	Silent	SNP	ENST00000395324.2	37	CCDS8757.1																																																																																			A|0.692;G|0.308	0.308	strong		0.642	VDR-001	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406433.1		
NOTCH1	4851	hgsc.bcm.edu	37	9	139391636	139391636	+	Silent	SNP	G	G	A	rs2229974	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:139391636G>A	ENST00000277541.6	-	34	6630	c.6555C>T	c.(6553-6555)gaC>gaT	p.D2185D		NM_017617.3	NP_060087.3	P46531	NOTC1_HUMAN	notch 1	2185					anagen (GO:0042640)|aortic valve morphogenesis (GO:0003180)|apoptotic process involved in embryonic digit morphogenesis (GO:1902263)|arterial endothelial cell differentiation (GO:0060842)|atrioventricular node development (GO:0003162)|atrioventricular valve morphogenesis (GO:0003181)|auditory receptor cell fate commitment (GO:0009912)|axonogenesis (GO:0007409)|branching morphogenesis of an epithelial tube (GO:0048754)|cardiac atrium morphogenesis (GO:0003209)|cardiac chamber formation (GO:0003207)|cardiac epithelial to mesenchymal transition (GO:0060317)|cardiac left ventricle morphogenesis (GO:0003214)|cardiac muscle cell proliferation (GO:0060038)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac right atrium morphogenesis (GO:0003213)|cardiac right ventricle formation (GO:0003219)|cardiac septum morphogenesis (GO:0060411)|cardiac vascular smooth muscle cell development (GO:0060948)|cardiac ventricle morphogenesis (GO:0003208)|cell fate specification (GO:0001708)|cell migration involved in endocardial cushion formation (GO:0003273)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|cilium morphogenesis (GO:0060271)|collecting duct development (GO:0072044)|compartment pattern specification (GO:0007386)|coronary artery morphogenesis (GO:0060982)|coronary vein morphogenesis (GO:0003169)|determination of left/right symmetry (GO:0007368)|distal tubule development (GO:0072017)|embryonic hindlimb morphogenesis (GO:0035116)|endocardial cell differentiation (GO:0060956)|endocardial cushion morphogenesis (GO:0003203)|endocardium development (GO:0003157)|endocardium morphogenesis (GO:0003160)|endoderm development (GO:0007492)|epithelial to mesenchymal transition (GO:0001837)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|forebrain development (GO:0030900)|foregut morphogenesis (GO:0007440)|gene expression (GO:0010467)|glial cell differentiation (GO:0010001)|glomerular mesangial cell development (GO:0072144)|growth involved in heart morphogenesis (GO:0003241)|hair follicle morphogenesis (GO:0031069)|heart development (GO:0007507)|heart looping (GO:0001947)|heart trabecula morphogenesis (GO:0061384)|humoral immune response (GO:0006959)|immune response (GO:0006955)|in utero embryonic development (GO:0001701)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-4 secretion (GO:0072602)|keratinocyte differentiation (GO:0030216)|left/right axis specification (GO:0070986)|liver development (GO:0001889)|lung development (GO:0030324)|mesenchymal cell development (GO:0014031)|mitral valve formation (GO:0003192)|negative regulation of anoikis (GO:2000811)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of calcium ion-dependent exocytosis (GO:0045955)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cell migration involved in sprouting angiogenesis (GO:0090051)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of endothelial cell chemotaxis (GO:2001027)|negative regulation of glial cell proliferation (GO:0060253)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of neurogenesis (GO:0050768)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of ossification (GO:0030279)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of photoreceptor cell differentiation (GO:0046533)|negative regulation of pro-B cell differentiation (GO:2000974)|negative regulation of stem cell differentiation (GO:2000737)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube development (GO:0021915)|neuronal stem cell maintenance (GO:0097150)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|Notch signaling pathway involved in regulation of secondary heart field cardioblast proliferation (GO:0003270)|pericardium morphogenesis (GO:0003344)|positive regulation of apoptotic process (GO:0043065)|positive regulation of astrocyte differentiation (GO:0048711)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061419)|positive regulation of transcription of Notch receptor target (GO:0007221)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland epithelium morphogenesis (GO:0060740)|pulmonary valve morphogenesis (GO:0003184)|regulation of epithelial cell proliferation involved in prostate gland development (GO:0060768)|regulation of extracellular matrix assembly (GO:1901201)|regulation of somitogenesis (GO:0014807)|regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation (GO:0003256)|regulation of transcription, DNA-templated (GO:0006355)|response to muramyl dipeptide (GO:0032495)|secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development (GO:0060528)|skeletal muscle cell differentiation (GO:0035914)|somatic stem cell division (GO:0048103)|sprouting angiogenesis (GO:0002040)|transcription initiation from RNA polymerase II promoter (GO:0006367)|tube formation (GO:0035148)|vasculogenesis involved in coronary vascular morphogenesis (GO:0060979)|venous endothelial cell differentiation (GO:0060843)|ventricular septum morphogenesis (GO:0060412)|ventricular trabecula myocardium morphogenesis (GO:0003222)	cell surface (GO:0009986)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|MAML1-RBP-Jkappa- ICN1 complex (GO:0002193)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)|receptor activity (GO:0004872)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.K2182fs*61(1)|p.S2163_T2283del(1)		breast(16)|central_nervous_system(17)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1183)|kidney(4)|large_intestine(1)|lung(57)|oesophagus(2)|ovary(3)|pancreas(1)|prostate(3)|skin(21)|upper_aerodigestive_tract(39)|urinary_tract(3)	1359	all_cancers(76;0.223)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;5.34e-06)|Epithelial(140;7.77e-06)		AGCCCTTGCCGTCCTGGGACT	0.662			"""T, Mis, O"""	TRB@	T-ALL					HNSCC(8;0.001)			G|||	3481	0.695088	0.6278	0.6542	5008	,	,		16337	0.9494		0.5775	False		,,,				2504	0.6738				p.D2185D		Atlas-SNP	.		Dom	yes		9	9q34.3	4851	"""Notch homolog 1, translocation-associated (Drosophila) (TAN1)"""		L	.	NOTCH1	1980	.	2	Deletion - Frameshift(1)|Deletion - In frame(1)	haematopoietic_and_lymphoid_tissue(2)	c.C6555T						PASS	.	G		2777,1589		891,995,297	47.0	54.0	52.0		6555	-0.8	1.0	9	dbSNP_98	52	4726,3816		1319,2088,864	no	coding-synonymous	NOTCH1	NM_017617.3		2210,3083,1161	AA,AG,GG		44.6734,36.3949,41.8733		2185/2556	139391636	7503,5405	2183	4271	6454	SO:0001819	synonymous_variant	4851	exon34			CTTGCCGTCCTGG	AF308602	CCDS43905.1	9q34.3	2013-01-10	2010-06-24		ENSG00000148400	ENSG00000148400		"""Ankyrin repeat domain containing"""	7881	protein-coding gene	gene with protein product		190198	"""Notch (Drosophila) homolog 1 (translocation-associated)"", ""Notch homolog 1, translocation-associated (Drosophila)"""	TAN1		1831692	Standard	NM_017617		Approved		uc004chz.3	P46531	OTTHUMG00000020935	ENST00000277541.6:c.6555C>T	9.37:g.139391636G>A		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	125	56	0.448	NM_017617	Q59ED8|Q5SXM3	Silent	SNP	ENST00000277541.6	37	CCDS43905.1																																																																																			G|0.341;A|0.659	0.659	strong		0.662	NOTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055087.1	NM_017617	
C3orf30	152405	hgsc.bcm.edu	37	3	118865609	118865609	+	Silent	SNP	C	C	T	rs10934483	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:118865609C>T	ENST00000295622.1	+	1	613	c.573C>T	c.(571-573)tcC>tcT	p.S191S	IGSF11_ENST00000354673.2_5'Flank|IGSF11_ENST00000441144.2_5'Flank|RP11-484M3.5_ENST00000490594.1_5'Flank|IGSF11_ENST00000425327.2_5'Flank	NM_152539.2	NP_689752.2	Q96M34	CC030_HUMAN	chromosome 3 open reading frame 30	191										NS(1)|breast(1)|cervix(1)|endometrium(1)|large_intestine(6)|lung(20)|ovary(2)|prostate(1)|urinary_tract(1)	34				GBM - Glioblastoma multiforme(114;0.222)		GAAGAGCTTCCGAGCAGATGG	0.517													c|||	717	0.143171	0.1331	0.0663	5008	,	,		22755	0.2361		0.1531	False		,,,				2504	0.1053				p.S191S		Atlas-SNP	.											C3orf30,rectum,carcinoma,0,1	C3orf30	64	1	0			c.C573T						PASS	.	T		519,3887	239.3+/-250.5	28,463,1712	91.0	94.0	93.0		573	-8.2	0.0	3	dbSNP_120	93	1187,7413	242.1+/-272.2	73,1041,3186	no	coding-synonymous	C3orf30	NM_152539.2		101,1504,4898	TT,TC,CC		13.8023,11.7794,13.117		191/537	118865609	1706,11300	2203	4300	6503	SO:0001819	synonymous_variant	152405	exon1			AGCTTCCGAGCAG	AK057421	CCDS2984.1	3q13.32	2011-08-09			ENSG00000163424	ENSG00000163424			26553	protein-coding gene	gene with protein product							Standard	NM_152539		Approved	FLJ32859	uc003ecb.1	Q96M34	OTTHUMG00000159349	ENST00000295622.1:c.573C>T	3.37:g.118865609C>T		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	84	44	0.52381	NM_152539	A1L4B7	Silent	SNP	ENST00000295622.1	37	CCDS2984.1	359	0.16437728937728938	79	0.16056910569105692	22	0.06077348066298342	131	0.229020979020979	127	0.16754617414248021	c	4.219	0.039534	0.08148	0.117794	0.138023	ENSG00000163424	ENST00000460150	.	.	.	4.09	-8.17	0.01057	.	.	.	.	.	.	.	.	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	.	.	.	.	.	.	.	-14.7772	9.1284	0.36830	0.0:0.4138:0.1026:0.4836	rs10934483;rs10934483	.	.	.	X	155	.	.	R	+	1	2	C3orf30	120348299	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.657000	0.01979	-1.809000	0.01232	-1.402000	0.01139	CGA	C|0.855;T|0.145	0.145	strong		0.517	C3orf30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354838.1	NM_152539	
MCM10	55388	hgsc.bcm.edu	37	10	13230950	13230950	+	Silent	SNP	C	C	T	rs2296222	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:13230950C>T	ENST00000484800.2	+	10	1391	c.1288C>T	c.(1288-1290)Ctg>Ttg	p.L430L	MCM10_ENST00000378714.3_Silent_p.L429L|MCM10_ENST00000378694.1_Silent_p.L429L			Q7L590	MCM10_HUMAN	minichromosome maintenance complex component 10	430					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)			central_nervous_system(1)|large_intestine(4)|ovary(2)|skin(1)|stomach(1)	9						GCGTGCGGATCTGCAGTCCAC	0.542													T|||	983	0.196286	0.1293	0.2896	5008	,	,		17923	0.1954		0.174	False		,,,				2504	0.2444				p.L430L		Atlas-SNP	.											.	MCM10	76	.	0			c.C1288T						PASS	.	T	,	624,3782	768.8+/-413.6	35,554,1614	140.0	130.0	133.0		1285,1288	-6.7	0.0	10	dbSNP_100	133	1255,7345	761.3+/-407.6	88,1079,3133	no	coding-synonymous,coding-synonymous	MCM10	NM_018518.4,NM_182751.2	,	123,1633,4747	TT,TC,CC		14.593,14.1625,14.4472	,	429/875,430/876	13230950	1879,11127	2203	4300	6503	SO:0001819	synonymous_variant	55388	exon10			GCGGATCTGCAGT	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.1288C>T	10.37:g.13230950C>T		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	90	49	0.544444	NM_182751	A8K9I6|B7ZKZ8|Q3MIR3|Q7LD55|Q96GX4|Q96NB6|Q9H0D7|Q9H3P9|Q9P177	Silent	SNP	ENST00000484800.2	37	CCDS7096.1																																																																																			C|0.837;T|0.163	0.163	strong		0.542	MCM10-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356853.1	NM_182751	
PKHD1	5314	hgsc.bcm.edu	37	6	51491884	51491884	+	Missense_Mutation	SNP	T	T	C	rs4715227	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:51491884T>C	ENST00000371117.3	-	66	11971	c.11696A>G	c.(11695-11697)cAg>cGg	p.Q3899R		NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	3899			Q -> R (in dbSNP:rs4715227). {ECO:0000269|PubMed:12846734, ECO:0000269|PubMed:12874454}.		cellular calcium ion homeostasis (GO:0006874)|cilium assembly (GO:0042384)|homeostatic process (GO:0042592)|kidney development (GO:0001822)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular component movement (GO:0051271)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein kinase B signaling (GO:0051898)|positive regulation of cell proliferation (GO:0008284)|regulation of centrosome duplication (GO:0010824)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of TOR signaling (GO:0032006)|single organismal cell-cell adhesion (GO:0016337)	anchored component of external side of plasma membrane (GO:0031362)|apical plasma membrane (GO:0016324)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitotic spindle (GO:0072686)|perinuclear region of cytoplasm (GO:0048471)|primary cilium (GO:0072372)	receptor activity (GO:0004872)			NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(5)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(59)|lung(139)|ovary(16)|prostate(8)|skin(20)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(7)|urinary_tract(5)	304	Lung NSC(77;0.0605)					ATTATTAGTCTGGGATTCAGG	0.388													T|||	2771	0.553315	0.4569	0.5937	5008	,	,		18238	0.5813		0.5358	False		,,,				2504	0.6442				p.Q3899R		Atlas-SNP	.											.	PKHD1	927	.	0			c.A11696G						PASS	.	T	ARG/GLN	2120,2286	577.4+/-384.4	528,1064,611	241.0	243.0	243.0		11696	4.0	1.0	6	dbSNP_111	243	4690,3910	605.3+/-394.9	1270,2150,880	yes	missense	PKHD1	NM_138694.3	43	1798,3214,1491	CC,CT,TT		45.4651,48.1162,47.6396	benign	3899/4075	51491884	6810,6196	2203	4300	6503	SO:0001583	missense	5314	exon66			TTAGTCTGGGATT	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.11696A>G	6.37:g.51491884T>C	ENSP00000360158:p.Gln3899Arg	Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	129	127	0.984496	NM_138694	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Missense_Mutation	SNP	ENST00000371117.3	37	CCDS4935.1	1181	0.5407509157509157	222	0.45121951219512196	213	0.5883977900552486	332	0.5804195804195804	414	0.5461741424802111	T	10.02	1.237296	0.22711	0.481162	0.545349	ENSG00000170927	ENST00000371117	D	0.87809	-2.3	5.19	3.99	0.46301	.	0.707453	0.12437	N	0.469060	T	0.75925	0.3916	L	0.59436	1.845	0.09310	P	0.99999999935508	B	0.30793	0.295	B	0.31686	0.134	T	0.72151	-0.4377	9	0.66056	D	0.02	.	8.2376	0.31636	0.1768:0.0:0.0:0.8232	rs4715227;rs52814903;rs56452478;rs58387623;rs4715227	3899	P08F94	PKHD1_HUMAN	R	3899	ENSP00000360158:Q3899R	ENSP00000360158:Q3899R	Q	-	2	0	PKHD1	51599843	0.981000	0.34729	0.954000	0.39281	0.169000	0.22640	1.965000	0.40471	1.048000	0.40298	0.533000	0.62120	CAG	T|0.467;C|0.533	0.533	strong		0.388	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694	
ULBP3	79465	hgsc.bcm.edu	37	6	150386752	150386752	+	Missense_Mutation	SNP	C	C	T	rs34547018	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:150386752C>T	ENST00000367339.2	-	3	438	c.410G>A	c.(409-411)cGt>cAt	p.R137H	ULBP3_ENST00000438272.2_Missense_Mutation_p.R137H			Q9BZM4	N2DL3_HUMAN	UL16 binding protein 3	137	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)|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)			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)		CCAAGATCCACGGATGTATCC	0.517													C|||	25	0.00499201	0.0091	0.0029	5008	,	,		22692	0.0		0.008	False		,,,				2504	0.0031				p.R137H		Atlas-SNP	.											.	ULBP3	22	.	0			c.G410A						PASS	.	C	HIS/ARG	26,4380	32.6+/-62.9	0,26,2177	128.0	119.0	122.0		410	-6.7	0.0	6	dbSNP_126	122	22,8578	15.3+/-51.7	0,22,4278	yes	missense	ULBP3	NM_024518.1	29	0,48,6455	TT,TC,CC		0.2558,0.5901,0.3691	benign	137/245	150386752	48,12958	2203	4300	6503	SO:0001583	missense	79465	exon3			GATCCACGGATGT	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.410G>A	6.37:g.150386752C>T	ENSP00000356308:p.Arg137His	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	69	19	0.275362	NM_024518	Q5VY82|Q8IZX5|Q8TE75	Missense_Mutation	SNP	ENST00000367339.2	37	CCDS5225.1	10	0.004578754578754579	2	0.0040650406504065045	1	0.0027624309392265192	0	0.0	7	0.009234828496042216	C	1.414	-0.574714	0.03882	0.005901	0.002558	ENSG00000131019	ENST00000399812;ENST00000253335;ENST00000367339;ENST00000438272	T;T	0.08102	3.13;3.13	3.34	-6.69	0.01772	MHC class I, alpha chain, alpha1/alpha2 (1);MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);	.	.	.	.	T	0.01765	0.0056	M	0.71581	2.175	0.09310	N	1	B;B	0.25206	0.12;0.12	B;B	0.11329	0.006;0.006	T	0.24333	-1.0163	9	0.39692	T	0.17	1.34	0.3216	0.00304	0.3017:0.137:0.2037:0.3577	rs34547018	137;137	Q5VY82;Q9BZM4	.;N2DL3_HUMAN	H	88;137;137;137	ENSP00000356308:R137H;ENSP00000403562:R137H	ENSP00000253335:R137H	R	-	2	0	ULBP3	150428445	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.449000	0.01008	-3.228000	0.00210	-1.434000	0.01081	CGT	C|0.997;T|0.003	0.003	strong		0.517	ULBP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042678.2		
NLRP8	126205	hgsc.bcm.edu	37	19	56487603	56487603	+	Missense_Mutation	SNP	A	A	G	rs306481	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:56487603A>G	ENST00000291971.3	+	8	2881	c.2810A>G	c.(2809-2811)aAg>aGg	p.K937R	NLRP8_ENST00000590542.1_Missense_Mutation_p.K918R	NM_176811.2	NP_789781.2	Q86W28	NALP8_HUMAN	NLR family, pyrin domain containing 8	937			K -> R (in dbSNP:rs306481).		neuron death (GO:0070997)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)			breast(4)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(14)|ovary(5)|skin(2)|stomach(3)|upper_aerodigestive_tract(2)	35		Colorectal(82;0.000147)|Ovarian(87;0.17)		GBM - Glioblastoma multiforme(193;0.0695)		AATAGCCTGAAGGATGATGGG	0.463													A|||	2820	0.563099	0.4024	0.6037	5008	,	,		17430	0.6657		0.5537	False		,,,				2504	0.6554				p.K937R		Atlas-SNP	.											.	NLRP8	225	.	0			c.A2810G						PASS	.	A	ARG/LYS	1801,2605	529.8+/-372.8	357,1087,759	137.0	134.0	135.0		2810	-5.0	0.0	19	dbSNP_79	135	4778,3822	611.3+/-395.8	1314,2150,836	yes	missense	NLRP8	NM_176811.2	26	1671,3237,1595	GG,GA,AA		44.4419,40.8761,49.4157	benign	937/1049	56487603	6579,6427	2203	4300	6503	SO:0001583	missense	126205	exon8			GCCTGAAGGATGA	AY154463	CCDS12937.1	19q13.43	2008-02-05	2006-12-08	2006-12-08		ENSG00000179709		"""Nucleotide-binding domain and leucine rich repeat containing"""	22940	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 8"""	609659	"""NACHT, leucine rich repeat and PYD containing 8"""	NALP8		12563287	Standard	NM_176811		Approved	NOD16, PAN4, CLR19.2	uc002qmh.3	Q86W28		ENST00000291971.3:c.2810A>G	19.37:g.56487603A>G	ENSP00000291971:p.Lys937Arg	Somatic	220	1	0.00454545		WXS	Illumina HiSeq	Phase_I	186	186	1	NM_176811	Q7RTR4	Missense_Mutation	SNP	ENST00000291971.3	37	CCDS12937.1	1208	0.5531135531135531	200	0.4065040650406504	216	0.5966850828729282	370	0.6468531468531469	422	0.5567282321899736	A	0.018	-1.470150	0.01044	0.408761	0.555581	ENSG00000179709	ENST00000291971	T	0.63096	-0.02	2.94	-5.02	0.02982	.	.	.	.	.	T	0.00012	0.0000	N	0.12182	0.205	0.80722	P	0.0	B;B	0.16603	0.007;0.018	B;B	0.20577	0.018;0.03	T	0.41324	-0.9515	8	0.09590	T	0.72	.	2.5502	0.04747	0.2329:0.1605:0.4488:0.1578	rs306481;rs52827447;rs58300306;rs306481	918;937	Q86W28-2;Q86W28	.;NALP8_HUMAN	R	937	ENSP00000291971:K937R	ENSP00000291971:K937R	K	+	2	0	NLRP8	61179415	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-0.429000	0.06982	-1.533000	0.01745	-0.476000	0.04901	AAG	A|0.474;G|0.526	0.526	strong		0.463	NLRP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457462.1	NM_176811	
RAD51AP2	729475	hgsc.bcm.edu	37	2	17697635	17697635	+	Missense_Mutation	SNP	T	T	C	rs181531922	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:17697635T>C	ENST00000399080.2	-	1	2071	c.2048A>G	c.(2047-2049)gAa>gGa	p.E683G		NM_001099218.2	NP_001092688.1	Q09MP3	R51A2_HUMAN	RAD51 associated protein 2	683										endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(10)|liver(1)|lung(17)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	49	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)					TTCATATGTTTCAAAAATCGG	0.289													T|||	13	0.00259585	0.0008	0.0043	5008	,	,		17559	0.0		0.0089	False		,,,				2504	0.0				p.E683G		Atlas-SNP	.											.	RAD51AP2	134	.	0			c.A2048G						PASS	.	T	GLY/GLU	10,3590		0,10,1790	38.0	36.0	37.0		2048	4.6	0.0	2		37	115,7961		0,115,3923	yes	missense	RAD51AP2	NM_001099218.2	98	0,125,5713	CC,CT,TT		1.424,0.2778,1.0706	possibly-damaging	683/1160	17697635	125,11551	1800	4038	5838	SO:0001583	missense	729475	exon1			TATGTTTCAAAAA	AK310498	CCDS42656.1	2p24.2	2009-01-13			ENSG00000214842	ENSG00000214842			34417	protein-coding gene	gene with protein product						16990250	Standard	NM_001099218		Approved	FLJ17540	uc002rcl.1	Q09MP3	OTTHUMG00000151761	ENST00000399080.2:c.2048A>G	2.37:g.17697635T>C	ENSP00000382030:p.Glu683Gly	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	84	50	0.595238	NM_001099218		Missense_Mutation	SNP	ENST00000399080.2	37	CCDS42656.1	7	0.003205128205128205	0	0.0	1	0.0027624309392265192	0	0.0	6	0.0079155672823219	T	5.534	0.283387	0.10458	0.002778	0.01424	ENSG00000214842	ENST00000399080	T	0.25250	1.81	4.62	4.62	0.57501	.	.	.	.	.	T	0.15089	0.0364	N	0.14661	0.345	0.09310	N	1	P	0.44429	0.835	P	0.47645	0.553	T	0.05801	-1.0863	9	0.66056	D	0.02	-0.2662	8.6213	0.33861	0.0:0.0886:0.0:0.9114	.	683	Q09MP3	R51A2_HUMAN	G	683	ENSP00000382030:E683G	ENSP00000382030:E683G	E	-	2	0	RAD51AP2	17561116	0.532000	0.26346	0.003000	0.11579	0.009000	0.06853	2.814000	0.48010	2.012000	0.59069	0.482000	0.46254	GAA	T|0.994;C|0.006	0.006	strong		0.289	RAD51AP2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323801.3	NM_001099218	
ZNF91	7644	hgsc.bcm.edu	37	19	23542626	23542626	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:23542626C>T	ENST00000300619.7	-	4	3360	c.3155G>A	c.(3154-3156)tGt>tAt	p.C1052Y	ZNF91_ENST00000599743.1_Intron|ZNF91_ENST00000596528.1_5'Flank|ZNF91_ENST00000397082.2_Missense_Mutation_p.C1020Y	NM_003430.2	NP_003421.2	Q05481	ZNF91_HUMAN	zinc finger protein 91	1052					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)				ACATTCTTCACACTTGTAAGG	0.358																																					p.C1052Y		Atlas-SNP	.											.	ZNF91	349	.	0			c.G3155A						PASS	.						65.0	70.0	68.0					19																	23542626		2185	4292	6477	SO:0001583	missense	7644	exon4			TCTTCACACTTGT	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.3155G>A	19.37:g.23542626C>T	ENSP00000300619:p.Cys1052Tyr	Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	25	12	0.48	NM_003430	A8K5E1|B7Z6G6	Missense_Mutation	SNP	ENST00000300619.7	37	CCDS42541.1	.	.	.	.	.	.	.	.	.	.	C	12.28	1.889340	0.33348	.	.	ENSG00000167232	ENST00000300619;ENST00000397082	D;D	0.85088	-1.94;-1.94	1.31	-0.339	0.12647	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	D	0.94032	0.8088	H	0.97962	4.115	0.09310	N	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.83578	0.0116	9	0.87932	D	0	.	7.5061	0.27545	0.2521:0.7479:0.0:0.0	.	1020;1052	Q05481-2;Q05481	.;ZNF91_HUMAN	Y	1052;1020	ENSP00000300619:C1052Y;ENSP00000380272:C1020Y	ENSP00000300619:C1052Y	C	-	2	0	ZNF91	23334466	0.951000	0.32395	0.119000	0.21687	0.692000	0.40212	2.703000	0.47110	0.676000	0.31285	0.196000	0.17591	TGT	.	.	none		0.358	ZNF91-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465891.1	NM_003430	
PPP1R3A	5506	hgsc.bcm.edu	37	7	113518434	113518434	+	Missense_Mutation	SNP	C	C	A	rs1799999	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:113518434C>A	ENST00000284601.3	-	4	2781	c.2713G>T	c.(2713-2715)Gac>Tac	p.D905Y		NM_002711.3	NP_002702.2	Q16821	PPR3A_HUMAN	protein phosphatase 1, regulatory subunit 3A	905			D -> Y (common polymorphism; can be associated with insulin resistance; dbSNP:rs1799999). {ECO:0000269|PubMed:7581368, ECO:0000269|PubMed:9726244}.		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						CTATTAGTGTCTGAGTTAAAA	0.378													C|||	1546	0.308706	0.1793	0.2046	5008	,	,		18875	0.6409		0.1153	False		,,,				2504	0.4141				p.D905Y		Atlas-SNP	.											.	PPP1R3A	317	.	0			c.G2713T	GRCh37	CM950973	PPP1R3A	M	rs1799999	PASS	.	C	TYR/ASP	858,3548	336.5+/-304.4	77,704,1422	89.0	87.0	88.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	2713	5.6	1.0	7	dbSNP_89	88	902,7696	201.7+/-245.1	56,790,3453	yes	missense	PPP1R3A	NM_002711.3	160	133,1494,4875	AA,AC,CC		10.4908,19.4734,13.5343	probably-damaging	905/1123	113518434	1760,11244	2203	4299	6502	SO:0001583	missense	5506	exon4			TAGTGTCTGAGTT	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.2713G>T	7.37:g.113518434C>A	ENSP00000284601:p.Asp905Tyr	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	52	33	0.634615	NM_002711	A0AVQ2|A4D0T6|O43476|Q75LN8|Q7KYM8|Q86UI6	Missense_Mutation	SNP	ENST00000284601.3	37	CCDS5759.1	637	0.2916666666666667	75	0.1524390243902439	78	0.2154696132596685	392	0.6853146853146853	92	0.12137203166226913	C	12.29	1.893032	0.33442	0.194734	0.104908	ENSG00000154415	ENST00000284601	T	0.20738	2.05	5.64	5.64	0.86602	.	0.367148	0.26414	N	0.024511	T	0.00012	0.0000	L	0.56769	1.78	0.35982	P	0.16393800000000003	D	0.56521	0.976	P	0.53185	0.72	T	0.30504	-0.9976	9	0.72032	D	0.01	-3.5799	11.6403	0.51228	0.0:0.9117:0.0:0.0883	rs1799999;rs8192685;rs17847379;rs59907640;rs1799999	905	Q16821	PPR3A_HUMAN	Y	905	ENSP00000284601:D905Y	ENSP00000284601:D905Y	D	-	1	0	PPP1R3A	113305670	1.000000	0.71417	0.997000	0.53966	0.368000	0.29767	3.209000	0.51122	2.646000	0.89796	0.603000	0.83216	GAC	C|0.769;N|0.000	.	strong		0.378	PPP1R3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346724.1	NM_002711	
ATP10D	57205	hgsc.bcm.edu	37	4	47514685	47514685	+	Missense_Mutation	SNP	C	C	T	rs33995001	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:47514685C>T	ENST00000273859.3	+	2	397	c.128C>T	c.(127-129)aCc>aTc	p.T43I	ATP10D_ENST00000504445.1_Missense_Mutation_p.T43I	NM_020453.3	NP_065186.3	Q9P241	AT10D_HUMAN	ATPase, class V, type 10D	43			T -> I (in dbSNP:rs33995001). {ECO:0000269|PubMed:15489334}.		cation transport (GO:0006812)|ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(2)|endometrium(5)|kidney(5)|large_intestine(14)|liver(2)|lung(26)|ovary(2)|pancreas(1)|prostate(5)|skin(2)|stomach(1)|urinary_tract(1)	66						TCCTCTCAGACCCCTAAACTG	0.522													C|||	1527	0.304912	0.2958	0.4352	5008	,	,		17210	0.1558		0.4374	False		,,,				2504	0.2423				p.T43I		Atlas-SNP	.											.	ATP10D	168	.	0			c.C128T						PASS	.	C	ILE/THR	1382,3024	455.7+/-351.1	219,944,1040	95.0	89.0	91.0		128	3.3	0.7	4	dbSNP_126	91	3686,4914	527.7+/-381.2	801,2084,1415	yes	missense	ATP10D	NM_020453.3	89	1020,3028,2455	TT,TC,CC		42.8605,31.3663,38.9666	benign	43/1427	47514685	5068,7938	2203	4300	6503	SO:0001583	missense	57205	exon2			CTCAGACCCCTAA	AB040920	CCDS3476.1	4p12	2010-04-20	2007-09-19		ENSG00000145246	ENSG00000145246		"""ATPases / P-type"""	13549	protein-coding gene	gene with protein product			"""ATPase, Class V, type 10D"""			12532265	Standard	NM_020453		Approved	ATPVD, KIAA1487	uc003gxk.1	Q9P241	OTTHUMG00000160784	ENST00000273859.3:c.128C>T	4.37:g.47514685C>T	ENSP00000273859:p.Thr43Ile	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	100	43	0.43	NM_020453	A2RRC8|D6REN2|Q8NC70|Q96SR3	Missense_Mutation	SNP	ENST00000273859.3	37	CCDS3476.1	751	0.34386446886446886	146	0.2967479674796748	165	0.4558011049723757	109	0.19055944055944055	331	0.4366754617414248	C	5.653	0.305108	0.10678	0.313663	0.428605	ENSG00000145246	ENST00000273859;ENST00000504445	T;T	0.38722	1.12;4.02	5.1	3.3	0.37823	.	0.615971	0.17070	N	0.188207	T	0.00012	0.0000	M	0.62723	1.935	0.80722	P	0.0	P;B	0.35481	0.504;0.006	B;B	0.28916	0.096;0.008	T	0.47560	-0.9108	9	0.22109	T	0.4	-4.9928	6.758	0.23524	0.0:0.5692:0.2837:0.147	rs33995001	43;43	Q9P241;Q6PEW3	AT10D_HUMAN;.	I	43	ENSP00000273859:T43I;ENSP00000420909:T43I	ENSP00000273859:T43I	T	+	2	0	ATP10D	47209442	0.000000	0.05858	0.689000	0.30133	0.059000	0.15707	0.341000	0.19909	0.604000	0.29930	-0.310000	0.09108	ACC	C|0.623;T|0.377	0.377	strong		0.522	ATP10D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216900.1	NM_020453	
LRRC8A	56262	hgsc.bcm.edu	37	9	131670457	131670457	+	Silent	SNP	T	T	C	rs3750320	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:131670457T>C	ENST00000259324.5	+	3	1537	c.1014T>C	c.(1012-1014)taT>taC	p.Y338Y	LRRC8A_ENST00000372600.4_Silent_p.Y338Y|LRRC8A_ENST00000372599.3_Silent_p.Y338Y	NM_001127244.1	NP_001120716.1	Q8IWT6	LRC8A_HUMAN	leucine rich repeat containing 8 family, member A	338					anion transport (GO:0006820)|cell volume homeostasis (GO:0006884)|pre-B cell differentiation (GO:0002329)|response to osmotic stress (GO:0006970)	cell surface (GO:0009986)|ion channel complex (GO:0034702)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(8)|ovary(1)|pancreas(1)|skin(3)	28						TCTGCATGTATACACTGTGGT	0.562													C|||	1324	0.264377	0.4297	0.1513	5008	,	,		20578	0.1746		0.2008	False		,,,				2504	0.2791				p.Y338Y		Atlas-SNP	.											.	LRRC8A	69	.	0			c.T1014C						PASS	.	C	,,	1735,2671	648.2+/-398.7	308,1119,776	199.0	145.0	164.0		1014,1014,1014	4.3	1.0	9	dbSNP_107	164	1596,7004	743.6+/-407.2	141,1314,2845	no	coding-synonymous,coding-synonymous,coding-synonymous	LRRC8A	NM_001127244.1,NM_001127245.1,NM_019594.3	,,	449,2433,3621	CC,CT,TT		18.5581,39.3781,25.6113	,,	338/811,338/811,338/811	131670457	3331,9675	2203	4300	6503	SO:0001819	synonymous_variant	56262	exon3			CATGTATACACTG	AB037858	CCDS35155.1	9q34.2	2014-09-17	2005-06-29	2005-06-29	ENSG00000136802	ENSG00000136802			19027	protein-coding gene	gene with protein product		608360	"""leucine rich repeat containing 8"""	LRRC8			Standard	NM_001127244		Approved	KIAA1437, FLJ10337	uc010myp.3	Q8IWT6	OTTHUMG00000020766	ENST00000259324.5:c.1014T>C	9.37:g.131670457T>C		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	92	45	0.48913	NM_001127244	Q6UXM2|Q8NCI0|Q9P2B1	Silent	SNP	ENST00000259324.5	37	CCDS35155.1																																																																																			T|0.745;C|0.255	0.255	strong		0.562	LRRC8A-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054516.2	NM_019594	
C6	729	hgsc.bcm.edu	37	5	41155088	41155088	+	Missense_Mutation	SNP	T	T	C	rs41271067	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:41155088T>C	ENST00000263413.3	-	14	2351	c.2087A>G	c.(2086-2088)gAt>gGt	p.D696G	C6_ENST00000337836.5_Missense_Mutation_p.D696G	NM_001115131.1	NP_001108603.2	P13671	CO6_HUMAN	complement component 6	696	C5b-binding domain.|CCP 2.|Sushi 1. {ECO:0000255|PROSITE- ProRule:PRU00302}.				complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|cytolysis (GO:0019835)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane attack complex (GO:0005579)				central_nervous_system(2)|cervix(2)|endometrium(2)|kidney(7)|large_intestine(16)|liver(1)|lung(51)|ovary(3)|prostate(1)|skin(9)|upper_aerodigestive_tract(2)	96		Breast(839;1.07e-05)|Ovarian(839;0.0228)|Lung SC(612;0.0548)|Lung NSC(810;0.128)|all_neural(839;0.157)				GCATTCCACATCCCCTTGTCT	0.413													T|||	17	0.00339457	0.0	0.0086	5008	,	,		19476	0.001		0.008	False		,,,				2504	0.002				p.D696G		Atlas-SNP	.											.	C6	197	.	0			c.A2087G						PASS	.	T	GLY/ASP,GLY/ASP	8,4398	14.3+/-33.2	0,8,2195	148.0	138.0	142.0		2087,2087	3.5	1.0	5	dbSNP_127	142	115,8485	60.6+/-122.4	1,113,4186	yes	missense,missense	C6	NM_000065.2,NM_001115131.1	94,94	1,121,6381	CC,CT,TT		1.3372,0.1816,0.9457	benign,benign	696/935,696/935	41155088	123,12883	2203	4300	6503	SO:0001583	missense	729	exon14			TCCACATCCCCTT	J05024	CCDS3936.1	5p13.1	2014-09-17			ENSG00000039537	ENSG00000039537		"""Complement system"""	1339	protein-coding gene	gene with protein product		217050					Standard	NM_001115131		Approved		uc003jmk.3	P13671	OTTHUMG00000094781	ENST00000263413.3:c.2087A>G	5.37:g.41155088T>C	ENSP00000263413:p.Asp696Gly	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	107	38	0.35514	NM_001115131		Missense_Mutation	SNP	ENST00000263413.3	37	CCDS3936.1	12	0.005494505494505495	0	0.0	5	0.013812154696132596	1	0.0017482517482517483	6	0.0079155672823219	T	13.64	2.298824	0.40694	0.001816	0.013372	ENSG00000039537	ENST00000337836;ENST00000263413	T;T	0.41758	0.99;0.99	5.82	3.51	0.40186	Complement control module (2);Sushi/SCR/CCP (2);	0.475155	0.24788	N	0.035595	T	0.26048	0.0635	L	0.47190	1.495	0.34230	D	0.676444	B	0.17852	0.024	B	0.25759	0.063	T	0.36939	-0.9727	10	0.36615	T	0.2	-24.0381	7.4848	0.27425	0.0:0.1133:0.1879:0.6988	rs41271067;rs61733157	696	P13671	CO6_HUMAN	G	696	ENSP00000338861:D696G;ENSP00000263413:D696G	ENSP00000263413:D696G	D	-	2	0	C6	41190845	0.576000	0.26700	0.999000	0.59377	0.992000	0.81027	0.724000	0.25954	2.232000	0.73038	0.528000	0.53228	GAT	T|0.992;C|0.008	0.008	strong		0.413	C6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211592.1		
C5orf60	285679	hgsc.bcm.edu	37	5	179071893	179071893	+	Silent	SNP	A	A	G	rs4990388	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:179071893A>G	ENST00000448248.2	-	1	154	c.129T>C	c.(127-129)ttT>ttC	p.F43F	C5orf60_ENST00000506142.1_Intron	NM_001142306.1	NP_001135778.1	A6NFR6	CE060_HUMAN	chromosome 5 open reading frame 60	43						integral component of membrane (GO:0016021)		p.F43F(2)		NS(1)|breast(1)|kidney(5)	7						TGAACACAACAAAGAGGACGA	0.517													-|||	83	0.0165735	0.0575	0.0058	5008	,	,		23296	0.0		0.002	False		,,,				2504	0.001				p.F43F		Atlas-SNP	.											C5orf60,NS,carcinoma,0,2	C5orf60	24	2	2	Substitution - coding silent(2)	kidney(2)	c.T129C						scavenged	.						89.0	84.0	86.0					5																	179071893		692	1591	2283	SO:0001819	synonymous_variant	285679	exon1			CACAACAAAGAGG	BC043435	CCDS47353.1	5q35.3	2010-08-19			ENSG00000204661	ENSG00000204661			27753	protein-coding gene	gene with protein product						12477932	Standard	NM_001142306		Approved		uc003mki.3	A6NFR6	OTTHUMG00000163221	ENST00000448248.2:c.129T>C	5.37:g.179071893A>G		Somatic	327	0	0		WXS	Illumina HiSeq	Phase_I	235	11	0.0468085	NM_001142306	A1L488|B7ZM52|B7ZM53	Silent	SNP	ENST00000448248.2	37	CCDS47353.1																																																																																			A|0.993;G|0.007	0.007	strong		0.517	C5orf60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372148.2	NM_001142306	
OR5L2	26338	hgsc.bcm.edu	37	11	55595018	55595018	+	Silent	SNP	A	A	G	rs61745634|rs34954823|rs386753700	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:55595018A>G	ENST00000378397.1	+	1	324	c.324A>G	c.(322-324)ggA>ggG	p.G108G		NM_001004739.1	NP_001004739.1	Q8NGL0	OR5L2_HUMAN	olfactory receptor, family 5, subfamily L, member 2	108						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.G108G(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)				GCACATGTGGAGTCACTGAGG	0.488										HNSCC(27;0.073)			N|||	342	0.0682907	0.0938	0.036	5008	,	,		22005	0.0704		0.0736	False		,,,				2504	0.0491				p.G108G		Atlas-SNP	.											OR5L2,NS,carcinoma,0,2	OR5L2	135	2	1	Substitution - coding silent(1)	stomach(1)	c.A324G						PASS	.						183.0	172.0	176.0					11																	55595018		2197	4293	6490	SO:0001819	synonymous_variant	26338	exon1			ATGTGGAGTCACT	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.324A>G	11.37:g.55595018A>G		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	71	37	0.521127	NM_001004739	Q6IF66|Q96RB2	Silent	SNP	ENST00000378397.1	37	CCDS31511.1																																																																																			A|0.993;G|0.007	0.007	strong		0.488	OR5L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391516.1	NM_001004739	
MST1R	4486	hgsc.bcm.edu	37	3	49936102	49936102	+	Missense_Mutation	SNP	T	T	C	rs2230590	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:49936102T>C	ENST00000296474.3	-	4	1595	c.1568A>G	c.(1567-1569)cAa>cGa	p.Q523R	CTD-2330K9.2_ENST00000435478.1_RNA|MST1R_ENST00000344206.4_Missense_Mutation_p.Q523R	NM_002447.2	NP_002438	Q04912	RON_HUMAN	macrophage stimulating 1 receptor (c-met-related tyrosine kinase)	523			Q -> R (in dbSNP:rs2230590). {ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:8386824}.		cellular component movement (GO:0006928)|defense response (GO:0006952)|innate immune response (GO:0045087)|macrophage colony-stimulating factor signaling pathway (GO:0038145)|multicellular organismal development (GO:0007275)|positive regulation of cell proliferation (GO:0008284)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein kinase B signaling (GO:0051897)|response to virus (GO:0009615)|signal transduction (GO:0007165)|single fertilization (GO:0007338)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|stress fiber (GO:0001725)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|macrophage colony-stimulating factor receptor activity (GO:0005011)			cervix(1)|endometrium(5)|large_intestine(3)|lung(17)|ovary(5)|prostate(2)|skin(1)|urinary_tract(3)	37				BRCA - Breast invasive adenocarcinoma(193;4.65e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.00553)|Kidney(197;0.00625)		GCCAGGGCCTTGGATAGGTAC	0.597													C|||	2086	0.416534	0.7368	0.3761	5008	,	,		19719	0.1429		0.497	False		,,,				2504	0.2117				p.Q523R		Atlas-SNP	.											.	MST1R	205	.	0			c.A1568G						PASS	.	C	ARG/GLN	2941,1465	467.9+/-355.0	1002,937,264	49.0	58.0	55.0		1568	-6.8	0.1	3	dbSNP_98	55	4350,4250	570.7+/-389.4	1100,2150,1050	yes	missense	MST1R	NM_002447.2	43	2102,3087,1314	CC,CT,TT		49.4186,33.2501,43.9413	benign	523/1401	49936102	7291,5715	2203	4300	6503	SO:0001583	missense	4486	exon4			GGGCCTTGGATAG	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.1568A>G	3.37:g.49936102T>C	ENSP00000296474:p.Gln523Arg	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	76	53	0.697368	NM_001244937	B5A944|B5A945|B5A946|B5A947	Missense_Mutation	SNP	ENST00000296474.3	37	CCDS2807.1	916	0.4194139194139194	340	0.6910569105691057	132	0.36464088397790057	82	0.14335664335664336	362	0.47757255936675463	C	0.005	-2.227231	0.00280	0.667499	0.505814	ENSG00000164078	ENST00000296474;ENST00000344206	T;T	0.39997	1.05;3.01	5.84	-6.78	0.01721	WD40/YVTN repeat-like-containing domain (1);	0.557246	0.19719	N	0.107633	T	0.00012	0.0000	L	0.35487	1.065	0.80722	P	0.0	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.08055	0.001;0.003;0.002;0.0	T	0.36311	-0.9753	9	0.05959	T	0.93	-0.871	7.5474	0.27775	0.0646:0.3007:0.0998:0.5348	rs2230590;rs2293019;rs57396014;rs2230590	417;523;523;523	Q04912-4;Q04912-6;Q04912-5;Q04912	.;.;.;RON_HUMAN	R	523	ENSP00000296474:Q523R;ENSP00000341325:Q523R	ENSP00000296474:Q523R	Q	-	2	0	MST1R	49911106	0.000000	0.05858	0.139000	0.22197	0.049000	0.14656	-1.163000	0.03138	-1.703000	0.01409	-2.395000	0.00226	CAA	T|0.495;C|0.505	0.505	strong		0.597	MST1R-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000345403.1		
MUC20	200958	hgsc.bcm.edu	37	3	195453244	195453244	+	Silent	SNP	G	G	A	rs140946665	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195453244G>A	ENST00000447234.2	+	2	1896	c.1770G>A	c.(1768-1770)ccG>ccA	p.P590P	MUC20_ENST00000436408.1_Silent_p.P590P|MUC20_ENST00000445522.2_Silent_p.P555P|MUC20_ENST00000320736.6_Silent_p.P419P	NM_001282506.1	NP_001269435.1	Q8N307	MUC20_HUMAN	mucin 20, cell surface associated	590	Involved in oligomerization.|Thr-rich.		P -> L (in dbSNP:rs3828408). {ECO:0000269|PubMed:15489334}.		activation of MAPK activity (GO:0000187)|cellular protein metabolic process (GO:0044267)|hepatocyte growth factor receptor signaling pathway (GO:0048012)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein homooligomerization (GO:0051260)	basal plasma membrane (GO:0009925)|cell projection (GO:0042995)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)				NS(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(4)|skin(4)|stomach(3)|upper_aerodigestive_tract(1)	23	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)	Lung NSC(153;0.191)	Epithelial(36;1e-21)|all cancers(36;9.02e-20)|OV - Ovarian serous cystadenocarcinoma(49;1.6e-18)|Lung(62;0.000104)|LUSC - Lung squamous cell carcinoma(58;0.000128)	GBM - Glioblastoma multiforme(46;1.66e-05)		CAGAGACACCGACCATGGACA	0.597													g|||	154	0.0307508	0.0393	0.0403	5008	,	,		27759	0.0		0.0656	False		,,,				2504	0.0082				p.P419P		Atlas-SNP	.											.	MUC20	84	.	0			c.G1257A						PASS	.		,	163,3939		0,163,1888	63.0	59.0	60.0		1152,1257	-6.8	0.0	3	dbSNP_134	60	434,7948		0,434,3757	no	coding-synonymous,coding-synonymous	MUC20	NM_001098516.1,NM_152673.2	,	0,597,5645	AA,AG,GG		5.1778,3.9737,4.7821	,	384/504,419/539	195453244	597,11887	2051	4191	6242	SO:0001819	synonymous_variant	200958	exon3			GACACCGACCATG	AB037780	CCDS63877.1	3q29	2008-08-07	2006-03-14		ENSG00000176945	ENSG00000176945		"""Mucins"""	23282	protein-coding gene	gene with protein product		610360				14565953	Standard	NM_001282506		Approved	FLJ14408, KIAA1359	uc010hzo.3	Q8N307	OTTHUMG00000155823	ENST00000447234.2:c.1770G>A	3.37:g.195453244G>A		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	135	46	0.340741	NM_152673	Q6UX97|Q76I83|Q76I85|Q86ST8|Q8NBY6|Q96KA1|Q9P2I8	Silent	SNP	ENST00000447234.2	37		77	0.035256410256410256	17	0.034552845528455285	11	0.03038674033149171	0	0.0	49	0.06464379947229551	G	2.431	-0.330955	0.05314	0.039737	0.051778	ENSG00000176945	ENST00000423938	.	.	.	4.69	-6.77	0.01727	.	.	.	.	.	T	0.01489	0.0048	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.20505	-1.0273	4	.	.	.	1.2966	0.3197	0.00301	0.2575:0.2514:0.2569:0.2342	.	.	.	.	N	2	.	.	D	+	1	0	MUC20	196938915	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.325000	0.01115	-1.392000	0.02082	-1.345000	0.01243	GAC	G|0.965;A|0.035	0.035	strong		0.597	MUC20-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000341835.1	NM_152673	
TCN2	6948	hgsc.bcm.edu	37	22	31006860	31006860	+	Missense_Mutation	SNP	A	A	G	rs9606756	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:31006860A>G	ENST00000215838.3	+	2	561	c.67A>G	c.(67-69)Ata>Gta	p.I23V	TCN2_ENST00000407817.3_Missense_Mutation_p.I23V|TCN2_ENST00000405742.3_Missense_Mutation_p.I23V			P20062	TCO2_HUMAN	transcobalamin II	23			I -> V (in dbSNP:rs9606756).		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)	endosome (GO:0005768)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)	cobalamin binding (GO:0031419)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(6)|prostate(2)|urinary_tract(1)	22					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	TTTCTAAGAAATACCAGAGAT	0.502													A|||	566	0.113019	0.1581	0.196	5008	,	,		21709	0.0129		0.1133	False		,,,				2504	0.0961				p.I23V		Atlas-SNP	.											.	TCN2	44	.	0			c.A67G						PASS	.	A	VAL/ILE,VAL/ILE	678,3728	284.0+/-277.4	57,564,1582	78.0	76.0	77.0		67,67	1.3	0.0	22	dbSNP_119	77	1001,7599	213.6+/-253.5	60,881,3359	yes	missense,missense	TCN2	NM_000355.3,NM_001184726.1	29,29	117,1445,4941	GG,GA,AA		11.6395,15.3881,12.9094	benign,benign	23/428,23/401	31006860	1679,11327	2203	4300	6503	SO:0001583	missense	6948	exon2			TAAGAAATACCAG		CCDS13881.1, CCDS54519.1	22q12.2	2014-09-17	2010-05-11		ENSG00000185339	ENSG00000185339			11653	protein-coding gene	gene with protein product	"""macrocytic anemia"""	613441	"""transcobalamin II; macrocytic anemia"""			1708393, 7742531	Standard	NM_000355		Approved	D22S676, D22S750, TC2	uc003aip.2	P20062	OTTHUMG00000151095	ENST00000215838.3:c.67A>G	22.37:g.31006860A>G	ENSP00000215838:p.Ile23Val	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	87	50	0.574713	NM_001184726	Q96FD4|Q9BVI8|Q9UCI5|Q9UCI6|Q9UDM0	Missense_Mutation	SNP	ENST00000215838.3	37	CCDS13881.1	223	0.1021062271062271	75	0.1524390243902439	52	0.143646408839779	4	0.006993006993006993	92	0.12137203166226913	A	13.93	2.382508	0.42207	0.153881	0.116395	ENSG00000185339	ENST00000215838;ENST00000423350;ENST00000405742;ENST00000407817	T;T;T;T	0.37235	1.54;1.54;1.54;1.21	5.94	1.27	0.21489	.	0.228775	0.44902	N	0.000409	T	0.00144	0.0004	L	0.47016	1.485	0.29483	P	0.856208	B;B;B	0.17038	0.02;0.002;0.002	B;B;B	0.22601	0.04;0.026;0.026	T	0.09574	-1.0668	9	0.37606	T	0.19	-2.8261	2.0113	0.03489	0.5892:0.1357:0.1451:0.1301	rs9606756;rs11557599;rs61003488;rs9606756	23;23;23	Q96FD4;B5MBX2;P20062	.;.;TCO2_HUMAN	V	23	ENSP00000215838:I23V;ENSP00000411529:I23V;ENSP00000385914:I23V;ENSP00000384914:I23V	ENSP00000215838:I23V	I	+	1	0	TCN2	29336860	0.122000	0.22280	0.003000	0.11579	0.378000	0.30076	0.182000	0.16900	-0.109000	0.12044	0.528000	0.53228	ATA	A|0.885;G|0.115	0.115	strong		0.502	TCN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000321282.2	NM_000355	
MRGPRX4	117196	hgsc.bcm.edu	37	11	18195348	18195348	+	Missense_Mutation	SNP	C	C	T	rs11024532	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:18195348C>T	ENST00000314254.3	+	1	965	c.545C>T	c.(544-546)gCg>gTg	p.A182V	RP11-113D6.6_ENST00000527671.1_Intron	NM_054032.3	NP_473373.2	Q96LA9	MRGX4_HUMAN	MAS-related GPR, member X4	182			A -> V (in dbSNP:rs11024532). {ECO:0000269|PubMed:11850634, ECO:0000269|PubMed:15489334}.			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						ATCCCAGTCGCGTGGCTGATT	0.512													C|||	636	0.126997	0.0461	0.1441	5008	,	,		20406	0.0347		0.2644	False		,,,				2504	0.1779				p.A182V		Atlas-SNP	.											.	MRGPRX4	68	.	0			c.C545T						PASS	.	C	VAL/ALA	389,4009	193.6+/-218.7	12,365,1822	210.0	199.0	203.0		545	-0.4	0.0	11	dbSNP_120	203	2493,6093	409.6+/-349.9	390,1713,2190	yes	missense	MRGPRX4	NM_054032.3	64	402,2078,4012	TT,TC,CC		29.0356,8.8449,22.1965	benign	182/323	18195348	2882,10102	2199	4293	6492	SO:0001583	missense	117196	exon1			CAGTCGCGTGGCT	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.545C>T	11.37:g.18195348C>T	ENSP00000314042:p.Ala182Val	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	115	24	0.208696	NM_054032	Q3KNU3|Q3KNU4|Q502W0|Q8TDD6|Q8TDD7	Missense_Mutation	SNP	ENST00000314254.3	37	CCDS7831.1	307	0.14056776556776557	28	0.056910569105691054	61	0.1685082872928177	17	0.02972027972027972	201	0.26517150395778366	C	10.12	1.263710	0.23136	0.088449	0.290356	ENSG00000179817	ENST00000314254	T	0.33865	1.39	2.85	-0.447	0.12234	GPCR, rhodopsin-like superfamily (1);	1.195330	0.05937	N	0.636357	T	0.00012	0.0000	L	0.28740	0.885	0.80722	P	0.0	B	0.24963	0.115	B	0.28385	0.089	T	0.37888	-0.9686	9	0.30854	T	0.27	.	3.211	0.06682	0.0:0.4219:0.2751:0.303	rs11024532;rs52828189;rs58386901;rs11024532	182	Q96LA9	MRGX4_HUMAN	V	182	ENSP00000314042:A182V	ENSP00000314042:A182V	A	+	2	0	MRGPRX4	18151924	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	-0.465000	0.06680	0.074000	0.16767	-0.573000	0.04149	GCG	C|0.817;T|0.183	0.183	strong		0.512	MRGPRX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389788.1	NM_054032	
RP1L1	94137	hgsc.bcm.edu	37	8	10469292	10469292	+	Silent	SNP	C	C	T	rs62490857	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:10469292C>T	ENST00000382483.3	-	4	2539	c.2316G>A	c.(2314-2316)tcG>tcA	p.S772S		NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	772					cell projection organization (GO:0030030)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|visual perception (GO:0007601)	axoneme (GO:0005930)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|photoreceptor connecting cilium (GO:0032391)|photoreceptor outer segment (GO:0001750)				breast(5)|central_nervous_system(2)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(16)|lung(82)|ovary(8)|prostate(5)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(3)	148				COAD - Colon adenocarcinoma(149;0.0811)		TGGGGGCCGGCGAGCATGTCC	0.662													C|||	152	0.0303514	0.0023	0.0288	5008	,	,		16095	0.001		0.1083	False		,,,				2504	0.0194				p.S772S		Atlas-SNP	.											.	RP1L1	453	.	0			c.G2316A						PASS	.	C		64,3840		0,64,1888	50.0	57.0	55.0		2316	-10.2	0.0	8	dbSNP_129	55	681,7581		25,631,3475	no	coding-synonymous	RP1L1	NM_178857.5		25,695,5363	TT,TC,CC		8.2426,1.6393,6.1236		772/2401	10469292	745,11421	1952	4131	6083	SO:0001819	synonymous_variant	94137	exon4			GGCCGGCGAGCAT	AY168346	CCDS43708.1	8p23.1	2011-12-06			ENSG00000183638	ENSG00000183638			15946	protein-coding gene	gene with protein product		608581				12634863	Standard	NM_178857		Approved	DCDC4B	uc003wtc.3	Q8IWN7	OTTHUMG00000163806	ENST00000382483.3:c.2316G>A	8.37:g.10469292C>T		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	97	74	0.762887	NM_178857	Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	Silent	SNP	ENST00000382483.3	37	CCDS43708.1																																																																																			C|0.945;T|0.055	0.055	strong		0.662	RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375673.1		
TTN	7273	hgsc.bcm.edu	37	2	179440029	179440029	+	Silent	SNP	G	G	A	rs12464787	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:179440029G>A	ENST00000591111.1	-	276	66131	c.65907C>T	c.(65905-65907)agC>agT	p.S21969S	TTN-AS1_ENST00000438095.1_RNA|TTN_ENST00000359218.5_Silent_p.S14670S|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN_ENST00000342992.6_Silent_p.S21042S|TTN-AS1_ENST00000586452.1_RNA|TTN_ENST00000460472.2_Silent_p.S14545S|TTN-AS1_ENST00000591332.1_RNA|TTN_ENST00000589042.1_Silent_p.S23610S|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN_ENST00000342175.6_Silent_p.S14737S|TTN-AS1_ENST00000586707.1_RNA|RP11-171I2.5_ENST00000604215.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590932.1_RNA			Q8WZ42	TITIN_HUMAN	titin	21969	Fibronectin type-III 59. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TTCTCCCCGCGCTGTTCACTG	0.502													G|||	734	0.146565	0.0779	0.1167	5008	,	,		20676	0.0417		0.3052	False		,,,				2504	0.2055				p.S23610S		Atlas-SNP	.											.	TTN	18412	.	0			c.C70830T						PASS	.	G	,,,	480,3602		29,422,1590	65.0	66.0	66.0		43635,63126,44010,44211	-2.6	0.8	2	dbSNP_120	66	2497,5897		364,1769,2064	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	,,,	393,2191,3654	AA,AG,GG		29.7474,11.7589,23.8618	,,,	14545/26927,21042/33424,14670/27052,14737/27119	179440029	2977,9499	2041	4197	6238	SO:0001819	synonymous_variant	7273	exon326			CCCCGCGCTGTTC	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.65907C>T	2.37:g.179440029G>A		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	124	61	0.491935	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	
AP4B1	10717	hgsc.bcm.edu	37	1	114444444	114444444	+	Silent	SNP	T	T	G	rs34751342	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:114444444T>G	ENST00000369569.1	-	3	682	c.402A>C	c.(400-402)tcA>tcC	p.S134S	AP4B1_ENST00000369566.3_Intron|AP4B1_ENST00000256658.4_Silent_p.S134S|AP4B1-AS1_ENST00000419536.1_RNA|AP4B1_ENST00000369567.1_Intron	NM_001253852.1	NP_001240781.1	Q9Y6B7	AP4B1_HUMAN	adaptor-related protein complex 4, beta 1 subunit	134					intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	clathrin adaptor complex (GO:0030131)|coated pit (GO:0005905)|trans-Golgi network (GO:0005802)	protein transporter activity (GO:0008565)|transporter activity (GO:0005215)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(9)|ovary(3)|prostate(3)	25	Lung SC(450;0.184)	all_cancers(81;4.5e-08)|all_epithelial(167;1.1e-07)|all_lung(203;1.53e-05)|Lung NSC(69;2.76e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		TCCTGACATATGAAGCCTTAT	0.453													T|||	108	0.0215655	0.0023	0.0389	5008	,	,		20112	0.0		0.0239	False		,,,				2504	0.0552				p.S134S		Atlas-SNP	.											.	AP4B1	72	.	0			c.A402C						PASS	.	T		27,4379	35.2+/-66.4	0,27,2176	175.0	145.0	155.0		402	-10.9	0.0	1	dbSNP_126	155	361,8239	122.2+/-181.2	3,355,3942	no	coding-synonymous	AP4B1	NM_006594.2		3,382,6118	GG,GT,TT		4.1977,0.6128,2.9832		134/740	114444444	388,12618	2203	4300	6503	SO:0001819	synonymous_variant	10717	exon4			GACATATGAAGCC	AF092094	CCDS865.1	1p13.2	2012-03-30			ENSG00000134262	ENSG00000134262			572	protein-coding gene	gene with protein product	"""beta 4 subunit of AP-4"""	607245	"""spastic paraplegia 47"""	SPG47		10066790	Standard	NM_006594		Approved	BETA-4	uc001eeb.3	Q9Y6B7	OTTHUMG00000011943	ENST00000369569.1:c.402A>C	1.37:g.114444444T>G		Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	132	60	0.454545	NM_006594	B7Z4X3|Q59EJ4|Q96CL6	Silent	SNP	ENST00000369569.1	37	CCDS865.1																																																																																			T|0.971;G|0.029	0.029	strong		0.453	AP4B1-009	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033037.1	NM_006594	
BPIFC	254240	hgsc.bcm.edu	37	22	32831711	32831711	+	Missense_Mutation	SNP	C	C	G	rs5994570	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:32831711C>G	ENST00000397452.1	-	9	1014	c.904G>C	c.(904-906)Gtc>Ctc	p.V302L	BPIFC_ENST00000300399.3_Missense_Mutation_p.V302L|BPIFC_ENST00000432451.2_Missense_Mutation_p.V116L|BPIFC_ENST00000534972.1_Missense_Mutation_p.V26L			Q8NFQ6	BPIFC_HUMAN	BPI fold containing family C	302			V -> L (in dbSNP:rs5994570).			extracellular region (GO:0005576)	lipopolysaccharide binding (GO:0001530)|phospholipid binding (GO:0005543)										GAGAGAGTGACATTGAAAACC	0.438													C|||	685	0.136781	0.4153	0.0576	5008	,	,		19585	0.001		0.0517	False		,,,				2504	0.044				p.V302L		Atlas-SNP	.											.	.	.	.	0			c.G904C						PASS	.	C	LEU/VAL	1490,2916	475.3+/-357.3	273,944,986	65.0	67.0	66.0		904	2.2	0.9	22	dbSNP_114	66	573,8027	153.4+/-207.8	16,541,3743	yes	missense	BPIFC	NM_174932.2	32	289,1485,4729	GG,GC,CC		6.6628,33.8175,15.8619	benign	302/508	32831711	2063,10943	2203	4300	6503	SO:0001583	missense	254240	exon8			GAGTGACATTGAA	AF465766	CCDS13906.1	22q12.3	2011-08-04	2011-08-01	2011-08-01	ENSG00000184459	ENSG00000184459		"""BPI fold containing"""	16503	protein-coding gene	gene with protein product		614109	"""bactericidal/permeability-increasing protein-like 2"""	BPIL2			Standard	NM_174932		Approved	dJ149A16.7	uc003amn.2	Q8NFQ6	OTTHUMG00000058273	ENST00000397452.1:c.904G>C	22.37:g.32831711C>G	ENSP00000380594:p.Val302Leu	Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	23	13	0.565217	NM_174932	A2RRF1	Missense_Mutation	SNP	ENST00000397452.1	37	CCDS13906.1	280	0.1282051282051282	210	0.4268292682926829	27	0.07458563535911603	0	0.0	43	0.05672823218997362	C	6.593	0.477859	0.12521	0.338175	0.066628	ENSG00000184459	ENST00000397452;ENST00000300399;ENST00000534972;ENST00000432451	T;T;T;T	0.07800	3.16;3.16;3.16;3.16	5.65	2.15	0.27550	.	0.534254	0.20228	N	0.096548	T	0.00012	0.0000	L	0.39020	1.185	0.47511	P	5.519999999999969E-4	B;B	0.19583	0.009;0.037	B;B	0.28232	0.01;0.087	T	0.46373	-0.9196	9	0.02654	T	1	-9.1936	4.6875	0.12764	0.1763:0.5996:0.0:0.2241	rs5994570;rs52793051;rs5994570	116;302	A2RRF1;Q8NFQ6	.;BPIFC_HUMAN	L	302;302;26;116	ENSP00000380594:V302L;ENSP00000300399:V302L;ENSP00000439123:V26L;ENSP00000408920:V116L	ENSP00000300399:V302L	V	-	1	0	BPIFC	31161711	0.001000	0.12720	0.865000	0.33974	0.893000	0.52053	-0.417000	0.07088	0.731000	0.32448	0.650000	0.86243	GTC	C|0.857;G|0.143	0.143	strong		0.438	BPIFC-010	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129029.2	NM_174932	
NBPF14	25832	hgsc.bcm.edu	37	1	148009510	148009510	+	Silent	SNP	G	G	A	rs587690666	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:148009510G>A	ENST00000369219.1	-	16	1813	c.1797C>T	c.(1795-1797)agC>agT	p.S599S				Q5TI25	NBPFE_HUMAN	neuroblastoma breakpoint family, member 14	599	NBPF 7. {ECO:0000255|PROSITE- ProRule:PRU00647}.					cytoplasm (GO:0005737)		p.S599S(1)		NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(1)|lung(23)|ovary(2)|pancreas(2)|prostate(2)|skin(1)|stomach(2)|urinary_tract(1)	42	all_hematologic(923;0.032)					ACAGCTCCCCGCTGAGCCTGG	0.463													-|||	58	0.0115815	0.0015	0.0043	5008	,	,		57574	0.0506		0.001	False		,,,				2504	0.001				p.S599S		Atlas-SNP	.											NBPF14,NS,carcinoma,0,1	NBPF14	107	1	1	Substitution - coding silent(1)	stomach(1)	c.C1797T						PASS	.						110.0	201.0	177.0					1																	148009510		1440	4051	5491	SO:0001819	synonymous_variant	25832	exon16			CTCCCCGCTGAGC	AK092351		1q21.1	2013-01-17			ENSG00000122497			"""neuroblastoma breakpoint family"""	25232	protein-coding gene	gene with protein product		614003				8619474, 9110174, 16079250	Standard	NM_015383		Approved	DJ328E19.C1.1	uc021owp.2	Q5TI25	OTTHUMG00000013900	ENST00000369219.1:c.1797C>T	1.37:g.148009510G>A		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	53	7	0.132075	NM_015383	Q5TI23|Q8IX76|Q9UJI9	Silent	SNP	ENST00000369219.1	37		.	.	.	.	.	.	.	.	.	.	g	2.154	-0.393869	0.04899	.	.	ENSG00000122497	ENST00000310701	.	.	.	.	.	.	.	.	.	.	.	T	0.14270	0.0345	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.28808	-1.0032	1	.	.	.	.	.	.	.	rs56160124	.	.	.	V	605	.	.	A	-	2	0	NBPF14	146476134	0.993000	0.37304	.	.	.	.	0.748000	0.26305	.	.	.	.	GCG	G|0.500;A|0.500	0.500	weak		0.463	NBPF14-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_015383	
ADNP2	22850	hgsc.bcm.edu	37	18	77894844	77894844	+	Silent	SNP	G	G	A	rs3744877	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:77894844G>A	ENST00000262198.4	+	4	2003	c.1548G>A	c.(1546-1548)ccG>ccA	p.P516P		NM_014913.3	NP_055728.1	Q6IQ32	ADNP2_HUMAN	ADNP homeobox 2	516					cellular response to oxidative stress (GO:0034599)|cellular response to retinoic acid (GO:0071300)|negative regulation of cell death (GO:0060548)|neuron differentiation (GO:0030182)|positive regulation of cell growth (GO:0030307)|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)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(9)|liver(1)|lung(15)|ovary(5)|prostate(2)	42		all_cancers(4;1.06e-15)|all_epithelial(4;2.36e-10)|all_lung(4;0.000302)|Lung NSC(4;0.000518)|Esophageal squamous(42;0.0212)|Ovarian(4;0.0256)|all_hematologic(56;0.15)|Melanoma(33;0.2)		Epithelial(2;1.1e-11)|OV - Ovarian serous cystadenocarcinoma(15;7.54e-09)|BRCA - Breast invasive adenocarcinoma(31;0.00247)|STAD - Stomach adenocarcinoma(84;0.164)		AGGTGGTCCCGTCTGGGCTTC	0.577													G|||	2097	0.41873	0.1528	0.5086	5008	,	,		18450	0.5764		0.4771	False		,,,				2504	0.4918				p.P516P		Atlas-SNP	.											.	ADNP2	102	.	0			c.G1548A						PASS	.	G		900,3506	346.7+/-309.1	86,728,1389	83.0	83.0	83.0		1548	-9.9	0.0	18	dbSNP_107	83	4096,4504	559.3+/-387.4	967,2162,1171	yes	coding-synonymous	ADNP2	NM_014913.3		1053,2890,2560	AA,AG,GG		47.6279,20.4267,38.413		516/1132	77894844	4996,8010	2203	4300	6503	SO:0001819	synonymous_variant	22850	exon4			GGTCCCGTCTGGG	AB020670	CCDS32853.1	18q23	2013-01-07	2007-07-17	2007-07-17	ENSG00000101544	ENSG00000101544		"""Homeoboxes / ZF class"", ""Zinc fingers, C2H2-type"""	23803	protein-coding gene	gene with protein product			"""zinc finger protein 508"""	ZNF508			Standard	NM_014913		Approved	KIAA0863	uc002lnw.3	Q6IQ32	OTTHUMG00000172535	ENST00000262198.4:c.1548G>A	18.37:g.77894844G>A		Somatic	214	0	0		WXS	Illumina HiSeq	Phase_I	140	47	0.335714	NM_014913	A8K951|O94943|Q9H9P3	Silent	SNP	ENST00000262198.4	37	CCDS32853.1																																																																																			G|0.596;A|0.404	0.404	strong		0.577	ADNP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418979.1	NM_014913	
PLEC	5339	hgsc.bcm.edu	37	8	145001588	145001588	+	Missense_Mutation	SNP	C	C	T	rs11136334	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:145001588C>T	ENST00000322810.4	-	27	4326	c.4157G>A	c.(4156-4158)cGg>cAg	p.R1386Q	PLEC_ENST00000357649.2_Missense_Mutation_p.R1253Q|PLEC_ENST00000398774.2_Missense_Mutation_p.R1217Q|PLEC_ENST00000436759.2_Missense_Mutation_p.R1276Q|PLEC_ENST00000354958.2_Missense_Mutation_p.R1227Q|PLEC_ENST00000527096.1_Missense_Mutation_p.R1272Q|PLEC_ENST00000354589.3_Missense_Mutation_p.R1249Q|PLEC_ENST00000345136.3_Missense_Mutation_p.R1249Q|PLEC_ENST00000356346.3_Missense_Mutation_p.R1235Q	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						scavenged	.	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	3	1	0.333333		WXS	Illumina HiSeq	Phase_I	3	3	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	
HEG1	57493	hgsc.bcm.edu	37	3	124739892	124739892	+	Silent	SNP	G	G	A	rs6438874	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	223	0	0		WXS	Illumina HiSeq	Phase_I	195	97	0.497436	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	
NPHS1	4868	hgsc.bcm.edu	37	19	36322601	36322601	+	Missense_Mutation	SNP	T	T	C	rs4806213	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:36322601T>C	ENST00000378910.5	-	24	3229	c.3230A>G	c.(3229-3231)aAt>aGt	p.N1077S	NPHS1_ENST00000353632.6_Intron	NM_004646.3	NP_004637.1	O60500	NPHN_HUMAN	nephrosis 1, congenital, Finnish type (nephrin)	1077			N -> S (in dbSNP:rs4806213). {ECO:0000269|PubMed:11317351, ECO:0000269|PubMed:9915943}.		cell adhesion (GO:0007155)|excretion (GO:0007588)|glomerular basement membrane development (GO:0032836)|glomerular visceral epithelial cell development (GO:0072015)|JNK cascade (GO:0007254)|myoblast fusion (GO:0007520)|positive regulation of actin filament polymerization (GO:0030838)|regulation of excretion (GO:0044062)|skeletal muscle tissue development (GO:0007519)	cell projection (GO:0042995)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|slit diaphragm (GO:0036057)	myosin binding (GO:0017022)			NS(2)|breast(1)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(16)|liver(1)|lung(26)|ovary(5)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	74	all_lung(56;7.14e-07)|Lung NSC(56;1.12e-06)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			ACAGGAGGCATTGGAGAGGAG	0.647													T|||	463	0.0924521	0.1415	0.0749	5008	,	,		14438	0.0198		0.0934	False		,,,				2504	0.1125				p.N1077S		Atlas-SNP	.											.	NPHS1	165	.	0			c.A3230G	GRCh37	CM024138	NPHS1	M	rs4806213	PASS	.	T	SER/ASN	547,3859		36,475,1692	22.0	24.0	23.0		3230	1.7	0.9	19	dbSNP_111	23	831,7769		47,737,3516	yes	missense	NPHS1	NM_004646.3	46	83,1212,5208	CC,CT,TT		9.6628,12.4149,10.5951	probably-damaging	1077/1242	36322601	1378,11628	2203	4300	6503	SO:0001583	missense	4868	exon24			GAGGCATTGGAGA		CCDS32996.1	19q12-q13.1	2014-09-17				ENSG00000161270		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	7908	protein-coding gene	gene with protein product		602716				9915943, 9660941	Standard	NM_004646		Approved	CNF, NPHN	uc002oby.3	O60500		ENST00000378910.5:c.3230A>G	19.37:g.36322601T>C	ENSP00000368190:p.Asn1077Ser	Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	31	13	0.419355	NM_004646	A6NDH2|C3RX61	Missense_Mutation	SNP	ENST00000378910.5	37	CCDS32996.1	181	0.08287545787545787	81	0.16463414634146342	30	0.08287292817679558	7	0.012237762237762238	63	0.08311345646437995	T	8.787	0.929698	0.18131	0.124149	0.096628	ENSG00000161270	ENST00000378910	T	0.73363	-0.74	5.09	1.7	0.24286	.	0.378995	0.25929	N	0.027398	T	0.00300	0.0009	L	0.27053	0.805	0.09310	P	0.99999666761	B	0.14438	0.01	B	0.14023	0.01	T	0.06180	-1.0841	9	0.62326	D	0.03	-8.2252	2.093	0.03661	0.158:0.0884:0.1645:0.589	rs4806213;rs4806213	1077	O60500	NPHN_HUMAN	S	1077	ENSP00000368190:N1077S	ENSP00000368190:N1077S	N	-	2	0	NPHS1	41014441	0.872000	0.30054	0.886000	0.34754	0.127000	0.20565	0.919000	0.28692	0.416000	0.25844	-0.762000	0.03455	AAT	T|0.897;C|0.103	0.103	strong		0.647	NPHS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452553.1		
TAOK2	9344	hgsc.bcm.edu	37	16	29994922	29994922	+	Silent	SNP	C	C	T	rs3814883	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:29994922C>T	ENST00000308893.4	+	13	2402	c.1359C>T	c.(1357-1359)tcC>tcT	p.S453S	TAOK2_ENST00000543033.1_Silent_p.S453S|TAOK2_ENST00000416441.2_Silent_p.S280S|TAOK2_ENST00000279394.3_Silent_p.S453S	NM_001252043.1|NM_016151.3	NP_001238972.1|NP_057235.2	Q9UL54	TAOK2_HUMAN	TAO kinase 2	453					actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|apoptotic process (GO:0006915)|cell migration (GO:0016477)|cellular response to DNA damage stimulus (GO:0006974)|focal adhesion assembly (GO:0048041)|G2 DNA damage checkpoint (GO:0031572)|positive regulation of JNK cascade (GO:0046330)|positive regulation of stress-activated MAPK cascade (GO:0032874)|protein targeting to membrane (GO:0006612)|regulation of cell growth (GO:0001558)|regulation of cell shape (GO:0008360)|response to stress (GO:0006950)|stress-activated MAPK cascade (GO:0051403)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|nucleolus (GO:0005730)|nucleus (GO:0005634)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|mitogen-activated protein kinase kinase binding (GO:0031434)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(3)|large_intestine(5)|lung(8)|ovary(1)|prostate(3)|skin(1)	22						CCACCTCTTCCGCCCGCCGCC	0.637													c|||	1840	0.367412	0.1286	0.3804	5008	,	,		14141	0.4444		0.4602	False		,,,				2504	0.5061				p.S453S		Atlas-SNP	.											.	TAOK2	142	.	0			c.C1359T						PASS	.	T	,	731,3663	296.1+/-284.1	74,583,1540	128.0	162.0	151.0		1359,1359	-1.3	1.0	16	dbSNP_107	151	4008,4592	546.4+/-385.0	944,2120,1236	no	coding-synonymous,coding-synonymous	TAOK2	NM_004783.2,NM_016151.2	,	1018,2703,2776	TT,TC,CC		46.6047,16.6363,36.4707	,	453/1050,453/1236	29994922	4739,8255	2197	4300	6497	SO:0001819	synonymous_variant	9344	exon13			CTCTTCCGCCCGC	AB020688	CCDS10662.1, CCDS10663.1, CCDS58448.1	16p11.2	2008-02-05			ENSG00000149930	ENSG00000149930			16835	protein-coding gene	gene with protein product		613199				10048485, 9786855	Standard	NM_016151		Approved	TAO1, KIAA0881, PSK, PSK1, TAO2, MAP3K17	uc002dva.2	Q9UL54	OTTHUMG00000132111	ENST00000308893.4:c.1359C>T	16.37:g.29994922C>T		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	62	61	0.983871	NM_004783	A5PKY1|A7MCZ2|B2RN35|B7ZM88|O94957|Q6UW73|Q7LC09|Q9NSW2	Silent	SNP	ENST00000308893.4	37	CCDS10663.1																																																																																			C|0.622;T|0.378	0.378	strong		0.637	TAOK2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255152.2	NM_016151	
RPGR	6103	hgsc.bcm.edu	37	X	38158290	38158290	+	Silent	SNP	C	C	T	rs1801686	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:38158290C>T	ENST00000339363.3	-	10	1331	c.1164G>A	c.(1162-1164)gcG>gcA	p.A388A	RPGR_ENST00000342811.3_Silent_p.A388A|TM4SF2_ENST00000465127.1_Intron|RPGR_ENST00000318842.7_Silent_p.A388A|RPGR_ENST00000378505.2_Silent_p.A388A|RPGR_ENST00000309513.3_Intron|RPGR_ENST00000338898.3_Silent_p.A388A			Q92834	RPGR_HUMAN	retinitis pigmentosa GTPase regulator	388					cilium assembly (GO:0042384)|eye photoreceptor cell development (GO:0042462)|intracellular protein transport (GO:0006886)|intraciliary transport (GO:0042073)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|Golgi apparatus (GO:0005794)|photoreceptor outer segment (GO:0001750)|sperm flagellum (GO:0036126)	guanyl-nucleotide exchange factor activity (GO:0005085)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	25						GCAGAAAAGTCGCCACAGATA	0.443													C|||	249	0.0659603	0.0522	0.0476	3775	,	,		13625	0.0		0.1252	False		,,,				2504	0.0215				p.A388A		Atlas-SNP	.											.	RPGR	175	.	0			c.G1164A						PASS	.	C	,	263,3570		9,202,43,1420,528	99.0	78.0	85.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1164,1164	-9.1	0.0	X	dbSNP_89	85	1041,5687		63,605,310,1760,1562	no	coding-synonymous,coding-synonymous	RPGR	NM_000328.2,NM_001034853.1	,	72,807,353,3180,2090	TT,TC,T,CC,C		15.4727,6.8615,12.3473	,	388/816,388/1153	38158290	1304,9257	2202	4300	6502	SO:0001819	synonymous_variant	6103	exon10			AAAAGTCGCCACA	U57629	CCDS14246.1, CCDS35229.1	Xp11.4	2013-06-06	2004-02-13		ENSG00000156313	ENSG00000156313			10295	protein-coding gene	gene with protein product		312610	"""retinitis pigmentosa 15"", ""cone dystrophy 1 (X-linked)"""	CRD, RP3, RP15, COD1		8673101, 8817343	Standard	XM_005272633		Approved	CORDX1	uc004ded.1	Q92834	OTTHUMG00000021361	ENST00000339363.3:c.1164G>A	X.37:g.38158290C>T		Somatic	153	1	0.00653595		WXS	Illumina HiSeq	Phase_I	94	91	0.968085	NM_001034853	B1ARN3|E9PE28|O00702|O00737|Q3KN84|Q8N5T6|Q93039|Q9HD29|Q9UMR1	Silent	SNP	ENST00000339363.3	37		157	0.09463532248342375	23	0.04811715481171548	15	0.04335260115606936	0	0.0	71	0.10289855072463767	C	5.533	0.283315	0.10458	0.068615	0.154727	ENSG00000156313	ENST00000464437	.	.	.	4.95	-9.12	0.00707	.	.	.	.	.	T	0.00073	0.0002	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.12837	-1.0532	3	.	.	.	.	2.9469	0.05849	0.3529:0.1251:0.0722:0.4497	rs1801686	.	.	.	Q	77	.	.	R	-	2	0	RPGR	38043234	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.506000	0.00962	-1.756000	0.01318	-0.522000	0.04353	CGA	C|0.887;T|0.113	0.113	strong		0.443	RPGR-203	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_000328	
DDX47	51202	hgsc.bcm.edu	37	12	12967127	12967127	+	Silent	SNP	C	C	T	rs1051374	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:12967127C>T	ENST00000358007.3	+	2	172	c.150C>T	c.(148-150)atC>atT	p.I50I	DDX47_ENST00000352940.4_Silent_p.I50I	NM_016355.3	NP_057439.2	Q9H0S4	DDX47_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 47	50					extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|mRNA processing (GO:0006397)|RNA splicing (GO:0008380)|rRNA processing (GO:0006364)	membrane (GO:0016020)|nucleolus (GO:0005730)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(5)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	16		Prostate(47;0.0526)		BRCA - Breast invasive adenocarcinoma(232;0.0354)		CCACCAAGATCCAGATTGAAG	0.398													C|||	1937	0.386781	0.2511	0.4121	5008	,	,		23125	0.5992		0.2734	False		,,,				2504	0.4499				p.I50I		Atlas-SNP	.											.	DDX47	37	.	0			c.C150T						PASS	.	C	,	1166,3240	412.4+/-336.1	168,830,1205	308.0	290.0	296.0		150,150	5.3	1.0	12	dbSNP_86	296	2385,6215	397.3+/-345.7	330,1725,2245	yes	coding-synonymous,coding-synonymous	DDX47	NM_016355.3,NM_201224.1	,	498,2555,3450	TT,TC,CC		27.7326,26.4639,27.3028	,	50/456,50/407	12967127	3551,9455	2203	4300	6503	SO:0001819	synonymous_variant	51202	exon2			CAAGATCCAGATT	AK127712	CCDS8655.1, CCDS8656.1	12p13.2	2010-07-06			ENSG00000213782	ENSG00000213782		"""DEAD-boxes"""	18682	protein-coding gene	gene with protein product		615428					Standard	NM_016355		Approved	DKFZp564O176, FLJ30012, HQ0256, RRP3	uc001rax.3	Q9H0S4	OTTHUMG00000168709	ENST00000358007.3:c.150C>T	12.37:g.12967127C>T		Somatic	230	0	0		WXS	Illumina HiSeq	Phase_I	165	163	0.987879	NM_201224	B3KXP4|G5E955|Q96GM0|Q96NV8|Q9UI98	Silent	SNP	ENST00000358007.3	37	CCDS8655.1																																																																																			C|0.686;T|0.314	0.314	strong		0.398	DDX47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400674.1	NM_016355	
NCAN	1463	hgsc.bcm.edu	37	19	19335135	19335135	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:19335135G>A	ENST00000252575.6	+	5	770	c.671G>A	c.(670-672)cGt>cAt	p.R224H	NCAN_ENST00000538881.1_5'Flank	NM_004386.2	NP_004377.2	O14594	NCAN_HUMAN	neurocan	224	Link 1. {ECO:0000255|PROSITE- ProRule:PRU00323}.				axon guidance (GO:0007411)|carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|regulation of synapse structural plasticity (GO:0051823)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|hyaluronic acid binding (GO:0005540)			breast(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(32)|ovary(5)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	64			Epithelial(12;0.00544)		Hyaluronan(DB08818)	ACCCAGTCCCGTCCTGGTTGC	0.587																																					p.R224H		Atlas-SNP	.											.	NCAN	277	.	0			c.G671A						PASS	.						157.0	140.0	146.0					19																	19335135		2203	4300	6503	SO:0001583	missense	1463	exon5			AGTCCCGTCCTGG	AF026547	CCDS12397.1	19p12	2014-01-30	2007-02-15	2007-02-15	ENSG00000130287	ENSG00000130287		"""Immunoglobulin superfamily / V-set domain containing"", ""Proteoglycans / Extracellular Matrix : Hyalectans"", ""Endogenous ligands"""	2465	protein-coding gene	gene with protein product	"""neurocan proteoglycan"""	600826	"""chondroitin sulfate proteoglycan 3"""	CSPG3		1326557, 21353194	Standard	NM_004386		Approved		uc002nlz.3	O14594		ENST00000252575.6:c.671G>A	19.37:g.19335135G>A	ENSP00000252575:p.Arg224His	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	88	20	0.227273	NM_004386	Q9UPK6	Missense_Mutation	SNP	ENST00000252575.6	37	CCDS12397.1	.	.	.	.	.	.	.	.	.	.	G	29.3	4.996086	0.93167	.	.	ENSG00000130287	ENST00000539499;ENST00000252575	T	0.13657	2.57	4.83	4.83	0.62350	C-type lectin fold (1);Link (5);C-type lectin-like (1);	0.000000	0.34853	N	0.003626	T	0.49338	0.1551	H	0.94734	3.575	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.65026	-0.6268	10	0.87932	D	0	-14.3002	15.4278	0.75069	0.0:0.0:1.0:0.0	.	224	O14594	NCAN_HUMAN	H	238;224	ENSP00000252575:R224H	ENSP00000252575:R224H	R	+	2	0	NCAN	19196135	0.943000	0.32029	0.642000	0.29436	0.926000	0.56050	4.868000	0.63021	2.240000	0.73641	0.561000	0.74099	CGT	.	.	none		0.587	NCAN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460111.2	NM_004386	
ARL13B	200894	hgsc.bcm.edu	37	3	93768268	93768268	+	Missense_Mutation	SNP	C	C	G	rs33944211	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:93768268C>G	ENST00000394222.3	+	8	1318	c.1043C>G	c.(1042-1044)aCt>aGt	p.T348S	ARL13B_ENST00000303097.7_Missense_Mutation_p.T241S|ARL13B_ENST00000471138.1_Missense_Mutation_p.T348S|ARL13B_ENST00000535334.1_Missense_Mutation_p.T245S|DHFRL1_ENST00000481631.1_Intron|ARL13B_ENST00000539730.1_Missense_Mutation_p.T69S	NM_001174150.1	NP_001167621.1	Q3SXY8	AR13B_HUMAN	ADP-ribosylation factor-like 13B	348			T -> S (in dbSNP:rs33944211).		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						AAAAAGAAAACTAAGAAACTA	0.373													C|||	389	0.0776757	0.003	0.0764	5008	,	,		12859	0.0863		0.1103	False		,,,				2504	0.137				p.T348S		Atlas-SNP	.											.	ARL13B	52	.	0			c.C1043G						PASS	.	C	SER/THR,SER/THR,SER/THR,SER/THR	98,4308	79.3+/-117.8	0,98,2105	59.0	57.0	58.0		1043,734,722,1043	3.0	1.0	3	dbSNP_126	58	1033,7567	217.4+/-256.1	64,905,3331	yes	missense,missense,missense,missense	ARL13B	NM_001174150.1,NM_001174151.1,NM_144996.3,NM_182896.2	58,58,58,58	64,1003,5436	GG,GC,CC		12.0116,2.2242,8.696	benign,benign,benign,benign	348/429,245/326,241/322,348/429	93768268	1131,11875	2203	4300	6503	SO:0001583	missense	200894	exon8			AGAAAACTAAGAA	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.1043C>G	3.37:g.93768268C>G	ENSP00000377769:p.Thr348Ser	Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	143	63	0.440559	NM_182896	D3DN29|G3V1S8|Q504W8|Q8TCL5	Missense_Mutation	SNP	ENST00000394222.3	37	CCDS2925.1	161	0.07371794871794872	3	0.006097560975609756	31	0.0856353591160221	50	0.08741258741258741	77	0.10158311345646438	C	11.56	1.674564	0.29693	0.022242	0.120116	ENSG00000169379	ENST00000535334;ENST00000303097;ENST00000394222;ENST00000471138;ENST00000539730	T;T;T;T;T	0.64260	1.71;-0.09;0.14;0.14;0.86	5.08	3.02	0.34903	.	0.598474	0.16356	N	0.217984	T	0.01320	0.0043	L	0.59436	1.845	0.09310	P	0.999999891691	B;B;B;B	0.23806	0.091;0.016;0.073;0.012	B;B;B;B	0.24394	0.045;0.02;0.053;0.022	T	0.40924	-0.9537	9	0.49607	T	0.09	-1.4318	12.4339	0.55588	0.1716:0.7229:0.1055:0.0	rs33944211	245;348;241;348	G3V1S8;B4DLH1;Q3SXY8-2;Q3SXY8	.;.;.;AR13B_HUMAN	S	245;241;348;348;69	ENSP00000445145:T245S;ENSP00000306225:T241S;ENSP00000377769:T348S;ENSP00000420780:T348S;ENSP00000437977:T69S	ENSP00000306225:T241S	T	+	2	0	ARL13B	95250958	0.958000	0.32768	1.000000	0.80357	0.820000	0.46376	0.592000	0.23984	1.127000	0.42034	0.585000	0.79938	ACT	C|0.914;G|0.086	0.086	strong		0.373	ARL13B-005	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352904.1	NM_182896	
MUC20	200958	hgsc.bcm.edu	37	3	195452783	195452783	+	Missense_Mutation	SNP	C	C	T	rs199620417	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195452783C>T	ENST00000447234.2	+	2	1435	c.1309C>T	c.(1309-1311)Cct>Tct	p.P437S	MUC20_ENST00000436408.1_Missense_Mutation_p.P437S|MUC20_ENST00000445522.2_Missense_Mutation_p.P402S|MUC20_ENST00000320736.6_Missense_Mutation_p.P266S	NM_001282506.1	NP_001269435.1	Q8N307	MUC20_HUMAN	mucin 20, cell surface associated	437					activation of MAPK activity (GO:0000187)|cellular protein metabolic process (GO:0044267)|hepatocyte growth factor receptor signaling pathway (GO:0048012)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein homooligomerization (GO:0051260)	basal plasma membrane (GO:0009925)|cell projection (GO:0042995)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)				NS(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(4)|skin(4)|stomach(3)|upper_aerodigestive_tract(1)	23	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)	Lung NSC(153;0.191)	Epithelial(36;1e-21)|all cancers(36;9.02e-20)|OV - Ovarian serous cystadenocarcinoma(49;1.6e-18)|Lung(62;0.000104)|LUSC - Lung squamous cell carcinoma(58;0.000128)	GBM - Glioblastoma multiforme(46;1.66e-05)		TTCCAGCATCCCTGGGGCCTC	0.532																																					p.P266S		Atlas-SNP	.											MUC20,caecum,carcinoma,0,1	MUC20	84	1	0			c.C796T						PASS	.						29.0	25.0	26.0					3																	195452783		1951	4103	6054	SO:0001583	missense	200958	exon3			AGCATCCCTGGGG	AB037780	CCDS63877.1	3q29	2008-08-07	2006-03-14		ENSG00000176945	ENSG00000176945		"""Mucins"""	23282	protein-coding gene	gene with protein product		610360				14565953	Standard	NM_001282506		Approved	FLJ14408, KIAA1359	uc010hzo.3	Q8N307	OTTHUMG00000155823	ENST00000447234.2:c.1309C>T	3.37:g.195452783C>T	ENSP00000414350:p.Pro437Ser	Somatic	576	1	0.00173611		WXS	Illumina HiSeq	Phase_I	543	124	0.228361	NM_152673	Q6UX97|Q76I83|Q76I85|Q86ST8|Q8NBY6|Q96KA1|Q9P2I8	Missense_Mutation	SNP	ENST00000447234.2	37		.	.	.	.	.	.	.	.	.	.	C	11.87	1.767506	0.31320	.	.	ENSG00000176945	ENST00000447234;ENST00000320736;ENST00000436408;ENST00000445522	T;T;T;T	0.11495	3.17;3.12;3.34;2.77	3.75	-2.79	0.05841	.	0.561022	0.15092	N	0.281004	T	0.04679	0.0127	N	0.12746	0.255	0.80722	P	0.0	B	0.24576	0.106	B	0.20384	0.029	T	0.20907	-1.0261	9	0.62326	D	0.03	0.2839	5.1652	0.15082	0.0:0.2352:0.167:0.5977	.	266	E9PH32	.	S	437;266;437;402	ENSP00000414350:P437S;ENSP00000325431:P266S;ENSP00000396774:P437S;ENSP00000405629:P402S	ENSP00000325431:P266S	P	+	1	0	MUC20	196938454	0.002000	0.14202	0.000000	0.03702	0.002000	0.02628	-0.117000	0.10708	-0.587000	0.05890	-1.129000	0.01985	CCT	C|0.955;T|0.045	0.045	strong		0.532	MUC20-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000341835.1	NM_152673	
ACACB	32	hgsc.bcm.edu	37	12	109617728	109617728	+	Missense_Mutation	SNP	A	A	G	rs16940029	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:109617728A>G	ENST00000338432.7	+	11	1773	c.1654A>G	c.(1654-1656)Atc>Gtc	p.I552V	ACACB_ENST00000543080.1_3'UTR|ACACB_ENST00000377848.3_Missense_Mutation_p.I552V|ACACB_ENST00000377854.5_Missense_Mutation_p.I552V			O00763	ACACB_HUMAN	acetyl-CoA carboxylase beta	552	ATP-grasp. {ECO:0000255|PROSITE- ProRule:PRU00409}.|Biotin carboxylation.		I -> V (in dbSNP:rs16940029).		acetyl-CoA metabolic process (GO:0006084)|biotin metabolic process (GO:0006768)|carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|malonyl-CoA biosynthetic process (GO:2001295)|positive regulation of cellular metabolic process (GO:0031325)|protein homotetramerization (GO:0051289)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	acetyl-CoA carboxylase activity (GO:0003989)|ATP binding (GO:0005524)|biotin binding (GO:0009374)|biotin carboxylase activity (GO:0004075)|metal ion binding (GO:0046872)			NS(1)|breast(2)|endometrium(9)|kidney(5)|large_intestine(20)|lung(40)|ovary(6)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95					Adenine(DB00173)|Biotin(DB00121)	ACAGTGTGCCATCCGCCTGGC	0.512													G|||	395	0.0788738	0.2375	0.0403	5008	,	,		18543	0.0179		0.0239	False		,,,				2504	0.0112				p.I552V		Atlas-SNP	.											.	ACACB	330	.	0			c.A1654G						PASS	.	G	VAL/ILE	909,3497	739.8+/-411.1	96,717,1390	80.0	69.0	73.0		1654	4.9	0.9	12	dbSNP_123	73	154,8446	812.4+/-407.1	0,154,4146	yes	missense	ACACB	NM_001093.3	29	96,871,5536	GG,GA,AA		1.7907,20.631,8.1732	benign	552/2459	109617728	1063,11943	2203	4300	6503	SO:0001583	missense	32	exon10			TGTGCCATCCGCC	U89344	CCDS31898.1	12q24.1	2010-05-07	2010-04-30		ENSG00000076555	ENSG00000076555	6.4.1.2		85	protein-coding gene	gene with protein product	"""acetyl-CoA carboxylase 2"""	601557	"""acetyl-Coenzyme A carboxylase beta"""			8670171	Standard	NM_001093		Approved	HACC275, ACC2, ACCB	uc001toc.3	O00763	OTTHUMG00000169250	ENST00000338432.7:c.1654A>G	12.37:g.109617728A>G	ENSP00000341044:p.Ile552Val	Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	184	85	0.461957	NM_001093	A6NK36|Q16852|Q1HEC1|Q6KE87|Q6KE89|Q6TY48	Missense_Mutation	SNP	ENST00000338432.7	37	CCDS31898.1	170	0.07783882783882784	129	0.2621951219512195	11	0.03038674033149171	13	0.022727272727272728	17	0.022427440633245383	G	4.992	0.184305	0.09495	0.20631	0.017907	ENSG00000076555	ENST00000338432;ENST00000377848;ENST00000377854	D;D;D	0.96802	-4.13;-4.13;-4.13	4.86	4.86	0.63082	ATP-grasp fold (1);ATP-grasp fold, subdomain 2 (1);Carbamoyl-phosphate synthetase, large subunit, ATP-binding (1);Biotin carboxylation domain (1);	0.000000	0.85682	N	0.000000	T	0.00039	0.0001	N	0.00419	-1.52	0.09310	P	1.0	B	0.02656	0.0	B	0.04013	0.001	T	0.50816	-0.8783	9	0.02654	T	1	.	13.3307	0.60485	0.077:0.0:0.923:0.0	rs16940029;rs17848853;rs60034155;rs16940029	552	O00763	ACACB_HUMAN	V	552	ENSP00000341044:I552V;ENSP00000367079:I552V;ENSP00000367085:I552V	ENSP00000341044:I552V	I	+	1	0	ACACB	108102111	1.000000	0.71417	0.950000	0.38849	0.515000	0.34225	6.663000	0.74431	1.049000	0.40321	-0.119000	0.15052	ATC	A|0.917;G|0.083	0.083	strong		0.512	ACACB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403077.1	NM_001093	
TBX5	6910	hgsc.bcm.edu	37	12	114793414	114793414	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:114793414G>A	ENST00000310346.4	-	9	2146	c.1480C>T	c.(1480-1482)Cca>Tca	p.P494S	TBX5_ENST00000349716.5_Missense_Mutation_p.P444S|TBX5_ENST00000405440.2_Missense_Mutation_p.P494S	NM_000192.3	NP_000183.2	Q99593	TBX5_HUMAN	T-box 5	494				PRTLSPHQYHSVHGVGMVPEWSDNS -> QGLYPLISTTLC TELAWCRVERQ (in Ref. 1; CAA70592). {ECO:0000305}.	apoptotic nuclear changes (GO:0030262)|atrial septum morphogenesis (GO:0060413)|atrioventricular valve morphogenesis (GO:0003181)|bundle of His development (GO:0003166)|cardiac left ventricle formation (GO:0003218)|cardiac muscle cell differentiation (GO:0055007)|cell migration involved in coronary vasculogenesis (GO:0060980)|cell-cell signaling (GO:0007267)|embryonic forelimb morphogenesis (GO:0035115)|embryonic limb morphogenesis (GO:0030326)|endocardial cushion development (GO:0003197)|forelimb morphogenesis (GO:0035136)|gene expression (GO:0010467)|heart development (GO:0007507)|lung development (GO:0030324)|morphogenesis of an epithelium (GO:0002009)|negative regulation of cardiac muscle cell proliferation (GO:0060044)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|pattern specification process (GO:0007389)|pericardium development (GO:0060039)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cardioblast differentiation (GO:0051891)|positive regulation of secondary heart field cardioblast proliferation (GO:0072513)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of execution phase of apoptosis (GO:1900117)|transcription initiation from RNA polymerase II promoter (GO:0006367)|ventricular cardiac muscle tissue development (GO:0003229)|ventricular septum development (GO:0003281)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(7)|lung(29)|ovary(6)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	56	Medulloblastoma(191;0.163)|all_neural(191;0.178)			BRCA - Breast invasive adenocarcinoma(302;0.0893)		AGAGTCCTTGGCACGCCATGA	0.597																																					p.P494S	NSCLC(152;1358 1980 4050 23898 40356)	Atlas-SNP	.											.	TBX5	188	.	0			c.C1480T						PASS	.						57.0	55.0	56.0					12																	114793414		2203	4300	6503	SO:0001583	missense	6910	exon9			TCCTTGGCACGCC	U89353	CCDS9173.1, CCDS9174.1	12q24.1	2014-09-17			ENSG00000089225	ENSG00000089225		"""T-boxes"""	11604	protein-coding gene	gene with protein product		601620		HOS		8988165, 8054982	Standard	NM_000192		Approved		uc001tvo.4	Q99593	OTTHUMG00000166191	ENST00000310346.4:c.1480C>T	12.37:g.114793414G>A	ENSP00000309913:p.Pro494Ser	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	87	42	0.482759	NM_000192	A6ND77|O15301|Q96TB0|Q9Y4I2	Missense_Mutation	SNP	ENST00000310346.4	37	CCDS9173.1	.	.	.	.	.	.	.	.	.	.	G	3.093	-0.186357	0.06340	.	.	ENSG00000089225	ENST00000349716;ENST00000310346;ENST00000405440	D;D;D	0.86694	-2.15;-2.16;-2.16	5.42	3.6	0.41247	.	0.168870	0.53938	N	0.000057	T	0.76586	0.4008	L	0.31664	0.95	0.49130	D	0.999753	B	0.12013	0.005	B	0.10450	0.005	T	0.64935	-0.6290	10	0.06757	T	0.87	.	11.3993	0.49860	0.145:0.0:0.855:0.0	.	494	Q99593	TBX5_HUMAN	S	444;494;494	ENSP00000337723:P444S;ENSP00000309913:P494S;ENSP00000384152:P494S	ENSP00000309913:P494S	P	-	1	0	TBX5	113277797	1.000000	0.71417	0.916000	0.36221	0.860000	0.49131	5.471000	0.66762	0.667000	0.31107	0.655000	0.94253	CCA	.	.	none		0.597	TBX5-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388297.1	NM_080717	
SPAG7	9552	hgsc.bcm.edu	37	17	4864114	4864114	+	Silent	SNP	T	T	C	rs61749470	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:4864114T>C	ENST00000206020.3	-	2	187	c.120A>G	c.(118-120)caA>caG	p.Q40Q	SPAG7_ENST00000573366.1_5'UTR|SPAG7_ENST00000575142.1_Silent_p.Q29Q	NM_004890.2	NP_004881.2	O75391	SPAG7_HUMAN	sperm associated antigen 7	40						nucleus (GO:0005634)	nucleic acid binding (GO:0003676)			central_nervous_system(1)|endometrium(1)|kidney(2)|lung(3)|ovary(2)|urinary_tract(1)	10						GTTGTTTCTCTTGCTCTTGTA	0.478													T|||	103	0.0205671	0.028	0.013	5008	,	,		19443	0.0099		0.0388	False		,,,				2504	0.0082				p.Q40Q		Atlas-SNP	.											.	SPAG7	22	.	0			c.A120G						PASS	.	T		94,3648		0,94,1777	161.0	155.0	157.0		120	1.7	1.0	17	dbSNP_129	157	279,7943		6,267,3838	no	coding-synonymous	SPAG7	NM_004890.2		6,361,5615	CC,CT,TT		3.3933,2.512,3.1177		40/228	4864114	373,11591	1871	4111	5982	SO:0001819	synonymous_variant	9552	exon2			TTTCTCTTGCTCT	AF047437	CCDS42240.1	17p13.2	2008-07-18				ENSG00000091640			11216	protein-coding gene	gene with protein product		610056				9653160	Standard	NM_004890		Approved	FSA-1, ACRP, MGC20134	uc002gae.3	O75391		ENST00000206020.3:c.120A>G	17.37:g.4864114T>C		Somatic	250	0	0		WXS	Illumina HiSeq	Phase_I	245	105	0.428571	NM_004890	Q96EU5	Silent	SNP	ENST00000206020.3	37	CCDS42240.1																																																																																			T|0.975;C|0.025	0.025	strong		0.478	SPAG7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438747.1	NM_004890	
LCE1E	353135	hgsc.bcm.edu	37	1	152760075	152760075	+	Silent	SNP	A	A	G	rs201660535	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:152760075A>G	ENST00000368770.3	+	2	353	c.300A>G	c.(298-300)tcA>tcG	p.S100S	LCE1E_ENST00000368771.1_Silent_p.S100S	NM_178353.1	NP_848130.1	Q5T753	LCE1E_HUMAN	late cornified envelope 1E	100	Cys-rich.				keratinization (GO:0031424)					lung(5)|stomach(1)	6	Lung NSC(65;3.97e-29)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)			GCCAGCCCTCAGGGGGCTCCA	0.642													G|||	1333	0.266174	0.3654	0.2406	5008	,	,		14498	0.3313		0.1064	False		,,,				2504	0.2474				p.S100S		Atlas-SNP	.											.	LCE1E	26	.	0			c.A300G						PASS	.	G		355,3853		89,177,1838	36.0	52.0	47.0		300	-4.6	0.5	1	dbSNP_132	47	177,8331		25,127,4102	no	coding-synonymous	LCE1E	NM_178353.1		114,304,5940	GG,GA,AA		2.0804,8.4363,4.1837		100/119	152760075	532,12184	2104	4254	6358	SO:0001819	synonymous_variant	353135	exon2			GCCCTCAGGGGGC	BC038391	CCDS1024.1	1q21.3	2008-02-05			ENSG00000186226	ENSG00000186226		"""Late cornified envelopes"""	29466	protein-coding gene	gene with protein product		612607				11698679	Standard	NM_178353		Approved	LEP5	uc001fan.3	Q5T753	OTTHUMG00000012405	ENST00000368770.3:c.300A>G	1.37:g.152760075A>G		Somatic	404	0	0		WXS	Illumina HiSeq	Phase_I	209	39	0.186603	NM_178353	D3DV30	Silent	SNP	ENST00000368770.3	37	CCDS1024.1																																																																																			A|0.995;G|0.005	0.005	strong		0.642	LCE1E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034525.1	NM_178353	
KDR	3791	hgsc.bcm.edu	37	4	55972974	55972974	+	Missense_Mutation	SNP	T	T	A	rs1870377	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:55972974T>A	ENST00000263923.4	-	11	1711	c.1416A>T	c.(1414-1416)caA>caT	p.Q472H		NM_002253.2	NP_002244.1	P35968	VGFR2_HUMAN	kinase insert domain receptor (a type III receptor tyrosine kinase)	472	Ig-like C2-type 5.		Q -> H (in dbSNP:rs1870377). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17344846}.		angiogenesis (GO:0001525)|branching morphogenesis of an epithelial tube (GO:0048754)|calcium ion homeostasis (GO:0055074)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|cell fate commitment (GO:0045165)|cell maturation (GO:0048469)|cell migration involved in sprouting angiogenesis (GO:0002042)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|embryonic hemopoiesis (GO:0035162)|endothelial cell differentiation (GO:0045446)|endothelium development (GO:0003158)|extracellular matrix organization (GO:0030198)|lung alveolus development (GO:0048286)|lymph vessel development (GO:0001945)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|ovarian follicle development (GO:0001541)|peptidyl-tyrosine autophosphorylation (GO:0038083)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of vasculogenesis (GO:2001214)|protein autophosphorylation (GO:0046777)|regulation of cell shape (GO:0008360)|signal transduction by phosphorylation (GO:0023014)|surfactant homeostasis (GO:0043129)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|vascular endothelial growth factor signaling pathway (GO:0038084)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sorting endosome (GO:0097443)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|Hsp90 protein binding (GO:0051879)|integrin binding (GO:0005178)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor binding (GO:0038085)|vascular endothelial growth factor-activated receptor activity (GO:0005021)	p.Q472H(1)		NS(1)|breast(3)|central_nervous_system(4)|endometrium(2)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(16)|lung(71)|ovary(2)|prostate(2)|skin(10)|soft_tissue(4)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	135	all_cancers(7;0.0255)|all_lung(4;0.00175)|Lung NSC(11;0.00384)|all_epithelial(27;0.034)|Glioma(25;0.08)|all_neural(26;0.101)		Epithelial(7;0.189)		Axitinib(DB06626)|Cabozantinib(DB08875)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	CTGAGACAGCTTGGCTATAAG	0.343			Mis		"""NSCLC, angiosarcoma"""					TSP Lung(20;0.16)			T|||	1061	0.211861	0.09	0.1311	5008	,	,		17888	0.4653		0.2346	False		,,,				2504	0.1493				p.Q472H		Atlas-SNP	.		Dom	yes		4	4q11-q12	3791	vascular endothelial growth factor receptor 2		E	KDR,NS,carcinoma,0,1	KDR	307	1	1	Substitution - Missense(1)	stomach(1)	c.A1416T	GRCh37	CM074306	KDR	M	rs1870377	PASS	.	T	HIS/GLN	485,3921	221.0+/-238.3	28,429,1746	79.0	82.0	81.0		1416	-1.8	0.0	4	dbSNP_92	81	2037,6563	353.6+/-329.2	246,1545,2509	yes	missense	KDR	NM_002253.2	24	274,1974,4255	AA,AT,TT		23.686,11.0077,19.3911	benign	472/1357	55972974	2522,10484	2203	4300	6503	SO:0001583	missense	3791	exon11			GACAGCTTGGCTA	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.1416A>T	4.37:g.55972974T>A	ENSP00000263923:p.Gln472His	Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	139	66	0.47482	NM_002253	A2RRS0|B5A925|C5IFA0|O60723|Q14178	Missense_Mutation	SNP	ENST00000263923.4	37	CCDS3497.1	513	0.2348901098901099	41	0.08333333333333333	52	0.143646408839779	248	0.43356643356643354	172	0.22691292875989447	T	4.227	0.041015	0.08196	0.110077	0.23686	ENSG00000128052	ENST00000263923	T	0.76448	-1.02	5.67	-1.82	0.07857	Immunoglobulin subtype (1);Immunoglobulin-like (1);	0.974058	0.08489	N	0.938324	T	0.00012	0.0000	L	0.49350	1.555	0.80722	P	0.0	P;B	0.52692	0.955;0.003	P;B	0.56514	0.8;0.011	T	0.14699	-1.0463	9	0.25106	T	0.35	.	5.5298	0.16978	0.0:0.2646:0.2451:0.4903	rs1870377;rs52810770;rs1870377	472;472	P35968-2;P35968	.;VGFR2_HUMAN	H	472	ENSP00000263923:Q472H	ENSP00000263923:Q472H	Q	-	3	2	KDR	55667731	0.011000	0.17503	0.005000	0.12908	0.006000	0.05464	-0.046000	0.11983	-0.160000	0.11002	-0.290000	0.09829	CAA	T|0.781;A|0.219	0.219	strong		0.343	KDR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250645.1		
MYO9B	4650	hgsc.bcm.edu	37	19	17306074	17306074	+	Missense_Mutation	SNP	G	G	A	rs112900956	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	38	0	0		WXS	Illumina HiSeq	Phase_I	57	29	0.508772	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		
LRPAP1	4043	hgsc.bcm.edu	37	4	3519762	3519762	+	Splice_Site	SNP	A	A	G	rs13325	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:3519762A>G	ENST00000500728.2	-	5	896	c.750T>C	c.(748-750)gcT>gcC	p.A250A	LRPAP1_ENST00000296325.5_5'UTR	NM_002337.3	NP_002328.1	P30533	AMRP_HUMAN	low density lipoprotein receptor-related protein associated protein 1	250	LDL receptor binding. {ECO:0000255}.				extracellular negative regulation of signal transduction (GO:1900116)|negative regulation of beta-amyloid clearance (GO:1900222)|negative regulation of protein binding (GO:0032091)|negative regulation of very-low-density lipoprotein particle clearance (GO:0010916)|protein folding (GO:0006457)|receptor-mediated endocytosis (GO:0006898)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|rough endoplasmic reticulum lumen (GO:0048237)|vesicle (GO:0031982)	asialoglycoprotein receptor activity (GO:0004873)|heparin binding (GO:0008201)|low-density lipoprotein particle receptor binding (GO:0050750)|receptor antagonist activity (GO:0048019)|unfolded protein binding (GO:0051082)|very-low-density lipoprotein particle receptor binding (GO:0070326)			breast(1)|endometrium(2)|large_intestine(2)|lung(5)|ovary(1)|prostate(1)|skin(2)	14				UCEC - Uterine corpus endometrioid carcinoma (64;0.165)		GGCACTCACCAGCCTCAGTGC	0.652													.|||	492	0.0982428	0.1263	0.1369	5008	,	,		16586	0.0		0.161	False		,,,				2504	0.0695				p.A250A		Atlas-SNP	.											.	LRPAP1	29	.	0			c.T750C						PASS	.	G		691,3715	749.8+/-412.1	53,585,1565	38.0	36.0	36.0		750	-8.2	0.0	4	dbSNP_52	36	1466,7134	742.2+/-407.2	122,1222,2956	no	coding-synonymous-near-splice	LRPAP1	NM_002337.3		175,1807,4521	GG,GA,AA		17.0465,15.6832,16.5847		250/358	3519762	2157,10849	2203	4300	6503	SO:0001630	splice_region_variant	4043	exon5			CTCACCAGCCTCA		CCDS3371.1	4p16.3	2008-05-02	2003-03-17		ENSG00000163956	ENSG00000163956			6701	protein-coding gene	gene with protein product		104225	"""low density lipoprotein-related protein-associated protein 1 (alpha-2-macroglobulin receptor-associated protein 1)"""	A2MRAP		1712782	Standard	NM_002337		Approved	HBP44	uc003ghh.4	P30533	OTTHUMG00000090299	ENST00000500728.2:c.751+1T>C	4.37:g.3519762A>G		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	38	20	0.526316	NM_002337	D3DVR9|Q2M310|Q53HQ3|Q53HS6	Silent	SNP	ENST00000500728.2	37	CCDS3371.1																																																																																			A|0.853;G|0.147	0.147	strong		0.652	LRPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206659.4		Silent
DCTN4	51164	hgsc.bcm.edu	37	5	150097883	150097883	+	Missense_Mutation	SNP	G	G	C	rs11954652	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:150097883G>C	ENST00000447998.2	-	11	1141	c.1026C>G	c.(1024-1026)ttC>ttG	p.F342L	DCTN4_ENST00000424236.1_Missense_Mutation_p.F285L|DCTN4_ENST00000446090.2_Missense_Mutation_p.F349L	NM_016221.3	NP_057305.1	Q9UJW0	DCTN4_HUMAN	dynactin 4 (p62)	342			F -> L (in dbSNP:rs11954652). {ECO:0000269|PubMed:14702039}.		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)|nucleus (GO:0005634)	protein N-terminus binding (GO:0047485)			breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(1)	10		Medulloblastoma(196;0.167)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			CCTCACACTCGAAGAGAGTCA	0.522													C|||	1356	0.270767	0.6142	0.0893	5008	,	,		19789	0.2589		0.0606	False		,,,				2504	0.1636				p.F349L		Atlas-SNP	.											.	DCTN4	35	.	0			c.C1047G						PASS	.	C	LEU/PHE,LEU/PHE,LEU/PHE	2334,2072	568.8+/-382.5	638,1058,507	138.0	119.0	125.0		1026,855,1047	4.1	1.0	5	dbSNP_120	125	410,8190	801.0+/-407.4	6,398,3896	yes	missense,missense,missense	DCTN4	NM_016221.3,NM_001135644.1,NM_001135643.1	22,22,22	644,1456,4403	CC,CG,GG		4.7674,47.0268,21.098	benign,benign,benign	342/461,285/404,349/468	150097883	2744,10262	2203	4300	6503	SO:0001583	missense	51164	exon12			ACACTCGAAGAGA	AF195120	CCDS4310.1, CCDS47310.1, CCDS47311.1	5q31-q32	2008-05-23			ENSG00000132912	ENSG00000132912			15518	protein-coding gene	gene with protein product		614758				10843801, 16554302	Standard	NM_016221		Approved		uc010jhi.3	Q9UJW0	OTTHUMG00000130079	ENST00000447998.2:c.1026C>G	5.37:g.150097883G>C	ENSP00000416968:p.Phe342Leu	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	118	44	0.372881	NM_001135643	B3KWW0|D3DQH0|E5RGT5|Q8TAN8	Missense_Mutation	SNP	ENST00000447998.2	37	CCDS4310.1	509	0.23305860805860806	281	0.5711382113821138	37	0.10220994475138122	146	0.25524475524475526	45	0.059366754617414245	C	5.578	0.291418	0.10567	0.529732	0.047674	ENSG00000132912	ENST00000447998;ENST00000424236;ENST00000446090	T;T;T	0.21734	1.99;1.99;1.99	5.83	4.05	0.47172	.	0.448446	0.25192	N	0.032456	T	0.00012	0.0000	N	0.00258	-1.755	0.58432	P	1.999999999946489E-6	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.43426	-0.9392	9	0.06236	T	0.91	-1.0278	5.3363	0.15959	0.1213:0.636:0.1168:0.1258	rs11954652;rs11954652	349;342	Q9UJW0-3;Q9UJW0	.;DCTN4_HUMAN	L	342;285;349	ENSP00000416968:F342L;ENSP00000411251:F285L;ENSP00000414906:F349L	ENSP00000411251:F285L	F	-	3	2	DCTN4	150078076	0.994000	0.37717	0.970000	0.41538	0.976000	0.68499	0.443000	0.21644	0.487000	0.27698	-0.125000	0.14975	TTC	G|0.780;C|0.220	0.220	strong		0.522	DCTN4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252372.1		
OR52E2	119678	hgsc.bcm.edu	37	11	5080337	5080337	+	Missense_Mutation	SNP	T	T	C	rs61746343	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	74	0	0		WXS	Illumina HiSeq	Phase_I	69	14	0.202899	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	
RTP2	344892	hgsc.bcm.edu	37	3	187419816	187419816	+	Missense_Mutation	SNP	T	T	C	rs61754877	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	201	1	0.00497512		WXS	Illumina HiSeq	Phase_I	163	88	0.539877	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	
SERPINB10	5273	hgsc.bcm.edu	37	18	61600384	61600384	+	Missense_Mutation	SNP	C	C	T	rs963075	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:61600384C>T	ENST00000238508.3	+	7	795	c.736C>T	c.(736-738)Cgt>Tgt	p.R246C		NM_005024.1	NP_005015.1	P48595	SPB10_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 10	246			R -> C (in dbSNP:rs963075).		negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|nucleus (GO:0005634)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(6)|prostate(1)|skin(3)|stomach(2)	24		Esophageal squamous(42;0.131)				CTACAAAAGCCGTGACCTCAG	0.413													C|||	2367	0.472644	0.7731	0.4193	5008	,	,		19382	0.4623		0.2942	False		,,,				2504	0.2986				p.R246C		Atlas-SNP	.											SERPINB10,colon,carcinoma,0,1	SERPINB10	53	1	0			c.C736T						PASS	.	C	CYS/ARG	3064,1342	693.0+/-405.6	1057,950,196	123.0	137.0	132.0		736	0.7	0.0	18	dbSNP_86	132	2224,6376	377.7+/-338.6	310,1604,2386	yes	missense	SERPINB10	NM_005024.1	180	1367,2554,2582	TT,TC,CC		25.8605,30.4585,40.6582		246/398	61600384	5288,7718	2203	4300	6503	SO:0001583	missense	5273	exon6			AAAAGCCGTGACC	U35459	CCDS11990.1	18q21.3	2014-02-18	2005-08-18		ENSG00000242550	ENSG00000242550		"""Serine (or cysteine) peptidase inhibitors"""	8942	protein-coding gene	gene with protein product	"""protease inhibitor 10 (ovalbumin type, bomapin)"""	602058	"""serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 10"""	PI10		9268635, 10871600, 24172014	Standard	NM_005024		Approved	bomapin		P48595	OTTHUMG00000060594	ENST00000238508.3:c.736C>T	18.37:g.61600384C>T	ENSP00000238508:p.Arg246Cys	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	84	38	0.452381	NM_005024	Q4VAX4|Q4VAX7	Missense_Mutation	SNP	ENST00000238508.3	37	CCDS11990.1	959	0.4391025641025641	357	0.725609756097561	144	0.39779005524861877	243	0.42482517482517484	215	0.2836411609498681	C	6.757	0.508440	0.12883	0.695415	0.258605	ENSG00000242550	ENST00000238508	D	0.83250	-1.7	5.95	0.68	0.17980	Serpin domain (3);	0.740672	0.13840	N	0.359069	T	0.00012	0.0000	M	0.78916	2.43	0.80722	P	0.0	B	0.22346	0.068	B	0.15484	0.013	T	0.41574	-0.9501	9	0.52906	T	0.07	.	1.2349	0.01951	0.2737:0.303:0.2636:0.1597	rs963075;rs58118394;rs963075	246	P48595	SPB10_HUMAN	C	246	ENSP00000238508:R246C	ENSP00000238508:R246C	R	+	1	0	SERPINB10	59751364	0.000000	0.05858	0.018000	0.16275	0.041000	0.13682	-0.160000	0.10041	0.380000	0.24823	0.655000	0.94253	CGT	C|0.570;T|0.430	0.430	strong		0.413	SERPINB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000134012.3	NM_005024	
PKD1L1	168507	hgsc.bcm.edu	37	7	47874630	47874630	+	Missense_Mutation	SNP	G	G	A	rs66755489	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:47874630G>A	ENST00000289672.2	-	39	6112	c.6062C>T	c.(6061-6063)cCg>cTg	p.P2021L		NM_138295.3	NP_612152.1	Q8TDX9	PK1L1_HUMAN	polycystic kidney disease 1 like 1	2021					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						GGCAGACCCCGGGGCTTCCTG	0.572													G|||	679	0.135583	0.2814	0.1052	5008	,	,		16637	0.0496		0.1243	False		,,,				2504	0.0603				p.P2021L		Atlas-SNP	.											PKD1L1,caecum,carcinoma,+1,1	PKD1L1	328	1	0			c.C6062T						PASS	.	G	LEU/PRO	1226,3180	422.5+/-339.8	184,858,1161	62.0	66.0	65.0		6062	-5.6	0.0	7	dbSNP_130	65	1104,7496	230.0+/-264.5	65,974,3261	yes	missense	PKD1L1	NM_138295.3	98	249,1832,4422	AA,AG,GG		12.8372,27.8257,17.9148	benign	2021/2850	47874630	2330,10676	2203	4300	6503	SO:0001583	missense	168507	exon39			GACCCCGGGGCTT	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.6062C>T	7.37:g.47874630G>A	ENSP00000289672:p.Pro2021Leu	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	56	38	0.678571	NM_138295	Q6UWK1	Missense_Mutation	SNP	ENST00000289672.2	37	CCDS34633.1	290	0.13278388278388278	125	0.2540650406504065	46	0.1270718232044199	26	0.045454545454545456	93	0.12269129287598944	G	4.277	0.050576	0.08243	0.278257	0.128372	ENSG00000158683	ENST00000289672	T	0.20738	2.05	3.68	-5.62	0.02481	.	.	.	.	.	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	B	0.21225	0.053	B	0.09377	0.004	T	0.45760	-0.9239	8	0.27785	T	0.31	2.6368	0.4611	0.00516	0.2946:0.3038:0.1747:0.2269	.	2021	Q8TDX9	PK1L1_HUMAN	L	2021	ENSP00000289672:P2021L	ENSP00000289672:P2021L	P	-	2	0	PKD1L1	47841155	0.000000	0.05858	0.000000	0.03702	0.072000	0.16883	-1.101000	0.03336	-1.317000	0.02292	0.563000	0.77884	CCG	G|0.831;A|0.169	0.169	strong		0.572	PKD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340974.1	NM_138295	
OR5L2	26338	hgsc.bcm.edu	37	11	55595012	55595012	+	Silent	SNP	A	A	T	rs35645945	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:55595012A>T	ENST00000378397.1	+	1	318	c.318A>T	c.(316-318)acA>acT	p.T106T		NM_001004739.1	NP_001004739.1	Q8NGL0	OR5L2_HUMAN	olfactory receptor, family 5, subfamily L, member 2	106						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)|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)				TGTTTTGCACATGTGGAGTCA	0.483										HNSCC(27;0.073)																											p.T106T		Atlas-SNP	.											.	OR5L2	135	.	0			c.A318T						PASS	.						187.0	175.0	179.0					11																	55595012		2199	4295	6494	SO:0001819	synonymous_variant	26338	exon1			TTGCACATGTGGA	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.318A>T	11.37:g.55595012A>T		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	68	39	0.573529	NM_001004739	Q6IF66|Q96RB2	Silent	SNP	ENST00000378397.1	37	CCDS31511.1																																																																																			A|0.934;T|0.066	0.066	strong		0.483	OR5L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391516.1	NM_001004739	
BOC	91653	hgsc.bcm.edu	37	3	112991959	112991959	+	Silent	SNP	C	C	T	rs11710894	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:112991959C>T	ENST00000495514.1	+	8	1709	c.1005C>T	c.(1003-1005)ccC>ccT	p.P335P	BOC_ENST00000355385.3_Silent_p.P335P|BOC_ENST00000273395.4_Silent_p.P335P			Q9BWV1	BOC_HUMAN	BOC cell adhesion associated, oncogene regulated	335	Ig-like C2-type 4.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|muscle cell differentiation (GO:0042692)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of myoblast differentiation (GO:0045663)|smoothened signaling pathway (GO:0007224)	axonal growth cone (GO:0044295)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)				NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(17)|lung(18)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	68			Epithelial(53;0.227)			TGGTCATCCCCTGGGGCCAGA	0.637													C|||	1496	0.298722	0.2231	0.3948	5008	,	,		18599	0.4107		0.1998	False		,,,				2504	0.319				p.P335P		Atlas-SNP	.											.	BOC	139	.	0			c.C1005T						PASS	.	C		976,3430	367.1+/-318.1	110,756,1337	73.0	72.0	73.0		1005	-8.1	0.5	3	dbSNP_120	73	1488,7112	281.8+/-295.3	138,1212,2950	no	coding-synonymous	BOC	NM_033254.2		248,1968,4287	TT,TC,CC		17.3023,22.1516,18.9451		335/1115	112991959	2464,10542	2203	4300	6503	SO:0001819	synonymous_variant	91653	exon8			CATCCCCTGGGGC	AY027658	CCDS2971.1	3q13.2	2013-02-11	2012-12-07		ENSG00000144857	ENSG00000144857		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	17173	protein-coding gene	gene with protein product	"""brother of CDO"", ""brother of CDON"", ""cell adhesion associated, oncogene regulated 2"""	608708	"""Boc homolog (mouse)"""			11782431	Standard	NM_033254		Approved	CDON2	uc003dzy.3	Q9BWV1	OTTHUMG00000159305	ENST00000495514.1:c.1005C>T	3.37:g.112991959C>T		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	165	94	0.569697	NM_033254	A6NJ30|B2RMS8|D3DN70|Q6UXJ5|Q8N2P7|Q8NF26	Silent	SNP	ENST00000495514.1	37	CCDS2971.1																																																																																			C|0.773;T|0.227	0.227	strong		0.637	BOC-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000354485.3	NM_033254	
CLEC18A	348174	hgsc.bcm.edu	37	16	69988463	69988463	+	Missense_Mutation	SNP	C	C	G	rs78531533	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:69988463C>G	ENST00000288040.6	+	3	630	c.443C>G	c.(442-444)aCc>aGc	p.T148S	CLEC18A_ENST00000393701.2_Missense_Mutation_p.T148S|CLEC18A_ENST00000449317.2_Missense_Mutation_p.T148S|CLEC18A_ENST00000568461.1_Missense_Mutation_p.T148S	NM_001136214.2	NP_001129686.1	A5D8T8	CL18A_HUMAN	C-type lectin domain family 18, member A	148	SCP.					extracellular region (GO:0005576)	carbohydrate binding (GO:0030246)			NS(1)|endometrium(2)|lung(1)|skin(1)	5						GCCACCTGCACCCACTACACG	0.602																																					p.T148S		Atlas-SNP	.											CLEC18A,NS,carcinoid-endocrine_tumour,0,1	CLEC18A	9	1	0			c.C443G						scavenged	.						22.0	21.0	21.0					16																	69988463		2198	4297	6495	SO:0001583	missense	348174	exon4			CCTGCACCCACTA	AF428259	CCDS10886.1	16q22.1	2010-04-27	2009-03-10	2009-03-10		ENSG00000157322		"""C-type lectin domain containing"""	30388	protein-coding gene	gene with protein product	"""mannose receptor-like"""					12975309	Standard	NM_001136214		Approved	MRCL	uc010vlo.3	A5D8T8		ENST00000288040.6:c.443C>G	16.37:g.69988463C>G	ENSP00000288040:p.Thr148Ser	Somatic	308	0	0		WXS	Illumina HiSeq	Phase_I	346	44	0.127168	NM_001271197	A8K1G9|Q6DCB3|Q7Z5K9|Q96HH2	Missense_Mutation	SNP	ENST00000288040.6	37	CCDS10886.1	.	.	.	.	.	.	.	.	.	.	.	8.343	0.829050	0.16749	.	.	ENSG00000157322	ENST00000393701;ENST00000539957;ENST00000545150;ENST00000449317;ENST00000288040	T;T;T	0.07688	3.17;3.17;3.17	1.97	1.97	0.26223	CAP domain (3);	0.557277	0.19650	N	0.109248	T	0.03959	0.0111	N	0.12502	0.225	0.21782	N	0.999542	B;B;B	0.27068	0.005;0.003;0.167	B;B;B	0.24394	0.02;0.008;0.053	T	0.43734	-0.9373	9	.	.	.	.	7.5137	0.27587	0.0:1.0:0.0:0.0	.	148;148;148	B4DPF2;A5D8T8;F8W692	.;CL18A_HUMAN;.	S	148;148;145;148;148	ENSP00000377304:T148S;ENSP00000413990:T148S;ENSP00000288040:T148S	.	T	+	2	0	CLEC18A	68545964	0.596000	0.26866	0.995000	0.50966	0.088000	0.18126	1.195000	0.32186	1.424000	0.47217	0.184000	0.17185	ACC	C|0.997;G|0.003	0.003	strong		0.602	CLEC18A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000268955.2	NM_182619	
ATP2B4	493	hgsc.bcm.edu	37	1	203669371	203669371	+	Silent	SNP	G	G	A	rs2228446	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:203669371G>A	ENST00000357681.5	+	5	1810	c.687G>A	c.(685-687)ggG>ggA	p.G229G	ATP2B4_ENST00000391954.2_Silent_p.G229G|ATP2B4_ENST00000367219.3_Silent_p.G229G|ATP2B4_ENST00000367218.3_Silent_p.G229G|ATP2B4_ENST00000341360.2_Silent_p.G229G	NM_001684.4	NP_001675.3	P23634	AT2B4_HUMAN	ATPase, Ca++ transporting, plasma membrane 4	229					blood coagulation (GO:0007596)|calcium ion homeostasis (GO:0055074)|calcium ion import across plasma membrane (GO:0098703)|calcium ion transmembrane transport (GO:0070588)|cellular calcium ion homeostasis (GO:0006874)|cellular response to epinephrine stimulus (GO:0071872)|ion transmembrane transport (GO:0034220)|negative regulation of adrenergic receptor signaling pathway involved in heart process (GO:1901205)|negative regulation of arginine catabolic process (GO:1900082)|negative regulation of calcineurin-NFAT signaling cascade (GO:0070885)|negative regulation of cardiac muscle hypertrophy in response to stress (GO:1903243)|negative regulation of citrulline biosynthetic process (GO:1903249)|negative regulation of nitric oxide biosynthetic process (GO:0045019)|negative regulation of nitric oxide mediated signal transduction (GO:0010751)|negative regulation of nitric-oxide synthase activity (GO:0051001)|negative regulation of peptidyl-cysteine S-nitrosylation (GO:1902083)|negative regulation of the force of heart contraction (GO:0098736)|positive regulation of cAMP-dependent protein kinase activity (GO:2000481)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|regulation of sodium ion transmembrane transport (GO:1902305)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to hydrostatic pressure (GO:0051599)|transmembrane transport (GO:0055085)	caveola (GO:0005901)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|T-tubule (GO:0030315)|Z disc (GO:0030018)	ATP binding (GO:0005524)|calcium-transporting ATPase activity (GO:0005388)|calmodulin binding (GO:0005516)|metal ion binding (GO:0046872)|nitric-oxide synthase binding (GO:0050998)|protein phosphatase 2B binding (GO:0030346)|scaffold protein binding (GO:0097110)			NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(5)|kidney(2)|large_intestine(10)|lung(20)|ovary(2)|prostate(6)|skin(1)|stomach(1)|urinary_tract(3)	56	all_cancers(21;0.071)|all_epithelial(62;0.228)		BRCA - Breast invasive adenocarcinoma(75;0.109)			TGATCCAAGGGAATGATCTGA	0.517													G|||	25	0.00499201	0.0008	0.0072	5008	,	,		20092	0.0		0.0139	False		,,,				2504	0.0051				p.G229G		Atlas-SNP	.											.	ATP2B4	226	.	0			c.G687A						PASS	.	G	,	12,4394	19.1+/-41.9	0,12,2191	114.0	110.0	112.0		687,687	-9.8	0.8	1	dbSNP_98	112	171,8429	78.6+/-141.3	0,171,4129	no	coding-synonymous,coding-synonymous	ATP2B4	NM_001001396.2,NM_001684.4	,	0,183,6320	AA,AG,GG		1.9884,0.2724,1.407	,	229/1171,229/1206	203669371	183,12823	2203	4300	6503	SO:0001819	synonymous_variant	493	exon5			CCAAGGGAATGAT	M25874	CCDS1440.1, CCDS30977.1	1q32.1	2010-04-20	2005-05-26		ENSG00000058668	ENSG00000058668	3.6.3.8	"""ATPases / P-type"""	817	protein-coding gene	gene with protein product	"""plasma membrane calcium-transporting ATPase 4"""	108732	"""matrix-remodelling associated 1"""	ATP2B2, MXRA1		1674727	Standard	NM_001001396		Approved	PMCA4	uc001gzw.3	P23634	OTTHUMG00000035906	ENST00000357681.5:c.687G>A	1.37:g.203669371G>A		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	97	49	0.505155	NM_001001396	B1APW5|B1APW6|Q13450|Q13452|Q13455|Q16817|Q7Z3S1	Silent	SNP	ENST00000357681.5	37	CCDS1440.1																																																																																			G|0.987;A|0.013	0.013	strong		0.517	ATP2B4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087462.1	NM_001001396	
AQP12B	653437	hgsc.bcm.edu	37	2	241622195	241622195	+	Silent	SNP	T	T	C	rs184458523	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:241622195T>C	ENST00000407834.3	-	1	122	c.60A>G	c.(58-60)gcA>gcG	p.A20A		NM_001102467.1	NP_001095937.1	A6NM10	AQ12B_HUMAN	aquaporin 12B	20						integral component of membrane (GO:0016021)	transporter activity (GO:0005215)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|lung(8)|ovary(1)	13		all_epithelial(40;1.71e-15)|Breast(86;2.14e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0294)|all_neural(83;0.0459)|Lung NSC(271;0.094)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;2.2e-31)|all cancers(36;1.08e-28)|OV - Ovarian serous cystadenocarcinoma(60;2.13e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;7.52e-06)|Lung(119;0.00163)|LUSC - Lung squamous cell carcinoma(224;0.008)|Colorectal(34;0.0124)|COAD - Colon adenocarcinoma(134;0.0757)		CCCGCCTGGCTGCCTCACAGA	0.672																																					p.A20A		Atlas-SNP	.											.	AQP12B	33	.	0			c.A60G						PASS	.			66,4230		3,60,2085	43.0	50.0	48.0		60	1.3	0.2	2		48	171,8367		8,155,4106	no	coding-synonymous	AQP12B	NM_001102467.1		11,215,6191	CC,CT,TT		2.0028,1.5363,1.8467		20/308	241622195	237,12597	2148	4269	6417	SO:0001819	synonymous_variant	653437	exon1			CCTGGCTGCCTCA	BC041460	CCDS46560.1	2q37.3	2007-12-14	2005-05-26	2005-05-26	ENSG00000185176	ENSG00000185176		"""Ion channels / Aquaporins"""	6096	protein-coding gene	gene with protein product			"""insulin synthesis associated 3"""	INSSA3			Standard	NM_001102467		Approved		uc010fzj.3	A6NM10	OTTHUMG00000152263	ENST00000407834.3:c.60A>G	2.37:g.241622195T>C		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	150	71	0.473333	NM_001102467	A4QPB9	Silent	SNP	ENST00000407834.3	37	CCDS46560.1																																																																																			T|0.907;C|0.093	0.093	strong		0.672	AQP12B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325625.1		
CD22	933	hgsc.bcm.edu	37	19	35831986	35831986	+	Silent	SNP	C	C	T	rs25677	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:35831986C>T	ENST00000085219.5	+	7	1518	c.1452C>T	c.(1450-1452)tgC>tgT	p.C484C	CD22_ENST00000544992.2_Silent_p.C484C|CD22_ENST00000419549.2_Silent_p.C312C|CD22_ENST00000341773.6_Silent_p.C307C|CD22_ENST00000270311.6_Silent_p.C364C|CD22_ENST00000536635.2_Silent_p.C396C|CD22_ENST00000594250.1_Silent_p.C307C	NM_001771.3	NP_001762.2	P20273	CD22_HUMAN	CD22 molecule	484	Ig-like C2-type 4.				cell adhesion (GO:0007155)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	carbohydrate binding (GO:0030246)			breast(2)|endometrium(2)|kidney(3)|large_intestine(14)|lung(21)|ovary(5)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	54	all_lung(56;9.78e-09)|Lung NSC(56;1.46e-08)|Esophageal squamous(110;0.162)		Epithelial(14;5.83e-19)|OV - Ovarian serous cystadenocarcinoma(14;3.19e-18)|all cancers(14;3.41e-16)|LUSC - Lung squamous cell carcinoma(66;0.0417)			CCATCGCCTGCGCAGCTTGTA	0.607													C|||	294	0.0587061	0.1936	0.0403	5008	,	,		17505	0.0		0.0099	False		,,,				2504	0.0				p.C484C	Ovarian(42;1009 1133 23674 26041)	Atlas-SNP	.											.	CD22	129	.	0			c.C1452T						PASS	.	C	,,,	761,3645	308.0+/-290.3	67,627,1509	95.0	84.0	88.0		1188,1452,921,1452	-2.3	0.0	19	dbSNP_72	88	105,8495	56.8+/-118.0	1,103,4196	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CD22	NM_001185099.1,NM_001185100.1,NM_001185101.1,NM_001771.3	,,,	68,730,5705	TT,TC,CC		1.2209,17.2719,6.6585	,,,	396/760,484/752,307/671,484/848	35831986	866,12140	2203	4300	6503	SO:0001819	synonymous_variant	933	exon7			CGCCTGCGCAGCT	X52785	CCDS12457.1, CCDS54247.1, CCDS54248.1, CCDS54249.1, CCDS62634.1	19q13.1	2013-01-29	2006-03-28		ENSG00000012124	ENSG00000012124		"""CD molecules"", ""Sialic acid binding Ig-like lectins"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	1643	protein-coding gene	gene with protein product	"""sialic acid binding Ig-like lectin 2"""	107266	"""CD22 antigen"""			8496602, 1691828	Standard	NM_001185099		Approved	SIGLEC-2, SIGLEC2	uc010edt.3	P20273		ENST00000085219.5:c.1452C>T	19.37:g.35831986C>T		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	126	64	0.507937	NM_001185100	F5GYU4|F5H7U3|O95699|O95701|O95702|O95703|Q01665|Q32M46|Q92872|Q92873|Q9UQA6|Q9UQA7|Q9UQA8|Q9UQA9|Q9UQB0|Q9Y2A6	Silent	SNP	ENST00000085219.5	37	CCDS12457.1																																																																																			A|0.015;C|0.932;T|0.053	0.053	strong		0.607	CD22-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466099.1	NM_001771	
KCNA2	3737	hgsc.bcm.edu	37	1	111144661	111144661	+	3'UTR	SNP	A	A	G	rs12407942	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:111144661A>G	ENST00000485317.1	-	0	3417				KCNA2_ENST00000369770.3_Silent_p.D342D|KCNA2_ENST00000525120.1_5'Flank			P16389	KCNA2_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 2						optic nerve structural organization (GO:0021633)|potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	juxtaparanode region of axon (GO:0044224)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|outward rectifier potassium channel activity (GO:0015271)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)			endometrium(1)|kidney(1)|large_intestine(6)|liver(1)|lung(18)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	32		all_cancers(81;5.55e-06)|all_epithelial(167;1.87e-05)|all_lung(203;0.000199)|Lung NSC(277;0.000398)		Colorectal(144;0.00878)|Lung(183;0.0234)|all cancers(265;0.0492)|Epithelial(280;0.0529)|COAD - Colon adenocarcinoma(174;0.131)|LUSC - Lung squamous cell carcinoma(189;0.133)|READ - Rectum adenocarcinoma(129;0.191)	Dalfampridine(DB06637)	CCTGCCTGTCATCAGGACCAG	0.468													G|||	1080	0.215655	0.1377	0.3473	5008	,	,		16150	0.3879		0.0706	False		,,,				2504	0.1994				p.D342D	Pancreas(18;568 735 10587 23710 36357)	Atlas-SNP	.											.	KCNA2	61	.	0			c.T1026C						PASS	.																																			SO:0001624	3_prime_UTR_variant	3737	exon4			CCTGTCATCAGGA	L02752	CCDS827.1, CCDS55625.1	1p13	2012-07-05			ENSG00000177301	ENSG00000177301		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6220	protein-coding gene	gene with protein product		176262				16382104	Standard	NM_004974		Approved	Kv1.2, HK4	uc009wfw.3	P16389	OTTHUMG00000011567	ENST00000485317.1:c.*1244T>C	1.37:g.111144661A>G		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	59	37	0.627119	NM_001204269	Q86XG6	Silent	SNP	ENST00000485317.1	37	CCDS827.1																																																																																			A|0.800;G|0.200	0.200	strong		0.468	KCNA2-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128001.2	NM_004974	
MEGF11	84465	hgsc.bcm.edu	37	15	66411441	66411441	+	Missense_Mutation	SNP	C	C	T	rs16949528	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:66411441C>T	ENST00000409699.2	-	4	456	c.284G>A	c.(283-285)aGc>aAc	p.S95N	MEGF11_ENST00000395614.1_5'UTR|MEGF11_ENST00000422354.1_Missense_Mutation_p.S95N|MEGF11_ENST00000288745.3_Intron|MEGF11_ENST00000395625.2_Intron|MEGF11_ENST00000360698.4_Missense_Mutation_p.S95N			A6BM72	MEG11_HUMAN	multiple EGF-like-domains 11	95	EGF-like 1. {ECO:0000255|PROSITE- ProRule:PRU00076}.|EMI. {ECO:0000255|PROSITE- ProRule:PRU00384}.		S -> N (in dbSNP:rs16949528). {ECO:0000269|PubMed:15489334}.		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						GAAGTCTCCGCTCTCATAGTA	0.607													T|||	2141	0.427516	0.5545	0.2867	5008	,	,		15476	0.4762		0.2555	False		,,,				2504	0.4826				p.S95N		Atlas-SNP	.											.	MEGF11	70	.	0			c.G284A						PASS	.	T	ASN/SER	732,648		187,358,145	68.0	70.0	70.0		284	1.7	0.3	15	dbSNP_123	70	889,2291		135,619,836	yes	missense	MEGF11	NM_032445.2	46	322,977,981	TT,TC,CC		27.956,46.9565,35.5482	benign	95/1045	66411441	1621,2939	690	1590	2280	SO:0001583	missense	84465	exon4			TCTCCGCTCTCAT	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.284G>A	15.37:g.66411441C>T	ENSP00000386908:p.Ser95Asn	Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	29	29	1	NM_032445	Q17R86|Q6UXS5|Q8ND91|Q96KG6	Missense_Mutation	SNP	ENST00000409699.2	37	CCDS10213.2	834	0.38186813186813184	278	0.5650406504065041	95	0.26243093922651933	268	0.46853146853146854	193	0.2546174142480211	T	11.20	1.569365	0.28003	0.530435	0.27956	ENSG00000157890	ENST00000409699;ENST00000422354;ENST00000360698	D;D;D	0.87029	-2.2;-2.2;-2.13	5.29	1.74	0.24563	EMI domain (1);Epidermal growth factor-like, type 3 (1);	.	.	.	.	T	0.00012	0.0000	M	0.65498	2.005	0.44798	P	0.0021970000000000045	B	0.02656	0.0	B	0.08055	0.003	T	0.45600	-0.9250	8	0.20046	T	0.44	.	9.9341	0.41541	0.0:0.4872:0.0:0.5128	rs16949528;rs56708944	95	A6BM72	MEG11_HUMAN	N	95	ENSP00000386908:S95N;ENSP00000414475:S95N;ENSP00000353919:S95N	ENSP00000353919:S95N	S	-	2	0	MEGF11	64198495	0.920000	0.31207	0.279000	0.24732	0.913000	0.54294	1.643000	0.37217	-0.184000	0.10567	-0.269000	0.10298	AGC	C|0.642;T|0.358	0.358	strong		0.607	MEGF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329307.2	NM_032445	
FBN3	84467	hgsc.bcm.edu	37	19	8196499	8196499	+	Silent	SNP	G	G	A	rs3813774	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:8196499G>A	ENST00000600128.1	-	15	2343	c.1929C>T	c.(1927-1929)tgC>tgT	p.C643C	FBN3_ENST00000270509.2_Silent_p.C643C|FBN3_ENST00000601739.1_Silent_p.C643C			Q75N90	FBN3_HUMAN	fibrillin 3	643	TB 3.					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						GATTGGCACAGCAGCACTCGG	0.652													G|||	690	0.13778	0.2103	0.0533	5008	,	,		16673	0.2262		0.0805	False		,,,				2504	0.0675				p.C643C		Atlas-SNP	.											.	FBN3	300	.	0			c.C1929T						PASS	.	G		783,3623	314.7+/-293.7	64,655,1484	59.0	60.0	60.0		1929	1.6	0.9	19	dbSNP_107	60	504,8096	144.7+/-200.5	16,472,3812	no	coding-synonymous	FBN3	NM_032447.3		80,1127,5296	AA,AG,GG		5.8605,17.7712,9.8954		643/2810	8196499	1287,11719	2203	4300	6503	SO:0001819	synonymous_variant	84467	exon14			GGCACAGCAGCAC		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.1929C>T	19.37:g.8196499G>A		Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	184	80	0.434783	NM_032447	Q75N91|Q75N92|Q75N93|Q86SJ5|Q96JP8	Silent	SNP	ENST00000600128.1	37	CCDS12196.1																																																																																			G|0.878;A|0.122	0.122	strong		0.652	FBN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461428.2	NM_032447	
BFSP1	631	hgsc.bcm.edu	37	20	17475217	17475217	+	Silent	SNP	C	C	T	rs6136118	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:17475217C>T	ENST00000377873.3	-	8	1539	c.1500G>A	c.(1498-1500)gcG>gcA	p.A500A	BFSP1_ENST00000544874.1_Silent_p.A361A|BFSP1_ENST00000536626.1_Silent_p.A361A|BFSP1_ENST00000377868.2_Silent_p.A375A	NM_001195.3	NP_001186.1	Q12934	BFSP1_HUMAN	beaded filament structural protein 1, filensin	500	Tail.				cell maturation (GO:0048469)|lens fiber cell development (GO:0070307)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|intermediate filament (GO:0005882)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	structural constituent of cytoskeleton (GO:0005200)|structural constituent of eye lens (GO:0005212)			central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(7)|prostate(2)|skin(1)|stomach(1)	18						CAGAGTCTTCCGCAACAGAAA	0.552													C|||	1700	0.339457	0.3404	0.3069	5008	,	,		15488	0.4038		0.2435	False		,,,				2504	0.3937				p.A500A		Atlas-SNP	.											.	BFSP1	55	.	0			c.G1500A						PASS	.	C	,	1458,2948	472.8+/-356.5	251,956,996	64.0	56.0	58.0		1125,1500	0.3	0.2	20	dbSNP_114	58	2028,6572	353.6+/-329.2	246,1536,2518	no	coding-synonymous,coding-synonymous	BFSP1	NM_001161705.1,NM_001195.3	,	497,2492,3514	TT,TC,CC		23.5814,33.0912,26.803	,	375/541,500/666	17475217	3486,9520	2203	4300	6503	SO:0001819	synonymous_variant	631	exon8			GTCTTCCGCAACA	Y16717	CCDS13126.1, CCDS54448.1, CCDS63229.1	20p12.1	2014-06-05			ENSG00000125864	ENSG00000125864		"""Intermediate filaments type VI, eye lens intermediate filaments"""	1040	protein-coding gene	gene with protein product		603307				9787085	Standard	NM_001161705		Approved	CP94, CP115, LIFL-H, filensin	uc002wpo.3	Q12934	OTTHUMG00000031940	ENST00000377873.3:c.1500G>A	20.37:g.17475217C>T		Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	125	63	0.504	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	
DIDO1	11083	hgsc.bcm.edu	37	20	61538601	61538601	+	Silent	SNP	C	C	T	rs34820000	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:61538601C>T	ENST00000266070.4	-	5	1597	c.1272G>A	c.(1270-1272)gcG>gcA	p.A424A	DIDO1_ENST00000395335.2_Silent_p.A424A|DIDO1_ENST00000370371.4_Silent_p.A424A|DIDO1_ENST00000266071.5_Silent_p.A424A|DIDO1_ENST00000370368.1_Silent_p.A424A|DIDO1_ENST00000354665.4_Silent_p.A424A|DIDO1_ENST00000370366.1_Silent_p.A424A|DIDO1_ENST00000395340.1_Silent_p.A424A|DIDO1_ENST00000395343.1_Silent_p.A424A	NM_033081.2	NP_149072.2	Q9BTC0	DIDO1_HUMAN	death inducer-obliterator 1	424					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)					ACTTCATTGTCGCTGCGGCGT	0.522													C|||	330	0.0658946	0.1218	0.0447	5008	,	,		18192	0.0238		0.0497	False		,,,				2504	0.0654				p.A424A	Melanoma(25;381 482 3385 5362 7955 17159 17174 40604 47095)	Atlas-SNP	.											DIDO1_ENST00000370371,NS,carcinoma,-1,2	DIDO1	321	2	0			c.G1272A						PASS	.	C	,,,,,	535,3871	243.1+/-252.9	31,473,1699	225.0	216.0	219.0		1272,1272,1272,1272,1272,1272	-7.2	0.1	20	dbSNP_126	219	485,8115	140.6+/-197.1	13,459,3828	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	DIDO1	NM_001193369.1,NM_001193370.1,NM_022105.4,NM_033081.2,NM_080796.3,NM_080797.3	,,,,,	44,932,5527	TT,TC,CC		5.6395,12.1425,7.8425	,,,,,	424/2241,424/1190,424/563,424/2241,424/563,424/1190	61538601	1020,11986	2203	4300	6503	SO:0001819	synonymous_variant	11083	exon5			CATTGTCGCTGCG	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.1272G>A	20.37:g.61538601C>T		Somatic	267	1	0.00374532		WXS	Illumina HiSeq	Phase_I	224	109	0.486607	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																																																																																			C|0.924;T|0.076	0.076	strong		0.522	DIDO1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080091.2	NM_080796	
HLA-A	3105	hgsc.bcm.edu	37	6	29910759	29910759	+	Missense_Mutation	SNP	T	T	C	rs1071742	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:29910759T>C	ENST00000396634.1	+	4	640	c.299T>C	c.(298-300)gTg>gCg	p.V100A	HLA-A_ENST00000376802.2_Missense_Mutation_p.V100A|HLA-A_ENST00000376809.5_Missense_Mutation_p.V100A|HLA-A_ENST00000376806.5_Missense_Mutation_p.V100A			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	100	Alpha-1.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	beta-2-microglobulin binding (GO:0030881)|peptide antigen binding (GO:0042605)|TAP binding (GO:0046977)			central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	30						ACTGACCGAGTGGACCTGGGG	0.687									Osteosarcoma, Familial Clustering of;Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of;Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of	Multiple Myeloma(9;0.094)			N|||	774	0.154553	0.1445	0.1225	5008	,	,		10249	0.0704		0.1928	False		,,,				2504	0.2382				p.V100A		Atlas-SNP	.											HLA-A,rectum,carcinoma,0,1	HLA-A	89	1	0			c.T299C						PASS	.	C	ALA/VAL	656,3732		158,340,1696	60.0	64.0	63.0		299	-6.7	0.0	6	dbSNP_86	63	2286,6282		597,1092,2595	yes	missense	HLA-A	NM_002116.7	64	755,1432,4291	CC,CT,TT		26.6807,14.9499,22.7076	benign	100/366	29910759	2942,10014	2194	4284	6478	SO:0001583	missense	3105	exon2	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	ACCGAGTGGACCT	D32129	CCDS34373.1	6p21.3	2013-01-11			ENSG00000206503	ENSG00000206503		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4931	protein-coding gene	gene with protein product		142800				8838351	Standard	NM_001242758		Approved		uc003nol.3	P01891	OTTHUMG00000130501	ENST00000396634.1:c.299T>C	6.37:g.29910759T>C	ENSP00000379873:p.Val100Ala	Somatic	235	0	0		WXS	Illumina HiSeq	Phase_I	144	142	0.986111	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Missense_Mutation	SNP	ENST00000396634.1	37	CCDS34373.1	.	.	.	.	.	.	.	.	.	.	.	5.521	0.280982	0.10458	0.149499	0.266807	ENSG00000206503	ENST00000396634;ENST00000376806;ENST00000376809;ENST00000355767;ENST00000376802	T;T;T;T	0.00792	5.69;5.69;5.69;5.69	3.33	-6.67	0.01783	MHC class I, alpha chain, alpha1/alpha2 (6);MHC classes I/II-like antigen recognition protein (3);MHC class I-like antigen recognition (3);	15.776400	0.01836	N	0.034989	T	0.00300	0.0009	M	0.67625	2.065	0.80722	P	0.0	B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0	B;B;B;B;B	0.09377	0.004;0.003;0.002;0.001;0.004	T	0.46289	-0.9202	9	0.38643	T	0.18	.	0.4643	0.00521	0.2856:0.2905:0.146:0.2778	rs1071742;rs2231002;rs3129019;rs3173422;rs3200152;rs3200155;rs9256981;rs17423971;rs41551313	100;100;100;100;100	P13746;Q5SRN7;P16188;Q5SRN5;P04439	1A11_HUMAN;.;1A30_HUMAN;.;1A03_HUMAN	A	100	ENSP00000379873:V100A;ENSP00000366002:V100A;ENSP00000366005:V100A;ENSP00000365998:V100A	ENSP00000348012:V100A	V	+	2	0	HLA-A	30018738	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.538000	0.00938	-1.834000	0.01193	-3.111000	0.00062	GTG	A|0.129;C|0.082;T|0.790	0.082	strong		0.687	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
TRAPPC12	51112	hgsc.bcm.edu	37	2	3483205	3483205	+	Silent	SNP	C	C	T	rs6767	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	174	0	0		WXS	Illumina HiSeq	Phase_I	221	82	0.371041	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	
SH3BP4	23677	hgsc.bcm.edu	37	2	235950284	235950284	+	Silent	SNP	A	A	C	rs3731648	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:235950284A>C	ENST00000409212.1	+	4	1378	c.871A>C	c.(871-873)Agg>Cgg	p.R291R	SH3BP4_ENST00000344528.4_Silent_p.R291R|SH3BP4_ENST00000392011.2_Silent_p.R291R			Q9P0V3	SH3B4_HUMAN	SH3-domain binding protein 4	291					cellular response to amino acid stimulus (GO:0071230)|endocytosis (GO:0006897)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of GTPase activity (GO:0034260)|negative regulation of TOR signaling (GO:0032007)|positive regulation of autophagy (GO:0010508)|protein localization to lysosome (GO:0061462)|regulation of catalytic activity (GO:0050790)	coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	GDP-dissociation inhibitor activity (GO:0005092)|identical protein binding (GO:0042802)|Ras GTPase binding (GO:0017016)	p.R291R(1)		central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(6)|lung(13)|ovary(4)|prostate(2)|skin(6)|stomach(3)|urinary_tract(2)	44		Breast(86;0.000332)|Renal(207;0.00339)|all_lung(227;0.00458)|all_hematologic(139;0.0296)|Lung NSC(271;0.0419)		Epithelial(121;7.66e-20)|BRCA - Breast invasive adenocarcinoma(100;0.000402)|Lung(119;0.00299)|LUSC - Lung squamous cell carcinoma(224;0.00645)|GBM - Glioblastoma multiforme(43;0.237)		GCTAAACCACAGGAAGCTGGC	0.582													C|||	1494	0.298323	0.2867	0.3256	5008	,	,		17048	0.4077		0.0915	False		,,,				2504	0.3947				p.R291R		Atlas-SNP	.											SH3BP4,NS,carcinoma,0,1	SH3BP4	109	1	1	Substitution - coding silent(1)	stomach(1)	c.A871C						scavenged	.	C		1115,3287		134,847,1220	40.0	50.0	46.0		871	4.6	1.0	2	dbSNP_107	46	888,7712		47,794,3459	no	coding-synonymous	SH3BP4	NM_014521.2		181,1641,4679	CC,CA,AA		10.3256,25.3294,15.4053		291/964	235950284	2003,10999	2201	4300	6501	SO:0001819	synonymous_variant	23677	exon4			AACCACAGGAAGC	AF147747	CCDS2513.1	2q37.1-q37.2	2008-05-15			ENSG00000130147	ENSG00000130147			10826	protein-coding gene	gene with protein product		605611				10644451	Standard	NM_014521		Approved		uc002vvp.3	Q9P0V3	OTTHUMG00000133292	ENST00000409212.1:c.871A>C	2.37:g.235950284A>C		Somatic	97	1	0.0103093		WXS	Illumina HiSeq	Phase_I	92	41	0.445652	NM_014521	O95082|Q309A3|Q53QD0|Q53TD1	Silent	SNP	ENST00000409212.1	37	CCDS2513.1																																																																																			A|0.797;C|0.203	0.203	strong		0.582	SH3BP4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329763.1		
SLC22A4	6583	hgsc.bcm.edu	37	5	131676320	131676320	+	Missense_Mutation	SNP	C	C	T	rs1050152	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:131676320C>T	ENST00000200652.3	+	9	1681	c.1507C>T	c.(1507-1509)Ctc>Ttc	p.L503F	AC034220.3_ENST00000417795.1_RNA|AC034220.3_ENST00000437091.1_RNA	NM_003059.2	NP_003050.2	Q9H015	S22A4_HUMAN	solute carrier family 22 (organic cation/zwitterion transporter), member 4	503			L -> F (reduces the ability to transport carnitine; dbSNP:rs1050152). {ECO:0000269|PubMed:15107849, ECO:0000269|PubMed:9426230}.		body fluid secretion (GO:0007589)|carnitine metabolic process (GO:0009437)|carnitine transmembrane transport (GO:1902603)|carnitine transport (GO:0015879)|cation transmembrane transport (GO:0098655)|organic cation transport (GO:0015695)|quaternary ammonium group transport (GO:0015697)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)|triglyceride metabolic process (GO:0006641)	apical plasma membrane (GO:0016324)|integral component of plasma membrane (GO:0005887)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|carnitine transmembrane transporter activity (GO:0015226)|cation:cation antiporter activity (GO:0015491)|nucleotide binding (GO:0000166)|PDZ domain binding (GO:0030165)|quaternary ammonium group transmembrane transporter activity (GO:0015651)|secondary active organic cation transmembrane transporter activity (GO:0008513)|symporter activity (GO:0015293)			endometrium(1)|kidney(3)|large_intestine(2)|lung(8)|ovary(1)|urinary_tract(1)	16		all_cancers(142;0.0752)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)		Amiloride(DB00594)|Aminohippurate(DB00345)|Benzylpenicillin(DB01053)|Choline(DB00122)|Cimetidine(DB00501)|Clonidine(DB00575)|Desipramine(DB01151)|Guanidine(DB00536)|Imipramine(DB00458)|Ipratropium bromide(DB00332)|L-Arginine(DB00125)|L-Carnitine(DB00583)|L-Lysine(DB00123)|Levofloxacin(DB01137)|Mepyramine(DB06691)|Nicotine(DB00184)|Ofloxacin(DB01165)|Procainamide(DB01035)|Quinidine(DB00908)|Quinine(DB00468)|Spermine(DB00127)|Testosterone(DB00624)|Tiotropium(DB01409)|Verapamil(DB00661)	GATTGGAATCCTCACCCTTTT	0.423													C|||	673	0.134385	0.0212	0.2435	5008	,	,		18689	0.001		0.3867	False		,,,				2504	0.0879				p.L503F		Atlas-SNP	.											SLC22A4,NS,carcinoma,-2,1	SLC22A4	45	1	0			c.C1507T	GRCh37	CM041074	SLC22A4	M	rs1050152	scavenged	.	C	PHE/LEU	367,4039	183.6+/-211.2	22,323,1858	237.0	218.0	225.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1507	-4.6	0.5	5	dbSNP_86	225	3607,4993	522.2+/-380.1	747,2113,1440	yes	missense	SLC22A4	NM_003059.2	22	769,2436,3298	TT,TC,CC		41.9419,8.3296,30.5551	benign	503/552	131676320	3974,9032	2203	4300	6503	SO:0001583	missense	6583	exon9			GGAATCCTCACCC	AB007448	CCDS4153.1	5q23.3	2013-07-18	2013-07-18		ENSG00000197208	ENSG00000197208		"""Solute carriers"""	10968	protein-coding gene	gene with protein product		604190	"""solute carrier family 22 (organic cation/ergothioneine transporter), member 4"""			9426230, 15795384	Standard	NM_003059		Approved	OCTN1, MGC34546	uc003kwq.3	Q9H015	OTTHUMG00000059648	ENST00000200652.3:c.1507C>T	5.37:g.131676320C>T	ENSP00000200652:p.Leu503Phe	Somatic	190	1	0.00526316		WXS	Illumina HiSeq	Phase_I	153	71	0.464052	NM_003059	O14546	Missense_Mutation	SNP	ENST00000200652.3	37	CCDS4153.1	403	0.18452380952380953	15	0.03048780487804878	105	0.2900552486187845	0	0.0	283	0.3733509234828496	C	9.415	1.081608	0.20309	0.083296	0.419419	ENSG00000197208	ENST00000200652	T	0.74526	-0.85	5.22	-4.62	0.03370	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.782657	0.12072	N	0.502162	T	0.00012	0.0000	L	0.52206	1.635	0.42947	P	0.005637000000000003	B	0.12630	0.006	B	0.23419	0.046	T	0.35176	-0.9799	9	0.54805	T	0.06	.	6.0229	0.19638	0.1479:0.2382:0.5244:0.0894	rs1050152;rs17680807;rs52829495;rs57045625;rs1050152	503	Q9H015	S22A4_HUMAN	F	503	ENSP00000200652:L503F	ENSP00000200652:L503F	L	+	1	0	SLC22A4	131704219	0.001000	0.12720	0.543000	0.28128	0.313000	0.28021	-0.079000	0.11357	-0.729000	0.04875	-0.388000	0.06559	CTC	C|0.748;T|0.252	0.252	strong		0.423	SLC22A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132661.1	NM_003059	
CRACR2A	84766	hgsc.bcm.edu	37	12	3806147	3806147	+	Missense_Mutation	SNP	T	T	C	rs200051200|rs9788233	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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						PASS	.	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	36	0	0		WXS	Illumina HiSeq	Phase_I	33	17	0.515152	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		
DNAH8	1769	hgsc.bcm.edu	37	6	38980081	38980081	+	Missense_Mutation	SNP	A	A	G	rs10484847	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:38980081A>G	ENST00000359357.3	+	88	13065	c.12811A>G	c.(12811-12813)Ata>Gta	p.I4271V	DNAH8_ENST00000441566.1_Missense_Mutation_p.I4235V			Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy chain 8	4271			I -> V (in dbSNP:rs10484847). {ECO:0000269|PubMed:12297094}.		cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(7)|breast(9)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(16)|large_intestine(44)|liver(4)|lung(101)|ovary(7)|pancreas(2)|prostate(8)|skin(28)|stomach(4)|upper_aerodigestive_tract(6)|urinary_tract(4)	260						AGTCATTTCAATACTCCGCAG	0.358													A|||	533	0.10643	0.1188	0.1225	5008	,	,		20665	0.002		0.1769	False		,,,				2504	0.1135				p.I4488V		Atlas-SNP	.											DNAH8_ENST00000359357,NS,carcinoma,-1,2	DNAH8	1239	2	0			c.A13462G						PASS	.	A	VAL/ILE	642,3764	273.7+/-271.5	45,552,1606	157.0	145.0	149.0		13462	2.5	0.1	6	dbSNP_119	149	1549,7051	291.5+/-300.3	136,1277,2887	yes	missense	DNAH8	NM_001206927.1	29	181,1829,4493	GG,GA,AA		18.0116,14.571,16.8461	benign	4488/4708	38980081	2191,10815	2203	4300	6503	SO:0001583	missense	1769	exon90			ATTTCAATACTCC	Z83806	CCDS75447.1	6p21.2	2012-04-19	2006-09-04		ENSG00000124721	ENSG00000124721		"""Axonemal dyneins"""	2952	protein-coding gene	gene with protein product		603337	"""dynein, axonemal, heavy polypeptide 8"""			9373155	Standard	NM_001206927		Approved	hdhc9	uc021yzh.1	Q96JB1	OTTHUMG00000016253	ENST00000359357.3:c.12811A>G	6.37:g.38980081A>G	ENSP00000352312:p.Ile4271Val	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	126	67	0.531746	NM_001206927	O00438|Q5JYI2|Q5T2M3|Q5T2M4|Q5TG00|Q9UEM4	Missense_Mutation	SNP	ENST00000359357.3	37		243	0.11126373626373626	61	0.12398373983739837	51	0.1408839779005525	2	0.0034965034965034965	129	0.17018469656992086	A	7.940	0.742626	0.15642	0.14571	0.180116	ENSG00000124721	ENST00000327475;ENST00000359357;ENST00000441566	T;T;T	0.08102	3.13;3.13;3.13	6.16	2.45	0.29901	Dynein heavy chain (1);	0.554802	0.19449	N	0.113988	T	0.00815	0.0027	N	0.02736	-0.51	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.48175	-0.9058	9	0.27785	T	0.31	.	1.9397	0.03344	0.5499:0.1244:0.206:0.1197	rs10484847;rs17422343;rs52803138;rs57264205;rs10484847	4271	Q96JB1	DYH8_HUMAN	V	4476;4271;4235	ENSP00000333363:I4476V;ENSP00000352312:I4271V;ENSP00000402294:I4235V	ENSP00000333363:I4476V	I	+	1	0	DNAH8	39088059	0.013000	0.17824	0.079000	0.20413	0.978000	0.69477	0.402000	0.20965	0.187000	0.20147	0.528000	0.53228	ATA	A|0.890;G|0.110	0.110	strong		0.358	DNAH8-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000043574.1	NM_001206927	
ACTL7B	10880	hgsc.bcm.edu	37	9	111618163	111618163	+	Silent	SNP	G	G	A	rs3750468	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:111618163G>A	ENST00000374667.3	-	1	1076	c.48C>T	c.(46-48)gaC>gaT	p.D16D		NM_006686.3	NP_006677.1	Q9Y614	ACL7B_HUMAN	actin-like 7B	16						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						CCTCTCCAGGGTCACCCTGAG	0.652													G|||	1134	0.226438	0.2247	0.2349	5008	,	,		17053	0.2113		0.2028	False		,,,				2504	0.2628				p.D16D		Atlas-SNP	.											.	ACTL7B	57	.	0			c.C48T						PASS	.	G		969,3437	365.6+/-317.5	108,753,1342	56.0	58.0	58.0		48	0.9	1.0	9	dbSNP_107	58	1767,6833	320.7+/-314.7	174,1419,2707	no	coding-synonymous	ACTL7B	NM_006686.3		282,2172,4049	AA,AG,GG		20.5465,21.9927,21.0364		16/416	111618163	2736,10270	2203	4300	6503	SO:0001819	synonymous_variant	10880	exon1			TCCAGGGTCACCC	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.48C>T	9.37:g.111618163G>A		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	48	14	0.291667	NM_006686	B2R9Q2|Q5JSV1	Silent	SNP	ENST00000374667.3	37	CCDS6771.1																																																																																			G|0.783;A|0.217	0.217	strong		0.652	ACTL7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053571.1	NM_006686	
OR2AG2	338755	hgsc.bcm.edu	37	11	6789492	6789492	+	Missense_Mutation	SNP	C	C	T	rs143018775	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:6789492C>T	ENST00000338569.2	-	1	794	c.697G>A	c.(697-699)Ggg>Agg	p.G233R		NM_001004490.1	NP_001004490.1	A6NM03	O2AG2_HUMAN	olfactory receptor, family 2, subfamily AG, member 2	233						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(13)|ovary(1)|skin(5)|stomach(1)|urinary_tract(1)	28		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)		Epithelial(150;2.15e-08)|BRCA - Breast invasive adenocarcinoma(625;0.129)		TTCTTCCTCCCCTCATTTGAT	0.502													C|||	8	0.00159744	0.0	0.0086	5008	,	,		19208	0.0		0.002	False		,,,				2504	0.0				p.G233R		Atlas-SNP	.											.	OR2AG2	55	.	0			c.G697A						PASS	.	C	ARG/GLY	2,4400	4.2+/-10.8	0,2,2199	110.0	95.0	100.0		697	3.5	0.1	11	dbSNP_134	100	19,8573	14.0+/-48.4	0,19,4277	yes	missense	OR2AG2	NM_001004490.1	125	0,21,6476	TT,TC,CC		0.2211,0.0454,0.1616	probably-damaging	233/317	6789492	21,12973	2201	4296	6497	SO:0001583	missense	338755	exon1			TCCTCCCCTCATT	AB065539	CCDS31413.1	11p15.4	2012-08-09		2004-03-10	ENSG00000188124	ENSG00000188124		"""GPCR / Class A : Olfactory receptors"""	15143	protein-coding gene	gene with protein product				OR2AG2P			Standard	NM_001004490		Approved		uc001meq.1	A6NM03	OTTHUMG00000165868	ENST00000338569.2:c.697G>A	11.37:g.6789492C>T	ENSP00000342697:p.Gly233Arg	Somatic	199	0	0		WXS	Illumina HiSeq	Phase_I	179	145	0.810056	NM_001004490		Missense_Mutation	SNP	ENST00000338569.2	37	CCDS31413.1	4	0.0018315018315018315	0	0.0	3	0.008287292817679558	0	0.0	1	0.0013192612137203166	C	12.95	2.092121	0.36952	4.54E-4	0.002211	ENSG00000188124	ENST00000338569	T	0.00295	8.25	4.47	3.55	0.40652	GPCR, rhodopsin-like superfamily (1);	0.000000	0.51477	D	0.000084	T	0.00496	0.0016	M	0.85197	2.74	0.09310	N	1	D	0.89917	1.0	D	0.85130	0.997	T	0.28554	-1.0040	10	0.87932	D	0	.	10.7934	0.46447	0.0:0.9061:0.0:0.0939	.	233	A6NM03	O2AG2_HUMAN	R	233	ENSP00000342697:G233R	ENSP00000342697:G233R	G	-	1	0	OR2AG2	6746068	0.000000	0.05858	0.111000	0.21465	0.605000	0.37080	0.158000	0.16422	1.480000	0.48289	0.655000	0.94253	GGG	C|0.999;T|0.001	0.001	strong		0.502	OR2AG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386775.1	NM_001004490	
PRAMEF1	65121	hgsc.bcm.edu	37	1	12854428	12854428	+	Missense_Mutation	SNP	C	C	T	rs1769774		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:12854428C>T	ENST00000332296.7	+	3	755	c.652C>T	c.(652-654)Cca>Tca	p.P218S	PRAMEF1_ENST00000400814.3_5'Flank	NM_023013.2	NP_075389.1	O95521	PRAM1_HUMAN	PRAME family member 1	218			P -> S (in dbSNP:rs1769774).		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)		CATGTCCTGGCCACGTCTGAT	0.393																																					p.P218S		Atlas-SNP	.											.	PRAMEF1	78	.	0			c.C652T						PASS	.	G	SER/PRO	959,3447		7,945,1251	298.0	273.0	282.0		652	-0.5	0.0	1	dbSNP_89	282	2715,5885		261,2193,1846	no	missense	PRAMEF1	NM_023013.2	74	268,3138,3097	TT,TC,CC		31.5698,21.7658,28.2485	benign	218/475	12854428	3674,9332	2203	4300	6503	SO:0001583	missense	65121	exon3			TCCTGGCCACGTC	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.652C>T	1.37:g.12854428C>T	ENSP00000332134:p.Pro218Ser	Somatic	482	1	0.00207469		WXS	Illumina HiSeq	Phase_I	355	156	0.439437	NM_023013	Q9UQP2	Missense_Mutation	SNP	ENST00000332296.7	37	CCDS148.1	626	0.2866300366300366	87	0.17682926829268292	101	0.27900552486187846	215	0.3758741258741259	223	0.2941952506596306	.	0.007	-2.005143	0.00426	0.217658	0.315698	ENSG00000116721	ENST00000332296	T	0.14640	2.49	1.61	-0.486	0.12064	.	2.279790	0.02045	N	0.049591	T	0.00012	0.0000	N	0.05230	-0.09	0.80722	P	0.0	B	0.15719	0.014	B	0.20384	0.029	T	0.47328	-0.9126	9	0.20046	T	0.44	.	2.601	0.04867	0.0:0.4561:0.3162:0.2277	rs1769774	218	O95521	PRAM1_HUMAN	S	218	ENSP00000332134:P218S	ENSP00000332134:P218S	P	+	1	0	PRAMEF1	12777015	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.115000	0.10741	-0.146000	0.11274	-0.445000	0.05633	CCA	C|0.713;T|0.287	0.287	strong		0.393	PRAMEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005458.1	NM_023013	
FRRS1	391059	hgsc.bcm.edu	37	1	100181147	100181147	+	Missense_Mutation	SNP	T	T	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:100181147T>A	ENST00000414213.1	-	12	1919	c.1318A>T	c.(1318-1320)Agt>Tgt	p.S440C	FRRS1_ENST00000492943.1_5'UTR|FRRS1_ENST00000287474.5_Missense_Mutation_p.S440C			Q6ZNA5	FRRS1_HUMAN	ferric-chelate reductase 1	440	Cytochrome b561. {ECO:0000255|PROSITE- ProRule:PRU00242}.					integral component of membrane (GO:0016021)	ferric-chelate reductase activity (GO:0000293)|metal ion binding (GO:0046872)			breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(12)|pancreas(1)|skin(1)|urinary_tract(1)	26		all_epithelial(167;2.09e-06)|all_lung(203;0.000435)|Lung NSC(277;0.00201)		Epithelial(280;0.0718)|all cancers(265;0.126)|COAD - Colon adenocarcinoma(174;0.148)|Lung(183;0.206)		CTTACCCTACTCCAGCCTCCC	0.358																																					p.S440C		Atlas-SNP	.											FRRS1,NS,carcinoma,0,1	FRRS1	50	1	0			c.A1318T						scavenged	.						91.0	90.0	90.0					1																	100181147		2203	4300	6503	SO:0001583	missense	391059	exon12			CCCTACTCCAGCC	AK131302	CCDS30780.1	1p21.3	2009-11-30	2006-02-22	2006-02-22	ENSG00000156869	ENSG00000156869			27622	protein-coding gene	gene with protein product		611578	"""stromal cell derived factor receptor 2 homolog (mouse)"""	SDFR2			Standard	NM_001013660		Approved	SDR2	uc001dsh.1	Q6ZNA5	OTTHUMG00000010768	ENST00000414213.1:c.1318A>T	1.37:g.100181147T>A	ENSP00000393884:p.Ser440Cys	Somatic	320	0	0		WXS	Illumina HiSeq	Phase_I	241	4	0.0165975	NM_001013660	A6NLN7	Missense_Mutation	SNP	ENST00000414213.1	37		.	.	.	.	.	.	.	.	.	.	T	15.37	2.813893	0.50527	.	.	ENSG00000156869	ENST00000414213;ENST00000287474	.	.	.	5.47	5.47	0.80525	.	0.000000	0.85682	D	0.000000	T	0.77491	0.4138	M	0.87180	2.865	0.80722	D	1	D	0.76494	0.999	D	0.72625	0.978	T	0.82242	-0.0554	9	0.72032	D	0.01	-19.92	14.6634	0.68891	0.0:0.0:0.0:1.0	.	440	Q6ZNA5-2	.	C	440	.	ENSP00000287474:S440C	S	-	1	0	FRRS1	99953735	1.000000	0.71417	1.000000	0.80357	0.102000	0.19082	5.407000	0.66363	2.194000	0.70268	0.377000	0.23210	AGT	.	.	none		0.358	FRRS1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001013660	
FBLN2	2199	hgsc.bcm.edu	37	3	13612936	13612936	+	Missense_Mutation	SNP	A	A	G	rs3732666	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:13612936A>G	ENST00000295760.7	+	2	1150	c.1081A>G	c.(1081-1083)Agc>Ggc	p.S361G	FBLN2_ENST00000535798.1_Missense_Mutation_p.S387G|FBLN2_ENST00000404922.3_Missense_Mutation_p.S361G|FBLN2_ENST00000492059.1_Missense_Mutation_p.S361G	NM_001998.2	NP_001989.2	P98095	FBLN2_HUMAN	fibulin 2	361	N.|Subdomain NB (Cys-free).		S -> G (in dbSNP:rs3732666).		extracellular matrix organization (GO:0030198)|positive regulation of cell-substrate adhesion (GO:0010811)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	calcium ion binding (GO:0005509)|extracellular matrix binding (GO:0050840)|extracellular matrix structural constituent (GO:0005201)			haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(10)|ovary(3)|prostate(3)|urinary_tract(1)	24			UCEC - Uterine corpus endometrioid carcinoma (1;0.00416)			GCATGCACCGAGCCTGGGCAA	0.662													G|||	2341	0.467452	0.7587	0.2824	5008	,	,		16187	0.5496		0.1869	False		,,,				2504	0.409				p.S361G		Atlas-SNP	.											.	FBLN2	137	.	0			c.A1081G						PASS	.	G	GLY/SER,GLY/SER,GLY/SER	2822,1480		954,914,283	35.0	47.0	43.0		1081,1081,1081	1.9	0.0	3	dbSNP_107	43	1671,6801		179,1313,2744	no	missense,missense,missense	FBLN2	NM_001004019.1,NM_001165035.1,NM_001998.2	56,56,56	1133,2227,3027	GG,GA,AA		19.7238,34.4026,35.173	benign,benign,benign	361/1232,361/1232,361/1185	13612936	4493,8281	2151	4236	6387	SO:0001583	missense	2199	exon2			GCACCGAGCCTGG	X82494	CCDS46761.1, CCDS46762.1	3p25-p24	2010-06-15			ENSG00000163520	ENSG00000163520		"""Fibulins"""	3601	protein-coding gene	gene with protein product		135821				7806230	Standard	NM_001165035		Approved		uc011ava.2	P98095	OTTHUMG00000155437	ENST00000295760.7:c.1081A>G	3.37:g.13612936A>G	ENSP00000295760:p.Ser361Gly	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	87	50	0.574713	NM_001998	B7Z9C5|Q8IUI0|Q8IUI1	Missense_Mutation	SNP	ENST00000295760.7	37	CCDS46762.1	913	0.41804029304029305	342	0.6951219512195121	98	0.27071823204419887	340	0.5944055944055944	133	0.17546174142480211	G	5.775	0.327445	0.10956	0.655974	0.197238	ENSG00000163520	ENST00000535798;ENST00000404922;ENST00000295760;ENST00000492059	T;T;T;T	0.79554	-1.28;-1.23;-1.19;-1.23	4.82	1.9	0.25705	.	2.938210	0.00827	N	0.001632	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	0.42949	-0.9421	9	0.20519	T	0.43	.	4.8974	0.13757	0.2617:0.1534:0.5849:0.0	rs3732666;rs3732666	361;361;387	P98095;P98095-2;F5H1F3	FBLN2_HUMAN;.;.	G	387;361;361;361	ENSP00000445705:S387G;ENSP00000384169:S361G;ENSP00000295760:S361G;ENSP00000420042:S361G	ENSP00000295760:S361G	S	+	1	0	FBLN2	13587937	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.151000	0.10175	-0.056000	0.13221	-0.124000	0.14976	AGC	A|0.603;G|0.397	0.397	strong		0.662	FBLN2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000340083.3	NM_001004019	
OR52R1	119695	hgsc.bcm.edu	37	11	4825225	4825225	+	Missense_Mutation	SNP	A	A	G	rs7941731	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:4825225A>G	ENST00000356069.2	-	1	385	c.386T>C	c.(385-387)aTc>aCc	p.I129T	OR52R1_ENST00000380382.1_Missense_Mutation_p.I208T|MMP26_ENST00000477339.1_Intron|MMP26_ENST00000380390.1_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	70	0	0		WXS	Illumina HiSeq	Phase_I	76	16	0.210526	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	
KCTD1	284252	hgsc.bcm.edu	37	18	24035788	24035788	+	Silent	SNP	G	G	A	rs3755	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:24035788G>A	ENST00000408011.3	-	5	1252	c.693C>T	c.(691-693)agC>agT	p.S231S	KCTD1_ENST00000580059.1_Silent_p.S231S|KCTD1_ENST00000417602.1_Silent_p.S839S|KCTD1_ENST00000579973.1_Silent_p.S231S|KCTD1_ENST00000317932.7_Silent_p.S231S	NM_001136205.2	NP_001129677.1	Q719H9	KCTD1_HUMAN	potassium channel tetramerization domain containing 1	231					negative regulation of transcription, DNA-templated (GO:0045892)|protein homooligomerization (GO:0051260)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)			endometrium(2)|large_intestine(3)|lung(3)|ovary(1)|prostate(3)	12	all_cancers(21;0.00191)|Lung NSC(5;0.000698)|all_lung(6;0.0019)|Ovarian(20;0.0848)		Epithelial(2;7.8e-06)|OV - Ovarian serous cystadenocarcinoma(3;9.02e-06)|all cancers(3;3.37e-05)			GGACGTATTCGCTGAACTGGG	0.547													G|||	358	0.0714856	0.0772	0.0893	5008	,	,		16036	0.004		0.1511	False		,,,				2504	0.0389				p.S839S		Atlas-SNP	.											.	KCTD1	76	.	0			c.C2517T						PASS	.	G	,,	495,3911	230.1+/-244.4	28,439,1736	84.0	80.0	82.0		693,2517,693	-6.9	0.9	18	dbSNP_36	82	1311,7289	258.8+/-282.3	117,1077,3106	yes	coding-synonymous,coding-synonymous,coding-synonymous	KCTD1	NM_001136205.1,NM_001142730.1,NM_198991.2	,,	145,1516,4842	AA,AG,GG		15.2442,11.2347,13.8859	,,	231/258,839/866,231/258	24035788	1806,11200	2203	4300	6503	SO:0001819	synonymous_variant	284252	exon5			GTATTCGCTGAAC	AF542549	CCDS11888.1	18q11.2	2013-09-20	2013-06-20		ENSG00000134504	ENSG00000134504			18249	protein-coding gene	gene with protein product		613420	"""potassium channel tetramerisation domain containing 1"""	C18orf5			Standard	NM_001142730		Approved		uc010xbj.3	Q719H9	OTTHUMG00000131947	ENST00000408011.3:c.693C>T	18.37:g.24035788G>A		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	92	45	0.48913	NM_001142730	A8K1F5	Silent	SNP	ENST00000408011.3	37	CCDS11888.1																																																																																			G|0.889;A|0.111	0.111	strong		0.547	KCTD1-003	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000446265.1	XM_209091	
ITPR1	3708	hgsc.bcm.edu	37	3	4709131	4709131	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:4709131T>C	ENST00000443694.2	+	15	1739	c.1739T>C	c.(1738-1740)aTc>aCc	p.I580T	ITPR1_ENST00000456211.2_Missense_Mutation_p.I580T|ITPR1_ENST00000357086.4_Missense_Mutation_p.I595T|ITPR1_ENST00000423119.2_Missense_Mutation_p.I595T|ITPR1_ENST00000302640.8_Missense_Mutation_p.I580T|ITPR1_ENST00000544951.1_Intron|ITPR1_ENST00000354582.6_Missense_Mutation_p.I595T			Q14643	ITPR1_HUMAN	inositol 1,4,5-trisphosphate receptor, type 1	595					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|calcium ion transport (GO:0006816)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|negative regulation of calcium-mediated signaling (GO:0050849)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|post-embryonic development (GO:0009791)|regulation of insulin secretion (GO:0050796)|release of sequestered calcium ion into cytosol (GO:0051209)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|voluntary musculoskeletal movement (GO:0050882)	calcineurin complex (GO:0005955)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear inner membrane (GO:0005637)|nucleolus (GO:0005730)|platelet dense granule membrane (GO:0031088)|platelet dense tubular network (GO:0031094)|platelet dense tubular network membrane (GO:0031095)|postsynaptic density (GO:0014069)|sarcoplasmic reticulum (GO:0016529)	calcium channel inhibitor activity (GO:0019855)|calcium ion transmembrane transporter activity (GO:0015085)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|intracellular ligand-gated calcium channel activity (GO:0005218)|phosphatidylinositol binding (GO:0035091)			NS(1)|autonomic_ganglia(1)|breast(10)|endometrium(15)|kidney(6)|large_intestine(27)|liver(1)|lung(27)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|urinary_tract(2)	106				Epithelial(13;0.0199)|OV - Ovarian serous cystadenocarcinoma(96;0.0361)|all cancers(10;0.0982)	Caffeine(DB00201)	GAAGACACTATCACTGCCCTG	0.468																																					p.I595T		Atlas-SNP	.											ITPR1,NS,carcinoma,-1,1	ITPR1	659	1	0			c.T1784C						scavenged	.						67.0	62.0	63.0					3																	4709131		1944	4173	6117	SO:0001583	missense	3708	exon18			ACACTATCACTGC	D26070	CCDS46740.1, CCDS46740.2, CCDS54550.1, CCDS54551.1	3p26.1	2014-06-12	2011-04-28			ENSG00000150995		"""Ion channels / Inositol triphosphate receptors"""	6180	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 94"""	147265	"""spinocerebellar ataxia 15"", ""spinocerebellar ataxia 16"", ""spinocerebellar ataxia 29"""	SCA15, SCA16, SCA29		7945203, 7500840, 17590087, 17932120, 22986007	Standard	NM_001099952		Approved	Insp3r1, IP3R1, ACV, PPP1R94	uc003bqc.3	Q14643		ENST00000443694.2:c.1739T>C	3.37:g.4709131T>C	ENSP00000401671:p.Ile580Thr	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	117	2	0.017094	NM_001099952	E7EPX7|E9PDE9|Q14660|Q99897	Missense_Mutation	SNP	ENST00000443694.2	37	CCDS54551.1	.	.	.	.	.	.	.	.	.	.	T	22.1	4.245160	0.80024	.	.	ENSG00000150995	ENST00000356617;ENST00000302640;ENST00000354582;ENST00000423119;ENST00000357086;ENST00000456211;ENST00000443694	D;D;D;D;D;D	0.91295	-2.82;-2.82;-2.82;-2.82;-2.82;-2.82	4.74	4.74	0.60224	Intracellular calcium-release channel (1);	0.000000	0.85682	D	0.000000	D	0.95604	0.8571	M	0.86864	2.845	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;1.0;0.994	D	0.96349	0.9257	10	0.87932	D	0	.	14.4311	0.67251	0.0:0.0:0.0:1.0	.	580;595;595	E7EPX7;Q14643;G5E9P1	.;ITPR1_HUMAN;.	T	595;580;595;595;595;580;580	ENSP00000306253:I580T;ENSP00000346595:I595T;ENSP00000405934:I595T;ENSP00000349597:I595T;ENSP00000397885:I580T;ENSP00000401671:I580T	ENSP00000306253:I580T	I	+	2	0	ITPR1	4684131	1.000000	0.71417	0.996000	0.52242	0.920000	0.55202	7.792000	0.85828	1.994000	0.58287	0.454000	0.30748	ATC	.	.	none		0.468	ITPR1-004	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337982.3	NM_002222	
PDE6C	5146	hgsc.bcm.edu	37	10	95372764	95372764	+	Silent	SNP	C	C	T	rs12781149	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:95372764C>T	ENST00000371447.3	+	1	420	c.282C>T	c.(280-282)gaC>gaT	p.D94D		NM_006204.3	NP_006195.3	P51160	PDE6C_HUMAN	phosphodiesterase 6C, cGMP-specific, cone, alpha prime	94	GAF 1.				phototransduction, visible light (GO:0007603)|retinal cone cell development (GO:0046549)|visual perception (GO:0007601)	plasma membrane (GO:0005886)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|cGMP binding (GO:0030553)|metal ion binding (GO:0046872)			breast(3)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(12)|ovary(2)|pancreas(1)|skin(4)|upper_aerodigestive_tract(1)	42		Colorectal(252;0.123)			Caffeine(DB00201)	TCCAGGCTGACCGCTGCAGCA	0.652													C|||	215	0.0429313	0.0053	0.0793	5008	,	,		17246	0.001		0.0885	False		,,,				2504	0.0644				p.D94D		Atlas-SNP	.											.	PDE6C	97	.	0			c.C282T						PASS	.	C		106,4300	83.4+/-121.9	0,106,2097	34.0	35.0	35.0		282	1.4	1.0	10	dbSNP_121	35	832,7768	192.8+/-238.7	38,756,3506	no	coding-synonymous	PDE6C	NM_006204.3		38,862,5603	TT,TC,CC		9.6744,2.4058,7.2121		94/859	95372764	938,12068	2203	4300	6503	SO:0001819	synonymous_variant	5146	exon1			GGCTGACCGCTGC	U31973	CCDS7429.1	10q24	2013-01-23			ENSG00000095464	ENSG00000095464	3.1.4.17	"""Phosphodiesterases"""	8787	protein-coding gene	gene with protein product		600827					Standard	NM_006204		Approved	PDEA2, ACHM5, COD4	uc001kiu.4	P51160	OTTHUMG00000018775	ENST00000371447.3:c.282C>T	10.37:g.95372764C>T		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	39	21	0.538462	NM_006204	A6NCR6|Q5VY29	Silent	SNP	ENST00000371447.3	37	CCDS7429.1																																																																																			C|0.939;T|0.061	0.061	strong		0.652	PDE6C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049437.1	NM_006204	
PIGG	54872	hgsc.bcm.edu	37	4	517376	517376	+	Silent	SNP	T	T	C	rs7666226	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:517376T>C	ENST00000453061.2	+	9	1849	c.1743T>C	c.(1741-1743)ctT>ctC	p.L581L	PIGG_ENST00000383028.4_Silent_p.L448L|PIGG_ENST00000296306.7_3'UTR|PIGG_ENST00000504346.1_Silent_p.L492L|PIGG_ENST00000310340.5_Silent_p.L573L	NM_001127178.1	NP_001120650.1	Q5H8A4	PIGG_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class G	581					C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|GPI anchor biosynthetic process (GO:0006506)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	CP2 mannose-ethanolamine phosphotransferase activity (GO:0051267)|phosphotransferase activity, for other substituted phosphate groups (GO:0016780)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(5)|lung(16)|ovary(3)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	39						GGTACTTCCTTGTGAACACCC	0.572													C|||	1123	0.224241	0.3956	0.0994	5008	,	,		19532	0.2202		0.1312	False		,,,				2504	0.181				p.L581L		Atlas-SNP	.											.	PIGG	86	.	0			c.T1743C						PASS	.	C	,	1505,2901	676.4+/-403.2	271,963,969	140.0	135.0	137.0		1743,1719	-11.3	0.0	4	dbSNP_116	137	1050,7550	771.1+/-407.7	69,912,3319	no	coding-synonymous,coding-synonymous	PIGG	NM_001127178.1,NM_017733.3	,	340,1875,4288	CC,CT,TT		12.2093,34.158,19.6448	,	581/984,573/976	517376	2555,10451	2203	4300	6503	SO:0001819	synonymous_variant	54872	exon9			CTTCCTTGTGAAC		CCDS3336.1, CCDS46992.1, CCDS75080.1, CCDS75081.1, CCDS75082.1, CCDS75083.1	4p16.3	2013-02-26	2006-06-28		ENSG00000174227	ENSG00000174227		"""Phosphatidylinositol glycan anchor biosynthesis"""	25985	protein-coding gene	gene with protein product			"""phosphatidylinositol glycan, class G"""			15632136	Standard	XM_005272287		Approved	FLJ20265, GPI7, LAS21	uc003gak.4	Q5H8A4	OTTHUMG00000112457	ENST00000453061.2:c.1743T>C	4.37:g.517376T>C		Somatic	192	1	0.00520833		WXS	Illumina HiSeq	Phase_I	142	80	0.56338	NM_001127178	B4DKC7|Q2TAK5|Q6UX31|Q7L5Y4|Q8N866|Q8NCC9|Q96SY9|Q9BVT7|Q9NXG5	Silent	SNP	ENST00000453061.2	37	CCDS46992.1																																																																																			T|0.780;C|0.220	0.220	strong		0.572	PIGG-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000357494.1	NM_017733	
AXDND1	126859	hgsc.bcm.edu	37	1	179504043	179504043	+	Missense_Mutation	SNP	C	C	G	rs6658180	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:179504043C>G	ENST00000367618.3	+	25	3364	c.2977C>G	c.(2977-2979)Caa>Gaa	p.Q993E		NM_144696.4	NP_653297.3	Q5T1B0	AXDN1_HUMAN	axonemal dynein light chain domain containing 1	993	Glu-rich.		Q -> E (in dbSNP:rs6658180).							NS(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(27)|ovary(1)|pancreas(1)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)	59						agaagaacaacaagaagaaga	0.323													C|||	1910	0.38139	0.2496	0.4035	5008	,	,		17574	0.4256		0.4115	False		,,,				2504	0.4673				p.Q993E		Atlas-SNP	.											.	AXDND1	142	.	0			c.C2977G						PASS	.	C	GLU/GLN	1137,3151		169,799,1176	50.0	54.0	53.0		2977	-4.9	0.0	1	dbSNP_116	53	3113,5457		585,1943,1757	yes	missense	AXDND1	NM_144696.4	29	754,2742,2933	GG,GC,CC		36.3244,26.5159,33.0534	benign	993/1013	179504043	4250,8608	2144	4285	6429	SO:0001583	missense	126859	exon25			GAACAACAAGAAG	BX647935	CCDS30948.1	1q25.2	2011-02-18	2011-02-18	2011-02-18	ENSG00000162779	ENSG00000162779			26564	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 125"""	C1orf125		14702039	Standard	NM_144696		Approved	FLJ32940	uc001gmo.3	Q5T1B0	OTTHUMG00000035266	ENST00000367618.3:c.2977C>G	1.37:g.179504043C>G	ENSP00000356590:p.Gln993Glu	Somatic	243	0	0		WXS	Illumina HiSeq	Phase_I	185	92	0.497297	NM_144696	Q6AWB2|Q96LJ3|Q96M01	Missense_Mutation	SNP	ENST00000367618.3	37	CCDS30948.1	825	0.37774725274725274	103	0.20934959349593496	157	0.43370165745856354	263	0.4597902097902098	302	0.39841688654353563	C	0.003	-2.521003	0.00149	0.265159	0.363244	ENSG00000162779	ENST00000367618;ENST00000360322;ENST00000434088	T;T	0.15256	2.44;2.46	2.47	-4.94	0.03057	.	2.583780	0.01561	N	0.020132	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	0.43310	-0.9399	9	0.10111	T	0.7	-6.7708	0.9261	0.01325	0.4226:0.1628:0.2568:0.1578	rs6658180;rs6658180	877;993	E9PCJ4;Q5T1B0	.;AXDN1_HUMAN	E	993;877;853	ENSP00000356590:Q993E;ENSP00000391716:Q853E	ENSP00000353471:Q877E	Q	+	1	0	AXDND1	177770666	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-1.633000	0.02022	-1.372000	0.02137	-1.284000	0.01376	CAA	C|0.671;G|0.329	0.329	strong		0.323	AXDND1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085312.1	NM_144696	
NEK4	6787	hgsc.bcm.edu	37	3	52800284	52800284	+	Silent	SNP	T	T	C	rs2230535	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:52800284T>C	ENST00000233027.5	-	3	670	c.468A>G	c.(466-468)ttA>ttG	p.L156L	NEK4_ENST00000383721.4_Silent_p.L156L|NEK4_ENST00000535191.1_Silent_p.L67L	NM_001193533.1|NM_003157.4	NP_001180462.1|NP_003148.2	P51957	NEK4_HUMAN	NIMA-related kinase 4	156	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				mitotic nuclear division (GO:0007067)|protein phosphorylation (GO:0006468)	nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(9)|lung(10)	26				BRCA - Breast invasive adenocarcinoma(193;7.44e-05)|Kidney(197;0.000711)|KIRC - Kidney renal clear cell carcinoma(197;0.00086)|OV - Ovarian serous cystadenocarcinoma(275;0.0513)		AGTGGTTCTCTAACACTCGGG	0.428													T|||	1664	0.332268	0.1475	0.4597	5008	,	,		18334	0.4296		0.4195	False		,,,				2504	0.3016				p.L156L		Atlas-SNP	.											.	NEK4	51	.	0			c.A468G						PASS	.	T	,	781,3625	317.2+/-295.0	69,643,1491	255.0	210.0	225.0		201,468	-8.0	0.7	3	dbSNP_98	225	3517,5083	512.6+/-378.0	738,2041,1521	no	coding-synonymous,coding-synonymous	NEK4	NM_001193533.1,NM_003157.4	,	807,2684,3012	CC,CT,TT		40.8953,17.7258,33.0463	,	67/753,156/842	52800284	4298,8708	2203	4300	6503	SO:0001819	synonymous_variant	6787	exon3			GTTCTCTAACACT	L20321	CCDS2863.1, CCDS54593.1	3p21.1	2012-11-15	2012-11-15	2002-05-10	ENSG00000114904	ENSG00000114904	2.7.11.1		11399	protein-coding gene	gene with protein product	"""serine/threonine protein kinase-2"""	601959	"""serine/threonine kinase 2"", ""NIMA (never in mitosis gene a)-related kinase 4"""	STK2		8208544	Standard	NM_001193533		Approved	NRK2, pp12301	uc003dfq.4	P51957	OTTHUMG00000158836	ENST00000233027.5:c.468A>G	3.37:g.52800284T>C		Somatic	309	1	0.00323625		WXS	Illumina HiSeq	Phase_I	272	271	0.996324	NM_003157	A5YM70|B2R633|B7Z200|Q6P576	Silent	SNP	ENST00000233027.5	37	CCDS2863.1																																																																																			T|0.652;C|0.348	0.348	strong		0.428	NEK4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000352386.2	NM_003157	
GSDMC	56169	hgsc.bcm.edu	37	8	130774897	130774897	+	Silent	SNP	T	T	C	rs17190932	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:130774897T>C	ENST00000276708.4	-	5	1532	c.651A>G	c.(649-651)agA>agG	p.R217R		NM_031415.2	NP_113603.1	Q9BYG8	GSDMC_HUMAN	gasdermin C	217						cytoplasm (GO:0005737)|microtubule organizing center (GO:0005815)|mitochondrion (GO:0005739)		p.R217R(1)		autonomic_ganglia(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(5)|ovary(2)|pancreas(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)	26						CCAGCTGCTTTCTCTTATAAG	0.527													T|||	472	0.0942492	0.0287	0.2003	5008	,	,		20432	0.0268		0.1899	False		,,,				2504	0.0787				p.R217R		Atlas-SNP	.											GSDMC,NS,carcinoma,0,1	GSDMC	71	1	1	Substitution - coding silent(1)	stomach(1)	c.A651G						scavenged	.	T		244,4162	141.5+/-176.9	12,220,1971	257.0	230.0	239.0		651	2.9	0.2	8	dbSNP_123	239	1678,6922	306.9+/-308.1	181,1316,2803	no	coding-synonymous	GSDMC	NM_031415.2		193,1536,4774	CC,CT,TT		19.5116,5.5379,14.7778		217/509	130774897	1922,11084	2203	4300	6503	SO:0001819	synonymous_variant	56169	exon5			CTGCTTTCTCTTA	AB042405	CCDS6360.1	8q24.21	2014-05-14	2008-07-31	2008-07-31	ENSG00000147697	ENSG00000147697			7151	protein-coding gene	gene with protein product		608384	"""melanoma-derived leucine zipper, extra-nuclear factor"""	MLZE		17350798	Standard	NM_031415		Approved		uc003ysr.3	Q9BYG8	OTTHUMG00000164851	ENST00000276708.4:c.651A>G	8.37:g.130774897T>C		Somatic	82	1	0.0121951		WXS	Illumina HiSeq	Phase_I	67	19	0.283582	NM_031415	Q5XKF3|Q6P494	Silent	SNP	ENST00000276708.4	37	CCDS6360.1																																																																																			C|0.125;N|0.000	0.125	strong		0.527	GSDMC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380586.1		
FCRLA	84824	hgsc.bcm.edu	37	1	161683136	161683136	+	Missense_Mutation	SNP	G	G	A	rs11746	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:161683136G>A	ENST00000236938.6	+	5	1339	c.1097G>A	c.(1096-1098)cGg>cAg	p.R366Q	FCRLA_ENST00000367953.3_Missense_Mutation_p.R355Q|FCRLA_ENST00000367949.2_Missense_Mutation_p.R182Q|FCRLA_ENST00000349527.4_Missense_Mutation_p.R254Q|FCRLA_ENST00000350710.3_Missense_Mutation_p.R131Q|FCRLA_ENST00000309691.6_Missense_Mutation_p.R260Q|FCRLA_ENST00000546024.1_Missense_Mutation_p.R277Q|FCRLA_ENST00000540926.1_Missense_Mutation_p.R355Q|FCRLA_ENST00000294796.4_Missense_Mutation_p.R215Q|FCRLA_ENST00000367959.2_Missense_Mutation_p.R372Q|FCRLA_ENST00000470841.1_3'UTR|FCRLA_ENST00000367957.2_Missense_Mutation_p.R226Q|FCRLA_ENST00000540521.1_Missense_Mutation_p.R232Q|FCRLA_ENST00000367950.1_Missense_Mutation_p.R142Q	NM_032738.3	NP_116127.3	Q7L513	FCRLA_HUMAN	Fc receptor-like A	349					cell differentiation (GO:0030154)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)		p.R349Q(1)		breast(1)|kidney(12)|large_intestine(4)|lung(13)|prostate(1)|skin(2)|stomach(1)	34	all_cancers(52;2.55e-15)|all_hematologic(112;0.0359)		BRCA - Breast invasive adenocarcinoma(70;0.00301)			TCTGGCCACCGGAAGCCTGGG	0.463													G|||	1488	0.297125	0.0469	0.3444	5008	,	,		18540	0.2371		0.5129	False		,,,				2504	0.4417				p.R372Q		Atlas-SNP	.											FCRLA,NS,carcinoma,0,1	FCRLA	101	1	1	Substitution - Missense(1)	stomach(1)	c.G1115A						PASS	.	G	GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG	533,3873	241.5+/-251.9	40,453,1710	70.0	66.0	67.0		1115,830,695,392,677,545,1097	-3.4	0.0	1	dbSNP_52	67	4144,4456	564.3+/-388.3	985,2174,1141	yes	missense,missense,missense,missense,missense,missense,missense	FCRLA	NM_001184866.1,NM_001184867.1,NM_001184870.1,NM_001184871.1,NM_001184872.1,NM_001184873.1,NM_032738.3	43,43,43,43,43,43,43	1025,2627,2851	AA,AG,GG		48.186,12.0971,35.9603	benign,benign,benign,benign,benign,benign,benign	372/383,277/288,232/243,131/142,226/237,182/193,366/377	161683136	4677,8329	2203	4300	6503	SO:0001583	missense	84824	exon6			GCCACCGGAAGCC	AF531423	CCDS30926.1, CCDS53415.1, CCDS53416.1, CCDS53417.1, CCDS53418.1, CCDS53419.1, CCDS53420.1	1q23.3	2014-01-28	2006-09-26	2006-09-26	ENSG00000132185	ENSG00000132185		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	18504	protein-coding gene	gene with protein product		606891	"""Fc receptor-like and mucin-like 1"""	FCRLM1		11754007	Standard	NM_001184866		Approved	MGC4595, FCRLc2, FCRLb, FCRLc1, FCRLd, FCRLe, FCRL, FCRLa, FREB, FCRLX	uc001gbe.3	Q7L513	OTTHUMG00000034537	ENST00000236938.6:c.1097G>A	1.37:g.161683136G>A	ENSP00000236938:p.Arg366Gln	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	99	98	0.989899	NM_001184866	A0N0M1|A6NC03|A6NL20|F5H720|F8W743|G3V1J2|Q5VXA1|Q5VXA2|Q5VXA3|Q5VXA4|Q5VXB0|Q5VXB1|Q8NEW4|Q8WXH3|Q96PC6|Q96PJ0|Q96PJ1|Q96PJ2|Q96PJ4|Q9BR57	Missense_Mutation	SNP	ENST00000236938.6	37	CCDS30926.1	690	0.3159340659340659	27	0.054878048780487805	135	0.3729281767955801	148	0.25874125874125875	380	0.5013192612137203	G	6.278	0.419487	0.11928	0.120971	0.48186	ENSG00000132185	ENST00000236938;ENST00000367959;ENST00000546024;ENST00000540521;ENST00000367949;ENST00000350710;ENST00000540926;ENST00000367957;ENST00000349527;ENST00000309691;ENST00000294796;ENST00000367953;ENST00000367950	T;T;T;T;T;T;T;T;T;T;T;T;T	0.44881	0.91;0.91;0.91;0.91;0.91;0.91;0.91;0.91;0.91;0.91;0.91;0.91;0.91	5.23	-3.37	0.04898	.	0.909229	0.09180	N	0.837550	T	0.07188	0.0182	N	0.14661	0.345	0.80722	P	0.0	B;B;B;B;B;B;B	0.25235	0.003;0.121;0.087;0.052;0.032;0.021;0.009	B;B;B;B;B;B;B	0.15870	0.001;0.01;0.014;0.004;0.005;0.004;0.006	T	0.25882	-1.0119	9	0.25751	T	0.34	.	7.078	0.25215	0.3066:0.0:0.4801:0.2133	rs11746;rs1105125;rs3202905;rs17413841;rs17850109;rs52825965;rs56459424;rs11746	131;182;232;226;277;372;366	F8W743;A6NL20;F5H720;Q5VXB1;G3V1J2;A6NC03;Q7L513-9	.;.;.;.;.;.;.	Q	366;372;277;232;182;131;355;226;254;260;215;355;142	ENSP00000236938:R366Q;ENSP00000356936:R372Q;ENSP00000439838:R277Q;ENSP00000442870:R232Q;ENSP00000356926:R182Q;ENSP00000344808:R131Q;ENSP00000446380:R355Q;ENSP00000356934:R226Q;ENSP00000294798:R254Q;ENSP00000309596:R260Q;ENSP00000294796:R215Q;ENSP00000356930:R355Q;ENSP00000356927:R142Q	ENSP00000236938:R366Q	R	+	2	0	FCRLA	159949760	0.000000	0.05858	0.003000	0.11579	0.223000	0.24884	-0.770000	0.04705	-0.846000	0.04174	-0.880000	0.02959	CGG	G|0.661;A|0.339	0.339	strong		0.463	FCRLA-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083574.1	NM_032738	
MYOF	26509	hgsc.bcm.edu	37	10	95082882	95082882	+	Silent	SNP	G	G	A	rs34048939	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:95082882G>A	ENST00000359263.4	-	48	5408	c.5409C>T	c.(5407-5409)gaC>gaT	p.D1803D	MYOF_ENST00000358334.5_Silent_p.D1790D|MYOF_ENST00000371502.4_Silent_p.D1793D|MYOF_ENST00000485212.1_5'Flank|MYOF_ENST00000371501.4_Silent_p.D1803D	NM_013451.3	NP_038479.1	Q9NZM1	MYOF_HUMAN	myoferlin	1803					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)			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						TGCTTTTCTCGTCCAAGATAA	0.468													G|||	140	0.0279553	0.0098	0.049	5008	,	,		21093	0.0		0.0765	False		,,,				2504	0.0164				p.D1803D		Atlas-SNP	.											.	MYOF	177	.	0			c.C5409T						PASS	.	G	,	78,3876		2,74,1901	304.0	285.0	291.0		5409,5370	-3.8	1.0	10	dbSNP_126	291	533,7797		21,491,3653	no	coding-synonymous,coding-synonymous	MYOF	NM_013451.3,NM_133337.2	,	23,565,5554	AA,AG,GG		6.3986,1.9727,4.9739	,	1803/2062,1790/2049	95082882	611,11673	1977	4165	6142	SO:0001819	synonymous_variant	26509	exon48			TTTCTCGTCCAAG	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.5409C>T	10.37:g.95082882G>A		Somatic	241	1	0.00414938		WXS	Illumina HiSeq	Phase_I	172	88	0.511628	NM_013451	B3KQN5|Q5VWW2|Q5VWW3|Q5VWW4|Q5VWW5|Q7Z642|Q8IWH0|Q9HBU3|Q9NZM0|Q9ULL3|Q9Y4U4	Silent	SNP	ENST00000359263.4	37	CCDS41551.1																																																																																			G|0.958;A|0.042	0.042	strong		0.468	MYOF-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000049423.2	NM_013451	
MYO3B	140469	hgsc.bcm.edu	37	2	171073887	171073887	+	Silent	SNP	G	G	A	rs2161916	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:171073887G>A	ENST00000408978.4	+	6	728	c.585G>A	c.(583-585)ccG>ccA	p.P195P	MYO3B_ENST00000602629.1_3'UTR|MYO3B_ENST00000334231.6_Silent_p.P204P|MYO3B_ENST00000409044.3_Silent_p.P195P	NM_138995.4	NP_620482.3	Q8WXR4	MYO3B_HUMAN	myosin IIIB	195	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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						TTGGCACCCCGTTCTGGATGG	0.433													A|||	2888	0.576677	0.6316	0.4179	5008	,	,		19832	0.5714		0.5636	False		,,,				2504	0.6339				p.P195P		Atlas-SNP	.											.	MYO3B	320	.	0			c.G585A						PASS	.	A	,,	2426,1418		753,920,249	226.0	221.0	222.0		585,585,585	-7.8	0.5	2	dbSNP_96	222	4542,3728		1261,2020,854	no	coding-synonymous,coding-synonymous,coding-synonymous	MYO3B	NM_001083615.2,NM_001171642.1,NM_138995.3	,,	2014,2940,1103	AA,AG,GG		45.0786,36.8887,42.4798	,,	195/1315,195/1276,195/1342	171073887	6968,5146	1922	4135	6057	SO:0001819	synonymous_variant	140469	exon6			CACCCCGTTCTGG		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.585G>A	2.37:g.171073887G>A		Somatic	271	0	0		WXS	Illumina HiSeq	Phase_I	219	106	0.484018	NM_001083615	B8ZZR2|Q53QE1|Q53T08|Q8IX64|Q8IX65|Q8IX66|Q8IX67|Q8IX68|Q96N94	Silent	SNP	ENST00000408978.4	37	CCDS42773.1	1227	0.5618131868131868	290	0.5894308943089431	170	0.4696132596685083	327	0.5716783216783217	440	0.5804749340369393	A	7.686	0.690037	0.15039	0.631113	0.549214	ENSG00000071909	ENST00000442690	.	.	.	6.06	-7.85	0.01192	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999954	.	.	.	.	.	.	T	0.04178	-1.0971	3	.	.	.	.	12.0644	0.53580	0.1929:0.4715:0.3356:0.0	rs2161916;rs17496561;rs58706986;rs2161916	.	.	.	I	195	.	.	V	+	1	0	MYO3B	170782133	0.000000	0.05858	0.468000	0.27192	0.841000	0.47740	-1.854000	0.01664	-2.287000	0.00669	-0.254000	0.11334	GTT	G|0.433;A|0.567	0.567	strong		0.433	MYO3B-004	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333410.1		
OGFOD3	79701	hgsc.bcm.edu	37	17	80352303	80352303	+	Intron	SNP	G	G	A	rs62079523	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:80352303G>A	ENST00000313056.5	-	9	975				OGFOD3_ENST00000578287.1_5'Flank|OGFOD3_ENST00000329197.5_Missense_Mutation_p.P314S	NM_024648.2|NM_175902.4	NP_078924.1|NP_787098.3	Q6PK18	OGFD3_HUMAN	2-oxoglutarate and iron-dependent oxygenase domain containing 3							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)										CCCCTCTCGGGCGGGTGGTGA	0.547													-|||	938	0.1873	0.1543	0.1974	5008	,	,		18469	0.003		0.325	False		,,,				2504	0.273				p.P314S		Atlas-SNP	.											.	.	.	.	0			c.C940T						PASS	.	G	,SER/PRO	845,3561	334.7+/-303.5	85,675,1443	160.0	148.0	152.0		,940	-0.6	0.0	17	dbSNP_129	152	2997,5603	464.6+/-366.3	533,1931,1836	yes	intron,missense	C17orf101	NM_024648.2,NM_175902.4	,74	618,2606,3279	AA,AG,GG		34.8488,19.1784,29.5402	,	,314/332	80352303	3842,9164	2203	4300	6503	SO:0001627	intron_variant	79701	exon9			TCTCGGGCGGGTG	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.824-1893C>T	17.37:g.80352303G>A		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	71	32	0.450704	NM_175902	C9JDC8|Q8IZ37|Q9H6J2	Missense_Mutation	SNP	ENST00000313056.5	37	CCDS11811.1	406	0.1858974358974359	80	0.16260162601626016	77	0.212707182320442	1	0.0017482517482517483	248	0.32717678100263853	G	7.804	0.714279	0.15306	0.191784	0.348488	ENSG00000181396	ENST00000329197	T	0.33438	1.41	0.894	-0.635	0.11512	.	0.154371	0.43747	D	0.000533	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	P	0.38800	0.648	B	0.31290	0.127	T	0.44802	-0.9304	8	0.59425	D	0.04	.	3.6609	0.08238	0.0:0.0:0.5663:0.4337	rs62079523	314	Q6PK18-2	.	S	314	ENSP00000330075:P314S	ENSP00000330075:P314S	P	-	1	0	C17orf101	77945592	0.000000	0.05858	0.002000	0.10522	0.013000	0.08279	-0.380000	0.07427	-0.123000	0.11745	0.420000	0.28162	CCC	G|0.728;A|0.272	0.272	strong		0.547	OGFOD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442895.1	NM_175902	
CCDC64B	146439	hgsc.bcm.edu	37	16	3085326	3085326	+	Missense_Mutation	SNP	C	C	T	rs71386699	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:3085326C>T	ENST00000572449.1	-	2	234	c.172G>A	c.(172-174)Gag>Aag	p.E58K	CCDC64B_ENST00000573514.1_5'Flank|RP11-473M20.5_ENST00000382225.3_RNA|CCDC64B_ENST00000389347.4_Missense_Mutation_p.E58K			A1A5D9	BICR2_HUMAN	coiled-coil domain containing 64B	58										breast(1)|endometrium(2)|large_intestine(1)	4						AGGTCTTTCTCCTTCTGCTGC	0.647													C|||	45	0.00898562	0.0023	0.0173	5008	,	,		11912	0.0		0.0258	False		,,,				2504	0.0041				p.E58K		Atlas-SNP	.											.	CCDC64B	19	.	0			c.G172A						PASS	.	C	LYS/GLU	12,3838		0,12,1913	10.0	11.0	11.0		172	5.1	1.0	16	dbSNP_130	11	204,8038		3,198,3920	yes	missense	CCDC64B	NM_001103175.1	56	3,210,5833	TT,TC,CC		2.4751,0.3117,1.7863	benign	58/509	3085326	216,11876	1925	4121	6046	SO:0001583	missense	146439	exon1			CTTTCTCCTTCTG	BC128602	CCDS45393.1	16p13.3	2008-07-04				ENSG00000162069			33584	protein-coding gene	gene with protein product							Standard	NM_001103175		Approved		uc002ctf.4	A1A5D9		ENST00000572449.1:c.172G>A	16.37:g.3085326C>T	ENSP00000459043:p.Glu58Lys	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	132	17	0.128788	NM_001103175	Q658L9	Missense_Mutation	SNP	ENST00000572449.1	37	CCDS45393.1	31	0.014194139194139194	2	0.0040650406504065045	9	0.024861878453038673	0	0.0	20	0.026385224274406333	c	21.5	4.163784	0.78226	0.003117	0.024751	ENSG00000162069	ENST00000389347	T	0.05513	3.43	5.08	5.08	0.68730	.	0.063133	0.64402	D	0.000009	T	0.08088	0.0202	M	0.71036	2.16	0.50813	D	0.999892	D	0.64830	0.994	D	0.63488	0.915	T	0.00044	-1.2219	10	0.62326	D	0.03	-26.8836	15.9724	0.80031	0.0:1.0:0.0:0.0	.	58	A1A5D9	BICR2_HUMAN	K	58	ENSP00000373998:E58K	ENSP00000373998:E58K	E	-	1	0	CCDC64B	3025327	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	6.271000	0.72569	2.361000	0.80049	0.457000	0.33378	GAG	C|0.985;T|0.015	0.015	strong		0.647	CCDC64B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436991.1		
PDCD11	22984	hgsc.bcm.edu	37	10	105205260	105205260	+	Missense_Mutation	SNP	A	A	G	rs151054853		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:105205260A>G	ENST00000369797.3	+	36	5664	c.5570A>G	c.(5569-5571)aAg>aGg	p.K1857R		NM_014976.1	NP_055791.1	Q14690	RRP5_HUMAN	programmed cell death 11	1857					mRNA processing (GO:0006397)|rRNA processing (GO:0006364)	cytosol (GO:0005829)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|transcription factor binding (GO:0008134)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(10)|lung(29)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	64		Colorectal(252;0.0747)|Breast(234;0.128)		Epithelial(162;7.21e-09)|all cancers(201;1.17e-08)|BRCA - Breast invasive adenocarcinoma(275;0.208)		GTCAAGGCCAAGGCCCTGGAG	0.587													A|||	1	0.000199681	0.0	0.0	5008	,	,		19265	0.0		0.001	False		,,,				2504	0.0				p.K1857R		Atlas-SNP	.											.	PDCD11	160	.	0			c.A5570G						PASS	.	A	ARG/LYS	1,4405	2.1+/-5.4	0,1,2202	115.0	96.0	102.0		5570	5.6	1.0	10	dbSNP_134	102	31,8569	19.8+/-62.0	0,31,4269	yes	missense	PDCD11	NM_014976.1	26	0,32,6471	GG,GA,AA		0.3605,0.0227,0.246	probably-damaging	1857/1872	105205260	32,12974	2203	4300	6503	SO:0001583	missense	22984	exon36			AGGCCAAGGCCCT	D80007	CCDS31276.1	10q24.32	2010-07-06			ENSG00000148843	ENSG00000148843			13408	protein-coding gene	gene with protein product		612333				10229231	Standard	XM_005269647		Approved	KIAA0185, ALG-4, RRP5	uc001kwy.1	Q14690	OTTHUMG00000018988	ENST00000369797.3:c.5570A>G	10.37:g.105205260A>G	ENSP00000358812:p.Lys1857Arg	Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	134	78	0.58209	NM_014976	Q2TA92|Q5W093|Q6P2J3|Q86VQ8|Q9H4P1	Missense_Mutation	SNP	ENST00000369797.3	37	CCDS31276.1	.	.	.	.	.	.	.	.	.	.	A	19.36	3.812885	0.70912	2.27E-4	0.003605	ENSG00000148843	ENST00000369797	T	0.22743	1.94	5.6	5.6	0.85130	Suppressor of forked (1);	0.087859	0.85682	D	0.000000	T	0.34077	0.0885	L	0.41027	1.25	0.58432	D	0.999993	D	0.89917	1.0	D	0.77557	0.99	T	0.03739	-1.1008	10	0.23302	T	0.38	-26.404	12.0882	0.53710	0.8159:0.1841:0.0:0.0	.	1857	Q14690	RRP5_HUMAN	R	1857	ENSP00000358812:K1857R	ENSP00000358812:K1857R	K	+	2	0	PDCD11	105195250	1.000000	0.71417	0.998000	0.56505	0.993000	0.82548	7.030000	0.76484	2.143000	0.66587	0.459000	0.35465	AAG	A|0.998;G|0.002	0.002	strong		0.587	PDCD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050151.1		
ZC3H7B	23264	hgsc.bcm.edu	37	22	41752747	41752747	+	Silent	SNP	G	G	A	rs12484074	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:41752747G>A	ENST00000352645.4	+	22	2873	c.2616G>A	c.(2614-2616)acG>acA	p.T872T	ZC3H7B_ENST00000351589.4_Silent_p.T872T	NM_017590.4	NP_060060.3	Q9UGR2	Z3H7B_HUMAN	zinc finger CCCH-type containing 7B	888					viral process (GO:0016032)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(11)|ovary(3)|prostate(3)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(3)	38						AGGTCTTCACGTCCGACAGTG	0.637													G|||	1102	0.220048	0.0537	0.5159	5008	,	,		16711	0.0764		0.2396	False		,,,				2504	0.363				p.T872T		Atlas-SNP	.											.	ZC3H7B	82	.	0			c.G2616A						PASS	.	G		364,4042	187.1+/-213.8	16,332,1855	123.0	104.0	110.0		2616	-7.9	0.3	22	dbSNP_120	110	2004,6596	351.5+/-328.3	251,1502,2547	yes	coding-synonymous	ZC3H7B	NM_017590.4		267,1834,4402	AA,AG,GG		23.3023,8.2615,18.207		872/978	41752747	2368,10638	2203	4300	6503	SO:0001819	synonymous_variant	23264	exon22			CTTCACGTCCGAC		CCDS14013.1	22q13.2	2013-01-10		2005-08-09	ENSG00000100403	ENSG00000100403		"""Zinc fingers, CCCH-type domain containing"", ""Tetratricopeptide (TTC) repeat domain containing"""	30869	protein-coding gene	gene with protein product						10470851, 11230166	Standard	NM_017590		Approved	RoXaN, FLJ13787, DKFZp434K0920, KIAA1031	uc003azw.4	Q9UGR2	OTTHUMG00000150969	ENST00000352645.4:c.2616G>A	22.37:g.41752747G>A		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	144	73	0.506944	NM_017590	A7YY88|B2RCA4|Q5TFX9|Q8TBT9|Q9H8B6|Q9UGQ9|Q9UGR0|Q9UGR1|Q9UK03|Q9UPW9	Silent	SNP	ENST00000352645.4	37	CCDS14013.1																																																																																			G|0.810;A|0.190	0.190	strong		0.637	ZC3H7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320696.1	NM_017590	
PAXIP1	22976	hgsc.bcm.edu	37	7	154760666	154760666	+	Silent	SNP	C	C	T	rs61752011	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	85	0	0		WXS	Illumina HiSeq	Phase_I	75	31	0.413333	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	
TET1	80312	hgsc.bcm.edu	37	10	70332312	70332312	+	Missense_Mutation	SNP	C	C	T	rs138684329		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:70332312C>T	ENST00000373644.4	+	2	426	c.217C>T	c.(217-219)Ctt>Ttt	p.L73F		NM_030625.2	NP_085128.2	Q8NFU7	TET1_HUMAN	tet methylcytosine dioxygenase 1	73					chromatin modification (GO:0016568)|DNA demethylation (GO:0080111)|inner cell mass cell differentiation (GO:0001826)|negative regulation of methylation-dependent chromatin silencing (GO:0090310)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein O-linked glycosylation (GO:0006493)|regulation of DNA methylation (GO:0044030)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	iron ion binding (GO:0005506)|methylcytosine dioxygenase activity (GO:0070579)|structure-specific DNA binding (GO:0043566)|zinc ion binding (GO:0008270)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(2)|ovary(5)|prostate(1)|upper_aerodigestive_tract(2)	21						AGTCAGAAGCCTTCTGACAAG	0.423													C|||	1	0.000199681	0.0008	0.0	5008	,	,		19958	0.0		0.0	False		,,,				2504	0.0				p.L73F		Atlas-SNP	.											.	TET1	255	.	0			c.C217T						PASS	.	C	PHE/LEU	1,4405	2.1+/-5.4	0,1,2202	71.0	77.0	75.0		217	4.3	1.0	10	dbSNP_134	75	2,8598	2.2+/-6.3	0,2,4298	yes	missense	TET1	NM_030625.2	22	0,3,6500	TT,TC,CC		0.0233,0.0227,0.0231	benign	73/2137	70332312	3,13003	2203	4300	6503	SO:0001583	missense	80312	exon2			AGAAGCCTTCTGA	AF430147	CCDS7281.1	10q21	2014-02-18	2011-09-30	2008-03-12	ENSG00000138336	ENSG00000138336			29484	protein-coding gene	gene with protein product	"""leukemia-associated protein with a CXXC domain"", ""ten-eleven translocation-1"""	607790	"""CXXC zinc finger 6"", ""tet oncogene 1"""	CXXC6		12124344, 12646957	Standard	NM_030625		Approved	LCX, KIAA1676, bA119F7.1	uc001jok.4	Q8NFU7	OTTHUMG00000018359	ENST00000373644.4:c.217C>T	10.37:g.70332312C>T	ENSP00000362748:p.Leu73Phe	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	97	43	0.443299	NM_030625	Q5VUP7|Q7Z6B6|Q8TCR1|Q9C0I7	Missense_Mutation	SNP	ENST00000373644.4	37	CCDS7281.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	14.23	2.472520	0.43942	2.27E-4	2.33E-4	ENSG00000138336	ENST00000373644	T	0.08984	3.03	5.24	4.32	0.51571	.	0.000000	0.44902	D	0.000417	T	0.05135	0.0137	N	0.19112	0.55	0.24628	N	0.993634	B	0.33748	0.423	B	0.31751	0.135	T	0.37865	-0.9687	10	0.27082	T	0.32	.	7.5134	0.27587	0.2035:0.7101:0.0:0.0864	.	73	Q8NFU7	TET1_HUMAN	F	73	ENSP00000362748:L73F	ENSP00000362748:L73F	L	+	1	0	TET1	70002318	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	2.411000	0.44600	1.168000	0.42723	0.563000	0.77884	CTT	C|1.000;T|0.000	0.000	strong		0.423	TET1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048354.1	NM_030625	
ABHD4	63874	hgsc.bcm.edu	37	14	23072905	23072905	+	Silent	SNP	C	C	G	rs540141952		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:23072905C>G	ENST00000428304.2	+	4	631	c.561C>G	c.(559-561)ccC>ccG	p.P187P	ABHD4_ENST00000544562.1_3'UTR	NM_022060.2	NP_071343.2	Q8TB40	ABHD4_HUMAN	abhydrolase domain containing 4	187					lipid catabolic process (GO:0016042)		hydrolase activity (GO:0016787)			breast(1)|central_nervous_system(1)|endometrium(5)|large_intestine(3)|lung(3)|prostate(1)	14	all_cancers(95;5.49e-05)			GBM - Glioblastoma multiforme(265;0.0153)		TCCGTGCACCCCCAGCCTGGG	0.557																																					p.P187P		Atlas-SNP	.											.	ABHD4	30	.	0			c.C561G						PASS	.						109.0	102.0	105.0					14																	23072905		2203	4300	6503	SO:0001819	synonymous_variant	63874	exon4			TGCACCCCCAGCC	AK022878	CCDS9572.1	14q11.1	2006-10-06			ENSG00000100439	ENSG00000100439		"""Abhydrolase domain containing"""	20154	protein-coding gene	gene with protein product							Standard	NM_022060		Approved	FLJ12816	uc001wgm.3	Q8TB40	OTTHUMG00000028686	ENST00000428304.2:c.561C>G	14.37:g.23072905C>G		Somatic	198	0	0		WXS	Illumina HiSeq	Phase_I	183	91	0.497268	NM_022060	B4DDH7|Q9H9E0	Silent	SNP	ENST00000428304.2	37	CCDS9572.1																																																																																			.	.	none		0.557	ABHD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071623.3		
GMIP	51291	hgsc.bcm.edu	37	19	19745962	19745962	+	Missense_Mutation	SNP	G	G	A	rs372547969		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:19745962G>A	ENST00000203556.4	-	16	1758	c.1621C>T	c.(1621-1623)Cgg>Tgg	p.R541W	GMIP_ENST00000586269.1_5'UTR|GMIP_ENST00000587238.1_Missense_Mutation_p.R515W|GMIP_ENST00000445806.2_Missense_Mutation_p.R512W	NM_016573.2	NP_057657.2	Q9P107	GMIP_HUMAN	GEM interacting protein	541					intracellular signal transduction (GO:0035556)|negative regulation of Rho GTPase activity (GO:0034259)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|intracellular (GO:0005622)	metal ion binding (GO:0046872)|Rho GTPase activator activity (GO:0005100)			breast(1)|endometrium(6)|kidney(1)|large_intestine(2)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	24						GCTGGGAGCCGCCTGTGTCCA	0.607																																					p.R541W		Atlas-SNP	.											.	GMIP	55	.	0			c.C1621T						PASS	.	G	TRP/ARG	0,4406		0,0,2203	29.0	31.0	30.0		1621	1.2	0.8	19		30	1,8599	1.2+/-3.3	0,1,4299	no	missense	GMIP	NM_016573.2	101	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	541/971	19745962	1,13005	2203	4300	6503	SO:0001583	missense	51291	exon16			GGAGCCGCCTGTG	AF132541	CCDS12408.1, CCDS74318.1	19p13.11	2011-09-07				ENSG00000089639		"""Rho GTPase activating proteins"""	24852	protein-coding gene	gene with protein product		609694				12093360, 16086184	Standard	XM_005259927		Approved	ARHGAP46	uc002nnd.3	Q9P107		ENST00000203556.4:c.1621C>T	19.37:g.19745962G>A	ENSP00000203556:p.Arg541Trp	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	94	6	0.0638298	NM_016573	A0AVN9|B7ZLZ0	Missense_Mutation	SNP	ENST00000203556.4	37	CCDS12408.1	.	.	.	.	.	.	.	.	.	.	G	16.31	3.086928	0.55861	0.0	1.16E-4	ENSG00000089639	ENST00000203556;ENST00000445806	T;T	0.23147	1.93;1.92	4.93	1.24	0.21308	.	0.558941	0.13840	N	0.359079	T	0.25901	0.0631	N	0.14661	0.345	0.35031	D	0.758787	D;D;D	0.71674	0.998;0.998;0.998	P;P;P	0.56648	0.803;0.702;0.803	T	0.41787	-0.9489	10	0.87932	D	0	-14.6413	11.5425	0.50675	0.0:0.0:0.2902:0.7098	.	512;515;541	E7ERB7;B7ZLZ0;Q9P107	.;.;GMIP_HUMAN	W	541;512	ENSP00000203556:R541W;ENSP00000397075:R512W	ENSP00000203556:R541W	R	-	1	2	GMIP	19606962	1.000000	0.71417	0.752000	0.31206	0.569000	0.35902	4.044000	0.57361	0.419000	0.25927	0.462000	0.41574	CGG	.	.	weak		0.607	GMIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460551.1	NM_016573	
LILRA2	11027	hgsc.bcm.edu	37	19	55086873	55086873	+	Nonsense_Mutation	SNP	G	G	A	rs575246367	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:55086873G>A	ENST00000251377.3	+	6	939	c.806G>A	c.(805-807)tGg>tAg	p.W269*	LILRB1_ENST00000448689.1_Intron|LILRA2_ENST00000251376.3_Nonsense_Mutation_p.W269*|LILRA2_ENST00000391737.1_Nonsense_Mutation_p.W257*|LILRB1_ENST00000396321.2_Intron|LILRA2_ENST00000391738.3_Nonsense_Mutation_p.W269*|LILRB1_ENST00000418536.2_Intron			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	204	0	0		WXS	Illumina HiSeq	Phase_I	198	4	0.020202	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		
PDE11A	50940	hgsc.bcm.edu	37	2	178528641	178528641	+	Missense_Mutation	SNP	G	G	C	rs61306957	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:178528641G>C	ENST00000286063.6	-	19	2916	c.2599C>G	c.(2599-2601)Cgg>Ggg	p.R867G	PDE11A_ENST00000409504.1_Missense_Mutation_p.R509G|PDE11A_ENST00000450799.2_Missense_Mutation_p.R58G|PDE11A_ENST00000449286.2_Missense_Mutation_p.R509G|PDE11A_ENST00000358450.4_Missense_Mutation_p.R617G|PDE11A_ENST00000389683.3_Missense_Mutation_p.R423G	NM_016953.3	NP_058649.3	Q9HCR9	PDE11_HUMAN	phosphodiesterase 11A	867	Catalytic. {ECO:0000250}.		R -> G (in dbSNP:rs61306957). {ECO:0000269|PubMed:16767104}.		blood coagulation (GO:0007596)|cAMP catabolic process (GO:0006198)|cGMP catabolic process (GO:0046069)|signal transduction (GO:0007165)	cytosol (GO:0005829)|perikaryon (GO:0043204)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|cAMP binding (GO:0030552)|cGMP binding (GO:0030553)|cGMP-stimulated cyclic-nucleotide phosphodiesterase activity (GO:0004118)|cyclic-nucleotide phosphodiesterase activity (GO:0004112)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(13)|lung(28)|ovary(4)|skin(3)|upper_aerodigestive_tract(3)	58			OV - Ovarian serous cystadenocarcinoma(117;0.00121)|Epithelial(96;0.00455)|all cancers(119;0.02)		Caffeine(DB00201)|Tadalafil(DB00820)	AGTTGCAACCGAGGCAGTTCA	0.453									Primary Pigmented Nodular Adrenocortical Disease, Familial				G|||	160	0.0319489	0.0393	0.0115	5008	,	,		18868	0.0109		0.0199	False		,,,				2504	0.0706				p.R867G		Atlas-SNP	.											.	PDE11A	283	.	0			c.C2599G	GRCh37	CM067442	PDE11A	M	rs61306957	PASS	.	G	GLY/ARG,GLY/ARG,GLY/ARG,GLY/ARG	190,4216	122.1+/-159.5	5,180,2018	114.0	100.0	104.0		1267,1849,1525,2599	4.1	1.0	2	dbSNP_129	104	149,8451	72.3+/-134.9	2,145,4153	yes	missense,missense,missense,missense	PDE11A	NM_001077196.1,NM_001077197.1,NM_001077358.1,NM_016953.3	125,125,125,125	7,325,6171	CC,CG,GG		1.7326,4.3123,2.6065	benign,benign,benign,benign	423/490,617/684,509/576,867/934	178528641	339,12667	2203	4300	6503	SO:0001583	missense	50940	exon19	Familial Cancer Database	iPPNAD, PPNAD1, incl. familial micronodular adrenocortical hyperplasia, PPNAD2	GCAACCGAGGCAG	AJ251509	CCDS33334.1, CCDS42785.1, CCDS42786.1, CCDS46459.1	2q31.3	2010-06-22			ENSG00000128655	ENSG00000128655	3.1.4.17	"""Phosphodiesterases"""	8773	protein-coding gene	gene with protein product		604961				10725373	Standard	NM_001077196		Approved		uc002ulq.3	Q9HCR9	OTTHUMG00000154188	ENST00000286063.6:c.2599C>G	2.37:g.178528641G>C	ENSP00000286063:p.Arg867Gly	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	70	34	0.485714	NM_016953	Q14CD1|Q53T16|Q96S76|Q9GZY7|Q9HB46|Q9NY45	Missense_Mutation	SNP	ENST00000286063.6	37	CCDS33334.1	38|38	0.0173992673992674|0.0173992673992674	14|14	0.028455284552845527|0.028455284552845527	5|5	0.013812154696132596|0.013812154696132596	5|5	0.008741258741258742|0.008741258741258742	14|14	0.018469656992084433|0.018469656992084433	G|G	10.44|10.44	1.352134|1.352134	0.24512|0.24512	0.043123|0.043123	0.017326|0.017326	ENSG00000128655|ENSG00000128655	ENST00000286063;ENST00000358450;ENST00000450799;ENST00000409504;ENST00000389683;ENST00000449286|ENST00000436700	T;T;T;T;T;T|.	0.76578|.	-1.03;-1.03;-1.03;-1.03;-1.03;-1.03|.	6.07|6.07	4.14|4.14	0.48551|0.48551	5&apos (2);-cyclic nucleotide phosphodiesterase, catalytic domain (2);3&apos (2);|.	0.101356|.	0.64402|.	D|.	0.000003|.	T|T	0.11836|0.11836	0.0288|0.0288	N|N	0.12569|0.12569	0.235|0.235	0.41027|0.41027	D|D	0.985121|0.985121	B;B|.	0.06786|.	0.001;0.001|.	B;B|.	0.08055|.	0.001;0.003|.	T|T	0.05767|0.05767	-1.0865|-1.0865	10|5	0.23302|.	T|.	0.38|.	.|.	11.939|11.939	0.52890|0.52890	0.0:0.1083:0.6827:0.2089|0.0:0.1083:0.6827:0.2089	rs61306957|rs61306957	617;867|.	Q9HCR9-2;Q9HCR9|.	.;PDE11_HUMAN|.	G|W	867;617;58;509;423;509|69	ENSP00000286063:R867G;ENSP00000351232:R617G;ENSP00000387964:R58G;ENSP00000386539:R509G;ENSP00000374333:R423G;ENSP00000390599:R509G|.	ENSP00000286063:R867G|.	R|S	-|-	1|2	2|0	PDE11A|PDE11A	178236887|178236887	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.994000|0.994000	0.84299|0.84299	2.923000|2.923000	0.48868|0.48868	1.529000|1.529000	0.49120|0.49120	0.655000|0.655000	0.94253|0.94253	CGG|TCG	G|0.975;C|0.025	0.025	strong		0.453	PDE11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334313.2		
TMEM2	23670	hgsc.bcm.edu	37	9	74360395	74360395	+	Silent	SNP	T	T	C	rs76670837	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:74360395T>C	ENST00000377044.4	-	4	1112	c.573A>G	c.(571-573)gcA>gcG	p.A191A	TMEM2_ENST00000377066.5_Silent_p.A191A	NM_001135820.1|NM_013390.2	NP_001129292.1|NP_037522.1	Q9UHN6	TMEM2_HUMAN	transmembrane protein 2	191	G8. {ECO:0000255|PROSITE- ProRule:PRU00817}.				multicellular organismal development (GO:0007275)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(15)|liver(1)|lung(19)|ovary(2)|prostate(5)|skin(1)|stomach(1)|urinary_tract(2)	56		all_epithelial(88;4.56e-14)|Myeloproliferative disorder(762;0.0255)		GBM - Glioblastoma multiforme(74;7.45e-21)|OV - Ovarian serous cystadenocarcinoma(323;1.02e-16)		GGCATTTTTCTGCTCCAATAT	0.413													T|||	302	0.0603035	0.0998	0.0591	5008	,	,		18601	0.0		0.0934	False		,,,				2504	0.0358				p.A191A		Atlas-SNP	.											.	TMEM2	112	.	0			c.A573G						PASS	.	T	,	364,4042	186.4+/-213.3	16,332,1855	100.0	101.0	101.0		573,573	5.9	1.0	9	dbSNP_132	101	576,8024	155.2+/-209.3	25,526,3749	no	coding-synonymous,coding-synonymous	TMEM2	NM_001135820.1,NM_013390.2	,	41,858,5604	CC,CT,TT		6.6977,8.2615,7.2274	,	191/1321,191/1384	74360395	940,12066	2203	4300	6503	SO:0001819	synonymous_variant	23670	exon4			TTTTTCTGCTCCA		CCDS6638.1, CCDS47979.1	9q21.13	2011-07-19			ENSG00000135048	ENSG00000135048			11869	protein-coding gene	gene with protein product		605835					Standard	NM_013390		Approved		uc011lsa.1	Q9UHN6	OTTHUMG00000020000	ENST00000377044.4:c.573A>G	9.37:g.74360395T>C		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	78	78	1	NM_001135820	A6H8W9|B2RTQ6|Q5T838|Q5T839|Q5T840|Q5T841|Q8NBP6|Q9P2D5	Silent	SNP	ENST00000377044.4	37	CCDS6638.1																																																																																			T|0.926;C|0.074	0.074	strong		0.413	TMEM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052618.2	NM_013390	
SEH1L	81929	hgsc.bcm.edu	37	18	12955467	12955467	+	Silent	SNP	T	T	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:12955467T>C	ENST00000262124.11	+	3	295	c.168T>C	c.(166-168)caT>caC	p.H56H	SEH1L_ENST00000399892.2_Silent_p.H56H	NM_031216.3	NP_112493.2	Q96EE3	SEH1_HUMAN	SEH1-like (S. cerevisiae)	56					attachment of spindle microtubules to kinetochore involved in mitotic sister chromatid segregation (GO:0051315)|carbohydrate metabolic process (GO:0005975)|cytokine production involved in inflammatory response (GO:0002534)|cytokine-mediated signaling pathway (GO:0019221)|defense response to Gram-positive bacterium (GO:0050830)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic metaphase plate congression (GO:0007080)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|nuclear pore organization (GO:0006999)|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)|nuclear envelope (GO:0005635)|nuclear pore outer ring (GO:0031080)		p.H56H(2)		central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(5)|pancreas(1)|prostate(1)	11						CCCAGACACATAGTGGATCTG	0.398																																					p.H56H		Atlas-SNP	.											SEH1L,NS,carcinoma,0,3	SEH1L	33	3	2	Substitution - coding silent(2)	prostate(1)|central_nervous_system(1)	c.T168C						PASS	.						150.0	135.0	140.0					18																	12955467		2203	4300	6503	SO:0001819	synonymous_variant	81929	exon3			GACACATAGTGGA	BC012430	CCDS32791.1, CCDS45832.1	18p11.21	2013-01-10				ENSG00000085415		"""WD repeat domain containing"""	30379	protein-coding gene	gene with protein product	"""sec13 like protein"", ""nucleoporin Seh1"""	609263				12196509, 14517296	Standard	XM_005258152		Approved	SEH1A, SEH1B, Seh1, SEC13L	uc002krq.3	Q96EE3		ENST00000262124.11:c.168T>C	18.37:g.12955467T>C		Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	132	7	0.0530303	NM_001013437	A8K5B1|Q8NFU6|Q96MH3|Q9C069	Silent	SNP	ENST00000262124.11	37	CCDS45832.1																																																																																			.	.	weak		0.398	SEH1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458254.1	NM_031216	
BCS1L	617	hgsc.bcm.edu	37	2	219527857	219527857	+	Splice_Site	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:219527857G>A	ENST00000431802.1	+	8	1707	c.1008G>A	c.(1006-1008)agG>agA	p.R336R	BCS1L_ENST00000412366.1_Splice_Site_p.R336R|BCS1L_ENST00000392111.2_Splice_Site_p.R336R|BCS1L_ENST00000392109.1_Splice_Site_p.R336R|BCS1L_ENST00000465706.1_3'UTR|BCS1L_ENST00000359273.3_Splice_Site_p.R336R|BCS1L_ENST00000439945.1_Splice_Site_p.R336R|BCS1L_ENST00000392110.2_Splice_Site_p.R336R			Q9Y276	BCS1_HUMAN	BC1 (ubiquinol-cytochrome c reductase) synthesis-like	336					mitochondrial respiratory chain complex I assembly (GO:0032981)|mitochondrial respiratory chain complex III assembly (GO:0034551)|mitochondrial respiratory chain complex IV assembly (GO:0033617)|mitochondrion organization (GO:0007005)	mitochondrial respiratory chain complex III (GO:0005750)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)			endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|prostate(1)	8		Renal(207;0.0474)		Epithelial(149;7.12e-07)|all cancers(144;0.000131)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		CTTCTCTCAGGCTGGACCCTG	0.602																																					p.R336R		Atlas-SNP	.											.	BCS1L	22	.	0			c.G1008A						PASS	.						73.0	76.0	75.0					2																	219527857		2203	4300	6503	SO:0001630	splice_region_variant	617	exon9			TCTCAGGCTGGAC	AF026849	CCDS2419.1	2q35	2014-09-17	2012-10-12		ENSG00000074582	ENSG00000074582		"""ATPases / AAA-type"", ""Mitochondrial respiratory chain complex assembly factors"""	1020	protein-coding gene	gene with protein product	"""GRACILE syndrome"", ""Bjornstad syndrome"""	603647	"""BCS1 (yeast homolog)-like"", ""BCS1-like (yeast)"", ""BCS1-like (S. cerevisiae)"""			9878253, 17314340	Standard	NM_001079866		Approved	Hs.6719, BCS, h-BCS, BJS	uc002viq.3	Q9Y276	OTTHUMG00000133114	ENST00000431802.1:c.1008-1G>A	2.37:g.219527857G>A		Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	146	39	0.267123	NM_001257343	B3KTW9|Q7Z2V7	Silent	SNP	ENST00000431802.1	37	CCDS2419.1	.	.	.	.	.	.	.	.	.	.	G	4.628	0.116645	0.08881	.	.	ENSG00000074582	ENST00000426649	.	.	.	5.12	2.05	0.26809	.	.	.	.	.	T	0.57651	0.2068	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.49542	-0.8929	4	.	.	.	.	8.9926	0.36033	0.2679:0.0:0.7321:0.0	.	.	.	.	T	118	.	.	A	+	1	0	BCS1L	219236101	1.000000	0.71417	0.998000	0.56505	0.156000	0.22039	3.543000	0.53633	0.207000	0.20607	-0.291000	0.09656	GCT	.	.	none		0.602	BCS1L-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336756.1	NM_004328	Silent
BTG2	7832	hgsc.bcm.edu	37	1	203274826	203274826	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:203274826G>A	ENST00000290551.4	+	1	163	c.92G>A	c.(91-93)aGc>aAc	p.S31N	RP11-134P9.1_ENST00000457348.1_lincRNA	NM_006763.2	NP_006754.1	P78543	BTG2_HUMAN	BTG family, member 2	31					anterior/posterior pattern specification (GO:0009952)|associative learning (GO:0008306)|cellular response to DNA damage stimulus (GO:0006974)|central nervous system neuron development (GO:0021954)|dentate gyrus development (GO:0021542)|DNA repair (GO:0006281)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neural precursor cell proliferation (GO:2000178)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of translation (GO:0017148)|neuron projection development (GO:0031175)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|protein methylation (GO:0006479)|response to electrical stimulus (GO:0051602)|response to mechanical stimulus (GO:0009612)|response to organic cyclic compound (GO:0014070)|response to peptide hormone (GO:0043434)|skeletal muscle cell differentiation (GO:0035914)	extracellular vesicular exosome (GO:0070062)	RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(1)|lung(2)|ovary(1)|skin(1)	9			BRCA - Breast invasive adenocarcinoma(75;0.203)			GGCTGCGTGAGCGAGCAGAGG	0.711																																					p.S31N		Atlas-SNP	.											.	BTG2	16	.	0			c.G92A						PASS	.						16.0	16.0	16.0					1																	203274826		2157	4238	6395	SO:0001583	missense	7832	exon1			GCGTGAGCGAGCA		CCDS1437.1	1q32	2008-07-18			ENSG00000159388	ENSG00000159388			1131	protein-coding gene	gene with protein product	"""B-cell translocation gene 2"", ""pheochromacytoma cell-3"", ""NGF-inducible anti-proliferative protein PC3"", ""nerve growth factor-inducible anti-proliferative"""	601597				8944033	Standard	NM_006763		Approved	PC3, TIS21, MGC126063, MGC126064	uc001gzq.3	P78543	OTTHUMG00000035834	ENST00000290551.4:c.92G>A	1.37:g.203274826G>A	ENSP00000290551:p.Ser31Asn	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	165	44	0.266667	NM_006763	A0A024R986|Q3KR25|Q5VUT0	Missense_Mutation	SNP	ENST00000290551.4	37	CCDS1437.1	.	.	.	.	.	.	.	.	.	.	G	9.276	1.046979	0.19748	.	.	ENSG00000159388	ENST00000290551	T	0.22539	1.95	4.66	3.75	0.43078	Anti-proliferative protein (3);	0.175253	0.47455	N	0.000221	T	0.11324	0.0276	N	0.17800	0.525	0.32144	N	0.585114	B	0.02656	0.0	B	0.04013	0.001	T	0.18272	-1.0342	10	0.14656	T	0.56	-0.1987	8.0794	0.30735	0.1867:0.0:0.8133:0.0	.	31	P78543	BTG2_HUMAN	N	31	ENSP00000290551:S31N	ENSP00000290551:S31N	S	+	2	0	BTG2	201541449	1.000000	0.71417	1.000000	0.80357	0.902000	0.53008	2.876000	0.48498	1.194000	0.43101	0.478000	0.44815	AGC	.	.	none		0.711	BTG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087168.1	NM_006763	
ATE1	11101	hgsc.bcm.edu	37	10	123549691	123549691	+	Silent	SNP	T	T	G	rs35350755	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:123549691T>G	ENST00000224652.6	-	11	1456	c.1371A>C	c.(1369-1371)ccA>ccC	p.P457P	ATE1_ENST00000369043.3_Silent_p.P457P|ATE1_ENST00000535655.1_Silent_p.P158P|ATE1_ENST00000369040.3_Silent_p.P361P|ATE1_ENST00000540606.1_Silent_p.P450P|ATE1_ENST00000543447.1_Silent_p.P342P	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	86	0	0		WXS	Illumina HiSeq	Phase_I	79	78	0.987342	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	
PSAPL1	768239	hgsc.bcm.edu	37	4	7436486	7436486	+	Missense_Mutation	SNP	C	C	A	rs11548325	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:7436486C>A	ENST00000319098.4	-	1	214	c.121G>T	c.(121-123)Gcc>Tcc	p.A41S	SORCS2_ENST00000511199.1_Intron|SORCS2_ENST00000507866.2_Intron|SORCS2_ENST00000329016.9_Intron	NM_001085382.1	NP_001078851.1	Q6NUJ1	SAPL1_HUMAN	prosaposin-like 1 (gene/pseudogene)	41	Saposin A-type 1. {ECO:0000255|PROSITE- ProRule:PRU00414}.		A -> S (in dbSNP:rs11548325).		sphingolipid metabolic process (GO:0006665)	extracellular region (GO:0005576)|lysosome (GO:0005764)				lung(4)	4						CCGCACCTGGCAGCTGTCTGC	0.677													C|||	1002	0.20008	0.1543	0.2795	5008	,	,		17157	0.2946		0.1252	False		,,,				2504	0.1851				p.A41S		Atlas-SNP	.											.	PSAPL1	51	.	0			c.G121T						PASS	.	C	SER/ALA,	573,3421		36,501,1460	21.0	25.0	24.0		121,	1.6	0.0	4	dbSNP_120	24	908,7426		45,818,3304	yes	missense,intron	SORCS2,PSAPL1	NM_001085382.1,NM_020777.2	99,	81,1319,4764	AA,AC,CC		10.8951,14.3465,12.0133	benign,	41/522,	7436486	1481,10847	1997	4167	6164	SO:0001583	missense	768239	exon1			ACCTGGCAGCTGT	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.121G>T	4.37:g.7436486C>A	ENSP00000317445:p.Ala41Ser	Somatic	187	0	0		WXS	Illumina HiSeq	Phase_I	132	66	0.5	NM_001085382	A0A184|Q8N7T4	Missense_Mutation	SNP	ENST00000319098.4	37	CCDS47009.1	401	0.18360805860805862	65	0.13211382113821138	88	0.2430939226519337	150	0.26223776223776224	98	0.12928759894459102	C	0.005	-2.189265	0.00302	0.143465	0.108951	ENSG00000178597	ENST00000319098	T	0.54866	0.55	2.67	1.63	0.23807	Saposin type A (3);	.	.	.	.	T	0.00012	0.0000	L	0.29908	0.895	0.80722	P	0.0	B	0.34181	0.44	B	0.32090	0.14	T	0.17501	-1.0367	8	0.09084	T	0.74	.	4.6842	0.12750	0.0:0.7638:0.0:0.2362	rs11548325	41	Q6NUJ1	SAPL1_HUMAN	S	41	ENSP00000317445:A41S	ENSP00000317445:A41S	A	-	1	0	PSAPL1	7487387	0.003000	0.15002	0.001000	0.08648	0.035000	0.12851	0.676000	0.25247	0.487000	0.27698	0.561000	0.74099	GCC	C|0.820;A|0.180	0.180	strong		0.677	PSAPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358859.1		
SAMSN1	64092	hgsc.bcm.edu	37	21	15954528	15954528	+	Missense_Mutation	SNP	G	G	A	rs2822785	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:15954528G>A	ENST00000285670.2	-	2	364	c.190C>T	c.(190-192)Cac>Tac	p.H64Y	SAMSN1-AS1_ENST00000449214.1_RNA	NM_001256370.1	NP_001243299.1	Q9NSI8	SAMN1_HUMAN	SAM domain, SH3 domain and nuclear localization signals 1	0					negative regulation of adaptive immune response (GO:0002820)|negative regulation of B cell activation (GO:0050869)|negative regulation of peptidyl-tyrosine phosphorylation (GO:0050732)	cell projection (GO:0042995)|cytosol (GO:0005829)|nucleus (GO:0005634)	phosphotyrosine binding (GO:0001784)|poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(1)|kidney(1)|large_intestine(3)|lung(9)|ovary(3)|pancreas(1)|prostate(3)|urinary_tract(1)	24				Epithelial(23;0.000155)|COAD - Colon adenocarcinoma(22;0.00118)|Colorectal(24;0.00961)|Lung(58;0.164)		GAGGAGCAGTGGTCCCAGGGT	0.468													G|||	1439	0.28734	0.1974	0.4654	5008	,	,		19067	0.1458		0.4384	False		,,,				2504	0.273				p.H64Y		Atlas-SNP	.											.	SAMSN1	112	.	0			c.C190T						PASS	.																																			SO:0001583	missense	64092	exon2			AGCAGTGGTCCCA	AF222927	CCDS42906.1, CCDS58786.1, CCDS74774.1	21q11	2013-01-10	2006-12-13		ENSG00000155307	ENSG00000155307		"""SAM and SH3 domain containing"", ""Sterile alpha motif (SAM) domain containing"""	10528	protein-coding gene	gene with protein product	"""nuclear localization signals, SAM and SH3 domain containing 1"", ""SAM and SH3 domain containing 2"", ""hematopoietic adapter-containing SH3 and sterile &#945;-motif (SAM) domains 1"", ""Src homology domain 3 (SH3)-containing adapter protein SH3 lymphocyte protein 2"""	607978				11536050, 11594764	Standard	NM_022136		Approved	NASH1, SASH2, SH3D6B, HACS1, SLy2	uc002yjv.1	Q9NSI8	OTTHUMG00000074317	ENST00000285670.2:c.190C>T	21.37:g.15954528G>A	ENSP00000285670:p.His64Tyr	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	121	120	0.991736	NM_001256370	B3KWJ3|F8WAA1|Q8NFF7|Q9C041	Missense_Mutation	SNP	ENST00000285670.2	37	CCDS58786.1	687|687	0.31456043956043955|0.31456043956043955	98|98	0.1991869918699187|0.1991869918699187	174|174	0.48066298342541436|0.48066298342541436	89|89	0.1555944055944056|0.1555944055944056	326|326	0.43007915567282323|0.43007915567282323	G|G	8.528|8.528	0.870416|0.870416	0.17322|0.17322	.|.	.|.	ENSG00000155307|ENSG00000243440	ENST00000285670|ENST00000442499;ENST00000389438	T|.	0.42513|.	0.97|.	5.65|5.65	-2.47|-2.47	0.06442|0.06442	.|.	0.518762|.	0.17792|.	N|.	0.161851|.	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.58432|0.58432	P|P	8.000000000008E-6|8.000000000008E-6	B|.	0.02656|.	0.0|.	B|.	0.01281|.	0.0|.	T|T	0.47368|0.47368	-0.9123|-0.9123	8|3	0.59425|.	D|.	0.04|.	-8.5588|-8.5588	1.9003|1.9003	0.03266|0.03266	0.1033:0.2036:0.2507:0.4425|0.1033:0.2036:0.2507:0.4425	rs2822785;rs17274353;rs52815372;rs60384084;rs2822785|rs2822785;rs17274353;rs52815372;rs60384084;rs2822785	64|.	F8WAA1|.	.|.	Y|L	64|271;150	ENSP00000285670:H64Y|.	ENSP00000285670:H64Y|.	H|P	-|-	1|2	0|0	SAMSN1|AF165138.7	14876399|14876399	0.801000|0.801000	0.28930|0.28930	0.000000|0.000000	0.03702|0.03702	0.016000|0.016000	0.09150|0.09150	0.372000|0.372000	0.20467|0.20467	-0.604000|-0.604000	0.05760|0.05760	-0.136000|-0.136000	0.14681|0.14681	CAC|CCA	G|0.692;A|0.307	0.307	strong		0.468	SAMSN1-001	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000157913.1		
CEACAM19	56971	hgsc.bcm.edu	37	19	45176003	45176003	+	Missense_Mutation	SNP	A	A	G	rs201929208		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:45176003A>G	ENST00000403660.3	+	2	401	c.191A>G	c.(190-192)aAc>aGc	p.N64S	CEACAM19_ENST00000480278.1_3'UTR|CTB-171A8.1_ENST00000590796.1_RNA|CEACAM19_ENST00000358777.4_Missense_Mutation_p.N64S			Q7Z692	CEA19_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 19	64						integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(5)	11	Lung NSC(12;0.00308)|all_lung(12;0.00806)	Prostate(69;0.0376)				CAGGACTTCAACTGGTACCTG	0.567																																					p.N64S		Atlas-SNP	.											.	CEACAM19	27	.	0			c.A191G						PASS	.						103.0	75.0	84.0					19																	45176003		2203	4300	6503	SO:0001583	missense	56971	exon2			ACTTCAACTGGTA	AF406955	CCDS12641.1, CCDS46108.1	19q13.31	2013-01-11			ENSG00000186567	ENSG00000186567		"""Immunoglobulin superfamily / V-set domain containing"""	31951	protein-coding gene	gene with protein product		606691					Standard	NM_020219		Approved	CEAL1	uc002ozo.4	Q7Z692	OTTHUMG00000151528	ENST00000403660.3:c.191A>G	19.37:g.45176003A>G	ENSP00000384887:p.Asn64Ser	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	151	76	0.503311	NM_001127893	Q5XJ15|Q7Z693	Missense_Mutation	SNP	ENST00000403660.3	37	CCDS12641.1	.	.	.	.	.	.	.	.	.	.	A	6.496	0.459717	0.12342	.	.	ENSG00000186567	ENST00000358777;ENST00000403660	T;T	0.62941	-0.01;-0.01	4.18	-0.79	0.10932	Immunoglobulin V-set (1);Immunoglobulin-like fold (1);	0.319679	0.22466	N	0.059684	T	0.34774	0.0909	N	0.17764	0.52	0.21386	N	0.999705	B;B	0.17268	0.021;0.021	B;B	0.18871	0.023;0.023	T	0.08932	-1.0698	10	0.21014	T	0.42	-5.3844	1.0166	0.01509	0.296:0.1476:0.1065:0.4499	.	64;64	Q5XJ15;Q7Z692	.;CEA19_HUMAN	S	64	ENSP00000351627:N64S;ENSP00000384887:N64S	ENSP00000351627:N64S	N	+	2	0	CEACAM19	49867843	0.003000	0.15002	0.944000	0.38274	0.969000	0.65631	-0.536000	0.06135	-0.547000	0.06207	0.454000	0.30748	AAC	.	.	weak		0.567	CEACAM19-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000323022.1	NM_020219	
C9orf84	158401	hgsc.bcm.edu	37	9	114454544	114454544	+	Missense_Mutation	SNP	T	T	C	rs7869279	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:114454544T>C	ENST00000318737.4	-	25	3649	c.3521A>G	c.(3520-3522)gAa>gGa	p.E1174G	C9orf84_ENST00000374287.3_Missense_Mutation_p.E1174G|C9orf84_ENST00000394777.4_Missense_Mutation_p.E1100G|C9orf84_ENST00000394779.3_Missense_Mutation_p.E1135G	NM_173521.3	NP_775792.3	Q5VXU9	CI084_HUMAN	chromosome 9 open reading frame 84	1174			E -> G (in dbSNP:rs7869279).							breast(1)|cervix(1)|endometrium(3)|kidney(7)|large_intestine(10)|liver(1)|lung(7)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	35						ACTTGAGATTTCTTTTAGTTC	0.358													T|||	2489	0.497005	0.3911	0.5994	5008	,	,		18606	0.7728		0.4404	False		,,,				2504	0.3415				p.E1174G		Atlas-SNP	.											.	C9orf84	207	.	0			c.A3521G						PASS	.	T	GLY/GLU,GLY/GLU	1817,2589	531.9+/-373.3	402,1013,788	94.0	96.0	95.0		3404,3521	4.2	0.1	9	dbSNP_116	95	3834,4766	539.0+/-383.5	867,2100,1333	yes	missense,missense	C9orf84	NM_001080551.1,NM_173521.3	98,98	1269,3113,2121	CC,CT,TT		44.5814,41.2392,43.4492	benign,benign	1135/1406,1174/1445	114454544	5651,7355	2203	4300	6503	SO:0001583	missense	158401	exon25			GAGATTTCTTTTA	AL833535	CCDS6781.3, CCDS43863.1	9q32	2012-03-16			ENSG00000165181	ENSG00000165181			26535	protein-coding gene	gene with protein product							Standard	XM_005251738		Approved	FLJ32779	uc004bfr.3	Q5VXU9	OTTHUMG00000020495	ENST00000318737.4:c.3521A>G	9.37:g.114454544T>C	ENSP00000322108:p.Glu1174Gly	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	124	48	0.387097	NM_173521	A2A2V3|Q2M1H8|Q96M73	Missense_Mutation	SNP	ENST00000318737.4	37	CCDS6781.3	1144	0.5238095238095238	178	0.3617886178861789	211	0.5828729281767956	427	0.7465034965034965	328	0.43271767810026385	T	11.24	1.580204	0.28180	0.412392	0.445814	ENSG00000165181	ENST00000394779;ENST00000394777;ENST00000394778;ENST00000374287;ENST00000318737	T;T;T;T	0.05996	3.37;3.36;3.38;3.38	5.4	4.24	0.50183	.	0.672855	0.13625	N	0.374124	T	0.00012	0.0000	L	0.29908	0.895	0.49130	P	2.4599999999996847E-4	P;P;P	0.47302	0.893;0.893;0.893	P;P;P	0.47981	0.563;0.563;0.563	T	0.00138	-1.2003	9	0.54805	T	0.06	-1.1518	10.7936	0.46447	0.0:0.0:0.1584:0.8416	rs7869279;rs57126656;rs7869279	1100;1174;1135	A6PVK7;Q5VXU9;A2A2V3	.;CI084_HUMAN;.	G	1135;1100;788;1174;1174	ENSP00000378259:E1135G;ENSP00000378257:E1100G;ENSP00000363405:E1174G;ENSP00000322108:E1174G	ENSP00000322108:E1174G	E	-	2	0	C9orf84	113494365	0.986000	0.35501	0.074000	0.20217	0.050000	0.14768	2.033000	0.41136	0.955000	0.37878	0.383000	0.25322	GAA	T|0.528;C|0.472	0.472	strong		0.358	C9orf84-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053656.2	NM_173521	
SCRIB	23513	hgsc.bcm.edu	37	8	144874554	144874554	+	Silent	SNP	T	T	C	rs6991873	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:144874554T>C	ENST00000320476.3	-	32	4356	c.4350A>G	c.(4348-4350)ccA>ccG	p.P1450P	SCRIB_ENST00000377533.3_Silent_p.P1369P|SCRIB_ENST00000356994.2_Silent_p.P1450P|RP11-429J17.8_ENST00000527139.1_RNA|RP11-429J17.8_ENST00000534089.1_RNA|RP11-429J17.8_ENST00000532625.1_RNA|SCRIB_ENST00000546337.1_5'Flank	NM_015356.4	NP_056171	Q14160	SCRIB_HUMAN	scribbled planar cell polarity protein	1450					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)			CTCCCAGGGGTGGGGGGGACG	0.751													T|||	4958	0.990016	0.9652	0.9971	5008	,	,		8428	1.0		0.998	False		,,,				2504	1.0				p.P1450P	Pancreas(51;966 1133 10533 14576 29674)	Atlas-SNP	.											SCRIB_ENST00000356994,colon,carcinoma,-2,2	SCRIB	192	2	0			c.A4350G						scavenged	.	T	,	3300,62		1619,62,0	3.0	4.0	4.0		4350,4350	-2.9	0.0	8	dbSNP_116	4	7076,4		3536,4,0	no	coding-synonymous,coding-synonymous	SCRIB	NM_015356.3,NM_182706.3	,	5155,66,0	CC,CT,TT		0.0565,1.8441,0.6321	,	1450/1631,1450/1656	144874554	10376,66	1681	3540	5221	SO:0001819	synonymous_variant	23513	exon32			CAGGGGTGGGGGG	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.4350A>G	8.37:g.144874554T>C		Somatic	2	1	0.5		WXS	Illumina HiSeq	Phase_I	2	2	1	NM_015356	Q6P496|Q7Z5D1|Q8WWV8|Q96C69|Q96GG1	Silent	SNP	ENST00000320476.3	37	CCDS6411.1	2162	0.98992673992674	472	0.959349593495935	361	0.9972375690607734	572	1.0	757	0.9986807387862797	T	5.986	0.365776	0.11352	0.981559	0.999435	ENSG00000180900	ENST00000526832	.	.	.	4.01	-2.89	0.05665	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.20773	-1.0265	3	.	.	.	.	6.6143	0.22769	0.0:0.6476:0.1513:0.201	rs6991873	.	.	.	A	470	.	.	T	-	1	0	SCRIB	144946542	0.000000	0.05858	0.000000	0.03702	0.031000	0.12232	-0.411000	0.07142	-0.857000	0.04115	-0.386000	0.06593	ACC	T|0.010;C|0.990	0.990	strong		0.751	SCRIB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000382215.1	NM_015356	
ARHGAP44	9912	hgsc.bcm.edu	37	17	12888086	12888086	+	Silent	SNP	G	G	A	rs143756943	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:12888086G>A	ENST00000379672.5	+	20	2478	c.2178G>A	c.(2176-2178)tcG>tcA	p.S726S	ARHGAP44_ENST00000340825.3_Silent_p.S720S|ARHGAP44_ENST00000262444.9_Silent_p.S726S	NM_014859.4	NP_055674.4	Q17R89	RHG44_HUMAN	Rho GTPase activating protein 44	726					exocytosis (GO:0006887)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytosol (GO:0005829)|endosome (GO:0005768)|leading edge membrane (GO:0031256)|synapse (GO:0045202)	GTPase activator activity (GO:0005096)|phospholipid binding (GO:0005543)			NS(2)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(7)|skin(1)|urinary_tract(1)	31						TGAGCAAATCGCGGCCCACTC	0.627													G|||	10	0.00199681	0.0	0.0014	5008	,	,		12916	0.0		0.0089	False		,,,				2504	0.0				p.S726S		Atlas-SNP	.											ARHGAP44,NS,carcinoma,+1,1	ARHGAP44	55	1	0			c.G2178A						PASS	.	G		5,3927		0,5,1961	36.0	40.0	38.0		2178	-10.7	0.0	17	dbSNP_134	38	54,8244		0,54,4095	no	coding-synonymous	ARHGAP44	NM_014859.4		0,59,6056	AA,AG,GG		0.6508,0.1272,0.4824		726/819	12888086	59,12171	1966	4149	6115	SO:0001819	synonymous_variant	9912	exon20			CAAATCGCGGCCC		CCDS45616.1	17p12	2011-06-29			ENSG00000006740	ENSG00000006740		"""Rho GTPase activating proteins"""	29096	protein-coding gene	gene with protein product						19273615	Standard	NM_014859		Approved	KIAA0672, RICH-2, RICH2	uc002gnr.4	Q17R89	OTTHUMG00000058765	ENST00000379672.5:c.2178G>A	17.37:g.12888086G>A		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	103	51	0.495146	NM_014859	A6NCP5|A8MQB2|O75160|Q7Z5Z7|Q9Y4Q4	Silent	SNP	ENST00000379672.5	37	CCDS45616.1																																																																																			G|0.998;A|0.002	0.002	strong		0.627	ARHGAP44-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441566.1	NM_014859	
DCLK2	166614	hgsc.bcm.edu	37	4	151141918	151141918	+	Missense_Mutation	SNP	A	A	C	rs148315360	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:151141918A>C	ENST00000296550.7	+	6	1874	c.1120A>C	c.(1120-1122)Ata>Cta	p.I374L	DCLK2_ENST00000506325.1_Missense_Mutation_p.I373L|DCLK2_ENST00000302176.8_Missense_Mutation_p.I391L	NM_001040260.3	NP_001035350.2	Q8N568	DCLK2_HUMAN	doublecortin-like kinase 2	374					intracellular signal transduction (GO:0035556)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(7)|ovary(3)|pancreas(1)|prostate(1)|skin(1)	26	all_hematologic(180;0.151)					TGACCGTTGCATAAGTCCTGA	0.413													A|||	4	0.000798722	0.0	0.0029	5008	,	,		19679	0.0		0.002	False		,,,				2504	0.0				p.I391L	GBM(195;186 2215 13375 16801 37459)	Atlas-SNP	.											.	DCLK2	168	.	0			c.A1171C						PASS	.	A	LEU/ILE,LEU/ILE	4,4402	8.1+/-20.4	0,4,2199	131.0	105.0	114.0		1120,1171	-6.0	1.0	4	dbSNP_134	114	18,8582	13.3+/-46.6	0,18,4282	yes	missense,missense	DCLK2	NM_001040260.3,NM_001040261.4	5,5	0,22,6481	CC,CA,AA		0.2093,0.0908,0.1692	benign,benign	374/767,391/784	151141918	22,12984	2203	4300	6503	SO:0001583	missense	166614	exon7			CGTTGCATAAGTC	BC032726	CCDS34076.1, CCDS47142.1, CCDS47142.2	4q31.3	2008-02-05	2007-04-02	2007-04-02	ENSG00000170390	ENSG00000170390			19002	protein-coding gene	gene with protein product		613166	"""doublecortin and CaM kinase-like 2"""	DCAMKL2		12477932	Standard	NM_001040260		Approved	MGC45428, DCDC3, DCDC3B, DCK2	uc003ilo.4	Q8N568	OTTHUMG00000161444	ENST00000296550.7:c.1120A>C	4.37:g.151141918A>C	ENSP00000296550:p.Ile374Leu	Somatic	215	0	0		WXS	Illumina HiSeq	Phase_I	134	71	0.529851	NM_001040261	C9J5Q9|Q59GC8|Q8N399	Missense_Mutation	SNP	ENST00000296550.7	37	CCDS34076.1	4	0.0018315018315018315	0	0.0	3	0.008287292817679558	0	0.0	1	0.0013192612137203166	A	10.88	1.475306	0.26511	9.08E-4	0.002093	ENSG00000170390	ENST00000296550;ENST00000506325;ENST00000302176	T;T;T	0.63913	0.94;0.94;-0.07	5.49	-5.99	0.02213	.	0.793091	0.12274	N	0.483509	T	0.19327	0.0464	N	0.03608	-0.345	0.09310	N	0.999994	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.0;0.0	T	0.39742	-0.9599	10	0.06494	T	0.89	.	8.557	0.33487	0.1693:0.6518:0.08:0.0989	.	391;373;374	Q8N568-3;Q8N568-2;Q8N568	.;.;DCLK2_HUMAN	L	374;373;391	ENSP00000296550:I374L;ENSP00000427235:I373L;ENSP00000303887:I391L	ENSP00000296550:I374L	I	+	1	0	DCLK2	151361368	0.004000	0.15560	0.970000	0.41538	0.777000	0.43975	-1.810000	0.01729	-0.498000	0.06632	0.533000	0.62120	ATA	A|0.998;C|0.002	0.002	strong		0.413	DCLK2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000364952.1	NM_001040260	
JAKMIP2	9832	hgsc.bcm.edu	37	5	147051334	147051334	+	Silent	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:147051334G>A	ENST00000265272.5	-	2	503	c.36C>T	c.(34-36)ccC>ccT	p.P12P	JAKMIP2_ENST00000333010.6_Intron|JAKMIP2_ENST00000507386.1_Silent_p.P12P	NM_001270941.1|NM_014790.4	NP_001257870.1|NP_055605.2	Q96AA8	JKIP2_HUMAN	janus kinase and microtubule interacting protein 2	12						Golgi apparatus (GO:0005794)				NS(1)|autonomic_ganglia(1)|breast(3)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(22)|lung(18)|ovary(3)|pancreas(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(2)	64			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGAGTGCCTCGGGCTTCTCGC	0.473																																					p.P12P		Atlas-SNP	.											JAKMIP2,right_upper_lobe,carcinoma,0,1	JAKMIP2	154	1	0			c.C36T						scavenged	.						147.0	134.0	138.0					5																	147051334		2203	4300	6503	SO:0001819	synonymous_variant	9832	exon2			TGCCTCGGGCTTC	AB011127	CCDS4285.1, CCDS59495.1, CCDS64284.1, CCDS75352.1	5q32	2009-08-13	2009-08-13		ENSG00000176049	ENSG00000176049			29067	protein-coding gene	gene with protein product		611197				9628581	Standard	NM_001270941		Approved	JAMIP2, KIAA0555	uc010jgo.2	Q96AA8	OTTHUMG00000129731	ENST00000265272.5:c.36C>T	5.37:g.147051334G>A		Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	152	3	0.0197368	NM_001270941	A4ZZA7|A8K5G5|B4DSG0|G5E9Y0|O60302|Q548S1	Silent	SNP	ENST00000265272.5	37	CCDS4285.1																																																																																			.	.	none		0.473	JAKMIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251941.1	NM_014790	
ZNF17	7565	hgsc.bcm.edu	37	19	57931553	57931553	+	Silent	SNP	C	C	T	rs10417533	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	69	0	0		WXS	Illumina HiSeq	Phase_I	89	89	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	
ULK1	8408	hgsc.bcm.edu	37	12	132401058	132401058	+	Missense_Mutation	SNP	C	C	T	rs55815560	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:132401058C>T	ENST00000321867.4	+	20	2345	c.1994C>T	c.(1993-1995)tCg>tTg	p.S665L	ULK1_ENST00000540647.1_5'Flank	NM_003565.2	NP_003556	O75385	ULK1_HUMAN	unc-51 like autophagy activating kinase 1	665			S -> L (in dbSNP:rs55815560). {ECO:0000269|PubMed:17344846}.		autophagic vacuole assembly (GO:0000045)|axon extension (GO:0048675)|cellular response to nutrient levels (GO:0031669)|cerebellar granule cell differentiation (GO:0021707)|negative regulation of collateral sprouting (GO:0048671)|neuron projection development (GO:0031175)|neuron projection regeneration (GO:0031102)|positive regulation of autophagy (GO:0010508)|positive regulation of macroautophagy (GO:0016239)|protein autophosphorylation (GO:0046777)|protein localization (GO:0008104)|protein phosphorylation (GO:0006468)|radial glia guided migration of cerebellar granule cell (GO:0021933)|Ras protein signal transduction (GO:0007265)|receptor internalization (GO:0031623)|regulation of autophagy (GO:0010506)|regulation of neurotrophin TRK receptor signaling pathway (GO:0051386)|response to starvation (GO:0042594)	ATG1/UKL1 signaling complex (GO:0034273)|autophagic vacuole (GO:0005776)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|extrinsic component of autophagic vacuole membrane (GO:0097635)|extrinsic component of omegasome membrane (GO:0097629)|extrinsic component of pre-autophagosomal structure membrane (GO:0097632)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|pre-autophagosomal structure membrane (GO:0034045)|ULK1-ATG13-FIP200 complex (GO:0070969)	ATP binding (GO:0005524)|protein complex binding (GO:0032403)|protein serine/threonine kinase activity (GO:0004674)|Rab GTPase binding (GO:0017137)			breast(1)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(11)|ovary(1)|prostate(2)|skin(2)|urinary_tract(2)	29	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;2.07e-08)|Epithelial(86;2.56e-07)|all cancers(50;3.01e-07)		CCCGACCTCTCGGAGGTGGGA	0.697													C|||	5	0.000998403	0.0	0.0	5008	,	,		15038	0.001		0.003	False		,,,				2504	0.001				p.S665L		Atlas-SNP	.											.	ULK1	92	.	0			c.C1994T						PASS	.	C	LEU/SER	1,4397	2.1+/-5.4	0,1,2198	37.0	43.0	41.0		1994	3.8	0.9	12	dbSNP_129	41	22,8572	16.6+/-54.9	0,22,4275	yes	missense	ULK1	NM_003565.2	145	0,23,6473	TT,TC,CC		0.256,0.0227,0.177	benign	665/1051	132401058	23,12969	2199	4297	6496	SO:0001583	missense	8408	exon20			ACCTCTCGGAGGT	AF045458	CCDS9274.1	12q24.3	2014-02-12	2013-07-02		ENSG00000177169	ENSG00000177169			12558	protein-coding gene	gene with protein product	"""ATG1 autophagy related 1 homolog (S. cerevisiae)"""	603168	"""unc-51 (C. elegans)-like kinase 1"", ""unc-51-like kinase 1 (C. elegans)"""			9693035	Standard	NM_003565		Approved	ATG1, ATG1A	uc001uje.3	O75385	OTTHUMG00000168052	ENST00000321867.4:c.1994C>T	12.37:g.132401058C>T	ENSP00000324560:p.Ser665Leu	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	61	30	0.491803	NM_003565	Q9UQ28	Missense_Mutation	SNP	ENST00000321867.4	37	CCDS9274.1	8	0.003663003663003663	3	0.006097560975609756	0	0.0	1	0.0017482517482517483	4	0.005277044854881266	C	11.31	1.599607	0.28534	2.27E-4	0.00256	ENSG00000177169	ENST00000321867;ENST00000541761	T;T	0.29397	1.57;2.5	5.69	3.79	0.43588	.	1.033790	0.07680	N	0.936898	T	0.19685	0.0473	L	0.44542	1.39	0.20873	N	0.999836	B	0.09022	0.002	B	0.04013	0.001	T	0.04165	-1.0972	10	0.35671	T	0.21	-11.4096	7.8361	0.29371	0.365:0.5069:0.1281:0.0	rs55815560	665	O75385	ULK1_HUMAN	L	665;13	ENSP00000324560:S665L;ENSP00000444298:S13L	ENSP00000324560:S665L	S	+	2	0	ULK1	130967011	0.866000	0.29940	0.897000	0.35233	0.013000	0.08279	2.057000	0.41365	2.684000	0.91462	0.655000	0.94253	TCG	C|0.998;T|0.002	0.002	strong		0.697	ULK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397769.3		
MYO3B	140469	hgsc.bcm.edu	37	2	171070912	171070912	+	Silent	SNP	T	T	C	rs13385825	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:171070912T>C	ENST00000408978.4	+	4	488	c.345T>C	c.(343-345)acT>acC	p.T115T	MYO3B_ENST00000602629.1_3'UTR|MYO3B_ENST00000334231.6_Silent_p.T124T|MYO3B_ENST00000409044.3_Silent_p.T115T	NM_138995.4	NP_620482.3	Q8WXR4	MYO3B_HUMAN	myosin IIIB	115	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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						GCTCAGTCACTGAGCTTGTCA	0.453													t|||	2092	0.417732	0.447	0.33	5008	,	,		18082	0.4494		0.3787	False		,,,				2504	0.4479				p.T115T		Atlas-SNP	.											.	MYO3B	320	.	0			c.T345C						PASS	.	T	,,	1612,2324		333,946,689	85.0	83.0	83.0		345,345,345	-11.0	0.0	2	dbSNP_121	83	3233,5099		656,1921,1589	no	coding-synonymous,coding-synonymous,coding-synonymous	MYO3B	NM_001083615.2,NM_001171642.1,NM_138995.3	,,	989,2867,2278	CC,CT,TT		38.8022,40.9553,39.493	,,	115/1315,115/1276,115/1342	171070912	4845,7423	1968	4166	6134	SO:0001819	synonymous_variant	140469	exon4			AGTCACTGAGCTT		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.345T>C	2.37:g.171070912T>C		Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	115	55	0.478261	NM_001083615	B8ZZR2|Q53QE1|Q53T08|Q8IX64|Q8IX65|Q8IX66|Q8IX67|Q8IX68|Q96N94	Silent	SNP	ENST00000408978.4	37	CCDS42773.1	892	0.4084249084249084	199	0.40447154471544716	142	0.39226519337016574	262	0.458041958041958	289	0.3812664907651715	t	8.911	0.958801	0.18507	0.409553	0.388022	ENSG00000071909	ENST00000442690	.	.	.	5.5	-11.0	0.00169	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	0.9999999999999605	.	.	.	.	.	.	.	.	.	.	.	.	.	.	3.259	0.06842	0.1656:0.1538:0.1755:0.5051	rs13385825;rs17496528	.	.	.	R	115	.	.	X	+	1	0	MYO3B	170779158	0.000000	0.05858	0.025000	0.17156	0.975000	0.68041	-3.150000	0.00582	-3.781000	0.00107	-0.802000	0.03209	TGA	T|0.608;C|0.392	0.392	strong		0.453	MYO3B-004	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333410.1		
ANKRD30A	91074	hgsc.bcm.edu	37	10	37486235	37486235	+	Missense_Mutation	SNP	G	G	A	rs201775035	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:37486235G>A	ENST00000602533.1	+	28	2572	c.2473G>A	c.(2473-2475)Gag>Aag	p.E825K	ANKRD30A_ENST00000361713.1_Missense_Mutation_p.E825K|ANKRD30A_ENST00000374660.1_Missense_Mutation_p.E944K			Q9BXX3	AN30A_HUMAN	ankyrin repeat domain 30A	881					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						ATCTGCCTTCGAGGTATTTAG	0.333													.|||	4	0.000798722	0.0	0.0	5008	,	,		18178	0.003		0.001	False		,,,				2504	0.0				p.E825K		Atlas-SNP	.											ANKRD30A,NS,carcinoma,0,1	ANKRD30A	448	1	0			c.G2473A						scavenged	.	G	LYS/GLU	1,3605		0,1,1802	164.0	139.0	147.0		2473	-2.7	0.0	10		147	3,8151		0,3,4074	no	missense	ANKRD30A	NM_052997.2	56	0,4,5876	AA,AG,GG		0.0368,0.0277,0.034	possibly-damaging	825/1342	37486235	4,11756	1803	4077	5880	SO:0001583	missense	91074	exon28			GCCTTCGAGGTAT	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.2473G>A	10.37:g.37486235G>A	ENSP00000473551:p.Glu825Lys	Somatic	328	1	0.00304878		WXS	Illumina HiSeq	Phase_I	292	18	0.0616438	NM_052997	Q5W025	Missense_Mutation	SNP	ENST00000602533.1	37		.	.	.	.	.	.	.	.	.	.	.	0.011	-1.726410	0.00694	2.77E-4	3.68E-4	ENSG00000148513	ENST00000361713;ENST00000374660	T;T	0.07114	3.22;3.22	1.36	-2.73	0.05950	.	.	.	.	.	T	0.02929	0.0087	N	0.01576	-0.805	0.09310	N	1	P	0.50272	0.933	P	0.52189	0.692	T	0.15838	-1.0423	9	0.02654	T	1	.	2.1426	0.03778	0.4051:0.3297:0.2652:0.0	.	881	Q9BXX3	AN30A_HUMAN	K	825;944	ENSP00000354432:E825K;ENSP00000363792:E944K	ENSP00000354432:E825K	E	+	1	0	ANKRD30A	37526241	0.016000	0.18221	0.008000	0.14137	0.002000	0.02628	-0.757000	0.04772	-0.171000	0.10797	-0.482000	0.04802	GAG	.	.	weak		0.333	ANKRD30A-001	KNOWN	NMD_exception|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000047588.2	NM_052997	
DOCK1	1793	hgsc.bcm.edu	37	10	129160458	129160458	+	Silent	SNP	G	G	A	rs2296635	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:129160458G>A	ENST00000280333.6	+	33	3460	c.3351G>A	c.(3349-3351)tcG>tcA	p.S1117S		NM_001380.3	NP_001371.1	Q14185	DOCK1_HUMAN	dedicator of cytokinesis 1	1117					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)		AATTCCATTCGACCCGAAGCT	0.493													G|||	1023	0.204273	0.1747	0.1628	5008	,	,		17732	0.1359		0.2684	False		,,,				2504	0.2781				p.S1117S		Atlas-SNP	.											.	DOCK1	188	.	0			c.G3351A						PASS	.	G		732,3446		67,598,1424	62.0	61.0	62.0		3306	-10.3	0.0	10	dbSNP_100	62	2277,6223		315,1647,2288	no	coding-synonymous	DOCK1	NM_001380.3		382,2245,3712	AA,AG,GG		26.7882,17.5203,23.734		1102/1851	129160458	3009,9669	2089	4250	6339	SO:0001819	synonymous_variant	1793	exon33			CCATTCGACCCGA	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.3351G>A	10.37:g.129160458G>A		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	81	40	0.493827	NM_001380	A9Z1Z5	Silent	SNP	ENST00000280333.6	37																																																																																				G|0.808;A|0.192	0.192	strong		0.493	DOCK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050979.2	NM_001380	
FAM205A	259308	hgsc.bcm.edu	37	9	34726671	34726671	+	Missense_Mutation	SNP	G	G	A	rs1854574	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:34726671G>A	ENST00000378788.3	-	4	605	c.566C>T	c.(565-567)aCg>aTg	p.T189M		NM_001141917.1	NP_001135389.1	Q6ZU69	F205A_HUMAN	family with sequence similarity 205, member A	189						integral component of membrane (GO:0016021)|nucleus (GO:0005634)				breast(1)|endometrium(2)|kidney(1)	4						ATCTGCATACGTTGACTGGGC	0.493													G|||	1348	0.269169	0.1657	0.3818	5008	,	,		21277	0.3006		0.3439	False		,,,				2504	0.2198				p.T189M		Atlas-SNP	.											.	FAM205A	45	.	0			c.C566T						PASS	.						107.0	91.0	96.0					9																	34726671		692	1590	2282	SO:0001583	missense	259308	exon4			GCATACGTTGACT		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.566C>T	9.37:g.34726671G>A	ENSP00000417711:p.Thr189Met	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	85	44	0.517647	NM_001141917	A8MVW7	Missense_Mutation	SNP	ENST00000378788.3	37	CCDS55305.1	683	0.31272893772893773	90	0.18292682926829268	135	0.3729281767955801	204	0.35664335664335667	254	0.33509234828496043	G	10.40	1.340468	0.24339	.	.	ENSG00000205108	ENST00000378788	T	0.26957	1.7	3.09	1.22	0.21188	.	1.925660	0.03166	U	0.170045	T	0.00012	0.0000	L	0.42245	1.32	0.80722	P	0.0	D	0.60575	0.988	P	0.47744	0.556	T	0.28106	-1.0054	9	0.62326	D	0.03	.	3.7287	0.08484	0.1325:0.0:0.6256:0.2419	rs1854574;rs1854574	189	Q6ZU69	F205A_HUMAN	M	189	ENSP00000417711:T189M	ENSP00000417711:T189M	T	-	2	0	RP11-195F19.10	34716671	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	0.368000	0.20399	0.334000	0.23590	-0.234000	0.12200	ACG	G|0.708;A|0.292	0.292	strong		0.493	FAM205A-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001150.2	NM_001141917	
PPAP2C	8612	hgsc.bcm.edu	37	19	282753	282753	+	Splice_Site	SNP	G	G	A	rs1138439	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	41	20	0.487805	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
OR52I1	390037	hgsc.bcm.edu	37	11	4615508	4615508	+	Silent	SNP	C	C	G	rs2010719	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:4615508C>G	ENST00000530443.2	+	1	240	c.240C>G	c.(238-240)tcC>tcG	p.S80S	OR52I1_ENST00000450052.2_Silent_p.S104S	NM_001005169.1	NP_001005169.1	Q8NGK6	O52I1_HUMAN	olfactory receptor, family 52, subfamily I, member 1	80						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)	15		Medulloblastoma(188;0.0075)|Breast(177;0.0461)|all_neural(188;0.0577)		Epithelial(150;7.98e-12)|BRCA - Breast invasive adenocarcinoma(625;0.0284)|LUSC - Lung squamous cell carcinoma(625;0.19)		TGGCCTCCTCCGTGGTACCCA	0.507													G|||	3065	0.612021	0.5303	0.7046	5008	,	,		21113	0.5595		0.659	False		,,,				2504	0.6626				p.S80S		Atlas-SNP	.											OR52I1,NS,carcinoma,+1,1	OR52I1	29	1	0			c.C240G						PASS	.	G		2031,2371		664,703,834	166.0	141.0	149.0		240	-9.8	0.0	11	dbSNP_92	149	5255,3337		1955,1345,996	no	coding-synonymous	OR52I1	NM_001005169.1		2619,2048,1830	GG,GC,CC		38.8385,46.1381,43.928		80/325	4615508	7286,5708	2201	4296	6497	SO:0001819	synonymous_variant	390037	exon1			CTCCTCCGTGGTA	BK004371	CCDS59223.1	11p15.4	2012-08-09				ENSG00000232268		"""GPCR / Class A : Olfactory receptors"""	15220	protein-coding gene	gene with protein product							Standard	NM_001005169		Approved		uc010qyi.2	Q8NGK6		ENST00000530443.2:c.240C>G	11.37:g.4615508C>G		Somatic	336	0	0		WXS	Illumina HiSeq	Phase_I	335	52	0.155224	NM_001005169	Q6IF91	Silent	SNP	ENST00000530443.2	37	CCDS59223.1																																																																																			C|0.416;G|0.584	0.584	strong		0.507	OR52I1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385947.2	NM_001005169	
KANK2	25959	hgsc.bcm.edu	37	19	11305161	11305161	+	Silent	SNP	A	A	G	rs754529	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:11305161A>G	ENST00000586659.1	-	3	341	c.27T>C	c.(25-27)gcT>gcC	p.A9A	KANK2_ENST00000432929.2_Silent_p.A9A|KANK2_ENST00000589359.1_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	43	0	0		WXS	Illumina HiSeq	Phase_I	47	22	0.468085	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	
LILRA6	79168	hgsc.bcm.edu	37	19	54744210	54744210	+	Missense_Mutation	SNP	A	A	G	rs8104206	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:54744210A>G	ENST00000396365.2	-	6	1237	c.1198T>C	c.(1198-1200)Tac>Cac	p.Y400H	LILRA6_ENST00000245621.5_Missense_Mutation_p.Y400H|LILRA6_ENST00000440558.2_Intron|LILRA6_ENST00000270464.5_Intron|LILRB3_ENST00000407860.2_Intron|LILRA6_ENST00000419410.2_Missense_Mutation_p.Y400H|LILRA6_ENST00000391735.3_3'UTR	NM_024318.2	NP_077294	Q6PI73	LIRA6_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 6	400	Ig-like C2-type 2.		Y -> H (in dbSNP:rs8104206).		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)		TTGGAGCTGTATGAGCCGTAG	0.592													.|||	1466	0.292732	0.3041	0.2205	5008	,	,		24658	0.2411		0.2664	False		,,,				2504	0.409				p.Y400H		Atlas-SNP	.											.	LILRA6	75	.	0			c.T1198C						PASS	.						82.0	114.0	103.0					19																	54744210		2198	4300	6498	SO:0001583	missense	79168	exon6			AGCTGTATGAGCC	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.1198T>C	19.37:g.54744210A>G	ENSP00000379651:p.Tyr400His	Somatic	294	0	0		WXS	Illumina HiSeq	Phase_I	188	54	0.287234	NM_024318		Missense_Mutation	SNP	ENST00000396365.2	37	CCDS42610.1	319	0.14606227106227107	68	0.13821138211382114	55	0.15193370165745856	77	0.1346153846153846	119	0.15699208443271767	A	0.303	-0.972591	0.02215	.	.	ENSG00000244482	ENST00000419410;ENST00000421123;ENST00000396365;ENST00000245621	T;T;T	0.00730	5.77;5.77;5.77	2.39	-1.47	0.08772	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	6.834670	0.00465	N	0.000119	T	0.00012	0.0000	N	0.05050	-0.12	0.80722	P	0.0	B;B;B	0.22480	0.008;0.07;0.001	B;B;B	0.18561	0.008;0.022;0.012	T	0.44065	-0.9352	9	0.14252	T	0.57	.	5.4146	0.16365	0.4611:0.0:0.5389:0.0	rs8104206	400;400;400	C9JFH3;Q6PI73;D3YTC4	.;LIRA6_HUMAN;.	H	400	ENSP00000411227:Y400H;ENSP00000379651:Y400H;ENSP00000245621:Y400H	ENSP00000245621:Y400H	Y	-	1	0	LILRA6	59436022	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-1.563000	0.02154	-0.381000	0.07882	-1.232000	0.01568	TAC	A|0.830;G|0.170	0.170	strong		0.592	LILRA6-003	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000313725.1	NM_024318	
PCDHB7	56129	hgsc.bcm.edu	37	5	140553919	140553919	+	Silent	SNP	C	C	A	rs17844456|rs386692906	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:140553919C>A	ENST00000231137.3	+	1	1677	c.1503C>A	c.(1501-1503)gcC>gcA	p.A501A		NM_018940.2	NP_061763.1	Q9Y5E2	PCDB7_HUMAN	protocadherin beta 7	501	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)			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)			TGCCCCTCGCCTCCCTGGTCT	0.672													C|||	759	0.151558	0.2572	0.1902	5008	,	,		16995	0.0417		0.1531	False		,,,				2504	0.093				p.A501A		Atlas-SNP	.											.	PCDHB7	231	.	0			c.C1503A						PASS	.	C		1021,3385	360.1+/-315.1	113,795,1295	86.0	89.0	88.0		1503	3.5	0.0	5	dbSNP_123	88	1409,7191	257.0+/-281.3	121,1167,3012	no	coding-synonymous	PCDHB7	NM_018940.2		234,1962,4307	AA,AC,CC		16.3837,23.1729,18.6837		501/794	140553919	2430,10576	2203	4300	6503	SO:0001819	synonymous_variant	56129	exon1			CCTCGCCTCCCTG	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.1503C>A	5.37:g.140553919C>A		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	100	50	0.5	NM_018940	A1L3Y8	Silent	SNP	ENST00000231137.3	37	CCDS4249.1																																																																																			C|0.826;A|0.174	0.174	strong		0.672	PCDHB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251803.2	NM_018940	
KDM7A	80853	hgsc.bcm.edu	37	7	139797431	139797431	+	Missense_Mutation	SNP	G	G	T	rs6950119	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:139797431G>T	ENST00000397560.2	-	15	2027	c.1930C>A	c.(1930-1932)Cgt>Agt	p.R644S	Y_RNA_ENST00000515919.1_RNA|JHDM1D_ENST00000006967.5_Missense_Mutation_p.R644S	NM_030647.1	NP_085150.1	Q6ZMT4	KDM7A_HUMAN		644			R -> S (in dbSNP:rs6950119). {ECO:0000269|PubMed:11214970}.		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)	p.R644S(1)		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)					GATTTCACACGTGTAAAAAAC	0.433													G|||	1640	0.327476	0.4039	0.2767	5008	,	,		20930	0.245		0.334	False		,,,				2504	0.3384				p.R644S		Atlas-SNP	.											JHDM1D,NS,carcinoma,0,1	JHDM1D	54	1	1	Substitution - Missense(1)	lung(1)	c.C1930A						PASS	.	G	SER/ARG	1415,2283		266,883,700	67.0	64.0	65.0		1930	3.2	1.0	7	dbSNP_116	65	2782,5404		475,1832,1786	yes	missense	JHDM1D	NM_030647.1	110	741,2715,2486	TT,TG,GG		33.9849,38.2639,35.3164	benign	644/942	139797431	4197,7687	1849	4093	5942	SO:0001583	missense	80853	exon15			TCACACGTGTAAA																												ENST00000397560.2:c.1930C>A	7.37:g.139797431G>T	ENSP00000380692:p.Arg644Ser	Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	106	45	0.424528	NM_030647	A4D1S9|C9JJH9|C9JQU2|Q6MZL8|Q9C0E5	Missense_Mutation	SNP	ENST00000397560.2	37	CCDS43658.1	664	0.304029304029304	188	0.3821138211382114	103	0.2845303867403315	137	0.2395104895104895	236	0.3113456464379947	G	4.224	0.040418	0.08148	0.382639	0.339849	ENSG00000006459	ENST00000397560;ENST00000006967	T;T	0.12465	2.92;2.68	5.53	3.18	0.36537	.	0.323397	0.40469	N	0.001093	T	0.00012	0.0000	N	0.00146	-1.995	0.34970	P	0.24697000000000002	B	0.02656	0.0	B	0.01281	0.0	T	0.43147	-0.9409	9	0.20519	T	0.43	-3.5099	8.5295	0.33326	0.1204:0.0:0.1557:0.7239	rs6950119;rs52801179;rs60741643;rs6950119	644	Q6ZMT4	KDM7_HUMAN	S	644	ENSP00000380692:R644S;ENSP00000006967:R644S	ENSP00000006967:R644S	R	-	1	0	JHDM1D	139443900	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	2.472000	0.45136	0.399000	0.25367	-0.237000	0.12165	CGT	A|0.000;G|0.670;T|0.330	0.330	strong		0.433	JHDM1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348460.1		
AKAP6	9472	hgsc.bcm.edu	37	14	33015397	33015397	+	Missense_Mutation	SNP	G	G	T	rs45477296	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:33015397G>T	ENST00000280979.4	+	4	1708	c.1538G>T	c.(1537-1539)cGg>cTg	p.R513L	AKAP6_ENST00000557272.1_Missense_Mutation_p.R513L|AKAP6_ENST00000557354.1_Missense_Mutation_p.R513L	NM_004274.4	NP_004265.3	Q13023	AKAP6_HUMAN	A kinase (PRKA) anchor protein 6	513					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)		ACACCTAAACGGGGGACTGGT	0.478													G|||	174	0.0347444	0.0401	0.0389	5008	,	,		20287	0.001		0.0586	False		,,,				2504	0.0348				p.R513L	Melanoma(49;821 1200 7288 13647 42351)	Atlas-SNP	.											.	AKAP6	308	.	0			c.G1538T						PASS	.	G	LEU/ARG	232,4174	134.9+/-171.1	5,222,1976	64.0	68.0	67.0		1538	-5.0	0.0	14	dbSNP_127	67	488,8112	139.0+/-195.8	13,462,3825	no	missense	AKAP6	NM_004274.4	102	18,684,5801	TT,TG,GG		5.6744,5.2655,5.5359	benign	513/2320	33015397	720,12286	2203	4300	6503	SO:0001583	missense	9472	exon4			CTAAACGGGGGAC	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.1538G>T	14.37:g.33015397G>T	ENSP00000280979:p.Arg513Leu	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	79	78	0.987342	NM_004274	A7E242|A7E2D4|O15028	Missense_Mutation	SNP	ENST00000280979.4	37	CCDS9644.1	89	0.04075091575091575	18	0.036585365853658534	19	0.052486187845303865	0	0.0	52	0.06860158311345646	G	9.851	1.193544	0.22037	0.052655	0.056744	ENSG00000151320	ENST00000280979;ENST00000557354;ENST00000557272;ENST00000553547	T;T;T;T	0.49720	0.77;0.77;0.77;0.77	5.89	-5.03	0.02973	.	1.100850	0.06798	N	0.788311	T	0.02494	0.0076	L	0.40543	1.245	0.09310	N	1	B;B	0.25007	0.033;0.116	B;B	0.17433	0.007;0.018	T	0.17992	-1.0351	10	0.72032	D	0.01	1.0023	2.3782	0.04347	0.3556:0.2853:0.262:0.0971	rs45477296;rs59656153;rs61754293	513;513	A7E242;Q13023	.;AKAP6_HUMAN	L	513;513;513;271	ENSP00000280979:R513L;ENSP00000450531:R513L;ENSP00000451247:R513L;ENSP00000451239:R271L	ENSP00000280979:R513L	R	+	2	0	AKAP6	32085148	0.000000	0.05858	0.000000	0.03702	0.559000	0.35586	-0.885000	0.04161	-1.085000	0.03088	0.655000	0.94253	CGG	G|0.952;T|0.048	0.048	strong		0.478	AKAP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276617.2	NM_004274	
MUC4	4585	hgsc.bcm.edu	37	3	195511390	195511390	+	Missense_Mutation	SNP	T	T	G	rs75692609	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195511390T>G	ENST00000463781.3	-	2	7520	c.7061A>C	c.(7060-7062)cAt>cCt	p.H2354P	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.H2354P	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.H2354P(2)|p.H2354L(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)		GTCGGTGACATGAAGAGGGGT	0.582													.|||	288	0.057508	0.1505	0.0216	5008	,	,		22743	0.004		0.0288	False		,,,				2504	0.0419				p.H2354P		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,3	MUC4	1505	3	3	Substitution - Missense(3)	stomach(2)|endometrium(1)	c.A7061C						PASS	.						18.0	15.0	16.0					3																	195511390		675	1569	2244	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.7061A>C	3.37:g.195511390T>G	ENSP00000417498:p.His2354Pro	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	49	26	0.530612	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	t	2.704	-0.270348	0.05716	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.28666	1.61;1.6	.	.	.	.	.	.	.	.	T	0.08935	0.0221	N	0.02539	-0.55	0.09310	N	1	B	0.10296	0.003	B	0.01281	0.0	T	0.28267	-1.0049	7	.	.	.	.	5.2163	0.15344	0.0:0.0:0.5975:0.4024	.	2354	E7ESK3	.	P	2354	ENSP00000417498:H2354P;ENSP00000420243:H2354P	.	H	-	2	0	MUC4	196995785	0.004000	0.15560	0.001000	0.08648	0.045000	0.14185	-2.399000	0.01050	-2.179000	0.00767	-2.418000	0.00219	CAT	T|0.928;G|0.072	0.072	strong		0.582	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
CR1	1378	hgsc.bcm.edu	37	1	207753621	207753621	+	Missense_Mutation	SNP	A	A	G	rs2274567	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:207753621A>G	ENST00000367049.4	+	30	4973	c.4973A>G	c.(4972-4974)cAt>cGt	p.H1658R	CR1_ENST00000367053.1_Missense_Mutation_p.H1208R|CR1_ENST00000367052.1_Missense_Mutation_p.H1208R|RP11-78B10.2_ENST00000597497.1_RNA|CR1_ENST00000367051.1_Missense_Mutation_p.H1208R|RP11-78B10.2_ENST00000596003.1_RNA|CR1_ENST00000400960.2_Missense_Mutation_p.H1208R	NM_000651.4	NP_000642.3	P17927	CR1_HUMAN	complement component (3b/4b) receptor 1 (Knops blood group)	1208	Sushi 26. {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						CATGGTGAGCATACCCCAAGC	0.522													A|||	1474	0.294329	0.2186	0.2709	5008	,	,		18110	0.3274		0.1819	False		,,,				2504	0.4949				p.H1658R		Atlas-SNP	.											.	CR1	354	.	0			c.A4973G						PASS	.	A	ARG/HIS,ARG/HIS	875,3049		94,687,1181	126.0	127.0	126.0		3623,4973	0.2	0.0	1	dbSNP_100	126	1524,6788		129,1266,2761	no	missense,missense	CR1	NM_000573.3,NM_000651.4	29,29	223,1953,3942	GG,GA,AA		18.3349,22.2987,19.6061	probably-damaging,probably-damaging	1208/2040,1658/2490	207753621	2399,9837	1962	4156	6118	SO:0001583	missense	1378	exon30			GTGAGCATACCCC	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.4973A>G	1.37:g.207753621A>G	ENSP00000356016:p.His1658Arg	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	115	51	0.443478	NM_000651	Q16744|Q16745|Q5SR43|Q5SR45|Q9UQV2	Missense_Mutation	SNP	ENST00000367049.4	37	CCDS44308.1	487	0.222985347985348	114	0.23170731707317074	108	0.2983425414364641	134	0.23426573426573427	131	0.17282321899736147	A	0.454	-0.892160	0.02491	0.222987	0.183349	ENSG00000203710	ENST00000367052;ENST00000367051;ENST00000367053;ENST00000400960;ENST00000534202;ENST00000367049	T;T;T;T;T;T	0.63255	-0.03;-0.03;-0.03;-0.03;-0.03;-0.03	4.34	0.182	0.15077	Complement control module (2);Sushi/SCR/CCP (3);	.	.	.	.	T	0.00012	0.0000	N	0.17674	0.51	0.80722	P	0.0	B;B;D	0.65815	0.147;0.08;0.995	B;B;D	0.74674	0.168;0.049;0.984	T	0.09907	-1.0653	8	0.25106	T	0.35	.	1.2006	0.01884	0.5248:0.1803:0.1191:0.1757	rs2274567;rs3860293;rs17047280;rs52826014;rs60859711;rs2274567	1208;1208;1658	Q5SR44;P17927;E9PDY4	.;CR1_HUMAN;.	R	1208;1208;1208;1208;758;1658	ENSP00000356019:H1208R;ENSP00000356018:H1208R;ENSP00000356020:H1208R;ENSP00000383744:H1208R;ENSP00000436139:H758R;ENSP00000356016:H1658R	ENSP00000356016:H1658R	H	+	2	0	CR1	205820244	0.000000	0.05858	0.001000	0.08648	0.091000	0.18340	0.814000	0.27239	0.164000	0.19529	0.529000	0.55759	CAT	A|0.785;G|0.214	0.214	strong		0.522	CR1-012	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382527.1	NM_000573	
CARD10	29775	hgsc.bcm.edu	37	22	37900771	37900771	+	Silent	SNP	A	A	G	rs3817806	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:37900771A>G	ENST00000403299.1	-	9	1605	c.1389T>C	c.(1387-1389)tgT>tgC	p.C463C	CARD10_ENST00000251973.5_Silent_p.C463C|CARD10_ENST00000406271.3_Silent_p.C177C			Q9BWT7	CAR10_HUMAN	caspase recruitment domain family, member 10	463					activation of NF-kappaB-inducing kinase activity (GO:0007250)|protein complex assembly (GO:0006461)|regulation of apoptotic process (GO:0042981)	CBM complex (GO:0032449)|cytoplasm (GO:0005737)	receptor signaling complex scaffold activity (GO:0030159)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	17	Melanoma(58;0.0574)					GGGAGGAGGCACAGGCCTGGA	0.622													A|||	551	0.110024	0.053	0.0461	5008	,	,		17960	0.125		0.0755	False		,,,				2504	0.2526				p.C463C		Atlas-SNP	.											.	CARD10	55	.	0			c.T1389C						PASS	.	A		226,4180	132.9+/-169.3	4,218,1981	52.0	39.0	43.0		1389	-3.5	0.9	22	dbSNP_107	43	519,8081	144.8+/-200.6	13,493,3794	no	coding-synonymous	CARD10	NM_014550.3		17,711,5775	GG,GA,AA		6.0349,5.1294,5.7281		463/1033	37900771	745,12261	2203	4300	6503	SO:0001819	synonymous_variant	29775	exon8			GGAGGCACAGGCC	AF086324	CCDS13948.1	22q13.1	2008-05-22			ENSG00000100065	ENSG00000100065			16422	protein-coding gene	gene with protein product		607209				11259443, 11356195	Standard	NM_014550		Approved	CARMA3, BIMP1	uc003asu.1	Q9BWT7	OTTHUMG00000150592	ENST00000403299.1:c.1389T>C	22.37:g.37900771A>G		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	58	29	0.5	NM_014550	Q14CQ8|Q5TFG6|Q8NC81|Q9UGR5|Q9UGR6|Q9Y3H0	Silent	SNP	ENST00000403299.1	37	CCDS13948.1																																																																																			A|0.934;G|0.066	0.066	strong		0.622	CARD10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318997.1	NM_014550	
PPAN	56342	hgsc.bcm.edu	37	19	10221642	10221642	+	Missense_Mutation	SNP	A	A	G	rs11559188	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:10221642A>G	ENST00000253107.7	+	12	1329	c.1223A>G	c.(1222-1224)cAg>cGg	p.Q408R	SNORD105B_ENST00000458770.1_RNA|P2RY11_ENST00000321826.4_5'Flank|PPAN_ENST00000556468.1_Missense_Mutation_p.Q408R|PPAN-P2RY11_ENST00000428358.1_Missense_Mutation_p.Q408R|PPAN-P2RY11_ENST00000393796.4_Missense_Mutation_p.Q408R|PPAN_ENST00000393793.1_Missense_Mutation_p.Q355R	NM_020230.5	NP_064615.3	Q9NQ55	SSF1_HUMAN	peter pan homolog (Drosophila)	408			Q -> R (in dbSNP:rs11559188).		RNA splicing (GO:0008380)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(3)|liver(2)|lung(7)|prostate(1)|skin(1)|urinary_tract(1)	15			OV - Ovarian serous cystadenocarcinoma(20;2.19e-08)|Epithelial(33;1.76e-05)|all cancers(31;3.54e-05)			GAGGCCAAGCAGAAACGGCTT	0.617													G|||	338	0.067492	0.1868	0.0086	5008	,	,		15016	0.0248		0.001	False		,,,				2504	0.0603				p.Q408R		Atlas-SNP	.											.	PPAN	43	.	0			c.A1223G						PASS	.	G	ARG/GLN,ARG/GLN,ARG/GLN	600,3804	749.0+/-412.0	45,510,1647	50.0	55.0	53.0		1223,1223,1223	0.3	0.0	19	dbSNP_120	53	13,8587	804.3+/-407.3	1,11,4288	yes	missense,missense,missense	PPAN,PPAN-P2RY11	NM_001040664.2,NM_001198690.1,NM_020230.5	43,43,43	46,521,5935	GG,GA,AA		0.1512,13.624,4.7139	benign,benign,benign	408/795,408/521,408/474	10221642	613,12391	2202	4300	6502	SO:0001583	missense	56342	exon12			CCAAGCAGAAACG	BC033202	CCDS12225.1	19p13.2	2008-02-05	2001-11-28		ENSG00000130810	ENSG00000130810			9227	protein-coding gene	gene with protein product		607793	"""peter pan (Drosophila) homolog"""			10873382	Standard	NM_020230		Approved	SSF1, SSF2, SSF, BXDC3		Q9NQ55	OTTHUMG00000156826	ENST00000253107.7:c.1223A>G	19.37:g.10221642A>G	ENSP00000253107:p.Gln408Arg	Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	35	17	0.485714	NM_020230	C9J3F9|Q9BW97|Q9H170	Missense_Mutation	SNP	ENST00000253107.7	37	CCDS12225.1	108|108	0.04945054945054945|0.04945054945054945	83|83	0.16869918699186992|0.16869918699186992	6|6	0.016574585635359115|0.016574585635359115	18|18	0.03146853146853147|0.03146853146853147	1|1	0.0013192612137203166|0.0013192612137203166	G|G	0.267|0.267	-0.995545|-0.995545	0.02145|0.02145	0.13624|0.13624	0.001512|0.001512	ENSG00000243207;ENSG00000243207;ENSG00000130810;ENSG00000130810;ENSG00000130810;ENSG00000130810|ENSG00000130810	ENST00000428358;ENST00000393796;ENST00000253107;ENST00000556468;ENST00000342696;ENST00000393793|ENST00000444703	T;T;T;T;T|.	0.60548|.	1.6;0.18;1.63;0.18;1.63|.	4.9|4.9	0.3|0.3	0.15776|0.15776	.|.	.|.	.|.	.|.	.|.	T|T	0.00039|0.00039	0.0001|0.0001	N|N	0.03209|0.03209	-0.39|-0.39	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	0.34502|0.34502	-0.9826|-0.9826	8|4	0.02654|.	T|.	1|.	-10.6805|-10.6805	4.6937|4.6937	0.12793|0.12793	0.3502:0.1497:0.5:0.0|0.3502:0.1497:0.5:0.0	rs11559188;rs11559188|rs11559188;rs11559188	408;408;408|.	C9J3F9;C9JW41;Q9NQ55|.	.;.;SSF1_HUMAN|.	R|G	408;408;408;408;408;355|143	ENSP00000411918:Q408R;ENSP00000377385:Q408R;ENSP00000253107:Q408R;ENSP00000450710:Q408R;ENSP00000377382:Q355R|.	ENSP00000253107:Q408R|.	Q|R	+|+	2|1	0|2	PPAN;PPAN-P2RY11|PPAN	10082642|10082642	0.217000|0.217000	0.23597|0.23597	0.000000|0.000000	0.03702|0.03702	0.001000|0.001000	0.01503|0.01503	0.119000|0.119000	0.15626|0.15626	-0.332000|-0.332000	0.08489|0.08489	-2.224000|-2.224000	0.00294|0.00294	CAG|AGA	A|0.943;G|0.057	0.057	strong		0.617	PPAN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316658.1	NM_020230	
PCCB	5096	hgsc.bcm.edu	37	3	136012637	136012637	+	Nonsense_Mutation	SNP	A	A	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:136012637A>T	ENST00000251654.4	+	7	764	c.694A>T	c.(694-696)Aag>Tag	p.K232*	PCCB_ENST00000478469.1_Nonsense_Mutation_p.K232*|PCCB_ENST00000468777.1_Nonsense_Mutation_p.K263*|PCCB_ENST00000471595.1_Nonsense_Mutation_p.K232*|PCCB_ENST00000462637.1_Nonsense_Mutation_p.K209*|PCCB_ENST00000482086.1_Nonsense_Mutation_p.K116*|PCCB_ENST00000483687.1_Nonsense_Mutation_p.K213*|PCCB_ENST00000474833.1_3'UTR|PCCB_ENST00000490504.1_Nonsense_Mutation_p.K175*|PCCB_ENST00000466072.1_Nonsense_Mutation_p.K232*|PCCB_ENST00000469217.1_Nonsense_Mutation_p.K252*	NM_000532.4	NP_000523.2	P05166	PCCB_HUMAN	propionyl CoA carboxylase, beta polypeptide	232	Carboxyltransferase.				biotin metabolic process (GO:0006768)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|short-chain fatty acid catabolic process (GO:0019626)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|propionyl-CoA carboxylase activity (GO:0004658)			breast(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(10)|ovary(1)|urinary_tract(1)	25					Biotin(DB00121)|L-Valine(DB00161)	TGATGTTGTGAAGTCTGTCAC	0.507																																					p.K252X		Atlas-SNP	.											.	PCCB	52	.	0			c.A754T						PASS	.						216.0	204.0	208.0					3																	136012637		2203	4300	6503	SO:0001587	stop_gained	5096	exon8			GTTGTGAAGTCTG		CCDS3089.1, CCDS54643.1	3q21-q22	2010-07-01	2010-04-30		ENSG00000114054	ENSG00000114054	6.4.1.3		8654	protein-coding gene	gene with protein product		232050	"""propionyl Coenzyme A carboxylase, beta polypeptide"""			2895916	Standard	NM_000532		Approved		uc003eqy.2	P05166	OTTHUMG00000159792	ENST00000251654.4:c.694A>T	3.37:g.136012637A>T	ENSP00000251654:p.Lys232*	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	58	17	0.293103	NM_001178014	B7Z2Z4|Q16813|Q96CX0	Nonsense_Mutation	SNP	ENST00000251654.4	37	CCDS3089.1	.	.	.	.	.	.	.	.	.	.	A	36	5.673289	0.96754	.	.	ENSG00000114054	ENST00000251654;ENST00000490504;ENST00000483687;ENST00000468777;ENST00000462637;ENST00000466072;ENST00000482086;ENST00000471595;ENST00000469217;ENST00000478469	.	.	.	5.02	5.02	0.67125	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	14.7115	0.69235	1.0:0.0:0.0:0.0	.	.	.	.	X	232;175;213;263;209;232;116;232;252;232	.	ENSP00000251654:K232X	K	+	1	0	PCCB	137495327	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	8.520000	0.90566	2.009000	0.58944	0.528000	0.53228	AAG	.	.	none		0.507	PCCB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000357335.1		
TMC6	11322	hgsc.bcm.edu	37	17	76117136	76117136	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:76117136G>A	ENST00000590602.1	-	12	1652	c.1493C>T	c.(1492-1494)cCg>cTg	p.P498L	TMC6_ENST00000322933.4_Missense_Mutation_p.P137L|TMC6_ENST00000306591.7_Intron|TMC6_ENST00000592076.1_Intron|TMC6_ENST00000589553.1_Missense_Mutation_p.P271L|TMC6_ENST00000591436.1_Missense_Mutation_p.P137L|TMC6_ENST00000322914.3_Missense_Mutation_p.P498L|TMC6_ENST00000392467.3_Missense_Mutation_p.P498L			Q7Z403	TMC6_HUMAN	transmembrane channel-like 6	498					ion transport (GO:0006811)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear membrane (GO:0031965)				NS(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(5)|upper_aerodigestive_tract(1)	14			BRCA - Breast invasive adenocarcinoma(99;0.00269)|Lung(188;0.0973)			GGAGTCATGCGGCTCCAGGGC	0.632																																					p.P498L		Atlas-SNP	.											.	TMC6	42	.	0			c.C1493T						PASS	.						40.0	39.0	39.0					17																	76117136		2203	4300	6503	SO:0001583	missense	11322	exon12			TCATGCGGCTCCA	AY057379	CCDS32748.1	17q25.3	2014-09-17	2005-11-10	2005-11-10	ENSG00000141524	ENSG00000141524			18021	protein-coding gene	gene with protein product		605828	"""epidermodysplasia verruciformis 1"""	EVER1		12426567	Standard	NM_007267		Approved	LAK-4P, EVIN1	uc002juk.2	Q7Z403	OTTHUMG00000177466	ENST00000590602.1:c.1493C>T	17.37:g.76117136G>A	ENSP00000465261:p.Pro498Leu	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	129	71	0.550388	NM_001127198	O43284|Q45VJ2|Q8IU98|Q8IUI7|Q8IWU8|Q8TEQ7|Q9HAG5	Missense_Mutation	SNP	ENST00000590602.1	37	CCDS32748.1	.	.	.	.	.	.	.	.	.	.	G	4.500	0.092789	0.08632	.	.	ENSG00000141524	ENST00000322914;ENST00000392467;ENST00000322933	T;T;T	0.70399	-0.1;-0.1;-0.48	3.93	0.273	0.15650	.	0.837178	0.10830	N	0.629444	T	0.44414	0.1292	N	0.19112	0.55	0.33151	D	0.545754	B;P;B;B	0.39094	0.099;0.659;0.09;0.259	B;B;B;B	0.24848	0.033;0.056;0.005;0.027	T	0.48080	-0.9066	10	0.42905	T	0.14	-12.4351	4.296	0.10901	0.0:0.191:0.2303:0.5788	.	271;498;498;137	Q7Z403-4;B3KTU5;Q7Z403;Q7Z403-3	.;.;TMC6_HUMAN;.	L	498;498;137	ENSP00000313408:P498L;ENSP00000376260:P498L;ENSP00000313479:P137L	ENSP00000313408:P498L	P	-	2	0	TMC6	73628731	0.022000	0.18835	0.402000	0.26371	0.729000	0.41735	-0.010000	0.12743	-0.092000	0.12417	0.462000	0.41574	CCG	.	.	none		0.632	TMC6-007	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437146.1		
GRM6	2916	hgsc.bcm.edu	37	5	178410151	178410151	+	Silent	SNP	C	C	T	rs2071247	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:178410151C>T	ENST00000517717.1	-	10	2234	c.2196G>A	c.(2194-2196)acG>acA	p.T732T	RP11-281O15.4_ENST00000519491.1_RNA|GRM6_ENST00000231188.5_Silent_p.T732T			O15303	GRM6_HUMAN	glutamate receptor, metabotropic 6	732					adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|detection of light stimulus involved in visual perception (GO:0050908)|detection of visible light (GO:0009584)|G-protein coupled glutamate receptor signaling pathway (GO:0007216)|locomotory behavior (GO:0007626)|positive regulation of calcium ion import (GO:0090280)|regulation of synaptic transmission, glutamatergic (GO:0051966)|retina development in camera-type eye (GO:0060041)|synaptic transmission (GO:0007268)	cell projection (GO:0042995)|endoplasmic reticulum membrane (GO:0005789)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|new growing cell tip (GO:0035841)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)|group III metabotropic glutamate receptor activity (GO:0001642)|protein homodimerization activity (GO:0042803)			NS(2)|breast(4)|endometrium(9)|large_intestine(12)|lung(21)|ovary(2)|pancreas(1)|prostate(3)|urinary_tract(1)	55	all_cancers(89;0.000828)|Renal(175;0.000159)|all_epithelial(37;0.000167)|Lung NSC(126;0.00199)|all_lung(126;0.00351)	all_cancers(40;0.0156)|all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.245)		CGGGGTCCACCGTCCGCTGTT	0.622													c|||	1258	0.251198	0.2171	0.2003	5008	,	,		18687	0.372		0.168	False		,,,				2504	0.2945				p.T732T		Atlas-SNP	.											.	GRM6	149	.	0			c.G2196A						PASS	.	T		890,3516	346.4+/-309.0	87,716,1400	87.0	70.0	76.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	2196	-5.9	0.8	5	dbSNP_96	76	1419,7181	272.3+/-290.0	129,1161,3010	no	coding-synonymous	GRM6	NM_000843.3		216,1877,4410	TT,TC,CC		16.5,20.1997,17.7533		732/878	178410151	2309,10697	2203	4300	6503	SO:0001819	synonymous_variant	2916	exon9			GTCCACCGTCCGC	U82083	CCDS4442.1	5q35	2014-01-28						"""GPCR / Class C : Glutamate receptors, metabotropic"", ""Glutamate receptors"""	4598	protein-coding gene	gene with protein product		604096				9215706	Standard	NM_000843		Approved	GPRC1F, mGlu6, MGLUR6, CSNB1B	uc003mjr.3	O15303	OTTHUMG00000130889	ENST00000517717.1:c.2196G>A	5.37:g.178410151C>T		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	96	59	0.614583	NM_000843		Silent	SNP	ENST00000517717.1	37	CCDS4442.1																																																																																			C|0.792;T|0.208	0.208	strong		0.622	GRM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253474.2		
ASCC3	10973	hgsc.bcm.edu	37	6	101166095	101166095	+	Silent	SNP	G	G	A	rs41288423	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:101166095G>A	ENST00000369162.2	-	12	2279	c.1935C>T	c.(1933-1935)ctC>ctT	p.L645L	ASCC3_ENST00000522650.1_Silent_p.L645L	NM_006828.2	NP_006819.2	Q8N3C0	ASCC3_HUMAN	activating signal cointegrator 1 complex subunit 3	645	Helicase ATP-binding 1. {ECO:0000255|PROSITE-ProRule:PRU00541}.				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.L645L(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)		CAGACAGTCCGAGAATCCTTA	0.323													G|||	2297	0.458666	0.4735	0.3948	5008	,	,		15981	0.3135		0.4771	False		,,,				2504	0.6145				p.L645L		Atlas-SNP	.											ASCC3,NS,carcinoma,0,2	ASCC3	205	2	1	Substitution - coding silent(1)	stomach(1)	c.C1935T						PASS	.	G		2022,2384	562.7+/-381.0	475,1072,656	112.0	108.0	109.0		1935	0.4	1.0	6	dbSNP_127	109	4273,4327	575.0+/-390.2	1079,2115,1106	no	coding-synonymous	ASCC3	NM_006828.2		1554,3187,1762	AA,AG,GG		49.686,45.892,48.4007		645/2203	101166095	6295,6711	2203	4300	6503	SO:0001819	synonymous_variant	10973	exon12			CAGTCCGAGAATC	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.1935C>T	6.37:g.101166095G>A		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	67	67	1	NM_006828	E7EW23|O43738|Q4G1A0|Q5VTN2|Q9H1I9|Q9H5A2|Q9NTR0	Silent	SNP	ENST00000369162.2	37	CCDS5046.1																																																																																			G|0.528;A|0.472	0.472	strong		0.323	ASCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041632.2	NM_006828	
SLC38A8	146167	hgsc.bcm.edu	37	16	84050209	84050209	+	Silent	SNP	G	G	A	rs77876966	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:84050209G>A	ENST00000299709.3	-	8	1076	c.1077C>T	c.(1075-1077)ctC>ctT	p.L359L		NM_001080442.1	NP_001073911.1	A6NNN8	S38A8_HUMAN	solute carrier family 38, member 8	359					amino acid transport (GO:0006865)|sodium ion transport (GO:0006814)	integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(12)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	26						GCGCCATGGCGAGCGTCACGG	0.637													G|||	137	0.0273562	0.0265	0.0317	5008	,	,		20610	0.0		0.0716	False		,,,				2504	0.0082				p.L359L		Atlas-SNP	.											.	SLC38A8	60	.	0			c.C1077T						PASS	.	G		131,4269	95.3+/-134.0	1,129,2070	81.0	72.0	75.0		1077	-2.2	0.3	16	dbSNP_132	75	467,8133	138.4+/-195.2	17,433,3850	no	coding-synonymous	SLC38A8	NM_001080442.1		18,562,5920	AA,AG,GG		5.4302,2.9773,4.6		359/436	84050209	598,12402	2200	4300	6500	SO:0001819	synonymous_variant	146167	exon8			CATGGCGAGCGTC		CCDS32495.1	16q23.3	2013-05-22				ENSG00000166558		"""Solute carriers"""	32434	protein-coding gene	gene with protein product		615585					Standard	XM_006721135		Approved		uc002fhg.1	A6NNN8		ENST00000299709.3:c.1077C>T	16.37:g.84050209G>A		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	62	30	0.483871	NM_001080442		Silent	SNP	ENST00000299709.3	37	CCDS32495.1																																																																																			G|0.954;A|0.046	0.046	strong		0.637	SLC38A8-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432623.1	NM_001080442	
CTH	1491	hgsc.bcm.edu	37	1	70904800	70904800	+	Missense_Mutation	SNP	G	G	T	rs1021737	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	176	0	0		WXS	Illumina HiSeq	Phase_I	172	73	0.424419	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	
OR51B6	390058	hgsc.bcm.edu	37	11	5372863	5372863	+	Silent	SNP	T	T	A	rs10837882	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:5372863T>A	ENST00000380219.1	+	1	126	c.126T>A	c.(124-126)acT>acA	p.T42T	HBE1_ENST00000380237.1_Intron|HBG2_ENST00000380252.1_Intron|AC104389.28_ENST00000415970.1_RNA|HBG2_ENST00000380259.2_Intron	NM_001004750.1	NP_001004750.1	Q9H340	O51B6_HUMAN	olfactory receptor, family 51, subfamily B, member 6	42					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)		GCAATGGCACTCTTCTCTTTC	0.468													T|||	750	0.14976	0.0658	0.0937	5008	,	,		22274	0.2351		0.1193	False		,,,				2504	0.2464				p.T42T		Atlas-SNP	.											.	OR51B6	53	.	0			c.T126A						PASS	.	T		412,3990	202.1+/-225.0	19,374,1808	175.0	139.0	151.0		126	-5.6	0.1	11	dbSNP_120	151	1090,7504	228.0+/-263.2	80,930,3287	no	coding-synonymous	OR51B6	NM_001004750.1		99,1304,5095	AA,AT,TT		12.6833,9.3594,11.5574		42/313	5372863	1502,11494	2201	4297	6498	SO:0001819	synonymous_variant	390058	exon1			TGGCACTCTTCTC		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.126T>A	11.37:g.5372863T>A		Somatic	282	0	0		WXS	Illumina HiSeq	Phase_I	350	276	0.788571	NM_001004750		Silent	SNP	ENST00000380219.1	37	CCDS31379.1																																																																																			T|0.871;A|0.129	0.129	strong		0.468	OR51B6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142960.1	NM_001004750	
KCNG4	93107	hgsc.bcm.edu	37	16	84256410	84256410	+	Missense_Mutation	SNP	C	C	T	rs7196482	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	93	0	0		WXS	Illumina HiSeq	Phase_I	85	51	0.6	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	
OR4M2	390538	hgsc.bcm.edu	37	15	22369290	22369290	+	Missense_Mutation	SNP	A	A	G	rs12593418	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:22369290A>G	ENST00000332663.2	+	1	813	c.715A>G	c.(715-717)Atg>Gtg	p.M239V	RP11-69H14.6_ENST00000558896.1_RNA	NM_001004719.2	NP_001004719.2	Q8NGB6	OR4M2_HUMAN	olfactory receptor, family 4, subfamily M, member 2	239			M -> V (in dbSNP:rs12593418).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.M239V(1)		NS(2)|endometrium(2)|kidney(4)|large_intestine(6)|lung(38)|ovary(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)	63		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)		CAACAGGGCCATGTCCACCTG	0.453																																					p.M239V		Atlas-SNP	.											OR4M2,NS,carcinoma,0,1	OR4M2	140	1	1	Substitution - Missense(1)	stomach(1)	c.A715G						PASS	.						288.0	199.0	229.0					15																	22369290		2203	4300	6503	SO:0001583	missense	390538	exon1			AGGGCCATGTCCA	AC060768	CCDS32172.1	15q11.2	2013-09-23			ENSG00000182974	ENSG00000182974		"""GPCR / Class A : Olfactory receptors"""	15373	protein-coding gene	gene with protein product							Standard	NM_001004719		Approved		uc010tzu.2	Q8NGB6	OTTHUMG00000171738	ENST00000332663.2:c.715A>G	15.37:g.22369290A>G	ENSP00000329467:p.Met239Val	Somatic	242	0	0		WXS	Illumina HiSeq	Phase_I	328	86	0.262195	NM_001004719	B9EH16|Q6IEY2	Missense_Mutation	SNP	ENST00000332663.2	37	CCDS32172.1	566	0.2591575091575092	57	0.11585365853658537	114	0.3149171270718232	177	0.3094405594405594	218	0.287598944591029	.	6.608	0.480486	0.12581	.	.	ENSG00000182974	ENST00000332663	T	0.00044	8.83	2.28	-0.1	0.13621	GPCR, rhodopsin-like superfamily (1);	0.309717	0.27139	N	0.020757	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.06405	0.002	T	0.31806	-0.9930	9	0.72032	D	0.01	-4.5993	5.3649	0.16107	0.6814:0.0:0.3186:0.0	rs12593418	239	Q8NGB6	OR4M2_HUMAN	V	239	ENSP00000329467:M239V	ENSP00000329467:M239V	M	+	1	0	OR4M2	19870654	0.000000	0.05858	0.993000	0.49108	0.973000	0.67179	-1.357000	0.02607	0.160000	0.19432	0.368000	0.22195	ATG	.	.	weak		0.453	OR4M2-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414921.1		
DVL2	1856	hgsc.bcm.edu	37	17	7133609	7133609	+	Silent	SNP	G	G	A	rs2074216	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	75	0	0		WXS	Illumina HiSeq	Phase_I	54	29	0.537037	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	
MOXD1	26002	hgsc.bcm.edu	37	6	132636820	132636820	+	Missense_Mutation	SNP	C	C	G	rs36075540	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:132636820C>G	ENST00000367963.3	-	10	1580	c.1462G>C	c.(1462-1464)Gaa>Caa	p.E488Q	MOXD1_ENST00000336749.3_Missense_Mutation_p.E420Q|MOXD1_ENST00000489128.1_5'Flank	NM_015529.2	NP_056344.2	Q6UVY6	MOXD1_HUMAN	monooxygenase, DBH-like 1	488			E -> Q (in dbSNP:rs36075540).			endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	copper ion binding (GO:0005507)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced ascorbate as one donor, and incorporation of one atom of oxygen (GO:0016715)			breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(15)|ovary(1)|prostate(3)|skin(1)	37	Breast(56;0.0495)			OV - Ovarian serous cystadenocarcinoma(155;0.0132)|GBM - Glioblastoma multiforme(226;0.0191)		TGAAGTTGTTCCATAATGTCT	0.398													C|||	58	0.0115815	0.0023	0.013	5008	,	,		18184	0.0		0.0437	False		,,,				2504	0.002				p.E488Q		Atlas-SNP	.											.	MOXD1	136	.	0			c.G1462C						PASS	.	C	GLN/GLU	40,4366	43.8+/-77.6	0,40,2163	209.0	204.0	206.0		1462	5.6	1.0	6	dbSNP_126	206	409,8191	129.0+/-187.1	15,379,3906	yes	missense	MOXD1	NM_015529.2	29	15,419,6069	GG,GC,CC		4.7558,0.9079,3.4523	benign	488/614	132636820	449,12557	2203	4300	6503	SO:0001583	missense	26002	exon10			GTTGTTCCATAAT	AY007239	CCDS5152.2	6q23.2	2010-09-24			ENSG00000079931	ENSG00000079931			21063	protein-coding gene	gene with protein product		609000				9751809	Standard	XM_006715456		Approved	DKFZP564G202, MOX, dJ248E1.1	uc003qdf.3	Q6UVY6	OTTHUMG00000055853	ENST00000367963.3:c.1462G>C	6.37:g.132636820C>G	ENSP00000356940:p.Glu488Gln	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	57	35	0.614035	NM_015529	Q5THU6|Q8NC97|Q8WV49|Q9H4M6|Q9Y4U3	Missense_Mutation	SNP	ENST00000367963.3	37	CCDS5152.2	45	0.020604395604395604	0	0.0	6	0.016574585635359115	0	0.0	39	0.051451187335092345	C	12.67	2.009021	0.35415	0.009079	0.047558	ENSG00000079931	ENST00000367963;ENST00000336749	T;T	0.63417	-0.04;-0.04	5.56	5.56	0.83823	PHM/PNGase F domain (1);	0.153267	0.44097	D	0.000496	T	0.22898	0.0553	N	0.04508	-0.205	0.80722	D	1	B;B	0.22003	0.008;0.063	B;B	0.21151	0.02;0.033	T	0.16660	-1.0395	10	0.14656	T	0.56	-15.0892	15.0664	0.71999	0.0:0.8585:0.1415:0.0	rs36075540	488;420	Q6UVY6;Q6UVY6-2	MOXD1_HUMAN;.	Q	488;420	ENSP00000356940:E488Q;ENSP00000336998:E420Q	ENSP00000336998:E420Q	E	-	1	0	MOXD1	132678513	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	4.488000	0.60300	2.608000	0.88229	0.563000	0.77884	GAA	C|0.971;G|0.029	0.029	strong		0.398	MOXD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000125837.1	NM_015529	
UNC5C	8633	hgsc.bcm.edu	37	4	96106322	96106322	+	Missense_Mutation	SNP	A	A	G	rs2289043	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:96106322A>G	ENST00000453304.1	-	13	2510	c.2162T>C	c.(2161-2163)aTg>aCg	p.M721T		NM_003728.3	NP_003719.3	O95185	UNC5C_HUMAN	unc-5 homolog C (C. elegans)	721			M -> T (in dbSNP:rs2289043). {ECO:0000269|PubMed:9782087}.		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)		CTGTCCTCCCATCTGTCTCTC	0.448													A|||	2477	0.494609	0.0923	0.7507	5008	,	,		17114	0.5694		0.7147	False		,,,				2504	0.5532				p.M721T		Atlas-SNP	.											.	UNC5C	141	.	0			c.T2162C						PASS	.	A	THR/MET	816,3590	325.0+/-298.9	93,630,1480	109.0	103.0	105.0		2162	4.7	1.0	4	dbSNP_100	105	6041,2559	691.7+/-404.5	2147,1747,406	yes	missense	UNC5C	NM_003728.3	81	2240,2377,1886	GG,GA,AA		29.7558,18.5202,47.2782	benign	721/932	96106322	6857,6149	2203	4300	6503	SO:0001583	missense	8633	exon13			CCTCCCATCTGTC	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.2162T>C	4.37:g.96106322A>G	ENSP00000406022:p.Met721Thr	Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	101	98	0.970297	NM_003728	Q8IUT0	Missense_Mutation	SNP	ENST00000453304.1	37	CCDS3643.1	1191	0.5453296703296703	46	0.09349593495934959	260	0.7182320441988951	341	0.5961538461538461	544	0.7176781002638523	A	15.05	2.718955	0.48622	0.185202	0.702442	ENSG00000182168	ENST00000453304;ENST00000331502;ENST00000513796	T;T	0.55413	0.84;0.52	5.87	4.71	0.59529	.	0.129840	0.64402	D	0.000001	T	0.00012	0.0000	L	0.47716	1.5	0.09310	P	1.0	B	0.27791	0.189	B	0.22386	0.039	T	0.41305	-0.9516	9	0.72032	D	0.01	.	11.4162	0.49954	0.9303:0.0:0.0697:0.0	rs2289043;rs52803176;rs57517044;rs2289043	721	O95185	UNC5C_HUMAN	T	721;680;740	ENSP00000406022:M721T;ENSP00000426924:M740T	ENSP00000328673:M680T	M	-	2	0	UNC5C	96325345	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	6.106000	0.71511	2.251000	0.74343	0.529000	0.55759	ATG	G|0.520;N|0.000	0.520	strong		0.448	UNC5C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253607.1	NM_003728	
RTP4	64108	hgsc.bcm.edu	37	3	187088812	187088812	+	Missense_Mutation	SNP	C	C	T	rs3821812	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	124	0	0		WXS	Illumina HiSeq	Phase_I	118	67	0.567797	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	
NFATC4	4776	hgsc.bcm.edu	37	14	24838953	24838953	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:24838953C>T	ENST00000250373.4	+	2	490	c.349C>T	c.(349-351)Cgc>Tgc	p.R117C	NFATC4_ENST00000422617.3_Missense_Mutation_p.R105C|NFATC4_ENST00000555590.1_Missense_Mutation_p.R130C|NFATC4_ENST00000440487.2_3'UTR|NFATC4_ENST00000553879.1_Missense_Mutation_p.R47C|NFATC4_ENST00000554050.1_Missense_Mutation_p.R117C|NFATC4_ENST00000553708.1_Missense_Mutation_p.R117C|NFATC4_ENST00000554661.1_Missense_Mutation_p.R47C|NFATC4_ENST00000556279.1_Missense_Mutation_p.R149C|NFATC4_ENST00000554344.1_Missense_Mutation_p.R47C|NFATC4_ENST00000413692.2_Missense_Mutation_p.R180C|NFATC4_ENST00000539237.2_Missense_Mutation_p.R149C|NFATC4_ENST00000554966.1_Missense_Mutation_p.R130C|NFATC4_ENST00000555453.1_Missense_Mutation_p.R105C|NFATC4_ENST00000553469.1_Missense_Mutation_p.R149C|NFATC4_ENST00000424781.2_Missense_Mutation_p.R130C|NFATC4_ENST00000554591.1_Missense_Mutation_p.R180C|NFATC4_ENST00000557451.1_Missense_Mutation_p.R47C|NFATC4_ENST00000556169.1_Missense_Mutation_p.R105C	NM_004554.4	NP_004545.2	Q14934	NFAC4_HUMAN	nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 4	117	Calcineurin-binding.|Pro-rich.				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)		TCCCAGCATCCGCATCACCTC	0.687																																					p.R180C		Atlas-SNP	.											.	NFATC4	115	.	0			c.C538T						PASS	.						12.0	14.0	13.0					14																	24838953		2190	4254	6444	SO:0001583	missense	4776	exon3			AGCATCCGCATCA	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.349C>T	14.37:g.24838953C>T	ENSP00000250373:p.Arg117Cys	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	70	4	0.0571429	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	Missense_Mutation	SNP	ENST00000250373.4	37	CCDS9629.1	.	.	.	.	.	.	.	.	.	.	C	24.1	4.491135	0.84962	.	.	ENSG00000100968	ENST00000413692;ENST00000554591;ENST00000555590;ENST00000554966;ENST00000424781;ENST00000539237;ENST00000556279;ENST00000553469;ENST00000554050;ENST00000554903;ENST00000250373;ENST00000553708;ENST00000557674;ENST00000553879;ENST00000554344;ENST00000554661;ENST00000556169;ENST00000557451;ENST00000422617;ENST00000555453	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.16324	2.35;2.35;2.35;2.35;2.35;2.35;2.35;2.35;2.35;2.35;2.35;2.35;2.35;2.35;2.35;2.35;2.35;2.35;2.35;2.35	3.76	3.76	0.43208	.	0.096786	0.44097	D	0.000481	T	0.27384	0.0672	L	0.29908	0.895	0.80722	D	1	D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;0.999;1.0;0.999	D;D;D;D;D;D;D;D;D;D;D;D;D;P	0.67725	0.93;0.93;0.93;0.93;0.93;0.93;0.93;0.953;0.953;0.93;0.953;0.93;0.93;0.853	T	0.04579	-1.0941	10	0.87932	D	0	-5.8251	13.1624	0.59552	0.0:1.0:0.0:0.0	.	105;105;149;149;130;130;130;180;180;105;149;94;180;117	Q14934-17;Q14934-9;Q14934-14;Q14934-4;Q14934-15;Q14934-6;Q14934-7;Q14934-2;Q14934-3;Q14934-10;Q14934-5;B4DU09;Q14934-11;Q14934	.;.;.;.;.;.;.;.;.;.;.;.;.;NFAC4_HUMAN	C	180;180;130;130;130;149;149;149;117;117;117;117;94;47;47;47;105;47;105;105	ENSP00000388910:R180C;ENSP00000452039:R180C;ENSP00000451224:R130C;ENSP00000450644:R130C;ENSP00000388668:R130C;ENSP00000439350:R149C;ENSP00000452270:R149C;ENSP00000451502:R149C;ENSP00000451151:R117C;ENSP00000451853:R117C;ENSP00000250373:R117C;ENSP00000450590:R117C;ENSP00000452352:R94C;ENSP00000452349:R47C;ENSP00000450469:R47C;ENSP00000450733:R47C;ENSP00000451454:R105C;ENSP00000451284:R47C;ENSP00000396788:R105C;ENSP00000450686:R105C	ENSP00000250373:R117C	R	+	1	0	NFATC4	23908793	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	6.890000	0.75633	1.943000	0.56356	0.558000	0.71614	CGC	.	.	none		0.687	NFATC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000073206.6	NM_004554	
OPLAH	26873	hgsc.bcm.edu	37	8	145114844	145114844	+	Missense_Mutation	SNP	C	C	T	rs7004867	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:145114844C>T	ENST00000426825.1	-	2	173	c.92G>A	c.(91-93)cGg>cAg	p.R31Q	OPLAH_ENST00000534424.1_5'UTR	NM_017570.3	NP_060040.1	O14841	OPLA_HUMAN	5-oxoprolinase (ATP-hydrolysing)	31					glutathione biosynthetic process (GO:0006750)|glutathione derivative biosynthetic process (GO:1901687)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	5-oxoprolinase (ATP-hydrolyzing) activity (GO:0017168)|ATP binding (GO:0005524)			breast(1)|central_nervous_system(1)|endometrium(1)|lung(13)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	20	all_cancers(97;1.06e-10)|all_epithelial(106;1.5e-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;6.79e-41)|Epithelial(56;1.02e-39)|all cancers(56;2.24e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			TTTTAAGACCCGCACGTGCCC	0.667													C|||	309	0.0617013	0.1195	0.0504	5008	,	,		16649	0.001		0.0865	False		,,,				2504	0.0286				p.R31Q		Atlas-SNP	.											OPLAH,NS,carcinoma,0,2	OPLAH	78	2	0			c.G92A						PASS	.	C	GLN/ARG	424,3430		22,380,1525	34.0	40.0	38.0		92	4.4	1.0	8	dbSNP_116	38	584,7650		18,548,3551	yes	missense	OPLAH	NM_017570.3	43	40,928,5076	TT,TC,CC		7.0925,11.0016,8.3388	possibly-damaging	31/1289	145114844	1008,11080	1927	4117	6044	SO:0001583	missense	26873	exon2			AAGACCCGCACGT	AF024672, AB122018	CCDS75802.1	8q24.3	2010-11-23			ENSG00000178814	ENSG00000178814	3.5.2.9		8149	protein-coding gene	gene with protein product		614243				14993790	Standard	NM_017570		Approved	OPLA, 5-Opase	uc003zar.3	O14841		ENST00000426825.1:c.92G>A	8.37:g.145114844C>T	ENSP00000475943:p.Arg31Gln	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	76	75	0.986842	NM_017570	A5PKY8|Q75W65|Q9Y4Q0	Missense_Mutation	SNP	ENST00000426825.1	37		155	0.07097069597069597	68	0.13821138211382114	23	0.06353591160220995	1	0.0017482517482517483	63	0.08311345646437995	C	10.24	1.294808	0.23564	0.110016	0.070925	ENSG00000178814	ENST00000426825	.	.	.	5.24	4.37	0.52481	Hydantoinaseoxoprolinase, N-terminal (1);	0.100597	0.64402	N	0.000007	T	0.00271	0.0008	.	.	.	0.43771	P	0.003707000000000016	P	0.43169	0.8	B	0.37198	0.243	T	0.08207	-1.0733	7	0.29301	T	0.29	.	11.8979	0.52665	0.0:0.914:0.0:0.086	rs7004867;rs7004867	31	O14841	OPLA_HUMAN	Q	31	.	ENSP00000412071:R31Q	R	-	2	0	OPLAH	145186832	0.998000	0.40836	0.992000	0.48379	0.136000	0.21042	4.204000	0.58460	1.221000	0.43506	-0.369000	0.07265	CGG	C|0.921;T|0.079	0.079	strong		0.667	OPLAH-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_017570	
MTOR	2475	hgsc.bcm.edu	37	1	11181327	11181327	+	Silent	SNP	C	C	T	rs11121691	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:11181327C>T	ENST00000361445.4	-	49	6985	c.6909G>A	c.(6907-6909)ctG>ctA	p.L2303L	MTOR_ENST00000376838.1_Silent_p.L508L	NM_004958.3	NP_004949.1	P42345	MTOR_HUMAN	mechanistic target of rapamycin (serine/threonine kinase)	2303	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.				cell growth (GO:0016049)|cellular response to hypoxia (GO:0071456)|cellular response to nutrient levels (GO:0031669)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|germ cell development (GO:0007281)|growth (GO:0040007)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|negative regulation of autophagy (GO:0010507)|negative regulation of cell size (GO:0045792)|negative regulation of macroautophagy (GO:0016242)|negative regulation of NFAT protein import into nucleus (GO:0051534)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|phosphatidylinositol-mediated signaling (GO:0048015)|phosphorylation (GO:0016310)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of gene expression (GO:0010628)|positive regulation of lamellipodium assembly (GO:0010592)|positive regulation of lipid biosynthetic process (GO:0046889)|positive regulation of myotube differentiation (GO:0010831)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein catabolic process (GO:0030163)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of carbohydrate utilization (GO:0043610)|regulation of fatty acid beta-oxidation (GO:0031998)|regulation of glycogen biosynthetic process (GO:0005979)|regulation of protein kinase activity (GO:0045859)|regulation of Rac GTPase activity (GO:0032314)|regulation of response to food (GO:0032095)|response to amino acid (GO:0043200)|response to nutrient (GO:0007584)|response to stress (GO:0006950)|ruffle organization (GO:0031529)|signal transduction (GO:0007165)|T cell costimulation (GO:0031295)|TOR signaling (GO:0031929)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endomembrane system (GO:0012505)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|phosphatidylinositol 3-kinase complex (GO:0005942)|PML body (GO:0016605)|TORC1 complex (GO:0031931)|TORC2 complex (GO:0031932)	ATP binding (GO:0005524)|drug binding (GO:0008144)|kinase activity (GO:0016301)|phosphoprotein binding (GO:0051219)|protein serine/threonine kinase activity (GO:0004674)|ribosome binding (GO:0043022)|RNA polymerase III type 1 promoter DNA binding (GO:0001030)|RNA polymerase III type 2 promoter DNA binding (GO:0001031)|RNA polymerase III type 3 promoter DNA binding (GO:0001032)|TFIIIC-class transcription factor binding (GO:0001156)			breast(5)|central_nervous_system(7)|endometrium(20)|kidney(34)|large_intestine(21)|lung(43)|ovary(9)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	149					Everolimus(DB01590)|Pimecrolimus(DB00337)|Sirolimus(DB00877)|Temsirolimus(DB06287)	TTTTCAGCCACAGCAGCTTGG	0.587													C|||	1105	0.220647	0.4365	0.1542	5008	,	,		17412	0.0565		0.2356	False		,,,				2504	0.1299				p.L2303L		Atlas-SNP	.											.	MTOR	327	.	0			c.G6909A						PASS	.	C		1875,2531	541.3+/-375.7	383,1109,711	80.0	68.0	72.0		6909	3.9	1.0	1	dbSNP_120	72	2054,6546	356.9+/-330.5	249,1556,2495	no	coding-synonymous	MTOR	NM_004958.3		632,2665,3206	TT,TC,CC		23.8837,42.5556,30.2091		2303/2550	11181327	3929,9077	2203	4300	6503	SO:0001819	synonymous_variant	2475	exon49			CAGCCACAGCAGC	L34075	CCDS127.1	1p36	2014-09-17	2009-05-29	2009-05-29	ENSG00000198793	ENSG00000198793			3942	protein-coding gene	gene with protein product	"""FK506 binding protein 12-rapamycin associated protein 2"", ""rapamycin target protein"", ""FKBP12-rapamycin complex-associated protein 1"", ""FKBP-rapamycin associated protein"", ""rapamycin associated protein FRAP2"", ""dJ576K7.1 (FK506 binding protein 12-rapamycin associated protein 1)"", ""rapamycin and FKBP12 target 1"", ""mammalian target of rapamycin"""	601231	"""FK506 binding protein 12-rapamycin associated protein 1"""	FRAP, FRAP2, FRAP1		8008069, 8660990	Standard	NM_004958		Approved	RAFT1, RAPT1, FLJ44809	uc001asd.3	P42345	OTTHUMG00000002001	ENST00000361445.4:c.6909G>A	1.37:g.11181327C>T		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	64	39	0.609375	NM_004958	Q4LE76|Q5TER1|Q6LE87|Q96QG3|Q9Y4I3	Silent	SNP	ENST00000361445.4	37	CCDS127.1																																																																																			C|0.721;T|0.279	0.279	strong		0.587	MTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005558.1	NM_004958	
ARID4B	51742	hgsc.bcm.edu	37	1	235392546	235392546	+	Splice_Site	SNP	T	T	C	rs17846600|rs12731746	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:235392546T>C	ENST00000264183.3	-	11	1394	c.897A>G	c.(895-897)gaA>gaG	p.E299E	ARID4B_ENST00000366603.2_Splice_Site_p.E299E|ARID4B_ENST00000349213.3_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	168	0	0		WXS	Illumina HiSeq	Phase_I	103	103	1	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
ZNF598	90850	hgsc.bcm.edu	37	16	2049728	2049728	+	Missense_Mutation	SNP	C	C	T	rs11248905	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:2049728C>T	ENST00000563630.1	-	9	1899	c.1657G>A	c.(1657-1659)Gct>Act	p.A553T	AC005606.15_ENST00000567515.1_lincRNA|ZNF598_ENST00000431526.1_Missense_Mutation_p.A608T|ZNF598_ENST00000562103.1_Missense_Mutation_p.A553T			Q86UK7	ZN598_HUMAN	zinc finger protein 598	608							poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|lung(7)|skin(1)|urinary_tract(1)	16						GGACAGGTAGCGGGCGGGGGC	0.647													T|||	633	0.126398	0.0068	0.2147	5008	,	,		14808	0.0437		0.1839	False		,,,				2504	0.2515				p.A608T		Atlas-SNP	.											ZNF598,NS,carcinoma,0,1	ZNF598	55	1	0			c.G1822A						PASS	.	T	THR/ALA	131,3591		6,119,1736	15.0	18.0	17.0		1824	-5.3	0.0	16	dbSNP_120	17	1364,6758		105,1154,2802	no	missense	ZNF598	NM_178167.2	58	111,1273,4538	TT,TC,CC		16.7939,3.5196,12.6224	benign	608/905	2049728	1495,10349	1861	4061	5922	SO:0001583	missense	90850	exon11			AGGTAGCGGGCGG	BC029270		16p13.3	2008-05-02				ENSG00000167962		"""Zinc fingers, C2H2-type"""	28079	protein-coding gene	gene with protein product							Standard	NM_178167		Approved	FLJ00086	uc002cof.2	Q86UK7		ENST00000563630.1:c.1657G>A	16.37:g.2049728C>T	ENSP00000455882:p.Ala553Thr	Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	53	41	0.773585	NM_178167	Q8IW49|Q8N3D9|Q96FG3|Q9H7J3	Missense_Mutation	SNP	ENST00000563630.1	37		223	0.1021062271062271	4	0.008130081300813009	59	0.16298342541436464	21	0.03671328671328671	139	0.18337730870712401	.	0.491	-0.875344	0.02550	0.035196	0.167939	ENSG00000167962	ENST00000431526	T	0.18174	2.23	4.41	-5.35	0.02697	.	2.431040	0.00991	N	0.003532	T	0.00012	0.0000	N	0.02011	-0.69	0.80722	P	0.0	B	0.10296	0.003	B	0.10450	0.005	T	0.31336	-0.9947	9	0.18276	T	0.48	0.0464	3.0977	0.06315	0.1207:0.3431:0.1867:0.3495	rs11248905	608	Q86UK7	ZN598_HUMAN	T	608	ENSP00000411409:A608T	ENSP00000411409:A608T	A	-	1	0	ZNF598	1989729	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.518000	0.06267	-1.119000	0.02958	-2.362000	0.00238	GCT	C|0.890;T|0.110	0.110	strong		0.647	ZNF598-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000434439.1	NM_178167	
TMEM86B	255043	hgsc.bcm.edu	37	19	55738746	55738746	+	Silent	SNP	G	G	A	rs4374298	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:55738746G>A	ENST00000327042.4	-	3	1006	c.484C>T	c.(484-486)Ctg>Ttg	p.L162L	AC010327.2_ENST00000598855.1_Silent_p.Q36Q	NM_173804.4	NP_776165.3	Q8N661	TM86B_HUMAN	transmembrane protein 86B	162					ether lipid metabolic process (GO:0046485)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	alkenylglycerophosphocholine hydrolase activity (GO:0047408)|alkenylglycerophosphoethanolamine hydrolase activity (GO:0047409)			skin(2)	2			BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0443)		CCGCGCCACAGCATGGCCATC	0.697													G|||	856	0.170927	0.205	0.2219	5008	,	,		16124	0.0764		0.1968	False		,,,				2504	0.1595				p.L162L		Atlas-SNP	.											.	TMEM86B	12	.	0			c.C484T						PASS	.	G		827,3545		76,675,1435	14.0	15.0	15.0		484	2.4	1.0	19	dbSNP_111	15	1676,6902		166,1344,2779	no	coding-synonymous	TMEM86B	NM_173804.4		242,2019,4214	AA,AG,GG		19.5384,18.9158,19.3282		162/227	55738746	2503,10447	2186	4289	6475	SO:0001819	synonymous_variant	255043	exon3			GCCACAGCATGGC	BC023000	CCDS12920.1	19q13.42	2011-07-12					3.3.2.2, 3.3.2.5		28448	protein-coding gene	gene with protein product						21515882	Standard	NM_173804		Approved	MGC30208	uc002qju.3	Q8N661		ENST00000327042.4:c.484C>T	19.37:g.55738746G>A		Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	56	27	0.482143	NM_173804		Silent	SNP	ENST00000327042.4	37	CCDS12920.1																																																																																			G|0.828;A|0.172	0.172	strong		0.697	TMEM86B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452659.1	NM_173804	
UNC5C	8633	hgsc.bcm.edu	37	4	96123981	96123981	+	Silent	SNP	C	C	T	rs3733212	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:96123981C>T	ENST00000453304.1	-	12	2385	c.2037G>A	c.(2035-2037)gcG>gcA	p.A679A		NM_003728.3	NP_003719.3	O95185	UNC5C_HUMAN	unc-5 homolog C (C. elegans)	679					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)		TGAGGCGCTTCGCAGCCGCTT	0.602													C|||	2926	0.584265	0.73	0.5375	5008	,	,		19095	0.3601		0.7167	False		,,,				2504	0.5153				p.A679A		Atlas-SNP	.											.	UNC5C	141	.	0			c.G2037A						PASS	.	C		3146,1260	701.8+/-406.8	1121,904,178	114.0	109.0	111.0		2037	-10.7	0.0	4	dbSNP_107	111	5962,2638	687.1+/-404.2	2073,1816,411	no	coding-synonymous	UNC5C	NM_003728.3		3194,2720,589	TT,TC,CC		30.6744,28.5974,29.9708		679/932	96123981	9108,3898	2203	4300	6503	SO:0001819	synonymous_variant	8633	exon12			GCGCTTCGCAGCC	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.2037G>A	4.37:g.96123981C>T		Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	154	61	0.396104	NM_003728	Q8IUT0	Silent	SNP	ENST00000453304.1	37	CCDS3643.1																																																																																			C|0.347;T|0.653	0.653	strong		0.602	UNC5C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253607.1	NM_003728	
TNC	3371	hgsc.bcm.edu	37	9	117797597	117797597	+	Silent	SNP	T	T	C	rs12347433	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:117797597T>C	ENST00000350763.4	-	22	6084	c.5673A>G	c.(5671-5673)agA>agG	p.R1891R	TNC_ENST00000340094.3_Silent_p.R1527R|TNC_ENST00000423613.2_Silent_p.R1618R|TNC_ENST00000542877.1_Silent_p.R1528R|TNC_ENST00000537320.1_Silent_p.R1254R|TNC_ENST00000346706.3_Silent_p.R1345R|TNC_ENST00000345230.3_Silent_p.R1254R|TNC_ENST00000341037.4_Silent_p.R1709R|TNC_ENST00000535648.1_Silent_p.R1436R	NM_002160.3	NP_002151.2	P24821	TENA_HUMAN	tenascin C	1891	Fibronectin type-III 15. {ECO:0000255|PROSITE-ProRule:PRU00316}.				bud outgrowth involved in lung branching (GO:0060447)|cell adhesion (GO:0007155)|cellular response to prostaglandin D stimulus (GO:0071799)|cellular response to retinoic acid (GO:0071300)|cellular response to vitamin D (GO:0071305)|extracellular matrix organization (GO:0030198)|mesenchymal-epithelial cell signaling involved in prostate gland development (GO:0060739)|negative regulation of cell adhesion (GO:0007162)|neuromuscular junction development (GO:0007528)|odontogenesis of dentin-containing tooth (GO:0042475)|osteoblast differentiation (GO:0001649)|peripheral nervous system axon regeneration (GO:0014012)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|prostate gland epithelium morphogenesis (GO:0060740)|response to ethanol (GO:0045471)|response to fibroblast growth factor (GO:0071774)|response to mechanical stimulus (GO:0009612)|response to wounding (GO:0009611)|wound healing (GO:0042060)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|interstitial matrix (GO:0005614)|membrane (GO:0016020)	syndecan binding (GO:0045545)	p.R1891R(1)		NS(3)|breast(5)|central_nervous_system(4)|endometrium(8)|kidney(6)|large_intestine(32)|liver(1)|lung(39)|ovary(1)|pancreas(2)|prostate(5)|skin(5)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	120						CAGTCAAGTCTCTTGGAGAAT	0.512													T|||	773	0.154353	0.0666	0.1484	5008	,	,		19335	0.129		0.2793	False		,,,				2504	0.1748				p.R1891R		Atlas-SNP	.											TNC,NS,carcinoma,0,1	TNC	282	1	1	Substitution - coding silent(1)	stomach(1)	c.A5673G						PASS	.	T		404,4002	199.4+/-223.0	21,362,1820	72.0	72.0	72.0		5673	6.0	1.0	9	dbSNP_120	72	2313,6287	389.1+/-342.8	320,1673,2307	no	coding-synonymous	TNC	NM_002160.3		341,2035,4127	CC,CT,TT		26.8953,9.1693,20.8904		1891/2202	117797597	2717,10289	2203	4300	6503	SO:0001819	synonymous_variant	3371	exon22			CAAGTCTCTTGGA		CCDS6811.1	9q33.1	2014-01-28	2008-07-31	2002-06-07	ENSG00000041982	ENSG00000041982		"""Fibrinogen C domain containing"", ""Fibronectin type III domain containing"""	5318	protein-coding gene	gene with protein product	"""hexabrachion (tenascin)"""	187380	"""hexabrachion (tenascin C, cytotactin)"", ""deafness, autosomal dominant 56"""	HXB, DFNA56		1704365, 1707164, 23936043	Standard	NM_002160		Approved	TN, MGC167029	uc004bjj.4	P24821	OTTHUMG00000021010	ENST00000350763.4:c.5673A>G	9.37:g.117797597T>C		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	43	19	0.44186	NM_002160	C9IYT7|C9J575|C9J6D9|C9J848|Q14583|Q15567|Q5T7S3	Silent	SNP	ENST00000350763.4	37	CCDS6811.1	383	0.17536630036630035	40	0.08130081300813008	46	0.1270718232044199	85	0.1486013986013986	212	0.2796833773087071	T	10.49	1.365894	0.24684	0.091693	0.268953	ENSG00000041982	ENST00000544972	T	0.57436	0.4	5.97	5.97	0.96955	.	0.206129	0.51477	D	0.000084	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.22034	-1.0228	6	0.48119	T	0.1	.	10.4647	0.44600	0.0:0.1145:0.0:0.8855	rs12347433;rs17240303;rs12347433	.	.	.	G	454	ENSP00000445380:R454G	ENSP00000445380:R454G	R	-	1	2	TNC	116837418	1.000000	0.71417	1.000000	0.80357	0.936000	0.57629	3.042000	0.49815	2.274000	0.75844	0.533000	0.62120	AGA	T|0.813;C|0.187	0.187	strong		0.512	TNC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055418.2	NM_002160	
IFITM2	10581	hgsc.bcm.edu	37	11	308314	308314	+	Missense_Mutation	SNP	T	T	C	rs14408	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:308314T>C	ENST00000399817.4	+	1	152	c.122T>C	c.(121-123)aTg>aCg	p.M41T	RP11-326C3.7_ENST00000526612.1_RNA|IFITM2_ENST00000533141.1_Missense_Mutation_p.M21T|IFITM2_ENST00000602569.1_Missense_Mutation_p.M21T	NM_006435.2	NP_006426.2	Q01629	IFM2_HUMAN	interferon induced transmembrane protein 2	41			M -> T (in dbSNP:rs14408). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:1906403}.		cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|immune response (GO:0006955)|negative regulation of viral entry into host cell (GO:0046597)|negative regulation of viral genome replication (GO:0045071)|response to interferon-alpha (GO:0035455)|response to interferon-beta (GO:0035456)|response to interferon-gamma (GO:0034341)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(1)|kidney(1)|large_intestine(1)|lung(1)	4		all_cancers(49;2e-09)|all_epithelial(84;3.36e-06)|Breast(177;0.000162)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.0538)|all_lung(207;0.0713)		all cancers(45;5.73e-28)|Epithelial(43;3.42e-27)|OV - Ovarian serous cystadenocarcinoma(40;1.14e-20)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0328)|LUSC - Lung squamous cell carcinoma(625;0.122)		GCTCCCCCGATGTCCACCGTG	0.607													t|||	3531	0.705072	0.7617	0.6657	5008	,	,		14037	0.9593		0.3787	False		,,,				2504	0.7301				p.M41T		Atlas-SNP	.											IFITM2,rectum,carcinoma,0,1	IFITM2	21	1	0			c.T122C						scavenged	.	T	THR/MET	2520,1396		857,806,295	63.0	88.0	80.0		122	-2.8	0.0	11	dbSNP_52	80	3019,5275		590,1839,1718	no	missense	IFITM2	NM_006435.2	81	1447,2645,2013	CC,CT,TT		36.3998,35.6486,45.3645	benign	41/133	308314	5539,6671	1958	4147	6105	SO:0001583	missense	10581	exon1			CCCCGATGTCCAC	X57351	CCDS41583.1	11p15.5	2012-03-13	2012-03-13		ENSG00000185201	ENSG00000185201			5413	protein-coding gene	gene with protein product		605578	"""interferon induced transmembrane protein 2 (1-8D)"""			1906403	Standard	NM_006435		Approved	1-8D	uc001lox.4	Q01629		ENST00000399817.4:c.122T>C	11.37:g.308314T>C	ENSP00000382714:p.Met41Thr	Somatic	134	1	0.00746269		WXS	Illumina HiSeq	Phase_I	151	109	0.721854	NM_006435	Q6FH82|Q96DA8	Missense_Mutation	SNP	ENST00000399817.4	37	CCDS41583.1	1298	0.5943223443223443	337	0.6849593495934959	199	0.5497237569060773	523	0.9143356643356644	239	0.3153034300791557	T	0.004	-2.266536	0.00259	0.643514	0.363998	ENSG00000185201	ENST00000533141;ENST00000399817;ENST00000327366	T;T	0.76709	-1.04;-0.8	2.59	-2.76	0.05896	.	1.327100	0.06148	N	0.673694	T	0.00012	0.0000	N	0.00010	-3.02	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.45644	-0.9247	9	0.02654	T	1	2.4836	3.407	0.07344	0.3221:0.496:0.0:0.1819	rs14408;rs3179090;rs17850538;rs58885107;rs14408	41	Q01629	IFM2_HUMAN	T	21;41;41	ENSP00000434443:M21T;ENSP00000382714:M41T	ENSP00000327996:M41T	M	+	2	0	IFITM2	298314	0.000000	0.05858	0.000000	0.03702	0.028000	0.11728	-2.620000	0.00879	-0.998000	0.03446	-3.056000	0.00068	ATG	.	.	weak		0.607	IFITM2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000383591.1	NM_006435	
TTC7B	145567	hgsc.bcm.edu	37	14	91161862	91161862	+	Silent	SNP	C	C	T	rs10146731	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:91161862C>T	ENST00000328459.6	-	6	880	c.759G>A	c.(757-759)acG>acA	p.T253T	RP11-661G16.2_ENST00000553712.1_RNA|TTC7B_ENST00000357056.2_Silent_p.T253T	NM_001010854.1	NP_001010854.1	Q86TV6	TTC7B_HUMAN	tetratricopeptide repeat domain 7B	253										NS(1)|breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(8)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	36		Melanoma(154;0.222)				GGTTTTGAGTCGTTCTTGTTT	0.413													C|||	3102	0.619409	0.4909	0.6585	5008	,	,		12641	0.6885		0.6302	False		,,,				2504	0.683				p.T253T		Atlas-SNP	.											.	TTC7B	93	.	0			c.G759A						PASS	.	C		2335,2071	606.0+/-390.6	614,1107,482	147.0	116.0	126.0		759	-7.3	0.4	14	dbSNP_119	126	5554,3044	662.3+/-402.0	1775,2004,520	no	coding-synonymous	TTC7B	NM_001010854.1		2389,3111,1002	TT,TC,CC		35.4036,47.0041,39.3341		253/844	91161862	7889,5115	2203	4299	6502	SO:0001819	synonymous_variant	145567	exon6			TTGAGTCGTTCTT	BC035865	CCDS32140.1	14q32.12	2013-01-11	2004-06-02	2004-06-04		ENSG00000165914		"""Tetratricopeptide (TTC) repeat domain containing"""	19858	protein-coding gene	gene with protein product			"""tetratricopeptide repeat domain 7 like 1"""	TTC7L1			Standard	XM_005267367		Approved		uc001xyp.3	Q86TV6		ENST00000328459.6:c.759G>A	14.37:g.91161862C>T		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	121	120	0.991736	NM_001010854	Q86U24|Q86VT3	Silent	SNP	ENST00000328459.6	37	CCDS32140.1																																																																																			C|0.384;T|0.616	0.616	strong		0.413	TTC7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411364.2		
KIAA0226	9711	hgsc.bcm.edu	37	3	197427557	197427557	+	Silent	SNP	A	A	G	rs28394098	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:197427557A>G	ENST00000296343.5	-	7	1187	c.1188T>C	c.(1186-1188)acT>acC	p.T396T	KIAA0226_ENST00000449205.1_Silent_p.T396T|KIAA0226_ENST00000273582.5_Silent_p.T336T|KIAA0226_ENST00000389665.5_Silent_p.T396T|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	200	0	0		WXS	Illumina HiSeq	Phase_I	168	83	0.494048	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	
RAI1	10743	hgsc.bcm.edu	37	17	17700573	17700573	+	Silent	SNP	T	T	C	rs4925112	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:17700573T>C	ENST00000353383.1	+	3	4780	c.4311T>C	c.(4309-4311)ccT>ccC	p.P1437P	RAI1_ENST00000261641.6_Silent_p.P1437P	NM_030665.3	NP_109590.3	Q7Z5J4	RAI1_HUMAN	retinoic acid induced 1	1437					circadian regulation of gene expression (GO:0032922)|negative regulation of multicellular organism growth (GO:0040015)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	enhancer binding (GO:0035326)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(14)|ovary(1)|prostate(1)|skin(5)|urinary_tract(7)	48				READ - Rectum adenocarcinoma(1115;0.0276)		CCCTGCAGCCTGGGGGGACTG	0.587													C|||	474	0.0946486	0.2655	0.0447	5008	,	,		16820	0.0069		0.0577	False		,,,				2504	0.0276				p.P1437P		Atlas-SNP	.											.	RAI1	121	.	0			c.T4311C						PASS	.	C		1089,3317	685.0+/-404.5	142,805,1256	30.0	35.0	33.0		4311	-1.9	0.0	17	dbSNP_111	33	518,8082	771.5+/-407.7	19,480,3801	no	coding-synonymous	RAI1	NM_030665.3		161,1285,5057	CC,CT,TT		6.0233,24.7163,12.3558		1437/1907	17700573	1607,11399	2203	4300	6503	SO:0001819	synonymous_variant	10743	exon3			GCAGCCTGGGGGG	AJ230819	CCDS11188.1	17p11.2	2011-02-08			ENSG00000108557	ENSG00000108557			9834	protein-coding gene	gene with protein product		607642	"""Smith-Magenis syndrome chromosome region"""	SMCR		10036180	Standard	NM_030665		Approved	DKFZP434A139, SMS, KIAA1820, MGC12824	uc002grm.3	Q7Z5J4	OTTHUMG00000059314	ENST00000353383.1:c.4311T>C	17.37:g.17700573T>C		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	38	18	0.473684	NM_030665	Q8N3B4|Q8ND08|Q8WU64|Q96JK5|Q9H1C1|Q9H1C2|Q9UF69	Silent	SNP	ENST00000353383.1	37	CCDS11188.1																																																																																			T|0.888;C|0.112	0.112	strong		0.587	RAI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131775.1	NM_030665	
CEP131	22994	hgsc.bcm.edu	37	17	79164488	79164488	+	Missense_Mutation	SNP	C	C	T	rs117616373	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:79164488C>T	ENST00000269392.4	-	24	3314	c.3067G>A	c.(3067-3069)Gcc>Acc	p.A1023T	AZI1_ENST00000374782.3_Missense_Mutation_p.A984T|AZI1_ENST00000450824.2_Missense_Mutation_p.A1020T|AZI1_ENST00000575907.1_Missense_Mutation_p.A987T	NM_014984.2	NP_055799.2	Q9UPN4	CP131_HUMAN		1023					cell differentiation (GO:0030154)|G2/M transition of mitotic cell cycle (GO:0000086)|intraciliary transport involved in cilium morphogenesis (GO:0035735)|mitotic cell cycle (GO:0000278)|multicellular organismal development (GO:0007275)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular protein transport (GO:0090316)|regulation of centrosome duplication (GO:0010824)|spermatogenesis (GO:0007283)	BBSome (GO:0034464)|cell projection (GO:0042995)|centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)	protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(3)|endometrium(6)|kidney(3)|large_intestine(1)|lung(12)|ovary(2)|prostate(3)|urinary_tract(5)	36	all_neural(118;0.0804)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0272)|OV - Ovarian serous cystadenocarcinoma(97;0.117)			TGCAGCGTGGCCAGCTCGGCC	0.731													C|||	76	0.0151757	0.0023	0.0317	5008	,	,		11555	0.0		0.0427	False		,,,				2504	0.0082				p.A1020T		Atlas-SNP	.											.	AZI1	145	.	0			c.G3058A						PASS	.	C	THR/ALA,THR/ALA	38,4312		0,38,2137	9.0	11.0	11.0		2950,3058	1.1	0.9	17	dbSNP_132	11	408,8104		13,382,3861	no	missense,missense	AZI1	NM_001009811.2,NM_014984.2	58,58	13,420,5998	TT,TC,CC		4.7932,0.8736,3.4676	probably-damaging,probably-damaging	984/1045,1020/1081	79164488	446,12416	2175	4256	6431	SO:0001583	missense	22994	exon24			GCGTGGCCAGCTC																												ENST00000269392.4:c.3067G>A	17.37:g.79164488C>T	ENSP00000269392:p.Ala1023Thr	Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	39	28	0.717949	NM_014984	A6NHI8|B2RN11|Q96F50	Missense_Mutation	SNP	ENST00000269392.4	37		46	0.021062271062271064	1	0.0020325203252032522	11	0.03038674033149171	0	0.0	34	0.044854881266490766	C	14.54	2.564835	0.45694	0.008736	0.047932	ENSG00000141577	ENST00000450824;ENST00000374782;ENST00000269392	T;T;T	0.15256	2.46;2.44;2.46	4.4	1.11	0.20524	.	0.361388	0.26248	N	0.025463	T	0.03564	0.0102	L	0.47716	1.5	0.40310	D	0.978706	D;P;P;P	0.63880	0.993;0.716;0.577;0.577	P;B;B;B	0.58172	0.834;0.407;0.187;0.187	T	0.01337	-1.1381	10	0.52906	T	0.07	-0.7262	4.9522	0.14021	0.2875:0.5524:0.0:0.1602	.	1020;1023;984;1020	B2RN10;Q9UPN4;Q9UPN4-3;Q9UPN4-2	.;AZI1_HUMAN;.;.	T	1020;984;1023	ENSP00000393583:A1020T;ENSP00000363914:A984T;ENSP00000269392:A1023T	ENSP00000269392:A1023T	A	-	1	0	AZI1	76779083	0.958000	0.32768	0.933000	0.37362	0.010000	0.07245	0.274000	0.18680	0.506000	0.28125	-0.218000	0.12543	GCC	C|0.979;T|0.021	0.021	strong		0.731	AZI1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000256070.1		
ELN	2006	hgsc.bcm.edu	37	7	73470714	73470714	+	Missense_Mutation	SNP	G	G	A	rs2071307	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:73470714G>A	ENST00000252034.7	+	20	1663	c.1264G>A	c.(1264-1266)Ggt>Agt	p.G422S	ELN_ENST00000357036.5_Missense_Mutation_p.G427S|ELN_ENST00000320492.7_Intron|ELN_ENST00000458204.1_Missense_Mutation_p.G412S|ELN_ENST00000380584.4_Missense_Mutation_p.G408S|ELN_ENST00000429192.1_Missense_Mutation_p.G427S|ELN_ENST00000445912.1_Missense_Mutation_p.G422S|ELN_ENST00000320399.6_Missense_Mutation_p.G422S|ELN_ENST00000414324.1_Missense_Mutation_p.G417S|ELN_ENST00000380575.4_Missense_Mutation_p.G412S|ELN_ENST00000380553.4_Missense_Mutation_p.G305S|ELN_ENST00000380562.4_Missense_Mutation_p.G422S|ELN_ENST00000358929.4_Missense_Mutation_p.G422S|ELN_ENST00000380576.5_Missense_Mutation_p.G422S	NM_000501.2|NM_001278915.1	NP_000492.2|NP_001265844.1	P15502	ELN_HUMAN	elastin	0	Ala-rich.		G -> S (in dbSNP:rs2071307). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:2831431, ECO:0000269|PubMed:3039501, ECO:0000269|PubMed:3171221, ECO:0000269|PubMed:8689688, ECO:0000269|PubMed:9215670}.		blood circulation (GO:0008015)|blood vessel remodeling (GO:0001974)|cell proliferation (GO:0008283)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|organ morphogenesis (GO:0009887)|regulation of actin filament polymerization (GO:0030833)|respiratory gaseous exchange (GO:0007585)|skeletal muscle tissue development (GO:0007519)|stress fiber assembly (GO:0043149)	elastic fiber (GO:0071953)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix binding (GO:0050840)|extracellular matrix constituent conferring elasticity (GO:0030023)|extracellular matrix structural constituent (GO:0005201)	p.G422S(1)		breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(10)|ovary(4)|pancreas(2)|prostate(1)|skin(2)|stomach(1)	32		Lung NSC(55;0.159)				AGGTGTCCCTGGTGTCGGAGG	0.617			T	PAX5	B-ALL		"""Supravalvular Aortic Stenosis, Cutis laxa , Williams-Beuren Syndrome"""						A|||	1104	0.220447	0.1339	0.2464	5008	,	,		15486	0.1081		0.4205	False		,,,				2504	0.229				p.G427S		Atlas-SNP	.		Dom	yes		7	7q11.23	2006	elastin	yes	L	ELN,NS,carcinoma,0,1	ELN	81	1	1	Substitution - Missense(1)	stomach(1)	c.G1279A						PASS	.	A	SER/GLY,SER/GLY,SER/GLY,SER/GLY,SER/GLY	779,3627	753.3+/-412.4	72,635,1496	110.0	108.0	108.0		1264,1279,1279,1234,1264	1.2	0.0	7	dbSNP_96	108	3551,5049	630.5+/-398.4	728,2095,1477	yes	missense,missense,missense,missense,missense	ELN	NM_001081755.1,NM_001081754.1,NM_001081753.1,NM_001081752.1,NM_000501.2	56,56,56,56,56	800,2730,2973	AA,AG,GG		41.2907,17.6804,33.2923	benign,benign,benign,benign,benign	422/706,427/712,427/693,412/678,422/725	73470714	4330,8676	2203	4300	6503	SO:0001583	missense	2006	exon20			GTCCCTGGTGTCG		CCDS5562.2, CCDS43598.1, CCDS43599.1, CCDS47611.1, CCDS47612.1, CCDS64673.1, CCDS64674.1, CCDS64675.1, CCDS64676.1, CCDS64677.1, CCDS64678.1, CCDS75616.1, CCDS75617.1	7q11.1-q21.1	2008-08-01	2008-08-01		ENSG00000049540	ENSG00000049540			3327	protein-coding gene	gene with protein product	"""tropoelastin"", ""supravalvular aortic stenosis"", ""Williams-Beuren syndrome"""	130160				8096434	Standard	NM_001278939		Approved	WBS, WS, SVAS	uc003tzn.3	P15502	OTTHUMG00000150229	ENST00000252034.7:c.1264G>A	7.37:g.73470714G>A	ENSP00000252034:p.Gly422Ser	Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	131	51	0.389313	NM_001081753	B3KTS6|O15336|O15337|Q14233|Q14234|Q14235|Q14238|Q6P0L4|Q6ZWJ6|Q75MU5|Q7Z316|Q7Z3F5|Q9UMF5	Missense_Mutation	SNP	ENST00000252034.7	37	CCDS5562.2	559	0.25595238095238093	74	0.15040650406504066	108	0.2983425414364641	78	0.13636363636363635	299	0.3944591029023747	A	10.41	1.343509	0.24339	0.176804	0.412907	ENSG00000049540	ENST00000445912;ENST00000252034;ENST00000358929;ENST00000414324;ENST00000380562;ENST00000380575;ENST00000380584;ENST00000458204;ENST00000357036;ENST00000429192;ENST00000442462;ENST00000380553;ENST00000380576;ENST00000320399	T;T;T;T;T;T;T;T;T;T;T;T;T	0.58652	1.13;1.16;0.32;1.18;1.14;1.25;1.38;1.14;1.11;1.27;1.31;1.28;1.16	2.18	1.2	0.21068	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B;B;B;B;B;B;B;B;B;B;B;B	0.15141	0.012;0.012;0.012;0.012;0.007;0.012;0.012;0.012;0.012;0.012;0.012;0.012	B;B;B;B;B;B;B;B;B;B;B;B	0.06405	0.002;0.002;0.002;0.002;0.002;0.002;0.002;0.002;0.002;0.002;0.002;0.002	T	0.36237	-0.9756	7	0.49607	T	0.09	.	7.3905	0.26907	0.1691:0.0:0.8309:0.0	rs2071307;rs11567855;rs17855987;rs58147333;rs2071307	422;391;417;412;422;412;427;427;422;305;408;422	E7ENM0;E9PBM4;G3V0G6;E7EN65;P15502-1;P15502-7;P15502-12;P15502-5;P15502-13;P15502-11;P15502-8;P15502-2	.;.;.;.;.;.;.;.;.;.;.;.	S	422;422;422;417;422;412;408;412;427;427;391;305;422;422	ENSP00000389857:G422S;ENSP00000252034:G422S;ENSP00000351807:G422S;ENSP00000392575:G417S;ENSP00000369936:G422S;ENSP00000369949:G412S;ENSP00000369958:G408S;ENSP00000403162:G412S;ENSP00000349540:G427S;ENSP00000391129:G427S;ENSP00000369926:G305S;ENSP00000369950:G422S;ENSP00000313565:G422S	ENSP00000252034:G422S	G	+	1	0	ELN	73108650	0.111000	0.22076	0.002000	0.10522	0.002000	0.02628	0.532000	0.23067	-0.267000	0.09325	-1.446000	0.01064	GGT	G|0.704;A|0.296	0.296	strong		0.617	ELN-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000316913.1	NM_000501	
BABAM1	29086	hgsc.bcm.edu	37	19	17389704	17389704	+	Silent	SNP	G	G	A	rs8170	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:17389704G>A	ENST00000359435.4	+	9	1030	c.837G>A	c.(835-837)aaG>aaA	p.K279K	CTD-2278I10.6_ENST00000596542.1_Intron|BABAM1_ENST00000601043.1_Silent_p.K279K|ANKLE1_ENST00000404085.1_5'Flank|ANKLE1_ENST00000394458.3_5'Flank|BABAM1_ENST00000595632.1_Silent_p.K204K|ANKLE1_ENST00000594072.1_5'Flank|BABAM1_ENST00000598188.1_Silent_p.K279K|BABAM1_ENST00000447614.2_Silent_p.K279K|ANKLE1_ENST00000433424.2_5'Flank	NM_001033549.1	NP_001028721.1	Q9NWV8	BABA1_HUMAN	BRISC and BRCA1 A complex member 1	279	VWFA-like.				chromatin modification (GO:0016568)|double-strand break repair (GO:0006302)|G2 DNA damage checkpoint (GO:0031572)|positive regulation of DNA repair (GO:0045739)|protein K63-linked deubiquitination (GO:0070536)|response to ionizing radiation (GO:0010212)	BRCA1-A complex (GO:0070531)|BRISC complex (GO:0070552)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(1)	5						CCAGCTACAAGTATGAGGTGG	0.612													G|||	563	0.11242	0.1861	0.0951	5008	,	,		17800	0.001		0.163	False		,,,				2504	0.0879				p.K279K		Atlas-SNP	.											C19orf62,NS,carcinoma,0,2	BABAM1	14	2	0			c.G837A						PASS	.	G	,	723,3299		60,603,1348	35.0	40.0	38.0	http://www.ncbi.nlm.nih.gov/pubmed?term	837,837	2.8	1.0	19	dbSNP_52	38	1503,6797		145,1213,2792	yes	coding-synonymous,coding-synonymous	BABAM1	NM_001033549.1,NM_014173.2	,	205,1816,4140	AA,AG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	18.1084,17.9761,18.0652	,	279/330,279/330	17389704	2226,10096	2011	4150	6161	SO:0001819	synonymous_variant	29086	exon9			CTACAAGTATGAG	AK000578	CCDS46012.1, CCDS74310.1	19p13.11	2011-02-21	2011-02-21	2011-01-31	ENSG00000105393	ENSG00000105393			25008	protein-coding gene	gene with protein product	"""Mediator of Rap80 Interactions and Targeting 40 kD"", ""new component of the BRCA1 A complex"""	612766	"""chromosome 19 open reading frame 62"""	C19orf62		11042152	Standard	NM_001288756		Approved	FLJ20571, HSPC142, NBA1, MERIT40	uc002nfv.3	Q9NWV8		ENST00000359435.4:c.837G>A	19.37:g.17389704G>A		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	61	26	0.42623	NM_014173	A8MQT0|B4DRY9|B4DVR1|Q6FIA0|Q9P018	Silent	SNP	ENST00000359435.4	37	CCDS46012.1																																																																																			G|0.869;A|0.131	0.131	strong		0.612	BABAM1-005	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000463471.1	NM_014173	
NAT2	10	hgsc.bcm.edu	37	8	18257795	18257795	+	Silent	SNP	C	C	T	rs1041983	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:18257795C>T	ENST00000286479.3	+	2	389	c.282C>T	c.(280-282)taC>taT	p.Y94Y	NAT2_ENST00000520116.1_Intron	NM_000015.2	NP_000006.2	P11245	ARY2_HUMAN	N-acetyltransferase 2 (arylamine N-acetyltransferase)	94					small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	arylamine N-acetyltransferase activity (GO:0004060)			kidney(1)|large_intestine(1)|lung(6)|ovary(1)|prostate(1)|skin(2)	12				Colorectal(111;0.0531)|COAD - Colon adenocarcinoma(73;0.21)	Acetaminophen(DB00316)|Clonazepam(DB01068)|Dapsone(DB00250)|Ezogabine(DB04953)|Isoniazid(DB00951)|Sulfamethoxazole(DB01015)	GGTATTTTTACATCCCTCCAG	0.493									Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of				C|||	1990	0.397364	0.4682	0.2911	5008	,	,		18016	0.4395		0.3052	False		,,,				2504	0.4284				p.Y94Y		Atlas-SNP	.											.	NAT2	34	.	0			c.C282T	GRCh37	CM001251	NAT2	M	rs1041983	PASS	.	C		1951,2455	551.8+/-378.4	421,1109,673	91.0	95.0	94.0		282	1.5	0.0	8	dbSNP_86	94	2697,5903	431.2+/-356.7	418,1861,2021	yes	coding-synonymous	NAT2	NM_000015.2		839,2970,2694	TT,TC,CC		31.3605,44.2805,35.7374		94/291	18257795	4648,8358	2203	4300	6503	SO:0001819	synonymous_variant	10	exon2	Familial Cancer Database	incl.: Familial Head and Neck Cancer	TTTTTACATCCCT	D90042	CCDS6008.1	8p22	2012-01-18			ENSG00000156006	ENSG00000156006	2.3.1.5		7646	protein-coding gene	gene with protein product		612182		AAC2		7773298	Standard	NM_000015		Approved		uc003wyw.1	P11245	OTTHUMG00000130826	ENST00000286479.3:c.282C>T	8.37:g.18257795C>T		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	129	32	0.248062	NM_000015	O43637|O60654|O60655|Q13146|Q16697|Q2MLE4|Q2MLF5|Q2MLG8|Q2MLJ6|Q2MLK4|Q2MLK6|Q2MLN7|Q6LET4|Q86XS0|Q86XS1|Q96KY8|Q96T64|Q96T65|Q9H220	Silent	SNP	ENST00000286479.3	37	CCDS6008.1																																																																																			C|0.637;T|0.363	0.363	strong		0.493	NAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253380.1	NM_000015	
MUC16	94025	hgsc.bcm.edu	37	19	9013905	9013905	+	Missense_Mutation	SNP	C	C	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:9013905C>G	ENST00000397910.4	-	33	38688	c.38485G>C	c.(38485-38487)Ggg>Cgg	p.G12829R		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	12831				Missing (in Ref. 3; AAK74120). {ECO:0000305}.	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						GTGGAGGTCCCAGGAGCTGAA	0.502																																					p.G12829R		Atlas-SNP	.											.	MUC16	4315	.	0			c.G38485C						PASS	.						68.0	61.0	63.0					19																	9013905		1920	4127	6047	SO:0001583	missense	94025	exon33			AGGTCCCAGGAGC	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.38485G>C	19.37:g.9013905C>G	ENSP00000381008:p.Gly12829Arg	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	83	18	0.216867	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	.	9.580	1.123389	0.20959	.	.	ENSG00000181143	ENST00000397910	T	0.01918	4.56	1.48	1.48	0.22813	.	.	.	.	.	T	0.07458	0.0188	M	0.73962	2.25	.	.	.	D	0.71674	0.998	P	0.58520	0.84	T	0.10730	-1.0617	8	0.87932	D	0	.	6.367	0.21461	0.0:1.0:0.0:0.0	.	12829	B5ME49	.	R	12829	ENSP00000381008:G12829R	ENSP00000381008:G12829R	G	-	1	0	MUC16	8874905	0.000000	0.05858	0.075000	0.20258	0.028000	0.11728	-0.025000	0.12413	1.121000	0.41925	0.484000	0.47621	GGG	.	.	none		0.502	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
LRRC4B	94030	hgsc.bcm.edu	37	19	51022073	51022073	+	Silent	SNP	G	G	A	rs61745055	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:51022073G>A	ENST00000599957.1	-	3	1094	c.897C>T	c.(895-897)ccC>ccT	p.P299P	LRRC4B_ENST00000389201.3_Silent_p.P299P			Q9NT99	LRC4B_HUMAN	leucine rich repeat containing 4B	299					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)		GGCGGTGCAGGGGCGTGAAGA	0.637													G|||	27	0.00539137	0.0	0.0144	5008	,	,		18771	0.0		0.0159	False		,,,				2504	0.001				p.P299P		Atlas-SNP	.											.	LRRC4B	89	.	0			c.C897T						PASS	.	G		8,4330		0,8,2161	85.0	102.0	96.0		897	0.1	1.0	19	dbSNP_129	96	99,8421		0,99,4161	no	coding-synonymous	LRRC4B	NM_001080457.1		0,107,6322	AA,AG,GG		1.162,0.1844,0.8322		299/714	51022073	107,12751	2169	4260	6429	SO:0001819	synonymous_variant	94030	exon3			GTGCAGGGGCGTG	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.897C>T	19.37:g.51022073G>A		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	108	61	0.564815	NM_001080457	Q3ZCQ4|Q58F20	Silent	SNP	ENST00000599957.1	37	CCDS42595.1																																																																																			G|0.993;A|0.007	0.007	strong		0.637	LRRC4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464907.1	NM_001080457	
LINC00283	100874057	hgsc.bcm.edu	37	13	103392562	103392562	+	RNA	SNP	C	C	A	rs12585626	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:103392562C>A	ENST00000430111.1	+	0	0									long intergenic non-protein coding RNA 283																		CTGATGATTTCATTCCTTTTG	0.333													C|||	371	0.0740815	0.1573	0.0159	5008	,	,		21018	0.1052		0.0268	False		,,,				2504	0.0194				p.M3495I		Atlas-SNP	.											.	.	.	.	0			c.G10485T						PASS	.	C	ILE/MET	187,1197		14,159,519	72.0	58.0	62.0		10485	0.3	0.0	13	dbSNP_120	62	68,3112		2,64,1524	yes	missense	CCDC168	NM_001146197.1	10	16,223,2043	AA,AC,CC		2.1384,13.5116,5.5872		3495/7082	103392562	255,4309	692	1590	2282			643677	exon4			TGATTTCATTCCT			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.103392562C>A		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	60	29	0.483333	NM_001146197		Missense_Mutation	SNP	ENST00000430111.1	37																																																																																				C|0.905;A|0.095	0.095	strong		0.333	LINC00283-001	KNOWN	not_organism_supported|basic	antisense	antisense	OTTHUMT00000045714.1		
KANK2	25959	hgsc.bcm.edu	37	19	11303618	11303618	+	Missense_Mutation	SNP	G	G	A	rs144821191		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:11303618G>A	ENST00000586659.1	-	4	1452	c.1138C>T	c.(1138-1140)Cgc>Tgc	p.R380C	KANK2_ENST00000432929.2_Missense_Mutation_p.R380C|KANK2_ENST00000589359.1_Missense_Mutation_p.R380C|KANK2_ENST00000589894.1_Missense_Mutation_p.R380C|KANK2_ENST00000355150.5_Missense_Mutation_p.R380C			Q63ZY3	KANK2_HUMAN	KN motif and ankyrin repeat domains 2	380					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						TCCTGGCTGCGGAACACAGGT	0.642													G|||	1	0.000199681	0.0	0.0	5008	,	,		16197	0.0		0.001	False		,,,				2504	0.0				p.R380C		Atlas-SNP	.											.	KANK2	47	.	0			c.C1138T						PASS	.	G	CYS/ARG,CYS/ARG	1,4405	2.1+/-5.4	0,1,2202	70.0	74.0	72.0		1138,1138	0.2	1.0	19	dbSNP_134	72	10,8590	7.7+/-29.5	0,10,4290	yes	missense,missense	KANK2	NM_001136191.2,NM_015493.6	180,180	0,11,6492	AA,AG,GG		0.1163,0.0227,0.0846	benign,benign	380/852,380/860	11303618	11,12995	2203	4300	6503	SO:0001583	missense	25959	exon2			GGCTGCGGAACAC	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.1138C>T	19.37:g.11303618G>A	ENSP00000465650:p.Arg380Cys	Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	131	65	0.496183	NM_015493	B0I1P4|Q3KQZ3|Q6GUF5|Q9H8S4|Q9NUP0|Q9P210	Missense_Mutation	SNP	ENST00000586659.1	37	CCDS12255.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	6.976	0.550018	0.13374	2.27E-4	0.001163	ENSG00000197256	ENST00000432929;ENST00000355150	T;T	0.37235	1.21;1.21	4.11	0.147	0.14838	.	0.085848	0.43747	D	0.000540	T	0.24774	0.0601	L	0.45581	1.43	0.33354	D	0.571462	B;B;B	0.13145	0.001;0.001;0.007	B;B;B	0.06405	0.002;0.0;0.002	T	0.10474	-1.0628	10	0.37606	T	0.19	-34.2083	5.155	0.15031	0.305:0.0:0.546:0.149	.	380;380;380	Q63ZY3-3;Q63ZY3;Q63ZY3-2	.;KANK2_HUMAN;.	C	380	ENSP00000395650:R380C;ENSP00000347276:R380C	ENSP00000347276:R380C	R	-	1	0	KANK2	11164618	0.023000	0.18921	0.998000	0.56505	0.366000	0.29705	0.248000	0.18198	0.224000	0.20940	-0.448000	0.05591	CGC	G|0.999;A|0.001	0.001	strong		0.642	KANK2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000453066.2	NM_015493	
OR51F1	256892	hgsc.bcm.edu	37	11	4790482	4790482	+	Silent	SNP	T	T	C	rs12792898	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:4790482T>C	ENST00000380383.1	-	1	686	c.687A>G	c.(685-687)ttA>ttG	p.L229L	OR51F1_ENST00000343430.3_Silent_p.L222L|MMP26_ENST00000477339.1_Intron|MMP26_ENST00000380390.1_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	172	0	0		WXS	Illumina HiSeq	Phase_I	181	39	0.21547	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	
CCDC27	148870	hgsc.bcm.edu	37	1	3669205	3669205	+	Missense_Mutation	SNP	C	C	G	rs10910021	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:3669205C>G	ENST00000294600.2	+	1	244	c.160C>G	c.(160-162)Cag>Gag	p.Q54E		NM_152492.2	NP_689705.2	Q2M243	CCD27_HUMAN	coiled-coil domain containing 27	54			Q -> E (in dbSNP:rs10910021). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.							breast(1)|endometrium(2)|kidney(1)|large_intestine(8)|liver(2)|lung(17)|prostate(1)|skin(2)|urinary_tract(2)	36	all_cancers(77;0.0385)|Ovarian(185;0.0634)|Lung NSC(156;0.21)|all_lung(157;0.218)	all_epithelial(116;5.52e-17)|all_lung(118;1.04e-06)|Lung NSC(185;0.000214)|Renal(390;0.00357)|Breast(487;0.00446)|Hepatocellular(190;0.0218)|Lung SC(97;0.0367)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.127)		Epithelial(90;1.11e-38)|OV - Ovarian serous cystadenocarcinoma(86;1.35e-22)|GBM - Glioblastoma multiforme(42;3.46e-16)|Colorectal(212;1.17e-05)|COAD - Colon adenocarcinoma(227;5.76e-05)|Kidney(185;0.00036)|BRCA - Breast invasive adenocarcinoma(365;0.000696)|KIRC - Kidney renal clear cell carcinoma(229;0.00558)|STAD - Stomach adenocarcinoma(132;0.00645)|Lung(427;0.203)		CAGCCCATCTCAGAGGCACAG	0.602													G|||	1939	0.387181	0.4017	0.4078	5008	,	,		17772	0.2897		0.3946	False		,,,				2504	0.4458				p.Q54E		Atlas-SNP	.											.	CCDC27	79	.	0			c.C160G						PASS	.	G	GLU/GLN	1728,2678	648.5+/-398.7	345,1038,820	132.0	113.0	119.0		160	-5.5	0.0	1	dbSNP_120	119	3176,5424	653.6+/-401.1	589,1998,1713	yes	missense	CCDC27	NM_152492.2	29	934,3036,2533	GG,GC,CC		36.9302,39.2192,37.7057	benign	54/657	3669205	4904,8102	2203	4300	6503	SO:0001583	missense	148870	exon1			CCATCTCAGAGGC		CCDS50.1	1p36.32	2008-02-05			ENSG00000162592	ENSG00000162592			26546	protein-coding gene	gene with protein product							Standard	NM_152492		Approved	FLJ32825	uc001akv.2	Q2M243	OTTHUMG00000003504	ENST00000294600.2:c.160C>G	1.37:g.3669205C>G	ENSP00000294600:p.Gln54Glu	Somatic	174	1	0.00574713		WXS	Illumina HiSeq	Phase_I	95	67	0.705263	NM_152492	Q5TBV3|Q96M50	Missense_Mutation	SNP	ENST00000294600.2	37	CCDS50.1	790	0.3617216117216117	200	0.4065040650406504	135	0.3729281767955801	159	0.27797202797202797	296	0.39050131926121373	G	5.832	0.337707	0.11013	0.392192	0.369302	ENSG00000162592	ENST00000294600	T	0.17691	2.26	3.95	-5.54	0.02544	.	1.231100	0.06015	N	0.650230	T	0.00012	0.0000	N	0.12182	0.205	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.47341	-0.9125	9	0.08179	T	0.78	-5.2542	7.9089	0.29778	0.3185:0.4778:0.2037:0.0	rs10910021	54	Q2M243	CCD27_HUMAN	E	54	ENSP00000294600:Q54E	ENSP00000294600:Q54E	Q	+	1	0	CCDC27	3659065	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.374000	0.02566	-1.647000	0.01511	-0.829000	0.03081	CAG	C|0.625;G|0.375	0.375	strong		0.602	CCDC27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009740.1	NM_152492	
KRTAP10-10	353333	hgsc.bcm.edu	37	21	46057720	46057720	+	Missense_Mutation	SNP	A	A	C	rs4818949	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:46057720A>C	ENST00000380095.1	+	1	448	c.386A>C	c.(385-387)cAg>cCg	p.Q129P	TSPEAR_ENST00000323084.4_Intron	NM_181688.1	NP_859016.1	P60014	KR10A_HUMAN	keratin associated protein 10-10	129	15 X 5 AA repeats of C-C-X(3).		Q -> P (in dbSNP:rs4818949).			keratin filament (GO:0045095)				NS(1)|endometrium(2)|kidney(1)|lung(6)|prostate(1)|skin(2)	13						TGCTGCCAGCAGTCTAGCTGC	0.607													A|||	1395	0.278554	0.4773	0.2233	5008	,	,		23323	0.0526		0.2425	False		,,,				2504	0.319				p.Q129P		Atlas-SNP	.											.	KRTAP10-10	37	.	0			c.A386C						PASS	.	A	,PRO/GLN	1971,2435	556.5+/-379.5	445,1081,677	259.0	234.0	243.0		,386	-0.1	1.0	21	dbSNP_111	243	2165,6435	369.3+/-335.4	281,1603,2416	yes	intron,missense	TSPEAR,KRTAP10-10	NM_144991.2,NM_181688.1	,76	726,2684,3093	CC,CA,AA		25.1744,44.7345,31.8007	,benign	,129/252	46057720	4136,8870	2203	4300	6503	SO:0001583	missense	353333	exon1			GCCAGCAGTCTAG	AJ566387	CCDS33585.1	21q22.3	2006-03-13			ENSG00000221859	ENSG00000221859		"""Keratin associated proteins"""	22972	protein-coding gene	gene with protein product							Standard	NM_181688		Approved	KAP10.10, KAP18.10, KRTAP18-10	uc002zfq.3	P60014	OTTHUMG00000057631	ENST00000380095.1:c.386A>C	21.37:g.46057720A>C	ENSP00000369438:p.Gln129Pro	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	165	50	0.30303	NM_181688		Missense_Mutation	SNP	ENST00000380095.1	37	CCDS33585.1	541	0.24771062271062272	232	0.4715447154471545	88	0.2430939226519337	31	0.05419580419580419	190	0.25065963060686014	a	6.718	0.501193	0.12822	0.447345	0.251744	ENSG00000221859	ENST00000380095	T	0.01165	5.24	3.04	-0.0501	0.13832	.	.	.	.	.	T	0.00012	0.0000	L	0.52364	1.645	0.37030	P	0.10338099999999995	B	0.15141	0.012	B	0.14023	0.01	T	0.17167	-1.0378	8	0.16896	T	0.51	.	4.4006	0.11385	0.4554:0.3648:0.0:0.1798	rs4818949;rs56858729	129	P60014	KR10A_HUMAN	P	129	ENSP00000369438:Q129P	ENSP00000369438:Q129P	Q	+	2	0	KRTAP10-10	44882148	0.000000	0.05858	0.998000	0.56505	0.378000	0.30076	0.029000	0.13666	0.190000	0.20209	0.378000	0.23410	CAG	A|0.711;C|0.289	0.289	strong		0.607	KRTAP10-10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128034.1	NM_181688	
BPHL	670	hgsc.bcm.edu	37	6	3123983	3123983	+	Missense_Mutation	SNP	C	C	T	rs372718817		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:3123983C>T	ENST00000380379.5	+	2	249	c.200C>T	c.(199-201)cCt>cTt	p.P67L	BPHL_ENST00000380375.3_Missense_Mutation_p.P50L|BPHL_ENST00000434640.1_Missense_Mutation_p.P50L|BPHL_ENST00000380368.2_Missense_Mutation_p.P50L	NM_004332.2	NP_004323.2	Q86WA6	BPHL_HUMAN	biphenyl hydrolase-like (serine hydrolase)	67					cellular amino acid metabolic process (GO:0006520)|response to toxic substance (GO:0009636)	extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	hydrolase activity (GO:0016787)			endometrium(4)|kidney(1)|large_intestine(2)|lung(6)	13	Ovarian(93;0.0386)	all_hematologic(90;0.108)				CTGCTACTTCCTGGGATGTTA	0.438																																					p.P67L		Atlas-SNP	.											BPHL,NS,carcinoma,0,1	BPHL	32	1	0			c.C200T						scavenged	.	C	LEU/PRO	0,4406		0,0,2203	137.0	116.0	123.0		200	5.6	1.0	6		123	1,8599	1.2+/-3.3	0,1,4299	no	missense	BPHL	NM_004332.2	98	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	67/292	3123983	1,13005	2203	4300	6503	SO:0001583	missense	670	exon2			TACTTCCTGGGAT	X81372	CCDS4483.2	6p25	2008-08-29	2008-08-29		ENSG00000137274	ENSG00000137274			1094	protein-coding gene	gene with protein product	"""breast epithelial mucin-associated antigen"""	603156		MCNAA		7759552, 9721218, 15832508	Standard	NM_004332		Approved	Bph-rp	uc003mva.3	Q86WA6	OTTHUMG00000014140	ENST00000380379.5:c.200C>T	6.37:g.3123983C>T	ENSP00000369739:p.Pro67Leu	Somatic	226	0	0		WXS	Illumina HiSeq	Phase_I	230	3	0.0130435	NM_004332	Q00306|Q13855|Q3KP51	Missense_Mutation	SNP	ENST00000380379.5	37	CCDS4483.2	.	.	.	.	.	.	.	.	.	.	C	27.6	4.846068	0.91277	0.0	1.16E-4	ENSG00000137274	ENST00000434640;ENST00000380375;ENST00000380368;ENST00000380379	T;T;T;T	0.69806	-0.43;-0.43;-0.43;-0.43	5.55	5.55	0.83447	.	0.000000	0.85682	D	0.000000	T	0.81365	0.4807	M	0.84219	2.685	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.81152	-0.1063	10	0.46703	T	0.11	-2.5525	19.4939	0.95064	0.0:1.0:0.0:0.0	.	67;50	Q86WA6;Q86WA6-2	BPHL_HUMAN;.	L	50;50;50;67	ENSP00000390472:P50L;ENSP00000369734:P50L;ENSP00000369726:P50L;ENSP00000369739:P67L	ENSP00000369726:P50L	P	+	2	0	BPHL	3068982	1.000000	0.71417	0.991000	0.47740	0.880000	0.50808	6.702000	0.74628	2.606000	0.88127	0.563000	0.77884	CCT	.	.	weak		0.438	BPHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039670.5		
DYNC2LI1	51626	hgsc.bcm.edu	37	2	44021826	44021826	+	Intron	SNP	T	T	A	rs9309107	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:44021826T>A	ENST00000260605.8	+	6	607				DYNC2LI1_ENST00000398823.2_3'UTR|DYNC2LI1_ENST00000406852.3_Missense_Mutation_p.F184Y|DYNC2LI1_ENST00000605786.1_Intron|DYNC2LI1_ENST00000443170.3_Intron|DYNC2LI1_ENST00000489222.2_Intron	NM_001193464.1|NM_016008.3	NP_001180393.1|NP_057092.2	Q8TCX1	DC2L1_HUMAN	dynein, cytoplasmic 2, light intermediate chain 1						antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cilium assembly (GO:0042384)|determination of left/right symmetry (GO:0007368)	apical part of cell (GO:0045177)|axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|cytosol (GO:0005829)|intraciliary transport particle (GO:0030990)|microtubule (GO:0005874)|motile primary cilium (GO:0031512)|primary cilium (GO:0072372)	motor activity (GO:0003774)			breast(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(12)|ovary(1)|pancreas(1)|skin(1)	26		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)				TTAGTCCCATTTATAGTTAAT	0.343													A|||	2262	0.451677	0.7262	0.4654	5008	,	,		18661	0.1895		0.326	False		,,,				2504	0.4703				p.F184Y		Atlas-SNP	.											.	DYNC2LI1	46	.	0			c.T551A						PASS	.	A	,TYR/PHE,	2915,1491	456.1+/-351.2	990,935,278	92.0	99.0	96.0		,551,	0.9	0.0	2	dbSNP_119	96	2828,5772	675.0+/-403.2	471,1886,1943	yes	intron,missense,intron	DYNC2LI1	NM_001193464.1,NM_015522.3,NM_016008.3	,22,	1461,2821,2221	AA,AT,TT		32.8837,33.8402,44.1565	,,	,184/202,	44021826	5743,7263	2203	4300	6503	SO:0001627	intron_variant	51626	exon6			TCCCATTTATAGT		CCDS1813.1, CCDS46270.1, CCDS62903.1	2p25.1-p24.1	2008-02-05			ENSG00000138036	ENSG00000138036		"""Cytoplasmic dyneins"""	24595	protein-coding gene	gene with protein product						10810093, 11907264	Standard	NM_016008		Approved	D2LIC, LIC3, CGI-60, DKFZP564A033	uc002rtl.3	Q8TCX1	OTTHUMG00000128656	ENST00000260605.8:c.507+44T>A	2.37:g.44021826T>A		Somatic	250	0	0		WXS	Illumina HiSeq	Phase_I	404	402	0.995049	NM_015522	A8MVJ5|Q53F57|Q6PDB2|Q8IWA3|Q96B03|Q96J00|Q9Y370|Q9Y3S9	Missense_Mutation	SNP	ENST00000260605.8	37	CCDS1813.1	884	0.40476190476190477	361	0.733739837398374	172	0.47513812154696133	108	0.1888111888111888	243	0.32058047493403696	A	4.001	-0.002468	0.07819	0.661598	0.328837	ENSG00000138036	ENST00000406852	T	0.32023	1.47	4.45	0.913	0.19354	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.22591	-1.0212	7	0.87932	D	0	.	5.1073	0.14790	0.6522:0.0:0.2213:0.1265	rs9309107;rs52802708;rs59663186;rs9309107	184	Q8TCX1-4	.	Y	184	ENSP00000385738:F184Y	ENSP00000385738:F184Y	F	+	2	0	DYNC2LI1	43875330	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	0.411000	0.21115	0.048000	0.15891	-1.185000	0.01705	TTT	A|0.389;N|0.001	0.389	strong		0.343	DYNC2LI1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000250536.2	NM_016008	
RFTN2	130132	hgsc.bcm.edu	37	2	198460748	198460748	+	Silent	SNP	T	T	G	rs77442629	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:198460748T>G	ENST00000295049.4	-	8	1736	c.1200A>C	c.(1198-1200)ccA>ccC	p.P400P		NM_144629.2	NP_653230.2	Q52LD8	RFTN2_HUMAN	raftlin family member 2	400					dsRNA transport (GO:0033227)|response to exogenous dsRNA (GO:0043330)	plasma membrane (GO:0005886)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(6)|lung(13)|urinary_tract(3)	30						TCCACATAACTGGCCTCTGAA	0.328													T|||	12	0.00239617	0.0008	0.0	5008	,	,		17368	0.0		0.0109	False		,,,				2504	0.0				p.P400P		Atlas-SNP	.											.	RFTN2	68	.	0			c.A1200C						PASS	.	T		5,4401	9.9+/-24.2	0,5,2198	100.0	90.0	93.0		1200	-4.7	0.0	2	dbSNP_132	93	64,8536	38.8+/-94.9	0,64,4236	no	coding-synonymous	RFTN2	NM_144629.2		0,69,6434	GG,GT,TT		0.7442,0.1135,0.5305		400/502	198460748	69,12937	2203	4300	6503	SO:0001819	synonymous_variant	130132	exon8			CATAACTGGCCTC	AK055136	CCDS2323.1	2q33.1	2008-02-05	2006-09-28	2006-09-28	ENSG00000162944	ENSG00000162944			26402	protein-coding gene	gene with protein product			"""chromosome 2 open reading frame 11"""	C2orf11			Standard	NM_144629		Approved	FLJ30574, Raftlin-2	uc002uuo.4	Q52LD8	OTTHUMG00000132746	ENST00000295049.4:c.1200A>C	2.37:g.198460748T>G		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	65	30	0.461538	NM_144629	Q14DH4|Q2TA69|Q53QE0|Q53SE1|Q96NM3	Silent	SNP	ENST00000295049.4	37	CCDS2323.1																																																																																			T|0.995;G|0.005	0.005	strong		0.328	RFTN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256106.2	NM_144629	
OR13C9	286362	hgsc.bcm.edu	37	9	107379895	107379895	+	Missense_Mutation	SNP	G	G	T	rs10761054	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	205	0	0		WXS	Illumina HiSeq	Phase_I	166	77	0.463855	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		
SETX	23064	hgsc.bcm.edu	37	9	135172412	135172412	+	Silent	SNP	A	A	G	rs2296869	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:135172412A>G	ENST00000224140.5	-	14	5993	c.5811T>C	c.(5809-5811)gaT>gaC	p.D1937D	SETX_ENST00000393220.1_Silent_p.D1937D|SETX_ENST00000372169.2_Silent_p.D1937D	NM_015046.5	NP_055861.3	Q7Z333	SETX_HUMAN	senataxin	1937					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)		CTTTCTTTTGATCTTCATTGA	0.348													G|||	2212	0.441693	0.6921	0.2262	5008	,	,		21263	0.6329		0.1382	False		,,,				2504	0.3712				p.D1937D		Atlas-SNP	.											.	SETX	234	.	0			c.T5811C						PASS	.	G		2658,1748	518.6+/-369.8	823,1012,368	134.0	110.0	118.0		5811	-0.0	1.0	9	dbSNP_100	118	1337,7263	755.9+/-407.5	97,1143,3060	no	coding-synonymous	SETX	NM_015046.5		920,2155,3428	GG,GA,AA		15.5465,39.6732,30.7166		1937/2678	135172412	3995,9011	2203	4300	6503	SO:0001819	synonymous_variant	23064	exon14			CTTTTGATCTTCA	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.5811T>C	9.37:g.135172412A>G		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	95	44	0.463158	NM_015046	A2A396|B2RPB2|B5ME16|C9JQ10|O75120|Q3KQX4|Q5JUJ1|Q68DW5|Q6AZD7|Q7Z3J6|Q8WX33|Q9H9D1|Q9NVP9	Silent	SNP	ENST00000224140.5	37	CCDS6947.1																																																																																			A|0.628;G|0.372	0.372	strong		0.348	SETX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054774.3	NM_015046	
STOX1	219736	hgsc.bcm.edu	37	10	70645376	70645376	+	Missense_Mutation	SNP	A	A	C	rs10509305	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:70645376A>C	ENST00000298596.6	+	3	1907	c.1824A>C	c.(1822-1824)gaA>gaC	p.E608D	STOX1_ENST00000421961.2_Missense_Mutation_p.E498D|STOX1_ENST00000399169.4_Missense_Mutation_p.E608D|STOX1_ENST00000399162.2_Intron|STOX1_ENST00000399165.4_Intron	NM_152709.4	NP_689922.3	Q6ZVD7	STOX1_HUMAN	storkhead box 1	608			E -> D (in dbSNP:rs10509305). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15806103}.			cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(5)|endometrium(2)|kidney(2)|large_intestine(5)|liver(2)|lung(8)|prostate(1)|skin(3)	28						TGAGATATGAAGTGTATGGTG	0.428													A|||	722	0.144169	0.0318	0.2161	5008	,	,		23136	0.0804		0.2187	False		,,,				2504	0.2342				p.E608D		Atlas-SNP	.											.	STOX1	75	.	0			c.A1824C	GRCh37	CM057372	STOX1	M	rs10509305	PASS	.	A	,,ASP/GLU,ASP/GLU,ASP/GLU	225,3635		5,215,1710	159.0	143.0	148.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	,,1824,1494,1824	1.1	0.0	10	dbSNP_119	148	1779,6497		196,1387,2555	yes	intron,intron,missense,missense,missense	STOX1	NM_001130159.2,NM_001130160.2,NM_001130161.2,NM_001130162.2,NM_152709.4	,,45,45,45	201,1602,4265	CC,CA,AA		21.4959,5.829,16.5129	,,benign,benign,benign	,,608/990,498/880,608/990	70645376	2004,10132	1930	4138	6068	SO:0001583	missense	219736	exon3			ATATGAAGTGTAT	AK057891	CCDS41535.1, CCDS44416.1, CCDS44417.1	10q22.1	2005-11-29	2005-04-04	2005-04-04	ENSG00000165730	ENSG00000165730			23508	protein-coding gene	gene with protein product		609397	"""chromosome 10 open reading frame 24"""	C10orf24			Standard	NM_152709		Approved	FLJ25162	uc001joq.3	Q6ZVD7	OTTHUMG00000018367	ENST00000298596.6:c.1824A>C	10.37:g.70645376A>C	ENSP00000298596:p.Glu608Asp	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	90	39	0.433333	NM_152709	A2A3Q9|A5D6Y7|B0QZA4|B0QZA5|B0QZA6|Q4F8Q6|Q5I946|Q5I947|Q5I948|Q5VX38|Q5VX39|Q6ZRY3|Q96LR3|Q96LS0	Missense_Mutation	SNP	ENST00000298596.6	37	CCDS41535.1	315	0.14423076923076922	14	0.028455284552845527	86	0.23756906077348067	55	0.09615384615384616	160	0.21108179419525067	A	0	-2.847190	0.00067	0.05829	0.214959	ENSG00000165730	ENST00000399169;ENST00000298596;ENST00000421961	T;T;T	0.74106	-0.81;-0.81;-0.49	6.07	1.14	0.20703	.	1.071960	0.07228	N	0.861947	T	0.00012	0.0000	N	0.00162	-1.95	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.06075	-1.0847	9	0.09338	T	0.73	.	0.0409	0.00008	0.2825:0.1869:0.213:0.3176	rs10509305;rs17470548;rs52799917;rs61365255;rs10509305	608	Q6ZVD7	STOX1_HUMAN	D	608;608;498	ENSP00000382121:E608D;ENSP00000298596:E608D;ENSP00000394509:E498D	ENSP00000298596:E608D	E	+	3	2	STOX1	70315382	0.000000	0.05858	0.003000	0.11579	0.001000	0.01503	-0.860000	0.04272	-0.040000	0.13580	-2.501000	0.00191	GAA	A|0.858;C|0.142	0.142	strong		0.428	STOX1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276849.3	NM_152709	
NT5DC3	51559	hgsc.bcm.edu	37	12	104186995	104186995	+	Silent	SNP	G	G	A	rs61748068	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:104186995G>A	ENST00000392876.3	-	9	1006	c.966C>T	c.(964-966)ttC>ttT	p.F322F		NM_001031701.2	NP_001026871.1	Q86UY8	NT5D3_HUMAN	5'-nucleotidase domain containing 3	322						cytosol (GO:0005829)|mitochondrion (GO:0005739)|receptor complex (GO:0043235)	hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(1)|kidney(4)|large_intestine(3)|lung(15)|ovary(2)|skin(1)|stomach(2)	30						TGACCACATCGAACAGGTCCC	0.423													G|||	561	0.112021	0.0038	0.1585	5008	,	,		21006	0.2639		0.0974	False		,,,				2504	0.0838				p.F322F		Atlas-SNP	.											.	NT5DC3	113	.	0			c.C966T						PASS	.	G		97,4309	80.4+/-118.8	0,97,2106	196.0	205.0	202.0		966	-3.5	0.9	12	dbSNP_129	202	842,7758	194.1+/-239.6	49,744,3507	no	coding-synonymous	NT5DC3	NM_001031701.2		49,841,5613	AA,AG,GG		9.7907,2.2015,7.2197		322/549	104186995	939,12067	2203	4300	6503	SO:0001819	synonymous_variant	51559	exon9			CACATCGAACAGG	AB032786	CCDS41824.1	12q22-q23.1	2006-02-03			ENSG00000111696	ENSG00000111696			30826	protein-coding gene	gene with protein product		611076					Standard	NM_001031701		Approved	TU12B1-TY, FLJ11266	uc010swe.1	Q86UY8	OTTHUMG00000157017	ENST00000392876.3:c.966C>T	12.37:g.104186995G>A		Somatic	239	0	0		WXS	Illumina HiSeq	Phase_I	225	108	0.48	NM_001031701	Q9NUM7|Q9P2T2|Q9P2T3	Silent	SNP	ENST00000392876.3	37	CCDS41824.1																																																																																			G|0.908;A|0.092	0.092	strong		0.423	NT5DC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347118.2	NM_016575	
ZNF416	55659	hgsc.bcm.edu	37	19	58084605	58084605	+	Missense_Mutation	SNP	C	C	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:58084605C>G	ENST00000196489.3	-	4	889	c.667G>C	c.(667-669)Gag>Cag	p.E223Q		NM_017879.1	NP_060349.1	Q9BWM5	ZN416_HUMAN	zinc finger protein 416	223					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(3)|large_intestine(5)|lung(12)|prostate(1)	22		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0259)		TGGCTGGACTCTCTCCTGCAT	0.438																																					p.E223Q		Atlas-SNP	.											.	ZNF416	50	.	0			c.G667C						PASS	.						140.0	142.0	141.0					19																	58084605		2203	4300	6503	SO:0001583	missense	55659	exon4			TGGACTCTCTCCT	BC000130	CCDS12954.1	19q13.4	2013-01-08				ENSG00000083817		"""Zinc fingers, C2H2-type"", ""-"""	20645	protein-coding gene	gene with protein product							Standard	NM_017879		Approved	FLJ20557	uc002qpf.3	Q9BWM5		ENST00000196489.3:c.667G>C	19.37:g.58084605C>G	ENSP00000196489:p.Glu223Gln	Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	174	108	0.62069	NM_017879	Q9NWW8	Missense_Mutation	SNP	ENST00000196489.3	37	CCDS12954.1	.	.	.	.	.	.	.	.	.	.	C	8.461	0.855209	0.17106	.	.	ENSG00000083817	ENST00000196489;ENST00000359489;ENST00000428052	T	0.07444	3.19	3.65	1.43	0.22495	.	.	.	.	.	T	0.05502	0.0145	L	0.27053	0.805	0.09310	N	1	B	0.30361	0.277	B	0.25759	0.063	T	0.36720	-0.9736	9	0.66056	D	0.02	.	4.8172	0.13372	0.1732:0.6307:0.0:0.1961	.	223	Q9BWM5	ZN416_HUMAN	Q	223;209;203	ENSP00000196489:E223Q	ENSP00000196489:E223Q	E	-	1	0	ZNF416	62776417	0.000000	0.05858	0.002000	0.10522	0.021000	0.10359	-0.488000	0.06497	0.334000	0.23590	0.655000	0.94253	GAG	.	.	none		0.438	ZNF416-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466787.1	NM_017879	
DNA2	1763	hgsc.bcm.edu	37	10	70191970	70191970	+	Silent	SNP	A	A	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:70191970A>G	ENST00000358410.3	-	12	1916	c.1866T>C	c.(1864-1866)atT>atC	p.I622I	DNA2_ENST00000399179.2_Silent_p.I622I|DNA2_ENST00000399180.2_Silent_p.I708I	NM_001080449.2	NP_001073918.2	P51530	DNA2_HUMAN	DNA replication helicase/nuclease 2	622	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						TACCCTTTAGAATGCAGGCAA	0.323																																					p.I622I		Atlas-SNP	.											.	DNA2	76	.	0			c.T1866C						PASS	.						132.0	126.0	128.0					10																	70191970		1836	4087	5923	SO:0001819	synonymous_variant	1763	exon12			CTTTAGAATGCAG	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.1866T>C	10.37:g.70191970A>G		Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	150	6	0.04	NM_001080449	Q2NKM1|Q5TC49|Q5TC50|Q6P455|Q6PI80|Q7Z6H9|Q8N346	Silent	SNP	ENST00000358410.3	37																																																																																				.	.	none		0.323	DNA2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000048334.2		
CAND2	23066	hgsc.bcm.edu	37	3	12856856	12856856	+	Missense_Mutation	SNP	A	A	G	rs2305398	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:12856856A>G	ENST00000456430.2	+	8	1264	c.1223A>G	c.(1222-1224)cAg>cGg	p.Q408R	CAND2_ENST00000295989.5_Missense_Mutation_p.Q315R	NM_001162499.1	NP_001155971.1	O75155	CAND2_HUMAN	cullin-associated and neddylation-dissociated 2 (putative)	408			Q -> R (in dbSNP:rs2305398). {ECO:0000269|PubMed:9734811}.		positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	intracellular (GO:0005622)|nucleus (GO:0005634)				breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(8)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	37						CGGCAAACACAGCCCCCGAAG	0.617													G|||	2887	0.576478	0.972	0.4986	5008	,	,		20497	0.2907		0.6551	False		,,,				2504	0.3108				p.Q408R	GBM(43;676 868 1633 6395 37496)	Atlas-SNP	.											.	CAND2	138	.	0			c.A1223G						PASS	.	G	ARG/GLN,ARG/GLN	3844,376		1752,340,18	46.0	54.0	51.0		1223,944	3.8	1.0	3	dbSNP_100	51	5225,3213		1621,1983,615	yes	missense,missense	CAND2	NM_001162499.1,NM_012298.2	43,43	3373,2323,633	GG,GA,AA		38.0777,8.91,28.3536	benign,benign	408/1237,315/1120	12856856	9069,3589	2110	4219	6329	SO:0001583	missense	23066	exon8			AAACACAGCCCCC		CCDS43053.1, CCDS54554.1	3p25.2	2008-02-05			ENSG00000144712	ENSG00000144712			30689	protein-coding gene	gene with protein product	"""TBP interacting protein"""	610403				9734811, 10441524	Standard	NM_012298		Approved	TIP120B, KIAA0667, Tp120b	uc003bxk.2	O75155	OTTHUMG00000155397	ENST00000456430.2:c.1223A>G	3.37:g.12856856A>G	ENSP00000387641:p.Gln408Arg	Somatic	263	1	0.00380228		WXS	Illumina HiSeq	Phase_I	212	99	0.466981	NM_001162499	B9EGM9|E9KL24	Missense_Mutation	SNP	ENST00000456430.2	37	CCDS54554.1	1283	0.5874542124542125	469	0.9532520325203252	180	0.4972375690607735	150	0.26223776223776224	484	0.6385224274406333	G	0.066	-1.213618	0.01555	0.9109	0.619223	ENSG00000144712	ENST00000295989;ENST00000456430	T;T	0.64991	-0.13;-0.13	4.86	3.85	0.44370	Armadillo-like helical (1);Armadillo-type fold (1);	0.296572	0.26016	N	0.026849	T	0.00012	0.0000	N	0.00399	-1.545	0.09310	P	0.999996978	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.36504	-0.9745	9	0.07482	T	0.82	-22.8675	7.173	0.25728	0.2702:0.0:0.7298:0.0	rs2305398;rs17824975;rs59611646;rs2305398	408;315	O75155;O75155-2	CAND2_HUMAN;.	R	315;408	ENSP00000295989:Q315R;ENSP00000387641:Q408R	ENSP00000295989:Q315R	Q	+	2	0	CAND2	12831856	0.994000	0.37717	0.955000	0.39395	0.098000	0.18820	0.601000	0.24119	1.046000	0.40249	-0.215000	0.12644	CAG	G|0.597;N|0.001	0.597	strong		0.617	CAND2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339856.4	XM_371617	
TTLL12	23170	hgsc.bcm.edu	37	22	43576904	43576904	+	Silent	SNP	G	G	A	rs2071723	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:43576904G>A	ENST00000216129.6	-	3	453	c.390C>T	c.(388-390)caC>caT	p.H130H		NM_015140.3	NP_055955.1	Q14166	TTL12_HUMAN	tubulin tyrosine ligase-like family, member 12	130					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)				GCTGGCGCGCGTGCTCCACAC	0.662													G|||	1641	0.327676	0.2383	0.3905	5008	,	,		17213	0.3165		0.4105	False		,,,				2504	0.3303				p.H130H		Atlas-SNP	.											TTLL12,NS,carcinoma,0,1	TTLL12	50	1	0			c.C390T						PASS	.	G		1081,3325	377.5+/-322.5	126,829,1248	47.0	42.0	44.0		390	-10.7	0.4	22	dbSNP_96	44	3465,5131	494.2+/-373.8	718,2029,1551	no	coding-synonymous	TTLL12	NM_015140.3		844,2858,2799	AA,AG,GG		40.3094,24.5347,34.9639		130/645	43576904	4546,8456	2203	4298	6501	SO:0001819	synonymous_variant	23170	exon3			GCGCGCGTGCTCC	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.390C>T	22.37:g.43576904G>A		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	112	53	0.473214	NM_015140	Q20WK5|Q9UGU3	Silent	SNP	ENST00000216129.6	37	CCDS14047.1																																																																																			A|0.339;C|0.000;G|0.661	0.339	strong		0.662	TTLL12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319611.1	NM_015140	
CCDC176	80127	hgsc.bcm.edu	37	14	74523949	74523949	+	Silent	SNP	G	G	A	rs3742808	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:74523949G>A	ENST00000394009.3	+	11	1689	c.1566G>A	c.(1564-1566)caG>caA	p.Q522Q	ALDH6A1_ENST00000553458.1_3'UTR|AC005484.5_ENST00000492026.1_RNA|CCDC176_ENST00000553773.1_Silent_p.Q247Q|CCDC176_ENST00000492247.2_Silent_p.Q66Q	NM_025057.2	NP_079333.2	Q8ND07	BBOF1_HUMAN	coiled-coil domain containing 176	522					motile cilium assembly (GO:0044458)	ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)											AAGAACCTCAGGAGTCTGACA	0.398													A|||	1505	0.300519	0.3555	0.1801	5008	,	,		20419	0.2381		0.1909	False		,,,				2504	0.4888				p.Q522Q		Atlas-SNP	.											.	.	.	.	0			c.G1566A						PASS	.	A		1483,2923	676.6+/-403.3	263,957,983	63.0	61.0	62.0		1566	-2.0	0.0	14	dbSNP_107	62	1616,6984	741.2+/-407.1	147,1322,2831	no	coding-synonymous	C14orf45	NM_025057.2		410,2279,3814	AA,AG,GG		18.7907,33.6586,23.8275		522/530	74523949	3099,9907	2203	4300	6503	SO:0001819	synonymous_variant	80127	exon11			ACCTCAGGAGTCT	BI457605	CCDS32119.2	14q24.3	2013-01-04	2012-09-25	2012-09-25	ENSG00000119636	ENSG00000119636			19855	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 45"""	C14orf45			Standard	NM_025057		Approved		uc010tup.2	Q8ND07	OTTHUMG00000152786	ENST00000394009.3:c.1566G>A	14.37:g.74523949G>A		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	108	53	0.490741	NM_025057	Q0P604|Q9H5P8	Silent	SNP	ENST00000394009.3	37	CCDS32119.2																																																																																			G|0.755;A|0.245	0.245	strong		0.398	CCDC176-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327863.1	NM_025057	
DIDO1	11083	hgsc.bcm.edu	37	20	61512185	61512185	+	Missense_Mutation	SNP	G	G	C	rs41282984	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:61512185G>C	ENST00000266070.4	-	16	5448	c.5123C>G	c.(5122-5124)tCt>tGt	p.S1708C	DIDO1_ENST00000395343.1_Missense_Mutation_p.S1708C	NM_033081.2	NP_149072.2	Q9BTC0	DIDO1_HUMAN	death inducer-obliterator 1	1708			S -> C (in dbSNP:rs41282984).		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)					CCTTCCAGCAGAATGAAGATT	0.652													G|||	277	0.0553115	0.1097	0.0216	5008	,	,		15522	0.0198		0.0596	False		,,,				2504	0.0378				p.S1708C	Melanoma(25;381 482 3385 5362 7955 17159 17174 40604 47095)	Atlas-SNP	.											.	DIDO1	321	.	0			c.C5123G						PASS	.	G	CYS/SER,CYS/SER	505,3901	229.1+/-243.8	20,465,1718	58.0	68.0	64.0		5123,5123	1.8	0.0	20	dbSNP_127	64	678,7922	167.4+/-219.2	33,612,3655	yes	missense,missense	DIDO1	NM_001193369.1,NM_033081.2	112,112	53,1077,5373	CC,CG,GG		7.8837,11.4616,9.0958	possibly-damaging,possibly-damaging	1708/2241,1708/2241	61512185	1183,11823	2203	4300	6503	SO:0001583	missense	11083	exon16			CCAGCAGAATGAA	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.5123C>G	20.37:g.61512185G>C	ENSP00000266070:p.Ser1708Cys	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	100	49	0.49	NM_001193369	A8MY65|B9EH82|E1P5I1|O15043|Q3ZTL7|Q3ZTL8|Q4VXS1|Q4VXS2|Q4VXV8|Q4VXV9|Q96D72|Q9BQW0|Q9BW03|Q9H4G6|Q9H4G7|Q9NTU8|Q9NUM8|Q9UFB6	Missense_Mutation	SNP	ENST00000266070.4	37	CCDS33506.1	127	0.05815018315018315	53	0.10772357723577236	12	0.03314917127071823	10	0.017482517482517484	52	0.06860158311345646	G	11.14	1.550129	0.27652	0.114616	0.078837	ENSG00000101191	ENST00000266070;ENST00000395343	T;T	0.08896	3.04;3.04	5.31	1.8	0.24995	.	0.165815	0.28371	N	0.015596	T	0.00109	0.0003	N	0.19112	0.55	0.58432	P	5.000000000032756E-6	B	0.09022	0.002	B	0.04013	0.001	T	0.31861	-0.9928	9	0.54805	T	0.06	-0.623	4.2819	0.10836	0.4482:0.4274:0.1244:0.0	rs41282984	1708	Q9BTC0	DIDO1_HUMAN	C	1708	ENSP00000266070:S1708C;ENSP00000378752:S1708C	ENSP00000266070:S1708C	S	-	2	0	DIDO1	60982630	0.903000	0.30736	0.001000	0.08648	0.047000	0.14425	2.065000	0.41442	0.071000	0.16664	0.655000	0.94253	TCT	G|0.921;C|0.079	0.079	strong		0.652	DIDO1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080091.2	NM_080796	
IGSF8	93185	hgsc.bcm.edu	37	1	160064697	160064697	+	Missense_Mutation	SNP	C	C	T	rs200550632		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:160064697C>T	ENST00000368086.1	-	2	620	c.404G>A	c.(403-405)cGc>cAc	p.R135H	IGSF8_ENST00000460351.1_5'UTR|IGSF8_ENST00000314485.7_Missense_Mutation_p.R135H			Q969P0	IGSF8_HUMAN	immunoglobulin superfamily, member 8	135	Ig-like C2-type 1.				cell proliferation (GO:0008283)|cellular component movement (GO:0006928)|nervous system development (GO:0007399)|single fertilization (GO:0007338)|skeletal muscle tissue development (GO:0007519)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(19)|pancreas(1)|prostate(1)|skin(1)	33	all_cancers(52;1.11e-16)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)|LUSC - Lung squamous cell carcinoma(543;0.246)			GCCCAGGTAGCGGGTATCAGT	0.627													C|||	1	0.000199681	0.0	0.0	5008	,	,		18151	0.0		0.001	False		,,,				2504	0.0				p.R135H		Atlas-SNP	.											.	IGSF8	59	.	0			c.G404A						PASS	.	C	HIS/ARG,HIS/ARG	0,4406		0,0,2203	34.0	37.0	36.0		404,404	-1.3	0.9	1		36	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense	IGSF8	NM_001206665.2,NM_052868.4	29,29	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging,possibly-damaging	135/614,135/614	160064697	1,13005	2203	4300	6503	SO:0001583	missense	93185	exon2			AGGTAGCGGGTAT	AF407274	CCDS1195.1	1q23.1	2013-01-11			ENSG00000162729	ENSG00000162729		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"""	17813	protein-coding gene	gene with protein product		606644				11504738, 11673522	Standard	NM_001206665		Approved	CD81P3, EWI2, PGRL, CD316	uc009wtf.3	Q969P0	OTTHUMG00000024075	ENST00000368086.1:c.404G>A	1.37:g.160064697C>T	ENSP00000357065:p.Arg135His	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	86	54	0.627907	NM_052868	Q8NG09|Q96DP4|Q9BTG9	Missense_Mutation	SNP	ENST00000368086.1	37	CCDS1195.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	18.12	3.552769	0.65425	0.0	1.16E-4	ENSG00000162729	ENST00000314485;ENST00000368086;ENST00000358475;ENST00000448417	T;T;T	0.10382	3.47;3.47;2.88	4.89	-1.29	0.09288	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.619503	0.14945	N	0.289261	T	0.03390	0.0098	L	0.42245	1.32	0.26281	N	0.978279	P	0.48694	0.914	B	0.43251	0.413	T	0.35101	-0.9802	10	0.56958	D	0.05	-5.5588	6.2467	0.20823	0.0:0.2743:0.1448:0.5809	.	135	Q969P0	IGSF8_HUMAN	H	135	ENSP00000316664:R135H;ENSP00000357065:R135H;ENSP00000397464:R135H	ENSP00000316664:R135H	R	-	2	0	IGSF8	158331321	0.085000	0.21516	0.917000	0.36280	0.965000	0.64279	-0.605000	0.05661	-0.104000	0.12154	0.563000	0.77884	CGC	C|1.000;T|0.000	0.000	strong		0.627	IGSF8-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060636.1	NM_052868	
APLF	200558	hgsc.bcm.edu	37	2	68765205	68765205	+	Missense_Mutation	SNP	C	C	T	rs13404469	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:68765205C>T	ENST00000303795.4	+	7	1177	c.1006C>T	c.(1006-1008)Ctt>Ttt	p.L336F	APLF_ENST00000471727.1_3'UTR	NM_173545.2	NP_775816.1	Q8IW19	APLF_HUMAN	aprataxin and PNKP like factor	336			L -> F (in dbSNP:rs13404469).		cellular response to DNA damage stimulus (GO:0006974)|DNA catabolic process, endonucleolytic (GO:0000737)|double-strand break repair (GO:0006302)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|positive regulation of DNA ligation (GO:0051106)|regulation of isotype switching (GO:0045191)|single strand break repair (GO:0000012)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|site of double-strand break (GO:0035861)	3'-5' exonuclease activity (GO:0008408)|DNA-(apurinic or apyrimidinic site) lyase activity (GO:0003906)|endodeoxyribonuclease activity (GO:0004520)|metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)			autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|liver(2)|lung(9)|ovary(3)|prostate(1)|skin(1)	25						GGGCGACTCACTTCAGGATGA	0.423													T|||	395	0.0788738	0.1483	0.0735	5008	,	,		18007	0.005		0.0726	False		,,,				2504	0.0716				p.L336F		Atlas-SNP	.											.	APLF	69	.	0			c.C1006T						PASS	.	T	PHE/LEU	637,3769		51,535,1617	92.0	86.0	88.0		1006	4.0	0.0	2	dbSNP_121	88	695,7905		33,629,3638	yes	missense	APLF	NM_173545.2	22	84,1164,5255	TT,TC,CC		8.0814,14.4576,10.2414	benign	336/512	68765205	1332,11674	2203	4300	6503	SO:0001583	missense	200558	exon7			GACTCACTTCAGG	BC030711	CCDS1888.1	2p14	2014-02-20	2008-10-01	2008-10-01	ENSG00000169621	ENSG00000169621			28724	protein-coding gene	gene with protein product	"""XRCC1-interacting protein 1"", ""zinc finger, CX5CX6HX5H motif containing 1"""	611035	"""chromosome 2 open reading frame 13"""	C2orf13		18474613, 18077224, 17353262	Standard	NM_173545		Approved	MGC47799, Xip1, ZCCHH1	uc002sep.3	Q8IW19	OTTHUMG00000129566	ENST00000303795.4:c.1006C>T	2.37:g.68765205C>T	ENSP00000307004:p.Leu336Phe	Somatic	203	1	0.00492611		WXS	Illumina HiSeq	Phase_I	187	94	0.502674	NM_173545	A8K476|Q53P47|Q53PB9|Q53QU0	Missense_Mutation	SNP	ENST00000303795.4	37	CCDS1888.1	151	0.06913919413919414	62	0.12601626016260162	28	0.07734806629834254	4	0.006993006993006993	57	0.07519788918205805	.	0.181	-1.061812	0.01950	0.144576	0.080814	ENSG00000169621	ENST00000303795	T	0.23950	1.88	5.19	4.0	0.46444	.	1.310930	0.04804	N	0.434102	T	0.00073	0.0002	N	0.00289	-1.7	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.30475	-0.9977	9	0.26408	T	0.33	.	8.0877	0.30782	0.0:0.1667:0.0:0.8333	rs13404469;rs52799369;rs13404469	336	Q8IW19	APLF_HUMAN	F	336	ENSP00000307004:L336F	ENSP00000307004:L336F	L	+	1	0	APLF	68618709	0.006000	0.16342	0.002000	0.10522	0.063000	0.16089	0.651000	0.24873	0.274000	0.22072	-0.381000	0.06696	CTT	C|0.910;T|0.090	0.090	strong		0.423	APLF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251759.1	NM_173545	
SIGLEC6	946	hgsc.bcm.edu	37	19	52034469	52034469	+	Silent	SNP	C	C	T	rs1993462	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:52034469C>T	ENST00000425629.3	-	2	526	c.372G>A	c.(370-372)aaG>aaA	p.K124K	SIGLEC6_ENST00000436458.1_Silent_p.K88K|SIGLEC6_ENST00000474054.1_5'Flank|SIGLEC6_ENST00000343300.4_Silent_p.K124K|SIGLEC6_ENST00000391797.3_Silent_p.K124K|SIGLEC6_ENST00000359982.4_Silent_p.K124K|SIGLEC6_ENST00000346477.3_Silent_p.K124K	NM_001245.5	NP_001236.4	O43699	SIGL6_HUMAN	sialic acid binding Ig-like lectin 6	124					cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)			endometrium(3)|kidney(1)|large_intestine(6)|liver(1)|lung(15)|ovary(1)|stomach(1)	28		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.00115)|OV - Ovarian serous cystadenocarcinoma(262;0.0165)		TCCATTTGGACTTCAACCGAA	0.532													C|||	616	0.123003	0.0908	0.1268	5008	,	,		19650	0.0952		0.162	False		,,,				2504	0.1524				p.K124K		Atlas-SNP	.											.	SIGLEC6	142	.	0			c.G372A						PASS	.	C	,,,,,	430,3902		18,394,1754	99.0	103.0	101.0		264,372,372,372,372,372	-1.8	0.0	19	dbSNP_92	101	1363,7189		103,1157,3016	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SIGLEC6	NM_001177547.1,NM_001177548.1,NM_001177549.1,NM_001245.5,NM_198845.4,NM_198846.4	,,,,,	121,1551,4770	TT,TC,CC		15.9378,9.9261,13.9165	,,,,,	88/402,124/390,124/343,124/454,124/438,124/354	52034469	1793,11091	2166	4276	6442	SO:0001819	synonymous_variant	946	exon2			TTTGGACTTCAAC	D86358	CCDS12834.3, CCDS12835.3, CCDS12836.3, CCDS54307.1, CCDS54308.1, CCDS59417.1	19q13.3	2013-01-29			ENSG00000105492	ENSG00000105492		"""Sialic acid binding Ig-like lectins"", ""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	10875	protein-coding gene	gene with protein product		604405		CD33L, CD33L1		9465907	Standard	NM_001245		Approved	OB-BP1, SIGLEC-6, CD327	uc002pwy.3	O43699	OTTHUMG00000133571	ENST00000425629.3:c.372G>A	19.37:g.52034469C>T		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	40	16	0.4	NM_001177549	A8MV71|B2RTS8|C9JBE5|F8WA78|O15388|O43700	Silent	SNP	ENST00000425629.3	37	CCDS12834.3																																																																																			C|0.860;N|0.000	.	strong		0.532	SIGLEC6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257670.3	NM_001245	
RELN	5649	hgsc.bcm.edu	37	7	103251161	103251161	+	Missense_Mutation	SNP	G	G	C	rs362691	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:103251161G>C	ENST00000428762.1	-	22	3148	c.2989C>G	c.(2989-2991)Ctt>Gtt	p.L997V	RELN_ENST00000424685.2_Missense_Mutation_p.L997V|RELN_ENST00000343529.5_Missense_Mutation_p.L997V	NM_005045.3	NP_005036.2	P78509	RELN_HUMAN	reelin	997			L -> V (in dbSNP:rs362691).		associative learning (GO:0008306)|axon guidance (GO:0007411)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cell morphogenesis involved in differentiation (GO:0000904)|central nervous system development (GO:0007417)|cerebral cortex tangential migration (GO:0021800)|dendrite development (GO:0016358)|glial cell differentiation (GO:0010001)|hippocampus development (GO:0021766)|lateral motor column neuron migration (GO:0097477)|layer formation in cerebral cortex (GO:0021819)|long-term memory (GO:0007616)|N-methyl-D-aspartate receptor clustering (GO:0097114)|neuron migration (GO:0001764)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000969)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of dendritic spine morphogenesis (GO:0061003)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of lateral motor column neuron migration (GO:1902078)|positive regulation of long-term synaptic potentiation (GO:1900273)|positive regulation of neuron projection development (GO:0010976)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of TOR signaling (GO:0032008)|postsynaptic density protein 95 clustering (GO:0097119)|receptor localization to synapse (GO:0097120)|reelin-mediated signaling pathway (GO:0038026)|regulation of behavior (GO:0050795)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of synaptic transmission (GO:0050804)|response to pain (GO:0048265)|spinal cord patterning (GO:0021511)|ventral spinal cord development (GO:0021517)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	lipoprotein particle receptor binding (GO:0070325)|metal ion binding (GO:0046872)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|serine-type peptidase activity (GO:0008236)|very-low-density lipoprotein particle receptor binding (GO:0070326)			NS(3)|breast(8)|central_nervous_system(3)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(43)|lung(101)|ovary(9)|pancreas(2)|prostate(4)|skin(14)|stomach(2)|upper_aerodigestive_tract(12)|urinary_tract(2)	227				COAD - Colon adenocarcinoma(1;8.98e-05)|Colorectal(1;0.00184)		TGGGGAAGAAGCACTATGACT	0.398													G|||	606	0.121006	0.0658	0.121	5008	,	,		18694	0.1458		0.1054	False		,,,				2504	0.1861				p.L997V	NSCLC(146;835 1944 15585 22231 52158)	Atlas-SNP	.											.	RELN	593	.	0			c.C2989G						PASS	.	G	VAL/LEU,VAL/LEU	367,4039	186.4+/-213.3	15,337,1851	175.0	140.0	152.0		2989,2989	4.4	0.1	7	dbSNP_79	152	893,7707	200.7+/-244.4	53,787,3460	yes	missense,missense	RELN	NM_005045.3,NM_173054.2	32,32	68,1124,5311	CC,CG,GG		10.3837,8.3296,9.6878	benign,benign	997/3461,997/3459	103251161	1260,11746	2203	4300	6503	SO:0001583	missense	5649	exon22			GAAGAAGCACTAT		CCDS34722.1, CCDS47680.1	7q22	2008-07-18			ENSG00000189056	ENSG00000189056			9957	protein-coding gene	gene with protein product		600514				9049633	Standard	NM_005045		Approved	RL, PRO1598	uc010liz.3	P78509	OTTHUMG00000157247	ENST00000428762.1:c.2989C>G	7.37:g.103251161G>C	ENSP00000392423:p.Leu997Val	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	54	28	0.518519	NM_173054	A4D0P9|A4D0Q0|Q86UJ0|Q86UJ8|Q8NDV0|Q9UDQ2	Missense_Mutation	SNP	ENST00000428762.1	37	CCDS47680.1	227	0.10393772893772894	33	0.06707317073170732	44	0.12154696132596685	67	0.11713286713286714	83	0.10949868073878628	G	8.848	0.943780	0.18281	0.083296	0.103837	ENSG00000189056	ENST00000428762;ENST00000343529;ENST00000424685;ENST00000448171	T;T;T	0.22539	1.99;1.98;1.95	6.17	4.36	0.52297	.	0.314360	0.36034	N	0.002827	T	0.00178	0.0005	N	0.14661	0.345	0.43787	P	0.00367099999999998	B;B	0.27791	0.185;0.189	B;B	0.31101	0.124;0.073	T	0.29488	-1.0010	9	0.15066	T	0.55	.	12.0604	0.53559	0.0:0.1302:0.734:0.1358	rs362691;rs17310959;rs52796689;rs362691	997;997	P78509-2;P78509	.;RELN_HUMAN	V	997	ENSP00000392423:L997V;ENSP00000345694:L997V;ENSP00000388446:L997V	ENSP00000345694:L997V	L	-	1	0	RELN	103038397	1.000000	0.71417	0.062000	0.19696	0.993000	0.82548	4.021000	0.57196	0.916000	0.36871	0.655000	0.94253	CTT	C|0.101;G|0.899;N|0.000	0.101	strong		0.398	RELN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348148.1	NM_005045	
HIST1H2BF	8343	hgsc.bcm.edu	37	6	26199822	26199822	+	Silent	SNP	A	A	G	rs41266807	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:26199822A>G	ENST00000359985.1	+	1	75	c.36A>G	c.(34-36)aaA>aaG	p.K12K	HIST1H3D_ENST00000356476.2_5'Flank|HIST1H2AD_ENST00000341023.1_5'Flank|HIST1H3D_ENST00000377831.5_5'Flank	NM_003522.3	NP_003513.1	P62807	H2B1C_HUMAN	histone cluster 1, H2bf	12					antibacterial humoral response (GO:0019731)|chromatin organization (GO:0006325)|defense response to Gram-positive bacterium (GO:0050830)|innate immune response in mucosa (GO:0002227)|nucleosome assembly (GO:0006334)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|liver(2)|lung(7)|upper_aerodigestive_tract(3)	17		all_hematologic(11;0.196)				CTGCTCCAAAAAAGGGCTCCA	0.502													G|||	869	0.173522	0.2315	0.1138	5008	,	,		19823	0.1161		0.161	False		,,,				2504	0.2096				p.K12K		Atlas-SNP	.											.	HIST1H2BF	25	.	0			c.A36G						PASS	.	G		870,3536		86,698,1419	101.0	99.0	99.0		36	-0.3	0.7	6	dbSNP_127	99	1196,7404		75,1046,3179	no	coding-synonymous	HIST1H2BF	NM_003522.3		161,1744,4598	GG,GA,AA		13.907,19.7458,15.885		12/127	26199822	2066,10940	2203	4300	6503	SO:0001819	synonymous_variant	8343	exon1			TCCAAAAAAGGGC	Z80779	CCDS4592.1	6p22.1	2011-01-27	2006-10-11	2003-02-14	ENSG00000197846	ENSG00000277224		"""Histones / Replication-dependent"""	4752	protein-coding gene	gene with protein product		602804	"""H2B histone family, member G"", ""histone 1, H2bf"""	H2BFG		9119399, 12408966	Standard	NM_003522		Approved	H2B/g	uc003ngx.3	P62807	OTTHUMG00000014445	ENST00000359985.1:c.36A>G	6.37:g.26199822A>G		Somatic	191	1	0.0052356		WXS	Illumina HiSeq	Phase_I	167	110	0.658683	NM_003522	P02278|Q3B872|Q4VB69|Q93078|Q93080	Silent	SNP	ENST00000359985.1	37	CCDS4592.1																																																																																			A|0.844;G|0.156	0.156	strong		0.502	HIST1H2BF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040108.1	NM_003522	
LYSMD3	116068	hgsc.bcm.edu	37	5	89820984	89820984	+	Silent	SNP	T	T	C	rs10069050	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:89820984T>C	ENST00000315948.6	-	2	267	c.123A>G	c.(121-123)gaA>gaG	p.E41E	LYSMD3_ENST00000509384.1_Silent_p.E41E|LYSMD3_ENST00000500869.2_Silent_p.E41E	NM_198273.1	NP_938014.1	Q7Z3D4	LYSM3_HUMAN	LysM, putative peptidoglycan-binding, domain containing 3	41						integral component of membrane (GO:0016021)				breast(2)|large_intestine(1)|lung(2)|prostate(1)|urinary_tract(1)	7		all_cancers(142;5.03e-09)|all_epithelial(76;1.23e-11)|Lung NSC(167;2.46e-05)|all_lung(232;3.25e-05)|Ovarian(174;0.00832)|Colorectal(57;0.122)|Breast(839;0.198)		OV - Ovarian serous cystadenocarcinoma(54;1.94e-31)|Epithelial(54;5.22e-26)|all cancers(79;2.42e-22)		TGGATCGAAGTTCATACACTT	0.378													C|||	3068	0.61262	0.7678	0.428	5008	,	,		17152	0.6081		0.5408	False		,,,				2504	0.6125				p.E41E		Atlas-SNP	.											.	LYSMD3	25	.	0			c.A123G						PASS	.	C		2727,1049		983,761,144	151.0	137.0	141.0		123	1.7	1.0	5	dbSNP_119	141	4636,3612		1309,2018,797	no	coding-synonymous	LYSMD3	NM_198273.1		2292,2779,941	CC,CT,TT		43.7924,27.7807,38.7641		41/307	89820984	7363,4661	1888	4124	6012	SO:0001819	synonymous_variant	116068	exon2			TCGAAGTTCATAC	BX537972	CCDS43338.1, CCDS68911.1	5q14.3	2010-12-09			ENSG00000176018	ENSG00000176018			26969	protein-coding gene	gene with protein product							Standard	NM_001286812		Approved	FLJ13542	uc003kjr.3	Q7Z3D4	OTTHUMG00000162667	ENST00000315948.6:c.123A>G	5.37:g.89820984T>C		Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	183	66	0.360656	NM_198273	Q5H9U0|Q6PEK0|Q9NTE9	Silent	SNP	ENST00000315948.6	37	CCDS43338.1																																																																																			T|0.410;C|0.590	0.590	strong		0.378	LYSMD3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369987.2	XM_371760	
CALU	813	hgsc.bcm.edu	37	7	128394606	128394606	+	Intron	SNP	C	C	T	rs2307040	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:128394606C>T	ENST00000249364.4	+	3	517				CALU_ENST00000535623.1_3'UTR|CALU_ENST00000538546.1_Intron|CALU_ENST00000542996.2_Missense_Mutation_p.A90V|CALU_ENST00000479257.1_Intron|CALU_ENST00000535011.2_Intron|CALU_ENST00000449187.2_Missense_Mutation_p.A82V	NM_001219.4	NP_001210.1	O43852	CALU_HUMAN	calumenin						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)	p.A90V(1)		kidney(2)|large_intestine(3)|lung(5)	10						AAAATAGACGCGGATAAAGAT	0.443													C|||	888	0.177316	0.1127	0.2233	5008	,	,		19129	0.0585		0.3728	False		,,,				2504	0.1534				p.A90V		Atlas-SNP	.											CALU_ENST00000542996,NS,carcinoma,0,1	CALU	42	1	1	Substitution - Missense(1)	stomach(1)	c.C269T						PASS	.	C	VAL/ALA,,VAL/ALA,,,	181,1203		11,159,522	83.0	74.0	76.0		245,,269,,,	0.2	1.0	7	dbSNP_100	76	1182,2000		224,734,633	yes	missense,intron,missense,intron,intron,intron	CALU	NM_001130674.2,NM_001199671.1,NM_001199672.1,NM_001199673.1,NM_001199674.1,NM_001219.4	64,,64,,,	235,893,1155	TT,TC,CC		37.1464,13.078,29.8511	,,,,,	82/316,,90/324,,,	128394606	1363,3203	692	1591	2283	SO:0001627	intron_variant	813	exon4			TAGACGCGGATAA	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.415+97C>T	7.37:g.128394606C>T		Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	117	57	0.487179	NM_001199672	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	459	0.21016483516483517	62	0.12601626016260162	95	0.26243093922651933	28	0.04895104895104895	274	0.36147757255936674	C	10.84	1.465452	0.26335	0.13078	0.371464	ENSG00000128595	ENST00000542996;ENST00000537667;ENST00000537014;ENST00000449187	T;T	0.70399	-0.48;-0.48	5.96	0.244	0.15507	.	.	.	.	.	T	0.00012	0.0000	N	0.11201	0.11	0.80722	P	0.0	B	0.13145	0.007	B	0.12837	0.008	T	0.32693	-0.9897	8	0.22109	T	0.4	.	5.664	0.17684	0.0:0.4412:0.1377:0.4211	rs2307040;rs11545530;rs52803804;rs2307040	90	D6QS48	.	V	90;82;82;82	ENSP00000438248:A90V;ENSP00000408838:A82V	ENSP00000408838:A82V	A	+	2	0	CALU	128181842	0.000000	0.05858	0.959000	0.39883	0.990000	0.78478	-0.365000	0.07573	0.092000	0.17331	-0.136000	0.14681	GCG	C|0.785;T|0.215	0.215	strong		0.443	CALU-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350533.1	NM_001219	
CNTN6	27255	hgsc.bcm.edu	37	3	1424850	1424850	+	Silent	SNP	T	T	G	rs2291100	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:1424850T>G	ENST00000446702.2	+	18	3018	c.2391T>G	c.(2389-2391)tcT>tcG	p.S797S	CNTN6_ENST00000539053.1_Silent_p.S725S|CNTN6_ENST00000350110.2_Silent_p.S797S			Q9UQ52	CNTN6_HUMAN	contactin 6	797	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|central nervous system development (GO:0007417)|Notch signaling pathway (GO:0007219)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)				breast(6)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(25)|lung(34)|ovary(1)|pancreas(1)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	90		all_cancers(2;0.000164)|all_epithelial(2;0.107)		Epithelial(13;0.000233)|all cancers(10;0.0013)|OV - Ovarian serous cystadenocarcinoma(96;0.0139)		TTGTCTACTCTGGGGAAGATG	0.418													T|||	1325	0.264577	0.0386	0.2781	5008	,	,		20256	0.3452		0.3877	False		,,,				2504	0.3507				p.S797S		Atlas-SNP	.											.	CNTN6	245	.	0			c.T2391G						PASS	.	T		404,4002	200.8+/-224.0	17,370,1816	123.0	109.0	114.0		2391	-12.2	0.2	3	dbSNP_100	114	3216,5384	485.5+/-371.6	597,2022,1681	no	coding-synonymous	CNTN6	NM_014461.2		614,2392,3497	GG,GT,TT		37.3953,9.1693,27.8333		797/1029	1424850	3620,9386	2203	4300	6503	SO:0001819	synonymous_variant	27255	exon18			CTACTCTGGGGAA	AB003592	CCDS2557.1	3p26-p25	2013-02-11			ENSG00000134115	ENSG00000134115		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	2176	protein-coding gene	gene with protein product	"""neural adhesion molecule"""	607220				9486763	Standard	NM_014461		Approved	NB-3	uc003bpa.3	Q9UQ52	OTTHUMG00000119030	ENST00000446702.2:c.2391T>G	3.37:g.1424850T>G		Somatic	214	0	0		WXS	Illumina HiSeq	Phase_I	177	87	0.491525	NM_014461	Q2KHM2	Silent	SNP	ENST00000446702.2	37	CCDS2557.1																																																																																			T|0.724;G|0.276	0.276	strong		0.418	CNTN6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239235.2	NM_014461	
TDG	6996	hgsc.bcm.edu	37	12	104376700	104376700	+	Missense_Mutation	SNP	A	A	C	rs61937630		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:104376700A>C	ENST00000392872.3	+	5	836	c.602A>C	c.(601-603)aAa>aCa	p.K201T	TDG_ENST00000544861.1_Missense_Mutation_p.K58T|AC078819.1_ENST00000401157.1_RNA|TDG_ENST00000542036.1_Missense_Mutation_p.K25Q|TDG_ENST00000266775.9_Missense_Mutation_p.K197T	NM_003211.4	NP_003202.3	Q13569	TDG_HUMAN	thymine-DNA glycosylase	201					base-excision repair (GO:0006284)|base-excision repair, AP site formation (GO:0006285)|chromatin modification (GO:0016568)|depyrimidination (GO:0045008)|DNA demethylation (GO:0080111)|DNA repair (GO:0006281)|embryo development (GO:0009790)|mismatch repair (GO:0006298)|negative regulation of chromatin binding (GO:0035562)|negative regulation of protein binding (GO:0032091)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of gene expression, epigenetic (GO:0040029)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|PML body (GO:0016605)	damaged DNA binding (GO:0003684)|DNA N-glycosylase activity (GO:0019104)|double-stranded DNA binding (GO:0003690)|mismatched DNA binding (GO:0030983)|protein homodimerization activity (GO:0042803)|pyrimidine-specific mismatch base pair DNA N-glycosylase activity (GO:0008263)|RNA polymerase II transcription cofactor activity (GO:0001104)|structure-specific DNA binding (GO:0043566)	p.K201T(1)		large_intestine(2)|lung(14)|ovary(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	24				BRCA - Breast invasive adenocarcinoma(302;0.00114)		CCCGGCAGCAAAGATCTCTCC	0.458								Base excision repair (BER), DNA glycosylases																													p.K201T		Atlas-SNP	.											TDG,extremity,malignant_melanoma,0,1	TDG	43	1	1	Substitution - Missense(1)	skin(1)	c.A602C						PASS	.						81.0	78.0	79.0					12																	104376700		2203	4300	6503	SO:0001583	missense	6996	exon5			GCAGCAAAGATCT	U51166	CCDS9095.1	12q24.1	2014-05-14			ENSG00000139372	ENSG00000139372	3.2.2.29		11700	protein-coding gene	gene with protein product	"""G/T mismatch-specific thymine DNA glycosylase"""	601423				8662714, 9299239	Standard	NM_003211		Approved		uc001tkg.3	Q13569	OTTHUMG00000168418	ENST00000392872.3:c.602A>C	12.37:g.104376700A>C	ENSP00000376611:p.Lys201Thr	Somatic	212	0	0		WXS	Illumina HiSeq	Phase_I	242	14	0.0578512	NM_003211	Q8IUZ6|Q8IZM3	Missense_Mutation	SNP	ENST00000392872.3	37	CCDS9095.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	17.68|17.68	3.450099|3.450099	0.63290|0.63290	.|.	.|.	ENSG00000139372|ENSG00000139372	ENST00000542036|ENST00000392872;ENST00000266775;ENST00000544861;ENST00000537100	T|T;T;T;T	0.22539|0.45276	1.95|0.9;0.9;0.9;0.9	5.4|5.4	5.4|5.4	0.78164|0.78164	.|Uracil-DNA glycosylase-like (3);	0.000000|0.000000	0.85682|0.85682	D|D	0.000000|0.000000	T|T	0.47116|0.47116	0.1428|0.1428	L|L	0.36672|0.36672	1.1|1.1	0.29181|0.29181	N|N	0.876493|0.876493	B|P;P	0.22346|0.42692	0.068|0.787;0.787	B|P;P	0.12837|0.52159	0.008|0.691;0.581	T|T	0.42699|0.42699	-0.9436|-0.9436	10|10	0.87932|0.31617	D|T	0|0.26	-25.7328|-25.7328	15.4266|15.4266	0.75055|0.75055	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	rs61937630|rs61937630	25|201;201	B4DI29|B2R848;Q13569	.|.;TDG_HUMAN	Q|T	25|201;197;58;194	ENSP00000439054:K25Q|ENSP00000376611:K201T;ENSP00000266775:K197T;ENSP00000445899:K58T;ENSP00000439825:K194T	ENSP00000439054:K25Q|ENSP00000266775:K197T	K|K	+|+	1|2	0|0	TDG|TDG	102900830|102900830	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.736000|0.736000	0.42039|0.42039	9.271000|9.271000	0.95698|0.95698	2.037000|2.037000	0.60232|0.60232	0.460000|0.460000	0.39030|0.39030	AAG|AAA	.	.	weak		0.458	TDG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399673.2		
CENPQ	55166	hgsc.bcm.edu	37	6	49439805	49439805	+	Missense_Mutation	SNP	G	G	A	rs4267943	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:49439805G>A	ENST00000335783.3	+	4	281	c.187G>A	c.(187-189)Gga>Aga	p.G63R		NM_018132.3	NP_060602.2	Q7L2Z9	CENPQ_HUMAN	centromere protein Q	63			G -> R (in dbSNP:rs4267943).		CENP-A containing nucleosome assembly (GO:0034080)|mitotic cell cycle (GO:0000278)|nucleosome assembly (GO:0006334)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intermediate filament cytoskeleton (GO:0045111)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(4)|ovary(2)|prostate(1)	11	Lung NSC(77;0.0128)					CCTAAAACACGGAAAGACAGC	0.378													G|||	1674	0.334265	0.4191	0.2305	5008	,	,		14881	0.2103		0.332	False		,,,				2504	0.4233				p.G63R		Atlas-SNP	.											.	CENPQ	23	.	0			c.G187A						PASS	.	G	ARG/GLY	1724,2682	516.8+/-369.3	331,1062,810	121.0	124.0	123.0		187	-6.5	0.0	6	dbSNP_111	123	3158,5442	479.9+/-370.2	584,1990,1726	yes	missense	CENPQ	NM_018132.3	125	915,3052,2536	AA,AG,GG		36.7209,39.1285,37.5365	benign	63/269	49439805	4882,8124	2203	4300	6503	SO:0001583	missense	55166	exon4			AAACACGGAAAGA	AK001407	CCDS4925.1	6p12.3	2013-11-05	2006-06-15	2006-06-15	ENSG00000031691	ENSG00000031691			21347	protein-coding gene	gene with protein product		611506	"""chromosome 6 open reading frame 139"""	C6orf139		16622420, 16622419	Standard	NM_018132		Approved	FLJ10545, CENP-Q	uc003ozh.1	Q7L2Z9	OTTHUMG00000014815	ENST00000335783.3:c.187G>A	6.37:g.49439805G>A	ENSP00000337289:p.Gly63Arg	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	46	26	0.565217	NM_018132	A8KAF1|Q6IN61|Q9NVS5	Missense_Mutation	SNP	ENST00000335783.3	37	CCDS4925.1	690	0.3159340659340659	205	0.4166666666666667	89	0.24585635359116023	112	0.1958041958041958	284	0.37467018469656993	G	4.427	0.079036	0.08533	0.391285	0.367209	ENSG00000031691	ENST00000335783;ENST00000371200	T	0.29142	1.58	4.44	-6.48	0.01896	.	0.695143	0.13866	N	0.357330	T	0.04363	0.0120	N	0.08118	0	0.80722	P	0.0	B	0.10296	0.003	B	0.01281	0.0	T	0.33954	-0.9848	9	0.87932	D	0	-0.2957	9.5128	0.39087	0.5713:0.0989:0.3297:0.0	rs4267943;rs17186767;rs56644708;rs58394552;rs4267943	63	Q7L2Z9	CENPQ_HUMAN	R	63	ENSP00000337289:G63R	ENSP00000337289:G63R	G	+	1	0	CENPQ	49547764	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.832000	0.04400	-1.779000	0.01280	-1.345000	0.01243	GGA	G|0.653;A|0.347	0.347	strong		0.378	CENPQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040855.2	NM_018132	
CENPU	79682	hgsc.bcm.edu	37	4	185634144	185634144	+	Missense_Mutation	SNP	T	T	C	rs4616798	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:185634144T>C	ENST00000281453.5	-	7	712	c.642A>G	c.(640-642)atA>atG	p.I214M	MLF1IP_ENST00000541971.1_Missense_Mutation_p.I214M|MLF1IP_ENST00000506535.1_5'UTR	NM_024629.3	NP_078905.2														endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|stomach(1)	13		all_lung(41;7.57e-14)|Lung NSC(41;1.81e-13)|Hepatocellular(41;0.000519)|Colorectal(36;0.00172)|Renal(120;0.00988)|Prostate(90;0.0235)|all_neural(102;0.0299)|all_hematologic(60;0.0592)|Medulloblastoma(177;0.146)		all cancers(43;7.83e-28)|Epithelial(43;2.56e-24)|OV - Ovarian serous cystadenocarcinoma(60;4.5e-11)|Colorectal(24;3.27e-06)|STAD - Stomach adenocarcinoma(60;2.66e-05)|GBM - Glioblastoma multiforme(59;3.16e-05)|BRCA - Breast invasive adenocarcinoma(30;0.000252)|COAD - Colon adenocarcinoma(29;0.000512)|LUSC - Lung squamous cell carcinoma(40;0.01)|READ - Rectum adenocarcinoma(43;0.0419)		TGTCATGAGATATCTTCCCTT	0.299													C|||	724	0.144569	0.295	0.1354	5008	,	,		16274	0.001		0.1481	False		,,,				2504	0.092				p.I214M		Atlas-SNP	.											.	MLF1IP	33	.	0			c.A642G						PASS	.	C	MET/ILE	1189,3215	708.9+/-407.7	161,867,1174	113.0	109.0	111.0		642	0.4	0.0	4	dbSNP_111	111	1406,7190	750.3+/-407.4	119,1168,3011	yes	missense	MLF1IP	NM_024629.3	10	280,2035,4185	CC,CT,TT		16.3564,26.9982,19.9615	benign	214/419	185634144	2595,10405	2202	4298	6500	SO:0001583	missense	79682	exon7			ATGAGATATCTTC																												ENST00000281453.5:c.642A>G	4.37:g.185634144T>C	ENSP00000281453:p.Ile214Met	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	39	22	0.564103	NM_024629		Missense_Mutation	SNP	ENST00000281453.5	37	CCDS3838.1	306	0.1401098901098901	145	0.29471544715447157	56	0.15469613259668508	0	0.0	105	0.13852242744063326	C	0.001	-2.945452	0.00052	0.269982	0.163564	ENSG00000151725	ENST00000281453;ENST00000541665;ENST00000541971	T;T	0.22134	1.97;1.97	4.03	0.371	0.16168	.	1.079220	0.07109	N	0.841860	T	0.00012	0.0000	N	0.01267	-0.92	0.80722	P	0.0	B;B	0.09022	0.0;0.002	B;B	0.09377	0.002;0.004	T	0.43621	-0.9380	9	0.44086	T	0.13	-20.3821	8.2661	0.31815	0.0:0.6043:0.0:0.3957	rs4616798;rs58095997;rs4616798	214;214	Q09GN1;Q71F23	.;CENPU_HUMAN	M	214	ENSP00000281453:I214M;ENSP00000445862:I214M	ENSP00000281453:I214M	I	-	3	3	MLF1IP	185871138	0.000000	0.05858	0.000000	0.03702	0.049000	0.14656	-3.075000	0.00616	-0.189000	0.10482	-0.722000	0.03604	ATA	T|0.826;C|0.174	0.174	strong		0.299	MLF1IP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000360841.2		
E2F1	1869	hgsc.bcm.edu	37	20	32266134	32266134	+	Missense_Mutation	SNP	C	C	T	rs35385772	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:32266134C>T	ENST00000343380.5	-	4	737	c.598G>A	c.(598-600)Ggc>Agc	p.G200S	RP1-63M2.5_ENST00000606866.1_RNA	NM_005225.2	NP_005216.1	Q01094	E2F1_HUMAN	E2F transcription factor 1	200	Dimerization. {ECO:0000255}.|Required for interaction with TRIM28.		G -> S (in dbSNP:rs35385772).		anoikis (GO:0043276)|apoptotic process (GO:0006915)|cellular response to fatty acid (GO:0071398)|cellular response to hypoxia (GO:0071456)|DNA damage checkpoint (GO:0000077)|forebrain development (GO:0030900)|G1/S transition of mitotic cell cycle (GO:0000082)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|lens fiber cell apoptotic process (GO:1990086)|mitotic cell cycle (GO:0000278)|mRNA stabilization (GO:0048255)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0071930)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of gene expression (GO:0010628)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of G1/S transition of mitotic cell cycle (GO:2000045)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Rb-E2F complex (GO:0035189)	core promoter binding (GO:0001047)|DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			NS(2)|breast(1)|endometrium(3)|lung(8)|prostate(1)|upper_aerodigestive_tract(1)	16						AGCCGTCCGCCGACGCCCACT	0.652													C|||	64	0.0127796	0.0015	0.0274	5008	,	,		18426	0.0		0.0408	False		,,,				2504	0.002				p.G200S		Atlas-SNP	.											.	E2F1	41	.	0			c.G598A						PASS	.	C	SER/GLY	30,4376	36.0+/-67.5	0,30,2173	36.0	34.0	34.0		598	-3.4	0.0	20	dbSNP_126	34	224,8374	91.4+/-153.5	0,224,4075	yes	missense	E2F1	NM_005225.2	56	0,254,6248	TT,TC,CC		2.6053,0.6809,1.9532	benign	200/438	32266134	254,12750	2203	4299	6502	SO:0001583	missense	1869	exon4			GTCCGCCGACGCC		CCDS13224.1	20q11	2008-05-14			ENSG00000101412	ENSG00000101412			3113	protein-coding gene	gene with protein product		189971		RBBP3		8964493	Standard	NM_005225		Approved	RBP3	uc002wzu.4	Q01094	OTTHUMG00000032265	ENST00000343380.5:c.598G>A	20.37:g.32266134C>T	ENSP00000345571:p.Gly200Ser	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	98	45	0.459184	NM_005225	Q13143|Q92768	Missense_Mutation	SNP	ENST00000343380.5	37	CCDS13224.1	41	0.018772893772893772	1	0.0020325203252032522	8	0.022099447513812154	0	0.0	32	0.04221635883905013	C	0.011	-1.707208	0.00719	0.006809	0.026053	ENSG00000101412	ENST00000343380	T	0.07908	3.15	5.16	-3.42	0.04825	.	1.060050	0.07264	N	0.867922	T	0.00998	0.0033	N	0.24115	0.695	0.09310	N	1	B	0.17465	0.022	B	0.04013	0.001	T	0.46133	-0.9213	10	0.07644	T	0.81	-2.1827	9.5138	0.39093	0.0:0.2833:0.1035:0.6132	rs35385772;rs61752051	200	Q01094	E2F1_HUMAN	S	200	ENSP00000345571:G200S	ENSP00000345571:G200S	G	-	1	0	E2F1	31729795	0.000000	0.05858	0.001000	0.08648	0.002000	0.02628	-0.376000	0.07465	-0.774000	0.04590	-1.945000	0.00491	GGC	C|0.980;T|0.020	0.020	strong		0.652	E2F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078731.2		
IRX1	79192	hgsc.bcm.edu	37	5	3600136	3600136	+	Silent	SNP	G	G	A	rs61746094	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:3600136G>A	ENST00000302006.3	+	2	1126	c.1074G>A	c.(1072-1074)ctG>ctA	p.L358L	CTD-2012M11.3_ENST00000559410.1_RNA	NM_024337.3	NP_077313.3	P78414	IRX1_HUMAN	iroquois homeobox 1	358					proximal/distal pattern formation involved in metanephric nephron development (GO:0072272)|regulation of transcription, DNA-templated (GO:0006355)|specification of loop of Henle identity (GO:0072086)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			biliary_tract(1)|endometrium(5)|kidney(2)|large_intestine(5)|lung(18)|ovary(2)|pancreas(1)|prostate(5)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	43						CCGCCTTCCTGCCTAGCCACG	0.706													G|||	430	0.0858626	0.003	0.2464	5008	,	,		11212	0.005		0.1014	False		,,,				2504	0.1513				p.L358L		Atlas-SNP	.											.	IRX1	106	.	0			c.G1074A						PASS	.	G		114,4260		1,112,2074	29.0	21.0	24.0		1074	2.7	1.0	5	dbSNP_129	24	961,7629		54,853,3388	no	coding-synonymous	IRX1	NM_024337.3		55,965,5462	AA,AG,GG		11.1874,2.6063,8.2922		358/481	3600136	1075,11889	2187	4295	6482	SO:0001819	synonymous_variant	79192	exon2			CTTCCTGCCTAGC	U90307	CCDS34132.1	5p15.33	2011-12-16	2007-07-13		ENSG00000170549	ENSG00000170549		"""Homeoboxes / TALE class"""	14358	protein-coding gene	gene with protein product		606197					Standard	NM_024337		Approved	IRX-5	uc003jde.3	P78414	OTTHUMG00000161632	ENST00000302006.3:c.1074G>A	5.37:g.3600136G>A		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	125	116	0.928	NM_024337	Q7Z2F8|Q8N312	Silent	SNP	ENST00000302006.3	37	CCDS34132.1																																																																																			G|0.920;A|0.080	0.080	strong		0.706	IRX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365546.1	NM_024337	
TRAPPC10	7109	hgsc.bcm.edu	37	21	45502844	45502844	+	Missense_Mutation	SNP	T	T	G	rs915877	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:45502844T>G	ENST00000291574.4	+	14	2074	c.1899T>G	c.(1897-1899)atT>atG	p.I633M		NM_003274.4	NP_003265.3	P48553	TPC10_HUMAN	trafficking protein particle complex 10	633			I -> M (in dbSNP:rs915877). {ECO:0000269|PubMed:9370297}.		sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|vesicle-mediated transport (GO:0016192)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	sodium ion transmembrane transporter activity (GO:0015081)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(8)|ovary(1)|prostate(2)|skin(2)|urinary_tract(4)	41						ACTTCAGCATTGAGAAAAACA	0.517													T|||	245	0.0489217	0.0825	0.0389	5008	,	,		21901	0.0		0.0626	False		,,,				2504	0.047				p.I633M		Atlas-SNP	.											.	TRAPPC10	109	.	0			c.T1899G						PASS	.	T	MET/ILE	377,4029	193.3+/-218.5	15,347,1841	168.0	149.0	156.0		1899	-10.8	0.2	21	dbSNP_86	156	531,8069	148.6+/-203.8	20,491,3789	yes	missense	TRAPPC10	NM_003274.4	10	35,838,5630	GG,GT,TT		6.1744,8.5565,6.9814	possibly-damaging	633/1260	45502844	908,12098	2203	4300	6503	SO:0001583	missense	7109	exon14			CAGCATTGAGAAA	U19252	CCDS13704.1	21q22.3	2008-05-07	2008-05-07	2008-05-07	ENSG00000160218	ENSG00000160218		"""Trafficking protein particle complex"""	11868	protein-coding gene	gene with protein product	"""trafficking protein particle complex subunit 130"", ""TRAPP 130 kDa subunit"""	602103	"""transmembrane protein 1"""	TMEM1		7633421	Standard	NM_003274		Approved	EHOC-1, TRS130	uc002zea.3	P48553	OTTHUMG00000086894	ENST00000291574.4:c.1899T>G	21.37:g.45502844T>G	ENSP00000291574:p.Ile633Met	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	136	41	0.301471	NM_003274	Q3MIR2|Q86SI7|Q9UMD4|Q9Y4L3	Missense_Mutation	SNP	ENST00000291574.4	37	CCDS13704.1	98	0.04487179487179487	35	0.07113821138211382	13	0.03591160220994475	0	0.0	50	0.06596306068601583	T	15.27	2.783165	0.49891	0.085565	0.061744	ENSG00000160218	ENST00000291574	T	0.46451	0.87	5.58	-10.8	0.00216	.	0.351400	0.30667	N	0.009139	T	0.00496	0.0016	N	0.14661	0.345	0.31699	N	0.640884	P	0.42735	0.788	B	0.35971	0.215	T	0.38023	-0.9680	10	0.46703	T	0.11	.	7.8181	0.29271	0.084:0.0992:0.1674:0.6494	rs915877;rs17178647;rs52822086;rs915877	633	P48553	TPC10_HUMAN	M	633	ENSP00000291574:I633M	ENSP00000291574:I633M	I	+	3	3	TRAPPC10	44327272	0.046000	0.20272	0.230000	0.23976	0.954000	0.61252	-0.971000	0.03806	-2.204000	0.00743	-1.151000	0.01829	ATT	T|0.954;G|0.046	0.046	strong		0.517	TRAPPC10-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000195737.1	NM_003274	
ADRA1A	148	hgsc.bcm.edu	37	8	26628028	26628028	+	Missense_Mutation	SNP	A	A	G	rs1048101	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:26628028A>G	ENST00000519229.1	-	2	1045	c.1039T>C	c.(1039-1041)Tgc>Cgc	p.C347R	ADRA1A_ENST00000354550.4_Missense_Mutation_p.C347R|ADRA1A_ENST00000380586.1_Missense_Mutation_p.C347R|ADRA1A_ENST00000380582.3_Missense_Mutation_p.C347R|ADRA1A_ENST00000380573.3_Missense_Mutation_p.C347R|ADRA1A_ENST00000276393.4_Missense_Mutation_p.C347R|ADRA1A_ENST00000380587.1_Intron|ADRA1A_ENST00000380581.2_Intron			P25100	ADA1D_HUMAN	adrenoceptor alpha 1A	310					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|adrenergic receptor signaling pathway (GO:0071875)|cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|DNA metabolic process (GO:0006259)|G-protein coupled receptor signaling pathway (GO:0007186)|multicellular organismal development (GO:0007275)|negative regulation of the force of heart contraction involved in baroreceptor response to increased systemic arterial blood pressure (GO:0001986)|norepinephrine-epinephrine vasoconstriction involved in regulation of systemic arterial blood pressure (GO:0001994)|positive regulation of cell proliferation (GO:0008284)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	alpha1-adrenergic receptor activity (GO:0004937)			breast(2)|endometrium(3)|kidney(1)|large_intestine(10)|lung(17)|ovary(1)|prostate(1)|skin(1)	36		all_cancers(63;0.122)|Ovarian(32;2.61e-05)|all_epithelial(46;0.118)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0228)|Epithelial(17;4.92e-10)|Colorectal(74;0.0132)|READ - Rectum adenocarcinoma(644;0.115)	Alfuzosin(DB00346)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Amphetamine(DB00182)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Carvedilol(DB01136)|Chlorpromazine(DB00477)|Clonidine(DB00575)|Dapiprazole(DB00298)|Desipramine(DB01151)|Doxazosin(DB00590)|Doxepin(DB01142)|Dronedarone(DB04855)|Droxidopa(DB06262)|Epinephrine(DB00668)|Ergoloid mesylate(DB01049)|Ergotamine(DB00696)|Fenoldopam(DB00800)|Imipramine(DB00458)|Labetalol(DB00598)|Maprotiline(DB00934)|Mephentermine(DB01365)|Methotrimeprazine(DB01403)|Methoxamine(DB00723)|Mianserin(DB06148)|Midodrine(DB00211)|Mirtazapine(DB00370)|Nicardipine(DB00622)|Norepinephrine(DB00368)|Nortriptyline(DB00540)|Oxymetazoline(DB00935)|Pergolide(DB01186)|Phenoxybenzamine(DB00925)|Phenylephrine(DB00388)|Prazosin(DB00457)|Promazine(DB00420)|Propiomazine(DB00777)|Quetiapine(DB01224)|Sertindole(DB06144)|Silodosin(DB06207)|Tamsulosin(DB00706)|Terazosin(DB01162)|Xylometazoline(DB06694)	TGCTTTCTGCAGAGACACTGG	0.547													G|||	3246	0.648163	0.7844	0.4928	5008	,	,		17261	0.8929		0.4334	False		,,,				2504	0.5429				p.C347R		Atlas-SNP	.											.	ADRA1A	337	.	0			c.T1039C	GRCh37	CM064954	ADRA1A	M	rs1048101	PASS	.	G	ARG/CYS,ARG/CYS,ARG/CYS,ARG/CYS	3258,1148	406.6+/-333.9	1199,860,144	152.0	155.0	154.0		1039,1039,1039,1039	5.8	1.0	8	dbSNP_86	154	3831,4769	611.7+/-395.9	833,2165,1302	yes	missense,missense,missense,missense	ADRA1A	NM_000680.2,NM_033302.2,NM_033303.3,NM_033304.2	180,180,180,180	2032,3025,1446	GG,GA,AA		44.5465,26.0554,45.4944	benign,benign,benign,benign	347/467,347/430,347/476,347/456	26628028	7089,5917	2203	4300	6503	SO:0001583	missense	148	exon2			TTCTGCAGAGACA	L31774	CCDS6052.1, CCDS6053.1, CCDS6054.1, CCDS34869.1	8p21.2	2012-08-08	2012-05-09		ENSG00000120907	ENSG00000120907		"""GPCR / Class A : Adrenoceptors : alpha"""	277	protein-coding gene	gene with protein product		104221	"""adrenergic, alpha-1A-, receptor"""	ADRA1C			Standard	NM_033303		Approved	ADRA1L1	uc003xfh.1	P35348	OTTHUMG00000099459	ENST00000519229.1:c.1039T>C	8.37:g.26628028A>G	ENSP00000430793:p.Cys347Arg	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	85	24	0.282353	NM_033303	Q9NPY0	Missense_Mutation	SNP	ENST00000519229.1	37		1397	0.6396520146520146	381	0.774390243902439	178	0.49171270718232046	506	0.8846153846153846	332	0.43799472295514513	G	6.452	0.451582	0.12223	0.739446	0.445465	ENSG00000120907	ENST00000380586;ENST00000380582;ENST00000519229;ENST00000354550;ENST00000276393;ENST00000380573	T;T;T;T;T;T	0.33654	1.4;1.4;1.4;1.4;1.4;1.4	5.83	5.83	0.93111	.	0.069666	0.53938	N	0.000059	T	0.00012	0.0000	N	0.00823	-1.155	0.19945	P	0.9999494131	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	0.35674	-0.9779	9	0.05959	T	0.93	.	14.8702	0.70450	0.0692:0.0:0.9308:0.0	rs1048101;rs3188081;rs3729633;rs17425094;rs52806290;rs57898697;rs1048101	347;347;347;347	P35348;P35348-4;P35348-3;B0ZBD3	ADA1A_HUMAN;.;.;.	R	347	ENSP00000369960:C347R;ENSP00000369956:C347R;ENSP00000430793:C347R;ENSP00000346557:C347R;ENSP00000276393:C347R;ENSP00000369947:C347R	ENSP00000276393:C347R	C	-	1	0	ADRA1A	26683945	0.631000	0.27164	0.995000	0.50966	0.875000	0.50365	2.915000	0.48805	1.498000	0.48600	-0.119000	0.15052	TGC	T|0.003;G|0.595	0.595	strong		0.547	ADRA1A-009	PUTATIVE	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000376207.1	NM_033303	
PCNT	5116	hgsc.bcm.edu	37	21	47808679	47808679	+	Missense_Mutation	SNP	C	C	T	rs7279204	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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						PASS	.	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	78	0	0		WXS	Illumina HiSeq	Phase_I	89	27	0.303371	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	
CEP72	55722	hgsc.bcm.edu	37	5	640705	640705	+	Missense_Mutation	SNP	A	A	G	rs868649|rs386684282	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:640705A>G	ENST00000264935.5	+	9	1615	c.1525A>G	c.(1525-1527)Aca>Gca	p.T509A	CEP72_ENST00000444221.1_3'UTR	NM_018140.3	NP_060610.2	Q9P209	CEP72_HUMAN	centrosomal protein 72kDa	509			T -> A (in dbSNP:rs868649). {ECO:0000269|PubMed:10819331}.		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)			GCTGCACCACACACACAAGGA	0.627													A|||	1346	0.26877	0.2579	0.2507	5008	,	,		17932	0.4683		0.2286	False		,,,				2504	0.1319				p.T509A		Atlas-SNP	.											.	CEP72	53	.	0			c.A1525G						PASS	.	A	ALA/THR	878,3528		149,580,1474	43.0	46.0	45.0		1525	-2.3	0.0	5	dbSNP_89	45	1946,6654		238,1470,2592	yes	missense	CEP72	NM_018140.3	58	387,2050,4066	GG,GA,AA		22.6279,19.9274,21.7131	benign	509/648	640705	2824,10182	2203	4300	6503	SO:0001583	missense	55722	exon9			CACCACACACACA	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.1525A>G	5.37:g.640705A>G	ENSP00000264935:p.Thr509Ala	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	71	42	0.591549	NM_018140	B4DR26|Q9BV03|Q9BWM3|Q9NVR4	Missense_Mutation	SNP	ENST00000264935.5	37	CCDS34126.1	622	0.2847985347985348	117	0.23780487804878048	90	0.24861878453038674	243	0.42482517482517484	172	0.22691292875989447	A	3.791	-0.043731	0.07452	0.199274	0.226279	ENSG00000112877	ENST00000264935	T	0.33865	1.39	5.02	-2.31	0.06765	.	0.317210	0.32444	N	0.006085	T	0.00012	0.0000	N	0.25201	0.72	0.58432	P	1.0000000000287557E-6	B	0.09022	0.002	B	0.08055	0.003	T	0.48234	-0.9053	9	0.15066	T	0.55	-1.275	10.9594	0.47376	0.3702:0.0:0.6298:0.0	rs868649;rs58588705;rs868649	509	Q9P209	CEP72_HUMAN	A	509	ENSP00000264935:T509A	ENSP00000264935:T509A	T	+	1	0	CEP72	693705	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-2.852000	0.00731	-0.271000	0.09272	0.459000	0.35465	ACA	T|0.001;G|0.251	0.251	strong		0.627	CEP72-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000365967.3	NM_018140	
SLC9C1	285335	hgsc.bcm.edu	37	3	111985107	111985107	+	Missense_Mutation	SNP	T	T	C	rs9872691	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:111985107T>C	ENST00000305815.5	-	8	1108	c.856A>G	c.(856-858)Att>Gtt	p.I286V	SLC9C1_ENST00000487372.1_Missense_Mutation_p.I286V	NM_183061.1	NP_898884.1	Q4G0N8	SL9C1_HUMAN	solute carrier family 9, subfamily C (Na+-transporting carboxylic acid decarboxylase), member 1	286			I -> V (in dbSNP:rs9872691). {ECO:0000269|PubMed:14702039}.		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)										GTTTCTTCAATTGCTGCTTTA	0.289													T|||	1648	0.329073	0.3449	0.4035	5008	,	,		15497	0.3393		0.2376	False		,,,				2504	0.3384				p.I286V		Atlas-SNP	.											.	.	.	.	0			c.A856G						PASS	.	T	VAL/ILE	1483,2923	464.7+/-354.0	256,971,976	67.0	75.0	72.0		856	3.2	1.0	3	dbSNP_119	72	2324,6268	385.5+/-341.5	322,1680,2294	yes	missense	SLC9A10	NM_183061.1	29	578,2651,3270	CC,CT,TT		27.0484,33.6586,29.2891	benign	286/1178	111985107	3807,9191	2203	4296	6499	SO:0001583	missense	285335	exon8			CTTCAATTGCTGC	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.856A>G	3.37:g.111985107T>C	ENSP00000306627:p.Ile286Val	Somatic	246	0	0		WXS	Illumina HiSeq	Phase_I	208	207	0.995192	NM_183061	Q6ZRP4|Q7RTP2	Missense_Mutation	SNP	ENST00000305815.5	37	CCDS33817.1	679	0.3108974358974359	171	0.3475609756097561	138	0.3812154696132597	185	0.32342657342657344	185	0.24406332453825857	T	0.009	-1.855283	0.00558	0.336586	0.270484	ENSG00000172139	ENST00000305815;ENST00000487372	T;T	0.03386	3.95;3.95	5.04	3.23	0.37069	Cation/H+ exchanger (1);	0.574613	0.15538	N	0.257133	T	0.00012	0.0000	N	0.01297	-0.9	0.53005	P	3.500000000000725E-5	B;B	0.06786	0.001;0.0	B;B	0.06405	0.002;0.002	T	0.37526	-0.9702	9	0.09843	T	0.71	-2.2326	7.8574	0.29491	0.0:0.8079:0.0:0.1921	rs9872691;rs52814342;rs56679245;rs9872691	286;286	Q4G0N8-2;Q4G0N8	.;S9A10_HUMAN	V	286	ENSP00000306627:I286V;ENSP00000420688:I286V	ENSP00000306627:I286V	I	-	1	0	SLC9A10	113467797	0.992000	0.36948	0.997000	0.53966	0.235000	0.25334	0.291000	0.18994	0.647000	0.30713	-0.186000	0.12905	ATT	T|0.705;C|0.295	0.295	strong		0.289	SLC9C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354066.1	NM_183061	
ZNF750	79755	hgsc.bcm.edu	37	17	80789468	80789468	+	Missense_Mutation	SNP	G	G	A	rs35653278	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:80789468G>A	ENST00000269394.3	-	2	1696	c.863C>T	c.(862-864)cCg>cTg	p.P288L	TBCD_ENST00000355528.4_Intron|ZNF750_ENST00000572562.1_Intron|TBCD_ENST00000539345.2_Intron|TBCD_ENST00000397466.2_Intron	NM_024702.2	NP_078978.2	Q32MQ0	ZN750_HUMAN	zinc finger protein 750	288			P -> L (in dbSNP:rs35653278).		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)			GATCGGCCCCGGGTGAGGCAG	0.567													G|||	103	0.0205671	0.0038	0.036	5008	,	,		16043	0.001		0.0656	False		,,,				2504	0.0061				p.P288L		Atlas-SNP	.											.	ZNF750	60	.	0			c.C863T						PASS	.	G	,LEU/PRO	82,4324	70.3+/-108.2	1,80,2122	132.0	145.0	141.0		,863	5.3	0.0	17	dbSNP_126	141	904,7696	202.1+/-245.5	46,812,3442	yes	intron,missense	TBCD,ZNF750	NM_005993.4,NM_024702.2	,98	47,892,5564	AA,AG,GG		10.5116,1.8611,7.5811	,probably-damaging	,288/724	80789468	986,12020	2203	4300	6503	SO:0001583	missense	79755	exon2			GGCCCCGGGTGAG	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.863C>T	17.37:g.80789468G>A	ENSP00000269394:p.Pro288Leu	Somatic	207	1	0.00483092		WXS	Illumina HiSeq	Phase_I	171	85	0.497076	NM_024702	Q9H899	Missense_Mutation	SNP	ENST00000269394.3	37	CCDS11819.1	69	0.03159340659340659	0	0.0	14	0.03867403314917127	0	0.0	55	0.07255936675461741	G	15.38	2.817490	0.50633	0.018611	0.105116	ENSG00000141579	ENST00000269394	T	0.14766	2.48	5.34	5.34	0.76211	.	0.085246	0.49916	D	0.000122	T	0.00666	0.0022	M	0.71581	2.175	0.80722	D	1	D	0.76494	0.999	P	0.60236	0.871	T	0.00006	-1.2510	9	.	.	.	-19.1297	18.0265	0.89270	0.0:0.0:1.0:0.0	rs35653278	288	Q32MQ0	ZN750_HUMAN	L	288	ENSP00000269394:P288L	.	P	-	2	0	ZNF750	78382757	1.000000	0.71417	0.029000	0.17559	0.460000	0.32559	5.112000	0.64634	2.507000	0.84556	0.655000	0.94253	CCG	G|0.934;A|0.066	0.066	strong		0.567	ZNF750-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439074.2	NM_024702	
MANSC1	54682	hgsc.bcm.edu	37	12	12483030	12483030	+	Silent	SNP	C	C	T	rs75750739	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:12483030C>T	ENST00000535902.1	-	4	1790	c.1227G>A	c.(1225-1227)tcG>tcA	p.S409S	MANSC1_ENST00000545735.1_Silent_p.S328S|MANSC1_ENST00000396349.3_Silent_p.S375S			Q9H8J5	MANS1_HUMAN	MANSC domain containing 1	409						integral component of membrane (GO:0016021)				breast(2)|endometrium(1)|kidney(2)|large_intestine(4)|lung(9)|skin(1)|stomach(4)	23		Prostate(47;0.0865)		BRCA - Breast invasive adenocarcinoma(232;0.185)		GGAGTGATTCCGAGAGGATTC	0.463													C|||	13	0.00259585	0.0	0.0043	5008	,	,		18645	0.0		0.005	False		,,,				2504	0.0051				p.S409S		Atlas-SNP	.											.	MANSC1	38	.	0			c.G1227A						PASS	.	C		8,4398	14.3+/-33.2	0,8,2195	86.0	86.0	86.0		1227	-10.1	0.0	12	dbSNP_133	86	86,8514	49.8+/-109.6	0,86,4214	no	coding-synonymous	MANSC1	NM_018050.2		0,94,6409	TT,TC,CC		1.0,0.1816,0.7227		409/432	12483030	94,12912	2203	4300	6503	SO:0001819	synonymous_variant	54682	exon4			TGATTCCGAGAGG	AK001160	CCDS8648.1	12p13.2	2006-04-12				ENSG00000111261			25505	protein-coding gene	gene with protein product						12975309	Standard	NM_018050		Approved	FLJ10298, LOH12CR3	uc001rai.1	Q9H8J5		ENST00000535902.1:c.1227G>A	12.37:g.12483030C>T		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	80	38	0.475	NM_018050	Q8NEC1|Q9NW60	Silent	SNP	ENST00000535902.1	37	CCDS8648.1																																																																																			C|0.995;T|0.005	0.005	strong		0.463	MANSC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400144.1	NM_018050	
WWP2	11060	hgsc.bcm.edu	37	16	69963355	69963355	+	Silent	SNP	G	G	A	rs1566452	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:69963355G>A	ENST00000359154.2	+	12	1340	c.1239G>A	c.(1237-1239)aaG>aaA	p.K413K	WWP2_ENST00000568684.1_5'UTR|WWP2_ENST00000544162.1_3'UTR|WWP2_ENST00000448661.1_Silent_p.K413K|WWP2_ENST00000356003.2_Silent_p.K413K|WWP2_ENST00000542271.1_Silent_p.K297K	NM_001270454.1|NM_007014.4	NP_001257383.1|NP_008945.2	O00308	WWP2_HUMAN	WW domain containing E3 ubiquitin protein ligase 2	413	WW 3. {ECO:0000255|PROSITE- ProRule:PRU00224}.				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						TGGCAGAGAAGAGACAGGACA	0.557													G|||	4282	0.855032	0.9455	0.7493	5008	,	,		17978	0.9683		0.7535	False		,,,				2504	0.7955				p.K413K		Atlas-SNP	.											.	WWP2	88	.	0			c.G1239A						PASS	.	G	,	3933,463	777.5+/-414.2	1759,415,24	51.0	47.0	49.0		1239,	4.3	1.0	16	dbSNP_88	49	6376,2224	703.7+/-405.4	2379,1618,303	no	coding-synonymous,utr-5	WWP2	NM_007014.3,NM_199424.1	,	4138,2033,327	AA,AG,GG		25.8605,10.5323,20.6756	,	413/871,	69963355	10309,2687	2198	4300	6498	SO:0001819	synonymous_variant	11060	exon12			AGAGAAGAGACAG	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.1239G>A	16.37:g.69963355G>A		Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	150	150	1	NM_001270454	A6NEP1|B2R706|B4DTL5|F5H213|H3BRF3|I3RSG8|Q6ZTQ5|Q96CZ2|Q9BWN6	Silent	SNP	ENST00000359154.2	37	CCDS10885.1																																																																																			A|0.812;C|0.000	0.812	strong		0.557	WWP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268954.1	NM_007014	
MUC4	4585	hgsc.bcm.edu	37	3	195508115	195508115	+	Missense_Mutation	SNP	T	T	G	rs77145082	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195508115T>G	ENST00000463781.3	-	2	10795	c.10336A>C	c.(10336-10338)Act>Cct	p.T3446P	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.T3446P	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)		GCTGAGGAAGTGCTGGTGACA	0.597													.|||	46	0.0091853	0.0015	0.0014	5008	,	,		20035	0.001		0.002	False		,,,				2504	0.0409				p.T3446P		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	0			c.A10336C						scavenged	.						27.0	23.0	24.0					3																	195508115		684	1577	2261	SO:0001583	missense	4585	exon2			AGGAAGTGCTGGT	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.10336A>C	3.37:g.195508115T>G	ENSP00000417498:p.Thr3446Pro	Somatic	65	2	0.0307692		WXS	Illumina HiSeq	Phase_I	82	13	0.158537	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	3.677	-0.066237	0.07273	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.37915	1.17;1.23	0.743	-1.49	0.08718	.	.	.	.	.	T	0.19167	0.0460	N	0.03608	-0.345	0.09310	N	1	D	0.57257	0.979	P	0.51487	0.671	T	0.37314	-0.9711	8	.	.	.	.	3.3392	0.07113	0.0:0.4056:0.2303:0.3641	.	3318	E7ESK3	.	P	3446	ENSP00000417498:T3446P;ENSP00000420243:T3446P	.	T	-	1	0	MUC4	196992894	0.001000	0.12720	0.001000	0.08648	0.001000	0.01503	0.063000	0.14410	-4.128000	0.00071	-4.106000	0.00011	ACT	G|1.000;|0.000	1.000	weak		0.597	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
NDRG4	65009	hgsc.bcm.edu	37	16	58542901	58542901	+	Silent	SNP	G	G	A	rs867583	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:58542901G>A	ENST00000570248.1	+	11	871	c.765G>A	c.(763-765)acG>acA	p.T255T	NDRG4_ENST00000568640.1_Silent_p.T273T|NDRG4_ENST00000394282.4_Silent_p.T307T|NDRG4_ENST00000566192.1_Silent_p.T255T|NDRG4_ENST00000356752.4_Silent_p.T285T|NDRG4_ENST00000394279.2_Silent_p.T287T|NDRG4_ENST00000569923.1_Silent_p.T200T|NDRG4_ENST00000563799.1_Silent_p.T273T|NDRG4_ENST00000562999.1_Silent_p.T255T|NDRG4_ENST00000258187.5_Silent_p.T287T	NM_001242835.1	NP_001229764.1	Q9ULP0	NDRG4_HUMAN	NDRG family member 4	255	Poly-Thr.				cell differentiation (GO:0030154)|cell growth (GO:0016049)|response to stress (GO:0006950)	cytoplasm (GO:0005737)				breast(1)|endometrium(3)|large_intestine(1)|lung(3)|ovary(1)|skin(1)|urinary_tract(1)	11						CGACCACTACGACCTTCCTGA	0.632													G|||	1797	0.358826	0.379	0.2392	5008	,	,		18235	0.5694		0.2127	False		,,,				2504	0.3497				p.T307T		Atlas-SNP	.											.	NDRG4	29	.	0			c.G921A						PASS	.	G	,,,,,,	1646,2750	501.2+/-364.9	320,1006,872	68.0	70.0	69.0		921,855,819,765,765,861,861	-7.5	0.8	16	dbSNP_86	69	1716,6884	313.1+/-311.2	163,1390,2747	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NDRG4	NM_001130487.1,NM_001242833.1,NM_001242834.1,NM_001242835.1,NM_001242836.1,NM_020465.3,NM_022910.3	,,,,,,	483,2396,3619	AA,AG,GG		19.9535,37.4431,25.8695	,,,,,,	307/392,285/370,273/358,255/353,255/340,287/372,287/372	58542901	3362,9634	2198	4300	6498	SO:0001819	synonymous_variant	65009	exon13			CACTACGACCTTC	AB044947	CCDS10797.1, CCDS45500.1, CCDS55999.1, CCDS58465.1, CCDS58466.1, CCDS58467.1	16q21-q22.3	2008-07-04			ENSG00000103034	ENSG00000103034			14466	protein-coding gene	gene with protein product		614463				11352569, 16408304	Standard	NM_020465		Approved	KIAA1180, SMAP-8	uc002enk.3	Q9ULP0	OTTHUMG00000133485	ENST00000570248.1:c.765G>A	16.37:g.58542901G>A		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	107	43	0.401869	NM_001130487	B3KNU2|B4DK66|B4DSW5|H7C600|Q6ZNE7|Q6ZTI7|Q96PL9|Q9GZM1|Q9GZN3|Q9GZX0	Silent	SNP	ENST00000570248.1	37	CCDS58466.1																																																																																			G|0.696;A|0.304	0.304	strong		0.632	NDRG4-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000422671.2		
SFSWAP	6433	hgsc.bcm.edu	37	12	132237750	132237750	+	Silent	SNP	C	C	T	rs1051219	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:132237750C>T	ENST00000261674.4	+	8	1305	c.1164C>T	c.(1162-1164)gaC>gaT	p.D388D	SFSWAP_ENST00000541286.1_Silent_p.D388D	NM_004592.3	NP_004583.2	Q12872	SFSWA_HUMAN	splicing factor, suppressor of white-apricot family	388					mRNA processing (GO:0006397)|mRNA splice site selection (GO:0006376)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	RNA binding (GO:0003723)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(8)|ovary(1)|skin(2)	25						CCGGAATCGACGTGACTACTT	0.612													C|||	515	0.102835	0.0091	0.2147	5008	,	,		17969	0.001		0.2565	False		,,,				2504	0.0971				p.D388D		Atlas-SNP	.											.	SFSWAP	69	.	0			c.C1164T						PASS	.	C		211,4195	129.0+/-165.8	6,199,1998	160.0	140.0	147.0		1164	-4.4	0.1	12	dbSNP_86	147	2395,6205	399.4+/-346.4	321,1753,2226	no	coding-synonymous	SFSWAP	NM_004592.2		327,1952,4224	TT,TC,CC		27.8488,4.7889,20.0369		388/952	132237750	2606,10400	2203	4300	6503	SO:0001819	synonymous_variant	6433	exon8			AATCGACGTGACT	U08377	CCDS9273.1, CCDS58290.1	12q24.33	2014-04-14	2014-04-14	2010-09-15	ENSG00000061936	ENSG00000061936			10790	protein-coding gene	gene with protein product		601945	"""splicing factor, arginine/serine-rich 8 (suppressor-of-white-apricot, Drosophila homolog)"", ""splicing factor, arginine/serine-rich 8 (suppressor-of-white-apricot homolog, Drosophila)"", ""splicing factor, suppressor of white-apricot homolog (Drosophila)"""	SFRS8		8940107	Standard	NM_004592		Approved	SWAP	uc010tbn.2	Q12872	OTTHUMG00000168319	ENST00000261674.4:c.1164C>T	12.37:g.132237750C>T		Somatic	196	0	0		WXS	Illumina HiSeq	Phase_I	155	90	0.580645	NM_001261411	B2RN45|B7ZM97|F5H6B8|Q6PJF7	Silent	SNP	ENST00000261674.4	37	CCDS9273.1	293	0.13415750915750915	6	0.012195121951219513	94	0.2596685082872928	0	0.0	193	0.2546174142480211	C	3.164	-0.171526	0.06421	0.047889	0.278488	ENSG00000061936	ENST00000537164	.	.	.	5.28	-4.44	0.03557	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.999999777251	.	.	.	.	.	.	T	0.28427	-1.0044	3	.	.	.	-26.8037	8.7176	0.34421	0.0:0.2818:0.1823:0.5358	rs1051219;rs17678035;rs60659244;rs1051219	.	.	.	M	28	.	.	T	+	2	0	SFSWAP	130803703	0.016000	0.18221	0.112000	0.21494	0.302000	0.27658	-0.993000	0.03720	-0.865000	0.04073	-0.369000	0.07265	ACG	C|0.832;T|0.168	0.168	strong		0.612	SFSWAP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399276.1	NM_004592	
PPP1R21	129285	hgsc.bcm.edu	37	2	48687054	48687054	+	Silent	SNP	A	A	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:48687054A>C	ENST00000294952.8	+	5	694	c.537A>C	c.(535-537)ctA>ctC	p.L179L	PPP1R21_ENST00000449090.2_Silent_p.L179L|PPP1R21_ENST00000281394.4_Silent_p.L179L	NM_001135629.2	NP_001129101.1	Q6ZMI0	PPR21_HUMAN	protein phosphatase 1, regulatory subunit 21	179						membrane (GO:0016020)	phosphatase binding (GO:0019902)			endometrium(2)|kidney(4)|lung(9)	15						AGGCTAAACTAGAAGTAAGCC	0.433																																					p.L179L		Atlas-SNP	.											.	PPP1R21	47	.	0			c.A537C						PASS	.						59.0	56.0	57.0					2																	48687054		2203	4300	6503	SO:0001819	synonymous_variant	129285	exon5			TAAACTAGAAGTA	AY134855	CCDS1839.1, CCDS46278.1, CCDS54358.1	2p16.3	2012-04-17	2011-10-11	2011-10-11	ENSG00000162869	ENSG00000162869		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	30595	protein-coding gene	gene with protein product			"""coiled-coil domain containing 128"", ""KLRAQ motif containing 1"""	CCDC128, KLRAQ1		12477932	Standard	NM_001135629		Approved	FLJ16566	uc002rwm.3	Q6ZMI0	OTTHUMG00000129167	ENST00000294952.8:c.537A>C	2.37:g.48687054A>C		Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	334	33	0.0988024	NM_152994	B7ZKY5|B7ZKY7|E1B6W7|Q2TA78|Q6ZMI6|Q8IW83|Q8J029|Q96ES8	Silent	SNP	ENST00000294952.8	37	CCDS46278.1																																																																																			.	.	none		0.433	PPP1R21-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251238.4	NM_152994	
METTL11B	149281	hgsc.bcm.edu	37	1	170135669	170135669	+	Silent	SNP	C	C	T	rs6427234	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:170135669C>T	ENST00000439373.2	+	3	464	c.357C>T	c.(355-357)tgC>tgT	p.C119C	METTL11B_ENST00000367764.3_3'UTR	NM_001136107.1	NP_001129579.1	Q5VVY1	NTM1B_HUMAN	methyltransferase like 11B	119						nucleus (GO:0005634)	methyltransferase activity (GO:0008168)			NS(1)|breast(2)|endometrium(3)|prostate(2)	8						GAACAGACTGCGCCTTGGACT	0.542													C|||	1458	0.291134	0.5076	0.2421	5008	,	,		16699	0.1349		0.2724	False		,,,				2504	0.2137				p.C119C		Atlas-SNP	.											.	METTL11B	18	.	0			c.C357T						PASS	.	C		657,727		159,339,194	85.0	80.0	82.0		357	-7.7	0.7	1	dbSNP_116	82	885,2297		133,619,839	no	coding-synonymous	METTL11B	NM_001136107.1		292,958,1033	TT,TC,CC		27.8127,47.4711,33.7714		119/284	170135669	1542,3024	692	1591	2283	SO:0001819	synonymous_variant	149281	exon3			AGACTGCGCCTTG	AL445203, CAH72139	CCDS44275.1	1q24.2	2012-11-05	2008-06-11	2008-06-11	ENSG00000203740	ENSG00000203740			31932	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 184"""	C1orf184			Standard	NM_001136107		Approved	HOMT1B	uc009wvv.1	Q5VVY1	OTTHUMG00000035959	ENST00000439373.2:c.357C>T	1.37:g.170135669C>T		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	50	31	0.62	NM_001136107	B2RXI0	Silent	SNP	ENST00000439373.2	37	CCDS44275.1																																																																																			C|0.725;T|0.275	0.275	strong		0.542	METTL11B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087586.2	NM_001136107	
FBN3	84467	hgsc.bcm.edu	37	19	8145928	8145928	+	Missense_Mutation	SNP	C	C	T	rs3848570|rs398088717	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:8145928C>T	ENST00000600128.1	-	59	7826	c.7412G>A	c.(7411-7413)cGc>cAc	p.R2471H	FBN3_ENST00000270509.2_Missense_Mutation_p.R2471H|FBN3_ENST00000601739.1_Missense_Mutation_p.R2471H			Q75N90	FBN3_HUMAN	fibrillin 3	2471	EGF-like 40; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.		R -> H (in dbSNP:rs3848570).			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						GGGCGGACAGCGGCAGGTGAA	0.622													C|||	111	0.0221645	0.0083	0.0403	5008	,	,		17290	0.0		0.0467	False		,,,				2504	0.0256				p.R2471H		Atlas-SNP	.											.	FBN3	300	.	0			c.G7412A						PASS	.	C	HIS/ARG	55,4351	51.6+/-87.1	1,53,2149	60.0	55.0	56.0		7412	0.9	1.0	19	dbSNP_108	56	406,8194	126.0+/-184.5	7,392,3901	yes	missense	FBN3	NM_032447.3	29	8,445,6050	TT,TC,CC		4.7209,1.2483,3.5445	benign	2471/2810	8145928	461,12545	2203	4300	6503	SO:0001583	missense	84467	exon58			GGACAGCGGCAGG		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.7412G>A	19.37:g.8145928C>T	ENSP00000470498:p.Arg2471His	Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	23	9	0.391304	NM_032447	Q75N91|Q75N92|Q75N93|Q86SJ5|Q96JP8	Missense_Mutation	SNP	ENST00000600128.1	37	CCDS12196.1	55	0.025183150183150184	3	0.006097560975609756	14	0.03867403314917127	0	0.0	38	0.05013192612137203	C	12.22	1.871409	0.33069	0.012483	0.047209	ENSG00000142449	ENST00000270509;ENST00000341066	D	0.92545	-3.06	4.06	0.915	0.19366	EGF-like region, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	0.310571	0.28436	N	0.015342	T	0.47691	0.1459	N	0.17312	0.475	0.27752	N	0.944128	B;B	0.21452	0.032;0.056	B;B	0.22753	0.041;0.027	T	0.62492	-0.6843	10	0.41790	T	0.15	.	5.5084	0.16866	0.0:0.3205:0.0:0.6795	rs3848570;rs3848570	2471;577	Q75N90;Q6ZNB8	FBN3_HUMAN;.	H	2471;577	ENSP00000270509:R2471H	ENSP00000270509:R2471H	R	-	2	0	FBN3	8051928	1.000000	0.71417	1.000000	0.80357	0.167000	0.22549	3.177000	0.50871	0.551000	0.29008	0.297000	0.19635	CGC	C|0.971;T|0.029	0.029	strong		0.622	FBN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461428.2	NM_032447	
MUC4	4585	hgsc.bcm.edu	37	3	195507228	195507228	+	Missense_Mutation	SNP	G	G	C	rs375915811|rs74187968		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195507228G>C	ENST00000463781.3	-	2	11682	c.11223C>G	c.(11221-11223)caC>caG	p.H3741Q	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.H3741Q	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.H3741Q(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)		GAGGGGTGACGTGACCTGTGG	0.582																																					p.H3741Q		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	1	Substitution - Missense(1)	kidney(1)	c.C11223G						PASS	.						26.0	26.0	26.0					3																	195507228		668	1583	2251	SO:0001583	missense	4585	exon2			GGTGACGTGACCT	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.11223C>G	3.37:g.195507228G>C	ENSP00000417498:p.His3741Gln	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	78	19	0.24359	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	7.779	0.709128	0.15239	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.32753	1.52;1.44	0.885	-1.56	0.08532	.	0.000000	0.25267	U	0.031920	T	0.16514	0.0397	N	0.19112	0.55	0.09310	N	1	D	0.52996	0.957	P	0.45071	0.468	T	0.25328	-1.0135	9	.	.	.	.	5.328	0.15917	0.2604:0.0:0.7396:0.0	.	3613	E7ESK3	.	Q	3741	ENSP00000417498:H3741Q;ENSP00000420243:H3741Q	.	H	-	3	2	MUC4	196992007	0.000000	0.05858	0.032000	0.17829	0.049000	0.14656	0.317000	0.19487	-0.535000	0.06307	0.064000	0.15345	CAC	.	.	weak		0.582	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
ITPR2	3709	hgsc.bcm.edu	37	12	26648092	26648092	+	Silent	SNP	C	C	T	rs2230381	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:26648092C>T	ENST00000381340.3	-	38	5591	c.5175G>A	c.(5173-5175)caG>caA	p.Q1725Q		NM_002223.2	NP_002214.2	Q14571	ITPR2_HUMAN	inositol 1,4,5-trisphosphate receptor, type 2	1725					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)	TACCTCCCACCTGTGCAGTTT	0.363													C|||	446	0.0890575	0.0113	0.1412	5008	,	,		18270	0.0248		0.2346	False		,,,				2504	0.0736				p.Q1725Q		Atlas-SNP	.											.	ITPR2	270	.	0			c.G5175A						PASS	.	C		135,3625		1,133,1746	118.0	110.0	112.0		5175	0.4	0.2	12	dbSNP_98	112	1812,6412		199,1414,2499	no	coding-synonymous	ITPR2	NM_002223.2		200,1547,4245	TT,TC,CC		22.0331,3.5904,16.2467		1725/2702	26648092	1947,10037	1880	4112	5992	SO:0001819	synonymous_variant	3709	exon38			TCCCACCTGTGCA	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.5175G>A	12.37:g.26648092C>T		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	87	50	0.574713	NM_002223	O94773	Silent	SNP	ENST00000381340.3	37	CCDS41764.1																																																																																			C|0.868;T|0.132	0.132	strong		0.363	ITPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402732.1	NM_002223	
COL9A1	1297	hgsc.bcm.edu	37	6	70984436	70984436	+	Missense_Mutation	SNP	A	A	G	rs592121	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:70984436A>G	ENST00000357250.6	-	11	1173	c.1015T>C	c.(1015-1017)Tca>Cca	p.S339P	COL9A1_ENST00000370499.4_Missense_Mutation_p.S96P|COL9A1_ENST00000320755.7_Missense_Mutation_p.S96P|COL9A1_ENST00000489611.1_5'UTR	NM_001851.4	NP_001842.3	P20849	CO9A1_HUMAN	collagen, type IX, alpha 1	339	Collagen-like 2.|Triple-helical region (COL3).		S -> P (in dbSNP:rs592121). {ECO:0000269|PubMed:11565064}.		axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|growth plate cartilage development (GO:0003417)|organ morphogenesis (GO:0009887)|tissue homeostasis (GO:0001894)	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)|metal ion binding (GO:0046872)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(44)|ovary(5)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(4)	80						TGTCCCTTTGACCCAATGGAG	0.383													G|||	2416	0.482428	0.7231	0.4294	5008	,	,		19229	0.3145		0.3628	False		,,,				2504	0.4908				p.S339P		Atlas-SNP	.											COL9A1_ENST00000320755,NS,adenoma,0,2	COL9A1	228	2	0			c.T1015C						PASS	.	G	PRO/SER,PRO/SER	2993,1413	460.5+/-352.6	1017,959,227	109.0	104.0	105.0		1015,286	5.0	1.0	6	dbSNP_83	105	3247,5353	649.4+/-400.6	610,2027,1663	yes	missense,missense	COL9A1	NM_001851.4,NM_078485.3	74,74	1627,2986,1890	GG,GA,AA		37.7558,32.0699,47.9779	benign,benign	339/922,96/679	70984436	6240,6766	2203	4300	6503	SO:0001583	missense	1297	exon11			CCTTTGACCCAAT		CCDS4971.1, CCDS47447.1	6q13	2013-05-07			ENSG00000112280	ENSG00000112280		"""Proteoglycans / Extracellular Matrix : Collagen proteoglycans"", ""Collagens"""	2217	protein-coding gene	gene with protein product		120210				1429648	Standard	NM_001851		Approved		uc003pfg.4	P20849	OTTHUMG00000014988	ENST00000357250.6:c.1015T>C	6.37:g.70984436A>G	ENSP00000349790:p.Ser339Pro	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	28	12	0.428571	NM_001851	Q13699|Q13700|Q5TF52|Q6P467|Q96BM8|Q99225|Q9H151|Q9H152|Q9Y6P2|Q9Y6P3	Missense_Mutation	SNP	ENST00000357250.6	37	CCDS4971.1	952	0.4358974358974359	349	0.709349593495935	146	0.40331491712707185	182	0.3181818181818182	275	0.3627968337730871	G	11.66	1.705769	0.30232	0.679301	0.377558	ENSG00000112280	ENST00000357250;ENST00000320755;ENST00000370499	D;D;D	0.93811	-3.29;-2.63;-3.29	5.85	4.98	0.66077	.	0.049158	0.85682	N	0.000000	T	0.49525	0.1562	N	0.00069	-2.28	0.43782	P	0.0036840000000000206	B;B	0.06786	0.001;0.0	B;B	0.01281	0.0;0.0	T	0.48559	-0.9025	9	0.06099	T	0.92	.	12.1197	0.53885	0.1427:0.0:0.8573:0.0	rs592121;rs1753199;rs17582574;rs61160542;rs592121	339;96	P20849;P20849-2	CO9A1_HUMAN;.	P	339;96;96	ENSP00000349790:S339P;ENSP00000315252:S96P;ENSP00000359530:S96P	ENSP00000315252:S96P	S	-	1	0	COL9A1	71041157	1.000000	0.71417	1.000000	0.80357	0.759000	0.43091	2.383000	0.44354	1.496000	0.48567	-0.119000	0.15052	TCA	A|0.531;G|0.469	0.469	strong		0.383	COL9A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041131.2		
TSPAN17	26262	hgsc.bcm.edu	37	5	176081907	176081907	+	Silent	SNP	C	C	T	rs11267007	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:176081907C>T	ENST00000503045.1	+	5	454	c.399C>T	c.(397-399)tgC>tgT	p.C133C	TSPAN17_ENST00000508164.1_Silent_p.C156C|TSPAN17_ENST00000310032.8_Silent_p.C156C|TSPAN17_ENST00000405525.2_Silent_p.C156C|TSPAN17_ENST00000515708.1_Silent_p.C156C|TSPAN17_ENST00000298564.10_Intron			Q96FV3	TSN17_HUMAN	tetraspanin 17	156					establishment of protein localization to organelle (GO:0072594)|protein ubiquitination (GO:0016567)	integral component of membrane (GO:0016021)|ubiquitin ligase complex (GO:0000151)	enzyme binding (GO:0019899)|ubiquitin-protein transferase activity (GO:0004842)			endometrium(4)|kidney(1)|large_intestine(2)|lung(5)|urinary_tract(1)	13	all_cancers(89;0.00141)|Renal(175;0.000269)|Lung NSC(126;0.00814)|all_lung(126;0.0133)	Medulloblastoma(196;0.00498)|all_neural(177;0.0212)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			GGTCTTGCTGCGGAGCCCGAG	0.632													c|||	1155	0.230631	0.0227	0.1484	5008	,	,		17541	0.4504		0.2604	False		,,,				2504	0.3129				p.C156C		Atlas-SNP	.											TSPAN17,NS,carcinoma,0,1	TSPAN17	33	1	0			c.C468T						PASS	.	T	,,	225,4181	133.3+/-169.7	7,211,1985	33.0	35.0	34.0		468,468,468	-3.4	1.0	5	dbSNP_120	34	2194,6406	365.8+/-334.1	269,1656,2375	no	coding-synonymous,coding-synonymous,coding-synonymous	TSPAN17	NM_001006616.2,NM_012171.2,NM_130465.4	,,	276,1867,4360	TT,TC,CC		25.5116,5.1067,18.5991	,,	156/264,156/333,156/330	176081907	2419,10587	2203	4300	6503	SO:0001819	synonymous_variant	26262	exon5			TTGCTGCGGAGCC	AF174603	CCDS34298.1, CCDS47346.1, CCDS47346.2, CCDS54952.1	5q35.3	2013-02-14	2005-03-21	2005-03-21	ENSG00000048140	ENSG00000048140		"""Tetraspanins"""	13594	protein-coding gene	gene with protein product			"""F-box only protein 23, transmembrane 4 superfamily member 17"""	FBXO23, TM4SF17		10531035, 10531037	Standard	NM_012171		Approved	FBX23	uc003met.3	Q96FV3	OTTHUMG00000163230	ENST00000503045.1:c.399C>T	5.37:g.176081907C>T		Somatic	207	1	0.00483092		WXS	Illumina HiSeq	Phase_I	218	119	0.545872	NM_001006616	Q6NXF7|Q96S98|Q9UKB9	Silent	SNP	ENST00000503045.1	37		525	0.2403846153846154	13	0.026422764227642278	57	0.1574585635359116	272	0.4755244755244755	183	0.24142480211081793	c	9.190	1.025885	0.19512	0.051067	0.255116	ENSG00000048140	ENST00000507471	.	.	.	5.23	-3.44	0.04796	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.39702	-0.9601	3	.	.	.	-8.0088	13.4813	0.61336	0.0:0.1708:0.0:0.8292	rs11267007;rs13183488;rs61477696;rs13183488	.	.	.	V	89	.	.	A	+	2	0	TSPAN17	176014513	0.112000	0.22096	0.976000	0.42696	0.904000	0.53231	-0.590000	0.05760	-0.590000	0.05866	-1.402000	0.01139	GCG	C|0.791;G|0.000;N|0.001;T|0.208	0.208	strong		0.632	TSPAN17-008	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000372215.1		
TLN2	83660	hgsc.bcm.edu	37	15	63102153	63102153	+	Silent	SNP	C	C	T	rs150114385	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:63102153C>T	ENST00000561311.1	+	51	6923	c.6693C>T	c.(6691-6693)gaC>gaT	p.D2231D	TLN2_ENST00000306829.6_Silent_p.D2231D			Q9Y4G6	TLN2_HUMAN	talin 2	2231					cell adhesion (GO:0007155)|cell-cell junction assembly (GO:0007043)|cytoskeletal anchoring at plasma membrane (GO:0007016)	actin cytoskeleton (GO:0015629)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|synapse (GO:0045202)	actin binding (GO:0003779)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			NS(3)|breast(6)|central_nervous_system(3)|endometrium(8)|kidney(8)|large_intestine(20)|lung(34)|ovary(6)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)	99						ATGTCAGTGACGAGGTGAGAA	0.547													C|||	3	0.000599042	0.0015	0.0	5008	,	,		22983	0.0		0.001	False		,,,				2504	0.0				p.D2231D		Atlas-SNP	.											.	TLN2	253	.	0			c.C6693T						PASS	.	C		3,4403	6.2+/-15.9	0,3,2200	128.0	94.0	106.0		6693	-4.9	0.9	15	dbSNP_134	106	29,8571	20.4+/-63.3	0,29,4271	no	coding-synonymous	TLN2	NM_015059.2		0,32,6471	TT,TC,CC		0.3372,0.0681,0.246		2231/2543	63102153	32,12974	2203	4300	6503	SO:0001819	synonymous_variant	83660	exon49			CAGTGACGAGGTG	AB002318	CCDS32261.1	15q15-q21	2008-07-03			ENSG00000171914	ENSG00000171914			15447	protein-coding gene	gene with protein product		607349				9205841, 11527381	Standard	NM_015059		Approved	KIAA0320, ILWEQ	uc002alb.4	Q9Y4G6	OTTHUMG00000133679	ENST00000561311.1:c.6693C>T	15.37:g.63102153C>T		Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	201	123	0.61194	NM_015059	A6NLB8	Silent	SNP	ENST00000561311.1	37	CCDS32261.1																																																																																			C|0.997;T|0.003	0.003	strong		0.547	TLN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257878.2		
OPLAH	26873	hgsc.bcm.edu	37	8	145113241	145113241	+	Missense_Mutation	SNP	T	T	G	rs3935209	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:145113241T>G	ENST00000426825.1	-	7	931	c.850A>C	c.(850-852)Agt>Cgt	p.S284R	OPLAH_ENST00000534424.1_5'UTR	NM_017570.3	NP_060040.1	O14841	OPLA_HUMAN	5-oxoprolinase (ATP-hydrolysing)	284			S -> R (in dbSNP:rs3935209).		glutathione biosynthetic process (GO:0006750)|glutathione derivative biosynthetic process (GO:1901687)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	5-oxoprolinase (ATP-hydrolyzing) activity (GO:0017168)|ATP binding (GO:0005524)			breast(1)|central_nervous_system(1)|endometrium(1)|lung(13)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	20	all_cancers(97;1.06e-10)|all_epithelial(106;1.5e-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;6.79e-41)|Epithelial(56;1.02e-39)|all cancers(56;2.24e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			AGCACAGCACTGGAGCCGCTG	0.687													G|||	1014	0.202476	0.5998	0.0893	5008	,	,		15381	0.003		0.0984	False		,,,				2504	0.0583				p.S284R		Atlas-SNP	.											OPLAH,NS,carcinoma,0,1	OPLAH	78	1	0			c.A850C						scavenged	.	G	ARG/SER	1818,2076		465,888,594	6.0	9.0	8.0		850	2.9	1.0	8	dbSNP_108	8	604,7624		25,554,3535	yes	missense	OPLAH	NM_017570.3	110	490,1442,4129	GG,GT,TT		7.3408,46.6872,19.9802	benign	284/1289	145113241	2422,9700	1947	4114	6061	SO:0001583	missense	26873	exon7			CAGCACTGGAGCC	AF024672, AB122018	CCDS75802.1	8q24.3	2010-11-23			ENSG00000178814	ENSG00000178814	3.5.2.9		8149	protein-coding gene	gene with protein product		614243				14993790	Standard	NM_017570		Approved	OPLA, 5-Opase	uc003zar.3	O14841		ENST00000426825.1:c.850A>C	8.37:g.145113241T>G	ENSP00000475943:p.Ser284Arg	Somatic	30	1	0.0333333		WXS	Illumina HiSeq	Phase_I	28	28	1	NM_017570	A5PKY8|Q75W65|Q9Y4Q0	Missense_Mutation	SNP	ENST00000426825.1	37		421	0.19276556776556777	297	0.6036585365853658	37	0.10220994475138122	13	0.022727272727272728	74	0.09762532981530343	G	11.48	1.649903	0.29336	0.466872	0.073408	ENSG00000178814	ENST00000426825	.	.	.	3.95	2.94	0.34122	.	0.000000	0.85682	N	0.000000	T	0.00012	0.0000	.	.	.	0.19575	N	0.999967	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.44421	-0.9329	7	0.02654	T	1	.	11.4387	0.50083	0.0:0.0:0.6654:0.3346	rs3935209;rs3935209	284;284	A7E261;O14841	.;OPLA_HUMAN	R	284	.	ENSP00000412071:S284R	S	-	1	0	OPLAH	145185229	0.940000	0.31905	0.981000	0.43875	0.538000	0.34931	0.568000	0.23623	0.652000	0.30806	-0.352000	0.07741	AGT	T|0.812;G|0.188	0.188	strong		0.687	OPLAH-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_017570	
TOP2A	7153	hgsc.bcm.edu	37	17	38547868	38547868	+	Missense_Mutation	SNP	C	C	T	rs34300454	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:38547868C>T	ENST00000423485.1	-	33	4315	c.4157G>A	c.(4156-4158)gGc>gAc	p.G1386D	Y_RNA_ENST00000410949.1_RNA	NM_001067.3	NP_001058.2	P11388	TOP2A_HUMAN	topoisomerase (DNA) II alpha 170kDa	1386			G -> D (in dbSNP:rs34300454).		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)	TGGTACACTGCCCTTAACATC	0.383													T|||	171	0.0341454	0.0998	0.0173	5008	,	,		18632	0.0		0.0209	False		,,,				2504	0.0061				p.G1386D		Atlas-SNP	.											.	TOP2A	124	.	0			c.G4157A						PASS	.	T	ASP/GLY	302,3452		11,280,1586	110.0	97.0	101.0		4157	4.2	0.0	17	dbSNP_126	101	184,8064		4,176,3944	yes	missense	TOP2A	NM_001067.3	94	15,456,5530	TT,TC,CC		2.2308,8.0448,4.0493	benign	1386/1532	38547868	486,11516	1877	4124	6001	SO:0001583	missense	7153	exon33			ACACTGCCCTTAA		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.4157G>A	17.37:g.38547868C>T	ENSP00000411532:p.Gly1386Asp	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	136	60	0.441176	NM_001067	B2RTS1|Q71UN1|Q71UQ5|Q9HB24|Q9HB25|Q9HB26|Q9UP44|Q9UQP9	Missense_Mutation	SNP	ENST00000423485.1	37	CCDS45672.1	82	0.037545787545787544	60	0.12195121951219512	9	0.024861878453038673	0	0.0	13	0.017150395778364115	T	0.491	-0.875336	0.02550	0.080448	0.022308	ENSG00000131747	ENST00000423485;ENST00000269577;ENST00000348049;ENST00000357601	T	0.20881	2.04	5.27	4.2	0.49525	.	0.693346	0.14593	N	0.310128	T	0.00109	0.0003	N	0.00926	-1.1	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.34229	-0.9837	9	0.10902	T	0.67	.	6.872	0.24125	0.0:0.1793:0.0:0.8207	rs34300454;rs34300454	1386	P11388	TOP2A_HUMAN	D	1386;1466;1409;1423	ENSP00000411532:G1386D	ENSP00000269577:G1466D	G	-	2	0	TOP2A	35801394	0.281000	0.24258	0.001000	0.08648	0.015000	0.08874	1.349000	0.33998	0.466000	0.27193	-1.007000	0.02485	GGC	C|0.955;T|0.045	0.045	strong		0.383	TOP2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338035.1		
AOC1	26	hgsc.bcm.edu	37	7	150555915	150555915	+	Silent	SNP	A	A	G	rs10893	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:150555915A>G	ENST00000493429.1	+	5	2219	c.1635A>G	c.(1633-1635)ccA>ccG	p.P545P	AOC1_ENST00000360937.4_Silent_p.P545P|AOC1_ENST00000416793.2_Silent_p.P545P|AOC1_ENST00000467291.1_Silent_p.P545P|AOC1_ENST00000480582.1_3'UTR			P19801	AOC1_HUMAN	amine oxidase, copper containing 1	545					amine metabolic process (GO:0009308)|cellular response to azide (GO:0097185)|cellular response to copper ion (GO:0071280)|cellular response to copper ion starvation (GO:0035874)|cellular response to heparin (GO:0071504)|cellular response to histamine (GO:0071420)|oxidation-reduction process (GO:0055114)|response to antibiotic (GO:0046677)|response to drug (GO:0042493)|sodium ion transmembrane transport (GO:0035725)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|peroxisome (GO:0005777)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	calcium ion binding (GO:0005509)|cation channel activity (GO:0005261)|copper ion binding (GO:0005507)|diamine oxidase activity (GO:0052597)|drug binding (GO:0008144)|heparin binding (GO:0008201)|histamine oxidase activity (GO:0052598)|methylputrescine oxidase activity (GO:0052599)|primary amine oxidase activity (GO:0008131)|propane-1,3-diamine oxidase activity (GO:0052600)|protein complex binding (GO:0032403)|protein homodimerization activity (GO:0042803)|quinone binding (GO:0048038)|receptor activity (GO:0004872)|sodium channel activity (GO:0005272)|zinc ion binding (GO:0008270)									Amiloride(DB00594)	CCTGGAGCCCAAGACACCGCG	0.562													G|||	2299	0.459065	0.5643	0.3977	5008	,	,		18858	0.4792		0.2734	False		,,,				2504	0.5307				p.P545P		Atlas-SNP	.											.	ABP1	92	.	0			c.A1635G						PASS	.	G		1898,2130		462,974,578	39.0	44.0	42.0		1635	-10.8	0.0	7	dbSNP_52	42	2525,5833		408,1709,2062	no	coding-synonymous	ABP1	NM_001091.2		870,2683,2640	GG,GA,AA		30.2106,47.1202,35.7097		545/752	150555915	4423,7963	2014	4179	6193	SO:0001819	synonymous_variant	26	exon3			GAGCCCAAGACAC	AK092514	CCDS43679.1, CCDS64797.1	7q36.1	2013-06-19	2013-06-19	2013-06-19	ENSG00000002726	ENSG00000002726	1.4.3.22		80	protein-coding gene	gene with protein product	"""diamine oxidase"""	104610	"""amiloride binding protein 1 (amine oxidase (copper-containing))"""	ABP1		8182053	Standard	NM_001091		Approved	DAO	uc003wia.2	P19801	OTTHUMG00000158306	ENST00000493429.1:c.1635A>G	7.37:g.150555915A>G		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	154	69	0.448052	NM_001091	C9J690|Q16683|Q16684|Q56II4|Q6GU42	Silent	SNP	ENST00000493429.1	37	CCDS43679.1																																																																																			A|0.571;G|0.429	0.429	strong		0.562	AOC1-009	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350628.1	NM_001091	
ITGAM	3684	hgsc.bcm.edu	37	16	31343005	31343005	+	Missense_Mutation	SNP	C	C	T	rs1143678	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:31343005C>T	ENST00000287497.8	+	30	3511	c.3436C>T	c.(3436-3438)Ccc>Tcc	p.P1146S	ITGAM_ENST00000544665.3_Missense_Mutation_p.P1147S			P11215	ITAM_HUMAN	integrin, alpha M (complement component 3 receptor 3 subunit)	1146			P -> S (in dbSNP:rs1143678). {ECO:0000269|PubMed:15489334}.		activated T cell proliferation (GO:0050798)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cellular extravasation (GO:0045123)|ectodermal cell differentiation (GO:0010668)|extracellular matrix organization (GO:0030198)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|leukocyte migration involved in inflammatory response (GO:0002523)|microglia development (GO:0014005)|neutrophil chemotaxis (GO:0030593)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integrin complex (GO:0008305)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	glycoprotein binding (GO:0001948)|heparin binding (GO:0008201)|metal ion binding (GO:0046872)			endometrium(7)|kidney(1)|large_intestine(10)|lung(32)|ovary(1)|prostate(4)|skin(1)	56						TGAAGGGGGTCCCCCGGGGGC	0.672													C|||	849	0.169529	0.2194	0.1282	5008	,	,		13181	0.0278		0.1809	False		,,,				2504	0.2658				p.P1147S		Atlas-SNP	.											.	ITGAM	137	.	0			c.C3439T						PASS	.	C	SER/PRO,SER/PRO	755,3143		75,605,1269	20.0	25.0	23.0		3436,3439	3.2	0.0	16	dbSNP_86	23	1262,6994		113,1036,2979	yes	missense,missense	ITGAM	NM_000632.3,NM_001145808.1	74,74	188,1641,4248	TT,TC,CC		15.2859,19.3689,16.5954	benign,benign	1146/1153,1147/1154	31343005	2017,10137	1949	4128	6077	SO:0001583	missense	3684	exon30			GGGGGTCCCCCGG	J03925	CCDS45470.1, CCDS54004.1	16p11.2	2010-03-23	2006-02-10			ENSG00000169896		"""CD molecules"", ""Complement system"", ""Integrins"""	6149	protein-coding gene	gene with protein product		120980	"""integrin, alpha M (complement component receptor 3, alpha; also known as CD11b (p170), macrophage antigen alpha polypeptide)"""	CR3A, CD11B			Standard	NM_001145808		Approved	MAC-1, CD11b	uc002ebr.3	P11215		ENST00000287497.8:c.3436C>T	16.37:g.31343005C>T	ENSP00000287497:p.Pro1146Ser	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	157	86	0.547771	NM_001145808	Q4VAK0|Q4VAK1|Q4VAK2	Missense_Mutation	SNP	ENST00000287497.8	37	CCDS45470.1	275	0.1259157509157509	91	0.18495934959349594	46	0.1270718232044199	1	0.0017482517482517483	137	0.18073878627968337	C	11.04	1.521360	0.27211	0.193689	0.152859	ENSG00000169896	ENST00000544665;ENST00000287497	T;T	0.59083	0.29;0.29	4.24	3.25	0.37280	.	.	.	.	.	T	0.00073	0.0002	L	0.50333	1.59	0.80722	P	0.0	P	0.40578	0.722	B	0.36719	0.231	T	0.03910	-1.0993	8	0.39692	T	0.17	.	7.0467	0.25050	0.3449:0.4872:0.1679:0.0	rs1143678;rs59972379;rs1143678	1146	P11215	ITAM_HUMAN	S	1147;1146	ENSP00000441691:P1147S;ENSP00000287497:P1146S	ENSP00000287497:P1146S	P	+	1	0	ITGAM	31250506	0.079000	0.21365	0.029000	0.17559	0.071000	0.16799	1.952000	0.40343	1.075000	0.40932	0.650000	0.86243	CCC	C|0.864;T|0.136	0.136	strong		0.672	ITGAM-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000432816.1	NM_000632	
ZNF462	58499	hgsc.bcm.edu	37	9	109691676	109691676	+	Missense_Mutation	SNP	A	A	G	rs3814538	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:109691676A>G	ENST00000277225.5	+	3	5772	c.5483A>G	c.(5482-5484)aAc>aGc	p.N1828S	ZNF462_ENST00000457913.1_Missense_Mutation_p.N1828S|ZNF462_ENST00000441147.2_Missense_Mutation_p.N673S			Q96JM2	ZN462_HUMAN	zinc finger protein 462	1828			N -> S (in dbSNP:rs3814538).		chromatin organization (GO:0006325)|negative regulation of DNA binding (GO:0043392)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|autonomic_ganglia(2)|breast(5)|central_nervous_system(4)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(17)|large_intestine(20)|lung(32)|ovary(5)|prostate(6)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	119						GAGAGAGGCAACTTTGAGAAA	0.542													G|||	2802	0.559505	0.8623	0.4625	5008	,	,		19918	0.4782		0.3917	False		,,,				2504	0.4755				p.N1828S		Atlas-SNP	.											.	ZNF462	322	.	0			c.A5483G						PASS	.	G	SER/ASN	3402,1004	361.6+/-315.8	1329,744,130	83.0	73.0	77.0		5483	3.9	1.0	9	dbSNP_107	77	3126,5474	647.7+/-400.4	542,2042,1716	yes	missense	ZNF462	NM_021224.4	46	1871,2786,1846	GG,GA,AA		36.3488,22.7871,49.8078	benign	1828/2507	109691676	6528,6478	2203	4300	6503	SO:0001583	missense	58499	exon3			GAGGCAACTTTGA	AB058706	CCDS35096.1	9q31.3	2008-02-05			ENSG00000148143	ENSG00000148143		"""Zinc fingers, C2H2-type"""	21684	protein-coding gene	gene with protein product							Standard	NM_021224		Approved	DKFZP762N2316, KIAA1803, Zfp462	uc004bcz.3	Q96JM2	OTTHUMG00000020438	ENST00000277225.5:c.5483A>G	9.37:g.109691676A>G	ENSP00000277225:p.Asn1828Ser	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	60	26	0.433333	NM_021224	Q5T0T4|Q8N408	Missense_Mutation	SNP	ENST00000277225.5	37	CCDS35096.1	1134	0.5192307692307693	411	0.8353658536585366	170	0.4696132596685083	258	0.45104895104895104	295	0.3891820580474934	G	0.006	-2.046486	0.00398	0.772129	0.363488	ENSG00000148143	ENST00000277225;ENST00000457913;ENST00000374686;ENST00000441147	T;T;T;T	0.04654	3.58;4.03;4.14;4.16	5.92	3.86	0.44501	.	0.653773	0.17254	N	0.181055	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	0.19353	-1.0308	9	0.07030	T	0.85	.	5.0988	0.14749	0.4595:0.0:0.5405:0.0	rs3814538;rs17788089;rs17846198;rs17859213;rs52813323;rs57069281;rs3814538	1828;1828	Q96JM2-3;Q96JM2	.;ZN462_HUMAN	S	1828;1828;711;673	ENSP00000277225:N1828S;ENSP00000414570:N1828S;ENSP00000363818:N711S;ENSP00000397306:N673S	ENSP00000277225:N1828S	N	+	2	0	ZNF462	108731497	0.013000	0.17824	0.991000	0.47740	0.824000	0.46624	1.305000	0.33493	0.858000	0.35431	-0.215000	0.12644	AAC	G|0.519;N|0.001	0.519	strong		0.542	ZNF462-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000053532.2	NM_021224	
CYP4F12	66002	hgsc.bcm.edu	37	19	15784377	15784377	+	Missense_Mutation	SNP	C	C	T	rs16995376	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:15784377C>T	ENST00000550308.1	+	2	418	c.38C>T	c.(37-39)cCg>cTg	p.P13L	CYP4F12_ENST00000324632.10_Missense_Mutation_p.P13L	NM_023944.3	NP_076433	Q9HCS2	CP4FC_HUMAN	cytochrome P450, family 4, subfamily F, polypeptide 12	13			P -> L (in dbSNP:rs16995376). {ECO:0000269|PubMed:11162645}.		arachidonic acid metabolic process (GO:0019369)|drug metabolic process (GO:0017144)|epoxygenase P450 pathway (GO:0019373)|leukotriene B4 catabolic process (GO:0036101)|long-chain fatty acid metabolic process (GO:0001676)|negative regulation of blood coagulation (GO:0030195)|oxidation-reduction process (GO:0055114)|pressure natriuresis (GO:0003095)|renal water homeostasis (GO:0003091)|small molecule metabolic process (GO:0044281)|sodium ion homeostasis (GO:0055078)|very long-chain fatty acid metabolic process (GO:0000038)|vitamin E metabolic process (GO:0042360)|vitamin K biosynthetic process (GO:0042371)|xenobiotic metabolic process (GO:0006805)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)	alkane 1-monooxygenase activity (GO:0018685)|arachidonic acid epoxygenase activity (GO:0008392)|aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|leukotriene-B4 20-monooxygenase activity (GO:0050051)|vitamin-K-epoxide reductase (warfarin-sensitive) activity (GO:0047057)			NS(1)|central_nervous_system(3)|endometrium(4)|kidney(2)|large_intestine(7)|lung(12)|ovary(3)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	41	Acute lymphoblastic leukemia(2;0.0367)				Fingolimod(DB08868)	GGCCTCAGACCGGTGGCAACG	0.647													.|||	1030	0.205671	0.3139	0.2161	5008	,	,		6485	0.0109		0.2584	False		,,,				2504	0.1984				p.P13L		Atlas-SNP	.											.	CYP4F12	89	.	0			c.C38T						PASS	.	A	LEU/PRO	1513,2883		226,1061,911	57.0	62.0	60.0		38	-4.9	0.0	19	dbSNP_123	60	2065,6533		282,1501,2516	yes	missense	CYP4F12	NM_023944.3	98	508,2562,3427	TT,TC,CC		24.0172,34.4177,27.5358	benign	13/525	15784377	3578,9416	2198	4299	6497	SO:0001583	missense	66002	exon2			TCAGACCGGTGGC	AB035130	CCDS42517.1	19p13.1	2008-02-05	2003-01-14		ENSG00000186204	ENSG00000186204		"""Cytochrome P450s"""	18857	protein-coding gene	gene with protein product		611485	"""cytochrome P450, subfamily IVF, polypeptide 12"""			11162607	Standard	NM_023944		Approved		uc002nbl.3	Q9HCS2	OTTHUMG00000164477	ENST00000550308.1:c.38C>T	19.37:g.15784377C>T	ENSP00000448998:p.Pro13Leu	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	90	49	0.544444	NM_023944	E7ET51|O60389|Q5JPJ7|Q9HCS1	Missense_Mutation	SNP	ENST00000550308.1	37	CCDS42517.1	477	0.2184065934065934	164	0.3333333333333333	95	0.26243093922651933	11	0.019230769230769232	207	0.27308707124010556	.	6.370	0.436299	0.12104	0.344177	0.240172	ENSG00000186204	ENST00000550308;ENST00000324632	D;D	0.92048	-2.96;-2.96	2.46	-4.92	0.03075	.	1.096560	0.07077	U	0.836348	T	0.00012	0.0000	L	0.56769	1.78	0.80722	P	0.0	B;B;B	0.31256	0.316;0.05;0.028	B;B;B	0.26969	0.075;0.021;0.014	T	0.08166	-1.0735	9	0.27785	T	0.31	.	3.7556	0.08584	0.3401:0.2669:0.0:0.393	rs16995376;rs16995376	13;13;13	B4E2R2;B4E270;Q9HCS2	.;.;CP4FC_HUMAN	L	13	ENSP00000448998:P13L;ENSP00000321821:P13L	ENSP00000321821:P13L	P	+	2	0	CYP4F12	15645377	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-4.371000	0.00244	-2.258000	0.00694	-1.284000	0.01376	CCG	C|0.775;T|0.225	0.225	strong		0.647	CYP4F12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378938.9		
NUMB	8650	hgsc.bcm.edu	37	14	73753886	73753886	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:73753886C>T	ENST00000355058.3	-	9	865	c.587G>A	c.(586-588)cGt>cAt	p.R196H	NUMB_ENST00000555238.1_Missense_Mutation_p.R196H|NUMB_ENST00000555738.2_Missense_Mutation_p.R185H|NUMB_ENST00000359560.3_Missense_Mutation_p.R185H|NUMB_ENST00000559312.1_Missense_Mutation_p.R196H|NUMB_ENST00000554521.2_Missense_Mutation_p.R185H|NUMB_ENST00000535282.1_Missense_Mutation_p.R185H|NUMB_ENST00000555394.1_Missense_Mutation_p.R196H|NUMB_ENST00000554546.1_Missense_Mutation_p.R185H|NUMB_ENST00000556772.1_Missense_Mutation_p.R52H|NUMB_ENST00000560335.1_Missense_Mutation_p.R196H|NUMB_ENST00000356296.4_Missense_Mutation_p.R196H|NUMB_ENST00000454166.4_Missense_Mutation_p.R196H|NUMB_ENST00000544991.3_Missense_Mutation_p.R196H|NUMB_ENST00000557597.1_Missense_Mutation_p.R185H			P49757	NUMB_HUMAN	numb homolog (Drosophila)	196					adherens junction organization (GO:0034332)|axon guidance (GO:0007411)|lateral ventricle development (GO:0021670)|lung epithelial cell differentiation (GO:0060487)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of protein localization to plasma membrane (GO:1903077)|neuroblast division in subventricular zone (GO:0021849)|Notch signaling pathway (GO:0007219)|positive regulation of cell migration (GO:0030335)|positive regulation of neurogenesis (GO:0050769)|positive regulation of polarized epithelial cell differentiation (GO:0030862)	apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|clathrin-coated vesicle (GO:0030136)|early endosome (GO:0005769)|extrinsic component of plasma membrane (GO:0019897)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(4)|lung(8)|ovary(3)|prostate(1)|skin(3)|urinary_tract(1)	28				BRCA - Breast invasive adenocarcinoma(234;0.00471)|OV - Ovarian serous cystadenocarcinoma(108;0.161)		TGTTGTGACACGGAATGATCC	0.448																																					p.R196H		Atlas-SNP	.											NUMB,NS,lymphoid_neoplasm,0,1	NUMB	56	1	0			c.G587A						scavenged	.						226.0	188.0	201.0					14																	73753886		2203	4300	6503	SO:0001583	missense	8650	exon9			GTGACACGGAATG	L40393	CCDS9814.1, CCDS32115.1, CCDS32116.1, CCDS55927.1	14q24.3	2011-11-25	2001-11-28			ENSG00000133961			8060	protein-coding gene	gene with protein product		603728	"""numb (Drosophila) homolog"", ""chromosome 14 open reading frame 41"""	C14orf41			Standard	NM_003744		Approved		uc001xny.1	P49757		ENST00000355058.3:c.587G>A	14.37:g.73753886C>T	ENSP00000347169:p.Arg196His	Somatic	419	0	0		WXS	Illumina HiSeq	Phase_I	396	4	0.010101	NM_001005744	B1P2N5|B1P2N6|B1P2N7|B1P2N8|B1P2N9|B4E2B1|Q6NUQ7|Q86SY1|Q8WW73|Q9UBG1|Q9UEQ4|Q9UKE8|Q9UKE9|Q9UKF0|Q9UQJ4	Missense_Mutation	SNP	ENST00000355058.3	37	CCDS32116.1	.	.	.	.	.	.	.	.	.	.	C	36	5.618602	0.96649	.	.	ENSG00000133961	ENST00000554546;ENST00000356296;ENST00000557597;ENST00000555238;ENST00000556772;ENST00000355058;ENST00000359560;ENST00000555394;ENST00000544991;ENST00000454166;ENST00000555738;ENST00000554521;ENST00000535282;ENST00000326018;ENST00000555859;ENST00000555307;ENST00000554394	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.72835	0.2;0.08;0.62;0.51;0.88;0.51;0.62;0.08;0.04;-0.42;0.01;0.21;0.62;-0.69;-0.69	5.5	5.5	0.81552	.	0.000000	0.85682	D	0.000000	D	0.83353	0.5236	L	0.61036	1.89	0.80722	D	1	D;D;D;D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;0.999;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D;D;D;D	0.91635	0.998;0.999;0.999;0.964;0.999;0.991;0.995;0.999;0.999;0.996;0.995	D	0.83970	0.0326	10	0.87932	D	0	-10.9822	19.5916	0.95514	0.0:1.0:0.0:0.0	.	185;196;185;196;196;185;185;185;196;185;196	B1P2N6;B1P2N5;B1P2N8;B1P2N7;G3V3R1;Q86SW5;B2RCI6;P49757-4;P49757-2;P49757-3;P49757	.;.;.;.;.;.;.;.;.;.;NUMB_HUMAN	H	185;196;185;196;52;196;185;196;196;196;185;185;185;160;160;196;196	ENSP00000452416:R185H;ENSP00000348644:R196H;ENSP00000451117:R185H;ENSP00000451300:R196H;ENSP00000451513:R52H;ENSP00000347169:R196H;ENSP00000352563:R185H;ENSP00000451625:R196H;ENSP00000446001:R196H;ENSP00000394025:R196H;ENSP00000452069:R185H;ENSP00000450817:R185H;ENSP00000441258:R185H;ENSP00000452357:R196H;ENSP00000451374:R196H	ENSP00000315193:R160H	R	-	2	0	NUMB	72823639	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.651000	0.83577	2.861000	0.98227	0.655000	0.94253	CGT	.	.	none		0.448	NUMB-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000414416.1		
BTN3A2	11118	hgsc.bcm.edu	37	6	26370572	26370572	+	Silent	SNP	C	C	T	rs34878490	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:26370572C>T	ENST00000356386.2	+	5	644	c.456C>T	c.(454-456)gtC>gtT	p.V152V	BTN3A2_ENST00000396948.1_Silent_p.V152V|BTN3A2_ENST00000396934.3_Silent_p.V129V|BTN3A2_ENST00000532994.1_3'UTR|BTN3A2_ENST00000527422.1_Silent_p.V152V|BTN3A2_ENST00000508906.2_Silent_p.V110V|BTN3A2_ENST00000377708.2_Silent_p.V152V	NM_001197246.2|NM_001197247.1|NM_007047.3	NP_001184175.1|NP_001184176.1|NP_008978.2	P78410	BT3A2_HUMAN	butyrophilin, subfamily 3, member A2	152					interferon-gamma secretion (GO:0072643)|T cell mediated immunity (GO:0002456)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(5)	10						ATCTTCACGTCGAAGTGAAGG	0.512													C|||	422	0.0842652	0.0287	0.0403	5008	,	,		19875	0.1101		0.1123	False		,,,				2504	0.135				p.V152V		Atlas-SNP	.											.	BTN3A2	44	.	0			c.C456T						PASS	.	C	,,,,	168,4238	111.2+/-149.4	2,164,2037	94.0	85.0	88.0		456,456,387,330,456	-5.7	0.0	6	dbSNP_126	88	939,7661	205.9+/-248.2	50,839,3411	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	BTN3A2	NM_001197246.1,NM_001197247.1,NM_001197248.1,NM_001197249.1,NM_007047.3	,,,,	52,1003,5448	TT,TC,CC		10.9186,3.813,8.5115	,,,,	152/335,152/335,129/312,110/293,152/335	26370572	1107,11899	2203	4300	6503	SO:0001819	synonymous_variant	11118	exon3			TCACGTCGAAGTG	U90546	CCDS4605.1, CCDS56399.1, CCDS56400.1	6p22.1	2014-01-14			ENSG00000186470	ENSG00000186470		"""Immunoglobulin superfamily / V-set domain containing"", ""Butyrophilins"""	1139	protein-coding gene	gene with protein product		613594				9149941	Standard	NM_007047		Approved	BTN3.2	uc010jqi.2	P78410	OTTHUMG00000014450	ENST00000356386.2:c.456C>T	6.37:g.26370572C>T		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	81	80	0.987654	NM_001197246	B4DRT7|B4E103|F5H791|F8W6E0|O00477|O15338|O75658|Q76PA0|Q9BU81|Q9NR44	Silent	SNP	ENST00000356386.2	37	CCDS4605.1																																																																																			C|0.923;T|0.077	0.077	strong		0.512	BTN3A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040113.2		
MFAP3	4238	hgsc.bcm.edu	37	5	153432970	153432970	+	Silent	SNP	C	C	T	rs2255493	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:153432970C>T	ENST00000436816.1	+	3	1005	c.786C>T	c.(784-786)gaC>gaT	p.D262D	MFAP3_ENST00000322602.5_Silent_p.D262D|MFAP3_ENST00000439768.2_Silent_p.D116D	NM_001242336.1|NM_005927.4	NP_001229265.1|NP_005918.1	P55082	MFAP3_HUMAN	microfibrillar-associated protein 3	262					extracellular matrix organization (GO:0030198)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|kidney(2)|large_intestine(1)|lung(2)|pancreas(1)	7	Renal(175;0.00488)	Lung NSC(249;0.00145)|all_lung(500;0.00226)|all_neural(177;0.122)|Breast(839;0.14)	Kidney(363;0.000173)|KIRC - Kidney renal clear cell carcinoma(527;0.000785)	OV - Ovarian serous cystadenocarcinoma(192;9.69e-06)|GBM - Glioblastoma multiforme(465;0.0201)		TGCGAGTGGACGACCCTGATG	0.468													T|||	3585	0.715855	0.6241	0.7161	5008	,	,		20272	0.8581		0.6252	False		,,,				2504	0.7863				p.D262D		Atlas-SNP	.											.	MFAP3	20	.	0			c.C786T						PASS	.	T	,,	2859,1547	489.0+/-361.4	931,997,275	105.0	99.0	101.0		348,786,786	4.0	1.0	5	dbSNP_100	101	5349,3251	488.7+/-372.4	1663,2023,614	no	coding-synonymous,coding-synonymous,coding-synonymous	MFAP3	NM_001135037.1,NM_001242336.1,NM_005927.4	,,	2594,3020,889	TT,TC,CC		37.8023,35.1112,36.8907	,,	116/217,262/363,262/363	153432970	8208,4798	2203	4300	6503	SO:0001819	synonymous_variant	4238	exon3			AGTGGACGACCCT		CCDS4324.1, CCDS47319.1	5q32-q33.2	2013-01-11			ENSG00000037749	ENSG00000037749		"""Immunoglobulin superfamily / I-set domain containing"""	7034	protein-coding gene	gene with protein product		600491				7782085	Standard	NM_005927		Approved		uc010jib.2	P55082	OTTHUMG00000130149	ENST00000436816.1:c.786C>T	5.37:g.153432970C>T		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	94	52	0.553191	NM_005927	B2RDK0|B4DKA1|Q9NXA7	Silent	SNP	ENST00000436816.1	37	CCDS4324.1																																																																																			C|0.346;T|0.654	0.654	strong		0.468	MFAP3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252457.2	NM_005927	
IL27RA	9466	hgsc.bcm.edu	37	19	14142705	14142705	+	Silent	SNP	C	C	T	rs113593439	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:14142705C>T	ENST00000263379.2	+	1	146	c.21C>T	c.(19-21)gcC>gcT	p.A7A	CTB-55O6.4_ENST00000590528.1_RNA	NM_004843.3	NP_004834.1	Q6UWB1	I27RA_HUMAN	interleukin 27 receptor, alpha	7				A -> G (in Ref. 3; AAG27297 and 5; AAQ89235). {ECO:0000305}.	cell surface receptor signaling pathway (GO:0007166)|defense response to Gram-positive bacterium (GO:0050830)|immune response (GO:0006955)|negative regulation of type 2 immune response (GO:0002829)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of T-helper 1 type immune response (GO:0002827)|regulation of isotype switching to IgG isotypes (GO:0048302)	integral component of plasma membrane (GO:0005887)	interleukin-27 receptor activity (GO:0045509)|transmembrane signaling receptor activity (GO:0004888)			breast(3)|endometrium(3)|kidney(2)|large_intestine(8)|lung(7)|ovary(1)|skin(1)|urinary_tract(1)	26						GCAGGGGCGCCCCTTTCTGGC	0.721													C|||	588	0.117412	0.1641	0.1282	5008	,	,		11265	0.12		0.0517	False		,,,				2504	0.1115				p.A7A	Colon(164;1849 1896 4443 37792 47834)	Atlas-SNP	.											IL27RA,NS,haematopoietic_neoplasm,0,2	IL27RA	56	2	0			c.C21T						PASS	.	C		560,3818		37,486,1666	11.0	13.0	12.0		21	-1.2	0.0	19	dbSNP_132	12	524,8042		18,488,3777	no	coding-synonymous	IL27RA	NM_004843.2		55,974,5443	TT,TC,CC		6.1172,12.7912,8.3745		7/637	14142705	1084,11860	2189	4283	6472	SO:0001819	synonymous_variant	9466	exon1			GGGCGCCCCTTTC	AF053004	CCDS12303.1	19p13.11	2013-02-11				ENSG00000104998		"""Interleukins and interleukin receptors"", ""Fibronectin type III domain containing"""	17290	protein-coding gene	gene with protein product	"""T-cell cytokine receptor type 1"""	605350				9600072, 11057672	Standard	NM_004843		Approved	WSX-1, TCCR, CRL1, WSX1, zcytor1, IL-27R	uc002mxx.4	Q6UWB1		ENST00000263379.2:c.21C>T	19.37:g.14142705C>T		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	68	42	0.617647	NM_004843	A0N0L1|O60624	Silent	SNP	ENST00000263379.2	37	CCDS12303.1																																																																																			C|0.891;T|0.109	0.109	strong		0.721	IL27RA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458539.1	NM_004843	
MRPL28	10573	hgsc.bcm.edu	37	16	420140	420140	+	Missense_Mutation	SNP	G	G	A	rs3194151	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:420140G>A	ENST00000199706.8	-	2	114	c.79C>T	c.(79-81)Cac>Tac	p.H27Y	MRPL28_ENST00000389675.2_Missense_Mutation_p.H27Y|MRPL28_ENST00000429738.1_5'Flank	NM_006428.4	NP_006419.2	Q13084	RM28_HUMAN	mitochondrial ribosomal protein L28	27			H -> Y (in dbSNP:rs3194151). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		translation (GO:0006412)	cytoplasm (GO:0005737)|mitochondrial ribosome (GO:0005761)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			breast(1)|kidney(1)|lung(1)|ovary(1)|prostate(1)	5		Hepatocellular(16;0.000105)|Lung NSC(18;0.0324)|all_lung(18;0.064)				CGCAGGTAGTGGCCGGGCAGG	0.662													G|||	565	0.112819	0.0151	0.085	5008	,	,		10068	0.1508		0.163	False		,,,				2504	0.1738				p.H27Y		Atlas-SNP	.											.	MRPL28	15	.	0			c.C79T						PASS	.	G	TYR/HIS	170,4194		7,156,2019	34.0	33.0	33.0		79	4.7	0.7	16	dbSNP_105	33	1457,7129		111,1235,2947	yes	missense	MRPL28	NM_006428.4	83	118,1391,4966	AA,AG,GG		16.9695,3.8955,12.5637	probably-damaging	27/257	420140	1627,11323	2182	4293	6475	SO:0001583	missense	10573	exon2			GGTAGTGGCCGGG	U19796	CCDS32349.1	16p13.12	2012-09-26	2002-11-13		ENSG00000086504	ENSG00000086504		"""Mitochondrial ribosomal proteins / large subunits"""	14484	protein-coding gene	gene with protein product		604853	"""melanoma-associated antigen recognised by cytotoxic T lymphocytes"""	MAAT1		11551941, 19753307	Standard	NM_006428		Approved	p15	uc002cgs.2	Q13084	OTTHUMG00000047994	ENST00000199706.8:c.79C>T	16.37:g.420140G>A	ENSP00000199706:p.His27Tyr	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	40	40	1	NM_006428	B2RCM4|D3DU46|Q4TT39|Q96S26|Q9BQD8|Q9BR04	Missense_Mutation	SNP	ENST00000199706.8	37	CCDS32349.1	225	0.10302197802197802	7	0.014227642276422764	33	0.09116022099447514	69	0.12062937062937062	116	0.15303430079155672	G	15.59	2.880014	0.51801	0.038955	0.169695	ENSG00000086504	ENST00000397735;ENST00000199706;ENST00000397734;ENST00000389675;ENST00000441883;ENST00000447696;ENST00000450882	T;T;T;T;T	0.33438	1.82;1.82;1.83;1.41;1.41	4.71	4.71	0.59529	.	0.000000	0.85682	D	0.000000	T	0.00300	0.0009	M	0.90595	3.13	0.22639	P	0.99890068	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.74023	0.966;0.966;0.982	T	0.13710	-1.0499	9	0.52906	T	0.07	-49.4999	13.0978	0.59202	0.0805:0.0:0.9195:0.0	rs3194151;rs17849390;rs3194151	27;27;27	A2IDC6;Q13084;Q4TT38	.;RM28_HUMAN;.	Y	27	ENSP00000199706:H27Y;ENSP00000374326:H27Y;ENSP00000398684:H27Y;ENSP00000390399:H27Y;ENSP00000395305:H27Y	ENSP00000199706:H27Y	H	-	1	0	MRPL28	360141	1.000000	0.71417	0.733000	0.30861	0.077000	0.17291	5.096000	0.64535	2.175000	0.68902	0.561000	0.74099	CAC	G|0.896;A|0.104	0.104	strong		0.662	MRPL28-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139285.2		
SNRNP48	154007	hgsc.bcm.edu	37	6	7590624	7590624	+	Missense_Mutation	SNP	C	C	T	rs2757594	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:7590624C>T	ENST00000342415.5	+	1	193	c.134C>T	c.(133-135)cCc>cTc	p.P45L		NM_152551.3	NP_689764.3	Q6IEG0	SNR48_HUMAN	small nuclear ribonucleoprotein 48kDa (U11/U12)	45			P -> L (in dbSNP:rs2757594). {ECO:0000269|PubMed:15489334}.		mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	U12-type spliceosomal complex (GO:0005689)	metal ion binding (GO:0046872)			kidney(2)|lung(5)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	10						AGTCTGGATCCCGGGGAAGAG	0.687													C|||	1070	0.213658	0.1415	0.2435	5008	,	,		12876	0.0744		0.3817	False		,,,				2504	0.2607				p.P45L		Atlas-SNP	.											.	SNRNP48	32	.	0			c.C134T						PASS	.	C	LEU/PRO	702,3610		72,558,1526	11.0	13.0	13.0		134	2.3	0.7	6	dbSNP_100	13	3045,5415		579,1887,1764	yes	missense	SNRNP48	NM_152551.3	98	651,2445,3290	TT,TC,CC		35.9929,16.2801,29.3376	benign	45/340	7590624	3747,9025	2156	4230	6386	SO:0001583	missense	154007	exon1			TGGATCCCGGGGA	AK056796	CCDS4502.1	6p24.3	2011-10-11	2008-10-29	2008-10-29	ENSG00000168566	ENSG00000168566			21368	protein-coding gene	gene with protein product	"""U11/U12 snRNP 48K"""		"""chromosome 6 open reading frame 151"""	C6orf151		15146077	Standard	XR_427825		Approved	FLJ32234, dJ512B11.2, dJ336K20B.1	uc003mxr.3	Q6IEG0	OTTHUMG00000014213	ENST00000342415.5:c.134C>T	6.37:g.7590624C>T	ENSP00000339834:p.Pro45Leu	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	100	58	0.58	NM_152551	A8K8P4|Q14C91|Q5T339|Q5THM1|Q5THM2|Q96MK1	Missense_Mutation	SNP	ENST00000342415.5	37	CCDS4502.1	507	0.23214285714285715	77	0.1565040650406504	103	0.2845303867403315	36	0.06293706293706294	291	0.3839050131926121	C	15.96	2.985607	0.53934	0.162801	0.359929	ENSG00000168566	ENST00000342415;ENST00000397475	T	0.30182	1.54	5.16	2.33	0.28932	.	0.471174	0.19972	N	0.101950	T	0.06325	0.0163	N	0.19112	0.55	0.28431	P	0.9172821	B	0.02656	0.0	B	0.06405	0.002	T	0.24584	-1.0156	9	0.33940	T	0.23	-0.0562	5.8231	0.18538	0.0:0.6621:0.1573:0.1807	rs2757594;rs17397753;rs52799491;rs59594751;rs2757594	45	Q6IEG0	SNR48_HUMAN	L	45	ENSP00000339834:P45L	ENSP00000339834:P45L	P	+	2	0	SNRNP48	7535623	0.012000	0.17670	0.748000	0.31131	0.993000	0.82548	0.390000	0.20768	0.545000	0.28902	0.563000	0.77884	CCC	C|0.778;T|0.222	0.222	strong		0.687	SNRNP48-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039787.3	NM_152551	
ZNF426	79088	hgsc.bcm.edu	37	19	9641722	9641722	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:9641722G>A	ENST00000535489.1	-	5	683	c.347C>T	c.(346-348)aCc>aTc	p.T116I	ZNF426_ENST00000253115.2_Missense_Mutation_p.T116I|ZNF426_ENST00000593003.1_Missense_Mutation_p.T78I|ZNF426_ENST00000589289.1_Intron			Q9BUY5	ZN426_HUMAN	zinc finger protein 426	116					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(7)|lung(3)|ovary(1)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	20						AGACCACTGGGTTTCAAGTCG	0.418																																					p.T116I		Atlas-SNP	.											.	ZNF426	56	.	0			c.C347T						PASS	.						110.0	104.0	106.0					19																	9641722		2203	4300	6503	SO:0001583	missense	79088	exon7			CACTGGGTTTCAA	AK095759	CCDS12215.1, CCDS74279.1	19p13.2	2013-01-08				ENSG00000130818		"""Zinc fingers, C2H2-type"", ""-"""	20725	protein-coding gene	gene with protein product							Standard	NM_024106		Approved	MGC2663	uc002mlq.3	Q9BUY5		ENST00000535489.1:c.347C>T	19.37:g.9641722G>A	ENSP00000439017:p.Thr116Ile	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	111	27	0.243243	NM_024106	B3KTL2	Missense_Mutation	SNP	ENST00000535489.1	37	CCDS12215.1	.	.	.	.	.	.	.	.	.	.	G	5.359	0.251581	0.10185	.	.	ENSG00000130818	ENST00000545189;ENST00000253115;ENST00000535489	T;T	0.06608	3.28;3.28	1.53	0.414	0.16406	.	.	.	.	.	T	0.04679	0.0127	L	0.29908	0.895	0.09310	N	1	B;B	0.21688	0.059;0.017	B;B	0.14023	0.01;0.006	T	0.39881	-0.9592	9	0.41790	T	0.15	.	5.6008	0.17353	0.0:0.3499:0.6501:0.0	.	103;116	Q59EH4;Q9BUY5	.;ZN426_HUMAN	I	103;116;116	ENSP00000253115:T116I;ENSP00000439017:T116I	ENSP00000253115:T116I	T	-	2	0	ZNF426	9502722	0.000000	0.05858	0.001000	0.08648	0.036000	0.12997	-0.134000	0.10436	0.183000	0.20059	0.460000	0.39030	ACC	.	.	none		0.418	ZNF426-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449905.1	NM_024106	
DYSF	8291	hgsc.bcm.edu	37	2	71795152	71795152	+	Silent	SNP	A	A	T	rs2288355	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:71795152A>T	ENST00000258104.3	+	25	2860	c.2583A>T	c.(2581-2583)tcA>tcT	p.S861S	DYSF_ENST00000413539.2_Silent_p.S892S|DYSF_ENST00000394120.2_Silent_p.S862S|DYSF_ENST00000409651.1_Silent_p.S893S|DYSF_ENST00000409366.1_Silent_p.S862S|DYSF_ENST00000409762.1_Silent_p.S878S|DYSF_ENST00000429174.2_Silent_p.S861S|DYSF_ENST00000409582.3_Silent_p.S878S|DYSF_ENST00000410020.3_Silent_p.S879S|DYSF_ENST00000410041.1_Silent_p.S879S|DYSF_ENST00000409744.1_Silent_p.S848S	NM_001130976.1|NM_003494.3	NP_001124448.1|NP_003485.1	O75923	DYSF_HUMAN	dysferlin	861					plasma membrane repair (GO:0001778)|vesicle fusion (GO:0006906)	cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|phospholipid binding (GO:0005543)			autonomic_ganglia(2)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|lung(57)|ovary(3)|pancreas(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(2)	111						TTGGGCTCTCAGTGGATGAGA	0.572													T|||	2757	0.550519	0.8147	0.5634	5008	,	,		17834	0.1925		0.663	False		,,,				2504	0.4376				p.S893S		Atlas-SNP	.											.	DYSF	536	.	0			c.A2679T						PASS	.	T	,,,,,,,,,,,,,	3563,843	332.0+/-302.3	1435,693,75	169.0	156.0	160.0		2586,2541,2541,2583,2676,2634,2634,2679,2586,2544,2637,2544,2637,2583	-0.7	1.0	2	dbSNP_100	160	5752,2848	447.7+/-361.6	1923,1906,471	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	DYSF	NM_001130455.1,NM_001130976.1,NM_001130977.1,NM_001130978.1,NM_001130979.1,NM_001130980.1,NM_001130981.1,NM_001130982.1,NM_001130983.1,NM_001130984.1,NM_001130985.1,NM_001130986.1,NM_001130987.1,NM_003494.3	,,,,,,,,,,,,,	3358,2599,546	TT,TA,AA		33.1163,19.133,28.3792	,,,,,,,,,,,,,	862/2082,847/2067,847/2088,861/2102,892/2112,878/2098,878/2119,893/2113,862/2103,848/2089,879/2099,848/2068,879/2120,861/2081	71795152	9315,3691	2203	4300	6503	SO:0001819	synonymous_variant	8291	exon26			GCTCTCAGTGGAT	AF075575	CCDS1918.1, CCDS46323.1, CCDS46324.1, CCDS46325.1, CCDS46326.1, CCDS46327.1, CCDS46328.1, CCDS46329.1, CCDS46330.1, CCDS46331.1, CCDS46332.1	2p13.3	2014-09-17	2013-09-12		ENSG00000135636	ENSG00000135636			3097	protein-coding gene	gene with protein product	"""fer-1-like family member 1"""	603009	"""limb girdle muscular dystrophy 2B (autosomal recessive)"""	LGMD2B		8320700	Standard	NM_003494		Approved	FER1L1	uc010fen.3	O75923	OTTHUMG00000129757	ENST00000258104.3:c.2583A>T	2.37:g.71795152A>T		Somatic	245	0	0		WXS	Illumina HiSeq	Phase_I	247	117	0.473684	NM_001130982	A0FK00|B1PZ70|B1PZ71|B1PZ72|B1PZ73|B1PZ74|B1PZ75|B1PZ76|B1PZ77|B1PZ78|B1PZ79|B1PZ80|B1PZ81|B3KQB9|O75696|Q09EX5|Q0H395|Q53QY3|Q53TD2|Q8TEL8|Q9UEN7	Silent	SNP	ENST00000258104.3	37	CCDS1918.1																																																																																			A|0.354;T|0.646	0.646	strong		0.572	DYSF-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251970.3	NM_003494	
MUC6	4588	hgsc.bcm.edu	37	11	1016851	1016851	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:1016851T>C	ENST00000421673.2	-	31	6000	c.5950A>G	c.(5950-5952)Atg>Gtg	p.M1984V		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming	1984	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)		GTTGCAGTCATAGGACCTGTG	0.582																																					p.M1984V		Atlas-SNP	.											MUC6_ENST00000421673,NS,carcinoma,+2,2	MUC6	408	2	0			c.A5950G						scavenged	.						1531.0	1522.0	1525.0					11																	1016851		2203	4298	6501	SO:0001583	missense	4588	exon31			CAGTCATAGGACC	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.5950A>G	11.37:g.1016851T>C	ENSP00000406861:p.Met1984Val	Somatic	754	22	0.0291777		WXS	Illumina HiSeq	Phase_I	1061	37	0.0348728	NM_005961	O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	Missense_Mutation	SNP	ENST00000421673.2	37	CCDS44513.1	.	.	.	.	.	.	.	.	.	.	C	1.757	-0.487796	0.04352	.	.	ENSG00000184956	ENST00000421673	T	0.17370	2.28	2.75	-1.23	0.09465	.	.	.	.	.	T	0.10809	0.0264	L	0.43152	1.355	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.45205	-0.9277	9	0.06365	T	0.9	.	7.0983	0.25321	0.0:0.1589:0.2688:0.5723	.	1984	Q6W4X9	MUC6_HUMAN	V	1984	ENSP00000406861:M1984V	ENSP00000406861:M1984V	M	-	1	0	MUC6	1006851	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-3.137000	0.00588	-0.732000	0.04856	-2.319000	0.00253	ATG	.	.	none		0.582	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382120.2	XM_290540	
TTLL4	9654	hgsc.bcm.edu	37	2	219602499	219602499	+	Missense_Mutation	SNP	G	G	C	rs3731877	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:219602499G>C	ENST00000392102.1	+	3	440	c.100G>C	c.(100-102)Gag>Cag	p.E34Q	TTLL4_ENST00000258398.4_Missense_Mutation_p.E34Q|TTLL4_ENST00000442769.1_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	141	0	0		WXS	Illumina HiSeq	Phase_I	144	144	1	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	
KIAA0226	9711	hgsc.bcm.edu	37	3	197432029	197432029	+	Silent	SNP	C	C	A	rs60457064	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:197432029C>A	ENST00000296343.5	-	3	236	c.237G>T	c.(235-237)acG>acT	p.T79T	KIAA0226_ENST00000449205.1_Silent_p.T79T|KIAA0226_ENST00000273582.5_Silent_p.T19T|KIAA0226_ENST00000389665.5_Silent_p.T79T|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	62	0	0		WXS	Illumina HiSeq	Phase_I	54	32	0.592593	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	
OR2D3	120775	hgsc.bcm.edu	37	11	6942628	6942628	+	Silent	SNP	A	A	C	rs11605995	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:6942628A>C	ENST00000317834.3	+	1	424	c.396A>C	c.(394-396)gcA>gcC	p.A132A		NM_001004684.1	NP_001004684.1	Q8NGH3	OR2D3_HUMAN	olfactory receptor, family 2, subfamily D, member 3	132						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(2)|large_intestine(7)|lung(12)|prostate(3)|skin(1)|stomach(1)	27		Medulloblastoma(188;0.0523)|all_neural(188;0.236)		Epithelial(150;4.78e-08)|BRCA - Breast invasive adenocarcinoma(625;0.129)		CGCTGCTGGCAGTGATGTCCT	0.483													C|||	2040	0.407348	0.6241	0.3329	5008	,	,		19923	0.4464		0.1948	False		,,,				2504	0.3456				p.A132A		Atlas-SNP	.											.	OR2D3	51	.	0			c.A396C						PASS	.	C		2479,1923	547.5+/-377.3	692,1095,414	165.0	155.0	158.0		396	-10.1	0.0	11	dbSNP_120	158	1701,6891	738.4+/-407.1	172,1357,2767	no	coding-synonymous	OR2D3	NM_001004684.1		864,2452,3181	CC,CA,AA		19.7975,43.6847,32.1687		132/331	6942628	4180,8814	2201	4296	6497	SO:0001819	synonymous_variant	120775	exon1			GCTGGCAGTGATG	BK004294	CCDS31417.1	11p15.4	2012-08-09			ENSG00000178358	ENSG00000178358		"""GPCR / Class A : Olfactory receptors"""	15146	protein-coding gene	gene with protein product							Standard	NM_001004684		Approved		uc010rav.2	Q8NGH3	OTTHUMG00000165742	ENST00000317834.3:c.396A>C	11.37:g.6942628A>C		Somatic	283	0	0		WXS	Illumina HiSeq	Phase_I	268	223	0.83209	NM_001004684	B2RP06|Q6IFG8|Q96R51	Silent	SNP	ENST00000317834.3	37	CCDS31417.1																																																																																			A|0.655;C|0.345	0.345	strong		0.483	OR2D3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385987.1	NM_001004684	
CHRNA3	1136	hgsc.bcm.edu	37	15	78911181	78911181	+	Silent	SNP	T	T	C	rs8040868	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:78911181T>C	ENST00000326828.5	-	2	543	c.159A>G	c.(157-159)gtA>gtG	p.V53V	CHRNA3_ENST00000559941.1_5'Flank|CHRNA3_ENST00000348639.3_Silent_p.V53V	NM_000743.4	NP_000734.2	P32297	ACHA3_HUMAN	cholinergic receptor, nicotinic, alpha 3 (neuronal)	53					activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|behavioral response to nicotine (GO:0035095)|cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|locomotory behavior (GO:0007626)|nervous system development (GO:0007399)|regulation of acetylcholine secretion, neurotransmission (GO:0014056)|regulation of dendrite morphogenesis (GO:0048814)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of membrane potential (GO:0042391)|regulation of smooth muscle contraction (GO:0006940)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission involved in micturition (GO:0060084)|synaptic transmission, cholinergic (GO:0007271)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|ligand-gated ion channel activity (GO:0015276)			central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18					Bupropion(DB01156)|Dextromethorphan(DB00514)|Galantamine(DB00674)|Levomethadyl Acetate(DB01227)|Nicotine(DB00184)|Pentolinium(DB01090)|Varenicline(DB01273)	ACACGTTGGCTACAGGCCGGA	0.572											OREG0023334	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	1645	0.328474	0.3533	0.2795	5008	,	,		18663	0.3542		0.4165	False		,,,				2504	0.2127				p.V53V		Atlas-SNP	.											.	CHRNA3	56	.	0			c.A159G						PASS	.	C	,	1475,2917	677.4+/-403.4	235,1005,956	87.0	76.0	80.0		159,159	3.9	1.0	15	dbSNP_116	80	3524,5062	631.5+/-398.5	754,2016,1523	no	coding-synonymous,coding-synonymous	CHRNA3	NM_000743.4,NM_001166694.1	,	989,3021,2479	CC,CT,TT	http://www.ncbi.nlm.nih.gov/pubmed?term	41.0436,33.5838,38.519	,	53/506,53/490	78911181	4999,7979	2196	4293	6489	SO:0001819	synonymous_variant	1136	exon2			GTTGGCTACAGGC		CCDS10305.1, CCDS53964.1	15q24	2012-02-11	2012-02-07		ENSG00000080644	ENSG00000080644		"""Cholinergic receptors"", ""Ligand-gated ion channels / Acetylcholine receptors, nicotinic"""	1957	protein-coding gene	gene with protein product	"""acetylcholine receptor, nicotinic, alpha 3 (neuronal)"""	118503	"""cholinergic receptor, nicotinic, alpha polypeptide 3"""			2004777	Standard	NM_000743		Approved		uc002bec.3	P32297	OTTHUMG00000143863	ENST00000326828.5:c.159A>G	15.37:g.78911181T>C		Somatic	93	0	0	1187	WXS	Illumina HiSeq	Phase_I	90	90	1	NM_000743	Q15823|Q4KMN8|Q86U77|Q96RH3|Q99553|Q9BQ93|Q9BRR4	Silent	SNP	ENST00000326828.5	37	CCDS10305.1																																																																																			T|0.616;C|0.384	0.384	strong		0.572	CHRNA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000290111.3		
WDFY4	57705	hgsc.bcm.edu	37	10	49998824	49998824	+	Silent	SNP	C	C	T	rs10857644	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:49998824C>T	ENST00000325239.5	+	22	4146	c.4119C>T	c.(4117-4119)ggC>ggT	p.G1373G	WDFY4_ENST00000413659.2_Intron	NM_020945.1	NP_065996.1	Q6ZS81	WDFY4_HUMAN	WDFY family member 4	1373						integral component of membrane (GO:0016021)				NS(2)|breast(5)|central_nervous_system(4)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|lung(3)|pancreas(2)|prostate(5)|skin(6)|stomach(1)	48						ACTTCATTGGCGGGCCTGCCA	0.547													C|||	849	0.169529	0.3147	0.0922	5008	,	,		21863	0.1577		0.0924	False		,,,				2504	0.1196				p.G1373G		Atlas-SNP	.											WDFY4,colon,carcinoma,0,1	WDFY4	205	1	0			c.C4119T						scavenged	.						72.0	62.0	65.0					10																	49998824		692	1591	2283	SO:0001819	synonymous_variant	57705	exon23			CATTGGCGGGCCT	AK074085	CCDS44385.1	10q11.23	2013-01-10			ENSG00000128815	ENSG00000128815		"""WD repeat domain containing"""	29323	protein-coding gene	gene with protein product		613316	"""chromosome 10 open reading frame 64"""	C10orf64		10997877	Standard	NM_020945		Approved	KIAA1607, Em:AC060234.3, FLJ45748	uc001jha.4	Q6ZS81	OTTHUMG00000018180	ENST00000325239.5:c.4119C>T	10.37:g.49998824C>T		Somatic	165	1	0.00606061		WXS	Illumina HiSeq	Phase_I	161	79	0.490683	NM_020945	B9ZVP2|Q86WZ4|Q8N4A3|Q8TEN7|Q96BE1|Q9H7H8|Q9HCG5	Silent	SNP	ENST00000325239.5	37	CCDS44385.1	364	0.16666666666666666	153	0.31097560975609756	40	0.11049723756906077	95	0.1660839160839161	76	0.10026385224274406	C	9.198	1.027641	0.19512	.	.	ENSG00000128815	ENST00000312002	.	.	.	5.18	-8.28	0.01013	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.99999985119	.	.	.	.	.	.	T	0.20605	-1.0270	3	.	.	.	.	7.56	0.27845	0.275:0.1759:0.0:0.5492	rs10857644;rs56445870;rs10857644	.	.	.	W	464	.	.	R	+	1	2	WDFY4	49668830	0.000000	0.05858	0.272000	0.24630	0.996000	0.88848	-2.359000	0.01085	-1.729000	0.01364	0.557000	0.71058	CGG	C|0.834;T|0.166	0.166	strong		0.547	WDFY4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		XM_033379	
UGT2B7	7364	hgsc.bcm.edu	37	4	69964337	69964337	+	Silent	SNP	A	A	T	rs7438284|rs386675647	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:69964337A>T	ENST00000508661.1	+	2	828	c.801A>T	c.(799-801)ccA>ccT	p.P267P	UGT2B7_ENST00000305231.7_Silent_p.P267P|UGT2B7_ENST00000509763.1_3'UTR			P16662	UD2B7_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide B7	267					androgen metabolic process (GO:0008209)|cellular glucuronidation (GO:0052695)|lipid metabolic process (GO:0006629)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	glucuronosyltransferase activity (GO:0015020)	p.P267P(1)		autonomic_ganglia(1)|endometrium(3)|kidney(4)|large_intestine(6)|lung(16)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	38					Atorvastatin(DB01076)|Carbamazepine(DB00564)|Chenodeoxycholic acid(DB06777)|Codeine(DB00318)|Dabigatran etexilate(DB06695)|Dapagliflozin(DB06292)|Diclofenac(DB00586)|Epirubicin(DB00445)|Etodolac(DB00749)|Ezetimibe(DB00973)|Flunitrazepam(DB01544)|Flurbiprofen(DB00712)|Fluvastatin(DB01095)|Ibuprofen(DB01050)|Indomethacin(DB00328)|Losartan(DB00678)|Lovastatin(DB00227)|Mitiglinide(DB01252)|Morphine(DB00295)|Mycophenolate mofetil(DB00688)|Mycophenolic acid(DB01024)|Naproxen(DB00788)|Oxazepam(DB00842)|Pitavastatin(DB08860)|Silodosin(DB06207)|Simvastatin(DB00641)|Suprofen(DB00870)|Tapentadol(DB06204)|Valproic Acid(DB00313)|Zidovudine(DB00495)	TTCAGTTTCCATATCCACTCT	0.393													A|||	3331	0.665136	0.7731	0.6801	5008	,	,		15416	0.7252		0.5149	False		,,,				2504	0.6012				p.P267P		Atlas-SNP	.											UGT2B7,NS,carcinoma,0,1	UGT2B7	79	1	1	Substitution - coding silent(1)	prostate(1)	c.A801T						PASS	.	A		1148,3258		400,348,1455	156.0	160.0	159.0		801	-0.1	0.2	4	dbSNP_116	159	986,7614		316,354,3630	no	coding-synonymous	UGT2B7	NM_001074.2		716,702,5085	TT,TA,AA		11.4651,26.0554,16.4078		267/530	69964337	2134,10872	2203	4300	6503	SO:0001819	synonymous_variant	7364	exon2			GTTTCCATATCCA	BC030974	CCDS3526.1	4q13	2008-02-05	2005-07-20		ENSG00000171234	ENSG00000171234		"""UDP glucuronosyltransferases"""	12554	protein-coding gene	gene with protein product		600068	"""UDP glycosyltransferase 2 family, polypeptide B7"""			2159463, 7835904	Standard	NM_001074		Approved	UGT2B9	uc003heg.4	P16662	OTTHUMG00000129404	ENST00000508661.1:c.801A>T	4.37:g.69964337A>T		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	138	90	0.652174	NM_001074	B2R810|Q6GTW0	Silent	SNP	ENST00000508661.1	37																																																																																				A|0.452;T|0.548	0.548	strong		0.393	UGT2B7-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000362103.1	NM_001074	
CDH23	64072	hgsc.bcm.edu	37	10	73434888	73434888	+	Missense_Mutation	SNP	G	G	C	rs1227049	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:73434888G>C	ENST00000224721.6	+	14	1489	c.1484G>C	c.(1483-1485)gGc>gCc	p.G495A	CDH23_ENST00000299366.7_Missense_Mutation_p.G535A	NM_022124.5	NP_071407.4	Q9H251	CAD23_HUMAN	cadherin-related 23	490	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium ion transport (GO:0006816)|calcium-dependent cell-cell adhesion (GO:0016339)|cytosolic calcium ion homeostasis (GO:0051480)|equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(6)|endometrium(15)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(27)|lung(49)|ovary(3)|pancreas(1)|prostate(7)|stomach(7)|upper_aerodigestive_tract(3)	133						AATGATGCAGGCACCTTTGGG	0.582													G|||	928	0.185304	0.0113	0.1455	5008	,	,		21889	0.2887		0.1948	False		,,,				2504	0.3323				p.G490A		Atlas-SNP	.											.	CDH23	365	.	0			c.G1469C						PASS	.	G	ALA/GLY,ALA/GLY,ALA/GLY	149,4055		5,139,1958	93.0	97.0	95.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1469,1469,1469	5.7	1.0	10	dbSNP_87	95	1387,7083		113,1161,2961	yes	missense,missense,missense	CDH23	NM_001171930.1,NM_001171931.1,NM_022124.5	60,60,60	118,1300,4919	CC,CG,GG		16.3754,3.5442,12.1193	probably-damaging,probably-damaging,probably-damaging	490/1382,490/1062,490/3355	73434888	1536,11138	2102	4235	6337	SO:0001583	missense	64072	exon14			ATGCAGGCACCTT	AY010111	CCDS53540.1, CCDS73146.1	10q22.1	2014-08-08	2010-01-25		ENSG00000107736	ENSG00000107736		"""Cadherins / Cadherin-related"""	13733	protein-coding gene	gene with protein product	"""cadherin-related family member 23"""	605516	"""cadherin related 23"", ""cadherin-like 23"""	DFNB12, USH1D		11090341	Standard	NM_022124		Approved	CDHR23	uc001jrx.4	Q9H251	OTTHUMG00000019347	ENST00000224721.6:c.1484G>C	10.37:g.73434888G>C	ENSP00000224721:p.Gly495Ala	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	58	26	0.448276	NM_022124	C4IXS9|F6U049|Q5QGS1|Q5QGS2|Q5QGS5|Q5QGS6|Q5XKN2|Q6UWW1|Q96JL3|Q9H4K9	Missense_Mutation	SNP	ENST00000224721.6	37		365	0.1671245421245421	7	0.014227642276422764	46	0.1270718232044199	158	0.2762237762237762	154	0.20316622691292877	G	21.9	4.222763	0.79464	0.035442	0.163754	ENSG00000107736	ENST00000398860;ENST00000398855;ENST00000398828;ENST00000299366;ENST00000224721;ENST00000442677	.	.	.	5.72	5.72	0.89469	Cadherin (4);Cadherin-like (1);	0.000000	0.85682	D	0.000000	T	0.00039	0.0001	M	0.88310	2.945	0.09310	P	1.0	P;D;D	0.89917	0.855;1.0;1.0	P;D;D	0.91635	0.842;0.998;0.999	T	0.00210	-1.1916	8	0.66056	D	0.02	.	19.8786	0.96886	0.0:0.0:1.0:0.0	rs1227049;rs1665702;rs52829568;rs1227049	490;493;490	Q6P152;G3XCN8;Q9H251	.;.;CAD23_HUMAN	A	495;490;490;493;493;7	.	ENSP00000224721:G495A	G	+	2	0	CDH23	73104894	1.000000	0.71417	1.000000	0.80357	0.594000	0.36715	8.658000	0.91110	2.693000	0.91896	0.655000	0.94253	GGC	G|0.821;C|0.179	0.179	strong		0.582	CDH23-001	PUTATIVE	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051227.4	NM_052836	
OR5P2	120065	hgsc.bcm.edu	37	11	7817852	7817852	+	Missense_Mutation	SNP	C	C	G	rs76615008	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:7817852C>G	ENST00000329434.2	-	1	668	c.638G>C	c.(637-639)tGc>tCc	p.C213S	RP11-35J10.5_ENST00000527565.1_lincRNA	NM_153444.1	NP_703145.1	Q8WZ92	OR5P2_HUMAN	olfactory receptor, family 5, subfamily P, member 2	213						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(4)	22				Epithelial(150;8.62e-08)|BRCA - Breast invasive adenocarcinoma(625;0.189)		ATAGATGTAGCAGACGGCTAT	0.493													G|||	1185	0.236621	0.3472	0.2911	5008	,	,		18597	0.128		0.2763	False		,,,				2504	0.1196				p.C213S		Atlas-SNP	.											.	OR5P2	68	.	0			c.G638C						PASS	.	G	SER/CYS	1372,2840		401,570,1135	99.0	103.0	102.0		638	5.5	1.0	11	dbSNP_131	102	2424,6160		393,1638,2261	no	missense	OR5P2	NM_153444.1	112	794,2208,3396	GG,GC,CC		28.2386,32.5736,29.6655	benign	213/323	7817852	3796,9000	2106	4292	6398	SO:0001583	missense	120065	exon1			ATGTAGCAGACGG	AF173006	CCDS7782.1	11p15.4	2012-08-09			ENSG00000183303	ENSG00000183303		"""GPCR / Class A : Olfactory receptors"""	14783	protein-coding gene	gene with protein product							Standard	NM_153444		Approved	JCG3	uc001mfp.1	Q8WZ92	OTTHUMG00000165668	ENST00000329434.2:c.638G>C	11.37:g.7817852C>G	ENSP00000331823:p.Cys213Ser	Somatic	197	0	0		WXS	Illumina HiSeq	Phase_I	178	141	0.792135	NM_153444	Q3MIS8	Missense_Mutation	SNP	ENST00000329434.2	37	CCDS7782.1	586	0.2683150183150183	180	0.36585365853658536	100	0.27624309392265195	84	0.14685314685314685	222	0.2928759894459103	G	1.419	-0.573385	0.03882	0.325736	0.282386	ENSG00000183303	ENST00000329434	T	0.35048	1.33	5.5	5.5	0.81552	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	N	0.000004	T	0.00012	0.0000	N	0.00000	-3.99	0.48975	P	2.609999999999557E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.48514	-0.9029	9	0.02654	T	1	-60.4257	14.3625	0.66782	0.0:0.1489:0.8511:0.0	.	213	Q8WZ92	OR5P2_HUMAN	S	213	ENSP00000331823:C213S	ENSP00000331823:C213S	C	-	2	0	OR5P2	7774428	1.000000	0.71417	0.985000	0.45067	0.597000	0.36814	3.226000	0.51254	1.580000	0.49851	-0.225000	0.12378	TGC	C|0.738;G|0.262	0.262	strong		0.493	OR5P2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385696.1	NM_153444	
OR2T4	127074	hgsc.bcm.edu	37	1	248525639	248525639	+	Missense_Mutation	SNP	A	A	T	rs34079073|rs76878172	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:248525639A>T	ENST00000366475.1	+	1	757	c.757A>T	c.(757-759)Atc>Ttc	p.I253F		NM_001004696.1	NP_001004696.1	Q8NH00	OR2T4_HUMAN	olfactory receptor, family 2, subfamily T, member 4	253						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|liver(2)|lung(47)	56	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			CTATTTACTCATCCTCCTCAC	0.522																																					p.I253F		Atlas-SNP	.											OR2T4,brain,glioma,0,1	OR2T4	126	1	0			c.A757T						scavenged	.						94.0	74.0	81.0					1																	248525639		2024	3426	5450	SO:0001583	missense	127074	exon1			TTACTCATCCTCC	BK004464	CCDS31113.1	1q44	2012-08-09			ENSG00000196944	ENSG00000196944		"""GPCR / Class A : Olfactory receptors"""	15016	protein-coding gene	gene with protein product							Standard	NM_001004696		Approved	OR2T4Q	uc001ieh.1	Q8NH00	OTTHUMG00000040453	ENST00000366475.1:c.757A>T	1.37:g.248525639A>T	ENSP00000355431:p.Ile253Phe	Somatic	662	312	0.471299		WXS	Illumina HiSeq	Phase_I	508	225	0.442913	NM_001004696	Q6IEZ8	Missense_Mutation	SNP	ENST00000366475.1	37	CCDS31113.1	.	.	.	.	.	.	.	.	.	.	A	13.48	2.250012	0.39797	.	.	ENSG00000196944	ENST00000366475	T	0.00414	7.52	3.09	3.09	0.35607	GPCR, rhodopsin-like superfamily (1);	0.000000	0.47852	D	0.000219	T	0.01835	0.0058	H	0.96142	3.775	0.40727	D	0.98271	D	0.89917	1.0	D	0.85130	0.997	T	0.25117	-1.0141	10	0.87932	D	0	.	11.1471	0.48436	1.0:0.0:0.0:0.0	.	253	Q8NH00	OR2T4_HUMAN	F	253	ENSP00000355431:I253F	ENSP00000355431:I253F	I	+	1	0	OR2T4	246592262	1.000000	0.71417	0.050000	0.19076	0.010000	0.07245	7.329000	0.79170	1.264000	0.44198	0.477000	0.44152	ATC	.	.	alt		0.522	OR2T4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097349.2	NM_001004696	
KCTD16	57528	hgsc.bcm.edu	37	5	143853421	143853421	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:143853421G>A	ENST00000507359.3	+	3	2122	c.1031G>A	c.(1030-1032)cGt>cAt	p.R344H	KCTD16_ENST00000512467.1_Missense_Mutation_p.R344H	NM_020768.3	NP_065819.1	Q68DU8	KCD16_HUMAN	potassium channel tetramerization domain containing 16	344					protein homooligomerization (GO:0051260)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	cell junction (GO:0030054)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|receptor complex (GO:0043235)		p.R344H(1)		large_intestine(5)|lung(9)|ovary(2)|prostate(1)|skin(3)|urinary_tract(1)	21		all_hematologic(541;0.118)	KIRC - Kidney renal clear cell carcinoma(527;0.00111)|Kidney(363;0.00176)			ACTCTGGACCGTCCCATCAAG	0.587																																					p.R344H		Atlas-SNP	.											KCTD16,NS,carcinoma,+1,3	KCTD16	70	3	1	Substitution - Missense(1)	large_intestine(1)	c.G1031A						scavenged	.						76.0	74.0	74.0					5																	143853421		2203	4300	6503	SO:0001583	missense	57528	exon4			TGGACCGTCCCAT	AB037738	CCDS34260.1	5q32	2013-06-20	2013-06-20		ENSG00000183775	ENSG00000183775			29244	protein-coding gene	gene with protein product		613423	"""potassium channel tetramerisation domain containing 16"""			10718198	Standard	NM_020768		Approved	KIAA1317	uc003lnm.1	Q68DU8	OTTHUMG00000163172	ENST00000507359.3:c.1031G>A	5.37:g.143853421G>A	ENSP00000426548:p.Arg344His	Somatic	190	0	0		WXS	Illumina HiSeq	Phase_I	198	3	0.0151515	NM_020768	Q9P2M9	Missense_Mutation	SNP	ENST00000507359.3	37	CCDS34260.1	.	.	.	.	.	.	.	.	.	.	G	29.0	4.966455	0.92855	.	.	ENSG00000183775	ENST00000512467;ENST00000507359	T;T	0.52526	0.66;0.66	6.17	6.17	0.99709	.	0.067878	0.52532	D	0.000065	T	0.62986	0.2473	L	0.36672	1.1	0.54753	D	0.999983	D	0.76494	0.999	D	0.73380	0.98	T	0.62129	-0.6919	10	0.87932	D	0	.	20.8794	0.99867	0.0:0.0:1.0:0.0	.	344	Q68DU8	KCD16_HUMAN	H	344	ENSP00000424151:R344H;ENSP00000426548:R344H	ENSP00000426548:R344H	R	+	2	0	KCTD16	143833614	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.363000	0.97131	2.941000	0.99782	0.655000	0.94253	CGT	.	.	none		0.587	KCTD16-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371898.3	XM_098368	
IL12RB1	3594	hgsc.bcm.edu	37	19	18188408	18188408	+	Missense_Mutation	SNP	C	C	T	rs11575926	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:18188408C>T	ENST00000600835.2	-	6	765	c.467G>A	c.(466-468)cGt>cAt	p.R156H	IL12RB1_ENST00000593993.2_Missense_Mutation_p.R156H|IL12RB1_ENST00000322153.7_Missense_Mutation_p.R156H			P42701	I12R1_HUMAN	interleukin 12 receptor, beta 1	156	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.		R -> H (in dbSNP:rs11575926). {ECO:0000269|Ref.3}.		cellular response to interferon-gamma (GO:0071346)|cytokine-mediated signaling pathway (GO:0019221)|interleukin-12-mediated signaling pathway (GO:0035722)|interleukin-23-mediated signaling pathway (GO:0038155)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of memory T cell differentiation (GO:0043382)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|positive regulation of T-helper 1 type immune response (GO:0002827)|positive regulation of T-helper 17 cell lineage commitment (GO:2000330)|positive regulation of T-helper 17 type immune response (GO:2000318)|signal transduction (GO:0007165)	external side of plasma membrane (GO:0009897)|interleukin-12 receptor complex (GO:0042022)|interleukin-23 receptor complex (GO:0072536)	cytokine receptor activity (GO:0004896)			endometrium(1)|kidney(1)|lung(3)|pancreas(1)|skin(2)	8						CCACTCCATACGCAGCTGCCC	0.582													C|||	280	0.0559105	0.0068	0.0692	5008	,	,		16517	0.001		0.1551	False		,,,				2504	0.0675				p.R156H		Atlas-SNP	.											.	IL12RB1	92	.	0			c.G467A						PASS	.	C	HIS/ARG,HIS/ARG	158,4248	107.8+/-146.2	3,152,2048	65.0	54.0	58.0		467,467	-7.8	0.0	19	dbSNP_120	58	1494,7106	283.3+/-296.1	127,1240,2933	no	missense,missense	IL12RB1	NM_005535.1,NM_153701.1	29,29	130,1392,4981	TT,TC,CC		17.3721,3.586,12.7018	benign,benign	156/663,156/382	18188408	1652,11354	2203	4300	6503	SO:0001583	missense	3594	exon5			TCCATACGCAGCT	U03187	CCDS32957.1, CCDS54232.1	19p13.1	2014-09-17						"""Interleukins and interleukin receptors"", ""CD molecules"", ""Fibronectin type III domain containing"""	5971	protein-coding gene	gene with protein product		601604		IL12RB		9284929	Standard	XM_005259893		Approved	CD212	uc002nhw.1	P42701		ENST00000600835.2:c.467G>A	19.37:g.18188408C>T	ENSP00000470788:p.Arg156His	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	94	47	0.5	NM_153701	A8K308|B2RPF1|B7ZKK3|Q8N6Q7	Missense_Mutation	SNP	ENST00000600835.2	37	CCDS54232.1	146	0.06684981684981685	2	0.0040650406504065045	26	0.0718232044198895	1	0.0017482517482517483	117	0.15435356200527706	C	9.619	1.133424	0.21041	0.03586	0.173721	ENSG00000096996	ENST00000430026;ENST00000322153	T;D	0.85955	-1.49;-2.05	3.9	-7.79	0.01218	Immunoglobulin-like fold (1);	1.817980	0.03453	N	0.210996	T	0.00440	0.0014	L	0.29908	0.895	0.09310	N	1	B;B;B	0.29862	0.025;0.259;0.014	B;B;B	0.17433	0.007;0.018;0.003	T	0.18023	-1.0350	10	0.30854	T	0.27	-1.1907	6.7248	0.23350	0.6568:0.1478:0.0:0.1953	rs11575926;rs17884715	156;156;156	P42701-2;P42701-3;P42701	.;.;I12R1_HUMAN	H	156	ENSP00000403103:R156H;ENSP00000314425:R156H	ENSP00000314425:R156H	R	-	2	0	IL12RB1	18049408	0.000000	0.05858	0.001000	0.08648	0.015000	0.08874	-1.507000	0.02268	-1.510000	0.01796	-0.302000	0.09304	CGT	C|0.900;T|0.100	0.100	strong		0.582	IL12RB1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466525.3		
OR1S2	219958	hgsc.bcm.edu	37	11	57970981	57970981	+	Missense_Mutation	SNP	C	C	T	rs11229278|rs34249289	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:57970981C>T	ENST00000302592.6	-	1	672	c.673G>A	c.(673-675)Gta>Ata	p.V225I		NM_001004459.1	NP_001004459.1	Q8NGQ3	OR1S2_HUMAN	olfactory receptor, family 1, subfamily S, member 2	225			V -> A (in dbSNP:rs11229277).|V -> I (in dbSNP:rs11229278).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(11)|kidney(1)|large_intestine(4)|lung(23)|ovary(2)|skin(2)|stomach(2)|urinary_tract(1)	46		Breast(21;0.0589)				AAGATGAGTACAAAGGGGAAG	0.458													C|||	426	0.0850639	0.0265	0.1138	5008	,	,		23191	0.0556		0.1083	False		,,,				2504	0.1503				p.V225I		Atlas-SNP	.											.	OR1S2	119	.	0			c.G673A						PASS	.						165.0	137.0	146.0					11																	57970981		2201	4296	6497	SO:0001583	missense	219958	exon1			TGAGTACAAAGGG	BK004297	CCDS31545.1	11q12.1	2012-08-09			ENSG00000197887	ENSG00000197887		"""GPCR / Class A : Olfactory receptors"""	15141	protein-coding gene	gene with protein product							Standard	NM_001004459		Approved		uc010rkb.2	Q8NGQ3	OTTHUMG00000167541	ENST00000302592.6:c.673G>A	11.37:g.57970981C>T	ENSP00000305469:p.Val225Ile	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	103	24	0.23301	NM_001004459	Q6IFG5|Q96R85	Missense_Mutation	SNP	ENST00000302592.6	37	CCDS31545.1	109	0.04990842490842491	13	0.026422764227642278	27	0.07458563535911603	19	0.033216783216783216	50	0.06596306068601583	C	0.180	-1.063021	0.01950	.	.	ENSG00000197887	ENST00000302592	T	0.36699	1.24	4.75	2.83	0.33086	GPCR, rhodopsin-like superfamily (1);	0.471664	0.17897	N	0.158338	T	0.01387	0.0045	N	0.05383	-0.06	0.80722	P	0.0	B	0.14805	0.011	B	0.23852	0.049	T	0.12426	-1.0548	9	0.17369	T	0.5	.	12.7854	0.57502	0.2978:0.7022:0.0:0.0	rs11229278;rs52811080;rs11229278	225	Q8NGQ3	OR1S2_HUMAN	I	225	ENSP00000305469:V225I	ENSP00000305469:V225I	V	-	1	0	OR1S2	57727557	0.000000	0.05858	0.426000	0.26672	0.853000	0.48598	-1.185000	0.03073	0.691000	0.31592	0.655000	0.94253	GTA	C|0.931;T|0.069	0.069	strong		0.458	OR1S2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394703.2	NM_001004459	
UBR2	23304	hgsc.bcm.edu	37	6	42627430	42627430	+	Silent	SNP	C	C	T	rs6916713	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:42627430C>T	ENST00000372899.1	+	30	3537	c.3279C>T	c.(3277-3279)ggC>ggT	p.G1093G	UBR2_ENST00000372901.1_Silent_p.G1093G|UBR2_ENST00000372883.3_3'UTR	NM_015255.2	NP_056070.1	Q8IWV8	UBR2_HUMAN	ubiquitin protein ligase E3 component n-recognin 2	1093					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)			CAGCACTGGGCCCCGCACAAA	0.398													C|||	1265	0.252596	0.2042	0.1988	5008	,	,		16291	0.3026		0.2972	False		,,,				2504	0.2587				p.G1093G		Atlas-SNP	.											.	UBR2	134	.	0			c.C3279T						PASS	.	C		949,3457	359.9+/-315.0	105,739,1359	86.0	79.0	81.0		3279	0.6	1.0	6	dbSNP_116	81	2484,6116	405.5+/-348.5	360,1764,2176	no	coding-synonymous	UBR2	NM_015255.2		465,2503,3535	TT,TC,CC		28.8837,21.5388,26.3955		1093/1756	42627430	3433,9573	2203	4300	6503	SO:0001819	synonymous_variant	23304	exon30			ACTGGGCCCCGCA	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.3279C>T	6.37:g.42627430C>T		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	77	40	0.519481	NM_015255	O15057|Q4VXK2|Q5TFH6|Q6P2I2|Q6ZUD0	Silent	SNP	ENST00000372899.1	37	CCDS4870.1																																																																																			C|0.739;T|0.261	0.261	strong		0.398	UBR2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040558.2	NM_015255	
LTN1	26046	hgsc.bcm.edu	37	21	30339120	30339120	+	Missense_Mutation	SNP	C	C	A	rs34191159	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:30339120C>A	ENST00000361371.5	-	10	1772	c.1693G>T	c.(1693-1695)Ggc>Tgc	p.G565C	LTN1_ENST00000389195.2_Missense_Mutation_p.G611C|LTN1_ENST00000389194.2_Missense_Mutation_p.G611C			O94822	LTN1_HUMAN	listerin E3 ubiquitin protein ligase 1	565			G -> C (in dbSNP:rs34191159).		protein ubiquitination (GO:0016567)		ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(1)|endometrium(4)|kidney(5)|large_intestine(12)|lung(19)|ovary(5)|pancreas(1)|prostate(2)|skin(6)|stomach(2)|upper_aerodigestive_tract(2)	60						AATTCCCAGCCTTCAATCTTC	0.353													C|||	970	0.19369	0.087	0.255	5008	,	,		20229	0.3849		0.1779	False		,,,				2504	0.1135				p.G611C		Atlas-SNP	.											.	LTN1	141	.	0			c.G1831T						PASS	.	C	CYS/GLY	422,3984	205.8+/-227.6	20,382,1801	60.0	55.0	57.0		1831	2.0	0.0	21	dbSNP_126	57	1351,7249	262.1+/-284.2	110,1131,3059	yes	missense	LTN1	NM_015565.2	159	130,1513,4860	AA,AC,CC		15.7093,9.5778,13.6322	probably-damaging	611/1813	30339120	1773,11233	2203	4300	6503	SO:0001583	missense	26046	exon10			CCCAGCCTTCAAT	AK001915	CCDS33527.1, CCDS33527.2	21q21.3	2013-01-09	2010-09-17	2010-09-17	ENSG00000198862	ENSG00000198862		"""RING-type (C3HC4) zinc fingers"""	13082	protein-coding gene	gene with protein product	"""listerin"""	613083	"""chromosome 21 open reading frame 98"", ""zinc finger protein 294"", ""ring finger protein 160"""	C21orf98, C21orf10, ZNF294, RNF160		20835226, 19196968	Standard	NM_015565		Approved	KIAA0714, FLJ11053, LISTERIN	uc002ymr.2	O94822	OTTHUMG00000078803	ENST00000361371.5:c.1693G>T	21.37:g.30339120C>A	ENSP00000354977:p.Gly565Cys	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	75	25	0.333333	NM_015565	A6NL41|A7E2D0|B2RTS0|C9J7U3|J3KPL4|Q05C47|Q9H8M4|Q9NUY5|Q9P0E9	Missense_Mutation	SNP	ENST00000361371.5	37		505	0.23122710622710624	49	0.09959349593495935	86	0.23756906077348067	233	0.40734265734265734	137	0.18073878627968337	C	9.941	1.217596	0.22373	0.095778	0.157093	ENSG00000198862	ENST00000389194;ENST00000361371;ENST00000389195	T;T;T	0.25414	2.15;2.16;1.8	4.75	1.97	0.26223	.	0.980624	0.08386	N	0.953805	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	D	0.69078	0.997	P	0.55667	0.781	T	0.47812	-0.9088	9	0.48119	T	0.1	.	6.5089	0.22210	0.0:0.7009:0.0:0.2991	rs34191159	565	O94822	LTN1_HUMAN	C	611;565;611	ENSP00000373846:G611C;ENSP00000354977:G565C;ENSP00000373847:G611C	ENSP00000354977:G565C	G	-	1	0	LTN1	29260991	0.010000	0.17322	0.002000	0.10522	0.002000	0.02628	0.745000	0.26259	0.318000	0.23185	-0.145000	0.13849	GGC	C|0.836;A|0.164	0.164	strong		0.353	LTN1-008	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000472108.1	NM_015565	
ROBO1	6091	hgsc.bcm.edu	37	3	78717343	78717343	+	Silent	SNP	C	C	T	rs2271151	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:78717343C>T	ENST00000464233.1	-	13	1853	c.1740G>A	c.(1738-1740)tcG>tcA	p.S580S	ROBO1_ENST00000436010.2_Silent_p.S541S|ROBO1_ENST00000495273.1_Silent_p.S544S|ROBO1_ENST00000467549.1_Silent_p.S544S	NM_002941.3	NP_002932.1	Q9Y6N7	ROBO1_HUMAN	roundabout, axon guidance receptor, homolog 1 (Drosophila)	580	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|axon guidance (GO:0007411)|axon midline choice point recognition (GO:0016199)|cell adhesion (GO:0007155)|cell migration involved in sprouting angiogenesis (GO:0002042)|chemorepulsion involved in postnatal olfactory bulb interneuron migration (GO:0021836)|homophilic cell adhesion (GO:0007156)|mammary duct terminal end bud growth (GO:0060763)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|negative regulation of negative chemotaxis (GO:0050925)|nervous system development (GO:0007399)|positive regulation of axonogenesis (GO:0050772)|Roundabout signaling pathway (GO:0035385)	axolemma (GO:0030673)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	axon guidance receptor activity (GO:0008046)|identical protein binding (GO:0042802)|LRR domain binding (GO:0030275)			breast(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(2)|lung(25)|urinary_tract(1)	44		Lung SC(41;0.0257)|Lung NSC(201;0.0439)		LUSC - Lung squamous cell carcinoma(21;0.008)|Epithelial(33;0.00999)|Lung(72;0.0177)|BRCA - Breast invasive adenocarcinoma(55;0.0274)		TTGGTTGCCACGATAATGTGA	0.408													T|||	1415	0.282548	0.4297	0.2435	5008	,	,		18832	0.2192		0.2485	False		,,,				2504	0.2117				p.S580S		Atlas-SNP	.											.	ROBO1	833	.	0			c.G1740A						PASS	.	T	,,	1364,2332		251,862,735	113.0	103.0	106.0		1632,1740,1632	0.8	0.8	3	dbSNP_100	106	1960,6240		237,1486,2377	no	coding-synonymous,coding-synonymous,coding-synonymous	ROBO1	NM_001145845.1,NM_002941.3,NM_133631.3	,,	488,2348,3112	TT,TC,CC		23.9024,36.9048,27.9422	,,	544/1552,580/1652,544/1607	78717343	3324,8572	1848	4100	5948	SO:0001819	synonymous_variant	6091	exon13			TTGCCACGATAAT	AF040990	CCDS46872.1, CCDS46872.2, CCDS54610.1, CCDS54611.1	3p12.3	2013-02-11	2001-11-28		ENSG00000169855	ENSG00000169855		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	10249	protein-coding gene	gene with protein product		602430	"""roundabout (axon guidance receptor, Drosophila) homolog 1"""			9458045, 9608531	Standard	NM_002941		Approved	DUTT1, FLJ21882, SAX3	uc003dqe.2	Q9Y6N7	OTTHUMG00000158843	ENST00000464233.1:c.1740G>A	3.37:g.78717343C>T		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	96	52	0.541667	NM_002941	B2RXI1|D3DU36|E9PD49|Q1RMC7|Q7Z300|Q9BUS7	Silent	SNP	ENST00000464233.1	37	CCDS54611.1																																																																																			C|0.699;T|0.301	0.301	strong		0.408	ROBO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352610.1	NM_002941	
PGLYRP2	114770	hgsc.bcm.edu	37	19	15580658	15580658	+	Missense_Mutation	SNP	G	G	A	rs2304200	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:15580658G>A	ENST00000340880.4	-	4	1906	c.1426C>T	c.(1426-1428)Cgg>Tgg	p.R476W	PGLYRP2_ENST00000292609.4_Missense_Mutation_p.R476W	NM_052890.3	NP_443122.3	Q96PD5	PGRP2_HUMAN	peptidoglycan recognition protein 2	476			R -> W (in dbSNP:rs2304200).		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)			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						CCGAAGCCCCGGGAGTTGTGG	0.711													G|||	236	0.0471246	0.0061	0.0821	5008	,	,		14087	0.005		0.1044	False		,,,				2504	0.0624				p.R476W		Atlas-SNP	.											.	PGLYRP2	116	.	0			c.C1426T						PASS	.	G	TRP/ARG	57,4287		0,57,2115	10.0	13.0	12.0		1426	4.1	0.1	19	dbSNP_100	12	688,7812		26,636,3588	no	missense	PGLYRP2	NM_052890.3	101	26,693,5703	AA,AG,GG		8.0941,1.3122,5.8004	probably-damaging	476/577	15580658	745,12099	2172	4250	6422	SO:0001583	missense	114770	exon4			AGCCCCGGGAGTT	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.1426C>T	19.37:g.15580658G>A	ENSP00000345968:p.Arg476Trp	Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	33	25	0.757576	NM_052890	A8K050|A8K8C7|B2RMZ2|B7ZM33|Q68CK1|Q96N74|Q9UC60	Missense_Mutation	SNP	ENST00000340880.4	37	CCDS12330.2	110	0.05036630036630037	2	0.0040650406504065045	33	0.09116022099447514	4	0.006993006993006993	71	0.09366754617414248	G	12.98	2.101870	0.37048	0.013122	0.080941	ENSG00000161031	ENST00000340880;ENST00000292609	T;T	0.14640	2.49;2.49	5.2	4.1	0.47936	Peptidoglycan recognition protein family domain, metazoa/bacteria (1);N-acetylmuramoyl-L-alanine amidase domain (4);	1.069120	0.07197	N	0.856787	T	0.00666	0.0022	M	0.66297	2.02	0.80722	P	0.0	B;P	0.36010	0.432;0.532	B;B	0.37047	0.035;0.24	T	0.10064	-1.0646	9	0.66056	D	0.02	-22.2927	8.0407	0.30519	0.0:0.1727:0.6489:0.1785	rs2304200	476;476	Q96PD5-2;Q96PD5	.;PGRP2_HUMAN	W	476	ENSP00000345968:R476W;ENSP00000292609:R476W	ENSP00000292609:R476W	R	-	1	2	PGLYRP2	15441658	0.003000	0.15002	0.099000	0.21106	0.032000	0.12392	0.819000	0.27308	2.432000	0.82394	0.462000	0.41574	CGG	G|0.952;A|0.048	0.048	strong		0.711	PGLYRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319626.1	NM_052890	
ANKRD27	84079	hgsc.bcm.edu	37	19	33096786	33096786	+	Silent	SNP	G	G	A	rs7247420	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:33096786G>A	ENST00000306065.4	-	24	2606	c.2448C>T	c.(2446-2448)taC>taT	p.Y816Y	SNORA68_ENST00000364518.1_RNA	NM_032139.2	NP_115515.2	Q96NW4	ANR27_HUMAN	ankyrin repeat domain 27 (VPS9 domain)	816					early endosome to late endosome transport (GO:0045022)|positive regulation of GTPase activity (GO:0043547)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|lysosome (GO:0005764)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)			breast(3)|endometrium(7)|kidney(2)|large_intestine(6)|lung(15)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(2)	42	Esophageal squamous(110;0.137)					CGGAGCAGGCGTAAATGAGGG	0.552													G|||	1175	0.234625	0.3434	0.1427	5008	,	,		13004	0.3393		0.1153	False		,,,				2504	0.1677				p.Y816Y		Atlas-SNP	.											.	ANKRD27	86	.	0			c.C2448T						PASS	.	G		1377,3029	454.9+/-350.8	223,931,1049	137.0	125.0	129.0		2448	-4.8	0.9	19	dbSNP_116	129	1049,7551	221.0+/-258.6	64,921,3315	no	coding-synonymous	ANKRD27	NM_032139.2		287,1852,4364	AA,AG,GG		12.1977,31.2528,18.6529		816/1051	33096786	2426,10580	2203	4300	6503	SO:0001819	synonymous_variant	84079	exon24			GCAGGCGTAAATG	AK054561	CCDS32986.1	19q13.12	2013-01-10				ENSG00000105186		"""Ankyrin repeat domain containing"""	25310	protein-coding gene	gene with protein product	"""Vps9 domain and ankyrin-repeat-containing protein"""					11230166, 16525121	Standard	NM_032139		Approved	FLJ00040, DKFZp434L0718, VARP	uc002ntn.1	Q96NW4		ENST00000306065.4:c.2448C>T	19.37:g.33096786G>A		Somatic	220	0	0		WXS	Illumina HiSeq	Phase_I	122	47	0.385246	NM_032139	Q71MF5|Q86UC3|Q8ND80|Q9H0I4	Silent	SNP	ENST00000306065.4	37	CCDS32986.1																																																																																			G|0.792;A|0.208	0.208	strong		0.552	ANKRD27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450329.1	NM_032139	
CHRNA9	55584	hgsc.bcm.edu	37	4	40339250	40339250	+	Silent	SNP	T	T	C	rs55998310	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:40339250T>C	ENST00000310169.2	+	3	373	c.234T>C	c.(232-234)acT>acC	p.T78T		NM_017581.3	NP_060051.2	Q9UGM1	ACHA9_HUMAN	cholinergic receptor, nicotinic, alpha 9 (neuronal)	78					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)	AAATTCTGACTGCTTATTTGT	0.468													T|||	20	0.00399361	0.0008	0.0014	5008	,	,		20941	0.0		0.0149	False		,,,				2504	0.0031				p.T78T	Esophageal Squamous(115;1297 1602 22235 25158 43327)	Atlas-SNP	.											.	CHRNA9	53	.	0			c.T234C						PASS	.	T		3,4403	6.2+/-15.9	0,3,2200	103.0	80.0	88.0		234	-11.7	0.0	4	dbSNP_129	88	93,8507	51.9+/-112.3	0,93,4207	no	coding-synonymous	CHRNA9	NM_017581.2		0,96,6407	CC,CT,TT		1.0814,0.0681,0.7381		78/480	40339250	96,12910	2203	4300	6503	SO:0001819	synonymous_variant	55584	exon3			TCTGACTGCTTAT	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.234T>C	4.37:g.40339250T>C		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	156	70	0.448718	NM_017581	Q14CY7|Q4W5A2|Q9NYV2	Silent	SNP	ENST00000310169.2	37	CCDS3459.1																																																																																			T|0.993;C|0.007	0.007	strong		0.468	CHRNA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216822.1		
SLC5A10	125206	hgsc.bcm.edu	37	17	18855611	18855611	+	Silent	SNP	T	T	C	rs2076562	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:18855611T>C	ENST00000395645.3	+	1	111	c.93T>C	c.(91-93)aaT>aaC	p.N31N	SLC5A10_ENST00000317977.6_Intron|SLC5A10_ENST00000395647.2_Silent_p.N31N|SLC5A10_ENST00000395642.1_5'UTR|AC090286.4_ENST00000354432.3_RNA|SLC5A10_ENST00000417251.2_Silent_p.N31N|SLC5A10_ENST00000395643.2_Silent_p.N31N	NM_001042450.2	NP_001035915.1	A0PJK1	SC5AA_HUMAN	solute carrier family 5 (sodium/sugar cotransporter), member 10	31					sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(3)|ovary(3)|prostate(3)|skin(3)	24						TTGCTCTGAATGTGGCCGTGG	0.612													T|||	1865	0.372404	0.1687	0.513	5008	,	,		19904	0.2331		0.6173	False		,,,				2504	0.4397				p.N31N		Atlas-SNP	.											SLC5A10,NS,carcinoma,0,1	SLC5A10	55	1	0			c.T93C						PASS	.	T	,	1042,3288		151,740,1274	121.0	127.0	125.0		93,93	-6.7	0.9	17	dbSNP_96	125	5247,3273		1605,2037,618	no	coding-synonymous,coding-synonymous	SLC5A10	NM_001042450.1,NM_152351.3	,	1756,2777,1892	CC,CT,TT		38.4155,24.0647,48.9416	,	31/597,31/613	18855611	6289,6561	2165	4260	6425	SO:0001819	synonymous_variant	125206	exon1			TCTGAATGTGGCC		CCDS11201.2, CCDS42275.1, CCDS59277.1, CCDS59278.1, CCDS74008.1	17p11.2	2013-07-19	2013-07-19		ENSG00000154025	ENSG00000154025		"""Solute carriers"""	23155	protein-coding gene	gene with protein product			"""solute carrier family 5 (sodium/glucose cotransporter), member 10"""				Standard	NM_152351		Approved	SGLT5	uc002gut.2	A0PJK1	OTTHUMG00000178143	ENST00000395645.3:c.93T>C	17.37:g.18855611T>C		Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	190	92	0.484211	NM_001042450	A8MUC9|B4DPI0|B7WPR4|Q6P5X0|Q8IXM4|Q96LQ1	Silent	SNP	ENST00000395645.3	37	CCDS42275.1																																																																																			T|0.605;C|0.395	0.395	strong		0.612	SLC5A10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132129.2	NM_152351	
ATAD5	79915	hgsc.bcm.edu	37	17	29187497	29187497	+	Silent	SNP	A	A	G	rs9896095	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:29187497A>G	ENST00000321990.4	+	10	3381	c.3003A>G	c.(3001-3003)gtA>gtG	p.V1001V	RNU6-298P_ENST00000390888.1_RNA|CTD-2349P21.11_ENST00000580873.1_RNA	NM_024857.3	NP_079133.3	Q96QE3	ATAD5_HUMAN	ATPase family, AAA domain containing 5	1001					cellular response to DNA damage stimulus (GO:0006974)	nucleus (GO:0005634)	ATP binding (GO:0005524)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(3)|large_intestine(18)|lung(13)|ovary(3)|pancreas(1)	51		all_hematologic(16;0.0202)|Acute lymphoblastic leukemia(14;0.0238)|Myeloproliferative disorder(56;0.0393)				GGAAACTCGTAGAAGCAGAAA	0.353													G|||	864	0.172524	0.1762	0.1902	5008	,	,		16243	0.1359		0.1074	False		,,,				2504	0.2597				p.V1001V		Atlas-SNP	.											.	ATAD5	150	.	0			c.A3003G						PASS	.	G		730,3674	744.8+/-411.6	60,610,1532	66.0	66.0	66.0		3003	-3.3	0.0	17	dbSNP_119	66	902,7698	773.0+/-407.7	37,828,3435	no	coding-synonymous	ATAD5	NM_024857.3		97,1438,4967	GG,GA,AA		10.4884,16.5758,12.55		1001/1845	29187497	1632,11372	2202	4300	6502	SO:0001819	synonymous_variant	79915	exon10			ACTCGTAGAAGCA		CCDS11260.1	17q11.2	2010-04-21	2007-02-08	2007-02-08	ENSG00000176208	ENSG00000176208		"""ATPases / AAA-type"""	25752	protein-coding gene	gene with protein product	"""enhanced level of genomic instability 1 homolog (S. cerevisiae)"""	609534	"""chromosome 17 open reading frame 41"""	C17orf41		15983387, 11468690, 19755857	Standard	NM_024857		Approved	FLJ12735, FRAG1, ELG1	uc002hfs.1	Q96QE3	OTTHUMG00000132794	ENST00000321990.4:c.3003A>G	17.37:g.29187497A>G		Somatic	217	0	0		WXS	Illumina HiSeq	Phase_I	150	78	0.52	NM_024857	Q05DH0|Q69YR6|Q9H9I1	Silent	SNP	ENST00000321990.4	37	CCDS11260.1																																																																																			A|0.862;G|0.138	0.138	strong		0.353	ATAD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256206.2	NM_024857	
CTDP1	9150	hgsc.bcm.edu	37	18	77455227	77455227	+	Missense_Mutation	SNP	C	C	T	rs115044443	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:77455227C>T	ENST00000299543.7	+	2	464	c.317C>T	c.(316-318)gCg>gTg	p.A106V	CTDP1_ENST00000075430.7_Missense_Mutation_p.A106V	NM_001202504.1|NM_004715.4	NP_001189433.1|NP_004706.3	Q9Y5B0	CTDP1_HUMAN	CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) phosphatase, subunit 1	106					exit from mitosis (GO:0010458)|gene expression (GO:0010467)|positive regulation of viral transcription (GO:0050434)|protein dephosphorylation (GO:0006470)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	actin cytoskeleton (GO:0015629)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|midbody (GO:0030496)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)|spindle midzone (GO:0051233)|spindle pole (GO:0000922)	CTD phosphatase activity (GO:0008420)|DNA-directed RNA polymerase activity (GO:0003899)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(14)|ovary(2)|prostate(2)|urinary_tract(1)	35		Esophageal squamous(42;0.0157)|Melanoma(33;0.144)		OV - Ovarian serous cystadenocarcinoma(15;5.2e-06)|BRCA - Breast invasive adenocarcinoma(31;0.0277)		TTTTGTAGAGCGGTTCTGGTG	0.438													C|||	99	0.0197684	0.0613	0.0072	5008	,	,		16271	0.0		0.0119	False		,,,				2504	0.001				p.A106V		Atlas-SNP	.											.	CTDP1	67	.	0			c.C317T						PASS	.	C	,VAL/ALA,VAL/ALA	222,4184	135.7+/-171.8	5,212,1986	121.0	109.0	113.0		,317,317	3.9	0.0	18	dbSNP_132	113	125,8475	64.2+/-126.4	0,125,4175	yes	utr-5,missense,missense	CTDP1	NM_001202504.1,NM_004715.4,NM_048368.3	,64,64	5,337,6161	TT,TC,CC		1.4535,5.0386,2.668	,benign,benign	,106/962,106/868	77455227	347,12659	2203	4300	6503	SO:0001583	missense	9150	exon2			GTAGAGCGGTTCT	AF081287	CCDS12017.1, CCDS12018.1, CCDS74239.1	18q23	2014-09-17			ENSG00000060069	ENSG00000060069		"""Serine/threonine phosphatases / CTD aspartate-based phosphatases"""	2498	protein-coding gene	gene with protein product		604927				9405607, 9765293	Standard	NM_004715		Approved	FCP1	uc002lnh.2	Q9Y5B0	OTTHUMG00000132920	ENST00000299543.7:c.317C>T	18.37:g.77455227C>T	ENSP00000299543:p.Ala106Val	Somatic	193	0	0		WXS	Illumina HiSeq	Phase_I	119	40	0.336134	NM_004715	A8MY97|Q7Z644|Q96BZ1|Q9Y6F5	Missense_Mutation	SNP	ENST00000299543.7	37	CCDS12017.1	43	0.019688644688644688	29	0.05894308943089431	2	0.0055248618784530384	0	0.0	12	0.0158311345646438	C	14.60	2.584590	0.46110	0.050386	0.014535	ENSG00000060069	ENST00000299543;ENST00000075430	T;T	0.10382	2.9;2.88	4.8	3.86	0.44501	.	0.283877	0.39615	N	0.001318	T	0.01254	0.0041	M	0.65975	2.015	0.21256	N	0.999743	D;P	0.53312	0.959;0.931	B;B	0.40165	0.321;0.171	T	0.20075	-1.0286	10	0.27785	T	0.31	-21.0839	14.1115	0.65123	0.0:0.6821:0.3179:0.0	.	106;106	Q9Y5B0-4;Q9Y5B0	.;CTDP1_HUMAN	V	106	ENSP00000299543:A106V;ENSP00000075430:A106V	ENSP00000075430:A106V	A	+	2	0	CTDP1	75556215	0.964000	0.33143	0.008000	0.14137	0.004000	0.04260	2.608000	0.46308	2.376000	0.81061	0.655000	0.94253	GCG	C|0.977;T|0.023	0.023	strong		0.438	CTDP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256432.1	NM_004715	
PTPRG	5793	hgsc.bcm.edu	37	3	61975382	61975382	+	Missense_Mutation	SNP	T	T	C	rs62620047	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:61975382T>C	ENST00000474889.1	+	3	651	c.274T>C	c.(274-276)Tat>Cat	p.Y92H	PTPRG_ENST00000295874.10_Missense_Mutation_p.Y92H	NM_002841.3	NP_002832.3	P23470	PTPRG_HUMAN	protein tyrosine phosphatase, receptor type, G	92	Alpha-carbonic anhydrase.		Y -> H (in dbSNP:rs62620047). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:8833149}.		brain development (GO:0007420)|negative regulation of epithelial cell migration (GO:0010633)|negative regulation of neuron projection development (GO:0010977)|peptidyl-tyrosine dephosphorylation (GO:0035335)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	identical protein binding (GO:0042802)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(12)|liver(2)|lung(15)|ovary(7)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	62				BRCA - Breast invasive adenocarcinoma(55;0.000376)|KIRC - Kidney renal clear cell carcinoma(10;0.0499)|Kidney(10;0.065)		TTTAGACCAGTATGCGCGTGT	0.488													T|||	440	0.0878594	0.0696	0.0879	5008	,	,		18472	0.002		0.1441	False		,,,				2504	0.1431				p.Y92H		Atlas-SNP	.											.	PTPRG	153	.	0			c.T274C						PASS	.	T	HIS/TYR	337,4069	178.0+/-206.8	14,309,1880	115.0	105.0	108.0		274	4.1	1.0	3	dbSNP_129	108	1225,7375	247.4+/-275.4	96,1033,3171	yes	missense	PTPRG	NM_002841.3	83	110,1342,5051	CC,CT,TT		14.2442,7.6487,12.0098	benign	92/1446	61975382	1562,11444	2203	4300	6503	SO:0001583	missense	5793	exon3			GACCAGTATGCGC	L09247	CCDS2895.1	3p21-p14	2013-02-11			ENSG00000144724	ENSG00000144724		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9671	protein-coding gene	gene with protein product		176886		PTPG		1711217	Standard	NM_002841		Approved	RPTPG	uc003dlb.3	P23470	OTTHUMG00000158660	ENST00000474889.1:c.274T>C	3.37:g.61975382T>C	ENSP00000418112:p.Tyr92His	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	127	63	0.496063	NM_002841	B2RU12|B7ZLX5|Q15623|Q59EE0|Q68DU5	Missense_Mutation	SNP	ENST00000474889.1	37	CCDS2895.1	191	0.08745421245421245	26	0.052845528455284556	41	0.1132596685082873	2	0.0034965034965034965	122	0.16094986807387862	T	9.548	1.115287	0.20795	0.076487	0.142442	ENSG00000144724	ENST00000474889;ENST00000295874	T;T	0.66099	-0.19;-0.19	5.92	4.14	0.48551	Carbonic anhydrase, alpha-class, catalytic domain (4);	0.415282	0.27705	N	0.018194	T	0.00178	0.0005	N	0.11131	0.1	0.51012	P	9.80000000000425E-5	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.03534	-1.1027	9	0.38643	T	0.18	.	7.6336	0.28253	0.133:0.7303:0.0:0.1366	rs62620047	92;92	P23470-2;P23470	.;PTPRG_HUMAN	H	92	ENSP00000418112:Y92H;ENSP00000295874:Y92H	ENSP00000295874:Y92H	Y	+	1	0	PTPRG	61950422	0.141000	0.22595	1.000000	0.80357	0.983000	0.72400	0.550000	0.23345	0.846000	0.35142	-0.132000	0.14878	TAT	T|0.887;C|0.113	0.113	strong		0.488	PTPRG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351674.1	NM_002841	
MUC4	4585	hgsc.bcm.edu	37	3	195513812	195513812	+	Missense_Mutation	SNP	T	T	A	rs201142885	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195513812T>A	ENST00000463781.3	-	2	5098	c.4639A>T	c.(4639-4641)Aca>Tca	p.T1547S	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.T1547S	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0	VWFD. {ECO:0000255|PROSITE- ProRule:PRU00580}.				cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.M1535_T1550delMPLPVTSPSSASTGDT(4)|p.T1547S(1)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GTGTCACCTGTGGATGCTGAG	0.582																																					p.T1547S		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	5	Deletion - In frame(4)|Substitution - Missense(1)	stomach(4)|kidney(1)	c.A4639T						scavenged	.																																			SO:0001583	missense	4585	exon2			CACCTGTGGATGC	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.4639A>T	3.37:g.195513812T>A	ENSP00000417498:p.Thr1547Ser	Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	21	2	0.0952381	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	-	6.021	0.372220	0.11409	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.32272	1.48;1.46	0.844	-0.658	0.11428	.	.	.	.	.	T	0.22437	0.0541	N	0.19112	0.55	0.09310	N	1	P	0.46578	0.88	P	0.50270	0.636	T	0.13764	-1.0497	8	.	.	.	.	3.6421	0.08170	0.0:0.3306:0.0:0.6694	.	1547	E7ESK3	.	S	1547	ENSP00000417498:T1547S;ENSP00000420243:T1547S	.	T	-	1	0	MUC4	196998207	0.034000	0.19679	0.062000	0.19696	0.063000	0.16089	-0.041000	0.12084	0.077000	0.16863	0.076000	0.15429	ACA	T|0.976;A|0.023	0.023	strong		0.582	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
FUT5	2527	hgsc.bcm.edu	37	19	5867154	5867154	+	Missense_Mutation	SNP	G	G	A	rs140776824	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:5867154G>A	ENST00000588525.1	-	2	670	c.583C>T	c.(583-585)Cca>Tca	p.P195S	FUT5_ENST00000252675.5_Missense_Mutation_p.P195S	NM_002034.2	NP_002025.2	Q11128	FUT5_HUMAN	fucosyltransferase 5 (alpha (1,3) fucosyltransferase)	195					carbohydrate metabolic process (GO:0005975)|fucosylation (GO:0036065)|L-fucose catabolic process (GO:0042355)|protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	3-galactosyl-N-acetylglucosaminide 4-alpha-L-fucosyltransferase activity (GO:0017060)|alpha-(1->3)-fucosyltransferase activity (GO:0046920)|fucosyltransferase activity (GO:0008417)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(8)|upper_aerodigestive_tract(1)	12						TTGAGCGGTGGGTGGGCAGGC	0.662													G|||	104	0.0207668	0.0015	0.0259	5008	,	,		12928	0.0079		0.0656	False		,,,				2504	0.0102				p.P195S		Atlas-SNP	.											.	FUT5	29	.	0			c.C583T						PASS	.	G	SER/PRO	47,4169		1,45,2062	15.0	16.0	15.0		583	-4.3	0.0	19	dbSNP_134	15	585,7781		23,539,3621	no	missense	FUT5	NM_002034.2	74	24,584,5683	AA,AG,GG		6.9926,1.1148,5.023	benign	195/375	5867154	632,11950	2108	4183	6291	SO:0001583	missense	2527	exon2			GCGGTGGGTGGGC		CCDS12154.1	19p13.3	2013-02-26				ENSG00000130383	2.4.1.65	"""Fucosyltransferases"""	4016	protein-coding gene	gene with protein product		136835				1740457	Standard	NM_002034		Approved	FUC-TV	uc002mdo.4	Q11128	OTTHUMG00000180616	ENST00000588525.1:c.583C>T	19.37:g.5867154G>A	ENSP00000466880:p.Pro195Ser	Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	97	49	0.505155	NM_002034	A8K4X2	Missense_Mutation	SNP	ENST00000588525.1	37	CCDS12154.1	63	0.028846153846153848	1	0.0020325203252032522	10	0.027624309392265192	1	0.0017482517482517483	51	0.06728232189973615	G	0.053	-1.243341	0.01481	0.011148	0.069926	ENSG00000130383	ENST00000252675	T	0.22743	1.94	2.17	-4.35	0.03656	.	1.868570	0.03005	U	0.148748	T	0.00815	0.0027	N	0.20685	0.6	0.09310	N	1	B	0.21225	0.053	B	0.29440	0.102	T	0.20773	-1.0265	10	0.08837	T	0.75	.	5.3404	0.15981	0.0:0.2057:0.4987:0.2956	.	195	Q11128	FUT5_HUMAN	S	195	ENSP00000252675:P195S	ENSP00000252675:P195S	P	-	1	0	FUT5	5818154	0.000000	0.05858	0.000000	0.03702	0.031000	0.12232	-1.395000	0.02516	-1.422000	0.02004	-0.693000	0.03709	CCA	G|0.900;A|0.100	0.100	strong		0.662	FUT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452213.1	NM_002034	
SMYD4	114826	hgsc.bcm.edu	37	17	1690752	1690752	+	Missense_Mutation	SNP	G	G	A	rs11549830	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:1690752G>A	ENST00000305513.7	-	6	1851	c.1684C>T	c.(1684-1686)Cgg>Tgg	p.R562W		NM_052928.2	NP_443160.2	Q8IYR2	SMYD4_HUMAN	SET and MYND domain containing 4	562	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.		R -> W (in dbSNP:rs11549830). {ECO:0000269|PubMed:11572484}.				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						TTTCTAATCCGCTGTGACGCC	0.572													G|||	2206	0.440495	0.4047	0.4914	5008	,	,		22833	0.5268		0.3439	False		,,,				2504	0.4632				p.R562W		Atlas-SNP	.											.	SMYD4	50	.	0			c.C1684T						PASS	.	G	TRP/ARG	1729,2671		353,1023,824	86.0	68.0	74.0		1684	2.5	0.3	17	dbSNP_120	74	2823,5767		463,1897,1935	yes	missense	SMYD4	NM_052928.2	101	816,2920,2759	AA,AG,GG		32.8638,39.2955,35.0423	probably-damaging	562/805	1690752	4552,8438	2200	4295	6495	SO:0001583	missense	114826	exon6			TAATCCGCTGTGA	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.1684C>T	17.37:g.1690752G>A	ENSP00000304360:p.Arg562Trp	Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	126	125	0.992063	NM_052928	Q8N1P2|Q8NAT0|Q96LV4|Q96PV2	Missense_Mutation	SNP	ENST00000305513.7	37	CCDS11013.1	953	0.43635531135531136	224	0.45528455284552843	152	0.4198895027624309	308	0.5384615384615384	269	0.3548812664907652	G	18.51	3.640410	0.67244	0.392955	0.328638	ENSG00000186532	ENST00000305513	T	0.80393	-1.37	5.86	2.54	0.30619	SET domain (3);	1.405560	0.04087	N	0.310634	T	0.00012	0.0000	L	0.48642	1.525	0.38185	P	0.06025999999999998	D	0.69078	0.997	P	0.56916	0.809	T	0.33523	-0.9865	9	0.45353	T	0.12	4.6685	11.3134	0.49377	0.0:0.1111:0.4818:0.4072	rs11549830	562	Q8IYR2	SMYD4_HUMAN	W	562	ENSP00000304360:R562W	ENSP00000304360:R562W	R	-	1	2	SMYD4	1637502	0.456000	0.25744	0.266000	0.24541	0.743000	0.42351	0.773000	0.26661	0.244000	0.21351	0.655000	0.94253	CGG	G|0.609;A|0.391	0.391	strong		0.572	SMYD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207108.4	XM_056082	
COL4A3	1285	hgsc.bcm.edu	37	2	228131752	228131752	+	Silent	SNP	G	G	A	rs34019152	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:228131752G>A	ENST00000396578.3	+	23	1614	c.1452G>A	c.(1450-1452)ggG>ggA	p.G484G	AC097662.2_ENST00000433324.1_RNA|AC097662.2_ENST00000439598.2_RNA|AC097662.2_ENST00000396588.2_RNA|AC097662.2_ENST00000437673.1_RNA	NM_000091.4	NP_000082.2	Q01955	CO4A3_HUMAN	collagen, type IV, alpha 3 (Goodpasture antigen)	484	Triple-helical region.				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)		ATATCCCAGGGCCTCCCGGTC	0.463													G|||	527	0.105232	0.0454	0.1787	5008	,	,		16826	0.1577		0.0686	False		,,,				2504	0.1176				p.G484G		Atlas-SNP	.											.	COL4A3	293	.	0			c.G1452A						PASS	.	G		176,3554		4,168,1693	66.0	66.0	66.0		1452	-2.1	0.1	2	dbSNP_126	66	636,7560		21,594,3483	no	coding-synonymous	COL4A3	NM_000091.4		25,762,5176	AA,AG,GG		7.7599,4.7185,6.8087		484/1671	228131752	812,11114	1865	4098	5963	SO:0001819	synonymous_variant	1285	exon23			CCCAGGGCCTCCC		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.1452G>A	2.37:g.228131752G>A		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	47	24	0.510638	NM_000091	Q53QQ1|Q53R14|Q53RW8|Q9BQT2|Q9NYC4|Q9UDJ9|Q9UDK9|Q9UDL0|Q9UDL1	Silent	SNP	ENST00000396578.3	37	CCDS42829.1																																																																																			G|0.905;A|0.095	0.095	strong		0.463	COL4A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331409.2	NM_000091	
MMP3	4314	hgsc.bcm.edu	37	11	102709425	102709425	+	Silent	SNP	A	A	G	rs520540	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:102709425A>G	ENST00000299855.5	-	8	1342	c.1086T>C	c.(1084-1086)gcT>gcC	p.A362A	WTAPP1_ENST00000525739.2_RNA	NM_002422.3	NP_002413.1	P08254	MMP3_HUMAN	matrix metallopeptidase 3 (stromelysin 1, progelatinase)	362					cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of hydrogen peroxide metabolic process (GO:0010727)|positive regulation of oxidative stress-induced cell death (GO:1903209)|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)|endopeptidase activity (GO:0004175)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(3)|large_intestine(3)|liver(1)|lung(7)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	22		all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)		BRCA - Breast invasive adenocarcinoma(274;0.0142)	Marimastat(DB00786)	TTCCTCTGATAGCCCAGAATT	0.398													G|||	3117	0.622404	0.5598	0.6643	5008	,	,		17460	0.6706		0.5298	False		,,,				2504	0.7229				p.A362A		Atlas-SNP	.											.	MMP3	60	.	0			c.T1086C						PASS	.	G		2389,2017	561.6+/-380.8	643,1103,457	69.0	64.0	66.0		1086	2.2	1.0	11	dbSNP_83	66	4298,4300	577.8+/-390.6	1064,2170,1065	no	coding-synonymous	MMP3	NM_002422.3		1707,3273,1522	GG,GA,AA		49.9884,45.7785,48.5774		362/478	102709425	6687,6317	2203	4299	6502	SO:0001819	synonymous_variant	4314	exon8			TCTGATAGCCCAG	X05232	CCDS8323.1	11q22.3	2012-10-02	2005-08-08		ENSG00000149968	ENSG00000149968	3.4.24.17		7173	protein-coding gene	gene with protein product		185250	"""matrix metalloproteinase 3 (stromelysin 1, progelatinase)"""	STMY1, STMY			Standard	NM_002422		Approved		uc001phj.1	P08254	OTTHUMG00000048254	ENST00000299855.5:c.1086T>C	11.37:g.102709425A>G		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	62	62	1	NM_002422	B2R8B8|Q3B7S0|Q6GRF8	Silent	SNP	ENST00000299855.5	37	CCDS8323.1	1308	0.5989010989010989	285	0.5792682926829268	226	0.6243093922651933	387	0.6765734265734266	410	0.5408970976253298	G	8.240	0.806639	0.16467	0.542215	0.499884	ENSG00000149968	ENST00000434103	.	.	.	5.07	2.15	0.27550	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999977	.	.	.	.	.	.	T	0.38436	-0.9661	3	.	.	.	.	6.7088	0.23266	0.5951:0.0:0.4049:0.0	rs520540;rs3740933;rs60233336;rs520540	.	.	.	P	6	.	.	L	-	2	0	MMP3	102214635	0.374000	0.25081	1.000000	0.80357	0.655000	0.38815	1.162000	0.31786	0.394000	0.25230	-0.186000	0.12905	CTA	A|0.461;G|0.539	0.539	strong		0.398	MMP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109758.2	NM_002422	
TMEM25	84866	hgsc.bcm.edu	37	11	118404804	118404804	+	Silent	SNP	G	G	A	rs6589664	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:118404804G>A	ENST00000313236.5	+	7	950	c.897G>A	c.(895-897)ccG>ccA	p.P299P	TMEM25_ENST00000411589.2_Silent_p.P255P|TMEM25_ENST00000533102.1_Silent_p.P299P|RP11-770J1.3_ENST00000556583.1_RNA|TMEM25_ENST00000442938.2_Silent_p.P255P|TMEM25_ENST00000359862.4_Silent_p.P255P|TMEM25_ENST00000544878.1_Silent_p.P202P|TMEM25_ENST00000354064.7_Silent_p.P151P|TMEM25_ENST00000524725.1_Silent_p.P255P|TMEM25_ENST00000354284.4_Silent_p.P299P	NM_032780.3	NP_116169.2	Q86YD3	TMM25_HUMAN	transmembrane protein 25	299						extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.P299P(1)		endometrium(2)|kidney(2)|large_intestine(2)|lung(4)|prostate(1)|skin(1)|stomach(1)	13	all_hematologic(175;0.0349)	Medulloblastoma(222;0.0523)|all_hematologic(192;0.0735)		BRCA - Breast invasive adenocarcinoma(274;3.04e-05)		TGTCCCTCCCGTCCAACCTTC	0.517													G|||	1202	0.240016	0.1921	0.4337	5008	,	,		18727	0.2302		0.2932	False		,,,				2504	0.1227				p.P299P		Atlas-SNP	.											TMEM25,NS,carcinoma,0,1	TMEM25	24	1	1	Substitution - coding silent(1)	stomach(1)	c.G897A						PASS	.	G	,,,,,	862,3538	336.8+/-304.5	84,694,1422	114.0	96.0	102.0		765,765,453,897,765,897	-4.2	1.0	11	dbSNP_116	102	2554,6036	416.7+/-352.2	375,1804,2116	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TMEM25	NM_001144034.1,NM_001144035.1,NM_001144036.1,NM_001144037.1,NM_001144038.1,NM_032780.3	,,,,,	459,2498,3538	AA,AG,GG		29.7322,19.5909,26.2972	,,,,,	255/323,255/323,151/219,299/352,255/307,299/367	118404804	3416,9574	2200	4295	6495	SO:0001819	synonymous_variant	84866	exon7			CCTCCCGTCCAAC	AK075437	CCDS8398.1, CCDS44745.1, CCDS44746.1, CCDS44747.1, CCDS44748.1	11q23.3	2013-01-11			ENSG00000149582	ENSG00000149582		"""Immunoglobulin superfamily / C2-set domain containing"""	25890	protein-coding gene	gene with protein product		613934				15254712, 12975309	Standard	NM_001144034		Approved	FLJ14399	uc010rye.2	Q86YD3	OTTHUMG00000166339	ENST00000313236.5:c.897G>A	11.37:g.118404804G>A		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	108	75	0.694444	NM_032780	A8K8J4|B0YJA6|B0YJA7|B0YJA9|G5E9U4|Q6UW89|Q86UA7|Q8NBL5|Q96KA6|Q96MW9	Silent	SNP	ENST00000313236.5	37	CCDS8398.1	607|607	0.27793040293040294|0.27793040293040294	86|86	0.17479674796747968|0.17479674796747968	134|134	0.3701657458563536|0.3701657458563536	151|151	0.263986013986014|0.263986013986014	236|236	0.3113456464379947|0.3113456464379947	G|G	9.953|9.953	1.220799|1.220799	0.22457|0.22457	0.195909|0.195909	0.297322|0.297322	ENSG00000149582|ENSG00000149582	ENST00000526973|ENST00000526853	.|.	.|.	.|.	5.92|5.92	-4.17|-4.17	0.03857|0.03857	.|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.09310|0.09310	P|P	0.999999999999998|0.999999999999998	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.46303|0.46303	-0.9201|-0.9201	3|3	.|.	.|.	.|.	-25.1125|-25.1125	1.2064|1.2064	0.01896|0.01896	0.4382:0.1483:0.2062:0.2073|0.4382:0.1483:0.2062:0.2073	rs6589664;rs6589664|rs6589664;rs6589664	.|.	.|.	.|.	H|I	139|134	.|.	.|.	R|V	+|+	2|1	0|0	TMEM25|TMEM25	117910014|117910014	0.000000|0.000000	0.05858|0.05858	0.987000|0.987000	0.45799|0.45799	0.963000|0.963000	0.63663|0.63663	-2.732000|-2.732000	0.00804|0.00804	-0.317000|-0.317000	0.08677|0.08677	-1.101000|-1.101000	0.02118|0.02118	CGT|GTC	G|0.738;A|0.262	0.262	strong		0.517	TMEM25-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389266.1	NM_032780	
GCNT1	2650	hgsc.bcm.edu	37	9	79118329	79118329	+	Silent	SNP	G	G	A	rs1057406	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:79118329G>A	ENST00000376730.4	+	4	1515	c.1032G>A	c.(1030-1032)ctG>ctA	p.L344L	GCNT1_ENST00000442371.1_Silent_p.L344L|GCNT1_ENST00000444201.2_Silent_p.L344L|GCNT1_ENST00000536223.1_Silent_p.L344L	NM_001097636.1|NM_001490.4	NP_001091105.1|NP_001481.2	Q02742	GCNT1_HUMAN	glucosaminyl (N-acetyl) transferase 1, core 2	344	Catalytic. {ECO:0000250}.				cell adhesion molecule production (GO:0060352)|cellular protein metabolic process (GO:0044267)|glycoprotein biosynthetic process (GO:0009101)|kidney morphogenesis (GO:0060993)|leukocyte tethering or rolling (GO:0050901)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|response to insulin (GO:0032868)|tissue morphogenesis (GO:0048729)	extracellular space (GO:0005615)|Golgi cisterna (GO:0031985)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|trans-Golgi network (GO:0005802)	beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase activity (GO:0003829)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(6)|lung(11)|prostate(2)|urinary_tract(1)	30						AGTATGATCTGTCTGACATGC	0.547													G|||	1180	0.235623	0.239	0.2493	5008	,	,		20510	0.1974		0.2276	False		,,,				2504	0.2689				p.L344L		Atlas-SNP	.											.	GCNT1	52	.	0			c.G1032A						PASS	.	G	,,,,	972,3434	364.6+/-317.1	126,720,1357	84.0	78.0	80.0		1032,1032,1032,1032,1032	3.1	1.0	9	dbSNP_86	80	1849,6751	329.3+/-318.7	192,1465,2643	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	GCNT1	NM_001097633.1,NM_001097634.1,NM_001097635.1,NM_001097636.1,NM_001490.4	,,,,	318,2185,4000	AA,AG,GG		21.5,22.0608,21.69	,,,,	344/429,344/429,344/429,344/429,344/429	79118329	2821,10185	2203	4300	6503	SO:0001819	synonymous_variant	2650	exon4			TGATCTGTCTGAC	L41415	CCDS6653.1	9q13	2013-02-25	2010-03-16		ENSG00000187210	ENSG00000187210	2.4.1.102	"""Glucosaminyl (N-acetyl) transferase and xylosyltransferase family"""	4203	protein-coding gene	gene with protein product	"""core 2 beta1,6 N-acetylglucosaminyltransferase-I"", ""beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N--acetylglucosaminyltransferase"""	600391	"""glucosaminyl (N-acetyl) transferase 1, core 2 (beta-1,6-N-acetylglucosaminyltransferase)"""	NACGT2		8449405, 9915862	Standard	NM_001490		Approved	C2GNT, NAGCT2	uc004akf.4	Q02742	OTTHUMG00000020044	ENST00000376730.4:c.1032G>A	9.37:g.79118329G>A		Somatic	273	0	0		WXS	Illumina HiSeq	Phase_I	210	91	0.433333	NM_001490	Q6DJZ4	Silent	SNP	ENST00000376730.4	37	CCDS6653.1																																																																																			G|0.774;A|0.226	0.226	strong		0.547	GCNT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052725.1	NM_001097634	
OR7D4	125958	hgsc.bcm.edu	37	19	9324863	9324863	+	Silent	SNP	G	G	A	rs8109935	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:9324863G>A	ENST00000308682.2	-	1	679	c.651C>T	c.(649-651)tcC>tcT	p.S217S		NM_001005191.2	NP_001005191.1	Q8NG98	OR7D4_HUMAN	olfactory receptor, family 7, subfamily D, member 4	217						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(4)|kidney(1)|large_intestine(2)|lung(10)|ovary(2)|skin(3)|stomach(1)	26						TCTGAGAGTAGGAGAAGAGGA	0.512													G|||	880	0.175719	0.3578	0.134	5008	,	,		21686	0.0407		0.0626	False		,,,				2504	0.2147				p.S217S		Atlas-SNP	.											OR7D4,NS,malignant_melanoma,-1,2	OR7D4	66	2	0			c.C651T						PASS	.	G		1368,3038	446.3+/-348.0	212,944,1047	82.0	77.0	79.0		651	-1.2	0.0	19	dbSNP_116	79	677,7923	169.3+/-220.7	31,615,3654	no	coding-synonymous	OR7D4	NM_001005191.2		243,1559,4701	AA,AG,GG		7.8721,31.0486,15.7235		217/313	9324863	2045,10961	2203	4300	6503	SO:0001819	synonymous_variant	125958	exon1			AGAGTAGGAGAAG		CCDS32901.1	19p13.2	2013-12-17		2004-03-10	ENSG00000174667	ENSG00000174667		"""GPCR / Class A : Olfactory receptors"""	8380	protein-coding gene	gene with protein product		611538		OR7D4P			Standard	NM_001005191		Approved	hg105, OR19-B	uc002mla.2	Q8NG98	OTTHUMG00000179936	ENST00000308682.2:c.651C>T	19.37:g.9324863G>A		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	75	39	0.52	NM_001005191	A8CAH8|A8CAH9|A8CAI0|A8CAI1|B9EH79	Silent	SNP	ENST00000308682.2	37	CCDS32901.1																																																																																			G|0.833;A|0.167	0.167	strong		0.512	OR7D4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449004.1		
FDXACB1	91893	hgsc.bcm.edu	37	11	111747297	111747297	+	Silent	SNP	A	A	G	rs7124696	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:111747297A>G	ENST00000260257.4	-	4	647	c.600T>C	c.(598-600)ttT>ttC	p.F200F	C11orf1_ENST00000530214.1_5'Flank|ALG9_ENST00000524880.1_Silent_p.F200F|C11orf1_ENST00000260276.3_5'Flank|ALG9_ENST00000527377.1_5'UTR|FDXACB1_ENST00000542429.1_Silent_p.F51F|C11orf1_ENST00000528125.1_5'Flank	NM_138378.2	NP_612387.1	Q9BRP7	FDXA1_HUMAN	ferredoxin-fold anticodon binding domain containing 1	200					phenylalanyl-tRNA aminoacylation (GO:0006432)|tRNA processing (GO:0008033)		ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|phenylalanine-tRNA ligase activity (GO:0004826)|tRNA binding (GO:0000049)			endometrium(1)|kidney(3)|large_intestine(2)|lung(9)|ovary(1)|upper_aerodigestive_tract(3)	19						GAGAACCTTCAAAAGGTAAGC	0.423													G|||	1228	0.245208	0.1982	0.3228	5008	,	,		20985	0.1944		0.33	False		,,,				2504	0.2188				p.F200F		Atlas-SNP	.											.	FDXACB1	74	.	0			c.T600C						PASS	.	G		805,2911		85,635,1138	127.0	123.0	124.0		600	0.9	0.0	11	dbSNP_116	124	2534,5660		397,1740,1960	no	coding-synonymous	FDXACB1	NM_138378.2		482,2375,3098	GG,GA,AA		30.9251,21.6631,28.0353		200/625	111747297	3339,8571	1858	4097	5955	SO:0001819	synonymous_variant	91893	exon4			ACCTTCAAAAGGT		CCDS44729.1	11q23.1	2011-04-15			ENSG00000255561	ENSG00000255561			25110	protein-coding gene	gene with protein product	"""hypothetical protein BC006136"""						Standard	NR_038364		Approved	LOC91893, hCG_2033039	uc001pmc.4	Q9BRP7	OTTHUMG00000166795	ENST00000260257.4:c.600T>C	11.37:g.111747297A>G		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	99	28	0.282828	NM_138378	A0PJW7|B4DUU2	Silent	SNP	ENST00000260257.4	37	CCDS44729.1																																																																																			A|0.738;G|0.262	0.262	strong		0.423	FDXACB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391497.1	NM_138378	
HEMGN	55363	hgsc.bcm.edu	37	9	100692648	100692648	+	Silent	SNP	G	G	T	rs35527067	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	268	1	0.00373134		WXS	Illumina HiSeq	Phase_I	214	114	0.53271	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	
HJURP	55355	hgsc.bcm.edu	37	2	234749258	234749258	+	Missense_Mutation	SNP	T	T	C	rs10511	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:234749258T>C	ENST00000411486.2	-	8	2233	c.2168A>G	c.(2167-2169)gAg>gGg	p.E723G	HJURP_ENST00000434039.1_5'Flank|HJURP_ENST00000441687.1_Missense_Mutation_p.E638G|HJURP_ENST00000432087.1_Missense_Mutation_p.E669G	NM_018410.3	NP_060880.3	Q8NCD3	HJURP_HUMAN	Holliday junction recognition protein	723			E -> G (in dbSNP:rs10511). {ECO:0000269|PubMed:14702039}.		cell cycle (GO:0007049)|CENP-A containing nucleosome assembly (GO:0034080)|chromosome segregation (GO:0007059)|nucleosome assembly (GO:0006334)|regulation of DNA binding (GO:0051101)|regulation of protein complex assembly (GO:0043254)	chromosome, centromeric region (GO:0000775)|condensed chromosome kinetochore (GO:0000777)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone binding (GO:0042393)|identical protein binding (GO:0042802)			NS(2)|breast(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(3)|lung(11)|ovary(2)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	38		Breast(86;0.00204)|all_lung(227;0.00433)|Renal(207;0.00685)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0719)|Lung SC(224;0.128)		Epithelial(121;2.01e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000186)|Lung(119;0.00521)|LUSC - Lung squamous cell carcinoma(224;0.00829)		CACCTACCTCTCTTCTGAGTT	0.537													T|||	796	0.158946	0.2027	0.121	5008	,	,		20359	0.2837		0.0885	False		,,,				2504	0.0706				p.E723G		Atlas-SNP	.											.	HJURP	72	.	0			c.A2168G						PASS	.	T	GLY/GLU	696,3710	291.8+/-281.7	53,590,1560	104.0	106.0	105.0		2168	3.0	0.1	2	dbSNP_52	105	828,7772	190.8+/-237.2	40,748,3512	yes	missense	HJURP	NM_018410.3	98	93,1338,5072	CC,CT,TT		9.6279,15.7966,11.7177	probably-damaging	723/749	234749258	1524,11482	2203	4300	6503	SO:0001583	missense	55355	exon8			TACCTCTCTTCTG		CCDS33406.1, CCDS63166.1, CCDS63167.1	2q37.1	2007-12-06			ENSG00000123485	ENSG00000123485			25444	protein-coding gene	gene with protein product		612667				17823411	Standard	NM_001282962		Approved	DKFZp762E1312, URLC9, hFLEG1, FAKTS	uc002vvg.3	Q8NCD3	OTTHUMG00000059125	ENST00000411486.2:c.2168A>G	2.37:g.234749258T>C	ENSP00000414109:p.Glu723Gly	Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	124	57	0.459677	NM_018410	A8IRH5|B4DWR0|B4DZV4|Q9BUT2|Q9NSL8	Missense_Mutation	SNP	ENST00000411486.2	37	CCDS33406.1	398	0.18223443223443223	98	0.1991869918699187	39	0.10773480662983426	188	0.32867132867132864	73	0.09630606860158311	T	13.33	2.204373	0.38905	0.157966	0.096279	ENSG00000123485	ENST00000411486;ENST00000432087;ENST00000441687	T;T;T	0.08282	3.11;3.11;3.11	2.97	2.97	0.34412	.	0.926456	0.08847	N	0.884946	T	0.00012	0.0000	L	0.44542	1.39	0.80722	P	0.0	D;D;D	0.71674	0.998;0.998;0.997	D;D;D	0.69824	0.966;0.966;0.925	T	0.49011	-0.8983	9	0.46703	T	0.11	.	7.749	0.28886	0.0:0.0:0.0:1.0	rs10511;rs3178178;rs3193379;rs3771335;rs11546247;rs17342485;rs17350131;rs52831384;rs59962961;rs3178178	638;669;723	Q8NCD3-3;Q8NCD3-2;Q8NCD3	.;.;HJURP_HUMAN	G	723;669;638	ENSP00000414109:E723G;ENSP00000407208:E669G;ENSP00000401944:E638G	ENSP00000414109:E723G	E	-	2	0	HJURP	234413997	0.000000	0.05858	0.088000	0.20740	0.225000	0.24961	-0.036000	0.12185	1.570000	0.49709	0.460000	0.39030	GAG	A|0.153;C|0.110	0.110	strong		0.537	HJURP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000130996.6	NM_018410	
HLA-G	3135	hgsc.bcm.edu	37	6	29795993	29795993	+	Silent	SNP	G	G	A	rs1130355	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:29795993G>A	ENST00000360323.6	+	2	267	c.243G>A	c.(241-243)ccG>ccA	p.P81P	HLA-G_ENST00000376818.3_Silent_p.P81P|HLA-G_ENST00000376815.3_Silent_p.P81P|HLA-G_ENST00000428701.1_Silent_p.P81P|HLA-G_ENST00000376828.2_Silent_p.P86P			P17693	HLAG_HUMAN	major histocompatibility complex, class I, G	81	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)|cellular defense response (GO:0006968)|cytokine-mediated signaling pathway (GO:0019221)|immune response-inhibiting cell surface receptor signaling pathway (GO:0002767)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of dendritic cell differentiation (GO:2001199)|negative regulation of T cell proliferation (GO:0042130)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of regulatory T cell differentiation (GO:0045591)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|positive regulation of T cell tolerance induction (GO:0002666)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)	early endosome membrane (GO:0031901)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|membrane (GO:0016020)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	peptide antigen binding (GO:0042605)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)			central_nervous_system(1)|endometrium(1)|large_intestine(5)|lung(4)|ovary(3)|pancreas(1)|prostate(5)|skin(1)	21						AGGAGGGGCCGGAGTATTGGG	0.647													g|||	2726	0.544329	0.5083	0.4654	5008	,	,		13086	0.6032		0.4324	False		,,,				2504	0.7035				p.P81P		Atlas-SNP	.											.	HLA-G	90	.	0			c.G243A						PASS	.	G		1537,1485		391,755,365	55.0	35.0	42.0		243	0.8	1.0	6	dbSNP_86	42	2509,2909		599,1311,799	no	coding-synonymous	HLA-G	NM_002127.5		990,2066,1164	AA,AG,GG		46.3086,49.1396,47.9384		81/339	29795993	4046,4394	1511	2709	4220	SO:0001819	synonymous_variant	3135	exon3			GGGGCCGGAGTAT		CCDS4668.1	6p21.3	2013-01-11	2007-12-12		ENSG00000204632	ENSG00000204632		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4964	protein-coding gene	gene with protein product	"""b2 microglobulin"""	142871	"""HLA-G histocompatibility antigen, class I, G"""				Standard	NM_002127		Approved		uc003nnw.2	P17693	OTTHUMG00000031157	ENST00000360323.6:c.243G>A	6.37:g.29795993G>A		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	101	98	0.970297	NM_002127		Silent	SNP	ENST00000360323.6	37	CCDS4668.1																																																																																			G|0.500;A|0.500	0.500	strong		0.647	HLA-G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076286.2	NM_002127	
GPATCH1	55094	hgsc.bcm.edu	37	19	33600764	33600764	+	Missense_Mutation	SNP	T	T	C	rs2287679	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	85	0	0		WXS	Illumina HiSeq	Phase_I	47	21	0.446809	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	
PBRM1	55193	hgsc.bcm.edu	37	3	52643685	52643685	+	Silent	SNP	T	T	C	rs3755806	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:52643685T>C	ENST00000296302.7	-	16	2212	c.2211A>G	c.(2209-2211)acA>acG	p.T737T	PBRM1_ENST00000409114.3_Silent_p.T752T|PBRM1_ENST00000409767.1_Silent_p.T752T|PBRM1_ENST00000356770.4_Silent_p.T705T|PBRM1_ENST00000409057.1_Silent_p.T737T|PBRM1_ENST00000337303.4_Silent_p.T737T|PBRM1_ENST00000410007.1_Silent_p.T737T|PBRM1_ENST00000394830.3_Silent_p.T737T			Q86U86	PB1_HUMAN	polybromo 1	737	Bromo 5. {ECO:0000255|PROSITE- ProRule:PRU00035}.				chromatin remodeling (GO:0006338)|heart development (GO:0007507)|mitotic nuclear division (GO:0007067)|negative regulation of cell proliferation (GO:0008285)|placenta development (GO:0001890)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	kinetochore (GO:0000776)|nuclear chromosome (GO:0000228)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)	p.A735fs*7(2)|p.A703fs*7(1)		breast(5)|endometrium(5)|kidney(301)|liver(1)|lung(22)|pancreas(1)	335				BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)		GCTCATTGTATGTACAGGCAT	0.423			"""Mis, N, F, S, D, O"""		"""clear cell renal carcinoma, breast"""								T|||	1615	0.322484	0.1483	0.4611	5008	,	,		22548	0.4276		0.4215	False		,,,				2504	0.2495				p.T737T		Atlas-SNP	.		Rec	yes		3	3p21	55193	polybromo 1		E	PBRM1_ENST00000356770,rectum,carcinoma,0,3	PBRM1	1252	3	3	Deletion - Frameshift(3)	kidney(3)	c.A2211G						PASS	.	T	,,	771,3635	314.4+/-293.6	64,643,1496	141.0	135.0	137.0		2115,2211,2211	-2.2	1.0	3	dbSNP_107	137	3516,5084	512.1+/-377.9	737,2042,1521	no	coding-synonymous,coding-synonymous,coding-synonymous	PBRM1	NM_018165.4,NM_018313.4,NM_181042.3	,,	801,2685,3017	CC,CT,TT		40.8837,17.4989,32.9617	,,	705/1603,737/1583,737/1583	52643685	4287,8719	2203	4300	6503	SO:0001819	synonymous_variant	55193	exon17			ATTGTATGTACAG	BC015323	CCDS43099.1	3p21	2007-03-29			ENSG00000163939	ENSG00000163939			30064	protein-coding gene	gene with protein product		606083				11078522, 11483580	Standard	NM_018313		Approved	BAF180, PB1	uc003der.2	Q86U86	OTTHUMG00000152663	ENST00000296302.7:c.2211A>G	3.37:g.52643685T>C		Somatic	187	0	0		WXS	Illumina HiSeq	Phase_I	181	179	0.98895	NM_018313	A1L381|A1L382|A4FUJ7|Q1RMD1|Q1RMD2|Q96MS2|Q9H2T3|Q9H2T4|Q9H2T5|Q9H301|Q9H314	Silent	SNP	ENST00000296302.7	37																																																																																				T|0.658;C|0.342	0.342	strong		0.423	PBRM1-008	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000327232.1	NM_018165	
SLC2A11	66035	hgsc.bcm.edu	37	22	24224655	24224655	+	Missense_Mutation	SNP	G	G	A	rs9608213	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:24224655G>A	ENST00000345044.6	+	7	963	c.695G>A	c.(694-696)cGg>cAg	p.R232Q	SLC2A11_ENST00000316185.8_Missense_Mutation_p.R235Q|SLC2A11_ENST00000398356.2_Missense_Mutation_p.R239Q|AP000350.10_ENST00000433835.3_Intron|SLC2A11_ENST00000467660.1_3'UTR|RN7SL268P_ENST00000491172.2_RNA			Q9BYW1	GTR11_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 11	232			R -> Q (in dbSNP:rs9608213). {ECO:0000269|PubMed:11741323, ECO:0000269|PubMed:14702039}.		carbohydrate transport (GO:0008643)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	substrate-specific transmembrane transporter activity (GO:0022891)			endometrium(2)|kidney(1)|large_intestine(2)|lung(3)|ovary(1)|prostate(1)|skin(2)	12						GCACTACGGCGGCTCCGGGGC	0.706													g|||	1721	0.34365	0.1899	0.3689	5008	,	,		13898	0.3194		0.4076	False		,,,				2504	0.4928				p.R239Q		Atlas-SNP	.											.	SLC2A11	32	.	0			c.G716A						PASS	.		GLN/ARG,GLN/ARG,GLN/ARG	713,2925		129,455,1235	3.0	4.0	3.0		695,704,716	-2.0	0.6	22	dbSNP_119	3	2666,4600		613,1440,1580	yes	missense,missense,missense	SLC2A11	NM_001024938.2,NM_001024939.2,NM_030807.3	43,43,43	742,1895,2815	AA,AG,GG		36.6914,19.5987,30.9886	possibly-damaging,possibly-damaging,possibly-damaging	232/497,235/500,239/504	24224655	3379,7525	1819	3633	5452	SO:0001583	missense	66035	exon8			TACGGCGGCTCCG	AJ271290	CCDS13818.1, CCDS33616.1, CCDS46673.1, CCDS74828.1	22q11.23	2013-05-22			ENSG00000133460	ENSG00000133460		"""Solute carriers"""	14239	protein-coding gene	gene with protein product		610367					Standard	NM_001024938		Approved	GLUT11, GLUT10	uc002zyp.4	Q9BYW1	OTTHUMG00000166469	ENST00000345044.6:c.695G>A	22.37:g.24224655G>A	ENSP00000342542:p.Arg232Gln	Somatic	15	0	0		WXS	Illumina HiSeq	Phase_I	21	19	0.904762	NM_030807	E9PH55|Q542Y4|Q6ICJ5|Q8WXF9|Q8WYM4	Missense_Mutation	SNP	ENST00000345044.6	37	CCDS46673.1	712|712	0.326007326007326|0.326007326007326	102|102	0.2073170731707317|0.2073170731707317	114|114	0.3149171270718232|0.3149171270718232	183|183	0.31993006993006995|0.31993006993006995	313|313	0.4129287598944591|0.4129287598944591	g|g	9.117|9.117	1.008112|1.008112	0.19199|0.19199	0.195987|0.195987	0.366914|0.366914	ENSG00000251357|ENSG00000133460	ENST00000502845|ENST00000345044;ENST00000398356;ENST00000398359;ENST00000407566;ENST00000316185	.|T;T;T	.|0.75477	.|-0.94;-0.94;-0.94	3.92|3.92	-2.05|-2.05	0.07321|0.07321	.|Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	.|0.356230	.|0.28332	.|N	.|0.015729	T|T	0.00012|0.00012	0.0000|0.0000	M|M	0.63208|0.63208	1.945|1.945	0.35342|0.35342	P|P	0.21342700000000003|0.21342700000000003	.|B;B;B;B;B	.|0.23937	.|0.04;0.068;0.094;0.047;0.083	.|B;B;B;B;B	.|0.24394	.|0.004;0.006;0.053;0.011;0.016	T|T	0.34179|0.34179	-0.9839|-0.9839	4|8	.|.	.|.	.|.	.|.	9.941|9.941	0.41580|0.41580	0.3218:0.0:0.6782:0.0|0.3218:0.0:0.6782:0.0	rs9608213|rs9608213	.|239;235;232;239;239	.|E7ENI4;Q9BYW1-3;Q9BYW1;E9PH55;Q6P4C1	.|.;.;GTR11_HUMAN;.;.	S|Q	4|232;239;239;239;235	.|ENSP00000342542:R232Q;ENSP00000381399:R239Q;ENSP00000326748:R235Q	.|.	G|R	+|+	1|2	0|0	AP000350.10|SLC2A11	22554655|22554655	0.274000|0.274000	0.24191|0.24191	0.617000|0.617000	0.29091|0.29091	0.001000|0.001000	0.01503|0.01503	0.798000|0.798000	0.27014|0.27014	-0.175000|-0.175000	0.10725|0.10725	-1.188000|-1.188000	0.01700|0.01700	GGC|CGG	G|0.678;A|0.322	0.322	strong		0.706	SLC2A11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319889.3	NM_030807	
HLA-A	3105	hgsc.bcm.edu	37	6	29910742	29910742	+	Missense_Mutation	SNP	G	G	C	rs281864739|rs78306866	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:29910742G>C	ENST00000396634.1	+	4	623	c.282G>C	c.(280-282)caG>caC	p.Q94H	HLA-A_ENST00000376802.2_Missense_Mutation_p.Q94H|HLA-A_ENST00000376809.5_Missense_Mutation_p.Q94H|HLA-A_ENST00000376806.5_Missense_Mutation_p.Q94H			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	94	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						TGAAGGCCCAGTCACAGACTG	0.687									Osteosarcoma, Familial Clustering of;Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of;Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of	Multiple Myeloma(9;0.094)			N|||	3409	0.680711	0.6634	0.7133	5008	,	,		10638	0.6706		0.6899	False		,,,				2504	0.682				p.Q94H		Atlas-SNP	.											HLA-A,NS,carcinoma,0,1	HLA-A	89	1	0			c.G282C						PASS	.	C	HIS/GLN	2661,1735		897,867,434	74.0	79.0	78.0		282	-0.6	0.0	6	dbSNP_131	78	5625,2961		2043,1539,711	no	missense	HLA-A	NM_002116.7	24	2940,2406,1145	CC,CG,GG		34.4864,39.4677,36.1732	benign	94/366	29910742	8286,4696	2198	4293	6491	SO:0001583	missense	3105	exon2	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	GGCCCAGTCACAG	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.282G>C	6.37:g.29910742G>C	ENSP00000379873:p.Gln94His	Somatic	261	0	0		WXS	Illumina HiSeq	Phase_I	170	165	0.970588	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Missense_Mutation	SNP	ENST00000396634.1	37	CCDS34373.1	1430	0.6547619047619048	289	0.5873983739837398	244	0.6740331491712708	399	0.6975524475524476	498	0.6569920844327177	.	7.320	0.616730	0.14129	0.605323	0.655136	ENSG00000206503	ENST00000396634;ENST00000376806;ENST00000376809;ENST00000355767;ENST00000376802	T;T;T;T	0.00737	5.76;5.76;5.76;5.76	3.57	-0.587	0.11690	MHC class I, alpha chain, alpha1/alpha2 (6);MHC classes I/II-like antigen recognition protein (3);MHC class I-like antigen recognition (3);	31.095600	0.01235	N	0.008471	T	0.00073	0.0002	N	0.01493	-0.835	0.80722	P	0.0	B;B;B;B;B	0.06786	0.0;0.0;0.0;0.001;0.0	B;B;B;B;B	0.08055	0.001;0.003;0.001;0.001;0.001	T	0.35025	-0.9805	9	0.02654	T	1	.	0.4979	0.00575	0.1804:0.2941:0.1771:0.3484	rs1059463;rs1065458;rs3129020;rs3173425;rs9260134;rs41549017	94;94;94;94;94	P13746;Q5SRN7;P16188;Q5SRN5;P04439	1A11_HUMAN;.;1A30_HUMAN;.;1A03_HUMAN	H	94	ENSP00000379873:Q94H;ENSP00000366002:Q94H;ENSP00000366005:Q94H;ENSP00000365998:Q94H	ENSP00000348012:Q94H	Q	+	3	2	HLA-A	30018721	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.480000	0.00457	-0.256000	0.09473	-1.243000	0.01532	CAG	C|0.643;G|0.357	0.643	strong		0.687	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
ABCG5	64240	hgsc.bcm.edu	37	2	44040401	44040401	+	Missense_Mutation	SNP	G	G	C	rs6720173	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	128	0	0		WXS	Illumina HiSeq	Phase_I	213	213	1	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	
MISP	126353	hgsc.bcm.edu	37	19	757234	757234	+	Silent	SNP	C	C	T	rs34384654	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:757234C>T	ENST00000215582.6	+	2	391	c.288C>T	c.(286-288)cgC>cgT	p.R96R		NM_173481.2	NP_775752.1	Q8IVT2	MISP_HUMAN	mitotic spindle positioning	96					mitotic nuclear division (GO:0007067)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)											AGGTTTACCGCCTGGGCGCCA	0.667													C|||	41	0.0081869	0.0008	0.0043	5008	,	,		17750	0.0		0.0328	False		,,,				2504	0.0041				p.R96R		Atlas-SNP	.											C19orf21,NS,carcinoma,+2,1	C19orf21	56	1	0			c.C288T						PASS	.	C		14,4392	21.2+/-45.6	0,14,2189	60.0	53.0	55.0		288	1.2	0.0	19	dbSNP_126	55	188,8412	82.9+/-145.4	2,184,4114	no	coding-synonymous	C19orf21	NM_173481.2		2,198,6303	TT,TC,CC		2.186,0.3177,1.5531		96/680	757234	202,12804	2203	4300	6503	SO:0001819	synonymous_variant	126353	exon2			TTACCGCCTGGGC	BC052236	CCDS12042.1	19p13.3	2014-06-25	2013-05-03	2013-05-03	ENSG00000099812	ENSG00000099812			27000	protein-coding gene	gene with protein product	"""mitotic interactor and substrate of Plk1"""	615289	"""chromosome 19 open reading frame 21"""	C19orf21		23574715, 23509069, 24475924	Standard	NM_173481		Approved	DKFZp686H18209, Caprice		Q8IVT2	OTTHUMG00000181786	ENST00000215582.6:c.288C>T	19.37:g.757234C>T		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	63	31	0.492063	NM_173481		Silent	SNP	ENST00000215582.6	37	CCDS12042.1																																																																																			C|0.986;T|0.014	0.014	strong		0.667	MISP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457600.2	NM_173481	
CCDC168	643677	hgsc.bcm.edu	37	13	103390322	103390322	+	5'Flank	SNP	T	T	C	rs112442443	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:103390322T>C	ENST00000322527.2	-	0	0					NM_001146197.1	NP_001139669.1	Q8NDH2	CC168_HUMAN	coiled-coil domain containing 168																		tttctgttgctcttcaacttc	0.438													T|||	10	0.00199681	0.0	0.0029	5008	,	,		21687	0.0		0.006	False		,,,				2504	0.002				p.E4242G		Atlas-SNP	.											.	.	.	.	0			c.A12725G						PASS	.	T	GLY/GLU	2,1382		0,2,690	140.0	111.0	120.0		12725	-0.2	0.0	13	dbSNP_132	120	24,3158		0,24,1567	yes	missense	CCDC168	NM_001146197.1	98	0,26,2257	CC,CT,TT		0.7542,0.1445,0.5694		4242/7082	103390322	26,4540	692	1591	2283	SO:0001631	upstream_gene_variant	643677	exon4			TGTTGCTCTTCAA		CCDS73596.1	13q33.1	2014-06-17	2011-08-09	2011-08-09	ENSG00000175820	ENSG00000175820			26851	protein-coding gene	gene with protein product			"""chromosome 13 open reading frame 40"""	C13orf40			Standard	NM_001146197		Approved	FLJ40176	uc001vpm.3	Q8NDH2	OTTHUMG00000187287		13.37:g.103390322T>C	Exception_encountered	Somatic	301	1	0.00332226		WXS	Illumina HiSeq	Phase_I	245	124	0.506122	NM_001146197	Q8N800	Missense_Mutation	SNP	ENST00000322527.2	37																																																																																				T|0.995;C|0.005	0.005	strong		0.438	CCDC168-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001146197	
ARHGAP42	143872	hgsc.bcm.edu	37	11	100814570	100814570	+	Silent	SNP	A	A	G	rs543146	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:100814570A>G	ENST00000298815.8	+	10	1017	c.1014A>G	c.(1012-1014)cgA>cgG	p.R338R	ARHGAP42_ENST00000524892.2_Silent_p.R304R	NM_152432.2	NP_689645.2	A6NI28	RHG42_HUMAN	Rho GTPase activating protein 42	338	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				signal transduction (GO:0007165)	intracellular (GO:0005622)	GTPase activator activity (GO:0005096)			endometrium(3)|skin(2)	5						TTGACAAACGATTCTGCTTTG	0.328													A|||	2058	0.410942	0.1362	0.4308	5008	,	,		17776	0.7312		0.2565	False		,,,				2504	0.5971				p.R338R		Atlas-SNP	.											.	ARHGAP42	32	.	0			c.A1014G						PASS	.	A		276,1108		24,228,440	120.0	97.0	104.0		1014	-1.1	1.0	11	dbSNP_83	104	911,2271		127,657,807	no	coding-synonymous	ARHGAP42	NM_152432.2		151,885,1247	GG,GA,AA		28.6298,19.9422,25.9965		338/875	100814570	1187,3379	692	1591	2283	SO:0001819	synonymous_variant	143872	exon10			CAAACGATTCTGC			11q22.1	2012-04-19			ENSG00000165895	ENSG00000165895		"""Rho GTPase activating proteins"""	26545	protein-coding gene	gene with protein product		615936				18954304	Standard	NM_152432		Approved	FLJ32810, GRAF3	uc001pge.2	A6NI28	OTTHUMG00000167530	ENST00000298815.8:c.1014A>G	11.37:g.100814570A>G		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	43	7	0.162791	NM_152432	Q96M56	Silent	SNP	ENST00000298815.8	37																																																																																				A|0.643;G|0.357	0.357	strong		0.328	ARHGAP42-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_152432	
WRAP53	55135	hgsc.bcm.edu	37	17	7606722	7606722	+	Missense_Mutation	SNP	C	C	G	rs7640|rs373064567	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:7606722C>G	ENST00000316024.5	+	10	3913	c.1565C>G	c.(1564-1566)gCg>gGg	p.A522G	WRAP53_ENST00000534050.1_Missense_Mutation_p.A489G|WRAP53_ENST00000396463.2_Missense_Mutation_p.A522G|WRAP53_ENST00000431639.2_Missense_Mutation_p.A522G|EFNB3_ENST00000226091.2_5'Flank|WRAP53_ENST00000457584.2_Missense_Mutation_p.A522G			Q9BUR4	WAP53_HUMAN	WD repeat containing, antisense to TP53	522			A -> G (in dbSNP:rs7640). {ECO:0000269|PubMed:21205863}.		positive regulation of telomerase activity (GO:0051973)|telomere formation via telomerase (GO:0032203)	Cajal body (GO:0015030)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|telomerase holoenzyme complex (GO:0005697)	RNA binding (GO:0003723)	p.A522G(1)		endometrium(4)|kidney(1)|large_intestine(2)|lung(7)|prostate(2)|stomach(2)	18						TGTGGGGGGGCGCCAGACTCC	0.582													G|||	2560	0.511182	0.9327	0.3069	5008	,	,		15581	0.4077		0.2336	False		,,,				2504	0.4785				p.A522G		Atlas-SNP	.											WRAP53,NS,carcinoma,0,1	WRAP53	35	1	1	Substitution - Missense(1)	stomach(1)	c.C1565G						PASS	.	G	GLY/ALA,GLY/ALA,GLY/ALA,GLY/ALA	3470,936		1423,624,156	47.0	48.0	48.0		1565,1565,1565,1565	-6.6	0.0	17	dbSNP_52	48	1675,6925		185,1305,2810	yes	missense,missense,missense,missense	WRAP53	NM_001143990.1,NM_001143991.1,NM_001143992.1,NM_018081.2	60,60,60,60	1608,1929,2966	GG,GC,CC		19.4767,21.2438,39.5587	benign,benign,benign,benign	522/549,522/549,522/549,522/549	7606722	5145,7861	2203	4300	6503	SO:0001583	missense	55135	exon11			GGGGGGCGCCAGA	AK001247, DQ431240	CCDS11119.1	17p13.1	2014-09-17	2009-02-16	2009-02-16	ENSG00000141499	ENSG00000141499		"""WD repeat domain containing"""	25522	protein-coding gene	gene with protein product	"""telomerase cajal body protein 1"", ""WD-encoding RNA antisense to p53"""	612661	"""WD repeat domain 79"""	WDR79		19179534, 19250907, 19571673, 19342896, 20494116, 21441950	Standard	NM_018081		Approved	FLJ10385, TCAB1	uc010vuh.2	Q9BUR4	OTTHUMG00000134323	ENST00000316024.5:c.1565C>G	17.37:g.7606722C>G	ENSP00000324203:p.Ala522Gly	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	58	23	0.396552	NM_001143991	B3KPR9|D3DTQ4|Q08ET9|Q9NW09	Missense_Mutation	SNP	ENST00000316024.5	37	CCDS11119.1	938	0.42948717948717946	446	0.9065040650406504	97	0.26795580110497236	219	0.38286713286713286	176	0.23218997361477572	G	0.042	-1.279172	0.01410	0.787562	0.194767	ENSG00000141499	ENST00000431639;ENST00000316024;ENST00000457584;ENST00000396463;ENST00000534050	T;T;T;T;T	0.52295	0.67;0.67;0.67;0.67;0.76	5.45	-6.63	0.01807	.	0.942750	0.08843	N	0.885533	T	0.00012	0.0000	N	0.01410	-0.885	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.31833	-0.9929	9	0.02654	T	1	0.5657	8.5577	0.33492	0.4452:0.331:0.2237:0.0	rs7640;rs3186836;rs7640	489;522	E9PMG4;Q9BUR4	.;WAP53_HUMAN	G	522;522;522;522;489	ENSP00000397219:A522G;ENSP00000324203:A522G;ENSP00000411061:A522G;ENSP00000379727:A522G;ENSP00000434999:A489G	ENSP00000324203:A522G	A	+	2	0	WRAP53	7547447	0.000000	0.05858	0.000000	0.03702	0.172000	0.22775	-1.904000	0.01593	-1.379000	0.02118	-0.232000	0.12228	GCG	C|0.591;G|0.409	0.409	strong		0.582	WRAP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259385.2	NM_018081	
FAM86C1	55199	hgsc.bcm.edu	37	11	71507158	71507158	+	Silent	SNP	A	A	G	rs138882787	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:71507158A>G	ENST00000359244.4	+	4	380	c.357A>G	c.(355-357)acA>acG	p.T119T	FAM86C1_ENST00000346333.6_Silent_p.T85T|FAM86C1_ENST00000426628.2_Silent_p.T112T	NM_018172.2	NP_060642.2	Q9NVL1	FA86C_HUMAN	family with sequence similarity 86, member C1	119										lung(1)	1						TCAATTCTACATGGCCCTTAC	0.647													.|||	23	0.00459265	0.0023	0.0043	5008	,	,		16631	0.0089		0.006	False		,,,				2504	0.002				p.T119T		Atlas-SNP	.											.	FAM86C1	27	.	0			c.A357G						PASS	.						100.0	106.0	104.0					11																	71507158		2200	4293	6493	SO:0001819	synonymous_variant	55199	exon4			TTCTACATGGCCC	AK130709	CCDS8202.1, CCDS41686.1, CCDS44664.1	11q13.4	2011-07-07	2011-07-07	2011-07-07	ENSG00000158483	ENSG00000158483			25561	protein-coding gene	gene with protein product			"""family with sequence similarity 86, member C"""	FAM86C		12477932	Standard	NM_152563		Approved	FLJ10661, FLJ27199	uc001oqv.4	Q9NVL1	OTTHUMG00000160552	ENST00000359244.4:c.357A>G	11.37:g.71507158A>G		Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	187	39	0.208556	NM_018172	Q8N5D3	Silent	SNP	ENST00000359244.4	37	CCDS41686.1																																																																																			A|0.998;G|0.002	0.002	strong		0.647	FAM86C1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000361120.1	NM_152563	
GDPGP1	390637	hgsc.bcm.edu	37	15	90784930	90784930	+	Missense_Mutation	SNP	C	C	A	rs10152994	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:90784930C>A	ENST00000558017.1	+	4	1210	c.790C>A	c.(790-792)Cct>Act	p.P264T	GDPGP1_ENST00000329600.6_Missense_Mutation_p.P264T	NM_001013657.2	NP_001013679.2	Q6ZNW5	GDPP1_HUMAN	GDP-D-glucose phosphorylase 1	264			P -> T (in dbSNP:rs10152994). {ECO:0000269|PubMed:14702039}.		glucose metabolic process (GO:0006006)	cytoplasm (GO:0005737)	GDP-D-glucose phosphorylase activity (GO:0080048)|guanyl-nucleotide exchange factor activity (GO:0005085)|hydrolase activity (GO:0016787)|nucleotide binding (GO:0000166)|nucleotidyltransferase activity (GO:0016779)										TGGGCCAGGGCCTGACTTGGA	0.587													C|||	662	0.132188	0.2436	0.1398	5008	,	,		19088	0.0		0.1789	False		,,,				2504	0.0644				p.P264T		Atlas-SNP	.											.	.	.	.	0			c.C790A						PASS	.	C	THR/PRO	872,3526	340.7+/-306.4	90,692,1417	76.0	68.0	71.0		790	4.0	0.0	15	dbSNP_119	71	1435,7161	275.6+/-291.8	131,1173,2994	yes	missense	C15orf58	NM_001013657.2	38	221,1865,4411	AA,AC,CC		16.6938,19.8272,17.7543	possibly-damaging	264/386	90784930	2307,10687	2199	4298	6497	SO:0001583	missense	390637	exon4			CCAGGGCCTGACT		CCDS32327.1	15q26.1	2012-05-04	2012-05-04	2012-05-04	ENSG00000183208	ENSG00000183208	2.7.7.78		34360	protein-coding gene	gene with protein product			"""chromosome 15 open reading frame 58"""	C15orf58		21507950	Standard	NM_001013657		Approved		uc002bpc.3	Q6ZNW5		ENST00000558017.1:c.790C>A	15.37:g.90784930C>A	ENSP00000452793:p.Pro264Thr	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	119	47	0.394958	NM_001013657		Missense_Mutation	SNP	ENST00000558017.1	37	CCDS32327.1	311	0.1423992673992674	114	0.23170731707317074	61	0.1685082872928177	0	0.0	136	0.17941952506596306	C	0.104	-1.147311	0.01714	0.198272	0.166938	ENSG00000183208	ENST00000329600	T	0.21031	2.03	5.95	4.0	0.46444	.	0.529862	0.20055	N	0.100211	T	0.00012	0.0000	L	0.32530	0.975	0.80722	P	0.0	P	0.41848	0.763	B	0.36608	0.229	T	0.36792	-0.9733	9	0.12103	T	0.63	-2.3515	15.5393	0.76027	0.0:0.608:0.392:0.0	rs10152994;rs60285158;rs10152994	264	Q6ZNW5	VTC2_HUMAN	T	264	ENSP00000368405:P264T	ENSP00000368405:P264T	P	+	1	0	C15orf58	88585934	0.098000	0.21812	0.009000	0.14445	0.008000	0.06430	2.045000	0.41250	0.787000	0.33731	0.655000	0.94253	CCT	C|0.833;A|0.167	0.167	strong		0.587	GDPGP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416973.1	NM_001013657	
CCDC53	51019	hgsc.bcm.edu	37	12	102455729	102455729	+	Silent	SNP	G	G	A	rs3751129	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:102455729G>A	ENST00000240079.6	-	1	173	c.12C>T	c.(10-12)gaC>gaT	p.D4D	RP11-554E23.4_ENST00000552707.1_RNA|CCDC53_ENST00000539515.1_Intron|CCDC53_ENST00000545679.1_Silent_p.D4D	NM_016053.2	NP_057137.1	Q9Y3C0	CCD53_HUMAN	coiled-coil domain containing 53	4						actin cytoskeleton (GO:0015629)|intracellular membrane-bounded organelle (GO:0043231)|WASH complex (GO:0071203)				endometrium(1)|kidney(1)|large_intestine(1)|lung(1)	4						GAGGAAGCCCGTCCTCATCCA	0.612													G|||	1404	0.280351	0.3003	0.2464	5008	,	,		16728	0.4276		0.2157	False		,,,				2504	0.1922				p.D4D		Atlas-SNP	.											.	CCDC53	14	.	0			c.C12T						PASS	.	G		1183,2651		195,793,929	26.0	31.0	29.0		12	-0.9	1.0	12	dbSNP_107	29	1782,6448		209,1364,2542	no	coding-synonymous	CCDC53	NM_016053.2		404,2157,3471	AA,AG,GG		21.6525,30.8555,24.5773		4/195	102455729	2965,9099	1917	4115	6032	SO:0001819	synonymous_variant	51019	exon1			AAGCCCGTCCTCA	AF151874	CCDS44959.1, CCDS73512.1	12q23.3	2014-05-09			ENSG00000120860	ENSG00000120860			24256	protein-coding gene	gene with protein product						10810093, 20498093	Standard	XM_005268939		Approved	CGI-116	uc010svw.2	Q9Y3C0	OTTHUMG00000168187	ENST00000240079.6:c.12C>T	12.37:g.102455729G>A		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	38	20	0.526316	NM_016053	B2RC74|Q53FF0|Q6IAI4|Q96QK0	Silent	SNP	ENST00000240079.6	37	CCDS44959.1																																																																																			G|0.694;A|0.306	0.306	strong		0.612	CCDC53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398685.1	NM_016053	
F2R	2149	hgsc.bcm.edu	37	5	76028669	76028669	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:76028669C>T	ENST00000319211.4	+	2	884	c.619C>T	c.(619-621)Ccc>Tcc	p.P207S		NM_001992.3	NP_001983.2	P25116	PAR1_HUMAN	coagulation factor II (thrombin) receptor	207					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of MAPKK activity (GO:0000186)|anatomical structure morphogenesis (GO:0009653)|blood coagulation (GO:0007596)|connective tissue replacement involved in inflammatory response wound healing (GO:0002248)|establishment of synaptic specificity at neuromuscular junction (GO:0007529)|G-protein coupled receptor signaling pathway (GO:0007186)|homeostasis of number of cells within a tissue (GO:0048873)|inflammatory response (GO:0006954)|negative regulation of cell proliferation (GO:0008285)|negative regulation of glomerular filtration (GO:0003105)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of renin secretion into blood stream (GO:1900134)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|platelet activation (GO:0030168)|platelet dense granule organization (GO:0060155)|positive regulation of blood coagulation (GO:0030194)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of collagen biosynthetic process (GO:0032967)|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 cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-6 secretion (GO:2000778)|positive regulation of interleukin-8 secretion (GO:2000484)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|positive regulation of Rho protein signal transduction (GO:0035025)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of vasoconstriction (GO:0045907)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of blood coagulation (GO:0030193)|regulation of interleukin-1 beta production (GO:0032651)|regulation of sensory perception of pain (GO:0051930)|release of sequestered calcium ion into cytosol (GO:0051209)|response to lipopolysaccharide (GO:0032496)|response to wounding (GO:0009611)|STAT protein import into nucleus (GO:0007262)|tyrosine phosphorylation of STAT protein (GO:0007260)	caveola (GO:0005901)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)|platelet dense tubular network (GO:0031094)|postsynaptic membrane (GO:0045211)	G-protein alpha-subunit binding (GO:0001965)|G-protein beta-subunit binding (GO:0031681)|G-protein coupled receptor activity (GO:0004930)|receptor binding (GO:0005102)|thrombin receptor activity (GO:0015057)			NS(1)|breast(1)|endometrium(3)|kidney(1)|lung(7)|ovary(3)	16		all_lung(232;0.000414)|Lung NSC(167;0.0011)|Prostate(461;0.00955)|Ovarian(174;0.0129)		all cancers(79;4.43e-43)	Streptokinase(DB00086)	TGTGGTGTATCCCATGCAGTC	0.527																																					p.P207S		Atlas-SNP	.											.	F2R	58	.	0			c.C619T						PASS	.						184.0	181.0	182.0					5																	76028669		2203	4300	6503	SO:0001583	missense	2149	exon2			GTGTATCCCATGC	M62424	CCDS4032.1	5q13	2012-08-08			ENSG00000181104	ENSG00000181104		"""GPCR / Class A : Protease activated receptors"""	3537	protein-coding gene	gene with protein product		187930				8395910	Standard	NM_001992		Approved	TR, CF2R, PAR1, PAR-1	uc003ken.4	P25116	OTTHUMG00000131299	ENST00000319211.4:c.619C>T	5.37:g.76028669C>T	ENSP00000321326:p.Pro207Ser	Somatic	249	0	0		WXS	Illumina HiSeq	Phase_I	250	49	0.196	NM_001992	Q53XV0|Q96RF7|Q9BUN4	Missense_Mutation	SNP	ENST00000319211.4	37	CCDS4032.1	.	.	.	.	.	.	.	.	.	.	C	28.4	4.913750	0.92178	.	.	ENSG00000181104	ENST00000319211	T	0.60920	0.15	5.07	5.07	0.68467	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.80849	0.4702	M	0.88181	2.935	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.84195	0.0447	10	0.87932	D	0	-44.8056	19.0012	0.92834	0.0:1.0:0.0:0.0	.	207	P25116	PAR1_HUMAN	S	207	ENSP00000321326:P207S	ENSP00000321326:P207S	P	+	1	0	F2R	76064425	1.000000	0.71417	0.998000	0.56505	0.988000	0.76386	7.502000	0.81614	2.786000	0.95864	0.561000	0.74099	CCC	.	.	none		0.527	F2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254068.2		
CMYA5	202333	hgsc.bcm.edu	37	5	79032562	79032562	+	Silent	SNP	A	A	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:79032562A>G	ENST00000446378.2	+	2	8005	c.7974A>G	c.(7972-7974)gtA>gtG	p.V2658V		NM_153610.3	NP_705838.3	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	2658					negative regulation of calcineurin-NFAT signaling cascade (GO:0070885)|negative regulation of protein phosphatase type 2B activity (GO:0032513)|regulation of skeletal muscle adaptation (GO:0014733)	costamere (GO:0043034)				NS(2)|breast(4)|central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(37)|lung(34)|ovary(6)|pancreas(2)|prostate(5)|skin(5)|stomach(11)|upper_aerodigestive_tract(3)|urinary_tract(1)	128		Lung NSC(167;0.00296)|all_lung(232;0.00327)|Ovarian(174;0.0262)		OV - Ovarian serous cystadenocarcinoma(54;9.85e-46)|Epithelial(54;3.38e-40)|all cancers(79;3.43e-35)		GAAATCTAGTATTAGAAAAGT	0.408																																					p.V2658V		Atlas-SNP	.											CMYA5_ENST00000446378,lower_third,carcinoma,0,2	CMYA5	643	2	0			c.A7974G						scavenged	.						48.0	48.0	48.0					5																	79032562		1831	4091	5922	SO:0001819	synonymous_variant	202333	exon2			TCTAGTATTAGAA	AW755254, AL831986	CCDS47238.1	5q14.1	2013-02-11			ENSG00000164309	ENSG00000164309		"""Tripartite motif containing / Tripartite motif containing"", ""A-kinase anchor proteins"", ""Fibronectin type III domain containing"""	14305	protein-coding gene	gene with protein product	"""genethonin-3"", ""tripartite motif-containing 76"""	612193	"""chromosome 5 open reading frame 10"""	C5orf10		14688250	Standard	NM_153610		Approved	myospryn, SPRYD2, DKFZp451G223, TRIM76	uc003kgc.3	Q8N3K9	OTTHUMG00000162548	ENST00000446378.2:c.7974A>G	5.37:g.79032562A>G		Somatic	128	1	0.0078125		WXS	Illumina HiSeq	Phase_I	106	3	0.0283019	NM_153610	A0PJB7|Q05CT4|Q2NKX1|Q2T9G9|Q69YQ8|Q69YQ9|Q6P517|Q6P5U3|Q7Z4I1|Q86T34|Q86T49|Q8N3S4|Q8N3S7|Q8NAG8|Q9UK88	Silent	SNP	ENST00000446378.2	37	CCDS47238.1																																																																																			.	.	none		0.408	CMYA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369497.1	NM_153610	
DTX2	113878	hgsc.bcm.edu	37	7	76111938	76111938	+	Missense_Mutation	SNP	G	G	A	rs12534498	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:76111938G>A	ENST00000324432.5	+	5	892	c.382G>A	c.(382-384)Gtc>Atc	p.V128I	DTX2_ENST00000413936.2_Missense_Mutation_p.V128I|DTX2_ENST00000307569.8_Missense_Mutation_p.V128I|DTX2_ENST00000446820.2_Missense_Mutation_p.V128I|DTX2_ENST00000446600.1_Missense_Mutation_p.V37I|DTX2_ENST00000430490.2_Missense_Mutation_p.V128I	NM_020892.2	NP_065943.2	Q86UW9	DTX2_HUMAN	deltex 2, E3 ubiquitin ligase	128	WWE 2. {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						TGAAGCCAGCGTCTGTGACTA	0.627													.|||	41	0.0081869	0.0008	0.013	5008	,	,		15104	0.0		0.0278	False		,,,				2504	0.0031				p.V128I		Atlas-SNP	.											.	DTX2	64	.	0			c.G382A						PASS	.	G	ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL	18,4388		0,18,2185	57.0	52.0	53.0		382,382,382,382	-1.8	0.2	7	dbSNP_120	53	164,8436		2,160,4138	yes	missense,missense,missense,missense	DTX2	NM_001102594.1,NM_001102595.1,NM_001102596.1,NM_020892.2	29,29,29,29	2,178,6323	AA,AG,GG		1.907,0.4085,1.3994	benign,benign,benign,benign	128/623,128/623,128/576,128/623	76111938	182,12824	2203	4300	6503	SO:0001583	missense	113878	exon2			GCCAGCGTCTGTG		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.382G>A	7.37:g.76111938G>A	ENSP00000322885:p.Val128Ile	Somatic	182	0	0		WXS	Illumina HiSeq	Phase_I	136	68	0.5	NM_001102596	Q6XM87|Q6XM88|Q96H69|Q9H890|Q9P200	Missense_Mutation	SNP	ENST00000324432.5	37	CCDS5587.1	20	0.009157509157509158	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	18	0.023746701846965697	.	2.386	-0.340930	0.05243	0.004085	0.01907	ENSG00000091073	ENST00000324432;ENST00000307569;ENST00000541989;ENST00000446600;ENST00000413936;ENST00000423646;ENST00000430490;ENST00000446820	T;T;T;T;T;T;T	0.48522	0.81;0.81;0.81;0.81;0.81;0.81;0.81	5.41	-1.8	0.07907	WWE domain (2);WWE domain, subgroup (1);	0.499471	0.22570	N	0.058341	T	0.11665	0.0284	N	0.16833	0.445	0.09310	N	0.999998	B;B;B	0.22604	0.072;0.041;0.038	B;B;B	0.23716	0.048;0.012;0.021	T	0.17592	-1.0364	10	0.12766	T	0.61	-18.6177	6.1106	0.20097	0.4918:0.0:0.387:0.1211	rs12534498;rs12534498	37;128;128	F5GX89;Q86UW9-2;Q86UW9	.;.;DTX2_HUMAN	I	128;128;37;37;128;128;128;128	ENSP00000322885:V128I;ENSP00000305242:V128I;ENSP00000397648:V37I;ENSP00000390218:V128I;ENSP00000415838:V128I;ENSP00000411986:V128I;ENSP00000392545:V128I	ENSP00000305242:V128I	V	+	1	0	AC005522.1	75949874	0.003000	0.15002	0.212000	0.23672	0.350000	0.29205	0.080000	0.14802	-0.374000	0.07967	-0.291000	0.09656	GTC	G|0.988;A|0.012	0.012	strong		0.627	DTX2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253104.2		
ADAMTS18	170692	hgsc.bcm.edu	37	16	77328990	77328990	+	Missense_Mutation	SNP	C	C	A	rs12935394	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	90	0	0		WXS	Illumina HiSeq	Phase_I	104	35	0.336538	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		
KLHL1	57626	hgsc.bcm.edu	37	13	70293616	70293616	+	Missense_Mutation	SNP	A	A	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:70293616A>T	ENST00000377844.4	-	9	2659	c.1900T>A	c.(1900-1902)Tgt>Agt	p.C634S	KLHL1_ENST00000545028.1_Missense_Mutation_p.C441S	NM_020866.2	NP_065917.1	Q9NR64	KLHL1_HUMAN	kelch-like family member 1	634					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)		CTCCTCTTACACATGGGAGCA	0.458																																					p.C634S		Atlas-SNP	.											.	KLHL1	164	.	0			c.T1900A						PASS	.						124.0	107.0	113.0					13																	70293616		2203	4300	6503	SO:0001583	missense	57626	exon9			TCTTACACATGGG	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.1900T>A	13.37:g.70293616A>T	ENSP00000367075:p.Cys634Ser	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	82	15	0.182927	NM_020866	A8K5X0|Q5VZ64|Q9H4X4|Q9NR65|Q9P238	Missense_Mutation	SNP	ENST00000377844.4	37	CCDS9445.1	.	.	.	.	.	.	.	.	.	.	A	6.361	0.434642	0.12045	.	.	ENSG00000150361	ENST00000377844;ENST00000545028	T;T	0.64991	-0.13;-0.13	5.82	5.82	0.92795	Galactose oxidase, beta-propeller (1);	0.082942	0.52532	D	0.000067	T	0.24236	0.0587	N	0.00178	-1.915	0.45261	D	0.998261	B;B	0.09022	0.002;0.002	B;B	0.15052	0.012;0.012	T	0.49688	-0.8913	10	0.02654	T	1	.	16.171	0.81817	1.0:0.0:0.0:0.0	.	634;634	Q8TBJ7;Q9NR64	.;KLHL1_HUMAN	S	634;441	ENSP00000367075:C634S;ENSP00000439602:C441S	ENSP00000367075:C634S	C	-	1	0	KLHL1	69191617	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.228000	0.51270	2.211000	0.71520	0.533000	0.62120	TGT	.	.	none		0.458	KLHL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045231.3	NM_020866	
CCDC67	159989	hgsc.bcm.edu	37	11	93129483	93129483	+	Missense_Mutation	SNP	G	G	C	rs386756254|rs12288277	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	154	0	0		WXS	Illumina HiSeq	Phase_I	116	115	0.991379	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	
PARL	55486	hgsc.bcm.edu	37	3	183560195	183560195	+	Silent	SNP	A	A	G	rs13091	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:183560195A>G	ENST00000317096.4	-	6	708	c.648T>C	c.(646-648)caT>caC	p.H216H	PARL_ENST00000435888.1_Intron|PARL_ENST00000311101.5_Intron	NM_018622.5	NP_061092.3	Q9H300	PARL_HUMAN	presenilin associated, rhomboid-like	216					membrane protein proteolysis (GO:0033619)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|negative regulation of release of cytochrome c from mitochondria (GO:0090201)|proteolysis (GO:0006508)|regulation of protein targeting to mitochondrion (GO:1903214)|regulation of reactive oxygen species metabolic process (GO:2000377)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	endopeptidase activity (GO:0004175)|serine-type endopeptidase activity (GO:0004252)	p.H216H(1)		endometrium(2)|large_intestine(3)|liver(1)|lung(6)|prostate(1)|skin(1)|stomach(2)|urinary_tract(1)	17	all_cancers(143;6.55e-10)|Ovarian(172;0.0303)		all cancers(12;2.21e-41)|Epithelial(37;1.34e-36)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)			ATAAGGAGAAATGACTGAATG	0.403													A|||	2288	0.456869	0.4962	0.4986	5008	,	,		19755	0.4077		0.4781	False		,,,				2504	0.4029				p.H216H		Atlas-SNP	.											PARL,NS,carcinoma,0,1	PARL	32	1	1	Substitution - coding silent(1)	stomach(1)	c.T648C						PASS	.	A	,	2173,2233	584.5+/-386.0	535,1103,565	103.0	98.0	99.0		,648	0.4	1.0	3	dbSNP_52	99	4163,4437	566.5+/-388.7	1007,2149,1144	no	intron,coding-synonymous	PARL	NM_001037639.1,NM_018622.5	,	1542,3252,1709	GG,GA,AA		48.407,49.3191,48.716	,	,216/380	183560195	6336,6670	2203	4300	6503	SO:0001819	synonymous_variant	55486	exon6			GGAGAAATGACTG	AF116692	CCDS3248.1, CCDS33897.1	3q27.3	2008-02-05		2006-02-28	ENSG00000175193	ENSG00000175193			18253	protein-coding gene	gene with protein product	"""rhomboid 7 homolog 1 (Drosophila)"""	607858		PSARL			Standard	XM_005247587		Approved	PRO2207, PSARL1, RHBDS1	uc003fmd.3	Q9H300	OTTHUMG00000156890	ENST00000317096.4:c.648T>C	3.37:g.183560195A>G		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	64	32	0.5	NM_018622	Q96CQ4|Q9BTJ6|Q9P1E3	Silent	SNP	ENST00000317096.4	37	CCDS3248.1																																																																																			A|0.512;G|0.488	0.488	strong		0.403	PARL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346465.1	NM_018622	
CINP	51550	hgsc.bcm.edu	37	14	102815042	102815042	+	Missense_Mutation	SNP	C	C	T	rs7011	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:102815042C>T	ENST00000216756.6	-	5	531	c.491G>A	c.(490-492)cGc>cAc	p.R164H	CINP_ENST00000560326.1_5'Flank|CINP_ENST00000536961.2_Missense_Mutation_p.R179H|CINP_ENST00000541568.2_3'UTR	NM_032630.2	NP_116019.1	Q9BW66	CINP_HUMAN	cyclin-dependent kinase 2 interacting protein	164			R -> H (in dbSNP:rs7011).		cell cycle (GO:0007049)|cell division (GO:0051301)|DNA repair (GO:0006281)|DNA replication (GO:0006260)	nucleus (GO:0005634)				large_intestine(2)|lung(2)	4						GGCCACCGTGCGCTTCAGGAG	0.552													C|||	826	0.164936	0.0756	0.1643	5008	,	,		20078	0.1081		0.2654	False		,,,				2504	0.2413				p.R179H		Atlas-SNP	.											CINP,NS,carcinoma,-1,1	CINP	17	1	0			c.G536A						PASS	.	C	HIS/ARG,,HIS/ARG	462,3944	220.7+/-238.1	35,392,1776	78.0	53.0	61.0		536,,491	2.8	0.7	14	dbSNP_52	61	2570,6030	417.0+/-352.3	371,1828,2101	yes	missense,utr-3,missense	CINP	NM_001177611.1,NM_001177612.1,NM_032630.2	29,,29	406,2220,3877	TT,TC,CC		29.8837,10.4857,23.3123	benign,,benign	179/228,,164/213	102815042	3032,9974	2203	4300	6503	SO:0001583	missense	51550	exon5			ACCGTGCGCTTCA	AK056112, AF228148, AF228149	CCDS9972.1	14q32.33	2010-02-17			ENSG00000100865	ENSG00000100865			23789	protein-coding gene	gene with protein product		613362				16082200	Standard	NM_032630		Approved	MGC849	uc021sea.1	Q9BW66		ENST00000216756.6:c.491G>A	14.37:g.102815042C>T	ENSP00000216756:p.Arg164His	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	84	42	0.5	NM_001177611	F5H7P3|F5H8A7|Q9NPF9	Missense_Mutation	SNP	ENST00000216756.6	37	CCDS9972.1	349	0.15979853479853479	37	0.07520325203252033	61	0.1685082872928177	52	0.09090909090909091	199	0.262532981530343	C	10.76	1.440241	0.25900	0.104857	0.298837	ENSG00000100865	ENST00000216756;ENST00000536961	T;T	0.53206	0.67;0.63	6.07	2.76	0.32466	.	0.355408	0.30101	N	0.010410	T	0.00012	0.0000	L	0.50919	1.6	0.09310	P	0.999999999841401	B	0.21309	0.054	B	0.09377	0.004	T	0.23940	-1.0174	9	0.30854	T	0.27	-2.3364	9.4492	0.38717	0.0:0.6095:0.0:0.3905	rs7011;rs17664746;rs52824323;rs59427525;rs7011	164	Q9BW66	CINP_HUMAN	H	164;179	ENSP00000216756:R164H;ENSP00000442057:R179H	ENSP00000216756:R164H	R	-	2	0	CINP	101884795	0.999000	0.42202	0.701000	0.30321	0.134000	0.20937	0.621000	0.24418	0.644000	0.30656	-0.140000	0.14226	CGC	C|0.795;N|0.000	.	strong		0.552	CINP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415055.1	NM_032630	
CALB2	794	hgsc.bcm.edu	37	16	71411636	71411636	+	Missense_Mutation	SNP	G	G	A	rs11545954	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:71411636G>A	ENST00000302628.4	+	4	405	c.328G>A	c.(328-330)Gcc>Acc	p.A110T	CALB2_ENST00000349553.5_Missense_Mutation_p.A110T	NM_001740.4	NP_001731.2	P22676	CALB2_HUMAN	calbindin 2	110	EF-hand 3. {ECO:0000255|PROSITE- ProRule:PRU00448}.			A -> T (in Ref. 5; AAH15484). {ECO:0000305}.	cytosolic calcium ion homeostasis (GO:0051480)	cytoplasm (GO:0005737)|gap junction (GO:0005921)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(7)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	18		Ovarian(137;0.125)				GGGCTCCAGCGCCGAGTTTAT	0.572													G|||	690	0.13778	0.1861	0.1052	5008	,	,		19624	0.0298		0.1292	False		,,,				2504	0.2157				p.A110T		Atlas-SNP	.											.	CALB2	46	.	0			c.G328A						PASS	.	G	THR/ALA,THR/ALA	751,3645	306.9+/-289.7	63,625,1510	94.0	84.0	88.0		328,328	1.2	0.9	16	dbSNP_120	88	1117,7483	232.6+/-266.2	72,973,3255	yes	missense,missense	CALB2	NM_001740.4,NM_007088.3	58,58	135,1598,4765	AA,AG,GG		12.9884,17.0837,14.3737	benign,benign	110/272,110/193	71411636	1868,11128	2198	4300	6498	SO:0001583	missense	794	exon4			TCCAGCGCCGAGT	X56667	CCDS10899.1	16q22.2	2013-01-10	2008-05-19		ENSG00000172137	ENSG00000172137		"""EF-hand domain containing"""	1435	protein-coding gene	gene with protein product	"""calretinin"""	114051	"""calbindin 2, 29kDa (calretinin)"""			1906795	Standard	NM_001740		Approved	CAL2	uc002faa.4	P22676	OTTHUMG00000137589	ENST00000302628.4:c.328G>A	16.37:g.71411636G>A	ENSP00000307508:p.Ala110Thr	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	91	54	0.593407	NM_007088	A8K4Y1|Q53HD2|Q96BK4	Missense_Mutation	SNP	ENST00000302628.4	37	CCDS10899.1	264	0.12087912087912088	103	0.20934959349593496	51	0.1408839779005525	21	0.03671328671328671	89	0.11741424802110818	G	10.06	1.246691	0.22796	0.170837	0.129884	ENSG00000172137	ENST00000349553;ENST00000302628	T;T	0.68479	-0.33;-0.33	5.48	1.17	0.20885	EF-hand-like domain (1);	0.565985	0.20929	N	0.083122	T	0.00039	0.0001	L	0.41573	1.285	0.38374	P	0.05504600000000004	B;B	0.12013	0.005;0.003	B;B	0.11329	0.006;0.002	T	0.05517	-1.0880	9	0.27785	T	0.31	-1.4052	7.9909	0.30239	0.4237:0.0:0.5763:0.0	rs11545954;rs17851296;rs58508901	110;110	A6NER6;P22676	.;CALB2_HUMAN	T	110	ENSP00000340294:A110T;ENSP00000307508:A110T	ENSP00000307508:A110T	A	+	1	0	CALB2	69969137	0.811000	0.29063	0.926000	0.36857	0.935000	0.57460	0.203000	0.17315	0.057000	0.16193	0.603000	0.83216	GCC	G|0.867;A|0.133	0.133	strong		0.572	CALB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268988.1	NM_001740	
LRRK2	120892	hgsc.bcm.edu	37	12	40677936	40677936	+	Splice_Site	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:40677936G>A	ENST00000298910.7	+	19	2558		c.e19+1		LRRK2_ENST00000343742.2_Splice_Site	NM_198578.3	NP_940980	Q5S007	LRRK2_HUMAN	leucine-rich repeat kinase 2						activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|autophagy (GO:0006914)|cellular protein localization (GO:0034613)|cellular response to dopamine (GO:1903351)|cellular response to manganese ion (GO:0071287)|cellular response to oxidative stress (GO:0034599)|determination of adult lifespan (GO:0008340)|endocytosis (GO:0006897)|exploration behavior (GO:0035640)|GTP catabolic process (GO:0006184)|intracellular distribution of mitochondria (GO:0048312)|intracellular signal transduction (GO:0035556)|locomotory exploration behavior (GO:0035641)|MAPK cascade (GO:0000165)|negative regulation of GTPase activity (GO:0034260)|negative regulation of hydrogen peroxide-induced cell death (GO:1903206)|negative regulation of late endosome to lysosome transport (GO:1902823)|negative regulation of peroxidase activity (GO:2000469)|negative regulation of protein binding (GO:0032091)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein processing (GO:0010955)|negative regulation of protein processing involved in protein targeting to mitochondrion (GO:1903217)|negative regulation of protein targeting to mitochondrion (GO:1903215)|negative regulation of thioredoxin peroxidase activity by peptidyl-threonine phosphorylation (GO:1903125)|neuromuscular junction development (GO:0007528)|neuron death (GO:0070997)|neuron projection morphogenesis (GO:0048812)|olfactory bulb development (GO:0021772)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of autophagy (GO:0010508)|positive regulation of dopamine receptor signaling pathway (GO:0060161)|positive regulation of GTPase activity (GO:0043547)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of programmed cell death (GO:0043068)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein autoubiquitination (GO:1902499)|positive regulation of protein binding (GO:0032092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reactive oxygen species metabolic process (GO:0072593)|regulation of branching morphogenesis of a nerve (GO:2000172)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of dopamine receptor signaling pathway (GO:0060159)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of kidney size (GO:0035564)|regulation of locomotion (GO:0040012)|regulation of membrane potential (GO:0042391)|regulation of mitochondrial depolarization (GO:0051900)|regulation of neuroblast proliferation (GO:1902692)|regulation of neuron death (GO:1901214)|regulation of neuron maturation (GO:0014041)|regulation of protein kinase A signaling (GO:0010738)|regulation of synaptic transmission, glutamatergic (GO:0051966)|regulation of synaptic vesicle exocytosis (GO:2000300)|regulation of synaptic vesicle transport (GO:1902803)|response to oxidative stress (GO:0006979)|small GTPase mediated signal transduction (GO:0007264)|tangential migration from the subventricular zone to the olfactory bulb (GO:0022028)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytoplasmic side of mitochondrial outer membrane (GO:0032473)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendrite (GO:0030425)|dendrite cytoplasm (GO:0032839)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|inclusion body (GO:0016234)|lysosome (GO:0005764)|membrane raft (GO:0045121)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial membrane (GO:0031966)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)|terminal bouton (GO:0043195)|trans-Golgi network (GO:0005802)	actin binding (GO:0003779)|ATP binding (GO:0005524)|clathrin binding (GO:0030276)|glycoprotein binding (GO:0001948)|GTP binding (GO:0005525)|GTP-dependent protein kinase activity (GO:0034211)|GTPase activator activity (GO:0005096)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|kinase activity (GO:0016301)|MAP kinase kinase activity (GO:0004708)|peroxidase inhibitor activity (GO:0036479)|protein homodimerization activity (GO:0042803)|protein kinase A binding (GO:0051018)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|Rho GTPase binding (GO:0017048)|SNARE binding (GO:0000149)|syntaxin-1 binding (GO:0017075)|tubulin binding (GO:0015631)			NS(3)|biliary_tract(1)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(23)|large_intestine(31)|lung(55)|ovary(15)|pancreas(2)|prostate(4)|skin(4)|stomach(9)|upper_aerodigestive_tract(7)|urinary_tract(2)	181	all_cancers(12;0.00108)|Breast(8;0.218)	Lung NSC(34;0.0942)|all_lung(34;0.11)				AAACAAACAAGTAAGTAACAA	0.308																																					.		Atlas-SNP	.											.	LRRK2	763	.	0			c.2500+1G>A						PASS	.						65.0	71.0	69.0					12																	40677936		2202	4300	6502	SO:0001630	splice_region_variant	120892	exon19			AAACAAGTAAGTA	AK026776	CCDS31774.1	12q12	2011-07-21			ENSG00000188906	ENSG00000188906		"""Parkinson disease"""	18618	protein-coding gene	gene with protein product		609007	"""Parkinson disease (autosomal dominant) 8"""	PARK8		15541308	Standard	NM_198578		Approved	ROCO2, DKFZp434H2111, FLJ45829, RIPK7	uc001rmg.4	Q5S007	OTTHUMG00000059742	ENST00000298910.7:c.2500+1G>A	12.37:g.40677936G>A		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	43	13	0.302326	NM_198578	A6NJU2|Q6ZS50|Q8NCX9	Splice_Site	SNP	ENST00000298910.7	37	CCDS31774.1	.	.	.	.	.	.	.	.	.	.	G	17.94	3.510681	0.64522	.	.	ENSG00000188906	ENST00000343742;ENST00000298910	.	.	.	5.05	5.05	0.67936	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.7573	0.91837	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	LRRK2	38964203	1.000000	0.71417	0.993000	0.49108	0.716000	0.41182	5.970000	0.70431	2.498000	0.84270	0.591000	0.81541	.	.	.	none		0.308	LRRK2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277179.1	XM_058513	Intron
GAS2L2	246176	hgsc.bcm.edu	37	17	34072555	34072555	+	Missense_Mutation	SNP	G	G	A	rs3744374	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:34072555G>A	ENST00000254466.6	-	6	1988	c.1961C>T	c.(1960-1962)gCc>gTc	p.A654V	GAS2L2_ENST00000587565.1_Missense_Mutation_p.A638V	NM_139285.3	NP_644814.1	Q8NHY3	GA2L2_HUMAN	growth arrest-specific 2 like 2	654			A -> V (in dbSNP:rs3744374).		cell cycle arrest (GO:0007050)|microtubule bundle formation (GO:0001578)|negative regulation of microtubule depolymerization (GO:0007026)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	actin filament binding (GO:0051015)|cytoskeletal adaptor activity (GO:0008093)|microtubule binding (GO:0008017)	p.A654V(2)		central_nervous_system(1)|endometrium(1)|large_intestine(7)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	35		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		TTCTTGGATGGCTTTGTCATA	0.627													A|||	1011	0.201877	0.3714	0.1297	5008	,	,		18244	0.127		0.2068	False		,,,				2504	0.0961				p.A654V		Atlas-SNP	.											GAS2L2,NS,carcinoma,0,1	GAS2L2	94	1	2	Substitution - Missense(2)	prostate(2)	c.C1961T						PASS	.	A	VAL/ALA	1418,2988	678.6+/-403.6	226,966,1011	80.0	93.0	89.0		1961	4.6	1.0	17	dbSNP_107	89	2112,6488	709.5+/-405.7	268,1576,2456	yes	missense	GAS2L2	NM_139285.3	64	494,2542,3467	AA,AG,GG		24.5581,32.1834,27.1413	benign	654/881	34072555	3530,9476	2203	4300	6503	SO:0001583	missense	246176	exon6			TGGATGGCTTTGT	AF508784	CCDS11298.1	17q21	2014-05-06			ENSG00000132139	ENSG00000270765			24846	protein-coding gene	gene with protein product		611398				12584248	Standard	NM_139285		Approved	GAR17	uc002hjv.2	Q8NHY3	OTTHUMG00000188386	ENST00000254466.6:c.1961C>T	17.37:g.34072555G>A	ENSP00000254466:p.Ala654Val	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	48	19	0.395833	NM_139285	Q8NHY4	Missense_Mutation	SNP	ENST00000254466.6	37	CCDS11298.1	478	0.21886446886446886	173	0.3516260162601626	60	0.16574585635359115	87	0.1520979020979021	158	0.20844327176781002	A	0.227	-1.024236	0.02061	0.321834	0.245581	ENSG00000132139	ENST00000254466	T	0.07800	3.16	4.58	4.58	0.56647	.	0.000000	0.51477	N	0.000087	T	0.00012	0.0000	N	0.00926	-1.1	0.58432	P	1.999999999946489E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.45731	-0.9241	9	0.02654	T	1	-21.9719	6.1261	0.20180	0.8016:0.0:0.1984:0.0	rs3744374;rs61222146;rs3744374	654	Q8NHY3	GA2L2_HUMAN	V	654	ENSP00000254466:A654V	ENSP00000254466:A654V	A	-	2	0	GAS2L2	31096668	0.998000	0.40836	1.000000	0.80357	0.273000	0.26683	1.310000	0.33551	0.807000	0.34208	-0.817000	0.03123	GCC	G|0.753;A|0.247	0.247	strong		0.627	GAS2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256497.1	NM_139285	
FAM120B	84498	hgsc.bcm.edu	37	6	170627761	170627761	+	Missense_Mutation	SNP	A	A	G	rs6900199	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:170627761A>G	ENST00000476287.1	+	2	1391	c.1283A>G	c.(1282-1284)tAt>tGt	p.Y428C	FAM120B_ENST00000537664.1_Missense_Mutation_p.Y451C|FAM120B_ENST00000540480.1_Missense_Mutation_p.Y440C|FAM120B_ENST00000252510.9_Intron	NM_032448.1	NP_115824.1	Q96EK7	F120B_HUMAN	family with sequence similarity 120B	428			Y -> C (in dbSNP:rs6900199).		cell differentiation (GO:0030154)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(11)|liver(1)|lung(15)|ovary(1)|prostate(2)|skin(2)	44		Breast(66;0.000338)|Esophageal squamous(34;0.241)		OV - Ovarian serous cystadenocarcinoma(33;3.94e-22)|BRCA - Breast invasive adenocarcinoma(81;6.47e-06)|GBM - Glioblastoma multiforme(31;0.0899)		GTTCCCATGTATACAGACTCT	0.507													G|||	820	0.163738	0.0885	0.2075	5008	,	,		20552	0.2817		0.1262	False		,,,				2504	0.1513				p.Y428C		Atlas-SNP	.											.	FAM120B	108	.	0			c.A1283G						PASS	.	A	CYS/TYR	520,3886	777.7+/-414.2	33,454,1716	183.0	199.0	194.0		1283	-2.0	0.0	6	dbSNP_116	194	1214,7386	762.3+/-407.6	95,1024,3181	no	missense	FAM120B	NM_032448.1	194	128,1478,4897	GG,GA,AA		14.1163,11.8021,13.3323	benign	428/911	170627761	1734,11272	2203	4300	6503	SO:0001583	missense	84498	exon2			CCATGTATACAGA	AB058741	CCDS5314.1, CCDS75555.1	6q27	2011-04-13	2006-07-04	2006-07-04	ENSG00000112584	ENSG00000112584			21109	protein-coding gene	gene with protein product	"""PPARgamma constitutive coactivator 1"", ""constitutive coactivator of PPAR-gamma"""	612266	"""KIAA1838"""	KIAA1838		14585507	Standard	NM_032448		Approved	PGCC1, CCPG	uc003qxp.3	Q96EK7	OTTHUMG00000016080	ENST00000476287.1:c.1283A>G	6.37:g.170627761A>G	ENSP00000417970:p.Tyr428Cys	Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	36	15	0.416667	NM_032448	B4DL34|Q86V68|Q96JI9	Missense_Mutation	SNP	ENST00000476287.1	37	CCDS5314.1	388	0.17765567765567766	64	0.13008130081300814	61	0.1685082872928177	164	0.2867132867132867	99	0.13060686015831136	G	3.367	-0.129275	0.06753	0.118021	0.141163	ENSG00000112584	ENST00000540480;ENST00000537664;ENST00000476287	T;T;T	0.08102	3.13;3.13;3.13	3.07	-2.02	0.07388	.	1.085760	0.06844	N	0.796216	T	0.00524	0.0017	N	0.00159	-1.955	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.47573	-0.9107	9	0.54805	T	0.06	1.1396	4.8427	0.13498	0.4009:0.0:0.4558:0.1433	rs6900199;rs17860762;rs6900199	428;428	Q96EK7;F2Z2E1	F120B_HUMAN;.	C	440;451;428	ENSP00000444125:Y440C;ENSP00000440125:Y451C;ENSP00000417970:Y428C	ENSP00000436640:Y428C	Y	+	2	0	FAM120B	170469686	0.000000	0.05858	0.000000	0.03702	0.012000	0.07955	-1.638000	0.02013	-0.544000	0.06232	-0.734000	0.03567	TAT	A|0.862;G|0.138	0.138	strong		0.507	FAM120B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000043259.2	NM_032448	
CHST10	9486	hgsc.bcm.edu	37	2	101009869	101009869	+	Silent	SNP	C	C	T	rs148920749	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:101009869C>T	ENST00000264249.3	-	7	1294	c.909G>A	c.(907-909)gtG>gtA	p.V303V	CHST10_ENST00000542617.1_Silent_p.V351V|CHST10_ENST00000409701.1_Silent_p.V303V	NM_004854.4	NP_004845.1	O43529	CHSTA_HUMAN	carbohydrate sulfotransferase 10	303					carbohydrate biosynthetic process (GO:0016051)|cell adhesion (GO:0007155)|learning (GO:0007612)|long-term memory (GO:0007616)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	HNK-1 sulfotransferase activity (GO:0016232)|sulfotransferase activity (GO:0008146)			breast(1)|endometrium(1)|large_intestine(9)|lung(4)|ovary(1)	16						TCGGGTATGACACCAGGTGGT	0.522													C|||	16	0.00319489	0.0	0.0014	5008	,	,		17713	0.0		0.0099	False		,,,				2504	0.0051				p.V303V		Atlas-SNP	.											.	CHST10	42	.	0			c.G909A						PASS	.	C		7,4399	12.9+/-30.5	0,7,2196	174.0	143.0	154.0		909	1.6	1.0	2	dbSNP_134	154	95,8505	53.6+/-114.3	0,95,4205	no	coding-synonymous	CHST10	NM_004854.4		0,102,6401	TT,TC,CC		1.1047,0.1589,0.7843		303/357	101009869	102,12904	2203	4300	6503	SO:0001819	synonymous_variant	9486	exon7			GTATGACACCAGG	BC010441	CCDS2047.1	2q11.2	2008-02-05			ENSG00000115526	ENSG00000115526		"""Sulfotransferases, membrane-bound"""	19650	protein-coding gene	gene with protein product		606376				12080076	Standard	NM_004854		Approved	HNK-1ST	uc002tam.3	O43529	OTTHUMG00000130669	ENST00000264249.3:c.909G>A	2.37:g.101009869C>T		Somatic	296	0	0		WXS	Illumina HiSeq	Phase_I	249	117	0.46988	NM_004854	Q53T18	Silent	SNP	ENST00000264249.3	37	CCDS2047.1																																																																																			C|0.993;T|0.007	0.007	strong		0.522	CHST10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253162.1	NM_004854	
TRIM31	11074	hgsc.bcm.edu	37	6	30080231	30080231	+	Missense_Mutation	SNP	G	G	A	rs3734838	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:30080231G>A	ENST00000376734.3	-	2	477	c.352C>T	c.(352-354)Cgt>Tgt	p.R118C	TRIM31_ENST00000540829.1_Missense_Mutation_p.R118C|TRIM31-AS1_ENST00000440874.1_RNA|TRIM31_ENST00000485864.1_5'Flank	NM_007028.3	NP_008959.3	Q9BZY9	TRI31_HUMAN	tripartite motif containing 31	118			R -> C (in dbSNP:rs3734838). {ECO:0000269|PubMed:14574404}.		innate immune response (GO:0045087)|negative regulation of viral entry into host cell (GO:0046597)|negative regulation of viral transcription (GO:0032897)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein ubiquitination (GO:0016567)|regulation of viral release from host cell (GO:1902186)	mitochondrion (GO:0005739)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(5)|ovary(2)|prostate(2)|skin(2)	15						TTGGATTCACGACACACAAAA	0.488													G|||	348	0.0694888	0.0333	0.0605	5008	,	,		22308	0.1141		0.0775	False		,,,				2504	0.0706				p.R118C		Atlas-SNP	.											.	TRIM31	40	.	0			c.C352T						PASS	.	G	CYS/ARG	141,2881		0,141,1370	116.0	105.0	109.0		352	1.1	0.0	6	dbSNP_107	109	477,4941		17,443,2249	yes	missense	TRIM31	NM_007028.3	180	17,584,3619	AA,AG,GG		8.804,4.6658,7.3223	possibly-damaging	118/426	30080231	618,7822	1511	2709	4220	SO:0001583	missense	11074	exon2			ATTCACGACACAC	AF230386	CCDS34374.1	6p21.3	2013-01-09	2011-01-25		ENSG00000204616	ENSG00000204616		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	16289	protein-coding gene	gene with protein product		609316	"""tripartite motif-containing 31"""			11331580	Standard	XM_006714977		Approved	RNF, HCGI, C6orf13, HCG1	uc003npg.1	Q9BZY9	OTTHUMG00000031064	ENST00000376734.3:c.352C>T	6.37:g.30080231G>A	ENSP00000365924:p.Arg118Cys	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	109	71	0.651376	NM_007028	A6NLX6|A9R9Q4|Q53H52|Q5RI37|Q5SRJ7|Q5SRJ8|Q5SS28|Q96AK4|Q96AP8|Q99579|Q9BZY8	Missense_Mutation	SNP	ENST00000376734.3	37	CCDS34374.1	169	0.07738095238095238	12	0.024390243902439025	22	0.06077348066298342	73	0.12762237762237763	62	0.08179419525065963	G	7.995	0.754104	0.15778	0.046658	0.08804	ENSG00000204616	ENST00000376734;ENST00000376728;ENST00000540829	T;T	0.44083	0.93;0.93	3.94	1.08	0.20341	Zinc finger, B-box, chordata (1);Zinc finger, B-box (3);	0.477822	0.15757	N	0.246142	T	0.12135	0.0295	N	0.24115	0.695	0.80722	P	0.0	P	0.42203	0.773	B	0.39531	0.302	T	0.05784	-1.0864	9	0.44086	T	0.13	.	7.8705	0.29563	0.2949:0.0:0.7051:0.0	rs3734838;rs17839990;rs52824167;rs61420333;rs3734838	118	Q9BZY9	TRI31_HUMAN	C	118	ENSP00000365924:R118C;ENSP00000444311:R118C	ENSP00000365918:R118C	R	-	1	0	TRIM31	30188210	0.000000	0.05858	0.002000	0.10522	0.006000	0.05464	-3.431000	0.00473	0.073000	0.16731	0.643000	0.83706	CGT	A|0.078;G|0.922	0.078	strong		0.488	TRIM31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076081.2		
SYNE1	23345	hgsc.bcm.edu	37	6	152668215	152668215	+	Silent	SNP	C	C	T	rs144596829	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:152668215C>T	ENST00000367255.5	-	73	12658	c.12057G>A	c.(12055-12057)gcG>gcA	p.A4019A	SYNE1_ENST00000265368.4_Silent_p.A4019A|SYNE1_ENST00000448038.1_Silent_p.A3948A|SYNE1_ENST00000423061.1_Silent_p.A3948A|SYNE1_ENST00000341594.5_Intron	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	4019					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)		TGCTGCAGATCGCTGAGTAGC	0.488										HNSCC(10;0.0054)			C|||	24	0.00479233	0.0015	0.0072	5008	,	,		17951	0.0		0.0139	False		,,,				2504	0.0031				p.A4019A		Atlas-SNP	.											SYNE1_ENST00000423061,right_upper_lobe,carcinoma,0,3	SYNE1	3227	3	0			c.G12057A						PASS	.	C	,	7,4399	12.9+/-30.5	0,7,2196	162.0	134.0	144.0		11844,12057	-11.8	0.0	6	dbSNP_134	144	112,8488	59.8+/-121.6	0,112,4188	no	coding-synonymous,coding-synonymous	SYNE1	NM_033071.3,NM_182961.3	,	0,119,6384	TT,TC,CC		1.3023,0.1589,0.915	,	3948/8750,4019/8798	152668215	119,12887	2203	4300	6503	SO:0001819	synonymous_variant	23345	exon73			GCAGATCGCTGAG	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.12057G>A	6.37:g.152668215C>T		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	96	70	0.729167	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																																																																																			C|0.991;T|0.009	0.009	strong		0.488	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961	
PSPH	5723	hgsc.bcm.edu	37	7	56088789	56088789	+	Silent	SNP	G	G	A	rs199851385	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:56088789G>A	ENST00000395471.3	-	4	922	c.117C>T	c.(115-117)ggC>ggT	p.G39G	PSPH_ENST00000275605.3_Silent_p.G39G|PSPH_ENST00000459834.1_Intron			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	140	0	0		WXS	Illumina HiSeq	Phase_I	165	27	0.163636	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	
DDIAS	220042	hgsc.bcm.edu	37	11	82643760	82643760	+	Missense_Mutation	SNP	G	G	T	rs7947780	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:82643760G>T	ENST00000533655.1	+	6	1592	c.1380G>T	c.(1378-1380)agG>agT	p.R460S	C11orf82_ENST00000528759.1_3'UTR|C11orf82_ENST00000329143.3_Missense_Mutation_p.R159S|C11orf82_ENST00000430323.2_Missense_Mutation_p.R460S|C11orf82_ENST00000525361.1_Intron	NM_145018.3	NP_659455.3	Q8IXT1	DDIAS_HUMAN		460			R -> S (in dbSNP:rs7947780). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		apoptotic process (GO:0006915)|cellular response to cytokine stimulus (GO:0071345)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|cellular response to hydroperoxide (GO:0071447)|cellular response to UV (GO:0034644)|hemopoiesis (GO:0030097)|mitotic cell cycle arrest (GO:0071850)|negative regulation of fibroblast apoptotic process (GO:2000270)|spermatid development (GO:0007286)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(17)|ovary(3)|prostate(1)|skin(1)|urinary_tract(1)	33						ACCACAGCAGGTTATCTGTGA	0.413													G|||	1540	0.307508	0.1793	0.4049	5008	,	,		22107	0.3244		0.3579	False		,,,				2504	0.3425				p.R460S		Atlas-SNP	.											.	C11orf82	71	.	0			c.G1380T						PASS	.	G	SER/ARG	984,3422	368.1+/-318.5	105,774,1324	77.0	76.0	76.0		1380	2.4	0.1	11	dbSNP_116	76	3028,5572	467.0+/-366.9	521,1986,1793	yes	missense	C11orf82	NM_145018.3	110	626,2760,3117	TT,TG,GG		35.2093,22.3332,30.8473	benign	460/999	82643760	4012,8994	2203	4300	6503	SO:0001583	missense	220042	exon6			CAGCAGGTTATCT																												ENST00000533655.1:c.1380G>T	11.37:g.82643760G>T	ENSP00000435421:p.Arg460Ser	Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	38	10	0.263158	NM_145018	Q96LK6|Q9H856	Missense_Mutation	SNP	ENST00000533655.1	37	CCDS8263.1	665	0.30448717948717946	93	0.18902439024390244	128	0.35359116022099446	172	0.3006993006993007	272	0.35883905013192613	G	3.944	-0.013559	0.07727	0.223332	0.352093	ENSG00000165490	ENST00000430323;ENST00000533655;ENST00000329143	T;T;T	0.38722	1.12;1.12;1.12	5.84	2.37	0.29283	.	0.621729	0.16187	N	0.225579	T	0.00012	0.0000	L	0.50333	1.59	0.80722	P	0.0	B	0.20780	0.048	B	0.15870	0.014	T	0.38265	-0.9669	8	.	.	.	.	5.6558	0.17642	0.2556:0.0:0.6159:0.1285	rs7947780;rs17571913;rs17857189;rs59924014;rs7947780	460	Q8IXT1	NOXIN_HUMAN	S	460;460;159	ENSP00000414687:R460S;ENSP00000435421:R460S;ENSP00000329930:R159S	.	R	+	3	2	C11orf82	82321408	0.001000	0.12720	0.089000	0.20774	0.053000	0.15095	0.093000	0.15086	0.534000	0.28695	0.655000	0.94253	AGG	G|0.697;N|0.000	.	strong		0.413	C11orf82-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391936.1		
PPP1R26	9858	hgsc.bcm.edu	37	9	138376649	138376649	+	Missense_Mutation	SNP	T	T	C	rs3748192	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:138376649T>C	ENST00000356818.2	+	4	842	c.293T>C	c.(292-294)gTc>gCc	p.V98A	PPP1R26_ENST00000604351.1_Missense_Mutation_p.V98A|PPP1R26_ENST00000401470.3_Missense_Mutation_p.V98A|PPP1R26_ENST00000602993.1_Intron|PPP1R26_ENST00000605660.1_Missense_Mutation_p.V98A|PPP1R26_ENST00000605286.1_Missense_Mutation_p.V98A	NM_014811.3	NP_055626.3	Q5T8A7	PPR26_HUMAN	protein phosphatase 1, regulatory subunit 26	98			V -> A (in dbSNP:rs3748192). {ECO:0000269|PubMed:15489334}.		negative regulation of phosphatase activity (GO:0010923)	nucleus (GO:0005634)	phosphatase binding (GO:0019902)|protein phosphatase inhibitor activity (GO:0004864)										GCGTTGGCTGTCTGTGGTCTC	0.627													C|||	2095	0.418331	0.2905	0.4899	5008	,	,		16315	0.6528		0.2117	False		,,,				2504	0.5112				p.V98A		Atlas-SNP	.											KIAA0649,NS,carcinoma,0,1	.	.	1	0			c.T293C						PASS	.	C	ALA/VAL	1113,3291		132,849,1221	41.0	48.0	46.0		293	3.4	0.1	9	dbSNP_107	46	1777,6821		195,1387,2717	no	missense	KIAA0649	NM_014811.3	64	327,2236,3938	CC,CT,TT		20.6676,25.2725,22.2273	benign	98/1210	138376649	2890,10112	2202	4299	6501	SO:0001583	missense	9858	exon4			TGGCTGTCTGTGG	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.293T>C	9.37:g.138376649T>C	ENSP00000349274:p.Val98Ala	Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	35	19	0.542857	NM_014811	Q86WU0|Q8WVV0|Q9Y4D3	Missense_Mutation	SNP	ENST00000356818.2	37	CCDS6988.1	833	0.3814102564102564	122	0.24796747967479674	158	0.43646408839779005	394	0.6888111888111889	159	0.20976253298153033	C	0.007	-2.011636	0.00422	0.252725	0.206676	ENSG00000196422	ENST00000356818;ENST00000401470	T;T	0.46063	0.88;0.88	4.39	3.41	0.39046	.	0.854487	0.10136	N	0.711490	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	0.45116	-0.9283	9	0.02654	T	1	-12.6961	7.3836	0.26870	0.2105:0.6922:0.0:0.0973	rs3748192;rs17846422;rs17859468;rs3748192	98	Q5T8A7	PPR26_HUMAN	A	98	ENSP00000349274:V98A;ENSP00000385826:V98A	ENSP00000349274:V98A	V	+	2	0	KIAA0649	137516470	0.006000	0.16342	0.106000	0.21319	0.067000	0.16453	1.185000	0.32065	1.085000	0.41206	-0.119000	0.15052	GTC	T|0.723;C|0.277	0.277	strong		0.627	PPP1R26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054987.1	NM_014811	
MTMR3	8897	hgsc.bcm.edu	37	22	30403996	30403996	+	Silent	SNP	C	C	T	rs2074204	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:30403996C>T	ENST00000401950.2	+	11	1326	c.984C>T	c.(982-984)gcC>gcT	p.A328A	MTMR3_ENST00000351488.3_Silent_p.A328A|MTMR3_ENST00000323630.5_Silent_p.A192A|MTMR3_ENST00000406629.1_Silent_p.A328A|CTA-85E5.10_ENST00000429350.1_RNA|MTMR3_ENST00000333027.3_Silent_p.A328A	NM_021090.3	NP_066576.1	Q13615	MTMR3_HUMAN	myotubularin related protein 3	328	Myotubularin phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00669}.|Substrate binding. {ECO:0000250}.				peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|protein dephosphorylation (GO:0006470)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extrinsic component of membrane (GO:0019898)|membrane (GO:0016020)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity (GO:0052629)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)			breast(3)|large_intestine(3)|ovary(2)|skin(8)|upper_aerodigestive_tract(1)	17			OV - Ovarian serous cystadenocarcinoma(5;0.00204)|Epithelial(10;0.06)|all cancers(5;0.107)			CAAACCGAGCCAAAGGAGGAG	0.522													C|||	1670	0.333466	0.5356	0.2392	5008	,	,		20059	0.2629		0.2256	False		,,,				2504	0.3108				p.A328A		Atlas-SNP	.											.	MTMR3	106	.	0			c.C984T						PASS	.	C	,,	2114,2292	576.2+/-384.2	494,1126,583	102.0	90.0	94.0		984,984,984	4.7	1.0	22	dbSNP_96	94	2133,6467	366.8+/-334.5	249,1635,2416	no	coding-synonymous,coding-synonymous,coding-synonymous	MTMR3	NM_021090.3,NM_153050.2,NM_153051.2	,,	743,2761,2999	TT,TC,CC		24.8023,47.98,32.6542	,,	328/1199,328/1171,328/1162	30403996	4247,8759	2203	4300	6503	SO:0001819	synonymous_variant	8897	exon11			CCGAGCCAAAGGA	U58034	CCDS13870.1, CCDS13871.1, CCDS46682.1	22q12.2	2011-06-09			ENSG00000100330	ENSG00000100330		"""Zinc fingers, FYVE domain containing"", ""Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"""	7451	protein-coding gene	gene with protein product		603558				8640223, 9736772	Standard	NM_153050		Approved	KIAA0371, ZFYVE10, FYVE-DSP1	uc003agv.4	Q13615	OTTHUMG00000151278	ENST00000401950.2:c.984C>T	22.37:g.30403996C>T		Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	159	81	0.509434	NM_021090	A5PL26|A7MD32|Q9NYN5|Q9NYN6|Q9UDX6|Q9UEG3	Silent	SNP	ENST00000401950.2	37	CCDS13870.1																																																																																			C|0.678;T|0.322	0.322	strong		0.522	MTMR3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000322066.1	NM_021090	
SEL1L2	80343	hgsc.bcm.edu	37	20	13912309	13912309	+	Missense_Mutation	SNP	G	G	A	rs41275404	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:13912309G>A	ENST00000284951.5	-	3	297	c.223C>T	c.(223-225)Cgt>Tgt	p.R75C	SEL1L2_ENST00000486903.1_5'UTR|SEL1L2_ENST00000378072.5_Missense_Mutation_p.R75C			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	165	0	0		WXS	Illumina HiSeq	Phase_I	117	66	0.564103	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	
CYP8B1	1582	hgsc.bcm.edu	37	3	42915878	42915878	+	Silent	SNP	C	C	T	rs735320	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:42915878C>T	ENST00000316161.4	-	1	1755	c.1431G>A	c.(1429-1431)ccG>ccA	p.P477P	CYP8B1_ENST00000437102.1_Intron|KRBOX1_ENST00000426937.1_Intron|RP11-141M3.5_ENST00000471537.1_RNA	NM_004391.2	NP_004382.2	Q9UNU6	CP8B1_HUMAN	cytochrome P450, family 8, subfamily B, polypeptide 1	477					bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|lipid metabolic process (GO:0006629)|small molecule metabolic process (GO:0044281)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	7alpha-hydroxycholest-4-en-3-one 12alpha-hydroxylase activity (GO:0033778)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxygen binding (GO:0019825)|sterol 12-alpha-hydroxylase activity (GO:0008397)			NS(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(5)|ovary(2)|prostate(2)|skin(5)	23				KIRC - Kidney renal clear cell carcinoma(284;0.213)|Kidney(284;0.249)		CCCAGCGCTGCGGGTCAACAT	0.557													C|||	577	0.115216	0.1747	0.1196	5008	,	,		17878	0.002		0.168	False		,,,				2504	0.0941				p.P477P		Atlas-SNP	.											.	CYP8B1	59	.	0			c.G1431A						PASS	.	C		744,3662	305.2+/-288.9	58,628,1517	75.0	69.0	71.0		1431	-9.1	0.0	3	dbSNP_86	71	1479,7121	280.3+/-294.4	120,1239,2941	no	coding-synonymous	CYP8B1	NM_004391.2		178,1867,4458	TT,TC,CC		17.1977,16.8861,17.0921		477/502	42915878	2223,10783	2203	4300	6503	SO:0001819	synonymous_variant	1582	exon1			GCGCTGCGGGTCA	AF090318	CCDS2707.1	3p22.1	2004-02-27	2003-01-14		ENSG00000180432	ENSG00000180432		"""Cytochrome P450s"""	2653	protein-coding gene	gene with protein product		602172	"""cytochrome P450, subfamily VIIIB (sterol 12-alpha-hydroxylase), polypeptide 1"""			10051404	Standard	NM_004391		Approved	CYP12	uc003cmh.3	Q9UNU6	OTTHUMG00000133047	ENST00000316161.4:c.1431G>A	3.37:g.42915878C>T		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	109	58	0.53211	NM_004391	B2RCY3|O75958|Q6NWT2|Q6NWT3	Silent	SNP	ENST00000316161.4	37	CCDS2707.1																																																																																			C|0.861;T|0.139	0.139	strong		0.557	CYP8B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256653.1	NM_004391	
CCDC73	493860	hgsc.bcm.edu	37	11	32624405	32624405	+	Silent	SNP	C	C	T	rs201893	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:32624405C>T	ENST00000335185.5	-	18	3235	c.3192G>A	c.(3190-3192)aaG>aaA	p.K1064K	EIF3M_ENST00000531120.1_3'UTR	NM_001008391.2	NP_001008392.2	Q6ZRK6	CCD73_HUMAN	coiled-coil domain containing 73	1064										NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(9)|lung(20)|ovary(2)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	51	Breast(20;0.112)					CTTTTCTTTTCTTTGGCTGGT	0.313													C|||	933	0.186302	0.211	0.2061	5008	,	,		17249	0.0665		0.2813	False		,,,				2504	0.1646				p.R1064R		Atlas-SNP	.											.	CCDC73	136	.	0			c.A3192A						PASS	.	C		791,2811		92,607,1102	139.0	118.0	124.0		3192	3.3	1.0	11	dbSNP_79	124	2135,5991		271,1593,2199	no	coding-synonymous	CCDC73	NM_001008391.2		363,2200,3301	TT,TC,CC		26.2737,21.96,24.9488		1064/1080	32624405	2926,8802	1801	4063	5864	SO:0001819	synonymous_variant	493860	exon18			TCTTTTCTTTGGC	AK128159	CCDS41630.1	11p13	2006-02-11			ENSG00000186714	ENSG00000186714			23261	protein-coding gene	gene with protein product		612328					Standard	NM_001008391		Approved	NY-SAR-79	uc001mtv.4	Q6ZRK6	OTTHUMG00000166279	ENST00000335185.5:c.3192G>A	11.37:g.32624405C>T		Somatic	137	1	0.00729927		WXS	Illumina HiSeq	Phase_I	87	87	1	NM_001008391	Q6P5Q7|Q6ZMW0|Q86WE7	Silent	SNP	ENST00000335185.5	37	CCDS41630.1	429	0.19642857142857142	111	0.22560975609756098	86	0.23756906077348067	39	0.06818181818181818	193	0.2546174142480211	C	1.358	-0.589427	0.03799	0.2196	0.262737	ENSG00000186714	ENST00000528333	.	.	.	5.65	3.3	0.37823	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999997946	.	.	.	.	.	.	T	0.12578	-1.0542	3	.	.	.	.	8.1133	0.30928	0.0:0.1677:0.0:0.8323	rs201893;rs201893	.	.	.	K	100	.	.	R	-	2	0	CCDC73	32580981	1.000000	0.71417	0.991000	0.47740	0.265000	0.26407	1.259000	0.32956	0.416000	0.25844	-0.312000	0.09012	AGA	C|0.791;T|0.209	0.209	strong		0.313	CCDC73-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388874.2	NM_001008391	
MAP3K6	9064	hgsc.bcm.edu	37	1	27687466	27687466	+	Missense_Mutation	SNP	G	G	T	rs35659744	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:27687466G>T	ENST00000493901.1	-	15	2105	c.1866C>A	c.(1864-1866)aaC>aaA	p.N622K	MAP3K6_ENST00000357582.2_Missense_Mutation_p.N622K|MAP3K6_ENST00000374040.3_Missense_Mutation_p.N614K	NM_004672.3	NP_004663.3	O95382	M3K6_HUMAN	mitogen-activated protein kinase kinase kinase 6	622			N -> K (in dbSNP:rs35659744). {ECO:0000269|PubMed:17344846, ECO:0000269|Ref.4}.		activation of JUN kinase activity (GO:0007257)|activation of MAPKK activity (GO:0000186)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)		ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|MAP kinase kinase kinase activity (GO:0004709)			breast(4)|central_nervous_system(2)|lung(3)|ovary(1)	10		all_lung(284;1.6e-05)|Lung NSC(340;2.92e-05)|Colorectal(325;3.46e-05)|Renal(390;0.0007)|Breast(348;0.0021)|Ovarian(437;0.0175)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0416)|OV - Ovarian serous cystadenocarcinoma(117;1.69e-27)|Colorectal(126;1.24e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00132)|KIRC - Kidney renal clear cell carcinoma(1967;0.00163)|STAD - Stomach adenocarcinoma(196;0.00303)|READ - Rectum adenocarcinoma(331;0.0419)		TGGAATCCGGGTTCGTCACCC	0.716													G|||	611	0.122005	0.0182	0.1571	5008	,	,		14370	0.0823		0.2684	False		,,,				2504	0.1278				p.N622K		Atlas-SNP	.											MAP3K6_ENST00000493901,brain,glioma,0,16	MAP3K6	134	16	0			c.C1866A						scavenged	.	G	LYS/ASN	243,4005		10,223,1891	11.0	15.0	14.0		1866	-0.3	0.6	1	dbSNP_126	14	2513,5979		407,1699,2140	yes	missense	MAP3K6	NM_004672.3	94	417,1922,4031	TT,TG,GG		29.5926,5.7203,21.6327	benign	622/1289	27687466	2756,9984	2124	4246	6370	SO:0001583	missense	9064	exon14			ATCCGGGTTCGTC	AF100318	CCDS299.1, CCDS72738.1	1p36.11	2011-06-09			ENSG00000142733	ENSG00000142733		"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	6858	protein-coding gene	gene with protein product	"""apoptosis signal regulating kinase 2"""	604468				9875215	Standard	XM_005246029		Approved	MAPKKK6, ASK2, MEKK6	uc001bny.1	O95382	OTTHUMG00000004631	ENST00000493901.1:c.1866C>A	1.37:g.27687466G>T	ENSP00000419591:p.Asn622Lys	Somatic	85	2	0.0235294		WXS	Illumina HiSeq	Phase_I	65	35	0.538462	NM_004672	A2ACE8|A2VDG4|A2VDG5|Q59HF4|Q5SSD4|Q75PK3|Q96B75	Missense_Mutation	SNP	ENST00000493901.1	37	CCDS299.1	324|324	0.14835164835164835|0.14835164835164835	7|7	0.014227642276422764|0.014227642276422764	60|60	0.16574585635359115|0.16574585635359115	57|57	0.09965034965034965|0.09965034965034965	200|200	0.2638522427440633|0.2638522427440633	G|G	11.29|11.29	1.595660|1.595660	0.28445|0.28445	0.057203|0.057203	0.295926|0.295926	ENSG00000142733|ENSG00000142733	ENST00000374040;ENST00000493901;ENST00000545447;ENST00000357582|ENST00000472410	T;T;T|.	0.65549|.	-0.16;-0.16;-0.16|.	5.2|5.2	-0.342|-0.342	0.12635|0.12635	.|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	L|L	0.43152|0.43152	1.355|1.355	0.80722|0.80722	P|P	0.0|0.0	B;B|.	0.10296|.	0.003;0.001|.	B;B|.	0.09377|.	0.004;0.002|.	T|T	0.35025|0.35025	-0.9805|-0.9805	8|4	0.41790|.	T|.	0.15|.	.|.	4.454|4.454	0.11635|0.11635	0.4176:0.2041:0.3783:0.0|0.4176:0.2041:0.3783:0.0	rs35659744;rs35659744|rs35659744;rs35659744	614;622|.	O95382-3;O95382|.	.;M3K6_HUMAN|.	K|N	614;622;345;622|346	ENSP00000363152:N614K;ENSP00000419591:N622K;ENSP00000350195:N622K|.	ENSP00000350195:N622K|.	N|T	-|-	3|2	2|0	MAP3K6|MAP3K6	27560053|27560053	0.001000|0.001000	0.12720|0.12720	0.648000|0.648000	0.29521|0.29521	0.791000|0.791000	0.44710|0.44710	0.029000|0.029000	0.13666|0.13666	0.246000|0.246000	0.21394|0.21394	-0.345000|-0.345000	0.07892|0.07892	AAC|ACC	G|0.846;T|0.154	0.154	strong		0.716	MAP3K6-001	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000013469.2	NM_004672	
UNC13D	201294	hgsc.bcm.edu	37	17	73827205	73827205	+	Missense_Mutation	SNP	T	T	C	rs1135688	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:73827205T>C	ENST00000207549.4	-	27	2978	c.2599A>G	c.(2599-2601)Aag>Gag	p.K867E	UNC13D_ENST00000412096.2_Missense_Mutation_p.K867E	NM_199242.2	NP_954712.1	Q70J99	UN13D_HUMAN	unc-13 homolog D (C. elegans)	867	MHD2. {ECO:0000255|PROSITE- ProRule:PRU00588}.		K -> E (in dbSNP:rs1135688).		defense response to virus (GO:0051607)|germinal center formation (GO:0002467)|granuloma formation (GO:0002432)|natural killer cell degranulation (GO:0043320)|phagocytosis (GO:0006909)|positive regulation of exocytosis (GO:0045921)|regulation of mast cell degranulation (GO:0043304)	endosome (GO:0005768)|exocytic vesicle (GO:0070382)|lysosome (GO:0005764)|membrane (GO:0016020)				central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(9)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29			all cancers(21;2.11e-06)|Epithelial(20;2.32e-06)|BRCA - Breast invasive adenocarcinoma(9;0.000618)|LUSC - Lung squamous cell carcinoma(166;0.154)			TGCAGGGCCTTGGGTGGCAGG	0.612									Familial Hemophagocytic Lymphohistiocytosis				C|||	2501	0.499401	0.9032	0.2968	5008	,	,		13362	0.4266		0.336	False		,,,				2504	0.3405				p.K867E		Atlas-SNP	.											.	UNC13D	68	.	0			c.A2599G						PASS	.	C	GLU/LYS	3612,794	315.2+/-294.0	1486,640,77	63.0	64.0	63.0		2599	3.7	0.3	17	dbSNP_86	63	2800,5798	676.1+/-403.3	458,1884,1957	yes	missense	UNC13D	NM_199242.2	56	1944,2524,2034	CC,CT,TT		32.5657,18.0209,49.3079	benign	867/1091	73827205	6412,6592	2203	4299	6502	SO:0001583	missense	201294	exon27	Familial Cancer Database	FHLH, FHL, Familial Hemophagocytic Reticulosis, FHR	GGGCCTTGGGTGG	AK024474	CCDS11730.1	17q25.3	2014-09-17				ENSG00000092929			23147	protein-coding gene	gene with protein product		608897					Standard	NM_199242		Approved	Munc13-4	uc002jpp.3	Q70J99		ENST00000207549.4:c.2599A>G	17.37:g.73827205T>C	ENSP00000207549:p.Lys867Glu	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	66	33	0.5	NM_199242	B4DWG9|Q9H7K5	Missense_Mutation	SNP	ENST00000207549.4	37	CCDS11730.1	1082	0.49542124542124544	441	0.8963414634146342	119	0.3287292817679558	280	0.48951048951048953	242	0.31926121372031663	C	0.028	-1.352212	0.01256	0.819791	0.325657	ENSG00000092929	ENST00000207549;ENST00000412096;ENST00000448606	T;T	0.72282	-0.64;-0.64	4.67	3.7	0.42460	Mammalian uncoordinated homology 13, domain 2 (1);Mammalian uncoordinated homology 13, subgroup, domain 2 (1);	0.389639	0.26394	N	0.024634	T	0.00012	0.0000	N	0.00193	-1.875	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.41875	-0.9484	9	0.02654	T	1	-0.9421	9.48	0.38895	0.0:0.835:0.0:0.165	rs1135688;rs3198548;rs28622144;rs61662805	867	Q70J99	UN13D_HUMAN	E	867	ENSP00000207549:K867E;ENSP00000388093:K867E	ENSP00000207549:K867E	K	-	1	0	UNC13D	71338800	0.073000	0.21202	0.342000	0.25602	0.004000	0.04260	1.088000	0.30877	0.583000	0.29574	-0.733000	0.03571	AAG	T|0.510;C|0.490	0.490	strong		0.612	UNC13D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448847.2	XM_113950	
MCUR1	63933	hgsc.bcm.edu	37	6	13801615	13801615	+	Missense_Mutation	SNP	T	T	C	rs3180196	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:13801615T>C	ENST00000379170.4	-	4	784	c.646A>G	c.(646-648)Act>Gct	p.T216A		NM_001031713.3	NP_001026883.1	Q96AQ8	MCUR1_HUMAN	mitochondrial calcium uniporter regulator 1	216			T -> A (in dbSNP:rs3180196).		calcium ion import (GO:0070509)|mitochondrial calcium ion transport (GO:0006851)|positive regulation of mitochondrial calcium ion concentration (GO:0051561)	integral component of mitochondrial inner membrane (GO:0031305)		p.T216A(1)									TGCTGAAAAGTGATTTCCTAG	0.353													T|||	625	0.1248	0.0068	0.0879	5008	,	,		20323	0.3026		0.1779	False		,,,				2504	0.0726				p.T216A		Atlas-SNP	.											CCDC90A,NS,carcinoma,0,1	CCDC90A	15	1	1	Substitution - Missense(1)	stomach(1)	c.A646G						PASS	.	T	ALA/THR	150,4254	101.2+/-139.8	5,140,2057	90.0	93.0	92.0		646	4.0	1.0	6	dbSNP_105	92	1312,7286	259.1+/-282.5	102,1108,3089	yes	missense	CCDC90A	NM_001031713.3	58	107,1248,5146	CC,CT,TT		15.2594,3.406,11.2444	benign	216/360	13801615	1462,11540	2202	4299	6501	SO:0001583	missense	63933	exon4			GAAAAGTGATTTC	BC016850	CCDS35495.1	6p23	2013-03-13	2013-03-13	2013-03-13	ENSG00000050393	ENSG00000050393			21097	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 79"", ""coiled-coil domain containing 90A"""	C6orf79, CCDC90A		23178883	Standard	NM_001031713		Approved	FLJ20958	uc003nbc.2	Q96AQ8	OTTHUMG00000014279	ENST00000379170.4:c.646A>G	6.37:g.13801615T>C	ENSP00000368468:p.Thr216Ala	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	57	29	0.508772	NM_001031713	Q96JS7|Q9H7F8	Missense_Mutation	SNP	ENST00000379170.4	37	CCDS35495.1	344	0.1575091575091575	6	0.012195121951219513	43	0.11878453038674033	160	0.27972027972027974	135	0.17810026385224276	T	11.88	1.771192	0.31320	0.03406	0.152594	ENSG00000050393	ENST00000379170	T	0.40756	1.02	5.18	3.97	0.46021	.	0.379516	0.32134	N	0.006529	T	0.06872	0.0175	N	0.11560	0.145	0.09310	P	0.9999999999999991	B	0.30068	0.267	B	0.24701	0.055	T	0.22312	-1.0220	9	0.08837	T	0.75	-6.6486	8.5551	0.33476	0.0:0.1617:0.0:0.8383	rs3180196;rs3207308;rs57009899;rs3180196	216	Q96AQ8	CC90A_HUMAN	A	216	ENSP00000368468:T216A	ENSP00000368468:T216A	T	-	1	0	CCDC90A	13909594	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	2.978000	0.49305	0.874000	0.35823	0.533000	0.62120	ACT	T|0.880;C|0.120	0.120	strong		0.353	MCUR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039909.3	NM_022102	
CUL9	23113	hgsc.bcm.edu	37	6	43182906	43182906	+	Silent	SNP	C	C	T	rs76552409	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:43182906C>T	ENST00000252050.4	+	30	5862	c.5778C>T	c.(5776-5778)gtC>gtT	p.V1926V	CUL9_ENST00000354495.3_Silent_p.V1816V|RP3-330M21.5_ENST00000500590.1_RNA|CUL9_ENST00000372647.2_Silent_p.V1898V	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	98	0	0		WXS	Illumina HiSeq	Phase_I	89	39	0.438202	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	
CPS1	1373	hgsc.bcm.edu	37	2	211540507	211540507	+	Missense_Mutation	SNP	C	C	A	rs1047891	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:211540507C>A	ENST00000233072.5	+	36	4413	c.4217C>A	c.(4216-4218)aCc>aAc	p.T1406N	CPS1_ENST00000430249.2_Missense_Mutation_p.T1412N|CPS1_ENST00000451903.2_Missense_Mutation_p.T955N	NM_001875.4	NP_001866.2	P31327	CPSM_HUMAN	carbamoyl-phosphate synthase 1, mitochondrial	1406			T -> N (associated with PHN susceptibility; 30-40% higher activity; also highly associated with hepatocellular carcinoma (HCC) progression; dbSNP:rs1047891). {ECO:0000269|PubMed:11407344, ECO:0000269|PubMed:12853138, ECO:0000269|PubMed:12955727, ECO:0000269|PubMed:1840546, ECO:0000269|PubMed:20520828, ECO:0000269|PubMed:21767969, ECO:0000269|PubMed:24237036}.		anion homeostasis (GO:0055081)|carbamoyl phosphate biosynthetic process (GO:0070409)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to cAMP (GO:0071320)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cellular response to glucagon stimulus (GO:0071377)|cellular response to oleic acid (GO:0071400)|citrulline biosynthetic process (GO:0019240)|glutamine catabolic process (GO:0006543)|glycogen catabolic process (GO:0005980)|hepatocyte differentiation (GO:0070365)|homocysteine metabolic process (GO:0050667)|midgut development (GO:0007494)|nitric oxide metabolic process (GO:0046209)|positive regulation of vasodilation (GO:0045909)|response to amine (GO:0014075)|response to amino acid (GO:0043200)|response to dexamethasone (GO:0071548)|response to drug (GO:0042493)|response to food (GO:0032094)|response to growth hormone (GO:0060416)|response to lipopolysaccharide (GO:0032496)|response to starvation (GO:0042594)|response to toxic substance (GO:0009636)|response to zinc ion (GO:0010043)|small molecule metabolic process (GO:0044281)|triglyceride catabolic process (GO:0019433)|urea cycle (GO:0000050)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|carbamoyl-phosphate synthase (ammonia) activity (GO:0004087)|endopeptidase activity (GO:0004175)|glutamate binding (GO:0016595)|modified amino acid binding (GO:0072341)|phospholipid binding (GO:0005543)			breast(1)|central_nervous_system(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(17)|lung(85)|ovary(8)|pancreas(1)|prostate(6)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	142				Epithelial(149;0.00697)|Lung(261;0.0521)|LUSC - Lung squamous cell carcinoma(261;0.0544)|all cancers(144;0.0843)	Carglumic Acid(DB06775)	GTCCCTGCCACCCCAGTGGCA	0.443													C|||	1445	0.288538	0.3684	0.3429	5008	,	,		16610	0.1389		0.3012	False		,,,				2504	0.2832				p.T1412N		Atlas-SNP	.											.	CPS1	485	.	0			c.C4235A						PASS	.	C	ASN/THR,ASN/THR,ASN/THR	1605,2801	497.2+/-363.8	305,995,903	68.0	68.0	68.0	http://www.ncbi.nlm.nih.gov/pubmed?term	4235,2864,4217	5.2	1.0	2	dbSNP_86	68	2676,5924	428.0+/-355.8	422,1832,2046	yes	missense,missense,missense	CPS1	NM_001122633.2,NM_001122634.2,NM_001875.4	65,65,65	727,2827,2949	AA,AC,CC	http://www.ncbi.nlm.nih.gov/pubmed?term	31.1163,36.4276,32.9156	benign,benign,benign	1412/1507,955/1050,1406/1501	211540507	4281,8725	2203	4300	6503	SO:0001583	missense	1373	exon37			CTGCCACCCCAGT	AF154830	CCDS2393.1, CCDS46505.1, CCDS46506.1	2p	2014-09-17	2010-05-11		ENSG00000021826	ENSG00000021826	6.3.4.16		2323	protein-coding gene	gene with protein product		608307	"""carbamoyl-phosphate synthetase 1, mitochondrial"""				Standard	NM_001122633		Approved		uc002vee.4	P31327	OTTHUMG00000132994	ENST00000233072.5:c.4217C>A	2.37:g.211540507C>A	ENSP00000233072:p.Thr1406Asn	Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	127	66	0.519685	NM_001122633	B7Z818|J3KQL0|O43774|Q53TL5|Q59HF8|Q7Z5I5	Missense_Mutation	SNP	ENST00000233072.5	37	CCDS2393.1	586	0.2683150183150183	154	0.3130081300813008	122	0.3370165745856354	81	0.14160839160839161	229	0.3021108179419525	C	14.03	2.413514	0.42817	0.364276	0.311163	ENSG00000021826	ENST00000430249;ENST00000539150;ENST00000233072;ENST00000451903	D;D;D	0.82984	-1.67;-1.67;-1.67	6.08	5.2	0.72013	Methylglyoxal synthase-like domain (4);	0.301714	0.35124	N	0.003423	T	0.00012	0.0000	L	0.48877	1.53	0.37459	P	0.08485100000000001	B;B	0.14012	0.009;0.009	B;B	0.19391	0.025;0.025	T	0.08371	-1.0725	9	0.32370	T	0.25	-11.1012	9.5512	0.39310	0.1496:0.7771:0.0:0.0732	rs1047891;rs2229587;rs3187890;rs7422339;rs52831019;rs7422339	1416;1406	Q59HF8;P31327	.;CPSM_HUMAN	N	1412;1414;1406;955	ENSP00000402608:T1412N;ENSP00000233072:T1406N;ENSP00000406136:T955N	ENSP00000233072:T1406N	T	+	2	0	CPS1	211248752	0.977000	0.34250	1.000000	0.80357	0.981000	0.71138	1.756000	0.38390	1.580000	0.49851	0.591000	0.81541	ACC	C|0.699;A|0.301	0.301	strong		0.443	CPS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256569.5		
PEX6	5190	hgsc.bcm.edu	37	6	42932200	42932200	+	Missense_Mutation	SNP	G	G	T	rs386700658|rs1129187	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:42932200G>T	ENST00000304611.8	-	17	2885	c.2816C>A	c.(2815-2817)cCa>cAa	p.P939Q	PEX6_ENST00000244546.4_3'UTR	NM_000287.3	NP_000278.3	Q13608	PEX6_HUMAN	peroxisomal biogenesis factor 6	939			P -> Q (in dbSNP:rs1129187). {ECO:0000269|PubMed:11355018, ECO:0000269|PubMed:19105186}.		ATP catabolic process (GO:0006200)|peroxisome organization (GO:0007031)|protein import into peroxisome matrix, translocation (GO:0016561)|protein stabilization (GO:0050821)|protein targeting to peroxisome (GO:0006625)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled (GO:0042623)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)			NS(1)|breast(1)|endometrium(2)|large_intestine(2)|lung(5)|ovary(1)|prostate(3)	15			all cancers(41;0.00235)|Colorectal(64;0.00237)|COAD - Colon adenocarcinoma(64;0.00473)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.0562)			TGAGCTACCTGGCTCCAGCCC	0.632													G|||	1660	0.33147	0.3699	0.3516	5008	,	,		18582	0.1012		0.4622	False		,,,				2504	0.3681				p.P939Q		Atlas-SNP	.											PEX6,colon,carcinoma,0,1	PEX6	44	1	0			c.C2816A						PASS	.	G	GLN/PRO	1720,2686	496.0+/-363.4	332,1056,815	48.0	45.0	46.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	2816	0.6	0.0	6	dbSNP_86	46	3832,4768	515.8+/-378.7	834,2164,1302	yes	missense	PEX6	NM_000287.3	76	1166,3220,2117	TT,TG,GG		44.5581,39.0377,42.688	benign	939/981	42932200	5552,7454	2203	4300	6503	SO:0001583	missense	5190	exon17			CTACCTGGCTCCA	U56602	CCDS4877.1	6p22-p11	2010-04-21			ENSG00000124587	ENSG00000124587		"""ATPases / AAA-type"""	8859	protein-coding gene	gene with protein product		601498				8670792	Standard	NM_000287		Approved	PXAAA1, PAF-2	uc003otf.3	Q13608	OTTHUMG00000014713	ENST00000304611.8:c.2816C>A	6.37:g.42932200G>T	ENSP00000303511:p.Pro939Gln	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	103	101	0.980583	NM_000287	Q5T8W1|Q8WYQ0|Q8WYQ1|Q8WYQ2|Q99476	Missense_Mutation	SNP	ENST00000304611.8	37	CCDS4877.1	719	0.3292124542124542	169	0.3434959349593496	130	0.35911602209944754	71	0.12412587412587413	349	0.4604221635883905	G	12.52	1.963729	0.34659	0.390377	0.445581	ENSG00000124587	ENST00000304611	D	0.94758	-3.51	5.96	0.549	0.17213	.	0.978492	0.08443	N	0.945108	T	0.82116	0.4967	L	0.48362	1.52	0.09310	P	1.0	B	0.11235	0.004	B	0.11329	0.006	T	0.63989	-0.6512	9	0.37606	T	0.19	-1.1722	2.5906	0.04841	0.2743:0.1118:0.4992:0.1148	rs1129187;rs3186790;rs9471979;rs17415506;rs59470433;rs1129187	939	Q13608	PEX6_HUMAN	Q	939	ENSP00000303511:P939Q	ENSP00000303511:P939Q	P	-	2	0	PEX6	43040178	0.000000	0.05858	0.008000	0.14137	0.910000	0.53928	0.232000	0.17891	-0.182000	0.10602	0.650000	0.86243	CCA	G|0.617;T|0.383	0.383	strong		0.632	PEX6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040569.1	NM_000287	
RFX3	5991	hgsc.bcm.edu	37	9	3247895	3247895	+	Intron	SNP	A	A	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:3247895A>G	ENST00000382004.3	-	16	2280				RFX3_ENST00000358730.2_Missense_Mutation_p.V702A|RFX3_ENST00000302303.1_Missense_Mutation_p.V702A	NM_001282116.1|NM_134428.1	NP_001269045.1|NP_602304.1	P48380	RFX3_HUMAN	regulatory factor X, 3 (influences HLA class II expression)						cell maturation (GO:0048469)|cilium assembly (GO:0042384)|cilium-dependent cell motility (GO:0060285)|endocrine pancreas development (GO:0031018)|epithelial cilium movement involved in determination of left/right asymmetry (GO:0060287)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type B pancreatic cell development (GO:2000078)|regulation of insulin secretion (GO:0050796)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)|type B pancreatic cell maturation (GO:0072560)	nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	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)|transcription regulatory region DNA binding (GO:0044212)			central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(11)|large_intestine(3)|lung(14)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	40				GBM - Glioblastoma multiforme(50;0.00124)|Lung(2;0.0337)		tcttgcaataactccacagtc	0.348																																					p.V702A		Atlas-SNP	.											.	RFX3	156	.	0			c.T2105C						PASS	.						79.0	80.0	79.0					9																	3247895		2203	4300	6503	SO:0001627	intron_variant	5991	exon16			GCAATAACTCCAC	AI811824	CCDS6449.1, CCDS6450.1, CCDS75809.1	9p24.2	2008-02-05			ENSG00000080298	ENSG00000080298			9984	protein-coding gene	gene with protein product		601337				8289803	Standard	XM_005251534		Approved		uc003zhr.3	P48380	OTTHUMG00000019456	ENST00000382004.3:c.1968+136T>C	9.37:g.3247895A>G		Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	22	13	0.590909	NM_002919	A8K0H5|D3DRH8|D3DRH9|Q5JTL7|Q5JTL8|Q6NW13|Q8WTU4|Q95HL5|Q95HL6	Missense_Mutation	SNP	ENST00000382004.3	37	CCDS6449.1	.	.	.	.	.	.	.	.	.	.	A	10.67	1.415133	0.25552	.	.	ENSG00000080298	ENST00000358730;ENST00000302303	T;T	0.59502	0.26;0.26	3.82	-0.0572	0.13802	.	.	.	.	.	T	0.42787	0.1218	.	.	.	0.09310	N	1	B	0.12630	0.006	B	0.09377	0.004	T	0.37957	-0.9683	8	0.87932	D	0	.	5.4108	0.16346	0.5649:0.3387:0.0964:0.0	.	702	P48380-2	.	A	702	ENSP00000351574:V702A;ENSP00000303847:V702A	ENSP00000303847:V702A	V	-	2	0	RFX3	3237895	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.141000	0.10327	-0.009000	0.14296	-0.435000	0.05868	GTT	.	.	none		0.348	RFX3-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051545.1	NM_002919	
NOTCH1	4851	hgsc.bcm.edu	37	9	139407932	139407932	+	Silent	SNP	A	A	G	rs2229971|rs587778559	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:139407932A>G	ENST00000277541.6	-	14	2340	c.2265T>C	c.(2263-2265)aaT>aaC	p.N755N		NM_017617.3	NP_060087.3	P46531	NOTC1_HUMAN	notch 1	755	EGF-like 20. {ECO:0000255|PROSITE- ProRule:PRU00076}.				anagen (GO:0042640)|aortic valve morphogenesis (GO:0003180)|apoptotic process involved in embryonic digit morphogenesis (GO:1902263)|arterial endothelial cell differentiation (GO:0060842)|atrioventricular node development (GO:0003162)|atrioventricular valve morphogenesis (GO:0003181)|auditory receptor cell fate commitment (GO:0009912)|axonogenesis (GO:0007409)|branching morphogenesis of an epithelial tube (GO:0048754)|cardiac atrium morphogenesis (GO:0003209)|cardiac chamber formation (GO:0003207)|cardiac epithelial to mesenchymal transition (GO:0060317)|cardiac left ventricle morphogenesis (GO:0003214)|cardiac muscle cell proliferation (GO:0060038)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac right atrium morphogenesis (GO:0003213)|cardiac right ventricle formation (GO:0003219)|cardiac septum morphogenesis (GO:0060411)|cardiac vascular smooth muscle cell development (GO:0060948)|cardiac ventricle morphogenesis (GO:0003208)|cell fate specification (GO:0001708)|cell migration involved in endocardial cushion formation (GO:0003273)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|cilium morphogenesis (GO:0060271)|collecting duct development (GO:0072044)|compartment pattern specification (GO:0007386)|coronary artery morphogenesis (GO:0060982)|coronary vein morphogenesis (GO:0003169)|determination of left/right symmetry (GO:0007368)|distal tubule development (GO:0072017)|embryonic hindlimb morphogenesis (GO:0035116)|endocardial cell differentiation (GO:0060956)|endocardial cushion morphogenesis (GO:0003203)|endocardium development (GO:0003157)|endocardium morphogenesis (GO:0003160)|endoderm development (GO:0007492)|epithelial to mesenchymal transition (GO:0001837)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|forebrain development (GO:0030900)|foregut morphogenesis (GO:0007440)|gene expression (GO:0010467)|glial cell differentiation (GO:0010001)|glomerular mesangial cell development (GO:0072144)|growth involved in heart morphogenesis (GO:0003241)|hair follicle morphogenesis (GO:0031069)|heart development (GO:0007507)|heart looping (GO:0001947)|heart trabecula morphogenesis (GO:0061384)|humoral immune response (GO:0006959)|immune response (GO:0006955)|in utero embryonic development (GO:0001701)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-4 secretion (GO:0072602)|keratinocyte differentiation (GO:0030216)|left/right axis specification (GO:0070986)|liver development (GO:0001889)|lung development (GO:0030324)|mesenchymal cell development (GO:0014031)|mitral valve formation (GO:0003192)|negative regulation of anoikis (GO:2000811)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of calcium ion-dependent exocytosis (GO:0045955)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cell migration involved in sprouting angiogenesis (GO:0090051)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of endothelial cell chemotaxis (GO:2001027)|negative regulation of glial cell proliferation (GO:0060253)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of neurogenesis (GO:0050768)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of ossification (GO:0030279)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of photoreceptor cell differentiation (GO:0046533)|negative regulation of pro-B cell differentiation (GO:2000974)|negative regulation of stem cell differentiation (GO:2000737)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube development (GO:0021915)|neuronal stem cell maintenance (GO:0097150)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|Notch signaling pathway involved in regulation of secondary heart field cardioblast proliferation (GO:0003270)|pericardium morphogenesis (GO:0003344)|positive regulation of apoptotic process (GO:0043065)|positive regulation of astrocyte differentiation (GO:0048711)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061419)|positive regulation of transcription of Notch receptor target (GO:0007221)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland epithelium morphogenesis (GO:0060740)|pulmonary valve morphogenesis (GO:0003184)|regulation of epithelial cell proliferation involved in prostate gland development (GO:0060768)|regulation of extracellular matrix assembly (GO:1901201)|regulation of somitogenesis (GO:0014807)|regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation (GO:0003256)|regulation of transcription, DNA-templated (GO:0006355)|response to muramyl dipeptide (GO:0032495)|secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development (GO:0060528)|skeletal muscle cell differentiation (GO:0035914)|somatic stem cell division (GO:0048103)|sprouting angiogenesis (GO:0002040)|transcription initiation from RNA polymerase II promoter (GO:0006367)|tube formation (GO:0035148)|vasculogenesis involved in coronary vascular morphogenesis (GO:0060979)|venous endothelial cell differentiation (GO:0060843)|ventricular septum morphogenesis (GO:0060412)|ventricular trabecula myocardium morphogenesis (GO:0003222)	cell surface (GO:0009986)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|MAML1-RBP-Jkappa- ICN1 complex (GO:0002193)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)|receptor activity (GO:0004872)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(16)|central_nervous_system(17)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1183)|kidney(4)|large_intestine(1)|lung(57)|oesophagus(2)|ovary(3)|pancreas(1)|prostate(3)|skin(21)|upper_aerodigestive_tract(39)|urinary_tract(3)	1359	all_cancers(76;0.223)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;5.34e-06)|Epithelial(140;7.77e-06)		ATTCACACTCATTGTTGTTGA	0.602			"""T, Mis, O"""	TRB@	T-ALL					HNSCC(8;0.001)			G|||	2643	0.527756	0.6997	0.4784	5008	,	,		19531	0.7768		0.335	False		,,,				2504	0.272				p.N755N		Atlas-SNP	.		Dom	yes		9	9q34.3	4851	"""Notch homolog 1, translocation-associated (Drosophila) (TAN1)"""		L	.	NOTCH1	1980	.	0			c.T2265C						PASS	.	G		2695,1683		864,967,358	109.0	123.0	118.0		2265	-2.3	0.0	9	dbSNP_98	118	2445,6109		358,1729,2190	no	coding-synonymous	NOTCH1	NM_017617.3		1222,2696,2548	GG,GA,AA		28.5831,38.4422,39.7464		755/2556	139407932	5140,7792	2189	4277	6466	SO:0001819	synonymous_variant	4851	exon14			ACACTCATTGTTG	AF308602	CCDS43905.1	9q34.3	2013-01-10	2010-06-24		ENSG00000148400	ENSG00000148400		"""Ankyrin repeat domain containing"""	7881	protein-coding gene	gene with protein product		190198	"""Notch (Drosophila) homolog 1 (translocation-associated)"", ""Notch homolog 1, translocation-associated (Drosophila)"""	TAN1		1831692	Standard	NM_017617		Approved		uc004chz.3	P46531	OTTHUMG00000020935	ENST00000277541.6:c.2265T>C	9.37:g.139407932A>G		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	113	51	0.451327	NM_017617	Q59ED8|Q5SXM3	Silent	SNP	ENST00000277541.6	37	CCDS43905.1																																																																																			A|0.484;G|0.516	0.516	strong		0.602	NOTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055087.1	NM_017617	
MYO5A	4644	hgsc.bcm.edu	37	15	52611451	52611451	+	Silent	SNP	A	A	G	rs2290332	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:52611451A>G	ENST00000399231.3	-	38	5208	c.4965T>C	c.(4963-4965)gaT>gaC	p.D1655D	MYO5A_ENST00000358212.6_Silent_p.D1680D|MYO5A_ENST00000553916.1_Silent_p.D1653D|MYO5A_ENST00000356338.6_Silent_p.D1628D|MYO5A_ENST00000399233.2_Silent_p.D1652D	NM_000259.3	NP_000250	Q9Y4I1	MYO5A_HUMAN	myosin VA (heavy chain 12, myoxin)	1655	Dilute. {ECO:0000255|PROSITE- ProRule:PRU00503}.				actin filament-based movement (GO:0030048)|anagen (GO:0042640)|cellular protein metabolic process (GO:0044267)|cellular response to insulin stimulus (GO:0032869)|endoplasmic reticulum localization (GO:0051643)|exocytosis (GO:0006887)|insulin secretion (GO:0030073)|locomotion involved in locomotory behavior (GO:0031987)|long-chain fatty acid biosynthetic process (GO:0042759)|melanin biosynthetic process (GO:0042438)|melanocyte differentiation (GO:0030318)|melanosome transport (GO:0032402)|membrane organization (GO:0061024)|myelination (GO:0042552)|odontogenesis (GO:0042476)|post-Golgi vesicle-mediated transport (GO:0006892)|protein localization to plasma membrane (GO:0072659)|protein transport (GO:0015031)|regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0031585)|secretory granule localization (GO:0032252)|synapse organization (GO:0050808)|synaptic transmission (GO:0007268)|transport (GO:0006810)|vesicle transport along actin filament (GO:0030050)|vesicle-mediated transport (GO:0016192)|visual perception (GO:0007601)	actomyosin (GO:0042641)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filopodium tip (GO:0032433)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|insulin-responsive compartment (GO:0032593)|intermediate filament (GO:0005882)|melanosome (GO:0042470)|membrane (GO:0016020)|microtubule plus-end (GO:0035371)|myosin complex (GO:0016459)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|photoreceptor outer segment (GO:0001750)|ruffle (GO:0001726)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|microfilament motor activity (GO:0000146)|poly(A) RNA binding (GO:0044822)|Rab GTPase binding (GO:0017137)			breast(4)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(7)|large_intestine(12)|lung(19)|ovary(3)|skin(3)|stomach(1)	57				all cancers(107;0.0085)|Colorectal(133;0.077)|READ - Rectum adenocarcinoma(133;0.196)		AGGTGCCCTCATCGGCGATAC	0.562													A|||	1646	0.328674	0.2867	0.2939	5008	,	,		20516	0.5774		0.1163	False		,,,				2504	0.3722				p.D1655D		Atlas-SNP	.											.	MYO5A	145	.	0			c.T4965C						PASS	.	A	,	1091,3259		143,805,1227	130.0	137.0	134.0		4965,4884	-11.4	0.1	15	dbSNP_100	134	1267,7291		107,1053,3119	no	coding-synonymous,coding-synonymous	MYO5A	NM_000259.3,NM_001142495.1	,	250,1858,4346	GG,GA,AA		14.8049,25.0805,18.2677	,	1655/1856,1628/1829	52611451	2358,10550	2175	4279	6454	SO:0001819	synonymous_variant	4644	exon38			GCCCTCATCGGCG		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.4965T>C	15.37:g.52611451A>G		Somatic	217	0	0		WXS	Illumina HiSeq	Phase_I	250	249	0.996	NM_000259	A8MZC5|O60653|Q07902|Q16249|Q9UE30|Q9UE31	Silent	SNP	ENST00000399231.3	37	CCDS42037.1																																																																																			A|0.716;G|0.284	0.284	strong		0.562	MYO5A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000268102.1	NM_000259	
COL4A4	1286	hgsc.bcm.edu	37	2	227917090	227917090	+	Missense_Mutation	SNP	T	T	C	rs80243096	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:227917090T>C	ENST00000396625.3	-	32	3106	c.2899A>G	c.(2899-2901)Atc>Gtc	p.I967V	COL4A4_ENST00000329662.7_Missense_Mutation_p.I967V	NM_000092.4	NP_000083.3	P53420	CO4A4_HUMAN	collagen, type IV, alpha 4	967	Triple-helical region.				axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glomerular basement membrane development (GO:0032836)	basal lamina (GO:0005605)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(15)|lung(35)|ovary(5)|pancreas(3)|prostate(2)|skin(12)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	98		Renal(207;0.00844)|all_lung(227;0.0187)|Lung NSC(271;0.0879)|all_hematologic(139;0.21)|Esophageal squamous(248;0.242)		Epithelial(121;6.7e-11)|all cancers(144;5.39e-08)|Lung(261;0.0132)|LUSC - Lung squamous cell carcinoma(224;0.0181)		TGTGAAATGATAGCCATTTCT	0.408													T|||	82	0.0163738	0.0545	0.0043	5008	,	,		18824	0.0		0.006	False		,,,				2504	0.001				p.I967V		Atlas-SNP	.											.	COL4A4	215	.	0			c.A2899G						PASS	.	T	VAL/ILE	145,3549		3,139,1705	118.0	116.0	117.0		2899	-0.4	0.0	2	dbSNP_131	117	53,8129		0,53,4038	yes	missense	COL4A4	NM_000092.4	29	3,192,5743	CC,CT,TT		0.6478,3.9253,1.6672	benign	967/1691	227917090	198,11678	1847	4091	5938	SO:0001583	missense	1286	exon32			AAATGATAGCCAT		CCDS42828.1	2q35-q37	2014-09-17			ENSG00000081052	ENSG00000081052		"""Collagens"""	2206	protein-coding gene	gene with protein product	"""collagen of basement membrane, alpha-4 chain"""	120131				1639407	Standard	NM_000092		Approved	CA44	uc021vxs.1	P53420	OTTHUMG00000149892	ENST00000396625.3:c.2899A>G	2.37:g.227917090T>C	ENSP00000379866:p.Ile967Val	Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	123	57	0.463415	NM_000092	A8MTZ1|Q53RW9|Q53S42|Q53WR1	Missense_Mutation	SNP	ENST00000396625.3	37	CCDS42828.1	36	0.016483516483516484	30	0.06097560975609756	1	0.0027624309392265192	0	0.0	5	0.006596306068601583	T	9.125	1.009997	0.19277	0.039253	0.006478	ENSG00000081052	ENST00000396625;ENST00000329662	D;D	0.93189	-3.18;-3.18	4.95	-0.429	0.12303	.	.	.	.	.	T	0.40595	0.1123	N	0.12182	0.205	0.09310	N	1	B	0.06786	0.001	B	0.12156	0.007	T	0.56872	-0.7907	9	0.17832	T	0.49	.	4.3506	0.11153	0.0:0.2894:0.1665:0.5441	.	967	P53420	CO4A4_HUMAN	V	967	ENSP00000379866:I967V;ENSP00000328553:I967V	ENSP00000328553:I967V	I	-	1	0	COL4A4	227625334	0.000000	0.05858	0.000000	0.03702	0.687000	0.40016	-0.111000	0.10807	-0.320000	0.08640	0.455000	0.32223	ATC	T|0.988;C|0.012	0.012	strong		0.408	COL4A4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313770.1	NM_000092	
OR4N4	283694	hgsc.bcm.edu	37	15	22383189	22383189	+	Silent	SNP	G	G	A	rs1820851	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:22383189G>A	ENST00000328795.4	+	1	808	c.717G>A	c.(715-717)acG>acA	p.T239T	RP11-69H14.6_ENST00000558896.1_RNA	NM_001005241.2	NP_001005241.2	Q8N0Y3	OR4N4_HUMAN	olfactory receptor, family 4, subfamily N, member 4	239			T -> M (in dbSNP:rs475947). {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)	p.T239T(2)		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)		CCATGTCCACGTGCACCACTC	0.493																																					p.T239T		Atlas-SNP	.											OR4N4,NS,carcinoma,0,2	OR4N4	108	2	2	Substitution - coding silent(2)	prostate(1)|stomach(1)	c.G717A						PASS	.	G		1427,2955		150,1127,914	226.0	191.0	203.0		717	-5.3	0.9	15	dbSNP_92	203	4118,4406		767,2584,911	no	coding-synonymous	OR4N4	NM_001005241.2		917,3711,1825	AA,AG,GG		48.3107,32.565,42.9645		239/317	22383189	5545,7361	2191	4262	6453	SO:0001819	synonymous_variant	283694	exon1			GTCCACGTGCACC	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.717G>A	15.37:g.22383189G>A		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	141	71	0.503546	NM_001005241	Q6IEY3|Q6IF56	Silent	SNP	ENST00000328795.4	37	CCDS32173.1																																																																																			G|0.536;A|0.464	0.464	strong		0.493	OR4N4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414922.1		
PCDHB16	57717	hgsc.bcm.edu	37	5	140563173	140563173	+	Missense_Mutation	SNP	G	G	T	rs28664170	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:140563173G>T	ENST00000361016.2	+	1	2194	c.1039G>T	c.(1039-1041)Gtg>Ttg	p.V347L		NM_020957.1	NP_066008.1	Q9NRJ7	PCDBG_HUMAN	protocadherin beta 16	347	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.		V -> L (in dbSNP:rs28664170).		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)			TCCCCCACAGGTGACCATGTC	0.522													g|||	763	0.152356	0.2579	0.1902	5008	,	,		17783	0.0407		0.1571	False		,,,				2504	0.093				p.V347L		Atlas-SNP	.											.	PCDHB16	159	.	0			c.G1039T						PASS	.	T	LEU/VAL	1042,3364	384.9+/-325.5	115,812,1276	90.0	95.0	93.0		1039	-2.2	0.0	5	dbSNP_125	93	1474,7126	281.2+/-294.9	136,1202,2962	yes	missense	PCDHB16	NM_020957.1	32	251,2014,4238	TT,TG,GG		17.1395,23.6496,19.3449	benign	347/777	140563173	2516,10490	2203	4300	6503	SO:0001583	missense	57717	exon1			CCACAGGTGACCA	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.1039G>T	5.37:g.140563173G>T	ENSP00000354293:p.Val347Leu	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	94	46	0.489362	NM_020957	B3KPK5|Q8IYD5|Q96SE9|Q9HCF1	Missense_Mutation	SNP	ENST00000361016.2	37	CCDS4251.1	329	0.15064102564102563	119	0.241869918699187	63	0.17403314917127072	26	0.045454545454545456	121	0.15963060686015831	G	0.041	-1.283588	0.01398	0.236496	0.171395	ENSG00000196963	ENST00000361016	T	0.01787	4.64	4.47	-2.21	0.06973	Cadherin (2);Cadherin-like (1);	0.600314	0.12637	N	0.451640	T	0.00012	0.0000	N	0.03253	-0.375	0.80722	P	0.0	B;B	0.09022	0.002;0.001	B;B	0.09377	0.004;0.003	T	0.42498	-0.9448	9	0.02654	T	1	.	0.421	0.00456	0.2557:0.2432:0.1326:0.3685	rs28664170;rs59526747	37;347	O15199;Q9NRJ7	.;PCDBG_HUMAN	L	347	ENSP00000354293:V347L	ENSP00000354293:V347L	V	+	1	0	PCDHB16	140543357	0.000000	0.05858	0.011000	0.14972	0.556000	0.35491	-1.001000	0.03690	0.020000	0.15106	-0.188000	0.12872	GTG	C|0.000;G|0.818;T|0.182	0.182	strong		0.522	PCDHB16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251800.1	NM_020957	
TSNARE1	203062	hgsc.bcm.edu	37	8	143427178	143427178	+	Missense_Mutation	SNP	C	C	G	rs33970858	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:143427178C>G	ENST00000307180.3	-	3	281	c.164G>C	c.(163-165)cGc>cCc	p.R55P	TSNARE1_ENST00000519651.1_Intron|TSNARE1_ENST00000520166.1_Missense_Mutation_p.R55P|TSNARE1_ENST00000524325.1_Missense_Mutation_p.R55P	NM_145003.3	NP_659440.2	Q96NA8	TSNA1_HUMAN	t-SNARE domain containing 1	55			R -> P (in dbSNP:rs33970858). {ECO:0000269|PubMed:14702039}.		intracellular protein transport (GO:0006886)|synaptic vesicle exocytosis (GO:0016079)	integral component of membrane (GO:0016021)|SNARE complex (GO:0031201)	SNAP receptor activity (GO:0005484)|SNARE binding (GO:0000149)	p.R55P(1)		breast(1)|endometrium(3)|kidney(4)|large_intestine(1)|lung(6)|ovary(2)|stomach(2)|urinary_tract(1)	20	all_cancers(97;7.39e-11)|all_epithelial(106;8.98e-09)|Lung NSC(106;0.000167)|all_lung(105;0.000332)|Ovarian(258;0.0315)|Acute lymphoblastic leukemia(118;0.155)					CCCCACACAGCGGTTCTGCAG	0.607													G|||	1814	0.36222	0.652	0.2896	5008	,	,		21165	0.3472		0.1978	False		,,,				2504	0.2065				p.R55P		Atlas-SNP	.											TSNARE1,NS,carcinoma,0,1	TSNARE1	59	1	1	Substitution - Missense(1)	stomach(1)	c.G164C						PASS	.	G	PRO/ARG	2522,1884	543.6+/-376.3	730,1062,411	111.0	92.0	99.0		164	-0.3	0.0	8	dbSNP_126	99	1806,6794	732.8+/-406.9	185,1436,2679	yes	missense	TSNARE1	NM_145003.3	103	915,2498,3090	GG,GC,CC		21.0,42.7599,33.2769	benign	55/514	143427178	4328,8678	2203	4300	6503	SO:0001583	missense	203062	exon3			ACACAGCGGTTCT			8q24.3	2005-08-18							26437	protein-coding gene	gene with protein product						14702039	Standard	XM_005250828		Approved	FLJ31164	uc003ywk.3	Q96NA8		ENST00000307180.3:c.164G>C	8.37:g.143427178C>G	ENSP00000303437:p.Arg55Pro	Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	149	24	0.161074	NM_145003	B7ZLB0|Q14D03	Missense_Mutation	SNP	ENST00000307180.3	37	CCDS6384.1	734	0.3360805860805861	284	0.5772357723577236	96	0.26519337016574585	216	0.3776223776223776	138	0.1820580474934037	G	0.008	-1.876825	0.00537	0.572401	0.21	ENSG00000171045	ENST00000524325;ENST00000307180;ENST00000520166;ENST00000520462;ENST00000518720	T;T;T;T;T	0.25414	2.68;2.67;2.68;1.82;1.8	2.62	-0.305	0.12784	.	0.698313	0.10997	N	0.610948	T	0.00012	0.0000	N	0.01352	-0.895	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.43147	-0.9409	9	0.02654	T	1	.	3.8909	0.09119	0.258:0.3986:0.3434:0.0	rs33970858	55;55;55	B7ZLB0;Q96NA8;A0AVG3	.;TSNA1_HUMAN;.	P	55;55;55;55;71	ENSP00000428763:R55P;ENSP00000303437:R55P;ENSP00000427770:R55P;ENSP00000429626:R55P;ENSP00000430789:R71P	ENSP00000303437:R55P	R	-	2	0	TSNARE1	143425085	0.005000	0.15991	0.000000	0.03702	0.730000	0.41778	0.493000	0.22451	-0.386000	0.07821	-0.744000	0.03518	CGC	C|0.671;G|0.329	0.329	strong		0.607	TSNARE1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_145003	
MUC4	4585	hgsc.bcm.edu	37	3	195509689	195509689	+	Missense_Mutation	SNP	G	G	A	rs59620726		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195509689G>A	ENST00000463781.3	-	2	9221	c.8762C>T	c.(8761-8763)gCa>gTa	p.A2921V	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.A2921V	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.A2921V(2)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		ACCTGTGGATGCTGAGGAAGT	0.577																																					p.A2921V		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	2	Substitution - Missense(2)	stomach(2)	c.C8762T						scavenged	.						13.0	9.0	10.0					3																	195509689		673	1544	2217	SO:0001583	missense	4585	exon2			GTGGATGCTGAGG	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.8762C>T	3.37:g.195509689G>A	ENSP00000417498:p.Ala2921Val	Somatic	56	1	0.0178571		WXS	Illumina HiSeq	Phase_I	126	62	0.492063	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	g	1.188	-0.636095	0.03557	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.30182	1.54;1.59	.	.	.	.	.	.	.	.	T	0.14442	0.0349	N	0.19112	0.55	0.09310	N	1	B	0.28128	0.201	B	0.24848	0.056	T	0.25187	-1.0139	7	.	.	.	.	2.1665	0.03838	0.3292:0.3381:0.3327:0.0	rs59620726	2793	E7ESK3	.	V	2921	ENSP00000417498:A2921V;ENSP00000420243:A2921V	.	A	-	2	0	MUC4	196994468	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.843000	0.01680	-0.000000	0.14550	0.000000	0.15137	GCA	G|0.997;A|0.003	0.003	weak		0.577	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
NCAM1	4684	hgsc.bcm.edu	37	11	113146033	113146033	+	Missense_Mutation	SNP	C	C	T	rs17174409	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:113146033C>T	ENST00000316851.7	+	18	2471	c.2471C>T	c.(2470-2472)aCg>aTg	p.T824M	NCAM1_ENST00000397957.4_3'UTR|NCAM1-AS1_ENST00000533638.1_RNA|NCAM1-AS1_ENST00000526229.1_RNA	NM_001242607.1|NM_181351.4	NP_001229536.1|NP_851996.2	P13591	NCAM1_HUMAN	neural cell adhesion molecule 1	834					axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cytokine-mediated signaling pathway (GO:0019221)|extracellular matrix organization (GO:0030198)|interferon-gamma-mediated signaling pathway (GO:0060333)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)			breast(1)|endometrium(3)|kidney(1)|large_intestine(11)|lung(27)|ovary(3)|prostate(2)|upper_aerodigestive_tract(1)	49		all_cancers(61;5.82e-19)|all_epithelial(67;6.87e-12)|Melanoma(852;1.99e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;0.00119)|Breast(348;0.0109)|all_neural(223;0.0299)|Medulloblastoma(222;0.0458)|Renal(330;0.198)|Prostate(24;0.207)		BRCA - Breast invasive adenocarcinoma(274;1.78e-05)|Epithelial(105;0.000114)|all cancers(92;0.000467)|OV - Ovarian serous cystadenocarcinoma(223;0.212)		GAGACAGAAACGAAGCCAGCG	0.552													C|||	15	0.00299521	0.0008	0.0014	5008	,	,		16990	0.0		0.0109	False		,,,				2504	0.002				p.T860M		Atlas-SNP	.											.	NCAM1	372	.	0			c.C2579T						PASS	.	C	MET/THR,MET/THR,MET/THR	4,4228		0,4,2112	67.0	90.0	82.0		2502,2580,2472	4.5	1.0	11	dbSNP_123	82	107,8365		1,105,4130	yes	missense,missense,missense	NCAM1	NM_181351.4,NM_001242607.1,NM_000615.6	81,81,81	1,109,6242	TT,TC,CC		1.263,0.0945,0.8737	benign,benign,benign	834/859,860/885,824/849	113146033	111,12593	2116	4236	6352	SO:0001583	missense	4684	exon21			CAGAAACGAAGCC		CCDS73384.1, CCDS73385.1, CCDS73386.1, CCDS73387.1, CCDS73388.1	11q23.2	2013-02-11			ENSG00000149294	ENSG00000149294		"""CD molecules"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	7656	protein-coding gene	gene with protein product		116930					Standard	NM_000615		Approved	NCAM, CD56	uc021qqp.1	P13591	OTTHUMG00000167196	ENST00000316851.7:c.2471C>T	11.37:g.113146033C>T	ENSP00000318472:p.Thr824Met	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	65	52	0.8	NM_001242607	A8K8T8|P13592|P13593|Q05C58|Q15829|Q16180|Q16209|Q59FL7|Q86X47|Q96CJ3	Missense_Mutation	SNP	ENST00000316851.7	37		7	0.003205128205128205	0	0.0	1	0.0027624309392265192	0	0.0	6	0.0079155672823219	C	10.28	1.307927	0.23821	9.45E-4	0.01263	ENSG00000149294	ENST00000316851;ENST00000433634	T	0.46451	0.87	5.45	4.54	0.55810	.	0.879712	0.09422	U	0.804201	T	0.17789	0.0427	.	.	.	0.25662	N	0.985987	P;B;B	0.35959	0.53;0.036;0.021	B;B;B	0.23574	0.047;0.011;0.005	T	0.06092	-1.0846	9	0.26408	T	0.33	.	7.6034	0.28089	0.0:0.7189:0.1366:0.1445	rs17174409;rs57590747	289;824;834	B4DSQ7;P13591-1;P13591	.;.;NCAM1_HUMAN	M	824;289	ENSP00000318472:T824M	ENSP00000318472:T824M	T	+	2	0	NCAM1	112651243	0.996000	0.38824	0.999000	0.59377	0.989000	0.77384	3.018000	0.49625	1.525000	0.49052	0.655000	0.94253	ACG	C|0.995;T|0.005	0.005	strong		0.552	NCAM1-201	KNOWN	basic	protein_coding	protein_coding		NM_000615	
FMNL2	114793	hgsc.bcm.edu	37	2	153378487	153378487	+	Missense_Mutation	SNP	A	A	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:153378487A>T	ENST00000288670.9	+	2	515	c.148A>T	c.(148-150)Agg>Tgg	p.R50W		NM_052905.3	NP_443137.2	Q96PY5	FMNL2_HUMAN	formin-like 2	50	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						TGACAAAGCCAGGTTACTGCG	0.363																																					p.R50W		Atlas-SNP	.											.	FMNL2	75	.	0			c.A148T						PASS	.						84.0	80.0	81.0					2																	153378487		1847	4093	5940	SO:0001583	missense	114793	exon2			AAAGCCAGGTTAC	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.148A>T	2.37:g.153378487A>T	ENSP00000288670:p.Arg50Trp	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	107	21	0.196262	NM_052905	B2RZH5|Q14CC9|Q4ZG52|Q8N3E0	Missense_Mutation	SNP	ENST00000288670.9	37	CCDS46429.1	.	.	.	.	.	.	.	.	.	.	A	17.49	3.402207	0.62288	.	.	ENSG00000157827	ENST00000288670	D	0.90261	-2.64	5.93	5.93	0.95920	.	0.000000	0.85682	D	0.000000	D	0.94918	0.8357	M	0.73962	2.25	0.80722	D	1	D	0.76494	0.999	D	0.79108	0.992	D	0.95337	0.8435	10	0.87932	D	0	.	15.3697	0.74554	1.0:0.0:0.0:0.0	.	50	Q96PY5-3	.	W	50	ENSP00000288670:R50W	ENSP00000288670:R50W	R	+	1	2	FMNL2	153086733	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.999000	0.57031	2.270000	0.75569	0.482000	0.46254	AGG	.	.	none		0.363	FMNL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333582.2	NM_052905	
PDGFRB	5159	hgsc.bcm.edu	37	5	149511636	149511636	+	Silent	SNP	C	C	G	rs2228439	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:149511636C>G	ENST00000261799.4	-	8	1618	c.1149G>C	c.(1147-1149)ctG>ctC	p.L383L		NM_002609.3	NP_002600.1	P09619	PGFRB_HUMAN	platelet-derived growth factor receptor, beta polypeptide	383	Ig-like C2-type 4.				adrenal gland development (GO:0030325)|aorta morphogenesis (GO:0035909)|cardiac myofibril assembly (GO:0055003)|cell chemotaxis (GO:0060326)|cell migration (GO:0016477)|cell migration involved in coronary angiogenesis (GO:0060981)|cell migration involved in vasculogenesis (GO:0035441)|cellular response to platelet-derived growth factor stimulus (GO:0036120)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|glycosaminoglycan biosynthetic process (GO:0006024)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|inner ear development (GO:0048839)|metanephric comma-shaped body morphogenesis (GO:0072278)|metanephric glomerular capillary formation (GO:0072277)|metanephric glomerular mesangial cell proliferation involved in metanephros development (GO:0072262)|metanephric mesenchymal cell migration (GO:0035789)|metanephric mesenchyme development (GO:0072075)|metanephric S-shaped body morphogenesis (GO:0072284)|negative regulation of apoptotic process (GO:0043066)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol metabolic process (GO:0046488)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|platelet-derived growth factor receptor-beta signaling pathway (GO:0035791)|positive regulation of calcium ion import (GO:0090280)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signaling pathway (GO:0038091)|positive regulation of chemotaxis (GO:0050921)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of metanephric mesenchymal cell migration by platelet-derived growth factor receptor-beta signaling pathway (GO:0035793)|positive regulation of mitosis (GO:0045840)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of smooth muscle cell migration (GO:0014911)|positive regulation of smooth muscle cell proliferation (GO:0048661)|protein autophosphorylation (GO:0046777)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|response to estradiol (GO:0032355)|response to fluid shear stress (GO:0034405)|response to hydrogen peroxide (GO:0042542)|response to hyperoxia (GO:0055093)|response to retinoic acid (GO:0032526)|response to toxic substance (GO:0009636)|retina vasculature development in camera-type eye (GO:0061298)|signal transduction (GO:0007165)|skeletal system morphogenesis (GO:0048705)|smooth muscle cell chemotaxis (GO:0071670)|smooth muscle tissue development (GO:0048745)|tissue homeostasis (GO:0001894)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intrinsic component of plasma membrane (GO:0031226)|lysosome (GO:0005764)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|platelet activating factor receptor activity (GO:0004992)|platelet-derived growth factor beta-receptor activity (GO:0005019)|platelet-derived growth factor binding (GO:0048407)|platelet-derived growth factor receptor binding (GO:0005161)|platelet-derived growth factor-activated receptor activity (GO:0005017)|protein kinase binding (GO:0019901)|protein tyrosine kinase activity (GO:0004713)|receptor binding (GO:0005102)|vascular endothelial growth factor binding (GO:0038085)			breast(3)|central_nervous_system(5)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(9)|kidney(3)|large_intestine(12)|lung(20)|ovary(3)|prostate(3)|skin(3)|stomach(6)|urinary_tract(1)	75		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		Becaplermin(DB00102)|Dasatinib(DB01254)|Imatinib(DB00619)|Pazopanib(DB06589)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	TCACGCGAACCAGTGTCAGCT	0.557			T	"""ETV6, TRIP11, HIP1, RAB5EP, H4, NIN, HCMOGT-1, PDE4DIP"""	"""MPD, AML, CMML, CML"""								C|||	24	0.00479233	0.0	0.0115	5008	,	,		20833	0.0		0.0159	False		,,,				2504	0.0				p.L383L		Atlas-SNP	.		Dom	yes		5	5q31-q32	5159	"""platelet-derived growth factor receptor, beta polypeptide"""		L	.	PDGFRB	142	.	0			c.G1149C						PASS	.	C		9,4397	14.3+/-33.2	0,9,2194	93.0	80.0	84.0		1149	1.1	0.9	5	dbSNP_98	84	100,8500	54.4+/-115.2	0,100,4200	no	coding-synonymous	PDGFRB	NM_002609.3		0,109,6394	GG,GC,CC		1.1628,0.2043,0.8381		383/1107	149511636	109,12897	2203	4300	6503	SO:0001819	synonymous_variant	5159	exon8			GCGAACCAGTGTC	M21616	CCDS4303.1	5q33.1	2013-01-29			ENSG00000113721	ENSG00000113721		"""CD molecules"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	8804	protein-coding gene	gene with protein product		173410		PDGFR			Standard	XM_005268464		Approved	JTK12, CD140b, PDGFR1	uc003lro.3	P09619	OTTHUMG00000130053	ENST00000261799.4:c.1149G>C	5.37:g.149511636C>G		Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	151	68	0.450331	NM_002609	B5A957|Q8N5L4	Silent	SNP	ENST00000261799.4	37	CCDS4303.1																																																																																			C|0.992;G|0.008	0.008	strong		0.557	PDGFRB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252332.1	NM_002609	
KRTAP4-6	81871	hgsc.bcm.edu	37	17	39296152	39296152	+	Silent	SNP	A	A	G	rs551614044	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:39296152A>G	ENST00000345847.4	-	1	587	c.588T>C	c.(586-588)cgT>cgC	p.R196R		NM_030976.1	NP_112238.1	Q9BYQ5	KRA46_HUMAN	keratin associated protein 4-6	196						keratin filament (GO:0045095)				endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|lung(1)|prostate(1)|urinary_tract(1)	9						AGCACAAGGGACGGGGGCAGG	0.597													a|||	234	0.0467252	0.0726	0.0504	5008	,	,		18042	0.0179		0.0298	False		,,,				2504	0.0562				p.R196R		Atlas-SNP	.											KRTAP4-6,NS,carcinoma,0,1	KRTAP4-6	46	1	0			c.T588C						scavenged	.																																			SO:0001819	synonymous_variant	81871	exon1			CAAGGGACGGGGG	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.588T>C	17.37:g.39296152A>G		Somatic	140	1	0.00714286		WXS	Illumina HiSeq	Phase_I	148	7	0.0472973	NM_030976	Q9BYR1	Silent	SNP	ENST00000345847.4	37	CCDS54125.1																																																																																			.	.	none		0.597	KRTAP4-6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257779.1		
ESPNL	339768	hgsc.bcm.edu	37	2	239039075	239039075	+	Missense_Mutation	SNP	G	G	T	rs13006204	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:239039075G>T	ENST00000343063.3	+	9	1983	c.1720G>T	c.(1720-1722)Gca>Tca	p.A574S	ESPNL_ENST00000477241.1_3'UTR|ESPNL_ENST00000409506.1_Missense_Mutation_p.A206S|ESPNL_ENST00000409169.1_Missense_Mutation_p.A530S	NM_194312.2	NP_919288.2	Q6ZVH7	ESPNL_HUMAN	espin-like	574			A -> S (in dbSNP:rs13006204). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.							endometrium(1)|lung(8)|pancreas(2)|skin(2)	13		Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0481)|all_hematologic(139;0.158)|all_lung(227;0.198)|Melanoma(123;0.203)|Hepatocellular(293;0.244)		Epithelial(121;4.71e-24)|OV - Ovarian serous cystadenocarcinoma(60;3.02e-12)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;5.63e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000109)|Lung(119;0.0108)|LUSC - Lung squamous cell carcinoma(224;0.0253)		GGCTGAGCCCGCAGGGTCTGC	0.706													G|||	1954	0.390176	0.3411	0.3876	5008	,	,		13997	0.4415		0.3827	False		,,,				2504	0.4131				p.A574S		Atlas-SNP	.											.	ESPNL	63	.	0			c.G1720T						PASS	.	G	SER/ALA	1547,2753		314,919,917	7.0	10.0	9.0		1720	-5.0	0.0	2	dbSNP_121	9	3307,5193		687,1933,1630	no	missense	ESPNL	NM_194312.2	99	1001,2852,2547	TT,TG,GG		38.9059,35.9767,37.9219	benign	574/1006	239039075	4854,7946	2150	4250	6400	SO:0001583	missense	339768	exon9			GAGCCCGCAGGGT	AK124559	CCDS2525.1	2q37.3	2013-01-10			ENSG00000144488	ENSG00000144488		"""Ankyrin repeat domain containing"""	27937	protein-coding gene	gene with protein product						12975309	Standard	NM_194312		Approved	FLJ42568	uc002vxq.4	Q6ZVH7	OTTHUMG00000133335	ENST00000343063.3:c.1720G>T	2.37:g.239039075G>T	ENSP00000339115:p.Ala574Ser	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	47	26	0.553191	NM_194312	Q66K27|Q6ZVG1|Q8IVU2	Missense_Mutation	SNP	ENST00000343063.3	37	CCDS2525.1	846	0.3873626373626374	177	0.3597560975609756	150	0.4143646408839779	236	0.4125874125874126	283	0.3733509234828496	G	0.019	-1.458749	0.01062	0.359767	0.389059	ENSG00000144488	ENST00000343063;ENST00000409169;ENST00000409506	T;T;T	0.62105	0.05;1.15;0.74	2.52	-5.03	0.02973	.	8.367350	0.00721	N	0.000888	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B	0.16603	0.001;0.018	B;B	0.06405	0.001;0.002	T	0.16867	-1.0388	9	0.13853	T	0.58	-0.9182	1.4149	0.02299	0.3048:0.148:0.3979:0.1493	rs13006204	530;574	Q6ZVH7-2;Q6ZVH7	.;ESPNL_HUMAN	S	574;530;206	ENSP00000339115:A574S;ENSP00000386577:A530S;ENSP00000386579:A206S	ENSP00000339115:A574S	A	+	1	0	ESPNL	238703814	0.000000	0.05858	0.000000	0.03702	0.018000	0.09664	-3.396000	0.00485	-1.405000	0.02048	-1.763000	0.00667	GCA	G|0.611;T|0.389	0.389	strong		0.706	ESPNL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257164.2	NM_194312	
DERL1	79139	hgsc.bcm.edu	37	8	124031541	124031541	+	Missense_Mutation	SNP	T	T	C	rs2272722	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:124031541T>C	ENST00000259512.4	-	7	811	c.511A>G	c.(511-513)Atc>Gtc	p.I171V	DERL1_ENST00000419562.2_Missense_Mutation_p.I71V|DERL1_ENST00000405944.3_Intron|DERL1_ENST00000523036.1_Missense_Mutation_p.I71V|RP11-557C18.3_ENST00000521258.1_RNA|DERL1_ENST00000519018.1_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	94	0	0		WXS	Illumina HiSeq	Phase_I	100	67	0.67	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	
SGK1	6446	hgsc.bcm.edu	37	6	134495159	134495159	+	Missense_Mutation	SNP	G	G	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:134495159G>C	ENST00000237305.7	-	3	300	c.212C>G	c.(211-213)gCc>gGc	p.A71G	SGK1_ENST00000475719.2_Missense_Mutation_p.A71G|SGK1_ENST00000489458.2_5'UTR|SGK1_ENST00000528577.1_Missense_Mutation_p.A99G|SGK1_ENST00000367858.5_Missense_Mutation_p.A166G|SGK1_ENST00000367857.5_Missense_Mutation_p.A61G|SGK1_ENST00000413996.3_Missense_Mutation_p.A85G	NM_005627.3	NP_005618.2	O00141	SGK1_HUMAN	serum/glucocorticoid regulated kinase 1	71					apoptotic process (GO:0006915)|cellular response to DNA damage stimulus (GO:0006974)|ion transmembrane transport (GO:0034220)|long-term memory (GO:0007616)|positive regulation of transporter activity (GO:0032411)|protein phosphorylation (GO:0006468)|regulation of apoptotic process (GO:0042981)|regulation of blood pressure (GO:0008217)|regulation of catalytic activity (GO:0050790)|regulation of cell growth (GO:0001558)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of gastric acid secretion (GO:0060453)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|renal sodium ion absorption (GO:0070294)|response to stress (GO:0006950)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium channel regulator activity (GO:0005246)|chloride channel regulator activity (GO:0017081)|potassium channel regulator activity (GO:0015459)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|sodium channel regulator activity (GO:0017080)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(21)|kidney(3)|large_intestine(3)|lung(10)|ovary(1)|skin(4)|stomach(1)	46	Colorectal(23;0.221)			OV - Ovarian serous cystadenocarcinoma(155;0.00317)|GBM - Glioblastoma multiforme(68;0.00847)		AGAAGGGTTGGCATTCATAAG	0.453																																					p.A166G		Atlas-SNP	.											SGK1_ENST00000528577,NS,lymphoid_neoplasm,0,5	SGK1	387	5	0			c.C497G						PASS	.						152.0	146.0	148.0					6																	134495159		2203	4300	6503	SO:0001583	missense	6446	exon5			GGGTTGGCATTCA	AJ000512	CCDS5170.1, CCDS47476.1, CCDS47477.1, CCDS47478.1	6q23	2008-02-05	2007-12-05	2007-12-05	ENSG00000118515	ENSG00000118515			10810	protein-coding gene	gene with protein product		602958	"""serum/glucocorticoid regulated kinase"""	SGK		9114008, 9722955	Standard	NM_005627		Approved		uc003qeo.4	O00141	OTTHUMG00000015613	ENST00000237305.7:c.212C>G	6.37:g.134495159G>C	ENSP00000237305:p.Ala71Gly	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	58	15	0.258621	NM_001143676	B7UUP7|B7UUP8|B7UUP9|B7Z5B2|E1P583|Q5TCN2|Q5TCN3|Q5TCN4|Q5VY65|Q9UN56	Missense_Mutation	SNP	ENST00000237305.7	37	CCDS5170.1	.	.	.	.	.	.	.	.	.	.	G	13.00	2.107682	0.37242	.	.	ENSG00000118515	ENST00000367858;ENST00000413996;ENST00000237305;ENST00000367857;ENST00000528577;ENST00000475719;ENST00000461976	T;T;T;T;T;T	0.72942	-0.69;-0.69;-0.69;-0.67;-0.68;-0.7	5.99	5.12	0.69794	.	0.399737	0.30076	N	0.010479	T	0.40171	0.1106	N	0.22421	0.69	0.80722	D	1	B;B;B;B;B;B	0.27559	0.001;0.0;0.0;0.019;0.181;0.0	B;B;B;B;B;B	0.26693	0.005;0.001;0.001;0.039;0.072;0.001	T	0.36625	-0.9740	10	0.20519	T	0.43	.	14.2908	0.66275	0.0:0.0:0.7295:0.2705	.	99;85;71;61;166;71	O00141-5;O00141-3;E9PR89;O00141-4;O00141-2;O00141	.;.;.;.;.;SGK1_HUMAN	G	166;85;71;61;99;71;135	ENSP00000356832:A166G;ENSP00000396242:A85G;ENSP00000237305:A71G;ENSP00000356831:A61G;ENSP00000434450:A99G;ENSP00000434302:A71G	ENSP00000237305:A71G	A	-	2	0	SGK1	134536852	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.654000	0.54453	1.523000	0.49018	0.655000	0.94253	GCC	.	.	none		0.453	SGK1-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042312.2		
MTBP	27085	hgsc.bcm.edu	37	8	121530190	121530190	+	Silent	SNP	A	A	G	rs13258848	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:121530190A>G	ENST00000305949.1	+	19	2391	c.2346A>G	c.(2344-2346)gaA>gaG	p.E782E		NM_022045.4	NP_071328.2	Q96DY7	MTBP_HUMAN	MDM2 binding protein	782	Interaction with MDM2. {ECO:0000250}.				cell cycle arrest (GO:0007050)|mitotic spindle checkpoint (GO:0071174)|negative regulation of cell proliferation (GO:0008285)|protein localization to kinetochore (GO:0034501)|traversing start control point of mitotic cell cycle (GO:0007089)	chromatin (GO:0000785)|kinetochore (GO:0000776)				NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	30	Lung NSC(37;5.68e-08)|Ovarian(258;0.00769)|all_neural(195;0.0804)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00503)			CACAAACAGAACGGTCCTTAC	0.398													G|||	2397	0.478634	0.1483	0.6066	5008	,	,		14446	0.5774		0.6869	False		,,,				2504	0.5184				p.E782E		Atlas-SNP	.											.	MTBP	77	.	0			c.A2346G						PASS	.	G		1026,3380	726.6+/-409.7	118,790,1295	140.0	107.0	118.0		2346	0.9	0.0	8	dbSNP_121	118	5785,2815	445.5+/-361.0	1931,1923,446	no	coding-synonymous	MTBP	NM_022045.3		2049,2713,1741	GG,GA,AA		32.7326,23.2864,47.6319		782/905	121530190	6811,6195	2203	4300	6503	SO:0001819	synonymous_variant	27085	exon19			AACAGAACGGTCC		CCDS6333.1	8q24.1-q24.2	2014-03-03	2014-03-03		ENSG00000172167	ENSG00000172167			7417	protein-coding gene	gene with protein product		605927	"""MDM2 (mouse double minute 2)-binding protein, 104kD"", ""Mdm2, transformed 3T3 cell double minute 2, p53 binding protein (mouse) binding protein, 104kDa"""			10906133, 11060448	Standard	NM_022045		Approved		uc003ypc.2	Q96DY7	OTTHUMG00000165040	ENST00000305949.1:c.2346A>G	8.37:g.121530190A>G		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	86	86	1	NM_022045	B4DUR5|Q9HA89	Silent	SNP	ENST00000305949.1	37	CCDS6333.1																																																																																			A|0.493;G|0.507	0.507	strong		0.398	MTBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381530.1	NM_022045	
CATSPER1	117144	hgsc.bcm.edu	37	11	65793797	65793797	+	Silent	SNP	G	G	A	rs1893316	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:65793797G>A	ENST00000312106.5	-	1	191	c.54C>T	c.(52-54)aaC>aaT	p.N18N		NM_053054.3	NP_444282.3	Q8NEC5	CTSR1_HUMAN	cation channel, sperm associated 1	18					calcium ion import (GO:0070509)|cell differentiation (GO:0030154)|fusion of sperm to egg plasma membrane (GO:0007342)|membrane depolarization during action potential (GO:0086010)|multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|regulation of calcium ion transport (GO:0051924)|regulation of cilium beat frequency involved in ciliary motility (GO:0060296)|single fertilization (GO:0007338)|sperm motility (GO:0030317)|sperm-egg recognition (GO:0035036)|spermatogenesis (GO:0007283)	CatSper complex (GO:0036128)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|voltage-gated calcium channel activity (GO:0005245)			breast(3)|central_nervous_system(1)|endometrium(9)|kidney(3)|large_intestine(6)|liver(3)|lung(12)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	44						ACCTATCTGCGTTATTGGTGT	0.557													G|||	831	0.165935	0.0106	0.389	5008	,	,		21811	0.2292		0.2435	False		,,,				2504	0.0726				p.N18N		Atlas-SNP	.											.	CATSPER1	101	.	0			c.C54T						PASS	.	G		237,4165	139.6+/-175.2	6,225,1970	181.0	139.0	153.0		54	0.7	0.0	11	dbSNP_92	153	2079,6513	359.0+/-331.4	241,1597,2458	no	coding-synonymous	CATSPER1	NM_053054.3		247,1822,4428	AA,AG,GG		24.1969,5.3839,17.8236		18/781	65793797	2316,10678	2201	4296	6497	SO:0001819	synonymous_variant	117144	exon1			ATCTGCGTTATTG	AF407333	CCDS8127.1	11q12.1	2011-07-05			ENSG00000175294	ENSG00000175294		"""Voltage-gated ion channels / Cation channels, sperm associated"""	17116	protein-coding gene	gene with protein product		606389				11675491, 11595941, 16382101	Standard	NM_053054		Approved	CATSPER	uc001ogt.3	Q8NEC5	OTTHUMG00000166668	ENST00000312106.5:c.54C>T	11.37:g.65793797G>A		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	86	73	0.848837	NM_053054	Q96P76	Silent	SNP	ENST00000312106.5	37	CCDS8127.1																																																																																			G|0.825;A|0.175	0.175	strong		0.557	CATSPER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391055.1	NM_053054	
CENPE	1062	hgsc.bcm.edu	37	4	104061993	104061993	+	Missense_Mutation	SNP	C	C	G	rs1381657|rs34789392	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:104061993C>G	ENST00000265148.3	-	36	5821	c.5732G>C	c.(5731-5733)aGc>aCc	p.S1911T	CENPE_ENST00000380026.3_Missense_Mutation_p.S1886T	NM_001813.2	NP_001804.2	Q02224	CENPE_HUMAN	centromere protein E, 312kDa	1911			S -> T (in dbSNP:rs1381657).		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)		TTCTTGCAGGCTTTCCTTGAG	0.388													C|||	1056	0.210863	0.1831	0.2176	5008	,	,		18277	0.1548		0.1799	False		,,,				2504	0.3333				p.S1911T		Atlas-SNP	.											.	CENPE	253	.	0			c.G5732C						PASS	.	C	THR/SER	780,3626	313.3+/-293.0	67,646,1490	136.0	119.0	125.0		5732	-1.3	0.0	4	dbSNP_88	125	1580,7020	295.5+/-302.4	146,1288,2866	yes	missense	CENPE	NM_001813.2	58	213,1934,4356	GG,GC,CC		18.3721,17.7031,18.1455	benign	1911/2702	104061993	2360,10646	2203	4300	6503	SO:0001583	missense	1062	exon36			TGCAGGCTTTCCT	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.5732G>C	4.37:g.104061993C>G	ENSP00000265148:p.Ser1911Thr	Somatic	227	0	0		WXS	Illumina HiSeq	Phase_I	177	79	0.446328	NM_001813	A6NKY9|A8K2U7|Q4LE75	Missense_Mutation	SNP	ENST00000265148.3	37	CCDS34042.1	371	0.16987179487179488	87	0.17682926829268292	75	0.20718232044198895	78	0.13636363636363635	131	0.17282321899736147	C	1.869	-0.460761	0.04508	0.177031	0.183721	ENSG00000138778	ENST00000265148;ENST00000394771;ENST00000380026	T;T	0.72394	-0.65;-0.65	5.21	-1.34	0.09143	.	.	.	.	.	T	0.00039	0.0001	N	0.12746	0.255	0.80722	P	0.0	B;B	0.29531	0.247;0.001	B;B	0.28638	0.092;0.005	T	0.03933	-1.0991	8	0.37606	T	0.19	.	9.7662	0.40563	0.0:0.3975:0.0:0.6025	rs1381657;rs52832792;rs60126258;rs1381657	1886;1911	Q02224-3;Q02224	.;CENPE_HUMAN	T	1911;1911;1886	ENSP00000265148:S1911T;ENSP00000369365:S1886T	ENSP00000265148:S1911T	S	-	2	0	CENPE	104281442	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.757000	0.04772	-0.150000	0.11195	-0.334000	0.08254	AGC	C|0.816;G|0.184	0.184	strong		0.388	CENPE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
ALPI	248	hgsc.bcm.edu	37	2	233322286	233322286	+	Silent	SNP	C	C	T	rs139371546		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:233322286C>T	ENST00000295463.3	+	6	737	c.660C>T	c.(658-660)ggC>ggT	p.G220G		NM_001631.3	NP_001622.2	P09923	PPBI_HUMAN	alkaline phosphatase, intestinal	220					dephosphorylation (GO:0016311)	anchored component of membrane (GO:0031225)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alkaline phosphatase activity (GO:0004035)|magnesium ion binding (GO:0000287)|protease binding (GO:0002020)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(2)|lung(10)|prostate(2)|upper_aerodigestive_tract(1)	24		all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0449)|Lung NSC(271;0.132)		Epithelial(121;1.64e-16)|Kidney(3;9.71e-08)|KIRC - Kidney renal clear cell carcinoma(3;2.74e-06)|BRCA - Breast invasive adenocarcinoma(100;0.000763)|Lung(119;0.00564)|LUSC - Lung squamous cell carcinoma(224;0.00746)		TGATCCTTGGCGGAGGCCGCA	0.642													C|||	1	0.000199681	0.0	0.0014	5008	,	,		19244	0.0		0.0	False		,,,				2504	0.0				p.G220G		Atlas-SNP	.											.	ALPI	64	.	0			c.C660T						PASS	.	C		2,4404	2.1+/-5.4	0,2,2201	56.0	59.0	58.0		660	-11.2	0.0	2	dbSNP_134	58	10,8590	7.7+/-29.5	0,10,4290	no	coding-synonymous	ALPI	NM_001631.3		0,12,6491	TT,TC,CC		0.1163,0.0454,0.0923		220/529	233322286	12,12994	2203	4300	6503	SO:0001819	synonymous_variant	248	exon6			CCTTGGCGGAGGC	M15694	CCDS2492.1	2q37.1	2008-02-05			ENSG00000163295	ENSG00000163295	3.1.3.1		437	protein-coding gene	gene with protein product		171740				3468508, 3469665	Standard	NM_001631		Approved		uc002vst.4	P09923	OTTHUMG00000133258	ENST00000295463.3:c.660C>T	2.37:g.233322286C>T		Somatic	240	1	0.00416667		WXS	Illumina HiSeq	Phase_I	228	129	0.565789	NM_001631	B2R7Y4|Q53S80|Q9UBV5|Q9UCL2	Silent	SNP	ENST00000295463.3	37	CCDS2492.1																																																																																			C|0.999;T|0.001	0.001	strong		0.642	ALPI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257035.2	NM_001631	
MUC4	4585	hgsc.bcm.edu	37	3	195513442	195513442	+	Missense_Mutation	SNP	G	G	T	rs537252759	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195513442G>T	ENST00000463781.3	-	2	5468	c.5009C>A	c.(5008-5010)aCt>aAt	p.T1670N	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.T1670N	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0	VWFD. {ECO:0000255|PROSITE- ProRule:PRU00580}.				cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		TGCTGAGGAAGTGCTGGTGAC	0.587													.|||	125	0.0249601	0.0545	0.0058	5008	,	,		20701	0.0228		0.0169	False		,,,				2504	0.0092				p.T1670N		Atlas-SNP	.											.	MUC4	1505	.	0			c.C5009A						PASS	.						39.0	37.0	37.0					3																	195513442		689	1584	2273	SO:0001583	missense	4585	exon2			GAGGAAGTGCTGG	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.5009C>A	3.37:g.195513442G>T	ENSP00000417498:p.Thr1670Asn	Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	160	34	0.2125	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	-	6.440	0.449408	0.12223	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.32515	1.45;1.46	0.595	-1.19	0.09585	.	.	.	.	.	T	0.13970	0.0338	N	0.19112	0.55	0.09310	N	1	B	0.14438	0.01	B	0.04013	0.001	T	0.27872	-1.0061	8	.	.	.	.	1.5348	0.02543	0.2829:0.0:0.3766:0.3405	.	1670	E7ESK3	.	N	1670	ENSP00000417498:T1670N;ENSP00000420243:T1670N	.	T	-	2	0	MUC4	196997837	0.000000	0.05858	0.001000	0.08648	0.004000	0.04260	0.600000	0.24104	-0.385000	0.07833	0.089000	0.15464	ACT	.	.	none		0.587	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
ANKRD13A	88455	hgsc.bcm.edu	37	12	110474070	110474070	+	Missense_Mutation	SNP	T	T	C	rs2287174	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	196	0	0		WXS	Illumina HiSeq	Phase_I	167	81	0.48503	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	
MYH7B	57644	hgsc.bcm.edu	37	20	33578899	33578899	+	Silent	SNP	T	T	C	rs2425009	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:33578899T>C	ENST00000262873.7	+	22	2376	c.2284T>C	c.(2284-2286)Ttg>Ctg	p.L762L	MIR499A_ENST00000384903.1_RNA	NM_020884.3	NP_065935.2	A7E2Y1	MYH7B_HUMAN	myosin, heavy chain 7B, cardiac muscle, beta	720	Myosin motor.					membrane (GO:0016020)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(2)|breast(5)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(19)|ovary(5)|prostate(3)|upper_aerodigestive_tract(2)|urinary_tract(3)	54			BRCA - Breast invasive adenocarcinoma(18;0.00691)			CCCCAACAGGTTGCTCTACAC	0.642													C|||	3933	0.785343	0.8389	0.8646	5008	,	,		17712	0.7867		0.7684	False		,,,				2504	0.6728				p.L762L		Atlas-SNP	.											.	MYH7B	145	.	0			c.T2284C						PASS	.	C		3455,777		1416,623,77	55.0	62.0	60.0		2284	3.7	1.0	20	dbSNP_100	60	6228,2302		2279,1670,316	no	coding-synonymous	MYH7B	NM_020884.3		3695,2293,393	CC,CT,TT		26.9871,18.3601,24.1263		762/1984	33578899	9683,3079	2116	4265	6381	SO:0001819	synonymous_variant	57644	exon24			AACAGGTTGCTCT	AB040945	CCDS42869.1	20q11	2011-09-27	2006-09-29		ENSG00000078814	ENSG00000078814		"""Myosins / Myosin superfamily : Class II"""	15906	protein-coding gene	gene with protein product		609928	"""myosin, heavy polypeptide 7B, cardiac muscle, beta"""			11919279, 15014174	Standard	XM_006723839		Approved	KIAA1512, dJ756N5.1, MYH14, MHC14	uc002xbi.2	A7E2Y1	OTTHUMG00000032320	ENST00000262873.7:c.2284T>C	20.37:g.33578899T>C		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	39	39	1	NM_020884	Q5JVW7|Q6NT44|Q6NT57|Q6WG75|Q96I57|Q9NWE2|Q9P216	Silent	SNP	ENST00000262873.7	37	CCDS42869.1																																																																																			T|0.217;C|0.783	0.783	strong		0.642	MYH7B-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000078833.2	NM_020884	
DYNC2H1	79659	hgsc.bcm.edu	37	11	103057048	103057048	+	Silent	SNP	A	A	G	rs658804	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:103057048A>G	ENST00000375735.2	+	42	6855	c.6711A>G	c.(6709-6711)cgA>cgG	p.R2237R	DYNC2H1_ENST00000398093.3_Silent_p.R2237R|DYNC2H1_ENST00000334267.7_Intron	NM_001080463.1|NM_001377.2	NP_001073932.1|NP_001368.2	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1	2237					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)		CTAGGGGTCGATTAGCAACAT	0.418													A|||	2862	0.571486	0.4985	0.67	5008	,	,		16424	0.5526		0.6223	False		,,,				2504	0.5675				p.R2237R		Atlas-SNP	.											.	DYNC2H1	246	.	0			c.A6711G						PASS	.	A	,	1987,1741		536,915,413	92.0	83.0	86.0		6711,6711	-10.7	0.0	11	dbSNP_83	86	5137,3057		1611,1915,571	no	coding-synonymous,coding-synonymous	DYNC2H1	NM_001080463.1,NM_001377.2	,	2147,2830,984	GG,GA,AA		37.3078,46.7006,40.2449	,	2237/4315,2237/4308	103057048	7124,4798	1864	4097	5961	SO:0001819	synonymous_variant	79659	exon42			GGGTCGATTAGCA	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.6711A>G	11.37:g.103057048A>G		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	74	74	1	NM_001377	O00432|Q16693|Q3C1U8|Q4AC93|Q6ZMX7|Q6ZUM6|Q7Z363|Q8N977|Q92815|Q9HAE4	Silent	SNP	ENST00000375735.2	37	CCDS53701.1																																																																																			A|0.420;G|0.580	0.580	strong		0.418	DYNC2H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387196.1	XM_370652	
LILRA6	79168	hgsc.bcm.edu	37	19	54744387	54744387	+	Missense_Mutation	SNP	C	C	T	rs71263238	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:54744387C>T	ENST00000396365.2	-	6	1060	c.1021G>A	c.(1021-1023)Gtg>Atg	p.V341M	LILRA6_ENST00000245621.5_Missense_Mutation_p.V341M|LILRA6_ENST00000440558.2_Intron|LILRA6_ENST00000270464.5_Intron|LILRB3_ENST00000407860.2_Intron|LILRA6_ENST00000419410.2_Missense_Mutation_p.V341M|LILRA6_ENST00000391735.3_3'UTR	NM_024318.2	NP_077294	Q6PI73	LIRA6_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 6	341	Ig-like C2-type 2.				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)		AGCAGGGTCACGTTCTCTCCT	0.582																																					p.V341M		Atlas-SNP	.											.	LILRA6	75	.	0			c.G1021A						PASS	.	C	MET/VAL	1667,2543		384,899,822	40.0	57.0	51.0		1021	1.1	0.4	19	dbSNP_130	51	3076,5426		408,2260,1583	yes	missense	LILRA6	NM_024318.2	21	792,3159,2405	TT,TC,CC		36.1797,39.5962,37.3112		341/482	54744387	4743,7969	2105	4251	6356	SO:0001583	missense	79168	exon6			GGGTCACGTTCTC	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.1021G>A	19.37:g.54744387C>T	ENSP00000379651:p.Val341Met	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	209	96	0.45933	NM_024318		Missense_Mutation	SNP	ENST00000396365.2	37	CCDS42610.1	744	0.34065934065934067	195	0.39634146341463417	123	0.3397790055248619	162	0.28321678321678323	264	0.3482849604221636	C	13.36	2.213853	0.39102	0.395962	0.361797	ENSG00000244482	ENST00000419410;ENST00000421123;ENST00000396365;ENST00000245621	T;T;T	0.01215	5.16;5.16;5.16	2.16	1.1	0.20463	Immunoglobulin subtype (1);Immunoglobulin (1);Immunoglobulin-like fold (1);	1.027150	0.07816	N	0.958912	T	0.00012	0.0000	M	0.86651	2.83	0.31233	P	0.696064	D;D;D	0.89917	1.0;0.974;1.0	P;P;D	0.83275	0.906;0.703;0.996	T	0.44877	-0.9299	9	0.48119	T	0.1	.	4.6406	0.12546	0.0:0.8064:0.0:0.1936	.	341;341;341	C9JFH3;Q6PI73;D3YTC4	.;LIRA6_HUMAN;.	M	341	ENSP00000411227:V341M;ENSP00000379651:V341M;ENSP00000245621:V341M	ENSP00000245621:V341M	V	-	1	0	LILRA6	59436199	0.006000	0.16342	0.448000	0.26945	0.180000	0.23129	0.793000	0.26944	0.470000	0.27294	0.195000	0.17529	GTG	C|0.659;T|0.341	0.341	strong		0.582	LILRA6-003	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000313725.1	NM_024318	
METTL11B	149281	hgsc.bcm.edu	37	1	170135760	170135760	+	Missense_Mutation	SNP	T	T	C	rs6427235	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:170135760T>C	ENST00000439373.2	+	3	555	c.448T>C	c.(448-450)Tcc>Ccc	p.S150P	METTL11B_ENST00000367764.3_3'UTR	NM_001136107.1	NP_001129579.1	Q5VVY1	NTM1B_HUMAN	methyltransferase like 11B	150			S -> P (in dbSNP:rs6427235).			nucleus (GO:0005634)	methyltransferase activity (GO:0008168)			NS(1)|breast(2)|endometrium(3)|prostate(2)	8						TATGATGGAATCCTTTCTCCT	0.517													T|||	1459	0.291334	0.5076	0.2435	5008	,	,		18050	0.1349		0.2724	False		,,,				2504	0.2137				p.S150P		Atlas-SNP	.											.	METTL11B	18	.	0			c.T448C						PASS	.	T	PRO/SER	657,727		159,339,194	116.0	107.0	110.0		448	-1.3	0.6	1	dbSNP_116	110	885,2297		133,619,839	yes	missense	METTL11B	NM_001136107.1	74	292,958,1033	CC,CT,TT		27.8127,47.4711,33.7714	benign	150/284	170135760	1542,3024	692	1591	2283	SO:0001583	missense	149281	exon3			ATGGAATCCTTTC	AL445203, CAH72139	CCDS44275.1	1q24.2	2012-11-05	2008-06-11	2008-06-11	ENSG00000203740	ENSG00000203740			31932	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 184"""	C1orf184			Standard	NM_001136107		Approved	HOMT1B	uc009wvv.1	Q5VVY1	OTTHUMG00000035959	ENST00000439373.2:c.448T>C	1.37:g.170135760T>C	ENSP00000408058:p.Ser150Pro	Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	132	74	0.560606	NM_001136107	B2RXI0	Missense_Mutation	SNP	ENST00000439373.2	37	CCDS44275.1	610	0.2793040293040293	227	0.4613821138211382	93	0.2569060773480663	70	0.12237762237762238	220	0.29023746701846964	T	10.56	1.383329	0.25031	0.474711	0.278127	ENSG00000203740	ENST00000439373	T	0.22539	1.95	5.25	-1.26	0.09376	.	0.478630	0.25096	N	0.033178	T	0.01940	0.0061	N	0.02697	-0.525	0.80722	P	0.0	B	0.06786	0.001	B	0.04013	0.001	T	0.44421	-0.9329	9	0.28530	T	0.3	-0.9035	5.4805	0.16721	0.2123:0.435:0.0:0.3527	rs6427235	150	Q5VVY1	NTM1B_HUMAN	P	150	ENSP00000408058:S150P	ENSP00000408058:S150P	S	+	1	0	METTL11B	168402384	0.799000	0.28903	0.609000	0.28983	0.989000	0.77384	0.422000	0.21296	0.078000	0.16900	0.533000	0.62120	TCC	T|0.719;C|0.281	0.281	strong		0.517	METTL11B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087586.2	NM_001136107	
PIGZ	80235	hgsc.bcm.edu	37	3	196674916	196674916	+	Silent	SNP	A	A	C	rs1147240	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:196674916A>C	ENST00000412723.1	-	3	998	c.852T>G	c.(850-852)gcT>gcG	p.A284A		NM_025163.2	NP_079439.2	Q86VD9	PIGZ_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class Z	284					GPI anchor biosynthetic process (GO:0006506)|mannosylation (GO:0097502)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	alpha-1,2-mannosyltransferase activity (GO:0000026)|mannosyltransferase activity (GO:0000030)			breast(1)|endometrium(1)|lung(7)|ovary(3)|prostate(1)|urinary_tract(1)	14	all_cancers(143;1.05e-08)|Ovarian(172;0.0634)|Breast(254;0.0838)		Epithelial(36;4.29e-24)|all cancers(36;2.79e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.03e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00603)		TCCTGGATGTAGCGGGGCTGG	0.607													A|||	2891	0.577276	0.6672	0.4568	5008	,	,		18756	0.7698		0.3976	False		,,,				2504	0.5276				p.A284A		Atlas-SNP	.											.	PIGZ	34	.	0			c.T852G						PASS	.	A		2723,1683	639.9+/-397.2	832,1059,312	104.0	110.0	108.0		852	-8.1	0.0	3	dbSNP_87	108	3228,5372	471.3+/-368.1	617,1994,1689	no	coding-synonymous	PIGZ	NM_025163.2		1449,3053,2001	CC,CA,AA		37.5349,38.1979,45.7558		284/580	196674916	5951,7055	2203	4300	6503	SO:0001819	synonymous_variant	80235	exon3			GGATGTAGCGGGG	BC018804	CCDS3324.1	3q29	2013-02-26	2006-06-28		ENSG00000119227	ENSG00000119227		"""Dolichyl D-mannosyl phosphate dependent mannosyltransferases"", ""Phosphatidylinositol glycan anchor biosynthesis"""	30596	protein-coding gene	gene with protein product	"""GPI mannosyltransferase 4"", ""dol-P-Man dependent GPI mannosyltransferase"""	611671	"""phosphatidylinositol glycan, class Z"""			15208306	Standard	NM_025163		Approved	FLJ12768, MGC52163, SMP3	uc003fxh.3	Q86VD9	OTTHUMG00000155522	ENST00000412723.1:c.852T>G	3.37:g.196674916A>C		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	50	49	0.98	NM_025163	Q9H9G6	Silent	SNP	ENST00000412723.1	37	CCDS3324.1																																																																																			A|0.479;C|0.521	0.521	strong		0.607	PIGZ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340486.2	NM_025163	
EMC10	284361	hgsc.bcm.edu	37	19	50983930	50983930	+	Silent	SNP	C	C	T	rs10409679	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:50983930C>T	ENST00000334976.6	+	5	541	c.495C>T	c.(493-495)ccC>ccT	p.P165P	CTD-2545M3.2_ENST00000598194.1_RNA|EMC10_ENST00000376918.3_Silent_p.P165P|EMC10_ENST00000598585.1_Silent_p.P165P	NM_206538.2	NP_996261.1	Q5UCC4	EMC10_HUMAN	ER membrane protein complex subunit 10	165						ER membrane protein complex (GO:0072546)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)											TGACGCACCCCGGGGGCTGCC	0.697													C|||	2712	0.541534	0.3389	0.6297	5008	,	,		13105	0.5556		0.5875	False		,,,				2504	0.6912				p.P165P		Atlas-SNP	.											C19orf63_ENST00000376918,rectum,carcinoma,0,2	.	.	2	0			c.C495T						PASS	.	C	,	1652,2732		318,1016,858	24.0	25.0	25.0		495,495	-8.5	0.1	19	dbSNP_119	25	5033,3555		1498,2037,759	no	coding-synonymous,coding-synonymous	C19orf63	NM_175063.4,NM_206538.2	,	1816,3053,1617	TT,TC,CC		41.395,37.6825,48.4659	,	165/255,165/263	50983930	6685,6287	2192	4294	6486	SO:0001819	synonymous_variant	284361	exon5			GCACCCCGGGGGC	BC062607	CCDS12796.1, CCDS42594.1	19q13.33	2012-05-30	2012-05-30	2012-05-30	ENSG00000161671	ENSG00000161671			27609	protein-coding gene	gene with protein product	"""hematopoietic signal peptide-containing secreted 1"", ""hematopoietic signal peptide-containing membrane domain-containing 1"""	614545	"""chromosome 19 open reading frame 63"""	C19orf63		12975309, 22119785	Standard	NM_175063		Approved	INM02, HSS1, HSM1	uc002psl.3	Q5UCC4		ENST00000334976.6:c.495C>T	19.37:g.50983930C>T		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	60	33	0.55	NM_175063	Q5UCC6|Q69YT5|Q6UWP3|Q86YL4|Q8N541	Silent	SNP	ENST00000334976.6	37	CCDS12796.1																																																																																			C|0.493;T|0.507	0.507	strong		0.697	EMC10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464760.2	NM_175063	
FSIP1	161835	hgsc.bcm.edu	37	15	39910431	39910431	+	Missense_Mutation	SNP	A	A	G	rs10152640	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:39910431A>G	ENST00000350221.3	-	11	1413	c.1204T>C	c.(1204-1206)Tgt>Cgt	p.C402R		NM_152597.4	NP_689810.3	Q8NA03	FSIP1_HUMAN	fibrous sheath interacting protein 1	402			C -> R (in dbSNP:rs10152640). {ECO:0000269|Ref.3}.					p.C402R(1)		NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(4)|ovary(2)|skin(4)|stomach(2)|urinary_tract(1)	23		all_cancers(109;2.66e-19)|all_epithelial(112;2.66e-16)|Lung NSC(122;1.5e-11)|all_lung(180;4.03e-10)|Melanoma(134;0.0575)|Ovarian(310;0.0827)|Colorectal(260;0.119)		GBM - Glioblastoma multiforme(113;8.22e-06)|BRCA - Breast invasive adenocarcinoma(123;0.142)		TCAGAGAGACATGATGTGGAC	0.318													G|||	2063	0.411941	0.7458	0.2594	5008	,	,		20215	0.3095		0.3072	False		,,,				2504	0.2822				p.C402R		Atlas-SNP	.											FSIP1,NS,carcinoma,0,2	FSIP1	53	2	1	Substitution - Missense(1)	stomach(1)	c.T1204C						PASS	.	G	ARG/CYS	2789,1577		917,955,311	44.0	48.0	47.0		1204	-0.4	0.1	15	dbSNP_119	47	2544,5964		382,1780,2092	yes	missense	FSIP1	NM_152597.4	180	1299,2735,2403	GG,GA,AA		29.9013,36.12,41.4246	benign	402/582	39910431	5333,7541	2183	4254	6437	SO:0001583	missense	161835	exon11			AGAGACATGATGT	BC045191	CCDS10050.1	15q14	2012-11-19			ENSG00000150667	ENSG00000150667			21674	protein-coding gene	gene with protein product		615795				14702039	Standard	NM_152597		Approved	FLJ35989	uc001zki.3	Q8NA03	OTTHUMG00000172456	ENST00000350221.3:c.1204T>C	15.37:g.39910431A>G	ENSP00000280236:p.Cys402Arg	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	91	91	1	NM_152597	Q6X2C8|Q86Y89	Missense_Mutation	SNP	ENST00000350221.3	37	CCDS10050.1	872	0.3992673992673993	346	0.7032520325203252	106	0.292817679558011	188	0.32867132867132864	232	0.30606860158311344	G	0.009	-1.857666	0.00558	0.6388	0.299013	ENSG00000150667	ENST00000350221	T	0.10668	2.85	5.06	-0.452	0.12205	.	0.738656	0.11694	N	0.538597	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	0.15723	-1.0427	8	.	.	.	8.7668	2.7672	0.05323	0.2845:0.4014:0.2062:0.1079	rs10152640;rs52803468;rs57454183;rs10152640	402	Q8NA03	FSIP1_HUMAN	R	402	ENSP00000280236:C402R	.	C	-	1	0	FSIP1	37697723	0.001000	0.12720	0.088000	0.20740	0.012000	0.07955	-0.124000	0.10595	-0.082000	0.12640	-0.726000	0.03593	TGT	A|0.599;G|0.401	0.401	strong		0.318	FSIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252118.2	NM_152597	
MOCS1	4337	hgsc.bcm.edu	37	6	39881568	39881568	+	Missense_Mutation	SNP	C	C	A	rs377241570		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:39881568C>A	ENST00000340692.5	-	5	598	c.595G>T	c.(595-597)Gtc>Ttc	p.V199F	MOCS1_ENST00000432280.2_Missense_Mutation_p.V170F|MOCS1_ENST00000373186.4_Missense_Mutation_p.V199F|MOCS1_ENST00000425303.2_Missense_Mutation_p.V199F|MOCS1_ENST00000373188.2_Missense_Mutation_p.V199F|MOCS1_ENST00000308559.7_Missense_Mutation_p.V199F|MOCS1_ENST00000373195.3_Missense_Mutation_p.V112F|MOCS1_ENST00000373175.4_Missense_Mutation_p.V170F			Q9NZB8	MOCS1_HUMAN	molybdenum cofactor synthesis 1	199	Molybdenum cofactor biosynthesis protein A.				Mo-molybdopterin cofactor biosynthetic process (GO:0006777)|molybdopterin cofactor biosynthetic process (GO:0032324)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|molybdopterin synthase complex (GO:0019008)|nucleus (GO:0005634)	4 iron, 4 sulfur cluster binding (GO:0051539)|cyclic pyranopterin monophosphate synthase activity (GO:0061597)|GTP binding (GO:0005525)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(1)|liver(2)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|skin(2)	21	Ovarian(28;0.0355)|Colorectal(47;0.196)					CCCTCCATGACCTTGTGGAAG	0.592																																					p.V199F	NSCLC(84;861 1413 23785 24908 42279)|Melanoma(182;611 2047 9114 11847 26639)	Atlas-SNP	.											.	MOCS1	87	.	0			c.G595T						PASS	.						120.0	101.0	107.0					6																	39881568		2203	4300	6503	SO:0001583	missense	4337	exon4			CCATGACCTTGTG	AJ224328	CCDS4846.1, CCDS43460.1	6p21.2	2012-05-08			ENSG00000124615	ENSG00000124615			7190	protein-coding gene	gene with protein product		603707				9731530, 10053004	Standard	NM_001075098		Approved	MOCOD	uc003opb.3	Q9NZB8	OTTHUMG00000014656	ENST00000340692.5:c.595G>T	6.37:g.39881568C>A	ENSP00000344794:p.Val199Phe	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	66	16	0.242424	NM_005943	B3KPT7|B4DTP1|O14940|O14941|O75710|Q5J7W0|Q5TCE1|Q5TCE2|Q5TCE6|Q5TCE9|Q5TCF0|Q5TCF1|Q8N418|Q9NZB7|Q9UEM1	Missense_Mutation	SNP	ENST00000340692.5	37		.	.	.	.	.	.	.	.	.	.	C	27.2	4.806025	0.90623	.	.	ENSG00000124615	ENST00000373186;ENST00000308559;ENST00000373175;ENST00000373188;ENST00000373195;ENST00000340692;ENST00000425303;ENST00000432280	T;T;T;T;T;T;T;T	0.80566	-1.39;-1.39;-1.39;-1.39;-1.39;-1.39;-1.39;-1.39	4.84	4.84	0.62591	Elongator protein 3/MiaB/NifB (1);Aldolase-type TIM barrel (1);Radical SAM (1);	0.000000	0.85682	D	0.000000	D	0.93996	0.8077	H	0.99357	4.53	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;0.999	D;D;D;D;D	0.91635	0.999;0.995;0.999;0.999;0.995	D	0.96772	0.9569	9	.	.	.	-19.377	17.5587	0.87900	0.0:1.0:0.0:0.0	.	199;199;199;199;199	Q9NZB8-2;Q9NZB8-5;Q9NZB8;Q9NZB8-8;Q9NZB8-6	.;.;MOCS1_HUMAN;.;.	F	199;199;170;199;112;199;199;170	ENSP00000362282:V199F;ENSP00000309843:V199F;ENSP00000362270:V170F;ENSP00000362284:V199F;ENSP00000362291:V112F;ENSP00000344794:V199F;ENSP00000416478:V199F;ENSP00000410809:V170F	.	V	-	1	0	MOCS1	39989546	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	7.601000	0.82783	2.245000	0.73994	0.655000	0.94253	GTC	.	.	alt		0.592	MOCS1-005	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000040476.2	NM_005943	
LY75	4065	hgsc.bcm.edu	37	2	160732019	160732019	+	Missense_Mutation	SNP	G	G	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:160732019G>C	ENST00000263636.4	-	12	1937	c.1910C>G	c.(1909-1911)cCt>cGt	p.P637R	LY75_ENST00000554112.1_Missense_Mutation_p.P637R|LY75_ENST00000553424.1_Missense_Mutation_p.P637R|LY75-CD302_ENST00000504764.1_Missense_Mutation_p.P637R|LY75-CD302_ENST00000505052.1_Missense_Mutation_p.P637R	NM_002349.3	NP_002340.2	O60449	LY75_HUMAN	lymphocyte antigen 75	637					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)		ATCAGGCTTAGGGGATGCTTC	0.463																																					p.P637R		Atlas-SNP	.											.	LY75	151	.	0			c.C1910G						PASS	.						119.0	126.0	123.0					2																	160732019		2203	4300	6503	SO:0001583	missense	4065	exon12			GGCTTAGGGGATG	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.1910C>G	2.37:g.160732019G>C	ENSP00000263636:p.Pro637Arg	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	99	58	0.585859	NM_002349	O75913|Q53R46|Q53TF5|Q7Z575|Q7Z577	Missense_Mutation	SNP	ENST00000263636.4	37	CCDS2211.1	.	.	.	.	.	.	.	.	.	.	G	18.02	3.529779	0.64860	.	.	ENSG00000054219;ENSG00000054219;ENSG00000054219;ENSG00000248672;ENSG00000248672	ENST00000554112;ENST00000553424;ENST00000263636;ENST00000504764;ENST00000505052	T;T;T;T;T	0.08720	3.06;3.06;3.06;3.06;3.06	4.77	4.77	0.60923	C-type lectin-like (1);	0.000000	0.34959	N	0.003545	T	0.27384	0.0672	M	0.64630	1.985	0.80722	D	1	D;D;D;D	0.89917	0.983;1.0;1.0;1.0	D;D;D;D	0.97110	0.928;1.0;0.999;0.999	T	0.01033	-1.1474	10	0.66056	D	0.02	-9.9671	16.9332	0.86196	0.0:0.0:1.0:0.0	.	255;637;637;637	Q59H44;O60449-3;O60449;O60449-2	.;.;LY75_HUMAN;.	R	637	ENSP00000451511:P637R;ENSP00000451446:P637R;ENSP00000263636:P637R;ENSP00000423463:P637R;ENSP00000421035:P637R	ENSP00000423463:P637R	P	-	2	0	LY75;LY75-CD302	160440265	1.000000	0.71417	0.987000	0.45799	0.952000	0.60782	4.393000	0.59665	2.356000	0.79943	0.455000	0.32223	CCT	.	.	none		0.463	LY75-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255035.1		
ULK4	54986	hgsc.bcm.edu	37	3	41952852	41952852	+	Missense_Mutation	SNP	T	T	C	rs35263917	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:41952852T>C	ENST00000301831.4	-	11	1504	c.1042A>G	c.(1042-1044)Agt>Ggt	p.S348G	ULK4_ENST00000420927.1_Missense_Mutation_p.S348G	NM_017886.2	NP_060356.2	Q96C45	ULK4_HUMAN	unc-51 like kinase 4	348			S -> G (in dbSNP:rs35263917). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:17344846}.		cilium morphogenesis (GO:0060271)|epithelial cilium movement (GO:0003351)|microtubule cytoskeleton organization (GO:0000226)|regulation of JNK cascade (GO:0046328)|regulation of MAPK cascade (GO:0043408)|regulation of neuron migration (GO:2001222)|regulation of neuron projection development (GO:0010975)|regulation of p38MAPK cascade (GO:1900744)|regulation of protein kinase C signaling (GO:0090036)|ventricular system development (GO:0021591)		ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|cervix(1)|large_intestine(6)|lung(7)|prostate(5)|skin(1)	22				KIRC - Kidney renal clear cell carcinoma(284;0.214)		TCAAGAGTACTCTTAGGCCGA	0.343													T|||	421	0.0840655	0.0635	0.0908	5008	,	,		20625	0.002		0.166	False		,,,				2504	0.1074				p.S348G		Atlas-SNP	.											ULK4_ENST00000301831,colon,carcinoma,+1,2	ULK4	150	2	0			c.A1042G						PASS	.	T	GLY/SER	283,3385		9,265,1560	94.0	88.0	90.0		1042	5.2	0.9	3	dbSNP_126	90	1227,6941		90,1047,2947	yes	missense	ULK4	NM_017886.2	56	99,1312,4507	CC,CT,TT		15.022,7.7154,12.7577	possibly-damaging	348/1276	41952852	1510,10326	1834	4084	5918	SO:0001583	missense	54986	exon11			GAGTACTCTTAGG	AK000581	CCDS43071.1	3p22.1	2013-07-02	2013-07-02		ENSG00000168038	ENSG00000168038			15784	protein-coding gene	gene with protein product			"""unc-51-like kinase 4 (C. elegans)"""			12477932	Standard	NM_017886		Approved	FLJ20574, REC01035, FAM7C1	uc003ckv.4	Q96C45	OTTHUMG00000156210	ENST00000301831.4:c.1042A>G	3.37:g.41952852T>C	ENSP00000301831:p.Ser348Gly	Somatic	265	0	0		WXS	Illumina HiSeq	Phase_I	237	138	0.582278	NM_017886	A6NF15|Q8IW79|Q9NWV6|Q9UF96	Missense_Mutation	SNP	ENST00000301831.4	37	CCDS43071.1	198	0.09065934065934066	31	0.06300813008130081	32	0.08839779005524862	2	0.0034965034965034965	133	0.17546174142480211	T	21.5	4.164150	0.78339	0.077154	0.15022	ENSG00000168038	ENST00000301831;ENST00000420927	T;T	0.69040	0.42;-0.37	5.22	5.22	0.72569	.	0.707959	0.15193	N	0.275422	T	0.00300	0.0009	M	0.71581	2.175	0.09310	P	1.0	P	0.48911	0.917	B	0.43950	0.437	T	0.20907	-1.0261	9	0.62326	D	0.03	.	14.1258	0.65219	0.0:0.0:0.0:1.0	rs35263917;rs61740620	348	Q96C45	ULK4_HUMAN	G	348	ENSP00000301831:S348G;ENSP00000412187:S348G	ENSP00000301831:S348G	S	-	1	0	ULK4	41927856	1.000000	0.71417	0.918000	0.36340	0.766000	0.43426	5.411000	0.66386	1.979000	0.57680	0.529000	0.55759	AGT	T|0.887;C|0.113	0.113	strong		0.343	ULK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343490.1	XM_929989	
ZNF30	90075	hgsc.bcm.edu	37	19	35435069	35435069	+	Missense_Mutation	SNP	A	A	G	rs765746	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:35435069A>G	ENST00000601142.1	+	5	1436	c.1199A>G	c.(1198-1200)tAt>tGt	p.Y400C	ZNF30_ENST00000439785.1_Missense_Mutation_p.Y401C|ZNF30_ENST00000601957.1_3'UTR|ZNF30_ENST00000426813.2_Missense_Mutation_p.Y319C|ZNF30_ENST00000303586.7_Missense_Mutation_p.Y401C			P17039	ZNF30_HUMAN	zinc finger protein 30	400			Y -> C (in dbSNP:rs765746). {ECO:0000269|PubMed:14702039}.		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(3)|ovary(1)|prostate(2)	16	all_lung(56;8.38e-08)|Lung NSC(56;1.31e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0849)	GBM - Glioblastoma multiforme(1328;0.0265)		GAGAAGCCCTATGAATGTAAG	0.478													A|||	1146	0.228834	0.1815	0.1873	5008	,	,		24479	0.3909		0.1819	False		,,,				2504	0.2035				p.Y401C		Atlas-SNP	.											.	ZNF30	44	.	0			c.A1202G						PASS	.	A	CYS/TYR,CYS/TYR,CYS/TYR	841,3563	308.8+/-290.8	86,669,1447	64.0	73.0	70.0		1202,1202,1199	1.0	0.0	19	dbSNP_86	70	1454,7146	272.6+/-290.2	117,1220,2963	yes	missense,missense,missense	ZNF30	NM_001099437.1,NM_001099438.1,NM_194325.2	194,194,194	203,1889,4410	GG,GA,AA		16.907,19.0963,17.6484	probably-damaging,probably-damaging,probably-damaging	401/625,401/625,400/624	35435069	2295,10709	2202	4300	6502	SO:0001583	missense	90075	exon5			AGCCCTATGAATG	X52359	CCDS46044.1, CCDS46045.1	19q13.13	2013-01-08	2006-05-10			ENSG00000168661		"""Zinc fingers, C2H2-type"", ""-"""	13090	protein-coding gene	gene with protein product			"""zinc finger protein 30 (KOX 28)"""				Standard	NM_001099437		Approved	KOX28, DKFZp686N19164, FLJ20562	uc010edq.1	P17039		ENST00000601142.1:c.1199A>G	19.37:g.35435069A>G	ENSP00000469954:p.Tyr400Cys	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	85	50	0.588235	NM_001099438	A5PLP1|A8K320|B4DIC0|Q6N068	Missense_Mutation	SNP	ENST00000601142.1	37	CCDS46045.1	545	0.24954212454212454	102	0.2073170731707317	77	0.212707182320442	236	0.4125874125874126	130	0.17150395778364116	a	12.34	1.908703	0.33721	0.190963	0.16907	ENSG00000168661	ENST00000439785;ENST00000303586;ENST00000426813;ENST00000342559	T;T	0.25414	1.8;1.8	2.11	1.04	0.20106	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	M	0.85041	2.73	0.58432	P	2.9999999999752447E-6	P;D	0.89917	0.954;1.0	P;D	0.79108	0.498;0.992	T	0.35351	-0.9792	8	0.87932	D	0	.	1.865	0.03196	0.5516:0.0:0.1751:0.2733	rs765746;rs3746237;rs52817507;rs60077728;rs765746	401;400	P17039-2;P17039	.;ZNF30_HUMAN	C	401;400;319;109	ENSP00000403441:Y401C;ENSP00000416457:Y319C	ENSP00000303889:Y400C	Y	+	2	0	ZNF30	40126909	0.000000	0.05858	0.040000	0.18447	0.171000	0.22731	0.036000	0.13819	0.092000	0.17331	0.332000	0.21555	TAT	A|0.758;G|0.242	0.242	strong		0.478	ZNF30-003	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464432.1	NM_194325	
KRTAP10-11	386678	hgsc.bcm.edu	37	21	46066764	46066764	+	Missense_Mutation	SNP	C	C	T	rs4818952	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:46066764C>T	ENST00000334670.8	+	1	434	c.389C>T	c.(388-390)tCt>tTt	p.S130F	TSPEAR_ENST00000323084.4_Intron	NM_198692.2	NP_941965.2	P60412	KR10B_HUMAN	keratin associated protein 10-11	130	25 X 5 AA repeats of C-C-X(3).		S -> F (in dbSNP:rs4818952).			keratin filament (GO:0045095)				NS(1)|endometrium(1)|large_intestine(1)|lung(6)|ovary(2)|prostate(1)	12						tgccggcagtctagctgccag	0.632													C|||	3893	0.777356	0.8896	0.7493	5008	,	,		20378	0.6548		0.7694	False		,,,				2504	0.7802				p.S130F		Atlas-SNP	.											.	KRTAP10-11	36	.	0			c.C389T						PASS	.	C	PHE/SER,	3813,593	760.8+/-413.0	1652,509,42	107.0	115.0	113.0		389,	3.3	0.4	21	dbSNP_111	113	6216,2384	694.3+/-404.7	2260,1696,344	no	missense,intron	TSPEAR,KRTAP10-11	NM_198692.2,NM_144991.2	155,	3912,2205,386	TT,TC,CC		27.7209,13.4589,22.8894	probably-damaging,	130/299,	46066764	10029,2977	2203	4300	6503	SO:0001583	missense	386678	exon1			GGCAGTCTAGCTG	AB076359	CCDS42962.1	21q22.3	2006-03-13	2004-07-12	2004-07-14	ENSG00000243489	ENSG00000243489		"""Keratin associated proteins"""	20528	protein-coding gene	gene with protein product			"""keratin associated protein 10-11"""	KRTAP18-11			Standard	NM_198692		Approved	KRTAP18.11, KAP18.11, KAP10.11	uc002zfr.4	P60412	OTTHUMG00000057626	ENST00000334670.8:c.389C>T	21.37:g.46066764C>T	ENSP00000334197:p.Ser130Phe	Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	239	236	0.987448	NM_198692	A2RRF9	Missense_Mutation	SNP	ENST00000334670.8	37	CCDS42962.1	1658	0.7591575091575091	440	0.8943089430894309	280	0.7734806629834254	358	0.6258741258741258	580	0.7651715039577837	c	11.95	1.790471	0.31685	0.865411	0.722791	ENSG00000243489	ENST00000334670	T	0.01981	4.52	3.32	3.32	0.38043	.	.	.	.	.	T	0.00012	0.0000	M	0.92604	3.325	0.28924	P	0.891943	D	0.89917	1.0	D	0.91635	0.999	T	0.03534	-1.1027	8	0.87932	D	0	.	10.528	0.44960	0.0:1.0:0.0:0.0	rs4818952	130	P60412	KR10B_HUMAN	F	130	ENSP00000334197:S130F	ENSP00000334197:S130F	S	+	2	0	KRTAP10-11	44891192	0.002000	0.14202	0.358000	0.25811	0.496000	0.33645	0.618000	0.24373	1.583000	0.49898	0.456000	0.33151	TCT	C|0.241;T|0.759	0.759	strong		0.632	KRTAP10-11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128029.1	NM_198692	
MEP1B	4225	hgsc.bcm.edu	37	18	29772759	29772759	+	Silent	SNP	G	G	A	rs2289544	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:29772759G>A	ENST00000269202.6	+	4	197	c.150G>A	c.(148-150)gaG>gaA	p.E50E	MEP1B_ENST00000581447.1_Silent_p.E50E	NM_005925.2	NP_005916.2	Q16820	MEP1B_HUMAN	meprin A, beta	50					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						ATCTTTTTGAGGGTGACATCA	0.343													G|||	343	0.0684904	0.0749	0.0274	5008	,	,		18009	0.129		0.0249	False		,,,				2504	0.0716				p.E50E		Atlas-SNP	.											.	MEP1B	54	.	0			c.G150A						PASS	.	G		205,3453		5,195,1629	120.0	110.0	113.0		150	2.3	1.0	18	dbSNP_100	113	227,7957		6,215,3871	no	coding-synonymous	MEP1B	NM_005925.2		11,410,5500	AA,AG,GG		2.7737,5.6042,3.648		50/702	29772759	432,11410	1829	4092	5921	SO:0001819	synonymous_variant	4225	exon4			TTTTGAGGGTGAC	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.150G>A	18.37:g.29772759G>A		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	65	35	0.538462	NM_005925	B7ZM35|B9EGL6|Q670J1	Silent	SNP	ENST00000269202.6	37	CCDS45846.1																																																																																			G|0.924;A|0.076	0.076	strong		0.343	MEP1B-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447755.1	NM_005925	
KLK11	11012	hgsc.bcm.edu	37	19	51527942	51527942	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:51527942G>A	ENST00000594768.1	-	3	430	c.245C>T	c.(244-246)aCg>aTg	p.T82M	KLK11_ENST00000319720.7_Missense_Mutation_p.T50M|KLK11_ENST00000391804.3_Missense_Mutation_p.T50M|KLK11_ENST00000453757.3_Missense_Mutation_p.T50M|KLK11_ENST00000594458.1_5'UTR|KLK11_ENST00000600362.1_Intron	NM_144947.1	NP_659196.1	Q9UBX7	KLK11_HUMAN	kallikrein-related peptidase 11	82	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			breast(1)|endometrium(2)|large_intestine(1)|lung(2)|skin(1)	7		all_neural(266;0.026)		OV - Ovarian serous cystadenocarcinoma(262;0.00327)|GBM - Glioblastoma multiforme(134;0.00878)		GGCGATGAGCGTCGCCCCACA	0.687																																					p.T82M		Atlas-SNP	.											.	KLK11	28	.	0			c.C245T						PASS	.						22.0	20.0	20.0					19																	51527942		2203	4300	6503	SO:0001583	missense	11012	exon3			ATGAGCGTCGCCC	AB012917	CCDS12818.1, CCDS12819.1, CCDS54297.1	19q13.33	2011-09-07	2006-10-27			ENSG00000167757		"""Kallikreins"", ""Serine peptidases / Serine peptidases"""	6359	protein-coding gene	gene with protein product		604434	"""kallikrein 11"""	PRSS20		9765601, 10662548, 16800724, 16800723	Standard	NM_006853		Approved	TLSP	uc002pvb.2	Q9UBX7		ENST00000594768.1:c.245C>T	19.37:g.51527942G>A	ENSP00000473047:p.Thr82Met	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	65	25	0.384615	NM_144947	O75837|Q0WXX5|Q8IXD7|Q9NS65	Missense_Mutation	SNP	ENST00000594768.1	37	CCDS12818.1	.	.	.	.	.	.	.	.	.	.	g	13.04	2.118342	0.37339	.	.	ENSG00000167757	ENST00000391804;ENST00000319720;ENST00000453757;ENST00000319756	D;D;D;T	0.94330	-3.4;-3.4;-3.4;1.27	4.21	3.18	0.36537	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.000000	0.37669	U	0.001986	D	0.94466	0.8219	M	0.79123	2.44	0.27238	N	0.959219	P;P;P	0.50156	0.932;0.932;0.932	P;P;P	0.56823	0.751;0.807;0.807	D	0.88748	0.3248	10	0.66056	D	0.02	.	6.1447	0.20278	0.2243:0.0:0.7757:0.0	.	50;82;50	Q0WXX5;Q9UBX7;Q8IXD7	.;KLK11_HUMAN;.	M	50;50;50;82	ENSP00000375680:T50M;ENSP00000324269:T50M;ENSP00000413958:T50M;ENSP00000324414:T82M	ENSP00000324269:T50M	T	-	2	0	KLK11	56219754	0.796000	0.28864	0.801000	0.32222	0.039000	0.13416	1.752000	0.38349	0.977000	0.38444	0.455000	0.32223	ACG	.	.	none		0.687	KLK11-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000464314.2	NM_006853	
DOCK1	1793	hgsc.bcm.edu	37	10	129249676	129249676	+	Silent	SNP	C	C	T	rs2229604	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:129249676C>T	ENST00000280333.6	+	52	5692	c.5583C>T	c.(5581-5583)tcC>tcT	p.S1861S		NM_001380.3	NP_001371.1	Q14185	DOCK1_HUMAN	dedicator of cytokinesis 1	1861					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)		CGGTGGACTCCGGGATCGTGC	0.582													C|||	2116	0.422524	0.2337	0.4986	5008	,	,		17386	0.4593		0.497	False		,,,				2504	0.5092				p.S1861S		Atlas-SNP	.											.	DOCK1	188	.	0			c.C5583T						PASS	.	C		1097,3077		154,789,1144	43.0	51.0	48.0		5538	-10.4	0.1	10	dbSNP_98	48	4170,4256		1036,2098,1079	no	coding-synonymous	DOCK1	NM_001380.3		1190,2887,2223	TT,TC,CC		49.4897,26.2817,41.8016		1846/1851	129249676	5267,7333	2087	4213	6300	SO:0001819	synonymous_variant	1793	exon52			GGACTCCGGGATC	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.5583C>T	10.37:g.129249676C>T		Somatic	17	0	0		WXS	Illumina HiSeq	Phase_I	22	15	0.681818	NM_001380	A9Z1Z5	Silent	SNP	ENST00000280333.6	37																																																																																				C|0.571;T|0.429	0.429	strong		0.582	DOCK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050979.2	NM_001380	
ARHGAP5	394	hgsc.bcm.edu	37	14	32561340	32561340	+	Missense_Mutation	SNP	G	G	A	rs78337553		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:32561340G>A	ENST00000345122.3	+	2	1780	c.1465G>A	c.(1465-1467)Gag>Aag	p.E489K	ARHGAP5_ENST00000432921.1_Missense_Mutation_p.E489K|ARHGAP5_ENST00000539826.2_Missense_Mutation_p.E489K|ARHGAP5_ENST00000556611.1_Missense_Mutation_p.E489K|ARHGAP5_ENST00000433497.1_Intron|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						scavenged	.						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	101	0	0		WXS	Illumina HiSeq	Phase_I	102	15	0.147059	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	
PATE2	399967	hgsc.bcm.edu	37	11	125647286	125647286	+	Silent	SNP	C	C	T	rs76476146	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:125647286C>T	ENST00000358524.3	-	4	378	c.333G>A	c.(331-333)gaG>gaA	p.E111E	PATE2_ENST00000436890.2_Silent_p.E68E	NM_212555.2	NP_997720.1	Q6UY27	PATE2_HUMAN	prostate and testis expressed 2	111						extracellular space (GO:0005615)				endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|prostate(1)	6						ACTAAACTCCCTCAGGGAGGT	0.463													C|||	299	0.0597045	0.0991	0.0288	5008	,	,		21808	0.002		0.0636	False		,,,				2504	0.0838				p.E111E		Atlas-SNP	.											.	PATE2	14	.	0			c.G333A						PASS	.	C		405,3997	199.4+/-223.0	13,379,1809	125.0	102.0	110.0		333	-6.8	0.0	11	dbSNP_132	110	509,8089	143.4+/-199.5	13,483,3803	no	coding-synonymous	PATE2	NM_212555.2		26,862,5612	TT,TC,CC		5.92,9.2004,7.0308		111/114	125647286	914,12086	2201	4299	6500	SO:0001819	synonymous_variant	399967	exon4			AACTCCCTCAGGG	AY358105	CCDS8465.1	11q24.2	2008-12-17	2008-12-17	2008-12-17		ENSG00000196844		"""PATE family"""	32249	protein-coding gene	gene with protein product			"""chromosome 11 open reading frame 38"""	C11orf38			Standard	NM_212555		Approved	UNQ3112, LVLF3112, PATE-M	uc001qcu.3	Q6UY27		ENST00000358524.3:c.333G>A	11.37:g.125647286C>T		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	118	87	0.737288	NM_212555	B2RNZ2|B7ZMG4	Silent	SNP	ENST00000358524.3	37	CCDS8465.1																																																																																			C|0.936;T|0.064	0.064	strong		0.463	PATE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386729.1	NM_212555	
SERHL2	253190	hgsc.bcm.edu	37	22	42970004	42970004	+	Silent	SNP	G	G	C	rs147451679	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:42970004G>C	ENST00000327678.5	+	12	990	c.888G>C	c.(886-888)gtG>gtC	p.V296V	SERHL2_ENST00000407614.4_Silent_p.V116V|SERHL2_ENST00000340239.4_3'UTR|SERHL2_ENST00000335879.5_Silent_p.V232V|RRP7B_ENST00000357802.2_RNA	NM_014509.3	NP_055324.2	Q9NQF3	SERHL_HUMAN	serine hydrolase-like 2	169							hydrolase activity (GO:0016787)			breast(1)|endometrium(2)|lung(3)|skin(1)|stomach(1)	8						CCCAGCACGTGGCCAGTATCA	0.577																																					p.V296V		Atlas-SNP	.											SERHL2,NS,carcinoma,0,3	SERHL2	23	3	0			c.G888C						scavenged	.						132.0	116.0	121.0					22																	42970004		2203	4299	6502	SO:0001819	synonymous_variant	253190	exon12			GCACGTGGCCAGT		CCDS14037.1, CCDS63498.1	22q13	2005-08-09			ENSG00000183569	ENSG00000183569			29446	protein-coding gene	gene with protein product							Standard	NM_014509		Approved		uc003bcr.3	Q9H4I8	OTTHUMG00000150892	ENST00000327678.5:c.888G>C	22.37:g.42970004G>C		Somatic	477	0	0		WXS	Illumina HiSeq	Phase_I	502	78	0.155378	NM_014509	Q5JZ95|Q9UH21	Silent	SNP	ENST00000327678.5	37	CCDS14037.1																																																																																			G|0.998;C|0.002	0.002	strong		0.577	SERHL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320454.1	NM_014509	
ASAP3	55616	hgsc.bcm.edu	37	1	23767669	23767669	+	Silent	SNP	A	A	G	rs12117542	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:23767669A>G	ENST00000336689.3	-	10	914	c.870T>C	c.(868-870)taT>taC	p.Y290Y	ASAP3_ENST00000437606.2_Silent_p.Y281Y	NM_017707.3	NP_060177.2	Q8TDY4	ASAP3_HUMAN	ArfGAP with SH3 domain, ankyrin repeat and PH domain 3	290					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						GGTGGATGCTATAGCCACATC	0.517													G|||	109	0.0217652	0.0083	0.0403	5008	,	,		18845	0.0		0.0437	False		,,,				2504	0.0266				p.Y290Y		Atlas-SNP	.											.	ASAP3	65	.	0			c.T870C						PASS	.	G	,	83,4323	818.9+/-416.3	3,77,2123	166.0	155.0	159.0		843,870	4.6	1.0	1	dbSNP_120	159	418,8182	800.6+/-407.4	5,408,3887	no	coding-synonymous,coding-synonymous	ASAP3	NM_001143778.1,NM_017707.3	,	8,485,6010	GG,GA,AA		4.8605,1.8838,3.8521	,	281/895,290/904	23767669	501,12505	2203	4300	6503	SO:0001819	synonymous_variant	55616	exon10			GATGCTATAGCCA	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.870T>C	1.37:g.23767669A>G		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	100	48	0.48	NM_017707	B3KRW0|B4DHH4|Q6P9F4|Q86UY1|Q9NXK2	Silent	SNP	ENST00000336689.3	37	CCDS235.1																																																																																			A|0.967;G|0.033	0.033	strong		0.517	ASAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008916.2	NM_017707	
HLX	3142	hgsc.bcm.edu	37	1	221053545	221053545	+	Missense_Mutation	SNP	T	T	C	rs12141189	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:221053545T>C	ENST00000366903.6	+	1	1847	c.346T>C	c.(346-348)Tca>Cca	p.S116P	HLA-AS1_ENST00000552026.1_RNA|HLX_ENST00000549319.1_5'Flank	NM_021958.3	NP_068777.1	Q14774	HLX_HUMAN	H2.0-like homeobox	116	Pro-rich.		S -> P (in dbSNP:rs12141189). {ECO:0000269|PubMed:7806220}.		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)		GTCTCCGCTCTCAGCCGCCTA	0.706													T|||	1056	0.210863	0.171	0.2767	5008	,	,		10735	0.2252		0.2505	False		,,,				2504	0.1626				p.S116P		Atlas-SNP	.											HLX,NS,carcinoma,0,1	HLX	67	1	0			c.T346C						scavenged	.	T	PRO/SER	846,3544		97,652,1446	13.0	18.0	16.0		346	3.4	1.0	1	dbSNP_120	16	1904,6676		215,1474,2601	no	missense	HLX	NM_021958.3	74	312,2126,4047	CC,CT,TT		22.1911,19.2711,21.2028	probably-damaging	116/489	221053545	2750,10220	2195	4290	6485	SO:0001583	missense	3142	exon1			CCGCTCTCAGCCG	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.346T>C	1.37:g.221053545T>C	ENSP00000355870:p.Ser116Pro	Somatic	51	1	0.0196078		WXS	Illumina HiSeq	Phase_I	57	57	1	NM_021958	B2R8A8|Q15988|Q59HE7|Q9NZ75	Missense_Mutation	SNP	ENST00000366903.6	37	CCDS1527.1	511	0.23397435897435898	87	0.17682926829268292	104	0.287292817679558	124	0.21678321678321677	196	0.25857519788918204	T	20.7	4.040183	0.75732	0.192711	0.221911	ENSG00000136630	ENST00000366903	T	0.34472	1.36	4.57	3.44	0.39384	.	0.000000	0.39083	N	0.001465	T	0.00012	0.0000	N	0.11560	0.145	0.09310	P	1.0	B	0.20780	0.048	B	0.18871	0.023	T	0.40251	-0.9573	9	0.26408	T	0.33	-6.9827	7.6547	0.28369	0.0:0.1681:0.0:0.8319	rs12141189;rs12141189	116	Q14774	HLX_HUMAN	P	116	ENSP00000355870:S116P	ENSP00000355870:S116P	S	+	1	0	HLX	219120168	0.713000	0.27926	0.991000	0.47740	0.943000	0.58893	1.154000	0.31688	0.894000	0.36317	0.533000	0.62120	TCA	T|0.782;C|0.218	0.218	strong		0.706	HLX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090902.3	NM_021958	
MDGA1	266727	hgsc.bcm.edu	37	6	37623626	37623626	+	Silent	SNP	C	C	T	rs13204070	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:37623626C>T	ENST00000434837.3	-	4	1607	c.429G>A	c.(427-429)gtG>gtA	p.V143V	MDGA1_ENST00000505425.1_Silent_p.V143V|MDGA1_ENST00000297153.7_Silent_p.V143V	NM_153487.3	NP_705691.1	Q8NFP4	MDGA1_HUMAN	MAM domain containing glycosylphosphatidylinositol anchor 1	143	Ig-like 2.				brain development (GO:0007420)|cerebral cortex radially oriented cell migration (GO:0021799)|neuron migration (GO:0001764)|spinal cord association neuron differentiation (GO:0021527)	anchored component of plasma membrane (GO:0046658)|extracellular space (GO:0005615)				central_nervous_system(2)|endometrium(6)|kidney(3)|large_intestine(12)|lung(11)|prostate(1)|skin(2)|urinary_tract(1)	38						AGTTGCCTCGCACATCGCTCA	0.607													C|||	681	0.135982	0.0454	0.1499	5008	,	,		18497	0.1627		0.1988	False		,,,				2504	0.1564				p.V143V		Atlas-SNP	.											.	MDGA1	104	.	0			c.G429A						PASS	.	C		292,3960		12,268,1846	46.0	48.0	47.0		429	-7.2	0.3	6	dbSNP_121	47	1638,6808		162,1314,2747	no	coding-synonymous	MDGA1	NM_153487.3		174,1582,4593	TT,TC,CC		19.3938,6.8674,15.1992		143/956	37623626	1930,10768	2126	4223	6349	SO:0001819	synonymous_variant	266727	exon4			GCCTCGCACATCG	AF478693	CCDS47417.1	6p21	2013-01-29			ENSG00000112139	ENSG00000112139		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	19267	protein-coding gene	gene with protein product		609626				15922729, 15019943	Standard	NM_153487		Approved	GPIM, MAMDC3	uc003onu.1	Q8NFP4	OTTHUMG00000014626	ENST00000434837.3:c.429G>A	6.37:g.37623626C>T		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	102	57	0.558824	NM_153487	A6NHG0|Q8NBE3	Silent	SNP	ENST00000434837.3	37	CCDS47417.1																																																																																			C|0.847;T|0.153	0.153	strong		0.607	MDGA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040419.3		
ITPKC	80271	hgsc.bcm.edu	37	19	41243671	41243671	+	Silent	SNP	C	C	T	rs145921796	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:41243671C>T	ENST00000263370.2	+	6	1878	c.1845C>T	c.(1843-1845)caC>caT	p.H615H		NM_025194.2	NP_079470.1	Q96DU7	IP3KC_HUMAN	inositol-trisphosphate 3-kinase C	615					inositol phosphate metabolic process (GO:0043647)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|inositol-1,4,5-trisphosphate 3-kinase activity (GO:0008440)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(7)|ovary(1)|prostate(1)	14			LUSC - Lung squamous cell carcinoma(20;0.000219)|Lung(22;0.000959)			TCAAGACCCACGAGGTGCGAG	0.512													T|||	3	0.000599042	0.0	0.0	5008	,	,		18395	0.0		0.003	False		,,,				2504	0.0				p.H615H		Atlas-SNP	.											.	ITPKC	36	.	0			c.C1845T						PASS	.	T		1,4405	825.9+/-416.6	0,1,2202	152.0	140.0	144.0		1845	-10.9	0.1	19	dbSNP_134	144	2,8598	819.2+/-406.8	0,2,4298	no	coding-synonymous	ITPKC	NM_025194.2		0,3,6500	TT,TC,CC		0.0233,0.0227,0.0231		615/684	41243671	3,13003	2203	4300	6503	SO:0001819	synonymous_variant	80271	exon6			GACCCACGAGGTG	Y11999	CCDS12563.1	19q13.1	2011-04-28	2011-04-28		ENSG00000086544	ENSG00000086544	2.7.1.127		14897	protein-coding gene	gene with protein product		606476	"""inositol 1,4,5-trisphosphate 3-kinase C"""			11085927	Standard	NM_025194		Approved	IP3KC, IP3-3KC	uc002oot.3	Q96DU7		ENST00000263370.2:c.1845C>T	19.37:g.41243671C>T		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	103	49	0.475728	NM_025194	Q9UE25|Q9Y475	Silent	SNP	ENST00000263370.2	37	CCDS12563.1																																																																																			C|1.000;T|0.000	0.000	strong		0.512	ITPKC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463104.1	NM_025194	
PSG8	440533	hgsc.bcm.edu	37	19	43269705	43269705	+	Missense_Mutation	SNP	G	G	A	rs71337226|rs34129574|rs7245423	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	24	0	0		WXS	Illumina HiSeq	Phase_I	15	10	0.666667	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		
KIAA1524	57650	hgsc.bcm.edu	37	3	108303958	108303958	+	Silent	SNP	T	T	G	rs79888562	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:108303958T>G	ENST00000295746.8	-	2	280	c.204A>C	c.(202-204)atA>atC	p.I68I	KIAA1524_ENST00000487834.1_5'UTR|KIAA1524_ENST00000491772.1_5'UTR	NM_020890.2	NP_065941.2	Q8TCG1	CIP2A_HUMAN	KIAA1524	68					positive regulation of neural precursor cell proliferation (GO:2000179)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(21)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						GTGAAGCACTTATGTTGGGGT	0.338													T|||	72	0.014377	0.0023	0.0403	5008	,	,		19545	0.0		0.0328	False		,,,				2504	0.0082				p.I68I		Atlas-SNP	.											.	KIAA1524	82	.	0			c.A204C						PASS	.	T		33,4373	40.0+/-72.8	0,33,2170	160.0	153.0	155.0		204	4.3	1.0	3	dbSNP_132	155	343,8257	118.1+/-177.6	7,329,3964	no	coding-synonymous	KIAA1524	NM_020890.2		7,362,6134	GG,GT,TT		3.9884,0.749,2.891		68/906	108303958	376,12630	2203	4300	6503	SO:0001819	synonymous_variant	57650	exon2			AGCACTTATGTTG	AB040957	CCDS33812.1	3q13.13	2014-01-14			ENSG00000163507	ENSG00000163507			29302	protein-coding gene	gene with protein product	"""cancerous inhibitor of protein phosphatase 2A"""	610643				10819331, 24214971	Standard	NM_020890		Approved	CIP2A	uc003dxb.4	Q8TCG1	OTTHUMG00000159233	ENST00000295746.8:c.204A>C	3.37:g.108303958T>G		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	112	57	0.508929	NM_020890	A1L4J7|B9EGC3|Q6P4G6|Q8WVP8|Q96PI2|Q9H9C6|Q9P204	Silent	SNP	ENST00000295746.8	37	CCDS33812.1																																																																																			T|0.976;G|0.024	0.024	strong		0.338	KIAA1524-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353975.2	NM_020890	
DEPTOR	64798	hgsc.bcm.edu	37	8	120940652	120940652	+	Silent	SNP	C	C	T	rs16893299	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:120940652C>T	ENST00000286234.5	+	2	265	c.135C>T	c.(133-135)caC>caT	p.H45H	DEPTOR_ENST00000523492.1_Intron	NM_022783.2	NP_073620.2	Q8TB45	DPTOR_HUMAN	DEP domain containing MTOR-interacting protein	45	DEP 1. {ECO:0000255|PROSITE- ProRule:PRU00066}.				intracellular signal transduction (GO:0035556)|negative regulation of cell size (GO:0045792)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of TOR signaling (GO:0032007)|regulation of extrinsic apoptotic signaling pathway (GO:2001236)	intracellular (GO:0005622)				endometrium(1)|kidney(1)|large_intestine(5)|lung(5)|ovary(3)|skin(1)|upper_aerodigestive_tract(2)	18						TCAGGCTGCACGAAGAAAAGG	0.373													T|||	1246	0.248802	0.379	0.1873	5008	,	,		19141	0.0367		0.2416	False		,,,				2504	0.3425				p.H45H		Atlas-SNP	.											.	DEPTOR	41	.	0			c.C135T						PASS	.	T		1585,2821	666.2+/-401.7	285,1015,903	91.0	93.0	92.0		135	2.3	1.0	8	dbSNP_123	92	2268,6332	708.0+/-405.6	292,1684,2324	no	coding-synonymous	DEPTOR	NM_022783.2		577,2699,3227	TT,TC,CC		26.3721,35.9737,29.6248		45/410	120940652	3853,9153	2203	4300	6503	SO:0001819	synonymous_variant	64798	exon2			GCTGCACGAAGAA		CCDS6331.1, CCDS64960.1	8q24.12	2011-12-13	2010-12-08	2010-12-08	ENSG00000155792	ENSG00000155792			22953	protein-coding gene	gene with protein product		612974	"""DEP domain containing 6"""	DEPDC6		19446321	Standard	NM_022783		Approved	DEP.6, FLJ12428	uc003yow.4	Q8TB45	OTTHUMG00000165052	ENST00000286234.5:c.135C>T	8.37:g.120940652C>T		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	58	19	0.327586	NM_022783	B2RCL9|B4DN97|E7EV87|Q96EQ1|Q9H0R7|Q9H894|Q9HA07	Silent	SNP	ENST00000286234.5	37	CCDS6331.1																																																																																			C|0.743;T|0.257	0.257	strong		0.373	DEPTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381601.1	NM_022783	
SHC3	53358	hgsc.bcm.edu	37	9	91690082	91690082	+	Missense_Mutation	SNP	C	C	T	rs35046724	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:91690082C>T	ENST00000375835.4	-	4	977	c.671G>A	c.(670-672)aGc>aAc	p.S224N	SHC3_ENST00000375830.1_5'UTR	NM_016848.5	NP_058544.3	Q92529	SHC3_HUMAN	SHC (Src homology 2 domain containing) transforming protein 3	224	PID. {ECO:0000255|PROSITE- ProRule:PRU00148}.				central nervous system development (GO:0007417)|epidermal growth factor receptor signaling pathway (GO:0007173)|insulin receptor signaling pathway (GO:0008286)|learning or memory (GO:0007611)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Ras protein signal transduction (GO:0007265)|synaptic transmission, glutamatergic (GO:0035249)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytosol (GO:0005829)	signal transducer activity (GO:0004871)			breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(13)|skin(3)	28						CAGAGAGATGCTCATTCCCGC	0.512													C|||	33	0.00658946	0.0	0.0043	5008	,	,		18720	0.0		0.0179	False		,,,				2504	0.0123				p.S224N		Atlas-SNP	.											.	SHC3	66	.	0			c.G671A						PASS	.	C	ASN/SER	8,4398	14.3+/-33.2	0,8,2195	171.0	144.0	153.0		671	2.7	1.0	9	dbSNP_126	153	167,8433	78.6+/-141.3	0,167,4133	yes	missense	SHC3	NM_016848.5	46	0,175,6328	TT,TC,CC		1.9419,0.1816,1.3455	benign	224/595	91690082	175,12831	2203	4300	6503	SO:0001583	missense	53358	exon4			GAGATGCTCATTC	D84361	CCDS6681.1	9q22.1	2013-02-14	2005-05-24		ENSG00000148082	ENSG00000148082		"""SH2 domain containing"""	18181	protein-coding gene	gene with protein product		605263	"""src homology 2 domain containing transforming protein C3"""			8808684	Standard	NM_016848		Approved	N-Shc, NSHC, SHCC	uc004aqf.2	Q92529	OTTHUMG00000020179	ENST00000375835.4:c.671G>A	9.37:g.91690082C>T	ENSP00000364995:p.Ser224Asn	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	133	67	0.503759	NM_016848	Q5T7I7|Q8TAP2|Q9UCX5	Missense_Mutation	SNP	ENST00000375835.4	37	CCDS6681.1	16	0.007326007326007326	0	0.0	2	0.0055248618784530384	0	0.0	14	0.018469656992084433	C	8.160	0.789310	0.16258	0.001816	0.019419	ENSG00000148082	ENST00000375835	T	0.13901	2.55	4.58	2.69	0.31865	Phosphotyrosine interaction (PID/PI) (1);Phosphotyrosine interaction domain (3);Pleckstrin homology-type (1);	0.214361	0.46442	N	0.000287	T	0.03220	0.0094	N	0.04686	-0.185	0.80722	D	1	B	0.31655	0.334	B	0.42245	0.381	T	0.28396	-1.0045	10	0.06625	T	0.88	-12.9406	8.5843	0.33649	0.0:0.7446:0.0:0.2554	rs35046724;rs61761936	224	Q92529	SHC3_HUMAN	N	224	ENSP00000364995:S224N	ENSP00000364995:S224N	S	-	2	0	SHC3	90879902	0.995000	0.38212	1.000000	0.80357	0.722000	0.41435	0.288000	0.18939	1.151000	0.42436	0.563000	0.77884	AGC	C|0.987;T|0.013	0.013	strong		0.512	SHC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052986.1	NM_016848	
OR5L1	219437	hgsc.bcm.edu	37	11	55578987	55578987	+	Silent	SNP	T	T	C	rs386753698|rs67727364	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:55578987T>C	ENST00000333973.2	+	1	134	c.45T>C	c.(43-45)ctT>ctC	p.L15L		NM_001004738.1	NP_001004738.1	Q8NGL2	OR5L1_HUMAN	olfactory receptor, family 5, subfamily L, 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)	p.L15L(1)		NS(1)|breast(2)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(4)|liver(4)|lung(36)|ovary(2)|pancreas(1)|prostate(5)|skin(9)|stomach(4)|upper_aerodigestive_tract(3)	78		all_epithelial(135;0.208)				TCATTCTCCTTGGACTATCAG	0.433													N|||	525	0.104832	0.1884	0.0461	5008	,	,		18304	0.0813		0.0924	False		,,,				2504	0.0706				p.L15L		Atlas-SNP	.											OR5L1,NS,carcinoma,0,1	OR5L1	145	1	1	Substitution - coding silent(1)	stomach(1)	c.T45C						PASS	.	C		670,3730		63,544,1593	201.0	191.0	194.0		45	-2.8	0.0	11	dbSNP_130	194	724,7862		32,660,3601	no	coding-synonymous	OR5L1	NM_001004738.1		95,1204,5194	CC,CT,TT		8.4323,15.2273,10.7346		15/312	55578987	1394,11592	2200	4293	6493	SO:0001819	synonymous_variant	219437	exon1			TCTCCTTGGACTA	AB065780	CCDS31509.1	11q11	2012-08-09			ENSG00000186117	ENSG00000186117		"""GPCR / Class A : Olfactory receptors"""	8350	protein-coding gene	gene with protein product							Standard	NM_001004738		Approved	OST262	uc001nhw.1	Q8NGL2	OTTHUMG00000166810	ENST00000333973.2:c.45T>C	11.37:g.55578987T>C		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	61	42	0.688525	NM_001004738	B2RNK6|Q6IFD0	Silent	SNP	ENST00000333973.2	37	CCDS31509.1																																																																																			T|0.898;C|0.102	0.102	strong		0.433	OR5L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391514.1	NM_001004738	
OR13C2	392376	hgsc.bcm.edu	37	9	107367132	107367132	+	Silent	SNP	G	G	A	rs10820679	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	210	0	0		WXS	Illumina HiSeq	Phase_I	136	69	0.507353	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	
FYCO1	79443	hgsc.bcm.edu	37	3	46007825	46007825	+	Missense_Mutation	SNP	T	T	C	rs71622515|rs13059238	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:46007825T>C	ENST00000296137.2	-	8	3206	c.3001A>G	c.(3001-3003)Aac>Gac	p.N1001D	FYCO1_ENST00000535325.1_Missense_Mutation_p.N1001D	NM_024513.3	NP_078789.2	Q9BQS8	FYCO1_HUMAN	FYVE and coiled-coil domain containing 1	1001			N -> D (in dbSNP:rs13059238).		plus-end-directed vesicle transport along microtubule (GO:0072383)	autophagic vacuole (GO:0005776)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)	metal ion binding (GO:0046872)			NS(4)|breast(3)|central_nervous_system(1)|endometrium(11)|kidney(2)|large_intestine(9)|lung(17)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	54				BRCA - Breast invasive adenocarcinoma(193;0.00147)|KIRC - Kidney renal clear cell carcinoma(197;0.0272)|Kidney(197;0.0323)		TTGAGGGTGTTGAGCTCCTGG	0.617													C|||	548	0.109425	0.0189	0.0634	5008	,	,		19562	0.004		0.1233	False		,,,				2504	0.3589				p.N1001D		Atlas-SNP	.											.	FYCO1	115	.	0			c.A3001G						PASS	.	C	ASP/ASN	40,4366	819.4+/-416.4	1,38,2164	95.0	82.0	86.0		3001	2.3	0.2	3	dbSNP_121	86	35,8565	809.3+/-407.2	5,25,4270	no	missense	FYCO1	NM_024513.2	23	6,63,6434	CC,CT,TT		0.407,0.9079,0.5767	benign	1001/1479	46007825	75,12931	2203	4300	6503	SO:0001583	missense	79443	exon8			GGGTGTTGAGCTC	AJ292348	CCDS2734.1	3p21.3	2008-02-05			ENSG00000163820	ENSG00000163820		"""Zinc fingers, FYVE domain containing"""	14673	protein-coding gene	gene with protein product		607182				11896456	Standard	NM_024513		Approved	FLJ13335, ZFYVE7	uc003cpb.5	Q9BQS8	OTTHUMG00000133447	ENST00000296137.2:c.3001A>G	3.37:g.46007825T>C	ENSP00000296137:p.Asn1001Asp	Somatic	187	0	0		WXS	Illumina HiSeq	Phase_I	185	72	0.389189	NM_024513	B7ZKT7|Q3MJE6|Q86T41|Q86TB1|Q8TEF9|Q96IV5|Q9H8P9	Missense_Mutation	SNP	ENST00000296137.2	37	CCDS2734.1	136	0.06227106227106227	10	0.02032520325203252	21	0.058011049723756904	0	0.0	105	0.13852242744063326	C	0.383	-0.927848	0.02377	0.009079	0.00407	ENSG00000163820	ENST00000296137;ENST00000535325	T;T	0.79554	-1.28;-1.28	5.49	2.29	0.28610	.	0.437095	0.25572	N	0.029755	T	0.00468	0.0015	N	0.02916	-0.46	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.04781	-1.0927	9	0.06625	T	0.88	-17.5834	4.0771	0.09909	0.2588:0.4452:0.0:0.296	rs13059238;rs13059238	1001;1001	B7ZKT7;Q9BQS8	.;FYCO1_HUMAN	D	1001	ENSP00000296137:N1001D;ENSP00000441178:N1001D	ENSP00000296137:N1001D	N	-	1	0	FYCO1	45982829	0.017000	0.18338	0.216000	0.23742	0.995000	0.86356	0.889000	0.28282	0.260000	0.21731	-0.119000	0.15052	AAC	T|0.928;C|0.072	0.072	strong		0.617	FYCO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257320.2	NM_024513	
IGHMBP2	3508	hgsc.bcm.edu	37	11	68704264	68704264	+	Silent	SNP	C	C	T	rs546382	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:68704264C>T	ENST00000255078.3	+	13	2427	c.2316C>T	c.(2314-2316)tcC>tcT	p.S772S		NM_002180.2	NP_002171.2	P38935	SMBP2_HUMAN	immunoglobulin mu binding protein 2	772	R3H. {ECO:0000255|PROSITE- ProRule:PRU00382}.|SS DNA-binding. {ECO:0000250}.				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)			ACGACAGTTCCGGGGAAGGGA	0.647													C|||	1233	0.246206	0.0991	0.1571	5008	,	,		18079	0.2133		0.3042	False		,,,				2504	0.4826				p.S772S		Atlas-SNP	.											.	IGHMBP2	83	.	0			c.C2316T						PASS	.	C		561,3839	249.0+/-256.6	46,469,1685	56.0	52.0	53.0		2316	-3.7	0.1	11	dbSNP_83	53	2655,5933	425.3+/-354.9	408,1839,2047	no	coding-synonymous	IGHMBP2	NM_002180.2		454,2308,3732	TT,TC,CC		30.9152,12.75,24.7613		772/994	68704264	3216,9772	2200	4294	6494	SO:0001819	synonymous_variant	3508	exon13			CAGTTCCGGGGAA	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.2316C>T	11.37:g.68704264C>T		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	84	20	0.238095	NM_002180	A0PJD2|Q00443|Q14177	Silent	SNP	ENST00000255078.3	37	CCDS8187.1																																																																																			C|0.761;T|0.239	0.239	strong		0.647	IGHMBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396862.1	NM_002180	
TLE1	7088	hgsc.bcm.edu	37	9	84200529	84200529	+	Silent	SNP	T	T	C	rs2228172	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:84200529T>C	ENST00000376499.3	-	18	3083	c.2019A>G	c.(2017-2019)gcA>gcG	p.A673A		NM_005077.3	NP_005068.2	Q04724	TLE1_HUMAN	transducin-like enhancer of split 1 (E(sp1) homolog, Drosophila)	673					multicellular organismal development (GO:0007275)|negative regulation of anoikis (GO:2000811)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of Wnt signaling pathway (GO:0030178)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|positive regulation of gene expression (GO:0010628)|signal transduction (GO:0007165)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|identical protein binding (GO:0042802)|RNA polymerase II transcription corepressor activity (GO:0001106)|transcription factor binding (GO:0008134)			NS(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(11)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	29						CCATGCCCACTGCCAGCCACT	0.557													C|||	228	0.0455272	0.0098	0.0562	5008	,	,		16995	0.0317		0.0636	False		,,,				2504	0.0818				p.A673A	NSCLC(155;1437 1995 30668 39354 45875)|Melanoma(16;266 781 14000 47728 51870)	Atlas-SNP	.											.	TLE1	81	.	0			c.A2019G						PASS	.	C		67,4339	819.7+/-416.4	1,65,2137	76.0	56.0	63.0		2019	-7.4	0.6	9	dbSNP_98	63	635,7965	789.6+/-407.6	23,589,3688	no	coding-synonymous	TLE1	NM_005077.3		24,654,5825	CC,CT,TT		7.3837,1.5207,5.3975		673/771	84200529	702,12304	2203	4300	6503	SO:0001819	synonymous_variant	7088	exon18			GCCCACTGCCAGC		CCDS6661.1	9q21.32	2013-01-10	2001-11-28		ENSG00000196781	ENSG00000196781		"""WD repeat domain containing"""	11837	protein-coding gene	gene with protein product	"""enhancer of split groucho 1"""	600189	"""transducin-like enhancer of split 1, homolog of Drosophila E(sp1)"""			8365415, 8808280	Standard	NM_005077		Approved	ESG1, GRG1, ESG	uc004aly.3	Q04724	OTTHUMG00000021008	ENST00000376499.3:c.2019A>G	9.37:g.84200529T>C		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	72	37	0.513889	NM_005077	A8K495|Q5T3G4|Q969V9	Silent	SNP	ENST00000376499.3	37	CCDS6661.1																																																																																			T|0.948;C|0.052	0.052	strong		0.557	TLE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055407.1	NM_005077	
PCDHB4	56131	hgsc.bcm.edu	37	5	140502344	140502344	+	Missense_Mutation	SNP	C	C	T	rs3733697|rs377479392	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:140502344C>T	ENST00000194152.1	+	1	764	c.764C>T	c.(763-765)cCc>cTc	p.P255L	AC005754.8_ENST00000606030.1_lincRNA	NM_018938.2	NP_061761.1	Q9Y5E5	PCDB4_HUMAN	protocadherin beta 4	255	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.		P -> L (in dbSNP:rs3733697).|P -> S (in dbSNP:rs3733698).		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)			GAAAACAGCCCCCTAGACTCT	0.453													C|||	743	0.148363	0.1657	0.1974	5008	,	,		19662	0.119		0.159	False		,,,				2504	0.1094				p.P255L		Atlas-SNP	.											.	PCDHB4	177	.	0			c.C764T						PASS	.	C	LEU/PRO	853,3553		77,699,1427	100.0	108.0	105.0		764	4.4	0.9	5	dbSNP_107	105	1444,7156		140,1164,2996	yes	missense	PCDHB4	NM_018938.2	98	217,1863,4423	TT,TC,CC		16.7907,19.36,17.6611	benign	255/796	140502344	2297,10709	2203	4300	6503	SO:0001583	missense	56131	exon1			ACAGCCCCCTAGA	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.764C>T	5.37:g.140502344C>T	ENSP00000194152:p.Pro255Leu	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	107	50	0.46729	NM_018938	Q4V761	Missense_Mutation	SNP	ENST00000194152.1	37	CCDS4246.1	270	0.12362637362637363	67	0.13617886178861788	60	0.16574585635359115	49	0.08566433566433566	94	0.12401055408970976	C	12.38	1.920384	0.33908	0.1936	0.167907	ENSG00000081818	ENST00000194152	T	0.54071	0.59	4.41	4.41	0.53225	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.00178	0.0005	M	0.85041	2.73	0.09310	P	0.999999655108	B	0.26902	0.163	B	0.37451	0.25	T	0.34204	-0.9838	8	0.66056	D	0.02	.	17.5536	0.87884	0.0:1.0:0.0:0.0	rs3733697;rs17844410;rs60052876;rs3733697	255	Q9Y5E5	PCDB4_HUMAN	L	255	ENSP00000194152:P255L	ENSP00000194152:P255L	P	+	2	0	PCDHB4	140482528	0.571000	0.26659	0.868000	0.34077	0.324000	0.28378	4.604000	0.61112	2.449000	0.82847	0.650000	0.86243	CCC	.	.	alt		0.453	PCDHB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251812.2	NM_018938	
CHD5	26038	hgsc.bcm.edu	37	1	6196869	6196869	+	Silent	SNP	A	A	G	rs2250358	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:6196869A>G	ENST00000262450.3	-	16	2592	c.2493T>C	c.(2491-2493)atT>atC	p.I831I	CHD5_ENST00000378021.1_5'UTR	NM_015557.2	NP_056372.1	O00258	WRB_HUMAN	chromodomain helicase DNA binding protein 5	0					tail-anchored membrane protein insertion into ER membrane (GO:0071816)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)				breast(3)|central_nervous_system(3)|liver(1)|lung(1)|ovary(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)	16	Ovarian(185;0.0634)	all_cancers(23;5.36e-32)|all_epithelial(116;2.32e-17)|all_neural(13;3.68e-06)|all_lung(118;3.94e-06)|all_hematologic(16;2.39e-05)|Lung NSC(185;5.33e-05)|Acute lymphoblastic leukemia(12;0.000372)|Glioma(11;0.00127)|Renal(390;0.00188)|Colorectal(325;0.00342)|Breast(487;0.00373)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.15)		Epithelial(90;3.08e-37)|GBM - Glioblastoma multiforme(13;1.36e-31)|OV - Ovarian serous cystadenocarcinoma(86;7.7e-19)|Colorectal(212;9.97e-08)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(185;6.16e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.00109)|BRCA - Breast invasive adenocarcinoma(365;0.0012)|STAD - Stomach adenocarcinoma(132;0.00346)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.193)		TGGCCTGGTCAATGGTGATGA	0.587													G|||	2593	0.517772	0.3366	0.4697	5008	,	,		18356	0.7996		0.3946	False		,,,				2504	0.6329				p.I831I		Atlas-SNP	.											.	CHD5	267	.	0			c.T2493C						PASS	.	G		1509,2897	675.5+/-403.1	249,1011,943	72.0	71.0	72.0		2493	1.1	1.0	1	dbSNP_100	72	3563,5037	628.8+/-398.2	733,2097,1470	no	coding-synonymous	CHD5	NM_015557.2		982,3108,2413	GG,GA,AA		41.4302,34.2488,38.9974		831/1955	6196869	5072,7934	2203	4300	6503	SO:0001819	synonymous_variant	26038	exon16			CTGGTCAATGGTG	AF425231	CCDS57.1	1p36.3	2013-01-28			ENSG00000116254	ENSG00000116254		"""Zinc fingers, PHD-type"""	16816	protein-coding gene	gene with protein product		610771				11889561, 12592387	Standard	NM_015557		Approved		uc001amb.2	Q8TDI0	OTTHUMG00000000952	ENST00000262450.3:c.2493T>C	1.37:g.6196869A>G		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	70	20	0.285714	NM_015557	A8KAP8|A8MQ44|D3DSH9|O60740	Silent	SNP	ENST00000262450.3	37	CCDS57.1																																																																																			A|0.550;G|0.450	0.450	strong		0.587	CHD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002823.2	NM_015557	
LOXHD1	125336	hgsc.bcm.edu	37	18	44137400	44137400	+	Missense_Mutation	SNP	C	C	T	rs118174674	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:44137400C>T	ENST00000398722.4	-	14	2434	c.2435G>A	c.(2434-2436)cGg>cAg	p.R812Q	LOXHD1_ENST00000300591.6_5'UTR|LOXHD1_ENST00000579038.1_5'Flank|LOXHD1_ENST00000441551.2_Missense_Mutation_p.R884Q|LOXHD1_ENST00000536736.1_Missense_Mutation_p.R1090Q|LOXHD1_ENST00000582408.1_5'UTR|LOXHD1_ENST00000441893.2_Missense_Mutation_p.R23Q			Q8IVV2	LOXH1_HUMAN	lipoxygenase homology domains 1	812	PLAT 6. {ECO:0000255|PROSITE- ProRule:PRU00152}.				calcium ion transmembrane transport (GO:0070588)|detection of mechanical stimulus (GO:0050982)|sensory perception of sound (GO:0007605)	membrane (GO:0016020)|stereocilium (GO:0032420)	calcium channel activity (GO:0005262)			NS(3)|autonomic_ganglia(1)|breast(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|lung(2)|pancreas(1)|prostate(4)|skin(4)|stomach(1)	36						GTGGCGAATCCGAATCTTGGT	0.562													C|||	36	0.0071885	0.0008	0.0173	5008	,	,		19065	0.0		0.0229	False		,,,				2504	0.0				p.R1090Q		Atlas-SNP	.											LOXHD1_ENST00000398722,NS,carcinoma,-1,2	LOXHD1	367	2	0			c.G3269A						PASS	.	C	GLN/ARG,	0,1384		0,0,692	244.0	220.0	227.0		3269,	5.2	1.0	18	dbSNP_132	227	61,3121		0,61,1530	yes	missense,utr-5	LOXHD1	NM_144612.6,NM_001145472.2	43,	0,61,2222	TT,TC,CC		1.917,0.0,1.336	probably-damaging,	1090/2212,	44137400	61,4505	692	1591	2283	SO:0001583	missense	125336	exon21			CGAATCCGAATCT	AK057232	CCDS45861.1, CCDS45862.1, CCDS54184.1	18q21.1	2009-09-11			ENSG00000167210	ENSG00000167210			26521	protein-coding gene	gene with protein product		613072	"""deafness, autosomal recessive 77"""	DFNB77		19732867	Standard	NM_144612		Approved	FLJ32670, LH2D1	uc010xcw.1	Q8IVV2	OTTHUMG00000132644	ENST00000398722.4:c.2435G>A	18.37:g.44137400C>T	ENSP00000381707:p.Arg812Gln	Somatic	377	1	0.00265252		WXS	Illumina HiSeq	Phase_I	344	174	0.505814	NM_144612	B7WNN3|B7WNT1|B7WPI9|Q6ZRY7|Q86WW9|Q96DL7	Missense_Mutation	SNP	ENST00000398722.4	37		26	0.011904761904761904	0	0.0	8	0.022099447513812154	0	0.0	18	0.023746701846965697	C	17.58	3.424203	0.62733	0.0	0.01917	ENSG00000167210	ENST00000398722;ENST00000536736;ENST00000441893;ENST00000335730	T;T;T	0.66099	-0.19;-0.19;-0.19	5.21	5.21	0.72293	.	0.058685	0.64402	D	0.000005	T	0.61874	0.2382	L	0.58583	1.82	0.44754	D	0.997757	D;D;D	0.76494	0.999;0.998;0.995	D;D;P	0.76575	0.96;0.988;0.891	T	0.68205	-0.5470	10	0.34782	T	0.22	.	16.5328	0.84366	0.0:1.0:0.0:0.0	.	1090;23;812	F5GZB4;F8WA52;Q8IVV2-2	.;.;.	Q	812;1090;23;812	ENSP00000381707:R812Q;ENSP00000444586:R1090Q;ENSP00000409062:R23Q	ENSP00000338222:R812Q	R	-	2	0	LOXHD1	42391398	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	4.902000	0.63266	2.440000	0.82611	0.491000	0.48974	CGG	C|0.986;T|0.014	0.014	strong		0.562	LOXHD1-201	KNOWN	basic	protein_coding	protein_coding		NM_144612	
OR1S2	219958	hgsc.bcm.edu	37	11	57970980	57970980	+	Missense_Mutation	SNP	A	A	G	rs34249289|rs11229277	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:57970980A>G	ENST00000302592.6	-	1	673	c.674T>C	c.(673-675)gTa>gCa	p.V225A		NM_001004459.1	NP_001004459.1	Q8NGQ3	OR1S2_HUMAN	olfactory receptor, family 1, subfamily S, member 2	225			V -> A (in dbSNP:rs11229277).|V -> I (in dbSNP:rs11229278).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(11)|kidney(1)|large_intestine(4)|lung(23)|ovary(2)|skin(2)|stomach(2)|urinary_tract(1)	46		Breast(21;0.0589)				GAAGATGAGTACAAAGGGGAA	0.458													a|||	423	0.0844649	0.0257	0.1138	5008	,	,		23120	0.0536		0.1083	False		,,,				2504	0.1503				p.V225A		Atlas-SNP	.											.	OR1S2	119	.	0			c.T674C						PASS	.						164.0	137.0	146.0					11																	57970980		2201	4296	6497	SO:0001583	missense	219958	exon1			ATGAGTACAAAGG	BK004297	CCDS31545.1	11q12.1	2012-08-09			ENSG00000197887	ENSG00000197887		"""GPCR / Class A : Olfactory receptors"""	15141	protein-coding gene	gene with protein product							Standard	NM_001004459		Approved		uc010rkb.2	Q8NGQ3	OTTHUMG00000167541	ENST00000302592.6:c.674T>C	11.37:g.57970980A>G	ENSP00000305469:p.Val225Ala	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	104	24	0.230769	NM_001004459	Q6IFG5|Q96R85	Missense_Mutation	SNP	ENST00000302592.6	37	CCDS31545.1	109	0.04990842490842491	13	0.026422764227642278	27	0.07458563535911603	19	0.033216783216783216	50	0.06596306068601583	a	5.168	0.216627	0.09810	.	.	ENSG00000197887	ENST00000302592	T	0.38240	1.15	4.75	-0.698	0.11280	GPCR, rhodopsin-like superfamily (1);	0.471664	0.17897	N	0.158338	T	0.01029	0.0034	N	0.17674	0.51	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.30238	-0.9985	9	0.02654	T	1	.	5.3927	0.16253	0.337:0.3756:0.2875:0.0	rs11229277;rs52800241;rs11229277	225	Q8NGQ3	OR1S2_HUMAN	A	225	ENSP00000305469:V225A	ENSP00000305469:V225A	V	-	2	0	OR1S2	57727556	0.000000	0.05858	0.260000	0.24451	0.836000	0.47400	0.422000	0.21296	0.053000	0.16036	-0.866000	0.03004	GTA	AC|0.500;GT|0.500	.	alt		0.458	OR1S2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394703.2	NM_001004459	
PKHD1L1	93035	hgsc.bcm.edu	37	8	110416813	110416813	+	Silent	SNP	C	C	T	rs1457286	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:110416813C>T	ENST00000378402.5	+	15	1508	c.1404C>T	c.(1402-1404)taC>taT	p.Y468Y		NM_177531.4	NP_803875.2	Q86WI1	PKHL1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1	468					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)			TGCAGGAGTACAGATTAAGTG	0.313										HNSCC(38;0.096)			T|||	2996	0.598243	0.6929	0.6556	5008	,	,		16328	0.3968		0.5239	False		,,,				2504	0.7137				p.Y468Y		Atlas-SNP	.											.	PKHD1L1	522	.	0			c.C1404T						PASS	.	T		2556,1170		888,780,195	99.0	92.0	94.0		1404	-7.1	0.0	8	dbSNP_88	94	4451,3757		1220,2011,873	no	coding-synonymous	PKHD1L1	NM_177531.4		2108,2791,1068	TT,TC,CC		45.7724,31.401,41.2854		468/4244	110416813	7007,4927	1863	4104	5967	SO:0001819	synonymous_variant	93035	exon15			GGAGTACAGATTA	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.1404C>T	8.37:g.110416813C>T		Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	156	95	0.608974	NM_177531	Q567P2|Q9UF27	Silent	SNP	ENST00000378402.5	37	CCDS47911.1																																																																																			C|0.434;T|0.566	0.566	strong		0.313	PKHD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381017.1	NM_177531	
SNED1	25992	hgsc.bcm.edu	37	2	241991875	241991875	+	Silent	SNP	G	G	A	rs57214830	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:241991875G>A	ENST00000310397.8	+	15	2073	c.2073G>A	c.(2071-2073)cgG>cgA	p.R691R	SNED1_ENST00000342631.6_Silent_p.R691R|SNED1_ENST00000401884.1_Silent_p.R691R|AC005237.4_ENST00000458377.1_RNA|SNED1_ENST00000469006.1_3'UTR|SNED1_ENST00000405547.3_Silent_p.R691R	NM_001080437.1	NP_001073906.1	Q8TER0	SNED1_HUMAN	sushi, nidogen and EGF-like domains 1	691	EGF-like 10. {ECO:0000255|PROSITE- ProRule:PRU00076}.				cell-matrix adhesion (GO:0007160)	extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|central_nervous_system(3)|kidney(2)|large_intestine(6)|lung(4)|ovary(3)|prostate(3)|upper_aerodigestive_tract(1)	24		all_cancers(19;7.48e-31)|all_epithelial(40;1.35e-12)|Breast(86;0.000148)|Renal(207;0.00528)|Ovarian(221;0.104)|Esophageal squamous(248;0.131)|all_lung(227;0.17)|all_hematologic(139;0.182)|Melanoma(123;0.238)		Epithelial(32;6.46e-32)|all cancers(36;6.23e-29)|OV - Ovarian serous cystadenocarcinoma(60;2.1e-14)|Kidney(56;6.35e-09)|KIRC - Kidney renal clear cell carcinoma(57;5.98e-08)|BRCA - Breast invasive adenocarcinoma(100;3.66e-06)|Lung(119;0.00072)|LUSC - Lung squamous cell carcinoma(224;0.00553)|Colorectal(34;0.0162)|COAD - Colon adenocarcinoma(134;0.109)		TGGGACGCCGGTGCCAGGCAG	0.637													G|||	1286	0.256789	0.2126	0.245	5008	,	,		17592	0.4067		0.1928	False		,,,				2504	0.2362				p.R691R		Atlas-SNP	.											.	SNED1	76	.	0			c.G2073A						PASS	.	G		800,3316		93,614,1351	43.0	49.0	47.0		2073	2.2	1.0	2	dbSNP_129	47	1433,6939		134,1165,2887	yes	coding-synonymous	SNED1	NM_001080437.1		227,1779,4238	AA,AG,GG		17.1166,19.4363,17.8812		691/1414	241991875	2233,10255	2058	4186	6244	SO:0001819	synonymous_variant	25992	exon15			ACGCCGGTGCCAG	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.2073G>A	2.37:g.241991875G>A		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	65	36	0.553846	NM_001080437	B5MDC3|B7WNK6|B7WPM0|Q336F4|Q336F5|Q8N369|Q8TEP7	Silent	SNP	ENST00000310397.8	37	CCDS46562.1																																																																																			G|0.756;A|0.244	0.244	strong		0.637	SNED1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323935.2	XM_059482	
USP53	54532	hgsc.bcm.edu	37	4	120214030	120214030	+	Missense_Mutation	SNP	T	T	G	rs3749591	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:120214030T>G	ENST00000274030.6	+	19	4065	c.2886T>G	c.(2884-2886)agT>agG	p.S962R	USP53_ENST00000450251.1_Missense_Mutation_p.S962R	NM_019050.2	NP_061923.2			ubiquitin specific peptidase 53									p.S961R(1)		breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(5)|ovary(1)|pancreas(1)|skin(2)|stomach(1)	27						CGAAGCACAGTTTAAGTACAG	0.388													T|||	1226	0.244808	0.1195	0.2824	5008	,	,		21325	0.3859		0.3032	False		,,,				2504	0.182				p.S962R		Atlas-SNP	.											USP53,NS,carcinoma,0,1	USP53	69	1	1	Substitution - Missense(1)	stomach(1)	c.T2886G						scavenged	.	T	ARG/SER	527,3265		37,453,1406	81.0	73.0	76.0		2886	-1.7	0.0	4	dbSNP_107	76	2598,5662		400,1798,1932	yes	missense	USP53	NM_019050.2	110	437,2251,3338	GG,GT,TT		31.4528,13.8977,25.9293	benign	962/1074	120214030	3125,8927	1896	4130	6026	SO:0001583	missense	54532	exon18			GCACAGTTTAAGT	BC017382	CCDS43265.1	4q26	2010-05-12	2005-08-08		ENSG00000145390	ENSG00000145390		"""Ubiquitin-specific peptidases"""	29255	protein-coding gene	gene with protein product			"""ubiquitin specific protease 53"""			10718198, 14715245	Standard	NM_019050		Approved	KIAA1350	uc003ics.4	Q70EK8	OTTHUMG00000161331	ENST00000274030.6:c.2886T>G	4.37:g.120214030T>G	ENSP00000274030:p.Ser962Arg	Somatic	74	1	0.0135135		WXS	Illumina HiSeq	Phase_I	83	82	0.987952	NM_019050		Missense_Mutation	SNP	ENST00000274030.6	37	CCDS43265.1	601	0.2751831501831502	52	0.10569105691056911	87	0.24033149171270718	231	0.40384615384615385	231	0.30474934036939316	T	12.58	1.979529	0.34942	0.138977	0.314528	ENSG00000145390	ENST00000274030;ENST00000450251	T;T	0.47869	0.83;0.83	5.02	-1.66	0.08265	.	0.901431	0.09698	N	0.767375	T	0.00012	0.0000	L	0.59436	1.845	0.80722	P	0.0	P	0.35433	0.501	B	0.27500	0.08	T	0.34850	-0.9812	9	0.54805	T	0.06	-6.1731	6.3273	0.21251	0.1345:0.43:0.0:0.4356	rs3749591;rs17595370;rs52832840;rs59311247;rs3749591	962	Q70EK8	UBP53_HUMAN	R	962	ENSP00000274030:S962R;ENSP00000409906:S962R	ENSP00000274030:S962R	S	+	3	2	USP53	120433478	0.000000	0.05858	0.000000	0.03702	0.977000	0.68977	-0.174000	0.09839	-0.151000	0.11176	-0.361000	0.07541	AGT	T|0.725;G|0.275	0.275	strong		0.388	USP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364564.2	XM_052597	
RP1L1	94137	hgsc.bcm.edu	37	8	10467604	10467604	+	Missense_Mutation	SNP	C	C	A	rs74366179		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:10467604C>A	ENST00000382483.3	-	4	4227	c.4004G>T	c.(4003-4005)gGg>gTg	p.G1335V		NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	1351	8 X 16 AA approximate tandem repeats of T-E-E-G-L-Q-E-E-G-V-Q-L-E-E-T-K.		G -> R (in allele RP1L1-2 and allele RP1L1-3; dbSNP:rs61503212).|Missing (in allele RP1L1-1).		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)		taactgcaccccctcttcttg	0.463																																					p.G1335V		Atlas-SNP	.											RP1L1,NS,carcinoma,0,1	RP1L1	453	1	0			c.G4004T						PASS	.	C	VAL/GLY	516,3388		31,454,1467	118.0	115.0	116.0		4004	-0.4	0.0	8	dbSNP_131	116	1257,7009		110,1037,2986	yes	missense	RP1L1	NM_178857.5	109	141,1491,4453	AA,AC,CC		15.2069,13.2172,14.5686	probably-damaging	1335/2401	10467604	1773,10397	1952	4133	6085	SO:0001583	missense	94137	exon4			TGCACCCCCTCTT	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.4004G>T	8.37:g.10467604C>A	ENSP00000371923:p.Gly1335Val	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	118	24	0.20339	NM_178857	Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	Missense_Mutation	SNP	ENST00000382483.3	37	CCDS43708.1	383	0.17536630036630035	73	0.1483739837398374	68	0.1878453038674033	127	0.22202797202797203	115	0.1517150395778364	c	10.70	1.422679	0.25639	0.132172	0.152069	ENSG00000183638	ENST00000382483	T	0.05855	3.38	2.91	-0.449	0.12226	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.58432	P	5.999999999950489E-6	D	0.65815	0.995	P	0.53185	0.72	T	0.51060	-0.8753	8	0.72032	D	0.01	.	6.5765	0.22569	0.0:0.4875:0.0:0.5125	.	1335	A6NKC6	.	V	1335	ENSP00000371923:G1335V	ENSP00000371923:G1335V	G	-	2	0	RP1L1	10505014	0.000000	0.05858	0.004000	0.12327	0.297000	0.27493	-0.865000	0.04250	0.008000	0.14787	0.462000	0.41574	GGG	C|0.824;A|0.176	0.176	strong		0.463	RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375673.1		
WDR93	56964	hgsc.bcm.edu	37	15	90246336	90246336	+	Silent	SNP	A	A	G	rs16974175	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:90246336A>G	ENST00000268130.7	+	3	560	c.459A>G	c.(457-459)ttA>ttG	p.L153L	WDR93_ENST00000560294.1_Silent_p.L153L|RP11-300G22.2_ENST00000557964.1_RNA|WDR93_ENST00000558000.1_Silent_p.L153L	NM_020212.1	NP_064597.1	Q6P2C0	WDR93_HUMAN	WD repeat domain 93	153					electron transport chain (GO:0022900)		oxidoreductase activity, acting on NAD(P)H (GO:0016651)			NS(1)|breast(3)|endometrium(2)|kidney(4)|large_intestine(5)|liver(2)|lung(8)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	33	Lung NSC(78;0.0237)|all_lung(78;0.0478)		KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|BRCA - Breast invasive adenocarcinoma(143;0.128)			CCACAGATTTAGGGAATGAAA	0.388													G|||	1964	0.392173	0.5061	0.3631	5008	,	,		20249	0.2063		0.4016	False		,,,				2504	0.4407				p.L153L		Atlas-SNP	.											.	WDR93	63	.	0			c.A459G						PASS	.	G		2142,2258	594.6+/-388.3	529,1084,587	187.0	183.0	185.0		459	0.2	1.0	15	dbSNP_123	185	3848,4750	609.9+/-395.6	846,2156,1297	no	coding-synonymous	WDR93	NM_020212.1		1375,3240,1884	GG,GA,AA		44.7546,48.6818,46.084		153/687	90246336	5990,7008	2200	4299	6499	SO:0001819	synonymous_variant	56964	exon3			AGATTTAGGGAAT		CCDS32326.1, CCDS66862.1, CCDS73779.1	15q26.1	2012-11-02						"""WD repeat domain containing"""	26924	protein-coding gene	gene with protein product							Standard	NM_020212		Approved		uc002boj.3	Q6P2C0		ENST00000268130.7:c.459A>G	15.37:g.90246336A>G		Somatic	195	0	0		WXS	Illumina HiSeq	Phase_I	252	93	0.369048	NM_020212	Q8N7Y8|Q9NP89	Silent	SNP	ENST00000268130.7	37	CCDS32326.1																																																																																			A|0.575;G|0.425	0.425	strong		0.388	WDR93-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000416369.1	NM_020212	
KAZN	23254	hgsc.bcm.edu	37	1	15382667	15382667	+	Silent	SNP	T	T	C	rs2076570	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:15382667T>C	ENST00000376030.2	+	5	1101	c.807T>C	c.(805-807)aaT>aaC	p.N269N	KAZN_ENST00000400798.2_Silent_p.N175N|KAZN_ENST00000422387.2_Silent_p.N269N|KAZN_ENST00000503743.1_Silent_p.N269N|KAZN_ENST00000400797.3_Silent_p.N175N|KAZN_ENST00000361144.5_Silent_p.N263N	NM_201628.2	NP_963922.2	Q674X7	KAZRN_HUMAN	kazrin, periplakin interacting protein	269	Interaction with PPL.				keratinization (GO:0031424)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|desmosome (GO:0030057)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(9)|liver(1)|lung(6)|ovary(1)|prostate(2)	25						CGGTGCTCAATGGCAACCAGG	0.632													C|||	190	0.0379393	0.0318	0.0043	5008	,	,		19818	0.0675		0.007	False		,,,				2504	0.0716				p.N269N		Atlas-SNP	.											.	KAZN	57	.	0			c.T807C						PASS	.	C	,,,,	110,4296	816.4+/-416.2	1,108,2094	72.0	67.0	69.0		525,789,525,807,807	-1.8	1.0	1	dbSNP_96	69	39,8561	817.5+/-406.9	0,39,4261	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	KAZN	NM_001017999.2,NM_001018000.3,NM_001018001.2,NM_015209.2,NM_201628.2	,,,,	1,147,6355	CC,CT,TT		0.4535,2.4966,1.1456	,,,,	175/328,263/416,175/328,269/422,269/776	15382667	149,12857	2203	4300	6503	SO:0001819	synonymous_variant	23254	exon5			GCTCAATGGCAAC	AY505119	CCDS30604.1, CCDS41267.1, CCDS152.2, CCDS41268.1	1p36.21	2014-02-12	2011-01-31		ENSG00000189337	ENSG00000189337		"""Sterile alpha motif (SAM) domain containing"""	29173	protein-coding gene	gene with protein product						15337775, 18840647	Standard	NM_015209		Approved	KIAA1026, KAZRIN, FLJ43806	uc001avm.4	Q674X7	OTTHUMG00000002042	ENST00000376030.2:c.807T>C	1.37:g.15382667T>C		Somatic	252	0	0		WXS	Illumina HiSeq	Phase_I	199	101	0.507538	NM_015209	B0QYQ0|B1AK78|Q5TGF1|Q674X4|Q674X6|Q6ZUD1|Q8IYN7|Q8N409|Q9UIL2|Q9UPX4	Silent	SNP	ENST00000376030.2	37	CCDS152.2																																																																																			T|0.984;C|0.016	0.016	strong		0.632	KAZN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005690.2	NM_001017999	
EPS8L2	64787	hgsc.bcm.edu	37	11	721570	721570	+	Silent	SNP	C	C	T	rs7635	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:721570C>T	ENST00000533256.1	+	11	1149	c.774C>T	c.(772-774)atC>atT	p.I258I	EPS8L2_ENST00000530636.1_Silent_p.I258I|EPS8L2_ENST00000526198.1_Silent_p.I274I|EPS8L2_ENST00000318562.8_Silent_p.I258I|AP006621.9_ENST00000527021.2_RNA			Q9H6S3	ES8L2_HUMAN	EPS8-like 2	258					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)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|ruffle membrane (GO:0032587)|vesicle (GO:0031982)	actin binding (GO:0003779)			NS(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(2)|pancreas(1)|prostate(2)|soft_tissue(1)|urinary_tract(1)	13		all_cancers(49;1.24e-08)|all_epithelial(84;1.87e-05)|Breast(177;0.000286)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.106)|all_lung(207;0.136)		all cancers(45;4.37e-27)|Epithelial(43;2.81e-26)|OV - Ovarian serous cystadenocarcinoma(40;1.33e-20)|BRCA - Breast invasive adenocarcinoma(625;4.29e-05)|Lung(200;0.0582)|LUSC - Lung squamous cell carcinoma(625;0.0703)		CCCAGCAAATCCTCAACTGCG	0.637													c|||	1401	0.279752	0.1884	0.5648	5008	,	,		14025	0.1746		0.4155	False		,,,				2504	0.1697				p.I258I		Atlas-SNP	.											EPS8L2,colon,carcinoma,0,1	EPS8L2	42	1	0			c.C774T						PASS	.			970,3408		127,716,1346	22.0	27.0	26.0		774	3.8	1.0	11	dbSNP_52	26	3854,4700		888,2078,1311	no	coding-synonymous	EPS8L2	NM_022772.3		1015,2794,2657	TT,TC,CC		45.0549,22.1562,37.3028		258/716	721570	4824,8108	2189	4277	6466	SO:0001819	synonymous_variant	64787	exon10			GCAAATCCTCAAC	AF318331	CCDS31328.1	11p15.5	2008-02-05				ENSG00000177106			21296	protein-coding gene	gene with protein product		614988				12620401	Standard	NM_022772		Approved	FLJ21935, FLJ22171, MGC3088	uc001lqt.3	Q9H6S3		ENST00000533256.1:c.774C>T	11.37:g.721570C>T		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	109	22	0.201835	NM_022772	B3KSX1|B7ZKL3|Q53GM8|Q8WYW7|Q96K06|Q9H6K9	Silent	SNP	ENST00000533256.1	37	CCDS31328.1																																																																																			C|0.687;T|0.313	0.313	strong		0.637	EPS8L2-003	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382344.1	NM_022772	
HRH3	11255	hgsc.bcm.edu	37	20	60791422	60791422	+	Silent	SNP	C	C	T	rs3787430	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:60791422C>T	ENST00000340177.5	-	3	1262	c.978G>A	c.(976-978)ccG>ccA	p.P326P	HRH3_ENST00000317393.6_Silent_p.P326P	NM_007232.2	NP_009163.2	Q9Y5N1	HRH3_HUMAN	histamine receptor H3	326					brain development (GO:0007420)|drinking behavior (GO:0042756)|eating behavior (GO:0042755)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|learning (GO:0007612)|memory (GO:0007613)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of blood pressure (GO:0045776)|negative regulation of gamma-aminobutyric acid secretion (GO:0014053)|negative regulation of glutamate secretion (GO:0014050)|negative regulation of serotonin secretion (GO:0014063)|neurotransmitter secretion (GO:0007269)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of epithelial cell proliferation (GO:0050679)|regulation of norepinephrine secretion (GO:0014061)|response to organic cyclic compound (GO:0014070)	integral component of plasma membrane (GO:0005887)|myelin sheath (GO:0043209)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	drug binding (GO:0008144)|histamine receptor activity (GO:0004969)			breast(1)|endometrium(1)|lung(4)|skin(2)|upper_aerodigestive_tract(1)	9	Breast(26;7.76e-09)		BRCA - Breast invasive adenocarcinoma(19;7.08e-07)		Betahistine(DB06698)|Histamine Phosphate(DB00667)|Mirtazapine(DB00370)	AGGACGCCGACGGCTTGGAGC	0.677													C|||	891	0.177915	0.1846	0.1513	5008	,	,		14281	0.1815		0.1441	False		,,,				2504	0.2188				p.P326P		Atlas-SNP	.											.	HRH3	25	.	0			c.G978A						PASS	.	C		787,3601		82,623,1489	11.0	11.0	11.0		978	-9.1	0.2	20	dbSNP_107	11	1221,7339		105,1011,3164	no	coding-synonymous	HRH3	NM_007232.2		187,1634,4653	TT,TC,CC		14.264,17.9353,15.5082		326/446	60791422	2008,10940	2194	4280	6474	SO:0001819	synonymous_variant	11255	exon3			CGCCGACGGCTTG	AF140538	CCDS13493.1	20q13.33	2013-09-19			ENSG00000101180	ENSG00000101180		"""GPCR / Class A : Histamine receptors"""	5184	protein-coding gene	gene with protein product		604525				10347254	Standard	NM_007232		Approved	GPCR97	uc002ycf.2	Q9Y5N1	OTTHUMG00000032899	ENST00000340177.5:c.978G>A	20.37:g.60791422C>T		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	83	43	0.518072	NM_007232	Q4QRI7|Q9GZX2|Q9H4K8	Silent	SNP	ENST00000340177.5	37	CCDS13493.1																																																																																			C|0.833;T|0.167	0.167	strong		0.677	HRH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079994.1	NM_007232	
ALMS1	7840	hgsc.bcm.edu	37	2	73746923	73746923	+	Silent	SNP	C	C	T	rs11884776	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:73746923C>T	ENST00000264448.6	+	11	9669	c.9558C>T	c.(9556-9558)acC>acT	p.T3186T	ALMS1_ENST00000409009.1_Silent_p.T3144T	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	3186					endosomal transport (GO:0016197)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of stress fiber assembly (GO:0051492)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)				breast(4)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(31)|lung(68)|ovary(4)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	147						AGATGAAGACCCCACTTTCTG	0.363													T|||	1286	0.256789	0.5741	0.2349	5008	,	,		17135	0.005		0.2137	False		,,,				2504	0.1472				p.T3186T		Atlas-SNP	.											.	ALMS1	384	.	0			c.C9558T						PASS	.			1737,1889		416,905,492	79.0	77.0	77.0		9558	-2.7	0.0	2	dbSNP_120	77	1840,6310		197,1446,2432	no	coding-synonymous	ALMS1	NM_015120.4		613,2351,2924	TT,TC,CC		22.5767,47.904,30.3753		3186/4168	73746923	3577,8199	1813	4075	5888	SO:0001819	synonymous_variant	7840	exon11			GAAGACCCCACTT	AB002326	CCDS42697.1	2p13.1	2014-09-17			ENSG00000116127	ENSG00000116127			428	protein-coding gene	gene with protein product		606844				9063741	Standard	NM_015120		Approved	KIAA0328	uc002sje.1	Q8TCU4	OTTHUMG00000152812	ENST00000264448.6:c.9558C>T	2.37:g.73746923C>T		Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	124	124	1	NM_015120	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Silent	SNP	ENST00000264448.6	37	CCDS42697.1																																																																																			C|0.742;T|0.258	0.258	strong		0.363	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120	
OR10H4	126541	hgsc.bcm.edu	37	19	16060021	16060021	+	Silent	SNP	C	C	T	rs16980821	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:16060021C>T	ENST00000322107.1	+	1	204	c.204C>T	c.(202-204)tcC>tcT	p.S68S		NM_001004465.1	NP_001004465.1	Q8NGA5	O10H4_HUMAN	olfactory receptor, family 10, subfamily H, member 4	68						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)|large_intestine(3)|lung(8)|ovary(1)|pancreas(1)|urinary_tract(1)	17						GCACCCTCTCCGTCTCTGAGA	0.512													.|||	1210	0.241613	0.4629	0.1772	5008	,	,		22980	0.0526		0.2644	False		,,,				2504	0.1595				p.S68S		Atlas-SNP	.											.	OR10H4	48	.	0			c.C204T						PASS	.	C		1849,2557	537.5+/-374.7	384,1081,738	425.0	392.0	403.0		204	0.1	0.6	19	dbSNP_123	403	2050,6550	357.3+/-330.7	236,1578,2486	no	coding-synonymous	OR10H4	NM_001004465.1		620,2659,3224	TT,TC,CC		23.8372,41.9655,29.9785		68/317	16060021	3899,9107	2203	4300	6503	SO:0001819	synonymous_variant	126541	exon1			CCTCTCCGTCTCT	AC011517	CCDS32941.1	19p13.12	2013-09-24			ENSG00000176231	ENSG00000176231		"""GPCR / Class A : Olfactory receptors"""	15388	protein-coding gene	gene with protein product							Standard	NM_001004465		Approved		uc010xov.2	Q8NGA5	OTTHUMG00000182268	ENST00000322107.1:c.204C>T	19.37:g.16060021C>T		Somatic	226	0	0		WXS	Illumina HiSeq	Phase_I	223	108	0.484305	NM_001004465	Q6IFJ2|Q96R57	Silent	SNP	ENST00000322107.1	37	CCDS32941.1																																																																																			C|0.723;T|0.277	0.277	strong		0.512	OR10H4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460311.1		
TMEM173	340061	hgsc.bcm.edu	37	5	138861078	138861078	+	Missense_Mutation	SNP	C	C	T	rs11554776	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:138861078C>T	ENST00000330794.4	-	3	545	c.212G>A	c.(211-213)cGc>cAc	p.R71H	TMEM173_ENST00000511850.1_5'UTR	NM_198282.2	NP_938023.1	Q86WV6	STING_HUMAN	transmembrane protein 173	71			R -> H (in dbSNP:rs11554776).		activation of innate immune response (GO:0002218)|apoptotic process (GO:0006915)|cellular response to exogenous dsRNA (GO:0071360)|cellular response to interferon-beta (GO:0035458)|defense response to virus (GO:0051607)|innate immune response (GO:0045087)|interferon-beta production (GO:0032608)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of protein binding (GO:0032092)|positive regulation of protein import into nucleus, translocation (GO:0033160)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|regulation of type I interferon production (GO:0032479)	cytoplasmic vesicle membrane (GO:0030659)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)|perinuclear region of cytoplasm (GO:0048471)|peroxisome (GO:0005777)|plasma membrane (GO:0005886)	cyclic-di-GMP binding (GO:0035438)|cyclic-GMP-AMP binding (GO:0061507)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|transcription factor binding (GO:0008134)			endometrium(1)|kidney(1)|lung(6)|upper_aerodigestive_tract(1)	9			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			GTGGATGTGGCGCAGCTCCTC	0.617													C|||	1017	0.203075	0.0121	0.2781	5008	,	,		18966	0.4008		0.1471	False		,,,				2504	0.2618				p.R71H		Atlas-SNP	.											TMEM173,NS,carcinoma,0,1	TMEM173	19	1	0			c.G212A						PASS	.	C	HIS/ARG	163,4243	103.8+/-142.4	5,153,2045	53.0	53.0	53.0		212	1.8	0.0	5	dbSNP_120	53	1200,7400	236.4+/-268.6	89,1022,3189	yes	missense	TMEM173	NM_198282.2	29	94,1175,5234	TT,TC,CC		13.9535,3.6995,10.4798	possibly-damaging	71/380	138861078	1363,11643	2203	4300	6503	SO:0001583	missense	340061	exon3			ATGTGGCGCAGCT		CCDS4215.1	5q31.2	2009-11-06			ENSG00000184584	ENSG00000184584			27962	protein-coding gene	gene with protein product		612374				12477932	Standard	XM_005268445		Approved	FLJ38577, NET23	uc003lep.3	Q86WV6	OTTHUMG00000129239	ENST00000330794.4:c.212G>A	5.37:g.138861078C>T	ENSP00000331288:p.Arg71His	Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	116	52	0.448276	NM_198282	A8K3P6|B6EB35|D6RBX0|D6RE01|D6RID9	Missense_Mutation	SNP	ENST00000330794.4	37	CCDS4215.1	438	0.20054945054945056	11	0.022357723577235773	82	0.2265193370165746	232	0.40559440559440557	113	0.14907651715039577	C	4.677	0.125829	0.08931	0.036995	0.139535	ENSG00000184584	ENST00000330794;ENST00000510817	T;T	0.41758	0.99;0.99	5.58	1.84	0.25277	.	0.590726	0.19132	N	0.121905	T	0.00012	0.0000	L	0.29908	0.895	0.80722	P	0.0	B	0.13594	0.008	B	0.06405	0.002	T	0.43278	-0.9401	9	0.40728	T	0.16	-1.9834	3.65	0.08199	0.2713:0.4307:0.0:0.2979	rs11554776;rs11742049;rs52823365;rs57564432;rs11554776	71	Q86WV6	TM173_HUMAN	H	71	ENSP00000331288:R71H;ENSP00000427455:R71H	ENSP00000331288:R71H	R	-	2	0	TMEM173	138841262	0.000000	0.05858	0.028000	0.17463	0.331000	0.28603	-0.120000	0.10660	0.053000	0.16036	0.561000	0.74099	CGC	C|0.867;T|0.133	0.133	strong		0.617	TMEM173-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251338.1	NM_198282	
SNX30	401548	hgsc.bcm.edu	37	9	115600827	115600827	+	Silent	SNP	C	C	T	rs41280189	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:115600827C>T	ENST00000374232.3	+	6	1028	c.864C>T	c.(862-864)agC>agT	p.S288S		NM_001012994.1	NP_001013012.1	Q5VWJ9	SNX30_HUMAN	sorting nexin family member 30	288					apoptotic process (GO:0006915)|intracellular protein transport (GO:0006886)	endosome (GO:0005768)	phosphatidylinositol binding (GO:0035091)			large_intestine(1)|lung(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	8						CCACATGGAGCGCCTTGGAGG	0.522													C|||	283	0.0565096	0.0023	0.0793	5008	,	,		19457	0.0655		0.1093	False		,,,				2504	0.0501				p.S288S		Atlas-SNP	.											.	SNX30	32	.	0			c.C864T						PASS	.	C		97,3771		1,95,1838	92.0	95.0	94.0		864	-4.8	0.0	9	dbSNP_127	94	799,7459		41,717,3371	no	coding-synonymous	SNX30	NM_001012994.1		42,812,5209	TT,TC,CC		9.6755,2.5078,7.3891		288/438	115600827	896,11230	1934	4129	6063	SO:0001819	synonymous_variant	401548	exon6			ATGGAGCGCCTTG	AK126644	CCDS43865.1	9q33.1	2014-02-12			ENSG00000148158	ENSG00000148158		"""Sorting nexins"""	23685	protein-coding gene	gene with protein product							Standard	NM_001012994		Approved	ATG24A	uc004bgj.4	Q5VWJ9	OTTHUMG00000020512	ENST00000374232.3:c.864C>T	9.37:g.115600827C>T		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	119	63	0.529412	NM_001012994		Silent	SNP	ENST00000374232.3	37	CCDS43865.1																																																																																			C|0.922;T|0.078	0.078	strong		0.522	SNX30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053700.1		
BOC	91653	hgsc.bcm.edu	37	3	112991312	112991312	+	Silent	SNP	C	C	T	rs3814398	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:112991312C>T	ENST00000495514.1	+	7	1427	c.723C>T	c.(721-723)atC>atT	p.I241I	BOC_ENST00000355385.3_Silent_p.I241I|BOC_ENST00000273395.4_Silent_p.I241I			Q9BWV1	BOC_HUMAN	BOC cell adhesion associated, oncogene regulated	241	Ig-like C2-type 3.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|muscle cell differentiation (GO:0042692)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of myoblast differentiation (GO:0045663)|smoothened signaling pathway (GO:0007224)	axonal growth cone (GO:0044295)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)				NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(17)|lung(18)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	68			Epithelial(53;0.227)			AAACCATCATCGTCACCAAAG	0.627													C|||	1386	0.276757	0.2073	0.3732	5008	,	,		18873	0.3978		0.1879	False		,,,				2504	0.2689				p.I241I		Atlas-SNP	.											.	BOC	139	.	0			c.C723T						PASS	.	C		902,3504	348.0+/-309.7	94,714,1395	162.0	154.0	157.0		723	-5.9	0.9	3	dbSNP_107	157	1332,7268	261.2+/-283.7	111,1110,3079	no	coding-synonymous	BOC	NM_033254.2		205,1824,4474	TT,TC,CC		15.4884,20.4721,17.1767		241/1115	112991312	2234,10772	2203	4300	6503	SO:0001819	synonymous_variant	91653	exon7			CATCATCGTCACC	AY027658	CCDS2971.1	3q13.2	2013-02-11	2012-12-07		ENSG00000144857	ENSG00000144857		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	17173	protein-coding gene	gene with protein product	"""brother of CDO"", ""brother of CDON"", ""cell adhesion associated, oncogene regulated 2"""	608708	"""Boc homolog (mouse)"""			11782431	Standard	NM_033254		Approved	CDON2	uc003dzy.3	Q9BWV1	OTTHUMG00000159305	ENST00000495514.1:c.723C>T	3.37:g.112991312C>T		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	116	64	0.551724	NM_033254	A6NJ30|B2RMS8|D3DN70|Q6UXJ5|Q8N2P7|Q8NF26	Silent	SNP	ENST00000495514.1	37	CCDS2971.1																																																																																			C|0.788;T|0.212	0.212	strong		0.627	BOC-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000354485.3	NM_033254	
ZNF761	388561	hgsc.bcm.edu	37	19	53959804	53959804	+	RNA	SNP	T	T	C	rs4803129	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:53959804T>C	ENST00000454407.1	+	0	2496							Q86XN6	ZN761_HUMAN	zinc finger protein 761						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.H627H(1)		endometrium(1)|kidney(2)|large_intestine(5)|lung(13)|ovary(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	30				GBM - Glioblastoma multiforme(134;0.00786)		TATGCCATCATAGACTTCATA	0.393													t|||	731	0.145966	0.1914	0.1066	5008	,	,		22447	0.1349		0.165	False		,,,				2504	0.1043				p.H681H		Atlas-SNP	.											ZNF761,NS,carcinoma,0,1	ZNF761	104	1	1	Substitution - coding silent(1)	stomach(1)	c.T2043C						PASS	.	T		683,3723	286.0+/-278.5	50,583,1570	89.0	93.0	91.0		2044	-0.7	0.0	19	dbSNP_111	91	1572,7028	291.7+/-300.5	131,1310,2859	no	coding-synonymous	ZNF761	NM_001008401.3		181,1893,4429	CC,CT,TT		18.2791,15.5016,17.3382		681/747	53959804	2255,10751	2203	4300	6503			388561	exon7			CCATCATAGACTT	AB107355		19q13.42	2007-10-05	2006-08-11	2006-08-11	ENSG00000160336	ENSG00000160336		"""Zinc fingers, C2H2-type"""	23179	protein-coding gene	gene with protein product							Standard	NM_001008401		Approved	KIAA2033, FLJ16231, FLJ35333	uc010eqp.3	Q86XN6	OTTHUMG00000156999		19.37:g.53959804T>C		Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	18	12	0.666667	NM_001008401	Q6ZNB9	Silent	SNP	ENST00000454407.1	37																																																																																				T|0.823;C|0.177	0.177	strong		0.393	ZNF761-203	KNOWN	basic	processed_transcript	processed_transcript		NM_001008401	
LCE1D	353134	hgsc.bcm.edu	37	1	152770589	152770589	+	Missense_Mutation	SNP	A	A	G	rs11485496	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:152770589A>G	ENST00000326233.6	+	2	362	c.319A>G	c.(319-321)Agc>Ggc	p.S107G		NM_178352.2	NP_848129.1	Q5T752	LCE1D_HUMAN	late cornified envelope 1D	107	Cys-rich.				cellular response to calcium ion (GO:0071277)|cognition (GO:0050890)|keratinization (GO:0031424)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|perinuclear region of cytoplasm (GO:0048471)				large_intestine(1)	1	Lung NSC(65;3.97e-29)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)			TGGGGGCAGCAGCCAGCACTC	0.617																																					p.S107G		Atlas-SNP	.											.	LCE1D	19	.	0			c.A319G						PASS	.	G	GLY/SER	1517,2503		250,1017,743	42.0	38.0	40.0		319	-4.4	0.0	1	dbSNP_120	40	1515,5915		354,807,2554	no	missense	LCE1D	NM_178352.2	56	604,1824,3297	GG,GA,AA		20.3903,37.7363,26.4803	benign	107/115	152770589	3032,8418	2010	3715	5725	SO:0001583	missense	353134	exon2			GGCAGCAGCCAGC		CCDS1025.1	1q21.3	2008-02-05			ENSG00000172155	ENSG00000172155		"""Late cornified envelopes"""	29465	protein-coding gene	gene with protein product		612606				11698679	Standard	NM_178352		Approved	LEP4	uc009wnp.3	Q5T752	OTTHUMG00000012444	ENST00000326233.6:c.319A>G	1.37:g.152770589A>G	ENSP00000316737:p.Ser107Gly	Somatic	500	1	0.002		WXS	Illumina HiSeq	Phase_I	560	368	0.657143	NM_178352		Missense_Mutation	SNP	ENST00000326233.6	37	CCDS1025.1	755	0.3456959706959707	221	0.4491869918699187	133	0.3674033149171271	209	0.36538461538461536	192	0.2532981530343008	G	2.075	-0.412012	0.04799	0.377363	0.203903	ENSG00000172155	ENST00000326233	T	0.02395	4.31	4.52	-4.45	0.03546	.	0.709364	0.11211	N	0.587727	T	0.00328	0.0010	N	0.00583	-1.355	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.48043	-0.9069	9	0.87932	D	0	.	7.5651	0.27874	0.6643:0.0:0.2156:0.1201	rs11485496	107	Q5T752	LCE1D_HUMAN	G	107	ENSP00000316737:S107G	ENSP00000316737:S107G	S	+	1	0	LCE1D	151037213	0.000000	0.05858	0.000000	0.03702	0.131000	0.20780	-0.754000	0.04787	-1.102000	0.03023	-1.087000	0.02190	AGC	A|0.659;G|0.341	0.341	strong		0.617	LCE1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034657.2	NM_178352	
AFF2	2334	hgsc.bcm.edu	37	X	148048494	148048494	+	Missense_Mutation	SNP	A	A	C	rs149653283	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:148048494A>C	ENST00000370460.2	+	14	3567	c.3088A>C	c.(3088-3090)Atc>Ctc	p.I1030L	AFF2_ENST00000342251.3_Missense_Mutation_p.I997L|AFF2_ENST00000370457.5_Missense_Mutation_p.I995L|AFF2_ENST00000286437.5_Missense_Mutation_p.I671L	NM_001169123.1|NM_002025.3	NP_001162594.1|NP_002016.2	P51816	AFF2_HUMAN	AF4/FMR2 family, member 2	1030					brain development (GO:0007420)|learning or memory (GO:0007611)|mRNA processing (GO:0006397)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)	nuclear speck (GO:0016607)	G-quadruplex RNA binding (GO:0002151)			breast(5)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(29)|liver(2)|lung(39)|ovary(4)|pancreas(5)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	109	Acute lymphoblastic leukemia(192;6.56e-05)					cacctctaccatcactacTGG	0.567													A|||	2	0.000529801	0.0	0.0014	3775	,	,		13632	0.0		0.001	False		,,,				2504	0.0				p.I1030L		Atlas-SNP	.											.	AFF2	679	.	0			c.A3088C						PASS	.	A	LEU/ILE,LEU/ILE,LEU/ILE,LEU/ILE,LEU/ILE,LEU/ILE	1,3834		0,0,1,1632,570	380.0	264.0	304.0		2983,3058,2983,2971,2011,3088	4.2	1.0	X	dbSNP_134	304	5,6723		0,4,1,2424,1871	yes	missense,missense,missense,missense,missense,missense	AFF2	NM_001169122.1,NM_001169123.1,NM_001169124.1,NM_001169125.1,NM_001170628.1,NM_002025.3	5,5,5,5,5,5	0,4,2,4056,2441	CC,CA,C,AA,A		0.0743,0.0261,0.0568	benign,benign,benign,benign,benign,benign	995/1277,1020/1302,995/1277,991/1273,671/953,1030/1312	148048494	6,10557	2203	4300	6503	SO:0001583	missense	2334	exon14			TCTACCATCACTA	U48436	CCDS14684.1, CCDS55521.1, CCDS76040.1	Xq28	2008-02-05	2005-06-27	2005-06-27	ENSG00000155966	ENSG00000155966			3776	protein-coding gene	gene with protein product		300806	"""fragile X mental retardation 2"""	FMR2			Standard	NM_002025		Approved	FRAXE	uc004fcp.3	P51816	OTTHUMG00000022613	ENST00000370460.2:c.3088A>C	X.37:g.148048494A>C	ENSP00000359489:p.Ile1030Leu	Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	91	89	0.978022	NM_002025	A2RTY4|B4DXD5|B7WNQ1|B7ZLD6|B7ZLD9|O43786|O60215|P78407|Q13521|Q14323|Q7Z2F7|Q7Z400|Q9UNA5	Missense_Mutation	SNP	ENST00000370460.2	37	CCDS14684.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	A	14.61	2.587998	0.46110	2.61E-4	7.43E-4	ENSG00000155966	ENST00000370460;ENST00000370457;ENST00000342251;ENST00000286437	T;T;T;T	0.71934	-0.01;-0.27;-0.27;-0.61	4.18	4.18	0.49190	.	0.089728	0.42053	D	0.000773	T	0.47710	0.1460	N	0.08118	0	0.24214	N	0.995466	P;P;P;P;P;P	0.38473	0.633;0.579;0.579;0.579;0.579;0.633	B;B;B;B;B;B	0.40782	0.34;0.23;0.23;0.23;0.23;0.34	T	0.32851	-0.9891	10	0.27785	T	0.31	.	5.4451	0.16531	0.8777:0.0:0.1223:0.0	.	671;995;995;991;1020;1030	B4DXD5;P51816-6;P51816-3;P51816-2;P51816-5;P51816	.;.;.;.;.;AFF2_HUMAN	L	1030;995;997;671	ENSP00000359489:I1030L;ENSP00000359486:I995L;ENSP00000345459:I997L;ENSP00000286437:I671L	ENSP00000286437:I671L	I	+	1	0	AFF2	147856188	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	3.240000	0.51368	1.860000	0.53959	0.417000	0.27973	ATC	A|1.000;C|0.000	0.000	strong		0.567	AFF2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058673.2	NM_002025	
MCC	4163	hgsc.bcm.edu	37	5	112406862	112406862	+	Silent	SNP	G	G	A	rs2227950	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:112406862G>A	ENST00000302475.4	-	10	1847	c.1284C>T	c.(1282-1284)gcC>gcT	p.A428A	MCC_ENST00000408903.3_Silent_p.A618A|MCC_ENST00000515367.2_Silent_p.A365A|MCC_ENST00000514701.3_5'UTR	NM_002387.2	NP_002378	P23508	CRCM_HUMAN	mutated in colorectal cancers	428					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)	p.A618A(1)|p.A428A(1)		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)		TCATCCTCTCGGCATTGCTTT	0.483													G|||	1671	0.333666	0.354	0.2853	5008	,	,		19595	0.3462		0.3151	False		,,,				2504	0.3466				p.A618A		Atlas-SNP	.											MCC_ENST00000408903,colon,carcinoma,-1,4	MCC	234	4	2	Substitution - coding silent(2)	stomach(2)	c.C1854T						PASS	.	G	,	1380,3024	455.1+/-350.9	223,934,1045	265.0	221.0	236.0		1854,1284	-9.4	0.1	5	dbSNP_98	236	2825,5775	446.1+/-361.2	460,1905,1935	no	coding-synonymous,coding-synonymous	MCC	NM_001085377.1,NM_002387.2	,	683,2839,2980	AA,AG,GG		32.8488,31.3351,32.3362	,	618/1020,428/830	112406862	4205,8799	2202	4300	6502	SO:0001819	synonymous_variant	4163	exon12			CCTCTCGGCATTG		CCDS4111.1, CCDS43351.1	5q21-q22	2013-01-10			ENSG00000171444	ENSG00000171444		"""EF-hand domain containing"""	6935	protein-coding gene	gene with protein product		159350				1848370	Standard	NM_002387		Approved		uc003kql.4	P23508	OTTHUMG00000128804	ENST00000302475.4:c.1284C>T	5.37:g.112406862G>A		Somatic	222	0	0		WXS	Illumina HiSeq	Phase_I	222	99	0.445946	NM_001085377	D3DT05|Q6ZR04	Silent	SNP	ENST00000302475.4	37	CCDS4111.1																																																																																			T|0.062;G|0.554;C|0.125;A|0.259	0.259	strong		0.483	MCC-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250736.3	NM_001085377	
CFLAR	8837	hgsc.bcm.edu	37	2	202006096	202006096	+	Intron	SNP	G	G	A	rs10190751	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:202006096G>A	ENST00000309955.3	+	5	1121				CFLAR_ENST00000479953.2_Intron|CFLAR_ENST00000341222.6_Splice_Site|CFLAR_ENST00000342795.5_Intron|CFLAR_ENST00000341582.6_Intron|CFLAR-AS1_ENST00000594911.1_RNA|CFLAR-AS1_ENST00000415011.2_RNA|CFLAR_ENST00000440180.1_Splice_Site|RNU7-45P_ENST00000459460.1_RNA|CFLAR_ENST00000340870.5_Intron|CFLAR_ENST00000423241.2_Intron|CFLAR_ENST00000443227.1_Intron|CFLAR_ENST00000355558.4_Intron|CFLAR_ENST00000457277.1_Intron|CFLAR-AS1_ENST00000598453.1_RNA|CFLAR-AS1_ENST00000474886.2_RNA	NM_001202515.1|NM_003879.5	NP_001189444.1|NP_003870.4	O15519	CFLAR_HUMAN	CASP8 and FADD-like apoptosis regulator						apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of myoblast fusion (GO:1901740)|positive regulation of catalytic activity (GO:0043085)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001239)|regulation of necroptotic process (GO:0060544)|regulation of satellite cell proliferation (GO:0014842)|skeletal muscle atrophy (GO:0014732)|skeletal muscle tissue development (GO:0007519)|skeletal muscle tissue regeneration (GO:0043403)|skeletal myofibril assembly (GO:0014866)|viral process (GO:0016032)	CD95 death-inducing signaling complex (GO:0031265)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|death-inducing signaling complex (GO:0031264)|ripoptosome (GO:0097342)	cysteine-type peptidase activity (GO:0008234)|death effector domain binding (GO:0035877)|enzyme activator activity (GO:0008047)|protease binding (GO:0002020)			breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(6)|stomach(1)	13						ctcttctacagatgataacac	0.338													A|||	1084	0.216454	0.4622	0.147	5008	,	,		18717	0.0516		0.2147	False		,,,				2504	0.1053				.	Pancreas(16;548 657 22190 32864 42338)	Atlas-SNP	.											.	CFLAR	37	.	0			c.607-1G>A						PASS	.	A	,,,,,,,	1221,1891		265,691,600	115.0	94.0	100.0		,,,,,,,	-4.6	0.0	2	dbSNP_119	100	1377,5755		145,1087,2334	yes	intron,splice-3,intron,intron,intron,intron,intron,intron	CFLAR	NM_001127183.2,NM_001127184.2,NM_001202515.1,NM_001202516.1,NM_001202517.1,NM_001202518.1,NM_001202519.1,NM_003879.5	,,,,,,,	410,1778,2934	AA,AG,GG		19.3073,39.2352,25.3612	,,,,,,,	,,,,,,,	202006096	2598,7646	1556	3566	5122	SO:0001627	intron_variant	8837	exon6			TCTACAGATGATA	AF005774	CCDS2337.1, CCDS46487.1, CCDS56157.1, CCDS56158.1, CCDS59436.1	2q33-q34	2014-01-30			ENSG00000003402	ENSG00000003402		"""Endogenous ligands"""	1876	protein-coding gene	gene with protein product		603599		CASP8AP1		9208847, 9217161	Standard	NM_003879		Approved	CASH, Casper, CLARP, FLAME, FLIP, I-FLICE, MRIT, c-FLIP	uc002uxb.4	O15519	OTTHUMG00000132819	ENST00000309955.3:c.606+934G>A	2.37:g.202006096G>A		Somatic	193	0	0		WXS	Illumina HiSeq	Phase_I	165	73	0.442424	NM_001127184	B4DJE0|B7Z9F9|O14673|O14674|O14675|O15137|O15138|O15356|O15510|O43618|O43619|O43620|O60458|O60459|Q53TS6|Q54AF1|Q96TE4|Q9UEW1	Splice_Site	SNP	ENST00000309955.3	37	CCDS2337.1																																																																																			G|0.764;A|0.236	0.236	strong		0.338	CFLAR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256276.3	NM_003879	
DMBT1	1755	hgsc.bcm.edu	37	10	124345796	124345796	+	Missense_Mutation	SNP	C	C	G	rs143892520	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:124345796C>G	ENST00000338354.3	+	16	1786	c.1680C>G	c.(1678-1680)gaC>gaG	p.D560E	DMBT1_ENST00000368909.3_Missense_Mutation_p.D560E|DMBT1_ENST00000359586.6_Intron|DMBT1_ENST00000344338.3_Missense_Mutation_p.D550E|DMBT1_ENST00000368955.3_Missense_Mutation_p.D550E|DMBT1_ENST00000330163.4_Intron|DMBT1_ENST00000368956.2_Intron			Q9UGM3	DMBT1_HUMAN	deleted in malignant brain tumors 1	560	SRCR 4. {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)	p.D560D(1)		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)				TCCTGGATGACGTGCGCTGCT	0.592													c|||	30	0.00599042	0.0	0.0058	5008	,	,		18199	0.0		0.0169	False		,,,				2504	0.0092				p.D560E	Ovarian(182;93 2026 18125 22222 38972)	Atlas-SNP	.											DMBT1_ENST00000368915,caecum,carcinoma,0,13	DMBT1	677	13	1	Substitution - coding silent(1)	central_nervous_system(1)	c.C1680G						PASS	.	C	,GLU/ASP,GLU/ASP	6,4040		0,6,2017	186.0	137.0	153.0		,1680,1650	-9.0	0.0	10	dbSNP_134	153	155,8111		17,121,3995	no	intron,missense,missense	DMBT1	NM_004406.2,NM_007329.2,NM_017579.2	,45,45	17,127,6012	GG,GC,CC		1.8752,0.1483,1.3077	,possibly-damaging,possibly-damaging	,560/2414,550/2404	124345796	161,12151	2023	4133	6156	SO:0001583	missense	1755	exon16			GGATGACGTGCGC		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.1680C>G	10.37:g.124345796C>G	ENSP00000342210:p.Asp560Glu	Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	134	64	0.477612	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		18	0.008241758241758242	0	0.0	2	0.0055248618784530384	0	0.0	16	0.021108179419525065	C	13.74	2.326283	0.41197	0.001483	0.018752	ENSG00000187908	ENST00000338354;ENST00000368915;ENST00000341278;ENST00000368953;ENST00000339871;ENST00000368942;ENST00000344338;ENST00000368909;ENST00000368955	T;T;T;T	0.44083	0.93;0.93;0.93;0.93	4.5	-9.0	0.00747	Speract/scavenger receptor (3);Speract/scavenger receptor-related (2);	.	.	.	.	T	0.13243	0.0321	L	0.33753	1.03	0.80722	D	1	B;B;B	0.33266	0.351;0.351;0.404	B;B;B	0.34489	0.115;0.115;0.184	T	0.29941	-0.9995	9	0.25751	T	0.34	.	10.9976	0.47585	0.1665:0.1817:0.0:0.6517	.	560;550;560	Q9UGM3-6;Q9UGM3-3;Q9UGM3	.;.;DMBT1_HUMAN	E	560;560;560;560;560;560;550;560;550	ENSP00000342210:D560E;ENSP00000343175:D550E;ENSP00000357905:D560E;ENSP00000357951:D550E	ENSP00000342210:D560E	D	+	3	2	DMBT1	124335786	0.000000	0.05858	0.000000	0.03702	0.425000	0.31504	-5.882000	0.00092	-2.782000	0.00360	-0.680000	0.03767	GAC	C|0.989;G|0.011	0.011	strong		0.592	DMBT1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050792.2	NM_004406	
CEL	1056	hgsc.bcm.edu	37	9	135945997	135945997	+	Missense_Mutation	SNP	C	C	T	rs201677850	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:135945997C>T	ENST00000372080.4	+	10	1461	c.1445C>T	c.(1444-1446)aCa>aTa	p.T482I	CEL_ENST00000351304.7_Intron	NM_001807.3	NP_001798.2	P19835	CEL_HUMAN	carboxyl ester lipase	479					cholesterol catabolic process (GO:0006707)|fatty acid catabolic process (GO:0009062)|intestinal cholesterol absorption (GO:0030299)|intestinal lipid catabolic process (GO:0044258)|lipid digestion (GO:0044241)|lipid metabolic process (GO:0006629)|pancreatic juice secretion (GO:0030157)|protein esterification (GO:0018350)|small molecule metabolic process (GO:0044281)|triglyceride metabolic process (GO:0006641)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	acylglycerol lipase activity (GO:0047372)|catalytic activity (GO:0003824)|heparin binding (GO:0008201)|hydrolase activity (GO:0016787)|sterol esterase activity (GO:0004771)|triglyceride lipase activity (GO:0004806)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(9)|pancreas(2)|skin(1)	20				OV - Ovarian serous cystadenocarcinoma(145;1.03e-40)|Epithelial(140;3.58e-37)|GBM - Glioblastoma multiforme(294;0.00164)|READ - Rectum adenocarcinoma(205;0.196)		CAAGACAGGACAGTCTCTAAG	0.607																																					p.T482I		Atlas-SNP	.											CEL,NS,carcinoma,+1,1	CEL	71	1	0			c.C1445T						scavenged	.						83.0	95.0	91.0					9																	135945997		2003	4163	6166	SO:0001583	missense	1056	exon10			ACAGGACAGTCTC	M54994	CCDS43896.1	9q34.3	2013-03-13	2013-03-13		ENSG00000170835	ENSG00000170835	3.1.1.3, 3.1.1.13		1848	protein-coding gene	gene with protein product	"""bile salt-stimulated lipase"""	114840				1676983	Standard	NM_001807		Approved	BSSL, MODY8	uc010naa.2	P19835	OTTHUMG00000020855	ENST00000372080.4:c.1445C>T	9.37:g.135945997C>T	ENSP00000361151:p.Thr482Ile	Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	244	9	0.0368852	NM_001807	Q16398|Q5T7U7|Q9UCH1|Q9UP41	Missense_Mutation	SNP	ENST00000372080.4	37	CCDS43896.1	.	.	.	.	.	.	.	.	.	.	C	17.46	3.395574	0.62177	.	.	ENSG00000170835	ENST00000372080;ENST00000303626	T	0.67171	-0.25	5.69	5.69	0.88448	Carboxylesterase, type B (1);	0.296062	0.38058	N	0.001840	T	0.57344	0.2047	N	0.13327	0.33	0.80722	D	1	D	0.54397	0.966	P	0.50352	0.638	T	0.55386	-0.8149	10	0.26408	T	0.33	.	13.7707	0.63023	0.1534:0.8466:0.0:0.0	.	479	P19835	CEL_HUMAN	I	482;481	ENSP00000361151:T482I	ENSP00000304021:T481I	T	+	2	0	CEL	134935818	0.940000	0.31905	0.109000	0.21407	0.603000	0.37013	2.046000	0.41260	2.698000	0.92095	0.472000	0.43445	ACA	C|0.998;T|0.002	0.002	strong		0.607	CEL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054823.1		
HLA-A	3105	hgsc.bcm.edu	37	6	29911240	29911240	+	Missense_Mutation	SNP	T	T	G	rs9260156	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:29911240T>G	ENST00000396634.1	+	5	880	c.539T>G	c.(538-540)tTg>tGg	p.L180W	HLA-A_ENST00000376802.2_Missense_Mutation_p.L180W|HLA-A_ENST00000376809.5_Missense_Mutation_p.L180W|HLA-A_ENST00000376806.5_Missense_Mutation_p.L180W			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	180	Alpha-2.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	beta-2-microglobulin binding (GO:0030881)|peptide antigen binding (GO:0042605)|TAP binding (GO:0046977)	p.L180*(1)		central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	30						GCGGAGCAGTTGAGAGCCTAC	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)			N|||	1166	0.232827	0.2988	0.1902	5008	,	,		12147	0.12		0.2207	False		,,,				2504	0.3027				p.L180W		Atlas-SNP	.											HLA-A,mouth,carcinoma,0,1	HLA-A	89	1	1	Substitution - Nonsense(1)	upper_aerodigestive_tract(1)	c.T539G						PASS	.	A	TRP/LEU	851,2167		163,525,821	40.0	29.0	33.0		539	-7.6	0.0	6	dbSNP_131	33	1445,3945		348,749,1598	no	missense	HLA-A	NM_002116.7	61	511,1274,2419	GG,GT,TT		26.8089,28.1975,27.3073	benign	180/366	29911240	2296,6112	1509	2695	4204	SO:0001583	missense	3105	exon3	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	AGCAGTTGAGAGC	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.539T>G	6.37:g.29911240T>G	ENSP00000379873:p.Leu180Trp	Somatic	257	2	0.0077821		WXS	Illumina HiSeq	Phase_I	130	107	0.823077	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Missense_Mutation	SNP	ENST00000396634.1	37	CCDS34373.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	2.728|2.728	-0.264990|-0.264990	0.05754|0.05754	0.281975|0.281975	0.268089|0.268089	ENSG00000206503|ENSG00000206503	ENST00000396634;ENST00000376806;ENST00000376809;ENST00000376802|ENST00000355767	T;T;T;T|.	0.00010|.	9.41;9.41;9.41;9.41|.	3.78|3.78	-7.56|-7.56	0.01322|0.01322	MHC class I, alpha chain, alpha1/alpha2 (2);MHC classes I/II-like antigen recognition protein (2);MHC class I-like antigen recognition (2);|.	4.873430|.	0.01566|.	N|.	0.020372|.	T|.	0.02888|.	0.0086|.	N|N	0.04636|0.04636	-0.2|-0.2	0.09310|0.09310	N|N	1|1	B;B;B;B;B|.	0.14805|.	0.011;0.0;0.002;0.0;0.002|.	B;B;B;B;B|.	0.13407|.	0.009;0.001;0.001;0.001;0.001|.	T|.	0.15178|.	-1.0446|.	10|.	0.14252|.	T|.	0.57|.	.|.	6.7832|6.7832	0.23659|0.23659	0.5534:0.0:0.1127:0.3339|0.5534:0.0:0.1127:0.3339	rs9260156;rs11539955;rs16896023;rs41555815|rs9260156;rs11539955;rs16896023;rs41555815	59;180;180;180;180|.	B4DVB9;Q5SRN7;P16188;Q5SRN5;P04439|.	.;.;1A30_HUMAN;.;1A03_HUMAN|.	W|G	180|155	ENSP00000379873:L180W;ENSP00000366002:L180W;ENSP00000366005:L180W;ENSP00000365998:L180W|.	ENSP00000365998:L180W|.	L|X	+|+	2|1	0|0	HLA-A|HLA-A	30019219|30019219	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.001000|0.001000	0.01503|0.01503	-12.720000|-12.720000	0.00001|0.00001	-3.712000|-3.712000	0.00117|0.00117	-2.599000|-2.599000	0.00162|0.00162	TTG|TGA	A|0.250;G|0.070;T|0.680	0.070	strong		0.667	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
STT3A	3703	hgsc.bcm.edu	37	11	125465862	125465862	+	Silent	SNP	T	T	C	rs10082632	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:125465862T>C	ENST00000529196.1	+	3	258	c.52T>C	c.(52-54)Ttg>Ctg	p.L18L	STT3A_ENST00000392708.4_Silent_p.L18L|STT3A_ENST00000531491.1_Intron			P46977	STT3A_HUMAN	STT3A, subunit of the oligosaccharyltransferase complex (catalytic)	18					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)		GGACACACTTTTGAAGCTTCT	0.393													C|||	524	0.104633	0.2436	0.062	5008	,	,		20413	0.0308		0.0755	False		,,,				2504	0.0532				p.L18L		Atlas-SNP	.											.	STT3A	52	.	0			c.T52C						PASS	.	C		922,3480	737.7+/-410.9	91,740,1370	227.0	194.0	205.0		52	1.6	1.0	11	dbSNP_119	205	582,8016	793.1+/-407.5	17,548,3734	no	coding-synonymous	STT3A	NM_152713.3		108,1288,5104	CC,CT,TT		6.769,20.945,11.5692		18/706	125465862	1504,11496	2201	4299	6500	SO:0001819	synonymous_variant	3703	exon2			ACACTTTTGAAGC	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.52T>C	11.37:g.125465862T>C		Somatic	234	0	0		WXS	Illumina HiSeq	Phase_I	168	117	0.696429	NM_152713	B4DJ24|E9PNQ1|Q86XU9|Q8TE35|Q8WUB4	Silent	SNP	ENST00000529196.1	37	CCDS8458.1																																																																																			T|0.885;C|0.115	0.115	strong		0.393	STT3A-002	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000386691.1	NM_152713	
SH2D3A	10045	hgsc.bcm.edu	37	19	6763718	6763718	+	Silent	SNP	A	A	G	rs2305805	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:6763718A>G	ENST00000245908.6	-	2	311	c.42T>C	c.(40-42)ccT>ccC	p.P14P	SH2D3A_ENST00000599563.1_5'Flank|SH2D3A_ENST00000437152.3_Missense_Mutation_p.L9P	NM_005490.2	NP_005481.2	Q9BRG2	SH23A_HUMAN	SH2 domain containing 3A	14					JNK cascade (GO:0007254)|positive regulation of signal transduction (GO:0009967)|small GTPase mediated signal transduction (GO:0007264)		guanyl-nucleotide exchange factor activity (GO:0005085)|SH3/SH2 adaptor activity (GO:0005070)			breast(3)|endometrium(3)|kidney(1)|large_intestine(4)|lung(9)|skin(3)|urinary_tract(1)	24						CGTGGTACCAAGGTTGGCCAG	0.617													G|||	1303	0.260184	0.4682	0.1571	5008	,	,		14692	0.0565		0.2247	False		,,,				2504	0.2986				p.P14P		Atlas-SNP	.											.	SH2D3A	53	.	0			c.T42C						PASS	.	G		1863,2543	628.9+/-395.2	393,1077,733	90.0	72.0	78.0		42	2.0	1.0	19	dbSNP_100	78	1866,6734	725.7+/-406.6	208,1450,2642	no	coding-synonymous	SH2D3A	NM_005490.2		601,2527,3375	GG,GA,AA		21.6977,42.2833,28.6714		14/577	6763718	3729,9277	2203	4300	6503	SO:0001819	synonymous_variant	10045	exon2			GTACCAAGGTTGG	AF124249	CCDS12173.1	19p13.3	2013-02-14	2002-01-14			ENSG00000125731		"""SH2 domain containing"""	16885	protein-coding gene	gene with protein product		604721	"""SH2 domain-containing 3A"""			10187783	Standard	NM_005490		Approved	NSP1	uc002mft.3	Q9BRG2		ENST00000245908.6:c.42T>C	19.37:g.6763718A>G		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	46	19	0.413043	NM_005490	A8K9R6|B4DRS7|Q9Y2X4	Silent	SNP	ENST00000245908.6	37	CCDS12173.1	480	0.21978021978021978	204	0.4146341463414634	64	0.17679558011049723	37	0.06468531468531469	175	0.23087071240105542	G	8.380	0.837313	0.16891	0.422833	0.216977	ENSG00000125731	ENST00000437152	T	0.32272	1.46	4.21	2.03	0.26663	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.26469	P	0.9753131	B	0.02656	0.0	B	0.01281	0.0	T	0.48151	-0.9060	6	.	.	.	-7.4148	4.1083	0.10047	0.2892:0.1735:0.5373:0.0	rs2305805;rs58578745;rs2305805	9	B4DRS7	.	P	9	ENSP00000393303:L9P	.	L	-	2	0	SH2D3A	6714718	1.000000	0.71417	0.998000	0.56505	0.453000	0.32348	0.586000	0.23894	0.175000	0.19841	-0.119000	0.15052	CTT	A|0.742;G|0.258	0.258	strong		0.617	SH2D3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458016.1	NM_005490	
CEACAM20	125931	hgsc.bcm.edu	37	19	45033485	45033485	+	RNA	SNP	A	A	G	rs62116895	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:45033485A>G	ENST00000454753.1	-	0	326							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)				ACTCACCTGAAAGCAGGATTC	0.587													g|||	1067	0.213059	0.4569	0.1657	5008	,	,		16546	0.1587		0.0954	False		,,,				2504	0.0941				p.L16L		Atlas-SNP	.											.	CEACAM20	31	.	0			c.T48C						PASS	.		,,,	1683,2519		343,997,761	53.0	59.0	57.0		48,48,48,48	1.2	0.8	19	dbSNP_129	57	730,7710		38,654,3528	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CEACAM20	NM_001102597.1,NM_001102598.1,NM_001102599.1,NM_001102600.1	,,,	381,1651,4289	GG,GA,AA		8.6493,40.0524,19.0872	,,,	16/597,16/492,16/504,16/585	45033485	2413,10229	2101	4220	6321			125931	exon1			ACCTGAAAGCAGG	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.45033485A>G		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	83	83	1	NM_001102600		Silent	SNP	ENST00000454753.1	37																																																																																				A|0.815;G|0.185	0.185	strong		0.587	CEACAM20-001	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000323032.1	NM_198444	
TDRD9	122402	hgsc.bcm.edu	37	14	104452640	104452640	+	Silent	SNP	G	G	A	rs10143389	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:104452640G>A	ENST00000409874.4	+	8	1146	c.1098G>A	c.(1096-1098)ttG>ttA	p.L366L	TDRD9_ENST00000339063.5_Silent_p.L366L	NM_153046.2	NP_694591.2	Q8NDG6	TDRD9_HUMAN	tudor domain containing 9	366					cell differentiation (GO:0030154)|DNA methylation involved in gamete generation (GO:0043046)|fertilization (GO:0009566)|gene silencing by RNA (GO:0031047)|male meiosis (GO:0007140)|multicellular organismal development (GO:0007275)|piRNA metabolic process (GO:0034587)|spermatogenesis (GO:0007283)	nucleus (GO:0005634)|piP-body (GO:0071547)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)	p.L366L(1)|p.L81L(1)		breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(10)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)	33		all_cancers(154;0.109)|Melanoma(154;0.0525)|all_epithelial(191;0.0768)				TTGATGACTTGGATATGAAGG	0.348													G|||	1613	0.322085	0.2731	0.3516	5008	,	,		18906	0.3343		0.3588	False		,,,				2504	0.317				p.L366L		Atlas-SNP	.											TDRD9_ENST00000409874,NS,carcinoma,0,2	TDRD9	175	2	2	Substitution - coding silent(2)	stomach(2)	c.G1098A						PASS	.	G		1326,3080	446.7+/-348.1	190,946,1067	113.0	104.0	107.0		1098	3.9	1.0	14	dbSNP_119	107	2984,5616	460.9+/-365.3	518,1948,1834	no	coding-synonymous	TDRD9	NM_153046.2		708,2894,2901	AA,AG,GG		34.6977,30.0953,33.1386		366/1383	104452640	4310,8696	2203	4300	6503	SO:0001819	synonymous_variant	122402	exon8			TGACTTGGATATG	AK093483	CCDS9987.2	14q32.33	2013-01-23	2004-04-01	2004-04-02	ENSG00000156414	ENSG00000156414		"""Tudor domain containing"""	20122	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 75"""	C14orf75			Standard	NM_153046		Approved	DKFZp434N0820, FLJ36164, NET54	uc001yom.4	Q8NDG6	OTTHUMG00000152876	ENST00000409874.4:c.1098G>A	14.37:g.104452640G>A		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	119	52	0.436975	NM_153046	A1A4S7|Q6ZU54|Q8N7T3|Q8N827|Q8N9V5|Q96AS9	Silent	SNP	ENST00000409874.4	37	CCDS9987.2	706	0.3232600732600733	131	0.266260162601626	118	0.3259668508287293	183	0.31993006993006995	274	0.36147757255936674	G	8.454	0.853663	0.17106	0.300953	0.346977	ENSG00000156414	ENST00000557332	.	.	.	5.71	3.9	0.45041	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.38200	-0.9672	3	.	.	.	.	7.929	0.29891	0.25:0.0:0.75:0.0	rs10143389;rs58504835;rs10143389	.	.	.	R	93	.	.	G	+	1	0	TDRD9	103522393	1.000000	0.71417	0.986000	0.45419	0.988000	0.76386	1.987000	0.40687	0.772000	0.33382	0.650000	0.86243	GGA	G|0.674;A|0.326	0.326	strong		0.348	TDRD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328325.3	NM_153046	
MFGE8	4240	hgsc.bcm.edu	37	15	89450587	89450587	+	Missense_Mutation	SNP	G	G	T	rs1878326	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:89450587G>T	ENST00000566497.1	-	3	287	c.226C>A	c.(226-228)Ctg>Atg	p.L76M	MFGE8_ENST00000559997.1_5'UTR|MFGE8_ENST00000268150.8_Missense_Mutation_p.L76M|MFGE8_ENST00000539437.1_Missense_Mutation_p.L68M|MFGE8_ENST00000542878.1_Missense_Mutation_p.L32M|MFGE8_ENST00000268151.7_Missense_Mutation_p.L76M			Q08431	MFGM_HUMAN	milk fat globule-EGF factor 8 protein	76	F5/8 type C 1. {ECO:0000255|PROSITE- ProRule:PRU00081}.		M -> L (in dbSNP:rs1878326). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:16572171, ECO:0000269|Ref.5}.		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.L76M(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)					CCATTCTCCAGGCCCAGTGGC	0.612													T|||	3197	0.638379	0.8011	0.6167	5008	,	,		18586	0.4554		0.6372	False		,,,				2504	0.6237				p.L76M		Atlas-SNP	.											MFGE8,NS,carcinoma,0,2	MFGE8	60	2	1	Substitution - Missense(1)	stomach(1)	c.C226A						PASS	.	T	MET/LEU,MET/LEU	3453,947	359.9+/-315.0	1351,751,98	107.0	78.0	88.0		226,226	4.2	1.0	15	dbSNP_92	88	5609,2989	463.0+/-365.8	1812,1985,502	yes	missense,missense	MFGE8	NM_001114614.1,NM_005928.2	15,15	3163,2736,600	TT,TG,GG		34.7639,21.5227,30.2816	benign,benign	76/336,76/388	89450587	9062,3936	2200	4299	6499	SO:0001583	missense	4240	exon3			TCTCCAGGCCCAG	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.226C>A	15.37:g.89450587G>T	ENSP00000456281:p.Leu76Met	Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	203	202	0.995074	NM_001114614	B2R6M7|Q53FU9|Q7Z3D2|Q9BTL9	Missense_Mutation	SNP	ENST00000566497.1	37	CCDS10347.1	1336	0.6117216117216118	376	0.7642276422764228	220	0.6077348066298343	260	0.45454545454545453	480	0.633245382585752	T	0.010	-1.772135	0.00645	0.784773	0.652361	ENSG00000140545	ENST00000268150;ENST00000268151;ENST00000539437;ENST00000542878	D;D;D;D	0.97209	-4.29;-4.29;-4.29;-1.62	5.32	4.18	0.49190	.	0.036199	0.85682	N	0.000000	T	0.00012	0.0000	.	.	.	0.50813	P	1.0100000000001774E-4	B;B	0.14438	0.01;0.0	B;B	0.16722	0.016;0.005	T	0.46498	-0.9187	8	0.02654	T	1	-48.0241	8.268	0.31827	0.1319:0.0:0.1384:0.7297	rs1878326;rs11557314;rs17202746;rs17856089;rs60806175;rs1878326	32;68	F5GZN3;F5H7N9	.;.	M	76;76;68;32	ENSP00000268150:L76M;ENSP00000268151:L76M;ENSP00000442386:L68M;ENSP00000444332:L32M	ENSP00000268150:L76M	L	-	1	2	MFGE8	87251591	1.000000	0.71417	1.000000	0.80357	0.029000	0.11900	2.742000	0.47434	0.319000	0.23209	-0.525000	0.04345	CTG	G|0.336;T|0.658	0.658	strong		0.612	MFGE8-015	NOVEL	alternative_3_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000432804.1	NM_005928	
ERO1LB	56605	hgsc.bcm.edu	37	1	236381825	236381825	+	Missense_Mutation	SNP	G	G	C	rs1055851	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	266	0	0		WXS	Illumina HiSeq	Phase_I	177	177	1	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	
GLYATL3	389396	hgsc.bcm.edu	37	6	49494241	49494241	+	Missense_Mutation	SNP	A	A	G	rs9367359	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:49494241A>G	ENST00000371197.4	+	6	594	c.481A>G	c.(481-483)Aat>Gat	p.N161D		NM_001010904.1	NP_001010904.1	Q5SZD4	GLYL3_HUMAN	glycine-N-acyltransferase-like 3	161						mitochondrion (GO:0005739)	glycine N-acyltransferase activity (GO:0047961)			NS(1)|endometrium(1)|kidney(3)|lung(1)|skin(3)|stomach(2)	11						GAGTGTTGCCAATGCGGATCT	0.507													G|||	2439	0.487021	0.407	0.3674	5008	,	,		19001	0.4573		0.6322	False		,,,				2504	0.5613				p.N161D		Atlas-SNP	.											.	GLYATL3	19	.	0			c.A481G						PASS	.	G	ASP/ASN	625,759		132,361,199	86.0	75.0	78.0		481	6.1	0.6	6	dbSNP_119	78	2050,1132		660,730,201	yes	missense	GLYATL3	NM_001010904.1	23	792,1091,400	GG,GA,AA		35.5751,45.159,41.4148	benign	161/289	49494241	2675,1891	692	1591	2283	SO:0001583	missense	389396	exon6			GTTGCCAATGCGG		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.481A>G	6.37:g.49494241A>G	ENSP00000360240:p.Asn161Asp	Somatic	211	0	0		WXS	Illumina HiSeq	Phase_I	166	75	0.451807	NM_001010904		Missense_Mutation	SNP	ENST00000371197.4	37	CCDS47440.1	1054	0.4826007326007326	198	0.4024390243902439	147	0.40607734806629836	222	0.3881118881118881	487	0.6424802110817942	G	0.274	-0.991050	0.02162	0.45159	0.644249	ENSG00000203972	ENST00000371197	T	0.11712	2.75	6.06	6.06	0.98353	Acyl-CoA N-acyltransferase (2);Glycine N-acyltransferase, N-terminal (1);	0.157276	0.56097	N	0.000033	T	0.00936	0.0031	N	0.00483	-1.445	0.53005	P	3.399999999997849E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.45775	-0.9238	9	0.11794	T	0.64	-1.7093	11.5712	0.50834	0.0814:0.0:0.9186:0.0	rs9367359;rs52799300;rs9367359	161	Q5SZD4	GLYL3_HUMAN	D	161	ENSP00000360240:N161D	ENSP00000360240:N161D	N	+	1	0	GLYATL3	49602200	0.992000	0.36948	0.589000	0.28718	0.003000	0.03518	3.040000	0.49799	1.593000	0.50029	-0.119000	0.15052	AAT	A|0.510;G|0.490	0.490	strong		0.507	GLYATL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040866.3	NM_001010904	
SYNE1	23345	hgsc.bcm.edu	37	6	152772264	152772264	+	Missense_Mutation	SNP	A	A	G	rs214976	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:152772264A>G	ENST00000367255.5	-	26	3705	c.3104T>C	c.(3103-3105)gTa>gCa	p.V1035A	SYNE1_ENST00000367253.4_Missense_Mutation_p.V1035A|SYNE1_ENST00000367248.3_Missense_Mutation_p.V1025A|SYNE1_ENST00000265368.4_Missense_Mutation_p.V1035A|SYNE1_ENST00000413186.2_Missense_Mutation_p.V1035A|SYNE1_ENST00000448038.1_Missense_Mutation_p.V1042A|SYNE1_ENST00000423061.1_Missense_Mutation_p.V1042A|SYNE1_ENST00000341594.5_Missense_Mutation_p.V1101A	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	1035			V -> A (in dbSNP:rs214976).		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)		GCATTCTTCTACAGAGGCTAA	0.453										HNSCC(10;0.0054)			a|||	3041	0.607228	0.8086	0.3732	5008	,	,		17297	0.749		0.4473	False		,,,				2504	0.5194				p.V1042A		Atlas-SNP	.											.	SYNE1	3227	.	0			c.T3125C						PASS	.		ALA/VAL,ALA/VAL	3232,1174	711.6+/-408.0	1188,856,159	177.0	159.0	165.0		3125,3104	5.8	0.0	6	dbSNP_79	165	3694,4906	529.1+/-381.5	807,2080,1413	yes	missense,missense	SYNE1	NM_033071.3,NM_182961.3	64,64	1995,2936,1572	GG,GA,AA		42.9535,26.6455,46.7477	possibly-damaging,possibly-damaging	1042/8750,1035/8798	152772264	6926,6080	2203	4300	6503	SO:0001583	missense	23345	exon26			TCTTCTACAGAGG	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.3104T>C	6.37:g.152772264A>G	ENSP00000356224:p.Val1035Ala	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	79	79	1	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	1279	0.5856227106227107	380	0.7723577235772358	143	0.39502762430939226	425	0.743006993006993	331	0.4366754617414248	A	19.02	3.745785	0.69418	0.733545	0.429535	ENSG00000131018	ENST00000367255;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594;ENST00000367253;ENST00000367248;ENST00000413186	T;T;T;T;T;D;D;D	0.88896	0.55;0.54;0.46;0.54;0.63;-2.29;-2.44;-2.43	5.84	5.84	0.93424	.	0.636632	0.14357	N	0.324693	D	0.83917	0.5358	M	0.63843	1.955	0.09310	P	1.0	B;B;B;B;B;P	0.35033	0.033;0.009;0.11;0.18;0.009;0.481	B;B;B;B;B;B	0.33454	0.045;0.011;0.157;0.157;0.011;0.164	D	0.85312	0.1079	9	0.54805	T	0.06	.	16.5601	0.84551	1.0:0.0:0.0:0.0	rs214976;rs530857;rs17463800;rs58629854;rs214976	1018;1035;1025;1035;1035;1042	B3W695;Q8NF91;F5GXQ8;Q8NF91-6;E7EQI5;Q8NF91-4	.;SYNE1_HUMAN;.;.;.;.	A	1035;1042;1035;1042;1101;1035;1025;1035	ENSP00000356224:V1035A;ENSP00000396024:V1042A;ENSP00000265368:V1035A;ENSP00000390975:V1042A;ENSP00000341887:V1101A;ENSP00000356222:V1035A;ENSP00000356217:V1025A;ENSP00000414510:V1035A	ENSP00000265368:V1035A	V	-	2	0	SYNE1	152813957	0.985000	0.35326	0.005000	0.12908	0.991000	0.79684	8.644000	0.91044	2.367000	0.80283	0.529000	0.55759	GTA	G|0.567;N|0.000	0.567	strong		0.453	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961	
ZNF880	400713	hgsc.bcm.edu	37	19	52888245	52888245	+	Missense_Mutation	SNP	A	A	G	rs55748277	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:52888245A>G	ENST00000422689.2	+	4	1427	c.1412A>G	c.(1411-1413)aAg>aGg	p.K471R		NM_001145434.1	NP_001138906.1	Q6PDB4	ZN880_HUMAN	zinc finger protein 880	471					regulation of transcription, DNA-templated (GO:0006355)	intracellular (GO:0005622)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(2)|skin(1)	10						GAATGTGGCAAGGACTTCACT	0.388													A|||	2061	0.411542	0.3555	0.3919	5008	,	,		22737	0.3492		0.4205	False		,,,				2504	0.5562				p.K471R		Atlas-SNP	.											.	ZNF880	45	.	0			c.A1412G						PASS	.	A	ARG/LYS	529,855		102,325,265	83.0	75.0	77.0		1412	-0.5	0.0	19	dbSNP_129	77	1216,1966		222,772,597	no	missense	ZNF880	NM_001145434.1	26	324,1097,862	GG,GA,AA		38.215,38.2225,38.2173	possibly-damaging	471/578	52888245	1745,2821	692	1591	2283	SO:0001583	missense	400713	exon4			GTGGCAAGGACTT	BC058819	CCDS46164.1	19q13.41	2013-01-08			ENSG00000221923	ENSG00000221923		"""Zinc fingers, C2H2-type"", ""-"""	37249	protein-coding gene	gene with protein product							Standard	NM_001145434		Approved		uc002pzc.3	Q6PDB4	OTTHUMG00000167972	ENST00000422689.2:c.1412A>G	19.37:g.52888245A>G	ENSP00000406318:p.Lys471Arg	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	32	32	1	NM_001145434	B4DNA6	Missense_Mutation	SNP	ENST00000422689.2	37	CCDS46164.1	802	0.36721611721611724	164	0.3333333333333333	148	0.4088397790055249	179	0.3129370629370629	311	0.4102902374670185	A	13.64	2.296527	0.40594	0.382225	0.38215	ENSG00000221923	ENST00000422689	T	0.26223	1.75	2.03	-0.46	0.12175	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	L	0.35854	1.095	0.58432	P	9.99999999995449E-6	D	0.62365	0.991	D	0.63703	0.917	T	0.43750	-0.9372	7	.	.	.	.	6.4253	0.21766	0.7772:0.0:0.2228:0.0	rs55748277;rs62108357	471	Q6PDB4	ZN880_HUMAN	R	471	ENSP00000406318:K471R	.	K	+	2	0	ZNF880	57580057	0.060000	0.20803	0.007000	0.13788	0.010000	0.07245	1.664000	0.37439	-0.387000	0.07809	0.450000	0.29827	AAG	A|0.631;G|0.369	0.369	strong		0.388	ZNF880-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397374.1	NM_001145434	
WNK1	65125	hgsc.bcm.edu	37	12	993930	993930	+	Silent	SNP	C	C	T	rs7300444	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:993930C>T	ENST00000315939.6	+	19	4603	c.3960C>T	c.(3958-3960)aaC>aaT	p.N1320N	WNK1_ENST00000530271.2_Silent_p.N1818N|WNK1_ENST00000537687.1_Silent_p.N1580N|WNK1_ENST00000535572.1_Silent_p.N1073N|WNK1_ENST00000340908.4_Silent_p.N913N	NM_018979.3	NP_061852.3	Q9H4A3	WNK1_HUMAN	WNK lysine deficient protein kinase 1	1320					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)			AAGGACCCAACACAGCACCTC	0.483													T|||	1998	0.398962	0.2685	0.428	5008	,	,		20670	0.5377		0.4404	False		,,,				2504	0.3691				p.N1580N	Colon(19;451 567 6672 12618 28860)	Atlas-SNP	.											.	WNK1	403	.	0			c.C4740T						PASS	.	T	,,,	1307,3099	698.6+/-406.4	187,933,1083	130.0	113.0	119.0		4740,3219,3960,4716	-1.8	0.1	12	dbSNP_116	119	3787,4813	614.3+/-396.2	847,2093,1360	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	WNK1	NM_001184985.1,NM_014823.2,NM_018979.3,NM_213655.4	,,,	1034,3026,2443	TT,TC,CC		44.0349,29.6641,39.1665	,,,	1580/2643,1073/2135,1320/2383,1572/2635	993930	5094,7912	2203	4300	6503	SO:0001819	synonymous_variant	65125	exon19			ACCCAACACAGCA	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.3960C>T	12.37:g.993930C>T		Somatic	289	1	0.00346021		WXS	Illumina HiSeq	Phase_I	278	135	0.485611	NM_001184985	A1L4B0|C5HTZ5|C5HTZ6|C5HTZ7|H6WZW3|O15052|P54963|Q4VBX9|Q6IFS5|Q86WL5|Q8N673|Q96CZ6|Q9P1S9	Silent	SNP	ENST00000315939.6	37	CCDS8506.1																																																																																			C|0.597;T|0.403	0.403	strong		0.483	WNK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206683.1	NM_018979	
TMEM82	388595	hgsc.bcm.edu	37	1	16070912	16070912	+	Silent	SNP	T	T	C	rs7525747	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:16070912T>C	ENST00000375782.1	+	4	732	c.594T>C	c.(592-594)caT>caC	p.H198H	RP11-169K16.4_ENST00000418525.1_RNA|TMEM82_ENST00000465575.1_3'UTR	NM_001013641.1	NP_001013663.1	A0PJX8	TMM82_HUMAN	transmembrane protein 82	198	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)		CCCATGCACATGGCCTCCCCC	0.692													C|||	566	0.113019	0.2723	0.0937	5008	,	,		17642	0.0099		0.1034	False		,,,				2504	0.0276				p.H198H		Atlas-SNP	.											.	TMEM82	30	.	0			c.T594C						PASS	.	C		1098,3286		153,792,1247	22.0	19.0	20.0		594	1.3	0.0	1	dbSNP_116	20	683,7905		30,623,3641	no	coding-synonymous	TMEM82	NM_001013641.1		183,1415,4888	CC,CT,TT		7.953,25.0456,13.7296		198/344	16070912	1781,11191	2192	4294	6486	SO:0001819	synonymous_variant	388595	exon4			TGCACATGGCCTC		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.594T>C	1.37:g.16070912T>C		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	34	16	0.470588	NM_001013641	B2RP27|Q5VVD4	Silent	SNP	ENST00000375782.1	37	CCDS30608.1																																																																																			T|0.848;C|0.152	0.152	strong		0.692	TMEM82-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008471.2	NM_001013641	
SART1	9092	hgsc.bcm.edu	37	11	65735174	65735174	+	Missense_Mutation	SNP	G	G	C	rs660118	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:65735174G>C	ENST00000312397.5	+	12	1546	c.1454G>C	c.(1453-1455)gGg>gCg	p.G485A		NM_005146.4	NP_005137.1	O43290	SNUT1_HUMAN	squamous cell carcinoma antigen recognized by T cells	485			G -> A (in dbSNP:rs660118). {ECO:0000269|Ref.4}.		cell cycle arrest (GO:0007050)|intrinsic apoptotic signaling pathway (GO:0097193)|mRNA splicing, via spliceosome (GO:0000398)|positive regulation of cytotoxic T cell differentiation (GO:0045585)|spliceosomal snRNP assembly (GO:0000387)	Cajal body (GO:0015030)|catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(1)|large_intestine(1)|lung(5)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	11						CCACCGCCGGGGTCCCCGCAG	0.677													G|||	1834	0.366214	0.0393	0.5793	5008	,	,		13594	0.5218		0.4404	False		,,,				2504	0.4202				p.G485A		Atlas-SNP	.											.	SART1	41	.	0			c.G1454C	GRCh37	CM024558	SART1	M	rs660118	PASS	.	G	ALA/GLY	442,3874		37,368,1753	11.0	12.0	12.0		1454	4.2	0.8	11	dbSNP_83	12	3506,4952		754,1998,1477	no	missense	SART1	NM_005146.4	60	791,2366,3230	CC,CG,GG		41.4519,10.241,30.9065	possibly-damaging	485/801	65735174	3948,8826	2158	4229	6387	SO:0001583	missense	9092	exon12			CGCCGGGGTCCCC	AB006198	CCDS31611.1	11q13.1	2009-01-06	2006-12-07		ENSG00000175467	ENSG00000175467			10538	protein-coding gene	gene with protein product	"""small nuclear ribonucleoprotein 110kDa (U4/U6.U5)"""	605941	"""squamous cell carcinoma antigen recognised by T cells"""			9449708	Standard	NM_005146		Approved	Ara1, Snu66, SNRNP110	uc001ogl.3	O43290	OTTHUMG00000166771	ENST00000312397.5:c.1454G>C	11.37:g.65735174G>C	ENSP00000310448:p.Gly485Ala	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	66	65	0.984848	NM_005146	A6NDN1|Q53GB5	Missense_Mutation	SNP	ENST00000312397.5	37	CCDS31611.1	882	0.40384615384615385	30	0.06097560975609756	194	0.5359116022099447	323	0.5646853146853147	335	0.4419525065963061	G	6.367	0.435751	0.12104	0.10241	0.414519	ENSG00000175467	ENST00000312397;ENST00000542816	T	0.21543	2.0	5.12	4.17	0.49024	.	0.349123	0.25532	N	0.030034	T	0.00012	0.0000	L	0.46157	1.445	0.24437	P	0.99454935	B	0.30179	0.271	B	0.24541	0.054	T	0.39901	-0.9591	9	0.87932	D	0	-48.9249	11.2382	0.48953	0.0:0.1857:0.8143:0.0	rs660118;rs61398889;rs660118	485	O43290	SNUT1_HUMAN	A	485;327	ENSP00000310448:G485A	ENSP00000310448:G485A	G	+	2	0	SART1	65491750	0.633000	0.27181	0.837000	0.33122	0.452000	0.32318	-0.229000	0.09098	1.090000	0.41315	0.491000	0.48974	GGG	G|0.591;C|0.409	0.409	strong		0.677	SART1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391409.1		
SPATA17	128153	hgsc.bcm.edu	37	1	217856626	217856626	+	Silent	SNP	G	G	A	rs12068167	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:217856626G>A	ENST00000366933.4	+	5	373	c.318G>A	c.(316-318)agG>agA	p.R106R		NM_138796.2	NP_620151.1	Q96L03	SPT17_HUMAN	spermatogenesis associated 17	106	IQ 3. {ECO:0000255|PROSITE- ProRule:PRU00116}.					cytoplasm (GO:0005737)				endometrium(1)|kidney(1)|large_intestine(9)|lung(6)|pancreas(2)|prostate(1)|urinary_tract(1)	21				OV - Ovarian serous cystadenocarcinoma(81;0.0516)|all cancers(67;0.0891)|GBM - Glioblastoma multiforme(131;0.117)		GAGGCTATAGGGTTCGGAAGT	0.313													G|||	877	0.17512	0.3011	0.1268	5008	,	,		11797	0.0962		0.173	False		,,,				2504	0.1227				p.R106R		Atlas-SNP	.											.	SPATA17	59	.	0			c.G318A						PASS	.	G		1198,3200	373.4+/-320.8	166,866,1167	91.0	109.0	103.0		318	3.5	0.9	1	dbSNP_120	103	1365,7233	258.6+/-282.2	110,1145,3044	no	coding-synonymous	SPATA17	NM_138796.2		276,2011,4211	AA,AG,GG		15.8758,27.2397,19.7215		106/362	217856626	2563,10433	2199	4299	6498	SO:0001819	synonymous_variant	128153	exon5			CTATAGGGTTCGG	AK098591	CCDS1519.1	1q41	2008-02-05			ENSG00000162814	ENSG00000162814			25184	protein-coding gene	gene with protein product	"""IQ motif containing H"""	611032				16395525	Standard	NM_138796		Approved	IQCH	uc001hlh.1	Q96L03	OTTHUMG00000037875	ENST00000366933.4:c.318G>A	1.37:g.217856626G>A		Somatic	187	0	0		WXS	Illumina HiSeq	Phase_I	169	68	0.402367	NM_138796	A5D6N2	Silent	SNP	ENST00000366933.4	37	CCDS1519.1																																																																																			G|0.826;A|0.174	0.174	strong		0.313	SPATA17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092433.2	NM_138796	
STXBP2	6813	hgsc.bcm.edu	37	19	7712277	7712277	+	Missense_Mutation	SNP	A	A	G	rs6791	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:7712277A>G	ENST00000221283.5	+	18	1607	c.1576A>G	c.(1576-1578)Ata>Gta	p.I526V	STXBP2_ENST00000602355.1_Missense_Mutation_p.I61V|STXBP2_ENST00000414284.2_Missense_Mutation_p.I523V|STXBP2_ENST00000441779.2_Missense_Mutation_p.I537V	NM_006949.2	NP_008880.2	Q15833	STXB2_HUMAN	syntaxin binding protein 2	526			I -> V (in dbSNP:rs6791). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:8921365}.		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						CAAGGCTGGCATAGAAGCCCG	0.682													a|||	3536	0.70607	0.8071	0.6859	5008	,	,		13311	0.8185		0.664	False		,,,				2504	0.5112				p.I537V		Atlas-SNP	.											STXBP2,NS,carcinoma,0,1	STXBP2	63	1	0			c.A1609G						PASS	.	G	VAL/ILE,VAL/ILE	3404,990		1328,748,121	23.0	31.0	28.0		1567,1576	-0.8	0.0	19	dbSNP_52	28	5251,3325		1620,2011,657	yes	missense,missense	STXBP2	NM_001127396.1,NM_006949.2	29,29	2948,2759,778	GG,GA,AA		38.771,22.5307,33.2691	benign,benign	523/591,526/594	7712277	8655,4315	2197	4288	6485	SO:0001583	missense	6813	exon18			GCTGGCATAGAAG	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.1576A>G	19.37:g.7712277A>G	ENSP00000221283:p.Ile526Val	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	36	35	0.972222	NM_001272034	B4E175|E7EQD5|Q9BU65	Missense_Mutation	SNP	ENST00000221283.5	37	CCDS12181.1	1608	0.7362637362637363	387	0.7865853658536586	237	0.6546961325966851	479	0.8374125874125874	505	0.6662269129287599	a	0.138	-1.105234	0.01828	0.774693	0.61229	ENSG00000076944	ENST00000221283;ENST00000414284;ENST00000441779;ENST00000543902	T;T;T	0.76060	-0.99;-0.99;-0.99	5.26	-0.767	0.11016	.	0.726199	0.13129	N	0.411628	T	0.00012	0.0000	N	0.00483	-1.445	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	0.32188	-0.9916	9	0.10636	T	0.68	5.3107	6.8461	0.23988	0.2883:0.0:0.6014:0.1103	rs6791;rs710952;rs1051801;rs1674031;rs3192176;rs17258757;rs56612527;rs56879654;rs6791	537;492;523;526	E7EQD5;B4DY46;Q15833-2;Q15833	.;.;.;STXB2_HUMAN	V	526;523;537;526	ENSP00000221283:I526V;ENSP00000409471:I523V;ENSP00000413606:I537V	ENSP00000221283:I526V	I	+	1	0	STXBP2	7618277	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.176000	0.09811	-0.523000	0.06409	-2.371000	0.00235	ATA	A|0.305;C|0.008	.	strong		0.682	STXBP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460963.1	NM_006949	
RGMA	56963	hgsc.bcm.edu	37	15	93588264	93588264	+	Silent	SNP	G	G	C	rs4299103	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:93588264G>C	ENST00000329082.7	-	4	1588	c.1317C>G	c.(1315-1317)ctC>ctG	p.L439L	RGMA_ENST00000425933.2_Silent_p.L423L|RGMA_ENST00000556658.1_Silent_p.L330L|RGMA_ENST00000543599.1_Silent_p.L423L|RGMA_ENST00000542321.2_Silent_p.L423L|RGMA_ENST00000557420.1_3'UTR|RGMA_ENST00000557301.1_Silent_p.L447L|RGMA_ENST00000538818.1_Silent_p.L330L	NM_020211.2	NP_064596	Q96B86	RGMA_HUMAN	repulsive guidance molecule family member a	439					axon guidance (GO:0007411)|BMP signaling pathway (GO:0030509)|neural tube closure (GO:0001843)|regulation of BMP signaling pathway (GO:0030510)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	coreceptor activity (GO:0015026)			breast(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(2)|prostate(1)	9	Lung NSC(78;0.0542)|all_lung(78;0.0786)		BRCA - Breast invasive adenocarcinoma(143;0.0312)|OV - Ovarian serous cystadenocarcinoma(32;0.108)			GGAGCGGGACGAGGGCGCCCA	0.692													G|||	2379	0.47504	0.3313	0.4856	5008	,	,		13715	0.7073		0.4215	False		,,,				2504	0.4775				p.L447L		Atlas-SNP	.											.	RGMA	49	.	0			c.C1341G						PASS	.	G	,,,,,	1354,2486		258,838,824	14.0	15.0	15.0		1341,1269,1269,1269,1269,1317	-2.0	0.0	15	dbSNP_111	15	3538,4650		771,1996,1327	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	RGMA	NM_001166283.1,NM_001166286.1,NM_001166287.1,NM_001166288.1,NM_001166289.1,NM_020211.2	,,,,,	1029,2834,2151	CC,CG,GG		43.2096,35.2604,40.6718	,,,,,	447/459,423/435,423/435,423/435,423/435,439/451	93588264	4892,7136	1920	4094	6014	SO:0001819	synonymous_variant	56963	exon4			CGGGACGAGGGCG	AL390083	CCDS45357.1, CCDS53973.1, CCDS53974.1	15q26.1	2013-11-06	2013-11-06			ENSG00000182175			30308	protein-coding gene	gene with protein product		607362	"""RGM domain family, member A"""			15975920	Standard	NM_020211		Approved	RGM, RGMa	uc010urc.2	Q96B86		ENST00000329082.7:c.1317C>G	15.37:g.93588264G>C		Somatic	18	0	0		WXS	Illumina HiSeq	Phase_I	30	14	0.466667	NM_001166283	B2RTW1|B7Z5S8|F5GXQ7|F5GZU6|G3V518|Q0JV97|Q8NC80|Q9H0E6|Q9NPM3	Silent	SNP	ENST00000329082.7	37	CCDS45357.1																																																																																			G|0.523;C|0.477	0.477	strong		0.692	RGMA-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000415091.1	NM_020211	
DCC	1630	hgsc.bcm.edu	37	18	49867246	49867246	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:49867246C>T	ENST00000442544.2	+	1	705	c.89C>T	c.(88-90)aCc>aTc	p.T30I	RP11-25O3.1_ENST00000582700.1_lincRNA	NM_005215.3	NP_005206.2	P43146	DCC_HUMAN	DCC netrin 1 receptor	30	Ig-like C2-type 1.				anterior/posterior axon guidance (GO:0033564)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|axonogenesis (GO:0007409)|dorsal/ventral axon guidance (GO:0033563)|negative regulation of collateral sprouting (GO:0048671)|negative regulation of dendrite development (GO:2000171)|negative regulation of neuron projection development (GO:0010977)|neuron migration (GO:0001764)|positive regulation of apoptotic process (GO:0043065)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of neuron projection development (GO:0010976)|regulation of apoptotic process (GO:0042981)|response to amphetamine (GO:0001975)|spinal cord ventral commissure morphogenesis (GO:0021965)	axon (GO:0030424)|cytosol (GO:0005829)|growth cone membrane (GO:0032584)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	netrin receptor activity (GO:0005042)|transcription coactivator activity (GO:0003713)|transmembrane signaling receptor activity (GO:0004888)			NS(3)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(23)|liver(1)|lung(56)|ovary(7)|pancreas(3)|prostate(2)|skin(16)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(6)	148		all_cancers(7;0.11)|all_epithelial(6;0.00126)		Colorectal(16;0.0251)|COAD - Colon adenocarcinoma(17;0.0942)		CTTCAAGTAACCGGTAAGTGG	0.493																																					p.T30I		Atlas-SNP	.											.	DCC	360	.	0			c.C89T						PASS	.						180.0	160.0	167.0					18																	49867246		2203	4300	6503	SO:0001583	missense	1630	exon1			AAGTAACCGGTAA	X76132	CCDS11952.1	18q21.1	2014-06-20	2014-06-20		ENSG00000187323	ENSG00000187323		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	2701	protein-coding gene	gene with protein product	"""immunoglobulin superfamily, DCC subclass, member 1"""	120470	"""deleted in colorectal carcinoma"""			2294591, 24400119	Standard	NM_005215		Approved	IGDCC1, NTN1R1	uc002lfe.2	P43146	OTTHUMG00000132698	ENST00000442544.2:c.89C>T	18.37:g.49867246C>T	ENSP00000389140:p.Thr30Ile	Somatic	247	0	0		WXS	Illumina HiSeq	Phase_I	190	37	0.194737	NM_005215		Missense_Mutation	SNP	ENST00000442544.2	37	CCDS11952.1	.	.	.	.	.	.	.	.	.	.	C	12.53	1.964768	0.34659	.	.	ENSG00000187323	ENST00000442544	T	0.50548	0.74	5.73	5.73	0.89815	Immunoglobulin-like (1);	1.199860	0.05969	N	0.642001	T	0.42630	0.1211	N	0.22421	0.69	0.80722	D	1	B	0.06786	0.001	B	0.10450	0.005	T	0.03910	-1.0993	10	0.22706	T	0.39	.	18.6711	0.91512	0.0:1.0:0.0:0.0	.	30	P43146	DCC_HUMAN	I	30	ENSP00000389140:T30I	ENSP00000389140:T30I	T	+	2	0	DCC	48121244	0.992000	0.36948	1.000000	0.80357	0.965000	0.64279	2.219000	0.42899	2.709000	0.92574	0.561000	0.74099	ACC	.	.	none		0.493	DCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255996.3	NM_005215	
SLC35B1	10237	hgsc.bcm.edu	37	17	47783663	47783663	+	Missense_Mutation	SNP	C	C	T	rs1135034	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:47783663C>T	ENST00000240333.6	-	3	363	c.242G>A	c.(241-243)cGt>cAt	p.R81H	SLC35B1_ENST00000415270.2_Missense_Mutation_p.R118H|RP11-613C6.2_ENST00000512720.1_RNA			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	97	0	0		WXS	Illumina HiSeq	Phase_I	84	36	0.428571	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	
UNC5C	8633	hgsc.bcm.edu	37	4	96166270	96166270	+	Silent	SNP	C	C	T	rs35120448	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:96166270C>T	ENST00000453304.1	-	6	1149	c.801G>A	c.(799-801)acG>acA	p.T267T	UNC5C_ENST00000506749.1_Silent_p.T267T	NM_003728.3	NP_003719.3	O95185	UNC5C_HUMAN	unc-5 homolog C (C. elegans)	267	TSP type-1 1. {ECO:0000255|PROSITE- ProRule:PRU00210}.				anterior/posterior axon guidance (GO:0033564)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|brain development (GO:0007420)|positive regulation of apoptotic process (GO:0043065)|regulation of cell migration (GO:0030334)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	netrin receptor activity (GO:0005042)			NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(14)|lung(25)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	55		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;8.72e-10)		CAGACCACTCCGTCCAGGTGG	0.512													C|||	116	0.0231629	0.0159	0.0346	5008	,	,		17093	0.0		0.0537	False		,,,				2504	0.0174				p.T267T		Atlas-SNP	.											UNC5C,NS,carcinoma,-1,1	UNC5C	141	1	0			c.G801A						PASS	.	C		97,4309	78.3+/-116.7	3,91,2109	64.0	55.0	58.0		801	-5.9	1.0	4	dbSNP_126	58	444,8156	133.1+/-190.7	8,428,3864	no	coding-synonymous	UNC5C	NM_003728.3		11,519,5973	TT,TC,CC		5.1628,2.2015,4.1596		267/932	96166270	541,12465	2203	4300	6503	SO:0001819	synonymous_variant	8633	exon6			CCACTCCGTCCAG	AF055634	CCDS3643.1	4q21-q23	2013-01-11	2001-11-28		ENSG00000182168	ENSG00000182168		"""Immunoglobulin superfamily / I-set domain containing"""	12569	protein-coding gene	gene with protein product		603610	"""unc5 (C.elegans homolog) c"""			9126742, 9782087	Standard	NM_003728		Approved		uc003hto.3	O95185	OTTHUMG00000130989	ENST00000453304.1:c.801G>A	4.37:g.96166270C>T		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	82	41	0.5	NM_003728	Q8IUT0	Silent	SNP	ENST00000453304.1	37	CCDS3643.1																																																																																			C|0.961;T|0.039	0.039	strong		0.512	UNC5C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253607.1	NM_003728	
TTN	7273	hgsc.bcm.edu	37	2	179396573	179396573	+	Silent	SNP	T	T	G	rs56375087	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:179396573T>G	ENST00000591111.1	-	308	100070	c.99846A>C	c.(99844-99846)acA>acC	p.T33282T	TTN-AS1_ENST00000585358.1_RNA|TTN-AS1_ENST00000588804.1_RNA|TTN_ENST00000359218.5_Silent_p.T25983T|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000589391.1_RNA|TTN-AS1_ENST00000588244.1_RNA|TTN-AS1_ENST00000585487.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000589355.1_RNA|TTN_ENST00000342992.6_Silent_p.T32355T|TTN-AS1_ENST00000592182.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000588716.1_RNA|TTN-AS1_ENST00000442329.2_RNA|TTN_ENST00000460472.2_Silent_p.T25858T|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592836.1_RNA|TTN-AS1_ENST00000588257.1_RNA|TTN-AS1_ENST00000589842.1_RNA|TTN-AS1_ENST00000431259.2_RNA|TTN-AS1_ENST00000589434.1_RNA|TTN_ENST00000589042.1_Silent_p.T34923T|TTN-AS1_ENST00000591867.1_RNA|TTN-AS1_ENST00000604571.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000450692.2_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN_ENST00000342175.6_Silent_p.T26050T|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000591466.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000590040.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000587568.1_RNA|TTN-AS1_ENST00000587944.1_RNA|TTN-AS1_ENST00000585625.1_RNA			Q8WZ42	TITIN_HUMAN	titin	33282					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)			TCCTTTCTGATGTCTTCTGAG	0.458													T|||	19	0.00379393	0.0	0.0043	5008	,	,		21340	0.0		0.0159	False		,,,				2504	0.0				p.T34923T		Atlas-SNP	.											.	TTN	18412	.	0			c.A104769C						PASS	.	T	,,,	2,3864		0,2,1931	51.0	49.0	50.0		77574,97065,77949,78150	-2.6	1.0	2	dbSNP_129	50	56,8214		1,54,4080	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	,,,	1,56,6011	GG,GT,TT		0.6771,0.0517,0.4779	,,,	25858/26927,32355/33424,25983/27052,26050/27119	179396573	58,12078	1933	4135	6068	SO:0001819	synonymous_variant	7273	exon358			TTCTGATGTCTTC	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.99846A>C	2.37:g.179396573T>G		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	126	57	0.452381	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																																																																																				T|0.993;G|0.007	0.007	strong		0.458	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
ACSM4	341392	hgsc.bcm.edu	37	12	7463241	7463241	+	Silent	SNP	A	A	T	rs7968241	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	88	0	0		WXS	Illumina HiSeq	Phase_I	67	29	0.432836	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	
IL31	386653	hgsc.bcm.edu	37	12	122657271	122657271	+	Silent	SNP	G	G	C	rs7974857	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:122657271G>C	ENST00000377035.1	-	3	209	c.183C>G	c.(181-183)ggC>ggG	p.G61G		NM_001014336.1	NP_001014358.1	Q6EBC2	IL31_HUMAN	interleukin 31	61					immune system process (GO:0002376)	extracellular space (GO:0005615)				central_nervous_system(2)|kidney(1)|large_intestine(4)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	13	all_neural(191;0.0837)|Medulloblastoma(191;0.163)	Lung NSC(355;6.93e-05)|Breast(359;0.0544)		OV - Ovarian serous cystadenocarcinoma(86;3.27e-29)|Epithelial(86;4.86e-27)|BRCA - Breast invasive adenocarcinoma(302;0.223)		ACACGAGCACGCCCTTCTCTT	0.537													C|||	748	0.149361	0.0386	0.2882	5008	,	,		18956	0.1002		0.1551	False		,,,				2504	0.2454				p.G61G		Atlas-SNP	.											.	IL31	23	.	0			c.C183G						PASS	.	C	,	283,4123	785.4+/-414.7	8,267,1928	90.0	68.0	75.0		183,	-7.8	0.0	12	dbSNP_116	75	1353,7247	740.6+/-407.1	113,1127,3060	no	coding-synonymous,intron	LRRC43,IL31	NM_001014336.1,NM_152759.4	,	121,1394,4988	CC,CG,GG		15.7326,6.4231,12.5788	,	61/165,	122657271	1636,11370	2203	4300	6503	SO:0001819	synonymous_variant	386653	exon3			GAGCACGCCCTTC	AY499343	CCDS31919.1	12q24.31	2011-07-21			ENSG00000204671	ENSG00000204671		"""Interleukins and interleukin receptors"""	19372	protein-coding gene	gene with protein product		609509				15184896	Standard	NM_001014336		Approved	IL-31	uc001ubv.3	Q6EBC2	OTTHUMG00000168916	ENST00000377035.1:c.183C>G	12.37:g.122657271G>C		Somatic	173	1	0.00578035		WXS	Illumina HiSeq	Phase_I	163	160	0.981595	NM_001014336	A2RUQ1	Silent	SNP	ENST00000377035.1	37	CCDS31919.1																																																																																			G|0.882;C|0.118	0.118	strong		0.537	IL31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401594.1	NM_001014336	
ACOT4	122970	hgsc.bcm.edu	37	14	74060508	74060508	+	Missense_Mutation	SNP	C	C	A	rs35724886	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:74060508C>A	ENST00000326303.4	+	2	814	c.560C>A	c.(559-561)gCt>gAt	p.A187D		NM_152331.3	NP_689544.3	Q8N9L9	ACOT4_HUMAN	acyl-CoA thioesterase 4	187			A -> D (in dbSNP:rs35724886).	ALAY -> DLQS (in Ref. 1; BAC04313). {ECO:0000305}.	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)		GCCACGTTGGCTCTAGCTTAT	0.498													C|||	372	0.0742812	0.0325	0.0965	5008	,	,		16972	0.003		0.2028	False		,,,				2504	0.0562				p.A187D		Atlas-SNP	.											.	ACOT4	25	.	0			c.C560A						PASS	.	C	ASP/ALA	76,4330		5,66,2132	132.0	117.0	122.0		560	5.2	1.0	14	dbSNP_126	122	837,7759		159,519,3620	yes	missense	ACOT4	NM_152331.3	126	164,585,5752	AA,AC,CC		9.7371,1.7249,7.022	probably-damaging	187/422	74060508	913,12089	2203	4298	6501	SO:0001583	missense	122970	exon2			CGTTGGCTCTAGC	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.560C>A	14.37:g.74060508C>A	ENSP00000323071:p.Ala187Asp	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	85	23	0.270588	NM_152331	Q17RF4|Q5BKT6|Q86TX0|Q86TX1|Q96N88	Missense_Mutation	SNP	ENST00000326303.4	37	CCDS9817.1	184	0.08424908424908426	16	0.032520325203252036	33	0.09116022099447514	0	0.0	135	0.17810026385224276	C	29.0	4.967766	0.92855	0.017249	0.097371	ENSG00000177465	ENST00000326303	T	0.53640	0.61	5.25	5.25	0.73442	.	0.052433	0.85682	D	0.000000	T	0.00552	0.0018	H	0.97186	3.955	0.09310	P	0.99999999708979	D	0.89917	1.0	D	0.91635	0.999	T	0.48103	-0.9064	9	0.72032	D	0.01	4.5875	18.4245	0.90605	0.0:1.0:0.0:0.0	rs35724886	187	Q8N9L9	ACOT4_HUMAN	D	187	ENSP00000323071:A187D	ENSP00000323071:A187D	A	+	2	0	ACOT4	73130261	0.998000	0.40836	0.998000	0.56505	0.988000	0.76386	3.955000	0.56715	2.442000	0.82660	0.561000	0.74099	GCT	C|0.889;A|0.111	0.111	strong		0.498	ACOT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404298.2	NM_152331	
ATP13A4	84239	hgsc.bcm.edu	37	3	193180592	193180592	+	Silent	SNP	G	G	A	rs59451116	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:193180592G>A	ENST00000342695.4	-	13	1804	c.1482C>T	c.(1480-1482)gaC>gaT	p.D494D	ATP13A4_ENST00000295548.3_Silent_p.D494D|ATP13A4_ENST00000392443.3_Silent_p.D475D	NM_032279.2	NP_115655.2	Q4VNC1	AT134_HUMAN	ATPase type 13A4	494						integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(9)|lung(27)|ovary(2)|prostate(3)|skin(11)|upper_aerodigestive_tract(2)	71	all_cancers(143;1.76e-08)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(49;2.72e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;0.000109)		GGTCCAAGCCGTCCCTTGTTA	0.488													A|||	1477	0.294928	0.2905	0.3141	5008	,	,		17830	0.3046		0.1918	False		,,,				2504	0.3834				p.D494D		Atlas-SNP	.											.	ATP13A4	154	.	0			c.C1482T						PASS	.	A		1191,3215	710.1+/-407.8	142,907,1154	111.0	99.0	103.0		1482	2.0	1.0	3	dbSNP_129	103	1706,6894	737.6+/-407.0	169,1368,2763	no	coding-synonymous	ATP13A4	NM_032279.2		311,2275,3917	AA,AG,GG		19.8372,27.0313,22.2743		494/1197	193180592	2897,10109	2203	4300	6503	SO:0001819	synonymous_variant	84239	exon13			CAAGCCGTCCCTT	AK095277	CCDS3304.2	3q29	2010-04-20			ENSG00000127249	ENSG00000127249		"""ATPases / P-type"""	25422	protein-coding gene	gene with protein product		609556				14702039, 12975309	Standard	XM_005247829		Approved	DKFZp761I1011, FLJ37958	uc003ftd.3	Q4VNC1	OTTHUMG00000074067	ENST00000342695.4:c.1482C>T	3.37:g.193180592G>A		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	92	45	0.48913	NM_032279	B7WPC7|Q6UY23|Q8N1Q9|Q9H043	Silent	SNP	ENST00000342695.4	37	CCDS3304.2																																																																																			G|0.762;A|0.238	0.238	strong		0.488	ATP13A4-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157244.4	NM_032279	
TCEB3B	51224	hgsc.bcm.edu	37	18	44560300	44560300	+	Missense_Mutation	SNP	C	C	T	rs3744863	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:44560300C>T	ENST00000332567.4	-	1	1688	c.1336G>A	c.(1336-1338)Gct>Act	p.A446T	KATNAL2_ENST00000356157.7_Intron|KATNAL2_ENST00000245121.5_Intron|KATNAL2_ENST00000592005.1_Intron	NM_016427.2	NP_057511.2	Q8IYF1	ELOA2_HUMAN	transcription elongation factor B polypeptide 3B (elongin A2)	446			A -> T (in dbSNP:rs3744863). {ECO:0000269|PubMed:10692460}.		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						GCGGAATCAGCGCCGGCCGCC	0.597													C|||	2675	0.534145	0.4349	0.6239	5008	,	,		15220	0.6448		0.4433	False		,,,				2504	0.5838				p.A446T		Atlas-SNP	.											.	TCEB3B	141	.	0			c.G1336A						PASS	.	C	THR/ALA,	1952,2454	547.5+/-377.3	450,1052,701	46.0	52.0	50.0		1336,	-0.1	0.0	18	dbSNP_107	50	3910,4684	541.0+/-383.9	925,2060,1312	no	missense,intron	TCEB3B,KATNAL2	NM_016427.2,NM_031303.2	58,	1375,3112,2013	TT,TC,CC		45.4969,44.3032,45.0923	probably-damaging,	446/754,	44560300	5862,7138	2203	4297	6500	SO:0001583	missense	51224	exon1			AATCAGCGCCGGC	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.1336G>A	18.37:g.44560300C>T	ENSP00000331302:p.Ala446Thr	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	60	24	0.4	NM_016427	Q9P2V9	Missense_Mutation	SNP	ENST00000332567.4	37	CCDS11932.1	1116	0.510989010989011	211	0.42886178861788615	209	0.5773480662983426	362	0.6328671328671329	334	0.44063324538258575	C	13.31	2.198727	0.38806	0.443032	0.454969	ENSG00000206181	ENST00000332567	T	0.07800	3.16	1.92	-0.0472	0.13844	.	0.534294	0.15445	N	0.261986	T	0.00012	0.0000	L	0.39898	1.24	0.80722	P	0.0	D	0.76494	0.999	P	0.61874	0.895	T	0.36504	-0.9745	9	0.24483	T	0.36	-5.4296	4.0756	0.09902	0.0:0.5626:0.0:0.4374	rs3744863;rs7236505;rs60450549	446	Q8IYF1	ELOA2_HUMAN	T	446	ENSP00000331302:A446T	ENSP00000331302:A446T	A	-	1	0	TCEB3B	42814298	0.001000	0.12720	0.000000	0.03702	0.001000	0.01503	0.052000	0.14163	-0.022000	0.13986	-0.346000	0.07831	GCT	.	.	weak		0.597	TCEB3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255900.1	NM_016427	
ADGB	79747	hgsc.bcm.edu	37	6	146993445	146993445	+	Missense_Mutation	SNP	T	T	C	rs9497606	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:146993445T>C	ENST00000397944.3	+	8	1005	c.929T>C	c.(928-930)aTa>aCa	p.I310T	ADGB_ENST00000367493.3_5'UTR	NM_024694.3	NP_078970.3	Q8N7X0	ADGB_HUMAN	androglobin	310	Calpain catalytic. {ECO:0000255|PROSITE- ProRule:PRU00239}.		I -> T (in dbSNP:rs9497606). {ECO:0000269|PubMed:14702039}.		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						GAAAGCAAAATAGCAGTGTTA	0.393													T|||	1423	0.284145	0.416	0.3372	5008	,	,		17282	0.124		0.2127	False		,,,				2504	0.3067				p.I310T		Atlas-SNP	.											.	ADGB	93	.	0			c.T929C						PASS	.	T	THR/ILE	537,847		101,335,256	71.0	62.0	65.0		929	-4.2	0.0	6	dbSNP_119	65	649,2533		71,507,1013	yes	missense	C6orf103	NM_024694.3	89	172,842,1269	CC,CT,TT		20.396,38.8006,25.9746	probably-damaging	310/1668	146993445	1186,3380	692	1591	2283	SO:0001583	missense	79747	exon8			GCAAAATAGCAGT	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.929T>C	6.37:g.146993445T>C	ENSP00000381036:p.Ile310Thr	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	69	42	0.608696	NM_024694	Q5T402|Q5T904|Q5T905	Missense_Mutation	SNP	ENST00000397944.3	37		528	0.24175824175824176	196	0.3983739837398374	107	0.2955801104972376	62	0.10839160839160839	163	0.21503957783641162	T	10.40	1.340751	0.24339	0.388006	0.20396	ENSG00000118492	ENST00000397944	D	0.87256	-2.23	5.01	-4.19	0.03835	Peptidase C2, calpain, catalytic domain (3);	1.559840	0.03266	N	0.184008	T	0.67040	0.2851	L	0.54323	1.7	0.80722	P	0.0	B	0.23735	0.09	B	0.23150	0.044	T	0.52586	-0.8556	9	0.13108	T	0.6	-2.3532	8.9248	0.35634	0.0:0.512:0.126:0.362	rs9497606;rs52829379;rs56454038;rs56826710;rs9497606	310	Q8N7X0	CAN7L_HUMAN	T	310	ENSP00000381036:I310T	ENSP00000381036:I310T	I	+	2	0	C6orf103	147035138	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.390000	0.07332	-0.492000	0.06687	-0.462000	0.05337	ATA	T|0.734;C|0.266	0.266	strong		0.393	ADGB-009	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000376350.2	NM_024694	
SKA3	221150	hgsc.bcm.edu	37	13	21729267	21729267	+	3'UTR	SNP	G	G	A	rs11147977	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:21729267G>A	ENST00000314759.5	-	0	1385				SKA3_ENST00000400018.3_Missense_Mutation_p.T381I	NM_145061.5	NP_659498.4	Q8IX90	SKA3_HUMAN	spindle and kinetochore associated complex subunit 3						chromosome segregation (GO:0007059)|mitotic nuclear division (GO:0007067)|regulation of microtubule polymerization or depolymerization (GO:0031110)	condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|spindle microtubule (GO:0005876)				breast(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	19						CAGTTTCTGTGTTGGATAGAT	0.363																																					p.T381I		Atlas-SNP	.											.	SKA3	76	.	0			c.C1142T						PASS	.						141.0	146.0	144.0					13																	21729267		2202	4300	6502	SO:0001624	3_prime_UTR_variant	221150	exon8			TTCTGTGTTGGAT	AF361358	CCDS31946.1, CCDS53856.1	13q11	2013-01-17	2009-08-19	2009-08-19	ENSG00000165480	ENSG00000165480			20262	protein-coding gene	gene with protein product			"""chromosome 13 open reading frame 3"""	C13orf3		19387489, 19289083, 19646878, 19360002	Standard	NM_145061		Approved	MGC4832, RAMA1	uc001unt.3	Q8IX90	OTTHUMG00000016539	ENST00000314759.5:c.*22C>T	13.37:g.21729267G>A		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	81	15	0.185185	NM_001166017	A2A330|A2A331|B2RBY2|Q5VZV5|Q86WR2|Q8NBG1|Q96D22	Missense_Mutation	SNP	ENST00000314759.5	37	CCDS31946.1	234	0.10714285714285714	10	0.02032520325203252	48	0.13259668508287292	96	0.16783216783216784	80	0.10554089709762533	A	1.991	-0.431860	0.04669	.	.	ENSG00000165480	ENST00000400018	T	0.22945	1.93	4.07	-0.905	0.10527	.	.	.	.	.	T	0.00039	0.0001	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.30357	-0.9981	8	0.41790	T	0.15	.	4.7384	0.13001	0.4657:0.1694:0.365:0.0	rs11147977;rs52815571;rs61114986;rs11147977	381	Q8IX90-3	.	I	381	ENSP00000382896:T381I	ENSP00000382896:T381I	T	-	2	0	SKA3	20627267	0.001000	0.12720	0.000000	0.03702	0.014000	0.08584	0.200000	0.17257	-0.416000	0.07473	-0.893000	0.02921	ACA	G|0.905;A|0.095	0.095	strong		0.363	SKA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000272912.1	NM_145061	
CD300LD	100131439	hgsc.bcm.edu	37	17	72584764	72584764	+	Missense_Mutation	SNP	C	C	T	rs783239	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:72584764C>T	ENST00000375352.1	-	2	345	c.265G>A	c.(265-267)Gtg>Atg	p.V89M	C17orf77_ENST00000392620.1_Intron|C17orf77_ENST00000328023.2_5'Flank	NM_001115152.1	NP_001108624.1	Q6UXZ3	CLM4_HUMAN	CD300 molecule-like family member d	89	Ig-like V-type.		V -> M (in dbSNP:rs783239).		immune system process (GO:0002376)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.V89M(1)		large_intestine(1)|lung(2)|prostate(1)|stomach(1)	5						ACGGTGAACACGTGGTTTTTC	0.423													T|||	1715	0.342452	0.6604	0.2161	5008	,	,		24754	0.249		0.1829	False		,,,				2504	0.2628				p.V89M		Atlas-SNP	.											CD300LD,NS,carcinoma,0,1	CD300LD	16	1	1	Substitution - Missense(1)	stomach(1)	c.G265A						PASS	.	T	MET/VAL,	1777,1359		504,769,295	370.0	303.0	324.0		265,	-0.5	0.0	17	dbSNP_86	324	1529,5635		168,1193,2221	yes	missense,intron	C17orf77,CD300LD	NM_001115152.1,NM_152460.2	21,	672,1962,2516	TT,TC,CC		21.3428,43.3355,32.0971	benign,	89/195,	72584764	3306,6994	1568	3582	5150	SO:0001583	missense	100131439	exon2			TGAACACGTGGTT		CCDS42379.1	17q25.1	2014-05-15			ENSG00000204345	ENSG00000204345		"""Immunoglobulin superfamily / V-set domain containing"""	16848	protein-coding gene	gene with protein product						22291008	Standard	NM_001115152		Approved	CMRF35A4, CD300D	uc002jkz.2	Q6UXZ3	OTTHUMG00000067614	ENST00000375352.1:c.265G>A	17.37:g.72584764C>T	ENSP00000364501:p.Val89Met	Somatic	258	1	0.00387597		WXS	Illumina HiSeq	Phase_I	228	117	0.513158	NM_001115152		Missense_Mutation	SNP	ENST00000375352.1	37	CCDS42379.1	695	0.3182234432234432	332	0.6747967479674797	87	0.24033149171270718	133	0.23251748251748253	143	0.18865435356200527	T	9.306	1.054409	0.19907	0.566645	0.213428	ENSG00000204345	ENST00000375352	T	0.65364	-0.15	4.67	-0.509	0.11977	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	2.005160	0.03034	N	0.152512	T	0.00012	0.0000	L	0.58810	1.83	0.80722	P	0.0	B	0.23316	0.083	B	0.23419	0.046	T	0.47983	-0.9074	9	0.37606	T	0.19	.	4.8858	0.13703	0.142:0.326:0.0:0.532	rs783239;rs58833921;rs783239	89	Q6UXZ3	CLM4_HUMAN	M	89	ENSP00000364501:V89M	ENSP00000364501:V89M	V	-	1	0	CD300LD	70096359	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.650000	0.05378	-0.727000	0.04888	-0.361000	0.07541	GTG	C|0.680;T|0.320	0.320	strong		0.423	CD300LD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000145099.1	NM_001115152	
ARHGEF28	64283	hgsc.bcm.edu	37	5	73205337	73205337	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:73205337C>A	ENST00000426542.2	+	33	4282	c.4262C>A	c.(4261-4263)cCc>cAc	p.P1421H	ARHGEF28_ENST00000512883.1_Missense_Mutation_p.P341H|ARHGEF28_ENST00000296794.6_Missense_Mutation_p.P1421H|ARHGEF28_ENST00000287898.5_Missense_Mutation_p.P1377H|ARHGEF28_ENST00000513042.2_Missense_Mutation_p.P1421H|ARHGEF28_ENST00000296799.4_Missense_Mutation_p.P1108H|ARHGEF28_ENST00000545377.1_Missense_Mutation_p.P1421H|ARHGEF28_ENST00000437974.1_Missense_Mutation_p.P1421H			Q8N1W1	ARG28_HUMAN	Rho guanine nucleotide exchange factor (GEF) 28	1421					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)										CGAGGCGGCCCCTTGCAGGAC	0.642																																					p.P1421H		Atlas-SNP	.											.	.	.	.	0			c.C4262A						PASS	.						17.0	20.0	19.0					5																	73205337		2040	4194	6234	SO:0001583	missense	64283	exon34			GCGGCCCCTTGCA		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.4262C>A	5.37:g.73205337C>A	ENSP00000412175:p.Pro1421His	Somatic	198	0	0		WXS	Illumina HiSeq	Phase_I	270	108	0.4	NM_001080479	B2RXG7|B4E3K4|B5MDA3|B7ZW32|E9PC75|Q8NCM7|Q96E37|Q9H6L3|Q9H6W0	Missense_Mutation	SNP	ENST00000426542.2	37	CCDS54870.1	.	.	.	.	.	.	.	.	.	.	C	4.756	0.140576	0.09083	.	.	ENSG00000214944	ENST00000296794;ENST00000545377;ENST00000513042;ENST00000287898;ENST00000437974;ENST00000426542;ENST00000296799;ENST00000512883	T;T;T;T;T;T;T;T	0.21543	2.0;2.0;2.0;2.0;2.0;2.0;2.0;2.0	5.34	1.35	0.21983	.	0.670385	0.11270	U	0.581554	T	0.26011	0.0634	L	0.54323	1.7	0.09310	N	1	D;P;P;D;P	0.54047	0.964;0.836;0.836;0.963;0.898	P;P;P;P;P	0.52424	0.619;0.497;0.497;0.698;0.694	T	0.14008	-1.0488	10	0.56958	D	0.05	.	2.765	0.05317	0.2109:0.2926:0.0:0.4965	.	1108;1421;1421;341;1421	B5MDA3;Q8N1W1;E9PC75;D6RGZ3;Q8N1W1-4	.;RGNEF_HUMAN;.;.;.	H	1421;1421;1421;1377;1421;1421;1108;341	ENSP00000296794:P1421H;ENSP00000441913:P1421H;ENSP00000441436:P1421H;ENSP00000287898:P1377H;ENSP00000411459:P1421H;ENSP00000412175:P1421H;ENSP00000296799:P1108H;ENSP00000421081:P341H	ENSP00000287898:P1377H	P	+	2	0	RP11-428C6.1	73241093	0.038000	0.19896	0.001000	0.08648	0.010000	0.07245	1.372000	0.34261	0.246000	0.21394	-0.324000	0.08512	CCC	.	.	none		0.642	ARHGEF28-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000368975.1		
TNFRSF13B	23495	hgsc.bcm.edu	37	17	16842991	16842991	+	Missense_Mutation	SNP	G	G	A	rs34562254	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:16842991G>A	ENST00000261652.2	-	5	764	c.752C>T	c.(751-753)cCc>cTc	p.P251L	TNFRSF13B_ENST00000437538.2_Missense_Mutation_p.P205L|TNFRSF13B_ENST00000579315.1_Intron|TNFRSF13B_ENST00000583789.1_Missense_Mutation_p.P205L|TNFRSF13B_ENST00000581616.2_5'Flank	NM_012452.2	NP_036584.1	O14836	TR13B_HUMAN	tumor necrosis factor receptor superfamily, member 13B	251			P -> L (in dbSNP:rs34562254). {ECO:0000269|PubMed:14702039}.		B cell homeostasis (GO:0001782)|cell surface receptor signaling pathway (GO:0007166)|hematopoietic progenitor cell differentiation (GO:0002244)|negative regulation of B cell proliferation (GO:0030889)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)	receptor activity (GO:0004872)			endometrium(1)|kidney(2)|large_intestine(4)|liver(1)|lung(7)|skin(1)	16						AGTGGGGTCGGGGGTCCCAGG	0.652									IgA Deficiency, Selective				.|||	955	0.190695	0.1399	0.1182	5008	,	,		15407	0.4236		0.1064	False		,,,				2504	0.1575				p.P251L		Atlas-SNP	.											.	TNFRSF13B	34	.	0			c.C752T						PASS	.	G	LEU/PRO	589,3817	253.7+/-259.5	41,507,1655	37.0	34.0	35.0		752	0.9	0.0	17	dbSNP_126	35	945,7655	203.0+/-246.1	51,843,3406	yes	missense	TNFRSF13B	NM_012452.2	98	92,1350,5061	AA,AG,GG		10.9884,13.3681,11.7946	probably-damaging	251/294	16842991	1534,11472	2203	4300	6503	SO:0001583	missense	23495	exon5	Familial Cancer Database	IGAD1, IGAD2	GGGTCGGGGGTCC	AF023614	CCDS11181.1	17p11.2	2014-09-17			ENSG00000240505	ENSG00000240505		"""Tumor necrosis factor receptor superfamily"", ""CD molecules"""	18153	protein-coding gene	gene with protein product		604907				9311921	Standard	NM_012452		Approved	TACI, CD267	uc002gqs.1	O14836	OTTHUMG00000059262	ENST00000261652.2:c.752C>T	17.37:g.16842991G>A	ENSP00000261652:p.Pro251Leu	Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	168	167	0.994048	NM_012452	B2R8B0|B7Z6V8|Q32LX4|Q7Z6F5	Missense_Mutation	SNP	ENST00000261652.2	37	CCDS11181.1	395	0.18086080586080586	59	0.11991869918699187	35	0.09668508287292818	222	0.3881118881118881	79	0.10422163588390501	G	5.925	0.354776	0.11239	0.133681	0.109884	ENSG00000240505	ENST00000437538;ENST00000261652	D;D	0.92647	-3.03;-3.08	3.12	0.879	0.19155	.	0.652988	0.14091	N	0.342023	T	0.00012	0.0000	L	0.38175	1.15	0.80722	P	0.0	P;P	0.40731	0.698;0.728	P;B	0.45310	0.476;0.284	T	0.46965	-0.9153	9	0.02654	T	1	-1.6478	2.8954	0.05689	0.1597:0.0:0.5137:0.3266	rs34562254	205;251	O14836-2;O14836	.;TR13B_HUMAN	L	205;251	ENSP00000413453:P205L;ENSP00000261652:P251L	ENSP00000261652:P251L	P	-	2	0	TNFRSF13B	16783716	0.001000	0.12720	0.003000	0.11579	0.013000	0.08279	-0.051000	0.11885	0.505000	0.28104	0.448000	0.29417	CCC	G|0.865;A|0.135	0.135	strong		0.652	TNFRSF13B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131474.2		
OPLAH	26873	hgsc.bcm.edu	37	8	145107915	145107915	+	Missense_Mutation	SNP	G	G	A	rs200620019	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:145107915G>A	ENST00000426825.1	-	21	3070	c.2989C>T	c.(2989-2991)Cgc>Tgc	p.R997C	CTD-3065J16.6_ENST00000528912.1_RNA|OPLAH_ENST00000534424.1_5'UTR|CTD-3065J16.6_ENST00000561181.1_RNA	NM_017570.3	NP_060040.1	O14841	OPLA_HUMAN	5-oxoprolinase (ATP-hydrolysing)	997					glutathione biosynthetic process (GO:0006750)|glutathione derivative biosynthetic process (GO:1901687)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	5-oxoprolinase (ATP-hydrolyzing) activity (GO:0017168)|ATP binding (GO:0005524)			breast(1)|central_nervous_system(1)|endometrium(1)|lung(13)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	20	all_cancers(97;1.06e-10)|all_epithelial(106;1.5e-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;6.79e-41)|Epithelial(56;1.02e-39)|all cancers(56;2.24e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			ACACGGAGGCGGATGGGGGAA	0.687													G|||	5	0.000998403	0.0008	0.0014	5008	,	,		14517	0.0		0.002	False		,,,				2504	0.001				p.R997C		Atlas-SNP	.											.	OPLAH	78	.	0			c.C2989T						PASS	.	G	CYS/ARG	1,4293		0,1,2146	19.0	23.0	22.0		2989	0.7	0.9	8		22	8,8440		0,8,4216	yes	missense	OPLAH	NM_017570.3	180	0,9,6362	AA,AG,GG		0.0947,0.0233,0.0706	benign	997/1289	145107915	9,12733	2147	4224	6371	SO:0001583	missense	26873	exon21			GGAGGCGGATGGG	AF024672, AB122018	CCDS75802.1	8q24.3	2010-11-23			ENSG00000178814	ENSG00000178814	3.5.2.9		8149	protein-coding gene	gene with protein product		614243				14993790	Standard	NM_017570		Approved	OPLA, 5-Opase	uc003zar.3	O14841		ENST00000426825.1:c.2989C>T	8.37:g.145107915G>A	ENSP00000475943:p.Arg997Cys	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	103	26	0.252427	NM_017570	A5PKY8|Q75W65|Q9Y4Q0	Missense_Mutation	SNP	ENST00000426825.1	37		.	.	.	.	.	.	.	.	.	.	G	3.876	-0.026921	0.07589	2.33E-4	9.47E-4	ENSG00000178814	ENST00000426825	.	.	.	4.68	0.665	0.17896	.	0.224693	0.42682	N	0.000665	T	0.28034	0.0691	.	.	.	0.37399	D	0.912761	B	0.06786	0.001	B	0.01281	0.0	T	0.08953	-1.0697	7	0.33940	T	0.23	.	3.9788	0.09486	0.387:0.0:0.4565:0.1565	.	997	O14841	OPLA_HUMAN	C	997	.	ENSP00000412071:R997C	R	-	1	0	OPLAH	145179903	0.886000	0.30341	0.905000	0.35620	0.031000	0.12232	1.258000	0.32944	0.058000	0.16222	-0.480000	0.04831	CGC	.	.	weak		0.687	OPLAH-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_017570	
PANK1	53354	hgsc.bcm.edu	37	10	91405044	91405044	+	Missense_Mutation	SNP	C	C	T	rs61853459	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:91405044C>T	ENST00000307534.4	-	1	171	c.16G>A	c.(16-18)Ggt>Agt	p.G6S	PANK1_ENST00000371774.2_5'Flank|PANK1_ENST00000342512.3_5'Flank|PANK1_ENST00000488482.1_5'Flank|RP11-80H5.6_ENST00000428166.1_lincRNA|PANK1_ENST00000322191.6_5'Flank|RP11-80H5.2_ENST00000451733.1_RNA|RP11-80H5.2_ENST00000454174.1_RNA	NM_148977.2	NP_683878.1	Q8TE04	PANK1_HUMAN	pantothenate kinase 1	6					coenzyme A biosynthetic process (GO:0015937)|coenzyme biosynthetic process (GO:0009108)|pantothenate metabolic process (GO:0015939)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cell periphery (GO:0071944)|clathrin coat (GO:0030118)|cytosol (GO:0005829)|nucleus (GO:0005634)|recycling endosome (GO:0055037)	ATP binding (GO:0005524)|pantothenate kinase activity (GO:0004594)			cervix(1)|kidney(1)|large_intestine(3)|lung(4)|prostate(2)	11						CCACCGCCACCGACGAGTTTC	0.617													C|||	235	0.0469249	0.0968	0.0187	5008	,	,		12970	0.0069		0.0258	False		,,,				2504	0.0624				p.G6S		Atlas-SNP	.											.	PANK1	35	.	0			c.G16A						PASS	.	C	SER/GLY	204,3446		11,182,1632	18.0	20.0	20.0		16	2.0	1.0	10	dbSNP_129	20	215,7319		4,207,3556	yes	missense	PANK1	NM_148977.2	56	15,389,5188	TT,TC,CC		2.8537,5.589,3.7464	possibly-damaging	6/599	91405044	419,10765	1825	3767	5592	SO:0001583	missense	53354	exon1			CGCCACCGACGAG	AF355198	CCDS7405.1, CCDS7406.1, CCDS31244.1	10q23.31	2008-05-14	2002-11-13	2002-11-15	ENSG00000152782	ENSG00000152782			8598	protein-coding gene	gene with protein product		606160	"""pantothenate kinase"""	PANK		11809413	Standard	NM_148977		Approved	MGC24596, PANK1a, PANK1b	uc001kgp.2	Q8TE04	OTTHUMG00000018718	ENST00000307534.4:c.16G>A	10.37:g.91405044C>T	ENSP00000302108:p.Gly6Ser	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	85	42	0.494118	NM_148977	A6NIP0|Q7RTX6|Q7Z495|Q8TBQ8	Missense_Mutation	SNP	ENST00000307534.4	37	CCDS31244.1	71	0.03250915750915751	42	0.08536585365853659	9	0.024861878453038673	2	0.0034965034965034965	18	0.023746701846965697	C	18.39	3.613066	0.66672	0.05589	0.028537	ENSG00000152782	ENST00000307534	D	0.99683	-6.39	3.86	2.02	0.26589	.	0.787399	0.10403	N	0.678916	T	0.61073	0.2318	N	0.03608	-0.345	0.80722	D	1	P	0.36874	0.572	B	0.23574	0.047	D	0.87291	0.2299	10	0.10377	T	0.69	-4.9995	6.1261	0.20180	0.0:0.7719:0.0:0.2281	rs61853459	6	Q8TE04	PANK1_HUMAN	S	6	ENSP00000302108:G6S	ENSP00000302108:G6S	G	-	1	0	PANK1	91395024	0.394000	0.25246	0.998000	0.56505	0.971000	0.66376	-0.164000	0.09983	0.603000	0.29913	-0.137000	0.14449	GGT	C|0.967;T|0.033	0.033	strong		0.617	PANK1-201	KNOWN	basic|CCDS	protein_coding	protein_coding			
CHIA	27159	hgsc.bcm.edu	37	1	111862042	111862042	+	Missense_Mutation	SNP	T	T	C	rs36011905	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:111862042T>C	ENST00000369740.1	+	11	1232	c.1129T>C	c.(1129-1131)Ttt>Ctt	p.F377L	CHIA_ENST00000451398.2_Missense_Mutation_p.F216L|CHIA_ENST00000353665.6_Missense_Mutation_p.F216L|RP5-1125M8.2_ENST00000426321.1_RNA|CHIA_ENST00000343320.6_Missense_Mutation_p.F377L|CHIA_ENST00000483391.1_Missense_Mutation_p.F216L|CHIA_ENST00000430615.1_Missense_Mutation_p.F269L	NM_001258001.1|NM_201653.3	NP_001244930.1|NP_970615.2	Q9BZP6	CHIA_HUMAN	chitinase, acidic	377			F -> L (in dbSNP:rs36011905).		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)		CCAGGGCAAGTTTCCCCTAAT	0.517													T|||	62	0.0123802	0.0015	0.0144	5008	,	,		19632	0.0		0.0408	False		,,,				2504	0.0092				p.F377L		Atlas-SNP	.											.	CHIA	115	.	0			c.T1129C						PASS	.	T	LEU/PHE,LEU/PHE	49,4357	50.2+/-85.5	0,49,2154	85.0	78.0	80.0		805,1129	5.2	1.0	1	dbSNP_126	80	368,8232	120.6+/-179.8	8,352,3940	yes	missense,missense	CHIA	NM_021797.2,NM_201653.2	22,22	8,401,6094	CC,CT,TT		4.2791,1.1121,3.2062	possibly-damaging,possibly-damaging	269/369,377/477	111862042	417,12589	2203	4300	6503	SO:0001583	missense	27159	exon11			GGCAAGTTTCCCC	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.1129T>C	1.37:g.111862042T>C	ENSP00000358755:p.Phe377Leu	Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	137	65	0.474453	NM_201653	Q32W79|Q32W80|Q3B866|Q5U5Z5|Q5VUV4|Q86UD8|Q9ULY3|Q9ULY4	Missense_Mutation	SNP	ENST00000369740.1	37	CCDS41368.1	41	0.018772893772893772	1	0.0020325203252032522	5	0.013812154696132596	0	0.0	35	0.04617414248021108	T	23.7	4.451775	0.84209	0.011121	0.042791	ENSG00000134216	ENST00000422815;ENST00000483391;ENST00000369740;ENST00000343320;ENST00000451398;ENST00000353665;ENST00000489524;ENST00000430615	T;T;T;T;T;T;T;T	0.04360	3.64;3.64;3.64;3.64;3.64;3.64;3.64;3.64	5.19	5.19	0.71726	Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.187147	0.35096	U	0.003442	T	0.06371	0.0164	M	0.67397	2.05	0.39143	D	0.962083	P	0.51537	0.946	P	0.48677	0.586	T	0.04565	-1.0942	10	0.87932	D	0	-20.2058	13.2842	0.60232	0.0:0.0:0.0:1.0	rs36011905	377	Q9BZP6	CHIA_HUMAN	L	321;216;377;377;216;216;216;269	ENSP00000387671:F321L;ENSP00000436946:F216L;ENSP00000358755:F377L;ENSP00000341828:F377L;ENSP00000390476:F216L;ENSP00000338970:F216L;ENSP00000433309:F216L;ENSP00000391132:F269L	ENSP00000341828:F377L	F	+	1	0	CHIA	111663565	0.916000	0.31088	0.969000	0.41365	0.956000	0.61745	1.445000	0.35079	2.070000	0.61991	0.533000	0.62120	TTT	T|0.971;C|0.029	0.029	strong		0.517	CHIA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030710.1		
SPTBN1	6711	hgsc.bcm.edu	37	2	54844790	54844790	+	Silent	SNP	C	C	T	rs2229506	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:54844790C>T	ENST00000356805.4	+	6	893	c.612C>T	c.(610-612)gaC>gaT	p.D204D	SPTBN1_ENST00000333896.5_Silent_p.D191D	NM_003128.2	NP_003119.2	Q01082	SPTB2_HUMAN	spectrin, beta, non-erythrocytic 1	204	Actin-binding.|CH 2. {ECO:0000255|PROSITE- ProRule:PRU00044}.				actin filament capping (GO:0051693)|axon guidance (GO:0007411)|Golgi to plasma membrane protein transport (GO:0043001)|membrane assembly (GO:0071709)|mitotic cytokinesis (GO:0000281)|plasma membrane organization (GO:0007009)|protein targeting to plasma membrane (GO:0072661)	axolemma (GO:0030673)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|protein complex (GO:0043234)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin binding (GO:0003779)|ankyrin binding (GO:0030506)|phospholipid binding (GO:0005543)|poly(A) RNA binding (GO:0044822)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|breast(8)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(11)|lung(27)|ovary(4)|prostate(2)|skin(5)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	82			Lung(47;0.24)			GCTGGAGGGACGGCATGGCCT	0.458													C|||	568	0.113419	0.1165	0.1052	5008	,	,		19328	0.0506		0.167	False		,,,				2504	0.1247				p.D204D		Atlas-SNP	.											.	SPTBN1	378	.	0			c.C612T						PASS	.	C	,	533,3873	241.5+/-251.9	35,463,1705	179.0	144.0	156.0		612,573	-3.5	1.0	2	dbSNP_98	156	1334,7266	262.4+/-284.4	116,1102,3082	no	coding-synonymous,coding-synonymous	SPTBN1	NM_003128.2,NM_178313.2	,	151,1565,4787	TT,TC,CC		15.5116,12.0971,14.3549	,	204/2365,191/2156	54844790	1867,11139	2203	4300	6503	SO:0001819	synonymous_variant	6711	exon6			GAGGGACGGCATG		CCDS33198.1, CCDS33199.1	2p21	2013-01-10			ENSG00000115306	ENSG00000115306		"""Pleckstrin homology (PH) domain containing"""	11275	protein-coding gene	gene with protein product		182790					Standard	NM_003128		Approved		uc002rxu.3	Q01082	OTTHUMG00000133746	ENST00000356805.4:c.612C>T	2.37:g.54844790C>T		Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	480	115	0.239583	NM_003128	B2RP63|O60837|Q16057|Q53R99|Q59ER3|Q8IX99	Silent	SNP	ENST00000356805.4	37	CCDS33198.1																																																																																			C|0.859;G|0.000;T|0.140	0.140	strong		0.458	SPTBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258115.3		
KANK2	25959	hgsc.bcm.edu	37	19	11304404	11304404	+	Missense_Mutation	SNP	C	C	T	rs755237	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:11304404C>T	ENST00000586659.1	-	4	666	c.352G>A	c.(352-354)Ggt>Agt	p.G118S	KANK2_ENST00000432929.2_Missense_Mutation_p.G118S|KANK2_ENST00000589359.1_Missense_Mutation_p.G118S|KANK2_ENST00000589894.1_Missense_Mutation_p.G118S|KANK2_ENST00000355150.5_Missense_Mutation_p.G118S			Q63ZY3	KANK2_HUMAN	KN motif and ankyrin repeat domains 2	118			G -> S (in dbSNP:rs755237).		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						TTGAAGCCACCGCGGGTCTCC	0.677													C|||	258	0.0515176	0.0492	0.1081	5008	,	,		14456	0.0129		0.0706	False		,,,				2504	0.0348				p.G118S		Atlas-SNP	.											.	KANK2	47	.	0			c.G352A						PASS	.	C	SER/GLY,SER/GLY	255,4137		6,243,1947	34.0	40.0	38.0		352,352	1.6	0.0	19	dbSNP_86	38	718,7870		31,656,3607	yes	missense,missense	KANK2	NM_001136191.2,NM_015493.6	56,56	37,899,5554	TT,TC,CC		8.3605,5.806,7.4961	benign,benign	118/852,118/860	11304404	973,12007	2196	4294	6490	SO:0001583	missense	25959	exon2			AGCCACCGCGGGT	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.352G>A	19.37:g.11304404C>T	ENSP00000465650:p.Gly118Ser	Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	28	14	0.5	NM_015493	B0I1P4|Q3KQZ3|Q6GUF5|Q9H8S4|Q9NUP0|Q9P210	Missense_Mutation	SNP	ENST00000586659.1	37	CCDS12255.1	126	0.057692307692307696	23	0.046747967479674794	39	0.10773480662983426	9	0.015734265734265736	55	0.07255936675461741	C	0.182	-1.061089	0.01950	0.05806	0.083605	ENSG00000197256	ENST00000432929;ENST00000355150	T;T	0.36157	1.27;1.29	4.23	1.59	0.23543	.	0.759762	0.11880	N	0.520610	T	0.00328	0.0010	N	0.22421	0.69	0.80722	P	0.0	B;B;B	0.06786	0.0;0.001;0.001	B;B;B	0.08055	0.002;0.001;0.003	T	0.27872	-1.0061	9	0.06757	T	0.87	-10.3937	4.9743	0.14133	0.0:0.6423:0.1965:0.1612	rs755237;rs56711195;rs755237	118;118;118	Q63ZY3-3;Q63ZY3;Q63ZY3-2	.;KANK2_HUMAN;.	S	118	ENSP00000395650:G118S;ENSP00000347276:G118S	ENSP00000347276:G118S	G	-	1	0	KANK2	11165404	0.000000	0.05858	0.003000	0.11579	0.026000	0.11368	-0.296000	0.08287	0.073000	0.16731	0.462000	0.41574	GGT	C|0.936;T|0.064	0.064	strong		0.677	KANK2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000453066.2	NM_015493	
JARID2	3720	hgsc.bcm.edu	37	6	15513482	15513482	+	Silent	SNP	G	G	A	rs2235258	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:15513482G>A	ENST00000341776.2	+	16	3523	c.3279G>A	c.(3277-3279)ctG>ctA	p.L1093L	JARID2_ENST00000397311.3_Silent_p.L921L	NM_004973.3	NP_004964.2	Q92833	JARD2_HUMAN	jumonji, AT rich interactive domain 2	1093					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)				ATACAGAGCTGCGGCAGCGCA	0.667													G|||	2929	0.584864	0.3003	0.6513	5008	,	,		16258	0.6667		0.7465	False		,,,				2504	0.6718				p.L1093L		Atlas-SNP	.											JARID2,NS,carcinoma,0,1	JARID2	135	1	0			c.G3279A						PASS	.	G		1670,2696		354,962,867	16.0	15.0	15.0		3279	2.5	1.0	6	dbSNP_98	15	6569,1975		2569,1431,272	no	coding-synonymous	JARID2	NM_004973.2		2923,2393,1139	AA,AG,GG		23.1156,38.2501,36.1813		1093/1247	15513482	8239,4671	2183	4272	6455	SO:0001819	synonymous_variant	3720	exon16			AGAGCTGCGGCAG	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.3279G>A	6.37:g.15513482G>A		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	62	62	1	NM_004973	A8K9Z6|B7Z5S5|B7Z8L0|Q5U5L5|Q86X63	Silent	SNP	ENST00000341776.2	37	CCDS4533.1																																																																																			G|0.410;A|0.590	0.590	strong		0.667	JARID2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000039926.1	NM_004973	
SCARF1	8578	hgsc.bcm.edu	37	17	1538714	1538714	+	Missense_Mutation	SNP	T	T	G	rs61738531	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:1538714T>G	ENST00000263071.4	-	11	1880	c.1831A>C	c.(1831-1833)Agc>Cgc	p.S611R	SCARF1_ENST00000571272.1_3'UTR|SCARF1_ENST00000348987.3_Missense_Mutation_p.S525R	NM_003693.2|NM_145350.1	NP_003684.2|NP_663325.1	Q14162	SREC_HUMAN	scavenger receptor class F, member 1	611	Pro/Ser-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)		CGGAGCGGGCTGGAGAGCTCC	0.677													T|||	55	0.0109824	0.0008	0.0101	5008	,	,		15189	0.001		0.0149	False		,,,				2504	0.0317				p.S611R		Atlas-SNP	.											.	SCARF1	46	.	0			c.A1831C						PASS	.	T	ARG/SER,,ARG/SER	21,4385	27.2+/-55.0	0,21,2182	51.0	55.0	53.0		1831,,1573	5.2	1.0	17	dbSNP_129	53	214,8386	89.2+/-151.4	3,208,4089	yes	missense,utr-3,missense	SCARF1	NM_003693.2,NM_145350.1,NM_145352.2	110,,110	3,229,6271	GG,GT,TT		2.4884,0.4766,1.8069	probably-damaging,,probably-damaging	611/831,,525/745	1538714	235,12771	2203	4300	6503	SO:0001583	missense	8578	exon11			GCGGGCTGGAGAG	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.1831A>C	17.37:g.1538714T>G	ENSP00000263071:p.Ser611Arg	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	77	22	0.285714	NM_003693	A8MQ05|O43701|Q8NHD2|Q8NHD3|Q8NHD4|Q8NHD5	Missense_Mutation	SNP	ENST00000263071.4	37	CCDS11007.1	17	0.007783882783882784	0	0.0	5	0.013812154696132596	1	0.0017482517482517483	11	0.014511873350923483	T	22.4	4.289498	0.80914	0.004766	0.024884	ENSG00000074660	ENST00000263071;ENST00000348987	T;T	0.37411	1.2;1.2	5.21	5.21	0.72293	.	0.124140	0.36628	N	0.002484	T	0.35364	0.0929	M	0.63428	1.95	0.27223	N	0.959619	D;P	0.63046	0.992;0.947	P;P	0.56648	0.803;0.622	T	0.43669	-0.9377	10	0.72032	D	0.01	-22.476	15.1104	0.72351	0.0:0.0:0.0:1.0	.	525;611	Q14162-2;Q14162	.;SREC_HUMAN	R	611;525	ENSP00000263071:S611R;ENSP00000323964:S525R	ENSP00000263071:S611R	S	-	1	0	SCARF1	1485464	1.000000	0.71417	0.998000	0.56505	0.954000	0.61252	4.194000	0.58393	1.965000	0.57142	0.454000	0.30748	AGC	T|0.984;G|0.016	0.016	strong		0.677	SCARF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207081.4	NM_003693	
UMODL1	89766	hgsc.bcm.edu	37	21	43543098	43543098	+	Silent	SNP	C	C	T	rs58867895	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:43543098C>T	ENST00000408910.2	+	17	2985	c.2985C>T	c.(2983-2985)atC>atT	p.I995I	UMODL1_ENST00000400427.1_Silent_p.I1051I|UMODL1_ENST00000400424.2_Silent_p.I923I|UMODL1_ENST00000408989.2_Silent_p.I1123I|UMODL1_ENST00000400423.2_3'UTR	NM_001004416.2	NP_001004416	Q5DID0	UROL1_HUMAN	uromodulin-like 1	995	ZP. {ECO:0000255|PROSITE- ProRule:PRU00375}.				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						TCTGTGAGATCGAGAAGGTGG	0.632													C|||	142	0.0283546	0.1006	0.0086	5008	,	,		20433	0.0		0.003	False		,,,				2504	0.0				p.I1123I	Pancreas(122;680 807 13940 14411 22888 25505 31742 36028 36332 38435)	Atlas-SNP	.											.	UMODL1	186	.	0			c.C3369T						PASS	.	C	,,,	370,3912		11,348,1782	75.0	80.0	78.0		2985,3153,2769,3369	-6.2	0.9	21	dbSNP_129	78	6,8496		0,6,4245	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	UMODL1	NM_001004416.2,NM_001199527.1,NM_001199528.2,NM_173568.3	,,,	11,354,6027	TT,TC,CC		0.0706,8.6408,2.9412	,,,	995/1319,1051/1375,923/1247,1123/1447	43543098	376,12408	2141	4251	6392	SO:0001819	synonymous_variant	89766	exon16			TGAGATCGAGAAG		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.2985C>T	21.37:g.43543098C>T		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	93	35	0.376344	NM_173568	C9JCE6|Q5DIC9|Q6LA40|Q6LA41|Q8N216	Silent	SNP	ENST00000408910.2	37	CCDS42936.1																																																																																			C|0.985;T|0.015	0.015	strong		0.632	UMODL1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195292.2		
PTCH1	5727	hgsc.bcm.edu	37	9	98209594	98209594	+	Missense_Mutation	SNP	G	G	A	rs357564	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:98209594G>A	ENST00000331920.6	-	23	4243	c.3944C>T	c.(3943-3945)cCc>cTc	p.P1315L	PTCH1_ENST00000430669.2_Missense_Mutation_p.P1249L|PTCH1_ENST00000375274.2_Missense_Mutation_p.P1314L|PTCH1_ENST00000418258.1_Missense_Mutation_p.P1164L|PTCH1_ENST00000429896.2_Missense_Mutation_p.P1164L|PTCH1_ENST00000437951.1_Missense_Mutation_p.P1249L|PTCH1_ENST00000421141.1_Missense_Mutation_p.P1164L	NM_000264.3	NP_000255.2	Q13635	PTC1_HUMAN	patched 1	1315			P -> L (in dbSNP:rs357564). {ECO:0000269|PubMed:10200051, ECO:0000269|PubMed:10874314, ECO:0000269|PubMed:8647801, ECO:0000269|PubMed:8658145}.		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)				CGGTCTGTAGGGGGGTGGCCA	0.667													G|||	1987	0.396765	0.2254	0.4063	5008	,	,		14889	0.5863		0.3529	False		,,,				2504	0.4714				p.P1315L		Atlas-SNP	.											PTCH1_ENST00000430669,NS,NS,0,4	PTCH1	1850	4	0			c.C3944T	GRCh37	CM056376	PTCH1	M	rs357564	PASS	.	G	LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO	1009,3215		149,711,1252	36.0	44.0	42.0		3944,3746,3941,3491,3491,3491,3491	4.8	1.0	9	dbSNP_79	42	2752,5592		483,1786,1903	yes	missense,missense,missense,missense,missense,missense,missense	PTCH1	NM_000264.3,NM_001083602.1,NM_001083603.1,NM_001083604.1,NM_001083605.1,NM_001083606.1,NM_001083607.1	98,98,98,98,98,98,98	632,2497,3155	AA,AG,GG		32.9818,23.8873,29.9252	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	1315/1448,1249/1382,1314/1447,1164/1297,1164/1297,1164/1297,1164/1297	98209594	3761,8807	2112	4172	6284	SO:0001583	missense	5727	exon23			CTGTAGGGGGGTG	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.3944C>T	9.37:g.98209594G>A	ENSP00000332353:p.Pro1315Leu	Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	40	19	0.475	NM_000264	A3KBI9|E9PEJ8|Q13463|Q5R1U7|Q5R1U9|Q5R1V0|Q5VZC0|Q5VZC2|Q86XG7	Missense_Mutation	SNP	ENST00000331920.6	37	CCDS6714.1	833	0.3814102564102564	109	0.22154471544715448	139	0.3839779005524862	325	0.5681818181818182	260	0.34300791556728233	G	26.2	4.715015	0.89112	0.238873	0.329818	ENSG00000185920	ENST00000331920;ENST00000437951;ENST00000421141;ENST00000418258;ENST00000430669;ENST00000375284;ENST00000429896;ENST00000375274	D;D;D;D;D;D;D	0.91011	-2.76;-2.74;-2.73;-2.73;-2.74;-2.73;-2.77	4.83	4.83	0.62350	.	0.055734	0.64402	D	0.000001	T	0.00012	0.0000	M	0.62723	1.935	0.09310	P	0.9999999999746184	P;P;P	0.51351	0.944;0.944;0.906	P;P;B	0.52957	0.646;0.714;0.444	T	0.29792	-1.0000	9	0.34782	T	0.22	-23.7809	18.1026	0.89510	0.0:0.0:1.0:0.0	rs357564;rs701002;rs52794414;rs357564	1249;1314;1315	Q13635-3;Q13635-2;Q13635	.;.;PTC1_HUMAN	L	1315;1249;1164;1164;1249;107;1164;1314	ENSP00000332353:P1315L;ENSP00000389744:P1249L;ENSP00000399981:P1164L;ENSP00000396135:P1164L;ENSP00000410287:P1249L;ENSP00000414823:P1164L;ENSP00000364423:P1314L	ENSP00000332353:P1315L	P	-	2	0	PTCH1	97249415	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	9.405000	0.97313	2.506000	0.84524	0.655000	0.94253	CCC	G|0.661;A|0.339	0.339	strong		0.667	PTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053229.2	NM_000264	
HLA-A	3105	hgsc.bcm.edu	37	6	29911124	29911124	+	Silent	SNP	C	C	T	rs3173418	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:29911124C>T	ENST00000396634.1	+	5	764	c.423C>T	c.(421-423)gcC>gcT	p.A141A	HLA-A_ENST00000376802.2_Silent_p.A141A|HLA-A_ENST00000376809.5_Silent_p.A141A|HLA-A_ENST00000376806.5_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	263	0	0		WXS	Illumina HiSeq	Phase_I	166	67	0.403614	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	
RIPPLY2	134701	hgsc.bcm.edu	37	6	84563147	84563147	+	Silent	SNP	G	G	A	rs9353143	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:84563147G>A	ENST00000369689.1	+	1	163	c.12G>A	c.(10-12)gcG>gcA	p.A4A	RIPPLY2_ENST00000369687.1_5'Flank	NM_001009994.1	NP_001009994.1	Q5TAB7	RIPP2_HUMAN	ripply transcriptional repressor 2	4					bone morphogenesis (GO:0060349)|determination of left/right symmetry (GO:0007368)|Notch signaling pathway (GO:0007219)|ossification (GO:0001503)|post-anal tail morphogenesis (GO:0036342)|regulation of gene expression (GO:0010468)|somite rostral/caudal axis specification (GO:0032525)|somitogenesis (GO:0001756)	nucleus (GO:0005634)				large_intestine(2)|lung(4)|urinary_tract(1)	7						TGGAGAACGCGGGAGGCGCAG	0.697													A|||	1469	0.293331	0.6596	0.2752	5008	,	,		13517	0.2619		0.0825	False		,,,				2504	0.0603				p.A4A		Atlas-SNP	.											RIPPLY2,rectum,carcinoma,0,1	RIPPLY2	17	1	0			c.G12A						PASS	.	A		1259,1859		244,771,544	3.0	4.0	4.0		12	-3.7	0.0	6	dbSNP_119	4	433,5751		28,377,2687	no	coding-synonymous	RIPPLY2	NM_001009994.1		272,1148,3231	AA,AG,GG		7.0019,40.3784,18.1896		4/129	84563147	1692,7610	1559	3092	4651	SO:0001819	synonymous_variant	134701	exon1			GAACGCGGGAGGC	BC130460	CCDS34493.1	6q14.2	2013-07-23	2013-07-23	2008-05-07	ENSG00000203877	ENSG00000203877			21390	protein-coding gene	gene with protein product		609891	"""chromosome 6 open reading frame 159"", ""ripply2 homolog (zebrafish)"""	C6orf159			Standard	NM_001009994		Approved	dJ237I15.1	uc003pke.3	Q5TAB7	OTTHUMG00000015117	ENST00000369689.1:c.12G>A	6.37:g.84563147G>A		Somatic	11	0	0		WXS	Illumina HiSeq	Phase_I	20	10	0.5	NM_001009994	Q5TAB6	Silent	SNP	ENST00000369689.1	37	CCDS34493.1																																																																																			G|0.692;A|0.308	0.308	strong		0.697	RIPPLY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041360.1	NM_001009994	
RFX7	64864	hgsc.bcm.edu	37	15	56387142	56387142	+	Silent	SNP	G	G	A	rs34361729	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:56387142G>A	ENST00000559447.2	-	9	2764	c.2493C>T	c.(2491-2493)caC>caT	p.H831H	RFX7_ENST00000317318.6_Silent_p.H928H|RFX7_ENST00000423270.1_Silent_p.H928H|RFX7_ENST00000422057.1_Silent_p.H831H			Q2KHR2	RFX7_HUMAN	regulatory factor X, 7	831					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	DNA binding (GO:0003677)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(3)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	19						TGCTGGAAGTGTGAGATGACA	0.502													G|||	617	0.123203	0.1051	0.0836	5008	,	,		18677	0.1002		0.1491	False		,,,				2504	0.1728				p.H928H		Atlas-SNP	.											RFX7_ENST00000423270,NS,carcinoma,-1,2	RFX7	170	2	0			c.C2784T						PASS	.	G		387,3783		24,339,1722	104.0	113.0	110.0		2784	-6.1	0.1	15	dbSNP_126	110	1122,7304		78,966,3169	no	coding-synonymous	RFX7	NM_022841.5		102,1305,4891	AA,AG,GG		13.3159,9.2806,11.98		928/1461	56387142	1509,11087	2085	4213	6298	SO:0001819	synonymous_variant	64864	exon9			GGAAGTGTGAGAT			15q21.3	2008-08-04	2008-08-04	2008-08-04		ENSG00000181827			25777	protein-coding gene	gene with protein product		612660	"""regulatory factor X domain containing 2"""	RFXDC2			Standard	NM_022841		Approved	FLJ12994	uc010bfn.3	Q2KHR2		ENST00000559447.2:c.2493C>T	15.37:g.56387142G>A		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	109	69	0.633027	NM_022841	Q6ZRR1|Q6ZTY6|Q8N3J0|Q9H7A9|Q9H956	Silent	SNP	ENST00000559447.2	37																																																																																				G|0.879;A|0.121	0.121	strong		0.502	RFX7-001	KNOWN	non_canonical_U12|basic	protein_coding	protein_coding	OTTHUMT00000418841.3	NM_022841	
DOC2A	8448	hgsc.bcm.edu	37	16	30018500	30018500	+	Silent	SNP	C	C	T	rs3935873	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:30018500C>T	ENST00000350119.4	-	6	838	c.648G>A	c.(646-648)caG>caA	p.Q216Q	DOC2A_ENST00000564944.1_Silent_p.Q216Q|DOC2A_ENST00000564979.1_Silent_p.Q216Q	NM_001282062.1|NM_001282063.1|NM_001282068.1|NM_003586.2	NP_001268991.1|NP_001268992.1|NP_001268997.1|NP_003577.2	Q14183	DOC2A_HUMAN	double C2-like domains, alpha	216	Interaction with UNC13D.				nervous system development (GO:0007399)|regulation of calcium ion-dependent exocytosis (GO:0017158)|synaptic transmission (GO:0007268)|synaptic vesicle exocytosis (GO:0016079)	cell junction (GO:0030054)|lysosome (GO:0005764)|membrane (GO:0016020)|neuron projection (GO:0043005)|synaptic vesicle (GO:0008021)	calcium-dependent phospholipid binding (GO:0005544)|transporter activity (GO:0005215)			central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(2)|ovary(2)	9						AGACCGGGACCTGGCGCTCGA	0.642													C|||	1749	0.349241	0.1573	0.3141	5008	,	,		15186	0.378		0.4414	False		,,,				2504	0.5092				p.Q216Q		Atlas-SNP	.											.	DOC2A	40	.	0			c.G648A						PASS	.	C		774,3620	304.4+/-288.4	78,618,1501	31.0	34.0	33.0		648	4.2	1.0	16	dbSNP_108	33	3823,4777	525.6+/-380.8	864,2095,1341	no	coding-synonymous	DOC2A	NM_003586.2		942,2713,2842	TT,TC,CC		44.4535,17.6149,35.3779		216/401	30018500	4597,8397	2197	4300	6497	SO:0001819	synonymous_variant	8448	exon6			CGGGACCTGGCGC	D31897	CCDS10666.1	16p11.2	2014-07-02			ENSG00000149927	ENSG00000149927		"""Synaptotagmins"""	2985	protein-coding gene	gene with protein product		604567				7826360, 9736751	Standard	NM_003586		Approved		uc002dvn.3	Q14183	OTTHUMG00000132109	ENST00000350119.4:c.648G>A	16.37:g.30018500C>T		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	58	58	1	NM_003586	B4DEJ2|H3BNH6|Q6P4G4|Q7Z5G0|Q8IVX0	Silent	SNP	ENST00000350119.4	37	CCDS10666.1																																																																																			C|0.660;T|0.340	0.340	strong		0.642	DOC2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255148.2	NM_003586	
CNR1	1268	hgsc.bcm.edu	37	6	88853635	88853635	+	Silent	SNP	C	C	T	rs1049353	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:88853635C>T	ENST00000537554.1	-	2	4921	c.1359G>A	c.(1357-1359)acG>acA	p.T453T	CNR1_ENST00000549890.1_Silent_p.T453T|CNR1_ENST00000535130.1_Silent_p.T453T|CNR1_ENST00000369499.2_Silent_p.T453T|CNR1_ENST00000428600.2_Silent_p.T453T|CNR1_ENST00000369501.2_Silent_p.T453T|CNR1_ENST00000468898.1_Silent_p.T420T|CNR1_ENST00000362094.5_3'UTR|CNR1_ENST00000549716.1_Silent_p.T392T	NM_001160226.1|NM_001160258.1	NP_001153698.1|NP_001153730.1	P21554	CNR1_HUMAN	cannabinoid receptor 1 (brain)	453					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|aging (GO:0007568)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|glucose homeostasis (GO:0042593)|maternal process involved in female pregnancy (GO:0060135)|memory (GO:0007613)|negative regulation of action potential (GO:0045759)|negative regulation of blood pressure (GO:0045776)|negative regulation of dopamine secretion (GO:0033602)|negative regulation of fatty acid beta-oxidation (GO:0031999)|negative regulation of mast cell activation (GO:0033004)|negative regulation of nitric-oxide synthase activity (GO:0051001)|positive regulation of acute inflammatory response to antigenic stimulus (GO:0002866)|positive regulation of apoptotic process (GO:0043065)|positive regulation of blood pressure (GO:0045777)|positive regulation of fever generation (GO:0031622)|positive regulation of neuron projection development (GO:0010976)|regulation of feeding behavior (GO:0060259)|regulation of insulin secretion (GO:0050796)|regulation of penile erection (GO:0060405)|regulation of synaptic transmission, GABAergic (GO:0032228)|regulation of synaptic transmission, glutamatergic (GO:0051966)|response to cocaine (GO:0042220)|response to ethanol (GO:0045471)|response to lipopolysaccharide (GO:0032496)|response to morphine (GO:0043278)|response to nicotine (GO:0035094)|response to nutrient (GO:0007584)|sensory perception of pain (GO:0019233)|spermatogenesis (GO:0007283)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cannabinoid receptor activity (GO:0004949)|drug binding (GO:0008144)			breast(2)|endometrium(3)|kidney(1)|large_intestine(7)|liver(1)|lung(11)|prostate(1)|skin(10)|urinary_tract(1)	37		all_cancers(76;8.24e-09)|Acute lymphoblastic leukemia(125;2.15e-10)|Prostate(29;4.11e-10)|all_hematologic(105;1.08e-06)|all_epithelial(107;0.00011)		BRCA - Breast invasive adenocarcinoma(108;0.15)	Dronabinol(DB00470)|Nabilone(DB00486)|Rimonabant(DB06155)	CAATCTTGACCGTGCTCTTGA	0.537													C|||	648	0.129393	0.0287	0.147	5008	,	,		20357	0.0764		0.2584	False		,,,				2504	0.1748				p.T453T		Atlas-SNP	.											CNR1,NS,carcinoma,-1,1	CNR1	91	1	0			c.G1359A	GRCh37	CM074755	CNR1	M	rs1049353	PASS	.	C	,,,,	314,4092	168.0+/-198.9	16,282,1905	226.0	204.0	212.0		1359,1359,1359,1359,1260	-7.6	0.6	6	dbSNP_86	212	2330,6270	390.2+/-343.2	338,1654,2308	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CNR1	NM_001160226.1,NM_001160258.1,NM_001160259.1,NM_016083.4,NM_033181.3	,,,,	354,1936,4213	TT,TC,CC		27.093,7.1266,20.3291	,,,,	453/473,453/473,453/473,453/473,420/440	88853635	2644,10362	2203	4300	6503	SO:0001819	synonymous_variant	1268	exon4			CTTGACCGTGCTC	AF107262	CCDS5015.1, CCDS5016.1, CCDS5016.2	6q14-q15	2012-08-08			ENSG00000118432	ENSG00000118432		"""GPCR / Class A : Cannabinoid receptors"""	2159	protein-coding gene	gene with protein product		114610		CNR			Standard	NM_016083		Approved	CB1K5, CB-R, CB1, CANN6, CB1A	uc003pmq.4	P21554	OTTHUMG00000015184	ENST00000537554.1:c.1359G>A	6.37:g.88853635C>T		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	146	77	0.527397	NM_001160258	B2R9T4|E1P512|Q13949|Q495Z0|Q4PLI4|Q4VBM6|Q5JVL5|Q5UB37|Q9UNN0	Silent	SNP	ENST00000537554.1	37	CCDS5015.1																																																																																			C|0.840;T|0.160	0.160	strong		0.537	CNR1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354204.2		
MUC4	4585	hgsc.bcm.edu	37	3	195507324	195507324	+	Missense_Mutation	SNP	G	G	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195507324G>C	ENST00000463781.3	-	2	11586	c.11127C>G	c.(11125-11127)caC>caG	p.H3709Q	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.H3709Q	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.H3709Q(1)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GAGGGGTGGTGTGACCTGAGG	0.572																																					p.H3709Q		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	1	Substitution - Missense(1)	kidney(1)	c.C11127G						PASS	.						66.0	57.0	59.0					3																	195507324		660	1591	2251	SO:0001583	missense	4585	exon2			GGTGGTGTGACCT	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.11127C>G	3.37:g.195507324G>C	ENSP00000417498:p.His3709Gln	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	95	12	0.126316	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	g	4.440	0.081383	0.08533	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.32753	1.52;1.44	0.885	-1.56	0.08532	.	.	.	.	.	T	0.22244	0.0536	N	0.19112	0.55	0.09310	N	1	P	0.44006	0.824	P	0.48770	0.589	T	0.18116	-1.0347	8	.	.	.	.	5.328	0.15917	0.2604:0.0:0.7396:0.0	.	3581	E7ESK3	.	Q	3709	ENSP00000417498:H3709Q;ENSP00000420243:H3709Q	.	H	-	3	2	MUC4	196992103	0.869000	0.29996	0.010000	0.14722	0.046000	0.14306	1.281000	0.33214	-0.535000	0.06307	0.064000	0.15345	CAC	.	.	none		0.572	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
RECK	8434	hgsc.bcm.edu	37	9	36105264	36105264	+	Silent	SNP	A	A	G	rs11788747	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:36105264A>G	ENST00000377966.3	+	13	2126	c.1560A>G	c.(1558-1560)ccA>ccG	p.P520P		NM_021111.2	NP_066934.1	O95980	RECK_HUMAN	reversion-inducing-cysteine-rich protein with kazal motifs	520					blood vessel maturation (GO:0001955)|embryo implantation (GO:0007566)|extracellular matrix organization (GO:0030198)|negative regulation of endopeptidase activity (GO:0010951)	anchored component of membrane (GO:0031225)|membrane (GO:0016020)|plasma membrane (GO:0005886)	endopeptidase inhibitor activity (GO:0004866)|metalloendopeptidase inhibitor activity (GO:0008191)|serine-type endopeptidase inhibitor activity (GO:0004867)			cervix(1)|endometrium(7)|kidney(3)|large_intestine(6)|lung(10)|ovary(1)|pancreas(1)|skin(2)|stomach(1)	32			LUSC - Lung squamous cell carcinoma(32;0.112)|STAD - Stomach adenocarcinoma(86;0.228)			CCTGTCTTCCATACTTTTGTG	0.438													A|||	1279	0.255391	0.0469	0.2464	5008	,	,		18176	0.3075		0.3907	False		,,,				2504	0.3507				p.P520P		Atlas-SNP	.											.	RECK	73	.	0			c.A1560G						PASS	.	A		449,3957	214.8+/-234.0	27,395,1781	148.0	134.0	139.0		1560	-4.0	1.0	9	dbSNP_120	139	3450,5150	507.1+/-376.8	724,2002,1574	no	coding-synonymous	RECK	NM_021111.2		751,2397,3355	GG,GA,AA		40.1163,10.1906,29.9785		520/972	36105264	3899,9107	2203	4300	6503	SO:0001819	synonymous_variant	8434	exon13			TCTTCCATACTTT	E13833	CCDS6597.1	9p13.3	2008-05-15			ENSG00000122707	ENSG00000122707			11345	protein-coding gene	gene with protein product		605227		ST15		9789069	Standard	NM_021111		Approved	hRECK	uc003zyv.3	O95980	OTTHUMG00000019898	ENST00000377966.3:c.1560A>G	9.37:g.36105264A>G		Somatic	204	0	0		WXS	Illumina HiSeq	Phase_I	166	66	0.39759	NM_021111	B2RNS1|Q5W0K6|Q8WX37	Silent	SNP	ENST00000377966.3	37	CCDS6597.1																																																																																			A|0.721;G|0.279	0.279	strong		0.438	RECK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052409.1		
OR51F1	256892	hgsc.bcm.edu	37	11	4790575	4790575	+	Silent	SNP	A	A	G	rs12788102	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:4790575A>G	ENST00000380383.1	-	1	593	c.594T>C	c.(592-594)tgT>tgC	p.C198C	OR51F1_ENST00000343430.3_Silent_p.C191C|MMP26_ENST00000477339.1_Intron|MMP26_ENST00000380390.1_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	244	0	0		WXS	Illumina HiSeq	Phase_I	289	58	0.200692	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	
SLC20A2	6575	hgsc.bcm.edu	37	8	42294592	42294592	+	Missense_Mutation	SNP	C	C	T	rs79577461	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:42294592C>T	ENST00000342228.3	-	8	1807	c.1438G>A	c.(1438-1440)Gca>Aca	p.A480T	SLC20A2_ENST00000520262.1_Missense_Mutation_p.A480T|SLC20A2_ENST00000520179.1_Missense_Mutation_p.A480T	NM_006749.4	NP_006740.1	Q08357	S20A2_HUMAN	solute carrier family 20 (phosphate transporter), member 2	480					ion transport (GO:0006811)|phosphate ion transmembrane transport (GO:0035435)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)|transport (GO:0006810)|viral process (GO:0016032)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	inorganic phosphate transmembrane transporter activity (GO:0005315)|receptor activity (GO:0004872)|sodium:phosphate symporter activity (GO:0005436)|virus receptor activity (GO:0001618)			breast(1)|endometrium(6)|large_intestine(5)|lung(9)|ovary(3)|prostate(1)|stomach(1)	26	all_lung(13;8.33e-12)|Lung NSC(13;1.41e-10)|Ovarian(28;0.00579)|Prostate(17;0.0119)|Lung SC(25;0.211)	all_lung(54;0.00671)|Lung NSC(58;0.0184)|Esophageal squamous(32;0.131)|Hepatocellular(245;0.133)|Renal(179;0.151)	BRCA - Breast invasive adenocarcinoma(8;5.73e-10)|OV - Ovarian serous cystadenocarcinoma(14;0.00419)|Lung(22;0.0302)|LUSC - Lung squamous cell carcinoma(45;0.0869)			ACCTCGGGTGCGTCCTTCTCC	0.637													C|||	29	0.00579073	0.0008	0.013	5008	,	,		16739	0.0		0.0159	False		,,,				2504	0.0031				p.A480T		Atlas-SNP	.											.	SLC20A2	64	.	0			c.G1438A						PASS	.	C	THR/ALA	26,4380	32.6+/-62.9	0,26,2177	89.0	58.0	69.0		1438	-4.0	0.0	8	dbSNP_132	69	187,8413	83.7+/-146.2	3,181,4116	yes	missense	SLC20A2	NM_006749.3	58	3,207,6293	TT,TC,CC		2.1744,0.5901,1.6377	benign	480/653	42294592	213,12793	2203	4300	6503	SO:0001583	missense	6575	exon8			CGGGTGCGTCCTT		CCDS6132.1	8p11.21	2013-05-22			ENSG00000168575	ENSG00000168575		"""Solute carriers"""	10947	protein-coding gene	gene with protein product		158378		MLVAR, GLVR2		7745689, 16790504	Standard	NM_001257180		Approved	PiT-2, Glvr-2	uc010lxm.4	Q08357	OTTHUMG00000164169	ENST00000342228.3:c.1438G>A	8.37:g.42294592C>T	ENSP00000340465:p.Ala480Thr	Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	17	4	0.235294	NM_001257181		Missense_Mutation	SNP	ENST00000342228.3	37	CCDS6132.1	15	0.006868131868131868	0	0.0	6	0.016574585635359115	0	0.0	9	0.011873350923482849	C	4.778	0.144587	0.09134	0.005901	0.021744	ENSG00000168575	ENST00000342228;ENST00000520262;ENST00000520179	D;D;D	0.89746	-2.56;-2.56;-2.56	5.63	-4.0	0.04057	.	0.358640	0.34828	N	0.003654	T	0.44871	0.1314	N	0.01438	-0.865	0.09310	N	0.999999	B	0.02656	0.0	B	0.04013	0.001	T	0.59118	-0.7514	10	0.11485	T	0.65	-2.0977	4.5824	0.12266	0.2622:0.3593:0.0:0.3785	.	480	Q08357	S20A2_HUMAN	T	480	ENSP00000340465:A480T;ENSP00000429754:A480T;ENSP00000429712:A480T	ENSP00000340465:A480T	A	-	1	0	SLC20A2	42413749	0.999000	0.42202	0.015000	0.15790	0.157000	0.22087	0.734000	0.26101	-1.008000	0.03404	-0.482000	0.04802	GCA	C|0.985;T|0.015	0.015	strong		0.637	SLC20A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377578.1		
TMPRSS11A	339967	hgsc.bcm.edu	37	4	68829109	68829109	+	Start_Codon_SNP	SNP	C	C	T	rs977728	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:68829109C>T	ENST00000334830.7	-	1	749	c.3G>A	c.(1-3)atG>atA	p.M1I	UBA6-AS1_ENST00000500538.2_RNA|TMPRSS11A_ENST00000508048.1_5'UTR|TMPRSS11A_ENST00000396188.2_Start_Codon_SNP_p.M1I			Q6ZMR5	TM11A_HUMAN	transmembrane protease, serine 11A	1					cell cycle (GO:0007049)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	serine-type endopeptidase activity (GO:0004252)	p.M1I(1)		breast(1)|cervix(2)|kidney(1)|large_intestine(8)|lung(11)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)	29						ACCGATACATCATGTACAGGA	0.423													C|||	1018	0.203275	0.115	0.3473	5008	,	,		17605	0.1835		0.2177	False		,,,				2504	0.226				p.M1I	NSCLC(26;2 894 10941 14480 22546)	Atlas-SNP	.											TMPRSS11A,NS,carcinoma,0,1	TMPRSS11A	74	1	1	Substitution - Missense(1)	stomach(1)	c.G3A						scavenged	.	C	ILE/MET,ILE/MET	591,3815	260.4+/-263.7	40,511,1652	173.0	153.0	160.0		3,3	1.3	0.2	4	dbSNP_86	160	1425,7175	273.7+/-290.8	116,1193,2991	yes	missense,missense	TMPRSS11A	NM_001114387.1,NM_182606.3	10,10	156,1704,4643	TT,TC,CC		16.5698,13.4135,15.5005	benign,benign	1/419,1/422	68829109	2016,10990	2203	4300	6503	SO:0001582	initiator_codon_variant	339967	exon1			ATACATCATGTAC	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.3G>A	4.37:g.68829109C>T	ENSP00000334611:p.Met1Ile	Somatic	120	1	0.00833333		WXS	Illumina HiSeq	Phase_I	95	45	0.473684	NM_001114387	J3KNQ8|Q2NKI9|Q6JE90|Q7RTY4|Q86TK8	Missense_Mutation	SNP	ENST00000334830.7	37	CCDS3519.1	431	0.19734432234432234	55	0.11178861788617886	107	0.2955801104972376	107	0.18706293706293706	162	0.21372031662269128	C	0.015	-1.547850	0.00926	0.134135	0.165698	ENSG00000187054	ENST00000334830;ENST00000396188	D;D	0.87966	-2.32;-2.32	5.95	1.27	0.21489	.	2.557560	0.01300	N	0.010266	T	0.00012	0.0000	.	.	.	0.58432	P	8.000000000008E-6	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.13469	-1.0508	8	0.56958	D	0.05	.	5.8662	0.18777	0.0:0.59:0.1312:0.2788	rs977728;rs52800649;rs61432757;rs977728	1;1	B5MDI9;Q6ZMR5	.;TM11A_HUMAN	I	1	ENSP00000334611:M1I;ENSP00000379491:M1I	ENSP00000334611:M1I	M	-	3	0	TMPRSS11A	68511704	0.041000	0.20044	0.178000	0.23040	0.018000	0.09664	-0.011000	0.12721	0.133000	0.18654	-0.182000	0.12963	ATG	C|0.829;T|0.171	0.171	strong		0.423	TMPRSS11A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251433.3	NM_182606	Missense_Mutation
ZNF611	81856	hgsc.bcm.edu	37	19	53209554	53209554	+	Missense_Mutation	SNP	G	G	T	rs4085565|rs34846371	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:53209554G>T	ENST00000319783.1	-	7	1070	c.754C>A	c.(754-756)Ccc>Acc	p.P252T	ZNF611_ENST00000602162.1_Missense_Mutation_p.P183T|ZNF611_ENST00000595798.1_Missense_Mutation_p.P183T|ZNF611_ENST00000540744.1_Missense_Mutation_p.P252T|ZNF611_ENST00000602046.1_5'Flank|ZNF611_ENST00000453741.2_Missense_Mutation_p.P183T|ZNF611_ENST00000543227.1_Missense_Mutation_p.P252T	NM_030972.3	NP_112234.3	Q8N823	ZN611_HUMAN	zinc finger protein 611	252			P -> I (requires 2 nucleotide substitutions; dbSNP:rs34846371). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:17974005}.|P -> L (in dbSNP:rs4085566).|P -> T (in dbSNP:rs4085565).		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(4)|large_intestine(10)|lung(12)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	36				OV - Ovarian serous cystadenocarcinoma(262;0.0233)|GBM - Glioblastoma multiforme(134;0.04)		CCTAAATGGGGTATCTGGTGT	0.383													-|||	2197	0.438698	0.7012	0.3285	5008	,	,		21189	0.3681		0.4105	False		,,,				2504	0.2638				p.P252T		Atlas-SNP	.											ZNF611,NS,carcinoma,+1,1	ZNF611	72	1	0			c.C754A						PASS	.	T	THR/PRO,THR/PRO,THR/PRO,THR/PRO	2862,1544		1004,854,345	137.0	145.0	142.0		754,754,547,754	1.2	0.0	19	dbSNP_108	142	3197,5397		725,1747,1825	no	missense,missense,missense,missense	ZNF611	NM_001161499.1,NM_001161500.1,NM_001161501.1,NM_030972.3	38,38,38,38	1729,2601,2170	TT,TG,GG		37.2004,35.0431,46.6077	benign,benign,benign,benign	252/706,252/706,183/637,252/706	53209554	6059,6941	2203	4297	6500	SO:0001583	missense	81856	exon7			AATGGGGTATCTG	AK091389	CCDS12855.1, CCDS54312.1	19q13.42	2013-01-08			ENSG00000213020	ENSG00000213020		"""Zinc fingers, C2H2-type"", ""-"""	28766	protein-coding gene	gene with protein product						12477932	Standard	NM_030972		Approved	MGC5384	uc010ydq.2	Q8N823	OTTHUMG00000154908	ENST00000319783.1:c.754C>A	19.37:g.53209554G>T	ENSP00000322427:p.Pro252Thr	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	92	37	0.402174	NM_030972	B3KRD5|Q69YG9	Missense_Mutation	SNP	ENST00000319783.1	37	CCDS12855.1	930	0.4258241758241758	314	0.6382113821138211	126	0.34806629834254144	214	0.3741258741258741	276	0.3641160949868074	.	1.705	-0.500665	0.04261	0.649569	0.372004	ENSG00000213020	ENST00000543227;ENST00000540744;ENST00000453741;ENST00000319783	T;T;T;T	0.12879	2.64;2.64;2.64;2.64	1.2	1.2	0.21068	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	N	0.00595	-1.35	0.80722	P	0.0	B	0.02656	0.0	B	0.06405	0.002	T	0.18178	-1.0345	8	0.39692	T	0.17	.	6.3535	0.21389	0.0:0.0:0.5087:0.4913	rs4085565;rs60261865;rs4085565	252	Q8N823	ZN611_HUMAN	T	252;252;183;252	ENSP00000437616:P252T;ENSP00000439211:P252T;ENSP00000443505:P183T;ENSP00000322427:P252T	ENSP00000322427:P252T	P	-	1	0	ZNF611	57901366	0.000000	0.05858	0.010000	0.14722	0.004000	0.04260	0.006000	0.13152	-0.306000	0.08818	-1.228000	0.01579	CCC	.	.	weak		0.383	ZNF611-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337612.1	NM_030972	
ITPR1	3708	hgsc.bcm.edu	37	3	4842231	4842231	+	Silent	SNP	C	C	T	rs2291862	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:4842231C>T	ENST00000443694.2	+	51	7009	c.7009C>T	c.(7009-7011)Ctg>Ttg	p.L2337L	ITPR1_ENST00000423119.2_Silent_p.L2304L|ITPR1_ENST00000544951.1_Intron|ITPR1_ENST00000354582.6_Silent_p.L2337L|ITPR1_ENST00000456211.2_Silent_p.L2289L|ITPR1_ENST00000302640.8_Silent_p.L2337L|ITPR1_ENST00000463980.1_3'UTR|ITPR1_ENST00000357086.4_Silent_p.L2304L			Q14643	ITPR1_HUMAN	inositol 1,4,5-trisphosphate receptor, type 1	2352					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|calcium ion transport (GO:0006816)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|negative regulation of calcium-mediated signaling (GO:0050849)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|post-embryonic development (GO:0009791)|regulation of insulin secretion (GO:0050796)|release of sequestered calcium ion into cytosol (GO:0051209)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|voluntary musculoskeletal movement (GO:0050882)	calcineurin complex (GO:0005955)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear inner membrane (GO:0005637)|nucleolus (GO:0005730)|platelet dense granule membrane (GO:0031088)|platelet dense tubular network (GO:0031094)|platelet dense tubular network membrane (GO:0031095)|postsynaptic density (GO:0014069)|sarcoplasmic reticulum (GO:0016529)	calcium channel inhibitor activity (GO:0019855)|calcium ion transmembrane transporter activity (GO:0015085)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|intracellular ligand-gated calcium channel activity (GO:0005218)|phosphatidylinositol binding (GO:0035091)			NS(1)|autonomic_ganglia(1)|breast(10)|endometrium(15)|kidney(6)|large_intestine(27)|liver(1)|lung(27)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|urinary_tract(2)	106				Epithelial(13;0.0199)|OV - Ovarian serous cystadenocarcinoma(96;0.0361)|all cancers(10;0.0982)	Caffeine(DB00201)	AATTCTACGACTGATATTTTC	0.493													T|||	1325	0.264577	0.1165	0.3617	5008	,	,		20031	0.377		0.3062	False		,,,				2504	0.2372				p.L2337L		Atlas-SNP	.											.	ITPR1	659	.	0			c.C7009T						PASS	.	T	,,	524,3364		32,460,1452	105.0	105.0	105.0		6910,7009,6865	-0.9	0.1	3	dbSNP_100	105	2284,5992		320,1644,2174	no	coding-synonymous,coding-synonymous,coding-synonymous	ITPR1	NM_001099952.2,NM_001168272.1,NM_002222.5	,,	352,2104,3626	TT,TC,CC		27.5979,13.4774,23.0845	,,	2304/2711,2337/2744,2289/2696	4842231	2808,9356	1944	4138	6082	SO:0001819	synonymous_variant	3708	exon53			CTACGACTGATAT	D26070	CCDS46740.1, CCDS46740.2, CCDS54550.1, CCDS54551.1	3p26.1	2014-06-12	2011-04-28			ENSG00000150995		"""Ion channels / Inositol triphosphate receptors"""	6180	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 94"""	147265	"""spinocerebellar ataxia 15"", ""spinocerebellar ataxia 16"", ""spinocerebellar ataxia 29"""	SCA15, SCA16, SCA29		7945203, 7500840, 17590087, 17932120, 22986007	Standard	NM_001099952		Approved	Insp3r1, IP3R1, ACV, PPP1R94	uc003bqc.3	Q14643		ENST00000443694.2:c.7009C>T	3.37:g.4842231C>T		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	103	50	0.485437	NM_001168272	E7EPX7|E9PDE9|Q14660|Q99897	Silent	SNP	ENST00000443694.2	37	CCDS54551.1																																																																																			C|0.722;T|0.278	0.278	strong		0.493	ITPR1-004	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337982.3	NM_002222	
LCA5	167691	hgsc.bcm.edu	37	6	80196848	80196848	+	Missense_Mutation	SNP	C	C	T	rs1875845	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:80196848C>T	ENST00000392959.1	-	9	2578	c.1967G>A	c.(1966-1968)gGc>gAc	p.G656D	LCA5_ENST00000369846.4_Missense_Mutation_p.G656D	NM_181714.3	NP_859065.2	Q86VQ0	LCA5_HUMAN	Leber congenital amaurosis 5	656			G -> D (in dbSNP:rs1875845).		intraciliary transport (GO:0042073)|photoreceptor cell maintenance (GO:0045494)|protein transport (GO:0015031)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	protein complex binding (GO:0032403)			haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(11)|lung(15)|prostate(2)|skin(1)	32		all_cancers(76;3.32e-05)|Acute lymphoblastic leukemia(125;1.1e-05)|all_hematologic(105;0.00117)|all_epithelial(107;0.0176)		BRCA - Breast invasive adenocarcinoma(397;0.0657)		GAGGAAAAAGCCTTCATCTTC	0.408													T|||	1779	0.355232	0.553	0.3444	5008	,	,		15995	0.2698		0.2674	False		,,,				2504	0.274				p.G656D		Atlas-SNP	.											.	LCA5	71	.	0			c.G1967A						PASS	.	T	ASP/GLY,ASP/GLY	2268,2138	578.8+/-384.8	578,1112,513	121.0	129.0	126.0		1967,1967	4.4	1.0	6	dbSNP_92	126	2653,5945	685.2+/-404.0	392,1869,2038	yes	missense,missense	LCA5	NM_001122769.2,NM_181714.3	94,94	970,2981,2551	TT,TC,CC		30.856,48.5247,37.8422	benign,benign	656/698,656/698	80196848	4921,8083	2203	4299	6502	SO:0001583	missense	167691	exon8			AAAAAGCCTTCAT		CCDS4990.1	6q14	2014-01-28			ENSG00000135338	ENSG00000135338			31923	protein-coding gene	gene with protein product	"""lebercilin"""	611408	"""chromosome 6 open reading frame 152"""	C6orf152		10631161, 17546029	Standard	NM_181714		Approved		uc003pix.3	Q86VQ0	OTTHUMG00000015080	ENST00000392959.1:c.1967G>A	6.37:g.80196848C>T	ENSP00000376686:p.Gly656Asp	Somatic	249	1	0.00401606		WXS	Illumina HiSeq	Phase_I	177	77	0.435028	NM_001122769	E1P542|Q9BWX7	Missense_Mutation	SNP	ENST00000392959.1	37	CCDS4990.1	767	0.35119047619047616	272	0.5528455284552846	128	0.35359116022099446	163	0.28496503496503495	204	0.2691292875989446	T	0.018	-1.483550	0.01027	0.514753	0.30856	ENSG00000135338	ENST00000369846;ENST00000392959	T;T	0.26660	1.72;1.72	5.53	4.38	0.52667	.	0.401274	0.26812	N	0.022363	T	0.01353	0.0044	N	0.00436	-1.5	0.48135	P	4.049999999999887E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.45977	-0.9224	9	0.02654	T	1	-8.7317	6.6827	0.23129	0.0:0.1827:0.0:0.8173	rs1875845;rs52828917;rs58895262;rs1875845	656	Q86VQ0	LCA5_HUMAN	D	656	ENSP00000358861:G656D;ENSP00000376686:G656D	ENSP00000358861:G656D	G	-	2	0	LCA5	80253567	0.987000	0.35691	0.999000	0.59377	0.175000	0.22909	1.009000	0.29886	0.909000	0.36697	-0.409000	0.06214	GGC	C|0.626;T|0.374	0.374	strong		0.408	LCA5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259269.1	NM_181714	
DPYS	1807	hgsc.bcm.edu	37	8	105478933	105478933	+	Silent	SNP	G	G	A	rs2298840	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:105478933G>A	ENST00000351513.2	-	1	348	c.216C>T	c.(214-216)ttC>ttT	p.F72F		NM_001385.2	NP_001376.1	Q14117	DPYS_HUMAN	dihydropyrimidinase	72					beta-alanine metabolic process (GO:0019482)|nucleobase-containing small molecule metabolic process (GO:0055086)|protein homotetramerization (GO:0051289)|pyrimidine nucleobase catabolic process (GO:0006208)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside catabolic process (GO:0046135)|small molecule metabolic process (GO:0044281)|thymine catabolic process (GO:0006210)|uracil catabolic process (GO:0006212)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	amino acid binding (GO:0016597)|dihydropyrimidinase activity (GO:0004157)|thymine binding (GO:0002059)|uracil binding (GO:0002058)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(23)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	41			OV - Ovarian serous cystadenocarcinoma(57;1.61e-06)|STAD - Stomach adenocarcinoma(118;0.229)			CCATGAAGGGGAACTGCATGT	0.736													G|||	1160	0.231629	0.2867	0.2133	5008	,	,		9267	0.3085		0.175	False		,,,				2504	0.1493				p.F72F		Atlas-SNP	.											.	DPYS	107	.	0			c.C216T						PASS	.	G		728,2942		64,600,1171	18.0	11.0	14.0		216	3.0	1.0	8	dbSNP_100	14	1026,5972		73,880,2546	no	coding-synonymous	DPYS	NM_001385.2		137,1480,3717	AA,AG,GG		14.6613,19.8365,16.4417		72/520	105478933	1754,8914	1835	3499	5334	SO:0001819	synonymous_variant	1807	exon1			GAAGGGGAACTGC	D78011	CCDS6302.1	8q22	2004-01-22			ENSG00000147647	ENSG00000147647			3013	protein-coding gene	gene with protein product		613326				8973361	Standard	NM_001385		Approved	DHPase	uc003yly.4	Q14117	OTTHUMG00000164891	ENST00000351513.2:c.216C>T	8.37:g.105478933G>A		Somatic	20	0	0		WXS	Illumina HiSeq	Phase_I	17	17	1	NM_001385		Silent	SNP	ENST00000351513.2	37	CCDS6302.1																																																																																			G|0.763;A|0.237	0.237	strong		0.736	DPYS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380814.1	NM_001385	
FCGBP	8857	hgsc.bcm.edu	37	19	40408532	40408532	+	Missense_Mutation	SNP	G	G	A	rs36106401	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:40408532G>A	ENST00000221347.6	-	8	4314	c.4307C>T	c.(4306-4308)cCg>cTg	p.P1436L		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	1436	VWFD 3. {ECO:0000255|PROSITE- ProRule:PRU00580}.		P -> L (in dbSNP:rs36106401).			extracellular vesicular exosome (GO:0070062)		p.P1436L(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)			CTCGCTCCCCGGCGGGCAAGG	0.642													G|||	562	0.11222	0.0363	0.2003	5008	,	,		17719	0.0387		0.1839	False		,,,				2504	0.1544				p.P1436L		Atlas-SNP	.											FCGBP,NS,carcinoma,0,1	FCGBP	416	1	1	Substitution - Missense(1)	stomach(1)	c.C4307T						PASS	.	G	LEU/PRO	356,4050	181.9+/-209.8	15,326,1862	53.0	57.0	55.0		4307	4.8	0.0	19	dbSNP_126	55	1750,6850	318.2+/-313.6	182,1386,2732	no	missense	FCGBP	NM_003890.2	98	197,1712,4594	AA,AG,GG		20.3488,8.0799,16.1925	probably-damaging	1436/5406	40408532	2106,10900	2203	4300	6503	SO:0001583	missense	8857	exon8			CTCCCCGGCGGGC	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.4307C>T	19.37:g.40408532G>A	ENSP00000221347:p.Pro1436Leu	Somatic	363	0	0		WXS	Illumina HiSeq	Phase_I	294	141	0.479592	NM_003890	O95784	Missense_Mutation	SNP	ENST00000221347.6	37	CCDS12546.1	237	0.10851648351648352	21	0.042682926829268296	50	0.13812154696132597	19	0.033216783216783216	147	0.19393139841688653	G	13.46	2.242442	0.39598	0.080799	0.203488	ENSG00000090920	ENST00000221347	T	0.19532	2.14	4.8	4.8	0.61643	von Willebrand factor, type D domain (1);	.	.	.	.	T	0.00012	0.0000	L	0.39566	1.225	0.80722	P	0.0	P	0.37864	0.61	B	0.24701	0.055	T	0.30707	-0.9969	8	0.12103	T	0.63	.	11.0692	0.47993	0.0916:0.0:0.9084:0.0	rs36106401	1436	Q9Y6R7	FCGBP_HUMAN	L	1436	ENSP00000221347:P1436L	ENSP00000221347:P1436L	P	-	2	0	FCGBP	45100372	.	.	0.046000	0.18839	0.004000	0.04260	.	.	2.240000	0.73641	0.644000	0.83932	CCG	G|0.853;A|0.147	0.147	strong		0.642	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890	
SPTAN1	6709	hgsc.bcm.edu	37	9	131379998	131379998	+	Silent	SNP	C	C	A	rs3750333	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:131379998C>A	ENST00000372731.4	+	41	5532	c.5422C>A	c.(5422-5424)Cgg>Agg	p.R1808R	SPTAN1_ENST00000372739.3_Silent_p.R1813R|SPTAN1_ENST00000358161.5_Silent_p.R1813R	NM_001195532.1|NM_003127.3	NP_001182461.1|NP_003118.2	Q13813	SPTN1_HUMAN	spectrin, alpha, non-erythrocytic 1	1808					actin filament capping (GO:0051693)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)	cuticular plate (GO:0032437)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|intracellular membrane-bounded organelle (GO:0043231)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|spectrin (GO:0008091)|vesicle (GO:0031982)|Z disc (GO:0030018)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)			NS(2)|breast(8)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(21)|liver(1)|lung(25)|ovary(5)|pancreas(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	87						GAAGCACAAGCGGCTGGAAGC	0.602													C|||	158	0.0315495	0.0023	0.0562	5008	,	,		17767	0.0804		0.0159	False		,,,				2504	0.0194				p.R1813R	NSCLC(120;833 1744 2558 35612 37579)	Atlas-SNP	.											.	SPTAN1	266	.	0			c.C5437A						PASS	.	C	,,	22,4384	29.0+/-57.7	0,22,2181	56.0	60.0	58.0		5437,5362,5422	5.8	1.0	9	dbSNP_107	58	131,8469	67.7+/-130.1	0,131,4169	no	coding-synonymous,coding-synonymous,coding-synonymous	SPTAN1	NM_001130438.2,NM_001195532.1,NM_003127.3	,,	0,153,6350	AA,AC,CC		1.5233,0.4993,1.1764	,,	1813/2478,1788/2453,1808/2473	131379998	153,12853	2203	4300	6503	SO:0001819	synonymous_variant	6709	exon42			CACAAGCGGCTGG	M19725	CCDS6905.1, CCDS48036.1, CCDS75914.1	9q34.11	2013-01-10	2012-06-15		ENSG00000197694	ENSG00000197694		"""EF-hand domain containing"""	11273	protein-coding gene	gene with protein product	"""alpha-fodrin"""	182810				3336352	Standard	NM_003127		Approved		uc004bvm.4	Q13813	OTTHUMG00000020754	ENST00000372731.4:c.5422C>A	9.37:g.131379998C>A		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	85	47	0.552941	NM_001130438	Q13186|Q15324|Q16606|Q59EF1|Q5VXV5|Q5VXV6|Q7Z6M5|Q9P0V0	Silent	SNP	ENST00000372731.4	37	CCDS6905.1																																																																																			C|0.977;A|0.023	0.023	strong		0.602	SPTAN1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054472.1	NM_003127	
KDELR3	11015	hgsc.bcm.edu	37	22	38877461	38877461	+	Missense_Mutation	SNP	T	T	G	rs12004	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:38877461T>G	ENST00000216014.4	+	4	768	c.596T>G	c.(595-597)gTg>gGg	p.V199G	KDELR3_ENST00000471268.1_3'UTR|KDELR3_ENST00000409006.3_Missense_Mutation_p.V199G	NM_006855.2	NP_006846.1	O43731	ERD23_HUMAN	KDEL (Lys-Asp-Glu-Leu) endoplasmic reticulum protein retention receptor 3	199			V -> G (in dbSNP:rs12004). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.4}.		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)|protein retention in ER lumen (GO:0006621)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	ER retention sequence binding (GO:0046923)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|ovary(2)|prostate(1)	13	Melanoma(58;0.0286)					TACTTGTATGTGACCAAAGGT	0.438													T|||	1278	0.255192	0.1657	0.1974	5008	,	,		20556	0.3542		0.3062	False		,,,				2504	0.2628				p.V199G	Ovarian(11;103 529 24120 28493 32980)	Atlas-SNP	.											.	KDELR3	39	.	0			c.T596G						PASS	.	T	GLY/VAL,GLY/VAL	824,3582	325.3+/-299.0	73,678,1452	138.0	125.0	129.0		596,596	4.7	1.0	22	dbSNP_52	129	2634,5966	426.6+/-355.3	402,1830,2068	yes	missense,missense	KDELR3	NM_006855.2,NM_016657.1	109,109	475,2508,3520	GG,GT,TT		30.6279,18.7018,26.5877	possibly-damaging,possibly-damaging	199/215,199/221	38877461	3458,9548	2203	4300	6503	SO:0001583	missense	11015	exon4			TGTATGTGACCAA	AL035081	CCDS13972.1, CCDS46705.1	22q13	2008-05-02			ENSG00000100196	ENSG00000100196			6306	protein-coding gene	gene with protein product							Standard	NM_006855		Approved		uc003avu.3	O43731	OTTHUMG00000153520	ENST00000216014.4:c.596T>G	22.37:g.38877461T>G	ENSP00000216014:p.Val199Gly	Somatic	237	1	0.00421941		WXS	Illumina HiSeq	Phase_I	178	86	0.483146	NM_016657	A8K7T7|B8ZZ26|O95557|Q4V750|Q4V767|Q53FP4|Q53GK1	Missense_Mutation	SNP	ENST00000216014.4	37	CCDS13972.1	630	0.28846153846153844	89	0.18089430894308944	81	0.22375690607734808	219	0.38286713286713286	241	0.3179419525065963	T	16.69	3.193945	0.58017	0.187018	0.306279	ENSG00000100196	ENST00000216014;ENST00000409006	T;T	0.75704	-0.96;-0.96	4.65	4.65	0.58169	.	0.218747	0.39475	N	0.001353	T	0.00012	0.0000	M	0.81802	2.56	0.09310	P	0.999999999789922	B;P	0.43973	0.356;0.823	B;P	0.48141	0.197;0.568	T	0.01159	-1.1433	9	0.62326	D	0.03	-10.4461	14.226	0.65860	0.0:0.0:0.0:1.0	rs12004;rs3180098;rs17173760;rs17402570;rs52804343;rs57393871;rs12004	199;199	O43731;O43731-2	ERD23_HUMAN;.	G	199	ENSP00000216014:V199G;ENSP00000386918:V199G	ENSP00000216014:V199G	V	+	2	0	KDELR3	37207407	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.868000	0.87116	1.950000	0.56595	0.477000	0.44152	GTG	A|0.004;C|0.002	.	strong		0.438	KDELR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331474.1		
ALOX15B	247	hgsc.bcm.edu	37	17	7950009	7950009	+	Nonsense_Mutation	SNP	C	C	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:7950009C>G	ENST00000380183.4	+	9	1363	c.1224C>G	c.(1222-1224)taC>taG	p.Y408*	ALOX15B_ENST00000572022.1_Nonsense_Mutation_p.Y408*|ALOX15B_ENST00000380173.2_Intron|ALOX15B_ENST00000573359.1_Intron	NM_001141.2	NP_001132.2	O15296	LX15B_HUMAN	arachidonate 15-lipoxygenase, type B	408	Lipoxygenase. {ECO:0000255|PROSITE- ProRule:PRU00726}.				apoptotic process (GO:0006915)|arachidonic acid metabolic process (GO:0019369)|hepoxilin biosynthetic process (GO:0051122)|linoleic acid metabolic process (GO:0043651)|lipid metabolic process (GO:0006629)|lipoxygenase pathway (GO:0019372)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of growth (GO:0045926)|positive regulation of chemokine secretion (GO:0090197)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|positive regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035360)|prostate gland development (GO:0030850)|regulation of epithelial cell differentiation (GO:0030856)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|intracellular (GO:0005622)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	arachidonate 15-lipoxygenase activity (GO:0050473)|arachidonate 8(S)-lipoxygenase activity (GO:0036403)|calcium ion binding (GO:0005509)|iron ion binding (GO:0005506)|linoleate 13S-lipoxygenase activity (GO:0016165)|lipid binding (GO:0008289)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(3)|ovary(1)|prostate(2)|skin(2)|stomach(4)|upper_aerodigestive_tract(1)	24						ACACCCGATACACCCTGCACA	0.627																																					p.Y408X		Atlas-SNP	.											.	ALOX15B	66	.	0			c.C1224G						PASS	.						64.0	54.0	57.0					17																	7950009		2203	4300	6503	SO:0001587	stop_gained	247	exon9			CCGATACACCCTG	U78294	CCDS11128.1, CCDS32558.1, CCDS32559.1	17p13.1	2013-03-20	2006-01-16		ENSG00000179593	ENSG00000179593	1.13.11.33	"""Arachidonate lipoxygenases"""	434	protein-coding gene	gene with protein product		603697	"""arachidonate 15-lipoxygenase, second type"""			9177185	Standard	NM_001039130		Approved	15-LOX-2	uc002gju.3	O15296	OTTHUMG00000108181	ENST00000380183.4:c.1224C>G	17.37:g.7950009C>G	ENSP00000369530:p.Tyr408*	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	61	31	0.508197	NM_001141	D3DTR2|Q8IYQ2|Q8TEV3|Q8TEV4|Q8TEV5|Q8TEV6|Q9UKM4	Nonsense_Mutation	SNP	ENST00000380183.4	37	CCDS11128.1	.	.	.	.	.	.	.	.	.	.	C	16.09	3.025494	0.54683	.	.	ENSG00000179593	ENST00000380183	.	.	.	4.99	-2.88	0.05682	.	0.264891	0.39020	N	0.001493	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-7.1679	11.9463	0.52930	0.0:0.5497:0.0:0.4503	.	.	.	.	X	408	.	ENSP00000369530:Y408X	Y	+	3	2	ALOX15B	7890734	0.222000	0.23652	0.004000	0.12327	0.007000	0.05969	0.543000	0.23237	-0.334000	0.08463	-0.140000	0.14226	TAC	.	.	none		0.627	ALOX15B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226985.2		
DAPL1	92196	hgsc.bcm.edu	37	2	159660870	159660870	+	Silent	SNP	C	C	T	rs17810398	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:159660870C>T	ENST00000309950.3	+	2	191	c.135C>T	c.(133-135)ttC>ttT	p.F45F	DAPL1_ENST00000409042.1_Silent_p.F45F	NM_001017920.2	NP_001017920.2	A0PJW8	DAPL1_HUMAN	death associated protein-like 1	45					apoptotic process (GO:0006915)|cell differentiation (GO:0030154)					prostate(1)	1						AAACAGGATTCGAGAAAACAA	0.388													C|||	292	0.0583067	0.0159	0.1023	5008	,	,		15777	0.0		0.1561	False		,,,				2504	0.044				p.F45F		Atlas-SNP	.											.	DAPL1	11	.	0			c.C135T						PASS	.	C		139,4267	93.9+/-132.6	1,137,2065	55.0	54.0	54.0		135	-5.9	0.4	2	dbSNP_123	54	1155,7445	228.3+/-263.4	82,991,3227	no	coding-synonymous	DAPL1	NM_001017920.2		83,1128,5292	TT,TC,CC		13.4302,3.1548,9.9493		45/108	159660870	1294,11712	2203	4300	6503	SO:0001819	synonymous_variant	92196	exon2			AGGATTCGAGAAA		CCDS33307.1	2q24	2007-06-26			ENSG00000163331	ENSG00000163331			21490	protein-coding gene	gene with protein product							Standard	NM_001017920		Approved		uc002uaf.3	A0PJW8	OTTHUMG00000153970	ENST00000309950.3:c.135C>T	2.37:g.159660870C>T		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	97	36	0.371134	NM_001017920	A0PJW9|B9EIK6	Silent	SNP	ENST00000309950.3	37	CCDS33307.1	166	0.076007326007326	12	0.024390243902439025	48	0.13259668508287292	0	0.0	106	0.13984168865435356	C	7.900	0.734156	0.15574	0.031548	0.134302	ENSG00000163331	ENST00000343761	.	.	.	5.83	-5.87	0.02297	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	0.99999990897	.	.	.	.	.	.	.	.	.	.	.	.	.	.	2.6942	0.05129	0.2775:0.2467:0.3631:0.1127	rs17810398;rs17810398	.	.	.	X	21	.	.	R	+	1	2	DAPL1	159369116	0.515000	0.26210	0.405000	0.26409	0.821000	0.46438	-0.281000	0.08456	-1.474000	0.01879	-0.271000	0.10264	CGA	C|0.916;T|0.084	0.084	strong		0.388	DAPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333265.1	NM_001017920	
PPWD1	23398	hgsc.bcm.edu	37	5	64863426	64863426	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:64863426C>T	ENST00000261308.5	+	2	355	c.283C>T	c.(283-285)Cat>Tat	p.H95Y	PPWD1_ENST00000535264.1_Missense_Mutation_p.H65Y|PPWD1_ENST00000538977.1_Intron	NM_015342.3	NP_056157.1	Q96BP3	PPWD1_HUMAN	peptidylprolyl isomerase domain and WD repeat containing 1	95					mRNA splicing, via spliceosome (GO:0000398)|protein folding (GO:0006457)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)	peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)	19		Lung NSC(167;7.21e-05)|Prostate(74;0.0174)|Ovarian(174;0.186)		Lung(70;0.00451)		TGTTATCACCCATGTGGTATG	0.328																																					p.H95Y		Atlas-SNP	.											PPWD1,NS,carcinoma,-2,1	PPWD1	47	1	0			c.C283T						scavenged	.						111.0	112.0	112.0					5																	64863426		2203	4300	6503	SO:0001583	missense	23398	exon2			ATCACCCATGTGG	AK025679	CCDS3985.1, CCDS64161.1, CCDS64162.1	5q12.3	2013-01-09			ENSG00000113593	ENSG00000113593		"""WD repeat domain containing"""	28954	protein-coding gene	gene with protein product						7584044	Standard	NM_015342		Approved	KIAA0073	uc003jtv.5	Q96BP3	OTTHUMG00000131226	ENST00000261308.5:c.283C>T	5.37:g.64863426C>T	ENSP00000261308:p.His95Tyr	Somatic	400	0	0		WXS	Illumina HiSeq	Phase_I	454	5	0.0110132	NM_015342	B4DWR9|Q15002|Q7KZ89	Missense_Mutation	SNP	ENST00000261308.5	37	CCDS3985.1	.	.	.	.	.	.	.	.	.	.	C	26.0	4.695460	0.88830	.	.	ENSG00000113593	ENST00000261308;ENST00000535264;ENST00000505380	T;T;T	0.62941	-0.01;-0.01;0.21	5.62	5.62	0.85841	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.044921	0.85682	D	0.000000	T	0.67552	0.2905	L	0.59436	1.845	0.80722	D	1	B;B	0.27625	0.151;0.183	B;B	0.39531	0.089;0.302	T	0.61821	-0.6984	10	0.27082	T	0.32	.	19.6517	0.95819	0.0:1.0:0.0:0.0	.	65;95	F5H7P7;Q96BP3	.;PPWD1_HUMAN	Y	95;65;14	ENSP00000261308:H95Y;ENSP00000442371:H65Y;ENSP00000423234:H14Y	ENSP00000261308:H95Y	H	+	1	0	PPWD1	64899182	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	7.794000	0.85869	2.662000	0.90505	0.655000	0.94253	CAT	.	.	none		0.328	PPWD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253970.2	NM_015342	
TRIM2	23321	hgsc.bcm.edu	37	4	154197234	154197234	+	Silent	SNP	T	T	G	rs2289409	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:154197234T>G	ENST00000437508.2	+	3	525	c.324T>G	c.(322-324)acT>acG	p.T108T	TRIM2_ENST00000338700.5_Silent_p.T135T|TRIM2_ENST00000494872.1_3'UTR	NM_001130067.1	NP_001123539.1	Q9C040	TRIM2_HUMAN	tripartite motif containing 2	108					cell death (GO:0008219)|regulation of neuron apoptotic process (GO:0043523)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(7)|prostate(1)	19	all_hematologic(180;0.093)	Medulloblastoma(177;0.00225)		GBM - Glioblastoma multiforme(119;0.0102)|LUSC - Lung squamous cell carcinoma(193;0.0703)		AGACAGTCACTGCTGTGGCTG	0.562													T|||	952	0.190096	0.3525	0.2161	5008	,	,		20029	0.0556		0.162	False		,,,				2504	0.1196				p.T135T		Atlas-SNP	.											.	TRIM2	105	.	0			c.T405G						PASS	.	T	,	1439,2967	465.9+/-354.3	242,955,1006	76.0	68.0	71.0		324,405	2.8	1.0	4	dbSNP_100	71	1573,7027	295.7+/-302.5	142,1289,2869	no	coding-synonymous,coding-synonymous	TRIM2	NM_001130067.1,NM_015271.3	,	384,2244,3875	GG,GT,TT		18.2907,32.66,23.1585	,	108/745,135/772	154197234	3012,9994	2203	4300	6503	SO:0001819	synonymous_variant	23321	exon3			AGTCACTGCTGTG	AF220018	CCDS3781.2, CCDS47147.1	4q31.3	2013-01-09	2011-01-25		ENSG00000109654	ENSG00000109654		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	15974	protein-coding gene	gene with protein product		614141	"""tripartite motif-containing 2"""			9628581, 11331580	Standard	NM_015271		Approved	KIAA0517, RNF86	uc003inh.2	Q9C040	OTTHUMG00000155991	ENST00000437508.2:c.324T>G	4.37:g.154197234T>G		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	81	41	0.506173	NM_015271	D3DP09|O60272|Q9BSI9|Q9UFZ1	Silent	SNP	ENST00000437508.2	37	CCDS47147.1																																																																																			T|0.783;G|0.217	0.217	strong		0.562	TRIM2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342652.1		
CYP4F12	66002	hgsc.bcm.edu	37	19	15793235	15793235	+	Missense_Mutation	SNP	T	T	C	rs2285888	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:15793235T>C	ENST00000550308.1	+	6	942	c.562T>C	c.(562-564)Tgt>Cgt	p.C188R	CYP4F12_ENST00000324632.10_Missense_Mutation_p.C188R	NM_023944.3	NP_076433	Q9HCS2	CP4FC_HUMAN	cytochrome P450, family 4, subfamily F, polypeptide 12	188			C -> R (in dbSNP:rs2285888). {ECO:0000269|PubMed:11162607, ECO:0000269|PubMed:11162645, ECO:0000269|PubMed:12975309, ECO:0000269|Ref.7}.		arachidonic acid metabolic process (GO:0019369)|drug metabolic process (GO:0017144)|epoxygenase P450 pathway (GO:0019373)|leukotriene B4 catabolic process (GO:0036101)|long-chain fatty acid metabolic process (GO:0001676)|negative regulation of blood coagulation (GO:0030195)|oxidation-reduction process (GO:0055114)|pressure natriuresis (GO:0003095)|renal water homeostasis (GO:0003091)|small molecule metabolic process (GO:0044281)|sodium ion homeostasis (GO:0055078)|very long-chain fatty acid metabolic process (GO:0000038)|vitamin E metabolic process (GO:0042360)|vitamin K biosynthetic process (GO:0042371)|xenobiotic metabolic process (GO:0006805)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)	alkane 1-monooxygenase activity (GO:0018685)|arachidonic acid epoxygenase activity (GO:0008392)|aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|leukotriene-B4 20-monooxygenase activity (GO:0050051)|vitamin-K-epoxide reductase (warfarin-sensitive) activity (GO:0047057)			NS(1)|central_nervous_system(3)|endometrium(4)|kidney(2)|large_intestine(7)|lung(12)|ovary(3)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	41	Acute lymphoblastic leukemia(2;0.0367)				Fingolimod(DB08868)	GGGCAGCAGTTGTCTGGACAT	0.557													.|||	3105	0.620008	0.6006	0.6599	5008	,	,		20612	0.745		0.5288	False		,,,				2504	0.5828				p.C188R		Atlas-SNP	.											.	CYP4F12	89	.	0			c.T562C	GRCh37	CM043944	CYP4F12	M	rs2285888	PASS	.	C	ARG/CYS	2646,1760		816,1014,373	76.0	73.0	74.0		562	0.1	0.0	19	dbSNP_100	74	4593,4007		1266,2061,973	no	missense	CYP4F12	NM_023944.3	180	2082,3075,1346	CC,CT,TT		46.593,39.9455,44.3411	benign	188/525	15793235	7239,5767	2203	4300	6503	SO:0001583	missense	66002	exon6			AGCAGTTGTCTGG	AB035130	CCDS42517.1	19p13.1	2008-02-05	2003-01-14		ENSG00000186204	ENSG00000186204		"""Cytochrome P450s"""	18857	protein-coding gene	gene with protein product		611485	"""cytochrome P450, subfamily IVF, polypeptide 12"""			11162607	Standard	NM_023944		Approved		uc002nbl.3	Q9HCS2	OTTHUMG00000164477	ENST00000550308.1:c.562T>C	19.37:g.15793235T>C	ENSP00000448998:p.Cys188Arg	Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	174	171	0.982759	NM_023944	E7ET51|O60389|Q5JPJ7|Q9HCS1	Missense_Mutation	SNP	ENST00000550308.1	37	CCDS42517.1	1248	0.5714285714285714	261	0.5304878048780488	216	0.5966850828729282	402	0.7027972027972028	369	0.4868073878627968	.	0.004	-2.378912	0.00205	0.600545	0.53407	ENSG00000186204	ENST00000550308;ENST00000324632	T;T	0.78481	-1.18;-1.18	2.36	0.14	0.14804	.	0.927018	0.08869	N	0.881865	T	0.00012	0.0000	N	0.00563	-1.375	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.40213	-0.9575	9	0.02654	T	1	.	2.5919	0.04845	0.2156:0.39:0.0:0.3944	rs2285888;rs10909318	188	Q9HCS2	CP4FC_HUMAN	R	188	ENSP00000448998:C188R;ENSP00000321821:C188R	ENSP00000321821:C188R	C	+	1	0	CYP4F12	15654235	0.000000	0.05858	0.004000	0.12327	0.015000	0.08874	0.306000	0.19279	-0.146000	0.11274	-1.374000	0.01184	TGT	.	.	weak		0.557	CYP4F12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378938.9		
RCAN3	11123	hgsc.bcm.edu	37	1	24859617	24859617	+	Silent	SNP	G	G	A	rs196429	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:24859617G>A	ENST00000374395.4	+	4	727	c.414G>A	c.(412-414)ccG>ccA	p.P138P	RCAN3_ENST00000538532.1_Silent_p.P80P|RCAN3_ENST00000374393.2_Intron|RCAN3_ENST00000412742.2_Intron|RCAN3_ENST00000436717.2_Silent_p.P128P	NM_001251978.1|NM_001251979.1|NM_001251984.1	NP_001238907.1|NP_001238908.1|NP_001238913.1	Q9UKA8	RCAN3_HUMAN	RCAN family member 3	138					anatomical structure morphogenesis (GO:0009653)|calcium-mediated signaling (GO:0019722)		RNA binding (GO:0003723)|troponin I binding (GO:0031013)			central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(2)	7		Colorectal(325;3.46e-05)|Renal(390;0.0007)|Lung NSC(340;0.000946)|all_lung(284;0.00125)|Ovarian(437;0.00473)|Breast(348;0.0148)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.19)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0427)|OV - Ovarian serous cystadenocarcinoma(117;1.13e-24)|Colorectal(126;6.09e-08)|COAD - Colon adenocarcinoma(152;3.33e-06)|GBM - Glioblastoma multiforme(114;0.000923)|BRCA - Breast invasive adenocarcinoma(304;0.0018)|KIRC - Kidney renal clear cell carcinoma(1967;0.00359)|STAD - Stomach adenocarcinoma(196;0.00493)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.14)		ATCTCCTGCCGCCCCAGCCTG	0.557													G|||	1921	0.383586	0.2458	0.3314	5008	,	,		12764	0.6786		0.3221	False		,,,				2504	0.3661				p.P138P		Atlas-SNP	.											.	RCAN3	22	.	0			c.G414A						PASS	.	G		1175,3231	414.8+/-337.0	148,879,1176	69.0	61.0	64.0		414	-10.2	0.0	1	dbSNP_79	64	2747,5853	437.3+/-358.6	432,1883,1985	no	coding-synonymous	RCAN3	NM_013441.2		580,2762,3161	AA,AG,GG		31.9419,26.6682,30.1553		138/242	24859617	3922,9084	2203	4300	6503	SO:0001819	synonymous_variant	11123	exon4			CCTGCCGCCCCAG		CCDS254.1, CCDS57980.1, CCDS57981.1, CCDS57982.1, CCDS72730.1	1p35.3-p33	2008-02-05	2007-06-26	2007-06-26	ENSG00000117602	ENSG00000117602			3042	protein-coding gene	gene with protein product		605860	"""Down syndrome critical region gene 1-like 2"""	DSCR1L2		10756093	Standard	NM_001251984		Approved		uc001bjj.3	Q9UKA8	OTTHUMG00000003298	ENST00000374395.4:c.414G>A	1.37:g.24859617G>A		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	48	19	0.395833	NM_001251979	A4GU14|A4LA69|E3VWE2|E5L4P0|E5L4P7|E7ENV1|E7EWD8|G1FI66|G1FLF0|Q5ECL3|Q5TGC6|Q9NUC8|Q9UKA7	Silent	SNP	ENST00000374395.4	37	CCDS254.1																																																																																			G|0.669;A|0.331	0.331	strong		0.557	RCAN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009176.2		
CNOT4	4850	hgsc.bcm.edu	37	7	135123060	135123060	+	Missense_Mutation	SNP	G	G	C	rs17480616	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:135123060G>C	ENST00000315544.5	-	2	299	c.20C>G	c.(19-21)gCg>gGg	p.A7G	CNOT4_ENST00000361528.4_Missense_Mutation_p.A7G|CNOT4_ENST00000541284.1_Missense_Mutation_p.A7G|CNOT4_ENST00000356162.4_Missense_Mutation_p.A7G|CNOT4_ENST00000428680.2_Missense_Mutation_p.A7G|CNOT4_ENST00000451834.1_Missense_Mutation_p.A7G|CNOT4_ENST00000423368.2_Missense_Mutation_p.A7G|CNOT4_ENST00000414802.1_Missense_Mutation_p.A7G	NM_001190848.1	NP_001177777.1	O95628	CNOT4_HUMAN	CCR4-NOT transcription complex, subunit 4	7			A -> G (in dbSNP:rs17480616). {ECO:0000269|Ref.3}.		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						GTCTTCCTTCGCATCAGGACT	0.433													G|||	37	0.00738818	0.0023	0.0173	5008	,	,		17128	0.0		0.0209	False		,,,				2504	0.001				p.A7G	Ovarian(51;766 1130 5502 35047 50875)	Atlas-SNP	.											.	CNOT4	146	.	0			c.C20G						PASS	.	G	GLY/ALA,GLY/ALA,GLY/ALA,GLY/ALA,GLY/ALA,GLY/ALA	17,3759		0,17,1871	67.0	63.0	65.0		20,20,20,20,20,20	1.5	1.0	7	dbSNP_123	65	228,7992		4,220,3886	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	60,60,60,60,60,60	4,237,5757	CC,CG,GG		2.7737,0.4502,2.0423	benign,benign,benign,benign,benign,benign	7/573,7/643,7/576,7/711,7/714,7/640	135123060	245,11751	1888	4110	5998	SO:0001583	missense	4850	exon2			TCCTTCGCATCAG	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.20C>G	7.37:g.135123060G>C	ENSP00000326731:p.Ala7Gly	Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	98	39	0.397959	NM_001190850	B7Z6I4|E7ET38|F8VQP3|O95339|O95627|Q8IYM7|Q8NCL0|Q9NPQ1|Q9NZN6	Missense_Mutation	SNP	ENST00000315544.5	37	CCDS55166.1	27	0.012362637362637362	2	0.0040650406504065045	11	0.03038674033149171	0	0.0	14	0.018469656992084433	G	12.53	1.964625	0.34659	0.004502	0.027737	ENSG00000080802	ENST00000541284;ENST00000451834;ENST00000423368;ENST00000262563;ENST00000361528;ENST00000414802;ENST00000356162;ENST00000428680;ENST00000315544	D;D;D;D;D;D;D;D	0.86164	-2.08;-2.08;-2.08;-2.08;-2.08;-2.08;-2.08;-2.08	5.87	1.55	0.23275	Zinc finger, RING/FYVE/PHD-type (1);	0.373548	0.33938	N	0.004417	T	0.50103	0.1596	N	0.14661	0.345	0.21290	N	0.999735	B;B;B;P;B;B	0.34997	0.211;0.315;0.405;0.479;0.019;0.019	B;B;B;B;B;B	0.31946	0.071;0.138;0.102;0.119;0.022;0.022	T	0.54063	-0.8349	10	0.32370	T	0.25	0.5143	9.3711	0.38254	0.4834:0.0:0.5166:0.0	rs17480616;rs52814664;rs17480616	7;7;7;7;7;7	E7ET38;F8VQP3;O95628;O95628-2;O95628-4;O95628-8	.;.;CNOT4_HUMAN;.;.;.	G	7	ENSP00000445508:A7G;ENSP00000388491:A7G;ENSP00000406777:A7G;ENSP00000354673:A7G;ENSP00000416532:A7G;ENSP00000348485:A7G;ENSP00000399108:A7G;ENSP00000326731:A7G	ENSP00000262563:A7G	A	-	2	0	CNOT4	134773600	0.999000	0.42202	0.976000	0.42696	0.929000	0.56500	1.442000	0.35046	-0.007000	0.14345	0.655000	0.94253	GCG	G|0.983;C|0.017	0.017	strong		0.433	CNOT4-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_013316	
OR5AR1	219493	hgsc.bcm.edu	37	11	56431834	56431834	+	Missense_Mutation	SNP	A	A	G	rs56067375	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:56431834A>G	ENST00000302969.2	+	1	697	c.673A>G	c.(673-675)Atc>Gtc	p.I225V		NM_001004730.1	NP_001004730.1	Q8NGP9	O5AR1_HUMAN	olfactory receptor, family 5, subfamily AR, member 1 (gene/pseudogene)	225			I -> V (in dbSNP:rs56067375).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.I225V(1)		NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(1)|lung(12)|prostate(1)|skin(3)|stomach(1)	26						CCTTGTTGCAATCATCAGAAT	0.468													A|||	270	0.0539137	0.0287	0.0159	5008	,	,		22087	0.0913		0.0547	False		,,,				2504	0.0757				p.I225V		Atlas-SNP	.											OR5AR1,NS,carcinoma,0,1	OR5AR1	68	1	1	Substitution - Missense(1)	stomach(1)	c.A673G						PASS	.	A	VAL/ILE	135,4267	96.2+/-134.9	1,133,2067	165.0	140.0	148.0		673	4.9	0.9	11	dbSNP_129	148	481,8111	140.8+/-197.2	13,455,3828	yes	missense	OR5AR1	NM_001004730.1	29	14,588,5895	GG,GA,AA		5.5982,3.0668,4.7406	benign	225/311	56431834	616,12378	2201	4296	6497	SO:0001583	missense	219493	exon1			GTTGCAATCATCA	AB065740	CCDS31535.1	11q11	2013-10-10	2013-10-10		ENSG00000172459	ENSG00000172459		"""GPCR / Class A : Olfactory receptors"""	15260	protein-coding gene	gene with protein product			"""olfactory receptor, family 5, subfamily AR, member 1"""				Standard	NM_001004730		Approved		uc010rjm.2	Q8NGP9	OTTHUMG00000154213	ENST00000302969.2:c.673A>G	11.37:g.56431834A>G	ENSP00000302639:p.Ile225Val	Somatic	190	0	0		WXS	Illumina HiSeq	Phase_I	136	103	0.757353	NM_001004730	Q6IF61	Missense_Mutation	SNP	ENST00000302969.2	37	CCDS31535.1	96	0.04395604395604396	12	0.024390243902439025	6	0.016574585635359115	41	0.07167832167832168	37	0.048812664907651716	A	9.001	0.980067	0.18812	0.030668	0.055982	ENSG00000172459	ENST00000302969	T	0.00024	8.98	4.91	4.91	0.64330	GPCR, rhodopsin-like superfamily (1);	0.000000	0.48286	D	0.000181	T	0.00012	0.0000	N	0.12502	0.225	0.26938	N	0.966306	B	0.24882	0.113	B	0.23574	0.047	T	0.10870	-1.0611	10	0.40728	T	0.16	.	8.2745	0.31864	0.9023:0.0:0.0977:0.0	rs56067375;rs61743856	225	Q8NGP9	O5AR1_HUMAN	V	225	ENSP00000302639:I225V	ENSP00000302639:I225V	I	+	1	0	OR5AR1	56188410	0.001000	0.12720	0.915000	0.36163	0.217000	0.24651	0.024000	0.13555	2.064000	0.61679	0.467000	0.42956	ATC	A|0.952;G|0.048	0.048	strong		0.468	OR5AR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334434.1	NM_001004730	
ALMS1	7840	hgsc.bcm.edu	37	2	73679280	73679280	+	Missense_Mutation	SNP	A	A	G	rs6546838	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:73679280A>G	ENST00000264448.6	+	8	5734	c.5623A>G	c.(5623-5625)Ata>Gta	p.I1875V	ALMS1_ENST00000377715.1_Missense_Mutation_p.I1875V|ALMS1_ENST00000409009.1_Missense_Mutation_p.I1833V	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	1875	34 X 47 AA approximate tandem repeat.		I -> V (in dbSNP:rs6546838).		endosomal transport (GO:0016197)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of stress fiber assembly (GO:0051492)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)				breast(4)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(31)|lung(68)|ovary(4)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	147						TTTGAAAGCAATAGGGGTTCC	0.443													G|||	1797	0.358826	0.8585	0.3919	5008	,	,		18751	0.0089		0.2276	False		,,,				2504	0.1554				p.I1875V		Atlas-SNP	.											.	ALMS1	384	.	0			c.A5623G						PASS	.	G	VAL/ILE	2708,1020		995,718,151	62.0	61.0	62.0		5623	-3.3	0.0	2	dbSNP_116	62	1951,6229		221,1509,2360	yes	missense	ALMS1	NM_015120.4	29	1216,2227,2511	GG,GA,AA		23.8509,27.3605,39.125	benign	1875/4168	73679280	4659,7249	1864	4090	5954	SO:0001583	missense	7840	exon8			AAAGCAATAGGGG	AB002326	CCDS42697.1	2p13.1	2014-09-17			ENSG00000116127	ENSG00000116127			428	protein-coding gene	gene with protein product		606844				9063741	Standard	NM_015120		Approved	KIAA0328	uc002sje.1	Q8TCU4	OTTHUMG00000152812	ENST00000264448.6:c.5623A>G	2.37:g.73679280A>G	ENSP00000264448:p.Ile1875Val	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	66	66	1	NM_015120	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Missense_Mutation	SNP	ENST00000264448.6	37	CCDS42697.1	731	0.3347069597069597	419	0.8516260162601627	126	0.34806629834254144	8	0.013986013986013986	178	0.23482849604221637	G	0.013	-1.607239	0.00842	0.726395	0.238509	ENSG00000116127	ENST00000409009;ENST00000264448;ENST00000377715	T;T;T	0.12879	3.53;3.53;2.64	4.38	-3.33	0.04958	.	2.320940	0.02370	N	0.077734	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	0.06405	0.002;0.0;0.001	T	0.33137	-0.9880	9	0.02654	T	1	.	5.2394	0.15464	0.2773:0.0:0.2757:0.447	rs6546838;rs17434110;rs52790418;rs60669356;rs6546838	1875;1833;1875	Q8TCU4-3;B8ZZJ3;Q8TCU4	.;.;ALMS1_HUMAN	V	1833;1875;1875	ENSP00000386627:I1833V;ENSP00000264448:I1875V;ENSP00000366944:I1875V	ENSP00000264448:I1875V	I	+	1	0	ALMS1	73532788	0.000000	0.05858	0.000000	0.03702	0.013000	0.08279	-0.185000	0.09684	-0.997000	0.03450	-1.234000	0.01563	ATA	A|0.663;G|0.337	0.337	strong		0.443	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120	
BTBD16	118663	hgsc.bcm.edu	37	10	124096061	124096061	+	Missense_Mutation	SNP	A	A	C	rs1048347	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:124096061A>C	ENST00000260723.4	+	15	1567	c.1316A>C	c.(1315-1317)cAc>cCc	p.H439P	BTBD16_ENST00000495370.2_3'UTR|BTBD16_ENST00000368994.2_Missense_Mutation_p.H440P	NM_144587.2	NP_653188.2	Q32M84	BTBDG_HUMAN	BTB (POZ) domain containing 16	439			H -> P (in dbSNP:rs1048347).							breast(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(5)|lung(3)|skin(2)|stomach(1)|urinary_tract(1)	15		all_neural(114;0.107)|Lung NSC(174;0.175)|all_lung(145;0.222)|Breast(234;0.238)				GAGCACAACCACGTCAGCCTG	0.557													C|||	2300	0.459265	0.3956	0.487	5008	,	,		17696	0.6935		0.325	False		,,,				2504	0.4223				p.H439P		Atlas-SNP	.											.	BTBD16	44	.	0			c.A1316C						PASS	.	C	PRO/HIS	1583,2823	661.8+/-401.0	293,997,913	89.0	73.0	78.0		1316	1.4	0.0	10	dbSNP_86	78	2766,5834	676.0+/-403.3	446,1874,1980	yes	missense	BTBD16	NM_144587.2	77	739,2871,2893	CC,CA,AA		32.1628,35.9283,33.4384	benign	439/507	124096061	4349,8657	2203	4300	6503	SO:0001583	missense	118663	exon15			ACAACCACGTCAG	AK058088	CCDS31301.1	10q26.13	2013-01-24	2006-07-04	2006-07-04	ENSG00000138152	ENSG00000138152		"""BTB/POZ domain containing"""	26340	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 87"""	C10orf87			Standard	NM_144587		Approved	FLJ25359, Em:AC061711.1	uc001lgc.1	Q32M84	OTTHUMG00000019182	ENST00000260723.4:c.1316A>C	10.37:g.124096061A>C	ENSP00000260723:p.His439Pro	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	68	34	0.5	NM_144587	A6NM63|Q4VXL1|Q96LN0	Missense_Mutation	SNP	ENST00000260723.4	37	CCDS31301.1	1023	0.4684065934065934	208	0.42276422764227645	165	0.4558011049723757	403	0.7045454545454546	247	0.3258575197889182	C	0.040	-1.289364	0.01387	0.359283	0.321628	ENSG00000138152	ENST00000260723;ENST00000368994	T;T	0.16073	2.37;2.37	5.5	1.38	0.22167	.	0.189287	0.32852	N	0.005580	T	0.00012	0.0000	N	0.01168	-0.975	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.33574	-0.9863	9	0.05721	T	0.95	-2.4471	4.2236	0.10570	0.1484:0.4976:0.0:0.354	rs1048347;rs3167835;rs3817283;rs17642636;rs58942580;rs1048347	440;439	Q32M84-2;Q32M84	.;BTBDG_HUMAN	P	439;440	ENSP00000260723:H439P;ENSP00000357990:H440P	ENSP00000260723:H439P	H	+	2	0	BTBD16	124086051	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.113000	0.15499	-0.223000	0.09943	-0.729000	0.03580	CAC	A|0.608;C|0.392	0.392	strong		0.557	BTBD16-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000050780.3	NM_144587	
TAF1L	138474	hgsc.bcm.edu	37	9	32630472	32630472	+	Silent	SNP	T	T	C	rs10758145	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:32630472T>C	ENST00000242310.4	-	1	5195	c.5106A>G	c.(5104-5106)aaA>aaG	p.K1702K	RP11-555J4.4_ENST00000430787.1_RNA	NM_153809.2	NP_722516.1	Q8IZX4	TAF1L_HUMAN	TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 210kDa-like	1702					DNA-templated transcription, initiation (GO:0006352)|histone acetylation (GO:0016573)|male meiosis (GO:0007140)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	transcription factor TFIID complex (GO:0005669)	DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|lysine-acetylated histone binding (GO:0070577)|protein serine/threonine kinase activity (GO:0004674)|TBP-class protein binding (GO:0017025)			breast(6)|central_nervous_system(4)|endometrium(14)|kidney(11)|large_intestine(32)|liver(2)|lung(68)|ovary(2)|pancreas(2)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(1)	159			LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.00301)		GGCACATCTGTTTTTCTGGAG	0.483													C|||	1733	0.346046	0.5106	0.245	5008	,	,		24091	0.3681		0.2435	False		,,,				2504	0.2781				p.K1702K		Atlas-SNP	.											.	TAF1L	382	.	0			c.A5106G						PASS	.	C		2107,2299	601.6+/-389.7	488,1131,584	167.0	154.0	158.0		5106	0.5	0.5	9	dbSNP_120	158	1986,6614	722.6+/-406.4	230,1526,2544	no	coding-synonymous	TAF1L	NM_153809.2		718,2657,3128	CC,CT,TT		23.093,47.8212,31.4701		1702/1827	32630472	4093,8913	2203	4300	6503	SO:0001819	synonymous_variant	138474	exon1			CATCTGTTTTTCT	AF390562	CCDS35003.1	9p12	2007-07-27	2007-07-27		ENSG00000122728	ENSG00000122728			18056	protein-coding gene	gene with protein product		607798	"""TAF1-like RNA polymerase II, TATA box binding protein (TBP)-associated factor, 210kDa"""			12217962	Standard	NM_153809		Approved		uc003zrg.1	Q8IZX4	OTTHUMG00000019747	ENST00000242310.4:c.5106A>G	9.37:g.32630472T>C		Somatic	227	0	0		WXS	Illumina HiSeq	Phase_I	216	117	0.541667	NM_153809	Q0VG57	Silent	SNP	ENST00000242310.4	37	CCDS35003.1																																																																																			T|0.672;C|0.328	0.328	strong		0.483	TAF1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052012.2		
TOM1	10043	hgsc.bcm.edu	37	22	35717988	35717988	+	Silent	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:35717988C>T	ENST00000449058.2	+	3	299	c.174C>T	c.(172-174)atC>atT	p.I58I	TOM1_ENST00000447733.1_Silent_p.I25I|TOM1_ENST00000425375.1_Silent_p.I58I|TOM1_ENST00000382034.5_5'UTR|TOM1_ENST00000436462.2_Intron|TOM1_ENST00000411850.1_Silent_p.I58I	NM_005488.2	NP_005479.1	O60784	TOM1_HUMAN	target of myb1 (chicken)	58	VHS. {ECO:0000255|PROSITE- ProRule:PRU00218}.				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)			NS(1)|breast(2)|kidney(2)|large_intestine(2)|lung(7)|ovary(3)|prostate(2)	19						AGAAGAGAATCGTGGGGAATA	0.532																																					p.I58I		Atlas-SNP	.											TOM1,NS,carcinoma,0,1	TOM1	43	1	0			c.C174T						scavenged	.						127.0	110.0	116.0					22																	35717988		2203	4300	6503	SO:0001819	synonymous_variant	10043	exon3			GAGAATCGTGGGG	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.174C>T	22.37:g.35717988C>T		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	145	2	0.0137931	NM_001135732	B4DEL9|B4DNA1|Q5TIJ6|Q86X74	Silent	SNP	ENST00000449058.2	37	CCDS13913.1																																																																																			.	.	none		0.532	TOM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000320641.1	NM_005488	
SLC35E2	9906	hgsc.bcm.edu	37	1	1663960	1663960	+	Silent	SNP	G	G	A	rs147265331	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:1663960G>A	ENST00000246421.4	-	6	1150	c.735C>T	c.(733-735)gtC>gtT	p.V245V	RP1-283E3.4_ENST00000417099.1_RNA|SLC35E2_ENST00000475229.1_5'UTR|SLC35E2_ENST00000400924.1_Intron|SLC35E2_ENST00000355439.2_Intron|RP1-283E3.8_ENST00000598846.1_RNA	NM_182838.2	NP_878258.1	P0CK97	S35E2_HUMAN	solute carrier family 35, member E2	245						integral component of membrane (GO:0016021)				endometrium(2)|lung(4)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	9	all_cancers(77;0.000708)|all_epithelial(69;0.000943)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;5.61e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		Epithelial(90;5.26e-37)|OV - Ovarian serous cystadenocarcinoma(86;2.54e-23)|GBM - Glioblastoma multiforme(42;9e-08)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|STAD - Stomach adenocarcinoma(132;0.00644)|BRCA - Breast invasive adenocarcinoma(365;0.00786)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.199)		GGGCCTGCGGGACCTGCAGGT	0.607													-|||	25	0.00499201	0.0015	0.0086	5008	,	,		16644	0.0		0.0099	False		,,,				2504	0.0072				p.V245V		Atlas-SNP	.											.	SLC35E2	13	.	0			c.C735T						PASS	.		,	16,4378	23.3+/-48.9	1,14,2182	41.0	37.0	38.0		,735	-2.3	0.0	1	dbSNP_134	38	168,8396	71.0+/-133.6	5,158,4119	no	intron,coding-synonymous	SLC35E2	NM_001199787.1,NM_182838.2	,	6,172,6301	AA,AG,GG		1.9617,0.3641,1.42	,	,245/267	1663960	184,12774	2197	4282	6479	SO:0001819	synonymous_variant	9906	exon6			CTGCGGGACCTGC	AB007916	CCDS33.1, CCDS55560.1	1p36.33	2013-05-22			ENSG00000215790	ENSG00000215790		"""Solute carriers"""	20863	protein-coding gene	gene with protein product							Standard	NM_182838		Approved	KIAA0447	uc001aia.2	P0CK97	OTTHUMG00000000823	ENST00000246421.4:c.735C>T	1.37:g.1663960G>A		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	82	61	0.743902	NM_182838	B3KWR0|O75035|Q2TAY8|Q569F8|Q5CZA4|Q5QPR8|Q9Y3J8	Silent	SNP	ENST00000246421.4	37	CCDS33.1																																																																																			G|0.987;A|0.013	0.013	strong		0.607	SLC35E2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000002210.3	XM_049733	
CSGALNACT1	55790	hgsc.bcm.edu	37	8	19316086	19316086	+	Silent	SNP	G	G	A	rs12155539	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:19316086G>A	ENST00000454498.2	-	5	1715	c.702C>T	c.(700-702)caC>caT	p.H234H	CSGALNACT1_ENST00000311540.4_Silent_p.H234H|CSGALNACT1_ENST00000544602.1_Silent_p.H234H|CSGALNACT1_ENST00000332246.6_Silent_p.H234H|CSGALNACT1_ENST00000522854.1_Silent_p.H234H|CSGALNACT1_ENST00000518542.1_5'UTR	NM_001130518.1	NP_001123990.1	Q8TDX6	CGAT1_HUMAN	chondroitin sulfate N-acetylgalactosaminyltransferase 1	234					anatomical structure morphogenesis (GO:0009653)|carbohydrate metabolic process (GO:0005975)|cartilage development (GO:0051216)|cell proliferation (GO:0008283)|cell recognition (GO:0008037)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|chondroitin sulfate proteoglycan biosynthetic process (GO:0050650)|chondroitin sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process (GO:0050653)|dermatan sulfate proteoglycan biosynthetic process (GO:0050651)|endochondral ossification (GO:0001958)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process (GO:0015014)|heparin biosynthetic process (GO:0030210)|nervous system development (GO:0007399)|proteoglycan biosynthetic process (GO:0030166)|small molecule metabolic process (GO:0044281)|UDP-glucuronate metabolic process (GO:0046398)|UDP-N-acetylgalactosamine metabolic process (GO:0019276)	Golgi cisterna membrane (GO:0032580)|Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)|intracellular (GO:0005622)	acetylgalactosaminyltransferase activity (GO:0008376)|glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity (GO:0047238)|glucuronosyltransferase activity (GO:0015020)|glucuronylgalactosylproteoglycan 4-beta-N-acetylgalactosaminyltransferase activity (GO:0047237)|metal ion binding (GO:0046872)|peptidoglycan glycosyltransferase activity (GO:0008955)			NS(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(15)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31				Colorectal(111;0.182)		GTTTGAATTCGTGTTTGTGGT	0.423													G|||	2298	0.458866	0.1997	0.5576	5008	,	,		18551	0.8581		0.3519	False		,,,				2504	0.4376				p.H234H		Atlas-SNP	.											CSGALNACT1,colon,carcinoma,0,1	CSGALNACT1	72	1	0			c.C702T						PASS	.	G	,	977,3429	365.9+/-317.6	95,787,1321	301.0	276.0	284.0		702,702	-6.8	0.5	8	dbSNP_120	284	3104,5496	475.7+/-369.2	532,2040,1728	no	coding-synonymous,coding-synonymous	CSGALNACT1	NM_001130518.1,NM_018371.4	,	627,2827,3049	AA,AG,GG		36.093,22.1743,31.3778	,	234/533,234/533	19316086	4081,8925	2203	4300	6503	SO:0001819	synonymous_variant	55790	exon5			GAATTCGTGTTTG	AK002126	CCDS6010.1	8p21.3	2013-02-19				ENSG00000147408		"""Beta 4-glycosyltransferases"""	24290	protein-coding gene	gene with protein product	"""chondroitin beta1,4 N-acetylgalactosaminyltransferase"""					17145758, 12446672	Standard	NM_018371		Approved	CSGalNAcT-1, FLJ11264, ChGn	uc011kyo.2	Q8TDX6		ENST00000454498.2:c.702C>T	8.37:g.19316086G>A		Somatic	317	0	0		WXS	Illumina HiSeq	Phase_I	285	211	0.740351	NM_018371	B2RBE4|Q6P9G6|Q8IUF9|Q9NSQ7|Q9NUM9	Silent	SNP	ENST00000454498.2	37	CCDS6010.1																																																																																			G|0.616;A|0.384	0.384	strong		0.423	CSGALNACT1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375204.1	NM_018371	
TPTE2	93492	hgsc.bcm.edu	37	13	20067011	20067011	+	Missense_Mutation	SNP	A	A	C	rs76437836	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:20067011A>C	ENST00000400230.2	-	3	142	c.98T>G	c.(97-99)cTg>cGg	p.L33R	TPTE2_ENST00000382977.4_Missense_Mutation_p.L33R|TPTE2_ENST00000382978.1_Missense_Mutation_p.L33R|TPTE2_ENST00000457266.2_Missense_Mutation_p.L33R|TPTE2_ENST00000400103.2_Missense_Mutation_p.L33R|TPTE2_ENST00000255310.6_Missense_Mutation_p.L33R|TPTE2_ENST00000382975.4_Missense_Mutation_p.L33R|TPTE2_ENST00000390680.2_Missense_Mutation_p.L33R			Q6XPS3	TPTE2_HUMAN	transmembrane phosphoinositide 3-phosphatase and tensin homolog 2	33					phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	ion channel activity (GO:0005216)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.L33R(1)		NS(2)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(8)|lung(21)|pancreas(1)|prostate(8)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	65		all_cancers(29;1.23e-20)|all_lung(29;1.97e-20)|all_epithelial(30;5.86e-20)|Lung NSC(5;3.36e-17)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;1.73e-05)|Epithelial(112;7.42e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000785)|Lung(94;0.0176)|LUSC - Lung squamous cell carcinoma(192;0.089)		AGGTGACACCAGGGCTGCTCC	0.373																																					p.L33R		Atlas-SNP	.											TPTE2_ENST00000400230,adrenal_gland,adrenal_cortical_adenoma,0,3	TPTE2	225	3	1	Substitution - Missense(1)	pancreas(1)	c.T98G						scavenged	.						135.0	115.0	122.0					13																	20067011		2203	4300	6503	SO:0001583	missense	93492	exon4			GACACCAGGGCTG	AJ421032	CCDS9285.1, CCDS45013.1, CCDS45014.1	13q12.11	2012-12-10			ENSG00000132958	ENSG00000132958		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"""	17299	protein-coding gene	gene with protein product		606791				11716755, 12717346, 15057823	Standard	NM_130785		Approved	TPIP	uc001umd.3	Q6XPS3	OTTHUMG00000016493	ENST00000400230.2:c.98T>G	13.37:g.20067011A>C	ENSP00000383089:p.Leu33Arg	Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	174	20	0.114943	NM_199254	A1A4X0|A1A4X1|A8MX64|B1AQ16|B4DWZ2|Q5VUH2|Q8WWL4|Q8WWL5	Missense_Mutation	SNP	ENST00000400230.2	37	CCDS45014.1	.	.	.	.	.	.	.	.	.	.	a	0.031	-1.334344	0.01287	.	.	ENSG00000132958	ENST00000382978;ENST00000400103;ENST00000400230;ENST00000255310;ENST00000390680;ENST00000382977;ENST00000382975;ENST00000457266;ENST00000343548;ENST00000419256	D;D;D;D;D;D;D;D	0.95171	-3.53;-3.51;-3.43;-3.63;-3.63;-3.43;-3.53;-3.51	0.785	-1.57	0.08506	.	0.817016	0.10002	N	0.728341	D	0.84629	0.5514	N	0.16478	0.41	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.0;0.001;0.0	T	0.68591	-0.5368	9	.	.	.	5.8346	1.8764	0.03219	0.3863:0.3084:0.0:0.3053	.	33;33;33	A8MX64;Q6XPS3-3;Q6XPS3	.;.;TPTE2_HUMAN	R	33	ENSP00000372438:L33R;ENSP00000382974:L33R;ENSP00000383089:L33R;ENSP00000255310:L33R;ENSP00000375098:L33R;ENSP00000372437:L33R;ENSP00000372435:L33R;ENSP00000442218:L33R	.	L	-	2	0	TPTE2	18965011	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.053000	0.01400	-1.334000	0.02244	-2.170000	0.00323	CTG	A|0.375;C|0.625	0.625	strong		0.373	TPTE2-205	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_199254	
DTX1	1840	hgsc.bcm.edu	37	12	113496182	113496182	+	Missense_Mutation	SNP	T	T	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:113496182T>G	ENST00000257600.3	+	1	688	c.185T>G	c.(184-186)cTg>cGg	p.L62R		NM_004416.2	NP_004407.2	Q86Y01	DTX1_HUMAN	deltex 1, E3 ubiquitin ligase	62	WWE 1. {ECO:0000255|PROSITE- ProRule:PRU00248}.				cell surface receptor signaling pathway (GO:0007166)|glial cell differentiation (GO:0010001)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of T cell differentiation (GO:0045581)|Notch signaling pathway (GO:0007219)|protein ubiquitination (GO:0016567)|regulation of Notch signaling pathway (GO:0008593)|regulation of RNA biosynthetic process (GO:2001141)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ligase activity (GO:0016874)|Notch binding (GO:0005112)|transcription coactivator activity (GO:0003713)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(2)|lung(11)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	32						TCCGTGGTCCTGGGGCAGGTG	0.637																																					p.L62R		Atlas-SNP	.											.	DTX1	83	.	0			c.T185G						PASS	.						123.0	112.0	116.0					12																	113496182		2203	4300	6503	SO:0001583	missense	1840	exon1			TGGTCCTGGGGCA	AF053700	CCDS9164.1	12q24	2014-01-28	2014-01-28			ENSG00000135144			3060	protein-coding gene	gene with protein product		602582	"""deltex homolog 1 (Drosophila)"""			9590294, 12670957	Standard	NM_004416		Approved	hDx-1	uc001tuk.1	Q86Y01	OTTHUMG00000169610	ENST00000257600.3:c.185T>G	12.37:g.113496182T>G	ENSP00000257600:p.Leu62Arg	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	58	12	0.206897	NM_004416	O60630|Q9BS04	Missense_Mutation	SNP	ENST00000257600.3	37	CCDS9164.1	.	.	.	.	.	.	.	.	.	.	T	23.6	4.436253	0.83885	.	.	ENSG00000135144	ENST00000257600	T	0.64438	-0.1	4.05	4.05	0.47172	WWE domain (2);WWE domain, subgroup (1);	0.000000	0.56097	D	0.000033	T	0.81288	0.4791	M	0.89840	3.065	0.47862	D	0.999538	D	0.76494	0.999	D	0.87578	0.998	D	0.85075	0.0942	10	0.87932	D	0	-9.9988	12.1675	0.54138	0.0:0.0:0.0:1.0	.	62	Q86Y01	DTX1_HUMAN	R	62	ENSP00000257600:L62R	ENSP00000257600:L62R	L	+	2	0	DTX1	111980565	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	7.286000	0.78671	1.710000	0.51325	0.454000	0.30748	CTG	.	.	none		0.637	DTX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405045.2		
GRIN3A	116443	hgsc.bcm.edu	37	9	104385712	104385712	+	Silent	SNP	A	A	G	rs35768024|rs10989564	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:104385712A>G	ENST00000361820.3	-	5	3102	c.2502T>C	c.(2500-2502)aaT>aaC	p.N834N		NM_133445.2	NP_597702.2	Q8TCU5	NMD3A_HUMAN	glutamate receptor, ionotropic, N-methyl-D-aspartate 3A	834					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)	TCTCTGGATCATTCCTATATT	0.443													A|||	2526	0.504393	0.5847	0.4524	5008	,	,		19002	0.5308		0.4722	False		,,,				2504	0.4387				p.N834N		Atlas-SNP	.											.	GRIN3A	186	.	0			c.T2502C						PASS	.	A		2472,1934		712,1048,443	111.0	102.0	105.0		2502	3.4	1.0	9	dbSNP_120	105	3778,4822		934,1910,1456	no	coding-synonymous	GRIN3A	NM_133445.2		1646,2958,1899	GG,GA,AA		43.9302,43.8947,48.0547		834/1116	104385712	6250,6756	2203	4300	6503	SO:0001819	synonymous_variant	116443	exon5			TGGATCATTCCTA		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.2502T>C	9.37:g.104385712A>G		Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	140	138	0.985714	NM_133445	B3DLF9|Q5VTR3|Q8TF29|Q8WXI6	Silent	SNP	ENST00000361820.3	37	CCDS6758.1																																																																																			A|0.501;G|0.499	0.499	strong		0.443	GRIN3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053453.1		
OR4M1	441670	hgsc.bcm.edu	37	14	20248828	20248828	+	Missense_Mutation	SNP	C	C	T	rs2635535	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:20248828C>T	ENST00000315957.4	+	1	428	c.347C>T	c.(346-348)aCa>aTa	p.T116I		NM_001005500.1	NP_001005500.1	Q8NGD0	OR4M1_HUMAN	olfactory receptor, family 4, subfamily M, member 1	116			T -> I (in dbSNP:rs2635535).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(1)|endometrium(1)|large_intestine(4)|lung(32)|prostate(1)|skin(2)	42	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)		TTCTTGCTCACAGTGATGGCC	0.493													.|||	1274	0.254393	0.0847	0.3242	5008	,	,		27958	0.2937		0.3439	False		,,,				2504	0.3016				p.T116I		Atlas-SNP	.											.	OR4M1	104	.	0			c.C347T						PASS	.		ILE/THR	587,3819		18,551,1634	237.0	249.0	245.0		347	3.4	1.0	14	dbSNP_100	245	2790,5810		266,2258,1776	no	missense	OR4M1	NM_001005500.1	89	284,2809,3410	TT,TC,CC		32.4419,13.3227,25.9649	possibly-damaging	116/314	20248828	3377,9629	2203	4300	6503	SO:0001583	missense	441670	exon1			TGCTCACAGTGAT		CCDS32021.1	14q11.2	2013-09-23			ENSG00000176299	ENSG00000176299		"""GPCR / Class A : Olfactory receptors"""	14735	protein-coding gene	gene with protein product							Standard	NM_001005500		Approved		uc010tku.2	Q8NGD0	OTTHUMG00000170599	ENST00000315957.4:c.347C>T	14.37:g.20248828C>T	ENSP00000319654:p.Thr116Ile	Somatic	310	0	0		WXS	Illumina HiSeq	Phase_I	308	93	0.301948	NM_001005500	B9EH18|Q6IFA3	Missense_Mutation	SNP	ENST00000315957.4	37	CCDS32021.1	599	0.2742673992673993	40	0.08130081300813008	115	0.31767955801104975	169	0.29545454545454547	275	0.3627968337730871	.	11.72	1.723491	0.30593	0.133227	0.324419	ENSG00000176299	ENST00000315957	T	0.00380	7.64	4.33	3.43	0.39272	GPCR, rhodopsin-like superfamily (1);	0.000000	0.49916	D	0.000124	T	0.00012	0.0000	L	0.38649	1.16	0.36142	P	0.15317000000000003	B	0.18741	0.03	B	0.15052	0.012	T	0.03148	-1.1067	9	0.08599	T	0.76	-7.5579	9.9477	0.41621	0.0:0.8968:0.0:0.1032	rs2635535;rs52798113	116	Q8NGD0	OR4M1_HUMAN	I	116	ENSP00000319654:T116I	ENSP00000319654:T116I	T	+	2	0	OR4M1	19318668	0.000000	0.05858	1.000000	0.80357	0.990000	0.78478	1.306000	0.33505	2.407000	0.81776	0.506000	0.49869	ACA	C|0.736;T|0.264	0.264	strong		0.493	OR4M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409770.1		
FAM205A	259308	hgsc.bcm.edu	37	9	34725112	34725112	+	Missense_Mutation	SNP	C	C	T	rs200209883	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:34725112C>T	ENST00000378788.3	-	4	2164	c.2125G>A	c.(2125-2127)Gca>Aca	p.A709T		NM_001141917.1	NP_001135389.1	Q6ZU69	F205A_HUMAN	family with sequence similarity 205, member A	709						integral component of membrane (GO:0016021)|nucleus (GO:0005634)				breast(1)|endometrium(2)|kidney(1)	4						GGAGCCACTGCCAGGACCCCA	0.552																																					p.A709T		Atlas-SNP	.											FAM205A_ENST00000378788,NS,haematopoietic_neoplasm,0,2	FAM205A	45	2	0			c.G2125A						PASS	.						22.0	16.0	18.0					9																	34725112		692	1591	2283	SO:0001583	missense	259308	exon4			CCACTGCCAGGAC		CCDS55305.1	9p13.3	2014-05-16			ENSG00000205108	ENSG00000205108			41911	protein-coding gene	gene with protein product							Standard	NM_001141917		Approved	C9orf144B	uc011lor.2	Q6ZU69	OTTHUMG00000000448	ENST00000378788.3:c.2125G>A	9.37:g.34725112C>T	ENSP00000417711:p.Ala709Thr	Somatic	473	0	0		WXS	Illumina HiSeq	Phase_I	395	126	0.318987	NM_001141917	A8MVW7	Missense_Mutation	SNP	ENST00000378788.3	37	CCDS55305.1	.	.	.	.	.	.	.	.	.	.	C	15.09	2.730297	0.48939	.	.	ENSG00000205108	ENST00000378788	T	0.54279	0.58	4.43	-2.72	0.05968	.	.	.	.	.	T	0.42268	0.1195	L	0.29908	0.895	0.09310	N	1	D	0.54207	0.965	P	0.50659	0.647	T	0.34900	-0.9810	9	0.35671	T	0.21	.	5.4131	0.16358	0.0:0.2766:0.4419:0.2815	.	709	Q6ZU69	F205A_HUMAN	T	709	ENSP00000417711:A709T	ENSP00000417711:A709T	A	-	1	0	RP11-195F19.10	34715112	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.932000	0.03963	-0.528000	0.06366	-0.300000	0.09419	GCA	C|0.978;T|0.022	0.022	strong		0.552	FAM205A-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001150.2	NM_001141917	
C2orf83	56918	hgsc.bcm.edu	37	2	228493211	228493211	+	Missense_Mutation	SNP	G	G	A	rs28739019	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:228493211G>A	ENST00000264387.4	-	2	220	c.134C>T	c.(133-135)tCg>tTg	p.S45L	C2orf83_ENST00000409066.1_Missense_Mutation_p.S45L	NM_020161.3	NP_064546.3	Q53S99	CB083_HUMAN	chromosome 2 open reading frame 83	45			S -> L (in dbSNP:rs28739019).		transport (GO:0006810)	membrane (GO:0016020)		p.S45L(1)		endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|stomach(2)	11						ggcttttggcgagggctttgc	0.453													G|||	1702	0.339856	0.466	0.3084	5008	,	,		18142	0.2143		0.2575	False		,,,				2504	0.4059				p.S45L		Atlas-SNP	.											C2orf83,NS,carcinoma,0,1	C2orf83	15	1	1	Substitution - Missense(1)	stomach(1)	c.C134T						PASS	.	G	LEU/SER,LEU/SER	1129,1525		247,635,445	237.0	203.0	215.0		134,134	-1.4	0.0	2	dbSNP_125	215	1185,3433		172,841,1296	yes	missense,missense	C2orf83	NM_001162483.1,NM_020161.3	145,145	419,1476,1741	AA,AG,GG		25.6605,42.5396,31.8207	possibly-damaging,possibly-damaging	45/97,45/151	228493211	2314,4958	1327	2309	3636	SO:0001583	missense	56918	exon2			TTTGGCGAGGGCT		CCDS33388.1, CCDS54434.1	2q36.3	2008-09-16			ENSG00000042304	ENSG00000042304			25344	protein-coding gene	gene with protein product							Standard	NM_020161		Approved	DKFZp547H025	uc002vph.3	Q53S99	OTTHUMG00000153550	ENST00000264387.4:c.134C>T	2.37:g.228493211G>A	ENSP00000264387:p.Ser45Leu	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	78	28	0.358974	NM_020161	A2RRG6|B8ZZI8|Q9NPW4	Missense_Mutation	SNP	ENST00000264387.4	37	CCDS33388.1	627	0.28708791208791207	208	0.42276422764227645	108	0.2983425414364641	127	0.22202797202797203	184	0.24274406332453827	.	4.677	0.125929	0.08931	0.425396	0.256605	ENSG00000042304	ENST00000264387;ENST00000409066	T;T	0.69806	0.17;-0.43	0.694	-1.36	0.09085	.	.	.	.	.	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B;B	0.06786	0.001;0.001	B;B	0.01281	0.0;0.0	T	0.35151	-0.9800	7	0.56958	D	0.05	.	.	.	.	rs28739019	45;45	B8ZZI8;Q53S99	.;CB083_HUMAN	L	45	ENSP00000264387:S45L;ENSP00000387149:S45L	ENSP00000264387:S45L	S	-	2	0	C2orf83	228201455	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.928000	0.00332	-0.756000	0.04703	-0.751000	0.03497	TCG	G|0.709;A|0.291	0.291	strong		0.453	C2orf83-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331607.1	NM_020161	
WDR87	83889	hgsc.bcm.edu	37	19	38376103	38376103	+	Silent	SNP	A	A	G	rs73027454	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:38376103A>G	ENST00000303868.5	-	6	8315	c.8091T>C	c.(8089-8091)ttT>ttC	p.F2697F	WDR87_ENST00000447313.2_Silent_p.F2736F	NM_031951.3	NP_114157.3	Q6ZQQ6	WDR87_HUMAN	WD repeat domain 87	2697										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						GTTTATCCTTAAAATCCCAGA	0.423													A|||	961	0.191893	0.0998	0.2622	5008	,	,		20467	0.0298		0.3469	False		,,,				2504	0.274				p.F2697F		Atlas-SNP	.											.	WDR87	191	.	0			c.T8091C						PASS	.	A		197,1187		16,165,511	20.0	18.0	19.0		8091	-5.0	0.0	19	dbSNP_130	19	1123,2059		213,697,681	no	coding-synonymous	WDR87	NM_031951.3		229,862,1192	GG,GA,AA		35.2923,14.2341,28.9093		2697/2874	38376103	1320,3246	692	1591	2283	SO:0001819	synonymous_variant	83889	exon6			ATCCTTAAAATCC	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.8091T>C	19.37:g.38376103A>G		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	58	28	0.482759	NM_031951	Q9BWV9	Silent	SNP	ENST00000303868.5	37	CCDS46063.1																																																																																			A|0.775;G|0.225	0.225	strong		0.423	WDR87-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000314628.2	XM_940478	
PTPRH	5794	hgsc.bcm.edu	37	19	55715309	55715309	+	Missense_Mutation	SNP	C	C	T	rs45535035	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:55715309C>T	ENST00000376350.3	-	5	749	c.727G>A	c.(727-729)Gtt>Att	p.V243I	PTPRH_ENST00000588559.1_5'UTR|PTPRH_ENST00000263434.5_Intron	NM_002842.3	NP_002833.3	Q9HD43	PTPRH_HUMAN	protein tyrosine phosphatase, receptor type, H	243	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.		V -> I (in dbSNP:rs45535035).		apoptotic process (GO:0006915)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(2)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(8)|lung(27)|ovary(2)|prostate(5)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(2)	67		Renal(1328;0.245)	BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0479)		GTGCACTGAACGCAGTAGGTC	0.577													C|||	623	0.124401	0.1558	0.0994	5008	,	,		15751	0.0327		0.1978	False		,,,				2504	0.1186				p.V243I		Atlas-SNP	.											.	PTPRH	139	.	0			c.G727A						PASS	.	C	,ILE/VAL	718,3688	300.4+/-286.3	70,578,1555	184.0	150.0	162.0		,727	2.5	0.5	19	dbSNP_127	162	1526,7074	288.9+/-299.0	145,1236,2919	yes	intron,missense	PTPRH	NM_001161440.1,NM_002842.3	,29	215,1814,4474	TT,TC,CC		17.7442,16.296,17.2536	,benign	,243/1116	55715309	2244,10762	2203	4300	6503	SO:0001583	missense	5794	exon5			ACTGAACGCAGTA		CCDS33110.1, CCDS54321.1	19q13.4	2013-02-11				ENSG00000080031		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9672	protein-coding gene	gene with protein product		602510				8294459	Standard	XM_006723312		Approved	SAP-1	uc002qjq.3	Q9HD43		ENST00000376350.3:c.727G>A	19.37:g.55715309C>T	ENSP00000365528:p.Val243Ile	Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	115	55	0.478261	NM_002842	C9JCH2|Q15426|Q2NKN9|Q2NKP0	Missense_Mutation	SNP	ENST00000376350.3	37	CCDS33110.1	277	0.12683150183150182	66	0.13414634146341464	42	0.11602209944751381	12	0.02097902097902098	157	0.20712401055408972	C	0.029	-1.344619	0.01277	0.16296	0.177442	ENSG00000080031	ENST00000376350	T	0.60672	0.17	3.75	2.49	0.30216	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.964989	0.08388	N	0.953456	T	0.00039	0.0001	N	0.11313	0.125	0.23204	P	0.99812677	P;B	0.41159	0.74;0.369	B;B	0.28305	0.088;0.042	T	0.04191	-1.0970	9	0.02654	T	1	.	6.8978	0.24265	0.0:0.8304:0.0:0.1696	rs45535035;rs61734209	65;243	Q9HD43-2;Q9HD43	.;PTPRH_HUMAN	I	243	ENSP00000365528:V243I	ENSP00000365528:V243I	V	-	1	0	PTPRH	60407121	0.006000	0.16342	0.473000	0.27253	0.136000	0.21042	-0.050000	0.11904	0.582000	0.29556	0.511000	0.50034	GTT	C|0.840;T|0.160	0.160	strong		0.577	PTPRH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452649.1		
FAM179A	165186	hgsc.bcm.edu	37	2	29240060	29240060	+	Missense_Mutation	SNP	A	A	G	rs11127202	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:29240060A>G	ENST00000379558.4	+	9	1436	c.1085A>G	c.(1084-1086)cAg>cGg	p.Q362R	FAM179A_ENST00000403861.2_Missense_Mutation_p.Q362R|FAM179A_ENST00000465300.1_Intron	NM_199280.2	NP_954974.2	Q6ZUX3	F179A_HUMAN	family with sequence similarity 179, member A	362			Q -> R (in dbSNP:rs11127202).							breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(5)|lung(9)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	26						GAGAAGATGCAGCTGAAGCAG	0.542													G|||	1065	0.21266	0.267	0.1859	5008	,	,		16571	0.1567		0.2485	False		,,,				2504	0.1789				p.Q362R		Atlas-SNP	.											.	FAM179A	106	.	0			c.A1085G						PASS	.	G	ARG/GLN	920,3124		106,708,1208	108.0	112.0	110.0		1085	3.8	1.0	2	dbSNP_120	110	1979,6397		243,1493,2452	yes	missense	FAM179A	NM_199280.2	43	349,2201,3660	GG,GA,AA		23.627,22.7498,23.3414	benign	362/1020	29240060	2899,9521	2022	4188	6210	SO:0001583	missense	165186	exon9			AGATGCAGCTGAA	AK125239, AK125744	CCDS1769.2	2p23.2	2008-10-30			ENSG00000189350	ENSG00000189350			33715	protein-coding gene	gene with protein product						16344560	Standard	NM_199280		Approved	FLJ43249, LOC165186	uc010ezl.3	Q6ZUX3	OTTHUMG00000128432	ENST00000379558.4:c.1085A>G	2.37:g.29240060A>G	ENSP00000368876:p.Gln362Arg	Somatic	316	0	0		WXS	Illumina HiSeq	Phase_I	379	227	0.598945	NM_199280	Q6ZUF5	Missense_Mutation	SNP	ENST00000379558.4	37	CCDS1769.2	463	0.211996336996337	126	0.25609756097560976	69	0.19060773480662985	80	0.13986013986013987	188	0.24802110817941952	G	0.634	-0.815920	0.02776	0.227498	0.23627	ENSG00000189350	ENST00000379558;ENST00000403861	T;T	0.14766	3.73;2.48	4.75	3.85	0.44370	.	.	.	.	.	T	0.00012	0.0000	N	0.01048	-1.04	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.44544	-0.9321	8	0.02654	T	1	.	10.3911	0.44168	0.1669:0.0:0.8331:0.0	rs11127202;rs59508471;rs11127202	362;362	F8W8E4;Q6ZUX3	.;F179A_HUMAN	R	362	ENSP00000368876:Q362R;ENSP00000384699:Q362R	ENSP00000368876:Q362R	Q	+	2	0	FAM179A	29093564	1.000000	0.71417	0.999000	0.59377	0.396000	0.30629	1.748000	0.38308	0.510000	0.28216	-0.186000	0.12905	CAG	A|0.778;G|0.222	0.222	strong		0.542	FAM179A-003	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317848.4	NM_199280	
CYP39A1	51302	hgsc.bcm.edu	37	6	46563817	46563817	+	Missense_Mutation	SNP	A	A	T	rs7761731	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:46563817A>T	ENST00000275016.2	-	8	1175	c.972T>A	c.(970-972)aaT>aaA	p.N324K		NM_016593.3	NP_057677.2	Q9NYL5	CP39A_HUMAN	cytochrome P450, family 39, subfamily A, polypeptide 1	324			N -> K (in dbSNP:rs7761731). {ECO:0000269|PubMed:10748047}.		bile acid biosynthetic process (GO:0006699)|bile acid catabolic process (GO:0030573)|bile acid metabolic process (GO:0008206)|cholesterol catabolic process (GO:0006707)|digestion (GO:0007586)|small molecule metabolic process (GO:0044281)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|intracellular membrane-bounded organelle (GO:0043231)	24-hydroxycholesterol 7alpha-hydroxylase activity (GO:0033782)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxysterol 7-alpha-hydroxylase activity (GO:0008396)|steroid 7-alpha-hydroxylase activity (GO:0008387)		EIF3K/CYP39A1(2)	NS(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(6)|ovary(1)|prostate(2)|skin(2)	21						TTAGAAGGAGATTCTCCAGGT	0.353													T|||	2459	0.491014	0.7035	0.3833	5008	,	,		15400	0.3859		0.2684	False		,,,				2504	0.6176				p.N324K		Atlas-SNP	.											.	CYP39A1	41	.	0			c.T972A						PASS	.	T	LYS/ASN	2767,1639	496.9+/-363.7	869,1029,305	82.0	87.0	85.0		972	-0.5	1.0	6	dbSNP_116	85	2293,6307	703.7+/-405.4	312,1669,2319	yes	missense	CYP39A1	NM_016593.3	94	1181,2698,2624	TT,TA,AA		26.6628,37.1993,38.9051	benign	324/470	46563817	5060,7946	2203	4300	6503	SO:0001583	missense	51302	exon8			AAGGAGATTCTCC	AF237982	CCDS4916.1, CCDS75465.1	6p21.1-p11.2	2008-02-05	2003-01-14		ENSG00000146233	ENSG00000146233		"""Cytochrome P450s"""	17449	protein-coding gene	gene with protein product		605994	"""cytochrome P450, subfamily XXXIX (oxysterol 7 alpha-hydroxylase), polypeptide 1"""			10748047	Standard	NM_016593		Approved		uc003oyf.1	Q9NYL5	OTTHUMG00000014785	ENST00000275016.2:c.972T>A	6.37:g.46563817A>T	ENSP00000275016:p.Asn324Lys	Somatic	237	1	0.00421941		WXS	Illumina HiSeq	Phase_I	201	102	0.507463	NM_016593	Q5VTT0|Q96FW5	Missense_Mutation	SNP	ENST00000275016.2	37	CCDS4916.1	914	0.4184981684981685	375	0.7621951219512195	135	0.3729281767955801	205	0.3583916083916084	199	0.262532981530343	T	1.157	-0.644802	0.03531	0.628007	0.266628	ENSG00000146233	ENST00000275016	D	0.84442	-1.85	5.64	-0.545	0.11843	.	0.191501	0.44285	N	0.000470	T	0.24314	0.0589	N	0.00788	-1.185	0.53005	P	3.100000000000325E-5	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.17776	-1.0358	9	0.02654	T	1	-12.3399	3.8072	0.08782	0.1147:0.4417:0.1896:0.254	rs7761731;rs52826280;rs61011153;rs7761731	304;324	B7Z786;Q9NYL5	.;CP39A_HUMAN	K	324	ENSP00000275016:N324K	ENSP00000275016:N324K	N	-	3	2	CYP39A1	46671776	0.973000	0.33851	0.964000	0.40570	0.654000	0.38779	-0.051000	0.11885	-0.349000	0.08274	-0.375000	0.07067	AAT	A|0.592;T|0.408	0.408	strong		0.353	CYP39A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040787.1		
NDUFA7	4701	hgsc.bcm.edu	37	19	8376431	8376431	+	Silent	SNP	G	G	A	rs561	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:8376431G>A	ENST00000301457.2	-	4	337	c.300C>T	c.(298-300)ccC>ccT	p.P100P	NDUFA7_ENST00000598884.1_Silent_p.P100P	NM_005001.3	NP_004992.2	O95182	NDUA7_HUMAN	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 7, 14.5kDa	100					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 respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			NS(1)|central_nervous_system(1)|lung(2)|ovary(1)	5						ACCTCTTTATGGGAGGAGCTG	0.557													G|||	692	0.138179	0.0303	0.2666	5008	,	,		16617	0.2083		0.1859	False		,,,				2504	0.0716				p.P100P		Atlas-SNP	.											.	NDUFA7	11	.	0			c.C300T						PASS	.	G		227,3867		6,215,1826	88.0	95.0	92.0		300	-1.1	0.6	19	dbSNP_36	92	1592,6782		153,1286,2748	no	coding-synonymous	NDUFA7	NM_005001.3		159,1501,4574	AA,AG,GG		19.0112,5.5447,14.5893		100/114	8376431	1819,10649	2047	4187	6234	SO:0001819	synonymous_variant	4701	exon4			CTTTATGGGAGGA	AF050637	CCDS42492.1	19p13.2	2013-05-14	2002-08-29		ENSG00000267855	ENSG00000267855		"""Mitochondrial respiratory chain complex / Complex I"""	7691	protein-coding gene	gene with protein product	"""complex I B14.5a subunit"""	602139	"""NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 7 (14.5kD, B14.5a)"""			9763676	Standard	NM_005001		Approved	B14.5a	uc002mjm.2	O95182	OTTHUMG00000182459	ENST00000301457.2:c.300C>T	19.37:g.8376431G>A		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	117	65	0.555556	NM_005001		Silent	SNP	ENST00000301457.2	37	CCDS42492.1																																																																																			G|0.844;A|0.156	0.156	strong		0.557	NDUFA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461373.1	NM_005001	
OR51F1	256892	hgsc.bcm.edu	37	11	4790410	4790410	+	Silent	SNP	A	A	G	rs1030724	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:4790410A>G	ENST00000380383.1	-	1	758	c.759T>C	c.(757-759)caT>caC	p.H253H	OR51F1_ENST00000343430.3_Silent_p.H246H|MMP26_ENST00000477339.1_Intron|MMP26_ENST00000380390.1_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	168	0	0		WXS	Illumina HiSeq	Phase_I	171	42	0.245614	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	
GABRB3	2562	hgsc.bcm.edu	37	15	26806154	26806154	+	Silent	SNP	G	G	A	rs74907974	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:26806154G>A	ENST00000311550.5	-	8	1116	c.1005C>T	c.(1003-1005)ggC>ggT	p.G335G	GABRB3_ENST00000400188.3_Silent_p.G264G|GABRB3_ENST00000299267.4_Silent_p.G335G|GABRB3_ENST00000545868.1_Silent_p.G250G|GABRB3_ENST00000541819.2_Silent_p.G391G	NM_000814.5|NM_001278631.1	NP_000805.1|NP_001265560.1	P28472	GBRB3_HUMAN	gamma-aminobutyric acid (GABA) A receptor, beta 3	335					cellular response to histamine (GO:0071420)|chloride transmembrane transport (GO:1902476)|cochlea development (GO:0090102)|inner ear receptor cell development (GO:0060119)|innervation (GO:0060384)|ion transmembrane transport (GO:0034220)|negative regulation of neuron apoptotic process (GO:0043524)|palate development (GO:0060021)|sensory perception of sound (GO:0007605)|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)|GABA-gated chloride ion channel activity (GO:0022851)			NS(2)|breast(1)|central_nervous_system(1)|cervix(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(11)|liver(1)|lung(41)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	68		all_cancers(20;1.89e-22)|all_lung(180;6.35e-15)|Breast(32;0.000279)|Colorectal(260;0.232)		all cancers(64;1.46e-07)|Epithelial(43;2.89e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0251)|COAD - Colon adenocarcinoma(236;0.235)|Lung(196;0.243)	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)|Fospropofol(DB06716)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Ivermectin(DB00602)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Piperazine(DB00592)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	GCCTTTGAGGGCCTCTTCCAA	0.493													G|||	55	0.0109824	0.034	0.0115	5008	,	,		18829	0.0		0.002	False		,,,				2504	0.0				p.G335G		Atlas-SNP	.											GABRB3_ENST00000541819,right_upper_lobe,carcinoma,-2,6	GABRB3	338	6	0			c.C1005T						PASS	.	G	,,,	122,4284	90.6+/-129.3	1,120,2082	156.0	163.0	161.0		1005,750,792,1005	2.1	1.0	15	dbSNP_131	161	16,8584	11.9+/-42.8	0,16,4284	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	GABRB3	NM_000814.5,NM_001191320.1,NM_001191321.1,NM_021912.4	,,,	1,136,6366	AA,AG,GG		0.186,2.769,1.061	,,,	335/474,250/389,264/403,335/474	26806154	138,12868	2203	4300	6503	SO:0001819	synonymous_variant	2562	exon8			TTGAGGGCCTCTT		CCDS10018.1, CCDS10019.1, CCDS53920.1, CCDS53921.1	15q12	2012-06-22			ENSG00000166206	ENSG00000166206		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	4083	protein-coding gene	gene with protein product	"""GABA(A) receptor, beta 3"""	137192					Standard	NM_000814		Approved		uc001zaz.3	P28472	OTTHUMG00000129231	ENST00000311550.5:c.1005C>T	15.37:g.26806154G>A		Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	129	53	0.410853	NM_021912	B7Z2W1|B7Z825|F5H3D2|H7BYV8|Q14352|Q96FM5	Silent	SNP	ENST00000311550.5	37	CCDS10019.1																																																																																			G|0.991;A|0.009	0.009	strong		0.493	GABRB3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251352.2		
LINGO1	84894	hgsc.bcm.edu	37	15	77907775	77907775	+	Silent	SNP	T	T	C	rs2271397	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:77907775T>C	ENST00000355300.6	-	2	648	c.474A>G	c.(472-474)ctA>ctG	p.L158L	LINGO1_ENST00000561030.1_Silent_p.L152L	NM_032808.5	NP_116197.4	Q96FE5	LIGO1_HUMAN	leucine rich repeat and Ig domain containing 1	158					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						TGTAGTCCAGTAGGATAACGA	0.552													C|||	3626	0.724042	0.6838	0.6556	5008	,	,		21838	0.8304		0.6461	False		,,,				2504	0.7975				p.L158L		Atlas-SNP	.											.	LINGO1	76	.	0			c.A474G						PASS	.	C		2934,1348		1017,900,224	130.0	135.0	133.0		474	3.7	1.0	15	dbSNP_100	133	5399,3075		1703,1993,541	no	coding-synonymous	LINGO1	NM_032808.5		2720,2893,765	CC,CT,TT		36.2875,31.4806,34.6739		158/621	77907775	8333,4423	2141	4237	6378	SO:0001819	synonymous_variant	84894	exon2			GTCCAGTAGGATA	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.474A>G	15.37:g.77907775T>C		Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	182	181	0.994505	NM_032808	D3DW80|Q6NUK3|Q6UXM3|Q6VVG0|Q6VVG1|Q6VVG2|Q8N3K5|Q96K52	Silent	SNP	ENST00000355300.6	37	CCDS45313.1																																																																																			T|0.292;C|0.708	0.708	strong		0.552	LINGO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419546.1	NM_032808	
SLFN13	146857	hgsc.bcm.edu	37	17	33772550	33772550	+	Silent	SNP	C	C	T	rs76192030	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:33772550C>T	ENST00000285013.6	-	3	425	c.150G>A	c.(148-150)gcG>gcA	p.A50A	SLFN13_ENST00000526861.1_Silent_p.A50A|SLFN13_ENST00000533791.1_Silent_p.A50A|SLFN13_ENST00000534689.1_Intron|SLFN13_ENST00000360502.2_Intron|SLFN13_ENST00000542635.1_Silent_p.A50A	NM_144682.5	NP_653283.3	Q68D06	SLN13_HUMAN	schlafen family member 13	50			A -> T (in dbSNP:rs7216628).			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)		ATAAAGCACACGCGGCCCGTA	0.478													C|||	545	0.108826	0.0197	0.0749	5008	,	,		16941	0.0208		0.0994	False		,,,				2504	0.3538				p.A50A		Atlas-SNP	.											SLFN13,rectum,carcinoma,-2,1	SLFN13	79	1	0			c.G150A						PASS	.	C		147,4259	102.1+/-140.7	4,139,2060	118.0	122.0	121.0		150	-6.6	0.1	17	dbSNP_132	121	765,7835	182.6+/-231.0	28,709,3563	no	coding-synonymous	SLFN13	NM_144682.5		32,848,5623	TT,TC,CC		8.8953,3.3364,7.0121		50/898	33772550	912,12094	2203	4300	6503	SO:0001819	synonymous_variant	146857	exon3			AGCACACGCGGCC	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.150G>A	17.37:g.33772550C>T		Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	141	80	0.567376	NM_144682	E1P645|Q658M1|Q6ZS51|Q96A81	Silent	SNP	ENST00000285013.6	37	CCDS32620.1																																																																																			C|0.930;T|0.070	0.070	strong		0.478	SLFN13-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381883.1	NM_144682	
COL6A2	1292	hgsc.bcm.edu	37	21	47552130	47552130	+	Silent	SNP	A	A	G	rs9977394	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:47552130A>G	ENST00000300527.4	+	28	2828	c.2724A>G	c.(2722-2724)acA>acG	p.T908T		NM_001849.3	NP_001840.3	P12110	CO6A2_HUMAN	collagen, type VI, alpha 2	908	Nonhelical region.|VWFA 3. {ECO:0000255|PROSITE- ProRule:PRU00219}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|protein heterotrimerization (GO:0070208)|response to glucose (GO:0009749)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)				NS(1)|breast(1)|central_nervous_system(7)|endometrium(7)|kidney(5)|liver(1)|lung(15)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	43	Breast(49;0.245)			Colorectal(79;0.0303)|READ - Rectum adenocarcinoma(84;0.0649)		TGGAGACCACACAATACCTGA	0.692													G|||	700	0.139776	0.2602	0.0519	5008	,	,		16671	0.0308		0.1024	False		,,,				2504	0.1902				p.T908T		Atlas-SNP	.											.	COL6A2	351	.	0			c.A2724G						PASS	.	G		1106,3272		145,816,1228	18.0	18.0	18.0		2724	-0.3	0.0	21	dbSNP_119	18	849,7737		34,781,3478	no	coding-synonymous	COL6A2	NM_001849.3		179,1597,4706	GG,GA,AA		9.8882,25.2627,15.0802		908/1020	47552130	1955,11009	2189	4293	6482	SO:0001819	synonymous_variant	1292	exon28			GACCACACAATAC	M20777	CCDS13728.1, CCDS13729.1, CCDS13730.1	21q22.3	2014-09-17			ENSG00000142173	ENSG00000142173		"""Collagens"""	2212	protein-coding gene	gene with protein product		120240					Standard	NM_001849		Approved		uc002zia.1	P12110	OTTHUMG00000090489	ENST00000300527.4:c.2724A>G	21.37:g.47552130A>G		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	59	28	0.474576	NM_001849	Q13909|Q13910|Q13911|Q14048|Q14049|Q16259|Q16597|Q6P0Q1|Q9UML3|Q9Y4S8	Silent	SNP	ENST00000300527.4	37	CCDS13728.1																																																																																			A|0.879;G|0.121	0.121	strong		0.692	COL6A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206971.1		
HELB	92797	hgsc.bcm.edu	37	12	66704225	66704225	+	Missense_Mutation	SNP	A	A	G	rs75770066	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:66704225A>G	ENST00000247815.4	+	4	1576	c.1517A>G	c.(1516-1518)gAt>gGt	p.D506G		NM_033647.3	NP_387467.2	Q8NG08	HELB_HUMAN	helicase (DNA) B	506					DNA duplex unwinding (GO:0032508)|DNA replication (GO:0006260)|DNA replication, synthesis of RNA primer (GO:0006269)		ATP binding (GO:0005524)|ATP-dependent 5'-3' DNA helicase activity (GO:0043141)|single-stranded DNA-dependent ATP-dependent DNA helicase activity (GO:0017116)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(10)|lung(15)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)	40			GBM - Glioblastoma multiforme(2;0.000142)	GBM - Glioblastoma multiforme(28;0.0265)		GCCTGTGAAGATTTTGAACAA	0.413													A|||	109	0.0217652	0.0015	0.0245	5008	,	,		18810	0.003		0.0348	False		,,,				2504	0.0532				p.D506G		Atlas-SNP	.											.	HELB	90	.	0			c.A1517G						PASS	.	A	GLY/ASP	25,4381	29.9+/-59.1	0,25,2178	82.0	90.0	87.0		1517	6.0	1.0	12	dbSNP_132	87	323,8277	114.2+/-174.2	9,305,3986	yes	missense	HELB	NM_033647.2	94	9,330,6164	GG,GA,AA		3.7558,0.5674,2.6757	probably-damaging	506/1088	66704225	348,12658	2203	4300	6503	SO:0001583	missense	92797	exon4			GTGAAGATTTTGA	AF319995	CCDS8976.1	12q14.2	2009-01-15			ENSG00000127311	ENSG00000127311			17196	protein-coding gene	gene with protein product		614539				12181327	Standard	NM_033647		Approved		uc001sti.3	Q8NG08	OTTHUMG00000169006	ENST00000247815.4:c.1517A>G	12.37:g.66704225A>G	ENSP00000247815:p.Asp506Gly	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	118	50	0.423729	NM_033647	A8K4C9|Q4G0T2|Q9H7L5	Missense_Mutation	SNP	ENST00000247815.4	37	CCDS8976.1	35	0.016025641025641024	2	0.0040650406504065045	9	0.024861878453038673	1	0.0017482517482517483	23	0.030343007915567283	A	20.9	4.062652	0.76187	0.005674	0.037558	ENSG00000127311	ENST00000247815	T	0.13538	2.58	6.04	6.04	0.98038	.	0.052112	0.64402	D	0.000001	T	0.08537	0.0212	L	0.52905	1.665	0.42985	D	0.994478	D	0.89917	1.0	D	0.76071	0.987	T	0.00238	-1.1889	9	.	.	.	-34.5351	12.4259	0.55546	0.8602:0.1398:0.0:0.0	.	506	Q8NG08	HELB_HUMAN	G	506	ENSP00000247815:D506G	.	D	+	2	0	HELB	64990492	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	2.644000	0.46613	2.317000	0.78254	0.459000	0.35465	GAT	A|0.975;G|0.025	0.025	strong		0.413	HELB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401919.1		
MUC4	4585	hgsc.bcm.edu	37	3	195506007	195506007	+	Silent	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195506007G>A	ENST00000463781.3	-	2	12903	c.12444C>T	c.(12442-12444)acC>acT	p.T4148T	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Silent_p.T4148T	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.T4148T(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)		AGGAAGGGATGGTGACAGGAA	0.587																																					p.T4148T		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	2	Substitution - coding silent(2)	kidney(1)|endometrium(1)	c.C12444T						scavenged	.						40.0	22.0	27.0					3																	195506007		646	1562	2208	SO:0001819	synonymous_variant	4585	exon2			AGGGATGGTGACA	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.12444C>T	3.37:g.195506007G>A		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	112	2	0.0178571	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|1.000;|0.000	.	weak		0.587	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
MACF1	23499	hgsc.bcm.edu	37	1	39816546	39816546	+	Silent	SNP	G	G	A	rs41270815	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:39816546G>A	ENST00000372915.3	+	42	11157	c.11070G>A	c.(11068-11070)aaG>aaA	p.K3690K	MACF1_ENST00000567887.1_Silent_p.K3722K|MACF1_ENST00000564288.1_Silent_p.K3685K|MACF1_ENST00000289893.4_Silent_p.K2125K|MACF1_ENST00000361689.2_Silent_p.K1623K|MACF1_ENST00000545844.1_Silent_p.K1623K|MACF1_ENST00000539005.1_Silent_p.K1623K|MACF1_ENST00000476350.1_3'UTR|MACF1_ENST00000317713.7_Silent_p.K1623K			Q9UPN3	MACF1_HUMAN	microtubule-actin crosslinking factor 1	3690					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)			ATCAGACCAAGCTGAGCCCAC	0.498													G|||	274	0.0547125	0.0038	0.0605	5008	,	,		18848	0.0119		0.0915	False		,,,				2504	0.1258				p.K1623K		Atlas-SNP	.											.	MACF1	909	.	0			c.G4869A						PASS	.	G	,	80,4326	70.3+/-108.2	1,78,2124	107.0	99.0	102.0		4869,6375	-1.8	1.0	1	dbSNP_127	102	661,7939	166.7+/-218.6	25,611,3664	no	coding-synonymous,coding-synonymous	MACF1	NM_012090.4,NM_033044.3	,	26,689,5788	AA,AG,GG		7.686,1.8157,5.6974	,	1623/5431,2125/5939	39816546	741,12265	2203	4300	6503	SO:0001819	synonymous_variant	23499	exon39			GACCAAGCTGAGC	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.11070G>A	1.37:g.39816546G>A		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	91	40	0.43956	NM_012090	B1ALC5|E9PJT0|O75053|Q5VW20|Q8WXY1|Q8WXY2|Q96PK2|Q9H540|Q9UKP0|Q9ULG9	Silent	SNP	ENST00000372915.3	37		106	0.048534798534798536	5	0.01016260162601626	28	0.07734806629834254	3	0.005244755244755245	70	0.09234828496042216	G	10.11	1.260269	0.23051	0.018157	0.07686	ENSG00000127603	ENST00000372925	.	.	.	6.06	-1.81	0.07882	.	.	.	.	.	T	0.02929	0.0087	.	.	.	0.09310	P	0.99999999895488	.	.	.	.	.	.	T	0.44081	-0.9351	3	.	.	.	.	12.5544	0.56244	0.5121:0.0:0.4879:0.0	rs41270815	.	.	.	T	757	.	.	A	+	1	0	MACF1	39589133	0.343000	0.24818	0.993000	0.49108	0.996000	0.88848	0.481000	0.22260	-0.194000	0.10399	0.650000	0.86243	GCT	G|0.947;A|0.053	0.053	strong		0.498	MACF1-028	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000392096.1	NM_033044	
FMO1	2326	hgsc.bcm.edu	37	1	171252287	171252287	+	Silent	SNP	A	A	G	rs1126692	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:171252287A>G	ENST00000354841.4	+	7	1319	c.1188A>G	c.(1186-1188)gtA>gtG	p.V396V	FMO1_ENST00000402921.2_Silent_p.V333V|FMO1_ENST00000367750.3_Silent_p.V396V|FMO1_ENST00000469112.1_3'UTR	NM_001282692.1	NP_001269621.1	Q01740	FMO1_HUMAN	flavin containing monooxygenase 1	396					NADPH oxidation (GO:0070995)|organic acid metabolic process (GO:0006082)|small molecule metabolic process (GO:0044281)|toxin metabolic process (GO:0009404)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum lumen (GO:0005788)|integral component of membrane (GO:0016021)	flavin adenine dinucleotide binding (GO:0050660)|monooxygenase activity (GO:0004497)|N,N-dimethylaniline monooxygenase activity (GO:0004499)|NADP binding (GO:0050661)			NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(13)|prostate(2)|skin(2)	27	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)				Cevimeline(DB00185)|Cimetidine(DB00501)|Lorcaserin(DB04871)|Tamoxifen(DB00675)|Vandetanib(DB05294)|Voriconazole(DB00582)	CTACAGGTGTAAATAAGTTAC	0.353													A|||	1255	0.250599	0.593	0.121	5008	,	,		15383	0.0367		0.1412	False		,,,				2504	0.2127				p.V396V		Atlas-SNP	.											FMO1,left_upper_lobe,carcinoma,+2,1	FMO1	79	1	0			c.A1188G						PASS	.	A		2260,2146	595.1+/-388.4	580,1100,523	119.0	121.0	120.0		1188	-10.3	0.0	1	dbSNP_86	120	1166,7434	237.5+/-269.3	78,1010,3212	no	coding-synonymous	FMO1	NM_002021.1		658,2110,3735	GG,GA,AA		13.5581,48.7063,26.3417		396/533	171252287	3426,9580	2203	4300	6503	SO:0001819	synonymous_variant	2326	exon8			AGGTGTAAATAAG	M64082	CCDS1294.1, CCDS60351.1	1q24.3	2011-08-04			ENSG00000010932	ENSG00000010932	1.14.13.8		3769	protein-coding gene	gene with protein product		136130					Standard	XM_005245037		Approved		uc001ghl.3	Q01740	OTTHUMG00000035502	ENST00000354841.4:c.1188A>G	1.37:g.171252287A>G		Somatic	279	0	0		WXS	Illumina HiSeq	Phase_I	293	165	0.56314	NM_002021	A8K248|B7Z3P4|Q5QPT2|Q9UJC2	Silent	SNP	ENST00000354841.4	37	CCDS1294.1																																																																																			A|0.769;C|0.000;G|0.231	0.231	strong		0.353	FMO1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086212.1	NM_002021	
NLRP2	55655	hgsc.bcm.edu	37	19	55494262	55494262	+	Missense_Mutation	SNP	C	C	T	rs142821233		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:55494262C>T	ENST00000543010.1	+	6	1339	c.1196C>T	c.(1195-1197)gCg>gTg	p.A399V	NLRP2_ENST00000448584.2_Missense_Mutation_p.A399V|NLRP2_ENST00000263437.6_Missense_Mutation_p.A396V|NLRP2_ENST00000391721.4_Missense_Mutation_p.A375V|NLRP2_ENST00000427260.2_Missense_Mutation_p.A376V|NLRP2_ENST00000538819.1_Missense_Mutation_p.A375V|NLRP2_ENST00000339757.7_Missense_Mutation_p.A377V|NLRP2_ENST00000537859.1_Missense_Mutation_p.A377V	NM_001174081.1	NP_001167552.1	Q9NX02	NALP2_HUMAN	NLR family, pyrin domain containing 2	399	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)		TCGGCCCCCGCGGTGTGCTGG	0.632																																					p.A399V		Atlas-SNP	.											NLRP2_ENST00000543010,caecum,carcinoma,0,1	NLRP2	161	1	0			c.C1196T						scavenged	.	C	VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA	2,4404	4.2+/-10.8	0,2,2201	37.0	36.0	36.0		1196,1130,1127,1196	0.4	0.0	19	dbSNP_134	36	0,8600		0,0,4300	no	missense,missense,missense,missense	NLRP2	NM_001174081.1,NM_001174082.1,NM_001174083.1,NM_017852.3	64,64,64,64	0,2,6501	TT,TC,CC		0.0,0.0454,0.0154	probably-damaging,probably-damaging,probably-damaging,probably-damaging	399/1063,377/1041,376/1040,399/1063	55494262	2,13004	2203	4300	6503	SO:0001583	missense	55655	exon6			CCCCCGCGGTGTG	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.1196C>T	19.37:g.55494262C>T	ENSP00000445135:p.Ala399Val	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	117	3	0.025641	NM_017852	B4DZL7|I3L0G4|Q53FL5|Q59G09|Q8IXT0|Q9BVN5|Q9H6G6|Q9HAV9|Q9NWK3	Missense_Mutation	SNP	ENST00000543010.1	37	CCDS12913.1	.	.	.	.	.	.	.	.	.	.	C	12.63	1.995137	0.35226	4.54E-4	0.0	ENSG00000022556	ENST00000543010;ENST00000391721;ENST00000339757;ENST00000448584;ENST00000537859;ENST00000427260;ENST00000538819;ENST00000263437	T;T;T;T;T;T;T;T	0.70164	-0.41;-0.35;-0.34;-0.41;-0.34;-0.46;-0.35;-0.41	1.64	0.375	0.16188	NACHT nucleoside triphosphatase (1);	1.219470	0.06379	N	0.714829	T	0.59224	0.2178	N	0.16478	0.41	0.09310	N	1	D;D;D;D;D	0.71674	0.99;0.998;0.996;0.994;0.996	P;D;P;P;P	0.65233	0.727;0.933;0.859;0.896;0.859	T	0.51849	-0.8653	10	0.02654	T	1	.	5.2705	0.15622	0.0:0.7186:0.0:0.2814	.	376;377;396;375;399	B4DZL7;Q9NX02-2;A8K9G6;Q9NX02-4;Q9NX02	.;.;.;.;NALP2_HUMAN	V	399;375;377;399;377;376;375;396	ENSP00000445135:A399V;ENSP00000375601:A375V;ENSP00000344074:A377V;ENSP00000409370:A399V;ENSP00000440601:A377V;ENSP00000402474:A376V;ENSP00000441133:A375V;ENSP00000263437:A396V	ENSP00000263437:A396V	A	+	2	0	NLRP2	60186074	0.000000	0.05858	0.033000	0.17914	0.039000	0.13416	0.519000	0.22862	0.146000	0.19002	0.556000	0.70494	GCG	C|1.000;T|0.000	0.000	weak		0.632	NLRP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396152.1	NM_017852	
MYH4	4622	hgsc.bcm.edu	37	17	10355371	10355371	+	Missense_Mutation	SNP	C	C	T	rs11651295	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:10355371C>T	ENST00000255381.2	-	27	3735	c.3625G>A	c.(3625-3627)Gag>Aag	p.E1209K	CTC-297N7.11_ENST00000587182.2_RNA|RP11-799N11.1_ENST00000399342.2_RNA|RP11-799N11.1_ENST00000581304.1_RNA	NM_017533.2	NP_060003.2	Q9Y623	MYH4_HUMAN	myosin, heavy chain 4, skeletal muscle	1209			E -> K (in dbSNP:rs11651295). {ECO:0000269|PubMed:10388558}.		actin filament-based movement (GO:0030048)|ATP catabolic process (GO:0006200)|membrane organization (GO:0061024)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|response to activity (GO:0014823)	muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin filament (GO:0032982)|sarcomere (GO:0030017)	ATP binding (GO:0005524)|double-stranded RNA binding (GO:0003725)|microfilament motor activity (GO:0000146)			NS(4)|breast(8)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(13)|lung(72)|ovary(10)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	149						TCAATCTGCTCCCCAAGCTCA	0.542													C|||	2544	0.507987	0.3011	0.4841	5008	,	,		18293	0.8631		0.334	False		,,,				2504	0.6176				p.E1209K		Atlas-SNP	.											.	MYH4	349	.	0			c.G3625A						PASS	.	C	LYS/GLU	1391,3015	458.6+/-352.0	222,947,1034	105.0	85.0	92.0		3625	5.5	1.0	17	dbSNP_120	92	3130,5470	476.6+/-369.4	595,1940,1765	yes	missense	MYH4	NM_017533.2	56	817,2887,2799	TT,TC,CC		36.3953,31.5706,34.7609	probably-damaging	1209/1940	10355371	4521,8485	2203	4300	6503	SO:0001583	missense	4622	exon27			TCTGCTCCCCAAG		CCDS11154.1	17p13.1	2013-09-19	2006-09-29		ENSG00000264424	ENSG00000264424		"""Myosins / Myosin superfamily : Class II"""	7574	protein-coding gene	gene with protein product		160742	"""myosin, heavy polypeptide 4, skeletal muscle"""			8518795	Standard	NM_017533		Approved	MYH2B, MyHC-2B, MyHC-IIb	uc002gmn.3	Q9Y623	OTTHUMG00000130365	ENST00000255381.2:c.3625G>A	17.37:g.10355371C>T	ENSP00000255381:p.Glu1209Lys	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	86	43	0.5	NM_017533		Missense_Mutation	SNP	ENST00000255381.2	37	CCDS11154.1	1069	0.48946886446886445	147	0.29878048780487804	170	0.4696132596685083	498	0.8706293706293706	254	0.33509234828496043	C	34	5.299995	0.95574	0.315706	0.363953	ENSG00000141048	ENST00000255381	T	0.80480	-1.38	5.51	5.51	0.81932	Myosin tail (1);	0.000000	0.37577	U	0.002023	T	0.00012	0.0000	H	0.94847	3.59	0.09310	P	0.999999800477	D	0.58970	0.984	D	0.63113	0.911	T	0.48525	-0.9028	9	0.87932	D	0	.	19.7768	0.96398	0.0:1.0:0.0:0.0	rs11651295;rs52799277;rs58579935;rs11651295	1209	Q9Y623	MYH4_HUMAN	K	1209	ENSP00000255381:E1209K	ENSP00000255381:E1209K	E	-	1	0	MYH4	10296096	1.000000	0.71417	1.000000	0.80357	0.879000	0.50718	7.722000	0.84778	2.745000	0.94114	0.655000	0.94253	GAG	C|0.616;T|0.384	0.384	strong		0.542	MYH4-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252731.1	NM_017533	
PPM1E	22843	hgsc.bcm.edu	37	17	56833612	56833612	+	Missense_Mutation	SNP	C	C	G	rs116991234	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:56833612C>G	ENST00000308249.2	+	1	383	c.254C>G	c.(253-255)cCg>cGg	p.P85R		NM_014906.4	NP_055721.3	Q96MI6	PPM1M_HUMAN	protein phosphatase, Mg2+/Mn2+ dependent, 1E	0	PP2C-like.				protein dephosphorylation (GO:0006470)	nucleus (GO:0005634)	CTD phosphatase activity (GO:0008420)|manganese ion binding (GO:0030145)			biliary_tract(1)|breast(3)|endometrium(4)|kidney(2)|large_intestine(8)|lung(10)|ovary(2)|prostate(1)|skin(2)	33	Medulloblastoma(34;0.127)|all_neural(34;0.237)		BRCA - Breast invasive adenocarcinoma(1;5.76e-11)			gagcaagacccggagcccgag	0.756													c|||	23	0.00459265	0.0	0.0101	5008	,	,		8364	0.0		0.0129	False		,,,				2504	0.0031				p.P85R		Atlas-SNP	.											.	PPM1E	97	.	0			c.C254G						PASS	.		ARG/PRO	4,3962		0,4,1979	8.0	7.0	7.0		254	2.4	1.0	17	dbSNP_132	7	43,7859		0,43,3908	no	missense	PPM1E	NM_014906.3	103	0,47,5887	GG,GC,CC		0.5442,0.1009,0.396	benign	85/756	56833612	47,11821	1983	3951	5934	SO:0001583	missense	22843	exon1			AAGACCCGGAGCC	AB028995	CCDS11613.1	17q24.2	2012-04-17	2010-03-05		ENSG00000175175	ENSG00000175175		"""Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent"""	19322	protein-coding gene	gene with protein product	"""partner of PIX 1"", ""nuclear calmodulin-dependent protein kinase phosphatase"""		"""protein phosphatase 1E (PP2C domain containing)"""			11864573, 10470851	Standard	NR_048561		Approved	POPX1, KIAA1072, PP2CH, CaMKP-N	uc002iwx.4	Q8WY54		ENST00000308249.2:c.254C>G	17.37:g.56833612C>G	ENSP00000312411:p.Pro85Arg	Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	57	25	0.438596	NM_014906	Q8N8J9|Q96DB8	Missense_Mutation	SNP	ENST00000308249.2	37	CCDS11613.1	13	0.005952380952380952	0	0.0	5	0.013812154696132596	0	0.0	8	0.010554089709762533	c	11.88	1.770544	0.31320	0.001009	0.005442	ENSG00000175175	ENST00000308249	T	0.27256	1.68	3.53	2.43	0.29744	.	.	.	.	.	T	0.11750	0.0286	N	0.19112	0.55	0.20638	N	0.999879	B	0.26775	0.159	B	0.31614	0.133	T	0.18335	-1.0340	9	0.34782	T	0.22	-3.1579	7.5016	0.27522	0.2562:0.7438:0.0:0.0	.	85	Q8WY54-2	.	R	85	ENSP00000312411:P85R	ENSP00000312411:P85R	P	+	2	0	PPM1E	54188611	.	.	0.997000	0.53966	0.470000	0.32858	.	.	1.690000	0.51089	0.457000	0.33378	CCG	C|0.993;G|0.007	0.007	strong		0.756	PPM1E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445458.1	NM_014906	
MTA1	9112	hgsc.bcm.edu	37	14	105936204	105936204	+	Silent	SNP	C	C	T	rs373034822		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:105936204C>T	ENST00000331320.7	+	20	2086	c.1872C>T	c.(1870-1872)aaC>aaT	p.N624N	MTA1_ENST00000406191.1_Silent_p.N612N|RP11-521B24.5_ENST00000552675.1_RNA|MTA1_ENST00000435036.2_Silent_p.N164N|MTA1_ENST00000405646.1_Silent_p.N607N	NM_001203258.1|NM_004689.3	NP_001190187.1|NP_004680.2	Q13330	MTA1_HUMAN	metastasis associated 1	624					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)			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)		TCCTGCTCAACGGGAAGTCCT	0.682																																					p.N624N		Atlas-SNP	.											.	MTA1	61	.	0			c.C1872T						PASS	.	C	,	0,4384		0,0,2192	27.0	26.0	27.0		,1872	-6.0	0.9	14		27	1,8585		0,1,4292	no	utr-3,coding-synonymous	MTA1	NM_001203258.1,NM_004689.3	,	0,1,6484	TT,TC,CC		0.0116,0.0,0.0077	,	,624/716	105936204	1,12969	2192	4293	6485	SO:0001819	synonymous_variant	9112	exon20			GCTCAACGGGAAG	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.1872C>T	14.37:g.105936204C>T		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	97	53	0.546392	NM_004689	A5PLK4|Q86SW2|Q8NFI8|Q96GI8	Silent	SNP	ENST00000331320.7	37	CCDS32169.1	.	.	.	.	.	.	.	.	.	.	C	9.588	1.125368	0.20959	0.0	1.16E-4	ENSG00000182979	ENST00000494981	.	.	.	5.27	-6.01	0.02199	.	.	.	.	.	T	0.51924	0.1703	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.55231	-0.8173	4	.	.	.	-33.3685	10.6162	0.45451	0.0:0.1432:0.115:0.7418	.	.	.	.	W	51	.	.	R	+	1	2	MTA1	105007249	0.007000	0.16637	0.911000	0.35937	0.890000	0.51754	-1.491000	0.02302	-1.078000	0.03117	-0.350000	0.07774	CGG	.	.	weak		0.682	MTA1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000317849.15		
WNK1	65125	hgsc.bcm.edu	37	12	999632	999632	+	Missense_Mutation	SNP	C	C	A	rs371264719		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:999632C>A	ENST00000315939.6	+	22	6105	c.5462C>A	c.(5461-5463)gCg>gAg	p.A1821E	WNK1_ENST00000530271.2_Missense_Mutation_p.A2319E|WNK1_ENST00000537687.1_Missense_Mutation_p.A2081E|WNK1_ENST00000535572.1_Missense_Mutation_p.A1574E|WNK1_ENST00000340908.4_Missense_Mutation_p.A1414E	NM_018979.3	NP_061852.3	Q9H4A3	WNK1_HUMAN	WNK lysine deficient protein kinase 1	1821					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)			GTGTCCATGGCGGCTCCAACA	0.463																																					p.A2081E	Colon(19;451 567 6672 12618 28860)	Atlas-SNP	.											.	WNK1	403	.	0			c.C6242A						PASS	.						137.0	125.0	129.0					12																	999632		2203	4300	6503	SO:0001583	missense	65125	exon22			CCATGGCGGCTCC	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.5462C>A	12.37:g.999632C>A	ENSP00000313059:p.Ala1821Glu	Somatic	312	0	0		WXS	Illumina HiSeq	Phase_I	249	55	0.220884	NM_001184985	A1L4B0|C5HTZ5|C5HTZ6|C5HTZ7|H6WZW3|O15052|P54963|Q4VBX9|Q6IFS5|Q86WL5|Q8N673|Q96CZ6|Q9P1S9	Missense_Mutation	SNP	ENST00000315939.6	37	CCDS8506.1	.	.	.	.	.	.	.	.	.	.	T	8.007	0.756729	0.15846	.	.	ENSG00000060237	ENST00000535572;ENST00000315939;ENST00000537687;ENST00000252477;ENST00000530271;ENST00000340908	T;T;T;T;T	0.30981	1.51;1.51;1.51;1.51;1.51	5.06	1.3	0.21679	.	0.576229	0.16749	N	0.201105	T	0.13756	0.0333	N	0.14661	0.345	0.09310	N	0.999997	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.06405	0.001;0.002;0.001	T	0.23084	-1.0198	10	0.23891	T	0.37	0.0017	3.5613	0.07884	0.1573:0.2635:0.0:0.5792	.	1574;1574;1821	Q9H4A3-2;F5GWT4;Q9H4A3	.;.;WNK1_HUMAN	E	1574;1821;2081;994;2319;1414	ENSP00000441972:A1574E;ENSP00000313059:A1821E;ENSP00000444465:A2081E;ENSP00000433548:A2319E;ENSP00000341292:A1414E	ENSP00000252477:A994E	A	+	2	0	WNK1	869893	0.996000	0.38824	0.746000	0.31095	0.091000	0.18340	0.353000	0.20130	-0.096000	0.12329	-0.254000	0.11334	GCG	.	.	alt		0.463	WNK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206683.1	NM_018979	
MUC4	4585	hgsc.bcm.edu	37	3	195513461	195513461	+	Missense_Mutation	SNP	G	G	A	rs199513183		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195513461G>A	ENST00000463781.3	-	2	5449	c.4990C>T	c.(4990-4992)Cct>Tct	p.P1664S	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.P1664S	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0	VWFD. {ECO:0000255|PROSITE- ProRule:PRU00580}.				cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		ACAGGAAGAGGGGTGGCGTGA	0.592																																					p.P1664S		Atlas-SNP	.											.	MUC4	1505	.	0			c.C4990T						PASS	.						21.0	28.0	26.0					3																	195513461		688	1577	2265	SO:0001583	missense	4585	exon2			GAAGAGGGGTGGC	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.4990C>T	3.37:g.195513461G>A	ENSP00000417498:p.Pro1664Ser	Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	207	23	0.111111	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	.	.	.	.	.	.	.	.	.	.	-	5.823	0.336149	0.11013	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.30448	1.53;1.53	0.595	0.595	0.17490	.	.	.	.	.	T	0.15825	0.0381	N	0.19112	0.55	0.09310	N	1	P	0.51933	0.949	B	0.39094	0.29	T	0.13737	-1.0498	8	.	.	.	.	7.1208	0.25444	1.0E-4:0.0:0.9999:0.0	.	1664	E7ESK3	.	S	1664	ENSP00000417498:P1664S;ENSP00000420243:P1664S	.	P	-	1	0	MUC4	196997856	0.000000	0.05858	0.008000	0.14137	0.032000	0.12392	-0.500000	0.06405	0.625000	0.30304	0.089000	0.15464	CCT	.	.	weak		0.592	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
RNASE11	122651	hgsc.bcm.edu	37	14	21052259	21052259	+	Silent	SNP	T	T	C	rs1429539	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:21052259T>C	ENST00000610205.1	-	3	558	c.375A>G	c.(373-375)acA>acG	p.T125T	RNASE11_ENST00000398009.2_Silent_p.T125T|RNASE11_ENST00000555841.1_Silent_p.T125T|RNASE11_ENST00000432835.2_Silent_p.T125T|RNASE11_ENST00000553849.1_Silent_p.T125T|RNASE11_ENST00000398008.2_Silent_p.T125T	NM_145250.3	NP_660293.1	Q8TAA1	RNS11_HUMAN	ribonuclease, RNase A family, 11 (non-active)	125						extracellular region (GO:0005576)	endonuclease activity (GO:0004519)|nucleic acid binding (GO:0003676)			endometrium(1)|large_intestine(6)|lung(7)|ovary(3)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	21	all_cancers(95;0.00238)	all_lung(585;0.235)	Epithelial(56;1.85e-06)|all cancers(55;1.46e-05)	GBM - Glioblastoma multiforme(265;0.0139)		GCATCACTTCTGTGGAGCTGC	0.493													C|||	1842	0.367812	0.5484	0.2723	5008	,	,		21015	0.1905		0.3539	False		,,,				2504	0.3885				p.T125T		Atlas-SNP	.											.	RNASE11	44	.	0			c.A375G						PASS	.	C		2223,2183	585.8+/-386.3	575,1073,555	86.0	74.0	78.0		375	-1.9	0.0	14	dbSNP_88	78	3189,5411	653.4+/-401.0	604,1981,1715	no	coding-synonymous	RNASE11	NM_145250.3		1179,3054,2270	CC,CT,TT		37.0814,49.5461,41.6116		125/200	21052259	5412,7594	2203	4300	6503	SO:0001819	synonymous_variant	122651	exon3			CACTTCTGTGGAG	BC025410	CCDS9553.1	14q11.1	2013-08-05	2004-11-18	2004-11-18	ENSG00000173464	ENSG00000173464		"""Ribonucleases, RNase A"""	19269	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 6"""	C14orf6			Standard	NM_145250		Approved		uc001vxs.3	Q8TAA1	OTTHUMG00000170990	ENST00000610205.1:c.375A>G	14.37:g.21052259T>C		Somatic	242	0	0		WXS	Illumina HiSeq	Phase_I	229	229	1	NM_145250		Silent	SNP	ENST00000610205.1	37	CCDS9553.1																																																																																			T|0.613;C|0.387	0.387	strong		0.493	RNASE11-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073662.3	NM_145250	
TTN	7273	hgsc.bcm.edu	37	2	179659912	179659912	+	Missense_Mutation	SNP	G	G	A	rs16866538	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:179659912G>A	ENST00000591111.1	-	7	1206	c.982C>T	c.(982-984)Cgt>Tgt	p.R328C	TTN_ENST00000359218.5_Missense_Mutation_p.R328C|TTN_ENST00000342992.6_Missense_Mutation_p.R328C|TTN_ENST00000460472.2_Missense_Mutation_p.R328C|TTN_ENST00000589042.1_Missense_Mutation_p.R328C|TTN_ENST00000342175.6_Missense_Mutation_p.R328C|TTN_ENST00000360870.5_Missense_Mutation_p.R328C			Q8WZ42	TITIN_HUMAN	titin	0	ZIS1.		R -> C (in dbSNP:rs16866538). {ECO:0000269|PubMed:11846417, 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)			TGAGTCTTACGCATGAGCAAT	0.547													G|||	1182	0.236022	0.1974	0.098	5008	,	,		20301	0.5883		0.0477	False		,,,				2504	0.2168				p.R328C		Atlas-SNP	.											TTN_ENST00000360870,NS,carcinoma,+1,16	TTN	18412	16	0			c.C982T						PASS	.	G	CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG	689,3717	289.5+/-280.5	54,581,1568	102.0	93.0	96.0		982,982,982,982,982	5.3	0.1	2	dbSNP_123	96	457,8143	136.5+/-193.6	16,425,3859	yes	missense,missense,missense,missense,missense	TTN	NM_133437.3,NM_133432.3,NM_133379.3,NM_133378.4,NM_003319.4	180,180,180,180,180	70,1006,5427	AA,AG,GG		5.314,15.6378,8.8113	benign,benign,benign,benign,benign	328/27119,328/27052,328/5605,328/33424,328/26927	179659912	1146,11860	2203	4300	6503	SO:0001583	missense	7273	exon7			TCTTACGCATGAG	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.982C>T	2.37:g.179659912G>A	ENSP00000465570:p.Arg328Cys	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	78	42	0.538462	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		506	0.2316849816849817	101	0.20528455284552846	34	0.09392265193370165	337	0.5891608391608392	34	0.044854881266490766	G	8.050	0.765811	0.15983	0.156378	0.05314	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127;ENST00000360870	T;T;T;T;T	0.72942	-0.7;-0.33;-0.38;-0.39;-0.36	6.17	5.3	0.74995	.	.	.	.	.	T	0.00012	0.0000	L	0.50333	1.59	0.24831	P	0.99252889	B;B;B;B;P	0.41947	0.08;0.08;0.08;0.14;0.766	B;B;B;B;B	0.33121	0.01;0.01;0.01;0.01;0.158	T	0.49670	-0.8915	8	0.87932	D	0	.	11.7311	0.51737	0.1343:0.0:0.8657:0.0	rs16866538;rs52818462;rs57423160;rs16866538	328;328;328;328;328	D3DPF9;E7EQE6;E7ET18;Q8WZ42;Q8WZ42-6	.;.;.;TITIN_HUMAN;.	C	328	ENSP00000343764:R328C;ENSP00000434586:R328C;ENSP00000340554:R328C;ENSP00000352154:R328C;ENSP00000354117:R328C	ENSP00000340554:R328C	R	-	1	0	TTN	179368157	1.000000	0.71417	0.102000	0.21198	0.028000	0.11728	5.683000	0.68189	1.626000	0.50381	0.655000	0.94253	CGT	G|0.845;A|0.155	0.155	strong		0.547	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
CACNA2D4	93589	hgsc.bcm.edu	37	12	1902905	1902905	+	Silent	SNP	G	G	A	rs33912216	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:1902905G>A	ENST00000382722.5	-	38	3692	c.3330C>T	c.(3328-3330)ggC>ggT	p.G1110G	CACNA2D4_ENST00000538027.2_Silent_p.G255G|CACNA2D4_ENST00000588077.1_Silent_p.G1046G|CACNA2D4_ENST00000587995.1_Silent_p.G1085G|CACNA2D4_ENST00000538450.1_Silent_p.G240G	NM_172364.4	NP_758952.4	Q7Z3S7	CA2D4_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 4	1110					calcium ion transmembrane transport (GO:0070588)|detection of light stimulus involved in visual perception (GO:0050908)	voltage-gated calcium channel complex (GO:0005891)	metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			endometrium(3)|kidney(2)|large_intestine(1)|liver(1)|lung(27)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	39	Ovarian(42;0.107)	Myeloproliferative disorder(1001;0.206)	OV - Ovarian serous cystadenocarcinoma(31;0.00113)	Kidney(2;0.0205)|KIRC - Kidney renal clear cell carcinoma(2;0.0451)		CCGAGGCGCCGCCGCAGTCCT	0.657													G|||	613	0.122404	0.1218	0.2478	5008	,	,		17428	0.0774		0.1044	False		,,,				2504	0.0992				p.G1110G	Colon(2;101 179 21030 23310 28141)	Atlas-SNP	.											.	CACNA2D4	220	.	0			c.C3330T						PASS	.	G		484,3520		35,414,1553	25.0	30.0	28.0		3330	-9.6	0.0	12	dbSNP_126	28	716,7636		22,672,3482	no	coding-synonymous	CACNA2D4	NM_172364.4		57,1086,5035	AA,AG,GG		8.5728,12.0879,9.7119		1110/1138	1902905	1200,11156	2002	4176	6178	SO:0001819	synonymous_variant	93589	exon38			GGCGCCGCCGCAG	AF516695	CCDS44785.1	12p13.33	2003-03-05			ENSG00000151062	ENSG00000151062		"""Calcium channel subunits"""	20202	protein-coding gene	gene with protein product		608171				12181424	Standard	NM_172364		Approved		uc021qsx.1	Q7Z3S7	OTTHUMG00000168111	ENST00000382722.5:c.3330C>T	12.37:g.1902905G>A		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	184	94	0.51087	NM_172364	Q7Z3S8|Q86XZ5|Q8IZS9	Silent	SNP	ENST00000382722.5	37	CCDS44785.1																																																																																			G|0.891;A|0.109	0.109	strong		0.657	CACNA2D4-001	KNOWN	non_canonical_U12|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000398230.2		
CCT2	10576	hgsc.bcm.edu	37	12	69986788	69986788	+	Silent	SNP	A	A	G	rs1043434	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:69986788A>G	ENST00000299300.6	+	9	971	c.783A>G	c.(781-783)acA>acG	p.T261T	CCT2_ENST00000543146.2_Silent_p.T214T|CCT2_ENST00000544368.2_Silent_p.T261T	NM_006431.2	NP_006422.1	P78371	TCPB_HUMAN	chaperonin containing TCP1, subunit 2 (beta)	261					'de novo' posttranslational protein folding (GO:0051084)|binding of sperm to zona pellucida (GO:0007339)|cellular protein metabolic process (GO:0044267)|chaperone-mediated protein complex assembly (GO:0051131)|protein folding (GO:0006457)	cell body (GO:0044297)|chaperonin-containing T-complex (GO:0005832)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|zona pellucida receptor complex (GO:0002199)	ATP binding (GO:0005524)|unfolded protein binding (GO:0051082)			central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(1)|lung(10)|ovary(1)|prostate(2)|skin(2)|stomach(1)	24	all_cancers(2;7.7e-106)|Breast(13;2.15e-06)|Esophageal squamous(21;0.187)		Epithelial(6;2.72e-18)|GBM - Glioblastoma multiforme(2;2.58e-10)|Lung(24;0.000185)|OV - Ovarian serous cystadenocarcinoma(12;0.00126)|STAD - Stomach adenocarcinoma(21;0.00501)|Kidney(9;0.143)|LUSC - Lung squamous cell carcinoma(43;0.24)			TTGACTCTACAGCAAAGGTTG	0.363													A|||	1086	0.216853	0.084	0.1888	5008	,	,		19934	0.3026		0.2565	False		,,,				2504	0.2873				p.T261T		Atlas-SNP	.											.	CCT2	49	.	0			c.A783G						PASS	.	A	,	459,3947	218.1+/-236.3	20,419,1764	81.0	82.0	82.0		642,783	4.6	1.0	12	dbSNP_86	82	1954,6646	345.9+/-325.9	204,1546,2550	no	coding-synonymous,coding-synonymous	CCT2	NM_001198842.1,NM_006431.2	,	224,1965,4314	GG,GA,AA		22.7209,10.4176,18.553	,	214/489,261/536	69986788	2413,10593	2203	4300	6503	SO:0001819	synonymous_variant	10576	exon9			CTCTACAGCAAAG	AF026293	CCDS8991.1, CCDS55843.1	12q14	2011-09-02						"""Heat Shock Proteins / Chaperonins"""	1615	protein-coding gene	gene with protein product		605139				9819444	Standard	NM_001198842		Approved	Cctb	uc001svb.1	P78371	OTTHUMG00000169383	ENST00000299300.6:c.783A>G	12.37:g.69986788A>G		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	61	24	0.393443	NM_006431	A8K402|B5BTY7|B7Z243|B7Z7K4|B7ZAT2|Q14D36|Q6IAT3	Silent	SNP	ENST00000299300.6	37	CCDS8991.1																																																																																			A|0.800;G|0.200	0.200	strong		0.363	CCT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403818.1	NM_006431	
WDFY4	57705	hgsc.bcm.edu	37	10	50183042	50183042	+	Missense_Mutation	SNP	G	G	A	rs61733240	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:50183042G>A	ENST00000325239.5	+	57	9091	c.9064G>A	c.(9064-9066)Gcc>Acc	p.A3022T	WDFY4_ENST00000465910.1_3'UTR|WDFY4_ENST00000413659.2_3'UTR|RP11-523O18.5_ENST00000428825.4_RNA	NM_020945.1	NP_065996.1	Q6ZS81	WDFY4_HUMAN	WDFY family member 4	3022						integral component of membrane (GO:0016021)				NS(2)|breast(5)|central_nervous_system(4)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|lung(3)|pancreas(2)|prostate(5)|skin(6)|stomach(1)	48						CCGCCTGCCCGCCCATCGGGA	0.607													A|||	598	0.119409	0.2496	0.1239	5008	,	,		19367	0.006		0.0706	False		,,,				2504	0.1074				p.A3022T		Atlas-SNP	.											.	WDFY4	205	.	0			c.G9064A						PASS	.	A	THR/ALA	331,1053		41,249,402	60.0	65.0	64.0		9064	-1.2	0.0	10	dbSNP_129	64	202,2980		5,192,1394	yes	missense	WDFY4	NM_020945.1	58	46,441,1796	AA,AG,GG		6.3482,23.9162,11.6732	benign	3022/3185	50183042	533,4033	692	1591	2283	SO:0001583	missense	57705	exon58			CTGCCCGCCCATC	AK074085	CCDS44385.1	10q11.23	2013-01-10			ENSG00000128815	ENSG00000128815		"""WD repeat domain containing"""	29323	protein-coding gene	gene with protein product		613316	"""chromosome 10 open reading frame 64"""	C10orf64		10997877	Standard	NM_020945		Approved	KIAA1607, Em:AC060234.3, FLJ45748	uc001jha.4	Q6ZS81	OTTHUMG00000018180	ENST00000325239.5:c.9064G>A	10.37:g.50183042G>A	ENSP00000320563:p.Ala3022Thr	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	118	58	0.491525	NM_020945	B9ZVP2|Q86WZ4|Q8N4A3|Q8TEN7|Q96BE1|Q9H7H8|Q9HCG5	Missense_Mutation	SNP	ENST00000325239.5	37	CCDS44385.1	215|215	0.09844322344322344|0.09844322344322344	120|120	0.24390243902439024|0.24390243902439024	43|43	0.11878453038674033|0.11878453038674033	4|4	0.006993006993006993|0.006993006993006993	48|48	0.0633245382585752|0.0633245382585752	A|A	8.330|8.330	0.826276|0.826276	0.16749|0.16749	0.239162|0.239162	0.063482|0.063482	ENSG00000128815|ENSG00000128815	ENST00000426033;ENST00000325239;ENST00000544136|ENST00000312002	T|.	0.29142|.	1.58|.	5.61|5.61	-1.18|-1.18	0.09617|0.09617	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);|.	0.590841|.	0.17291|.	N|.	0.179628|.	T|T	0.00012|0.00012	0.0000|0.0000	L|L	0.38531|0.38531	1.155|1.155	0.58432|0.58432	P|P	1.0000000000287557E-6|1.0000000000287557E-6	B;B|.	0.23591|.	0.013;0.088|.	B;B|.	0.10450|.	0.003;0.005|.	T|T	0.24977|0.24977	-1.0145|-1.0145	8|4	.|.	.|.	.|.	.|.	8.4404|8.4404	0.32812|0.32812	0.3567:0.0985:0.5448:0.0|0.3567:0.0985:0.5448:0.0	rs61733240|rs61733240	485;3022|.	B4DWY9;Q6ZS81|.	.;WDFY4_HUMAN|.	T|H	3022;3022;485|2112	ENSP00000320563:A3022T|.	.|.	A|R	+|+	1|2	0|0	WDFY4|WDFY4	49853048|49853048	0.000000|0.000000	0.05858|0.05858	0.003000|0.003000	0.11579|0.11579	0.003000|0.003000	0.03518|0.03518	0.572000|0.572000	0.23684|0.23684	-0.654000|-0.654000	0.05394|0.05394	-0.834000|-0.834000	0.03071|0.03071	GCC|CGC	G|0.901;A|0.099	0.099	strong		0.607	WDFY4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		XM_033379	
TSEN54	283989	hgsc.bcm.edu	37	17	73520435	73520435	+	Missense_Mutation	SNP	G	G	A	rs200275380		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:73520435G>A	ENST00000333213.6	+	11	1559	c.1523G>A	c.(1522-1524)gGt>gAt	p.G508D	LLGL2_ENST00000578363.1_5'Flank|LLGL2_ENST00000392550.3_5'Flank|LLGL2_ENST00000167462.5_5'Flank|LLGL2_ENST00000375227.4_5'Flank	NM_207346.2	NP_997229.2	Q7Z6J9	SEN54_HUMAN	TSEN54 tRNA splicing endonuclease subunit	508					mRNA processing (GO:0006397)|tRNA splicing, via endonucleolytic cleavage and ligation (GO:0006388)	nucleus (GO:0005634)				endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(1)|lung(5)|ovary(2)	13	all_cancers(13;3.15e-09)|all_epithelial(9;5.78e-10)|Breast(9;5.8e-10)|all_lung(278;0.246)		all cancers(21;4.57e-07)|Epithelial(20;2.92e-06)|Lung(188;0.0809)|LUSC - Lung squamous cell carcinoma(166;0.154)			GTGGATCATGGTGACATCTCC	0.582																																					p.G508D		Atlas-SNP	.											.	TSEN54	27	.	0			c.G1523A						PASS	.						178.0	144.0	155.0					17																	73520435		2203	4300	6503	SO:0001583	missense	283989	exon11			ATCATGGTGACAT	AK097583	CCDS11724.1	17q25.1	2013-08-06	2013-08-06		ENSG00000182173	ENSG00000182173		"""tRNA splicing endonuclease subunits"""	27561	protein-coding gene	gene with protein product		608755	"""tRNA splicing endonuclease 54 homolog (SEN54, S. cerevisiae)"", ""tRNA splicing endonuclease 54 homolog (S. cerevisiae)"""			15109492	Standard	NM_207346		Approved	SEN54, SEN54L	uc002jof.1	Q7Z6J9		ENST00000333213.6:c.1523G>A	17.37:g.73520435G>A	ENSP00000327487:p.Gly508Asp	Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	150	83	0.553333	NM_207346	Q86WV3|Q86XE4|Q8N9H2	Missense_Mutation	SNP	ENST00000333213.6	37	CCDS11724.1	.	.	.	.	.	.	.	.	.	.	G	35	5.485368	0.96323	.	.	ENSG00000182173	ENST00000333213	T	0.60424	0.19	5.6	5.6	0.85130	.	0.000000	0.85682	D	0.000000	T	0.77638	0.4160	M	0.74258	2.255	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.79179	-0.1910	10	0.72032	D	0.01	-14.4051	19.6034	0.95572	0.0:0.0:1.0:0.0	.	508	Q7Z6J9	SEN54_HUMAN	D	508	ENSP00000327487:G508D	ENSP00000327487:G508D	G	+	2	0	TSEN54	71032030	1.000000	0.71417	0.970000	0.41538	0.988000	0.76386	9.171000	0.94802	2.637000	0.89404	0.561000	0.74099	GGT	G|0.999;A|0.001	0.001	weak		0.582	TSEN54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447618.1	NM_207346	
PIEZO1	9780	hgsc.bcm.edu	37	16	88783521	88783521	+	Silent	SNP	T	T	C	rs6500491	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:88783521T>C	ENST00000301015.9	-	45	6816	c.6570A>G	c.(6568-6570)ccA>ccG	p.P2190P	MIR4722_ENST00000578292.1_RNA|PIEZO1_ENST00000327397.7_Silent_p.P58P|RP5-1142A6.9_ENST00000564984.1_RNA	NM_001142864.2	NP_001136336.2	Q92508	PIEZ1_HUMAN	piezo-type mechanosensitive ion channel component 1	2190					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						TGAAGAGCAGTGGGAACCAGA	0.562													C|||	4467	0.891973	0.8805	0.9107	5008	,	,		21238	0.9256		0.8946	False		,,,				2504	0.8569				p.P2190P		Atlas-SNP	.											.	PIEZO1	79	.	0			c.A6570G						PASS	.	C		1233,151		550,133,9	275.0	281.0	279.0		6570	-9.4	0.0	16	dbSNP_116	279	2907,275		1330,247,14	no	coding-synonymous	PIEZO1	NM_001142864.2		1880,380,23	CC,CT,TT		8.6424,10.9104,9.3298		2190/2522	88783521	4140,426	692	1591	2283	SO:0001819	synonymous_variant	9780	exon45			GAGCAGTGGGAAC	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.6570A>G	16.37:g.88783521T>C		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	97	97	1	NM_001142864	A6NHT9|A7E2B7|Q0KKZ9	Silent	SNP	ENST00000301015.9	37	CCDS54058.1	1968	0.9010989010989011	427	0.8678861788617886	331	0.914364640883978	535	0.9353146853146853	675	0.8905013192612137	C	3.010	-0.204171	0.06180	0.890896	0.913576	ENSG00000103335	ENST00000451779	.	.	.	4.68	-9.36	0.00629	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999671	.	.	.	.	.	.	T	0.04579	-1.0941	3	.	.	.	-20.0584	4.9532	0.14025	0.0667:0.2513:0.2576:0.4245	rs6500491;rs61024122	.	.	.	A	2136	.	.	T	-	1	0	FAM38A	87311022	0.000000	0.05858	0.038000	0.18304	0.527000	0.34593	-11.502000	0.00003	-4.408000	0.00051	-4.327000	0.00007	ACT	C|0.901;G|0.000;T|0.099	0.901	strong		0.562	PIEZO1-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000345699.4	NM_014745	
LCA5L	150082	hgsc.bcm.edu	37	21	40800368	40800368	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:40800368C>T	ENST00000358268.2	-	4	580	c.52G>A	c.(52-54)Gtg>Atg	p.V18M	LCA5L_ENST00000288350.3_Missense_Mutation_p.V18M|LCA5L_ENST00000485895.2_Missense_Mutation_p.V18M|LCA5L_ENST00000380671.2_Missense_Mutation_p.V18M			O95447	LCA5L_HUMAN	Leber congenital amaurosis 5-like	18										breast(1)|cervix(1)|endometrium(3)|large_intestine(8)|lung(4)|pancreas(2)|prostate(2)|skin(2)|urinary_tract(1)	24		Prostate(19;1.2e-06)				TCTAATGCCACGCCGAAGAAA	0.368																																					p.V18M		Atlas-SNP	.											.	LCA5L	57	.	0			c.G52A						PASS	.						112.0	109.0	110.0					21																	40800368		2203	4300	6503	SO:0001583	missense	150082	exon4			ATGCCACGCCGAA	AF121781	CCDS13665.1	21q22.2	2007-12-18	2007-12-18	2007-12-18	ENSG00000157578	ENSG00000157578			1255	protein-coding gene	gene with protein product			"""chromosome 21 open reading frame 13"""	C21orf13			Standard	XM_005260926		Approved	MGC33295	uc002yxu.3	O95447	OTTHUMG00000066280	ENST00000358268.2:c.52G>A	21.37:g.40800368C>T	ENSP00000351008:p.Val18Met	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	124	23	0.185484	NM_152505	D3DSI0|Q3ZCT0	Missense_Mutation	SNP	ENST00000358268.2	37	CCDS13665.1	.	.	.	.	.	.	.	.	.	.	c	14.53	2.562098	0.45590	.	.	ENSG00000157578	ENST00000288350;ENST00000380671;ENST00000358268;ENST00000418018;ENST00000448288;ENST00000434281;ENST00000438404;ENST00000411566;ENST00000415863;ENST00000426783;ENST00000456017	T;T;T;T;T;T;T;T;T;T;T	0.66099	0.19;0.19;0.19;0.62;0.58;0.57;0.56;0.56;0.47;0.42;-0.19	5.65	1.67	0.24075	.	1.008340	0.07969	N	0.983624	T	0.65852	0.2731	L	0.47716	1.5	0.09310	N	1	D;D	0.67145	0.993;0.996	P;P	0.61397	0.743;0.888	T	0.51132	-0.8744	10	0.72032	D	0.01	-2.9629	1.7285	0.02927	0.2757:0.4233:0.1428:0.1582	.	18;18	C9JFB6;O95447	.;LCA5L_HUMAN	M	18	ENSP00000288350:V18M;ENSP00000370046:V18M;ENSP00000351008:V18M;ENSP00000404521:V18M;ENSP00000405598:V18M;ENSP00000400086:V18M;ENSP00000405130:V18M;ENSP00000412691:V18M;ENSP00000395593:V18M;ENSP00000414784:V18M;ENSP00000407065:V18M	ENSP00000288350:V18M	V	-	1	0	LCA5L	39722238	0.000000	0.05858	0.001000	0.08648	0.007000	0.05969	-0.181000	0.09740	0.032000	0.15435	-0.119000	0.15052	GTG	.	.	none		0.368	LCA5L-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141807.2	NM_152505	
CARD10	29775	hgsc.bcm.edu	37	22	37906262	37906262	+	Missense_Mutation	SNP	C	C	T	rs9610775	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:37906262C>T	ENST00000403299.1	-	5	1082	c.866G>A	c.(865-867)cGg>cAg	p.R289Q	CARD10_ENST00000494166.1_5'UTR|CARD10_ENST00000251973.5_Missense_Mutation_p.R289Q|CARD10_ENST00000406271.3_5'Flank			Q9BWT7	CAR10_HUMAN	caspase recruitment domain family, member 10	289			R -> Q (in dbSNP:rs9610775). {ECO:0000269|PubMed:11259443, ECO:0000269|PubMed:11356195}.		activation of NF-kappaB-inducing kinase activity (GO:0007250)|protein complex assembly (GO:0006461)|regulation of apoptotic process (GO:0042981)	CBM complex (GO:0032449)|cytoplasm (GO:0005737)	receptor signaling complex scaffold activity (GO:0030159)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	17	Melanoma(58;0.0574)					CGCCGTCAGCCGCTGGTTCTC	0.662													C|||	1085	0.216653	0.2579	0.1282	5008	,	,		14625	0.1915		0.1948	False		,,,				2504	0.272				p.R289Q		Atlas-SNP	.											.	CARD10	55	.	0			c.G866A						PASS	.	C	GLN/ARG	1053,3353	366.6+/-317.9	134,785,1284	38.0	38.0	38.0		866	4.9	1.0	22	dbSNP_119	38	1557,7039	278.4+/-293.4	166,1225,2907	yes	missense	CARD10	NM_014550.3	43	300,2010,4191	TT,TC,CC		18.1131,23.8992,20.0738	probably-damaging	289/1033	37906262	2610,10392	2203	4298	6501	SO:0001583	missense	29775	exon4			GTCAGCCGCTGGT	AF086324	CCDS13948.1	22q13.1	2008-05-22			ENSG00000100065	ENSG00000100065			16422	protein-coding gene	gene with protein product		607209				11259443, 11356195	Standard	NM_014550		Approved	CARMA3, BIMP1	uc003asu.1	Q9BWT7	OTTHUMG00000150592	ENST00000403299.1:c.866G>A	22.37:g.37906262C>T	ENSP00000384570:p.Arg289Gln	Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	16	9	0.5625	NM_014550	Q14CQ8|Q5TFG6|Q8NC81|Q9UGR5|Q9UGR6|Q9Y3H0	Missense_Mutation	SNP	ENST00000403299.1	37	CCDS13948.1	392	0.1794871794871795	94	0.1910569105691057	46	0.1270718232044199	104	0.18181818181818182	148	0.19525065963060687	C	15.72	2.915945	0.52546	0.238992	0.181131	ENSG00000100065	ENST00000403299;ENST00000251973	T;T	0.34472	1.36;1.36	4.86	4.86	0.63082	.	0.252547	0.31909	N	0.006875	T	0.00012	0.0000	L	0.60455	1.87	0.35512	P	0.199303	D	0.67145	0.996	P	0.45829	0.494	T	0.20739	-1.0266	9	0.19590	T	0.45	-16.9506	18.0032	0.89203	0.0:1.0:0.0:0.0	rs9610775;rs9610775	289	Q9BWT7	CAR10_HUMAN	Q	289	ENSP00000384570:R289Q;ENSP00000251973:R289Q	ENSP00000251973:R289Q	R	-	2	0	CARD10	36236208	1.000000	0.71417	1.000000	0.80357	0.676000	0.39594	4.785000	0.62418	2.250000	0.74265	0.655000	0.94253	CGG	C|0.806;T|0.194	0.194	strong		0.662	CARD10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318997.1	NM_014550	
PKHD1	5314	hgsc.bcm.edu	37	6	51524681	51524681	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:51524681G>A	ENST00000371117.3	-	61	10518	c.10243C>T	c.(10243-10245)Ctt>Ttt	p.L3415F		NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	3415					cellular calcium ion homeostasis (GO:0006874)|cilium assembly (GO:0042384)|homeostatic process (GO:0042592)|kidney development (GO:0001822)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular component movement (GO:0051271)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein kinase B signaling (GO:0051898)|positive regulation of cell proliferation (GO:0008284)|regulation of centrosome duplication (GO:0010824)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of TOR signaling (GO:0032006)|single organismal cell-cell adhesion (GO:0016337)	anchored component of external side of plasma membrane (GO:0031362)|apical plasma membrane (GO:0016324)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitotic spindle (GO:0072686)|perinuclear region of cytoplasm (GO:0048471)|primary cilium (GO:0072372)	receptor activity (GO:0004872)	p.L3415F(1)		NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(5)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(59)|lung(139)|ovary(16)|prostate(8)|skin(20)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(7)|urinary_tract(5)	304	Lung NSC(77;0.0605)					GCGCTATCAAGAATTAGGACC	0.368																																					p.L3415F		Atlas-SNP	.											PKHD1,NS,carcinoma,0,1	PKHD1	927	1	1	Substitution - Missense(1)	lung(1)	c.C10243T						PASS	.						74.0	66.0	69.0					6																	51524681		2203	4300	6503	SO:0001583	missense	5314	exon61			TATCAAGAATTAG	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.10243C>T	6.37:g.51524681G>A	ENSP00000360158:p.Leu3415Phe	Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	167	42	0.251497	NM_138694	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Missense_Mutation	SNP	ENST00000371117.3	37	CCDS4935.1	.	.	.	.	.	.	.	.	.	.	G	13.40	2.226393	0.39300	.	.	ENSG00000170927	ENST00000371117	D	0.86497	-2.13	5.48	4.6	0.57074	.	0.000000	0.56097	D	0.000021	D	0.85669	0.5750	L	0.34521	1.04	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.84345	0.0529	10	0.34782	T	0.22	.	11.1417	0.48406	0.1436:0.0:0.8564:0.0	.	3415	P08F94	PKHD1_HUMAN	F	3415	ENSP00000360158:L3415F	ENSP00000360158:L3415F	L	-	1	0	PKHD1	51632640	1.000000	0.71417	1.000000	0.80357	0.192000	0.23643	1.690000	0.37711	2.580000	0.87095	0.655000	0.94253	CTT	.	.	none		0.368	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694	
KIAA0226	9711	hgsc.bcm.edu	37	3	197401952	197401952	+	Silent	SNP	T	T	C	rs28562770	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	86	0	0		WXS	Illumina HiSeq	Phase_I	70	31	0.442857	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	
MUC5B	727897	hgsc.bcm.edu	37	11	1263776	1263776	+	Missense_Mutation	SNP	C	C	T	rs2943510	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:1263776C>T	ENST00000529681.1	+	31	5724	c.5666C>T	c.(5665-5667)cCa>cTa	p.P1889L	MUC5B_ENST00000447027.1_Missense_Mutation_p.P1892L|RP11-532E4.2_ENST00000532061.2_RNA	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	213	0	0		WXS	Illumina HiSeq	Phase_I	204	38	0.186275	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	
GPER1	2852	hgsc.bcm.edu	37	7	1132153	1132153	+	Silent	SNP	G	G	A	rs3808352	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:1132153G>A	ENST00000297469.3	+	2	1480	c.789G>A	c.(787-789)gcG>gcA	p.A263A	GPER1_ENST00000401670.1_Silent_p.A263A|C7orf50_ENST00000488073.1_Intron|GPER1_ENST00000397092.1_Silent_p.A263A|GPER1_ENST00000397088.3_Silent_p.A263A|C7orf50_ENST00000397100.2_Intron|C7orf50_ENST00000357429.6_Intron|C7orf50_ENST00000397098.3_Intron	NM_001505.2	NP_001496.1	Q99527	GPER1_HUMAN	G protein-coupled estrogen receptor 1	263					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)										TGATCCTCGCGGTGGTGCTGG	0.687													G|||	572	0.114217	0.0287	0.1427	5008	,	,		17727	0.1121		0.1759	False		,,,				2504	0.1483				p.A263A		Atlas-SNP	.											.	GPER	25	.	0			c.G789A						PASS	.		,,,,,	211,4195	126.6+/-163.6	10,191,2002	50.0	53.0	52.0		789,789,,,789,	-10.9	0.0	7	dbSNP_107	52	1599,7001	295.8+/-302.6	155,1289,2856	no	coding-synonymous,coding-synonymous,intron,intron,coding-synonymous,intron	GPER,C7orf50	NM_001039966.1,NM_001098201.1,NM_001134395.1,NM_001134396.1,NM_001505.2,NM_032350.5	,,,,,	165,1480,4858	AA,AG,GG		18.593,4.7889,13.9167	,,,,,	263/376,263/376,,,263/376,	1132153	1810,11196	2203	4300	6503	SO:0001819	synonymous_variant	2852	exon2			CCTCGCGGTGGTG	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.789G>A	7.37:g.1132153G>A		Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	24	10	0.416667	NM_001505	A8K6C5|B5BUJ1|O00143|O43494|Q13631|Q6FHL1|Q96F42|Q99981	Silent	SNP	ENST00000297469.3	37	CCDS5322.1																																																																																			G|0.875;A|0.125	0.125	strong		0.687	GPER1-030	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060001.1	NM_001039966	
KRT77	374454	hgsc.bcm.edu	37	12	53086645	53086645	+	Missense_Mutation	SNP	G	G	A	rs3782489	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:53086645G>A	ENST00000341809.3	-	6	1128	c.1100C>T	c.(1099-1101)aCg>aTg	p.T367M	KRT77_ENST00000537195.1_Missense_Mutation_p.T134M|RP11-641A6.3_ENST00000547533.1_RNA	NM_175078.2	NP_778253.2	Q7Z794	K2C1B_HUMAN	keratin 77	367	Coil 2.|Rod.					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						TCTCCCTGCCGTGATCTGGAG	0.587													G|||	1900	0.379393	0.4584	0.3703	5008	,	,		20084	0.245		0.3499	False		,,,				2504	0.4479				p.T367M		Atlas-SNP	.											.	KRT77	58	.	0			c.C1100T						PASS	.	G	MET/THR	1850,2554		392,1066,744	145.0	105.0	118.0		1100	1.4	0.0	12	dbSNP_107	118	3151,5391		728,1695,1848	yes	missense	KRT77	NM_175078.2	81	1120,2761,2592	AA,AG,GG		36.8883,42.0073,38.6297	probably-damaging	367/579	53086645	5001,7945	2202	4271	6473	SO:0001583	missense	374454	exon6			CCTGCCGTGATCT	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.1100C>T	12.37:g.53086645G>A	ENSP00000342710:p.Thr367Met	Somatic	210	0	0		WXS	Illumina HiSeq	Phase_I	172	74	0.430233	NM_175078	Q7RTS8	Missense_Mutation	SNP	ENST00000341809.3	37	CCDS8837.1	729	0.33379120879120877	211	0.42886178861788615	119	0.3287292817679558	128	0.22377622377622378	271	0.3575197889182058	G	16.26	3.073422	0.55646	0.420073	0.368883	ENSG00000189182	ENST00000341809;ENST00000537195	D;D	0.89196	-2.48;-1.64	3.44	1.41	0.22369	Filament (1);	.	.	.	.	T	0.00012	0.0000	M	0.92367	3.3	0.80722	P	0.0	D	0.76494	0.999	D	0.69479	0.964	T	0.00010	-1.2454	8	0.72032	D	0.01	.	8.8356	0.35111	0.2067:0.0:0.7933:0.0	rs3782489;rs58781522;rs3782489	367	Q7Z794	K2C1B_HUMAN	M	367;134	ENSP00000342710:T367M;ENSP00000440803:T134M	ENSP00000342710:T367M	T	-	2	0	KRT77	51372912	0.002000	0.14202	0.000000	0.03702	0.359000	0.29487	1.188000	0.32102	0.371000	0.24564	0.456000	0.33151	ACG	G|0.631;A|0.369	0.369	strong		0.587	KRT77-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404111.1	NM_175078	
RPP21	79897	hgsc.bcm.edu	37	6	30314567	30314567	+	Missense_Mutation	SNP	C	C	A	rs974963|rs35287137	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:30314567C>A	ENST00000442966.2	+	5	458	c.445C>A	c.(445-447)Cag>Aag	p.Q149K	TRIM39-RPP21_ENST00000513556.1_Missense_Mutation_p.Q410K|RPP21_ENST00000428040.2_Missense_Mutation_p.Q172K|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						PASS	.	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	96	0	0		WXS	Illumina HiSeq	Phase_I	97	40	0.412371	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	
FANCE	2178	hgsc.bcm.edu	37	6	35426175	35426175	+	Silent	SNP	C	C	T	rs3823434	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:35426175C>T	ENST00000229769.2	+	5	1256	c.1071C>T	c.(1069-1071)ctC>ctT	p.L357L		NM_021922.2	NP_068741.1	Q9HB96	FANCE_HUMAN	Fanconi anemia, complementation group E	357	Interaction with FANCC.				DNA repair (GO:0006281)	Fanconi anaemia nuclear complex (GO:0043240)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(3)|ovary(1)|skin(2)	13						ATCTCAGCCTCAGCAATGCTA	0.587			"""N, F, S"""			"""AML, leukemia"""		Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia				C|||	292	0.0583067	0.0061	0.0331	5008	,	,		19522	0.1687		0.0258	False		,,,				2504	0.0665				p.L357L		Atlas-SNP	.	yes	Rec		Fanconi anaemia E	6	6p21-p22	2178	"""Fanconi anemia, complementation group E"""		L	.	FANCE	45	.	0			c.C1071T						PASS	.	C		35,4371	39.2+/-71.8	0,35,2168	177.0	167.0	171.0		1071	-0.8	0.0	6	dbSNP_107	171	197,8403	86.3+/-148.7	4,189,4107	no	coding-synonymous	FANCE	NM_021922.2		4,224,6275	TT,TC,CC		2.2907,0.7944,1.7838		357/537	35426175	232,12774	2203	4300	6503	SO:0001819	synonymous_variant	2178	exon5	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	CAGCCTCAGCAAT	AF265210	CCDS4805.1	6p22-p21	2014-09-17			ENSG00000112039	ENSG00000112039		"""Fanconi anemia, complementation groups"""	3586	protein-coding gene	gene with protein product		613976		FACE		7662964, 11001585	Standard	XM_005248885		Approved	FAE	uc003oko.1	Q9HB96	OTTHUMG00000014565	ENST00000229769.2:c.1071C>T	6.37:g.35426175C>T		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	96	38	0.395833	NM_021922	A8K907|Q4ZGH2	Silent	SNP	ENST00000229769.2	37	CCDS4805.1																																																																																			C|0.960;T|0.040	0.040	strong		0.587	FANCE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040282.1		
SLC35A1	10559	hgsc.bcm.edu	37	6	88218282	88218282	+	Missense_Mutation	SNP	A	A	G	rs188216651		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:88218282A>G	ENST00000369552.4	+	6	746	c.719A>G	c.(718-720)tAt>tGt	p.Y240C	SLC35A1_ENST00000544441.1_Missense_Mutation_p.Y106C|SLC35A1_ENST00000369556.3_Intron|C6orf165_ENST00000506888.1_3'UTR|SLC35A1_ENST00000369557.5_Intron|SLC35A1_ENST00000464978.1_3'UTR	NM_006416.4	NP_006407.1	P78382	S35A1_HUMAN	solute carrier family 35 (CMP-sialic acid transporter), member A1	240					carbohydrate metabolic process (GO:0005975)|cellular protein modification process (GO:0006464)|CMP-N-acetylneuraminate transport (GO:0015782)|transmembrane transport (GO:0055085)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)	CMP-N-acetylneuraminate transmembrane transporter activity (GO:0005456)|sugar:proton symporter activity (GO:0005351)			breast(1)|kidney(3)|large_intestine(2)|lung(3)	9		all_cancers(76;3.93e-06)|Acute lymphoblastic leukemia(125;3.55e-10)|Prostate(29;3.51e-09)|all_hematologic(105;3.29e-06)|all_epithelial(107;0.00575)		BRCA - Breast invasive adenocarcinoma(108;0.0429)		GGATTTTTCTATGGTTACACA	0.323																																					p.Y240C	NSCLC(183;214 2117 17033 22638 44782)|Ovarian(87;1008 1343 9644 42916 50932)	Atlas-SNP	.											.	SLC35A1	29	.	0			c.A719G						PASS	.						89.0	92.0	91.0					6																	88218282		2203	4298	6501	SO:0001583	missense	10559	exon6			TTTTCTATGGTTA	D87969	CCDS5010.1, CCDS55043.1	6q15	2013-05-22			ENSG00000164414	ENSG00000164414		"""Solute carriers"""	11021	protein-coding gene	gene with protein product		605634	"""solute carrier family 35 (UDP-galactose transporter), member 1"""			9010752, 9644260	Standard	NM_006416		Approved	CMPST, hCST	uc011dzj.2	P78382	OTTHUMG00000015177	ENST00000369552.4:c.719A>G	6.37:g.88218282A>G	ENSP00000358565:p.Tyr240Cys	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	52	31	0.596154	NM_006416	Q5W1L8	Missense_Mutation	SNP	ENST00000369552.4	37	CCDS5010.1	1|1	4.578754578754579E-4|4.578754578754579E-4	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	1|1	0.0013192612137203166|0.0013192612137203166	A|A	15.17|15.17	2.754984|2.754984	0.49362|0.49362	.|.	.|.	ENSG00000164414|ENSG00000164414	ENST00000429605|ENST00000544441;ENST00000369552	.|T;T	.|0.44881	.|0.91;0.91	5.64|5.64	3.21|3.21	0.36854|0.36854	.|.	.|0.214545	.|0.40908	.|U	.|0.000998	T|T	0.42585|0.42585	0.1209|0.1209	M|M	0.68593|0.68593	2.085|2.085	0.48901|0.48901	D|D	0.99972|0.99972	.|D;D	.|0.62365	.|0.991;0.978	.|P;P	.|0.62089	.|0.898;0.762	T|T	0.39800|0.39800	-0.9596|-0.9596	6|10	0.30078|0.54805	T|T	0.28|0.06	-56.8193|-56.8193	7.7786|7.7786	0.29051|0.29051	0.8085:0.0:0.0674:0.1241|0.8085:0.0:0.0674:0.1241	.|.	.|240;106	.|P78382;B4DEM1	.|S35A1_HUMAN;.	V|C	150|106;240	.|ENSP00000438603:Y106C;ENSP00000358565:Y240C	ENSP00000413148:M150V|ENSP00000358565:Y240C	M|Y	+|+	1|2	0|0	SLC35A1|SLC35A1	88275001|88275001	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	2.961000|2.961000	0.49168|0.49168	0.412000|0.412000	0.25729|0.25729	0.459000|0.459000	0.35465|0.35465	ATG|TAT	A|1.000;G|0.000	0.000	strong		0.323	SLC35A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041446.1		
CD33	945	hgsc.bcm.edu	37	19	51728641	51728641	+	Missense_Mutation	SNP	A	A	G	rs2455069	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:51728641A>G	ENST00000262262.4	+	2	226	c.205A>G	c.(205-207)Agg>Ggg	p.R69G	CD33_ENST00000421133.2_Intron|CD33_ENST00000391796.3_Missense_Mutation_p.R69G|CD33_ENST00000436584.2_Intron	NM_001772.3	NP_001763.3	P20138	CD33_HUMAN	CD33 molecule	69	Ig-like V-type.		R -> G (in dbSNP:rs2455069). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:3139766}.		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.R69G(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)	CATTATATCCAGGGACTCTCC	0.537													N|||	1678	0.335064	0.5318	0.2983	5008	,	,		19238	0.1042		0.4483	False		,,,				2504	0.2168				p.R69G		Atlas-SNP	.											CD33,NS,carcinoma,0,1	CD33	55	1	1	Substitution - Missense(1)	stomach(1)	c.A205G						scavenged	.	G	,GLY/ARG,GLY/ARG	2210,2196		567,1076,560	80.0	81.0	81.0		,205,205	-7.0	0.0	19	dbSNP_100	81	3698,4902		800,2098,1402	yes	intron,missense,missense	CD33	NM_001082618.1,NM_001177608.1,NM_001772.3	,125,125	1367,3174,1962	GG,GA,AA		43.0,49.8411,45.4252	,benign,benign	,69/311,69/365	51728641	5908,7098	2203	4300	6503	SO:0001583	missense	945	exon2			ATATCCAGGGACT	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.205A>G	19.37:g.51728641A>G	ENSP00000262262:p.Arg69Gly	Somatic	149	1	0.00671141		WXS	Illumina HiSeq	Phase_I	140	73	0.521429	NM_001772	B4E3P8|C9JEN7|F8WAL2|Q8TD24	Missense_Mutation	SNP	ENST00000262262.4	37	CCDS33084.1	762	0.3489010989010989	246	0.5	118	0.3259668508287293	53	0.09265734265734266	345	0.4551451187335092	.	5.312	0.242838	0.10077	0.501589	0.43	ENSG00000105383	ENST00000262262;ENST00000391796	T;T	0.45276	0.9;0.9	3.49	-6.98	0.01611	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	8.617480	0.00763	N	0.001149	T	0.00012	0.0000	L	0.36672	1.1	0.54753	P	1.2000000000012001E-5	B;B	0.06786	0.0;0.001	B;B	0.13407	0.003;0.009	T	0.36114	-0.9761	9	0.25751	T	0.34	.	1.204	0.01891	0.4573:0.1499:0.1144:0.2784	rs2455069;rs17659491;rs17856792;rs56575195;rs59927365;rs2455069	69;69	F8WAL2;P20138	.;CD33_HUMAN	G	69	ENSP00000262262:R69G;ENSP00000375673:R69G	ENSP00000262262:R69G	R	+	1	2	CD33	56420453	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.931000	0.00688	-1.842000	0.01181	-4.293000	0.00008	AGG	A|0.596;G|0.404	0.404	strong		0.537	CD33-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464199.2	NM_001772	
CWF19L2	143884	hgsc.bcm.edu	37	11	107224415	107224415	+	Silent	SNP	A	A	G	rs35543671	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:107224415A>G	ENST00000282251.5	-	13	1947	c.1920T>C	c.(1918-1920)ttT>ttC	p.F640F	CWF19L2_ENST00000433523.1_Silent_p.F640F	NM_152434.2	NP_689647.2	Q2TBE0	C19L2_HUMAN	CWF19-like 2, cell cycle control (S. pombe)	640							catalytic activity (GO:0003824)			endometrium(4)|kidney(2)|large_intestine(13)|lung(21)	40		Melanoma(852;1.75e-05)|all_epithelial(67;6.27e-05)|Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Breast(348;0.0258)		Epithelial(105;7.18e-06)|BRCA - Breast invasive adenocarcinoma(274;1.65e-05)|all cancers(92;1.76e-05)		CTTTGGAGACAAACATGTCAT	0.393													A|||	67	0.0133786	0.0023	0.0331	5008	,	,		17536	0.002		0.0278	False		,,,				2504	0.0112				p.F640F		Atlas-SNP	.											.	CWF19L2	135	.	0			c.T1920C						PASS	.	A		17,4385	25.3+/-52.1	0,17,2184	99.0	97.0	98.0		1920	2.4	1.0	11	dbSNP_126	98	217,8379	89.4+/-151.6	3,211,4084	no	coding-synonymous	CWF19L2	NM_152434.2		3,228,6268	GG,GA,AA		2.5244,0.3862,1.8003		640/895	107224415	234,12764	2201	4298	6499	SO:0001819	synonymous_variant	143884	exon13			GGAGACAAACATG	AK056905	CCDS8336.2	11q23.1	2005-09-22			ENSG00000152404	ENSG00000152404			26508	protein-coding gene	gene with protein product						14702039	Standard	NM_152434		Approved	FLJ32343	uc010rvp.2	Q2TBE0	OTTHUMG00000152975	ENST00000282251.5:c.1920T>C	11.37:g.107224415A>G		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	100	27	0.27	NM_152434	A4FU66|A4FU67|A4FU68|Q6PHW1|Q96MI1	Silent	SNP	ENST00000282251.5	37	CCDS8336.2																																																																																			A|0.983;G|0.017	0.017	strong		0.393	CWF19L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328825.2	NM_152434	
TRPM1	4308	hgsc.bcm.edu	37	15	31327779	31327779	+	Silent	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:31327779G>A	ENST00000256552.6	-	21	2817	c.2670C>T	c.(2668-2670)atC>atT	p.I890I	TRPM1_ENST00000397795.2_Silent_p.I868I|RP11-348B17.1_ENST00000558755.1_RNA|RP11-348B17.1_ENST00000561299.1_RNA|TRPM1_ENST00000542188.1_Silent_p.I907I	NM_001252024.1	NP_001238953.1			transient receptor potential cation channel, subfamily M, member 1											NS(2)|breast(3)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(15)|lung(48)|ovary(2)|pancreas(1)|prostate(3)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(3)	99		all_lung(180;1.92e-11)		all cancers(64;3.52e-16)|Epithelial(43;1.65e-11)|GBM - Glioblastoma multiforme(186;3.57e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00533)|COAD - Colon adenocarcinoma(236;0.0609)|Lung(196;0.199)		CCAGGCTCACGATGTAGGAGA	0.542																																					p.I907I		Atlas-SNP	.											.	TRPM1	183	.	0			c.C2721T						PASS	.						87.0	89.0	88.0					15																	31327779		2054	4193	6247	SO:0001819	synonymous_variant	4308	exon20			GCTCACGATGTAG	AF071787	CCDS10024.2, CCDS58345.1, CCDS58346.1, CCDS58347.1	15q13.3	2014-01-28		2002-01-18	ENSG00000134160	ENSG00000134160		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	7146	protein-coding gene	gene with protein product		603576	"""melastatin 1"""	MLSN1		9806836, 9537257, 16382100	Standard	NM_001252020		Approved	LTRPC1, CSNB1C	uc021sia.1	Q7Z4N2	OTTHUMG00000129267	ENST00000256552.6:c.2670C>T	15.37:g.31327779G>A		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	93	5	0.0537634	NM_001252020		Silent	SNP	ENST00000256552.6	37	CCDS58346.1																																																																																			.	.	none		0.542	TRPM1-004	PUTATIVE	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417166.2	NM_002420	
FAM109B	150368	hgsc.bcm.edu	37	22	42473860	42473860	+	Missense_Mutation	SNP	C	C	G	rs1807493	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:42473860C>G	ENST00000321753.3	+	3	750	c.563C>G	c.(562-564)gCg>gGg	p.A188G	SMDT1_ENST00000331479.3_5'Flank|snoU13_ENST00000458891.1_RNA	NM_001002034.2	NP_001002034.2	Q6ICB4	SESQ2_HUMAN	family with sequence similarity 109, member B	188			A -> G (in dbSNP:rs1807493). {ECO:0000269|PubMed:15489334}.		endosome organization (GO:0007032)|receptor recycling (GO:0001881)|retrograde transport, endosome to Golgi (GO:0042147)	clathrin-coated vesicle (GO:0030136)|early endosome (GO:0005769)|recycling endosome (GO:0055037)|trans-Golgi network (GO:0005802)	protein homodimerization activity (GO:0042803)			endometrium(2)|large_intestine(2)|liver(2)|lung(1)|prostate(1)	8						GTTGAAGAAGCGGGCAGCAGG	0.667													C|||	808	0.161342	0.0484	0.2363	5008	,	,		17874	0.1101		0.2396	False		,,,				2504	0.2331				p.A188G		Atlas-SNP	.											.	FAM109B	22	.	0			c.C563G						PASS	.	C	GLY/ALA	308,4096		14,280,1908	28.0	29.0	29.0		563	-2.4	0.0	22	dbSNP_92	29	1915,6685		246,1423,2631	yes	missense	FAM109B	NM_001002034.2	60	260,1703,4539	GG,GC,CC		22.2674,6.9936,17.0947	benign	188/260	42473860	2223,10781	2202	4300	6502	SO:0001583	missense	150368	exon3			AAGAAGCGGGCAG	BX648402	CCDS33655.1	22q13.2	2013-01-10			ENSG00000177096	ENSG00000177096		"""Pleckstrin homology (PH) domain containing"""	27161	protein-coding gene	gene with protein product		614240				12477932	Standard	NM_001002034		Approved	DKFZp686J07229	uc003bbz.3	Q6ICB4	OTTHUMG00000151285	ENST00000321753.3:c.563C>G	22.37:g.42473860C>G	ENSP00000312753:p.Ala188Gly	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	37	37	1	NM_001002034	Q3SXQ3|Q8N6L9	Missense_Mutation	SNP	ENST00000321753.3	37	CCDS33655.1	367	0.16804029304029305	28	0.056910569105691054	78	0.2154696132596685	78	0.13636363636363635	183	0.24142480211081793	C	0.005	-2.164310	0.00318	0.069936	0.222674	ENSG00000177096	ENST00000321753	T	0.42513	0.97	4.37	-2.38	0.06622	.	1.543610	0.05328	N	0.527815	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.23226	-1.0194	9	0.17369	T	0.5	-8.7261	2.597	0.04856	0.1219:0.3229:0.3358:0.2193	rs1807493;rs17845905;rs17858880	188	Q6ICB4	SESQ2_HUMAN	G	188	ENSP00000312753:A188G	ENSP00000312753:A188G	A	+	2	0	FAM109B	40803806	0.000000	0.05858	0.003000	0.11579	0.000000	0.00434	-0.591000	0.05753	-0.397000	0.07691	-4.145000	0.00010	GCG	C|0.837;G|0.163	0.163	strong		0.667	FAM109B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322084.1	NM_001002034	
MAP4K1	11184	hgsc.bcm.edu	37	19	39092142	39092142	+	Silent	SNP	C	C	T	rs35423612	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:39092142C>T	ENST00000591517.1	-	20	1498	c.1470G>A	c.(1468-1470)ttG>ttA	p.L490L	MAP4K1_ENST00000423454.2_Silent_p.L152L|MAP4K1_ENST00000396857.2_Silent_p.L490L|MAP4K1_ENST00000586296.1_Intron|CTB-186G2.1_ENST00000589557.1_RNA|MAP4K1_ENST00000589130.1_Silent_p.L486L	NM_007181.4	NP_009112.1	Q92918	M4K1_HUMAN	mitogen-activated protein kinase kinase kinase kinase 1	490					activation of JUN kinase activity (GO:0007257)|activation of MAPKKK activity (GO:0000185)|cell proliferation (GO:0008283)|intracellular signal transduction (GO:0035556)|peptidyl-serine phosphorylation (GO:0018105)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|response to stress (GO:0006950)	membrane (GO:0016020)	ATP binding (GO:0005524)|MAP kinase kinase kinase kinase activity (GO:0008349)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(3)|lung(24)|ovary(1)|prostate(1)|skin(5)|stomach(1)|urinary_tract(1)	44	all_cancers(60;6.42e-06)|Ovarian(47;0.103)		Lung(45;0.000751)|LUSC - Lung squamous cell carcinoma(53;0.00272)			AGCCATTGAACAACTTTACGA	0.617													C|||	45	0.00898562	0.0008	0.0058	5008	,	,		15542	0.0		0.0199	False		,,,				2504	0.0204				p.L490L		Atlas-SNP	.											.	MAP4K1	165	.	0			c.G1470A						PASS	.	C	,	18,4112		0,18,2047	29.0	33.0	32.0		1470,1470	-1.3	0.7	19	dbSNP_126	32	268,8106		5,258,3924	no	coding-synonymous,coding-synonymous	MAP4K1	NM_001042600.1,NM_007181.4	,	5,276,5971	TT,TC,CC		3.2004,0.4358,2.2873	,	490/822,490/834	39092142	286,12218	2065	4187	6252	SO:0001819	synonymous_variant	11184	exon20			ATTGAACAACTTT	U66464	CCDS42564.1, CCDS59385.1	19q13.1-q13.4	2011-06-09				ENSG00000104814	2.7.11.1	"""Mitogen-activated protein kinase cascade / Kinase kinase kinase kinases"""	6863	protein-coding gene	gene with protein product	"""hematopoietic progenitor kinase 1"""	601983				8824585	Standard	NM_001042600		Approved	HPK1	uc002oix.1	Q92918		ENST00000591517.1:c.1470G>A	19.37:g.39092142C>T		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	43	22	0.511628	NM_007181		Silent	SNP	ENST00000591517.1	37	CCDS59385.1																																																																																			C|0.990;T|0.010	0.010	strong		0.617	MAP4K1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000453390.1	NM_001042600	
FRZB	2487	hgsc.bcm.edu	37	2	183699584	183699584	+	Missense_Mutation	SNP	G	G	C	rs7775	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:183699584G>C	ENST00000295113.4	-	6	1579	c.970C>G	c.(970-972)Cgc>Ggc	p.R324G		NM_001463.3	NP_001454.2	Q92765	SFRP3_HUMAN	frizzled-related protein	324			R -> G (in hip OA susceptibility; has diminished ability to antagonize Wnt signaling, in vitro; dbSNP:rs7775). {ECO:0000269|PubMed:15210948}.		brain development (GO:0007420)|cochlea morphogenesis (GO:0090103)|convergent extension involved in organogenesis (GO:0060029)|epithelium development (GO:0060429)|gonad development (GO:0008406)|mammary gland involution (GO:0060056)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cartilage development (GO:0061037)|negative regulation of cell development (GO:0010721)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of hepatocyte differentiation (GO:0070367)|negative regulation of Wnt signaling pathway (GO:0030178)|neural crest cell differentiation (GO:0014033)|positive regulation of apoptotic process (GO:0043065)|positive regulation of fat cell differentiation (GO:0045600)|skeletal system development (GO:0001501)|somite development (GO:0061053)|vasculature development (GO:0001944)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|membrane (GO:0016020)	PDZ domain binding (GO:0030165)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(12)|ovary(2)|prostate(1)|skin(1)	21			OV - Ovarian serous cystadenocarcinoma(117;0.109)|Epithelial(96;0.231)			ATTTAGTTGCGTGCTTGCCGG	0.428													G|||	643	0.128395	0.323	0.0908	5008	,	,		17685	0.005		0.0895	False		,,,				2504	0.0593				p.R324G		Atlas-SNP	.											FRZB,NS,carcinoma,+1,1	FRZB	42	1	0			c.C970G	GRCh37	CM042052	FRZB	M	rs7775	PASS	.	G	GLY/ARG	1250,3156	428.0+/-341.7	185,880,1138	127.0	122.0	124.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	970	3.6	1.0	2	dbSNP_52	124	757,7843	181.8+/-230.4	37,683,3580	yes	missense	FRZB	NM_001463.3	125	222,1563,4718	CC,CG,GG		8.8023,28.3704,15.4313	probably-damaging	324/326	183699584	2007,10999	2203	4300	6503	SO:0001583	missense	2487	exon6			AGTTGCGTGCTTG	U24163	CCDS2286.1	2q32.1	2013-09-19			ENSG00000162998	ENSG00000162998		"""Secreted frizzled-related proteins"""	3959	protein-coding gene	gene with protein product		605083				8824257, 9118218	Standard	NM_001463		Approved	FRZB-PEN, FRZB1, SRFP3, FRP-3, SFRP3, FRE, FRITZ, FRZB-1, FZRB, hFIZ	uc002upa.2	Q92765	OTTHUMG00000132597	ENST00000295113.4:c.970C>G	2.37:g.183699584G>C	ENSP00000295113:p.Arg324Gly	Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	160	62	0.3875	NM_001463	O00181|Q99686	Missense_Mutation	SNP	ENST00000295113.4	37	CCDS2286.1	247	0.1130952380952381	142	0.2886178861788618	36	0.09944751381215469	4	0.006993006993006993	65	0.08575197889182058	G	14.09	2.431060	0.43122	0.283704	0.088023	ENSG00000162998	ENST00000295113	T	0.74209	-0.82	5.4	3.6	0.41247	.	0.098933	0.43416	D	0.000579	T	0.00012	0.0000	L	0.29908	0.895	0.25498	P	0.9875874	B	0.24920	0.114	B	0.24394	0.053	T	0.06716	-1.0811	9	0.52906	T	0.07	.	10.6319	0.45541	0.0683:0.0:0.7994:0.1324	rs7775;rs3197283;rs52801397;rs7775	324	Q92765	SFRP3_HUMAN	G	324	ENSP00000295113:R324G	ENSP00000295113:R324G	R	-	1	0	FRZB	183407829	1.000000	0.71417	0.999000	0.59377	0.999000	0.98932	3.843000	0.55865	0.852000	0.35287	0.650000	0.86243	CGC	G|0.865;C|0.135	0.135	strong		0.428	FRZB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255808.1	NM_001463	
GPR4	2828	hgsc.bcm.edu	37	19	46094597	46094597	+	Silent	SNP	G	G	A	rs3745820	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:46094597G>A	ENST00000323040.4	-	2	1472	c.528C>T	c.(526-528)ggC>ggT	p.G176G	GPR4_ENST00000591614.1_5'Flank|OPA3_ENST00000544371.1_Intron	NM_005282.2	NP_005273.1	P46093	GPR4_HUMAN	G protein-coupled receptor 4	176					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)			breast(2)|endometrium(1)|kidney(3)|large_intestine(1)|lung(11)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	23				OV - Ovarian serous cystadenocarcinoma(262;0.0071)|GBM - Glioblastoma multiforme(486;0.128)|Epithelial(262;0.223)		AGGCCACCCAGCCTTCCATGG	0.642													g|||	827	0.165136	0.0303	0.1787	5008	,	,		15664	0.1895		0.2763	False		,,,				2504	0.1984				p.G176G	Esophageal Squamous(117;181 1612 1673 14956 42937)	Atlas-SNP	.											.	GPR4	54	.	0			c.C528T						PASS	.			305,4097		11,283,1907	72.0	64.0	67.0		528	4.2	1.0	19	dbSNP_107	67	2283,6311		311,1661,2325	no	coding-synonymous	GPR4	NM_005282.2		322,1944,4232	AA,AG,GG		26.565,6.9287,19.9138		176/363	46094597	2588,10408	2201	4297	6498	SO:0001819	synonymous_variant	2828	exon2			CACCCAGCCTTCC	BC067536	CCDS12669.1	19q13.3	2012-08-21				ENSG00000177464		"""GPCR / Class A : Orphans"""	4497	protein-coding gene	gene with protein product		600551				8595909	Standard	NM_005282		Approved		uc002pcm.3	P46093		ENST00000323040.4:c.528C>T	19.37:g.46094597G>A		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	96	93	0.96875	NM_005282	A8K3T3|B0M0K1|Q6NWM4	Silent	SNP	ENST00000323040.4	37	CCDS12669.1																																																																																			G|0.820;A|0.180	0.180	strong		0.642	GPR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459603.1	NM_005282	
GCNT2	2651	hgsc.bcm.edu	37	6	10586727	10586727	+	Intron	SNP	G	G	A	rs56106312	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:10586727G>A	ENST00000379597.3	+	2	1481				GCNT2_ENST00000397423.2_Intron|GCNT2_ENST00000410107.1_Intron|GCNT2_ENST00000316170.3_Intron|GCNT2_ENST00000265012.4_Missense_Mutation_p.A169T|GCNT2_ENST00000495262.1_Intron			Q8N0V5	GNT2A_HUMAN	glucosaminyl (N-acetyl) transferase 2, I-branching enzyme (I blood group)						maintenance of lens transparency (GO:0036438)|negative regulation of cell-substrate adhesion (GO:0010812)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of heterotypic cell-cell adhesion (GO:0034116)|positive regulation of protein kinase B signaling (GO:0051897)|posttranscriptional regulation of gene expression (GO:0010608)|protein glycosylation (GO:0006486)|transforming growth factor beta receptor signaling pathway (GO:0007179)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	N-acetyllactosaminide beta-1,6-N-acetylglucosaminyltransferase activity (GO:0008109)			endometrium(2)|kidney(1)|large_intestine(5)|lung(2)|ovary(2)	12	Ovarian(93;0.107)|Breast(50;0.148)	all_hematologic(90;0.107)		KIRC - Kidney renal clear cell carcinoma(1;0.099)|Kidney(1;0.119)		CAGACTCCAGGCTGACCTGAA	0.483													G|||	12	0.00239617	0.0008	0.0058	5008	,	,		19773	0.0		0.006	False		,,,				2504	0.001				p.A169T		Atlas-SNP	.											.	GCNT2	123	.	0			c.G505A						PASS	.	G	,,THR/ALA	3,4403	6.2+/-15.9	0,3,2200	127.0	123.0	124.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	,,505	5.6	1.0	6	dbSNP_129	124	45,8555	30.1+/-81.4	0,45,4255	yes	intron,intron,missense	GCNT2	NM_001491.2,NM_145649.4,NM_145655.3	,,58	0,48,6455	AA,AG,GG		0.5233,0.0681,0.3691	,,probably-damaging	,,169/403	10586727	48,12958	2203	4300	6503	SO:0001627	intron_variant	2651	exon1			CTCCAGGCTGACC	L41605	CCDS4512.1, CCDS4513.1, CCDS34338.1	6p24.2	2014-07-18	2006-02-23		ENSG00000111846	ENSG00000111846	2.4.1.150	"""Blood group antigens"", ""Glucosaminyl (N-acetyl) transferase and xylosyltransferase family"""	4204	protein-coding gene	gene with protein product	"""Ii blood group"", ""unassigned linkage group 3"""	600429	"""glucosaminyl (N-acetyl) transferase 5"", ""glucosaminyl (N-acetyl) transferase 2, I-branching enzyme"", ""glucosaminyl (N-acetyl) transferase 2, I-branching enzyme (Ii blood group)"", ""cataract, congenital"""	NACGT1, II, GCNT5, CCAT		8449405, 9915862	Standard	NM_145649		Approved	IGNT, NAGCT1, bA421M1.1, bA360O19.2, ULG3	uc003mze.3	Q06430	OTTHUMG00000014244	ENST00000379597.3:c.926-34857G>A	6.37:g.10586727G>A		Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	163	111	0.680982	NM_145655		Missense_Mutation	SNP	ENST00000379597.3	37	CCDS34338.1	7	0.003205128205128205	0	0.0	2	0.0055248618784530384	0	0.0	5	0.006596306068601583	G	18.84	3.709073	0.68615	6.81E-4	0.005233	ENSG00000111846	ENST00000265012	T	0.20332	2.08	5.58	5.58	0.84498	.	.	.	.	.	T	0.45836	0.1362	M	0.88842	2.985	0.58432	D	0.999996	D	0.76494	0.999	D	0.77557	0.99	T	0.53920	-0.8370	9	0.87932	D	0	.	14.7518	0.69530	0.0709:0.0:0.9291:0.0	rs56106312	169	Q8NFS9	GNT2C_HUMAN	T	169	ENSP00000265012:A169T	ENSP00000265012:A169T	A	+	1	0	GCNT2	10694713	1.000000	0.71417	1.000000	0.80357	0.110000	0.19582	6.558000	0.73942	2.624000	0.88883	0.655000	0.94253	GCT	G|0.996;A|0.004	0.004	strong		0.483	GCNT2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327912.3	NM_145649	
D2HGDH	728294	hgsc.bcm.edu	37	2	242690770	242690770	+	Silent	SNP	T	T	C	rs141343442	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:242690770T>C	ENST00000321264.4	+	8	1316	c.1107T>C	c.(1105-1107)gaT>gaC	p.D369D	D2HGDH_ENST00000486953.1_Intron|D2HGDH_ENST00000403782.1_Silent_p.D235D	NM_152783.3	NP_689996.4	Q8N465	D2HDH_HUMAN	D-2-hydroxyglutarate dehydrogenase	369					2-oxoglutarate metabolic process (GO:0006103)|cellular metabolic process (GO:0044237)|cellular protein metabolic process (GO:0044267)|response to cobalt ion (GO:0032025)|response to manganese ion (GO:0010042)|response to zinc ion (GO:0010043)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	(R)-2-hydroxyglutarate dehydrogenase activity (GO:0051990)|flavin adenine dinucleotide binding (GO:0050660)|UDP-N-acetylmuramate dehydrogenase activity (GO:0008762)			breast(1)|endometrium(3)|lung(10)|skin(1)|urinary_tract(1)	16		all_cancers(19;1.09e-40)|all_epithelial(40;2.03e-18)|Breast(86;1.53e-05)|all_lung(227;0.00338)|Renal(207;0.00502)|Ovarian(221;0.00716)|Lung NSC(271;0.012)|Esophageal squamous(248;0.129)|Melanoma(123;0.144)|all_hematologic(139;0.158)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;4.59e-33)|all cancers(36;9.89e-31)|OV - Ovarian serous cystadenocarcinoma(60;7.89e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.63e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0833)		TGGTGACCGATGGGACCATGG	0.627													T|||	156	0.0311502	0.0	0.0288	5008	,	,		18957	0.0079		0.0497	False		,,,				2504	0.0798				p.D369D		Atlas-SNP	.											.	D2HGDH	39	.	0			c.T1107C						PASS	.	T		27,4379	33.5+/-64.1	0,27,2176	46.0	43.0	44.0		1107	-10.2	0.0	2	dbSNP_134	44	414,8178	129.0+/-187.1	8,398,3890	no	coding-synonymous	D2HGDH	NM_152783.3		8,425,6066	CC,CT,TT		4.8184,0.6128,3.3928		369/522	242690770	441,12557	2203	4296	6499	SO:0001819	synonymous_variant	728294	exon8			GACCGATGGGACC	AK091725	CCDS33426.1, CCDS74684.1	2p25.3	2010-05-11			ENSG00000180902	ENSG00000180902	1.1.99.-		28358	protein-coding gene	gene with protein product		609186				15070399, 15609246	Standard	NM_152783		Approved	MGC25181, D2HGD, FLJ42195	uc002wce.1	Q8N465	OTTHUMG00000151474	ENST00000321264.4:c.1107T>C	2.37:g.242690770T>C		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	81	34	0.419753	NM_152783	B4E3L6|E7ENP2|Q6IQ24|Q8N5Q8	Silent	SNP	ENST00000321264.4	37	CCDS33426.1	60	0.027472527472527472	0	0.0	12	0.03314917127071823	5	0.008741258741258742	43	0.05672823218997362	T	1.488	-0.555485	0.03967	0.006128	0.048184	ENSG00000180902	ENST00000432449	.	.	.	5.1	-10.2	0.00374	.	.	.	.	.	T	0.09468	0.0233	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.59182	-0.7502	4	.	.	.	1.0142	11.2638	0.49099	0.0737:0.0822:0.0736:0.7705	.	.	.	.	R	123	.	.	W	+	1	0	D2HGDH	242339443	0.001000	0.12720	0.040000	0.18447	0.141000	0.21300	-2.318000	0.01121	-2.441000	0.00550	-1.017000	0.02453	TGG	T|0.973;C|0.027	0.027	strong		0.627	D2HGDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322794.2	NM_152783	
SLC25A27	9481	hgsc.bcm.edu	37	6	46632594	46632594	+	Missense_Mutation	SNP	T	T	C	rs35884480	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:46632594T>C	ENST00000371347.5	+	5	842	c.590T>C	c.(589-591)aTa>aCa	p.I197T	SLC25A27_ENST00000411689.2_Missense_Mutation_p.I197T|SLC25A27_ENST00000452689.2_Missense_Mutation_p.I111T|SLC25A27_ENST00000604908.1_Intron	NM_001204051.1|NM_004277.4	NP_001190980.1|NP_004268.3	O95847	UCP4_HUMAN	solute carrier family 25, member 27	197			I -> T (in dbSNP:rs35884480).		cellular triglyceride homeostasis (GO:0035356)|generation of precursor metabolites and energy (GO:0006091)|inner ear development (GO:0048839)|negative regulation of apoptotic process (GO:0043066)|negative regulation of mitochondrial calcium ion concentration (GO:0051562)|negative regulation of mitochondrial membrane potential (GO:0010917)|neuron death (GO:0070997)|positive regulation of cell proliferation (GO:0008284)|regulation of glucose import (GO:0046324)|transport (GO:0006810)	apical part of cell (GO:0045177)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)				central_nervous_system(1)|kidney(1)|lung(4)|prostate(1)|urinary_tract(1)	8			Lung(136;0.192)			GTACCCAATATACAAAGAGCA	0.378													T|||	147	0.029353	0.0038	0.036	5008	,	,		13909	0.0		0.0577	False		,,,				2504	0.0603				p.I197T		Atlas-SNP	.											.	SLC25A27	22	.	0			c.T590C						PASS	.	T	THR/ILE,THR/ILE,THR/ILE	40,3668		1,38,1815	86.0	84.0	84.0		590,590,590	5.1	1.0	6	dbSNP_126	84	522,7670		24,474,3598	yes	missense,missense,missense	SLC25A27	NM_001204051.1,NM_001204052.1,NM_004277.4	89,89,89	25,512,5413	CC,CT,TT		6.3721,1.0787,4.7227	benign,benign,benign	197/301,197/246,197/324	46632594	562,11338	1854	4096	5950	SO:0001583	missense	9481	exon5			CCAATATACAAAG	AK090871	CCDS43470.1, CCDS56431.1	6p12.3	2013-05-22			ENSG00000153291	ENSG00000153291		"""Solute carriers"""	21065	protein-coding gene	gene with protein product		613725				10025957, 10772343	Standard	NM_004277		Approved	UCP4, FLJ33552	uc003oyh.3	O95847	OTTHUMG00000014786	ENST00000371347.5:c.590T>C	6.37:g.46632594T>C	ENSP00000360398:p.Ile197Thr	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	64	39	0.609375	NM_001204051	F5GWR4|Q5VTS9|Q8N518	Missense_Mutation	SNP	ENST00000371347.5	37	CCDS43470.1	69	0.03159340659340659	3	0.006097560975609756	18	0.049723756906077346	0	0.0	48	0.0633245382585752	T	13.48	2.250203	0.39797	0.010787	0.063721	ENSG00000153291	ENST00000371347;ENST00000411689;ENST00000355073;ENST00000452689;ENST00000425120	T;T;T	0.80738	-1.41;-1.41;-1.41	5.13	5.13	0.70059	Mitochondrial carrier domain (2);	0.229133	0.33916	N	0.004432	T	0.56891	0.2016	N	0.25201	0.72	0.37212	D	0.904839	B;B;B;B	0.21071	0.028;0.051;0.051;0.01	B;B;B;B	0.25405	0.042;0.06;0.06;0.015	T	0.58120	-0.7692	10	0.35671	T	0.21	-12.6418	12.9054	0.58149	0.0:0.0:0.0:1.0	rs35884480;rs62401180	111;197;197;197	B4DZG4;Q5VTS9;O95847;F5GWR4	.;.;UCP4_HUMAN;.	T	197;197;41;111;127	ENSP00000360398:I197T;ENSP00000412024:I197T;ENSP00000412223:I111T	ENSP00000347185:I41T	I	+	2	0	SLC25A27	46740553	1.000000	0.71417	0.999000	0.59377	0.989000	0.77384	5.876000	0.69667	1.929000	0.55896	0.533000	0.62120	ATA	T|0.951;C|0.049	0.049	strong		0.378	SLC25A27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040791.1	NM_004277	
PER3	8863	hgsc.bcm.edu	37	1	7890026	7890026	+	Missense_Mutation	SNP	A	A	G	rs199947375|rs57875989		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:7890026A>G	ENST00000361923.2	+	18	3167	c.2992A>G	c.(2992-2994)Aag>Gag	p.K998E	RP3-467L1.4_ENST00000451646.1_RNA|PER3_ENST00000377532.3_Missense_Mutation_p.K1007E	NM_016831.1	NP_058515.1	P56645	PER3_HUMAN	period circadian clock 3	998	5 X 18 AA tandem repeats of S-[HP]-[AP]- T-[AT]-[GST]-[ATV]-L-S-[MT]-G-[LS]-P-P- [MRS]-[EKR]-[NST]-P.|Ser-rich.				circadian regulation of gene expression (GO:0032922)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of circadian sleep/wake cycle, sleep (GO:0045187)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	signal transducer activity (GO:0004871)	p.K998E(1)		breast(4)|central_nervous_system(3)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(9)|lung(8)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	39	Ovarian(185;0.0634)|all_lung(157;0.178)	all_epithelial(116;9.35e-21)|all_lung(118;7.57e-07)|Lung NSC(185;4.52e-06)|Renal(390;0.000147)|Breast(487;0.00086)|Colorectal(325;0.000959)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0234)|all cancers(8;8.58e-70)|GBM - Glioblastoma multiforme(8;1.81e-35)|Colorectal(212;2.06e-07)|COAD - Colon adenocarcinoma(227;1.92e-05)|Kidney(185;7.18e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000472)|STAD - Stomach adenocarcinoma(132;0.00118)|KIRC - Kidney renal clear cell carcinoma(229;0.00122)|READ - Rectum adenocarcinoma(331;0.0649)		GCCTCCCATGAAGAATCCATC	0.587																																					p.K998E		Atlas-SNP	.											PER3,NS,carcinoma,0,4	PER3	95	4	1	Substitution - Missense(1)	central_nervous_system(1)	c.A2992G						scavenged	.						84.0	69.0	74.0					1																	7890026		1999	3897	5896	SO:0001583	missense	8863	exon18			CCCATGAAGAATC	BC026102	CCDS89.1, CCDS72695.1	1p36.23	2012-12-13	2012-12-13		ENSG00000049246	ENSG00000049246			8847	protein-coding gene	gene with protein product		603427	"""period (Drosophila) homolog 3"", ""period homolog 3 (Drosophila)"""			9427249	Standard	XM_005263520		Approved		uc001aoo.3	P56645	OTTHUMG00000001216	ENST00000361923.2:c.2992A>G	1.37:g.7890026A>G	ENSP00000355031:p.Lys998Glu	Somatic	154	1	0.00649351		WXS	Illumina HiSeq	Phase_I	86	18	0.209302	NM_016831	Q5H8X4|Q5H8X5|Q969K6|Q96S77|Q96S78|Q9C0J3|Q9NSP9|Q9UGU8	Missense_Mutation	SNP	ENST00000361923.2	37	CCDS89.1	.	.	.	.	.	.	.	.	.	.	G	0.003	-2.434686	0.00182	.	.	ENSG00000049246	ENST00000377532;ENST00000361923	T;T	0.13538	2.58;2.58	.	.	.	Period circadian-like, C-terminal (1);	5.912170	0.01354	N	0.012011	T	0.04724	0.0128	N	0.04508	-0.205	0.09310	N	1	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.26503	-1.0101	8	0.02654	T	1	.	.	.	.	.	998;1007;1007;998	A2I2N5;A6H8X0;P56645-2;P56645	.;.;.;PER3_HUMAN	E	1007;998	ENSP00000366755:K1007E;ENSP00000355031:K998E	ENSP00000355031:K998E	K	+	1	0	PER3	7812613	0.002000	0.14202	0.013000	0.15412	0.014000	0.08584	-0.844000	0.04345	-0.911000	0.03843	-0.891000	0.02926	AAG	.	.	weak		0.587	PER3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000003607.1	NM_016831	
ELSPBP1	64100	hgsc.bcm.edu	37	19	48519244	48519244	+	Silent	SNP	A	A	G	rs35792818	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:48519244A>G	ENST00000339841.2	+	4	481	c.303A>G	c.(301-303)tcA>tcG	p.S101S	ELSPBP1_ENST00000597519.1_Intron	NM_022142.4	NP_071425.3	Q96BH3	ESPB1_HUMAN	epididymal sperm binding protein 1	101	Fibronectin type-II 2. {ECO:0000255|PROSITE-ProRule:PRU00479}.				single fertilization (GO:0007338)	extracellular region (GO:0005576)				NS(1)|breast(1)|kidney(1)|large_intestine(1)|lung(6)	10		all_cancers(25;8.7e-09)|all_lung(116;1.15e-06)|all_epithelial(76;1.17e-06)|Lung NSC(112;2.56e-06)|all_neural(266;0.0138)|Ovarian(192;0.0261)|Breast(70;0.203)		OV - Ovarian serous cystadenocarcinoma(262;0.000253)|all cancers(93;0.00129)|Epithelial(262;0.0314)|GBM - Glioblastoma multiforme(486;0.0606)		TGTGGTGCTCAGTCACCTCTG	0.507													g|||	810	0.161741	0.2103	0.1254	5008	,	,		21204	0.0724		0.1531	False		,,,				2504	0.2229				p.S101S		Atlas-SNP	.											ELSPBP1,NS,NS,+1,1	ELSPBP1	29	1	0			c.A303G						PASS	.	G		885,3521	742.5+/-411.4	86,713,1404	136.0	115.0	122.0		303	-7.1	0.3	19	dbSNP_126	122	1294,7306	759.1+/-407.5	91,1112,3097	no	coding-synonymous	ELSPBP1	NM_022142.4		177,1825,4501	GG,GA,AA		15.0465,20.0862,16.7538		101/224	48519244	2179,10827	2203	4300	6503	SO:0001819	synonymous_variant	64100	exon4			GTGCTCAGTCACC	AJ278478	CCDS12708.1	19q13.33	2009-09-17							14417	protein-coding gene	gene with protein product	"""epididymal protein 12"""	607443					Standard	NM_022142		Approved	HE12, E12, EDDM12	uc002pht.3	Q96BH3		ENST00000339841.2:c.303A>G	19.37:g.48519244A>G		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	90	50	0.555556	NM_022142	Q96RT0|Q9H4C8	Silent	SNP	ENST00000339841.2	37	CCDS12708.1																																																																																			A|0.837;G|0.163	0.163	strong		0.507	ELSPBP1-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465207.1		
FUT2	2524	hgsc.bcm.edu	37	19	49206603	49206603	+	Silent	SNP	C	C	T	rs281377	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	62	0	0		WXS	Illumina HiSeq	Phase_I	48	25	0.520833	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	
ZAN	7455	hgsc.bcm.edu	37	7	100377373	100377373	+	RNA	SNP	G	G	A	rs482308	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:100377373G>A	ENST00000348028.3	+	0	6786				ZAN_ENST00000546213.1_RNA|ZAN_ENST00000542585.1_RNA|ZAN_ENST00000443370.1_RNA|ZAN_ENST00000546292.1_RNA|ZAN_ENST00000449052.1_RNA|ZAN_ENST00000538115.1_RNA|ZAN_ENST00000427578.1_RNA|ZAN_ENST00000421100.1_RNA|ZAN_ENST00000349350.6_RNA			Q9Y493	ZAN_HUMAN	zonadhesin (gene/pseudogene)						binding of sperm to zona pellucida (GO:0007339)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(2)|breast(3)|central_nervous_system(3)|endometrium(21)|kidney(6)|large_intestine(18)|lung(60)|ovary(4)|pancreas(3)|prostate(5)|skin(8)|stomach(3)|upper_aerodigestive_tract(3)	139	Lung NSC(181;0.041)|all_lung(186;0.0581)		STAD - Stomach adenocarcinoma(171;0.19)			AGCTTCTGCCGTGAGTGTGCC	0.622													G|||	1308	0.261182	0.1838	0.2565	5008	,	,		11897	0.2778		0.332	False		,,,				2504	0.2791				.		Atlas-SNP	.											.	ZAN	658	.	0			c.6621+1G>A						PASS	.	G	,	691,3099		68,555,1272	10.0	12.0	11.0		,	4.1	1.0	7	dbSNP_83	11	2707,5393		468,1771,1811	yes	splice-5,splice-5	ZAN	NM_003386.1,NM_173059.1	,	536,2326,3083	AA,AG,GG		33.4198,18.2322,28.5786	,	,	100377373	3398,8492	1895	4050	5945			7455	exon35			TCTGCCGTGAGTG	U83191		7q22.1	2013-10-10	2013-10-10		ENSG00000146839	ENSG00000146839			12857	protein-coding gene	gene with protein product		602372	"""zonadhesin"""			9799793, 17033959	Standard	NM_003386		Approved		uc003uwk.3	Q9Y493	OTTHUMG00000157037		7.37:g.100377373G>A		Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	20	12	0.6	NM_003386	A0FKC8|D6W5W4|O00218|Q96L85|Q96L86|Q96L87|Q96L88|Q96L89|Q96L90|Q9BXN9|Q9BZ83|Q9BZ84|Q9BZ85|Q9BZ86|Q9BZ87|Q9BZ88	Splice_Site	SNP	ENST00000348028.3	37		648	0.2967032967032967	93	0.18902439024390244	114	0.3149171270718232	180	0.3146853146853147	261	0.34432717678100266	G	20.6	4.010531	0.75046	0.182322	0.334198	ENSG00000146839	ENST00000546292;ENST00000538115;ENST00000542585	.	.	.	4.08	4.08	0.47627	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.1438	0.54012	0.0:0.0:1.0:0.0	rs482308;rs10378059;rs482308	.	.	.	.	-1	.	.	.	+	.	.	ZAN	100215309	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	6.815000	0.75242	2.586000	0.87340	0.558000	0.71614	.	G|0.690;T|0.002	.	strong		0.622	ZAN-006	KNOWN	basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000347214.1	NM_003386	
WDR78	79819	hgsc.bcm.edu	37	1	67327894	67327894	+	Silent	SNP	A	A	G	rs34182923	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:67327894A>G	ENST00000371026.3	-	7	1087	c.1032T>C	c.(1030-1032)agT>agC	p.S344S	WDR78_ENST00000431318.1_Silent_p.S90S|WDR78_ENST00000493572.1_5'UTR|WDR78_ENST00000371023.3_Silent_p.S344S	NM_024763.4	NP_079039.4	Q5VTH9	WDR78_HUMAN	WD repeat domain 78	344					hematopoietic progenitor cell differentiation (GO:0002244)					NS(1)|endometrium(3)|kidney(6)|large_intestine(6)|lung(10)|ovary(3)|skin(3)	32						TTGCTTTACTACTTGACTCAA	0.338													A|||	87	0.0173722	0.0023	0.0159	5008	,	,		18825	0.0228		0.0189	False		,,,				2504	0.0317				p.S344S		Atlas-SNP	.											.	WDR78	102	.	0			c.T1032C						PASS	.	A	,	26,4380	33.5+/-64.1	0,26,2177	108.0	108.0	108.0		1032,1032	-2.6	0.0	1	dbSNP_126	108	218,8382	91.9+/-153.9	1,216,4083	yes	coding-synonymous,coding-synonymous	WDR78	NM_024763.4,NM_207014.2	,	1,242,6260	GG,GA,AA		2.5349,0.5901,1.8761	,	344/849,344/546	67327894	244,12762	2203	4300	6503	SO:0001819	synonymous_variant	79819	exon7			TTTACTACTTGAC	BX648840	CCDS635.1, CCDS44157.1	1p31.2	2014-02-21	2013-02-19	2013-02-19	ENSG00000152763	ENSG00000152763		"""WD repeat domain containing"""	26252	protein-coding gene	gene with protein product						21953912	Standard	NM_207014		Approved	DIC4, FLJ23129	uc001dcx.3	Q5VTH9	OTTHUMG00000009165	ENST00000371026.3:c.1032T>C	1.37:g.67327894A>G		Somatic	424	1	0.00235849		WXS	Illumina HiSeq	Phase_I	316	159	0.503165	NM_207014	A8K9W5|B5MDT3|H7BY80|Q5VTI0|Q8N5G5|Q9H5R9|Q9UF44	Silent	SNP	ENST00000371026.3	37	CCDS635.1	33	0.01510989010989011	2	0.0040650406504065045	8	0.022099447513812154	12	0.02097902097902098	11	0.014511873350923483	A	3.430	-0.116389	0.06881	0.005901	0.025349	ENSG00000152763	ENST00000469450	.	.	.	4.38	-2.56	0.06268	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	4.3879	5.1919	0.15214	0.5182:0.0:0.3481:0.1337	rs34182923	.	.	.	Q	78	.	.	X	-	1	0	WDR78	67100482	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.878000	0.04192	-0.390000	0.07774	-1.120000	0.02017	TAG	A|0.982;G|0.018	0.018	strong		0.338	WDR78-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025404.1	NM_024763	
ZNF737	100129842	hgsc.bcm.edu	37	19	20727463	20727463	+	Missense_Mutation	SNP	T	T	C	rs10411329	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:20727463T>C	ENST00000427401.4	-	4	1640	c.1546A>G	c.(1546-1548)Aaa>Gaa	p.K516E		NM_001159293.1	NP_001152765.1	O75373	ZN737_HUMAN	zinc finger protein 737	516			K -> E (in dbSNP:rs10411329). {ECO:0000269|PubMed:15489334}.		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|kidney(1)|lung(7)|ovary(1)|stomach(1)|urinary_tract(1)	13						TTAAAGCCTTTGCCACATTCT	0.403													-|||	2092	0.417732	0.3449	0.5202	5008	,	,		20903	0.4395		0.4185	False		,,,				2504	0.4202				p.K516E		Atlas-SNP	.											.	ZNF737	50	.	0			c.A1546G						PASS	.	T	GLU/LYS	490,894		87,316,289	46.0	47.0	47.0		1546	0.8	0.3	19	dbSNP_119	47	1191,1991		221,749,621	no	missense	ZNF737	NM_001159293.1	56	308,1065,910	CC,CT,TT		37.4293,35.4046,36.8156	benign	516/537	20727463	1681,2885	692	1591	2283	SO:0001583	missense	100129842	exon4			AGCCTTTGCCACA	BC015765	CCDS54238.1	19p12	2013-01-08						"""Zinc fingers, C2H2-type"", ""-"""	32468	protein-coding gene	gene with protein product		603984					Standard	NM_001159293		Approved	ZNF102	uc002npa.3	O75373		ENST00000427401.4:c.1546A>G	19.37:g.20727463T>C	ENSP00000395733:p.Lys516Glu	Somatic	22	0	0		WXS	Illumina HiSeq	Phase_I	9	9	1	NM_001159293	C9JHM3	Missense_Mutation	SNP	ENST00000427401.4	37	CCDS54238.1	939	0.42994505494505497	168	0.34146341463414637	179	0.494475138121547	267	0.46678321678321677	325	0.4287598944591029	N	12.59	1.984912	0.35036	0.354046	0.374293	ENSG00000237440	ENST00000427401	T	0.27104	1.69	0.801	0.801	0.18679	.	.	.	.	.	T	0.00012	0.0000	L	0.60904	1.88	0.37937	P	0.06779599999999997	B	0.25743	0.133	B	0.30401	0.115	T	0.42666	-0.9438	8	0.87932	D	0	.	3.7037	0.08392	0.0:0.0:0.0:1.0	rs10411329;rs52819273;rs10411329	516	C9JHM3	.	E	516	ENSP00000395733:K516E	ENSP00000395733:K516E	K	-	1	0	ZNF737	20519303	0.006000	0.16342	0.286000	0.24833	0.282000	0.26991	-2.106000	0.01338	0.147000	0.19030	0.145000	0.16022	AAA	T|0.588;C|0.412	0.412	strong		0.403	ZNF737-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447844.2	NM_145289	
FAT1	2195	hgsc.bcm.edu	37	4	187525020	187525020	+	Missense_Mutation	SNP	A	A	C	rs2637777	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:187525020A>C	ENST00000441802.2	-	19	10869	c.10660T>G	c.(10660-10662)Tct>Gct	p.S3554A		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	3554	Cadherin 33. {ECO:0000255|PROSITE- ProRule:PRU00043}.				actin filament organization (GO:0007015)|anatomical structure morphogenesis (GO:0009653)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(38)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(33)|lung(88)|ovary(13)|pancreas(2)|prostate(16)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	228						TCTCCAGAAGAGGTGATGAAA	0.473										HNSCC(5;0.00058)			c|||	2568	0.51278	0.7844	0.5389	5008	,	,		19363	0.5774		0.3688	False		,,,				2504	0.2086				p.S3554A	Colon(197;1040 2055 4143 4984 49344)	Atlas-SNP	.											.	FAT1	500	.	0			c.T10660G						PASS	.	T	ALA/SER	2723,1125		958,807,159	80.0	81.0	80.0		10660	2.2	0.0	4	dbSNP_100	80	2990,5276		559,1872,1702	yes	missense	FAT1	NM_005245.3	99	1517,2679,1861	CC,CA,AA		36.1723,29.236,47.1603	benign	3554/4589	187525020	5713,6401	1924	4133	6057	SO:0001583	missense	2195	exon19			CAGAAGAGGTGAT	X87241	CCDS47177.1	4q35.2	2013-05-31	2013-05-31	2008-10-30	ENSG00000083857	ENSG00000083857		"""Cadherins / Cadherin-related"""	3595	protein-coding gene	gene with protein product	"""cadherin-related family member 8"""	600976	"""FAT tumor suppressor (Drosophila) homolog"", ""FAT tumor suppressor homolog 1 (Drosophila)"""	FAT		8586420	Standard	XM_005262834		Approved	CDHF7, CDHR8	uc003izf.3	Q14517	OTTHUMG00000160320	ENST00000441802.2:c.10660T>G	4.37:g.187525020A>C	ENSP00000406229:p.Ser3554Ala	Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	117	57	0.487179	NM_005245		Missense_Mutation	SNP	ENST00000441802.2	37	CCDS47177.1	1210	0.5540293040293041	373	0.758130081300813	193	0.5331491712707183	357	0.6241258741258742	287	0.3786279683377309	c	0.683	-0.797573	0.02862	0.70764	0.361723	ENSG00000083857	ENST00000441802;ENST00000260147	T	0.37411	1.2	5.06	2.19	0.27852	Cadherin-like (1);	0.225081	0.45867	N	0.000335	T	0.00012	0.0000	N	0.25245	0.725	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.29212	-1.0019	9	0.16896	T	0.51	.	5.7344	0.18059	0.1328:0.5731:0.0:0.2941	rs2637777;rs3733404;rs17635884;rs52812769;rs57359486;rs2637777	3554	Q14517	FAT1_HUMAN	A	3554;3556	ENSP00000406229:S3554A	ENSP00000260147:S3556A	S	-	1	0	FAT1	187762014	0.027000	0.19231	0.007000	0.13788	0.053000	0.15095	0.136000	0.15974	0.336000	0.23639	-0.905000	0.02835	TCT	T|0.007;G|0.007	.	strong		0.473	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245	
OR1S1	219959	hgsc.bcm.edu	37	11	57983162	57983162	+	Missense_Mutation	SNP	A	A	G	rs7103026	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:57983162A>G	ENST00000309433.6	+	1	946	c.946A>G	c.(946-948)Aag>Gag	p.K316E		NM_001004458.1	NP_001004458.1	Q8NH92	OR1S1_HUMAN	olfactory receptor, family 1, subfamily S, member 1	316						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.K316E(1)		breast(1)|central_nervous_system(1)|endometrium(24)|kidney(1)|large_intestine(1)|liver(1)|lung(10)|prostate(1)|skin(2)|stomach(3)|urinary_tract(3)	48		Breast(21;0.0589)				TGCCCTGAGAAAGCTCATCAA	0.423													A|||	689	0.13758	0.0772	0.2205	5008	,	,		19269	0.0635		0.2386	False		,,,				2504	0.1329				p.K316E		Atlas-SNP	.											OR1S1,NS,carcinoma,0,2	OR1S1	139	2	1	Substitution - Missense(1)	prostate(1)	c.A946G						PASS	.	A	GLU/LYS	475,3927	224.6+/-240.7	28,419,1754	139.0	139.0	139.0		946	3.2	0.0	11	dbSNP_116	139	2223,6363	375.4+/-337.8	294,1635,2364	no	missense	OR1S1	NM_001004458.1	56	322,2054,4118	GG,GA,AA		25.891,10.7905,20.773	possibly-damaging	316/326	57983162	2698,10290	2201	4293	6494	SO:0001583	missense	219959	exon1			CTGAGAAAGCTCA	BK004299	CCDS31546.1	11q12.1	2012-08-09			ENSG00000172774	ENSG00000172774		"""GPCR / Class A : Olfactory receptors"""	8227	protein-coding gene	gene with protein product							Standard	NM_001004458		Approved	OST034	uc010rkc.2	Q8NH92	OTTHUMG00000167463	ENST00000309433.6:c.946A>G	11.37:g.57983162A>G	ENSP00000311688:p.Lys316Glu	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	104	67	0.644231	NM_001004458	Q6IFG3	Missense_Mutation	SNP	ENST00000309433.6	37	CCDS31546.1	334	0.15293040293040294	32	0.06504065040650407	75	0.20718232044198895	47	0.08216783216783216	180	0.23746701846965698	A	8.760	0.923264	0.18056	0.107905	0.25891	ENSG00000172774	ENST00000309433	T	0.40476	1.03	3.23	3.23	0.37069	.	0.251674	0.27778	N	0.017891	T	0.00012	0.0000	M	0.76838	2.35	0.80722	P	0.0	P	0.44627	0.839	B	0.36719	0.231	T	0.14559	-1.0468	9	0.66056	D	0.02	.	10.883	0.46951	1.0:0.0:0.0:0.0	rs7103026	316	Q8NH92	OR1S1_HUMAN	E	316	ENSP00000311688:K316E	ENSP00000311688:K316E	K	+	1	0	OR1S1	57739738	0.007000	0.16637	0.011000	0.14972	0.479000	0.33129	2.259000	0.43259	1.345000	0.45676	0.392000	0.25879	AAG	A|0.817;G|0.183	0.183	strong		0.423	OR1S1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394705.1	NM_001004458	
MAGEA12	4111	hgsc.bcm.edu	37	X	151899913	151899913	+	Silent	SNP	T	T	C	rs2233055	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:151899913T>C	ENST00000357916.4	-	2	1043	c.888A>G	c.(886-888)ggA>ggG	p.G296G	MAGEA12_ENST00000393869.3_Silent_p.G296G|CSAG4_ENST00000361201.4_RNA|MAGEA12_ENST00000393900.3_Silent_p.G296G	NM_005367.5	NP_005358.2	P43365	MAGAC_HUMAN	melanoma antigen family A, 12	296	MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.									breast(5)|large_intestine(5)|liver(1)|lung(14)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	28	Acute lymphoblastic leukemia(192;6.56e-05)					AAATGTGAGGTCCTCCACTGA	0.557													.|||	1595	0.422517	0.1793	0.1758	3775	,	,		15587	0.4891		0.329	False		,,,				2504	0.4213				p.G296G		Atlas-SNP	.											.	MAGEA12	125	.	0			c.A888G						PASS	.	T	,,	1023,2812		109,647,158,876,413	177.0	166.0	170.0		888,888,888	-1.6	0.0	X	dbSNP_98	170	2796,3932		420,1204,752,804,1120	no	coding-synonymous,coding-synonymous,coding-synonymous	MAGEA12	NM_001166386.1,NM_001166387.1,NM_005367.5	,,	529,1851,910,1680,1533	CC,CT,C,TT,T		41.5577,26.6754,36.1545	,,	296/315,296/315,296/315	151899913	3819,6744	2203	4300	6503	SO:0001819	synonymous_variant	4111	exon2			GTGAGGTCCTCCA		CCDS76048.1	Xq28	2009-03-13			ENSG00000213401	ENSG00000213401			6799	protein-coding gene	gene with protein product	"""cancer/testis antigen family 1, member 12"""	300177		MAGE12		8575766	Standard	NM_001166386		Approved	CT1.12	uc004fgc.3	P43365	OTTHUMG00000022650	ENST00000357916.4:c.888A>G	X.37:g.151899913T>C		Somatic	555	2	0.0036036		WXS	Illumina HiSeq	Phase_I	336	335	0.997024	NM_005367	Q9NSD3	Silent	SNP	ENST00000357916.4	37	CCDS14710.1																																																																																			T|0.627;C|0.373	0.373	strong		0.557	MAGEA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058764.1	NM_005367	
KRTAP10-11	386678	hgsc.bcm.edu	37	21	46067193	46067193	+	Missense_Mutation	SNP	G	G	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:46067193G>C	ENST00000334670.8	+	1	863	c.818G>C	c.(817-819)tGc>tCc	p.C273S	TSPEAR_ENST00000323084.4_Intron	NM_198692.2	NP_941965.2	P60412	KR10B_HUMAN	keratin associated protein 10-11	273						keratin filament (GO:0045095)				NS(1)|endometrium(1)|large_intestine(1)|lung(6)|ovary(2)|prostate(1)	12						CCGGCCTCCTGCGTGTCCCTC	0.677																																					p.C273S		Atlas-SNP	.											KRTAP10-11,NS,carcinoma,-1,1	KRTAP10-11	36	1	0			c.G818C						scavenged	.						41.0	52.0	48.0					21																	46067193		2200	4292	6492	SO:0001583	missense	386678	exon1			CCTCCTGCGTGTC	AB076359	CCDS42962.1	21q22.3	2006-03-13	2004-07-12	2004-07-14	ENSG00000243489	ENSG00000243489		"""Keratin associated proteins"""	20528	protein-coding gene	gene with protein product			"""keratin associated protein 10-11"""	KRTAP18-11			Standard	NM_198692		Approved	KRTAP18.11, KAP18.11, KAP10.11	uc002zfr.4	P60412	OTTHUMG00000057626	ENST00000334670.8:c.818G>C	21.37:g.46067193G>C	ENSP00000334197:p.Cys273Ser	Somatic	89	1	0.011236		WXS	Illumina HiSeq	Phase_I	107	4	0.0373832	NM_198692	A2RRF9	Missense_Mutation	SNP	ENST00000334670.8	37	CCDS42962.1	.	.	.	.	.	.	.	.	.	.	g	10.35	1.326226	0.24080	.	.	ENSG00000243489	ENST00000334670	T	0.00648	5.99	3.93	1.85	0.25348	.	.	.	.	.	T	0.00724	0.0024	L	0.45051	1.395	0.21527	N	0.999652	B	0.21071	0.051	B	0.24541	0.054	T	0.44314	-0.9336	9	0.16896	T	0.51	.	7.0501	0.25069	0.1131:0.3795:0.5075:0.0	.	273	P60412	KR10B_HUMAN	S	273	ENSP00000334197:C273S	ENSP00000334197:C273S	C	+	2	0	KRTAP10-11	44891621	0.000000	0.05858	0.035000	0.18076	0.597000	0.36814	-0.005000	0.12855	0.627000	0.30340	0.462000	0.41574	TGC	.	.	none		0.677	KRTAP10-11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128029.1	NM_198692	
PITPNM3	83394	hgsc.bcm.edu	37	17	6441376	6441376	+	Missense_Mutation	SNP	G	G	A	rs28493751	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:6441376G>A	ENST00000262483.8	-	2	136	c.49C>T	c.(49-51)Ccc>Tcc	p.P17S	PITPNM3_ENST00000421306.3_Missense_Mutation_p.P17S	NM_031220.3	NP_112497.2	Q9BZ71	PITM3_HUMAN	PITPNM family member 3	17			P -> S (in dbSNP:rs28493751).		phosphatidylinositol metabolic process (GO:0046488)|phospholipid transport (GO:0015914)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)	calcium ion binding (GO:0005509)|lipid binding (GO:0008289)|phosphatidylinositol transporter activity (GO:0008526)|receptor tyrosine kinase binding (GO:0030971)	p.P17S(1)		autonomic_ganglia(1)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(9)|lung(10)|ovary(3)|prostate(3)|skin(2)	36				Colorectal(2;0.000372)|READ - Rectum adenocarcinoma(2;0.0276)|LUAD - Lung adenocarcinoma(2;0.0836)|COAD - Colon adenocarcinoma(228;0.185)		AGGTGCCAGGGGGCACCGCCG	0.552													G|||	267	0.0533147	0.0265	0.0648	5008	,	,		18689	0.002		0.1103	False		,,,				2504	0.0757				p.P17S		Atlas-SNP	.											PITPNM3,brain,glioma,0,1	PITPNM3	91	1	1	Substitution - Missense(1)	central_nervous_system(1)	c.C49T						scavenged	.	G	SER/PRO,SER/PRO	196,4210	119.6+/-157.3	4,188,2011	39.0	37.0	38.0		49,49	4.9	1.0	17	dbSNP_125	38	939,7661	200.3+/-244.1	62,815,3423	yes	missense,missense	PITPNM3	NM_001165966.1,NM_031220.3	74,74	66,1003,5434	AA,AG,GG		10.9186,4.4485,8.7267	possibly-damaging,possibly-damaging	17/939,17/975	6441376	1135,11871	2203	4300	6503	SO:0001583	missense	83394	exon2			GCCAGGGGGCACC	AF334586	CCDS11076.1, CCDS54080.1	17p13	2013-07-18	2013-07-18	2013-07-18	ENSG00000091622	ENSG00000091622		"""GPCR / Class A : Chemokine receptors : Atypical"""	21043	protein-coding gene	gene with protein product	"""atypical chemokine receptor 6"""	608921	"""cone rod dystrophy 5"""	CORD5		10022914	Standard	NM_031220		Approved	NIR1, RDGBA3, ACKR6	uc002gdd.4	Q9BZ71	OTTHUMG00000102039	ENST00000262483.8:c.49C>T	17.37:g.6441376G>A	ENSP00000262483:p.Pro17Ser	Somatic	218	1	0.00458716		WXS	Illumina HiSeq	Phase_I	175	78	0.445714	NM_031220	A1A5D0|F8WEW5|Q59GH9|Q9NPQ4	Missense_Mutation	SNP	ENST00000262483.8	37	CCDS11076.1	127	0.05815018315018315	15	0.03048780487804878	28	0.07734806629834254	1	0.0017482517482517483	83	0.10949868073878628	G	18.04	3.534439	0.64972	0.044485	0.109186	ENSG00000091622	ENST00000262483;ENST00000421306	T;T	0.41065	1.03;1.01	4.89	4.89	0.63831	.	0.182670	0.37219	N	0.002190	T	0.00496	0.0016	N	0.08118	0	0.36580	P	0.12648700000000002	P;P	0.42518	0.782;0.675	B;B	0.41174	0.349;0.19	T	0.08659	-1.0711	9	0.48119	T	0.1	0.2887	13.9315	0.63998	0.0:0.0:1.0:0.0	rs28493751	17;17	F8WEW5;Q9BZ71	.;PITM3_HUMAN	S	17	ENSP00000262483:P17S;ENSP00000407882:P17S	ENSP00000262483:P17S	P	-	1	0	PITPNM3	6382100	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.677000	0.54619	2.439000	0.82584	0.655000	0.94253	CCC	G|0.926;A|0.074	0.074	strong		0.552	PITPNM3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000219824.2	NM_031220	
CEP68	23177	hgsc.bcm.edu	37	2	65299298	65299298	+	Missense_Mutation	SNP	C	C	A	rs2723088	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:65299298C>A	ENST00000377990.2	+	3	1271	c.1068C>A	c.(1066-1068)aaC>aaA	p.N356K	CEP68_ENST00000260569.4_Missense_Mutation_p.N356K|RAB1A_ENST00000494188.1_Intron|CEP68_ENST00000537589.1_5'UTR|CEP68_ENST00000546106.1_Missense_Mutation_p.N356K|CEP68_ENST00000497039.1_3'UTR	NM_015147.2	NP_055962.2	Q76N32	CEP68_HUMAN	centrosomal protein 68kDa	356					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						TCTCCCCCAACTGCCCACCAG	0.592													C|||	371	0.0740815	0.0681	0.0749	5008	,	,		17673	0.0		0.1233	False		,,,				2504	0.1074				p.N356K		Atlas-SNP	.											.	CEP68	69	.	0			c.C1068A						PASS	.	C	LYS/ASN	378,4028	176.6+/-205.7	15,348,1840	103.0	110.0	108.0		1068	-0.8	0.1	2	dbSNP_100	108	1046,7554	204.4+/-247.1	64,918,3318	yes	missense	CEP68	NM_015147.2	94	79,1266,5158	AA,AC,CC		12.1628,8.5792,10.9488	possibly-damaging	356/758	65299298	1424,11582	2203	4300	6503	SO:0001583	missense	23177	exon3			CCCCAACTGCCCA	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.1068C>A	2.37:g.65299298C>A	ENSP00000367229:p.Asn356Lys	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	205	153	0.746341	NM_015147	B4DRQ1|D6W5F1|D6W5F2|O60326|Q9BQ18|Q9UDM9	Missense_Mutation	SNP	ENST00000377990.2	37	CCDS1880.2	150	0.06868131868131869	26	0.052845528455284556	37	0.10220994475138122	0	0.0	87	0.11477572559366754	C	11.34	1.610210	0.28712	0.085792	0.121628	ENSG00000011523	ENST00000377990;ENST00000546106;ENST00000260569;ENST00000545501	T;T;T	0.14640	2.49;2.51;2.51	5.66	-0.786	0.10946	.	0.876803	0.10296	N	0.691750	T	0.00210	0.0006	L	0.51422	1.61	0.58432	P	5.000000000032756E-6	P;B;B;P;P	0.52316	0.589;0.358;0.053;0.952;0.589	B;B;B;P;B	0.46659	0.173;0.124;0.032;0.523;0.173	T	0.29731	-1.0002	9	0.38643	T	0.18	-2.5225	10.0031	0.41940	0.0:0.6553:0.0:0.3447	rs2723088	344;356;356;356;356	F5H3N9;F5H2Y2;Q76N32;Q76N32-2;Q05C09	.;.;CEP68_HUMAN;.;.	K	356;356;356;344	ENSP00000367229:N356K;ENSP00000438306:N356K;ENSP00000260569:N356K	ENSP00000260569:N356K	N	+	3	2	CEP68	65152802	0.083000	0.21467	0.079000	0.20413	0.614000	0.37383	0.132000	0.15891	-0.095000	0.12351	-0.339000	0.08088	AAC	C|0.905;A|0.095	0.095	strong		0.592	CEP68-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251727.2	NM_015147	
TMEM8A	58986	hgsc.bcm.edu	37	16	427516	427516	+	Silent	SNP	T	T	C	rs11649031	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:427516T>C	ENST00000431232.2	-	3	529	c.369A>G	c.(367-369)gtA>gtG	p.V123V	TMEM8A_ENST00000476735.1_5'UTR|TMEM8A_ENST00000250930.3_5'UTR	NM_021259.2	NP_067082.2	Q9HCN3	TMM8A_HUMAN	transmembrane protein 8A	123					cell adhesion (GO:0007155)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)				central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|pancreas(1)|prostate(1)	14						AGGAGGGCTGTACCGCGGTGT	0.692											OREG0003703	type=REGULATORY REGION|Gene=TMEM8|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	C|||	2859	0.570887	0.736	0.4885	5008	,	,		15299	0.3036		0.5437	False		,,,				2504	0.7096				p.V123V		Atlas-SNP	.											TMEM8A,colon,carcinoma,0,2	TMEM8A	49	2	0			c.A369G						PASS	.	C		3129,1243		1125,879,182	19.0	19.0	19.0		369	-0.5	0.0	16	dbSNP_120	19	4870,3712		1419,2032,840	no	coding-synonymous	TMEM8A	NM_021259.2		2544,2911,1022	CC,CT,TT		43.2533,28.4309,38.2507		123/772	427516	7999,4955	2186	4291	6477	SO:0001819	synonymous_variant	58986	exon3			GGGCTGTACCGCG	AB045292	CCDS10407.1	16p13.3	2009-06-12	2009-06-12	2009-06-12	ENSG00000129925	ENSG00000129925			17205	protein-coding gene	gene with protein product			"""transmembrane protein 6"", ""transmembrane protein 8 (five membrane-spanning domains)"""	TMEM6, TMEM8		11006113	Standard	NM_021259		Approved	M83	uc002cgu.4	Q9HCN3	OTTHUMG00000047996	ENST00000431232.2:c.369A>G	16.37:g.427516T>C		Somatic	152	1	0.00657895	588	WXS	Illumina HiSeq	Phase_I	78	76	0.974359	NM_021259	D3DU49|Q4TT35|Q8WU24|Q96S25|Q9BR03|Q9BT97|Q9H7B9	Silent	SNP	ENST00000431232.2	37	CCDS10407.1																																																																																			T|0.429;C|0.571	0.571	strong		0.692	TMEM8A-001	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000109257.2	NM_021259	
CDH17	1015	hgsc.bcm.edu	37	8	95186382	95186382	+	Silent	SNP	G	G	A	rs3214050	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:95186382G>A	ENST00000027335.3	-	6	655	c.531C>T	c.(529-531)gtC>gtT	p.V177V	CDH17_ENST00000441892.2_Intron|CDH17_ENST00000450165.2_Silent_p.V177V	NM_004063.3	NP_004054.3	Q12864	CAD17_HUMAN	cadherin 17, LI cadherin (liver-intestine)	177	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|oligopeptide transmembrane transport (GO:0035672)|oligopeptide transport (GO:0006857)|transport (GO:0006810)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|proton-dependent oligopeptide secondary active transmembrane transporter activity (GO:0005427)|transporter activity (GO:0005215)	p.V177V(1)		NS(1)|endometrium(5)|kidney(3)|large_intestine(10)|lung(18)|ovary(6)|prostate(3)|skin(4)|stomach(2)	52	Breast(36;4.65e-06)		BRCA - Breast invasive adenocarcinoma(8;0.00691)			GAAAGTACATGACATTGTTGA	0.488													G|||	1732	0.345847	0.2307	0.281	5008	,	,		17966	0.3165		0.4384	False		,,,				2504	0.4826				p.V177V		Atlas-SNP	.											CDH17,NS,carcinoma,0,1	CDH17	119	1	1	Substitution - coding silent(1)	stomach(1)	c.C531T						scavenged	.	G	,	1045,3361	384.2+/-325.2	103,839,1261	179.0	172.0	174.0		531,531	-2.8	0.5	8	dbSNP_106	174	4029,4571	555.7+/-386.7	933,2163,1204	no	coding-synonymous,coding-synonymous	CDH17	NM_001144663.1,NM_004063.3	,	1036,3002,2465	AA,AG,GG		46.8488,23.7177,39.0128	,	177/833,177/833	95186382	5074,7932	2203	4300	6503	SO:0001819	synonymous_variant	1015	exon6			GTACATGACATTG	X83228	CCDS6260.1	8q22.1	2010-01-26			ENSG00000079112	ENSG00000079112		"""Cadherins / Major cadherins"""	1756	protein-coding gene	gene with protein product		603017				9615235, 10191097	Standard	NM_004063		Approved	HPT-1, cadherin	uc003ygh.2	Q12864	OTTHUMG00000164391	ENST00000027335.3:c.531C>T	8.37:g.95186382G>A		Somatic	124	1	0.00806452		WXS	Illumina HiSeq	Phase_I	135	31	0.22963	NM_004063	Q15336|Q2M2E0	Silent	SNP	ENST00000027335.3	37	CCDS6260.1																																																																																			G|0.634;A|0.366	0.366	strong		0.488	CDH17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378560.1	NM_004063	
FAM13A	10144	hgsc.bcm.edu	37	4	89668859	89668859	+	Missense_Mutation	SNP	C	C	T	rs7657817	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:89668859C>T	ENST00000264344.5	-	18	2512	c.2305G>A	c.(2305-2307)Gtt>Att	p.V769I	FAM13A_ENST00000511976.1_Missense_Mutation_p.V355I|FAM13A_ENST00000503556.1_Missense_Mutation_p.V429I|FAM13A_ENST00000508369.1_Missense_Mutation_p.V443I|FAM13A_ENST00000513837.1_Missense_Mutation_p.V415I|FAM13A_ENST00000395002.2_Missense_Mutation_p.V443I	NM_014883.3	NP_055698.2	O94988	FA13A_HUMAN	family with sequence similarity 13, member A	769			V -> I (in dbSNP:rs7657817). {ECO:0000269|PubMed:15489334}.		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						GTGGCTTCAACACTGGGCTTT	0.498													C|||	1405	0.280551	0.4705	0.232	5008	,	,		17339	0.246		0.1769	False		,,,				2504	0.2004				p.V769I		Atlas-SNP	.											.	FAM13A	181	.	0			c.G2305A						PASS	.	C	ILE/VAL,ILE/VAL	1878,2528	542.2+/-376.0	402,1074,727	158.0	178.0	171.0		1327,2305	2.6	0.0	4	dbSNP_116	171	1473,7127	280.8+/-294.7	131,1211,2958	yes	missense,missense	FAM13A	NM_001015045.1,NM_014883.2	29,29	533,2285,3685	TT,TC,CC		17.1279,42.6237,25.765	benign,benign	443/698,769/1024	89668859	3351,9655	2203	4300	6503	SO:0001583	missense	10144	exon18			CTTCAACACTGGG	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.2305G>A	4.37:g.89668859C>T	ENSP00000264344:p.Val769Ile	Somatic	213	0	0		WXS	Illumina HiSeq	Phase_I	174	80	0.45977	NM_014883	B4DLC1|Q24JP0|Q5PR21|Q8NBA3	Missense_Mutation	SNP	ENST00000264344.5	37	CCDS34029.1	563	0.25778388278388276	212	0.43089430894308944	76	0.20994475138121546	142	0.24825174825174826	133	0.17546174142480211	C	6.635	0.485567	0.12641	0.426237	0.171279	ENSG00000138640	ENST00000395002;ENST00000264344;ENST00000503556;ENST00000511976;ENST00000508369;ENST00000513837	T;T;T;T;T;T	0.47528	0.84;2.12;1.43;1.46;1.43;1.43	5.26	2.56	0.30785	.	0.382752	0.26594	N	0.023510	T	0.00012	0.0000	N	0.25647	0.755	0.23430	P	0.9976995	B;B;B;B;B;B	0.31077	0.052;0.11;0.307;0.084;0.041;0.052	B;B;B;B;B;B	0.24155	0.05;0.028;0.051;0.037;0.037;0.037	T	0.47649	-0.9101	9	0.35671	T	0.21	.	6.4235	0.21756	0.0:0.6571:0.132:0.2109	rs7657817;rs52825255;rs58300926;rs7657817	415;355;769;443;429;443	O94988-6;E9PGM7;O94988;O94988-3;O94988-5;O94988-1	.;.;FA13A_HUMAN;.;.;.	I	443;769;429;355;443;415	ENSP00000378450:V443I;ENSP00000264344:V769I;ENSP00000427189:V429I;ENSP00000421914:V355I;ENSP00000421562:V443I;ENSP00000423252:V415I	ENSP00000264344:V769I	V	-	1	0	FAM13A	89887882	0.977000	0.34250	0.009000	0.14445	0.003000	0.03518	2.603000	0.46266	0.790000	0.33803	-0.878000	0.02970	GTT	C|0.745;T|0.255	0.255	strong		0.498	FAM13A-022	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363371.1		
RAD21L1	642636	hgsc.bcm.edu	37	20	1224774	1224774	+	Missense_Mutation	SNP	A	A	C	rs17717241	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:1224774A>C	ENST00000409241.1	+	11	1361	c.1268A>C	c.(1267-1269)cAt>cCt	p.H423P	RAD21L1_ENST00000381882.2_Missense_Mutation_p.H423P|RAD21L1_ENST00000402452.1_Missense_Mutation_p.H423P	NM_001136566.2	NP_001130038.2	Q9H4I0	RD21L_HUMAN	RAD21-like 1 (S. pombe)	423			H -> P (in dbSNP:rs17717241).		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						GGATCTCAGCATAGCTCTCAT	0.353													A|||	298	0.0595048	0.0787	0.0836	5008	,	,		17319	0.0159		0.0964	False		,,,				2504	0.0235				p.H423P		Atlas-SNP	.											.	RAD21L1	51	.	0			c.A1268C						PASS	.	A	PRO/HIS	127,1257		8,111,573	135.0	116.0	122.0		1268	3.6	0.0	20	dbSNP_123	122	271,2911		10,251,1330	yes	missense	RAD21L1	NM_001136566.2	77	18,362,1903	CC,CA,AA		8.5167,9.1763,8.7166	benign	423/557	1224774	398,4168	692	1591	2283	SO:0001583	missense	642636	exon11			CTCAGCATAGCTC	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.1268A>C	20.37:g.1224774A>C	ENSP00000386414:p.His423Pro	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	81	39	0.481481	NM_001136566	B2RXL0|B7ZBB1|B7ZW76|Q5W0X5	Missense_Mutation	SNP	ENST00000409241.1	37	CCDS46568.1	158	0.07234432234432235	49	0.09959349593495935	29	0.08011049723756906	8	0.013986013986013986	72	0.09498680738786279	A	0.874	-0.731023	0.03135	0.091763	0.085167	ENSG00000244588	ENST00000402452;ENST00000409241;ENST00000381882	T;T;T	0.62639	0.01;0.09;0.01	5.5	3.56	0.40772	.	.	.	.	.	T	0.01092	0.0036	N	0.08118	0	0.80722	P	0.0	B	0.21309	0.054	B	0.08055	0.003	T	0.07028	-1.0794	8	0.30854	T	0.27	.	7.6764	0.28488	0.191:0.0:0.809:0.0	rs17717241;rs52834781;rs61377268;rs17717241	423	Q9H4I0	RD21L_HUMAN	P	423	ENSP00000385925:H423P;ENSP00000386414:H423P;ENSP00000371306:H423P	ENSP00000371306:H423P	H	+	2	0	RAD21L1	1172774	0.002000	0.14202	0.001000	0.08648	0.001000	0.01503	0.307000	0.19296	0.865000	0.35603	-0.242000	0.12053	CAT	A|0.928;C|0.072	0.072	strong		0.353	RAD21L1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334022.1		
NLRP7	199713	hgsc.bcm.edu	37	19	55451797	55451797	+	Silent	SNP	C	C	T	rs775883	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:55451797C>T	ENST00000590030.1	-	3	430	c.390G>A	c.(388-390)caG>caA	p.Q130Q	NLRP7_ENST00000340844.2_Silent_p.Q130Q|NLRP7_ENST00000448121.2_Silent_p.Q130Q|NLRP7_ENST00000588756.1_Silent_p.Q130Q|NLRP7_ENST00000592784.1_Silent_p.Q130Q|NLRP7_ENST00000328092.5_Silent_p.Q130Q|NLRP7_ENST00000446217.1_Silent_p.Q158Q			Q8WX94	NALP7_HUMAN	NLR family, pyrin domain containing 7	130							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)		AGACCAAAGACTGTTTCTCCA	0.418													.|||	1780	0.355431	0.5204	0.3746	5008	,	,		21599	0.1905		0.3956	False		,,,				2504	0.2474				p.Q130Q		Atlas-SNP	.											.	NLRP7	411	.	0			c.G390A						PASS	.	T	,,	2185,2221	576.7+/-384.3	544,1097,562	291.0	320.0	310.0		390,390,390	-2.9	0.0	19	dbSNP_86	310	2871,5729	663.0+/-402.0	490,1891,1919	no	coding-synonymous,coding-synonymous,coding-synonymous	NLRP7	NM_001127255.1,NM_139176.3,NM_206828.3	,,	1034,2988,2481	TT,TC,CC		33.3837,49.5915,38.8744	,,	130/1038,130/1010,130/981	55451797	5056,7950	2203	4300	6503	SO:0001819	synonymous_variant	199713	exon4			CAAAGACTGTTTC	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.390G>A	19.37:g.55451797C>T		Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	117	50	0.42735	NM_001127255	E9PE16|Q32MH8|Q7RTR1	Silent	SNP	ENST00000590030.1	37	CCDS33109.1																																																																																			C|0.623;T|0.377	0.377	strong		0.418	NLRP7-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000451396.1	NM_139176	
LAMB2	3913	hgsc.bcm.edu	37	3	49162284	49162284	+	Missense_Mutation	SNP	C	C	T	rs34759087	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:49162284C>T	ENST00000418109.1	-	22	3123	c.2959G>A	c.(2959-2961)Gag>Aag	p.E987K	LAMB2_ENST00000464891.1_5'UTR|LAMB2_ENST00000305544.4_Missense_Mutation_p.E987K	NM_002292.3	NP_002283.3	P55268	LAMB2_HUMAN	laminin, beta 2 (laminin S)	987	Laminin EGF-like 10. {ECO:0000255|PROSITE-ProRule:PRU00460}.		E -> K (in dbSNP:rs34759087).		astrocyte development (GO:0014002)|axon extension involved in regeneration (GO:0048677)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|metanephric glomerular basement membrane development (GO:0072274)|metanephric glomerular visceral epithelial cell development (GO:0072249)|neuromuscular junction development (GO:0007528)|retina development in camera-type eye (GO:0060041)|Schwann cell development (GO:0014044)|visual perception (GO:0007601)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-11 complex (GO:0043260)|laminin-3 complex (GO:0005608)|synapse (GO:0045202)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|endometrium(15)|kidney(3)|large_intestine(6)|lung(21)|ovary(4)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	61				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00219)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)		CCACTGCACTCACACAGTTGG	0.602													C|||	297	0.0593051	0.0091	0.0418	5008	,	,		21062	0.002		0.1133	False		,,,				2504	0.1431				p.E987K		Atlas-SNP	.											.	LAMB2	156	.	0			c.G2959A						PASS	.	C	LYS/GLU	91,4315	76.2+/-114.5	0,91,2112	110.0	90.0	97.0		2959	4.6	1.0	3	dbSNP_126	97	1139,7461	234.9+/-267.6	75,989,3236	yes	missense	LAMB2	NM_002292.3	56	75,1080,5348	TT,TC,CC		13.2442,2.0654,9.4572	benign	987/1799	49162284	1230,11776	2203	4300	6503	SO:0001583	missense	3913	exon21			TGCACTCACACAG		CCDS2789.1	3p21.3-p21.2	2013-03-01			ENSG00000172037	ENSG00000172037		"""Laminins"""	6487	protein-coding gene	gene with protein product	"""laminin S"""	150325		LAMS		2922051, 10393422	Standard	NM_002292		Approved		uc003cwe.3	P55268	OTTHUMG00000156807	ENST00000418109.1:c.2959G>A	3.37:g.49162284C>T	ENSP00000388325:p.Glu987Lys	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	83	49	0.590361	NM_002292	Q16321	Missense_Mutation	SNP	ENST00000418109.1	37	CCDS2789.1	112	0.05128205128205128	8	0.016260162601626018	18	0.049723756906077346	1	0.0017482517482517483	85	0.11213720316622691	C	19.71	3.879194	0.72294	0.020654	0.132442	ENSG00000172037	ENST00000418109;ENST00000305544	T;T	0.61742	0.08;0.08	5.53	4.6	0.57074	EGF-like, laminin (4);	0.122950	0.56097	D	0.000023	T	0.00580	0.0019	L	0.48218	1.51	0.45452	D	0.998421	P	0.40144	0.704	B	0.34931	0.192	T	0.01178	-1.1427	10	0.15952	T	0.53	.	15.1555	0.72739	0.0:0.7314:0.2686:0.0	rs34759087;rs34759087	987	P55268	LAMB2_HUMAN	K	987	ENSP00000388325:E987K;ENSP00000307156:E987K	ENSP00000307156:E987K	E	-	1	0	LAMB2	49137288	1.000000	0.71417	1.000000	0.80357	0.913000	0.54294	3.294000	0.51787	2.628000	0.89032	0.561000	0.74099	GAG	C|0.920;T|0.080	0.080	strong		0.602	LAMB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345939.1	NM_002292	
PAMR1	25891	hgsc.bcm.edu	37	11	35463043	35463043	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:35463043G>A	ENST00000378880.2	-	7	1464	c.1019C>T	c.(1018-1020)cCc>cTc	p.P340L	PAMR1_ENST00000278360.3_Missense_Mutation_p.P357L|PAMR1_ENST00000378878.3_Missense_Mutation_p.P229L|PAMR1_ENST00000532848.1_Missense_Mutation_p.P300L	NM_001001991.1	NP_001001991.1	Q6UXH9	PAMR1_HUMAN	peptidase domain containing associated with muscle regeneration 1	340	Sushi 1. {ECO:0000255|PROSITE- ProRule:PRU00302}.					extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(8)|ovary(3)|upper_aerodigestive_tract(1)	26						TATGCAGATGGGCTGTTTCCC	0.418																																					p.P357L		Atlas-SNP	.											.	PAMR1	85	.	0			c.C1070T						PASS	.						195.0	189.0	191.0					11																	35463043		2202	4298	6500	SO:0001583	missense	25891	exon8			CAGATGGGCTGTT		CCDS7898.1, CCDS31460.1, CCDS60759.1, CCDS60760.1	11p13	2009-09-30			ENSG00000149090	ENSG00000149090			24554	protein-coding gene	gene with protein product	"""regeneration-associated muscle protease"""					15111323	Standard	NM_001282675		Approved	RAMP, DKFZP586H2123	uc001mwf.3	Q6UXH9	OTTHUMG00000166328	ENST00000378880.2:c.1019C>T	11.37:g.35463043G>A	ENSP00000368158:p.Pro340Leu	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	129	65	0.503876	NM_015430	A8MQ58|B7ZA73|Q5EBL7|Q5JPI4|Q6N062|Q71RE9|Q96JW2|Q9Y432	Missense_Mutation	SNP	ENST00000378880.2	37	CCDS31460.1	.	.	.	.	.	.	.	.	.	.	G	29.7	5.031221	0.93575	.	.	ENSG00000149090	ENST00000278360;ENST00000378880;ENST00000378878;ENST00000532848;ENST00000527605	T;T;T;T;T	0.77358	-1.09;-1.09;-1.09;-1.09;-1.09	5.84	5.84	0.93424	Complement control module (2);Sushi/SCR/CCP (3);	0.000000	0.85682	D	0.000000	D	0.92306	0.7559	H	0.95187	3.635	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	D	0.93784	0.7086	10	0.87932	D	0	.	20.139	0.98050	0.0:0.0:1.0:0.0	.	229;340;357	A8MQ58;Q6UXH9;Q6UXH9-2	.;PAMR1_HUMAN;.	L	357;340;229;300;317	ENSP00000278360:P357L;ENSP00000368158:P340L;ENSP00000368156:P229L;ENSP00000433868:P300L;ENSP00000432591:P317L	ENSP00000278360:P357L	P	-	2	0	PAMR1	35419619	1.000000	0.71417	0.991000	0.47740	0.987000	0.75469	8.755000	0.91646	2.764000	0.94973	0.655000	0.94253	CCC	.	.	none		0.418	PAMR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389177.1	NM_015430	
ZFPM1	161882	hgsc.bcm.edu	37	16	88599023	88599023	+	Splice_Site	SNP	A	A	G	rs56041036	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:88599023A>G	ENST00000319555.3	+	8	1270	c.948A>G	c.(946-948)ggA>ggG	p.G316G	RP11-21B21.4_ENST00000563243.1_RNA	NM_153813.2	NP_722520.2	Q8IX07	FOG1_HUMAN	zinc finger protein, FOG family member 1	316					atrial septum morphogenesis (GO:0060413)|atrioventricular valve morphogenesis (GO:0003181)|blood coagulation (GO:0007596)|cardiac muscle tissue morphogenesis (GO:0055008)|definitive erythrocyte differentiation (GO:0060318)|embryonic hemopoiesis (GO:0035162)|erythrocyte differentiation (GO:0030218)|granulocyte differentiation (GO:0030851)|megakaryocyte development (GO:0035855)|megakaryocyte differentiation (GO:0030219)|mitral valve formation (GO:0003192)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of interleukin-4 biosynthetic process (GO:0045403)|negative regulation of mast cell differentiation (GO:0060377)|negative regulation of protein binding (GO:0032091)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|outflow tract morphogenesis (GO:0003151)|platelet formation (GO:0030220)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|primitive erythrocyte differentiation (GO:0060319)|regulation of chemokine production (GO:0032642)|regulation of definitive erythrocyte differentiation (GO:0010724)|T-helper cell lineage commitment (GO:0002295)|transcriptional activation by promoter-enhancer looping (GO:0071733)|tricuspid valve formation (GO:0003195)|ventricular septum morphogenesis (GO:0060412)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|transcription factor complex (GO:0005667)|transcriptional repressor complex (GO:0017053)	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)|RNA polymerase II transcription factor binding (GO:0001085)|transcription factor binding (GO:0008134)			central_nervous_system(1)|ovary(2)|urinary_tract(1)	4				BRCA - Breast invasive adenocarcinoma(80;0.0478)		GTGTTCCAGGAGAGCGGCCCT	0.662													a|||	741	0.147963	0.0741	0.1484	5008	,	,		16600	0.3591		0.0974	False		,,,				2504	0.0818				p.G316G	Pancreas(49;850 1106 29641 32847 38344)	Atlas-SNP	.											ZFPM1,NS,carcinoma,0,1	ZFPM1	32	1	0			c.A948G						PASS	.	A		345,4013		17,311,1851	29.0	27.0	28.0		948	0.6	1.0	16	dbSNP_129	28	652,7914		21,610,3652	yes	coding-synonymous-near-splice	ZFPM1	NM_153813.2		38,921,5503	GG,GA,AA		7.6115,7.9165,7.7143		316/1007	88599023	997,11927	2179	4283	6462	SO:0001630	splice_region_variant	161882	exon8			TCCAGGAGAGCGG	AF488691	CCDS32502.1	16q24.2	2013-01-10	2012-11-27		ENSG00000179588	ENSG00000179588		"""Zinc fingers, C2H2-type"", ""Zinc fingers, C2HC-type containing"""	19762	protein-coding gene	gene with protein product		601950	"""zinc finger protein, multitype 1"""				Standard	NM_153813		Approved	FOG1, FOG, ZNF89A, ZC2HC11A	uc002fkv.3	Q8IX07	OTTHUMG00000173152	ENST00000319555.3:c.947-1A>G	16.37:g.88599023A>G		Somatic	179	0	0		WXS	Illumina HiSeq	Phase_I	196	194	0.989796	NM_153813		Silent	SNP	ENST00000319555.3	37	CCDS32502.1																																																																																			A|0.879;G|0.121	0.121	strong		0.662	ZFPM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422270.2		Silent
DNAH8	1769	hgsc.bcm.edu	37	6	38800209	38800209	+	Silent	SNP	T	T	C	rs1678729	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:38800209T>C	ENST00000359357.3	+	29	3903	c.3649T>C	c.(3649-3651)Ttg>Ctg	p.L1217L	DNAH8_ENST00000441566.1_Silent_p.L1217L|DNAH8_ENST00000449981.2_Silent_p.L1434L			Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy chain 8	1217					cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(7)|breast(9)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(16)|large_intestine(44)|liver(4)|lung(101)|ovary(7)|pancreas(2)|prostate(8)|skin(28)|stomach(4)|upper_aerodigestive_tract(6)|urinary_tract(4)	260						AGCATATGAATTGGTAATTTA	0.363													T|||	1365	0.272564	0.4259	0.2161	5008	,	,		18954	0.2917		0.1272	False		,,,				2504	0.2352				p.L1434L		Atlas-SNP	.											.	DNAH8	1239	.	0			c.T4300C						PASS	.	T		1614,2792	497.2+/-363.8	299,1016,888	109.0	107.0	108.0		4300	-5.7	0.0	6	dbSNP_89	108	1175,7425	238.1+/-269.7	78,1019,3203	no	coding-synonymous	DNAH8	NM_001206927.1		377,2035,4091	CC,CT,TT		13.6628,36.6319,21.4439		1434/4708	38800209	2789,10217	2203	4300	6503	SO:0001819	synonymous_variant	1769	exon31			TATGAATTGGTAA	Z83806	CCDS75447.1	6p21.2	2012-04-19	2006-09-04		ENSG00000124721	ENSG00000124721		"""Axonemal dyneins"""	2952	protein-coding gene	gene with protein product		603337	"""dynein, axonemal, heavy polypeptide 8"""			9373155	Standard	NM_001206927		Approved	hdhc9	uc021yzh.1	Q96JB1	OTTHUMG00000016253	ENST00000359357.3:c.3649T>C	6.37:g.38800209T>C		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	76	35	0.460526	NM_001206927	O00438|Q5JYI2|Q5T2M3|Q5T2M4|Q5TG00|Q9UEM4	Silent	SNP	ENST00000359357.3	37																																																																																				T|0.758;C|0.242	0.242	strong		0.363	DNAH8-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000043574.1	NM_001206927	
HYPK	25764	hgsc.bcm.edu	37	15	44093927	44093927	+	Missense_Mutation	SNP	T	T	C	rs12702	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:44093927T>C	ENST00000406925.1	+	5	4424	c.313T>C	c.(313-315)Tct>Cct	p.S105P	SERINC4_ENST00000299969.6_5'Flank|SERINC4_ENST00000249714.3_5'Flank|SERF2_ENST00000594896.1_Missense_Mutation_p.S151P|HYPK_ENST00000442995.2_Missense_Mutation_p.S105P|RP11-296A16.1_ENST00000417761.2_5'Flank|SERF2_ENST00000600633.1_Missense_Mutation_p.S105P|SERINC4_ENST00000319327.6_5'Flank|HYPK_ENST00000458412.1_3'UTR			Q9NX55	HYPK_HUMAN	huntingtin interacting protein K	105			S -> P (in dbSNP:rs12702). {ECO:0000269|PubMed:11042152}.			cytoplasm (GO:0005737)|nucleus (GO:0005634)							all_cancers(109;3.26e-11)|all_epithelial(112;4.82e-09)|Lung NSC(122;1.61e-06)|all_lung(180;1.5e-05)|Melanoma(134;0.0417)		GBM - Glioblastoma multiforme(94;8.1e-07)		GATGGAGATATCTCGAGCAGC	0.458													T|||	1047	0.209065	0.3177	0.1801	5008	,	,		17222	0.2599		0.0954	False		,,,				2504	0.1472				p.S105P		Atlas-SNP	.											.	.	.	.	0			c.T313C						PASS	.	T	,PRO/SER	1154,3242	407.3+/-334.2	142,870,1186	96.0	90.0	92.0		,313	5.3	1.0	15	dbSNP_52	92	817,7779	189.8+/-236.5	39,739,3520	yes	utr-3,missense	C15orf63	NM_001199885.1,NM_016400.3	,74	181,1609,4706	CC,CT,TT		9.5044,26.2511,15.1709	,	,105/130	44093927	1971,11021	2198	4298	6496	SO:0001583	missense	25764	exon4			GAGATATCTCGAG	AF049613	CCDS10104.1	15q14	2012-10-08	2012-10-08	2012-10-08	ENSG00000242028	ENSG00000242028			18418	protein-coding gene	gene with protein product	"""Huntingtin yeast partner K"""	612784	"""chromosome 15 open reading frame 63"""	C15orf63		9700202, 20154145	Standard	NM_016400		Approved	HSPC136, FLJ20431	uc001ztf.3	Q9NX55	OTTHUMG00000060146	ENST00000406925.1:c.313T>C	15.37:g.44093927T>C	ENSP00000384474:p.Ser105Pro	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	85	30	0.352941	NM_016400	C9JKJ0|O75408|Q8WUW8|Q9P024	Missense_Mutation	SNP	ENST00000406925.1	37	CCDS10104.1	464	0.21245421245421245	157	0.31910569105691056	68	0.1878453038674033	174	0.3041958041958042	65	0.08575197889182058	T	18.05	3.537166	0.65085	0.262511	0.095044	ENSG00000242028	ENST00000406925;ENST00000442995	T;T	0.52057	0.68;0.68	5.34	5.34	0.76211	.	0.054450	0.85682	D	0.000000	T	0.00012	0.0000	N	0.16567	0.415	0.09310	P	1.0	B	0.06786	0.001	B	0.11329	0.006	T	0.18745	-1.0327	9	0.45353	T	0.12	-8.4758	9.9009	0.41346	0.0:0.0754:0.0:0.9246	rs12702;rs1071657;rs3191169;rs8028332;rs52804577;rs56425911;rs12702	105	Q9NX55	HYPK_HUMAN	P	105	ENSP00000384474:S105P;ENSP00000401155:S105P	ENSP00000384474:S105P	S	+	1	0	C15orf63	41881219	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.965000	0.56788	2.248000	0.74166	0.533000	0.62120	TCT	T|0.812;C|0.188	0.188	strong		0.458	HYPK-007	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000133876.3	NM_016400	
HYAL4	23553	hgsc.bcm.edu	37	7	123514896	123514896	+	Missense_Mutation	SNP	G	G	T	rs6949082	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:123514896G>T	ENST00000223026.4	+	4	1674	c.1036G>T	c.(1036-1038)Gca>Tca	p.A346S	HYAL4_ENST00000476325.1_Missense_Mutation_p.A346S	NM_012269.2	NP_036401.2	Q2M3T9	HYAL4_HUMAN	hyaluronoglucosaminidase 4	346			A -> S (in dbSNP:rs6949082). {ECO:0000269|PubMed:15489334}.		carbohydrate metabolic process (GO:0005975)|chondroitin sulfate catabolic process (GO:0030207)|glycosaminoglycan catabolic process (GO:0006027)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)	hyalurononglucosaminidase activity (GO:0004415)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(8)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	23						GAATTTAACTGCATCCAAGGT	0.393													T|||	569	0.113618	0.1293	0.0994	5008	,	,		17605	0.001		0.1779	False		,,,				2504	0.1524				p.A346S		Atlas-SNP	.											.	HYAL4	65	.	0			c.G1036T						PASS	.	T	SER/ALA	660,3746	764.9+/-413.3	55,550,1598	117.0	109.0	112.0		1036	4.9	0.9	7	dbSNP_116	112	1464,7136	749.6+/-407.4	107,1250,2943	yes	missense	HYAL4	NM_012269.2	99	162,1800,4541	TT,TG,GG		17.0233,14.9796,16.3309	benign	346/482	123514896	2124,10882	2203	4300	6503	SO:0001583	missense	23553	exon4			TTAACTGCATCCA	AF009010	CCDS5789.1	7q31.3	2010-01-14			ENSG00000106302	ENSG00000106302			5323	protein-coding gene	gene with protein product	"""hyaluronidase 4"""	604510				10493834	Standard	NM_012269		Approved		uc003vlc.3	Q2M3T9	OTTHUMG00000157349	ENST00000223026.4:c.1036G>T	7.37:g.123514896G>T	ENSP00000223026:p.Ala346Ser	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	59	59	1	NM_012269	D0VXG1|Q9UL99|Q9Y6T9	Missense_Mutation	SNP	ENST00000223026.4	37	CCDS5789.1	251	0.11492673992673992	79	0.16056910569105692	36	0.09944751381215469	1	0.0017482517482517483	135	0.17810026385224276	T	1.595	-0.528098	0.04112	0.149796	0.170233	ENSG00000106302	ENST00000223026;ENST00000476325	T;T	0.20738	2.05;2.05	6.06	4.89	0.63831	Aldolase-type TIM barrel (1);Glycoside hydrolase, superfamily (1);	0.076912	0.53938	N	0.000044	T	0.00012	0.0000	N	0.00119	-2.075	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.33163	-0.9879	9	0.02654	T	1	-5.186	7.8202	0.29284	0.0:0.065:0.266:0.669	rs6949082;rs17703276;rs52837968;rs60489599;rs6949082	346;346	F8WDH9;Q2M3T9	.;HYAL4_HUMAN	S	346	ENSP00000223026:A346S;ENSP00000417186:A346S	ENSP00000223026:A346S	A	+	1	0	HYAL4	123302132	0.998000	0.40836	0.929000	0.37066	0.879000	0.50718	2.040000	0.41203	0.508000	0.28173	-0.256000	0.11100	GCA	G|0.852;T|0.148	0.148	strong		0.393	HYAL4-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348545.1	NM_012269	
YTHDF1	54915	hgsc.bcm.edu	37	20	61834695	61834695	+	Silent	SNP	G	G	A	rs6122103	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:61834695G>A	ENST00000370339.3	-	4	938	c.597C>T	c.(595-597)gcC>gcT	p.A199A	YTHDF1_ENST00000370334.4_Intron|YTHDF1_ENST00000370333.4_Silent_p.A149A	NM_017798.3	NP_060268.2	Q9BYJ9	YTHD1_HUMAN	YTH domain family, member 1	199							N6-methyladenosine-containing RNA binding (GO:1990247)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|endometrium(6)|kidney(1)|large_intestine(5)|lung(7)|ovary(2)	24						CCGTCTTGACGGCGGAGGAGC	0.602													A|||	1608	0.321086	0.3056	0.2478	5008	,	,		18362	0.369		0.3032	False		,,,				2504	0.363				p.A199A		Atlas-SNP	.											.	YTHDF1	66	.	0			c.C597T						PASS	.	A		1428,2978	671.6+/-402.5	237,954,1012	42.0	39.0	40.0		597	-5.8	0.1	20	dbSNP_114	40	2642,5958	675.3+/-403.2	408,1826,2066	no	coding-synonymous	YTHDF1	NM_017798.3		645,2780,3078	AA,AG,GG		30.7209,32.4103,31.2932		199/560	61834695	4070,8936	2203	4300	6503	SO:0001819	synonymous_variant	54915	exon4			CTTGACGGCGGAG	AK000398	CCDS13511.1	20q13.33	2010-03-15	2004-11-16	2004-06-04	ENSG00000149658	ENSG00000149658			15867	protein-coding gene	gene with protein product			"""YTH domain family 1"""	C20orf21			Standard	NM_017798		Approved	FLJ20391	uc002yeh.3	Q9BYJ9	OTTHUMG00000032955	ENST00000370339.3:c.597C>T	20.37:g.61834695G>A		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	51	23	0.45098	NM_017798	Q8N3G5|Q8TBT1|Q96AN4|Q96S57|Q9BTI7|Q9NX79	Silent	SNP	ENST00000370339.3	37	CCDS13511.1																																																																																			G|0.680;A|0.320	0.320	strong		0.602	YTHDF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080110.2	NM_017798	
SLC16A8	23539	hgsc.bcm.edu	37	22	38477930	38477930	+	Silent	SNP	G	G	A	rs2235573	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:38477930G>A	ENST00000320521.5	-	3	432	c.324C>T	c.(322-324)ctC>ctT	p.L108L	SLC16A8_ENST00000469516.1_Intron	NM_013356.2	NP_037488.2	O95907	MOT3_HUMAN	solute carrier family 16 (monocarboxylate transporter), member 8	108					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)	AGAGCTCCAGGAGGCGCGTGG	0.667													G|||	2180	0.435304	0.4145	0.4524	5008	,	,		13694	0.4831		0.493	False		,,,				2504	0.3425				p.L108L		Atlas-SNP	.											SLC16A8,NS,carcinoma,0,1	SLC16A8	13	1	0			c.C324T						scavenged	.	G		1838,2528		406,1026,751	30.0	32.0	32.0		324	0.1	1.0	22	dbSNP_98	32	4098,4478		988,2122,1178	no	coding-synonymous	SLC16A8	NM_013356.2		1394,3148,1929	AA,AG,GG		47.7845,42.098,45.8662		108/505	38477930	5936,7006	2183	4288	6471	SO:0001819	synonymous_variant	23539	exon3			CTCCAGGAGGCGC	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.324C>T	22.37:g.38477930G>A		Somatic	229	1	0.00436681		WXS	Illumina HiSeq	Phase_I	208	85	0.408654	NM_013356	Q9UBE2	Silent	SNP	ENST00000320521.5	37	CCDS13966.1																																																																																			G|0.551;A|0.449	0.449	strong		0.667	SLC16A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321724.1	NM_013356	
FAM13A	10144	hgsc.bcm.edu	37	4	89772321	89772321	+	Missense_Mutation	SNP	C	C	T	rs115194267	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:89772321C>T	ENST00000264344.5	-	7	1064	c.857G>A	c.(856-858)aGg>aAg	p.R286K	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	286					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						TCCCTCACTCCTGGATTTTGG	0.403													C|||	32	0.00638978	0.0	0.0159	5008	,	,		15453	0.0		0.0189	False		,,,				2504	0.002				p.R286K		Atlas-SNP	.											.	FAM13A	181	.	0			c.G857A						PASS	.	C	LYS/ARG	6,4400	12.9+/-30.5	0,6,2197	76.0	84.0	81.0		857	0.2	1.0	4	dbSNP_132	81	111,8489	57.5+/-118.9	2,107,4191	yes	missense	FAM13A	NM_014883.2	26	2,113,6388	TT,TC,CC		1.2907,0.1362,0.8996	benign	286/1024	89772321	117,12889	2203	4300	6503	SO:0001583	missense	10144	exon7			TCACTCCTGGATT	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.857G>A	4.37:g.89772321C>T	ENSP00000264344:p.Arg286Lys	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	60	28	0.466667	NM_014883	B4DLC1|Q24JP0|Q5PR21|Q8NBA3	Missense_Mutation	SNP	ENST00000264344.5	37	CCDS34029.1	17	0.007783882783882784	0	0.0	2	0.0055248618784530384	0	0.0	15	0.01978891820580475	C	0.754	-0.771903	0.02951	0.001362	0.012907	ENSG00000138640	ENST00000264344	T	0.15952	2.38	4.42	0.189	0.15119	.	0.429803	0.24303	N	0.039703	T	0.02494	0.0076	N	0.08118	0	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.40608	-0.9554	10	0.05959	T	0.93	.	6.6573	0.22994	0.0:0.4833:0.0:0.5167	.	286	O94988	FA13A_HUMAN	K	286	ENSP00000264344:R286K	ENSP00000264344:R286K	R	-	2	0	FAM13A	89991344	0.704000	0.27836	0.994000	0.49952	0.550000	0.35303	-0.196000	0.09532	-0.006000	0.14370	0.650000	0.86243	AGG	C|0.990;T|0.010	0.010	strong		0.403	FAM13A-022	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363371.1		
DMRTC2	63946	hgsc.bcm.edu	37	19	42354629	42354629	+	Silent	SNP	T	T	C	rs2305809	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:42354629T>C	ENST00000269945.3	+	8	903	c.852T>C	c.(850-852)ggT>ggC	p.G284G	DMRTC2_ENST00000596827.1_Silent_p.G335G	NM_001040283.1	NP_001035373.1	Q8IXT2	DMRTD_HUMAN	DMRT-like family C2	284	Pro-rich.				male meiosis I (GO:0007141)|positive regulation of histone H3-K9 dimethylation (GO:1900111)|positive regulation of histone H3-K9 trimethylation (GO:1900114)|sex differentiation (GO:0007548)|spermatid nucleus elongation (GO:0007290)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|XY body (GO:0001741)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|large_intestine(2)|lung(5)|prostate(1)|skin(1)	10						GGACATCTGGTCCCTCAGAGT	0.627													C|||	3047	0.608427	0.916	0.572	5008	,	,		16805	0.5258		0.4702	False		,,,				2504	0.4458				p.G284G		Atlas-SNP	.											.	DMRTC2	31	.	0			c.T852C						PASS	.	C		3676,730	288.4+/-279.8	1545,586,72	44.0	51.0	48.0		852	2.3	0.3	19	dbSNP_100	48	4114,4486	575.9+/-390.3	963,2188,1149	no	coding-synonymous	DMRTC2	NM_001040283.1		2508,2774,1221	CC,CT,TT		47.8372,16.5683,40.1046		284/368	42354629	7790,5216	2203	4300	6503	SO:0001819	synonymous_variant	63946	exon8			ATCTGGTCCCTCA	AJ291669	CCDS33034.1	19q13.2	2008-07-16				ENSG00000142025			13911	protein-coding gene	gene with protein product		614806				11863363	Standard	NM_001040283		Approved		uc002ors.3	Q8IXT2		ENST00000269945.3:c.852T>C	19.37:g.42354629T>C		Somatic	26	0	0		WXS	Illumina HiSeq	Phase_I	27	25	0.925926	NM_001040283	Q8N6Q2|Q96M39|Q96SD4	Silent	SNP	ENST00000269945.3	37	CCDS33034.1																																																																																			T|0.398;C|0.602	0.602	strong		0.627	DMRTC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463045.1	NM_001040283	
FREM1	158326	hgsc.bcm.edu	37	9	14801725	14801725	+	Missense_Mutation	SNP	C	C	G	rs61744094	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:14801725C>G	ENST00000380880.3	-	20	4402	c.3619G>C	c.(3619-3621)Gag>Cag	p.E1207Q	FREM1_ENST00000380881.4_Missense_Mutation_p.E1208Q|FREM1_ENST00000422223.2_Missense_Mutation_p.E1207Q			Q5H8C1	FREM1_HUMAN	FRAS1 related extracellular matrix 1	1207					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)		TGCTTATTCTCAGAGAAGTCT	0.512																																					p.E1207Q		Atlas-SNP	.											.	FREM1	261	.	0			c.G3619C						PASS	.	C	GLN/GLU	1,3989		0,1,1994	147.0	145.0	145.0		3619	1.5	0.0	9	dbSNP_129	145	2,8356		0,2,4177	no	missense	FREM1	NM_144966.5	29	0,3,6171	GG,GC,CC		0.0239,0.0251,0.0243	benign	1207/2180	14801725	3,12345	1995	4179	6174	SO:0001583	missense	158326	exon21			TATTCTCAGAGAA	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.3619G>C	9.37:g.14801725C>G	ENSP00000370262:p.Glu1207Gln	Somatic	238	0	0		WXS	Illumina HiSeq	Phase_I	221	97	0.438914	NM_144966	B7ZBX4|Q5VV00|Q5VV01|Q6MZI4|Q8NEG9|Q96LI3	Missense_Mutation	SNP	ENST00000380880.3	37	CCDS47952.1	.	.	.	.	.	.	.	.	.	.	C	0.332	-0.955355	0.02267	2.51E-4	2.39E-4	ENSG00000164946	ENST00000380881;ENST00000422223;ENST00000380880	T;T;T	0.51574	0.7;0.7;0.7	5.51	1.53	0.23141	.	0.815509	0.11476	N	0.560211	T	0.12902	0.0313	N	0.00436	-1.5	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.31166	-0.9953	10	0.11794	T	0.64	0.2002	5.6173	0.17438	0.072:0.2719:0.5253:0.1308	rs61744094	1207	Q5H8C1	FREM1_HUMAN	Q	1208;1207;1207	ENSP00000370263:E1208Q;ENSP00000412940:E1207Q;ENSP00000370262:E1207Q	ENSP00000370257:E1210Q	E	-	1	0	FREM1	14791725	0.011000	0.17503	0.001000	0.08648	0.053000	0.15095	1.753000	0.38359	0.262000	0.21774	-0.340000	0.08031	GAG	C|0.889;G|0.111	0.111	strong		0.512	FREM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339474.2	NM_144966	
JAK1	3716	hgsc.bcm.edu	37	1	65335095	65335095	+	Silent	SNP	T	T	C	rs11585932	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:65335095T>C	ENST00000342505.4	-	6	794	c.546A>G	c.(544-546)ggA>ggG	p.G182G		NM_002227.2	NP_002218.2	P23458	JAK1_HUMAN	Janus kinase 1	182	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				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)	CAATATCATGTCCATCCTGCT	0.522			Mis		ALL								T|||	176	0.0351438	0.0015	0.1297	5008	,	,		20298	0.0069		0.0408	False		,,,				2504	0.0368				p.G182G		Atlas-SNP	.		Dom	yes		1	1p32.3-p31.3	3716	Janus kinase 1		L	.	JAK1	209	.	0			c.A546G						PASS	.	T		48,3982		1,46,1968	139.0	134.0	135.0		546	-3.8	0.9	1	dbSNP_120	135	504,7844		13,478,3683	no	coding-synonymous	JAK1	NM_002227.2		14,524,5651	CC,CT,TT		6.0374,1.1911,4.4595		182/1155	65335095	552,11826	2015	4174	6189	SO:0001819	synonymous_variant	3716	exon6			ATCATGTCCATCC	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.546A>G	1.37:g.65335095T>C		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	106	46	0.433962	NM_002227	Q59GQ2|Q9UD26	Silent	SNP	ENST00000342505.4	37	CCDS41346.1																																																																																			T|0.963;C|0.037	0.037	strong		0.522	JAK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025791.1	NM_002227	
NUP62CL	54830	hgsc.bcm.edu	37	X	106396455	106396455	+	Silent	SNP	A	A	G	rs1285590	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:106396455A>G	ENST00000372466.4	-	7	728	c.477T>C	c.(475-477)cgT>cgC	p.R159R	NUP62CL_ENST00000372461.3_3'UTR	NM_017681.2	NP_060151.2	Q9H1M0	N62CL_HUMAN	nucleoporin 62kDa C-terminal like	159					protein transport (GO:0015031)	nuclear pore (GO:0005643)	structural constituent of nuclear pore (GO:0017056)			lung(4)	4						CACTCTGGTCACGCGTAGACT	0.388													G|||	1811	0.479735	0.6566	0.3199	3775	,	,		14359	0.3333		0.1521	False		,,,				2504	0.2372				p.R159R		Atlas-SNP	.											.	NUP62CL	10	.	0			c.T477C						PASS	.	G		2886,949		925,604,432,103,139	149.0	164.0	159.0		477	-1.8	0.0	X	dbSNP_87	159	1226,5502		66,739,355,1623,1517	no	coding-synonymous	NUP62CL	NM_017681.2		991,1343,787,1726,1656	GG,GA,G,AA,A		18.2224,24.7458,38.9283		159/185	106396455	4112,6451	2203	4300	6503	SO:0001819	synonymous_variant	54830	exon7			CTGGTCACGCGTA	AK000137	CCDS14527.1	Xq22.3	2008-02-05			ENSG00000198088	ENSG00000198088			25960	protein-coding gene	gene with protein product						12477932	Standard	NM_017681		Approved	FLJ20130	uc004ena.3	Q9H1M0	OTTHUMG00000022159	ENST00000372466.4:c.477T>C	X.37:g.106396455A>G		Somatic	349	0	0		WXS	Illumina HiSeq	Phase_I	214	212	0.990654	NM_017681	D3DUX4|Q8WVL6|Q9NXP2	Silent	SNP	ENST00000372466.4	37	CCDS14527.1	738	0.4448462929475588	217	0.7138157894736842	67	0.23591549295774647	137	0.315668202764977	77	0.11290322580645161	G	5.024	0.190194	0.09547	0.752542	0.182224	ENSG00000198088	ENST00000432145	.	.	.	5.44	-1.77	0.07982	.	.	.	.	.	.	.	.	.	.	.	0.32452	P	0.5452330000000001	.	.	.	.	.	.	.	.	.	.	.	.	.	-0.6833	1.1076	0.01698	0.4443:0.1715:0.1106:0.2735	rs1285590;rs56440588;rs1285590	.	.	.	R	91	.	.	X	-	1	0	NUP62CL	106283111	0.824000	0.29247	0.000000	0.03702	0.000000	0.00434	-0.019000	0.12546	-1.064000	0.03172	-4.419000	0.00006	TGA	A|0.553;G|0.447	0.447	strong		0.388	NUP62CL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057828.1	NM_017681	
HSD17B14	51171	hgsc.bcm.edu	37	19	49318380	49318380	+	Missense_Mutation	SNP	G	G	A	rs35299026	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:49318380G>A	ENST00000263278.4	-	6	654	c.388C>T	c.(388-390)Cgg>Tgg	p.R130W	HSD17B14_ENST00000599157.1_Missense_Mutation_p.R106W	NM_016246.2	NP_057330.2	Q9BPX1	DHB14_HUMAN	hydroxysteroid (17-beta) dehydrogenase 14	130			R -> W (in dbSNP:rs35299026).		steroid catabolic process (GO:0006706)	cytosol (GO:0005829)	estradiol 17-beta-dehydrogenase activity (GO:0004303)|testosterone 17-beta-dehydrogenase (NADP+) activity (GO:0047045)			large_intestine(3)|lung(1)|skin(1)	5		all_epithelial(76;7e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000341)|all cancers(93;0.000764)|GBM - Glioblastoma multiforme(486;0.0233)|Epithelial(262;0.0346)		TGACTCTTCCGCAGGTAGGGG	0.587													G|||	79	0.0157748	0.0	0.0245	5008	,	,		18332	0.0		0.0427	False		,,,				2504	0.0194				p.R130W		Atlas-SNP	.											.	HSD17B14	25	.	0			c.C388T						PASS	.	G	TRP/ARG	37,4369	42.3+/-75.8	0,37,2166	98.0	75.0	83.0		388	1.8	1.0	19	dbSNP_126	83	423,8177	131.8+/-189.6	14,395,3891	yes	missense	HSD17B14	NM_016246.2	101	14,432,6057	AA,AG,GG		4.9186,0.8398,3.5368	probably-damaging	130/271	49318380	460,12546	2203	4300	6503	SO:0001583	missense	51171	exon6			TCTTCCGCAGGTA	AF126781	CCDS12736.1	19q13.33	2011-09-14	2006-11-22	2006-11-22		ENSG00000087076		"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"""	23238	protein-coding gene	gene with protein product	"""retinal short-chain dehydrogenase/reductase 3"", ""short chain dehydrogenase/reductase family 47C, member 1"""	612832	"""dehydrogenase/reductase (SDR family) member 10"""	DHRS10		10800688, 17067289, 19027726	Standard	XM_005258969		Approved	retSDR3, SDR47C1	uc002pkv.1	Q9BPX1		ENST00000263278.4:c.388C>T	19.37:g.49318380G>A	ENSP00000263278:p.Arg130Trp	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	36	15	0.416667	NM_016246	Q9UKU3	Missense_Mutation	SNP	ENST00000263278.4	37	CCDS12736.1	41	0.018772893772893772	0	0.0	12	0.03314917127071823	0	0.0	29	0.03825857519788918	G	17.05	3.289263	0.59976	0.008398	0.049186	ENSG00000087076	ENST00000263278	T	0.24538	1.85	4.07	1.83	0.25207	NAD(P)-binding domain (1);	0.000000	0.64402	D	0.000001	T	0.12263	0.0298	M	0.79011	2.435	0.51012	D	0.999902	D	0.89917	1.0	D	0.91635	0.999	T	0.06041	-1.0849	10	0.72032	D	0.01	.	9.9558	0.41666	0.0:0.0:0.4607:0.5393	rs35299026	130	Q9BPX1	DHB14_HUMAN	W	130	ENSP00000263278:R130W	ENSP00000263278:R130W	R	-	1	2	HSD17B14	54010192	0.950000	0.32346	0.988000	0.46212	0.813000	0.45954	1.187000	0.32090	0.448000	0.26722	0.558000	0.71614	CGG	G|0.966;A|0.034	0.034	strong		0.587	HSD17B14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466212.1	NM_016246	
LHB	3972	hgsc.bcm.edu	37	19	49519873	49519873	+	Silent	SNP	G	G	C	rs6521	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:49519873G>C	ENST00000221421.2	-	2	113	c.114C>G	c.(112-114)gtC>gtG	p.V38V	CTB-60B18.10_ENST00000600007.1_lincRNA	NM_000894.2	NP_000885.1	P01229	LSHB_HUMAN	luteinizing hormone beta polypeptide	38					cell-cell signaling (GO:0007267)|cellular protein metabolic process (GO:0044267)|male gonad development (GO:0008584)|peptide hormone processing (GO:0016486)|progesterone biosynthetic process (GO:0006701)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	receptor binding (GO:0005102)			cervix(1)|endometrium(1)|large_intestine(1)|lung(4)|prostate(1)	8		all_epithelial(76;9.62e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		all cancers(93;0.000371)|OV - Ovarian serous cystadenocarcinoma(262;0.000503)|GBM - Glioblastoma multiforme(486;0.00518)|Epithelial(262;0.0427)		CCTCCTTCTCGACAGCCAGGA	0.657													G|||	2469	0.493011	0.4569	0.6081	5008	,	,		16514	0.3343		0.5835	False		,,,				2504	0.5307				p.V38V		Atlas-SNP	.											.	LHB	20	.	0			c.C114G						PASS	.	G		1945,2461		480,985,738	85.0	70.0	75.0		114	-8.4	0.0	19	dbSNP_52	75	4650,3950		1377,1896,1027	no	coding-synonymous	LHB	NM_000894.2		1857,2881,1765	CC,CG,GG		45.9302,44.1443,49.2926		38/142	49519873	6595,6411	2203	4300	6503	SO:0001819	synonymous_variant	3972	exon2			CTTCTCGACAGCC		CCDS12748.1	19q13.3	2013-02-26				ENSG00000104826		"""Endogenous ligands"""	6584	protein-coding gene	gene with protein product	"""lutropin, beta chain"", ""interstitial cell stimulating hormone, beta chain"", ""luteinizing hormone beta subunit"""	152780				1191677	Standard	NM_000894		Approved	LSH-B, CGB4, hLHB	uc002plt.3	P01229		ENST00000221421.2:c.114C>G	19.37:g.49519873G>C		Somatic	362	0	0		WXS	Illumina HiSeq	Phase_I	253	34	0.134387	NM_000894	Q9UDI0	Silent	SNP	ENST00000221421.2	37	CCDS12748.1																																																																																			.	.	weak		0.657	LHB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466246.1	NM_000894	
CDON	50937	hgsc.bcm.edu	37	11	125851055	125851055	+	Silent	SNP	A	A	G	rs564214	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:125851055A>G	ENST00000392693.3	-	17	3292	c.3165T>C	c.(3163-3165)aaT>aaC	p.N1055N	CDON_ENST00000531738.1_Silent_p.N432N|CDON_ENST00000263577.7_Silent_p.N1055N	NM_001243597.1|NM_016952.4	NP_001230526.1|NP_058648.4	Q4KMG0	CDON_HUMAN	cell adhesion associated, oncogene regulated	1055					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)		CATTGACTGCATTGGGGACCT	0.493													G|||	1343	0.268171	0.497	0.2161	5008	,	,		18390	0.0665		0.2604	False		,,,				2504	0.2117				p.N1055N		Atlas-SNP	.											CDON,brain,glioma,0,1	CDON	137	1	0			c.T3165C						scavenged	.	G		2016,2386	613.5+/-392.2	466,1084,651	103.0	94.0	97.0		3165	-4.4	0.0	11	dbSNP_83	97	2326,6272	703.7+/-405.4	318,1690,2291	no	coding-synonymous	CDON	NM_016952.4		784,2774,2942	GG,GA,AA		27.0528,45.7974,33.4		1055/1265	125851055	4342,8658	2201	4299	6500	SO:0001819	synonymous_variant	50937	exon17			GACTGCATTGGGG	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.3165T>C	11.37:g.125851055A>G		Somatic	141	1	0.0070922		WXS	Illumina HiSeq	Phase_I	109	18	0.165138	NM_016952	O14631	Silent	SNP	ENST00000392693.3	37	CCDS58192.1																																																																																			A|0.698;G|0.302	0.302	strong		0.493	CDON-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386749.2	NM_016952	
LAMA3	3909	hgsc.bcm.edu	37	18	21437931	21437931	+	Silent	SNP	G	G	C	rs867449	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:21437931G>C	ENST00000313654.9	+	33	4501	c.4260G>C	c.(4258-4260)ggG>ggC	p.G1420G	LAMA3_ENST00000399516.3_Silent_p.G1420G	NM_198129.1	NP_937762.1	Q16787	LAMA3_HUMAN	laminin, alpha 3	1420	Domain III B.|Laminin EGF-like 12. {ECO:0000255|PROSITE-ProRule:PRU00460}.				cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-5 complex (GO:0005610)	structural molecule activity (GO:0005198)			NS(2)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(24)|lung(54)|ovary(8)|prostate(6)|skin(7)|urinary_tract(4)	128	all_cancers(21;7.81e-05)|all_epithelial(16;4.45e-07)|Lung NSC(20;0.00156)|all_lung(20;0.00508)|Colorectal(14;0.0202)|Ovarian(20;0.17)					GTGACCCAGGGACCGGGGCTT	0.537													G|||	1721	0.34365	0.202	0.415	5008	,	,		19662	0.1736		0.6123	False		,,,				2504	0.3834				p.G1420G		Atlas-SNP	.											.	LAMA3	397	.	0			c.G4260C						PASS	.	G	,	1217,2857		199,819,1019	101.0	101.0	101.0		4260,4260	1.5	0.0	18	dbSNP_86	101	5218,3148		1633,1952,598	no	coding-synonymous,coding-synonymous	LAMA3	NM_001127717.1,NM_198129.1	,	1832,2771,1617	CC,CG,GG		37.6285,29.8724,48.2717	,	1420/3278,1420/3334	21437931	6435,6005	2037	4183	6220	SO:0001819	synonymous_variant	3909	exon33			CCCAGGGACCGGG	L34155	CCDS11880.1, CCDS42419.1, CCDS45838.1, CCDS59307.1	18q11.2	2013-03-01	2002-08-29		ENSG00000053747	ENSG00000053747		"""Laminins"""	6483	protein-coding gene	gene with protein product		600805	"""laminin, alpha 3 (nicein (150kD), kalinin (165kD), BM600 (150kD), epilegrin)"""	LAMNA		8077230	Standard	NM_000227		Approved	nicein-150kDa, kalinin-165kDa, BM600-150kDa, epiligrin	uc002kuq.3	Q16787	OTTHUMG00000131874	ENST00000313654.9:c.4260G>C	18.37:g.21437931G>C		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	91	41	0.450549	NM_001127717	B0YJ33|Q13679|Q13680|Q6VU67|Q6VU68|Q6VU69|Q76E14|Q96TG0	Silent	SNP	ENST00000313654.9	37	CCDS42419.1																																																																																			G|0.488;C|0.512	0.512	strong		0.537	LAMA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254824.3	NM_000227, NM_198129	
PALLD	23022	hgsc.bcm.edu	37	4	169433333	169433333	+	Silent	SNP	C	C	T	rs7673220	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:169433333C>T	ENST00000505667.1	+	2	851	c.678C>T	c.(676-678)gaC>gaT	p.D226D	PALLD_ENST00000261509.6_Silent_p.D226D|PALLD_ENST00000335742.7_5'UTR|PALLD_ENST00000333488.4_Silent_p.D103D			Q8WX93	PALLD_HUMAN	palladin, cytoskeletal associated protein	226					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)		CTATGGAAGACCAAGGGGAGA	0.582									Pancreatic Cancer, Familial Clustering of				C|||	1200	0.239617	0.2368	0.1844	5008	,	,		17119	0.1935		0.33	False		,,,				2504	0.2372				p.D226D	Esophageal Squamous(109;1482 1532 18347 40239 51172)	Atlas-SNP	.											.	PALLD	179	.	0			c.C678T						PASS	.	C	,	1117,3289	398.5+/-330.9	151,815,1237	101.0	104.0	103.0		678,678	-5.9	0.0	4	dbSNP_116	103	2811,5789	444.9+/-360.8	461,1889,1950	no	coding-synonymous,coding-synonymous	PALLD	NM_001166108.1,NM_016081.3	,	612,2704,3187	TT,TC,CC		32.686,25.3518,30.2014	,	226/1124,226/1107	169433333	3928,9078	2203	4300	6503	SO:0001819	synonymous_variant	23022	exon2	Familial Cancer Database	incl.: Hereditary Pancreatic Adenocarcinoma, Insulin-Dependent Diabetes Mellitus - Exocrine Insufficiency - Familial Pancreatic Cancer, PNCA1	GGAAGACCAAGGG	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.678C>T	4.37:g.169433333C>T		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	60	60	1	NM_001166108	B3KTG2|B5MD56|B7ZMM5|Q7L3E0|Q7Z3W0|Q86WE8|Q8N1M2|Q9UGA0|Q9UQF5|Q9Y2J6|Q9Y3E9	Silent	SNP	ENST00000505667.1	37	CCDS54818.1																																																																																			C|0.724;T|0.276	0.276	strong		0.582	PALLD-002	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000363762.1	NM_016081	
EXO5	64789	hgsc.bcm.edu	37	1	40980731	40980731	+	Missense_Mutation	SNP	G	G	T	rs11208299	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:40980731G>T	ENST00000372703.1	+	2	1589	c.515G>T	c.(514-516)gGg>gTg	p.G172V	EXO5_ENST00000358527.2_Missense_Mutation_p.G172V|RP11-656D10.6_ENST00000437060.1_RNA|RP11-656D10.5_ENST00000453437.1_RNA|EXO5_ENST00000296380.4_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	137	0	0		WXS	Illumina HiSeq	Phase_I	87	87	1	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	
SMEK1	55671	hgsc.bcm.edu	37	14	91948043	91948043	+	Silent	SNP	T	T	C	rs17127374	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:91948043T>C	ENST00000554943.1	-	4	907	c.792A>G	c.(790-792)acA>acG	p.T264T	SMEK1_ENST00000554684.1_Silent_p.T264T|SMEK1_ENST00000555462.1_Intron|SMEK1_ENST00000428424.2_Intron|SMEK1_ENST00000337238.4_Silent_p.T264T			Q6IN85	P4R3A_HUMAN	SMEK homolog 1, suppressor of mek1 (Dictyostelium)	264					positive regulation of gluconeogenesis (GO:0045722)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)|protein phosphatase 4 complex (GO:0030289)				NS(1)|endometrium(1)|kidney(1)|liver(1)|lung(1)|stomach(1)	6		all_cancers(154;0.0691)|all_epithelial(191;0.219)		COAD - Colon adenocarcinoma(157;0.221)		GAACTCTGTATGTCTGATGAA	0.348													T|||	233	0.0465256	0.0204	0.0605	5008	,	,		17946	0.003		0.1163	False		,,,				2504	0.045				p.T264T		Atlas-SNP	.											.	SMEK1	94	.	0			c.A792G						PASS	.	T		163,4243	109.5+/-147.8	6,151,2046	158.0	147.0	151.0		792	-2.8	1.0	14	dbSNP_123	151	896,7704	199.7+/-243.7	53,790,3457	yes	coding-synonymous	SMEK1	NM_032560.4		59,941,5503	CC,CT,TT		10.4186,3.6995,8.1424		264/821	91948043	1059,11947	2203	4300	6503	SO:0001819	synonymous_variant	55671	exon5			TCTGTATGTCTGA	AK000714	CCDS9895.1, CCDS61532.1	14q32.12	2008-09-15	2006-10-12	2006-10-12		ENSG00000100796			20219	protein-coding gene	gene with protein product		610351	"""KIAA2010"""	KIAA2010		16085932, 18487071	Standard	XM_005267842		Approved	FLJ20707, MSTP033, FLFL1, smk-1, smk1	uc001xzm.3	Q6IN85		ENST00000554943.1:c.792A>G	14.37:g.91948043T>C		Somatic	360	0	0		WXS	Illumina HiSeq	Phase_I	266	127	0.477444	NM_032560	Q69YK6|Q86U23|Q86YI7|Q8IVG1|Q9H3F1|Q9H7U8|Q9NV01|Q9NWP1	Silent	SNP	ENST00000554943.1	37		113	0.051739926739926737	10	0.02032520325203252	24	0.06629834254143646	3	0.005244755244755245	76	0.10026385224274406	T	8.401	0.841920	0.16963	0.036995	0.104186	ENSG00000100796	ENST00000555470	.	.	.	6.03	-2.82	0.05787	.	.	.	.	.	T	0.01124	0.0037	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.18840	-1.0324	4	.	.	.	-14.8432	1.3143	0.02104	0.1967:0.2318:0.1018:0.4697	rs17127374;rs52791686;rs59536884;rs17127374	.	.	.	V	59	.	.	I	-	1	0	SMEK1	91017796	0.980000	0.34600	0.992000	0.48379	0.977000	0.68977	0.101000	0.15251	-0.337000	0.08426	-0.313000	0.08912	ATA	T|0.932;C|0.068	0.068	strong		0.348	SMEK1-007	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000411665.1	NM_032560	
SPEG	10290	hgsc.bcm.edu	37	2	220353532	220353532	+	Missense_Mutation	SNP	C	C	A	rs13026308	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:220353532C>A	ENST00000312358.7	+	34	8191	c.8059C>A	c.(8059-8061)Ccc>Acc	p.P2687T	AC053503.11_ENST00000429882.1_RNA|SPEG_ENST00000485813.1_3'UTR	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	221	0	0		WXS	Illumina HiSeq	Phase_I	193	104	0.53886	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	
DUSP27	92235	hgsc.bcm.edu	37	1	167095163	167095163	+	Missense_Mutation	SNP	G	G	C	rs267745	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:167095163G>C	ENST00000361200.2	+	6	961	c.795G>C	c.(793-795)gaG>gaC	p.E265D	DUSP27_ENST00000443333.1_Missense_Mutation_p.E265D|DUSP27_ENST00000485151.1_3'UTR|DUSP27_ENST00000271385.5_Missense_Mutation_p.E265D			Q5VZP5	DUS27_HUMAN	dual specificity phosphatase 27 (putative)	265			E -> D (in dbSNP:rs267745). {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						ACCCCAATGAGGGCTTCCTGA	0.587													C|||	3215	0.641973	0.888	0.4597	5008	,	,		19822	0.872		0.4751	False		,,,				2504	0.3732				p.E265D		Atlas-SNP	.											.	DUSP27	235	.	0			c.G795C						PASS	.	C	ASP/GLU	3677,729	302.1+/-287.2	1536,605,62	77.0	76.0	76.0		795	-4.6	0.8	1	dbSNP_79	76	4153,4447	588.8+/-392.4	1003,2147,1150	yes	missense	DUSP27	NM_001080426.1	45	2539,2752,1212	CC,CG,GG		48.2907,16.5456,39.797	benign	265/1159	167095163	7830,5176	2203	4300	6503	SO:0001583	missense	92235	exon5			CAATGAGGGCTTC	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.795G>C	1.37:g.167095163G>C	ENSP00000354483:p.Glu265Asp	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	71	37	0.521127	NM_001080426	A0AUM4|Q9C074	Missense_Mutation	SNP	ENST00000361200.2	37	CCDS30932.1	1439	0.6588827838827839	417	0.8475609756097561	181	0.5	508	0.8881118881118881	333	0.4393139841688654	C	2.612	-0.290557	0.05568	0.834544	0.482907	ENSG00000198842	ENST00000361200;ENST00000271385;ENST00000443333	D;D;D	0.85484	-1.99;-1.99;-1.99	5.55	-4.59	0.03400	Dual specificity phosphatase, catalytic domain (1);Dual specificity phosphatase, subgroup, catalytic domain (2);	0.312145	0.34802	N	0.003677	T	0.30386	0.0763	N	0.04787	-0.16	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.34428	-0.9829	9	0.02654	T	1	-28.9626	2.8034	0.05421	0.1828:0.2921:0.0838:0.4413	rs267745;rs12734908;rs52812145;rs61430367;rs267745	265	Q5VZP5	DUS27_HUMAN	D	265	ENSP00000354483:E265D;ENSP00000271385:E265D;ENSP00000404874:E265D	ENSP00000271385:E265D	E	+	3	2	DUSP27	165361787	0.000000	0.05858	0.815000	0.32552	0.967000	0.64934	-2.213000	0.01224	-0.793000	0.04475	-0.756000	0.03474	GAG	G|0.373;C|0.627	0.627	strong		0.587	DUSP27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083244.1	NM_001080426	
MAPKAPK2	9261	hgsc.bcm.edu	37	1	206905043	206905043	+	Silent	SNP	C	C	T	rs4073250	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:206905043C>T	ENST00000367103.3	+	8	1144	c.951C>T	c.(949-951)acC>acT	p.T317T	MAPKAPK2_ENST00000479009.1_3'UTR|MAPKAPK2_ENST00000294981.4_Silent_p.T317T	NM_004759.4|NM_032960.3	NP_004750.1|NP_116584.2	P49137	MAPK2_HUMAN	mitogen-activated protein kinase-activated protein kinase 2	317	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				3'-UTR-mediated mRNA stabilization (GO:0070935)|activation of MAPK activity (GO:0000187)|arachidonic acid metabolic process (GO:0019369)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|G2 DNA damage checkpoint (GO:0031572)|gene expression (GO:0010467)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|inner ear development (GO:0048839)|leukotriene metabolic process (GO:0006691)|macropinocytosis (GO:0044351)|MAPK cascade (GO:0000165)|mRNA metabolic process (GO:0016071)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|protein phosphorylation (GO:0006468)|Ras protein signal transduction (GO:0007265)|regulation of interleukin-6 production (GO:0032675)|regulation of tumor necrosis factor production (GO:0032680)|response to cytokine (GO:0034097)|response to lipopolysaccharide (GO:0032496)|response to stress (GO:0006950)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|signal transducer activity (GO:0004871)			central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(8)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	19	Breast(84;0.183)		BRCA - Breast invasive adenocarcinoma(75;0.211)			TGACCATCACCGAGTTTATGA	0.562													C|||	979	0.195487	0.1838	0.1729	5008	,	,		18715	0.0526		0.2137	False		,,,				2504	0.3558				p.T317T		Atlas-SNP	.											.	MAPKAPK2	45	.	0			c.C951T						PASS	.	C	,	847,3559	334.9+/-303.7	95,657,1451	132.0	131.0	131.0		951,951	-10.2	0.0	1	dbSNP_108	131	1652,6948	305.2+/-307.3	168,1316,2816	no	coding-synonymous,coding-synonymous	MAPKAPK2	NM_004759.4,NM_032960.3	,	263,1973,4267	TT,TC,CC		19.2093,19.2238,19.2142	,	317/371,317/401	206905043	2499,10507	2203	4300	6503	SO:0001819	synonymous_variant	9261	exon8			CATCACCGAGTTT	U12779	CCDS1466.1, CCDS31001.1	1q32	2008-02-05			ENSG00000162889	ENSG00000162889			6887	protein-coding gene	gene with protein product		602006				8179591, 8280084	Standard	NM_004759		Approved		uc001hem.2	P49137	OTTHUMG00000036342	ENST00000367103.3:c.951C>T	1.37:g.206905043C>T		Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	152	80	0.526316	NM_004759	Q5SY30|Q5SY41|Q8IYD6	Silent	SNP	ENST00000367103.3	37	CCDS31001.1																																																																																			C|0.820;T|0.180	0.180	strong		0.562	MAPKAPK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088465.1	NM_004759	
ZNF695	57116	hgsc.bcm.edu	37	1	247151035	247151035	+	Missense_Mutation	SNP	T	T	G	rs2642993	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:247151035T>G	ENST00000339986.7	-	4	929	c.782A>C	c.(781-783)aAt>aCt	p.N261T	ZNF695_ENST00000487338.2_Intron|ZNF695_ENST00000498046.2_Intron	NM_020394.4	NP_065127	Q8IW36	ZN695_HUMAN	zinc finger protein 695	261					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			endometrium(1)|large_intestine(1)|lung(9)|prostate(1)|urinary_tract(1)	13	all_cancers(71;4.01e-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)			TTCAGTATGATTTTTCTCAAC	0.333													T|||	432	0.086262	0.1853	0.0274	5008	,	,		20980	0.0169		0.0378	False		,,,				2504	0.1155				p.N261T		Atlas-SNP	.											.	ZNF695	55	.	0			c.A782C						PASS	.	T	,THR/ASN	650,3438		53,544,1447	48.0	49.0	49.0		,782	-1.3	0.0	1	dbSNP_100	49	350,8108		4,342,3883	yes	intron,missense	ZNF695	NM_001204221.1,NM_020394.4	,65	57,886,5330	GG,GT,TT		4.1381,15.9002,7.9707	,benign	,261/516	247151035	1000,11546	2044	4229	6273	SO:0001583	missense	57116	exon4			GTATGATTTTTCT		CCDS44344.1, CCDS55694.1	1q44	2013-01-08			ENSG00000197472	ENSG00000197472		"""Zinc fingers, C2H2-type"", ""-"""	30954	protein-coding gene	gene with protein product						12477932	Standard	NM_020394		Approved	SBZF3	uc009xgu.3	Q8IW36	OTTHUMG00000040707	ENST00000339986.7:c.782A>C	1.37:g.247151035T>G	ENSP00000341236:p.Asn261Thr	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	128	63	0.492188	NM_020394	Q5T0N9|Q5T0P1|Q5T0P3|Q7Z2W8|Q7Z648	Missense_Mutation	SNP	ENST00000339986.7	37	CCDS44344.1	124	0.056776556776556776	78	0.15853658536585366	9	0.024861878453038673	10	0.017482517482517484	27	0.03562005277044855	T	0.990	-0.694439	0.03303	0.159002	0.041381	ENSG00000197472	ENST00000339986	T	0.12774	2.65	0.642	-1.28	0.09318	Zinc finger, C2H2 (1);	.	.	.	.	T	0.00012	0.0000	N	0.01219	-0.95	0.53688	P	2.1000000000048757E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.40720	-0.9548	8	0.52906	T	0.07	.	2.3094	0.04183	0.3798:0.0:0.1929:0.4273	rs2642993;rs3805090;rs16848864;rs52792655;rs59348183;rs2642993	261	Q8IW36	ZN695_HUMAN	T	261	ENSP00000341236:N261T	ENSP00000341236:N261T	N	-	2	0	ZNF695	245217658	0.000000	0.05858	0.002000	0.10522	0.162000	0.22319	-3.420000	0.00477	-2.353000	0.00615	-1.285000	0.01374	AAT	T|0.936;G|0.064	0.064	strong		0.333	ZNF695-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097823.5	NM_020394	
ACAN	176	hgsc.bcm.edu	37	15	89401615	89401615	+	Silent	SNP	T	T	G	rs3825994	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:89401615T>G	ENST00000561243.1	+	11	5799	c.5799T>G	c.(5797-5799)acT>acG	p.T1933T	ACAN_ENST00000439576.2_Silent_p.T1933T|ACAN_ENST00000559004.1_Silent_p.T1933T|ACAN_ENST00000352105.7_Silent_p.T1933T			P16112	PGCA_HUMAN	aggrecan	1918	CS-2.				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|proteolysis (GO:0006508)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)	carbohydrate binding (GO:0030246)|extracellular matrix structural constituent (GO:0005201)|hyaluronic acid binding (GO:0005540)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(4)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(15)|liver(2)|lung(40)|ovary(2)|prostate(5)|skin(5)|stomach(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	93	Lung NSC(78;0.0392)|all_lung(78;0.077)		BRCA - Breast invasive adenocarcinoma(143;0.146)			GTTTCCCCACTGTCTCTCTTG	0.527													T|||	2667	0.532548	0.3593	0.5879	5008	,	,		18110	0.5427		0.7326	False		,,,				2504	0.5112				p.T1933T		Atlas-SNP	.											.	ACAN	220	.	0			c.T5799G						PASS	.	T	,	1689,2171		365,959,606	54.0	56.0	55.0		5799,5799	-9.8	0.0	15	dbSNP_107	55	6159,2095		2301,1557,269	no	coding-synonymous,coding-synonymous	ACAN	NM_001135.3,NM_013227.3	,	2666,2516,875	GG,GT,TT		25.3816,43.7565,35.2155	,	1933/2432,1933/2531	89401615	7848,4266	1930	4127	6057	SO:0001819	synonymous_variant	176	exon12			CCCCACTGTCTCT	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.5799T>G	15.37:g.89401615T>G		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	148	147	0.993243	NM_001135	Q13650|Q9UCD3|Q9UCP4|Q9UCP5|Q9UDE0	Silent	SNP	ENST00000561243.1	37	CCDS53970.1																																																																																			T|0.431;G|0.569	0.569	strong		0.527	ACAN-006	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416267.2	NM_001135	
TCN1	6947	hgsc.bcm.edu	37	11	59623433	59623433	+	Silent	SNP	G	G	A	rs1042613	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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						scavenged	.			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	144	2	0.0138889		WXS	Illumina HiSeq	Phase_I	159	117	0.735849	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	
MAN2B2	23324	hgsc.bcm.edu	37	4	6596360	6596360	+	Missense_Mutation	SNP	G	G	A	rs2301795	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:6596360G>A	ENST00000285599.3	+	7	994	c.958G>A	c.(958-960)Gtg>Atg	p.V320M	MAN2B2_ENST00000504248.1_Missense_Mutation_p.V269M	NM_015274.1	NP_056089.1	Q9Y2E5	MA2B2_HUMAN	mannosidase, alpha, class 2B, member 2	320			V -> M (in dbSNP:rs2301795). {ECO:0000269|PubMed:17974005}.		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						CGGTGTCTCGGTGCAGTATGC	0.602													G|||	2281	0.455471	0.4387	0.4755	5008	,	,		20498	0.3879		0.5388	False		,,,				2504	0.4479				p.V320M		Atlas-SNP	.											.	MAN2B2	80	.	0			c.G958A						PASS	.	G	MET/VAL	1930,2476	549.9+/-377.9	431,1068,704	127.0	95.0	106.0		958	2.8	0.0	4	dbSNP_100	106	4455,4145	588.1+/-392.3	1138,2179,983	yes	missense	MAN2B2	NM_015274.1	21	1569,3247,1687	AA,AG,GG		48.1977,43.8039,49.0927	benign	320/1010	6596360	6385,6621	2203	4300	6503	SO:0001583	missense	23324	exon7			GTCTCGGTGCAGT	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.958G>A	4.37:g.6596360G>A	ENSP00000285599:p.Val320Met	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	102	101	0.990196	NM_015274	Q66MP2|Q86T67	Missense_Mutation	SNP	ENST00000285599.3	37	CCDS33951.1	1021	0.4674908424908425	233	0.4735772357723577	169	0.46685082872928174	216	0.3776223776223776	403	0.5316622691292876	G	6.829	0.522162	0.13066	0.438039	0.518023	ENSG00000013288	ENST00000285599;ENST00000504248	T;T	0.76709	-1.04;-1.04	4.52	2.76	0.32466	Glycoside hydrolase/deacetylase, beta/alpha-barrel (1);Glycoside hydrolase, family 38, core (2);	0.350241	0.28927	N	0.013700	T	0.00012	0.0000	L	0.53671	1.685	0.39621	P	0.029962000000000044	B;B;B	0.33299	0.37;0.126;0.407	B;B;B	0.40477	0.33;0.138;0.167	T	0.45833	-0.9234	9	0.40728	T	0.16	-6.2654	8.0974	0.30837	0.0849:0.0:0.7574:0.1577	rs2301795;rs17724940;rs60981402;rs2301795	269;320;320	E9PCD7;Q9Y2E5;Q9Y2E5-2	.;MA2B2_HUMAN;.	M	320;269	ENSP00000285599:V320M;ENSP00000423129:V269M	ENSP00000285599:V320M	V	+	1	0	MAN2B2	6647261	0.998000	0.40836	0.001000	0.08648	0.090000	0.18270	3.562000	0.53777	0.341000	0.23771	0.543000	0.68304	GTG	G|0.522;A|0.478	0.478	strong		0.602	MAN2B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359106.2	NM_015274	
SESN1	27244	hgsc.bcm.edu	37	6	109322554	109322554	+	Silent	SNP	C	C	T	rs12214121	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:109322554C>T	ENST00000356644.7	-	3	400	c.306G>A	c.(304-306)caG>caA	p.Q102Q	SESN1_ENST00000302071.2_Silent_p.Q36Q|SESN1_ENST00000436639.2_Silent_p.Q161Q|RP11-787I22.3_ENST00000605885.1_RNA	NM_001199933.1	NP_001186862.1	Q9Y6P5	SESN1_HUMAN	sestrin 1	102					cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|negative regulation of cell proliferation (GO:0008285)|regulation of protein kinase B signaling (GO:0051896)|regulation of response to reactive oxygen species (GO:1901031)	nucleus (GO:0005634)				cervix(1)|large_intestine(3)|lung(3)|ovary(1)|skin(1)|urinary_tract(1)	10		all_cancers(87;6.45e-05)|Acute lymphoblastic leukemia(125;3.55e-10)|all_hematologic(75;1.68e-07)|all_epithelial(87;0.0106)|Colorectal(196;0.0637)		Epithelial(106;0.0014)|BRCA - Breast invasive adenocarcinoma(108;0.00146)|all cancers(137;0.0031)|OV - Ovarian serous cystadenocarcinoma(136;0.0117)		GTAGATAGTGCTGAGTTTTTA	0.363													T|||	482	0.096246	0.0431	0.0735	5008	,	,		18104	0.0407		0.1352	False		,,,				2504	0.2014				p.Q161Q		Atlas-SNP	.											.	SESN1	29	.	0			c.G483A						PASS	.	T	,,	224,4182	804.7+/-415.8	6,212,1985	84.0	80.0	82.0		306,108,483	0.5	1.0	6	dbSNP_120	82	1005,7593	771.8+/-407.7	72,861,3366	no	coding-synonymous,coding-synonymous,coding-synonymous	SESN1	NM_001199933.1,NM_001199934.1,NM_014454.2	,,	78,1073,5351	TT,TC,CC		11.6888,5.084,9.4509	,,	102/493,36/427,161/552	109322554	1229,11775	2203	4299	6502	SO:0001819	synonymous_variant	27244	exon3			ATAGTGCTGAGTT	AF033120	CCDS5070.1, CCDS56444.1, CCDS56445.1	6q21	2008-10-23			ENSG00000080546	ENSG00000080546			21595	protein-coding gene	gene with protein product		606103				9926927, 7938006	Standard	NM_014454		Approved	SEST1, PA26	uc003psu.3	Q9Y6P5	OTTHUMG00000015338	ENST00000356644.7:c.306G>A	6.37:g.109322554C>T		Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	124	54	0.435484	NM_014454	Q2M2B7|Q5T316|Q9NV00|Q9UPD5|Q9Y6P6	Silent	SNP	ENST00000356644.7	37	CCDS56445.1																																																																																			C|0.915;T|0.085	0.085	strong		0.363	SESN1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000041738.4	NM_014454	
DDIT4L	115265	hgsc.bcm.edu	37	4	101109161	101109161	+	Silent	SNP	G	G	C	rs3749604	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:101109161G>C	ENST00000273990.2	-	3	469	c.255C>G	c.(253-255)acC>acG	p.T85T	RP11-588P8.1_ENST00000515782.1_RNA|RP11-15B17.1_ENST00000515026.1_RNA	NM_145244.3	NP_660287.1	Q96D03	DDT4L_HUMAN	DNA-damage-inducible transcript 4-like	85					negative regulation of signal transduction (GO:0009968)	cytoplasm (GO:0005737)				breast(2)|endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|pancreas(2)	12				OV - Ovarian serous cystadenocarcinoma(123;5.75e-09)		CAATTCTCTGGGTCAGTTTCT	0.453													G|||	631	0.125998	0.1626	0.1254	5008	,	,		19326	0.006		0.2316	False		,,,				2504	0.092				p.T85T		Atlas-SNP	.											DDIT4L,NS,carcinoma,-1,1	DDIT4L	33	1	0			c.C255G						PASS	.	G		785,3621	316.1+/-294.4	60,665,1478	139.0	133.0	135.0		255	2.9	1.0	4	dbSNP_107	135	1940,6660	342.1+/-324.3	215,1510,2575	no	coding-synonymous	DDIT4L	NM_145244.3		275,2175,4053	CC,CG,GG		22.5581,17.8166,20.9519		85/194	101109161	2725,10281	2203	4300	6503	SO:0001819	synonymous_variant	115265	exon3			TCTCTGGGTCAGT	BC013592	CCDS34036.1	4q23	2008-02-05				ENSG00000145358			30555	protein-coding gene	gene with protein product	"""regulated in development and DNA damage response 2"", "" similar to Smhs1 protein"""	607730				12477932	Standard	NM_145244		Approved	REDD2, Rtp801L	uc003hvq.3	Q96D03		ENST00000273990.2:c.255C>G	4.37:g.101109161G>C		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	76	32	0.421053	NM_145244	B2R7C3	Silent	SNP	ENST00000273990.2	37	CCDS34036.1																																																																																			G|0.813;C|0.187	0.187	strong		0.453	DDIT4L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363423.1	NM_145244	
ZNF516	9658	hgsc.bcm.edu	37	18	74155000	74155000	+	Missense_Mutation	SNP	T	T	C	rs3752097	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:74155000T>C	ENST00000443185.2	-	3	328	c.11A>G	c.(10-12)aAc>aGc	p.N4S	ZNF516_ENST00000524431.2_5'UTR	NM_014643.3	NP_055458.1	Q92618	ZN516_HUMAN	zinc finger protein 516	4			N -> S (in dbSNP:rs3752097).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(7)|lung(11)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	32		Prostate(75;0.0869)|Esophageal squamous(42;0.129)		OV - Ovarian serous cystadenocarcinoma(15;7.64e-06)|BRCA - Breast invasive adenocarcinoma(31;0.238)		GGCCTCTCTGTTGCGATCCAT	0.692													C|||	412	0.0822684	0.2126	0.0519	5008	,	,		14071	0.0109		0.0328	False		,,,				2504	0.0521				p.N4S		Atlas-SNP	.											.	ZNF516	102	.	0			c.A11G						PASS	.	C	SER/ASN	701,3263		63,575,1344	11.0	14.0	13.0		11	-9.5	0.0	18	dbSNP_107	13	245,8041		5,235,3903	yes	missense	ZNF516	NM_014643.3	46	68,810,5247	CC,CT,TT		2.9568,17.6842,7.7224	benign	4/1164	74155000	946,11304	1982	4143	6125	SO:0001583	missense	9658	exon3			TCTCTGTTGCGAT	D86975	CCDS74234.1	18q23	2013-01-08				ENSG00000101493		"""Zinc fingers, C2H2-type"""	28990	protein-coding gene	gene with protein product		615114				9039502	Standard	NM_014643		Approved	HsT287, KIAA0222	uc021ulp.1	Q92618		ENST00000443185.2:c.11A>G	18.37:g.74155000T>C	ENSP00000394757:p.Asn4Ser	Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	14	14	1	NM_014643		Missense_Mutation	SNP	ENST00000443185.2	37		151	0.06913919413919414	105	0.21341463414634146	18	0.049723756906077346	6	0.01048951048951049	22	0.029023746701846966	C	0.033	-1.325070	0.01309	0.176842	0.029568	ENSG00000101493	ENST00000443185;ENST00000532857	T;T	0.08458	3.09;3.26	4.75	-9.5	0.00584	.	1.121590	0.06659	N	0.764104	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.06786	0.001	B	0.04013	0.001	T	0.37753	-0.9692	8	0.07482	T	0.82	.	10.9167	0.47139	0.0:0.2924:0.2547:0.4529	rs3752097;rs3752097	4	Q92618	ZN516_HUMAN	S	4	ENSP00000394757:N4S;ENSP00000446211:N4S	ENSP00000394757:N4S	N	-	2	0	ZNF516	72283988	0.000000	0.05858	0.003000	0.11579	0.680000	0.39746	-4.956000	0.00166	-3.651000	0.00126	-2.400000	0.00224	AAC	T|0.920;C|0.080	0.080	strong		0.692	ZNF516-201	KNOWN	basic|appris_principal|exp_conf	protein_coding	protein_coding		NM_014643	
MMS19	64210	hgsc.bcm.edu	37	10	99219885	99219885	+	Silent	SNP	G	G	A	rs2152092	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:99219885G>A	ENST00000438925.2	-	26	2909	c.2574C>T	c.(2572-2574)gcC>gcT	p.A858A	MMS19_ENST00000327277.7_3'UTR|MMS19_ENST00000327238.10_Silent_p.A760A|MMS19_ENST00000355839.6_Silent_p.A815A|MMS19_ENST00000370782.2_Silent_p.A858A	NM_022362.4	NP_071757.4	Q96T76	MMS19_HUMAN	MMS19 nucleotide excision repair homolog (S. cerevisiae)	858					cellular response to DNA damage stimulus (GO:0006974)|chromosome segregation (GO:0007059)|DNA metabolic process (GO:0006259)|DNA repair (GO:0006281)|iron-sulfur cluster assembly (GO:0016226)|nucleotide-excision repair (GO:0006289)|phosphorelay signal transduction system (GO:0000160)|positive regulation of transcription, DNA-templated (GO:0045893)|response to hormone (GO:0009725)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	CIA complex (GO:0097361)|cytoplasm (GO:0005737)|holo TFIIH complex (GO:0005675)|membrane (GO:0016020)|MMXD complex (GO:0071817)|nucleus (GO:0005634)|spindle (GO:0005819)	estrogen receptor binding (GO:0030331)|protein binding, bridging (GO:0030674)|receptor signaling complex scaffold activity (GO:0030159)|transcription coactivator activity (GO:0003713)			endometrium(1)|kidney(2)|large_intestine(5)|lung(6)|prostate(1)|stomach(1)	16		Colorectal(252;0.0846)		Epithelial(162;3.33e-10)|all cancers(201;2.74e-08)		TCCGCACTTCGGCATGGCCAG	0.557								Direct reversal of damage					A|||	2630	0.52516	0.4153	0.5548	5008	,	,		20335	0.5863		0.5189	False		,,,				2504	0.5961				p.A858A		Atlas-SNP	.											.	MMS19	36	.	0			c.C2574T						PASS	.	A		1862,2544	633.2+/-396.0	397,1068,738	96.0	83.0	87.0		2574	-6.0	0.9	10	dbSNP_96	87	4675,3925	548.7+/-385.4	1252,2171,877	yes	coding-synonymous	MMS19	NM_022362.4		1649,3239,1615	AA,AG,GG		45.6395,42.2606,49.7386		858/1031	99219885	6537,6469	2203	4300	6503	SO:0001819	synonymous_variant	64210	exon26			CACTTCGGCATGG	AF007151	CCDS7464.1, CCDS73177.1	10q24-q25	2007-08-15	2007-08-15	2007-08-15	ENSG00000155229	ENSG00000155229			13824	protein-coding gene	gene with protein product	"""MET18 homolog (S. cerevisiae)"""	614777		MMS19L		11071939	Standard	NM_022362		Approved	MET18, hMMS19	uc001kns.4	Q96T76	OTTHUMG00000018857	ENST00000438925.2:c.2574C>T	10.37:g.99219885G>A		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	128	127	0.992188	NM_022362	B0QZ75|B3KPE5|B4DQX2|B4E2I3|D3DR55|F8W9Y2|Q17RZ8|Q5T455|Q66K82|Q7L4W8|Q969Z1|Q96DF1|Q96MR1|Q96RK5|Q96SK1|Q9BUE2|Q9BYS9	Silent	SNP	ENST00000438925.2	37	CCDS7464.1	1116	0.510989010989011	200	0.4065040650406504	187	0.5165745856353591	338	0.5909090909090909	391	0.5158311345646438	A	8.185	0.794666	0.16327	0.422606	0.543605	ENSG00000155229	ENST00000434538	.	.	.	5.65	-5.96	0.02234	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999998	.	.	.	.	.	.	T	0.46317	-0.9200	3	.	.	.	.	2.905	0.05718	0.2198:0.0843:0.3664:0.3294	rs2152092;rs17415339;rs59059271;rs2152092	.	.	.	L	433	.	.	P	-	2	0	MMS19	99209875	0.014000	0.17966	0.905000	0.35620	0.912000	0.54170	-0.942000	0.03921	-0.885000	0.03971	-1.177000	0.01723	CCG	G|0.506;A|0.494	0.494	strong		0.557	MMS19-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049706.2		
ZFHX3	463	hgsc.bcm.edu	37	16	72993397	72993397	+	Silent	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:72993397C>T	ENST00000268489.5	-	2	1320	c.648G>A	c.(646-648)ccG>ccA	p.P216P	ZFHX3_ENST00000397992.5_Intron	NM_006885.3	NP_008816.3	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3	216					brain development (GO:0007420)|cell cycle arrest (GO:0007050)|muscle organ development (GO:0007517)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of myoblast differentiation (GO:0045663)|regulation of neuron differentiation (GO:0045664)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	enzyme binding (GO:0019899)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			NS(3)|breast(7)|cervix(2)|endometrium(18)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(22)|liver(1)|lung(46)|ovary(5)|pancreas(1)|prostate(15)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(11)	153		Ovarian(137;0.13)				CTGAGGTATTCGGGAAAGCCT	0.572																																					p.P216P		Atlas-SNP	.											.	ZFHX3	404	.	0			c.G648A						PASS	.						85.0	86.0	85.0					16																	72993397		2198	4300	6498	SO:0001819	synonymous_variant	463	exon2			GGTATTCGGGAAA	D10250	CCDS10908.1, CCDS54035.1	16q22.3	2012-03-09	2007-08-09	2007-08-09	ENSG00000140836	ENSG00000140836		"""Zinc fingers, C2H2-type"", ""Homeoboxes / ZF class"""	777	protein-coding gene	gene with protein product		104155	"""AT-binding transcription factor 1"""	ATBF1		1719379, 7592926	Standard	NM_006885		Approved	ZNF927	uc002fck.3	Q15911	OTTHUMG00000137599	ENST00000268489.5:c.648G>A	16.37:g.72993397C>T		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	100	38	0.38	NM_006885	D3DWS8|O15101|Q13719	Silent	SNP	ENST00000268489.5	37	CCDS10908.1																																																																																			.	.	none		0.572	ZFHX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269008.1	NM_006885	
C1S	716	hgsc.bcm.edu	37	12	7175762	7175762	+	Missense_Mutation	SNP	G	G	C	rs150549869		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:7175762G>C	ENST00000406697.1	+	14	1826	c.1198G>C	c.(1198-1200)Gag>Cag	p.E400Q	C1S_ENST00000495061.1_3'UTR|C1S_ENST00000360817.5_Missense_Mutation_p.E400Q|C1S_ENST00000402681.3_Missense_Mutation_p.E233Q|C1S_ENST00000328916.3_Missense_Mutation_p.E400Q			P09871	C1S_HUMAN	complement component 1, s subcomponent	400	Sushi 2. {ECO:0000255|PROSITE- ProRule:PRU00302}.				complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|innate immune response (GO:0045087)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|serine-type endopeptidase activity (GO:0004252)			breast(1)|endometrium(5)|kidney(2)|large_intestine(8)|liver(4)|lung(8)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	33					Abciximab(DB00054)|Adalimumab(DB00051)|Basiliximab(DB00074)|Cetuximab(DB00002)|Etanercept(DB00005)|Gemtuzumab ozogamicin(DB00056)|Ibritumomab(DB00078)|Muromonab(DB00075)|Rituximab(DB00073)|Trastuzumab(DB00072)	TATTCCAGGGGAGTATCACTG	0.587																																					p.E400Q	GBM(156;750 1943 12971 24779 31015)	Atlas-SNP	.											.	C1S	93	.	0			c.G1198C						PASS	.	G	GLN/GLU,GLN/GLU	0,4406		0,0,2203	246.0	189.0	208.0		1198,1198	4.4	0.7	12	dbSNP_134	208	5,8595	4.3+/-15.6	0,5,4295	yes	missense,missense	C1S	NM_001734.3,NM_201442.2	29,29	0,5,6498	CC,CG,GG		0.0581,0.0,0.0384	benign,benign	400/689,400/689	7175762	5,13001	2203	4300	6503	SO:0001583	missense	716	exon11			CCAGGGGAGTATC		CCDS31735.1	12p13	2014-09-17			ENSG00000182326	ENSG00000182326	3.4.21.42	"""Complement system"""	1247	protein-coding gene	gene with protein product		120580					Standard	NM_201442		Approved		uc001qsl.3	P09871	OTTHUMG00000150305	ENST00000406697.1:c.1198G>C	12.37:g.7175762G>C	ENSP00000385035:p.Glu400Gln	Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	120	56	0.466667	NM_201442	D3DUT4|Q9UCU7|Q9UCU8|Q9UCU9|Q9UCV0|Q9UCV1|Q9UCV2|Q9UCV3|Q9UCV4|Q9UCV5|Q9UM14	Missense_Mutation	SNP	ENST00000406697.1	37	CCDS31735.1	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	G	2.603	-0.292472	0.05568	0.0	5.81E-4	ENSG00000182326	ENST00000406697;ENST00000328916;ENST00000360817;ENST00000382222;ENST00000402681	T;T;T;T	0.65364	-0.15;-0.15;-0.15;-0.15	5.28	4.39	0.52855	Complement control module (2);Sushi/SCR/CCP (3);	0.768045	0.11079	N	0.601989	T	0.57651	0.2068	L	0.55834	1.745	0.09310	N	1	B	0.23650	0.089	B	0.24974	0.057	T	0.47209	-0.9135	10	0.32370	T	0.25	.	10.104	0.42521	0.1176:0.1284:0.7539:0.0	.	400	P09871	C1S_HUMAN	Q	400;400;400;394;233	ENSP00000385035:E400Q;ENSP00000328173:E400Q;ENSP00000354057:E400Q;ENSP00000384171:E233Q	ENSP00000328173:E400Q	E	+	1	0	C1S	7046023	0.001000	0.12720	0.664000	0.29753	0.013000	0.08279	0.933000	0.28897	0.617000	0.30160	-2.178000	0.00318	GAG	G|1.000;C|0.000	0.000	strong		0.587	C1S-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317481.1	NM_001734	
TDRD6	221400	hgsc.bcm.edu	37	6	46658905	46658905	+	Missense_Mutation	SNP	C	C	G	rs9381472	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:46658905C>G	ENST00000316081.6	+	1	3040	c.3040C>G	c.(3040-3042)Cag>Gag	p.Q1014E	TDRD6_ENST00000544460.1_Missense_Mutation_p.Q1014E	NM_001010870.2	NP_001010870.1	O60522	TDRD6_HUMAN	tudor domain containing 6	1014			Q -> E (in dbSNP:rs9381472). {ECO:0000269|PubMed:14702039}.		germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|P granule (GO:0043186)				NS(1)|breast(9)|central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(25)|ovary(2)|pancreas(1)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	80			Lung(136;0.192)			TATTTTAGAACAGTTGTCATG	0.343													C|||	2092	0.417732	0.3631	0.4323	5008	,	,		19636	0.3492		0.329	False		,,,				2504	0.6431				p.Q1014E		Atlas-SNP	.											.	TDRD6	205	.	0			c.C3040G						PASS	.	C	GLU/GLN,GLU/GLN	1684,2722	490.4+/-361.8	322,1040,841	47.0	52.0	50.0		3040,3040	3.5	1.0	6	dbSNP_119	50	2856,5744	442.8+/-360.2	504,1848,1948	yes	missense,missense	TDRD6	NM_001010870.2,NM_001168359.1	29,29	826,2888,2789	GG,GC,CC		33.2093,38.2206,34.907	possibly-damaging,possibly-damaging	1014/2097,1014/2067	46658905	4540,8466	2203	4300	6503	SO:0001583	missense	221400	exon1			TTAGAACAGTTGT	AF039442	CCDS34470.1, CCDS55017.1	6p12.3	2013-01-23			ENSG00000180113	ENSG00000180113		"""Tudor domain containing"""	21339	protein-coding gene	gene with protein product	"""cancer/testis antigen 41.2"", ""spermatogenesis associated 36"""	611200				9610721	Standard	NM_001010870		Approved	NY-CO-45, bA446F17.4, CT41.2, SPATA36	uc003oyj.3	O60522	OTTHUMG00000014788	ENST00000316081.6:c.3040C>G	6.37:g.46658905C>G	ENSP00000346065:p.Gln1014Glu	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	53	17	0.320755	NM_001168359	B3KWU2|F5H5M3|Q5HYB1|Q5VTS4|Q6ZMX5	Missense_Mutation	SNP	ENST00000316081.6	37	CCDS34470.1	786	0.3598901098901099	180	0.36585365853658536	148	0.4088397790055249	202	0.3531468531468531	256	0.33773087071240104	C	8.698	0.908949	0.17833	0.382206	0.332093	ENSG00000180113	ENST00000544460;ENST00000316081	T;T	0.08370	3.1;3.1	5.36	3.52	0.40303	Maternal tudor protein (1);	1.417590	0.03640	N	0.239271	T	0.02083	0.0065	L	0.28608	0.87	0.42236	P	0.008086999999999955	B;B	0.12013	0.004;0.005	B;B	0.18561	0.013;0.022	T	0.43861	-0.9365	9	0.09338	T	0.73	-21.7981	10.0578	0.42255	0.2788:0.5867:0.1345:0.0	rs9381472;rs56926189;rs9381472	1014;1014	F5H5M3;O60522	.;TDRD6_HUMAN	E	1014	ENSP00000443299:Q1014E;ENSP00000346065:Q1014E	ENSP00000346065:Q1014E	Q	+	1	0	TDRD6	46766864	0.930000	0.31532	0.992000	0.48379	0.871000	0.50021	1.590000	0.36654	0.576000	0.29452	0.655000	0.94253	CAG	C|0.649;G|0.351	0.351	strong		0.343	TDRD6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040800.1	XM_166443	
OR5T2	219464	hgsc.bcm.edu	37	11	56000079	56000079	+	Missense_Mutation	SNP	C	C	T	rs77295387	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:56000079C>T	ENST00000313264.4	-	1	658	c.583G>A	c.(583-585)Gct>Act	p.A195T		NM_001004746.1	NP_001004746.1	Q8NGG2	OR5T2_HUMAN	olfactory receptor, family 5, subfamily T, member 2	195						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)					TGTATAGTAGCATGTAAAATG	0.433													c|||	34	0.00678914	0.0015	0.0029	5008	,	,		23389	0.0		0.0268	False		,,,				2504	0.0031				p.A195T		Atlas-SNP	.											.	OR5T2	107	.	0			c.G583A						PASS	.	C	THR/ALA	21,4381	26.2+/-53.5	0,21,2180	193.0	169.0	177.0		583	4.1	0.1	11	dbSNP_131	177	237,8355	96.6+/-158.3	1,235,4060	yes	missense	OR5T2	NM_001004746.1	58	1,256,6240	TT,TC,CC		2.7584,0.4771,1.9855	probably-damaging	195/360	56000079	258,12736	2201	4296	6497	SO:0001583	missense	219464	exon1			TAGTAGCATGTAA	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.583G>A	11.37:g.56000079C>T	ENSP00000323688:p.Ala195Thr	Somatic	264	0	0		WXS	Illumina HiSeq	Phase_I	207	157	0.758454	NM_001004746	B9EGX5|Q6IFC8	Missense_Mutation	SNP	ENST00000313264.4	37	CCDS31523.1	21	0.009615384615384616	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	19	0.025065963060686015	C	12.15	1.852226	0.32699	0.004771	0.027584	ENSG00000181718	ENST00000313264	T	0.39056	1.1	5.07	4.13	0.48395	GPCR, rhodopsin-like superfamily (1);	0.184659	0.26013	U	0.026862	T	0.23054	0.0557	L	0.41356	1.27	0.09310	N	1	P	0.45986	0.87	P	0.53102	0.718	T	0.11155	-1.0599	10	0.49607	T	0.09	.	12.8779	0.57999	0.3516:0.6484:0.0:0.0	.	195	Q8NGG2	OR5T2_HUMAN	T	195	ENSP00000323688:A195T	ENSP00000323688:A195T	A	-	1	0	OR5T2	55756655	0.000000	0.05858	0.078000	0.20375	0.029000	0.11900	-0.966000	0.03825	1.207000	0.43291	0.478000	0.44815	GCT	C|0.981;T|0.019	0.019	strong		0.433	OR5T2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391598.1	NM_001004746	
ESYT2	57488	hgsc.bcm.edu	37	7	158590740	158590740	+	Missense_Mutation	SNP	A	A	T	rs13233513	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:158590740A>T	ENST00000251527.5	-	3	609	c.544T>A	c.(544-546)Tgc>Agc	p.C182S	ESYT2_ENST00000497111.1_5'UTR	NM_020728.2	NP_065779.1	A0FGR8	ESYT2_HUMAN	extended synaptotagmin-like protein 2	210					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						ATAAATTGGCAAATGAAAGGC	0.428													A|||	488	0.0974441	0.1316	0.0519	5008	,	,		16595	0.1101		0.1054	False		,,,				2504	0.0624				p.C182S		Atlas-SNP	.											.	ESYT2	70	.	0			c.T544A						PASS	.		SER/CYS	578,3828	254.3+/-259.9	32,514,1657	71.0	72.0	71.0		544	5.2	1.0	7	dbSNP_121	71	929,7671	204.5+/-247.2	48,833,3419	yes	missense	ESYT2	NM_020728.2	112	80,1347,5076	TT,TA,AA		10.8023,13.1185,11.587	probably-damaging	182/894	158590740	1507,11499	2203	4300	6503	SO:0001583	missense	57488	exon3			ATTGGCAAATGAA	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.544T>A	7.37:g.158590740A>T	ENSP00000251527:p.Cys182Ser	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	69	29	0.42029	NM_020728	A4D229|Q69YJ2|Q6UKI4|Q6ZTU0|Q6ZVU1|Q9BQS0|Q9NW47|Q9ULJ2	Missense_Mutation	SNP	ENST00000251527.5	37	CCDS34791.1	221	0.10119047619047619	54	0.10975609756097561	23	0.06353591160220995	63	0.11013986013986014	81	0.10686015831134564	A	15.27	2.783083	0.49891	0.131185	0.108023	ENSG00000117868	ENST00000251527;ENST00000421679;ENST00000275418;ENST00000429474	T;T	0.76709	-1.04;-1.04	5.16	5.16	0.70880	.	0.000000	0.85682	D	0.000000	T	0.04048	0.0113	L	0.42245	1.32	0.09310	P	1.0	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.51601	-0.8685	9	0.15066	T	0.55	-0.7953	14.4687	0.67501	1.0:0.0:0.0:0.0	rs13233513;rs52821058;rs13233513	210;182	A0FGR8-6;A0FGR8-2	.;.	S	182;210;152;6	ENSP00000251527:C182S;ENSP00000275418:C152S	ENSP00000251527:C182S	C	-	1	0	ESYT2	158283501	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.559000	0.90708	2.072000	0.62099	0.454000	0.30748	TGC	A|0.887;T|0.113	0.113	strong		0.428	ESYT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322647.1	NM_020728	
CCDC185	164127	hgsc.bcm.edu	37	1	223566876	223566876	+	Missense_Mutation	SNP	G	G	A	rs75945379	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:223566876G>A	ENST00000366875.3	+	1	162	c.59G>A	c.(58-60)cGg>cAg	p.R20Q		NM_152610.2	NP_689823.2	Q8N715	CC185_HUMAN		20										breast(4)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(12)|skin(3)	29				GBM - Glioblastoma multiforme(131;0.0704)		GAACCCCCGCGGCCCGGCGGA	0.736													G|||	406	0.0810703	0.0832	0.0648	5008	,	,		10145	0.131		0.0398	False		,,,				2504	0.0808				p.R20Q		Atlas-SNP	.											C1orf65,NS,carcinoma,0,1	C1orf65	71	1	0			c.G59A						PASS	.	G	GLN/ARG	233,3717		5,223,1747	4.0	6.0	5.0		59	-0.5	0.0	1	dbSNP_131	5	244,7682		2,240,3721	yes	missense	C1orf65	NM_152610.2	43	7,463,5468	AA,AG,GG		3.0785,5.8987,4.0165	possibly-damaging	20/624	223566876	477,11399	1975	3963	5938	SO:0001583	missense	164127	exon1			CCCCGCGGCCCGG																												ENST00000366875.3:c.59G>A	1.37:g.223566876G>A	ENSP00000355840:p.Arg20Gln	Somatic	23	0	0		WXS	Illumina HiSeq	Phase_I	11	8	0.727273	NM_152610	Q8N746|Q8NA93	Missense_Mutation	SNP	ENST00000366875.3	37	CCDS1537.1	136	0.06227106227106227	27	0.054878048780487805	17	0.04696132596685083	65	0.11363636363636363	27	0.03562005277044855	G	9.585	1.124649	0.20959	0.058987	0.030785	ENSG00000178395	ENST00000366875	T	0.17854	2.25	3.7	-0.51	0.11973	.	.	.	.	.	T	0.00109	0.0003	N	0.14661	0.345	0.80722	P	0.0	P	0.44006	0.824	B	0.28916	0.096	T	0.37957	-0.9683	8	0.16896	T	0.51	.	3.9747	0.09468	0.0:0.4708:0.1905:0.3387	.	20	Q8N715	CA065_HUMAN	Q	20	ENSP00000355840:R20Q	ENSP00000355840:R20Q	R	+	2	0	C1orf65	221633499	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.361000	0.07612	-0.318000	0.08665	-1.097000	0.02148	CGG	G|0.937;A|0.063	0.063	strong		0.736	C1orf65-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092718.1		
HLA-DQA1	3117	hgsc.bcm.edu	37	6	32609094	32609094	+	Silent	SNP	C	C	T	rs550717566	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:32609094C>T	ENST00000343139.5	+	2	192	c.90C>T	c.(88-90)caC>caT	p.H30H	HLA-DQA1_ENST00000395363.1_Silent_p.H30H|HLA-DQA1_ENST00000374949.2_Silent_p.H30H	NM_002122.3	NP_002113.2	P01909	DQA1_HUMAN	major histocompatibility complex, class II, DQ alpha 1	30	Alpha-1.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			NS(1)|lung(3)|skin(1)|upper_aerodigestive_tract(1)	6						CAGCTGACCACGTTGCCTCTT	0.453													.|||	1698	0.339058	0.239	0.3991	5008	,	,		17899	0.4514		0.2684	False		,,,				2504	0.3885				p.H30H		Atlas-SNP	.											.	HLA-DQA1	52	.	0			c.C90T						PASS	.	C		922,3484		131,660,1412	145.0	125.0	132.0		90	-3.5	0.0	6	dbSNP_126	132	1916,6672		341,1234,2719	no	coding-synonymous	HLA-DQA1	NM_002122.3		472,1894,4131	TT,TC,CC		22.3102,20.926,21.8408		30/256	32609094	2838,10156	2203	4294	6497	SO:0001819	synonymous_variant	3117	exon2			TGACCACGTTGCC		CCDS4752.1	6p21.3	2013-01-11			ENSG00000196735	ENSG00000196735		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4942	protein-coding gene	gene with protein product		146880		HLA-DQA			Standard	NM_002122		Approved	CELIAC1	uc003obr.3	P01909	OTTHUMG00000031106	ENST00000343139.5:c.90C>T	6.37:g.32609094C>T		Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	126	82	0.650794	NM_002122	O19630|O19706|P01907|P01908|P04225|P04226|P05536|P79553|Q06751|Q29876|Q29994|Q2Q6Y6|Q2Q6Y7|Q2Q6Y8|Q2WCM3|Q30064|Q30067|Q30068|Q30070|Q30071|Q30072|Q30073|Q30086|Q30101|Q5Y7D5|Q5Y7F5|Q6ICU6|Q6PR46|Q6QDB1|Q860W2|Q860W4|Q9BD37|Q9TPM3|Q9UM31	Silent	SNP	ENST00000343139.5	37	CCDS4752.1	768	0.3516483516483517	114	0.23170731707317074	137	0.3784530386740331	292	0.5104895104895105	225	0.29683377308707126	.	2.853	-0.237898	0.05944	0.20926	0.223102	ENSG00000196735	ENST00000486548	.	.	.	3.84	-3.45	0.04781	.	.	.	.	.	T	0.22936	0.0554	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.22730	-1.0208	3	.	.	.	.	10.9663	0.47414	0.0:0.3747:0.0:0.6253	rs12722043;rs17415840	.	.	.	M	3	.	.	T	+	2	0	HLA-DQA1	32717072	0.000000	0.05858	0.020000	0.16555	0.047000	0.14425	-4.803000	0.00184	-0.758000	0.04690	0.462000	0.41574	ACG	C|0.706;T|0.294	0.294	strong		0.453	HLA-DQA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076176.3	NM_002122	
DYNC1I1	1780	hgsc.bcm.edu	37	7	95668664	95668664	+	Silent	SNP	C	C	A	rs1048666	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:95668664C>A	ENST00000324972.6	+	14	1684	c.1491C>A	c.(1489-1491)ggC>ggA	p.G497G	DYNC1I1_ENST00000359388.4_Silent_p.G460G|DYNC1I1_ENST00000537881.1_Silent_p.G460G|DYNC1I1_ENST00000447467.2_Silent_p.G480G|DYNC1I1_ENST00000497626.1_3'UTR|DYNC1I1_ENST00000457059.1_Silent_p.G480G|DYNC1I1_ENST00000437599.1_Silent_p.G477G	NM_004411.4	NP_004402.1	O14576	DC1I1_HUMAN	dynein, cytoplasmic 1, intermediate chain 1	497					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|metabolic process (GO:0008152)|vesicle transport along microtubule (GO:0047496)	cytoplasmic dynein complex (GO:0005868)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|kinetochore (GO:0000776)|microtubule (GO:0005874)|perinuclear region of cytoplasm (GO:0048471)|spindle pole (GO:0000922)|vesicle (GO:0031982)	microtubule binding (GO:0008017)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)|spectrin binding (GO:0030507)			NS(2)|autonomic_ganglia(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(10)|lung(27)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	54	all_cancers(62;9.39e-10)|all_epithelial(64;2.28e-09)|Lung NSC(181;0.165)|all_lung(186;0.191)		STAD - Stomach adenocarcinoma(171;0.0957)			TGGCAGTGGGCCCAATCGACT	0.463													C|||	1061	0.211861	0.23	0.2061	5008	,	,		14926	0.3006		0.2356	False		,,,				2504	0.0757				p.G497G		Atlas-SNP	.											.	DYNC1I1	111	.	0			c.C1491A						PASS	.	C	,,	999,3407	371.2+/-319.9	113,773,1317	141.0	128.0	133.0		1440,1380,1491	-4.5	0.7	7	dbSNP_86	133	1926,6674	339.8+/-323.3	204,1518,2578	no	coding-synonymous,coding-synonymous,coding-synonymous	DYNC1I1	NM_001135556.1,NM_001135557.1,NM_004411.4	,,	317,2291,3895	AA,AC,CC		22.3953,22.6736,22.4896	,,	480/629,460/609,497/646	95668664	2925,10081	2203	4300	6503	SO:0001819	synonymous_variant	1780	exon14			AGTGGGCCCAATC	AF063228	CCDS5644.1, CCDS47645.1, CCDS47646.1, CCDS64718.1	7q21.3-q22.1	2013-01-18	2005-11-24	2005-11-24	ENSG00000158560	ENSG00000158560		"""Cytoplasmic dyneins"", ""WD repeat domain containing"""	2963	protein-coding gene	gene with protein product		603772	"""dynein, cytoplasmic, intermediate polypeptide 1"""	DNCI1		10049579, 16260502	Standard	NM_004411		Approved	DNCIC1	uc003uoc.4	O14576	OTTHUMG00000153983	ENST00000324972.6:c.1491C>A	7.37:g.95668664C>A		Somatic	199	1	0.00502513		WXS	Illumina HiSeq	Phase_I	159	158	0.993711	NM_004411	B4DME3|F5H050|G5E9K1|Q8TBF7|Q9Y2X1	Silent	SNP	ENST00000324972.6	37	CCDS5644.1																																																																																			C|0.760;A|0.240	0.240	strong		0.463	DYNC1I1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333432.1	NM_004411	
RGL3	57139	hgsc.bcm.edu	37	19	11516007	11516007	+	Silent	SNP	T	T	G	rs10416704	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:11516007T>G	ENST00000380456.3	-	8	1155	c.1092A>C	c.(1090-1092)gcA>gcC	p.A364A	RGL3_ENST00000393423.3_Silent_p.A364A	NM_001035223.2|NM_001161616.1	NP_001030300.2|NP_001155088.1	Q3MIN7	RGL3_HUMAN	ral guanine nucleotide dissociation stimulator-like 3	364	Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00168}.				small GTPase mediated signal transduction (GO:0007264)	intracellular (GO:0005622)	Ral guanyl-nucleotide exchange factor activity (GO:0008321)			breast(1)|endometrium(4)|large_intestine(2)|lung(9)|ovary(1)|skin(1)	18						ACCGGCTCACTGCCCCCCAGC	0.662													t|||	1197	0.239018	0.5219	0.1023	5008	,	,		11868	0.251		0.0795	False		,,,				2504	0.1053				p.A364A	GBM(174;751 2067 17998 27979 33959)	Atlas-SNP	.											.	RGL3	100	.	0			c.A1092C						PASS	.	T	,	1990,2416	507.9+/-366.8	447,1096,660	23.0	27.0	25.0		1092,1092	-10.3	0.1	19	dbSNP_119	25	677,7923	159.8+/-213.0	30,617,3653	no	coding-synonymous,coding-synonymous	RGL3	NM_001035223.2,NM_001161616.1	,	477,1713,4313	GG,GT,TT		7.8721,45.1657,20.5059	,	364/711,364/717	11516007	2667,10339	2203	4300	6503	SO:0001819	synonymous_variant	57139	exon8			GCTCACTGCCCCC	BC014426	CCDS32910.1, CCDS54221.1	19p13.2	2008-02-05				ENSG00000205517			30282	protein-coding gene	gene with protein product						10869344	Standard	NM_001035223		Approved	FLJ32585	uc002mro.2	Q3MIN7		ENST00000380456.3:c.1092A>C	19.37:g.11516007T>G		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	55	31	0.563636	NM_001035223	B5ME84|B7ZL22|Q0P6G0	Silent	SNP	ENST00000380456.3	37	CCDS32910.1																																																																																			T|0.794;G|0.206	0.206	strong		0.662	RGL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421208.3	XM_290867	
TMPRSS6	164656	hgsc.bcm.edu	37	22	37466565	37466565	+	Silent	SNP	G	G	A	rs145814440	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:37466565G>A	ENST00000346753.3	-	15	1943	c.1827C>T	c.(1825-1827)gaC>gaT	p.D609D	TMPRSS6_ENST00000406856.1_Silent_p.D600D|TMPRSS6_ENST00000406725.1_Silent_p.D600D|TMPRSS6_ENST00000381792.2_Silent_p.D600D	NM_153609.2	NP_705837.1	Q8IU80	TMPS6_HUMAN	transmembrane protease, serine 6	609	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)			breast(5)|central_nervous_system(4)|endometrium(4)|kidney(4)|large_intestine(3)|lung(13)|ovary(1)|prostate(1)|skin(2)|stomach(3)	40						TCACCCAGCGGTCAGCGATGA	0.652													G|||	25	0.00499201	0.0015	0.0159	5008	,	,		15444	0.0		0.0119	False		,,,				2504	0.0				p.D609D		Atlas-SNP	.											.	TMPRSS6	99	.	0			c.C1827T						PASS	.	G		14,4392	21.2+/-45.6	0,14,2189	68.0	72.0	71.0		1827	3.0	1.0	22	dbSNP_134	71	90,8510	51.1+/-111.2	0,90,4210	no	coding-synonymous	TMPRSS6	NM_153609.2		0,104,6399	AA,AG,GG		1.0465,0.3177,0.7996		609/812	37466565	104,12902	2203	4300	6503	SO:0001819	synonymous_variant	164656	exon15			CCAGCGGTCAGCG	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.1827C>T	22.37:g.37466565G>A		Somatic	207	0	0		WXS	Illumina HiSeq	Phase_I	153	67	0.437909	NM_153609	B0QYB4|B0QYB7|B0QYB8|Q5TI06|Q6ICC2|Q6UXD8|Q8IUE2|Q8IXV8	Silent	SNP	ENST00000346753.3	37	CCDS13941.1																																																																																			G|0.992;A|0.008	0.008	strong		0.652	TMPRSS6-003	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000318822.1	NM_153609	
APOBEC3F	200316	hgsc.bcm.edu	37	22	39441203	39441203	+	Silent	SNP	C	C	T	rs4821862	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:39441203C>T	ENST00000308521.5	+	3	786	c.429C>T	c.(427-429)cgC>cgT	p.R143R	APOBEC3G_ENST00000452957.2_Intron	NM_145298.5	NP_660341.2	Q8IUX4	ABC3F_HUMAN	apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3F	143					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)					CAGGGGCCCGCGTGAAGATTA	0.592													C|||	2972	0.59345	0.5454	0.6427	5008	,	,		16814	0.7123		0.492	False		,,,				2504	0.6053				p.R143R		Atlas-SNP	.											APOBEC3F,NS,carcinoma,+2,2	APOBEC3F	37	2	0			c.C429T						scavenged	.	C		2401,2005		631,1139,433	43.0	46.0	45.0		429	-3.7	0.0	22	dbSNP_111	45	4575,4025		1214,2147,939	no	coding-synonymous	APOBEC3F	NM_145298.5		1845,3286,1372	TT,TC,CC		46.8023,45.5061,46.3632		143/374	39441203	6976,6030	2203	4300	6503	SO:0001819	synonymous_variant	200316	exon3			GGCCCGCGTGAAG	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.429C>T	22.37:g.39441203C>T		Somatic	135	1	0.00740741		WXS	Illumina HiSeq	Phase_I	101	51	0.504951	NM_145298	B0QYD4|Q45F03|Q6ICH3|Q7Z2N2|Q7Z2N5	Silent	SNP	ENST00000308521.5	37	CCDS33648.1																																																																																			C|0.439;T|0.561	0.561	strong		0.592	APOBEC3F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321216.1	NM_145298	
TTLL6	284076	hgsc.bcm.edu	37	17	46894377	46894377	+	Missense_Mutation	SNP	A	A	C	rs3959442	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	28	0	0		WXS	Illumina HiSeq	Phase_I	25	15	0.6	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	
ACO2	50	hgsc.bcm.edu	37	22	41903813	41903813	+	Silent	SNP	A	A	C	rs137831	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:41903813A>C	ENST00000216254.4	+	3	214	c.192A>C	c.(190-192)acA>acC	p.T64T	ACO2_ENST00000396512.3_Silent_p.T64T	NM_001098.2	NP_001089.1	Q99798	ACON_HUMAN	aconitase 2, mitochondrial	64					cell death (GO:0008219)|cellular metabolic process (GO:0044237)|citrate metabolic process (GO:0006101)|generation of precursor metabolites and energy (GO:0006091)|isocitrate metabolic process (GO:0006102)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	3 iron, 4 sulfur cluster binding (GO:0051538)|4 iron, 4 sulfur cluster binding (GO:0051539)|aconitate hydratase activity (GO:0003994)|iron ion binding (GO:0005506)			breast(3)|endometrium(5)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(2)	23						GGCCGCTGACACTCTCGGAGA	0.637													C|||	2095	0.418331	0.3714	0.5418	5008	,	,		18535	0.5734		0.2306	False		,,,				2504	0.4274				p.T64T		Atlas-SNP	.											.	ACO2	58	.	0			c.A192C						PASS	.	C		1536,2870	638.6+/-397.0	276,984,943	25.0	26.0	25.0		192	1.3	1.0	22	dbSNP_78	25	1819,6781	698.8+/-405.0	213,1393,2694	no	coding-synonymous	ACO2	NM_001098.2		489,2377,3637	CC,CA,AA		21.1512,34.8616,25.7958		64/781	41903813	3355,9651	2203	4300	6503	SO:0001819	synonymous_variant	50	exon3			GCTGACACTCTCG	AH006514	CCDS14017.1	22q13.2	2013-05-21			ENSG00000100412	ENSG00000100412	4.2.1.3		118	protein-coding gene	gene with protein product	"""aconitate hydratase, mitochondrial"""	100850				10591208	Standard	NM_001098		Approved	ACONM	uc003bac.3	Q99798	OTTHUMG00000030544	ENST00000216254.4:c.192A>C	22.37:g.41903813A>C		Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	96	56	0.583333	NM_001098	O75809|Q5JZ41|Q6FHX0|Q8TAQ6	Silent	SNP	ENST00000216254.4	37	CCDS14017.1																																																																																			A|0.669;C|0.331	0.331	strong		0.637	ACO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259151.1	NM_001098	
ALB	213	hgsc.bcm.edu	37	4	74285263	74285263	+	Silent	SNP	A	A	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:74285263A>G	ENST00000503124.1	+	11	1449	c.1242A>G	c.(1240-1242)acA>acG	p.T414T	ALB_ENST00000509063.1_Silent_p.T564T|ALB_ENST00000505649.1_3'UTR|ALB_ENST00000401494.3_Silent_p.T449T|ALB_ENST00000415165.2_Silent_p.T372T|ALB_ENST00000295897.4_Silent_p.T564T			Q8TES7	FBF1_HUMAN	albumin	0					apical junction assembly (GO:0043297)|cilium assembly (GO:0042384)|establishment of epithelial cell polarity (GO:0090162)	cell junction (GO:0030054)|centriole (GO:0005814)|ciliary transition fiber (GO:0097539)|spindle pole (GO:0000922)				NS(1)|endometrium(4)|kidney(1)|large_intestine(6)|liver(9)|lung(16)|ovary(3)|prostate(2)|skin(4)|stomach(1)|urinary_tract(1)	48	Breast(15;0.00102)		Epithelial(6;4.8e-05)|OV - Ovarian serous cystadenocarcinoma(6;0.000263)|all cancers(17;0.000472)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			CCAAGGCAACAAAAGAGCAAC	0.408																																					p.T564T		Atlas-SNP	.											.	ALB	132	.	0			c.A1692G						PASS	.						93.0	89.0	90.0					4																	74285263		2203	4300	6503	SO:0001819	synonymous_variant	213	exon13			GGCAACAAAAGAG	V00494	CCDS3555.1	4q13.3	2008-02-05	2006-06-30	2006-06-30	ENSG00000163631	ENSG00000163631			399	protein-coding gene	gene with protein product		103600				6292049, 6192711	Standard	NM_000477		Approved		uc003hgs.4	P02768	OTTHUMG00000129919	ENST00000503124.1:c.1242A>G	4.37:g.74285263A>G		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	101	22	0.217822	NM_000477	B5MEM5|Q96IF6|Q96JG4|Q96MA8	Silent	SNP	ENST00000503124.1	37		.	.	.	.	.	.	.	.	.	.	A	10.22	1.290736	0.23564	.	.	ENSG00000163631	ENST00000511370	.	.	.	6.06	-2.4	0.06583	.	.	.	.	.	T	0.21801	0.0525	.	.	.	0.25935	N	0.982943	.	.	.	.	.	.	T	0.31724	-0.9933	4	.	.	.	-29.7385	4.5011	0.11865	0.4432:0.0:0.2016:0.3552	.	.	.	.	E	409	.	.	K	+	1	0	ALB	74504127	0.001000	0.12720	0.046000	0.18839	0.538000	0.34931	-0.230000	0.09083	-0.111000	0.12001	0.533000	0.62120	AAA	.	.	none		0.408	ALB-011	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000365419.1	NM_000477	
TCP11	6954	hgsc.bcm.edu	37	6	35090097	35090097	+	Silent	SNP	T	T	C	rs2234044	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:35090097T>C	ENST00000512012.1	-	4	531	c.375A>G	c.(373-375)ctA>ctG	p.L125L	TCP11_ENST00000418521.2_Silent_p.L62L|TCP11_ENST00000444780.2_Silent_p.L133L|TCP11_ENST00000244645.3_Silent_p.L63L|TCP11_ENST00000412155.2_Silent_p.L87L|TCP11_ENST00000311875.5_Silent_p.L138L|TCP11_ENST00000373979.2_Silent_p.L63L|TCP11_ENST00000373974.4_Silent_p.L92L			Q8WWU5	TCP11_HUMAN	t-complex 11, testis-specific	125					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)				breast(1)|kidney(5)|large_intestine(3)|lung(10)|ovary(3)|prostate(1)|skin(4)	27						GGCGTGGTAATAGCAGTGATA	0.468													T|||	797	0.159145	0.2799	0.1412	5008	,	,		17764	0.119		0.1501	False		,,,				2504	0.0593				p.L138L		Atlas-SNP	.											.	TCP11	94	.	0			c.A414G						PASS	.	T	,	1292,3114	438.4+/-345.3	183,926,1094	80.0	77.0	78.0		414,189	-7.3	0.8	6	dbSNP_98	78	1335,7265	261.9+/-284.1	106,1123,3071	no	coding-synonymous,coding-synonymous	TCP11	NM_001093728.1,NM_018679.4	,	289,2049,4165	CC,CT,TT		15.5233,29.3236,20.1984	,	138/517,63/442	35090097	2627,10379	2203	4300	6503	SO:0001819	synonymous_variant	6954	exon5			TGGTAATAGCAGT		CCDS4799.1, CCDS47413.1, CCDS59015.1, CCDS59016.1, CCDS59017.1, CCDS59018.1	6p21.31	2012-09-20	2012-09-20		ENSG00000124678	ENSG00000124678			11658	protein-coding gene	gene with protein product	"""fertilization-promoting peptide receptor"""	186982	"""t-complex 11 (a murine tcp homolog)"", ""t-complex 11 homolog (mouse)"""	D6S230E		1427894, 11756566, 21597245	Standard	NM_001093728		Approved	KIAA0229, FPPR	uc003okd.2	Q8WWU5	OTTHUMG00000014560	ENST00000512012.1:c.375A>G	6.37:g.35090097T>C		Somatic	409	0	0		WXS	Illumina HiSeq	Phase_I	345	153	0.443478	NM_001093728	B2RCE9|B3KQ27|B7Z7B5|B7Z7G1|B7Z7H4|B7Z7S8|E7EP29|J3KNG1|Q8NF85|Q9NQZ9|Q9NR39	Silent	SNP	ENST00000512012.1	37																																																																																				T|0.808;C|0.192	0.192	strong		0.468	TCP11-014	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000370354.1	NM_001093728	
CHSY3	337876	hgsc.bcm.edu	37	5	129520679	129520679	+	Missense_Mutation	SNP	G	G	A	rs10068403	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:129520679G>A	ENST00000305031.4	+	3	2202	c.1844G>A	c.(1843-1845)gGg>gAg	p.G615E		NM_175856.4	NP_787052.3	Q70JA7	CHSS3_HUMAN	chondroitin sulfate synthase 3	615			G -> E (in dbSNP:rs10068403).		carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi cisterna membrane (GO:0032580)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity (GO:0047238)|metal ion binding (GO:0046872)|N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase activity (GO:0050510)	p.G615E(1)		central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(7)|lung(9)|ovary(2)|pancreas(1)|prostate(2)|stomach(1)|urinary_tract(1)	28		all_cancers(142;0.0227)|Breast(839;0.198)|Prostate(80;0.215)|Lung NSC(810;0.239)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	OV - Ovarian serous cystadenocarcinoma(64;0.136)		GAAATGGGAGGGCACAATGAA	0.358													G|||	854	0.170527	0.2965	0.1643	5008	,	,		21395	0.2579		0.006	False		,,,				2504	0.0838				p.G615E		Atlas-SNP	.											CHSY3,right_upper_lobe,carcinoma,+1,2	CHSY3	92	2	1	Substitution - Missense(1)	stomach(1)	c.G1844A						PASS	.	G	GLU/GLY	970,3436	357.1+/-313.8	103,764,1336	56.0	57.0	57.0		1844	0.3	0.0	5	dbSNP_119	57	60,8540	35.9+/-90.5	0,60,4240	yes	missense	CHSY3	NM_175856.4	98	103,824,5576	AA,AG,GG		0.6977,22.0154,7.9194	benign	615/883	129520679	1030,11976	2203	4300	6503	SO:0001583	missense	337876	exon3			TGGGAGGGCACAA	AB086062	CCDS34223.1	5q13	2013-02-19			ENSG00000198108	ENSG00000198108	2.4.1.175, 2.4.1.226	"""Beta 3-glycosyltransferases"", ""Beta 4-glycosyltransferases"""	24293	protein-coding gene	gene with protein product		609963				12907687	Standard	XM_005271982		Approved	CSS3, CHSY-2	uc003kvd.3	Q70JA7	OTTHUMG00000163043	ENST00000305031.4:c.1844G>A	5.37:g.129520679G>A	ENSP00000302629:p.Gly615Glu	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	75	49	0.653333	NM_175856	B2RP97|Q76L22|Q86Y52	Missense_Mutation	SNP	ENST00000305031.4	37	CCDS34223.1	376	0.17216117216117216	171	0.3475609756097561	48	0.13259668508287292	151	0.263986013986014	6	0.0079155672823219	G	0.003	-2.405052	0.00195	0.220154	0.006977	ENSG00000198108	ENST00000305031	T	0.34472	1.36	4.12	0.333	0.15943	.	0.342006	0.24727	N	0.036100	T	0.00012	0.0000	N	0.01003	-1.06	0.34603	P	0.28325900000000004	B	0.11235	0.004	B	0.17098	0.017	T	0.43410	-0.9393	8	.	.	.	-1.8064	2.315	0.04196	0.2187:0.1294:0.5187:0.1331	rs10068403;rs17769784;rs10068403	615	Q70JA7	CHSS3_HUMAN	E	615	ENSP00000302629:G615E	.	G	+	2	0	CHSY3	129548578	0.995000	0.38212	0.008000	0.14137	0.710000	0.40934	2.503000	0.45407	0.028000	0.15324	-0.157000	0.13467	GGG	G|0.878;A|0.122	0.122	strong		0.358	CHSY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371453.1	NM_175856	
GPRIN1	114787	hgsc.bcm.edu	37	5	176026143	176026143	+	Silent	SNP	C	C	T	rs142779818|rs550332435|rs77245696|rs371149640|rs386695335	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:176026143C>T	ENST00000303991.4	-	2	870	c.693G>A	c.(691-693)agG>agA	p.R231R		NM_052899.2	NP_443131.2	Q7Z2K8	GRIN1_HUMAN	G protein regulated inducer of neurite outgrowth 1	231				Missing (in Ref. 4; CAD38868). {ECO:0000305}.	neuron projection development (GO:0031175)	cell projection (GO:0042995)|plasma membrane (GO:0005886)				NS(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(3)|liver(1)|lung(15)|ovary(2)|prostate(5)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	35	all_cancers(89;0.00263)|Renal(175;0.000269)|Lung NSC(126;0.00902)|all_lung(126;0.0142)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			GATCCTCCTTCCTCGGTGACA	0.493																																					p.R231R		Atlas-SNP	.											.	GPRIN1	77	.	0			c.G693A						PASS	.						84.0	86.0	85.0					5																	176026143		2157	4218	6375	SO:0001819	synonymous_variant	114787	exon2			CTCCTTCCTCGGT	AB067480	CCDS4405.1	5q35.2	2008-02-05			ENSG00000169258	ENSG00000169258			24835	protein-coding gene	gene with protein product		611239				11572484	Standard	NM_052899		Approved	GRIN1, KIAA1893	uc003meo.1	Q7Z2K8	OTTHUMG00000130659	ENST00000303991.4:c.693G>A	5.37:g.176026143C>T		Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	134	44	0.328358	NM_052899	C9JM70|Q8ND74|Q96PZ4	Silent	SNP	ENST00000303991.4	37	CCDS4405.1																																																																																			C|0.778;T|0.222	0.222	strong		0.493	GPRIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253149.1	NM_052899	
ASPM	259266	hgsc.bcm.edu	37	1	197094030	197094030	+	Silent	SNP	C	C	T	rs6676084	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:197094030C>T	ENST00000367409.4	-	12	3394	c.3138G>A	c.(3136-3138)agG>agA	p.R1046R	ASPM_ENST00000367408.1_Silent_p.R296R|ASPM_ENST00000294732.7_Silent_p.R1046R	NM_018136.4	NP_060606.3	Q8IZT6	ASPM_HUMAN	asp (abnormal spindle) homolog, microcephaly associated (Drosophila)	1046	CH 1. {ECO:0000255|PROSITE- ProRule:PRU00044}.				developmental growth (GO:0048589)|forebrain neuroblast division (GO:0021873)|maintenance of centrosome location (GO:0051661)|mitotic nuclear division (GO:0007067)|negative regulation of asymmetric cell division (GO:0045769)|negative regulation of neuron differentiation (GO:0045665)|neuron migration (GO:0001764)|oogenesis (GO:0048477)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of neuroblast proliferation (GO:0002052)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|midbody (GO:0030496)|nucleus (GO:0005634)|spindle pole (GO:0000922)				breast(6)|central_nervous_system(2)|cervix(2)|endometrium(10)|kidney(9)|large_intestine(28)|liver(1)|lung(87)|ovary(5)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(3)	165						TCCAAAGCAACCTGAGAGTTT	0.294													C|||	1085	0.216653	0.1324	0.2147	5008	,	,		15024	0.1488		0.328	False		,,,				2504	0.2873				p.R1046R		Atlas-SNP	.											.	ASPM	444	.	0			c.G3138A						PASS	.	C	,	692,3714	285.7+/-278.4	70,552,1581	146.0	156.0	153.0		3138,3138	-5.4	0.0	1	dbSNP_116	153	2735,5863	433.6+/-357.5	421,1893,1985	no	coding-synonymous,coding-synonymous	ASPM	NM_001206846.1,NM_018136.4	,	491,2445,3566	TT,TC,CC		31.8097,15.7059,26.3534	,	1046/1893,1046/3478	197094030	3427,9577	2203	4299	6502	SO:0001819	synonymous_variant	259266	exon12			AAGCAACCTGAGA	AY367065	CCDS1389.1, CCDS55672.1	1q31	2008-02-05	2006-09-12		ENSG00000066279	ENSG00000066279			19048	protein-coding gene	gene with protein product		605481	"""microcephaly, primary autosomal recessive 5"", ""asp (abnormal spindle)-like, microcephaly associated (Drosophila)"""	MCPH5		11078481	Standard	NM_018136		Approved	Calmbp1, ASP, FLJ10517, FLJ10549	uc001gtu.3	Q8IZT6	OTTHUMG00000036277	ENST00000367409.4:c.3138G>A	1.37:g.197094030C>T		Somatic	213	0	0		WXS	Illumina HiSeq	Phase_I	142	142	1	NM_001206846	Q4G1H1|Q5VYL3|Q86UX4|Q8IUL2|Q8IZJ7|Q8IZJ8|Q8IZJ9|Q8N4D1|Q9NVS1|Q9NVT6	Silent	SNP	ENST00000367409.4	37	CCDS1389.1																																																																																			C|0.754;N|0.000	.	strong		0.294	ASPM-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000088256.1	NM_018136	
IFT81	28981	hgsc.bcm.edu	37	12	110618235	110618235	+	Silent	SNP	A	A	G	rs16940805	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:110618235A>G	ENST00000242591.5	+	12	1703	c.1197A>G	c.(1195-1197)cgA>cgG	p.R399R	IFT81_ENST00000552912.1_Silent_p.R399R	NM_014055.3	NP_054774.2	Q8WYA0	IFT81_HUMAN	intraflagellar transport 81	399					cilium assembly (GO:0042384)|intraciliary transport involved in cilium morphogenesis (GO:0035735)|spermatogenesis (GO:0007283)	centrosome (GO:0005813)|cilium (GO:0005929)|intraciliary transport particle B (GO:0030992)|motile cilium (GO:0031514)|sperm midpiece (GO:0097225)|sperm principal piece (GO:0097228)	tubulin binding (GO:0015631)			endometrium(1)|large_intestine(2)|lung(5)|ovary(1)|stomach(1)	10						AGTTCAAACGATATGTCAATA	0.299													A|||	120	0.0239617	0.0008	0.0173	5008	,	,		13711	0.0		0.0676	False		,,,				2504	0.0399				p.R399R		Atlas-SNP	.											IFT81_ENST00000242591,caecum,carcinoma,+2,1	IFT81	86	1	0			c.A1197G						PASS	.	A	,	47,3569		0,47,1761	65.0	57.0	60.0		1197,1197	-1.0	1.0	12	dbSNP_123	60	561,7583		16,529,3527	no	coding-synonymous,coding-synonymous	IFT81	NM_001143779.1,NM_014055.3	,	16,576,5288	GG,GA,AA		6.8885,1.2998,5.1701	,	399/677,399/677	110618235	608,11152	1808	4072	5880	SO:0001819	synonymous_variant	28981	exon12			CAAACGATATGTC	AF139540	CCDS9142.1, CCDS41831.1	12q24.13	2014-07-03	2014-07-03	2005-11-02		ENSG00000122970		"""Intraflagellar transport homologs"""	14313	protein-coding gene	gene with protein product		605489	"""carnitine deficiency-associated, expressed in ventricle 1"", ""intraflagellar transport 81 homolog (Chlamydomonas)"""	CDV1		11130971	Standard	NM_014055		Approved	CDV-1R, MGC4027	uc001tqi.3	Q8WYA0	OTTHUMG00000169326	ENST00000242591.5:c.1197A>G	12.37:g.110618235A>G		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	58	30	0.517241	NM_014055	Q2YDY1|Q8NB51|Q9BSV2|Q9UNY8	Silent	SNP	ENST00000242591.5	37	CCDS41831.1																																																																																			A|0.963;G|0.037	0.037	strong		0.299	IFT81-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403529.1	NM_014055	
COL6A2	1292	hgsc.bcm.edu	37	21	47552385	47552385	+	Silent	SNP	C	C	T	rs6652	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:47552385C>T	ENST00000300527.4	+	28	3083	c.2979C>T	c.(2977-2979)cgC>cgT	p.R993R		NM_001849.3	NP_001840.3	P12110	CO6A2_HUMAN	collagen, type VI, alpha 2	993	Nonhelical region.|VWFA 3. {ECO:0000255|PROSITE- ProRule:PRU00219}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|protein heterotrimerization (GO:0070208)|response to glucose (GO:0009749)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)				NS(1)|breast(1)|central_nervous_system(7)|endometrium(7)|kidney(5)|liver(1)|lung(15)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	43	Breast(49;0.245)			Colorectal(79;0.0303)|READ - Rectum adenocarcinoma(84;0.0649)		TGGGTGACCGCGCCGCCGTGT	0.682													C|||	463	0.0924521	0.0893	0.0749	5008	,	,		15128	0.0288		0.1978	False		,,,				2504	0.0665				p.R993R		Atlas-SNP	.											.	COL6A2	351	.	0			c.C2979T						PASS	.	C		497,3905	215.8+/-234.7	29,439,1733	54.0	45.0	49.0		2979	1.4	1.0	21	dbSNP_52	49	1678,6920	297.1+/-303.3	145,1388,2766	no	coding-synonymous	COL6A2	NM_001849.3		174,1827,4499	TT,TC,CC		19.5162,11.2903,16.7308		993/1020	47552385	2175,10825	2201	4299	6500	SO:0001819	synonymous_variant	1292	exon28			TGACCGCGCCGCC	M20777	CCDS13728.1, CCDS13729.1, CCDS13730.1	21q22.3	2014-09-17			ENSG00000142173	ENSG00000142173		"""Collagens"""	2212	protein-coding gene	gene with protein product		120240					Standard	NM_001849		Approved		uc002zia.1	P12110	OTTHUMG00000090489	ENST00000300527.4:c.2979C>T	21.37:g.47552385C>T		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	85	53	0.623529	NM_001849	Q13909|Q13910|Q13911|Q14048|Q14049|Q16259|Q16597|Q6P0Q1|Q9UML3|Q9Y4S8	Silent	SNP	ENST00000300527.4	37	CCDS13728.1																																																																																			C|0.863;T|0.137	0.137	strong		0.682	COL6A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206971.1		
KRT14	3861	hgsc.bcm.edu	37	17	39742921	39742921	+	Missense_Mutation	SNP	G	G	A	rs117484558	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:39742921G>A	ENST00000167586.6	-	1	252	c.166C>T	c.(166-168)Cgc>Tgc	p.R56C		NM_000526.4	NP_000517	P02533	K1C14_HUMAN	keratin 14	56	Head.				aging (GO:0007568)|cell junction assembly (GO:0034329)|epidermis development (GO:0008544)|epithelial cell differentiation (GO:0030855)|hair cycle (GO:0042633)|hemidesmosome assembly (GO:0031581)|intermediate filament bundle assembly (GO:0045110)|response to ionizing radiation (GO:0010212)|response to zinc ion (GO:0010043)	cell periphery (GO:0071944)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)|nucleus (GO:0005634)	keratin filament binding (GO:1990254)|structural constituent of cytoskeleton (GO:0005200)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(5)|large_intestine(3)|lung(7)|ovary(1)|prostate(5)|skin(1)|stomach(1)	25		Breast(137;0.000307)				GAGGAGAAGCGGGAGGATGAG	0.706													G|||	31	0.0061901	0.0008	0.0043	5008	,	,		13635	0.0		0.0149	False		,,,				2504	0.0123				p.R56C		Atlas-SNP	.											KRT14,NS,carcinoma,+1,1	KRT14	65	1	0			c.C166T						PASS	.	G	CYS/ARG	8,4356		0,8,2174	25.0	30.0	28.0		166	3.4	1.0	17	dbSNP_132	28	57,8505		0,57,4224	no	missense	KRT14	NM_000526.4	180	0,65,6398	AA,AG,GG		0.6657,0.1833,0.5029	benign	56/473	39742921	65,12861	2182	4281	6463	SO:0001583	missense	3861	exon1			AGAAGCGGGAGGA	BC002690	CCDS11400.1	17q21.2	2013-06-20	2008-09-19		ENSG00000186847	ENSG00000186847		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6416	protein-coding gene	gene with protein product	"""epidermolysis bullosa simplex, Dowling-Meara, Koebner"""	148066	"""keratin 14 (epidermolysis bullosa simplex, Dowling-Meara, Koebner)"""	EBS3, EBS4		1717157, 16831889	Standard	NM_000526		Approved		uc002hxf.2	P02533	OTTHUMG00000133426	ENST00000167586.6:c.166C>T	17.37:g.39742921G>A	ENSP00000167586:p.Arg56Cys	Somatic	22	0	0		WXS	Illumina HiSeq	Phase_I	25	10	0.4	NM_000526	Q14715|Q53XY3|Q9BUE3|Q9UBN2|Q9UBN3|Q9UCY4	Missense_Mutation	SNP	ENST00000167586.6	37	CCDS11400.1	15	0.006868131868131868	0	0.0	3	0.008287292817679558	0	0.0	12	0.0158311345646438	G	7.992	0.753456	0.15778	0.001833	0.006657	ENSG00000186847	ENST00000167586	D	0.84070	-1.8	4.37	3.4	0.38934	.	0.000000	0.53938	D	0.000053	T	0.61726	0.2370	L	0.47716	1.5	0.53005	D	0.999962	B	0.02656	0.0	B	0.01281	0.0	T	0.65623	-0.6123	10	0.36615	T	0.2	.	9.0759	0.36522	0.1706:0.0:0.8294:0.0	.	56	P02533	K1C14_HUMAN	C	56	ENSP00000167586:R56C	ENSP00000167586:R56C	R	-	1	0	KRT14	36996447	0.997000	0.39634	1.000000	0.80357	0.012000	0.07955	0.082000	0.14847	1.210000	0.43336	-0.235000	0.12190	CGC	G|0.994;A|0.006	0.006	strong		0.706	KRT14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257289.1	NM_000526	
FKBP15	23307	hgsc.bcm.edu	37	9	115931703	115931703	+	Silent	SNP	G	G	A	rs3810910	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:115931703G>A	ENST00000238256.3	-	26	3403	c.3286C>T	c.(3286-3288)Ctg>Ttg	p.L1096L		NM_015258.1	NP_056073.1	Q5T1M5	FKB15_HUMAN	FK506 binding protein 15, 133kDa	1096					endocytosis (GO:0006897)|negative regulation of phosphatase activity (GO:0010923)|protein folding (GO:0006457)	actin filament (GO:0005884)|axon (GO:0030424)|endosome (GO:0005768)|growth cone (GO:0030426)|membrane (GO:0016020)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(3)|lung(9)|ovary(3)|urinary_tract(1)	26						GTCAGGGACAGTCTTGTGGAG	0.577													G|||	1420	0.283546	0.3351	0.2954	5008	,	,		17925	0.1617		0.3489	False		,,,				2504	0.2638				p.L1096L		Atlas-SNP	.											.	FKBP15	128	.	0			c.C3286T						PASS	.	G		1174,2710		177,820,945	96.0	98.0	98.0		3286	3.5	0.0	9	dbSNP_107	98	2704,5574		443,1818,1878	no	coding-synonymous	FKBP15	NM_015258.1		620,2638,2823	AA,AG,GG		32.6649,30.2266,31.8862		1096/1220	115931703	3878,8284	1942	4139	6081	SO:0001819	synonymous_variant	23307	exon26			GGGACAGTCTTGT	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.3286C>T	9.37:g.115931703G>A		Somatic	207	0	0		WXS	Illumina HiSeq	Phase_I	196	98	0.5	NM_015258	Q05DK8|Q5T1M2|Q6DD85|Q9Y4D0	Silent	SNP	ENST00000238256.3	37	CCDS48007.1																																																																																			G|0.712;A|0.288	0.288	strong		0.577	FKBP15-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_015258	
MUC4	4585	hgsc.bcm.edu	37	3	195505874	195505874	+	Missense_Mutation	SNP	G	G	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195505874G>C	ENST00000463781.3	-	2	13036	c.12577C>G	c.(12577-12579)Ctt>Gtt	p.L4193V	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.L4193V	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.L4193V(1)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GTGACAGGAAGAGGGGTGGTG	0.602																																					p.L4193V		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	1	Substitution - Missense(1)	kidney(1)	c.C12577G						scavenged	.						21.0	15.0	17.0					3																	195505874		689	1580	2269	SO:0001583	missense	4585	exon2			CAGGAAGAGGGGT	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.12577C>G	3.37:g.195505874G>C	ENSP00000417498:p.Leu4193Val	Somatic	64	1	0.015625		WXS	Illumina HiSeq	Phase_I	84	6	0.0714286	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	0.230	-1.021560	0.02061	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.33865	1.42;1.39	.	.	.	.	.	.	.	.	T	0.26629	0.0651	N	0.19112	0.55	0.09310	N	1	P	0.43973	0.823	P	0.48952	0.596	T	0.10245	-1.0638	7	.	.	.	.	3.3879	0.07278	1.0E-4:1.0E-4:0.5468:0.453	.	4065	E7ESK3	.	V	4193	ENSP00000417498:L4193V;ENSP00000420243:L4193V	.	L	-	1	0	MUC4	196990653	0.000000	0.05858	0.128000	0.21923	0.050000	0.14768	-0.106000	0.10890	0.452000	0.26830	0.074000	0.15403	CTT	.	.	none		0.602	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
PABPC1L	80336	hgsc.bcm.edu	37	20	43547677	43547677	+	Missense_Mutation	SNP	T	T	G	rs2075960	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:43547677T>G	ENST00000217073.2	+	4	634	c.634T>G	c.(634-636)Tcc>Gcc	p.S212A	PABPC1L_ENST00000537323.1_Missense_Mutation_p.S212A|PABPC1L_ENST00000255136.3_Missense_Mutation_p.S212A|PABPC1L_ENST00000217074.4_Missense_Mutation_p.S212A			Q4VXU2	PAP1L_HUMAN	poly(A) binding protein, cytoplasmic 1-like	212	RRM 3. {ECO:0000255|PROSITE- ProRule:PRU00176}.		S -> A (in dbSNP:rs2075960).		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						GGACCTCTTCTCCCAGTTTGG	0.627													T|||	1159	0.23143	0.1838	0.3458	5008	,	,		17408	0.2123		0.2515	False		,,,				2504	0.2137				p.S212A		Atlas-SNP	.											.	PABPC1L	59	.	0			c.T634G						PASS	.	T	ALA/SER	541,2595		43,455,1070	97.0	95.0	96.0		634	3.9	1.0	20	dbSNP_96	96	1744,5420		214,1316,2052	yes	missense	PABPC1L	NM_001124756.1	99	257,1771,3122	GG,GT,TT		24.3439,17.2513,22.1845	benign	212/615	43547677	2285,8015	1568	3582	5150	SO:0001583	missense	80336	exon4			CTCTTCTCCCAGT	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.634T>G	20.37:g.43547677T>G	ENSP00000217073:p.Ser212Ala	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	106	102	0.962264	NM_001124756	Q4VY17	Missense_Mutation	SNP	ENST00000217073.2	37	CCDS42878.1	513	0.2348901098901099	83	0.16869918699186992	121	0.3342541436464088	125	0.21853146853146854	184	0.24274406332453827	T	10.66	1.411498	0.25465	0.172513	0.243439	ENSG00000101104	ENST00000217074;ENST00000255136;ENST00000537323;ENST00000217073	D;D;D;D	0.85556	-2.0;-2.0;-2.0;-2.0	5.06	3.94	0.45596	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.281067	0.41097	D	0.000956	T	0.00012	0.0000	N	0.21583	0.68	0.31114	P	0.709589	B	0.15473	0.013	B	0.26094	0.066	T	0.04693	-1.0933	9	0.29301	T	0.29	.	12.1282	0.53928	0.0:0.0:0.1436:0.8564	rs2075960;rs60813358;rs2075960	212	Q4VXU2	PAP1L_HUMAN	A	212	ENSP00000217074:S212A;ENSP00000255136:S212A;ENSP00000445661:S212A;ENSP00000217073:S212A	ENSP00000217073:S212A	S	+	1	0	PABPC1L	42981091	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	3.107000	0.50329	0.929000	0.37192	0.460000	0.39030	TCC	T|0.781;G|0.219	0.219	strong		0.627	PABPC1L-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127816.2		
ABCA4	24	hgsc.bcm.edu	37	1	94544233	94544233	+	Silent	SNP	G	G	A	rs4147831	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:94544233G>A	ENST00000370225.3	-	10	1355	c.1269C>T	c.(1267-1269)caC>caT	p.H423H	ABCA4_ENST00000535735.1_Silent_p.H423H	NM_000350.2	NP_000341.2	P78363	ABCA4_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 4	423			H -> R (in dbSNP:rs3112831). {ECO:0000269|PubMed:10958763, ECO:0000269|PubMed:11379881, ECO:0000269|PubMed:11384574, ECO:0000269|PubMed:11527935, ECO:0000269|PubMed:12111378}.		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.H423H(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)		ACTTCCTAACGTGTTCCAGTT	0.458													G|||	574	0.114617	0.152	0.1095	5008	,	,		13998	0.13		0.0636	False		,,,				2504	0.1043				p.H423H		Atlas-SNP	.											ABCA4,NS,carcinoma,-2,2	ABCA4	275	2	1	Substitution - coding silent(1)	stomach(1)	c.C1269T						PASS	.	G		585,3821	259.8+/-263.3	39,507,1657	198.0	186.0	190.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1269	-11.0	0.0	1	dbSNP_110	190	645,7955	165.1+/-217.3	27,591,3682	no	coding-synonymous	ABCA4	NM_000350.2		66,1098,5339	AA,AG,GG		7.5,13.2773,9.4572		423/2274	94544233	1230,11776	2203	4300	6503	SO:0001819	synonymous_variant	24	exon10			CCTAACGTGTTCC	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.1269C>T	1.37:g.94544233G>A		Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	155	64	0.412903	NM_000350	O15112|O60438|O60915|Q0QD48|Q4LE31	Silent	SNP	ENST00000370225.3	37	CCDS747.1																																																																																			G|0.896;A|0.104	0.104	strong		0.458	ABCA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029320.1	NM_000350	
CPSF1	29894	hgsc.bcm.edu	37	8	145624578	145624578	+	Silent	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:145624578G>A	ENST00000349769.3	-	15	1501	c.1407C>T	c.(1405-1407)atC>atT	p.I469I	MIR1234_ENST00000408875.1_RNA	NM_013291.2	NP_037423.2	Q10570	CPSF1_HUMAN	cleavage and polyadenylation specific factor 1, 160kDa	469					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)			CAATGTTCAGGATGCTGTCAC	0.672																																					p.I469I	NSCLC(133;1088 1848 27708 34777 35269)	Atlas-SNP	.											.	CPSF1	92	.	0			c.C1407T						PASS	.						11.0	12.0	12.0					8																	145624578		2196	4290	6486	SO:0001819	synonymous_variant	29894	exon15			GTTCAGGATGCTG	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.1407C>T	8.37:g.145624578G>A		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	89	40	0.449438	NM_013291	Q96AF0	Silent	SNP	ENST00000349769.3	37	CCDS34966.1																																																																																			.	.	none		0.672	CPSF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382422.2	NM_013291	
PTPRR	5801	hgsc.bcm.edu	37	12	71286606	71286606	+	Silent	SNP	G	G	A	rs149684669	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:71286606G>A	ENST00000283228.2	-	2	662	c.210C>T	c.(208-210)tcC>tcT	p.S70S		NM_002849.3	NP_002840.2	Q15256	PTPRR_HUMAN	protein tyrosine phosphatase, receptor type, R	70					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)		CTTGAGCTTCGGAAGAGGAAT	0.458													G|||	10	0.00199681	0.0	0.0014	5008	,	,		18216	0.0		0.006	False		,,,				2504	0.0031				p.S70S		Atlas-SNP	.											.	PTPRR	109	.	0			c.C210T						PASS	.	G		6,4400	11.4+/-27.6	0,6,2197	230.0	233.0	232.0		210	-3.7	0.0	12	dbSNP_134	232	32,8568	22.8+/-68.1	0,32,4268	no	coding-synonymous	PTPRR	NM_002849.3		0,38,6465	AA,AG,GG		0.3721,0.1362,0.2922		70/658	71286606	38,12968	2203	4300	6503	SO:0001819	synonymous_variant	5801	exon2			AGCTTCGGAAGAG	D64053	CCDS8998.1, CCDS44945.1, CCDS55847.1, CCDS55848.1	12q15	2011-10-07			ENSG00000153233	ENSG00000153233		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"""	9680	protein-coding gene	gene with protein product		602853		PTPRQ		7557444, 10393441	Standard	NM_002849		Approved	PTPBR7, PTP-SL, EC-PTP, PCPTP1	uc001swi.2	Q15256	OTTHUMG00000169502	ENST00000283228.2:c.210C>T	12.37:g.71286606G>A		Somatic	371	0	0		WXS	Illumina HiSeq	Phase_I	295	139	0.471186	NM_002849	B2R5Z7|B7Z3J1|F5GXR7|O00342|Q92682|Q9UE65	Silent	SNP	ENST00000283228.2	37	CCDS8998.1																																																																																			G|0.997;A|0.003	0.003	strong		0.458	PTPRR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404485.1	NM_002849	
KIAA0355	9710	hgsc.bcm.edu	37	19	34843761	34843761	+	Silent	SNP	C	C	A	rs527829371|rs397414	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:34843761C>A	ENST00000299505.6	+	14	3987	c.3114C>A	c.(3112-3114)ccC>ccA	p.P1038P	AC010504.2_ENST00000591311.1_RNA	NM_014686.3	NP_055501.2	O15063	K0355_HUMAN	KIAA0355	1038	Poly-Pro.									breast(1)|endometrium(7)|kidney(1)|large_intestine(4)|lung(15)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	41	Esophageal squamous(110;0.162)					AGACCCCACCCCAGCCCCCAC	0.647													A|||	3154	0.629792	0.8313	0.4179	5008	,	,		13217	0.8165		0.3907	False		,,,				2504	0.5613				p.P1038P		Atlas-SNP	.											.	KIAA0355	105	.	0			c.C3114A						PASS	.	A		3359,1041		1301,757,142	30.0	19.0	23.0		3114	-11.2	0.2	19	dbSNP_80	23	3308,5264		739,1830,1717	no	coding-synonymous	KIAA0355	NM_014686.3		2040,2587,1859	AA,AC,CC		38.5908,23.6591,48.6047		1038/1071	34843761	6667,6305	2200	4286	6486	SO:0001819	synonymous_variant	9710	exon14			CCCACCCCAGCCC		CCDS12436.1	19q13.12	2012-11-29			ENSG00000166398	ENSG00000166398			29016	protein-coding gene	gene with protein product						9205841	Standard	NM_014686		Approved		uc002nvd.4	O15063	OTTHUMG00000180505	ENST00000299505.6:c.3114C>A	19.37:g.34843761C>A		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	112	58	0.517857	NM_014686	Q2M3W4	Silent	SNP	ENST00000299505.6	37	CCDS12436.1																																																																																			C|0.378;A|0.622	0.622	strong		0.647	KIAA0355-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451678.4	NM_014686	
ATG13	9776	hgsc.bcm.edu	37	11	46690413	46690413	+	Missense_Mutation	SNP	G	G	A	rs35619591	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:46690413G>A	ENST00000434074.1	+	15	1989	c.1300G>A	c.(1300-1302)Ggg>Agg	p.G434R	ATG13_ENST00000524625.1_Missense_Mutation_p.G397R|ATG13_ENST00000359513.4_Missense_Mutation_p.G434R|ATG13_ENST00000529655.1_Missense_Mutation_p.G397R|ATG13_ENST00000312040.4_Missense_Mutation_p.G434R|ATG13_ENST00000451945.1_Missense_Mutation_p.G397R|ATG13_ENST00000530500.1_Missense_Mutation_p.G318R|ATG13_ENST00000526508.1_Missense_Mutation_p.G434R|ATG13_ENST00000528494.1_Missense_Mutation_p.G467R	NM_001205120.1	NP_001192049.1	O75143	ATG13_HUMAN	autophagy related 13	434					autophagic vacuole assembly (GO:0000045)	ATG1/UKL1 signaling complex (GO:0034273)|cytosol (GO:0005829)|pre-autophagosomal structure (GO:0000407)|ULK1-ATG13-FIP200 complex (GO:0070969)	protein kinase binding (GO:0019901)			NS(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(1)|lung(5)|prostate(1)|skin(1)	15						TGGCTCCAGCGGGGGCAGCAG	0.532													G|||	40	0.00798722	0.0	0.0014	5008	,	,		19713	0.001		0.0109	False		,,,				2504	0.0276				p.G467R		Atlas-SNP	.											.	ATG13	60	.	0			c.G1399A						PASS	.	G	ARG/GLY,ARG/GLY,ARG/GLY,ARG/GLY,ARG/GLY,ARG/GLY	6,4396	11.4+/-27.6	0,6,2195	136.0	122.0	127.0		1300,1399,1300,1189,952,1189	4.9	0.8	11	dbSNP_126	127	67,8531	41.7+/-99.0	1,65,4233	yes	missense,missense,missense,missense,missense,missense	ATG13	NM_001142673.2,NM_001205119.1,NM_001205120.1,NM_001205121.1,NM_001205122.1,NM_014741.4	125,125,125,125,125,125	1,71,6428	AA,AG,GG		0.7793,0.1363,0.5615	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	434/518,467/551,434/518,397/481,318/402,397/481	46690413	73,12927	2201	4299	6500	SO:0001583	missense	9776	exon16			TCCAGCGGGGGCA	AB014552	CCDS7921.1, CCDS44582.1, CCDS55760.1, CCDS55761.1	11p11.2	2014-02-12	2012-06-06	2010-06-29	ENSG00000175224	ENSG00000175224			29091	protein-coding gene	gene with protein product		615088	"""KIAA0652"", ""ATG13 autophagy related 13 homolog (S. cerevisiae)"""	KIAA0652		15169610, 18339812, 17204848	Standard	NM_001205120		Approved		uc001nda.3	O75143	OTTHUMG00000166538	ENST00000434074.1:c.1300G>A	11.37:g.46690413G>A	ENSP00000400642:p.Gly434Arg	Somatic	26	0	0		WXS	Illumina HiSeq	Phase_I	24	19	0.791667	NM_001205119	B4DFI4|D3DQQ1|D3DQQ2|E9PQZ8|Q53EN6|Q9BRL3|Q9H8B0	Missense_Mutation	SNP	ENST00000434074.1	37	CCDS44582.1	10	0.004578754578754579	0	0.0	1	0.0027624309392265192	0	0.0	9	0.011873350923482849	G	15.32	2.797457	0.50208	0.001363	0.007793	ENSG00000175224	ENST00000434074;ENST00000312040;ENST00000451945;ENST00000529655;ENST00000530500;ENST00000526508;ENST00000524625;ENST00000359513;ENST00000528494;ENST00000525009	.	.	.	5.8	4.88	0.63580	.	0.345068	0.38111	N	0.001815	T	0.33962	0.0881	L	0.29908	0.895	0.41529	D	0.988441	B;B;B;B	0.25390	0.047;0.003;0.014;0.125	B;B;B;B	0.19148	0.005;0.002;0.003;0.024	T	0.23833	-1.0177	9	0.30854	T	0.27	-14.1572	9.9398	0.41574	0.0698:0.0:0.7929:0.1373	rs35619591;rs35619591	318;434;467;397	B4DFI4;O75143;E9PQZ8;O75143-2	.;ATG13_HUMAN;.;.	R	434;434;397;397;318;434;397;434;467;166	.	ENSP00000310321:G434R	G	+	1	0	ATG13	46646989	1.000000	0.71417	0.765000	0.31456	0.721000	0.41392	4.226000	0.58606	1.452000	0.47756	0.655000	0.94253	GGG	G|0.994;A|0.006	0.006	strong		0.532	ATG13-202	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000390300.2	NM_014741	
PRPS1L1	221823	hgsc.bcm.edu	37	7	18066569	18066569	+	Missense_Mutation	SNP	C	C	A	rs3800962	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:18066569C>A	ENST00000506618.2	-	1	917	c.837G>T	c.(835-837)gaG>gaT	p.E279D		NM_175886.2	NP_787082	P21108	PRPS3_HUMAN	phosphoribosyl pyrophosphate synthetase 1-like 1	279			E -> D (in dbSNP:rs3800962). {ECO:0000269|PubMed:15489334}.		5-phosphoribose 1-diphosphate biosynthetic process (GO:0006015)|nucleotide biosynthetic process (GO:0009165)|ribonucleoside monophosphate biosynthetic process (GO:0009156)		ATP binding (GO:0005524)|kinase activity (GO:0016301)|magnesium ion binding (GO:0000287)|protein homodimerization activity (GO:0042803)|ribose phosphate diphosphokinase activity (GO:0004749)			endometrium(1)|kidney(1)|large_intestine(3)|lung(9)|ovary(1)|prostate(3)	18	Lung NSC(10;0.0385)|all_lung(11;0.0736)					GCTTCATCTTCTCATCTTGAG	0.433													A|||	1326	0.264776	0.1974	0.3977	5008	,	,		19661	0.1548		0.4165	False		,,,				2504	0.2188				p.E279D		Atlas-SNP	.											.	PRPS1L1	90	.	0			c.G837T						PASS	.	A	ASP/GLU	1003,3399	717.9+/-408.8	108,787,1306	189.0	188.0	189.0		837	-2.1	1.0	7	dbSNP_107	189	3641,4959	622.0+/-397.3	738,2165,1397	yes	missense	PRPS1L1	NM_175886.2	45	846,2952,2703	AA,AC,CC		42.3372,22.7851,35.7176	benign	279/319	18066569	4644,8358	2201	4300	6501	SO:0001583	missense	221823	exon1			CATCTTCTCATCT	M57423	CCDS47552.1	7p21.1	2010-12-10			ENSG00000229937	ENSG00000229937			9463	protein-coding gene	gene with protein product		611566		PRPSL		2168892	Standard	NM_175886		Approved	PRPS3	uc003stz.3	P21108	OTTHUMG00000152742	ENST00000506618.2:c.837G>T	7.37:g.18066569C>A	ENSP00000424595:p.Glu279Asp	Somatic	204	1	0.00490196		WXS	Illumina HiSeq	Phase_I	197	197	1	NM_175886	Q6P5P6	Missense_Mutation	SNP	ENST00000506618.2	37	CCDS47552.1	657	0.3008241758241758	85	0.17276422764227642	154	0.425414364640884	93	0.16258741258741258	325	0.4287598944591029	A	0.593	-0.832338	0.02713	0.227851	0.423372	ENSG00000229937	ENST00000506618	T	0.71934	-0.61	4.44	-2.11	0.07187	.	.	.	.	.	T	0.00012	0.0000	N	0.13198	0.31	.	.	.	B	0.02656	0.0	B	0.04013	0.001	T	0.22138	-1.0225	8	0.02654	T	1	.	7.6097	0.28122	0.2:0.5365:0.2635:0.0	rs3800962;rs11567145;rs12699958;rs17846612;rs17859698;rs3800962	279	P21108	PRPS3_HUMAN	D	279	ENSP00000424595:E279D	ENSP00000424595:E279D	E	-	3	2	PRPS1L1	18033094	0.993000	0.37304	0.965000	0.40720	0.801000	0.45260	0.374000	0.20501	-0.531000	0.06340	-0.264000	0.10439	GAG	C|0.709;A|0.291	0.291	strong		0.433	PRPS1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327667.1	NM_175886	
ADAM18	8749	hgsc.bcm.edu	37	8	39525607	39525607	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:39525607C>T	ENST00000265707.5	+	14	1462	c.1417C>T	c.(1417-1419)Cct>Tct	p.P473S	ADAM18_ENST00000541111.1_5'UTR|ADAM18_ENST00000379866.1_Missense_Mutation_p.P449S	NM_014237.2	NP_055052.1	Q9Y3Q7	ADA18_HUMAN	ADAM metallopeptidase domain 18	473	Disintegrin. {ECO:0000255|PROSITE- ProRule:PRU00068}.				cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.P473A(1)		NS(2)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(31)|ovary(1)|prostate(1)|skin(12)|stomach(1)|upper_aerodigestive_tract(3)	71		all_cancers(7;1.32e-05)|all_epithelial(6;3.08e-10)|all_lung(54;0.00187)|Hepatocellular(245;0.00745)|Lung NSC(58;0.00769)|Breast(189;0.0112)	LUSC - Lung squamous cell carcinoma(45;0.000199)			TAATTGTGTTCCTGACACTTA	0.418																																					p.P473S		Atlas-SNP	.											ADAM18,NS,carcinoma,0,1	ADAM18	169	1	1	Substitution - Missense(1)	lung(1)	c.C1417T						scavenged	.						225.0	205.0	212.0					8																	39525607		2203	4300	6503	SO:0001583	missense	8749	exon14			TGTGTTCCTGACA	AJ133004	CCDS6113.1, CCDS55225.1	8p11.22	2008-08-07	2005-08-18		ENSG00000168619	ENSG00000168619		"""ADAM metallopeptidase domain containing"""	196	protein-coding gene	gene with protein product			"""a disintegrin and metalloproteinase domain 18"""			12200459	Standard	NM_014237		Approved	tMDCIII, ADAM27	uc003xni.3	Q9Y3Q7	OTTHUMG00000164040	ENST00000265707.5:c.1417C>T	8.37:g.39525607C>T	ENSP00000265707:p.Pro473Ser	Somatic	303	0	0		WXS	Illumina HiSeq	Phase_I	323	4	0.0123839	NM_014237	B2R9Y0|Q0VAI4|Q6IRW9|Q6UXJ9	Missense_Mutation	SNP	ENST00000265707.5	37	CCDS6113.1	.	.	.	.	.	.	.	.	.	.	C	17.98	3.521000	0.64747	.	.	ENSG00000168619	ENST00000265707;ENST00000379866;ENST00000522198	T;T	0.10763	2.84;2.84	5.35	4.44	0.53790	Blood coagulation inhibitor, Disintegrin (5);	0.000000	0.47093	D	0.000245	T	0.23766	0.0575	L	0.56124	1.755	0.80722	D	1	D;D	0.67145	0.995;0.996	D;D	0.72338	0.962;0.977	T	0.00412	-1.1755	10	0.21540	T	0.41	.	12.0491	0.53498	0.0:0.8276:0.1724:0.0	.	449;473	Q9Y3Q7-2;Q9Y3Q7	.;ADA18_HUMAN	S	473;449;405	ENSP00000265707:P473S;ENSP00000369195:P449S	ENSP00000265707:P473S	P	+	1	0	ADAM18	39644764	0.929000	0.31497	1.000000	0.80357	0.907000	0.53573	0.691000	0.25467	2.792000	0.96026	0.555000	0.69702	CCT	.	.	none		0.418	ADAM18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376916.1	NM_014237	
TBX10	347853	hgsc.bcm.edu	37	11	67402362	67402362	+	Missense_Mutation	SNP	T	T	G	rs3758938	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:67402362T>G	ENST00000335385.3	-	3	389	c.302A>C	c.(301-303)aAg>aCg	p.K101T		NM_005995.4	NP_005986.2	O75333	TBX10_HUMAN	T-box 10	101			K -> T (in dbSNP:rs3758938).		anatomical structure morphogenesis (GO:0009653)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|lung(4)|ovary(1)	7						GCCCAGGATCTTCACCTGGAA	0.677													T|||	1088	0.217252	0.1626	0.4236	5008	,	,		19390	0.131		0.3042	False		,,,				2504	0.1442				p.K101T		Atlas-SNP	.											.	TBX10	25	.	0			c.A302C	GRCh37	CM067720	TBX10	M	rs3758938	PASS	.	T	THR/LYS	765,3635	310.0+/-291.3	61,643,1496	54.0	54.0	54.0		302	1.7	0.9	11	dbSNP_107	54	2520,6068	410.2+/-350.1	399,1722,2173	yes	missense	TBX10	NM_005995.4	78	460,2365,3669	GG,GT,TT		29.3433,17.3864,25.2926	possibly-damaging	101/386	67402362	3285,9703	2200	4294	6494	SO:0001583	missense	347853	exon3			AGGATCTTCACCT	AH006177	CCDS31621.1	11q13.2	2005-10-11	2004-10-05		ENSG00000167800	ENSG00000167800		"""T-boxes"""	11593	protein-coding gene	gene with protein product		604648	"""T-box 7"""	TBX7		9545502	Standard	NM_005995		Approved	TBX13	uc001omp.3	O75333	OTTHUMG00000167291	ENST00000335385.3:c.302A>C	11.37:g.67402362T>G	ENSP00000335191:p.Lys101Thr	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	87	66	0.758621	NM_005995	Q14D64|Q86XS3	Missense_Mutation	SNP	ENST00000335385.3	37	CCDS31621.1	523	0.23946886446886448	89	0.18089430894308944	141	0.38950276243093923	66	0.11538461538461539	227	0.2994722955145119	T	13.44	2.237093	0.39498	0.173864	0.293433	ENSG00000167800	ENST00000335385	D	0.87809	-2.3	5.3	1.7	0.24286	p53-like transcription factor, DNA-binding (1);	0.078492	0.50627	D	0.000111	T	0.00012	0.0000	L	0.50993	1.605	0.28232	P	0.9260502	D	0.76494	0.999	D	0.75484	0.986	T	0.04191	-1.0970	9	0.87932	D	0	.	8.5722	0.33576	0.0:0.2305:0.0:0.7695	rs3758938;rs17508969;rs58569464;rs3758938	101	O75333	TBX10_HUMAN	T	101	ENSP00000335191:K101T	ENSP00000335191:K101T	K	-	2	0	TBX10	67158938	1.000000	0.71417	0.889000	0.34880	0.007000	0.05969	7.595000	0.82710	0.039000	0.15632	-0.371000	0.07208	AAG	T|0.753;G|0.247	0.247	strong		0.677	TBX10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394034.1	NM_005995	
ZNF625	90589	hgsc.bcm.edu	37	19	12256358	12256358	+	Silent	SNP	T	T	G	rs12972621	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:12256358T>G	ENST00000355738.1	-	4	1024	c.675A>C	c.(673-675)cgA>cgC	p.R225R	ZNF625_ENST00000542938.1_Silent_p.R225R|ZNF625_ENST00000455799.1_3'UTR|CTC-359D24.3_ENST00000472362.1_RNA|ZNF625_ENST00000439556.2_Silent_p.R291R|ZNF625-ZNF20_ENST00000430024.1_Intron			Q96I27	ZN625_HUMAN	zinc finger protein 625	225					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|kidney(1)|large_intestine(6)|lung(4)|skin(2)	14						TTTCATGATATCGAACGGAAT	0.453													T|||	2003	0.39996	0.0295	0.3862	5008	,	,		22544	0.6369		0.4533	False		,,,				2504	0.6115				p.R291R		Atlas-SNP	.											ZNF625,trunk,malignant_melanoma,-2,1	ZNF625	37	1	0			c.A873C						PASS	.	T		433,3973	210.2+/-230.7	24,385,1794	123.0	117.0	119.0		873	0.9	0.0	19	dbSNP_121	119	4008,4592	554.9+/-386.6	928,2152,1220	no	coding-synonymous	ZNF625	NM_145233.3		952,2537,3014	GG,GT,TT		46.6047,9.8275,34.1458		291/373	12256358	4441,8565	2203	4300	6503	SO:0001819	synonymous_variant	90589	exon4			ATGATATCGAACG	BC007868	CCDS12269.1, CCDS12269.2	19p13.2	2013-01-08			ENSG00000257591	ENSG00000257591		"""Zinc fingers, C2H2-type"", ""-"""	30571	protein-coding gene	gene with protein product						12477932	Standard	NM_145233		Approved		uc010dyo.2	Q96I27	OTTHUMG00000156407	ENST00000355738.1:c.675A>C	19.37:g.12256358T>G		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	58	26	0.448276	NM_145233	A4FU45|I3L0E9	Silent	SNP	ENST00000355738.1	37																																																																																				G|0.365;N|0.000	0.365	strong		0.453	ZNF625-201	KNOWN	basic	protein_coding	protein_coding		NM_145233	
CEP85	64793	hgsc.bcm.edu	37	1	26596080	26596080	+	Missense_Mutation	SNP	G	G	A	rs7550997	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:26596080G>A	ENST00000252992.4	+	9	1755	c.1624G>A	c.(1624-1626)Gca>Aca	p.A542T	CEP85_ENST00000469609.1_3'UTR|CEP85_ENST00000451429.2_Missense_Mutation_p.A491T	NM_001281517.1|NM_022778.2	NP_001268446.1|NP_073615.2	Q6P2H3	CEP85_HUMAN	centrosomal protein 85kDa	542			A -> T (in dbSNP:rs7550997).			centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|spindle pole (GO:0000922)				breast(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(11)|skin(2)	25						GCAGAGAGAAGCAGAATTCTC	0.502													G|||	648	0.129393	0.2027	0.1052	5008	,	,		16924	0.0228		0.1889	False		,,,				2504	0.0961				p.A542T		Atlas-SNP	.											.	CEP85	61	.	0			c.G1624A						PASS	.	G	THR/ALA	701,3705	292.4+/-282.0	60,581,1562	59.0	57.0	58.0		1624	3.1	1.0	1	dbSNP_116	58	1432,7168	273.7+/-290.8	110,1212,2978	yes	missense	CEP85	NM_022778.2	58	170,1793,4540	AA,AG,GG		16.6512,15.9101,16.4001	benign	542/763	26596080	2133,10873	2203	4300	6503	SO:0001583	missense	64793	exon9			AGAGAAGCAGAAT	AK024038	CCDS277.1, CCDS60038.1	1p36.11	2014-02-20	2011-05-06	2011-05-06	ENSG00000130695	ENSG00000130695			25309	protein-coding gene	gene with protein product			"""coiled-coil domain containing 21"""	CCDC21		12477932	Standard	NM_022778		Approved	DKFZP434L0117	uc001bls.1	Q6P2H3	OTTHUMG00000003380	ENST00000252992.4:c.1624G>A	1.37:g.26596080G>A	ENSP00000252992:p.Ala542Thr	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	73	25	0.342466	NM_022778	B4DRL1|D3DPK4|F8W7K4|Q5VY68|Q5VY70|Q9H6Q1|Q9H828|Q9UF52	Missense_Mutation	SNP	ENST00000252992.4	37	CCDS277.1	287	0.13141025641025642	80	0.16260162601626016	41	0.1132596685082873	12	0.02097902097902098	154	0.20316622691292877	G	8.915	0.959619	0.18507	0.159101	0.166512	ENSG00000130695	ENST00000451429;ENST00000252992	T;T	0.10960	2.82;2.82	5.06	3.11	0.35812	.	0.570233	0.20173	N	0.097692	T	0.00012	0.0000	L	0.36672	1.1	0.44946	P	0.0020320000000000338	B;B;B	0.06786	0.0;0.001;0.001	B;B;B	0.06405	0.001;0.002;0.002	T	0.36261	-0.9755	9	0.27785	T	0.31	-2.0585	5.216	0.15342	0.193:0.2319:0.5751:0.0	rs7550997;rs17257183;rs35972494;rs59910526;rs7550997	491;542;542	F8W7K4;Q6P2H3;Q6P2H3-2	.;CEP85_HUMAN;.	T	491;542	ENSP00000417002:A491T;ENSP00000252992:A542T	ENSP00000252992:A542T	A	+	1	0	CEP85	26468667	0.981000	0.34729	1.000000	0.80357	0.126000	0.20510	0.154000	0.16343	1.365000	0.46057	0.561000	0.74099	GCA	G|0.849;A|0.151	0.151	strong		0.502	CEP85-002	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009492.2	NM_022778	
SEH1L	81929	hgsc.bcm.edu	37	18	12984144	12984144	+	Missense_Mutation	SNP	C	C	A	rs6505776	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:12984144C>A	ENST00000262124.11	+	8	1152	c.1025C>A	c.(1024-1026)aCt>aAt	p.T342N	SEH1L_ENST00000592582.1_3'UTR|SEH1L_ENST00000399892.2_Missense_Mutation_p.T342N|RP11-773H22.4_ENST00000588211.1_RNA	NM_031216.3	NP_112493.2	Q96EE3	SEH1_HUMAN	SEH1-like (S. cerevisiae)	342			T -> N (in dbSNP:rs6505776). {ECO:0000269|PubMed:14702039, ECO:0000269|Ref.3}.		attachment of spindle microtubules to kinetochore involved in mitotic sister chromatid segregation (GO:0051315)|carbohydrate metabolic process (GO:0005975)|cytokine production involved in inflammatory response (GO:0002534)|cytokine-mediated signaling pathway (GO:0019221)|defense response to Gram-positive bacterium (GO:0050830)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic metaphase plate congression (GO:0007080)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|nuclear pore organization (GO:0006999)|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)|nuclear envelope (GO:0005635)|nuclear pore outer ring (GO:0031080)				central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(5)|pancreas(1)|prostate(1)	11						CTAGGTTCAACTATTCCAAGT	0.408													A|||	3917	0.782149	0.9788	0.6441	5008	,	,		18285	0.8105		0.6203	False		,,,				2504	0.7515				p.T342N		Atlas-SNP	.											.	SEH1L	33	.	0			c.C1025A						PASS	.	A	ASN/THR,ASN/THR	4059,347	177.3+/-206.3	1870,319,14	104.0	114.0	111.0		1025,1025	1.0	0.9	18	dbSNP_116	111	5337,3261	488.5+/-372.4	1661,2015,623	yes	missense,missense	SEH1L	NM_001013437.1,NM_031216.3	65,65	3531,2334,637	AA,AC,CC		37.9274,7.8756,27.7453	benign,benign	342/422,342/361	12984144	9396,3608	2203	4299	6502	SO:0001583	missense	81929	exon8			GTTCAACTATTCC	BC012430	CCDS32791.1, CCDS45832.1	18p11.21	2013-01-10				ENSG00000085415		"""WD repeat domain containing"""	30379	protein-coding gene	gene with protein product	"""sec13 like protein"", ""nucleoporin Seh1"""	609263				12196509, 14517296	Standard	XM_005258152		Approved	SEH1A, SEH1B, Seh1, SEC13L	uc002krq.3	Q96EE3		ENST00000262124.11:c.1025C>A	18.37:g.12984144C>A	ENSP00000262124:p.Thr342Asn	Somatic	231	0	0		WXS	Illumina HiSeq	Phase_I	193	96	0.497409	NM_001013437	A8K5B1|Q8NFU6|Q96MH3|Q9C069	Missense_Mutation	SNP	ENST00000262124.11	37	CCDS45832.1	1647	0.7541208791208791	476	0.967479674796748	237	0.6546961325966851	462	0.8076923076923077	472	0.6226912928759895	A	3.658	-0.070133	0.07228	0.921244	0.620726	ENSG00000085415	ENST00000399892;ENST00000262124	T;T	0.68765	-0.29;-0.35	6.04	1.0	0.19881	.	0.378371	0.31884	N	0.006907	T	0.00012	0.0000	N	0.00926	-1.1	0.58432	P	4.000000000004E-6	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.32134	-0.9918	9	0.10377	T	0.69	-10.2768	7.0792	0.25221	0.3928:0.3408:0.2663:0.0	rs6505776;rs52825360;rs58418692;rs6505776	342;342	Q96EE3;Q96EE3-1	SEH1_HUMAN;.	N	342	ENSP00000382779:T342N;ENSP00000262124:T342N	ENSP00000262124:T342N	T	+	2	0	SEH1L	12974144	1.000000	0.71417	0.929000	0.37066	0.983000	0.72400	1.686000	0.37669	-0.279000	0.09167	-0.362000	0.07510	ACT	C|0.252;A|0.748	0.748	strong		0.408	SEH1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458254.1	NM_031216	
TEX101	83639	hgsc.bcm.edu	37	19	43922061	43922061	+	Silent	SNP	A	A	G	rs3816438	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:43922061A>G	ENST00000598265.1	+	5	589	c.423A>G	c.(421-423)ccA>ccG	p.P141P	TEX101_ENST00000602198.1_Silent_p.P159P|TEX101_ENST00000253435.7_Silent_p.P159P|TEX101_ENST00000601707.1_3'UTR	NM_001130011.1	NP_001123483.1	Q9BY14	TX101_HUMAN	testis expressed 101	141	UPAR/Ly6.					acrosomal membrane (GO:0002080)|anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)				large_intestine(1)|lung(12)|ovary(1)|skin(1)	15		Prostate(69;0.0199)				TCCATTGTCCAACCTGTGTGG	0.512													A|||	1440	0.28754	0.0287	0.2839	5008	,	,		21738	0.6091		0.2366	False		,,,				2504	0.3609				p.P159P		Atlas-SNP	.											.	TEX101	28	.	0			c.A477G						PASS	.	A	,	257,4149	146.1+/-180.8	5,247,1951	325.0	268.0	287.0		423,477	1.5	1.0	19	dbSNP_107	287	1964,6636	345.5+/-325.8	253,1458,2589	no	coding-synonymous,coding-synonymous	TEX101	NM_001130011.1,NM_031451.4	,	258,1705,4540	GG,GA,AA		22.8372,5.833,17.0767	,	141/250,159/268	43922061	2221,10785	2203	4300	6503	SO:0001819	synonymous_variant	83639	exon8			TTGTCCAACCTGT	AF241268	CCDS12619.1, CCDS59393.1	19q13.31	2013-06-06	2007-03-13			ENSG00000131126			30722	protein-coding gene	gene with protein product	"""cancer/testis antigen 131"", ""spermatogenesis associated 44"""	612665	"""testis expressed sequence 101"""			16388701, 16516155	Standard	NM_031451		Approved	MGC4766, SGRG, CT131, SPATA44	uc010xwo.2	Q9BY14		ENST00000598265.1:c.423A>G	19.37:g.43922061A>G		Somatic	375	0	0		WXS	Illumina HiSeq	Phase_I	345	152	0.44058	NM_031451	Q7L5R2|Q9BPY7	Silent	SNP	ENST00000598265.1	37	CCDS59393.1																																																																																			A|0.783;G|0.217	0.217	strong		0.512	TEX101-004	KNOWN	non_canonical_other|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000463176.1	NM_031451	
PTCH1	5727	hgsc.bcm.edu	37	9	98238358	98238358	+	Silent	SNP	G	G	A	rs2066836	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:98238358G>A	ENST00000331920.6	-	12	1985	c.1686C>T	c.(1684-1686)gcC>gcT	p.A562A	PTCH1_ENST00000430669.2_Silent_p.A496A|PTCH1_ENST00000375274.2_Silent_p.A561A|PTCH1_ENST00000418258.1_Silent_p.A411A|PTCH1_ENST00000429896.2_Silent_p.A411A|PTCH1_ENST00000437951.1_Silent_p.A496A|PTCH1_ENST00000421141.1_Silent_p.A411A	NM_000264.3	NP_000255.2	Q13635	PTC1_HUMAN	patched 1	562	SSD. {ECO:0000255|PROSITE- ProRule:PRU00199}.				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)				GGATTAACGCGGCCATGAAGA	0.577													G|||	460	0.091853	0.0106	0.098	5008	,	,		17758	0.0833		0.1948	False		,,,				2504	0.1002				p.A562A		Atlas-SNP	.											.	PTCH1	1850	.	0			c.C1686T						PASS	.	G	,,,,,,	146,4260	99.8+/-138.5	3,140,2060	84.0	63.0	70.0		1686,1488,1683,1233,1233,1233,1233	-11.3	0.0	9	dbSNP_94	70	1903,6697	335.3+/-321.3	207,1489,2604	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	,,,,,,	210,1629,4664	AA,AG,GG		22.1279,3.3137,15.7543	,,,,,,	562/1448,496/1382,561/1447,411/1297,411/1297,411/1297,411/1297	98238358	2049,10957	2203	4300	6503	SO:0001819	synonymous_variant	5727	exon12			TAACGCGGCCATG	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.1686C>T	9.37:g.98238358G>A		Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	31	12	0.387097	NM_000264	A3KBI9|E9PEJ8|Q13463|Q5R1U7|Q5R1U9|Q5R1V0|Q5VZC0|Q5VZC2|Q86XG7	Silent	SNP	ENST00000331920.6	37	CCDS6714.1																																																																																			G|0.865;A|0.135	0.135	strong		0.577	PTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053229.2	NM_000264	
CYP4F12	66002	hgsc.bcm.edu	37	19	15807884	15807884	+	Missense_Mutation	SNP	A	A	G	rs593818	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:15807884A>G	ENST00000550308.1	+	13	1944	c.1564A>G	c.(1564-1566)Agc>Ggc	p.S522G	CYP4F12_ENST00000324632.10_Missense_Mutation_p.S522G	NM_023944.3	NP_076433	Q9HCS2	CP4FC_HUMAN	cytochrome P450, family 4, subfamily F, polypeptide 12	522			S -> G (in dbSNP:rs593818). {ECO:0000269|PubMed:11162607, ECO:0000269|PubMed:11162645, ECO:0000269|PubMed:12975309, ECO:0000269|Ref.7}.		arachidonic acid metabolic process (GO:0019369)|drug metabolic process (GO:0017144)|epoxygenase P450 pathway (GO:0019373)|leukotriene B4 catabolic process (GO:0036101)|long-chain fatty acid metabolic process (GO:0001676)|negative regulation of blood coagulation (GO:0030195)|oxidation-reduction process (GO:0055114)|pressure natriuresis (GO:0003095)|renal water homeostasis (GO:0003091)|small molecule metabolic process (GO:0044281)|sodium ion homeostasis (GO:0055078)|very long-chain fatty acid metabolic process (GO:0000038)|vitamin E metabolic process (GO:0042360)|vitamin K biosynthetic process (GO:0042371)|xenobiotic metabolic process (GO:0006805)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)	alkane 1-monooxygenase activity (GO:0018685)|arachidonic acid epoxygenase activity (GO:0008392)|aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|leukotriene-B4 20-monooxygenase activity (GO:0050051)|vitamin-K-epoxide reductase (warfarin-sensitive) activity (GO:0047057)			NS(1)|central_nervous_system(3)|endometrium(4)|kidney(2)|large_intestine(7)|lung(12)|ovary(3)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	41	Acute lymphoblastic leukemia(2;0.0367)				Fingolimod(DB08868)	CCTGAATGTAAGCTTGCAGTG	0.572													G|||	3076	0.614217	0.6006	0.647	5008	,	,		18672	0.7421		0.5129	False		,,,				2504	0.5818				p.S522G		Atlas-SNP	.											.	CYP4F12	89	.	0			c.A1564G						PASS	.	G	GLY/SER	2663,1695		834,995,350	58.0	62.0	61.0		1564	-1.8	0.0	19	dbSNP_83	61	4510,4074		1211,2088,993	yes	missense	CYP4F12	NM_023944.3	56	2045,3083,1343	GG,GA,AA		47.4604,38.894,44.5758	benign	522/525	15807884	7173,5769	2179	4292	6471	SO:0001583	missense	66002	exon13			AATGTAAGCTTGC	AB035130	CCDS42517.1	19p13.1	2008-02-05	2003-01-14		ENSG00000186204	ENSG00000186204		"""Cytochrome P450s"""	18857	protein-coding gene	gene with protein product		611485	"""cytochrome P450, subfamily IVF, polypeptide 12"""			11162607	Standard	NM_023944		Approved		uc002nbl.3	Q9HCS2	OTTHUMG00000164477	ENST00000550308.1:c.1564A>G	19.37:g.15807884A>G	ENSP00000448998:p.Ser522Gly	Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	137	137	1	NM_023944	E7ET51|O60389|Q5JPJ7|Q9HCS1	Missense_Mutation	SNP	ENST00000550308.1	37	CCDS42517.1	1320	0.6043956043956044	282	0.573170731707317	226	0.6243093922651933	420	0.7342657342657343	392	0.5171503957783641	.	0.009	-1.820459	0.00595	0.61106	0.525396	ENSG00000186204	ENST00000550308;ENST00000324632	T;T	0.68479	-0.33;-0.33	2.23	-1.81	0.07882	.	3.388060	0.03644	N	0.239949	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	0.39502	-0.9611	9	0.02654	T	1	.	3.753	0.08573	0.2902:0.4077:0.3022:0.0	rs593818;rs1059447;rs3170514;rs52811306;rs57321119;rs593818	522	Q9HCS2	CP4FC_HUMAN	G	522	ENSP00000448998:S522G;ENSP00000321821:S522G	ENSP00000321821:S522G	S	+	1	0	CYP4F12	15668884	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.458000	0.02372	-0.729000	0.04875	-0.642000	0.03964	AGC	A|0.395;G|0.605	0.605	strong		0.572	CYP4F12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378938.9		
CES1	1066	hgsc.bcm.edu	37	16	55862836	55862836	+	Silent	SNP	G	G	A	rs3826191		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:55862836G>A	ENST00000361503.4	-	2	230	c.100C>T	c.(100-102)Ctg>Ttg	p.L34L	CES1_ENST00000360526.3_Silent_p.L35L|CES1_ENST00000422046.2_Silent_p.L34L|CES1_ENST00000566555.1_5'Flank			P23141	EST1_HUMAN	carboxylesterase 1	34					epithelial cell differentiation (GO:0030855)|metabolic process (GO:0008152)|response to toxic substance (GO:0009636)	endoplasmic reticulum (GO:0005783)	carboxylic ester hydrolase activity (GO:0052689)|methylumbelliferyl-acetate deacetylase activity (GO:0047374)								all cancers(182;0.13)|Epithelial(162;0.137)	Benzocaine(DB01086)|Capecitabine(DB01101)|Ciclesonide(DB01410)|Clopidogrel(DB00758)|Cyclandelate(DB04838)|Dabigatran etexilate(DB06695)|Indomethacin(DB00328)|Irinotecan(DB00762)|L-Carnitine(DB00583)|Mycophenolate mofetil(DB00688)|Oseltamivir(DB00198)|Probucol(DB01599)|Rufinamide(DB06201)|Tamoxifen(DB00675)|Trandolapril(DB00519)	AACTTCCCCAGCACTTTGCCA	0.557																																					p.L35L	NSCLC(162;1801 2756 42904 52896)	Atlas-SNP	.											CES1_ENST00000360526,colon,carcinoma,0,1	CES1	78	1	0			c.C103T						PASS	.						64.0	50.0	55.0					16																	55862836		2198	4300	6498	SO:0001819	synonymous_variant	1066	exon2			TCCCCAGCACTTT	BC012418	CCDS32450.1, CCDS45488.1, CCDS45489.1	16q22.2	2010-10-12	2010-10-12		ENSG00000198848	ENSG00000198848	3.1.1.1	"""Carboxylesterases"""	1863	protein-coding gene	gene with protein product	"""human monocyte/macrophage serine esterase 1"""	114835	"""carboxylesterase 1 (monocyte/macrophage serine esterase 1)"""			2070086, 20931200	Standard	XM_005255774		Approved	HMSE, CES2, HMSE1, SES1, CEH, CES1A1, CES1A2	uc002eil.3	P23141		ENST00000361503.4:c.100C>T	16.37:g.55862836G>A		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	78	13	0.166667	NM_001025195	A6NIM1|A8K3K8|A8K844|E9PAU8|P82127|Q00015|Q13657|Q14062|Q16737|Q16788|Q549X7|Q549X8|Q86UK2|Q96EE8|Q9UC52|Q9UDG8|Q9UK77|Q9ULY2	Silent	SNP	ENST00000361503.4	37	CCDS45488.1																																																																																			G|0.500;A|0.500	0.500	strong		0.557	CES1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000433285.1	NM_001266	
SLC2A14	144195	hgsc.bcm.edu	37	12	7966958	7966958	+	Missense_Mutation	SNP	C	C	T	rs10845981	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:7966958C>T	ENST00000543909.1	-	16	2276	c.1517G>A	c.(1516-1518)gGg>gAg	p.G506E	SLC2A14_ENST00000431042.2_Missense_Mutation_p.G483E|SLC2A14_ENST00000535295.1_Missense_Mutation_p.G397E|SLC2A14_ENST00000542546.1_Missense_Mutation_p.G397E|SLC2A14_ENST00000340749.5_Missense_Mutation_p.G483E|SLC2A14_ENST00000396589.2_Missense_Mutation_p.G506E|SLC2A14_ENST00000542505.1_Missense_Mutation_p.G147E|SLC2A14_ENST00000539924.1_Missense_Mutation_p.G521E			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	180	0	0		WXS	Illumina HiSeq	Phase_I	201	88	0.437811	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	
TIPIN	54962	hgsc.bcm.edu	37	15	66641732	66641732	+	Missense_Mutation	SNP	G	G	C	rs2063690	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:66641732G>C	ENST00000261881.4	-	5	417	c.332C>G	c.(331-333)gCa>gGa	p.A111G	Y_RNA_ENST00000411339.1_RNA|SCARNA14_ENST00000516903.1_RNA|TIPIN_ENST00000367709.4_Missense_Mutation_p.A10G	NM_017858.2	NP_060328	Q9BVW5	TIPIN_HUMAN	TIMELESS interacting protein	111	Interaction with TIMELESS.		A -> G (in dbSNP:rs2063690). {ECO:0000269|Ref.2}.		cell cycle phase transition (GO:0044770)|DNA replication checkpoint (GO:0000076)|intra-S DNA damage checkpoint (GO:0031573)|mitotic nuclear division (GO:0007067)|positive regulation of cell proliferation (GO:0008284)|regulation of nuclear cell cycle DNA replication (GO:0033262)|replication fork protection (GO:0048478)|response to UV (GO:0009411)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)				autonomic_ganglia(1)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|ovary(1)|skin(1)|stomach(1)	7						TAGCCTATGTGCCCAGTGCTC	0.408													G|||	701	0.139976	0.0666	0.1297	5008	,	,		17463	0.3214		0.0855	False		,,,				2504	0.1155				p.A111G		Atlas-SNP	.											.	TIPIN	23	.	0			c.C332G						PASS	.	G	GLY/ALA	330,4072	171.9+/-202.1	9,312,1880	120.0	116.0	117.0		332	5.5	1.0	15	dbSNP_94	117	739,7859	176.8+/-226.5	28,683,3588	yes	missense	TIPIN	NM_017858.2	60	37,995,5468	CC,CG,GG		8.595,7.4966,8.2231	probably-damaging	111/302	66641732	1069,11931	2201	4299	6500	SO:0001583	missense	54962	exon5			CTATGTGCCCAGT	BK001386	CCDS10215.1	15q22.31	2012-03-02	2006-08-08		ENSG00000075131	ENSG00000075131			30750	protein-coding gene	gene with protein product	"""CSM3 homolog (S. cerevisiae)"""	610716				12875843, 17102137	Standard	NM_017858		Approved	FLJ20516	uc002apr.2	Q9BVW5	OTTHUMG00000133188	ENST00000261881.4:c.332C>G	15.37:g.66641732G>C	ENSP00000261881:p.Ala111Gly	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	118	64	0.542373	NM_017858	B2CW64|Q9NWZ6	Missense_Mutation	SNP	ENST00000261881.4	37	CCDS10215.1	362	0.16575091575091574	38	0.07723577235772358	37	0.10220994475138122	223	0.38986013986013984	64	0.08443271767810026	G	16.01	3.002140	0.54254	0.074966	0.08595	ENSG00000075131	ENST00000367709;ENST00000261881	T;T	0.49720	0.77;0.77	5.54	5.54	0.83059	Replication fork protection component Swi3 (2);	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	L	0.37697	1.125	0.09310	P	0.9999999875026	P	0.37663	0.604	B	0.38954	0.286	T	0.42396	-0.9454	9	0.41790	T	0.15	-20.1045	18.0484	0.89340	0.0:0.0:1.0:0.0	rs2063690;rs17686704;rs2063690	111	Q9BVW5	TIPIN_HUMAN	G	10;111	ENSP00000356682:A10G;ENSP00000261881:A111G	ENSP00000261881:A111G	A	-	2	0	TIPIN	64428786	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.354000	0.97083	2.610000	0.88304	0.555000	0.69702	GCA	G|0.877;C|0.123	0.123	strong		0.408	TIPIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256897.2	NM_017858	
OR10H5	284433	hgsc.bcm.edu	37	19	15905002	15905002	+	Silent	SNP	T	T	C	rs4808379	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:15905002T>C	ENST00000308940.8	+	1	242	c.144T>C	c.(142-144)acT>acC	p.T48T		NM_001004466.1	NP_001004466.1	Q8NGA6	O10H5_HUMAN	olfactory receptor, family 10, subfamily H, member 5	48						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(1)|lung(9)|ovary(1)	20						TCATGGCCACTGTCTGGAGCG	0.597													.|||	2431	0.485423	0.4433	0.4841	5008	,	,		19819	0.7907		0.3052	False		,,,				2504	0.4141				p.T48T		Atlas-SNP	.											.	OR10H5	49	.	0			c.T144C						PASS	.	C		1909,2497		406,1097,700	205.0	166.0	179.0		144	-6.8	0.0	19	dbSNP_111	179	2918,5682		510,1898,1892	no	coding-synonymous	OR10H5	NM_001004466.1		916,2995,2592	CC,CT,TT		33.9302,43.3273,37.1136		48/316	15905002	4827,8179	2203	4300	6503	SO:0001819	synonymous_variant	284433	exon1			GGCCACTGTCTGG	AC011537	CCDS32940.1	19p13.12	2013-09-24			ENSG00000172519	ENSG00000172519		"""GPCR / Class A : Olfactory receptors"""	15389	protein-coding gene	gene with protein product							Standard	NM_001004466		Approved		uc010xos.2	Q8NGA6	OTTHUMG00000182284	ENST00000308940.8:c.144T>C	19.37:g.15905002T>C		Somatic	208	0	0		WXS	Illumina HiSeq	Phase_I	187	88	0.470588	NM_001004466	Q6IFJ0|Q96R60	Silent	SNP	ENST00000308940.8	37	CCDS32940.1																																																																																			.	.	weak		0.597	OR10H5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460363.1		
IPO13	9670	hgsc.bcm.edu	37	1	44415415	44415415	+	Silent	SNP	C	C	T	rs2240447	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:44415415C>T	ENST00000372343.3	+	2	1073	c.411C>T	c.(409-411)gaC>gaT	p.D137D		NM_014652.3	NP_055467.3	O94829	IPO13_HUMAN	importin 13	137					protein import into nucleus (GO:0006606)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(6)|lung(13)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	40	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0821)				TGATGCCTGACGCTTGGCCAT	0.592													C|||	2530	0.505192	0.0877	0.6167	5008	,	,		20937	0.6161		0.7634	False		,,,				2504	0.6104				p.D137D		Atlas-SNP	.											.	IPO13	86	.	0			c.C411T						PASS	.	C		901,3505	348.0+/-309.7	101,699,1403	79.0	67.0	71.0		411	-9.4	0.6	1	dbSNP_98	71	6752,1848	730.0+/-406.7	2666,1420,214	no	coding-synonymous	IPO13	NM_014652.3		2767,2119,1617	TT,TC,CC		21.4884,20.4494,41.1579		137/964	44415415	7653,5353	2203	4300	6503	SO:0001819	synonymous_variant	9670	exon2			GCCTGACGCTTGG	AB018267	CCDS503.1	1p34.1	2008-02-05			ENSG00000117408	ENSG00000117408		"""Importins"""	16853	protein-coding gene	gene with protein product		610411				9872452, 11447110	Standard	NM_014652		Approved	IMP13, KIAA0724, RANBP13	uc001ckx.3	O94829	OTTHUMG00000008297	ENST00000372343.3:c.411C>T	1.37:g.44415415C>T		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	117	116	0.991453	NM_014652	D3DPY4|Q5T4X3|Q7LC04|Q96HS3|Q9H8N3|Q9UFR1	Silent	SNP	ENST00000372343.3	37	CCDS503.1																																																																																			C|0.416;T|0.584	0.584	strong		0.592	IPO13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022846.1	NM_014652	
ARSH	347527	hgsc.bcm.edu	37	X	2942109	2942109	+	Silent	SNP	T	T	C	rs5939407	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:2942109T>C	ENST00000381130.2	+	6	949	c.949T>C	c.(949-951)Ttg>Ctg	p.L317L		NM_001011719.1	NP_001011719.1	Q5FYA8	ARSH_HUMAN	arylsulfatase family, member H	317					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)|integral component of membrane (GO:0016021)	arylsulfatase activity (GO:0004065)|metal ion binding (GO:0046872)			breast(3)|endometrium(8)|kidney(2)|large_intestine(6)|lung(13)|skin(1)|stomach(1)	34		all_cancers(21;9e-05)|all_epithelial(21;6.22e-06)|all_lung(23;0.000597)|Lung NSC(23;0.00901)|Lung SC(21;0.186)				CAACCACACCTTGGTGTACTT	0.572													T|||	2820	0.74702	0.4554	0.5706	3775	,	,		8094	0.7331		0.4911	False		,,,				2504	0.6022				p.L317L		Atlas-SNP	.											.	ARSH	72	.	0			c.T949C						PASS	.	T		2326,1509		613,768,332,251,239	51.0	47.0	48.0		949	2.0	0.1	X	dbSNP_114	48	4345,2383		998,1127,1222,303,650	no	coding-synonymous	ARSH	NM_001011719.1		1611,1895,1554,554,889	CC,CT,C,TT,T		35.4191,39.3481,36.8456		317/563	2942109	6671,3892	2203	4300	6503	SO:0001819	synonymous_variant	347527	exon6			CACACCTTGGTGT	AY875940	CCDS35198.1	Xp22.33	2013-02-14	2006-03-07		ENSG00000205667	ENSG00000205667		"""Arylsulfatase family"""	32488	protein-coding gene	gene with protein product		300586	"""arylsulfatase H"""			16174644	Standard	NM_001011719		Approved		uc011mhj.2	Q5FYA8	OTTHUMG00000159612	ENST00000381130.2:c.949T>C	X.37:g.2942109T>C		Somatic	273	0	0		WXS	Illumina HiSeq	Phase_I	209	207	0.990431	NM_001011719		Silent	SNP	ENST00000381130.2	37	CCDS35198.1																																																																																			T|0.346;C|0.654	0.654	strong		0.572	ARSH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356489.1	NM_001011719	
OBSCN	84033	hgsc.bcm.edu	37	1	228482010	228482010	+	Silent	SNP	C	C	T	rs449133	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:228482010C>T	ENST00000422127.1	+	42	11333	c.11289C>T	c.(11287-11289)gaC>gaT	p.D3763D	OBSCN_ENST00000284548.11_Silent_p.D3763D|RP5-1139B12.4_ENST00000602778.1_RNA|OBSCN_ENST00000359599.6_Silent_p.D2610D|OBSCN_ENST00000570156.2_Silent_p.D4192D|OBSCN_ENST00000366709.4_Silent_p.D882D|OBSCN_ENST00000366707.4_Silent_p.D882D	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	3763	Ig-like 38.				apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				TGAGGCAGGACGGGTCCAGGT	0.652													C|||	1913	0.381989	0.472	0.4179	5008	,	,		20851	0.247		0.4821	False		,,,				2504	0.271				p.D4192D		Atlas-SNP	.											.	OBSCN	2142	.	0			c.C12576T						PASS	.	C	,	1786,2524		398,990,767	144.0	151.0	149.0		11289,11289	-9.9	0.0	1	dbSNP_80	149	4209,4289		1075,2059,1115	no	coding-synonymous,coding-synonymous	OBSCN	NM_001098623.1,NM_052843.2	,	1473,3049,1882	TT,TC,CC		49.5293,41.4385,46.8067	,	3763/7969,3763/6621	228482010	5995,6813	2155	4249	6404	SO:0001819	synonymous_variant	84033	exon47			GCAGGACGGGTCC	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"""Rho guanine nucleotide exchange factors"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.11289C>T	1.37:g.228482010C>T		Somatic	185	1	0.00540541		WXS	Illumina HiSeq	Phase_I	174	99	0.568965	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Silent	SNP	ENST00000422127.1	37	CCDS58065.1																																																																																			C|0.595;T|0.405	0.405	strong		0.652	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
KIRREL3	84623	hgsc.bcm.edu	37	11	126391297	126391297	+	Silent	SNP	T	T	G	rs12269776	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:126391297T>G	ENST00000525144.2	-	4	595	c.346A>C	c.(346-348)Agg>Cgg	p.R116R	KIRREL3_ENST00000525704.2_Silent_p.R116R|KIRREL3_ENST00000529097.2_Silent_p.R116R	NM_032531.3	NP_115920.1	Q8IZU9	KIRR3_HUMAN	kin of IRRE like 3 (Drosophila)	116	Ig-like C2-type 1.				hemopoiesis (GO:0030097)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				central_nervous_system(1)|endometrium(5)|large_intestine(11)|lung(8)|ovary(3)|prostate(1)	29	all_hematologic(175;0.145)	Lung NSC(97;0.0484)|all_lung(97;0.0522)|Medulloblastoma(222;0.0523)|Breast(109;0.0949)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;6.03e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.12)		AGCTCTGCCCTCAGGATCTTC	0.632													G|||	1126	0.22484	0.5015	0.2075	5008	,	,		15796	0.0446		0.2008	False		,,,				2504	0.0736				p.R116R		Atlas-SNP	.											.	KIRREL3	183	.	0			c.A346C						PASS	.	G	,	1786,2446		387,1012,717	42.0	54.0	50.0		346,346	2.5	1.0	11	dbSNP_120	50	1771,6703		184,1403,2650	no	coding-synonymous,coding-synonymous	KIRREL3	NM_001161707.1,NM_032531.3	,	571,2415,3367	GG,GT,TT		20.8992,42.2023,27.9946	,	116/601,116/779	126391297	3557,9149	2116	4237	6353	SO:0001819	synonymous_variant	84623	exon4			CTGCCCTCAGGAT	AB058770	CCDS53723.1, CCDS55796.1, CCDS73413.1	11q24	2013-01-29			ENSG00000149571	ENSG00000149571		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	23204	protein-coding gene	gene with protein product		607761				12424224, 11347906	Standard	NM_032531		Approved	NEPH2, KIAA1867, KIRRE	uc001qea.3	Q8IZU9	OTTHUMG00000165831	ENST00000525144.2:c.346A>C	11.37:g.126391297T>G		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	112	26	0.232143	NM_032531	Q3MIJ7|Q6UWJ9|Q6UWL5|Q96JG0	Silent	SNP	ENST00000525144.2	37	CCDS53723.1																																																																																			T|0.764;G|0.236	0.236	strong		0.632	KIRREL3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386479.2	NM_032531	
CUX1	1523	hgsc.bcm.edu	37	7	101921292	101921292	+	Missense_Mutation	SNP	A	A	C	rs118010189	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:101921292A>C	ENST00000437600.4	+	18	1982	c.1630A>C	c.(1630-1632)Aag>Cag	p.K544Q	CUX1_ENST00000547394.2_Missense_Mutation_p.K530Q|CUX1_ENST00000425244.2_Missense_Mutation_p.K500Q|CUX1_ENST00000393824.3_Missense_Mutation_p.K507Q|CUX1_ENST00000560541.1_3'UTR|CUX1_ENST00000292538.4_Missense_Mutation_p.K546Q	NM_181500.2	NP_852477.1	P39880	CUX1_HUMAN	cut-like homeobox 1	353					auditory receptor cell differentiation (GO:0042491)|kidney development (GO:0001822)|lung development (GO:0030324)|multicellular organismal development (GO:0007275)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of dendrite morphogenesis (GO:0050775)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|retrograde transport, vesicle recycling within Golgi (GO:0000301)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi membrane (GO:0000139)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding (GO:0043565)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(3)|large_intestine(8)|lung(26)|ovary(7)|pancreas(1)|prostate(6)|skin(2)|stomach(1)|urinary_tract(5)	70						CGACAACATCAAGCTCTTTGA	0.662													A|||	18	0.00359425	0.0	0.0101	5008	,	,		12632	0.0		0.007	False		,,,				2504	0.0041				p.K546Q		Atlas-SNP	.											.	CUX1	253	.	0			c.A1636C						PASS	.	A	GLN/LYS,GLN/LYS,GLN/LYS,GLN/LYS,GLN/LYS	5,4401	8.1+/-20.4	0,5,2198	42.0	36.0	38.0		1588,1498,1519,1636,1630	4.6	1.0	7	dbSNP_133	38	88,8510	45.8+/-104.6	0,88,4211	yes	missense,missense,missense,missense,missense	CUX1	NM_001202544.1,NM_001202545.1,NM_001202546.1,NM_001913.3,NM_181500.2	53,53,53,53,53	0,93,6409	CC,CA,AA		1.0235,0.1135,0.7152	,,,,	530/663,500/633,507/640,546/679,544/677	101921292	93,12911	2203	4299	6502	SO:0001583	missense	1523	exon18			AACATCAAGCTCT	M74099	CCDS5720.1, CCDS5721.1, CCDS47672.1, CCDS56498.1, CCDS56499.1, CCDS56500.1, CCDS59071.1	7q22.1	2012-10-03	2007-11-07	2007-11-07	ENSG00000257923	ENSG00000257923		"""Homeoboxes / CUT class"""	2557	protein-coding gene	gene with protein product	"""golgi integral membrane protein 6"""	116896	"""cut (Drosophila)-like 1 (CCAAT displacement protein)"", ""cut-like 1, CCAAT displacement protein (Drosophila)"""	CUTL1		8468066, 9799793, 15004235	Standard	NM_001202543		Approved	CDP, CDP1, CUX, CUT, Clox, CDP/Cut, CDP/Cux, Cux/CDP, CASP, GOLIM6	uc003uyx.4	P39880	OTTHUMG00000157129	ENST00000437600.4:c.1630A>C	7.37:g.101921292A>C	ENSP00000414091:p.Lys544Gln	Somatic	282	0	0		WXS	Illumina HiSeq	Phase_I	244	120	0.491803	NM_001913	B3KV79|J3KQV9|Q6NYH4|Q75LE5|Q75MT2|Q75MT3|Q86UJ7|Q9UEV5	Missense_Mutation	SNP	ENST00000437600.4	37	CCDS47672.1	9	0.004120879120879121	0	0.0	5	0.013812154696132596	0	0.0	4	0.005277044854881266	A	21.6	4.169486	0.78452	0.001135	0.010235	ENSG00000257923	ENST00000292538;ENST00000547394;ENST00000425244;ENST00000437600	T;T;T;T	0.32753	1.44;1.44;1.44;1.44	4.55	4.55	0.56014	CASP, C-terminal (1);	.	.	.	.	T	0.45796	0.1360	M	0.66560	2.04	0.28388	N	0.919234	D;D;D;D;D	0.89917	1.0;0.999;0.972;1.0;0.998	D;D;P;D;D	0.85130	0.99;0.997;0.861;0.989;0.963	T	0.45220	-0.9276	9	0.52906	T	0.07	.	14.2558	0.66051	1.0:0.0:0.0:0.0	.	507;500;530;544;546	B4DZZ2;B3KV79;G3V1Z6;Q13948-2;Q13948	.;.;.;.;CASP_HUMAN	Q	546;530;500;544	ENSP00000292538:K546Q;ENSP00000449371:K530Q;ENSP00000409745:K500Q;ENSP00000414091:K544Q	ENSP00000292538:K546Q	K	+	1	0	CUX1	101708012	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	8.671000	0.91174	1.849000	0.53698	0.374000	0.22700	AAG	A|0.993;C|0.007	0.007	strong		0.662	CUX1-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347534.3	NM_001913	
CFAP74	85452	hgsc.bcm.edu	37	1	1916890	1916890	+	IGR	SNP	C	C	T	rs3795280	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:1916890C>T	ENST00000434971.2	-	0	339							Q69YW0	CA222_HUMAN												breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|stomach(1)	11	all_cancers(77;0.000708)|all_epithelial(69;0.000943)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;6.04e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Medulloblastoma(700;0.151)|Lung SC(97;0.217)		Epithelial(90;1.82e-37)|OV - Ovarian serous cystadenocarcinoma(86;2.75e-23)|GBM - Glioblastoma multiforme(42;9e-08)|Colorectal(212;3.94e-05)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.00435)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.199)		GCTCTGCAAACAGGCGTCTGG	0.662													c|||	2196	0.438498	0.6573	0.2795	5008	,	,		18797	0.4335		0.3082	False		,,,				2504	0.3947				p.L145L		Atlas-SNP	.											.	KIAA1751	92	.	0			c.G435A						PASS	.	T		2382,1730		693,996,367	67.0	73.0	71.0		435	2.8	0.6	1	dbSNP_107	71	2744,5634		450,1844,1895	no	coding-synonymous	KIAA1751	NM_001080484.1		1143,2840,2262	TT,TC,CC		32.7524,42.072,41.0408		145/763	1916890	5126,7364	2056	4189	6245	SO:0001628	intergenic_variant	85452	exon6			TGCAAACAGGCGT																													1.37:g.1916890C>T		Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	91	28	0.307692	NM_001080484		Silent	SNP	ENST00000434971.2	37																																																																																				C|0.606;T|0.394	0.394	strong		0.662	C1orf222-201	KNOWN	basic	protein_coding	protein_coding			
DNAH17	8632	hgsc.bcm.edu	37	17	76472768	76472768	+	Silent	SNP	G	G	A	rs7405830	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:76472768G>A	ENST00000585328.1	-	52	8149	c.8025C>T	c.(8023-8025)ctC>ctT	p.L2675L	DNAH17_ENST00000389840.5_Silent_p.L2666L|DNAH17_ENST00000586052.1_Intron	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	263	0	0		WXS	Illumina HiSeq	Phase_I	211	113	0.535545	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	
BTN3A2	11118	hgsc.bcm.edu	37	6	26370659	26370659	+	Silent	SNP	C	C	T	rs71544290|rs9393711	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:26370659C>T	ENST00000356386.2	+	5	731	c.543C>T	c.(541-543)aaC>aaT	p.N181N	BTN3A2_ENST00000396948.1_Silent_p.N181N|BTN3A2_ENST00000396934.3_Silent_p.N158N|BTN3A2_ENST00000532994.1_3'UTR|BTN3A2_ENST00000527422.1_Silent_p.N181N|BTN3A2_ENST00000508906.2_Silent_p.N139N|BTN3A2_ENST00000377708.2_Silent_p.N181N	NM_001197246.2|NM_001197247.1|NM_007047.3	NP_001184175.1|NP_001184176.1|NP_008978.2	P78410	BT3A2_HUMAN	butyrophilin, subfamily 3, member A2	181			N -> D (in dbSNP:rs9358936). {ECO:0000269|PubMed:14702039}.		interferon-gamma secretion (GO:0072643)|T cell mediated immunity (GO:0002456)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(5)	10						AGTGGAGCAACGCCAAGGGAG	0.552													C|||	410	0.081869	0.0287	0.0418	5008	,	,		18398	0.0992		0.1123	False		,,,				2504	0.1329				p.N181N		Atlas-SNP	.											.	BTN3A2	44	.	0			c.C543T						PASS	.	C	,,,,	168,4238	111.2+/-149.4	2,164,2037	131.0	117.0	122.0		543,543,474,417,543	-4.6	0.0	6	dbSNP_119	122	944,7656	206.8+/-248.7	51,842,3407	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	BTN3A2	NM_001197246.1,NM_001197247.1,NM_001197248.1,NM_001197249.1,NM_007047.3	,,,,	53,1006,5444	TT,TC,CC		10.9767,3.813,8.5499	,,,,	181/335,181/335,158/312,139/293,181/335	26370659	1112,11894	2203	4300	6503	SO:0001819	synonymous_variant	11118	exon3			GAGCAACGCCAAG	U90546	CCDS4605.1, CCDS56399.1, CCDS56400.1	6p22.1	2014-01-14			ENSG00000186470	ENSG00000186470		"""Immunoglobulin superfamily / V-set domain containing"", ""Butyrophilins"""	1139	protein-coding gene	gene with protein product		613594				9149941	Standard	NM_007047		Approved	BTN3.2	uc010jqi.2	P78410	OTTHUMG00000014450	ENST00000356386.2:c.543C>T	6.37:g.26370659C>T		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	115	114	0.991304	NM_001197246	B4DRT7|B4E103|F5H791|F8W6E0|O00477|O15338|O75658|Q76PA0|Q9BU81|Q9NR44	Silent	SNP	ENST00000356386.2	37	CCDS4605.1																																																																																			C|0.923;T|0.077	0.077	strong		0.552	BTN3A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040113.2		
MUC4	4585	hgsc.bcm.edu	37	3	195506076	195506076	+	Missense_Mutation	SNP	C	C	G	rs547812110	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195506076C>G	ENST00000463781.3	-	2	12834	c.12375G>C	c.(12373-12375)caG>caC	p.Q4125H	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.Q4125H	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.Q4125H(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)		GAGGGGTGGCCTGACCTGTGG	0.582													.|||	590	0.117812	0.2995	0.0937	5008	,	,		9585	0.0288		0.0825	False		,,,				2504	0.0174				p.Q4125H		Atlas-SNP	.											MUC4_ENST00000463781,brain,primitive_neuroectodermal_tumour-medulloblastoma,0,1	MUC4	1505	1	1	Substitution - Missense(1)	central_nervous_system(1)	c.G12375C						scavenged	.						12.0	9.0	10.0					3																	195506076		599	1486	2085	SO:0001583	missense	4585	exon2			GGTGGCCTGACCT	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.12375G>C	3.37:g.195506076C>G	ENSP00000417498:p.Gln4125His	Somatic	105	4	0.0380952		WXS	Illumina HiSeq	Phase_I	48	20	0.416667	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	N	0.505	-0.869207	0.02570	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.31510	1.49;1.49	0.423	0.423	0.16463	.	.	.	.	.	T	0.12220	0.0297	N	0.08118	0	0.09310	N	1	B	0.26876	0.162	B	0.08055	0.003	T	0.29671	-1.0004	8	.	.	.	.	5.9813	0.19409	0.0:0.3299:0.6701:0.0	.	3997	E7ESK3	.	H	4125	ENSP00000417498:Q4125H;ENSP00000420243:Q4125H	.	Q	-	3	2	MUC4	196990855	0.006000	0.16342	0.001000	0.08648	0.007000	0.05969	0.550000	0.23345	-1.409000	0.02038	-1.964000	0.00472	CAG	.	.	none		0.582	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
MMAB	326625	hgsc.bcm.edu	37	12	109994870	109994870	+	Missense_Mutation	SNP	A	A	T	rs9593	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	123	0	0		WXS	Illumina HiSeq	Phase_I	119	53	0.445378	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		
ERICH6B	220081	hgsc.bcm.edu	37	13	46170621	46170621	+	Missense_Mutation	SNP	A	A	T	rs17066954	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:46170621A>T	ENST00000298738.2	-	3	684	c.520T>A	c.(520-522)Tca>Aca	p.S174T		NM_182542.2	NP_872348.2	Q5W0A0	ERI6B_HUMAN		174	Glu-rich.		S -> T (in dbSNP:rs17066954).							breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)	5						TCTAGATATGATTTCTTCCCC	0.448													T|||	896	0.178914	0.1679	0.1974	5008	,	,		21174	0.3204		0.0815	False		,,,				2504	0.135				p.S174T		Atlas-SNP	.											.	FAM194B	42	.	0			c.T520A						PASS	.	A	THR/SER	215,1169		20,175,497	107.0	85.0	92.0		520	-2.2	0.0	13	dbSNP_123	92	208,2974		5,198,1388	yes	missense	FAM194B	NM_182542.2	58	25,373,1885	TT,TA,AA		6.5368,15.5347,9.2641	possibly-damaging	174/697	46170621	423,4143	692	1591	2283	SO:0001583	missense	220081	exon3			GATATGATTTCTT																												ENST00000298738.2:c.520T>A	13.37:g.46170621A>T	ENSP00000298738:p.Ser174Thr	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	95	51	0.536842	NM_182542	Q96MB5	Missense_Mutation	SNP	ENST00000298738.2	37	CCDS45045.1	408	0.18681318681318682	95	0.19308943089430894	66	0.18232044198895028	185	0.32342657342657344	62	0.08179419525065963	a	0.032	-1.326941	0.01309	0.155347	0.065368	ENSG00000165837	ENST00000298738	T	0.05996	3.36	1.08	-2.15	0.07102	.	.	.	.	.	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B;B	0.12013	0.005;0.005	B;B	0.08055	0.003;0.003	T	0.48547	-0.9026	8	0.87932	D	0	.	0.5496	0.00660	0.376:0.2694:0.1804:0.1743	rs17066954;rs17066954	174;174	A2VDI6;Q5W0A0	.;F194B_HUMAN	T	174	ENSP00000298738:S174T	ENSP00000298738:S174T	S	-	1	0	FAM194B	45068622	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.601000	0.00892	-2.071000	0.00880	-1.433000	0.01084	TCA	A|0.833;T|0.167	0.167	strong		0.448	FAM194B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044781.3		
SLITRK1	114798	hgsc.bcm.edu	37	13	84455214	84455214	+	Silent	SNP	T	T	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:84455214T>C	ENST00000377084.2	-	1	1314	c.429A>G	c.(427-429)cgA>cgG	p.R143R		NM_001281503.1|NM_052910.1	NP_001268432.1|NP_443142.1	Q96PX8	SLIK1_HUMAN	SLIT and NTRK-like family, member 1	143					adult behavior (GO:0030534)|axonogenesis (GO:0007409)|homeostatic process (GO:0042592)|multicellular organism growth (GO:0035264)	integral component of membrane (GO:0016021)				NS(2)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(22)|liver(1)|lung(36)|ovary(4)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	80	Medulloblastoma(90;0.18)	Breast(118;0.212)		GBM - Glioblastoma multiforme(99;0.07)		GGTCTATATCTCGTAATAAAT	0.458																																					p.R143R		Atlas-SNP	.											.	SLITRK1	196	.	0			c.A429G						PASS	.						60.0	65.0	64.0					13																	84455214		2203	4300	6503	SO:0001819	synonymous_variant	114798	exon1			TATATCTCGTAAT	AB067497	CCDS9464.1	13q31.1	2004-01-08	2004-01-08		ENSG00000178235	ENSG00000178235			20297	protein-coding gene	gene with protein product		609678	"""leucine rich repeat containing 12"""	LRRC12		14557068, 12975309	Standard	NM_001281503		Approved	KIAA1910	uc001vlk.3	Q96PX8	OTTHUMG00000017149	ENST00000377084.2:c.429A>G	13.37:g.84455214T>C		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	61	14	0.229508	NM_052910	Q5U5I6|Q96SF9	Silent	SNP	ENST00000377084.2	37	CCDS9464.1																																																																																			.	.	none		0.458	SLITRK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045396.1	NM_052910	
NLRP6	171389	hgsc.bcm.edu	37	11	284257	284257	+	Silent	SNP	G	G	A	rs11246050	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:284257G>A	ENST00000312165.5	+	6	2229	c.2229G>A	c.(2227-2229)gcG>gcA	p.A743A	NLRP6_ENST00000534750.1_Silent_p.A742A	NM_138329.1	NP_612202.2	P59044	NALP6_HUMAN	NLR family, pyrin domain containing 6	743					G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of immune response (GO:0050777)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of toll-like receptor signaling pathway (GO:0034122)|regulation of inflammatory response (GO:0050727)|response to bacterium (GO:0009617)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|vasopressin receptor activity (GO:0005000)			breast(1)|skin(1)|upper_aerodigestive_tract(2)	4		all_cancers(49;1.12e-06)|all_epithelial(84;0.000375)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;4.28e-28)|Epithelial(43;2.47e-27)|OV - Ovarian serous cystadenocarcinoma(40;4.66e-21)|BRCA - Breast invasive adenocarcinoma(625;3.57e-05)|Lung(200;0.0485)|LUSC - Lung squamous cell carcinoma(625;0.122)		TCCCTGACGCGGTCTGCCGAG	0.617													A|||	697	0.139177	0.0454	0.1138	5008	,	,		17272	0.1905		0.1551	False		,,,				2504	0.2147				p.A743A		Atlas-SNP	.											.	NLRP6	4	.	0			c.G2229A						PASS	.	A		297,4109	797.7+/-415.4	10,277,1916	43.0	42.0	43.0		2229	-5.2	0.0	11	dbSNP_120	43	1348,7252	754.5+/-407.5	106,1136,3058	no	coding-synonymous	NLRP6	NM_138329.1		116,1413,4974	AA,AG,GG		15.6744,6.7408,12.648		743/893	284257	1645,11361	2203	4300	6503	SO:0001819	synonymous_variant	171389	exon6			TGACGCGGTCTGC	AF479748	CCDS7693.1, CCDS60680.1	11p15	2006-12-08	2006-12-08	2006-12-08	ENSG00000174885	ENSG00000174885		"""Nucleotide-binding domain and leucine rich repeat containing"""	22944	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 6"""	609650	"""NACHT, leucine rich repeat and PYD containing 6"""	NALP6		12563287, 12019269	Standard	NM_138329		Approved	PYPAF5, PAN3, CLR11.4	uc010qvs.3	P59044	OTTHUMG00000119070	ENST00000312165.5:c.2229G>A	11.37:g.284257G>A		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	111	18	0.162162	NM_138329	A8K9F3|E9PJZ8	Silent	SNP	ENST00000312165.5	37	CCDS7693.1																																																																																			G|0.866;A|0.134	0.134	strong		0.617	NLRP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239283.1	NM_138329	
CTDP1	9150	hgsc.bcm.edu	37	18	77474921	77474921	+	Silent	SNP	G	G	A	rs2126082	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:77474921G>A	ENST00000299543.7	+	8	1608	c.1461G>A	c.(1459-1461)ccG>ccA	p.P487P	CTDP1_ENST00000075430.7_Silent_p.P487P	NM_001202504.1|NM_004715.4	NP_001189433.1|NP_004706.3	Q9Y5B0	CTDP1_HUMAN	CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) phosphatase, subunit 1	487				KP -> NA (in Ref. 5; AAC64549). {ECO:0000305}.	exit from mitosis (GO:0010458)|gene expression (GO:0010467)|positive regulation of viral transcription (GO:0050434)|protein dephosphorylation (GO:0006470)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	actin cytoskeleton (GO:0015629)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|midbody (GO:0030496)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)|spindle midzone (GO:0051233)|spindle pole (GO:0000922)	CTD phosphatase activity (GO:0008420)|DNA-directed RNA polymerase activity (GO:0003899)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(14)|ovary(2)|prostate(2)|urinary_tract(1)	35		Esophageal squamous(42;0.0157)|Melanoma(33;0.144)		OV - Ovarian serous cystadenocarcinoma(15;5.2e-06)|BRCA - Breast invasive adenocarcinoma(31;0.0277)		GGCAGAAGCCGAAGGCTGCCC	0.697													G|||	927	0.185104	0.2307	0.2075	5008	,	,		14787	0.1389		0.1759	False		,,,				2504	0.1646				p.P487P		Atlas-SNP	.											.	CTDP1	67	.	0			c.G1461A						PASS	.	G	,,	784,3440		78,628,1406	7.0	8.0	7.0		1104,1461,1461	-9.2	0.0	18	dbSNP_96	7	1297,7041		111,1075,2983	no	coding-synonymous,coding-synonymous,coding-synonymous	CTDP1	NM_001202504.1,NM_004715.4,NM_048368.3	,,	189,1703,4389	AA,AG,GG		15.5553,18.5606,16.5658	,,	368/843,487/962,487/868	77474921	2081,10481	2112	4169	6281	SO:0001819	synonymous_variant	9150	exon8			GAAGCCGAAGGCT	AF081287	CCDS12017.1, CCDS12018.1, CCDS74239.1	18q23	2014-09-17			ENSG00000060069	ENSG00000060069		"""Serine/threonine phosphatases / CTD aspartate-based phosphatases"""	2498	protein-coding gene	gene with protein product		604927				9405607, 9765293	Standard	NM_004715		Approved	FCP1	uc002lnh.2	Q9Y5B0	OTTHUMG00000132920	ENST00000299543.7:c.1461G>A	18.37:g.77474921G>A		Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	17	4	0.235294	NM_004715	A8MY97|Q7Z644|Q96BZ1|Q9Y6F5	Silent	SNP	ENST00000299543.7	37	CCDS12017.1																																																																																			G|0.813;A|0.187	0.187	strong		0.697	CTDP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256432.1	NM_004715	
PCDHB8	56128	hgsc.bcm.edu	37	5	140559148	140559148	+	Silent	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:140559148C>T	ENST00000239444.2	+	1	1778	c.1533C>T	c.(1531-1533)aaC>aaT	p.N511N	PCDHB16_ENST00000361016.2_5'Flank	NM_019120.3	NP_061993.2	Q9UN66	PCDB8_HUMAN	protocadherin beta 8	511	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)			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)			ACACAGACAACGGCCACCTGT	0.677																																					p.N511N		Atlas-SNP	.											.	PCDHB8	199	.	0			c.C1533T						PASS	.						94.0	148.0	130.0					5																	140559148		2203	4298	6501	SO:0001819	synonymous_variant	56128	exon1			AGACAACGGCCAC	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.1533C>T	5.37:g.140559148C>T		Somatic	305	0	0		WXS	Illumina HiSeq	Phase_I	423	50	0.118203	NM_019120	B9EGV1	Silent	SNP	ENST00000239444.2	37	CCDS4250.1																																																																																			.	.	none		0.677	PCDHB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251816.2	NM_019120	
TAF3	83860	hgsc.bcm.edu	37	10	8007559	8007559	+	Missense_Mutation	SNP	G	G	C	rs386740632|rs10795583	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:8007559G>C	ENST00000344293.5	+	3	2292	c.2086G>C	c.(2086-2088)Gtg>Ctg	p.V696L		NM_031923.3	NP_114129.1	Q5VWG9	TAF3_HUMAN	TAF3 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 140kDa	696	Lys-rich.		V -> A (in dbSNP:rs1244229). {ECO:0000269|PubMed:17974005}.|V -> L (in dbSNP:rs10795583).	V -> P (in Ref. 3; AAH62352). {ECO:0000305}.	maintenance of protein location in nucleus (GO:0051457)|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)|transcription factor TFIID complex (GO:0005669)	zinc ion binding (GO:0008270)			NS(2)|breast(4)|endometrium(2)|kidney(1)|large_intestine(6)|lung(16)|ovary(3)|prostate(4)|skin(2)	40						gaaagagaaggtgaaggagaa	0.463													C|||	2891	0.577276	0.3275	0.7651	5008	,	,		16853	0.7183		0.6372	False		,,,				2504	0.5746				p.V696L		Atlas-SNP	.											.	TAF3	93	.	0			c.G2086C						PASS	.	C	LEU/VAL	1461,2233		299,863,685	35.0	36.0	35.0		2086	5.8	0.1	10	dbSNP_120	35	5057,3115		1600,1857,629	yes	missense	TAF3	NM_031923.2	32	1899,2720,1314	CC,CG,GG		38.118,39.5506,45.0699	benign	696/930	8007559	6518,5348	1847	4086	5933	SO:0001583	missense	83860	exon3			GAGAAGGTGAAGG	AJ292190	CCDS41487.1	10p15.1	2013-01-28	2002-08-29		ENSG00000165632	ENSG00000165632		"""Zinc fingers, PHD-type"""	17303	protein-coding gene	gene with protein product		606576	"""TAF3 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 140 kD"""			11438666, 18549481	Standard	NM_031923		Approved	TAF140, TAFII140	uc010qbd.3	Q5VWG9	OTTHUMG00000017643	ENST00000344293.5:c.2086G>C	10.37:g.8007559G>C	ENSP00000340271:p.Val696Leu	Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	34	18	0.529412	NM_031923	Q05DA0|Q6GMS5|Q6P6B5|Q86VY6|Q9BQS9|Q9UFI8	Missense_Mutation	SNP	ENST00000344293.5	37	CCDS41487.1	1135	0.5196886446886447	118	0.23983739837398374	235	0.649171270718232	379	0.6625874125874126	403	0.5316622691292876	C	10.69	1.420748	0.25639	0.395506	0.61882	ENSG00000165632	ENST00000344293	T	0.08546	3.08	5.83	5.83	0.93111	.	0.000000	0.64402	D	0.000004	T	0.00012	0.0000	N	0.08118	0	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.21655	-1.0239	9	0.30078	T	0.28	-5.0432	16.8339	0.85952	0.0:0.8712:0.1288:0.0	rs10795583;rs52820101;rs10795583	696	Q5VWG9	TAF3_HUMAN	L	696	ENSP00000340271:V696L	ENSP00000340271:V696L	V	+	1	0	TAF3	8047565	0.993000	0.37304	0.087000	0.20705	0.679000	0.39708	4.668000	0.61568	1.496000	0.48567	-0.120000	0.15030	GTG	G|0.471;C|0.529	0.529	strong		0.463	TAF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046725.1	NM_031923	
CCL4	6351	hgsc.bcm.edu	37	17	34432664	34432664	+	Missense_Mutation	SNP	T	T	A	rs1719152|rs386796798	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:34432664T>A	ENST00000250151.4	+	3	554	c.238T>A	c.(238-240)Tcc>Acc	p.S80T	CCL4_ENST00000394495.1_Missense_Mutation_p.N41K	NM_002984.2	NP_002975.1	P13236	CCL4_HUMAN	chemokine (C-C motif) ligand 4	80			S -> T (in dbSNP:rs1719152). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:2809212}.		cell adhesion (GO:0007155)|cell chemotaxis (GO:0060326)|cell-cell signaling (GO:0007267)|cellular component movement (GO:0006928)|establishment or maintenance of cell polarity (GO:0007163)|immune response (GO:0006955)|inflammatory response (GO:0006954)|negative regulation by host of viral transcription (GO:0043922)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of natural killer cell chemotaxis (GO:2000503)|response to toxic substance (GO:0009636)|response to virus (GO:0009615)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	CCR1 chemokine receptor binding (GO:0031726)|CCR5 chemokine receptor binding (GO:0031730)|chemokine activity (GO:0008009)|cytokine activity (GO:0005125)|identical protein binding (GO:0042802)			endometrium(1)|large_intestine(1)|lung(2)	4		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		TCCCAGTGAATCCTGGGTCCA	0.498													A|||	898	0.179313	0.0492	0.1182	5008	,	,		21017	0.2758		0.2485	False		,,,				2504	0.228				p.S80T	Colon(139;824 1752 21188 21615 24765)	Atlas-SNP	.											.	CCL4	14	.	0			c.T238A						PASS	.	A	THR/SER	14,4392		3,8,2192	199.0	183.0	188.0		238	-10.1	0.7	17	dbSNP_89	188	113,8487		33,47,4220	no	missense	CCL4	NM_002984.2	58	36,55,6412	AA,AT,TT		1.314,0.3177,0.9765	benign	80/93	34432664	127,12879	2203	4300	6503	SO:0001583	missense	6351	exon3			AGTGAATCCTGGG	M23502	CCDS11308.1	17q21-q23	2014-05-06	2002-08-22	2002-08-23	ENSG00000129277	ENSG00000275302		"""Chemokine ligands"", ""Endogenous ligands"""	10630	protein-coding gene	gene with protein product		182284	"""small inducible cytokine A4 (homologous to mouse Mip-1b)"""	LAG1, SCYA4		1972563	Standard	NM_002984		Approved	MIP-1-beta, Act-2, AT744.1	uc002hkw.1	P13236	OTTHUMG00000188414	ENST00000250151.4:c.238T>A	17.37:g.34432664T>A	ENSP00000250151:p.Ser80Thr	Somatic	412	0	0		WXS	Illumina HiSeq	Phase_I	386	205	0.531088	NM_002984	P22617|Q13704|Q3SXL8|Q6FGI8	Missense_Mutation	SNP	ENST00000250151.4	37	CCDS11308.1	314|314	0.14377289377289376|0.14377289377289376	13|13	0.026422764227642278|0.026422764227642278	43|43	0.11878453038674033|0.11878453038674033	122|122	0.21328671328671328|0.21328671328671328	136|136	0.17941952506596306|0.17941952506596306	.|.	0.132|0.132	-1.112281|-1.112281	0.01799|0.01799	0.003177|0.003177	0.01314|0.01314	ENSG00000129277|ENSG00000129277	ENST00000394495|ENST00000250151	T|T	0.71698|0.04551	-0.59|3.6	5.03|5.03	-10.1|-10.1	0.00402|0.00402	.|Chemokine interleukin-8-like domain (3);	.|0.947069	.|0.08503	.|N	.|0.936124	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.50813|0.50813	P|P	1.020000000000465E-4|1.020000000000465E-4	.|B	.|0.02656	.|0.0	.|B	.|0.04013	.|0.001	T|T	0.40098|0.40098	-0.9581|-0.9581	5|8	0.87932|0.20519	D|T	0|0.43	.|.	2.6529|2.6529	0.05003|0.05003	0.1602:0.1173:0.3049:0.4176|0.1602:0.1173:0.3049:0.4176	rs1719152;rs52821607;rs1719152|rs1719152;rs52821607;rs1719152	.|80	.|P13236	.|CCL4_HUMAN	K|T	41|80	ENSP00000378004:N41K|ENSP00000250151:S80T	ENSP00000378004:N41K|ENSP00000250151:S80T	N|S	+|+	3|1	2|0	CCL4|CCL4	31456777|31456777	0.000000|0.000000	0.05858|0.05858	0.651000|0.651000	0.29564|0.29564	0.096000|0.096000	0.18686|0.18686	-6.619000|-6.619000	0.00059|0.00059	-3.661000|-3.661000	0.00124|0.00124	-2.948000|-2.948000	0.00085|0.00085	AAT|TCC	T|0.845;A|0.155	0.155	strong		0.498	CCL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256592.2	NM_002984	
ASCC3	10973	hgsc.bcm.edu	37	6	101100745	101100745	+	Silent	SNP	C	C	T	rs41288409	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:101100745C>T	ENST00000369162.2	-	18	3188	c.2844G>A	c.(2842-2844)aaG>aaA	p.K948K		NM_006828.2	NP_006819.2	Q8N3C0	ASCC3_HUMAN	activating signal cointegrator 1 complex subunit 3	948					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)		GTTCTCGATGCTTTCTTAATG	0.338													C|||	172	0.034345	0.0726	0.0101	5008	,	,		14635	0.0437		0.0159	False		,,,				2504	0.0092				p.K948K		Atlas-SNP	.											.	ASCC3	205	.	0			c.G2844A						PASS	.	C		205,4199	120.8+/-158.4	4,197,2001	78.0	73.0	74.0		2844	-2.9	1.0	6	dbSNP_127	74	171,8429	75.4+/-138.0	4,163,4133	no	coding-synonymous	ASCC3	NM_006828.2		8,360,6134	TT,TC,CC		1.9884,4.6549,2.8914		948/2203	101100745	376,12628	2202	4300	6502	SO:0001819	synonymous_variant	10973	exon18			TCGATGCTTTCTT	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.2844G>A	6.37:g.101100745C>T		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	90	49	0.544444	NM_006828	E7EW23|O43738|Q4G1A0|Q5VTN2|Q9H1I9|Q9H5A2|Q9NTR0	Silent	SNP	ENST00000369162.2	37	CCDS5046.1																																																																																			C|0.970;T|0.030	0.030	strong		0.338	ASCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041632.2	NM_006828	
ZBED1	9189	hgsc.bcm.edu	37	X	2408437	2408437	+	Silent	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:2408437G>A	ENST00000381223.4	-	2	527	c.324C>T	c.(322-324)gaC>gaT	p.D108D	ZBED1_ENST00000515319.1_5'Flank|DHRSX_ENST00000334651.5_Intron|ZBED1_ENST00000381218.3_Silent_p.D108D|ZBED1_ENST00000381222.2_Silent_p.D108D	NM_001171135.1|NM_001171136.1|NM_004729.3	NP_001164606.1|NP_001164607.1|NP_004720.1	O96006	ZBED1_HUMAN	zinc finger, BED-type containing 1	108					metabolic process (GO:0008152)	nuclear chromosome (GO:0000228)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|transposase activity (GO:0004803)			endometrium(8)|kidney(1)|large_intestine(3)|lung(11)|prostate(1)|upper_aerodigestive_tract(1)	25		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)				CGGCCAGCGCGTCCTGCCCGG	0.667													G|||	977	0.195088	0.0605	0.1787	5008	,	,		14525	0.1756		0.2644	False		,,,				2504	0.3374				p.D108D		Atlas-SNP	.											.	ZBED1	64	.	0			c.C324T						PASS	.	G	,,,	463,3943		30,403,1770	66.0	65.0	65.0		324,324,324,	2.6	0.0	X	dbSNP_134	65	2421,6171		347,1727,2222	no	coding-synonymous,coding-synonymous,coding-synonymous,intron	ZBED1,DHRSX	NM_001171135.1,NM_001171136.1,NM_004729.3,NM_145177.2	,,,	377,2130,3992	AA,AG,GG		28.1774,10.5084,22.188	,,,	108/695,108/695,108/695,	2408437	2884,10114	2203	4296	6499	SO:0001819	synonymous_variant	9189	exon2			CAGCGCGTCCTGC	AB018328	CCDS14118.1	Xp22.33 and Yp11	2013-05-03	2004-01-14	2004-01-16	ENSG00000214717	ENSG00000214717		"""Pseudoautosomal regions / PAR1"", ""Zinc fingers, BED-type"""	447	protein-coding gene	gene with protein product		300178	"""Ac-like transposable element"""	ALTE		9872452, 9887332, 23533661	Standard	NM_001171135		Approved	TRAMP, KIAA0785, DREF, hDREF	uc004cqh.2	O96006	OTTHUMG00000021069	ENST00000381223.4:c.324C>T	X.37:g.2408437G>A		Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	164	164	1	NM_001171135	Q96BY4	Silent	SNP	ENST00000381223.4	37	CCDS14118.1																																																																																			G|0.779;A|0.221	0.221	strong		0.667	ZBED1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000144310.3	NM_004729	
AKNA	80709	hgsc.bcm.edu	37	9	117110046	117110046	+	Missense_Mutation	SNP	C	C	T	rs3748178	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:117110046C>T	ENST00000307564.4	-	16	3517	c.3356G>A	c.(3355-3357)cGg>cAg	p.R1119Q	AKNA_ENST00000374075.5_Missense_Mutation_p.R1038Q|AKNA_ENST00000374088.3_Missense_Mutation_p.R1119Q|AKNA_ENST00000223791.3_Missense_Mutation_p.R579Q|AKNA_ENST00000374079.4_Missense_Mutation_p.R64Q|AKNA_ENST00000492875.1_5'Flank	NM_030767.4	NP_110394.3	Q7Z591	AKNA_HUMAN	AT-hook transcription factor	1119			R -> Q (in dbSNP:rs3748178). {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)			breast(3)|central_nervous_system(4)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(7)|liver(2)|lung(22)|ovary(4)|stomach(2)	51						GTCTGCTGGCCGGCCGCGGGT	0.662													C|||	533	0.10643	0.0106	0.1427	5008	,	,		13674	0.0685		0.2624	False		,,,				2504	0.089				p.R1119Q		Atlas-SNP	.											.	AKNA	119	.	0			c.G3356A						PASS	.	C	GLN/ARG	179,3903		8,163,1870	7.0	8.0	8.0		3356	1.0	0.0	9	dbSNP_107	8	1759,6341		177,1405,2468	yes	missense	AKNA	NM_030767.4	43	185,1568,4338	TT,TC,CC		21.716,4.3851,15.9087	probably-damaging	1119/1440	117110046	1938,10244	2041	4050	6091	SO:0001583	missense	80709	exon16			GCTGGCCGGCCGC	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.3356G>A	9.37:g.117110046C>T	ENSP00000303769:p.Arg1119Gln	Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	77	44	0.571429	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	300	0.13736263736263737	8	0.016260162601626018	62	0.1712707182320442	31	0.05419580419580419	199	0.262532981530343	C	18.55	3.649336	0.67358	0.043851	0.21716	ENSG00000106948	ENST00000307564;ENST00000374079;ENST00000320310;ENST00000374088;ENST00000223791;ENST00000374075	T;T;T;T;T	0.24350	2.37;1.86;2.37;2.13;2.36	5.01	0.963	0.19649	.	0.323271	0.22341	N	0.061322	T	0.00012	0.0000	M	0.65975	2.015	0.80722	P	0.0	B;P	0.36874	0.436;0.572	B;B	0.29267	0.027;0.1	T	0.24621	-1.0155	9	0.62326	D	0.03	-11.2927	4.2153	0.10531	0.0:0.5399:0.1702:0.2899	rs3748178;rs17230383;rs3748178	1119;1038	Q7Z591;Q7Z591-2	AKNA_HUMAN;.	Q	1119;64;131;1119;579;1038	ENSP00000303769:R1119Q;ENSP00000363192:R64Q;ENSP00000363201:R1119Q;ENSP00000223791:R579Q;ENSP00000363188:R1038Q	ENSP00000223791:R579Q	R	-	2	0	AKNA	116149867	0.004000	0.15560	0.001000	0.08648	0.013000	0.08279	0.196000	0.17176	0.084000	0.17077	0.655000	0.94253	CGG	C|0.891;T|0.109	0.109	strong		0.662	AKNA-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053767.2	NM_030767	
GLT6D1	360203	hgsc.bcm.edu	37	9	138516190	138516190	+	Missense_Mutation	SNP	T	T	C	rs35762223	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:138516190T>C	ENST00000371763.1	-	5	837	c.584A>G	c.(583-585)cAc>cGc	p.H195R		NM_182974.2	NP_892019.2	Q7Z4J2	GL6D1_HUMAN	glycosyltransferase 6 domain containing 1	195			H -> R (in dbSNP:rs35762223). {ECO:0000269|PubMed:19218399}.		carbohydrate metabolic process (GO:0005975)	integral component of membrane (GO:0016021)	transferase activity, transferring hexosyl groups (GO:0016758)	p.H195R(1)		endometrium(2)|large_intestine(5)|lung(3)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(1)	15		Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;4.3e-07)|Epithelial(140;1.58e-06)|all cancers(34;5.36e-05)		CCACCAGGCGTGGAGCTGGGC	0.562													T|||	618	0.123403	0.1157	0.1369	5008	,	,		17218	0.1538		0.1372	False		,,,				2504	0.0787				p.H195R		Atlas-SNP	.											GLT6D1,NS,carcinoma,0,3	GLT6D1	56	3	1	Substitution - Missense(1)	stomach(1)	c.A584G						scavenged	.	T	ARG/HIS	477,3339		25,427,1456	67.0	66.0	66.0		584	2.3	0.2	9	dbSNP_126	66	1065,7177		78,909,3134	yes	missense	GLT6D1	NM_182974.2	29	103,1336,4590	CC,CT,TT		12.9216,12.5,12.7882	probably-damaging	195/277	138516190	1542,10516	1908	4121	6029	SO:0001583	missense	360203	exon5			CAGGCGTGGAGCT	AY336054	CCDS43900.1	9q34.3	2013-02-22	2004-09-16	2004-09-17	ENSG00000204007	ENSG00000204007		"""Glycosyltransferase family 6 domain containing"""	23671	protein-coding gene	gene with protein product		613699	"""galactosyltransferase family 6 domain containing 1"""	GLTDC1			Standard	NM_182974		Approved		uc010nbd.1	Q7Z4J2	OTTHUMG00000020911	ENST00000371763.1:c.584A>G	9.37:g.138516190T>C	ENSP00000360829:p.His195Arg	Somatic	77	1	0.012987		WXS	Illumina HiSeq	Phase_I	48	23	0.479167	NM_182974		Missense_Mutation	SNP	ENST00000371763.1	37	CCDS43900.1	265	0.12133699633699634	47	0.09552845528455285	54	0.14917127071823205	76	0.13286713286713286	88	0.11609498680738786	T	16.45	3.125657	0.56721	0.125	0.129216	ENSG00000204007	ENST00000371763	T	0.01265	5.08	3.49	2.34	0.29019	.	0.320352	0.27143	N	0.020737	T	0.00039	0.0001	M	0.90425	3.115	0.33970	P	0.35331900000000005	D	0.76494	0.999	D	0.75484	0.986	T	0.04216	-1.0968	9	0.87932	D	0	-41.268	7.3204	0.26523	0.0:0.1105:0.0:0.8895	rs35762223	195	Q7Z4J2	GL6D1_HUMAN	R	195	ENSP00000360829:H195R	ENSP00000360829:H195R	H	-	2	0	GLT6D1	137656011	1.000000	0.71417	0.225000	0.23894	0.059000	0.15707	5.890000	0.69774	0.719000	0.32188	0.533000	0.62120	CAC	T|0.870;C|0.130	0.130	strong		0.562	GLT6D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055005.2	NM_182974	
ITGA1	3672	hgsc.bcm.edu	37	5	52157374	52157374	+	Silent	SNP	T	T	C	rs2447867	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:52157374T>C	ENST00000282588.6	+	3	734	c.276T>C	c.(274-276)tgT>tgC	p.C92C		NM_181501.1	NP_852478.1	P56199	ITA1_HUMAN	integrin, alpha 1	92					activation of MAPK activity (GO:0000187)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell-matrix adhesion (GO:0007160)|cellular extravasation (GO:0045123)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|muscle contraction (GO:0006936)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|neutrophil chemotaxis (GO:0030593)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|vasodilation (GO:0042311)	acrosomal vesicle (GO:0001669)|basal part of cell (GO:0045178)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integrin alpha1-beta1 complex (GO:0034665)|integrin complex (GO:0008305)|membrane (GO:0016020)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)	collagen binding (GO:0005518)|collagen binding involved in cell-matrix adhesion (GO:0098639)|metal ion binding (GO:0046872)|protein phosphatase binding (GO:0019903)			NS(1)|breast(3)|central_nervous_system(4)|endometrium(3)|kidney(4)|large_intestine(6)|liver(2)|lung(19)|ovary(2)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	51		Lung NSC(810;5.05e-05)|Breast(144;0.0851)				CATTACCTTGTGTAAAGTTGG	0.438													C|||	3818	0.76238	0.8396	0.7147	5008	,	,		17656	0.5992		0.833	False		,,,				2504	0.7873				p.C92C		Atlas-SNP	.											.	ITGA1	112	.	0			c.T276C						PASS	.	C		3761,645	276.3+/-273.0	1596,569,38	115.0	113.0	114.0		276	-1.2	0.2	5	dbSNP_100	114	7222,1378	267.9+/-287.5	3039,1144,117	no	coding-synonymous	ITGA1	NM_181501.1		4635,1713,155	CC,CT,TT		16.0233,14.6391,15.5544		92/1180	52157374	10983,2023	2203	4300	6503	SO:0001819	synonymous_variant	3672	exon3			ACCTTGTGTAAAG	X68742	CCDS3955.1	5q11.1	2010-03-23			ENSG00000213949	ENSG00000213949		"""CD molecules"", ""Integrins"""	6134	protein-coding gene	gene with protein product		192968				8428973, 11937138	Standard	NM_181501		Approved	VLA1, CD49a	uc003jou.3	P56199	OTTHUMG00000131163	ENST00000282588.6:c.276T>C	5.37:g.52157374T>C		Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	129	128	0.992248	NM_181501	B2RNU0	Silent	SNP	ENST00000282588.6	37	CCDS3955.1																																																																																			T|0.204;C|0.796	0.796	strong		0.438	ITGA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253855.3	NM_181501	
TCHP	84260	hgsc.bcm.edu	37	12	110341933	110341933	+	Missense_Mutation	SNP	A	A	G	rs10774978	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:110341933A>G	ENST00000312777.5	+	3	594	c.380A>G	c.(379-381)aAa>aGa	p.K127R	TCHP_ENST00000405876.4_Missense_Mutation_p.K127R	NM_032300.4	NP_115676.1			trichoplein, keratin filament binding											NS(1)|breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(8)|ovary(1)|skin(2)	22						AAATCAGCCAAAGAAGAGCAG	0.562													G|||	1562	0.311901	0.674	0.1844	5008	,	,		19945	0.1438		0.1769	False		,,,				2504	0.2249				p.K127R		Atlas-SNP	.											.	TCHP	45	.	0			c.A380G						PASS	.	G	ARG/LYS,ARG/LYS	2603,1787		779,1045,371	50.0	45.0	47.0		380,380	3.3	1.0	12	dbSNP_120	47	1357,7219		108,1141,3039	yes	missense,missense	TCHP	NM_001143852.1,NM_032300.4	26,26	887,2186,3410	GG,GA,AA		15.8232,40.7062,30.5414	benign,benign	127/499,127/499	110341933	3960,9006	2195	4288	6483	SO:0001583	missense	84260	exon3			CAGCCAAAGAAGA	AK092736	CCDS9137.1	12q24.11	2011-08-25	2006-01-27			ENSG00000139437			28135	protein-coding gene	gene with protein product	"""mitostatin"""	612654				15731013, 20930847	Standard	NM_032300		Approved	MGC10854, TpMs	uc001tpn.3	Q9BT92		ENST00000312777.5:c.380A>G	12.37:g.110341933A>G	ENSP00000324404:p.Lys127Arg	Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	55	25	0.454545	NM_001143852		Missense_Mutation	SNP	ENST00000312777.5	37	CCDS9137.1	554	0.25366300366300365	301	0.6117886178861789	70	0.19337016574585636	54	0.0944055944055944	129	0.17018469656992086	G	0.176	-1.067266	0.01934	0.592938	0.158232	ENSG00000139437	ENST00000405876;ENST00000536868;ENST00000312777;ENST00000536408	T;T;T	0.33865	2.2;2.2;1.39	5.21	3.3	0.37823	.	0.117657	0.56097	N	0.000036	T	0.00012	0.0000	N	0.00230	-1.795	0.09310	P	0.9999999999948324	B	0.02656	0.0	B	0.01281	0.0	T	0.47736	-0.9094	9	0.02654	T	1	-0.1723	8.7459	0.34587	0.2659:0.0:0.7341:0.0	rs10774978;rs61441019;rs10774978	127	Q9BT92	TCHP_HUMAN	R	127	ENSP00000384520:K127R;ENSP00000324404:K127R;ENSP00000441835:K127R	ENSP00000324404:K127R	K	+	2	0	TCHP	108826316	0.826000	0.29277	0.968000	0.41197	0.210000	0.24377	1.397000	0.34543	0.268000	0.21939	-1.101000	0.02118	AAA	A|0.700;G|0.300	0.300	strong		0.562	TCHP-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403289.1	NM_032300	
CPN1	1369	hgsc.bcm.edu	37	10	101808540	101808540	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:101808540G>A	ENST00000370418.3	-	8	1456	c.1205C>T	c.(1204-1206)aCc>aTc	p.T402I		NM_001308.2	NP_001299.1	P15169	CBPN_HUMAN	carboxypeptidase N, polypeptide 1	402					response to glucocorticoid (GO:0051384)	extracellular space (GO:0005615)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(14)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	33		Colorectal(252;0.234)		Epithelial(162;4.77e-10)|all cancers(201;3.82e-08)		AGGACCCACGGTCACAGTTAC	0.512																																					p.T402I		Atlas-SNP	.											.	CPN1	62	.	0			c.C1205T						PASS	.						181.0	142.0	156.0					10																	101808540		2203	4300	6503	SO:0001583	missense	1369	exon8			CCCACGGTCACAG	X14329	CCDS7486.1	10q24.2	2012-02-10	2007-02-23		ENSG00000120054	ENSG00000120054	3.4.17.3		2312	protein-coding gene	gene with protein product	"""anaphylatoxin inactivator"", ""arginine carboxypeptidase"", ""carboxypeptidase K"", ""kininase I"", ""lysine carboxypeptidase"""	603103	"""carboxypeptidase N, polypeptide 1, 50kD"""			9628828, 2912725	Standard	NM_001308		Approved		uc001kql.2	P15169	OTTHUMG00000018896	ENST00000370418.3:c.1205C>T	10.37:g.101808540G>A	ENSP00000359446:p.Thr402Ile	Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	113	26	0.230089	NM_001308	B1AP59	Missense_Mutation	SNP	ENST00000370418.3	37	CCDS7486.1	.	.	.	.	.	.	.	.	.	.	G	11.80	1.745365	0.30955	.	.	ENSG00000120054	ENST00000370418;ENST00000441382	T;T	0.49139	0.79;0.79	5.5	4.6	0.57074	Peptidase M14, carboxypeptidase A (1);Carboxypeptidase-like, regulatory domain (1);Carboxypeptidase, regulatory domain (1);	0.099528	0.64402	N	0.000002	T	0.45256	0.1333	M	0.66560	2.04	0.52099	D	0.999945	B	0.14438	0.01	B	0.19148	0.024	T	0.38824	-0.9643	10	0.38643	T	0.18	-16.477	10.2462	0.43343	0.1601:0.0:0.8399:0.0	.	402	P15169	CBPN_HUMAN	I	402;199	ENSP00000359446:T402I;ENSP00000410895:T199I	ENSP00000359446:T402I	T	-	2	0	CPN1	101798530	0.998000	0.40836	0.992000	0.48379	0.342000	0.28953	2.976000	0.49289	1.339000	0.45563	0.644000	0.83932	ACC	.	.	none		0.512	CPN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049828.1	NM_001308	
OR8B4	283162	hgsc.bcm.edu	37	11	124294703	124294703	+	Missense_Mutation	SNP	T	T	C	rs10750270	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:124294703T>C	ENST00000356130.3	-	1	86	c.65A>G	c.(64-66)gAg>gGg	p.E22G		NM_001005196.1	NP_001005196.1	Q96RC9	OR8B4_HUMAN	olfactory receptor, family 8, subfamily B, member 4	22			E -> G (in dbSNP:rs10750270).			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(7)|lung(15)|ovary(1)|skin(6)|stomach(1)|urinary_tract(1)	32		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;0.0279)		GAGCTGGAGCTCTGGCTGTTC	0.483													T|||	1735	0.346446	0.2874	0.3242	5008	,	,		19677	0.5952		0.3121	False		,,,				2504	0.2209				p.E22G		Atlas-SNP	.											.	OR8B4	60	.	0			c.A65G						PASS	.	T	GLY/GLU	1209,3193	413.0+/-336.3	176,857,1168	53.0	52.0	52.0		65	2.2	0.0	11	dbSNP_120	52	2675,5923	416.8+/-352.2	419,1837,2043	yes	missense	OR8B4	NM_001005196.1	98	595,2694,3211	CC,CT,TT		31.1119,27.4648,29.8769	benign	22/310	124294703	3884,9116	2201	4299	6500	SO:0001583	missense	283162	exon1			TGGAGCTCTGGCT	AB065831	CCDS31710.1	11q24	2012-08-09		2001-06-29	ENSG00000198657	ENSG00000198657		"""GPCR / Class A : Olfactory receptors"""	8473	protein-coding gene	gene with protein product				OR8B4P			Standard	NM_001005196		Approved		uc010sak.2	Q96RC9	OTTHUMG00000165916	ENST00000356130.3:c.65A>G	11.37:g.124294703T>C	ENSP00000348449:p.Glu22Gly	Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	40	9	0.225	NM_001005196	B2RNF8|Q6IFQ7	Missense_Mutation	SNP	ENST00000356130.3	37	CCDS31710.1	832	0.38095238095238093	123	0.25	125	0.3453038674033149	352	0.6153846153846154	232	0.30606860158311344	t	2.515	-0.312118	0.05422	0.274648	0.311119	ENSG00000198657	ENST00000356130	T	0.00444	7.4	4.62	2.16	0.27623	.	0.264994	0.26899	N	0.021931	T	0.00012	0.0000	L	0.39467	1.215	0.80722	P	0.0	B	0.12630	0.006	B	0.15052	0.012	T	0.02743	-1.1116	9	0.37606	T	0.19	.	11.1631	0.48526	0.0:0.0:0.2894:0.7106	rs10750270;rs52830364;rs58760348;rs10750270	22	Q96RC9	OR8B4_HUMAN	G	22	ENSP00000348449:E22G	ENSP00000348449:E22G	E	-	2	0	OR8B4	123799913	0.000000	0.05858	0.014000	0.15608	0.159000	0.22180	0.167000	0.16602	0.337000	0.23665	0.533000	0.62120	GAG	T|0.675;C|0.325	0.325	strong		0.483	OR8B4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387055.1	NM_001005196	
STT3A	3703	hgsc.bcm.edu	37	11	125488404	125488404	+	Silent	SNP	C	C	T	rs17140116	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:125488404C>T	ENST00000529196.1	+	17	2117	c.1911C>T	c.(1909-1911)tgC>tgT	p.C637C	STT3A_ENST00000392708.4_Silent_p.C637C|STT3A_ENST00000531491.1_Silent_p.C545C			P46977	STT3A_HUMAN	STT3A, subunit of the oligosaccharyltransferase complex (catalytic)	637					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)		TGCTCAACTGCCTCATGTACA	0.413													C|||	557	0.111222	0.27	0.062	5008	,	,		16908	0.0308		0.0736	False		,,,				2504	0.0532				p.C637C		Atlas-SNP	.											.	STT3A	52	.	0			c.C1911T						PASS	.	C		1016,3386	377.5+/-322.5	113,790,1298	153.0	137.0	142.0		1911	2.4	1.0	11	dbSNP_123	142	579,8019	155.1+/-209.2	18,543,3738	no	coding-synonymous	STT3A	NM_152713.3		131,1333,5036	TT,TC,CC		6.7341,23.0804,12.2692		637/706	125488404	1595,11405	2201	4299	6500	SO:0001819	synonymous_variant	3703	exon16			CAACTGCCTCATG	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.1911C>T	11.37:g.125488404C>T		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	83	65	0.783133	NM_152713	B4DJ24|E9PNQ1|Q86XU9|Q8TE35|Q8WUB4	Silent	SNP	ENST00000529196.1	37	CCDS8458.1																																																																																			C|0.878;T|0.122	0.122	strong		0.413	STT3A-002	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000386691.1	NM_152713	
ACAN	176	hgsc.bcm.edu	37	15	89398407	89398407	+	Missense_Mutation	SNP	C	C	T	rs3743398	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:89398407C>T	ENST00000561243.1	+	11	2591	c.2591C>T	c.(2590-2592)cCt>cTt	p.P864L	ACAN_ENST00000439576.2_Missense_Mutation_p.P864L|ACAN_ENST00000559004.1_Missense_Mutation_p.P864L|ACAN_ENST00000352105.7_Missense_Mutation_p.P864L			P16112	PGCA_HUMAN	aggrecan	863	CS-1.				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|proteolysis (GO:0006508)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)	carbohydrate binding (GO:0030246)|extracellular matrix structural constituent (GO:0005201)|hyaluronic acid binding (GO:0005540)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(4)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(15)|liver(2)|lung(40)|ovary(2)|prostate(5)|skin(5)|stomach(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	93	Lung NSC(78;0.0392)|all_lung(78;0.077)		BRCA - Breast invasive adenocarcinoma(143;0.146)			TCTGGGGCCCCTGATGTCAGT	0.607													C|||	409	0.0816693	0.0151	0.1081	5008	,	,		19429	0.0952		0.1909	False		,,,				2504	0.0266				p.P864L		Atlas-SNP	.											.	ACAN	220	.	0			c.C2591T						PASS	.	C	LEU/PRO,LEU/PRO	138,3846		4,130,1858	47.0	53.0	51.0		2591,2591	4.9	0.5	15	dbSNP_107	51	1673,6659		152,1369,2645	yes	missense,missense	ACAN	NM_001135.3,NM_013227.3	98,98	156,1499,4503	TT,TC,CC		20.0792,3.4639,14.7044	probably-damaging,probably-damaging	864/2432,864/2531	89398407	1811,10505	1992	4166	6158	SO:0001583	missense	176	exon12			GGGCCCCTGATGT	M55172	CCDS53970.1, CCDS53971.1	15q26.1	2013-05-07	2007-02-16	2007-02-16	ENSG00000157766	ENSG00000157766		"""Immunoglobulin superfamily / V-set domain containing"", ""Proteoglycans / Extracellular Matrix : Hyalectans"""	319	protein-coding gene	gene with protein product	"""aggrecan proteoglycan"""	155760	"""chondroitin sulfate proteoglycan 1"", ""aggrecan 1"""	MSK16, CSPG1, AGC1		1985970	Standard	NM_013227		Approved	CSPGCP	uc010upo.1	P16112	OTTHUMG00000171989	ENST00000561243.1:c.2591C>T	15.37:g.89398407C>T	ENSP00000453342:p.Pro864Leu	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	75	49	0.653333	NM_001135	Q13650|Q9UCD3|Q9UCP4|Q9UCP5|Q9UDE0	Missense_Mutation	SNP	ENST00000561243.1	37	CCDS53970.1	256	0.11721611721611722	11	0.022357723577235773	49	0.13535911602209943	55	0.09615384615384616	141	0.18601583113456466	C	15.30	2.793935	0.50102	0.034639	0.200792	ENSG00000157766	ENST00000439576;ENST00000352105;ENST00000268134	T;T	0.03468	4.19;3.92	5.79	4.87	0.63330	.	0.000000	0.32343	N	0.006224	T	0.00012	0.0000	M	0.65975	2.015	0.53005	P	3.799999999998249E-5	P;D	0.76494	0.584;0.999	B;D	0.71184	0.16;0.972	T	0.33599	-0.9862	9	0.09338	T	0.73	-12.1183	9.3039	0.37863	0.1416:0.7849:0.0:0.0735	rs3743398;rs60866336;rs3743398	864;864	E7ENV9;E7EX88	.;.	L	864	ENSP00000387356:P864L;ENSP00000341615:P864L	ENSP00000268134:P864L	P	+	2	0	ACAN	87199411	0.372000	0.25064	0.480000	0.27341	0.521000	0.34408	1.014000	0.29950	2.722000	0.93159	0.655000	0.94253	CCT	C|0.871;T|0.129	0.129	strong		0.607	ACAN-006	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416267.2	NM_001135	
CPA4	51200	hgsc.bcm.edu	37	7	129938598	129938598	+	Missense_Mutation	SNP	G	G	T	rs34587586	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:129938598G>T	ENST00000222482.4	+	2	109	c.81G>T	c.(79-81)ttG>ttT	p.L27F	CPA4_ENST00000445470.2_Missense_Mutation_p.L27F|CPA4_ENST00000493259.1_Intron	NM_016352.3	NP_057436.2	Q9UI42	CBPA4_HUMAN	carboxypeptidase A4	27			L -> F (in dbSNP:rs34587586).		histone acetylation (GO:0016573)	extracellular region (GO:0005576)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	21	Melanoma(18;0.0435)					ACCAAGTTTTGAGGATTAATG	0.428													T|||	1783	0.35603	0.3253	0.3458	5008	,	,		20606	0.3581		0.3877	False		,,,				2504	0.3701				p.L27F		Atlas-SNP	.											.	CPA4	47	.	0			c.G81T						PASS	.	T	PHE/LEU,PHE/LEU	1486,2920	676.9+/-403.3	252,982,969	126.0	125.0	125.0		81,81	4.5	1.0	7	dbSNP_126	125	3453,5147	636.4+/-399.1	715,2023,1562	yes	missense,missense	CPA4	NM_001163446.1,NM_016352.3	22,22	967,3005,2531	TT,TG,GG		40.1512,33.7267,37.9748	benign,benign	27/389,27/422	129938598	4939,8067	2203	4300	6503	SO:0001583	missense	51200	exon2			AGTTTTGAGGATT	AF095719	CCDS5818.1, CCDS55163.1	7q32	2008-07-18			ENSG00000128510	ENSG00000128510			15740	protein-coding gene	gene with protein product	"""carboxypeptidase A3"""	607635				10383164, 10860668	Standard	NM_016352		Approved	CPA3	uc003vpr.3	Q9UI42	OTTHUMG00000157825	ENST00000222482.4:c.81G>T	7.37:g.129938598G>T	ENSP00000222482:p.Leu27Phe	Somatic	236	0	0		WXS	Illumina HiSeq	Phase_I	237	110	0.464135	NM_016352	B7Z576|Q86UY9	Missense_Mutation	SNP	ENST00000222482.4	37	CCDS5818.1	793	0.3630952380952381	159	0.3231707317073171	141	0.38950276243093923	213	0.3723776223776224	280	0.36939313984168864	T	7.318	0.616383	0.14129	0.337267	0.401512	ENSG00000128510	ENST00000445470;ENST00000222482;ENST00000492072;ENST00000473956	T;T;T;T	0.14893	2.47;2.47;2.47;2.47	5.61	4.47	0.54385	Proteinase inhibitor, propeptide (1);Proteinase inhibitor, carboxypeptidase propeptide (2);	0.227453	0.39146	N	0.001446	T	0.00012	0.0000	N	0.20483	0.58	0.42641	P	0.006581999999999977	B;B	0.13594	0.008;0.002	B;B	0.36186	0.219;0.023	T	0.48906	-0.8993	9	0.12103	T	0.63	.	5.3961	0.16271	0.0:0.0931:0.1772:0.7297	rs34587586	27;27	B7Z576;Q9UI42	.;CBPA4_HUMAN	F	27	ENSP00000412947:L27F;ENSP00000222482:L27F;ENSP00000417255:L27F;ENSP00000418392:L27F	ENSP00000222482:L27F	L	+	3	2	CPA4	129725834	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	0.604000	0.24164	0.512000	0.28257	-0.525000	0.04345	TTG	G|0.630;T|0.370	0.370	strong		0.428	CPA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349725.1	NM_016352	
ZNF812	729648	hgsc.bcm.edu	37	19	9801257	9801257	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:9801257T>C	ENST00000457674.2	-	5	1440	c.922A>G	c.(922-924)Aag>Gag	p.K308E	ZNF812_ENST00000536819.1_5'UTR	NM_001199814.1	NP_001186743.1	P0C7V5	ZN812_HUMAN	zinc finger protein 812	308					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			ovary(1)	1						CCACATTCCTTACATTCATAG	0.428																																					p.K308E		Atlas-SNP	.											.	ZNF812	27	.	0			c.A922G						PASS	.																																			SO:0001583	missense	729648	exon6			ATTCCTTACATTC		CCDS54215.1	19p13.2	2014-04-02			ENSG00000224689	ENSG00000224689		"""Zinc fingers, C2H2-type"", ""-"""	33242	protein-coding gene	gene with protein product							Standard	NM_001199814		Approved		uc021uop.1	P0C7V5	OTTHUMG00000167867	ENST00000457674.2:c.922A>G	19.37:g.9801257T>C	ENSP00000395629:p.Lys308Glu	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	87	24	0.275862	NM_001199814		Missense_Mutation	SNP	ENST00000457674.2	37	CCDS54215.1	.	.	.	.	.	.	.	.	.	.	t	14.71	2.617516	0.46736	.	.	ENSG00000224689	ENST00000457674	T	0.08370	3.1	1.42	0.35	0.16037	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.09598	0.0236	N	0.16098	0.37	0.09310	N	1	D	0.64830	0.994	P	0.62298	0.9	T	0.30060	-0.9991	9	0.40728	T	0.16	.	4.7675	0.13139	0.0:0.1949:0.0:0.8051	.	308	P0C7V5	ZN812_HUMAN	E	308	ENSP00000395629:K308E	ENSP00000395629:K308E	K	-	1	0	ZNF812	9662257	0.000000	0.05858	0.147000	0.22382	0.506000	0.33950	-5.502000	0.00117	0.031000	0.15407	0.164000	0.16699	AAG	.	.	none		0.428	ZNF812-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396726.1		
TNN	63923	hgsc.bcm.edu	37	1	175049379	175049379	+	Missense_Mutation	SNP	G	G	A	rs16847812	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:175049379G>A	ENST00000239462.4	+	4	978	c.865G>A	c.(865-867)Gat>Aat	p.D289N		NM_022093.1	NP_071376.1	Q9UQP3	TENN_HUMAN	tenascin N	289	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.		D -> N (in dbSNP:rs16847812).		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)		CAGCCAGGTGGATCACTACCT	0.582													G|||	639	0.127596	0.0053	0.0735	5008	,	,		17710	0.251		0.1272	False		,,,				2504	0.2045				p.D289N		Atlas-SNP	.											.	TNN	297	.	0			c.G865A						PASS	.	G	ASN/ASP	120,4286	91.1+/-129.8	2,116,2085	68.0	68.0	68.0		865	5.7	1.0	1	dbSNP_123	68	1287,7313	255.4+/-280.3	85,1117,3098	yes	missense	TNN	NM_022093.1	23	87,1233,5183	AA,AG,GG		14.9651,2.7236,10.8181	benign	289/1300	175049379	1407,11599	2203	4300	6503	SO:0001583	missense	63923	exon4			CAGGTGGATCACT	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.865G>A	1.37:g.175049379G>A	ENSP00000239462:p.Asp289Asn	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	83	36	0.433735	NM_022093	B9EGP3|Q5R360	Missense_Mutation	SNP	ENST00000239462.4	37	CCDS30943.1	309	0.14148351648351648	6	0.012195121951219513	29	0.08011049723756906	160	0.27972027972027974	114	0.1503957783641161	G	19.23	3.786596	0.70337	0.027236	0.149651	ENSG00000120332	ENST00000239462;ENST00000539081	T	0.58940	0.3	5.69	5.69	0.88448	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.046701	0.85682	D	0.000000	T	0.00012	0.0000	M	0.87971	2.92	0.20975	P	0.999815479	B;B	0.24675	0.109;0.016	B;B	0.37451	0.25;0.098	T	0.04495	-1.0947	9	0.48119	T	0.1	.	19.4166	0.94703	0.0:0.0:1.0:0.0	rs16847812;rs52834449;rs16847812	289;289	B3KXB6;Q9UQP3	.;TENN_HUMAN	N	289	ENSP00000239462:D289N	ENSP00000239462:D289N	D	+	1	0	TNN	173316002	1.000000	0.71417	1.000000	0.80357	0.815000	0.46073	8.072000	0.89496	2.679000	0.91253	0.650000	0.86243	GAT	G|0.872;A|0.128	0.128	strong		0.582	TNN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084422.1	XM_040527	
FUT10	84750	hgsc.bcm.edu	37	8	33246685	33246685	+	Silent	SNP	G	G	A	rs16880852	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:33246685G>A	ENST00000327671.5	-	4	1639	c.1008C>T	c.(1006-1008)taC>taT	p.Y336Y	FUT10_ENST00000524021.1_Silent_p.Y308Y|FUT10_ENST00000518076.1_5'UTR|FUT10_ENST00000335589.3_Silent_p.Y274Y|FUT10_ENST00000518672.1_Silent_p.Y308Y	NM_032664.3	NP_116053.3	Q6P4F1	FUT10_HUMAN	fucosyltransferase 10 (alpha (1,3) fucosyltransferase)	336					embryo development (GO:0009790)|fertilization (GO:0009566)|fucosylation (GO:0036065)|hemopoiesis (GO:0030097)|L-fucose catabolic process (GO:0042355)|nervous system development (GO:0007399)|protein folding (GO:0006457)|protein glycosylation (GO:0006486)|protein targeting (GO:0006605)|wound healing (GO:0042060)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	alpha-(1->3)-fucosyltransferase activity (GO:0046920)	p.Y336Y(1)		cervix(1)|endometrium(1)|large_intestine(7)|liver(1)|lung(9)|ovary(1)|pancreas(1)|prostate(3)|stomach(3)|upper_aerodigestive_tract(2)	29				KIRC - Kidney renal clear cell carcinoma(67;0.129)|Kidney(114;0.154)		GTCGTCTGATGTAACTTGCCA	0.463													G|||	1496	0.298722	0.1808	0.17	5008	,	,		21121	0.4683		0.1938	False		,,,				2504	0.4826				p.Y336Y		Atlas-SNP	.											FUT10,NS,carcinoma,0,1	FUT10	62	1	1	Substitution - coding silent(1)	stomach(1)	c.C1008T						PASS	.	G		916,3490	349.5+/-310.4	76,764,1363	96.0	89.0	91.0		1008	3.2	0.4	8	dbSNP_123	91	1747,6853	316.6+/-312.8	177,1393,2730	no	coding-synonymous	FUT10	NM_032664.3		253,2157,4093	AA,AG,GG		20.314,20.7898,20.4752		336/480	33246685	2663,10343	2203	4300	6503	SO:0001819	synonymous_variant	84750	exon4			TCTGATGTAACTT	AJ512465	CCDS6088.1	8p12	2013-02-26			ENSG00000172728	ENSG00000172728		"""Fucosyltransferases"""	19234	protein-coding gene	gene with protein product							Standard	NM_032664		Approved		uc003xje.3	Q6P4F1	OTTHUMG00000163954	ENST00000327671.5:c.1008C>T	8.37:g.33246685G>A		Somatic	318	1	0.00314465		WXS	Illumina HiSeq	Phase_I	289	287	0.99308	NM_032664	A8KAC8|Q70GG3|Q8IVI6|Q8IVI7|Q8IVJ3|Q8TE43|Q9BSR3	Silent	SNP	ENST00000327671.5	37	CCDS6088.1																																																																																			G|0.768;A|0.232	0.232	strong		0.463	FUT10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376540.1	NM_032664	
PRKRIR	5612	hgsc.bcm.edu	37	11	76072085	76072085	+	Missense_Mutation	SNP	C	C	T	rs76214254	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:76072085C>T	ENST00000260045.3	-	3	338	c.233G>A	c.(232-234)cGa>cAa	p.R78Q	PRKRIR_ENST00000531878.1_5'UTR	NM_004705.2	NP_004696.2	O43422	P52K_HUMAN	protein-kinase, interferon-inducible double stranded RNA dependent inhibitor, repressor of (P58 repressor)	78					negative regulation of cell proliferation (GO:0008285)|response to stress (GO:0006950)|signal transduction (GO:0007165)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			cervix(1)|endometrium(3)|large_intestine(4)|lung(12)|ovary(2)|pancreas(1)|prostate(1)|skin(1)	25						TGCATTATCTCGAAGAACTGT	0.308																																					p.R78Q		Atlas-SNP	.											PRKRIR,caecum,adenoma,0,1	PRKRIR	65	1	0			c.G233A						scavenged	.						114.0	110.0	112.0					11																	76072085		2200	4292	6492	SO:0001583	missense	5612	exon3			TTATCTCGAAGAA	AF007393	CCDS8243.1	11q13.5	2013-01-25			ENSG00000137492	ENSG00000137492		"""THAP (C2CH-type zinc finger) domain containing"""	9440	protein-coding gene	gene with protein product	"""THAP domain containing 12"""	607374				9447982	Standard	NM_004705		Approved	P52rIPK, DAP4, THAP12	uc001oxh.1	O43422	OTTHUMG00000165280	ENST00000260045.3:c.233G>A	11.37:g.76072085C>T	ENSP00000260045:p.Arg78Gln	Somatic	115	1	0.00869565		WXS	Illumina HiSeq	Phase_I	106	8	0.0754717	NM_004705	A8K728|Q17RY9|Q8WTW1|Q9Y3Z4	Missense_Mutation	SNP	ENST00000260045.3	37	CCDS8243.1	.	.	.	.	.	.	.	.	.	.	C	18.12	3.552130	0.65311	.	.	ENSG00000137492	ENST00000260045	D	0.96459	-4.02	5.44	5.44	0.79542	Zinc finger, C2CH-type (4);	0.052263	0.85682	D	0.000000	D	0.93035	0.7783	L	0.31526	0.94	0.44899	D	0.997917	B	0.28470	0.213	B	0.20184	0.028	D	0.90113	0.4193	10	0.36615	T	0.2	.	19.6212	0.95656	0.0:1.0:0.0:0.0	.	78	O43422	P52K_HUMAN	Q	78	ENSP00000260045:R78Q	ENSP00000260045:R78Q	R	-	2	0	PRKRIR	75749733	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.216000	0.58540	2.723000	0.93209	0.655000	0.94253	CGA	C|0.999;T|0.001	0.001	strong		0.308	PRKRIR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383188.1	NM_004705	
PKHD1	5314	hgsc.bcm.edu	37	6	51890754	51890754	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:51890754C>T	ENST00000371117.3	-	32	4129	c.3854G>A	c.(3853-3855)aGc>aAc	p.S1285N	PKHD1_ENST00000340994.4_Missense_Mutation_p.S1285N	NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	1285	IPT/TIG 7.				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)					CCCCACCAAGCTTGGTGAAGG	0.587																																					p.S1285N		Atlas-SNP	.											.	PKHD1	927	.	0			c.G3854A						PASS	.						88.0	78.0	82.0					6																	51890754		2203	4300	6503	SO:0001583	missense	5314	exon32			ACCAAGCTTGGTG	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.3854G>A	6.37:g.51890754C>T	ENSP00000360158:p.Ser1285Asn	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	103	27	0.262136	NM_170724	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Missense_Mutation	SNP	ENST00000371117.3	37	CCDS4935.1	.	.	.	.	.	.	.	.	.	.	C	8.648	0.897477	0.17686	.	.	ENSG00000170927	ENST00000371117;ENST00000340994;ENST00000393616	D;D	0.87412	-2.05;-2.25	5.79	-0.718	0.11205	Cell surface receptor IPT/TIG (1);	1.934510	0.01638	N	0.023911	T	0.64962	0.2646	M	0.63428	1.95	0.09310	N	1	B;B	0.34015	0.435;0.011	B;B	0.25140	0.058;0.002	T	0.52873	-0.8517	10	0.12766	T	0.61	.	3.7658	0.08622	0.2648:0.4257:0.0:0.3094	.	1285;1285	P08F94-2;P08F94	.;PKHD1_HUMAN	N	1285	ENSP00000360158:S1285N;ENSP00000341097:S1285N	ENSP00000341097:S1285N	S	-	2	0	PKHD1	51998713	0.000000	0.05858	0.000000	0.03702	0.071000	0.16799	-0.748000	0.04818	0.080000	0.16959	-0.169000	0.13324	AGC	.	.	none		0.587	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694	
WDR82	80335	hgsc.bcm.edu	37	3	52293859	52293859	+	Silent	SNP	A	A	G	rs3210487	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:52293859A>G	ENST00000296490.3	-	6	854	c.573T>C	c.(571-573)taT>taC	p.Y191Y		NM_025222.3	NP_079498.2	Q6UXN9	WDR82_HUMAN	WD repeat domain 82	191					histone H3-K4 methylation (GO:0051568)	chromatin (GO:0000785)|histone methyltransferase complex (GO:0035097)|PTW/PP1 phosphatase complex (GO:0072357)|Set1C/COMPASS complex (GO:0048188)	chromatin binding (GO:0003682)								BRCA - Breast invasive adenocarcinoma(193;2.67e-05)|Kidney(197;0.00198)|KIRC - Kidney renal clear cell carcinoma(197;0.00223)|OV - Ovarian serous cystadenocarcinoma(275;0.246)		AAGTTCGATCATACTGCATCT	0.423													A|||	667	0.133187	0.3381	0.0937	5008	,	,		19939	0.0		0.1024	False		,,,				2504	0.0532				p.Y191Y		Atlas-SNP	.											WDR82_ENST00000296490,NS,adenoma,-2,1	WDR82	19	1	0			c.T573C						PASS	.	A		919,2903		104,711,1096	150.0	139.0	143.0		573	-0.8	1.0	3	dbSNP_105	143	982,7274		58,866,3204	no	coding-synonymous	WDR82	NM_025222.3		162,1577,4300	GG,GA,AA		11.8944,24.045,15.7394		191/314	52293859	1901,10177	1911	4128	6039	SO:0001819	synonymous_variant	80335	exon6			TCGATCATACTGC	AF132207	CCDS2851.2	3p21.2	2013-01-10	2007-07-04	2007-07-04	ENSG00000164091	ENSG00000164091		"""WD repeat domain containing"""	28826	protein-coding gene	gene with protein product		611059	"""transmembrane protein 113"""	TMEM113		17355966	Standard	NM_025222		Approved	PRO2730, MST107, MSTP107, PRO34047, WDR82A, SWD2	uc003ddl.2	Q6UXN9	OTTHUMG00000150391	ENST00000296490.3:c.573T>C	3.37:g.52293859A>G		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	59	26	0.440678	NM_025222	A8K5R5|Q8TEB2	Silent	SNP	ENST00000296490.3	37	CCDS2851.2																																																																																			A|0.888;G|0.112	0.112	strong		0.423	WDR82-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317919.1	NM_025222	
KRTAP21-2	337978	hgsc.bcm.edu	37	21	32119495	32119495	+	Missense_Mutation	SNP	C	C	G	rs12053674	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	130	0	0		WXS	Illumina HiSeq	Phase_I	120	49	0.408333	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		
BIN1	274	hgsc.bcm.edu	37	2	127826533	127826533	+	Silent	SNP	A	A	G	rs1060743	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:127826533A>G	ENST00000316724.5	-	6	897	c.486T>C	c.(484-486)acT>acC	p.T162T	BIN1_ENST00000346226.3_Silent_p.T162T|BIN1_ENST00000393040.3_Silent_p.T162T|BIN1_ENST00000351659.3_Silent_p.T162T|BIN1_ENST00000348750.4_Silent_p.T162T|BIN1_ENST00000352848.3_Silent_p.T162T|BIN1_ENST00000376113.2_Silent_p.T162T|BIN1_ENST00000357970.3_Silent_p.T162T|BIN1_ENST00000393041.3_Silent_p.T162T|BIN1_ENST00000409400.1_Silent_p.T162T|BIN1_ENST00000259238.4_Silent_p.T162T	NM_139343.2	NP_647593.1	O00499	BIN1_HUMAN	bridging integrator 1	162	BAR. {ECO:0000255|PROSITE- ProRule:PRU00361}.				cell proliferation (GO:0008283)|endocytosis (GO:0006897)|lipid tube assembly (GO:0060988)|muscle cell differentiation (GO:0042692)|positive regulation of apoptotic process (GO:0043065)|positive regulation of astrocyte differentiation (GO:0048711)|positive regulation of endocytosis (GO:0045807)|positive regulation of GTPase activity (GO:0043547)|regulation of cell cycle arrest (GO:0071156)|regulation of neuron differentiation (GO:0045664)|viral process (GO:0016032)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|axon initial segment (GO:0043194)|axon terminus (GO:0043679)|cerebellar mossy fiber (GO:0044300)|cytoplasm (GO:0005737)|I band (GO:0031674)|lipid tube (GO:0060987)|node of Ranvier (GO:0033268)|nucleus (GO:0005634)|synaptic vesicle (GO:0008021)|T-tubule (GO:0030315)|varicosity (GO:0043196)|Z disc (GO:0030018)	identical protein binding (GO:0042802)|tau protein binding (GO:0048156)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(3)|lung(6)|ovary(3)|prostate(3)|skin(3)	24	Colorectal(110;0.0831)			BRCA - Breast invasive adenocarcinoma(221;0.073)		TCTTTTTGGCAGTTTGAAGGG	0.617													A|||	1776	0.354633	0.2443	0.366	5008	,	,		17643	0.4534		0.2913	False		,,,				2504	0.4591				p.T162T		Atlas-SNP	.											.	BIN1	85	.	0			c.T486C						PASS	.	A	,,,,,,,,,	1037,3369		132,773,1298	147.0	135.0	139.0		486,486,486,486,486,486,486,486,486,486	-7.0	0.7	2	dbSNP_86	139	2498,6102		366,1766,2168	yes	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	BIN1	NM_004305.3,NM_139343.2,NM_139344.2,NM_139345.2,NM_139346.2,NM_139347.2,NM_139348.2,NM_139349.2,NM_139350.2,NM_139351.2	,,,,,,,,,	498,2539,3466	GG,GA,AA		29.0465,23.5361,27.1798	,,,,,,,,,	162/455,162/594,162/551,162/507,162/498,162/519,162/483,162/476,162/440,162/410	127826533	3535,9471	2203	4300	6503	SO:0001819	synonymous_variant	274	exon6			TTTGGCAGTTTGA	U68485	CCDS2137.1, CCDS2138.1, CCDS2139.1, CCDS2140.1, CCDS2141.1, CCDS2142.1, CCDS2143.1, CCDS42743.1, CCDS42744.1, CCDS46403.1	2q14	2014-09-17			ENSG00000136717	ENSG00000136717			1052	protein-coding gene	gene with protein product	"""amphiphysin II"""	601248		AMPHL		8725406, 8782822, 17676042	Standard	NM_004305		Approved	SH3P9, AMPH2	uc002tns.2	O00499	OTTHUMG00000131465	ENST00000316724.5:c.486T>C	2.37:g.127826533A>G		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	106	46	0.433962	NM_139346	O00297|O00545|O43867|O60552|O60553|O60554|O60555|O75514|O75515|O75516|O75517|O75518|Q659B7|Q92944|Q99688	Silent	SNP	ENST00000316724.5	37	CCDS2138.1																																																																																			A|0.702;G|0.298	0.298	strong		0.617	BIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254298.2	NM_139343	
PRKCH	5583	hgsc.bcm.edu	37	14	61857969	61857969	+	Silent	SNP	A	A	G	rs2230499	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:61857969A>G	ENST00000332981.5	+	2	775	c.390A>G	c.(388-390)gtA>gtG	p.V130V	PRKCH_ENST00000555082.1_5'UTR	NM_006255.3	NP_006246.2	P24723	KPCL_HUMAN	protein kinase C, eta	130					blood coagulation (GO:0007596)|negative regulation of glial cell apoptotic process (GO:0034351)|platelet activation (GO:0030168)|positive regulation of B cell receptor signaling pathway (GO:0050861)|positive regulation of glial cell proliferation (GO:0060252)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein kinase C signaling (GO:0070528)|protein phosphorylation (GO:0006468)|regulation of tight junction assembly (GO:2000810)|signal transduction (GO:0007165)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium-independent protein kinase C activity (GO:0004699)|enzyme binding (GO:0019899)|metal ion binding (GO:0046872)|protein kinase C activity (GO:0004697)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(4)|ovary(2)|pancreas(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	25				OV - Ovarian serous cystadenocarcinoma(108;0.045)|BRCA - Breast invasive adenocarcinoma(234;0.0906)|KIRC - Kidney renal clear cell carcinoma(182;0.182)		AGGGGAAAGTATTTGTGGTAA	0.348													A|||	1390	0.277556	0.4955	0.1873	5008	,	,		17836	0.248		0.163	False		,,,				2504	0.1953				p.V130V	Melanoma(135;863 1779 8064 14443 26348)	Atlas-SNP	.											.	PRKCH	89	.	0			c.A390G						PASS	.	A		1787,2619	523.9+/-371.2	364,1059,780	86.0	84.0	85.0		390	-2.9	1.0	14	dbSNP_107	85	1375,7225	265.8+/-286.4	103,1169,3028	no	coding-synonymous	PRKCH	NM_006255.3		467,2228,3808	GG,GA,AA		15.9884,40.5583,24.3119		130/684	61857969	3162,9844	2203	4300	6503	SO:0001819	synonymous_variant	5583	exon2			GAAAGTATTTGTG	M55284	CCDS9752.1	14q23.1	2009-07-10			ENSG00000027075	ENSG00000027075	2.7.11.1		9403	protein-coding gene	gene with protein product		605437		PRKCL		1986216, 1545821	Standard	NM_006255		Approved	PKC-L, PKCL	uc001xfn.3	P24723	OTTHUMG00000152341	ENST00000332981.5:c.390A>G	14.37:g.61857969A>G		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	54	20	0.37037	NM_006255	B4DJN5|Q16246|Q8NE03	Silent	SNP	ENST00000332981.5	37	CCDS9752.1																																																																																			A|0.743;G|0.257	0.257	strong		0.348	PRKCH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276974.2	NM_006255	
TPR	7175	hgsc.bcm.edu	37	1	186321242	186321242	+	Splice_Site	SNP	C	C	T	rs61744267	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:186321242C>T	ENST00000367478.4	-	19	2631	c.2335G>A	c.(2335-2337)Gta>Ata	p.V779I	TPR_ENST00000474852.1_5'UTR	NM_003292.2	NP_003283.2	P12270	TPR_HUMAN	translocated promoter region, nuclear basket protein	779				V -> I (in Ref. 3; AAB48030). {ECO:0000305}.	carbohydrate metabolic process (GO:0005975)|cellular response to heat (GO:0034605)|cellular response to interferon-alpha (GO:0035457)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|MAPK import into nucleus (GO:0000189)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope disassembly (GO:0007077)|mitotic spindle assembly checkpoint (GO:0007094)|mRNA export from nucleus in response to heat stress (GO:0031990)|negative regulation of RNA export from nucleus (GO:0046832)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of translational initiation (GO:0045947)|nuclear pore organization (GO:0006999)|positive regulation of heterochromatin assembly (GO:0031453)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of mitotic cell cycle spindle assembly checkpoint (GO:0090267)|positive regulation of protein export from nucleus (GO:0046827)|positive regulation of protein import into nucleus (GO:0042307)|protein import into nucleus (GO:0006606)|regulation of glucose transport (GO:0010827)|regulation of mitotic sister chromatid separation (GO:0010965)|regulation of spindle assembly involved in mitosis (GO:1901673)|response to epidermal growth factor (GO:0070849)|RNA export from nucleus (GO:0006405)|RNA import into nucleus (GO:0006404)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoplasmic dynein complex (GO:0005868)|extrinsic component of membrane (GO:0019898)|kinetochore (GO:0000776)|mitotic spindle (GO:0072686)|nuclear envelope (GO:0005635)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|dynein complex binding (GO:0070840)|heat shock protein binding (GO:0031072)|mitogen-activated protein kinase binding (GO:0051019)|mRNA binding (GO:0003729)|nucleocytoplasmic transporter activity (GO:0005487)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)|tubulin binding (GO:0015631)	p.V780I(2)|p.V779I(1)		autonomic_ganglia(1)|breast(5)|central_nervous_system(4)|cervix(2)|endometrium(9)|kidney(12)|large_intestine(23)|liver(1)|lung(45)|ovary(2)|pancreas(1)|prostate(6)|skin(3)|stomach(1)|urinary_tract(8)	123		Breast(1374;0.000659)|Lung SC(1967;0.0262)|Prostate(1639;0.157)		Colorectal(1306;1.12e-05)|KIRC - Kidney renal clear cell carcinoma(1967;0.00553)		TCTGCTCTTACCTAAACATAA	0.303			T	NTRK1	papillary thyroid								C|||	436	0.0870607	0.0234	0.121	5008	,	,		14946	0.0714		0.1849	False		,,,				2504	0.0644				p.V779I		Atlas-SNP	.		Dom	yes		1	1q25	7175	translocated promoter region		E	TPR_ENST00000367478,NS,carcinoma,0,3	TPR	441	3	3	Substitution - Missense(3)	pancreas(2)|stomach(1)	c.G2335A						PASS	.	C	ILE/VAL	189,3415		5,179,1618	73.0	68.0	70.0		2335	5.8	1.0	1	dbSNP_129	70	1469,6669		123,1223,2723	yes	missense-near-splice	TPR	NM_003292.2	29	128,1402,4341	TT,TC,CC		18.0511,5.2442,14.1203	probably-damaging	779/2364	186321242	1658,10084	1802	4069	5871	SO:0001630	splice_region_variant	7175	exon19			CTCTTACCTAAAC	U69668	CCDS41446.1	1q25	2012-03-13	2012-03-13		ENSG00000047410	ENSG00000047410			12017	protein-coding gene	gene with protein product		189940	"""translocated promoter region (to activated MET oncogene)"""			1611909, 15229283	Standard	NM_003292		Approved		uc001grv.3	P12270	OTTHUMG00000035580	ENST00000367478.4:c.2335-1G>A	1.37:g.186321242C>T		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	41	18	0.439024	NM_003292	Q15655|Q5SWY0|Q99968	Missense_Mutation	SNP	ENST00000367478.4	37	CCDS41446.1	239	0.10943223443223443	7	0.014227642276422764	45	0.12430939226519337	36	0.06293706293706294	151	0.19920844327176782	C	23.5	4.421789	0.83559	0.052442	0.180511	ENSG00000047410	ENST00000367478	T	0.24908	1.83	5.75	5.75	0.90469	.	0.242826	0.41194	D	0.000931	T	0.00039	0.0001	L	0.54323	1.7	0.20703	P	0.999866087	D	0.59357	0.985	B	0.43950	0.437	T	0.15037	-1.0451	9	0.21540	T	0.41	.	19.5445	0.95285	0.0:1.0:0.0:0.0	.	779	P12270	TPR_HUMAN	I	779	ENSP00000356448:V779I	ENSP00000356448:V779I	V	-	1	0	TPR	184587865	1.000000	0.71417	1.000000	0.80357	0.801000	0.45260	4.876000	0.63079	2.711000	0.92665	0.563000	0.77884	GTA	C|0.871;T|0.129	0.129	strong		0.303	TPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086353.2	NM_003292	Missense_Mutation
DSPP	1834	hgsc.bcm.edu	37	4	88536448	88536448	+	Silent	SNP	C	C	T	rs111205175		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:88536448C>T	ENST00000282478.7	+	4	2667	c.2634C>T	c.(2632-2634)gaC>gaT	p.D878D	RP11-742B18.1_ENST00000506480.1_RNA|DSPP_ENST00000399271.1_Silent_p.D878D			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	878	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)		acagcagtgacagcagtgata	0.498																																					p.D878D		Atlas-SNP	.											.	DSPP	174	.	0			c.C2634T						PASS	.						70.0	84.0	79.0					4																	88536448		1633	2930	4563	SO:0001819	synonymous_variant	1834	exon5			CAGTGACAGCAGT	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.2634C>T	4.37:g.88536448C>T		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	73	12	0.164384	NM_014208	A8MUI0|O95815	Silent	SNP	ENST00000282478.7	37	CCDS43248.1																																																																																			.	.	weak		0.498	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208	
BPIFB4	149954	hgsc.bcm.edu	37	20	31671599	31671599	+	Missense_Mutation	SNP	A	A	G	rs4339026	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:31671599A>G	ENST00000375483.3	+	3	596	c.596A>G	c.(595-597)gAt>gGt	p.D199G		NM_182519.2	NP_872325.2	P59827	BPIB4_HUMAN	BPI fold containing family B, member 4	199	Gly-rich.		D -> G (in dbSNP:rs4339026).			cytoplasm (GO:0005737)|extracellular region (GO:0005576)	lipid binding (GO:0008289)										CTCCTTGGTGATGGAGGACTT	0.657													A|||	1168	0.233227	0.2572	0.3127	5008	,	,		16499	0.1518		0.2296	False		,,,				2504	0.2321				p.D199G		Atlas-SNP	.											.	.	.	.	0			c.A596G						PASS	.	A	GLY/ASP	1159,3241		171,817,1212	34.0	40.0	38.0		596	3.3	0.1	20	dbSNP_111	38	1960,6632		225,1510,2561	yes	missense	BPIFB4	NM_182519.2	94	396,2327,3773	GG,GA,AA		22.8119,26.3409,24.0071	probably-damaging	199/615	31671599	3119,9873	2200	4296	6496	SO:0001583	missense	149954	exon3			TTGGTGATGGAGG	AF549190	CCDS13213.2	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000186191	ENSG00000186191		"""BPI fold containing"""	16179	protein-coding gene	gene with protein product		615718	"""chromosome 20 open reading frame 186"""	C20orf186		11971875, 21787333	Standard	NM_182519		Approved	dJ726C3.5, LPLUNC4	uc010zue.2	P59827	OTTHUMG00000032235	ENST00000375483.3:c.596A>G	20.37:g.31671599A>G	ENSP00000364632:p.Asp199Gly	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	68	40	0.588235	NM_182519	Q5TDX6	Missense_Mutation	SNP	ENST00000375483.3	37	CCDS13213.2	499	0.22847985347985347	111	0.22560975609756098	115	0.31767955801104975	97	0.16958041958041958	176	0.23218997361477572	A	12.08	1.830971	0.32329	0.263409	0.228119	ENSG00000186191	ENST00000375483	T	0.01092	5.35	3.33	3.33	0.38152	.	0.145342	0.30771	N	0.008918	T	0.00012	0.0000	L	0.29908	0.895	0.80722	P	0.0	P	0.34587	0.458	B	0.37267	0.245	T	0.51725	-0.8669	9	0.40728	T	0.16	-8.96	8.2721	0.31851	1.0:0.0:0.0:0.0	rs4339026;rs52799415;rs59902902;rs4339026	199	P59827	BPIB4_HUMAN	G	199	ENSP00000364632:D199G	ENSP00000364632:D199G	D	+	2	0	BPIFB4	31135260	0.072000	0.21174	0.106000	0.21319	0.375000	0.29983	2.137000	0.42130	1.516000	0.48900	0.334000	0.21626	GAT	A|0.777;G|0.223	0.223	strong		0.657	BPIFB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078655.5	NM_182519	
IL16	3603	hgsc.bcm.edu	37	15	81584925	81584925	+	Silent	SNP	C	C	T	rs61752774	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:81584925C>T	ENST00000302987.4	+	11	1449	c.1449C>T	c.(1447-1449)caC>caT	p.H483H	IL16_ENST00000394660.2_Silent_p.H483H			Q14005	IL16_HUMAN	interleukin 16	483					immune response (GO:0006955)|induction of positive chemotaxis (GO:0050930)|leukocyte chemotaxis (GO:0030595)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(12)|lung(20)|ovary(3)|skin(3)|stomach(1)|urinary_tract(1)	57						GCAGTTGGCACGGGCGGCCCA	0.557													C|||	837	0.167133	0.0673	0.1931	5008	,	,		19115	0.1885		0.0994	False		,,,				2504	0.3313				p.H483H		Atlas-SNP	.											IL16_ENST00000302987,caecum,carcinoma,0,2	IL16	254	2	0			c.C1449T						PASS	.	C	,	274,3694		11,252,1721	54.0	60.0	58.0		1449,1449	-8.4	0.5	15	dbSNP_129	58	870,7440		43,784,3328	no	coding-synonymous,coding-synonymous	IL16	NM_001172128.1,NM_172217.3	,	54,1036,5049	TT,TC,CC		10.4693,6.9052,9.3175	,	483/1332,483/1333	81584925	1144,11134	1984	4155	6139	SO:0001819	synonymous_variant	3603	exon12			TTGGCACGGGCGG	U82972	CCDS10317.1, CCDS42069.1, CCDS53966.1	15q26.3	2011-07-14	2011-07-14		ENSG00000172349	ENSG00000172349		"""Interleukins and interleukin receptors"""	5980	protein-coding gene	gene with protein product	"""prointerleukin 16"", ""lymphocyte chemoattractant factor"""	603035	"""interleukin 16 (lymphocyte chemoattractant factor)"""			9144227	Standard	NM_004513		Approved	LCF, IL-16, prIL-16, HsT19289, FLJ42735, FLJ16806	uc021ssh.1	Q14005	OTTHUMG00000144186	ENST00000302987.4:c.1449C>T	15.37:g.81584925C>T		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	52	15	0.288462	NM_001172128	A6NM20|A8MU65|B5TY35|B9EGR6|H3BVH5|Q16435|Q6VVE6|Q6ZMQ7|Q9UP18	Silent	SNP	ENST00000302987.4	37	CCDS42069.1																																																																																			C|0.881;T|0.119	0.119	strong		0.557	IL16-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000303952.1	NM_172217	
ISYNA1	51477	hgsc.bcm.edu	37	19	18546678	18546678	+	Silent	SNP	T	T	C	rs2303697	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:18546678T>C	ENST00000338128.8	-	8	1246	c.1029A>G	c.(1027-1029)ctA>ctG	p.L343L	ISYNA1_ENST00000457269.4_Silent_p.L289L|ISYNA1_ENST00000317018.6_Silent_p.L141L|ISYNA1_ENST00000578963.1_Silent_p.L215L|ISYNA1_ENST00000545187.1_Silent_p.L193L	NM_001170938.1|NM_016368.4	NP_001164409.1|NP_057452.1	Q9NPH2	INO1_HUMAN	inositol-3-phosphate synthase 1	343					inositol biosynthetic process (GO:0006021)|inositol phosphate metabolic process (GO:0043647)|phospholipid biosynthetic process (GO:0008654)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	inositol-3-phosphate synthase activity (GO:0004512)			breast(1)|endometrium(1)|kidney(2)|lung(4)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(2)	12						ATGGCGCCGATAGGTTCTCCC	0.602													C|||	2366	0.472444	0.8298	0.3732	5008	,	,		15663	0.2163		0.3479	False		,,,				2504	0.4519				p.L343L		Atlas-SNP	.											.	ISYNA1	31	.	0			c.A1029G	GRCh37	CM044082	ISYNA1	M	rs2303697	PASS	.	C	,,	3313,1093	394.0+/-329.1	1253,807,143	163.0	176.0	172.0		867,579,1029	0.8	1.0	19	dbSNP_100	172	2947,5653	668.2+/-402.5	537,1873,1890	no	coding-synonymous,coding-synonymous,coding-synonymous	ISYNA1	NM_001170938.1,NM_001170939.1,NM_016368.4	,,	1790,2680,2033	CC,CT,TT		34.2674,24.8071,48.1316	,,	289/505,193/409,343/559	18546678	6260,6746	2203	4300	6503	SO:0001819	synonymous_variant	51477	exon8			CGCCGATAGGTTC		CCDS12379.1, CCDS54234.1, CCDS62603.1	19p13.11	2014-09-04			ENSG00000105655	ENSG00000105655	5.5.1.4		29821	protein-coding gene	gene with protein product	"""myo-inositol 1-phosphate synthase"""	611670				15024000, 12941308	Standard	NM_016368		Approved	Ino1, INOS, IPS	uc002njd.2	Q9NPH2	OTTHUMG00000179027	ENST00000338128.8:c.1029A>G	19.37:g.18546678T>C		Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	116	116	1	NM_016368	B3KRT1|G5E9U0|Q6NXT5|Q7Z525|Q9BT65|Q9H2Y2|Q9NSU0|Q9NVW7	Silent	SNP	ENST00000338128.8	37	CCDS12379.1																																																																																			T|0.535;C|0.465	0.465	strong		0.602	ISYNA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444469.2	NM_016368	
WDR35	57539	hgsc.bcm.edu	37	2	20133221	20133221	+	Missense_Mutation	SNP	C	C	T	rs2293669	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:20133221C>T	ENST00000345530.3	-	23	2747	c.2632G>A	c.(2632-2634)Gca>Aca	p.A878T	WDR35_ENST00000416055.2_Intron|WDR35_ENST00000281405.4_Missense_Mutation_p.A867T	NM_001006657.1	NP_001006658.1	Q9P2L0	WDR35_HUMAN	WD repeat domain 35	878			A -> P (in dbSNP:rs2293669).|A -> T (in dbSNP:rs2293669). {ECO:0000269|PubMed:15489334}.		cilium assembly (GO:0042384)|intraciliary retrograde transport (GO:0035721)	axoneme (GO:0005930)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|intraciliary transport particle A (GO:0030991)				breast(1)|endometrium(5)|kidney(8)|large_intestine(8)|lung(16)|ovary(2)|prostate(1)|skin(1)|stomach(1)	43	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TTCAAAAATGCAGTCACTGCT	0.383													C|||	210	0.0419329	0.0439	0.0403	5008	,	,		19241	0.0298		0.0666	False		,,,				2504	0.0276				p.A878T		Atlas-SNP	.											.	WDR35	92	.	0			c.G2632A						PASS	.	C	THR/ALA,THR/ALA	163,4243	108.6+/-147.0	3,157,2043	160.0	137.0	144.0		2632,2599	5.3	0.5	2	dbSNP_100	144	676,7924	168.7+/-220.2	29,618,3653	yes	missense,missense	WDR35	NM_001006657.1,NM_020779.3	58,58	32,775,5696	TT,TC,CC		7.8605,3.6995,6.4509	possibly-damaging,possibly-damaging	878/1182,867/1171	20133221	839,12167	2203	4300	6503	SO:0001583	missense	57539	exon23			AAAATGCAGTCAC	AB037757	CCDS1695.1, CCDS33152.1	2p24.3	2014-02-21			ENSG00000118965	ENSG00000118965		"""WD repeat domain containing"", ""Intraflagellar transport homologs"""	29250	protein-coding gene	gene with protein product		613602				10718198	Standard	NM_001006657		Approved	MGC33196, KIAA1336, IFT121, IFTA1	uc002rdi.3	Q9P2L0	OTTHUMG00000090737	ENST00000345530.3:c.2632G>A	2.37:g.20133221C>T	ENSP00000314444:p.Ala878Thr	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	100	29	0.29	NM_001006657	B3KVI5|Q4ZG01|Q8NE11	Missense_Mutation	SNP	ENST00000345530.3	37	CCDS33152.1	106	0.048534798534798536	23	0.046747967479674794	19	0.052486187845303865	13	0.022727272727272728	51	0.06728232189973615	C	34	5.368739	0.95900	0.036995	0.078605	ENSG00000118965	ENST00000345530;ENST00000281405	T;T	0.23950	1.88;1.88	5.29	5.29	0.74685	.	0.000000	0.85682	D	0.000000	T	0.03011	0.0089	M	0.81179	2.53	0.80722	D	1	B;D	0.56968	0.36;0.978	B;P	0.50136	0.161;0.632	T	0.01013	-1.1481	10	0.27082	T	0.32	-13.1646	18.2704	0.90066	0.0:1.0:0.0:0.0	rs2293669;rs17853686;rs52816513;rs56934726;rs2293669	867;878	Q9P2L0-2;Q9P2L0	.;WDR35_HUMAN	T	878;867	ENSP00000314444:A878T;ENSP00000281405:A867T	ENSP00000281405:A867T	A	-	1	0	WDR35	19996702	1.000000	0.71417	0.490000	0.27465	0.979000	0.70002	5.610000	0.67668	2.635000	0.89317	0.563000	0.77884	GCA	C|0.942;G|0.000;T|0.058	0.058	strong		0.383	WDR35-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000207472.2	NM_020779	
GRIA2	2891	hgsc.bcm.edu	37	4	158242630	158242630	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:158242630G>T	ENST00000264426.9	+	6	1040	c.761G>T	c.(760-762)gGt>gTt	p.G254V	GRIA2_ENST00000393815.2_Missense_Mutation_p.G207V|GRIA2_ENST00000507898.1_Missense_Mutation_p.G207V|GRIA2_ENST00000449365.1_Missense_Mutation_p.G207V|GRIA2_ENST00000296526.7_Missense_Mutation_p.G254V	NM_001083619.1	NP_001077088	P42262	GRIA2_HUMAN	glutamate receptor, ionotropic, AMPA 2	254					ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|synaptic vesicle (GO:0008021)	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:0004971)|extracellular-glutamate-gated ion channel activity (GO:0005234)|ionotropic glutamate receptor activity (GO:0004970)			NS(1)|breast(2)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(16)|liver(2)|lung(32)|ovary(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	79	all_hematologic(180;0.24)	Renal(120;0.0458)		COAD - Colon adenocarcinoma(41;0.0294)	Amobarbital(DB01351)|Aprobarbital(DB01352)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Methylphenobarbital(DB00849)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Primidone(DB00794)|Quinidine barbiturate(DB01346)|Secobarbital(DB00418)|Talbutal(DB00306)|Thiopental(DB00599)	CAGTTTGGAGGTGCAAATGTC	0.348																																					p.G254V		Atlas-SNP	.											.	GRIA2	358	.	0			c.G761T						PASS	.						192.0	203.0	199.0					4																	158242630		2203	4300	6503	SO:0001583	missense	2891	exon6			TTGGAGGTGCAAA		CCDS3797.1, CCDS43274.1, CCDS43275.1	4q32.1	2012-08-29			ENSG00000120251	ENSG00000120251		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4572	protein-coding gene	gene with protein product		138247		GLUR2		1311100	Standard	NM_001083619		Approved	GluA2, GLURB	uc003ipl.4	P42262	OTTHUMG00000133836	ENST00000264426.9:c.761G>T	4.37:g.158242630G>T	ENSP00000264426:p.Gly254Val	Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	131	29	0.221374	NM_000826	A8MT92|I6L997|Q96FP6	Missense_Mutation	SNP	ENST00000264426.9	37	CCDS43274.1	.	.	.	.	.	.	.	.	.	.	G	25.2	4.616977	0.87359	.	.	ENSG00000120251	ENST00000507898;ENST00000393815;ENST00000296526;ENST00000264426;ENST00000449365	D;D;D;D;D	0.81821	-1.54;-1.54;-1.54;-1.54;-1.54	5.74	5.74	0.90152	Extracellular ligand-binding receptor (1);	0.000000	0.85682	D	0.000000	D	0.89150	0.6633	M	0.62723	1.935	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.99;0.94;1.0	D	0.89340	0.3653	10	0.87932	D	0	.	19.9317	0.97122	0.0:0.0:1.0:0.0	.	254;254;207	P42262;P42262-2;A8MT92	GRIA2_HUMAN;.;.	V	207;207;254;254;207	ENSP00000426845:G207V;ENSP00000377403:G207V;ENSP00000296526:G254V;ENSP00000264426:G254V;ENSP00000389837:G207V	ENSP00000264426:G254V	G	+	2	0	GRIA2	158462080	1.000000	0.71417	0.983000	0.44433	0.964000	0.63967	9.238000	0.95380	2.716000	0.92895	0.591000	0.81541	GGT	.	.	none		0.348	GRIA2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000258367.2		
C6orf15	29113	hgsc.bcm.edu	37	6	31079644	31079644	+	Silent	SNP	G	G	A	rs2233980	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:31079644G>A	ENST00000259870.3	-	2	495	c.492C>T	c.(490-492)ccC>ccT	p.P164P	PSORS1C1_ENST00000259881.9_5'Flank	NM_014070.2	NP_054789.2	Q6UXA7	CF015_HUMAN	chromosome 6 open reading frame 15	164					extracellular matrix organization (GO:0030198)	interstitial matrix (GO:0005614)	heparin binding (GO:0008201)|hyaluronic acid binding (GO:0005540)			endometrium(3)|large_intestine(2)|lung(9)|prostate(1)|skin(1)|stomach(1)	17						GTGAAGCCTTGGGTGAGAGGC	0.617													G|||	119	0.023762	0.0083	0.0317	5008	,	,		16520	0.0		0.0855	False		,,,				2504	0.0				p.P164P		Atlas-SNP	.											.	C6orf15	29	.	0			c.C492T						PASS	.	G		103,3523		2,99,1712	32.0	36.0	34.0		492	-9.1	0.0	6	dbSNP_98	34	726,6374		42,642,2866	no	coding-synonymous	C6orf15	NM_014070.2		44,741,4578	AA,AG,GG		10.2254,2.8406,7.7289		164/326	31079644	829,9897	1813	3550	5363	SO:0001819	synonymous_variant	29113	exon2			AGCCTTGGGTGAG	AB031481	CCDS4693.1	6p21	2011-12-12			ENSG00000204542	ENSG00000204542			13927	protein-coding gene	gene with protein product		611401					Standard	NM_014070		Approved	STG	uc003nsk.1	Q6UXA7	OTTHUMG00000031111	ENST00000259870.3:c.492C>T	6.37:g.31079644G>A		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	83	30	0.361446	NM_014070	B0S7V8|Q0EFA6|Q2L6G7|Q5SQ81|Q86Z05|Q9UIG3	Silent	SNP	ENST00000259870.3	37	CCDS4693.1																																																																																			G|0.926;A|0.074	0.074	strong		0.617	C6orf15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076184.2	NM_014070	
AATK	9625	hgsc.bcm.edu	37	17	79100340	79100340	+	Silent	SNP	C	C	T	rs139267162	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:79100340C>T	ENST00000326724.4	-	7	666	c.642G>A	c.(640-642)ctG>ctA	p.L214L	MIR657_ENST00000385003.1_RNA|AATK_ENST00000417379.1_Silent_p.L111L|AATK_ENST00000572339.1_5'UTR|MIR338_ENST00000390137.2_RNA	NM_001080395.2	NP_001073864.2	Q6ZMQ8	LMTK1_HUMAN	apoptosis-associated tyrosine kinase	214	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				brain development (GO:0007420)|negative regulation of axon extension (GO:0030517)|neuron apoptotic process (GO:0051402)|peptidyl-tyrosine autophosphorylation (GO:0038083)|Rab protein signal transduction (GO:0032482)	axonal growth cone (GO:0044295)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|recycling endosome (GO:0055037)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)			endometrium(2)|kidney(2)|lung(8)|ovary(3)|prostate(1)|stomach(4)|upper_aerodigestive_tract(1)	21	all_neural(118;0.101)		BRCA - Breast invasive adenocarcinoma(99;0.0228)|OV - Ovarian serous cystadenocarcinoma(97;0.0524)			GGCAGCTCCGCAGGTAGCCCT	0.692													C|||	28	0.00559105	0.0008	0.0144	5008	,	,		15493	0.0		0.0119	False		,,,				2504	0.0051				p.L214L		Atlas-SNP	.											.	AATK	102	.	0			c.G642A						PASS	.	C	,	6,3592		0,6,1793	5.0	7.0	6.0		642,333	2.0	1.0	17	dbSNP_134	6	87,7669		1,85,3792	no	coding-synonymous,coding-synonymous	AATK	NM_001080395.2,NM_004920.2	,	1,91,5585	TT,TC,CC		1.1217,0.1668,0.8191	,	214/1375,111/1272	79100340	93,11261	1799	3878	5677	SO:0001819	synonymous_variant	9625	exon7			GCTCCGCAGGTAG	AB014541	CCDS45807.1, CCDS58607.1	17q25.3	2014-06-12			ENSG00000181409	ENSG00000181409			21	protein-coding gene	gene with protein product	"""lemur tyrosine kinase 1"", ""protein phosphatase 1, regulatory subunit 77"""	605276				9734811, 10083745	Standard	NM_001080395		Approved	AATYK, KIAA0641, LMTK1, LMR1, AATYK1, PPP1R77	uc010dia.3	Q6ZMQ8	OTTHUMG00000132717	ENST00000326724.4:c.642G>A	17.37:g.79100340C>T		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	59	31	0.525424	NM_001080395	O75136|Q6ZN31|Q86X28	Silent	SNP	ENST00000326724.4	37	CCDS45807.1	14	0.00641025641025641	0	0.0	6	0.016574585635359115	0	0.0	8	0.010554089709762533	C	10.62	1.402433	0.25291	0.001668	0.011217	ENSG00000181409	ENST00000417379	.	.	.	4.07	2.0	0.26442	.	.	.	.	.	T	0.26412	0.0645	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.15925	-1.0420	4	.	.	.	.	1.1434	0.01770	0.162:0.3873:0.2417:0.2089	.	.	.	.	Y	167	.	.	C	-	2	0	AATK	76714935	0.991000	0.36638	0.999000	0.59377	0.919000	0.55068	0.370000	0.20433	0.330000	0.23485	0.467000	0.42956	TGC	C|0.994;T|0.006	0.006	strong		0.692	AATK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256055.1	NM_004920	
CACNB2	783	hgsc.bcm.edu	37	10	18828371	18828371	+	Silent	SNP	C	C	T	rs2228645	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:18828371C>T	ENST00000324631.7	+	14	1761	c.1701C>T	c.(1699-1701)taC>taT	p.Y567Y	CACNB2_ENST00000377329.4_Silent_p.Y513Y|CACNB2_ENST00000377319.3_Silent_p.Y474Y|RP11-499P20.2_ENST00000436485.1_RNA|RP11-499P20.2_ENST00000425669.1_RNA|CACNB2_ENST00000377315.4_Silent_p.Y519Y|CACNB2_ENST00000352115.6_Silent_p.Y543Y|CACNB2_ENST00000377331.2_Silent_p.Y515Y|CACNB2_ENST00000396576.2_Silent_p.Y512Y|CACNB2_ENST00000282343.8_Silent_p.Y539Y|CACNB2_ENST00000377328.1_Silent_p.Y317Y	NM_201593.2|NM_201596.2	NP_963887.2|NP_963890.2	Q08289	CACB2_HUMAN	calcium channel, voltage-dependent, beta 2 subunit	567					axon guidance (GO:0007411)|calcium ion import (GO:0070509)|neuromuscular junction development (GO:0007528)|positive regulation of calcium ion transport (GO:0051928)|synaptic transmission (GO:0007268)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|voltage-gated calcium channel complex (GO:0005891)	calcium channel activity (GO:0005262)|voltage-gated calcium channel activity (GO:0005245)	p.Y512Y(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(12)|prostate(1)|skin(3)|stomach(2)	31					Amlodipine(DB00381)|Dronedarone(DB04855)|Felodipine(DB01023)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	ACTCTGCCTACGTAGAGCCAA	0.572													C|||	1188	0.23722	0.1899	0.3314	5008	,	,		19055	0.2381		0.161	False		,,,				2504	0.3119				p.Y567Y		Atlas-SNP	.											CACNB2_ENST00000352115,NS,carcinoma,+2,3	CACNB2	220	3	1	Substitution - coding silent(1)	stomach(1)	c.C1701T						PASS	.	C	,,,,,,,,	920,3486	352.1+/-311.5	86,748,1369	99.0	79.0	86.0		1536,1503,1557,1617,1545,1539,1587,1701,1629	-7.9	0.0	10	dbSNP_98	86	1389,7211	269.0+/-288.2	113,1163,3024	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CACNB2	NM_000724.3,NM_001167945.1,NM_201570.2,NM_201571.3,NM_201572.3,NM_201590.2,NM_201593.2,NM_201596.2,NM_201597.2	,,,,,,,,	199,1911,4393	TT,TC,CC		16.1512,20.8806,17.7533	,,,,,,,,	512/606,501/595,519/613,539/633,515/609,513/607,529/623,567/661,543/637	18828371	2309,10697	2203	4300	6503	SO:0001819	synonymous_variant	783	exon14			TGCCTACGTAGAG	U95019	CCDS7125.1, CCDS7126.1, CCDS7127.1, CCDS7128.1, CCDS7129.1, CCDS41493.1, CCDS41494.1	10p12	2014-09-17			ENSG00000165995	ENSG00000165995		"""Calcium channel subunits"""	1402	protein-coding gene	gene with protein product		600003		MYSB, CACNLB2		9254841, 8494331	Standard	NM_201596		Approved		uc001ipr.2	Q08289	OTTHUMG00000017764	ENST00000324631.7:c.1701C>T	10.37:g.18828371C>T		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	112	51	0.455357	NM_201596	A6PVM5|A6PVM7|A6PVM8|O00304|Q5QJ99|Q5QJA0|Q5VVG9|Q5VVH0|Q5VWV6|Q6TME1|Q6TME2|Q6TME3|Q8WX81|Q96NZ3|Q96NZ4|Q96NZ5|Q9BWU2|Q9HD32|Q9Y340|Q9Y341	Silent	SNP	ENST00000324631.7	37	CCDS7125.1																																																																																			C|0.810;T|0.190	0.190	strong		0.572	CACNB2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047072.2	NM_000724	
CAMTA1	23261	hgsc.bcm.edu	37	1	7723957	7723957	+	Silent	SNP	G	G	A	rs12128526	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:7723957G>A	ENST00000303635.7	+	9	1557	c.1350G>A	c.(1348-1350)tcG>tcA	p.S450S	CAMTA1_ENST00000439411.2_Silent_p.S450S	NM_015215.2	NP_056030.1	Q9Y6Y1	CMTA1_HUMAN	calmodulin binding transcription activator 1	450					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(5)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(11)|lung(29)|ovary(5)|pancreas(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	85	Ovarian(185;0.0634)	all_epithelial(116;8.38e-23)|all_lung(118;5.87e-07)|Lung NSC(185;3.43e-06)|Renal(390;0.000219)|Breast(487;0.000307)|Colorectal(325;0.000615)|Hepatocellular(190;0.0088)|Myeloproliferative disorder(586;0.0303)|Ovarian(437;0.0388)		UCEC - Uterine corpus endometrioid carcinoma (279;0.101)|Colorectal(212;1.33e-05)|COAD - Colon adenocarcinoma(227;0.000235)|BRCA - Breast invasive adenocarcinoma(304;0.000864)|Kidney(185;0.00244)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0179)|READ - Rectum adenocarcinoma(331;0.133)		CGGGCAGCTCGGAGAGCCTGT	0.627			T	WWTR1	epitheliod hemangioendothelioma								G|||	2004	0.40016	0.3873	0.4539	5008	,	,		18084	0.3313		0.4304	False		,,,				2504	0.4192				p.S450S		Atlas-SNP	.		Dom	yes		1	1p36.31-p36.23	611501	calmodulin binding transcription activator 1		M	.	CAMTA1	226	.	0			c.G1350A						PASS	.	G		1648,2758	504.4+/-365.8	297,1054,852	73.0	77.0	76.0		1350	-2.1	1.0	1	dbSNP_120	76	3944,4656	549.5+/-385.6	906,2132,1262	no	coding-synonymous	CAMTA1	NM_015215.2		1203,3186,2114	AA,AG,GG		45.8605,37.4035,42.9955		450/1674	7723957	5592,7414	2203	4300	6503	SO:0001819	synonymous_variant	23261	exon9			CAGCTCGGAGAGC	AB020640	CCDS30576.1, CCDS55574.1, CCDS55575.1	1p36.31-p36.23	2008-07-18			ENSG00000171735	ENSG00000171735			18806	protein-coding gene	gene with protein product		611501				11925432	Standard	NM_001195563		Approved	KIAA0833	uc001aoi.3	Q9Y6Y1	OTTHUMG00000001212	ENST00000303635.7:c.1350G>A	1.37:g.7723957G>A		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	63	31	0.492063	NM_015215	A7MBM4|G3V3Z7|Q5VUE1|Q6V701|Q8WYI3|Q96S92	Silent	SNP	ENST00000303635.7	37	CCDS30576.1																																																																																			G|0.581;A|0.419	0.419	strong		0.627	CAMTA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000003588.3	NM_015215	
TBC1D29	26083	hgsc.bcm.edu	37	17	28890361	28890361	+	Missense_Mutation	SNP	G	G	A	rs372824382		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:28890361G>A	ENST00000580161.1	+	6	2868	c.371G>A	c.(370-372)cGg>cAg	p.R124Q	TBC1D29_ENST00000579181.1_Missense_Mutation_p.R124Q|RP11-218M11.1_ENST00000563063.1_lincRNA|TBC1D29_ENST00000584297.1_3'UTR			Q9UFV1	TBC29_HUMAN	TBC1 domain family, member 29	124							Rab GTPase activator activity (GO:0005097)	p.R124Q(1)		breast(1)|kidney(1)|lung(3)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	9		Myeloproliferative disorder(56;0.0255)				GCCTTGAGCCGGGGAGACAAG	0.567																																					p.R124Q		Atlas-SNP	.											TBC1D29,NS,carcinoma,0,3	TBC1D29	19	3	1	Substitution - Missense(1)	prostate(1)	c.G371A						scavenged	.						78.0	68.0	71.0					17																	28890361		2203	4300	6503	SO:0001583	missense	26083	exon5			TGAGCCGGGGAGA	BC096718	CCDS32606.1	17q11.2	2014-09-04			ENSG00000266733	ENSG00000266733			24509	protein-coding gene	gene with protein product						12618308	Standard	XM_006721805		Approved	DKFZP434O047	uc002hfh.3	Q9UFV1	OTTHUMG00000178857	ENST00000580161.1:c.371G>A	17.37:g.28890361G>A	ENSP00000462799:p.Arg124Gln	Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	166	4	0.0240964	NM_015594		Missense_Mutation	SNP	ENST00000580161.1	37	CCDS32606.1	.	.	.	.	.	.	.	.	.	.	.	2.991	-0.208219	0.06180	.	.	ENSG00000197689	ENST00000329040	.	.	.	.	.	.	.	.	.	.	.	T	0.14399	0.0348	N	0.08118	0	0.09310	N	0.999998	B	0.02656	0.0	B	0.01281	0.0	T	0.14559	-1.0468	7	0.33141	T	0.24	.	3.9265	0.09265	0.6657:0.0:0.3343:0.0	.	124	Q9UFV1	TBC29_HUMAN	Q	124	.	ENSP00000330052:R124Q	R	+	2	0	TBC1D29	25914487	0.090000	0.21635	0.024000	0.17045	0.025000	0.11179	-1.180000	0.03088	-1.657000	0.01492	-1.643000	0.00768	CGG	.	.	alt		0.567	TBC1D29-004	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000443632.1	NM_015594	
KRTAP3-1	83896	hgsc.bcm.edu	37	17	39165174	39165174	+	Silent	SNP	G	G	A	rs112432710	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:39165174G>A	ENST00000391588.1	-	1	192	c.153C>T	c.(151-153)tgC>tgT	p.C51C	KRTAP3-1_ENST00000581033.1_5'UTR	NM_031958.1	NP_114164.1	Q9BYR8	KRA31_HUMAN	keratin associated protein 3-1	51	4 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			autonomic_ganglia(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(4)	8		Breast(137;0.00043)				AGGGTGGGGGGCAGGTGTCAC	0.577													g|||	386	0.0770767	0.0386	0.0778	5008	,	,		18684	0.0288		0.1143	False		,,,				2504	0.1401				p.C51C		Atlas-SNP	.											.	KRTAP3-1	11	.	0			c.C153T						PASS	.	G		224,4182	135.7+/-171.8	6,212,1985	78.0	68.0	71.0		153	3.4	1.0	17	dbSNP_132	71	785,7807	185.6+/-233.3	40,705,3551	no	coding-synonymous	KRTAP3-1	NM_031958.1		46,917,5536	AA,AG,GG		9.1364,5.084,7.7627		51/99	39165174	1009,11989	2203	4296	6499	SO:0001819	synonymous_variant	83896	exon1			TGGGGGGCAGGTG	AJ406931	CCDS32645.1	17q21.2	2013-06-25			ENSG00000212901	ENSG00000212901		"""Keratin associated proteins"""	16778	protein-coding gene	gene with protein product						11279113	Standard	NM_031958		Approved	KAP3.1	uc002hvt.1	Q9BYR8	OTTHUMG00000133595	ENST00000391588.1:c.153C>T	17.37:g.39165174G>A		Somatic	182	0	0		WXS	Illumina HiSeq	Phase_I	156	79	0.50641	NM_031958	Q14DM4	Silent	SNP	ENST00000391588.1	37	CCDS32645.1																																																																																			G|0.925;A|0.075	0.075	strong		0.577	KRTAP3-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257699.1		
FGFR3	2261	hgsc.bcm.edu	37	4	1801511	1801511	+	Silent	SNP	C	C	T	rs3135867	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:1801511C>T	ENST00000260795.2	+	3	519	c.417C>T	c.(415-417)gaC>gaT	p.D139D	FGFR3_ENST00000481110.2_Silent_p.D139D|FGFR3_ENST00000412135.2_Silent_p.D139D|FGFR3_ENST00000340107.4_Silent_p.D139D|FGFR3_ENST00000352904.1_Silent_p.D139D|FGFR3_ENST00000440486.2_Silent_p.D139D			P22607	FGFR3_HUMAN	fibroblast growth factor receptor 3	139					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)			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)	ACGGGGAGGACGAGGCTGAGG	0.677		1	"""Mis, T"""	"""IGH@, ETV6"""	"""bladder, MM, T-cell lymphoma"""		"""Hypochondroplasia, Thanatophoric dysplasia"""		Saethre-Chotzen syndrome;Muenke syndrome				c|||	101	0.0201677	0.0015	0.0331	5008	,	,		17142	0.0		0.0487	False		,,,				2504	0.0276				p.D139D		Atlas-SNP	.		Dom	yes		4	4p16.3	2261	fibroblast growth factor receptor 3	yes	"""L, E"""	.	FGFR3	3320	.	0			c.C417T						PASS	.	C	,,	38,4360	42.3+/-75.8	1,36,2162	88.0	69.0	75.0		417,417,417	-1.1	1.0	4	dbSNP_103	75	447,8147	134.1+/-191.5	10,427,3860	no	coding-synonymous,coding-synonymous,coding-synonymous	FGFR3	NM_000142.4,NM_001163213.1,NM_022965.3	,,	11,463,6022	TT,TC,CC		5.2013,0.864,3.7331	,,	139/807,139/809,139/695	1801511	485,12507	2199	4297	6496	SO:0001819	synonymous_variant	2261	exon4	Familial Cancer Database	Acrocephalosyndactyly type III;Muenke Nonsyndromic Coronal Craniosynostosis, FGFR3-related Craniosynostosis	GGAGGACGAGGCT	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.417C>T	4.37:g.1801511C>T		Somatic	196	0	0		WXS	Illumina HiSeq	Phase_I	156	78	0.5	NM_001163213	D3DVP9|D3DVQ0|Q14308|Q16294|Q16608|Q59FL9	Silent	SNP	ENST00000260795.2	37	CCDS3353.1																																																																																			C|0.965;T|0.035	0.035	strong		0.677	FGFR3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000241632.2	NM_000142	
OR10G2	26534	hgsc.bcm.edu	37	14	22102745	22102745	+	Missense_Mutation	SNP	C	C	A	rs41314525	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	218	0	0		WXS	Illumina HiSeq	Phase_I	212	104	0.490566	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		
SLC25A22	79751	hgsc.bcm.edu	37	11	792692	792692	+	Missense_Mutation	SNP	G	G	C	rs111277421	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:792692G>C	ENST00000320230.5	-	7	929	c.448C>G	c.(448-450)Ctc>Gtc	p.L150V	CEND1_ENST00000330106.4_5'Flank|SLC25A22_ENST00000531214.1_Missense_Mutation_p.L150V|CEND1_ENST00000524587.1_5'Flank	NM_001191061.1|NM_024698.5	NP_001177990.1|NP_078974.1	Q9H936	GHC1_HUMAN	solute carrier family 25 (mitochondrial carrier: glutamate), member 22	150					L-glutamate transport (GO:0015813)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	L-glutamate transmembrane transporter activity (GO:0005313)|symporter activity (GO:0015293)			endometrium(1)|kidney(1)|lung(2)|urinary_tract(1)	5		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;6.27e-26)|Epithelial(43;4.84e-25)|OV - Ovarian serous cystadenocarcinoma(40;2.72e-19)|BRCA - Breast invasive adenocarcinoma(625;4.23e-05)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		TGGGCCGAGAGCTGGCCCTGG	0.706													G|||	160	0.0319489	0.0393	0.0375	5008	,	,		11778	0.001		0.0676	False		,,,				2504	0.0133				p.L150V	Colon(93;848 1468 3270 23355 49636)	Atlas-SNP	.											.	SLC25A22	19	.	0			c.C448G						PASS	.	G	VAL/LEU,VAL/LEU,VAL/LEU	147,4113		1,145,1984	9.0	11.0	10.0		448,448,448	3.4	0.9	11	dbSNP_132	10	607,7751		24,559,3596	no	missense,missense,missense	SLC25A22	NM_001191060.1,NM_001191061.1,NM_024698.5	32,32,32	25,704,5580	CC,CG,GG		7.2625,3.4507,5.9756	benign,benign,benign	150/324,150/324,150/324	792692	754,11864	2130	4179	6309	SO:0001583	missense	79751	exon7			CCGAGAGCTGGCC	AJ428202	CCDS7715.1	11p15.5	2013-05-22			ENSG00000177542	ENSG00000177542		"""Solute carriers"""	19954	protein-coding gene	gene with protein product		609302				11897791	Standard	NM_024698		Approved	GC1, FLJ13044, NET44, EIEE3	uc001lrj.3	Q9H936	OTTHUMG00000133310	ENST00000320230.5:c.448C>G	11.37:g.792692G>C	ENSP00000322020:p.Leu150Val	Somatic	13	0	0		WXS	Illumina HiSeq	Phase_I	20	12	0.6	NM_001191061	A8K366|C9J1H6|E9PJD3|E9PKB2|E9PL68|E9PN26|E9PNQ3|E9PP01|E9PR97|Q8TBU8	Missense_Mutation	SNP	ENST00000320230.5	37	CCDS7715.1	78	0.03571428571428571	11	0.022357723577235773	15	0.04143646408839779	1	0.0017482517482517483	51	0.06728232189973615	G	3.513	-0.099295	0.07010	0.034507	0.072625	ENSG00000177542	ENST00000320230;ENST00000531214;ENST00000481290;ENST00000531437	T;T;D;T	0.82619	-1.29;-1.29;-1.63;-1.18	3.43	3.43	0.39272	Mitochondrial carrier domain (2);	0.428251	0.20562	U	0.089898	T	0.16557	0.0398	N	0.25485	0.75	0.31752	N	0.634443	B	0.09022	0.002	B	0.14578	0.011	T	0.48980	-0.8986	10	0.13470	T	0.59	-17.6935	10.6343	0.45556	0.0:0.0:0.8093:0.1907	.	150	Q9H936	GHC1_HUMAN	V	150;150;175;146	ENSP00000322020:L150V;ENSP00000437236:L150V;ENSP00000431829:L175V;ENSP00000435862:L146V	ENSP00000322020:L150V	L	-	1	0	SLC25A22	782692	0.765000	0.28485	0.949000	0.38748	0.180000	0.23129	3.402000	0.52608	1.909000	0.55274	0.436000	0.28706	CTC	G|0.963;C|0.037	0.037	strong		0.706	SLC25A22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257107.2		
OR5P2	120065	hgsc.bcm.edu	37	11	7817665	7817665	+	Silent	SNP	T	T	C	rs72484720	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:7817665T>C	ENST00000329434.2	-	1	855	c.825A>G	c.(823-825)acA>acG	p.T275T	RP11-35J10.5_ENST00000527565.1_lincRNA	NM_153444.1	NP_703145.1	Q8WZ92	OR5P2_HUMAN	olfactory receptor, family 5, subfamily P, member 2	275						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(4)	22				Epithelial(150;8.62e-08)|BRCA - Breast invasive adenocarcinoma(625;0.189)		GAATCACCACTGTGTACAACA	0.448													C|||	1185	0.236621	0.3472	0.2911	5008	,	,		18498	0.128		0.2763	False		,,,				2504	0.1196				p.T275T		Atlas-SNP	.											.	OR5P2	68	.	0			c.A825G						PASS	.	C		1371,2845		401,569,1138	114.0	122.0	120.0		825	2.4	1.0	11	dbSNP_130	120	2425,6159		393,1639,2260	no	coding-synonymous	OR5P2	NM_153444.1		794,2208,3398	CC,CT,TT		28.2502,32.519,29.6562		275/323	7817665	3796,9004	2108	4292	6400	SO:0001819	synonymous_variant	120065	exon1			CACCACTGTGTAC	AF173006	CCDS7782.1	11p15.4	2012-08-09			ENSG00000183303	ENSG00000183303		"""GPCR / Class A : Olfactory receptors"""	14783	protein-coding gene	gene with protein product							Standard	NM_153444		Approved	JCG3	uc001mfp.1	Q8WZ92	OTTHUMG00000165668	ENST00000329434.2:c.825A>G	11.37:g.7817665T>C		Somatic	201	0	0		WXS	Illumina HiSeq	Phase_I	228	185	0.811404	NM_153444	Q3MIS8	Silent	SNP	ENST00000329434.2	37	CCDS7782.1																																																																																			T|0.738;C|0.262	0.262	strong		0.448	OR5P2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385696.1	NM_153444	
P2RY2	5029	hgsc.bcm.edu	37	11	72946204	72946204	+	Missense_Mutation	SNP	C	C	T	rs1626154	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:72946204C>T	ENST00000311131.2	+	3	1467	c.1000C>T	c.(1000-1002)Cgc>Tgc	p.R334C	P2RY2_ENST00000393596.2_Missense_Mutation_p.R334C|P2RY2_ENST00000393597.2_Missense_Mutation_p.R334C	NM_002564.2|NM_176072.1	NP_002555|NP_788086	P41231	P2RY2_HUMAN	purinergic receptor P2Y, G-protein coupled, 2	334			R -> C (in dbSNP:rs1626154). {ECO:0000269|PubMed:14702039, ECO:0000269|Ref.6}.		cellular ion homeostasis (GO:0006873)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of mucus secretion (GO:0070257)|regulation of vasodilation (GO:0042312)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled purinergic nucleotide receptor activity (GO:0045028)|receptor activity (GO:0004872)			endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(3)|lung(8)|ovary(2)|prostate(1)|skin(2)|urinary_tract(2)	25					Suramin(DB04786)	CCCGGCTCGCCGCAGGCTGGG	0.652													C|||	457	0.091254	0.0212	0.1571	5008	,	,		14819	0.0506		0.2087	False		,,,				2504	0.0603				p.R334C		Atlas-SNP	.											.	P2RY2	54	.	0			c.C1000T						PASS	.	C	CYS/ARG,CYS/ARG,CYS/ARG	178,4220		6,166,2027	29.0	34.0	32.0		1000,1000,1000	3.4	0.9	11	dbSNP_89	32	1595,6989		152,1291,2849	yes	missense,missense,missense	P2RY2	NM_002564.2,NM_176071.1,NM_176072.1	180,180,180	158,1457,4876	TT,TC,CC		18.5811,4.0473,13.6574	probably-damaging,probably-damaging,probably-damaging	334/378,334/378,334/378	72946204	1773,11209	2199	4292	6491	SO:0001583	missense	5029	exon3			GCTCGCCGCAGGC	U07225	CCDS8219.1	11q13.5-q14.1	2012-08-08				ENSG00000175591		"""Purinergic receptors"", ""GPCR / Class A : Purinergic receptors, P2Y"""	8541	protein-coding gene	gene with protein product		600041				8159738, 9286708	Standard	NM_002564		Approved	P2U	uc001otj.4	P41231		ENST00000311131.2:c.1000C>T	11.37:g.72946204C>T	ENSP00000310305:p.Arg334Cys	Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	34	27	0.794118	NM_176071	B2R9W3|Q96EM8	Missense_Mutation	SNP	ENST00000311131.2	37	CCDS8219.1	263	0.12042124542124542	16	0.032520325203252036	62	0.1712707182320442	34	0.05944055944055944	151	0.19920844327176782	C	10.24	1.296099	0.23650	0.040473	0.185811	ENSG00000175591	ENST00000393597;ENST00000311131;ENST00000393596	T;T;T	0.26660	1.72;1.72;1.72	4.44	3.44	0.39384	.	1.660570	0.03269	N	0.184484	T	0.00012	0.0000	N	0.08118	0	0.27732	P	0.9447875	D	0.61697	0.99	B	0.43809	0.432	T	0.19031	-1.0318	9	0.59425	D	0.04	.	9.8209	0.40883	0.0:0.7905:0.2095:0.0	rs1626154;rs1626154	334	P41231	P2RY2_HUMAN	C	334	ENSP00000377222:R334C;ENSP00000310305:R334C;ENSP00000377221:R334C	ENSP00000310305:R334C	R	+	1	0	P2RY2	72623852	0.012000	0.17670	0.929000	0.37066	0.293000	0.27360	1.895000	0.39778	2.196000	0.70406	0.561000	0.74099	CGC	C|0.873;T|0.127	0.127	strong		0.652	P2RY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397336.1	NM_176072	
LCE1D	353134	hgsc.bcm.edu	37	1	152770533	152770533	+	Missense_Mutation	SNP	G	G	A	rs41268494	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:152770533G>A	ENST00000326233.6	+	2	306	c.263G>A	c.(262-264)aGc>aAc	p.S88N		NM_178352.2	NP_848129.1	Q5T752	LCE1D_HUMAN	late cornified envelope 1D	88	Cys-rich.				cellular response to calcium ion (GO:0071277)|cognition (GO:0050890)|keratinization (GO:0031424)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|perinuclear region of cytoplasm (GO:0048471)				large_intestine(1)	1	Lung NSC(65;3.97e-29)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)			AGACCCCAGAGCTCTGACTGC	0.687																																					p.S88N		Atlas-SNP	.											.	LCE1D	19	.	0			c.G263A						PASS	.	G	ASN/SER	571,3459		9,553,1453	25.0	25.0	25.0		263	3.6	0.9	1	dbSNP_127	25	806,6728		15,776,2976	no	missense	LCE1D	NM_178352.2	46	24,1329,4429	AA,AG,GG		10.6982,14.1687,11.9076	benign	88/115	152770533	1377,10187	2015	3767	5782	SO:0001583	missense	353134	exon2			CCCAGAGCTCTGA		CCDS1025.1	1q21.3	2008-02-05			ENSG00000172155	ENSG00000172155		"""Late cornified envelopes"""	29465	protein-coding gene	gene with protein product		612606				11698679	Standard	NM_178352		Approved	LEP4	uc009wnp.3	Q5T752	OTTHUMG00000012444	ENST00000326233.6:c.263G>A	1.37:g.152770533G>A	ENSP00000316737:p.Ser88Asn	Somatic	241	0	0		WXS	Illumina HiSeq	Phase_I	257	102	0.396887	NM_178352		Missense_Mutation	SNP	ENST00000326233.6	37	CCDS1025.1	433	0.19826007326007325	93	0.18902439024390244	75	0.20718232044198895	178	0.3111888111888112	87	0.11477572559366754	G	10.52	1.372816	0.24857	0.141687	0.106982	ENSG00000172155	ENST00000326233	T	0.05717	3.4	4.52	3.6	0.41247	.	0.170939	0.28388	N	0.015527	T	0.02380	0.0073	L	0.42487	1.325	0.53688	P	2.8000000000028002E-5	B	0.02656	0.0	B	0.06405	0.002	T	0.24799	-1.0150	9	0.87932	D	0	.	8.6	0.33738	0.1094:0.0:0.8906:0.0	rs41268494	88	Q5T752	LCE1D_HUMAN	N	88	ENSP00000316737:S88N	ENSP00000316737:S88N	S	+	2	0	LCE1D	151037157	0.947000	0.32204	0.903000	0.35520	0.829000	0.46940	1.910000	0.39927	1.005000	0.39183	0.555000	0.69702	AGC	G|0.806;A|0.194	0.194	strong		0.687	LCE1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034657.2	NM_178352	
DNAH17	8632	hgsc.bcm.edu	37	17	76446872	76446872	+	Silent	SNP	A	A	G	rs35957404	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:76446872A>G	ENST00000585328.1	-	67	10900	c.10776T>C	c.(10774-10776)gaT>gaC	p.D3592D	DNAH17_ENST00000389840.5_Silent_p.D3583D|DNAH17_ENST00000586052.1_5'UTR	NM_173628.3	NP_775899.3	Q9UFH2	DYH17_HUMAN	dynein, axonemal, heavy chain 17	3583	AAA 5. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(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)			CCAGGAGCGAATCTTCCAGCT	0.557													A|||	140	0.0279553	0.0045	0.0288	5008	,	,		20863	0.001		0.0408	False		,,,				2504	0.0736				p.D3597D		Atlas-SNP	.											.	DNAH17	347	.	0			c.T10791C						PASS	.	A		36,4370	42.3+/-75.8	0,36,2167	88.0	90.0	89.0		10791	-10.7	0.1	17	dbSNP_126	89	390,8210	125.5+/-184.1	9,372,3919	no	coding-synonymous	DNAH17	NM_173628.3		9,408,6086	GG,GA,AA		4.5349,0.8171,3.2754		3597/4463	76446872	426,12580	2203	4300	6503	SO:0001819	synonymous_variant	8632	exon67			GAGCGAATCTTCC	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.10776T>C	17.37:g.76446872A>G		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	67	24	0.358209	NM_173628	O00431|O15206|Q2M2Y1|Q6ZRQ2|Q8N7Q7	Silent	SNP	ENST00000585328.1	37																																																																																				A|0.971;G|0.029	0.029	strong		0.557	DNAH17-001	PUTATIVE	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000318962.2	NM_173628	
CR2	1380	hgsc.bcm.edu	37	1	207653364	207653364	+	Missense_Mutation	SNP	A	A	G	rs17618	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:207653364A>G	ENST00000367058.3	+	17	3166	c.2977A>G	c.(2977-2979)Att>Gtt	p.I993V	CR2_ENST00000367059.3_Missense_Mutation_p.I931V|CR2_ENST00000458541.2_Missense_Mutation_p.I966V|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	228	1	0.00438596		WXS	Illumina HiSeq	Phase_I	183	182	0.994536	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	
AEBP1	165	hgsc.bcm.edu	37	7	44147485	44147485	+	Missense_Mutation	SNP	C	C	A	rs2537188	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:44147485C>A	ENST00000223357.3	+	5	1122	c.817C>A	c.(817-819)Ccc>Acc	p.P273T	AEBP1_ENST00000450684.2_5'Flank|MIR4649_ENST00000582839.1_RNA	NM_001129.3	NP_001120.3	Q8IUX7	AEBP1_HUMAN	AE binding protein 1	273	Pro-rich.		P -> T (in dbSNP:rs2537188).		cell adhesion (GO:0007155)|muscle organ development (GO:0007517)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	carboxypeptidase activity (GO:0004180)|metallocarboxypeptidase activity (GO:0004181)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(13)|upper_aerodigestive_tract(2)	33						CTGGCCAGAGCCCCCTGAGGA	0.697													C|||	1790	0.357428	0.3684	0.2695	5008	,	,		13134	0.2738		0.3519	False		,,,				2504	0.4969				p.P273T		Atlas-SNP	.											AEBP1,NS,carcinoma,0,1	AEBP1	102	1	0			c.C817A						PASS	.	C	THR/PRO	1512,2824		285,942,941	10.0	13.0	12.0		817	1.4	0.1	7	dbSNP_100	12	3187,5327		639,1909,1709	no	missense	AEBP1	NM_001129.3	38	924,2851,2650	AA,AC,CC		37.4325,34.8708,36.5681	possibly-damaging	273/1159	44147485	4699,8151	2168	4257	6425	SO:0001583	missense	165	exon5			CCAGAGCCCCCTG	D86479	CCDS5476.1	7p	2008-07-18	2001-11-28		ENSG00000106624	ENSG00000106624			303	protein-coding gene	gene with protein product	"""aortic carboxypeptidase-like protein"", ""adipocyte enhancer binding protein 1"""	602981	"""AE-binding protein 1"""			8920928	Standard	NM_001129		Approved	ACLP	uc003tkb.4	Q8IUX7	OTTHUMG00000023362	ENST00000223357.3:c.817C>A	7.37:g.44147485C>A	ENSP00000223357:p.Pro273Thr	Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	157	108	0.687898	NM_001129	Q14113|Q59ER7|Q6ZSC7|Q7KZ79	Missense_Mutation	SNP	ENST00000223357.3	37	CCDS5476.1	697	0.3191391941391941	148	0.3008130081300813	113	0.31215469613259667	155	0.270979020979021	281	0.370712401055409	C	8.109	0.778353	0.16120	0.348708	0.374325	ENSG00000106624	ENST00000223357	T	0.39997	1.05	4.54	1.41	0.22369	.	7.491200	0.00166	N	0.000008	T	0.00012	0.0000	N	0.19112	0.55	0.58432	P	9.000000000036756E-6	B	0.19817	0.039	B	0.14023	0.01	T	0.34950	-0.9808	9	0.48119	T	0.1	-0.4184	7.7789	0.29054	0.1715:0.4951:0.3335:0.0	rs2537188;rs60349212	273	Q8IUX7	AEBP1_HUMAN	T	273	ENSP00000223357:P273T	ENSP00000223357:P273T	P	+	1	0	AEBP1	44114010	0.001000	0.12720	0.074000	0.20217	0.361000	0.29550	0.387000	0.20718	0.318000	0.23185	0.491000	0.48974	CCC	C|0.678;A|0.322	0.322	strong		0.697	AEBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250993.2	NM_001129	
CEP164	22897	hgsc.bcm.edu	37	11	117266312	117266312	+	Missense_Mutation	SNP	C	C	G	rs2305830	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	134	0	0		WXS	Illumina HiSeq	Phase_I	101	18	0.178218	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	
MUC21	394263	hgsc.bcm.edu	37	6	30954873	30954873	+	Silent	SNP	G	G	A	rs1625781	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:30954873G>A	ENST00000376296.3	+	2	1162	c.921G>A	c.(919-921)acG>acA	p.T307T	MUC21_ENST00000486149.2_5'UTR	NM_001010909.2	NP_001010909.2	Q5SSG8	MUC21_HUMAN	mucin 21, cell surface associated	307	28 X 15 AA approximate tandem repeats.|Ser-rich.				cellular protein metabolic process (GO:0044267)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of cell-substrate adhesion (GO:0010812)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(4)|breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(4)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	42						AGTCCAGTACGACCTCCAGTG	0.597													g|||	707	0.141174	0.1059	0.2594	5008	,	,		21191	0.0427		0.2386	False		,,,				2504	0.1063				p.T307T		Atlas-SNP	.											.	MUC21	98	.	0			c.G921A						PASS	.	G		688,3718	289.2+/-280.3	41,606,1556	166.0	160.0	162.0		921	-8.6	0.0	6	dbSNP_89	162	2411,6189	400.9+/-346.9	330,1751,2219	no	coding-synonymous	MUC21	NM_001010909.2		371,2357,3775	AA,AG,GG		28.0349,15.6151,23.8275		307/567	30954873	3099,9907	2203	4300	6503	SO:0001819	synonymous_variant	394263	exon2			CAGTACGACCTCC	AK056612	CCDS34388.1	6p21.33	2008-05-14	2008-05-14	2008-05-14	ENSG00000204544	ENSG00000204544		"""Mucins"""	21661	protein-coding gene	gene with protein product	"""epiglycanin"""		"""chromosome 6 open reading frame 205"""	C6orf205		17977904	Standard	NM_001010909		Approved	bCX31G15.2	uc003nsh.2	Q5SSG8	OTTHUMG00000031216	ENST00000376296.3:c.921G>A	6.37:g.30954873G>A		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	64	31	0.484375	NM_001010909	B0UZT7|B4DQ55|C9JMK2|D9N007|Q0VGF1|Q3B7T2|Q5SS94|Q6UXC5	Silent	SNP	ENST00000376296.3	37	CCDS34388.1																																																																																			G|0.774;A|0.226	0.226	strong		0.597	MUC21-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000128579.3	NM_001010909	
ATP9B	374868	hgsc.bcm.edu	37	18	76870397	76870397	+	Silent	SNP	G	G	A	rs492657	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:76870397G>A	ENST00000426216.2	+	3	353	c.336G>A	c.(334-336)gaG>gaA	p.E112E	ATP9B_ENST00000458297.2_Silent_p.E60E|ATP9B_ENST00000586722.1_Silent_p.E112E|ATP9B_ENST00000591464.1_Intron|ATP9B_ENST00000307671.7_Silent_p.E112E	NM_198531.3	NP_940933.3	O43861	ATP9B_HUMAN	ATPase, class II, type 9B	112					establishment of protein localization to Golgi (GO:0072600)|phospholipid translocation (GO:0045332)	integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|trans-Golgi network (GO:0005802)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(15)|ovary(3)|prostate(1)|skin(2)|stomach(1)	38		Esophageal squamous(42;0.018)|Melanoma(33;0.0964)|Prostate(75;0.171)		OV - Ovarian serous cystadenocarcinoma(15;1.44e-07)|BRCA - Breast invasive adenocarcinoma(31;0.0405)		GAAAGAAAGAGCTGAAAGCTC	0.318													A|||	578	0.115415	0.2882	0.0749	5008	,	,		18999	0.0228		0.1034	False		,,,				2504	0.0184				p.E112E		Atlas-SNP	.											.	ATP9B	96	.	0			c.G336A						PASS	.	A		1196,3210	705.1+/-407.2	143,910,1150	70.0	76.0	74.0		336	-1.9	0.9	18	dbSNP_83	74	809,7791	781.8+/-407.6	43,723,3534	no	coding-synonymous	ATP9B	NM_198531.3		186,1633,4684	AA,AG,GG		9.407,27.1448,15.416		112/1148	76870397	2005,11001	2203	4300	6503	SO:0001819	synonymous_variant	374868	exon3			GAAAGAGCTGAAA	R51412	CCDS12014.1	18q23	2010-04-20	2007-09-19		ENSG00000166377	ENSG00000166377		"""ATPases / P-type"""	13541	protein-coding gene	gene with protein product		614446	"""ATPase, Class II, type 9B"""			9548971, 11015572	Standard	NM_198531		Approved	ATPIIB	uc002lmx.3	O43861	OTTHUMG00000132898	ENST00000426216.2:c.336G>A	18.37:g.76870397G>A		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	48	18	0.375	NM_198531	O60872|Q08AD8|Q08AD9	Silent	SNP	ENST00000426216.2	37	CCDS12014.1																																																																																			G|0.862;A|0.138	0.138	strong		0.318	ATP9B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256402.3	NM_198531	
CLEC1B	51266	hgsc.bcm.edu	37	12	10150961	10150961	+	Missense_Mutation	SNP	G	G	A	rs2273987	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:10150961G>A	ENST00000298527.6	-	2	262	c.83C>T	c.(82-84)tCc>tTc	p.S28F	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	28			S -> F (in dbSNP:rs2273987).		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)	p.S28F(1)		NS(1)|breast(1)|central_nervous_system(1)|large_intestine(2)|lung(12)|stomach(1)|urinary_tract(1)	19						ACGCCACCAGGAGGAGGATGC	0.562													G|||	450	0.0898562	0.0522	0.0504	5008	,	,		18063	0.1706		0.0865	False		,,,				2504	0.089				p.S28F		Atlas-SNP	.											CLEC1B,NS,carcinoma,+1,2	CLEC1B	39	2	1	Substitution - Missense(1)	stomach(1)	c.C83T						PASS	.	G	,PHE/SER	212,3992		9,194,1899	99.0	106.0	104.0		,83	4.4	0.4	12	dbSNP_100	104	683,7739		23,637,3551	yes	intron,missense	CLEC1B	NM_001099431.1,NM_016509.3	,155	32,831,5450	AA,AG,GG		8.1097,5.0428,7.0885	,possibly-damaging	,28/230	10150961	895,11731	2102	4211	6313	SO:0001583	missense	51266	exon2			CACCAGGAGGAGG	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.83C>T	12.37:g.10150961G>A	ENSP00000298527:p.Ser28Phe	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	101	48	0.475248	NM_016509	Q6UWX7|Q8NHR6	Missense_Mutation	SNP	ENST00000298527.6	37	CCDS41752.1	214	0.09798534798534798	25	0.0508130081300813	15	0.04143646408839779	113	0.19755244755244755	61	0.08047493403693931	G	13.74	2.328352	0.41197	0.050428	0.081097	ENSG00000165682	ENST00000298527	T	0.01516	4.81	4.37	4.37	0.52481	.	0.418107	0.20454	N	0.092030	T	0.00012	0.0000	M	0.76838	2.35	0.20489	P	0.999893407	D	0.61080	0.989	P	0.57283	0.817	T	0.49679	-0.8914	9	0.40728	T	0.16	.	12.3952	0.55380	0.0:0.0:1.0:0.0	rs2273987;rs61392058;rs2273987	28	Q9P126	CLC1B_HUMAN	F	28	ENSP00000298527:S28F	ENSP00000298527:S28F	S	-	2	0	CLEC1B	10042228	0.177000	0.23109	0.430000	0.26722	0.414000	0.31173	4.546000	0.60705	1.968000	0.57251	0.305000	0.20034	TCC	G|0.909;A|0.091	0.091	strong		0.562	CLEC1B-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399922.1	NM_016509	
OSCP1	127700	hgsc.bcm.edu	37	1	36888462	36888462	+	Missense_Mutation	SNP	A	A	G	rs1416840	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:36888462A>G	ENST00000356637.5	-	7	749	c.686T>C	c.(685-687)aTa>aCa	p.I229T	OSCP1_ENST00000315643.9_Missense_Mutation_p.I229T|OSCP1_ENST00000235532.5_Missense_Mutation_p.I219T|OSCP1_ENST00000495222.1_5'UTR|OSCP1_ENST00000433045.2_Missense_Mutation_p.I174T			Q8WVF1	OSCP1_HUMAN	organic solute carrier partner 1	229					transport (GO:0006810)	plasma membrane (GO:0005886)				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						CTTGAATTCTATCCTCTTCAC	0.408													A|||	678	0.135383	0.0726	0.1311	5008	,	,		16539	0.3065		0.0934	False		,,,				2504	0.09				p.I219T		Atlas-SNP	.											.	OSCP1	48	.	0			c.T656C						PASS	.	A	THR/ILE	360,4046	184.7+/-212.0	8,344,1851	147.0	130.0	136.0		656	-2.2	0.0	1	dbSNP_88	136	833,7767	191.7+/-237.8	34,765,3501	yes	missense	OSCP1	NM_145047.4	89	42,1109,5352	GG,GA,AA		9.686,8.1707,9.1727	benign	219/380	36888462	1193,11813	2203	4300	6503	SO:0001583	missense	127700	exon6			AATTCTATCCTCT		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.686T>C	1.37:g.36888462A>G	ENSP00000349052:p.Ile229Thr	Somatic	208	0	0		WXS	Illumina HiSeq	Phase_I	152	67	0.440789	NM_145047	A6NHM5|A6NHS9|A6NIN9|Q4AEJ0|Q8N7G2|Q8TDF1	Missense_Mutation	SNP	ENST00000356637.5	37		332	0.152014652014652	52	0.10569105691056911	48	0.13259668508287292	161	0.28146853146853146	71	0.09366754617414248	A	1.217	-0.628034	0.03610	0.081707	0.09686	ENSG00000116885	ENST00000235532;ENST00000356637;ENST00000433045;ENST00000445843;ENST00000315643	T;T;T;T;T	0.28454	2.05;2.04;1.63;1.61;2.03	5.61	-2.25	0.06888	.	1.063570	0.07168	N	0.851936	T	0.00012	0.0000	N	0.01109	-1.01	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.45086	-0.9285	9	0.07482	T	0.82	.	12.6072	0.56529	0.5095:0.0:0.4905:0.0	rs1416840;rs52794055;rs58162730;rs1416840	219;229	Q8WVF1-3;Q8WVF1	.;OSCP1_HUMAN	T	219;229;174;189;229	ENSP00000235532:I219T;ENSP00000349052:I229T;ENSP00000390820:I174T;ENSP00000396417:I189T;ENSP00000314541:I229T	ENSP00000235532:I219T	I	-	2	0	OSCP1	36661049	0.000000	0.05858	0.000000	0.03702	0.861000	0.49209	0.148000	0.16224	-0.708000	0.05015	-0.290000	0.09829	ATA	A|0.882;G|0.118	0.118	strong		0.408	OSCP1-010	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000389759.1	NM_145047	
MYH8	4626	hgsc.bcm.edu	37	17	10312472	10312472	+	Missense_Mutation	SNP	G	G	A	rs34693726	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:10312472G>A	ENST00000403437.2	-	17	2001	c.1907C>T	c.(1906-1908)gCg>gTg	p.A636V	CTC-297N7.11_ENST00000587182.2_RNA|RP11-799N11.1_ENST00000399342.2_RNA|RP11-799N11.1_ENST00000581304.1_RNA	NM_002472.2	NP_002463.2	P13535	MYH8_HUMAN	myosin, heavy chain 8, skeletal muscle, perinatal	636	Myosin motor.		A -> V (in dbSNP:rs34693726).		ATP catabolic process (GO:0006200)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|skeletal muscle contraction (GO:0003009)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|sarcomere (GO:0030017)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)|myosin light chain binding (GO:0032027)|structural constituent of muscle (GO:0008307)			NS(3)|breast(8)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(61)|ovary(3)|prostate(3)|skin(10)|upper_aerodigestive_tract(2)|urinary_tract(2)	134						ACCTTTCTTCGCGCTGCTATC	0.343									Trismus-Pseudocamptodactyly Syndrome with Cardiac Myxoma and Freckling				G|||	299	0.0597045	0.0408	0.0375	5008	,	,		18253	0.0427		0.0517	False		,,,				2504	0.1268				p.A636V		Atlas-SNP	.											MYH8,NS,carcinoma,+1,1	MYH8	346	1	0			c.C1907T						PASS	.	G	VAL/ALA	199,4207	121.3+/-158.8	4,191,2008	52.0	55.0	54.0		1907	5.2	0.9	17	dbSNP_126	54	525,8075	146.5+/-202.0	16,493,3791	yes	missense	MYH8	NM_002472.2	64	20,684,5799	AA,AG,GG		6.1047,4.5166,5.5667	benign	636/1938	10312472	724,12282	2203	4300	6503	SO:0001583	missense	4626	exon17	Familial Cancer Database	Carney Complex Variant	TTCTTCGCGCTGC		CCDS11153.1	17p13.1	2013-09-19	2006-09-29		ENSG00000133020	ENSG00000133020		"""Myosins / Myosin superfamily : Class II"""	7578	protein-coding gene	gene with protein product		160741	"""myosin, heavy polypeptide 8, skeletal muscle, perinatal"""			2373371	Standard	NM_002472		Approved	MyHC-peri, MyHC-pn	uc002gmm.2	P13535	OTTHUMG00000130361	ENST00000403437.2:c.1907C>T	17.37:g.10312472G>A	ENSP00000384330:p.Ala636Val	Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	104	53	0.509615	NM_002472	Q14910	Missense_Mutation	SNP	ENST00000403437.2	37	CCDS11153.1	110	0.05036630036630037	21	0.042682926829268296	17	0.04696132596685083	26	0.045454545454545456	46	0.06068601583113457	G	9.307	1.054554	0.19907	0.045166	0.061047	ENSG00000133020	ENST00000252173;ENST00000403437	T	0.72394	-0.65	5.23	5.23	0.72850	Myosin head, motor domain (2);	0.657409	0.11973	U	0.511511	T	0.17746	0.0426	L	0.39147	1.195	0.30323	N	0.787406	B	0.02656	0.0	B	0.08055	0.003	T	0.48019	-0.9071	10	0.66056	D	0.02	.	13.1246	0.59346	0.0:0.2884:0.7116:0.0	rs34693726	636	P13535	MYH8_HUMAN	V	636	ENSP00000384330:A636V	ENSP00000252173:A636V	A	-	2	0	MYH8	10253197	0.018000	0.18449	0.876000	0.34364	0.006000	0.05464	0.660000	0.25009	2.736000	0.93811	0.655000	0.94253	GCG	G|0.944;A|0.056	0.056	strong		0.343	MYH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252724.2	NM_002472	
SEMA5A	9037	hgsc.bcm.edu	37	5	9154659	9154659	+	Silent	SNP	G	G	C	rs1806151	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:9154659G>C	ENST00000382496.5	-	12	2087	c.1422C>G	c.(1420-1422)ggC>ggG	p.G474G		NM_003966.2	NP_003957.2	Q13591	SEM5A_HUMAN	sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5A	474	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|blood vessel endothelial cell proliferation involved in sprouting angiogenesis (GO:0002043)|cell adhesion (GO:0007155)|cell chemotaxis (GO:0060326)|cell-cell signaling (GO:0007267)|diencephalon development (GO:0021536)|negative regulation of axon extension involved in axon guidance (GO:0048843)|negative regulation of cell adhesion (GO:0007162)|negative regulation of endothelial cell apoptotic process (GO:2000352)|nervous system development (GO:0007399)|patterning of blood vessels (GO:0001569)|positive chemotaxis (GO:0050918)|positive regulation of actin filament depolymerization (GO:0030836)|positive regulation of angiogenesis (GO:0045766)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of endothelial cell chemotaxis (GO:2001028)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of protein kinase B signaling (GO:0051897)|signal clustering (GO:1990256)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	axon guidance receptor activity (GO:0008046)|chondroitin sulfate proteoglycan binding (GO:0035373)|heparan sulfate proteoglycan binding (GO:0043395)|semaphorin receptor binding (GO:0030215)|syndecan binding (GO:0045545)			biliary_tract(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(13)|lung(40)|ovary(2)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	81						GCTCCCGCAGGCCCACGAACA	0.612													G|||	1372	0.273962	0.0371	0.3199	5008	,	,		17575	0.2312		0.5676	False		,,,				2504	0.3037				p.G474G		Atlas-SNP	.											SEMA5A,lymph_node,lymphoid_neoplasm,-1,1	SEMA5A	236	1	0			c.C1422G						PASS	.	G		506,3900	232.3+/-245.9	29,448,1726	82.0	75.0	78.0		1422	-2.8	1.0	5	dbSNP_92	78	4728,3872	607.0+/-395.2	1306,2116,878	no	coding-synonymous	SEMA5A	NM_003966.2		1335,2564,2604	CC,CG,GG		45.0233,11.4843,40.243		474/1075	9154659	5234,7772	2203	4300	6503	SO:0001819	synonymous_variant	9037	exon12			CCGCAGGCCCACG	U52840	CCDS3875.1	5p15.2	2008-05-15			ENSG00000112902	ENSG00000112902		"""Semaphorins"""	10736	protein-coding gene	gene with protein product		609297		SEMAF		8817451, 9464278	Standard	NM_003966		Approved	semF	uc003jek.2	Q13591	OTTHUMG00000090501	ENST00000382496.5:c.1422C>G	5.37:g.9154659G>C		Somatic	190	1	0.00526316		WXS	Illumina HiSeq	Phase_I	135	133	0.985185	NM_003966	D3DTC6|O60408|Q1RLL9	Silent	SNP	ENST00000382496.5	37	CCDS3875.1																																																																																			G|0.619;C|0.381	0.381	strong		0.612	SEMA5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206989.2		
MDN1	23195	hgsc.bcm.edu	37	6	90499502	90499502	+	Silent	SNP	G	G	A	rs1036853	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	112	0	0		WXS	Illumina HiSeq	Phase_I	95	44	0.463158	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		
MKI67	4288	hgsc.bcm.edu	37	10	129900858	129900858	+	Silent	SNP	C	C	T	rs3191122	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:129900858C>T	ENST00000368654.3	-	13	9621	c.9246G>A	c.(9244-9246)tcG>tcA	p.S3082S	MKI67_ENST00000368653.3_Silent_p.S2722S	NM_002417.4	NP_002408.3	P46013	KI67_HUMAN	marker of proliferation Ki-67	3082					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.S3082S(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)				TTTCAGGGACCGAGTCTTGTA	0.398													C|||	892	0.178115	0.0711	0.3112	5008	,	,		21849	0.121		0.2684	False		,,,				2504	0.1943				p.S3082S		Atlas-SNP	.											MKI67,NS,carcinoma,0,1	MKI67	363	1	1	Substitution - coding silent(1)	stomach(1)	c.G9246A						PASS	.	C	,	392,4014	194.3+/-219.2	16,360,1827	316.0	276.0	290.0		8166,9246	-2.2	0.0	10	dbSNP_105	290	2129,6471	366.1+/-334.2	267,1595,2438	yes	coding-synonymous,coding-synonymous	MKI67	NM_001145966.1,NM_002417.4	,	283,1955,4265	TT,TC,CC		24.7558,8.897,19.3834	,	2722/2897,3082/3257	129900858	2521,10485	2203	4300	6503	SO:0001819	synonymous_variant	4288	exon13			AGGGACCGAGTCT	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.9246G>A	10.37:g.129900858C>T		Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	127	74	0.582677	NM_002417	Q5VWH2	Silent	SNP	ENST00000368654.3	37	CCDS7659.1																																																																																			C|0.803;T|0.197	0.197	strong		0.398	MKI67-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050999.1	NM_002417	
COL4A1	1282	hgsc.bcm.edu	37	13	110827574	110827574	+	Silent	SNP	T	T	A	rs874203	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:110827574T>A	ENST00000375820.4	-	37	3310	c.3189A>T	c.(3187-3189)cgA>cgT	p.R1063R		NM_001845.4	NP_001836.2	P02462	CO4A1_HUMAN	collagen, type IV, alpha 1	1063	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)			CCTTTTCACCTCGCAGCCCTG	0.567													A|||	1592	0.317891	0.2549	0.3501	5008	,	,		22228	0.2788		0.3668	False		,,,				2504	0.3701				p.R1063R		Atlas-SNP	.											COL4A1_ENST00000375815,NS,carcinoma,-1,2	COL4A1	372	2	0			c.A3189T						PASS	.	A		1251,3155	703.5+/-407.0	181,889,1133	150.0	115.0	127.0		3189	-6.8	0.1	13	dbSNP_86	127	3118,5482	658.0+/-401.5	568,1982,1750	no	coding-synonymous	COL4A1	NM_001845.4		749,2871,2883	AA,AT,TT		36.2558,28.3931,33.5922		1063/1670	110827574	4369,8637	2203	4300	6503	SO:0001819	synonymous_variant	1282	exon37			TTCACCTCGCAGC	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.3189A>T	13.37:g.110827574T>A		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	94	48	0.510638	NM_001845	A7E2W4|B1AM70|Q1P9S9|Q5VWF6|Q86X41|Q8NF88|Q9NYC5	Silent	SNP	ENST00000375820.4	37	CCDS9511.1																																																																																			T|0.665;A|0.335	0.335	strong		0.567	COL4A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045759.3		
FAM188B	84182	hgsc.bcm.edu	37	7	30818142	30818142	+	Missense_Mutation	SNP	T	T	G	rs201946407	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:30818142T>G	ENST00000265299.6	+	2	235	c.158T>G	c.(157-159)cTt>cGt	p.L53R	INMT-FAM188B_ENST00000458257.1_3'UTR	NM_032222.2	NP_115598.2	Q4G0A6	F188B_HUMAN	family with sequence similarity 188, member B	53										endometrium(1)|large_intestine(5)|lung(19)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						GTTTTGCATCTTGAATTTCTC	0.478													T|||	5	0.000998403	0.0	0.0014	5008	,	,		21672	0.0		0.004	False		,,,				2504	0.0				p.L53R		Atlas-SNP	.											.	FAM188B	62	.	0			c.T158G						PASS	.	T	ARG/LEU	5,3861		0,5,1928	125.0	120.0	122.0		158	4.4	0.9	7		122	62,8212		0,62,4075	yes	missense	FAM188B	NM_032222.2	102	0,67,6003	GG,GT,TT		0.7493,0.1293,0.5519	probably-damaging	53/758	30818142	67,12073	1933	4137	6070	SO:0001583	missense	84182	exon2			TGCATCTTGAATT	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.158T>G	7.37:g.30818142T>G	ENSP00000265299:p.Leu53Arg	Somatic	226	0	0		WXS	Illumina HiSeq	Phase_I	209	47	0.22488	NM_032222	Q71AZ7|Q9H6D2	Missense_Mutation	SNP	ENST00000265299.6	37	CCDS43565.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	T	16.55	3.153666	0.57259	0.001293	0.007493	ENSG00000106125	ENST00000265299	T	0.24723	1.84	4.43	4.43	0.53597	.	0.070363	0.56097	D	0.000037	T	0.41236	0.1150	M	0.77103	2.36	0.58432	D	0.999995	D	0.89917	1.0	D	0.87578	0.998	T	0.49707	-0.8911	10	0.87932	D	0	1.9565	10.2353	0.43280	0.0:0.0:0.0:1.0	.	53	Q4G0A6	F188B_HUMAN	R	53	ENSP00000265299:L53R	ENSP00000265299:L53R	L	+	2	0	FAM188B	30784667	0.997000	0.39634	0.891000	0.34965	0.613000	0.37349	4.603000	0.61105	1.998000	0.58463	0.459000	0.35465	CTT	T|0.998;G|0.002	0.002	strong		0.478	FAM188B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327962.1	NM_032222	
PKHD1L1	93035	hgsc.bcm.edu	37	8	110476993	110476993	+	Silent	SNP	A	A	G	rs1673398	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:110476993A>G	ENST00000378402.5	+	49	8036	c.7932A>G	c.(7930-7932)gcA>gcG	p.A2644A		NM_177531.4	NP_803875.2	Q86WI1	PKHL1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1	2644					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)			CAGTGCCTGCACCTGCAATAT	0.403										HNSCC(38;0.096)			G|||	2582	0.515575	0.3918	0.634	5008	,	,		20498	0.4147		0.504	False		,,,				2504	0.7147				p.A2644A		Atlas-SNP	.											.	PKHD1L1	522	.	0			c.A7932G						PASS	.	G		1533,2239		321,891,674	131.0	127.0	128.0		7932	-0.9	0.0	8	dbSNP_89	128	4282,3952		1134,2014,969	no	coding-synonymous	PKHD1L1	NM_177531.4		1455,2905,1643	GG,GA,AA		47.9961,40.6416,48.4341		2644/4244	110476993	5815,6191	1886	4117	6003	SO:0001819	synonymous_variant	93035	exon49			GCCTGCACCTGCA	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.7932A>G	8.37:g.110476993A>G		Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	109	86	0.788991	NM_177531	Q567P2|Q9UF27	Silent	SNP	ENST00000378402.5	37	CCDS47911.1																																																																																			A|0.525;G|0.475	0.475	strong		0.403	PKHD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381017.1	NM_177531	
AXIN1	8312	hgsc.bcm.edu	37	16	348222	348222	+	Silent	SNP	C	C	T	rs214250	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:348222C>T	ENST00000262320.3	-	6	1655	c.1284G>A	c.(1282-1284)tcG>tcA	p.S428S	AXIN1_ENST00000481769.1_5'UTR|AXIN1_ENST00000354866.3_Silent_p.S428S	NM_003502.3	NP_003493.1	O15169	AXIN1_HUMAN	axin 1	428	Interaction with GSK3B. {ECO:0000250}.				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)	p.S428S(1)		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)				GGGGCCCTGACGATGGATCGC	0.647											OREG0003699	type=REGULATORY REGION|Gene=AXIN1|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	G|||	1053	0.210264	0.4304	0.1671	5008	,	,		15375	0.0556		0.2227	False		,,,				2504	0.09				p.S428S		Atlas-SNP	.											AXIN1,cerebellum,primitive_neuroectodermal_tumour-medulloblastoma,0,1	AXIN1	290	1	1	Substitution - coding silent(1)	central_nervous_system(1)	c.G1284A						PASS	.	G	,	1441,2729		260,921,904	14.0	6.0	9.0		1284,1284	-1.9	0.0	16	dbSNP_79	9	1635,6563		205,1225,2669	no	coding-synonymous,coding-synonymous	AXIN1	NM_003502.3,NM_181050.2	,	465,2146,3573	TT,TC,CC		19.9439,34.5564,24.8706	,	428/863,428/827	348222	3076,9292	2085	4099	6184	SO:0001819	synonymous_variant	8312	exon6			CCCTGACGATGGA	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.1284G>A	16.37:g.348222C>T		Somatic	26	0	0	587	WXS	Illumina HiSeq	Phase_I	40	14	0.35	NM_181050	Q4TT26|Q4TT27|Q86YA7|Q8WVW6|Q96S28	Silent	SNP	ENST00000262320.3	37	CCDS10405.1																																																																																			C|0.770;T|0.230	0.230	strong		0.647	AXIN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139441.3		
ENGASE	64772	hgsc.bcm.edu	37	17	77078069	77078069	+	Missense_Mutation	SNP	G	G	A	rs12937557	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:77078069G>A	ENST00000579016.1	+	7	962	c.962G>A	c.(961-963)cGc>cAc	p.R321H	ENGASE_ENST00000539857.2_Missense_Mutation_p.R135H	NM_001042573.2	NP_001036038.1	Q8NFI3	ENASE_HUMAN	endo-beta-N-acetylglucosaminidase	321	BRCT. {ECO:0000255|PROSITE- ProRule:PRU00033}.					cytoplasm (GO:0005737)	mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase activity (GO:0033925)			breast(2)|endometrium(4)|large_intestine(1)|lung(15)|prostate(2)|skin(1)	25						GCTGGGGAGCGCCGGGCTGAT	0.592													G|||	276	0.0551118	0.0658	0.0447	5008	,	,		9299	0.0466		0.0547	False		,,,				2504	0.0573				p.R321H		Atlas-SNP	.											.	ENGASE	55	.	0			c.G962A						PASS	.	G	HIS/ARG	252,3974		9,234,1870	112.0	145.0	134.0		962	4.3	0.9	17	dbSNP_121	134	450,8004		9,432,3786	yes	missense	ENGASE	NM_001042573.1	29	18,666,5656	AA,AG,GG		5.3229,5.9631,5.5363	probably-damaging	321/744	77078069	702,11978	2113	4227	6340	SO:0001583	missense	64772	exon7			GGGAGCGCCGGGC	AF512564	CCDS42394.1	17q25.3	2009-03-03			ENSG00000167280	ENSG00000167280	3.2.1.96		24622	protein-coding gene	gene with protein product	"""Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase"", ""Di-N-acetylchitobiosyl beta-N-acetylglucosaminidase"""	611898				12114544, 18586680	Standard	NM_001042573		Approved	FLJ21865	uc002jwv.4	Q8NFI3	OTTHUMG00000167714	ENST00000579016.1:c.962G>A	17.37:g.77078069G>A	ENSP00000462333:p.Arg321His	Somatic	269	0	0		WXS	Illumina HiSeq	Phase_I	218	89	0.408257	NM_001042573	Q659F0|Q8TB86|Q9H6U4	Missense_Mutation	SNP	ENST00000579016.1	37	CCDS42394.1	117	0.05357142857142857	31	0.06300813008130081	19	0.052486187845303865	23	0.04020979020979021	44	0.05804749340369393	G	24.6	4.553661	0.86231	0.059631	0.053229	ENSG00000167280	ENST00000311595;ENST00000545583	.	.	.	4.34	4.34	0.51931	Glycoside hydrolase, family 85 (1);	0.000000	0.85682	D	0.000000	T	0.48241	0.1489	M	0.92970	3.365	0.58432	D	0.999993	D;D;P	0.89917	1.0;1.0;0.947	D;D;P	0.91635	0.999;0.998;0.657	T	0.78909	-0.2018	9	0.87932	D	0	-16.7454	17.0368	0.86478	0.0:0.0:1.0:0.0	rs12937557	135;321;321	B4DVK0;Q8NFI3;Q8NFI3-3	.;ENASE_HUMAN;.	H	321	.	ENSP00000308158:R321H	R	+	2	0	ENGASE	74589664	1.000000	0.71417	0.924000	0.36721	0.350000	0.29205	9.065000	0.93941	2.263000	0.75096	0.313000	0.20887	CGC	G|0.943;A|0.057	0.057	strong		0.592	ENGASE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395807.1	NM_022759	
KIAA1522	57648	hgsc.bcm.edu	37	1	33236824	33236824	+	Missense_Mutation	SNP	C	C	T	rs199566536	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:33236824C>T	ENST00000373480.1	+	6	1970	c.1867C>T	c.(1867-1869)Cca>Tca	p.P623S	KIAA1522_ENST00000373481.3_Missense_Mutation_p.P634S|KIAA1522_ENST00000401073.2_Missense_Mutation_p.P682S|KIAA1522_ENST00000294521.3_Intron	NM_001198972.1	NP_001185901.1	Q9P206	K1522_HUMAN	KIAA1522	623	Pro-rich.									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)				GAGCCCTAACCCAGCTGCCCC	0.627													C|||	3	0.000599042	0.0008	0.0029	5008	,	,		7970	0.0		0.0	False		,,,				2504	0.0				p.P682S		Atlas-SNP	.											.	KIAA1522	68	.	0			c.C2044T						PASS	.	C	,SER/PRO,SER/PRO	1,3823		0,1,1911	49.0	56.0	54.0		,2044,1867	3.8	0.8	1		54	17,8217		0,17,4100	yes	intron,missense,missense	KIAA1522	NM_001198973.1,NM_020888.2,NM_001198972.1	,74,74	0,18,6011	TT,TC,CC		0.2065,0.0262,0.1493	,benign,benign	,682/1095,623/1036	33236824	18,12040	1912	4117	6029	SO:0001583	missense	57648	exon6			CCTAACCCAGCTG	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.1867C>T	1.37:g.33236824C>T	ENSP00000362579:p.Pro623Ser	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	71	36	0.507042	NM_020888	B4DQU8|B5MDY0|C9JH84|Q8TCQ0	Missense_Mutation	SNP	ENST00000373480.1	37	CCDS55588.1	5	0.0022893772893772895	2	0.0040650406504065045	2	0.0055248618784530384	0	0.0	1	0.0013192612137203166	C	2.344	-0.350520	0.05173	2.62E-4	0.002065	ENSG00000162522	ENST00000401073;ENST00000373481;ENST00000373480	T;T;T	0.12569	2.67;2.69;2.7	3.78	3.78	0.43462	.	0.637153	0.12767	N	0.440802	T	0.05868	0.0153	N	0.22421	0.69	0.09310	N	1	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.09377	0.004;0.004;0.004	T	0.32640	-0.9899	10	0.10111	T	0.7	-0.4029	10.0745	0.42351	0.2011:0.7989:0.0:0.0	.	634;623;682	Q9P206-3;Q9P206;Q9P206-2	.;K1522_HUMAN;.	S	682;634;623	ENSP00000383851:P682S;ENSP00000362580:P634S;ENSP00000362579:P623S	ENSP00000362579:P623S	P	+	1	0	KIAA1522	33009411	0.002000	0.14202	0.843000	0.33291	0.062000	0.15995	1.732000	0.38146	1.802000	0.52723	0.655000	0.94253	CCA	C|0.997;T|0.003	0.003	strong		0.627	KIAA1522-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000022130.1		
TYMSOS	494514	hgsc.bcm.edu	37	18	658064	658064	+	Missense_Mutation	SNP	G	G	C	rs2853533	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:658064G>C	ENST00000323813.3	-	1	276	c.184C>G	c.(184-186)Cgc>Ggc	p.R62G	RP11-806L2.5_ENST00000584679.1_RNA|C18orf56_ENST00000585033.1_Missense_Mutation_p.R62G|TYMS_ENST00000323250.5_Intron|TYMS_ENST00000323274.10_Intron|TYMS_ENST00000323224.7_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	20	0	0		WXS	Illumina HiSeq	Phase_I	16	13	0.8125	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		
MED25	81857	hgsc.bcm.edu	37	19	50339548	50339548	+	Silent	SNP	G	G	A	rs57854058	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:50339548G>A	ENST00000312865.6	+	17	2084	c.2031G>A	c.(2029-2031)gcG>gcA	p.A677A	PTOV1-AS1_ENST00000600742.1_RNA|PTOV1-AS1_ENST00000596521.1_RNA|MED25_ENST00000538643.1_Silent_p.A464A	NM_030973.3	NP_112235.2	Q71SY5	MED25_HUMAN	mediator complex subunit 25	677	Interaction with RARA.|Pro-rich.				cell death (GO:0008219)|gene expression (GO:0010467)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of chromatin binding (GO:0035563)|positive regulation of mediator complex assembly (GO:2001178)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)	retinoic acid receptor binding (GO:0042974)|retinoid X receptor binding (GO:0046965)|transcription factor binding (GO:0008134)	p.A677A(1)		NS(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(6)|ovary(1)|stomach(1)|urinary_tract(1)	17		all_lung(116;3.24e-07)|Lung NSC(112;1.6e-06)|all_neural(266;0.0459)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.00822)|GBM - Glioblastoma multiforme(134;0.0122)		GGGCTCCTGCGCTGCTGCCTC	0.716													G|||	50	0.00998403	0.0212	0.0159	5008	,	,		12697	0.0		0.0099	False		,,,				2504	0.001				p.A677A	GBM(51;894 1657 37868)	Atlas-SNP	.											MED25,NS,lymphoid_neoplasm,0,1	MED25	98	1	1	Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(1)	c.G2031A						PASS	.	G		110,4244		0,110,2067	10.0	13.0	12.0		2031	-6.8	0.0	19	dbSNP_129	12	66,8434		0,66,4184	no	coding-synonymous	MED25	NM_030973.3		0,176,6251	AA,AG,GG		0.7765,2.5264,1.3692		677/748	50339548	176,12678	2177	4250	6427	SO:0001819	synonymous_variant	81857	exon17			TCCTGCGCTGCTG	AL136746	CCDS33075.1	19q13.3	2014-09-17	2007-07-30			ENSG00000104973			28845	protein-coding gene	gene with protein product		610197	"""mediator of RNA polymerase II transcription, subunit 25 homolog (S. cerevisiae)"""			9110174, 11230166	Standard	NM_030973		Approved	ARC92, ACID1, TCBAP0758, DKFZp434K0512	uc002ppw.2	Q71SY5		ENST00000312865.6:c.2031G>A	19.37:g.50339548G>A		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	60	37	0.616667	NM_030973	A8K095|B9TX30|O95783|Q6P143|Q6QMH5|Q707U4|Q8TB55|Q9H0L5|Q9HB34	Silent	SNP	ENST00000312865.6	37	CCDS33075.1	19	0.0086996336996337	7	0.014227642276422764	5	0.013812154696132596	0	0.0	7	0.009234828496042216	G	7.972	0.749348	0.15710	0.025264	0.007765	ENSG00000104973	ENST00000536547	.	.	.	5.26	-6.83	0.01693	.	.	.	.	.	T	0.07999	0.0200	.	.	.	0.09310	N	0.999998	.	.	.	.	.	.	T	0.28490	-1.0042	5	0.51188	T	0.08	.	0.7099	0.00922	0.3522:0.167:0.2781:0.2028	rs57854058	.	.	.	H	166	.	ENSP00000443425:R166H	R	+	2	0	MED25	55031360	0.000000	0.05858	0.003000	0.11579	0.893000	0.52053	-1.724000	0.01865	-1.392000	0.02082	-0.311000	0.09066	CGC	G|0.991;A|0.009	0.009	strong		0.716	MED25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465316.1	NM_030973	
PAPLN	89932	hgsc.bcm.edu	37	14	73720604	73720604	+	Missense_Mutation	SNP	C	C	A	rs146030488	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:73720604C>A	ENST00000554301.1	+	11	1400	c.1237C>A	c.(1237-1239)Ccc>Acc	p.P413T	PAPLN_ENST00000555445.1_Missense_Mutation_p.P413T|PAPLN_ENST00000340738.5_Missense_Mutation_p.P386T|PAPLN_ENST00000381166.3_Missense_Mutation_p.P413T|PAPLN_ENST00000427855.1_Missense_Mutation_p.P413T			O95428	PPN_HUMAN	papilin, proteoglycan-like sulfated glycoprotein	413	TSP type-1 3. {ECO:0000255|PROSITE- ProRule:PRU00210}.					basement membrane (GO:0005604)	metalloendopeptidase activity (GO:0004222)|serine-type endopeptidase inhibitor activity (GO:0004867)|zinc ion binding (GO:0008270)			NS(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(4)|lung(11)|ovary(3)|pancreas(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(3)	42				BRCA - Breast invasive adenocarcinoma(234;0.00394)|OV - Ovarian serous cystadenocarcinoma(108;0.0468)		GCCTGGGAAGCCCCCTGCCAT	0.701													C|||	16	0.00319489	0.0015	0.0058	5008	,	,		17022	0.0		0.0089	False		,,,				2504	0.001				p.P386T		Atlas-SNP	.											.	PAPLN	180	.	0			c.C1156A						PASS	.	C	THR/PRO	4,4398		0,4,2197	27.0	29.0	28.0		1156	4.6	1.0	14	dbSNP_134	28	40,8558		0,40,4259	yes	missense	PAPLN	NM_173462.3	38	0,44,6456	AA,AC,CC		0.4652,0.0909,0.3385	probably-damaging	386/1252	73720604	44,12956	2201	4299	6500	SO:0001583	missense	89932	exon11			GGGAAGCCCCCTG	BC042057	CCDS32114.1	14q24.2	2013-01-11				ENSG00000100767		"""Immunoglobulin superfamily / I-set domain containing"""	19262	protein-coding gene	gene with protein product						11076767, 19734141	Standard	NM_173462		Approved	MGC50452	uc001xnw.4	O95428		ENST00000554301.1:c.1237C>A	14.37:g.73720604C>A	ENSP00000451803:p.Pro413Thr	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	116	55	0.474138	NM_173462	B4DES8|B4DGE6|Q659F2|Q6UXJ4|Q6ZNM1|Q6ZUJ0|Q7Z681|Q8IVU0	Missense_Mutation	SNP	ENST00000554301.1	37		14	0.00641025641025641	3	0.006097560975609756	3	0.008287292817679558	0	0.0	8	0.010554089709762533	C	19.78	3.890634	0.72524	9.09E-4	0.004652	ENSG00000100767	ENST00000340738;ENST00000427855;ENST00000381166;ENST00000554301;ENST00000555445	T;T;T;T;T	0.63255	-0.03;-0.03;-0.03;-0.03;-0.03	4.57	4.57	0.56435	.	.	.	.	.	T	0.76506	0.3997	M	0.85945	2.785	0.49798	D	0.999828	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.83565	0.0109	9	0.87932	D	0	.	17.5437	0.87855	0.0:1.0:0.0:0.0	.	413;413;386	O95428-5;O95428;O95428-6	.;PPN_HUMAN;.	T	386;413;413;413;413	ENSP00000345395:P386T;ENSP00000403403:P413T;ENSP00000370558:P413T;ENSP00000451803:P413T;ENSP00000451729:P413T	ENSP00000216658:P413T	P	+	1	0	PAPLN	72790357	1.000000	0.71417	0.998000	0.56505	0.599000	0.36880	7.053000	0.76641	2.385000	0.81259	0.462000	0.41574	CCC	C|0.996;A|0.004	0.004	strong		0.701	PAPLN-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000413182.1	NM_173462	
KNTC1	9735	hgsc.bcm.edu	37	12	123057792	123057792	+	Missense_Mutation	SNP	A	A	G	rs61751322	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:123057792A>G	ENST00000333479.7	+	26	2420	c.2243A>G	c.(2242-2244)cAt>cGt	p.H748R	KNTC1_ENST00000450485.2_Missense_Mutation_p.H711R	NM_014708.4	NP_055523.1	P50748	KNTC1_HUMAN	kinetochore associated 1	748					mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|mitotic nuclear division (GO:0007067)|protein complex assembly (GO:0006461)|regulation of exit from mitosis (GO:0007096)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|kinetochore microtubule (GO:0005828)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|spindle pole (GO:0000922)				breast(1)|central_nervous_system(1)|cervix(2)|endometrium(12)|kidney(8)|large_intestine(12)|lung(20)|ovary(7)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(4)	72	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;7.21e-05)|Epithelial(86;0.000178)|BRCA - Breast invasive adenocarcinoma(302;0.217)		ATGAGAGAACATGACTTGCAA	0.393													A|||	92	0.0183706	0.003	0.0331	5008	,	,		19334	0.0		0.0616	False		,,,				2504	0.0031				p.H748R		Atlas-SNP	.											.	KNTC1	182	.	0			c.A2243G						PASS	.	A	ARG/HIS	50,3634		0,50,1792	172.0	170.0	171.0		2243	5.7	0.6	12	dbSNP_129	171	531,7657		14,503,3577	yes	missense	KNTC1	NM_014708.4	29	14,553,5369	GG,GA,AA		6.4851,1.3572,4.8939	possibly-damaging	748/2210	123057792	581,11291	1842	4094	5936	SO:0001583	missense	9735	exon26			GAGAACATGACTT		CCDS45002.1	12q24.31	2013-01-17			ENSG00000184445	ENSG00000184445			17255	protein-coding gene	gene with protein product	"""rough deal homolog (Drosophila)"""	607363				11146660, 11590237	Standard	NM_014708		Approved	KIAA0166, ROD	uc001ucv.3	P50748	OTTHUMG00000168861	ENST00000333479.7:c.2243A>G	12.37:g.123057792A>G	ENSP00000328236:p.His748Arg	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	117	53	0.452991	NM_014708	A7E2C4|B3KSG2	Missense_Mutation	SNP	ENST00000333479.7	37	CCDS45002.1	70	0.03205128205128205	1	0.0020325203252032522	11	0.03038674033149171	0	0.0	58	0.07651715039577836	A	13.54	2.268225	0.40095	0.013572	0.064851	ENSG00000184445	ENST00000450485;ENST00000333479	T;T	0.24350	1.86;2.35	5.66	5.66	0.87406	.	0.104253	0.64402	D	0.000004	T	0.02119	0.0066	L	0.54323	1.7	0.80722	D	1	P;P	0.47106	0.89;0.827	P;B	0.49047	0.599;0.344	T	0.00048	-1.2206	10	0.41790	T	0.15	-13.7702	15.8843	0.79232	1.0:0.0:0.0:0.0	rs61751322	711;748	E7ES84;P50748	.;KNTC1_HUMAN	R	711;748	ENSP00000397992:H711R;ENSP00000328236:H748R	ENSP00000328236:H748R	H	+	2	0	KNTC1	121623745	1.000000	0.71417	0.614000	0.29051	0.255000	0.26057	7.838000	0.86804	2.164000	0.68074	0.533000	0.62120	CAT	A|0.962;G|0.038	0.038	strong		0.393	KNTC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396110.2		
VPS13A	23230	hgsc.bcm.edu	37	9	79986057	79986057	+	Silent	SNP	A	A	G	rs3737289	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:79986057A>G	ENST00000360280.3	+	67	9329	c.9069A>G	c.(9067-9069)ggA>ggG	p.G3023G	VPS13A_ENST00000376636.3_Silent_p.G2984G|VPS13A_ENST00000357409.5_Silent_p.G3023G|VPS13A_ENST00000376634.4_Silent_p.G3023G	NM_033305.2	NP_150648.2	Q96RL7	VP13A_HUMAN	vacuolar protein sorting 13 homolog A (S. cerevisiae)	3023					cell death (GO:0008219)|Golgi to endosome transport (GO:0006895)|locomotory behavior (GO:0007626)|nervous system development (GO:0007399)|protein localization (GO:0008104)|protein transport (GO:0015031)|social behavior (GO:0035176)	dense core granule (GO:0031045)|intracellular (GO:0005622)				breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(28)|liver(1)|lung(42)|ovary(3)|pancreas(3)|prostate(3)|skin(9)|upper_aerodigestive_tract(1)|urinary_tract(1)	104						CATTTCAGGGAATAAAAAGGT	0.408													A|||	2079	0.415136	0.2958	0.5159	5008	,	,		17902	0.3542		0.4394	False		,,,				2504	0.5429				p.G3023G		Atlas-SNP	.											.	VPS13A	735	.	0			c.A9069G						PASS	.	A	,,,	1432,2974	461.1+/-352.8	239,954,1010	83.0	75.0	78.0		8952,9069,9069,9069	3.3	1.0	9	dbSNP_107	78	3740,4860	527.3+/-381.1	796,2148,1356	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	VPS13A	NM_001018037.1,NM_001018038.2,NM_015186.3,NM_033305.2	,,,	1035,3102,2366	GG,GA,AA		43.4884,32.5011,39.7663	,,,	2984/3136,3023/3070,3023/3096,3023/3175	79986057	5172,7834	2203	4300	6503	SO:0001819	synonymous_variant	23230	exon67			TCAGGGAATAAAA	AB023203	CCDS6655.1, CCDS6656.1, CCDS47983.1, CCDS55321.1	9q21	2014-01-30	2006-04-04	2004-02-11	ENSG00000197969	ENSG00000197969			1908	protein-coding gene	gene with protein product	"""chorein"""	605978	"""chorea acanthocytosis"", ""vacuolar protein sorting 13A (yeast)"""	CHAC		9382101, 11381253	Standard	NM_001018038		Approved	KIAA0986	uc004akr.3	Q96RL7	OTTHUMG00000020055	ENST00000360280.3:c.9069A>G	9.37:g.79986057A>G		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	72	43	0.597222	NM_001018038	Q5JSX9|Q5JSY0|Q5VYR5|Q702P4|Q709D0|Q86YF8|Q96S61|Q9H995|Q9Y2J1	Silent	SNP	ENST00000360280.3	37	CCDS6655.1																																																																																			A|0.606;G|0.394	0.394	strong		0.408	VPS13A-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052753.2	NM_015186	
CALML5	51806	hgsc.bcm.edu	37	10	5541183	5541183	+	Silent	SNP	C	C	T	rs10904517|rs202221308|rs373657626|rs386740368	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:5541183C>T	ENST00000380332.3	-	1	350	c.219G>A	c.(217-219)gcG>gcA	p.A73A		NM_017422.4	NP_059118.2	Q9NZT1	CALL5_HUMAN	calmodulin-like 5	73	EF-hand 2. {ECO:0000255|PROSITE- ProRule:PRU00448}.				epidermis development (GO:0008544)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			biliary_tract(1)|large_intestine(2)|lung(2)|ovary(1)|skin(1)|stomach(1)	8						TGGCCTTCTTCGCCGCCGTCA	0.662													C|||	1780	0.355431	0.5182	0.2334	5008	,	,		16136	0.3065		0.3231	False		,,,				2504	0.3057				p.A73A	GBM(149;1055 3356 43077)	Atlas-SNP	.											CALML5,rectum,carcinoma,0,1	CALML5	25	1	0			c.G219A						PASS	.	C		407,3999		128,151,1924	42.0	45.0	44.0		219	0.5	0.0	10	dbSNP_120	44	354,8246		109,136,4055	no	coding-synonymous	CALML5	NM_017422.4		237,287,5979	TT,TC,CC		4.1163,9.2374,5.8511		73/147	5541183	761,12245	2203	4300	6503	SO:0001819	synonymous_variant	51806	exon1			CTTCTTCGCCGCC	AF172852	CCDS7068.1	10p15.1	2013-01-10			ENSG00000178372	ENSG00000178372		"""EF-hand domain containing"""	18180	protein-coding gene	gene with protein product	"""calmodulin-like skin protein"""	605183				10777582	Standard	NM_017422		Approved	CLSP	uc001iic.2	Q9NZT1	OTTHUMG00000017598	ENST00000380332.3:c.219G>A	10.37:g.5541183C>T		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	58	29	0.5	NM_017422	Q5SQI3|Q8IXU8	Silent	SNP	ENST00000380332.3	37	CCDS7068.1																																																																																			C|0.622;T|0.378	0.378	strong		0.662	CALML5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046556.1	NM_017422	
TBC1D9	23158	hgsc.bcm.edu	37	4	141583176	141583176	+	Silent	SNP	C	C	T	rs28465061	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:141583176C>T	ENST00000442267.2	-	10	1748	c.1674G>A	c.(1672-1674)gaG>gaA	p.E558E		NM_015130.2	NP_055945.2	Q6ZT07	TBCD9_HUMAN	TBC1 domain family, member 9 (with GRAM domain)	558	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.						calcium ion binding (GO:0005509)|Rab GTPase activator activity (GO:0005097)			endometrium(3)|kidney(2)|large_intestine(3)|lung(18)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)	31	all_hematologic(180;0.162)	Medulloblastoma(177;0.00498)				TCTCAATCTCCTCCGTGGCGA	0.473													C|||	316	0.063099	0.1672	0.0476	5008	,	,		17185	0.0		0.0487	False		,,,				2504	0.0133				p.E558E		Atlas-SNP	.											.	TBC1D9	198	.	0			c.G1674A						PASS	.	C		548,3346		41,466,1440	171.0	166.0	167.0		1674	3.1	1.0	4	dbSNP_125	167	328,7974		12,304,3835	no	coding-synonymous	TBC1D9	NM_015130.2		53,770,5275	TT,TC,CC		3.9509,14.0729,7.1827		558/1267	141583176	876,11320	1947	4151	6098	SO:0001819	synonymous_variant	23158	exon10			AATCTCCTCCGTG	AB020689	CCDS47136.1	4q31.1	2013-01-10	2006-07-12		ENSG00000109436	ENSG00000109436		"""EF-hand domain containing"""	21710	protein-coding gene	gene with protein product			"""TBC1 domain family, member 9"""			12970790	Standard	NM_015130		Approved	KIAA0882, MDR1	uc010ioj.3	Q6ZT07	OTTHUMG00000161405	ENST00000442267.2:c.1674G>A	4.37:g.141583176C>T		Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	182	90	0.494505	NM_015130	A6H8U8|D3DNZ1|O94958	Silent	SNP	ENST00000442267.2	37	CCDS47136.1																																																																																			C|0.945;T|0.055	0.055	strong		0.473	TBC1D9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364806.1	NM_015130	
BTBD6	90135	hgsc.bcm.edu	37	14	105716034	105716034	+	Silent	SNP	C	C	T	rs2816606	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:105716034C>T	ENST00000392554.3	+	4	780	c.483C>T	c.(481-483)taC>taT	p.Y161Y	BRF1_ENST00000440513.3_Intron|BRF1_ENST00000379937.2_Intron|BRF1_ENST00000546474.1_Intron|BRF1_ENST00000379932.4_5'Flank|BRF1_ENST00000392557.4_5'Flank|BTBD6_ENST00000327471.3_Silent_p.Y86Y|BRF1_ENST00000446501.2_5'Flank|BRF1_ENST00000551787.1_5'Flank|BRF1_ENST00000327359.3_Intron|BTBD6_ENST00000463376.2_Silent_p.Y86Y|BTBD6_ENST00000536364.1_Silent_p.Y161Y			Q96KE9	BTBD6_HUMAN	BTB (POZ) domain containing 6	161						cytoplasm (GO:0005737)				endometrium(1)|lung(3)	4		Melanoma(154;0.226)	OV - Ovarian serous cystadenocarcinoma(23;0.0163)|Epithelial(46;0.0391)	Epithelial(152;0.18)		CCACTCTGTACGCTGCTAAGA	0.572													C|||	917	0.183107	0.1248	0.1801	5008	,	,		18024	0.1091		0.2833	False		,,,				2504	0.2372				p.Y161Y		Atlas-SNP	.											.	BTBD6	24	.	0			c.C483T						PASS	.	C	,,,,	644,3760	274.3+/-271.8	44,556,1602	55.0	56.0	56.0		,,,,483	-3.5	0.6	14	dbSNP_100	56	2328,6272	388.6+/-342.6	301,1726,2273	no	intron,intron,intron,intron,coding-synonymous	BRF1,BTBD6	NM_001242786.1,NM_001242787.1,NM_001242788.1,NM_001519.3,NM_033271.2	,,,,	345,2282,3875	TT,TC,CC		27.0698,14.6231,22.8545	,,,,	,,,,161/486	105716034	2972,10032	2202	4300	6502	SO:0001819	synonymous_variant	90135	exon5			TCTGTACGCTGCT	AF353674	CCDS10002.1, CCDS10002.2	14q32.33	2013-01-08			ENSG00000184887	ENSG00000184887		"""BTB/POZ domain containing"""	19897	protein-coding gene	gene with protein product							Standard	NM_033271		Approved	BDPL	uc010tyq.2	Q96KE9	OTTHUMG00000029887	ENST00000392554.3:c.483C>T	14.37:g.105716034C>T		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	76	41	0.539474	NM_033271	Q8IVQ7|Q9BR94	Silent	SNP	ENST00000392554.3	37	CCDS10002.2																																																																																			C|0.776;T|0.224	0.224	strong		0.572	BTBD6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000074556.4		
DSPP	1834	hgsc.bcm.edu	37	4	88535830	88535830	+	Silent	SNP	T	T	C	rs202057495|rs142316753		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:88535830T>C	ENST00000282478.7	+	4	2049	c.2016T>C	c.(2014-2016)agT>agC	p.S672S	RP11-742B18.1_ENST00000506480.1_RNA|DSPP_ENST00000399271.1_Silent_p.S672S			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	672	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)		gtgacagcagtgatagcagtg	0.488																																					p.S672S		Atlas-SNP	.											.	DSPP	174	.	0			c.T2016C						PASS	.						121.0	137.0	131.0					4																	88535830		1707	3117	4824	SO:0001819	synonymous_variant	1834	exon5			CAGCAGTGATAGC	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.2016T>C	4.37:g.88535830T>C		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	113	16	0.141593	NM_014208	A8MUI0|O95815	Silent	SNP	ENST00000282478.7	37	CCDS43248.1																																																																																			.	.	weak		0.488	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208	
FRY	10129	hgsc.bcm.edu	37	13	32776153	32776153	+	Silent	SNP	T	T	C	rs9567420	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:32776153T>C	ENST00000380250.3	+	30	4318	c.3822T>C	c.(3820-3822)taT>taC	p.Y1274Y		NM_023037.2	NP_075463.2	Q5TBA9	FRY_HUMAN	furry homolog (Drosophila)	1274						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)		GAGAGATTTATGAAATCTCCA	0.368													T|||	495	0.0988419	0.003	0.0389	5008	,	,		18615	0.2649		0.0358	False		,,,				2504	0.1646				p.Y1274Y		Atlas-SNP	.											.	FRY	312	.	0			c.T3822C						PASS	.	T		36,3746		0,36,1855	139.0	124.0	129.0		3822	3.2	1.0	13	dbSNP_119	129	357,7873		10,337,3768	no	coding-synonymous	FRY	NM_023037.2		10,373,5623	CC,CT,TT		4.3378,0.9519,3.2717		1274/3014	32776153	393,11619	1891	4115	6006	SO:0001819	synonymous_variant	10129	exon30			GATTTATGAAATC	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.3822T>C	13.37:g.32776153T>C		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	82	37	0.451219	NM_023037	Q9Y3N6	Silent	SNP	ENST00000380250.3	37	CCDS41875.1																																																																																			T|0.918;C|0.082	0.082	strong		0.368	FRY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044405.1	NM_023037	
MS4A6E	245802	hgsc.bcm.edu	37	11	60102384	60102384	+	Missense_Mutation	SNP	A	A	G	rs2304935	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:60102384A>G	ENST00000300182.4	+	1	81	c.16A>G	c.(16-18)Att>Gtt	p.I6V		NM_139249.2	NP_640342.1	Q96DS6	M4A6E_HUMAN	membrane-spanning 4-domains, subfamily A, member 6E	6			I -> V (in dbSNP:rs2304935).			integral component of membrane (GO:0016021)				endometrium(2)|kidney(1)|lung(9)|stomach(1)	13						ATCACAACCTATTTCCAATGA	0.438													G|||	1293	0.258187	0.2269	0.4236	5008	,	,		21109	0.254		0.3121	False		,,,				2504	0.1319				p.I6V		Atlas-SNP	.											.	MS4A6E	22	.	0			c.A16G						PASS	.	G	VAL/ILE	1144,3262	714.8+/-408.4	148,848,1207	159.0	142.0	148.0		16	-3.9	0.0	11	dbSNP_100	148	2888,5712	672.6+/-402.9	507,1874,1919	yes	missense	MS4A6E	NM_139249.2	29	655,2722,3126	GG,GA,AA		33.5814,25.9646,31.0011	benign	6/148	60102384	4032,8974	2203	4300	6503	SO:0001583	missense	245802	exon1			CAACCTATTTCCA	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.16A>G	11.37:g.60102384A>G	ENSP00000300182:p.Ile6Val	Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	172	119	0.69186	NM_139249	Q3MIL2|Q8NE56|Q96PG4|Q96PG5	Missense_Mutation	SNP	ENST00000300182.4	37	CCDS7984.1	650	0.2976190476190476	128	0.2601626016260163	127	0.35082872928176795	148	0.25874125874125875	247	0.3258575197889182	G	0.004	-2.247485	0.00271	0.259646	0.335814	ENSG00000166926	ENST00000300182	T	0.07908	3.15	2.4	-3.92	0.04155	.	1.490400	0.03780	N	0.261176	T	0.00012	0.0000	N	0.01209	-0.955	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.44636	-0.9315	9	0.02654	T	1	.	8.785	0.34814	0.4387:0.0:0.5613:0.0	rs2304935;rs56640510;rs59632903;rs2304935	6	Q96DS6	M4A6E_HUMAN	V	6	ENSP00000300182:I6V	ENSP00000300182:I6V	I	+	1	0	MS4A6E	59858960	0.000000	0.05858	0.000000	0.03702	0.014000	0.08584	-0.662000	0.05305	-1.240000	0.02529	-1.840000	0.00586	ATT	A|0.705;G|0.295	0.295	strong		0.438	MS4A6E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394296.1		
OR10H3	26532	hgsc.bcm.edu	37	19	15852223	15852223	+	Missense_Mutation	SNP	A	A	C	rs1966357	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:15852223A>C	ENST00000305892.1	+	1	21	c.21A>C	c.(19-21)agA>agC	p.R7S		NM_013938.1	NP_039226.1	O60404	O10H3_HUMAN	olfactory receptor, family 10, subfamily H, member 3	7			R -> S (in dbSNP:rs1966357).			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)|kidney(2)|large_intestine(1)|liver(1)|lung(6)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	17						AGAACTACAGAACCATATCTG	0.453													N|||	3285	0.65595	0.8064	0.598	5008	,	,		22187	0.3323		0.7624	False		,,,				2504	0.7178				p.R7S		Atlas-SNP	.											OR10H3,colon,carcinoma,0,3	OR10H3	53	3	0			c.A21C						PASS	.	C	SER/ARG	3542,864		1428,686,89	167.0	156.0	159.0		21	-1.7	0.0	19	dbSNP_92	159	6321,2279		2337,1647,316	yes	missense	OR10H3	NM_013938.1	110	3765,2333,405	CC,CA,AA		26.5,19.6096,24.1658	benign	7/317	15852223	9863,3143	2203	4300	6503	SO:0001583	missense	26532	exon1			CTACAGAACCATA		CCDS12334.1	19p13.1	2012-08-09				ENSG00000171936		"""GPCR / Class A : Olfactory receptors"""	8174	protein-coding gene	gene with protein product							Standard	NM_013938		Approved		uc010xoq.2	O60404		ENST00000305892.1:c.21A>C	19.37:g.15852223A>C	ENSP00000307130:p.Arg7Ser	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	78	78	1	NM_013938	Q2HIZ3|Q6IFQ0	Missense_Mutation	SNP	ENST00000305892.1	37	CCDS12334.1	1417	0.6488095238095238	401	0.8150406504065041	234	0.6464088397790055	202	0.3531468531468531	580	0.7651715039577837	.	4.831	0.154468	0.09236	0.803904	0.735	ENSG00000171936	ENST00000305892	T	0.01221	5.15	2.35	-1.7	0.08159	.	0.199448	0.24762	N	0.035801	T	0.00012	0.0000	N	0.00084	-2.205	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.11767	-1.0574	9	0.22706	T	0.39	.	3.0412	0.06139	0.4897:0.2346:0.0:0.2758	rs1966357;rs17829384;rs52806856;rs1966357	7	O60404	O10H3_HUMAN	S	7	ENSP00000307130:R7S	ENSP00000307130:R7S	R	+	3	2	OR10H3	15713223	0.000000	0.05858	0.000000	0.03702	0.067000	0.16453	-0.234000	0.09028	-0.391000	0.07763	-1.096000	0.02151	AGA	A|0.300;C|0.700	0.700	strong		0.453	OR10H3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460918.1		
KIR3DL3	115653	hgsc.bcm.edu	37	19	55246731	55246731	+	Missense_Mutation	SNP	C	C	A	rs602444	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:55246731C>A	ENST00000291860.1	+	6	979	c.961C>A	c.(961-963)Cac>Aac	p.H321N	KIR3DL1_ENST00000538269.1_Intron|KIR3DL1_ENST00000402254.2_Intron|KIR3DL1_ENST00000541392.1_Intron|KIR2DL4_ENST00000396284.2_Intron|CTB-61M7.1_ENST00000400864.3_RNA	NM_153443.3	NP_703144.2	Q8N743	KI3L3_HUMAN	killer cell immunoglobulin-like receptor, three domains, long cytoplasmic tail, 3	321			H -> N (in allele KIR3DL3*00101, allele KIR3DL3*00102, allele KIR3DL3*00103, allele KIR3DL3*00601, allele KIR3DL3*00602, allele KIR3DL3*01302, allele KIR3DL3*01305, allele KIR3DL3*01306, allele KIR3DL3*01307, allele KIR3DL3*017 and allele KIR3DL3*026; dbSNP:rs77241525). {ECO:0000269|PubMed:9862332}.|H -> Y (in allele KIR3DL3*00101, allele KIR3DL3*0030101, allele KIR3DL3*00401, allele KIR3DL3*00402, allele KIR3DL3*007, allele KIR3DL3*01404, allele KIR3DL3*01405, allele KIR3DL3*01601 and allele KIR3DL3*028; dbSNP:rs602444). {ECO:0000269|PubMed:11513144}.			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(5)|ovary(3)|prostate(1)|skin(1)	21				GBM - Glioblastoma multiforme(193;0.0192)		TAACTCCAGACACCTGCACGT	0.448													.|||	1177	0.235024	0.0318	0.2118	5008	,	,		15547	0.1339		0.4801	False		,,,				2504	0.3783				p.H321N		Atlas-SNP	.											KIR3DL3,NS,carcinoma,0,1	KIR3DL3	46	1	0			c.C961A						PASS	.	C	ASN/HIS	382,3632		96,190,1721	289.0	223.0	245.0		961	-0.6	0.0	19	dbSNP_83	245	3917,3999		1412,1093,1453	no	missense	KIR3DL3	NM_153443.3	68	1508,1283,3174	AA,AC,CC		49.4821,9.5167,36.0352	probably-damaging	321/411	55246731	4299,7631	2007	3958	5965	SO:0001583	missense	115653	exon6			TCCAGACACCTGC	AF352324	CCDS12903.1	19q13.4	2014-05-22			ENSG00000242019	ENSG00000242019		"""Killer cell immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	16312	protein-coding gene	gene with protein product		610095				11513144	Standard	NM_153443		Approved	KIRC1, KIR3DL7, KIR44, CD158z	uc002qgu.1	Q8N743	OTTHUMG00000065884	ENST00000291860.1:c.961C>A	19.37:g.55246731C>A	ENSP00000291860:p.His321Asn	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	84	84	1	NM_153443	A9PL62|A9PL64|A9PL65|A9PL66|A9PL67|A9PL68|A9PZV4|A9PZV7|A9PZV8|A9Q066|A9Q0R5|A9Q242|A9Q250|A9Q251|O95056|Q1X775|Q1X777|Q1X778|Q1X779|Q1X780|Q1X781|Q1X782|Q1X783|Q7Z7N4|Q8NHI2|Q8NHI3|Q9UEI4	Missense_Mutation	SNP	ENST00000291860.1	37	CCDS12903.1	546	0.25	25	0.0508130081300813	88	0.2430939226519337	69	0.12062937062937062	364	0.48021108179419525	c	2.032	-0.422252	0.04734	0.095167	0.494821	ENSG00000242019	ENST00000291860	T	0.00468	7.22	0.929	-0.622	0.11560	Immunoglobulin subtype (1);	.	.	.	.	T	0.00012	0.0000	M	0.76938	2.355	0.80722	P	0.0	B	0.24258	0.1	B	0.26864	0.074	T	0.26815	-1.0092	8	0.66056	D	0.02	.	3.6449	0.08181	0.4353:0.5647:0.0:0.0	.	321	Q8N743	KI3L3_HUMAN	N	321	ENSP00000291860:H321N	ENSP00000291860:H321N	H	+	1	0	KIR3DL3	59938543	0.000000	0.05858	0.002000	0.10522	0.026000	0.11368	0.011000	0.13264	-0.127000	0.11661	0.184000	0.17185	CAC	A|0.254;C|0.746	0.254	strong		0.448	KIR3DL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141147.1	NM_153443	
MYH15	22989	hgsc.bcm.edu	37	3	108189627	108189627	+	Missense_Mutation	SNP	C	C	T	rs4299484	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:108189627C>T	ENST00000273353.3	-	14	1417	c.1361G>A	c.(1360-1362)cGg>cAg	p.R454Q		NM_014981.1	NP_055796.1	Q9Y2K3	MYH15_HUMAN	myosin, heavy chain 15	454	Myosin motor.		R -> Q (in dbSNP:rs4299484).			cytoplasm (GO:0005737)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)	p.R454Q(1)		NS(1)|breast(3)|central_nervous_system(2)|cervix(4)|endometrium(10)|kidney(4)|large_intestine(14)|lung(47)|ovary(5)|pancreas(2)|prostate(6)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	105						CCTGTTGATCCGTGCCACTAG	0.458													C|||	505	0.100839	0.0098	0.1873	5008	,	,		14327	0.0		0.2932	False		,,,				2504	0.0685				p.R454Q		Atlas-SNP	.											MYH15,NS,carcinoma,0,1	MYH15	223	1	1	Substitution - Missense(1)	prostate(1)	c.G1361A						PASS	.	C	GLN/ARG	222,3770		8,206,1782	94.0	89.0	90.0		1361	2.6	0.0	3	dbSNP_111	90	2495,5801		374,1747,2027	yes	missense	MYH15	NM_014981.1	43	382,1953,3809	TT,TC,CC		30.0747,5.5611,22.111	probably-damaging	454/1947	108189627	2717,9571	1996	4148	6144	SO:0001583	missense	22989	exon14			TTGATCCGTGCCA	AB023217	CCDS43127.1	3q13	2011-09-27	2006-09-29		ENSG00000144821	ENSG00000144821		"""Myosins / Myosin superfamily : Class II"""	31073	protein-coding gene	gene with protein product		609929	"""myosin, heavy polypeptide 15"""			15014174, 15042088	Standard	NM_014981		Approved	KIAA1000	uc003dxa.1	Q9Y2K3	OTTHUMG00000159226	ENST00000273353.3:c.1361G>A	3.37:g.108189627C>T	ENSP00000273353:p.Arg454Gln	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	92	37	0.402174	NM_014981		Missense_Mutation	SNP	ENST00000273353.3	37	CCDS43127.1	318	0.14560439560439561	10	0.02032520325203252	79	0.21823204419889503	0	0.0	229	0.3021108179419525	C	23.4	4.411069	0.83340	0.055611	0.300747	ENSG00000144821	ENST00000273353	D	0.88431	-2.38	5.77	2.58	0.30949	Myosin head, motor domain (2);	.	.	.	.	T	0.00039	0.0001	M	0.88181	2.935	0.80722	P	0.0	D	0.89917	1.0	D	0.91635	0.999	T	0.00015	-1.2392	8	0.87932	D	0	.	7.0191	0.24904	0.1319:0.6992:0.0:0.1689	rs4299484;rs17538845;rs52826675;rs56656800;rs4299484	454	Q9Y2K3	MYH15_HUMAN	Q	454	ENSP00000273353:R454Q	ENSP00000273353:R454Q	R	-	2	0	MYH15	109672317	0.000000	0.05858	0.001000	0.08648	0.977000	0.68977	0.405000	0.21015	0.557000	0.29117	0.650000	0.86243	CGG	C|0.833;T|0.167	0.167	strong		0.458	MYH15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353935.1	XM_036988	
ABCA7	10347	hgsc.bcm.edu	37	19	1047002	1047002	+	Silent	SNP	A	A	G	rs3752234	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:1047002A>G	ENST00000263094.6	+	14	2055	c.1824A>G	c.(1822-1824)gcA>gcG	p.A608A	ABCA7_ENST00000435683.2_Silent_p.A470A|ABCA7_ENST00000533574.1_Intron|ABCA7_ENST00000433129.1_Silent_p.A608A	NM_019112.3	NP_061985.2	Q8IZY2	ABCA7_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 7	608					apolipoprotein A-I-mediated signaling pathway (GO:0038027)|ATP catabolic process (GO:0006200)|cholesterol efflux (GO:0033344)|high-density lipoprotein particle assembly (GO:0034380)|memory (GO:0007613)|negative regulation of amyloid precursor protein biosynthetic process (GO:0042985)|negative regulation of ATPase activity (GO:0032780)|negative regulation of beta-amyloid formation (GO:1902430)|peptide cross-linking (GO:0018149)|phagocytosis (GO:0006909)|phospholipid efflux (GO:0033700)|phospholipid scrambling (GO:0017121)|positive regulation of ATPase activity (GO:0032781)|positive regulation of beta-amyloid clearance (GO:1900223)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of engulfment of apoptotic cell (GO:1901076)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of phagocytosis (GO:0050766)|positive regulation of phospholipid efflux (GO:1902995)|protein localization to nucleus (GO:0034504)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|ATP-binding cassette (ABC) transporter complex (GO:0043190)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|phagocytic cup (GO:0001891)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	apolipoprotein A-I receptor activity (GO:0034188)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|phospholipid transporter activity (GO:0005548)|transporter activity (GO:0005215)			NS(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(7)|lung(22)|ovary(1)|pancreas(7)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	65		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		TCAGCGCCGCACTGCTGGTTC	0.726													G|||	2899	0.578874	0.4637	0.7104	5008	,	,		13766	0.75		0.5199	False		,,,				2504	0.5256				p.A608A		Atlas-SNP	.											ABCA7,NS,carcinoma,0,1	ABCA7	174	1	0			c.A1824G						PASS	.			2219,2141		606,1007,567	14.0	13.0	13.0		1824	-2.7	0.3	19	dbSNP_107	13	4663,3873		1348,1967,953	no	coding-synonymous	ABCA7	NM_019112.3		1954,2974,1520	GG,GA,AA		45.3725,49.1055,46.6346		608/2147	1047002	6882,6014	2180	4268	6448	SO:0001819	synonymous_variant	10347	exon14			CGCCGCACTGCTG	AF328787	CCDS12055.1	19p13.3	2012-03-14			ENSG00000064687	ENSG00000064687		"""ATP binding cassette transporters / subfamily A"""	37	protein-coding gene	gene with protein product		605414					Standard	NM_019112		Approved	ABCX	uc002lqw.4	Q8IZY2	OTTHUMG00000167547	ENST00000263094.6:c.1824A>G	19.37:g.1047002A>G		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	38	11	0.289474	NM_019112	Q96S58|Q9BZC4|Q9NR73|Q9UKP8	Silent	SNP	ENST00000263094.6	37	CCDS12055.1																																																																																			A|0.401;G|0.599	0.599	strong		0.726	ABCA7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000394993.1	NM_019112	
VCX	26609	hgsc.bcm.edu	37	X	7811760	7811760	+	Silent	SNP	C	C	A	rs202230674		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:7811760C>A	ENST00000381059.3	+	3	543	c.324C>A	c.(322-324)gcC>gcA	p.A108A	VCX_ENST00000341408.4_Silent_p.A108A	NM_013452.2	NP_038480.2	Q9H320	VCX1_HUMAN	variable charge, X-linked	108	10 X 10 AA tandem repeats of L-S-Q-E-S- [EQ]-V-E-E-P.|Glu-rich.			A -> S (in Ref. 3; AAH98123). {ECO:0000305}.	chromatin organization (GO:0006325)|ribosome assembly (GO:0042255)|spermatogenesis (GO:0007283)	nucleolus (GO:0005730)|nucleus (GO:0005634)	chromatin binding (GO:0003682)			NS(1)|endometrium(4)|large_intestine(2)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	10		Colorectal(8;0.0136)|Medulloblastoma(8;0.184)				GTCAGGAGGCCGAGCTGGAGG	0.662																																					p.A108A		Atlas-SNP	.											.	VCX	28	.	0			c.C324A						PASS	.						83.0	103.0	96.0					X																	7811760		2133	4081	6214	SO:0001819	synonymous_variant	26609	exon3			GGAGGCCGAGCTG	AF167081	CCDS14128.1	Xp22.31	2008-02-05	2003-09-12		ENSG00000182583	ENSG00000182583			12667	protein-coding gene	gene with protein product		300229	"""variable charge, X chromosome"""			10607842, 10903929	Standard	NM_013452		Approved	VCX1, VCX10R, VCX-10r, VCX-B1	uc004crz.3	Q9H320	OTTHUMG00000028608	ENST00000381059.3:c.324C>A	X.37:g.7811760C>A		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	77	18	0.233766	NM_013452	A0JNS5|Q4V774|Q9P0H3	Silent	SNP	ENST00000381059.3	37	CCDS14128.1																																																																																			.	.	alt		0.662	VCX-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000071474.1	NM_013452	
SUN2	25777	hgsc.bcm.edu	37	22	39134715	39134715	+	Silent	SNP	T	T	C	rs1062687	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:39134715T>C	ENST00000405510.1	-	17	2182	c.1824A>G	c.(1822-1824)caA>caG	p.Q608Q	SUN2_ENST00000405018.1_Silent_p.Q629Q|RP3-508I15.18_ENST00000420118.1_RNA|RP3-508I15.20_ENST00000609428.1_RNA|RP3-508I15.14_ENST00000416406.1_RNA|SUN2_ENST00000411587.2_Silent_p.Q597Q|SUN2_ENST00000216064.4_Silent_p.Q608Q|SUN2_ENST00000406622.1_Silent_p.Q608Q|RP3-508I15.19_ENST00000418803.1_RNA	NM_001199580.1	NP_001186509.1	Q9UH99	SUN2_HUMAN	Sad1 and UNC84 domain containing 2	608	SUN. {ECO:0000255|PROSITE- ProRule:PRU00802}.				centrosome localization (GO:0051642)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|mitotic spindle organization (GO:0007052)|nuclear envelope organization (GO:0006998)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nuclear migration (GO:0007097)|nuclear migration along microfilament (GO:0031022)|positive regulation of cell migration (GO:0030335)	condensed nuclear chromosome (GO:0000794)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|nuclear chromosome, telomeric region (GO:0000784)|nuclear envelope (GO:0005635)|nuclear inner membrane (GO:0005637)|nuclear membrane (GO:0031965)|SUN-KASH complex (GO:0034993)	identical protein binding (GO:0042802)|lamin binding (GO:0005521)|microtubule binding (GO:0008017)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(3)|ovary(1)|skin(2)|stomach(1)	15						CGGCGAAGCCTTGTGGCCCCT	0.622													C|||	1923	0.383986	0.556	0.2046	5008	,	,		17697	0.4603		0.2982	False		,,,				2504	0.2883				p.Q629Q		Atlas-SNP	.											.	SUN2	59	.	0			c.A1887G						PASS	.	C	,,	2258,2148	573.8+/-383.6	577,1104,522	66.0	70.0	69.0		1887,1824,1824	2.4	1.0	22	dbSNP_86	69	2565,6035	685.2+/-404.0	375,1815,2110	no	coding-synonymous,coding-synonymous,coding-synonymous	SUN2	NM_001199579.1,NM_001199580.1,NM_015374.2	,,	952,2919,2632	CC,CT,TT		29.8256,48.7517,37.0829	,,	629/739,608/718,608/718	39134715	4823,8183	2203	4300	6503	SO:0001819	synonymous_variant	25777	exon16			GAAGCCTTGTGGC	AF202723	CCDS13978.1, CCDS56231.1	22q12-q13	2010-05-18	2010-05-18	2010-01-27	ENSG00000100242	ENSG00000100242			14210	protein-coding gene	gene with protein product		613569	"""unc-84 homolog B (C. elegans)"""	UNC84B		10508607, 10375507	Standard	NM_015374		Approved		uc010gxq.2	Q9UH99	OTTHUMG00000151031	ENST00000405510.1:c.1824A>G	22.37:g.39134715T>C		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	63	30	0.47619	NM_001199579	B0QY62|O75156|Q2NKN8|Q2T9F7|Q504T5|Q6B4H1|Q7Z3E3	Silent	SNP	ENST00000405510.1	37	CCDS13978.1																																																																																			T|0.620;C|0.380;A|0.000	0.380	strong		0.622	SUN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321057.1	XM_039332	
KPRP	448834	hgsc.bcm.edu	37	1	152732436	152732436	+	Silent	SNP	G	G	C	rs4845480	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:152732436G>C	ENST00000606109.1	+	1	400	c.372G>C	c.(370-372)gcG>gcC	p.A124A	KPRP_ENST00000368773.1_Silent_p.A124A			Q5T749	KPRP_HUMAN	keratinocyte proline-rich protein	124	Gln-rich.					cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)				NS(1)|breast(1)|endometrium(9)|kidney(1)|large_intestine(10)|lung(21)|ovary(6)|pancreas(1)|prostate(6)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	60	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)			AGTGCGAAGCGTCACAACCTG	0.502													C|||	2456	0.490415	0.5787	0.4914	5008	,	,		23278	0.4187		0.5159	False		,,,				2504	0.4182				p.A124A		Atlas-SNP	.											KPRP,NS,carcinoma,+1,1	KPRP	152	1	0			c.G372C						PASS	.	C		2439,1967	554.9+/-379.1	676,1087,440	259.0	245.0	250.0		372	-0.8	0.0	1	dbSNP_111	250	4322,4278	575.7+/-390.3	1096,2130,1074	no	coding-synonymous	KPRP	NM_001025231.1		1772,3217,1514	CC,CG,GG		49.7442,44.6437,48.0163		124/580	152732436	6761,6245	2203	4300	6503	SO:0001819	synonymous_variant	448834	exon2			CGAAGCGTCACAA	AY960854	CCDS30862.1	1q21.3	2008-02-05	2007-02-02	2006-12-07	ENSG00000203786	ENSG00000203786			31823	protein-coding gene	gene with protein product		613260	"""chromosome 1 open reading frame 45"""	C1orf45		16297201	Standard	NM_001025231		Approved		uc001fal.1	Q5T749	OTTHUMG00000012402	ENST00000606109.1:c.372G>C	1.37:g.152732436G>C		Somatic	281	0	0		WXS	Illumina HiSeq	Phase_I	236	108	0.457627	NM_001025231		Silent	SNP	ENST00000606109.1	37	CCDS30862.1																																																																																			G|0.490;C|0.510	0.510	strong		0.502	KPRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034522.2	NM_001025231	
SORCS3	22986	hgsc.bcm.edu	37	10	106907440	106907440	+	Silent	SNP	C	C	T	rs791125	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:106907440C>T	ENST00000369701.3	+	9	1595	c.1368C>T	c.(1366-1368)aaC>aaT	p.N456N		NM_014978.1	NP_055793.1	Q9UPU3	SORC3_HUMAN	sortilin-related VPS10 domain containing receptor 3	456					learning (GO:0007612)|memory (GO:0007613)|neuropeptide signaling pathway (GO:0007218)|regulation of long term synaptic depression (GO:1900452)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|neuronal postsynaptic density (GO:0097481)	neuropeptide receptor activity (GO:0008188)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(19)|lung(63)|ovary(6)|pancreas(1)|prostate(6)|skin(8)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	131		Colorectal(252;0.134)|Breast(234;0.142)|Lung NSC(174;0.191)		Epithelial(162;1.58e-07)|all cancers(201;1.02e-05)|BRCA - Breast invasive adenocarcinoma(275;0.0628)		GGAACCAGAACGACACGTACA	0.473													C|||	2449	0.489018	0.4803	0.6268	5008	,	,		21040	0.3492		0.5467	False		,,,				2504	0.4877				p.N456N	NSCLC(116;1497 1690 7108 13108 14106)	Atlas-SNP	.											.	SORCS3	282	.	0			c.C1368T						PASS	.	C		2143,2263	580.5+/-385.1	528,1087,588	261.0	207.0	225.0		1368	-7.3	0.8	10	dbSNP_86	225	4688,3912	604.4+/-394.8	1274,2140,886	no	coding-synonymous	SORCS3	NM_014978.1		1802,3227,1474	TT,TC,CC		45.4884,48.6382,47.4781		456/1223	106907440	6831,6175	2203	4300	6503	SO:0001819	synonymous_variant	22986	exon9			CCAGAACGACACG	AB028982	CCDS7558.1	10q23-q25	2006-04-12			ENSG00000156395	ENSG00000156395			16699	protein-coding gene	gene with protein product		606285				11499680	Standard	NM_014978		Approved	KIAA1059, SORCS	uc001kyi.1	Q9UPU3	OTTHUMG00000019011	ENST00000369701.3:c.1368C>T	10.37:g.106907440C>T		Somatic	179	0	0		WXS	Illumina HiSeq	Phase_I	178	178	1	NM_014978	Q5VXF9|Q9NQJ2	Silent	SNP	ENST00000369701.3	37	CCDS7558.1																																																																																			C|0.497;T|0.503	0.503	strong		0.473	SORCS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050221.1	NM_014978	
MAPRE1	22919	hgsc.bcm.edu	37	20	31427635	31427635	+	Silent	SNP	C	C	T	rs2070090	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	94	0	0		WXS	Illumina HiSeq	Phase_I	82	32	0.390244	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	
MYCBPAP	84073	hgsc.bcm.edu	37	17	48594691	48594691	+	Missense_Mutation	SNP	G	G	A	rs61749930	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:48594691G>A	ENST00000323776.5	+	3	533	c.371G>A	c.(370-372)cGt>cAt	p.R124H	MYCBPAP_ENST00000436259.2_Missense_Mutation_p.R87H	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)			GAAGATAAACGTGTCATCACC	0.463													G|||	58	0.0115815	0.0008	0.0274	5008	,	,		21900	0.0		0.0328	False		,,,				2504	0.0051				p.R124H		Atlas-SNP	.											.	MYCBPAP	135	.	0			c.G371A						PASS	.	G	HIS/ARG	39,4367	44.6+/-78.6	0,39,2164	136.0	133.0	134.0		371	2.1	0.0	17	dbSNP_129	134	230,8370	94.2+/-156.2	3,224,4073	yes	missense	MYCBPAP	NM_032133.4	29	3,263,6237	AA,AG,GG		2.6744,0.8852,2.0683	benign	124/985	48594691	269,12737	2203	4300	6503	SO:0001583	missense	84073	exon3			ATAAACGTGTCAT	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.371G>A	17.37:g.48594691G>A	ENSP00000323184:p.Arg124His	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	101	47	0.465347	NM_032133		Missense_Mutation	SNP	ENST00000323776.5	37	CCDS32680.2	32	0.014652014652014652	1	0.0020325203252032522	11	0.03038674033149171	0	0.0	20	0.026385224274406333	G	3.408	-0.120716	0.06838	0.008852	0.026744	ENSG00000136449	ENST00000323776;ENST00000452039;ENST00000436259	T;T	0.23754	1.89;1.89	5.45	2.11	0.27256	.	0.776720	0.12153	N	0.494646	T	0.02688	0.0081	N	0.02011	-0.69	0.09310	N	1	B;B	0.06786	0.0;0.001	B;B	0.04013	0.001;0.001	T	0.26430	-1.0103	10	0.35671	T	0.21	-1.106	5.8945	0.18931	0.1274:0.543:0.2559:0.0737	rs61749930	87;124	Q8TBZ2;B4DZQ1	MYBPP_HUMAN;.	H	124;124;87	ENSP00000323184:R124H;ENSP00000397209:R87H	ENSP00000323184:R124H	R	+	2	0	MYCBPAP	45949690	0.001000	0.12720	0.003000	0.11579	0.044000	0.14063	0.395000	0.20850	0.767000	0.33267	-0.256000	0.11100	CGT	G|0.980;A|0.020	0.020	strong		0.463	MYCBPAP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347814.1	NM_032133	
PAX5	5079	hgsc.bcm.edu	37	9	37033983	37033983	+	Splice_Site	SNP	C	C	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:37033983C>G	ENST00000358127.4	-	1	120	c.46G>C	c.(46-48)Gga>Cga	p.G16R	PAX5_ENST00000520281.1_Splice_Site_p.G16R|PAX5_ENST00000377853.2_Splice_Site_p.G16R|PAX5_ENST00000523241.1_Splice_Site_p.G16R|PAX5_ENST00000414447.1_Splice_Site_p.G16R|PAX5_ENST00000446742.1_Splice_Site_p.G16R|PAX5_ENST00000520154.1_Splice_Site_p.G16R|PAX5_ENST00000522003.1_5'UTR|PAX5_ENST00000523145.1_5'UTR|PAX5_ENST00000377852.2_Splice_Site_p.G16R|PAX5_ENST00000377847.2_Splice_Site_p.G16R	NM_001280554.1|NM_001280556.1|NM_016734.1	NP_001267483.1|NP_001267485.1|NP_057953.1	Q02548	PAX5_HUMAN	paired box 5	16	Paired. {ECO:0000255|PROSITE- ProRule:PRU00381}.				humoral immune response (GO:0006959)|multicellular organismal development (GO:0007275)|negative regulation of histone H3-K9 methylation (GO:0051573)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|organ morphogenesis (GO:0009887)|skeletal muscle cell differentiation (GO:0035914)|spermatogenesis (GO:0007283)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)	p.?(10)	PAX5/JAK2(18)	NS(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(151)|kidney(1)|lung(10)|prostate(1)|skin(1)	171		all_cancers(2;3.46e-10)|Acute lymphoblastic leukemia(2;7.09e-56)|all_hematologic(2;6.65e-44)		GBM - Glioblastoma multiforme(29;0.0108)		GCGGTCCTACCTGTCCTGCTG	0.552			"""T, Mis, D, F, S"""	"""IGH@, ETV6, PML, FOXP1, ZNF521, ELN"""	"""NHL, ALL, B-ALL"""																																p.G16R		Atlas-SNP	.		Dom	yes		9	9p13	5079	paired box gene 5 (B-cell lineage specific activator protein)		L	.	PAX5	250	.	10	Unknown(10)	haematopoietic_and_lymphoid_tissue(10)	c.G46C						PASS	.						70.0	65.0	66.0					9																	37033983		2203	4300	6503	SO:0001630	splice_region_variant	5079	exon1			TCCTACCTGTCCT		CCDS6607.1, CCDS65039.1, CCDS65040.1, CCDS65041.1, CCDS65042.1, CCDS65043.1, CCDS65044.1, CCDS65045.1, CCDS65046.1, CCDS65047.1, CCDS65048.1	9p13.2	2011-06-20	2007-07-12		ENSG00000196092	ENSG00000196092		"""Paired boxes"", ""Homeoboxes / PRD class"""	8619	protein-coding gene	gene with protein product	"""B-cell lineage specific activator"""	167414	"""paired box gene 5 (B-cell lineage specific activator protein)"", ""paired box gene 5 (B-cell lineage specific activator)"""			1516825, 8431641	Standard	NM_016734		Approved	BSAP	uc003zzo.1	Q02548	OTTHUMG00000019907	ENST00000358127.4:c.46+1G>C	9.37:g.37033983C>G		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	98	29	0.295918	NM_016734	A3QVP6|A3QVP7|A3QVP8|C0KTF6|C0KTF7|C0KTF8|C0KTF9|C0KTG0|O75933|Q5SFM2|Q6S728|Q6S729|Q6S730|Q6S731|Q6S732	Missense_Mutation	SNP	ENST00000358127.4	37	CCDS6607.1	.	.	.	.	.	.	.	.	.	.	C	25.6	4.650847	0.87958	.	.	ENSG00000196092	ENST00000358127;ENST00000377853;ENST00000377852;ENST00000523241;ENST00000520154;ENST00000520281;ENST00000446742;ENST00000414447;ENST00000377847	D;D;D;D;D;D;D;D;D	0.99474	-5.97;-5.97;-5.97;-5.97;-5.97;-5.97;-5.97;-5.97;-5.97	6.08	6.08	0.98989	Paired box protein, N-terminal (3);	0.000000	0.64402	D	0.000001	D	0.99557	0.9841	M	0.82923	2.615	0.80722	D	1	D;B;P;D;P;P;D;D;D	0.89917	1.0;0.439;0.752;1.0;0.56;0.727;1.0;1.0;1.0	D;B;P;D;P;P;D;D;D	0.91635	0.999;0.196;0.627;0.999;0.533;0.664;0.999;0.999;0.999	D	0.99007	1.0813	9	.	.	.	.	20.2751	0.98485	0.0:1.0:0.0:0.0	.	16;16;16;16;16;16;16;16;16	C0KTF8;C0KTF7;C0KTF9;C0KTF6;E7ERW5;E7EQT0;Q6S730;Q6S731;Q02548	.;.;.;.;.;.;.;.;PAX5_HUMAN	R	16	ENSP00000350844:G16R;ENSP00000367084:G16R;ENSP00000367083:G16R;ENSP00000429637:G16R;ENSP00000429291:G16R;ENSP00000430773:G16R;ENSP00000404687:G16R;ENSP00000412188:G16R;ENSP00000367078:G16R	.	G	-	1	0	PAX5	37023983	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.083000	0.71326	2.890000	0.99128	0.655000	0.94253	GGA	.	.	none		0.552	PAX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052433.1		Missense_Mutation
BANK1	55024	hgsc.bcm.edu	37	4	102839287	102839287	+	Missense_Mutation	SNP	G	G	A	rs3733197	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:102839287G>A	ENST00000322953.4	+	7	1421	c.1147G>A	c.(1147-1149)Gca>Aca	p.A383T	BANK1_ENST00000508653.1_Missense_Mutation_p.A250T|BANK1_ENST00000428908.1_Missense_Mutation_p.A250T|BANK1_ENST00000444316.2_Missense_Mutation_p.A353T|BANK1_ENST00000504592.1_Missense_Mutation_p.A368T	NM_017935.4	NP_060405	Q8NDB2	BANK1_HUMAN	B-cell scaffold protein with ankyrin repeats 1	383			A -> T (influences susceptibility to SLE; dbSNP:rs3733197). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:18204447}.		B cell activation (GO:0042113)					NS(1)|breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|liver(2)|lung(16)|ovary(2)|skin(2)|urinary_tract(1)	44		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;2.7e-07)		TTCAGACCCCGCACATATTGC	0.363													G|||	1136	0.226837	0.1498	0.219	5008	,	,		15219	0.254		0.3489	False		,,,				2504	0.183				p.A383T		Atlas-SNP	.											.	BANK1	95	.	0			c.G1147A	GRCh37	CM080096	BANK1	M	rs3733197	PASS	.	G	THR/ALA,THR/ALA,THR/ALA	812,3592	310.0+/-291.3	85,642,1475	63.0	66.0	65.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1057,748,1147	1.9	0.1	4	dbSNP_107	65	3053,5547	465.6+/-366.6	542,1969,1789	yes	missense,missense,missense	BANK1	NM_001083907.2,NM_001127507.2,NM_017935.4	58,58,58	627,2611,3264	AA,AG,GG		35.5,18.4378,29.7216	benign,benign,benign	353/756,250/653,383/786	102839287	3865,9139	2202	4300	6502	SO:0001583	missense	55024	exon7			GACCCCGCACATA	AB063170	CCDS34038.1, CCDS47115.1, CCDS47116.1	4q23	2013-01-11						"""Ankyrin repeat domain containing"""	18233	protein-coding gene	gene with protein product		610292				11782428, 21208380, 21480188	Standard	NM_017935		Approved	BANK, FLJ20706	uc003hvy.4	Q8NDB2		ENST00000322953.4:c.1147G>A	4.37:g.102839287G>A	ENSP00000320509:p.Ala383Thr	Somatic	193	0	0		WXS	Illumina HiSeq	Phase_I	135	60	0.444444	NM_017935	A8K7W8|B0F3S2|Q8N5K8|Q8NB56|Q8WYN5|Q9NWP2	Missense_Mutation	SNP	ENST00000322953.4	37	CCDS34038.1	547	0.25045787545787546	70	0.14227642276422764	83	0.2292817679558011	125	0.21853146853146854	269	0.3548812664907652	G	4.252	0.045840	0.08196	0.184378	0.355	ENSG00000153064	ENST00000504592;ENST00000322953;ENST00000428908;ENST00000508653;ENST00000444316	T;T;T;T;T	0.53423	0.62;0.62;0.62;0.62;0.62	4.55	1.85	0.25348	Ankyrin repeat-containing domain (1);	0.537909	0.15287	N	0.270369	T	0.00012	0.0000	L	0.52573	1.65	0.80722	P	0.0	D;D;D	0.76494	0.999;0.983;0.983	P;P;P	0.59357	0.856;0.608;0.608	T	0.29671	-1.0004	9	0.08381	T	0.77	.	4.0106	0.09621	0.2958:0.1862:0.518:0.0	rs3733197;rs52823400;rs3733197	250;383;368	Q8NDB2-4;Q8NDB2;Q8NDB2-2	.;BANK1_HUMAN;.	T	368;383;250;250;353	ENSP00000421443:A368T;ENSP00000320509:A383T;ENSP00000412748:A250T;ENSP00000422314:A250T;ENSP00000388817:A353T	ENSP00000320509:A383T	A	+	1	0	BANK1	103058310	0.059000	0.20769	0.056000	0.19401	0.127000	0.20565	0.723000	0.25939	0.163000	0.19507	-0.126000	0.14955	GCA	G|0.725;A|0.275	0.275	strong		0.363	BANK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363161.1	NM_017935	
ARMC9	80210	hgsc.bcm.edu	37	2	232072912	232072912	+	Silent	SNP	T	T	C	rs11558174	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:232072912T>C	ENST00000349938.4	+	3	318	c.124T>C	c.(124-126)Ttg>Ctg	p.L42L	ARMC9_ENST00000483477.1_3'UTR	NM_001271466.1|NM_025139.4	NP_001258395.1|NP_079415	Q7Z3E5	ARMC9_HUMAN	armadillo repeat containing 9	42						extracellular vesicular exosome (GO:0070062)		p.L42L(2)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(5)|ovary(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	22		Renal(207;0.0112)|all_lung(227;0.0744)|all_hematologic(139;0.0749)|Acute lymphoblastic leukemia(138;0.167)|Medulloblastoma(418;0.184)|Lung NSC(271;0.205)		Epithelial(121;1.43e-10)|LUSC - Lung squamous cell carcinoma(224;0.017)|Lung(119;0.0189)		AGGAAAACCATTGTGTAAAAC	0.299													T|||	1242	0.248003	0.3563	0.2349	5008	,	,		18620	0.1409		0.2853	False		,,,				2504	0.183				p.L42L		Atlas-SNP	.											ARMC9_ENST00000359743,NS,carcinoma,0,2	ARMC9	129	2	2	Substitution - coding silent(2)	stomach(2)	c.T124C						PASS	.	T		1601,2803	494.6+/-363.0	285,1031,886	80.0	81.0	80.0		124	-2.8	0.0	2	dbSNP_120	80	2199,6401	374.2+/-337.3	281,1637,2382	no	coding-synonymous	ARMC9	NM_025139.3		566,2668,3268	CC,CT,TT		25.5698,36.3533,29.2218		42/666	232072912	3800,9204	2202	4300	6502	SO:0001819	synonymous_variant	80210	exon3			AAACCATTGTGTA	BC004514	CCDS2484.1, CCDS74666.1	2q37.1	2013-02-14			ENSG00000135931	ENSG00000135931		"""Armadillo repeat containing"""	20730	protein-coding gene	gene with protein product						11347906	Standard	NM_025139		Approved	FLJ12584, KIAA1868, ARM, KU-MEL-1	uc031rrs.1	Q7Z3E5	OTTHUMG00000133229	ENST00000349938.4:c.124T>C	2.37:g.232072912T>C		Somatic	303	0	0		WXS	Illumina HiSeq	Phase_I	227	116	0.511013	NM_025139	Q53TI3|Q6P162|Q7L594|Q86WG2|Q96JF9|Q9H9R8	Silent	SNP	ENST00000349938.4	37	CCDS2484.1																																																																																			T|0.713;C|0.287	0.287	strong		0.299	ARMC9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256966.3	NM_025139	
ENPP7	339221	hgsc.bcm.edu	37	17	77709339	77709339	+	Silent	SNP	C	C	G	rs11657217	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:77709339C>G	ENST00000328313.5	+	3	1118	c.897C>G	c.(895-897)gcC>gcG	p.A299A		NM_178543.3	NP_848638.3			ectonucleotide pyrophosphatase/phosphodiesterase 7											breast(1)|central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(3)|lung(12)|ovary(2)|prostate(6)|skin(3)	34			OV - Ovarian serous cystadenocarcinoma(97;0.016)|BRCA - Breast invasive adenocarcinoma(99;0.0224)			TGTACGATGCCCTCAAGGACG	0.592													G|||	1599	0.319289	0.4864	0.2435	5008	,	,		5034	0.1101		0.2942	False		,,,				2504	0.3885				p.A299A		Atlas-SNP	.											.	ENPP7	63	.	0			c.C897G						PASS	.	G		2062,2344	607.3+/-390.9	479,1104,620	94.0	76.0	82.0		897	-0.9	0.0	17	dbSNP_120	82	2625,5975	686.6+/-404.1	414,1797,2089	no	coding-synonymous	ENPP7	NM_178543.3		893,2901,2709	GG,GC,CC		30.5233,46.7998,36.0372		299/459	77709339	4687,8319	2203	4300	6503	SO:0001819	synonymous_variant	339221	exon3			CGATGCCCTCAAG	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.897C>G	17.37:g.77709339C>G		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	70	36	0.514286	NM_178543		Silent	SNP	ENST00000328313.5	37	CCDS11763.1																																																																																			C|0.672;G|0.328	0.328	strong		0.592	ENPP7-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437038.1	NM_178543	
IGSF22	283284	hgsc.bcm.edu	37	11	18729367	18729367	+	Silent	SNP	G	G	T	rs57253324	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:18729367G>T	ENST00000513874.1	-	20	3403	c.3264C>A	c.(3262-3264)atC>atA	p.I1088I	RP11-1081L13.4_ENST00000527285.1_RNA|IGSF22_ENST00000510673.1_5'Flank	NM_173588.3	NP_775859	Q8N9C0	IGS22_HUMAN	immunoglobulin superfamily, member 22	693										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						CGCGCACATGGATGTCATAGC	0.532													G|||	553	0.110423	0.1778	0.1239	5008	,	,		21190	0.0615		0.0686	False		,,,				2504	0.1033				p.I1088I		Atlas-SNP	.											.	IGSF22	211	.	0			c.C3264A						PASS	.	G		237,1147		17,203,472	152.0	124.0	133.0		3264	3.0	0.0	11	dbSNP_129	133	218,2964		7,204,1380	no	coding-synonymous	IGSF22	NM_173588.3		24,407,1852	TT,TG,GG		6.851,17.1243,9.965		1088/1327	18729367	455,4111	692	1591	2283	SO:0001819	synonymous_variant	283284	exon20			CACATGGATGTCA	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.3264C>A	11.37:g.18729367G>T		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	65	22	0.338462	NM_173588	A6NNA0|D6RGV7	Silent	SNP	ENST00000513874.1	37	CCDS41625.2																																																																																			G|0.901;T|0.099	0.099	strong		0.532	IGSF22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360850.2	NM_173588	
MRPL22	29093	hgsc.bcm.edu	37	5	154346259	154346259	+	Silent	SNP	A	A	G	rs14922	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:154346259A>G	ENST00000523037.1	+	7	464	c.423A>G	c.(421-423)tcA>tcG	p.S141S	MRPL22_ENST00000522038.1_Silent_p.S147S|MRPL22_ENST00000518364.1_3'UTR|MRPL22_ENST00000265229.8_Silent_p.S61S|MRPL22_ENST00000439747.3_Silent_p.S167S	NM_014180.3	NP_054899.2	Q9NWU5	RM22_HUMAN	mitochondrial ribosomal protein L22	141					translation (GO:0006412)	large ribosomal subunit (GO:0015934)|mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|urinary_tract(2)	10	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)			AGTCCACCTCAGGACGAGGCC	0.468													A|||	611	0.122005	0.0961	0.2219	5008	,	,		21141	0.0645		0.1252	False		,,,				2504	0.1421				p.S141S		Atlas-SNP	.											.	MRPL22	18	.	0			c.A423G						PASS	.	A	,	468,3938	221.0+/-238.3	24,420,1759	119.0	111.0	114.0		183,423	-2.7	0.9	5	dbSNP_52	114	1034,7566	219.1+/-257.3	49,936,3315	no	coding-synonymous,coding-synonymous	MRPL22	NM_001014990.2,NM_014180.3	,	73,1356,5074	GG,GA,AA		12.0233,10.6219,11.5485	,	61/127,141/207	154346259	1502,11504	2203	4300	6503	SO:0001819	synonymous_variant	29093	exon7			CACCTCAGGACGA	AB051622	CCDS4331.1, CCDS43391.1	5q33.2	2012-09-13			ENSG00000082515	ENSG00000082515		"""Mitochondrial ribosomal proteins / large subunits"""	14480	protein-coding gene	gene with protein product		611835					Standard	NM_014180		Approved	MRP-L25, RPML25, HSPC158	uc003lvy.4	Q9NWU5	OTTHUMG00000130190	ENST00000523037.1:c.423A>G	5.37:g.154346259A>G		Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	127	44	0.346457	NM_014180	A6NGJ8|Q5H9Q1|Q96Q51|Q9P006	Silent	SNP	ENST00000523037.1	37	CCDS4331.1																																																																																			T|0.168;G|0.092	0.092	strong		0.468	MRPL22-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252508.2		
RTEL1	51750	hgsc.bcm.edu	37	20	62294236	62294236	+	Missense_Mutation	SNP	G	G	A	rs184051277	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:62294236G>A	ENST00000360203.5	+	6	857	c.532G>A	c.(532-534)Gta>Ata	p.V178I	RTEL1_ENST00000370018.3_Missense_Mutation_p.V178I|RTEL1_ENST00000318100.4_Missense_Mutation_p.V178I|RTEL1_ENST00000508582.2_Missense_Mutation_p.V202I|RTEL1-TNFRSF6B_ENST00000482936.1_Missense_Mutation_p.V178I					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)			CTACAACAACGTAGAAGGTAC	0.577													G|||	2	0.000399361	0.0	0.0014	5008	,	,		18896	0.001		0.0	False		,,,				2504	0.0				p.V202I		Atlas-SNP	.											.	RTEL1	114	.	0			c.G604A						PASS	.						85.0	74.0	78.0					20																	62294236		2203	4300	6503	SO:0001583	missense	51750	exon6			AACAACGTAGAAG	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.532G>A	20.37:g.62294236G>A	ENSP00000353332:p.Val178Ile	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	83	29	0.349398	NM_032957		Missense_Mutation	SNP	ENST00000360203.5	37		1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	13.04	2.119146	0.37436	.	.	ENSG00000258366	ENST00000370018;ENST00000318100;ENST00000508582;ENST00000360203;ENST00000356810	T;T;T;T;T	0.70986	-0.53;-0.53;-0.53;-0.53;-0.53	5.05	4.1	0.47936	DEAD2 (1);Helicase-like, DEXD box c2 type (1);Helicase, superfamily 1/2, ATP-binding domain, DinG/Rad3-type (1);	0.137530	0.47455	D	0.000232	T	0.63534	0.2519	L	0.49571	1.57	0.42644	D	0.993425	B;B;B;B	0.33637	0.237;0.129;0.42;0.108	B;B;B;B	0.29942	0.105;0.059;0.109;0.015	T	0.64525	-0.6387	10	0.42905	T	0.14	-13.4976	14.0662	0.64831	0.0739:0.0:0.9261:0.0	.	202;202;178;178	Q9NZ71-7;D6RBA3;Q9NZ71;Q9NZ71-6	.;.;RTEL1_HUMAN;.	I	178;178;202;178;228	ENSP00000359035:V178I;ENSP00000322287:V178I;ENSP00000424307:V202I;ENSP00000353332:V178I;ENSP00000349265:V228I	ENSP00000349265:V228I	V	+	1	0	AL353715.1	61764680	1.000000	0.71417	0.746000	0.31095	0.277000	0.26821	4.731000	0.62022	1.266000	0.44231	0.511000	0.50034	GTA	G|1.000;A|0.000	0.000	strong		0.577	RTEL1-011	NOVEL	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000289781.1	NM_032957	
TAAR6	319100	hgsc.bcm.edu	37	6	132892253	132892253	+	Missense_Mutation	SNP	G	G	A	rs8192624	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:132892253G>A	ENST00000275198.1	+	1	793	c.793G>A	c.(793-795)Gta>Ata	p.V265I		NM_175067.1	NP_778237.1	Q96RI8	TAAR6_HUMAN	trace amine associated receptor 6	265			V -> I (in dbSNP:rs8192624). {ECO:0000269|PubMed:15329799}.		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)|trace-amine receptor activity (GO:0001594)			cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(2)|lung(19)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	41	Breast(56;0.112)			OV - Ovarian serous cystadenocarcinoma(155;0.006)|GBM - Glioblastoma multiforme(226;0.00792)		GGTCACAGTGGTAGCATTTAT	0.413													G|||	286	0.0571086	0.0507	0.0562	5008	,	,		18805	0.0188		0.0865	False		,,,				2504	0.0757				p.V265I		Atlas-SNP	.											.	TAAR6	68	.	0			c.G793A						PASS	.	G	ILE/VAL	277,4129	152.9+/-186.6	8,261,1934	113.0	108.0	110.0		793	-6.0	0.2	6	dbSNP_117	110	694,7906	171.7+/-222.6	25,644,3631	yes	missense	TAAR6	NM_175067.1	29	33,905,5565	AA,AG,GG		8.0698,6.2869,7.4658	benign	265/346	132892253	971,12035	2203	4300	6503	SO:0001583	missense	319100	exon1			ACAGTGGTAGCAT	AF380192	CCDS5155.1	6q23.1	2012-08-08	2005-02-23	2005-02-24	ENSG00000146383	ENSG00000146383		"""GPCR / Class A : Trace amine associated receptors"""	20978	protein-coding gene	gene with protein product		608923	"""trace amine receptor 4"""	TRAR4		11459929, 15718104	Standard	NM_175067		Approved	TA4	uc011eck.2	Q96RI8	OTTHUMG00000015579	ENST00000275198.1:c.793G>A	6.37:g.132892253G>A	ENSP00000275198:p.Val265Ile	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	42	42	1	NM_175067	Q5VUQ4	Missense_Mutation	SNP	ENST00000275198.1	37	CCDS5155.1	121	0.0554029304029304	21	0.042682926829268296	20	0.055248618784530384	14	0.024475524475524476	66	0.0870712401055409	G	8.127	0.782195	0.16189	0.062869	0.080698	ENSG00000146383	ENST00000275198;ENST00000539228	T	0.36699	1.24	5.11	-6.03	0.02185	GPCR, rhodopsin-like superfamily (1);	0.918543	0.08994	N	0.864057	T	0.06096	0.0158	N	0.11364	0.135	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.38993	-0.9635	10	0.45353	T	0.12	-1.6922	10.0006	0.41927	0.5104:0.0903:0.3993:0.0	rs8192624;rs17061455;rs57755475;rs8192624	265	Q96RI8	TAAR6_HUMAN	I	265;240	ENSP00000275198:V265I	ENSP00000275198:V265I	V	+	1	0	TAAR6	132933946	0.000000	0.05858	0.184000	0.23157	0.942000	0.58702	-1.322000	0.02695	-1.264000	0.02452	0.650000	0.86243	GTA	G|0.937;A|0.063	0.063	strong		0.413	TAAR6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042255.1	NM_175067	
ATRNL1	26033	hgsc.bcm.edu	37	10	117075140	117075140	+	Silent	SNP	A	A	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:117075140A>C	ENST00000355044.3	+	18	3057	c.2931A>C	c.(2929-2931)tcA>tcC	p.S977S	ATRNL1_ENST00000423111.2_Silent_p.S74S|ATRNL1_ENST00000303745.7_5'UTR	NM_207303.2	NP_997186.1	Q5VV63	ATRN1_HUMAN	attractin-like 1	977	PSI 5.				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)		AAGGTTCTTCACGGGGACCAA	0.458																																					p.S977S		Atlas-SNP	.											.	ATRNL1	219	.	0			c.A2931C						PASS	.						151.0	134.0	140.0					10																	117075140		2203	4300	6503	SO:0001819	synonymous_variant	26033	exon18			TTCTTCACGGGGA	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.2931A>C	10.37:g.117075140A>C		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	121	27	0.22314	NM_207303	O60283|Q5JSE8|Q5T5Y9|Q6T256|Q6ZSN4|Q86WX2	Silent	SNP	ENST00000355044.3	37	CCDS7592.1	.	.	.	.	.	.	.	.	.	.	A	9.126	1.010135	0.19277	.	.	ENSG00000107518	ENST00000526373	.	.	.	5.34	-3.83	0.04269	.	.	.	.	.	T	0.61974	0.2390	.	.	.	0.53688	D	0.999979	.	.	.	.	.	.	T	0.61806	-0.6987	4	.	.	.	-11.3344	12.8927	0.58080	0.2191:0.6573:0.1236:0.0	.	.	.	.	P	107	.	.	T	+	1	0	ATRNL1	117065130	0.000000	0.05858	0.587000	0.28692	0.980000	0.70556	-2.912000	0.00698	-0.532000	0.06332	0.374000	0.22700	ACG	.	.	none		0.458	ATRNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050507.3	XM_049349	
C17orf77	146723	hgsc.bcm.edu	37	17	72588778	72588778	+	Missense_Mutation	SNP	C	C	T	rs58253413	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:72588778C>T	ENST00000392620.1	+	3	955	c.593C>T	c.(592-594)aCa>aTa	p.T198I	CD300LD_ENST00000375352.1_5'Flank|C17orf77_ENST00000328023.2_Missense_Mutation_p.T198I	NM_152460.2	NP_689673.2	Q96MU5	CQ077_HUMAN	chromosome 17 open reading frame 77	198						extracellular region (GO:0005576)		p.T198I(1)		breast(2)|large_intestine(2)|lung(5)|prostate(1)|stomach(1)	11						ACAGGACTCACACCCAGCCTT	0.602													C|||	549	0.109625	0.1074	0.0692	5008	,	,		19613	0.2024		0.0437	False		,,,				2504	0.1135				p.T198I		Atlas-SNP	.											C17orf77,NS,carcinoma,0,1	C17orf77	31	1	1	Substitution - Missense(1)	stomach(1)	c.C593T						PASS	.	C	ILE/THR	396,4010	198.4+/-222.2	16,364,1823	87.0	84.0	85.0		593	-2.7	0.0	17	dbSNP_129	85	364,8236	120.2+/-179.5	10,344,3946	yes	missense	C17orf77	NM_152460.2	89	26,708,5769	TT,TC,CC		4.2326,8.9877,5.8435	benign	198/244	72588778	760,12246	2203	4300	6503	SO:0001583	missense	146723	exon3			GACTCACACCCAG		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.593C>T	17.37:g.72588778C>T	ENSP00000376396:p.Thr198Ile	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	71	44	0.619718	NM_152460		Missense_Mutation	SNP	ENST00000392620.1	37	CCDS32721.1	224	0.10256410256410256	57	0.11585365853658537	20	0.055248618784530384	112	0.1958041958041958	35	0.04617414248021108	C	2.765	-0.256921	0.05829	0.089877	0.042326	ENSG00000182352	ENST00000392620;ENST00000328023	T;T	0.52754	0.65;0.65	2.29	-2.72	0.05968	.	.	.	.	.	T	0.00039	0.0001	N	0.08118	0	0.80722	P	0.0	B	0.27166	0.17	B	0.30316	0.114	T	0.25328	-1.0135	7	.	.	.	.	3.3787	0.07247	0.0:0.3507:0.2116:0.4378	rs58253413	198	Q96MU5	CQ077_HUMAN	I	198	ENSP00000376396:T198I;ENSP00000329353:T198I	.	T	+	2	0	C17orf77	70100373	0.001000	0.12720	0.000000	0.03702	0.034000	0.12701	-0.120000	0.10660	-0.613000	0.05694	-0.436000	0.05848	ACA	C|0.928;T|0.072	0.072	strong		0.602	C17orf77-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000145090.2	NM_152460	
UBXN11	91544	hgsc.bcm.edu	37	1	26608883	26608883	+	Silent	SNP	A	A	G	rs1134580|rs140364749	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:26608883A>G	ENST00000374222.1	-	16	1934	c.1470T>C	c.(1468-1470)ggT>ggC	p.G490G	UBXN11_ENST00000314675.7_Silent_p.G370G|UBXN11_ENST00000374221.3_Silent_p.G490G|UBXN11_ENST00000374217.2_Silent_p.G457G|UBXN11_ENST00000357089.4_Silent_p.G457G|UBXN11_ENST00000374223.1_Silent_p.G247G			Q5T124	UBX11_HUMAN	UBX domain protein 11	490	3 X 8 AA tandem repeats of P-G-P-G-P-G-P- S.|Pro-rich.		Missing.|Missing. {ECO:0000269|PubMed:14702039, ECO:0000269|Ref.2}.			cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)		p.G490_P515delGPGPSPGPGPGPSPGPGPGPSPCPGP(1)		endometrium(3)|kidney(2)|large_intestine(4)|lung(6)|ovary(2)|prostate(3)|upper_aerodigestive_tract(3)	23						tggggccgggaccgggaccgg	0.711																																					p.G490G		Atlas-SNP	.											UBXN11,NS,carcinoma,-2,2	UBXN11	54	2	1	Deletion - In frame(1)	ovary(1)	c.T1470C						scavenged	.						33.0	42.0	39.0					1																	26608883		1797	4025	5822	SO:0001819	synonymous_variant	91544	exon16			GCCGGGACCGGGA	AF521017	CCDS41286.1, CCDS41287.1, CCDS41288.1	1p36.11	2008-07-25	2008-07-25	2008-07-25	ENSG00000158062	ENSG00000158062		"""UBX domain containing"""	30600	protein-coding gene	gene with protein product	"""socius"""	609151	"""UBX domain containing 5"""	UBXD5		11940653	Standard	NM_183008		Approved	SOC, SOCI	uc001blw.3	Q5T124	OTTHUMG00000003382	ENST00000374222.1:c.1470T>C	1.37:g.26608883A>G		Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	26	9	0.346154	NM_183008	D3DPK6|Q5T117|Q5T120|Q5T125|Q5T126|Q5T129|Q5T131|Q5T133|Q63HM6|Q71RB3|Q8IY27|Q8N1L6|Q8N9M4|Q8NA18|Q8NFE3|Q8NFE4|Q8NFE6	Silent	SNP	ENST00000374222.1	37	CCDS41288.1																																																																																			A|0.773;G|0.227	0.227	strong		0.711	UBXN11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000009500.1	NM_145345	
PRDM7	11105	hgsc.bcm.edu	37	16	90141355	90141355	+	Missense_Mutation	SNP	A	A	C	rs12925933	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:90141355A>C	ENST00000449207.2	-	3	289	c.270T>G	c.(268-270)gaT>gaG	p.D90E	PRDM7_ENST00000407825.1_5'UTR|PRDM7_ENST00000569206.1_5'Flank	NM_001098173.1	NP_001091643.1	Q9NQW5	PRDM7_HUMAN	PR domain containing 7	90			D -> E (in dbSNP:rs12925933). {ECO:0000269|PubMed:17916234}.		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)		CTTCATCGGAATCTTCTGTGT	0.473													.|||	1956	0.390575	0.1551	0.513	5008	,	,		20681	0.1905		0.6779	False		,,,				2504	0.5327				p.D90E		Atlas-SNP	.											.	PRDM7	53	.	0			c.T270G						PASS	.	A	GLU/ASP	887,2885		101,685,1100	121.0	109.0	113.0		270	0.1	0.0	16	dbSNP_121	113	5630,2620		1927,1776,422	yes	missense	PRDM7	NM_001098173.1	45	2028,2461,1522	CC,CA,AA		31.7576,23.5154,45.791	probably-damaging	90/493	90141355	6517,5505	1886	4125	6011	SO:0001583	missense	11105	exon3			ATCGGAATCTTCT	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.270T>G	16.37:g.90141355A>C	ENSP00000396732:p.Asp90Glu	Somatic	276	1	0.00362319		WXS	Illumina HiSeq	Phase_I	348	211	0.606322	NM_001098173	A4Q9G8|Q08EM4|Q9NQW4	Missense_Mutation	SNP	ENST00000449207.2	37	CCDS45557.1	888	0.4065934065934066	64	0.13008130081300814	212	0.585635359116022	114	0.1993006993006993	498	0.6569920844327177	.	15.43	2.832471	0.50845	0.235154	0.682424	ENSG00000126856	ENST00000449207;ENST00000414728	T	0.11495	2.77	1.4	0.141	0.14811	.	.	.	.	.	T	0.00012	0.0000	L	0.44542	1.39	0.58432	P	5.000000000032756E-6	D	0.76494	0.999	D	0.78314	0.991	T	0.40194	-0.9576	7	.	.	.	-5.3786	3.4724	0.07571	0.758:0.0:0.242:0.0	rs12925933;rs17784802;rs58414729;rs12925933	90	Q9NQW5	PRDM7_HUMAN	E	90	ENSP00000396732:D90E	.	D	-	3	2	PRDM7	88668856	1.000000	0.71417	0.017000	0.16124	0.517000	0.34286	1.107000	0.31110	0.019000	0.15079	0.397000	0.26171	GAT	A|0.605;C|0.395	0.395	strong		0.473	PRDM7-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000420560.1		
FGD3	89846	hgsc.bcm.edu	37	9	95782667	95782667	+	Silent	SNP	C	C	T	rs11790517	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:95782667C>T	ENST00000375482.3	+	13	1951	c.1455C>T	c.(1453-1455)ttC>ttT	p.F485F	FGD3_ENST00000538555.1_Silent_p.F88F|FGD3_ENST00000416701.2_Silent_p.F485F|FGD3_ENST00000337352.6_Silent_p.F485F	NM_001083536.1	NP_001077005.1	Q5JSP0	FGD3_HUMAN	FYVE, RhoGEF and PH domain containing 3	485					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)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|ruffle (GO:0001726)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|small GTPase binding (GO:0031267)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(4)|ovary(2)|prostate(1)|urinary_tract(1)	17						GTGGCGCCTTCAGCCAGGATG	0.577													C|||	1414	0.282348	0.3812	0.3876	5008	,	,		16496	0.2411		0.2903	False		,,,				2504	0.1084				p.F485F		Atlas-SNP	.											.	FGD3	116	.	0			c.C1455T						PASS	.	C	,	1536,2680		298,940,870	60.0	66.0	64.0		1455,1455	0.2	0.0	9	dbSNP_120	64	2352,6102		331,1690,2206	no	coding-synonymous,coding-synonymous	FGD3	NM_001083536.1,NM_033086.2	,	629,2630,3076	TT,TC,CC		27.8211,36.4326,30.6867	,	485/726,485/726	95782667	3888,8782	2108	4227	6335	SO:0001819	synonymous_variant	89846	exon13			CGCCTTCAGCCAG	AK000004	CCDS43849.1, CCDS69619.1	9q22	2013-01-10	2004-08-24		ENSG00000127084	ENSG00000127084		"""Zinc fingers, FYVE domain containing"", ""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	16027	protein-coding gene	gene with protein product			"""FGD1 family, member 3"""			11214971	Standard	NM_001083536		Approved	FLJ00004, ZFYVE5	uc004asz.2	Q5JSP0	OTTHUMG00000021032	ENST00000375482.3:c.1455C>T	9.37:g.95782667C>T		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	73	27	0.369863	NM_001083536	F8W7P2|Q4VX84|Q7Z7D9|Q8N5G1	Silent	SNP	ENST00000375482.3	37	CCDS43849.1																																																																																			C|0.684;T|0.316	0.316	strong		0.577	FGD3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055493.1	NM_033086	
DSP	1832	hgsc.bcm.edu	37	6	7585967	7585967	+	Silent	SNP	G	G	C	rs397516968|rs2744380|rs397516967	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:7585967G>C	ENST00000379802.3	+	24	8813	c.8472G>C	c.(8470-8472)ggG>ggC	p.G2824G	DSP_ENST00000418664.2_Silent_p.G2225G	NM_004415.2	NP_004406.2	P15924	DESP_HUMAN	desmoplakin	2824	6 X 4 AA tandem repeats of G-S-R-[SR].|Globular 2.				adherens junction organization (GO:0034332)|apoptotic process (GO:0006915)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|desmosome organization (GO:0002934)|epidermis development (GO:0008544)|intermediate filament organization (GO:0045109)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)|protein localization to adherens junction (GO:0071896)|regulation of heart rate by cardiac conduction (GO:0086091)|single organismal cell-cell adhesion (GO:0016337)|ventricular cardiac muscle cell action potential (GO:0086005)|ventricular compact myocardium morphogenesis (GO:0003223)|wound healing (GO:0042060)	basolateral plasma membrane (GO:0016323)|cornified envelope (GO:0001533)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|intercalated disc (GO:0014704)|intermediate filament (GO:0005882)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)|protein binding, bridging (GO:0030674)|protein kinase C binding (GO:0005080)|scaffold protein binding (GO:0097110)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			biliary_tract(1)|breast(6)|central_nervous_system(7)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(16)|liver(2)|lung(27)|ovary(4)|prostate(1)|skin(8)|stomach(3)|upper_aerodigestive_tract(7)|urinary_tract(5)	101	Ovarian(93;0.0584)	all_hematologic(90;0.236)		OV - Ovarian serous cystadenocarcinoma(45;0.000508)		CGGCTCCGGGGtcccgctccg	0.637													C|||	3553	0.709465	0.6051	0.7478	5008	,	,		14877	0.8046		0.7127	False		,,,				2504	0.7219				p.G2824G		Atlas-SNP	.											.	DSP	306	.	0			c.G8472C						PASS	.	C	,	2780,1626	460.9+/-352.8	882,1016,305	61.0	73.0	69.0		6675,8472	3.0	1.0	6	dbSNP_100	69	6169,2431	391.7+/-343.7	2203,1763,334	no	coding-synonymous,coding-synonymous	DSP	NM_001008844.1,NM_004415.2	,	3085,2779,639	CC,CG,GG		28.2674,36.9042,31.1933	,	2225/2273,2824/2872	7585967	8949,4057	2203	4300	6503	SO:0001819	synonymous_variant	1832	exon24			TCCGGGGTCCCGC	J05211	CCDS4501.1, CCDS47368.1	6p24.3	2014-09-17	2003-05-20		ENSG00000096696	ENSG00000096696			3052	protein-coding gene	gene with protein product		125647	"""desmoplakin (DPI, DPII)"""			1889810	Standard	NM_004415		Approved	KPPS2, PPKS2, DPI, DPII	uc003mxp.1	P15924	OTTHUMG00000014212	ENST00000379802.3:c.8472G>C	6.37:g.7585967G>C		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	41	24	0.585366	NM_004415	B2RTT2|D7RX09|O75993|Q14189|Q9UHN4	Silent	SNP	ENST00000379802.3	37	CCDS4501.1																																																																																			G|0.303;C|0.697	0.697	strong		0.637	DSP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039786.2	NM_004415	
FAM160B2	64760	hgsc.bcm.edu	37	8	21960096	21960096	+	Missense_Mutation	SNP	C	C	T	rs117802113	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:21960096C>T	ENST00000289921.7	+	16	2096	c.2050C>T	c.(2050-2052)Ctc>Ttc	p.L684F		NM_022749.5	NP_073586.5	Q86V87	F16B2_HUMAN	family with sequence similarity 160, member B2	684				L -> F (in Ref. 2; AAH12865/AAH13350). {ECO:0000305}.						endometrium(2)|kidney(1)|lung(2)|prostate(3)|urinary_tract(1)	9						AGGCAAGCTGCTCCTGGTGCG	0.617													.|||	183	0.0365415	0.0076	0.0476	5008	,	,		14506	0.001		0.1233	False		,,,				2504	0.0153				p.L684F		Atlas-SNP	.											.	FAM160B2	35	.	0			c.C2050T						PASS	.	C	PHE/LEU	79,3821		1,77,1872	23.0	26.0	25.0		2050	5.0	1.0	8	dbSNP_132	25	999,7267		43,913,3177	yes	missense	FAM160B2	NM_022749.5	22	44,990,5049	TT,TC,CC		12.0857,2.0256,8.8608	benign	684/744	21960096	1078,11088	1950	4133	6083	SO:0001583	missense	64760	exon16			AAGCTGCTCCTGG	AK025454	CCDS6021.2	8p21.3	2012-11-30	2008-06-05	2008-06-05	ENSG00000158863	ENSG00000158863			16492	protein-coding gene	gene with protein product			"""retinoic acid induced 16"""	RAI16		22971576, 15626329	Standard	XR_247128		Approved	FLJ21801	uc011kyx.2	Q86V87	OTTHUMG00000097088	ENST00000289921.7:c.2050C>T	8.37:g.21960096C>T	ENSP00000289921:p.Leu684Phe	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	70	70	1	NM_022749	B2RDQ5|B3KNX1|Q2M211|Q71JB5|Q7L3J6|Q969T0|Q9H6W4	Missense_Mutation	SNP	ENST00000289921.7	37	CCDS6021.2	116	0.05311355311355311	4	0.008130081300813009	17	0.04696132596685083	1	0.0017482517482517483	94	0.12401055408970976	C	21.7	4.182786	0.78677	0.020256	0.120857	ENSG00000158863	ENST00000289921;ENST00000356512	T	0.57107	0.42	4.98	4.98	0.66077	.	0.075316	0.52532	D	0.000062	T	0.01254	0.0041	M	0.63843	1.955	0.23381	P	0.99779929	P	0.42483	0.781	P	0.44732	0.459	T	0.23583	-1.0184	9	0.49607	T	0.09	-29.1676	15.7616	0.78087	0.0:1.0:0.0:0.0	.	684	Q86V87	F16B2_HUMAN	F	684;102	ENSP00000289921:L684F	ENSP00000289921:L684F	L	+	1	0	FAM160B2	22016041	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	2.353000	0.44089	2.318000	0.78349	0.561000	0.74099	CTC	C|0.945;T|0.055	0.055	strong		0.617	FAM160B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375334.2		
FGFR2	2263	hgsc.bcm.edu	37	10	123279643	123279643	+	Silent	SNP	C	C	T	rs138315382		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:123279643C>T	ENST00000358487.5	-	7	1061	c.789G>A	c.(787-789)ccG>ccA	p.P263P	FGFR2_ENST00000369061.4_Intron|FGFR2_ENST00000346997.2_Silent_p.P263P|FGFR2_ENST00000369059.1_Silent_p.P148P|FGFR2_ENST00000490349.1_5'UTR|FGFR2_ENST00000369060.4_Silent_p.P263P|FGFR2_ENST00000478859.1_Silent_p.P35P|FGFR2_ENST00000360144.3_Silent_p.P174P|FGFR2_ENST00000369056.1_Silent_p.P263P|FGFR2_ENST00000457416.2_Silent_p.P263P|FGFR2_ENST00000356226.4_Silent_p.P148P|FGFR2_ENST00000351936.6_Silent_p.P263P|FGFR2_ENST00000357555.5_Silent_p.P174P	NM_000141.4	NP_000132.3	P21802	FGFR2_HUMAN	fibroblast growth factor receptor 2	263	Ig-like C2-type 3.		P -> L (in CS). {ECO:0000269|PubMed:11173845}.		angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|axonogenesis (GO:0007409)|bone development (GO:0060348)|bone mineralization (GO:0030282)|bone morphogenesis (GO:0060349)|branch elongation involved in salivary gland morphogenesis (GO:0060667)|branching involved in labyrinthine layer morphogenesis (GO:0060670)|branching involved in prostate gland morphogenesis (GO:0060442)|branching involved in salivary gland morphogenesis (GO:0060445)|branching morphogenesis of a nerve (GO:0048755)|bud elongation involved in lung branching (GO:0060449)|cell fate commitment (GO:0045165)|cell-cell signaling (GO:0007267)|coronal suture morphogenesis (GO:0060365)|digestive tract development (GO:0048565)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic organ development (GO:0048568)|embryonic organ morphogenesis (GO:0048562)|embryonic pattern specification (GO:0009880)|endodermal digestive tract morphogenesis (GO:0061031)|epidermal growth factor receptor signaling pathway (GO:0007173)|epidermis morphogenesis (GO:0048730)|epithelial cell differentiation (GO:0030855)|epithelial cell proliferation involved in salivary gland morphogenesis (GO:0060664)|epithelial to mesenchymal transition (GO:0001837)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|fibroblast growth factor receptor signaling pathway involved in hemopoiesis (GO:0035603)|fibroblast growth factor receptor signaling pathway involved in mammary gland specification (GO:0060595)|fibroblast growth factor receptor signaling pathway involved in negative regulation of apoptotic process in bone marrow (GO:0035602)|fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development (GO:0035607)|fibroblast growth factor receptor signaling pathway involved in positive regulation of cell proliferation in bone marrow (GO:0035604)|gland morphogenesis (GO:0022612)|hair follicle morphogenesis (GO:0031069)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|inner ear morphogenesis (GO:0042472)|insulin receptor signaling pathway (GO:0008286)|lacrimal gland development (GO:0032808)|lateral sprouting from an epithelium (GO:0060601)|lens fiber cell development (GO:0070307)|limb bud formation (GO:0060174)|lung alveolus development (GO:0048286)|lung development (GO:0030324)|lung lobe morphogenesis (GO:0060463)|lung-associated mesenchyme development (GO:0060484)|mammary gland bud formation (GO:0060615)|membranous septum morphogenesis (GO:0003149)|mesenchymal cell differentiation (GO:0048762)|mesenchymal cell differentiation involved in lung development (GO:0060915)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesodermal cell differentiation (GO:0048333)|midbrain development (GO:0030901)|morphogenesis of embryonic epithelium (GO:0016331)|multicellular organism growth (GO:0035264)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of mitosis (GO:0045839)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuromuscular junction development (GO:0007528)|neurotrophin TRK receptor signaling pathway (GO:0048011)|odontogenesis (GO:0042476)|orbitofrontal cortex development (GO:0021769)|organ growth (GO:0035265)|organ morphogenesis (GO:0009887)|otic vesicle formation (GO:0030916)|outflow tract septum morphogenesis (GO:0003148)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of epithelial cell proliferation involved in lung morphogenesis (GO:0060501)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of Wnt signaling pathway (GO:0030177)|post-embryonic development (GO:0009791)|prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis (GO:0060527)|prostate epithelial cord elongation (GO:0060523)|prostate gland morphogenesis (GO:0060512)|protein autophosphorylation (GO:0046777)|pyramidal neuron development (GO:0021860)|regulation of branching involved in prostate gland morphogenesis (GO:0060687)|regulation of cell fate commitment (GO:0010453)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)|regulation of morphogenesis of a branching structure (GO:0060688)|regulation of multicellular organism growth (GO:0040014)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoblast proliferation (GO:0033688)|regulation of smooth muscle cell differentiation (GO:0051150)|regulation of smoothened signaling pathway (GO:0008589)|reproductive structure development (GO:0048608)|skeletal system morphogenesis (GO:0048705)|squamous basal epithelial stem cell differentiation involved in prostate gland acinus development (GO:0060529)|synaptic vesicle transport (GO:0048489)|ureteric bud development (GO:0001657)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|ventricular zone neuroblast division (GO:0021847)	cell cortex (GO:0005938)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|excitatory synapse (GO:0060076)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|fibroblast growth factor binding (GO:0017134)|fibroblast growth factor-activated receptor activity (GO:0005007)|heparin binding (GO:0008201)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)			breast(3)|central_nervous_system(3)|cervix(2)|endometrium(98)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(7)|lung(21)|ovary(4)|skin(30)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(2)	181		Lung NSC(174;0.0841)|all_lung(145;0.106)|all_neural(114;0.107)	STAD - Stomach adenocarcinoma(1;7.52e-05)|all cancers(1;0.0722)	all cancers(201;9.73e-05)|GBM - Glioblastoma multiforme(135;0.0845)	Palifermin(DB00039)|Ponatinib(DB08901)|Regorafenib(DB08896)|Thalidomide(DB01041)	AGGCATTTGCCGGCAGTCCGG	0.552		5	Mis		"""gastric. NSCLC, endometrial"""		"""Crouzon, Pfeiffer, and Apert syndromes"""		Saethre-Chotzen syndrome;Apert syndrome				C|||	1	0.000199681	0.0	0.0014	5008	,	,		18486	0.0		0.0	False		,,,				2504	0.0				p.P263P		Atlas-SNP	.		Dom	yes		10	10q26	2263	fibroblast growth factor receptor 2	yes	E	.	FGFR2	758	.	0			c.G789A						PASS	.	C	,,,,,,,,	0,4406		0,0,2203	81.0	68.0	72.0		789,789,,522,444,789,444,522,789	-11.6	0.0	10	dbSNP_134	72	1,8599	1.2+/-3.3	0,1,4299	yes	coding-synonymous,coding-synonymous,intron,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	FGFR2	NM_000141.4,NM_001144913.1,NM_001144914.1,NM_001144915.1,NM_001144916.1,NM_001144917.1,NM_001144918.1,NM_001144919.1,NM_022970.3	,,,,,,,,	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,,,,,,,,	263/822,263/770,,174/708,148/707,263/706,148/705,174/681,263/823	123279643	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	2263	exon7	Familial Cancer Database	Acrocephalosyndactyly type III;Acrocephalosyndactyly type I and II, ACS1. ACS2, incl Apert-Crouzon s.	ATTTGCCGGCAGT	AK026508	CCDS7620.2, CCDS31298.1, CCDS44485.1, CCDS44486.1, CCDS44487.1, CCDS44488.1, CCDS44489.1, CCDS53584.1, CCDS73210.1	10q25.3-q26	2013-01-11	2008-08-01		ENSG00000066468	ENSG00000066468		"""CD molecules"", ""Immunoglobulin superfamily / I-set domain containing"""	3689	protein-coding gene	gene with protein product	"""Crouzon syndrome"", ""Pfeiffer syndrome"""	176943	"""bacteria-expressed kinase"", ""keratinocyte growth factor receptor"", ""craniofacial dysostosis 1"", ""Jackson-Weiss syndrome"""	KGFR, BEK, CFD1, JWS			Standard	NM_022970		Approved	CEK3, TK14, TK25, ECT1, K-SAM, CD332	uc021pzy.1	P21802	OTTHUMG00000019175	ENST00000358487.5:c.789G>A	10.37:g.123279643C>T		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	63	18	0.285714	NM_022970	B4DFC2|E7EVR6|E9PCR0|P18443|Q01742|Q12922|Q14300|Q14301|Q14302|Q14303|Q14304|Q14305|Q14672|Q14718|Q14719|Q1KHY5|Q86YI4|Q8IXC7|Q96KL9|Q96KM0|Q96KM1|Q96KM2|Q9NZU2|Q9NZU3|Q9UD01|Q9UD02|Q9UIH3|Q9UIH4|Q9UIH5|Q9UIH6|Q9UIH7|Q9UIH8|Q9UM87|Q9UMC6|Q9UNS7|Q9UQH7|Q9UQH8|Q9UQH9|Q9UQI0	Silent	SNP	ENST00000358487.5	37	CCDS31298.1																																																																																			C|1.000;T|0.000	0.000	strong		0.552	FGFR2-001	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000050715.1	NM_022976, NM_000141	
STIP1	10963	hgsc.bcm.edu	37	11	63970625	63970625	+	Silent	SNP	G	G	A	rs2070232	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:63970625G>A	ENST00000305218.4	+	12	1458	c.1311G>A	c.(1309-1311)gcG>gcA	p.A437A	STIP1_ENST00000538945.1_Silent_p.A413A|STIP1_ENST00000358794.5_Silent_p.A484A	NM_006819.2	NP_006810.1	P31948	STIP1_HUMAN	stress-induced phosphoprotein 1	437					response to stress (GO:0006950)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(4)|large_intestine(3)|liver(1)|lung(15)|ovary(2)|prostate(1)|skin(1)	27						AAGCCGCTGCGCTGGAAGCGA	0.577													G|||	347	0.0692891	0.0136	0.1239	5008	,	,		20508	0.0456		0.0636	False		,,,				2504	0.136				p.A437A		Atlas-SNP	.											STIP1,NS,carcinoma,+1,1	STIP1	63	1	0			c.G1311A						PASS	.	G		108,4294	83.4+/-121.9	1,106,2094	66.0	64.0	64.0		1311	-5.3	0.1	11	dbSNP_96	64	593,8001	157.5+/-211.1	22,549,3726	no	coding-synonymous	STIP1	NM_006819.2		23,655,5820	AA,AG,GG		6.9002,2.4534,5.394		437/544	63970625	701,12295	2201	4297	6498	SO:0001819	synonymous_variant	10963	exon12			CGCTGCGCTGGAA	BC039299	CCDS8058.1, CCDS60827.1, CCDS60828.1	11q13	2014-01-13	2014-01-13		ENSG00000168439	ENSG00000168439		"""Tetratricopeptide (TTC) repeat domain containing"""	11387	protein-coding gene	gene with protein product	"""Hsp70/Hsp90-organizing protein"""	605063	"""stress-induced-phosphoprotein 1"""			1569099	Standard	NM_006819		Approved	HOP, STI1	uc001nyk.1	P31948	OTTHUMG00000167789	ENST00000305218.4:c.1311G>A	11.37:g.63970625G>A		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	49	35	0.714286	NM_006819	B4DM70|F5H0T1|G3XAD8|Q3ZCU9|Q5TZU9	Silent	SNP	ENST00000305218.4	37	CCDS8058.1																																																																																			A|0.052;C|0.008	0.052	strong		0.577	STIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396289.2	NM_006819	
SPPL2C	162540	hgsc.bcm.edu	37	17	43922640	43922640	+	Missense_Mutation	SNP	G	G	A	rs17763658	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:43922640G>A	ENST00000329196.5	+	1	385	c.368G>A	c.(367-369)cGg>cAg	p.R123Q	MAPT-AS1_ENST00000579244.1_RNA|MAPT-AS1_ENST00000579599.1_RNA|MAPT-AS1_ENST00000581125.1_RNA	NM_175882.2	NP_787078.2	Q8IUH8	SPP2C_HUMAN	signal peptide peptidase like 2C	123	PA.		R -> Q (in dbSNP:rs17763658).			endoplasmic reticulum membrane (GO:0005789)|integral component of cytoplasmic side of endoplasmic reticulum membrane (GO:0071458)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)	aspartic-type endopeptidase activity (GO:0004190)|protein homodimerization activity (GO:0042803)										ATCGTGAGCCGGGTCAGTGAC	0.637													G|||	454	0.090655	0.0734	0.0663	5008	,	,		17382	0.1181		0.0805	False		,,,				2504	0.1135				p.R123Q		Atlas-SNP	.											.	.	.	.	0			c.G368A						PASS	.	G	GLN/ARG	344,4062	178.0+/-206.8	15,314,1874	53.0	53.0	53.0		368	0.5	0.1	17	dbSNP_123	53	589,8011	155.8+/-209.8	23,543,3734	yes	missense	IMP5	NM_175882.2	43	38,857,5608	AA,AG,GG		6.8488,7.8075,7.1736	probably-damaging	123/685	43922640	933,12073	2203	4300	6503	SO:0001583	missense	162540	exon1			TGAGCCGGGTCAG		CCDS32673.1	17q21.31	2014-02-12			ENSG00000185294	ENSG00000185294			28902	protein-coding gene	gene with protein product	"""intramembrane protease 5"""	608284				12139484	Standard	NM_175882		Approved	IMP5	uc010wka.2	Q8IUH8		ENST00000329196.5:c.368G>A	17.37:g.43922640G>A	ENSP00000332488:p.Arg123Gln	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	102	47	0.460784	NM_175882	Q8TC67|Q8WVZ6	Missense_Mutation	SNP	ENST00000329196.5	37	CCDS32673.1	191	0.08745421245421245	39	0.07926829268292683	29	0.08011049723756906	63	0.11013986013986014	60	0.079155672823219	G	8.681	0.905052	0.17760	0.078075	0.068488	ENSG00000185294	ENST00000329196	T	0.07688	3.17	4.64	0.472	0.16758	Protease-associated domain, PA (1);	0.368339	0.19781	N	0.106216	T	0.00241	0.0007	L	0.49350	1.555	0.26367	P	0.9769541	P	0.52842	0.956	P	0.51453	0.67	T	0.19943	-1.0290	9	0.37606	T	0.19	-3.1037	6.8244	0.23874	0.3859:0.0:0.6141:0.0	rs17763658;rs52794767;rs17763658	123	Q8IUH8	IMP5_HUMAN	Q	123	ENSP00000332488:R123Q	ENSP00000332488:R123Q	R	+	2	0	AC217771.1	41278420	1.000000	0.71417	0.141000	0.22245	0.005000	0.04900	1.345000	0.33953	-0.018000	0.14079	-0.808000	0.03180	CGG	G|0.922;A|0.078	0.078	strong		0.637	SPPL2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441156.1	NM_175882	
BCKDHA	593	hgsc.bcm.edu	37	19	41932063	41932063	+	IGR	SNP	A	A	G	rs45563938	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:41932063A>G	ENST00000269980.2	+	0	2103				CTC-435M10.6_ENST00000598887.1_RNA|B3GNT8_ENST00000321702.2_Silent_p.S207S|B3GNT8_ENST00000601379.1_5'UTR	NM_000709.3|NM_001164783.1	NP_000700.1|NP_001158255.1	P12694	ODBA_HUMAN	branched chain keto acid dehydrogenase E1, alpha polypeptide						branched-chain amino acid catabolic process (GO:0009083)|cellular nitrogen compound metabolic process (GO:0034641)|response to cAMP (GO:0051591)|response to glucocorticoid (GO:0051384)|response to nutrient (GO:0007584)|small molecule metabolic process (GO:0044281)	mitochondrial alpha-ketoglutarate dehydrogenase complex (GO:0005947)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) activity (GO:0003863)|alpha-ketoacid dehydrogenase activity (GO:0003826)|carboxy-lyase activity (GO:0016831)|metal ion binding (GO:0046872)			central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(4)|prostate(1)	10						GCAGCAGGTCACTGTAGCGAC	0.647													A|||	314	0.0626997	0.0257	0.0778	5008	,	,		15953	0.001		0.1272	False		,,,				2504	0.0992				p.S207S		Atlas-SNP	.											.	B3GNT8	20	.	0			c.T621C						PASS	.	A		167,4239	111.2+/-149.4	4,159,2040	66.0	67.0	67.0		621	-4.0	0.2	19	dbSNP_127	67	1206,7394	243.9+/-273.3	94,1018,3188	no	coding-synonymous	B3GNT8	NM_198540.2		98,1177,5228	GG,GA,AA		14.0233,3.7903,10.5567		207/398	41932063	1373,11633	2203	4300	6503	SO:0001628	intergenic_variant	374907	exon3			CAGGTCACTGTAG	J04474	CCDS12581.1	19q13.1-q13.2	2008-07-09	2005-11-29		ENSG00000248098	ENSG00000248098			986	protein-coding gene	gene with protein product	"""maple syrup urine disease"""	608348	"""branched chain keto acid dehydrogenase E1, alpha polypeptide (maple syrup urine disease)"", ""2-oxoisovalerate dehydrogenase (lipoamide)"""	OVD1A			Standard	NM_000709		Approved	MSU	uc002oqq.3	P12694	OTTHUMG00000168128		19.37:g.41932063A>G		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	78	34	0.435897	NM_198540	B4DP47|E7EW46|Q16034|Q16472	Silent	SNP	ENST00000269980.2	37	CCDS12581.1																																																																																			A|0.905;G|0.095	0.095	strong		0.647	BCKDHA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398313.3	NM_000709	
ZNF280D	54816	hgsc.bcm.edu	37	15	56959028	56959028	+	Missense_Mutation	SNP	C	C	T	rs28620278	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:56959028C>T	ENST00000267807.7	-	15	1918	c.1702G>A	c.(1702-1704)Gtc>Atc	p.V568I	ZNF280D_ENST00000559237.1_Missense_Mutation_p.V555I|ZNF280D_ENST00000559000.1_Missense_Mutation_p.V555I|ZNF280D_ENST00000396245.1_Missense_Mutation_p.V272I	NM_017661.2	NP_060131.2	Q6N043	Z280D_HUMAN	zinc finger protein 280D	568			V -> I (in dbSNP:rs28620278). {ECO:0000269|PubMed:10997877, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005}.		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(5)|kidney(4)|large_intestine(7)|lung(12)|ovary(1)|skin(1)	30				all cancers(107;0.0399)|GBM - Glioblastoma multiforme(80;0.0787)		TTGGATTTGACTGTATTAGGT	0.333													T|||	2640	0.527157	0.7141	0.6225	5008	,	,		15602	0.3829		0.4066	False		,,,				2504	0.4796				p.V568I		Atlas-SNP	.											.	ZNF280D	82	.	0			c.G1702A						PASS	.	T	ILE/VAL,ILE/VAL	2803,1581	486.2+/-360.5	917,969,306	139.0	145.0	143.0		1663,1702	-0.9	0.0	15	dbSNP_125	143	3481,5103	631.5+/-398.5	697,2087,1508	yes	missense,missense	ZNF280D	NM_001002843.1,NM_017661.2	29,29	1614,3056,1814	TT,TC,CC		40.5522,36.063,48.4577	benign,benign	555/967,568/980	56959028	6284,6684	2192	4292	6484	SO:0001583	missense	54816	exon15			ATTTGACTGTATT	AB046804	CCDS32245.1, CCDS42041.1, CCDS58364.1	15q21.2	2008-05-02	2007-09-20	2007-09-20					25953	protein-coding gene	gene with protein product			"""suppressor of hairy wing homolog 4 (Drosophila)"""	SUHW4		10997877	Standard	XM_005254481		Approved	FLJ20086, ZNF634	uc002adu.3	Q6N043		ENST00000267807.7:c.1702G>A	15.37:g.56959028C>T	ENSP00000267807:p.Val568Ile	Somatic	328	0	0		WXS	Illumina HiSeq	Phase_I	313	169	0.539936	NM_017661	A1L495|B2RMT6|Q6MZM6|Q6N085|Q6P2R6|Q7Z6J5|Q9H0U5|Q9HCI8|Q9NXS0	Missense_Mutation	SNP	ENST00000267807.7	37	CCDS32245.1	1099	0.5032051282051282	370	0.7520325203252033	214	0.5911602209944752	225	0.39335664335664333	290	0.38258575197889183	T	1.441	-0.567698	0.03910	0.63937	0.405522	ENSG00000137871	ENST00000267807;ENST00000455329;ENST00000396245	T;T	0.03004	4.08;4.5	4.58	-0.931	0.10438	.	.	.	.	.	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B	0.09022	0.002	B	0.04013	0.001	T	0.05305	-1.0893	8	0.17832	T	0.49	0.0847	6.768	0.23579	0.0:0.4082:0.1329:0.459	rs28620278;rs28620278	568	Q6N043	Z280D_HUMAN	I	568;555;272	ENSP00000267807:V568I;ENSP00000379545:V272I	ENSP00000267807:V568I	V	-	1	0	ZNF280D	54746320	0.059000	0.20769	0.018000	0.16275	0.511000	0.34104	-0.286000	0.08399	-0.282000	0.09128	-0.332000	0.08345	GTC	C|0.495;T|0.505	0.505	strong		0.333	ZNF280D-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000418891.2	XM_370867	
C9orf114	51490	hgsc.bcm.edu	37	9	131588888	131588888	+	Missense_Mutation	SNP	G	G	C	rs6478854	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:131588888G>C	ENST00000361256.5	-	5	429	c.389C>G	c.(388-390)aCa>aGa	p.T130R		NM_016390.3	NP_057474.2	Q5T280	CI114_HUMAN	chromosome 9 open reading frame 114	130			T -> R (in dbSNP:rs6478854). {ECO:0000269|PubMed:15489334}.				poly(A) RNA binding (GO:0044822)			kidney(2)|large_intestine(4)|ovary(1)	7						CCCAACTCCTGTGAATTCCCC	0.587													G|||	2311	0.461462	0.7602	0.2536	5008	,	,		18444	0.3601		0.2942	False		,,,				2504	0.4816				p.T130R		Atlas-SNP	.											.	C9orf114	28	.	0			c.C389G						PASS	.	G	ARG/THR	2973,1433	683.1+/-404.2	996,981,226	56.0	56.0	56.0		389	-4.3	0.9	9	dbSNP_116	56	2493,6107	409.2+/-349.7	337,1819,2144	yes	missense	C9orf114	NM_016390.2	71	1333,2800,2370	CC,CG,GG		28.9884,32.5238,42.0268	benign	130/377	131588888	5466,7540	2203	4300	6503	SO:0001583	missense	51490	exon5			ACTCCTGTGAATT		CCDS6913.1	9q34.11	2014-05-29			ENSG00000198917	ENSG00000198917			26933	protein-coding gene	gene with protein product	"""centromere protein 32"""					20813266	Standard	NM_016390		Approved	HSPC109, CENP-32	uc004bwd.3	Q5T280	OTTHUMG00000020762	ENST00000361256.5:c.389C>G	9.37:g.131588888G>C	ENSP00000354812:p.Thr130Arg	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	60	26	0.433333	NM_016390	Q0D2P6|Q6P469|Q6PGP9|Q6PIJ1|Q6PJV9	Missense_Mutation	SNP	ENST00000361256.5	37	CCDS6913.1	870|870	0.3983516483516483|0.3983516483516483	370|370	0.7520325203252033|0.7520325203252033	101|101	0.27900552486187846|0.27900552486187846	208|208	0.36363636363636365|0.36363636363636365	191|191	0.2519788918205805|0.2519788918205805	G|G	10.12|10.12	1.263936|1.263936	0.23136|0.23136	0.674762|0.674762	0.289884|0.289884	ENSG00000198917|ENSG00000198917	ENST00000372618|ENST00000361256	.|T	.|0.41065	.|1.01	5.62|5.62	-4.31|-4.31	0.03698|0.03698	.|.	0.428510|.	0.28914|.	N|.	0.013729|.	T|T	0.00012|0.00012	0.0000|0.0000	L|L	0.39633|0.39633	1.23|1.23	0.52099|0.52099	P|P	5.999999999994898E-5|5.999999999994898E-5	.|B	.|0.02656	.|0.0	.|B	.|0.06405	.|0.002	T|T	0.44436|0.44436	-0.9328|-0.9328	6|8	0.02654|0.15952	T|T	1|0.53	-0.1618|-0.1618	1.7504|1.7504	0.02970|0.02970	0.2463:0.1486:0.1088:0.4963|0.2463:0.1486:0.1088:0.4963	rs6478854;rs11540575;rs17855860;rs56866944;rs6478854|rs6478854;rs11540575;rs17855860;rs56866944;rs6478854	.|130	.|Q5T280	.|CI114_HUMAN	E|R	130|130	.|ENSP00000354812:T130R	ENSP00000361701:Q130E|ENSP00000354812:T130R	Q|T	-|-	1|2	0|0	C9orf114|C9orf114	130628709|130628709	0.001000|0.001000	0.12720|0.12720	0.892000|0.892000	0.35008|0.35008	0.880000|0.880000	0.50808|0.50808	-0.159000|-0.159000	0.10056|0.10056	-0.654000|-0.654000	0.05394|0.05394	-0.143000|-0.143000	0.13931|0.13931	CAG|ACA	G|0.583;C|0.417	0.417	strong		0.587	C9orf114-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054500.1	NM_016390	
ITIH1	3697	hgsc.bcm.edu	37	3	52821011	52821011	+	Missense_Mutation	SNP	A	A	G	rs1042779	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:52821011A>G	ENST00000273283.2	+	14	1808	c.1784A>G	c.(1783-1785)cAg>cGg	p.Q595R	ITIH1_ENST00000542827.1_Missense_Mutation_p.Q595R|ITIH1_ENST00000540715.1_Missense_Mutation_p.Q453R|ITIH1_ENST00000405128.3_5'Flank|ITIH1_ENST00000537050.1_Missense_Mutation_p.Q307R	NM_002215.3	NP_002206.2	P19827	ITIH1_HUMAN	inter-alpha-trypsin inhibitor heavy chain 1	595	Hyaluronan-binding.		Q -> R (in allele ITIH1*2 and allele ITIH1*3; dbSNP:rs1042779). {ECO:0000269|PubMed:1380832, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:7535743}.		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)		CAGGCCCTGCAGATGTCGCTG	0.617													G|||	2127	0.42472	0.5393	0.487	5008	,	,		17314	0.379		0.3986	False		,,,				2504	0.2996				p.Q595R		Atlas-SNP	.											.	ITIH1	108	.	0			c.A1784G						PASS	.	G	ARG/GLN,ARG/GLN,ARG/GLN,ARG/GLN	2127,2279	597.4+/-388.9	508,1111,584	91.0	84.0	86.0	http://www.ncbi.nlm.nih.gov/pubmed?term	1358,920,920,1784	3.0	0.4	3	dbSNP_86	86	3330,5270	645.1+/-400.1	670,1990,1640	yes	missense,missense,missense,missense	ITIH1	NM_001166434.1,NM_001166435.1,NM_001166436.1,NM_002215.2	43,43,43,43	1178,3101,2224	GG,GA,AA	http://www.ncbi.nlm.nih.gov/pubmed?term	38.7209,48.2751,41.9576	benign,benign,benign,benign	453/770,307/624,307/624,595/912	52821011	5457,7549	2203	4300	6503	SO:0001583	missense	3697	exon14			CCCTGCAGATGTC		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.1784A>G	3.37:g.52821011A>G	ENSP00000273283:p.Gln595Arg	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	111	110	0.990991	NM_002215	A8K9N5|B2RAH9|B7Z558|B7Z8C0|F5H165|F5H7Y8|P78455|Q01746|Q562G1	Missense_Mutation	SNP	ENST00000273283.2	37	CCDS2864.1	1006	0.4606227106227106	271	0.5508130081300813	176	0.4861878453038674	254	0.44405594405594406	305	0.4023746701846966	G	4.384	0.070936	0.08436	0.482751	0.387209	ENSG00000055957	ENST00000542827;ENST00000273283;ENST00000540715;ENST00000537050;ENST00000428133	T;T;T;T;T	0.29917	1.55;1.55;1.55;1.55;1.55	5.44	2.96	0.34315	.	0.733154	0.14237	N	0.332314	T	0.00012	0.0000	M	0.68593	2.085	0.80722	P	0.0	B;B;B	0.24882	0.008;0.113;0.0	B;B;B	0.22880	0.042;0.033;0.002	T	0.41998	-0.9477	9	0.27082	T	0.32	-3.4004	7.1456	0.25581	0.7294:0.1253:0.1452:0.0	rs1042779;rs3182234;rs17418937;rs52791326;rs57378468;rs1042779	453;196;595	F5H165;Q9P1C5;P19827	.;.;ITIH1_HUMAN	R	595;595;453;307;148	ENSP00000442584:Q595R;ENSP00000273283:Q595R;ENSP00000443973:Q453R;ENSP00000443847:Q307R;ENSP00000395836:Q148R	ENSP00000273283:Q595R	Q	+	2	0	ITIH1	52796051	1.000000	0.71417	0.438000	0.26821	0.003000	0.03518	2.813000	0.48002	0.165000	0.19558	-1.088000	0.02184	CAG	A|0.564;G|0.436	0.436	strong		0.617	ITIH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317522.1	NM_002215	
SIRPD	128646	hgsc.bcm.edu	37	20	1538249	1538249	+	Silent	SNP	C	C	T	rs2250055	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:1538249C>T	ENST00000381623.3	-	1	1240	c.51G>A	c.(49-51)ctG>ctA	p.L17L	RP4-576H24.4_ENST00000564763.1_Intron|SIRPD_ENST00000381621.1_Silent_p.L17L			Q9H106	SIRPD_HUMAN	signal-regulatory protein delta	17						extracellular region (GO:0005576)				breast(1)|kidney(2)|large_intestine(3)|lung(6)|ovary(2)|skin(1)	15						GCAGCAGATACAGCAGTAAGG	0.572													C|||	536	0.107029	0.0219	0.1153	5008	,	,		17762	0.0188		0.2306	False		,,,				2504	0.18				p.L17L		Atlas-SNP	.											.	SIRPD	34	.	0			c.G51A						PASS	.	C		252,4154		10,232,1961	238.0	176.0	197.0		51	-0.0	0.2	20	dbSNP_100	197	2055,6545		254,1547,2499	yes	coding-synonymous	SIRPD	NM_178460.2		264,1779,4460	TT,TC,CC		23.8953,5.7195,17.738		17/198	1538249	2307,10699	2203	4300	6503	SO:0001819	synonymous_variant	128646	exon1			CAGATACAGCAGT	AL049634	CCDS13018.1	20p13	2013-01-11	2006-02-03	2006-02-03	ENSG00000125900	ENSG00000125900		"""Signal-regulatory proteins"", ""Immunoglobulin superfamily / V-set domain containing"""	16248	protein-coding gene	gene with protein product			"""protein tyrosine phosphatase, non-receptor type substrate 1-like 2"""	PTPNS1L2		16339511	Standard	NM_178460		Approved	dJ576H24.4	uc002wfi.3	Q9H106	OTTHUMG00000031674	ENST00000381623.3:c.51G>A	20.37:g.1538249C>T		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	59	22	0.372881	NM_178460	B3KS88|Q5TFQ6	Silent	SNP	ENST00000381623.3	37	CCDS13018.1																																																																																			C|0.856;T|0.144	0.144	strong		0.572	SIRPD-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000077552.1	NM_178460	
ARHGEF19	128272	hgsc.bcm.edu	37	1	16532803	16532803	+	Silent	SNP	G	G	A	rs221050	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:16532803G>A	ENST00000270747.3	-	7	1306	c.1170C>T	c.(1168-1170)tcC>tcT	p.S390S	ARHGEF19_ENST00000478117.1_5'UTR	NM_153213.3	NP_694945.2	Q8IW93	ARHGJ_HUMAN	Rho guanine nucleotide exchange factor (GEF) 19	390	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				regulation of actin cytoskeleton organization (GO:0032956)|wound healing (GO:0042060)		GTPase activator activity (GO:0005096)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			cervix(1)|endometrium(1)|lung(3)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	12		Colorectal(325;0.000147)|Renal(390;0.00145)|Breast(348;0.00224)|Lung NSC(340;0.00566)|all_lung(284;0.00831)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.018)|Colorectal(212;3.48e-07)|COAD - Colon adenocarcinoma(227;2.19e-05)|BRCA - Breast invasive adenocarcinoma(304;9.46e-05)|Kidney(64;0.000171)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(313;0.0117)|READ - Rectum adenocarcinoma(331;0.0649)		TGTGGATGTAGGAGGCCTCGG	0.622													G|||	1346	0.26877	0.1747	0.4049	5008	,	,		13256	0.1518		0.2654	False		,,,				2504	0.4233				p.S390S		Atlas-SNP	.											.	ARHGEF19	49	.	0			c.C1170T						PASS	.	G		786,3618		80,626,1496	32.0	29.0	30.0		1170	-9.7	0.6	1	dbSNP_79	30	2186,6404		297,1592,2406	no	coding-synonymous	ARHGEF19	NM_153213.3		377,2218,3902	AA,AG,GG		25.4482,17.8474,22.8721		390/803	16532803	2972,10022	2202	4295	6497	SO:0001819	synonymous_variant	128272	exon7			GATGTAGGAGGCC	BC012982	CCDS170.1	1p36.13	2011-11-16			ENSG00000142632	ENSG00000142632		"""Rho guanine nucleotide exchange factors"""	26604	protein-coding gene	gene with protein product		612496				12477932	Standard	NM_153213		Approved	FLJ33962, WGEF	uc001ayc.1	Q8IW93	OTTHUMG00000002219	ENST00000270747.3:c.1170C>T	1.37:g.16532803G>A		Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	107	48	0.448598	NM_153213	A6NJ04|Q5TEV2|Q6PJQ4|Q8N244	Silent	SNP	ENST00000270747.3	37	CCDS170.1	485	0.22206959706959706	79	0.16056910569105692	123	0.3397790055248619	73	0.12762237762237763	210	0.2770448548812665	G	11.21	1.571221	0.28003	0.178474	0.254482	ENSG00000142632	ENST00000449495	.	.	.	4.85	-9.7	0.00521	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.999999999926941	.	.	.	.	.	.	T	0.06197	-1.0840	3	.	.	.	.	12.7933	0.57547	0.0:0.2802:0.5479:0.1719	rs221050;rs3738623	.	.	.	L	79	.	.	P	-	2	0	ARHGEF19	16405390	0.005000	0.15991	0.630000	0.29268	0.995000	0.86356	-1.891000	0.01611	-2.358000	0.00611	0.555000	0.69702	CCT	G|0.786;A|0.214	0.214	strong		0.622	ARHGEF19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006289.1	NM_153213	
KIAA1522	57648	hgsc.bcm.edu	37	1	33235651	33235651	+	Missense_Mutation	SNP	A	A	G	rs12730560	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:33235651A>G	ENST00000373480.1	+	6	797	c.694A>G	c.(694-696)Atg>Gtg	p.M232V	KIAA1522_ENST00000373481.3_Missense_Mutation_p.M243V|KIAA1522_ENST00000401073.2_Missense_Mutation_p.M291V|KIAA1522_ENST00000294521.3_Intron	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	107	0	0		WXS	Illumina HiSeq	Phase_I	124	67	0.540323	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		
CRIPAK	285464	hgsc.bcm.edu	37	4	1388697	1388697	+	Missense_Mutation	SNP	C	C	T	rs113316888	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:1388697C>T	ENST00000324803.4	+	1	3358	c.398C>T	c.(397-399)gCg>gTg	p.A133V		NM_175918.3	NP_787114.2	Q8N1N5	CRPAK_HUMAN	cysteine-rich PAK1 inhibitor	133					negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of protein kinase activity (GO:0006469)|regulation of cytoskeleton organization (GO:0051493)|response to estrogen (GO:0043627)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(3)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(11)|ovary(1)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(1)	35			OV - Ovarian serous cystadenocarcinoma(23;0.0106)			CGTGCCCATGCGGAGTGCCCG	0.701													N|||	623	0.124401	0.1399	0.1527	5008	,	,		12463	0.2083		0.0736	False		,,,				2504	0.0491				p.A133V		Atlas-SNP	.											CRIPAK,NS,carcinoma,0,1	CRIPAK	185	1	0			c.C398T						scavenged	.						57.0	58.0	58.0					4																	1388697		2192	4288	6480	SO:0001583	missense	285464	exon1			CCCATGCGGAGTG	AK096209	CCDS3349.1	4p16.3	2011-02-10	2006-09-04		ENSG00000179979	ENSG00000179979			26619	protein-coding gene	gene with protein product		610203	"""cysteine-rich PAK1inhibitor"""			16278681	Standard	NM_175918		Approved	FLJ34443	uc003gdf.2	Q8N1N5	OTTHUMG00000121131	ENST00000324803.4:c.398C>T	4.37:g.1388697C>T	ENSP00000323978:p.Ala133Val	Somatic	42	1	0.0238095		WXS	Illumina HiSeq	Phase_I	25	8	0.32	NM_175918	Q8NB03	Missense_Mutation	SNP	ENST00000324803.4	37	CCDS3349.1	.	.	.	.	.	.	.	.	.	.	-	11.32	1.604146	0.28534	.	.	ENSG00000179979	ENST00000324803	T	0.18810	2.19	0.948	-1.08	0.09936	.	.	.	.	.	T	0.06645	0.0170	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.34378	-0.9831	9	0.02654	T	1	.	2.1758	0.03862	0.2485:0.1979:0.0:0.5536	.	133	Q8N1N5	CRPAK_HUMAN	V	133	ENSP00000323978:A133V	ENSP00000323978:A133V	A	+	2	0	CRIPAK	1378697	0.001000	0.12720	0.001000	0.08648	0.006000	0.05464	-2.200000	0.01237	-1.804000	0.01241	-1.950000	0.00486	GCG	C|0.500;T|0.500	0.500	weak		0.701	CRIPAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241607.2	NM_175918	
SOAT1	6646	hgsc.bcm.edu	37	1	179310439	179310439	+	Silent	SNP	C	C	T	rs7547733	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:179310439C>T	ENST00000367619.3	+	7	917	c.774C>T	c.(772-774)ttC>ttT	p.F258F	SOAT1_ENST00000539888.1_Silent_p.F193F|SOAT1_ENST00000540564.1_Silent_p.F200F|SOAT1_ENST00000535686.1_5'UTR	NM_003101.5	NP_003092.4	P35610	SOAT1_HUMAN	sterol O-acyltransferase 1	258					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)	TCATTATATTCGAGCAGGTAA	0.373													C|||	331	0.0660942	0.0061	0.1167	5008	,	,		17814	0.0		0.2087	False		,,,				2504	0.0327				p.F258F		Atlas-SNP	.											.	SOAT1	53	.	0			c.C774T						PASS	.	C		179,4227	112.1+/-150.2	3,173,2027	130.0	129.0	129.0		774	-6.3	0.0	1	dbSNP_116	129	1684,6914	287.5+/-298.3	163,1358,2778	no	coding-synonymous	SOAT1	NM_003101.4		166,1531,4805	TT,TC,CC		19.586,4.0626,14.3264		258/551	179310439	1863,11141	2203	4299	6502	SO:0001819	synonymous_variant	6646	exon7			TATATTCGAGCAG	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.774C>T	1.37:g.179310439C>T		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	83	42	0.506024	NM_003101	A6NC40|A8K3P4|A9Z1V7|B4DU95|Q5T0X4|Q8N1E4	Silent	SNP	ENST00000367619.3	37	CCDS1330.1																																																																																			C|0.881;T|0.119	0.119	strong		0.373	SOAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085286.2	NM_003101	
MUC4	4585	hgsc.bcm.edu	37	3	195513433	195513433	+	Missense_Mutation	SNP	G	G	A	rs74419078	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195513433G>A	ENST00000463781.3	-	2	5477	c.5018C>T	c.(5017-5019)gCa>gTa	p.A1673V	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.A1673V	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.A1673V(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)		ACCGGTGGATGCTGAGGAAGT	0.597													.|||	524	0.104633	0.1573	0.0576	5008	,	,		20654	0.0972		0.0954	False		,,,				2504	0.0838				p.A1673V		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	2	Substitution - Missense(2)	stomach(2)	c.C5018T						scavenged	.						37.0	35.0	36.0					3																	195513433		689	1584	2273	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.5018C>T	3.37:g.195513433G>A	ENSP00000417498:p.Ala1673Val	Somatic	183	1	0.00546448		WXS	Illumina HiSeq	Phase_I	159	67	0.421384	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	-	7.616	0.675809	0.14841	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.30714	1.52;1.56	0.595	-1.19	0.09585	.	.	.	.	.	T	0.09992	0.0245	N	0.02539	-0.55	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.27262	-1.0079	8	.	.	.	.	5.415	0.16368	0.571:0.0:0.429:0.0	.	1673	E7ESK3	.	V	1673	ENSP00000417498:A1673V;ENSP00000420243:A1673V	.	A	-	2	0	MUC4	196997828	0.000000	0.05858	0.001000	0.08648	0.006000	0.05464	-1.992000	0.01476	-2.026000	0.00934	-2.047000	0.00414	GCA	G|0.986;A|0.014	0.014	strong		0.597	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
RAVER2	55225	hgsc.bcm.edu	37	1	65243466	65243466	+	Silent	SNP	A	A	G	rs41285400	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:65243466A>G	ENST00000294428.3	+	3	555	c.477A>G	c.(475-477)gaA>gaG	p.E159E	RAVER2_ENST00000430964.2_5'Flank|RAVER2_ENST00000371072.4_Silent_p.E159E			Q9HCJ3	RAVR2_HUMAN	ribonucleoprotein, PTB-binding 2	159	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.					cytoplasm (GO:0005737)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(2)|kidney(1)|large_intestine(7)|lung(6)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	24						AAGAGTTTGAAGAACTTGTTC	0.368													A|||	13	0.00259585	0.0015	0.0029	5008	,	,		18846	0.001		0.007	False		,,,				2504	0.001				p.E159E		Atlas-SNP	.											.	RAVER2	56	.	0			c.A477G						PASS	.	A		9,3707		0,9,1849	208.0	187.0	194.0		477	1.4	1.0	1	dbSNP_127	194	119,8097		0,119,3989	no	coding-synonymous	RAVER2	NM_018211.3		0,128,5838	GG,GA,AA		1.4484,0.2422,1.0727		159/679	65243466	128,11804	1858	4108	5966	SO:0001819	synonymous_variant	55225	exon3			GTTTGAAGAACTT	AB046799	CCDS41345.1	1p31.3	2013-02-12			ENSG00000162437	ENSG00000162437		"""RNA binding motif (RRM) containing"""	25577	protein-coding gene	gene with protein product		609953				16051233	Standard	NM_018211		Approved	KIAA1579, FLJ10770	uc001dbs.2	Q9HCJ3	OTTHUMG00000009102	ENST00000294428.3:c.477A>G	1.37:g.65243466A>G		Somatic	249	0	0		WXS	Illumina HiSeq	Phase_I	237	120	0.506329	NM_018211	Q6P141|Q9NPV7	Silent	SNP	ENST00000294428.3	37																																																																																				A|0.994;G|0.006	0.006	strong		0.368	RAVER2-201	KNOWN	basic	protein_coding	protein_coding		NM_018211	
MAT1A	4143	hgsc.bcm.edu	37	10	82033594	82033594	+	Silent	SNP	G	G	A	rs2993763	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:82033594G>A	ENST00000372213.3	-	9	1391	c.1131C>T	c.(1129-1131)taC>taT	p.Y377Y	MAT1A_ENST00000485270.1_5'UTR	NM_000429.2	NP_000420.1	Q00266	METK1_HUMAN	methionine adenosyltransferase I, alpha	377					cellular amino acid metabolic process (GO:0006520)|cellular nitrogen compound metabolic process (GO:0034641)|methylation (GO:0032259)|one-carbon metabolic process (GO:0006730)|S-adenosylmethionine biosynthetic process (GO:0006556)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|methionine adenosyltransferase activity (GO:0004478)			endometrium(4)|large_intestine(7)|lung(10)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	26			Colorectal(32;0.229)		L-Methionine(DB00134)|S-Adenosylmethionine(DB00118)	CGAAATGGCCGTAGCATGCTG	0.552													G|||	2939	0.586861	0.7874	0.5187	5008	,	,		17763	0.4861		0.4245	False		,,,				2504	0.635				p.Y377Y		Atlas-SNP	.											.	MAT1A	52	.	0			c.C1131T						PASS	.	G		3186,1220	707.5+/-407.5	1155,876,172	189.0	176.0	180.0		1131	-8.9	0.5	10	dbSNP_101	180	3810,4790	539.6+/-383.6	817,2176,1307	no	coding-synonymous	MAT1A	NM_000429.2		1972,3052,1479	AA,AG,GG		44.3023,27.6895,46.2094		377/396	82033594	6996,6010	2203	4300	6503	SO:0001819	synonymous_variant	4143	exon9			ATGGCCGTAGCAT		CCDS7365.1	10q22	2008-08-01			ENSG00000151224	ENSG00000151224			6903	protein-coding gene	gene with protein product	"""S-adenosylmethionine synthetase"""	610550				8393662	Standard	XM_005269842		Approved	MAT, SAMS, MATA1, SAMS1	uc001kbw.3	Q00266	OTTHUMG00000018613	ENST00000372213.3:c.1131C>T	10.37:g.82033594G>A		Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	131	60	0.458015	NM_000429	D3DWD5|Q5QP09	Silent	SNP	ENST00000372213.3	37	CCDS7365.1																																																																																			G|0.458;A|0.542	0.542	strong		0.552	MAT1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049070.1	NM_000429	
AK9	221264	hgsc.bcm.edu	37	6	109894773	109894773	+	Missense_Mutation	SNP	T	T	A	rs12175588	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:109894773T>A	ENST00000424296.2	-	21	2292	c.2216A>T	c.(2215-2217)gAt>gTt	p.D739V	AK9_ENST00000341338.6_5'UTR	NM_001145128.2	NP_001138600.2	Q5TCS8	KAD9_HUMAN	adenylate kinase 9	739					ADP phosphorylation (GO:0006757)|AMP phosphorylation (GO:0006756)|CDP phosphorylation (GO:0061508)|CMP phosphorylation (GO:0061566)|dADP phosphorylation (GO:0006174)|dAMP phosphorylation (GO:0061565)|dCDP phosphorylation (GO:0061570)|dCMP phosphorylation (GO:0061567)|dGDP phosphorylation (GO:0006186)|GDP phosphorylation (GO:0061568)|TDP phosphorylation (GO:0061571)|UDP phosphorylation (GO:0061569)	cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|nucleoside diphosphate kinase activity (GO:0004550)|nucleoside phosphate kinase activity (GO:0050145)										CTCCTCTTCATCCTCATTATC	0.388													T|||	1223	0.244209	0.1089	0.2839	5008	,	,		18633	0.3433		0.2197	False		,,,				2504	0.3221				p.D739V		Atlas-SNP	.											.	AKD1	223	.	0			c.A2216T						PASS	.	T	VAL/ASP	167,1217		13,141,538	143.0	117.0	125.0		2216	-2.1	0.0	6	dbSNP_120	125	751,2431		87,577,927	yes	missense	AKD1	NM_001145128.2	152	100,718,1465	AA,AT,TT		23.6015,12.0665,20.1051	benign	739/1912	109894773	918,3648	692	1591	2283	SO:0001583	missense	221264	exon21			TCTTCATCCTCAT	AK131244, BC146443, BC087860	CCDS5077.1, CCDS55048.1	6q21	2013-04-29	2013-04-29	2013-04-29			2.7.4.3		33814	protein-coding gene	gene with protein product		615358	"""chromosome 6 open reading frame 224"", ""adenylate kinase domain containing 2"", ""chromosome 6 open reading frame 199"", ""adenylate kinase domain containing 1"""	C6orf224, AKD2, C6orf199, AKD1		23416111	Standard	NM_145025		Approved	FLJ42177, FLJ25791, dJ70A9.1, MGC26954		Q5TCS8		ENST00000424296.2:c.2216A>T	6.37:g.109894773T>A	ENSP00000410186:p.Asp739Val	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	119	115	0.966387	NM_001145128	A6NL75|B2RDJ0|B6ZDM7|Q3MIS4|Q5I0W8|Q6ZNF1|Q6ZVR7|Q8N7C6|Q8WW00|Q96NF4	Missense_Mutation	SNP	ENST00000424296.2	37	CCDS55048.1	476	0.21794871794871795	51	0.10365853658536585	94	0.2596685082872928	163	0.28496503496503495	168	0.22163588390501318	T	18.06	3.539938	0.65085	0.120665	0.236015	ENSG00000155085	ENST00000424296	T	0.64991	-0.13	4.26	-2.13	0.07144	.	.	.	.	.	T	0.14313	0.0346	N	0.14661	0.345	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.10042	-1.0647	7	.	.	.	-1.5517	2.0014	0.03468	0.1298:0.1374:0.225:0.5078	rs12175588;rs52832625;rs12175588	739	Q5TCS8	AKD1_HUMAN	V	739	ENSP00000410186:D739V	.	D	-	2	0	AKD1	110001466	0.000000	0.05858	0.000000	0.03702	0.683000	0.39861	0.167000	0.16602	-0.415000	0.07484	-0.445000	0.05633	GAT	T|0.780;A|0.220	0.220	strong		0.388	AK9-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001145128	
DFNA5	1687	hgsc.bcm.edu	37	7	24758753	24758753	+	Silent	SNP	C	C	T	rs754555	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:24758753C>T	ENST00000342947.3	-	4	914	c.489G>A	c.(487-489)acG>acA	p.T163T	DFNA5_ENST00000409775.3_Silent_p.T163T|DFNA5_ENST00000559637.1_5'UTR|DFNA5_ENST00000419307.1_5'UTR|DFNA5_ENST00000545231.1_5'UTR|DFNA5_ENST00000409970.1_5'UTR	NM_004403.2	NP_004394.1	O60443	DFNA5_HUMAN	deafness, autosomal dominant 5	163					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						TCTGCATCGTCGTGATCTTCT	0.517													C|||	1298	0.259185	0.1982	0.1383	5008	,	,		22645	0.4435		0.1501	False		,,,				2504	0.3497				p.T163T	GBM(78;184 1250 20134 20900 23600)	Atlas-SNP	.											.	DFNA5	51	.	0			c.G489A						PASS	.	C	,,	925,3481	355.1+/-312.9	106,713,1384	227.0	182.0	197.0		489,,489	4.3	0.2	7	dbSNP_86	197	1230,7370	247.4+/-275.4	79,1072,3149	no	coding-synonymous,utr-5,coding-synonymous	DFNA5	NM_001127453.1,NM_001127454.1,NM_004403.2	,,	185,1785,4533	TT,TC,CC		14.3023,20.9941,16.5693	,,	163/497,,163/497	24758753	2155,10851	2203	4300	6503	SO:0001819	synonymous_variant	1687	exon4			CATCGTCGTGATC	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.489G>A	7.37:g.24758753C>T		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	82	15	0.182927	NM_001127453	A4D156|B2RAX9|B3KT05|O14590|Q08AQ8|Q9UBV3	Silent	SNP	ENST00000342947.3	37	CCDS5389.1																																																																																			C|0.802;T|0.198	0.198	strong		0.517	DFNA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214060.2	NM_004403	
SLC6A19	340024	hgsc.bcm.edu	37	5	1208964	1208964	+	Silent	SNP	T	T	C	rs60992377	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:1208964T>C	ENST00000304460.10	+	2	362	c.306T>C	c.(304-306)ggT>ggC	p.G102G		NM_001003841.2	NP_001003841.1	Q695T7	S6A19_HUMAN	solute carrier family 6 (neutral amino acid transporter), member 19	102					amino acid transport (GO:0006865)|ion transport (GO:0006811)|response to nutrient (GO:0007584)|transmembrane transport (GO:0055085)	brush border membrane (GO:0031526)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	neurotransmitter:sodium symporter activity (GO:0005328)|neutral amino acid transmembrane transporter activity (GO:0015175)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|lung(25)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	44	all_cancers(3;3.55e-15)|Lung NSC(6;2.89e-14)|all_lung(6;2.2e-13)|all_epithelial(6;3.75e-10)		Epithelial(17;0.000356)|all cancers(22;0.00137)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|Lung(60;0.185)			GCAGCCTGGGTGTGTGGAGCT	0.682																																					p.G102G		Atlas-SNP	.											SLC6A19,NS,carcinoma,+2,2	SLC6A19	99	2	0			c.T306C						scavenged	.	C		2407,1997	546.1+/-377.0	672,1063,467	39.0	40.0	40.0		306	-3.2	0.9	5	dbSNP_129	40	2649,5949	674.3+/-403.1	447,1755,2097	no	coding-synonymous	SLC6A19	NM_001003841.2		1119,2818,2564	CC,CT,TT		30.8095,45.3451,38.8863		102/635	1208964	5056,7946	2202	4299	6501	SO:0001819	synonymous_variant	340024	exon2			CCTGGGTGTGTGG	AK096054	CCDS34130.1	5p15	2013-07-19			ENSG00000174358	ENSG00000174358		"""Solute carriers"""	27960	protein-coding gene	gene with protein product	"""Hartnup disease"""	608893					Standard	NM_001003841		Approved		uc003jbw.4	Q695T7	OTTHUMG00000161636	ENST00000304460.10:c.306T>C	5.37:g.1208964T>C		Somatic	104	1	0.00961538		WXS	Illumina HiSeq	Phase_I	88	39	0.443182	NM_001003841	A8K446	Silent	SNP	ENST00000304460.10	37	CCDS34130.1																																																																																			T|0.608;C|0.392	0.392	strong		0.682	SLC6A19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365557.1	XM_291120	
OR5P2	120065	hgsc.bcm.edu	37	11	7818056	7818056	+	Missense_Mutation	SNP	T	T	C	rs73406604	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:7818056T>C	ENST00000329434.2	-	1	464	c.434A>G	c.(433-435)tAc>tGc	p.Y145C	RP11-35J10.5_ENST00000527565.1_lincRNA	NM_153444.1	NP_703145.1	Q8WZ92	OR5P2_HUMAN	olfactory receptor, family 5, subfamily P, member 2	145						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(4)	22				Epithelial(150;8.62e-08)|BRCA - Breast invasive adenocarcinoma(625;0.189)		ACCAGCTATGTAAACTACTAA	0.408													T|||	1184	0.236422	0.3472	0.2911	5008	,	,		19685	0.128		0.2763	False		,,,				2504	0.1186				p.Y145C		Atlas-SNP	.											OR5P2,brain,glioma,0,2	OR5P2	68	2	0			c.A434G						PASS	.	T	CYS/TYR	1369,2829		401,567,1131	63.0	75.0	71.0		434	3.2	0.2	11	dbSNP_130	71	2425,6159		393,1639,2260	yes	missense	OR5P2	NM_153444.1	194	794,2206,3391	CC,CT,TT		28.2502,32.6108,29.6824	benign	145/323	7818056	3794,8988	2099	4292	6391	SO:0001583	missense	120065	exon1			GCTATGTAAACTA	AF173006	CCDS7782.1	11p15.4	2012-08-09			ENSG00000183303	ENSG00000183303		"""GPCR / Class A : Olfactory receptors"""	14783	protein-coding gene	gene with protein product							Standard	NM_153444		Approved	JCG3	uc001mfp.1	Q8WZ92	OTTHUMG00000165668	ENST00000329434.2:c.434A>G	11.37:g.7818056T>C	ENSP00000331823:p.Tyr145Cys	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	58	48	0.827586	NM_153444	Q3MIS8	Missense_Mutation	SNP	ENST00000329434.2	37	CCDS7782.1	586	0.2683150183150183	180	0.36585365853658536	100	0.27624309392265195	84	0.14685314685314685	222	0.2928759894459103	T	5.438	0.265978	0.10294	0.326108	0.282502	ENSG00000183303	ENST00000329434	T	0.38240	1.15	5.5	3.18	0.36537	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	D	0.000015	T	0.00012	0.0000	M	0.68952	2.095	0.80722	P	0.0	B	0.17667	0.023	B	0.33750	0.169	T	0.32402	-0.9908	9	0.66056	D	0.02	-38.8562	4.4769	0.11748	0.3014:0.0807:0.0:0.6179	.	145	Q8WZ92	OR5P2_HUMAN	C	145	ENSP00000331823:Y145C	ENSP00000331823:Y145C	Y	-	2	0	OR5P2	7774632	0.000000	0.05858	0.166000	0.22797	0.001000	0.01503	0.078000	0.14761	0.511000	0.28236	-0.456000	0.05471	TAC	T|0.738;C|0.262	0.262	strong		0.408	OR5P2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385696.1	NM_153444	
TMEM63B	55362	hgsc.bcm.edu	37	6	44117664	44117664	+	Silent	SNP	C	C	T	rs4714762	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:44117664C>T	ENST00000259746.9	+	16	1665	c.1482C>T	c.(1480-1482)atC>atT	p.I494I	TMEM63B_ENST00000323267.6_Silent_p.I494I			Q5T3F8	CSCL2_HUMAN	transmembrane protein 63B	494					ion transport (GO:0006811)	integral component of membrane (GO:0016021)	nucleotide binding (GO:0000166)	p.I494I(1)		breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(8)|ovary(1)|pancreas(2)|prostate(2)|stomach(4)	35	all_cancers(18;1.66e-06)|Lung NSC(15;0.00108)|all_lung(25;0.00278)|Hepatocellular(11;0.00309)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0215)			TTCCCACCATCGTCTACTACT	0.612													C|||	528	0.105431	0.0061	0.0965	5008	,	,		20116	0.2321		0.0984	False		,,,				2504	0.1227				p.I494I		Atlas-SNP	.											TMEM63B,NS,carcinoma,0,1	TMEM63B	77	1	1	Substitution - coding silent(1)	stomach(1)	c.C1482T						PASS	.	C		108,4298	85.3+/-124.0	2,104,2097	205.0	144.0	165.0		1482	0.3	1.0	6	dbSNP_111	165	914,7686	201.8+/-245.2	53,808,3439	no	coding-synonymous	TMEM63B	NM_018426.1		55,912,5536	TT,TC,CC		10.6279,2.4512,7.8579		494/833	44117664	1022,11984	2203	4300	6503	SO:0001819	synonymous_variant	55362	exon16			CACCATCGTCTAC	BC022095	CCDS34461.1	6p21.1	2008-02-05	2005-07-25	2005-07-25	ENSG00000137216	ENSG00000137216			17735	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 110"""	C6orf110			Standard	XM_005249211		Approved	DKFZp434P0531, dJ421H19.2	uc003owr.3	Q5T3F8	OTTHUMG00000014757	ENST00000259746.9:c.1482C>T	6.37:g.44117664C>T		Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	127	60	0.472441	NM_018426	B9EGU3|Q5T3F9|Q6AHX4|Q6P5A0|Q8N219|Q8NDE1|Q9NSG5	Silent	SNP	ENST00000259746.9	37	CCDS34461.1	257	0.11767399267399267	2	0.0040650406504065045	38	0.10497237569060773	146	0.25524475524475526	71	0.09366754617414248	C	10.43	1.347414	0.24426	0.024512	0.106279	ENSG00000137216	ENST00000371893	.	.	.	4.42	0.341	0.15991	.	.	.	.	.	T	0.24547	0.0595	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.10706	-1.0618	3	.	.	.	.	8.5159	0.33246	0.0:0.4934:0.0:0.5066	rs4714762;rs57455510	.	.	.	L	423	.	.	S	+	2	0	TMEM63B	44225642	0.001000	0.12720	0.998000	0.56505	0.985000	0.73830	-1.277000	0.02812	-0.057000	0.13199	-0.437000	0.05841	TCG	C|0.910;G|0.000;T|0.089	0.089	strong		0.612	TMEM63B-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040712.2	XM_166410	
LRRC43	254050	hgsc.bcm.edu	37	12	122674780	122674780	+	Missense_Mutation	SNP	C	C	A	rs11060094	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:122674780C>A	ENST00000339777.4	+	5	794	c.766C>A	c.(766-768)Cag>Aag	p.Q256K	LRRC43_ENST00000425921.1_Missense_Mutation_p.Q71K	NM_152759.4	NP_689972.3	Q8N309	LRC43_HUMAN	leucine rich repeat containing 43	256			Q -> K (in dbSNP:rs11060094). {ECO:0000269|PubMed:14702039}.							NS(1)|endometrium(1)|large_intestine(4)|lung(10)|skin(1)|upper_aerodigestive_tract(2)	19	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000312)|Epithelial(86;0.000539)|BRCA - Breast invasive adenocarcinoma(302;0.225)		CCTGGTGCTGCAGGGAAACCC	0.637													C|||	671	0.133986	0.0953	0.2666	5008	,	,		20331	0.0357		0.2038	False		,,,				2504	0.1217				p.Q256K		Atlas-SNP	.											.	LRRC43	105	.	0			c.C766A						PASS	.	C	LYS/GLN,LYS/GLN	436,3902		20,396,1753	91.0	103.0	99.0		766,211	4.9	1.0	12	dbSNP_120	99	1763,6753		199,1365,2694	yes	missense,missense	LRRC43	NM_001098519.1,NM_152759.4	53,53	219,1761,4447	AA,AC,CC		20.7022,10.0507,17.1075	benign,benign	256/657,71/472	122674780	2199,10655	2169	4258	6427	SO:0001583	missense	254050	exon5			GTGCTGCAGGGAA	AK124107	CCDS45001.1	12q24.31	2014-09-11			ENSG00000158113	ENSG00000158113			28562	protein-coding gene	gene with protein product						12477932	Standard	NM_152759		Approved	MGC35140	uc009zxm.3	Q8N309	OTTHUMG00000168915	ENST00000339777.4:c.766C>A	12.37:g.122674780C>A	ENSP00000344233:p.Gln256Lys	Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	149	73	0.489933	NM_001098519	Q6ZVT9	Missense_Mutation	SNP	ENST00000339777.4	37	CCDS45001.1	303	0.13873626373626374	49	0.09959349593495935	98	0.27071823204419887	15	0.026223776223776224	141	0.18601583113456466	C	22.3	4.268532	0.80469	0.100507	0.207022	ENSG00000158113	ENST00000537729;ENST00000339777;ENST00000289014;ENST00000425921	T;T;T	0.23348	1.91;1.91;1.91	4.95	4.95	0.65309	.	0.068949	0.64402	D	0.000017	T	0.00012	0.0000	M	0.63208	1.945	0.26746	P	0.9702966	D	0.58268	0.982	D	0.70227	0.968	T	0.01294	-1.1393	9	0.48119	T	0.1	-55.8197	17.807	0.88604	0.0:1.0:0.0:0.0	rs11060094;rs57783714;rs11060094	256	Q8N309	LRC43_HUMAN	K	71;256;127;71	ENSP00000438751:Q71K;ENSP00000344233:Q256K;ENSP00000416628:Q71K	ENSP00000289014:Q127K	Q	+	1	0	LRRC43	121240733	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	4.532000	0.60608	2.309000	0.77851	0.561000	0.74099	CAG	C|0.865;A|0.135	0.135	strong		0.637	LRRC43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401589.1	NM_152759	
TLR6	10333	hgsc.bcm.edu	37	4	38830012	38830012	+	Silent	SNP	G	G	C	rs3821985	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:38830012G>C	ENST00000381950.1	-	1	1148	c.1083C>G	c.(1081-1083)acC>acG	p.T361T	TLR6_ENST00000436693.2_Silent_p.T361T			Q9Y2C9	TLR6_HUMAN	toll-like receptor 6	361					activation of NF-kappaB-inducing kinase activity (GO:0007250)|cellular response to diacyl bacterial lipopeptide (GO:0071726)|defense response to bacterium (GO:0042742)|detection of diacyl bacterial lipopeptide (GO:0042496)|immune response (GO:0006955)|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)|nitric oxide metabolic process (GO:0046209)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-6 biosynthetic process (GO:0045410)|positive regulation of JUN kinase activity (GO:0043507)|regulation of cytokine secretion (GO:0050707)|signal transduction (GO:0007165)|T-helper 1 type immune response (GO:0042088)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 6 signaling pathway (GO:0034150)|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)	cytoplasmic vesicle (GO:0031410)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|Toll-like receptor 2-Toll-like receptor 6 protein complex (GO:0035355)	diacyl lipopeptide binding (GO:0042498)|lipopeptide binding (GO:0071723)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(7)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						AAACGTTCTGGGTAAAGTTCA	0.328													G|||	2228	0.444888	0.6944	0.3112	5008	,	,		21947	0.3958		0.3141	False		,,,				2504	0.3875				p.T361T		Atlas-SNP	.											.	TLR6	67	.	0			c.C1083G						PASS	.	G		2785,1619	659.7+/-400.6	875,1035,292	54.0	54.0	54.0		1083	3.0	1.0	4	dbSNP_107	54	2939,5661	458.0+/-364.5	519,1901,1880	no	coding-synonymous	TLR6	NM_006068.4		1394,2936,2172	CC,CG,GG		34.1744,36.762,44.0172		361/797	38830012	5724,7280	2202	4300	6502	SO:0001819	synonymous_variant	10333	exon2			GTTCTGGGTAAAG		CCDS3446.1	4p16.1	2009-11-23			ENSG00000174130	ENSG00000174130		"""CD molecules"""	16711	protein-coding gene	gene with protein product		605403				10231569	Standard	NM_006068		Approved	CD286	uc010ifg.2	Q9Y2C9	OTTHUMG00000128579	ENST00000381950.1:c.1083C>G	4.37:g.38830012G>C		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	74	38	0.513514	NM_006068	B3Y640|B6CH35|B6RFS4|B6RFS5|Q2NKL3	Silent	SNP	ENST00000381950.1	37	CCDS3446.1																																																																																			G|0.583;C|0.417	0.417	strong		0.328	TLR6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250431.1		
OPN4	94233	hgsc.bcm.edu	37	10	88414569	88414569	+	Missense_Mutation	SNP	C	C	T	rs2675703	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:88414569C>T	ENST00000241891.5	+	1	196	c.29C>T	c.(28-30)cCg>cTg	p.P10L	OPN4_ENST00000372071.2_Missense_Mutation_p.P10L	NM_033282.3	NP_150598.1	Q9UHM6	OPN4_HUMAN	opsin 4	10			P -> L (in dbSNP:rs2675703). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.4}.		phototransduction (GO:0007602)|protein-chromophore linkage (GO:0018298)|regulation of circadian rhythm (GO:0042752)|rhodopsin mediated signaling pathway (GO:0016056)|rhythmic process (GO:0048511)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	11-cis retinal binding (GO:0005502)|G-protein coupled photoreceptor activity (GO:0008020)			breast(1)|endometrium(3)|kidney(2)|large_intestine(2)|liver(2)|lung(5)|ovary(3)	18						CCAAGAGTCCCGCCCAGCCCA	0.642													C|||	392	0.0782748	0.0227	0.1196	5008	,	,		16004	0.0446		0.1511	False		,,,				2504	0.0838				p.P10L		Atlas-SNP	.											OPN4,NS,carcinoma,0,1	OPN4	61	1	0			c.C29T						PASS	.	C	LEU/PRO,LEU/PRO	176,4230	115.9+/-153.8	6,164,2033	66.0	67.0	67.0		29,29	-2.1	0.0	10	dbSNP_100	67	1161,7439	236.8+/-268.9	69,1023,3208	yes	missense,missense	OPN4	NM_001030015.2,NM_033282.3	98,98	75,1187,5241	TT,TC,CC		13.5,3.9946,10.2799	possibly-damaging,possibly-damaging	10/490,10/479	88414569	1337,11669	2203	4300	6503	SO:0001583	missense	94233	exon1			GAGTCCCGCCCAG	AF147788	CCDS7376.1, CCDS31237.1	10q22	2012-08-08	2008-04-16		ENSG00000122375	ENSG00000122375		"""GPCR / Class A : Opsin receptors"""	14449	protein-coding gene	gene with protein product	"""melanopsin"""	606665	"""opsin 4 (melanopsin)"""			10632589	Standard	NM_001030015		Approved	MOP, melanopsin	uc001kdp.3	Q9UHM6	OTTHUMG00000018654	ENST00000241891.5:c.29C>T	10.37:g.88414569C>T	ENSP00000241891:p.Pro10Leu	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	76	76	1	NM_033282	B7ZLB3|Q14D01|Q2PP22|Q8NGQ9	Missense_Mutation	SNP	ENST00000241891.5	37	CCDS7376.1	209	0.09569597069597069	17	0.034552845528455285	52	0.143646408839779	30	0.05244755244755245	110	0.14511873350923482	C	2.718	-0.267266	0.05754	0.039946	0.135	ENSG00000122375	ENST00000372071;ENST00000241891;ENST00000443292	T;T;T	0.66460	-0.16;0.21;-0.21	4.65	-2.14	0.07123	.	0.680336	0.12954	N	0.425615	T	0.00241	0.0007	L	0.29908	0.895	0.80722	P	0.0	B;B;B	0.10296	0.001;0.002;0.003	B;B;B	0.06405	0.001;0.001;0.002	T	0.09618	-1.0666	9	0.02654	T	1	.	4.4654	0.11687	0.1568:0.3542:0.0:0.4889	rs2675703;rs3824747;rs2675703	10;10;10	C9JWU6;Q9UHM6;Q9UHM6-2	.;OPN4_HUMAN;.	L	10	ENSP00000361141:P10L;ENSP00000241891:P10L;ENSP00000393132:P10L	ENSP00000241891:P10L	P	+	2	0	OPN4	88404549	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.773000	0.04689	-0.273000	0.09246	-0.137000	0.14449	CCG	C|0.900;T|0.100	0.100	strong		0.642	OPN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049158.2	NM_033282	
TBC1D2B	23102	hgsc.bcm.edu	37	15	78369815	78369815	+	Silent	SNP	G	G	A	rs9047	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	41	0	0		WXS	Illumina HiSeq	Phase_I	39	21	0.538462	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	
COL6A5	256076	hgsc.bcm.edu	37	3	130103709	130103709	+	Missense_Mutation	SNP	G	G	A	rs1453241	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:130103709G>A	ENST00000432398.2	+	5	1857	c.1363G>A	c.(1363-1365)Gag>Aag	p.E455K	COL6A5_ENST00000265379.6_Missense_Mutation_p.E455K	NM_153264.5	NP_694996.5	A8TX70	CO6A5_HUMAN	collagen, type VI, alpha 5	455	Nonhelical region.|VWFA 3. {ECO:0000255|PROSITE- ProRule:PRU00219}.		E -> K (in dbSNP:rs1453241). {ECO:0000269|PubMed:18276594}.		cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				endometrium(6)|kidney(4)|large_intestine(8)|lung(19)|pancreas(2)|prostate(3)|stomach(1)|urinary_tract(1)	44						CAGCATCCAGGAGAAACAGTT	0.418													G|||	1987	0.396765	0.4728	0.4582	5008	,	,		19916	0.5149		0.2028	False		,,,				2504	0.3282				p.E455K		Atlas-SNP	.											.	COL6A5	205	.	0			c.G1363A	GRCh37	CM076121	COL6A5	M	rs1453241	PASS	.	G	LYS/GLU	586,798		116,354,222	86.0	78.0	81.0		1363	-6.1	0.0	3	dbSNP_88	81	697,2485		85,527,979	yes	missense	COL6A5	NM_153264.5	56	201,881,1201	AA,AG,GG		21.9045,42.341,28.099	benign	455/2527	130103709	1283,3283	692	1591	2283	SO:0001583	missense	256076	exon5			ATCCAGGAGAAAC	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.1363G>A	3.37:g.130103709G>A	ENSP00000390895:p.Glu455Lys	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	105	53	0.504762	NM_153264	A9J6L2|A9J6L4|A9J6L6|A9J6L7|A9J6M0|A9J6M1|A9J6M2|B5MEA7|Q6ZW26|Q8NA36	Missense_Mutation	SNP	ENST00000432398.2	37		795	0.364010989010989	206	0.4186991869918699	146	0.40331491712707185	294	0.513986013986014	149	0.19656992084432717	G	9.568	1.120335	0.20877	0.42341	0.219045	ENSG00000172752	ENST00000432398;ENST00000265379	D;D	0.83837	-1.77;-1.77	5.5	-6.05	0.02172	.	.	.	.	.	T	0.00012	0.0000	N	0.05554	-0.025	0.80722	P	0.0	B	0.02656	0.0	B	0.08055	0.003	T	0.16424	-1.0403	8	0.06365	T	0.9	.	3.7844	0.08694	0.289:0.1875:0.4308:0.0927	rs1453241;rs52804564;rs58043586;rs1453241	455	A8TX70-2	.	K	455	ENSP00000390895:E455K;ENSP00000265379:E455K	ENSP00000265379:E455K	E	+	1	0	COL6A5	131586399	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-2.626000	0.00874	-1.344000	0.02216	-0.262000	0.10625	GAG	G|0.619;A|0.381	0.381	strong		0.418	COL6A5-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_153264	
CR1	1378	hgsc.bcm.edu	37	1	207787831	207787831	+	Nonsense_Mutation	SNP	G	G	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:207787831G>T	ENST00000367049.4	+	40	6658	c.6658G>T	c.(6658-6660)Gaa>Taa	p.E2220*	CR1_ENST00000367053.1_Nonsense_Mutation_p.E1770*|CR1_ENST00000367052.1_Nonsense_Mutation_p.E1770*|CR1_ENST00000367051.1_Nonsense_Mutation_p.E1770*|CR1_ENST00000400960.2_Nonsense_Mutation_p.E1770*	NM_000651.4	NP_000642.3	P17927	CR1_HUMAN	complement component (3b/4b) receptor 1 (Knops blood group)	1770					complement activation, classical pathway (GO:0006958)|complement receptor mediated signaling pathway (GO:0002430)|innate immune response (GO:0045087)|negative regulation of complement activation, alternative pathway (GO:0045957)|negative regulation of complement activation, classical pathway (GO:0045959)|negative regulation of serine-type endopeptidase activity (GO:1900004)|positive regulation of serine-type endopeptidase activity (GO:1900005)|regulation of complement activation (GO:0030449)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	complement component C3b binding (GO:0001851)|complement component C3b receptor activity (GO:0004877)|complement component C4b binding (GO:0001855)|complement component C4b receptor activity (GO:0001861)	p.E2220*(6)|p.E1775*(6)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(9)|kidney(11)|large_intestine(13)|lung(33)|ovary(3)|prostate(6)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	82						TCCAGTGTGTGAACGTGAGTA	0.408																																					p.E2220X		Atlas-SNP	.											CR1_ENST00000367049,NS,carcinoma,0,12	CR1	354	12	12	Substitution - Nonsense(12)	kidney(8)|endometrium(4)	c.G6658T						scavenged	.						131.0	122.0	125.0					1																	207787831		1887	4127	6014	SO:0001587	stop_gained	1378	exon40			GTGTGTGAACGTG	Y00816	CCDS44308.1, CCDS44309.1	1q32	2014-07-19	2006-01-12		ENSG00000203710	ENSG00000203710		"""CD molecules"", ""Blood group antigens"", ""Complement system"""	2334	protein-coding gene	gene with protein product		120620	"""complement component (3b/4b) receptor 1, including Knops blood group system"""			1708809	Standard	XM_005273064		Approved	CD35, KN	uc001hfx.3	P17927	OTTHUMG00000036311	ENST00000367049.4:c.6658G>T	1.37:g.207787831G>T	ENSP00000356016:p.Glu2220*	Somatic	200	2	0.01		WXS	Illumina HiSeq	Phase_I	202	4	0.019802	NM_000651	Q16744|Q16745|Q5SR43|Q5SR45|Q9UQV2	Nonsense_Mutation	SNP	ENST00000367049.4	37	CCDS44308.1	.	.	.	.	.	.	.	.	.	.	G	45	12.061806	0.99632	.	.	ENSG00000203710	ENST00000367052;ENST00000367051;ENST00000367053;ENST00000400960;ENST00000367049	.	.	.	4.29	4.29	0.51040	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.06236	T	0.91	.	12.9543	0.58418	0.0:0.0:1.0:0.0	.	.	.	.	X	1770;1770;1770;1770;2220	.	ENSP00000356016:E2220X	E	+	1	0	CR1	205854454	1.000000	0.71417	0.999000	0.59377	0.893000	0.52053	2.536000	0.45693	2.316000	0.78162	0.436000	0.28706	GAA	.	.	none		0.408	CR1-012	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382527.1	NM_000573	
DAAM2	23500	hgsc.bcm.edu	37	6	39847197	39847197	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:39847197C>T	ENST00000398904.2	+	14	1971	c.1789C>T	c.(1789-1791)Cgt>Tgt	p.R597C	DAAM2_ENST00000538976.1_Missense_Mutation_p.R597C|RP11-61I13.3_ENST00000607675.1_RNA|DAAM2_ENST00000274867.4_Missense_Mutation_p.R597C			Q86T65	DAAM2_HUMAN	dishevelled associated activator of morphogenesis 2	597	FH2. {ECO:0000255|PROSITE- ProRule:PRU00774}.|Pro-rich.				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)					CAGGAAAAAGCGTGTCCCCCA	0.632																																					p.R597C		Atlas-SNP	.											DAAM2,rectum,carcinoma,-1,2	DAAM2	101	2	0			c.C1789T						scavenged	.						71.0	73.0	72.0					6																	39847197		1966	4130	6096	SO:0001583	missense	23500	exon14			AAAAAGCGTGTCC	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.1789C>T	6.37:g.39847197C>T	ENSP00000381876:p.Arg597Cys	Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	169	2	0.0118343	NM_015345	G5EA45|Q5T4T8|Q5T4U0|Q9NQI5|Q9Y4G0	Missense_Mutation	SNP	ENST00000398904.2	37	CCDS56426.1	.	.	.	.	.	.	.	.	.	.	C	4.897	0.166771	0.09339	.	.	ENSG00000146122	ENST00000274867;ENST00000398904;ENST00000538976	T;T;T	0.18174	2.23;2.23;2.23	5.15	1.55	0.23275	Actin-binding FH2/DRF autoregulatory (1);Actin-binding FH2 (3);	0.620813	0.16621	N	0.206470	T	0.01905	0.0060	N	0.04508	-0.205	0.54753	D	0.999983	B;B	0.33748	0.103;0.423	B;B	0.26517	0.003;0.07	T	0.42172	-0.9467	10	0.51188	T	0.08	.	2.5154	0.04667	0.3971:0.1758:0.0:0.4271	.	597;597	G5EA45;Q86T65	.;DAAM2_HUMAN	C	597	ENSP00000274867:R597C;ENSP00000381876:R597C;ENSP00000437808:R597C	ENSP00000274867:R597C	R	+	1	0	DAAM2	39955175	1.000000	0.71417	0.922000	0.36590	0.052000	0.14988	1.394000	0.34509	0.430000	0.26230	-0.175000	0.13238	CGT	.	.	none		0.632	DAAM2-003	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000280648.1		
SLIT3	6586	hgsc.bcm.edu	37	5	168098235	168098235	+	Silent	SNP	A	A	G	rs2277933	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:168098235A>G	ENST00000519560.1	-	34	4514	c.4095T>C	c.(4093-4095)gaT>gaC	p.D1365D	SLIT3_ENST00000332966.8_Silent_p.D1372D|SLIT3_ENST00000404867.3_Silent_p.D1365D	NM_001271946.1|NM_003062.2	NP_001258875.1|NP_003053	O75094	SLIT3_HUMAN	slit homolog 3 (Drosophila)	1365	EGF-like 7. {ECO:0000255|PROSITE- ProRule:PRU00076}.				apoptotic process involved in luteolysis (GO:0061364)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|cellular response to hormone stimulus (GO:0032870)|negative chemotaxis (GO:0050919)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of gene expression (GO:0010629)|organ morphogenesis (GO:0009887)|response to cortisol (GO:0051414)|Roundabout signaling pathway (GO:0035385)	extracellular space (GO:0005615)|mitochondrion (GO:0005739)	calcium ion binding (GO:0005509)|Roundabout binding (GO:0048495)			endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(15)|liver(2)|lung(48)|ovary(4)|prostate(7)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	100	Renal(175;0.000159)|Lung NSC(126;0.0174)|all_lung(126;0.0392)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			GGGCCTCCTGATCGCAGAGTG	0.687													G|||	1618	0.323083	0.4705	0.3934	5008	,	,		16999	0.3274		0.2435	False		,,,				2504	0.1513				p.D1372D	Ovarian(29;311 847 10864 17279 24903)	Atlas-SNP	.											.	SLIT3	224	.	0			c.T4116C						PASS	.	G		1943,2455		408,1127,664	24.0	25.0	24.0		4095	4.6	1.0	5	dbSNP_100	24	2006,6582		247,1512,2535	no	coding-synonymous	SLIT3	NM_003062.2		655,2639,3199	GG,GA,AA		23.3582,44.1792,30.4097		1365/1524	168098235	3949,9037	2199	4294	6493	SO:0001819	synonymous_variant	6586	exon34			CTCCTGATCGCAG	AB011538	CCDS4369.1, CCDS64311.1	5q35	2008-07-18	2001-11-28		ENSG00000184347	ENSG00000184347			11087	protein-coding gene	gene with protein product		603745	"""slit (Drosophila) homolog 3"""	SLIL2		9693030, 9813312	Standard	NM_001271946		Approved	slit2, MEGF5, SLIT1, Slit-3	uc010jjg.4	O75094	OTTHUMG00000130409	ENST00000519560.1:c.4095T>C	5.37:g.168098235A>G		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	93	32	0.344086	NM_001271946	A6H8U9|J3KNP3|O95804|Q9UFH5	Silent	SNP	ENST00000519560.1	37	CCDS4369.1																																																																																			A|0.689;G|0.311	0.311	strong		0.687	SLIT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252792.4	NM_003062	
OR1F1	4992	hgsc.bcm.edu	37	16	3254972	3254972	+	Silent	SNP	T	T	C	rs2075851	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	207	1	0.00483092		WXS	Illumina HiSeq	Phase_I	139	105	0.755396	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		
HLA-A	3105	hgsc.bcm.edu	37	6	29910358	29910358	+	Missense_Mutation	SNP	C	C	G	rs1143146	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:29910358C>G	ENST00000396634.1	+	3	369	c.28C>G	c.(28-30)Ctc>Gtc	p.L10V	HLA-A_ENST00000376802.2_Missense_Mutation_p.L10V|HLA-A_ENST00000376809.5_Missense_Mutation_p.L10V|HLA-A_ENST00000376806.5_Missense_Mutation_p.L10V			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	10					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						CCGAACCCTCCTCCTGCTACT	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)			g|||	2531	0.505391	0.4743	0.5965	5008	,	,		15681	0.5397		0.5119	False		,,,				2504	0.4407				p.L10V		Atlas-SNP	.											.	HLA-A	89	.	0			c.C28G						PASS	.	G	VAL/LEU	2094,2312		466,1162,575	33.0	36.0	35.0		28	-0.4	0.0	6	dbSNP_86	35	4132,4458		989,2154,1152	no	missense	HLA-A	NM_002116.7	32	1455,3316,1727	GG,GC,CC		48.1024,47.5261,47.907	benign	10/366	29910358	6226,6770	2203	4295	6498	SO:0001583	missense	3105	exon1	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	ACCCTCCTCCTGC	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.28C>G	6.37:g.29910358C>G	ENSP00000379873:p.Leu10Val	Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	141	61	0.432624	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Missense_Mutation	SNP	ENST00000396634.1	37	CCDS34373.1	1140	0.521978021978022	230	0.46747967479674796	198	0.5469613259668509	329	0.5751748251748252	383	0.5052770448548812	.	8.451	0.853152	0.17106	0.475261	0.481024	ENSG00000206503	ENST00000396634;ENST00000376806;ENST00000376809;ENST00000355767;ENST00000376802	T;T;T;T	0.00801	5.7;5.68;5.7;5.71	3.71	-0.398	0.12418	.	1.184600	0.07033	N	0.828726	T	0.00144	0.0004	.	.	.	0.80722	P	0.0	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.08055	0.001;0.003;0.001;0.003	T	0.34204	-0.9838	8	0.02654	T	1	.	4.1979	0.10452	0.0:0.5233:0.1702:0.3065	rs1143146;rs2230953;rs3115640;rs3173432;rs9260121;rs41540716	10;10;10;10	Q5SRN7;P16188;Q5SRN5;P04439	.;1A30_HUMAN;.;1A03_HUMAN	V	10	ENSP00000379873:L10V;ENSP00000366002:L10V;ENSP00000366005:L10V;ENSP00000365998:L10V	ENSP00000348012:L10V	L	+	1	0	HLA-A	30018337	0.000000	0.05858	0.002000	0.10522	0.137000	0.21094	-0.182000	0.09726	-0.192000	0.10432	-0.363000	0.07495	CTC	C|0.511;G|0.489	0.489	strong		0.697	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
ATP6V0A1	535	hgsc.bcm.edu	37	17	40665913	40665913	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:40665913T>C	ENST00000343619.4	+	20	2288	c.2165T>C	c.(2164-2166)aTc>aCc	p.I722T	MIR5010_ENST00000582846.1_RNA|ATP6V0A1_ENST00000393829.2_Missense_Mutation_p.I716T|ATP6V0A1_ENST00000585525.1_Missense_Mutation_p.I679T|ATP6V0A1_ENST00000264649.6_Missense_Mutation_p.I723T|RP11-400F19.18_ENST00000591237.1_RNA|ATP6V0A1_ENST00000544137.1_Missense_Mutation_p.I368T|ATP6V0A1_ENST00000537728.1_Missense_Mutation_p.I673T|ATP6V0A1_ENST00000546249.1_Missense_Mutation_p.I722T	NM_001130021.1	NP_001123493.1	Q93050	VPP1_HUMAN	ATPase, H+ transporting, lysosomal V0 subunit a1	722					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)		CACCAGGCCATCCACACCATC	0.577																																					p.I723T		Atlas-SNP	.											.	ATP6V0A1	67	.	0			c.T2168C						PASS	.						207.0	182.0	191.0					17																	40665913		2203	4300	6503	SO:0001583	missense	535	exon19			AGGCCATCCACAC	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.2165T>C	17.37:g.40665913T>C	ENSP00000342951:p.Ile722Thr	Somatic	210	0	0		WXS	Illumina HiSeq	Phase_I	193	58	0.300518	NM_001130020	B7Z3B7|Q8N5G7|Q9NSX0	Missense_Mutation	SNP	ENST00000343619.4	37	CCDS45684.1	.	.	.	.	.	.	.	.	.	.	T	23.9	4.468889	0.84533	.	.	ENSG00000033627	ENST00000343619;ENST00000546249;ENST00000393829;ENST00000264649;ENST00000537728;ENST00000544137	D;D;D;D;D;D	0.91351	-2.83;-2.83;-2.83;-2.83;-2.83;-2.83	4.92	4.92	0.64577	.	0.000000	0.85682	D	0.000000	D	0.97238	0.9097	H	0.98276	4.19	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;0.999;0.998;0.999;1.0	D	0.98713	1.0705	10	0.87932	D	0	-21.9263	14.7204	0.69302	0.0:0.0:0.0:1.0	.	673;679;723;722;716	B7Z641;B7Z2A9;B7Z3B7;Q93050;Q93050-1	.;.;.;VPP1_HUMAN;.	T	722;722;716;723;673;368	ENSP00000342951:I722T;ENSP00000444676:I722T;ENSP00000377415:I716T;ENSP00000264649:I723T;ENSP00000443991:I673T;ENSP00000446377:I368T	ENSP00000264649:I723T	I	+	2	0	ATP6V0A1	37919439	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	7.868000	0.87116	2.067000	0.61834	0.459000	0.35465	ATC	.	.	none		0.577	ATP6V0A1-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000450364.1	NM_001130020	
ZNF133	7692	hgsc.bcm.edu	37	20	18295730	18295730	+	Missense_Mutation	SNP	C	C	T	rs34099160	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:18295730C>T	ENST00000316358.4	+	4	332	c.235C>T	c.(235-237)Ctc>Ttc	p.L79F	ZNF133_ENST00000462170.1_3'UTR|ZNF133_ENST00000401790.1_Missense_Mutation_p.L79F|ZNF133_ENST00000396026.3_Missense_Mutation_p.L82F|RP4-568F9.3_ENST00000436848.1_RNA|ZNF133_ENST00000402618.2_Missense_Mutation_p.L16F|ZNF133_ENST00000377671.3_Missense_Mutation_p.L78F|ZNF133_ENST00000535822.1_5'UTR|ZNF133_ENST00000538547.1_5'UTR	NM_001282998.1|NM_001282999.1|NM_001283000.1|NM_001283001.1|NM_001283008.1	NP_001269927.1|NP_001269928.1|NP_001269929.1|NP_001269930.1|NP_001269937.1	P52736	ZN133_HUMAN	zinc finger protein 133	79					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.L78F(1)		autonomic_ganglia(1)|breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	26						AGAGCCAGAGCTCTACCTCGA	0.527													C|||	611	0.122005	0.1551	0.1037	5008	,	,		20314	0.1409		0.0825	False		,,,				2504	0.1115				p.L78F		Atlas-SNP	.											ZNF133,NS,carcinoma,0,1	ZNF133	63	1	1	Substitution - Missense(1)	stomach(1)	c.C232T						PASS	.	C	PHE/LEU,PHE/LEU	659,3747	281.6+/-276.1	53,553,1597	90.0	85.0	86.0		232,232	1.8	0.0	20	dbSNP_126	86	681,7919	169.7+/-221.0	30,621,3649	yes	missense,missense	ZNF133	NM_001083330.1,NM_003434.4	22,22	83,1174,5246	TT,TC,CC		7.9186,14.9569,10.3029	probably-damaging,probably-damaging	78/654,78/654	18295730	1340,11666	2203	4300	6503	SO:0001583	missense	7692	exon4			CCAGAGCTCTACC	AK123005	CCDS13134.1, CCDS63234.1, CCDS63235.1, CCDS74703.1, CCDS74704.1	20p11.23	2013-01-08	2006-06-13		ENSG00000125846	ENSG00000125846		"""Zinc fingers, C2H2-type"", ""-"""	12917	protein-coding gene	gene with protein product		604075	"""zinc finger protein 150 (pHZ-66)"", ""zinc finger protein 133 (clone pHZ-13)"""	ZNF150		7557990, 7649249	Standard	XM_005260819		Approved	pHZ-13, pHZ-66	uc010gcs.3	P52736	OTTHUMG00000031965	ENST00000316358.4:c.235C>T	20.37:g.18295730C>T	ENSP00000346090:p.Leu79Phe	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	80	29	0.3625	NM_001083330	A8K5S4|B4DHU7|B4DIB8|B7ZAS1|F5H289|J3KQ11|J3KQJ0|Q53XU1|Q5JXV8|Q9BUV2|Q9H443	Missense_Mutation	SNP	ENST00000316358.4	37		276	0.12637362637362637	94	0.1910569105691057	32	0.08839779005524862	87	0.1520979020979021	63	0.08311345646437995	C	2.553	-0.303546	0.05495	0.149569	0.079186	ENSG00000125846	ENST00000377671;ENST00000360010;ENST00000396026;ENST00000402618;ENST00000401790;ENST00000434018;ENST00000316358;ENST00000425686	T;T;T;T;T;T;T;T	0.08546	3.3;5.36;3.3;3.08;3.29;5.47;3.29;5.48	3.88	1.8	0.24995	.	0.851711	0.09860	N	0.746399	T	0.00012	0.0000	L	0.52573	1.65	0.53688	P	2.199999999996649E-5	B;B;B;B	0.20671	0.025;0.037;0.047;0.036	B;B;B;B	0.19666	0.011;0.011;0.017;0.026	T	0.30534	-0.9975	9	0.54805	T	0.06	-6.1499	5.9997	0.19513	0.2648:0.5487:0.1865:0.0	rs34099160	16;82;79;78	B4DIB8;B4DHU7;P52736;P52736-2	.;.;ZN133_HUMAN;.	F	78;93;82;16;79;79;79;79	ENSP00000366899:L78F;ENSP00000353105:L93F;ENSP00000400897:L82F;ENSP00000385279:L16F;ENSP00000383945:L79F;ENSP00000403835:L79F;ENSP00000346090:L79F;ENSP00000406638:L79F	ENSP00000346090:L79F	L	+	1	0	ZNF133	18243730	0.000000	0.05858	0.012000	0.15200	0.017000	0.09413	0.080000	0.14802	0.512000	0.28257	0.655000	0.94253	CTC	C|0.894;T|0.106	0.106	strong		0.527	ZNF133-002	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000127616.1	NM_003434	
USP45	85015	hgsc.bcm.edu	37	6	99893878	99893878	+	Silent	SNP	T	T	C	rs12203426	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:99893878T>C	ENST00000327681.6	-	14	2302	c.1770A>G	c.(1768-1770)ttA>ttG	p.L590L	USP45_ENST00000392738.2_Silent_p.L270L|USP45_ENST00000500704.2_Silent_p.L590L|USP45_ENST00000369233.2_Silent_p.L542L|USP45_ENST00000539675.1_Intron	NM_001080481.1	NP_001073950.1	Q70EL2	UBP45_HUMAN	ubiquitin specific peptidase 45	590	USP.				protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)		ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			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)		GCTTCCCCTCTAAAAAACATA	0.353													T|||	325	0.0648962	0.0038	0.1455	5008	,	,		17767	0.001		0.1879	False		,,,				2504	0.0297				p.L590L		Atlas-SNP	.											.	USP45	56	.	0			c.A1770G						PASS	.	T		181,4223	105.2+/-143.6	5,171,2026	35.0	39.0	38.0		1770	1.8	0.0	6	dbSNP_120	38	1728,6872	306.8+/-308.1	182,1364,2754	no	coding-synonymous	USP45	NM_001080481.1		187,1535,4780	CC,CT,TT		20.093,4.1099,14.6801		590/815	99893878	1909,11095	2202	4300	6502	SO:0001819	synonymous_variant	85015	exon14			CCCCTCTAAAAAA	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.1770A>G	6.37:g.99893878T>C		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	58	27	0.465517	NM_001080481	B2RXG0|Q5T062|Q86T44|Q86TC0|Q9BRU1	Silent	SNP	ENST00000327681.6	37	CCDS34501.1																																																																																			T|0.876;C|0.124	0.124	strong		0.353	USP45-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041609.2	NM_032929	
ZNF516	9658	hgsc.bcm.edu	37	18	74091766	74091766	+	Silent	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:74091766C>T	ENST00000443185.2	-	4	2621	c.2304G>A	c.(2302-2304)aaG>aaA	p.K768K	ZNF516_ENST00000524431.2_5'UTR|RP11-504I13.3_ENST00000583287.1_RNA	NM_014643.3	NP_055458.1	Q92618	ZN516_HUMAN	zinc finger protein 516	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)			central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(7)|lung(11)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	32		Prostate(75;0.0869)|Esophageal squamous(42;0.129)		OV - Ovarian serous cystadenocarcinoma(15;7.64e-06)|BRCA - Breast invasive adenocarcinoma(31;0.238)		GGTAGTAGGTCTTGTGGCTGC	0.592																																					p.K768K		Atlas-SNP	.											.	ZNF516	102	.	0			c.G2304A						PASS	.						35.0	40.0	38.0					18																	74091766		2038	4187	6225	SO:0001819	synonymous_variant	9658	exon4			GTAGGTCTTGTGG	D86975	CCDS74234.1	18q23	2013-01-08				ENSG00000101493		"""Zinc fingers, C2H2-type"""	28990	protein-coding gene	gene with protein product		615114				9039502	Standard	NM_014643		Approved	HsT287, KIAA0222	uc021ulp.1	Q92618		ENST00000443185.2:c.2304G>A	18.37:g.74091766C>T		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	89	26	0.292135	NM_014643		Silent	SNP	ENST00000443185.2	37																																																																																				.	.	none		0.592	ZNF516-201	KNOWN	basic|appris_principal|exp_conf	protein_coding	protein_coding		NM_014643	
ZNF749	388567	hgsc.bcm.edu	37	19	57956186	57956186	+	Missense_Mutation	SNP	T	T	C	rs2240040	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:57956186T>C	ENST00000334181.4	+	3	1920	c.1670T>C	c.(1669-1671)gTg>gCg	p.V557A	AC004076.9_ENST00000596831.1_Intron	NM_001023561.2	NP_001018855.2	O43361	ZN749_HUMAN	zinc finger protein 749	557					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(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)		AGGCCTTATGTGTGTAGTGAA	0.463													T|||	135	0.0269569	0.0159	0.0058	5008	,	,		23092	0.0218		0.0169	False		,,,				2504	0.0726				p.V557A		Atlas-SNP	.											.	ZNF749	75	.	0			c.T1670C						PASS	.	T	ALA/VAL	67,4339	62.9+/-100.1	0,67,2136	93.0	90.0	91.0		1670	-2.5	0.0	19	dbSNP_98	91	197,8403	86.6+/-149.0	2,193,4105	yes	missense	ZNF749	NM_001023561.2	64	2,260,6241	CC,CT,TT		2.2907,1.5207,2.0298	benign	557/779	57956186	264,12742	2203	4300	6503	SO:0001583	missense	388567	exon3			CTTATGTGTGTAG	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.1670T>C	19.37:g.57956186T>C	ENSP00000333980:p.Val557Ala	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	147	62	0.421769	NM_001023561		Missense_Mutation	SNP	ENST00000334181.4	37	CCDS33132.2	31	0.014194139194139194	6	0.012195121951219513	3	0.008287292817679558	8	0.013986013986013986	14	0.018469656992084433	T	2.640	-0.284353	0.05605	0.015207	0.022907	ENSG00000186230	ENST00000334181	T	0.15139	2.45	1.22	-2.45	0.06481	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.03651	0.0104	N	0.17082	0.46	0.09310	N	1	B	0.11235	0.004	B	0.12156	0.007	T	0.25779	-1.0122	9	0.44086	T	0.13	.	2.228	0.03989	0.3133:0.0:0.192:0.4947	rs2240040;rs2240040	557	O43361	ZN749_HUMAN	A	557	ENSP00000333980:V557A	ENSP00000333980:V557A	V	+	2	0	ZNF749	62647998	0.000000	0.05858	0.014000	0.15608	0.166000	0.22503	-5.888000	0.00092	-2.223000	0.00726	-1.258000	0.01471	GTG	T|0.982;C|0.018	0.018	strong		0.463	ZNF749-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317879.1	NM_001023561	
OTUD3	23252	hgsc.bcm.edu	37	1	20233086	20233086	+	Missense_Mutation	SNP	G	G	A	rs10916668	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:20233086G>A	ENST00000375120.3	+	7	998	c.997G>A	c.(997-999)Gca>Aca	p.A333T		NM_015207.1	NP_056022.1	Q5T2D3	OTUD3_HUMAN	OTU deubiquitinase 3	333			A -> T (in dbSNP:rs10916668).		protein K11-linked deubiquitination (GO:0035871)|protein K6-linked deubiquitination (GO:0044313)		ubiquitin-specific protease activity (GO:0004843)			breast(1)|kidney(2)|large_intestine(4)|lung(1)|skin(1)	9		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000276)|Lung NSC(340;0.000338)|Breast(348;0.000812)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0181)|COAD - Colon adenocarcinoma(152;1.12e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000142)|Kidney(64;0.000177)|GBM - Glioblastoma multiforme(114;0.000408)|KIRC - Kidney renal clear cell carcinoma(64;0.00262)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)		AGAAAACAAAGCAAATAAAAA	0.478													G|||	252	0.0503195	0.0091	0.1182	5008	,	,		19749	0.0208		0.0567	False		,,,				2504	0.0818				p.A333T		Atlas-SNP	.											OTUD3,NS,carcinoma,-2,1	OTUD3	25	1	0			c.G997A						PASS	.	G	THR/ALA	62,3844		1,60,1892	85.0	85.0	85.0		997	3.7	1.0	1	dbSNP_120	85	514,7752		14,486,3633	yes	missense	OTUD3	NM_015207.1	58	15,546,5525	AA,AG,GG		6.2182,1.5873,4.7322	benign	333/399	20233086	576,11596	1953	4133	6086	SO:0001583	missense	23252	exon7			AACAAAGCAAATA	AB007928	CCDS41279.1	1p36.13	2014-02-24	2014-02-24		ENSG00000169914	ENSG00000169914		"""OTU domain containing"""	29038	protein-coding gene	gene with protein product		611758	"""OTU domain containing 3"""			9455484, 23827681	Standard	NM_015207		Approved	KIAA0459, DUBA4	uc001bcs.4	Q5T2D3	OTTHUMG00000002696	ENST00000375120.3:c.997G>A	1.37:g.20233086G>A	ENSP00000364261:p.Ala333Thr	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	103	48	0.466019	NM_015207	O75047	Missense_Mutation	SNP	ENST00000375120.3	37	CCDS41279.1	116	0.05311355311355311	4	0.008130081300813009	43	0.11878453038674033	18	0.03146853146853147	51	0.06728232189973615	G	13.74	2.328108	0.41197	0.015873	0.062182	ENSG00000169914	ENST00000375120	T	0.23147	1.92	5.88	3.67	0.42095	.	0.163049	0.53938	D	0.000057	T	0.00241	0.0007	L	0.31752	0.955	0.44048	D	0.996788	B	0.11235	0.004	B	0.10450	0.005	T	0.20672	-1.0268	10	0.19590	T	0.45	.	10.0034	0.41942	0.0855:0.1437:0.7708:0.0	rs10916668;rs52818455;rs57768647;rs10916668	333	Q5T2D3	OTUD3_HUMAN	T	333	ENSP00000364261:A333T	ENSP00000364261:A333T	A	+	1	0	OTUD3	20105673	1.000000	0.71417	0.991000	0.47740	0.704000	0.40688	1.730000	0.38125	1.482000	0.48325	0.650000	0.86243	GCA	G|0.948;A|0.052	0.052	strong		0.478	OTUD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007655.1		
C7orf31	136895	hgsc.bcm.edu	37	7	25181912	25181912	+	Missense_Mutation	SNP	T	T	C	rs2285738	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:25181912T>C	ENST00000409280.1	-	9	1207	c.899A>G	c.(898-900)cAt>cGt	p.H300R	C7orf31_ENST00000283905.3_Missense_Mutation_p.H300R			Q8N865	CG031_HUMAN	chromosome 7 open reading frame 31	300			H -> R (in dbSNP:rs2285738). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005, ECO:0000269|Ref.3}.							autonomic_ganglia(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(6)|skin(2)|stomach(1)	14						CATCTTTTCATGGTAATCATC	0.433													T|||	2734	0.545927	0.388	0.6124	5008	,	,		17060	0.4732		0.6769	False		,,,				2504	0.6524				p.H300R		Atlas-SNP	.											.	C7orf31	53	.	0			c.A899G						PASS	.	T	ARG/HIS	1872,2534	540.4+/-375.5	405,1062,736	115.0	99.0	105.0		899	4.6	1.0	7	dbSNP_100	105	5872,2728	682.1+/-403.8	1994,1884,422	yes	missense	C7orf31	NM_138811.3	29	2399,2946,1158	CC,CT,TT		31.7209,42.4875,40.4583	benign	300/591	25181912	7744,5262	2203	4300	6503	SO:0001583	missense	136895	exon9			TTTTCATGGTAAT	AK097248	CCDS5394.1	7p15.2	2011-11-24			ENSG00000153790	ENSG00000153790			21722	protein-coding gene	gene with protein product							Standard	NM_138811		Approved		uc003sxn.1	Q8N865	OTTHUMG00000128497	ENST00000409280.1:c.899A>G	7.37:g.25181912T>C	ENSP00000386604:p.His300Arg	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	76	59	0.776316	NM_138811	A4D165|Q6MZV8|Q6P989|Q7LE28|Q86XK1|Q8N1H5|Q96BN4	Missense_Mutation	SNP	ENST00000409280.1	37	CCDS5394.1	1202	0.5503663003663004	198	0.4024390243902439	222	0.6132596685082873	275	0.4807692307692308	507	0.6688654353562006	T	13.52	2.262555	0.39995	0.424875	0.682791	ENSG00000153790	ENST00000409280;ENST00000283905	T;T	0.06142	3.34;3.34	5.78	4.6	0.57074	.	0.286512	0.34200	N	0.004179	T	0.00012	0.0000	L	0.41824	1.3	0.35543	P	0.19680699999999995	B	0.20671	0.047	B	0.20955	0.032	T	0.07986	-1.0744	9	0.37606	T	0.19	-7.474	10.4479	0.44505	0.0:0.0757:0.0:0.9243	rs2285738;rs52828497;rs57917951;rs2285738	300	Q8N865	CG031_HUMAN	R	300	ENSP00000386604:H300R;ENSP00000283905:H300R	ENSP00000283905:H300R	H	-	2	0	C7orf31	25148437	1.000000	0.71417	1.000000	0.80357	0.880000	0.50808	3.591000	0.53986	0.975000	0.38392	0.402000	0.26972	CAT	T|0.428;C|0.572	0.572	strong		0.433	C7orf31-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326929.1	NM_138811	
ZNF343	79175	hgsc.bcm.edu	37	20	2464353	2464353	+	Silent	SNP	A	A	G	rs73085334	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:2464353A>G	ENST00000278772.4	-	6	1741	c.1254T>C	c.(1252-1254)ttT>ttC	p.F418F	RP4-734P14.4_ENST00000461548.1_Intron	NM_001282495.1|NM_001282496.1|NM_024325.4	NP_001269424.1|NP_001269425.1|NP_077301.4	Q6P1L6	ZN343_HUMAN	zinc finger protein 343	418				F -> S (in Ref. 1; BAC04892). {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)			breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(11)|skin(4)|upper_aerodigestive_tract(1)	25						AGTTCTGGCTAAAGCCTCGCC	0.498													A|||	114	0.0227636	0.0	0.0115	5008	,	,		22554	0.0		0.0239	False		,,,				2504	0.0838				p.F418F		Atlas-SNP	.											.	ZNF343	47	.	0			c.T1254C						PASS	.	A		8,4398	12.9+/-30.5	0,8,2195	110.0	101.0	104.0		1254	1.5	0.0	20	dbSNP_130	104	122,8478	63.9+/-126.0	0,122,4178	no	coding-synonymous	ZNF343	NM_024325.4		0,130,6373	GG,GA,AA		1.4186,0.1816,0.9995		418/600	2464353	130,12876	2203	4300	6503	SO:0001819	synonymous_variant	79175	exon6			CTGGCTAAAGCCT	AK096911	CCDS13028.1, CCDS74692.1, CCDS74693.1, CCDS74694.1	20p13	2013-01-08			ENSG00000088876	ENSG00000088876		"""Zinc fingers, C2H2-type"", ""-"""	16017	protein-coding gene	gene with protein product							Standard	NM_001282498		Approved	MGC10715	uc002wge.1	Q6P1L6	OTTHUMG00000031701	ENST00000278772.4:c.1254T>C	20.37:g.2464353A>G		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	72	43	0.597222	NM_024325	Q5JXU8|Q5JXU9|Q8N8F2|Q96EX8|Q96NA5|Q9BQB0	Silent	SNP	ENST00000278772.4	37	CCDS13028.1																																																																																			A|0.989;G|0.011	0.011	strong		0.498	ZNF343-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077617.1	NM_024325	
PRAMEF2	65122	hgsc.bcm.edu	37	1	12921137	12921137	+	Missense_Mutation	SNP	T	T	A	rs17039283	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:12921137T>A	ENST00000240189.2	+	4	1015	c.928T>A	c.(928-930)Ttg>Atg	p.L310M		NM_023014.1	NP_075390.1	O60811	PRAM2_HUMAN	PRAME family member 2	310			L -> M (in dbSNP:rs17039283).		negative regulation of apoptotic process (GO:0043066)|negative regulation of cell differentiation (GO:0045596)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)					breast(2)|endometrium(1)|kidney(2)|large_intestine(2)|lung(22)|prostate(6)|skin(3)|upper_aerodigestive_tract(4)	42	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00143)|all_lung(284;0.00181)|Colorectal(325;0.00215)|Breast(348;0.00224)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Colorectal(212;2.4e-06)|Kidney(185;4.89e-05)|COAD - Colon adenocarcinoma(227;0.000152)|KIRC - Kidney renal clear cell carcinoma(229;0.000194)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		AGAAGAGGACTTGAAGTGTCT	0.493																																					p.L310M		Atlas-SNP	.											PRAMEF2,NS,carcinoma,0,1	PRAMEF2	85	1	0			c.T928A						scavenged	.						132.0	134.0	133.0					1																	12921137		2202	4297	6499	SO:0001583	missense	65122	exon4			GAGGACTTGAAGT		CCDS149.1	1p36.21	2013-01-17			ENSG00000120952	ENSG00000120952		"""-"""	28841	protein-coding gene	gene with protein product							Standard	NM_023014		Approved	FLJ43580	uc001aum.1	O60811	OTTHUMG00000001986	ENST00000240189.2:c.928T>A	1.37:g.12921137T>A	ENSP00000240189:p.Leu310Met	Somatic	134	1	0.00746269		WXS	Illumina HiSeq	Phase_I	119	4	0.0336134	NM_023014		Missense_Mutation	SNP	ENST00000240189.2	37	CCDS149.1	.	.	.	.	.	.	.	.	.	.	G	2.970	-0.212708	0.06140	.	.	ENSG00000120952	ENST00000240189	T	0.01076	5.37	0.824	-1.65	0.08291	.	0.471727	0.17963	N	0.156117	T	0.00936	0.0031	N	0.25825	0.765	0.09310	N	1	B	0.06786	0.001	B	0.21360	0.034	T	0.44742	-0.9308	10	0.38643	T	0.18	.	5.2047	0.15285	0.0:0.0:0.2907:0.7093	rs17039283	310	O60811	PRAM2_HUMAN	M	310	ENSP00000240189:L310M	ENSP00000240189:L310M	L	+	1	2	PRAMEF2	12843724	0.011000	0.17503	0.001000	0.08648	0.011000	0.07611	-0.072000	0.11486	-1.430000	0.01985	-1.205000	0.01647	TTG	T|1.000;|0.000	.	weak		0.493	PRAMEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005517.1	NM_023014	
PTPRU	10076	hgsc.bcm.edu	37	1	29606589	29606589	+	Missense_Mutation	SNP	G	G	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:29606589G>C	ENST00000345512.3	+	11	1933	c.1804G>C	c.(1804-1806)Ggc>Cgc	p.G602R	PTPRU_ENST00000428026.2_Missense_Mutation_p.G602R|PTPRU_ENST00000356870.3_Missense_Mutation_p.G602R|PTPRU_ENST00000415600.2_3'UTR|PTPRU_ENST00000323874.8_Missense_Mutation_p.G602R|PTPRU_ENST00000373779.3_Missense_Mutation_p.G602R|PTPRU_ENST00000460170.2_Missense_Mutation_p.G602R	NM_005704.4	NP_005695.3	Q92729	PTPRU_HUMAN	protein tyrosine phosphatase, receptor type, U	602	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.				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)		GTCACCCCTGGGCGAGTCTGA	0.652																																					p.G602R		Atlas-SNP	.											.	PTPRU	374	.	0			c.G1804C						PASS	.						65.0	66.0	65.0					1																	29606589		2203	4300	6503	SO:0001583	missense	10076	exon11			CCCCTGGGCGAGT	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.1804G>C	1.37:g.29606589G>C	ENSP00000334941:p.Gly602Arg	Somatic	277	0	0		WXS	Illumina HiSeq	Phase_I	239	53	0.221757	NM_001195001	A6H8L1|O00197|P78399|Q59HA4|Q5SYU4|Q5SYU5|Q92735|Q92850	Missense_Mutation	SNP	ENST00000345512.3	37	CCDS334.1	.	.	.	.	.	.	.	.	.	.	G	17.62	3.434280	0.62955	.	.	ENSG00000060656	ENST00000345512;ENST00000373779;ENST00000356870;ENST00000323874;ENST00000428026;ENST00000460170	T;T;T;T;T;T	0.31510	1.53;1.55;1.55;1.55;1.49;1.55	5.25	5.25	0.73442	.	0.059602	0.64402	D	0.000002	T	0.24044	0.0582	N	0.25647	0.755	0.38689	D	0.952724	P;P;P;P;P	0.48089	0.905;0.905;0.905;0.846;0.846	B;B;B;B;B	0.43251	0.413;0.413;0.413;0.235;0.235	T	0.04454	-1.0950	9	.	.	.	.	13.2132	0.59836	0.0793:0.0:0.9207:0.0	.	602;602;602;602;602	Q92729-3;Q92729-4;Q92729-2;E9PH42;Q92729	.;.;.;.;PTPRU_HUMAN	R	602	ENSP00000334941:G602R;ENSP00000362884:G602R;ENSP00000349333:G602R;ENSP00000314987:G602R;ENSP00000392332:G602R;ENSP00000432906:G602R	.	G	+	1	0	PTPRU	29479176	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	3.471000	0.53107	2.432000	0.82394	0.544000	0.68410	GGC	.	.	none		0.652	PTPRU-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010447.1		
TRAF3IP1	26146	hgsc.bcm.edu	37	2	239306268	239306268	+	Missense_Mutation	SNP	A	A	C	rs3739070	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:239306268A>C	ENST00000373327.4	+	16	2080	c.1858A>C	c.(1858-1860)Atg>Ctg	p.M620L	TRAF3IP1_ENST00000391993.3_Missense_Mutation_p.M554L|TRAF3IP1_ENST00000391994.2_Missense_Mutation_p.M620L	NM_015650.3	NP_056465.2	Q8TDR0	MIPT3_HUMAN	TNF receptor-associated factor 3 interacting protein 1	620	DISC1-interaction domain.		M -> L (in dbSNP:rs3739070).		cilium assembly (GO:0042384)|embryonic camera-type eye development (GO:0031076)|embryonic digit morphogenesis (GO:0042733)|embryonic heart tube development (GO:0035050)|intraciliary transport (GO:0042073)|negative regulation of defense response to virus (GO:0050687)|negative regulation of interferon-beta production (GO:0032688)|negative regulation of smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:1901621)|neural tube patterning (GO:0021532)|post-anal tail morphogenesis (GO:0036342)	axoneme (GO:0005930)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cilium (GO:0005929)|intraciliary transport particle B (GO:0030992)				breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(9)|ovary(2)|prostate(1)|skin(2)	23		all_epithelial(40;3.22e-10)|Breast(86;0.000523)|Renal(207;0.00571)|Ovarian(221;0.156)|all_hematologic(139;0.182)		Epithelial(121;9.92e-24)|OV - Ovarian serous cystadenocarcinoma(60;7.85e-12)|Kidney(56;3.21e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.01e-07)|BRCA - Breast invasive adenocarcinoma(100;7.72e-05)|Lung(119;0.00942)|LUSC - Lung squamous cell carcinoma(224;0.0184)		TGAGCTGCAGATGTGGCACAG	0.627													C|||	214	0.0427316	0.0106	0.0274	5008	,	,		15864	0.0516		0.0895	False		,,,				2504	0.0399				p.M620L		Atlas-SNP	.											.	TRAF3IP1	58	.	0			c.A1858C						PASS	.	C	LEU/MET,LEU/MET	103,4303	813.6+/-416.1	2,99,2102	74.0	71.0	72.0	http://www.ncbi.nlm.nih.gov/pubmed?term	1660,1858	2.6	1.0	2	dbSNP_107	72	667,7933	787.4+/-407.6	28,611,3661	yes	missense,missense	TRAF3IP1	NM_001139490.1,NM_015650.3	15,15	30,710,5763	CC,CA,AA	http://www.ncbi.nlm.nih.gov/pubmed?term	7.7558,2.3377,5.9203	benign,benign	554/626,620/692	239306268	770,12236	2203	4300	6503	SO:0001583	missense	26146	exon16			CTGCAGATGTGGC	AF230877	CCDS33415.1, CCDS46557.1	2q37.3	2014-02-21			ENSG00000204104	ENSG00000204104		"""Intraflagellar transport homologs"""	17861	protein-coding gene	gene with protein product	"""microtubule interacting protein that associates with TRAF3"""	607380				10791955, 12935900	Standard	NM_015650		Approved	MIP-T3, DKFZP434F124, MIPT3, IFT54	uc002vye.3	Q8TDR0	OTTHUMG00000152872	ENST00000373327.4:c.1858A>C	2.37:g.239306268A>C	ENSP00000362424:p.Met620Leu	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	99	41	0.414141	NM_015650	Q6PCT1|Q7L8N9|Q9NRD6|Q9Y4Q1	Missense_Mutation	SNP	ENST00000373327.4	37	CCDS33415.1	120	0.054945054945054944	6	0.012195121951219513	9	0.024861878453038673	33	0.057692307692307696	72	0.09498680738786279	C	2.785	-0.252637	0.05829	0.023377	0.077558	ENSG00000204104	ENST00000391993;ENST00000373327;ENST00000391994;ENST00000440998	T;T;T	0.14893	2.47;2.47;2.47	5.54	2.58	0.30949	.	0.690978	0.14509	N	0.315214	T	0.00210	0.0006	N	0.02775	-0.495	0.54753	P	1.6000000000016E-5	B;B	0.02656	0.0;0.0	B;B	0.06405	0.001;0.002	T	0.37549	-0.9701	9	0.05959	T	0.93	-11.6679	5.0849	0.14676	0.5262:0.2946:0.1062:0.073	rs3739070;rs52836335;rs58288257;rs3739070	554;620	Q8TDR0-2;Q8TDR0	.;MIPT3_HUMAN	L	554;620;620;554	ENSP00000375851:M554L;ENSP00000362424:M620L;ENSP00000375852:M620L	ENSP00000362424:M620L	M	+	1	0	TRAF3IP1	238971007	0.958000	0.32768	1.000000	0.80357	0.750000	0.42670	0.124000	0.15728	0.698000	0.31739	-0.121000	0.15023	ATG	A|0.944;C|0.056	0.056	strong		0.627	TRAF3IP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000328312.1	NM_015650	
VSX1	30813	hgsc.bcm.edu	37	20	25059442	25059442	+	Intron	SNP	C	C	T	rs6138482	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:25059442C>T	ENST00000376709.4	-	3	891				VSX1_ENST00000376707.3_Missense_Mutation_p.R217H|VSX1_ENST00000451258.1_Intron|VSX1_ENST00000429762.3_Intron|VSX1_ENST00000444511.2_Intron|VSX1_ENST00000424574.1_Intron	NM_014588.5	NP_055403.2	Q9NZR4	VSX1_HUMAN	visual system homeobox 1						neuron maturation (GO:0042551)|response to stimulus (GO:0050896)|retinal bipolar neuron differentiation (GO:0060040)|transcription, DNA-templated (GO:0006351)|visual perception (GO:0007601)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|large_intestine(3)|lung(2)	6						ATCTTTGGAGCGGAGAAAAGG	0.527													c|||	1080	0.215655	0.0098	0.2147	5008	,	,		17699	0.5268		0.2137	False		,,,				2504	0.1759				p.R217H		Atlas-SNP	.											.	VSX1	20	.	0			c.G650A						PASS	.	T	,HIS/ARG	191,4215	120.4+/-158.0	4,183,2016	204.0	203.0	203.0		,650	-4.9	0.0	20	dbSNP_114	203	1700,6900	312.0+/-310.6	161,1378,2761	yes	intron,missense	VSX1	NM_014588.4,NM_199425.1	,29	165,1561,4777	TT,TC,CC		19.7674,4.335,14.5394	,	,217/240	25059442	1891,11115	2203	4300	6503	SO:0001627	intron_variant	30813	exon3			TTGGAGCGGAGAA	AF176797	CCDS13168.1, CCDS13169.1, CCDS58766.1, CCDS58767.1	20p11.21	2014-02-14	2007-07-12		ENSG00000100987	ENSG00000100987		"""Homeoboxes / PRD class"""	12723	protein-coding gene	gene with protein product		605020	"""posterior polymorphous corneal dystrophy"", ""visual system homeobox 1 homolog, CHX10-like (zebrafish)"""	PPCD		10673340	Standard	NM_001256272		Approved	PPD, PPCD1	uc002wuf.4	Q9NZR4	OTTHUMG00000032111	ENST00000376709.4:c.627+22G>A	20.37:g.25059442C>T		Somatic	214	0	0		WXS	Illumina HiSeq	Phase_I	163	78	0.478528	NM_199425	B9EGJ4|D1MF28|Q0GM60|Q0GM61|Q0GM62|Q0GM63|Q0GM64|Q0GM65|Q5TF40|Q5TF41|Q9HCU3|Q9NU27	Missense_Mutation	SNP	ENST00000376709.4	37	CCDS13168.1	578	0.26465201465201466	14	0.028455284552845527	86	0.23756906077348067	321	0.5611888111888111	157	0.20712401055408972	c	11.23	1.577349	0.28180	0.04335	0.197674	ENSG00000100987	ENST00000376707	D	0.93366	-3.21	4.23	-4.87	0.03123	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.13594	0.008	B	0.04013	0.001	T	0.39722	-0.9600	7	0.87932	D	0	.	0.4641	0.00521	0.3084:0.1187:0.2286:0.3443	rs6138482;rs58752432;rs6138482	217	Q9NZR4-2	.	H	217	ENSP00000365897:R217H	ENSP00000365897:R217H	R	-	2	0	VSX1	25007442	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.065000	0.11617	-1.182000	0.02727	-1.590000	0.00845	CGC	C|0.759;T|0.241	0.241	strong		0.527	VSX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078384.3		
PITRM1	10531	hgsc.bcm.edu	37	10	3180298	3180298	+	Silent	SNP	C	C	T	rs10175	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:3180298C>T	ENST00000224949.4	-	27	3073	c.3039G>A	c.(3037-3039)aaG>aaA	p.K1013K	PITRM1_ENST00000380994.1_Silent_p.K571K|PITRM1_ENST00000380989.2_Silent_p.K1014K|PITRM1_ENST00000451104.2_Silent_p.K915K|PITRM1_ENST00000464395.1_5'UTR			Q5JRX3	PREP_HUMAN	pitrilysin metallopeptidase 1	1013					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						CGTGTGTGCTCTTCCCAGTGC	0.607													C|||	1180	0.235623	0.2027	0.3473	5008	,	,		17500	0.1617		0.3121	False		,,,				2504	0.1984				p.K1014K		Atlas-SNP	.											.	PITRM1	109	.	0			c.G3042A						PASS	.	C	,,	989,3275		113,763,1256	46.0	51.0	49.0		3042,2745,3039	1.8	0.2	10	dbSNP_52	49	2305,6179		314,1677,2251	no	coding-synonymous,coding-synonymous,coding-synonymous	PITRM1	NM_001242307.1,NM_001242309.1,NM_014889.3	,,	427,2440,3507	TT,TC,CC		27.1688,23.1942,25.8393	,,	1014/1039,915/940,1013/1038	3180298	3294,9454	2132	4242	6374	SO:0001819	synonymous_variant	10531	exon27			TGTGCTCTTCCCA	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.3039G>A	10.37:g.3180298C>T		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	77	34	0.441558	NM_001242307	B3KMJ6|B4E0J8|C9JSL2|E7ES23|O95204|Q2M2G6|Q4VBR1|Q5JRW7|Q7L5Z7|Q9BSI6|Q9BVJ5|Q9UPP8	Silent	SNP	ENST00000224949.4	37	CCDS59208.1																																																																																			C|0.756;T|0.244	0.244	strong		0.607	PITRM1-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000046469.2		
TMCO3	55002	hgsc.bcm.edu	37	13	114154419	114154419	+	Silent	SNP	G	G	A	rs2260159	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:114154419G>A	ENST00000434316.2	+	4	1130	c.771G>A	c.(769-771)aaG>aaA	p.K257K	TMCO3_ENST00000375391.1_Silent_p.K257K|TMCO3_ENST00000474393.1_3'UTR	NM_017905.4	NP_060375.4	Q6UWJ1	TMCO3_HUMAN	transmembrane and coiled-coil domains 3	257						integral component of membrane (GO:0016021)	solute:proton antiporter activity (GO:0015299)			NS(1)|endometrium(4)|large_intestine(9)|liver(1)|lung(8)|prostate(1)|stomach(1)	25	Lung NSC(43;0.0161)|all_neural(89;0.0337)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0145)|all_epithelial(44;0.00286)|all_lung(25;0.0273)|Breast(118;0.0411)|Lung NSC(25;0.0983)	all cancers(43;0.0317)			TTTTGACCAAGCCCAGAGATT	0.463													.|||	1019	0.203474	0.4092	0.1369	5008	,	,		16314	0.1488		0.1292	False		,,,				2504	0.1053				p.K257K		Atlas-SNP	.											.	TMCO3	77	.	0			c.G771A						PASS	.	G		1511,2895	481.5+/-359.1	256,999,948	119.0	120.0	120.0		771	1.5	0.9	13	dbSNP_100	120	1086,7514	226.2+/-262.0	62,962,3276	yes	coding-synonymous	TMCO3	NM_017905.4		318,1961,4224	AA,AG,GG		12.6279,34.2941,19.9677		257/678	114154419	2597,10409	2203	4300	6503	SO:0001819	synonymous_variant	55002	exon4			GACCAAGCCCAGA	BC012564	CCDS9537.1	13q34	2008-02-05	2005-07-22	2005-07-22	ENSG00000150403	ENSG00000150403			20329	protein-coding gene	gene with protein product			"""chromosome 13 open reading frame 11"""	C13orf11			Standard	NM_017905		Approved	FLJ20623	uc001vtu.4	Q6UWJ1	OTTHUMG00000017389	ENST00000434316.2:c.771G>A	13.37:g.114154419G>A		Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	141	76	0.539007	NM_017905	Q5JSB1|Q6NUN1|Q8NG29|Q8TCI6|Q96EA6|Q9NWT2	Silent	SNP	ENST00000434316.2	37	CCDS9537.1																																																																																			G|0.796;A|0.204	0.204	strong		0.463	TMCO3-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045931.3	NM_017905	
PRRT4	401399	hgsc.bcm.edu	37	7	127999645	127999645	+	Missense_Mutation	SNP	C	C	T	rs56272205	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:127999645C>T	ENST00000446477.2	-	3	714	c.401G>A	c.(400-402)cGg>cAg	p.R134Q	PRRT4_ENST00000489835.2_Missense_Mutation_p.R134Q|PRRT4_ENST00000435512.1_Missense_Mutation_p.R134Q|PRRT4_ENST00000535159.1_Missense_Mutation_p.R134Q	NM_001174164.1	NP_001167635.1	C9JH25	PRRT4_HUMAN	proline-rich transmembrane protein 4	134						integral component of membrane (GO:0016021)				endometrium(4)|prostate(1)	5						CCCAGAGCGCCGGGATGTGGA	0.647													C|||	612	0.122204	0.0847	0.0994	5008	,	,		14883	0.1131		0.162	False		,,,				2504	0.1575				p.R134Q		Atlas-SNP	.											PRRT4,caecum,carcinoma,0,1	PRRT4	31	1	0			c.G401A						PASS	.	C	GLN/ARG,GLN/ARG	102,1282		2,98,592	14.0	18.0	17.0		401,401	-0.4	0.0	7	dbSNP_129	17	507,2675		45,417,1129	yes	missense,missense	PRRT4	NM_001174164.1,NM_001114726.2	43,43	47,515,1721	TT,TC,CC		15.9334,7.3699,13.3377	benign,benign	134/900,134/430	127999645	609,3957	692	1591	2283	SO:0001583	missense	401399	exon3			GAGCGCCGGGATG	BC063892	CCDS47698.1, CCDS47698.2, CCDS55160.1	7q32.1	2011-10-10			ENSG00000224940	ENSG00000224940		"""Proline-rich transmembrane proteins"""	37280	protein-coding gene	gene with protein product							Standard	NM_001114726		Approved		uc022aky.1	C9JH25	OTTHUMG00000157714	ENST00000446477.2:c.401G>A	7.37:g.127999645C>T	ENSP00000415026:p.Arg134Gln	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	63	39	0.619048	NM_001174164	A4D0Z9|C9JVW7	Missense_Mutation	SNP	ENST00000446477.2	37	CCDS55160.1	273	0.125	45	0.09146341463414634	41	0.1132596685082873	82	0.14335664335664336	105	0.13852242744063326	C	5.695	0.312812	0.10789	0.073699	0.159334	ENSG00000224940	ENST00000489835;ENST00000446477;ENST00000535159;ENST00000435512;ENST00000489517;ENST00000464607;ENST00000495931	.	.	.	5.27	-0.37	0.12530	.	.	.	.	.	T	0.00109	0.0003	N	0.22421	0.69	0.80722	P	0.0	B;B	0.32128	0.357;0.307	B;B	0.26969	0.075;0.031	T	0.18023	-1.0350	7	0.25106	T	0.35	-0.5031	9.8115	0.40826	0.0916:0.5967:0.3116:0.0	rs56272205;rs61746550	134;134	C9JH25;C9JH25-2	PRRT4_HUMAN;.	Q	134	.	ENSP00000410779:R134Q	R	-	2	0	PRRT4	127786881	0.217000	0.23597	0.008000	0.14137	0.004000	0.04260	0.510000	0.22723	-0.060000	0.13132	-0.353000	0.07706	CGG	A|0.000;C|0.874;T|0.126	0.126	strong		0.647	PRRT4-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001114726	
UGT2B7	7364	hgsc.bcm.edu	37	4	69964338	69964338	+	Missense_Mutation	SNP	T	T	C	rs7439366|rs386675647	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:69964338T>C	ENST00000508661.1	+	2	829	c.802T>C	c.(802-804)Tat>Cat	p.Y268H	UGT2B7_ENST00000305231.7_Missense_Mutation_p.Y268H|UGT2B7_ENST00000509763.1_3'UTR			P16662	UD2B7_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide B7	268			H -> Y (in allele UGT2B7*2; dbSNP:rs7439366). {ECO:0000269|PubMed:11186130, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:15815621, ECO:0000269|Ref.3}.		androgen metabolic process (GO:0008209)|cellular glucuronidation (GO:0052695)|lipid metabolic process (GO:0006629)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	glucuronosyltransferase activity (GO:0015020)			autonomic_ganglia(1)|endometrium(3)|kidney(4)|large_intestine(6)|lung(16)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	38					Atorvastatin(DB01076)|Carbamazepine(DB00564)|Chenodeoxycholic acid(DB06777)|Codeine(DB00318)|Dabigatran etexilate(DB06695)|Dapagliflozin(DB06292)|Diclofenac(DB00586)|Epirubicin(DB00445)|Etodolac(DB00749)|Ezetimibe(DB00973)|Flunitrazepam(DB01544)|Flurbiprofen(DB00712)|Fluvastatin(DB01095)|Ibuprofen(DB01050)|Indomethacin(DB00328)|Losartan(DB00678)|Lovastatin(DB00227)|Mitiglinide(DB01252)|Morphine(DB00295)|Mycophenolate mofetil(DB00688)|Mycophenolic acid(DB01024)|Naproxen(DB00788)|Oxazepam(DB00842)|Pitavastatin(DB08860)|Silodosin(DB06207)|Simvastatin(DB00641)|Suprofen(DB00870)|Tapentadol(DB06204)|Valproic Acid(DB00313)|Zidovudine(DB00495)	TCAGTTTCCATATCCACTCTT	0.398													T|||	3331	0.665136	0.7731	0.6801	5008	,	,		15458	0.7252		0.5149	False		,,,				2504	0.6012				p.Y268H		Atlas-SNP	.											.	UGT2B7	79	.	0			c.T802C	GRCh37	CM057512	UGT2B7	M	rs7439366	PASS	.	T	HIS/TYR	1242,3164		471,300,1432	157.0	161.0	160.0		802	1.8	0.2	4	dbSNP_116	160	1078,7520		390,298,3611	no	missense	UGT2B7	NM_001074.2	83	861,598,5043	CC,CT,TT		12.5378,28.1888,17.8407	benign	268/530	69964338	2320,10684	2203	4299	6502	SO:0001583	missense	7364	exon2			TTTCCATATCCAC	BC030974	CCDS3526.1	4q13	2008-02-05	2005-07-20		ENSG00000171234	ENSG00000171234		"""UDP glucuronosyltransferases"""	12554	protein-coding gene	gene with protein product		600068	"""UDP glycosyltransferase 2 family, polypeptide B7"""			2159463, 7835904	Standard	NM_001074		Approved	UGT2B9	uc003heg.4	P16662	OTTHUMG00000129404	ENST00000508661.1:c.802T>C	4.37:g.69964338T>C	ENSP00000427659:p.Tyr268His	Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	140	91	0.65	NM_001074	B2R810|Q6GTW0	Missense_Mutation	SNP	ENST00000508661.1	37		1163	0.5325091575091575	291	0.5914634146341463	209	0.5773480662983426	353	0.6171328671328671	310	0.40897097625329815	T	0.705	-0.789279	0.02884	0.281888	0.125378	ENSG00000171234	ENST00000502942;ENST00000305231;ENST00000508661	T;T;T	0.59224	0.28;0.28;0.28	2.68	1.83	0.25207	.	0.223547	0.38381	N	0.001702	T	0.00012	0.0000	.	.	.	0.50313	P	1.3700000000005375E-4	B	0.02656	0.0	B	0.04013	0.001	T	0.46484	-0.9188	7	.	.	.	.	7.7078	0.28661	0.0:0.8631:0.0:0.1369	rs7439366;rs34924067;rs57980137;rs7439366	268	E9PBP8	.	H	19;268;268	ENSP00000426206:Y19H;ENSP00000304811:Y268H;ENSP00000427659:Y268H	.	Y	+	1	0	UGT2B7	69998927	0.022000	0.18835	0.172000	0.22920	0.003000	0.03518	1.919000	0.40015	0.441000	0.26529	-0.221000	0.12465	TAT	T|0.443;C|0.557	0.557	strong		0.398	UGT2B7-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000362103.1	NM_001074	
FSCB	84075	hgsc.bcm.edu	37	14	44974966	44974966	+	Missense_Mutation	SNP	G	G	A	rs1959379	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:44974966G>A	ENST00000340446.4	-	1	1516	c.1225C>T	c.(1225-1227)Cca>Tca	p.P409S	RP11-163M18.1_ENST00000557465.1_RNA|RP11-163M18.1_ENST00000555433.1_RNA	NM_032135.3	NP_115511.3	Q5H9T9	FSCB_HUMAN	fibrous sheath CABYR binding protein	409	Pro-rich.		P -> S (in dbSNP:rs1959379). {ECO:0000269|PubMed:15489334}.			sperm fibrous sheath (GO:0035686)|sperm principal piece (GO:0097228)	calcium ion binding (GO:0005509)			breast(4)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(10)|lung(47)|ovary(2)|pancreas(1)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(1)	89				GBM - Glioblastoma multiforme(112;0.128)		ACTTTAGCTGGGGCCTCTTCA	0.517													G|||	1358	0.271166	0.2859	0.3055	5008	,	,		17836	0.3968		0.1193	False		,,,				2504	0.2536				p.P409S		Atlas-SNP	.											.	FSCB	173	.	0			c.C1225T						PASS	.	G	SER/PRO	1149,3249		151,847,1201	39.0	44.0	42.0		1225	-8.3	0.0	14	dbSNP_92	42	933,7661		53,827,3417	yes	missense	FSCB	NM_032135.3	74	204,1674,4618	AA,AG,GG		10.8564,26.1255,16.0252	possibly-damaging	409/826	44974966	2082,10910	2199	4297	6496	SO:0001583	missense	84075	exon1			TAGCTGGGGCCTC	AK124110	CCDS9679.1	14q21.3	2007-11-22	2007-11-22	2007-11-22	ENSG00000189139	ENSG00000189139			20494	protein-coding gene	gene with protein product		611779	"""chromosome 14 open reading frame 155"""	C14orf155		17855365	Standard	NM_032135		Approved	DKFZP434F1017	uc001wvn.3	Q5H9T9	OTTHUMG00000140262	ENST00000340446.4:c.1225C>T	14.37:g.44974966G>A	ENSP00000344579:p.Pro409Ser	Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	77	23	0.298701	NM_032135	Q5H9U7|Q86YI2|Q9H0J3	Missense_Mutation	SNP	ENST00000340446.4	37	CCDS9679.1	542	0.24816849816849818	138	0.2804878048780488	97	0.26795580110497236	223	0.38986013986013984	84	0.11081794195250659	G	6.900	0.535552	0.13188	0.261255	0.108564	ENSG00000189139	ENST00000340446;ENST00000537803	T	0.19806	2.12	4.49	-8.33	0.00992	.	.	.	.	.	T	0.00012	0.0000	L	0.43152	1.355	0.80722	P	0.0	B	0.09022	0.002	B	0.08055	0.003	T	0.44711	-0.9310	8	0.31617	T	0.26	1.5439	3.3091	0.07010	0.4878:0.176:0.2415:0.0947	rs1959379;rs3825631;rs17855637;rs52807156;rs1959379	409	Q5H9T9	FSCB_HUMAN	S	409	ENSP00000344579:P409S	ENSP00000344579:P409S	P	-	1	0	FSCB	44044716	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-2.632000	0.00870	-1.724000	0.01373	-0.783000	0.03347	CCA	G|0.811;A|0.189	0.189	strong		0.517	FSCB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276788.1	NM_032135	
DDR1	780	hgsc.bcm.edu	37	6	30864829	30864829	+	Silent	SNP	T	T	C	rs1049623	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:30864829T>C	ENST00000324771.8	+	16	2456	c.1908T>C	c.(1906-1908)gtT>gtC	p.V636V	DDR1_ENST00000418800.2_Silent_p.V599V|DDR1_ENST00000376568.3_Silent_p.V636V|DDR1_ENST00000376570.4_Silent_p.V599V|DDR1_ENST00000376569.3_Silent_p.V599V|DDR1_ENST00000452441.1_Silent_p.V636V|DDR1_ENST00000513240.1_Silent_p.V636V|DDR1_ENST00000361741.4_Silent_p.V303V|DDR1_ENST00000376567.2_Silent_p.V599V|DDR1_ENST00000376575.3_Silent_p.V636V|DDR1_ENST00000454612.2_Silent_p.V599V|DDR1_ENST00000446312.1_3'UTR|DDR1_ENST00000508312.1_Silent_p.V617V			Q08345	DDR1_HUMAN	discoidin domain receptor tyrosine kinase 1	636	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				branching involved in mammary gland duct morphogenesis (GO:0060444)|cell adhesion (GO:0007155)|collagen-activated tyrosine kinase receptor signaling pathway (GO:0038063)|ear development (GO:0043583)|embryo implantation (GO:0007566)|extracellular matrix organization (GO:0030198)|lactation (GO:0007595)|mammary gland alveolus development (GO:0060749)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine autophosphorylation (GO:0038083)|protein autophosphorylation (GO:0046777)|regulation of cell growth (GO:0001558)|regulation of cell-matrix adhesion (GO:0001952)|regulation of extracellular matrix disassembly (GO:0010715)|smooth muscle cell migration (GO:0014909)|smooth muscle cell-matrix adhesion (GO:0061302)|wound healing, spreading of cells (GO:0044319)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|collagen binding (GO:0005518)|metal ion binding (GO:0046872)|protein tyrosine kinase collagen receptor activity (GO:0038062)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			central_nervous_system(3)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(14)|ovary(1)|prostate(1)|skin(1)	29					Imatinib(DB00619)	AAGATCTGGTTAGTCTTGATT	0.512													C|||	2683	0.535743	0.4531	0.5245	5008	,	,		14894	0.6667		0.3847	False		,,,				2504	0.6759				p.V636V		Atlas-SNP	.											DDR1_ENST00000376575,NS,adenoma,0,3	DDR1	213	3	0			c.T1908C	GRCh37	CM076148	DDR1	M	rs1049623	PASS	.	C	,,,,,	2008,2398	615.9+/-392.7	473,1062,668	203.0	181.0	189.0		,1470,1851,1797,1908,1908	5.3	1.0	6	dbSNP_86	189	3287,5313	648.3+/-400.5	620,2047,1633	no	utr-3,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	DDR1	NM_001202521.1,NM_001202522.1,NM_001202523.1,NM_001954.4,NM_013993.2,NM_013994.2	,,,,,	1093,3109,2301	CC,CT,TT		38.2209,45.5742,40.712	,,,,,	,490/768,617/895,599/877,636/914,636/920	30864829	5295,7711	2203	4300	6503	SO:0001819	synonymous_variant	780	exon13			TCTGGTTAGTCTT	X99031	CCDS4690.1, CCDS34385.1, CCDS47396.1, CCDS56411.1, CCDS75419.1	6p21.33	2010-02-17	2008-01-23		ENSG00000204580	ENSG00000204580	2.7.10.1	"""CD molecules"""	2730	protein-coding gene	gene with protein product		600408	"""discoidin domain receptor family, member 1"""	NTRK4, PTK3A, NEP, CAK, EDDR1		7789998	Standard	NM_001954		Approved	RTK6, CD167	uc003nrv.3	Q08345	OTTHUMG00000031236	ENST00000324771.8:c.1908T>C	6.37:g.30864829T>C		Somatic	208	0	0		WXS	Illumina HiSeq	Phase_I	168	86	0.511905	NM_013994	B5A975|B5A976|B7Z2K0|Q14196|Q16562|Q2L6H3|Q4LE50|Q5ST11|Q5ST12|Q6NSK4|Q9UD35|Q9UD36|Q9UD37|Q9UD86|Q9UDL2	Silent	SNP	ENST00000324771.8	37	CCDS34385.1	1109	0.5077838827838828	252	0.5121951219512195	189	0.5220994475138122	349	0.6101398601398601	319	0.420844327176781	C	10.41	1.343892	0.24339	0.455742	0.382209	ENSG00000204580	ENST00000514434	.	.	.	5.29	5.29	0.74685	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	0.9999999999999912	.	.	.	.	.	.	.	.	.	.	.	.	.	.	7.79	0.29114	0.0:0.7501:0.1626:0.0873	rs1049623;rs1264316;rs2228636;rs3173380;rs17413087;rs58133601;rs1049623	.	.	.	Q	128	.	.	X	+	1	0	DDR1	30972808	0.012000	0.17670	1.000000	0.80357	0.871000	0.50021	0.586000	0.23894	1.250000	0.43966	-0.215000	0.12644	TAG	T|0.539;C|0.461	0.461	strong		0.512	DDR1-005	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076494.3	NM_013994	
C10orf120	399814	hgsc.bcm.edu	37	10	124459139	124459139	+	Silent	SNP	T	T	C	rs11813597	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:124459139T>C	ENST00000329446.4	-	1	199	c.168A>G	c.(166-168)tcA>tcG	p.S56S		NM_001010912.1	NP_001010912.1	Q5SQS8	CJ120_HUMAN	chromosome 10 open reading frame 120	56								p.S56S(1)		endometrium(1)|kidney(1)|large_intestine(6)|lung(9)|skin(2)|stomach(1)|urinary_tract(1)	21		all_neural(114;0.169)|Glioma(114;0.222)				ACCGCAACGGTGAAGCAGAAC	0.478													T|||	2233	0.445887	0.4145	0.33	5008	,	,		19618	0.5327		0.4076	False		,,,				2504	0.5204				p.S56S		Atlas-SNP	.											C10orf120,NS,carcinoma,0,1	C10orf120	55	1	1	Substitution - coding silent(1)	stomach(1)	c.A168G						PASS	.	T		1827,2579	533.7+/-373.8	391,1045,767	99.0	86.0	90.0		168	-1.2	0.0	10	dbSNP_120	90	3560,5040	518.0+/-379.2	740,2080,1480	no	coding-synonymous	C10orf120	NM_001010912.1		1131,3125,2247	CC,CT,TT		41.3953,41.4662,41.4193		56/336	124459139	5387,7619	2203	4300	6503	SO:0001819	synonymous_variant	399814	exon1			CAACGGTGAAGCA		CCDS31302.1	10q26.13	2012-06-12			ENSG00000183559	ENSG00000183559			25707	protein-coding gene	gene with protein product							Standard	NM_001010912		Approved	bA318C4.1	uc001lgn.3	Q5SQS8	OTTHUMG00000019187	ENST00000329446.4:c.168A>G	10.37:g.124459139T>C		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	111	54	0.486486	NM_001010912	B2RU17	Silent	SNP	ENST00000329446.4	37	CCDS31302.1	966	0.4423076923076923	229	0.4654471544715447	143	0.39502762430939226	290	0.506993006993007	304	0.40105540897097625	T	4.042	0.005438	0.07866	0.414662	0.413953	ENSG00000183559	ENST00000432000	.	.	.	4.28	-1.2	0.09554	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.58432	P	1.0000000000287557E-6	.	.	.	.	.	.	T	0.47959	-0.9076	3	.	.	.	-0.4259	6.7398	0.23428	0.0:0.0978:0.5383:0.3639	rs11813597;rs17649853;rs11813597	.	.	.	R	49	.	.	H	-	2	0	C10orf120	124449129	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.094000	0.11094	-0.300000	0.08895	-0.323000	0.08544	CAC	C|0.427;N|0.000	0.427	strong		0.478	C10orf120-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050803.1	NM_001010912	
MMP13	4322	hgsc.bcm.edu	37	11	102825227	102825227	+	Silent	SNP	G	G	A	rs368161332		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:102825227G>A	ENST00000260302.3	-	3	499	c.471C>T	c.(469-471)caC>caT	p.H157H	MMP13_ENST00000340273.4_Silent_p.H157H	NM_002427.3	NP_002418.1	P45452	MMP13_HUMAN	matrix metallopeptidase 13 (collagenase 3)	157					bone mineralization (GO:0030282)|bone morphogenesis (GO:0060349)|cartilage development (GO:0051216)|cellular protein metabolic process (GO:0044267)|collagen catabolic process (GO:0030574)|endochondral ossification (GO:0001958)|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)|collagen binding (GO:0005518)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(15)|ovary(2)|skin(1)|stomach(1)	27		all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)		BRCA - Breast invasive adenocarcinoma(274;0.0144)	Marimastat(DB00786)	CAATGCCATCGTGAAGTCTGG	0.343																																					p.H157H		Atlas-SNP	.											MMP13,NS,malignant_melanoma,-2,1	MMP13	75	1	0			c.C471T						PASS	.	G		0,4404		0,0,2202	64.0	64.0	64.0		471	-2.8	0.0	11		64	2,8596	2.2+/-6.3	0,2,4297	no	coding-synonymous	MMP13	NM_002427.3		0,2,6499	AA,AG,GG		0.0233,0.0,0.0154		157/472	102825227	2,13000	2202	4299	6501	SO:0001819	synonymous_variant	4322	exon3			GCCATCGTGAAGT	X75308	CCDS8324.1	11q22.3	2014-01-30	2005-08-08		ENSG00000137745	ENSG00000137745		"""Endogenous ligands"""	7159	protein-coding gene	gene with protein product	"""collagenase 3"""	600108	"""matrix metalloproteinase 13 (collagenase 3)"""			8207000	Standard	NM_002427		Approved	CLG3	uc001phl.3	P45452	OTTHUMG00000165850	ENST00000260302.3:c.471C>T	11.37:g.102825227G>A		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	108	70	0.648148	NM_002427	A8K846|B2RCZ3|Q6NWN6	Silent	SNP	ENST00000260302.3	37	CCDS8324.1																																																																																			.	.	weak		0.343	MMP13-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000386648.1	NM_002427	
JMJD1C	221037	hgsc.bcm.edu	37	10	64927823	64927823	+	Missense_Mutation	SNP	C	C	G	rs1935	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:64927823C>G	ENST00000399262.2	-	26	7823	c.7605G>C	c.(7603-7605)gaG>gaC	p.E2535D	JMJD1C_ENST00000399251.1_3'UTR|JMJD1C_ENST00000542921.1_Missense_Mutation_p.E2353D|JMJD1C_ENST00000402544.1_Missense_Mutation_p.E2298D	NM_032776.1	NP_116165.1	Q15652	JHD2C_HUMAN	jumonji domain containing 1C	2535			E -> D (in dbSNP:rs1935). {ECO:0000269|PubMed:17974005}.		blood coagulation (GO:0007596)|chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	intracellular (GO:0005622)|nucleoplasm (GO:0005654)	dioxygenase activity (GO:0051213)|metal ion binding (GO:0046872)|thyroid hormone receptor binding (GO:0046966)	p.E2298D(2)|p.E2535D(1)		breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(8)|large_intestine(9)|lung(27)|ovary(6)|prostate(4)|skin(4)|stomach(3)|upper_aerodigestive_tract(3)	77	Prostate(12;0.0119)|all_hematologic(501;0.191)					CTTCCATATCCTCTACTTCAT	0.333													C|||	1964	0.392173	0.2859	0.3112	5008	,	,		17437	0.3601		0.4901	False		,,,				2504	0.5256				p.E2535D		Atlas-SNP	.											JMJD1C_ENST00000399262,NS,carcinoma,0,2	JMJD1C	347	2	3	Substitution - Missense(3)	prostate(3)	c.G7605C						PASS	.	C	ASP/GLU,ASP/GLU	1271,2471		208,855,808	174.0	159.0	164.0		6894,7605	3.6	1.0	10	dbSNP_36	164	3919,4275		952,2015,1130	yes	missense,missense	JMJD1C	NM_004241.2,NM_032776.1	45,45	1160,2870,1938	GG,GC,CC		47.8277,33.9658,43.4819	probably-damaging,probably-damaging	2298/2304,2535/2541	64927823	5190,6746	1871	4097	5968	SO:0001583	missense	221037	exon26			CATATCCTCTACT	L40411	CCDS41532.1, CCDS60538.1	10q22.1	2011-05-25	2004-03-31	2004-04-01	ENSG00000171988	ENSG00000171988			12313	protein-coding gene	gene with protein product		604503	"""thyroid hormone receptor interactor 8"""	TRIP8		7776974	Standard	XM_005269624		Approved	DKFZp761F0118, KIAA1380, FLJ14374	uc001jmn.3	Q15652	OTTHUMG00000018311	ENST00000399262.2:c.7605G>C	10.37:g.64927823C>G	ENSP00000382204:p.Glu2535Asp	Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	100	55	0.55	NM_032776	A0T124|Q5SQZ8|Q5SQZ9|Q5SR00|Q7Z3E7|Q8N3U0|Q96KB9|Q9P2G7	Missense_Mutation	SNP	ENST00000399262.2	37	CCDS41532.1	852	0.3901098901098901	135	0.27439024390243905	134	0.3701657458563536	225	0.39335664335664333	358	0.47229551451187335	C	15.29	2.788518	0.49997	0.339658	0.478277	ENSG00000171988	ENST00000399262;ENST00000402544;ENST00000542921	T;T;T	0.55930	0.83;0.49;0.83	5.42	3.57	0.40892	.	0.117118	0.56097	D	0.000029	T	0.00012	0.0000	L	0.40543	1.245	0.09310	P	0.9999999999965508	B;B	0.32071	0.355;0.152	B;B	0.24974	0.057;0.021	T	0.47674	-0.9099	9	0.42905	T	0.14	-14.8807	5.1962	0.15239	0.0:0.6035:0.0:0.3965	rs1935;rs17574273;rs52815148;rs1935	2535;2353	Q15652;A0T124	JHD2C_HUMAN;.	D	2535;2298;2353	ENSP00000382204:E2535D;ENSP00000384990:E2298D;ENSP00000444682:E2353D	ENSP00000382204:E2535D	E	-	3	2	JMJD1C	64597829	0.484000	0.25964	1.000000	0.80357	0.998000	0.95712	-0.006000	0.12833	1.279000	0.44446	0.591000	0.81541	GAG	C|0.570;G|0.430	0.430	strong		0.333	JMJD1C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048249.2	NM_004241	
OR2G2	81470	hgsc.bcm.edu	37	1	247752161	247752161	+	Missense_Mutation	SNP	T	T	C	rs10925085	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:247752161T>C	ENST00000320065.1	+	1	500	c.500T>C	c.(499-501)cTg>cCg	p.L167P	RP11-978I15.10_ENST00000446347.1_RNA|RP11-978I15.10_ENST00000435333.1_RNA	NM_001001915.1	NP_001001915.1	Q8NGZ5	OR2G2_HUMAN	olfactory receptor, family 2, subfamily G, member 2	167			L -> P (in dbSNP:rs10925085).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(4)|kidney(4)|large_intestine(3)|lung(30)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	45	all_cancers(71;3.24e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)		OV - Ovarian serous cystadenocarcinoma(106;0.017)			ACCCTCACCCTGCAGCTGCCC	0.542													T|||	1540	0.307508	0.0582	0.3501	5008	,	,		21547	0.5228		0.4125	False		,,,				2504	0.2843				p.L167P		Atlas-SNP	.											.	OR2G2	88	.	0			c.T500C						PASS	.	T	PRO/LEU	465,3941	220.4+/-237.8	28,409,1766	187.0	170.0	176.0		500	4.3	1.0	1	dbSNP_120	176	3464,5136	508.7+/-377.1	676,2112,1512	yes	missense	OR2G2	NM_001001915.1	98	704,2521,3278	CC,CT,TT		40.2791,10.5538,30.2091	probably-damaging	167/318	247752161	3929,9077	2203	4300	6503	SO:0001583	missense	81470	exon1			TCACCCTGCAGCT	BK004472	CCDS31092.1	1q44	2012-08-09	2008-05-23		ENSG00000177489	ENSG00000177489		"""GPCR / Class A : Olfactory receptors"""	15007	protein-coding gene	gene with protein product			"""olfactory receptor, family 2, subfamily G, member 2"", ""olfactory receptor, family 2, subfamily G, member 2 pseudogene"""				Standard	NM_001001915		Approved		uc010pyy.2	Q8NGZ5	OTTHUMG00000040575	ENST00000320065.1:c.500T>C	1.37:g.247752161T>C	ENSP00000326349:p.Leu167Pro	Somatic	197	0	0		WXS	Illumina HiSeq	Phase_I	163	71	0.435583	NM_001001915	Q5JQT2|Q6IEZ0	Missense_Mutation	SNP	ENST00000320065.1	37	CCDS31092.1	772	0.3534798534798535	31	0.06300813008130081	127	0.35082872928176795	303	0.5297202797202797	311	0.4102902374670185	T	14.84	2.655025	0.47467	0.105538	0.402791	ENSG00000177489	ENST00000320065	T	0.00235	8.48	4.29	4.29	0.51040	GPCR, rhodopsin-like superfamily (1);	0.000000	0.30890	U	0.008678	T	0.00012	0.0000	M	0.87180	2.865	0.34693	P	0.274065	D	0.76494	0.999	D	0.77557	0.99	T	0.04165	-1.0972	9	0.87932	D	0	.	11.4683	0.50252	0.0:0.0:0.0:1.0	rs10925085;rs52797659;rs61693533;rs10925085	167	Q8NGZ5	OR2G2_HUMAN	P	167	ENSP00000326349:L167P	ENSP00000326349:L167P	L	+	2	0	OR2G2	245818784	0.000000	0.05858	0.995000	0.50966	0.624000	0.37722	0.342000	0.19926	1.789000	0.52484	0.481000	0.45027	CTG	T|0.676;C|0.324	0.324	strong		0.542	OR2G2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097623.1		
DOCK8	81704	hgsc.bcm.edu	37	9	340230	340230	+	Missense_Mutation	SNP	G	G	A	rs373187839		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:340230G>A	ENST00000453981.1	+	14	1700	c.1588G>A	c.(1588-1590)Gtg>Atg	p.V530M	DOCK8_ENST00000469391.1_Missense_Mutation_p.V462M|DOCK8_ENST00000432829.2_Missense_Mutation_p.V462M			Q8NF50	DOCK8_HUMAN	dedicator of cytokinesis 8	530					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)		AATGCTGCCCGTGAAACCCTT	0.443																																					p.V530M		Atlas-SNP	.											DOCK8_ENST00000453981,NS,carcinoma,-2,2	DOCK8	401	2	0			c.G1588A						scavenged	.	G	MET/VAL,MET/VAL,MET/VAL	1,4405	2.1+/-5.4	0,1,2202	85.0	87.0	86.0		1384,1384,1588	5.5	0.9	9		86	0,8600		0,0,4300	no	missense,missense,missense	DOCK8	NM_001190458.1,NM_001193536.1,NM_203447.3	21,21,21	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging,probably-damaging,probably-damaging	462/2000,462/2032,530/2100	340230	1,13005	2203	4300	6503	SO:0001583	missense	81704	exon14			CTGCCCGTGAAAC	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.1588G>A	9.37:g.340230G>A	ENSP00000408464:p.Val530Met	Somatic	81	1	0.0123457		WXS	Illumina HiSeq	Phase_I	91	37	0.406593	NM_203447	A2A350|A2BDF2|A4FU78|B7ZLP0|E9PH09|Q3MV16|Q5JPJ1|Q8TEP1|Q8WUY2|Q9BYJ5|Q9H1Q2|Q9H1Q3|Q9H308|Q9H7P2	Missense_Mutation	SNP	ENST00000453981.1	37	CCDS6440.2	.	.	.	.	.	.	.	.	.	.	G	29.2	4.988063	0.93106	2.27E-4	0.0	ENSG00000107099	ENST00000453981;ENST00000287364;ENST00000432829;ENST00000469391	T;T;T	0.39229	1.09;1.09;1.09	5.49	5.49	0.81192	.	0.128635	0.52532	D	0.000073	T	0.63034	0.2477	M	0.62723	1.935	0.80722	D	1	D;D	0.89917	0.991;1.0	P;D	0.67725	0.878;0.953	T	0.61964	-0.6954	10	0.52906	T	0.07	.	19.7314	0.96182	0.0:0.0:1.0:0.0	.	462;530	E9PH09;Q8NF50	.;DOCK8_HUMAN	M	530;530;462;462	ENSP00000408464:V530M;ENSP00000394888:V462M;ENSP00000419438:V462M	ENSP00000287364:V530M	V	+	1	0	DOCK8	330230	1.000000	0.71417	0.917000	0.36280	0.951000	0.60555	3.219000	0.51200	2.727000	0.93392	0.655000	0.94253	GTG	.	.	weak		0.443	DOCK8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171792.5	XM_036307	
FBP1	2203	hgsc.bcm.edu	37	9	97369151	97369151	+	Silent	SNP	G	G	A	rs1042144|rs386736436	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:97369151G>A	ENST00000375326.4	-	5	847	c.651C>T	c.(649-651)gcC>gcT	p.A217A	FBP1_ENST00000415431.1_Silent_p.A217A	NM_000507.3	NP_000498.2	P09467	F16P1_HUMAN	fructose-1,6-bisphosphatase 1	217					carbohydrate metabolic process (GO:0005975)|cellular response to drug (GO:0035690)|cellular response to magnesium ion (GO:0071286)|dephosphorylation (GO:0016311)|fructose 6-phosphate metabolic process (GO:0006002)|fructose metabolic process (GO:0006000)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|negative regulation of cell growth (GO:0030308)|negative regulation of glycolytic process (GO:0045820)|negative regulation of Ras protein signal transduction (GO:0046580)|protein homotetramerization (GO:0051289)|regulation of gluconeogenesis (GO:0006111)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	AMP binding (GO:0016208)|fructose 1,6-bisphosphate 1-phosphatase activity (GO:0042132)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|monosaccharide binding (GO:0048029)			kidney(1)|liver(1)|lung(1)	3		Acute lymphoblastic leukemia(62;0.136)			Adenosine monophosphate(DB00131)	CAAAGTCCCTGGCGTAGCCCT	0.522													G|||	1765	0.352436	0.2716	0.2046	5008	,	,		20345	0.5496		0.3499	False		,,,				2504	0.3661				p.A217A	Ovarian(142;590 2466 25593 44496)	Atlas-SNP	.											.	FBP1	13	.	0			c.C651T						PASS	.	G	,	1229,3177	426.4+/-341.1	164,901,1138	120.0	109.0	113.0		651,651	3.6	1.0	9	dbSNP_86	113	2822,5778	445.1+/-360.9	456,1910,1934	no	coding-synonymous,coding-synonymous	FBP1	NM_000507.3,NM_001127628.1	,	620,2811,3072	AA,AG,GG		32.814,27.8938,31.1472	,	217/339,217/339	97369151	4051,8955	2203	4300	6503	SO:0001819	synonymous_variant	2203	exon5			GTCCCTGGCGTAG	M19922	CCDS6712.1	9q22.3	2012-08-13			ENSG00000165140	ENSG00000165140	3.1.3.11		3606	protein-coding gene	gene with protein product		611570		FBP		8387495	Standard	NM_000507		Approved		uc004auw.4	P09467	OTTHUMG00000020268	ENST00000375326.4:c.651C>T	9.37:g.97369151G>A		Somatic	193	0	0		WXS	Illumina HiSeq	Phase_I	153	72	0.470588	NM_000507	O75571|Q53F94|Q96E46	Silent	SNP	ENST00000375326.4	37	CCDS6712.1																																																																																			T|0.000;G|0.682;A|0.318	0.318	strong		0.522	FBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053187.1	NM_000507	
ALPK3	57538	hgsc.bcm.edu	37	15	85383640	85383640	+	Missense_Mutation	SNP	G	G	A	rs3803405	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:85383640G>A	ENST00000258888.5	+	5	1903	c.1736G>A	c.(1735-1737)gGg>gAg	p.G579E		NM_020778.4	NP_065829.3	Q96L96	ALPK3_HUMAN	alpha-kinase 3	579			G -> E (in dbSNP:rs3803405). {ECO:0000269|PubMed:17344846}.		heart development (GO:0007507)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(3)|breast(2)|central_nervous_system(2)|endometrium(12)|kidney(4)|large_intestine(9)|lung(27)|ovary(3)|prostate(5)|skin(8)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	81			BRCA - Breast invasive adenocarcinoma(143;0.0587)			GCTGCACGGGGGCCTGGGTCC	0.672													G|||	691	0.137979	0.0159	0.1643	5008	,	,		14771	0.1329		0.2575	False		,,,				2504	0.1667				p.G579E		Atlas-SNP	.											.	ALPK3	289	.	0			c.G1736A						PASS	.	G	GLU/GLY	243,4159		11,221,1969	21.0	24.0	23.0		1736	2.7	0.1	15	dbSNP_107	23	2322,6274		315,1692,2291	yes	missense	ALPK3	NM_020778.4	98	326,1913,4260	AA,AG,GG		27.0126,5.5202,19.7338	probably-damaging	579/1908	85383640	2565,10433	2201	4298	6499	SO:0001583	missense	57538	exon5			CACGGGGGCCTGG	AY044449	CCDS10333.1	15q25.2	2013-01-29			ENSG00000136383	ENSG00000136383		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	17574	protein-coding gene	gene with protein product	"""myocyte induction differentiation originator"", ""muscle alpha-kinase"""					10021370	Standard	NM_020778		Approved	MAK, KIAA1330, Midori	uc002ble.3	Q96L96	OTTHUMG00000148667	ENST00000258888.5:c.1736G>A	15.37:g.85383640G>A	ENSP00000258888:p.Gly579Glu	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	64	36	0.5625	NM_020778	Q9P2L6	Missense_Mutation	SNP	ENST00000258888.5	37	CCDS10333.1	359	0.16437728937728938	7	0.014227642276422764	72	0.19889502762430938	81	0.14160839160839161	199	0.262532981530343	G	15.43	2.831448	0.50845	0.055202	0.270126	ENSG00000136383	ENST00000258888	T	0.58797	0.31	4.63	2.68	0.31781	.	0.701763	0.13520	N	0.381774	T	0.00012	0.0000	L	0.32530	0.975	0.80722	P	0.0	B	0.27997	0.197	B	0.28638	0.092	T	0.12915	-1.0529	9	0.42905	T	0.14	-25.0097	6.5307	0.22326	0.1001:0.1836:0.7163:0.0	rs3803405;rs60841515;rs3803405	579	Q96L96	ALPK3_HUMAN	E	579	ENSP00000258888:G579E	ENSP00000258888:G579E	G	+	2	0	ALPK3	83184644	0.004000	0.15560	0.136000	0.22124	0.102000	0.19082	0.123000	0.15708	1.163000	0.42636	-0.300000	0.09419	GGG	G|0.815;A|0.185	0.185	strong		0.672	ALPK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000308997.1	NM_020778	
GNL3	26354	hgsc.bcm.edu	37	3	52721305	52721305	+	Missense_Mutation	SNP	G	G	A	rs11177	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:52721305G>A	ENST00000418458.1	+	3	289	c.116G>A	c.(115-117)cGg>cAg	p.R39Q	SNORD19B_ENST00000516978.1_RNA|GNL3_ENST00000394799.2_Missense_Mutation_p.R27Q|GNL3_ENST00000460073.1_3'UTR|PBRM1_ENST00000394830.3_5'Flank|SNORD19_ENST00000391191.1_RNA	NM_014366.4|NM_206826.1	NP_055181.3|NP_996562.1	Q9BVP2	GNL3_HUMAN	guanine nucleotide binding protein-like 3 (nucleolar)	39	Basic. {ECO:0000250}.		R -> Q (in dbSNP:rs11177). {ECO:0000269|PubMed:11085516, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:16012751}.		cell proliferation (GO:0008283)|GTP catabolic process (GO:0006184)|regulation of cell proliferation (GO:0042127)|ribosome biogenesis (GO:0042254)	extracellular space (GO:0005615)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)			breast(4)|endometrium(3)|large_intestine(3)|lung(2)	12				BRCA - Breast invasive adenocarcinoma(193;6.75e-05)|Kidney(197;0.000611)|KIRC - Kidney renal clear cell carcinoma(197;0.000773)|OV - Ovarian serous cystadenocarcinoma(275;0.048)		GCTAAAAAGCGGGGTCACAAG	0.398													G|||	1562	0.311901	0.1467	0.4582	5008	,	,		18389	0.4236		0.4175	False		,,,				2504	0.2076				p.R39Q		Atlas-SNP	.											.	GNL3	37	.	0			c.G116A						PASS	.	G	GLN/ARG,GLN/ARG,GLN/ARG	761,3645	290.1+/-280.8	62,637,1504	65.0	75.0	72.0		116,80,80	1.9	1.0	3	dbSNP_52	72	3465,5135	500.9+/-375.3	720,2025,1555	yes	missense,missense,missense	GNL3	NM_014366.4,NM_206825.1,NM_206826.1	43,43,43	782,2662,3059	AA,AG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	40.2907,17.2719,32.4927	benign,benign,benign	39/550,27/538,27/538	52721305	4226,8780	2203	4300	6503	SO:0001583	missense	26354	exon3			AAAAGCGGGGTCA	AK027514	CCDS2861.1, CCDS43100.1	3p21.1	2005-01-10			ENSG00000163938	ENSG00000163938			29931	protein-coding gene	gene with protein product		608011				11085516, 12464630	Standard	NM_014366		Approved	C77032, E2IG3, MGC800, NS, nucleostemin	uc003dfd.3	Q9BVP2	OTTHUMG00000158752	ENST00000418458.1:c.116G>A	3.37:g.52721305G>A	ENSP00000395772:p.Arg39Gln	Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	127	126	0.992126	NM_014366	B2RDC1|Q5PU80|Q96SV6|Q96SV7|Q9UJY0	Missense_Mutation	SNP	ENST00000418458.1	37	CCDS2861.1	848	0.3882783882783883	79	0.16056910569105692	171	0.4723756906077348	277	0.48426573426573427	321	0.4234828496042216	G	13.85	2.361061	0.41801	0.172719	0.402907	ENSG00000163938	ENST00000479230;ENST00000418458;ENST00000394799;ENST00000474423	T;T;T;T	0.41758	0.99;0.99;0.99;0.99	5.83	1.92	0.25849	GNL3L/Grn1 putative GTPase (1);	0.306688	0.37053	N	0.002263	T	0.00012	0.0000	N	0.22421	0.69	0.34398	P	0.305084	B	0.22080	0.064	B	0.16289	0.015	T	0.48768	-0.9006	9	0.15952	T	0.53	.	8.9856	0.35992	0.3608:0.0:0.6392:0.0	rs11177;rs1047396;rs3187401;rs17844878;rs17857595;rs52805757;rs60862326;rs11177	39	Q9BVP2	GNL3_HUMAN	Q	27;39;27;27	ENSP00000419734:R27Q;ENSP00000395772:R39Q;ENSP00000378278:R27Q;ENSP00000419895:R27Q	ENSP00000378278:R27Q	R	+	2	0	GNL3	52696345	1.000000	0.71417	0.997000	0.53966	0.991000	0.79684	2.766000	0.47629	0.346000	0.23899	0.655000	0.94253	CGG	G|0.658;A|0.342	0.342	strong		0.398	GNL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352032.1	NM_014366	
ZNF578	147660	hgsc.bcm.edu	37	19	53014752	53014752	+	Missense_Mutation	SNP	G	G	A	rs61739625	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:53014752G>A	ENST00000421239.2	+	6	1362	c.1118G>A	c.(1117-1119)tGt>tAt	p.C373Y	CTD-3099C6.5_ENST00000599143.1_RNA	NM_001099694.1	NP_001093164.1	Q96N58	ZN578_HUMAN	zinc finger protein 578	373					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)								GBM - Glioblastoma multiforme(134;0.00819)|OV - Ovarian serous cystadenocarcinoma(262;0.01)		CCTTACAAGTGTAATGAGTGT	0.378													G|||	14	0.00279553	0.0008	0.0072	5008	,	,		24766	0.0		0.008	False		,,,				2504	0.0				p.C373Y		Atlas-SNP	.											.	.	.	.	0			c.G1118A						PASS	.	G	TYR/CYS	3,4403		0,3,2200	101.0	106.0	104.0		1118	1.5	0.1	19	dbSNP_129	104	83,8515		0,83,4216	no	missense	ZNF578	NM_001099694.1	194	0,86,6416	AA,AG,GG		0.9653,0.0681,0.6613	probably-damaging	373/591	53014752	86,12918	2203	4299	6502	SO:0001583	missense	147660	exon6			ACAAGTGTAATGA	AK095562	CCDS54310.1	19q13.41	2013-09-20			ENSG00000258405	ENSG00000258405		"""Zinc fingers, C2H2-type"", ""-"""	26449	protein-coding gene	gene with protein product							Standard	NM_001099694		Approved	FLJ31384	uc002pzp.4	Q96N58	OTTHUMG00000156468	ENST00000421239.2:c.1118G>A	19.37:g.53014752G>A	ENSP00000459216:p.Cys373Tyr	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	45	24	0.533333	NM_001099694	B4DR51|I3L1Y6	Missense_Mutation	SNP	ENST00000421239.2	37	CCDS54310.1	8	0.003663003663003663	1	0.0020325203252032522	2	0.0055248618784530384	0	0.0	5	0.006596306068601583	-	15.33	2.800374	0.50315	6.81E-4	0.009653	ENSG00000258405	ENST00000553364	.	.	.	1.48	1.48	0.22813	.	.	.	.	.	T	0.77398	0.4124	H	0.97265	3.97	0.30366	N	0.78334	D	0.89917	1.0	D	0.91635	0.999	T	0.76666	-0.2875	7	.	.	.	.	10.0458	0.42186	0.0:0.0:1.0:0.0	rs61739625	373	G3V4F6	.	Y	373	.	.	C	+	2	0	ZNF578	57706564	1.000000	0.71417	0.059000	0.19551	0.164000	0.22412	7.591000	0.82666	0.835000	0.34877	0.297000	0.19635	TGT	G|0.995;A|0.005	0.005	strong		0.378	ZNF578-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344298.3	NM_152472	
VWA3A	146177	hgsc.bcm.edu	37	16	22144377	22144377	+	Silent	SNP	C	C	A	rs371670962		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:22144377C>A	ENST00000389398.5	+	20	2125	c.2029C>A	c.(2029-2031)Cgg>Agg	p.R677R	VWA3A_ENST00000389397.4_5'UTR	NM_173615.3	NP_775886.3	A6NCI4	VWA3A_HUMAN	von Willebrand factor A domain containing 3A	677	VWFA 1. {ECO:0000255|PROSITE- ProRule:PRU00219}.					extracellular region (GO:0005576)				haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(1)|skin(1)	7				GBM - Glioblastoma multiforme(48;0.0439)		GGAGGTCACCCGGGCTGCAGG	0.577																																					p.R677R		Atlas-SNP	.											.	VWA3A	115	.	0			c.C2029A						PASS	.						38.0	42.0	40.0					16																	22144377		2054	4187	6241	SO:0001819	synonymous_variant	146177	exon20			GTCACCCGGGCTG	AK128606, AK098260	CCDS45441.1	16p12.1	2008-02-05				ENSG00000175267			27088	protein-coding gene	gene with protein product						12477932	Standard	XM_006721021		Approved	FLJ46765, FLJ40941	uc010vbq.2	A6NCI4		ENST00000389398.5:c.2029C>A	16.37:g.22144377C>A		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	71	27	0.380282	NM_173615	A4QMU8|A6NNC0|Q6UTX4|Q6ZQZ9|Q8IUY6|Q8N9W1	Silent	SNP	ENST00000389398.5	37	CCDS45441.1																																																																																			.	.	alt		0.577	VWA3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430052.1		
EAPP	55837	hgsc.bcm.edu	37	14	34993982	34993982	+	Missense_Mutation	SNP	G	G	C	rs17352411	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:34993982G>C	ENST00000250454.3	-	5	583	c.502C>G	c.(502-504)Caa>Gaa	p.Q168E		NM_018453.3	NP_060923.2	Q56P03	EAPP_HUMAN	E2F-associated phosphoprotein	168			Q -> E (in dbSNP:rs17856038). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:15716352}.		negative regulation of transcription elongation from RNA polymerase II promoter (GO:0034244)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)				breast(1)|endometrium(1)|large_intestine(3)|lung(4)|ovary(1)|urinary_tract(2)	12	Breast(36;0.0473)|Hepatocellular(127;0.158)		LUAD - Lung adenocarcinoma(48;0.00169)|Lung(238;0.00342)|Epithelial(34;0.18)	GBM - Glioblastoma multiforme(112;0.0196)		GGCTGTTGTTGACGTGATCTC	0.423													G|||	294	0.0587061	0.1808	0.0346	5008	,	,		18142	0.003		0.0219	False		,,,				2504	0.0061				p.Q168E		Atlas-SNP	.											.	EAPP	28	.	0			c.C502G						PASS	.	G	GLU/GLN	657,3377		56,545,1416	147.0	138.0	141.0		502	4.5	0.8	14	dbSNP_123	141	204,8166		5,194,3986	yes	missense	EAPP	NM_018453.3	29	61,739,5402	CC,CG,GG		2.4373,16.2866,6.9413	benign	168/286	34993982	861,11543	2017	4185	6202	SO:0001583	missense	55837	exon5			GTTGTTGACGTGA	AF217512	CCDS41941.1	14q13	2007-03-26	2007-03-26	2007-03-26		ENSG00000129518			19312	protein-coding gene	gene with protein product		609486	"""chromosome 14 open reading frame 11"""	C14orf11		15716352	Standard	NM_018453		Approved	BM036, FLJ20578	uc001wsd.1	Q56P03		ENST00000250454.3:c.502C>G	14.37:g.34993982G>C	ENSP00000250454:p.Gln168Glu	Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	138	62	0.449275	NM_018453	Q9BVF4|Q9NWV5|Q9NZ86	Missense_Mutation	SNP	ENST00000250454.3	37	CCDS41941.1	132	0.06043956043956044	98	0.1991869918699187	15	0.04143646408839779	3	0.005244755244755245	16	0.021108179419525065	G	3.671	-0.067546	0.07273	0.162866	0.024373	ENSG00000129518	ENST00000250454;ENST00000554792	T;T	0.43294	0.95;0.95	5.49	4.49	0.54785	.	0.565900	0.19531	N	0.112052	T	0.00039	0.0001	M	0.76574	2.34	0.80722	P	0.0	B	0.24317	0.101	B	0.28385	0.089	T	0.09422	-1.0675	9	0.09084	T	0.74	-1.9939	10.1926	0.43035	0.0739:0.0:0.75:0.1761	rs17856038;rs17856038	168	Q56P03	EAPP_HUMAN	E	168;147	ENSP00000250454:Q168E;ENSP00000450908:Q147E	ENSP00000250454:Q168E	Q	-	1	0	EAPP	34063733	0.985000	0.35326	0.763000	0.31416	0.096000	0.18686	4.233000	0.58651	2.756000	0.94617	0.561000	0.74099	CAA	G|0.947;C|0.053	0.053	strong		0.423	EAPP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409847.1	NM_018453	
FCGBP	8857	hgsc.bcm.edu	37	19	40405999	40405999	+	Missense_Mutation	SNP	C	C	A	rs7248839	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:40405999C>A	ENST00000221347.6	-	10	4854	c.4847G>T	c.(4846-4848)gGc>gTc	p.G1616V		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	1616	Cys-rich.		G -> V (in dbSNP:rs7248839).			extracellular vesicular exosome (GO:0070062)				NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(5)|endometrium(13)|kidney(9)|large_intestine(27)|lung(49)|ovary(8)|pancreas(3)|prostate(13)|skin(9)|stomach(9)|upper_aerodigestive_tract(6)|urinary_tract(3)	165	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			GCACACCATGCCTTTACCCGC	0.642													C|||	659	0.131589	0.1324	0.1916	5008	,	,		19537	0.0357		0.172	False		,,,				2504	0.1452				p.G1616V		Atlas-SNP	.											FCGBP,mouth,carcinoma,+1,1	FCGBP	416	1	0			c.G4847T						scavenged	.						80.0	60.0	67.0					19																	40405999		2201	4292	6493	SO:0001583	missense	8857	exon10			ACCATGCCTTTAC	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.4847G>T	19.37:g.40405999C>A	ENSP00000221347:p.Gly1616Val	Somatic	721	18	0.0249653		WXS	Illumina HiSeq	Phase_I	448	48	0.107143	NM_003890	O95784	Missense_Mutation	SNP	ENST00000221347.6	37	CCDS12546.1	227	0.10393772893772894	60	0.12195121951219512	41	0.1132596685082873	18	0.03146853146853147	108	0.1424802110817942	C	9.121	1.008963	0.19199	.	.	ENSG00000090920	ENST00000221347	T	0.04454	3.62	3.4	1.07	0.20283	von Willebrand factor, type C (1);	.	.	.	.	T	0.00039	0.0001	L	0.61387	1.9	0.80722	P	0.0	B	0.24963	0.115	B	0.24269	0.052	T	0.32079	-0.9920	8	0.22706	T	0.39	.	7.7598	0.28946	0.4526:0.5474:0.0:0.0	rs7248839	1616	Q9Y6R7	FCGBP_HUMAN	V	1616	ENSP00000221347:G1616V	ENSP00000221347:G1616V	G	-	2	0	FCGBP	45097839	0.003000	0.15002	0.001000	0.08648	0.014000	0.08584	0.661000	0.25023	0.128000	0.18479	0.306000	0.20318	GGC	C|0.897;A|0.103	0.103	strong		0.642	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890	
ARAP2	116984	hgsc.bcm.edu	37	4	36069805	36069805	+	Silent	SNP	G	G	A	rs7657166	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:36069805G>A	ENST00000303965.4	-	33	5328	c.4839C>T	c.(4837-4839)gcC>gcT	p.A1613A		NM_015230.3	NP_056045.2	Q8WZ64	ARAP2_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 2	1613					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						CCAGGCAGTGGGCCACCATGG	0.517													G|||	778	0.155351	0.0204	0.2061	5008	,	,		18703	0.0913		0.2803	False		,,,				2504	0.2393				p.A1613A		Atlas-SNP	.											.	ARAP2	210	.	0			c.C4839T						PASS	.	G		314,4092	168.3+/-199.2	12,290,1901	102.0	103.0	103.0		4839	3.4	1.0	4	dbSNP_116	103	2765,5835	438.1+/-358.8	474,1817,2009	no	coding-synonymous	ARAP2	NM_015230.3		486,2107,3910	AA,AG,GG		32.1512,7.1266,23.6737		1613/1705	36069805	3079,9927	2203	4300	6503	SO:0001819	synonymous_variant	116984	exon33			GCAGTGGGCCACC	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.4839C>T	4.37:g.36069805G>A		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	104	103	0.990385	NM_015230	Q4W5D2|Q7Z2L5|Q96L70|Q96P49|Q9Y4E4	Silent	SNP	ENST00000303965.4	37	CCDS3441.1																																																																																			G|0.777;A|0.223	0.223	strong		0.517	ARAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215074.2	NM_015230	
CYP39A1	51302	hgsc.bcm.edu	37	6	46620252	46620252	+	Missense_Mutation	SNP	C	C	G	rs12192544	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:46620252C>G	ENST00000275016.2	-	1	271	c.68G>C	c.(67-69)cGg>cCg	p.R23P	SLC25A27_ENST00000371347.5_5'Flank|SLC25A27_ENST00000411689.2_5'Flank|SLC25A27_ENST00000452689.2_5'Flank	NM_016593.3	NP_057677.2	Q9NYL5	CP39A_HUMAN	cytochrome P450, family 39, subfamily A, polypeptide 1	23			R -> P (in dbSNP:rs12192544). {ECO:0000269|PubMed:15489334}.		bile acid biosynthetic process (GO:0006699)|bile acid catabolic process (GO:0030573)|bile acid metabolic process (GO:0008206)|cholesterol catabolic process (GO:0006707)|digestion (GO:0007586)|small molecule metabolic process (GO:0044281)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|intracellular membrane-bounded organelle (GO:0043231)	24-hydroxycholesterol 7alpha-hydroxylase activity (GO:0033782)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxysterol 7-alpha-hydroxylase activity (GO:0008396)|steroid 7-alpha-hydroxylase activity (GO:0008387)		EIF3K/CYP39A1(2)	NS(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(6)|ovary(1)|prostate(2)|skin(2)	21						CAAATTCTTCCGCTGAAGGAG	0.453													C|||	715	0.142772	0.0182	0.1441	5008	,	,		19051	0.1319		0.2087	False		,,,				2504	0.2536				p.R23P		Atlas-SNP	.											.	CYP39A1	41	.	0			c.G68C						PASS	.	C	PRO/ARG	229,4177	135.7+/-171.8	6,217,1980	225.0	237.0	233.0		68	3.4	0.1	6	dbSNP_120	233	1980,6620	347.2+/-326.5	247,1486,2567	yes	missense	CYP39A1	NM_016593.3	103	253,1703,4547	GG,GC,CC		23.0233,5.1975,16.9845	probably-damaging	23/470	46620252	2209,10797	2203	4300	6503	SO:0001583	missense	51302	exon1			TTCTTCCGCTGAA	AF237982	CCDS4916.1, CCDS75465.1	6p21.1-p11.2	2008-02-05	2003-01-14		ENSG00000146233	ENSG00000146233		"""Cytochrome P450s"""	17449	protein-coding gene	gene with protein product		605994	"""cytochrome P450, subfamily XXXIX (oxysterol 7 alpha-hydroxylase), polypeptide 1"""			10748047	Standard	NM_016593		Approved		uc003oyf.1	Q9NYL5	OTTHUMG00000014785	ENST00000275016.2:c.68G>C	6.37:g.46620252C>G	ENSP00000275016:p.Arg23Pro	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	79	40	0.506329	NM_016593	Q5VTT0|Q96FW5	Missense_Mutation	SNP	ENST00000275016.2	37	CCDS4916.1	303	0.13873626373626374	14	0.028455284552845527	62	0.1712707182320442	69	0.12062937062937062	158	0.20844327176781002	C	16.31	3.087548	0.55968	0.051975	0.230233	ENSG00000146233	ENST00000275016	T	0.76316	-1.01	5.29	3.36	0.38483	.	1.038340	0.07675	N	0.936181	T	0.62624	0.2443	M	0.64997	1.995	0.80722	P	0.0	D;D	0.53619	0.961;0.961	B;B	0.43155	0.41;0.41	T	0.50250	-0.8850	9	0.25751	T	0.34	1.7222	9.7041	0.40205	0.2729:0.5941:0.133:0.0	rs12192544;rs17850639;rs12192544	23;23	B7Z786;Q9NYL5	.;CP39A_HUMAN	P	23	ENSP00000275016:R23P	ENSP00000275016:R23P	R	-	2	0	CYP39A1	46728211	0.007000	0.16637	0.055000	0.19348	0.603000	0.37013	0.391000	0.20784	1.345000	0.45676	0.655000	0.94253	CGG	C|0.846;G|0.154	0.154	strong		0.453	CYP39A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040787.1		
AGAP11	119385	hgsc.bcm.edu	37	10	88768253	88768253	+	RNA	SNP	A	A	G	rs2641563	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:88768253A>G	ENST00000444431.1	+	0	2853				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)										ACCCACGCCCATTTGCAAGCA	0.517													G|||	3962	0.791134	0.8585	0.7522	5008	,	,		17889	0.9325		0.7048	False		,,,				2504	0.6708				p.I82V		Atlas-SNP	.											.	.	.	.	0			c.A244G						PASS	.	A	VAL/ILE	3640,728		1523,594,67	140.0	152.0	148.0		244	-0.3	0.0	10	dbSNP_100	148	5889,2701		1994,1901,400	no	missense	AGAP11	NM_133447.1	29	3517,2495,467	GG,GA,AA		31.4435,16.6667,26.4624	benign	82/551	88768253	9529,3429	2184	4295	6479			119385	exon12			ACGCCCATTTGCA			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.88768253A>G		Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	109	53	0.486239	NM_133447	B9EIP7|D3DWE4	Missense_Mutation	SNP	ENST00000444431.1	37																																																																																				A|0.215;G|0.785	0.785	strong		0.517	AGAP11-001	KNOWN	basic|readthrough_transcript	processed_transcript	processed_transcript	OTTHUMT00000049193.1	NM_133447	
PLEC	5339	hgsc.bcm.edu	37	8	145002070	145002070	+	Silent	SNP	G	G	A	rs145376880	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:145002070G>A	ENST00000322810.4	-	26	3931	c.3762C>T	c.(3760-3762)gcC>gcT	p.A1254A	PLEC_ENST00000357649.2_Silent_p.A1121A|PLEC_ENST00000398774.2_Silent_p.A1085A|PLEC_ENST00000436759.2_Silent_p.A1144A|PLEC_ENST00000354958.2_Silent_p.A1095A|PLEC_ENST00000527096.1_Silent_p.A1140A|PLEC_ENST00000354589.3_Silent_p.A1117A|PLEC_ENST00000345136.3_Silent_p.A1117A|PLEC_ENST00000356346.3_Silent_p.A1103A	NM_201380.2	NP_958782.1	Q15149	PLEC_HUMAN	plectin	1254	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						TGGCCGGCACGGCCTGGGCCT	0.692													G|||	21	0.00419329	0.0008	0.0029	5008	,	,		16164	0.001		0.0099	False		,,,				2504	0.0072				p.A1254A		Atlas-SNP	.											.	PLEC	1144	.	0			c.C3762T						PASS	.	G	,,,,,,,	6,3796		0,6,1895	12.0	17.0	16.0		3432,3309,3285,3762,3255,3351,3363,3351	-10.3	0.7	8	dbSNP_134	16	45,8157		0,45,4056	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	,,,,,,,	0,51,5951	AA,AG,GG		0.5486,0.1578,0.4249	,,,,,,,	1144/4575,1103/4534,1095/4526,1254/4685,1085/4516,1117/4548,1121/4552,1117/4548	145002070	51,11953	1901	4101	6002	SO:0001819	synonymous_variant	5339	exon26			CGGCACGGCCTGG	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.3762C>T	8.37:g.145002070G>A		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	78	26	0.333333	NM_201380	Q15148|Q16640|Q6S376|Q6S377|Q6S378|Q6S379|Q6S380|Q6S381|Q6S382|Q6S383	Silent	SNP	ENST00000322810.4	37	CCDS43772.1																																																																																			G|0.996;A|0.004	0.004	strong		0.692	PLEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383281.1	NM_000445	
OR52J3	119679	hgsc.bcm.edu	37	11	5067984	5067984	+	Missense_Mutation	SNP	A	A	G	rs2500016	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:5067984A>G	ENST00000380370.1	+	1	229	c.229A>G	c.(229-231)Aca>Gca	p.T77A		NM_001001916.2	NP_001001916.2	Q8NH60	O52J3_HUMAN	olfactory receptor, family 52, subfamily J, member 3	77			T -> A (in dbSNP:rs2500016). {ECO:0000269|PubMed:14983052, ECO:0000269|Ref.1, 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)			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)		GGCCCTTTCTACAACCTCTGT	0.488													A|||	2442	0.48762	0.5915	0.4971	5008	,	,		19708	0.2619		0.508	False		,,,				2504	0.5521				p.T77A		Atlas-SNP	.											.	OR52J3	77	.	0			c.A229G						PASS	.	A	ALA/THR	2443,1959	621.2+/-393.7	687,1069,445	129.0	110.0	117.0		229	4.2	1.0	11	dbSNP_100	117	4304,4292	577.8+/-390.6	1067,2170,1061	no	missense	OR52J3	NM_001001916.2	58	1754,3239,1506	GG,GA,AA		49.9302,44.5025,48.092	probably-damaging	77/312	5067984	6747,6251	2201	4298	6499	SO:0001583	missense	119679	exon1			CTTTCTACAACCT	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.229A>G	11.37:g.5067984A>G	ENSP00000369728:p.Thr77Ala	Somatic	232	0	0		WXS	Illumina HiSeq	Phase_I	251	247	0.984064	NM_001001916	Q6IFE4	Missense_Mutation	SNP	ENST00000380370.1	37	CCDS31370.1	995	0.4555860805860806	290	0.5894308943089431	170	0.4696132596685083	149	0.26048951048951047	386	0.5092348284960422	A	15.11	2.736934	0.49045	0.554975	0.500698	ENSG00000205495	ENST00000380370	T	0.04603	3.59	4.19	4.19	0.49359	GPCR, rhodopsin-like superfamily (1);	0.293409	0.24016	N	0.042331	T	0.00012	0.0000	M	0.74881	2.28	0.80722	P	0.0	P	0.47350	0.894	P	0.49301	0.606	T	0.24693	-1.0153	9	0.87932	D	0	.	12.2358	0.54514	1.0:0.0:0.0:0.0	rs2500016	77	Q8NH60	O52J3_HUMAN	A	77	ENSP00000369728:T77A	ENSP00000369728:T77A	T	+	1	0	OR52J3	5024560	0.001000	0.12720	0.986000	0.45419	0.937000	0.57800	0.843000	0.27640	1.742000	0.51746	0.533000	0.62120	ACA	A|0.493;G|0.507	0.507	strong		0.488	OR52J3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142807.1	NM_001001916	
THBD	7056	hgsc.bcm.edu	37	20	23028724	23028724	+	Missense_Mutation	SNP	G	G	A	rs1042579	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:23028724G>A	ENST00000377103.2	-	1	1654	c.1418C>T	c.(1417-1419)gCc>gTc	p.A473V		NM_000361.2	NP_000352.1	P07204	TRBM_HUMAN	thrombomodulin	473	EGF-like 6; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.		A -> V (in dbSNP:rs1042579). {ECO:0000269|PubMed:11245641, ECO:0000269|PubMed:12139752, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:19625716, ECO:0000269|PubMed:9157575, ECO:0000269|Ref.5}.		blood coagulation (GO:0007596)|female pregnancy (GO:0007565)|leukocyte migration (GO:0050900)|negative regulation of blood coagulation (GO:0030195)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of platelet activation (GO:0010544)|response to cAMP (GO:0051591)|response to lipopolysaccharide (GO:0032496)|response to X-ray (GO:0010165)	cell surface (GO:0009986)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			endometrium(2)|large_intestine(3)|ovary(1)|skin(1)	7	Colorectal(13;0.0518)|Lung NSC(19;0.0542)|all_lung(19;0.118)				Drotrecogin alfa(DB00055)|Ibuprofen(DB01050)	AATGTGGCGGGCAAGGGCCGA	0.692													G|||	824	0.164537	0.0219	0.147	5008	,	,		14788	0.3046		0.1928	False		,,,				2504	0.1963				p.A473V		Atlas-SNP	.											.	THBD	26	.	0			c.C1418T	GRCh37	CM971486	THBD	M	rs1042579	PASS	.	G	VAL/ALA	252,4152	133.7+/-170.0	10,232,1960	23.0	26.0	25.0		1418	-1.3	0.0	20	dbSNP_86	25	1541,7059	270.5+/-289.0	126,1289,2885	yes	missense	THBD	NM_000361.2	64	136,1521,4845	AA,AG,GG		17.9186,5.7221,13.7881	benign	473/576	23028724	1793,11211	2202	4300	6502	SO:0001583	missense	7056	exon1			TGGCGGGCAAGGG		CCDS13148.1	20p11.21	2014-09-17			ENSG00000178726	ENSG00000178726		"""CD molecules"""	11784	protein-coding gene	gene with protein product		188040					Standard	NM_000361		Approved	CD141	uc002wss.3	P07204	OTTHUMG00000032053	ENST00000377103.2:c.1418C>T	20.37:g.23028724G>A	ENSP00000366307:p.Ala473Val	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	56	30	0.535714	NM_000361	Q8IV29|Q9UC32	Missense_Mutation	SNP	ENST00000377103.2	37	CCDS13148.1	359	0.16437728937728938	6	0.012195121951219513	51	0.1408839779005525	147	0.256993006993007	155	0.20448548812664907	G	9.297	1.052227	0.19827	0.057221	0.179186	ENSG00000178726	ENST00000377103;ENST00000503590	T	0.79845	-1.31	4.73	-1.34	0.09143	Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	1.630370	0.04267	N	0.341366	T	0.00039	0.0001	L	0.28274	0.84	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.01215	-1.1416	9	0.21014	T	0.42	-3.9776	4.3108	0.10969	0.2609:0.0:0.4718:0.2673	rs1042579;rs3171313;rs17846140;rs17859148	473	P07204	TRBM_HUMAN	V	473;455	ENSP00000366307:A473V	ENSP00000366307:A473V	A	-	2	0	THBD	22976724	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.195000	0.09546	-0.087000	0.12528	-1.134000	0.01955	GCC	G|0.846;A|0.154	0.154	strong		0.692	THBD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078307.2		
PRX	57716	hgsc.bcm.edu	37	19	40901604	40901604	+	Silent	SNP	A	A	G	rs268672	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:40901604A>G	ENST00000324001.7	-	7	2925	c.2655T>C	c.(2653-2655)ccT>ccC	p.P885P	PRX_ENST00000291825.7_3'UTR	NM_181882.2	NP_870998.2	Q9BXM0	PRAX_HUMAN	periaxin	885					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)			CTGCCACCTCAGGGCCCTCCA	0.637													G|||	2664	0.531949	0.8427	0.4784	5008	,	,		17346	0.2401		0.506	False		,,,				2504	0.4775				p.P885P		Atlas-SNP	.											.	PRX	151	.	0			c.T2655C						PASS	.	G	,	3471,935	339.1+/-305.6	1385,701,117	40.0	49.0	46.0		,2655	-7.2	0.0	19	dbSNP_79	46	4451,4149	555.1+/-386.6	1155,2141,1004	no	utr-3,coding-synonymous	PRX	NM_020956.2,NM_181882.2	,	2540,2842,1121	GG,GA,AA		48.2442,21.2211,39.0897	,	,885/1462	40901604	7922,5084	2203	4300	6503	SO:0001819	synonymous_variant	57716	exon7			CACCTCAGGGCCC	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.2655T>C	19.37:g.40901604A>G		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	63	26	0.412698	NM_181882	Q9BXL9|Q9HCF2	Silent	SNP	ENST00000324001.7	37	CCDS33028.1																																																																																			A|0.457;G|0.543	0.543	strong		0.637	PRX-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000462582.1	NM_020956	
PCNX	22990	hgsc.bcm.edu	37	14	71443816	71443816	+	Silent	SNP	T	T	G	rs35702999	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:71443816T>G	ENST00000304743.2	+	6	1208	c.762T>G	c.(760-762)tcT>tcG	p.S254S	PCNX_ENST00000238570.5_Silent_p.S254S|PCNX_ENST00000439984.3_Silent_p.S254S	NM_014982.2	NP_055797.2	Q96RV3	PCX1_HUMAN	pecanex homolog (Drosophila)	254						integral component of membrane (GO:0016021)				NS(2)|biliary_tract(1)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(14)|liver(2)|lung(40)|ovary(1)|prostate(7)|skin(2)|urinary_tract(1)	87			KIRC - Kidney renal clear cell carcinoma(12;0.206)	all cancers(60;0.00835)|BRCA - Breast invasive adenocarcinoma(234;0.00951)|OV - Ovarian serous cystadenocarcinoma(108;0.0417)		TTGATCAGTCTCTGTCCAGCG	0.498													T|||	35	0.00698882	0.0	0.0043	5008	,	,		18137	0.0069		0.0199	False		,,,				2504	0.0051				p.S254S		Atlas-SNP	.											.	PCNX	198	.	0			c.T762G						PASS	.	T		10,4396	16.8+/-37.8	0,10,2193	141.0	119.0	126.0		762	0.8	1.0	14	dbSNP_126	126	86,8514	48.9+/-108.6	1,84,4215	no	coding-synonymous	PCNX	NM_014982.2		1,94,6408	GG,GT,TT		1.0,0.227,0.7381		254/2342	71443816	96,12910	2203	4300	6503	SO:0001819	synonymous_variant	22990	exon6			TCAGTCTCTGTCC	AF233450, AB018348	CCDS9806.1	14q24.2	2014-07-03							19740	protein-coding gene	gene with protein product			"""pecanex-like 1 (Drosophila)"""	PCNXL1		9244429, 15777640	Standard	NM_014982		Approved	KIAA0995, KIAA0805, pecanex	uc001xmo.2	Q96RV3		ENST00000304743.2:c.762T>G	14.37:g.71443816T>G		Somatic	227	0	0		WXS	Illumina HiSeq	Phase_I	218	94	0.431193	NM_014982	B2RTR6|O94897|Q96AI7|Q9Y2J9	Silent	SNP	ENST00000304743.2	37	CCDS9806.1																																																																																			T|0.991;G|0.009	0.009	strong		0.498	PCNX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412479.1	NM_014982	
BAZ2B	29994	hgsc.bcm.edu	37	2	160182302	160182302	+	Missense_Mutation	SNP	C	C	T	rs415793	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:160182302C>T	ENST00000392783.2	-	35	6566	c.6071G>A	c.(6070-6072)aGt>aAt	p.S2024N	BAZ2B_ENST00000355831.2_Missense_Mutation_p.S1990N|BAZ2B_ENST00000392782.1_Missense_Mutation_p.S1988N|BAZ2B_ENST00000343439.5_Missense_Mutation_p.S1924N	NM_013450.2	NP_038478.2	Q9UIF8	BAZ2B_HUMAN	bromodomain adjacent to zinc finger domain, 2B	2024			S -> N (in dbSNP:rs415793).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(7)|liver(2)|lung(41)|ovary(3)|prostate(1)|skin(2)|soft_tissue(1)|urinary_tract(1)	82						TTTTAGTGAACTACTTGTAGA	0.323													C|||	1255	0.250599	0.329	0.1801	5008	,	,		15308	0.2321		0.2097	False		,,,				2504	0.2556				p.S2024N		Atlas-SNP	.											.	BAZ2B	196	.	0			c.G6071A						PASS	.	C	ASN/SER	1037,2615		143,751,932	153.0	141.0	145.0		6071	5.8	1.0	2	dbSNP_80	145	1786,6372		189,1408,2482	yes	missense	BAZ2B	NM_013450.2	46	332,2159,3414	TT,TC,CC		21.8926,28.3954,23.9035	benign	2024/2169	160182302	2823,8987	1826	4079	5905	SO:0001583	missense	29994	exon35			AGTGAACTACTTG	AB032255	CCDS2209.2, CCDS74594.1	2q24.2	2013-01-28			ENSG00000123636	ENSG00000123636		"""Zinc fingers, PHD-type"""	963	protein-coding gene	gene with protein product		605683				10662543	Standard	XM_005246488		Approved	WALp4	uc002uao.3	Q9UIF8	OTTHUMG00000132027	ENST00000392783.2:c.6071G>A	2.37:g.160182302C>T	ENSP00000376534:p.Ser2024Asn	Somatic	226	0	0		WXS	Illumina HiSeq	Phase_I	173	173	1	NM_013450	D3DPA8|Q96EA1|Q96SQ8|Q9P252|Q9Y4N8	Missense_Mutation	SNP	ENST00000392783.2	37	CCDS2209.2	545	0.24954212454212454	180	0.36585365853658536	77	0.212707182320442	118	0.2062937062937063	170	0.22427440633245382	C	12.94	2.089690	0.36855	0.283954	0.218926	ENSG00000123636	ENST00000392782;ENST00000392783;ENST00000355831;ENST00000343439	T;T;T;T	0.58652	0.32;0.32;0.32;0.32	5.78	5.78	0.91487	.	0.000000	0.43110	U	0.000601	T	0.00012	0.0000	N	0.24115	0.695	0.27458	P	0.9532378	P;B	0.41848	0.763;0.209	B;B	0.36608	0.229;0.062	T	0.40590	-0.9555	9	0.26408	T	0.33	-12.2975	11.376	0.49728	0.1272:0.6343:0.2384:0.0	rs415793;rs52792009;rs58271129;rs415793	1988;2024	Q9UIF8-5;Q9UIF8	.;BAZ2B_HUMAN	N	1988;2024;1990;1924	ENSP00000376533:S1988N;ENSP00000376534:S2024N;ENSP00000348087:S1990N;ENSP00000339670:S1924N	ENSP00000339670:S1924N	S	-	2	0	BAZ2B	159890548	1.000000	0.71417	0.997000	0.53966	0.989000	0.77384	2.956000	0.49129	2.730000	0.93505	0.650000	0.86243	AGT	T|0.249;G|0.012	0.249	strong		0.323	BAZ2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255037.2		
LRRC38	126755	hgsc.bcm.edu	37	1	13802437	13802437	+	Silent	SNP	G	G	A	rs3013106	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:13802437G>A	ENST00000376085.3	-	2	1216	c.762C>T	c.(760-762)tcC>tcT	p.S254S		NM_001010847.1	NP_001010847.1	Q5VT99	LRC38_HUMAN	leucine rich repeat containing 38	254					ion transport (GO:0006811)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)											CGGCCACACCGGAGAAAATGA	0.582													G|||	1626	0.324681	0.4221	0.2262	5008	,	,		19646	0.3879		0.2505	False		,,,				2504	0.274				p.S254S		Atlas-SNP	.											.	LRRC38	12	.	0			c.C762T						PASS	.																																			SO:0001819	synonymous_variant	126755	exon2			CACACCGGAGAAA	BC016048	CCDS53269.1	1p36.21	2008-02-05			ENSG00000162494	ENSG00000162494			27005	protein-coding gene	gene with protein product		615212				12477932	Standard	NM_001010847		Approved		uc001avb.3	Q5VT99	OTTHUMG00000007918	ENST00000376085.3:c.762C>T	1.37:g.13802437G>A		Somatic	179	0	0		WXS	Illumina HiSeq	Phase_I	182	82	0.450549	NM_001010847	Q96B32	Silent	SNP	ENST00000376085.3	37	CCDS53269.1																																																																																			A|0.323;C|0.008	0.323	strong		0.582	LRRC38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021793.1		
APOPT1	84334	hgsc.bcm.edu	37	14	104029449	104029449	+	Silent	SNP	G	G	A	rs2274267	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:104029449G>A	ENST00000409074.2	+	1	151	c.150G>A	c.(148-150)acG>acA	p.T50T	APOPT1_ENST00000556253.2_Silent_p.T37T|APOPT1_ENST00000247618.4_Silent_p.T37T|BAG5_ENST00000299204.4_5'Flank|BAG5_ENST00000337322.4_5'Flank|BAG5_ENST00000445922.2_5'Flank|RP11-73M18.2_ENST00000472726.2_Silent_p.T50T|RP11-894P9.2_ENST00000556332.1_RNA	NM_032374.3	NP_115750.2	Q96IL0	APOP1_HUMAN	apoptogenic 1, mitochondrial	50					intrinsic apoptotic signaling pathway (GO:0097193)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of smooth muscle cell apoptotic process (GO:0034393)	mitochondrion (GO:0005739)											GCAGGGATACGGCGCCCAGCG	0.716													G|||	1108	0.221246	0.1074	0.3343	5008	,	,		12360	0.3512		0.2624	False		,,,				2504	0.1186				p.T50T		Atlas-SNP	.											.	.	.	.	0			c.G150A						PASS	.	G		557,3355		49,459,1448	4.0	6.0	5.0		150	-0.9	0.2	14	dbSNP_100	5	2012,5966		304,1404,2281	no	coding-synonymous	APOPT1	NM_032374.3		353,1863,3729	AA,AG,GG		25.2194,14.2382,21.6064		50/207	104029449	2569,9321	1956	3989	5945	SO:0001819	synonymous_variant	84334	exon1			GGATACGGCGCCC	BC007412	CCDS9983.2	14q32.33	2012-06-28	2012-06-28	2011-09-07	ENSG00000256053	ENSG00000256053			20492	protein-coding gene	gene with protein product	"""apoptogenic protein 1"""		"""chromosome 14 open reading frame 153"", ""apoptogenic 1"""	C14orf153		16782708, 18977203	Standard	NM_032374		Approved	MGC2562, APOP-1		Q96IL0	OTTHUMG00000153929	ENST00000409074.2:c.150G>A	14.37:g.104029449G>A		Somatic	11	0	0		WXS	Illumina HiSeq	Phase_I	18	11	0.611111	NM_032374	Q53G28	Silent	SNP	ENST00000409074.2	37	CCDS9983.2	553	0.2532051282051282	49	0.09959349593495935	118	0.3259668508287293	189	0.3304195804195804	197	0.2598944591029024	G	6.245	0.413378	0.11812	0.142382	0.252194	ENSG00000256053	ENST00000440963	.	.	.	3.37	-0.865	0.10662	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.53005	P	3.2999999999949736E-5	.	.	.	.	.	.	T	0.40213	-0.9575	4	0.09843	T	0.71	.	0.9102	0.01293	0.2249:0.1788:0.4131:0.1831	rs2274267;rs17095256;rs28362582	.	.	.	S	50	.	ENSP00000388067:G50S	G	+	1	0	C14orf153	103099202	0.296000	0.24398	0.214000	0.23707	0.083000	0.17756	-0.397000	0.07269	-0.499000	0.06623	-0.140000	0.14226	GGC	G|0.747;A|0.253	0.253	strong		0.716	APOPT1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333060.2	NM_032374	
PRSS55	203074	hgsc.bcm.edu	37	8	10396123	10396123	+	Silent	SNP	C	C	T	rs73195184	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:10396123C>T	ENST00000328655.3	+	5	919	c.879C>T	c.(877-879)ctC>ctT	p.L293L	PRSS51_ENST00000523024.1_RNA|PRSS55_ENST00000522210.1_Intron	NM_198464.3	NP_940866.2	Q6UWB4	PRS55_HUMAN	protease, serine, 55	293	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)	serine-type endopeptidase activity (GO:0004252)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(14)|ovary(1)|prostate(1)|skin(1)	31						ACTACAACCTCTGGATCGAGA	0.532													C|||	39	0.00778754	0.0	0.0086	5008	,	,		19220	0.001		0.0209	False		,,,				2504	0.0112				p.L293L		Atlas-SNP	.											PRSS55,NS,carcinoma,+2,2	PRSS55	67	2	0			c.C879T						PASS	.	C	,	27,4379	34.3+/-65.2	0,27,2176	109.0	114.0	112.0		,879	-2.3	0.0	8	dbSNP_130	112	221,8379	92.1+/-154.2	2,217,4081	no	intron,coding-synonymous	PRSS55	NM_001197020.1,NM_198464.3	,	2,244,6257	TT,TC,CC		2.5698,0.6128,1.9068	,	,293/353	10396123	248,12758	2203	4300	6503	SO:0001819	synonymous_variant	203074	exon5			CAACCTCTGGATC	AY358867	CCDS5976.1, CCDS56523.1	8p23.1	2014-01-21			ENSG00000184647	ENSG00000184647		"""Serine peptidases / Serine peptidases"""	30824	protein-coding gene	gene with protein product		615144				12975309, 18844450	Standard	NM_198464		Approved	T-SP1, UNQ9391, CT153	uc003wta.3	Q6UWB4	OTTHUMG00000129345	ENST00000328655.3:c.879C>T	8.37:g.10396123C>T		Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	139	27	0.194245	NM_198464	E5RJX5	Silent	SNP	ENST00000328655.3	37	CCDS5976.1																																																																																			C|0.985;T|0.015	0.015	strong		0.532	PRSS55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251493.3	NM_198464	
MUC4	4585	hgsc.bcm.edu	37	3	195512568	195512568	+	Silent	SNP	T	T	C	rs199625793|rs71254296		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195512568T>C	ENST00000463781.3	-	2	6342	c.5883A>G	c.(5881-5883)gtA>gtG	p.V1961V	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Silent_p.V1961V	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.P1952_T1967delPLPVTDASSVPTGHAT(4)|p.V1961V(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)		GACCTGTGGGTACTGAGGAAG	0.602																																					p.V1961V		Atlas-SNP	.											MUC4_ENST00000463781,bladder,carcinoma,0,2	MUC4	1505	2	5	Deletion - In frame(4)|Substitution - coding silent(1)	stomach(4)|endometrium(1)	c.A5883G						scavenged	.						55.0	43.0	46.0					3																	195512568		692	1591	2283	SO:0001819	synonymous_variant	4585	exon2			TGTGGGTACTGAG	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.5883A>G	3.37:g.195512568T>C		Somatic	55	1	0.0181818		WXS	Illumina HiSeq	Phase_I	117	21	0.179487	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																																																																																			GT|0.500;AC|0.500	.	alt		0.602	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
NPSR1	387129	hgsc.bcm.edu	37	7	34874038	34874038	+	Missense_Mutation	SNP	C	C	G	rs727162	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:34874038C>G	ENST00000360581.1	+	6	851	c.723C>G	c.(721-723)agC>agG	p.S241R	NPSR1_ENST00000531252.1_Missense_Mutation_p.S230R|NPSR1_ENST00000359791.1_Missense_Mutation_p.S241R|NPSR1_ENST00000381542.1_Missense_Mutation_p.S175R|NPSR1_ENST00000381539.3_Missense_Mutation_p.S241R	NM_207172.1	NP_997055.1	Q6W5P4	NPSR1_HUMAN	neuropeptide S receptor 1	241			S -> R (in dbSNP:rs727162). {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)	GGATTAAAAGCAAAACCTACG	0.423													C|||	1591	0.317692	0.2708	0.3516	5008	,	,		21956	0.3512		0.2177	False		,,,				2504	0.4254				p.S241R		Atlas-SNP	.											.	NPSR1	134	.	0			c.C723G						PASS	.	C	ARG/SER,ARG/SER	1179,3227	413.7+/-336.6	145,889,1169	193.0	172.0	179.0		723,723	4.8	1.0	7	dbSNP_86	179	1812,6788	325.5+/-317.0	209,1394,2697	yes	missense,missense	NPSR1	NM_207172.1,NM_207173.1	110,110	354,2283,3866	GG,GC,CC		21.0698,26.759,22.9971	probably-damaging,probably-damaging	241/372,241/378	34874038	2991,10015	2203	4300	6503	SO:0001583	missense	387129	exon6			TAAAAGCAAAACC	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.723C>G	7.37:g.34874038C>G	ENSP00000353788:p.Ser241Arg	Somatic	220	0	0		WXS	Illumina HiSeq	Phase_I	178	120	0.674157	NM_207172	A2RTZ4|Q2XP58|Q56H76|Q56H77|Q56H78|Q6JSL4|Q6JSL5|Q6JSL6|Q6JSL7|Q6JSL8|Q6W5P3|Q6ZMB8	Missense_Mutation	SNP	ENST00000360581.1	37	CCDS5444.1	619	0.2834249084249084	149	0.30284552845528456	115	0.31767955801104975	189	0.3304195804195804	166	0.21899736147757257	C	13.02	2.111304	0.37242	0.26759	0.210698	ENSG00000187258	ENST00000360581;ENST00000381542;ENST00000359791;ENST00000531252;ENST00000381539	T;T;T;T;T	0.37058	1.22;1.22;1.22;1.22;1.22	4.75	4.75	0.60458	GPCR, rhodopsin-like superfamily (1);	0.145297	0.49305	D	0.000142	T	0.00012	0.0000	L	0.56124	1.755	0.23449	P	0.99765779	D;D;D;D;D;D	0.76494	0.999;0.999;0.999;0.999;0.999;0.998	D;D;D;D;D;D	0.71656	0.966;0.974;0.943;0.973;0.974;0.973	T	0.30909	-0.9962	9	0.41790	T	0.15	-29.6163	10.1436	0.42749	0.0:0.908:0.0:0.092	rs727162;rs11489290;rs52823007;rs56605321;rs59161753;rs727162	175;230;175;241;241;241	B7ZMA2;Q6W5P4-5;Q6W5P4-2;Q6W5P4-4;Q6W5P4-3;Q6W5P4	.;.;.;.;.;NPSR1_HUMAN	R	241;175;241;230;241	ENSP00000353788:S241R;ENSP00000370953:S175R;ENSP00000352839:S241R;ENSP00000433258:S230R;ENSP00000370950:S241R	ENSP00000352839:S241R	S	+	3	2	NPSR1	34840563	1.000000	0.71417	1.000000	0.80357	0.772000	0.43724	1.415000	0.34748	2.456000	0.83038	0.555000	0.69702	AGC	C|0.744;G|0.256	0.256	strong		0.423	NPSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216837.1	NM_207173	
TREX2	11219	hgsc.bcm.edu	37	X	152710185	152710185	+	Missense_Mutation	SNP	T	T	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:152710185T>G	ENST00000334497.2	-	11	1974	c.833A>C	c.(832-834)gAg>gCg	p.E278A	TREX2_ENST00000393862.2_Missense_Mutation_p.E235A|TREX2_ENST00000370231.2_Missense_Mutation_p.E235A|HAUS7_ENST00000484394.1_5'Flank|TREX2_ENST00000330912.2_Missense_Mutation_p.E235A|TREX2_ENST00000370232.1_Missense_Mutation_p.E278A|TREX2_ENST00000414588.1_Missense_Mutation_p.E277A|TREX2_ENST00000338525.2_Missense_Mutation_p.E235A|TREX2_ENST00000402951.1_Missense_Mutation_p.E278A			Q9BQ50	TREX2_HUMAN	three prime repair exonuclease 2	278					DNA catabolic process, exonucleolytic (GO:0000738)|DNA metabolic process (GO:0006259)|DNA repair (GO:0006281)	nucleus (GO:0005634)	3'-5'-exodeoxyribonuclease activity (GO:0008296)|exodeoxyribonuclease III activity (GO:0008853)|magnesium ion binding (GO:0000287)|nucleic acid binding (GO:0003676)|protein homodimerization activity (GO:0042803)			endometrium(4)|large_intestine(2)|lung(3)|ovary(2)	11	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					TGCTCAGGCCTCCAGGCTGGG	0.692								Editing and processing nucleases																													p.E235A		Atlas-SNP	.											.	TREX2	36	.	0			c.A704C						PASS	.						13.0	10.0	11.0					X																	152710185		2176	4263	6439	SO:0001583	missense	11219	exon2			CAGGCCTCCAGGC	AF151107	CCDS35437.1	Xq28	2012-05-08			ENSG00000183479	ENSG00000183479			12270	protein-coding gene	gene with protein product		300370				10391904	Standard	NM_080701		Approved		uc011myp.2	Q9BQ50	OTTHUMG00000159319	ENST00000334497.2:c.833A>C	X.37:g.152710185T>G	ENSP00000334993:p.Glu278Ala	Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	50	18	0.36	NM_080701	Q45F08|Q9UN77	Missense_Mutation	SNP	ENST00000334497.2	37		.	.	.	.	.	.	.	.	.	.	T	14.14	2.445525	0.43429	.	.	ENSG00000183479	ENST00000393862;ENST00000330912;ENST00000338525;ENST00000334497;ENST00000370232;ENST00000402951;ENST00000414588;ENST00000370231	T;T;T;T;T;T;T;T	0.53640	0.81;0.81;0.81;0.65;0.65;0.65;0.61;0.81	4.35	4.35	0.52113	.	0.576106	0.12955	U	0.425475	T	0.33818	0.0876	L	0.27053	0.805	0.09310	N	1	P;P	0.46987	0.888;0.608	B;B	0.38985	0.287;0.08	T	0.17018	-1.0383	10	0.87932	D	0	-15.0026	9.2945	0.37806	0.0:0.0:0.0:1.0	.	277;278	Q06S70;Q9BQ50	.;TREX2_HUMAN	A	235;235;235;278;278;278;277;235	ENSP00000377442:E235A;ENSP00000333441:E235A;ENSP00000345218:E235A;ENSP00000334993:E278A;ENSP00000359252:E278A;ENSP00000386078:E278A;ENSP00000401692:E277A;ENSP00000359251:E235A	ENSP00000333441:E235A	E	-	2	0	TREX2	152363379	0.010000	0.17322	0.007000	0.13788	0.003000	0.03518	1.834000	0.39171	1.523000	0.49018	0.381000	0.24937	GAG	.	.	none		0.692	TREX2-001	KNOWN	alternative_5_UTR|basic	protein_coding	protein_coding	OTTHUMT00000060966.1	NM_080701	
NLRP5	126206	hgsc.bcm.edu	37	19	56552456	56552456	+	Silent	SNP	G	G	T	rs61732213	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:56552456G>T	ENST00000390649.3	+	11	2955	c.2955G>T	c.(2953-2955)ctG>ctT	p.L985L		NM_153447.4	NP_703148.4	P59047	NALP5_HUMAN	NLR family, pyrin domain containing 5	985					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)		TGCAGAGGCTGATGTGAGTCT	0.532													G|||	1125	0.224641	0.0272	0.2262	5008	,	,		22018	0.4792		0.1252	False		,,,				2504	0.3303				p.L985L		Atlas-SNP	.											.	NLRP5	217	.	0			c.G2955T						PASS	.	G		177,3947		1,175,1886	191.0	188.0	189.0		2955	2.0	0.4	19	dbSNP_129	189	1288,7142		105,1078,3032	no	coding-synonymous	NLRP5	NM_153447.4		106,1253,4918	TT,TG,GG		15.2788,4.2919,11.6696		985/1201	56552456	1465,11089	2062	4215	6277	SO:0001819	synonymous_variant	126206	exon11			GAGGCTGATGTGA	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.2955G>T	19.37:g.56552456G>T		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	146	83	0.568493	NM_153447	A8MTY4|Q86W29	Silent	SNP	ENST00000390649.3	37	CCDS12938.1																																																																																			G|0.815;T|0.185	0.185	strong		0.532	NLRP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313735.1	NM_153447	
C10orf54	64115	hgsc.bcm.edu	37	10	73521371	73521371	+	Silent	SNP	C	C	T	rs3747867	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:73521371C>T	ENST00000394957.3	-	2	553	c.495G>A	c.(493-495)gaG>gaA	p.E165E	CDH23_ENST00000224721.6_Intron|C10orf54_ENST00000481568.2_5'UTR	NM_022153.1	NP_071436.1	Q9H7M9	GI24_HUMAN	chromosome 10 open reading frame 54	165					BMP signaling pathway (GO:0030509)|negative regulation of CD4-positive, alpha-beta T cell proliferation (GO:2000562)|negative regulation of T cell cytokine production (GO:0002725)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of stem cell differentiation (GO:2000738)|stem cell differentiation (GO:0048863)	external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(2)|endometrium(1)|lung(1)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	9						GCACCTGCAGCTCCATGGCAC	0.622													C|||	934	0.186502	0.1551	0.1729	5008	,	,		23685	0.1935		0.2744	False		,,,				2504	0.1411				p.E165E		Atlas-SNP	.											.	C10orf54	29	.	0			c.G495A						PASS	.	C	,	800,3606	303.8+/-288.1	67,666,1470	37.0	29.0	32.0		,495	3.8	1.0	10	dbSNP_107	32	2175,6425	356.1+/-330.2	267,1641,2392	no	intron,coding-synonymous	CDH23,C10orf54	NM_022124.5,NM_022153.1	,	334,2307,3862	TT,TC,CC		25.2907,18.1571,22.8741	,	,165/312	73521371	2975,10031	2203	4300	6503	SO:0001819	synonymous_variant	64115	exon2			CTGCAGCTCCATG	AF193048	CCDS31218.1	10q22.1	2013-11-28			ENSG00000107738	ENSG00000107738		"""Immunoglobulin superfamily / V-set domain containing"""	30085	protein-coding gene	gene with protein product	"""stress induced secreted protein 1"""	615608				12975309	Standard	NM_022153		Approved	SISP1, GI24, B7-H5, B7H5	uc001jsd.3	Q9H7M9	OTTHUMG00000018426	ENST00000394957.3:c.495G>A	10.37:g.73521371C>T		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	46	29	0.630435	NM_022153	A1L0X9|A4ZYV1|A8MVH5|Q6UXF3|Q8WUG3|Q8WYZ8	Silent	SNP	ENST00000394957.3	37	CCDS31218.1																																																																																			C|0.779;T|0.221	0.221	strong		0.622	C10orf54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048548.1	NM_022153	
EGFR	1956	hgsc.bcm.edu	37	7	55238087	55238087	+	Intron	SNP	C	C	T	rs10258429	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:55238087C>T	ENST00000275493.2	+	16	2057				EGFR_ENST00000454757.2_Intron|EGFR_ENST00000455089.1_Intron|EGFR_ENST00000442591.1_Intron|EGFR_ENST00000344576.2_Silent_p.H656H	NM_005228.3	NP_005219.2	P00533	EGFR_HUMAN	epidermal growth factor receptor						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)	GCGTGTCCCACCAGAGCGGGA	0.512		8	"""A, O, Mis"""		"""glioma, NSCLC"""	NSCLC			Lung Cancer, Familial Clustering of	TCGA GBM(3;<1E-08)|TSP Lung(4;<1E-08)			C|||	563	0.11242	0.2398	0.049	5008	,	,		20745	0.0496		0.0736	False		,,,				2504	0.09				p.H656H		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.C1968T						PASS	.	C	,	922,3484	352.1+/-311.5	101,720,1382	108.0	89.0	95.0		,1968	2.4	0.0	7	dbSNP_119	95	606,7994	158.6+/-212.1	23,560,3717	no	intron,coding-synonymous	EGFR	NM_005228.3,NM_201284.1	,	124,1280,5099	TT,TC,CC		7.0465,20.926,11.7484	,	,656/706	55238087	1528,11478	2203	4300	6503	SO:0001627	intron_variant	1956	exon16	Familial Cancer Database	incl. Hereditary Lung cancer, Hereditary Non-Small Cell Lung cancer	GTCCCACCAGAGC		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.1881-781C>T	7.37:g.55238087C>T		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	145	66	0.455172	NM_201284	O00688|O00732|P06268|Q14225|Q68GS5|Q92795|Q9BZS2|Q9GZX1|Q9H2C9|Q9H3C9|Q9UMD7|Q9UMD8|Q9UMG5	Silent	SNP	ENST00000275493.2	37	CCDS5514.1																																																																																			C|0.889;T|0.111	0.111	strong		0.512	EGFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251456.2	NM_005228	
RABL6	55684	hgsc.bcm.edu	37	9	139731969	139731969	+	Silent	SNP	C	C	T	rs2811742	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:139731969C>T	ENST00000311502.7	+	9	1217	c.981C>T	c.(979-981)gcC>gcT	p.A327A	RABL6_ENST00000371675.3_Silent_p.A212A|RABL6_ENST00000357466.2_Silent_p.A327A|RABL6_ENST00000432842.2_Silent_p.A289A|RABL6_ENST00000371663.4_Silent_p.A328A			Q3YEC7	RABL6_HUMAN	RAB, member RAS oncogene family-like 6	327	Pro-rich.				small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	GTP binding (GO:0005525)										CCCTCAATGCCGCCCCACCAT	0.731													c|||	3839	0.766573	0.7057	0.7032	5008	,	,		9159	0.8155		0.8161	False		,,,				2504	0.7924				p.A328A		Atlas-SNP	.											C9orf86_ENST00000371663,NS,carcinoma,0,2	.	.	2	0			c.C984T						PASS	.	T	,	2550,840		965,620,110	4.0	4.0	4.0		984,981	0.4	0.0	9	dbSNP_100	4	6246,1344		2598,1050,147	no	coding-synonymous,coding-synonymous	C9orf86	NM_001173988.1,NM_024718.4	,	3563,1670,257	TT,TC,CC		17.7075,24.7788,19.8907	,	328/731,327/730	139731969	8796,2184	1695	3795	5490	SO:0001819	synonymous_variant	55684	exon9			CAATGCCGCCCCA	AK094382	CCDS48058.1, CCDS55352.1, CCDS55353.1	9q34.3	2012-06-28	2012-06-28	2012-06-28	ENSG00000196642	ENSG00000196642			24703	protein-coding gene	gene with protein product	"""Rab-like protein 1"", ""partner of ARF"""	610615	"""chromosome 9 open reading frame 86"""	C9orf86		14702039, 16582619, 17962191, 19433581	Standard	NM_024718		Approved	FLJ10101, FLJ13045, pp8875, bA216L13.9, Parf, RBEL1	uc004cjj.1	Q3YEC7	OTTHUMG00000020947	ENST00000311502.7:c.981C>T	9.37:g.139731969C>T		Somatic	15	0	0		WXS	Illumina HiSeq	Phase_I	26	9	0.346154	NM_001173988	A8QVZ7|A8QVZ8|C6K8I4|C6K8I5|Q4F968|Q5T5R7|Q8IWK1|Q8TCL4|Q8WU94|Q96SR8|Q9BU21|Q9H935	Silent	SNP	ENST00000311502.7	37	CCDS48058.1																																																																																			C|0.236;T|0.764	0.764	strong		0.731	RABL6-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000055141.4	NM_024718	
GALNT8	26290	hgsc.bcm.edu	37	12	4830000	4830000	+	Missense_Mutation	SNP	T	T	G	rs10849133	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:4830000T>G	ENST00000252318.2	+	1	494	c.157T>G	c.(157-159)Tac>Gac	p.Y53D	RP11-234B24.6_ENST00000544741.2_Intron|RP11-234B24.2_ENST00000527518.1_lincRNA	NM_017417.1	NP_059113.1	Q9NY28	GALT8_HUMAN	polypeptide N-acetylgalactosaminyltransferase 8	53			Y -> D (in dbSNP:rs10849133).|Y -> N. {ECO:0000269|PubMed:10767557}.		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)	p.Y53D(1)		central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(13)|ovary(2)|pancreas(1)|prostate(4)|skin(2)|urinary_tract(1)	35						GAATAAACGCTACGGGGCAGT	0.468													G|||	1913	0.381989	0.4977	0.415	5008	,	,		19958	0.3611		0.3777	False		,,,				2504	0.228				p.Y53D	Colon(108;631 1558 7270 20097 39846)	Atlas-SNP	.											GALNT8,NS,carcinoma,0,2	GALNT8	89	2	1	Substitution - Missense(1)	prostate(1)	c.T157G						PASS	.	G	ASP/TYR	2050,2356	609.2+/-391.3	481,1088,634	88.0	92.0	91.0		157	0.5	0.0	12	dbSNP_120	91	3284,5316	647.2+/-400.4	612,2060,1628	yes	missense	GALNT8	NM_017417.1	160	1093,3148,2262	GG,GT,TT		38.186,46.5275,41.0118	benign	53/638	4830000	5334,7672	2203	4300	6503	SO:0001583	missense	26290	exon1			AAACGCTACGGGG	AJ271385	CCDS8533.1	12p13.32	2014-03-13	2014-03-13		ENSG00000130035	ENSG00000130035	2.4.1.41	"""Glycosyltransferase family 2 domain containing"""	4130	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase 8"""	606250	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 8 (GalNAc-T8)"""			10767557	Standard	NM_017417		Approved	GALNAC-T8	uc001qne.1	Q9NY28	OTTHUMG00000166188	ENST00000252318.2:c.157T>G	12.37:g.4830000T>G	ENSP00000252318:p.Tyr53Asp	Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	118	70	0.59322	NM_017417	B2RU02	Missense_Mutation	SNP	ENST00000252318.2	37	CCDS8533.1	897	0.4107142857142857	249	0.5060975609756098	143	0.39502762430939226	226	0.3951048951048951	279	0.36807387862796836	G	0.963	-0.702517	0.03255	0.465275	0.38186	ENSG00000130035	ENST00000252318	T	0.51817	0.69	3.74	0.482	0.16815	.	104.897000	0.00166	N	0.000000	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	0.43589	-0.9382	9	0.11794	T	0.64	.	0.2754	0.00237	0.3052:0.2005:0.2915:0.2028	rs10849133;rs10849133	53	Q9NY28	GALT8_HUMAN	D	53	ENSP00000252318:Y53D	ENSP00000252318:Y53D	Y	+	1	0	GALNT8	4700261	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.341000	0.19909	-0.294000	0.08973	-1.720000	0.00707	TAC	G|0.410;N|0.000	0.410	strong		0.468	GALNT8-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388277.2	NM_017417	
MUC4	4585	hgsc.bcm.edu	37	3	195515449	195515449	+	Missense_Mutation	SNP	A	A	T	rs200672669	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195515449A>T	ENST00000463781.3	-	2	3461	c.3002T>A	c.(3001-3003)gTa>gAa	p.V1001E	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.V1001E	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	425	Ser-rich.				cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.V1001A(1)|p.V1001E(1)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		ACCTGTGGATACTGAGGAAGC	0.587																																					p.V1001E		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,12	MUC4	1505	12	2	Substitution - Missense(2)	prostate(1)|endometrium(1)	c.T3002A						PASS	.						45.0	36.0	39.0					3																	195515449		2193	4257	6450	SO:0001583	missense	4585	exon2			GTGGATACTGAGG	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.3002T>A	3.37:g.195515449A>T	ENSP00000417498:p.Val1001Glu	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	88	12	0.136364	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	A	7.806	0.714656	0.15306	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.37752	1.19;1.18	1.24	-2.48	0.06423	.	.	.	.	.	T	0.13543	0.0328	N	0.08118	0	0.09310	N	1	B	0.12630	0.006	B	0.01281	0.0	T	0.24261	-1.0165	8	.	.	.	.	2.7997	0.05411	0.2821:0.0:0.4902:0.2277	.	1001	E7ESK3	.	E	1001	ENSP00000417498:V1001E;ENSP00000420243:V1001E	.	V	-	2	0	MUC4	196999844	.	.	0.000000	0.03702	0.127000	0.20565	.	.	-0.712000	0.04988	0.055000	0.15244	GTA	A|0.956;G|0.036;T|0.008	0.008	strong		0.587	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
ERMARD	55780	hgsc.bcm.edu	37	6	170162537	170162537	+	Silent	SNP	C	C	T	rs11966349	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:170162537C>T	ENST00000366773.3	+	9	903	c.870C>T	c.(868-870)tgC>tgT	p.C290C	ERMARD_ENST00000392095.4_Silent_p.C164C|ERMARD_ENST00000588451.1_Silent_p.C164C|ERMARD_ENST00000366772.2_Silent_p.C290C|ERMARD_ENST00000418781.3_Silent_p.C290C	NM_001278532.1|NM_018341.1	NP_001265461.1|NP_060811.1	Q5T6L9	EMARD_HUMAN	ER membrane-associated RNA degradation	290					multicellular organismal development (GO:0007275)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)											TTGCTGACTGCGCCATATTGT	0.428													C|||	1007	0.201078	0.2436	0.17	5008	,	,		18512	0.2738		0.1014	False		,,,				2504	0.1933				p.C290C		Atlas-SNP	.											.	C6orf70	63	.	0			c.C870T						PASS	.	C		1060,3346	385.6+/-325.8	129,802,1272	134.0	128.0	130.0		870	-0.5	0.7	6	dbSNP_120	130	816,7784	188.3+/-235.3	46,724,3530	no	coding-synonymous	C6orf70	NM_018341.1		175,1526,4802	TT,TC,CC		9.4884,24.0581,14.4241		290/679	170162537	1876,11130	2203	4300	6503	SO:0001819	synonymous_variant	55780	exon9			TGACTGCGCCATA	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.870C>T	6.37:g.170162537C>T		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	57	12	0.210526	NM_018341	B4DFH0|F8WAF1|Q3ZCS8|Q5T6L8|Q9NUT5|Q9NVU2	Silent	SNP	ENST00000366773.3	37	CCDS34576.1																																																																																			C|0.838;T|0.162	0.162	strong		0.428	ERMARD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043238.2	NM_018341	
CXCR4	7852	hgsc.bcm.edu	37	2	136873084	136873084	+	Silent	SNP	G	G	A	rs2228014	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:136873084G>A	ENST00000241393.3	-	2	518	c.414C>T	c.(412-414)atC>atT	p.I138I	CXCR4_ENST00000466288.1_5'UTR|CXCR4_ENST00000409817.1_Silent_p.I142I	NM_003467.2	NP_003458.1	P61073	CXCR4_HUMAN	chemokine (C-X-C motif) receptor 4	138	Involved in dimerization; when bound to chemokine.				activation of MAPK activity (GO:0000187)|ameboidal cell migration (GO:0001667)|apoptotic process (GO:0006915)|brain development (GO:0007420)|calcium-mediated signaling (GO:0019722)|cellular response to cytokine stimulus (GO:0071345)|chemokine-mediated signaling pathway (GO:0070098)|dendritic cell chemotaxis (GO:0002407)|entry into host cell (GO:0030260)|G-protein coupled receptor signaling pathway (GO:0007186)|germ cell development (GO:0007281)|germ cell migration (GO:0008354)|inflammatory response (GO:0006954)|motor neuron axon guidance (GO:0008045)|myelin maintenance (GO:0043217)|neural precursor cell proliferation (GO:0061351)|neuron migration (GO:0001764)|neutrophil activation (GO:0042119)|patterning of blood vessels (GO:0001569)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of oligodendrocyte differentiation (GO:0048714)|regulation of cell migration (GO:0030334)|regulation of chemotaxis (GO:0050920)|response to hypoxia (GO:0001666)|response to virus (GO:0009615)|T cell proliferation (GO:0042098)|viral process (GO:0016032)	cell leading edge (GO:0031252)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|lysosome (GO:0005764)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|C-X-C chemokine receptor activity (GO:0016494)|coreceptor activity (GO:0015026)|G-protein coupled receptor activity (GO:0004930)|myosin light chain binding (GO:0032027)|ubiquitin binding (GO:0043130)|ubiquitin protein ligase binding (GO:0031625)|virus receptor activity (GO:0001618)	p.I142I(1)		haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(14)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25				BRCA - Breast invasive adenocarcinoma(221;0.155)	Framycetin(DB00452)|Plerixafor(DB06809)	TGGCGTGGACGATGGCCAGGT	0.552													g|||	315	0.0628994	0.0136	0.0288	5008	,	,		24356	0.1508		0.0427	False		,,,				2504	0.0838				p.I142I		Atlas-SNP	.											CXCR4,NS,carcinoma,0,1	CXCR4	51	1	1	Substitution - coding silent(1)	stomach(1)	c.C426T						PASS	.	A	,	86,4320	72.0+/-110.0	1,84,2118	173.0	148.0	157.0		426,414	-7.2	0.8	2	dbSNP_98	157	395,8205	126.5+/-185.0	15,365,3920	no	coding-synonymous,coding-synonymous	CXCR4	NM_001008540.1,NM_003467.2	,	16,449,6038	AA,AG,GG		4.593,1.9519,3.6983	,	142/357,138/353	136873084	481,12525	2203	4300	6503	SO:0001819	synonymous_variant	7852	exon1			GTGGACGATGGCC	AF005058	CCDS33295.1, CCDS46420.1	2q21	2014-09-17	2002-08-22		ENSG00000121966	ENSG00000121966		"""CD molecules"", ""GPCR / Class A : Chemokine receptors : C-X-C motif"""	2561	protein-coding gene	gene with protein product		162643	"""chemokine (C-X-C motif), receptor 4 (fusin)"""			9599023, 9379028	Standard	NM_001008540		Approved	LESTR, NPY3R, HM89, NPYY3R, D2S201E, fusin, HSY3RR, NPYR, CD184	uc002tuz.3	P61073	OTTHUMG00000153583	ENST00000241393.3:c.414C>T	2.37:g.136873084G>A		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	44	19	0.431818	NM_001008540	B2R5N0|O60835|P30991|P56438|Q53S69|Q9BXA0|Q9UKN2	Silent	SNP	ENST00000241393.3	37	CCDS46420.1																																																																																			G|0.955;A|0.045	0.045	strong		0.552	CXCR4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000331732.1		
PML	5371	hgsc.bcm.edu	37	15	74328116	74328116	+	Intron	SNP	A	A	G	rs743580	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:74328116A>G	ENST00000268058.3	+	7	1806				PML_ENST00000435786.2_3'UTR|PML_ENST00000563500.1_3'UTR|PML_ENST00000395135.3_Intron|PML_ENST00000268059.6_Missense_Mutation_p.S772G|PML_ENST00000565898.1_Intron|PML_ENST00000359928.4_Intron|PML_ENST00000436891.3_3'UTR|PML_ENST00000569965.1_Intron|PML_ENST00000395132.2_Intron|PML_ENST00000354026.6_Missense_Mutation_p.S724G|PML_ENST00000564428.1_Intron	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						GGCAGGGGAAAGCAGAGCCCA	0.577			T	"""RARA, PAX5"""	"""APL, ALL"""								G|||	2764	0.551917	0.5272	0.5346	5008	,	,		15561	0.6379		0.5189	False		,,,				2504	0.5429				p.S772G		Atlas-SNP	.		Dom	yes		15	15q22	5371	promyelocytic leukemia		L	.	PML	169	.	0			c.A2314G						PASS	.	G	,,GLY/SER,,,,,,GLY/SER	2250,2146	556.1+/-379.4	568,1114,516	47.0	55.0	53.0		,,2314,,,,,,2170	0.6	0.0	15	dbSNP_86	53	4233,4361	565.9+/-388.6	1023,2187,1087	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	,,56,,,,,,56	1591,3301,1603	GG,GA,AA		49.2553,48.8171,49.9076	,,,,,,,,	,,772/830,,,,,,724/782	74328116	6483,6507	2198	4297	6495	SO:0001627	intron_variant	5371	exon8			GGGGAAAGCAGAG	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+1245A>G	15.37:g.74328116A>G		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	86	63	0.732558	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	1199	0.548992673992674	248	0.5040650406504065	179	0.494475138121547	373	0.6520979020979021	399	0.5263852242744064	G	0.009	-1.857524	0.00558	0.511829	0.492553	ENSG00000140464	ENST00000268059;ENST00000354026	.	.	.	2.67	0.623	0.17654	.	.	.	.	.	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	0.44922	-0.9296	6	0.02654	T	1	.	2.4421	0.04497	0.2885:0.0:0.4641:0.2475	rs743580;rs3825940;rs17855993;rs17856627	724;772	P29590-13;P29590-8	.;.	G	772;724	.	ENSP00000268059:S772G	S	+	1	0	PML	72115169	0.000000	0.05858	0.002000	0.10522	0.023000	0.10783	0.137000	0.15995	-0.085000	0.12573	-0.355000	0.07637	AGC	A|0.492;C|0.000;G|0.508	0.508	strong		0.577	PML-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269021.3	NM_002675	
THSD1	55901	hgsc.bcm.edu	37	13	52971893	52971893	+	Silent	SNP	G	G	A	rs3803264	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:52971893G>A	ENST00000258613.4	-	3	673	c.495C>T	c.(493-495)atC>atT	p.I165I	THSD1_ENST00000349258.4_Silent_p.I165I|THSD1_ENST00000544466.1_Intron|RNY4P24_ENST00000362735.1_RNA	NM_018676.3	NP_061146.1	Q9NS62	THSD1_HUMAN	thrombospondin, type I, domain containing 1	165					hematopoietic progenitor cell differentiation (GO:0002244)	cell periphery (GO:0071944)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)				breast(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(11)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	30		Breast(56;0.000207)|Lung NSC(96;0.00145)|Hepatocellular(98;0.065)|Prostate(109;0.0771)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;2.8e-08)		CATCCACTACGATGTTGGGCT	0.488													G|||	2943	0.58766	0.4758	0.6383	5008	,	,		23174	0.6458		0.6889	False		,,,				2504	0.5389				p.I165I		Atlas-SNP	.											.	THSD1	89	.	0			c.C495T						PASS	.	G	,	2078,2328	569.8+/-382.7	496,1086,621	95.0	80.0	85.0		495,495	-0.2	0.0	13	dbSNP_107	85	5748,2852	674.3+/-403.1	1914,1920,466	no	coding-synonymous,coding-synonymous	THSD1	NM_018676.3,NM_199263.2	,	2410,3006,1087	AA,AG,GG		33.1628,47.163,39.8278	,	165/853,165/800	52971893	7826,5180	2203	4300	6503	SO:0001819	synonymous_variant	55901	exon3			CACTACGATGTTG	AK096289	CCDS9432.1, CCDS9433.1	13q14.13	2010-04-20	2004-03-11		ENSG00000136114	ENSG00000136114			17754	protein-coding gene	gene with protein product			"""thrombospondin, type I, domain 1"""				Standard	NM_018676		Approved	TMTSP	uc001vgo.3	Q9NS62	OTTHUMG00000016963	ENST00000258613.4:c.495C>T	13.37:g.52971893G>A		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	57	57	1	NM_199263	A2A3J3|B2RCF5|Q6P3U1|Q6UXZ2	Silent	SNP	ENST00000258613.4	37	CCDS9432.1																																																																																			G|0.397;A|0.603	0.603	strong		0.488	THSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045058.3		
COLEC12	81035	hgsc.bcm.edu	37	18	346821	346821	+	Silent	SNP	C	C	T	rs3826628	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:346821C>T	ENST00000400256.3	-	5	1008	c.801G>A	c.(799-801)acG>acA	p.T267T		NM_130386.2	NP_569057	Q5KU26	COL12_HUMAN	collectin sub-family member 12	267					carbohydrate mediated signaling (GO:0009756)|defense response (GO:0006952)|innate immune response (GO:0045087)|pattern recognition receptor signaling pathway (GO:0002221)|phagocytosis, recognition (GO:0006910)|protein homooligomerization (GO:0051260)|receptor-mediated endocytosis (GO:0006898)	collagen trimer (GO:0005581)|endocytic vesicle membrane (GO:0030666)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	galactose binding (GO:0005534)|low-density lipoprotein particle binding (GO:0030169)|metal ion binding (GO:0046872)|scavenger receptor activity (GO:0005044)|signaling pattern recognition receptor activity (GO:0008329)			cervix(2)|endometrium(3)|kidney(2)|large_intestine(10)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	46		all_cancers(4;0.0442)|Myeloproliferative disorder(11;0.0426)				TGGCAGCCAGCGTCTGCAAGC	0.498													C|||	1168	0.233227	0.177	0.2839	5008	,	,		21093	0.2153		0.2545	False		,,,				2504	0.2699				p.T267T		Atlas-SNP	.											COLEC12,colon,carcinoma,0,1	COLEC12	121	1	0			c.G801A						PASS	.	C		802,3604	324.2+/-298.5	93,616,1494	131.0	109.0	117.0		801	-7.0	0.6	18	dbSNP_107	117	2150,6450	369.5+/-335.5	270,1610,2420	no	coding-synonymous	COLEC12	NM_130386.2		363,2226,3914	TT,TC,CC		25.0,18.2025,22.6972		267/743	346821	2952,10054	2203	4300	6503	SO:0001819	synonymous_variant	81035	exon5			AGCCAGCGTCTGC	AB038518	CCDS32782.1	18p11.32	2013-09-19			ENSG00000158270	ENSG00000158270		"""Collectins"""	16016	protein-coding gene	gene with protein product		607621				11162630	Standard	NM_130386		Approved	SRCL, CL-P1, SCARA4	uc002kkm.3	Q5KU26	OTTHUMG00000178145	ENST00000400256.3:c.801G>A	18.37:g.346821C>T		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	89	41	0.460674	NM_130386	Q6P9F2|Q8TCR2|Q8WZA4|Q9BY85|Q9BYH7	Silent	SNP	ENST00000400256.3	37	CCDS32782.1																																																																																			C|0.763;T|0.237	0.237	strong		0.498	COLEC12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440746.1		
ADAM32	203102	hgsc.bcm.edu	37	8	39068684	39068684	+	Silent	SNP	T	T	A	rs61753544	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:39068684T>A	ENST00000379907.4	+	12	1201	c.1074T>A	c.(1072-1074)acT>acA	p.T358T	ADAM32_ENST00000437682.2_Intron|ADAM32_ENST00000519315.1_Intron	NM_145004.5	NP_659441	Q8TC27	ADA32_HUMAN	ADAM metallopeptidase domain 32	358	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.					integral component of membrane (GO:0016021)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(14)|ovary(1)|skin(2)	31		all_cancers(7;3e-05)|all_lung(54;0.00187)|Hepatocellular(245;0.00745)|Lung NSC(58;0.00771)|Breast(189;0.0503)	LUSC - Lung squamous cell carcinoma(45;6.2e-07)|Colorectal(1;0.00699)|READ - Rectum adenocarcinoma(1;0.146)			GTGTGAAGACTTTTAGCAGTT	0.323													T|||	2	0.000399361	0.0	0.0014	5008	,	,		16759	0.0		0.001	False		,,,				2504	0.0				p.T358T		Atlas-SNP	.											.	ADAM32	70	.	0			c.T1074A						PASS	.	T		5,3635		0,5,1815	102.0	101.0	101.0		1074	-2.5	1.0	8	dbSNP_129	101	25,8143		0,25,4059	no	coding-synonymous	ADAM32	NM_145004.5		0,30,5874	AA,AT,TT		0.3061,0.1374,0.2541		358/788	39068684	30,11778	1820	4084	5904	SO:0001819	synonymous_variant	203102	exon12			GAAGACTTTTAGC	BC026085	CCDS47846.1	8p11.22	2005-08-18	2005-08-18		ENSG00000197140	ENSG00000197140		"""ADAM metallopeptidase domain containing"""	15479	protein-coding gene	gene with protein product			"""a disintegrin and metalloproteinase domain 32"""			12568724	Standard	NM_145004		Approved		uc003xmt.4	Q8TC27	OTTHUMG00000164071	ENST00000379907.4:c.1074T>A	8.37:g.39068684T>A		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	71	56	0.788732	NM_145004	Q8TC42	Silent	SNP	ENST00000379907.4	37	CCDS47846.1																																																																																			T|0.999;A|0.001	0.001	strong		0.323	ADAM32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377089.1	NM_145004	
FAM135A	57579	hgsc.bcm.edu	37	6	71195892	71195892	+	Intron	SNP	A	A	G	rs142935920		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:71195892A>G	ENST00000418814.2	+	10	1437				FAM135A_ENST00000505868.1_Intron|FAM135A_ENST00000370479.3_Silent_p.L239L|FAM135A_ENST00000505769.1_Intron|FAM135A_ENST00000457062.2_Silent_p.L239L|FAM135A_ENST00000361499.3_Intron	NM_001105531.2|NM_001162529.1	NP_001099001.1|NP_001156001.1	Q9P2D6	F135A_HUMAN	family with sequence similarity 135, member A											breast(2)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(12)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	38						TGCAGCTCCTATATGAGCGTC	0.368													A|||	1	0.000199681	0.0	0.0	5008	,	,		16631	0.0		0.001	False		,,,				2504	0.0				p.L239L		Atlas-SNP	.											.	FAM135A	181	.	0			c.A717G						PASS	.	A	,,	0,4406		0,0,2203	88.0	79.0	82.0		,,717	-2.4	1.0	6	dbSNP_134	82	8,8592	6.4+/-24.3	0,8,4292	no	intron,intron,coding-synonymous	FAM135A	NM_001105531.2,NM_001162529.1,NM_020819.4	,,	0,8,6495	GG,GA,AA		0.093,0.0,0.0615	,,	,,239/1303	71195892	8,12998	2203	4300	6503	SO:0001627	intron_variant	57579	exon9			GCTCCTATATGAG	AK000183	CCDS34481.1, CCDS47448.1, CCDS55028.1	6q13	2008-10-30	2007-05-11	2007-05-11	ENSG00000082269	ENSG00000082269			21084	protein-coding gene	gene with protein product			"""KIAA1411"""	KIAA1411		10718198	Standard	NM_001105531		Approved	FLJ20176	uc003pfj.3	Q9P2D6	OTTHUMG00000014991	ENST00000418814.2:c.823+4035A>G	6.37:g.71195892A>G		Somatic	232	0	0		WXS	Illumina HiSeq	Phase_I	201	94	0.467662	NM_020819	A2RRQ5|Q3C0H3|Q5JXK0|Q5JXK1|Q68DW0|Q6P081|Q9H0F2|Q9NU48|Q9NUQ5|Q9NXL5	Silent	SNP	ENST00000418814.2	37	CCDS55028.1																																																																																			A|0.999;G|0.001	0.001	strong		0.368	FAM135A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000041137.2	NM_020819	
WRN	7486	hgsc.bcm.edu	37	8	31024638	31024638	+	Silent	SNP	C	C	T	rs1801196	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	212	0	0		WXS	Illumina HiSeq	Phase_I	159	117	0.735849	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		
TRPA1	8989	hgsc.bcm.edu	37	8	72958799	72958799	+	Silent	SNP	G	G	A	rs61757563	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:72958799G>A	ENST00000262209.4	-	17	2217	c.2010C>T	c.(2008-2010)acC>acT	p.T670T	RP11-383H13.1_ENST00000537896.1_Intron|RP11-383H13.1_ENST00000524152.1_Intron|RP11-383H13.1_ENST00000457356.4_Intron	NM_007332.2	NP_015628.2	O75762	TRPA1_HUMAN	transient receptor potential cation channel, subfamily A, member 1	670					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)	GTGTTTTTTTGGTGAATTCTA	0.284													G|||	90	0.0179712	0.0023	0.0187	5008	,	,		14599	0.0		0.0636	False		,,,				2504	0.0102				p.T670T		Atlas-SNP	.											.	TRPA1	256	.	0			c.C2010T						PASS	.	G		61,4345	59.3+/-96.0	0,61,2142	138.0	152.0	147.0		2010	-0.1	0.1	8	dbSNP_129	147	582,8016	154.3+/-208.6	14,554,3731	no	coding-synonymous	TRPA1	NM_007332.2		14,615,5873	AA,AG,GG		6.769,1.3845,4.9446		670/1120	72958799	643,12361	2203	4299	6502	SO:0001819	synonymous_variant	8989	exon17			TTTTTTGGTGAAT	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.2010C>T	8.37:g.72958799G>A		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	44	32	0.727273	NM_007332	A6NIN6	Silent	SNP	ENST00000262209.4	37	CCDS34908.1																																																																																			G|0.958;A|0.042	0.042	strong		0.284	TRPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379079.2	NM_007332	
PDILT	204474	hgsc.bcm.edu	37	16	20370810	20370810	+	Missense_Mutation	SNP	C	C	T	rs9652588	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:20370810C>T	ENST00000302451.4	-	12	1834	c.1586G>A	c.(1585-1587)gGg>gAg	p.G529E		NM_174924.1	NP_777584.1	Q8N807	PDILT_HUMAN	protein disulfide isomerase-like, testis expressed	529			G -> E (in dbSNP:rs9652588). {ECO:0000269|PubMed:14702039}.		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						TTCAGGTAACCCTTTCCTCAT	0.488													t|||	1767	0.352835	0.4017	0.3473	5008	,	,		18281	0.1538		0.4732	False		,,,				2504	0.3722				p.G529E		Atlas-SNP	.											.	PDILT	120	.	0			c.G1586A						PASS	.	T	GLU/GLY	1802,2604	641.6+/-397.5	373,1056,774	212.0	180.0	191.0		1586	2.8	0.0	16	dbSNP_119	191	4310,4290	575.9+/-390.3	1105,2100,1095	yes	missense	PDILT	NM_174924.1	98	1478,3156,1869	TT,TC,CC		49.8837,40.8988,46.9937	benign	529/585	20370810	6112,6894	2203	4300	6503	SO:0001583	missense	204474	exon12			GGTAACCCTTTCC		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.1586G>A	16.37:g.20370810C>T	ENSP00000305465:p.Gly529Glu	Somatic	233	0	0		WXS	Illumina HiSeq	Phase_I	279	103	0.369176	NM_174924	Q8IVQ5	Missense_Mutation	SNP	ENST00000302451.4	37	CCDS10584.1	769	0.35210622710622713	189	0.38414634146341464	128	0.35359116022099446	87	0.1520979020979021	365	0.4815303430079156	T	0.017	-1.492764	0.01009	0.408988	0.501163	ENSG00000169340	ENST00000302451	T	0.02812	4.15	3.86	2.75	0.32379	.	0.509670	0.16509	N	0.211332	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	0.37641	-0.9697	9	0.02654	T	1	.	3.4626	0.07539	0.1951:0.1078:0.0:0.6971	rs9652588;rs52825187;rs57070118;rs9652588	529	Q8N807	PDILT_HUMAN	E	529	ENSP00000305465:G529E	ENSP00000305465:G529E	G	-	2	0	PDILT	20278311	0.005000	0.15991	0.005000	0.12908	0.016000	0.09150	0.562000	0.23531	0.297000	0.22615	-0.409000	0.06214	GGG	C|0.575;T|0.425	0.425	strong		0.488	PDILT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254332.1	NM_174924	
MTMR2	8898	hgsc.bcm.edu	37	11	95571347	95571347	+	Missense_Mutation	SNP	C	C	G	rs61735578	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:95571347C>G	ENST00000346299.5	-	13	1844	c.1504G>C	c.(1504-1506)Gag>Cag	p.E502Q	RNA5SP345_ENST00000410646.1_RNA|MTMR2_ENST00000352297.7_Missense_Mutation_p.E430Q|MTMR2_ENST00000409459.1_Missense_Mutation_p.E430Q|MTMR2_ENST00000393223.3_Missense_Mutation_p.E430Q	NM_016156.5	NP_057240.3	Q13614	MTMR2_HUMAN	myotubularin related protein 2	502	Myotubularin phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00669}.				cell death (GO:0008219)|dendritic spine maintenance (GO:0097062)|inositol phosphate dephosphorylation (GO:0046855)|myelin assembly (GO:0032288)|negative regulation of endocytosis (GO:0045806)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of myelination (GO:0031642)|negative regulation of receptor catabolic process (GO:2000645)|negative regulation of receptor internalization (GO:0002091)|neuron development (GO:0048666)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|positive regulation of early endosome to late endosome transport (GO:2000643)|protein dephosphorylation (GO:0006470)|protein tetramerization (GO:0051262)|small molecule metabolic process (GO:0044281)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|endosome (GO:0005768)|neuronal postsynaptic density (GO:0097481)|nucleus (GO:0005634)|synaptic membrane (GO:0097060)|synaptic vesicle (GO:0008021)|vacuolar membrane (GO:0005774)	phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity (GO:0052629)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			autonomic_ganglia(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	19		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)				AGAAAATACTCATTGAATTCA	0.358													C|||	212	0.0423323	0.056	0.0202	5008	,	,		21110	0.002		0.0298	False		,,,				2504	0.0941				p.E502Q		Atlas-SNP	.											.	MTMR2	79	.	0			c.G1504C						PASS	.	C	GLN/GLU,GLN/GLU,GLN/GLU	247,4155	141.9+/-177.2	8,231,1962	120.0	120.0	120.0		1504,1288,1288	4.6	1.0	11	dbSNP_129	120	182,8414	82.6+/-145.2	0,182,4116	yes	missense,missense,missense	MTMR2	NM_016156.5,NM_201278.2,NM_201281.2	29,29,29	8,413,6078	GG,GC,CC		2.1173,5.6111,3.3005	probably-damaging,probably-damaging,probably-damaging	502/644,430/572,430/572	95571347	429,12569	2201	4298	6499	SO:0001583	missense	8898	exon13			AATACTCATTGAA	U58033	CCDS8305.1, CCDS8306.1	11q22	2014-09-17			ENSG00000087053	ENSG00000087053		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"""	7450	protein-coding gene	gene with protein product		603557		CMT4B		8640223, 9736772	Standard	NM_016156		Approved	KIAA1073	uc001pfu.3	Q13614	OTTHUMG00000153837	ENST00000346299.5:c.1504G>C	11.37:g.95571347C>G	ENSP00000345752:p.Glu502Gln	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	80	15	0.1875	NM_016156	A6NN98|Q9UPS9	Missense_Mutation	SNP	ENST00000346299.5	37	CCDS8305.1	53	0.024267399267399268	24	0.04878048780487805	7	0.019337016574585635	1	0.0017482517482517483	21	0.027704485488126648	C	18.20	3.572266	0.65765	0.056111	0.021173	ENSG00000087053	ENST00000346299;ENST00000393223;ENST00000409459;ENST00000352297;ENST00000444541	D;D;D;D;D	0.91792	-2.91;-2.91;-2.91;-2.91;-2.91	5.52	4.58	0.56647	Myotubularin phosphatase domain (1);	0.045995	0.85682	D	0.000000	T	0.68458	0.3003	M	0.85099	2.735	0.80722	D	1	P	0.39094	0.659	B	0.39185	0.293	T	0.82532	-0.0410	10	0.52906	T	0.07	.	16.4341	0.83869	0.0:0.8692:0.1308:0.0	rs61735578	502	Q13614	MTMR2_HUMAN	Q	502;430;430;430;430	ENSP00000345752:E502Q;ENSP00000376915:E430Q;ENSP00000386882:E430Q;ENSP00000343737:E430Q;ENSP00000396020:E430Q	ENSP00000345752:E502Q	E	-	1	0	MTMR2	95210995	1.000000	0.71417	0.998000	0.56505	0.565000	0.35776	6.012000	0.70767	2.599000	0.87857	0.563000	0.77884	GAG	C|0.960;G|0.040	0.040	strong		0.358	MTMR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332620.1	NM_016156	
ZDHHC11	79844	hgsc.bcm.edu	37	5	825280	825280	+	Splice_Site	SNP	C	C	T	rs1809008	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:825280C>T	ENST00000283441.8	-	8	1405	c.1022G>A	c.(1021-1023)cGg>cAg	p.R341Q	ZDHHC11_ENST00000503758.2_5'UTR|ZDHHC11_ENST00000424784.2_Splice_Site_p.R341Q	NM_024786.2	NP_079062.1	Q9H8X9	ZDH11_HUMAN	zinc finger, DHHC-type containing 11	341			R -> Q (in dbSNP:rs1809008).			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)			GCAACTTACCCGTGCCGTCGA	0.537													c|||	1874	0.374201	0.6422	0.3386	5008	,	,		27210	0.4127		0.1541	False		,,,				2504	0.2239				p.R341Q		Atlas-SNP	.											.	ZDHHC11	97	.	0			c.G1022A						PASS	.	C	GLN/ARG	2381,2025		580,1221,402	159.0	115.0	130.0		1022	-0.3	0.0	5	dbSNP_92	130	854,7732		60,734,3499	yes	missense-near-splice	ZDHHC11	NM_024786.2	43	640,1955,3901	TT,TC,CC		9.9464,45.9601,24.8999	benign	341/413	825280	3235,9757	2203	4293	6496	SO:0001630	splice_region_variant	79844	exon8			CTTACCCGTGCCG	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.1023+1G>A	5.37:g.825280C>T		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	103	11	0.106796	NM_024786	Q6UWR9	Missense_Mutation	SNP	ENST00000283441.8	37	CCDS3857.1	688	0.315018315018315	298	0.6056910569105691	93	0.2569060773480663	234	0.4090909090909091	63	0.08311345646437995	N	1.075	-0.668841	0.03403	0.540399	0.099464	ENSG00000188818	ENST00000424784;ENST00000283441	T;T	0.28069	1.63;1.63	0.131	-0.261	0.12963	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.06786	0.001	B	0.01281	0.0	T	0.43180	-0.9407	7	0.10902	T	0.67	.	.	.	.	rs1809008;rs61386472	341	Q9H8X9	ZDH11_HUMAN	Q	341	ENSP00000397719:R341Q;ENSP00000283441:R341Q	ENSP00000283441:R341Q	R	-	2	0	ZDHHC11	878280	0.003000	0.15002	0.002000	0.10522	0.002000	0.02628	-0.384000	0.07389	-1.204000	0.02648	-1.197000	0.01672	CGG	C|0.724;T|0.276	0.276	strong		0.537	ZDHHC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206681.3	NM_024786	Missense_Mutation
TEX35	84066	hgsc.bcm.edu	37	1	178492447	178492447	+	Silent	SNP	T	T	A	rs7527160	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:178492447T>A	ENST00000367639.1	+	9	666	c.621T>A	c.(619-621)gcT>gcA	p.A207A	TEX35_ENST00000258298.2_Intron	NM_001170722.1|NM_001170724.1	NP_001164193.1|NP_001164195.1			testis expressed 35																		gtatatacgctgcagtgggac	0.403													A|||	2880	0.57508	0.7239	0.5937	5008	,	,		21495	0.503		0.5547	False		,,,				2504	0.456				p.A207A		Atlas-SNP	.											.	TEX35	15	.	0			c.T621A						PASS	.	A	,	962,422		329,304,59	100.0	93.0	95.0		621,597	0.1	0.3	1	dbSNP_116	95	1648,1534		420,808,363	no	coding-synonymous,coding-synonymous	C1orf49	NM_001170722.1,NM_001170724.1	,	749,1112,422	AA,AT,TT		48.2087,30.4913,42.8384	,	207/216,199/208	178492447	2610,1956	692	1591	2283	SO:0001819	synonymous_variant	84066	exon9			ATACGCTGCAGTG	AL136694	CCDS1323.1, CCDS53433.1, CCDS53434.1	1q25.2	2014-01-28	2012-06-29	2012-06-29	ENSG00000240021	ENSG00000240021			25366	protein-coding gene	gene with protein product	"""Testis-Specific Conserved gene 24kDa"""		"""chromosome 1 open reading frame 49"""	C1orf49		11230166, 17077512	Standard	NM_032126		Approved	DKFZP564J047, TSC24	uc001glt.2	Q5T0J7	OTTHUMG00000035023	ENST00000367639.1:c.621T>A	1.37:g.178492447T>A		Somatic	17	0	0		WXS	Illumina HiSeq	Phase_I	11	11	1	NM_001170722		Silent	SNP	ENST00000367639.1	37	CCDS53434.1																																																																																			T|0.409;A|0.591	0.591	strong		0.403	TEX35-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000098170.1	NM_032126	
RADIL	55698	hgsc.bcm.edu	37	7	4843307	4843307	+	Missense_Mutation	SNP	T	T	C	rs187128776	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:4843307T>C	ENST00000399583.3	-	11	2556	c.2369A>G	c.(2368-2370)aAc>aGc	p.N790S	RADIL_ENST00000538469.1_Missense_Mutation_p.N550S|RADIL_ENST00000536091.1_3'UTR	NM_018059.4	NP_060529.4	Q96JH8	RADIL_HUMAN	Ras association and DIL domains	790					multicellular organismal development (GO:0007275)|signal transduction (GO:0007165)|substrate adhesion-dependent cell spreading (GO:0034446)	microtubule (GO:0005874)		p.N790S(1)		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)		GTCCAGGCAGTTGGCTTCCAA	0.647													T|||	63	0.0125799	0.0015	0.0187	5008	,	,		11788	0.0		0.0239	False		,,,				2504	0.0245				p.N790S		Atlas-SNP	.											RADIL,brain,glioma,0,1	RADIL	110	1	1	Substitution - Missense(1)	central_nervous_system(1)	c.A2369G						scavenged	.						19.0	26.0	24.0					7																	4843307		1977	4092	6069	SO:0001583	missense	55698	exon11			AGGCAGTTGGCTT	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.2369A>G	7.37:g.4843307T>C	ENSP00000382492:p.Asn790Ser	Somatic	111	1	0.00900901		WXS	Illumina HiSeq	Phase_I	116	26	0.224138	NM_018059	A4D1Z5|A5YM49|B7ZL20|Q0VFZ9|Q75LH3|Q9BSP5|Q9H0M6|Q9NW43|Q9NWC4	Missense_Mutation	SNP	ENST00000399583.3	37	CCDS43544.1	33	0.01510989010989011	2	0.0040650406504065045	13	0.03591160220994475	0	0.0	18	0.023746701846965697	T	0.543	-0.852823	0.02630	.	.	ENSG00000157927	ENST00000399583;ENST00000316919;ENST00000544486;ENST00000538469	T;T	0.06449	3.37;3.3	4.27	3.12	0.35913	.	0.502188	0.20854	N	0.084468	T	0.00695	0.0023	N	0.08118	0	0.19300	N	0.999978	B;B	0.09022	0.0;0.002	B;B	0.01281	0.0;0.0	T	0.46925	-0.9156	10	0.23302	T	0.38	-15.6944	6.6406	0.22906	0.0:0.187:0.0:0.813	.	790;98	Q96JH8;Q75LH2	RADIL_HUMAN;.	S	790;761;524;550	ENSP00000382492:N790S;ENSP00000442966:N550S	ENSP00000320946:N761S	N	-	2	0	RADIL	4809833	0.936000	0.31750	0.004000	0.12327	0.026000	0.11368	3.515000	0.53429	0.692000	0.31613	0.459000	0.35465	AAC	T|0.985;C|0.015	0.015	strong		0.647	RADIL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323769.2	NM_018059	
ASXL1	171023	hgsc.bcm.edu	37	20	31024274	31024274	+	Silent	SNP	T	T	C	rs4911231	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	67	0	0		WXS	Illumina HiSeq	Phase_I	57	25	0.438596	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	
FCGR3A	2214	hgsc.bcm.edu	37	1	161599693	161599693	+	Intron	SNP	T	T	C	rs448740	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:161599693T>C	ENST00000540048.1	-	2	94				FCGR3B_ENST00000367964.2_Missense_Mutation_p.N65S|FCGR3B_ENST00000531221.1_Missense_Mutation_p.N101S|FCGR3B_ENST00000294800.3_Missense_Mutation_p.N65S|FCGR2B_ENST00000428605.2_Intron|FCGR2B_ENST00000367962.4_Intron|FCGR2B_ENST00000403078.3_Intron|FCGR2B_ENST00000367960.5_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)	TGAGATGAGGTTCTCATTGTG	0.537													C|||	2669	0.532947	0.5628	0.4827	5008	,	,		9553	0.3383		0.664	False		,,,				2504	0.5941				p.N101S		Atlas-SNP	.											.	FCGR3B	35	.	0			c.A302G						PASS	.						70.0	67.0	68.0					1																	161599693		2161	4291	6452	SO:0001627	intron_variant	2215	exon3			ATGAGGTTCTCAT	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+464A>G	1.37:g.161599693T>C		Somatic	165	1	0.00606061		WXS	Illumina HiSeq	Phase_I	277	273	0.98556	NM_001244753	A2N6W9|Q53FJ0|Q53FL6|Q5EBR4|Q65ZM6|Q6PIJ0	Missense_Mutation	SNP	ENST00000540048.1	37		.	.	.	.	.	.	.	.	.	.	C	0.077	-1.191278	0.01607	.	.	ENSG00000162747	ENST00000367964;ENST00000294800;ENST00000531221;ENST00000534776	T;T;T;T	0.11712	2.75;2.75;2.75;2.75	2.79	-2.58	0.06228	.	.	.	.	.	T	0.00815	0.0027	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.45542	-0.9254	5	0.05833	T	0.94	.	5.2778	0.15659	0.0:0.2748:0.481:0.2442	.	.	.	.	S	65;65;101;48	ENSP00000356941:N65S;ENSP00000294800:N65S;ENSP00000433642:N101S;ENSP00000437084:N48S	ENSP00000294800:N65S	N	-	2	0	FCGR3B	159866317	0.000000	0.05858	0.000000	0.03702	0.202000	0.24057	-4.948000	0.00167	-0.657000	0.05373	-0.631000	0.03989	AAC	T|0.338;C|0.662	0.662	strong		0.537	FCGR3A-203	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_000569	
SLC12A6	9990	hgsc.bcm.edu	37	15	34551082	34551082	+	Silent	SNP	G	G	A	rs7164902	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:34551082G>A	ENST00000354181.3	-	5	967	c.475C>T	c.(475-477)Ctg>Ttg	p.L159L	SLC12A6_ENST00000290209.5_Silent_p.L108L|SLC12A6_ENST00000560164.1_Silent_p.L20L|RP11-1084A12.2_ENST00000559867.1_RNA|SLC12A6_ENST00000397707.2_Silent_p.L144L|SLC12A6_ENST00000458406.2_Silent_p.L100L|SLC12A6_ENST00000397702.2_Silent_p.L100L|SLC12A6_ENST00000451844.2_Silent_p.L20L|SLC12A6_ENST00000558667.1_Silent_p.L159L|SLC12A6_ENST00000560611.1_Silent_p.L159L|SLC12A6_ENST00000558589.1_Silent_p.L150L			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	366	2	0.00546448		WXS	Illumina HiSeq	Phase_I	298	297	0.996644	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	
DSC1	1823	hgsc.bcm.edu	37	18	28722103	28722103	+	Silent	SNP	T	T	C	rs2577074	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:28722103T>C	ENST00000257198.5	-	9	1380	c.1119A>G	c.(1117-1119)ttA>ttG	p.L373L	DSC1_ENST00000257197.3_Silent_p.L373L|RP11-408H20.2_ENST00000581836.1_RNA	NM_024421.2	NP_077739.1	Q08554	DSC1_HUMAN	desmocollin 1	373	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|gap junction (GO:0005921)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(20)|ovary(3)|skin(10)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	53			OV - Ovarian serous cystadenocarcinoma(10;0.00778)			CCTTCATTCGTAAAATCTCCA	0.338													T|||	1726	0.344649	0.4085	0.3746	5008	,	,		17144	0.5655		0.2127	False		,,,				2504	0.1452				p.L373L		Atlas-SNP	.											.	DSC1	240	.	0			c.A1119G						PASS	.	T	,	1771,2635	525.1+/-371.5	357,1057,789	167.0	154.0	158.0		1119,1119	-0.0	1.0	18	dbSNP_100	158	1611,6989	300.2+/-304.8	160,1291,2849	no	coding-synonymous,coding-synonymous	DSC1	NM_004948.3,NM_024421.2	,	517,2348,3638	CC,CT,TT		18.7326,40.1952,26.0034	,	373/841,373/895	28722103	3382,9624	2203	4300	6503	SO:0001819	synonymous_variant	1823	exon9			CATTCGTAAAATC	AF293358	CCDS11894.1, CCDS11895.1	18q12.1	2010-01-26			ENSG00000134765	ENSG00000134765		"""Cadherins / Major cadherins"""	3035	protein-coding gene	gene with protein product		125643				8486729	Standard	NM_024421		Approved	CDHF1	uc002kwn.3	Q08554	OTTHUMG00000131982	ENST00000257198.5:c.1119A>G	18.37:g.28722103T>C		Somatic	209	0	0		WXS	Illumina HiSeq	Phase_I	198	102	0.515152	NM_004948	Q9HB01	Silent	SNP	ENST00000257198.5	37	CCDS11894.1																																																																																			T|0.690;C|0.310	0.310	strong		0.338	DSC1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254946.1	NM_004948, NM_024421	
TOR2A	27433	hgsc.bcm.edu	37	9	130495633	130495633	+	Intron	SNP	C	C	G	rs564754	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:130495633C>G	ENST00000373284.5	-	3	640				TOR2A_ENST00000336067.6_Intron|TOR2A_ENST00000373281.5_Missense_Mutation_p.W208C|TOR2A_ENST00000458505.3_3'UTR|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	76	0	0		WXS	Illumina HiSeq	Phase_I	57	26	0.45614	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	
TMEM132E	124842	hgsc.bcm.edu	37	17	32962064	32962064	+	Missense_Mutation	SNP	C	C	A	rs111689642	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:32962064C>A	ENST00000321639.5	+	8	1993	c.1665C>A	c.(1663-1665)agC>agA	p.S555R		NM_207313.1	NP_997196.1	Q6IEE7	T132E_HUMAN	transmembrane protein 132E	555						integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(10)|lung(28)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	57				BRCA - Breast invasive adenocarcinoma(366;0.231)		TGGTGGACAGCAGCACGCTGG	0.607													C|||	39	0.00778754	0.0015	0.0058	5008	,	,		17892	0.0		0.0288	False		,,,				2504	0.0041				p.S555R		Atlas-SNP	.											.	TMEM132E	122	.	0			c.C1665A						PASS	.	C	ARG/SER	20,4386	27.2+/-55.0	0,20,2183	53.0	44.0	47.0		1665	2.0	1.0	17	dbSNP_132	47	242,8358	96.6+/-158.3	4,234,4062	yes	missense	TMEM132E	NM_207313.1	110	4,254,6245	AA,AC,CC		2.814,0.4539,2.0145	benign	555/985	32962064	262,12744	2203	4300	6503	SO:0001583	missense	124842	exon8			GGACAGCAGCACG	BN000149	CCDS11283.1	17q12	2012-11-01			ENSG00000181291	ENSG00000181291			26991	protein-coding gene	gene with protein product							Standard	NM_207313		Approved		uc002hif.3	Q6IEE7	OTTHUMG00000132927	ENST00000321639.5:c.1665C>A	17.37:g.32962064C>A	ENSP00000316532:p.Ser555Arg	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	58	30	0.517241	NM_207313	Q8WUF4|Q8WVA5	Missense_Mutation	SNP	ENST00000321639.5	37	CCDS11283.1	21	0.009615384615384616	1	0.0020325203252032522	0	0.0	0	0.0	20	0.026385224274406333	C	12.48	1.951245	0.34471	0.004539	0.02814	ENSG00000181291	ENST00000321639	T	0.43294	0.95	5.22	2.01	0.26516	.	0.085942	0.85682	D	0.000000	T	0.10165	0.0249	L	0.27053	0.805	0.45295	D	0.998293	B	0.15141	0.012	B	0.16722	0.016	T	0.04255	-1.0965	10	0.44086	T	0.13	-37.4952	8.3378	0.32225	0.0:0.6685:0.0:0.3315	.	555	Q6IEE7	T132E_HUMAN	R	555	ENSP00000316532:S555R	ENSP00000316532:S555R	S	+	3	2	TMEM132E	29986177	0.972000	0.33761	1.000000	0.80357	0.973000	0.67179	0.095000	0.15127	0.795000	0.33922	0.498000	0.49722	AGC	C|0.985;A|0.015	0.015	strong		0.607	TMEM132E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256440.2	NM_207313	
OR8D1	283159	hgsc.bcm.edu	37	11	124180282	124180282	+	Missense_Mutation	SNP	A	A	C	rs7107539	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:124180282A>C	ENST00000357821.2	-	1	451	c.381T>G	c.(379-381)tgT>tgG	p.C127W		NM_001002917.1	NP_001002917.1	Q8WZ84	OR8D1_HUMAN	olfactory receptor, family 8, subfamily D, member 1	127			C -> W (in dbSNP:rs7107539).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			kidney(1)|large_intestine(1)|lung(7)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	16		Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0528)		GCAGTGGGCTACAGATGGCAA	0.498													A|||	1340	0.267572	0.0893	0.3372	5008	,	,		20356	0.4177		0.4066	False		,,,				2504	0.1616				p.C127W		Atlas-SNP	.											.	OR8D1	53	.	0			c.T381G						PASS	.	A	TRP/CYS	619,3783	268.6+/-268.5	39,541,1621	84.0	74.0	78.0		381	-3.2	0.0	11	dbSNP_116	78	3381,5217	499.8+/-375.1	672,2037,1590	yes	missense	OR8D1	NM_001002917.1	215	711,2578,3211	CC,CA,AA		39.3231,14.0618,30.7692	probably-damaging	127/309	124180282	4000,9000	2201	4299	6500	SO:0001583	missense	283159	exon1			TGGGCTACAGATG	AF238489	CCDS31706.1	11q25	2012-08-09			ENSG00000196341	ENSG00000196341		"""GPCR / Class A : Olfactory receptors"""	8481	protein-coding gene	gene with protein product				OR8D3			Standard	NM_001002917		Approved	OST004	uc010sag.2	Q8WZ84	OTTHUMG00000165977	ENST00000357821.2:c.381T>G	11.37:g.124180282A>C	ENSP00000350474:p.Cys127Trp	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	49	14	0.285714	NM_001002917	B2RNL4|Q6IEW1|Q8NGH0	Missense_Mutation	SNP	ENST00000357821.2	37	CCDS31706.1	708	0.3241758241758242	35	0.07113821138211382	132	0.36464088397790057	243	0.42482517482517484	298	0.39313984168865435	a	14.89	2.670230	0.47677	0.140618	0.393231	ENSG00000196341	ENST00000357821	T	0.07327	3.2	4.29	-3.22	0.05125	GPCR, rhodopsin-like superfamily (1);	0.000000	0.40302	U	0.001137	T	0.00012	0.0000	H	0.96518	3.835	0.33753	P	0.37909400000000004	D	0.89917	1.0	D	0.97110	1.0	T	0.30446	-0.9978	9	0.72032	D	0.01	.	14.3721	0.66846	0.2778:0.0:0.7222:0.0	rs7107539;rs7107539	127	Q8WZ84	OR8D1_HUMAN	W	127	ENSP00000350474:C127W	ENSP00000350474:C127W	C	-	3	2	OR8D1	123685492	0.000000	0.05858	0.009000	0.14445	0.097000	0.18754	-1.117000	0.03283	-0.868000	0.04058	0.416000	0.27883	TGT	A|0.693;C|0.307	0.307	strong		0.498	OR8D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387285.1	NM_001002917	
KRTAP12-2	353323	hgsc.bcm.edu	37	21	46086757	46086757	+	Missense_Mutation	SNP	G	G	A	rs35163632|rs7275298	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:46086757G>A	ENST00000360770.3	-	1	87	c.47C>T	c.(46-48)gCg>gTg	p.A16V	TSPEAR_ENST00000323084.4_Intron	NM_181684.2	NP_859012.1	P59991	KR122_HUMAN	keratin associated protein 12-2	16	23 X 5 AA approximate repeats.		A -> T (in dbSNP:rs13046903).|A -> V (in dbSNP:rs7275298).			keratin filament (GO:0045095)				central_nervous_system(1)|endometrium(1)|lung(3)	5						GGGGCTGGGCGCGCAGCAGGC	0.672													A|||	3864	0.771565	0.8608	0.7493	5008	,	,		14563	0.6597		0.7634	False		,,,				2504	0.7904				p.A16V		Atlas-SNP	.											.	KRTAP12-2	10	.	0			c.C47T						PASS	.	A	,VAL/ALA	3597,679		1532,533,73	22.0	28.0	26.0		,47	-4.3	0.0	21	dbSNP_116	26	5995,2501		2178,1639,431	no	intron,missense	TSPEAR,KRTAP12-2	NM_144991.2,NM_181684.2	,64	3710,2172,504	AA,AG,GG		29.4374,15.8793,24.8982	,benign	,16/147	46086757	9592,3180	2138	4248	6386	SO:0001583	missense	353323	exon1			CTGGGCGCGCAGC	AJ566389	CCDS42965.1	21q22.3	2006-03-13			ENSG00000221864	ENSG00000221864		"""Keratin associated proteins"""	20530	protein-coding gene	gene with protein product							Standard	NM_181684		Approved	KRTAP12.2, KAP12.2	uc002zfu.3	P59991	OTTHUMG00000057636	ENST00000360770.3:c.47C>T	21.37:g.46086757G>A	ENSP00000354001:p.Ala16Val	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	114	113	0.991228	NM_181684	A6NIS1|A6NMS9|Q0VAS4	Missense_Mutation	SNP	ENST00000360770.3	37	CCDS42965.1	1496	0.684981684981685	385	0.782520325203252	258	0.712707182320442	335	0.5856643356643356	518	0.683377308707124	a	9.164	1.019523	0.19355	0.841207	0.705626	ENSG00000221864	ENST00000360770;ENST00000539483	T	0.03065	4.06	2.82	-4.35	0.03656	.	.	.	.	.	T	0.00012	0.0000	N	0.00808	-1.17	0.80722	P	0.0	B	0.09022	0.002	B	0.08055	0.003	T	0.08743	-1.0707	8	0.27785	T	0.31	.	6.4392	0.21841	0.5831:0.1332:0.2837:0.0	rs7275298;rs60851559	16	P59991	KR122_HUMAN	V	16	ENSP00000354001:A16V	ENSP00000354001:A16V	A	-	2	0	KRTAP12-2	44911185	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-0.534000	0.06150	-1.420000	0.02009	-1.896000	0.00531	GCG	G|0.314;A|0.686	0.686	strong		0.672	KRTAP12-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128039.1	NM_181684	
PCDHGC5	56097	hgsc.bcm.edu	37	5	140870949	140870949	+	Silent	SNP	G	G	T	rs918558	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:140870949G>T	ENST00000252087.1	+	1	2142	c.2142G>T	c.(2140-2142)gcG>gcT	p.A714A	PCDHGA3_ENST00000253812.6_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGC3_ENST00000308177.3_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA10_ENST00000398610.2_Intron|PCDHGA11_ENST00000518882.1_Intron|PCDHGB7_ENST00000398594.2_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA11_ENST00000398587.2_Intron|PCDHGA12_ENST00000252085.3_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGC4_ENST00000306593.1_Intron	NM_018929.2|NM_032403.2|NM_032407.1	NP_061752.1|NP_115779.1|NP_115783.1	Q9Y5F6	PCDGM_HUMAN	protocadherin gamma subfamily C, 5	714					homophilic cell adhesion (GO:0007156)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(2)|endometrium(6)|kidney(4)|large_intestine(4)|lung(10)|ovary(4)|prostate(1)|urinary_tract(2)	35			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TTCTGTCAGCGAAGTGCCTTC	0.582													T|||	935	0.186701	0.1437	0.3545	5008	,	,		19987	0.129		0.2127	False		,,,				2504	0.1585				p.A714A		Atlas-SNP	.											.	PCDHGC5	199	.	0			c.G2142T						PASS	.	T	,,,,,,,,,,,,,,,,,,,,,,,,	706,3700	759.6+/-412.9	57,592,1554	111.0	114.0	113.0		,,,,,,,,,,,,,,,,,,,,2142,,,,2142	2.1	1.0	5	dbSNP_86	113	1697,6903	737.6+/-407.0	156,1385,2759	no	intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,coding-synonymous,intron,intron,intron,coding-synonymous	PCDHGC3,PCDHGB4,PCDHGA8,PCDHGA12,PCDHGC5,PCDHGC4,PCDHGB7,PCDHGB6,PCDHGB5,PCDHGB3,PCDHGB2,PCDHGB1,PCDHGA11,PCDHGA10,PCDHGA9,PCDHGA7,PCDHGA6,PCDHGA5,PCDHGA4,PCDHGA3,PCDHGA2,PCDHGA1	NM_002588.2,NM_003735.2,NM_003736.2,NM_018912.2,NM_018913.2,NM_018914.2,NM_018915.2,NM_018916.3,NM_018917.2,NM_018918.2,NM_018919.2,NM_018920.2,NM_018921.2,NM_018922.2,NM_018923.2,NM_018924.2,NM_018925.2,NM_018926.2,NM_018927.3,NM_018928.2,NM_018929.2,NM_032088.1,NM_032092.1,NM_032403.1,NM_032407.1	,,,,,,,,,,,,,,,,,,,,,,,,	213,1977,4313	TT,TG,GG		19.7326,16.0236,18.4761	,,,,,,,,,,,,,,,,,,,,,,,,	,,,,,,,,,,,,,,,,,,,,714/945,,,,714/879	140870949	2403,10603	2203	4300	6503	SO:0001819	synonymous_variant	56097	exon1			GTCAGCGAAGTGC	AF152526	CCDS4263.1, CCDS75350.1	5q31	2010-01-26			ENSG00000240764	ENSG00000240764		"""Cadherins / Protocadherins : Clustered"""	8718	other	protocadherin		606306				10380929	Standard	NM_018929		Approved	PCDH-GAMMA-C5	uc003lla.2	Q9Y5F6	OTTHUMG00000129624	ENST00000252087.1:c.2142G>T	5.37:g.140870949G>T		Somatic	219	0	0		WXS	Illumina HiSeq	Phase_I	193	190	0.984456	NM_018929	Q9Y5C2	Silent	SNP	ENST00000252087.1	37	CCDS4263.1																																																																																			G|0.820;T|0.180	0.180	strong		0.582	PCDHGC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251819.1	NM_018929	
MOGS	7841	hgsc.bcm.edu	37	2	74692191	74692191	+	Missense_Mutation	SNP	C	C	T	rs79181168	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:74692191C>T	ENST00000233616.4	-	1	346	c.184G>A	c.(184-186)Gtg>Atg	p.V62M	MOGS_ENST00000409065.1_Missense_Mutation_p.V62M|MOGS_ENST00000462443.1_Intron|MOGS_ENST00000535045.1_Missense_Mutation_p.V62M|MOGS_ENST00000452063.2_Intron	NM_006302.2	NP_006293.2	Q13724	MOGS_HUMAN	mannosyl-oligosaccharide glucosidase	62					cellular protein metabolic process (GO:0044267)|oligosaccharide metabolic process (GO:0009311)|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)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	glucosidase activity (GO:0015926)|mannosyl-oligosaccharide glucosidase activity (GO:0004573)			cervix(1)|endometrium(6)|large_intestine(3)|lung(10)|prostate(1)|urinary_tract(2)	23						CACGCCAGCACCCAGCGCCCC	0.746													C|||	87	0.0173722	0.0015	0.0274	5008	,	,		9790	0.0		0.0567	False		,,,				2504	0.0092				p.V62M		Atlas-SNP	.											.	MOGS	58	.	0			c.G184A						PASS	.	C	,MET/VAL	50,3870		0,50,1910	9.0	15.0	13.0		,184	-0.9	1.0	2	dbSNP_131	13	446,7558		12,422,3568	yes	intron,missense	MOGS	NM_001146158.1,NM_006302.2	,21	12,472,5478	TT,TC,CC		5.5722,1.2755,4.1597	,benign	,62/838	74692191	496,11428	1960	4002	5962	SO:0001583	missense	7841	exon1			CCAGCACCCAGCG	X87237	CCDS42700.1, CCDS54370.1	2p13.1	2012-01-31			ENSG00000115275	ENSG00000115275	3.2.1.106		24862	protein-coding gene	gene with protein product	"""glucosidase I"", ""processing A-glucosidase I"""	601336				7635146, 8786151	Standard	NM_006302		Approved	GCS1, CWH41, DER7	uc010ffj.3	Q13724	OTTHUMG00000152886	ENST00000233616.4:c.184G>A	2.37:g.74692191C>T	ENSP00000233616:p.Val62Met	Somatic	6	0	0		WXS	Illumina HiSeq	Phase_I	9	7	0.777778	NM_006302	A8K938|F5H6D0|Q17RN9|Q8TCT5	Missense_Mutation	SNP	ENST00000233616.4	37	CCDS42700.1	63	0.028846153846153848	2	0.0040650406504065045	11	0.03038674033149171	5	0.008741258741258742	45	0.059366754617414245	C	9.467	1.094633	0.20471	0.012755	0.055722	ENSG00000115275	ENST00000233616;ENST00000409065;ENST00000535045	T;T;T	0.39406	1.08;1.08;1.08	5.09	-0.873	0.10635	.	0.789213	0.10860	N	0.626167	T	0.02380	0.0073	N	0.14661	0.345	0.22762	N	0.998761	B;B	0.10296	0.003;0.001	B;B	0.11329	0.006;0.002	T	0.12528	-1.0544	10	0.34782	T	0.22	-0.0347	6.9925	0.24763	0.0:0.1795:0.2259:0.5946	.	62;62	B4E3B8;Q13724	.;MOGS_HUMAN	M	62	ENSP00000233616:V62M;ENSP00000386493:V62M;ENSP00000439971:V62M	ENSP00000233616:V62M	V	-	1	0	MOGS	74545699	0.982000	0.34865	0.992000	0.48379	0.009000	0.06853	0.076000	0.14712	-0.017000	0.14103	-0.345000	0.07892	GTG	C|0.971;T|0.029	0.029	strong		0.746	MOGS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328382.1	NM_006302	
BAALC	79870	hgsc.bcm.edu	37	8	104153137	104153137	+	Silent	SNP	C	C	T	rs3736043	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:104153137C>T	ENST00000297574.6	+	1	151	c.12C>T	c.(10-12)ggC>ggT	p.G4G	BAALC_ENST00000330955.5_Silent_p.G4G|BAALC_ENST00000438105.2_Silent_p.G4G|C8orf56_ENST00000521246.1_Intron|C8orf56_ENST00000436771.1_Intron|BAALC_ENST00000306391.6_Silent_p.G4G|BAALC_ENST00000309982.5_Silent_p.G4G			Q8WXS3	BAALC_HUMAN	brain and acute leukemia, cytoplasmic	4	Interaction with CAMK2A. {ECO:0000250}.					cytoplasm (GO:0005737)|membrane (GO:0016020)				kidney(1)|large_intestine(3)|lung(3)	7			OV - Ovarian serous cystadenocarcinoma(57;3.49e-05)|STAD - Stomach adenocarcinoma(118;0.133)			TGGGCTGCGGCGGGAGCCGGG	0.751													C|||	159	0.0317492	0.0053	0.0403	5008	,	,		4112	0.0238		0.0765	False		,,,				2504	0.0235				p.G4G		Atlas-SNP	.											.	BAALC	15	.	0			c.C12T						PASS	.	C	,	106,3646		3,100,1773	4.0	6.0	6.0		12,12	-2.1	1.0	8	dbSNP_107	6	794,6762		49,696,3033	no	coding-synonymous,coding-synonymous	BAALC	NM_001024372.1,NM_024812.2	,	52,796,4806	TT,TC,CC		10.5082,2.8252,7.959	,	4/55,4/146	104153137	900,10408	1876	3778	5654	SO:0001819	synonymous_variant	79870	exon1			CTGCGGCGGGAGC	AF363578	CCDS6297.1, CCDS47906.1	8q22.3	2008-07-29			ENSG00000164929	ENSG00000164929			14333	protein-coding gene	gene with protein product		606602				11707601	Standard	NM_024812		Approved		uc003yld.3	Q8WXS3	OTTHUMG00000164782	ENST00000297574.6:c.12C>T	8.37:g.104153137C>T		Somatic	24	0	0		WXS	Illumina HiSeq	Phase_I	34	27	0.794118	NM_001024372	Q8WTP6|Q8WXS0|Q8WXS1|Q8WXS2|Q9HA93	Silent	SNP	ENST00000297574.6	37																																																																																				C|0.958;T|0.042	0.042	strong		0.751	BAALC-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000380257.1		
DPPA4	55211	hgsc.bcm.edu	37	3	109052732	109052732	+	Missense_Mutation	SNP	T	T	C	rs3762648	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:109052732T>C	ENST00000335658.6	-	2	217	c.163A>G	c.(163-165)Atc>Gtc	p.I55V	DPPA4_ENST00000478791.1_5'UTR	NM_018189.3	NP_060659.3	Q7L190	DPPA4_HUMAN	developmental pluripotency associated 4	55			I -> V (in dbSNP:rs3762648). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		lung-associated mesenchyme development (GO:0060484)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(17)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	25						CTGCCTTTGATAGACATTTTT	0.418													C|||	2424	0.484026	0.2231	0.4697	5008	,	,		20137	0.751		0.4831	False		,,,				2504	0.5726				p.I55V		Atlas-SNP	.											DPPA4,NS,carcinoma,+2,1	DPPA4	56	1	0			c.A163G						PASS	.	C	VAL/ILE	1104,3302	718.9+/-408.9	151,802,1250	246.0	234.0	238.0		163	-6.0	0.0	3	dbSNP_107	238	4023,4577	597.5+/-393.8	946,2131,1223	yes	missense	DPPA4	NM_018189.3	29	1097,2933,2473	CC,CT,TT		46.7791,25.0567,39.4203	benign	55/305	109052732	5127,7879	2203	4300	6503	SO:0001583	missense	55211	exon2			CTTTGATAGACAT	AK001575	CCDS33814.1	3q13.13	2014-01-28			ENSG00000121570	ENSG00000121570			19200	protein-coding gene	gene with protein product		614125					Standard	NM_018189		Approved	FLJ10713	uc003dxq.4	Q7L190	OTTHUMG00000159222	ENST00000335658.6:c.163A>G	3.37:g.109052732T>C	ENSP00000335306:p.Ile55Val	Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	109	108	0.990826	NM_018189	A8K4M7|Q9H9N5|Q9NVI6	Missense_Mutation	SNP	ENST00000335658.6	37	CCDS33814.1	1081	0.49496336996337	135	0.27439024390243905	167	0.4613259668508287	420	0.7342657342657343	359	0.4736147757255937	C	0.010	-1.753635	0.00663	0.250567	0.467791	ENSG00000121570	ENST00000335658;ENST00000477303	T;T	0.59083	2.01;0.29	3.37	-6.02	0.02192	.	3.611190	0.00735	N	0.000974	T	0.00012	0.0000	N	0.01352	-0.895	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.24941	-1.0146	8	.	.	.	7.0679	6.7032	0.23236	0.1207:0.4535:0.0:0.4259	rs3762648;rs52798077;rs56492819;rs60833201;rs3762648	55	Q7L190	DPPA4_HUMAN	V	55;3	ENSP00000335306:I55V;ENSP00000418313:I3V	.	I	-	1	0	DPPA4	110535422	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.085000	0.03390	-1.950000	0.01030	-0.233000	0.12211	ATC	T|0.557;C|0.443	0.443	strong		0.418	DPPA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353897.1	NM_018189	
GPLD1	2822	hgsc.bcm.edu	37	6	24445829	24445829	+	Silent	SNP	G	G	A	rs9358767	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:24445829G>A	ENST00000230036.1	-	20	2075	c.1965C>T	c.(1963-1965)caC>caT	p.H655H		NM_001503.3	NP_001494.2	P80108	PHLD_HUMAN	glycosylphosphatidylinositol specific phospholipase D1	655					cell migration involved in sprouting angiogenesis (GO:0002042)|cellular response to calcium ion (GO:0071277)|cellular response to cholesterol (GO:0071397)|cellular response to drug (GO:0035690)|cellular response to insulin stimulus (GO:0032869)|cellular response to pH (GO:0071467)|cellular response to triglyceride (GO:0071401)|chondrocyte differentiation (GO:0002062)|complement receptor mediated signaling pathway (GO:0002430)|GPI anchor release (GO:0006507)|hematopoietic stem cell migration (GO:0035701)|hematopoietic stem cell migration to bone marrow (GO:0097241)|insulin receptor signaling pathway (GO:0008286)|negative regulation of cell proliferation (GO:0008285)|negative regulation of triglyceride catabolic process (GO:0010897)|ossification (GO:0001503)|phosphatidylcholine metabolic process (GO:0046470)|positive regulation of alkaline phosphatase activity (GO:0010694)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cytolysis (GO:0045919)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of glucose metabolic process (GO:0010907)|positive regulation of high-density lipoprotein particle clearance (GO:0010983)|positive regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0035774)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|positive regulation of secretion (GO:0051047)|positive regulation of triglyceride biosynthetic process (GO:0010867)|regulation of cellular response to insulin stimulus (GO:1900076)|response to glucose (GO:0009749)|transepithelial transport (GO:0070633)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal membrane (GO:0005765)|proteinaceous extracellular matrix (GO:0005578)	glycosylphosphatidylinositol phospholipase D activity (GO:0004621)|phospholipase D activity (GO:0004630)|sodium channel regulator activity (GO:0017080)			breast(3)|endometrium(5)|kidney(1)|large_intestine(11)|lung(8)|ovary(2)|prostate(1)|urinary_tract(1)	32						TCATCAGTACGTGGCCACTGG	0.483													C|||	1012	0.202077	0.0643	0.2392	5008	,	,		19922	0.4524		0.0905	False		,,,				2504	0.2188				p.H655H		Atlas-SNP	.											.	GPLD1	91	.	0			c.C1965T						PASS	.	C		343,4063		14,315,1874	158.0	135.0	143.0		1965	-9.6	0.0	6	dbSNP_119	143	831,7769		39,753,3508	no	coding-synonymous	GPLD1	NM_001503.2		53,1068,5382	AA,AG,GG		9.6628,7.7848,9.0266		655/841	24445829	1174,11832	2203	4300	6503	SO:0001819	synonymous_variant	2822	exon20			CAGTACGTGGCCA	L11701	CCDS4553.1	6p22.1	2008-02-05			ENSG00000112293	ENSG00000112293			4459	protein-coding gene	gene with protein product		602515				11072085	Standard	NM_001503		Approved		uc003ned.2	P80108	OTTHUMG00000016104	ENST00000230036.1:c.1965C>T	6.37:g.24445829G>A		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	99	52	0.525253	NM_001503	Q15127|Q15128|Q2M2F2|Q5T3Y0|Q7Z6T8|Q8TCV0|Q8WW82|Q96ID6|Q9H167|Q9H4M1|Q9UJC9	Silent	SNP	ENST00000230036.1	37	CCDS4553.1																																																																																			G|0.859;A|0.140	0.140	strong		0.483	GPLD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043315.1	NM_001503	
ENTPD6	955	hgsc.bcm.edu	37	20	25187213	25187213	+	Missense_Mutation	SNP	G	G	A	rs2076559	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:25187213G>A	ENST00000376652.4	+	2	204	c.41G>A	c.(40-42)aGc>aAc	p.S14N	ENTPD6_ENST00000433259.2_Missense_Mutation_p.S14N|ENTPD6_ENST00000360031.2_Missense_Mutation_p.S14N|ENTPD6_ENST00000354989.5_Intron			O75354	ENTP6_HUMAN	ectonucleoside triphosphate diphosphohydrolase 6 (putative)	14			S -> N (in dbSNP:rs2076559). {ECO:0000269|PubMed:14529283}.		response to calcium ion (GO:0051592)|response to magnesium ion (GO:0032026)	cell surface (GO:0009986)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	guanosine-5'-triphosphate,3'-diphosphate diphosphatase activity (GO:0008894)|nucleoside-triphosphatase activity (GO:0017111)|uridine-diphosphatase activity (GO:0045134)			breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(16)|prostate(1)|skin(1)	27						AGAAAAACGAGCTACATTTTT	0.403													G|||	1562	0.311901	0.0983	0.2349	5008	,	,		20423	0.5903		0.3469	False		,,,				2504	0.3323				p.S14N		Atlas-SNP	.											.	ENTPD6	57	.	0			c.G41A						PASS	.	G	,ASN/SER	621,3785	269.5+/-269.1	42,537,1624	104.0	97.0	100.0		,41	-0.2	0.0	20	dbSNP_96	100	2767,5833	439.7+/-359.3	431,1905,1964	yes	intron,missense	ENTPD6	NM_001114089.1,NM_001247.2	,46	473,2442,3588	AA,AG,GG		32.1744,14.0944,26.0495	,benign	,14/485	25187213	3388,9618	2203	4300	6503	SO:0001583	missense	955	exon2			AAACGAGCTACAT	AF039916	CCDS13170.1, CCDS46586.1	20p11.21	2010-06-24	2010-06-24		ENSG00000197586	ENSG00000197586			3368	protein-coding gene	gene with protein product		603160	"""interleukin 6 signal transducer-2"""	CD39L2, IL6ST2		9676430	Standard	NM_001247		Approved	NTPDase-6, dJ738P15.3	uc002wuj.2	O75354	OTTHUMG00000032116	ENST00000376652.4:c.41G>A	20.37:g.25187213G>A	ENSP00000365840:p.Ser14Asn	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	96	51	0.53125	NM_001247	A6NCX6|D3DW49|Q5QPJ2|Q5QPJ5|Q7Z5B5|Q8N3H3|Q8TAS7|Q9UJD1	Missense_Mutation	SNP	ENST00000376652.4	37	CCDS13170.1	755	0.3456959706959707	59	0.11991869918699187	94	0.2596685082872928	344	0.6013986013986014	258	0.3403693931398417	G	8.922	0.961415	0.18583	0.140944	0.321744	ENSG00000197586	ENST00000360031;ENST00000376652;ENST00000433259;ENST00000435520;ENST00000425813	T;T;T;T;T	0.34275	2.18;2.18;2.05;1.37;2.35	2.98	-0.162	0.13367	.	.	.	.	.	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B;B;B;B;B	0.30482	0.281;0.18;0.18;0.18;0.18	B;B;B;B;B	0.22152	0.038;0.038;0.038;0.017;0.017	T	0.44283	-0.9338	8	0.19590	T	0.45	.	3.4656	0.07549	0.2556:0.2143:0.5302:0.0	rs2076559;rs11539327;rs17829504;rs52811761;rs60671666;rs2076559	14;14;14;14;14	E7EP89;Q5QPI9;D3DW49;Q5QPJ2;O75354	.;.;.;.;ENTP6_HUMAN	N	14	ENSP00000353131:S14N;ENSP00000365840:S14N;ENSP00000401895:S14N;ENSP00000398844:S14N;ENSP00000390646:S14N	ENSP00000353131:S14N	S	+	2	0	ENTPD6	25135213	0.001000	0.12720	0.000000	0.03702	0.007000	0.05969	0.214000	0.17541	0.004000	0.14682	-0.172000	0.13284	AGC	G|0.702;A|0.298	0.298	strong		0.403	ENTPD6-020	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078414.2		
RNF213	57674	hgsc.bcm.edu	37	17	78263486	78263486	+	Missense_Mutation	SNP	T	T	C	rs17853989	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:78263486T>C	ENST00000582970.1	+	6	1105	c.962T>C	c.(961-963)aTg>aCg	p.M321T	RNF213_ENST00000456466.1_Missense_Mutation_p.M321T|RNF213_ENST00000508628.2_Missense_Mutation_p.M370T|RNF213_ENST00000319921.4_Missense_Mutation_p.M321T	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						scavenged	.	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	117	1	0.00854701		WXS	Illumina HiSeq	Phase_I	102	50	0.490196	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	
ULK3	25989	hgsc.bcm.edu	37	15	75130093	75130093	+	Splice_Site	SNP	T	T	C	rs12898397	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:75130093T>C	ENST00000440863.2	-	14	1425	c.1334A>G	c.(1333-1335)aAg>aGg	p.K445R	ULK3_ENST00000568667.1_Splice_Site_p.K456R|ULK3_ENST00000569437.1_Intron	NM_001099436.1	NP_001092906	Q6PHR2	ULK3_HUMAN	unc-51 like kinase 3	445			K -> R (in dbSNP:rs12898397).		autophagic vacuole assembly (GO:0000045)|autophagy (GO:0006914)|cellular senescence (GO:0090398)|negative regulation of smoothened signaling pathway (GO:0045879)|positive regulation of smoothened signaling pathway (GO:0045880)|protein autophosphorylation (GO:0046777)|regulation of autophagy (GO:0010506)	ATG1/UKL1 signaling complex (GO:0034273)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|pre-autophagosomal structure (GO:0000407)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)	2						TGTGCCCACCTTGACCTGCTC	0.612													T|||	1940	0.38738	0.0915	0.5432	5008	,	,		16963	0.3403		0.5795	False		,,,				2504	0.5276				p.K445R		Atlas-SNP	.											.	ULK3	30	.	0			c.A1334G						PASS	.	T	ARG/LYS	709,3487		77,555,1466	41.0	50.0	47.0		1334	5.2	1.0	15	dbSNP_121	47	4977,3427		1499,1979,724	yes	missense-near-splice	ULK3	NM_001099436.1	26	1576,2534,2190	CC,CT,TT		40.7782,16.897,45.127	possibly-damaging	445/473	75130093	5686,6914	2098	4202	6300	SO:0001630	splice_region_variant	25989	exon14			CCCACCTTGACCT	BC048289		15q24.1	2013-07-02	2013-07-02			ENSG00000140474			19703	protein-coding gene	gene with protein product		613472	"""unc-51-like kinase 3 (C. elegans)"""				Standard	XM_005254289		Approved	DKFZP434C131, FLJ90566	uc010bkf.1	Q6PHR2		ENST00000440863.2:c.1335+1A>G	15.37:g.75130093T>C		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	89	89	1	NM_001099436	B2RXK3|B4DRQ7|D3DW68|Q9NPN5|Q9UFS4	Missense_Mutation	SNP	ENST00000440863.2	37	CCDS45305.1	880	0.40293040293040294	47	0.09552845528455285	197	0.5441988950276243	199	0.3479020979020979	437	0.5765171503957783	T	15.80	2.939286	0.52972	0.16897	0.592218	ENSG00000140474	ENST00000440863;ENST00000418051	T	0.30981	1.51	5.23	5.23	0.72850	MIT (1);	.	.	.	.	T	0.00012	0.0000	L	0.57536	1.79	0.22693	P	0.99884618	D;B	0.69078	0.997;0.294	D;B	0.75020	0.985;0.057	T	0.49457	-0.8938	8	0.27785	T	0.31	-16.8689	12.5013	0.55957	0.0:0.0:0.0:1.0	rs12898397	456;445	B4DFT0;Q6PHR2	.;ULK3_HUMAN	R	445;456	ENSP00000400312:K445R	ENSP00000393658:K456R	K	-	2	0	ULK3	72917146	1.000000	0.71417	1.000000	0.80357	0.670000	0.39368	5.637000	0.67854	1.978000	0.57642	0.459000	0.35465	AAG	T|0.596;C|0.404	0.404	strong		0.612	ULK3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000421734.4	NM_015518	Missense_Mutation
PRKAR1B	5575	hgsc.bcm.edu	37	7	618938	618938	+	Silent	SNP	A	A	G	rs3211362	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:618938A>G	ENST00000406797.1	-	9	1020	c.846T>C	c.(844-846)atT>atC	p.I282I	PRKAR1B_ENST00000403562.1_Silent_p.I282I|PRKAR1B_ENST00000537384.1_Silent_p.I282I|PRKAR1B_ENST00000360274.4_Silent_p.I282I|PRKAR1B_ENST00000544935.1_Silent_p.I282I	NM_001164761.1	NP_001158233.1	P31321	KAP1_HUMAN	protein kinase, cAMP-dependent, regulatory, type I, beta	282					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|blood coagulation (GO:0007596)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|learning or memory (GO:0007611)|negative regulation of cAMP-dependent protein kinase activity (GO:2000480)|neurotrophin TRK receptor signaling pathway (GO:0048011)|protein phosphorylation (GO:0006468)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cAMP-dependent protein kinase complex (GO:0005952)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	cAMP binding (GO:0030552)|cAMP-dependent protein kinase inhibitor activity (GO:0004862)|cAMP-dependent protein kinase regulator activity (GO:0008603)|protein kinase A catalytic subunit binding (GO:0034236)			endometrium(4)|large_intestine(1)|liver(1)|lung(10)|prostate(1)	17		Ovarian(82;0.0779)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0181)|Epithelial(4;5.75e-19)|OV - Ovarian serous cystadenocarcinoma(56;2.01e-18)|all cancers(6;3.96e-16)|BRCA - Breast invasive adenocarcinoma(126;0.152)		CCTGGACCACAATTTTCTCTC	0.612													G|||	1821	0.363618	0.5408	0.3357	5008	,	,		18716	0.2688		0.4443	False		,,,				2504	0.1585				p.I282I		Atlas-SNP	.											.	PRKAR1B	32	.	0			c.T846C						PASS	.	G	,,,,,	2209,2197	587.2+/-386.6	571,1067,565	163.0	127.0	139.0		846,846,846,846,846,846	-10.3	0.2	7	dbSNP_105	139	3420,5172	638.3+/-399.3	695,2030,1571	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PRKAR1B	NM_001164758.1,NM_001164759.1,NM_001164760.1,NM_001164761.1,NM_001164762.1,NM_002735.2	,,,,,	1266,3097,2136	GG,GA,AA		39.8045,49.8638,43.3067	,,,,,	282/382,282/382,282/382,282/382,282/382,282/382	618938	5629,7369	2203	4296	6499	SO:0001819	synonymous_variant	5575	exon9			GACCACAATTTTC	M65066	CCDS34579.1	7p22.3	2013-09-19			ENSG00000188191	ENSG00000188191	2.7.11.1		9390	protein-coding gene	gene with protein product		176911				1358799, 3479018	Standard	NM_002735		Approved		uc003siw.2	P31321	OTTHUMG00000151411	ENST00000406797.1:c.846T>C	7.37:g.618938A>G		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	140	103	0.735714	NM_001164760	Q8N422	Silent	SNP	ENST00000406797.1	37	CCDS34579.1	875	0.40064102564102566	263	0.5345528455284553	131	0.36187845303867405	144	0.2517482517482518	337	0.4445910290237467	G	2.413	-0.334936	0.05278	0.501362	0.398045	ENSG00000188191	ENST00000400758	.	.	.	5.14	-10.3	0.00346	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999998506	.	.	.	.	.	.	T	0.02852	-1.1102	3	.	.	.	0.1284	17.0595	0.86543	0.4771:0.0:0.5229:0.0	rs3211362;rs17411390;rs17781456;rs62431413	.	.	.	S	143	.	.	L	-	2	0	PRKAR1B	585464	0.000000	0.05858	0.186000	0.23195	0.161000	0.22273	-2.821000	0.00749	-2.912000	0.00307	-1.507000	0.00952	TTG	A|0.585;G|0.415	0.415	strong		0.612	PRKAR1B-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322525.1		
PREX2	80243	hgsc.bcm.edu	37	8	69058521	69058521	+	Nonsense_Mutation	SNP	G	G	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:69058521G>T	ENST00000288368.4	+	34	4442	c.4165G>T	c.(4165-4167)Gaa>Taa	p.E1389*		NM_024870.2|NM_025170.4	NP_079146.2|NP_079446.3	Q70Z35	PREX2_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 2	1389					adult locomotory behavior (GO:0008344)|dendrite morphogenesis (GO:0048813)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|positive regulation of Rac GTPase activity (GO:0032855)		Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)	p.E1389K(1)		NS(6)|biliary_tract(1)|breast(4)|endometrium(11)|kidney(16)|large_intestine(25)|liver(4)|lung(57)|ovary(2)|pancreas(4)|prostate(3)|skin(42)|upper_aerodigestive_tract(1)|urinary_tract(2)	178						TTATCATTTTGAACAACTTCC	0.343																																					p.E1389X		Atlas-SNP	.											PREX2,back,malignant_melanoma,0,1	PREX2	614	1	1	Substitution - Missense(1)	skin(1)	c.G4165T						scavenged	.						100.0	99.0	99.0					8																	69058521		2203	4299	6502	SO:0001587	stop_gained	80243	exon34			CATTTTGAACAAC	AK024079	CCDS6201.1	8q13.1	2014-06-13	2008-09-15	2008-09-15	ENSG00000046889	ENSG00000046889		"""Rho guanine nucleotide exchange factors"""	22950	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 129"""	612139	"""DEP domain containing 2"""	DEPDC2		15304342, 15304343	Standard	NM_024870		Approved	DEP.2, FLJ12987, P-REX2, PPP1R129	uc003xxv.1	Q70Z35	OTTHUMG00000164402	ENST00000288368.4:c.4165G>T	8.37:g.69058521G>T	ENSP00000288368:p.Glu1389*	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	106	4	0.0377358	NM_024870	B4DFX0|Q32KL0|Q32KL1|Q6R7Q3|Q6R7Q4|Q9H805|Q9H961	Nonsense_Mutation	SNP	ENST00000288368.4	37	CCDS6201.1	.	.	.	.	.	.	.	.	.	.	G	46	12.260236	0.99651	.	.	ENSG00000046889	ENST00000288368	.	.	.	5.62	5.62	0.85841	.	0.271260	0.38605	N	0.001638	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.38643	T	0.18	.	14.232	0.65898	0.0715:0.0:0.9285:0.0	.	.	.	.	X	1389	.	ENSP00000288368:E1389X	E	+	1	0	PREX2	69221075	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	3.119000	0.50422	2.810000	0.96702	0.650000	0.86243	GAA	.	.	none		0.343	PREX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378620.1	NM_025170	
C10orf25	220979	hgsc.bcm.edu	37	10	45496120	45496120	+	Missense_Mutation	SNP	A	A	T	rs12269028	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:45496120A>T	ENST00000298298.1	-	1	216	c.188T>A	c.(187-189)aTt>aAt	p.I63N	ZNF22_ENST00000298299.3_5'UTR|CEP164P1_ENST00000456938.2_RNA	NM_001039380.2	NP_001034469.2	Q5T742	CJ025_HUMAN	chromosome 10 open reading frame 25	63			I -> N (in dbSNP:rs12269028). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.3}.			extracellular region (GO:0005576)				endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|stomach(1)	6						AAATCTCAAAATTTGTGGAAA	0.453													A|||	2306	0.460463	0.2231	0.6945	5008	,	,		17395	0.371		0.6571	False		,,,				2504	0.5051				p.I63N		Atlas-SNP	.											.	C10orf25	11	.	0			c.T188A						PASS	.	A	ASN/ILE	1433,2973	456.3+/-351.3	251,931,1021	72.0	75.0	74.0		188	-2.8	0.0	10	dbSNP_120	74	5585,3015	660.5+/-401.8	1805,1975,520	yes	missense	C10orf25	NM_001039380.2	149	2056,2906,1541	TT,TA,AA		35.0581,32.5238,46.0403	possibly-damaging	63/123	45496120	7018,5988	2203	4300	6503	SO:0001583	missense	220979	exon1			CTCAAAATTTGTG	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.188T>A	10.37:g.45496120A>T	ENSP00000298298:p.Ile63Asn	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	86	85	0.988372	NM_001039380	A1L424|Q96NM5	Missense_Mutation	SNP	ENST00000298298.1	37	CCDS31187.1	1059	0.4848901098901099	127	0.258130081300813	241	0.6657458563535912	205	0.3583916083916084	486	0.6411609498680739	A	5.134	0.210400	0.09757	0.325238	0.649419	ENSG00000165511	ENST00000298298	T	0.38722	1.12	2.81	-2.84	0.05751	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.54753	P	1.399999999995849E-5	D	0.57899	0.981	P	0.50934	0.654	T	0.44267	-0.9339	8	0.87932	D	0	.	3.2317	0.06751	0.3825:0.0:0.4086:0.2089	rs12269028;rs12269028	63	Q5T742	CJ025_HUMAN	N	63	ENSP00000298298:I63N	ENSP00000298298:I63N	I	-	2	0	C10orf25	44816126	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.246000	0.18160	-0.646000	0.05452	-0.371000	0.07208	ATT	A|0.475;T|0.525	0.525	strong		0.453	C10orf25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047763.1	NM_145022	
TBC1D32	221322	hgsc.bcm.edu	37	6	121577370	121577370	+	Missense_Mutation	SNP	T	T	C	rs7745023	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:121577370T>C	ENST00000398212.2	-	16	1844	c.1795A>G	c.(1795-1797)Ata>Gta	p.I599V	TBC1D32_ENST00000275159.6_Missense_Mutation_p.I599V	NM_152730.4	NP_689943.4	Q96NH3	BROMI_HUMAN	TBC1 domain family, member 32	599			I -> V (in dbSNP:rs7745023).		cilium morphogenesis (GO:0060271)|embryonic digit morphogenesis (GO:0042733)|lens development in camera-type eye (GO:0002088)|protein localization to cilium (GO:0061512)|retinal pigment epithelium development (GO:0003406)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)	cilium (GO:0005929)|cytoplasm (GO:0005737)	Rab GTPase activator activity (GO:0005097)	p.I599V(1)									CCAGAAAATATAGAAATATCT	0.353													T|||	1306	0.260783	0.0424	0.2954	5008	,	,		18165	0.1111		0.5855	False		,,,				2504	0.3517				p.I599V		Atlas-SNP	.											C6orf170,NS,carcinoma,0,1	C6orf170	146	1	1	Substitution - Missense(1)	prostate(1)	c.A1795G						PASS	.	T	VAL/ILE	468,3146		39,390,1378	62.0	57.0	59.0		1795	-0.5	0.5	6	dbSNP_116	59	4710,3436		1354,2002,717	yes	missense	C6orf170	NM_152730.4	29	1393,2392,2095	CC,CT,TT		42.1802,12.9496,44.0306	benign	599/1258	121577370	5178,6582	1807	4073	5880	SO:0001583	missense	221322	exon16			AAAATATAGAAAT	AK055461	CCDS43501.1	6q22.31	2014-02-20	2013-07-10	2013-07-10	ENSG00000146350	ENSG00000146350			21485	protein-coding gene	gene with protein product	"""broad-minded homolog"""	615867	"""chromosome 6 open reading frame 171"", ""chromosome 6 open reading frame 170"""	C6orf171, C6orf170		20159594, 24285566	Standard	NM_152730		Approved	FLJ30899, dJ310J6.1, FLJ34235, bA57L9.1, BROMI	uc003pyo.1	Q96NH3	OTTHUMG00000015474	ENST00000398212.2:c.1795A>G	6.37:g.121577370T>C	ENSP00000381270:p.Ile599Val	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	65	64	0.984615	NM_152730	Q5SZD6|Q5SZM6|Q6ZMY4|Q6ZUR7|Q8NB47	Missense_Mutation	SNP	ENST00000398212.2	37	CCDS43501.1	639	0.2925824175824176	29	0.05894308943089431	121	0.3342541436464088	51	0.08916083916083917	438	0.5778364116094987	T	2.501	-0.315202	0.05422	0.129496	0.578198	ENSG00000146350	ENST00000275159;ENST00000398212	T;T	0.16073	2.37;2.37	5.21	-0.469	0.12142	.	0.775342	0.12424	N	0.470190	T	0.01695	0.0054	N	0.15975	0.35	0.44261	P	0.0028839999999999977	B;B	0.02656	0.0;0.0	B;B	0.06405	0.001;0.002	T	0.46762	-0.9168	9	0.02654	T	1	-15.6923	5.6919	0.17835	0.0:0.3939:0.3466:0.2596	rs7745023;rs13208594;rs52836518;rs58699322;rs7745023	599;599	Q96NH3-4;Q96NH3	.;BROMI_HUMAN	V	599	ENSP00000275159:I599V;ENSP00000381270:I599V	ENSP00000275159:I599V	I	-	1	0	C6orf170	121619069	0.857000	0.29778	0.468000	0.27192	0.460000	0.32559	0.019000	0.13444	0.057000	0.16193	-1.156000	0.01807	ATA	T|0.674;C|0.326	0.326	strong		0.353	TBC1D32-005	PUTATIVE	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380937.2	NM_152730	
GPR32	2854	hgsc.bcm.edu	37	19	51274836	51274836	+	Missense_Mutation	SNP	T	T	C	rs1864011	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:51274836T>C	ENST00000270590.4	+	1	1116	c.979T>C	c.(979-981)Ttt>Ctt	p.F327L		NM_001506.1	NP_001497.1	O75388	GPR32_HUMAN	G protein-coupled receptor 32	327			F -> L (in dbSNP:rs1864011).		G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)			breast(4)|endometrium(4)|kidney(1)|large_intestine(3)|lung(12)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	29		all_neural(266;0.131)		OV - Ovarian serous cystadenocarcinoma(262;0.00641)|GBM - Glioblastoma multiforme(134;0.028)		CCAAGAAAAGTTTTTCCAGTC	0.552													T|||	136	0.0271565	0.0023	0.0187	5008	,	,		17491	0.0139		0.0348	False		,,,				2504	0.0726				p.F327L	Esophageal Squamous(113;152 1581 5732 15840 44398)	Atlas-SNP	.											.	GPR32	68	.	0			c.T979C						PASS	.	T	LEU/PHE	31,4375	34.3+/-65.2	0,31,2172	67.0	69.0	69.0		979	-1.2	0.0	19	dbSNP_92	69	270,8330	97.2+/-158.9	6,258,4036	no	missense	GPR32	NM_001506.1	22	6,289,6208	CC,CT,TT		3.1395,0.7036,2.3143	benign	327/357	51274836	301,12705	2203	4300	6503	SO:0001583	missense	2854	exon1			GAAAAGTTTTTCC	AF045764	CCDS12801.1	19q13.33	2012-08-20			ENSG00000142511	ENSG00000142511		"""GPCR / Class A : Resolvin receptors"""	4487	protein-coding gene	gene with protein product	"""resolvin D1 receptor"""	603195				9653656	Standard	NM_001506		Approved	RVDR1	uc010ycf.3	O75388		ENST00000270590.4:c.979T>C	19.37:g.51274836T>C	ENSP00000270590:p.Phe327Leu	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	91	46	0.505495	NM_001506	Q502U7|Q6NWS5	Missense_Mutation	SNP	ENST00000270590.4	37	CCDS12801.1	47	0.02152014652014652	2	0.0040650406504065045	11	0.03038674033149171	10	0.017482517482517484	24	0.0316622691292876	T	0.007	-1.961372	0.00465	0.007036	0.031395	ENSG00000142511	ENST00000270590	T	0.34072	1.38	2.61	-1.18	0.09617	.	.	.	.	.	T	0.03783	0.0107	N	0.08118	0	0.09310	N	1	B	0.17465	0.022	B	0.11329	0.006	T	0.24621	-1.0155	9	0.02654	T	1	.	2.7231	0.05206	0.2129:0.2832:0.0:0.5039	rs1864011;rs1864011	327	O75388	GPR32_HUMAN	L	327	ENSP00000270590:F327L	ENSP00000270590:F327L	F	+	1	0	GPR32	55966648	0.259000	0.24043	0.000000	0.03702	0.399000	0.30720	0.005000	0.13129	-0.211000	0.10124	0.260000	0.18958	TTT	T|0.976;C|0.024	0.024	strong		0.552	GPR32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465016.1		
CHRND	1144	hgsc.bcm.edu	37	2	233390937	233390937	+	Silent	SNP	A	A	G	rs2245601	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:233390937A>G	ENST00000258385.3	+	1	44	c.12A>G	c.(10-12)ccA>ccG	p.P4P	CHRND_ENST00000536614.1_Silent_p.P4P|CHRND_ENST00000457943.2_5'UTR|CHRND_ENST00000543200.1_Silent_p.P4P	NM_000751.2	NP_000742.1	Q07001	ACHD_HUMAN	cholinergic receptor, nicotinic, delta (muscle)	4					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|muscle contraction (GO:0006936)|musculoskeletal movement (GO:0050881)|neuromuscular process (GO:0050905)|regulation of membrane potential (GO:0042391)|signal transduction (GO:0007165)|skeletal muscle tissue growth (GO:0048630)|synaptic transmission (GO:0007268)|transport (GO:0006810)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|acetylcholine-activated cation-selective channel activity (GO:0004889)	p.P4P(1)		breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(5)|liver(1)|lung(17)|ovary(3)|prostate(1)|skin(1)|stomach(1)	34		all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0449)|Lung NSC(271;0.132)		Epithelial(121;1.89e-16)|BRCA - Breast invasive adenocarcinoma(100;0.00078)|Lung(119;0.00579)|LUSC - Lung squamous cell carcinoma(224;0.00754)	Galantamine(DB00674)	TGGAGGGGCCAGTGCTGACAC	0.667													A|||	2421	0.483427	0.3502	0.5461	5008	,	,		11714	0.6518		0.4483	False		,,,				2504	0.4816				p.P4P		Atlas-SNP	.											CHRND,NS,carcinoma,0,1	CHRND	67	1	1	Substitution - coding silent(1)	stomach(1)	c.A12G						PASS	.	A		1676,2730	501.5+/-365.0	313,1050,840	60.0	61.0	61.0		12	-4.7	0.1	2	dbSNP_100	61	4159,4439	564.2+/-388.3	1024,2111,1164	no	coding-synonymous	CHRND	NM_000751.1		1337,3161,2004	GG,GA,AA		48.3717,38.039,44.8708		4/518	233390937	5835,7169	2203	4299	6502	SO:0001819	synonymous_variant	1144	exon1			GGGGCCAGTGCTG	X55019	CCDS2494.1, CCDS58754.1	2q37.1	2012-02-11	2012-02-07		ENSG00000135902	ENSG00000135902		"""Cholinergic receptors"", ""Ligand-gated ion channels / Acetylcholine receptors, nicotinic"""	1965	protein-coding gene	gene with protein product	"""acetylcholine receptor, nicotinic, delta (muscle)"""	100720	"""cholinergic receptor, nicotinic, delta"""	ACHRD			Standard	NM_000751		Approved		uc002vsw.4	Q07001	OTTHUMG00000133261	ENST00000258385.3:c.12A>G	2.37:g.233390937A>G		Somatic	200	0	0		WXS	Illumina HiSeq	Phase_I	215	100	0.465116	NM_000751	A8K661|B4DT92|Q52LH4	Silent	SNP	ENST00000258385.3	37	CCDS2494.1																																																																																			A|0.542;G|0.458	0.458	strong		0.667	CHRND-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257038.2		
ZKSCAN2	342357	hgsc.bcm.edu	37	16	25268368	25268368	+	Silent	SNP	A	A	G	rs4787310	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:25268368A>G	ENST00000328086.7	-	1	884	c.81T>C	c.(79-81)ccT>ccC	p.P27P		NM_001012981.4	NP_001012999.3	Q63HK3	ZKSC2_HUMAN	zinc finger with KRAB and SCAN domains 2	27					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)	p.P27P(1)		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)		ATGCCCACTCAGGGTCCTTTT	0.557											OREG0023690	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	2309	0.461062	0.6346	0.4481	5008	,	,		19215	0.4722		0.338	False		,,,				2504	0.3507				p.P27P		Atlas-SNP	.											ZKSCAN2,NS,carcinoma,0,1	ZKSCAN2	90	1	1	Substitution - coding silent(1)	stomach(1)	c.T81C						PASS	.	G		2596,1798	516.7+/-369.2	775,1046,376	73.0	79.0	77.0		81	2.0	0.9	16	dbSNP_111	77	3045,5555	655.5+/-401.3	540,1965,1795	no	coding-synonymous	ZKSCAN2	NM_001012981.4		1315,3011,2171	GG,GA,AA		35.407,40.9194,43.4123		27/968	25268368	5641,7353	2197	4300	6497	SO:0001819	synonymous_variant	342357	exon1			CCACTCAGGGTCC	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.81T>C	16.37:g.25268368A>G		Somatic	111	0	0	777	WXS	Illumina HiSeq	Phase_I	116	35	0.301724	NM_001012981	A1L3B4|Q6ZN77	Silent	SNP	ENST00000328086.7	37	CCDS32410.1																																																																																			A|0.562;G|0.438	0.438	strong		0.557	ZKSCAN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435739.1	NM_001012981	
UBXN11	91544	hgsc.bcm.edu	37	1	26612460	26612460	+	Silent	SNP	G	G	A	rs11247900	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:26612460G>A	ENST00000374222.1	-	10	1092	c.628C>T	c.(628-630)Ctg>Ttg	p.L210L	UBXN11_ENST00000535108.1_Silent_p.L52L|UBXN11_ENST00000357089.4_Silent_p.L177L|UBXN11_ENST00000436301.2_Silent_p.L135L|UBXN11_ENST00000314675.7_Silent_p.L90L|UBXN11_ENST00000374217.2_Silent_p.L177L|UBXN11_ENST00000374223.1_5'UTR|UBXN11_ENST00000374221.3_Silent_p.L210L			Q5T124	UBX11_HUMAN	UBX domain protein 11	210						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				endometrium(3)|kidney(2)|large_intestine(4)|lung(6)|ovary(2)|prostate(3)|upper_aerodigestive_tract(3)	23						TCTACCACCAGCTCACTAAGA	0.632											OREG0013265	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	646	0.128994	0.202	0.1066	5008	,	,		17288	0.0228		0.1909	False		,,,				2504	0.092				p.L210L		Atlas-SNP	.											.	UBXN11	54	.	0			c.C628T						PASS	.	G	,,	591,3317		48,495,1411	38.0	41.0	40.0		268,529,628	2.9	1.0	1	dbSNP_120	40	1366,6934		103,1160,2887	no	coding-synonymous,coding-synonymous,coding-synonymous	UBXN11	NM_001077262.1,NM_145345.2,NM_183008.2	,,	151,1655,4298	AA,AG,GG		16.4578,15.1228,16.0305	,,	90/401,177/488,210/521	26612460	1957,10251	1954	4150	6104	SO:0001819	synonymous_variant	91544	exon10			CCACCAGCTCACT	AF521017	CCDS41286.1, CCDS41287.1, CCDS41288.1	1p36.11	2008-07-25	2008-07-25	2008-07-25	ENSG00000158062	ENSG00000158062		"""UBX domain containing"""	30600	protein-coding gene	gene with protein product	"""socius"""	609151	"""UBX domain containing 5"""	UBXD5		11940653	Standard	NM_183008		Approved	SOC, SOCI	uc001blw.3	Q5T124	OTTHUMG00000003382	ENST00000374222.1:c.628C>T	1.37:g.26612460G>A		Somatic	151	0	0	788	WXS	Illumina HiSeq	Phase_I	152	68	0.447368	NM_183008	D3DPK6|Q5T117|Q5T120|Q5T125|Q5T126|Q5T129|Q5T131|Q5T133|Q63HM6|Q71RB3|Q8IY27|Q8N1L6|Q8N9M4|Q8NA18|Q8NFE3|Q8NFE4|Q8NFE6	Silent	SNP	ENST00000374222.1	37	CCDS41288.1																																																																																			G|0.862;A|0.138	0.138	strong		0.632	UBXN11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000009500.1	NM_145345	
KIAA2026	158358	hgsc.bcm.edu	37	9	5921844	5921844	+	Missense_Mutation	SNP	G	G	T	rs117286418	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:5921844G>T	ENST00000399933.3	-	8	4151	c.4152C>A	c.(4150-4152)caC>caA	p.H1384Q	KIAA2026_ENST00000381461.2_Missense_Mutation_p.H1354Q	NM_001017969.2	NP_001017969.2	Q5HYC2	K2026_HUMAN	KIAA2026	1384	Ser-rich.									breast(6)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(11)|lung(15)|ovary(2)|prostate(2)|skin(1)	46		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.00155)|Lung(218;0.124)		TATCTATCACGTGGCCCAAAT	0.443													G|||	167	0.0333466	0.0053	0.0461	5008	,	,		21842	0.001		0.0974	False		,,,				2504	0.0297				p.H1384Q		Atlas-SNP	.											KIAA2026_ENST00000399933,NS,carcinoma,0,2	KIAA2026	231	2	0			c.C4152A						PASS	.	G	GLN/HIS	78,3690		0,78,1806	156.0	150.0	152.0		4152	-0.7	0.5	9	dbSNP_132	152	936,7296		52,832,3232	yes	missense	KIAA2026	NM_001017969.2	24	52,910,5038	TT,TG,GG		11.3703,2.0701,8.45	benign	1384/2104	5921844	1014,10986	1884	4116	6000	SO:0001583	missense	158358	exon8			TATCACGTGGCCC	AB095946		9p24.1	2014-01-10			ENSG00000183354	ENSG00000183354			23378	protein-coding gene	gene with protein product							Standard	NM_001017969		Approved	FLJ20375	uc003zjq.4	Q5HYC2	OTTHUMG00000019507	ENST00000399933.3:c.4152C>A	9.37:g.5921844G>T	ENSP00000382815:p.His1384Gln	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	86	42	0.488372	NM_001017969	A8MTP2|B9EGW7|Q4VXA2|Q8IVE5	Missense_Mutation	SNP	ENST00000399933.3	37		115	0.052655677655677656	4	0.008130081300813009	23	0.06353591160220995	1	0.0017482517482517483	87	0.11477572559366754	G	0.015	-1.559182	0.00910	0.020701	0.113703	ENSG00000183354	ENST00000399933;ENST00000381461	.	.	.	4.08	-0.703	0.11261	.	0.243817	0.28612	N	0.014739	T	0.00241	0.0007	N	0.14661	0.345	0.58432	P	1.999999999946489E-6	B	0.10296	0.003	B	0.06405	0.002	T	0.12192	-1.0557	8	0.06494	T	0.89	-3.0597	0.5155	0.00602	0.353:0.123:0.2814:0.2426	.	1384	Q5HYC2	K2026_HUMAN	Q	1384;1354	.	ENSP00000370870:H1354Q	H	-	3	2	KIAA2026	5911844	0.955000	0.32602	0.463000	0.27130	0.627000	0.37826	0.235000	0.17948	0.026000	0.15269	0.484000	0.47621	CAC	A|0.001;G|0.937;T|0.062	0.062	strong		0.443	KIAA2026-002	NOVEL	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051652.2	NM_001017969	
PDE5A	8654	hgsc.bcm.edu	37	4	120474859	120474859	+	Silent	SNP	A	A	G	rs11947234	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:120474859A>G	ENST00000354960.3	-	8	1561	c.1242T>C	c.(1240-1242)taT>taC	p.Y414Y	PDE5A_ENST00000394439.1_Silent_p.Y362Y|RP11-33B1.1_ENST00000498873.1_RNA|PDE5A_ENST00000264805.5_Silent_p.Y372Y	NM_001083.3	NP_001074.2	O76074	PDE5A_HUMAN	phosphodiesterase 5A, cGMP-specific	414	GAF 2.				blood coagulation (GO:0007596)|cGMP catabolic process (GO:0046069)|negative regulation of cardiac muscle contraction (GO:0055118)|negative regulation of T cell proliferation (GO:0042130)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of oocyte development (GO:0060282)|relaxation of cardiac muscle (GO:0055119)|signal transduction (GO:0007165)	cytosol (GO:0005829)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|cGMP binding (GO:0030553)|metal ion binding (GO:0046872)			breast(4)|endometrium(2)|kidney(3)|large_intestine(8)|lung(7)|prostate(1)|skin(1)|urinary_tract(1)	27					Avanafil(DB06237)|Caffeine(DB00201)|Dipyridamole(DB00975)|Pentoxifylline(DB00806)|Sildenafil(DB00203)|Tadalafil(DB00820)|Theophylline(DB00277)|Udenafil(DB06267)|Vardenafil(DB00862)	TATTTTTGACATACTGAGCAT	0.358													A|||	1331	0.265775	0.2118	0.2867	5008	,	,		18474	0.3929		0.2863	False		,,,				2504	0.1718				p.Y414Y		Atlas-SNP	.											.	PDE5A	83	.	0			c.T1242C						PASS	.	A	,,	917,3489	351.8+/-311.4	104,709,1390	233.0	226.0	228.0		1242,1116,1086	3.3	1.0	4	dbSNP_120	228	2462,6138	404.9+/-348.3	347,1768,2185	no	coding-synonymous,coding-synonymous,coding-synonymous	PDE5A	NM_001083.3,NM_033430.2,NM_033437.3	,,	451,2477,3575	GG,GA,AA		28.6279,20.8125,25.9803	,,	414/876,372/834,362/824	120474859	3379,9627	2203	4300	6503	SO:0001819	synonymous_variant	8654	exon8			TTTGACATACTGA	D89094	CCDS3713.1, CCDS34055.1	4q27	2008-05-15			ENSG00000138735	ENSG00000138735	3.1.4.17	"""Phosphodiesterases"""	8784	protein-coding gene	gene with protein product		603310				9714779, 9642111	Standard	NM_033437		Approved		uc003idh.3	O76074	OTTHUMG00000132971	ENST00000354960.3:c.1242T>C	4.37:g.120474859A>G		Somatic	203	0	0		WXS	Illumina HiSeq	Phase_I	174	174	1	NM_001083	A0AV69|A8K2C4|O75026|O75887|Q86UI0|Q86V66|Q9Y6Z6	Silent	SNP	ENST00000354960.3	37	CCDS3713.1																																																																																			A|0.732;G|0.268	0.268	strong		0.358	PDE5A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256529.1	NM_001083	
OR52J3	119679	hgsc.bcm.edu	37	11	5068137	5068137	+	Missense_Mutation	SNP	G	G	A	rs2500017	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:5068137G>A	ENST00000380370.1	+	1	382	c.382G>A	c.(382-384)Gtc>Atc	p.V128I		NM_001001916.2	NP_001001916.2	Q8NH60	O52J3_HUMAN	olfactory receptor, family 52, subfamily J, member 3	128			V -> I (in dbSNP:rs2500017). {ECO:0000269|PubMed:14983052, ECO:0000269|Ref.1, 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)			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)		TTATGTGGCCGTCTGTGCTCC	0.483													A|||	2442	0.48762	0.5915	0.4971	5008	,	,		20351	0.2619		0.508	False		,,,				2504	0.5521				p.V128I		Atlas-SNP	.											.	OR52J3	77	.	0			c.G382A						PASS	.	A	ILE/VAL	2444,1958	553.0+/-378.7	688,1068,445	176.0	117.0	137.0		382	4.2	0.9	11	dbSNP_100	137	4303,4293	576.3+/-390.4	1068,2167,1063	yes	missense	OR52J3	NM_001001916.2	29	1756,3235,1508	AA,AG,GG		49.9418,44.4798,48.092	benign	128/312	5068137	6747,6251	2201	4298	6499	SO:0001583	missense	119679	exon1			GTGGCCGTCTGTG	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.382G>A	11.37:g.5068137G>A	ENSP00000369728:p.Val128Ile	Somatic	223	0	0		WXS	Illumina HiSeq	Phase_I	273	272	0.996337	NM_001001916	Q6IFE4	Missense_Mutation	SNP	ENST00000380370.1	37	CCDS31370.1	995	0.4555860805860806	290	0.5894308943089431	170	0.4696132596685083	149	0.26048951048951047	386	0.5092348284960422	A	0.017	-1.494256	0.01009	0.555202	0.500582	ENSG00000205495	ENST00000380370	T	0.26518	1.73	4.19	4.19	0.49359	GPCR, rhodopsin-like superfamily (1);	0.000000	0.47852	N	0.000211	T	0.00012	0.0000	N	0.00038	-2.52	0.58432	P	1.999999999946489E-6	B	0.02656	0.0	B	0.04013	0.001	T	0.46373	-0.9196	9	0.02654	T	1	.	8.6796	0.34201	0.9077:0.0:0.0923:0.0	rs2500017;rs17350722;rs52791516;rs60675916;rs2500017	128	Q8NH60	O52J3_HUMAN	I	128	ENSP00000369728:V128I	ENSP00000369728:V128I	V	+	1	0	OR52J3	5024713	0.985000	0.35326	0.891000	0.34965	0.100000	0.18952	2.872000	0.48467	0.651000	0.30788	-0.254000	0.11334	GTC	G|0.493;A|0.507	0.507	strong		0.483	OR52J3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142807.1	NM_001001916	
ESYT2	57488	hgsc.bcm.edu	37	7	158536345	158536345	+	Missense_Mutation	SNP	A	A	G	rs2305475	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	100	0	0		WXS	Illumina HiSeq	Phase_I	78	29	0.371795	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	
MUC4	4585	hgsc.bcm.edu	37	3	195508249	195508249	+	Missense_Mutation	SNP	A	A	G	rs201846606		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195508249A>G	ENST00000463781.3	-	2	10661	c.10202T>C	c.(10201-10203)gTa>gCa	p.V3401A	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.V3401A	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.V3401A(3)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		ACCTGTGGATACTGAGGAAGT	0.577																																					p.V3401A		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,7	MUC4	1505	7	3	Substitution - Missense(3)	stomach(2)|kidney(1)	c.T10202C						scavenged	.						33.0	25.0	27.0					3																	195508249		685	1579	2264	SO:0001583	missense	4585	exon2			GTGGATACTGAGG	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.10202T>C	3.37:g.195508249A>G	ENSP00000417498:p.Val3401Ala	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	90	8	0.0888889	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	a	0.030	-1.338402	0.01287	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.31769	1.54;1.48	0.743	-1.49	0.08718	.	.	.	.	.	T	0.07908	0.0198	N	0.02539	-0.55	0.09310	N	1	B	0.33494	0.414	B	0.19946	0.027	T	0.18366	-1.0339	8	.	.	.	.	2.8398	0.05525	0.2532:0.0:0.4936:0.2531	.	3273	E7ESK3	.	A	3401	ENSP00000417498:V3401A;ENSP00000420243:V3401A	.	V	-	2	0	MUC4	196993028	0.000000	0.05858	0.011000	0.14972	0.012000	0.07955	-0.712000	0.05013	-1.995000	0.00971	-2.001000	0.00444	GTA	A|0.500;G|0.500	0.500	weak		0.577	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
ELSPBP1	64100	hgsc.bcm.edu	37	19	48525507	48525507	+	Missense_Mutation	SNP	G	G	A	rs2303690	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:48525507G>A	ENST00000339841.2	+	6	773	c.595G>A	c.(595-597)Gaa>Aaa	p.E199K	ELSPBP1_ENST00000597519.1_Missense_Mutation_p.E51K	NM_022142.4	NP_071425.3	Q96BH3	ESPB1_HUMAN	epididymal sperm binding protein 1	199	Fibronectin type-II 4. {ECO:0000255|PROSITE-ProRule:PRU00479}.		E -> K (in dbSNP:rs2303690). {ECO:0000269|PubMed:11144225, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.2}.		single fertilization (GO:0007338)	extracellular region (GO:0005576)				NS(1)|breast(1)|kidney(1)|large_intestine(1)|lung(6)	10		all_cancers(25;8.7e-09)|all_lung(116;1.15e-06)|all_epithelial(76;1.17e-06)|Lung NSC(112;2.56e-06)|all_neural(266;0.0138)|Ovarian(192;0.0261)|Breast(70;0.203)		OV - Ovarian serous cystadenocarcinoma(262;0.000253)|all cancers(93;0.00129)|Epithelial(262;0.0314)|GBM - Glioblastoma multiforme(486;0.0606)		CTGCACTAACGAAGGATCAAA	0.458													a|||	3432	0.685304	0.6672	0.719	5008	,	,		21670	0.8671		0.5696	False		,,,				2504	0.6176				p.E199K		Atlas-SNP	.											ELSPBP1,NS,adenoma,0,1	ELSPBP1	29	1	0			c.G595A						PASS	.	A	LYS/GLU	2699,1707	514.5+/-368.7	854,991,358	172.0	160.0	164.0		595	1.5	0.0	19	dbSNP_100	164	4879,3721	530.3+/-381.8	1393,2093,814	yes	missense	ELSPBP1	NM_022142.4	56	2247,3084,1172	AA,AG,GG		43.2674,38.7426,41.7346	benign	199/224	48525507	7578,5428	2203	4300	6503	SO:0001583	missense	64100	exon6			ACTAACGAAGGAT	AJ278478	CCDS12708.1	19q13.33	2009-09-17							14417	protein-coding gene	gene with protein product	"""epididymal protein 12"""	607443					Standard	NM_022142		Approved	HE12, E12, EDDM12	uc002pht.3	Q96BH3		ENST00000339841.2:c.595G>A	19.37:g.48525507G>A	ENSP00000340660:p.Glu199Lys	Somatic	209	0	0		WXS	Illumina HiSeq	Phase_I	167	80	0.479042	NM_022142	Q96RT0|Q9H4C8	Missense_Mutation	SNP	ENST00000339841.2	37	CCDS12708.1	1512	0.6923076923076923	325	0.6605691056910569	242	0.6685082872928176	497	0.8688811188811189	448	0.5910290237467019	A	1.554	-0.538579	0.04053	0.612574	0.567326	ENSG00000169393	ENST00000339841	T	0.52295	0.67	3.66	1.54	0.23209	Fibronectin, type II, collagen-binding (5);Kringle-like fold (1);	0.248846	0.28031	N	0.016863	T	0.00012	0.0000	N	0.20401	0.57	0.80722	P	0.0	B	0.14805	0.011	B	0.15870	0.014	T	0.44651	-0.9314	9	0.02654	T	1	.	3.8049	0.08773	0.4456:0.2051:0.3493:0.0	rs2303690;rs17845467;rs17858345;rs59769918;rs2303690	199	Q96BH3	ESPB1_HUMAN	K	199	ENSP00000340660:E199K	ENSP00000340660:E199K	E	+	1	0	ELSPBP1	53217319	0.439000	0.25610	0.044000	0.18714	0.012000	0.07955	0.521000	0.22893	0.108000	0.17862	-0.308000	0.09152	GAA	G|0.365;A|0.635	0.635	strong		0.458	ELSPBP1-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465207.1		
DYNC2H1	79659	hgsc.bcm.edu	37	11	103116000	103116000	+	Silent	SNP	T	T	C	rs192003811	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:103116000T>C	ENST00000375735.2	+	65	10083	c.9939T>C	c.(9937-9939)gcT>gcC	p.A3313A	DYNC2H1_ENST00000398093.3_Silent_p.A3320A|DYNC2H1_ENST00000334267.7_Intron	NM_001080463.1|NM_001377.2	NP_001073932.1|NP_001368.2	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1	3313	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)		TTATCACAGCTCTTGAATTAG	0.303													T|||	8	0.00159744	0.0008	0.0029	5008	,	,		15868	0.0		0.004	False		,,,				2504	0.001				p.A3320A		Atlas-SNP	.											.	DYNC2H1	246	.	0			c.T9960C						PASS	.	T	,	3,3549		0,3,1773	58.0	51.0	54.0		9960,9939	5.6	1.0	11		54	40,8010		0,40,3985	no	coding-synonymous,coding-synonymous	DYNC2H1	NM_001080463.1,NM_001377.2	,	0,43,5758	CC,CT,TT		0.4969,0.0845,0.3706	,	3320/4315,3313/4308	103116000	43,11559	1776	4025	5801	SO:0001819	synonymous_variant	79659	exon66			CACAGCTCTTGAA	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.9939T>C	11.37:g.103116000T>C		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	51	8	0.156863	NM_001080463	O00432|Q16693|Q3C1U8|Q4AC93|Q6ZMX7|Q6ZUM6|Q7Z363|Q8N977|Q92815|Q9HAE4	Silent	SNP	ENST00000375735.2	37	CCDS53701.1																																																																																			T|0.997;C|0.003	0.003	strong		0.303	DYNC2H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387196.1	XM_370652	
ELF4	2000	hgsc.bcm.edu	37	X	129201179	129201179	+	Silent	SNP	C	C	T	rs2181440	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:129201179C>T	ENST00000308167.5	-	9	1888	c.1509G>A	c.(1507-1509)acG>acA	p.T503T	ELF4_ENST00000335997.7_Silent_p.T503T	NM_001421.3	NP_001412.1			E74-like factor 4 (ets domain transcription factor)											breast(2)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(6)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	22						CCCCTGTGACCGTGGGTGGCG	0.657			T	ERG	AML								c|||	772	0.204503	0.0348	0.317	3775	,	,		12362	0.1002		0.2286	False		,,,				2504	0.1789				p.T503T		Atlas-SNP	.		Dom	yes		X	Xq26	2000	E74-like factor 4 (ets domain transcription factor)		L	.	ELF4	67	.	0			c.G1509A						PASS	.		,	273,3558		10,215,38,1406,531	24.0	26.0	25.0		1509,1509	-7.2	0.0	X	dbSNP_96	25	1731,4977		158,919,496,1348,1362	no	coding-synonymous,coding-synonymous	ELF4	NM_001127197.1,NM_001421.3	,	168,1134,534,2754,1893	TT,TC,T,CC,C		25.805,7.1261,19.0151	,	503/664,503/664	129201179	2004,8535	2200	4283	6483	SO:0001819	synonymous_variant	2000	exon9			TGTGACCGTGGGT	U32645	CCDS14617.1	Xq26	2014-09-17			ENSG00000102034	ENSG00000102034			3319	protein-coding gene	gene with protein product		300775				8895518	Standard	NM_001421		Approved	MEF, ELFR	uc004eve.4	Q99607	OTTHUMG00000022390	ENST00000308167.5:c.1509G>A	X.37:g.129201179C>T		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	96	95	0.989583	NM_001421		Silent	SNP	ENST00000308167.5	37	CCDS14617.1																																																																																			C|0.813;T|0.187	0.187	strong		0.657	ELF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058243.1	NM_001421	
LINC00283	100874057	hgsc.bcm.edu	37	13	103394239	103394239	+	RNA	SNP	C	C	T	rs16960471	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:103394239C>T	ENST00000430111.1	+	0	0									long intergenic non-protein coding RNA 283																		TAATCCTTAACGGTCCAATAT	0.358													C|||	348	0.0694888	0.1399	0.0159	5008	,	,		21957	0.1052		0.0268	False		,,,				2504	0.0194				p.P2936P		Atlas-SNP	.											.	.	.	.	0			c.G8808A						PASS	.	C		158,1226		10,138,544	91.0	76.0	81.0		8808	-7.1	0.0	13	dbSNP_123	81	66,3116		2,62,1527	no	coding-synonymous	CCDC168	NM_001146197.1		12,200,2071	TT,TC,CC		2.0742,11.4162,4.9058		2936/7082	103394239	224,4342	692	1591	2283			643677	exon4			CCTTAACGGTCCA			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.103394239C>T		Somatic	188	0	0		WXS	Illumina HiSeq	Phase_I	162	83	0.512346	NM_001146197		Silent	SNP	ENST00000430111.1	37																																																																																				C|0.924;T|0.076	0.076	strong		0.358	LINC00283-001	KNOWN	not_organism_supported|basic	antisense	antisense	OTTHUMT00000045714.1		
DOCK4	9732	hgsc.bcm.edu	37	7	111375211	111375211	+	Missense_Mutation	SNP	G	G	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:111375211G>C	ENST00000437633.1	-	50	5547	c.5291C>G	c.(5290-5292)aCc>aGc	p.T1764S	DOCK4_ENST00000494651.2_Missense_Mutation_p.T647S|DOCK4_ENST00000428084.1_Missense_Mutation_p.T1773S	NM_014705.3	NP_055520.3	Q8N1I0	DOCK4_HUMAN	dedicator of cytokinesis 4	1764	Ser-rich.				cell chemotaxis (GO:0060326)|positive regulation of Rac GTPase activity (GO:0032855)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|membrane (GO:0016020)|stereocilium (GO:0032420)|stereocilium bundle (GO:0032421)	guanyl-nucleotide exchange factor activity (GO:0005085)|PDZ domain binding (GO:0030165)|Rac GTPase activator activity (GO:0030675)|Rac GTPase binding (GO:0048365)|receptor tyrosine kinase binding (GO:0030971)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(13)|lung(31)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(4)	72		Acute lymphoblastic leukemia(1;0.0441)				GCTGCTAGGGGTGGGGTTCAC	0.507																																					p.T1764S		Atlas-SNP	.											.	DOCK4	365	.	0			c.C5291G						PASS	.						38.0	38.0	38.0					7																	111375211		1905	4125	6030	SO:0001583	missense	9732	exon50			CTAGGGGTGGGGT		CCDS47688.1	7q31.1	2007-08-07			ENSG00000128512	ENSG00000128512			19192	protein-coding gene	gene with protein product		607679				12432077, 12628187	Standard	XM_006716188		Approved	FLJ34238, KIAA0716	uc003vfx.3	Q8N1I0	OTTHUMG00000155077	ENST00000437633.1:c.5291C>G	7.37:g.111375211G>C	ENSP00000404179:p.Thr1764Ser	Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	37	11	0.297297	NM_014705	O14584|O94824|Q8NB45	Missense_Mutation	SNP	ENST00000437633.1	37	CCDS47688.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	17.24|17.24	3.338601|3.338601	0.60963|0.60963	.|.	.|.	ENSG00000128512|ENSG00000128512	ENST00000445943|ENST00000352877;ENST00000428084;ENST00000494651;ENST00000437633	.|T;T;T	.|0.05717	.|4.13;3.4;4.14	6.04|6.04	5.16|5.16	0.70880|0.70880	.|.	.|0.093637	.|0.85682	.|D	.|0.000000	T|T	0.04182|0.04182	0.0116|0.0116	N|N	0.08118|0.08118	0|0	0.42876|0.42876	D|D	0.994156|0.994156	.|B;B;B;P	.|0.45902	.|0.206;0.146;0.146;0.868	.|B;B;B;B	.|0.41510	.|0.085;0.038;0.026;0.359	T|T	0.59348|0.59348	-0.7471|-0.7471	5|10	.|0.21540	.|T	.|0.41	.|.	14.7566|14.7566	0.69569|0.69569	0.0686:0.0:0.9314:0.0|0.0686:0.0:0.9314:0.0	.|.	.|647;1809;1764;77	.|F5GXW1;Q149N5;Q8N1I0;Q8N1I0-4	.|.;.;DOCK4_HUMAN;.	A|S	1797|1752;1773;647;1764	.|ENSP00000410746:T1773S;ENSP00000440944:T647S;ENSP00000404179:T1764S	.|ENSP00000262421:T1752S	P|T	-|-	1|2	0|0	DOCK4|DOCK4	111162447|111162447	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.995000|0.995000	0.86356|0.86356	7.062000|7.062000	0.76706|0.76706	2.876000|2.876000	0.98609|0.98609	0.650000|0.650000	0.86243|0.86243	CCC|ACC	.	.	none		0.507	DOCK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338369.4	NM_014705	
TAT	6898	hgsc.bcm.edu	37	16	71609856	71609856	+	Silent	SNP	C	C	T	rs78302875	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:71609856C>T	ENST00000355962.4	-	3	442	c.309G>A	c.(307-309)tcG>tcA	p.S103S	RP11-432I5.1_ENST00000561529.1_RNA	NM_000353.2	NP_000344.1	P17735	ATTY_HUMAN	tyrosine aminotransferase	103					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)	TATATTTGCCCGAGTCCAGGG	0.473													C|||	351	0.0700879	0.0983	0.0879	5008	,	,		20460	0.0069		0.0755	False		,,,				2504	0.0787				p.S103S	Melanoma(198;542 2142 10292 21661 50033)|Esophageal Squamous(48;487 1013 5572 44395 52594)	Atlas-SNP	.											TAT,colon,carcinoma,-1,1	TAT	80	1	0			c.G309A						scavenged	.	C		451,3945	215.8+/-234.7	26,399,1773	139.0	139.0	139.0		309	-11.7	0.0	16	dbSNP_131	139	552,8048	151.6+/-206.3	15,522,3763	no	coding-synonymous	TAT	NM_000353.2		41,921,5536	TT,TC,CC		6.4186,10.2593,7.7178		103/455	71609856	1003,11993	2198	4300	6498	SO:0001819	synonymous_variant	6898	exon3			TTTGCCCGAGTCC		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.309G>A	16.37:g.71609856C>T		Somatic	105	1	0.00952381		WXS	Illumina HiSeq	Phase_I	115	80	0.695652	NM_000353	B2R8I1|D3DWS2	Silent	SNP	ENST00000355962.4	37	CCDS10903.1																																																																																			C|0.928;T|0.072	0.072	strong		0.473	TAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268989.1		
TDRD9	122402	hgsc.bcm.edu	37	14	104436931	104436931	+	Silent	SNP	C	C	T	rs11851097	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:104436931C>T	ENST00000409874.4	+	6	867	c.819C>T	c.(817-819)ctC>ctT	p.L273L	TDRD9_ENST00000339063.5_Silent_p.L273L	NM_153046.2	NP_694591.2	Q8NDG6	TDRD9_HUMAN	tudor domain containing 9	273	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				cell differentiation (GO:0030154)|DNA methylation involved in gamete generation (GO:0043046)|fertilization (GO:0009566)|gene silencing by RNA (GO:0031047)|male meiosis (GO:0007140)|multicellular organismal development (GO:0007275)|piRNA metabolic process (GO:0034587)|spermatogenesis (GO:0007283)	nucleus (GO:0005634)|piP-body (GO:0071547)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)	p.L273L(1)		breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(10)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)	33		all_cancers(154;0.109)|Melanoma(154;0.0525)|all_epithelial(191;0.0768)				TCCGCAAACTCTTAAGAACAA	0.373													C|||	1760	0.351438	0.3631	0.3646	5008	,	,		19346	0.3353		0.3688	False		,,,				2504	0.3252				p.L273L		Atlas-SNP	.											TDRD9_ENST00000409874,NS,carcinoma,0,1	TDRD9	175	1	1	Substitution - coding silent(1)	stomach(1)	c.C819T						PASS	.	C		516,868		96,324,272	206.0	176.0	185.0		819	3.3	0.9	14	dbSNP_120	185	1127,2055		198,731,662	no	coding-synonymous	TDRD9	NM_153046.2		294,1055,934	TT,TC,CC		35.418,37.2832,35.9834		273/1383	104436931	1643,2923	692	1591	2283	SO:0001819	synonymous_variant	122402	exon6			CAAACTCTTAAGA	AK093483	CCDS9987.2	14q32.33	2013-01-23	2004-04-01	2004-04-02	ENSG00000156414	ENSG00000156414		"""Tudor domain containing"""	20122	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 75"""	C14orf75			Standard	NM_153046		Approved	DKFZp434N0820, FLJ36164, NET54	uc001yom.4	Q8NDG6	OTTHUMG00000152876	ENST00000409874.4:c.819C>T	14.37:g.104436931C>T		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	64	30	0.46875	NM_153046	A1A4S7|Q6ZU54|Q8N7T3|Q8N827|Q8N9V5|Q96AS9	Silent	SNP	ENST00000409874.4	37	CCDS9987.2																																																																																			C|0.648;T|0.352	0.352	strong		0.373	TDRD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328325.3	NM_153046	
OGFRL1	79627	hgsc.bcm.edu	37	6	72006512	72006512	+	Silent	SNP	T	T	C	rs2273888	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:72006512T>C	ENST00000370435.4	+	6	818	c.684T>C	c.(682-684)caT>caC	p.H228H	RP11-154D6.1_ENST00000586232.1_RNA|RP11-154D6.1_ENST00000586030.1_RNA|RP11-154D6.1_ENST00000587253.1_RNA|RP11-154D6.1_ENST00000588612.1_RNA|RP11-154D6.1_ENST00000423255.1_RNA|RP11-154D6.1_ENST00000591156.1_RNA|RP11-154D6.1_ENST00000432050.1_RNA|RP3-331H24.5_ENST00000602823.1_lincRNA|RP11-154D6.1_ENST00000412751.1_RNA	NM_024576.3	NP_078852.3	Q5TC84	OGRL1_HUMAN	opioid growth factor receptor-like 1	228						membrane (GO:0016020)	receptor activity (GO:0004872)			NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|upper_aerodigestive_tract(1)	13						GATTTCAGCATCTGAATGAGT	0.408													C|||	1081	0.215855	0.323	0.2104	5008	,	,		16017	0.2708		0.1044	False		,,,				2504	0.1329				p.H228H		Atlas-SNP	.											.	OGFRL1	44	.	0			c.T684C						PASS	.	C		1178,3212	639.8+/-397.2	150,878,1167	54.0	60.0	58.0		684	1.6	1.0	6	dbSNP_100	58	873,7719	765.6+/-407.6	51,771,3474	no	coding-synonymous	OGFRL1	NM_024576.3		201,1649,4641	CC,CT,TT		10.1606,26.8337,15.7988		228/452	72006512	2051,10931	2195	4296	6491	SO:0001819	synonymous_variant	79627	exon6			TCAGCATCTGAAT		CCDS34482.1	6q13	2008-02-05			ENSG00000119900	ENSG00000119900			21378	protein-coding gene	gene with protein product							Standard	NM_024576		Approved	dJ331H24.1	uc003pfx.1	Q5TC84	OTTHUMG00000015000	ENST00000370435.4:c.684T>C	6.37:g.72006512T>C		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	114	57	0.5	NM_024576	Q2TAC1|Q8NEQ4|Q9H7B5	Silent	SNP	ENST00000370435.4	37	CCDS34482.1																																																																																			T|0.820;C|0.180	0.180	strong		0.408	OGFRL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041153.2	NM_024576	
TBC1D25	4943	hgsc.bcm.edu	37	X	48418659	48418659	+	Missense_Mutation	SNP	G	G	A	rs235836	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	189	0	0		WXS	Illumina HiSeq	Phase_I	158	157	0.993671	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	
STON1	11037	hgsc.bcm.edu	37	2	48807976	48807976	+	Silent	SNP	T	T	C	rs3828340	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:48807976T>C	ENST00000406226.1	+	3	399	c.204T>C	c.(202-204)gaT>gaC	p.D68D	STON1_ENST00000309835.3_Silent_p.D68D|STON1_ENST00000404752.1_Silent_p.D68D|STON1-GTF2A1L_ENST00000394754.1_Silent_p.D68D|STON1-GTF2A1L_ENST00000309827.2_Silent_p.D68D|STON1-GTF2A1L_ENST00000402114.2_Silent_p.D68D|STON1-GTF2A1L_ENST00000394751.3_Silent_p.D68D|STON1-GTF2A1L_ENST00000405008.1_Silent_p.D68D	NM_001198595.1	NP_001185524.1	Q9Y6Q2	STON1_HUMAN	stonin 1	68					endocytosis (GO:0006897)|intracellular protein transport (GO:0006886)|regulation of endocytosis (GO:0030100)	clathrin adaptor complex (GO:0030131)				NS(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(19)|prostate(3)|skin(2)	37		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			CCATTGTAGATTTTTATTTCA	0.507													C|||	1700	0.339457	0.2791	0.3184	5008	,	,		8441	0.3919		0.326	False		,,,				2504	0.3957				p.D68D		Atlas-SNP	.											.	STON1	100	.	0			c.T204C						PASS	.	C	,,,,	1316,3090	697.2+/-406.2	195,926,1082	123.0	125.0	124.0		204,204,204,204,204	1.0	0.7	2	dbSNP_107	124	2829,5771	675.3+/-403.2	488,1853,1959	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	STON1,STON1-GTF2A1L	NM_001198593.1,NM_001198594.1,NM_001198595.1,NM_006873.3,NM_172311.2	,,,,	683,2779,3041	CC,CT,TT		32.8953,29.8684,31.8699	,,,,	68/1159,68/1136,68/736,68/736,68/1183	48807976	4145,8861	2203	4300	6503	SO:0001819	synonymous_variant	11037	exon3			TGTAGATTTTTAT	AF026169	CCDS1841.1	2p16.3	2008-02-05			ENSG00000243244	ENSG00000243244			17003	protein-coding gene	gene with protein product	"""stoned B homolog 1 (Drosophila)"""	605357				14504226, 10364255	Standard	NM_001198595		Approved	SBLF, stoned-b1		Q9Y6Q2	OTTHUMG00000129169	ENST00000406226.1:c.204T>C	2.37:g.48807976T>C		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	269	64	0.237918	NM_001198595	A8MXJ1|B5MCF5|B7ZL16|Q96JE3|Q9BYX3	Silent	SNP	ENST00000406226.1	37	CCDS1841.1																																																																																			T|0.674;C|0.326	0.326	strong		0.507	STON1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323848.2	NM_006873	
PPL	5493	hgsc.bcm.edu	37	16	4933907	4933907	+	Silent	SNP	T	T	C	rs17137389	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	162	0	0		WXS	Illumina HiSeq	Phase_I	125	84	0.672	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	
IFNAR1	3454	hgsc.bcm.edu	37	21	34715699	34715699	+	Missense_Mutation	SNP	G	G	C	rs2257167	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:34715699G>C	ENST00000270139.3	+	4	654	c.502G>C	c.(502-504)Gtt>Ctt	p.V168L	IFNAR1_ENST00000442357.2_Missense_Mutation_p.V168L|IFNAR1_ENST00000416947.2_Missense_Mutation_p.V99L	NM_000629.2	NP_000620.2	P17181	INAR1_HUMAN	interferon (alpha, beta and omega) receptor 1	168	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.		V -> L (in dbSNP:rs2257167). {ECO:0000269|PubMed:1370833, ECO:0000269|PubMed:2153461, ECO:0000269|Ref.4}.		cell surface receptor signaling pathway (GO:0007166)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|JAK-STAT cascade (GO:0007259)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-1 beta secretion (GO:0050718)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to virus (GO:0009615)|T cell activation (GO:0042110)|type I interferon biosynthetic process (GO:0045351)|type I interferon signaling pathway (GO:0060337)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	type I interferon receptor activity (GO:0004905)			breast(2)|central_nervous_system(1)|cervix(1)|kidney(2)|large_intestine(3)|liver(1)|lung(2)|skin(2)	14					"""""""Interferon Alfa-2a(DB00034)|""""Interferon Alfa-2b(DB00105)|Interferon alfa-n1(DB00011)|Interferon alfa-n3(DB00018)|Interferon alfacon-1(DB00069)|Interferon beta-1a(DB00060)|Interferon beta-1b(DB00068)|Natural alpha interferon(DB05258)|Peginterferon alfa-2a(DB00008)|Peginterferon alfa-2b(DB00022)"""	ATATAGCTTAGTTATCTGGAA	0.338													G|||	1146	0.228834	0.1626	0.2233	5008	,	,		18559	0.377		0.1292	False		,,,				2504	0.272				p.V168L	Esophageal Squamous(73;817 1211 32990 35667 42746)	Atlas-SNP	.											.	IFNAR1	44	.	0			c.G502C	GRCh37	CM035835	IFNAR1	M	rs2257167	PASS	.	G	LEU/VAL	701,3705	291.0+/-281.2	61,579,1563	140.0	149.0	146.0		502	0.8	0.0	21	dbSNP_100	146	1159,7441	237.1+/-269.0	61,1037,3202	yes	missense	IFNAR1	NM_000629.2	32	122,1616,4765	CC,CG,GG		13.4767,15.9101,14.3011	benign	168/558	34715699	1860,11146	2203	4300	6503	SO:0001583	missense	3454	exon4			AGCTTAGTTATCT		CCDS13624.1	21q22.1	2008-05-02			ENSG00000142166	ENSG00000142166		"""Interferons"""	5432	protein-coding gene	gene with protein product		107450		IFNAR		8181059	Standard	NM_000629		Approved	IFRC	uc002yrn.3	P17181	OTTHUMG00000065126	ENST00000270139.3:c.502G>C	21.37:g.34715699G>C	ENSP00000270139:p.Val168Leu	Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	127	43	0.338583	NM_000629	B2R6L9|B4DNT3|D3DSF0|Q53GW9|Q53H11|Q6PKD7|Q7M4L2|Q8WTZ2	Missense_Mutation	SNP	ENST00000270139.3	37	CCDS13624.1	455	0.20833333333333334	71	0.1443089430894309	84	0.23204419889502761	202	0.3531468531468531	98	0.12928759894459102	G	15.93	2.977718	0.53720	0.159101	0.134767	ENSG00000142166	ENST00000416947;ENST00000270139;ENST00000442357	T;T;T	0.28666	1.6;1.6;1.6	5.86	0.838	0.18902	Fibronectin, type III (2);Interferon alpha/beta receptor, beta chain (1);Immunoglobulin-like fold (1);	1.095030	0.06767	N	0.782750	T	0.00012	0.0000	L	0.46741	1.465	0.80722	P	0.0	P	0.41748	0.761	P	0.45474	0.482	T	0.28459	-1.0043	9	0.08381	T	0.77	-3.6636	4.8545	0.13552	0.3252:0.16:0.5148:0.0	rs2257167;rs17875817;rs52830923;rs2257167	168	P17181	INAR1_HUMAN	L	99;168;168	ENSP00000395606:V99L;ENSP00000270139:V168L;ENSP00000407406:V168L	ENSP00000270139:V168L	V	+	1	0	IFNAR1	33637569	0.000000	0.05858	0.000000	0.03702	0.374000	0.29953	0.111000	0.15458	0.360000	0.24265	0.650000	0.86243	GTT	G|0.831;C|0.169	0.169	strong		0.338	IFNAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139823.4		
MUC4	4585	hgsc.bcm.edu	37	3	195505955	195505955	+	Missense_Mutation	SNP	C	C	T	rs55789594	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195505955C>T	ENST00000463781.3	-	2	12955	c.12496G>A	c.(12496-12498)Gct>Act	p.A4166T	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.A4166T	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.A4166_S4181delASSVSTGHGTPLPVTS(2)|p.A4166T(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	0.582													.|||	29	0.00579073	0.0182	0.0014	5008	,	,		10866	0.0		0.001	False		,,,				2504	0.0031				p.A4166T		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	3	Deletion - In frame(2)|Substitution - Missense(1)	stomach(2)|upper_aerodigestive_tract(1)	c.G12496A						scavenged	.						17.0	10.0	12.0					3																	195505955		655	1495	2150	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.12496G>A	3.37:g.195505955C>T	ENSP00000417498:p.Ala4166Thr	Somatic	47	1	0.0212766		WXS	Illumina HiSeq	Phase_I	65	17	0.261538	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	8.223	0.802854	0.16397	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.32515	1.45;1.49	.	.	.	.	.	.	.	.	T	0.14399	0.0348	N	0.08118	0	0.09310	N	1	P	0.52463	0.953	B	0.43386	0.418	T	0.14699	-1.0463	7	.	.	.	.	5.8529	0.18704	0.0:0.9991:0.0:9.0E-4	rs55789594	4038	E7ESK3	.	T	4166	ENSP00000417498:A4166T;ENSP00000420243:A4166T	.	A	-	1	0	MUC4	196990734	0.000000	0.05858	0.017000	0.16124	0.012000	0.07955	-2.219000	0.01218	0.073000	0.16731	0.074000	0.15403	GCT	.	.	weak		0.582	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
ALMS1	7840	hgsc.bcm.edu	37	2	73651967	73651967	+	Missense_Mutation	SNP	C	C	T	rs3813227	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:73651967C>T	ENST00000264448.6	+	5	1285	c.1174C>T	c.(1174-1176)Cgt>Tgt	p.R392C	ALMS1_ENST00000409009.1_Missense_Mutation_p.R350C|ALMS1_ENST00000377715.1_Missense_Mutation_p.R392C	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	392					endosomal transport (GO:0016197)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of stress fiber assembly (GO:0051492)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)				breast(4)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(31)|lung(68)|ovary(4)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	147						TGATGCTGCTCGTTCATATGG	0.358													T|||	1821	0.363618	0.8782	0.3919	5008	,	,		21829	0.0089		0.2266	False		,,,				2504	0.1544				p.R392C		Atlas-SNP	.											.	ALMS1	384	.	0			c.C1174T						PASS	.	T	CYS/ARG	2778,990		1038,702,144	78.0	73.0	75.0		1174	0.2	0.0	2	dbSNP_107	75	1953,6271		220,1513,2379	yes	missense	ALMS1	NM_015120.4	180	1258,2215,2523	TT,TC,CC		23.7476,26.2739,39.4513	benign	392/4168	73651967	4731,7261	1884	4112	5996	SO:0001583	missense	7840	exon5			GCTGCTCGTTCAT	AB002326	CCDS42697.1	2p13.1	2014-09-17			ENSG00000116127	ENSG00000116127			428	protein-coding gene	gene with protein product		606844				9063741	Standard	NM_015120		Approved	KIAA0328	uc002sje.1	Q8TCU4	OTTHUMG00000152812	ENST00000264448.6:c.1174C>T	2.37:g.73651967C>T	ENSP00000264448:p.Arg392Cys	Somatic	283	0	0		WXS	Illumina HiSeq	Phase_I	215	213	0.990698	NM_015120	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Missense_Mutation	SNP	ENST00000264448.6	37	CCDS42697.1	739	0.3383699633699634	427	0.8678861788617886	126	0.34806629834254144	8	0.013986013986013986	178	0.23482849604221637	T	0.187	-1.056607	0.01965	0.737261	0.237476	ENSG00000116127	ENST00000409009;ENST00000264448;ENST00000377715	T;T;T	0.16073	3.26;3.26;2.37	4.17	0.185	0.15096	.	0.550399	0.15361	N	0.266386	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	0.28202	-1.0051	9	0.02654	T	1	.	1.7727	0.03015	0.1619:0.0947:0.335:0.4083	rs3813227;rs17349398;rs17848877;rs52832700;rs58256220;rs3813227	350;392	B8ZZJ3;Q8TCU4	.;ALMS1_HUMAN	C	350;392;392	ENSP00000386627:R350C;ENSP00000264448:R392C;ENSP00000366944:R392C	ENSP00000264448:R392C	R	+	1	0	ALMS1	73505475	0.383000	0.25156	0.009000	0.14445	0.009000	0.06853	0.260000	0.18424	-0.200000	0.10300	-0.381000	0.06696	CGT	C|0.661;T|0.339	0.339	strong		0.358	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120	
CNTN5	53942	hgsc.bcm.edu	37	11	99690450	99690450	+	Silent	SNP	T	T	C	rs12222337	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:99690450T>C	ENST00000524871.1	+	4	521	c.231T>C	c.(229-231)taT>taC	p.Y77Y	CNTN5_ENST00000418526.2_Intron|CNTN5_ENST00000528682.1_Silent_p.Y77Y|CNTN5_ENST00000279463.3_Silent_p.Y77Y|CNTN5_ENST00000527185.1_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	129	0	0		WXS	Illumina HiSeq	Phase_I	109	21	0.192661	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	
FAM170B	170370	hgsc.bcm.edu	37	10	50341954	50341954	+	Missense_Mutation	SNP	A	A	G	rs34110351	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:50341954A>G	ENST00000311787.5	-	1	99	c.10T>C	c.(10-12)Tac>Cac	p.Y4H	FAM170B-AS1_ENST00000443389.1_RNA|FAM170B-AS1_ENST00000435809.1_RNA|FAM170B-AS1_ENST00000442525.1_RNA	NM_001164484.1	NP_001157956.1	A6NMN3	F170B_HUMAN	family with sequence similarity 170, member B	4										central_nervous_system(1)|endometrium(1)|skin(1)	3						TCTGTGAAGTAGCATTTCATG	0.577													G|||	1228	0.245208	0.118	0.3444	5008	,	,		21931	0.3075		0.2684	False		,,,				2504	0.2587				p.Y4H		Atlas-SNP	.											.	FAM170B	20	.	0			c.T10C						PASS	.	G	HIS/TYR	223,1161		20,183,489	177.0	149.0	157.0		10	2.4	0.0	10	dbSNP_126	157	924,2258		149,626,816	yes	missense	FAM170B	NM_001164484.1	83	169,809,1305	GG,GA,AA		29.0383,16.1127,25.1205	benign	4/284	50341954	1147,3419	692	1591	2283	SO:0001583	missense	170370	exon1			TGAAGTAGCATTT		CCDS53536.1	10q11.23	2008-11-06	2008-06-12	2008-06-12	ENSG00000172538	ENSG00000172538			19736	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 73"""	C10orf73			Standard	NM_001164484		Approved	Em:AC084727.4	uc001jhj.3	A6NMN3	OTTHUMG00000018187	ENST00000311787.5:c.10T>C	10.37:g.50341954A>G	ENSP00000308292:p.Tyr4His	Somatic	202	1	0.00495049		WXS	Illumina HiSeq	Phase_I	173	86	0.49711	NM_001164484	Q86WY6|Q8N6K8	Missense_Mutation	SNP	ENST00000311787.5	37	CCDS53536.1	526	0.24084249084249085	61	0.12398373983739837	117	0.32320441988950277	147	0.256993006993007	201	0.26517150395778366	G	0.014	-1.574567	0.00887	0.161127	0.290383	ENSG00000172538	ENST00000311787	T	0.26067	1.76	4.29	2.42	0.29668	.	1.076690	0.07150	N	0.848962	T	0.00012	0.0000	N	0.00347	-1.61	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.44143	-0.9347	9	0.02654	T	1	-13.5173	6.5541	0.22450	0.3069:0.0:0.6931:0.0	rs34110351	4	A6NMN3	F170B_HUMAN	H	4	ENSP00000308292:Y4H	ENSP00000308292:Y4H	Y	-	1	0	FAM170B	50011960	0.001000	0.12720	0.000000	0.03702	0.001000	0.01503	0.772000	0.26647	0.201000	0.20466	-1.551000	0.00897	TAC	A|0.759;G|0.241	0.241	strong		0.577	FAM170B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047974.1	XM_096317	
ZFP69B	65243	hgsc.bcm.edu	37	1	40923019	40923019	+	Missense_Mutation	SNP	G	G	A	rs2272994	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:40923019G>A	ENST00000411995.2	+	5	719	c.344G>A	c.(343-345)tGt>tAt	p.C115Y	ZFP69B_ENST00000484445.1_Missense_Mutation_p.M86I|ZFP69B_ENST00000361584.3_Missense_Mutation_p.C13Y	NM_023070.2	NP_075558.2	Q9UJL9	ZF69B_HUMAN	ZFP69 zinc finger protein B	115	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.		C -> Y (in dbSNP:rs2272994).		transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)										TAAGCAGGATGTCAGCTTTCC	0.443													G|||	1110	0.221645	0.0212	0.3516	5008	,	,		20074	0.2986		0.2366	False		,,,				2504	0.3057				p.C115Y		Atlas-SNP	.											.	.	.	.	0			c.G344A						PASS	.	G	TYR/CYS	278,4128		6,266,1931	105.0	95.0	98.0		344	1.0	1.0	1	dbSNP_100	98	1873,6727		221,1431,2648	yes	missense	ZNF643	NM_023070.2	194	227,1697,4579	AA,AG,GG		21.7791,6.3096,16.5385	benign	115/535	40923019	2151,10855	2203	4300	6503	SO:0001583	missense	65243	exon4			CAGGATGTCAGCT	BC017498	CCDS452.1, CCDS452.2	1p34.2	2013-01-09	2012-11-27	2012-11-27	ENSG00000187801	ENSG00000187801		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	28053	protein-coding gene	gene with protein product			"""zinc finger protein 643"""	ZNF643			Standard	NM_023070		Approved	ZKSCAN23B, FLJ34293, ZSCAN54B	uc001cfn.2	Q9UJL9	OTTHUMG00000007302	ENST00000411995.2:c.344G>A	1.37:g.40923019G>A	ENSP00000399664:p.Cys115Tyr	Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	110	39	0.354545	NM_023070	Q5QPL4	Missense_Mutation	SNP	ENST00000411995.2	37	CCDS452.2	484|484	0.2216117216117216|0.2216117216117216	13|13	0.026422764227642278|0.026422764227642278	116|116	0.32044198895027626|0.32044198895027626	181|181	0.31643356643356646|0.31643356643356646	174|174	0.22955145118733508|0.22955145118733508	.|.	11.27|11.27	1.588414|1.588414	0.28357|0.28357	0.063096|0.063096	0.217791|0.217791	ENSG00000187801|ENSG00000187801	ENST00000411995;ENST00000361584|ENST00000431552;ENST00000484445	T;T|.	0.00730|.	5.77;5.77|.	3.4|3.4	0.988|0.988	0.19796|0.19796	Krueppel-associated box (3);|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.03881|0.03881	-0.34|-0.34	0.50813|0.50813	P|P	1.0399999999999299E-4|1.0399999999999299E-4	B|.	0.02656|.	0.0|.	B|.	0.01281|.	0.0|.	T|T	0.40608|0.40608	-0.9554|-0.9554	8|5	0.31617|0.66056	T|D	0.26|0.02	.|.	4.1937|4.1937	0.10433|0.10433	0.7155:0.0:0.1063:0.1782|0.7155:0.0:0.1063:0.1782	rs2272994;rs52813536;rs58074442;rs2272994|rs2272994;rs52813536;rs58074442;rs2272994	115|.	Q9UJL9|.	ZN643_HUMAN|.	Y|I	115;13|46;86	ENSP00000399664:C115Y;ENSP00000354547:C13Y|.	ENSP00000354547:C13Y|ENSP00000400051:M46I	C|M	+|+	2|3	0|0	ZNF643|ZNF643	40695606|40695606	0.002000|0.002000	0.14202|0.14202	0.987000|0.987000	0.45799|0.45799	0.679000|0.679000	0.39708|0.39708	-0.085000|-0.085000	0.11250|0.11250	0.174000|0.174000	0.19809|0.19809	-0.294000|-0.294000	0.09567|0.09567	TGT|ATG	G|0.815;A|0.185	0.185	strong		0.443	ZFP69B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019078.2	NM_023070	
OR1A2	26189	hgsc.bcm.edu	37	17	3101691	3101691	+	Missense_Mutation	SNP	G	G	T	rs12150427	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	117	0	0		WXS	Illumina HiSeq	Phase_I	89	89	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	
RIMS2	9699	hgsc.bcm.edu	37	8	105263979	105263979	+	Silent	SNP	C	C	T	rs10461	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:105263979C>T	ENST00000436393.2	+	28	4276	c.4035C>T	c.(4033-4035)gcC>gcT	p.A1345A	RIMS2_ENST00000507740.1_Silent_p.A1141A|RIMS2_ENST00000262231.10_Silent_p.A1166A|RIMS2_ENST00000339750.2_Silent_p.A263A|RIMS2_ENST00000406091.3_Silent_p.A1327A			Q9UQ26	RIMS2_HUMAN	regulating synaptic membrane exocytosis 2	1389	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|cAMP-mediated signaling (GO:0019933)|insulin secretion (GO:0030073)|intracellular protein transport (GO:0006886)|positive regulation of gene expression (GO:0010628)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)|regulation of exocytosis (GO:0017157)	cell junction (GO:0030054)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)	metal ion binding (GO:0046872)			NS(1)|breast(4)|central_nervous_system(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(22)|liver(1)|lung(68)|ovary(6)|pancreas(2)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(10)|urinary_tract(1)	144			OV - Ovarian serous cystadenocarcinoma(57;7.7e-07)|STAD - Stomach adenocarcinoma(118;0.229)			CAACCTTGGCCCCTCTGACAA	0.448										HNSCC(12;0.0054)			C|||	2394	0.478035	0.5227	0.536	5008	,	,		16632	0.6498		0.3529	False		,,,				2504	0.3282				p.A1327A		Atlas-SNP	.											.	RIMS2	1357	.	0			c.C3981T						PASS	.	C	,	1859,1877		476,907,485	149.0	149.0	149.0		3981,3423	0.4	1.0	8	dbSNP_52	149	2858,5328		525,1808,1760	no	coding-synonymous,coding-synonymous	RIMS2	NM_001100117.2,NM_014677.4	,	1001,2715,2245	TT,TC,CC		34.9133,49.7591,39.5655	,	1327/1350,1141/1164	105263979	4717,7205	1868	4093	5961	SO:0001819	synonymous_variant	9699	exon24			CTTGGCCCCTCTG	AB018294	CCDS43761.1, CCDS64948.1, CCDS64949.1	8q22.3	2008-08-08	2002-06-12	2002-06-14					17283	protein-coding gene	gene with protein product		606630	"""RAB3 interacting protein 3"""	RAB3IP3		9872452, 12578829	Standard	NM_014677		Approved	KIAA0751, RIM2, OBOE	uc003ylp.3	Q9UQ26		ENST00000436393.2:c.4035C>T	8.37:g.105263979C>T		Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	143	42	0.293706	NM_001100117	B3KX91|F8WD47|O43413|Q86XL9|Q8IWV9|Q8IWW1	Silent	SNP	ENST00000436393.2	37																																																																																				C|0.553;T|0.447	0.447	strong		0.448	RIMS2-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000367217.1	NM_001100117	
TTN	7273	hgsc.bcm.edu	37	2	179393691	179393691	+	Missense_Mutation	SNP	G	G	A	rs55842557	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:179393691G>A	ENST00000591111.1	-	310	102088	c.101864C>T	c.(101863-101865)aCa>aTa	p.T33955I	TTN-AS1_ENST00000585358.1_RNA|TTN-AS1_ENST00000588804.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.T26656I|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000589391.1_RNA|TTN-AS1_ENST00000588244.1_RNA|TTN-AS1_ENST00000585487.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000589355.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.T33028I|TTN-AS1_ENST00000592182.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000588716.1_RNA|TTN-AS1_ENST00000442329.2_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.T26531I|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592836.1_RNA|TTN-AS1_ENST00000588257.1_RNA|TTN-AS1_ENST00000589842.1_RNA|TTN-AS1_ENST00000592161.1_RNA|TTN-AS1_ENST00000431259.2_RNA|TTN-AS1_ENST00000589434.1_RNA|TTN-AS1_ENST00000587576.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.T35596I|TTN-AS1_ENST00000591867.1_RNA|TTN-AS1_ENST00000604571.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000450692.2_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.T26723I|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000591466.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000590040.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000587568.1_RNA|TTN-AS1_ENST00000587944.1_RNA|TTN-AS1_ENST00000585625.1_RNA			Q8WZ42	TITIN_HUMAN	titin	33955			T -> I. {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)			TGCCTGTGATGTTTTAGTGAT	0.398													G|||	19	0.00379393	0.0	0.0043	5008	,	,		22209	0.0		0.0159	False		,,,				2504	0.0				p.T35596I		Atlas-SNP	.											.	TTN	18412	.	0			c.C106787T						PASS	.	G	ILE/THR,ILE/THR,ILE/THR,ILE/THR	3,3779		0,3,1888	147.0	135.0	139.0		80168,79967,99083,79592	4.7	1.0	2	dbSNP_129	139	56,8158		1,54,4052	yes	missense,missense,missense,missense	TTN	NM_133437.3,NM_133432.3,NM_133378.4,NM_003319.4	89,89,89,89	1,57,5940	AA,AG,GG		0.6818,0.0793,0.4918	benign,benign,benign,benign	26723/27119,26656/27052,33028/33424,26531/26927	179393691	59,11937	1891	4107	5998	SO:0001583	missense	7273	exon360			TGTGATGTTTTAG	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.101864C>T	2.37:g.179393691G>A	ENSP00000465570:p.Thr33955Ile	Somatic	229	0	0		WXS	Illumina HiSeq	Phase_I	202	80	0.39604	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		17	0.007783882783882784	0	0.0	3	0.008287292817679558	0	0.0	14	0.018469656992084433	G	14.74	2.624609	0.46840	7.93E-4	0.006818	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.62941	-0.01;0.25;0.23;0.22	5.69	4.74	0.60224	Ribonuclease H-like (1);	.	.	.	.	T	0.32763	0.0840	N	0.24115	0.695	0.25561	N	0.986992	B;B;B;B;B	0.29805	0.026;0.026;0.026;0.026;0.257	B;B;B;B;B	0.26310	0.029;0.029;0.029;0.029;0.068	T	0.42565	-0.9444	9	0.87932	D	0	.	13.2479	0.60033	0.0:0.0:0.7689:0.2311	rs55842557	26531;26656;26723;33955;33028	D3DPF9;E7EQE6;E7ET18;Q8WZ42;A6NKB1	.;.;.;TITIN_HUMAN;.	I	33028;26531;26723;26656;26528	ENSP00000343764:T33028I;ENSP00000434586:T26531I;ENSP00000340554:T26723I;ENSP00000352154:T26656I	ENSP00000340554:T26723I	T	-	2	0	TTN	179101937	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	3.452000	0.52971	2.677000	0.91161	0.655000	0.94253	ACA	G|0.993;A|0.007	0.007	strong		0.398	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
NOM1	64434	hgsc.bcm.edu	37	7	156762224	156762224	+	Splice_Site	SNP	G	G	C	rs2302443	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:156762224G>C	ENST00000275820.3	+	11	2425	c.2410G>C	c.(2410-2412)Gta>Cta	p.V804L		NM_138400.1	NP_612409.1	Q5C9Z4	NOM1_HUMAN	nucleolar protein with MIF4G domain 1	804			V -> L (in dbSNP:rs2302443).			nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(5)|kidney(4)|large_intestine(9)|lung(7)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	31	Ovarian(565;0.218)	all_hematologic(28;0.0749)	OV - Ovarian serous cystadenocarcinoma(82;0.00301)	UCEC - Uterine corpus endometrioid carcinoma (81;0.169)		CCTTTCCAGAGTATCTGACAA	0.488													G|||	2290	0.457268	0.469	0.5274	5008	,	,		17390	0.2778		0.5706	False		,,,				2504	0.4601				p.V804L		Atlas-SNP	.											.	NOM1	73	.	0			c.G2410C						PASS	.	G	LEU/VAL	2095,2311	573.3+/-383.5	498,1099,606	87.0	88.0	87.0		2410	4.5	1.0	7	dbSNP_100	87	4903,3697	620.0+/-397.0	1387,2129,784	yes	missense-near-splice	NOM1	NM_138400.1	32	1885,3228,1390	CC,CG,GG		42.9884,47.5488,46.1941	benign	804/861	156762224	6998,6008	2203	4300	6503	SO:0001630	splice_region_variant	64434	exon11			TCCAGAGTATCTG	AF107455	CCDS34787.1	7q36.3	2014-06-13	2005-03-30	2005-03-30	ENSG00000146909	ENSG00000146909			13244	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 113"""	611269	"""chromosome 7 open reading frame 3"""	C7orf3		10329000	Standard	XM_005249560		Approved	SGD1, PPP1R113	uc003wmy.3	Q5C9Z4	OTTHUMG00000152639	ENST00000275820.3:c.2409-1G>C	7.37:g.156762224G>C		Somatic	22	0	0		WXS	Illumina HiSeq	Phase_I	15	15	1	NM_138400	Q96I08	Missense_Mutation	SNP	ENST00000275820.3	37	CCDS34787.1	1012	0.4633699633699634	240	0.4878048780487805	198	0.5469613259668509	154	0.2692307692307692	420	0.554089709762533	G	10.23	1.294211	0.23564	0.475488	0.570116	ENSG00000146909	ENST00000275820	T	0.12672	2.66	5.41	4.52	0.55395	.	0.196334	0.45867	D	0.000339	T	0.00012	0.0000	L	0.45051	1.395	0.22693	P	0.99884375	B	0.18013	0.025	B	0.19666	0.026	T	0.47328	-0.9126	9	0.09084	T	0.74	-30.1043	3.8301	0.08870	0.135:0.1401:0.5802:0.1447	rs2302443;rs56650505;rs58189922;rs2302443	804	Q5C9Z4	NOM1_HUMAN	L	804	ENSP00000275820:V804L	ENSP00000275820:V804L	V	+	1	0	NOM1	156454985	1.000000	0.71417	0.958000	0.39756	0.289000	0.27227	1.076000	0.30729	2.532000	0.85374	0.467000	0.42956	GTA	G|0.498;C|0.502	0.502	strong		0.488	NOM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327098.1	NM_138400	Missense_Mutation
CACNA1S	779	hgsc.bcm.edu	37	1	201047062	201047062	+	Silent	SNP	G	G	A	rs4915476	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:201047062G>A	ENST00000362061.3	-	11	1790	c.1564C>T	c.(1564-1566)Ctg>Ttg	p.L522L	CACNA1S_ENST00000367338.3_Silent_p.L522L	NM_000069.2	NP_000060.2	Q13698	CAC1S_HUMAN	calcium channel, voltage-dependent, L type, alpha 1S subunit	522					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)	GAGATGCCCAGGGGTGTCATG	0.622													G|||	956	0.190895	0.292	0.2695	5008	,	,		18414	0.0367		0.2425	False		,,,				2504	0.1043				p.L522L		Atlas-SNP	.											.	CACNA1S	249	.	0			c.C1564T	GRCh37	CM023570	CACNA1S	M	rs4915476	PASS	.	G		1172,3234	410.9+/-335.5	158,856,1189	77.0	61.0	66.0		1564	4.7	0.9	1	dbSNP_111	66	1915,6685	337.8+/-322.5	202,1511,2587	no	coding-synonymous	CACNA1S	NM_000069.2		360,2367,3776	AA,AG,GG		22.2674,26.6001,23.7352		522/1874	201047062	3087,9919	2203	4300	6503	SO:0001819	synonymous_variant	779	exon11			TGCCCAGGGGTGT	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.1564C>T	1.37:g.201047062G>A		Somatic	203	1	0.00492611		WXS	Illumina HiSeq	Phase_I	165	161	0.975758	NM_000069	A4IF51|B1ALM2|Q12896|Q13934	Silent	SNP	ENST00000362061.3	37	CCDS1407.1																																																																																			G|0.776;A|0.224	0.224	strong		0.622	CACNA1S-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087049.1	NM_000069	
ELFN2	114794	hgsc.bcm.edu	37	22	37771158	37771158	+	Silent	SNP	G	G	A	rs2071857	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:37771158G>A	ENST00000402918.2	-	3	1202	c.417C>T	c.(415-417)atC>atT	p.I139I	RP1-63G5.5_ENST00000430883.1_RNA|ELFN2_ENST00000435824.1_5'Flank|RP1-63G5.8_ENST00000609322.1_RNA	NM_052906.3	NP_443138.2	Q5R3F8	PPR29_HUMAN	extracellular leucine-rich repeat and fibronectin type III domain containing 2	139					negative regulation of phosphatase activity (GO:0010923)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	phosphatase binding (GO:0019902)|protein phosphatase inhibitor activity (GO:0004864)			NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(13)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	35	Melanoma(58;0.0574)					TCACCACCTCGATGAGGTTGT	0.632													G|||	2092	0.417732	0.4289	0.6556	5008	,	,		17766	0.3522		0.4274	False		,,,				2504	0.2914				p.I139I		Atlas-SNP	.											.	ELFN2	89	.	0			c.C417T						PASS	.	G		2070,2336	569.8+/-382.7	473,1124,606	94.0	87.0	89.0		417	-0.4	1.0	22	dbSNP_96	89	3736,4864	532.6+/-382.2	812,2112,1376	no	coding-synonymous	ELFN2	NM_052906.3		1285,3236,1982	AA,AG,GG		43.4419,46.9814,44.6409		139/821	37771158	5806,7200	2203	4300	6503	SO:0001819	synonymous_variant	114794	exon3			CACCTCGATGAGG	BC041596	CCDS33642.1	22q13.1	2013-02-11	2011-10-27	2011-10-27	ENSG00000166897	ENSG00000166897		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Fibronectin type III domain containing"""	29396	protein-coding gene	gene with protein product			"""leucine rich repeat containing 62"", ""extracellular leucine-rich repeat and fibronectin type III containing 2"", ""extracellular leucine-rich repeat and fibronectin type III domain containing 2"", ""protein phosphatase 1, regulatory subunit 29"""	LRRC62, PPP1R29		17868438	Standard	XR_244427		Approved	dJ63G5.3, KIAA1904	uc003asq.4	Q5R3F8	OTTHUMG00000150558	ENST00000402918.2:c.417C>T	22.37:g.37771158G>A		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	93	46	0.494624	NM_052906	Q96PY3	Silent	SNP	ENST00000402918.2	37	CCDS33642.1																																																																																			G|0.569;A|0.431	0.431	strong		0.632	ELFN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318900.2	NM_052906	
FAM193A	8603	hgsc.bcm.edu	37	4	2702115	2702115	+	Missense_Mutation	SNP	A	A	G	rs17681870	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:2702115A>G	ENST00000324666.5	+	17	3694	c.3343A>G	c.(3343-3345)Atc>Gtc	p.I1115V	FAM193A_ENST00000545951.1_Missense_Mutation_p.I1115V|FAM193A_ENST00000382839.3_Missense_Mutation_p.I1115V|FAM193A_ENST00000502458.1_Missense_Mutation_p.I1137V|FAM193A_ENST00000505311.1_Missense_Mutation_p.I1115V	NM_001256666.1	NP_001243595.1	P78312	F193A_HUMAN	family with sequence similarity 193, member A	1115			I -> V (in dbSNP:rs17681870). {ECO:0000269|PubMed:15489334}.							NS(2)|breast(1)|endometrium(4)|kidney(4)|large_intestine(3)|lung(12)|ovary(4)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(3)	40						GCTGAACCACATCAAGGACGA	0.498													A|||	195	0.0389377	0.0212	0.0389	5008	,	,		18637	0.0109		0.0378	False		,,,				2504	0.093				p.I1137V		Atlas-SNP	.											.	FAM193A	103	.	0			c.A3409G						PASS	.	A	VAL/ILE	74,4332	66.4+/-103.9	0,74,2129	70.0	65.0	67.0		3343	-0.8	0.0	4	dbSNP_123	67	344,8256	118.1+/-177.6	6,332,3962	yes	missense	FAM193A	NM_003704.3	29	6,406,6091	GG,GA,AA		4.0,1.6795,3.2139	benign	1115/1225	2702115	418,12588	2203	4300	6503	SO:0001583	missense	8603	exon18			AACCACATCAAGG	AB000459	CCDS33943.1, CCDS58874.1, CCDS58875.1, CCDS58876.1	4p16.3	2009-09-04	2009-09-04	2009-09-04					16822	protein-coding gene	gene with protein product			"""chromosome 4 open reading frame 8"""	C4orf8		9734812	Standard	NR_046335		Approved	RES4-22	uc010ick.3	P78312		ENST00000324666.5:c.3343A>G	4.37:g.2702115A>G	ENSP00000324587:p.Ile1115Val	Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	97	39	0.402062	NM_001256667	B7ZM85|B9EGR0|E9PFA1|O43607|P78311|P78313|Q9UEG8	Missense_Mutation	SNP	ENST00000324666.5	37	CCDS58875.1	62	0.028388278388278388	7	0.014227642276422764	18	0.049723756906077346	8	0.013986013986013986	29	0.03825857519788918	A	0.022	-1.410158	0.01145	0.016795	0.04	ENSG00000125386	ENST00000382839;ENST00000324666;ENST00000545951;ENST00000502458;ENST00000513350	T;T;T;T;T	0.40756	1.02;1.02;1.02;1.02;1.64	5.7	-0.831	0.10789	.	0.829063	0.11225	N	0.586236	T	0.02767	0.0083	N	0.02802	-0.49	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	0.15009	-1.0452	10	0.23302	T	0.38	-7.9755	12.0287	0.53386	0.4603:0.0:0.5397:0.0	rs17681870;rs56454507;rs61102381;rs17681870	1115;1137;1115;1115	B9EGR0;E9PFA1;P78312;P78312-2	.;.;F193A_HUMAN;.	V	1115;1115;1115;1137;969	ENSP00000372290:I1115V;ENSP00000324587:I1115V;ENSP00000443617:I1115V;ENSP00000427505:I1137V;ENSP00000427260:I969V	ENSP00000324587:I1115V	I	+	1	0	FAM193A	2671913	0.000000	0.05858	0.009000	0.14445	0.760000	0.43138	-0.152000	0.10159	-0.561000	0.06094	-1.032000	0.02404	ATC	A|0.965;G|0.035	0.035	strong		0.498	FAM193A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000360903.1	NM_003704	
TUBB4A	10382	hgsc.bcm.edu	37	19	6495199	6495199	+	Silent	SNP	C	C	T	rs369467354		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:6495199C>T	ENST00000264071.2	-	4	1682	c.1311G>A	c.(1309-1311)gaG>gaA	p.E437E	CTD-2396E7.9_ENST00000599292.1_RNA|TUBB4A_ENST00000540257.1_Silent_p.E437E|CTD-2396E7.10_ENST00000596027.1_RNA			P04350	TBB4A_HUMAN	tubulin, beta 4A class IVa	437					'de novo' posttranslational protein folding (GO:0051084)|cellular protein metabolic process (GO:0044267)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule-based process (GO:0007017)|mitotic cell cycle (GO:0000278)|protein folding (GO:0006457)|protein polymerization (GO:0051258)	cilium (GO:0005929)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|internode region of axon (GO:0033269)|microtubule (GO:0005874)|myelin sheath (GO:0043209)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)										CCTCCGCCTCCTCCTCGAACT	0.622																																					p.E437E		Atlas-SNP	.											.	.	.	.	0			c.G1311A						PASS	.	C		0,4406		0,0,2203	70.0	64.0	66.0		1311	2.9	1.0	19		66	6,8594	4.3+/-15.6	0,6,4294	no	coding-synonymous	TUBB4	NM_006087.2		0,6,6497	TT,TC,CC		0.0698,0.0,0.0461		437/445	6495199	6,13000	2203	4300	6503	SO:0001819	synonymous_variant	10382	exon4			CGCCTCCTCCTCG	AK075307	CCDS12168.1	19p13.3	2014-02-05	2011-10-11	2011-10-10	ENSG00000104833	ENSG00000104833		"""Tubulins"""	20774	protein-coding gene	gene with protein product	"""class IVa beta-tubulin"""	602662	"""tubulin, beta 4"", ""tubulin, beta 4 class IVa"", ""dystonia 4, torsion (autosomal dominant)"""	TUBB4, DYT4		6865944, 6462917, 23595291	Standard	NM_001289123		Approved	beta-5	uc002mfg.1	P04350		ENST00000264071.2:c.1311G>A	19.37:g.6495199C>T		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	49	18	0.367347	NM_006087	B3KQP4|Q969E5	Silent	SNP	ENST00000264071.2	37	CCDS12168.1																																																																																			.	.	weak		0.622	TUBB4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457841.1	NM_006087	
OR5H1	26341	hgsc.bcm.edu	37	3	97851645	97851645	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	450	1	0.00222222		WXS	Illumina HiSeq	Phase_I	369	9	0.0243902	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	
FAT4	79633	hgsc.bcm.edu	37	4	126336348	126336348	+	Missense_Mutation	SNP	C	C	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:126336348C>G	ENST00000394329.3	+	5	6243	c.6230C>G	c.(6229-6231)cCa>cGa	p.P2077R	FAT4_ENST00000335110.5_Missense_Mutation_p.P375R	NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	2077	Cadherin 20. {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.P2077>?(2)		NS(6)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(93)|liver(3)|lung(120)|ovary(9)|pancreas(2)|prostate(21)|skin(31)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(6)	355						GCAACTGACCCAGATAGTGGC	0.418																																					p.P2077R		Atlas-SNP	.											.	FAT4	1752	.	2	Complex(2)	large_intestine(2)	c.C6230G						PASS	.						137.0	140.0	139.0					4																	126336348		2203	4300	6503	SO:0001583	missense	79633	exon5			CTGACCCAGATAG	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.6230C>G	4.37:g.126336348C>G	ENSP00000377862:p.Pro2077Arg	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	107	7	0.0654206	NM_024582	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Missense_Mutation	SNP	ENST00000394329.3	37	CCDS3732.3	.	.	.	.	.	.	.	.	.	.	C	2.239	-0.374320	0.05034	.	.	ENSG00000196159	ENST00000394329;ENST00000335110	T;T	0.51574	0.7;0.7	5.0	4.11	0.48088	Cadherin (4);Cadherin-like (1);	0.000000	0.34314	U	0.004066	T	0.32763	0.0840	N	0.17379	0.485	0.42532	D	0.99304	B;B	0.09022	0.002;0.001	B;B	0.12837	0.008;0.004	T	0.10109	-1.0644	10	0.20519	T	0.43	.	16.9703	0.86297	0.0:0.8614:0.1386:0.0	.	375;2077	Q6V0I7-2;Q6V0I7	.;FAT4_HUMAN	R	2077;375	ENSP00000377862:P2077R;ENSP00000335169:P375R	ENSP00000335169:P375R	P	+	2	0	FAT4	126555798	1.000000	0.71417	1.000000	0.80357	0.906000	0.53458	5.908000	0.69916	2.308000	0.77769	0.557000	0.71058	CCA	.	.	none		0.418	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582	
SMO	6608	hgsc.bcm.edu	37	7	128843277	128843277	+	Silent	SNP	C	C	T	rs45571737	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:128843277C>T	ENST00000249373.3	+	2	664	c.384C>T	c.(382-384)gcC>gcT	p.A128A		NM_005631.4	NP_005622.1	Q99835	SMO_HUMAN	smoothened, frizzled class receptor	128	FZ. {ECO:0000255|PROSITE- ProRule:PRU00090}.				adenohypophysis development (GO:0021984)|anterior/posterior pattern specification (GO:0009952)|atrial septum morphogenesis (GO:0060413)|axon extension involved in axon guidance (GO:0048846)|canonical Wnt signaling pathway (GO:0060070)|cardioblast differentiation (GO:0010002)|cell fate specification (GO:0001708)|cellular response to cholesterol (GO:0071397)|central nervous system neuron differentiation (GO:0021953)|cerebellar cortex morphogenesis (GO:0021696)|ciliary receptor clustering involved in smoothened signaling pathway (GO:0060830)|detection of cell density by contact stimulus involved in contact inhibition (GO:0060248)|determination of left/right asymmetry in lateral mesoderm (GO:0003140)|determination of left/right symmetry (GO:0007368)|dorsal/ventral neural tube patterning (GO:0021904)|embryonic camera-type eye development (GO:0031076)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic neurocranium morphogenesis (GO:0048702)|embryonic viscerocranium morphogenesis (GO:0048703)|epithelial-mesenchymal cell signaling (GO:0060684)|exocrine pancreas development (GO:0031017)|facial nerve development (GO:0021561)|floor plate formation (GO:0021508)|forebrain morphogenesis (GO:0048853)|gonad development (GO:0008406)|hair follicle morphogenesis (GO:0031069)|heart looping (GO:0001947)|heart morphogenesis (GO:0003007)|in utero embryonic development (GO:0001701)|mammary gland epithelial cell differentiation (GO:0060644)|mesenchymal to epithelial transition involved in metanephric renal vesicle formation (GO:0072285)|midgut development (GO:0007494)|multicellular organism growth (GO:0035264)|muscle cell fate commitment (GO:0042693)|myoblast migration (GO:0051451)|negative regulation of apoptotic process (GO:0043066)|negative regulation of DNA binding (GO:0043392)|negative regulation of epithelial cell differentiation (GO:0030857)|negative regulation of gene expression (GO:0010629)|negative regulation of hair follicle development (GO:0051799)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural crest cell migration (GO:0001755)|neuron fate commitment (GO:0048663)|neuron projection regeneration (GO:0031102)|odontogenesis of dentin-containing tooth (GO:0042475)|osteoblast differentiation (GO:0001649)|otolith morphogenesis (GO:0032474)|pancreas morphogenesis (GO:0061113)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of gene expression (GO:0010628)|positive regulation of hh target transcription factor activity (GO:0007228)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of smoothened signaling pathway (GO:0045880)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein localization to nucleus (GO:0034504)|protein stabilization (GO:0050821)|regulation of heart morphogenesis (GO:2000826)|regulation of stem cell maintenance (GO:2000036)|renal system development (GO:0072001)|semicircular canal morphogenesis (GO:0048752)|skeletal muscle fiber development (GO:0048741)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in regulation of cerebellar granule cell precursor cell proliferation (GO:0021938)|smoothened signaling pathway involved in ventral spinal cord patterning (GO:0021910)|somite development (GO:0061053)|spermatogenesis (GO:0007283)|thalamus development (GO:0021794)|type B pancreatic cell development (GO:0003323)|vasculogenesis (GO:0001570)|ventral midline determination (GO:0007371)	ciliary membrane (GO:0060170)|cilium (GO:0005929)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|primary cilium (GO:0072372)	drug binding (GO:0008144)|G-protein coupled receptor activity (GO:0004930)|patched binding (GO:0005113)|PDZ domain binding (GO:0030165)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			biliary_tract(1)|central_nervous_system(5)|endometrium(1)|kidney(4)|large_intestine(14)|liver(1)|lung(11)|pancreas(2)|prostate(1)|skin(20)|upper_aerodigestive_tract(3)|urinary_tract(1)	64					Fluocinonide(DB01047)|Vismodegib(DB08828)	TGCTGTGTGCCGTATACATGC	0.667			Mis		skin basal cell								C|||	20	0.00399361	0.0	0.0058	5008	,	,		17322	0.0		0.0119	False		,,,				2504	0.0041				p.A128A		Atlas-SNP	.		Dom	yes		7	7q31-q32	6608	smoothened homolog (Drosophila)		E	.	SMO	145	.	0			c.C384T						PASS	.	C		5,4381		0,5,2188	26.0	22.0	23.0		384	-8.7	0.7	7	dbSNP_127	23	110,8456		0,110,4173	no	coding-synonymous	SMO	NM_005631.4		0,115,6361	TT,TC,CC		1.2841,0.114,0.8879		128/788	128843277	115,12837	2193	4283	6476	SO:0001819	synonymous_variant	6608	exon2			GTGTGCCGTATAC	U84401	CCDS5811.1	7q32.1	2014-01-29	2014-01-29	2003-01-17	ENSG00000128602	ENSG00000128602		"""GPCR / Class F : Frizzled receptors"""	11119	protein-coding gene	gene with protein product	"""frizzled family member 11"""	601500	"""smoothened (Drosophila) homolog"", ""smoothened homolog (Drosophila)"", ""smoothened, seven transmembrane spanning receptor"", ""smoothened, frizzled family receptor"""	SMOH		9628830	Standard	NM_005631		Approved	FZD11	uc003vor.3	Q99835	OTTHUMG00000158421	ENST00000249373.3:c.384C>T	7.37:g.128843277C>T		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	103	40	0.38835	NM_005631	A4D1K5	Silent	SNP	ENST00000249373.3	37	CCDS5811.1																																																																																			C|0.993;T|0.007	0.007	strong		0.667	SMO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350986.1	NM_005631	
ZNF221	7638	hgsc.bcm.edu	37	19	44471209	44471209	+	Missense_Mutation	SNP	T	T	A	rs365745	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:44471209T>A	ENST00000251269.5	+	6	1883	c.1555T>A	c.(1555-1557)Tca>Aca	p.S519T	ZNF221_ENST00000592350.1_Missense_Mutation_p.S519T|ZNF221_ENST00000587682.1_Missense_Mutation_p.S519T	NM_013359.2	NP_037491	Q9UK13	ZN221_HUMAN	zinc finger protein 221	519			S -> T (in dbSNP:rs365745). {ECO:0000269|PubMed:12743021, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.5}.		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(7)|lung(11)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	30		Prostate(69;0.0352)				TACTCAGAGTTCACAACTTCA	0.423													T|||	3688	0.736422	0.4841	0.8487	5008	,	,		21470	0.8452		0.8539	False		,,,				2504	0.7648				p.S519T		Atlas-SNP	.											.	ZNF221	59	.	0			c.T1555A						PASS	.	T	THR/SER	2409,1997	616.8+/-392.8	669,1071,463	95.0	89.0	91.0		1555	1.5	0.0	19	dbSNP_80	91	7391,1209	763.2+/-407.6	3167,1057,76	yes	missense	ZNF221	NM_013359.2	58	3836,2128,539	AA,AT,TT		14.0581,45.3246,24.6502	benign	519/618	44471209	9800,3206	2203	4300	6503	SO:0001583	missense	7638	exon6			CAGAGTTCACAAC	AF187987	CCDS12633.1	19q13.31	2013-01-08				ENSG00000159905		"""Zinc fingers, C2H2-type"", ""-"""	13014	protein-coding gene	gene with protein product							Standard	NM_013359		Approved		uc002oxx.2	Q9UK13		ENST00000251269.5:c.1555T>A	19.37:g.44471209T>A	ENSP00000251269:p.Ser519Thr	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	44	44	1	NM_013359	B2RAI6|Q2M2H2|Q9P1U8	Missense_Mutation	SNP	ENST00000251269.5	37	CCDS12633.1	1683	0.7706043956043956	265	0.5386178861788617	299	0.8259668508287292	480	0.8391608391608392	639	0.8430079155672823	t	13.31	2.198883	0.38806	0.546754	0.859419	ENSG00000159905	ENST00000251269	T	0.17854	2.25	2.63	1.55	0.23275	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	M	0.67517	2.055	0.80722	P	0.0	B	0.19706	0.038	B	0.15484	0.013	T	0.06917	-1.0800	8	0.56958	D	0.05	.	4.2693	0.10778	0.1895:0.0:0.2212:0.5893	rs365745;rs16976944;rs58720599;rs365745	519	Q9UK13	ZN221_HUMAN	T	519	ENSP00000251269:S519T	ENSP00000251269:S519T	S	+	1	0	ZNF221	49163049	0.000000	0.05858	0.003000	0.11579	0.899000	0.52679	-0.319000	0.08039	0.237000	0.21200	0.260000	0.18958	TCA	T|0.243;A|0.757	0.757	strong		0.423	ZNF221-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460068.1		
TLR1	7096	hgsc.bcm.edu	37	4	38798817	38798817	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:38798817C>T	ENST00000502213.2	-	3	1865	c.1636G>A	c.(1636-1638)Gtg>Atg	p.V546M	TLR1_ENST00000510552.1_5'Flank|TLR1_ENST00000308979.2_Missense_Mutation_p.V546M			Q15399	TLR1_HUMAN	toll-like receptor 1	546	LRRCT.				cellular response to triacyl bacterial lipopeptide (GO:0071727)|detection of triacyl bacterial lipopeptide (GO:0042495)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|macrophage activation (GO:0042116)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of interleukin-6 biosynthetic process (GO:0045410)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|regulation of cytokine secretion (GO:0050707)|signal transduction (GO:0007165)|toll-like receptor 1 signaling pathway (GO:0034130)	cytoplasmic vesicle (GO:0031410)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|Toll-like receptor 1-Toll-like receptor 2 protein complex (GO:0035354)	protein heterodimerization activity (GO:0046982)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|skin(4)|stomach(2)	28						CCCTCTAACACTTCACTTGAT	0.413																																					p.V546M	GBM(5;216 373 40795 46382)	Atlas-SNP	.											TLR1,right_upper_lobe,carcinoma,0,1	TLR1	70	1	0			c.G1636A						scavenged	.						185.0	196.0	192.0					4																	38798817		2203	4300	6503	SO:0001583	missense	7096	exon4			CTAACACTTCACT	U88540	CCDS33973.1	4p14	2008-02-05				ENSG00000174125		"""CD molecules"""	11847	protein-coding gene	gene with protein product		601194				9435236, 7584026	Standard	NM_003263		Approved	rsc786, KIAA0012, CD281	uc003gtl.3	Q15399		ENST00000502213.2:c.1636G>A	4.37:g.38798817C>T	ENSP00000421259:p.Val546Met	Somatic	280	1	0.00357143		WXS	Illumina HiSeq	Phase_I	249	3	0.0120482	NM_003263	D1CS39|D1CS41|O15452|Q32MK3|Q32MK4|Q9UG90	Missense_Mutation	SNP	ENST00000502213.2	37	CCDS33973.1	.	.	.	.	.	.	.	.	.	.	C	6.601	0.479174	0.12581	.	.	ENSG00000174125	ENST00000308979;ENST00000502213	T;T	0.02140	4.43;4.43	4.75	4.75	0.60458	Cysteine-rich flanking region, C-terminal (1);	0.463977	0.20076	N	0.099751	T	0.03739	0.0106	M	0.66939	2.045	0.25640	N	0.98622	B	0.33266	0.404	B	0.31495	0.131	T	0.37267	-0.9713	10	0.20519	T	0.43	.	13.4424	0.61121	0.0:1.0:0.0:0.0	.	546	Q15399	TLR1_HUMAN	M	546	ENSP00000354932:V546M;ENSP00000421259:V546M	ENSP00000354932:V546M	V	-	1	0	TLR1	38475212	0.000000	0.05858	0.838000	0.33150	0.435000	0.31806	0.128000	0.15810	2.636000	0.89361	0.650000	0.86243	GTG	.	.	none		0.413	TLR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360510.3		
PRKCG	5582	hgsc.bcm.edu	37	19	54403925	54403925	+	Silent	SNP	T	T	C	rs2242244	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:54403925T>C	ENST00000263431.3	+	14	1779	c.1497T>C	c.(1495-1497)ttT>ttC	p.F499F	PRKCG_ENST00000540413.1_Silent_p.F499F|PRKCG_ENST00000542049.1_Silent_p.F386F	NM_002739.3	NP_002730.1	P05129	KPCG_HUMAN	protein kinase C, gamma	499	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|cell death (GO:0008219)|chemosensory behavior (GO:0007635)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|innervation (GO:0060384)|intracellular signal transduction (GO:0035556)|learning or memory (GO:0007611)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of protein ubiquitination (GO:0031397)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphorylation (GO:0016310)|platelet activation (GO:0030168)|positive regulation of mismatch repair (GO:0032425)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|response to morphine (GO:0043278)|response to pain (GO:0048265)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	cell-cell junction (GO:0005911)|cytosol (GO:0005829)|dendrite (GO:0030425)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|synaptic membrane (GO:0097060)	ATP binding (GO:0005524)|calcium-dependent protein kinase C activity (GO:0004698)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|zinc ion binding (GO:0008270)			large_intestine(1)|lung(4)|ovary(2)|pancreas(2)|skin(1)	10	all_cancers(19;0.0462)|all_epithelial(19;0.0258)|all_lung(19;0.185)|Ovarian(34;0.19)|Lung NSC(19;0.218)			GBM - Glioblastoma multiforme(134;0.0521)	Tamoxifen(DB00675)	TCACTGACTTTGGCATGTGTA	0.577													C|||	303	0.0605032	0.093	0.0245	5008	,	,		20181	0.1081		0.005	False		,,,				2504	0.0501				p.F499F		Atlas-SNP	.											.	PRKCG	246	.	0			c.T1497C						PASS	.	C		356,4050	794.0+/-415.2	19,318,1866	233.0	222.0	226.0		1497	-7.6	0.8	19	dbSNP_98	226	46,8554	817.3+/-406.9	0,46,4254	no	coding-synonymous	PRKCG	NM_002739.3		19,364,6120	CC,CT,TT		0.5349,8.0799,3.0909		499/698	54403925	402,12604	2203	4300	6503	SO:0001819	synonymous_variant	5582	exon14			TGACTTTGGCATG	M13977	CCDS12867.1	19q13.4	2014-09-17			ENSG00000126583	ENSG00000126583	2.7.11.1		9402	protein-coding gene	gene with protein product	"""PKC-gamma"""	176980		PKCG, SCA14		8432525, 3755548	Standard	NM_002739		Approved	PKCC, MGC57564	uc002qcq.1	P05129	OTTHUMG00000064846	ENST00000263431.3:c.1497T>C	19.37:g.54403925T>C		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	95	46	0.484211	NM_002739	B7Z8Q0	Silent	SNP	ENST00000263431.3	37	CCDS12867.1																																																																																			T|0.949;C|0.051	0.051	strong		0.577	PRKCG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139233.3	NM_002739	
HIST1H2AA	221613	hgsc.bcm.edu	37	6	25726621	25726621	+	Silent	SNP	C	C	T	rs9467583	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	108	0	0		WXS	Illumina HiSeq	Phase_I	83	44	0.53012	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	
ZFAND4	93550	hgsc.bcm.edu	37	10	46143958	46143958	+	Missense_Mutation	SNP	T	T	G	rs17854567	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:46143958T>G	ENST00000344646.5	-	5	568	c.353A>C	c.(352-354)aAg>aCg	p.K118T	ZFAND4_ENST00000374370.1_5'UTR|ZFAND4_ENST00000374366.3_Missense_Mutation_p.K44T|ZFAND4_ENST00000374371.2_Missense_Mutation_p.K118T	NM_001128324.2|NM_174890.2	NP_001121796.1|NP_777550.2	Q86XD8	ZFAN4_HUMAN	zinc finger, AN1-type domain 4	118			K -> T (in dbSNP:rs17854567). {ECO:0000269|PubMed:14702039}.				zinc ion binding (GO:0008270)										CTCTGCCATCTTCCTAAGTGG	0.393													T|||	495	0.0988419	0.0068	0.2205	5008	,	,		18196	0.0317		0.1521	False		,,,				2504	0.1513				p.K118T		Atlas-SNP	.											.	.	.	.	0			c.A353C						PASS	.	T	THR/LYS,THR/LYS	133,4273	95.3+/-134.0	4,125,2074	101.0	97.0	98.0		353,353	5.8	1.0	10	dbSNP_123	98	1094,7506	228.0+/-263.2	69,956,3275	yes	missense,missense	ANUBL1	NM_001128324.1,NM_174890.2	78,78	73,1081,5349	GG,GT,TT		12.7209,3.0186,9.4341	benign,benign	118/728,118/728	46143958	1227,11779	2203	4300	6503	SO:0001583	missense	93550	exon5			GCCATCTTCCTAA	AF311324	CCDS7214.1, CCDS60520.1	10q11.22	2013-01-09	2011-11-10	2011-11-10	ENSG00000172671	ENSG00000172671		"""Zinc fingers, AN1-type domain containing"""	23504	protein-coding gene	gene with protein product			"""AN1, ubiquitin-like, homolog (Xenopus laevis)"""	ANUBL1			Standard	XM_005271837		Approved	FLJ40185	uc001jcp.4	Q86XD8	OTTHUMG00000018085	ENST00000344646.5:c.353A>C	10.37:g.46143958T>G	ENSP00000339484:p.Lys118Thr	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	74	34	0.459459	NM_001128324	A8K8V4|B2RAX2|Q5VVY5	Missense_Mutation	SNP	ENST00000344646.5	37	CCDS7214.1	201	0.09203296703296704	6	0.012195121951219513	67	0.1850828729281768	14	0.024475524475524476	114	0.1503957783641161	T	16.40	3.113419	0.56398	0.030186	0.127209	ENSG00000172671	ENST00000344646;ENST00000374371;ENST00000374366;ENST00000374376	T;T;T	0.46819	1.91;0.86;1.96	5.78	5.78	0.91487	.	2.856830	0.01859	N	0.036460	T	0.00073	0.0002	N	0.14661	0.345	0.29438	P	0.859326	B;B	0.23937	0.002;0.094	B;B	0.15870	0.001;0.014	T	0.04065	-1.0980	9	0.87932	D	0	-18.3348	14.0663	0.64831	0.0:0.0:0.0:1.0	rs17854567;rs17854567	118;118	Q5VVY4;Q86XD8	.;ANUB1_HUMAN	T	118;118;44;118	ENSP00000339484:K118T;ENSP00000363491:K118T;ENSP00000363486:K44T	ENSP00000339484:K118T	K	-	2	0	ANUBL1	45463964	1.000000	0.71417	1.000000	0.80357	0.359000	0.29487	4.665000	0.61547	2.198000	0.70561	0.477000	0.44152	AAG	T|0.909;G|0.091	0.091	strong		0.393	ZFAND4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047790.1	NM_174890	
CCDC158	339965	hgsc.bcm.edu	37	4	77272155	77272155	+	Silent	SNP	C	C	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:77272155C>A	ENST00000388914.3	-	17	2810	c.2658G>T	c.(2656-2658)ctG>ctT	p.L886L		NM_001042784.1	NP_001036249.1	Q5M9N0	CD158_HUMAN	coiled-coil domain containing 158	886										breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(28)|ovary(3)|pancreas(1)|prostate(1)|skin(6)|stomach(1)	56						TTACATGAGACAGGAAGCTGG	0.368																																					p.L886L		Atlas-SNP	.											.	CCDC158	114	.	0			c.G2658T						PASS	.						150.0	147.0	148.0					4																	77272155		1960	4149	6109	SO:0001819	synonymous_variant	339965	exon17			ATGAGACAGGAAG	BC035224	CCDS43242.1	4q21.1	2009-04-06			ENSG00000163749	ENSG00000163749			26374	protein-coding gene	gene with protein product						12477932	Standard	NM_001042784		Approved	FLJ25770	uc003hkb.4	Q5M9N0	OTTHUMG00000160916	ENST00000388914.3:c.2658G>T	4.37:g.77272155C>A		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	89	18	0.202247	NM_001042784	Q8IYQ1|Q8N7D4|Q8N7E3	Silent	SNP	ENST00000388914.3	37	CCDS43242.1																																																																																			.	.	none		0.368	CCDC158-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362694.2	NM_001042784	
MRGPRX1	259249	hgsc.bcm.edu	37	11	18956194	18956194	+	Silent	SNP	T	T	C	rs2014931	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	59	0	0		WXS	Illumina HiSeq	Phase_I	98	81	0.826531	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	
CNTNAP3	79937	hgsc.bcm.edu	37	9	39103743	39103743	+	Missense_Mutation	SNP	C	C	T	rs7852039	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:39103743C>T	ENST00000297668.6	-	16	2607	c.2534G>A	c.(2533-2535)cGt>cAt	p.R845H	CNTNAP3_ENST00000358144.2_Missense_Mutation_p.R757H|CNTNAP3_ENST00000377656.2_Missense_Mutation_p.R844H	NM_033655.3	NP_387504.2	Q9BZ76	CNTP3_HUMAN	contactin associated protein-like 3	845	Laminin G-like 3. {ECO:0000255|PROSITE- ProRule:PRU00122}.		R -> H (in dbSNP:rs7852039). {ECO:0000269|PubMed:11214970}.		cell adhesion (GO:0007155)|cell recognition (GO:0008037)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(3)|kidney(2)|large_intestine(5)|liver(2)|lung(8)|ovary(1)|upper_aerodigestive_tract(2)	24				GBM - Glioblastoma multiforme(29;0.02)|Lung(182;0.0681)		GAGCTTACCACGCAGCTCAAT	0.418													C|||	934	0.186502	0.062	0.1354	5008	,	,		15532	0.3036		0.2376	False		,,,				2504	0.2178				p.R845H		Atlas-SNP	.											.	CNTNAP3	82	.	0			c.G2534A						PASS	.	C	HIS/ARG	392,4014	190.5+/-216.4	24,344,1835	39.0	43.0	42.0		2534	-1.3	0.0	9	dbSNP_116	42	1860,6740	331.0+/-319.4	208,1444,2648	yes	missense	CNTNAP3	NM_033655.3	29	232,1788,4483	TT,TC,CC		21.6279,8.897,17.3151	benign	845/1289	39103743	2252,10754	2203	4300	6503	SO:0001583	missense	79937	exon16			TTACCACGCAGCT	AF333769	CCDS6616.1	9q12	2008-02-05			ENSG00000106714	ENSG00000106714			13834	protein-coding gene	gene with protein product	"""cell recognition molecule CASPR3 (FLJ14195, KIAA1714)"""	610517				12093160	Standard	NM_033655		Approved	CASPR3, KIAA1714, FLJ14195, CNTNAP3A	uc004abi.3	Q9BZ76	OTTHUMG00000019954	ENST00000297668.6:c.2534G>A	9.37:g.39103743C>T	ENSP00000297668:p.Arg845His	Somatic	377	2	0.00530504		WXS	Illumina HiSeq	Phase_I	336	335	0.997024	NM_033655	B1AMA0|Q9C0E9	Missense_Mutation	SNP	ENST00000297668.6	37	CCDS6616.1	439	0.20100732600732601	26	0.052845528455284556	58	0.16022099447513813	164	0.2867132867132867	191	0.2519788918205805	C	11.25	1.582659	0.28180	0.08897	0.216279	ENSG00000106714	ENST00000297668;ENST00000377656;ENST00000358144	T;T;T	0.42513	0.97;0.97;0.97	3.23	-1.29	0.09288	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	.	.	.	.	T	0.00012	0.0000	L	0.42487	1.325	0.50813	P	1.0299999999996423E-4	B;B;B	0.27286	0.174;0.076;0.032	B;B;B	0.30179	0.048;0.112;0.032	T	0.37596	-0.9699	8	0.16896	T	0.51	.	3.4899	0.07634	0.195:0.2478:0.0:0.5572	rs7852039;rs7852039	845;844;845	Q9BZ76-2;A6NC89;Q9BZ76	.;.;CNTP3_HUMAN	H	845;844;757	ENSP00000297668:R845H;ENSP00000366884:R844H;ENSP00000350863:R757H	ENSP00000297668:R845H	R	-	2	0	CNTNAP3	39093743	0.000000	0.05858	0.008000	0.14137	0.241000	0.25554	-0.236000	0.09003	-0.130000	0.11599	0.485000	0.47835	CGT	C|0.824;T|0.176	0.176	strong		0.418	CNTNAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052511.1	NM_033655	
PHRF1	57661	hgsc.bcm.edu	37	11	607175	607175	+	Silent	SNP	G	G	A	rs936468	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:607175G>A	ENST00000264555.5	+	14	1847	c.1719G>A	c.(1717-1719)ccG>ccA	p.P573P	PHRF1_ENST00000533464.1_Silent_p.P569P|PHRF1_ENST00000413872.2_Silent_p.P571P|PHRF1_ENST00000416188.2_Silent_p.P572P	NM_020901.2	NP_065952.2	Q9P1Y6	PHRF1_HUMAN	PHD and ring finger domains 1	573					mRNA processing (GO:0006397)|transcription from RNA polymerase II promoter (GO:0006366)	membrane (GO:0016020)	RNA polymerase binding (GO:0070063)|zinc ion binding (GO:0008270)			breast(1)|cervix(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(13)|urinary_tract(2)	28						CCCAAGGCCCGTCAGGAAACA	0.677													G|||	659	0.131589	0.1475	0.2305	5008	,	,		14275	0.0179		0.2048	False		,,,				2504	0.0818				p.P572P		Atlas-SNP	.											PHRF1_ENST00000264555,NS,carcinoma,0,2	PHRF1	188	2	0			c.G1716A						PASS	.	G		626,3092		45,536,1278	28.0	31.0	30.0		1716	-5.1	0.0	11	dbSNP_86	30	1896,6318		204,1488,2415	no	coding-synonymous	PHRF1	NM_020901.2		249,2024,3693	AA,AG,GG		23.0825,16.837,21.1364		572/1649	607175	2522,9410	1859	4107	5966	SO:0001819	synonymous_variant	57661	exon14			AGGCCCGTCAGGA	BC004950	CCDS44507.1, CCDS65987.1, CCDS65988.1, CCDS65989.1	11p15.5	2014-06-13			ENSG00000070047	ENSG00000070047		"""RING-type (C3HC4) zinc fingers"", ""Zinc fingers, PHD-type"""	24351	protein-coding gene	gene with protein product	"""CTD binding SR like protein rA9"", ""protein phosphatase 1, regulatory subunit 125"""	611780		RNF221			Standard	XM_005253027		Approved	KIAA1542, PPP1R125	uc010qwc.2	Q9P1Y6	OTTHUMG00000165141	ENST00000264555.5:c.1719G>A	11.37:g.607175G>A		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	67	54	0.80597	NM_020901	A6H8W1|B7ZM64|B9EGP0|C9JS82|Q6PJP2|Q8IVY2|Q8N2Y7|Q9BSM2	Silent	SNP	ENST00000264555.5	37																																																																																				G|0.828;A|0.172	0.172	strong		0.677	PHRF1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000382133.1	NM_020901	
PARP4	143	hgsc.bcm.edu	37	13	25029218	25029218	+	Missense_Mutation	SNP	C	C	T	rs2275660	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:25029218C>T	ENST00000381989.3	-	22	2800	c.2695G>A	c.(2695-2697)Gcc>Acc	p.A899T	PARP4_ENST00000480576.1_5'Flank	NM_006437.3	NP_006428.2	Q9UKK3	PARP4_HUMAN	poly (ADP-ribose) polymerase family, member 4	899	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.		A -> T (in dbSNP:rs2275660). {ECO:0000269|PubMed:10477748}.		cell death (GO:0008219)|cellular protein modification process (GO:0006464)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|inflammatory response (GO:0006954)|protein ADP-ribosylation (GO:0006471)|response to drug (GO:0042493)|transport (GO:0006810)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|spindle microtubule (GO:0005876)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|NAD+ ADP-ribosyltransferase activity (GO:0003950)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(14)|lung(18)|ovary(3)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	63		all_epithelial(30;7.67e-16)|Lung SC(185;0.0225)|Breast(139;0.052)		all cancers(112;0.000127)|Epithelial(112;0.000778)|Kidney(163;0.039)|OV - Ovarian serous cystadenocarcinoma(117;0.0578)|KIRC - Kidney renal clear cell carcinoma(186;0.135)|Lung(94;0.195)		GCATGCAAGGCGATTTGCTTG	0.527													c|||	3276	0.654153	0.4463	0.8098	5008	,	,		19950	0.6498		0.7763	False		,,,				2504	0.7035				p.A899T		Atlas-SNP	.											.	PARP4	142	.	0			c.G2695A						PASS	.	C	THR/ALA	2211,2195	589.6+/-387.2	582,1047,574	276.0	237.0	250.0		2695	4.7	0.2	13	dbSNP_100	250	6623,1977	723.6+/-406.5	2573,1477,250	yes	missense	PARP4	NM_006437.3	58	3155,2524,824	TT,TC,CC		22.9884,49.8184,32.0775	probably-damaging	899/1725	25029218	8834,4172	2203	4300	6503	SO:0001583	missense	143	exon22			GCAAGGCGATTTG	AF057160	CCDS9307.1	13q11	2010-09-29	2004-08-20	2004-08-26	ENSG00000102699	ENSG00000102699		"""Poly (ADP-ribose) polymerases"""	271	protein-coding gene	gene with protein product	"""von Willebrand factor A domain containing 5C"""	607519	"""ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase)-like 1"""	ADPRTL1		10644454	Standard	NM_006437		Approved	VAULT3, p193, VPARP, VWA5C	uc001upl.3	Q9UKK3	OTTHUMG00000016582	ENST00000381989.3:c.2695G>A	13.37:g.25029218C>T	ENSP00000371419:p.Ala899Thr	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	90	89	0.988889	NM_006437	O75903|Q14682|Q5QNZ9|Q9H1M6	Missense_Mutation	SNP	ENST00000381989.3	37	CCDS9307.1	1448	0.663003663003663	219	0.4451219512195122	285	0.787292817679558	359	0.6276223776223776	585	0.7717678100263852	C	17.10	3.303185	0.60195	0.501816	0.770116	ENSG00000102699	ENST00000381989	T	0.08282	3.11	4.72	4.72	0.59763	von Willebrand factor, type A (3);	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	M	0.66297	2.02	0.19300	P	0.9999721641	D	0.89917	1.0	D	0.91635	0.999	T	0.01767	-1.1278	9	0.45353	T	0.12	-17.4912	15.2852	0.73822	0.0:1.0:0.0:0.0	rs2275660;rs2275660	899	Q9UKK3	PARP4_HUMAN	T	899	ENSP00000371419:A899T	ENSP00000371419:A899T	A	-	1	0	PARP4	23927218	1.000000	0.71417	0.215000	0.23724	0.110000	0.19582	5.868000	0.69605	2.481000	0.83766	0.573000	0.79308	GCC	C|0.326;T|0.674	0.674	strong		0.527	PARP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044189.1	NM_006437	
LRRC75A	388341	hgsc.bcm.edu	37	17	16347325	16347325	+	Missense_Mutation	SNP	T	T	C	rs61745139	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:16347325T>C	ENST00000409083.3	-	3	658	c.496A>G	c.(496-498)Aga>Gga	p.R166G	C17orf76-AS1_ENST00000475953.1_RNA|C17orf76-AS1_ENST00000584141.1_RNA|C17orf76-AS1_ENST00000484836.1_RNA|C17orf76-AS1_ENST00000391079.1_RNA|C17orf76-AS1_ENST00000477249.2_RNA|C17orf76-AS1_ENST00000492250.1_RNA|C17orf76-AS1_ENST00000581718.1_RNA|C17orf76-AS1_ENST00000584926.1_RNA|C17orf76-AS1_ENST00000472367.1_RNA|FAM211A_ENST00000470794.1_Silent_p.V204V|C17orf76-AS1_ENST00000579473.1_RNA|C17orf76-AS1_ENST00000481027.1_RNA|C17orf76-AS1_ENST00000470491.2_RNA|C17orf76-AS1_ENST00000487066.1_RNA|C17orf76-AS1_ENST00000480811.1_RNA|C17orf76-AS1_ENST00000580180.1_RNA|C17orf76-AS1_ENST00000478103.2_RNA|C17orf76-AS1_ENST00000460249.1_RNA|C17orf76-AS1_ENST00000580770.1_RNA|C17orf76-AS1_ENST00000584177.1_RNA|C17orf76-AS1_ENST00000491009.1_RNA|C17orf76-AS1_ENST00000481898.1_RNA|C17orf76-AS1_ENST00000583400.2_RNA|C17orf76-AS1_ENST00000483140.1_RNA|C17orf76-AS1_ENST00000475947.2_RNA|C17orf76-AS1_ENST00000581913.1_RNA|C17orf76-AS1_ENST00000582911.1_RNA	NM_207387.3	NP_997270.2														lung(1)	1						CCACGCTGTCTACCTGCTCCC	0.647													T|||	241	0.048123	0.0083	0.0562	5008	,	,		18322	0.0		0.1203	False		,,,				2504	0.0716				p.R166G		Atlas-SNP	.											FAM211A_ENST00000470794,NS,carcinoma,0,3	FAM211A	21	3	0			c.A496G						PASS	.	T	,GLY/ARG	119,4287	87.3+/-125.9	3,113,2087	58.0	48.0	51.0		612,496	3.4	1.0	17	dbSNP_129	51	1153,7447	234.3+/-267.3	70,1013,3217	yes	coding-synonymous,missense	C17orf76	NM_001113567.1,NM_207387.2	,125	73,1126,5304	CC,CT,TT		13.407,2.7009,9.7801	,	204/345,166/213	16347325	1272,11734	2203	4300	6503	SO:0001583	missense	388341	exon3			GCTGTCTACCTGC																												ENST00000409083.3:c.496A>G	17.37:g.16347325T>C	ENSP00000386504:p.Arg166Gly	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	61	30	0.491803	NM_207387		Missense_Mutation	SNP	ENST00000409083.3	37	CCDS11178.2	130	0.05952380952380952	15	0.03048780487804878	22	0.06077348066298342	0	0.0	93	0.12269129287598944	T	14.35	2.510037	0.44660	0.027009	0.13407	ENSG00000181350	ENST00000409083	.	.	.	5.34	3.36	0.38483	.	1.464120	0.03657	N	0.242032	T	0.00496	0.0016	.	.	.	0.09310	P	1.0	B	0.02656	0.0	B	0.01281	0.0	T	0.10337	-1.0634	7	0.87932	D	0	.	10.0548	0.42239	0.0:0.8345:0.0:0.1655	.	166	Q8NAA5-2	.	G	166	.	ENSP00000386504:R166G	R	-	1	2	C17orf76	16288050	0.982000	0.34865	1.000000	0.80357	0.980000	0.70556	0.185000	0.16958	0.772000	0.33382	-0.232000	0.12228	AGA	T|0.918;C|0.082	0.082	strong		0.647	FAM211A-001	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000130461.2		
ZNF624	57547	hgsc.bcm.edu	37	17	16525824	16525824	+	Silent	SNP	T	T	C	rs62072858	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:16525824T>C	ENST00000311331.7	-	6	2467	c.2376A>G	c.(2374-2376)ctA>ctG	p.L792L		NM_020787.3	NP_065838.2	Q9P2J8	ZN624_HUMAN	zinc finger protein 624	792					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(4)|endometrium(1)|kidney(1)|large_intestine(8)|lung(9)|ovary(1)|prostate(1)|skin(1)	26				UCEC - Uterine corpus endometrioid carcinoma (92;0.0837)		TTAGCTGTGATAGAGTAATAC	0.433													T|||	151	0.0301518	0.0121	0.0432	5008	,	,		19376	0.0		0.0845	False		,,,				2504	0.0204				p.L792L	NSCLC(186;1023 2134 13330 38202 39800)	Atlas-SNP	.											.	ZNF624	91	.	0			c.A2376G						PASS	.	T		85,4321	73.6+/-111.7	0,85,2118	92.0	93.0	93.0		2376	1.0	1.0	17	dbSNP_129	93	579,8021	154.9+/-209.1	17,545,3738	no	coding-synonymous	ZNF624	NM_020787.3		17,630,5856	CC,CT,TT		6.7326,1.9292,5.1053		792/866	16525824	664,12342	2203	4300	6503	SO:0001819	synonymous_variant	57547	exon6			CTGTGATAGAGTA	AB037770	CCDS11180.1	17p11.2	2013-01-08			ENSG00000197566	ENSG00000197566		"""Zinc fingers, C2H2-type"", ""-"""	29254	protein-coding gene	gene with protein product						10718198	Standard	NM_020787		Approved	KIAA1349	uc010cpi.2	Q9P2J8	OTTHUMG00000058996	ENST00000311331.7:c.2376A>G	17.37:g.16525824T>C		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	65	30	0.461538	NM_020787	Q3SY62|Q3SY63|Q6ZN27	Silent	SNP	ENST00000311331.7	37	CCDS11180.1																																																																																			T|0.947;C|0.053	0.053	strong		0.433	ZNF624-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130512.3	XM_047617	
CCDC176	80127	hgsc.bcm.edu	37	14	74516497	74516497	+	Silent	SNP	G	G	A	rs34076068	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	158	0	0		WXS	Illumina HiSeq	Phase_I	155	77	0.496774	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	
SEZ6	124925	hgsc.bcm.edu	37	17	27286851	27286851	+	Missense_Mutation	SNP	T	T	C	rs1976165	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:27286851T>C	ENST00000317338.12	-	8	2064	c.1636A>G	c.(1636-1638)Aca>Gca	p.T546A	SEZ6_ENST00000360295.9_Missense_Mutation_p.T546A|PIPOX_ENST00000583215.1_Intron|SEZ6_ENST00000335960.6_Intron|SEZ6_ENST00000442608.3_Missense_Mutation_p.T546A			Q53EL9	SEZ6_HUMAN	seizure related 6 homolog (mouse)	546	Sushi 2. {ECO:0000255|PROSITE- ProRule:PRU00302}.		T -> A (in dbSNP:rs1976165).		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)			TAGGTGGGTGTGCTGCTGCTG	0.577													C|||	1805	0.360423	0.4977	0.317	5008	,	,		20834	0.244		0.2525	False		,,,				2504	0.4366				p.T546A		Atlas-SNP	.											.	SEZ6	61	.	0			c.A1636G	GRCh37	CM073339	SEZ6	M	rs1976165	PASS	.	C	ALA/THR,ALA/THR	1790,2384		381,1028,678	62.0	70.0	68.0		1636,1636	5.1	0.9	17	dbSNP_92	68	2162,6318		280,1602,2358	yes	missense,missense	SEZ6	NM_001098635.1,NM_178860.4	58,58	661,2630,3036	CC,CT,TT		25.4953,42.8845,31.2312	benign,benign	546/994,546/995	27286851	3952,8702	2087	4240	6327	SO:0001583	missense	124925	exon8			TGGGTGTGCTGCT	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.1636A>G	17.37:g.27286851T>C	ENSP00000312942:p.Thr546Ala	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	77	77	1	NM_001098635	B6ZDN1|Q8N701|Q8NB57|Q8ND50|Q8TD25|Q96NI5|Q96NQ3	Missense_Mutation	SNP	ENST00000317338.12	37	CCDS45639.1	677	0.309981684981685	243	0.49390243902439024	113	0.31215469613259667	145	0.2534965034965035	176	0.23218997361477572	C	12.14	1.848110	0.32699	0.428845	0.254953	ENSG00000063015	ENST00000442608;ENST00000360295;ENST00000317338;ENST00000541381	T;T	0.63744	-0.06;-0.06	5.07	5.07	0.68467	Complement control module (2);Sushi/SCR/CCP (3);	0.135388	0.48767	N	0.000180	T	0.00012	0.0000	L	0.34521	1.04	0.09310	P	1.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.43245	-0.9403	9	0.30854	T	0.27	.	11.8833	0.52587	0.0:0.9138:0.0:0.0862	rs1976165;rs52834488;rs60868464;rs1976165	546;546	Q53EL9-3;Q53EL9	.;SEZ6_HUMAN	A	546;546;421;546	ENSP00000403784:T546A;ENSP00000353440:T546A	ENSP00000312942:T421A	T	-	1	0	SEZ6	24310977	1.000000	0.71417	0.865000	0.33974	0.752000	0.42762	5.780000	0.68956	1.281000	0.44480	-0.215000	0.12644	ACA	T|0.664;C|0.336	0.336	strong		0.577	SEZ6-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397475.3		
HEG1	57493	hgsc.bcm.edu	37	3	124746049	124746049	+	Splice_Site	SNP	A	A	G	rs2981546	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	80	0	0		WXS	Illumina HiSeq	Phase_I	63	30	0.47619	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
HS6ST3	266722	hgsc.bcm.edu	37	13	96743584	96743584	+	Silent	SNP	G	G	T	rs144263527	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:96743584G>T	ENST00000376705.2	+	1	492	c.468G>T	c.(466-468)acG>acT	p.T156T		NM_153456.3	NP_703157.2	Q8IZP7	H6ST3_HUMAN	heparan sulfate 6-O-sulfotransferase 3	156	5'-phosphosulfate-binding. {ECO:0000255}.				heparan sulfate proteoglycan biosynthetic process, enzymatic modification (GO:0015015)	integral component of membrane (GO:0016021)	heparan sulfate 6-O-sulfotransferase activity (GO:0017095)	p.T156T(1)		NS(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(10)|ovary(1)|pancreas(1)|skin(1)	20	all_neural(89;0.0878)|Medulloblastoma(90;0.163)					TCCAGAAGACGGGGGGCACCA	0.602													c|||	6	0.00119808	0.0015	0.0	5008	,	,		11700	0.0		0.002	False		,,,				2504	0.002				p.T156T		Atlas-SNP	.											HS6ST3,NS,carcinoma,0,1	HS6ST3	54	1	1	Substitution - coding silent(1)	pancreas(1)	c.G468T						PASS	.	G		4,4402		0,4,2199	34.0	36.0	36.0		468	-0.6	1.0	13	dbSNP_134	36	18,8582		0,18,4282	no	coding-synonymous	HS6ST3	NM_153456.2		0,22,6481	TT,TG,GG		0.2093,0.0908,0.1692		156/472	96743584	22,12984	2203	4300	6503	SO:0001819	synonymous_variant	266722	exon1			GAAGACGGGGGGC	AF539426	CCDS9481.1	13q32.2	2007-12-04			ENSG00000185352	ENSG00000185352		"""Sulfotransferases, membrane-bound"""	19134	protein-coding gene	gene with protein product		609401					Standard	NM_153456		Approved		uc001vmw.4	Q8IZP7	OTTHUMG00000017232	ENST00000376705.2:c.468G>T	13.37:g.96743584G>T		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	41	18	0.439024	NM_153456	Q5W0L0|Q68CW6	Silent	SNP	ENST00000376705.2	37	CCDS9481.1																																																																																			G|0.998;T|0.002	0.002	strong		0.602	HS6ST3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045517.2	NM_153456	
TBC1D31	93594	hgsc.bcm.edu	37	8	124142489	124142489	+	Silent	SNP	T	T	C	rs2272724	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:124142489T>C	ENST00000287380.1	+	16	2412	c.2322T>C	c.(2320-2322)gaT>gaC	p.D774D	TBC1D31_ENST00000518805.1_Silent_p.D328D|TBC1D31_ENST00000327098.5_Silent_p.D774D|TBC1D31_ENST00000522420.1_Silent_p.D669D|TBC1D31_ENST00000309336.3_Silent_p.D774D|TBC1D31_ENST00000521676.1_Silent_p.D651D|TBC1D31_ENST00000378080.2_3'UTR	NM_145647.3	NP_663622.2	Q96DN5	TBC31_HUMAN	TBC1 domain family, member 31	774						centrosome (GO:0005813)	Rab GTPase activator activity (GO:0005097)										ACTTACAAGATGCTGCAAGAA	0.363													T|||	1679	0.335264	0.4244	0.4337	5008	,	,		19856	0.1825		0.337	False		,,,				2504	0.3006				p.D774D		Atlas-SNP	.											.	WDR67	97	.	0			c.T2322C						PASS	.	T	,	1880,2526	543.3+/-376.2	409,1062,732	132.0	128.0	129.0		2322,2322	-0.5	0.9	8	dbSNP_100	129	2976,5624	462.6+/-365.7	508,1960,1832	no	coding-synonymous,coding-synonymous	WDR67	NM_001145088.1,NM_145647.3	,	917,3022,2564	CC,CT,TT		34.6047,42.6691,37.3366	,	774/971,774/1067	124142489	4856,8150	2203	4300	6503	SO:0001819	synonymous_variant	93594	exon16			ACAAGATGCTGCA	AK094612	CCDS6338.1, CCDS47916.1	8q24.13	2013-07-10	2013-07-10	2013-07-10	ENSG00000156787	ENSG00000156787		"""WD repeat domain containing"""	30888	protein-coding gene	gene with protein product			"""WD repeat domain 67"""	WDR67		12477932	Standard	NM_001145088		Approved	MGC21654, Gm85	uc003ypp.2	Q96DN5	OTTHUMG00000165081	ENST00000287380.1:c.2322T>C	8.37:g.124142489T>C		Somatic	221	0	0		WXS	Illumina HiSeq	Phase_I	156	156	1	NM_001145088	B7ZL19|Q2M2J9|Q3MIR6|Q8TBP9	Silent	SNP	ENST00000287380.1	37	CCDS6338.1																																																																																			T|0.650;C|0.350	0.350	strong		0.363	TBC1D31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381721.1	NM_145647	
EXO5	64789	hgsc.bcm.edu	37	1	40980559	40980559	+	Missense_Mutation	SNP	G	G	A	rs1134586	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:40980559G>A	ENST00000372703.1	+	2	1417	c.343G>A	c.(343-345)Gac>Aac	p.D115N	EXO5_ENST00000358527.2_Missense_Mutation_p.D115N|RP11-656D10.6_ENST00000437060.1_RNA|RP11-656D10.5_ENST00000453437.1_RNA|EXO5_ENST00000296380.4_Missense_Mutation_p.D115N			Q9H790	EXO5_HUMAN	exonuclease 5	115			D -> N (polymorphism that does not affect exonuclease activity; dbSNP:rs1134586).		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)										AGCTGTGTTGGACACTGGTGC	0.473													G|||	534	0.106629	0.062	0.111	5008	,	,		21047	0.0288		0.1839	False		,,,				2504	0.1646				p.D115N		Atlas-SNP	.											.	.	.	.	0			c.G343A						PASS	.	G	ASN/ASP	421,3985	204.5+/-226.7	15,391,1797	85.0	83.0	84.0		343	3.7	1.0	1	dbSNP_86	84	1611,6989	298.7+/-304.1	141,1329,2830	yes	missense	DEM1	NM_022774.1	23	156,1720,4627	AA,AG,GG		18.7326,9.5552,15.6236	probably-damaging	115/374	40980559	2032,10974	2203	4300	6503	SO:0001583	missense	64789	exon3			GTGTTGGACACTG	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.343G>A	1.37:g.40980559G>A	ENSP00000361788:p.Asp115Asn	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	55	29	0.527273	NM_022774	D3DPV4|Q5SWM7|Q5SWM8|Q5SWM9|Q5SWN0|Q5SWN1|Q8WTW9	Missense_Mutation	SNP	ENST00000372703.1	37	CCDS453.1	232	0.10622710622710622	36	0.07317073170731707	48	0.13259668508287292	12	0.02097902097902098	136	0.17941952506596306	G	14.90	2.673797	0.47781	0.095552	0.187326	ENSG00000164002	ENST00000358527;ENST00000372703;ENST00000420209;ENST00000296380;ENST00000418186;ENST00000415550;ENST00000443729;ENST00000419161	T;T;T;T;T;T;T;T	0.29655	1.56;1.56;1.56;1.56;1.56;1.56;1.56;1.56	4.56	3.65	0.41850	.	0.746656	0.11573	N	0.550512	T	0.00039	0.0001	L	0.43152	1.355	0.32268	P	0.569258	B	0.34264	0.446	B	0.32677	0.15	T	0.12218	-1.0556	9	0.46703	T	0.11	.	8.585	0.33653	0.102:0.0:0.898:0.0	rs1134586;rs3196817;rs52810094;rs1134586	115	Q9H790	EXO5_HUMAN	N	115	ENSP00000351328:D115N;ENSP00000361788:D115N;ENSP00000398437:D115N;ENSP00000296380:D115N;ENSP00000391240:D115N;ENSP00000413565:D115N;ENSP00000409715:D115N;ENSP00000392115:D115N	ENSP00000296380:D115N	D	+	1	0	DEM1	40753146	0.986000	0.35501	0.980000	0.43619	0.649000	0.38597	1.363000	0.34159	1.523000	0.49018	0.650000	0.86243	GAC	G|0.866;A|0.134	0.134	strong		0.473	EXO5-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019087.1	NM_022774	
TSHZ2	128553	hgsc.bcm.edu	37	20	51870336	51870336	+	Missense_Mutation	SNP	G	G	C	rs739869	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:51870336G>C	ENST00000371497.5	+	2	1226	c.339G>C	c.(337-339)agG>agC	p.R113S	TSHZ2_ENST00000603338.2_Missense_Mutation_p.R110S|TSHZ2_ENST00000329613.6_Missense_Mutation_p.R110S|RP4-678D15.1_ENST00000606932.1_RNA	NM_001193421.1|NM_173485.5	NP_001180350.1|NP_775756.3	Q9NRE2	TSH2_HUMAN	teashirt zinc finger homeobox 2	113			R -> S (in dbSNP:rs739869). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:17974005}.		multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|breast(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(16)|lung(38)|ovary(5)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	84			STAD - Stomach adenocarcinoma(23;0.1)			CTCACGTCAGGCTTCCAAACG	0.532													G|||	264	0.0527157	0.0514	0.0591	5008	,	,		22214	0.0		0.1262	False		,,,				2504	0.0286				p.R113S		Atlas-SNP	.											.	TSHZ2	209	.	0			c.G339C						PASS	.	G	SER/ARG,SER/ARG	258,4148	148.0+/-182.4	5,248,1950	83.0	72.0	75.0		330,339	1.1	0.4	20	dbSNP_86	75	1023,7577	219.9+/-257.8	63,897,3340	yes	missense,missense	TSHZ2	NM_001193421.1,NM_173485.5	110,110	68,1145,5290	CC,CG,GG		11.8953,5.8557,9.8493	benign,benign	110/1032,113/1035	51870336	1281,11725	2203	4300	6503	SO:0001583	missense	128553	exon2			CGTCAGGCTTCCA	AF230201	CCDS33490.1, CCDS54474.1	20q13.2	2013-11-20	2007-07-16	2006-03-14	ENSG00000182463	ENSG00000182463		"""Teashirt zinc fingers"", ""Homeoboxes / ZF class"", ""Zinc fingers, C2H2-type"""	13010	protein-coding gene	gene with protein product		614118	"""chromosome 20 open reading frame 17"", ""zinc finger protein 218"", ""teashirt family zinc finger 2"""	C20orf17, ZNF218		9671742	Standard	NM_173485		Approved	ZABC2, OVC10-2, TSH2	uc021wex.1	Q9NRE2	OTTHUMG00000033058	ENST00000371497.5:c.339G>C	20.37:g.51870336G>C	ENSP00000360552:p.Arg113Ser	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	71	38	0.535211	NM_173485	B7Z7W1|J3KNQ0|Q4VXM4|Q6N003|Q8N260	Missense_Mutation	SNP	ENST00000371497.5	37	CCDS33490.1	135	0.061813186813186816	20	0.04065040650406504	26	0.0718232044198895	0	0.0	89	0.11741424802110818	G	0.268	-0.994872	0.02145	0.058557	0.118953	ENSG00000182463	ENST00000371497;ENST00000329613	T;T	0.12774	2.65;2.65	5.7	1.09	0.20402	.	0.141334	0.64402	D	0.000008	T	0.00109	0.0003	N	0.14661	0.345	0.53005	P	3.6999999999953737E-5	B	0.12630	0.006	B	0.14023	0.01	T	0.38564	-0.9655	9	0.23302	T	0.38	-30.2724	7.7223	0.28740	0.5865:0.0:0.4135:0.0	rs739869;rs52792789;rs739869	113	Q9NRE2	TSH2_HUMAN	S	113;110	ENSP00000360552:R113S;ENSP00000333114:R110S	ENSP00000333114:R110S	R	+	3	2	TSHZ2	51303743	0.899000	0.30636	0.370000	0.25965	0.020000	0.10135	0.479000	0.22228	0.285000	0.22329	0.643000	0.83706	AGG	G|0.921;C|0.079	0.079	strong		0.532	TSHZ2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080398.6	NM_173485	
CYFIP2	26999	hgsc.bcm.edu	37	5	156747669	156747669	+	Silent	SNP	A	A	G	rs1823035	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:156747669A>G	ENST00000521420.1	+	14	1543	c.1452A>G	c.(1450-1452)ctA>ctG	p.L484L	CYFIP2_ENST00000318218.6_Silent_p.L510L|CYFIP2_ENST00000442283.2_5'UTR|CYFIP2_ENST00000522463.1_Silent_p.L314L|CYFIP2_ENST00000541131.1_Silent_p.L435L|CYFIP2_ENST00000435847.2_Silent_p.L184L|CYFIP2_ENST00000347377.6_Silent_p.L510L|CYFIP2_ENST00000377576.3_Silent_p.L510L					cytoplasmic FMR1 interacting protein 2											breast(1)|endometrium(12)|kidney(2)|lung(23)	38	Renal(175;0.00212)	Medulloblastoma(196;0.0306)|all_neural(177;0.0897)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			CCAGCGTCCTACAGGCAATTC	0.532													A|||	1660	0.33147	0.525	0.2017	5008	,	,		21595	0.2738		0.2654	False		,,,				2504	0.2894				p.L510L		Atlas-SNP	.											.	CYFIP2	354	.	0			c.A1530G						PASS	.	A	,,	1851,2081		446,959,561	58.0	59.0	59.0		1530,1530,1530	-0.1	1.0	5	dbSNP_92	59	2228,6046		292,1644,2201	no	coding-synonymous,coding-synonymous,coding-synonymous	CYFIP2	NM_001037332.2,NM_001037333.1,NM_014376.2	,,	738,2603,2762	GG,GA,AA		26.9277,47.0753,33.418	,,	510/1254,510/1254,510/1254	156747669	4079,8127	1966	4137	6103	SO:0001819	synonymous_variant	26999	exon15			CGTCCTACAGGCA	AF160973	CCDS75364.1	5q34	2008-07-18				ENSG00000055163			13760	protein-coding gene	gene with protein product	"""p53 inducible protein"""	606323				11438699	Standard	NM_001037333		Approved	PIR121	uc021ygm.1	Q96F07		ENST00000521420.1:c.1452A>G	5.37:g.156747669A>G		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	77	42	0.545455	NM_001037332		Silent	SNP	ENST00000521420.1	37																																																																																				A|0.672;G|0.328	0.328	strong		0.532	CYFIP2-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000373710.1	NM_001037332	
IQUB	154865	hgsc.bcm.edu	37	7	123097468	123097468	+	Silent	SNP	T	T	C	rs10234745	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:123097468T>C	ENST00000466202.1	-	12	2736	c.2160A>G	c.(2158-2160)gcA>gcG	p.A720A	RNU6-296P_ENST00000384608.1_RNA|IQUB_ENST00000324698.6_Silent_p.A720A|RP11-332K15.1_ENST00000419832.1_RNA	NM_001282855.1	NP_001269784.1	Q8NA54	IQUB_HUMAN	IQ motif and ubiquitin domain containing	720					cilium morphogenesis (GO:0060271)|smoothened signaling pathway (GO:0007224)	acrosomal vesicle (GO:0001669)|motile cilium (GO:0031514)		p.A720A(1)		breast(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(18)|ovary(3)|prostate(2)|stomach(3)|upper_aerodigestive_tract(1)	45						GATGAGCAGCTGCTTCATCTT	0.403													C|||	1688	0.337061	0.3926	0.2781	5008	,	,		16262	0.3909		0.2972	False		,,,				2504	0.2894				p.A720A		Atlas-SNP	.											IQUB,colon,carcinoma,0,2	IQUB	117	2	1	Substitution - coding silent(1)	stomach(1)	c.A2160G						PASS	.	C		1779,2627	642.8+/-397.7	372,1035,796	98.0	102.0	100.0		2160	-11.7	0.0	7	dbSNP_119	100	2376,6224	700.4+/-405.1	324,1728,2248	no	coding-synonymous	IQUB	NM_178827.4		696,2763,3044	CC,CT,TT		27.6279,40.3768,31.9468		720/792	123097468	4155,8851	2203	4300	6503	SO:0001819	synonymous_variant	154865	exon12			AGCAGCTGCTTCA	AK093153	CCDS5787.1	7q31.32	2010-03-19			ENSG00000164675	ENSG00000164675			21995	protein-coding gene	gene with protein product							Standard	NM_178827		Approved	FLJ35834	uc003vko.3	Q8NA54	OTTHUMG00000157347	ENST00000466202.1:c.2160A>G	7.37:g.123097468T>C		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	99	48	0.484848	NM_178827	A4D0X0|Q49AL6|Q4G189|Q5BJD9|Q6NUH6|Q8N9Y2	Silent	SNP	ENST00000466202.1	37	CCDS5787.1																																																																																			T|0.682;C|0.318	0.318	strong		0.403	IQUB-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348529.1	NM_178827	
TMEFF1	8577	hgsc.bcm.edu	37	9	103235853	103235853	+	Silent	SNP	G	G	T	rs77849433	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:103235853G>T	ENST00000374879.4	+	1	459	c.27G>T	c.(25-27)ccG>ccT	p.P9P	TMEFF1_ENST00000334943.6_Intron|MSANTD3-TMEFF1_ENST00000502978.1_Intron	NM_003692.4	NP_003683.2	Q8IYR6	TEFF1_HUMAN	transmembrane protein with EGF-like and two follistatin-like domains 1	9					multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|kidney(1)|large_intestine(7)|lung(9)|stomach(1)	19		Acute lymphoblastic leukemia(62;0.0452)				CTGAGGCGCCGCTCCGGCTGC	0.751													G|||	400	0.0798722	0.0877	0.1138	5008	,	,		7642	0.001		0.1292	False		,,,				2504	0.0757				p.P9P		Atlas-SNP	.											.	TMEFF1	42	.	0			c.G27T						PASS	.	G	,	360,3810		24,312,1749	5.0	6.0	5.0		,27	3.1	1.0	9	dbSNP_131	5	1088,7026		89,910,3058	no	intron,coding-synonymous	TMEFF1,C9orf30-TMEFF1	NM_001198812.1,NM_003692.4	,	113,1222,4807	TT,TG,GG		13.4089,8.6331,11.7877	,	,9/381	103235853	1448,10836	2085	4057	6142	SO:0001819	synonymous_variant	8577	exon1			GGCGCCGCTCCGG	U19878	CCDS6750.1	9q31	2010-05-04			ENSG00000241697	ENSG00000241697			11866	protein-coding gene	gene with protein product	"""tomoregulin-1"", ""cancer/testis antigen family 120, member 1"""	603421		C9orf2		9730596	Standard	NM_003692		Approved	H7365, CT120.1		Q8IYR6	OTTHUMG00000020367	ENST00000374879.4:c.27G>T	9.37:g.103235853G>T		Somatic	4	0	0		WXS	Illumina HiSeq	Phase_I	16	9	0.5625	NM_003692	Q13086|Q8N3T8	Silent	SNP	ENST00000374879.4	37	CCDS6750.1																																																																																			G|0.915;T|0.085	0.085	strong		0.751	TMEFF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053418.1	NM_003692	
KCND1	3750	hgsc.bcm.edu	37	X	48826490	48826490	+	Silent	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:48826490G>A	ENST00000218176.3	-	1	1486	c.189C>T	c.(187-189)gaC>gaT	p.D63D	KCND1_ENST00000376477.1_5'Flank	NM_004979.4	NP_004970.3	Q9NSA2	KCND1_HUMAN	potassium voltage-gated channel, Shal-related subfamily, member 1	63					protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	cell projection (GO:0042995)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|metal ion binding (GO:0046872)			endometrium(3)|large_intestine(7)|lung(7)|ovary(2)|prostate(1)|skin(1)|soft_tissue(1)|upper_aerodigestive_tract(2)	24					Dalfampridine(DB06637)	CCAGCAAGGTGTCTGGGTAGC	0.567																																					p.D63D		Atlas-SNP	.											.	KCND1	63	.	0			c.C189T						PASS	.						46.0	31.0	36.0					X																	48826490		2203	4300	6503	SO:0001819	synonymous_variant	3750	exon1			CAAGGTGTCTGGG	AF166003	CCDS14314.1	Xp11.23	2012-07-05			ENSG00000102057	ENSG00000102057		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6237	protein-coding gene	gene with protein product		300281				10729221, 16382104	Standard	NM_004979		Approved	Kv4.1	uc004dlx.1	Q9NSA2	OTTHUMG00000024127	ENST00000218176.3:c.189C>T	X.37:g.48826490G>A		Somatic	254	0	0		WXS	Illumina HiSeq	Phase_I	166	53	0.319277	NM_004979	A6NEF1|B2RCG0|O75671	Silent	SNP	ENST00000218176.3	37	CCDS14314.1																																																																																			.	.	none		0.567	KCND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060774.1	NM_004979	
SLC7A3	84889	hgsc.bcm.edu	37	X	70146475	70146475	+	Missense_Mutation	SNP	G	G	C	rs6525447	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:70146475G>C	ENST00000374299.3	-	10	1666	c.1522C>G	c.(1522-1524)Ctg>Gtg	p.L508V	SLC7A3_ENST00000298085.4_Missense_Mutation_p.L508V			Q8WY07	CTR3_HUMAN	solute carrier family 7 (cationic amino acid transporter, y+ system), member 3	508			L -> V (in dbSNP:rs6525447). {ECO:0000269|PubMed:15489334}.		amino acid transport (GO:0006865)|ion transport (GO:0006811)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	arginine transmembrane transporter activity (GO:0015181)|L-lysine transmembrane transporter activity (GO:0015189)			breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|liver(1)|lung(9)|ovary(1)|urinary_tract(1)	31	Renal(35;0.156)				L-Arginine(DB00125)|L-Lysine(DB00123)|L-Ornithine(DB00129)	GCAGTCCACAGCAGGTCTCCA	0.517													C|||	1513	0.400795	0.4463	0.304	3775	,	,		14389	0.3512		0.0616	False		,,,				2504	0.3027				p.L508V		Atlas-SNP	.											.	SLC7A3	76	.	0			c.C1522G						PASS	.	C	VAL/LEU,VAL/LEU	2165,1669		533,772,327,327,243	45.0	37.0	40.0		1522,1522	4.2	1.0	X	dbSNP_116	40	638,6088		31,406,170,1991,1700	yes	missense,missense	SLC7A3	NM_001048164.2,NM_032803.5	32,32	564,1178,497,2318,1943	CC,CG,C,GG,G		9.4856,43.5316,26.5436	benign,benign	508/620,508/620	70146475	2803,7757	2202	4298	6500	SO:0001583	missense	84889	exon10			TCCACAGCAGGTC	AF320612	CCDS14404.1	Xq12	2013-05-22			ENSG00000165349	ENSG00000165349		"""Solute carriers"""	11061	protein-coding gene	gene with protein product		300443				11591158	Standard	NM_001048164		Approved	CAT-3, ATRC3, FLJ14541	uc004dyn.3	Q8WY07	OTTHUMG00000021780	ENST00000374299.3:c.1522C>G	X.37:g.70146475G>C	ENSP00000363417:p.Leu508Val	Somatic	190	1	0.00526316		WXS	Illumina HiSeq	Phase_I	150	149	0.993333	NM_032803	D3DVU7|Q5JQR2|Q8N185|Q8NCA7|Q96SZ7	Missense_Mutation	SNP	ENST00000374299.3	37	CCDS14404.1	575	0.3465943339361061	149	0.4281609195402299	77	0.275	115	0.279126213592233	34	0.04607046070460705	C	0.012	-1.681666	0.00745	0.564684	0.094856	ENSG00000165349	ENST00000374299;ENST00000298085	D;D	0.87571	-2.27;-2.27	5.01	4.15	0.48705	.	0.695584	0.14611	N	0.309011	T	0.00012	0.0000	N	0.00162	-1.95	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.44174	-0.9345	9	0.12430	T	0.62	.	7.8134	0.29245	0.0:0.612:0.3015:0.0866	rs6525447;rs17265153;rs17856987;rs52796906;rs6525447	508	Q8WY07	CTR3_HUMAN	V	508	ENSP00000363417:L508V;ENSP00000298085:L508V	ENSP00000298085:L508V	L	-	1	2	SLC7A3	70063200	0.000000	0.05858	0.999000	0.59377	0.016000	0.09150	-0.142000	0.10311	0.632000	0.30432	-0.252000	0.11476	CTG	0|0.018;C|0.306	0.306	strong		0.517	SLC7A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057080.1	NM_032803	
AP5Z1	9907	hgsc.bcm.edu	37	7	4825314	4825314	+	Splice_Site	SNP	C	C	T	rs11768079	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:4825314C>T	ENST00000348624.4	+	9	1225	c.1131C>T	c.(1129-1131)caC>caT	p.H377H	AP5Z1_ENST00000401897.1_Splice_Site_p.H377H|MIR4656_ENST00000579503.1_RNA	NM_014855.2	NP_055670.1	O43299	AP5Z1_HUMAN	adaptor-related protein complex 5, zeta 1 subunit	377					cell death (GO:0008219)|double-strand break repair via homologous recombination (GO:0000724)|endosomal transport (GO:0016197)|protein transport (GO:0015031)	AP-5 adaptor complex (GO:0044599)|AP-type membrane coat adaptor complex (GO:0030119)|cytoplasm (GO:0005737)|nucleus (GO:0005634)											TCCTGAGCCACGGTGAGCCCA	0.582													C|||	359	0.0716853	0.0091	0.0317	5008	,	,		13363	0.0506		0.0676	False		,,,				2504	0.2106				p.H377H		Atlas-SNP	.											.	.	.	.	0			c.C1131T						PASS	.	C		75,4103		0,75,2014	6.0	6.0	6.0		1131	-0.4	0.9	7	dbSNP_120	6	532,7858		19,494,3682	yes	coding-synonymous-near-splice	KIAA0415	NM_014855.2		19,569,5696	TT,TC,CC		6.3409,1.7951,4.8297		377/808	4825314	607,11961	2089	4195	6284	SO:0001630	splice_region_variant	9907	exon9			GAGCCACGGTGAG	AB007875	CCDS47528.1	7p22.1	2012-03-20	2012-03-20	2012-03-20	ENSG00000242802	ENSG00000242802			22197	protein-coding gene	gene with protein product		613653	"""KIAA0415"""	KIAA0415		20613862, 22022230	Standard	NM_014855		Approved	SPG48, zeta	uc003sne.3	O43299	OTTHUMG00000151754	ENST00000348624.4:c.1132+1C>T	7.37:g.4825314C>T		Somatic	20	0	0		WXS	Illumina HiSeq	Phase_I	27	16	0.592593	NM_014855	Q8N3X2|Q96H80	Silent	SNP	ENST00000348624.4	37	CCDS47528.1																																																																																			C|0.954;T|0.046	0.046	strong		0.582	AP5Z1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323771.1		Silent
CCL25	6370	hgsc.bcm.edu	37	19	8121096	8121096	+	Missense_Mutation	SNP	G	G	A	rs74959615	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:8121096G>A	ENST00000390669.3	+	2	184	c.134G>A	c.(133-135)cGc>cAc	p.R45H	CCL25_ENST00000253451.4_Missense_Mutation_p.R45H|CCL25_ENST00000315626.4_Missense_Mutation_p.R45H			O15444	CCL25_HUMAN	chemokine (C-C motif) ligand 25	45					cell chemotaxis (GO:0060326)|cell surface receptor signaling pathway (GO:0007166)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|inflammatory response (GO:0006954)|leukocyte migration (GO:0050900)|negative regulation of leukocyte tethering or rolling (GO:1903237)|positive regulation of cell-matrix adhesion (GO:0001954)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	CCR10 chemokine receptor binding (GO:0031735)|chemokine activity (GO:0008009)|chemokine receptor binding (GO:0042379)|hormone activity (GO:0005179)			NS(1)|endometrium(1)|lung(1)|skin(1)|urinary_tract(1)	5						GTGCTCCGGCGCGCCTGGACT	0.652													G|||	155	0.0309505	0.0113	0.049	5008	,	,		12450	0.001		0.0706	False		,,,				2504	0.0348				p.R45H		Atlas-SNP	.											.	CCL25	12	.	0			c.G134A						PASS	.	G	HIS/ARG,HIS/ARG	68,4120		1,66,2027	43.0	50.0	48.0		134,134	-7.6	0.0	19	dbSNP_131	48	671,7771		25,621,3575	yes	missense,missense	CCL25	NM_001201359.1,NM_005624.3	29,29	26,687,5602	AA,AG,GG		7.9484,1.6237,5.8511	benign,benign	45/150,45/151	8121096	739,11891	2094	4221	6315	SO:0001583	missense	6370	exon3			TCCGGCGCGCCTG	U86358	CCDS12194.1, CCDS56080.1	19p13.2	2013-02-25	2002-08-22	2002-08-23	ENSG00000131142	ENSG00000131142		"""Chemokine ligands"", ""Endogenous ligands"""	10624	protein-coding gene	gene with protein product	"""Ck beta-15"", ""thymus expressed chemokine"", ""TECKvar"""	602565	"""small inducible cytokine subfamily A (Cys-Cys), member 25"""	SCYA25		9285413, 9722960	Standard	NM_005624		Approved	TECK, Ckb15	uc002mjd.3	O15444	OTTHUMG00000141287	ENST00000390669.3:c.134G>A	19.37:g.8121096G>A	ENSP00000375086:p.Arg45His	Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	123	60	0.487805	NM_001201359	A1L4J4|A6NI52|A8K9E7|B5MCA5|Q96KJ7	Missense_Mutation	SNP	ENST00000390669.3	37	CCDS12194.1	83	0.038003663003663	4	0.008130081300813009	19	0.052486187845303865	1	0.0017482517482517483	59	0.07783641160949868	G	1.941	-0.443696	0.04604	0.016237	0.079484	ENSG00000131142	ENST00000253451;ENST00000315626;ENST00000390669	T;T;T	0.49720	3.53;0.77;3.53	3.81	-7.62	0.01294	Chemokine interleukin-8-like domain (3);	1.853610	0.02434	N	0.083878	T	0.01254	0.0041	N	0.12569	0.235	0.09310	N	1	B;B;B	0.11235	0.0;0.004;0.001	B;B;B	0.10450	0.001;0.005;0.002	T	0.09207	-1.0685	10	0.12430	T	0.62	-4.9607	8.4636	0.32942	0.6331:0.0:0.2574:0.1095	.	45;45;45	C9JDZ7;O15444;A6NI52	.;CCL25_HUMAN;.	H	45	ENSP00000253451:R45H;ENSP00000324756:R45H;ENSP00000375086:R45H	ENSP00000253451:R45H	R	+	2	0	CCL25	8027096	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-3.766000	0.00372	-2.312000	0.00648	-2.069000	0.00389	CGC	G|0.950;A|0.050	0.050	strong		0.652	CCL25-003	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000280522.1	NM_005624	
SYNE1	23345	hgsc.bcm.edu	37	6	152779933	152779933	+	Missense_Mutation	SNP	G	G	A	rs34610829	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:152779933G>A	ENST00000367255.5	-	22	3128	c.2527C>T	c.(2527-2529)Cgt>Tgt	p.R843C	SYNE1_ENST00000367253.4_Missense_Mutation_p.R843C|SYNE1_ENST00000367248.3_Missense_Mutation_p.R833C|SYNE1_ENST00000265368.4_Missense_Mutation_p.R843C|SYNE1_ENST00000413186.2_Missense_Mutation_p.R843C|SYNE1_ENST00000448038.1_Missense_Mutation_p.R850C|SYNE1_ENST00000423061.1_Missense_Mutation_p.R850C|SYNE1_ENST00000495090.2_Missense_Mutation_p.R410C|SYNE1_ENST00000341594.5_Missense_Mutation_p.R850C	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	843					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)		TGTGCCTCACGCTCAAGAACT	0.403										HNSCC(10;0.0054)			G|||	58	0.0115815	0.0015	0.0187	5008	,	,		19910	0.0		0.0209	False		,,,				2504	0.0225				p.R850C		Atlas-SNP	.											.	SYNE1	3227	.	0			c.C2548T						PASS	.	G	CYS/ARG,CYS/ARG	28,4378	33.5+/-64.1	0,28,2175	123.0	115.0	118.0		2548,2527	5.3	0.7	6	dbSNP_126	118	268,8332	102.5+/-163.7	8,252,4040	yes	missense,missense	SYNE1	NM_033071.3,NM_182961.3	180,180	8,280,6215	AA,AG,GG		3.1163,0.6355,2.2759	possibly-damaging,possibly-damaging	850/8750,843/8798	152779933	296,12710	2203	4300	6503	SO:0001583	missense	23345	exon22			CCTCACGCTCAAG	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.2527C>T	6.37:g.152779933G>A	ENSP00000356224:p.Arg843Cys	Somatic	196	0	0		WXS	Illumina HiSeq	Phase_I	113	37	0.327434	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	28	0.01282051282051282	1	0.0020325203252032522	10	0.027624309392265192	0	0.0	17	0.022427440633245383	G	21.7	4.186953	0.78789	0.006355	0.031163	ENSG00000131018	ENST00000367255;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594;ENST00000367253;ENST00000367248;ENST00000413186;ENST00000495090	T;T;T;T;T;T;T;T;T	0.50277	1.26;1.26;1.26;1.26;0.75;1.26;1.26;1.26;1.26	5.34	5.34	0.76211	.	0.833365	0.10450	N	0.673167	T	0.38268	0.1034	N	0.22421	0.69	0.80722	D	1	P;P;D;P;P;P;P	0.53151	0.9;0.917;0.958;0.95;0.95;0.917;0.95	B;B;P;P;P;B;P	0.50617	0.316;0.224;0.646;0.471;0.599;0.224;0.599	T	0.35276	-0.9795	10	0.37606	T	0.19	.	19.408	0.94656	0.0:0.0:1.0:0.0	rs34610829	826;843;410;833;843;843;850	B3W695;Q8NF91;F5H422;F5GXQ8;Q8NF91-6;E7EQI5;Q8NF91-4	.;SYNE1_HUMAN;.;.;.;.;.	C	843;850;843;850;850;843;833;843;410	ENSP00000356224:R843C;ENSP00000396024:R850C;ENSP00000265368:R843C;ENSP00000390975:R850C;ENSP00000341887:R850C;ENSP00000356222:R843C;ENSP00000356217:R833C;ENSP00000414510:R843C;ENSP00000438508:R410C	ENSP00000265368:R843C	R	-	1	0	SYNE1	152821626	1.000000	0.71417	0.717000	0.30585	0.938000	0.57974	5.143000	0.64826	2.643000	0.89663	0.650000	0.86243	CGT	G|0.981;A|0.019	0.019	strong		0.403	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961	
AGAP6	414189	hgsc.bcm.edu	37	10	51748584	51748584	+	Missense_Mutation	SNP	A	A	G	rs200504295		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:51748584A>G	ENST00000374056.4	+	1	507	c.109A>G	c.(109-111)Agg>Ggg	p.R37G	AGAP6_ENST00000412531.3_Missense_Mutation_p.R37G			Q5VW22	AGAP6_HUMAN	ArfGAP with GTPase domain, ankyrin repeat and PH domain 6	37				R -> G (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						GGCAGGAGCTAGGGACAGGAT	0.592																																					p.R37G		Atlas-SNP	.											AGAP6,NS,carcinoma,0,2	AGAP6	53	2	0			c.A109G						scavenged	.																																			SO:0001583	missense	414189	exon1			GGAGCTAGGGACA		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.109A>G	10.37:g.51748584A>G	ENSP00000363168:p.Arg37Gly	Somatic	6	0	0		WXS	Illumina HiSeq	Phase_I	3	3	1	NM_001077665		Missense_Mutation	SNP	ENST00000374056.4	37		.	.	.	.	.	.	.	.	.	.	G	0	-2.861803	0.00064	.	.	ENSG00000204149	ENST00000374056;ENST00000412531	D;D	0.87966	-2.32;-2.32	1.16	1.16	0.20824	.	0.060847	0.64402	N	0.000005	T	0.65637	0.2710	.	.	.	0.09310	N	0.999999	B	0.02656	0.0	B	0.01281	0.0	T	0.51340	-0.8718	9	0.06236	T	0.91	.	3.7746	0.08654	0.2646:0.0:0.7354:0.0	.	37	C9IYN2	.	G	37	ENSP00000363168:R37G;ENSP00000400972:R37G	ENSP00000363168:R37G	R	+	1	2	AGAP6	51418590	0.944000	0.32072	0.873000	0.34254	0.023000	0.10783	0.542000	0.23222	0.072000	0.16694	-1.352000	0.01234	AGG	G|1.000;|0.000	1.000	weak		0.592	AGAP6-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_001077665	
HLA-DPB1	3115	hgsc.bcm.edu	37	6	33048542	33048542	+	Missense_Mutation	SNP	C	C	T	rs1042121	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:33048542C>T	ENST00000418931.2	+	2	310	c.194C>T	c.(193-195)gCg>gTg	p.A65V	HLA-DPA1_ENST00000419277.1_5'Flank|HLA-DPB1_ENST00000471184.1_3'UTR|HLA-DPB1_ENST00000535465.1_Missense_Mutation_p.A65V	NM_002121.5	NP_002112.3	P04440	DPB1_HUMAN	major histocompatibility complex, class II, DP beta 1	65	Beta-1.		A -> V (in allele DPB1*01:02, allele DPB1*02:01, allele DPB1*02:02, allele DPB1*02:03, allele DPB1*03:01, allele DPB1*04:02, allele DPB1*04:03, allele DPB1*05:01, allele DPB1*05:02, allele DPB1*06:01, allele DPB1*06:02, allele DPB1*08:01, allele DPB1*08:02, allele DPB1*09:01, allele DPB1*10:01, allele DPB1*10:02, allele DPB1*11:02, allele DPB1*14:01, allele DPB1*14:02, allele DPB1*15:02, allele DPB1*16:01, allele DPB1*16:02, allele DPB1*17:01, allele DPB1*17:02, allele DPB1*18:01, allele DPB1*18:02, allele DPB1*19:01, allele DPB1*19:02, allele DPB1*21:01, allele DPB1*20:01, allele DPB1*22:01, allele DPB1*22:02, allele DPB1*23:01, allele DPB1*25:01, allele DPB1*26:02, allele DPB1*29:01, allele DPB1*30:01, allele DPB1*32:01, allele DPB1*34:01, allele DPB1*35:01, allele DPB1*36:01, allele DPB1*37:01, allele DPB1*38:01, allele DPB1*41:01, allele DPB1*44:01, allele DPB1*45:01, allele DPB1*46:01, allele DPB1*47:01, allele DPB1*48:01, allele DPB1*50:01, allele DPB1*52:01, allele DPB1*54:01, allele DPB1*55:01, allele DPB1*57:01, allele DPB1*58:01, allele DPB1*59:01, allele DPB1*60:01, allele DPB1*62:01, allele DPB1*63:01, allele DPB1*67:01, allele DPB1*68:01, allele DPB1*69:01, allele DPB1*70:01, allele DPB1*71:01, allele DPB1*73:01, allele DPB1*75:01, allele DPB1*77:01, allele DPB1*78:01, allele DPB1*79:01, allele DPB1*80:01, allele DPB1*82:01, allele DPB1*83:01, allele DPB1*84:01, allele DPB1*86:01, allele DPB1*87:01, allele DPB1*88:01, allele DPB1*91:01, allele DPB1*93:01, allele DPB1*94:01, allele DPB1*95:01, allele DPB1*97:01 and allele DPB1*98:01; dbSNP:rs1042121).		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell proliferation (GO:0042102)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	peptide antigen binding (GO:0042605)			cervix(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(3)|ovary(1)|skin(1)	11						GAGGAGTTCGCGCGCTTCGAC	0.607													.|||	2930	0.585064	0.4879	0.647	5008	,	,		14910	0.8452		0.497	False		,,,				2504	0.4949				p.A65V		Atlas-SNP	.											.	HLA-DPB1	28	.	0			c.C194T						PASS	.	C	,,VAL/ALA	1491,1531		353,785,373	69.0	69.0	69.0		,,194	-0.4	0.1	6	dbSNP_86	69	2569,2849		602,1365,742	no	utr-5,utr-5,missense	HLA-DPA1,HLA-DPB1	NM_001242524.1,NM_001242525.1,NM_002121.5	,,64	955,2150,1115	TT,TC,CC		47.416,49.3382,48.1043	,,benign	,,65/259	33048542	4060,4380	1511	2709	4220	SO:0001583	missense	3115	exon2			AGTTCGCGCGCTT		CCDS4765.1	6p21.3	2013-01-11			ENSG00000223865	ENSG00000223865		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4940	protein-coding gene	gene with protein product		142858		HLA-DP1B			Standard	NM_002121		Approved		uc003ocu.2	P04440	OTTHUMG00000031076	ENST00000418931.2:c.194C>T	6.37:g.33048542C>T	ENSP00000408146:p.Ala65Val	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	43	41	0.953488	NM_002121	A0PFJ7|A5I886|A8YPB3|B5U8B4|B7VF80|B7VF87|B8ZX68|B8ZYT0|B9W5S8|B9W6F7|B9W6F9|C0MPP5|C0MPQ2|C0MPQ3|C0MPQ5|C0MPQ6|C0MPQ7|C4R9J5|C5IZL1|O00259|O19698|O19700|O19702|O19749|O46884|O77952|O98215|O98216|O98217|O98218|O98219|O98222|O98223|P01916|P04232|P13763|P79493|P79608|Q0P0L4|Q0ZFN3|Q14279|Q27S71|Q29682|Q29684|Q29698|Q29714|Q29775|Q29776|Q29778|Q29779|Q29781|Q29827|Q29828|Q29879|Q29880|Q29898|Q29977|Q2MGW3|Q30015|Q30031|Q30032|Q30033|Q30034|Q30050|Q30051|Q30052|Q30053|Q30054|Q30055|Q30174|Q4GY31|Q4JHD8|Q5ENE0|Q5ENE1|Q5ENW3|Q5EP46|Q5EP47|Q5EP49|Q5EP51|Q5EP52|Q5EP53|Q5EP56|Q5I4H8|Q5I4H9|Q5ISH4|Q5ISH5|Q5SQ73|Q5STP2|Q5YLA6|Q6IVX1|Q6LBX2|Q6LBX3|Q6LBX4|Q6LBX5|Q6LBX6|Q6LBX7|Q6PWX6|Q6TAS4|Q714U1|Q714U2|Q7YQ10|Q860Z7|Q8HWL7|Q8HWT5|Q8SNC4|Q95HC1|Q95IT7|Q95IT8|Q9BD13|Q9GIM2|Q9GIM4|Q9GIX6|Q9GJ41|Q9MY67|Q9TNT7|Q9TQE2|Q9XS11|Q9XS12	Missense_Mutation	SNP	ENST00000418931.2	37	CCDS4765.1	1334|1334	0.6108058608058609|0.6108058608058609	245|245	0.49796747967479676|0.49796747967479676	231|231	0.638121546961326|0.638121546961326	493|493	0.8618881118881119|0.8618881118881119	365|365	0.4815303430079156|0.4815303430079156	c|c	0.009|0.009	-1.840626|-1.840626	0.00573|0.00573	0.493382|0.493382	0.47416|0.47416	ENSG00000223865|ENSG00000223865	ENST00000418931;ENST00000535465;ENST00000411942;ENST00000428835|ENST00000416804	T;T;T|.	0.00297|.	8.23;8.23;8.23|.	3.61|3.61	-0.406|-0.406	0.12389|0.12389	MHC class II, alpha/beta chain, N-terminal (1);MHC class II, beta chain, N-terminal (2);MHC classes I/II-like antigen recognition protein (1);|.	1.115630|.	0.06983|.	N|.	0.820251|.	T|T	0.02929|0.02929	0.0087|0.0087	N|N	0.01168|0.01168	-0.975|-0.975	0.80722|0.80722	P|P	0.0|0.0	B|.	0.02656|.	0.0|.	B|.	0.01281|.	0.0|.	T|T	0.44375|0.44375	-0.9332|-0.9332	9|4	0.02654|.	T|.	1|.	.|.	7.4734|7.4734	0.27361|0.27361	0.0:0.4284:0.0:0.5716|0.0:0.4284:0.0:0.5716	rs1042121;rs3173297;rs9277349;rs17221115;rs17855391;rs60359396|rs1042121;rs3173297;rs9277349;rs17221115;rs17855391;rs60359396	65|.	P04440|.	DPB1_HUMAN|.	V|C	65;65;65;42|32	ENSP00000408146:A65V;ENSP00000439674:A65V;ENSP00000412654:A42V|.	ENSP00000389210:A65V|.	A|R	+|+	2|1	0|0	HLA-DPB1|HLA-DPB1	33156520|33156520	0.000000|0.000000	0.05858|0.05858	0.075000|0.075000	0.20258|0.20258	0.011000|0.011000	0.07611|0.07611	-2.384000|-2.384000	0.01063|0.01063	-0.182000|-0.182000	0.10602|0.10602	-0.386000|-0.386000	0.06593|0.06593	GCG|CGC	C|0.477;T|0.523	0.523	strong		0.607	HLA-DPB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076106.2	NM_002121	
TUBG2	27175	hgsc.bcm.edu	37	17	40818353	40818353	+	Silent	SNP	C	C	T	rs523338	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:40818353C>T	ENST00000251412.7	+	10	1208	c.1009C>T	c.(1009-1011)Ctg>Ttg	p.L337L	PLEKHH3_ENST00000456950.2_5'Flank	NM_016437.2	NP_057521.1	Q9NRH3	TBG2_HUMAN	tubulin, gamma 2	337					cytoplasmic microtubule organization (GO:0031122)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule nucleation (GO:0007020)|mitotic cell cycle (GO:0000278)	cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|gamma-tubulin complex (GO:0000930)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|pericentriolar material (GO:0000242)|spindle microtubule (GO:0005876)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural molecule activity (GO:0005198)	p.L337L(1)		central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)	15		Breast(137;0.00116)		BRCA - Breast invasive adenocarcinoma(366;0.141)		CCACAAGAGCCTGCAGAGGAT	0.672																																					p.L337L		Atlas-SNP	.											TUBG2,brain,primitive_neuroectodermal_tumour-medulloblastoma,0,1	TUBG2	43	1	1	Substitution - coding silent(1)	central_nervous_system(1)	c.C1009T						scavenged	.						46.0	48.0	47.0					17																	40818353		2203	4300	6503	SO:0001819	synonymous_variant	27175	exon10			AAGAGCCTGCAGA	AF225971	CCDS32658.1	17q21.2	2014-09-04			ENSG00000037042	ENSG00000037042		"""Tubulins"""	12419	protein-coding gene	gene with protein product		605785					Standard	NM_016437		Approved		uc010wgr.2	Q9NRH3	OTTHUMG00000180640	ENST00000251412.7:c.1009C>T	17.37:g.40818353C>T		Somatic	249	0	0		WXS	Illumina HiSeq	Phase_I	238	15	0.0630252	NM_016437	A6NDI4|Q32NB2	Silent	SNP	ENST00000251412.7	37	CCDS32658.1																																																																																			C|0.801;T|0.199	0.199	strong		0.672	TUBG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452326.1	NM_016437	
ZBBX	79740	hgsc.bcm.edu	37	3	167045779	167045779	+	Silent	SNP	G	G	A	rs375095384		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:167045779G>A	ENST00000392766.2	-	11	1153	c.813C>T	c.(811-813)acC>acT	p.T271T	ZBBX_ENST00000469220.1_Intron|ZBBX_ENST00000392764.1_Silent_p.T242T|ZBBX_ENST00000392767.2_Silent_p.T271T|ZBBX_ENST00000455345.2_Silent_p.T271T|ZBBX_ENST00000307529.5_Silent_p.T271T	NM_001199201.1|NM_024687.3	NP_001186130.1|NP_078963.2	A8MT70	ZBBX_HUMAN	zinc finger, B-box domain containing	271						intracellular (GO:0005622)	zinc ion binding (GO:0008270)	p.T271T(2)		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						CATGATTTCCGGTTCTCCATT	0.378													G|||	1	0.000199681	0.0008	0.0	5008	,	,		15273	0.0		0.0	False		,,,				2504	0.0				p.T271T		Atlas-SNP	.											ZBBX_ENST00000455345,NS,carcinoma,0,2	ZBBX	299	2	2	Substitution - coding silent(2)	endometrium(2)	c.C813T						PASS	.	G	,,	1,3745		0,1,1872	218.0	199.0	205.0		813,726,813	-3.4	0.0	3		205	0,8220		0,0,4110	no	coding-synonymous,coding-synonymous,coding-synonymous	ZBBX	NM_001199201.1,NM_001199202.1,NM_024687.3	,,	0,1,5982	AA,AG,GG		0.0,0.0267,0.0084	,,	271/840,242/772,271/801	167045779	1,11965	1873	4110	5983	SO:0001819	synonymous_variant	79740	exon11			ATTTCCGGTTCTC	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.813C>T	3.37:g.167045779G>A		Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	123	26	0.211382	NM_024687	A8MV69|B3KSC1|B5MDJ6|F2Z370|Q9H5T8	Silent	SNP	ENST00000392766.2	37	CCDS3199.2																																																																																			.	.	weak		0.378	ZBBX-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000257657.3	NM_024687	
TTC16	158248	hgsc.bcm.edu	37	9	130489558	130489558	+	Silent	SNP	A	A	G	rs472144	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:130489558A>G	ENST00000373289.3	+	12	1658	c.1578A>G	c.(1576-1578)aaA>aaG	p.K526K	TTC16_ENST00000489226.1_3'UTR|PTRH1_ENST00000419060.1_5'Flank|PTRH1_ENST00000429848.1_5'Flank	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	142	0	0		WXS	Illumina HiSeq	Phase_I	100	54	0.54	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	
IQSEC3	440073	hgsc.bcm.edu	37	12	274647	274647	+	Silent	SNP	T	T	C	rs4980859	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:274647T>C	ENST00000538872.1	+	10	2875	c.2757T>C	c.(2755-2757)ttT>ttC	p.F919F	IQSEC3_ENST00000326261.4_Silent_p.F919F|RP11-598F7.6_ENST00000537295.1_lincRNA|IQSEC3_ENST00000382841.2_Silent_p.F616F|RP11-598F7.5_ENST00000540136.1_RNA			Q9UPP2	IQEC3_HUMAN	IQ motif and Sec7 domain 3	919	PH.				actin cytoskeleton organization (GO:0030036)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|inhibitory synapse (GO:0060077)|postsynaptic membrane (GO:0045211)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(6)|lung(18)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	35	all_cancers(10;0.016)|all_lung(10;0.0222)|all_epithelial(11;0.0262)|Lung NSC(10;0.031)		OV - Ovarian serous cystadenocarcinoma(31;0.00456)	LUAD - Lung adenocarcinoma(1;0.172)|Lung(1;0.179)		CGTACACCTTTTGCAAGTCAG	0.488													C|||	1306	0.260783	0.087	0.3199	5008	,	,		23066	0.3393		0.326	False		,,,				2504	0.3057				p.F919F		Atlas-SNP	.											.	IQSEC3	154	.	0			c.T2757C						PASS	.	C	,	593,3813	771.3+/-413.8	37,519,1647	189.0	176.0	180.0		2757,1848	4.9	1.0	12	dbSNP_111	180	2729,5871	680.5+/-403.6	434,1861,2005	yes	coding-synonymous,coding-synonymous	IQSEC3	NM_001170738.1,NM_015232.1	,	471,2380,3652	CC,CT,TT		31.7326,13.4589,25.5421	,	919/1183,616/760	274647	3322,9684	2203	4300	6503	SO:0001819	synonymous_variant	440073	exon10			CACCTTTTGCAAG	AB029033	CCDS31725.1, CCDS53728.1	12p13.33	2014-03-18			ENSG00000120645	ENSG00000120645			29193	protein-coding gene	gene with protein product		612118				10470851	Standard	NM_001170738		Approved	KIAA1110, MGC30156	uc001qhw.2	Q9UPP2	OTTHUMG00000167975	ENST00000538872.1:c.2757T>C	12.37:g.274647T>C		Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	138	64	0.463768	NM_001170738	A6NIF2|A6NKV9|Q8TB43	Silent	SNP	ENST00000538872.1	37	CCDS53728.1																																																																																			T|0.740;C|0.260	0.260	strong		0.488	IQSEC3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397382.3	XM_495902	
DCUN1D1	54165	hgsc.bcm.edu	37	3	182681740	182681740	+	Silent	SNP	C	C	T	rs4859146	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:182681740C>T	ENST00000292782.4	-	3	471	c.318G>A	c.(316-318)gcG>gcA	p.A106A	DCUN1D1_ENST00000469954.1_Silent_p.A91A	NM_020640.2	NP_065691.2	Q96GG9	DCNL1_HUMAN	DCN1, defective in cullin neddylation 1, domain containing 1	106	DCUN1. {ECO:0000255|PROSITE- ProRule:PRU00574}.					ubiquitin ligase complex (GO:0000151)				endometrium(2)|large_intestine(4)|lung(8)|ovary(1)	15	all_cancers(143;9.04e-15)|Ovarian(172;0.0355)		all cancers(12;2.54e-44)|Epithelial(37;4.71e-38)|LUSC - Lung squamous cell carcinoma(7;5.04e-25)|Lung(8;5.03e-23)|OV - Ovarian serous cystadenocarcinoma(80;7.41e-21)			TGAACTTCCACGCAATAATCA	0.423													T|||	3070	0.613019	0.7322	0.7017	5008	,	,		19773	0.2738		0.7425	False		,,,				2504	0.6053				p.A106A		Atlas-SNP	.											.	DCUN1D1	27	.	0			c.G318A						PASS	.	T		3275,1131	403.5+/-332.8	1219,837,147	151.0	126.0	134.0		318	-5.4	0.9	3	dbSNP_111	134	6567,2033	354.0+/-329.3	2510,1547,243	no	coding-synonymous	DCUN1D1	NM_020640.2		3729,2384,390	TT,TC,CC		23.6395,25.6695,24.3272		106/260	182681740	9842,3164	2203	4300	6503	SO:0001819	synonymous_variant	54165	exon3			CTTCCACGCAATA	AF292100, AK056335	CCDS3240.1	3q26.3	2013-06-10	2013-06-10		ENSG00000043093	ENSG00000043093			18184	protein-coding gene	gene with protein product	"""squamous cell carcinoma related oncogene"""	605905	"""DCN1, defective in cullin neddylation 1, domain containing 1 (S. cerevisiae)"""			10777668, 15988528	Standard	NM_020640		Approved	RP42, SCRO, DCUN1L1, Tes3, SCCRO	uc003fld.1	Q96GG9	OTTHUMG00000158314	ENST00000292782.4:c.318G>A	3.37:g.182681740C>T		Somatic	201	0	0		WXS	Illumina HiSeq	Phase_I	150	148	0.986667	NM_020640	B2RB37|Q7L3G9|Q8TEX7|Q9H6M1|Q9HCT3	Silent	SNP	ENST00000292782.4	37	CCDS3240.1																																																																																			C|0.308;T|0.692	0.692	strong		0.423	DCUN1D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350658.1	NM_020640	
TLDC2	140711	hgsc.bcm.edu	37	20	35507542	35507542	+	Silent	SNP	G	G	A	rs3748459	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:35507542G>A	ENST00000217320.3	+	3	332	c.288G>A	c.(286-288)cgG>cgA	p.R96R	TLDC2_ENST00000602922.1_Silent_p.R96R	NM_080628.1	NP_542195.1	A0PJX2	TLDC2_HUMAN	TBC/LysM-associated domain containing 2	96	TLD.																TGTACCGGCGGATGGAGGGCT	0.667													G|||	1164	0.232428	0.4092	0.2046	5008	,	,		16822	0.0069		0.2982	False		,,,				2504	0.1779				p.R96R		Atlas-SNP	.											.	C20orf118	21	.	0			c.G288A						PASS	.	G		1697,2709	511.2+/-367.7	310,1077,816	55.0	47.0	50.0		288	0.8	1.0	20	dbSNP_107	50	2360,6240	390.2+/-343.2	311,1738,2251	no	coding-synonymous	C20orf118	NM_080628.1		621,2815,3067	AA,AG,GG		27.4419,38.5157,31.1933		96/216	35507542	4057,8949	2203	4300	6503	SO:0001819	synonymous_variant	140711	exon3			CCGGCGGATGGAG	AL079335	CCDS33465.1	20q11.23	2013-03-14	2013-03-14	2013-03-14	ENSG00000101342	ENSG00000101342			16112	protein-coding gene	gene with protein product	"""hypothetical protein LOC140711"", ""TLD domain containing 2"""		"""chromosome 20 open reading frame 118"""	C20orf118			Standard	NM_080628		Approved	dJ132F21.2	uc002xgg.1	A0PJX2	OTTHUMG00000032400	ENST00000217320.3:c.288G>A	20.37:g.35507542G>A		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	59	35	0.59322	NM_080628	B3KVU8	Silent	SNP	ENST00000217320.3	37	CCDS33465.1																																																																																			G|0.723;A|0.277	0.277	strong		0.667	TLDC2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079060.2	NM_080628	
MFI2	4241	hgsc.bcm.edu	37	3	196742290	196742290	+	Silent	SNP	T	T	C	rs9855410	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	122	0	0		WXS	Illumina HiSeq	Phase_I	112	58	0.517857	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		
RAB3IL1	5866	hgsc.bcm.edu	37	11	61675644	61675644	+	Missense_Mutation	SNP	T	T	C	rs174477	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:61675644T>C	ENST00000394836.2	-	2	303	c.146A>G	c.(145-147)cAa>cGa	p.Q49R	RAB3IL1_ENST00000301773.5_Missense_Mutation_p.Q96R	NM_013401.2	NP_037533.2	Q8TBN0	R3GEF_HUMAN	RAB3A interacting protein (rabin3)-like 1	49			Q -> R (in dbSNP:rs174477).		positive regulation of Rab GTPase activity (GO:0032851)|protein transport (GO:0015031)		Rab guanyl-nucleotide exchange factor activity (GO:0017112)			central_nervous_system(1)|endometrium(2)|large_intestine(2)|liver(1)|lung(4)|skin(3)|urinary_tract(1)	14						CTCCTGGCCTTGGGCCTCCTC	0.682													T|||	369	0.0736821	0.0998	0.0807	5008	,	,		15756	0.0		0.1451	False		,,,				2504	0.0358				p.Q96R		Atlas-SNP	.											RAB3IL1,NS,carcinoma,0,1	RAB3IL1	39	1	0			c.A287G						scavenged	.	T	ARG/GLN	439,3883		20,399,1742	8.0	9.0	9.0		146	-1.3	0.1	11	dbSNP_79	9	1141,7311		89,963,3174	no	missense	RAB3IL1	NM_013401.2	43	109,1362,4916	CC,CT,TT		13.4998,10.1573,12.3689	benign	49/383	61675644	1580,11194	2161	4226	6387	SO:0001583	missense	5866	exon2			TGGCCTTGGGCCT	AF084557	CCDS8014.1, CCDS60809.1	11q12.2	2008-02-01			ENSG00000167994	ENSG00000167994			9780	protein-coding gene	gene with protein product							Standard	NM_013401		Approved		uc001nso.4	Q8TBN0	OTTHUMG00000167524	ENST00000394836.2:c.146A>G	11.37:g.61675644T>C	ENSP00000378313:p.Gln49Arg	Somatic	51	1	0.0196078		WXS	Illumina HiSeq	Phase_I	86	18	0.209302	NM_001271686	Q86V32|Q9P1Q8	Missense_Mutation	SNP	ENST00000394836.2	37	CCDS8014.1	193	0.08836996336996338	53	0.10772357723577236	34	0.09392265193370165	0	0.0	106	0.13984168865435356	T	6.248	0.413969	0.11870	0.101573	0.134998	ENSG00000167994	ENST00000394836;ENST00000301773;ENST00000531922	T;T;T	0.44881	0.91;0.91;0.91	4.73	-1.31	0.09230	.	0.527456	0.16430	N	0.214781	T	0.00144	0.0004	L	0.44542	1.39	0.80722	P	0.0	P;B	0.41265	0.744;0.089	B;B	0.31495	0.131;0.021	T	0.07385	-1.0775	9	0.41790	T	0.15	1.193	0.4651	0.00523	0.1991:0.3048:0.203:0.2931	rs174477	96;49	Q8TBN0-2;Q8TBN0	.;R3GEF_HUMAN	R	49;96;96	ENSP00000378313:Q49R;ENSP00000301773:Q96R;ENSP00000435444:Q96R	ENSP00000301773:Q96R	Q	-	2	0	RAB3IL1	61432220	0.013000	0.17824	0.103000	0.21229	0.109000	0.19521	-0.071000	0.11505	-0.066000	0.12998	0.459000	0.35465	CAA	T|0.917;C|0.083	0.083	strong		0.682	RAB3IL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394917.1	NM_013401	
PSG1	5669	hgsc.bcm.edu	37	19	43372941	43372941	+	Missense_Mutation	SNP	T	T	C	rs28374299	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:43372941T>C	ENST00000436291.2	-	4	1071	c.955A>G	c.(955-957)Atc>Gtc	p.I319V	PSG1_ENST00000403380.3_Missense_Mutation_p.I226V|PSG1_ENST00000595124.1_Missense_Mutation_p.I226V|PSG1_ENST00000595356.1_Missense_Mutation_p.I319V|PSG1_ENST00000312439.6_Missense_Mutation_p.I319V|PSG1_ENST00000244296.2_Missense_Mutation_p.I319V	NM_001184825.1|NM_001184826.1	NP_001171754.1|NP_001171755.1	P11464	PSG1_HUMAN	pregnancy specific beta-1-glycoprotein 1	319	Ig-like C2-type 2.			I -> V (in Ref. 5 and 6). {ECO:0000305}.	female pregnancy (GO:0007565)	extracellular region (GO:0005576)				breast(2)|endometrium(4)|kidney(2)|large_intestine(5)|lung(9)|ovary(3)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	30		Prostate(69;0.00682)				TCACTGCGGATGCCACCATAT	0.502													.|||	1426	0.284744	0.3094	0.1945	5008	,	,		20508	0.4167		0.1014	False		,,,				2504	0.3681				p.I319V		Atlas-SNP	.											.	PSG1	196	.	0			c.A955G						PASS	.	T	VAL/ILE,VAL/ILE,VAL/ILE	847,2169		130,587,791	49.0	56.0	53.0		955,955,955	-1.5	0.0	19	dbSNP_125	53	568,4832		42,484,2174	no	missense,missense,missense	PSG1	NM_001184825.1,NM_001184826.1,NM_006905.2	29,29,29	172,1071,2965	CC,CT,TT		10.5185,28.0836,16.8132	,,	319/420,319/418,319/427	43372941	1415,7001	1508	2700	4208	SO:0001583	missense	5669	exon4			TGCGGATGCCACC		CCDS12612.1, CCDS54275.1, CCDS59392.1, CCDS74380.1	19q13.2	2013-01-29			ENSG00000231924	ENSG00000231924		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9514	protein-coding gene	gene with protein product		176390		PSBG1			Standard	NM_006905		Approved	PSGGA, CD66f, PBG1		P11464	OTTHUMG00000151123	ENST00000436291.2:c.955A>G	19.37:g.43372941T>C	ENSP00000413041:p.Ile319Val	Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	42	19	0.452381	NM_001184826	O75236|P11462|P11463|Q15231|Q15241|Q15243|Q16660|Q6ICR4|Q9P1W5|Q9UQ79	Missense_Mutation	SNP	ENST00000436291.2	37	CCDS54275.1	495	0.22664835164835165	140	0.2845528455284553	52	0.143646408839779	226	0.3951048951048951	77	0.10158311345646438	N	1.087	-0.665276	0.03428	0.280836	0.105185	ENSG00000231924	ENST00000436291;ENST00000403380;ENST00000312439;ENST00000244296	T;T;T;T	0.12039	2.72;2.72;2.72;2.72	1.79	-1.49	0.08718	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00012	0.0000	L	0.49571	1.57	0.80722	P	0.0	B;B;B;B;B	0.14012	0.0;0.009;0.001;0.0;0.002	B;B;B;B;B	0.15484	0.005;0.013;0.008;0.005;0.008	T	0.47302	-0.9128	8	0.25106	T	0.35	.	2.4632	0.04547	0.2681:0.0:0.2731:0.4588	rs28374299;rs60861449	319;226;319;319;319	P11464-4;G5E9F7;P11464;P11464-3;P11464-2	.;.;PSG1_HUMAN;.;.	V	319;226;319;319	ENSP00000413041:I319V;ENSP00000385386:I226V;ENSP00000308970:I319V;ENSP00000244296:I319V	ENSP00000244296:I319V	I	-	1	0	PSG1	48064781	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.114000	0.01329	-0.750000	0.04740	0.352000	0.21897	ATC	T|0.830;C|0.170	0.170	strong		0.502	PSG1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000321426.1		
COL9A2	1298	hgsc.bcm.edu	37	1	40766923	40766923	+	Silent	SNP	G	G	A	rs2229826	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:40766923G>A	ENST00000372748.3	-	32	2097	c.2001C>T	c.(1999-2001)gcC>gcT	p.A667A	COL9A2_ENST00000466267.1_5'Flank	NM_001852.3	NP_001843.1	Q14055	CO9A2_HUMAN	collagen, type IX, alpha 2	667	Nonhelical region 1 (NC1).				axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	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)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(4)|stomach(2)|urinary_tract(2)	22	Lung NSC(20;4.38e-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;2.08e-17)			CAAGGCAGGCGGCAGGTTCAC	0.667													T|||	49	0.00978435	0.003	0.0058	5008	,	,		15366	0.0		0.0328	False		,,,				2504	0.0082				p.A667A		Atlas-SNP	.											.	COL9A2	63	.	0			c.C2001T						PASS	.	T		28,4378		0,28,2175	31.0	37.0	35.0		2001	-10.9	0.7	1	dbSNP_98	35	213,8387		3,207,4090	no	coding-synonymous	COL9A2	NM_001852.3		3,235,6265	AA,AG,GG		2.4767,0.6355,1.853		667/690	40766923	241,12765	2203	4300	6503	SO:0001819	synonymous_variant	1298	exon32			GCAGGCGGCAGGT	M95610	CCDS450.1	1p33-p32	2013-01-16			ENSG00000049089	ENSG00000049089		"""Proteoglycans / Extracellular Matrix : Collagen proteoglycans"", ""Collagens"""	2218	protein-coding gene	gene with protein product		120260		EDM2		8454052, 8528240, 1429648	Standard	NM_001852		Approved	MED	uc001cfh.1	Q14055	OTTHUMG00000005761	ENST00000372748.3:c.2001C>T	1.37:g.40766923G>A		Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	142	77	0.542253	NM_001852	B2RMP9	Silent	SNP	ENST00000372748.3	37	CCDS450.1																																																																																			G|0.984;A|0.016	0.016	strong		0.667	COL9A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000015764.3	NM_001852	
MS4A14	84689	hgsc.bcm.edu	37	11	60183483	60183483	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:60183483T>C	ENST00000300187.6	+	5	1319	c.1042T>C	c.(1042-1044)Tct>Cct	p.S348P	MS4A14_ENST00000395005.2_Missense_Mutation_p.S331P|MS4A14_ENST00000531783.1_Missense_Mutation_p.S381P|MS4A14_ENST00000531787.1_Missense_Mutation_p.S236P|MS4A14_ENST00000395001.1_3'UTR	NM_032597.4	NP_115986.3	Q96JA4	M4A14_HUMAN	membrane-spanning 4-domains, subfamily A, member 14	348						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						CAAACAGTCTTCTAATCTGAC	0.443																																					p.S381P		Atlas-SNP	.											.	MS4A14	120	.	0			c.T1141C						PASS	.						133.0	108.0	116.0					11																	60183483		2203	4300	6503	SO:0001583	missense	84689	exon6			CAGTCTTCTAATC	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.1042T>C	11.37:g.60183483T>C	ENSP00000300187:p.Ser348Pro	Somatic	230	0	0		WXS	Illumina HiSeq	Phase_I	214	162	0.757009	NM_001261828	E9PJE3|Q2TVT5|Q3B7W3|Q86XH8|Q9NTC2	Missense_Mutation	SNP	ENST00000300187.6	37	CCDS31569.1	.	.	.	.	.	.	.	.	.	.	T	7.724	0.697733	0.15106	.	.	ENSG00000166928	ENST00000531787;ENST00000300187;ENST00000395005;ENST00000531783	T;T;T;T	0.32023	1.47;2.69;1.47;3.05	3.68	-1.06	0.10002	.	18.346600	0.00424	N	0.000065	T	0.15609	0.0376	N	0.08118	0	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.12811	-1.0533	10	0.30078	T	0.28	-0.6079	3.9787	0.09486	0.2178:0.542:0.0:0.2402	.	331;348	Q96JA4-2;Q96JA4	.;M4A14_HUMAN	P	236;348;331;381	ENSP00000437222:S236P;ENSP00000300187:S348P;ENSP00000378453:S331P;ENSP00000433761:S381P	ENSP00000300187:S348P	S	+	1	0	MS4A14	59940059	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	0.134000	0.15932	-0.196000	0.10366	0.528000	0.53228	TCT	.	.	none		0.443	MS4A14-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000395383.2		
APOL6	80830	hgsc.bcm.edu	37	22	36055130	36055130	+	Missense_Mutation	SNP	T	T	A	rs5999923	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:36055130T>A	ENST00000409652.4	+	3	795	c.519T>A	c.(517-519)aaT>aaA	p.N173K		NM_030641.3	NP_085144.1	Q9BWW8	APOL6_HUMAN	apolipoprotein L, 6	173			N -> K (in dbSNP:rs5999923). {ECO:0000269|PubMed:17974005}.		lipid transport (GO:0006869)|lipoprotein metabolic process (GO:0042157)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)	lipid binding (GO:0008289)			haematopoietic_and_lymphoid_tissue(1)|lung(4)	5						TTATCTATAATCTTAGAAACA	0.493													T|||	120	0.0239617	0.0537	0.0086	5008	,	,		20620	0.002		0.0169	False		,,,				2504	0.0245				p.N173K		Atlas-SNP	.											.	APOL6	26	.	0			c.T519A						PASS	.	T	LYS/ASN	205,4201	124.1+/-161.4	7,191,2005	61.0	63.0	62.0		519	-8.1	0.0	22	dbSNP_114	62	168,8432	78.1+/-140.7	5,158,4137	yes	missense	APOL6	NM_030641.3	94	12,349,6142	AA,AT,TT		1.9535,4.6527,2.8679	benign	173/344	36055130	373,12633	2203	4300	6503	SO:0001583	missense	80830	exon3			CTATAATCTTAGA	AY014879	CCDS13919.1	22q12.3	2013-01-24			ENSG00000221963	ENSG00000221963		"""Apolipoproteins"""	14870	protein-coding gene	gene with protein product		607256				11374903, 15671246	Standard	NM_030641		Approved	APOL-VI, APOLVI	uc003aoe.3	Q9BWW8	OTTHUMG00000150615	ENST00000409652.4:c.519T>A	22.37:g.36055130T>A	ENSP00000386280:p.Asn173Lys	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	54	23	0.425926	NM_030641	Q5R3S1|Q658J1|Q8IXX6|Q9UGG1	Missense_Mutation	SNP	ENST00000409652.4	37	CCDS13919.1	42	0.019230769230769232	26	0.052845528455284556	5	0.013812154696132596	0	0.0	11	0.014511873350923483	T	0.015	-1.542021	0.00934	0.046527	0.019535	ENSG00000221963	ENST00000409652	T	0.03358	3.96	4.05	-8.09	0.01090	.	1.657170	0.04414	N	0.366552	T	0.00440	0.0014	L	0.41632	1.29	0.09310	N	1	B	0.10296	0.003	B	0.09377	0.004	T	0.43523	-0.9386	10	0.14252	T	0.57	-4.2671	1.0684	0.01616	0.2834:0.3061:0.2313:0.1793	rs5999923;rs52798245;rs5999923	173	Q9BWW8	APOL6_HUMAN	K	173	ENSP00000386280:N173K	ENSP00000386280:N173K	N	+	3	2	APOL6	34385076	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.755000	0.00375	-3.583000	0.00137	-1.567000	0.00876	AAT	T|0.973;A|0.027	0.027	strong		0.493	APOL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319081.2	NM_030641	
OR51F1	256892	hgsc.bcm.edu	37	11	4790857	4790857	+	Silent	SNP	A	A	G	rs11033797	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:4790857A>G	ENST00000380383.1	-	1	311	c.312T>C	c.(310-312)taT>taC	p.Y104Y	OR51F1_ENST00000343430.3_Silent_p.Y97Y|MMP26_ENST00000477339.1_Intron|MMP26_ENST00000380390.1_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	100	0	0		WXS	Illumina HiSeq	Phase_I	119	24	0.201681	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	
RHBDD3	25807	hgsc.bcm.edu	37	22	29659960	29659960	+	Silent	SNP	C	C	T	rs879580	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:29659960C>T	ENST00000216085.7	-	4	820	c.396G>A	c.(394-396)gaG>gaA	p.E132E	CTA-984G1.5_ENST00000433125.1_RNA	NM_012265.1	NP_036397.1	Q9Y3P4	RHBD3_HUMAN	rhomboid domain containing 3	132					liver development (GO:0001889)|MAPK cascade (GO:0000165)|negative regulation of natural killer cell activation (GO:0032815)|positive regulation of protein catabolic process (GO:0045732)|regulation of acute inflammatory response (GO:0002673)|regulation of protein secretion (GO:0050708)|response to xenobiotic stimulus (GO:0009410)	integral component of membrane (GO:0016021)	serine-type endopeptidase activity (GO:0004252)			lung(1)|ovary(1)	2						GGCGGTGTCCCTCCCCAGCCA	0.687													c|||	1197	0.239018	0.1225	0.3818	5008	,	,		17495	0.2837		0.1561	False		,,,				2504	0.3344				p.E132E		Atlas-SNP	.											.	RHBDD3	17	.	0			c.G396A						PASS	.			536,3720		42,452,1634	18.0	17.0	17.0		396	4.2	0.4	22	dbSNP_86	17	1215,7155		76,1063,3046	no	coding-synonymous	RHBDD3	NM_012265.1		118,1515,4680	TT,TC,CC		14.5161,12.594,13.8682		132/387	29659960	1751,10875	2128	4185	6313	SO:0001819	synonymous_variant	25807	exon4			GTGTCCCTCCCCA	AL050346	CCDS13850.1	22q12.2	2006-02-22	2006-02-22	2006-02-22	ENSG00000100263	ENSG00000100263			1308	protein-coding gene	gene with protein product			"""chromosome 22 open reading frame 3"""	C22orf3		10591208, 15105437	Standard	NM_012265		Approved	PTAG	uc003aeq.1	Q9Y3P4	OTTHUMG00000151032	ENST00000216085.7:c.396G>A	22.37:g.29659960C>T		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	69	25	0.362319	NM_012265	Q6I9X3|Q9UGQ7	Silent	SNP	ENST00000216085.7	37	CCDS13850.1																																																																																			C|0.814;T|0.186	0.186	strong		0.687	RHBDD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321085.1	NM_012265	
TUBA3E	112714	hgsc.bcm.edu	37	2	130951638	130951638	+	Silent	SNP	G	G	T	rs141240951	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:130951638G>T	ENST00000312988.7	-	4	877	c.777C>A	c.(775-777)ctC>ctA	p.L259L		NM_207312.2	NP_997195	Q6PEY2	TBA3E_HUMAN	tubulin, alpha 3e	259					microtubule-based process (GO:0007017)|protein polymerization (GO:0051258)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)	p.L259L(1)		endometrium(4)|kidney(7)|large_intestine(6)|lung(9)|skin(2)	28	Colorectal(110;0.1)					GGTACGGCACGAGGTTGGTCT	0.602																																					p.L259L		Atlas-SNP	.											TUBA3E,colon,carcinoma,0,1	TUBA3E	73	1	1	Substitution - coding silent(1)	large_intestine(1)	c.C777A						scavenged	.						203.0	144.0	164.0					2																	130951638		2203	4300	6503	SO:0001819	synonymous_variant	112714	exon4			CGGCACGAGGTTG	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.777C>A	2.37:g.130951638G>T		Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	145	18	0.124138	NM_207312		Silent	SNP	ENST00000312988.7	37	CCDS2158.1																																																																																			G|0.989;T|0.011	0.011	strong		0.602	TUBA3E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254519.1	NM_207312	
FAM120B	84498	hgsc.bcm.edu	37	6	170626943	170626943	+	Silent	SNP	T	T	C	rs3800266	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:170626943T>C	ENST00000476287.1	+	2	573	c.465T>C	c.(463-465)tcT>tcC	p.S155S	FAM120B_ENST00000537664.1_Silent_p.S178S|FAM120B_ENST00000540480.1_Silent_p.S167S|FAM120B_ENST00000252510.9_Intron	NM_032448.1	NP_115824.1	Q96EK7	F120B_HUMAN	family with sequence similarity 120B	155					cell differentiation (GO:0030154)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(11)|liver(1)|lung(15)|ovary(1)|prostate(2)|skin(2)	44		Breast(66;0.000338)|Esophageal squamous(34;0.241)		OV - Ovarian serous cystadenocarcinoma(33;3.94e-22)|BRCA - Breast invasive adenocarcinoma(81;6.47e-06)|GBM - Glioblastoma multiforme(31;0.0899)		CTTTGTGTTCTTTGCAGGAAG	0.468													C|||	799	0.159545	0.0749	0.2046	5008	,	,		20185	0.2817		0.1252	False		,,,				2504	0.1513				p.S155S		Atlas-SNP	.											.	FAM120B	108	.	0			c.T465C						PASS	.	C		421,3985	787.1+/-414.8	23,375,1805	81.0	79.0	80.0		465	-12.1	0.0	6	dbSNP_107	80	1214,7386	761.9+/-407.6	95,1024,3181	no	coding-synonymous	FAM120B	NM_032448.1		118,1399,4986	CC,CT,TT		14.1163,9.5552,12.5711		155/911	170626943	1635,11371	2203	4300	6503	SO:0001819	synonymous_variant	84498	exon2			GTGTTCTTTGCAG	AB058741	CCDS5314.1, CCDS75555.1	6q27	2011-04-13	2006-07-04	2006-07-04	ENSG00000112584	ENSG00000112584			21109	protein-coding gene	gene with protein product	"""PPARgamma constitutive coactivator 1"", ""constitutive coactivator of PPAR-gamma"""	612266	"""KIAA1838"""	KIAA1838		14585507	Standard	NM_032448		Approved	PGCC1, CCPG	uc003qxp.3	Q96EK7	OTTHUMG00000016080	ENST00000476287.1:c.465T>C	6.37:g.170626943T>C		Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	93	29	0.311828	NM_032448	B4DL34|Q86V68|Q96JI9	Silent	SNP	ENST00000476287.1	37	CCDS5314.1																																																																																			T|0.857;C|0.143	0.143	strong		0.468	FAM120B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000043259.2	NM_032448	
OR4M1	441670	hgsc.bcm.edu	37	14	20249176	20249176	+	Missense_Mutation	SNP	G	G	A	rs2815960	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:20249176G>A	ENST00000315957.4	+	1	776	c.695G>A	c.(694-696)gGt>gAt	p.G232D		NM_001005500.1	NP_001005500.1	Q8NGD0	OR4M1_HUMAN	olfactory receptor, family 4, subfamily M, member 1	232			G -> D (in dbSNP:rs2815960).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(1)|endometrium(1)|large_intestine(4)|lung(32)|prostate(1)|skin(2)	42	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)		TCAGGCTCAGGTGAGAATACC	0.463																																					p.G232D		Atlas-SNP	.											.	OR4M1	104	.	0			c.G695A						PASS	.		ASP/GLY	584,3822		18,548,1637	353.0	300.0	318.0		695	3.5	1.0	14	dbSNP_100	318	2769,5831		267,2235,1798	yes	missense	OR4M1	NM_001005500.1	94	285,2783,3435	AA,AG,GG		32.1977,13.2547,25.7804	benign	232/314	20249176	3353,9653	2203	4300	6503	SO:0001583	missense	441670	exon1			GCTCAGGTGAGAA		CCDS32021.1	14q11.2	2013-09-23			ENSG00000176299	ENSG00000176299		"""GPCR / Class A : Olfactory receptors"""	14735	protein-coding gene	gene with protein product							Standard	NM_001005500		Approved		uc010tku.2	Q8NGD0	OTTHUMG00000170599	ENST00000315957.4:c.695G>A	14.37:g.20249176G>A	ENSP00000319654:p.Gly232Asp	Somatic	345	0	0		WXS	Illumina HiSeq	Phase_I	426	125	0.293427	NM_001005500	B9EH18|Q6IFA3	Missense_Mutation	SNP	ENST00000315957.4	37	CCDS32021.1	595	0.2724358974358974	42	0.08536585365853659	120	0.3314917127071823	163	0.28496503496503495	270	0.3562005277044855	.	10.89	1.478364	0.26511	0.132547	0.321977	ENSG00000176299	ENST00000315957	T	0.00293	8.26	4.42	3.53	0.40419	GPCR, rhodopsin-like superfamily (1);	0.392518	0.21951	N	0.066723	T	0.00012	0.0000	N	0.08118	0	0.37415	P	0.08660699999999999	B	0.02656	0.0	B	0.08055	0.003	T	0.16571	-1.0398	9	0.72032	D	0.01	-1.8975	7.0717	0.25181	0.2025:0.0:0.7975:0.0	rs2815960;rs52830018	232	Q8NGD0	OR4M1_HUMAN	D	232	ENSP00000319654:G232D	ENSP00000319654:G232D	G	+	2	0	OR4M1	19319016	0.000000	0.05858	1.000000	0.80357	0.744000	0.42396	0.118000	0.15605	1.225000	0.43566	0.506000	0.49869	GGT	G|0.739;A|0.261	0.261	strong		0.463	OR4M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409770.1		
LMBRD1	55788	hgsc.bcm.edu	37	6	70407465	70407465	+	Missense_Mutation	SNP	A	A	T	rs12648	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:70407465A>T	ENST00000370577.3	-	14	1636	c.1407T>A	c.(1405-1407)gaT>gaA	p.D469E	LMBRD1_ENST00000370570.1_Missense_Mutation_p.D396E	NM_018368.3	NP_060838.3	Q9NUN5	LMBD1_HUMAN	LMBR1 domain containing 1	469			D -> E (in dbSNP:rs9354880).		cobalamin metabolic process (GO:0009235)|insulin receptor internalization (GO:0038016)|negative regulation of glucose import (GO:0046325)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of protein kinase B signaling (GO:0051898)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	clathrin-coated endocytic vesicle (GO:0045334)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cobalamin binding (GO:0031419)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(7)|lung(11)|ovary(2)|upper_aerodigestive_tract(1)	31						CTTCAGGAGCATCTGCATCAC	0.303													A|||	1927	0.384784	0.1203	0.4337	5008	,	,		15161	0.5645		0.4324	False		,,,				2504	0.4734				p.D469E		Atlas-SNP	.											.	LMBRD1	61	.	0			c.T1407A						PASS	.	A	GLU/ASP	681,3725	285.2+/-278.0	55,571,1577	105.0	106.0	106.0		1407	2.0	1.0	6	dbSNP_119	106	3437,5163	502.4+/-375.7	683,2071,1546	yes	missense	LMBRD1	NM_018368.3	45	738,2642,3123	TT,TA,AA		39.9651,15.4562,31.6623	benign	469/541	70407465	4118,8888	2203	4300	6503	SO:0001583	missense	55788	exon14			AGGAGCATCTGCA	AF113224	CCDS4969.1	6q13	2011-05-12	2005-07-25	2005-07-25	ENSG00000168216	ENSG00000168216			23038	protein-coding gene	gene with protein product		612625	"""chromosome 6 open reading frame 209"""	C6orf209		19136951	Standard	NM_018368		Approved	FLJ11240, bA810I22.1, cblF	uc003pfa.3	Q9NUN5	OTTHUMG00000014985	ENST00000370577.3:c.1407T>A	6.37:g.70407465A>T	ENSP00000359609:p.Asp469Glu	Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	38	24	0.631579	NM_018368	A8K204|E1P531|Q5VUN6|Q86Y70|Q96FW4|Q9BY56|Q9NZD6	Missense_Mutation	SNP	ENST00000370577.3	37	CCDS4969.1	860	0.39377289377289376	75	0.1524390243902439	143	0.39502762430939226	318	0.5559440559440559	324	0.42744063324538256	A	13.99	2.403229	0.42613	0.154562	0.399651	ENSG00000168216	ENST00000370577;ENST00000370570	T;T	0.16743	2.32;2.32	5.71	1.99	0.26369	.	0.138126	0.64402	D	0.000004	T	0.02083	0.0065	N	0.17723	0.515	0.23831	P	0.99672224	B	0.15473	0.013	B	0.13407	0.009	T	0.46105	-0.9215	9	0.05833	T	0.94	-15.4742	6.3237	0.21232	0.7224:0.1343:0.1434:0.0	rs9354880;rs52793334;rs9354880	469	Q9NUN5	LMBD1_HUMAN	E	469;396	ENSP00000359609:D469E;ENSP00000359602:D396E	ENSP00000359602:D396E	D	-	3	2	LMBRD1	70464186	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	3.360000	0.52299	0.111000	0.17947	-0.263000	0.10527	GAT	A|0.653;T|0.347	0.347	strong		0.303	LMBRD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041124.1	NM_018368	
CACTIN	58509	hgsc.bcm.edu	37	19	3612035	3612035	+	Silent	SNP	G	G	A	rs61738769		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:3612035G>A	ENST00000429344.2	-	10	2215	c.2163C>T	c.(2161-2163)ttC>ttT	p.F721F	CACTIN_ENST00000221899.3_Silent_p.F653F|CACTIN-AS1_ENST00000592274.1_RNA|CACTIN_ENST00000248420.5_Silent_p.F721F	NM_001080543.1	NP_001074012.1	Q8WUQ7	CATIN_HUMAN	cactin, spliceosome C complex subunit	721					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)										TGACGATCTTGAAAGCGATGT	0.617													G|||	1	0.000199681	0.0	0.0	5008	,	,		17582	0.0		0.001	False		,,,				2504	0.0				p.F721F		Atlas-SNP	.											C19orf29_ENST00000429344,NS,neuroblastoma,0,2	.	.	2	0			c.C2163T						PASS	.	G	,	0,4120		0,0,2060	110.0	126.0	121.0		2163,2163	3.3	1.0	19	dbSNP_129	121	3,8363		0,3,4180	no	coding-synonymous,coding-synonymous	C19orf29	NM_001080543.1,NM_021231.1	,	0,3,6240	AA,AG,GG		0.0359,0.0,0.024	,	721/759,721/759	3612035	3,12483	2060	4183	6243	SO:0001819	synonymous_variant	58509	exon10			GATCTTGAAAGCG	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.2163C>T	19.37:g.3612035G>A		Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	156	74	0.474359	NM_021231	A6NNA9|A9UL12|O75229|Q7LE08|Q9BTA6|Q9Y5A4	Silent	SNP	ENST00000429344.2	37	CCDS45920.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	15.54	2.863785	0.51482	0.0	3.59E-4	ENSG00000226800	ENST00000447295	.	.	.	4.31	3.27	0.37495	.	.	.	.	.	T	0.54711	0.1875	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.48603	-0.9021	5	0.30078	T	0.28	.	7.8484	0.29440	0.1936:0.0:0.8064:0.0	.	.	.	.	K	103	.	ENSP00000412459:E103K	E	+	1	0	C19orf29OS	3563035	1.000000	0.71417	1.000000	0.80357	0.912000	0.54170	2.449000	0.44935	1.171000	0.42768	0.643000	0.83706	GAA	G|0.999;A|0.001	0.001	strong		0.617	CACTIN-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000457370.2		
PLEKHG5	57449	hgsc.bcm.edu	37	1	6533393	6533393	+	Missense_Mutation	SNP	G	G	C	rs61741379	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:6533393G>C	ENST00000400915.3	-	9	947	c.881C>G	c.(880-882)aCt>aGt	p.T294S	PLEKHG5_ENST00000377728.3_Missense_Mutation_p.T238S|PLEKHG5_ENST00000535355.1_Missense_Mutation_p.T307S|PLEKHG5_ENST00000544978.1_Missense_Mutation_p.T238S|PLEKHG5_ENST00000400913.1_Missense_Mutation_p.T238S|PLEKHG5_ENST00000537245.1_Missense_Mutation_p.T317S|PLEKHG5_ENST00000377725.1_Missense_Mutation_p.T238S|PLEKHG5_ENST00000340850.5_Missense_Mutation_p.T238S|PLEKHG5_ENST00000377740.3_Missense_Mutation_p.T315S|PLEKHG5_ENST00000377732.1_Missense_Mutation_p.T275S|PLEKHG5_ENST00000377748.1_Missense_Mutation_p.T315S|PLEKHG5_ENST00000377737.2_Missense_Mutation_p.T238S	NM_001042663.1	NP_001036128.1	O94827	PKHG5_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 5	294				T -> S (in Ref. 1; BAA34440). {ECO:0000305}.	apoptotic signaling pathway (GO:0097190)|endothelial cell chemotaxis (GO:0035767)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)|signal transducer activity (GO:0004871)			liver(1)	1	Ovarian(185;0.02)|all_lung(157;0.154)	all_cancers(23;1.7e-35)|all_epithelial(116;2.78e-22)|all_lung(118;7.57e-07)|Lung NSC(185;4.26e-06)|Colorectal(325;4.47e-05)|all_hematologic(16;0.00014)|Breast(487;0.000688)|Renal(390;0.0007)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0448)		Epithelial(90;5.51e-35)|GBM - Glioblastoma multiforme(13;3.57e-27)|Colorectal(212;6.23e-08)|COAD - Colon adenocarcinoma(227;1.33e-05)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000894)|BRCA - Breast invasive adenocarcinoma(365;0.00107)|STAD - Stomach adenocarcinoma(132;0.00159)|READ - Rectum adenocarcinoma(331;0.0419)		GCTGTCGCCAGTGTTGGTGCT	0.682													N|||	1431	0.285743	0.7421	0.1499	5008	,	,		14243	0.0089		0.1481	False		,,,				2504	0.1922				p.T317S		Atlas-SNP	.											.	PLEKHG5	66	.	0			c.C950G						PASS	.	C	SER/THR,SER/THR,SER/THR,SER/THR,SER/THR	2342,1862		648,1046,408	12.0	16.0	15.0		881,713,713,713,944	1.0	0.0	1	dbSNP_129	15	1057,7203		78,901,3151	yes	missense,missense,missense,missense,missense	PLEKHG5	NM_001042663.1,NM_001042664.1,NM_001042665.1,NM_020631.3,NM_198681.2	58,58,58,58,58	726,1947,3559	CC,CG,GG		12.7966,44.2912,27.2705	benign,benign,benign,benign,benign	294/1063,238/1007,238/1007,238/1007,315/1084	6533393	3399,9065	2102	4130	6232	SO:0001583	missense	57449	exon9			TCGCCAGTGTTGG	AK024676	CCDS79.1, CCDS41240.1, CCDS41241.1, CCDS57967.1, CCDS57968.1, CCDS57969.1	1p36.31	2014-09-17		2005-08-09	ENSG00000171680	ENSG00000171680		"""Pleckstrin homology (PH) domain containing"""	29105	protein-coding gene	gene with protein product	"""synectin-binding guanine exchange factor"""	611101				17564964	Standard	NM_001042663		Approved	KIAA0720, Syx, GEF720, Tech	uc010nzr.1	O94827	OTTHUMG00000000905	ENST00000400915.3:c.881C>G	1.37:g.6533393G>C	ENSP00000383706:p.Thr294Ser	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	120	58	0.483333	NM_001265592	B3KU07|B7Z2M3|B7Z5X2|F5GZ21|F5H1I0|Q5SY17|Q5T8W5|Q5T8W9|Q6ZNM0|Q7Z436|Q86YD8|Q96BS1	Missense_Mutation	SNP	ENST00000400915.3	37	CCDS41241.1	530	0.24267399267399267	358	0.7276422764227642	62	0.1712707182320442	5	0.008741258741258742	105	0.13852242744063326	C	0.001	-3.092721	0.00034	0.557088	0.127966	ENSG00000171680	ENST00000377748;ENST00000340850;ENST00000400913;ENST00000400915;ENST00000377740;ENST00000377732;ENST00000377728;ENST00000377725;ENST00000535355;ENST00000377737;ENST00000535966;ENST00000537245;ENST00000544978	T;T;T;T;T;T;T;T;T;T;T;T	0.64260	-0.09;-0.08;-0.08;-0.08;-0.09;-0.08;-0.08;-0.09;-0.08;-0.08;-0.09;-0.09	1.95	0.976	0.19727	.	0.317898	0.32640	N	0.005824	T	0.00012	0.0000	N	0.00926	-1.1	0.80722	P	0.0	B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0	B;B;B;B;B	0.01281	0.0;0.0;0.0;0.0;0.0	T	0.38067	-0.9678	9	0.10377	T	0.69	-8.5483	4.351	0.11155	0.2592:0.4874:0.2535:0.0	rs61741379	307;238;315;315;294	F5GZ21;O94827-4;Q5SY18;O94827-2;O94827	.;.;.;.;PKHG5_HUMAN	S	315;238;238;294;315;275;238;238;307;238;144;317;238	ENSP00000366977:T315S;ENSP00000344570:T238S;ENSP00000383704:T238S;ENSP00000383706:T294S;ENSP00000366969:T315S;ENSP00000366961:T275S;ENSP00000366957:T238S;ENSP00000366954:T238S;ENSP00000441445:T307S;ENSP00000366966:T238S;ENSP00000439625:T317S;ENSP00000437710:T238S	ENSP00000344570:T238S	T	-	2	0	PLEKHG5	6455980	0.002000	0.14202	0.000000	0.03702	0.017000	0.09413	0.848000	0.27710	-0.027000	0.13873	-0.216000	0.12614	ACT	G|0.755;C|0.245	0.245	strong		0.682	PLEKHG5-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000002631.1	NM_020631	
OR5D16	390144	hgsc.bcm.edu	37	11	55606302	55606302	+	Silent	SNP	G	G	T	rs6591699	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:55606302G>T	ENST00000378396.1	+	1	75	c.75G>T	c.(73-75)ctG>ctT	p.L25L		NM_001005496.1	NP_001005496.1	Q8NGK9	OR5DG_HUMAN	olfactory receptor, family 5, subfamily D, member 16	25						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(2)|large_intestine(4)|lung(26)|ovary(5)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	44		all_epithelial(135;0.208)				ACCTGGAACTGCAAATTCCCC	0.418													N|||	3371	0.673123	0.6112	0.683	5008	,	,		17728	0.7718		0.6163	False		,,,				2504	0.7065				p.L25L		Atlas-SNP	.											OR5D16,NS,carcinoma,+1,1	OR5D16	94	1	0			c.G75T						scavenged	.	G		2788,1614		906,976,319	111.0	102.0	105.0		75	-3.2	0.0	11	dbSNP_116	105	5389,3203		1699,1991,606	no	coding-synonymous	OR5D16	NM_001005496.1		2605,2967,925	TT,TG,GG		37.2789,36.6652,37.071		25/329	55606302	8177,4817	2201	4296	6497	SO:0001819	synonymous_variant	390144	exon1			GGAACTGCAAATT	AB065783	CCDS31512.1	11q11	2012-08-09			ENSG00000205029	ENSG00000205029		"""GPCR / Class A : Olfactory receptors"""	15283	protein-coding gene	gene with protein product							Standard	NM_001005496		Approved		uc010rio.2	Q8NGK9	OTTHUMG00000154233	ENST00000378396.1:c.75G>T	11.37:g.55606302G>T		Somatic	339	3	0.00884956		WXS	Illumina HiSeq	Phase_I	291	51	0.175258	NM_001005496	Q6IF65|Q96RB4	Silent	SNP	ENST00000378396.1	37	CCDS31512.1																																																																																			G|0.350;T|0.650	0.650	strong		0.418	OR5D16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334506.1	NM_001005496	
TSSK2	23617	hgsc.bcm.edu	37	22	19119751	19119751	+	Missense_Mutation	SNP	C	C	T	rs1052763	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:19119751C>T	ENST00000399635.2	+	1	1431	c.839C>T	c.(838-840)aCg>aTg	p.T280M	DGCR14_ENST00000252137.6_3'UTR	NM_053006.4	NP_443732.3	Q96PF2	TSSK2_HUMAN	testis-specific serine kinase 2	280			T -> M (in dbSNP:rs1052763). {ECO:0000269|PubMed:17344846}.		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)					CCCAAAGCCACGTCTTCTGCC	0.642													T|||	1388	0.277157	0.3631	0.2233	5008	,	,		18784	0.2133		0.1948	False		,,,				2504	0.3497				p.T280M		Atlas-SNP	.											TSSK2,NS,carcinoma,-1,1	TSSK2	29	1	0			c.C839T						PASS	.	T	,MET/THR	1402,3004	674.8+/-403.0	210,982,1011	50.0	46.0	47.0		,839	4.7	1.0	22	dbSNP_86	47	1615,6985	729.7+/-406.7	170,1275,2855	yes	utr-3,missense	DGCR14,TSSK2	NM_022719.2,NM_053006.4	,81	380,2257,3866	TT,TC,CC		18.7791,31.8202,23.197	,benign	,280/359	19119751	3017,9989	2203	4300	6503	SO:0001583	missense	23617	exon1			AAGCCACGTCTTC	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.839C>T	22.37:g.19119751C>T	ENSP00000382544:p.Thr280Met	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	57	27	0.473684	NM_053006	Q8IY55	Missense_Mutation	SNP	ENST00000399635.2	37	CCDS13755.1	535	0.24496336996336995	178	0.3617886178861789	85	0.23480662983425415	121	0.21153846153846154	151	0.19920844327176782	T	6.138	0.393751	0.11638	0.318202	0.187791	ENSG00000206203	ENST00000399635	T	0.70516	-0.49	5.7	4.67	0.58626	.	0.328506	0.26549	N	0.023741	T	0.00012	0.0000	N	0.03608	-0.345	0.58432	P	4.000000000004E-6	B	0.09022	0.002	B	0.06405	0.002	T	0.23833	-1.0177	9	0.32370	T	0.25	.	7.8473	0.29433	0.0:0.1641:0.0:0.8359	rs1052763;rs3171566;rs17743850;rs1052763	280	Q96PF2	TSSK2_HUMAN	M	280	ENSP00000382544:T280M	ENSP00000382544:T280M	T	+	2	0	TSSK2	17499751	.	.	1.000000	0.80357	0.977000	0.68977	.	.	0.993000	0.38866	-0.254000	0.11334	ACG	C|0.762;T|0.238	0.238	strong		0.642	TSSK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316431.1		
KRT84	3890	hgsc.bcm.edu	37	12	52779159	52779159	+	Missense_Mutation	SNP	G	G	A	rs145217788	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:52779159G>A	ENST00000257951.3	-	1	277	c.211C>T	c.(211-213)Cgg>Tgg	p.R71W	RP3-416H24.4_ENST00000547174.1_RNA	NM_033045.3	NP_149034.2	Q9NSB2	KRT84_HUMAN	keratin 84	71	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)		TGGATGGGCCGAGAGCCTACA	0.597													G|||	6	0.00119808	0.0	0.0	5008	,	,		18426	0.0		0.005	False		,,,				2504	0.001				p.R71W		Atlas-SNP	.											.	KRT84	61	.	0			c.C211T						PASS	.	G	TRP/ARG	3,4403	6.2+/-15.9	0,3,2200	99.0	95.0	96.0		211	3.3	0.7	12	dbSNP_134	96	21,8579	15.3+/-51.7	0,21,4279	yes	missense	KRT84	NM_033045.3	101	0,24,6479	AA,AG,GG		0.2442,0.0681,0.1845	probably-damaging	71/601	52779159	24,12982	2203	4300	6503	SO:0001583	missense	3890	exon1			TGGGCCGAGAGCC	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.211C>T	12.37:g.52779159G>A	ENSP00000257951:p.Arg71Trp	Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	118	52	0.440678	NM_033045	B2RA43|Q6ISB0|Q701L6	Missense_Mutation	SNP	ENST00000257951.3	37	CCDS8825.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	G	9.259	1.042600	0.19748	6.81E-4	0.002442	ENSG00000161849	ENST00000257951	D	0.82344	-1.6	5.15	3.33	0.38152	.	0.736856	0.12245	N	0.486182	T	0.79341	0.4429	M	0.69358	2.11	0.09310	N	1	D	0.59357	0.985	B	0.37508	0.252	T	0.72243	-0.4350	10	0.62326	D	0.03	.	12.4648	0.55751	0.1438:0.0:0.8562:0.0	.	71	Q9NSB2	KRT84_HUMAN	W	71	ENSP00000257951:R71W	ENSP00000257951:R71W	R	-	1	2	KRT84	51065426	0.048000	0.20356	0.713000	0.30519	0.014000	0.08584	0.355000	0.20163	1.553000	0.49476	-0.192000	0.12808	CGG	G|0.998;A|0.002	0.002	strong		0.597	KRT84-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405187.1	NM_033045	
TTN	7273	hgsc.bcm.edu	37	2	179421609	179421609	+	Silent	SNP	C	C	T	rs9808036	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:179421609C>T	ENST00000591111.1	-	280	83573	c.83349G>A	c.(83347-83349)gaG>gaA	p.E27783E	TTN-AS1_ENST00000438095.1_RNA|TTN_ENST00000359218.5_Silent_p.E20484E|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN_ENST00000342992.6_Silent_p.E26856E|TTN-AS1_ENST00000586452.1_RNA|TTN_ENST00000460472.2_Silent_p.E20359E|TTN-AS1_ENST00000591332.1_RNA|TTN_ENST00000589042.1_Silent_p.E29424E|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN_ENST00000342175.6_Silent_p.E20551E|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590932.1_RNA			Q8WZ42	TITIN_HUMAN	titin	27783	Fibronectin type-III 102. {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)			GCCCTACAACCTCAGATGGAT	0.403													C|||	422	0.0842652	0.0378	0.1527	5008	,	,		22559	0.0248		0.0477	False		,,,				2504	0.1973				p.E29424E		Atlas-SNP	.											.	TTN	18412	.	0			c.G88272A						PASS	.	C	,,,	139,3671		0,139,1766	92.0	88.0	89.0		61077,80568,61452,61653	1.0	0.5	2	dbSNP_119	89	241,8033		8,225,3904	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	,,,	8,364,5670	TT,TC,CC		2.9127,3.6483,3.1447	,,,	20359/26927,26856/33424,20484/27052,20551/27119	179421609	380,11704	1905	4137	6042	SO:0001819	synonymous_variant	7273	exon330			TACAACCTCAGAT	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.83349G>A	2.37:g.179421609C>T		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	88	50	0.568182	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	37																																																																																				C|0.955;T|0.045	0.045	strong		0.403	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
TMPRSS3	64699	hgsc.bcm.edu	37	21	43803167	43803167	+	Missense_Mutation	SNP	T	T	C	rs2839500	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:43803167T>C	ENST00000291532.3	-	8	1712	c.757A>G	c.(757-759)Atc>Gtc	p.I253V	TMPRSS3_ENST00000433957.2_Missense_Mutation_p.I253V|TMPRSS3_ENST00000398405.1_Missense_Mutation_p.I251V|TMPRSS3_ENST00000380399.1_Missense_Mutation_p.I337V|TMPRSS3_ENST00000398397.3_Missense_Mutation_p.I253V|TMPRSS3_ENST00000474596.1_5'UTR	NM_032404.2	NP_115780.1	P57727	TMPS3_HUMAN	transmembrane protease, serine 3	253	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.		I -> V (in dbSNP:rs2839500). {ECO:0000269|PubMed:11424922}.		cellular sodium ion homeostasis (GO:0006883)|proteolysis (GO:0006508)|sensory perception of sound (GO:0007605)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)|sodium channel regulator activity (GO:0017080)			breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(2)|ovary(4)|skin(1)	13						GCAGCAGTGATGATCCACAGG	0.592													C|||	1208	0.241214	0.3041	0.134	5008	,	,		20674	0.3323		0.1113	False		,,,				2504	0.272				p.I253V		Atlas-SNP	.											.	TMPRSS3	40	.	0			c.A757G						PASS	.	C	VAL/ILE,VAL/ILE	1196,3210	708.6+/-407.6	161,874,1168	75.0	64.0	68.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	757,757	4.6	0.5	21	dbSNP_100	68	887,7713	778.9+/-407.7	37,813,3450	yes	missense,missense	TMPRSS3	NM_024022.2,NM_032405.1	29,29	198,1687,4618	CC,CT,TT		10.314,27.1448,16.0157	benign,benign	253/455,253/345	43803167	2083,10923	2203	4300	6503	SO:0001583	missense	64699	exon8			CAGTGATGATCCA	AF201380	CCDS13686.1, CCDS42939.1, CCDS58790.1	21q22.3	2010-04-13			ENSG00000160183	ENSG00000160183		"""Serine peptidases / Transmembrane"""	11877	protein-coding gene	gene with protein product		605511		DFNB10, DFNB8		11462234, 11907649	Standard	NM_032405		Approved		uc002zbc.3	P57727	OTTHUMG00000086796	ENST00000291532.3:c.757A>G	21.37:g.43803167T>C	ENSP00000291532:p.Ile253Val	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	81	80	0.987654	NM_001256317	D3DSJ6|Q5USC7|Q6ZMC3	Missense_Mutation	SNP	ENST00000291532.3	37	CCDS13686.1	494	0.2261904761904762	154	0.3130081300813008	54	0.14917127071823205	203	0.3548951048951049	83	0.10949868073878628	C	0.696	-0.792701	0.02884	0.271448	0.10314	ENSG00000160183	ENST00000291532;ENST00000433957;ENST00000398405;ENST00000380399;ENST00000398397	T;T;T;T;T	0.80994	0.25;-1.44;-1.44;0.25;-1.44	5.5	4.59	0.56863	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.159777	0.42053	N	0.000763	T	0.00012	0.0000	N	0.11698	0.16	0.58432	P	1.999999999946489E-6	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.06405	0.001;0.001;0.002	T	0.14980	-1.0453	8	.	.	.	.	8.2005	0.31421	0.0:0.5343:0.3254:0.1403	rs2839500;rs52817606;rs60045807;rs2839500	253;253;253	P57727-3;P57727-5;P57727	.;.;TMPS3_HUMAN	V	253;253;251;337;253	ENSP00000291532:I253V;ENSP00000411013:I253V;ENSP00000381442:I251V;ENSP00000369762:I337V;ENSP00000381434:I253V	.	I	-	1	0	TMPRSS3	42676236	0.025000	0.19082	0.465000	0.27155	0.794000	0.44872	0.113000	0.15499	0.658000	0.30925	-0.186000	0.12905	ATC	A|0.006;C|0.194	0.194	strong		0.592	TMPRSS3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000195347.1		
MARVELD3	91862	hgsc.bcm.edu	37	16	71660404	71660404	+	Missense_Mutation	SNP	G	G	A	rs61753635	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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|MARVELD3_ENST00000567566.1_Missense_Mutation_p.R91Q|MARVELD3_ENST00000299952.4_Missense_Mutation_p.R91Q|RP11-432I5.2_ENST00000562763.1_RNA|MARVELD3_ENST00000567501.1_5'Flank	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	21	0	0		WXS	Illumina HiSeq	Phase_I	35	15	0.428571	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	
RIN3	79890	hgsc.bcm.edu	37	14	93118198	93118198	+	Silent	SNP	C	C	T	rs3814830	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	103	0	0		WXS	Illumina HiSeq	Phase_I	57	27	0.473684	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		
NSD1	64324	hgsc.bcm.edu	37	5	176721119	176721119	+	Missense_Mutation	SNP	G	G	A	rs35848863	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:176721119G>A	ENST00000439151.2	+	23	6795	c.6750G>A	c.(6748-6750)atG>atA	p.M2250I	NSD1_ENST00000354179.4_Missense_Mutation_p.M1981I|NSD1_ENST00000361032.4_Missense_Mutation_p.M2147I|NSD1_ENST00000347982.4_Missense_Mutation_p.M1981I	NM_022455.4	NP_071900.2	Q96L73	NSD1_HUMAN	nuclear receptor binding SET domain protein 1	2250	Pro-rich.		M -> I (in dbSNP:rs35848863). {ECO:0000269|PubMed:12464997}.		gastrulation with mouth forming second (GO:0001702)|histone H3-K36 methylation (GO:0010452)|histone H4-K20 methylation (GO:0034770)|histone methylation (GO:0016571)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|estrogen receptor binding (GO:0030331)|histone methyltransferase activity (H3-K36 specific) (GO:0046975)|histone methyltransferase activity (H4-K20 specific) (GO:0042799)|retinoic acid receptor binding (GO:0042974)|retinoid X receptor binding (GO:0046965)|thyroid hormone receptor binding (GO:0046966)|transcription cofactor activity (GO:0003712)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(18)|lung(24)|ovary(2)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(3)	96	all_cancers(89;1.57e-05)|Renal(175;0.000269)|Lung NSC(126;0.00111)|all_lung(126;0.002)	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)|Epithelial(233;0.198)	Kidney(146;0.235)		CACCCAAAATGTCAGATAAAC	0.547			T	NUP98	AML		Sotos Syndrome		Weaver syndrome;Sotos syndrome;Beckwith-Wiedemann syndrome	HNSCC(47;0.14)			G|||	259	0.0517173	0.0734	0.0274	5008	,	,		18870	0.0179		0.0427	False		,,,				2504	0.0838				p.M2250I		Atlas-SNP	.		Dom	yes		5	5q35	64324	nuclear receptor binding SET domain protein 1	yes	L	.	NSD1	416	.	0			c.G6750A						PASS	.	G	ILE/MET,ILE/MET	260,4146	148.0+/-182.4	7,246,1950	80.0	80.0	80.0		6750,5943	1.5	0.2	5	dbSNP_126	80	420,8180	130.3+/-188.3	8,404,3888	yes	missense,missense	NSD1	NM_022455.4,NM_172349.2	10,10	15,650,5838	AA,AG,GG		4.8837,5.901,5.2284	benign,benign	2250/2697,1981/2428	176721119	680,12326	2203	4300	6503	SO:0001583	missense	64324	exon23	Familial Cancer Database	Weaver-Smith syndrome;Cerebral Gigantism;BWS, Exomphalos-Macroglossia-Gigantism (EMG) syndrome, Wiedemann-Beckwith syndrome, WBS	CAAAATGTCAGAT	AK026066	CCDS4412.1, CCDS4413.1	5q35	2014-09-17	2003-03-12		ENSG00000165671	ENSG00000165671		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	14234	protein-coding gene	gene with protein product		606681	"""Sotos syndrome"""	STO		9628876, 11896389	Standard	NM_022455		Approved	ARA267, FLJ22263, KMT3B	uc003mfr.4	Q96L73	OTTHUMG00000130846	ENST00000439151.2:c.6750G>A	5.37:g.176721119G>A	ENSP00000395929:p.Met2250Ile	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	60	21	0.35	NM_022455	Q96PD8|Q96RN7	Missense_Mutation	SNP	ENST00000439151.2	37	CCDS4412.1	87	0.03983516483516483	37	0.07520325203252033	10	0.027624309392265192	7	0.012237762237762238	33	0.04353562005277045	G	8.093	0.774950	0.16051	0.05901	0.048837	ENSG00000165671	ENST00000354179;ENST00000439151;ENST00000347982;ENST00000361032	T;T;T;T	0.78246	-1.16;-1.16;-1.16;-1.16	5.34	1.47	0.22746	.	0.517985	0.19554	N	0.111481	T	0.05914	0.0154	N	0.19112	0.55	0.09310	N	1	B;B	0.23990	0.095;0.057	B;B	0.21917	0.037;0.016	T	0.06807	-1.0806	10	0.37606	T	0.19	.	1.7561	0.02982	0.293:0.1286:0.4462:0.1323	rs35848863;rs61736340	1981;2250	Q96L73-2;Q96L73	.;NSD1_HUMAN	I	1981;2250;1981;2147	ENSP00000346111:M1981I;ENSP00000395929:M2250I;ENSP00000343209:M1981I;ENSP00000354310:M2147I	ENSP00000343209:M1981I	M	+	3	0	NSD1	176653725	0.000000	0.05858	0.182000	0.23118	0.775000	0.43874	0.050000	0.14120	0.081000	0.16988	0.655000	0.94253	ATG	G|0.952;A|0.048	0.048	strong		0.547	NSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253412.2	NM_172349	
C1orf85	112770	hgsc.bcm.edu	37	1	156263940	156263940	+	Missense_Mutation	SNP	T	T	C	rs10908495	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:156263940T>C	ENST00000362007.1	-	4	693	c.667A>G	c.(667-669)Att>Gtt	p.I223V	C1orf85_ENST00000482579.1_5'Flank	NM_001256604.1|NM_001256609.1|NM_144580.2	NP_001243533.1|NP_001243538.1|NP_653181.1	Q8WWB7	NCUG1_HUMAN	chromosome 1 open reading frame 85	223			I -> V (in dbSNP:rs10908495). {ECO:0000269|PubMed:15489334}.		intracellular receptor signaling pathway (GO:0030522)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|nucleus (GO:0005634)	ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|endometrium(2)|large_intestine(1)|lung(2)|ovary(2)|prostate(2)|skin(3)	14	Hepatocellular(266;0.158)					GAGGCTCCAATCAGGGCCACC	0.627													C|||	1034	0.20647	0.0923	0.2795	5008	,	,		18007	0.2272		0.2694	False		,,,				2504	0.2229				p.I223V		Atlas-SNP	.											.	C1orf85	41	.	0			c.A667G						PASS	.	C	VAL/ILE	544,3862	774.6+/-414.0	33,478,1692	57.0	58.0	58.0		667	2.5	0.9	1	dbSNP_120	58	2522,6078	693.0+/-404.6	385,1752,2163	yes	missense	C1orf85	NM_144580.1	29	418,2230,3855	CC,CT,TT		29.3256,12.3468,23.5737	benign	223/407	156263940	3066,9940	2203	4300	6503	SO:0001583	missense	112770	exon4			CTCCAATCAGGGC	BC011575	CCDS1139.1, CCDS72947.1, CCDS72948.1, CCDS72949.1	1q22	2014-08-07			ENSG00000198715	ENSG00000198715			29436	protein-coding gene	gene with protein product	"""kidney lysosomal membrane protein"""					12975309, 18021396, 19489740	Standard	NM_144580		Approved	MGC31963, NCU-G1	uc001foh.4	Q8WWB7	OTTHUMG00000019789	ENST00000362007.1:c.667A>G	1.37:g.156263940T>C	ENSP00000354553:p.Ile223Val	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	65	33	0.507692	NM_001256608	A6NH16|B4DJN4|Q5SZX4|Q6UX96|Q8IV07|Q96F65	Missense_Mutation	SNP	ENST00000362007.1	37	CCDS1139.1	468	0.21428571428571427	46	0.09349593495934959	82	0.2265193370165746	135	0.23601398601398602	205	0.2704485488126649	C	0.703	-0.790072	0.02884	0.123468	0.293256	ENSG00000198715	ENST00000362007;ENST00000368264	T;T	0.20598	2.06;2.06	5.53	2.5	0.30297	.	0.633137	0.15407	N	0.263993	T	0.01124	0.0037	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	0.47275	-0.9130	9	0.14656	T	0.56	-15.783	6.1842	0.20488	0.2601:0.5935:0.0:0.1463	rs10908495;rs59165206;rs10908495	142;223	Q8WWB7-2;Q8WWB7	.;NCUG1_HUMAN	V	223;137	ENSP00000354553:I223V;ENSP00000357247:I137V	ENSP00000354553:I223V	I	-	1	0	C1orf85	154530564	0.004000	0.15560	0.917000	0.36280	0.600000	0.36913	-0.073000	0.11468	0.301000	0.22738	-0.355000	0.07637	ATT	T|0.785;C|0.215	0.215	strong		0.627	C1orf85-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052108.1	NM_144580	
AGAP1	116987	hgsc.bcm.edu	37	2	236403462	236403462	+	Silent	SNP	C	C	T	rs8178993	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:236403462C>T	ENST00000304032.8	+	1	712	c.132C>T	c.(130-132)aaC>aaT	p.N44N	AGAP1_ENST00000409457.1_Silent_p.N44N|AGAP1_ENST00000336665.5_Silent_p.N44N	NM_001037131.2	NP_001032208.1	Q9UPQ3	AGAP1_HUMAN	ArfGAP with GTPase domain, ankyrin repeat and PH domain 1	44					protein transport (GO:0015031)|regulation of ARF GTPase activity (GO:0032312)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	ARF GTPase activator activity (GO:0008060)|GTP binding (GO:0005525)|phospholipid binding (GO:0005543)|zinc ion binding (GO:0008270)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(12)|lung(11)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	41						TGCTGCAGAACCAGATCCGGG	0.701													c|||	62	0.0123802	0.0015	0.0303	5008	,	,		6840	0.0		0.0338	False		,,,				2504	0.0051				p.N44N		Atlas-SNP	.											.	AGAP1	95	.	0			c.C132T						PASS	.	C	,	28,4376	33.5+/-64.1	0,28,2174	36.0	39.0	38.0		132,132	2.3	1.0	2	dbSNP_117	38	278,8322	102.5+/-163.7	3,272,4025	no	coding-synonymous,coding-synonymous	AGAP1	NM_001037131.2,NM_014914.4	,	3,300,6199	TT,TC,CC		3.2326,0.6358,2.3531	,	44/858,44/805	236403462	306,12698	2202	4300	6502	SO:0001819	synonymous_variant	116987	exon1			GCAGAACCAGATC	AF413078	CCDS2514.1, CCDS33408.1, CCDS58756.1	2q37	2013-01-10	2008-09-22	2008-09-22	ENSG00000157985	ENSG00000157985		"""ADP-ribosylation factor GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"", ""Ankyrin repeat domain containing"""	16922	protein-coding gene	gene with protein product		608651	"""centaurin, gamma 2"""	CENTG2			Standard	NM_001037131		Approved	KIAA1099, GGAP1	uc002vvs.3	Q9UPQ3	OTTHUMG00000133293	ENST00000304032.8:c.132C>T	2.37:g.236403462C>T		Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	126	59	0.468254	NM_014914	B2RTX7|Q541S5|Q6P9D7|Q9NV93	Silent	SNP	ENST00000304032.8	37	CCDS33408.1																																																																																			C|0.978;T|0.022	0.022	strong		0.701	AGAP1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000257076.2	NM_014914	
DISP1	84976	hgsc.bcm.edu	37	1	223176275	223176275	+	Silent	SNP	G	G	A	rs61738819	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:223176275G>A	ENST00000284476.6	+	8	1700	c.1536G>A	c.(1534-1536)gtG>gtA	p.V512V		NM_032890.3	NP_116279.2	Q96F81	DISP1_HUMAN	dispatched homolog 1 (Drosophila)	512	SSD. {ECO:0000255|PROSITE- ProRule:PRU00199}.				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)		TAGCCATTGTGATTGTCCTTT	0.383													G|||	287	0.0573083	0.0121	0.0692	5008	,	,		23825	0.0		0.1392	False		,,,				2504	0.0849				p.V512V		Atlas-SNP	.											.	DISP1	145	.	0			c.G1536A						PASS	.	G		177,4229	114.6+/-152.6	6,165,2032	129.0	121.0	124.0		1536	1.5	0.0	1	dbSNP_129	124	1299,7301	256.6+/-281.0	97,1105,3098	no	coding-synonymous	DISP1	NM_032890.3		103,1270,5130	AA,AG,GG		15.1047,4.0172,11.3486		512/1525	223176275	1476,11530	2203	4300	6503	SO:0001819	synonymous_variant	84976	exon10			CATTGTGATTGTC	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.1536G>A	1.37:g.223176275G>A		Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	148	49	0.331081	NM_032890	Q8N7C2|Q96I92|Q9H698|Q9H8H9|Q9UFA2	Silent	SNP	ENST00000284476.6	37	CCDS1536.1																																																																																			G|0.899;A|0.101	0.101	strong		0.383	DISP1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092512.1	NM_032890	
VIPR2	7434	hgsc.bcm.edu	37	7	158902567	158902567	+	Silent	SNP	G	G	A	rs3750071	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:158902567G>A	ENST00000262178.2	-	3	380	c.195C>T	c.(193-195)gcC>gcT	p.A65A	VIPR2_ENST00000402066.1_Silent_p.A206A	NM_003382.4	NP_003373.2	P41587	VIPR2_HUMAN	vasoactive intestinal peptide receptor 2	65					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)	p.A65A(1)		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)		CTCCCACATTGGCAGGCCGCC	0.557													G|||	494	0.0986422	0.1596	0.0519	5008	,	,		18715	0.0665		0.0875	False		,,,				2504	0.0941				p.A65A	Pancreas(154;1876 1931 2329 17914 20079)	Atlas-SNP	.											VIPR2,NS,carcinoma,0,1	VIPR2	53	1	1	Substitution - coding silent(1)	stomach(1)	c.C195T						PASS	.	G		611,3795	268.9+/-268.7	45,521,1637	90.0	82.0	85.0		195	-9.4	0.0	7	dbSNP_107	85	716,7884	175.5+/-225.5	33,650,3617	no	coding-synonymous	VIPR2	NM_003382.4		78,1171,5254	AA,AG,GG		8.3256,13.8675,10.203		65/439	158902567	1327,11679	2203	4300	6503	SO:0001819	synonymous_variant	7434	exon3			CACATTGGCAGGC	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.195C>T	7.37:g.158902567G>A		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	61	22	0.360656	NM_003382	Q13053|Q15870|Q53Y09|Q6ZN22|Q9UCW0	Silent	SNP	ENST00000262178.2	37	CCDS5950.1	196	0.08974358974358974	89	0.18089430894308944	21	0.058011049723756904	27	0.0472027972027972	59	0.07783641160949868	G	1.678	-0.507197	0.04231	0.138675	0.083256	ENSG00000106018	ENST00000418475	.	.	.	5.21	-9.37	0.00626	.	.	.	.	.	.	.	.	.	.	.	0.21822	P	0.999528623	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.7543	0.00996	0.214:0.2203:0.1648:0.401	rs3750071;rs3750071	.	.	.	X	61	.	.	Q	-	1	0	VIPR2	158595328	0.001000	0.12720	0.009000	0.14445	0.151000	0.21798	-2.358000	0.01085	-2.254000	0.00697	-1.083000	0.02208	CAA	G|0.898;A|0.102	0.102	strong		0.557	VIPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322675.1	NM_003382	
PDDC1	347862	hgsc.bcm.edu	37	11	772490	772490	+	Silent	SNP	G	G	A	rs12224894	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:772490G>A	ENST00000319863.8	-	5	408	c.387C>T	c.(385-387)gcC>gcT	p.A129A	PDDC1_ENST00000397472.2_Silent_p.A129A|PDDC1_ENST00000529966.1_5'UTR|PDDC1_ENST00000526325.1_Silent_p.A129A|PDDC1_ENST00000524550.1_Silent_p.A93A|PDDC1_ENST00000442059.2_Silent_p.A79A	NM_182612.2	NP_872418.1	Q8NB37	PDDC1_HUMAN	Parkinson disease 7 domain containing 1	129						extracellular vesicular exosome (GO:0070062)				kidney(1)|lung(3)|urinary_tract(1)	5		all_cancers(49;1.13e-08)|all_epithelial(84;2.95e-05)|Breast(177;0.000286)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.159)|all_lung(207;0.198)		all cancers(45;3.66e-26)|Epithelial(43;2.43e-25)|OV - Ovarian serous cystadenocarcinoma(40;1.33e-19)|BRCA - Breast invasive adenocarcinoma(625;4.29e-05)|Lung(200;0.0582)|LUSC - Lung squamous cell carcinoma(625;0.0703)		AGCACAGGGCGGCGACACCGT	0.667													g|||	1539	0.307308	0.1687	0.5893	5008	,	,		17437	0.2827		0.4354	False		,,,				2504	0.1881				p.A129A		Atlas-SNP	.											.	PDDC1	16	.	0			c.C387T						PASS	.			957,3449		101,755,1347	145.0	130.0	135.0		387	-8.5	0.1	11	dbSNP_120	135	4144,4456		1005,2134,1161	no	coding-synonymous	PDDC1	NM_182612.2		1106,2889,2508	AA,AG,GG		48.186,21.7204,39.2204		129/221	772490	5101,7905	2203	4300	6503	SO:0001819	synonymous_variant	347862	exon5			CAGGGCGGCGACA	AK128653	CCDS7713.1	11p15.5	2005-10-26			ENSG00000177225	ENSG00000177225			26616	protein-coding gene	gene with protein product							Standard	XM_005252898		Approved	FLJ34283	uc001lrc.3	Q8NB37	OTTHUMG00000133315	ENST00000319863.8:c.387C>T	11.37:g.772490G>A		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	86	11	0.127907	NM_182612	B7ZKW5|Q2NL76|Q6ZQY0|Q8NAE0	Silent	SNP	ENST00000319863.8	37	CCDS7713.1																																																																																			G|0.633;A|0.367	0.367	strong		0.667	PDDC1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258051.2	NM_182612	
COG1	9382	hgsc.bcm.edu	37	17	71193525	71193525	+	Missense_Mutation	SNP	G	G	C	rs117208167	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:71193525G>C	ENST00000299886.4	+	4	983	c.903G>C	c.(901-903)caG>caC	p.Q301H	RP11-143K11.5_ENST00000580671.1_RNA	NM_018714.2	NP_061184.1	Q8WTW3	COG1_HUMAN	component of oligomeric golgi complex 1	301					Golgi organization (GO:0007030)|intra-Golgi vesicle-mediated transport (GO:0006891)|protein transport (GO:0015031)	Golgi apparatus (GO:0005794)|Golgi transport complex (GO:0017119)|membrane (GO:0016020)				breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(3)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18			LUSC - Lung squamous cell carcinoma(166;0.197)			TCACAGGCCAGCATCCTGCCG	0.522													G|||	15	0.00299521	0.0008	0.0	5008	,	,		18880	0.001		0.0099	False		,,,				2504	0.0031				p.Q301H		Atlas-SNP	.											.	COG1	46	.	0			c.G903C						PASS	.	G	HIS/GLN	6,4400	11.4+/-27.6	0,6,2197	64.0	62.0	63.0		903	3.3	0.9	17	dbSNP_132	63	71,8529	43.1+/-100.9	0,71,4229	yes	missense	COG1	NM_018714.2	24	0,77,6426	CC,CG,GG		0.8256,0.1362,0.592	probably-damaging	301/981	71193525	77,12929	2203	4300	6503	SO:0001583	missense	9382	exon4			AGGCCAGCATCCT		CCDS11692.1	17q25.1	2008-05-14	2002-05-28	2002-05-31		ENSG00000166685		"""Components of oligomeric golgi complex"""	6545	protein-coding gene	gene with protein product		606973	"""low density lipoprotein receptor defect B complementing"""	LDLB		9927668	Standard	NM_018714		Approved	KIAA1381	uc002jjg.3	Q8WTW3		ENST00000299886.4:c.903G>C	17.37:g.71193525G>C	ENSP00000299886:p.Gln301His	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	49	24	0.489796	NM_018714	Q9NPV9|Q9P2G6	Missense_Mutation	SNP	ENST00000299886.4	37	CCDS11692.1	8	0.003663003663003663	0	0.0	0	0.0	1	0.0017482517482517483	7	0.009234828496042216	G	8.408	0.843455	0.16963	0.001362	0.008256	ENSG00000166685	ENST00000438720;ENST00000299886	T;T	0.24908	1.83;1.84	5.31	3.26	0.37387	.	0.492896	0.23176	N	0.051061	T	0.27798	0.0684	M	0.72479	2.2	0.40675	D	0.982259	D;D;D	0.57571	0.98;0.964;0.98	P;P;P	0.52267	0.694;0.679;0.694	T	0.06661	-1.0814	10	0.44086	T	0.13	-3.2025	7.9278	0.29885	0.1457:0.1339:0.7204:0.0	.	301;301;301	E9PBL8;Q8WTW3;Q4G0L8	.;COG1_HUMAN;.	H	301	ENSP00000400111:Q301H;ENSP00000299886:Q301H	ENSP00000299886:Q301H	Q	+	3	2	COG1	68705120	0.612000	0.27000	0.889000	0.34880	0.675000	0.39556	1.226000	0.32563	0.686000	0.31488	0.655000	0.94253	CAG	G|0.994;C|0.006	0.006	strong		0.522	COG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441638.1		
RIN2	54453	hgsc.bcm.edu	37	20	19955713	19955713	+	Silent	SNP	G	G	C	rs149398614	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:19955713G>C	ENST00000255006.6	+	8	1340	c.1191G>C	c.(1189-1191)ctG>ctC	p.L397L	RIN2_ENST00000484638.1_3'UTR|RIN2_ENST00000440354.2_Intron	NM_001242581.1|NM_018993.3	NP_001229510.1|NP_061866.1	Q8WYP3	RIN2_HUMAN	Ras and Rab interactor 2	348					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						ACGTAGCTCTGCCTGGAACGA	0.562													G|||	37	0.00738818	0.0015	0.0058	5008	,	,		333	0.0		0.0298	False		,,,				2504	0.001				p.L397L		Atlas-SNP	.											.	RIN2	126	.	0			c.G1191C						PASS	.	G	,	20,4018		0,20,1999	107.0	116.0	113.0		1191,1044	3.5	0.1	20	dbSNP_134	113	236,8124		5,226,3949	no	coding-synonymous,coding-synonymous	RIN2	NM_001242581.1,NM_018993.3	,	5,246,5948	CC,CG,GG		2.823,0.4953,2.0648	,	397/945,348/896	19955713	256,12142	2019	4180	6199	SO:0001819	synonymous_variant	54453	exon8			AGCTCTGCCTGGA	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.1191G>C	20.37:g.19955713G>C		Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	34	19	0.558824	NM_001242581	Q00425|Q5TFT8|Q9BQL3|Q9H071	Silent	SNP	ENST00000255006.6	37	CCDS56182.1																																																																																			G|0.983;C|0.017	0.017	strong		0.562	RIN2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078212.1		
DIP2C	22982	hgsc.bcm.edu	37	10	323283	323283	+	Silent	SNP	A	A	G	rs3740304	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:323283A>G	ENST00000280886.6	-	37	4740	c.4653T>C	c.(4651-4653)taT>taC	p.Y1551Y	AL603831.1_ENST00000579524.1_RNA	NM_014974.2	NP_055789.1	Q9Y2E4	DIP2C_HUMAN	DIP2 disco-interacting protein 2 homolog C (Drosophila)	1551						nucleus (GO:0005634)	catalytic activity (GO:0003824)			breast(8)|endometrium(6)|kidney(10)|large_intestine(13)|lung(26)|ovary(3)|prostate(6)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(4)	81		all_cancers(4;0.00336)|all_lung(4;0.00732)|Lung NSC(4;0.00785)|all_epithelial(10;0.0159)|Colorectal(49;0.235)	OV - Ovarian serous cystadenocarcinoma(33;0.136)	Epithelial(11;0.0123)|all cancers(11;0.0467)|Lung(33;0.0864)|OV - Ovarian serous cystadenocarcinoma(14;0.106)		TGTAGGCCACATAGATGGGGT	0.547													A|||	1423	0.284145	0.3116	0.2594	5008	,	,		19382	0.2381		0.2575	False		,,,				2504	0.3395				p.Y1551Y		Atlas-SNP	.											.	DIP2C	195	.	0			c.T4653C						PASS	.	A		1287,3119	437.2+/-344.9	181,925,1097	117.0	100.0	106.0		4653	-3.9	1.0	10	dbSNP_107	106	2153,6447	369.8+/-335.6	274,1605,2421	no	coding-synonymous	DIP2C	NM_014974.2		455,2530,3518	GG,GA,AA		25.0349,29.2102,26.4493		1551/1557	323283	3440,9566	2203	4300	6503	SO:0001819	synonymous_variant	22982	exon37			GGCCACATAGATG	BC035216	CCDS7054.1	10p15.3	2006-01-13	2006-01-13	2006-01-13	ENSG00000151240	ENSG00000151240			29150	protein-coding gene	gene with protein product		611380	"""KIAA0934"""	KIAA0934			Standard	NM_014974		Approved		uc001ifp.3	Q9Y2E4	OTTHUMG00000017532	ENST00000280886.6:c.4653T>C	10.37:g.323283A>G		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	45	13	0.288889	NM_014974	B4DPI5|Q5SS78	Silent	SNP	ENST00000280886.6	37	CCDS7054.1																																																																																			A|0.732;G|0.268	0.268	strong		0.547	DIP2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046389.1	NM_014974	
CARD11	84433	hgsc.bcm.edu	37	7	2946461	2946461	+	Silent	SNP	T	T	C	rs1124581	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:2946461T>C	ENST00000396946.4	-	25	3679	c.3276A>G	c.(3274-3276)cgA>cgG	p.R1092R		NM_032415.4	NP_115791.3	Q9BXL7	CAR11_HUMAN	caspase recruitment domain family, member 11	1092	Guanylate kinase-like.				Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|nucleotide phosphorylation (GO:0046939)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cytokine production (GO:0001819)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of T cell proliferation (GO:0042102)|regulation of apoptotic process (GO:0042981)|regulation of B cell differentiation (GO:0045577)|regulation of T cell differentiation (GO:0045580)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|thymic T cell selection (GO:0045061)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|immunological synapse (GO:0001772)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	CARD domain binding (GO:0050700)|guanylate kinase activity (GO:0004385)			NS(1)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(62)|kidney(11)|large_intestine(13)|lung(31)|ovary(4)|prostate(5)|skin(7)|upper_aerodigestive_tract(2)	150		Ovarian(82;0.0115)		OV - Ovarian serous cystadenocarcinoma(56;8.44e-14)		CCGTCTCAGGTCGGGGCAGCA	0.682			Mis		DLBCL								C|||	2987	0.596446	0.7012	0.5274	5008	,	,		15696	0.6508		0.4742	False		,,,				2504	0.5736				p.R1092R		Atlas-SNP	.		Dom	yes		7	7p22	84433	"""caspase recruitment domain family, member 11"""		L	.	CARD11	339	.	0			c.A3276G						PASS	.	C		2889,1517	463.0+/-353.4	971,947,285	34.0	29.0	31.0		3276	3.0	0.1	7	dbSNP_86	31	4220,4380	566.9+/-388.7	1067,2086,1147	no	coding-synonymous	CARD11	NM_032415.4		2038,3033,1432	CC,CT,TT		49.0698,34.4303,45.3406		1092/1155	2946461	7109,5897	2203	4300	6503	SO:0001819	synonymous_variant	84433	exon25			CTCAGGTCGGGGC	AF322641	CCDS5336.2	7p22	2014-09-17			ENSG00000198286	ENSG00000198286			16393	protein-coding gene	gene with protein product	"""card-maguk protein 1"", ""bcl10-interacting maguk protein 3"""	607210				11278692, 11356195	Standard	NM_032415		Approved	CARMA1, BIMP3	uc003smv.3	Q9BXL7	OTTHUMG00000023023	ENST00000396946.4:c.3276A>G	7.37:g.2946461T>C		Somatic	166	1	0.0060241		WXS	Illumina HiSeq	Phase_I	138	137	0.992754	NM_032415	A4D1Z7|Q2NKN7|Q548H3	Silent	SNP	ENST00000396946.4	37	CCDS5336.2																																																																																			T|0.439;C|0.561	0.561	strong		0.682	CARD11-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059344.4	NM_032415	
SUV39H2	79723	hgsc.bcm.edu	37	10	14943176	14943176	+	Silent	SNP	C	C	G	rs61730323	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:14943176C>G	ENST00000354919.6	+	5	1041	c.1041C>G	c.(1039-1041)ctC>ctG	p.L347L	SUV39H2_ENST00000378325.3_Silent_p.L167L|SUV39H2_ENST00000313519.5_Silent_p.L287L|DCLRE1C_ENST00000378289.4_Intron	NM_001193424.1	NP_001180353.1	Q9H5I1	SUV92_HUMAN	suppressor of variegation 3-9 homolog 2 (Drosophila)	347	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				cell differentiation (GO:0030154)|chromatin assembly or disassembly (GO:0006333)|chromatin remodeling (GO:0006338)|histone H3-K9 dimethylation (GO:0036123)|histone H3-K9 trimethylation (GO:0036124)|male meiosis (GO:0007140)|negative regulation of circadian rhythm (GO:0042754)|negative regulation of transcription, DNA-templated (GO:0045892)|rhythmic process (GO:0048511)|transcription, DNA-templated (GO:0006351)	chromatin (GO:0000785)|chromosome, centromeric region (GO:0000775)|nuclear heterochromatin (GO:0005720)	chromatin binding (GO:0003682)|histone methyltransferase activity (H3-K9 specific) (GO:0046974)|transcription regulatory region sequence-specific DNA binding (GO:0000976)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(6)|ovary(1)	19						TTGATAACCTCGATACTCGTC	0.373													C|||	234	0.0467252	0.0772	0.0994	5008	,	,		19345	0.0129		0.0338	False		,,,				2504	0.0164				p.L347L		Atlas-SNP	.											SUV39H2_ENST00000354919,NS,carcinoma,0,2	SUV39H2	72	2	0			c.C1041G						PASS	.	C	,,,,	285,4121	156.6+/-189.7	11,263,1929	152.0	137.0	142.0		1041,861,501,321,861	-6.4	0.8	10	dbSNP_129	142	274,8326	103.8+/-164.8	5,264,4031	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SUV39H2	NM_001193424.1,NM_001193425.1,NM_001193426.1,NM_001193427.1,NM_024670.3	,,,,	16,527,5960	GG,GC,CC		3.186,6.4685,4.298	,,,,	347/411,287/351,167/231,107/171,287/351	14943176	559,12447	2203	4300	6503	SO:0001819	synonymous_variant	79723	exon5			TAACCTCGATACT	AK027067	CCDS7104.1, CCDS53493.1, CCDS53494.1	10p13	2011-07-01			ENSG00000152455	ENSG00000152455		"""Chromatin-modifying enzymes / K-methyltransferases"""	17287	protein-coding gene	gene with protein product		606503				11094092	Standard	NM_001193424		Approved	FLJ23414, KMT1B	uc021png.1	Q9H5I1	OTTHUMG00000017718	ENST00000354919.6:c.1041C>G	10.37:g.14943176C>G		Somatic	213	0	0		WXS	Illumina HiSeq	Phase_I	164	81	0.493902	NM_001193424	D3DRT4|Q5JSS4|Q5JSS5|Q6I9Y3|Q8ND06	Silent	SNP	ENST00000354919.6	37	CCDS53494.1	101	0.04624542124542125	36	0.07317073170731707	30	0.08287292817679558	6	0.01048951048951049	29	0.03825857519788918	C	8.666	0.901692	0.17760	0.064685	0.03186	ENSG00000152455	ENST00000358298	.	.	.	5.87	-6.39	0.01951	.	.	.	.	.	T	0.09468	0.0233	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.61138	-0.7123	4	.	.	.	.	17.8458	0.88730	0.0:0.2355:0.0:0.7645	rs61730323	.	.	.	W	113	.	.	S	+	2	0	SUV39H2	14983182	0.000000	0.05858	0.821000	0.32701	0.996000	0.88848	-3.428000	0.00474	-1.256000	0.02478	-0.140000	0.14226	TCG	C|0.954;G|0.045	0.045	strong		0.373	SUV39H2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046947.2	NM_024670	
PYURF	100996939	hgsc.bcm.edu	37	4	89443162	89443162	+	Silent	SNP	G	G	A	rs3177413	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:89443162G>A	ENST00000273968.4	-	2	334	c.222C>T	c.(220-222)aaC>aaT	p.N74N	HERC3_ENST00000601319.1_3'UTR|PIGY_ENST00000527353.1_5'Flank	NM_001042616.2|NM_032906.4	NP_001036081.1|NP_116295.1	Q96I23	PREY_HUMAN	PIGY upstream reading frame	74	TRM112.				GPI anchor biosynthetic process (GO:0006506)|positive regulation of metabolic process (GO:0009893)	endoplasmic reticulum membrane (GO:0005789)|glycosylphosphatidylinositol-N-acetylglucosaminyltransferase (GPI-GnT) complex (GO:0000506)|mitochondrion (GO:0005739)											TAATCAATTCGTTTGTTGATG	0.368													A|||	888	0.177316	0.236	0.1888	5008	,	,		16888	0.1865		0.1153	False		,,,				2504	0.1442				p.N74N		Atlas-SNP	.											.	.	.	.	0			c.C222T						PASS	.	A	,	291,1093		26,239,427	161.0	118.0	131.0		,222	-0.3	1.0	4	dbSNP_105	131	311,2871		16,279,1296	no	utr-5,coding-synonymous	PIGY	NM_001042616.1,NM_032906.3	,	42,518,1723	AA,AG,GG		9.7737,21.026,13.1844	,	,74/115	89443162	602,3964	692	1591	2283	SO:0001819	synonymous_variant	100996939	exon2			CAATTCGTTTGTT			4q22.1	2012-08-14			ENSG00000145337	ENSG00000145337			44317	protein-coding gene	gene with protein product						16162815	Standard	NM_032906		Approved	PreY	uc003hru.2	Q96I23	OTTHUMG00000130949	ENST00000273968.4:c.222C>T	4.37:g.89443162G>A		Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	151	80	0.529801	NM_032906	B2R571	Silent	SNP	ENST00000273968.4	37	CCDS3631.1																																																																																			G|0.849;A|0.151	0.151	strong		0.368	PYURF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253550.1	NM_032906.4	
FNDC9	408263	hgsc.bcm.edu	37	5	156770133	156770133	+	Missense_Mutation	SNP	C	C	T	rs10037485	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:156770133C>T	ENST00000312349.4	-	2	599	c.412G>A	c.(412-414)Gtc>Atc	p.V138I	CYFIP2_ENST00000522463.1_Intron|CYFIP2_ENST00000347377.6_Intron|CYFIP2_ENST00000435847.2_Intron|CYFIP2_ENST00000442283.2_Intron|CYFIP2_ENST00000318218.6_Intron|CYFIP2_ENST00000521420.1_Intron|CYFIP2_ENST00000541131.1_Intron|CYFIP2_ENST00000377576.3_Intron	NM_001001343.3	NP_001001343.2	Q8TBE3	FNDC9_HUMAN	fibronectin type III domain containing 9	138			V -> I (in dbSNP:rs10037485).			integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|prostate(1)|skin(1)|urinary_tract(1)	9						TGGCAACGGACACACCAGAAC	0.607											OREG0016977	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	926	0.184904	0.379	0.1499	5008	,	,		19536	0.006		0.2048	False		,,,				2504	0.1115				p.V138I		Atlas-SNP	.											.	FNDC9	22	.	0			c.G412A						PASS	.	C	ILE/VAL,,,	1515,2891	480.6+/-358.9	263,989,951	63.0	61.0	62.0		412,,,	-3.8	1.0	5	dbSNP_119	62	1873,6727	332.9+/-320.3	198,1477,2625	yes	missense,intron,intron,intron	CYFIP2,FNDC9	NM_001001343.3,NM_001037332.2,NM_001037333.1,NM_014376.2	29,,,	461,2466,3576	TT,TC,CC		21.7791,34.3849,26.0495	benign,,,	138/225,,,	156770133	3388,9618	2203	4300	6503	SO:0001583	missense	408263	exon2			AACGGACACACCA	BC022570	CCDS4337.1	5q33.3	2013-02-11	2011-01-25	2011-01-25	ENSG00000172568	ENSG00000172568		"""Fibronectin type III domain containing"""	33547	protein-coding gene	gene with protein product			"""chromosome 5 open reading frame 40"""	C5orf40			Standard	NM_001001343		Approved	MGC27121	uc003lwu.2	Q8TBE3	OTTHUMG00000130248	ENST00000312349.4:c.412G>A	5.37:g.156770133C>T	ENSP00000310594:p.Val138Ile	Somatic	91	0	0	1781	WXS	Illumina HiSeq	Phase_I	75	36	0.48	NM_001001343	A8K0Y6	Missense_Mutation	SNP	ENST00000312349.4	37	CCDS4337.1	391	0.17902930402930403	177	0.3597560975609756	58	0.16022099447513813	3	0.005244755244755245	153	0.20184696569920843	C	2.095	-0.407568	0.04832	0.343849	0.217791	ENSG00000172568	ENST00000312349;ENST00000520782	T;T	0.64438	-0.1;-0.1	4.98	-3.79	0.04320	.	0.869052	0.09919	N	0.738787	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	0.09843	T	0.71	-25.0468	1.7212	0.02912	0.1406:0.3395:0.2868:0.2332	rs10037485;rs52826537;rs10037485	138	Q8TBE3	FNDC9_HUMAN	I	138	ENSP00000310594:V138I;ENSP00000429434:V138I	ENSP00000310594:V138I	V	-	1	0	FNDC9	156702711	0.000000	0.05858	0.987000	0.45799	0.658000	0.38924	-0.750000	0.04808	-0.056000	0.13221	-0.339000	0.08088	GTC	C|0.765;T|0.235	0.235	strong		0.607	FNDC9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252573.2	NM_001001343	
HOXC4	3221	hgsc.bcm.edu	37	12	54448106	54448106	+	Missense_Mutation	SNP	A	A	G	rs75256744	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:54448106A>G	ENST00000430889.2	+	1	446	c.400A>G	c.(400-402)Ata>Gta	p.I134V	HOXC4_ENST00000609810.1_Missense_Mutation_p.I134V|HOXC4_ENST00000303406.4_Missense_Mutation_p.I134V	NM_153633.2	NP_705897.1	P09017	HXC4_HUMAN	homeobox C4	134					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)			cervix(1)|kidney(2)|large_intestine(4)|lung(3)|ovary(1)|prostate(1)|urinary_tract(1)	13						CAAGCAACCCATAGTCTACCC	0.647													A|||	554	0.110623	0.0174	0.0908	5008	,	,		8955	0.0337		0.1769	False		,,,				2504	0.2618				p.I134V		Atlas-SNP	.											.	HOXC4	29	.	0			c.A400G						PASS	.	A	VAL/ILE,VAL/ILE	184,4222		6,172,2025	25.0	25.0	25.0		400,400	4.3	1.0	12	dbSNP_131	25	1507,7091		132,1243,2924	yes	missense,missense	HOXC4	NM_014620.4,NM_153633.2	29,29	138,1415,4949	GG,GA,AA		17.5273,4.1761,13.0037	benign,benign	134/265,134/265	54448106	1691,11313	2203	4299	6502	SO:0001583	missense	3221	exon3			CAACCCATAGTCT		CCDS8873.1	12q13.13	2011-06-20	2005-12-22		ENSG00000198353	ENSG00000198353		"""Homeoboxes / ANTP class : HOXL subclass"""	5126	protein-coding gene	gene with protein product		142974	"""homeo box C4"""	HOX3, HOX3E		1973146, 1358459	Standard	NM_014620		Approved		uc001sex.3	P09017	OTTHUMG00000160036	ENST00000430889.2:c.400A>G	12.37:g.54448106A>G	ENSP00000399808:p.Ile134Val	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	106	48	0.45283	NM_014620		Missense_Mutation	SNP	ENST00000430889.2	37	CCDS8873.1	217	0.09935897435897435	24	0.04878048780487805	38	0.10497237569060773	19	0.033216783216783216	136	0.17941952506596306	A	0.226	-1.024613	0.02061	0.041761	0.175273	ENSG00000198353	ENST00000303406;ENST00000430889	D;D	0.88354	-2.37;-2.37	4.26	4.26	0.50523	.	0.062472	0.64402	D	0.000007	T	0.00210	0.0006	N	0.00258	-1.755	0.26297	P	0.9780349	B	0.06786	0.001	B	0.08055	0.003	T	0.42032	-0.9475	9	0.02654	T	1	.	12.7918	0.57539	1.0:0.0:0.0:0.0	.	134	P09017	HXC4_HUMAN	V	134	ENSP00000305973:I134V;ENSP00000399808:I134V	ENSP00000305973:I134V	I	+	1	0	HOXC4	52734373	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.533000	0.45667	1.918000	0.55548	0.379000	0.24179	ATA	A|0.880;G|0.120	0.120	strong		0.647	HOXC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358963.1		
MUC4	4585	hgsc.bcm.edu	37	3	195513345	195513345	+	Silent	SNP	A	A	C	rs71321841	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195513345A>C	ENST00000463781.3	-	2	5565	c.5106T>G	c.(5104-5106)gtT>gtG	p.V1702V	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Silent_p.V1702V	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		ATGCCGAGGAAACGTCGGTGA	0.597																																					p.V1702V		Atlas-SNP	.											.	MUC4	1505	.	0			c.T5106G						PASS	.						31.0	33.0	33.0					3																	195513345		690	1583	2273	SO:0001819	synonymous_variant	4585	exon2			CGAGGAAACGTCG	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.5106T>G	3.37:g.195513345A>C		Somatic	237	0	0		WXS	Illumina HiSeq	Phase_I	185	83	0.448649	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Silent	SNP	ENST00000463781.3	37	CCDS54700.1																																																																																			A|0.500;C|0.500	0.500	strong		0.597	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
DNAH5	1767	hgsc.bcm.edu	37	5	13716797	13716797	+	Silent	SNP	A	A	G	rs61744054	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:13716797A>G	ENST00000265104.4	-	74	12812	c.12708T>C	c.(12706-12708)ggT>ggC	p.G4236G		NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	4236					cilium movement (GO:0003341)|lateral ventricle development (GO:0021670)|left/right axis specification (GO:0070986)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(6)|breast(14)|central_nervous_system(4)|cervix(2)|endometrium(23)|haematopoietic_and_lymphoid_tissue(8)|kidney(11)|large_intestine(85)|liver(1)|lung(129)|ovary(16)|pancreas(2)|prostate(5)|skin(48)|stomach(5)|upper_aerodigestive_tract(11)|urinary_tract(8)	378	Lung NSC(4;0.00476)					TCCAGGAGACACCCTGGGAAA	0.403									Kartagener syndrome				A|||	174	0.0347444	0.1097	0.0216	5008	,	,		16997	0.001		0.005	False		,,,				2504	0.0082				p.G4236G		Atlas-SNP	.											DNAH5,NS,carcinoma,-1,1	DNAH5	868	1	0			c.T12708C						scavenged	.	A		355,4051	180.5+/-208.7	16,323,1864	57.0	52.0	54.0		12708	-11.1	0.0	5	dbSNP_129	54	17,8583	12.6+/-44.7	0,17,4283	no	coding-synonymous	DNAH5	NM_001369.2		16,340,6147	GG,GA,AA		0.1977,8.0572,2.8602		4236/4625	13716797	372,12634	2203	4300	6503	SO:0001819	synonymous_variant	1767	exon74	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	GGAGACACCCTGG	AJ132090	CCDS3882.1	5p15.2	2008-07-18	2006-09-04		ENSG00000039139	ENSG00000039139		"""Axonemal dyneins"""	2950	protein-coding gene	gene with protein product	"""dynein heavy chain 5"""	603335	"""dynein, axonemal, heavy polypeptide 5"""			9256245, 11788826	Standard	NM_001369		Approved	Dnahc5, HL1, PCD, CILD3, KTGNR	uc003jfd.2	Q8TE73	OTTHUMG00000090533	ENST00000265104.4:c.12708T>C	5.37:g.13716797A>G		Somatic	88	1	0.0113636		WXS	Illumina HiSeq	Phase_I	101	42	0.415842	NM_001369	Q92860|Q96L74|Q9H5S7|Q9HCG9	Silent	SNP	ENST00000265104.4	37	CCDS3882.1																																																																																			A|0.971;G|0.029	0.029	strong		0.403	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369	
RPTN	126638	hgsc.bcm.edu	37	1	152129101	152129101	+	Silent	SNP	A	A	G	rs117596468	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:152129101A>G	ENST00000316073.3	-	3	538	c.474T>C	c.(472-474)caT>caC	p.H158H		NM_001122965.1	NP_001116437.1	Q6XPR3	RPTN_HUMAN	repetin	158	Gln-rich.					cornified envelope (GO:0001533)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)	p.G159_H170delGQSEKQDRDSHH(1)		breast(2)|central_nervous_system(1)|endometrium(14)|kidney(2)|large_intestine(1)|lung(32)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	59						CAGACTGACCATGGTGGGAAT	0.502																																					p.H158H		Atlas-SNP	.											RPTN,NS,carcinoma,0,1	RPTN	123	1	1	Deletion - In frame(1)	stomach(1)	c.T474C						scavenged	.						472.0	411.0	430.0					1																	152129101		1563	3567	5130	SO:0001819	synonymous_variant	126638	exon3			CTGACCATGGTGG	AK096436	CCDS41397.1	1q21.3	2013-01-10			ENSG00000215853	ENSG00000215853		"""EF-hand domain containing"""	26809	protein-coding gene	gene with protein product		613259				15854042	Standard	NM_001122965		Approved	FLJ39117	uc001ezs.1	Q6XPR3	OTTHUMG00000154095	ENST00000316073.3:c.474T>C	1.37:g.152129101A>G		Somatic	274	1	0.00364964		WXS	Illumina HiSeq	Phase_I	172	32	0.186047	NM_001122965	B7ZBZ3	Silent	SNP	ENST00000316073.3	37	CCDS41397.1																																																																																			A|0.953;G|0.047	0.047	strong		0.502	RPTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333867.1	XM_371312	
CTSE	1510	hgsc.bcm.edu	37	1	206327510	206327510	+	Silent	SNP	T	T	C	rs61742539	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:206327510T>C	ENST00000358184.2	+	6	817	c.699T>C	c.(697-699)ttT>ttC	p.F233F	CTSE_ENST00000361052.3_Silent_p.F238F|CTSE_ENST00000432969.2_Silent_p.F158F|CTSE_ENST00000360218.2_Silent_p.F233F|CTSE_ENST00000468617.1_3'UTR	NM_001910.3	NP_001901.1	P14091	CATE_HUMAN	cathepsin E	238					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|digestion (GO:0007586)|protein autoprocessing (GO:0016540)	endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)	aspartic-type endopeptidase activity (GO:0004190)			endometrium(2)|large_intestine(3)|lung(5)|ovary(2)|prostate(1)|skin(3)	16			BRCA - Breast invasive adenocarcinoma(75;0.0754)			AGCTGATTTTTGGAGGCTACG	0.527													c|||	879	0.175519	0.3744	0.1628	5008	,	,		19775	0.0169		0.2038	False		,,,				2504	0.0501				p.F233F		Atlas-SNP	.											.	CTSE	72	.	0			c.T699C						PASS	.	C	,	1617,2789	662.4+/-401.0	302,1013,888	171.0	173.0	172.0		699,699	-6.6	0.5	1	dbSNP_129	172	1568,7032	745.1+/-407.3	144,1280,2876	no	coding-synonymous,coding-synonymous	CTSE	NM_001910.3,NM_148964.2	,	446,2293,3764	CC,CT,TT		18.2326,36.7,24.4887	,	233/397,233/364	206327510	3185,9821	2203	4300	6503	SO:0001819	synonymous_variant	1510	exon6			GATTTTTGGAGGC	BC042537	CCDS73012.1, CCDS73013.1	1q32.1	2008-02-05			ENSG00000196188	ENSG00000196188	3.4.23.5	"""Cathepsins"""	2530	protein-coding gene	gene with protein product		116890				2369841, 2674141	Standard	NM_001910		Approved		uc001hdu.3	P14091	OTTHUMG00000036121	ENST00000358184.2:c.699T>C	1.37:g.206327510T>C		Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	138	62	0.449275	NM_001910	Q5TZ01|Q5TZ02|Q9NY58|Q9UCE3|Q9UCE4	Silent	SNP	ENST00000358184.2	37	CCDS1462.1																																																																																			T|0.778;C|0.222	0.222	strong		0.527	CTSE-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000087998.1	NM_001910	
DDX53	168400	hgsc.bcm.edu	37	X	23019317	23019317	+	Missense_Mutation	SNP	G	G	T	rs5925720	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:23019317G>T	ENST00000327968.5	+	1	1231	c.1143G>T	c.(1141-1143)atG>atT	p.M381I	RP11-40F8.2_ENST00000455399.1_lincRNA	NM_182699.3	NP_874358.2	Q86TM3	DDX53_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 53	381	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.		M -> I (in dbSNP:rs5925720).			nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|RNA binding (GO:0003723)			breast(2)|endometrium(5)|kidney(4)|large_intestine(3)|lung(15)|ovary(1)|prostate(1)|skin(2)|urinary_tract(2)	35						CAGATAAAATGCTGGATATGG	0.413													G|||	610	0.161589	0.0008	0.0432	3775	,	,		15089	0.2073		0.0885	False		,,,				2504	0.2873				p.M381I		Atlas-SNP	.											.	DDX53	76	.	0			c.G1143T						PASS	.	G	ILE/MET	67,3768		0,54,13,1578,558	112.0	110.0	110.0		1143	4.3	0.5	X	dbSNP_114	110	789,5939		28,494,239,1906,1633	yes	missense	DDX53	NM_182699.3	10	28,548,252,3484,2191	TT,TG,T,GG,G		11.7271,1.7471,8.1038	probably-damaging	381/632	23019317	856,9707	2203	4300	6503	SO:0001583	missense	168400	exon1			TAAAATGCTGGAT	AY039237	CCDS35214.1	Xp22.13	2009-03-25			ENSG00000184735	ENSG00000184735		"""DEAD-boxes"""	20083	protein-coding gene	gene with protein product	"""cancer associated gene"", ""cancer/testis antigen 26"""						Standard	NM_182699		Approved	CAGE, CT26	uc004daj.3	Q86TM3	OTTHUMG00000021248	ENST00000327968.5:c.1143G>T	X.37:g.23019317G>T	ENSP00000368667:p.Met381Ile	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	45	45	1	NM_182699	Q0D2N2|Q6NVV4	Missense_Mutation	SNP	ENST00000327968.5	37	CCDS35214.1	191	0.11512959614225438	0	0.0	11	0.03125	69	0.13745019920318724	52	0.07222222222222222	G	16.81	3.227200	0.58668	0.017471	0.117271	ENSG00000184735	ENST00000327968	T	0.14766	2.48	4.3	4.3	0.51218	RNA helicase, ATP-dependent, DEAD-box, conserved site (1);DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.00356	0.0011	M	0.84846	2.72	0.19575	P	0.9999620347	D	0.89917	1.0	D	0.91635	0.999	T	0.04467	-1.0949	9	0.87932	D	0	0.0312	13.7336	0.62804	0.0:0.0:1.0:0.0	rs5925720;rs58250497;rs5925720	381	Q86TM3	DDX53_HUMAN	I	381	ENSP00000368667:M381I	ENSP00000368667:M381I	M	+	3	0	DDX53	22929238	1.000000	0.71417	0.491000	0.27477	0.478000	0.33099	8.508000	0.90525	1.894000	0.54839	0.600000	0.82982	ATG	G|0.902;T|0.098	0.098	strong		0.413	DDX53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056043.1	NM_182699	
U2SURP	23350	hgsc.bcm.edu	37	3	142747227	142747227	+	Nonsense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:142747227G>A	ENST00000473835.2	+	15	1515	c.1425G>A	c.(1423-1425)tgG>tgA	p.W475*	U2SURP_ENST00000397933.2_Nonsense_Mutation_p.W66*|U2SURP_ENST00000493598.2_Nonsense_Mutation_p.W474*	NM_001080415.1	NP_001073884.1	O15042	SR140_HUMAN	U2 snRNP-associated SURP domain containing	475					RNA processing (GO:0006396)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(12)|ovary(2)|pancreas(1)|prostate(1)|skin(1)	31						ACTATAGGTGGAAGCTTTATT	0.313																																					p.W475X		Atlas-SNP	.											.	U2SURP	66	.	0			c.G1425A						PASS	.						75.0	70.0	72.0					3																	142747227		1796	4067	5863	SO:0001587	stop_gained	23350	exon15			TAGGTGGAAGCTT	BK000564	CCDS46928.1	3q23	2013-02-12			ENSG00000163714	ENSG00000163714		"""RNA binding motif (RRM) containing"""	30855	protein-coding gene	gene with protein product	"""functional spliceosome-associated protein a"", ""Ser/Arg-rich domain protein, 140 kDa"", ""U2 associated SR140 protein"""					9205841, 12234937	Standard	NM_001080415		Approved	fSAPa, SR140	uc003evh.1	O15042	OTTHUMG00000159323	ENST00000473835.2:c.1425G>A	3.37:g.142747227G>A	ENSP00000418563:p.Trp475*	Somatic	210	0	0		WXS	Illumina HiSeq	Phase_I	182	43	0.236264	NM_001080415	A0PJ60|Q0D2M1|Q2NKQ7|Q9BR70	Nonsense_Mutation	SNP	ENST00000473835.2	37	CCDS46928.1	.	.	.	.	.	.	.	.	.	.	G	39	7.674541	0.98425	.	.	ENSG00000163714	ENST00000473835;ENST00000319822;ENST00000397933;ENST00000493598;ENST00000480029	.	.	.	5.88	5.88	0.94601	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-6.0436	20.2187	0.98312	0.0:0.0:1.0:0.0	.	.	.	.	X	475;475;66;474;42	.	ENSP00000322376:W475X	W	+	3	0	U2SURP	144229917	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.444000	0.97578	2.780000	0.95670	0.655000	0.94253	TGG	.	.	none		0.313	U2SURP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354603.2	NM_001080415	
ADAMTS7	11173	hgsc.bcm.edu	37	15	79089111	79089111	+	Missense_Mutation	SNP	A	A	G	rs3825807	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:79089111A>G	ENST00000388820.4	-	4	850	c.640T>C	c.(640-642)Tct>Cct	p.S214P	ADAMTS7_ENST00000566303.1_5'UTR	NM_014272.3	NP_055087.2	Q9UKP4	ATS7_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 7	214			S -> P (in dbSNP:rs3825807).		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						tcccgtcgAGACTCCAGCTCT	0.657													G|||	1253	0.2502	0.1112	0.2968	5008	,	,		14046	0.1518		0.4274	False		,,,				2504	0.3241				p.S214P		Atlas-SNP	.											.	ADAMTS7	142	.	0			c.T640C						PASS	.	G	PRO/SER	678,3714		57,564,1575	22.0	21.0	22.0	http://www.ncbi.nlm.nih.gov/pubmed?term	640	-9.0	0.0	15	dbSNP_107	22	3816,4762		878,2060,1351	yes	missense	ADAMTS7	NM_014272.3	74	935,2624,2926	GG,GA,AA	http://www.ncbi.nlm.nih.gov/pubmed?term	44.4859,15.4372,34.6492	benign	214/1687	79089111	4494,8476	2196	4289	6485	SO:0001583	missense	11173	exon4			GTCGAGACTCCAG	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.640T>C	15.37:g.79089111A>G	ENSP00000373472:p.Ser214Pro	Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	64	39	0.609375	NM_014272	Q14F51|Q6P7J9	Missense_Mutation	SNP	ENST00000388820.4	37	CCDS32303.1	584	0.2673992673992674	63	0.12804878048780488	123	0.3397790055248619	77	0.1346153846153846	321	0.4234828496042216	G	12.54	1.968180	0.34754	0.154372	0.444859	ENSG00000136378	ENST00000388820;ENST00000456326	T	0.60920	0.15	5.11	-8.98	0.00754	.	0.967066	0.08499	N	0.936716	T	0.00012	0.0000	N	0.00436	-1.5	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.0;0.001	T	0.40384	-0.9566	9	0.30078	T	0.28	.	2.7518	0.05283	0.5523:0.0989:0.1616:0.1872	rs3825807;rs57075956;rs3825807	214;214;214	E7EP58;A8MQ00;Q9UKP4	.;.;ATS7_HUMAN	P	214	ENSP00000373472:S214P	ENSP00000373472:S214P	S	-	1	0	ADAMTS7	76876166	0.000000	0.05858	0.000000	0.03702	0.354000	0.29330	-1.471000	0.02344	-1.596000	0.01611	-1.382000	0.01172	TCT	A|0.704;G|0.296	0.296	strong		0.657	ADAMTS7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421331.1	NM_014272	
POLR3F	10621	hgsc.bcm.edu	37	20	18449662	18449662	+	Missense_Mutation	SNP	A	A	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:18449662A>C	ENST00000377603.4	+	2	517	c.137A>C	c.(136-138)gAa>gCa	p.E46A	DZANK1_ENST00000329494.5_5'Flank|DZANK1_ENST00000262547.5_5'Flank|MIR3192_ENST00000584920.1_RNA|DZANK1_ENST00000357236.4_5'Flank|POLR3F_ENST00000462997.1_3'UTR	NM_006466.2	NP_006457.2	Q9H1D9	RPC6_HUMAN	polymerase (RNA) III (DNA directed) polypeptide F, 39 kDa	46				HIEAQQRAVA -> QYRSPAAGSS (in Ref. 1; AAB63677). {ECO:0000305}.	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)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|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)			breast(2)	2						CCTCATATAGAAGCCCAGCAG	0.368																																					p.E46A	GBM(69;898 1468 19907 52011)	Atlas-SNP	.											.	POLR3F	14	.	0			c.A137C						PASS	.						100.0	100.0	100.0					20																	18449662		2203	4300	6503	SO:0001583	missense	10621	exon2			ATATAGAAGCCCA	U93869	CCDS13135.1	20p11.23	2013-01-21	2002-08-29		ENSG00000132664	ENSG00000132664		"""RNA polymerase subunits"""	15763	protein-coding gene	gene with protein product	"""RNA polymerase III C39 subunit"""		"""polymerase (RNA) III (DNA directed) polypeptide F (39 kDa)"""			9171375	Standard	NM_006466		Approved	RPC39, RPC6	uc002wqv.3	Q9H1D9	OTTHUMG00000031971	ENST00000377603.4:c.137A>C	20.37:g.18449662A>C	ENSP00000366828:p.Glu46Ala	Somatic	238	0	0		WXS	Illumina HiSeq	Phase_I	267	67	0.250936	NM_006466	A8K4C7|O15319	Missense_Mutation	SNP	ENST00000377603.4	37	CCDS13135.1	.	.	.	.	.	.	.	.	.	.	A	14.44	2.534697	0.45073	.	.	ENSG00000132664	ENST00000377603	.	.	.	6.08	6.08	0.98989	.	0.000000	0.85682	D	0.000000	T	0.59824	0.2222	L	0.51422	1.61	0.80722	D	1	B	0.25563	0.129	B	0.30251	0.113	T	0.55147	-0.8186	9	0.30078	T	0.28	.	16.3126	0.82898	1.0:0.0:0.0:0.0	.	46	Q9H1D9	RPC6_HUMAN	A	46	.	ENSP00000366828:E46A	E	+	2	0	POLR3F	18397662	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	8.904000	0.92590	2.333000	0.79357	0.482000	0.46254	GAA	.	.	none		0.368	POLR3F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078170.2	NM_006466	
SLC37A1	54020	hgsc.bcm.edu	37	21	43974226	43974226	+	Silent	SNP	T	T	C	rs2839550	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:43974226T>C	ENST00000352133.2	+	10	1805	c.823T>C	c.(823-825)Ttg>Ctg	p.L275L	SLC37A1_ENST00000398341.3_Silent_p.L275L			P57057	GLPT_HUMAN	solute carrier family 37 (glucose-6-phosphate transporter), member 1	275					carbohydrate transport (GO:0008643)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	transporter activity (GO:0005215)			breast(1)|endometrium(6)|kidney(1)|large_intestine(2)|liver(2)|lung(3)	15						GAAGCAAATCTTGAAGAGCGA	0.433													T|||	622	0.124201	0.3275	0.0893	5008	,	,		17220	0.001		0.1054	False		,,,				2504	0.0204				p.L275L		Atlas-SNP	.											.	SLC37A1	48	.	0			c.T823C						PASS	.	T		1207,3199	417.4+/-337.9	172,863,1168	61.0	57.0	58.0		823	-5.1	0.0	21	dbSNP_100	58	812,7788	188.1+/-235.2	33,746,3521	no	coding-synonymous	SLC37A1	NM_018964.3		205,1609,4689	CC,CT,TT		9.4419,27.3945,15.5236		275/534	43974226	2019,10987	2203	4300	6503	SO:0001819	synonymous_variant	54020	exon11			CAAATCTTGAAGA	AJ269529	CCDS13689.1	21q22.3	2013-07-17	2013-07-17		ENSG00000160190	ENSG00000160190		"""Solute carriers"""	11024	protein-coding gene	gene with protein product		608094	"""solute carrier family 37 (glycerol-3-phosphate transporter), member 1"""			11112347	Standard	NM_018964		Approved		uc002zbi.3	P57057	OTTHUMG00000086803	ENST00000352133.2:c.823T>C	21.37:g.43974226T>C		Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	31	16	0.516129	NM_018964	D3DSJ7|Q9HAQ1	Silent	SNP	ENST00000352133.2	37	CCDS13689.1																																																																																			T|0.848;C|0.152	0.152	strong		0.433	SLC37A1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195377.1		
TLR5	7100	hgsc.bcm.edu	37	1	223284528	223284528	+	Missense_Mutation	SNP	A	A	G	rs5744174	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:223284528A>G	ENST00000540964.1	-	4	2307	c.1846T>C	c.(1846-1848)Ttc>Ctc	p.F616L	TLR5_ENST00000342210.6_Missense_Mutation_p.F616L			O60602	TLR5_HUMAN	toll-like receptor 5	616	LRRCT.		F -> L (in dbSNP:rs5744174). {ECO:0000269|PubMed:14623910, ECO:0000269|PubMed:16027372, ECO:0000269|PubMed:9596645}.|Missing (in 10% of the population; abolishes flagellin signaling; associated with resistance to SLEB1). {ECO:0000269|PubMed:14623910}.		cellular response to lipopolysaccharide (GO:0071222)|cellular response to mechanical stimulus (GO:0071260)|defense response to bacterium (GO:0042742)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|male gonad development (GO:0008584)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of toll-like receptor signaling pathway (GO:0034123)|regulation of cytokine secretion (GO:0050707)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor signaling pathway (GO:0002224)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	interleukin-1 receptor binding (GO:0005149)|transmembrane signaling receptor activity (GO:0004888)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(4)|lung(8)|ovary(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	32				GBM - Glioblastoma multiforme(131;0.0851)		ACCCCAGAGAACGAGTCAGGG	0.433													G|||	1454	0.290335	0.1089	0.3487	5008	,	,		20738	0.1984		0.4095	False		,,,				2504	0.4663				p.F616L		Atlas-SNP	.											.	TLR5	86	.	0			c.T1846C						PASS	.	G	LEU/PHE	742,3664	756.3+/-412.6	61,620,1522	89.0	91.0	90.0		1846	-11.2	0.0	1	dbSNP_114	90	3610,4990	625.1+/-397.7	738,2134,1428	yes	missense	TLR5	NM_003268.5	22	799,2754,2950	GG,GA,AA		41.9767,16.8407,33.4615	benign	616/859	223284528	4352,8654	2203	4300	6503	SO:0001583	missense	7100	exon6			CAGAGAACGAGTC		CCDS31033.1	1q32.3-q42	2014-01-29			ENSG00000187554	ENSG00000187554			11851	protein-coding gene	gene with protein product	"""Toll/interleukin-1 receptor-like protein 3"""	603031	"""systemic lupus erythematosus susceptibility 1"""	SLEB1		9435236, 16027372	Standard	NM_003268		Approved	TIL3, FLJ10052, MGC126430, MGC126431	uc001hnw.2	O60602	OTTHUMG00000037937	ENST00000540964.1:c.1846T>C	1.37:g.223284528A>G	ENSP00000440643:p.Phe616Leu	Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	140	76	0.542857	NM_003268	B1AZ05|B3Y633|B9VJ63|D1CS80|D3DTB8|O15456|Q32MI2|Q32MI3	Missense_Mutation	SNP	ENST00000540964.1	37	CCDS31033.1	604	0.2765567765567766	69	0.1402439024390244	124	0.3425414364640884	104	0.18181818181818182	307	0.4050131926121372	G	0.008	-1.889258	0.00527	0.168407	0.419767	ENSG00000187554	ENST00000540964;ENST00000366881;ENST00000342210	T;T;T	0.17213	2.29;2.29;2.29	5.59	-11.2	0.00127	Cysteine-rich flanking region, C-terminal (1);	0.464610	0.24633	N	0.036880	T	0.00012	0.0000	N	0.01003	-1.06	0.80722	P	0.0	B	0.02656	0.0	B	0.06405	0.002	T	0.25187	-1.0139	9	0.02654	T	1	.	12.7011	0.57034	0.5768:0.2038:0.2194:0.0	rs5744174;rs17748224;rs5744174	616	O60602	TLR5_HUMAN	L	616	ENSP00000440643:F616L;ENSP00000355846:F616L;ENSP00000340089:F616L	ENSP00000340089:F616L	F	-	1	0	TLR5	221351151	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.885000	0.04161	-3.660000	0.00125	-1.702000	0.00720	TTC	A|0.691;G|0.309	0.309	strong		0.433	TLR5-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_003268	
NODAL	4838	hgsc.bcm.edu	37	10	72195439	72195439	+	Missense_Mutation	SNP	T	T	C	rs1904589	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:72195439T>C	ENST00000287139.3	-	2	493	c.494A>G	c.(493-495)cAc>cGc	p.H165R	AC022532.1_ENST00000420338.2_Missense_Mutation_p.V129A	NM_018055.4	NP_060525.3	Q96S42	NODAL_HUMAN	nodal growth differentiation factor	165			H -> R (in dbSNP:rs1904589). {ECO:0000269|Ref.1}.		axial mesodermal cell fate specification (GO:0048327)|brain development (GO:0007420)|cell migration involved in gastrulation (GO:0042074)|digestive tract morphogenesis (GO:0048546)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic pattern specification (GO:0009880)|embryonic placenta development (GO:0001892)|embryonic process involved in female pregnancy (GO:0060136)|endodermal cell differentiation (GO:0035987)|epiblast cell-extraembryonic ectoderm cell signaling involved in anterior/posterior axis specification (GO:0060802)|floor plate morphogenesis (GO:0033505)|formation of anatomical boundary (GO:0048859)|growth (GO:0040007)|heart looping (GO:0001947)|inhibition of neuroepithelial cell differentiation (GO:0002085)|left lung morphogenesis (GO:0060460)|liver development (GO:0001889)|maternal placenta development (GO:0001893)|maternal process involved in parturition (GO:0060137)|mesendoderm development (GO:0048382)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of chorionic trophoblast cell proliferation (GO:1901383)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of trophoblast cell migration (GO:1901164)|neural fold formation (GO:0001842)|nodal signaling pathway involved in determination of lateral mesoderm left/right asymmetry (GO:1900164)|placenta development (GO:0001890)|polarity specification of proximal/distal axis (GO:0010085)|positive regulation of activin receptor signaling pathway (GO:0032927)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of nodal signaling pathway involved in determination of lateral mesoderm left/right asymmetry (GO:1900224)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of gastrulation (GO:0010470)|regulation of stem cell maintenance (GO:2000036)|SMAD protein signal transduction (GO:0060395)|stem cell maintenance (GO:0019827)|transforming growth factor beta receptor signaling pathway involved in primitive streak formation (GO:0090010)|trophectodermal cellular morphogenesis (GO:0001831)|vasculature development (GO:0001944)	extracellular space (GO:0005615)	morphogen activity (GO:0016015)|type I activin receptor binding (GO:0070698)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(4)|upper_aerodigestive_tract(2)	15						GGCCCCAGGGTGCTTCAGCCA	0.587													C|||	3334	0.665735	0.5113	0.6816	5008	,	,		18872	0.9563		0.5308	False		,,,				2504	0.7025				p.H165R		Atlas-SNP	.											.	NODAL	32	.	0			c.A494G						PASS	.	C	ARG/HIS	2230,2176	581.8+/-385.5	583,1064,556	39.0	38.0	39.0		494	-2.8	0.8	10	dbSNP_92	39	4775,3825	534.6+/-382.6	1323,2129,848	yes	missense	NODAL	NM_018055.4	29	1906,3193,1404	CC,CT,TT		44.4767,49.3872,46.1402	benign	165/348	72195439	7005,6001	2203	4300	6503	SO:0001583	missense	4838	exon2			CCAGGGTGCTTCA	BC033585	CCDS7304.1	10q22.1	2012-12-07	2012-12-07		ENSG00000156574	ENSG00000156574			7865	protein-coding gene	gene with protein product		601265	"""nodal, mouse, homolog"", ""nodal homolog (mouse)"""			9354794	Standard	NM_018055		Approved		uc001jrc.2	Q96S42	OTTHUMG00000018408	ENST00000287139.3:c.494A>G	10.37:g.72195439T>C	ENSP00000287139:p.His165Arg	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	97	53	0.546392	NM_018055	Q2M3A5|Q8N4V3	Missense_Mutation	SNP	ENST00000287139.3	37	CCDS7304.1	1434|1434	0.6565934065934066|0.6565934065934066	238|238	0.483739837398374|0.483739837398374	241|241	0.6657458563535912|0.6657458563535912	545|545	0.9527972027972028|0.9527972027972028	410|410	0.5408970976253298|0.5408970976253298	C|C	2.365|2.365	-0.345616|-0.345616	0.05208|0.05208	0.506128|0.506128	0.555233|0.555233	ENSG00000156574|ENSG00000197604	ENST00000287139;ENST00000414871|ENST00000420338	T;T|.	0.63913|.	-0.07;-0.07|.	5.99|5.99	-2.83|-2.83	0.05769|0.05769	Transforming growth factor-beta, N-terminal (1);|.	0.896444|.	0.10001|.	N|.	0.728419|.	T|T	0.00012|0.00012	0.0000|0.0000	L|L	0.38175|0.38175	1.15|1.15	0.80722|0.80722	P|P	0.0|0.0	B|.	0.02656|.	0.0|.	B|.	0.01281|.	0.0|.	T|T	0.17776|0.17776	-1.0358|-1.0358	9|5	0.15499|0.87932	T|D	0.54|0	.|.	4.0111|4.0111	0.09623|0.09623	0.0932:0.2745:0.1016:0.5307|0.0932:0.2745:0.1016:0.5307	rs1904589;rs17846048;rs17859039;rs1904589|rs1904589;rs17846048;rs17859039;rs1904589	165|.	Q96S42|.	NODAL_HUMAN|.	R|A	165;110|129	ENSP00000287139:H165R;ENSP00000394468:H110R|.	ENSP00000287139:H165R|ENSP00000411125:V129A	H|V	-|+	2|2	0|0	NODAL|AC022532.1	71865445|71865445	0.000000|0.000000	0.05858|0.05858	0.789000|0.789000	0.31954|0.31954	0.006000|0.006000	0.05464|0.05464	0.049000|0.049000	0.14099|0.14099	-0.447000|-0.447000	0.07138|0.07138	-2.060000|-2.060000	0.00399|0.00399	CAC|GTG	T|0.424;C|0.576	0.576	strong		0.587	NODAL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048511.1	NM_018055	
ACAN	176	hgsc.bcm.edu	37	15	89386652	89386652	+	Missense_Mutation	SNP	G	G	A	rs34949187	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:89386652G>A	ENST00000561243.1	+	5	824	c.824G>A	c.(823-825)cGg>cAg	p.R275Q	ACAN_ENST00000439576.2_Missense_Mutation_p.R275Q|ACAN_ENST00000559004.1_Missense_Mutation_p.R275Q|ACAN_ENST00000352105.7_Missense_Mutation_p.R275Q|ACAN_ENST00000558207.1_Missense_Mutation_p.R275Q			P16112	PGCA_HUMAN	aggrecan	275	G1-B'.|Link 2. {ECO:0000255|PROSITE- ProRule:PRU00323}.		R -> Q (in dbSNP:rs34949187).		carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|proteolysis (GO:0006508)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)	carbohydrate binding (GO:0030246)|extracellular matrix structural constituent (GO:0005201)|hyaluronic acid binding (GO:0005540)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(4)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(15)|liver(2)|lung(40)|ovary(2)|prostate(5)|skin(5)|stomach(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	93	Lung NSC(78;0.0392)|all_lung(78;0.077)		BRCA - Breast invasive adenocarcinoma(143;0.146)			GAGTGCCGGCGGCTGGGTGCC	0.642													G|||	411	0.0820687	0.0076	0.0951	5008	,	,		16364	0.0764		0.165	False		,,,				2504	0.0941				p.R275Q		Atlas-SNP	.											.	ACAN	220	.	0			c.G824A						PASS	.	G	GLN/ARG,GLN/ARG	149,3725		0,149,1788	17.0	20.0	19.0		824,824	5.6	1.0	15	dbSNP_126	19	1467,6809		129,1209,2800	yes	missense,missense	ACAN	NM_001135.3,NM_013227.3	43,43	129,1358,4588	AA,AG,GG		17.726,3.8462,13.3004	possibly-damaging,possibly-damaging	275/2432,275/2531	89386652	1616,10534	1937	4138	6075	SO:0001583	missense	176	exon6			GCCGGCGGCTGGG	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.824G>A	15.37:g.89386652G>A	ENSP00000453342:p.Arg275Gln	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	124	47	0.379032	NM_001135	Q13650|Q9UCD3|Q9UCP4|Q9UCP5|Q9UDE0	Missense_Mutation	SNP	ENST00000561243.1	37	CCDS53970.1	205	0.09386446886446886	3	0.006097560975609756	42	0.11602209944751381	38	0.06643356643356643	122	0.16094986807387862	G	19.24	3.789786	0.70337	0.038462	0.17726	ENSG00000157766	ENST00000439576;ENST00000352105;ENST00000268134	T;T	0.09255	3.0;3.0	5.56	5.56	0.83823	.	0.000000	0.30593	N	0.009286	T	0.00039	0.0001	L	0.33485	1.01	0.36564	P	0.12737600000000004	D;D;P	0.89917	1.0;1.0;0.827	D;D;B	0.66716	0.946;0.946;0.418	T	0.15150	-1.0447	9	0.36615	T	0.2	-18.6464	18.5257	0.90971	0.0:0.0:1.0:0.0	rs34949187	275;275;275	E7ENV9;E7EX88;Q6PID9	.;.;.	Q	275	ENSP00000387356:R275Q;ENSP00000341615:R275Q	ENSP00000268134:R275Q	R	+	2	0	ACAN	87187656	1.000000	0.71417	0.999000	0.59377	0.983000	0.72400	5.756000	0.68757	2.626000	0.88956	0.650000	0.86243	CGG	G|0.889;A|0.111	0.111	strong		0.642	ACAN-006	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416267.2	NM_001135	
HIST1H4G	8369	hgsc.bcm.edu	37	6	26247198	26247198	+	Missense_Mutation	SNP	A	A	G	rs41266821	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	71	0	0		WXS	Illumina HiSeq	Phase_I	63	28	0.444444	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	
SDCCAG8	10806	hgsc.bcm.edu	37	1	243493907	243493907	+	Missense_Mutation	SNP	A	A	T	rs2275155	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:243493907A>T	ENST00000366541.3	+	10	1252	c.1134A>T	c.(1132-1134)gaA>gaT	p.E378D	SDCCAG8_ENST00000343783.6_Missense_Mutation_p.E233D|SDCCAG8_ENST00000355875.4_Missense_Mutation_p.E335D	NM_006642.3	NP_006633.1	Q86SQ7	SDCG8_HUMAN	serologically defined colon cancer antigen 8	378	Sufficient for homodimerization. {ECO:0000250}.		E -> D (in dbSNP:rs2275155).		establishment of cell polarity (GO:0030010)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|tube formation (GO:0035148)	cell-cell junction (GO:0005911)|centriole (GO:0005814)|centrosome (GO:0005813)|cytosol (GO:0005829)				breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(17)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29	all_cancers(71;0.000545)|all_epithelial(71;0.000509)|all_lung(81;0.0821)|Ovarian(71;0.0919)|all_neural(11;0.101)|Breast(184;0.218)	all_cancers(173;0.00395)	all cancers(7;1.58e-07)|GBM - Glioblastoma multiforme(7;5.12e-06)|OV - Ovarian serous cystadenocarcinoma(106;0.00392)	COAD - Colon adenocarcinoma(196;0.145)		TTGAAAAAGAACTTGCATCTC	0.448													A|||	1359	0.271366	0.1702	0.2147	5008	,	,		11478	0.1935		0.3231	False		,,,				2504	0.4755				p.E378D		Atlas-SNP	.											SDCCAG8,NS,carcinoma,+2,1	SDCCAG8	73	1	0			c.A1134T						PASS	.	A	ASP/GLU	843,3563	330.4+/-301.5	94,655,1454	81.0	76.0	77.0		1134	0.2	0.7	1	dbSNP_100	77	2645,5955	419.4+/-353.1	395,1855,2050	yes	missense	SDCCAG8	NM_006642.3	45	489,2510,3504	TT,TA,AA		30.7558,19.133,26.8184	benign	378/714	243493907	3488,9518	2203	4300	6503	SO:0001583	missense	10806	exon10			AAAAGAACTTGCA	AF039690	CCDS31075.1	1q43	2011-08-02			ENSG00000054282	ENSG00000054282			10671	protein-coding gene	gene with protein product		613524				9610721, 20835237	Standard	NM_006642		Approved	NY-CO-8, CCCAP, SLSN7, NPHP10, BBS16	uc001hzw.3	Q86SQ7	OTTHUMG00000039996	ENST00000366541.3:c.1134A>T	1.37:g.243493907A>T	ENSP00000355499:p.Glu378Asp	Somatic	219	0	0		WXS	Illumina HiSeq	Phase_I	193	82	0.42487	NM_006642	O60527|Q3ZCR6|Q8N5F2|Q9P0F1	Missense_Mutation	SNP	ENST00000366541.3	37	CCDS31075.1	507	0.23214285714285715	78	0.15853658536585366	79	0.21823204419889503	103	0.18006993006993008	247	0.3258575197889182	A	17.68	3.450269	0.63290	0.19133	0.307558	ENSG00000054282	ENST00000355875;ENST00000366541;ENST00000343783;ENST00000435549	T;T;T;T	0.49432	0.78;0.78;0.78;0.78	5.78	0.25	0.15535	.	0.100084	0.64402	D	0.000002	T	0.00012	0.0000	M	0.71581	2.175	0.34934	P	0.25036899999999995	P;B	0.50819	0.939;0.119	P;B	0.47075	0.536;0.084	T	0.24154	-1.0168	9	0.33141	T	0.24	-6.6197	8.5699	0.33563	0.6552:0.0:0.3448:0.0	rs2275155;rs52836454;rs2275155	335;378	E9PFS7;Q86SQ7	.;SDCG8_HUMAN	D	335;378;233;158	ENSP00000348137:E335D;ENSP00000355499:E378D;ENSP00000341260:E233D;ENSP00000410200:E158D	ENSP00000341260:E233D	E	+	3	2	SDCCAG8	241560530	0.996000	0.38824	0.707000	0.30419	0.873000	0.50193	0.375000	0.20518	-0.190000	0.10465	0.533000	0.62120	GAA	A|0.746;T|0.254	0.254	strong		0.448	SDCCAG8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096485.1	NM_006642	
CAMK2B	816	hgsc.bcm.edu	37	7	44282877	44282877	+	Silent	SNP	A	A	G	rs11542227	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:44282877A>G	ENST00000395749.2	-	8	649	c.573T>C	c.(571-573)taT>taC	p.Y191Y	CAMK2B_ENST00000347193.4_Silent_p.Y191Y|CAMK2B_ENST00000258682.6_Silent_p.Y191Y|CAMK2B_ENST00000440254.2_Silent_p.Y191Y|CAMK2B_ENST00000457475.1_Silent_p.Y191Y|CAMK2B_ENST00000358707.3_Silent_p.Y191Y|CAMK2B_ENST00000346990.4_Silent_p.Y191Y|CAMK2B_ENST00000502837.2_Silent_p.Y62Y|CAMK2B_ENST00000395747.2_Silent_p.Y191Y|CAMK2B_ENST00000350811.3_Silent_p.Y191Y|CAMK2B_ENST00000353625.4_Silent_p.Y191Y	NM_001220.4	NP_001211.3	Q13554	KCC2B_HUMAN	calcium/calmodulin-dependent protein kinase II beta	191	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						CAGGCTTGCCATACGCCTCTT	0.612													.|||	1051	0.209864	0.0976	0.2233	5008	,	,		19957	0.1131		0.3588	False		,,,				2504	0.2986				p.Y191Y		Atlas-SNP	.											.	CAMK2B	56	.	0			c.T573C						PASS	.	A	,,,,,,,	578,3828	255.2+/-260.5	34,510,1659	87.0	76.0	80.0		573,573,573,573,573,573,573,573	-1.5	0.9	7	dbSNP_120	80	3083,5517	471.3+/-368.1	543,1997,1760	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	,,,,,,,	577,2507,3419	GG,GA,AA		35.8488,13.1185,28.1485	,,,,,,,	191/667,191/543,191/519,191/518,191/504,191/493,191/480,191/450	44282877	3661,9345	2203	4300	6503	SO:0001819	synonymous_variant	816	exon8			CTTGCCATACGCC	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.573T>C	7.37:g.44282877A>G		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	115	80	0.695652	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																																																																																			A|0.735;G|0.265	0.265	strong		0.612	CAMK2B-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251138.2	NM_172084	
PAPPA	5069	hgsc.bcm.edu	37	9	118949998	118949998	+	Silent	SNP	C	C	T	rs12375498	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:118949998C>T	ENST00000328252.3	+	2	1350	c.981C>T	c.(979-981)tgC>tgT	p.C327C	PAPPA_ENST00000534838.1_5'Flank	NM_002581.3	NP_002572.2	Q13219	PAPP1_HUMAN	pregnancy-associated plasma protein A, pappalysin 1	327	Metalloprotease.				cell differentiation (GO:0030154)|cellular protein metabolic process (GO:0044267)|female pregnancy (GO:0007565)|response to follicle-stimulating hormone (GO:0032354)|response to glucocorticoid (GO:0051384)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)	endopeptidase activity (GO:0004175)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|endometrium(9)|kidney(2)|large_intestine(23)|lung(33)|ovary(4)|pancreas(2)|prostate(5)|skin(7)|stomach(1)|upper_aerodigestive_tract(6)|urinary_tract(1)	98						CTCCTCTGTGCGGACAGACAT	0.572													C|||	591	0.118011	0.0189	0.1499	5008	,	,		20359	0.0942		0.2555	False		,,,				2504	0.1125				p.C327C		Atlas-SNP	.											.	PAPPA	243	.	0			c.C981T						PASS	.	C		244,4162	141.9+/-177.2	7,230,1966	73.0	68.0	70.0		981	-11.8	0.5	9	dbSNP_120	70	2087,6513	361.4+/-332.3	246,1595,2459	no	coding-synonymous	PAPPA	NM_002581.3		253,1825,4425	TT,TC,CC		24.2674,5.5379,17.9225		327/1628	118949998	2331,10675	2203	4300	6503	SO:0001819	synonymous_variant	5069	exon2			TCTGTGCGGACAG		CCDS6813.1	9q33.1	2014-03-05			ENSG00000182752	ENSG00000182752			8602	protein-coding gene	gene with protein product	"""insulin-like growth factor-dependent IGF binding protein-4 protease"", ""aspecific BCL2 ARE-binding protein 2"", ""differentially placenta 1 expressed protein"""	176385				7679961	Standard	NM_002581		Approved	PAPP-A, PAPPA1, IGFBP-4ase, PAPA, ASBABP2, DIPLA1	uc004bjn.3	Q13219	OTTHUMG00000021045	ENST00000328252.3:c.981C>T	9.37:g.118949998C>T		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	82	31	0.378049	NM_002581	B1AMF9|Q08371|Q68G52|Q9UDK7	Silent	SNP	ENST00000328252.3	37	CCDS6813.1																																																																																			C|0.836;T|0.164	0.164	strong		0.572	PAPPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055546.1	NM_002581	
FAT2	2196	hgsc.bcm.edu	37	5	150908813	150908813	+	Missense_Mutation	SNP	G	G	A	rs2304024	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:150908813G>A	ENST00000261800.5	-	14	9964	c.9952C>T	c.(9952-9954)Cgg>Tgg	p.R3318W		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	3318	Cadherin 29. {ECO:0000255|PROSITE- ProRule:PRU00043}.		R -> Q (in dbSNP:rs7718054).|R -> W (in dbSNP:rs2304024).		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)			AATTGGGGCCGGTGTTCATTG	0.527													G|||	484	0.0966454	0.0083	0.1571	5008	,	,		21748	0.125		0.1938	False		,,,				2504	0.044				p.R3318W		Atlas-SNP	.											.	FAT2	465	.	0			c.C9952T						PASS	.	G	TRP/ARG	161,4245	107.3+/-145.7	6,149,2048	144.0	137.0	139.0		9952	3.9	1.0	5	dbSNP_100	139	1815,6785	328.0+/-318.1	201,1413,2686	yes	missense	FAT2	NM_001447.2	101	207,1562,4734	AA,AG,GG		21.1047,3.6541,15.193	probably-damaging	3318/4350	150908813	1976,11030	2203	4300	6503	SO:0001583	missense	2196	exon14			GGGGCCGGTGTTC	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.9952C>T	5.37:g.150908813G>A	ENSP00000261800:p.Arg3318Trp	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	103	56	0.543689	NM_001447	O75091|Q9NSR7	Missense_Mutation	SNP	ENST00000261800.5	37	CCDS4317.1	288|288	0.13186813186813187|0.13186813186813187	6|6	0.012195121951219513|0.012195121951219513	65|65	0.17955801104972377|0.17955801104972377	81|81	0.14160839160839161|0.14160839160839161	136|136	0.17941952506596306|0.17941952506596306	G|G	17.07|17.07	3.295417|3.295417	0.60086|0.60086	0.036541|0.036541	0.211047|0.211047	ENSG00000086570|ENSG00000086570	ENST00000520200|ENST00000261800	.|T	.|0.61392	.|0.11	5.78|5.78	3.9|3.9	0.45041|0.45041	.|Cadherin (3);Cadherin-like (1);	.|1.332910	.|0.04805	.|N	.|0.434197	T|T	0.00073|0.00073	0.0002|0.0002	L|L	0.61036|0.61036	1.89|1.89	0.39169|0.39169	P|P	0.03744499999999995|0.03744499999999995	.|D;D	.|0.62365	.|0.991;0.989	.|P;B	.|0.46452	.|0.517;0.409	T|T	0.04153|0.04153	-1.0973|-1.0973	4|9	.|0.87932	.|D	.|0	.|.	6.7277|6.7277	0.23365|0.23365	0.1644:0.2384:0.5973:0.0|0.1644:0.2384:0.5973:0.0	rs2304024;rs17404244;rs52798374;rs2304024|rs2304024;rs17404244;rs52798374;rs2304024	.|3318;509	.|Q9NYQ8;E9PDJ8	.|FAT2_HUMAN;.	L|W	176|3318	.|ENSP00000261800:R3318W	.|ENSP00000261800:R3318W	P|R	-|-	2|1	0|2	FAT2|FAT2	150889006|150889006	0.204000|0.204000	0.23447|0.23447	0.977000|0.977000	0.42913|0.42913	0.589000|0.589000	0.36550|0.36550	0.780000|0.780000	0.26760|0.26760	1.450000|1.450000	0.47717|0.47717	-0.170000|-0.170000	0.13304|0.13304	CCG|CGG	G|0.858;N|0.001	.	strong		0.527	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447	
PLXNA2	5362	hgsc.bcm.edu	37	1	208390469	208390469	+	Missense_Mutation	SNP	C	C	T	rs3748735	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:208390469C>T	ENST00000367033.3	-	2	1556	c.799G>A	c.(799-801)Gcc>Acc	p.A267T		NM_025179.3	NP_079455.3	O75051	PLXA2_HUMAN	plexin A2	267	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.		A -> T (in dbSNP:rs3748735).		axon guidance (GO:0007411)|centrosome localization (GO:0051642)|cerebellar granule cell precursor tangential migration (GO:0021935)|limb bud formation (GO:0060174)|neural tube development (GO:0021915)|pharyngeal system development (GO:0060037)|regulation of cell migration (GO:0030334)|semaphorin-plexin signaling pathway (GO:0071526)|somitogenesis (GO:0001756)	integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)			NS(1)|breast(3)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(28)|ovary(3)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)	80				OV - Ovarian serous cystadenocarcinoma(81;0.199)		GAGTTGATGGCCACACCCTCA	0.577													C|||	699	0.139577	0.0673	0.1715	5008	,	,		19639	0.1458		0.1988	False		,,,				2504	0.1472				p.A267T		Atlas-SNP	.											.	PLXNA2	178	.	0			c.G799A						PASS	.	C	THR/ALA	386,4020	195.3+/-220.0	19,348,1836	115.0	114.0	114.0		799	4.9	1.0	1	dbSNP_107	114	1686,6914	308.6+/-309.0	189,1308,2803	yes	missense	PLXNA2	NM_025179.3	58	208,1656,4639	TT,TC,CC		19.6047,8.7608,15.9311	benign	267/1895	208390469	2072,10934	2203	4300	6503	SO:0001583	missense	5362	exon2			TGATGGCCACACC	X87831	CCDS31013.1	1q32.2	2008-07-18			ENSG00000076356	ENSG00000076356		"""Plexins"""	9100	protein-coding gene	gene with protein product	"""plexin 2"", ""plexin-A2"", ""semaphorin receptor OCT"", ""transmembrane protein OCT"""	601054		PLXN2		8570614	Standard	NM_025179		Approved	OCT, FLJ11751, FLJ30634, KIAA0463	uc001hgz.3	O75051	OTTHUMG00000036564	ENST00000367033.3:c.799G>A	1.37:g.208390469C>T	ENSP00000356000:p.Ala267Thr	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	84	79	0.940476	NM_025179	A2RTX9|B2RMX7|Q6UX61|Q96GN9|Q9BRL1|Q9UIW1	Missense_Mutation	SNP	ENST00000367033.3	37	CCDS31013.1	308	0.14102564102564102	34	0.06910569105691057	55	0.15193370165745856	80	0.13986013986013987	139	0.18337730870712401	C	14.10	2.434528	0.43224	0.087608	0.196047	ENSG00000076356	ENST00000367033	T	0.10860	2.83	5.84	4.91	0.64330	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.472859	0.22674	N	0.057027	T	0.00012	0.0000	N	0.08118	0	0.25798	P	0.9845479	P;B	0.38827	0.649;0.053	B;B	0.41510	0.359;0.13	T	0.42464	-0.9450	9	0.07325	T	0.83	.	14.0881	0.64971	0.3283:0.6717:0.0:0.0	rs3748735;rs57678694;rs3748735	321;267	O75051-2;O75051	.;PLXA2_HUMAN	T	267	ENSP00000356000:A267T	ENSP00000356000:A267T	A	-	1	0	PLXNA2	206457092	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	3.531000	0.53546	1.433000	0.47394	0.655000	0.94253	GCC	C|0.850;T|0.150	0.150	strong		0.577	PLXNA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088932.6	NM_025179	
ZNF708	7562	hgsc.bcm.edu	37	19	21477431	21477431	+	Missense_Mutation	SNP	T	T	C	rs1781873	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:21477431T>C	ENST00000356929.3	-	4	534	c.337A>G	c.(337-339)Aaa>Gaa	p.K113E		NM_021269.2	NP_067092.2	P17019	ZN708_HUMAN	zinc finger protein 708	49					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						TCCACACTTTTACAGCCTTTC	0.393													T|||	3110	0.621006	0.7436	0.562	5008	,	,		17016	0.629		0.5089	False		,,,				2504	0.6043				p.K113E		Atlas-SNP	.											.	ZNF708	66	.	0			c.A337G						PASS	.	T	GLU/LYS	3110,1296		1100,910,193	152.0	138.0	143.0		337	-0.6	0.0	19	dbSNP_89	143	4486,4114		1227,2032,1041	yes	missense	ZNF708	NM_021269.2	56	2327,2942,1234	CC,CT,TT		47.8372,29.4144,41.5962	benign	113/564	21477431	7596,5410	2203	4300	6503	SO:0001583	missense	7562	exon4			CACTTTTACAGCC	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.337A>G	19.37:g.21477431T>C	ENSP00000349401:p.Lys113Glu	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	58	37	0.637931	NM_021269	Q6ZMR0	Missense_Mutation	SNP	ENST00000356929.3	37	CCDS32980.1	1334	0.6108058608058609	367	0.7459349593495935	208	0.574585635359116	380	0.6643356643356644	379	0.5	.	0.884	-0.727862	0.03158	0.705856	0.521628	ENSG00000182141	ENST00000356929	T	0.06218	3.33	1.07	-0.564	0.11774	.	.	.	.	.	T	0.00012	0.0000	N	0.11341	0.13	0.80722	P	0.0	B	0.11235	0.004	B	0.12837	0.008	T	0.08249	-1.0731	8	0.17369	T	0.5	.	3.2122	0.06686	0.0:0.3246:0.0:0.6753	rs1781873;rs52805708;rs59165625;rs1781873	113	P17019	ZN708_HUMAN	E	113	ENSP00000349401:K113E	ENSP00000349401:K113E	K	-	1	0	ZNF708	21269271	0.000000	0.05858	0.023000	0.16930	0.022000	0.10575	-0.330000	0.07925	-0.428000	0.07339	-0.436000	0.05848	AAA	T|0.407;C|0.593	0.593	strong		0.393	ZNF708-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463953.1	NM_021269	
KLHL4	56062	hgsc.bcm.edu	37	X	86877348	86877348	+	Silent	SNP	G	G	T	rs2273050	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:86877348G>T	ENST00000373119.4	+	5	1207	c.1062G>T	c.(1060-1062)ggG>ggT	p.G354G	KLHL4_ENST00000373114.4_Silent_p.G354G	NM_019117.4	NP_061990.2	Q9C0H6	KLHL4_HUMAN	kelch-like family member 4	354						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				NS(1)|biliary_tract(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(19)|lung(29)|ovary(2)|prostate(1)|skin(1)	67						AGTGGGTGGGGCATGATGTGC	0.433													G|||	717	0.189934	0.1513	0.0504	3775	,	,		12144	0.1448		0.1879	False		,,,				2504	0.1503				p.G354G		Atlas-SNP	.											.	KLHL4	263	.	0			c.G1062T						PASS	.	G	,	714,3121		53,505,103,1074,468	159.0	131.0	140.0		1062,1062	-6.9	0.3	X	dbSNP_100	140	1319,5409		93,760,373,1575,1499	no	coding-synonymous,coding-synonymous	KLHL4	NM_019117.4,NM_057162.2	,	146,1265,476,2649,1967	TT,TG,T,GG,G		19.6046,18.618,19.2464	,	354/719,354/721	86877348	2033,8530	2203	4300	6503	SO:0001819	synonymous_variant	56062	exon5			GGTGGGGCATGAT	AF284765	CCDS14456.1, CCDS14457.1	Xq21.3	2013-01-30	2013-01-30		ENSG00000102271	ENSG00000102271		"""Kelch-like"", ""BTB/POZ domain containing"""	6355	protein-coding gene	gene with protein product		300348	"""kelch (Drosophila)-like 4"", ""kelch-like 4 (Drosophila)"""			11401425	Standard	NM_019117		Approved	KIAA1687, DKELCHL, KHL4	uc004efa.2	Q9C0H6	OTTHUMG00000021946	ENST00000373119.4:c.1062G>T	X.37:g.86877348G>T		Somatic	396	1	0.00252525		WXS	Illumina HiSeq	Phase_I	243	243	1	NM_019117	B2RTW2|Q9Y3J5	Silent	SNP	ENST00000373119.4	37	CCDS14457.1																																																																																			G|0.807;T|0.193	0.193	strong		0.433	KLHL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057413.1		
MUC4	4585	hgsc.bcm.edu	37	3	195513180	195513180	+	Missense_Mutation	SNP	C	C	G	rs77724343	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195513180C>G	ENST00000463781.3	-	2	5730	c.5271G>C	c.(5269-5271)caG>caC	p.Q1757H	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.Q1757H	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.Q1757H(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)		GAGGGGTGGCCTGACCTGTGG	0.582																																					p.Q1757H		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	2	Substitution - Missense(2)	stomach(2)	c.G5271C						scavenged	.						49.0	44.0	45.0					3																	195513180		692	1590	2282	SO:0001583	missense	4585	exon2			GGTGGCCTGACCT	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.5271G>C	3.37:g.195513180C>G	ENSP00000417498:p.Gln1757His	Somatic	106	1	0.00943396		WXS	Illumina HiSeq	Phase_I	143	47	0.328671	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	-	1.229	-0.624622	0.03636	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.38722	1.23;1.12	.	.	.	.	.	.	.	.	T	0.12347	0.0300	N	0.02539	-0.55	0.09310	N	1	B	0.14438	0.01	B	0.01281	0.0	T	0.15838	-1.0423	7	.	.	.	.	2.2036	0.03930	0.0:0.3333:0.3352:0.3315	.	1757	E7ESK3	.	H	1757	ENSP00000417498:Q1757H;ENSP00000420243:Q1757H	.	Q	-	3	2	MUC4	196997575	0.000000	0.05858	0.010000	0.14722	0.010000	0.07245	-3.644000	0.00405	-1.916000	0.01075	-1.964000	0.00472	CAG	C|0.971;G|0.029	0.029	strong		0.582	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
RNF17	56163	hgsc.bcm.edu	37	13	25367282	25367282	+	Missense_Mutation	SNP	A	A	C	rs1451568	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:25367282A>C	ENST00000255324.5	+	10	1090	c.1038A>C	c.(1036-1038)aaA>aaC	p.K346N	RNF17_ENST00000255325.6_Missense_Mutation_p.K346N|RNF17_ENST00000381921.1_Missense_Mutation_p.K346N|RNF17_ENST00000255326.4_3'UTR	NM_001184993.1|NM_031277.2	NP_001171922.1|NP_112567.2	Q9BXT8	RNF17_HUMAN	ring finger protein 17	346			K -> N (in dbSNP:rs1451568).		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)		TAGAAAAGAAAAAGGTTGACA	0.373													A|||	788	0.157348	0.3411	0.1225	5008	,	,		20747	0.001		0.163	False		,,,				2504	0.089				p.K346N		Atlas-SNP	.											.	RNF17	259	.	0			c.A1038C						PASS	.	A	ASN/LYS,ASN/LYS	1432,2974	465.9+/-354.3	219,994,990	175.0	165.0	168.0		1038,1038	-0.1	0.1	13	dbSNP_88	168	1368,7232	266.5+/-286.8	99,1170,3031	yes	missense,missense	RNF17	NM_001184993.1,NM_031277.2	94,94	318,2164,4021	CC,CA,AA		15.907,32.5011,21.5285	benign,benign	346/1620,346/1624	25367282	2800,10206	2203	4300	6503	SO:0001583	missense	56163	exon10			AAAGAAAAAGGTT	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.1038A>C	13.37:g.25367282A>C	ENSP00000255324:p.Lys346Asn	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	57	27	0.473684	NM_001184993	Q5T2J9|Q6P1W3|Q9BXT7|Q9NUY9	Missense_Mutation	SNP	ENST00000255324.5	37	CCDS9308.2	329	0.15064102564102563	162	0.32926829268292684	41	0.1132596685082873	0	0.0	126	0.1662269129287599	A	2.686	-0.274285	0.05679	0.325011	0.15907	ENSG00000132972	ENST00000255324;ENST00000381921;ENST00000429047;ENST00000255325;ENST00000255326	T;T;T	0.19105	3.43;3.43;2.17	5.03	-0.125	0.13519	.	0.419347	0.22513	N	0.059069	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B;B	0.30281	0.001;0.275	B;B	0.26202	0.002;0.067	T	0.46470	-0.9189	9	0.31617	T	0.26	-8.7255	0.835	0.01138	0.5005:0.1659:0.1736:0.16	rs1451568;rs52829203;rs61594290;rs1451568	346;346	Q9BXT8;Q9BXT8-2	RNF17_HUMAN;.	N	346;346;205;347;346	ENSP00000255324:K346N;ENSP00000371346:K346N;ENSP00000255325:K347N	ENSP00000255324:K346N	K	+	3	2	RNF17	24265282	0.371000	0.25056	0.084000	0.20598	0.007000	0.05969	0.331000	0.19733	0.416000	0.25844	-1.007000	0.02485	AAA	A|0.801;C|0.199	0.199	strong		0.373	RNF17-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044217.1	NM_031994	
OR1E1	8387	hgsc.bcm.edu	37	17	3301549	3301549	+	Silent	SNP	G	G	A	rs150988	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:3301549G>A	ENST00000322608.2	-	1	155	c.156C>T	c.(154-156)gaC>gaT	p.D52D		NM_003553.2	NP_003544.2	P30953	OR1E1_HUMAN	olfactory receptor, family 1, subfamily E, member 1	52					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|large_intestine(2)|lung(5)	10						GGAGATGGGAGTCCAGTCGAA	0.498													G|||	2235	0.446286	0.3464	0.5663	5008	,	,		20648	0.4315		0.4016	False		,,,				2504	0.5573				p.D52D		Atlas-SNP	.											.	OR1E1	37	.	0			c.C156T						PASS	.	G		1631,2775	501.5+/-365.0	309,1013,881	127.0	119.0	122.0		156	3.3	1.0	17	dbSNP_79	122	3357,5243	498.3+/-374.7	651,2055,1594	no	coding-synonymous	OR1E1	NM_003553.2		960,3068,2475	AA,AG,GG		39.0349,37.0177,38.3515		52/315	3301549	4988,8018	2203	4300	6503	SO:0001819	synonymous_variant	8387	exon1			ATGGGAGTCCAGT	U04642	CCDS11024.1	17p13.3	2012-08-09			ENSG00000180016	ENSG00000180016		"""GPCR / Class A : Olfactory receptors"""	8189	protein-coding gene	gene with protein product				OR1E9P, OR1E5, OR1E6		8004088, 1370859	Standard	NM_003553		Approved	OR17-2, HGM071, OR17-32, OR13-66	uc002fvj.1	P30953	OTTHUMG00000090643	ENST00000322608.2:c.156C>T	17.37:g.3301549G>A		Somatic	268	0	0		WXS	Illumina HiSeq	Phase_I	225	103	0.457778	NM_003553	O43884|P47882|P47885|Q6IFA9|Q6IFM5|Q9UBJ1|Q9UM60	Silent	SNP	ENST00000322608.2	37	CCDS11024.1																																																																																			G|0.602;A|0.398	0.398	strong		0.498	OR1E1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207303.1	NM_003553	
ANKEF1	63926	hgsc.bcm.edu	37	20	10032413	10032413	+	Silent	SNP	T	T	G	rs683145	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:10032413T>G	ENST00000378380.3	+	7	2075	c.1746T>G	c.(1744-1746)gcT>gcG	p.A582A	SNAP25-AS1_ENST00000421143.2_RNA|SNAP25-AS1_ENST00000603542.1_RNA|ANKEF1_ENST00000378392.1_Silent_p.A582A|ANKEF1_ENST00000488991.1_3'UTR	NM_198798.1	NP_942093.1	Q9NU02	ANKE1_HUMAN	ankyrin repeat and EF-hand domain containing 1	582							calcium ion binding (GO:0005509)										AATCTGGAGCTTTAATAGATG	0.393													T|||	1005	0.200679	0.2791	0.1585	5008	,	,		17241	0.0069		0.2744	False		,,,				2504	0.2485				p.A582A		Atlas-SNP	.											.	.	.	.	0			c.T1746G						PASS	.	T	,	1192,3214	418.7+/-338.4	160,872,1171	89.0	83.0	85.0		1746,1746	-4.1	0.0	20	dbSNP_83	85	2415,6185	400.5+/-346.8	344,1727,2229	no	coding-synonymous,coding-synonymous	ANKRD5	NM_022096.4,NM_198798.1	,	504,2599,3400	GG,GT,TT		28.0814,27.054,27.7334	,	582/777,582/777	10032413	3607,9399	2203	4300	6503	SO:0001819	synonymous_variant	63926	exon7			TGGAGCTTTAATA	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.1746T>G	20.37:g.10032413T>G		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	67	36	0.537313	NM_198798	B3KUQ0|Q9H6Y9	Silent	SNP	ENST00000378380.3	37	CCDS13108.1																																																																																			T|0.752;G|0.248	0.248	strong		0.393	ANKEF1-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077968.2	NM_022096	
INPP4B	8821	hgsc.bcm.edu	37	4	143043397	143043397	+	Splice_Site	SNP	G	G	A	rs34561493	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:143043397G>A	ENST00000513000.1	-	22	2452	c.2019C>T	c.(2017-2019)agC>agT	p.S673S	INPP4B_ENST00000508116.1_Splice_Site_p.S673S|INPP4B_ENST00000308502.4_Splice_Site_p.S673S|INPP4B_ENST00000262992.4_Splice_Site_p.S673S|INPP4B_ENST00000509777.1_Splice_Site_p.S673S	NM_003866.2	NP_003857.2	O15327	INP4B_HUMAN	inositol polyphosphate-4-phosphatase, type II, 105kDa	673					cellular calcium ion homeostasis (GO:0006874)|inositol phosphate metabolic process (GO:0043647)|negative regulation of osteoclast differentiation (GO:0045671)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|regulation of bone remodeling (GO:0046850)|regulation of nucleocytoplasmic transport (GO:0046822)|regulation of protein kinase B signaling (GO:0051896)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|Golgi apparatus (GO:0005794)	lipid binding (GO:0008289)|phosphatidylinositol trisphosphate phosphatase activity (GO:0034594)|phosphatidylinositol-3,4-bisphosphate 4-phosphatase activity (GO:0016316)|phosphatidylinositol-4,5-bisphosphate 4-phosphatase activity (GO:0034597)			breast(3)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(8)|lung(29)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	58	all_hematologic(180;0.158)					CAATTTCATCGCCTAAACAAT	0.378													G|||	284	0.0567093	0.0431	0.0605	5008	,	,		19891	0.0506		0.0805	False		,,,				2504	0.0542				p.S673S		Atlas-SNP	.											.	INPP4B	132	.	0			c.C2019T						PASS	.	G	,	247,4159	142.7+/-177.9	7,233,1963	70.0	68.0	68.0		2019,2019	3.4	1.0	4	dbSNP_126	68	685,7915	170.3+/-221.5	32,621,3647	yes	coding-synonymous-near-splice,coding-synonymous-near-splice	INPP4B	NM_001101669.1,NM_003866.2	,	39,854,5610	AA,AG,GG		7.9651,5.606,7.1659	,	673/925,673/925	143043397	932,12074	2203	4300	6503	SO:0001630	splice_region_variant	8821	exon22			TTCATCGCCTAAA	U96922	CCDS3757.1	4q31.1	2008-02-05	2002-08-29			ENSG00000109452			6075	protein-coding gene	gene with protein product		607494	"""inositol polyphosphate-4-phosphatase, type II, 105kD"""			9295334	Standard	NM_003866		Approved		uc003iiw.4	O15327		ENST00000513000.1:c.2018-1C>T	4.37:g.143043397G>A		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	59	23	0.38983	NM_003866	Q2TAI2|Q5XLE7|Q6IN59|Q6PJB4	Silent	SNP	ENST00000513000.1	37	CCDS3757.1																																																																																			G|0.932;A|0.068	0.068	strong		0.378	INPP4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364587.1	NM_003866	Silent
FRG1	2483	hgsc.bcm.edu	37	4	190862182	190862182	+	Silent	SNP	C	C	T	rs2411530	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:190862182C>T	ENST00000226798.4	+	1	240	c.18C>T	c.(16-18)taC>taT	p.Y6Y	FRG1_ENST00000514482.1_3'UTR	NM_004477.2	NP_004468.1	Q14331	FRG1_HUMAN	FSHD region gene 1	6					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)		AGTACTCCTACGTGAAGTCTA	0.622											OREG0016457	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	.|||	2325	0.464257	0.7716	0.2752	5008	,	,		14875	0.3938		0.3231	False		,,,				2504	0.4008				p.Y6Y		Atlas-SNP	.											.	FRG1	76	.	0			c.C18T						PASS	.	T		3216,1190		1182,852,169	37.0	40.0	39.0		18	-8.0	0.0	4	dbSNP_100	39	2739,5861		419,1901,1980	no	coding-synonymous	FRG1	NM_004477.2		1601,2753,2149	TT,TC,CC		31.8488,27.0086,45.7866		6/259	190862182	5955,7051	2203	4300	6503	SO:0001819	synonymous_variant	2483	exon1			CTCCTACGTGAAG	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.18C>T	4.37:g.190862182C>T		Somatic	118	0	0	2041	WXS	Illumina HiSeq	Phase_I	123	43	0.349593	NM_004477	A8K775	Silent	SNP	ENST00000226798.4	37	CCDS34121.1																																																																																			C|0.506;T|0.494	0.494	strong		0.622	FRG1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000359622.4	NM_004477	
ALS2	57679	hgsc.bcm.edu	37	2	202626437	202626437	+	Missense_Mutation	SNP	T	T	C	rs3219154	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:202626437T>C	ENST00000264276.6	-	4	652	c.280A>G	c.(280-282)Att>Gtt	p.I94V	ALS2_ENST00000467448.1_Missense_Mutation_p.I94V|ALS2_ENST00000496244.1_5'UTR	NM_020919.3	NP_065970.2	Q96Q42	ALS2_HUMAN	amyotrophic lateral sclerosis 2 (juvenile)	94			I -> V (in dbSNP:rs3219154).		behavioral fear response (GO:0001662)|cell death (GO:0008219)|endosomal transport (GO:0016197)|endosome organization (GO:0007032)|locomotory behavior (GO:0007626)|neuromuscular junction development (GO:0007528)|neuron projection morphogenesis (GO:0048812)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of Rab GTPase activity (GO:0032851)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rac protein signal transduction (GO:0035022)|positive regulation of Ran GTPase activity (GO:0032853)|protein localization (GO:0008104)|receptor recycling (GO:0001881)|regulation of endosome size (GO:0051036)|response to oxidative stress (GO:0006979)|synaptic transmission, glutamatergic (GO:0035249)|vesicle organization (GO:0016050)	centrosome (GO:0005813)|cytosol (GO:0005829)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|early endosome (GO:0005769)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|postsynaptic density (GO:0014069)|protein complex (GO:0043234)|ruffle (GO:0001726)|vesicle (GO:0031982)	protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activator activity (GO:0043539)|Rab GTPase binding (GO:0017137)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|Ran guanyl-nucleotide exchange factor activity (GO:0005087)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(22)|ovary(1)|prostate(4)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)	72						GCCACAGTAATAACATATTGC	0.502													C|||	112	0.0223642	0.0408	0.0173	5008	,	,		15545	0.0		0.0219	False		,,,				2504	0.0245				p.I94V		Atlas-SNP	.											.	ALS2	172	.	0			c.A280G						PASS	.	C	VAL/ILE,VAL/ILE	198,3754		2,194,1780	120.0	117.0	118.0		280,280	2.8	0.9	2	dbSNP_106	118	213,8097		4,205,3946	yes	missense,missense	ALS2	NM_001135745.1,NM_020919.3	29,29	6,399,5726	CC,CT,TT		2.5632,5.0101,3.3518	benign,benign	94/397,94/1658	202626437	411,11851	1976	4155	6131	SO:0001583	missense	57679	exon4			CAGTAATAACATA	AB053305	CCDS42800.1, CCDS46492.1	2q33-q35	2014-09-17	2004-06-23		ENSG00000003393	ENSG00000003393		"""Rho guanine nucleotide exchange factors"""	443	protein-coding gene	gene with protein product	"""alsin"""	606352	"""amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 6"""	ALS2CR6		11586298	Standard	NM_020919		Approved		uc002uyo.3	Q96Q42	OTTHUMG00000154507	ENST00000264276.6:c.280A>G	2.37:g.202626437T>C	ENSP00000264276:p.Ile94Val	Somatic	254	0	0		WXS	Illumina HiSeq	Phase_I	227	117	0.515419	NM_001135745	Q53TT1|Q53TV2|Q8N1E0|Q96PC4|Q96Q41|Q9H973|Q9HCK9	Missense_Mutation	SNP	ENST00000264276.6	37	CCDS42800.1	34	0.015567765567765568	12	0.024390243902439025	9	0.024861878453038673	0	0.0	13	0.017150395778364115	C	2.719	-0.266955	0.05754	0.050101	0.025632	ENSG00000003393	ENST00000264276;ENST00000467448;ENST00000409632;ENST00000410052	T;T;T;T	0.79141	-1.24;-1.24;-1.24;-1.24	6.07	2.85	0.33270	Regulator of chromosome condensation/beta-lactamase-inhibitor protein II (2);	0.330203	0.31922	N	0.006850	T	0.13415	0.0325	N	0.04959	-0.14	0.80722	D	1	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.08055	0.003;0.001;0.0;0.0	T	0.23048	-1.0199	10	0.02654	T	1	.	8.3324	0.32195	0.0:0.5169:0.0:0.4831	rs3219154;rs52817011;rs59604713;rs3219154	94;94;94;94	Q96Q42-2;Q96Q42-3;Q6IQ41;Q96Q42	.;.;.;ALS2_HUMAN	V	94	ENSP00000264276:I94V;ENSP00000429223:I94V;ENSP00000386384:I94V;ENSP00000386948:I94V	ENSP00000264276:I94V	I	-	1	0	ALS2	202334682	0.894000	0.30519	0.945000	0.38365	0.993000	0.82548	0.863000	0.27913	0.443000	0.26582	-0.119000	0.15052	ATT	T|0.977;C|0.023	0.023	strong		0.502	ALS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335562.3	NM_020919	
METTL2B	55798	hgsc.bcm.edu	37	7	128119514	128119514	+	Missense_Mutation	SNP	G	G	A	rs1065267	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:128119514G>A	ENST00000262432.8	+	3	542	c.505G>A	c.(505-507)Gaa>Aaa	p.E169K	RP11-212P7.3_ENST00000462662.1_RNA|METTL2B_ENST00000480046.1_Missense_Mutation_p.E104K	NM_018396.2	NP_060866.2	Q6P1Q9	MET2B_HUMAN	methyltransferase like 2B	169			E -> K (in dbSNP:rs1065267).		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						TAGTGACCTGGAAATTTGTGC	0.408																																					p.E169K		Atlas-SNP	.											.	METTL2B	34	.	0			c.G505A						PASS	.						91.0	108.0	102.0					7																	128119514		2203	4299	6502	SO:0001583	missense	55798	exon3			GACCTGGAAATTT	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.505G>A	7.37:g.128119514G>A	ENSP00000262432:p.Glu169Lys	Somatic	432	1	0.00231481		WXS	Illumina HiSeq	Phase_I	358	107	0.298883	NM_018396	B4DZ68|Q0IJ54|Q3B7J1	Missense_Mutation	SNP	ENST00000262432.8	37	CCDS5803.2	188	0.08608058608058608	11	0.022357723577235773	46	0.1270718232044199	0	0.0	131	0.17282321899736147	G	5.147	0.212742	0.09757	.	.	ENSG00000165055	ENST00000462662;ENST00000262432;ENST00000480046	T;T;T	0.17691	2.26;2.8;2.79	2.65	1.7	0.24286	.	0.906623	0.09774	N	0.757606	T	0.00039	0.0001	L	0.31664	0.95	0.80722	P	0.0	B;B	0.14805	0.001;0.011	B;B	0.14578	0.006;0.011	T	0.40813	-0.9543	9	0.09590	T	0.72	-1.7228	7.2315	0.26045	0.0:0.2783:0.7217:0.0	rs1065267;rs1065267	104;169	Q6P1Q9-2;Q6P1Q9	.;MTL2B_HUMAN	K	163;169;104	ENSP00000418634:E163K;ENSP00000262432:E169K;ENSP00000418402:E104K	ENSP00000262432:E169K	E	+	1	0	METTL2B	127906750	0.652000	0.27349	0.721000	0.30653	0.035000	0.12851	1.379000	0.34340	0.405000	0.25532	0.405000	0.27470	GAA	G|0.906;A|0.094	0.094	strong		0.408	METTL2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000289817.1	NM_018396	
DMWD	1762	hgsc.bcm.edu	37	19	46289503	46289503	+	Silent	SNP	C	C	T	rs8109951	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:46289503C>T	ENST00000270223.6	-	3	1296	c.1251G>A	c.(1249-1251)ccG>ccA	p.P417P	DMWD_ENST00000377735.3_Silent_p.P417P|AC011530.4_ENST00000593999.1_5'Flank|DMWD_ENST00000601370.1_5'Flank	NM_004943.1	NP_004934.1	Q09019	DMWD_HUMAN	dystrophia myotonica, WD repeat containing	417										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)		GTGGAGAGAGCGGGGCGCCCC	0.692													C|||	1455	0.290535	0.3079	0.2291	5008	,	,		12564	0.2887		0.329	False		,,,				2504	0.273				p.P417P		Atlas-SNP	.											DMWD,rectum,carcinoma,0,1	DMWD	46	1	0			c.G1251A						PASS	.	C		1250,3120		209,832,1144	15.0	18.0	17.0		1251	-8.4	0.0	19	dbSNP_116	17	3086,5450		602,1882,1784	no	coding-synonymous	DMWD	NM_004943.1		811,2714,2928	TT,TC,CC		36.1528,28.6041,33.5968		417/675	46289503	4336,8570	2185	4268	6453	SO:0001819	synonymous_variant	1762	exon3			AGAGAGCGGGGCG	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.1251G>A	19.37:g.46289503C>T		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	84	39	0.464286	NM_004943		Silent	SNP	ENST00000270223.6	37	CCDS33054.1																																																																																			C|0.701;T|0.299	0.299	strong		0.692	DMWD-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402063.1	NM_004943	
GIT2	9815	hgsc.bcm.edu	37	12	110385079	110385079	+	Silent	SNP	G	G	T	rs2063388	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:110385079G>T	ENST00000355312.3	-	15	1622	c.1623C>A	c.(1621-1623)ctC>ctA	p.L541L	GIT2_ENST00000343646.5_Silent_p.L461L|GIT2_ENST00000338373.5_Intron|GIT2_ENST00000361006.5_Silent_p.L541L|GIT2_ENST00000551209.1_Silent_p.L490L|TCHP_ENST00000550780.1_Intron|GIT2_ENST00000553118.1_Intron|GIT2_ENST00000356259.4_Intron|GIT2_ENST00000360185.4_Silent_p.L491L|GIT2_ENST00000354574.4_Silent_p.L493L|GIT2_ENST00000457474.2_Silent_p.L493L	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	208	0	0		WXS	Illumina HiSeq	Phase_I	201	100	0.497512	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	
CDHR1	92211	hgsc.bcm.edu	37	10	85972043	85972043	+	Silent	SNP	A	A	G	rs10749482	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:85972043A>G	ENST00000372117.3	+	15	1765	c.1662A>G	c.(1660-1662)gaA>gaG	p.E554E	CDHR1_ENST00000440770.2_Silent_p.E258E|CDHR1_ENST00000332904.3_Silent_p.E554E	NM_033100.2	NP_149091.1	Q96JP9	CDHR1_HUMAN	cadherin-related family member 1	554	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cellular process (GO:0009987)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)	integral component of plasma membrane (GO:0005887)|photoreceptor outer segment membrane (GO:0042622)	calcium ion binding (GO:0005509)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(21)|ovary(1)|prostate(1)|skin(1)	36						AGGACATGGAAGGCAAGTACA	0.542													G|||	2149	0.429113	0.7542	0.3876	5008	,	,		20639	0.2619		0.2853	False		,,,				2504	0.3395				p.E554E		Atlas-SNP	.											.	CDHR1	122	.	0			c.A1662G						PASS	.	G	,	2938,1468	472.6+/-356.4	990,958,255	172.0	152.0	159.0		1662,1662	0.6	1.0	10	dbSNP_120	159	2503,6097	694.5+/-404.7	376,1751,2173	no	coding-synonymous,coding-synonymous	CDHR1	NM_001171971.1,NM_033100.2	,	1366,2709,2428	GG,GA,AA		29.1047,33.3182,41.8345	,	554/746,554/860	85972043	5441,7565	2203	4300	6503	SO:0001819	synonymous_variant	92211	exon15			CATGGAAGGCAAG	AB053448	CCDS7372.1, CCDS53548.1	10q23.1	2014-01-28	2010-01-25	2010-01-25	ENSG00000148600	ENSG00000148600		"""Cadherins / Cadherin-related"""	14550	protein-coding gene	gene with protein product		609502	"""protocadherin 21"""	PCDH21		11597768	Standard	NM_001171971		Approved	KIAA1775, CORD15, RP65	uc001kcv.3	Q96JP9	OTTHUMG00000018634	ENST00000372117.3:c.1662A>G	10.37:g.85972043A>G		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	126	58	0.460317	NM_001171971	Q69YZ8|Q8IXY5	Silent	SNP	ENST00000372117.3	37	CCDS7372.1																																																																																			A|0.585;G|0.415	0.415	strong		0.542	CDHR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049111.1	NM_033100	
MDN1	23195	hgsc.bcm.edu	37	6	90397132	90397132	+	Missense_Mutation	SNP	G	G	C	rs34766278	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	74	0	0		WXS	Illumina HiSeq	Phase_I	67	28	0.41791	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		
S1PR3	1903	hgsc.bcm.edu	37	9	91616843	91616843	+	Missense_Mutation	SNP	G	G	A	rs34075341	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:91616843G>A	ENST00000375846.3	+	1	5423	c.728G>A	c.(727-729)cGg>cAg	p.R243Q	S1PR3_ENST00000358157.2_Missense_Mutation_p.R243Q			Q99500	S1PR3_HUMAN	sphingosine-1-phosphate receptor 3	243			R -> Q (in dbSNP:rs34075341).		adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|anatomical structure morphogenesis (GO:0009653)|cytokine production (GO:0001816)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)|negative regulation of establishment of endothelial barrier (GO:1903141)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of interleukin-1 beta production (GO:0032651)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|integrin binding (GO:0005178)|lipid binding (GO:0008289)|sphingosine-1-phosphate receptor activity (GO:0038036)			NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(9)|ovary(3)|pancreas(1)|prostate(3)|skin(1)	34						GCACTGCTGCGGACCGTGGTG	0.592													G|||	148	0.0295527	0.0325	0.0245	5008	,	,		21413	0.0		0.0437	False		,,,				2504	0.045				p.R243Q		Atlas-SNP	.											.	S1PR3	49	.	0			c.G728A						PASS	.	G	GLN/ARG	160,4246	108.6+/-147.0	1,158,2044	156.0	103.0	121.0		728	2.3	0.9	9	dbSNP_126	121	331,8269	115.2+/-175.0	7,317,3976	yes	missense	S1PR3	NM_005226.2	43	8,475,6020	AA,AG,GG		3.8488,3.6314,3.7752	probably-damaging	243/379	91616843	491,12515	2203	4300	6503	SO:0001583	missense	1903	exon2			TGCTGCGGACCGT	AF022139	CCDS6680.1	9q22.1-q22.2	2012-08-08	2008-04-30	2008-04-30	ENSG00000213694	ENSG00000213694		"""GPCR / Class A : Lysophospholipid receptors : Sphingosine 1-phosphate"""	3167	protein-coding gene	gene with protein product	"""sphingosine-1-phosphate receptor 3"""	601965	"""endothelial differentiation, sphingolipid G-protein-coupled receptor, 3"""	EDG3		8878560, 9409733	Standard	NM_005226		Approved	EDG-3	uc004aqe.4	Q99500	OTTHUMG00000020173	ENST00000375846.3:c.728G>A	9.37:g.91616843G>A	ENSP00000365006:p.Arg243Gln	Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	146	69	0.472603	NM_005226	Q5SQD8|Q7Z5I2	Missense_Mutation	SNP	ENST00000375846.3	37	CCDS6680.1	53	0.024267399267399268	10	0.02032520325203252	11	0.03038674033149171	0	0.0	32	0.04221635883905013	G	20.8	4.052629	0.75960	0.036314	0.038488	ENSG00000213694	ENST00000358157;ENST00000375846	T;T	0.39592	1.07;1.07	5.11	2.3	0.28687	GPCR, rhodopsin-like superfamily (1);	0.126278	0.52532	N	0.000071	T	0.21921	0.0528	L	0.46741	1.465	0.44469	D	0.997404	D	0.89917	1.0	D	0.87578	0.998	T	0.22452	-1.0216	10	0.62326	D	0.03	.	10.5374	0.45013	0.1996:0.0:0.8004:0.0	rs34075341	243	Q99500	S1PR3_HUMAN	Q	243	ENSP00000350878:R243Q;ENSP00000365006:R243Q	ENSP00000350878:R243Q	R	+	2	0	S1PR3	90806663	1.000000	0.71417	0.908000	0.35775	0.877000	0.50540	5.439000	0.66556	0.431000	0.26258	0.561000	0.74099	CGG	G|0.964;A|0.036	0.036	strong		0.592	S1PR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052979.2	NM_005226	
RRP12	23223	hgsc.bcm.edu	37	10	99116903	99116903	+	Missense_Mutation	SNP	C	C	T	rs1048445	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:99116903C>T	ENST00000370992.4	-	34	3953	c.3842G>A	c.(3841-3843)cGg>cAg	p.R1281Q	RRP12_ENST00000315563.6_Missense_Mutation_p.R1181Q|RRP12_ENST00000479481.1_5'UTR|RRP12_ENST00000536831.1_Missense_Mutation_p.R999Q|RRP12_ENST00000414986.1_Missense_Mutation_p.R1220Q	NM_015179.3	NP_055994.2	Q5JTH9	RRP12_HUMAN	ribosomal RNA processing 12 homolog (S. cerevisiae)	1281			R -> Q (in dbSNP:rs1048445). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005}.			integral component of membrane (GO:0016021)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(5)|large_intestine(2)|lung(13)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	37		Colorectal(252;0.162)		Epithelial(162;2.72e-09)|all cancers(201;1.76e-07)		GGAACCTCGCCGGGCAGCCTT	0.612													C|||	1419	0.283347	0.1762	0.2853	5008	,	,		20496	0.3075		0.2813	False		,,,				2504	0.4039				p.R1281Q		Atlas-SNP	.											.	RRP12	97	.	0			c.G3842A						PASS	.	C	GLN/ARG,GLN/ARG	769,3637	314.1+/-293.5	70,629,1504	91.0	86.0	88.0		3659,3842	3.1	1.0	10	dbSNP_86	88	2304,6296	387.6+/-342.3	309,1686,2305	yes	missense,missense	RRP12	NM_001145114.1,NM_015179.3	43,43	379,2315,3809	TT,TC,CC		26.7907,17.4535,23.6276	benign,benign	1220/1237,1281/1298	99116903	3073,9933	2203	4300	6503	SO:0001583	missense	23223	exon34			CCTCGCCGGGCAG		CCDS7457.1, CCDS44467.1, CCDS60605.1	10q24.2	2006-11-06	2006-11-06	2006-11-06	ENSG00000052749	ENSG00000052749			29100	protein-coding gene	gene with protein product			"""KIAA0690"""	KIAA0690		9734811	Standard	NM_015179		Approved		uc001knf.3	Q5JTH9	OTTHUMG00000018855	ENST00000370992.4:c.3842G>A	10.37:g.99116903C>T	ENSP00000360031:p.Arg1281Gln	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	94	44	0.468085	NM_015179	B4DK00|E9PCK7|Q5JTH8|Q69YK4|Q96E87|Q9BUH3|Q9Y4C7	Missense_Mutation	SNP	ENST00000370992.4	37	CCDS7457.1	570	0.260989010989011	88	0.17886178861788618	106	0.292817679558011	162	0.28321678321678323	214	0.28232189973614774	C	11.11	1.542652	0.27563	0.174535	0.267907	ENSG00000052749	ENST00000370992;ENST00000315563;ENST00000414986;ENST00000536831	T;T;T;T	0.29917	1.56;1.55;1.56;1.55	5.4	3.1	0.35709	.	0.323342	0.34002	N	0.004349	T	0.00012	0.0000	N	0.00729	-1.24	0.35557	P	0.195639	B;B;B;B	0.15473	0.001;0.001;0.013;0.0	B;B;B;B	0.08055	0.001;0.002;0.003;0.0	T	0.41520	-0.9504	9	0.16420	T	0.52	-8.9726	10.3808	0.44110	0.0:0.1009:0.0:0.8991	rs1048445;rs3188453;rs17504948;rs17844956;rs17857696;rs60604007;rs1048445	1220;1181;999;1281	E9PCK7;Q5JTH9-2;F5H456;Q5JTH9	.;.;.;RRP12_HUMAN	Q	1281;1181;1220;999	ENSP00000360031:R1281Q;ENSP00000324315:R1181Q;ENSP00000414863:R1220Q;ENSP00000446184:R999Q	ENSP00000324315:R1181Q	R	-	2	0	RRP12	99106893	1.000000	0.71417	0.999000	0.59377	0.991000	0.79684	2.901000	0.48695	0.374000	0.24650	-0.258000	0.10820	CGG	C|0.753;T|0.247	0.247	strong		0.612	RRP12-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049699.4	NM_015179	
GALNTL5	168391	hgsc.bcm.edu	37	7	151684256	151684256	+	Missense_Mutation	SNP	A	A	G	rs61729490	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:151684256A>G	ENST00000392800.2	+	5	802	c.548A>G	c.(547-549)gAa>gGa	p.E183G	GALNTL5_ENST00000431418.2_Missense_Mutation_p.E183G	NM_145292.3	NP_660335.2	Q7Z4T8	GLTL5_HUMAN	polypeptide N-acetylgalactosaminyltransferase-like 5	183	Catalytic subdomain A.				spermatid development (GO:0007286)	endosome (GO:0005768)|integral component of membrane (GO:0016021)	metal ion binding (GO:0046872)			NS(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(11)|ovary(2)|prostate(2)|skin(3)	32	all_neural(206;0.187)	all_hematologic(28;0.0749)	OV - Ovarian serous cystadenocarcinoma(82;0.00427)	UCEC - Uterine corpus endometrioid carcinoma (81;0.18)|BRCA - Breast invasive adenocarcinoma(188;0.166)		GATTTGAAAGAAAAACTAGAC	0.343													A|||	1105	0.220647	0.2587	0.2334	5008	,	,		17777	0.2063		0.16	False		,,,				2504	0.2372				p.E183G		Atlas-SNP	.											.	GALNTL5	87	.	0			c.A548G						PASS	.	A	GLY/GLU	988,3418	345.4+/-308.5	118,752,1333	39.0	42.0	41.0		548	-2.6	0.1	7	dbSNP_129	41	1372,7228	253.6+/-279.2	116,1140,3044	yes	missense	GALNTL5	NM_145292.3	98	234,1892,4377	GG,GA,AA		15.9535,22.424,18.1455	benign	183/444	151684256	2360,10646	2203	4300	6503	SO:0001583	missense	168391	exon5			TGAAAGAAAAACT	AF440400	CCDS5929.1	7q36.2	2014-03-13	2014-03-13	2004-07-28	ENSG00000106648	ENSG00000106648		"""Glycosyltransferase family 2 domain containing"""	21725	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase-like 5"""	615133	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 15"", ""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase-like 5"""	GALNT15			Standard	NM_145292		Approved	GalNAc-T5L	uc003wkp.3	Q7Z4T8	OTTHUMG00000157306	ENST00000392800.2:c.548A>G	7.37:g.151684256A>G	ENSP00000376548:p.Glu183Gly	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	42	20	0.47619	NM_145292	Q75KN2|Q75MD3|Q8NCV4|Q8WW05|Q9UDR9	Missense_Mutation	SNP	ENST00000392800.2	37	CCDS5929.1	452	0.20695970695970695	129	0.2621951219512195	89	0.24585635359116023	109	0.19055944055944055	125	0.16490765171503957	a	10.49	1.364965	0.24684	0.22424	0.159535	ENSG00000106648	ENST00000431418;ENST00000392800	T;T	0.63744	-0.06;-0.06	4.3	-2.57	0.06248	Glycosyl transferase, family 2 (1);	0.713546	0.11949	N	0.513859	T	0.00012	0.0000	L	0.31157	0.91	0.58432	P	1.0000000000287557E-6	B	0.15719	0.014	B	0.17722	0.019	T	0.16660	-1.0395	9	0.21540	T	0.41	.	5.0715	0.14609	0.4889:0.2522:0.2588:0.0	rs61729490	183	Q7Z4T8	GLTL5_HUMAN	G	183	ENSP00000392582:E183G;ENSP00000376548:E183G	ENSP00000376548:E183G	E	+	2	0	GALNTL5	151315189	1.000000	0.71417	0.068000	0.19968	0.914000	0.54420	2.000000	0.40816	-0.301000	0.08882	0.454000	0.30748	GAA	A|0.814;G|0.186	0.186	strong		0.343	GALNTL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348395.1	NM_145292	
MYO18B	84700	hgsc.bcm.edu	37	22	26219605	26219605	+	Silent	SNP	G	G	A	rs4820658	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:26219605G>A	ENST00000407587.2	+	13	2824	c.2655G>A	c.(2653-2655)ggG>ggA	p.G885G	MYO18B_ENST00000335473.7_Silent_p.G885G|MYO18B_ENST00000536101.1_Silent_p.G885G			Q8IUG5	MY18B_HUMAN	myosin XVIIIB	885	Myosin motor.					cytoplasm (GO:0005737)|nucleus (GO:0005634)|unconventional myosin complex (GO:0016461)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(2)|breast(6)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(27)|liver(2)|lung(60)|ovary(7)|prostate(8)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	146						TGACGTTTGGGCCAAGCCGAT	0.607													G|||	797	0.159145	0.0136	0.3372	5008	,	,		17951	0.0258		0.3429	False		,,,				2504	0.1779				p.G885G		Atlas-SNP	.											.	MYO18B	322	.	0			c.G2655A						PASS	.	G		279,3877		14,251,1813	176.0	174.0	175.0		2655	2.5	0.2	22	dbSNP_111	175	3049,5359		561,1927,1716	no	coding-synonymous	MYO18B	NM_032608.5		575,2178,3529	AA,AG,GG		36.2631,6.7132,26.4884		885/2568	26219605	3328,9236	2078	4204	6282	SO:0001819	synonymous_variant	84700	exon13			GTTTGGGCCAAGC	AJ310931	CCDS54507.1	22q12.1	2011-09-27			ENSG00000133454	ENSG00000133454		"""Myosins / Myosin superfamily : Class XVIII"""	18150	protein-coding gene	gene with protein product		607295				12209013, 12547197	Standard	NM_032608		Approved	BK125H2.1	uc003abz.1	Q8IUG5	OTTHUMG00000151129	ENST00000407587.2:c.2655G>A	22.37:g.26219605G>A		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	105	45	0.428571	NM_032608	B2RWP3|F5GYU7|Q8NDI8|Q8TE65|Q8WWS0|Q96KH2|Q96KR8|Q96KR9	Silent	SNP	ENST00000407587.2	37																																																																																				G|0.815;A|0.185	0.185	strong		0.607	MYO18B-006	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000400691.1	NM_032608	
VWA3A	146177	hgsc.bcm.edu	37	16	22144378	22144378	+	Missense_Mutation	SNP	G	G	A	rs200086497		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:22144378G>A	ENST00000389398.5	+	20	2126	c.2030G>A	c.(2029-2031)cGg>cAg	p.R677Q	VWA3A_ENST00000389397.4_5'UTR	NM_173615.3	NP_775886.3	A6NCI4	VWA3A_HUMAN	von Willebrand factor A domain containing 3A	677	VWFA 1. {ECO:0000255|PROSITE- ProRule:PRU00219}.					extracellular region (GO:0005576)				haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(1)|skin(1)	7				GBM - Glioblastoma multiforme(48;0.0439)		GAGGTCACCCGGGCTGCAGGT	0.577													G|||	1	0.000199681	0.0	0.0	5008	,	,		17694	0.001		0.0	False		,,,				2504	0.0				p.R677Q		Atlas-SNP	.											.	VWA3A	115	.	0			c.G2030A						PASS	.						38.0	42.0	41.0					16																	22144378		2055	4184	6239	SO:0001583	missense	146177	exon20			TCACCCGGGCTGC	AK128606, AK098260	CCDS45441.1	16p12.1	2008-02-05				ENSG00000175267			27088	protein-coding gene	gene with protein product						12477932	Standard	XM_006721021		Approved	FLJ46765, FLJ40941	uc010vbq.2	A6NCI4		ENST00000389398.5:c.2030G>A	16.37:g.22144378G>A	ENSP00000374049:p.Arg677Gln	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	72	27	0.375	NM_173615	A4QMU8|A6NNC0|Q6UTX4|Q6ZQZ9|Q8IUY6|Q8N9W1	Missense_Mutation	SNP	ENST00000389398.5	37	CCDS45441.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	10.23	1.294063	0.23564	.	.	ENSG00000175267	ENST00000389398;ENST00000299840	T	0.10668	2.85	5.49	-3.57	0.04612	.	0.842998	0.10736	N	0.640019	T	0.04003	0.0112	N	0.04880	-0.145	0.80722	D	1	B;B	0.22080	0.04;0.064	B;B	0.12156	0.003;0.007	T	0.50136	-0.8863	10	0.02654	T	1	.	12.9659	0.58483	0.7034:0.0:0.2966:0.0	.	677;301	A6NCI4;A6NCI4-2	VWA3A_HUMAN;.	Q	677;300	ENSP00000374049:R677Q	ENSP00000299840:R300Q	R	+	2	0	VWA3A	22051879	0.545000	0.26449	0.959000	0.39883	0.756000	0.42949	-0.213000	0.09305	-0.507000	0.06549	-0.157000	0.13467	CGG	G|1.000;A|0.000	0.000	strong		0.577	VWA3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430052.1		
AP5M1	55745	hgsc.bcm.edu	37	14	57741550	57741550	+	Silent	SNP	A	A	G	rs1189899	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:57741550A>G	ENST00000261558.3	+	2	1069	c.663A>G	c.(661-663)caA>caG	p.Q221Q	AP5M1_ENST00000431972.2_Silent_p.Q235Q	NM_018229.3	NP_060699.3	Q9H0R1	AP5M1_HUMAN	adaptor-related protein complex 5, mu 1 subunit	221	MHD. {ECO:0000255|PROSITE- ProRule:PRU00404}.				endosomal transport (GO:0016197)|intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	AP-type membrane coat adaptor complex (GO:0030119)|clathrin adaptor complex (GO:0030131)|cytosol (GO:0005829)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)											AATCCATGCAATATGATAAAC	0.388													A|||	1364	0.272364	0.8321	0.0879	5008	,	,		17872	0.0655		0.0567	False		,,,				2504	0.0818				p.Q221Q		Atlas-SNP	.											.	.	.	.	0			c.A663G						PASS	.	A		2847,1505		956,935,285	85.0	94.0	91.0		663	-2.3	1.0	14	dbSNP_87	91	486,8090		12,462,3814	no	coding-synonymous	MUDENG	NM_018229.3		968,1397,4099	GG,GA,AA		5.667,34.5818,25.7812		221/491	57741550	3333,9595	2176	4288	6464	SO:0001819	synonymous_variant	55745	exon2			CATGCAATATGAT	AF094583	CCDS9729.1	14q22.2	2012-03-20	2012-03-20	2012-03-20	ENSG00000053770	ENSG00000053770			20192	protein-coding gene	gene with protein product	"""Mu-2 related death-inducing gene"""	614368	"""chromosome 14 open reading frame 108"", ""MU-2/AP1M2 domain containing, death-inducing"""	C14orf108, MUDENG		18395520	Standard	NM_018229		Approved	FLJ10813, MuD, mu5	uc001xcv.3	Q9H0R1	OTTHUMG00000140318	ENST00000261558.3:c.663A>G	14.37:g.57741550A>G		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	83	45	0.542169	NM_018229	O95354|Q6ZMD7|Q96DX3|Q9NVC5	Silent	SNP	ENST00000261558.3	37	CCDS9729.1																																																																																			A|0.764;G|0.236	0.236	strong		0.388	AP5M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276922.1	NM_018229	
ERMAP	114625	hgsc.bcm.edu	37	1	43296195	43296195	+	Missense_Mutation	SNP	C	C	T	rs33953680	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:43296195C>T	ENST00000372517.2	+	3	320	c.76C>T	c.(76-78)Cat>Tat	p.H26Y	ERMAP_ENST00000372514.3_Missense_Mutation_p.H26Y|ERMAP_ENST00000328249.3_5'UTR|ERMAP_ENST00000487556.1_Intron	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	96	0	0		WXS	Illumina HiSeq	Phase_I	83	83	1	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	
MR1	3140	hgsc.bcm.edu	37	1	181018236	181018236	+	Missense_Mutation	SNP	A	A	G	rs2236410	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	238	0	0		WXS	Illumina HiSeq	Phase_I	238	132	0.554622	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	
TP53I11	9537	hgsc.bcm.edu	37	11	44956459	44956459	+	Silent	SNP	G	G	A	rs61752934	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:44956459G>A	ENST00000533940.1	-	10	1150	c.546C>T	c.(544-546)gtC>gtT	p.V182V	TP53I11_ENST00000525680.1_Silent_p.V182V|TP53I11_ENST00000531130.2_5'Flank|TP53I11_ENST00000308212.5_Silent_p.V182V|TP53I11_ENST00000395648.3_Silent_p.V182V	NM_001258320.1	NP_001245249.1	O14683	P5I11_HUMAN	tumor protein p53 inducible protein 11	182					negative regulation of cell proliferation (GO:0008285)|response to stress (GO:0006950)	integral component of membrane (GO:0016021)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(2)|ovary(1)	5						GTCTTCGGCCGACTTGGTAAT	0.632													G|||	76	0.0151757	0.0008	0.013	5008	,	,		18130	0.0		0.0527	False		,,,				2504	0.0133				p.V182V		Atlas-SNP	.											.	TP53I11	17	.	0			c.C546T						PASS	.	G	,	42,4364	44.6+/-78.6	1,40,2162	79.0	79.0	79.0		546,546	-6.2	0.9	11	dbSNP_129	79	383,8215	124.4+/-183.2	10,363,3926	no	coding-synonymous,coding-synonymous	TP53I11	NM_001076787.1,NM_006034.3	,	11,403,6088	AA,AG,GG		4.4545,0.9532,3.2682	,	182/190,182/190	44956459	425,12579	2203	4299	6502	SO:0001819	synonymous_variant	9537	exon7			TCGGCCGACTTGG	AF010315	CCDS7911.1	11p11.2	2005-09-22				ENSG00000175274			16842	protein-coding gene	gene with protein product						9305847	Standard	NM_006034		Approved	PIG11	uc001myk.3	O14683		ENST00000533940.1:c.546C>T	11.37:g.44956459G>A		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	65	50	0.769231	NM_001258324	Q3ZCS0	Silent	SNP	ENST00000533940.1	37	CCDS7911.1																																																																																			G|0.970;A|0.030	0.030	strong		0.632	TP53I11-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389909.1	NM_006034	
FAM217A	222826	hgsc.bcm.edu	37	6	4069166	4069166	+	Missense_Mutation	SNP	C	C	T	rs595413	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:4069166C>T	ENST00000274673.3	-	7	1694	c.1291G>A	c.(1291-1293)Gtc>Atc	p.V431I	FAM217A_ENST00000380188.2_5'UTR	NM_173563.2	NP_775834.2	Q8IXS0	F217A_HUMAN	family with sequence similarity 217, member A	431			V -> I (in dbSNP:rs595413). {ECO:0000269|PubMed:15489334}.														CTTGTGGAGACCATTTTAACC	0.393													C|||	2734	0.545927	0.1362	0.634	5008	,	,		18674	0.6458		0.7406	False		,,,				2504	0.7342				p.V431I		Atlas-SNP	.											.	.	.	.	0			c.G1291A						PASS	.	C	ILE/VAL	964,3442	361.1+/-315.5	114,736,1353	110.0	106.0	107.0		1291	0.8	0.0	6	dbSNP_83	107	6347,2253	707.1+/-405.6	2343,1661,296	yes	missense	C6orf146	NM_173563.2	29	2457,2397,1649	TT,TC,CC		26.1977,21.8793,43.7875	benign	431/509	4069166	7311,5695	2203	4300	6503	SO:0001583	missense	222826	exon7			TGGAGACCATTTT	BC039349	CCDS4489.1	6p25.1	2012-02-07	2012-02-07	2012-02-07	ENSG00000145975	ENSG00000145975			21362	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 146"""	C6orf146			Standard	NM_173563		Approved	MGC43581	uc003mvx.3	Q8IXS0	OTTHUMG00000014159	ENST00000274673.3:c.1291G>A	6.37:g.4069166C>T	ENSP00000274673:p.Val431Ile	Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	142	67	0.471831	NM_173563	Q5JYK1	Missense_Mutation	SNP	ENST00000274673.3	37	CCDS4489.1	1233	0.5645604395604396	80	0.16260162601626016	233	0.643646408839779	360	0.6293706293706294	560	0.7387862796833773	C	6.145	0.395009	0.11638	0.218793	0.738023	ENSG00000145975	ENST00000274673;ENST00000538080;ENST00000470599	T	0.21031	2.03	4.66	0.752	0.18398	.	0.749251	0.11825	N	0.525834	T	0.05731	0.0150	L	0.49350	1.555	0.53688	P	2.599999999997049E-5	B	0.31318	0.319	B	0.26416	0.069	T	0.32134	-0.9918	9	0.33940	T	0.23	-1.3764	4.9623	0.14072	0.0:0.4752:0.3341:0.1907	rs595413;rs17853926;rs52806715;rs56587908;rs61019406;rs595413	431	Q8IXS0	CF146_HUMAN	I	431;278;559	ENSP00000274673:V431I	ENSP00000274673:V431I	V	-	1	0	C6orf146	4014165	0.299000	0.24426	0.012000	0.15200	0.247000	0.25773	0.212000	0.17497	-0.051000	0.13334	0.460000	0.39030	GTC	C|0.413;T|0.587	0.587	strong		0.393	FAM217A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352577.2	NM_173563	
SLC9C1	285335	hgsc.bcm.edu	37	3	111981878	111981878	+	Missense_Mutation	SNP	T	T	C	rs9809384	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:111981878T>C	ENST00000305815.5	-	10	1342	c.1090A>G	c.(1090-1092)Ata>Gta	p.I364V	SLC9C1_ENST00000487372.1_Missense_Mutation_p.I316V	NM_183061.1	NP_898884.1	Q4G0N8	SL9C1_HUMAN	solute carrier family 9, subfamily C (Na+-transporting carboxylic acid decarboxylase), member 1	364			I -> V (in dbSNP:rs9809384). {ECO:0000269|PubMed:14702039}.		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)										ATTATGAATATCCAGCGCCAA	0.368													C|||	3220	0.642971	0.4849	0.7118	5008	,	,		16692	0.7738		0.5964	False		,,,				2504	0.7209				p.I364V		Atlas-SNP	.											.	.	.	.	0			c.A1090G						PASS	.	C	VAL/ILE	2217,2189	585.8+/-386.3	536,1145,522	105.0	102.0	103.0		1090	4.9	1.0	3	dbSNP_119	103	5328,3272	489.1+/-372.5	1657,2014,629	yes	missense	SLC9A10	NM_183061.1	29	2193,3159,1151	CC,CT,TT		38.0465,49.6823,41.9883	benign	364/1178	111981878	7545,5461	2203	4300	6503	SO:0001583	missense	285335	exon10			TGAATATCCAGCG	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.1090A>G	3.37:g.111981878T>C	ENSP00000306627:p.Ile364Val	Somatic	336	1	0.00297619		WXS	Illumina HiSeq	Phase_I	255	254	0.996078	NM_183061	Q6ZRP4|Q7RTP2	Missense_Mutation	SNP	ENST00000305815.5	37	CCDS33817.1	1406	0.6437728937728938	247	0.5020325203252033	242	0.6685082872928176	455	0.7954545454545454	462	0.6094986807387863	C	8.870	0.949112	0.18356	0.503177	0.619535	ENSG00000172139	ENST00000305815;ENST00000487372	T;T	0.15372	2.43;2.52	5.78	4.91	0.64330	Cation/H+ exchanger (1);	0.209998	0.33457	N	0.004884	T	0.00012	0.0000	N	0.08118	0	0.58432	P	1.0000000000287557E-6	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.09840	-1.0656	9	0.32370	T	0.25	-10.7818	9.6347	0.39800	0.0:0.8509:0.0:0.1491	rs9809384;rs52826200;rs59855197;rs9809384	316;364	Q4G0N8-2;Q4G0N8	.;S9A10_HUMAN	V	364;316	ENSP00000306627:I364V;ENSP00000420688:I316V	ENSP00000306627:I364V	I	-	1	0	SLC9A10	113464568	1.000000	0.71417	0.987000	0.45799	0.371000	0.29859	1.712000	0.37940	0.806000	0.34183	-1.230000	0.01575	ATA	T|0.395;C|0.605	0.605	strong		0.368	SLC9C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354066.1	NM_183061	
B3GNT3	10331	hgsc.bcm.edu	37	19	17919024	17919024	+	Silent	SNP	A	A	T	rs2240813	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:17919024A>T	ENST00000318683.6	+	2	555	c.408A>T	c.(406-408)gtA>gtT	p.V136V	B3GNT3_ENST00000595387.1_Silent_p.V136V	NM_014256.3	NP_055071.2	Q9Y2A9	B3GN3_HUMAN	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 3	136					carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)	beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,3-N-acetylglucosaminyltransferase activity (GO:0047223)|galactosyltransferase activity (GO:0008378)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(7)|prostate(2)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(1)	21						AGCGCAAGGTACGGGGTTTGC	0.682													G|||	646	0.128994	0.1309	0.1931	5008	,	,		13801	0.1577		0.0696	False		,,,				2504	0.1125				p.V136V		Atlas-SNP	.											.	B3GNT3	40	.	0			c.A408T						PASS	.	G		493,3913		23,447,1733	26.0	28.0	28.0		408	-5.4	0.0	19	dbSNP_98	28	615,7983		27,561,3711	no	coding-synonymous	B3GNT3	NM_014256.3		50,1008,5444	TT,TA,AA		7.1528,11.1893,8.5205		136/373	17919024	1108,11896	2203	4299	6502	SO:0001819	synonymous_variant	10331	exon2			CAAGGTACGGGGT	AB015630	CCDS12364.1	19p13.1	2013-02-19				ENSG00000179913		"""Beta 3-glycosyltransferases"""	13528	protein-coding gene	gene with protein product	"""putative type II membrane protein"", ""beta-1,3-N-acetylglucosaminyltransferase bGnT-3"", ""transmembrane protein 3"""	605863		TMEM3		10072769, 11042166	Standard	NM_014256		Approved	B3GN-T3, beta3Gn-T3, HP10328, B3GNT-3	uc002nhl.1	Q9Y2A9		ENST00000318683.6:c.408A>T	19.37:g.17919024A>T		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	60	25	0.416667	NM_014256	B2RAS4|Q6NWU9|Q6NXU9|Q8WWR6|Q9C0J2	Silent	SNP	ENST00000318683.6	37	CCDS12364.1																																																																																			A|0.903;T|0.097	0.097	strong		0.682	B3GNT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466877.1	NM_014256	
ZNF493	284443	hgsc.bcm.edu	37	19	21606429	21606429	+	Missense_Mutation	SNP	G	G	T	rs4621113	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:21606429G>T	ENST00000355504.4	+	2	850	c.584G>T	c.(583-585)tGt>tTt	p.C195F	CTD-2561J22.3_ENST00000600810.1_Intron|ZNF493_ENST00000392288.2_Missense_Mutation_p.C323F	NM_175910.6	NP_787106.4	Q6ZR52	ZN493_HUMAN	zinc finger protein 493	195			C -> F (in dbSNP:rs4621113). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:17974005, ECO:0000269|Ref.2}.		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|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						CCCTATAAATGTGAAGAATGT	0.333													.|||	2943	0.58766	0.6589	0.5476	5008	,	,		19736	0.6319		0.5	False		,,,				2504	0.5644				p.C323F		Atlas-SNP	.											.	ZNF493	178	.	0			c.G968T						PASS	.	G	PHE/CYS,PHE/CYS	2757,1641		867,1023,309	32.0	37.0	35.0		968,584	1.0	0.2	19	dbSNP_111	35	4437,4151		1205,2027,1062	no	missense,missense	ZNF493	NM_001076678.2,NM_175910.6	205,205	2072,3050,1371	TT,TG,GG		48.3349,37.3124,44.6019	probably-damaging,probably-damaging	323/775,195/647	21606429	7194,5792	2199	4294	6493	SO:0001583	missense	284443	exon4			ATAAATGTGAAGA	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.584G>T	19.37:g.21606429G>T	ENSP00000347691:p.Cys195Phe	Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	19	8	0.421053	NM_001076678	G5E974|Q59GM3|Q6ZSF6|Q8N1Z6|Q8N965|Q9BR99	Missense_Mutation	SNP	ENST00000355504.4	37	CCDS12412.1	1284	0.5879120879120879	334	0.6788617886178862	202	0.5580110497237569	378	0.6608391608391608	370	0.48812664907651715	N	5.820	0.335504	0.11013	0.626876	0.516651	ENSG00000196268	ENST00000392288;ENST00000355504	D;D	0.85088	-1.94;-1.94	0.985	0.985	0.19779	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	M	0.94101	3.495	0.09310	P	1.0	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.46992	-0.9151	8	0.87932	D	0	.	8.7583	0.34658	0.0:0.0:1.0:0.0	rs4621113;rs4621113	195;323	Q6ZR52;Q6ZR52-2	ZN493_HUMAN;.	F	323;195	ENSP00000376110:C323F;ENSP00000347691:C195F	ENSP00000347691:C195F	C	+	2	0	ZNF493	21398269	1.000000	0.71417	0.194000	0.23346	0.190000	0.23558	6.598000	0.74122	0.399000	0.25367	0.404000	0.27445	TGT	G|0.458;T|0.542	0.542	strong		0.333	ZNF493-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000280563.1	NM_175910	
PKHD1L1	93035	hgsc.bcm.edu	37	8	110412519	110412519	+	Silent	SNP	G	G	A	rs1379369	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:110412519G>A	ENST00000378402.5	+	13	1331	c.1227G>A	c.(1225-1227)aaG>aaA	p.K409K		NM_177531.4	NP_803875.2	Q86WI1	PKHL1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1	409					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)			TCTACATCAAGGGTGATGACC	0.388										HNSCC(38;0.096)			A|||	2998	0.598642	0.6944	0.6556	5008	,	,		16147	0.3968		0.5239	False		,,,				2504	0.7137				p.K409K		Atlas-SNP	.											.	PKHD1L1	522	.	0			c.G1227A						PASS	.	A		2542,1166		884,774,196	226.0	212.0	217.0		1227	5.4	1.0	8	dbSNP_88	217	4431,3759		1219,1993,883	no	coding-synonymous	PKHD1L1	NM_177531.4		2103,2767,1079	AA,AG,GG		45.8974,31.4455,41.3935		409/4244	110412519	6973,4925	1854	4095	5949	SO:0001819	synonymous_variant	93035	exon13			CATCAAGGGTGAT	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.1227G>A	8.37:g.110412519G>A		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	108	81	0.75	NM_177531	Q567P2|Q9UF27	Silent	SNP	ENST00000378402.5	37	CCDS47911.1																																																																																			G|0.448;A|0.552	0.552	strong		0.388	PKHD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381017.1	NM_177531	
C19orf53	28974	hgsc.bcm.edu	37	19	13885309	13885309	+	Silent	SNP	C	C	T	rs1128749	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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_ENST00000591826.1_RNA|CTB-5E10.3_ENST00000586297.1_RNA|CTB-5E10.3_ENST00000586894.1_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	86	0	0		WXS	Illumina HiSeq	Phase_I	76	37	0.486842	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	
SSC5D	284297	hgsc.bcm.edu	37	19	56029489	56029489	+	Silent	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:56029489C>T	ENST00000389623.6	+	14	3869	c.3846C>T	c.(3844-3846)caC>caT	p.H1282H		NM_001144950.1	NP_001138422.1	A1L4H1	SRCRL_HUMAN	scavenger receptor cysteine rich family, 5 domains	1282	Pro-rich.|Thr-rich.				defense response to Gram-negative bacterium (GO:0050829)|defense response to Gram-positive bacterium (GO:0050830)|detection of bacterial lipoprotein (GO:0042494)|innate immune response (GO:0045087)|multicellular organismal development (GO:0007275)|negative regulation of interleukin-8 secretion (GO:2000483)|receptor-mediated endocytosis (GO:0006898)	cytoplasm (GO:0005737)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|intracellular (GO:0005622)|membrane (GO:0016020)	extracellular matrix binding (GO:0050840)|fibronectin binding (GO:0001968)|laminin binding (GO:0043236)|scavenger receptor activity (GO:0005044)			NS(1)|breast(1)|skin(2)	4						cgacccctcaccccaccacga	0.627																																					p.H1282H		Atlas-SNP	.											SSC5D,NS,carcinoma,+2,1	SSC5D	65	1	0			c.C3846T						scavenged	.						469.0	431.0	443.0					19																	56029489		692	1591	2283	SO:0001819	synonymous_variant	284297	exon14			CCCTCACCCCACC		CCDS46196.1, CCDS59424.1	19q13.42	2014-07-09	2014-07-09		ENSG00000179954	ENSG00000179954			26641	protein-coding gene	gene with protein product	"""soluble scavenger with 5 domains"""		"""scavenger receptor cysteine rich domain containing (5 domains)"""			19535143	Standard	NM_001144950		Approved	FLJ35258	uc002qlg.4	A1L4H1		ENST00000389623.6:c.3846C>T	19.37:g.56029489C>T		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	128	12	0.09375	NM_001144950	B5MDQ5|C7S7T9|C7S7U0|K7EP70	Silent	SNP	ENST00000389623.6	37	CCDS46196.1																																																																																			.	.	none		0.627	SSC5D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000453345.2	XM_001718392	
MEFV	4210	hgsc.bcm.edu	37	16	3297073	3297073	+	Silent	SNP	A	A	G	rs224206	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:3297073A>G	ENST00000219596.1	-	5	1569	c.1530T>C	c.(1528-1530)gaT>gaC	p.D510D	MEFV_ENST00000339854.4_Silent_p.D330D|MEFV_ENST00000541159.1_Silent_p.D299D|MEFV_ENST00000536379.1_Silent_p.D299D	NM_000243.2	NP_000234.1	O15553	MEFV_HUMAN	Mediterranean fever	510	Required for homotrimerization and induction of pyroptosomes.				inflammatory response (GO:0006954)|innate immune response (GO:0045087)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-1 beta production (GO:0032691)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of macrophage inflammatory protein 1 alpha production (GO:0071641)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of cysteine-type endopeptidase activity (GO:2001056)	cell projection (GO:0042995)|cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|nucleus (GO:0005634)	actin binding (GO:0003779)|zinc ion binding (GO:0008270)			NS(2)|biliary_tract(1)|breast(5)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(6)|lung(19)|ovary(3)|prostate(1)|skin(6)	50						CAATCAGCGCATCGAGCAGGG	0.597													G|||	3321	0.663139	0.6936	0.6297	5008	,	,		20097	0.6518		0.5577	False		,,,				2504	0.7658				p.D510D		Atlas-SNP	.											.	MEFV	170	.	0			c.T1530C						PASS	.	G	,	2994,1400	460.5+/-352.6	1013,968,216	147.0	126.0	133.0		1530,897	-10.6	0.0	16	dbSNP_79	133	4597,4003	554.3+/-386.5	1255,2087,958	no	coding-synonymous,coding-synonymous	MEFV	NM_000243.2,NM_001198536.1	,	2268,3055,1174	GG,GA,AA		46.5465,31.8616,41.5807	,	510/782,299/446	3297073	7591,5403	2197	4300	6497	SO:0001819	synonymous_variant	4210	exon5			CAGCGCATCGAGC	AF018080	CCDS10498.1, CCDS55981.1	16p13.3	2014-09-17			ENSG00000103313	ENSG00000103313		"""Tripartite motif containing / Tripartite motif containing"""	6998	protein-coding gene	gene with protein product	"""pyrin"""	608107		MEF		9288094	Standard	NM_000243		Approved	FMF, TRIM20	uc002cun.1	O15553	OTTHUMG00000129324	ENST00000219596.1:c.1530T>C	16.37:g.3297073A>G		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	121	20	0.165289	NM_000243	D3DUC0|F5H0Q3|Q3MJ84|Q96PN4|Q96PN5	Silent	SNP	ENST00000219596.1	37	CCDS10498.1																																																																																			A|0.391;G|0.609	0.609	strong		0.597	MEFV-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251464.1	NM_000243	
OR4C13	283092	hgsc.bcm.edu	37	11	49974626	49974626	+	Missense_Mutation	SNP	G	G	A	rs150606357		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:49974626G>A	ENST00000555099.1	+	1	684	c.652G>A	c.(652-654)Gtc>Atc	p.V218I		NM_001001955.2	NP_001001955.2	Q8NGP0	OR4CD_HUMAN	olfactory receptor, family 4, subfamily C, member 13	218						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			autonomic_ganglia(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(24)|ovary(2)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)	43						CTCCTGCGTGGTCATACTGTA	0.488													G|||	1	0.000199681	0.0	0.0	5008	,	,		17462	0.0		0.001	False		,,,				2504	0.0				p.V218I		Atlas-SNP	.											.	OR4C13	96	.	0			c.G652A						PASS	.	G	ILE/VAL	0,4402		0,0,2201	189.0	153.0	165.0		652	0.8	1.0	11	dbSNP_134	165	10,8582		0,10,4286	yes	missense	OR4C13	NM_001001955.2	29	0,10,6487	AA,AG,GG		0.1164,0.0,0.077	benign	218/310	49974626	10,12984	2201	4296	6497	SO:0001583	missense	283092	exon1			TGCGTGGTCATAC	AB065750	CCDS31495.1	11p11.12	2012-10-03			ENSG00000258817	ENSG00000258817		"""GPCR / Class A : Olfactory receptors"""	15169	protein-coding gene	gene with protein product							Standard	NM_001001955		Approved		uc010rhz.2	Q8NGP0	OTTHUMG00000166686	ENST00000555099.1:c.652G>A	11.37:g.49974626G>A	ENSP00000452277:p.Val218Ile	Somatic	219	0	0		WXS	Illumina HiSeq	Phase_I	157	111	0.707006	NM_001001955	A6NJJ3|B9EH30|Q6IF48|Q96R68	Missense_Mutation	SNP	ENST00000555099.1	37	CCDS31495.1	.	.	.	.	.	.	.	.	.	.	.	3.409	-0.120655	0.06838	0.0	0.001164	ENSG00000258817	ENST00000555099	T	0.00091	8.74	2.7	0.748	0.18376	GPCR, rhodopsin-like superfamily (1);	0.168066	0.28125	N	0.016511	T	0.00144	0.0004	L	0.60957	1.885	0.09310	N	0.999999	B	0.02656	0.0	B	0.17722	0.019	T	0.38714	-0.9648	9	.	.	.	.	2.838	0.05521	0.3033:0.2481:0.4486:0.0	.	218	Q8NGP0	OR4CD_HUMAN	I	218	ENSP00000452277:V218I	.	V	+	1	0	OR4C13	49931202	0.000000	0.05858	0.988000	0.46212	0.089000	0.18198	-2.155000	0.01284	0.474000	0.27392	0.186000	0.17326	GTC	G|0.999;A|0.001	0.001	strong		0.488	OR4C13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391103.1	NM_001001955	
FMO2	2327	hgsc.bcm.edu	37	1	171168585	171168585	+	Silent	SNP	A	A	G	rs2020861|rs386636736	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:171168585A>G	ENST00000209929.7	+	5	743	c.585A>G	c.(583-585)tcA>tcG	p.S195S	RP1-127D3.4_ENST00000445290.1_RNA|FMO2_ENST00000441535.1_Silent_p.S195S|FMO2_ENST00000529935.1_Intron|RP1-127D3.4_ENST00000445909.1_RNA|RP1-127D3.4_ENST00000422841.1_RNA			P31512	FMO4_HUMAN	flavin containing monooxygenase 2 (non-functional)	195					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)	p.S195S(1)		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)					TGGGAAACTCAGGCTCAGATA	0.488													G|||	2951	0.589257	0.7209	0.6167	5008	,	,		19431	0.6032		0.3877	False		,,,				2504	0.5849				p.S195S		Atlas-SNP	.											FMO2,NS,carcinoma,0,2	FMO2	66	2	1	Substitution - coding silent(1)	stomach(1)	c.A585G						scavenged	.	G		2951,1455	468.5+/-355.1	983,985,235	135.0	140.0	139.0		585	-12.3	0.0	1	dbSNP_98	139	3589,5011	627.2+/-397.9	765,2059,1476	no	coding-synonymous	FMO2	NM_001460.2		1748,3044,1711	GG,GA,AA		41.7326,33.0232,49.7155		195/472	171168585	6540,6466	2203	4300	6503	SO:0001819	synonymous_variant	2327	exon5			AAACTCAGGCTCA	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.585A>G	1.37:g.171168585A>G		Somatic	199	2	0.0100503		WXS	Illumina HiSeq	Phase_I	167	87	0.520958	NM_001460	Q53XR0	Silent	SNP	ENST00000209929.7	37	CCDS1293.1																																																																																			A|0.536;G|0.464	0.464	strong		0.488	FMO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086216.2	NM_001460	
ECD	11319	hgsc.bcm.edu	37	10	74899209	74899209	+	Silent	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:74899209G>A	ENST00000372979.4	-	11	1485	c.1279C>T	c.(1279-1281)Ctg>Ttg	p.L427L	ECD_ENST00000430082.2_Silent_p.L460L|ECD_ENST00000454759.2_Silent_p.L384L	NM_007265.2	NP_009196.1	O95905	SGT1_HUMAN	ecdysoneless homolog (Drosophila)	427					cell proliferation (GO:0008283)|regulation of G1/S transition of mitotic cell cycle (GO:2000045)|regulation of glycolytic process (GO:0006110)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)			breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(5)|pancreas(1)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	21	Prostate(51;0.0119)					GCTTCCTGCAGCAGCTGGTCC	0.438																																					p.L460L		Atlas-SNP	.											.	ECD	50	.	0			c.C1378T						PASS	.						89.0	92.0	91.0					10																	74899209		2203	4300	6503	SO:0001819	synonymous_variant	11319	exon12			CCTGCAGCAGCTG	BC000721	CCDS7321.1, CCDS44433.1, CCDS44434.1	10q22.3	2006-02-07				ENSG00000122882			17029	protein-coding gene	gene with protein product						9928932, 15128659	Standard	NM_007265		Approved	hSGT1, GCR2	uc001jtn.3	O95905		ENST00000372979.4:c.1279C>T	10.37:g.74899209G>A		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	77	18	0.233766	NM_001135752	C9JX46|E9PAW8	Silent	SNP	ENST00000372979.4	37	CCDS7321.1																																																																																			.	.	none		0.438	ECD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048606.1	NM_007265	
CLEC18C	283971	hgsc.bcm.edu	37	16	70211380	70211380	+	Silent	SNP	G	G	A	rs3869429	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:70211380G>A	ENST00000569347.2	+	3	707	c.453G>A	c.(451-453)acG>acA	p.T151T	CLEC18C_ENST00000536907.2_Silent_p.T151T|CLEC18C_ENST00000541793.2_Silent_p.T151T|CLEC18C_ENST00000561612.1_Intron|CLEC18C_ENST00000314151.8_Silent_p.T151T	NM_173619.2	NP_775890.2	Q8NCF0	CL18C_HUMAN	C-type lectin domain family 18, member C	151	SCP.					extracellular region (GO:0005576)	carbohydrate binding (GO:0030246)			endometrium(3)|large_intestine(6)|lung(1)	10						CCCACTACACGCAGGTGAGTG	0.582																																					p.T151T		Atlas-SNP	.											CLEC18C,NS,carcinoma,+1,1	CLEC18C	15	1	0			c.G453A						scavenged	.						12.0	10.0	11.0					16																	70211380		2077	4023	6100	SO:0001819	synonymous_variant	283971	exon3			CTACACGCAGGTG	AL833339	CCDS32473.1	16q22.1	2010-04-27	2009-03-10	2009-03-10		ENSG00000157335		"""C-type lectin domain containing"""	28538	protein-coding gene	gene with protein product						12477932	Standard	XM_005255906		Approved	MGC34761		Q8NCF0		ENST00000569347.2:c.453G>A	16.37:g.70211380G>A		Somatic	463	0	0		WXS	Illumina HiSeq	Phase_I	437	77	0.176201	NM_173619	Q8IUW8	Silent	SNP	ENST00000569347.2	37	CCDS32473.1																																																																																			.	.	weak		0.582	CLEC18C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000434588.2	NM_173619	
GPR123	84435	hgsc.bcm.edu	37	10	134942166	134942166	+	Silent	SNP	A	A	G	rs2806452	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:134942166A>G	ENST00000392607.3	+	7	1270	c.834A>G	c.(832-834)tcA>tcG	p.S278S	GPR123_ENST00000392606.2_Silent_p.S181S|GPR123_ENST00000607359.1_Silent_p.S997S	NM_001083909.1	NP_001077378.1	Q86SQ6	GP123_HUMAN	G protein-coupled receptor 123	278					G-protein coupled receptor signaling pathway (GO:0007186)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			endometrium(2)|kidney(2)|large_intestine(1)|lung(6)|prostate(3)	14		all_cancers(35;1.8e-10)|all_epithelial(44;8.95e-09)|Lung NSC(174;0.000845)|all_lung(145;0.00144)|all_neural(114;0.0299)|Colorectal(31;0.0585)|Melanoma(40;0.123)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;9.16e-06)|Epithelial(32;1.21e-05)|all cancers(32;1.63e-05)		TGGCGGTGTCACAGGGCCACT	0.652													G|||	2450	0.489217	0.4826	0.621	5008	,	,		13237	0.5357		0.4145	False		,,,				2504	0.4335				p.S278S		Atlas-SNP	.											.	GPR123	118	.	0			c.A834G						PASS	.	G		2082,2306		513,1056,625	29.0	22.0	25.0		834	-9.5	0.1	10	dbSNP_100	25	3242,5342		623,1996,1673	no	coding-synonymous	GPR123	NM_001083909.1		1136,3052,2298	GG,GA,AA		37.7679,47.4476,41.0422		278/561	134942166	5324,7648	2194	4292	6486	SO:0001819	synonymous_variant	84435	exon7			GGTGTCACAGGGC	AB058731	CCDS41580.1	10q26	2014-08-08			ENSG00000197177	ENSG00000197177		"""-"", ""GPCR / Class B : Orphans"""	13838	protein-coding gene	gene with protein product		612302				12565841	Standard	XM_005252695		Approved	KIAA1828	uc001llw.3	Q86SQ6	OTTHUMG00000019304	ENST00000392607.3:c.834A>G	10.37:g.134942166A>G		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	94	34	0.361702	NM_001083909	A5HL16|A6NG50|Q5T234|Q86SN7|Q96JJ9	Silent	SNP	ENST00000392607.3	37	CCDS41580.1																																																																																			A|0.559;G|0.441	0.441	strong		0.652	GPR123-003	NOVEL	basic|appris_candidate|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000051113.2		
FASTKD2	22868	hgsc.bcm.edu	37	2	207631446	207631446	+	Missense_Mutation	SNP	G	G	C	rs147727753	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:207631446G>C	ENST00000236980.6	+	2	377	c.29G>C	c.(28-30)aGt>aCt	p.S10T	MDH1B_ENST00000454776.2_5'Flank|MDH1B_ENST00000392214.2_5'Flank|MDH1B_ENST00000449792.1_5'Flank|MDH1B_ENST00000374412.3_5'Flank|FASTKD2_ENST00000403094.3_Missense_Mutation_p.S10T|FASTKD2_ENST00000402774.3_Missense_Mutation_p.S10T	NM_014929.3	NP_055744.2	Q9NYY8	FAKD2_HUMAN	FAST kinase domains 2	10					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)		CCATTTGGAAGTGTTTCAGTG	0.398													G|||	14	0.00279553	0.0	0.0029	5008	,	,		17193	0.0		0.0089	False		,,,				2504	0.0031				p.S10T		Atlas-SNP	.											.	FASTKD2	49	.	0			c.G29C						PASS	.	G	THR/SER,THR/SER,THR/SER	15,4391	22.3+/-47.3	0,15,2188	63.0	69.0	67.0		29,29,29	3.3	0.4	2	dbSNP_134	67	60,8540	35.9+/-90.5	1,58,4241	yes	missense,missense,missense	FASTKD2	NM_001136193.1,NM_001136194.1,NM_014929.3	58,58,58	1,73,6429	CC,CG,GG		0.6977,0.3404,0.5767	possibly-damaging,possibly-damaging,possibly-damaging	10/711,10/711,10/711	207631446	75,12931	2203	4300	6503	SO:0001583	missense	22868	exon2			TTGGAAGTGTTTC	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.29G>C	2.37:g.207631446G>C	ENSP00000236980:p.Ser10Thr	Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	148	79	0.533784	NM_001136193	Q9NVX6|Q9Y2H7	Missense_Mutation	SNP	ENST00000236980.6	37	CCDS2371.1	9	0.004120879120879121	0	0.0	1	0.0027624309392265192	0	0.0	8	0.010554089709762533	G	16.23	3.065708	0.55539	0.003404	0.006977	ENSG00000118246	ENST00000236980;ENST00000418289;ENST00000402774;ENST00000403094	T;T;T;T	0.50548	2.41;0.74;2.41;2.41	4.14	3.26	0.37387	.	1.872060	0.02814	N	0.124770	T	0.37812	0.1017	L	0.40543	1.245	0.09310	N	1	P;P	0.46512	0.879;0.808	P;B	0.46076	0.503;0.242	T	0.42327	-0.9458	10	0.87932	D	0	-2.845	4.6425	0.12556	0.1112:0.0:0.6698:0.219	.	10;10	Q9NYY8-2;Q9NYY8	.;FAKD2_HUMAN	T	10	ENSP00000236980:S10T;ENSP00000409927:S10T;ENSP00000385990:S10T;ENSP00000384929:S10T	ENSP00000236980:S10T	S	+	2	0	FASTKD2	207339691	0.019000	0.18553	0.385000	0.26158	0.482000	0.33219	1.205000	0.32308	2.316000	0.78162	0.491000	0.48974	AGT	G|0.996;C|0.004	0.004	strong		0.398	FASTKD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256428.2	NM_014929	
OR5L1	219437	hgsc.bcm.edu	37	11	55579182	55579182	+	Silent	SNP	A	A	G	rs139708815	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:55579182A>G	ENST00000333973.2	+	1	329	c.240A>G	c.(238-240)aaA>aaG	p.K80K		NM_001004738.1	NP_001004738.1	Q8NGL2	OR5L1_HUMAN	olfactory receptor, family 5, subfamily L, member 1	80						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.K80K(1)		NS(1)|breast(2)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(4)|liver(4)|lung(36)|ovary(2)|pancreas(1)|prostate(5)|skin(9)|stomach(4)|upper_aerodigestive_tract(3)	78		all_epithelial(135;0.208)				TTGTGCCAAAAATGTTGGCTA	0.458																																					p.K80K		Atlas-SNP	.											OR5L1,NS,carcinoma,0,3	OR5L1	145	3	1	Substitution - coding silent(1)	pancreas(1)	c.A240G						PASS	.						234.0	216.0	222.0					11																	55579182		2200	4296	6496	SO:0001819	synonymous_variant	219437	exon1			GCCAAAAATGTTG	AB065780	CCDS31509.1	11q11	2012-08-09			ENSG00000186117	ENSG00000186117		"""GPCR / Class A : Olfactory receptors"""	8350	protein-coding gene	gene with protein product							Standard	NM_001004738		Approved	OST262	uc001nhw.1	Q8NGL2	OTTHUMG00000166810	ENST00000333973.2:c.240A>G	11.37:g.55579182A>G		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	155	23	0.148387	NM_001004738	B2RNK6|Q6IFD0	Silent	SNP	ENST00000333973.2	37	CCDS31509.1																																																																																			A|1.000;G|0.000	0.000	strong		0.458	OR5L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391514.1	NM_001004738	
PIGG	54872	hgsc.bcm.edu	37	4	515489	515489	+	Missense_Mutation	SNP	G	G	A	rs13115344	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:515489G>A	ENST00000453061.2	+	8	1479	c.1373G>A	c.(1372-1374)cGc>cAc	p.R458H	PIGG_ENST00000383028.4_Missense_Mutation_p.R325H|PIGG_ENST00000503111.1_Silent_p.A296A|PIGG_ENST00000536264.1_Missense_Mutation_p.A321T|PIGG_ENST00000509768.1_Missense_Mutation_p.R369H|PIGG_ENST00000296306.7_Silent_p.A296A|PIGG_ENST00000504346.1_Missense_Mutation_p.R369H|PIGG_ENST00000310340.5_Missense_Mutation_p.R450H	NM_001127178.1	NP_001120650.1	Q5H8A4	PIGG_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class G	458			R -> H (in dbSNP:rs13115344). {ECO:0000269|PubMed:15489334}.		C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|GPI anchor biosynthetic process (GO:0006506)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	CP2 mannose-ethanolamine phosphotransferase activity (GO:0051267)|phosphotransferase activity, for other substituted phosphate groups (GO:0016780)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(5)|lung(16)|ovary(3)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	39						CAGGCACTGCGCAGAAAGGCT	0.527													G|||	1018	0.203275	0.3775	0.0836	5008	,	,		18123	0.2054		0.1233	False		,,,				2504	0.1329				p.R458H		Atlas-SNP	.											.	PIGG	86	.	0			c.G1373A						PASS	.	G	HIS/ARG,HIS/ARG	1467,2939	471.5+/-356.1	257,953,993	129.0	115.0	119.0		1373,1349	1.2	0.0	4	dbSNP_121	119	987,7613	213.4+/-253.3	65,857,3378	yes	missense,missense	PIGG	NM_001127178.1,NM_017733.3	29,29	322,1810,4371	AA,AG,GG		11.4767,33.2955,18.8682	benign,benign	458/984,450/976	515489	2454,10552	2203	4300	6503	SO:0001583	missense	54872	exon8			CACTGCGCAGAAA		CCDS3336.1, CCDS46992.1, CCDS75080.1, CCDS75081.1, CCDS75082.1, CCDS75083.1	4p16.3	2013-02-26	2006-06-28		ENSG00000174227	ENSG00000174227		"""Phosphatidylinositol glycan anchor biosynthesis"""	25985	protein-coding gene	gene with protein product			"""phosphatidylinositol glycan, class G"""			15632136	Standard	XM_005272287		Approved	FLJ20265, GPI7, LAS21	uc003gak.4	Q5H8A4	OTTHUMG00000112457	ENST00000453061.2:c.1373G>A	4.37:g.515489G>A	ENSP00000415203:p.Arg458His	Somatic	237	0	0		WXS	Illumina HiSeq	Phase_I	228	119	0.52193	NM_001127178	B4DKC7|Q2TAK5|Q6UX31|Q7L5Y4|Q8N866|Q8NCC9|Q96SY9|Q9BVT7|Q9NXG5	Missense_Mutation	SNP	ENST00000453061.2	37	CCDS46992.1	441|441	0.20192307692307693|0.20192307692307693	192|192	0.3902439024390244|0.3902439024390244	32|32	0.08839779005524862|0.08839779005524862	125|125	0.21853146853146854|0.21853146853146854	92|92	0.12137203166226913|0.12137203166226913	G|G	3.950|3.950	-0.012486|-0.012486	0.07727|0.07727	0.332955|0.332955	0.114767|0.114767	ENSG00000174227|ENSG00000174227	ENST00000536264|ENST00000310340;ENST00000453061;ENST00000504346;ENST00000383028;ENST00000509768	T|T;T;T;T;T	0.48201|0.45668	0.82|0.89;0.89;0.89;0.89;0.89	5.84|5.84	1.23|1.23	0.21249|0.21249	.|.	.|0.604056	.|0.19979	.|N	.|0.101811	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.08118|0.08118	0|0	0.80722|0.80722	P|P	0.0|0.0	B|B;B;B;B	0.09022|0.06786	0.002|0.0;0.001;0.0;0.0	B|B;B;B;B	0.04013|0.04013	0.001|0.001;0.001;0.001;0.001	T|T	0.46693|0.46693	-0.9173|-0.9173	8|9	0.20046|0.15499	T|T	0.44|0.54	.|.	12.2719|12.2719	0.54710|0.54710	0.2253:0.0:0.7747:0.0|0.2253:0.0:0.7747:0.0	rs13115344;rs61447247;rs13115344|rs13115344;rs61447247;rs13115344	321|325;369;458;450	B4DKC7|Q5H8A4-3;D6RFE8;Q5H8A4;Q5H8A4-2	.|.;.;PIGG_HUMAN;.	T|H	321|450;458;369;325;369	ENSP00000439240:A321T|ENSP00000311750:R450H;ENSP00000415203:R458H;ENSP00000424800:R369H;ENSP00000372494:R325H;ENSP00000421550:R369H	ENSP00000424619:A443T|ENSP00000311750:R450H	A|R	+|+	1|2	0|0	PIGG|PIGG	505489|505489	1.000000|1.000000	0.71417|0.71417	0.000000|0.000000	0.03702|0.03702	0.041000|0.041000	0.13682|0.13682	3.854000|3.854000	0.55949|0.55949	-0.081000|-0.081000	0.12662|0.12662	-1.166000|-1.166000	0.01754|0.01754	GCA|CGC	G|0.794;A|0.206	0.206	strong		0.527	PIGG-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000357494.1	NM_017733	
ZNF555	148254	hgsc.bcm.edu	37	19	2852744	2852744	+	Silent	SNP	C	C	T	rs35627030	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:2852744C>T	ENST00000334241.4	+	4	819	c.681C>T	c.(679-681)acC>acT	p.T227T	ZNF555_ENST00000591539.1_Silent_p.T226T|AC006130.3_ENST00000589365.1_RNA	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	50	0	0		WXS	Illumina HiSeq	Phase_I	42	21	0.5	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	
SCAP	22937	hgsc.bcm.edu	37	3	47467597	47467597	+	Missense_Mutation	SNP	C	C	T	rs149082564	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:47467597C>T	ENST00000265565.5	-	7	1212	c.800G>A	c.(799-801)cGg>cAg	p.R267Q	SCAP_ENST00000441517.2_Missense_Mutation_p.R12Q|SCAP_ENST00000545718.1_Intron	NM_012235.2	NP_036367.2	Q12770	SCAP_HUMAN	SREBF chaperone	267					aging (GO:0007568)|cholesterol metabolic process (GO:0008203)|negative regulation of cholesterol biosynthetic process (GO:0045541)|positive regulation of low-density lipoprotein particle receptor biosynthetic process (GO:0045716)|regulation of fatty acid biosynthetic process (GO:0042304)|response to hypoxia (GO:0001666)|response to insulin (GO:0032868)|small molecule metabolic process (GO:0044281)|SREBP signaling pathway (GO:0032933)	cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|protein complex (GO:0043234)	unfolded protein binding (GO:0051082)			endometrium(4)|kidney(1)|large_intestine(4)|liver(1)|lung(11)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	26				BRCA - Breast invasive adenocarcinoma(193;0.000278)|KIRC - Kidney renal clear cell carcinoma(197;0.00592)|Kidney(197;0.00679)		GCTCTCCGCCCGAAGGCTGCA	0.592													C|||	5	0.000998403	0.0	0.0	5008	,	,		16911	0.0		0.005	False		,,,				2504	0.0				p.R267Q	Pancreas(149;978 1908 29304 37806 46700)	Atlas-SNP	.											.	SCAP	88	.	0			c.G800A						PASS	.	C	GLN/ARG	5,4401	9.9+/-24.2	0,5,2198	100.0	84.0	90.0		800	4.1	0.7	3	dbSNP_134	90	42,8558	27.9+/-77.7	1,40,4259	yes	missense	SCAP	NM_012235.2	43	1,45,6457	TT,TC,CC		0.4884,0.1135,0.3614	benign	267/1280	47467597	47,12959	2203	4300	6503	SO:0001583	missense	22937	exon7			TCCGCCCGAAGGC	BC020987	CCDS2755.2	3p21.31	2013-01-10			ENSG00000114650	ENSG00000114650		"""WD repeat domain containing"""	30634	protein-coding gene	gene with protein product	"""SREBP cleavage activating protein"""	601510				8898195, 8724849, 10570913	Standard	XM_005264967		Approved	KIAA0199	uc003crh.1	Q12770	OTTHUMG00000125539	ENST00000265565.5:c.800G>A	3.37:g.47467597C>T	ENSP00000265565:p.Arg267Gln	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	63	32	0.507937	NM_012235	Q8N2E0|Q8WUA1	Missense_Mutation	SNP	ENST00000265565.5	37	CCDS2755.2	5	0.0022893772893772895	0	0.0	0	0.0	0	0.0	5	0.006596306068601583	C	15.61	2.885222	0.51908	0.001135	0.004884	ENSG00000114650	ENST00000339815;ENST00000265565;ENST00000441517	T;T	0.79653	-1.24;-1.29	5.02	4.12	0.48240	.	0.072632	0.56097	D	0.000038	T	0.56543	0.1992	N	0.22421	0.69	0.80722	D	1	B;B	0.22414	0.069;0.007	B;B	0.12156	0.007;0.004	T	0.55755	-0.8091	10	0.17832	T	0.49	-25.8852	9.534	0.39211	0.0:0.7822:0.1414:0.0764	.	12;267	F8W921;Q12770	.;SCAP_HUMAN	Q	267;267;12	ENSP00000265565:R267Q;ENSP00000416847:R12Q	ENSP00000265565:R267Q	R	-	2	0	SCAP	47442601	0.985000	0.35326	0.743000	0.31040	0.997000	0.91878	2.980000	0.49321	2.607000	0.88179	0.650000	0.86243	CGG	C|0.997;T|0.003	0.003	strong		0.592	SCAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246872.2	NM_012235	
STK39	27347	hgsc.bcm.edu	37	2	169020276	169020276	+	Missense_Mutation	SNP	T	T	C	rs201338418		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:169020276T>C	ENST00000355999.4	-	4	1250	c.545A>G	c.(544-546)tAt>tGt	p.Y182C		NM_013233.2	NP_037365.2	Q9UEW8	STK39_HUMAN	serine threonine kinase 39	182	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cellular hypotonic response (GO:0071476)|intracellular signal transduction (GO:0035556)|negative regulation of potassium ion transmembrane transport (GO:1901380)|negative regulation of potassium ion transmembrane transporter activity (GO:1901017)|negative regulation of rubidium ion transmembrane transporter activity (GO:2000687)|negative regulation of rubidium ion transport (GO:2000681)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of potassium ion transport (GO:0043268)|protein phosphorylation (GO:0006468)|regulation of inflammatory response (GO:0050727)|response to stress (GO:0006950)|signal transduction by phosphorylation (GO:0023014)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein serine/threonine kinase activity (GO:0004702)			central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(3)|prostate(2)|skin(2)	13						TCTGTGTAGATAGTCTAAGCC	0.378																																					p.Y182C		Atlas-SNP	.											STK39_ENST00000355999,bladder,carcinoma,0,8	STK39	95	8	0			c.A545G						scavenged	.						155.0	140.0	145.0					2																	169020276		1849	4092	5941	SO:0001583	missense	27347	exon4			TGTAGATAGTCTA	AF099989	CCDS42770.1	2q24.3	2010-06-25	2010-06-25		ENSG00000198648	ENSG00000198648			17717	protein-coding gene	gene with protein product	"""STE20/SPS1 homolog (yeast)"""	607648				10980603	Standard	NM_013233		Approved	DCHT, SPAK	uc002uea.3	Q9UEW8	OTTHUMG00000133745	ENST00000355999.4:c.545A>G	2.37:g.169020276T>C	ENSP00000348278:p.Tyr182Cys	Somatic	219	0	0		WXS	Illumina HiSeq	Phase_I	217	3	0.0138249	NM_013233	O14774|Q53S90|Q53SL7|Q53SS1|Q9UER4|X5D9C8	Missense_Mutation	SNP	ENST00000355999.4	37	CCDS42770.1	.	.	.	.	.	.	.	.	.	.	-	24.0	4.481085	0.84747	.	.	ENSG00000198648	ENST00000355999	T	0.75260	-0.92	6.03	6.03	0.97812	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.87853	0.6282	M	0.84683	2.71	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.89556	0.3803	10	0.87932	D	0	-0.6197	16.5582	0.84512	0.0:0.0:0.0:1.0	.	182	Q9UEW8	STK39_HUMAN	C	182	ENSP00000348278:Y182C	ENSP00000348278:Y182C	Y	-	2	0	STK39	168728522	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.960000	0.70348	2.308000	0.77769	0.533000	0.62120	TAT	.	.	weak		0.378	STK39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258112.2	NM_013233	
SPTBN4	57731	hgsc.bcm.edu	37	19	41008049	41008049	+	Silent	SNP	A	A	G	rs814526	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:41008049A>G	ENST00000352632.3	+	9	998	c.912A>G	c.(910-912)gtA>gtG	p.V304V	SPTBN4_ENST00000338932.3_Silent_p.V304V|SPTBN4_ENST00000344104.3_Silent_p.V304V|SPTBN4_ENST00000595535.1_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	69	0	0		WXS	Illumina HiSeq	Phase_I	53	53	1	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		
CBR3	874	hgsc.bcm.edu	37	21	37507501	37507501	+	Missense_Mutation	SNP	G	G	A	rs8133052	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:37507501G>A	ENST00000290354.5	+	1	292	c.11G>A	c.(10-12)tGc>tAc	p.C4Y	CBR3-AS1_ENST00000608641.1_RNA|CBR3-AS1_ENST00000608632.1_RNA|CBR3-AS1_ENST00000608622.1_RNA|CBR3-AS1_ENST00000608690.1_RNA|CBR3-AS1_ENST00000413862.1_RNA|CBR3-AS1_ENST00000453159.1_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	11	0	0		WXS	Illumina HiSeq	Phase_I	30	20	0.666667	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		
TNS1	7145	hgsc.bcm.edu	37	2	218682474	218682474	+	Silent	SNP	A	A	G	rs12694422	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:218682474A>G	ENST00000171887.4	-	24	4721	c.4269T>C	c.(4267-4269)agT>agC	p.S1423S	TNS1_ENST00000419504.1_Silent_p.S1410S|TNS1_ENST00000430930.1_Silent_p.S1402S	NM_022648.4	NP_072174.3	Q9HBL0	TENS1_HUMAN	tensin 1	1423					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)		TGCTGCCCCCACTGGGACTGG	0.612													G|||	1887	0.376797	0.4009	0.428	5008	,	,		18286	0.246		0.4056	False		,,,				2504	0.4131				p.S1423S		Atlas-SNP	.											.	TNS1	251	.	0			c.T4269C						PASS	.	G		1721,2685	649.9+/-399.0	357,1007,839	77.0	70.0	73.0		4269	-5.5	0.7	2	dbSNP_121	73	3560,5040	628.6+/-398.1	744,2072,1484	no	coding-synonymous	TNS1	NM_022648.4		1101,3079,2323	GG,GA,AA		41.3953,39.0604,40.6043		1423/1736	218682474	5281,7725	2203	4300	6503	SO:0001819	synonymous_variant	7145	exon24			GCCCCCACTGGGA	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.4269T>C	2.37:g.218682474A>G		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	60	28	0.466667	NM_022648	Q4ZG71|Q6IPI5	Silent	SNP	ENST00000171887.4	37	CCDS2407.1																																																																																			A|0.613;G|0.387	0.387	strong		0.612	TNS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256672.2	NM_022648	
TACC3	10460	hgsc.bcm.edu	37	4	1737502	1737502	+	Silent	SNP	C	C	T	rs11248073	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:1737502C>T	ENST00000313288.4	+	8	1795	c.1689C>T	c.(1687-1689)ttC>ttT	p.F563F		NM_006342.2	NP_006333.1	Q9Y6A5	TACC3_HUMAN	transforming, acidic coiled-coil containing protein 3	563					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)			ACCTCAAGTTCGACCCCCTCC	0.592													.|||	1954	0.390176	0.1263	0.3732	5008	,	,		17029	0.6935		0.3429	False		,,,				2504	0.4949				p.F563F	Ovarian(120;482 2294 11894 35824)	Atlas-SNP	.											.	TACC3	69	.	0			c.C1689T						PASS	.			790,3616	319.6+/-296.2	91,608,1504	137.0	110.0	119.0		1689	-7.1	0.0	4	dbSNP_120	119	3020,5580	465.7+/-366.6	533,1954,1813	no	coding-synonymous	TACC3	NM_006342.1		624,2562,3317	TT,TC,CC		35.1163,17.9301,29.2942		563/839	1737502	3810,9196	2203	4300	6503	SO:0001819	synonymous_variant	10460	exon8			CAAGTTCGACCCC	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.1689C>T	4.37:g.1737502C>T		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	48	36	0.75	NM_006342	Q2NKK4|Q3KQS5|Q9UMQ1	Silent	SNP	ENST00000313288.4	37	CCDS3352.1	861	0.3942307692307692	65	0.13211382113821138	132	0.36464088397790057	394	0.6888111888111889	270	0.3562005277044855	c	0.648	-0.810689	0.02798	0.179301	0.351163	ENSG00000013810	ENST00000470136	.	.	.	5.27	-7.14	0.01527	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	0.9999999999983626	.	.	.	.	.	.	.	.	.	.	.	.	.	-18.2683	16.5141	0.84294	0.0:0.1984:0.0:0.8016	rs11248073;rs11248073	.	.	.	X	200	.	.	R	+	1	2	TACC3	1707300	0.989000	0.36119	0.004000	0.12327	0.015000	0.08874	0.174000	0.16743	-1.407000	0.02043	-0.792000	0.03331	CGA	C|0.661;T|0.339	0.339	strong		0.592	TACC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000203730.2		
ACACA	31	hgsc.bcm.edu	37	17	35609866	35609866	+	Silent	SNP	C	C	T	rs2229416	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:35609866C>T	ENST00000394406.2	-	15	2002	c.1812G>A	c.(1810-1812)caG>caA	p.Q604Q	ACACA_ENST00000360679.3_Silent_p.Q546Q|ACACA_ENST00000353139.5_Silent_p.Q641Q|ACACA_ENST00000335166.5_Silent_p.Q526Q	NM_198836.1	NP_942133.1	Q13085	ACACA_HUMAN	acetyl-CoA carboxylase alpha	604	Biotin carboxylation.				acetyl-CoA metabolic process (GO:0006084)|biotin metabolic process (GO:0006768)|carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|lipid homeostasis (GO:0055088)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|malonyl-CoA biosynthetic process (GO:2001295)|multicellular organismal protein metabolic process (GO:0044268)|positive regulation of cellular metabolic process (GO:0031325)|protein homotetramerization (GO:0051289)|small molecule metabolic process (GO:0044281)|tissue homeostasis (GO:0001894)|triglyceride biosynthetic process (GO:0019432)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	acetyl-CoA carboxylase activity (GO:0003989)|ATP binding (GO:0005524)|biotin carboxylase activity (GO:0004075)|metal ion binding (GO:0046872)			NS(2)|breast(5)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(24)|lung(23)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	83		Breast(25;0.00157)|Ovarian(249;0.15)			Biotin(DB00121)	TTCTGTTCATCTGAAAGCTTT	0.423													C|||	1101	0.219848	0.0227	0.1412	5008	,	,		18528	0.4534		0.1561	False		,,,				2504	0.3671				p.Q641Q	Colon(23;82 258 739 2117 10493 24037 27661 34815 35438 36249)	Atlas-SNP	.											ACACA_ENST00000353139,right_upper_lobe,carcinoma,-2,2	ACACA	395	2	0			c.G1923A						PASS	.	C	,,,,	169,4237	111.6+/-149.8	2,165,2036	173.0	173.0	173.0		1923,1812,1638,1578,1812	4.1	1.0	17	dbSNP_98	173	1096,7504	228.7+/-263.7	60,976,3264	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ACACA	NM_198834.1,NM_198836.1,NM_198837.1,NM_198838.1,NM_198839.1	,,,,	62,1141,5300	TT,TC,CC		12.7442,3.8357,9.7263	,,,,	641/2384,604/2347,546/2289,526/2269,604/2347	35609866	1265,11741	2203	4300	6503	SO:0001819	synonymous_variant	31	exon15			GTTCATCTGAAAG	U19822	CCDS11317.1, CCDS11318.1, CCDS42302.1, CCDS42303.1	17q21	2014-05-06	2010-04-30		ENSG00000132142	ENSG00000278540	6.4.1.2		84	protein-coding gene	gene with protein product	"""acetyl-CoA carboxylase 1"""	200350	"""acetyl-Coenzyme A carboxylase alpha"""	ACAC, ACC			Standard	NM_198837		Approved	ACC1	uc002hno.3	Q13085	OTTHUMG00000188463	ENST00000394406.2:c.1812G>A	17.37:g.35609866C>T		Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	129	64	0.496124	NM_198834	B2RP68|Q6KEV6|Q6XDA8|Q7Z2G8|Q7Z561|Q7Z563|Q7Z564|Q86WB2|Q86WB3	Silent	SNP	ENST00000394406.2	37	CCDS11317.1																																																																																			T|0.139;C|0.861	0.139	strong		0.423	ACACA-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256696.1	NM_198836	
TMEM132A	54972	hgsc.bcm.edu	37	11	60701136	60701136	+	Silent	SNP	C	C	G	rs9513	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:60701136C>G	ENST00000453848.2	+	8	1637	c.1479C>G	c.(1477-1479)ccC>ccG	p.P493P	TMEM132A_ENST00000005286.4_Silent_p.P494P			Q24JP5	T132A_HUMAN	transmembrane protein 132A	493						endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				breast(1)|cervix(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(14)|ovary(3)|prostate(1)|skin(3)	32						TGTGGGCCCCCCTGCTACCGC	0.711													G|||	2109	0.421126	0.4713	0.4452	5008	,	,		14506	0.3165		0.4225	False		,,,				2504	0.4427				p.P494P		Atlas-SNP	.											.	TMEM132A	135	.	0			c.C1482G						PASS	.	G	,	2005,2385		470,1065,660	15.0	18.0	17.0		1482,1479	-3.5	0.4	11	dbSNP_52	17	3595,4969		793,2009,1480	no	coding-synonymous,coding-synonymous	TMEM132A	NM_017870.3,NM_178031.2	,	1263,3074,2140	GG,GC,CC		41.978,45.672,43.2299	,	494/1025,493/1024	60701136	5600,7354	2195	4282	6477	SO:0001819	synonymous_variant	54972	exon8			GGCCCCCCTGCTA	AK000546	CCDS7997.1, CCDS44618.1	11q12.2	2006-03-02	2006-03-02	2006-03-02	ENSG00000006118	ENSG00000006118			31092	protein-coding gene	gene with protein product			"""heat shock 70kDa protein 5 (glucose-regulated protein, 78kDa) binding protein 1"""	HSPA5BP1		12514190, 10997877	Standard	NM_017870		Approved	GBP, FLJ20539	uc001nqi.3	Q24JP5	OTTHUMG00000167803	ENST00000453848.2:c.1479C>G	11.37:g.60701136C>G		Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	21	21	1	NM_017870	Q69YU7|Q86VZ8|Q86W97|Q9H8K3|Q9HCI9|Q9NWY0	Silent	SNP	ENST00000453848.2	37	CCDS44618.1	902	0.413003663003663	233	0.4735772357723577	164	0.4530386740331492	185	0.32342657342657344	320	0.42216358839050133	G	1.214	-0.628838	0.03610	0.45672	0.41978	ENSG00000006118	ENST00000536409	T	0.28666	1.6	4.74	-3.54	0.04653	.	0.000000	0.64402	D	0.000006	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999881	.	.	.	.	.	.	T	0.38436	-0.9661	6	0.87932	D	0	-36.0168	7.8294	0.29334	0.532:0.2072:0.2608:0.0	rs9513;rs3180958;rs58804152	.	.	.	A	85	ENSP00000439717:P85A	ENSP00000439717:P85A	P	+	1	0	TMEM132A	60457712	0.000000	0.05858	0.438000	0.26821	0.129000	0.20672	-2.894000	0.00707	-1.522000	0.01769	-2.035000	0.00420	CCT	C|0.581;G|0.419	0.419	strong		0.711	TMEM132A-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000396352.1	NM_017870	
TRPA1	8989	hgsc.bcm.edu	37	8	72981327	72981327	+	Silent	SNP	A	A	G	rs1811457	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:72981327A>G	ENST00000262209.4	-	3	582	c.375T>C	c.(373-375)aaT>aaC	p.N125N		NM_007332.2	NP_015628.2	O75762	TRPA1_HUMAN	transient receptor potential cation channel, subfamily A, member 1	125					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)	AGTTTCGGAGATTTGGGTTTG	0.453													G|||	4041	0.806909	0.8964	0.7608	5008	,	,		19141	0.9752		0.6074	False		,,,				2504	0.7505				p.N125N		Atlas-SNP	.											.	TRPA1	256	.	0			c.T375C						PASS	.	G		3825,581	258.3+/-262.4	1653,519,31	220.0	232.0	228.0		375	2.9	1.0	8	dbSNP_92	228	5175,3425	505.3+/-376.3	1564,2047,689	no	coding-synonymous	TRPA1	NM_007332.2		3217,2566,720	GG,GA,AA		39.8256,13.1866,30.8012		125/1120	72981327	9000,4006	2203	4300	6503	SO:0001819	synonymous_variant	8989	exon3			TCGGAGATTTGGG	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.375T>C	8.37:g.72981327A>G		Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	123	93	0.756098	NM_007332	A6NIN6	Silent	SNP	ENST00000262209.4	37	CCDS34908.1																																																																																			A|0.277;G|0.723	0.723	strong		0.453	TRPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379079.2	NM_007332	
APOBEC2	10930	hgsc.bcm.edu	37	6	41029109	41029109	+	Silent	SNP	T	T	C	rs2073014	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	113	0	0		WXS	Illumina HiSeq	Phase_I	72	32	0.444444	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	
CRTAM	56253	hgsc.bcm.edu	37	11	122738261	122738261	+	Missense_Mutation	SNP	A	A	G	rs2272094	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:122738261A>G	ENST00000227348.4	+	8	1009	c.962A>G	c.(961-963)aAa>aGa	p.K321R	CRTAM_ENST00000533709.1_Missense_Mutation_p.K122R	NM_019604.2	NP_062550.2			cytotoxic and regulatory T cell molecule											breast(1)|endometrium(2)|large_intestine(5)|lung(7)|ovary(2)|pancreas(1)|prostate(1)	19		Breast(109;0.00249)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;5.28e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0308)		ATATGGAAGAAAGGTCAGTGG	0.453													A|||	2756	0.550319	0.3646	0.7478	5008	,	,		19717	0.4325		0.7316	False		,,,				2504	0.5961				p.K321R		Atlas-SNP	.											.	CRTAM	50	.	0			c.A962G						PASS	.	A	ARG/LYS	1855,2549	537.8+/-374.8	396,1063,743	80.0	71.0	74.0		962	-2.5	0.5	11	dbSNP_100	74	6226,2372	701.0+/-405.2	2248,1730,321	yes	missense	CRTAM	NM_019604.2	26	2644,2793,1064	GG,GA,AA		27.5878,42.1208,37.848	benign	321/394	122738261	8081,4921	2202	4299	6501	SO:0001583	missense	56253	exon8			GGAAGAAAGGTCA	AF001622	CCDS8437.1	11q24.1	2013-01-11			ENSG00000109943	ENSG00000109943		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"""	24313	protein-coding gene	gene with protein product	"""class I MHC restricted T cell associated molecule"""	612597				10811014, 16300832	Standard	NM_019604		Approved	CD355	uc001pyj.3	O95727	OTTHUMG00000166026	ENST00000227348.4:c.962A>G	11.37:g.122738261A>G	ENSP00000227348:p.Lys321Arg	Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	151	151	1	NM_019604		Missense_Mutation	SNP	ENST00000227348.4	37	CCDS8437.1	1282	0.586996336996337	203	0.41260162601626016	266	0.7348066298342542	252	0.4405594405594406	561	0.7401055408970977	A	5.176	0.217959	0.09810	0.421208	0.724122	ENSG00000109943	ENST00000227348;ENST00000533709	T;T	0.60672	0.17;1.08	5.62	-2.53	0.06326	.	0.235445	0.39985	N	0.001213	T	0.00012	0.0000	N	0.21282	0.65	0.25370	P	0.988702	B;B	0.21606	0.04;0.058	B;B	0.17433	0.018;0.012	T	0.39014	-0.9634	9	0.15499	T	0.54	.	11.3936	0.49827	0.5777:0.0:0.4223:0.0	rs2272094;rs58691097;rs2272094	122;321	O95727-2;O95727	.;CRTAM_HUMAN	R	321;122	ENSP00000227348:K321R;ENSP00000433728:K122R	ENSP00000227348:K321R	K	+	2	0	CRTAM	122243471	0.997000	0.39634	0.473000	0.27253	0.133000	0.20885	0.527000	0.22987	-0.410000	0.07542	-0.256000	0.11100	AAA	A|0.413;G|0.587	0.587	strong		0.453	CRTAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387507.1	NM_019604	
NAT8	9027	hgsc.bcm.edu	37	2	73868328	73868328	+	Missense_Mutation	SNP	A	A	G	rs13538	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:73868328A>G	ENST00000272425.3	-	2	577	c.428T>C	c.(427-429)tTt>tCt	p.F143S		NM_003960.3|NM_016347.2	NP_003951.3|NP_057431.2			N-acetyltransferase 8 (GCN5-related, putative)											breast(1)|endometrium(2)|kidney(2)|lung(2)|ovary(1)|prostate(1)	9						ACTGTCCACAAAGAGATGAAA	0.562													.|||	1350	0.269569	0.6172	0.2622	5008	,	,		19442	0.005		0.2097	False		,,,				2504	0.1391				p.F143S		Atlas-SNP	.											.	NAT8	26	.	0			c.T428C						PASS	.	A	SER/PHE	2321,2085	605.2+/-390.5	620,1081,502	73.0	76.0	75.0	http://www.ncbi.nlm.nih.gov/pubmed?term	428	-7.7	0.0	2	dbSNP_52	75	1917,6683	339.4+/-323.1	206,1505,2589	no	missense	NAT8	NM_003960.3	155	826,2586,3091	GG,GA,AA	http://www.ncbi.nlm.nih.gov/pubmed?term	22.2907,47.3218,32.585	benign	143/228	73868328	4238,8768	2203	4300	6503	SO:0001583	missense	9027	exon2			TCCACAAAGAGAT	AB013094	CCDS1926.1	2p13.2	2012-03-20	2008-09-24		ENSG00000144035	ENSG00000144035			18069	protein-coding gene	gene with protein product		606716	"""N-acetyltransferase 8"""			11397015, 9852678, 19011241	Standard	NM_003960		Approved	Hcml1, TSC501, GLA, ATase2	uc002sji.1	Q9UHE5	OTTHUMG00000129818	ENST00000272425.3:c.428T>C	2.37:g.73868328A>G	ENSP00000272425:p.Phe143Ser	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	88	88	1	NM_003960		Missense_Mutation	SNP	ENST00000272425.3	37	CCDS1926.1	548	0.2509157509157509	302	0.6138211382113821	81	0.22375690607734808	4	0.006993006993006993	161	0.21240105540897097	a	0.010	-1.771572	0.00645	0.526782	0.222907	ENSG00000144035	ENST00000272425	T	0.22539	1.95	3.86	-7.73	0.01245	GCN5-related N-acetyltransferase (GNAT) domain (2);Acyl-CoA N-acyltransferase (2);	0.610629	0.17818	N	0.160960	T	0.00012	0.0000	N	0.02960	-0.455	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.26018	-1.0115	9	0.09084	T	0.74	-0.7893	3.5914	0.07990	0.4:0.2826:0.2389:0.0785	rs13538;rs3174952;rs17009281;rs13538	143	Q9UHE5	NAT8_HUMAN	S	143	ENSP00000272425:F143S	ENSP00000272425:F143S	F	-	2	0	NAT8	73721836	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.187000	0.16998	-2.616000	0.00442	-3.803000	0.00020	TTT	A|0.708;G|0.292	0.292	strong		0.562	NAT8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327854.1	NM_003960	
C4orf45	152940	hgsc.bcm.edu	37	4	159881479	159881479	+	Silent	SNP	T	T	C	rs9784569	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:159881479T>C	ENST00000434826.2	-	3	399	c.315A>G	c.(313-315)caA>caG	p.Q105Q	C4orf45_ENST00000508011.1_Intron	NM_152543.2	NP_689756.2	Q96LM5	CD045_HUMAN	chromosome 4 open reading frame 45	105										large_intestine(2)|lung(3)	5						CAAGAGAAGCTTGACTTAGTT	0.303													T|||	1015	0.202676	0.1203	0.1974	5008	,	,		16244	0.2421		0.2744	False		,,,				2504	0.2035				p.Q105Q		Atlas-SNP	.											.	C4orf45	8	.	0			c.A315G						PASS	.	T		467,3129		28,411,1359	55.0	54.0	54.0		315	-5.8	0.0	4	dbSNP_119	54	2343,5783		339,1665,2059	no	coding-synonymous	C4orf45	NM_152543.2		367,2076,3418	CC,CT,TT		28.8334,12.9867,23.972		105/187	159881479	2810,8912	1798	4063	5861	SO:0001819	synonymous_variant	152940	exon3			AGAAGCTTGACTT		CCDS47156.1	4q32.1	2012-03-02			ENSG00000164123	ENSG00000164123			26342	protein-coding gene	gene with protein product							Standard	NM_152543		Approved	FLJ25371	uc003iqf.1	Q96LM5	OTTHUMG00000161988	ENST00000434826.2:c.315A>G	4.37:g.159881479T>C		Somatic	205	0	0		WXS	Illumina HiSeq	Phase_I	161	64	0.397516	NM_152543	A8MPU3|C9J0T8	Silent	SNP	ENST00000434826.2	37	CCDS47156.1																																																																																			T|0.781;C|0.219	0.219	strong		0.303	C4orf45-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366636.1	NM_152543	
GRHL3	57822	hgsc.bcm.edu	37	1	24690764	24690764	+	Missense_Mutation	SNP	T	T	A	rs545809	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:24690764T>A	ENST00000350501.5	+	16	1911	c.1784T>A	c.(1783-1785)aTg>aAg	p.M595K	STPG1_ENST00000003583.8_Intron|STPG1_ENST00000337248.4_Intron|STPG1_ENST00000374409.1_Intron|STPG1_ENST00000468303.1_Intron|STPG1_ENST00000440416.1_Intron	NM_198174.2	NP_937817.3	Q8TE85	GRHL3_HUMAN	grainyhead-like 3 (Drosophila)	595					central nervous system development (GO:0007417)|cochlea morphogenesis (GO:0090103)|ectoderm development (GO:0007398)|epidermis development (GO:0008544)|establishment of planar polarity (GO:0001736)|eyelid development in camera-type eye (GO:0061029)|pattern specification process (GO:0007389)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of actin cytoskeleton organization (GO:0032956)|wound healing (GO:0042060)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|pancreas(3)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20		Colorectal(325;3.46e-05)|Renal(390;0.0007)|Lung NSC(340;0.00171)|all_lung(284;0.00226)|Ovarian(437;0.00348)|Breast(348;0.0126)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.19)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;8.72e-25)|Colorectal(126;4.38e-08)|COAD - Colon adenocarcinoma(152;1.84e-06)|GBM - Glioblastoma multiforme(114;0.000132)|BRCA - Breast invasive adenocarcinoma(304;0.00105)|STAD - Stomach adenocarcinoma(196;0.00151)|KIRC - Kidney renal clear cell carcinoma(1967;0.00377)|READ - Rectum adenocarcinoma(331;0.0656)|Lung(427;0.143)		GTGAGGaacatgggttttgga	0.537													T|||	1497	0.298922	0.2247	0.2305	5008	,	,		15454	0.4127		0.2734	False		,,,				2504	0.3569				p.M595K		Atlas-SNP	.											.	GRHL3	69	.	0			c.T1784A						PASS	.																																			SO:0001583	missense	57822	exon16			GGAACATGGGTTT	AY231161	CCDS251.1, CCDS252.1, CCDS44088.1, CCDS252.2, CCDS53284.1	1p36	2008-02-05	2005-07-11	2005-07-11	ENSG00000158055	ENSG00000158055			25839	protein-coding gene	gene with protein product		608317	"""transcription factor CP2-like 4"""	TFCP2L4		12549979	Standard	NM_021180		Approved	SOM	uc021oiw.1	Q8TE85	OTTHUMG00000003040	ENST00000350501.5:c.1784T>A	1.37:g.24690764T>A	ENSP00000288955:p.Met595Lys	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	107	54	0.504673	NM_198174	A2A297|B2RCL1|G3XAF0|Q5TH78|Q86Y06|Q8N407	Missense_Mutation	SNP	ENST00000350501.5	37	CCDS252.2	647	0.29624542124542125	114	0.23170731707317074	90	0.24861878453038674	246	0.43006993006993005	197	0.2598944591029024	T	12.15	1.851371	0.32699	.	.	ENSG00000158055	ENST00000350501	T	0.09817	2.94	3.18	-1.22	0.09494	.	1.427050	0.03899	N	0.279931	T	0.00012	0.0000	L	0.38175	1.15	0.80722	P	0.0	.	.	.	.	.	.	T	0.44112	-0.9349	7	0.87932	D	0	-0.5292	0.3876	0.00405	0.2209:0.1397:0.2261:0.4132	rs545809;rs545809	.	.	.	K	595	ENSP00000288955:M595K	ENSP00000288955:M595K	M	+	2	0	GRHL3	24563351	0.000000	0.05858	0.002000	0.10522	0.400000	0.30750	-0.344000	0.07780	0.006000	0.14734	0.260000	0.18958	ATG	A|0.304;N|0.003	0.304	strong		0.537	GRHL3-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000009047.2	NM_021180	
BAZ2B	29994	hgsc.bcm.edu	37	2	160241785	160241785	+	Silent	SNP	T	T	C	rs372315034		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:160241785T>C	ENST00000392783.2	-	23	4062	c.3567A>G	c.(3565-3567)ggA>ggG	p.G1189G	BAZ2B_ENST00000355831.2_Silent_p.G1155G|BAZ2B_ENST00000392782.1_Silent_p.G1153G|BAZ2B_ENST00000343439.5_Silent_p.G1089G|AC008277.1_ENST00000420020.1_RNA	NM_013450.2	NP_038478.2	Q9UIF8	BAZ2B_HUMAN	bromodomain adjacent to zinc finger domain, 2B	1189					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(7)|liver(2)|lung(41)|ovary(3)|prostate(1)|skin(2)|soft_tissue(1)|urinary_tract(1)	82						GCTCAGTTTGTCCACAGTGGG	0.428													T|||	1	0.000199681	0.0	0.0	5008	,	,		15755	0.0		0.001	False		,,,				2504	0.0				p.G1189G		Atlas-SNP	.											.	BAZ2B	196	.	0			c.A3567G						PASS	.	T		2,3722		0,2,1860	120.0	117.0	118.0		3567	2.0	1.0	2		118	12,8192		0,12,4090	no	coding-synonymous	BAZ2B	NM_013450.2		0,14,5950	CC,CT,TT		0.1463,0.0537,0.1174		1189/2169	160241785	14,11914	1862	4102	5964	SO:0001819	synonymous_variant	29994	exon23			AGTTTGTCCACAG	AB032255	CCDS2209.2, CCDS74594.1	2q24.2	2013-01-28			ENSG00000123636	ENSG00000123636		"""Zinc fingers, PHD-type"""	963	protein-coding gene	gene with protein product		605683				10662543	Standard	XM_005246488		Approved	WALp4	uc002uao.3	Q9UIF8	OTTHUMG00000132027	ENST00000392783.2:c.3567A>G	2.37:g.160241785T>C		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	135	60	0.444444	NM_013450	D3DPA8|Q96EA1|Q96SQ8|Q9P252|Q9Y4N8	Silent	SNP	ENST00000392783.2	37	CCDS2209.2																																																																																			.	.	weak		0.428	BAZ2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255037.2		
TNFRSF6B	8771	hgsc.bcm.edu	37	20	62328742	62328742	+	Silent	SNP	C	C	T	rs909341	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:62328742C>T	ENST00000369996.1	+	2	586	c.486C>T	c.(484-486)agC>agT	p.S162S	ARFRP1_ENST00000485858.1_5'Flank|RTEL1-TNFRSF6B_ENST00000482936.1_3'UTR	NM_003823.3	NP_003814.1	O95407	TNF6B_HUMAN	tumor necrosis factor receptor superfamily, member 6b, decoy	162					apoptotic process (GO:0006915)|negative regulation of apoptotic process (GO:0043066)	extracellular space (GO:0005615)	receptor activity (GO:0004872)			central_nervous_system(1)|lung(2)|skin(1)	4	all_cancers(38;4.66e-12)|all_epithelial(29;2.56e-13)|Lung NSC(23;1.06e-08)|all_lung(23;3.34e-08)		Epithelial(9;1.78e-08)|all cancers(9;7.89e-08)|OV - Ovarian serous cystadenocarcinoma(5;0.00504)			CAGCCAGCAGCTCCAGCTCAG	0.667													C|||	1311	0.261781	0.0242	0.2637	5008	,	,		18523	0.6468		0.2018	False		,,,				2504	0.2464				p.S162S		Atlas-SNP	.											TNFRSF6B,caecum,carcinoma,0,2	TNFRSF6B	22	2	0			c.C486T						scavenged	.	C		304,4058	155.9+/-189.0	12,280,1889	35.0	30.0	32.0		486	3.3	1.0	20	dbSNP_92	32	1957,6607	314.6+/-311.9	229,1499,2554	no	coding-synonymous	TNFRSF6B	NM_003823.3		241,1779,4443	TT,TC,CC		22.8515,6.9693,17.4919		162/301	62328742	2261,10665	2181	4282	6463	SO:0001819	synonymous_variant	8771	exon2			CAGCAGCTCCAGC	AF104419	CCDS13532.1	20q13.33	2012-06-27						"""Tumor necrosis factor receptor superfamily"""	11921	protein-coding gene	gene with protein product		603361				9872321, 10318773	Standard	NM_003823		Approved	DcR3, DCR3, TR6, M68	uc002yfz.3	O95407	OTTHUMG00000143724	ENST00000369996.1:c.486C>T	20.37:g.62328742C>T		Somatic	173	1	0.00578035		WXS	Illumina HiSeq	Phase_I	149	79	0.530201	NM_003823		Silent	SNP	ENST00000369996.1	37	CCDS13532.1																																																																																			C|0.799;T|0.201	0.201	strong		0.667	TNFRSF6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080182.1		
TTN	7273	hgsc.bcm.edu	37	2	179642589	179642589	+	Missense_Mutation	SNP	C	C	G	rs72647876	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:179642589C>G	ENST00000591111.1	-	25	4546	c.4322G>C	c.(4321-4323)cGt>cCt	p.R1441P	TTN_ENST00000359218.5_Missense_Mutation_p.R1395P|RP11-88L24.4_ENST00000582038.2_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.R1441P|TTN_ENST00000460472.2_Missense_Mutation_p.R1395P|TTN_ENST00000589042.1_Missense_Mutation_p.R1441P|TTN_ENST00000342175.6_Missense_Mutation_p.R1395P|TTN_ENST00000360870.5_Missense_Mutation_p.R1441P			Q8WZ42	TITIN_HUMAN	titin	33637			R -> P. {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)			CTCCAGCCTACGTCCAGGGGA	0.488													C|||	52	0.0103834	0.0008	0.0101	5008	,	,		18433	0.0159		0.0119	False		,,,				2504	0.0164				p.R1441P		Atlas-SNP	.											.	TTN	18412	.	0			c.G4322C						PASS	.	C	PRO/ARG,PRO/ARG,PRO/ARG,PRO/ARG,PRO/ARG	10,4396	16.8+/-37.8	0,10,2193	71.0	72.0	72.0		4184,4322,4322,4184,4184	5.4	1.0	2	dbSNP_130	72	65,8535	40.3+/-97.0	0,65,4235	yes	missense,missense,missense,missense,missense	TTN	NM_003319.4,NM_133378.4,NM_133379.3,NM_133432.3,NM_133437.3	103,103,103,103,103	0,75,6428	GG,GC,CC		0.7558,0.227,0.5767	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	1395/26927,1441/33424,1441/5605,1395/27052,1395/27119	179642589	75,12931	2203	4300	6503	SO:0001583	missense	7273	exon25			AGCCTACGTCCAG	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.4322G>C	2.37:g.179642589C>G	ENSP00000465570:p.Arg1441Pro	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	126	49	0.388889	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		17	0.007783882783882784	0	0.0	6	0.016574585635359115	4	0.006993006993006993	7	0.009234828496042216	C	16.67	3.188469	0.57909	0.00227	0.007558	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127;ENST00000360870	T;T;T;T;T	0.65178	-0.14;0.12;0.1;0.09;0.24	5.45	5.45	0.79879	Ribonuclease H-like (1);	.	.	.	.	T	0.63200	0.2491	L	0.52759	1.655	0.47009	D	0.999288	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	0.997;0.997;0.997;0.997;1.0	T	0.73288	-0.4030	9	0.87932	D	0	.	19.2544	0.93940	0.0:1.0:0.0:0.0	.	1395;1395;1395;1441;1441	D3DPF9;E7EQE6;E7ET18;Q8WZ42;Q8WZ42-6	.;.;.;TITIN_HUMAN;.	P	1441;1395;1395;1395;1395;1441	ENSP00000343764:R1441P;ENSP00000434586:R1395P;ENSP00000340554:R1395P;ENSP00000352154:R1395P;ENSP00000354117:R1441P	ENSP00000340554:R1395P	R	-	2	0	TTN	179350834	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.584000	0.82572	2.723000	0.93209	0.650000	0.86243	CGT	C|0.993;G|0.007	0.007	strong		0.488	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
ACCS	84680	hgsc.bcm.edu	37	11	44101118	44101118	+	Silent	SNP	C	C	T	rs7950395	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:44101118C>T	ENST00000263776.8	+	10	1305	c.871C>T	c.(871-873)Ctg>Ttg	p.L291L		NM_001127219.1|NM_032592.3	NP_001120691.1|NP_115981.1	Q96QU6	1A1L1_HUMAN	1-aminocyclopropane-1-carboxylate synthase homolog (Arabidopsis)(non-functional)	291					biosynthetic process (GO:0009058)		catalytic activity (GO:0003824)|protein homodimerization activity (GO:0042803)|pyridoxal phosphate binding (GO:0030170)			breast(4)|endometrium(3)|large_intestine(11)|lung(15)|ovary(1)|skin(1)	35						GGTCTACATGCTGTCCGTGTT	0.567													C|||	572	0.114217	0.1203	0.0937	5008	,	,		18903	0.1151		0.1223	False		,,,				2504	0.1115				p.L291L	Esophageal Squamous(158;148 1889 8077 23160 41213)	Atlas-SNP	.											.	ACCS	64	.	0			c.C871T						PASS	.	C	,	580,3826	254.0+/-259.7	51,478,1674	216.0	139.0	165.0		871,871	1.9	1.0	11	dbSNP_116	165	1119,7481	229.8+/-264.4	66,987,3247	no	coding-synonymous,coding-synonymous	ACCS	NM_001127219.1,NM_032592.3	,	117,1465,4921	TT,TC,CC		13.0116,13.1639,13.0632	,	291/502,291/502	44101118	1699,11307	2203	4300	6503	SO:0001819	synonymous_variant	84680	exon10			TACATGCTGTCCG	AY026508	CCDS7907.1	11p11	2008-03-12	2008-01-28		ENSG00000110455	ENSG00000110455			23989	protein-coding gene	gene with protein product		608405				11470512	Standard	NM_032592		Approved	PHACS, ACS	uc009yks.1	Q96QU6	OTTHUMG00000166427	ENST00000263776.8:c.871C>T	11.37:g.44101118C>T		Somatic	207	0	0		WXS	Illumina HiSeq	Phase_I	174	124	0.712644	NM_032592	B4E219|Q8WUL4|Q96LX5	Silent	SNP	ENST00000263776.8	37	CCDS7907.1																																																																																			C|0.877;T|0.123	0.123	strong		0.567	ACCS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389721.1	NM_032592	
ZNF749	388567	hgsc.bcm.edu	37	19	57955719	57955719	+	Silent	SNP	G	G	A	rs2240037	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:57955719G>A	ENST00000334181.4	+	3	1453	c.1203G>A	c.(1201-1203)caG>caA	p.Q401Q	AC004076.9_ENST00000596831.1_Intron	NM_001023561.2	NP_001018855.2	O43361	ZN749_HUMAN	zinc finger protein 749	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)			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)		ATATGCACCAGAGAGTTCATG	0.423													G|||	216	0.043131	0.0855	0.0101	5008	,	,		22245	0.0218		0.0169	False		,,,				2504	0.0583				p.Q401Q		Atlas-SNP	.											.	ZNF749	75	.	0			c.G1203A						PASS	.	G		308,4098	165.4+/-196.9	13,282,1908	98.0	98.0	98.0		1203	-2.6	0.0	19	dbSNP_98	98	199,8401	87.1+/-149.5	2,195,4103	no	coding-synonymous	ZNF749	NM_001023561.2		15,477,6011	AA,AG,GG		2.314,6.9905,3.8982		401/779	57955719	507,12499	2203	4300	6503	SO:0001819	synonymous_variant	388567	exon3			GCACCAGAGAGTT	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.1203G>A	19.37:g.57955719G>A		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	118	46	0.38983	NM_001023561		Silent	SNP	ENST00000334181.4	37	CCDS33132.2																																																																																			G|0.959;A|0.041	0.041	strong		0.423	ZNF749-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317879.1	NM_001023561	
USH2A	7399	hgsc.bcm.edu	37	1	215848914	215848914	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:215848914C>A	ENST00000307340.3	-	63	12725	c.12339G>T	c.(12337-12339)ttG>ttT	p.L4113F	USH2A_ENST00000366943.2_Missense_Mutation_p.L4113F	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	4113	Fibronectin type-III 26. {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)		ACTGACGATTCAAACCAGAGT	0.507										HNSCC(13;0.011)																											p.L4113F		Atlas-SNP	.											.	USH2A	1168	.	0			c.G12339T						PASS	.						69.0	65.0	67.0					1																	215848914		2203	4300	6503	SO:0001583	missense	7399	exon63			ACGATTCAAACCA	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.12339G>T	1.37:g.215848914C>A	ENSP00000305941:p.Leu4113Phe	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	138	29	0.210145	NM_206933	Q5VVM9|Q6S362|Q9NS27	Missense_Mutation	SNP	ENST00000307340.3	37	CCDS31025.1	.	.	.	.	.	.	.	.	.	.	C	1.035	-0.680618	0.03353	.	.	ENSG00000042781	ENST00000307340;ENST00000366943	T;T	0.54279	0.58;0.58	5.25	1.15	0.20763	Fibronectin, type III (3);Immunoglobulin-like fold (1);	0.220262	0.22515	N	0.059043	T	0.41351	0.1155	M	0.72894	2.215	0.09310	N	1	B	0.23735	0.09	B	0.20384	0.029	T	0.21861	-1.0233	10	0.18710	T	0.47	.	2.3656	0.04318	0.1182:0.4436:0.2314:0.2067	.	4113	O75445	USH2A_HUMAN	F	4113	ENSP00000305941:L4113F;ENSP00000355910:L4113F	ENSP00000305941:L4113F	L	-	3	2	USH2A	213915537	0.001000	0.12720	0.000000	0.03702	0.084000	0.17831	0.243000	0.18106	0.205000	0.20568	-0.143000	0.13931	TTG	.	.	none		0.507	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123	
PCDHB14	56122	hgsc.bcm.edu	37	5	140604621	140604621	+	Missense_Mutation	SNP	C	C	T	rs144421802	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:140604621C>T	ENST00000239449.4	+	1	1544	c.1544C>T	c.(1543-1545)gCc>gTc	p.A515V	PCDHB14_ENST00000515856.2_Missense_Mutation_p.A362V	NM_018934.2	NP_061757.1	Q9Y5E9	PCDBE_HUMAN	protocadherin beta 14	515	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)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(21)|ovary(2)|prostate(3)|skin(6)|urinary_tract(1)	49			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CACCTGTTTGCCCTCAGGTCG	0.677													c|||	17	0.00339457	0.0	0.0014	5008	,	,		16912	0.0		0.007	False		,,,				2504	0.0092				p.A515V	Ovarian(141;50 1831 27899 33809 37648)	Atlas-SNP	.											.	PCDHB14	132	.	0			c.C1544T						PASS	.	C	VAL/ALA	8,4398		0,8,2195	96.0	100.0	99.0		1544	4.2	1.0	5	dbSNP_134	99	98,8502		0,98,4202	no	missense	PCDHB14	NM_018934.2	64	0,106,6397	TT,TC,CC		1.1395,0.1816,0.815	benign	515/799	140604621	106,12900	2203	4300	6503	SO:0001583	missense	56122	exon1			TGTTTGCCCTCAG	AF152493	CCDS4256.1	5q31	2010-01-26			ENSG00000120327	ENSG00000120327		"""Cadherins / Protocadherins : Clustered"""	8685	other	protocadherin		606340				10380929	Standard	NM_018934		Approved	PCDH-BETA14	uc003ljb.3	Q9Y5E9	OTTHUMG00000129619	ENST00000239449.4:c.1544C>T	5.37:g.140604621C>T	ENSP00000239449:p.Ala515Val	Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	169	92	0.544379	NM_018934	B4DPE2|Q4FZA4|Q4KN11	Missense_Mutation	SNP	ENST00000239449.4	37	CCDS4256.1	5	0.0022893772893772895	0	0.0	1	0.0027624309392265192	0	0.0	4	0.005277044854881266	-	14.32	2.499118	0.44455	0.001816	0.011395	ENSG00000120327	ENST00000515856;ENST00000239449	T;T	0.01647	4.71;4.71	4.15	4.15	0.48705	Cadherin (5);Cadherin-like (1);	.	.	.	.	T	0.02083	0.0065	L	0.41124	1.26	0.35681	D	0.814049	P	0.45957	0.869	B	0.43838	0.433	T	0.55835	-0.8078	9	0.62326	D	0.03	.	16.4819	0.84160	0.0:1.0:0.0:0.0	.	515	Q9Y5E9	PCDBE_HUMAN	V	362;515	ENSP00000444518:A362V;ENSP00000239449:A515V	ENSP00000239449:A515V	A	+	2	0	PCDHB14	140584805	0.027000	0.19231	0.956000	0.39512	0.165000	0.22458	1.595000	0.36708	2.048000	0.60808	0.556000	0.70494	GCC	C|0.994;T|0.006	0.006	strong		0.677	PCDHB14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251814.2	NM_018934	
SELPLG	6404	hgsc.bcm.edu	37	12	109017672	109017672	+	Missense_Mutation	SNP	G	G	C	rs63748999|rs372173288|rs540144714	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:109017672G>C	ENST00000550948.1	-	2	636	c.412C>G	c.(412-414)Ccc>Gcc	p.P138A	SELPLG_ENST00000228463.6_Missense_Mutation_p.P154A|SELPLG_ENST00000388962.3_Intron			Q14242	SELPL_HUMAN	selectin P ligand	138	12 X 10 AA tandem repeats.		Missing (in short form; not an alternative splicing; dbSNP:rs63748999). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:7505206}.		blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cellular response to interleukin-6 (GO:0071354)|leukocyte adhesive activation (GO:0050902)|leukocyte migration (GO:0050900)|leukocyte tethering or rolling (GO:0050901)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(3)|prostate(3)|skin(1)	12						GCCTCCGTGGGCACTGGTTGA	0.617													C|||	441	0.0880591	0.0272	0.0504	5008	,	,		19574	0.2034		0.0795	False		,,,				2504	0.0869				p.P154A		Atlas-SNP	.											SELPLG_ENST00000550948,NS,carcinoma,0,14	SELPLG	138	14	0			c.C460G						scavenged	.						160.0	124.0	137.0					12																	109017672		2199	4278	6477	SO:0001583	missense	6404	exon2			CCGTGGGCACTGG		CCDS31895.1, CCDS31895.2, CCDS55881.1	12q24	2014-01-30						"""CD molecules"", ""Endogenous ligands"""	10722	protein-coding gene	gene with protein product		600738				7505206	Standard	NM_003006		Approved	PSGL-1, CD162	uc010sxe.2	Q14242		ENST00000550948.1:c.412C>G	12.37:g.109017672G>C	ENSP00000447752:p.Pro138Ala	Somatic	116	3	0.0258621		WXS	Illumina HiSeq	Phase_I	91	36	0.395604	NM_001206609	A8K2Y0|B4DQC3|B7Z5C7|J3KMX6|Q12775|Q6GTW7|Q8N7J7	Missense_Mutation	SNP	ENST00000550948.1	37	CCDS31895.2	.	.	.	.	.	.	.	.	.	.	C	0.375	-0.932076	0.02359	.	.	ENSG00000110876	ENST00000550948;ENST00000228463	T;T	0.27402	1.67;1.67	3.23	-6.47	0.01902	.	.	.	.	.	T	0.07188	0.0182	N	0.02539	-0.55	0.09310	N	0.999999	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.24154	-1.0168	9	0.02654	T	1	-1.189	3.3056	0.06998	0.2007:0.2624:0.3957:0.1411	.	154;138	B7Z5C7;Q14242	.;SELPL_HUMAN	A	138;154	ENSP00000447752:P138A;ENSP00000228463:P154A	ENSP00000228463:P154A	P	-	1	0	SELPLG	107541801	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-3.940000	0.00329	-1.755000	0.01320	-0.339000	0.08088	CCC	.	.	none		0.617	SELPLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403904.1		
ONECUT2	9480	hgsc.bcm.edu	37	18	55103512	55103512	+	Silent	SNP	C	C	T	rs79019704	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:55103512C>T	ENST00000491143.2	+	1	596	c.564C>T	c.(562-564)tcC>tcT	p.S188S	AC090340.1_ENST00000581316.1_RNA	NM_004852.2	NP_004843.2	O95948	ONEC2_HUMAN	one cut homeobox 2	188					cell fate commitment (GO:0045165)|cilium assembly (GO:0042384)|endocrine pancreas development (GO:0031018)|epithelial cell development (GO:0002064)|liver development (GO:0001889)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|organ morphogenesis (GO:0009887)|peripheral nervous system neuron development (GO:0048935)|positive regulation of cell migration (GO:0030335)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell-matrix adhesion (GO:0001952)	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)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|lung(4)|ovary(2)|skin(1)	15		Colorectal(73;0.234)		READ - Rectum adenocarcinoma(59;0.227)|Colorectal(16;0.245)		aGCGCCTGTCCGGCAACGTCA	0.657													C|||	723	0.144369	0.1732	0.1427	5008	,	,		11273	0.1429		0.0646	False		,,,				2504	0.1902				p.S188S		Atlas-SNP	.											ONECUT2,brain,glioma,0,1	ONECUT2	42	1	0			c.C564T						PASS	.	C		541,3827		29,483,1672	25.0	32.0	29.0		564	-0.7	1.0	18	dbSNP_131	29	496,8070		16,464,3803	no	coding-synonymous	ONECUT2	NM_004852.2		45,947,5475	TT,TC,CC		5.7903,12.3855,8.0176		188/505	55103512	1037,11897	2184	4283	6467	SO:0001819	synonymous_variant	9480	exon1			CCTGTCCGGCAAC	Y18198	CCDS42440.1	18q21.31	2012-03-09	2007-07-16		ENSG00000119547	ENSG00000119547		"""Homeoboxes / CUT class"""	8139	protein-coding gene	gene with protein product		604894	"""one cut domain, family member 2"""			9915796	Standard	NM_004852		Approved	OC-2	uc002lgo.3	O95948	OTTHUMG00000159776	ENST00000491143.2:c.564C>T	18.37:g.55103512C>T		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	38	21	0.552632	NM_004852		Silent	SNP	ENST00000491143.2	37	CCDS42440.1																																																																																			C|0.906;T|0.094	0.094	strong		0.657	ONECUT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357264.3		
RRP12	23223	hgsc.bcm.edu	37	10	99126249	99126249	+	Silent	SNP	G	G	A	rs2275581	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:99126249G>A	ENST00000370992.4	-	28	3456	c.3345C>T	c.(3343-3345)gaC>gaT	p.D1115D	RRP12_ENST00000315563.6_Silent_p.D1015D|RRP12_ENST00000479481.1_5'UTR|RRP12_ENST00000536831.1_Silent_p.D833D|RRP12_ENST00000414986.1_Silent_p.D1054D	NM_015179.3	NP_055994.2	Q5JTH9	RRP12_HUMAN	ribosomal RNA processing 12 homolog (S. cerevisiae)	1115						integral component of membrane (GO:0016021)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(5)|large_intestine(2)|lung(13)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	37		Colorectal(252;0.162)		Epithelial(162;2.72e-09)|all cancers(201;1.76e-07)		TGAGGGGCTCGTCCCCACCGC	0.617													G|||	1367	0.272963	0.1815	0.2622	5008	,	,		15986	0.3095		0.2584	False		,,,				2504	0.3814				p.D1115D		Atlas-SNP	.											.	RRP12	97	.	0			c.C3345T						PASS	.	G	,	805,3601	323.7+/-298.2	75,655,1473	110.0	104.0	106.0		3162,3345	-10.4	0.0	10	dbSNP_100	106	2153,6447	368.9+/-335.3	279,1595,2426	no	coding-synonymous,coding-synonymous	RRP12	NM_001145114.1,NM_015179.3	,	354,2250,3899	AA,AG,GG		25.0349,18.2705,22.7433	,	1054/1237,1115/1298	99126249	2958,10048	2203	4300	6503	SO:0001819	synonymous_variant	23223	exon28			GGGCTCGTCCCCA		CCDS7457.1, CCDS44467.1, CCDS60605.1	10q24.2	2006-11-06	2006-11-06	2006-11-06	ENSG00000052749	ENSG00000052749			29100	protein-coding gene	gene with protein product			"""KIAA0690"""	KIAA0690		9734811	Standard	NM_015179		Approved		uc001knf.3	Q5JTH9	OTTHUMG00000018855	ENST00000370992.4:c.3345C>T	10.37:g.99126249G>A		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	73	25	0.342466	NM_015179	B4DK00|E9PCK7|Q5JTH8|Q69YK4|Q96E87|Q9BUH3|Q9Y4C7	Silent	SNP	ENST00000370992.4	37	CCDS7457.1																																																																																			G|0.762;A|0.238	0.238	strong		0.617	RRP12-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049699.4	NM_015179	
KIF21A	55605	hgsc.bcm.edu	37	12	39716675	39716675	+	Nonsense_Mutation	SNP	T	T	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:39716675T>A	ENST00000361418.5	-	27	3481	c.3466A>T	c.(3466-3468)Aga>Tga	p.R1156*	KIF21A_ENST00000541463.2_Nonsense_Mutation_p.R1120*|KIF21A_ENST00000544797.2_Nonsense_Mutation_p.R1136*|KIF21A_ENST00000361961.3_Nonsense_Mutation_p.R1143*|KIF21A_ENST00000547745.1_5'Flank|KIF21A_ENST00000395670.3_Nonsense_Mutation_p.R1156*			Q7Z4S6	KI21A_HUMAN	kinesin family member 21A	1156					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)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|lung(41)|ovary(5)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|urinary_tract(2)	86		Lung NSC(34;0.179)|all_lung(34;0.213)				GTGGTGGTTCTCCTTCGGGCC	0.453																																					p.R1156X		Atlas-SNP	.											.	KIF21A	238	.	0			c.A3466T						PASS	.						136.0	129.0	131.0					12																	39716675		2203	4300	6503	SO:0001587	stop_gained	55605	exon27			TGGTTCTCCTTCG	AK000059	CCDS31773.1, CCDS53774.1, CCDS53775.1, CCDS53776.1	12q12	2013-01-10						"""Kinesins"", ""WD repeat domain containing"""	19349	protein-coding gene	gene with protein product		608283	"""fibrosis of the extraocular muscles, congenital, 1"""	FEOM1		10225949	Standard	NM_017641		Approved	FLJ20052	uc001rly.3	Q7Z4S6	OTTHUMG00000169335	ENST00000361418.5:c.3466A>T	12.37:g.39716675T>A	ENSP00000354878:p.Arg1156*	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	117	28	0.239316	NM_001173464	A8MX28|B0I1R9|B9EGE4|F5H0C3|F5H219|Q2UVF1|Q6UKL9|Q7Z668|Q86WZ5|Q8IVZ8|Q9C0F5|Q9NXU4|Q9Y590	Nonsense_Mutation	SNP	ENST00000361418.5	37	CCDS53776.1	.	.	.	.	.	.	.	.	.	.	T	37	5.997374	0.97184	.	.	ENSG00000139116	ENST00000361961;ENST00000395670;ENST00000341813;ENST00000545778;ENST00000551264;ENST00000544797;ENST00000361418;ENST00000541463	.	.	.	5.36	5.36	0.76844	.	0.000000	0.64402	D	0.000016	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.3659	0.74523	0.0:0.0:0.0:1.0	.	.	.	.	X	1143;1156;1156;203;197;1136;1156;1120	.	ENSP00000344501:R1156X	R	-	1	2	KIF21A	38002942	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.732000	0.62029	2.020000	0.59435	0.528000	0.53228	AGA	.	.	none		0.453	KIF21A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403581.1	NM_017641	
HS3ST6	64711	hgsc.bcm.edu	37	16	1962047	1962047	+	Silent	SNP	G	G	A	rs1657140|rs386787777	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:1962047G>A	ENST00000293937.3	-	2	572	c.573C>T	c.(571-573)taC>taT	p.Y191Y	HS3ST6_ENST00000443547.1_Silent_p.Y160Y|HS3ST6_ENST00000454677.2_Silent_p.Y208Y			Q96QI5	HS3S6_HUMAN	heparan sulfate (glucosamine) 3-O-sulfotransferase 6	191					carbohydrate metabolic process (GO:0005975)|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 1 activity (GO:0008467)			endometrium(2)|lung(2)	4						GCGTCTGGGCGTAGTCGGAGA	0.726													g|||	1961	0.391573	0.2345	0.3386	5008	,	,		13691	0.4643		0.3767	False		,,,				2504	0.5818				p.Y160Y		Atlas-SNP	.											.	HS3ST6	26	.	0			c.C480T						PASS	.	G		983,3403		118,747,1328	17.0	22.0	20.0		480	-7.8	0.3	16	dbSNP_89	20	2967,5625		541,1885,1870	no	coding-synonymous	HS3ST6	NM_001009606.2		659,2632,3198	AA,AG,GG		34.5321,22.4122,30.4361		160/312	1962047	3950,9028	2193	4296	6489	SO:0001819	synonymous_variant	64711	exon2			CTGGGCGTAGTCG			16p13.3	2008-10-30	2003-06-11	2003-06-13	ENSG00000162040	ENSG00000162040		"""Sulfotransferases, membrane-bound"""	14178	protein-coding gene	gene with protein product			"""heparan sulfate (glucosamine) 3-O-sulfotransferase 5"""	HS3ST5		11157797	Standard	NM_001009606		Approved		uc002cnf.3	Q96QI5	OTTHUMG00000047860	ENST00000293937.3:c.573C>T	16.37:g.1962047G>A		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	48	38	0.791667	NM_001009606	Q96RX7	Silent	SNP	ENST00000293937.3	37																																																																																				G|0.664;A|0.336	0.336	strong		0.726	HS3ST6-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001009606	
TRIM26	7726	hgsc.bcm.edu	37	6	30166266	30166266	+	Silent	SNP	C	C	T	rs2523721	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:30166266C>T	ENST00000454678.2	-	5	910	c.474G>A	c.(472-474)agG>agA	p.R158R	TRIM26_ENST00000437089.1_Silent_p.R158R|TRIM26_ENST00000453195.1_Silent_p.R158R|TRIM26_ENST00000487829.1_5'Flank	NM_003449.4	NP_003440.1	Q12899	TRI26_HUMAN	tripartite motif containing 26	158					innate immune response (GO:0045087)|negative regulation of viral entry into host cell (GO:0046597)|negative regulation of viral release from host cell (GO:1902187)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)	cytoplasm (GO:0005737)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|zinc ion binding (GO:0008270)			lung(1)|ovary(2)	3						TGTCTCTGTCCCTCCTTAGGG	0.562													T|||	1153	0.230232	0.4017	0.1585	5008	,	,		20227	0.1081		0.1829	False		,,,				2504	0.2239				p.R158R		Atlas-SNP	.											.	TRIM26	74	.	0			c.G474A						PASS	.	T	,	1011,2011		166,679,666	133.0	141.0	138.0		474,474	2.2	1.0	6	dbSNP_100	138	1083,4335		116,851,1742	yes	coding-synonymous,coding-synonymous	TRIM26	NM_001242783.1,NM_003449.4	,	282,1530,2408	TT,TC,CC		19.9889,33.4547,24.8104	,	158/540,158/540	30166266	2094,6346	1511	2709	4220	SO:0001819	synonymous_variant	7726	exon4			TCTGTCCCTCCTT	AB088090	CCDS4678.1	6p21.3	2013-01-09	2011-01-25	2001-11-23	ENSG00000234127	ENSG00000234127		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	12962	protein-coding gene	gene with protein product		600830	"""tripartite motif-containing 26"""	ZNF173		8530076	Standard	NM_003449		Approved	RNF95	uc003npt.3	Q12899	OTTHUMG00000031041	ENST00000454678.2:c.474G>A	6.37:g.30166266C>T		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	97	45	0.463918	NM_001242783	A6NG96|Q5SRL2	Silent	SNP	ENST00000454678.2	37	CCDS4678.1																																																																																			C|0.765;T|0.235	0.235	strong		0.562	TRIM26-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253442.1	NM_003449	
CNBD2	140894	hgsc.bcm.edu	37	20	34596371	34596371	+	Missense_Mutation	SNP	C	C	T	rs6060750	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:34596371C>T	ENST00000373973.3	+	9	1296	c.1123C>T	c.(1123-1125)Ccc>Tcc	p.P375S	CNBD2_ENST00000349339.1_Missense_Mutation_p.P375S|CNBD2_ENST00000538900.1_Missense_Mutation_p.P375S			Q96M20	CNBD2_HUMAN	cyclic nucleotide binding domain containing 2	375			P -> S (in dbSNP:rs6060750). {ECO:0000269|PubMed:14702039}.														AGACACTCTCCCCAAGATGCT	0.507													C|||	1552	0.309904	0.3359	0.1859	5008	,	,		18022	0.3135		0.2018	False		,,,				2504	0.4703				p.P375S		Atlas-SNP	.											.	.	.	.	0			c.C1123T						PASS	.	C	SER/PRO,SER/PRO	1337,3069	445.9+/-347.8	208,921,1074	53.0	53.0	53.0		1123,1123	4.5	1.0	20	dbSNP_114	53	1737,6863	314.5+/-311.8	168,1401,2731	yes	missense,missense	C20orf152	NM_001207076.1,NM_080834.2	74,74	376,2322,3805	TT,TC,CC		20.1977,30.345,23.6352	probably-damaging,probably-damaging	375/424,375/573	34596371	3074,9932	2203	4300	6503	SO:0001583	missense	140894	exon9			ACTCTCCCCAAGA	AL359828	CCDS13270.1, CCDS56189.1	20q11.23	2012-11-15	2012-11-15	2012-11-15	ENSG00000149646	ENSG00000149646			16145	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 152"", ""cyclic nucleotide (cNMP) binding domain containing 1"""	C20orf152, CNMPD1		11780052	Standard	NM_080834		Approved	dJ954P9.1	uc002xer.1	Q96M20	OTTHUMG00000032371	ENST00000373973.3:c.1123C>T	20.37:g.34596371C>T	ENSP00000363084:p.Pro375Ser	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	60	60	1	NM_080834	Q14C79|Q5JWY7|Q5T3S1|Q9BR36|Q9BWY5	Missense_Mutation	SNP	ENST00000373973.3	37		523	0.23946886446886448	151	0.30691056910569103	80	0.22099447513812154	144	0.2517482517482518	148	0.19525065963060687	C	11.72	1.723698	0.30593	0.30345	0.201977	ENSG00000149646	ENST00000373973;ENST00000349339;ENST00000538900	T;T;T	0.12255	2.75;2.74;2.7	4.5	4.5	0.54988	Cyclic nucleotide-binding-like (1);	0.185586	0.36591	N	0.002515	T	0.00012	0.0000	M	0.67953	2.075	0.29895	P	0.824906	B;B	0.33637	0.15;0.42	B;B	0.28465	0.027;0.09	T	0.45906	-0.9229	9	0.25751	T	0.34	-12.0748	13.0094	0.58724	0.0:1.0:0.0:0.0	rs6060750;rs6579272;rs52810685;rs60984638;rs6060750	375;375	Q96M20;Q96M20-2	CT152_HUMAN;.	S	375	ENSP00000363084:P375S;ENSP00000340954:P375S;ENSP00000442729:P375S	ENSP00000340954:P375S	P	+	1	0	C20orf152	34059785	0.810000	0.29049	0.968000	0.41197	0.010000	0.07245	2.944000	0.49034	2.797000	0.96272	0.561000	0.74099	CCC	C|0.746;T|0.254	0.254	strong		0.507	CNBD2-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000078960.2	NM_080834	
UBQLN1	29979	hgsc.bcm.edu	37	9	86284178	86284178	+	Silent	SNP	C	C	A	rs1044175	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:86284178C>A	ENST00000376395.4	-	7	1693	c.1170G>T	c.(1168-1170)ctG>ctT	p.L390L	UBQLN1_ENST00000257468.7_Silent_p.L390L	NM_013438.4|NM_053067.2	NP_038466.2|NP_444295.1	Q9UMX0	UBQL1_HUMAN	ubiquilin 1	390					cellular response to hypoxia (GO:0071456)|regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902175)|regulation of protein ubiquitination (GO:0031396)|response to endoplasmic reticulum stress (GO:0034976)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|proteasome complex (GO:0000502)|protein complex (GO:0043234)	kinase binding (GO:0019900)			breast(4)|endometrium(2)|kidney(4)|large_intestine(6)|lung(10)|prostate(1)	27						TGTTTTGCATCAGTTGTGGGT	0.393													A|||	3851	0.76897	0.857	0.7104	5008	,	,		18442	0.8819		0.6203	False		,,,				2504	0.728				p.L390L	Melanoma(186;1284 2073 12755 14558 18426)	Atlas-SNP	.											UBQLN1,colon,carcinoma,0,1	UBQLN1	49	1	0			c.G1170T						PASS	.	A	,	3672,734	300.7+/-286.5	1535,602,66	144.0	127.0	133.0		1170,1170	2.0	1.0	9	dbSNP_86	133	5389,3211	484.9+/-371.5	1691,2007,602	no	coding-synonymous,coding-synonymous	UBQLN1	NM_013438.4,NM_053067.2	,	3226,2609,668	AA,AC,CC		37.3372,16.6591,30.3322	,	390/590,390/562	86284178	9061,3945	2203	4300	6503	SO:0001819	synonymous_variant	29979	exon7			TTGCATCAGTTGT	AF176069	CCDS6663.1, CCDS6664.1	9q22	2013-02-12			ENSG00000135018	ENSG00000135018		"""Ubiquilin family"""	12508	protein-coding gene	gene with protein product		605046				9303440, 10807547	Standard	NM_013438		Approved	DSK2, PLIC-1, XDRP1, DA41	uc004amv.3	Q9UMX0	OTTHUMG00000020104	ENST00000376395.4:c.1170G>T	9.37:g.86284178C>A		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	114	58	0.508772	NM_053067	Q5T6J5|Q5T6J9|Q8IXS9|Q8N2Q3|Q9H0T8|Q9H3R4|Q9HAZ5	Silent	SNP	ENST00000376395.4	37	CCDS6663.1	1637	0.7495421245421245	410	0.8333333333333334	263	0.7265193370165746	498	0.8706293706293706	466	0.6147757255936676	A	9.680	1.148963	0.21288	0.833409	0.626628	ENSG00000135018	ENST00000526134	.	.	.	5.72	1.98	0.26296	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	0.9999999999999999	.	.	.	.	.	.	.	.	.	.	.	.	.	.	5.881	0.18856	0.4008:0.3742:0.225:0.0	rs1044175;rs17323305;rs1044175	.	.	.	L	10	.	.	X	-	2	2	UBQLN1	85473998	1.000000	0.71417	0.997000	0.53966	0.987000	0.75469	0.900000	0.28431	-0.141000	0.11374	-0.256000	0.11100	TGA	C|0.276;A|0.724	0.724	strong		0.393	UBQLN1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000052834.1	NM_013438	
VWA5B1	127731	hgsc.bcm.edu	37	1	20645086	20645086	+	Missense_Mutation	SNP	T	T	A	rs35480773	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:20645086T>A	ENST00000375079.2	+	6	909	c.713T>A	c.(712-714)gTg>gAg	p.V238E	VWA5B1_ENST00000289825.4_5'UTR|VWA5B1_ENST00000375083.4_Missense_Mutation_p.V238E|VWA5B1_ENST00000289815.8_Missense_Mutation_p.V238E|RP4-745E8.2_ENST00000444923.1_RNA	NM_001039500.2	NP_001034589.2	Q5TIE3	VW5B1_HUMAN	von Willebrand factor A domain containing 5B1	238						extracellular region (GO:0005576)				central_nervous_system(1)|endometrium(3)|kidney(1)|prostate(1)|skin(1)	7						CACTCAGGGGTGGAGAGTCCC	0.592													T|||	96	0.0191693	0.0038	0.036	5008	,	,		18412	0.001		0.0487	False		,,,				2504	0.0164				p.V238E		Atlas-SNP	.											.	VWA5B1	44	.	0			c.T713A						PASS	.	T	GLU/VAL	15,1369		0,15,677	67.0	66.0	67.0		713	5.5	1.0	1	dbSNP_126	67	176,3006		6,164,1421	yes	missense	VWA5B1	NM_001039500.2	121	6,179,2098	AA,AT,TT		5.5311,1.0838,4.1831	probably-damaging	238/1216	20645086	191,4375	692	1591	2283	SO:0001583	missense	127731	exon6			CAGGGGTGGAGAG	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.713T>A	1.37:g.20645086T>A	ENSP00000364220:p.Val238Glu	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	43	24	0.55814	NM_001039500	A4IF35|A4IF36|Q3ZCM4|Q6ZUB4|Q96M71	Missense_Mutation	SNP	ENST00000375079.2	37		57	0.0260989010989011	1	0.0020325203252032522	17	0.04696132596685083	0	0.0	39	0.051451187335092345	T	23.0	4.366209	0.82463	0.010838	0.055311	ENSG00000158816	ENST00000375089;ENST00000289815;ENST00000375083;ENST00000375079	T;T;T	0.08984	3.32;3.03;3.3	5.54	5.54	0.83059	.	0.000000	0.85682	D	0.000000	T	0.03434	0.0099	M	0.73962	2.25	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.997;0.999	T	0.00029	-1.2293	10	0.62326	D	0.03	-16.4276	14.5046	0.67743	0.0:0.0:0.0:1.0	rs35480773;rs61742671	238;238	Q5TIE3;Q5TIE3-2	VW5B1_HUMAN;.	E	238	ENSP00000289815:V238E;ENSP00000364224:V238E;ENSP00000364220:V238E	ENSP00000289815:V238E	V	+	2	0	VWA5B1	20517673	1.000000	0.71417	1.000000	0.80357	0.707000	0.40811	7.459000	0.80802	2.107000	0.64212	0.377000	0.23210	GTG	T|0.963;A|0.037	0.037	strong		0.592	VWA5B1-001	NOVEL	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000007945.4	XM_001722222	
CCSER1	401145	hgsc.bcm.edu	37	4	92519814	92519814	+	Missense_Mutation	SNP	C	C	T	rs370719096		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:92519814C>T	ENST00000509176.1	+	11	2597	c.2309C>T	c.(2308-2310)tCg>tTg	p.S770L	CCSER1_ENST00000333691.8_Missense_Mutation_p.S770L	NM_001145065.1	NP_001138537.1	Q9C0I3	CCSE1_HUMAN	coiled-coil serine-rich protein 1	770																	TTTAGGTATTCGGCAGCGGAC	0.443																																					p.S770L		Atlas-SNP	.											.	.	.	.	0			c.C2309T						PASS	.						58.0	51.0	53.0					4																	92519814		692	1591	2283	SO:0001583	missense	401145	exon11			GGTATTCGGCAGC		CCDS47099.1, CCDS47100.1	4q22.1	2012-12-03	2012-12-03	2012-12-03	ENSG00000184305	ENSG00000184305			29349	protein-coding gene	gene with protein product			"""family with sequence similarity 190, member A"""	FAM190A		11214970	Standard	NM_001145065		Approved	KIAA1680	uc003hsv.4	Q9C0I3	OTTHUMG00000160950	ENST00000509176.1:c.2309C>T	4.37:g.92519814C>T	ENSP00000425040:p.Ser770Leu	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	74	21	0.283784	NM_001145065	Q4W5M0|Q86V57	Missense_Mutation	SNP	ENST00000509176.1	37	CCDS47099.1	.	.	.	.	.	.	.	.	.	.	C	14.08	2.429555	0.43122	.	.	ENSG00000184305	ENST00000509176;ENST00000333691	T;T	0.35973	1.28;1.28	5.77	4.93	0.64822	.	.	.	.	.	T	0.25494	0.0620	N	0.14661	0.345	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.22417	-1.0217	9	0.72032	D	0.01	-2.0E-4	13.2923	0.60278	0.0:0.9256:0.0:0.0744	.	770	Q9C0I3	F190A_HUMAN	L	770	ENSP00000425040:S770L;ENSP00000329482:S770L	ENSP00000329482:S770L	S	+	2	0	FAM190A	92738837	0.154000	0.22792	0.003000	0.11579	0.009000	0.06853	5.253000	0.65452	1.584000	0.49913	-0.157000	0.13467	TCG	.	.	weak		0.443	CCSER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363109.3	NM_001145065	
SFI1	9814	hgsc.bcm.edu	37	22	31998612	31998612	+	Missense_Mutation	SNP	G	G	A	rs2006771	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:31998612G>A	ENST00000400288.2	+	17	1751	c.1646G>A	c.(1645-1647)cGa>cAa	p.R549Q	SFI1_ENST00000432498.1_Missense_Mutation_p.R518Q|SFI1_ENST00000414585.1_Missense_Mutation_p.R396Q|SFI1_ENST00000443011.1_Missense_Mutation_p.R396Q|SFI1_ENST00000540643.1_Missense_Mutation_p.R494Q|SFI1_ENST00000400289.1_Missense_Mutation_p.R467Q|SFI1_ENST00000443326.1_Missense_Mutation_p.R467Q	NM_001007467.2	NP_001007468.1	A8K8P3	SFI1_HUMAN	Sfi1 homolog, spindle assembly associated (yeast)	549			R -> Q (in dbSNP:rs2006771). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|negative regulation of phosphatase activity (GO:0010923)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)	phosphatase binding (GO:0019902)			NS(2)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|large_intestine(7)|liver(1)|lung(11)|ovary(1)|prostate(3)|upper_aerodigestive_tract(3)	38						CACGCAGAGCGACAGCTTCTG	0.557													G|||	1762	0.351837	0.4138	0.3847	5008	,	,		21320	0.12		0.4612	False		,,,				2504	0.3712				p.R549Q		Atlas-SNP	.											.	SFI1	78	.	0			c.G1646A						PASS	.	G	GLN/ARG,GLN/ARG	1797,2479		413,971,754	85.0	93.0	91.0		1646,1553	-3.7	0.4	22	dbSNP_92	91	3934,4548		920,2094,1227	yes	missense,missense	SFI1	NM_001007467.1,NM_014775.2	43,43	1333,3065,1981	AA,AG,GG		46.3806,42.0253,44.9208	benign,benign	549/1243,518/1212	31998612	5731,7027	2138	4241	6379	SO:0001583	missense	9814	exon17			CAGAGCGACAGCT	AB011114	CCDS43004.1, CCDS43005.1, CCDS58803.1, CCDS58804.1	22q12.2	2014-06-13			ENSG00000198089	ENSG00000198089			29064	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 139"""	612765				14504268	Standard	NM_001007467		Approved	KIAA0542, PISD, PPP1R139	uc003ale.4	A8K8P3	OTTHUMG00000030249	ENST00000400288.2:c.1646G>A	22.37:g.31998612G>A	ENSP00000383145:p.Arg549Gln	Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	128	64	0.5	NM_001007467	A1L373|A1L387|A2A2L2|B1AKL9|B5MDB7|B7Z1V6|B7Z8G3|B7ZBE2|B7ZBE3|O60289|Q2TAN8|Q5W1B5|Q86TK0|Q8N4U8|Q8N8C1|Q8WU14	Missense_Mutation	SNP	ENST00000400288.2	37	CCDS43004.1	764	0.3498168498168498	200	0.4065040650406504	153	0.42265193370165743	70	0.12237762237762238	341	0.449868073878628	G	10.70	1.424511	0.25639	0.420253	0.463806	ENSG00000198089	ENST00000432498;ENST00000540643;ENST00000443326;ENST00000421060;ENST00000414585;ENST00000443011;ENST00000400289;ENST00000400288;ENST00000417682	T;T;T;T;T;T;T;T	0.28895	1.59;1.59;1.59;1.59;1.59;1.59;1.59;1.59	5.82	-3.74	0.04385	.	0.885835	0.10024	N	0.725566	T	0.00012	0.0000	N	0.08118	0	0.51482	P	7.199999999996098E-5	B;B;B;B;B;P	0.40931	0.023;0.115;0.41;0.138;0.236;0.733	B;B;B;B;B;B	0.30572	0.011;0.031;0.053;0.011;0.047;0.117	T	0.41179	-0.9523	9	0.11485	T	0.65	.	11.6767	0.51434	0.7757:0.0:0.2243:0.0	rs2006771;rs52793824;rs61276509;rs2006771	494;467;467;518;549;525	A8K8P3-9;A8K8P3-10;A8K8P3-3;A8K8P3-2;A8K8P3;A8K8P3-5	.;.;.;.;SFI1_HUMAN;.	Q	518;494;467;525;396;396;467;549;164	ENSP00000402679:R518Q;ENSP00000443025:R494Q;ENSP00000416469:R467Q;ENSP00000397148:R396Q;ENSP00000401199:R396Q;ENSP00000383146:R467Q;ENSP00000383145:R549Q;ENSP00000398871:R164Q	ENSP00000383145:R549Q	R	+	2	0	SFI1	30328612	0.018000	0.18449	0.428000	0.26697	0.574000	0.36063	-0.421000	0.07053	-0.393000	0.07739	0.561000	0.74099	CGA	G|0.614;A|0.386	0.386	strong		0.557	SFI1-023	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337180.3	NM_014775	
MEIOB	254528	hgsc.bcm.edu	37	16	1894912	1894912	+	Silent	SNP	C	C	T	rs9806826	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:1894912C>T	ENST00000397344.3	-	10	1025	c.831G>A	c.(829-831)acG>acA	p.T277T	MEIOB_ENST00000452149.2_Silent_p.T277T|LA16c-429E7.1_ENST00000570247.1_RNA|MEIOB_ENST00000470044.1_Silent_p.T70T|MEIOB_ENST00000412554.2_Silent_p.T277T|MEIOB_ENST00000325962.3_Silent_p.T277T	NM_152764.2	NP_689977.2	Q8N635	MEIOB_HUMAN	meiosis specific with OB domains	277					double-strand break repair via homologous recombination (GO:0000724)|female meiosis I (GO:0007144)|fertilization (GO:0009566)|male meiosis (GO:0007140)|male meiosis I (GO:0007141)|resolution of meiotic recombination intermediates (GO:0000712)|synapsis (GO:0007129)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|single-stranded DNA 3'-5' exodeoxyribonuclease activity (GO:0008310)|single-stranded DNA binding (GO:0003697)										CCAGAACATTCGTTTCTTTAT	0.279													T|||	1854	0.370208	0.3548	0.3242	5008	,	,		17509	0.4246		0.3141	False		,,,				2504	0.4254				p.T277T		Atlas-SNP	.											C16orf73_ENST00000412554,NS,carcinoma,-1,2	.	.	2	0			c.G831A						PASS	.	T	,	1467,2921	665.6+/-401.6	242,983,969	50.0	51.0	50.0		831,831	0.8	0.0	16	dbSNP_119	50	2459,6107	685.3+/-404.0	374,1711,2198	no	coding-synonymous,coding-synonymous	C16orf73	NM_001163560.2,NM_152764.2	,	616,2694,3167	TT,TC,CC		28.7065,33.4321,30.3072	,	277/472,277/443	1894912	3926,9028	2194	4283	6477	SO:0001819	synonymous_variant	254528	exon10			AACATTCGTTTCT	BC029829	CCDS10449.2, CCDS53983.1	16p13.3	2012-08-13	2012-08-13	2012-08-13	ENSG00000162039	ENSG00000162039			28569	protein-coding gene	gene with protein product			"""chromosome 16 open reading frame 73"""	C16orf73		12477932	Standard	NM_152764		Approved	MGC35212	uc010uvq.1	Q8N635	OTTHUMG00000128683	ENST00000397344.3:c.831G>A	16.37:g.1894912C>T		Somatic	284	1	0.00352113		WXS	Illumina HiSeq	Phase_I	190	131	0.689474	NM_001163560	B1AK39|C9J0S1|Q96RY0	Silent	SNP	ENST00000397344.3	37	CCDS10449.2																																																																																			C|0.681;T|0.319	0.319	strong		0.279	MEIOB-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250580.1	NM_152764	
ANO2	57101	hgsc.bcm.edu	37	12	5841733	5841733	+	Missense_Mutation	SNP	A	A	C	rs1860961	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:5841733A>C	ENST00000356134.5	-	16	1572	c.1501T>G	c.(1501-1503)Tct>Gct	p.S501A	ANO2_ENST00000546188.1_Missense_Mutation_p.S501A|ANO2_ENST00000327087.8_Missense_Mutation_p.S500A|ANO2_ENST00000538154.1_5'UTR	NM_001278596.1	NP_001265525.1	Q9NQ90	ANO2_HUMAN	anoctamin 2, calcium activated chloride channel	505					chloride transmembrane transport (GO:1902476)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	chloride channel complex (GO:0034707)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	intracellular calcium activated chloride channel activity (GO:0005229)	p.S501A(1)		central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(11)|lung(23)|ovary(4)|pancreas(1)|prostate(1)|skin(5)|stomach(3)|upper_aerodigestive_tract(1)	58						TGGACAGCAGACTGGTTGCTC	0.453													A|||	686	0.136981	0.2383	0.1311	5008	,	,		22847	0.1161		0.0746	False		,,,				2504	0.09				p.S500A		Atlas-SNP	.											ANO2,NS,carcinoma,0,1	ANO2	309	1	1	Substitution - Missense(1)	stomach(1)	c.T1498G						PASS	.	A	ALA/SER	872,3206		96,680,1263	128.0	124.0	125.0		1498	3.7	1.0	12	dbSNP_92	125	678,7696		35,608,3544	yes	missense	ANO2	NM_020373.2	99	131,1288,4807	CC,CA,AA		8.0965,21.383,12.4478	benign	500/999	5841733	1550,10902	2039	4187	6226	SO:0001583	missense	57101	exon15			CAGCAGACTGGTT	AJ272204	CCDS44807.1, CCDS44807.2	12p13.3	2014-04-09	2014-04-09	2008-08-28		ENSG00000047617		"""Ion channels / Chloride channels : Calcium activated : Anoctamins"""	1183	protein-coding gene	gene with protein product	"""transmembrane protein 16B (eight membrane-spanning domains)"""	610109	"""chromosome 12 open reading frame 3"", ""transmembrane protein 16B"", ""anoctamin 2"""	C12orf3, TMEM16B		12739008, 15067359, 24692353	Standard	NM_001278596		Approved		uc001qnm.2	Q9NQ90		ENST00000356134.5:c.1501T>G	12.37:g.5841733A>C	ENSP00000348453:p.Ser501Ala	Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	152	67	0.440789	NM_020373	C4N787|Q9H847	Missense_Mutation	SNP	ENST00000356134.5	37		270	0.12362637362637363	118	0.23983739837398374	35	0.09668508287292818	71	0.12412587412587413	46	0.06068601583113457	A	8.258	0.810552	0.16537	0.21383	0.080965	ENSG00000047617	ENST00000327087;ENST00000356134;ENST00000546188;ENST00000541277;ENST00000545860	T;T;T;T	0.65549	-0.16;-0.16;-0.16;0.68	4.84	3.66	0.41972	.	0.660666	0.15622	N	0.252809	T	0.00012	0.0000	N	0.04508	-0.205	0.48975	P	2.6199999999998447E-4	B	0.18741	0.03	B	0.15052	0.012	T	0.11203	-1.0597	9	0.09590	T	0.72	.	7.3722	0.26808	0.8984:0.0:0.1016:0.0	rs1860961;rs57832099;rs1860961	500	Q9NQ90-3	.	A	500;501;501;505;60	ENSP00000314048:S500A;ENSP00000348453:S501A;ENSP00000440981:S501A;ENSP00000443813:S60A	ENSP00000314048:S500A	S	-	1	0	ANO2	5711994	0.999000	0.42202	0.984000	0.44739	0.589000	0.36550	1.064000	0.30579	2.027000	0.59764	0.533000	0.62120	TCT	A|0.870;C|0.130	0.130	strong		0.453	ANO2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000399019.4	NM_020373	
KRTAP10-6	386674	hgsc.bcm.edu	37	21	46011718	46011718	+	Silent	SNP	T	T	C	rs587693578	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	227	2	0.00881057		WXS	Illumina HiSeq	Phase_I	246	17	0.0691057	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	
FMNL2	114793	hgsc.bcm.edu	37	2	153468107	153468107	+	Silent	SNP	C	C	T	rs35776654	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:153468107C>T	ENST00000288670.9	+	11	1417	c.1050C>T	c.(1048-1050)gaC>gaT	p.D350D		NM_052905.3	NP_443137.2	Q96PY5	FMNL2_HUMAN	formin-like 2	350	GBD/FH3. {ECO:0000255|PROSITE- ProRule:PRU00579}.				cortical actin cytoskeleton organization (GO:0030866)|cytoskeleton organization (GO:0007010)|regulation of cell morphogenesis (GO:0022604)	cytoplasm (GO:0005737)		p.D350D(1)		central_nervous_system(2)|endometrium(3)|large_intestine(5)|liver(2)|lung(3)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	23						TAGGCCTGGACGAATACTTGG	0.393													C|||	260	0.0519169	0.0053	0.0576	5008	,	,		18613	0.0069		0.1392	False		,,,				2504	0.0675				p.D350D		Atlas-SNP	.											FMNL2,NS,carcinoma,0,1	FMNL2	75	1	1	Substitution - coding silent(1)	prostate(1)	c.C1050T						PASS	.	C		86,3704		0,86,1809	86.0	76.0	79.0		1050	-0.6	1.0	2	dbSNP_126	79	1167,7075		91,985,3045	no	coding-synonymous	FMNL2	NM_052905.3		91,1071,4854	TT,TC,CC		14.1592,2.2691,10.4139		350/1093	153468107	1253,10779	1895	4121	6016	SO:0001819	synonymous_variant	114793	exon11			CCTGGACGAATAC	AB067489	CCDS46429.1	2q23.3	2008-02-05	2003-12-02	2003-12-03	ENSG00000157827	ENSG00000157827			18267	protein-coding gene	gene with protein product			"""formin homology 2 domain containing 2"""	FHOD2			Standard	XM_005246263		Approved	KIAA1902	uc002tye.3	Q96PY5	OTTHUMG00000154035	ENST00000288670.9:c.1050C>T	2.37:g.153468107C>T		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	62	29	0.467742	NM_052905	B2RZH5|Q14CC9|Q4ZG52|Q8N3E0	Silent	SNP	ENST00000288670.9	37	CCDS46429.1																																																																																			C|0.918;T|0.082	0.082	strong		0.393	FMNL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333582.2	NM_052905	
ZNF608	57507	hgsc.bcm.edu	37	5	123984763	123984763	+	Silent	SNP	C	C	T	rs7708070	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:123984763C>T	ENST00000306315.5	-	4	1749	c.1314G>A	c.(1312-1314)gcG>gcA	p.A438A	ZNF608_ENST00000504926.1_Silent_p.A11A	NM_020747.2	NP_065798.2	Q9ULD9	ZN608_HUMAN	zinc finger protein 608	438							metal ion binding (GO:0046872)			breast(4)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(8)|lung(12)|ovary(3)|skin(6)|urinary_tract(1)	46		all_cancers(142;0.186)|Prostate(80;0.081)	KIRC - Kidney renal clear cell carcinoma(527;0.159)|Kidney(363;0.221)	OV - Ovarian serous cystadenocarcinoma(64;0.00126)|Epithelial(69;0.00238)|all cancers(49;0.00783)		CAGCAGACCTCGCTCTCTTCC	0.592													T|||	3812	0.761182	0.885	0.5951	5008	,	,		16392	0.7609		0.7505	False		,,,				2504	0.7229				p.A438A		Atlas-SNP	.											.	ZNF608	117	.	0			c.G1314A						PASS	.	T		3820,584		1666,488,48	31.0	34.0	33.0		1314	-10.5	0.1	5	dbSNP_116	33	6393,2197		2403,1587,305	yes	coding-synonymous	ZNF608	NM_020747.2		4069,2075,353	TT,TC,CC		25.5763,13.2607,21.4022		438/1513	123984763	10213,2781	2202	4295	6497	SO:0001819	synonymous_variant	57507	exon4			AGACCTCGCTCTC	AB033107	CCDS34219.1	5q23.2	2008-05-02			ENSG00000168916	ENSG00000168916		"""Zinc fingers, C2H2-type"""	29238	protein-coding gene	gene with protein product						10574462, 10508479	Standard	NM_020747		Approved	KIAA1281, DKFZp434M098, NY-REN-36	uc003ktq.1	Q9ULD9	OTTHUMG00000162999	ENST00000306315.5:c.1314G>A	5.37:g.123984763C>T		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	95	94	0.989474	NM_020747	A7E2W9|Q3SYM6|Q68D12|Q8IY05|Q9Y5A1	Silent	SNP	ENST00000306315.5	37	CCDS34219.1																																																																																			C|0.228;T|0.772	0.772	strong		0.592	ZNF608-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371300.1	XM_114432	
DHX38	9785	hgsc.bcm.edu	37	16	72137561	72137561	+	Silent	SNP	G	G	A	rs2240243	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	111	0	0		WXS	Illumina HiSeq	Phase_I	156	62	0.397436	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	
KRAS	3845	hgsc.bcm.edu	37	12	25362777	25362777	+	3'UTR	SNP	A	A	G	rs1137282	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:25362777A>G	ENST00000256078.4	-	0	706				KRAS_ENST00000311936.3_Silent_p.D173D|KRAS_ENST00000557334.1_Silent_p.D60D	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog						actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to glucocorticoid (GO:0051384)|response to mineralocorticoid (GO:0051385)|small GTPase mediated signal transduction (GO:0007264)|social behavior (GO:0035176)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	focal adhesion (GO:0005925)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GMP binding (GO:0019002)|GTP binding (GO:0005525)|protein complex binding (GO:0032403)		UBE2L3/KRAS(2)	NS(6)|adrenal_gland(1)|autonomic_ganglia(3)|biliary_tract(532)|bone(2)|breast(32)|central_nervous_system(14)|cervix(50)|endometrium(411)|eye(4)|gastrointestinal_tract_(site_indeterminate)(7)|genital_tract(1)|haematopoietic_and_lymphoid_tissue(385)|kidney(8)|large_intestine(15267)|liver(29)|lung(3407)|oesophagus(16)|ovary(612)|pancreas(3739)|penis(1)|peritoneum(6)|prostate(96)|salivary_gland(6)|skin(45)|small_intestine(68)|soft_tissue(88)|stomach(207)|testis(17)|thymus(5)|thyroid(159)|upper_aerodigestive_tract(68)|urinary_tract(57)	25349	all_cancers(2;1e-35)|all_epithelial(2;1.97e-38)|all_lung(3;2.1e-23)|Lung NSC(3;1.16e-22)|Acute lymphoblastic leukemia(6;0.00231)|all_hematologic(7;0.00259)|Melanoma(3;0.0301)|Colorectal(261;0.11)|Ovarian(17;0.12)		OV - Ovarian serous cystadenocarcinoma(3;1.23e-21)|Epithelial(3;1.31e-20)|all cancers(3;5.45e-18)|STAD - Stomach adenocarcinoma(2;2.68e-05)			TCTTTTTACCATCTTTGCTCA	0.279		119	Mis		"""pancreatic, colorectal, lung, thyroid, AML, others"""				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)			A|||	879	0.175519	0.18	0.1931	5008	,	,		18305	0.0923		0.2187	False		,,,				2504	0.1984				p.D173D	Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)	Atlas-SNP	.		Dom	yes		12	12p12.1	3845	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog		"""L, E, M, O"""	.	KRAS	30930	.	0			c.T519C						PASS	.	A	,	753,3647	305.5+/-289.0	61,631,1508	68.0	64.0	65.0		519,	3.4	1.0	12	dbSNP_86	65	1853,6727	328.5+/-318.3	168,1517,2605	no	coding-synonymous,utr-3	KRAS	NM_004985.3,NM_033360.2	,	229,2148,4113	GG,GA,AA		21.5967,17.1136,20.077	,	173/189,	25362777	2606,10374	2200	4290	6490	SO:0001624	3_prime_UTR_variant	3845	exon5	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS	TTTACCATCTTTG	BC010502	CCDS8702.1, CCDS8703.1	12p12.1	2014-09-17	2013-07-08	2005-01-24	ENSG00000133703	ENSG00000133703			6407	protein-coding gene	gene with protein product		190070	"""v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog"", ""v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog"""	KRAS2			Standard	NM_004985		Approved	KRAS1	uc001rgp.1	P01116		ENST00000256078.4:c.*73T>C	12.37:g.25362777A>G		Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	127	126	0.992126	NM_004985	A8K8Z5|B0LPF9|P01118|Q96D10	Silent	SNP	ENST00000256078.4	37	CCDS8703.1																																																																																			T|0.136;G|0.154;C|0.028;A|0.682	0.154	strong		0.279	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	NM_033360	
CLUAP1	23059	hgsc.bcm.edu	37	16	3558381	3558381	+	Silent	SNP	T	T	C	rs11554091	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:3558381T>C	ENST00000576634.1	+	4	456	c.312T>C	c.(310-312)ctT>ctC	p.L104L	CLUAP1_ENST00000572600.1_5'Flank|CLUAP1_ENST00000341633.5_Silent_p.L104L|LA16c-306E5.3_ENST00000574423.2_RNA|CLUAP1_ENST00000417763.2_5'UTR|CLUAP1_ENST00000571025.1_Silent_p.L104L	NM_015041.2	NP_055856.1	Q96AJ1	CLUA1_HUMAN	clusterin associated protein 1	104					cilium assembly (GO:0042384)	centrosome (GO:0005813)|cilium (GO:0005929)|intracellular membrane-bounded organelle (GO:0043231)|intraciliary transport particle B (GO:0030992)|nucleus (GO:0005634)				breast(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(1)|ovary(1)|pancreas(1)|urinary_tract(2)	16						CATCTGTCCTTTATAATGCTA	0.408													T|||	284	0.0567093	0.0287	0.0519	5008	,	,		20476	0.1488		0.0089	False		,,,				2504	0.0521				p.L104L		Atlas-SNP	.											.	CLUAP1	32	.	0			c.T312C						PASS	.	T		87,4307	73.6+/-111.7	1,85,2111	135.0	120.0	125.0		312	1.2	1.0	16	dbSNP_120	125	36,8564	24.6+/-71.5	0,36,4264	no	coding-synonymous	CLUAP1	NM_015041.1		1,121,6375	CC,CT,TT		0.4186,1.98,0.9466		104/414	3558381	123,12871	2197	4300	6497	SO:0001819	synonymous_variant	23059	exon4			TGTCCTTTATAAT	BC017070	CCDS32381.1, CCDS45398.1	16p13.3	2014-07-18				ENSG00000103351		"""Intraflagellar transport homologs"""	19009	protein-coding gene	gene with protein product	"""flagellar associated protein 22, qilin-like protein, homolog (Chlamydomonas)"", ""cilia and flagella associated protein 22"""					15480429, 9734811, 19253336	Standard	NM_015041		Approved	FLJ13297, KIAA0643, FAP22, CFAP22	uc002cvk.2	Q96AJ1		ENST00000576634.1:c.312T>C	16.37:g.3558381T>C		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	83	66	0.795181	NM_015041	O75138|Q65ZA3|Q9H8R4|Q9H8T1	Silent	SNP	ENST00000576634.1	37	CCDS32381.1																																																																																			T|0.974;C|0.026	0.026	strong		0.408	CLUAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437883.2	NM_024793	
TROAP	10024	hgsc.bcm.edu	37	12	49721015	49721015	+	Missense_Mutation	SNP	C	C	T	rs78961476	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:49721015C>T	ENST00000257909.3	+	8	869	c.793C>T	c.(793-795)Cgc>Tgc	p.R265C	TROAP_ENST00000547923.1_5'UTR|RP11-161H23.9_ENST00000553259.1_RNA|TROAP_ENST00000551245.1_Missense_Mutation_p.R265C	NM_005480.3	NP_005471.3	Q12815	TROAP_HUMAN	trophinin associated protein	265					cell adhesion (GO:0007155)	cytoplasm (GO:0005737)				breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(14)|ovary(1)|prostate(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(4)	32						TAAAGGAGAACGCGAGGTTGT	0.473													C|||	102	0.0203674	0.0182	0.013	5008	,	,		21420	0.0139		0.0209	False		,,,				2504	0.0348				p.R265C		Atlas-SNP	.											.	TROAP	80	.	0			c.C793T						PASS	.	C	CYS/ARG	111,4295	85.3+/-124.0	1,109,2093	132.0	118.0	122.0		793	3.3	0.3	12	dbSNP_132	122	125,8475	65.3+/-127.6	0,125,4175	yes	missense	TROAP	NM_005480.3	180	1,234,6268	TT,TC,CC		1.4535,2.5193,1.8145	possibly-damaging	265/779	49721015	236,12770	2203	4300	6503	SO:0001583	missense	10024	exon8			GGAGAACGCGAGG	U04810	CCDS8784.1, CCDS41779.1, CCDS61117.1	12q13.12	2012-10-17	2012-10-17		ENSG00000135451	ENSG00000135451			12327	protein-coding gene	gene with protein product	"""tastin"""	603872				7758945	Standard	NM_005480		Approved	TASTIN	uc001rtx.4	Q12815	OTTHUMG00000169486	ENST00000257909.3:c.793C>T	12.37:g.49721015C>T	ENSP00000257909:p.Arg265Cys	Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	122	70	0.57377	NM_005480	F8VSF9|Q6PJU7|Q8N5B2	Missense_Mutation	SNP	ENST00000257909.3	37	CCDS8784.1	39	0.017857142857142856	6	0.012195121951219513	5	0.013812154696132596	13	0.022727272727272728	15	0.01978891820580475	C	13.82	2.351374	0.41700	0.025193	0.014535	ENSG00000135451	ENST00000551245;ENST00000550346;ENST00000257909;ENST00000547807	.	.	.	5.13	3.3	0.37823	.	0.845097	0.10278	N	0.693906	T	0.11537	0.0281	N	0.08118	0	0.33170	D	0.548185	B;B	0.32653	0.379;0.379	B;B	0.35510	0.204;0.172	T	0.30563	-0.9974	9	0.59425	D	0.04	0.4861	8.4833	0.33057	0.0:0.8165:0.0:0.1835	.	265;265	F8W130;Q12815	.;TROAP_HUMAN	C	265;148;265;259	.	ENSP00000257909:R265C	R	+	1	0	TROAP	48007282	0.169000	0.23002	0.293000	0.24932	0.934000	0.57294	1.209000	0.32357	0.826000	0.34661	0.655000	0.94253	CGC	C|0.981;T|0.019	0.019	strong		0.473	TROAP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000404300.1	NM_005480	
TSSK2	23617	hgsc.bcm.edu	37	22	19119938	19119938	+	Silent	SNP	G	G	A	rs1052773	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	39	0	0		WXS	Illumina HiSeq	Phase_I	33	20	0.606061	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		
PBRM1	55193	hgsc.bcm.edu	37	3	52661351	52661351	+	Silent	SNP	G	G	A	rs147488144	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:52661351G>A	ENST00000296302.7	-	13	1480	c.1479C>T	c.(1477-1479)atC>atT	p.I493I	PBRM1_ENST00000409114.3_Silent_p.I493I|PBRM1_ENST00000409767.1_Silent_p.I493I|PBRM1_ENST00000356770.4_Silent_p.I461I|PBRM1_ENST00000409057.1_Silent_p.I493I|PBRM1_ENST00000337303.4_Silent_p.I493I|PBRM1_ENST00000410007.1_Silent_p.I493I|PBRM1_ENST00000394830.3_Silent_p.I493I			Q86U86	PB1_HUMAN	polybromo 1	493					chromatin remodeling (GO:0006338)|heart development (GO:0007507)|mitotic nuclear division (GO:0007067)|negative regulation of cell proliferation (GO:0008285)|placenta development (GO:0001890)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	kinetochore (GO:0000776)|nuclear chromosome (GO:0000228)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)	p.I493I(2)|p.I461I(1)		breast(5)|endometrium(5)|kidney(301)|liver(1)|lung(22)|pancreas(1)	335				BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)		CTCCGTCCTCGATATCGTCTC	0.448			"""Mis, N, F, S, D, O"""		"""clear cell renal carcinoma, breast"""								G|||	13	0.00259585	0.0008	0.0072	5008	,	,		16411	0.0		0.007	False		,,,				2504	0.0				p.I493I		Atlas-SNP	.		Rec	yes		3	3p21	55193	polybromo 1		E	PBRM1_ENST00000356770,NS,carcinoma,0,3	PBRM1	1252	3	3	Substitution - coding silent(3)	pancreas(3)	c.C1479T						PASS	.	G	,,	10,4396	16.8+/-37.8	0,10,2193	140.0	124.0	130.0		1383,1479,1479	-1.1	1.0	3	dbSNP_134	130	81,8519	46.3+/-105.2	1,79,4220	no	coding-synonymous,coding-synonymous,coding-synonymous	PBRM1	NM_018165.4,NM_018313.4,NM_181042.3	,,	1,89,6413	AA,AG,GG		0.9419,0.227,0.6997	,,	461/1603,493/1583,493/1583	52661351	91,12915	2203	4300	6503	SO:0001819	synonymous_variant	55193	exon14			GTCCTCGATATCG	BC015323	CCDS43099.1	3p21	2007-03-29			ENSG00000163939	ENSG00000163939			30064	protein-coding gene	gene with protein product		606083				11078522, 11483580	Standard	NM_018313		Approved	BAF180, PB1	uc003der.2	Q86U86	OTTHUMG00000152663	ENST00000296302.7:c.1479C>T	3.37:g.52661351G>A		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	59	27	0.457627	NM_018313	A1L381|A1L382|A4FUJ7|Q1RMD1|Q1RMD2|Q96MS2|Q9H2T3|Q9H2T4|Q9H2T5|Q9H301|Q9H314	Silent	SNP	ENST00000296302.7	37																																																																																				G|0.995;A|0.005	0.005	strong		0.448	PBRM1-008	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000327232.1	NM_018165	
MAGEB3	4114	hgsc.bcm.edu	37	X	30254361	30254361	+	Missense_Mutation	SNP	G	G	A	rs2071308	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:30254361G>A	ENST00000361644.2	+	5	1057	c.320G>A	c.(319-321)cGc>cAc	p.R107H		NM_002365.4	NP_002356.2	O15480	MAGB3_HUMAN	melanoma antigen family B, 3	107			R -> H (in dbSNP:rs2071308). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9441743}.					p.R107H(1)		NS(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(12)|prostate(2)|skin(2)	25						GTGCAGTCTCGCACAGACCCT	0.393													G|||	1761	0.46649	0.2474	0.3746	3775	,	,		15649	0.4008		0.3648	False		,,,				2504	0.4121				p.R107H		Atlas-SNP	.											.	MAGEB3	54	.	1	Substitution - Missense(1)	prostate(1)	c.G320A						PASS	.	G	HIS/ARG	1296,2537		173,752,198,706,373	53.0	46.0	48.0		320	-8.2	0.0	X	dbSNP_96	48	3005,3723		470,1214,851,744,1021	yes	missense	MAGEB3	NM_002365.4	29	643,1966,1049,1450,1394	AA,AG,A,GG,G		44.6641,33.8116,40.7253	benign	107/347	30254361	4301,6260	2202	4300	6502	SO:0001583	missense	4114	exon5			AGTCTCGCACAGA	AK057441	CCDS14220.1	Xp21.3	2009-03-17			ENSG00000198798	ENSG00000198798			6810	protein-coding gene	gene with protein product	"""cancer/testis antigen family 3, member 5"""	300152				9441743	Standard	NM_002365		Approved	CT3.5	uc004dca.2	O15480	OTTHUMG00000021320	ENST00000361644.2:c.320G>A	X.37:g.30254361G>A	ENSP00000355198:p.Arg107His	Somatic	149	1	0.00671141		WXS	Illumina HiSeq	Phase_I	86	86	1	NM_002365	A0AVE4|B3KQ52|O75861	Missense_Mutation	SNP	ENST00000361644.2	37	CCDS14220.1	778	0.4689572031344183	91	0.21064814814814814	97	0.3592592592592593	142	0.355	200	0.3412969283276451	G	0.013	-1.639962	0.00799	0.338116	0.446641	ENSG00000198798	ENST00000378986;ENST00000361644	T;T	0.01804	4.63;4.63	4.1	-8.21	0.01041	.	1.050360	0.07707	U	0.941400	T	0.00012	0.0000	N	0.21324	0.655	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.44590	-0.9318	9	0.13108	T	0.6	.	14.2771	0.66187	0.0972:0.4816:0.4211:0.0	rs2071308;rs2071308	107	O15480	MAGB3_HUMAN	H	107	ENSP00000368271:R107H;ENSP00000355198:R107H	ENSP00000355198:R107H	R	+	2	0	MAGEB3	30164282	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.470000	0.00460	-6.183000	0.00006	-1.991000	0.00449	CGC	G|0.569;A|0.431	0.431	strong		0.393	MAGEB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056158.2	NM_002365	
AIFM2	84883	hgsc.bcm.edu	37	10	71874683	71874683	+	Silent	SNP	G	G	A	rs2271696	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:71874683G>A	ENST00000307864.1	-	8	1176	c.963C>T	c.(961-963)taC>taT	p.Y321Y	AIFM2_ENST00000373248.1_Silent_p.Y321Y|AIFM2_ENST00000482166.1_5'UTR	NM_001198696.1|NM_032797.5	NP_001185625.1|NP_116186.1	Q9BRQ8	AIFM2_HUMAN	apoptosis-inducing factor, mitochondrion-associated, 2	321					apoptotic mitochondrial changes (GO:0008637)|positive regulation of apoptotic process (GO:0043065)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|lipid particle (GO:0005811)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	DNA binding (GO:0003677)|electron-transferring-flavoprotein dehydrogenase activity (GO:0004174)|flavin adenine dinucleotide binding (GO:0050660)|NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(3)|prostate(1)|skin(2)|urinary_tract(2)	16						TACCCGGCTTGTAGGCCTGGA	0.557													G|||	710	0.141773	0.2088	0.2305	5008	,	,		19102	0.1716		0.0586	False		,,,				2504	0.0429				p.Y321Y		Atlas-SNP	.											.	AIFM2	33	.	0			c.C963T						PASS	.	G	,	792,3614	308.6+/-290.6	60,672,1471	32.0	32.0	32.0		963,963	2.0	1.0	10	dbSNP_100	32	555,8045	149.2+/-204.3	20,515,3765	no	coding-synonymous,coding-synonymous	AIFM2	NM_001198696.1,NM_032797.5	,	80,1187,5236	AA,AG,GG		6.4535,17.9755,10.3568	,	321/374,321/374	71874683	1347,11659	2203	4300	6503	SO:0001819	synonymous_variant	84883	exon8			CGGCTTGTAGGCC	AK027403	CCDS7297.1	10q22.2	2006-11-16	2006-11-16	2006-11-16	ENSG00000042286	ENSG00000042286			21411	protein-coding gene	gene with protein product		605159	"""apoptosis-inducing factor (AIF)-like mitochondrion-associated inducer of death"""	AMID		12135761, 11980907, 15958387	Standard	NM_001198696		Approved	FLJ14497, PRG3	uc001jqp.2	Q9BRQ8	OTTHUMG00000018398	ENST00000307864.1:c.963C>T	10.37:g.71874683G>A		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	42	22	0.52381	NM_001198696	B3KXI0|Q63Z39	Silent	SNP	ENST00000307864.1	37	CCDS7297.1																																																																																			G|0.882;A|0.118	0.118	strong		0.557	AIFM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048487.1	NM_032797	
JAK1	3716	hgsc.bcm.edu	37	1	65321250	65321250	+	Silent	SNP	G	G	A	rs2230586	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:65321250G>A	ENST00000342505.4	-	11	1838	c.1590C>T	c.(1588-1590)atC>atT	p.I530I		NM_002227.2	NP_002218.2	P23458	JAK1_HUMAN	Janus kinase 1	530	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				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)	CCGTGCGCAGGATCTGCTTCT	0.582			Mis		ALL								G|||	194	0.038738	0.0015	0.1311	5008	,	,		16784	0.0069		0.0408	False		,,,				2504	0.0542				p.I530I		Atlas-SNP	.		Dom	yes		1	1p32.3-p31.3	3716	Janus kinase 1		L	.	JAK1	209	.	0			c.C1590T						PASS	.	G		50,4182		1,48,2067	67.0	71.0	70.0		1590	3.6	1.0	1	dbSNP_98	70	510,7942		14,482,3730	no	coding-synonymous	JAK1	NM_002227.2		15,530,5797	AA,AG,GG		6.0341,1.1815,4.415		530/1155	65321250	560,12124	2116	4226	6342	SO:0001819	synonymous_variant	3716	exon11			GCGCAGGATCTGC	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.1590C>T	1.37:g.65321250G>A		Somatic	210	0	0		WXS	Illumina HiSeq	Phase_I	174	69	0.396552	NM_002227	Q59GQ2|Q9UD26	Silent	SNP	ENST00000342505.4	37	CCDS41346.1																																																																																			G|0.957;A|0.043	0.043	strong		0.582	JAK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025791.1	NM_002227	
DPYD	1806	hgsc.bcm.edu	37	1	98039419	98039419	+	Silent	SNP	C	C	T	rs56038477	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:98039419C>T	ENST00000370192.3	-	11	1336	c.1236G>A	c.(1234-1236)gaG>gaA	p.E412E		NM_000110.3	NP_000101	Q12882	DPYD_HUMAN	dihydropyrimidine dehydrogenase	412					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)	TTTCATCTTGCTCTGTCCGAA	0.433													c|||	48	0.00958466	0.0008	0.0058	5008	,	,		17825	0.0		0.0239	False		,,,				2504	0.0194				p.E412E		Atlas-SNP	.											.	DPYD	219	.	0			c.G1236A						PASS	.	C		16,4390	22.3+/-47.3	0,16,2187	210.0	176.0	187.0		1236	3.0	1.0	1	dbSNP_129	187	188,8412	84.2+/-146.7	2,184,4114	no	coding-synonymous	DPYD	NM_000110.3		2,200,6301	TT,TC,CC		2.186,0.3631,1.5685		412/1026	98039419	204,12802	2203	4300	6503	SO:0001819	synonymous_variant	1806	exon11			ATCTTGCTCTGTC	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.1236G>A	1.37:g.98039419C>T		Somatic	437	0	0		WXS	Illumina HiSeq	Phase_I	346	162	0.468208	NM_000110	A2RRQ2|A2RRQ3|A8K5A2|A8MWG9|B1AN21|E9PFN1|Q16694|Q16761|Q32NB0|Q96HL6|Q96TH1	Silent	SNP	ENST00000370192.3	37	CCDS30777.1																																																																																			C|0.986;T|0.014	0.014	strong		0.433	DPYD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095698.3	NM_000110	
ZNF133	7692	hgsc.bcm.edu	37	20	18296076	18296076	+	Missense_Mutation	SNP	G	G	A	rs2228273	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:18296076G>A	ENST00000316358.4	+	4	678	c.581G>A	c.(580-582)gGg>gAg	p.G194E	ZNF133_ENST00000462170.1_3'UTR|ZNF133_ENST00000401790.1_Missense_Mutation_p.G194E|ZNF133_ENST00000396026.3_Missense_Mutation_p.G197E|RP4-568F9.3_ENST00000436848.1_RNA|ZNF133_ENST00000402618.2_Missense_Mutation_p.G131E|ZNF133_ENST00000377671.3_Missense_Mutation_p.G193E|ZNF133_ENST00000535822.1_Missense_Mutation_p.G99E|ZNF133_ENST00000538547.1_Missense_Mutation_p.G99E	NM_001282998.1|NM_001282999.1|NM_001283000.1|NM_001283001.1|NM_001283008.1	NP_001269927.1|NP_001269928.1|NP_001269929.1|NP_001269930.1|NP_001269937.1	P52736	ZN133_HUMAN	zinc finger protein 133	194			G -> E (in dbSNP:rs2228273).		transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			autonomic_ganglia(1)|breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	26						GCTCAGTCAGGGAACCCTGAG	0.542													G|||	604	0.120607	0.1528	0.1037	5008	,	,		20164	0.1379		0.0825	False		,,,				2504	0.1104				p.G193E		Atlas-SNP	.											.	ZNF133	63	.	0			c.G578A						PASS	.	G	GLU/GLY,GLU/GLY	653,3753	259.5+/-263.1	52,549,1602	72.0	80.0	77.0		578,578	1.1	0.0	20	dbSNP_98	77	679,7921	163.8+/-216.2	29,621,3650	yes	missense,missense	ZNF133	NM_001083330.1,NM_003434.4	98,98	81,1170,5252	AA,AG,GG		7.8953,14.8207,10.2414	possibly-damaging,possibly-damaging	193/654,193/654	18296076	1332,11674	2203	4300	6503	SO:0001583	missense	7692	exon4			AGTCAGGGAACCC	AK123005	CCDS13134.1, CCDS63234.1, CCDS63235.1, CCDS74703.1, CCDS74704.1	20p11.23	2013-01-08	2006-06-13		ENSG00000125846	ENSG00000125846		"""Zinc fingers, C2H2-type"", ""-"""	12917	protein-coding gene	gene with protein product		604075	"""zinc finger protein 150 (pHZ-66)"", ""zinc finger protein 133 (clone pHZ-13)"""	ZNF150		7557990, 7649249	Standard	XM_005260819		Approved	pHZ-13, pHZ-66	uc010gcs.3	P52736	OTTHUMG00000031965	ENST00000316358.4:c.581G>A	20.37:g.18296076G>A	ENSP00000346090:p.Gly194Glu	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	59	38	0.644068	NM_001083330	A8K5S4|B4DHU7|B4DIB8|B7ZAS1|F5H289|J3KQ11|J3KQJ0|Q53XU1|Q5JXV8|Q9BUV2|Q9H443	Missense_Mutation	SNP	ENST00000316358.4	37		274	0.12545787545787546	93	0.18902439024390244	32	0.08839779005524862	86	0.15034965034965034	63	0.08311345646437995	G	0	-2.621583	0.00118	0.148207	0.078953	ENSG00000125846	ENST00000377671;ENST00000396026;ENST00000402618;ENST00000401790;ENST00000538547;ENST00000535822;ENST00000316358	T;T;T;T;T;T;T	0.06608	3.46;3.43;3.28;3.43;3.34;3.34;3.43	4.15	1.08	0.20341	.	0.266580	0.27168	N	0.020608	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	B;B;P;P	0.42375	0.105;0.126;0.67;0.778	B;B;B;B	0.41466	0.021;0.008;0.196;0.358	T	0.48258	-0.9051	9	0.72032	D	0.01	-7.1046	6.6448	0.22929	0.3:0.0:0.7:0.0	rs2228273;rs52800593;rs2228273	131;197;194;193	B4DIB8;B4DHU7;P52736;P52736-2	.;.;ZN133_HUMAN;.	E	193;197;131;194;99;99;194	ENSP00000366899:G193E;ENSP00000400897:G197E;ENSP00000385279:G131E;ENSP00000383945:G194E;ENSP00000442978:G99E;ENSP00000439427:G99E;ENSP00000346090:G194E	ENSP00000346090:G194E	G	+	2	0	ZNF133	18244076	0.000000	0.05858	0.007000	0.13788	0.186000	0.23388	0.082000	0.14847	0.287000	0.22375	0.561000	0.74099	GGG	A|0.112;C|0.006	0.112	strong		0.542	ZNF133-002	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000127616.1	NM_003434	
SKA3	221150	hgsc.bcm.edu	37	13	21729252	21729252	+	3'UTR	SNP	T	T	C	rs11147976	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:21729252T>C	ENST00000314759.5	-	0	1400				SKA3_ENST00000400018.3_Missense_Mutation_p.K386R	NM_145061.5	NP_659498.4	Q8IX90	SKA3_HUMAN	spindle and kinetochore associated complex subunit 3						chromosome segregation (GO:0007059)|mitotic nuclear division (GO:0007067)|regulation of microtubule polymerization or depolymerization (GO:0031110)	condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|spindle microtubule (GO:0005876)		p.K386R(1)		breast(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	19						TCATCTCATTTTGTTCAGTTT	0.353																																					p.K386R		Atlas-SNP	.											.	SKA3	76	.	1	Substitution - Missense(1)	endometrium(1)	c.A1157G						PASS	.						143.0	152.0	149.0					13																	21729252		2202	4300	6502	SO:0001624	3_prime_UTR_variant	221150	exon8			CTCATTTTGTTCA	AF361358	CCDS31946.1, CCDS53856.1	13q11	2013-01-17	2009-08-19	2009-08-19	ENSG00000165480	ENSG00000165480			20262	protein-coding gene	gene with protein product			"""chromosome 13 open reading frame 3"""	C13orf3		19387489, 19289083, 19646878, 19360002	Standard	NM_145061		Approved	MGC4832, RAMA1	uc001unt.3	Q8IX90	OTTHUMG00000016539	ENST00000314759.5:c.*37A>G	13.37:g.21729252T>C		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	86	15	0.174419	NM_001166017	A2A330|A2A331|B2RBY2|Q5VZV5|Q86WR2|Q8NBG1|Q96D22	Missense_Mutation	SNP	ENST00000314759.5	37	CCDS31946.1	285	0.1304945054945055	12	0.024390243902439025	53	0.1464088397790055	123	0.21503496503496503	97	0.1279683377308707	C	14.23	2.472714	0.43942	.	.	ENSG00000165480	ENST00000400018	T	0.23950	1.88	4.03	1.2	0.21068	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.34576	-0.9823	8	0.02654	T	1	.	6.6402	0.22904	0.0:0.549:0.0:0.451	rs11147976;rs52803875;rs56923931;rs11147976	386	Q8IX90-3	.	R	386	ENSP00000382896:K386R	ENSP00000382896:K386R	K	-	2	0	SKA3	20627252	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.064000	0.14437	-0.005000	0.14395	-1.473000	0.01005	AAA	T|0.889;C|0.111	0.111	strong		0.353	SKA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000272912.1	NM_145061	
IL3RA	3563	hgsc.bcm.edu	37	X	1497644	1497644	+	Missense_Mutation	SNP	G	G	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:1497644G>C	ENST00000331035.4	+	10	1316	c.967G>C	c.(967-969)Gtg>Ctg	p.V323L	IL3RA_ENST00000381469.2_Missense_Mutation_p.V245L	NM_001267713.1|NM_002183.3	NP_001254642.1|NP_002174.1	P26951	IL3RA_HUMAN	interleukin 3 receptor, alpha (low affinity)	323			V -> L (in dbSNP:rs17883366). {ECO:0000269|Ref.5}.		cellular response to interleukin-3 (GO:0036016)|interleukin-3-mediated signaling pathway (GO:0038156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	interleukin-3 receptor activity (GO:0004912)			lung(1)|skin(2)	3		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)			Sargramostim(DB00020)	CTGTGTCTTCGTGATCTGCAG	0.592													g|||	525	0.104832	0.0378	0.1297	5008	,	,		16681	0.0694		0.2058	False		,,,				2504	0.1104				p.V323L		Atlas-SNP	.											.	IL3RA	49	.	0			c.G967C						PASS	.		LEU/VAL	293,4109		12,269,1920	130.0	106.0	114.0		967	-1.6	0.0	X	dbSNP_134	114	1580,7012		144,1292,2860	no	missense	IL3RA	NM_002183.2	32	156,1561,4780	CC,CG,GG		18.3892,6.6561,14.4143	benign	323/379	1497644	1873,11121	2201	4296	6497	SO:0001583	missense	3563	exon10			GTCTTCGTGATCT	M74782	CCDS14113.1, CCDS59158.1	Xp22.3 and Yp13.3	2008-07-21			ENSG00000185291	ENSG00000185291		"""Pseudoautosomal regions / PAR1"", ""Interleukins and interleukin receptors"", ""CD molecules"""	6012	protein-coding gene	gene with protein product		308385, 430000				1833064	Standard	NM_002183		Approved	CD123	uc004cps.3	P26951	OTTHUMG00000021059	ENST00000331035.4:c.967G>C	X.37:g.1497644G>C	ENSP00000327890:p.Val323Leu	Somatic	261	0	0		WXS	Illumina HiSeq	Phase_I	232	174	0.75	NM_002183	A8K3F3|B9VI81|Q5HYQ7|Q5HYQ8|Q9UEH7	Missense_Mutation	SNP	ENST00000331035.4	37	CCDS14113.1	283	0.1295787545787546	21	0.042682926829268296	54	0.14917127071823205	53	0.09265734265734266	155	0.20448548812664907	.	0	-2.808565	0.00074	0.066561	0.183892	ENSG00000185291	ENST00000331035;ENST00000381469	T;D	0.96522	1.74;-4.04	0.798	-1.6	0.08426	.	0.471891	0.15240	N	0.272951	T	0.00271	0.0008	N	0.00841	-1.15	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.06405	0.0;0.002	T	0.51957	-0.8639	9	0.06757	T	0.87	.	.	.	.	.	244;323	P26951-2;P26951	.;IL3RA_HUMAN	L	323;245	ENSP00000327890:V323L;ENSP00000370878:V245L	ENSP00000327890:V323L	V	+	1	0	IL3RA	1457644	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.991000	0.03728	-2.554000	0.00477	-2.540000	0.00180	GTG	G|0.868;C|0.132	0.132	strong		0.592	IL3RA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055600.3		
CELA1	1990	hgsc.bcm.edu	37	12	51737562	51737562	+	Missense_Mutation	SNP	T	T	C	rs17860300	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	138	1	0.00724638		WXS	Illumina HiSeq	Phase_I	111	43	0.387387	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	
ZNF567	163081	hgsc.bcm.edu	37	19	37209866	37209866	+	Silent	SNP	T	T	C	rs34642314	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:37209866T>C	ENST00000536254.2	+	6	462	c.240T>C	c.(238-240)gcT>gcC	p.A80A	ZNF567_ENST00000360729.4_Silent_p.A49A|ZNF850_ENST00000589390.1_Intron|ZNF567_ENST00000392163.2_Silent_p.A49A|ZNF567_ENST00000585696.1_Silent_p.A49A|ZNF567_ENST00000588311.1_Silent_p.A49A			Q8N184	ZN567_HUMAN	zinc finger protein 567	80					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)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(6)|lung(8)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	24	Esophageal squamous(110;0.198)		COAD - Colon adenocarcinoma(19;0.0454)|Colorectal(19;0.065)			ACTGGAAAGCTGAAGACTTTT	0.328													T|||	262	0.0523163	0.0061	0.1297	5008	,	,		17030	0.003		0.1083	False		,,,				2504	0.0532				p.A49A		Atlas-SNP	.											.	ZNF567	61	.	0			c.T147C						PASS	.	T		110,4258		1,108,2075	36.0	39.0	38.0		147	1.4	1.0	19	dbSNP_126	38	1018,7554		59,900,3327	no	coding-synonymous	ZNF567	NM_152603.2		60,1008,5402	CC,CT,TT		11.8759,2.5183,8.7172		49/617	37209866	1128,11812	2184	4286	6470	SO:0001819	synonymous_variant	163081	exon4			GAAAGCTGAAGAC	AK093034	CCDS12495.1, CCDS74349.1	19q13.12	2013-10-08				ENSG00000189042		"""Zinc fingers, C2H2-type"", ""-"""	28696	protein-coding gene	gene with protein product						12477932	Standard	XM_006723064		Approved	MGC45586	uc002oep.4	Q8N184		ENST00000536254.2:c.240T>C	19.37:g.37209866T>C		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	96	53	0.552083	NM_152603	B3KX49|Q6N044	Silent	SNP	ENST00000536254.2	37																																																																																				T|0.917;C|0.083	0.083	strong		0.328	ZNF567-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000453549.1	NM_152603	
DCAF6	55827	hgsc.bcm.edu	37	1	167973976	167973976	+	Silent	SNP	C	C	T	rs1060041	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:167973976C>T	ENST00000312263.6	+	10	1527	c.1323C>T	c.(1321-1323)gaC>gaT	p.D441D	DCAF6_ENST00000432587.2_Silent_p.D410D|DCAF6_ENST00000367843.3_Silent_p.D441D|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	167	0	0		WXS	Illumina HiSeq	Phase_I	133	58	0.43609	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	
HLA-A	3105	hgsc.bcm.edu	37	6	29911239	29911239	+	Silent	SNP	T	T	C	rs9260155	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:29911239T>C	ENST00000396634.1	+	5	879	c.538T>C	c.(538-540)Ttg>Ctg	p.L180L	HLA-A_ENST00000376802.2_Silent_p.L180L|HLA-A_ENST00000376809.5_Silent_p.L180L|HLA-A_ENST00000376806.5_Silent_p.L180L			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	180	Alpha-2.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	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						GGCGGAGCAGTTGAGAGCCTA	0.662									Osteosarcoma, Familial Clustering of;Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of;Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of	Multiple Myeloma(9;0.094)			N|||	1927	0.384784	0.1982	0.3487	5008	,	,		12044	0.5397		0.3489	False		,,,				2504	0.5399				p.L180L		Atlas-SNP	.											HLA-A,mouth,carcinoma,-1,1	HLA-A	89	1	0			c.T538C						PASS	.						40.0	29.0	33.0					6																	29911239		1509	2697	4206	SO:0001819	synonymous_variant	3105	exon3	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	GAGCAGTTGAGAG	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.538T>C	6.37:g.29911239T>C		Somatic	257	1	0.00389105		WXS	Illumina HiSeq	Phase_I	131	61	0.465649	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Silent	SNP	ENST00000396634.1	37	CCDS34373.1																																																																																			C|0.290;T|0.710	0.290	strong		0.662	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
DLGAP1	9229	hgsc.bcm.edu	37	18	3534224	3534224	+	Missense_Mutation	SNP	C	C	T	rs35822832	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:3534224C>T	ENST00000315677.3	-	10	3042	c.2447G>A	c.(2446-2448)cGg>cAg	p.R816Q	DLGAP1_ENST00000534970.1_Missense_Mutation_p.R500Q|DLGAP1_ENST00000400150.3_Missense_Mutation_p.R532Q|DLGAP1_ENST00000539435.1_Missense_Mutation_p.R524Q|DLGAP1_ENST00000581699.1_Missense_Mutation_p.R522Q|DLGAP1_ENST00000515196.2_Missense_Mutation_p.R816Q|DLGAP1_ENST00000400147.2_Missense_Mutation_p.R514Q|DLGAP1_ENST00000584874.1_Missense_Mutation_p.R816Q|DLGAP1_ENST00000400155.1_Missense_Mutation_p.R522Q|DLGAP1_ENST00000400149.3_Missense_Mutation_p.R506Q|DLGAP1_ENST00000581527.1_Missense_Mutation_p.R816Q|DLGAP1_ENST00000400145.2_Missense_Mutation_p.R514Q	NM_004746.3	NP_004737.2	O14490	DLGP1_HUMAN	discs, large (Drosophila) homolog-associated protein 1	816			R -> Q (in dbSNP:rs35822832).		synaptic transmission (GO:0007268)	cell junction (GO:0030054)|neuronal postsynaptic density (GO:0097481)|postsynaptic membrane (GO:0045211)				breast(2)|endometrium(3)|kidney(1)|large_intestine(5)|lung(31)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(6)|urinary_tract(1)	56		Colorectal(8;0.0257)				CCGTTCTTCCCGCTCCATCTG	0.602													C|||	30	0.00599042	0.003	0.0101	5008	,	,		19947	0.0		0.0179	False		,,,				2504	0.001				p.R816Q		Atlas-SNP	.											.	DLGAP1	201	.	0			c.G2447A						PASS	.	C	GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG	15,4391	22.3+/-47.3	0,15,2188	109.0	99.0	103.0		1541,2447,1499,1613,1565,1541,1571,2447	5.9	1.0	18	dbSNP_126	103	219,8381	92.1+/-154.2	2,215,4083	yes	missense,missense,missense,missense,missense,missense,missense,missense	DLGAP1	NM_001003809.2,NM_001242761.1,NM_001242762.1,NM_001242763.1,NM_001242764.1,NM_001242765.1,NM_001242766.1,NM_004746.3	43,43,43,43,43,43,43,43	2,230,6271	TT,TC,CC		2.5465,0.3404,1.7992	benign,benign,benign,benign,benign,benign,benign,benign	514/676,816/930,500/662,538/700,522/684,514/628,524/686,816/978	3534224	234,12772	2203	4300	6503	SO:0001583	missense	9229	exon10			TCTTCCCGCTCCA	AB000277	CCDS11836.1, CCDS42406.1, CCDS56049.1, CCDS56050.1, CCDS56051.1, CCDS56052.1, CCDS56053.1, CCDS74191.1	18p11.3	2008-07-28	2001-11-28		ENSG00000170579	ENSG00000170579			2905	protein-coding gene	gene with protein product		605445	"""discs, large (Drosophila) homolog-associated protein 1"""			9024696, 9286858	Standard	NM_004746		Approved	GKAP, SAPAP1, DAP-1	uc002kmf.3	O14490	OTTHUMG00000131537	ENST00000315677.3:c.2447G>A	18.37:g.3534224C>T	ENSP00000316377:p.Arg816Gln	Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	160	70	0.4375	NM_001242761	A8MWN8|B2RMU8|B7WPA1|B7Z2H2|B7Z2I2|B7Z9Y4|O14489|P78335	Missense_Mutation	SNP	ENST00000315677.3	37	CCDS11836.1	20	0.009157509157509158	1	0.0020325203252032522	7	0.019337016574585635	0	0.0	12	0.0158311345646438	C	17.14	3.314540	0.60524	0.003404	0.025465	ENSG00000170579	ENST00000315677;ENST00000400147;ENST00000400150;ENST00000400149;ENST00000400155;ENST00000534970;ENST00000539435;ENST00000400145;ENST00000515196	T;T;T;T;T;T;T;T;T	0.17854	2.25;2.25;2.25;2.25;2.25;2.25;2.25;2.25;2.25	5.93	5.93	0.95920	.	0.106561	0.64402	D	0.000004	T	0.03915	0.0110	N	0.11724	0.165	0.45490	D	0.998455	B;B;B;B;B;B;B;B	0.21309	0.054;0.054;0.017;0.054;0.017;0.043;0.017;0.014	B;B;B;B;B;B;B;B	0.14578	0.006;0.011;0.01;0.006;0.01;0.002;0.004;0.006	T	0.24476	-1.0159	10	0.23891	T	0.37	-19.2872	20.3312	0.98718	0.0:1.0:0.0:0.0	rs35822832	816;500;512;522;524;514;816;514	B7Z9Y4;B7Z2H2;B7Z2J5;A8MWN8;B7Z2I2;O14490-3;O14490;O14490-2	.;.;.;.;.;.;DLGP1_HUMAN;.	Q	816;514;532;506;522;500;524;514;816	ENSP00000316377:R816Q;ENSP00000383011:R514Q;ENSP00000383014:R532Q;ENSP00000383013:R506Q;ENSP00000383019:R522Q;ENSP00000437817:R500Q;ENSP00000446312:R524Q;ENSP00000383010:R514Q;ENSP00000445973:R816Q	ENSP00000316377:R816Q	R	-	2	0	DLGAP1	3524224	1.000000	0.71417	0.988000	0.46212	0.986000	0.74619	4.810000	0.62598	2.797000	0.96272	0.655000	0.94253	CGG	C|0.984;T|0.016	0.016	strong		0.602	DLGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254394.4		
PSTPIP2	9050	hgsc.bcm.edu	37	18	43568717	43568717	+	Missense_Mutation	SNP	T	T	C	rs2276199	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:43568717T>C	ENST00000409746.5	-	14	1035	c.964A>G	c.(964-966)Aat>Gat	p.N322D	RN7SKP26_ENST00000410247.1_RNA|PSTPIP2_ENST00000588801.1_Intron|PSTPIP2_ENST00000589328.1_Silent_p.P289P	NM_024430.3	NP_077748.3	Q9H939	PPIP2_HUMAN	proline-serine-threonine phosphatase interacting protein 2	322			N -> D (in dbSNP:rs2276199).|N -> S (in dbSNP:rs16978507).			cytoskeleton (GO:0005856)|cytosol (GO:0005829)|membrane (GO:0016020)		p.P289P(1)		endometrium(1)|kidney(1)|large_intestine(1)|lung(8)|ovary(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)	17						AAAGAGTAATTGGGATCATCT	0.348													C|||	1558	0.311102	0.5855	0.2176	5008	,	,		20910	0.4127		0.1312	False		,,,				2504	0.0869				p.N322D		Atlas-SNP	.											PSTPIP2,NS,carcinoma,0,1	PSTPIP2	65	1	1	Substitution - coding silent(1)	stomach(1)	c.A964G						PASS	.	C	ASP/ASN	2251,2155	582.3+/-385.5	566,1119,518	100.0	95.0	96.0		964	4.9	0.7	18	dbSNP_100	96	1128,7472	766.9+/-407.6	81,966,3253	yes	missense	PSTPIP2	NM_024430.3	23	647,2085,3771	CC,CT,TT		13.1163,48.9106,25.9803	benign	322/335	43568717	3379,9627	2203	4300	6503	SO:0001583	missense	9050	exon14			AGTAATTGGGATC		CCDS32820.2	18q12	2008-07-28			ENSG00000152229	ENSG00000152229			9581	protein-coding gene	gene with protein product						9804817	Standard	NM_024430		Approved		uc002lbp.4	Q9H939	OTTHUMG00000152674	ENST00000409746.5:c.964A>G	18.37:g.43568717T>C	ENSP00000387261:p.Asn322Asp	Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	177	87	0.491525	NM_024430		Missense_Mutation	SNP	ENST00000409746.5	37	CCDS32820.2	702	0.32142857142857145	273	0.5548780487804879	79	0.21823204419889503	249	0.4353146853146853	101	0.13324538258575197	C	0.185	-1.058452	0.01950	0.510894	0.131163	ENSG00000152229	ENST00000409746	T	0.33865	1.39	5.74	4.87	0.63330	.	0.393817	0.28082	N	0.016664	T	0.00012	0.0000	N	0.00197	-1.87	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.46261	-0.9204	9	0.05525	T	0.97	.	8.9937	0.36039	0.0:0.8302:0.0:0.1698	rs2276199;rs3842867;rs52835505;rs60806783;rs2276199	322	Q9H939	PPIP2_HUMAN	D	322	ENSP00000387261:N322D	ENSP00000387261:N322D	N	-	1	0	PSTPIP2	41822715	0.980000	0.34600	0.674000	0.29902	0.002000	0.02628	1.864000	0.39469	0.788000	0.33755	-0.128000	0.14901	AAT	T|0.703;C|0.297	0.297	strong		0.348	PSTPIP2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327522.1		
CHGB	1114	hgsc.bcm.edu	37	20	5903848	5903848	+	Missense_Mutation	SNP	C	C	G	rs236152	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:5903848C>G	ENST00000378961.4	+	4	1262	c.1058C>G	c.(1057-1059)gCc>gGc	p.A353G		NM_001819.2	NP_001810.2	P05060	SCG1_HUMAN	chromogranin B (secretogranin 1)	353			A -> G (in dbSNP:rs236152). {ECO:0000269|PubMed:14702039, ECO:0000269|Ref.4}.			extracellular region (GO:0005576)|secretory granule (GO:0030141)	hormone activity (GO:0005179)			breast(7)|kidney(2)|large_intestine(8)|lung(19)|ovary(1)|pancreas(2)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)	47						GGCGTCCAGGCCCCTGAGGAC	0.527													C|||	2581	0.515375	0.6573	0.5231	5008	,	,		20028	0.5288		0.3499	False		,,,				2504	0.4744				p.A353G		Atlas-SNP	.											.	CHGB	112	.	0			c.C1058G	GRCh37	CM043990	CHGB	M	rs236152	PASS	.	C	GLY/ALA	2735,1671	645.1+/-398.1	870,995,338	76.0	80.0	79.0		1058	-1.1	0.0	20	dbSNP_79	79	3091,5509	456.5+/-364.1	553,1985,1762	yes	missense	CHGB	NM_001819.2	60	1423,2980,2100	GG,GC,CC		35.9419,37.9256,44.7947	benign	353/678	5903848	5826,7180	2203	4300	6503	SO:0001583	missense	1114	exon4			TCCAGGCCCCTGA		CCDS13092.1	20p12.3	2013-09-19			ENSG00000089199	ENSG00000089199			1930	protein-coding gene	gene with protein product	"""secretogranin B"""	118920		SCG1		3608978	Standard	NM_001819		Approved		uc002wmg.3	P05060	OTTHUMG00000031821	ENST00000378961.4:c.1058C>G	20.37:g.5903848C>G	ENSP00000368244:p.Ala353Gly	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	33	19	0.575758	NM_001819	A8K021|Q59EU9|Q6IBS6|Q9BQV6|Q9UC25|Q9UJA6	Missense_Mutation	SNP	ENST00000378961.4	37	CCDS13092.1	1025	0.4693223443223443	308	0.6260162601626016	163	0.45027624309392267	293	0.5122377622377622	261	0.34432717678100266	C	0.515	-0.864782	0.02590	0.620744	0.359419	ENSG00000089199	ENST00000378961	T	0.05580	3.42	5.27	-1.14	0.09741	.	0.712485	0.12872	N	0.432199	T	0.00012	0.0000	L	0.33485	1.01	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.30679	-0.9970	9	0.10377	T	0.69	-0.0614	4.5883	0.12294	0.188:0.3751:0.3568:0.0801	rs236152;rs236152	353	P05060	SCG1_HUMAN	G	353	ENSP00000368244:A353G	ENSP00000368244:A353G	A	+	2	0	CHGB	5851848	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.447000	0.06828	-0.043000	0.13513	-0.261000	0.10672	GCC	C|0.545;G|0.455	0.455	strong		0.527	CHGB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077897.2	NM_001819	
SMG1	23049	hgsc.bcm.edu	37	16	18853744	18853744	+	Silent	SNP	T	T	C	rs12926959	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:18853744T>C	ENST00000446231.2	-	40	6664	c.6252A>G	c.(6250-6252)aaA>aaG	p.K2084K	SMG1_ENST00000389467.3_Silent_p.K2084K			Q96Q15	SMG1_HUMAN	SMG1 phosphatidylinositol 3-kinase-related kinase	2084					DNA repair (GO:0006281)|gene expression (GO:0010467)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol phosphorylation (GO:0046854)|protein autophosphorylation (GO:0046777)|response to stress (GO:0006950)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(8)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(37)|ovary(1)|skin(1)|stomach(4)|urinary_tract(1)	92						AACTTGCACGTTTCTGTGCTC	0.388													T|||	253	0.0505192	0.0507	0.0692	5008	,	,		22357	0.001		0.0686	False		,,,				2504	0.0695				p.K2084K		Atlas-SNP	.											.	SMG1	401	.	0			c.A6252G						PASS	.	T		198,3630		8,182,1724	88.0	78.0	81.0		6252	3.3	1.0	16	dbSNP_121	81	723,7561		32,659,3451	no	coding-synonymous	SMG1	NM_015092.4		40,841,5175	CC,CT,TT		8.7277,5.1724,7.604		2084/3662	18853744	921,11191	1914	4142	6056	SO:0001819	synonymous_variant	23049	exon40			TGCACGTTTCTGT	AB061371	CCDS45430.1	16p12.3	2013-07-02	2013-07-02		ENSG00000157106	ENSG00000157106			30045	protein-coding gene	gene with protein product	"""phosphatidylinositol 3-kinase-related kinase"""	607032	"""smg-1 homolog, phosphatidylinositol 3-kinase-related kinase (C. elegans)"""			9455477, 11331269, 17229728	Standard	NM_015092		Approved	LIP, KIAA0421, ATX	uc002dfm.3	Q96Q15	OTTHUMG00000166900	ENST00000446231.2:c.6252A>G	16.37:g.18853744T>C		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	110	66	0.6	NM_015092	O43305|Q13284|Q8NFX2|Q96QV0|Q96RW3	Silent	SNP	ENST00000446231.2	37	CCDS45430.1																																																																																			T|0.942;C|0.058	0.058	strong		0.388	SMG1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000391817.1	NM_015092	
PRODH	5625	hgsc.bcm.edu	37	22	18905964	18905964	+	Missense_Mutation	SNP	C	C	T	rs2904552	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:18905964C>T	ENST00000357068.6	-	11	1557	c.1292G>A	c.(1291-1293)cGc>cAc	p.R431H	PRODH_ENST00000334029.2_Missense_Mutation_p.R323H|PRODH_ENST00000420436.1_Missense_Mutation_p.R323H	NM_016335.4	NP_057419	O43272	PROD_HUMAN	proline dehydrogenase (oxidase) 1	431			R -> H (associated with HP-1 in a subset of schizophrenia patients; moderate reduction of enzymatic activity; dbSNP:rs2904552). {ECO:0000269|PubMed:12217952, ECO:0000269|PubMed:17135275}.		4-hydroxyproline catabolic process (GO:0019470)|cellular nitrogen compound metabolic process (GO:0034641)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|proline catabolic process (GO:0006562)|proline catabolic process to glutamate (GO:0010133)|proline metabolic process (GO:0006560)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)	FAD binding (GO:0071949)|proline dehydrogenase activity (GO:0004657)			breast(1)|endometrium(3)|lung(4)|upper_aerodigestive_tract(1)	9					L-Proline(DB00172)	GCCCTCACGGCGAGCCAGCTC	0.642													.|||	215	0.0429313	0.0234	0.0576	5008	,	,		17166	0.001		0.1054	False		,,,				2504	0.0378				p.R431H		Atlas-SNP	.											.	PRODH	42	.	0			c.G1292A	GRCh37	CM057555	PRODH	M	rs2904552	PASS	.	C	HIS/ARG,HIS/ARG	161,4243	801.7+/-415.6	5,151,2046	58.0	51.0	54.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	968,1292	1.2	1.0	22	dbSNP_101	54	900,7700	773.2+/-407.7	43,814,3443	no	missense,missense	PRODH	NM_001195226.1,NM_016335.4	29,29	48,965,5489	TT,TC,CC		10.4651,3.6558,8.159	probably-damaging,probably-damaging	323/493,431/601	18905964	1061,11943	2202	4300	6502	SO:0001583	missense	5625	exon12			TCACGGCGAGCCA	AF010310	CCDS13754.1, CCDS56223.1	22q11.2	2014-07-10	2001-12-05		ENSG00000100033	ENSG00000100033	1.5.5.2		9453	protein-coding gene	gene with protein product		606810	"""proline dehydrogenase (proline oxidase )"""			9385373, 10192398	Standard	NM_001195226		Approved	HSPOX2, PRODH1, PIG6, PRODH2, TP53I6	uc002zok.4	O43272	OTTHUMG00000150163	ENST00000357068.6:c.1292G>A	22.37:g.18905964C>T	ENSP00000349577:p.Arg431His	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	80	34	0.425	NM_016335	A6NF53|O14680|Q0P507|Q147W8|Q504W1|Q59FI8|Q6NV86|Q9UF13	Missense_Mutation	SNP	ENST00000357068.6	37	CCDS13754.1	109	0.04990842490842491	12	0.024390243902439025	18	0.049723756906077346	0	0.0	79	0.10422163588390501	t	19.91	3.913871	0.72983	0.036558	0.104651	ENSG00000100033	ENST00000357068;ENST00000313755	T	0.35421	1.31	4.49	1.16	0.20824	Proline dehydrogenase (1);	0.229694	0.45606	N	0.000345	T	0.01870	0.0059	M	0.76574	2.34	0.47621	D	0.999478	P;D;P	0.67145	0.932;0.996;0.945	B;P;B	0.60173	0.286;0.87;0.408	T	0.00324	-1.1817	10	0.40728	T	0.16	-32.1286	8.7389	0.34545	0.0:0.7169:0.0:0.2831	rs2904552	347;431;323	O43272-1;O43272;E7EQL6	.;PROD_HUMAN;.	H	431;76	ENSP00000349577:R431H	ENSP00000318329:R76H	R	-	2	0	PRODH	17285964	0.994000	0.37717	1.000000	0.80357	0.977000	0.68977	1.178000	0.31981	0.474000	0.27392	-0.287000	0.09952	CGC	C|0.930;T|0.070	0.070	strong		0.642	PRODH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316637.2	NM_016335	
C3orf30	152405	hgsc.bcm.edu	37	3	118865801	118865801	+	Silent	SNP	C	C	T	rs4077931	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:118865801C>T	ENST00000295622.1	+	1	805	c.765C>T	c.(763-765)tcC>tcT	p.S255S	IGSF11_ENST00000354673.2_5'Flank|IGSF11_ENST00000441144.2_5'Flank|RP11-484M3.5_ENST00000490594.1_5'Flank|IGSF11_ENST00000425327.2_5'Flank	NM_152539.2	NP_689752.2	Q96M34	CC030_HUMAN	chromosome 3 open reading frame 30	255										NS(1)|breast(1)|cervix(1)|endometrium(1)|large_intestine(6)|lung(20)|ovary(2)|prostate(1)|urinary_tract(1)	34				GBM - Glioblastoma multiforme(114;0.222)		AAAGACCTTCCGTACAGATTG	0.502													C|||	1129	0.225439	0.2118	0.196	5008	,	,		24314	0.1994		0.2346	False		,,,				2504	0.2822				p.S255S		Atlas-SNP	.											C3orf30,NS,malignant_melanoma,+1,1	C3orf30	64	1	0			c.C765T						scavenged	.	C		1073,3333	389.8+/-327.4	128,817,1258	92.0	92.0	92.0		765	-7.1	0.0	3	dbSNP_108	92	2446,6154	404.2+/-348.1	345,1756,2199	no	coding-synonymous	C3orf30	NM_152539.2		473,2573,3457	TT,TC,CC		28.4419,24.3532,27.0567		255/537	118865801	3519,9487	2203	4300	6503	SO:0001819	synonymous_variant	152405	exon1			ACCTTCCGTACAG	AK057421	CCDS2984.1	3q13.32	2011-08-09			ENSG00000163424	ENSG00000163424			26553	protein-coding gene	gene with protein product							Standard	NM_152539		Approved	FLJ32859	uc003ecb.1	Q96M34	OTTHUMG00000159349	ENST00000295622.1:c.765C>T	3.37:g.118865801C>T		Somatic	49	1	0.0204082		WXS	Illumina HiSeq	Phase_I	51	27	0.529412	NM_152539	A1L4B7	Silent	SNP	ENST00000295622.1	37	CCDS2984.1	480	0.21978021978021978	103	0.20934959349593496	76	0.20994475138121546	120	0.2097902097902098	181	0.23878627968337732	C	3.881	-0.026039	0.07589	0.243532	0.284419	ENSG00000163424	ENST00000460150;ENST00000473121	.	.	.	4.45	-7.09	0.01553	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.41413	-0.9510	3	.	.	.	-0.3947	0.2055	0.00150	0.2265:0.2212:0.2309:0.3213	rs4077931;rs4077931	.	.	.	C	219;48	.	.	R	+	1	0	C3orf30	120348491	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.902000	0.04088	-1.239000	0.02532	-1.769000	0.00663	CGT	C|0.750;T|0.250	0.250	strong		0.502	C3orf30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354838.1	NM_152539	
PEAR1	375033	hgsc.bcm.edu	37	1	156883546	156883546	+	Missense_Mutation	SNP	A	A	G	rs12137505	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:156883546A>G	ENST00000338302.3	+	22	2932	c.2707A>G	c.(2707-2709)Aat>Gat	p.N903D	PEAR1_ENST00000292357.7_Missense_Mutation_p.N903D			Q5VY43	PEAR1_HUMAN	platelet endothelial aggregation receptor 1	903	Pro-rich.		N -> D (in dbSNP:rs12137505).		recognition of apoptotic cell (GO:0043654)	integral component of membrane (GO:0016021)|phagocytic cup (GO:0001891)				breast(1)|central_nervous_system(2)|endometrium(4)|large_intestine(6)|lung(22)|ovary(4)|skin(3)|upper_aerodigestive_tract(1)	43	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)					CCCATTCTACAATAAAGGTAT	0.582													A|||	2259	0.451078	0.2557	0.5591	5008	,	,		17614	0.5913		0.3926	False		,,,				2504	0.5542				p.N903D		Atlas-SNP	.											.	PEAR1	118	.	0			c.A2707G						PASS	.	A	ASP/ASN	1133,3273	402.6+/-332.4	145,843,1215	52.0	54.0	53.0		2707	-3.9	0.0	1	dbSNP_120	53	3483,5117	508.4+/-377.0	719,2045,1536	yes	missense	PEAR1	NM_001080471.1	23	864,2888,2751	GG,GA,AA		40.5,25.7149,35.4913	benign	903/1038	156883546	4616,8390	2203	4300	6503	SO:0001583	missense	375033	exon21			TTCTACAATAAAG	AK098809	CCDS30892.1	1q23.1	2008-02-05	2007-10-25	2007-10-25	ENSG00000187800	ENSG00000187800			33631	protein-coding gene	gene with protein product		610278	"""multiple EGF-like-domains 12"""	MEGF12		15851471	Standard	NM_001080471		Approved	JEDI, FLJ00193	uc001fqj.1	Q5VY43	OTTHUMG00000041293	ENST00000338302.3:c.2707A>G	1.37:g.156883546A>G	ENSP00000344465:p.Asn903Asp	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	119	119	1	NM_001080471	Q8TEK2	Missense_Mutation	SNP	ENST00000338302.3	37	CCDS30892.1	939	0.42994505494505497	139	0.28252032520325204	177	0.4889502762430939	317	0.5541958041958042	306	0.40369393139841686	A	7.885	0.731082	0.15507	0.257149	0.405	ENSG00000187800	ENST00000338302;ENST00000292357	D;D	0.88354	-2.37;-2.37	5.49	-3.91	0.04168	.	1.037990	0.07657	N	0.932935	T	0.56834	0.2012	N	0.14661	0.345	0.80722	P	0.0	B	0.23937	0.094	B	0.16722	0.016	T	0.32428	-0.9907	9	0.24483	T	0.36	.	6.234	0.20752	0.3626:0.2625:0.3749:0.0	rs12137505;rs56635659;rs58160272;rs12137505	903	Q5VY43	PEAR1_HUMAN	D	903	ENSP00000344465:N903D;ENSP00000292357:N903D	ENSP00000292357:N903D	N	+	1	0	PEAR1	155150170	0.012000	0.17670	0.000000	0.03702	0.009000	0.06853	0.203000	0.17315	-0.553000	0.06158	-0.461000	0.05368	AAT	A|0.621;G|0.379	0.379	strong		0.582	PEAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098937.2	NM_001080471	
SALL4	57167	hgsc.bcm.edu	37	20	50406630	50406630	+	Missense_Mutation	SNP	T	T	G	rs6091375	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:50406630T>G	ENST00000217086.4	-	2	2503	c.2392A>C	c.(2392-2394)Atc>Ctc	p.I798L	SALL4_ENST00000395997.3_Intron|SALL4_ENST00000371539.3_Intron|SALL4_ENST00000483130.1_5'Flank	NM_020436.3	NP_065169.1	Q9UJQ4	SALL4_HUMAN	spalt-like transcription factor 4	798			I -> L (in dbSNP:rs6091375). {ECO:0000269|PubMed:12395297}.		embryonic limb morphogenesis (GO:0030326)|inner cell mass cell proliferation (GO:0001833)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)|ventricular septum development (GO:0003281)	cytoplasm (GO:0005737)|heterochromatin (GO:0000792)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(27)|ovary(5)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						TTTGACTTGATGCTTTCGGCT	0.527													T|||	329	0.0656949	0.1619	0.049	5008	,	,		18816	0.0		0.0646	False		,,,				2504	0.0164				p.I798L		Atlas-SNP	.											.	SALL4	168	.	0			c.A2392C						PASS	.	T	LEU/ILE	696,3710	294.1+/-283.0	54,588,1561	81.0	78.0	79.0		2392	-5.1	0.2	20	dbSNP_114	79	498,8102	142.2+/-198.4	14,470,3816	yes	missense	SALL4	NM_020436.3	5	68,1058,5377	GG,GT,TT		5.7907,15.7966,9.1804	benign	798/1054	50406630	1194,11812	2203	4300	6503	SO:0001583	missense	57167	exon2			ACTTGATGCTTTC	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.2392A>C	20.37:g.50406630T>G	ENSP00000217086:p.Ile798Leu	Somatic	285	1	0.00350877		WXS	Illumina HiSeq	Phase_I	301	154	0.511628	NM_020436	A2A2D8|Q540H3|Q6Y8G6	Missense_Mutation	SNP	ENST00000217086.4	37	CCDS13438.1	159	0.07280219780219781	88	0.17886178861788618	22	0.06077348066298342	0	0.0	49	0.06464379947229551	T	4.686	0.127462	0.08981	0.157966	0.057907	ENSG00000101115	ENST00000217086	T	0.07800	3.16	5.67	-5.11	0.02901	.	0.990681	0.08190	N	0.984093	T	0.00012	0.0000	L	0.38175	1.15	0.20764	P	0.99985162	B	0.06786	0.001	B	0.06405	0.002	T	0.48258	-0.9051	9	0.10902	T	0.67	-18.3976	9.814	0.40840	0.0984:0.488:0.0:0.4137	rs6091375;rs52814636;rs56500327;rs6091375	798	Q9UJQ4	SALL4_HUMAN	L	798	ENSP00000217086:I798L	ENSP00000217086:I798L	I	-	1	0	SALL4	49840037	0.000000	0.05858	0.196000	0.23383	0.847000	0.48162	-1.163000	0.03138	-1.412000	0.02030	-0.408000	0.06270	ATC	T|0.917;G|0.083	0.083	strong		0.527	SALL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079738.3		
ABCG4	64137	hgsc.bcm.edu	37	11	119020719	119020719	+	Missense_Mutation	SNP	C	C	T	rs113286118	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:119020719C>T	ENST00000449422.2	+	2	232	c.44C>T	c.(43-45)cCg>cTg	p.P15L	ABCG4_ENST00000531739.1_Missense_Mutation_p.P15L|ABCG4_ENST00000307417.3_Missense_Mutation_p.P15L	NM_001142505.1	NP_001135977.1	Q9H172	ABCG4_HUMAN	ATP-binding cassette, sub-family G (WHITE), member 4	15					cholesterol efflux (GO:0033344)|transmembrane transport (GO:0055085)	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)|protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(28)|ovary(2)|prostate(1)|skin(1)	44	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)		GGACTAGGGCCGGGGGCTGTG	0.687													C|||	18	0.00359425	0.0	0.0029	5008	,	,		12936	0.0		0.0099	False		,,,				2504	0.0061				p.P15L		Atlas-SNP	.											.	ABCG4	77	.	0			c.C44T						PASS	.	C	LEU/PRO,LEU/PRO	18,4380	25.3+/-52.1	0,18,2181	40.0	48.0	45.0		44,44	4.9	1.0	11	dbSNP_132	45	80,8506	45.8+/-104.6	0,80,4213	no	missense,missense	ABCG4	NM_001142505.1,NM_022169.4	98,98	0,98,6394	TT,TC,CC		0.9317,0.4093,0.7548	benign,benign	15/647,15/647	119020719	98,12886	2199	4293	6492	SO:0001583	missense	64137	exon2			TAGGGCCGGGGGC	AJ300465	CCDS8415.1	11q23	2012-03-14			ENSG00000172350	ENSG00000172350		"""ATP binding cassette transporters / subfamily G"""	13884	protein-coding gene	gene with protein product	"""putative ABC transporter"", ""ATP-binding cassette, subfamily G, member 4"""	607784				11435397	Standard	NM_022169		Approved	WHITE2	uc001pvs.3	Q9H172	OTTHUMG00000166169	ENST00000449422.2:c.44C>T	11.37:g.119020719C>T	ENSP00000406874:p.Pro15Leu	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	93	66	0.709677	NM_022169	A8K1B5|Q8WWH0|Q8WWH1|Q8WWH2	Missense_Mutation	SNP	ENST00000449422.2	37	CCDS8415.1	7	0.003205128205128205	0	0.0	1	0.0027624309392265192	0	0.0	6	0.0079155672823219	C	16.82	3.228121	0.58777	0.004093	0.009317	ENSG00000172350	ENST00000307417;ENST00000524604;ENST00000449422;ENST00000531739	T;T;T;T	0.06933	3.24;3.24;3.24;3.24	4.9	4.9	0.64082	.	0.060836	0.64402	D	0.000002	T	0.04679	0.0127	L	0.43152	1.355	0.53005	D	0.999968	P	0.47545	0.897	B	0.30029	0.11	T	0.17653	-1.0362	10	0.87932	D	0	-22.1157	13.6442	0.62270	0.0:0.8456:0.1544:0.0	.	15	Q9H172	ABCG4_HUMAN	L	15	ENSP00000304111:P15L;ENSP00000431915:P15L;ENSP00000406874:P15L;ENSP00000434318:P15L	ENSP00000304111:P15L	P	+	2	0	ABCG4	118525929	0.061000	0.20836	0.996000	0.52242	0.896000	0.52359	0.364000	0.20325	2.269000	0.75478	0.555000	0.69702	CCG	C|0.994;T|0.006	0.006	strong		0.687	ABCG4-002	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388215.1	NM_022169	
SCAF1	58506	hgsc.bcm.edu	37	19	50161091	50161091	+	Missense_Mutation	SNP	A	A	G	rs61743199	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:50161091A>G	ENST00000360565.3	+	10	3816	c.3692A>G	c.(3691-3693)aAg>aGg	p.K1231R	IRF3_ENST00000599680.1_5'Flank	NM_021228.2	NP_067051.2	Q9H7N4	SFR19_HUMAN	SR-related CTD-associated factor 1	1231	Necessary for interaction with the CTD domain of POLR2A.				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)		TACTATCAGAAGAAGGACATC	0.612													A|||	95	0.0189696	0.0023	0.0274	5008	,	,		20646	0.0		0.0696	False		,,,				2504	0.0031				p.K1231R		Atlas-SNP	.											.	SCAF1	78	.	0			c.A3692G						PASS	.	A	ARG/LYS	65,4341	55.5+/-91.7	0,65,2138	97.0	66.0	76.0		3692	5.2	1.0	19	dbSNP_129	76	615,7985	154.0+/-208.3	19,577,3704	yes	missense	SCAF1	NM_021228.2	26	19,642,5842	GG,GA,AA		7.1512,1.4753,5.2284	possibly-damaging	1231/1313	50161091	680,12326	2203	4300	6503	SO:0001583	missense	58506	exon10			ATCAGAAGAAGGA	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.3692A>G	19.37:g.50161091A>G	ENSP00000353769:p.Lys1231Arg	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	107	44	0.411215	NM_021228	Q7Z5V7|Q8WVA1|Q9NR59	Missense_Mutation	SNP	ENST00000360565.3	37	CCDS33074.1	63	0.028846153846153848	3	0.006097560975609756	11	0.03038674033149171	0	0.0	49	0.06464379947229551	A	14.10	2.435439	0.43224	0.014753	0.071512	ENSG00000126461	ENST00000360565	T	0.34275	1.37	5.21	5.21	0.72293	.	0.255070	0.27349	N	0.019774	T	0.02047	0.0064	N	0.25890	0.77	0.40437	D	0.980001	B	0.33940	0.433	B	0.31686	0.134	T	0.02333	-1.1175	10	0.51188	T	0.08	-14.5273	14.2066	0.65739	1.0:0.0:0.0:0.0	rs61743199	1231	Q9H7N4	SFR19_HUMAN	R	1231	ENSP00000353769:K1231R	ENSP00000353769:K1231R	K	+	2	0	SCAF1	54852903	1.000000	0.71417	1.000000	0.80357	0.915000	0.54546	4.152000	0.58111	2.192000	0.70111	0.528000	0.53228	AAG	A|0.956;G|0.043;T|0.000	0.043	strong		0.612	SCAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465764.1	NM_021228	
RYR3	6263	hgsc.bcm.edu	37	15	33873751	33873751	+	Missense_Mutation	SNP	G	G	A	rs2077268	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:33873751G>A	ENST00000389232.4	+	14	1550	c.1480G>A	c.(1480-1482)Gtc>Atc	p.V494I	RYR3_ENST00000415757.3_Missense_Mutation_p.V494I	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	494			V -> I (in dbSNP:rs2077268). {ECO:0000269|PubMed:9515741}.		calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cellular response to ATP (GO:0071318)|cellular response to caffeine (GO:0071313)|cellular response to calcium ion (GO:0071277)|cellular response to magnesium ion (GO:0071286)|ion transmembrane transport (GO:0034220)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|protein homotetramerization (GO:0051289)|striated muscle contraction (GO:0006941)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|ryanodine-sensitive calcium-release channel activity (GO:0005219)			NS(3)|breast(9)|central_nervous_system(8)|cervix(2)|endometrium(29)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(55)|lung(148)|ovary(7)|pancreas(1)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(3)	311		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)		CCGCTTAAATGTCTACAATAG	0.438													A|||	721	0.14397	0.3601	0.0677	5008	,	,		22771	0.0427		0.1103	False		,,,				2504	0.045				p.V494I		Atlas-SNP	.											RYR3,NS,carcinoma,-1,1	RYR3	760	1	0			c.G1480A						PASS	.	A	ILE/VAL	1119,2717		171,777,970	138.0	138.0	138.0		1480	1.4	0.8	15	dbSNP_96	138	788,7500		38,712,3394	yes	missense	RYR3	NM_001036.3	29	209,1489,4364	AA,AG,GG		9.5077,29.171,15.7291	benign	494/4871	33873751	1907,10217	1918	4144	6062	SO:0001583	missense	6263	exon14			TTAAATGTCTACA		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.1480G>A	15.37:g.33873751G>A	ENSP00000373884:p.Val494Ile	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	101	31	0.306931	NM_001243996	O15175|Q15412	Missense_Mutation	SNP	ENST00000389232.4	37	CCDS45210.1	314	0.14377289377289376	176	0.35772357723577236	31	0.0856353591160221	23	0.04020979020979021	84	0.11081794195250659	A	10.64	1.406602	0.25378	0.29171	0.095077	ENSG00000198838	ENST00000389232;ENST00000415757;ENST00000361728	D;D	0.95342	-3.68;-3.68	5.41	1.39	0.22231	Intracellular calcium-release channel (1);	0.353051	0.25383	N	0.031074	T	0.00012	0.0000	L	0.42529	1.33	0.48830	P	2.870000000000372E-4	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.002	T	0.06092	-1.0846	9	0.22109	T	0.4	.	9.163	0.37035	0.4649:0.0:0.5351:0.0	rs2077268;rs16972762;rs56662888;rs2077268	494;494	Q15413-2;Q15413	.;RYR3_HUMAN	I	494	ENSP00000373884:V494I;ENSP00000399610:V494I	ENSP00000354735:V494I	V	+	1	0	RYR3	31661043	1.000000	0.71417	0.823000	0.32752	0.982000	0.71751	2.189000	0.42621	0.059000	0.16252	-0.360000	0.07572	GTC	G|0.846;A|0.154	0.154	strong		0.438	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1		
EXOSC7	23016	hgsc.bcm.edu	37	3	45052775	45052775	+	Missense_Mutation	SNP	G	G	C	rs6794	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:45052775G>C	ENST00000265564.7	+	8	868	c.820G>C	c.(820-822)Gtg>Ctg	p.V274L	EXOSC7_ENST00000461361.1_3'UTR|CLEC3B_ENST00000490386.1_Intron	NM_015004.3	NP_055819.2	Q15024	EXOS7_HUMAN	exosome component 7	274			V -> L (in dbSNP:rs6794). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:21269460, ECO:0000269|PubMed:7788527}.		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 catabolic process (GO:0006401)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|rRNA processing (GO:0006364)	cytosol (GO:0005829)|exosome (RNase complex) (GO:0000178)|nucleus (GO:0005634)	3'-5'-exoribonuclease activity (GO:0000175)|RNA binding (GO:0003723)			endometrium(3)|large_intestine(1)|lung(3)	7				BRCA - Breast invasive adenocarcinoma(193;0.00911)|KIRC - Kidney renal clear cell carcinoma(197;0.0509)|Kidney(197;0.064)		GCAGAGTGTTGTGCACAAGGA	0.517													C|||	3535	0.705871	0.7269	0.6239	5008	,	,		17322	0.9008		0.4841	False		,,,				2504	0.7628				p.V274L		Atlas-SNP	.											.	EXOSC7	19	.	0			c.G820C						PASS	.	C	LEU/VAL	2989,1417	462.4+/-353.2	1008,973,222	88.0	74.0	79.0		820	2.9	0.0	3	dbSNP_52	79	4411,4189	568.3+/-389.0	1124,2163,1013	yes	missense	EXOSC7	NM_015004.3	32	2132,3136,1235	CC,CG,GG		48.7093,32.1607,43.1032	benign	274/292	45052775	7400,5606	2203	4300	6503	SO:0001583	missense	23016	exon8			AGTGTTGTGCACA	BC012831	CCDS2725.1	3p21.32	2010-05-07			ENSG00000075914	ENSG00000075914	3.1.13.-		28112	protein-coding gene	gene with protein product		606488				11719186, 11812149	Standard	NR_023353		Approved	hRrp42p, Rrp42p, RRP42, EAP1, KIAA0116, p8	uc003coi.2	Q15024	OTTHUMG00000133095	ENST00000265564.7:c.820G>C	3.37:g.45052775G>C	ENSP00000265564:p.Val274Leu	Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	140	70	0.5	NM_015004	Q96E72	Missense_Mutation	SNP	ENST00000265564.7	37	CCDS2725.1	1472	0.673992673992674	352	0.7154471544715447	219	0.6049723756906077	525	0.9178321678321678	376	0.49604221635883905	C	0.007	-1.965217	0.00461	0.678393	0.512907	ENSG00000075914	ENST00000265564	T	0.35236	1.32	6.04	2.93	0.34026	.	0.000000	0.85682	N	0.000000	T	0.00012	0.0000	N	0.00010	-3.02	0.09310	P	0.999999868643	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.35325	-0.9793	9	0.02654	T	1	-2.5299	4.791	0.13248	0.0:0.4471:0.1569:0.3961	rs6794;rs1059918;rs3200759;rs17856408;rs58708695;rs6794	274;274	B2RDZ9;Q15024	.;EXOS7_HUMAN	L	274	ENSP00000265564:V274L	ENSP00000265564:V274L	V	+	1	0	EXOSC7	45027779	0.422000	0.25473	0.001000	0.08648	0.006000	0.05464	0.951000	0.29135	0.170000	0.19704	-2.319000	0.00253	GTG	G|0.396;C|0.604	0.604	strong		0.517	EXOSC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256754.2	NM_015004	
PPIL1	51645	hgsc.bcm.edu	37	6	36824399	36824399	+	Silent	SNP	C	C	T	rs2071823	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:36824399C>T	ENST00000373699.5	-	3	494	c.243G>A	c.(241-243)caG>caA	p.Q81Q	PPIL1_ENST00000483552.1_5'UTR	NM_016059.4	NP_057143.1	Q9Y3C6	PPIL1_HUMAN	peptidylprolyl isomerase (cyclophilin)-like 1	81	PPIase cyclophilin-type. {ECO:0000255|PROSITE-ProRule:PRU00156}.				mRNA splicing, via spliceosome (GO:0000398)|protein folding (GO:0006457)	catalytic step 2 spliceosome (GO:0071013)|extracellular vesicular exosome (GO:0070062)	peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			lung(1)|ovary(1)	2						CATCTTCAAACTGTTTGCCAT	0.453													C|||	914	0.182508	0.0136	0.2233	5008	,	,		21676	0.3542		0.2386	False		,,,				2504	0.1472				p.Q81Q		Atlas-SNP	.											.	PPIL1	6	.	0			c.G243A						PASS	.	C		248,4158	144.6+/-179.5	6,236,1961	127.0	113.0	118.0		243	4.9	1.0	6	dbSNP_96	118	2185,6415	372.7+/-336.7	268,1649,2383	no	coding-synonymous	PPIL1	NM_016059.4		274,1885,4344	TT,TC,CC		25.407,5.6287,18.7068		81/167	36824399	2433,10573	2203	4300	6503	SO:0001819	synonymous_variant	51645	exon3			TTCAAACTGTTTG	AF090992	CCDS4826.1	6p21.1	2008-08-29			ENSG00000137168	ENSG00000137168			9260	protein-coding gene	gene with protein product		601301				10072585, 8978786	Standard	NM_016059		Approved	CYPL1	uc003omu.2	Q9Y3C6	OTTHUMG00000014612	ENST00000373699.5:c.243G>A	6.37:g.36824399C>T		Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	159	82	0.515723	NM_016059	O15001|Q5TDC9	Silent	SNP	ENST00000373699.5	37	CCDS4826.1																																																																																			C|0.796;G|0.000;T|0.204	0.204	strong		0.453	PPIL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040382.1		
TNN	63923	hgsc.bcm.edu	37	1	175105996	175105996	+	Missense_Mutation	SNP	C	C	T	rs2072036	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	82	0	0		WXS	Illumina HiSeq	Phase_I	65	34	0.523077	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	
AHNAK2	113146	hgsc.bcm.edu	37	14	105419557	105419557	+	Missense_Mutation	SNP	G	G	A	rs78204285|rs386781105	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:105419557G>A	ENST00000333244.5	-	7	2350	c.2231C>T	c.(2230-2232)cCg>cTg	p.P744L	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	744						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)			GGGGCCCTCCGGAAGTTTCAC	0.632													G|||	1015	0.202676	0.2943	0.0807	5008	,	,		15957	0.2917		0.0467	False		,,,				2504	0.2342				p.P744L		Atlas-SNP	.											.	AHNAK2	719	.	0			c.C2231T						PASS	.	G	LEU/PRO	45,3743		13,19,1862	71.0	86.0	81.0		2231	-0.7	0.0	14	dbSNP_131	81	0,8216		0,0,4108	no	missense	AHNAK2	NM_138420.2	98	13,19,5970	AA,AG,GG		0.0,1.188,0.3749	benign	744/5796	105419557	45,11959	1894	4108	6002	SO:0001583	missense	113146	exon7			CCCTCCGGAAGTT	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.2231C>T	14.37:g.105419557G>A	ENSP00000353114:p.Pro744Leu	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	124	57	0.459677	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	.	.	.	.	.	.	.	.	.	.	g	0.593	-0.832018	0.02713	0.01188	0.0	ENSG00000185567	ENST00000333244	T	0.03094	4.05	2.59	-0.675	0.11364	.	.	.	.	.	T	0.05731	0.0150	M	0.92970	3.365	0.09310	N	1	D	0.56287	0.975	B	0.42214	0.38	T	0.11299	-1.0593	9	0.49607	T	0.09	-0.0068	5.3983	0.16281	0.1023:0.0:0.3935:0.5042	.	744	Q8IVF2	AHNK2_HUMAN	L	744	ENSP00000353114:P744L	ENSP00000353114:P744L	P	-	2	0	AHNAK2	104490602	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.004000	0.13106	-0.540000	0.06265	-3.300000	0.00046	CCG	G|0.968;A|0.032	0.032	strong		0.632	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
DNAH2	146754	hgsc.bcm.edu	37	17	7680159	7680159	+	Silent	SNP	G	G	A	rs62059684	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:7680159G>A	ENST00000572933.1	+	32	6470	c.5010G>A	c.(5008-5010)gcG>gcA	p.A1670A	DNAH2_ENST00000389173.2_Silent_p.A1670A			Q9P225	DYH2_HUMAN	dynein, axonemal, heavy chain 2	1670	Stem. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(3)|breast(11)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(53)|liver(2)|lung(49)|ovary(7)|prostate(7)|skin(15)|upper_aerodigestive_tract(1)|urinary_tract(1)	189		all_cancers(10;4.66e-07)|Prostate(122;0.081)				TGCTGACAGCGAAGGAGCGGG	0.572													G|||	603	0.120407	0.0113	0.2046	5008	,	,		18971	0.0		0.3579	False		,,,				2504	0.0879				p.A1670A		Atlas-SNP	.											.	DNAH2	498	.	0			c.G5010A						PASS	.	G		288,4118	158.1+/-190.9	11,266,1926	69.0	55.0	60.0		5010	-3.8	0.9	17	dbSNP_129	60	2942,5658	456.2+/-364.0	477,1988,1835	no	coding-synonymous	DNAH2	NM_020877.2		488,2254,3761	AA,AG,GG		34.2093,6.5365,24.8347		1670/4428	7680159	3230,9776	2203	4300	6503	SO:0001819	synonymous_variant	146754	exon31			GACAGCGAAGGAG	U83570, AK128517	CCDS32551.1	17p13.1	2007-10-05	2006-09-04			ENSG00000183914		"""Axonemal dyneins"""	2948	protein-coding gene	gene with protein product		603333	"""dynein, axonemal, heavy polypeptide 2"", ""dynein heavy chain domain 3"""	DNHD3		9256245	Standard	XM_005256470		Approved	KIAA1503, FLJ46675	uc002giu.1	Q9P225		ENST00000572933.1:c.5010G>A	17.37:g.7680159G>A		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	71	38	0.535211	NM_020877	A8K992|B5MDX5|O15434|Q6PIH3|Q6ZR42	Silent	SNP	ENST00000572933.1	37	CCDS32551.1																																																																																			G|0.764;A|0.236	0.236	strong		0.572	DNAH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440241.1	NM_020877	
TXNL1	9352	hgsc.bcm.edu	37	18	54281790	54281790	+	Silent	SNP	T	T	C	rs655539	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:54281790T>C	ENST00000217515.6	-	6	804	c.600A>G	c.(598-600)ctA>ctG	p.L200L	TXNL1_ENST00000540155.1_Silent_p.L77L|TXNL1_ENST00000590954.1_Silent_p.L200L	NM_004786.2	NP_004777.1	O43396	TXNL1_HUMAN	thioredoxin-like 1	200	PITH. {ECO:0000255|PROSITE- ProRule:PRU00864}.				cell redox homeostasis (GO:0045454)|glycerol ether metabolic process (GO:0006662)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|proteasome complex (GO:0000502)	disulfide oxidoreductase activity (GO:0015036)|protein disulfide oxidoreductase activity (GO:0015035)			endometrium(1)|large_intestine(1)|lung(1)|urinary_tract(1)	4				READ - Rectum adenocarcinoma(59;0.193)|Colorectal(16;0.211)		TAGATCGGGGTAGGTTGATAA	0.353													T|||	93	0.0185703	0.003	0.0216	5008	,	,		17755	0.0		0.0606	False		,,,				2504	0.0133				p.L200L		Atlas-SNP	.											.	TXNL1	30	.	0			c.A600G						PASS	.	T		56,4350	54.9+/-90.9	0,56,2147	95.0	90.0	92.0		600	-3.5	1.0	18	dbSNP_83	92	528,8072	148.2+/-203.4	13,502,3785	no	coding-synonymous	TXNL1	NM_004786.2		13,558,5932	CC,CT,TT		6.1395,1.271,4.4902		200/290	54281790	584,12422	2203	4300	6503	SO:0001819	synonymous_variant	9352	exon6			TCGGGGTAGGTTG	AF003938	CCDS11961.1	18q21.31	2011-01-17	2004-05-06	2004-05-07	ENSG00000091164	ENSG00000091164			12436	protein-coding gene	gene with protein product	"""thioredoxin-like, 32kD"""	603049	"""thioredoxin-like, 32kDa"""	TXNL		9473519, 9668102	Standard	NM_004786		Approved	Txl, TRP32	uc002lgg.3	O43396	OTTHUMG00000132722	ENST00000217515.6:c.600A>G	18.37:g.54281790T>C		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	78	75	0.961538	NM_004786		Silent	SNP	ENST00000217515.6	37	CCDS11961.1																																																																																			T|0.962;C|0.038	0.038	strong		0.353	TXNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256064.2		
CX3CR1	1524	hgsc.bcm.edu	37	3	39307162	39307162	+	Missense_Mutation	SNP	G	G	A	rs3732378	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:39307162G>A	ENST00000541347.1	-	2	1078	c.839C>T	c.(838-840)aCg>aTg	p.T280M	CX3CR1_ENST00000542107.1_Missense_Mutation_p.T280M|CX3CR1_ENST00000399220.2_Missense_Mutation_p.T280M|CX3CR1_ENST00000358309.3_Missense_Mutation_p.T312M	NM_001171171.1	NP_001164642.1	P49238	CX3C1_HUMAN	chemokine (C-X3-C motif) receptor 1	280			T -> M (common polymorphism in Caucasian population; associated with higher risk of developing ARMD12; chemotaxis of monocytes of individuals with homozygous Met-280 and Ile-249 genotypes is impaired in the presence of bound CX3CR1 protein; dbSNP:rs3732378). {ECO:0000269|PubMed:10731151, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15208270, ECO:0000269|Ref.6}.		cell adhesion (GO:0007155)|cellular defense response (GO:0006968)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to transforming growth factor beta stimulus (GO:0071560)|cerebral cortex cell migration (GO:0021795)|chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|macrophage chemotaxis (GO:0048246)|microglial cell activation involved in immune response (GO:0002282)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell migration (GO:0030336)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|positive regulation of angiogenesis (GO:0045766)|response to wounding (GO:0009611)|viral process (GO:0016032)	integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|neuronal cell body membrane (GO:0032809)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	C-X3-C chemokine receptor activity (GO:0016495)|chemokine receptor activity (GO:0004950)			endometrium(3)|kidney(1)|large_intestine(4)|lung(13)|prostate(1)|skin(1)|urinary_tract(1)	24				KIRC - Kidney renal clear cell carcinoma(284;0.0557)|Kidney(284;0.0699)		AAATGCAACCGTCTCAGTCAC	0.468													G|||	428	0.0854633	0.0083	0.1556	5008	,	,		22185	0.0288		0.172	False		,,,				2504	0.1094				p.T312M		Atlas-SNP	.											CX3CR1_ENST00000358309,NS,adenocarcinoma,+1,4	CX3CR1	91	4	0			c.C935T	GRCh37	CM000505	CX3CR1	M	rs3732378	PASS	.	G	MET/THR,MET/THR,MET/THR,MET/THR	126,3788		2,122,1833	138.0	136.0	137.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	839,839,935,839	4.0	0.7	3	dbSNP_107	137	1432,6886		124,1184,2851	yes	missense,missense,missense,missense	CX3CR1	NM_001171171.1,NM_001171172.1,NM_001171174.1,NM_001337.3	81,81,81,81	126,1306,4684	AA,AG,GG		17.2157,3.2192,12.7371	probably-damaging,probably-damaging,probably-damaging,probably-damaging	280/356,280/356,312/388,280/356	39307162	1558,10674	1957	4159	6116	SO:0001583	missense	1524	exon2			GCAACCGTCTCAG	BC028078	CCDS43069.1, CCDS54571.1	3p21.3	2012-08-08	2002-08-22		ENSG00000168329	ENSG00000168329		"""GPCR / Class A : Chemokine receptors : C-X-3-C motif"""	2558	protein-coding gene	gene with protein product		601470	"""chemokine (C-X3-C) receptor 1"""	GPR13, CMKBRL1		9726990, 7646814	Standard	NM_001171171		Approved	CMKDR1, V28, CCRL1	uc021wwc.1	P49238	OTTHUMG00000156249	ENST00000541347.1:c.839C>T	3.37:g.39307162G>A	ENSP00000439140:p.Thr280Met	Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	110	49	0.445455	NM_001171174	A0N0N6|B2R5Z4|J3KP17	Missense_Mutation	SNP	ENST00000541347.1	37	CCDS43069.1	211	0.09661172161172162	6	0.012195121951219513	57	0.1574585635359116	19	0.033216783216783216	129	0.17018469656992086	G	11.03	1.519699	0.27211	0.032192	0.172157	ENSG00000168329	ENST00000399220;ENST00000538756;ENST00000358309;ENST00000541347;ENST00000542107	T;T;T;T	0.71698	-0.59;-0.59;-0.59;-0.59	5.77	3.98	0.46160	GPCR, rhodopsin-like superfamily (1);	0.227311	0.45361	N	0.000375	T	0.00300	0.0009	M	0.80028	2.48	0.42331	P	0.007707000000000019	P	0.42248	0.774	B	0.28139	0.086	T	0.29027	-1.0025	9	0.59425	D	0.04	.	6.1781	0.20455	0.155:0.0:0.6947:0.1503	rs3732378;rs17792900;rs52789411;rs60081475;rs3732378	280	P49238	CX3C1_HUMAN	M	280;288;312;280;280	ENSP00000382166:T280M;ENSP00000351059:T312M;ENSP00000439140:T280M;ENSP00000444928:T280M	ENSP00000351059:T312M	T	-	2	0	CX3CR1	39282166	0.922000	0.31269	0.681000	0.30009	0.221000	0.24807	1.916000	0.39986	0.790000	0.33803	0.655000	0.94253	ACG	A|0.101;C|0.011	0.101	strong		0.468	CX3CR1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343613.1	NM_001337	
HIST1H1D	3007	hgsc.bcm.edu	37	6	26234735	26234735	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:26234735C>T	ENST00000244534.5	-	1	481	c.427G>A	c.(427-429)Gct>Act	p.A143T		NM_005320.2	NP_005311.1	P16402	H13_HUMAN	histone cluster 1, H1d	143					nucleosome assembly (GO:0006334)|nucleosome positioning (GO:0016584)	nuclear chromatin (GO:0000790)|nuclear euchromatin (GO:0005719)|nucleosome (GO:0000786)	chromatin DNA binding (GO:0031490)|poly(A) RNA binding (GO:0044822)			breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(5)|large_intestine(4)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	23		all_hematologic(11;0.0945)|Acute lymphoblastic leukemia(11;0.167)				GCGGCGCCAGCCACCTTCTTG	0.572																																					p.A143T		Atlas-SNP	.											.	HIST1H1D	40	.	0			c.G427A						PASS	.						65.0	71.0	69.0					6																	26234735		2203	4300	6503	SO:0001583	missense	3007	exon1			CGCCAGCCACCTT	M60747	CCDS4597.1	6p21.3	2012-10-02	2006-10-11	2003-02-21	ENSG00000124575	ENSG00000124575		"""Histones / Replication-dependent"""	4717	protein-coding gene	gene with protein product		142210	"""H1 histone family, member 3"", ""histone 1, H1d"""	H1F3		1916825, 12408966	Standard	NM_005320		Approved	H1.3, H1d, H1s-2	uc003nhd.3	P16402	OTTHUMG00000014432	ENST00000244534.5:c.427G>A	6.37:g.26234735C>T	ENSP00000244534:p.Ala143Thr	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	99	27	0.272727	NM_005320	B2R751|Q2M2I2	Missense_Mutation	SNP	ENST00000244534.5	37	CCDS4597.1	.	.	.	.	.	.	.	.	.	.	.	0.960	-0.703518	0.03255	.	.	ENSG00000124575	ENST00000244534	T	0.14022	2.54	4.7	-4.82	0.03171	.	0.725492	0.13325	N	0.396354	T	0.01061	0.0035	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.45396	-0.9264	10	0.06891	T	0.86	-17.2311	5.5857	0.17274	0.2338:0.4156:0.0:0.3506	.	143	P16402	H13_HUMAN	T	143	ENSP00000244534:A143T	ENSP00000244534:A143T	A	-	1	0	HIST1H1D	26342714	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.356000	0.07661	-0.537000	0.06290	-0.295000	0.09555	GCT	.	.	none		0.572	HIST1H1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040095.1	NM_005320	
RGPD3	653489	hgsc.bcm.edu	37	2	107041612	107041612	+	Missense_Mutation	SNP	A	A	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:107041612A>C	ENST00000409886.3	-	20	2898	c.2811T>G	c.(2809-2811)agT>agG	p.S937R	RGPD3_ENST00000304514.7_Missense_Mutation_p.S937R	NM_001144013.1	NP_001137485.1	A6NKT7	RGPD3_HUMAN	RANBP2-like and GRIP domain containing 3	937					protein targeting to Golgi (GO:0000042)					breast(2)|central_nervous_system(1)|endometrium(50)|kidney(4)|lung(11)|ovary(1)|urinary_tract(2)	71						GAGGCTTTTCACTTTTCTTTT	0.403																																					p.S937R		Atlas-SNP	.											RGPD3_ENST00000304514,NS,carcinoma,0,2	RGPD3	316	2	0			c.T2811G						scavenged	.						86.0	76.0	79.0					2																	107041612		692	1590	2282	SO:0001583	missense	653489	exon20			CTTTTCACTTTTC		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.2811T>G	2.37:g.107041612A>C	ENSP00000386588:p.Ser937Arg	Somatic	734	2	0.0027248		WXS	Illumina HiSeq	Phase_I	859	231	0.268917	NM_001144013	B8ZZM4	Missense_Mutation	SNP	ENST00000409886.3	37	CCDS46379.1	.	.	.	.	.	.	.	.	.	.	.	5.022	0.189738	0.09547	.	.	ENSG00000153165	ENST00000409886;ENST00000452099;ENST00000304514	T;T	0.40756	1.03;1.02	2.35	1.1	0.20463	.	.	.	.	.	T	0.34366	0.0895	L	0.54323	1.7	0.09310	N	1	P	0.49559	0.925	B	0.43575	0.424	T	0.16188	-1.0411	9	0.22706	T	0.39	-2.0278	5.5415	0.17041	0.844:0.0:0.156:0.0	.	937	A6NKT7	RGPD3_HUMAN	R	937;695;937	ENSP00000386588:S937R;ENSP00000303659:S937R	ENSP00000303659:S937R	S	-	3	2	RGPD3	106408044	0.541000	0.26417	0.031000	0.17742	0.516000	0.34256	1.090000	0.30902	0.167000	0.19631	0.156000	0.16432	AGT	.	.	weak		0.403	RGPD3-002	KNOWN	not_best_in_genome_evidence|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000329975.1	XM_929931	
BTN3A2	11118	hgsc.bcm.edu	37	6	26368279	26368279	+	Splice_Site	SNP	G	G	A	rs71557335	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:26368279G>A	ENST00000356386.2	+	2	183		c.e2+1		BTN3A2_ENST00000396948.1_Splice_Site|BTN3A2_ENST00000396934.3_Intron|AL021917.1_ENST00000401160.1_RNA|BTN3A2_ENST00000532994.1_Splice_Site|BTN3A2_ENST00000527422.1_Splice_Site|BTN3A2_ENST00000508906.2_Splice_Site|BTN3A2_ENST00000377708.2_Splice_Site	NM_001197246.2|NM_001197247.1|NM_007047.3	NP_001184175.1|NP_001184176.1|NP_008978.2	P78410	BT3A2_HUMAN	butyrophilin, subfamily 3, member A2						interferon-gamma secretion (GO:0072643)|T cell mediated immunity (GO:0002456)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(5)	10						TTTGGCAGAGGTAAGATCTTC	0.428													G|||	409	0.0816693	0.0287	0.0403	5008	,	,		19572	0.0992		0.1123	False		,,,				2504	0.1329				.		Atlas-SNP	.											.	BTN3A2	44	.	0			.						PASS	.																																			SO:0001630	splice_region_variant	11118	.			GCAGAGGTAAGAT	U90546	CCDS4605.1, CCDS56399.1, CCDS56400.1	6p22.1	2014-01-14			ENSG00000186470	ENSG00000186470		"""Immunoglobulin superfamily / V-set domain containing"", ""Butyrophilins"""	1139	protein-coding gene	gene with protein product		613594				9149941	Standard	NM_007047		Approved	BTN3.2	uc010jqi.2	P78410	OTTHUMG00000014450	ENST00000356386.2:c.-6+1G>A	6.37:g.26368279G>A		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	64	64	1	.	B4DRT7|B4E103|F5H791|F8W6E0|O00477|O15338|O75658|Q76PA0|Q9BU81|Q9NR44	Splice_Site	SNP	ENST00000356386.2	37	CCDS4605.1																																																																																			G|0.927;A|0.073	0.073	strong		0.428	BTN3A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040113.2		Intron
MUC4	4585	hgsc.bcm.edu	37	3	195508500	195508500	+	Missense_Mutation	SNP	G	G	C	rs374619108		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195508500G>C	ENST00000463781.3	-	2	10410	c.9951C>G	c.(9949-9951)gaC>gaG	p.D3317E	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.D3317E	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.D3317E(2)|p.V3305_S3320delVSTGHATPLLVTDASS(1)|p.V3305_S3336delVSTGHATPLLVTDASSASTGHATPLHVTSPSS(1)|p.S3317R(1)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		CTGAGGAAGCGTCGGTGACAA	0.577																																					p.D3317E		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,6	MUC4	1505	6	5	Substitution - Missense(3)|Deletion - In frame(2)	stomach(4)|kidney(1)	c.C9951G						PASS	.						9.0	12.0	11.0					3																	195508500		600	1514	2114	SO:0001583	missense	4585	exon2			GGAAGCGTCGGTG	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.9951C>G	3.37:g.195508500G>C	ENSP00000417498:p.Asp3317Glu	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	34	8	0.235294	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	g	6.278	0.419423	0.11928	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.30981	1.61;1.51	0.423	0.423	0.16463	.	.	.	.	.	T	0.14141	0.0342	N	0.19112	0.55	0.09310	N	1	P	0.43352	0.804	B	0.33196	0.159	T	0.14144	-1.0483	7	.	.	.	.	.	.	.	.	3189	E7ESK3	.	E	3317	ENSP00000417498:D3317E;ENSP00000420243:D3317E	.	D	-	3	2	MUC4	196993279	0.001000	0.12720	0.001000	0.08648	0.004000	0.04260	0.672000	0.25187	0.494000	0.27859	0.089000	0.15464	GAC	.	.	weak		0.577	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
PDIA2	64714	hgsc.bcm.edu	37	16	334890	334890	+	Missense_Mutation	SNP	G	G	A	rs419949	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:334890G>A	ENST00000219406.6	+	4	571	c.553G>A	c.(553-555)Gag>Aag	p.E185K	PDIA2_ENST00000404312.1_Missense_Mutation_p.E182K|PDIA2_ENST00000462950.1_3'UTR	NM_006849.2	NP_006840.2	Q13087	PDIA2_HUMAN	protein disulfide isomerase family A, member 2	185			E -> K (in dbSNP:rs419949).		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)				CCTGCAGGACGAGGACGTGGC	0.677													g|||	511	0.102037	0.1641	0.1023	5008	,	,		16673	0.001		0.1839	False		,,,				2504	0.0378				p.E185K		Atlas-SNP	.											.	PDIA2	51	.	0			c.G553A						PASS	.	G	LYS/GLU	607,3523		36,535,1494	39.0	47.0	45.0		553	0.3	0.1	16	dbSNP_80	45	1658,6698		175,1308,2695	yes	missense	PDIA2	NM_006849.2	56	211,1843,4189	AA,AG,GG		19.842,14.6973,18.1403	benign	185/526	334890	2265,10221	2065	4178	6243	SO:0001583	missense	64714	exon4			CAGGACGAGGACG	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.553G>A	16.37:g.334890G>A	ENSP00000219406:p.Glu185Lys	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	89	12	0.134831	NM_006849	A6ZJ64|B4DI27|Q2WGM4|Q4TT67|Q6B010|Q96KJ6|Q9BW95	Missense_Mutation	SNP	ENST00000219406.6	37	CCDS42089.1	271	0.12408424908424909	93	0.18902439024390244	41	0.1132596685082873	0	0.0	137	0.18073878627968337	g	6.194	0.403887	0.11754	0.146973	0.19842	ENSG00000185615	ENST00000219406;ENST00000455994;ENST00000404312	T;T	0.23147	1.92;1.92	3.66	0.305	0.15801	Thioredoxin-like fold (2);	0.433699	0.23706	N	0.045370	T	0.00039	0.0001	M	0.67700	2.07	0.33439	P	0.41782600000000003	B	0.17852	0.024	B	0.24269	0.052	T	0.12400	-1.0549	9	0.36615	T	0.2	.	5.0832	0.14668	0.3036:0.1519:0.5445:0.0	rs419949;rs59217529;rs419949	185	Q13087	PDIA2_HUMAN	K	185;154;182	ENSP00000219406:E185K;ENSP00000384410:E182K	ENSP00000219406:E185K	E	+	1	0	PDIA2	274891	0.006000	0.16342	0.118000	0.21660	0.118000	0.20060	0.523000	0.22925	-0.003000	0.14444	-0.389000	0.06534	GAG	G|0.849;A|0.151	0.151	strong		0.677	PDIA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139315.3	NM_006849	
SMG1	23049	hgsc.bcm.edu	37	16	18847416	18847416	+	Silent	SNP	G	G	A	rs3816919	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:18847416G>A	ENST00000446231.2	-	48	8308	c.7896C>T	c.(7894-7896)tcC>tcT	p.S2632S	SMG1_ENST00000389467.3_Silent_p.S2632S			Q96Q15	SMG1_HUMAN	SMG1 phosphatidylinositol 3-kinase-related kinase	2632					DNA repair (GO:0006281)|gene expression (GO:0010467)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol phosphorylation (GO:0046854)|protein autophosphorylation (GO:0046777)|response to stress (GO:0006950)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(8)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(37)|ovary(1)|skin(1)|stomach(4)|urinary_tract(1)	92						CACGGAGCACGGAGCGCCTCT	0.562													G|||	539	0.107628	0.0794	0.1657	5008	,	,		19236	0.1151		0.0765	False		,,,				2504	0.1288				p.S2632S		Atlas-SNP	.											.	SMG1	401	.	0			c.C7896T						PASS	.	G		345,3851		13,319,1766	43.0	42.0	42.0		7896	-11.6	0.0	16	dbSNP_107	42	771,7675		35,701,3487	no	coding-synonymous	SMG1	NM_015092.4		48,1020,5253	AA,AG,GG		9.1286,8.2221,8.8277		2632/3662	18847416	1116,11526	2098	4223	6321	SO:0001819	synonymous_variant	23049	exon48			GAGCACGGAGCGC	AB061371	CCDS45430.1	16p12.3	2013-07-02	2013-07-02		ENSG00000157106	ENSG00000157106			30045	protein-coding gene	gene with protein product	"""phosphatidylinositol 3-kinase-related kinase"""	607032	"""smg-1 homolog, phosphatidylinositol 3-kinase-related kinase (C. elegans)"""			9455477, 11331269, 17229728	Standard	NM_015092		Approved	LIP, KIAA0421, ATX	uc002dfm.3	Q96Q15	OTTHUMG00000166900	ENST00000446231.2:c.7896C>T	16.37:g.18847416G>A		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	130	76	0.584615	NM_015092	O43305|Q13284|Q8NFX2|Q96QV0|Q96RW3	Silent	SNP	ENST00000446231.2	37	CCDS45430.1																																																																																			G|0.899;A|0.101	0.101	strong		0.562	SMG1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000391817.1	NM_015092	
WWP2	11060	hgsc.bcm.edu	37	16	69970329	69970329	+	Silent	SNP	A	A	G	rs1983016	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:69970329A>G	ENST00000359154.2	+	19	2192	c.2091A>G	c.(2089-2091)acA>acG	p.T697T	WWP2_ENST00000568684.1_Silent_p.T258T|WWP2_ENST00000544162.1_3'UTR|WWP2_ENST00000448661.1_Silent_p.T697T|WWP2_ENST00000356003.2_Silent_p.T697T|WWP2_ENST00000542271.1_Silent_p.T581T	NM_001270454.1|NM_007014.4	NP_001257383.1|NP_008945.2	O00308	WWP2_HUMAN	WW domain containing E3 ubiquitin protein ligase 2	697	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						TCCGGGTCACAGAGGAGAACA	0.592													g|||	4234	0.845447	0.907	0.7565	5008	,	,		18658	0.9663		0.7515	False		,,,				2504	0.7975				p.T697T		Atlas-SNP	.											WWP2,NS,carcinoma,0,2	WWP2	88	2	0			c.A2091G						PASS	.		,	3794,602	265.0+/-266.4	1633,528,37	78.0	70.0	73.0		2091,774	-11.1	0.0	16	dbSNP_92	73	6405,2195	375.3+/-337.7	2394,1617,289	no	coding-synonymous,coding-synonymous	WWP2	NM_007014.3,NM_199424.1	,	4027,2145,326	GG,GA,AA		25.5233,13.6943,21.522	,	697/871,258/432	69970329	10199,2797	2198	4300	6498	SO:0001819	synonymous_variant	11060	exon19			GGTCACAGAGGAG	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.2091A>G	16.37:g.69970329A>G		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	106	106	1	NM_001270454	A6NEP1|B2R706|B4DTL5|F5H213|H3BRF3|I3RSG8|Q6ZTQ5|Q96CZ2|Q9BWN6	Silent	SNP	ENST00000359154.2	37	CCDS10885.1																																																																																			A|0.193;G|0.807	0.807	strong		0.592	WWP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268954.1	NM_007014	
ARMC2	84071	hgsc.bcm.edu	37	6	109274418	109274418	+	Silent	SNP	G	G	A	rs41287540	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:109274418G>A	ENST00000392644.4	+	13	1947	c.1779G>A	c.(1777-1779)gcG>gcA	p.A593A	ARMC2_ENST00000368972.3_Silent_p.A428A	NM_032131.4	NP_115507.4	Q8NEN0	ARMC2_HUMAN	armadillo repeat containing 2	593										endometrium(3)|large_intestine(8)|lung(10)|ovary(1)|prostate(1)|skin(1)	24		all_cancers(87;1.14e-07)|Acute lymphoblastic leukemia(125;2.3e-10)|all_hematologic(75;3.3e-08)|all_epithelial(87;0.000111)|Colorectal(196;0.03)|all_lung(197;0.11)		Epithelial(106;0.000197)|BRCA - Breast invasive adenocarcinoma(108;0.000236)|all cancers(137;0.000279)|OV - Ovarian serous cystadenocarcinoma(136;0.00434)		AGCACAGGGCGCAGAGGCCGC	0.627													G|||	59	0.0117812	0.0008	0.0144	5008	,	,		16206	0.0		0.0179	False		,,,				2504	0.0307				p.A593A		Atlas-SNP	.											.	ARMC2	56	.	0			c.G1779A						PASS	.	G		17,4389	22.3+/-47.3	0,17,2186	44.0	44.0	44.0		1779	-6.5	0.0	6	dbSNP_127	44	160,8440	74.8+/-137.4	2,156,4142	no	coding-synonymous	ARMC2	NM_032131.4		2,173,6328	AA,AG,GG		1.8605,0.3858,1.3609		593/868	109274418	177,12829	2203	4300	6503	SO:0001819	synonymous_variant	84071	exon13			CAGGGCGCAGAGG	BC030603	CCDS5069.2, CCDS69168.1	6q21	2013-02-14			ENSG00000118690	ENSG00000118690		"""Armadillo repeat containing"""	23045	protein-coding gene	gene with protein product							Standard	XM_005267154		Approved	DKFZp434P0714, bA787I22.1	uc003pss.4	Q8NEN0	OTTHUMG00000015335	ENST00000392644.4:c.1779G>A	6.37:g.109274418G>A		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	57	32	0.561404	NM_032131	A8K8Y4|B4DGF5|G5E993|Q5VVY8|Q9H0K9	Silent	SNP	ENST00000392644.4	37	CCDS5069.2																																																																																			G|0.986;A|0.014	0.014	strong		0.627	ARMC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041732.2	NM_032131	
TMEM72	643236	hgsc.bcm.edu	37	10	45430257	45430257	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:45430257C>T	ENST00000544540.1	+	4	633	c.149C>T	c.(148-150)aCc>aTc	p.T50I	TMEM72-AS1_ENST00000450287.2_RNA|RP11-285G1.9_ENST00000425541.2_lincRNA			A0PK05	TMM72_HUMAN	transmembrane protein 72	168						integral component of membrane (GO:0016021)				breast(2)|kidney(1)|large_intestine(2)|lung(10)	15						ACAGAGCAAACCTACACTTTC	0.607																																					p.T168I		Atlas-SNP	.											.	TMEM72	25	.	0			c.C503T						PASS	.						122.0	130.0	127.0					10																	45430257		1568	3582	5150	SO:0001583	missense	643236	exon5			AGCAAACCTACAC	AB235418	CCDS41504.1	10q11.21	2008-10-24	2008-08-21	2008-08-21	ENSG00000187783	ENSG00000187783			31658	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 127"""	C10orf127			Standard	NM_001123376		Approved	bA285G1.3, KSP37	uc001jbn.2	A0PK05	OTTHUMG00000018067	ENST00000544540.1:c.149C>T	10.37:g.45430257C>T	ENSP00000439911:p.Thr50Ile	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	86	37	0.430233	NM_001123376	A1L181|Q5T740	Missense_Mutation	SNP	ENST00000544540.1	37		.	.	.	.	.	.	.	.	.	.	C	14.56	2.570678	0.45798	.	.	ENSG00000187783	ENST00000389583;ENST00000544540	.	.	.	5.28	3.41	0.39046	.	0.000000	0.64402	D	0.000006	T	0.58736	0.2143	M	0.69823	2.125	0.39365	D	0.965998	B	0.15930	0.015	B	0.16722	0.016	T	0.61903	-0.6967	9	0.56958	D	0.05	-28.2717	9.2035	0.37275	0.0:0.8229:0.0:0.1771	.	168	A0PK05	TMM72_HUMAN	I	168;50	.	ENSP00000374234:T168I	T	+	2	0	TMEM72	44750263	1.000000	0.71417	0.997000	0.53966	0.991000	0.79684	3.002000	0.49496	1.372000	0.46190	0.563000	0.77884	ACC	.	.	none		0.607	TMEM72-201	KNOWN	basic	protein_coding	protein_coding		NM_001123376	
WWP2	11060	hgsc.bcm.edu	37	16	69973825	69973825	+	Silent	SNP	G	G	A	rs3748389	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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_ENST00000544162.1_3'UTR|WWP2_ENST00000448661.1_Silent_p.E865E|WWP2_ENST00000356003.2_Silent_p.E865E|WWP2_ENST00000542271.1_Silent_p.E749E	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	83	0	0		WXS	Illumina HiSeq	Phase_I	94	30	0.319149	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	
FAM13B	51306	hgsc.bcm.edu	37	5	137275968	137275968	+	Missense_Mutation	SNP	C	C	G	rs201094212	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:137275968C>G	ENST00000033079.3	-	23	3145	c.2694G>C	c.(2692-2694)aaG>aaC	p.K898N	PKD2L2_ENST00000290431.5_3'UTR|PKD2L2_ENST00000508883.1_Intron|PKD2L2_ENST00000508638.1_3'UTR|FAM13B_ENST00000425075.2_Missense_Mutation_p.K774N|PKD2L2_ENST00000502810.1_3'UTR|FAM13B_ENST00000420893.2_Missense_Mutation_p.K870N	NM_016603.2	NP_057687.2	Q9NYF5	FA13B_HUMAN	family with sequence similarity 13, member B	898					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						GAAGCCTAAGCTTGGCTTTAA	0.348													C|||	2	0.000399361	0.0	0.0014	5008	,	,		18964	0.0		0.001	False		,,,				2504	0.0				p.K898N		Atlas-SNP	.											FAM13B,NS,carcinoma,0,2	FAM13B	46	2	0			c.G2694C						PASS	.						112.0	110.0	111.0					5																	137275968		2203	4300	6503	SO:0001583	missense	51306	exon23			CCTAAGCTTGGCT	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.2694G>C	5.37:g.137275968C>G	ENSP00000033079:p.Lys898Asn	Somatic	197	0	0		WXS	Illumina HiSeq	Phase_I	163	83	0.509202	NM_016603	D3DQB5|G3V0H9|Q3ZCR0|Q6PGQ2|Q9P0I7	Missense_Mutation	SNP	ENST00000033079.3	37	CCDS4195.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	18.29	3.591185	0.66219	.	.	ENSG00000031003	ENST00000033079;ENST00000425075;ENST00000420893	T;T;T	0.37411	2.24;1.2;2.12	5.37	1.84	0.25277	.	0.000000	0.85682	D	0.000000	T	0.52741	0.1753	M	0.72894	2.215	0.58432	D	0.999999	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.997;0.999	T	0.51028	-0.8757	10	0.87932	D	0	-13.3199	7.0159	0.24887	0.0:0.4207:0.0:0.5793	.	774;870;898	G3V0H9;Q9NYF5-2;Q9NYF5	.;.;FA13B_HUMAN	N	898;774;870	ENSP00000033079:K898N;ENSP00000394669:K774N;ENSP00000388521:K870N	ENSP00000033079:K898N	K	-	3	2	FAM13B	137303867	0.468000	0.25839	1.000000	0.80357	0.997000	0.91878	-0.247000	0.08866	0.446000	0.26666	0.591000	0.81541	AAG	C|0.999;G|0.001	0.001	strong		0.348	FAM13B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251279.1		
ARSD	414	hgsc.bcm.edu	37	X	2833631	2833631	+	Silent	SNP	A	A	G	rs377542415		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	140	0	0		WXS	Illumina HiSeq	Phase_I	105	11	0.104762	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		
CCDC74A	90557	hgsc.bcm.edu	37	2	132288362	132288362	+	Missense_Mutation	SNP	T	T	C	rs201632382		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:132288362T>C	ENST00000295171.6	+	3	644	c.506T>C	c.(505-507)aTg>aCg	p.M169T	CCDC74A_ENST00000467992.2_Missense_Mutation_p.M271T|CCDC74A_ENST00000409856.3_Missense_Mutation_p.M103T	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	169										endometrium(4)|large_intestine(3)|lung(9)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19						AGCCTCTCCATGTCAAGCTTC	0.637																																					p.M211T		Atlas-SNP	.											CCDC74A,parotid,carcinoma,0,1	CCDC74A	44	1	0			c.T632C						scavenged	.						38.0	56.0	50.0					2																	132288362		2187	4290	6477	SO:0001583	missense	90557	exon3			TCTCCATGTCAAG		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.506T>C	2.37:g.132288362T>C	ENSP00000295171:p.Met169Thr	Somatic	477	0	0		WXS	Illumina HiSeq	Phase_I	527	31	0.0588235	NM_001258304	Q6P4I5	Missense_Mutation	SNP	ENST00000295171.6	37	CCDS2167.1	901	0.4125457875457875	256	0.5203252032520326	145	0.4005524861878453	317	0.5541958041958042	183	0.24142480211081793	.	0.004	-2.351374	0.00217	.	.	ENSG00000163040	ENST00000295171;ENST00000409856;ENST00000434330;ENST00000467992	T;T;T;T	0.43294	2.04;2.1;1.04;0.95	1.57	-0.67	0.11384	.	0.998261	0.08101	N	0.997806	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	0.04013	0.001;0.0	T	0.44651	-0.9314	9	0.02654	T	1	-0.4664	0.5182	0.00607	0.2701:0.3325:0.2175:0.1799	.	103;169	Q96AQ1-2;Q96AQ1	.;CC74A_HUMAN	T	169;103;98;271	ENSP00000295171:M169T;ENSP00000387009:M103T;ENSP00000406839:M98T;ENSP00000444610:M271T	ENSP00000295171:M169T	M	+	2	0	CCDC74A	132004832	0.000000	0.05858	0.001000	0.08648	0.067000	0.16453	-0.660000	0.05317	-0.687000	0.05162	-1.033000	0.02402	ATG	T|0.250;C|0.750	0.750	strong		0.637	CCDC74A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254570.2	NM_138770	
TMEM8A	58986	hgsc.bcm.edu	37	16	427820	427820	+	Silent	SNP	C	C	T	rs12922073	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:427820C>T	ENST00000431232.2	-	2	310	c.150G>A	c.(148-150)tcG>tcA	p.S50S	TMEM8A_ENST00000476735.1_5'UTR|TMEM8A_ENST00000250930.3_Intron	NM_021259.2	NP_067082.2	Q9HCN3	TMM8A_HUMAN	transmembrane protein 8A	50					cell adhesion (GO:0007155)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)				central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|pancreas(1)|prostate(1)	14						GCGGGGCCTGCGAGAAGTGCT	0.672													C|||	2580	0.515176	0.5582	0.4683	5008	,	,		14226	0.2996		0.5368	False		,,,				2504	0.6902				p.S50S		Atlas-SNP	.											.	TMEM8A	49	.	0			c.G150A						PASS	.	C		2520,1808		745,1030,389	33.0	39.0	37.0		150	-8.8	0.7	16	dbSNP_121	37	4850,3678		1444,1962,858	no	coding-synonymous	TMEM8A	NM_021259.2		2189,2992,1247	TT,TC,CC		43.1285,41.7745,42.6727		50/772	427820	7370,5486	2164	4264	6428	SO:0001819	synonymous_variant	58986	exon2			GGCCTGCGAGAAG	AB045292	CCDS10407.1	16p13.3	2009-06-12	2009-06-12	2009-06-12	ENSG00000129925	ENSG00000129925			17205	protein-coding gene	gene with protein product			"""transmembrane protein 6"", ""transmembrane protein 8 (five membrane-spanning domains)"""	TMEM6, TMEM8		11006113	Standard	NM_021259		Approved	M83	uc002cgu.4	Q9HCN3	OTTHUMG00000047996	ENST00000431232.2:c.150G>A	16.37:g.427820C>T		Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	133	130	0.977444	NM_021259	D3DU49|Q4TT35|Q8WU24|Q96S25|Q9BR03|Q9BT97|Q9H7B9	Silent	SNP	ENST00000431232.2	37	CCDS10407.1																																																																																			A|0.000;C|0.470;G|0.000;T|0.530	0.530	strong		0.672	TMEM8A-001	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000109257.2	NM_021259	
NEURL4	84461	hgsc.bcm.edu	37	17	7221385	7221385	+	Splice_Site	SNP	G	G	A	rs1127440|rs397798877	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:7221385G>A	ENST00000399464.2	-	25	4074	c.4059C>T	c.(4057-4059)ccC>ccT	p.P1353P	GPS2_ENST00000389167.5_5'Flank|NEURL4_ENST00000315614.7_Splice_Site_p.P1351P|GPS2_ENST00000391950.3_5'Flank|NEURL4_ENST00000574120.1_5'UTR|NEURL4_ENST00000570460.1_Splice_Site_p.P1329P|GPS2_ENST00000380728.2_5'Flank|RP11-542C16.2_ENST00000575474.1_Splice_Site_p.P167L	NM_032442.2	NP_115818.2	Q96JN8	NEUL4_HUMAN	neuralized E3 ubiquitin protein ligase 4	1353						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(12)|ovary(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						GGGACTCACCGGGAAGCAGCA	0.602													A|||	3532	0.705272	0.5953	0.7522	5008	,	,		18625	0.9286		0.5666	False		,,,				2504	0.7331				p.P1353P		Atlas-SNP	.											NEURL4_ENST00000315614,NS,carcinoma,0,4	NEURL4	192	4	0			c.C4059T						PASS	.	A	,	2470,1640		756,958,341	105.0	114.0	111.0		4053,4059	-1.9	1.0	17	dbSNP_86	111	4911,3507		1453,2005,751	yes	coding-synonymous-near-splice,coding-synonymous-near-splice	NEURL4	NM_001005408.1,NM_032442.2	,	2209,2963,1092	AA,AG,GG		41.6607,39.9027,41.084	,	1351/1561,1353/1563	7221385	7381,5147	2055	4209	6264	SO:0001630	splice_region_variant	84461	exon25			CTCACCGGGAAGC		CCDS42251.1, CCDS42252.1	17p13	2013-10-24	2013-10-24		ENSG00000215041	ENSG00000215041			34410	protein-coding gene	gene with protein product		615865	"""neuralized homolog 4 (Drosophila)"""			22261722, 22441691	Standard	NM_001005408		Approved	KIAA1787	uc002gga.1	Q96JN8	OTTHUMG00000132319	ENST00000399464.2:c.4060+1C>T	17.37:g.7221385G>A		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	93	93	1	NM_032442	Q6GPI8|Q96IU9|Q9H0B0	Silent	SNP	ENST00000399464.2	37	CCDS42251.1																																																																																			T|0.254;G|0.226;C|0.110;A|0.411	0.411	strong		0.602	NEURL4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255434.2	NM_032442	Silent
ZNF286B	729288	hgsc.bcm.edu	37	17	18565350	18565350	+	Missense_Mutation	SNP	G	G	C	rs9912644	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:18565350G>C	ENST00000545289.1	-	5	1719	c.1469C>G	c.(1468-1470)aCc>aGc	p.T490S	ZNF286B_ENST00000285274.5_3'UTR	NM_001145045.1	NP_001138517.1	P0CG31	Z286B_HUMAN	zinc finger protein 286B	490					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.T490S(2)		endometrium(1)|lung(1)	2						TTTCTCTCCGGTATGAGTTCT	0.393													.|||	1496	0.298722	0.2095	0.4092	5008	,	,		22635	0.3611		0.3827	False		,,,				2504	0.1902				p.T490S		Atlas-SNP	.											ZNF286B,NS,carcinoma,0,1	ZNF286B	75	1	2	Substitution - Missense(2)	endometrium(2)	c.C1469G						PASS	.						103.0	101.0	102.0					17																	18565350		692	1591	2283	SO:0001583	missense	729288	exon5			TCTCCGGTATGAG		CCDS58523.1	17p11.2	2013-01-08			ENSG00000249459	ENSG00000249459		"""Zinc fingers, C2H2-type"""	33241	protein-coding gene	gene with protein product	"""zinc finger protein 590"""		"""zinc finger protein 286-like"", ""zinc finger 286C pseudogene"""	ZNF286L, ZNF286C			Standard	NM_001145045		Approved	ZNF590	uc010vyd.1	P0CG31	OTTHUMG00000178136	ENST00000545289.1:c.1469C>G	17.37:g.18565350G>C	ENSP00000461413:p.Thr490Ser	Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	253	178	0.703557	NM_001145045		Missense_Mutation	SNP	ENST00000545289.1	37	CCDS58523.1																																																																																			G|0.648;C|0.352	0.352	strong		0.393	ZNF286B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		XM_001723047	
BIRC7	79444	hgsc.bcm.edu	37	20	61867454	61867454	+	Silent	SNP	A	A	G	rs6011691	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:61867454A>G	ENST00000217169.3	+	1	220	c.6A>G	c.(4-6)ggA>ggG	p.G2G	BIRC7_ENST00000342412.6_Silent_p.G2G|MIR3196_ENST00000579556.1_RNA|BIRC7_ENST00000395306.1_5'Flank	NM_139317.1	NP_647478.1	Q96CA5	BIRC7_HUMAN	baculoviral IAP repeat containing 7	2					activation of JUN kinase activity (GO:0007257)|apoptotic process (GO:0006915)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endopeptidase activity (GO:0010951)|protein ubiquitination (GO:0016567)|regulation of cell proliferation (GO:0042127)|regulation of natural killer cell apoptotic process (GO:0070247)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	cysteine-type endopeptidase inhibitor activity (GO:0004869)|enzyme binding (GO:0019899)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|lung(9)|ovary(1)	12	all_cancers(38;2.72e-09)					CCTCCATGGGACCTAAAGACA	0.622													G|||	594	0.11861	0.2247	0.0908	5008	,	,		16422	0.0149		0.0895	False		,,,				2504	0.1319				p.G2G		Atlas-SNP	.											.	BIRC7	25	.	0			c.A6G						PASS	.		,	768,3584		80,608,1488	13.0	11.0	12.0		6,6	-1.3	0.0	20	dbSNP_114	12	701,7863		40,621,3621	no	coding-synonymous,coding-synonymous	BIRC7	NM_022161.2,NM_139317.1	,	120,1229,5109	GG,GA,AA		8.1854,17.6471,11.3735	,	2/281,2/299	61867454	1469,11447	2176	4282	6458	SO:0001819	synonymous_variant	79444	exon1			CATGGGACCTAAA	AF301009	CCDS13512.1, CCDS13513.1	20q13.3	2011-01-25	2011-01-25		ENSG00000101197	ENSG00000101197		"""Baculoviral IAP repeat containing"", ""RING-type (C3HC4) zinc fingers"""	13702	protein-coding gene	gene with protein product	"""melanoma inhibitor of apoptosis protein"", ""kidney inhibitor of apoptosis protein"", ""livin inhibitor-of-apoptosis"", ""livin"""	605737	"""baculoviral IAP repeat-containing 7"""			11024045, 11162435	Standard	NM_139317		Approved	mliap, ML-IAP, KIAP, RNF50	uc002yej.3	Q96CA5	OTTHUMG00000032957	ENST00000217169.3:c.6A>G	20.37:g.61867454A>G		Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	137	77	0.562044	NM_139317	Q9BQV0|Q9H2A8|Q9HAP7	Silent	SNP	ENST00000217169.3	37	CCDS13513.1																																																																																			A|0.879;G|0.121	0.121	strong		0.622	BIRC7-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080114.2	NM_139317	
SLC35G5	83650	hgsc.bcm.edu	37	8	11188752	11188752	+	Missense_Mutation	SNP	G	G	A	rs6990563	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:11188752G>A	ENST00000382435.4	+	1	356	c.137G>A	c.(136-138)gGt>gAt	p.G46D		NM_001282300.1|NM_054028.1	NP_001269229.1|NP_473369.1	Q96KT7	S35G5_HUMAN	solute carrier family 35, member G5	46			G -> D (in dbSNP:rs6990563).			integral component of membrane (GO:0016021)											GCCCTGCTGGGTGGGGGCCTG	0.677													G|||	2136	0.426518	0.1467	0.3718	5008	,	,		16974	0.7351		0.4553	False		,,,				2504	0.4959				p.G46D		Atlas-SNP	.											.	.	.	.	0			c.G137A						PASS	.	G	ASP/GLY	896,3510	343.6+/-307.7	91,714,1398	48.0	55.0	52.0		137	0.3	1.0	8	dbSNP_116	52	4014,4586	552.0+/-386.0	952,2110,1238	no	missense	SLC35G5	NM_054028.1	94	1043,2824,2636	AA,AG,GG		46.6744,20.3359,37.7518	probably-damaging	46/339	11188752	4910,8096	2203	4300	6503	SO:0001583	missense	83650	exon1			TGCTGGGTGGGGG	AJ291677	CCDS5980.1	8p23.1	2013-05-22	2011-08-03	2011-08-03	ENSG00000177710	ENSG00000177710		"""Solute carriers"""	15546	protein-coding gene	gene with protein product		615199	"""acyl-malonyl condensing enzyme 1-like 2"""	AMAC, AMAC1L2			Standard	NM_054028		Approved		uc003wtp.1	Q96KT7	OTTHUMG00000090653	ENST00000382435.4:c.137G>A	8.37:g.11188752G>A	ENSP00000371872:p.Gly46Asp	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	84	20	0.238095	NM_054028	A2RRL6	Missense_Mutation	SNP	ENST00000382435.4	37	CCDS5980.1	904	0.4139194139194139	73	0.1483739837398374	134	0.3701657458563536	378	0.6608391608391608	319	0.420844327176781	G	15.55	2.867345	0.51588	0.203359	0.466744	ENSG00000177710	ENST00000382435	T	0.42900	0.96	0.34	0.34	0.15985	.	0.000000	0.45867	D	0.000330	T	0.00012	0.0000	L	0.27053	0.805	0.23391	P	0.99777562	D	0.71674	0.998	D	0.63597	0.916	T	0.42068	-0.9473	9	0.66056	D	0.02	-4.0269	6.5344	0.22344	2.0E-4:0.0:0.9998:0.0	rs6990563;rs58184334	46	Q96KT7	S35G5_HUMAN	D	46	ENSP00000371872:G46D	ENSP00000371872:G46D	G	+	2	0	SLC35G5	11226162	1.000000	0.71417	0.966000	0.40874	0.252000	0.25951	3.390000	0.52523	0.426000	0.26116	0.089000	0.15464	GGT	.	.	weak		0.677	SLC35G5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207313.2	NM_054028	
FRMD4B	23150	hgsc.bcm.edu	37	3	69271032	69271032	+	Silent	SNP	G	G	A	rs62254461	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:69271032G>A	ENST00000398540.3	-	9	791	c.708C>T	c.(706-708)ctC>ctT	p.L236L	FRMD4B_ENST00000542259.1_Silent_p.L182L	NM_015123.1	NP_055938	Q9Y2L6	FRM4B_HUMAN	FERM domain containing 4B	236	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				establishment of epithelial cell polarity (GO:0090162)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular space (GO:0005615)|ruffle (GO:0001726)				NS(2)|central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(3)|lung(1)|ovary(3)|prostate(3)|skin(2)	19		Lung NSC(201;0.0138)|Prostate(884;0.11)		BRCA - Breast invasive adenocarcinoma(55;0.000201)|Epithelial(33;0.00141)|LUSC - Lung squamous cell carcinoma(21;0.00999)|Lung(16;0.0182)		GACCTCGAGTGAGACCTTTGA	0.358													G|||	198	0.0395367	0.0068	0.0663	5008	,	,		18997	0.001		0.1183	False		,,,				2504	0.0235				p.L236L		Atlas-SNP	.											.	FRMD4B	90	.	0			c.C708T						PASS	.	G		74,3708		0,74,1817	82.0	77.0	79.0		708	2.5	1.0	3	dbSNP_129	79	967,7249		63,841,3204	no	coding-synonymous	FRMD4B	NM_015123.1		63,915,5021	AA,AG,GG		11.7697,1.9566,8.6764		236/1035	69271032	1041,10957	1891	4108	5999	SO:0001819	synonymous_variant	23150	exon9			TCGAGTGAGACCT	AL832231	CCDS46863.1	3p14.2	2006-04-12			ENSG00000114541	ENSG00000114541			24886	protein-coding gene	gene with protein product						10231032, 11445584	Standard	XM_005264720		Approved	KIAA1013, GRSP1	uc003dnv.2	Q9Y2L6	OTTHUMG00000158772	ENST00000398540.3:c.708C>T	3.37:g.69271032G>A		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	109	49	0.449541	NM_015123	Q8TAI3	Silent	SNP	ENST00000398540.3	37	CCDS46863.1																																																																																			G|0.928;A|0.072	0.072	strong		0.358	FRMD4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352111.1		
AIRE	326	hgsc.bcm.edu	37	21	45712977	45712977	+	Silent	SNP	T	T	C	rs1800521	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:45712977T>C	ENST00000291582.5	+	10	1324	c.1197T>C	c.(1195-1197)gcT>gcC	p.A399A	AIRE_ENST00000329347.4_Intron|AIRE_ENST00000355347.4_Silent_p.A192A	NM_000383.3	NP_000374.1	O43918	AIRE_HUMAN	autoimmune regulator	399					humoral immune response (GO:0006959)|immune response (GO:0006955)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|histone binding (GO:0042393)|transcription regulatory region DNA binding (GO:0044212)|translation regulator activity (GO:0045182)|zinc ion binding (GO:0008270)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(7)|skin(2)|urinary_tract(1)	14				Colorectal(79;0.0806)		ACCTGCCGGCTCCGCCTTCTG	0.682									Autoimmune PolyEndocrinopathy Candidiasis Ectodermal Dystrophy				C|||	1784	0.35623	0.4955	0.3184	5008	,	,		10777	0.247		0.3579	False		,,,				2504	0.3057				p.A399A		Atlas-SNP	.											AIRE_ENST00000397994,NS,carcinoma,0,2	AIRE	61	2	0			c.T1197C						PASS	.	C	,	2114,2268		543,1028,620	23.0	27.0	25.0		1197,606	2.0	0.0	21	dbSNP_89	25	2992,5602		519,1954,1824	no	coding-synonymous,coding-synonymous	AIRE	NM_000383.2,NM_000658.2	,	1062,2982,2444	CC,CT,TT		34.815,48.2428,39.3496	,	399/546,202/349	45712977	5106,7870	2191	4297	6488	SO:0001819	synonymous_variant	326	exon10	Familial Cancer Database	APECED	GCCGGCTCCGCCT	AB006684	CCDS13706.1	21q22.3	2014-09-17	2007-06-20		ENSG00000160224	ENSG00000160224		"""Zinc fingers, PHD-type"""	360	protein-coding gene	gene with protein product	"""autoimmune polyendocrinopathy candidiasis ectodermal dystrophy"""	607358	"""autoimmune regulator (autoimmune polyendocrinopathy candidiasis ectodermal dystrophy)"""	APECED		9398840	Standard	NM_000383		Approved	PGA1, APS1	uc002zei.3	O43918	OTTHUMG00000086921	ENST00000291582.5:c.1197T>C	21.37:g.45712977T>C		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	67	67	1	NM_000383	B2RP50|O43922|O43932|O75745	Silent	SNP	ENST00000291582.5	37	CCDS13706.1																																																																																			T|0.622;C|0.378	0.378	strong		0.682	AIRE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195842.2		
GRIN3A	116443	hgsc.bcm.edu	37	9	104432873	104432873	+	Silent	SNP	T	T	G	rs942142	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:104432873T>G	ENST00000361820.3	-	3	2421	c.1821A>C	c.(1819-1821)gcA>gcC	p.A607A		NM_133445.2	NP_597702.2	Q8TCU5	NMD3A_HUMAN	glutamate receptor, ionotropic, N-methyl-D-aspartate 3A	607					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)	CATTTTTCCATGCTCCATACT	0.483													G|||	1339	0.267372	0.1241	0.3617	5008	,	,		21363	0.2183		0.4056	False		,,,				2504	0.3027				p.A607A		Atlas-SNP	.											.	GRIN3A	186	.	0			c.A1821C						PASS	.	G		789,3617	752.7+/-412.3	73,643,1487	94.0	79.0	84.0		1821	1.3	1.0	9	dbSNP_86	84	3550,5050	630.2+/-398.3	726,2098,1476	no	coding-synonymous	GRIN3A	NM_133445.2		799,2741,2963	GG,GT,TT		41.2791,17.9074,33.3615		607/1116	104432873	4339,8667	2203	4300	6503	SO:0001819	synonymous_variant	116443	exon3			TTTCCATGCTCCA		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.1821A>C	9.37:g.104432873T>G		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	89	45	0.505618	NM_133445	B3DLF9|Q5VTR3|Q8TF29|Q8WXI6	Silent	SNP	ENST00000361820.3	37	CCDS6758.1																																																																																			T|0.683;G|0.317	0.317	strong		0.483	GRIN3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053453.1		
ZSCAN5A	79149	hgsc.bcm.edu	37	19	56736094	56736094	+	Missense_Mutation	SNP	C	C	T	rs143462624	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:56736094C>T	ENST00000587340.1	-	4	1017	c.322G>A	c.(322-324)Ggt>Agt	p.G108S	ZSCAN5A_ENST00000592355.1_Missense_Mutation_p.G108S|ZSCAN5A_ENST00000254165.3_Intron|ZSCAN5A_ENST00000391713.1_Missense_Mutation_p.G108S|ZSCAN5A_ENST00000587492.1_Intron			Q9BUG6	ZSA5A_HUMAN	zinc finger and SCAN domain containing 5A	108	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)			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						CTCTGCACACCGTTCATCATG	0.552																																					p.G108S		Atlas-SNP	.											ZSCAN5A,NS,carcinoma,0,1	ZSCAN5A	118	1	0			c.G322A						scavenged	.						19.0	19.0	19.0					19																	56736094		2134	4201	6335	SO:0001583	missense	79149	exon2			GCACACCGTTCAT	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.322G>A	19.37:g.56736094C>T	ENSP00000467631:p.Gly108Ser	Somatic	577	0	0		WXS	Illumina HiSeq	Phase_I	684	175	0.255848	NM_024303	B4DX98|Q49A73|Q53F04|Q8N7B3	Missense_Mutation	SNP	ENST00000587340.1	37	CCDS12941.1	26	0.011904761904761904	5	0.01016260162601626	3	0.008287292817679558	0	0.0	18	0.023746701846965697	C	9.170	1.020852	0.19433	.	.	ENSG00000131848	ENST00000391713	T	0.05447	3.44	2.27	-1.55	0.08558	Retrovirus capsid, C-terminal (1);Transcription regulator SCAN (3);	.	.	.	.	T	0.02156	0.0067	M	0.64676	1.99	0.09310	N	1	P	0.40731	0.728	B	0.27715	0.082	T	0.30208	-0.9986	9	0.44086	T	0.13	.	3.1545	0.06499	0.0:0.4753:0.2343:0.2904	.	108	Q9BUG6	ZSA5A_HUMAN	S	108	ENSP00000375593:G108S	ENSP00000375593:G108S	G	-	1	0	ZSCAN5A	61427906	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.015000	0.13355	-0.263000	0.09378	0.491000	0.48974	GGT	C|0.988;T|0.012	0.012	strong		0.552	ZSCAN5A-004	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458110.1	NM_024303	
MYO1C	4641	hgsc.bcm.edu	37	17	1377943	1377943	+	Silent	SNP	A	A	G	rs2286873	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:1377943A>G	ENST00000575158.1	-	17	1829	c.1653T>C	c.(1651-1653)ttT>ttC	p.F551F	MYO1C_ENST00000545534.2_Silent_p.F562F|MYO1C_ENST00000359786.5_Silent_p.F586F|MYO1C_ENST00000438665.2_Silent_p.F567F|MYO1C_ENST00000361007.2_Silent_p.F551F			Q12965	MYO1E_HUMAN	myosin IC	546	Myosin motor.				actin filament-based movement (GO:0030048)|ATP catabolic process (GO:0006200)|endocytosis (GO:0006897)|glomerular basement membrane development (GO:0032836)|glomerular filtration (GO:0003094)|glomerular visceral epithelial cell development (GO:0072015)|in utero embryonic development (GO:0001701)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|post-embryonic hemopoiesis (GO:0035166)|vasculogenesis (GO:0001570)	actin cytoskeleton (GO:0015629)|adherens junction (GO:0005912)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|motor activity (GO:0003774)|phosphatidylinositol binding (GO:0035091)			breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|liver(2)|lung(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	17				UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)		CGCTCCGGTCAAAGCACTGGC	0.637													G|||	2091	0.417532	0.7126	0.3977	5008	,	,		14329	0.2093		0.3847	False		,,,				2504	0.2812				p.F586F		Atlas-SNP	.											.	MYO1C	57	.	0			c.T1758C						PASS	.	G	,,	2888,1518	480.8+/-358.9	956,976,271	108.0	109.0	108.0		1758,1701,1653	-2.0	1.0	17	dbSNP_100	108	2983,5617	666.3+/-402.4	522,1939,1839	no	coding-synonymous,coding-synonymous,coding-synonymous	MYO1C	NM_001080779.1,NM_001080950.1,NM_033375.4	,,	1478,2915,2110	GG,GA,AA		34.686,34.453,45.1407	,,	586/1064,567/1045,551/1029	1377943	5871,7135	2203	4300	6503	SO:0001819	synonymous_variant	4641	exon17			CCGGTCAAAGCAC	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.1653T>C	17.37:g.1377943A>G		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	116	55	0.474138	NM_001080779	Q14778	Silent	SNP	ENST00000575158.1	37	CCDS11003.1																																																																																			A|0.554;G|0.446	0.446	strong		0.637	MYO1C-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438694.2		
CHMP7	91782	hgsc.bcm.edu	37	8	23118091	23118091	+	Silent	SNP	A	A	G	rs76771816|rs370978142		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:23118091A>G	ENST00000397677.1	+	11	1989	c.1341A>G	c.(1339-1341)gaA>gaG	p.E447E	CHMP7_ENST00000313219.7_Silent_p.E447E	NM_152272.3	NP_689485.1	Q8WUX9	CHMP7_HUMAN	charged multivesicular body protein 7	447					endosomal transport (GO:0016197)|late endosome to vacuole transport (GO:0045324)|membrane organization (GO:0061024)|viral life cycle (GO:0019058)|viral process (GO:0016032)	cytosol (GO:0005829)|ESCRT III complex (GO:0000815)	protein transporter activity (GO:0008565)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(1)|ovary(1)|prostate(1)|urinary_tract(1)	11		Prostate(55;0.0513)		Colorectal(74;0.0155)|COAD - Colon adenocarcinoma(73;0.0632)		GGCAATTGGAACCGACTCTAA	0.418																																					p.E447E		Atlas-SNP	.											CHMP7,NS,carcinoma,+1,1	CHMP7	34	1	0			c.A1341G						scavenged	.						118.0	114.0	115.0					8																	23118091		2203	4300	6503	SO:0001819	synonymous_variant	91782	exon11			ATTGGAACCGACT	BC019110	CCDS6040.1	8p21.2	2011-09-21	2011-09-21		ENSG00000147457	ENSG00000147457		"""Charged multivesicular body proteins"""	28439	protein-coding gene	gene with protein product		611130	"""CHMP family, member 7"""			16856878	Standard	NM_152272		Approved	MGC29816	uc003xdc.2	Q8WUX9	OTTHUMG00000131785	ENST00000397677.1:c.1341A>G	8.37:g.23118091A>G		Somatic	197	0	0		WXS	Illumina HiSeq	Phase_I	178	7	0.0393258	NM_152272	B2RDT3|B4DKJ6|D3DSS1|Q8NDM1|Q9BT50	Silent	SNP	ENST00000397677.1	37	CCDS6040.1																																																																																			.	.	alt		0.418	CHMP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254717.1	NM_152272	
ACSM5	54988	hgsc.bcm.edu	37	16	20441020	20441020	+	Missense_Mutation	SNP	G	G	A	rs12932087	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:20441020G>A	ENST00000331849.4	+	8	1169	c.1022G>A	c.(1021-1023)aGg>aAg	p.R341K		NM_017888.2	NP_060358.2	Q6NUN0	ACSM5_HUMAN	acyl-CoA synthetase medium-chain family member 5	341					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						CAGAGCCTGAGGCACTGTCTG	0.557													G|||	537	0.107228	0.0628	0.1066	5008	,	,		17883	0.1835		0.0537	False		,,,				2504	0.1442				p.R341K		Atlas-SNP	.											.	ACSM5	101	.	0			c.G1022A						PASS	.	G	LYS/ARG	311,4095	161.8+/-193.9	9,293,1901	101.0	101.0	101.0		1022	2.4	1.0	16	dbSNP_121	101	616,7984	156.9+/-210.6	19,578,3703	yes	missense	ACSM5	NM_017888.2	26	28,871,5604	AA,AG,GG		7.1628,7.0586,7.1275	benign	341/580	20441020	927,12079	2203	4300	6503	SO:0001583	missense	54988	exon8			GCCTGAGGCACTG		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.1022G>A	16.37:g.20441020G>A	ENSP00000327916:p.Arg341Lys	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	54	24	0.444444	NM_017888	Q96AV1|Q96CX8|Q9NWV3	Missense_Mutation	SNP	ENST00000331849.4	37	CCDS10585.1	233	0.10668498168498168	30	0.06097560975609756	40	0.11049723756906077	117	0.20454545454545456	46	0.06068601583113457	G	10.02	1.234993	0.22626	0.070586	0.071628	ENSG00000183549	ENST00000331849	T	0.49432	0.78	4.4	2.43	0.29744	AMP-dependent synthetase/ligase (1);	0.461000	0.19441	N	0.114166	T	0.00039	0.0001	L	0.28608	0.87	0.48901	P	2.7200000000005E-4	B	0.02656	0.0	B	0.09377	0.004	T	0.18650	-1.0330	9	0.13853	T	0.58	-6.2474	6.6372	0.22889	0.3838:0.0:0.6162:0.0	rs12932087	341	Q6NUN0	ACSM5_HUMAN	K	341	ENSP00000327916:R341K	ENSP00000327916:R341K	R	+	2	0	ACSM5	20348521	0.000000	0.05858	0.983000	0.44433	0.731000	0.41821	-0.019000	0.12546	0.413000	0.25759	0.551000	0.68910	AGG	G|0.913;A|0.087	0.087	strong		0.557	ACSM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254413.1	NM_017888	
ASPM	259266	hgsc.bcm.edu	37	1	197069640	197069640	+	Missense_Mutation	SNP	A	A	G	rs200856894		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:197069640A>G	ENST00000367409.4	-	18	8997	c.8741T>C	c.(8740-8742)aTc>aCc	p.I2914T	ASPM_ENST00000367408.1_Intron|ASPM_ENST00000294732.7_Intron	NM_018136.4	NP_060606.3	Q8IZT6	ASPM_HUMAN	asp (abnormal spindle) homolog, microcephaly associated (Drosophila)	2914	IQ 33. {ECO:0000255|PROSITE- ProRule:PRU00116}.				developmental growth (GO:0048589)|forebrain neuroblast division (GO:0021873)|maintenance of centrosome location (GO:0051661)|mitotic nuclear division (GO:0007067)|negative regulation of asymmetric cell division (GO:0045769)|negative regulation of neuron differentiation (GO:0045665)|neuron migration (GO:0001764)|oogenesis (GO:0048477)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of neuroblast proliferation (GO:0002052)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|midbody (GO:0030496)|nucleus (GO:0005634)|spindle pole (GO:0000922)				breast(6)|central_nervous_system(2)|cervix(2)|endometrium(10)|kidney(9)|large_intestine(28)|liver(1)|lung(87)|ovary(5)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(3)	165						TTGAATAATGATAACACTGCT	0.299																																					p.I2914T		Atlas-SNP	.											ASPM,NS,carcinoma,+1,1	ASPM	444	1	0			c.T8741C						PASS	.	A	,THR/ILE	0,4406		0,0,2203	59.0	62.0	61.0		,8741	2.7	0.0	1		61	2,8590	2.2+/-6.3	0,2,4294	yes	intron,missense	ASPM	NM_001206846.1,NM_018136.4	,89	0,2,6497	GG,GA,AA		0.0233,0.0,0.0154	,benign	,2914/3478	197069640	2,12996	2203	4296	6499	SO:0001583	missense	259266	exon18			ATAATGATAACAC	AY367065	CCDS1389.1, CCDS55672.1	1q31	2008-02-05	2006-09-12		ENSG00000066279	ENSG00000066279			19048	protein-coding gene	gene with protein product		605481	"""microcephaly, primary autosomal recessive 5"", ""asp (abnormal spindle)-like, microcephaly associated (Drosophila)"""	MCPH5		11078481	Standard	NM_018136		Approved	Calmbp1, ASP, FLJ10517, FLJ10549	uc001gtu.3	Q8IZT6	OTTHUMG00000036277	ENST00000367409.4:c.8741T>C	1.37:g.197069640A>G	ENSP00000356379:p.Ile2914Thr	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	48	17	0.354167	NM_018136	Q4G1H1|Q5VYL3|Q86UX4|Q8IUL2|Q8IZJ7|Q8IZJ8|Q8IZJ9|Q8N4D1|Q9NVS1|Q9NVT6	Missense_Mutation	SNP	ENST00000367409.4	37	CCDS1389.1	.	.	.	.	.	.	.	.	.	.	A	12.05	1.822080	0.32237	0.0	2.33E-4	ENSG00000066279	ENST00000367409;ENST00000367406	T	0.73897	-0.79	5.09	2.7	0.31948	.	0.360702	0.26708	N	0.022904	T	0.80778	0.4688	M	0.68317	2.08	0.09310	N	0.999996	B;D	0.71674	0.024;0.998	B;D	0.65987	0.012;0.94	T	0.70029	-0.4984	10	0.52906	T	0.07	.	7.9874	0.30220	0.7908:0.1371:0.0721:0.0	.	900;2914	E7EQ84;Q8IZT6	.;ASPM_HUMAN	T	2914;900	ENSP00000356379:I2914T	ENSP00000356376:I900T	I	-	2	0	ASPM	195336263	0.020000	0.18652	0.001000	0.08648	0.465000	0.32709	2.427000	0.44740	0.341000	0.23771	0.460000	0.39030	ATC	A|0.999;G|0.001	0.001	weak		0.299	ASPM-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000088256.1	NM_018136	
SLC9A9	285195	hgsc.bcm.edu	37	3	142985717	142985717	+	Missense_Mutation	SNP	T	T	C	rs2289491	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:142985717T>C	ENST00000316549.6	-	16	1973	c.1765A>G	c.(1765-1767)Ata>Gta	p.I589V		NM_173653.3	NP_775924.1	Q8IVB4	SL9A9_HUMAN	solute carrier family 9, subfamily A (NHE9, cation proton antiporter 9), member 9	589			I -> V (in dbSNP:rs2289491). {ECO:0000269|PubMed:17974005}.		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)	p.I589L(1)		breast(2)|endometrium(5)|kidney(2)|large_intestine(13)|lung(29)|ovary(2)|skin(3)|stomach(1)	57						TGGTAATTTATGGCTAGTTCA	0.488													T|||	145	0.0289537	0.0008	0.0303	5008	,	,		19361	0.0188		0.0229	False		,,,				2504	0.0828				p.I589V		Atlas-SNP	.											SLC9A9,caecum,carcinoma,0,3	SLC9A9	117	3	1	Substitution - Missense(1)	ovary(1)	c.A1765G						PASS	.	T	VAL/ILE	35,4371	39.2+/-71.8	0,35,2168	140.0	133.0	135.0		1765	4.6	0.9	3	dbSNP_100	135	243,8357	97.9+/-159.5	3,237,4060	yes	missense	SLC9A9	NM_173653.3	29	3,272,6228	CC,CT,TT		2.8256,0.7944,2.1375	benign	589/646	142985717	278,12728	2203	4300	6503	SO:0001583	missense	285195	exon16			AATTTATGGCTAG	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.1765A>G	3.37:g.142985717T>C	ENSP00000320246:p.Ile589Val	Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	139	52	0.374101	NM_173653	A6NMQ9|Q3LIC2|Q5JPI6|Q5WA58|Q8NAB9	Missense_Mutation	SNP	ENST00000316549.6	37	CCDS33872.1	40	0.018315018315018316	0	0.0	7	0.019337016574585635	13	0.022727272727272728	20	0.026385224274406333	T	7.351	0.622794	0.14193	0.007944	0.028256	ENSG00000181804	ENST00000316549	T	0.28454	1.61	5.7	4.55	0.56014	.	0.409505	0.28119	N	0.016522	T	0.03263	0.0095	N	0.02539	-0.55	0.09310	N	0.999999	B	0.02656	0.0	B	0.01281	0.0	T	0.21280	-1.0250	10	0.17832	T	0.49	.	6.6015	0.22703	0.0:0.1299:0.1377:0.7324	rs2289491;rs52817314;rs56517989;rs2289491	589	Q8IVB4	SL9A9_HUMAN	V	589	ENSP00000320246:I589V	ENSP00000320246:I589V	I	-	1	0	SLC9A9	144468407	1.000000	0.71417	0.930000	0.37139	0.085000	0.17905	0.747000	0.26290	2.168000	0.68352	0.533000	0.62120	ATA	T|0.977;C|0.023	0.023	strong		0.488	SLC9A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354994.1	NM_173653	
ISX	91464	hgsc.bcm.edu	37	22	35463249	35463249	+	Missense_Mutation	SNP	C	C	T	rs362090	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:35463249C>T	ENST00000308700.6	+	1	1121	c.169C>T	c.(169-171)Ccc>Tcc	p.P57S	RP1-272J12.1_ENST00000448318.4_RNA|ISX_ENST00000404699.2_Missense_Mutation_p.P57S	NM_001008494.1	NP_001008494.1	Q2M1V0	ISX_HUMAN	intestine-specific homeobox	57			P -> S (in dbSNP:rs362090). {ECO:0000269|PubMed:15489334}.		regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of vitamin A metabolic process (GO:1901738)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(12)|ovary(3)|prostate(1)|skin(4)	26						TGAAGAGGGCCCCGGAGAAGC	0.567													C|||	2880	0.57508	0.4448	0.5432	5008	,	,		17652	0.7827		0.507	False		,,,				2504	0.6299				p.P57S		Atlas-SNP	.											.	ISX	62	.	0			c.C169T						PASS	.	C	SER/PRO	2090,2314		491,1108,603	31.0	34.0	33.0		169	-6.2	0.0	22	dbSNP_79	33	4250,4350		1051,2148,1101	yes	missense	ISX	NM_001008494.1	74	1542,3256,1704	TT,TC,CC		49.4186,47.4569,48.7542	benign	57/246	35463249	6340,6664	2202	4300	6502	SO:0001583	missense	91464	exon1			GAGGGCCCCGGAG	AK025181	CCDS33640.1	22q12.3	2011-06-20			ENSG00000175329	ENSG00000175329		"""Homeoboxes / PRD class"""	28084	protein-coding gene	gene with protein product		612019					Standard	NM_001008494		Approved	RAXLX	uc003anj.3	Q2M1V0	OTTHUMG00000150962	ENST00000308700.6:c.169C>T	22.37:g.35463249C>T	ENSP00000311492:p.Pro57Ser	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	70	69	0.985714	NM_001008494	Q68DJ5	Missense_Mutation	SNP	ENST00000308700.6	37	CCDS33640.1	1262	0.5778388278388278	204	0.4146341463414634	210	0.580110497237569	452	0.7902097902097902	396	0.5224274406332454	C	8.515	0.867336	0.17250	0.474569	0.494186	ENSG00000175329	ENST00000308700;ENST00000404699	D;D	0.90732	-2.72;-2.72	4.9	-6.22	0.02058	.	1.523810	0.04048	N	0.304336	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	0.36432	-0.9748	9	0.08599	T	0.76	.	1.7971	0.03063	0.2911:0.389:0.1379:0.182	rs362090;rs362090	57	Q2M1V0	ISX_HUMAN	S	57	ENSP00000311492:P57S;ENSP00000386037:P57S	ENSP00000311492:P57S	P	+	1	0	ISX	33793249	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.951000	0.00678	-0.993000	0.03467	-0.140000	0.14226	CCC	C|0.453;T|0.547	0.547	strong		0.567	ISX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320662.1	NM_001008494	
IL17RC	84818	hgsc.bcm.edu	37	3	9959713	9959713	+	Silent	SNP	C	C	T	rs4686383	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:9959713C>T	ENST00000295981.3	+	3	665	c.447C>T	c.(445-447)acC>acT	p.T149T	RNU6-882P_ENST00000391025.1_RNA|IL17RC_ENST00000498214.1_3'UTR|IL17RC_ENST00000455057.1_Silent_p.T78T|IL17RC_ENST00000383812.4_Silent_p.T78T|IL17RC_ENST00000403601.3_Silent_p.T78T|IL17RC_ENST00000413608.1_Silent_p.T78T|IL17RC_ENST00000416074.2_5'UTR	NM_153461.3	NP_703191	Q8NAC3	I17RC_HUMAN	interleukin 17 receptor C	149					cytokine-mediated signaling pathway (GO:0019221)|positive regulation of cytokine production involved in inflammatory response (GO:1900017)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	interleukin-17 receptor activity (GO:0030368)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(3)|ovary(3)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	22						AGAAGGAGACCGACTGTGACC	0.617													C|||	382	0.076278	0.0091	0.1196	5008	,	,		18020	0.0149		0.1869	False		,,,				2504	0.0859				p.T149T		Atlas-SNP	.											.	IL17RC	55	.	0			c.C447T						PASS	.	C	,,,,,	204,4200	121.3+/-158.8	4,196,2002	78.0	76.0	76.0		234,234,234,234,234,447	-8.8	0.0	3	dbSNP_111	76	1787,6813	304.5+/-307.0	190,1407,2703	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	IL17RC	NM_001203263.1,NM_001203264.1,NM_001203265.1,NM_032732.5,NM_153460.3,NM_153461.3	,,,,,	194,1603,4705	TT,TC,CC		20.7791,4.6322,15.3107	,,,,,	78/708,78/691,78/689,78/706,78/721,149/792	9959713	1991,11013	2202	4300	6502	SO:0001819	synonymous_variant	84818	exon3			GGAGACCGACTGT	BC006411	CCDS2590.1, CCDS2591.2, CCDS46746.1, CCDS56240.1, CCDS56241.1, CCDS74898.1	3p25.3	2008-02-05			ENSG00000163702	ENSG00000163702		"""Interleukins and interleukin receptors"""	18358	protein-coding gene	gene with protein product		610925				11706037	Standard	NM_153460		Approved	IL17-RL	uc003bua.3	Q8NAC3	OTTHUMG00000128648	ENST00000295981.3:c.447C>T	3.37:g.9959713C>T		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	89	41	0.460674	NM_153461	E9PHG1|E9PHJ6|Q6UVY3|Q6UWD4|Q8NFS1|Q9BR97	Silent	SNP	ENST00000295981.3	37	CCDS2590.1																																																																																			C|0.889;T|0.111	0.111	strong		0.617	IL17RC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250526.2	NM_032732	
PER3	8863	hgsc.bcm.edu	37	1	7890055	7890055	+	Silent	SNP	T	T	A	rs11121034	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:7890055T>A	ENST00000361923.2	+	18	3196	c.3021T>A	c.(3019-3021)gcT>gcA	p.A1007A	RP3-467L1.4_ENST00000451646.1_RNA|PER3_ENST00000377532.3_Silent_p.A1016A	NM_016831.1	NP_058515.1	P56645	PER3_HUMAN	period circadian clock 3	1007	5 X 18 AA tandem repeats of S-[HP]-[AP]- T-[AT]-[GST]-[ATV]-L-S-[MT]-G-[LS]-P-P- [MRS]-[EKR]-[NST]-P.|Ser-rich.		A -> T (in dbSNP:rs1776342).|Missing (associated with eveningness and better cognitive performance during sleep deprivation exepriments; dbSNP:rs57875989).		circadian regulation of gene expression (GO:0032922)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of circadian sleep/wake cycle, sleep (GO:0045187)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	signal transducer activity (GO:0004871)			breast(4)|central_nervous_system(3)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(9)|lung(8)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	39	Ovarian(185;0.0634)|all_lung(157;0.178)	all_epithelial(116;9.35e-21)|all_lung(118;7.57e-07)|Lung NSC(185;4.52e-06)|Renal(390;0.000147)|Breast(487;0.00086)|Colorectal(325;0.000959)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0234)|all cancers(8;8.58e-70)|GBM - Glioblastoma multiforme(8;1.81e-35)|Colorectal(212;2.06e-07)|COAD - Colon adenocarcinoma(227;1.92e-05)|Kidney(185;7.18e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000472)|STAD - Stomach adenocarcinoma(132;0.00118)|KIRC - Kidney renal clear cell carcinoma(229;0.00122)|READ - Rectum adenocarcinoma(331;0.0649)		CTGCCAGCGCTCTGTCCACAG	0.587																																					p.A1007A		Atlas-SNP	.											PER3,NS,carcinoma,+2,1	PER3	95	1	0			c.T3021A						scavenged	.						90.0	71.0	77.0					1																	7890055		1995	3900	5895	SO:0001819	synonymous_variant	8863	exon18			CAGCGCTCTGTCC	BC026102	CCDS89.1, CCDS72695.1	1p36.23	2012-12-13	2012-12-13		ENSG00000049246	ENSG00000049246			8847	protein-coding gene	gene with protein product		603427	"""period (Drosophila) homolog 3"", ""period homolog 3 (Drosophila)"""			9427249	Standard	XM_005263520		Approved		uc001aoo.3	P56645	OTTHUMG00000001216	ENST00000361923.2:c.3021T>A	1.37:g.7890055T>A		Somatic	148	1	0.00675676		WXS	Illumina HiSeq	Phase_I	56	9	0.160714	NM_016831	Q5H8X4|Q5H8X5|Q969K6|Q96S77|Q96S78|Q9C0J3|Q9NSP9|Q9UGU8	Silent	SNP	ENST00000361923.2	37	CCDS89.1																																																																																			T|0.954;A|0.046	0.046	strong		0.587	PER3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000003607.1	NM_016831	
PLB1	151056	hgsc.bcm.edu	37	2	28814033	28814033	+	Missense_Mutation	SNP	A	A	G	rs11681826	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:28814033A>G	ENST00000327757.5	+	30	2166	c.2122A>G	c.(2122-2124)Atg>Gtg	p.M708V	PLB1_ENST00000329020.6_Missense_Mutation_p.M396V|PLB1_ENST00000422425.2_Missense_Mutation_p.M697V	NM_153021.4	NP_694566.4	Q6P1J6	PLB1_HUMAN	phospholipase B1	708	4 X 308-326 AA approximate repeats.		M -> V (in dbSNP:rs11681826).		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)	p.M708V(1)		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)					CAAGAACAGCATGCAGGTACC	0.582													G|||	1516	0.302716	0.3812	0.3184	5008	,	,		20437	0.3006		0.1899	False		,,,				2504	0.3037				p.M708V		Atlas-SNP	.											PLB1,NS,carcinoma,0,1	PLB1	255	1	1	Substitution - Missense(1)	stomach(1)	c.A2122G						PASS	.	G	VAL/MET,VAL/MET	1583,2823	667.0+/-401.8	290,1003,910	155.0	130.0	138.0		2089,2122	-1.1	0.0	2	dbSNP_120	138	1667,6933	739.9+/-407.1	175,1317,2808	yes	missense,missense	PLB1	NM_001170585.1,NM_153021.4	21,21	465,2320,3718	GG,GA,AA		19.3837,35.9283,24.9885	benign,benign	697/1448,708/1459	28814033	3250,9756	2203	4300	6503	SO:0001583	missense	151056	exon30			AACAGCATGCAGG		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.2122A>G	2.37:g.28814033A>G	ENSP00000330442:p.Met708Val	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	101	54	0.534653	NM_153021	A8KAX2|Q53S03|Q8IUP7|Q96DP9	Missense_Mutation	SNP	ENST00000327757.5	37	CCDS33168.1	599	0.2742673992673993	177	0.3597560975609756	104	0.287292817679558	173	0.30244755244755245	145	0.19129287598944592	G	8.047	0.765146	0.15914	0.359283	0.193837	ENSG00000163803	ENST00000327757;ENST00000422425;ENST00000436544;ENST00000329020	T;T;T;T	0.17528	2.27;2.27;2.27;2.27	5.02	-1.11	0.09840	.	1.562000	0.03736	N	0.254245	T	0.00012	0.0000	N	0.00583	-1.355	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	0.44081	-0.9351	9	0.10902	T	0.67	-0.0226	1.8633	0.03193	0.521:0.1486:0.1814:0.1491	rs11681826;rs59763477;rs11681826	697;708;396;708	Q6P1J6-3;Q6P1J6-4;Q6P1J6-2;Q6P1J6	.;.;.;PLB1_HUMAN	V	708;697;418;396	ENSP00000330442:M708V;ENSP00000416440:M697V;ENSP00000392493:M418V;ENSP00000330729:M396V	ENSP00000330442:M708V	M	+	1	0	PLB1	28667537	0.000000	0.05858	0.000000	0.03702	0.955000	0.61496	-0.520000	0.06252	-0.298000	0.08921	-0.735000	0.03563	ATG	A|0.739;G|0.261	0.261	strong		0.582	PLB1-012	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000353348.2		
CRACR2A	84766	hgsc.bcm.edu	37	12	3788222	3788222	+	Missense_Mutation	SNP	G	G	A	rs242017	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	114	0	0		WXS	Illumina HiSeq	Phase_I	100	41	0.41	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		
C7orf71	285941	hgsc.bcm.edu	37	7	26685934	26685934	+	Silent	SNP	T	T	C	rs12671270	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:26685934T>C	ENST00000409974.3	+	4	1001	c.285T>C	c.(283-285)tgT>tgC	p.C95C		NM_001145531.1	NP_001139003.1	A4D174	CG071_HUMAN	chromosome 7 open reading frame 71	95																	TCTCCGCATGTGGGACTCTCG	0.423													C|||	1413	0.282149	0.351	0.2176	5008	,	,		18149	0.3264		0.2724	False		,,,				2504	0.1994				p.C95C		Atlas-SNP	.											.	C7orf71	6	.	0			c.T285C						PASS	.	C		483,901		96,291,305	79.0	70.0	73.0		285	-1.3	0.0	7	dbSNP_120	73	967,2215		153,661,777	no	coding-synonymous	C7orf71	NM_001145531.1		249,952,1082	CC,CT,TT		30.3897,34.8988,31.7565		95/170	26685934	1450,3116	692	1591	2283	SO:0001819	synonymous_variant	285941	exon4			CGCATGTGGGACT		CCDS47565.1	7p15.2	2009-09-11			ENSG00000222004	ENSG00000222004			22364	protein-coding gene	gene with protein product							Standard	NM_001145531		Approved		uc003syb.3	A4D174	OTTHUMG00000152860	ENST00000409974.3:c.285T>C	7.37:g.26685934T>C		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	66	44	0.666667	NM_001145531		Silent	SNP	ENST00000409974.3	37	CCDS47565.1																																																																																			C|0.305;N|0.000	0.305	strong		0.423	C7orf71-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328272.1	NM_001145531	
NFKBIZ	64332	hgsc.bcm.edu	37	3	101571753	101571753	+	Missense_Mutation	SNP	A	A	G	rs61730026	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:101571753A>G	ENST00000326172.5	+	4	599	c.484A>G	c.(484-486)Agt>Ggt	p.S162G	NFKBIZ_ENST00000326151.5_Missense_Mutation_p.S162G|NFKBIZ_ENST00000394054.2_Missense_Mutation_p.S62G	NM_031419.3	NP_113607.1	Q9BYH8	IKBZ_HUMAN	nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, zeta	162					inflammatory response (GO:0006954)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				breast(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(8)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	24						AGTATCATACAGTGGGAAAAG	0.383													A|||	2	0.000399361	0.0	0.0014	5008	,	,		17347	0.0		0.001	False		,,,				2504	0.0				p.S162G		Atlas-SNP	.											.	NFKBIZ	55	.	0			c.A484G						PASS	.	A	GLY/SER,GLY/SER	4,4402	8.1+/-20.4	0,4,2199	135.0	135.0	135.0		184,484	2.0	0.2	3	dbSNP_129	135	17,8583	12.6+/-44.7	0,17,4283	yes	missense,missense	NFKBIZ	NM_001005474.2,NM_031419.3	56,56	0,21,6482	GG,GA,AA		0.1977,0.0908,0.1615	benign,benign	62/619,162/719	101571753	21,12985	2203	4300	6503	SO:0001583	missense	64332	exon4			TCATACAGTGGGA	AF548362	CCDS2946.1, CCDS43123.1	3p12-q12	2013-01-10			ENSG00000144802	ENSG00000144802		"""Ankyrin repeat domain containing"""	29805	protein-coding gene	gene with protein product	"""IL-1 inducible nuclear ankyrin-repeat protein"""	608004				12565889, 16513645	Standard	NM_031419		Approved	MAIL, FLJ34463, INAP	uc003dvp.3	Q9BYH8	OTTHUMG00000159194	ENST00000326172.5:c.484A>G	3.37:g.101571753A>G	ENSP00000325663:p.Ser162Gly	Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	155	78	0.503226	NM_031419	B3KNR2|D3DN54|Q8IUL4|Q8NAZ8	Missense_Mutation	SNP	ENST00000326172.5	37	CCDS2946.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	A	0.009	-1.840705	0.00573	9.08E-4	0.001977	ENSG00000144802	ENST00000483180;ENST00000394054;ENST00000326151;ENST00000326172;ENST00000491281	T;T;T;T	0.55760	0.57;0.53;0.5;0.56	5.62	1.98	0.26296	.	0.734859	0.13799	N	0.361934	T	0.29355	0.0731	N	0.08118	0	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.18178	-1.0345	10	0.18276	T	0.48	-12.5889	10.5998	0.45360	0.7332:0.0:0.2668:0.0	rs61730026	162;162	Q9BYH8-3;Q9BYH8	.;IKBZ_HUMAN	G	62;62;162;162;62	ENSP00000419800:S62G;ENSP00000377618:S62G;ENSP00000325593:S162G;ENSP00000325663:S162G	ENSP00000325593:S162G	S	+	1	0	NFKBIZ	103054443	0.619000	0.27059	0.159000	0.22649	0.020000	0.10135	1.190000	0.32126	0.081000	0.16988	-2.096000	0.00365	AGT	A|0.998;G|0.002	0.002	strong		0.383	NFKBIZ-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000353793.1	NM_031419	
GLI1	2735	hgsc.bcm.edu	37	12	57859431	57859431	+	Silent	SNP	G	G	A	rs2228225	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:57859431G>A	ENST00000228682.2	+	6	667	c.576G>A	c.(574-576)gaG>gaA	p.E192E	GLI1_ENST00000543426.1_Silent_p.E64E|GLI1_ENST00000546141.1_Silent_p.E151E	NM_005269.2	NP_005260.1	P08151	GLI1_HUMAN	GLI family zinc finger 1	192					cerebellar cortex morphogenesis (GO:0021696)|digestive tract morphogenesis (GO:0048546)|dorsal/ventral pattern formation (GO:0009953)|epidermal cell differentiation (GO:0009913)|lung development (GO:0030324)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|notochord regression (GO:0060032)|osteoblast differentiation (GO:0001649)|pituitary gland development (GO:0021983)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA replication (GO:0045740)|positive regulation of smoothened signaling pathway (GO:0045880)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|proximal/distal pattern formation (GO:0009954)|regulation of smoothened signaling pathway (GO:0008589)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in regulation of cerebellar granule cell precursor cell proliferation (GO:0021938)|spermatogenesis (GO:0007283)|ventral midline development (GO:0007418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|primary cilium (GO:0072372)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(8)|lung(22)|ovary(6)|pancreas(2)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	69			GBM - Glioblastoma multiforme(3;3.99e-32)			AGTGCCGGGAGGAACCCTTGG	0.547													G|||	1818	0.363019	0.1611	0.3934	5008	,	,		20121	0.3046		0.6233	False		,,,				2504	0.407				p.E192E	Pancreas(157;841 1936 10503 41495 50368)	Atlas-SNP	.											.	GLI1	141	.	0			c.G576A						PASS	.	G	,,	1066,3340	388.6+/-327.0	132,802,1269	78.0	66.0	70.0		192,453,576	1.3	0.9	12	dbSNP_98	70	5406,3194	652.7+/-401.0	1708,1990,602	yes	coding-synonymous,coding-synonymous,coding-synonymous	GLI1	NM_001160045.1,NM_001167609.1,NM_005269.2	,,	1840,2792,1871	AA,AG,GG		37.1395,24.1943,49.7616	,,	64/979,151/1066,192/1107	57859431	6472,6534	2203	4300	6503	SO:0001819	synonymous_variant	2735	exon6			CCGGGAGGAACCC		CCDS8940.1, CCDS53806.1, CCDS53807.1	12q13.2-q13.3	2013-01-25	2009-03-05	2005-01-14		ENSG00000111087		"""Zinc fingers, C2H2-type"""	4317	protein-coding gene	gene with protein product		165220	"""glioma-associated oncogene homolog 1 (zinc finger protein)"", ""glioma-associated oncogene family zinc finger 1"""	GLI		2850480	Standard	NM_005269		Approved		uc001snx.3	P08151		ENST00000228682.2:c.576G>A	12.37:g.57859431G>A		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	114	54	0.473684	NM_005269	D0EUY3|E9PQQ9|F5H6H8|Q8TDN9	Silent	SNP	ENST00000228682.2	37	CCDS8940.1																																																																																			A|0.449;C|0.000;G|0.551	0.449	strong		0.547	GLI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394197.1	NM_005269	
FAM83B	222584	hgsc.bcm.edu	37	6	54735301	54735301	+	Missense_Mutation	SNP	C	C	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:54735301C>G	ENST00000306858.7	+	2	373	c.257C>G	c.(256-258)aCc>aGc	p.T86S		NM_001010872.1	NP_001010872.1	Q5T0W9	FA83B_HUMAN	family with sequence similarity 83, member B	86										autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(6)|lung(28)|ovary(6)|prostate(6)|skin(6)|upper_aerodigestive_tract(1)	71	Lung NSC(77;0.0178)|Renal(3;0.122)					TGTGATGATACCTTATCTTCA	0.443																																					p.T86S		Atlas-SNP	.											.	FAM83B	186	.	0			c.C257G						PASS	.						130.0	131.0	131.0					6																	54735301		2203	4300	6503	SO:0001583	missense	222584	exon2			ATGATACCTTATC	AK055204	CCDS34479.1	6p12.1	2014-03-13	2006-03-23	2006-03-23	ENSG00000168143	ENSG00000168143			21357	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 143"""	C6orf143		22886302	Standard	NM_001010872		Approved	FLJ30642	uc003pck.4	Q5T0W9	OTTHUMG00000014899	ENST00000306858.7:c.257C>G	6.37:g.54735301C>G	ENSP00000304078:p.Thr86Ser	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	128	27	0.210938	NM_001010872	Q2M1P3|Q96DQ2	Missense_Mutation	SNP	ENST00000306858.7	37	CCDS34479.1	.	.	.	.	.	.	.	.	.	.	C	10.88	1.474403	0.26423	.	.	ENSG00000168143	ENST00000306858	T	0.10960	2.82	5.49	3.63	0.41609	.	0.784700	0.12264	N	0.484499	T	0.01765	0.0056	N	0.10782	0.045	0.09310	N	0.99999	B	0.24317	0.101	B	0.25506	0.061	T	0.48151	-0.9060	10	0.18710	T	0.47	-1.312	10.1089	0.42550	0.2692:0.5927:0.1381:0.0	.	86	Q5T0W9	FA83B_HUMAN	S	86	ENSP00000304078:T86S	ENSP00000304078:T86S	T	+	2	0	FAM83B	54843260	0.216000	0.23585	0.731000	0.30826	0.811000	0.45836	2.409000	0.44583	0.732000	0.32470	0.460000	0.39030	ACC	.	.	none		0.443	FAM83B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040994.1	XM_294139	
CES1	1066	hgsc.bcm.edu	37	16	55862791	55862791	+	Missense_Mutation	SNP	T	T	C	rs3826193	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:55862791T>C	ENST00000361503.4	-	2	275	c.145A>G	c.(145-147)Att>Gtt	p.I49V	CES1_ENST00000360526.3_Missense_Mutation_p.I50V|CES1_ENST00000422046.2_Missense_Mutation_p.I49V|CES1_ENST00000566555.1_5'Flank			P23141	EST1_HUMAN	carboxylesterase 1	49					epithelial cell differentiation (GO:0030855)|metabolic process (GO:0008152)|response to toxic substance (GO:0009636)	endoplasmic reticulum (GO:0005783)	carboxylic ester hydrolase activity (GO:0052689)|methylumbelliferyl-acetate deacetylase activity (GO:0047374)								all cancers(182;0.13)|Epithelial(162;0.137)	Benzocaine(DB01086)|Capecitabine(DB01101)|Ciclesonide(DB01410)|Clopidogrel(DB00758)|Cyclandelate(DB04838)|Dabigatran etexilate(DB06695)|Indomethacin(DB00328)|Irinotecan(DB00762)|L-Carnitine(DB00583)|Mycophenolate mofetil(DB00688)|Oseltamivir(DB00198)|Probucol(DB01599)|Rufinamide(DB06201)|Tamoxifen(DB00675)|Trandolapril(DB00519)	CCCAGGAAAATGGCCACAGGC	0.572																																					p.I50V	NSCLC(162;1801 2756 42904 52896)	Atlas-SNP	.											.	CES1	78	.	0			c.A148G						PASS	.						86.0	75.0	79.0					16																	55862791		2198	4300	6498	SO:0001583	missense	1066	exon2			GGAAAATGGCCAC	BC012418	CCDS32450.1, CCDS45488.1, CCDS45489.1	16q22.2	2010-10-12	2010-10-12		ENSG00000198848	ENSG00000198848	3.1.1.1	"""Carboxylesterases"""	1863	protein-coding gene	gene with protein product	"""human monocyte/macrophage serine esterase 1"""	114835	"""carboxylesterase 1 (monocyte/macrophage serine esterase 1)"""			2070086, 20931200	Standard	XM_005255774		Approved	HMSE, CES2, HMSE1, SES1, CEH, CES1A1, CES1A2	uc002eil.3	P23141		ENST00000361503.4:c.145A>G	16.37:g.55862791T>C	ENSP00000355193:p.Ile49Val	Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	99	14	0.141414	NM_001025195	A6NIM1|A8K3K8|A8K844|E9PAU8|P82127|Q00015|Q13657|Q14062|Q16737|Q16788|Q549X7|Q549X8|Q86UK2|Q96EE8|Q9UC52|Q9UDG8|Q9UK77|Q9ULY2	Missense_Mutation	SNP	ENST00000361503.4	37	CCDS45488.1	.	.	.	.	.	.	.	.	.	.	.	0.005	-2.119403	0.00346	.	.	ENSG00000198848	ENST00000360526;ENST00000361503;ENST00000422046	T;T;T	0.64438	-0.1;-0.1;-0.1	4.48	2.48	0.30137	Carboxylesterase, type B (1);	0.166939	0.28382	N	0.015560	T	0.19287	0.0463	N	0.00260	-1.75	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.001;0.0	T	0.38866	-0.9641	10	0.02654	T	1	.	8.5586	0.33496	0.0:0.727:0.0:0.273	rs3826193	49;49;50	E9PAU8;P23141;P23141-2	.;EST1_HUMAN;.	V	50;49;49	ENSP00000353720:I50V;ENSP00000355193:I49V;ENSP00000390492:I49V	ENSP00000353720:I50V	I	-	1	0	CES1	54420292	0.001000	0.12720	0.534000	0.28014	0.060000	0.15804	0.503000	0.22610	0.358000	0.24211	-0.534000	0.04291	ATT	.	.	weak		0.572	CES1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000433285.1	NM_001266	
HLA-A	3105	hgsc.bcm.edu	37	6	29912348	29912348	+	Missense_Mutation	SNP	A	A	G	rs1137078	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:29912348A>G	ENST00000396634.1	+	7	1308	c.967A>G	c.(967-969)Act>Gct	p.T323A	HLA-A_ENST00000376802.2_Intron|HLA-A_ENST00000376809.5_Missense_Mutation_p.T323A|HLA-A_ENST00000376806.5_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	211	0	0		WXS	Illumina HiSeq	Phase_I	157	58	0.369427	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	
FAM46C	54855	hgsc.bcm.edu	37	1	118165973	118165973	+	Silent	SNP	C	C	T	rs1627787	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:118165973C>T	ENST00000369448.3	+	2	730	c.483C>T	c.(481-483)aaC>aaT	p.N161N		NM_017709.3	NP_060179.2	Q5VWP2	FA46C_HUMAN	family with sequence similarity 46, member C	161										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)		CCAACAAGAACGGGAAGAACG	0.488			"""Mis, F, O"""		MM					Multiple Myeloma(3;1.13e-06)			T|||	1401	0.279752	0.3419	0.3127	5008	,	,		21929	0.2391		0.2266	False		,,,				2504	0.2689				p.N161N		Atlas-SNP	.		Rec	yes		1	1p12	54855	"""family with sequence similarity 46, member C"""		L	.	FAM46C	25	.	0			c.C483T						PASS	.	T		1424,2982	684.5+/-404.4	227,970,1006	141.0	133.0	136.0		483	-3.0	0.9	1	dbSNP_89	136	1925,6675	726.5+/-406.6	202,1521,2577	no	coding-synonymous	FAM46C	NM_017709.3		429,2491,3583	TT,TC,CC		22.3837,32.3196,25.7497		161/392	118165973	3349,9657	2203	4300	6503	SO:0001819	synonymous_variant	54855	exon2			CAAGAACGGGAAG	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.483C>T	1.37:g.118165973C>T		Somatic	238	0	0		WXS	Illumina HiSeq	Phase_I	177	177	1	NM_017709	A3KMG2|Q8NE25|Q9NXK0	Silent	SNP	ENST00000369448.3	37	CCDS896.1																																																																																			C|0.740;T|0.260	0.260	strong		0.488	FAM46C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038424.1	NM_017709	
PTBP1	5725	hgsc.bcm.edu	37	19	808742	808742	+	Silent	SNP	G	G	T	rs1135908	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:808742G>T	ENST00000349038.4	+	12	1438	c.1365G>T	c.(1363-1365)acG>acT	p.T455T	PTBP1_ENST00000350092.4_Silent_p.T121T|PTBP1_ENST00000356948.6_Silent_p.T481T|PTBP1_ENST00000394601.4_Silent_p.T474T	NM_031991.3	NP_114368.1	P26599	PTBP1_HUMAN	polypyrimidine tract binding protein 1	455	RRM 4. {ECO:0000255|PROSITE- ProRule:PRU00176}.				alternative mRNA splicing, via spliceosome (GO:0000380)|gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|negative regulation of muscle cell differentiation (GO:0051148)|negative regulation of RNA splicing (GO:0033119)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing (GO:0008380)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|poly-pyrimidine tract binding (GO:0008187)|pre-mRNA binding (GO:0036002)|RNA binding (GO:0003723)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|skin(2)|upper_aerodigestive_tract(4)	19		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;6.59e-06)|all_lung(49;9.97e-06)|Breast(49;0.000172)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CCTCGGCCACGCTGCACCTCT	0.662													G|||	799	0.159545	0.1331	0.2651	5008	,	,		9373	0.0218		0.1451	False		,,,				2504	0.2771				p.T481T		Atlas-SNP	.											.	PTBP1	43	.	0			c.G1443T						PASS	.	G	,,,	561,3835		43,475,1680	30.0	29.0	29.0		1443,1422,1365,363	0.0	1.0	19	dbSNP_86	29	1259,7327		83,1093,3117	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PTBP1	NM_002819.4,NM_031990.3,NM_031991.3,NM_175847.2	,,,	126,1568,4797	TT,TG,GG		14.6634,12.7616,14.0194	,,,	481/558,474/551,455/532,121/198	808742	1820,11162	2198	4293	6491	SO:0001819	synonymous_variant	5725	exon13			GGCCACGCTGCAC	X60648	CCDS32859.1, CCDS42456.1, CCDS45892.1	19p13.3	2013-07-16	2002-01-25	2002-01-25	ENSG00000011304	ENSG00000011304		"""RNA binding motif (RRM) containing"""	9583	protein-coding gene	gene with protein product	"""heterogeneous nuclear ribonucleoprotein I"""	600693	"""polypyrimidine tract binding protein (heterogeneous nuclear ribonucleoprotein I)"""	PTB		1906036, 11024286	Standard	NM_002819		Approved	HNRPI, HNRNP-I, PTB2, PTB3, PTB-1, PTB4, pPTB	uc002lpp.2	P26599		ENST00000349038.4:c.1365G>T	19.37:g.808742G>T		Somatic	200	1	0.005		WXS	Illumina HiSeq	Phase_I	176	174	0.988636	NM_002819	Q9BUQ0	Silent	SNP	ENST00000349038.4	37	CCDS32859.1																																																																																			G|0.864;T|0.136	0.136	strong		0.662	PTBP1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457605.1		
KRTAP10-6	386674	hgsc.bcm.edu	37	21	46011298	46011298	+	Silent	SNP	G	G	A	rs113437209	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	145	0	0		WXS	Illumina HiSeq	Phase_I	193	9	0.0466321	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	
C10orf90	118611	hgsc.bcm.edu	37	10	128202435	128202435	+	Silent	SNP	T	T	C	rs1436803	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:128202435T>C	ENST00000284694.7	-	2	216	c.96A>G	c.(94-96)gcA>gcG	p.A32A	C10orf90_ENST00000544758.1_Silent_p.A129A|C10orf90_ENST00000454341.1_Silent_p.A32A|C10orf90_ENST00000356858.3_5'UTR|C10orf90_ENST00000392694.1_5'UTR|C10orf90_ENST00000368674.1_5'UTR	NM_001004298.2	NP_001004298.2	Q96M02	CJ090_HUMAN	chromosome 10 open reading frame 90	32					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)		AGTCAGATTTTGCCTCTGTGA	0.378													C|||	4387	0.875998	0.9145	0.8631	5008	,	,		17004	0.8571		0.8569	False		,,,				2504	0.8722				p.A32A		Atlas-SNP	.											.	C10orf90	121	.	0			c.A96G						PASS	.	C		4010,396	197.7+/-221.8	1829,352,22	165.0	155.0	159.0		96	5.2	0.9	10	dbSNP_88	159	7311,1289	256.3+/-280.9	3112,1087,101	no	coding-synonymous	C10orf90	NM_001004298.2		4941,1439,123	CC,CT,TT		14.9884,8.9877,12.9556		32/700	128202435	11321,1685	2203	4300	6503	SO:0001819	synonymous_variant	118611	exon2			AGATTTTGCCTCT	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.96A>G	10.37:g.128202435T>C		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	77	76	0.987013	NM_001004298	B9EIQ9|Q5JRP6|Q5T023|Q8NCV5|Q8WU75	Silent	SNP	ENST00000284694.7	37	CCDS31310.1																																																																																			T|0.131;C|0.869	0.869	strong		0.378	C10orf90-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001004298	
CYP20A1	57404	hgsc.bcm.edu	37	2	204154552	204154552	+	Missense_Mutation	SNP	C	C	T	rs1048013	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:204154552C>T	ENST00000356079.4	+	10	1159	c.1036C>T	c.(1036-1038)Ctt>Ttt	p.L346F	CYP20A1_ENST00000461371.1_3'UTR|CYP20A1_ENST00000429815.2_Missense_Mutation_p.L354F	NM_177538.2	NP_803882.1	Q6UW02	CP20A_HUMAN	cytochrome P450, family 20, subfamily A, polypeptide 1	346			L -> F (in dbSNP:rs1048013). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.1}.			integral component of membrane (GO:0016021)|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)			cervix(1)|large_intestine(2)|lung(6)|ovary(1)|skin(1)	11						TTCTGCCCAGCTTCAAGATAT	0.318													C|||	2003	0.39996	0.149	0.4438	5008	,	,		13211	0.3194		0.5606	False		,,,				2504	0.6258				p.L346F		Atlas-SNP	.											.	CYP20A1	40	.	0			c.C1036T						PASS	.	C	PHE/LEU	979,3427	364.1+/-316.8	108,763,1332	61.0	58.0	59.0		1036	5.6	1.0	2	dbSNP_86	59	4837,3763	614.1+/-396.2	1365,2107,828	yes	missense	CYP20A1	NM_177538.2	22	1473,2870,2160	TT,TC,CC		43.7558,22.2197,44.7178	benign	346/463	204154552	5816,7190	2203	4300	6503	SO:0001583	missense	57404	exon10			GCCCAGCTTCAAG	AK021770	CCDS2357.1	2q33	2008-02-05			ENSG00000119004	ENSG00000119004		"""Cytochrome P450s"""	20576	protein-coding gene	gene with protein product							Standard	NM_177538		Approved	CYP-M	uc002uzv.4	Q6UW02	OTTHUMG00000132854	ENST00000356079.4:c.1036C>T	2.37:g.204154552C>T	ENSP00000348380:p.Leu346Phe	Somatic	292	0	0		WXS	Illumina HiSeq	Phase_I	262	144	0.549618	NM_177538	Q4ZG61|Q8N4Q8|Q8WWA9|Q9HC04	Missense_Mutation	SNP	ENST00000356079.4	37	CCDS2357.1	835	0.3823260073260073	84	0.17073170731707318	183	0.505524861878453	158	0.2762237762237762	410	0.5408970976253298	C	14.49	2.549672	0.45383	0.222197	0.562442	ENSG00000119004	ENST00000356079;ENST00000421618;ENST00000429815	T;T	0.70164	-0.46;-0.46	5.6	5.6	0.85130	.	0.060804	0.64402	D	0.000004	T	0.00012	0.0000	L	0.54323	1.7	0.20873	P	0.999831543	B;B	0.12013	0.003;0.005	B;B	0.18871	0.015;0.023	T	0.44997	-0.9291	9	0.12766	T	0.61	-8.4726	19.6715	0.95914	0.0:1.0:0.0:0.0	rs1048013;rs3188004;rs17415875;rs17858536;rs17859053;rs52814168;rs58200424;rs1048013	354;346	E9PHG5;Q6UW02	.;CP20A_HUMAN	F	346;319;354	ENSP00000348380:L346F;ENSP00000407860:L354F	ENSP00000348380:L346F	L	+	1	0	CYP20A1	203862797	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	4.719000	0.61937	2.667000	0.90743	0.580000	0.79431	CTT	C|0.598;T|0.402	0.402	strong		0.318	CYP20A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256328.3	NM_020674	
NUP88	4927	hgsc.bcm.edu	37	17	5294976	5294976	+	Silent	SNP	T	T	A	rs14231	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:5294976T>A	ENST00000573584.1	-	10	1898	c.1389A>T	c.(1387-1389)ccA>ccT	p.P463P		NM_002532.4	NP_002523.2	Q99567	NUP88_HUMAN	nucleoporin 88kDa	463					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA 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)	cytosol (GO:0005829)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	transporter activity (GO:0005215)			endometrium(4)|kidney(4)|large_intestine(4)|lung(3)	15						GAATTGGAGCTGGCTGCCTGG	0.478													T|||	2766	0.552316	0.3971	0.4236	5008	,	,		23299	0.8254		0.4404	False		,,,				2504	0.6871				p.P463P		Atlas-SNP	.											.	NUP88	47	.	0			c.A1389T						PASS	.	T		1846,2560	537.0+/-374.6	407,1032,764	106.0	93.0	97.0		1389	-3.3	0.9	17	dbSNP_52	97	3390,5210	501.8+/-375.5	665,2060,1575	no	coding-synonymous	NUP88	NM_002532.4		1072,3092,2339	AA,AT,TT		39.4186,41.8974,40.2583		463/742	5294976	5236,7770	2203	4300	6503	SO:0001819	synonymous_variant	4927	exon10			TGGAGCTGGCTGC	Y08612	CCDS11070.1	17p13	2004-02-18	2002-08-29		ENSG00000108559	ENSG00000108559			8067	protein-coding gene	gene with protein product		602552	"""nucleoporin 88kD"""			9049309	Standard	NM_002532		Approved	MGC8530	uc002gbo.2	Q99567	OTTHUMG00000099453	ENST00000573584.1:c.1389A>T	17.37:g.5294976T>A		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	47	25	0.531915	NM_002532	D3DTM2|Q9BWE5	Silent	SNP	ENST00000573584.1	37	CCDS11070.1																																																																																			T|0.571;A|0.429	0.429	strong		0.478	NUP88-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216918.3	NM_002532	
SLC35G6	643664	hgsc.bcm.edu	37	17	7385454	7385454	+	Missense_Mutation	SNP	G	G	A	rs3760422	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:7385454G>A	ENST00000412468.2	+	2	266	c.151G>A	c.(151-153)Gct>Act	p.A51T	POLR2A_ENST00000322644.6_5'Flank|ZBTB4_ENST00000380599.4_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	51	EamA 1.		A -> T (in dbSNP:rs3760422).			integral component of membrane (GO:0016021)											GGGCCTGCCTGCTGGCTTCGT	0.662													G|||	928	0.185304	0.1165	0.2392	5008	,	,		17801	0.1935		0.161	False		,,,				2504	0.2566				p.A51T		Atlas-SNP	.											.	.	.	.	0			c.G151A						PASS	.	G	THR/ALA,	587,3819	256.7+/-261.4	44,499,1660	55.0	62.0	60.0		151,	4.0	1.0	17	dbSNP_107	60	1268,7330	251.1+/-277.7	99,1070,3130	no	missense,intron	ZBTB4,SLC35G6	NM_001102614.1,NM_020899.3	58,	143,1569,4790	AA,AG,GG		14.7476,13.3227,14.2648	probably-damaging,	51/339,	7385454	1855,11149	2203	4299	6502	SO:0001583	missense	643664	exon2			CTGCCTGCTGGCT		CCDS45603.1	17p13.1	2013-05-22	2011-08-03	2011-08-03		ENSG00000259224		"""Solute carriers"""	31351	protein-coding gene	gene with protein product			"""transmembrane protein 21B"", ""acyl-malonyl condensing enzyme 1-like 3"""	TMEM21B, AMAC1L3			Standard	NM_001102614		Approved		uc010cmj.1	P0C7Q6		ENST00000412468.2:c.151G>A	17.37:g.7385454G>A	ENSP00000396523:p.Ala51Thr	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	105	48	0.457143	NM_001102614		Missense_Mutation	SNP	ENST00000412468.2	37	CCDS45603.1	387	0.1771978021978022	54	0.10975609756097561	91	0.2513812154696133	120	0.2097902097902098	122	0.16094986807387862	G	11.57	1.678465	0.29783	0.133227	0.147476	ENSG00000181222	ENST00000412468	T	0.27890	1.64	4.04	4.04	0.47022	.	.	.	.	.	T	0.00012	0.0000	N	0.24115	0.695	0.30395	P	0.780636	D	0.76494	0.999	D	0.85130	0.997	T	0.17899	-1.0354	8	0.23891	T	0.37	-4.4801	11.4032	0.49883	0.0:0.1843:0.8157:0.0	rs3760422;rs12945890;rs61072970;rs3760422	51	P0C7Q6	S35G6_HUMAN	T	51	ENSP00000396523:A51T	ENSP00000396523:A51T	A	+	1	0	SLC35G6	7326178	0.643000	0.27269	0.989000	0.46669	0.086000	0.17979	2.163000	0.42377	1.959000	0.56917	0.462000	0.41574	GCT	G|0.841;A|0.159	0.159	strong		0.662	SLC35G6-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001102614	
CFAP74	85452	hgsc.bcm.edu	37	1	1900225	1900225	+	IGR	SNP	C	C	T	rs72636304	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:1900225C>T								TMEM52 (49513 upstream) : C1orf222 (19337 downstream)																							TTTCAGAATCCGACTGATGAT	0.572													c|||	9	0.00179712	0.0	0.0029	5008	,	,		17712	0.0		0.007	False		,,,				2504	0.0				p.R365Q		Atlas-SNP	.											.	KIAA1751	92	.	0			c.G1094A						PASS	.	C	GLN/ARG	5,4041		0,5,2018	141.0	150.0	147.0		1094	1.7	0.0	1	dbSNP_130	147	78,8256		0,78,4089	no	missense	KIAA1751	NM_001080484.1	43	0,83,6107	TT,TC,CC		0.9359,0.1236,0.6704	possibly-damaging	365/763	1900225	83,12297	2023	4167	6190	SO:0001628	intergenic_variant	85452	exon11			AGAATCCGACTGA																													1.37:g.1900225C>T		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	59	17	0.288136	NM_001080484		Missense_Mutation	SNP		37		7	0.003205128205128205	0	0.0	1	0.0027624309392265192	0	0.0	6	0.0079155672823219	c	15.07	2.725287	0.48833	0.001236	0.009359	ENSG00000142609	ENST00000270720	.	.	.	3.67	1.74	0.24563	.	0.241675	0.27019	N	0.021330	T	0.19005	0.0456	L	0.41824	1.3	0.18873	N	0.999982	D;D	0.57571	0.973;0.98	B;B	0.41988	0.314;0.372	T	0.09729	-1.0661	9	0.39692	T	0.17	-15.2726	8.0725	0.30697	0.0:0.7846:0.0:0.2154	.	365;365	Q9C0B2-2;Q9C0B2	.;K1751_HUMAN	Q	365	.	ENSP00000270720:R365Q	R	-	2	0	C1orf222	1890085	0.231000	0.23751	0.001000	0.08648	0.004000	0.04260	1.053000	0.30442	0.309000	0.22966	0.556000	0.70494	CGG	C|0.994;T|0.006	0.006	strong	0	0.572								
OSCP1	127700	hgsc.bcm.edu	37	1	36898067	36898067	+	Missense_Mutation	SNP	T	T	C	rs34409118	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:36898067T>C	ENST00000356637.5	-	4	484	c.421A>G	c.(421-423)Acc>Gcc	p.T141A	OSCP1_ENST00000315643.9_Missense_Mutation_p.T141A|OSCP1_ENST00000235532.5_Missense_Mutation_p.T131A|OSCP1_ENST00000354267.3_Missense_Mutation_p.T131A|OSCP1_ENST00000433045.2_Missense_Mutation_p.T86A			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	163	0	0		WXS	Illumina HiSeq	Phase_I	157	65	0.414013	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	
STON1	11037	hgsc.bcm.edu	37	2	48808152	48808152	+	Missense_Mutation	SNP	G	G	C	rs940389	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:48808152G>C	ENST00000406226.1	+	3	575	c.380G>C	c.(379-381)aGa>aCa	p.R127T	STON1_ENST00000309835.3_Missense_Mutation_p.R127T|STON1_ENST00000404752.1_Missense_Mutation_p.R127T|STON1-GTF2A1L_ENST00000394754.1_Missense_Mutation_p.R127T|STON1-GTF2A1L_ENST00000309827.2_Missense_Mutation_p.R127T|STON1-GTF2A1L_ENST00000402114.2_Missense_Mutation_p.R127T|STON1-GTF2A1L_ENST00000394751.3_Missense_Mutation_p.R127T|STON1-GTF2A1L_ENST00000405008.1_Missense_Mutation_p.R127T	NM_001198595.1	NP_001185524.1	Q9Y6Q2	STON1_HUMAN	stonin 1	127			R -> T (in dbSNP:rs940389).		endocytosis (GO:0006897)|intracellular protein transport (GO:0006886)|regulation of endocytosis (GO:0030100)	clathrin adaptor complex (GO:0030131)				NS(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(19)|prostate(3)|skin(2)	37		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			CTGCCTACCAGACCAACATGT	0.463													G|||	1781	0.355631	0.3079	0.3271	5008	,	,		22141	0.3919		0.341	False		,,,				2504	0.4182				p.R127T		Atlas-SNP	.											.	STON1	100	.	0			c.G380C						PASS	.	G	THR/ARG,THR/ARG,THR/ARG,THR/ARG,THR/ARG	1400,3006	458.0+/-351.8	227,946,1030	110.0	106.0	108.0		380,380,380,380,380	2.8	0.0	2	dbSNP_86	108	2852,5748	448.7+/-361.9	492,1868,1940	yes	missense,missense,missense,missense,missense	STON1,STON1-GTF2A1L	NM_001198593.1,NM_001198594.1,NM_001198595.1,NM_006873.3,NM_172311.2	71,71,71,71,71	719,2814,2970	CC,CG,GG		33.1628,31.7749,32.6926	benign,benign,benign,benign,benign	127/1159,127/1136,127/736,127/736,127/1183	48808152	4252,8754	2203	4300	6503	SO:0001583	missense	11037	exon3			CTACCAGACCAAC	AF026169	CCDS1841.1	2p16.3	2008-02-05			ENSG00000243244	ENSG00000243244			17003	protein-coding gene	gene with protein product	"""stoned B homolog 1 (Drosophila)"""	605357				14504226, 10364255	Standard	NM_001198595		Approved	SBLF, stoned-b1		Q9Y6Q2	OTTHUMG00000129169	ENST00000406226.1:c.380G>C	2.37:g.48808152G>C	ENSP00000384615:p.Arg127Thr	Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	271	43	0.158672	NM_001198595	A8MXJ1|B5MCF5|B7ZL16|Q96JE3|Q9BYX3	Missense_Mutation	SNP	ENST00000406226.1	37	CCDS1841.1	768	0.3516483516483517	153	0.31097560975609756	105	0.2900552486187845	239	0.4178321678321678	271	0.3575197889182058	G	1.930	-0.446092	0.04604	0.317749	0.331628	ENSG00000243244;ENSG00000243244;ENSG00000243244;ENSG00000068781;ENSG00000068781;ENSG00000068781;ENSG00000068781;ENSG00000068781	ENST00000404752;ENST00000406226;ENST00000309835;ENST00000405008;ENST00000402114;ENST00000394754;ENST00000309827;ENST00000394751	T;T;T;T;T;T;T;T	0.10005	2.92;2.92;2.92;2.92;2.92;2.92;2.92;3.09	5.24	2.83	0.33086	.	0.643344	0.17146	N	0.185261	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B;B;B	0.27625	0.183;0.0;0.039	B;B;B	0.28011	0.085;0.0;0.034	T	0.47368	-0.9123	9	0.33141	T	0.24	.	7.6523	0.28354	0.7847:0.141:0.0743:0.0	rs940389;rs3749141;rs52795264;rs940389	127;127;127	A8MXJ1;Q53S48;Q9Y6Q2	.;.;STON1_HUMAN	T	127	ENSP00000385273:R127T;ENSP00000384615:R127T;ENSP00000310969:R127T;ENSP00000385499:R127T;ENSP00000385701:R127T;ENSP00000378236:R127T;ENSP00000311493:R127T;ENSP00000378234:R127T	ENSP00000310969:R127T	R	+	2	0	STON1-GTF2A1L;STON1	48661656	0.015000	0.18098	0.002000	0.10522	0.002000	0.02628	0.909000	0.28558	0.517000	0.28361	-0.302000	0.09304	AGA	G|0.659;C|0.341	0.341	strong		0.463	STON1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323848.2	NM_006873	
MUC4	4585	hgsc.bcm.edu	37	3	195513173	195513173	+	Missense_Mutation	SNP	G	G	A	rs77448757	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195513173G>A	ENST00000463781.3	-	2	5737	c.5278C>T	c.(5278-5280)Cct>Tct	p.P1760S	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.P1760S	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		ACAGGAAGAGGGGTGGCCTGA	0.587																																					p.P1760S		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	0			c.C5278T						PASS	.						53.0	49.0	50.0					3																	195513173		692	1591	2283	SO:0001583	missense	4585	exon2			GAAGAGGGGTGGC	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.5278C>T	3.37:g.195513173G>A	ENSP00000417498:p.Pro1760Ser	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	157	44	0.280255	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	-	3.212	-0.161316	0.06502	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.29142	1.58;1.58	.	.	.	.	.	.	.	.	T	0.08935	0.0221	N	0.02539	-0.55	0.09310	N	1	B	0.14438	0.01	B	0.04013	0.001	T	0.27872	-1.0061	7	.	.	.	.	4.5334	0.12017	0.332:0.0:0.668:0.0	.	1760	E7ESK3	.	S	1760	ENSP00000417498:P1760S;ENSP00000420243:P1760S	.	P	-	1	0	MUC4	196997568	0.080000	0.21391	0.007000	0.13788	0.007000	0.05969	2.260000	0.43267	-1.764000	0.01305	-1.783000	0.00646	CCT	G|0.967;A|0.033	0.033	strong		0.587	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
HLA-A	3105	hgsc.bcm.edu	37	6	29910721	29910721	+	Missense_Mutation	SNP	G	G	C	rs199474423|rs199474424	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:29910721G>C	ENST00000396634.1	+	4	602	c.261G>C	c.(259-261)gaG>gaC	p.E87D	HLA-A_ENST00000376802.2_Missense_Mutation_p.E87D|HLA-A_ENST00000376809.5_Missense_Mutation_p.E87D|HLA-A_ENST00000376806.5_Missense_Mutation_p.E87D			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	87	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						GGGACCAGGAGACACGGAATG	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)			g|||	924	0.184505	0.2791	0.1427	5008	,	,		11259	0.1369		0.1074	False		,,,				2504	0.2147				p.E87D		Atlas-SNP	.											.	HLA-A	89	.	0			c.G261C						PASS	.	G	ASP/GLU	162,4244		59,44,2100	75.0	80.0	78.0		261	0.5	0.0	6	dbSNP_132	78	75,8511		20,35,4238	no	missense	HLA-A	NM_002116.7	45	79,79,6338	CC,CG,GG		0.8735,3.6768,1.8242	possibly-damaging	87/366	29910721	237,12755	2203	4293	6496	SO:0001583	missense	3105	exon2	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	CCAGGAGACACGG	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.261G>C	6.37:g.29910721G>C	ENSP00000379873:p.Glu87Asp	Somatic	267	0	0		WXS	Illumina HiSeq	Phase_I	183	65	0.355191	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Missense_Mutation	SNP	ENST00000396634.1	37	CCDS34373.1	.	.	.	.	.	.	.	.	.	.	.	8.973	0.973488	0.18736	0.036768	0.008735	ENSG00000206503	ENST00000396634;ENST00000376806;ENST00000376809;ENST00000355767;ENST00000376802	T;T;T;T	0.00840	5.63;5.63;5.63;5.63	3.57	0.501	0.16925	MHC class I, alpha chain, alpha1/alpha2 (6);MHC classes I/II-like antigen recognition protein (3);MHC class I-like antigen recognition (3);	0.306974	0.16761	U	0.200603	T	0.02727	0.0082	H	0.94183	3.505	0.09310	N	1	B;P;B;P;B	0.52170	0.006;0.951;0.004;0.951;0.004	B;D;B;D;B	0.77004	0.032;0.989;0.06;0.989;0.032	T	0.17048	-1.0382	10	0.72032	D	0.01	.	6.102	0.20053	0.11:0.3603:0.5297:0.0	rs1059457;rs2230992;rs3179181;rs16867778;rs41551913	87;87;87;87;87	P13746;Q5SRN7;P16188;Q5SRN5;P04439	1A11_HUMAN;.;1A30_HUMAN;.;1A03_HUMAN	D	87	ENSP00000379873:E87D;ENSP00000366002:E87D;ENSP00000366005:E87D;ENSP00000365998:E87D	ENSP00000348012:E87D	E	+	3	2	HLA-A	30018700	0.000000	0.05858	0.001000	0.08648	0.009000	0.06853	-1.182000	0.03082	-0.013000	0.14199	0.478000	0.44815	GAG	C|0.156;G|0.844	0.156	strong		0.672	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
ATRIP	84126	hgsc.bcm.edu	37	3	48506279	48506279	+	Missense_Mutation	SNP	G	G	A	rs76493396	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:48506279G>A	ENST00000320211.3	+	12	2218	c.2105G>A	c.(2104-2106)cGg>cAg	p.R702Q	TREX1_ENST00000433541.1_5'Flank|TREX1_ENST00000436480.2_5'Flank|TREX1_ENST00000422277.2_5'Flank|ATRIP_ENST00000346691.4_Missense_Mutation_p.R675Q|ATRIP_ENST00000357105.6_Missense_Mutation_p.R575Q|SHISA5_ENST00000465449.1_5'Flank|ATRIP_ENST00000412052.1_Missense_Mutation_p.R609Q|TREX1_ENST00000296443.9_5'Flank|TREX1_ENST00000444177.1_5'Flank|TREX1_ENST00000456089.1_5'Flank	NM_130384.2	NP_569055.1	Q8WXE1	ATRIP_HUMAN	ATR interacting protein	702					DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)	microtubule cytoskeleton (GO:0015630)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				central_nervous_system(1)|cervix(2)|endometrium(1)|large_intestine(6)|lung(8)|ovary(3)|prostate(1)	22				BRCA - Breast invasive adenocarcinoma(193;0.000293)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		CTGACAGTGCGGAGGGCAGGG	0.662								Other conserved DNA damage response genes					G|||	17	0.00339457	0.0	0.0014	5008	,	,		19866	0.0		0.0159	False		,,,				2504	0.0				p.R702Q		Atlas-SNP	.											.	ATRIP	41	.	0			c.G2105A						PASS	.	G	GLN/ARG,GLN/ARG	10,4396	16.8+/-37.8	0,10,2193	48.0	44.0	45.0		2024,2105	4.8	1.0	3	dbSNP_131	45	73,8527	44.0+/-102.2	2,69,4229	yes	missense,missense	ATRIP	NM_032166.2,NM_130384.1	43,43	2,79,6422	AA,AG,GG		0.8488,0.227,0.6382	possibly-damaging,possibly-damaging	675/765,702/792	48506279	83,12923	2203	4300	6503	SO:0001583	missense	84126	exon12			CAGTGCGGAGGGC	AF451323	CCDS2767.1, CCDS2768.1, CCDS59449.1, CCDS59450.1	3p24.3-p22.1	2007-06-20			ENSG00000164053	ENSG00000164053			33499	protein-coding gene	gene with protein product		606605				11721054	Standard	NM_130384		Approved	FLJ12343, MGC20625, MGC21482, MGC26740	uc003ctf.2	Q8WXE1	OTTHUMG00000133532	ENST00000320211.3:c.2105G>A	3.37:g.48506279G>A	ENSP00000323099:p.Arg702Gln	Somatic	219	0	0		WXS	Illumina HiSeq	Phase_I	183	77	0.420765	NM_130384	A8K6A3|A8K714|B2RCE7|B4DU92|B5MEB7|Q69YK9|Q8NHQ2|Q8WUG7|Q96CL3|Q9HA30	Missense_Mutation	SNP	ENST00000320211.3	37	CCDS2768.1	16	0.007326007326007326	1	0.0020325203252032522	1	0.0027624309392265192	1	0.0017482517482517483	13	0.017150395778364115	G	20.1	3.933445	0.73442	0.00227	0.008488	ENSG00000164053	ENST00000320211;ENST00000346691;ENST00000357105;ENST00000412052	T;T;T;T	0.51325	1.27;1.44;0.71;1.28	5.65	4.78	0.61160	.	0.186359	0.45361	N	0.000372	T	0.20901	0.0503	L	0.43152	1.355	0.43588	D	0.995935	P;P	0.51653	0.947;0.947	B;B	0.35182	0.197;0.197	T	0.17410	-1.0370	10	0.66056	D	0.02	-11.776	12.3445	0.55114	0.0818:0.0:0.9182:0.0	.	675;702	Q8WXE1-2;Q8WXE1	.;ATRIP_HUMAN	Q	702;675;575;609	ENSP00000323099:R702Q;ENSP00000302338:R675Q;ENSP00000349620:R575Q;ENSP00000400930:R609Q	ENSP00000323099:R702Q	R	+	2	0	ATRIP	48481283	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	3.326000	0.52037	1.400000	0.46741	0.561000	0.74099	CGG	G|0.993;A|0.007	0.007	strong		0.662	ATRIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257507.2	NM_130384	
PRDM9	56979	hgsc.bcm.edu	37	5	23527324	23527324	+	Silent	SNP	T	T	A	rs200723191	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:23527324T>A	ENST00000296682.3	+	11	2309	c.2127T>A	c.(2125-2127)acT>acA	p.T709T		NM_020227.2	NP_064612.2	Q9NQV7	PRDM9_HUMAN	PR domain containing 9	709					meiotic gene conversion (GO:0006311)|positive regulation of meiosis I (GO:0060903)|positive regulation of reciprocal meiotic recombination (GO:0010845)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)	histone methyltransferase activity (H3-K4 specific) (GO:0042800)|metal ion binding (GO:0046872)|recombination hotspot binding (GO:0010844)|sequence-specific DNA binding (GO:0043565)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(15)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(27)|lung(87)|ovary(6)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(11)	172						TCCTCCTCACTCACCAGAGGA	0.582										HNSCC(3;0.000094)			T|||	492	0.0982428	0.2398	0.0893	5008	,	,		20918	0.0387		0.0298	False		,,,				2504	0.045				p.T709T		Atlas-SNP	.											PRDM9,NS,carcinoma,+1,1	PRDM9	344	1	0			c.T2127A						PASS	.						16.0	15.0	15.0					5																	23527324		1813	3616	5429	SO:0001819	synonymous_variant	56979	exon11			CCTCACTCACCAG	AF275816	CCDS43307.1	5p14.2	2014-06-03			ENSG00000164256	ENSG00000164256		"""-"", ""Zinc fingers, C2H2-type"""	13994	protein-coding gene	gene with protein product	"""PR-domain containing protein 9"""	609760	"""minisatellite binding protein 3, 115kDa"", ""minisatellite binding protein 3 (115kD)"""	MSBP3		10668202, 2062643, 24634223	Standard	NM_020227		Approved	PFM6, ZNF899	uc003jgo.3	Q9NQV7	OTTHUMG00000161918	ENST00000296682.3:c.2127T>A	5.37:g.23527324T>A		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	142	17	0.119718	NM_020227	B4DX22|Q27Q50	Silent	SNP	ENST00000296682.3	37	CCDS43307.1																																																																																			T|0.988;A|0.012	0.012	strong		0.582	PRDM9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366375.1	NM_020227	
BOC	91653	hgsc.bcm.edu	37	3	112998265	112998265	+	Silent	SNP	A	A	G	rs2649878	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:112998265A>G	ENST00000495514.1	+	12	2687	c.1983A>G	c.(1981-1983)ccA>ccG	p.P661P	BOC_ENST00000355385.3_Silent_p.P661P|BOC_ENST00000273395.4_Silent_p.P662P			Q9BWV1	BOC_HUMAN	BOC cell adhesion associated, oncogene regulated	661	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|muscle cell differentiation (GO:0042692)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of myoblast differentiation (GO:0045663)|smoothened signaling pathway (GO:0007224)	axonal growth cone (GO:0044295)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)				NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(17)|lung(18)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	68			Epithelial(53;0.227)			CCATCCCCCCATCGCGGCTGT	0.627													A|||	2798	0.558706	0.8359	0.4741	5008	,	,		17802	0.6101		0.336	False		,,,				2504	0.4202				p.P661P		Atlas-SNP	.											.	BOC	139	.	0			c.A1983G						PASS	.	A		3419,987	727.6+/-409.9	1346,727,130	43.0	52.0	49.0		1983	0.3	1.0	3	dbSNP_100	49	2586,6014	419.8+/-353.2	382,1822,2096	no	coding-synonymous	BOC	NM_033254.2		1728,2549,2226	GG,GA,AA		30.0698,22.4013,46.171		661/1115	112998265	6005,7001	2203	4300	6503	SO:0001819	synonymous_variant	91653	exon12			CCCCCCATCGCGG	AY027658	CCDS2971.1	3q13.2	2013-02-11	2012-12-07		ENSG00000144857	ENSG00000144857		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	17173	protein-coding gene	gene with protein product	"""brother of CDO"", ""brother of CDON"", ""cell adhesion associated, oncogene regulated 2"""	608708	"""Boc homolog (mouse)"""			11782431	Standard	NM_033254		Approved	CDON2	uc003dzy.3	Q9BWV1	OTTHUMG00000159305	ENST00000495514.1:c.1983A>G	3.37:g.112998265A>G		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	57	57	1	NM_033254	A6NJ30|B2RMS8|D3DN70|Q6UXJ5|Q8N2P7|Q8NF26	Silent	SNP	ENST00000495514.1	37	CCDS2971.1																																																																																			A|0.504;G|0.496	0.496	strong		0.627	BOC-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000354485.3	NM_033254	
SV2C	22987	hgsc.bcm.edu	37	5	75591710	75591710	+	Missense_Mutation	SNP	C	C	G	rs2270927	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:75591710C>G	ENST00000502798.2	+	9	1887	c.1445C>G	c.(1444-1446)aCt>aGt	p.T482S	RP11-466P24.6_ENST00000502589.1_RNA|SV2C_ENST00000322285.7_Missense_Mutation_p.T482S	NM_014979.1	NP_055794.1	Q496J9	SV2C_HUMAN	synaptic vesicle glycoprotein 2C	482			T -> S (in dbSNP:rs2270927).		neurotransmitter transport (GO:0006836)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|synaptic vesicle (GO:0008021)	transmembrane transporter activity (GO:0022857)			NS(1)|breast(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(14)|ovary(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	37		all_lung(232;0.007)|Lung NSC(167;0.0148)|Ovarian(174;0.0798)|Prostate(461;0.184)		OV - Ovarian serous cystadenocarcinoma(47;1.16e-50)|all cancers(79;7.25e-40)		GCAAATTTCACTATTAACTTT	0.348													G|||	891	0.177915	0.289	0.1599	5008	,	,		20707	0.1657		0.1044	False		,,,				2504	0.1288				p.T482S		Atlas-SNP	.											.	SV2C	97	.	0			c.C1445G						PASS	.	G	SER/THR	949,2731		120,709,1011	112.0	108.0	110.0		1445	0.7	0.9	5	dbSNP_100	110	821,7339		35,751,3294	yes	missense	SV2C	NM_014979.1	58	155,1460,4305	GG,GC,CC		10.0613,25.788,14.9493	benign	482/728	75591710	1770,10070	1840	4080	5920	SO:0001583	missense	22987	exon9			ATTTCACTATTAA	AB028977	CCDS43331.1, CCDS75261.1	5q13	2008-02-05			ENSG00000122012	ENSG00000122012			30670	protein-coding gene	gene with protein product		610291				10470851, 9801366	Standard	XM_005248470		Approved		uc003kei.1	Q496J9	OTTHUMG00000162384	ENST00000502798.2:c.1445C>G	5.37:g.75591710C>G	ENSP00000423541:p.Thr482Ser	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	115	50	0.434783	NM_014979	Q496K1|Q9UPU8	Missense_Mutation	SNP	ENST00000502798.2	37	CCDS43331.1	386	0.17673992673992675	148	0.3008130081300813	54	0.14917127071823205	107	0.18706293706293706	77	0.10158311345646438	G	11.83	1.756265	0.31137	0.25788	0.100613	ENSG00000122012	ENST00000502798;ENST00000322285	T;T	0.79352	-0.89;-1.26	5.87	0.657	0.17850	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.292064	0.43416	N	0.000565	T	0.00012	0.0000	M	0.75777	2.31	0.58432	P	2.9999999999752447E-6	B	0.02656	0.0	B	0.04013	0.001	T	0.09443	-1.0674	9	0.29301	T	0.29	-9.794	8.7831	0.34802	0.1029:0.5641:0.2338:0.0992	rs2270927;rs17674646;rs52802028;rs2270927	482	Q496J9	SV2C_HUMAN	S	482	ENSP00000423541:T482S;ENSP00000316983:T482S	ENSP00000316983:T482S	T	+	2	0	SV2C	75627466	0.102000	0.21896	0.890000	0.34922	0.985000	0.73830	0.506000	0.22658	-0.032000	0.13758	-0.120000	0.15030	ACT	C|0.830;G|0.170	0.170	strong		0.348	SV2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368700.4		
C9orf89	84270	hgsc.bcm.edu	37	9	95872885	95872885	+	Silent	SNP	C	C	T	rs17593496	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:95872885C>T	ENST00000375464.2	+	3	314	c.186C>T	c.(184-186)ctC>ctT	p.L62L	C9orf89_ENST00000488630.1_3'UTR	NM_032310.3	NP_115686.3	Q96LW7	BINCA_HUMAN	chromosome 9 open reading frame 89	62	CARD.				negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	CARD domain binding (GO:0050700)			endometrium(1)|kidney(1)|lung(3)|ovary(1)|skin(1)	7						GTGTGCGGCTCTGTGACCTCC	0.667													C|||	298	0.0595048	0.0356	0.062	5008	,	,		18997	0.002		0.161	False		,,,				2504	0.045				p.L62L		Atlas-SNP	.											C9orf89,NS,adenoma,0,1	C9orf89	12	1	0			c.C186T						PASS	.	C		207,4199	127.4+/-164.3	4,199,2000	93.0	93.0	93.0		186	-0.8	1.0	9	dbSNP_123	93	1267,7333	253.6+/-279.2	82,1103,3115	no	coding-synonymous	C9orf89	NM_032310.3		86,1302,5115	TT,TC,CC		14.7326,4.6981,11.3332		62/184	95872885	1474,11532	2203	4300	6503	SO:0001819	synonymous_variant	84270	exon3			GCGGCTCTGTGAC	AK057716	CCDS6702.2	9q22.32	2012-03-16			ENSG00000165233	ENSG00000165233			28148	protein-coding gene	gene with protein product	"""Bcl10-interacting protein with CARD"""					12477932	Standard	XM_005252273		Approved	MGC11115, bA370F5.1, BinCARD	uc004atd.3	Q96LW7	OTTHUMG00000020243	ENST00000375464.2:c.186C>T	9.37:g.95872885C>T		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	97	50	0.515464	NM_032310	Q5BJH8|Q9BSY2	Silent	SNP	ENST00000375464.2	37	CCDS6702.2																																																																																			C|0.908;T|0.092	0.092	strong		0.667	C9orf89-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053128.1	NM_032310	
TANC1	85461	hgsc.bcm.edu	37	2	160086653	160086653	+	Silent	SNP	C	C	T	rs67270488|rs4664277|rs4664276	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:160086653C>T	ENST00000263635.6	+	27	4953	c.4716C>T	c.(4714-4716)gcC>gcT	p.A1572A	TANC1_ENST00000454300.1_Silent_p.A1466A	NM_001145909.1|NM_033394.2	NP_001139381.1|NP_203752.2	Q9C0D5	TANC1_HUMAN	tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 1	1572					dendritic spine maintenance (GO:0097062)|myoblast fusion (GO:0007520)|visual learning (GO:0008542)	axon terminus (GO:0043679)|cell junction (GO:0030054)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)|postsynaptic membrane (GO:0045211)				breast(3)|central_nervous_system(4)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(9)|lung(25)|ovary(7)|pancreas(1)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(2)	77						GAATCGCTGCCACTCCTGCTG	0.562													C|||	2459	0.491014	0.3949	0.6037	5008	,	,		20482	0.6161		0.3718	False		,,,				2504	0.5348				p.A1572A		Atlas-SNP	.											.	TANC1	157	.	0			c.C4716T						PASS	.	C	,	1418,2472		287,844,814	54.0	60.0	58.0		,4716	-11.5	0.0	2	dbSNP_111	58	2746,5536		523,1700,1918	no	utr-3,coding-synonymous	TANC1	NM_001145909.1,NM_033394.2	,	810,2544,2732	TT,TC,CC		33.1562,36.4524,34.2097	,	,1572/1862	160086653	4164,8008	1945	4141	6086	SO:0001819	synonymous_variant	85461	exon27			CGCTGCCACTCCT	AB051515	CCDS42766.1	2q24.2	2013-01-11			ENSG00000115183	ENSG00000115183		"""Ankyrin repeat domain containing"", ""Tetratricopeptide (TTC) repeat domain containing"""	29364	protein-coding gene	gene with protein product	"""rolling pebbles homolog B (Drosophila)"""	611397				15673434	Standard	NM_033394		Approved	KIAA1728, ROLSB	uc002uag.3	Q9C0D5	OTTHUMG00000153945	ENST00000263635.6:c.4716C>T	2.37:g.160086653C>T		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	102	41	0.401961	NM_033394	C9JD88|Q49AI8	Silent	SNP	ENST00000263635.6	37	CCDS42766.1																																																																																			.	.	alt		0.562	TANC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333135.1		
NPY5R	4889	hgsc.bcm.edu	37	4	164272703	164272703	+	Silent	SNP	G	G	A	rs11946004	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:164272703G>A	ENST00000515560.1	+	4	2800	c.1278G>A	c.(1276-1278)ggG>ggA	p.G426G	NPY5R_ENST00000506953.1_Silent_p.G426G|NPY5R_ENST00000338566.3_Silent_p.G426G			Q15761	NPY5R_HUMAN	neuropeptide Y receptor Y5	426					cardiac left ventricle morphogenesis (GO:0003214)|eating behavior (GO:0042755)|G-protein coupled receptor signaling pathway (GO:0007186)|generation of ovulation cycle rhythm (GO:0060112)|negative regulation of apoptotic process (GO:0043066)|negative regulation of glutamate secretion (GO:0014050)|negative regulation of synaptic transmission, GABAergic (GO:0032229)|neuropeptide signaling pathway (GO:0007218)|outflow tract morphogenesis (GO:0003151)|positive regulation of acute inflammatory response (GO:0002675)|positive regulation of smooth muscle cell proliferation (GO:0048661)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	neuropeptide Y receptor activity (GO:0004983)|pancreatic polypeptide receptor activity (GO:0001602)|peptide YY receptor activity (GO:0001601)			NS(2)|biliary_tract(1)|breast(1)|endometrium(3)|large_intestine(4)|lung(26)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	42	all_hematologic(180;0.166)	Prostate(90;0.109)				TTCTATATGGGTTTCTTAATA	0.338													A|||	414	0.0826677	0.0787	0.0706	5008	,	,		16007	0.0546		0.1083	False		,,,				2504	0.0992				p.G426G	Melanoma(139;1287 1774 9781 19750 25599)	Atlas-SNP	.											.	NPY5R	101	.	0			c.G1278A						PASS	.	A		342,4062	780.8+/-414.5	12,318,1872	87.0	89.0	88.0		1278	-9.9	0.1	4	dbSNP_120	88	991,7609	767.7+/-407.6	43,905,3352	no	coding-synonymous	NPY5R	NM_006174.2		55,1223,5224	AA,AG,GG		11.5233,7.7657,10.2507		426/446	164272703	1333,11671	2202	4300	6502	SO:0001819	synonymous_variant	4889	exon4			ATATGGGTTTCTT	BC042416	CCDS3804.1	4q31-q32	2012-08-08				ENSG00000164129		"""GPCR / Class A : Neuropeptide receptors : Y"""	7958	protein-coding gene	gene with protein product		602001				8700207, 9417917	Standard	NM_006174		Approved	NPYR5	uc003iqn.3	Q15761		ENST00000515560.1:c.1278G>A	4.37:g.164272703G>A		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	114	56	0.491228	NM_006174	Q6GTR7|Q92916	Silent	SNP	ENST00000515560.1	37	CCDS3804.1																																																																																			G|0.899;A|0.101	0.101	strong		0.338	NPY5R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364633.1	NM_006174	
SPECC1	92521	hgsc.bcm.edu	37	17	20013802	20013802	+	Silent	SNP	G	G	A	rs3764436	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:20013802G>A	ENST00000261503.5	+	3	261	c.210G>A	c.(208-210)gtG>gtA	p.V70V	SPECC1_ENST00000395529.3_Silent_p.V70V|SPECC1_ENST00000395527.4_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	277	0	0		WXS	Illumina HiSeq	Phase_I	194	93	0.479381	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	
PRKCA	5578	hgsc.bcm.edu	37	17	64685078	64685078	+	Silent	SNP	G	G	A	rs2227857	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:64685078G>A	ENST00000413366.3	+	8	857	c.831G>A	c.(829-831)ttG>ttA	p.L277L		NM_002737.2	NP_002728	P17252	KPCA_HUMAN	protein kinase C, alpha	277					activation of adenylate cyclase activity (GO:0007190)|activation of phospholipase C activity (GO:0007202)|angiogenesis (GO:0001525)|apoptotic signaling pathway (GO:0097190)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cellular calcium ion homeostasis (GO:0006874)|cellular response to carbohydrate stimulus (GO:0071322)|chondrocyte differentiation (GO:0002062)|desmosome assembly (GO:0002159)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|extracellular matrix organization (GO:0030198)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|histone H3-T6 phosphorylation (GO:0035408)|inactivation of MAPK activity (GO:0000188)|induction of positive chemotaxis (GO:0050930)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway (GO:0097193)|mRNA metabolic process (GO:0016071)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of cell proliferation (GO:0008285)|negative regulation of glial cell apoptotic process (GO:0034351)|negative regulation of glucose import (GO:0046325)|negative regulation of insulin receptor signaling pathway (GO:0046627)|neurotrophin TRK receptor signaling pathway (GO:0048011)|neutrophil chemotaxis (GO:0030593)|peptidyl-serine autophosphorylation (GO:0036289)|phototransduction, visible light (GO:0007603)|platelet activation (GO:0030168)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell migration (GO:0030335)|positive regulation of dense core granule biogenesis (GO:2000707)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of inflammatory response (GO:0050729)|positive regulation of lipopolysaccharide-mediated signaling pathway (GO:0031666)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of protein phosphorylation (GO:0001934)|protein phosphorylation (GO:0006468)|regulation of insulin secretion (GO:0050796)|regulation of muscle contraction (GO:0006937)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|regulation of platelet aggregation (GO:0090330)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|regulation of the force of heart contraction (GO:0002026)|response to interleukin-1 (GO:0070555)|rhodopsin mediated signaling pathway (GO:0016056)|RNA metabolic process (GO:0016070)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	apical part of cell (GO:0045177)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)|nucleoplasm (GO:0005654)|perinuclear region of cytoplasm (GO:0048471)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium-dependent protein kinase C activity (GO:0004698)|enzyme binding (GO:0019899)|histone kinase activity (H3-T6 specific) (GO:0035403)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(4)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(17)|ovary(1)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	38			BRCA - Breast invasive adenocarcinoma(6;4.68e-09)		Ingenol Mebutate(DB05013)|Phosphatidylserine(DB00144)|Tamoxifen(DB00675)|Vitamin E(DB00163)	GGTACAAGTTGCTTAACCAAG	0.478													G|||	1150	0.229633	0.0908	0.3473	5008	,	,		17492	0.1081		0.3658	False		,,,				2504	0.319				p.L277L		Atlas-SNP	.											.	PRKCA	82	.	0			c.G831A						PASS	.	G		599,3807	260.1+/-263.5	50,499,1654	89.0	70.0	76.0		831	4.5	1.0	17	dbSNP_98	76	3146,5454	475.0+/-369.0	559,2028,1713	no	coding-synonymous	PRKCA	NM_002737.2		609,2527,3367	AA,AG,GG		36.5814,13.5951,28.7944		277/673	64685078	3745,9261	2203	4300	6503	SO:0001819	synonymous_variant	5578	exon8			CAAGTTGCTTAAC		CCDS11664.1	17q22-q24	2009-07-10				ENSG00000154229	2.7.11.1		9393	protein-coding gene	gene with protein product		176960		PKCA			Standard	NM_002737		Approved		uc002jfp.1	P17252		ENST00000413366.3:c.831G>A	17.37:g.64685078G>A		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	48	48	1	NM_002737	B5BU22|Q15137|Q32M72|Q96RE4	Silent	SNP	ENST00000413366.3	37	CCDS11664.1																																																																																			G|0.741;A|0.259	0.259	strong		0.478	PRKCA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446976.1		
ZNF529	57711	hgsc.bcm.edu	37	19	37039069	37039069	+	Missense_Mutation	SNP	A	A	C	rs2912444	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:37039069A>C	ENST00000591340.1	-	5	549	c.391T>G	c.(391-393)Tta>Gta	p.L131V	ZNF529_ENST00000334116.7_Missense_Mutation_p.L26V	NM_020951.4	NP_066002.3	Q6P280	ZN529_HUMAN	zinc finger protein 529	131			L -> V (in dbSNP:rs2912444). {ECO:0000269|PubMed:10997877, ECO:0000269|PubMed:15489334}.		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)	1	Esophageal squamous(110;0.198)					GGTCCTTGTAAGTCAATCTTG	0.398													C|||	3263	0.651558	0.8185	0.5735	5008	,	,		18259	0.4226		0.6948	False		,,,				2504	0.6728				p.L131V		Atlas-SNP	.											.	ZNF529	82	.	0			c.T391G						PASS	.	C	VAL/LEU,VAL/LEU,VAL/LEU	3020,714		1214,592,61	101.0	87.0	91.0		391,337,391	-7.7	0.0	19	dbSNP_101	91	5588,2600		1946,1696,452	yes	missense,missense,missense	ZNF529	NM_020951.4,NM_001145650.1,NM_001145649.1	32,32,32	3160,2288,513	CC,CA,AA		31.7538,19.1216,27.7973	benign,benign,benign	131/564,113/546,131/564	37039069	8608,3314	1867	4094	5961	SO:0001583	missense	57711	exon6			CTTGTAAGTCAAT	AK025110	CCDS54256.1	19q13.13	2014-08-22			ENSG00000186020	ENSG00000186020		"""Zinc fingers, C2H2-type"", ""-"""	29328	protein-coding gene	gene with protein product						10997877	Standard	NM_020951		Approved	KIAA1615	uc002oeh.4	Q6P280	OTTHUMG00000180714	ENST00000591340.1:c.391T>G	19.37:g.37039069A>C	ENSP00000465578:p.Leu131Val	Somatic	165	1	0.00606061		WXS	Illumina HiSeq	Phase_I	156	156	1	NM_001145649	K7EKE1|Q9H731|Q9HCF7	Missense_Mutation	SNP	ENST00000591340.1	37	CCDS54256.1	1401	0.6414835164835165	419	0.8516260162601627	219	0.6049723756906077	238	0.4160839160839161	525	0.6926121372031663	C	2.411	-0.335375	0.05278	0.808784	0.682462	ENSG00000186020	ENST00000334116	.	.	.	3.83	-7.66	0.01277	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.25676	-1.0125	4	0.22706	T	0.39	.	2.0601	0.03590	0.3039:0.1235:0.1005:0.472	rs2912444;rs3760827;rs17846672;rs17859771;rs52829338;rs60460845;rs2912444	.	.	.	V	131	.	ENSP00000334695:L131V	L	-	1	2	ZNF529	41730909	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-1.182000	0.03082	-1.556000	0.01695	-1.296000	0.01341	TTA	A|0.340;C|0.660	0.660	strong		0.398	ZNF529-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452730.1	NM_020951	
PRICKLE4	29964	hgsc.bcm.edu	37	6	41753084	41753084	+	Silent	SNP	C	C	T	rs9394831	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:41753084C>T	ENST00000394260.1	+	3	268	c.268C>T	c.(268-270)Ctg>Ttg	p.L90L	PRICKLE4_ENST00000394259.1_Silent_p.L90L|TOMM6_ENST00000398884.3_5'Flank|PRICKLE4_ENST00000394263.1_Silent_p.L130L|TOMM6_ENST00000398881.3_5'Flank|PRICKLE4_ENST00000359201.5_Silent_p.L130L|PRICKLE4_ENST00000458694.1_Silent_p.L130L|PRICKLE4_ENST00000463606.1_3'UTR			Q2TBC4	PRIC4_HUMAN	prickle homolog 4 (Drosophila)	90	LIM zinc-binding 1. {ECO:0000255|PROSITE- ProRule:PRU00125}.					nucleus (GO:0005634)	zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)	13	Ovarian(28;0.0355)|Colorectal(47;0.121)		Epithelial(12;8.38e-05)|STAD - Stomach adenocarcinoma(11;0.000204)|Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)			GTGTAGGGAGCTGCTGAAGCC	0.612													C|||	815	0.16274	0.0159	0.1297	5008	,	,		18817	0.3016		0.2525	False		,,,				2504	0.1493				p.L130L		Atlas-SNP	.											.	PRICKLE4	29	.	0			c.C388T						PASS	.	C		242,4164	141.5+/-176.9	12,218,1973	44.0	42.0	43.0		388	2.7	0.8	6	dbSNP_119	43	2210,6390	375.2+/-337.7	315,1580,2405	no	coding-synonymous	PRICKLE4	NM_013397.5		327,1798,4378	TT,TC,CC		25.6977,5.4925,18.8528		130/385	41753084	2452,10554	2203	4300	6503	SO:0001819	synonymous_variant	29964	exon6			AGGGAGCTGCTGA	AF216754	CCDS34449.1	6p21.1	2010-08-05	2007-09-18	2007-09-18	ENSG00000124593	ENSG00000124593			16805	protein-coding gene	gene with protein product		611389	"""chromosome 6 open reading frame 49"""	C6orf49		15702247	Standard	NM_013397		Approved	OEBT, DKFZp761H221	uc011duf.1	Q2TBC4	OTTHUMG00000014685	ENST00000394260.1:c.268C>T	6.37:g.41753084C>T		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	69	34	0.492754	NM_013397	A2A3M0|A6PVU1|B3KQ15|Q5T3D4|Q9NSV1	Silent	SNP	ENST00000394260.1	37																																																																																				C|0.821;T|0.179	0.179	strong		0.612	PRICKLE4-007	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000303948.1	NM_013397	
SLC6A5	9152	hgsc.bcm.edu	37	11	20622975	20622975	+	Missense_Mutation	SNP	G	G	A	rs1443547	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:20622975G>A	ENST00000525748.1	+	2	577	c.304G>A	c.(304-306)Ggc>Agc	p.G102S		NM_004211.3	NP_004202.2	Q9Y345	SC6A5_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 5	102			G -> S (in dbSNP:rs1443547). {ECO:0000269|PubMed:10381548}.		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)	AGAGGCGCAAGGCGCGCAGGC	0.701													G|||	2032	0.405751	0.447	0.3804	5008	,	,		14053	0.3651		0.3847	False		,,,				2504	0.4315				p.G102S		Atlas-SNP	.											.	SLC6A5	151	.	0			c.G304A						PASS	.	G	SER/GLY	1916,2474		441,1034,720	16.0	19.0	18.0		304	-4.0	0.0	11	dbSNP_88	18	2871,5697		529,1813,1942	no	missense	SLC6A5	NM_004211.3	56	970,2847,2662	AA,AG,GG		33.5084,43.6446,36.9424	benign	102/798	20622975	4787,8171	2195	4284	6479	SO:0001583	missense	9152	exon2			GCGCAAGGCGCGC	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.304G>A	11.37:g.20622975G>A	ENSP00000434364:p.Gly102Ser	Somatic	23	0	0		WXS	Illumina HiSeq	Phase_I	12	12	1	NM_004211	O95288|Q4VAM7|Q9BX77	Missense_Mutation	SNP	ENST00000525748.1	37	CCDS7854.1	806	0.36904761904761907	202	0.4105691056910569	126	0.34806629834254144	201	0.3513986013986014	277	0.3654353562005277	G	1.537	-0.542827	0.04053	0.436446	0.335084	ENSG00000165970	ENST00000525748	T	0.70631	-0.5	5.37	-3.96	0.04106	.	1.669100	0.02954	N	0.142135	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	0.13176	-1.0519	9	0.07175	T	0.84	.	6.8887	0.24216	0.5281:0.227:0.2449:0.0	rs1443547;rs1443547	102	Q9Y345	SC6A5_HUMAN	S	102	ENSP00000434364:G102S	ENSP00000298923:G102S	G	+	1	0	SLC6A5	20579551	0.000000	0.05858	0.000000	0.03702	0.164000	0.22412	-0.675000	0.05227	-0.904000	0.03876	0.462000	0.41574	GGC	G|0.607;A|0.393	0.393	strong		0.701	SLC6A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387497.2	NM_004211	
RRP12	23223	hgsc.bcm.edu	37	10	99160152	99160152	+	Silent	SNP	A	A	G	rs1048442	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:99160152A>G	ENST00000370992.4	-	2	390	c.279T>C	c.(277-279)ggT>ggC	p.G93G	RP11-452K12.7_ENST00000422848.1_RNA|RRP12_ENST00000315563.6_Silent_p.G93G|RRP12_ENST00000414986.1_Silent_p.G93G	NM_015179.3	NP_055994.2	Q5JTH9	RRP12_HUMAN	ribosomal RNA processing 12 homolog (S. cerevisiae)	93						integral component of membrane (GO:0016021)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(5)|large_intestine(2)|lung(13)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	37		Colorectal(252;0.162)		Epithelial(162;2.72e-09)|all cancers(201;1.76e-07)		TCAGGAAGGTACCCGAGGACT	0.597													G|||	2006	0.400559	0.5378	0.3444	5008	,	,		18936	0.3125		0.336	False		,,,				2504	0.4121				p.G93G		Atlas-SNP	.											.	RRP12	97	.	0			c.T279C						PASS	.	G	,	2190,2216	589.6+/-387.2	554,1082,567	127.0	123.0	125.0		279,279	1.5	0.1	10	dbSNP_86	125	2722,5878	681.7+/-403.7	430,1862,2008	no	coding-synonymous,coding-synonymous	RRP12	NM_001145114.1,NM_015179.3	,	984,2944,2575	GG,GA,AA		31.6512,49.7049,37.7672	,	93/1237,93/1298	99160152	4912,8094	2203	4300	6503	SO:0001819	synonymous_variant	23223	exon2			GAAGGTACCCGAG		CCDS7457.1, CCDS44467.1, CCDS60605.1	10q24.2	2006-11-06	2006-11-06	2006-11-06	ENSG00000052749	ENSG00000052749			29100	protein-coding gene	gene with protein product			"""KIAA0690"""	KIAA0690		9734811	Standard	NM_015179		Approved		uc001knf.3	Q5JTH9	OTTHUMG00000018855	ENST00000370992.4:c.279T>C	10.37:g.99160152A>G		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	75	36	0.48	NM_001145114	B4DK00|E9PCK7|Q5JTH8|Q69YK4|Q96E87|Q9BUH3|Q9Y4C7	Silent	SNP	ENST00000370992.4	37	CCDS7457.1																																																																																			A|0.622;G|0.378	0.378	strong		0.597	RRP12-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049699.4	NM_015179	
ADAM21	8747	hgsc.bcm.edu	37	14	70924955	70924955	+	Missense_Mutation	SNP	A	A	C	rs114864695	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:70924955A>C	ENST00000603540.1	+	2	997	c.739A>C	c.(739-741)Aag>Cag	p.K247Q	RP11-486O13.4_ENST00000556646.1_lincRNA|ADAM21_ENST00000267499.3_Missense_Mutation_p.K247Q	NM_003813.3	NP_003804.2	Q9UKJ8	ADA21_HUMAN	ADAM metallopeptidase domain 21	247	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.			K -> Q (in Ref. 1; AAD55255 and 3; AAI09025/AAI09026). {ECO:0000305}.	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.K247Q(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)		TTCCATGTATAAGCAGTTAGG	0.358													A|||	1381	0.275759	0.3495	0.147	5008	,	,		18988	0.5218		0.1292	False		,,,				2504	0.1646				p.K247Q		Atlas-SNP	.											ADAM21_ENST00000267499,NS,carcinoma,0,1	ADAM21	181	1	1	Substitution - Missense(1)	stomach(1)	c.A739C						PASS	.						65.0	76.0	72.0					14																	70924955		2202	4300	6502	SO:0001583	missense	8747	exon2			ATGTATAAGCAGT	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.739A>C	14.37:g.70924955A>C	ENSP00000474385:p.Lys247Gln	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	51	20	0.392157	NM_003813	O43507|Q2VPC6|Q32MR0	Missense_Mutation	SNP	ENST00000603540.1	37	CCDS9804.1	542	0.24816849816849818	119	0.241869918699187	54	0.14917127071823205	272	0.4755244755244755	97	0.1279683377308707	A	0	-2.595304	0.00125	.	.	ENSG00000139985	ENST00000267499	T	0.64260	-0.09	3.86	-1.13	0.09775	Metallopeptidase, catalytic domain (1);Peptidase M12B, ADAM/reprolysin (2);	0.883079	0.09333	N	0.816565	T	0.00012	0.0000	N	0.12920	0.275	0.80722	P	0.0	B	0.12013	0.005	B	0.14023	0.01	T	0.44436	-0.9328	9	0.10636	T	0.68	.	8.183	0.31322	0.508:0.3282:0.1639:0.0	.	247	Q9UKJ8	ADA21_HUMAN	Q	247	ENSP00000267499:K247Q	ENSP00000267499:K247Q	K	+	1	0	ADAM21	69994708	0.000000	0.05858	0.354000	0.25760	0.155000	0.21991	-0.543000	0.06084	-0.012000	0.14223	-1.611000	0.00801	AAG	.	.	weak		0.358	ADAM21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413008.3		
OR51L1	119682	hgsc.bcm.edu	37	11	5020832	5020832	+	Missense_Mutation	SNP	C	C	T	rs10768450	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:5020832C>T	ENST00000321543.1	+	1	620	c.620C>T	c.(619-621)gCc>gTc	p.A207V		NM_001004755.1	NP_001004755.1	Q8NGJ5	O51L1_HUMAN	olfactory receptor, family 51, subfamily L, member 1	207			A -> V (in dbSNP:rs10768450).			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)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(3)|lung(19)|skin(2)|stomach(1)	31		Medulloblastoma(188;0.0061)|all_neural(188;0.0479)|Breast(177;0.086)		Epithelial(150;1.75e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0285)|LUSC - Lung squamous cell carcinoma(625;0.19)		GTAGTCATTGCCACACTAGGT	0.428													C|||	1155	0.230631	0.3011	0.1599	5008	,	,		25398	0.0694		0.3131	False		,,,				2504	0.2669				p.A207V		Atlas-SNP	.											.	OR51L1	60	.	0			c.C620T						PASS	.	C	VAL/ALA	1371,3031	455.5+/-351.0	199,973,1029	247.0	212.0	224.0		620	-4.7	0.0	11	dbSNP_120	224	2566,6030	418.5+/-352.8	383,1800,2115	yes	missense	OR51L1	NM_001004755.1	64	582,2773,3144	TT,TC,CC		29.8511,31.1449,30.2893	benign	207/316	5020832	3937,9061	2201	4298	6499	SO:0001583	missense	119682	exon1			TCATTGCCACACT	AB065799	CCDS31369.1	11p15.4	2012-08-09			ENSG00000176798	ENSG00000176798		"""GPCR / Class A : Olfactory receptors"""	14759	protein-coding gene	gene with protein product							Standard	NM_001004755		Approved		uc010qyu.2	Q8NGJ5	OTTHUMG00000066605	ENST00000321543.1:c.620C>T	11.37:g.5020832C>T	ENSP00000322156:p.Ala207Val	Somatic	385	0	0		WXS	Illumina HiSeq	Phase_I	386	383	0.992228	NM_001004755	Q6IFE5	Missense_Mutation	SNP	ENST00000321543.1	37	CCDS31369.1	491	0.22481684981684982	143	0.29065040650406504	66	0.18232044198895028	41	0.07167832167832168	241	0.3179419525065963	C	0.005	-2.140741	0.00332	0.311449	0.298511	ENSG00000176798	ENST00000321543	T	0.34859	1.34	5.18	-4.71	0.03279	GPCR, rhodopsin-like superfamily (1);	1.479880	0.04460	N	0.374160	T	0.00012	0.0000	L	0.35341	1.055	0.80722	P	0.0	B	0.09022	0.002	B	0.06405	0.002	T	0.42899	-0.9424	9	0.02654	T	1	.	13.7055	0.62636	0.0:0.3172:0.0:0.6828	rs10768450;rs57593930;rs10768450	207	Q8NGJ5	O51L1_HUMAN	V	207	ENSP00000322156:A207V	ENSP00000322156:A207V	A	+	2	0	OR51L1	4977408	0.000000	0.05858	0.012000	0.15200	0.379000	0.30106	-3.800000	0.00363	-0.798000	0.04444	-0.259000	0.10710	GCC	C|0.721;T|0.279	0.279	strong		0.428	OR51L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142812.1	NM_001004755	
ZNF253	56242	hgsc.bcm.edu	37	19	20003109	20003109	+	Silent	SNP	A	A	G	rs8106559	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:20003109A>G	ENST00000589717.1	+	4	1145	c.1053A>G	c.(1051-1053)ctA>ctG	p.L351L	AC011477.1_ENST00000578823.1_RNA|ZNF253_ENST00000355650.4_Silent_p.L275L|CTC-559E9.8_ENST00000585571.1_RNA	NM_021047.2	NP_066385.2	O75346	ZN253_HUMAN	zinc finger protein 253	351				Missing (in Ref. 1; AAC26844). {ECO:0000305}.	negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(6)|lung(11)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						CCTTTCACCTATCCTCACACC	0.388													a|||	2422	0.483626	0.6762	0.379	5008	,	,		22620	0.6815		0.2376	False		,,,				2504	0.3466				p.L351L		Atlas-SNP	.											.	ZNF253	99	.	0			c.A1053G						PASS	.	A		2644,1696		840,964,366	46.0	50.0	49.0		1053	-1.8	0.0	19	dbSNP_116	49	2088,6472		252,1584,2444	no	coding-synonymous	ZNF253	NM_021047.2		1092,2548,2810	GG,GA,AA		24.3925,39.0783,36.6822		351/500	20003109	4732,8168	2170	4280	6450	SO:0001819	synonymous_variant	56242	exon4			TCACCTATCCTCA	AF038951	CCDS42532.1	19p12	2014-02-12	2003-12-17		ENSG00000256771	ENSG00000256771		"""Zinc fingers, C2H2-type"", ""-"""	13497	protein-coding gene	gene with protein product		606954	"""zinc finger protein 411"""	ZNF411		10585455	Standard	NM_021047		Approved	BMZF-1, FLJ90391	uc002noj.3	O75346	OTTHUMG00000182369	ENST00000589717.1:c.1053A>G	19.37:g.20003109A>G		Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	24	24	1	NM_021047	A4FVA7|Q0P6G3|Q6P0L2|Q8NCA3|Q8NCF9	Silent	SNP	ENST00000589717.1	37	CCDS42532.1																																																																																			A|0.602;G|0.398	0.398	strong		0.388	ZNF253-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460802.1	NM_021047	
PTPRN2	5799	hgsc.bcm.edu	37	7	157985149	157985149	+	Missense_Mutation	SNP	C	C	G	rs3800855	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:157985149C>G	ENST00000389418.4	-	5	428	c.419G>C	c.(418-420)aGt>aCt	p.S140T	PTPRN2_ENST00000409483.1_Missense_Mutation_p.S102T|PTPRN2_ENST00000389416.4_Missense_Mutation_p.S123T|PTPRN2_ENST00000389413.3_Missense_Mutation_p.S140T|PTPRN2_ENST00000404321.2_Missense_Mutation_p.S163T	NM_002847.3	NP_002838.2	Q92932	PTPR2_HUMAN	protein tyrosine phosphatase, receptor type, N polypeptide 2	140			S -> T (in dbSNP:rs3800855). {ECO:0000269|Ref.4}.		negative regulation of GTPase activity (GO:0034260)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	endoplasmic reticulum lumen (GO:0005788)|integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)|secretory granule (GO:0030141)|terminal bouton (GO:0043195)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|liver(1)|lung(42)|ovary(4)|pleura(1)|prostate(2)|skin(10)|upper_aerodigestive_tract(1)	86	all_neural(206;0.181)	all_cancers(7;8.99e-13)|all_epithelial(9;2.4e-06)|all_hematologic(28;0.0155)|Breast(660;0.132)	OV - Ovarian serous cystadenocarcinoma(82;0.00463)	STAD - Stomach adenocarcinoma(7;0.0875)		GCCCTCCCGACTGTACCTCCT	0.632													C|||	1224	0.244409	0.3752	0.1945	5008	,	,		15910	0.1944		0.169	False		,,,				2504	0.2321				p.S140T		Atlas-SNP	.											.	PTPRN2	243	.	0			c.G419C						PASS	.		THR/SER,THR/SER,THR/SER	1508,2898	454.9+/-350.8	273,962,968	51.0	60.0	57.0		419,368,419	1.4	0.0	7	dbSNP_107	57	1280,7320	243.1+/-272.8	91,1098,3111	yes	missense,missense,missense	PTPRN2	NM_002847.3,NM_130842.2,NM_130843.2	58,58,58	364,2060,4079	GG,GC,CC		14.8837,34.2261,21.4363	possibly-damaging,possibly-damaging,possibly-damaging	140/1016,123/999,140/987	157985149	2788,10218	2203	4300	6503	SO:0001583	missense	5799	exon5			TCCCGACTGTACC	AB002385	CCDS5947.1, CCDS5948.1, CCDS5949.1	7q36	2011-06-09			ENSG00000155093	ENSG00000155093		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"""	9677	protein-coding gene	gene with protein product	"""IAR PTPRP"""	601698				8954911, 9220540	Standard	NM_130842		Approved	KIAA0387, phogrin, ICAAR, IA-2beta	uc003wno.3	Q92932	OTTHUMG00000152646	ENST00000389418.4:c.419G>C	7.37:g.157985149C>G	ENSP00000374069:p.Ser140Thr	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	70	41	0.585714	NM_130843	E9PC57|Q8N4I5|Q92662|Q9Y4F8|Q9Y4I6	Missense_Mutation	SNP	ENST00000389418.4	37	CCDS5947.1	509	0.23305860805860806	188	0.3821138211382114	66	0.18232044198895028	128	0.22377622377622378	127	0.16754617414248021	C	5.064	0.197429	0.09652	0.342261	0.148837	ENSG00000155093	ENST00000409483;ENST00000389413;ENST00000389416;ENST00000389418;ENST00000404321	T;T;T;T;T	0.03524	3.94;3.9;3.95;3.97;3.96	4.17	1.36	0.22044	.	.	.	.	.	T	0.00012	0.0000	L	0.29908	0.895	0.80722	P	0.0	B;B;B;B;B	0.06786	0.001;0.001;0.001;0.001;0.001	B;B;B;B;B	0.09377	0.004;0.001;0.004;0.002;0.002	T	0.42816	-0.9429	8	0.12430	T	0.62	.	3.8043	0.08771	0.0:0.5724:0.2059:0.2217	rs3800855;rs10346808;rs17847434;rs3800855	163;102;140;123;140	Q92932-3;E7EM83;Q92932-2;E9PC57;Q92932	.;.;.;.;PTPR2_HUMAN	T	102;140;123;140;163	ENSP00000387114:S102T;ENSP00000374064:S140T;ENSP00000374067:S123T;ENSP00000374069:S140T;ENSP00000385464:S163T	ENSP00000374064:S140T	S	-	2	0	PTPRN2	157677910	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	-0.673000	0.05239	0.488000	0.27723	-0.189000	0.12847	AGT	C|0.780;G|0.220	0.220	strong		0.632	PTPRN2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000353214.1		
FRG2B	441581	hgsc.bcm.edu	37	10	135440123	135440123	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:135440123C>T	ENST00000425520.1	-	1	176	c.124G>A	c.(124-126)Gaa>Aaa	p.E42K	FRG2B_ENST00000443774.1_Missense_Mutation_p.E42K	NM_001080998.1	NP_001074467.1	Q96QU4	FRG2B_HUMAN	FSHD region gene 2 family, member B	42						nucleus (GO:0005634)				endometrium(2)|kidney(2)|lung(14)|ovary(1)|prostate(1)	20		all_cancers(35;7.01e-07)|all_epithelial(44;1.45e-05)|Lung NSC(174;0.027)|all_lung(145;0.0384)|all_neural(114;0.0726)|Glioma(114;0.172)|Melanoma(40;0.175)		OV - Ovarian serous cystadenocarcinoma(35;1.12e-06)|all cancers(32;1.43e-06)|Epithelial(32;1.71e-06)		TTGCCTTTTTCTTTGAATGGT	0.512																																					p.E42K		Atlas-SNP	.											FRG2B,NS,carcinoma,0,1	FRG2B	47	1	0			c.G124A						scavenged	.						6.0	7.0	6.0					10																	135440123		1818	3856	5674	SO:0001583	missense	441581	exon1			CTTTTTCTTTGAA	AY744466	CCDS44502.1	10q26.3	2012-10-02			ENSG00000225899	ENSG00000225899			33518	protein-coding gene	gene with protein product						15520407	Standard	NM_001080998		Approved		uc010qvg.2	Q96QU4	OTTHUMG00000019328	ENST00000425520.1:c.124G>A	10.37:g.135440123C>T	ENSP00000401310:p.Glu42Lys	Somatic	289	1	0.00346021		WXS	Illumina HiSeq	Phase_I	265	6	0.0226415	NM_001080998	Q5VSQ1	Missense_Mutation	SNP	ENST00000425520.1	37	CCDS44502.1	.	.	.	.	.	.	.	.	.	.	.	4.857	0.159324	0.09236	.	.	ENSG00000225899	ENST00000443774;ENST00000425520	T;T	0.37235	1.21;1.21	0.109	0.109	0.14578	.	.	.	.	.	T	0.19366	0.0465	N	0.14661	0.345	0.09310	N	1	B	0.13145	0.007	B	0.15870	0.014	T	0.20739	-1.0266	8	0.51188	T	0.08	-0.0822	.	.	.	.	42	Q96QU4	FRG2B_HUMAN	K	42	ENSP00000408343:E42K;ENSP00000401310:E42K	ENSP00000401310:E42K	E	-	1	0	FRG2B	135290113	0.953000	0.32496	0.013000	0.15412	0.013000	0.08279	-0.459000	0.06728	0.181000	0.19994	0.184000	0.17185	GAA	.	.	none		0.512	FRG2B-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000467780.1	NM_001080998	
ZC3H7B	23264	hgsc.bcm.edu	37	22	41726053	41726053	+	Silent	SNP	G	G	A	rs4822021	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:41726053G>A	ENST00000352645.4	+	6	728	c.471G>A	c.(469-471)caG>caA	p.Q157Q	ZC3H7B_ENST00000351589.4_Silent_p.Q157Q	NM_017590.4	NP_060060.3	Q9UGR2	Z3H7B_HUMAN	zinc finger CCCH-type containing 7B	157					viral process (GO:0016032)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(11)|ovary(3)|prostate(3)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(3)	38						AGCTTGGTCAGGAGCTGGCCC	0.627													G|||	1298	0.259185	0.1657	0.5447	5008	,	,		17078	0.0754		0.2624	False		,,,				2504	0.3691				p.Q157Q		Atlas-SNP	.											.	ZC3H7B	82	.	0			c.G471A						PASS	.	G		853,3553	335.5+/-303.9	78,697,1428	73.0	71.0	71.0		471	4.0	1.0	22	dbSNP_111	71	2203,6397	375.5+/-337.8	302,1599,2399	no	coding-synonymous	ZC3H7B	NM_017590.4		380,2296,3827	AA,AG,GG		25.6163,19.36,23.4968		157/978	41726053	3056,9950	2203	4300	6503	SO:0001819	synonymous_variant	23264	exon6			TGGTCAGGAGCTG		CCDS14013.1	22q13.2	2013-01-10		2005-08-09	ENSG00000100403	ENSG00000100403		"""Zinc fingers, CCCH-type domain containing"", ""Tetratricopeptide (TTC) repeat domain containing"""	30869	protein-coding gene	gene with protein product						10470851, 11230166	Standard	NM_017590		Approved	RoXaN, FLJ13787, DKFZp434K0920, KIAA1031	uc003azw.4	Q9UGR2	OTTHUMG00000150969	ENST00000352645.4:c.471G>A	22.37:g.41726053G>A		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	51	28	0.54902	NM_017590	A7YY88|B2RCA4|Q5TFX9|Q8TBT9|Q9H8B6|Q9UGQ9|Q9UGR0|Q9UGR1|Q9UK03|Q9UPW9	Silent	SNP	ENST00000352645.4	37	CCDS14013.1																																																																																			G|0.760;A|0.240	0.240	strong		0.627	ZC3H7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320696.1	NM_017590	
CDH17	1015	hgsc.bcm.edu	37	8	95143138	95143138	+	Silent	SNP	A	A	G	rs2513797	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:95143138A>G	ENST00000027335.3	-	16	2374	c.2250T>C	c.(2248-2250)ggT>ggC	p.G750G	CDH17_ENST00000441892.2_Silent_p.G536G|CDH17_ENST00000450165.2_Silent_p.G750G	NM_004063.3	NP_004054.3	Q12864	CAD17_HUMAN	cadherin 17, LI cadherin (liver-intestine)	750	Cadherin 7. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|oligopeptide transmembrane transport (GO:0035672)|oligopeptide transport (GO:0006857)|transport (GO:0006810)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|proton-dependent oligopeptide secondary active transmembrane transporter activity (GO:0005427)|transporter activity (GO:0005215)			NS(1)|endometrium(5)|kidney(3)|large_intestine(10)|lung(18)|ovary(6)|prostate(3)|skin(4)|stomach(2)	52	Breast(36;4.65e-06)		BRCA - Breast invasive adenocarcinoma(8;0.00691)			AGGGTGGCCGACCCCCATCAT	0.502													A|||	419	0.0836661	0.1339	0.1009	5008	,	,		18290	0.0		0.1153	False		,,,				2504	0.0573				p.G750G		Atlas-SNP	.											.	CDH17	119	.	0			c.T2250C						PASS	.	A	,	492,3914	230.1+/-244.4	32,428,1743	128.0	121.0	123.0		2250,2250	-11.7	0.0	8	dbSNP_100	123	1049,7551	222.4+/-259.5	71,907,3322	no	coding-synonymous,coding-synonymous	CDH17	NM_001144663.1,NM_004063.3	,	103,1335,5065	GG,GA,AA		12.1977,11.1666,11.8484	,	750/833,750/833	95143138	1541,11465	2203	4300	6503	SO:0001819	synonymous_variant	1015	exon16			TGGCCGACCCCCA	X83228	CCDS6260.1	8q22.1	2010-01-26			ENSG00000079112	ENSG00000079112		"""Cadherins / Major cadherins"""	1756	protein-coding gene	gene with protein product		603017				9615235, 10191097	Standard	NM_004063		Approved	HPT-1, cadherin	uc003ygh.2	Q12864	OTTHUMG00000164391	ENST00000027335.3:c.2250T>C	8.37:g.95143138A>G		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	48	13	0.270833	NM_004063	Q15336|Q2M2E0	Silent	SNP	ENST00000027335.3	37	CCDS6260.1																																																																																			A|0.892;G|0.108	0.108	strong		0.502	CDH17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378560.1	NM_004063	
KRTAP10-9	386676	hgsc.bcm.edu	37	21	46047710	46047710	+	Silent	SNP	T	T	C	rs8131142	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:46047710T>C	ENST00000397911.3	+	1	671	c.622T>C	c.(622-624)Ttg>Ctg	p.L208L	TSPEAR_ENST00000323084.4_Intron|KRTAP10-9_ENST00000484861.1_Intron	NM_198690.2	NP_941963.2	P60411	KR109_HUMAN	keratin associated protein 10-9	208	25 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				endometrium(1)|kidney(1)|large_intestine(1)|lung(6)	9						GGCTTCCTCTTTGTGCTGCCA	0.632													C|||	3246	0.648163	0.5711	0.6787	5008	,	,		20040	0.6637		0.7107	False		,,,				2504	0.6503				p.L208L		Atlas-SNP	.											.	KRTAP10-9	24	.	0			c.T622C						PASS	.	C	,	2517,1889	542.5+/-376.0	725,1067,411	192.0	214.0	206.0		,622	-1.4	0.0	21	dbSNP_116	206	5789,2811	442.8+/-360.2	1943,1903,454	no	intron,coding-synonymous	TSPEAR,KRTAP10-9	NM_144991.2,NM_198690.2	,	2668,2970,865	CC,CT,TT		32.686,42.8734,36.1372	,	,208/293	46047710	8306,4700	2203	4300	6503	SO:0001819	synonymous_variant	386676	exon1			TCCTCTTTGTGCT	AJ566386	CCDS42961.1	21q22.3	2007-10-05			ENSG00000221837	ENSG00000221837		"""Keratin associated proteins"""	22971	protein-coding gene	gene with protein product				KRTAP18-9			Standard	NM_198690		Approved	KAP10.9, KAP18.9	uc002zfp.4	P60411	OTTHUMG00000057637	ENST00000397911.3:c.622T>C	21.37:g.46047710T>C		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	123	119	0.96748	NM_198690	A2RRG1|A6NIR9|Q70LJ1	Silent	SNP	ENST00000397911.3	37	CCDS42961.1																																																																																			T|0.339;C|0.661	0.661	strong		0.632	KRTAP10-9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128040.1		
NOP58	51602	hgsc.bcm.edu	37	2	203155936	203155936	+	Silent	SNP	A	A	C	rs3731700	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	125	0	0		WXS	Illumina HiSeq	Phase_I	127	52	0.409449	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	
GPR116	221395	hgsc.bcm.edu	37	6	46826979	46826979	+	Silent	SNP	A	A	G	rs9381487	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:46826979A>G	ENST00000283296.7	-	17	2949	c.2661T>C	c.(2659-2661)taT>taC	p.Y887Y	GPR116_ENST00000362015.4_Silent_p.Y887Y|GPR116_ENST00000456426.2_Silent_p.Y745Y|GPR116_ENST00000265417.7_Silent_p.Y887Y|GPR116_ENST00000545669.1_Silent_p.Y316Y	NM_001098518.1	NP_001091988.1	Q8IZF2	GP116_HUMAN	G protein-coupled receptor 116	887					energy reserve metabolic process (GO:0006112)|fat cell differentiation (GO:0045444)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|neuropeptide signaling pathway (GO:0007218)|regulation of lipid metabolic process (GO:0019216)|surfactant homeostasis (GO:0043129)	cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(2)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|lung(21)|ovary(1)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	59			Lung(136;0.192)			AGTTTTCTAGATAGCTCTTGT	0.463													A|||	1609	0.321286	0.3714	0.2839	5008	,	,		20789	0.3621		0.1998	False		,,,				2504	0.363				p.Y887Y	NSCLC(59;410 1274 8751 36715 50546)	Atlas-SNP	.											.	GPR116	133	.	0			c.T2661C						PASS	.	A	,	1464,2942	472.6+/-356.4	224,1016,963	79.0	79.0	79.0		2661,2661	1.3	0.0	6	dbSNP_119	79	1784,6816	320.1+/-314.5	186,1412,2702	no	coding-synonymous,coding-synonymous	GPR116	NM_001098518.1,NM_015234.4	,	410,2428,3665	GG,GA,AA		20.7442,33.2274,24.9731	,	887/1347,887/1347	46826979	3248,9758	2203	4300	6503	SO:0001819	synonymous_variant	221395	exon17			TTCTAGATAGCTC	AB018301	CCDS4919.1	6p12.3	2014-08-08			ENSG00000069122	ENSG00000069122		"""-"", ""GPCR / Class B : Orphans"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	19030	protein-coding gene	gene with protein product						12435584	Standard	NM_001098518		Approved	DKFZp564O1923, KIAA0758	uc003oyo.3	Q8IZF2	OTTHUMG00000014793	ENST00000283296.7:c.2661T>C	6.37:g.46826979A>G		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	137	79	0.576642	NM_015234	O94858|Q5TF06|Q6RGN2|Q86SP0|Q9Y3Z2	Silent	SNP	ENST00000283296.7	37	CCDS4919.1																																																																																			A|0.733;G|0.267	0.267	strong		0.463	GPR116-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040806.2	NM_015234	
OR51F1	256892	hgsc.bcm.edu	37	11	4790671	4790671	+	Silent	SNP	C	C	T	rs11033795	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:4790671C>T	ENST00000380383.1	-	1	497	c.498G>A	c.(496-498)ttG>ttA	p.L166L	OR51F1_ENST00000343430.3_Silent_p.L159L|MMP26_ENST00000477339.1_Intron|MMP26_ENST00000380390.1_Intron			A6NGY5	O51F1_HUMAN	olfactory receptor, family 51, subfamily F, member 1	166						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)		AAAGTAGTGGCAATATTAGTA	0.403													T|||	1080	0.215655	0.4569	0.2017	5008	,	,		22619	0.0		0.2704	False		,,,				2504	0.0654				p.L159L		Atlas-SNP	.											.	OR51F1	60	.	0			c.G477A						PASS	.	T		1968,2434	618.7+/-393.2	445,1078,678	115.0	115.0	115.0		477	-8.8	0.0	11	dbSNP_120	115	2179,6417	712.2+/-405.9	291,1597,2410	no	coding-synonymous	OR51F1	NM_001004752.1		736,2675,3088	TT,TC,CC		25.349,44.707,31.9049		159/313	4790671	4147,8851	2201	4298	6499	SO:0001819	synonymous_variant	256892	exon1			TAGTGGCAATATT	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.498G>A	11.37:g.4790671C>T		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	140	35	0.25	NM_001004752		Silent	SNP	ENST00000380383.1	37																																																																																				C|0.706;T|0.294	0.294	strong		0.403	OR51F1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001004752	
SGK1	6446	hgsc.bcm.edu	37	6	134495725	134495725	+	Splice_Site	SNP	C	C	T	rs186450029		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:134495725C>T	ENST00000237305.7	-	2	165		c.e2-1		SGK1_ENST00000475719.2_Splice_Site|SGK1_ENST00000489458.2_5'Flank|SGK1_ENST00000528577.1_Splice_Site|SGK1_ENST00000367858.5_Splice_Site|SGK1_ENST00000367857.5_Missense_Mutation_p.A16T|SGK1_ENST00000413996.3_Splice_Site	NM_005627.3	NP_005618.2	O00141	SGK1_HUMAN	serum/glucocorticoid regulated kinase 1						apoptotic process (GO:0006915)|cellular response to DNA damage stimulus (GO:0006974)|ion transmembrane transport (GO:0034220)|long-term memory (GO:0007616)|positive regulation of transporter activity (GO:0032411)|protein phosphorylation (GO:0006468)|regulation of apoptotic process (GO:0042981)|regulation of blood pressure (GO:0008217)|regulation of catalytic activity (GO:0050790)|regulation of cell growth (GO:0001558)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of gastric acid secretion (GO:0060453)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|renal sodium ion absorption (GO:0070294)|response to stress (GO:0006950)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium channel regulator activity (GO:0005246)|chloride channel regulator activity (GO:0017081)|potassium channel regulator activity (GO:0015459)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|sodium channel regulator activity (GO:0017080)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(21)|kidney(3)|large_intestine(3)|lung(10)|ovary(1)|skin(4)|stomach(1)	46	Colorectal(23;0.221)			OV - Ovarian serous cystadenocarcinoma(155;0.00317)|GBM - Glioblastoma multiforme(68;0.00847)		TTCATGAAAGCTGTGGATGAA	0.433											OREG0017675	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									.		Atlas-SNP	.											SGK1_ENST00000528577,NS,lymphoid_neoplasm,0,4	SGK1	387	4	0			c.77-1G>A						PASS	.						73.0	73.0	73.0					6																	134495725		2203	4300	6503	SO:0001630	splice_region_variant	6446	exon3			TGAAAGCTGTGGA	AJ000512	CCDS5170.1, CCDS47476.1, CCDS47477.1, CCDS47478.1	6q23	2008-02-05	2007-12-05	2007-12-05	ENSG00000118515	ENSG00000118515			10810	protein-coding gene	gene with protein product		602958	"""serum/glucocorticoid regulated kinase"""	SGK		9114008, 9722955	Standard	NM_005627		Approved		uc003qeo.4	O00141	OTTHUMG00000015613	ENST00000237305.7:c.77-1G>A	6.37:g.134495725C>T		Somatic	84	0	0	1611	WXS	Illumina HiSeq	Phase_I	36	11	0.305556	NM_005627	B7UUP7|B7UUP8|B7UUP9|B7Z5B2|E1P583|Q5TCN2|Q5TCN3|Q5TCN4|Q5VY65|Q9UN56	Splice_Site	SNP	ENST00000237305.7	37	CCDS5170.1	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	C|C	29.2|29.2	4.985656|4.985656	0.93044|0.93044	.|.	.|.	ENSG00000118515|ENSG00000118515	ENST00000367858;ENST00000413996;ENST00000237305;ENST00000528577;ENST00000475719;ENST00000461976|ENST00000367857	.|T	.|0.30182	.|1.54	5.89|5.89	5.89|5.89	0.94794|0.94794	.|.	.|.	.|.	.|.	.|.	.|T	.|0.14399	.|0.0348	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|B	.|0.27971	.|0.196	.|B	.|0.25759	.|0.063	.|T	.|0.05419	.|-1.0886	.|7	.|.	.|.	.|.	.|.	20.2576|20.2576	0.98430|0.98430	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|16	.|O00141-4	.|.	.|T	-1|16	.|ENSP00000356831:A16T	.|.	.|A	-|-	.|1	.|0	SGK1|SGK1	134537418|134537418	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.926000|0.926000	0.56050|0.56050	7.818000|7.818000	0.86416|0.86416	2.783000|2.783000	0.95769|0.95769	0.655000|0.655000	0.94253|0.94253	.|GCT	C|1.000;T|0.000	0.000	strong		0.433	SGK1-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042312.2		Intron
OR5W2	390148	hgsc.bcm.edu	37	11	55681130	55681130	+	Missense_Mutation	SNP	A	A	T	rs34573569	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:55681130A>T	ENST00000344514.1	-	1	928	c.929T>A	c.(928-930)tTt>tAt	p.F310Y		NM_001001960.1	NP_001001960.1	Q8NH69	OR5W2_HUMAN	olfactory receptor, family 5, subfamily W, member 2	310			F -> Y (in dbSNP:rs34573569).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(28)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49						ATTTCCttaaaataaaatttt	0.299													A|||	454	0.090655	0.1278	0.0403	5008	,	,		13909	0.0903		0.0944	False		,,,				2504	0.0726				p.F310Y	Melanoma(48;171 1190 15239 43886 49348)	Atlas-SNP	.											.	OR5W2	112	.	0			c.T929A						PASS	.	A	TYR/PHE	402,3740		23,356,1692	12.0	13.0	13.0		929	-0.4	0.0	11	dbSNP_126	13	624,7858		22,580,3639	yes	missense	OR5W2	NM_001001960.1	22	45,936,5331	TT,TA,AA		7.3568,9.7055,8.1274	probably-damaging	310/311	55681130	1026,11598	2071	4241	6312	SO:0001583	missense	390148	exon1			CCTTAAAATAAAA	BK004398	CCDS31513.1	11q11	2012-08-09		2004-03-10	ENSG00000187612	ENSG00000187612		"""GPCR / Class A : Olfactory receptors"""	15299	protein-coding gene	gene with protein product				OR5W2P, OR5W3P			Standard	NM_001001960		Approved		uc010rir.2	Q8NH69	OTTHUMG00000166818	ENST00000344514.1:c.929T>A	11.37:g.55681130A>T	ENSP00000342448:p.Phe310Tyr	Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	27	14	0.518519	NM_001001960		Missense_Mutation	SNP	ENST00000344514.1	37	CCDS31513.1	205	0.09386446886446886	74	0.15040650406504066	18	0.049723756906077346	46	0.08041958041958042	67	0.08839050131926121	.	13.26	2.183817	0.38609	0.097055	0.073568	ENSG00000187612	ENST00000344514	T	0.02280	4.36	4.0	-0.387	0.12463	.	0.579014	0.13070	N	0.416199	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B	0.20164	0.042	B	0.21917	0.037	T	0.45716	-0.9242	9	0.59425	D	0.04	.	4.1446	0.10210	0.6166:0.0:0.2232:0.1602	rs34573569	310	Q8NH69	OR5W2_HUMAN	Y	310	ENSP00000342448:F310Y	ENSP00000342448:F310Y	F	-	2	0	OR5W2	55437706	.	.	0.027000	0.17364	0.423000	0.31445	.	.	0.003000	0.14656	0.448000	0.29417	TTT	A|0.877;T|0.123	0.123	strong		0.299	OR5W2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391523.1	NM_001001960	
TPBG	7162	hgsc.bcm.edu	37	6	83075914	83075914	+	Silent	SNP	G	G	A	rs700494	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:83075914G>A	ENST00000369750.3	+	2	1853	c.1236G>A	c.(1234-1236)acG>acA	p.T412T	TPBG_ENST00000535040.1_Silent_p.T412T|TPBG_ENST00000543496.1_Silent_p.T412T			Q13641	TPBG_HUMAN	trophoblast glycoprotein	412					cell adhesion (GO:0007155)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)				central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(6)|ovary(2)|prostate(1)|skin(1)|stomach(1)	15		all_cancers(76;0.000805)|Acute lymphoblastic leukemia(125;3.85e-06)|all_hematologic(105;0.0017)|all_epithelial(107;0.0897)		BRCA - Breast invasive adenocarcinoma(397;0.107)		CCAGATTAACGAACCTCAGTT	0.433													A|||	3434	0.685703	0.733	0.7161	5008	,	,		19959	0.5774		0.6889	False		,,,				2504	0.7086				p.T412T		Atlas-SNP	.											.	TPBG	37	.	0			c.G1236A						PASS	.	A	,	3216,1190	408.6+/-334.7	1174,868,161	56.0	58.0	57.0		1236,1236	-0.3	1.0	6	dbSNP_86	57	5833,2767	439.2+/-359.1	1962,1909,429	no	coding-synonymous,coding-synonymous	TPBG	NM_001166392.1,NM_006670.4	,	3136,2777,590	AA,AG,GG		32.1744,27.0086,30.4244	,	412/421,412/421	83075914	9049,3957	2203	4300	6503	SO:0001819	synonymous_variant	7162	exon2			ATTAACGAACCTC	AJ012159	CCDS4995.1	6q14-q15	2008-07-29			ENSG00000146242	ENSG00000146242			12004	protein-coding gene	gene with protein product		190920				8132670	Standard	NM_006670		Approved	5T4-AG, 5T4	uc003pjo.3	Q13641	OTTHUMG00000015103	ENST00000369750.3:c.1236G>A	6.37:g.83075914G>A		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	77	39	0.506494	NM_001166392	A8K555	Silent	SNP	ENST00000369750.3	37	CCDS4995.1																																																																																			G|0.316;A|0.684	0.684	strong		0.433	TPBG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041340.1		
TMPRSS5	80975	hgsc.bcm.edu	37	11	113561054	113561054	+	Missense_Mutation	SNP	A	A	G	rs7110736	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:113561054A>G	ENST00000299882.5	-	11	1253	c.1105T>C	c.(1105-1107)Ttc>Ctc	p.F369L	TMPRSS5_ENST00000545265.1_5'UTR|TMPRSS5_ENST00000540540.1_Missense_Mutation_p.F110L|TMPRSS5_ENST00000538955.1_Missense_Mutation_p.F325L|TMPRSS5_ENST00000536856.1_Missense_Mutation_p.F110L|TMPRSS5_ENST00000545579.1_Missense_Mutation_p.F360L|TMPRSS5_ENST00000544476.1_Missense_Mutation_p.F256L|TMPRSS5_ENST00000544634.1_Missense_Mutation_p.F300L	NM_030770.2	NP_110397.2	Q9H3S3	TMPS5_HUMAN	transmembrane protease, serine 5	369	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.		F -> L (common polymorphism; reduced proteolytic activity in a yeast-based protease assay; dbSNP:rs7110736). {ECO:0000269|PubMed:17918732}.		proteolysis (GO:0006508)	integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	peptidase activity (GO:0008233)|scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)			endometrium(2)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)	10		all_cancers(61;2.71e-16)|all_epithelial(67;1e-09)|Melanoma(852;1.46e-05)|all_hematologic(158;0.00014)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|all_neural(223;0.0281)|Prostate(24;0.0421)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;2.75e-06)|Epithelial(105;6.34e-05)|all cancers(92;0.000502)		TGAGTGCTGAACAAGGGCACC	0.592													G|||	3857	0.770168	0.9637	0.7594	5008	,	,		13848	0.748		0.6362	False		,,,				2504	0.6769				p.F369L		Atlas-SNP	.											.	TMPRSS5	69	.	0			c.T1105C						PASS	.	G	LEU/PHE	3868,366		1773,322,22	31.0	37.0	35.0		1105	3.2	1.0	11	dbSNP_116	35	5487,2987		1762,1963,512	yes	missense	TMPRSS5	NM_030770.2	22	3535,2285,534	GG,GA,AA		35.249,8.6443,26.385	benign	369/458	113561054	9355,3353	2117	4237	6354	SO:0001583	missense	80975	exon11			TGCTGAACAAGGG	AB028140	CCDS44735.1, CCDS73390.1, CCDS73391.1, CCDS73392.1, CCDS73393.1	11q	2010-04-13	2008-07-31		ENSG00000166682	ENSG00000166682		"""Serine peptidases / Transmembrane"""	14908	protein-coding gene	gene with protein product	"""spinesin"""	606751					Standard	NM_030770		Approved	MGC141886, MGC148044	uc001poc.4	Q9H3S3	OTTHUMG00000168186	ENST00000299882.5:c.1105T>C	11.37:g.113561054A>G	ENSP00000299882:p.Phe369Leu	Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	137	35	0.255474	NM_030770		Missense_Mutation	SNP	ENST00000299882.5	37	CCDS44735.1	1659	0.7596153846153846	473	0.9613821138211383	275	0.7596685082872928	433	0.756993006993007	478	0.6306068601583114	G	8.246	0.807900	0.16467	0.913557	0.64751	ENSG00000166682	ENST00000536856;ENST00000540540;ENST00000299882;ENST00000545579;ENST00000538955;ENST00000544634;ENST00000544476	D;D;D;D;D;D;D	0.87103	-2.21;-2.21;-2.21;-2.21;-2.21;-2.21;-2.21	4.21	3.21	0.36854	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.163922	0.37623	N	0.002004	T	0.00012	0.0000	N	0.00683	-1.26	0.44694	P	0.0023130000000000095	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	0.38929	-0.9638	9	0.27785	T	0.31	.	6.8897	0.24222	0.0988:0.0:0.6536:0.2476	rs7110736;rs57069367;rs7110736	300;110;360;369	F5GYA3;G5EA47;F5GX83;Q9H3S3	.;.;.;TMPS5_HUMAN	L	110;110;369;360;325;300;256	ENSP00000437937:F110L;ENSP00000437761:F110L;ENSP00000299882:F369L;ENSP00000441104:F360L;ENSP00000445528:F325L;ENSP00000440783:F300L;ENSP00000445930:F256L	ENSP00000299882:F369L	F	-	1	0	TMPRSS5	113066264	1.000000	0.71417	1.000000	0.80357	0.312000	0.27988	2.355000	0.44107	1.010000	0.39314	-0.684000	0.03749	TTC	A|0.250;G|0.750	0.750	strong		0.592	TMPRSS5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398652.1	NM_030770	
SLC5A8	160728	hgsc.bcm.edu	37	12	101587518	101587518	+	Missense_Mutation	SNP	C	C	T	rs1709189	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	165	0	0		WXS	Illumina HiSeq	Phase_I	151	71	0.470199	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	
THBS1	7057	hgsc.bcm.edu	37	15	39880818	39880818	+	Silent	SNP	C	C	T	rs41338344	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	76	0	0		WXS	Illumina HiSeq	Phase_I	70	34	0.485714	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	
MARC2	54996	hgsc.bcm.edu	37	1	220935081	220935081	+	Silent	SNP	G	G	A	rs2275575	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:220935081G>A	ENST00000366913.3	+	3	726	c.528G>A	c.(526-528)gcG>gcA	p.A176A	MARC2_ENST00000359316.2_Silent_p.A176A	NM_017898.3	NP_060368.2	Q969Z3	MARC2_HUMAN	mitochondrial amidoxime reducing component 2	176					detoxification of nitrogen compound (GO:0051410)|nitrate metabolic process (GO:0042126)|oxidation-reduction process (GO:0055114)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|peroxisome (GO:0005777)	molybdenum ion binding (GO:0030151)|molybdopterin cofactor binding (GO:0043546)|nitrate reductase activity (GO:0008940)|pyridoxal phosphate binding (GO:0030170)										AAACTGAAGCGTATAGATTGG	0.413													G|||	1042	0.208067	0.1649	0.3271	5008	,	,		21869	0.2312		0.1441	False		,,,				2504	0.2239				p.A176A		Atlas-SNP	.											.	.	.	.	0			c.G528A						PASS	.	G		740,3666	306.3+/-289.4	60,620,1523	120.0	107.0	112.0		528	-11.3	0.0	1	dbSNP_100	112	1159,7441	237.4+/-269.2	91,977,3232	no	coding-synonymous	MOSC2	NM_017898.3		151,1597,4755	AA,AG,GG		13.4767,16.7953,14.601		176/336	220935081	1899,11107	2203	4300	6503	SO:0001819	synonymous_variant	54996	exon3			TGAAGCGTATAGA		CCDS1525.1	1q41	2011-11-02	2011-11-02	2011-11-02	ENSG00000117791	ENSG00000117791			26064	protein-coding gene	gene with protein product		614127	"""MOCO sulphurase C-terminal domain containing 2"""	MOSC2		11886751	Standard	NM_017898		Approved	FLJ20605	uc001hmq.3	Q969Z3	OTTHUMG00000037354	ENST00000366913.3:c.528G>A	1.37:g.220935081G>A		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	89	45	0.505618	NM_017898	B2D0R5|D3DTB3|Q0JSK7|Q5VT67|Q5VXC7|Q7L317|Q9H066|Q9NWU0	Silent	SNP	ENST00000366913.3	37	CCDS1525.1																																																																																			G|0.831;A|0.169	0.169	strong		0.413	MARC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090911.1	NM_017898	
OVCH1	341350	hgsc.bcm.edu	37	12	29598292	29598292	+	Missense_Mutation	SNP	G	G	A	rs7967676	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:29598292G>A	ENST00000318184.5	-	23	2799	c.2800C>T	c.(2800-2802)Cct>Tct	p.P934S	OVCH1-AS1_ENST00000551108.1_Intron|OVCH1-AS1_ENST00000549411.1_Intron	NM_183378.2	NP_899234.2	Q7RTY7	OVCH1_HUMAN	ovochymase 1	934	CUB 3. {ECO:0000255|PROSITE- ProRule:PRU00059}.		P -> S (in dbSNP:rs7967676).			extracellular region (GO:0005576)	metal ion binding (GO:0046872)|serine-type endopeptidase activity (GO:0004252)			NS(2)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(15)|lung(43)|ovary(5)|pancreas(3)|prostate(2)|skin(1)|soft_tissue(1)|stomach(3)	92	Lung NSC(12;1.84e-09)|Acute lymphoblastic leukemia(23;0.00885)|all_hematologic(23;0.0155)					AGCGGTCCAGGACTCATGAAA	0.373													G|||	68	0.0135783	0.0023	0.0173	5008	,	,		17937	0.0		0.0437	False		,,,				2504	0.0092				p.P934S		Atlas-SNP	.											.	OVCH1	195	.	0			c.C2800T						PASS	.	G	SER/PRO	45,3681		1,43,1819	93.0	90.0	91.0		2800	-0.4	0.3	12	dbSNP_116	91	470,7740		18,434,3653	yes	missense	OVCH1	NM_183378.2	74	19,477,5472	AA,AG,GG		5.7247,1.2077,4.3147	benign	934/1135	29598292	515,11421	1863	4105	5968	SO:0001583	missense	341350	exon23			GTCCAGGACTCAT	BN000128		12p11.23	2012-11-08			ENSG00000187950	ENSG00000187950			23080	protein-coding gene	gene with protein product						12838346	Standard	NM_183378		Approved	OVCH	uc001rix.1	Q7RTY7	OTTHUMG00000167741	ENST00000318184.5:c.2800C>T	12.37:g.29598292G>A	ENSP00000326708:p.Pro934Ser	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	64	31	0.484375	NM_183378		Missense_Mutation	SNP	ENST00000318184.5	37		40	0.018315018315018316	2	0.0040650406504065045	7	0.019337016574585635	0	0.0	31	0.040897097625329816	G	0.001	-3.309245	0.00018	0.012077	0.057247	ENSG00000187950	ENST00000318184	T	0.15487	2.42	2.33	-0.389	0.12455	CUB (5);	.	.	.	.	T	0.00468	0.0015	N	0.01576	-0.805	0.09310	N	1	B	0.13594	0.008	B	0.14023	0.01	T	0.38067	-0.9678	9	0.02654	T	1	.	4.7287	0.12954	0.5315:0.0:0.4685:0.0	rs7967676;rs7967676	934	Q7RTY7	OVCH1_HUMAN	S	934	ENSP00000326708:P934S	ENSP00000326708:P934S	P	-	1	0	OVCH1	29489559	0.999000	0.42202	0.309000	0.25155	0.057000	0.15508	0.385000	0.20685	-0.080000	0.12685	-0.345000	0.07892	CCT	G|0.978;A|0.022	0.022	strong		0.373	OVCH1-001	KNOWN	non_canonical_TEC|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000395997.2	NM_183378	
TMEM173	340061	hgsc.bcm.edu	37	5	138856982	138856982	+	Missense_Mutation	SNP	C	C	T	rs7380824	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:138856982C>T	ENST00000330794.4	-	7	1211	c.878G>A	c.(877-879)cGg>cAg	p.R293Q	TMEM173_ENST00000511850.1_5'Flank	NM_198282.2	NP_938023.1	Q86WV6	STING_HUMAN	transmembrane protein 173	293	c-di-GMP-binding domain (CBD).		R -> Q (in dbSNP:rs7380824).		activation of innate immune response (GO:0002218)|apoptotic process (GO:0006915)|cellular response to exogenous dsRNA (GO:0071360)|cellular response to interferon-beta (GO:0035458)|defense response to virus (GO:0051607)|innate immune response (GO:0045087)|interferon-beta production (GO:0032608)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of protein binding (GO:0032092)|positive regulation of protein import into nucleus, translocation (GO:0033160)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|regulation of type I interferon production (GO:0032479)	cytoplasmic vesicle membrane (GO:0030659)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)|perinuclear region of cytoplasm (GO:0048471)|peroxisome (GO:0005777)|plasma membrane (GO:0005886)	cyclic-di-GMP binding (GO:0035438)|cyclic-GMP-AMP binding (GO:0061507)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|transcription factor binding (GO:0008134)			endometrium(1)|kidney(1)|lung(6)|upper_aerodigestive_tract(1)	9			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			CTCAAGTGTCCGGCAGAAGAG	0.562													C|||	1377	0.27496	0.2708	0.2882	5008	,	,		19161	0.4048		0.1531	False		,,,				2504	0.2628				p.R293Q		Atlas-SNP	.											.	TMEM173	19	.	0			c.G878A						PASS	.	C	GLN/ARG	1172,3234	412.6+/-336.2	151,870,1182	92.0	85.0	87.0		878	5.5	1.0	5	dbSNP_116	87	1214,7386	245.1+/-274.1	90,1034,3176	yes	missense	TMEM173	NM_198282.2	43	241,1904,4358	TT,TC,CC		14.1163,26.6001,18.3454	probably-damaging	293/380	138856982	2386,10620	2203	4300	6503	SO:0001583	missense	340061	exon7			AGTGTCCGGCAGA		CCDS4215.1	5q31.2	2009-11-06			ENSG00000184584	ENSG00000184584			27962	protein-coding gene	gene with protein product		612374				12477932	Standard	XM_005268445		Approved	FLJ38577, NET23	uc003lep.3	Q86WV6	OTTHUMG00000129239	ENST00000330794.4:c.878G>A	5.37:g.138856982C>T	ENSP00000331288:p.Arg293Gln	Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	122	56	0.459016	NM_198282	A8K3P6|B6EB35|D6RBX0|D6RE01|D6RID9	Missense_Mutation	SNP	ENST00000330794.4	37	CCDS4215.1	581	0.266025641025641	138	0.2804878048780488	92	0.2541436464088398	237	0.4143356643356643	114	0.1503957783641161	C	32	5.158298	0.94686	0.266001	0.141163	ENSG00000184584	ENST00000330794	T	0.26518	1.73	5.53	5.53	0.82687	.	0.062472	0.64402	D	0.000011	T	0.00012	0.0000	M	0.78049	2.395	0.09310	P	0.99999547022	D	0.89917	1.0	D	0.91635	0.999	T	0.26780	-1.0093	9	0.87932	D	0	-29.0556	19.0483	0.93030	0.0:1.0:0.0:0.0	rs7380824;rs59604760;rs7380824	293	Q86WV6	TM173_HUMAN	Q	293	ENSP00000331288:R293Q	ENSP00000331288:R293Q	R	-	2	0	TMEM173	138837166	1.000000	0.71417	1.000000	0.80357	0.877000	0.50540	3.440000	0.52886	2.617000	0.88574	0.561000	0.74099	CGG	C|0.780;T|0.220	0.220	strong		0.562	TMEM173-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251338.1	NM_198282	
SPOCD1	90853	hgsc.bcm.edu	37	1	32279629	32279629	+	Missense_Mutation	SNP	G	G	A	rs6669563	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:32279629G>A	ENST00000360482.2	-	2	1435	c.1306C>T	c.(1306-1308)Cgg>Tgg	p.R436W	SPOCD1_ENST00000373648.2_Missense_Mutation_p.R436W|SPOCD1_ENST00000257100.3_Intron|SPOCD1_ENST00000533231.1_Missense_Mutation_p.R436W	NM_144569.4	NP_653170.3	Q6ZMY3	SPOC1_HUMAN	SPOC domain containing 1	436			R -> W (in dbSNP:rs6669563).		negative regulation of phosphatase activity (GO:0010923)|transcription, DNA-templated (GO:0006351)			p.R436W(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|liver(1)|lung(7)|ovary(6)|prostate(1)|skin(3)|stomach(1)|urinary_tract(2)	37		Myeloproliferative disorder(586;0.0393)|all_neural(195;0.186)|Ovarian(437;0.199)		STAD - Stomach adenocarcinoma(196;0.18)		TCTGTGCCCCGGTCTTGGGCA	0.592													G|||	1734	0.346246	0.1876	0.4957	5008	,	,		18940	0.4226		0.4374	False		,,,				2504	0.2822				p.R436W		Atlas-SNP	.											SPOCD1,NS,carcinoma,0,2	SPOCD1	109	2	1	Substitution - Missense(1)	stomach(1)	c.C1306T						PASS	.	G	TRP/ARG	990,3416	365.9+/-317.6	118,754,1331	59.0	62.0	61.0		1306	0.2	0.0	1	dbSNP_116	61	3765,4835	527.7+/-381.2	804,2157,1339	yes	missense	SPOCD1	NM_144569.4	101	922,2911,2670	AA,AG,GG		43.7791,22.4694,36.56	probably-damaging	436/1217	32279629	4755,8251	2203	4300	6503	SO:0001583	missense	90853	exon2			TGCCCCGGTCTTG	AK058077	CCDS347.1, CCDS60066.1, CCDS72748.1	1p35.1	2014-06-13			ENSG00000134668	ENSG00000134668			26338	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 146"""					12477932	Standard	NM_144569		Approved	FLJ25348, PPP1R146	uc001bts.1	Q6ZMY3	OTTHUMG00000003879	ENST00000360482.2:c.1306C>T	1.37:g.32279629G>A	ENSP00000353670:p.Arg436Trp	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	94	42	0.446809	NM_144569	Q24JU3|Q6PI90|Q8N869|Q8N8U0|Q8NBC6|Q96LN6	Missense_Mutation	SNP	ENST00000360482.2	37	CCDS347.1	865	0.39606227106227104	106	0.21544715447154472	161	0.4447513812154696	260	0.45454545454545453	338	0.44591029023746703	G	10.09	1.254901	0.22965	0.224694	0.437791	ENSG00000134668	ENST00000360482;ENST00000373648;ENST00000533231	T;T;T	0.34275	1.84;1.37;1.84	3.25	0.152	0.14893	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	P;P	0.44044	0.825;0.733	B;B	0.36959	0.237;0.12	T	0.45011	-0.9290	8	0.87932	D	0	9.782	3.8093	0.08791	0.2419:0.202:0.556:0.0	rs6669563;rs6669563	436;436	Q6ZMY3-2;Q6ZMY3	.;SPOC1_HUMAN	W	436	ENSP00000353670:R436W;ENSP00000362752:R436W;ENSP00000435851:R436W	ENSP00000353670:R436W	R	-	1	2	SPOCD1	32052216	0.000000	0.05858	0.000000	0.03702	0.085000	0.17905	0.049000	0.14099	0.044000	0.15775	0.455000	0.32223	CGG	G|0.624;A|0.376	0.376	strong		0.592	SPOCD1-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000381912.1	NM_144569	
CNTN6	27255	hgsc.bcm.edu	37	3	1424718	1424718	+	Silent	SNP	G	G	A	rs2291101	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:1424718G>A	ENST00000446702.2	+	18	2886	c.2259G>A	c.(2257-2259)gtG>gtA	p.V753V	CNTN6_ENST00000539053.1_Silent_p.V681V|CNTN6_ENST00000350110.2_Silent_p.V753V			Q9UQ52	CNTN6_HUMAN	contactin 6	753	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|central nervous system development (GO:0007417)|Notch signaling pathway (GO:0007219)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)				breast(6)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(25)|lung(34)|ovary(1)|pancreas(1)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	90		all_cancers(2;0.000164)|all_epithelial(2;0.107)		Epithelial(13;0.000233)|all cancers(10;0.0013)|OV - Ovarian serous cystadenocarcinoma(96;0.0139)		AGGAGAAAGTGTCATCTGTGG	0.453													A|||	2421	0.483427	0.3684	0.5476	5008	,	,		17324	0.6508		0.3917	False		,,,				2504	0.5153				p.V753V		Atlas-SNP	.											.	CNTN6	245	.	0			c.G2259A						PASS	.	A		1643,2763	660.5+/-400.7	293,1057,853	158.0	145.0	150.0		2259	-8.8	0.0	3	dbSNP_100	150	3654,4946	623.5+/-397.5	786,2082,1432	no	coding-synonymous	CNTN6	NM_014461.2		1079,3139,2285	AA,AG,GG		42.4884,37.2901,40.7274		753/1029	1424718	5297,7709	2203	4300	6503	SO:0001819	synonymous_variant	27255	exon18			GAAAGTGTCATCT	AB003592	CCDS2557.1	3p26-p25	2013-02-11			ENSG00000134115	ENSG00000134115		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	2176	protein-coding gene	gene with protein product	"""neural adhesion molecule"""	607220				9486763	Standard	NM_014461		Approved	NB-3	uc003bpa.3	Q9UQ52	OTTHUMG00000119030	ENST00000446702.2:c.2259G>A	3.37:g.1424718G>A		Somatic	218	0	0		WXS	Illumina HiSeq	Phase_I	166	55	0.331325	NM_014461	Q2KHM2	Silent	SNP	ENST00000446702.2	37	CCDS2557.1																																																																																			G|0.557;A|0.443	0.443	strong		0.453	CNTN6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239235.2	NM_014461	
RAB11FIP5	26056	hgsc.bcm.edu	37	2	73339708	73339708	+	Silent	SNP	G	G	A	rs1864488	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:73339708G>A	ENST00000258098.6	-	1	438	c.198C>T	c.(196-198)tgC>tgT	p.C66C	RP11-44N22.3_ENST00000608612.1_RNA	NM_015470.2	NP_056285.1	Q9BXF6	RFIP5_HUMAN	RAB11 family interacting protein 5 (class I)	66	C2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				cellular response to acidic pH (GO:0071468)|insulin secretion involved in cellular response to glucose stimulus (GO:0035773)|protein transport (GO:0015031)|regulated secretory pathway (GO:0045055)|regulation of protein localization to cell surface (GO:2000008)	early endosome (GO:0005769)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|microtubule organizing center (GO:0005815)|mitochondrial outer membrane (GO:0005741)|recycling endosome (GO:0055037)|secretory granule (GO:0030141)	gamma-tubulin binding (GO:0043015)			biliary_tract(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(9)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	23						GCCACTCGGGGCAGCCGTGCG	0.731													G|||	2607	0.520567	0.2443	0.6671	5008	,	,		10002	0.4296		0.7137	False		,,,				2504	0.6851				p.C66C		Atlas-SNP	.											.	RAB11FIP5	66	.	0			c.C198T						PASS	.	G		1435,2957		255,925,1016	21.0	17.0	18.0		198	1.9	1.0	2	dbSNP_92	18	5954,2626		2072,1810,408	no	coding-synonymous	RAB11FIP5	NM_015470.2		2327,2735,1424	AA,AG,GG		30.6061,32.673,43.0389		66/654	73339708	7389,5583	2196	4290	6486	SO:0001819	synonymous_variant	26056	exon1			CTCGGGGCAGCCG	AF334812	CCDS1923.1	2p13	2008-02-05			ENSG00000135631	ENSG00000135631			24845	protein-coding gene	gene with protein product		605536				10048485, 11163216	Standard	NM_015470		Approved	GAF1, KIAA0857, RIP11, pp75	uc002sis.4	Q9BXF6	OTTHUMG00000129779	ENST00000258098.6:c.198C>T	2.37:g.73339708G>A		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	144	144	1	NM_015470	O94939|Q9P0M1	Silent	SNP	ENST00000258098.6	37	CCDS1923.1																																																																																			G|0.462;A|0.538	0.538	strong		0.731	RAB11FIP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251995.1	NM_015470	
PPP1R32	220004	hgsc.bcm.edu	37	11	61254455	61254455	+	Silent	SNP	T	T	C	rs77676987	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:61254455T>C	ENST00000338608.2	+	10	995	c.870T>C	c.(868-870)agT>agC	p.S290S	PPP1R32_ENST00000432063.2_Silent_p.S270S|PPP1R32_ENST00000538185.1_5'Flank|PPP1R32_ENST00000366212.4_5'Flank	NM_145017.2	NP_659454.2	Q7Z5V6	PPR32_HUMAN	protein phosphatase 1, regulatory subunit 32	290							phosphatase binding (GO:0019902)										GCAGCGTGAGTCACCAGCAGT	0.607													C|||	206	0.0411342	0.1392	0.0058	5008	,	,		19523	0.001		0.008	False		,,,				2504	0.0092				p.S290S		Atlas-SNP	.											.	.	.	.	0			c.T870C						PASS	.	C	,	514,3890	778.9+/-414.3	37,440,1725	213.0	213.0	213.0		810,870	2.9	0.1	11	dbSNP_131	213	62,8536	816.5+/-406.9	0,62,4237	no	coding-synonymous,coding-synonymous	C11orf66	NM_001170753.1,NM_145017.2	,	37,502,5962	CC,CT,TT		0.7211,11.6712,4.4301	,	270/406,290/426	61254455	576,12426	2202	4299	6501	SO:0001819	synonymous_variant	220004	exon10			CGTGAGTCACCAG	AK057333	CCDS8008.1, CCDS53641.1	11q12.2	2012-04-17	2011-10-11	2011-10-11	ENSG00000162148	ENSG00000162148		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	28869	protein-coding gene	gene with protein product			"""chromosome 11 open reading frame 66"""	C11orf66		12477932	Standard	NM_145017		Approved	IIIG9, FLJ32771	uc001nru.2	Q7Z5V6	OTTHUMG00000168176	ENST00000338608.2:c.870T>C	11.37:g.61254455T>C		Somatic	200	1	0.005		WXS	Illumina HiSeq	Phase_I	148	120	0.810811	NM_145017	Q4G0P4|Q96M77	Silent	SNP	ENST00000338608.2	37	CCDS8008.1																																																																																			T|0.960;C|0.040	0.040	strong		0.607	PPP1R32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398621.1	NM_145017	
ZNF83	55769	hgsc.bcm.edu	37	19	53117809	53117809	+	Silent	SNP	C	C	A	rs10406458	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:53117809C>A	ENST00000597597.1	-	2	2262	c.9G>T	c.(7-9)ggG>ggT	p.G3G	ZNF83_ENST00000601257.1_Intron|ZNF83_ENST00000545872.1_Silent_p.G3G|ZNF83_ENST00000600714.1_Intron|ZNF83_ENST00000541777.2_Silent_p.G3G|ZNF83_ENST00000391789.4_Silent_p.G3G|ZNF83_ENST00000594682.2_3'UTR|ZNF83_ENST00000536937.1_Silent_p.G3G|ZNF83_ENST00000301096.3_Silent_p.G3G|ZNF83_ENST00000544146.1_Silent_p.G3G			P51522	ZNF83_HUMAN	zinc finger protein 83	3					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(3)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	18				OV - Ovarian serous cystadenocarcinoma(262;0.00841)|GBM - Glioblastoma multiforme(134;0.0244)		CATCCTTTCTCCCATGCATGT	0.423													T|||	3569	0.71266	0.8888	0.7435	5008	,	,		18433	0.7044		0.6392	False		,,,				2504	0.5368				p.G3G		Atlas-SNP	.											.	ZNF83	73	.	0			c.G9T						PASS	.	T	,,,,,,,,	3586,820	733.2+/-410.4	1467,652,84	40.0	43.0	42.0		9,9,9,9,9,9,9,9,9	0.1	0.0	19	dbSNP_119	42	5117,3483	623.0+/-397.4	1529,2059,712	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ZNF83	NM_001105549.1,NM_001105550.1,NM_001105551.1,NM_001105552.1,NM_001105553.1,NM_001105554.1,NM_001242531.1,NM_001242538.1,NM_018300.3	,,,,,,,,	2996,2711,796	AA,AC,CC		40.5,18.611,33.0847	,,,,,,,,	3/517,3/517,3/517,3/517,3/489,3/489,3/489,3/489,3/517	53117809	8703,4303	2203	4300	6503	SO:0001819	synonymous_variant	55769	exon3			CTTTCTCCCATGC	M27877	CCDS12854.1	19q13.3	2013-01-08	2006-05-12			ENSG00000167766		"""Zinc fingers, C2H2-type"""	13158	protein-coding gene	gene with protein product		194558	"""zinc finger protein 83 (HPF1)"", ""zinc finger protein 816B"""	ZNF816B		8088807	Standard	NM_018300		Approved	FLJ11015, HPF1	uc010epy.3	P51522		ENST00000597597.1:c.9G>T	19.37:g.53117809C>A		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	58	58	1	NM_018300	A8MT75|Q3ZCX0|Q6PI08	Silent	SNP	ENST00000597597.1	37	CCDS12854.1																																																																																			C|0.304;A|0.696	0.696	strong		0.423	ZNF83-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463700.1	NM_018300	
GLP2R	9340	hgsc.bcm.edu	37	17	9792872	9792872	+	Silent	SNP	T	T	C	rs17681708	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:9792872T>C	ENST00000262441.5	+	13	2025	c.1512T>C	c.(1510-1512)caT>caC	p.H504H	GLP2R_ENST00000574745.1_Silent_p.H324H	NM_004246.1	NP_004237.1	O95838	GLP2R_HUMAN	glucagon-like peptide 2 receptor	504					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|positive regulation of cell proliferation (GO:0008284)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|glucagon receptor activity (GO:0004967)			endometrium(4)|large_intestine(7)|lung(22)|ovary(2)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)	44					Glucagon recombinant(DB00040)|Teduglutide(DB08900)	GGCTCCTACATCTAGCCATGC	0.627													C|||	504	0.100639	0.0212	0.1585	5008	,	,		18658	0.002		0.2763	False		,,,				2504	0.0879				p.H504H		Atlas-SNP	.											GLP2R,NS,carcinoma,0,1	GLP2R	90	1	0			c.T1512C						PASS	.	C		322,4084	771.1+/-413.8	11,300,1892	44.0	46.0	45.0		1512	-1.2	0.0	17	dbSNP_123	45	2702,5898	662.0+/-401.9	428,1846,2026	no	coding-synonymous	GLP2R	NM_004246.1		439,2146,3918	CC,CT,TT		31.4186,7.3082,23.2508		504/554	9792872	3024,9982	2203	4300	6503	SO:0001819	synonymous_variant	9340	exon13			CCTACATCTAGCC	AF105367	CCDS11150.1	17p13.3	2012-08-10			ENSG00000065325	ENSG00000065325		"""GPCR / Class B : Glucagon receptors"""	4325	protein-coding gene	gene with protein product		603659				9990065	Standard	NM_004246		Approved		uc002gmd.1	O95838	OTTHUMG00000130269	ENST00000262441.5:c.1512T>C	17.37:g.9792872T>C		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	57	31	0.54386	NM_004246	Q4VAT3	Silent	SNP	ENST00000262441.5	37	CCDS11150.1																																																																																			T|0.817;C|0.183	0.183	strong		0.627	GLP2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252601.4		
ADAMTSL3	57188	hgsc.bcm.edu	37	15	84581904	84581904	+	Silent	SNP	T	T	C	rs4842923	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:84581904T>C	ENST00000286744.5	+	16	1985	c.1761T>C	c.(1759-1761)cgT>cgC	p.R587R	ADAMTSL3_ENST00000567476.1_Silent_p.R587R	NM_207517.2	NP_997400.2	P82987	ATL3_HUMAN	ADAMTS-like 3	587	TSP type-1 4. {ECO:0000255|PROSITE- ProRule:PRU00210}.		R -> H (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.			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)			TGCAGGTCCGTGAGGTGAAGT	0.607													C|||	3436	0.686102	0.8306	0.7248	5008	,	,		17539	0.7202		0.5308	False		,,,				2504	0.5879				p.R587R		Atlas-SNP	.											ADAMTSL3,colon,carcinoma,+1,2	ADAMTSL3	290	2	0			c.T1761C						PASS	.	C		3417,989	369.8+/-319.3	1330,757,116	90.0	81.0	84.0		1761	-9.8	0.0	15	dbSNP_111	84	4624,3976	550.9+/-385.8	1252,2120,928	no	coding-synonymous	ADAMTSL3	NM_207517.2		2582,2877,1044	CC,CT,TT		46.2326,22.4467,38.1747		587/1692	84581904	8041,4965	2203	4300	6503	SO:0001819	synonymous_variant	57188	exon16			GGTCCGTGAGGTG	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.1761T>C	15.37:g.84581904T>C		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	117	117	1	NM_207517	A1A566|A1A567|Q9ULI7	Silent	SNP	ENST00000286744.5	37	CCDS10326.1																																																																																			T|0.354;C|0.646	0.646	strong		0.607	ADAMTSL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304007.2	NM_207517	
APOBEC3B	9582	hgsc.bcm.edu	37	22	39381936	39381936	+	Silent	SNP	G	G	A	rs138362043	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:39381936G>A	ENST00000333467.3	+	3	339	c.294G>A	c.(292-294)ccG>ccA	p.P98P	APOBEC3B_ENST00000407298.3_Silent_p.P98P|APOBEC3B_ENST00000402182.3_Silent_p.P98P	NM_001270411.1|NM_004900.4	NP_001257340.1|NP_004891	Q9UH17	ABC3B_HUMAN	apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3B	98	CMP/dCMP deaminase zinc-binding 1.		P -> L (in dbSNP:rs2076110).		defense response to virus (GO:0051607)|innate immune response (GO:0045087)|metabolic process (GO:0008152)|negative regulation of transposition (GO:0010529)	nucleus (GO:0005634)	deoxycytidine deaminase activity (GO:0047844)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			cervix(2)|endometrium(2)|kidney(3)|large_intestine(1)|lung(3)|ovary(1)|skin(1)	13	Melanoma(58;0.04)					CCCCCTGCCCGGACTGTGTGG	0.557													G|||	2	0.000399361	0.0015	0.0	5008	,	,		15975	0.0		0.0	False		,,,				2504	0.0				p.P98P		Atlas-SNP	.											APOBEC3B,colon,carcinoma,+1,1	APOBEC3B	32	1	0			c.G294A						PASS	.	G		1,4403		0,1,2201	139.0	133.0	135.0		294	-4.2	0.0	22	dbSNP_134	135	5,8591		0,5,4293	no	coding-synonymous	APOBEC3B	NM_004900.3		0,6,6494	AA,AG,GG		0.0582,0.0227,0.0462		98/383	39381936	6,12994	2202	4298	6500	SO:0001819	synonymous_variant	9582	exon3			CTGCCCGGACTGT	AK024854	CCDS13982.1, CCDS58807.1	22q13.1-q13.2	2008-05-15			ENSG00000179750	ENSG00000179750		"""Apolipoprotein B mRNA editing enzymes"""	17352	protein-coding gene	gene with protein product	"""phorbolin 3"""	607110				11863358, 10469298	Standard	NM_004900		Approved	PHRBNL, FLJ21201	uc003awo.2	Q9UH17	OTTHUMG00000151085	ENST00000333467.3:c.294G>A	22.37:g.39381936G>A		Somatic	244	0	0		WXS	Illumina HiSeq	Phase_I	168	117	0.696429	NM_004900	B0QYD2|O95618|Q20WL1|Q5IFJ4|Q7Z2N3|Q7Z6D6|Q9UE74	Silent	SNP	ENST00000333467.3	37	CCDS13982.1																																																																																			G|1.000;A|0.000	0.000	weak		0.557	APOBEC3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321233.1	NM_004900	
NOL8	55035	hgsc.bcm.edu	37	9	95069242	95069242	+	Silent	SNP	A	A	G	rs375530094		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:95069242A>G	ENST00000535387.1	-	9	2636	c.2637T>C	c.(2635-2637)aaT>aaC	p.N879N	NOL8_ENST00000442668.2_Silent_p.N917N|NOL8_ENST00000542053.1_Silent_p.N849N|NOL8_ENST00000545558.1_Silent_p.N917N|NOL8_ENST00000358855.4_Silent_p.N849N					nucleolar protein 8											endometrium(3)|kidney(2)|large_intestine(5)|lung(5)|ovary(1)	16						TTTGTACAACATTCAGGGCTT	0.343																																					p.N917N		Atlas-SNP	.											.	NOL8	118	.	0			c.T2751C						PASS	.	A		0,3634		0,0,1817	141.0	137.0	139.0		2751	3.4	0.5	9		139	1,8159		0,1,4079	no	coding-synonymous	NOL8	NM_017948.5		0,1,5896	GG,GA,AA		0.0123,0.0,0.0085		917/1168	95069242	1,11793	1817	4080	5897	SO:0001819	synonymous_variant	55035	exon11			TACAACATTCAGG	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.2637T>C	9.37:g.95069242A>G		Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	141	56	0.397163	NM_017948		Silent	SNP	ENST00000535387.1	37	CCDS47993.1																																																																																			.	.	weak		0.343	NOL8-010	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000053082.2	NM_017948	
RYR3	6263	hgsc.bcm.edu	37	15	33858935	33858935	+	Silent	SNP	G	G	A	rs11853872	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:33858935G>A	ENST00000389232.4	+	12	1273	c.1203G>A	c.(1201-1203)caG>caA	p.Q401Q	RYR3_ENST00000415757.3_Silent_p.Q401Q	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	401					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)		AGAGATGCCAGCGTGAGGAGT	0.512													G|||	531	0.10603	0.2579	0.0591	5008	,	,		20908	0.0188		0.0885	False		,,,				2504	0.0419				p.Q401Q		Atlas-SNP	.											.	RYR3	760	.	0			c.G1203A						PASS	.	G		896,3354		104,688,1333	176.0	180.0	178.0		1203	2.7	0.8	15	dbSNP_120	178	732,7744		31,670,3537	no	coding-synonymous	RYR3	NM_001036.3		135,1358,4870	AA,AG,GG		8.6361,21.0824,12.7927		401/4871	33858935	1628,11098	2125	4238	6363	SO:0001819	synonymous_variant	6263	exon12			ATGCCAGCGTGAG		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.1203G>A	15.37:g.33858935G>A		Somatic	237	0	0		WXS	Illumina HiSeq	Phase_I	173	89	0.514451	NM_001243996	O15175|Q15412	Silent	SNP	ENST00000389232.4	37	CCDS45210.1																																																																																			G|0.897;A|0.103	0.103	strong		0.512	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1		
PHRF1	57661	hgsc.bcm.edu	37	11	587425	587425	+	Silent	SNP	C	C	A	rs12800061	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:587425C>A	ENST00000264555.5	+	4	509	c.381C>A	c.(379-381)gcC>gcA	p.A127A	PHRF1_ENST00000533464.1_Silent_p.A123A|PHRF1_ENST00000413872.2_Silent_p.A126A|PHRF1_ENST00000416188.2_Silent_p.A127A	NM_020901.2	NP_065952.2	Q9P1Y6	PHRF1_HUMAN	PHD and ring finger domains 1	127					mRNA processing (GO:0006397)|transcription from RNA polymerase II promoter (GO:0006366)	membrane (GO:0016020)	RNA polymerase binding (GO:0070063)|zinc ion binding (GO:0008270)			breast(1)|cervix(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(13)|urinary_tract(2)	28						AGAACTGTGCCCATTACTTCT	0.542													C|||	822	0.164137	0.2504	0.245	5008	,	,		21033	0.0198		0.2147	False		,,,				2504	0.0869				p.A127A		Atlas-SNP	.											PHRF1_ENST00000264555,NS,NS,+2,1	PHRF1	188	1	0			c.C381A						PASS	.	C		1072,3148		132,808,1170	125.0	133.0	130.0		381	2.4	1.0	11	dbSNP_121	130	2007,6393		216,1575,2409	no	coding-synonymous	PHRF1	NM_020901.2		348,2383,3579	AA,AC,CC		23.8929,25.4028,24.3978		127/1649	587425	3079,9541	2110	4200	6310	SO:0001819	synonymous_variant	57661	exon4			CTGTGCCCATTAC	BC004950	CCDS44507.1, CCDS65987.1, CCDS65988.1, CCDS65989.1	11p15.5	2014-06-13			ENSG00000070047	ENSG00000070047		"""RING-type (C3HC4) zinc fingers"", ""Zinc fingers, PHD-type"""	24351	protein-coding gene	gene with protein product	"""CTD binding SR like protein rA9"", ""protein phosphatase 1, regulatory subunit 125"""	611780		RNF221			Standard	XM_005253027		Approved	KIAA1542, PPP1R125	uc010qwc.2	Q9P1Y6	OTTHUMG00000165141	ENST00000264555.5:c.381C>A	11.37:g.587425C>A		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	147	126	0.857143	NM_020901	A6H8W1|B7ZM64|B9EGP0|C9JS82|Q6PJP2|Q8IVY2|Q8N2Y7|Q9BSM2	Silent	SNP	ENST00000264555.5	37																																																																																				A|0.194;C|0.805;G|0.000	0.194	strong		0.542	PHRF1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000382133.1	NM_020901	
MFRP	83552	hgsc.bcm.edu	37	11	119215046	119215046	+	Silent	SNP	C	C	T	rs35885438	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:119215046C>T	ENST00000530681.1	-	8	1098	c.954G>A	c.(952-954)ctG>ctA	p.L318L	C1QTNF5_ENST00000445041.2_5'UTR|MFRP_ENST00000529147.1_5'Flank|MFRP_ENST00000555262.1_Silent_p.L318L|MFRP_ENST00000449574.2_Silent_p.L318L|MFRP_ENST00000360167.4_Intron	NM_001278431.1	NP_001265360.1	Q9BY79	MFRP_HUMAN	membrane frizzled-related protein	318	CUB 2. {ECO:0000255|PROSITE- ProRule:PRU00059}.				embryo development (GO:0009790)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(8)|prostate(1)|urinary_tract(1)	18		Medulloblastoma(222;0.0523)|Breast(348;0.174)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;3.84e-05)		GGTACTGCTGCAGGTAGCTGG	0.567													C|||	287	0.0573083	0.0295	0.0187	5008	,	,		19034	0.0357		0.0706	False		,,,				2504	0.1309				p.L318L		Atlas-SNP	.											.	MFRP	63	.	0			c.G954A						PASS	.	C	,	90,4308	76.2+/-114.5	0,90,2109	102.0	87.0	92.0		,954	1.5	0.6	11	dbSNP_126	92	401,8189	127.5+/-185.8	10,381,3904	no	utr-5,coding-synonymous	MFRP,C1QTNF5	NM_015645.3,NM_031433.2	,	10,471,6013	TT,TC,CC		4.6682,2.0464,3.7804	,	,318/580	119215046	491,12497	2199	4295	6494	SO:0001819	synonymous_variant	83552	exon8			CTGCTGCAGGTAG	AB055505	CCDS8421.1	11q23.3	2014-01-28			ENSG00000235718	ENSG00000235718			18121	protein-coding gene	gene with protein product	"""membrane-type frizzled-related protein"", ""complement C1q tumor necrosis factor-related protein 5 precursor variant 1"""	606227				11263980	Standard	NM_031433		Approved	FLJ30570, rd6, NNO2, C1QTNF5	uc001pwj.2	Q9BY79		ENST00000530681.1:c.954G>A	11.37:g.119215046C>T		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	92	10	0.108696	NM_031433	B0YJ36|B0YJ37|B4DHN8|Q335M3|Q96DQ9	Silent	SNP	ENST00000530681.1	37	CCDS8421.1																																																																																			C|0.962;T|0.038	0.038	strong		0.567	MFRP-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	nonsense_mediated_decay	protein_coding	OTTHUMT00000415179.1	NM_031433	
ZBTB4	57659	hgsc.bcm.edu	37	17	7366651	7366651	+	Missense_Mutation	SNP	C	C	G	rs871990	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:7366651C>G	ENST00000311403.4	-	4	1989	c.1650G>C	c.(1648-1650)atG>atC	p.M550I	ZBTB4_ENST00000380599.4_Missense_Mutation_p.M550I	NM_020899.3	NP_065950.2	Q9P1Z0	ZBTB4_HUMAN	zinc finger and BTB domain containing 4	550			M -> I (in dbSNP:rs871990).		cellular response to DNA damage stimulus (GO:0006974)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|methyl-CpG binding (GO:0008327)|methyl-CpNpG binding (GO:0010428)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|sequence-specific DNA binding (GO:0043565)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(7)|kidney(1)|large_intestine(4)|lung(7)|ovary(3)|prostate(3)|skin(6)	36		Colorectal(1115;3.46e-05)|Myeloproliferative disorder(207;0.0255)		COAD - Colon adenocarcinoma(228;4.1e-06)|READ - Rectum adenocarcinoma(115;0.0642)		TGGTGGTGGCCATGGCTGGCC	0.662													C|||	938	0.1873	0.1203	0.2277	5008	,	,		13827	0.1944		0.1571	False		,,,				2504	0.273				p.M550I		Atlas-SNP	.											.	ZBTB4	163	.	0			c.G1650C						PASS	.	C	ILE/MET,ILE/MET	586,3814		44,498,1658	14.0	17.0	16.0		1650,1650	-9.8	0.0	17	dbSNP_96	16	1227,7365		93,1041,3162	yes	missense,missense	ZBTB4	NM_001128833.1,NM_020899.3	10,10	137,1539,4820	GG,GC,CC		14.2807,13.3182,13.9547	benign,benign	550/1014,550/1014	7366651	1813,11179	2200	4296	6496	SO:0001583	missense	57659	exon4			GGTGGCCATGGCT	AB040971	CCDS11107.1	17p13.2	2013-01-09			ENSG00000174282	ENSG00000174282		"""-"", ""BTB/POZ domain containing"", ""Zinc fingers, C2H2-type"""	23847	protein-coding gene	gene with protein product		612308				12477932	Standard	NM_020899		Approved	KIAA1538, KAISO-L1, ZNF903	uc002ghd.4	Q9P1Z0	OTTHUMG00000108137	ENST00000311403.4:c.1650G>C	17.37:g.7366651C>G	ENSP00000307858:p.Met550Ile	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	74	35	0.472973	NM_001128833	B3KVL6|Q7Z697|Q86XJ4|Q8N4V8	Missense_Mutation	SNP	ENST00000311403.4	37	CCDS11107.1	373	0.1707875457875458	56	0.11382113821138211	85	0.23480662983425415	116	0.20279720279720279	116	0.15303430079155672	C	4.476	0.088158	0.08583	0.133182	0.142807	ENSG00000174282	ENST00000311403;ENST00000380599	T;T	0.03524	3.9;3.9	4.9	-9.81	0.00487	.	1.029510	0.07893	U	0.971512	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.49370	-0.8947	9	0.46703	T	0.11	.	4.0539	0.09808	0.1796:0.515:0.1813:0.1241	rs871990;rs3744546;rs3892359;rs871990	550	Q9P1Z0	ZBTB4_HUMAN	I	550	ENSP00000307858:M550I;ENSP00000369973:M550I	ENSP00000307858:M550I	M	-	3	0	ZBTB4	7307375	0.000000	0.05858	0.006000	0.13384	0.509000	0.34042	-3.455000	0.00465	-2.294000	0.00663	-0.448000	0.05591	ATG	C|0.861;G|0.139	0.139	strong		0.662	ZBTB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226940.2	NM_020899	
SLC26A7	115111	hgsc.bcm.edu	37	8	92364100	92364100	+	Silent	SNP	T	T	C	rs10109254	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:92364100T>C	ENST00000276609.3	+	10	1442	c.1203T>C	c.(1201-1203)ctT>ctC	p.L401L	SLC26A7_ENST00000523719.1_Silent_p.L401L|SLC26A7_ENST00000309536.2_Silent_p.L401L|SLC26A7_ENST00000520249.1_3'UTR	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	104	0	0		WXS	Illumina HiSeq	Phase_I	95	14	0.147368	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		
SH3TC1	54436	hgsc.bcm.edu	37	4	8207083	8207083	+	Silent	SNP	A	A	G	rs2677605	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:8207083A>G	ENST00000245105.3	+	2	229	c.162A>G	c.(160-162)ccA>ccG	p.P54P	SH3TC1_ENST00000382521.3_Silent_p.P54P|SH3TC1_ENST00000539824.1_5'UTR	NM_018986.3	NP_061859	Q8TE82	S3TC1_HUMAN	SH3 domain and tetratricopeptide repeats 1	54										NS(1)|breast(3)|endometrium(4)|kidney(4)|large_intestine(6)|lung(10)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	33						CCAAGGCGCCAGTGAGAGGCG	0.682													a|||	2287	0.456669	0.5499	0.4669	5008	,	,		13002	0.3036		0.5348	False		,,,				2504	0.4008				p.P54P	NSCLC(145;2298 2623 35616 37297)	Atlas-SNP	.											SH3TC1,NS,carcinoma,0,1	SH3TC1	105	1	0			c.A162G						PASS	.			2263,1703		685,893,405	30.0	32.0	31.0		162	-3.7	0.0	4	dbSNP_100	31	4325,3501		1258,1809,846	no	coding-synonymous	SH3TC1	NM_018986.3		1943,2702,1251	GG,GA,AA		44.7355,42.94,44.1316		54/1337	8207083	6588,5204	1983	3913	5896	SO:0001819	synonymous_variant	54436	exon2			GGCGCCAGTGAGA	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.162A>G	4.37:g.8207083A>G		Somatic	188	0	0		WXS	Illumina HiSeq	Phase_I	169	80	0.473373	NM_018986	Q4W5G5	Silent	SNP	ENST00000245105.3	37	CCDS3399.1																																																																																			A|0.516;G|0.484	0.484	strong		0.682	SH3TC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206991.2	NM_018986	
PTCHD4	442213	hgsc.bcm.edu	37	6	47847401	47847401	+	Silent	SNP	A	A	G	rs2068006	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:47847401A>G	ENST00000339488.4	-	3	1212	c.1179T>C	c.(1177-1179)gcT>gcC	p.A393A		NM_001013732.3	NP_001013754.3	Q6ZW05	PTHD4_HUMAN	patched domain containing 4	393						integral component of membrane (GO:0016021)	hedgehog receptor activity (GO:0008158)										CTAGTTGGCCAGCAAAGACCA	0.453													A|||	3250	0.648962	0.4592	0.7911	5008	,	,		19835	0.746		0.6769	False		,,,				2504	0.6759				p.A393A		Atlas-SNP	.											.	.	.	.	0			c.T1179C						PASS	.	A		2253,2153	594.9+/-388.3	577,1099,527	73.0	70.0	71.0		1179	-0.1	1.0	6	dbSNP_96	71	5888,2712	681.4+/-403.7	2016,1856,428	no	coding-synonymous	C6orf138	NM_001013732.3		2593,2955,955	GG,GA,AA		31.5349,48.8652,37.4058		393/847	47847401	8141,4865	2203	4300	6503	SO:0001819	synonymous_variant	442213	exon3			TTGGCCAGCAAAG		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.1179T>C	6.37:g.47847401A>G		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	59	58	0.983051	NM_001013732	B0QZ29|B4DRK3|Q5T884	Silent	SNP	ENST00000339488.4	37	CCDS34473.2																																																																																			A|0.358;G|0.642	0.642	strong		0.453	PTCHD4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317987.2	NM_001013732	
EMR1	2015	hgsc.bcm.edu	37	19	6926378	6926378	+	Splice_Site	SNP	T	T	C	rs2228539	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:6926378T>C	ENST00000312053.4	+	16	2025	c.1988T>C	c.(1987-1989)aTg>aCg	p.M663T	EMR1_ENST00000450315.3_Splice_Site_p.M486T|EMR1_ENST00000381404.4_Splice_Site_p.M611T|EMR1_ENST00000250572.8_Splice_Site_p.M598T|EMR1_ENST00000381407.5_Splice_Site_p.M522T	NM_001974.4	NP_001965.3	Q14246	EMR1_HUMAN	egf-like module containing, mucin-like, hormone receptor-like 1	663			M -> T (in dbSNP:rs2228539). {ECO:0000269|PubMed:7601460}.		cell adhesion (GO:0007155)|G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(11)|lung(31)|ovary(3)|prostate(1)|skin(8)	62	all_hematologic(4;0.166)					CCCCTCCAGATGGGCTGCGCC	0.532													t|||	1601	0.319688	0.6573	0.3746	5008	,	,		20941	0.0337		0.2694	False		,,,				2504	0.1708				p.M663T		Atlas-SNP	.											.	EMR1	153	.	0			c.T1988C						PASS	.	C	THR/MET	2568,1838	535.8+/-374.3	748,1072,383	107.0	104.0	105.0		1988	-8.4	0.0	19	dbSNP_98	105	2365,6235	702.5+/-405.3	308,1749,2243	yes	missense-near-splice	EMR1	NM_001974.3	81	1056,2821,2626	CC,CT,TT		27.5,41.7158,37.9286	benign	663/887	6926378	4933,8073	2203	4300	6503	SO:0001630	splice_region_variant	2015	exon16			TCCAGATGGGCTG	X81479	CCDS12175.1, CCDS58643.1, CCDS58644.1, CCDS58645.1, CCDS58646.1	19p13.3	2014-08-08	2003-11-26					"""-"", ""GPCR / Class B : Orphans"""	3336	protein-coding gene	gene with protein product		600493	"""egf-like module containing, mucin-like, hormone receptor-like sequence 1"""	TM7LN3		7601460, 9500513	Standard	NM_001974		Approved		uc002mfw.4	Q14246		ENST00000312053.4:c.1987-1T>C	19.37:g.6926378T>C		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	89	39	0.438202	NM_001974	A6NHV2|B7Z486|B7Z489|E7EPX9|E9PD45|H9KV79|Q2I7G5|Q6ZMN0|Q8NGA7	Missense_Mutation	SNP	ENST00000312053.4	37	CCDS12175.1	635	0.2907509157509158	304	0.6178861788617886	126	0.34806629834254144	10	0.017482517482517484	195	0.25725593667546176	C	2.685	-0.274379	0.05679	0.582842	0.275	ENSG00000174837	ENST00000543519;ENST00000312053;ENST00000381404;ENST00000250572;ENST00000381407;ENST00000450315	T;T;T;T;T	0.35605	1.3;1.3;1.3;1.3;1.3	4.18	-8.35	0.00984	GPCR, family 2-like (1);	.	.	.	.	T	0.00012	0.0000	N	0.00507	-1.42	0.80722	P	0.0	B;B;P;B;B	0.45827	0.0;0.0;0.867;0.0;0.0	B;B;B;B;B	0.42282	0.0;0.001;0.382;0.001;0.0	T	0.48559	-0.9025	8	0.66056	D	0.02	.	16.3517	0.83215	0.0:0.2016:0.0:0.7984	rs2228539;rs4807916;rs52819375;rs61570658;rs4807916	486;522;598;611;663	E7EPX9;B7Z486;Q14246-2;E9PD45;Q14246	.;.;.;.;EMR1_HUMAN	T	598;663;611;598;522;486	ENSP00000311545:M663T;ENSP00000370811:M611T;ENSP00000250572:M598T;ENSP00000370814:M522T;ENSP00000405974:M486T	ENSP00000250572:M598T	M	+	2	0	EMR1	6877378	0.000000	0.05858	0.000000	0.03702	0.389000	0.30415	-1.007000	0.03667	-2.524000	0.00495	-1.922000	0.00515	ATG	T|0.650;C|0.350	0.350	strong		0.532	EMR1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458485.1		Missense_Mutation
GFPT2	9945	hgsc.bcm.edu	37	5	179729519	179729519	+	Silent	SNP	A	A	G	rs1035411	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:179729519A>G	ENST00000253778.8	-	18	2077	c.1908T>C	c.(1906-1908)atT>atC	p.I636I		NM_005110.2	NP_005101.1	O94808	GFPT2_HUMAN	glutamine-fructose-6-phosphate transaminase 2	636	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)			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)	GGGGCAGCTCAATTGTCTTAT	0.517													G|||	3562	0.711262	0.6952	0.6527	5008	,	,		16952	0.9048		0.6571	False		,,,				2504	0.6309				p.I636I		Atlas-SNP	.											.	GFPT2	74	.	0			c.T1908C						PASS	.	G		3021,1189		1096,829,180	116.0	122.0	120.0		1908	-4.1	0.2	5	dbSNP_86	120	5258,3228		1645,1968,630	no	coding-synonymous	GFPT2	NM_005110.2		2741,2797,810	GG,GA,AA		38.0391,28.2423,34.7905		636/683	179729519	8279,4417	2105	4243	6348	SO:0001819	synonymous_variant	9945	exon18			CAGCTCAATTGTC	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.1908T>C	5.37:g.179729519A>G		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	70	31	0.442857	NM_005110	Q53XM2|Q9BWS4	Silent	SNP	ENST00000253778.8	37	CCDS43411.1																																																																																			A|0.292;G|0.708	0.708	strong		0.517	GFPT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373444.4	NM_005110	
CYP4F12	66002	hgsc.bcm.edu	37	19	15789098	15789098	+	Missense_Mutation	SNP	A	A	G	rs609636	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:15789098A>G	ENST00000550308.1	+	3	606	c.226A>G	c.(226-228)Aac>Gac	p.N76D	CYP4F12_ENST00000324632.10_Missense_Mutation_p.N76D	NM_023944.3	NP_076433	Q9HCS2	CP4FC_HUMAN	cytochrome P450, family 4, subfamily F, polypeptide 12	76			N -> D (in dbSNP:rs609636). {ECO:0000269|PubMed:11162607, ECO:0000269|PubMed:11162645, ECO:0000269|PubMed:12975309, ECO:0000269|PubMed:16303743, ECO:0000269|PubMed:17974005, ECO:0000269|Ref.7}.		arachidonic acid metabolic process (GO:0019369)|drug metabolic process (GO:0017144)|epoxygenase P450 pathway (GO:0019373)|leukotriene B4 catabolic process (GO:0036101)|long-chain fatty acid metabolic process (GO:0001676)|negative regulation of blood coagulation (GO:0030195)|oxidation-reduction process (GO:0055114)|pressure natriuresis (GO:0003095)|renal water homeostasis (GO:0003091)|small molecule metabolic process (GO:0044281)|sodium ion homeostasis (GO:0055078)|very long-chain fatty acid metabolic process (GO:0000038)|vitamin E metabolic process (GO:0042360)|vitamin K biosynthetic process (GO:0042371)|xenobiotic metabolic process (GO:0006805)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)	alkane 1-monooxygenase activity (GO:0018685)|arachidonic acid epoxygenase activity (GO:0008392)|aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|leukotriene-B4 20-monooxygenase activity (GO:0050051)|vitamin-K-epoxide reductase (warfarin-sensitive) activity (GO:0047057)			NS(1)|central_nervous_system(3)|endometrium(4)|kidney(2)|large_intestine(7)|lung(12)|ovary(3)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	41	Acute lymphoblastic leukemia(2;0.0367)				Fingolimod(DB08868)	GGGCTTGAAGAACTCGACCCA	0.517													.|||	4106	0.819888	0.7194	0.8818	5008	,	,		1740	0.9692		0.8221	False		,,,				2504	0.7556				p.N76D		Atlas-SNP	.											.	CYP4F12	89	.	0			c.A226G						PASS	.	G	ASP/ASN	3871,399		1755,361,19	140.0	141.0	141.0		226	-5.8	0.0	19	dbSNP_83	141	7913,583		3683,547,18	yes	missense	CYP4F12	NM_023944.3	23	5438,908,37	GG,GA,AA		6.8621,9.3443,7.6923	benign	76/525	15789098	11784,982	2135	4248	6383	SO:0001583	missense	66002	exon3			TTGAAGAACTCGA	AB035130	CCDS42517.1	19p13.1	2008-02-05	2003-01-14		ENSG00000186204	ENSG00000186204		"""Cytochrome P450s"""	18857	protein-coding gene	gene with protein product		611485	"""cytochrome P450, subfamily IVF, polypeptide 12"""			11162607	Standard	NM_023944		Approved		uc002nbl.3	Q9HCS2	OTTHUMG00000164477	ENST00000550308.1:c.226A>G	19.37:g.15789098A>G	ENSP00000448998:p.Asn76Asp	Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	118	118	1	NM_023944	E7ET51|O60389|Q5JPJ7|Q9HCS1	Missense_Mutation	SNP	ENST00000550308.1	37	CCDS42517.1	2050	0.9386446886446886	430	0.8739837398373984	350	0.9668508287292817	572	1.0	698	0.920844327176781	.	0.417	-0.910357	0.02434	0.906557	0.931379	ENSG00000186204	ENST00000550308;ENST00000551607;ENST00000324632	D;D;D	0.87966	-2.32;-2.32;-2.32	2.92	-5.84	0.02318	.	1.176180	0.06490	N	0.734359	T	0.00012	0.0000	N	0.21240	0.645	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.09377	0.001;0.004	T	0.25502	-1.0130	9	0.34782	T	0.22	.	6.2748	0.20975	0.2792:0.3463:0.3744:0.0	rs609636;rs17857062;rs52793471;rs60874827;rs609636	76;76	B4E2R2;Q9HCS2	.;CP4FC_HUMAN	D	76;29;76	ENSP00000448998:N76D;ENSP00000447922:N29D;ENSP00000321821:N76D	ENSP00000321821:N76D	N	+	1	0	CYP4F12	15650098	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-1.661000	0.01972	-2.298000	0.00660	-0.489000	0.04712	AAC	A|0.063;G|0.937	0.937	strong		0.517	CYP4F12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378938.9		
PEMT	10400	hgsc.bcm.edu	37	17	17415893	17415893	+	Silent	SNP	C	C	T	rs35277795	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:17415893C>T	ENST00000395783.1	-	4	464	c.285G>A	c.(283-285)gcG>gcA	p.A95A	PEMT_ENST00000395782.1_Silent_p.A95A|PEMT_ENST00000395781.2_Silent_p.A132A|PEMT_ENST00000435340.2_Silent_p.A110A|PEMT_ENST00000484838.2_5'UTR|PEMT_ENST00000255389.5_Silent_p.A132A	NM_007169.2	NP_009100.2	Q9UBM1	PEMT_HUMAN	phosphatidylethanolamine N-methyltransferase	95					cell proliferation (GO:0008283)|glycerophospholipid biosynthetic process (GO:0046474)|lipid metabolic process (GO:0006629)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	phosphatidyl-N-dimethylethanolamine N-methyltransferase activity (GO:0080101)|phosphatidyl-N-methylethanolamine N-methyltransferase activity (GO:0000773)|phosphatidylethanolamine N-methyltransferase activity (GO:0004608)			endometrium(1)|kidney(1)|large_intestine(2)|prostate(3)	7				Colorectal(2;0.0157)|READ - Rectum adenocarcinoma(2;0.0891)		GTCCCAGGAGCGCGAGGCCCA	0.657													C|||	161	0.0321486	0.0023	0.0375	5008	,	,		18395	0.006		0.0606	False		,,,				2504	0.0665				p.A132A		Atlas-SNP	.											.	PEMT	12	.	0			c.G396A						PASS	.	C	,,	69,4337	57.4+/-93.9	2,65,2136	33.0	32.0	32.0		285,396,285	-5.2	0.0	17	dbSNP_126	32	647,7953	159.4+/-212.7	26,595,3679	no	coding-synonymous,coding-synonymous,coding-synonymous	PEMT	NM_007169.2,NM_148172.1,NM_148173.1	,,	28,660,5815	TT,TC,CC		7.5233,1.566,5.5052	,,	95/200,132/237,95/200	17415893	716,12290	2203	4300	6503	SO:0001819	synonymous_variant	10400	exon4			CAGGAGCGCGAGG	AF176806	CCDS11186.1, CCDS11187.1, CCDS58520.1	17p11.2	2008-02-05			ENSG00000133027	ENSG00000133027	2.1.1.17		8830	protein-coding gene	gene with protein product		602391				9989271, 17881348	Standard	NM_148173		Approved	PEMPT, PEMT2	uc002grl.4	Q9UBM1	OTTHUMG00000059290	ENST00000395783.1:c.285G>A	17.37:g.17415893C>T		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	119	52	0.436975	NM_001267552	A8MZ66|B4DY41|D3DXC3|Q6IAQ5|Q86VL3|Q9BW86|Q9UHY6|Q9Y6V9	Silent	SNP	ENST00000395783.1	37	CCDS11187.1																																																																																			C|0.953;T|0.047	0.047	strong		0.657	PEMT-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131657.1	NM_007169	
AAK1	22848	hgsc.bcm.edu	37	2	69741801	69741801	+	Silent	SNP	C	C	T	rs6757825	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:69741801C>T	ENST00000409085.4	-	13	1954	c.1578G>A	c.(1576-1578)caG>caA	p.Q526Q	AAK1_ENST00000406297.3_Silent_p.Q526Q|AAK1_ENST00000409068.1_Silent_p.Q526Q|RN7SL604P_ENST00000492589.2_RNA	NM_014911.3	NP_055726	Q2M2I8	AAK1_HUMAN	AP2 associated kinase 1	526	Gln-rich.				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						TCTGCATTAGCTGCTGTTGAG	0.517													C|||	691	0.137979	0.1452	0.0994	5008	,	,		19233	0.0744		0.1869	False		,,,				2504	0.1708				p.Q526Q		Atlas-SNP	.											.	AAK1	121	.	0			c.G1578A						PASS	.	C		584,3802		46,492,1655	50.0	51.0	51.0		1578	3.6	1.0	2	dbSNP_116	51	1384,7216		115,1154,3031	no	coding-synonymous	AAK1	NM_014911.3		161,1646,4686	TT,TC,CC		16.093,13.3151,15.1548		526/962	69741801	1968,11018	2193	4300	6493	SO:0001819	synonymous_variant	22848	exon13			CATTAGCTGCTGT	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.1578G>A	2.37:g.69741801C>T		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	79	42	0.531646	NM_014911	Q4ZFZ3|Q53RX6|Q9UPV4	Silent	SNP	ENST00000409085.4	37	CCDS1893.2																																																																																			C|0.864;T|0.136	0.136	strong		0.517	AAK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251847.4	NM_014911	
MUC4	4585	hgsc.bcm.edu	37	3	195507365	195507365	+	Missense_Mutation	SNP	G	G	A	rs75737861	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195507365G>A	ENST00000463781.3	-	2	11545	c.11086C>T	c.(11086-11088)Cct>Tct	p.P3696S	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.P3696S	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		ACAGGAAGAGGGGTGGCCTGA	0.577													.|||	193	0.0385383	0.0613	0.0231	5008	,	,		9654	0.0317		0.0219	False		,,,				2504	0.0429				p.P3696S		Atlas-SNP	.											.	MUC4	1505	.	0			c.C11086T						PASS	.						33.0	31.0	32.0					3																	195507365		647	1587	2234	SO:0001583	missense	4585	exon2			GAAGAGGGGTGGC	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.11086C>T	3.37:g.195507365G>A	ENSP00000417498:p.Pro3696Ser	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	60	44	0.733333	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	1012	0.4633699633699634	233	0.4735772357723577	150	0.4143646408839779	281	0.49125874125874125	348	0.45910290237467016	g	5.502	0.277530	0.10403	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.57436	1.28;0.4	.	.	.	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.09022	0.002	B	0.01281	0.0	T	0.47509	-0.9112	6	.	.	.	.	2.6493	0.04994	0.4962:0.0:0.5038:0.0	.	3568	E7ESK3	.	S	3696	ENSP00000417498:P3696S;ENSP00000420243:P3696S	.	P	-	1	0	MUC4	196992144	0.000000	0.05858	0.032000	0.17829	0.032000	0.12392	-2.110000	0.01334	0.064000	0.16427	0.064000	0.15345	CCT	G|0.537;A|0.463	0.463	strong		0.577	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
MDN1	23195	hgsc.bcm.edu	37	6	90408589	90408589	+	Silent	SNP	A	A	G	rs3736984	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	68	0	0		WXS	Illumina HiSeq	Phase_I	69	32	0.463768	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		
PER3	8863	hgsc.bcm.edu	37	1	7890053	7890053	+	Missense_Mutation	SNP	G	G	A	rs1776342	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:7890053G>A	ENST00000361923.2	+	18	3194	c.3019G>A	c.(3019-3021)Gct>Act	p.A1007T	RP3-467L1.4_ENST00000451646.1_RNA|PER3_ENST00000377532.3_Missense_Mutation_p.A1016T	NM_016831.1	NP_058515.1	P56645	PER3_HUMAN	period circadian clock 3	1007	5 X 18 AA tandem repeats of S-[HP]-[AP]- T-[AT]-[GST]-[ATV]-L-S-[MT]-G-[LS]-P-P- [MRS]-[EKR]-[NST]-P.|Ser-rich.		A -> T (in dbSNP:rs1776342).|Missing (associated with eveningness and better cognitive performance during sleep deprivation exepriments; dbSNP:rs57875989).		circadian regulation of gene expression (GO:0032922)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of circadian sleep/wake cycle, sleep (GO:0045187)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	signal transducer activity (GO:0004871)	p.A1007T(1)		breast(4)|central_nervous_system(3)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(9)|lung(8)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	39	Ovarian(185;0.0634)|all_lung(157;0.178)	all_epithelial(116;9.35e-21)|all_lung(118;7.57e-07)|Lung NSC(185;4.52e-06)|Renal(390;0.000147)|Breast(487;0.00086)|Colorectal(325;0.000959)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0234)|all cancers(8;8.58e-70)|GBM - Glioblastoma multiforme(8;1.81e-35)|Colorectal(212;2.06e-07)|COAD - Colon adenocarcinoma(227;1.92e-05)|Kidney(185;7.18e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000472)|STAD - Stomach adenocarcinoma(132;0.00118)|KIRC - Kidney renal clear cell carcinoma(229;0.00122)|READ - Rectum adenocarcinoma(331;0.0649)		TACTGCCAGCGCTCTGTCCAC	0.587																																					p.A1007T		Atlas-SNP	.											PER3,NS,carcinoma,0,1	PER3	95	1	1	Substitution - Missense(1)	kidney(1)	c.G3019A						scavenged	.						87.0	69.0	75.0					1																	7890053		1995	3902	5897	SO:0001583	missense	8863	exon18			GCCAGCGCTCTGT	BC026102	CCDS89.1, CCDS72695.1	1p36.23	2012-12-13	2012-12-13		ENSG00000049246	ENSG00000049246			8847	protein-coding gene	gene with protein product		603427	"""period (Drosophila) homolog 3"", ""period homolog 3 (Drosophila)"""			9427249	Standard	XM_005263520		Approved		uc001aoo.3	P56645	OTTHUMG00000001216	ENST00000361923.2:c.3019G>A	1.37:g.7890053G>A	ENSP00000355031:p.Ala1007Thr	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	60	12	0.2	NM_016831	Q5H8X4|Q5H8X5|Q969K6|Q96S77|Q96S78|Q9C0J3|Q9NSP9|Q9UGU8	Missense_Mutation	SNP	ENST00000361923.2	37	CCDS89.1	.	.	.	.	.	.	.	.	.	.	g	0.668	-0.803078	0.02841	.	.	ENSG00000049246	ENST00000377532;ENST00000361923	T;T	0.14391	2.51;2.51	0.119	0.119	0.14685	Period circadian-like, C-terminal (1);	9.368370	0.00166	N	0.000019	T	0.09158	0.0226	N	0.20685	0.6	0.09310	N	1	B;B;B;B;B	0.25048	0.025;0.007;0.066;0.117;0.007	B;B;B;B;B	0.23018	0.002;0.004;0.004;0.043;0.004	T	0.25676	-1.0125	9	0.18710	T	0.47	.	.	.	.	rs1776342	56;1007;1016;1016;1007	B4DR65;A2I2N5;A6H8X0;P56645-2;P56645	.;.;.;.;PER3_HUMAN	T	1016;1007	ENSP00000366755:A1016T;ENSP00000355031:A1007T	ENSP00000355031:A1007T	A	+	1	0	PER3	7812640	0.000000	0.05858	0.068000	0.19968	0.074000	0.17049	-0.849000	0.04322	0.275000	0.22094	0.280000	0.19369	GCT	G|0.990;A|0.010	0.010	strong		0.587	PER3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000003607.1	NM_016831	
NCAPH	23397	hgsc.bcm.edu	37	2	97030247	97030247	+	Missense_Mutation	SNP	T	T	C	rs2305935	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:97030247T>C	ENST00000240423.4	+	13	1659	c.1616T>C	c.(1615-1617)gTa>gCa	p.V539A	NCAPH_ENST00000455200.1_Missense_Mutation_p.V528A|NCAPH_ENST00000427946.1_Missense_Mutation_p.V403A	NM_001281710.1|NM_001281711.1|NM_015341.3	NP_001268639.1|NP_001268640.1|NP_056156.2	Q15003	CND2_HUMAN	non-SMC condensin I complex, subunit H	539			V -> A (in dbSNP:rs2305935). {ECO:0000269|PubMed:15489334}.		mitotic cell cycle (GO:0000278)|mitotic chromosome condensation (GO:0007076)	condensin complex (GO:0000796)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)		p.V539A(1)		haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(1)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	28		Ovarian(717;0.0221)				GGCCATAGGGTAGAGACTGAG	0.398													C|||	1908	0.38099	0.2806	0.3184	5008	,	,		21877	0.2758		0.3221	False		,,,				2504	0.7301				p.V539A		Atlas-SNP	.											NCAPH,NS,carcinoma,0,1	NCAPH	67	1	1	Substitution - Missense(1)	stomach(1)	c.T1616C						PASS	.	C	ALA/VAL	1249,3157	704.7+/-407.2	179,891,1133	85.0	78.0	80.0		1616	4.2	0.0	2	dbSNP_100	80	2881,5719	672.7+/-403.0	508,1865,1927	yes	missense	NCAPH	NM_015341.3	64	687,2756,3060	CC,CT,TT		33.5,28.3477,31.7546	benign	539/742	97030247	4130,8876	2203	4300	6503	SO:0001583	missense	23397	exon13			ATAGGGTAGAGAC	BC024211	CCDS2021.1, CCDS62960.1	2q11.2	2008-02-05	2006-09-04	2006-09-04	ENSG00000121152	ENSG00000121152			1112	protein-coding gene	gene with protein product		602332	"""barren (Drosophila) homolog"", ""barren homolog (Drosophila)"", ""barren homolog 1 (Drosophila)"""	BRRN1		9417923	Standard	NM_015341		Approved	CAP-H, hCAP-H	uc002svz.1	Q15003	OTTHUMG00000130451	ENST00000240423.4:c.1616T>C	2.37:g.97030247T>C	ENSP00000240423:p.Val539Ala	Somatic	242	0	0		WXS	Illumina HiSeq	Phase_I	183	100	0.546448	NM_015341	B4E189|Q8TB87	Missense_Mutation	SNP	ENST00000240423.4	37	CCDS2021.1	633	0.28983516483516486	129	0.2621951219512195	113	0.31215469613259667	147	0.256993006993007	244	0.32189973614775724	C	0.833	-0.744640	0.03065	0.283477	0.335	ENSG00000121152	ENST00000240423;ENST00000427946;ENST00000435975;ENST00000455200	T;T;T;T	0.38722	1.12;1.12;1.12;1.12	5.03	4.16	0.48862	.	0.414407	0.26828	N	0.022283	T	0.00012	0.0000	N	0.01410	-0.885	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.38222	-0.9671	9	0.07990	T	0.79	-1.1494	9.5907	0.39543	0.0:0.8296:0.0:0.1704	rs2305935;rs17856718;rs56707886;rs2305935	528;539	E9PHA2;Q15003	.;CND2_HUMAN	A	539;403;528;528	ENSP00000240423:V539A;ENSP00000400774:V403A;ENSP00000405237:V528A;ENSP00000407308:V528A	ENSP00000240423:V539A	V	+	2	0	NCAPH	96393974	0.336000	0.24757	0.001000	0.08648	0.125000	0.20455	2.566000	0.45948	0.742000	0.32697	-0.733000	0.03571	GTA	T|0.688;C|0.312	0.312	strong		0.398	NCAPH-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252842.2	NM_015341	
FAM86C1	55199	hgsc.bcm.edu	37	11	71507157	71507157	+	Missense_Mutation	SNP	C	C	T	rs150702586	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:71507157C>T	ENST00000359244.4	+	4	379	c.356C>T	c.(355-357)aCa>aTa	p.T119I	FAM86C1_ENST00000346333.6_Missense_Mutation_p.T85I|FAM86C1_ENST00000426628.2_Missense_Mutation_p.T112I	NM_018172.2	NP_060642.2	Q9NVL1	FA86C_HUMAN	family with sequence similarity 86, member C1	119										lung(1)	1						CTCAATTCTACATGGCCCTTA	0.647													.|||	23	0.00459265	0.0023	0.0043	5008	,	,		17011	0.0089		0.006	False		,,,				2504	0.002				p.T119I		Atlas-SNP	.											.	FAM86C1	27	.	0			c.C356T						PASS	.						99.0	104.0	102.0					11																	71507157		2200	4293	6493	SO:0001583	missense	55199	exon4			ATTCTACATGGCC	AK130709	CCDS8202.1, CCDS41686.1, CCDS44664.1	11q13.4	2011-07-07	2011-07-07	2011-07-07	ENSG00000158483	ENSG00000158483			25561	protein-coding gene	gene with protein product			"""family with sequence similarity 86, member C"""	FAM86C		12477932	Standard	NM_152563		Approved	FLJ10661, FLJ27199	uc001oqv.4	Q9NVL1	OTTHUMG00000160552	ENST00000359244.4:c.356C>T	11.37:g.71507157C>T	ENSP00000352182:p.Thr119Ile	Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	185	37	0.2	NM_018172	Q8N5D3	Missense_Mutation	SNP	ENST00000359244.4	37	CCDS41686.1	.	.	.	.	.	.	.	.	.	.	.	7.719	0.696721	0.15106	.	.	ENSG00000158483	ENST00000346333;ENST00000359244;ENST00000426628;ENST00000528685	T;T;T;T	0.18502	2.24;2.52;2.24;2.21	1.49	-1.49	0.08718	.	.	.	.	.	T	0.05456	0.0144	N	0.08118	0	0.09310	N	0.999995	P;B;B	0.39809	0.689;0.103;0.061	B;B;B	0.28916	0.096;0.026;0.012	T	0.25537	-1.0129	9	0.72032	D	0.01	.	1.6998	0.02870	0.2939:0.3619:0.0:0.3442	.	112;85;119	G3V0F7;Q9NVL1-2;Q9NVL1	.;.;FA86C_HUMAN	I	85;119;112;85	ENSP00000325662:T85I;ENSP00000352182:T119I;ENSP00000391329:T112I;ENSP00000436598:T85I	ENSP00000325662:T85I	T	+	2	0	FAM86C1	71184805	0.014000	0.17966	0.007000	0.13788	0.001000	0.01503	-0.034000	0.12225	-0.442000	0.07190	-1.276000	0.01395	ACA	C|0.996;T|0.005	0.005	strong		0.647	FAM86C1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000361120.1	NM_152563	
AGXT2	64902	hgsc.bcm.edu	37	5	34998877	34998877	+	Missense_Mutation	SNP	C	C	A	rs16899974	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:34998877C>A	ENST00000231420.6	-	14	1692	c.1492G>T	c.(1492-1494)Gta>Tta	p.V498L		NM_031900.3	NP_114106.1	Q9BYV1	AGT2_HUMAN	alanine--glyoxylate aminotransferase 2	498			V -> L (in dbSNP:rs16899974). {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)	AATACTTCTACTGCAAAATCA	0.373													C|||	1180	0.235623	0.0461	0.2608	5008	,	,		21622	0.4216		0.2266	False		,,,				2504	0.2914				p.V498L		Atlas-SNP	.											.	AGXT2	89	.	0			c.G1492T						PASS	.	C	LEU/VAL	333,4073	175.1+/-204.6	9,315,1879	203.0	182.0	189.0		1492	3.8	1.0	5	dbSNP_123	189	1972,6628	346.5+/-326.2	219,1534,2547	yes	missense	AGXT2	NM_031900.3	32	228,1849,4426	AA,AC,CC		22.9302,7.5579,17.7226	benign	498/515	34998877	2305,10701	2203	4300	6503	SO:0001583	missense	64902	exon14			CTTCTACTGCAAA	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.1492G>T	5.37:g.34998877C>A	ENSP00000231420:p.Val498Leu	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	110	42	0.381818	NM_031900	B7ZM47|E9PDL7|Q53FB4|Q53FY7|Q53G03|Q5W7Q1	Missense_Mutation	SNP	ENST00000231420.6	37	CCDS3908.1	519	0.23763736263736263	20	0.04065040650406504	93	0.2569060773480663	240	0.4195804195804196	166	0.21899736147757257	C	9.105	1.005038	0.19199	0.075579	0.229302	ENSG00000113492	ENST00000231420	T	0.17691	2.26	5.69	3.85	0.44370	Pyridoxal phosphate-dependent transferase, major region, subdomain 2 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.481828	0.23060	N	0.052393	T	0.00012	0.0000	L	0.43152	1.355	0.42398	P	0.007441000000000031	B;B	0.23591	0.088;0.002	B;B	0.22753	0.041;0.006	T	0.46816	-0.9164	9	0.16420	T	0.52	-17.7656	10.6159	0.45449	0.1359:0.7889:0.0:0.0753	rs16899974;rs52832203;rs60642487;rs16899974	423;498	E9PDL7;Q9BYV1	.;AGT2_HUMAN	L	498	ENSP00000231420:V498L	ENSP00000231420:V498L	V	-	1	0	AGXT2	35034634	0.992000	0.36948	0.981000	0.43875	0.050000	0.14768	1.044000	0.30329	0.313000	0.23062	-0.813000	0.03139	GTA	C|0.795;A|0.205	0.205	strong		0.373	AGXT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207574.2	NM_031900	
SERPINB9	5272	hgsc.bcm.edu	37	6	2892130	2892130	+	Silent	SNP	G	G	A	rs61748573	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:2892130G>A	ENST00000380698.4	-	6	749	c.660C>T	c.(658-660)ccC>ccT	p.P220P		NM_004155.5	NP_004146.1	P50453	SPB9_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 9	220					cellular response to estrogen stimulus (GO:0071391)|immune response (GO:0006955)|mast cell mediated immunity (GO:0002448)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|protease binding (GO:0002020)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|endometrium(4)|large_intestine(3)|lung(5)|pancreas(1)|prostate(1)	15	Ovarian(93;0.0412)	all_hematologic(90;0.108)				TCCTGGCGTAGGGCAGCTCCA	0.657													G|||	66	0.0131789	0.0106	0.0144	5008	,	,		14420	0.0		0.0388	False		,,,				2504	0.0031				p.P220P		Atlas-SNP	.											.	SERPINB9	37	.	0			c.C660T						PASS	.	G		59,4347	54.9+/-90.9	1,57,2145	59.0	60.0	59.0		660	-0.3	0.9	6	dbSNP_129	59	239,8361	92.8+/-154.8	6,227,4067	no	coding-synonymous	SERPINB9	NM_004155.4		7,284,6212	AA,AG,GG		2.7791,1.3391,2.2913		220/377	2892130	298,12708	2203	4300	6503	SO:0001819	synonymous_variant	5272	exon6			GGCGTAGGGCAGC	L40378	CCDS4478.1	6p25.2	2014-02-18	2005-08-18		ENSG00000170542	ENSG00000170542		"""Serine (or cysteine) peptidase inhibitors"""	8955	protein-coding gene	gene with protein product		601799	"""serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 9"""	PI9		8530382, 9858835, 24172014	Standard	NM_004155		Approved	CAP3	uc003mug.4	P50453	OTTHUMG00000014131	ENST00000380698.4:c.660C>T	6.37:g.2892130G>A		Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	51	18	0.352941	NM_004155	B2RBW3|Q5TD03	Silent	SNP	ENST00000380698.4	37	CCDS4478.1																																																																																			G|0.976;A|0.024	0.024	strong		0.657	SERPINB9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039656.1		
MUC4	4585	hgsc.bcm.edu	37	3	195513413	195513413	+	Missense_Mutation	SNP	G	G	A	rs7374593		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195513413G>A	ENST00000463781.3	-	2	5497	c.5038C>T	c.(5038-5040)Cct>Tct	p.P1680S	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.P1680S	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.P1680S(4)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		ACAGGAAGAGGGGTGGCGTGA	0.612																																					p.P1680S		Atlas-SNP	.											MUC4_ENST00000463781,trunk,malignant_melanoma,0,4	MUC4	1505	4	4	Substitution - Missense(4)	skin(4)	c.C5038T						PASS	.						38.0	36.0	37.0					3																	195513413		690	1583	2273	SO:0001583	missense	4585	exon2			GAAGAGGGGTGGC	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.5038C>T	3.37:g.195513413G>A	ENSP00000417498:p.Pro1680Ser	Somatic	220	0	0		WXS	Illumina HiSeq	Phase_I	174	16	0.091954	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	-	7.096	0.573075	0.13623	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.29397	1.57;1.57	0.423	0.423	0.16463	.	.	.	.	.	T	0.13586	0.0329	N	0.19112	0.55	0.09310	N	1	P	0.36222	0.544	B	0.28849	0.095	T	0.15925	-1.0420	8	.	.	.	.	3.4645	0.07545	1.0E-4:1.0E-4:0.553:0.4469	.	1680	E7ESK3	.	S	1680	ENSP00000417498:P1680S;ENSP00000420243:P1680S	.	P	-	1	0	MUC4	196997808	0.000000	0.05858	0.156000	0.22583	0.031000	0.12232	-2.038000	0.01419	0.494000	0.27859	0.089000	0.15464	CCT	.	.	weak		0.612	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
DDX55	57696	hgsc.bcm.edu	37	12	124104686	124104686	+	Silent	SNP	G	G	A	rs3204541	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:124104686G>A	ENST00000238146.4	+	14	1852	c.1802G>A	c.(1801-1803)tGa>tAa	p.*601*	DDX55_ENST00000538744.1_Silent_p.*570*|DDX55_ENST00000421670.3_Silent_p.*208*	NM_020936.1	NP_065987.1	Q8NHQ9	DDX55_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 55	0						membrane (GO:0016020)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)			autonomic_ganglia(1)|breast(1)|endometrium(1)|large_intestine(3)|liver(1)|lung(4)|ovary(1)|prostate(1)|skin(1)	14	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000142)|Epithelial(86;0.000637)|all cancers(50;0.00772)		GATGACTGCTGATTCCAGTGC	0.418													G|||	1263	0.252196	0.4463	0.2205	5008	,	,		19827	0.0159		0.2654	False		,,,				2504	0.2423				p.X601X		Atlas-SNP	.											.	DDX55	51	.	0			c.G1802A						PASS	.	G		1828,2578	531.5+/-373.2	384,1060,759	75.0	75.0	75.0		1802	5.5	1.0	12	dbSNP_105	75	2376,6224	393.5+/-344.4	341,1694,2265	no	coding-synonymous	DDX55	NM_020936.1		725,2754,3024	AA,AG,GG		27.6279,41.4889,32.3235		601/601	124104686	4204,8802	2203	4300	6503	SO:0001819	synonymous_variant	57696	exon14			ACTGCTGATTCCA	AB046815	CCDS9251.1	12q24.31	2003-06-13			ENSG00000111364	ENSG00000111364		"""DEAD-boxes"""	20085	protein-coding gene	gene with protein product						10997877	Standard	NM_020936		Approved	KIAA1595	uc001ufi.3	Q8NHQ9	OTTHUMG00000168695	ENST00000238146.4:c.1802G>A	12.37:g.124104686G>A		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	114	113	0.991228	NM_020936	Q658L6|Q8IYH0|Q9HCH7	Silent	SNP	ENST00000238146.4	37	CCDS9251.1																																																																																			G|0.707;A|0.293	0.293	strong		0.418	DDX55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400616.2		
RABL6	55684	hgsc.bcm.edu	37	9	139732331	139732331	+	Missense_Mutation	SNP	G	G	C	rs2811741	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:139732331G>C	ENST00000311502.7	+	10	1380	c.1144G>C	c.(1144-1146)Gag>Cag	p.E382Q	RABL6_ENST00000371675.3_Missense_Mutation_p.E267Q|RABL6_ENST00000357466.2_Intron|RABL6_ENST00000432842.2_Missense_Mutation_p.E344Q|RABL6_ENST00000371663.4_Missense_Mutation_p.E383Q			Q3YEC7	RABL6_HUMAN	RAB, member RAS oncogene family-like 6	382	Pro-rich.		E -> Q (in dbSNP:rs2811741). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:16582619, ECO:0000269|Ref.5}.		small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	GTP binding (GO:0005525)										CCCGGCCGCAGAGGGCCCAGC	0.642													G|||	4034	0.805511	0.8079	0.7104	5008	,	,		14169	0.8681		0.8171	False		,,,				2504	0.7935				p.E383Q		Atlas-SNP	.											C9orf86_ENST00000371663,NS,carcinoma,0,2	.	.	2	0			c.G1147C						scavenged	.	G	GLN/GLU,GLN/GLU	3158,666		1295,568,49	20.0	23.0	22.0		1147,1144	4.3	0.2	9	dbSNP_100	22	6564,1434		2688,1188,123	yes	missense,missense	C9orf86	NM_001173988.1,NM_024718.4	29,29	3983,1756,172	CC,CG,GG		17.9295,17.4163,17.7635	probably-damaging,probably-damaging	383/731,382/730	139732331	9722,2100	1912	3999	5911	SO:0001583	missense	55684	exon10			GCCGCAGAGGGCC	AK094382	CCDS48058.1, CCDS55352.1, CCDS55353.1	9q34.3	2012-06-28	2012-06-28	2012-06-28	ENSG00000196642	ENSG00000196642			24703	protein-coding gene	gene with protein product	"""Rab-like protein 1"", ""partner of ARF"""	610615	"""chromosome 9 open reading frame 86"""	C9orf86		14702039, 16582619, 17962191, 19433581	Standard	NM_024718		Approved	FLJ10101, FLJ13045, pp8875, bA216L13.9, Parf, RBEL1	uc004cjj.1	Q3YEC7	OTTHUMG00000020947	ENST00000311502.7:c.1144G>C	9.37:g.139732331G>C	ENSP00000311134:p.Glu382Gln	Somatic	288	2	0.00694444		WXS	Illumina HiSeq	Phase_I	293	162	0.552901	NM_001173988	A8QVZ7|A8QVZ8|C6K8I4|C6K8I5|Q4F968|Q5T5R7|Q8IWK1|Q8TCL4|Q8WU94|Q96SR8|Q9BU21|Q9H935	Missense_Mutation	SNP	ENST00000311502.7	37	CCDS48058.1	1766	0.8086080586080586	383	0.7784552845528455	266	0.7348066298342542	494	0.8636363636363636	623	0.8218997361477572	.	15.54	2.865124	0.51482	0.825837	0.820705	ENSG00000196642	ENST00000371663;ENST00000311502;ENST00000432842;ENST00000371675;ENST00000435930	T;T;T;T;T	0.66099	-0.15;-0.15;0.86;-0.15;-0.19	4.29	4.29	0.51040	.	0.727918	0.12514	N	0.462204	T	0.00012	0.0000	M	0.63428	1.95	0.80722	P	0.0	D;D;D	0.76494	0.999;0.998;0.996	D;D;P	0.67382	0.943;0.951;0.895	T	0.21314	-1.0249	9	0.30854	T	0.27	-26.66	15.766	0.78126	0.0:0.0:1.0:0.0	rs2811741;rs3739953	176;383;382	B1AMX5;Q3YEC7-2;Q3YEC7	.;.;PARF_HUMAN	Q	383;382;344;267;176	ENSP00000360727:E383Q;ENSP00000311134:E382Q;ENSP00000414081:E344Q;ENSP00000360740:E267Q;ENSP00000408442:E176Q	ENSP00000311134:E382Q	E	+	1	0	C9orf86	138852152	1.000000	0.71417	0.192000	0.23308	0.005000	0.04900	3.689000	0.54706	1.950000	0.56595	0.313000	0.20887	GAG	G|0.193;C|0.807	0.807	strong		0.642	RABL6-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000055141.4	NM_024718	
OR8U1	219417	hgsc.bcm.edu	37	11	56143592	56143592	+	Missense_Mutation	SNP	C	C	T	rs17150411	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:56143592C>T	ENST00000302270.1	+	1	493	c.493C>T	c.(493-495)Cgc>Tgc	p.R165C		NM_001005204.1	NP_001005204.1	Q8NH10	OR8U1_HUMAN	olfactory receptor, family 8, subfamily U, member 1	165			R -> C (in dbSNP:rs17150411).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(1)|lung(23)|ovary(4)|skin(1)|stomach(1)	39	Esophageal squamous(21;0.00448)					CCTCACCTTCCGCCTCTCCTA	0.448																																					p.R165C		Atlas-SNP	.											OR8U1,colon,carcinoma,0,1	OR8U1	59	1	0			c.C493T						scavenged	.						217.0	209.0	211.0					11																	56143592		2105	4224	6329	SO:0001583	missense	219417	exon1			ACCTTCCGCCTCT	AB065603	CCDS41647.1	11q11	2012-08-09			ENSG00000172199	ENSG00000172199		"""GPCR / Class A : Olfactory receptors"""	19611	protein-coding gene	gene with protein product							Standard	NM_001005204		Approved			Q8NH10	OTTHUMG00000166860	ENST00000302270.1:c.493C>T	11.37:g.56143592C>T	ENSP00000304188:p.Arg165Cys	Somatic	239	2	0.0083682		WXS	Illumina HiSeq	Phase_I	170	19	0.111765	NM_001005204		Missense_Mutation	SNP	ENST00000302270.1	37	CCDS41647.1	696	0.31868131868131866	77	0.1565040650406504	152	0.4198895027624309	244	0.42657342657342656	223	0.2941952506596306	C	4.583	0.108223	0.08780	.	.	ENSG00000172199	ENST00000302270	T	0.00188	8.59	5.78	2.79	0.32731	GPCR, rhodopsin-like superfamily (1);	0.274133	0.26467	N	0.024205	T	0.00012	0.0000	L	0.41492	1.28	0.80722	P	0.0	B	0.18741	0.03	B	0.18561	0.022	T	0.13548	-1.0505	9	0.62326	D	0.03	.	7.7725	0.29017	0.1327:0.7267:0.0:0.1406	rs17150411;rs17150411	165	Q8NH10	OR8U1_HUMAN	C	165	ENSP00000304188:R165C	ENSP00000304188:R165C	R	+	1	0	OR8U1	55900168	0.000000	0.05858	0.590000	0.28732	0.002000	0.02628	-2.520000	0.00951	1.472000	0.48140	-0.135000	0.14842	CGC	C|0.653;N|0.000	.	strong		0.448	OR8U1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391607.1	NM_001005204	
OR10G9	219870	hgsc.bcm.edu	37	11	123894553	123894553	+	Silent	SNP	G	G	A	rs61908612	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:123894553G>A	ENST00000375024.1	+	1	834	c.834G>A	c.(832-834)ctG>ctA	p.L278L		NM_001001953.1	NP_001001953.1	Q8NGN4	O10G9_HUMAN	olfactory receptor, family 10, subfamily G, member 9	278						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(33)|prostate(2)|skin(4)|stomach(8)|urinary_tract(1)	61		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0399)		ACACTGTGCTGACACCCCTTC	0.478													G|||	199	0.0397364	0.0159	0.0447	5008	,	,		18729	0.0109		0.1004	False		,,,				2504	0.0358				p.L278L		Atlas-SNP	.											.	OR10G9	80	.	0			c.G834A						PASS	.	G		99,4303	79.9+/-118.3	1,97,2103	143.0	131.0	135.0		834	1.3	0.9	11	dbSNP_129	135	744,7854	179.0+/-228.3	37,670,3592	no	coding-synonymous	OR10G9	NM_001001953.1		38,767,5695	AA,AG,GG		8.6532,2.249,6.4846		278/312	123894553	843,12157	2201	4299	6500	SO:0001819	synonymous_variant	219870	exon1			TGTGCTGACACCC	AB065756	CCDS31703.1	11q24.1	2012-08-09			ENSG00000236981	ENSG00000236981		"""GPCR / Class A : Olfactory receptors"""	15129	protein-coding gene	gene with protein product				OR10G10P			Standard	NM_001001953		Approved		uc010sad.2	Q8NGN4	OTTHUMG00000165967	ENST00000375024.1:c.834G>A	11.37:g.123894553G>A		Somatic	166	1	0.0060241		WXS	Illumina HiSeq	Phase_I	156	115	0.737179	NM_001001953		Silent	SNP	ENST00000375024.1	37	CCDS31703.1																																																																																			G|0.941;A|0.059	0.059	strong		0.478	OR10G9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387269.1	NM_001001953	
DIS3L	115752	hgsc.bcm.edu	37	15	66625470	66625470	+	Silent	SNP	G	G	A	rs3759785	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:66625470G>A	ENST00000319212.4	+	17	3035	c.2985G>A	c.(2983-2985)gaG>gaA	p.E995E	DIS3L_ENST00000319194.5_Silent_p.E912E|RP11-352G18.2_ENST00000565993.1_RNA	NM_001143688.1	NP_001137160.1	Q8TF46	DI3L1_HUMAN	DIS3 like exosome 3'-5' exoribonuclease	995					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						TGAAGAGTGAGTTAGTGAAAG	0.368													G|||	150	0.0299521	0.0038	0.0749	5008	,	,		18740	0.0625		0.0258	False		,,,				2504	0.0041				p.E995E		Atlas-SNP	.											.	DIS3L	175	.	0			c.G2985A						PASS	.	G	,	30,4372	34.3+/-65.2	1,28,2172	93.0	93.0	93.0		2985,2736	-11.6	0.0	15	dbSNP_107	93	169,8429	77.8+/-140.4	4,161,4134	no	coding-synonymous,coding-synonymous	DIS3L	NM_001143688.1,NM_133375.3	,	5,189,6306	AA,AG,GG		1.9656,0.6815,1.5308	,	995/1055,912/972	66625470	199,12801	2201	4299	6500	SO:0001819	synonymous_variant	115752	exon17			GAGTGAGTTAGTG		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.2985G>A	15.37:g.66625470G>A		Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	51	28	0.54902	NM_001143688	Q8N1N8|Q8WTU9|Q96CM7	Silent	SNP	ENST00000319212.4	37	CCDS45286.1																																																																																			G|0.973;A|0.027	0.027	strong		0.368	DIS3L-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382792.2	NM_133375	
CLCN7	1186	hgsc.bcm.edu	37	16	1500567	1500567	+	Silent	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:1500567C>T	ENST00000382745.4	-	17	2153	c.1548G>A	c.(1546-1548)ccG>ccA	p.P516P	LA16c-390E6.4_ENST00000563610.1_RNA|CLCN7_ENST00000262318.8_Silent_p.P492P|CLCN7_ENST00000448525.1_Silent_p.P492P	NM_001287.5	NP_001278.1	P51798	CLCN7_HUMAN	chloride channel, voltage-sensitive 7	516					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)				TGAGCAGGGACGGGATGAAGA	0.687																																					p.P516P		Atlas-SNP	.											.	CLCN7	53	.	0			c.G1548A						PASS	.						38.0	42.0	41.0					16																	1500567		2181	4298	6479	SO:0001819	synonymous_variant	1186	exon17			CAGGGACGGGATG	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.1548G>A	16.37:g.1500567C>T		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	136	106	0.779412	NM_001287	A6NEJ7|A8K5T9|A8K7X1|B3KPN3|E9PDB9|Q9NYX5	Silent	SNP	ENST00000382745.4	37	CCDS32361.1																																																																																			.	.	none		0.687	CLCN7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103598.2	NM_001287	
DENND2C	163259	hgsc.bcm.edu	37	1	115168600	115168600	+	Missense_Mutation	SNP	A	A	T	rs7541738	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:115168600A>T	ENST00000393274.1	-	4	631	c.6T>A	c.(4-6)gaT>gaA	p.D2E	DENND2C_ENST00000393277.1_Missense_Mutation_p.D2E|DENND2C_ENST00000393276.3_Missense_Mutation_p.D2E|DENND2C_ENST00000481894.1_5'Flank	NM_001256404.1	NP_001243333.1	Q68D51	DEN2C_HUMAN	DENN/MADD domain containing 2C	2			D -> E (in dbSNP:rs7541738). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005}.		positive regulation of Rab GTPase activity (GO:0032851)		Rab guanyl-nucleotide exchange factor activity (GO:0017112)			NS(2)|breast(2)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(10)|pancreas(1)|skin(3)	37	all_epithelial(7;9.54e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;4.64e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)		AAAAACCAACATCCATGTTCC	0.363													A|||	572	0.114217	0.0182	0.1441	5008	,	,		18969	0.002		0.2863	False		,,,				2504	0.1616				p.D2E		Atlas-SNP	.											.	DENND2C	105	.	0			c.T6A						PASS	.	A	GLU/ASP	271,4135	145.0+/-179.8	16,239,1948	73.0	74.0	73.0		6	4.5	1.0	1	dbSNP_116	73	2373,6225	378.3+/-338.9	312,1749,2238	yes	missense	DENND2C	NM_198459.3	45	328,1988,4186	TT,TA,AA		27.5994,6.1507,20.3322	benign	2/872	115168600	2644,10360	2203	4299	6502	SO:0001583	missense	163259	exon4			ACCAACATCCATG		CCDS875.1, CCDS58018.1	1p13.2-p13.1	2012-10-03			ENSG00000175984	ENSG00000175984		"""DENN/MADD domain containing"""	24748	protein-coding gene	gene with protein product							Standard	NM_198459		Approved	FLJ37099, DKFZp686G0351, DKFZp779P1149, dJ1156J9.1, RP5-1156J9.1	uc001efd.1	Q68D51	OTTHUMG00000011893	ENST00000393274.1:c.6T>A	1.37:g.115168600A>T	ENSP00000376955:p.Asp2Glu	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	47	18	0.382979	NM_001256404	B1AL26|Q5TCX6|Q6P3R3	Missense_Mutation	SNP	ENST00000393274.1	37	CCDS58018.1	290	0.13278388278388278	8	0.016260162601626018	65	0.17955801104972377	0	0.0	217	0.2862796833773087	A	12.69	2.012818	0.35511	0.061507	0.275994	ENSG00000175984	ENST00000393276;ENST00000393274;ENST00000369540;ENST00000393277	T;T;T	0.09630	3.46;3.61;2.96	5.71	4.54	0.55810	.	0.439888	0.26556	N	0.023706	T	0.02807	0.0084	L	0.43152	1.355	0.31952	P	0.6095729999999999	B;B	0.23377	0.084;0.024	B;B	0.19148	0.024;0.016	T	0.34700	-0.9818	9	0.38643	T	0.18	.	1.8171	0.03102	0.5684:0.1674:0.1034:0.1607	rs7541738;rs17529624;rs52833856;rs7541738	2;2	Q68D51;Q68D51-3	DEN2C_HUMAN;.	E	2	ENSP00000376957:D2E;ENSP00000376955:D2E;ENSP00000376958:D2E	ENSP00000358553:D2E	D	-	3	2	DENND2C	114970123	0.277000	0.24220	1.000000	0.80357	0.998000	0.95712	0.645000	0.24782	2.187000	0.69744	0.524000	0.50904	GAT	A|0.824;T|0.176	0.176	strong		0.363	DENND2C-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000314822.1	NM_198459	
ADAMTS7	11173	hgsc.bcm.edu	37	15	79067055	79067055	+	Missense_Mutation	SNP	C	C	T	rs2277549	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:79067055C>T	ENST00000388820.4	-	12	1997	c.1787G>A	c.(1786-1788)cGc>cAc	p.R596H	ADAMTS7_ENST00000566303.1_Intron	NM_014272.3	NP_055087.2	Q9UKP4	ATS7_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 7	596	Cys-rich.				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						GAAGGAGGGGCGGCCAGCAGG	0.632													C|||	1262	0.251997	0.2005	0.2205	5008	,	,		21700	0.1825		0.3459	False		,,,				2504	0.319				p.R596H		Atlas-SNP	.											ADAMTS7,NS,carcinoma,-1,1	ADAMTS7	142	1	0			c.G1787A						PASS	.						47.0	53.0	51.0					15																	79067055		2196	4291	6487	SO:0001583	missense	11173	exon12			GAGGGGCGGCCAG	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.1787G>A	15.37:g.79067055C>T	ENSP00000373472:p.Arg596His	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	115	18	0.156522	NM_014272	Q14F51|Q6P7J9	Missense_Mutation	SNP	ENST00000388820.4	37	CCDS32303.1	596	0.27289377289377287	116	0.23577235772357724	97	0.26795580110497236	115	0.20104895104895104	268	0.35356200527704484	C	1.326	-0.598073	0.03744	.	.	ENSG00000136378	ENST00000388820	T	0.00438	7.42	3.3	-6.6	0.01824	.	1.548120	0.03595	N	0.232532	T	0.00012	0.0000	L	0.36672	1.1	0.80722	P	0.0	B;B	0.18461	0.003;0.028	B;B	0.09377	0.002;0.004	T	0.14090	-1.0485	9	0.36615	T	0.2	.	10.1071	0.42539	0.0:0.1661:0.1123:0.7216	rs2277549	596;596	A8MQ00;Q9UKP4	.;ATS7_HUMAN	H	596	ENSP00000373472:R596H	ENSP00000373472:R596H	R	-	2	0	ADAMTS7	76854110	0.000000	0.05858	0.007000	0.13788	0.727000	0.41649	-2.867000	0.00722	-1.837000	0.01189	-1.036000	0.02392	CGC	C|0.727;T|0.273	0.273	strong		0.632	ADAMTS7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421331.1	NM_014272	
NES	10763	hgsc.bcm.edu	37	1	156639753	156639753	+	Silent	SNP	G	G	A	rs11582300	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:156639753G>A	ENST00000368223.3	-	4	4359	c.4227C>T	c.(4225-4227)tcC>tcT	p.S1409S		NM_006617.1	NP_006608.1	P48681	NEST_HUMAN	nestin	1409	Tail.				brain development (GO:0007420)|cell projection morphogenesis (GO:0048858)|central nervous system development (GO:0007417)|embryonic camera-type eye development (GO:0031076)|G2/M transition of mitotic cell cycle (GO:0000086)|negative regulation of catalytic activity (GO:0043086)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of protein binding (GO:0032091)|positive regulation of intermediate filament depolymerization (GO:0030844)|positive regulation of neural precursor cell proliferation (GO:2000179)|stem cell proliferation (GO:0072089)	cytoplasm (GO:0005737)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)	intermediate filament binding (GO:0019215)|structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(30)|ovary(6)|prostate(1)|skin(3)|stomach(1)|urinary_tract(4)	64	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					CAAACCCATCGGACTCCCCAT	0.647													G|||	3097	0.618411	0.385	0.6787	5008	,	,		15954	0.8611		0.6312	False		,,,				2504	0.6278				p.S1409S		Atlas-SNP	.											.	NES	196	.	0			c.C4227T						PASS	.	G		1758,2648		355,1048,800	22.0	24.0	23.0		4227	0.8	1.0	1	dbSNP_120	23	5323,3269		1696,1931,669	no	coding-synonymous	NES	NM_006617.1		2051,2979,1469	AA,AG,GG		38.047,39.9001,45.5224		1409/1622	156639753	7081,5917	2203	4296	6499	SO:0001819	synonymous_variant	10763	exon4			CCCATCGGACTCC	X65964	CCDS1151.1	1q23	2013-01-16			ENSG00000132688	ENSG00000132688		"""Intermediate filaments type IV"""	7756	protein-coding gene	gene with protein product		600915				1478958, 9104587	Standard	NM_006617		Approved	FLJ21841	uc001fpq.3	P48681	OTTHUMG00000034299	ENST00000368223.3:c.4227C>T	1.37:g.156639753G>A		Somatic	235	0	0		WXS	Illumina HiSeq	Phase_I	200	101	0.505	NM_006617	O00552|Q3LIF5|Q5SYZ6	Silent	SNP	ENST00000368223.3	37	CCDS1151.1																																																																																			G|0.413;A|0.587	0.587	strong		0.647	NES-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000082844.2	NM_006617	
OR51A4	401666	hgsc.bcm.edu	37	11	4967834	4967834	+	Missense_Mutation	SNP	C	C	G	rs201205025	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:4967834C>G	ENST00000380373.2	-	1	522	c.497G>C	c.(496-498)aGa>aCa	p.R166T	MMP26_ENST00000477339.1_Intron|MMP26_ENST00000380390.1_Intron	NM_001005329.1	NP_001005329.1	Q8NGJ6	O51A4_HUMAN	olfactory receptor, family 51, subfamily A, member 4	166						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(15)|ovary(2)|skin(7)|stomach(1)|urinary_tract(1)	29		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)		TCTCAAGTTTCTTAAAGTGAA	0.413													.|||	12	0.00239617	0.003	0.0029	5008	,	,		24981	0.0		0.003	False		,,,				2504	0.0031				p.R166T		Atlas-SNP	.											OR51A4,colon,carcinoma,-1,1	OR51A4	73	1	0			c.G497C						scavenged	.						212.0	198.0	203.0					11																	4967834		2177	4245	6422	SO:0001583	missense	401666	exon1			AAGTTTCTTAAAG	AB065798	CCDS31367.1	11p15.4	2012-08-09			ENSG00000205497	ENSG00000205497		"""GPCR / Class A : Olfactory receptors"""	14795	protein-coding gene	gene with protein product							Standard	NM_001005329		Approved		uc010qys.2	Q8NGJ6	OTTHUMG00000066614	ENST00000380373.2:c.497G>C	11.37:g.4967834C>G	ENSP00000369731:p.Arg166Thr	Somatic	980	0	0		WXS	Illumina HiSeq	Phase_I	155	11	0.0709677	NM_001005329		Missense_Mutation	SNP	ENST00000380373.2	37	CCDS31367.1	.	.	.	.	.	.	.	.	.	.	C	9.411	1.080491	0.20309	.	.	ENSG00000205497	ENST00000380373	T	0.71817	-0.6	3.44	-3.66	0.04489	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.59046	0.2165	L	0.41027	1.25	0.09310	N	1	B	0.23249	0.082	B	0.27608	0.081	T	0.52041	-0.8628	9	0.66056	D	0.02	.	9.2359	0.37466	0.0:0.303:0.0:0.697	.	166	Q8NGJ6	O51A4_HUMAN	T	166	ENSP00000369731:R166T	ENSP00000369731:R166T	R	-	2	0	OR51A4	4924410	0.000000	0.05858	0.000000	0.03702	0.166000	0.22503	-0.905000	0.04075	-1.059000	0.03193	0.479000	0.44913	AGA	.	.	weak		0.413	OR51A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142821.1	NM_001005329	
PRX	57716	hgsc.bcm.edu	37	19	40904602	40904602	+	Silent	SNP	G	G	A	rs744389	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:40904602G>A	ENST00000324001.7	-	6	576	c.306C>T	c.(304-306)acC>acT	p.T102T	PRX_ENST00000291825.7_Silent_p.T102T	NM_181882.2	NP_870998.2	Q9BXM0	PRAX_HUMAN	periaxin	102					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)			CCAGGTCCCCGGTGGGCACAG	0.647													G|||	512	0.102236	0.0144	0.0821	5008	,	,		14022	0.0486		0.174	False		,,,				2504	0.2168				p.T102T		Atlas-SNP	.											.	PRX	151	.	0			c.C306T						PASS	.	G	,	193,4213	122.5+/-159.9	6,181,2016	48.0	44.0	45.0		306,306	4.1	1.0	19	dbSNP_86	45	1557,7043	289.8+/-299.5	131,1295,2874	no	coding-synonymous,coding-synonymous	PRX	NM_020956.2,NM_181882.2	,	137,1476,4890	AA,AG,GG		18.1047,4.3804,13.4553	,	102/148,102/1462	40904602	1750,11256	2203	4300	6503	SO:0001819	synonymous_variant	57716	exon6			GTCCCCGGTGGGC	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.306C>T	19.37:g.40904602G>A		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	113	64	0.566372	NM_181882	Q9BXL9|Q9HCF2	Silent	SNP	ENST00000324001.7	37	CCDS33028.1																																																																																			G|0.889;A|0.111	0.111	strong		0.647	PRX-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000462582.1	NM_020956	
OR1A2	26189	hgsc.bcm.edu	37	17	3101578	3101578	+	Missense_Mutation	SNP	G	G	T	rs2241091	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	175	1	0.00571429		WXS	Illumina HiSeq	Phase_I	151	148	0.980132	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	
CD3G	917	hgsc.bcm.edu	37	11	118219742	118219742	+	Splice_Site	SNP	G	G	A	rs146393315	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:118219742G>A	ENST00000532917.1	+	2	124	c.56G>A	c.(55-57)gGt>gAt	p.G19D	CD3G_ENST00000532903.1_3'UTR|CD3G_ENST00000392883.2_5'UTR	NM_000073.2	NP_000064.1	P09693	CD3G_HUMAN	CD3g molecule, gamma (CD3-TCR complex)	19					cell surface receptor signaling pathway (GO:0007166)|establishment or maintenance of cell polarity (GO:0007163)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|protein complex assembly (GO:0006461)|protein transport (GO:0015031)|regulation of immune response (GO:0050776)|regulation of lymphocyte apoptotic process (GO:0070228)|T cell activation (GO:0042110)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	alpha-beta T cell receptor complex (GO:0042105)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|T cell receptor complex (GO:0042101)	protein heterodimerization activity (GO:0046982)|receptor signaling complex scaffold activity (GO:0030159)|T cell receptor binding (GO:0042608)|transmembrane signaling receptor activity (GO:0004888)			breast(2)|kidney(1)|large_intestine(2)|skin(1)	6	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;3.04e-05)	Muromonab(DB00075)	GTCTTTACAGGTACTTTGGCC	0.413													G|||	2	0.000399361	0.0	0.0014	5008	,	,		21792	0.0		0.001	False		,,,				2504	0.0				p.G19D		Atlas-SNP	.											.	CD3G	31	.	0			c.G56A						PASS	.	G	ASP/GLY	0,4400		0,0,2200	183.0	172.0	176.0		56	4.5	0.7	11	dbSNP_134	176	11,8581	8.4+/-32.0	0,11,4285	yes	missense-near-splice	CD3G	NM_000073.2	94	0,11,6485	AA,AG,GG		0.128,0.0,0.0847	probably-damaging	19/183	118219742	11,12981	2200	4296	6496	SO:0001630	splice_region_variant	917	exon2			TTACAGGTACTTT	X60491	CCDS8395.1	11q23	2014-09-17	2006-03-28		ENSG00000160654	ENSG00000160654		"""CD molecules"""	1675	protein-coding gene	gene with protein product		186740	"""CD3g antigen, gamma polypeptide (TiT3 complex)"""				Standard	NM_000073		Approved		uc001psu.2	P09693	OTTHUMG00000166971	ENST00000532917.1:c.56-1G>A	11.37:g.118219742G>A		Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	192	43	0.223958	NM_000073	Q2HIZ6	Missense_Mutation	SNP	ENST00000532917.1	37	CCDS8395.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	G	18.08	3.543791	0.65198	0.0	0.00128	ENSG00000160654	ENST00000532917	T	0.59083	0.29	5.43	4.49	0.54785	.	0.356469	0.27327	N	0.019871	T	0.73644	0.3613	M	0.80183	2.485	0.80722	D	1	D	0.89917	1.0	D	0.79784	0.993	T	0.75077	-0.3445	9	.	.	.	.	9.1867	0.37174	0.1016:0.0:0.8984:0.0	.	19	P09693	CD3G_HUMAN	D	19	ENSP00000431445:G19D	.	G	+	2	0	CD3G	117724952	0.989000	0.36119	0.731000	0.30826	0.039000	0.13416	2.669000	0.46825	1.461000	0.47929	0.655000	0.94253	GGT	G|0.999;A|0.001	0.001	strong		0.413	CD3G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392135.1	NM_000073	Missense_Mutation
STARD8	9754	hgsc.bcm.edu	37	X	67937976	67937976	+	Missense_Mutation	SNP	G	G	A	rs55962426	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:67937976G>A	ENST00000252336.6	+	5	1352	c.980G>A	c.(979-981)cGg>cAg	p.R327Q	STARD8_ENST00000374599.3_Missense_Mutation_p.R407Q|STARD8_ENST00000374597.3_Missense_Mutation_p.R327Q	NM_014725.4	NP_055540.2	Q92502	STAR8_HUMAN	StAR-related lipid transfer (START) domain containing 8	327			R -> Q (in dbSNP:rs55962426).		regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell junction (GO:0030054)|cytosol (GO:0005829)	GTPase activator activity (GO:0005096)|lipid binding (GO:0008289)			NS(2)|breast(5)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(25)|ovary(3)|pancreas(1)|prostate(2)|skin(3)|urinary_tract(2)	50						CTGTGGTCTCGGGCCATGTAC	0.557													g|||	106	0.0280795	0.0008	0.0375	3775	,	,		13227	0.0		0.0726	False		,,,				2504	0.0061				p.R407Q		Atlas-SNP	.											.	STARD8	282	.	0			c.G1220A						PASS	.		GLN/ARG,GLN/ARG,GLN/ARG	71,3764		1,57,12,1574,559	51.0	45.0	47.0		1220,980,980	3.2	1.0	X	dbSNP_129	47	778,5950		38,489,213,1901,1659	yes	missense,missense,missense	STARD8	NM_001142503.2,NM_001142504.2,NM_014725.4	43,43,43	39,546,225,3475,2218	AA,AG,A,GG,G		11.5636,1.8514,8.0375	benign,benign,benign	407/1104,327/1024,327/1024	67937976	849,9714	2203	4300	6503	SO:0001583	missense	9754	exon6			GGTCTCGGGCCAT	D80011	CCDS14390.1, CCDS48134.1	Xq13.1	2011-09-13	2007-08-16		ENSG00000130052	ENSG00000130052		"""Rho GTPase activating proteins"", ""StAR-related lipid transfer (START) domain containing"""	19161	protein-coding gene	gene with protein product		300689	"""START domain containing 8"""			8724849	Standard	NM_001142504		Approved	KIAA0189, ARHGAP38	uc004dxb.3	Q92502	OTTHUMG00000021748	ENST00000252336.6:c.980G>A	X.37:g.67937976G>A	ENSP00000252336:p.Arg327Gln	Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	126	126	1	NM_001142503	A8K6T2|D3DVT9|Q5JST0|Q68DG7	Missense_Mutation	SNP	ENST00000252336.6	37	CCDS14390.1	69	0.04159132007233273	1	0.0020325203252032522	7	0.020114942528735632	0	0.0	45	0.06130790190735695	G	0.332	-0.955804	0.02267	0.018514	0.115636	ENSG00000130052	ENST00000252336;ENST00000374599;ENST00000374597	T;T;T	0.07021	3.23;3.23;3.23	4.4	3.25	0.37280	.	0.356436	0.27193	N	0.020481	T	0.00039	0.0001	N	0.00996	-1.065	0.53688	P	2.199999999996649E-5	B;B	0.10296	0.001;0.003	B;B	0.04013	0.001;0.001	T	0.38394	-0.9663	9	0.29301	T	0.29	.	5.0106	0.14310	0.7464:0.0:0.2536:0.0	rs55962426;rs61743102	407;327	Q92502-2;Q92502	.;STAR8_HUMAN	Q	327;407;327	ENSP00000252336:R327Q;ENSP00000363727:R407Q;ENSP00000363725:R327Q	ENSP00000252336:R327Q	R	+	2	0	STARD8	67854701	1.000000	0.71417	1.000000	0.80357	0.549000	0.35272	1.670000	0.37502	0.571000	0.29365	-0.340000	0.08031	CGG	G|0.938;A|0.062	0.062	strong		0.557	STARD8-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000057026.2	NM_014725	
CDH19	28513	hgsc.bcm.edu	37	18	64211251	64211251	+	Missense_Mutation	SNP	C	C	T	rs72954429	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:64211251C>T	ENST00000540086.1	-	7	1417	c.1171G>A	c.(1171-1173)Gtg>Atg	p.V391M	CDH19_ENST00000262150.2_Missense_Mutation_p.V391M	NM_001271028.1	NP_001257957.1	Q96JQ0	PCD16_HUMAN	cadherin 19, type 2	494	Cadherin 4. {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)				GCAGACACCACGCCTACAAAT	0.373													C|||	413	0.0824681	0.0053	0.1945	5008	,	,		15660	0.006		0.1491	False		,,,				2504	0.1176				p.V391M		Atlas-SNP	.											.	CDH19	141	.	0			c.G1171A						PASS	.	C	MET/VAL	159,4247	105.6+/-144.1	3,153,2047	49.0	49.0	49.0		1171	-3.3	0.0	18	dbSNP_130	49	1200,7400	242.5+/-272.5	84,1032,3184	yes	missense	CDH19	NM_021153.2	21	87,1185,5231	TT,TC,CC		13.9535,3.6087,10.449	benign	391/773	64211251	1359,11647	2203	4300	6503	SO:0001583	missense	28513	exon7			ACACCACGCCTAC	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	ENST00000540086.1:c.1171G>A	18.37:g.64211251C>T	ENSP00000439593:p.Val391Met	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	58	32	0.551724	NM_021153	O15098	Missense_Mutation	SNP	ENST00000540086.1	37	CCDS59325.1	187	0.08562271062271062	3	0.006097560975609756	64	0.17679558011049723	2	0.0034965034965034965	118	0.15567282321899736	C	8.876	0.950387	0.18431	0.036087	0.139535	ENSG00000071991	ENST00000262150;ENST00000540086;ENST00000454642	T;T	0.53206	0.63;0.63	5.62	-3.31	0.04988	Cadherin (3);Cadherin-like (1);	1.071720	0.07077	N	0.836414	T	0.00073	0.0002	N	0.05351	-0.065	0.80722	P	0.0	B;B	0.11235	0.003;0.004	B;B	0.13407	0.002;0.009	T	0.12016	-1.0564	9	0.49607	T	0.09	.	12.9706	0.58510	0.0:0.4921:0.0:0.5079	.	391;391	F5H1K0;Q9H159	.;CAD19_HUMAN	M	391;391;336	ENSP00000262150:V391M;ENSP00000439593:V391M	ENSP00000262150:V391M	V	-	1	0	CDH19	62362231	0.000000	0.05858	0.003000	0.11579	0.875000	0.50365	-1.158000	0.03153	-0.651000	0.05415	-0.300000	0.09419	GTG	C|0.896;T|0.104	0.104	strong		0.373	CDH19-005	PUTATIVE	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000442285.1	NM_021153	
TFB2M	64216	hgsc.bcm.edu	37	1	246707858	246707858	+	Silent	SNP	A	A	G	rs3129568	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:246707858A>G	ENST00000366514.4	-	7	1169	c.984T>C	c.(982-984)ttT>ttC	p.F328F		NM_022366.2	NP_071761.1	Q9H5Q4	TFB2M_HUMAN	transcription factor B2, mitochondrial	328					gene expression (GO:0010467)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from mitochondrial promoter (GO:0006390)|transcription initiation from mitochondrial promoter (GO:0006391)	mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)	poly(A) RNA binding (GO:0044822)|rRNA (adenine-N6,N6-)-dimethyltransferase activity (GO:0000179)|transcription cofactor activity (GO:0003712)			breast(1)|endometrium(1)|kidney(12)|large_intestine(3)|lung(5)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	28	all_cancers(71;4.25e-05)|all_epithelial(71;4.92e-06)|Ovarian(71;0.0254)|all_lung(81;0.0272)|Breast(184;0.0318)|Lung NSC(105;0.0376)		OV - Ovarian serous cystadenocarcinoma(106;0.00358)			TGCGCCTCCCAAAACAGTGCT	0.338													G|||	767	0.153155	0.1732	0.219	5008	,	,		17523	0.003		0.2803	False		,,,				2504	0.1033				p.F328F		Atlas-SNP	.											.	TFB2M	46	.	0			c.T984C						PASS	.	G		824,3582	743.6+/-411.5	88,648,1467	85.0	91.0	89.0		984	4.0	1.0	1	dbSNP_103	89	2307,6293	705.2+/-405.5	337,1633,2330	no	coding-synonymous	TFB2M	NM_022366.2		425,2281,3797	GG,GA,AA		26.8256,18.7018,24.0735		328/397	246707858	3131,9875	2203	4300	6503	SO:0001819	synonymous_variant	64216	exon7			CCTCCCAAAACAG	AK026835	CCDS1627.1	1q44	2008-02-05			ENSG00000162851	ENSG00000162851			18559	protein-coding gene	gene with protein product		607055					Standard	NM_022366		Approved	FLJ23182, FLJ22661, Hkp1	uc001ibn.3	Q9H5Q4	OTTHUMG00000040091	ENST00000366514.4:c.984T>C	1.37:g.246707858A>G		Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	115	52	0.452174	NM_022366	Q9H626	Silent	SNP	ENST00000366514.4	37	CCDS1627.1																																																																																			A|0.783;G|0.217	0.217	strong		0.338	TFB2M-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096673.1	NM_022366	
IGFL1	374918	hgsc.bcm.edu	37	19	46733409	46733409	+	Missense_Mutation	SNP	G	G	A	rs75105417	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:46733409G>A	ENST00000437936.1	+	2	93	c.70G>A	c.(70-72)Gga>Aga	p.G24R	AC006262.10_ENST00000597337.1_RNA	NM_198541.1	NP_940943.1	Q6UW32	IGFL1_HUMAN	IGF-like family member 1	24						extracellular space (GO:0005615)				lung(5)	5		Ovarian(192;0.0731)|all_neural(266;0.196)		OV - Ovarian serous cystadenocarcinoma(262;0.00242)|all cancers(93;0.0132)|GBM - Glioblastoma multiforme(486;0.0294)|Epithelial(262;0.201)		CTGCTCACACGGAGCCCCAGG	0.597													G|||	296	0.0591054	0.1021	0.0548	5008	,	,		18913	0.0079		0.0686	False		,,,				2504	0.047				p.G24R		Atlas-SNP	.											.	IGFL1	10	.	0			c.G70A						PASS	.	G	ARG/GLY	301,3493		10,281,1606	85.0	83.0	83.0		70	1.4	0.1	19	dbSNP_131	83	633,7615		28,577,3519	yes	missense	IGFL1	NM_198541.1	125	38,858,5125	AA,AG,GG		7.6746,7.9336,7.7562	probably-damaging	24/111	46733409	934,11108	1897	4124	6021	SO:0001583	missense	374918	exon2			TCACACGGAGCCC	AY359013	CCDS46123.1	19q13.32	2010-06-15			ENSG00000188293	ENSG00000188293			24093	protein-coding gene	gene with protein product		610544				12975309	Standard	NM_198541		Approved	UNQ644	uc002pee.3	Q6UW32		ENST00000437936.1:c.70G>A	19.37:g.46733409G>A	ENSP00000415823:p.Gly24Arg	Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	113	52	0.460177	NM_198541		Missense_Mutation	SNP	ENST00000437936.1	37	CCDS46123.1	134	0.06135531135531135	54	0.10975609756097561	24	0.06629834254143646	3	0.005244755244755245	53	0.06992084432717678	G	12.81	2.048324	0.36181	0.079336	0.076746	ENSG00000188293	ENST00000437936	T	0.28454	1.61	2.51	1.37	0.22104	.	0.599453	0.12640	N	0.451373	T	0.01029	0.0034	L	0.55481	1.735	0.80722	P	0.0	D	0.89917	1.0	D	0.69824	0.966	T	0.11665	-1.0578	9	0.59425	D	0.04	-1.9224	6.8538	0.24030	0.0:0.2926:0.7074:0.0	.	24	Q6UW32	IGFL1_HUMAN	R	24	ENSP00000415823:G24R	ENSP00000415823:G24R	G	+	1	0	IGFL1	51425249	0.008000	0.16893	0.113000	0.21522	0.123000	0.20343	0.594000	0.24014	0.555000	0.29079	0.455000	0.32223	GGA	G|0.932;A|0.068	0.068	strong		0.597	IGFL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461724.1	NM_198541	
LMO7	4008	hgsc.bcm.edu	37	13	76382100	76382100	+	Missense_Mutation	SNP	C	C	T	rs2241913	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:76382100C>T	ENST00000321797.8	+	8	1703	c.982C>T	c.(982-984)Ctt>Ttt	p.L328F	LMO7_ENST00000465261.2_Missense_Mutation_p.L328F|LMO7_ENST00000526202.1_Intron|LMO7_ENST00000341547.4_Intron|RP11-29G8.3_ENST00000563635.1_RNA|LMO7_ENST00000357063.3_Missense_Mutation_p.L613F|LMO7_ENST00000377534.3_Missense_Mutation_p.L613F			Q8WWI1	LMO7_HUMAN	LIM domain 7	613					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)		TCTCTGTGTACTTGAAAGGAC	0.443													C|||	644	0.128594	0.0083	0.2435	5008	,	,		18374	0.2252		0.1272	False		,,,				2504	0.1115				p.L328F		Atlas-SNP	.											.	LMO7	334	.	0			c.C982T						PASS	.	C	,PHE/LEU	77,3059		3,71,1494	86.0	85.0	86.0		,982	4.8	0.7	13	dbSNP_98	86	748,6416		40,668,2874	yes	intron,missense	LMO7	NM_005358.5,NM_015842.2	,22	43,739,4368	TT,TC,CC		10.4411,2.4554,8.0097	,probably-damaging	,328/1386	76382100	825,9475	1568	3582	5150	SO:0001583	missense	4008	exon7			TGTGTACTTGAAA	AF092557	CCDS9454.1, CCDS53876.1	13q22.2	2008-02-05	2004-06-15		ENSG00000136153	ENSG00000136153			6646	protein-coding gene	gene with protein product	"""F-box only protein 20"""	604362	"""LIM domain only 7"""	FBXO20		9826547, 10531035	Standard	NM_005358		Approved	FBX20, KIAA0858	uc021rkq.1	Q8WWI1	OTTHUMG00000017093	ENST00000321797.8:c.982C>T	13.37:g.76382100C>T	ENSP00000317802:p.Leu328Phe	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	75	27	0.36	NM_015842	E9PLH4|O15462|O95346|Q5TBK6|Q9UKC1|Q9UQM5|Q9Y6A7	Missense_Mutation	SNP	ENST00000321797.8	37		287|287	0.13141025641025642|0.13141025641025642	7|7	0.014227642276422764|0.014227642276422764	79|79	0.21823204419889503|0.21823204419889503	106|106	0.1853146853146853|0.1853146853146853	95|95	0.12532981530343007|0.12532981530343007	C|C	19.16|19.16	3.773455|3.773455	0.69992|0.69992	0.024554|0.024554	0.104411|0.104411	ENSG00000136153|ENSG00000136153	ENST00000357063;ENST00000377534;ENST00000321797;ENST00000465261|ENST00000447038	T;T;T;T|.	0.55588|.	0.51;0.51;0.51;0.51|.	5.67|5.67	4.83|4.83	0.62350|0.62350	.|.	0.125415|.	0.56097|.	D|.	0.000033|.	T|T	0.00039|0.00039	0.0001|0.0001	.|.	.|.	.|.	0.30770|0.30770	P|P	0.74318|0.74318	B|.	0.29508|.	0.246|.	B|.	0.26094|.	0.066|.	T|T	0.11251|0.11251	-1.0595|-1.0595	8|3	0.54805|.	T|.	0.06|.	-9.8046|-9.8046	9.9819|9.9819	0.41819|0.41819	0.1369:0.7936:0.0:0.0695|0.1369:0.7936:0.0:0.0695	rs2241913;rs60757334;rs2241913|rs2241913;rs60757334;rs2241913	328|.	E9PLH4|.	.|.	F|I	613;613;328;328|236	ENSP00000349571:L613F;ENSP00000366757:L613F;ENSP00000317802:L328F;ENSP00000433352:L328F|.	ENSP00000317802:L328F|.	L|T	+|+	1|2	0|0	LMO7|LMO7	75280101|75280101	1.000000|1.000000	0.71417|0.71417	0.732000|0.732000	0.30844|0.30844	0.993000|0.993000	0.82548|0.82548	4.505000|4.505000	0.60421|0.60421	1.536000|1.536000	0.49237|0.49237	0.655000|0.655000	0.94253|0.94253	CTT|ACT	C|0.885;T|0.115	0.115	strong		0.443	LMO7-005	PUTATIVE	alternative_5_UTR|not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000045301.3	NM_005358	
ZNF814	730051	hgsc.bcm.edu	37	19	58385714	58385714	+	Missense_Mutation	SNP	T	T	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:58385714T>G	ENST00000435989.2	-	3	1278	c.1044A>C	c.(1042-1044)gaA>gaC	p.E348D	ZNF814_ENST00000595295.1_Intron|ZNF814_ENST00000597342.1_Intron|ZNF814_ENST00000597832.1_Intron|ZNF814_ENST00000600634.1_Intron|ZNF814_ENST00000596604.1_Intron	NM_001144989.1	NP_001138461.1	B7Z6K7	ZN814_HUMAN	zinc finger protein 814	348					regulation of transcription, DNA-templated (GO:0006355)	intracellular (GO:0005622)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|central_nervous_system(2)|endometrium(3)|kidney(9)|lung(2)|prostate(4)|skin(1)|urinary_tract(3)	25						AATGTTTTTTTTCAGTGTGAA	0.368																																					p.E348D		Atlas-SNP	.											ZNF814,NS,carcinoma,0,2	ZNF814	93	2	0			c.A1044C						scavenged	.						192.0	147.0	160.0					19																	58385714		692	1591	2283	SO:0001583	missense	730051	exon3			TTTTTTTTCAGTG		CCDS46212.1	19q13.43	2013-01-08			ENSG00000204514	ENSG00000204514		"""Zinc fingers, C2H2-type"", ""-"""	33258	protein-coding gene	gene with protein product							Standard	NM_001144989		Approved		uc002qqo.2	B7Z6K7		ENST00000435989.2:c.1044A>C	19.37:g.58385714T>G	ENSP00000410545:p.Glu348Asp	Somatic	213	0	0		WXS	Illumina HiSeq	Phase_I	175	6	0.0342857	NM_001144989	A6NF35	Missense_Mutation	SNP	ENST00000435989.2	37	CCDS46212.1	.	.	.	.	.	.	.	.	.	.	.	13.49	2.252737	0.39797	.	.	ENSG00000204514	ENST00000435989	T	0.18502	2.21	2.01	0.932	0.19466	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.09468	0.0233	N	0.13371	0.34	0.19775	N	0.999954	B	0.15473	0.013	B	0.13407	0.009	T	0.30650	-0.9971	9	0.66056	D	0.02	.	5.8021	0.18420	0.0:0.152:0.0:0.848	.	348	B7Z6K7	ZN814_HUMAN	D	348	ENSP00000410545:E348D	ENSP00000410545:E348D	E	-	3	2	ZNF814	63077526	0.000000	0.05858	0.013000	0.15412	0.381000	0.30169	-0.928000	0.03980	0.089000	0.17243	0.113000	0.15668	GAA	.	.	none		0.368	ZNF814-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466976.1	XM_001725708	
PATE3	100169851	hgsc.bcm.edu	37	11	125659371	125659371	+	Missense_Mutation	SNP	G	G	A	rs78883072	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:125659371G>A	ENST00000445202.1	+	2	181	c.140G>A	c.(139-141)gGc>gAc	p.G47D		NM_001129883.3	NP_001123355.3	B3GLJ2	PATE3_HUMAN	prostate and testis expressed 3	47						extracellular region (GO:0005576)											GCTCAGAAGGGCGAGGCATGC	0.478													A|||	433	0.0864617	0.1778	0.0504	5008	,	,		21296	0.002		0.0736	False		,,,				2504	0.089				p.G47D		Atlas-SNP	.											.	PATE3	4	.	0			c.G140A						PASS	.						232.0	200.0	210.0					11																	125659371		692	1591	2283	SO:0001583	missense	100169851	exon2			AGAAGGGCGAGGC	EF426753	CCDS44764.1	11q24.2	2008-12-17			ENSG00000236027	ENSG00000236027		"""PATE family"""	35426	protein-coding gene	gene with protein product						18390568	Standard	NM_001129883		Approved	PATE-DJ, HEL-127	uc009zbs.3	B3GLJ2	OTTHUMG00000165857	ENST00000445202.1:c.140G>A	11.37:g.125659371G>A	ENSP00000395505:p.Gly47Asp	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	76	53	0.697368	NM_001129883	B5KFZ3	Missense_Mutation	SNP	ENST00000445202.1	37	CCDS44764.1	160	0.07326007326007326	87	0.17682926829268292	18	0.049723756906077346	0	0.0	55	0.07255936675461741	A	0.087	-1.173296	0.01646	.	.	ENSG00000236027	ENST00000445202	T	0.22134	1.97	4.08	1.72	0.24424	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.39035	-0.9633	7	0.02654	T	1	.	2.8217	0.05473	0.5916:0.0:0.2085:0.1998	.	47	B3GLJ2	PATE3_HUMAN	D	47	ENSP00000395505:G47D	ENSP00000395505:G47D	G	+	2	0	PATE3	125164581	0.000000	0.05858	0.000000	0.03702	0.022000	0.10575	0.234000	0.17930	0.048000	0.15891	-0.381000	0.06696	GGC	G|0.923;A|0.077	0.077	strong		0.478	PATE3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386731.1	NM_001129883	
KCNJ13	3769	hgsc.bcm.edu	37	2	233633460	233633460	+	Missense_Mutation	SNP	G	G	A	rs1801251	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:233633460G>A	ENST00000233826.3	-	3	663	c.524C>T	c.(523-525)aCa>aTa	p.T175I	GIGYF2_ENST00000373563.4_Intron|AC064852.4_ENST00000427571.1_RNA|GIGYF2_ENST00000409547.1_Intron|KCNJ13_ENST00000410029.1_Missense_Mutation_p.T175I|GIGYF2_ENST00000409451.3_Intron|KCNJ13_ENST00000409779.1_3'UTR|GIGYF2_ENST00000373566.3_Intron|GIGYF2_ENST00000409196.3_Intron|GIGYF2_ENST00000409480.1_Intron|GIGYF2_ENST00000452341.2_Intron	NM_002242.4	NP_002233.2	O60928	KCJ13_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 13	175			T -> I (in dbSNP:rs1801251). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9738472}.		potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)	integral component of membrane (GO:0016021)	inward rectifier potassium channel activity (GO:0005242)	p.T175I(1)		endometrium(3)|large_intestine(2)|lung(2)|stomach(1)|urinary_tract(1)	9		Breast(86;0.00279)|all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0306)|Lung NSC(271;0.0908)		Epithelial(121;5.9e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000311)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.00942)|GBM - Glioblastoma multiforme(43;0.0617)		TACTACTGCTGTGTCAGTAAA	0.433													A|||	1803	0.360024	0.2398	0.3055	5008	,	,		19578	0.3532		0.2873	False		,,,				2504	0.6431				p.T175I		Atlas-SNP	.											KCNJ13,NS,carcinoma,0,1	KCNJ13	18	1	1	Substitution - Missense(1)	stomach(1)	c.C524T						PASS	.	A	,,,,ILE/THR,ILE/THR,	1166,3240	712.8+/-408.2	156,854,1193	90.0	95.0	93.0		,,,,284,524,	2.3	0.9	2	dbSNP_89	93	3013,5587	663.9+/-402.1	530,1953,1817	yes	intron,intron,intron,utr-3,missense,missense,intron	KCNJ13,GIGYF2	NM_001103146.1,NM_001103147.1,NM_001103148.1,NM_001172416.1,NM_001172417.1,NM_002242.4,NM_015575.3	,,,,89,89,	686,2807,3010	AA,AG,GG		35.0349,26.4639,32.1313	,,,,benign,benign,	,,,,95/281,175/361,	233633460	4179,8827	2203	4300	6503	SO:0001583	missense	3769	exon3			ACTGCTGTGTCAG	AJ006128	CCDS2498.1, CCDS54437.1	2q37	2014-01-28			ENSG00000115474	ENSG00000115474		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Inwardly rectifying"""	6259	protein-coding gene	gene with protein product		603208				9878260, 9620703, 16382105	Standard	NM_002242		Approved	Kir7.1, Kir1.4, LCA16	uc002vtp.3	O60928	OTTHUMG00000153292	ENST00000233826.3:c.524C>T	2.37:g.233633460G>A	ENSP00000233826:p.Thr175Ile	Somatic	179	0	0		WXS	Illumina HiSeq	Phase_I	118	62	0.525424	NM_002242	A0PGH1|O76023|Q53SA1|Q8N3Y4	Missense_Mutation	SNP	ENST00000233826.3	37	CCDS2498.1	627	0.28708791208791207	125	0.2540650406504065	105	0.2900552486187845	181	0.31643356643356646	216	0.2849604221635884	A	0.094	-1.162850	0.01673	0.264639	0.350349	ENSG00000115474	ENST00000233826;ENST00000410029;ENST00000438786	T;T;D	0.91407	1.88;1.88;-2.84	5.86	2.27	0.28462	Immunoglobulin E-set (1);Potassium channel, inwardly rectifying, Kir, conserved region 2 (1);Potassium channel, inwardly rectifying, Kir, cytoplasmic (1);	0.947699	0.08918	N	0.874895	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.03139	-1.1068	9	0.54805	T	0.06	.	10.4877	0.44733	0.63:0.0:0.37:0.0	rs1801251;rs8192540;rs17846205;rs17859221;rs52812853;rs58979266;rs1801251	175	O60928	IRK13_HUMAN	I	175;175;95	ENSP00000233826:T175I;ENSP00000386251:T175I;ENSP00000407284:T95I	ENSP00000233826:T175I	T	-	2	0	KCNJ13	233341704	0.008000	0.16893	0.889000	0.34880	0.183000	0.23260	1.366000	0.34193	-0.082000	0.12640	-2.269000	0.00276	ACA	G|0.684;N|0.000	.	strong		0.433	KCNJ13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257036.1	NM_002242	
UTP20	27340	hgsc.bcm.edu	37	12	101693534	101693534	+	Missense_Mutation	SNP	C	C	G	rs4764643	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:101693534C>G	ENST00000261637.4	+	13	1679	c.1505C>G	c.(1504-1506)tCt>tGt	p.S502C		NM_014503.2	NP_055318.2	O75691	UTP20_HUMAN	UTP20, small subunit (SSU) processome component, homolog (yeast)	502			S -> C (in dbSNP:rs4764643).		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						CATCTTTTATCTATAATTAAG	0.338													C|||	529	0.105631	0.0439	0.1254	5008	,	,		19257	0.0288		0.1849	False		,,,				2504	0.1728				p.S502C		Atlas-SNP	.											.	UTP20	222	.	0			c.C1505G						PASS	.	C	CYS/SER	249,4157	140.8+/-176.2	7,235,1961	63.0	66.0	65.0		1505	5.8	0.0	12	dbSNP_111	65	1627,6971	300.4+/-304.9	169,1289,2841	yes	missense	UTP20	NM_014503.2	112	176,1524,4802	GG,GC,CC		18.923,5.6514,14.4263	probably-damaging	502/2786	101693534	1876,11128	2203	4299	6502	SO:0001583	missense	27340	exon13			TTTTATCTATAAT	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.1505C>G	12.37:g.101693534C>G	ENSP00000261637:p.Ser502Cys	Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	92	46	0.5	NM_014503	Q9H3H4	Missense_Mutation	SNP	ENST00000261637.4	37	CCDS9081.1	239	0.10943223443223443	27	0.054878048780487805	50	0.13812154696132597	17	0.02972027972027972	145	0.19129287598944592	C	13.57	2.277826	0.40294	0.056514	0.18923	ENSG00000120800	ENST00000261637	T	0.67698	-0.28	5.75	5.75	0.90469	Armadillo-type fold (1);	0.055091	0.85682	D	0.000000	T	0.00210	0.0006	L	0.36672	1.1	0.39688	P	0.028996000000000022	D	0.56521	0.976	P	0.49192	0.602	T	0.00885	-1.1527	9	0.51188	T	0.08	-11.3363	18.1211	0.89572	0.0:1.0:0.0:0.0	rs4764643;rs56577815;rs4764643	502	O75691	UTP20_HUMAN	C	502	ENSP00000261637:S502C	ENSP00000261637:S502C	S	+	2	0	UTP20	100217665	0.661000	0.27430	0.019000	0.16419	0.014000	0.08584	2.834000	0.48167	2.716000	0.92895	0.650000	0.86243	TCT	C|0.865;G|0.135	0.135	strong		0.338	UTP20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408242.1	NM_014503	
SLC7A11	23657	hgsc.bcm.edu	37	4	139140494	139140494	+	Silent	SNP	G	G	C	rs6838248	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:139140494G>C	ENST00000280612.5	-	5	951	c.672C>G	c.(670-672)gcC>gcG	p.A224A		NM_014331.3	NP_055146.1	Q9UPY5	XCT_HUMAN	solute carrier family 7 (anionic amino acid transporter light chain, xc- system), member 11	224					amino acid transport (GO:0006865)|blood coagulation (GO:0007596)|brain development (GO:0007420)|ion transport (GO:0006811)|L-glutamate transport (GO:0015813)|lens fiber cell differentiation (GO:0070306)|leukocyte migration (GO:0050900)|platelet aggregation (GO:0070527)|response to nicotine (GO:0035094)|response to oxidative stress (GO:0006979)|response to toxic substance (GO:0009636)|transmembrane transport (GO:0055085)	cell surface (GO:0009986)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|rough endoplasmic reticulum (GO:0005791)	cystine:glutamate antiporter activity (GO:0015327)			breast(1)|endometrium(4)|kidney(3)|large_intestine(3)|liver(1)|lung(3)|prostate(1)|skin(2)	18	all_hematologic(180;0.166)				Acetylcysteine(DB06151)|L-Cystine(DB00138)|Riluzole(DB00740)|Rosuvastatin(DB01098)|Sulfasalazine(DB00795)|Tauroursodeoxycholic acid(DB08834)	TTCCTGAAAAGGCGTCTTTAA	0.388													G|||	1713	0.342053	0.3018	0.366	5008	,	,		18813	0.0764		0.5099	False		,,,				2504	0.4806				p.A224A		Atlas-SNP	.											.	SLC7A11	40	.	0			c.C672G						PASS	.	G		1390,3016	456.1+/-351.2	207,976,1020	145.0	131.0	135.0		672	1.3	1.0	4	dbSNP_116	135	4176,4424	567.1+/-388.8	1016,2144,1140	no	coding-synonymous	SLC7A11	NM_014331.3		1223,3120,2160	CC,CG,GG		48.5581,31.5479,42.7956		224/502	139140494	5566,7440	2203	4300	6503	SO:0001819	synonymous_variant	23657	exon5			TGAAAAGGCGTCT	AB026891	CCDS3742.1	4q28-q32	2013-05-22	2011-07-12		ENSG00000151012	ENSG00000151012		"""Solute carriers"""	11059	protein-coding gene	gene with protein product		607933				10206947, 12763038	Standard	XM_005262875		Approved	xCT	uc021xrw.1	Q9UPY5	OTTHUMG00000133396	ENST00000280612.5:c.672C>G	4.37:g.139140494G>C		Somatic	202	0	0		WXS	Illumina HiSeq	Phase_I	121	52	0.429752	NM_014331	A8K2U4	Silent	SNP	ENST00000280612.5	37	CCDS3742.1																																																																																			G|0.601;C|0.399	0.399	strong		0.388	SLC7A11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257251.2		
USP34	9736	hgsc.bcm.edu	37	2	61647901	61647901	+	Silent	SNP	A	A	G	rs778155	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:61647901A>G	ENST00000398571.2	-	2	187	c.111T>C	c.(109-111)taT>taC	p.Y37Y		NM_014709.3	NP_055524.3	Q70CQ2	UBP34_HUMAN	ubiquitin specific peptidase 34	37					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)			AGGAATTGATATAAGTAAATA	0.303													A|||	1680	0.335463	0.2375	0.4467	5008	,	,		17643	0.3284		0.3499	False		,,,				2504	0.3814				p.Y37Y		Atlas-SNP	.											USP34,colon,carcinoma,0,1	USP34	334	1	0			c.T111C						PASS	.	A		915,2803		116,683,1060	111.0	109.0	109.0		111	4.6	1.0	2	dbSNP_86	109	3058,5150		571,1916,1617	no	coding-synonymous	USP34	NM_014709.3		687,2599,2677	GG,GA,AA		37.2563,24.61,33.3138		37/3547	61647901	3973,7953	1859	4104	5963	SO:0001819	synonymous_variant	9736	exon2			ATTGATATAAGTA	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.111T>C	2.37:g.61647901A>G		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	282	281	0.996454	NM_014709	A8MWD0|B3KWU9|O60316|O94834|Q3B777|Q6P6C9|Q7L8P6|Q8N3T9|Q8TBW2|Q9UGA1	Silent	SNP	ENST00000398571.2	37	CCDS42686.1																																																																																			A|0.679;G|0.320	0.320	strong		0.303	USP34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325650.4		
CXCR2	3579	hgsc.bcm.edu	37	2	219000310	219000310	+	Silent	SNP	C	C	T	rs2230054	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:219000310C>T	ENST00000318507.2	+	3	1213	c.786C>T	c.(784-786)ctC>ctT	p.L262L		NM_001557.3	NP_001548.1	P25025	CXCR2_HUMAN	chemokine (C-X-C motif) receptor 2	262					cell surface receptor signaling pathway (GO:0007166)|cellular defense response (GO:0006968)|chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|dendritic cell chemotaxis (GO:0002407)|inflammatory response (GO:0006954)|interleukin-8-mediated signaling pathway (GO:0038112)|neutrophil activation (GO:0042119)|neutrophil chemotaxis (GO:0030593)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cell proliferation (GO:0008284)|receptor internalization (GO:0031623)|signal transduction (GO:0007165)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|mast cell granule (GO:0042629)|membrane (GO:0016020)|plasma membrane (GO:0005886)	C-X-C chemokine receptor activity (GO:0016494)|interleukin-8 binding (GO:0019959)|interleukin-8 receptor activity (GO:0004918)|signal transducer activity (GO:0004871)	p.L262L(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(11)|skin(1)|stomach(1)	22						TCTTCCTGCTCTGCTGGCTGC	0.607													T|||	2566	0.51238	0.7315	0.5072	5008	,	,		20598	0.3175		0.4602	False		,,,				2504	0.4744				p.L262L		Atlas-SNP	.											CXCR2,NS,carcinoma,0,1	CXCR2	54	1	1	Substitution - coding silent(1)	stomach(1)	c.C786T						PASS	.	T	,	2852,1554	488.1+/-361.1	924,1004,275	128.0	124.0	125.0		786,786	4.5	1.0	2	dbSNP_98	125	4308,4292	576.8+/-390.4	1043,2222,1035	no	coding-synonymous,coding-synonymous	CXCR2	NM_001168298.1,NM_001557.3	,	1967,3226,1310	TT,TC,CC		49.907,35.2701,44.9485	,	262/361,262/361	219000310	7160,5846	2203	4300	6503	SO:0001819	synonymous_variant	3579	exon4			CCTGCTCTGCTGG	U11869	CCDS2408.1	2q35	2012-08-08	2009-11-25	2009-11-25	ENSG00000180871	ENSG00000180871		"""CD molecules"", ""GPCR / Class A : Chemokine receptors : C-X-C motif"", ""Interleukins and interleukin receptors"""	6027	protein-coding gene	gene with protein product		146928	"""interleukin 8 receptor, beta"""	IL8RB		1427896	Standard	NM_001557		Approved	CMKAR2, CD182	uc002vha.2	P25025	OTTHUMG00000133107	ENST00000318507.2:c.786C>T	2.37:g.219000310C>T		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	101	48	0.475248	NM_001168298	Q8IUZ1|Q9P2T6|Q9P2T7	Silent	SNP	ENST00000318507.2	37	CCDS2408.1																																																																																			C|0.465;T|0.535	0.535	strong		0.607	CXCR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256772.2	NM_001557	
LAMA5	3911	hgsc.bcm.edu	37	20	60926828	60926828	+	Silent	SNP	G	G	A	rs62204553	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:60926828G>A	ENST00000252999.3	-	6	954	c.888C>T	c.(886-888)atC>atT	p.I296I	LAMA5_ENST00000370677.3_Silent_p.I296I|RP11-157P1.5_ENST00000456721.2_RNA|RP11-157P1.5_ENST00000477848.1_RNA|LAMA5_ENST00000370692.3_Silent_p.I296I|RP11-157P1.5_ENST00000478167.1_RNA|RP11-157P1.5_ENST00000487421.1_RNA	NM_005560.3	NP_005551.3	O15230	LAMA5_HUMAN	laminin, alpha 5	296	Laminin N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00466}.				angiogenesis (GO:0001525)|branching involved in salivary gland morphogenesis (GO:0060445)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell differentiation (GO:0030154)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cell recognition (GO:0008037)|cilium assembly (GO:0042384)|cytoskeleton organization (GO:0007010)|embryo development (GO:0009790)|endothelial cell differentiation (GO:0045446)|establishment of protein localization to plasma membrane (GO:0090002)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|focal adhesion assembly (GO:0048041)|hair follicle development (GO:0001942)|integrin-mediated signaling pathway (GO:0007229)|lung development (GO:0030324)|morphogenesis of a polarized epithelium (GO:0001738)|morphogenesis of embryonic epithelium (GO:0016331)|muscle organ development (GO:0007517)|neural crest cell migration (GO:0001755)|odontogenesis of dentin-containing tooth (GO:0042475)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of embryonic development (GO:0045995)|substrate adhesion-dependent cell spreading (GO:0034446)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-11 complex (GO:0043260)|laminin-5 complex (GO:0005610)|nucleus (GO:0005634)	integrin binding (GO:0005178)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|lung(40)|ovary(1)|pancreas(1)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	81	Breast(26;1.57e-08)		BRCA - Breast invasive adenocarcinoma(19;4.36e-06)			AGCGGCCTCCGATGCTGATAT	0.657													g|||	336	0.0670927	0.1914	0.0447	5008	,	,		15930	0.001		0.0417	False		,,,				2504	0.0092				p.I296I		Atlas-SNP	.											.	LAMA5	268	.	0			c.C888T						PASS	.			692,3700	281.6+/-276.1	66,560,1570	34.0	36.0	36.0		888	-8.4	0.2	20	dbSNP_129	36	298,8278	106.8+/-167.6	7,284,3997	no	coding-synonymous	LAMA5	NM_005560.3		73,844,5567	AA,AG,GG		3.4748,15.7559,7.6342		296/3696	60926828	990,11978	2196	4288	6484	SO:0001819	synonymous_variant	3911	exon6			GCCTCCGATGCTG	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.888C>T	20.37:g.60926828G>A		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	58	32	0.551724	NM_005560	Q8TDF8|Q8WZA7|Q9H1P1	Silent	SNP	ENST00000252999.3	37	CCDS33502.1																																																																																			G|0.924;A|0.076	0.076	strong		0.657	LAMA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080014.2	NM_005560	
COL9A3	1299	hgsc.bcm.edu	37	20	61448933	61448933	+	Silent	SNP	C	C	A	rs544133282|rs2273078	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:61448933C>A	ENST00000343916.3	+	2	96	c.93C>A	c.(91-93)ccC>ccA	p.P31P		NM_001853.3	NP_001844.3	Q14050	CO9A3_HUMAN	collagen, type IX, alpha 3	31	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)					TGGGACTccccggcccccccg	0.731													A|||	804	0.160543	0.211	0.1484	5008	,	,		9815	0.251		0.0775	False		,,,				2504	0.093				p.P31P		Atlas-SNP	.											.	COL9A3	70	.	0			c.C93A						PASS	.	A		550,3092		33,484,1304	5.0	7.0	6.0		93	0.2	0.1	20	dbSNP_100	6	409,6799		10,389,3205	no	coding-synonymous	COL9A3	NM_001853.3		43,873,4509	AA,AC,CC		5.6743,15.1016,8.8387		31/685	61448933	959,9891	1821	3604	5425	SO:0001819	synonymous_variant	1299	exon2			ACTCCCCGGCCCC	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.93C>A	20.37:g.61448933C>A		Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	43	16	0.372093	NM_001853	Q13681|Q9H4G9|Q9UPE2	Silent	SNP	ENST00000343916.3	37	CCDS13505.1																																																																																			C|0.816;A|0.184	0.184	strong		0.731	COL9A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080071.2	NM_001853	
PGD	5226	hgsc.bcm.edu	37	1	10460485	10460485	+	Silent	SNP	T	T	C	rs1049887	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:10460485T>C	ENST00000270776.8	+	3	158	c.120T>C	c.(118-120)gaT>gaC	p.D40D	PGD_ENST00000538557.1_Silent_p.D27D|PGD_ENST00000541529.1_Silent_p.D40D	NM_002631.2	NP_002622.2	P52209	6PGD_HUMAN	phosphogluconate dehydrogenase	40					carbohydrate metabolic process (GO:0005975)|D-gluconate metabolic process (GO:0019521)|oxidation-reduction process (GO:0055114)|pentose biosynthetic process (GO:0019322)|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)|nucleus (GO:0005634)	NADP binding (GO:0050661)|phosphogluconate dehydrogenase (decarboxylating) activity (GO:0004616)	p.D40D(1)		NS(1)|breast(1)|cervix(1)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)	14	Ovarian(185;0.203)	all_lung(284;1.31e-05)|Lung NSC(185;2.19e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.14e-07)|COAD - Colon adenocarcinoma(227;7.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000294)|Kidney(185;0.000728)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(132;0.00832)|READ - Rectum adenocarcinoma(331;0.0487)	Dacarbazine(DB00851)|Furosemide(DB00695)|Gadopentetate dimeglumine(DB00789)|Ketotifen(DB00920)|Meloxicam(DB00814)|Methotrexate(DB00563)|Ritodrine(DB00867)	CCAAAGTTGATGATTTCTTGG	0.502													T|||	1171	0.233826	0.0658	0.3199	5008	,	,		19744	0.2817		0.3111	False		,,,				2504	0.271				p.D40D		Atlas-SNP	.											PGD,NS,adenoma,0,2	PGD	39	2	1	Substitution - coding silent(1)	stomach(1)	c.T120C						PASS	.	T		430,3976	206.5+/-228.1	33,364,1806	119.0	111.0	114.0		120	1.4	0.9	1	dbSNP_86	114	2603,5997	421.0+/-353.6	419,1765,2116	no	coding-synonymous	PGD	NM_002631.2		452,2129,3922	CC,CT,TT		30.2674,9.7594,23.32		40/484	10460485	3033,9973	2203	4300	6503	SO:0001819	synonymous_variant	5226	exon3			AGTTGATGATTTC	BC000368	CCDS113.1	1p36.22	2012-10-02			ENSG00000142657	ENSG00000142657	1.1.1.43		8891	protein-coding gene	gene with protein product		172200					Standard	NM_002631		Approved		uc001arc.3	P52209	OTTHUMG00000001905	ENST00000270776.8:c.120T>C	1.37:g.10460485T>C		Somatic	179	0	0		WXS	Illumina HiSeq	Phase_I	124	63	0.508065	NM_002631	A8K2Y9|B4DQJ8|Q9BWD8	Silent	SNP	ENST00000270776.8	37	CCDS113.1	577	0.2641941391941392	42	0.08536585365853659	126	0.34806629834254144	172	0.3006993006993007	237	0.31266490765171506	T	10.62	1.401045	0.25291	0.097594	0.302674	ENSG00000142657	ENST00000543846	.	.	.	5.18	1.38	0.22167	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999991	.	.	.	.	.	.	T	0.31308	-0.9948	4	0.87932	D	0	-24.6496	5.1933	0.15223	0.0:0.2189:0.1402:0.641	rs1049887;rs2070193;rs2229686;rs3190072;rs11547607;rs12754332	.	.	.	T	18	.	ENSP00000438783:M18T	M	+	2	0	PGD	10383072	0.999000	0.42202	0.913000	0.36048	0.993000	0.82548	0.528000	0.23002	0.038000	0.15604	0.533000	0.62120	ATG	T|0.754;C|0.246	0.246	strong		0.502	PGD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005398.1	NM_002631	
ANGPTL4	51129	hgsc.bcm.edu	37	19	8436289	8436289	+	Missense_Mutation	SNP	G	G	A	rs139998264	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:8436289G>A	ENST00000301455.2	+	6	1093	c.922G>A	c.(922-924)Gtg>Atg	p.V308M	ANGPTL4_ENST00000393962.2_Missense_Mutation_p.V270M|RAB11B-AS1_ENST00000597785.1_RNA|RAB11B-AS1_ENST00000593581.1_RNA|ANGPTL4_ENST00000541807.1_Missense_Mutation_p.V141M	NM_139314.1	NP_647475.1	Q9BY76	ANGL4_HUMAN	angiopoietin-like 4	308	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.		V -> M (in dbSNP:rs139998264). {ECO:0000269|PubMed:17322881}.		angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|cellular lipid metabolic process (GO:0044255)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of lipoprotein lipase activity (GO:0051005)|positive regulation of angiogenesis (GO:0045766)|protein homooligomerization (GO:0051260)|response to hypoxia (GO:0001666)|small molecule metabolic process (GO:0044281)|triglyceride homeostasis (GO:0070328)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	enzyme inhibitor activity (GO:0004857)			large_intestine(1)|lung(1)|ovary(2)|skin(2)	6						CACTGCACCCGTGGCCGGCCA	0.672													G|||	2	0.000399361	0.0	0.0	5008	,	,		16262	0.001		0.001	False		,,,				2504	0.0				p.V308M		Atlas-SNP	.											.	ANGPTL4	21	.	0			c.G922A						PASS	.	G	MET/VAL,MET/VAL	1,4405	2.1+/-5.4	0,1,2202	43.0	38.0	40.0		808,922	1.6	0.4	19	dbSNP_134	40	7,8591	5.7+/-21.5	0,7,4292	no	missense,missense	ANGPTL4	NM_001039667.1,NM_139314.1	21,21	0,8,6494	AA,AG,GG		0.0814,0.0227,0.0615	benign,benign	270/369,308/407	8436289	8,12996	2203	4299	6502	SO:0001583	missense	51129	exon6			GCACCCGTGGCCG	AF202636	CCDS12200.1, CCDS42493.1	19p13.3	2013-10-07				ENSG00000167772		"""Fibrinogen C domain containing"""	16039	protein-coding gene	gene with protein product	"""fasting-induced adipose factor"", ""hepatic angiopoietin-related protein"", ""PPARG angiopoietin related protein"", ""hepatic fibrinogen/angiopoietin-related protein"", ""peroxisome proliferator-activated receptor (PPAR) gamma induced angiopoietin-related protein"", ""angiopoietin-related protein 4"""	605910				10698685, 10866690, 23960078	Standard	NM_139314		Approved	pp1158, PGAR, ARP4, HFARP, FIAF, NL2	uc002mjq.1	Q9BY76		ENST00000301455.2:c.922G>A	19.37:g.8436289G>A	ENSP00000301455:p.Val308Met	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	81	40	0.493827	NM_139314	A8MY84|B4E089|D6W670|F5H0I2|Q53HQ6|Q53HU1|Q6UXN0|Q9HBV4|Q9NZU4|Q9Y5B3	Missense_Mutation	SNP	ENST00000301455.2	37	CCDS12200.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	5.392	0.257560	0.10239	2.27E-4	8.14E-4	ENSG00000167772	ENST00000301455;ENST00000393962;ENST00000541807	T;T;T	0.76709	-1.04;-1.04;-1.04	5.09	1.65	0.23941	Fibrinogen, alpha/beta/gamma chain, C-terminal globular (4);Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 (1);	2.318390	0.01258	N	0.009095	T	0.73938	0.3651	L	0.45422	1.42	0.09310	N	1	B;B	0.29646	0.253;0.253	B;B	0.34301	0.179;0.126	T	0.56836	-0.7913	10	0.49607	T	0.09	.	6.3492	0.21367	0.168:0.2821:0.5498:0.0	.	270;308	A8MY84;Q9BY76	.;ANGL4_HUMAN	M	308;270;141	ENSP00000301455:V308M;ENSP00000377534:V270M;ENSP00000439833:V141M	ENSP00000301455:V308M	V	+	1	0	ANGPTL4	8342289	0.038000	0.19896	0.434000	0.26772	0.003000	0.03518	1.289000	0.33307	0.130000	0.18549	-0.263000	0.10527	GTG	G|0.999;A|0.001	0.001	strong		0.672	ANGPTL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460322.1	NM_139314	
MUC4	4585	hgsc.bcm.edu	37	3	195505930	195505930	+	Missense_Mutation	SNP	C	C	G	rs201499581	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195505930C>G	ENST00000463781.3	-	2	12980	c.12521G>C	c.(12520-12522)gGc>gCc	p.G4174A	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.G4174A	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.A4166_S4181delASSVSTGHGTPLPVTS(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)		AAGAGGGGTGCCGTGACCTGT	0.597													.|||	279	0.0557109	0.0522	0.0447	5008	,	,		10180	0.0625		0.0517	False		,,,				2504	0.0654				p.G4174A		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	2	Deletion - In frame(2)	upper_aerodigestive_tract(1)|stomach(1)	c.G12521C						scavenged	.						18.0	11.0	13.0					3																	195505930		604	1338	1942	SO:0001583	missense	4585	exon2			GGGGTGCCGTGAC	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.12521G>C	3.37:g.195505930C>G	ENSP00000417498:p.Gly4174Ala	Somatic	46	2	0.0434783		WXS	Illumina HiSeq	Phase_I	51	19	0.372549	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	N	4.577	0.107284	0.08780	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.32023	1.51;1.47	.	.	.	.	.	.	.	.	T	0.10551	0.0258	N	0.08118	0	0.80722	P	0.0	B	0.13145	0.007	B	0.04013	0.001	T	0.20306	-1.0279	6	.	.	.	.	3.5856	0.07970	0.2505:0.4979:0.2516:0.0	.	4046	E7ESK3	.	A	4174	ENSP00000417498:G4174A;ENSP00000420243:G4174A	.	G	-	2	0	MUC4	196990709	0.000000	0.05858	0.001000	0.08648	0.005000	0.04900	-4.330000	0.00252	-2.654000	0.00422	-2.337000	0.00247	GGC	.	.	weak		0.597	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
EHD4	30844	hgsc.bcm.edu	37	15	42211486	42211486	+	Silent	SNP	A	A	G	rs1704396	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:42211486A>G	ENST00000220325.4	-	4	929	c.846T>C	c.(844-846)ttT>ttC	p.F282F	CTD-2382E5.4_ENST00000564168.1_RNA	NM_139265.3	NP_644670.1	Q9H223	EHD4_HUMAN	EH-domain containing 4	282	Dynamin-type G.				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)			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)		GGATGTCTCTAAAGAGGTCCT	0.632													G|||	2269	0.453075	0.6944	0.3775	5008	,	,		20051	0.1052		0.5	False		,,,				2504	0.4908				p.F282F		Atlas-SNP	.											.	EHD4	46	.	0			c.T846C						PASS	.	G		2839,1567	486.4+/-360.6	908,1023,272	50.0	49.0	49.0		846	5.1	1.0	15	dbSNP_89	49	4214,4384	574.6+/-390.1	1023,2168,1108	no	coding-synonymous	EHD4	NM_139265.3		1931,3191,1380	GG,GA,AA		49.0114,35.5651,45.7628		282/542	42211486	7053,5951	2203	4299	6502	SO:0001819	synonymous_variant	30844	exon4			GTCTCTAAAGAGG	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.846T>C	15.37:g.42211486A>G		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	62	37	0.596774	NM_139265	Q9HAR1|Q9NZN2	Silent	SNP	ENST00000220325.4	37	CCDS10081.1																																																																																			A|0.517;G|0.483	0.483	strong		0.632	EHD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252737.2	NM_139265	
ADAM28	10863	hgsc.bcm.edu	37	8	24177788	24177788	+	Missense_Mutation	SNP	A	A	G	rs200839167		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:24177788A>G	ENST00000265769.4	+	7	726	c.616A>G	c.(616-618)Ata>Gta	p.I206V	RP11-624C23.1_ENST00000523700.1_RNA|ADAM28_ENST00000540823.1_5'UTR|ADAM28_ENST00000437154.2_Missense_Mutation_p.I206V|RP11-624C23.1_ENST00000519689.1_RNA|RP11-624C23.1_ENST00000523578.1_RNA|ADAM28_ENST00000397649.3_5'UTR|RP11-624C23.1_ENST00000518988.1_RNA	NM_014265.4	NP_055080.2	Q9UKQ2	ADA28_HUMAN	ADAM metallopeptidase domain 28	206	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				spermatogenesis (GO:0007283)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(10)|lung(7)|prostate(1)|skin(12)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	42		Prostate(55;0.0959)		Colorectal(74;0.0129)|COAD - Colon adenocarcinoma(73;0.0434)|BRCA - Breast invasive adenocarcinoma(99;0.175)		TGAGAAATACATAGAATATTA	0.303																																					p.I206V	NSCLC(193;488 2149 22258 34798 40734)	Atlas-SNP	.											.	ADAM28	100	.	0			c.A616G						PASS	.	A	VAL/ILE,VAL/ILE	0,4406		0,0,2203	88.0	96.0	93.0		616,616	1.7	0.8	8		93	4,8578	3.7+/-12.6	0,4,4287	no	missense,missense	ADAM28	NM_014265.4,NM_021777.3	29,29	0,4,6490	GG,GA,AA		0.0466,0.0,0.0308	benign,benign	206/776,206/541	24177788	4,12984	2203	4291	6494	SO:0001583	missense	10863	exon7			AAATACATAGAAT	AJ242015	CCDS34865.1, CCDS47830.1	8p21.2	2005-11-29	2005-08-18		ENSG00000042980	ENSG00000042980		"""ADAM metallopeptidase domain containing"""	206	protein-coding gene	gene with protein product		606188	"""a disintegrin and metalloproteinase domain 28"""				Standard	XM_005273378		Approved	eMDCII, MDC-Lm, MDC-Ls, ADAM23	uc003xdy.3	Q9UKQ2	OTTHUMG00000163780	ENST00000265769.4:c.616A>G	8.37:g.24177788A>G	ENSP00000265769:p.Ile206Val	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	91	19	0.208791	NM_014265	B2RMV5|Q9Y339|Q9Y3S0	Missense_Mutation	SNP	ENST00000265769.4	37	CCDS34865.1	.	.	.	.	.	.	.	.	.	.	A	8.894	0.954625	0.18431	0.0	4.66E-4	ENSG00000042980	ENST00000265769;ENST00000437154	T;T	0.63580	-0.05;-0.05	5.34	1.71	0.24356	Metallopeptidase, catalytic domain (1);Peptidase M12B, ADAM/reprolysin (2);	.	.	.	.	T	0.34454	0.0898	N	0.05351	-0.065	0.58432	D	0.999999	B;B	0.18013	0.02;0.025	B;B	0.29862	0.068;0.108	T	0.21621	-1.0240	9	0.02654	T	1	.	6.5373	0.22361	0.7202:0.0:0.2798:0.0	.	206;206	Q9UKQ2;Q9UKQ2-2	ADA28_HUMAN;.	V	206	ENSP00000265769:I206V;ENSP00000393699:I206V	ENSP00000265769:I206V	I	+	1	0	ADAM28	24233733	0.039000	0.19947	0.825000	0.32803	0.758000	0.43043	0.086000	0.14935	0.429000	0.26202	0.533000	0.62120	ATA	A|0.999;G|0.001	0.001	weak		0.303	ADAM28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375441.2	NM_021778	
AKR1B10	57016	hgsc.bcm.edu	37	7	134215403	134215403	+	Silent	SNP	T	T	C	rs1722883	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:134215403T>C	ENST00000359579.4	+	2	395	c.75T>C	c.(73-75)ctT>ctC	p.L25L	AKR1B10_ENST00000475559.1_3'UTR	NM_020299.4	NP_064695.3	O60218	AK1BA_HUMAN	aldo-keto reductase family 1, member B10 (aldose reductase)	25					cellular aldehyde metabolic process (GO:0006081)|daunorubicin metabolic process (GO:0044597)|digestion (GO:0007586)|doxorubicin metabolic process (GO:0044598)|farnesol catabolic process (GO:0016488)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|steroid metabolic process (GO:0008202)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	aldo-keto reductase (NADP) activity (GO:0004033)|geranylgeranyl reductase activity (GO:0045550)|indanol dehydrogenase activity (GO:0047718)|retinal dehydrogenase activity (GO:0001758)			NS(1)|central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(9)|skin(5)	20						AGTCTCCTCTTGGCAAAGTGA	0.488													.|||	2670	0.533147	0.7753	0.3934	5008	,	,		20728	0.4137		0.4503	False		,,,				2504	0.5133				p.L25L		Atlas-SNP	.											.	AKR1B10	42	.	0			c.T75C						PASS	.	C		3261,1145		1209,843,151	80.0	81.0	81.0		75	-3.2	0.0	7	dbSNP_89	81	3954,4646		905,2144,1251	no	coding-synonymous	AKR1B10	NM_020299.4		2114,2987,1402	CC,CT,TT		45.9767,25.9873,44.5256		25/317	134215403	7215,5791	2203	4300	6503	SO:0001819	synonymous_variant	57016	exon2			TCCTCTTGGCAAA	AF052577	CCDS5832.1	7q33	2010-04-08			ENSG00000198074	ENSG00000198074		"""Aldo-keto reductases"""	382	protein-coding gene	gene with protein product	"""aldose reductase-like 1"", ""aldo-keto reductase family 1, member B11 (aldose reductase-like)"", ""aldose reductase-like peptide"", ""aldose reductase-related protein"", ""small intestine reductase"""	604707		AKR1B11		9765596, 9565553	Standard	NM_020299		Approved	AKR1B12, ARL-1, HIS, ARL1, HSI, ALDRLn	uc003vrr.3	O60218	OTTHUMG00000155356	ENST00000359579.4:c.75T>C	7.37:g.134215403T>C		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	119	116	0.97479	NM_020299	A4D1P1|O75890|Q6FHF3|Q8IWZ1	Silent	SNP	ENST00000359579.4	37	CCDS5832.1																																																																																			T|0.460;C|0.540	0.540	strong		0.488	AKR1B10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339615.1	NM_020299	
OR6M1	390261	hgsc.bcm.edu	37	11	123676413	123676413	+	Silent	SNP	G	G	A	rs7952150	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:123676413G>A	ENST00000309154.2	-	1	682	c.645C>T	c.(643-645)taC>taT	p.Y215Y		NM_001005325.1	NP_001005325.1	Q8NGM8	OR6M1_HUMAN	olfactory receptor, family 6, subfamily M, member 1	215						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			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)		TTATGTACACGTAGGACCCAG	0.488													G|||	1120	0.223642	0.3177	0.2666	5008	,	,		20315	0.1905		0.1869	False		,,,				2504	0.138				p.Y215Y		Atlas-SNP	.											.	OR6M1	60	.	0			c.C645T						PASS	.	G		1197,3207	417.8+/-338.1	173,851,1178	72.0	64.0	66.0		645	-0.8	0.1	11	dbSNP_116	66	1397,7201	270.9+/-289.3	107,1183,3009	no	coding-synonymous	OR6M1	NM_001005325.1		280,2034,4187	AA,AG,GG		16.248,27.1798,19.9508		215/314	123676413	2594,10408	2202	4299	6501	SO:0001819	synonymous_variant	390261	exon1			GTACACGTAGGAC	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.645C>T	11.37:g.123676413G>A		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	55	37	0.672727	NM_001005325	B2RNK0|Q6IEW9|Q96R37	Silent	SNP	ENST00000309154.2	37	CCDS31696.1																																																																																			G|0.788;A|0.212	0.212	strong		0.488	OR6M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387437.1	NM_001005325	
TRIM31	11074	hgsc.bcm.edu	37	6	30080496	30080496	+	Silent	SNP	G	G	A	rs2844793	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:30080496G>A	ENST00000376734.3	-	2	212	c.87C>T	c.(85-87)atC>atT	p.I29I	TRIM31_ENST00000540829.1_Silent_p.I29I|TRIM31-AS1_ENST00000440874.1_RNA|TRIM31_ENST00000485864.1_5'Flank	NM_007028.3	NP_008959.3	Q9BZY9	TRI31_HUMAN	tripartite motif containing 31	29					innate immune response (GO:0045087)|negative regulation of viral entry into host cell (GO:0046597)|negative regulation of viral transcription (GO:0032897)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein ubiquitination (GO:0016567)|regulation of viral release from host cell (GO:1902186)	mitochondrion (GO:0005739)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(5)|ovary(2)|prostate(2)|skin(2)	15						GCCCACAGTCGATGGTGACAG	0.478													G|||	381	0.0760783	0.0567	0.1182	5008	,	,		21211	0.0486		0.1213	False		,,,				2504	0.0542				p.I29I		Atlas-SNP	.											.	TRIM31	40	.	0			c.C87T						PASS	.	G		200,2820		8,184,1318	107.0	110.0	109.0		87	-5.1	0.0	6	dbSNP_100	109	760,4658		46,668,1995	yes	coding-synonymous	TRIM31	NM_007028.3		54,852,3313	AA,AG,GG		14.0273,6.6225,11.3771		29/426	30080496	960,7478	1510	2709	4219	SO:0001819	synonymous_variant	11074	exon2			ACAGTCGATGGTG	AF230386	CCDS34374.1	6p21.3	2013-01-09	2011-01-25		ENSG00000204616	ENSG00000204616		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	16289	protein-coding gene	gene with protein product		609316	"""tripartite motif-containing 31"""			11331580	Standard	XM_006714977		Approved	RNF, HCGI, C6orf13, HCG1	uc003npg.1	Q9BZY9	OTTHUMG00000031064	ENST00000376734.3:c.87C>T	6.37:g.30080496G>A		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	96	53	0.552083	NM_007028	A6NLX6|A9R9Q4|Q53H52|Q5RI37|Q5SRJ7|Q5SRJ8|Q5SS28|Q96AK4|Q96AP8|Q99579|Q9BZY8	Silent	SNP	ENST00000376734.3	37	CCDS34374.1																																																																																			G|0.893;A|0.107	0.107	strong		0.478	TRIM31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076081.2		
OR6S1	341799	hgsc.bcm.edu	37	14	21109671	21109671	+	Silent	SNP	A	A	G	rs11627574	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:21109671A>G	ENST00000320704.3	-	1	179	c.180T>C	c.(178-180)ccT>ccC	p.P60P		NM_001001968.1	NP_001001968.1	Q8NH40	OR6S1_HUMAN	olfactory receptor, family 6, subfamily S, member 1	60						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			kidney(1)|large_intestine(3)|lung(13)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	23	all_cancers(95;0.00304)		Epithelial(56;1.23e-06)|all cancers(55;1.01e-05)	GBM - Glioblastoma multiforme(265;0.0135)		AGAAGTACATAGGGGTCTGTA	0.443													G|||	2309	0.461062	0.4902	0.5461	5008	,	,		21262	0.2897		0.5378	False		,,,				2504	0.4591				p.P60P		Atlas-SNP	.											.	OR6S1	49	.	0			c.T180C						PASS	.	G		2257,2149	581.7+/-385.4	560,1137,506	102.0	96.0	98.0		180	1.4	1.0	14	dbSNP_120	98	4805,3795	537.6+/-383.2	1344,2117,839	no	coding-synonymous	OR6S1	NM_001001968.1		1904,3254,1345	GG,GA,AA		44.1279,48.7744,45.702		60/332	21109671	7062,5944	2203	4300	6503	SO:0001819	synonymous_variant	341799	exon1			GTACATAGGGGTC	AL163636	CCDS32038.1	14q11.2	2013-09-24			ENSG00000181803	ENSG00000181803		"""GPCR / Class A : Olfactory receptors"""	15363	protein-coding gene	gene with protein product							Standard	NM_001001968		Approved	OR6S1Q	uc001vxv.1	Q8NH40	OTTHUMG00000171010	ENST00000320704.3:c.180T>C	14.37:g.21109671A>G		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	106	53	0.5	NM_001001968	Q6IFJ9	Silent	SNP	ENST00000320704.3	37	CCDS32038.1																																																																																			A|0.484;G|0.516	0.516	strong		0.443	OR6S1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411227.1		
ANKRD13A	88455	hgsc.bcm.edu	37	12	110456175	110456175	+	Silent	SNP	A	A	G	rs2302689	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:110456175A>G	ENST00000261739.4	+	5	592	c.426A>G	c.(424-426)ccA>ccG	p.P142P	ANKRD13A_ENST00000550404.1_3'UTR	NM_033121.1	NP_149112.1	Q8IZ07	AN13A_HUMAN	ankyrin repeat domain 13A	142						endosome (GO:0005768)|plasma membrane (GO:0005886)				endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(8)|lung(3)|urinary_tract(1)	16						GAATATGCCCAAATGATGTCT	0.463													G|||	1560	0.311502	0.6717	0.183	5008	,	,		19584	0.1448		0.1769	False		,,,				2504	0.226				p.P142P		Atlas-SNP	.											.	ANKRD13A	39	.	0			c.A426G						PASS	.	G		2675,1731	518.3+/-369.7	814,1047,342	103.0	98.0	100.0		426	-11.2	0.1	12	dbSNP_100	100	1375,7225	755.3+/-407.5	102,1171,3027	no	coding-synonymous	ANKRD13A	NM_033121.1		916,2218,3369	GG,GA,AA		15.9884,39.2873,31.1395		142/591	110456175	4050,8956	2203	4300	6503	SO:0001819	synonymous_variant	88455	exon5			ATGCCCAAATGAT	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.426A>G	12.37:g.110456175A>G		Somatic	256	0	0		WXS	Illumina HiSeq	Phase_I	226	125	0.553097	NM_033121	O60736	Silent	SNP	ENST00000261739.4	37	CCDS9140.1																																																																																			A|0.706;G|0.294	0.294	strong		0.463	ANKRD13A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403430.1	NM_033121	
C1orf141	400757	hgsc.bcm.edu	37	1	67558739	67558739	+	Silent	SNP	C	C	T	rs6588237	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:67558739C>T	ENST00000371007.2	-	8	1261	c.1152G>A	c.(1150-1152)acG>acA	p.T384T	C1orf141_ENST00000544837.1_Silent_p.T384T|C1orf141_ENST00000371006.1_Silent_p.T384T	NM_001276351.1	NP_001263280.1	Q5JVX7	CA141_HUMAN	chromosome 1 open reading frame 141	384										NS(1)|breast(1)|endometrium(1)|large_intestine(5)|lung(8)|ovary(1)|skin(1)	18						TATCCAGTGGCGTTACATTAT	0.313													T|||	4611	0.920727	0.9228	0.9107	5008	,	,		16133	0.9722		0.8141	False		,,,				2504	0.9816				p.T384T		Atlas-SNP	.											.	C1orf141	58	.	0			c.G1152A						PASS	.	T		4030,374	178.7+/-207.4	1852,326,24	44.0	49.0	47.0		1152	-4.1	0.2	1	dbSNP_116	47	7367,1227	240.6+/-271.2	3163,1041,93	no	coding-synonymous	C1orf141	NM_001013674.1		5015,1367,117	TT,TC,CC		14.2774,8.4923,12.3173		384/401	67558739	11397,1601	2202	4297	6499	SO:0001819	synonymous_variant	400757	exon8			CAGTGGCGTTACA	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.1152G>A	1.37:g.67558739C>T		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	75	75	1	NM_001276351	Q0P5P5|Q5JVX5	Silent	SNP	ENST00000371007.2	37	CCDS30745.1																																																																																			C|0.118;T|0.882	0.882	strong		0.313	C1orf141-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026096.2	NM_001013674	
MUC4	4585	hgsc.bcm.edu	37	3	195507836	195507836	+	Missense_Mutation	SNP	C	C	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195507836C>G	ENST00000463781.3	-	2	11074	c.10615G>C	c.(10615-10617)Gtc>Ctc	p.V3539L	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.V3539L	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.V3539L(2)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		AGGCTGGTGACAGGAAGAGGC	0.617																																					p.V3539L		Atlas-SNP	.											MUC4_ENST00000463781,trunk,malignant_melanoma,0,2	MUC4	1505	2	2	Substitution - Missense(2)	skin(2)	c.G10615C						scavenged	.						27.0	27.0	27.0					3																	195507836		681	1578	2259	SO:0001583	missense	4585	exon2			TGGTGACAGGAAG	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.10615G>C	3.37:g.195507836C>G	ENSP00000417498:p.Val3539Leu	Somatic	176	2	0.0113636		WXS	Illumina HiSeq	Phase_I	231	19	0.0822511	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	c	3.354	-0.131924	0.06753	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.33865	1.4;1.39	0.743	-1.49	0.08718	.	0.000000	0.23275	U	0.049970	T	0.17831	0.0428	N	0.19112	0.55	0.09310	N	1	B	0.33494	0.414	B	0.35899	0.213	T	0.15665	-1.0429	9	.	.	.	.	4.8397	0.13483	0.3414:0.6586:0.0:1.0E-4	.	3411	E7ESK3	.	L	3539	ENSP00000417498:V3539L;ENSP00000420243:V3539L	.	V	-	1	0	MUC4	196992615	0.000000	0.05858	0.015000	0.15790	0.015000	0.08874	-0.219000	0.09228	0.088000	0.17205	0.089000	0.15464	GTC	.	.	none		0.617	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
ZNF782	158431	hgsc.bcm.edu	37	9	99581568	99581568	+	Missense_Mutation	SNP	T	T	C	rs34763627	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:99581568T>C	ENST00000481138.1	-	6	1398	c.737A>G	c.(736-738)aAt>aGt	p.N246S	ZNF782_ENST00000535338.1_Missense_Mutation_p.N114S|ZNF782_ENST00000466833.1_5'Flank	NM_001001662.1	NP_001001662.1	Q6ZMW2	ZN782_HUMAN	zinc finger protein 782	246			N -> S (in dbSNP:rs34763627).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|endometrium(2)|kidney(2)|large_intestine(12)|lung(8)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(3)	33		Acute lymphoblastic leukemia(62;0.0527)				CCCAAATTTATTGAAATTGTA	0.313													T|||	159	0.0317492	0.0023	0.0519	5008	,	,		19228	0.002		0.1064	False		,,,				2504	0.0112				p.N246S		Atlas-SNP	.											.	ZNF782	64	.	0			c.A737G						PASS	.	T	SER/ASN	88,4318	68.7+/-106.4	2,84,2117	70.0	76.0	74.0		737	-3.5	0.0	9	dbSNP_126	74	934,7664	203.4+/-246.4	57,820,3422	yes	missense	ZNF782	NM_001001662.1	46	59,904,5539	CC,CT,TT		10.863,1.9973,7.8591	benign	246/700	99581568	1022,11982	2203	4299	6502	SO:0001583	missense	158431	exon6			AATTTATTGAAAT	AK131468	CCDS35075.1	9q22.33	2013-01-08			ENSG00000196597	ENSG00000196597		"""Zinc fingers, C2H2-type"", ""-"""	33110	protein-coding gene	gene with protein product							Standard	NM_001001662		Approved	FLJ16636	uc004awp.1	Q6ZMW2	OTTHUMG00000020310	ENST00000481138.1:c.737A>G	9.37:g.99581568T>C	ENSP00000419397:p.Asn246Ser	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	75	28	0.373333	NM_001001662	B2RNR0	Missense_Mutation	SNP	ENST00000481138.1	37	CCDS35075.1	100	0.045787545787545784	1	0.0020325203252032522	23	0.06353591160220995	0	0.0	76	0.10026385224274406	T	8.866	0.948211	0.18356	0.019973	0.10863	ENSG00000196597	ENST00000481138;ENST00000535338	T;T	0.06528	3.51;3.29	3.33	-3.52	0.04682	.	0.697460	0.11782	N	0.530109	T	0.00073	0.0002	N	0.17764	0.52	0.09310	N	1	B	0.09022	0.002	B	0.06405	0.002	T	0.44205	-0.9343	10	0.28530	T	0.3	.	3.8127	0.08804	0.3002:0.3826:0.0:0.3171	rs34763627	246	Q6ZMW2	ZN782_HUMAN	S	246;114	ENSP00000419397:N246S;ENSP00000440624:N114S	ENSP00000419397:N246S	N	-	2	0	ZNF782	98621389	0.000000	0.05858	0.000000	0.03702	0.251000	0.25915	-1.910000	0.01584	-0.766000	0.04639	-0.296000	0.09543	AAT	T|0.930;C|0.070	0.070	strong		0.313	ZNF782-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356810.1	NM_001001662	
H2AFV	94239	hgsc.bcm.edu	37	7	44875203	44875203	+	Missense_Mutation	SNP	G	G	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:44875203G>C	ENST00000308153.4	-	4	341	c.250C>G	c.(250-252)Ccg>Gcg	p.P84A	H2AFV_ENST00000350771.3_Missense_Mutation_p.P58A|H2AFV_ENST00000349299.3_Missense_Mutation_p.P46A|H2AFV_ENST00000437072.1_Missense_Mutation_p.P46A|H2AFV_ENST00000446531.1_Missense_Mutation_p.P84A|H2AFV_ENST00000222690.6_Missense_Mutation_p.P84A|H2AFV_ENST00000521529.1_Intron|H2AFV_ENST00000381124.5_Intron	NM_012412.4	NP_036544.1	Q71UI9	H2AV_HUMAN	H2A histone family, member V	84						extracellular vesicular exosome (GO:0070062)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(2)|large_intestine(1)|lung(4)|prostate(1)|urinary_tract(1)	9						AAGTGACGCGGAGTGATACGC	0.453																																					p.P84A		Atlas-SNP	.											.	H2AFV	14	.	0			c.C250G						PASS	.						123.0	99.0	107.0					7																	44875203		2203	4300	6503	SO:0001583	missense	94239	exon4			GACGCGGAGTGAT	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.250C>G	7.37:g.44875203G>C	ENSP00000308405:p.Pro84Ala	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	56	15	0.267857	NM_012412	A6NFA8|A6NKY0|A6NN01|A8MQC5|Q59GV8|Q6PK98	Missense_Mutation	SNP	ENST00000308153.4	37	CCDS5496.1	.	.	.	.	.	.	.	.	.	.	G	19.56	3.850542	0.71719	.	.	ENSG00000105968	ENST00000222690;ENST00000437072;ENST00000349299;ENST00000308153;ENST00000350771;ENST00000446531	T;T;T;T;T;T	0.70749	-0.51;-0.51;-0.51;-0.51;-0.51;-0.51	5.68	5.68	0.88126	Histone-fold (2);Histone core (1);Histone H2A (2);	.	.	.	.	D	0.84415	0.5467	H	0.94698	3.57	0.80722	D	1	B;P;B;B	0.47302	0.118;0.893;0.083;0.235	B;P;B;B	0.49387	0.247;0.609;0.014;0.122	D	0.88628	0.3167	9	0.87932	D	0	-12.7012	17.2793	0.87124	0.0:0.0:1.0:0.0	.	58;46;84;84	A6NKY0;A6NFA8;Q71UI9;A6NN01	.;.;H2AV_HUMAN;.	A	84;46;46;84;58;84	ENSP00000222690:P84A;ENSP00000397115:P46A;ENSP00000342714:P46A;ENSP00000308405:P84A;ENSP00000340708:P58A;ENSP00000406901:P84A	ENSP00000222690:P84A	P	-	1	0	H2AFV	44841728	1.000000	0.71417	0.671000	0.29857	0.989000	0.77384	9.179000	0.94861	2.698000	0.92095	0.585000	0.79938	CCG	.	.	none		0.453	H2AFV-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251305.1	NM_012412	
PDE4DIP	9659	hgsc.bcm.edu	37	1	144916676	144916676	+	Nonsense_Mutation	SNP	C	C	T	rs1698683	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:144916676C>T	ENST00000369354.3	-	13	1868	c.1679G>A	c.(1678-1680)tGg>tAg	p.W560*	PDE4DIP_ENST00000369359.4_Nonsense_Mutation_p.W697*|PDE4DIP_ENST00000369349.3_Nonsense_Mutation_p.W560*|PDE4DIP_ENST00000313382.9_Nonsense_Mutation_p.W626*|PDE4DIP_ENST00000479408.2_Nonsense_Mutation_p.W347*|PDE4DIP_ENST00000529945.1_Nonsense_Mutation_p.W723*|PDE4DIP_ENST00000369356.4_Nonsense_Mutation_p.W560*|PDE4DIP_ENST00000530740.1_Nonsense_Mutation_p.W697*|PDE4DIP_ENST00000313431.9_Nonsense_Mutation_p.W723*|PDE4DIP_ENST00000369351.3_Nonsense_Mutation_p.W560*			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	560					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)		TTCTTTCAGCCACTGGAGGTT	0.433			T	PDGFRB	MPD																																p.W723X		Atlas-SNP	.		Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	.	PDE4DIP	817	.	0			c.G2168A						PASS	.	C	stop/TRP,stop/TRP,stop/TRP,stop/TRP,stop/TRP	1497,2909		0,1497,706	413.0	439.0	430.0		2168,1679,1877,1679,1679	5.8	1.0	1	dbSNP_89	430	2678,5914		0,2678,1618	yes	stop-gained,stop-gained,stop-gained,stop-gained,stop-gained	PDE4DIP	NM_001002811.1,NM_001002812.1,NM_001198832.1,NM_001198834.2,NM_014644.4	,,,,	0,4175,2324	TT,TC,CC		31.1685,33.9764,32.1203	,,,,	723/1133,560/970,626/2241,560/2363,560/2347	144916676	4175,8823	2203	4296	6499	SO:0001587	stop_gained	9659	exon9			TTCAGCCACTGGA	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.1679G>A	1.37:g.144916676C>T	ENSP00000358360:p.Trp560*	Somatic	318	0	0		WXS	Illumina HiSeq	Phase_I	283	68	0.240283	NM_001002811	A2RU15|O75042|O75065|Q2YDC1|Q5VU42|Q5VU44|Q5VU45|Q5VU46|Q5VU47|Q5VU48|Q5VU49|Q68DU2|Q6AZ93|Q6PK88|Q86T40|Q86TB2|Q8N3W0|Q8TAY9|Q9HCP2|Q9HCP3|Q9HCP4|Q9HCP5	Nonsense_Mutation	SNP	ENST00000369354.3	37	CCDS30824.1	582	0.2664835164835165	196	0.3983739837398374	95	0.26243093922651933	25	0.043706293706293704	266	0.35092348284960423	C	38	7.265646	0.98175	0.339764	0.311685	ENSG00000178104	ENST00000313382;ENST00000369354;ENST00000369356;ENST00000369353;ENST00000530740;ENST00000369359;ENST00000369351;ENST00000369349;ENST00000313431;ENST00000529945;ENST00000479408	.	.	.	5.83	5.83	0.93111	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.40728	T	0.16	.	18.0326	0.89290	0.0:1.0:0.0:0.0	rs1698683;rs61810875	.	.	.	X	626;560;560;723;697;697;560;560;723;723;347	.	ENSP00000327209:W626X	W	-	2	0	PDE4DIP	143628033	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.323000	0.59221	2.932000	0.99384	0.644000	0.83932	TGG	T|0.001;G|0.732	0.001	strong		0.433	PDE4DIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000038858.2	NM_022359	
CALCOCO2	10241	hgsc.bcm.edu	37	17	46939658	46939658	+	Missense_Mutation	SNP	C	C	G	rs10278	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:46939658C>G	ENST00000258947.3	+	12	1266	c.1165C>G	c.(1165-1167)Ccc>Gcc	p.P389A	CALCOCO2_ENST00000509507.1_Missense_Mutation_p.P410A|CALCOCO2_ENST00000416445.2_Missense_Mutation_p.P347A|CALCOCO2_ENST00000448105.2_Missense_Mutation_p.P413A|CALCOCO2_ENST00000508679.1_Missense_Mutation_p.P317A	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	171	0	0		WXS	Illumina HiSeq	Phase_I	158	74	0.468354	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	
GOLGB1	2804	hgsc.bcm.edu	37	3	121410844	121410844	+	Missense_Mutation	SNP	T	T	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:121410844T>G	ENST00000340645.5	-	14	7477	c.7352A>C	c.(7351-7353)gAa>gCa	p.E2451A	GOLGB1_ENST00000393667.3_Missense_Mutation_p.E2456A	NM_001256487.1|NM_001256488.1|NM_004487.4	NP_001243416.1|NP_001243417.1|NP_004478.3	Q14789	GOGB1_HUMAN	golgin B1	2451					Golgi organization (GO:0007030)	cis-Golgi network (GO:0005801)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(2)|cervix(2)|endometrium(12)|kidney(3)|large_intestine(26)|liver(2)|lung(36)|ovary(7)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(13)	119				GBM - Glioblastoma multiforme(114;0.0989)		CTGAATGTTTTCCTTTTTGAT	0.398																																					p.E2456A		Atlas-SNP	.											.	GOLGB1	319	.	0			c.A7367C						PASS	.						172.0	171.0	171.0					3																	121410844		2203	4300	6503	SO:0001583	missense	2804	exon14			ATGTTTTCCTTTT	X75304	CCDS3004.1, CCDS58847.1, CCDS74989.1	3q13	2010-02-12	2010-02-12	2007-07-27	ENSG00000173230	ENSG00000173230			4429	protein-coding gene	gene with protein product	"""macrogolgin"", ""golgi integral membrane protein 1"""	602500	"""golgi autoantigen, golgin subfamily b, macrogolgin (with transmembrane signal), 1"", ""golgin B1, golgi integral membrane protein"""			7691276, 15004235	Standard	NM_001256486		Approved	GCP, GCP372, giantin, GOLIM1	uc010hrc.4	Q14789	OTTHUMG00000159411	ENST00000340645.5:c.7352A>C	3.37:g.121410844T>G	ENSP00000341848:p.Glu2451Ala	Somatic	491	0	0		WXS	Illumina HiSeq	Phase_I	483	236	0.488613	NM_001256486	B2ZZ91|D3DN92|E7EP74|Q14398	Missense_Mutation	SNP	ENST00000340645.5	37	CCDS3004.1	.	.	.	.	.	.	.	.	.	.	T	12.49	1.952731	0.34471	.	.	ENSG00000173230	ENST00000340645;ENST00000393667	T;T	0.28255	1.62;1.62	5.79	5.79	0.91817	.	0.090631	0.47852	D	0.000201	T	0.44052	0.1275	L	0.56769	1.78	0.43588	D	0.995931	D;P;D	0.61697	0.972;0.925;0.99	P;P;P	0.55391	0.616;0.691;0.775	T	0.21552	-1.0242	10	0.30854	T	0.27	.	14.0831	0.64937	0.0:0.0:0.0:1.0	.	2456;2456;2451	E7EP74;B2ZZ91;Q14789	.;.;GOGB1_HUMAN	A	2451;2456	ENSP00000341848:E2451A;ENSP00000377275:E2456A	ENSP00000341848:E2451A	E	-	2	0	GOLGB1	122893534	1.000000	0.71417	0.908000	0.35775	0.972000	0.66771	5.884000	0.69729	2.208000	0.71279	0.460000	0.39030	GAA	.	.	none		0.398	GOLGB1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000355159.1	NM_004487	
TDRD9	122402	hgsc.bcm.edu	37	14	104497543	104497543	+	Silent	SNP	C	C	T	rs10135507	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:104497543C>T	ENST00000409874.4	+	29	3429	c.3381C>T	c.(3379-3381)ctC>ctT	p.L1127L	TDRD9_ENST00000339063.5_Intron	NM_153046.2	NP_694591.2	Q8NDG6	TDRD9_HUMAN	tudor domain containing 9	1127					cell differentiation (GO:0030154)|DNA methylation involved in gamete generation (GO:0043046)|fertilization (GO:0009566)|gene silencing by RNA (GO:0031047)|male meiosis (GO:0007140)|multicellular organismal development (GO:0007275)|piRNA metabolic process (GO:0034587)|spermatogenesis (GO:0007283)	nucleus (GO:0005634)|piP-body (GO:0071547)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)	p.L1127L(1)		breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(10)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)	33		all_cancers(154;0.109)|Melanoma(154;0.0525)|all_epithelial(191;0.0768)				AGAAATATCTCATCCGGATTT	0.393													C|||	1599	0.319289	0.2776	0.3429	5008	,	,		13729	0.3353		0.3469	False		,,,				2504	0.3139				p.L1127L		Atlas-SNP	.											TDRD9_ENST00000409874,NS,carcinoma,0,2	TDRD9	175	2	1	Substitution - coding silent(1)	stomach(1)	c.C3381T						PASS	.	C		424,960		63,298,331	128.0	110.0	115.0		3381	4.2	0.0	14	dbSNP_119	115	1047,2135		162,723,706	no	coding-synonymous	TDRD9	NM_153046.2		225,1021,1037	TT,TC,CC		32.9038,30.6358,32.2164		1127/1383	104497543	1471,3095	692	1591	2283	SO:0001819	synonymous_variant	122402	exon29			ATATCTCATCCGG	AK093483	CCDS9987.2	14q32.33	2013-01-23	2004-04-01	2004-04-02	ENSG00000156414	ENSG00000156414		"""Tudor domain containing"""	20122	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 75"""	C14orf75			Standard	NM_153046		Approved	DKFZp434N0820, FLJ36164, NET54	uc001yom.4	Q8NDG6	OTTHUMG00000152876	ENST00000409874.4:c.3381C>T	14.37:g.104497543C>T		Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	128	65	0.507812	NM_153046	A1A4S7|Q6ZU54|Q8N7T3|Q8N827|Q8N9V5|Q96AS9	Silent	SNP	ENST00000409874.4	37	CCDS9987.2																																																																																			C|0.684;T|0.316	0.316	strong		0.393	TDRD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328325.3	NM_153046	
CLDN20	49861	hgsc.bcm.edu	37	6	155597147	155597147	+	Silent	SNP	C	C	T	rs1555774	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:155597147C>T	ENST00000367165.3	+	2	674	c.294C>T	c.(292-294)tcC>tcT	p.S98S	TFB1M_ENST00000367166.4_Intron	NM_001001346.3	NP_001001346.1	P56880	CLD20_HUMAN	claudin 20	98					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)			endometrium(1)|lung(2)	3				OV - Ovarian serous cystadenocarcinoma(155;7.82e-13)|BRCA - Breast invasive adenocarcinoma(81;0.0114)		TCTGCACTTCCACAGTAGGAA	0.532													C|||	1993	0.397963	0.2572	0.5159	5008	,	,		22057	0.6528		0.2535	False		,,,				2504	0.3906				p.S98S		Atlas-SNP	.											.	CLDN20	10	.	0			c.C294T						PASS	.	C	,	1192,3214	414.6+/-336.9	166,860,1177	133.0	116.0	121.0		294,	0.2	0.0	6	dbSNP_88	121	2290,6310	386.5+/-341.9	312,1666,2322	no	coding-synonymous,intron	CLDN20,TFB1M	NM_001001346.3,NM_016020.3	,	478,2526,3499	TT,TC,CC		26.6279,27.054,26.7723	,	98/220,	155597147	3482,9524	2203	4300	6503	SO:0001819	synonymous_variant	49861	exon2			CACTTCCACAGTA	BC020838	CCDS5249.1	6q25	2008-08-01			ENSG00000171217	ENSG00000171217		"""Claudins"""	2042	protein-coding gene	gene with protein product						16836752	Standard	NM_001001346		Approved		uc003qql.2	P56880	OTTHUMG00000015882	ENST00000367165.3:c.294C>T	6.37:g.155597147C>T		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	111	76	0.684685	NM_001001346		Silent	SNP	ENST00000367165.3	37	CCDS5249.1																																																																																			C|0.681;T|0.319	0.319	strong		0.532	CLDN20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042818.1	NM_001001346	
MYOC	4653	hgsc.bcm.edu	37	1	171621525	171621525	+	Missense_Mutation	SNP	C	C	T	rs2234926	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:171621525C>T	ENST00000037502.6	-	1	298	c.227G>A	c.(226-228)aGa>aAa	p.R76K		NM_000261.1	NP_000252.1	Q99972	MYOC_HUMAN	myocilin, trabecular meshwork inducible glucocorticoid response	76			R -> K (in dbSNP:rs2234926). {ECO:0000269|PubMed:10798654, ECO:0000269|PubMed:10980537, ECO:0000269|PubMed:11004290, ECO:0000269|PubMed:12189160, ECO:0000269|PubMed:12356829, ECO:0000269|PubMed:12442283, ECO:0000269|PubMed:12872267, ECO:0000269|PubMed:15025728, ECO:0000269|PubMed:9863594}.		bone development (GO:0060348)|clustering of voltage-gated sodium channels (GO:0045162)|ERBB2-ERBB3 signaling pathway (GO:0038133)|myelination in peripheral nervous system (GO:0022011)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of Rho protein signal transduction (GO:0035024)|negative regulation of stress fiber assembly (GO:0051497)|neuron projection development (GO:0031175)|non-canonical Wnt signaling pathway via JNK cascade (GO:0038031)|osteoblast differentiation (GO:0001649)|positive regulation of cell migration (GO:0030335)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of mitochondrial depolarization (GO:0051901)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|regulation of MAPK cascade (GO:0043408)|skeletal muscle hypertrophy (GO:0014734)	cilium (GO:0005929)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrial outer membrane (GO:0005741)|node of Ranvier (GO:0033268)|proteinaceous extracellular matrix (GO:0005578)	fibronectin binding (GO:0001968)|frizzled binding (GO:0005109)|myosin light chain binding (GO:0032027)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(4)|lung(12)|ovary(2)|prostate(1)|urinary_tract(2)	28	all_cancers(6;5.47e-10)|all_hematologic(923;0.088)|Acute lymphoblastic leukemia(37;0.181)					GCTGCTGTCTCTCTGTAAGTT	0.577													C|||	682	0.136182	0.0068	0.1023	5008	,	,		18797	0.0794		0.1412	False		,,,				2504	0.3885				p.R76K		Atlas-SNP	.											.	MYOC	69	.	0			c.G227A	GRCh37	CM085579	MYOC	M	rs2234926	PASS	.	C	LYS/ARG	122,4284	91.1+/-129.8	2,118,2083	130.0	102.0	111.0		227	3.4	1.0	1	dbSNP_98	111	1155,7445	237.1+/-269.0	76,1003,3221	yes	missense	MYOC	NM_000261.1	26	78,1121,5304	TT,TC,CC		13.4302,2.769,9.8185	probably-damaging	76/505	171621525	1277,11729	2203	4300	6503	SO:0001583	missense	4653	exon1			CTGTCTCTCTGTA	BC029261	CCDS1297.1	1q23-q24	2008-02-05			ENSG00000034971	ENSG00000034971			7610	protein-coding gene	gene with protein product		601652		GLC1A		9169133, 9005853	Standard	NM_000261		Approved	TIGR, JOAG1	uc001ghu.3	Q99972	OTTHUMG00000034789	ENST00000037502.6:c.227G>A	1.37:g.171621525C>T	ENSP00000037502:p.Arg76Lys	Somatic	300	0	0		WXS	Illumina HiSeq	Phase_I	264	122	0.462121	NM_000261	B2RD84|O00620|Q7Z6Q9	Missense_Mutation	SNP	ENST00000037502.6	37	CCDS1297.1	175	0.08012820512820513	7	0.014227642276422764	31	0.0856353591160221	27	0.0472027972027972	110	0.14511873350923482	C	8.539	0.872785	0.17322	0.02769	0.134302	ENSG00000034971	ENST00000037502;ENST00000357746;ENST00000536591;ENST00000537133	T	0.60299	0.2	5.31	3.43	0.39272	.	0.072208	0.56097	N	0.000037	T	0.60274	0.2256	M	0.64997	1.995	0.43080	P	0.00526099999999996	D;B	0.58970	0.984;0.018	D;B	0.68192	0.956;0.012	T	0.65549	-0.6141	9	0.62326	D	0.03	.	11.2975	0.49286	0.0:0.8356:0.0:0.1644	rs2234926	76;76	B4DV44;Q99972	.;MYOC_HUMAN	K	76;76;9;76	ENSP00000037502:R76K	ENSP00000037502:R76K	R	-	2	0	MYOC	169888148	1.000000	0.71417	0.998000	0.56505	0.070000	0.16714	2.640000	0.46579	0.332000	0.23536	-0.797000	0.03246	AGA	C|0.909;T|0.091	0.091	strong		0.577	MYOC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084178.2	NM_000261	
UBR2	23304	hgsc.bcm.edu	37	6	42627434	42627434	+	Missense_Mutation	SNP	G	G	A	rs6917033	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:42627434G>A	ENST00000372899.1	+	30	3541	c.3283G>A	c.(3283-3285)Gca>Aca	p.A1095T	UBR2_ENST00000372901.1_Missense_Mutation_p.A1095T|UBR2_ENST00000372883.3_3'UTR	NM_015255.2	NP_056070.1	Q8IWV8	UBR2_HUMAN	ubiquitin protein ligase E3 component n-recognin 2	1095			A -> P (in dbSNP:rs6917033).|A -> S (in dbSNP:rs6917033).|A -> T (in dbSNP:rs6917033). {ECO:0000269|PubMed:9205841}.		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)			ACTGGGCCCCGCACAAACTCA	0.408													G|||	2163	0.431909	0.5015	0.389	5008	,	,		16383	0.4385		0.3857	False		,,,				2504	0.409				p.A1095T		Atlas-SNP	.											.	UBR2	134	.	0			c.G3283A						PASS	.	G	THR/ALA	2124,2282	577.4+/-384.4	509,1106,588	88.0	81.0	83.0		3283	2.8	0.8	6	dbSNP_116	83	3370,5230	498.4+/-374.7	682,2006,1612	yes	missense	UBR2	NM_015255.2	58	1191,3112,2200	AA,AG,GG		39.186,48.207,42.242	benign	1095/1756	42627434	5494,7512	2203	4300	6503	SO:0001583	missense	23304	exon30			GGCCCCGCACAAA	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.3283G>A	6.37:g.42627434G>A	ENSP00000361990:p.Ala1095Thr	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	78	38	0.487179	NM_015255	O15057|Q4VXK2|Q5TFH6|Q6P2I2|Q6ZUD0	Missense_Mutation	SNP	ENST00000372899.1	37	CCDS4870.1	952	0.4358974358974359	235	0.47764227642276424	152	0.4198895027624309	258	0.45104895104895104	307	0.4050131926121372	G	9.977	1.227046	0.22542	0.48207	0.39186	ENSG00000024048	ENST00000372899;ENST00000372901	T;T	0.42131	0.98;0.98	5.56	2.77	0.32553	.	0.364840	0.34291	N	0.004086	T	0.10508	0.0257	N	0.22421	0.69	0.09310	P	0.9999999850984	B;B	0.29115	0.233;0.091	B;B	0.21708	0.036;0.025	T	0.14035	-1.0487	9	0.16896	T	0.51	3.3783	11.6187	0.51104	0.0687:0.2336:0.6977:0.0	rs6917033;rs60034483;rs6917033	1095;1095	Q8IWV8-4;Q8IWV8	.;UBR2_HUMAN	T	1095	ENSP00000361990:A1095T;ENSP00000361992:A1095T	ENSP00000361990:A1095T	A	+	1	0	UBR2	42735412	0.962000	0.33011	0.836000	0.33094	0.428000	0.31595	1.338000	0.33873	0.290000	0.22444	-1.516000	0.00938	GCA	A|0.421;G|0.579	0.421	strong		0.408	UBR2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040558.2	NM_015255	
C17orf104	284071	hgsc.bcm.edu	37	17	42745180	42745180	+	Missense_Mutation	SNP	A	A	G	rs77416189	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:42745180A>G	ENST00000409122.2	+	5	2043	c.1901A>G	c.(1900-1902)tAc>tGc	p.Y634C	C17orf104_ENST00000409464.1_Missense_Mutation_p.Y468C|C17orf104_ENST00000359945.3_Missense_Mutation_p.Y634C	NM_001145080.2	NP_001138552.2	A2RUB1	CQ104_HUMAN	chromosome 17 open reading frame 104	634										autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(7)|ovary(2)|pancreas(1)|skin(1)	24						CAAAATACATACCAAGATCTA	0.413													A|||	31	0.0061901	0.0	0.0014	5008	,	,		18324	0.0		0.0298	False		,,,				2504	0.0				p.Y634C		Atlas-SNP	.											.	C17orf104	75	.	0			c.A1901G						PASS	.	A	CYS/TYR	10,4396	16.8+/-37.8	0,10,2193	60.0	59.0	59.0		1901	5.7	0.9	17	dbSNP_131	59	111,8489	59.5+/-121.1	1,109,4190	yes	missense	C17orf104	NM_001145080.2	194	1,119,6383	GG,GA,AA		1.2907,0.227,0.9303	probably-damaging	634/953	42745180	121,12885	2203	4300	6503	SO:0001583	missense	284071	exon5			ATACATACCAAGA		CCDS45703.1, CCDS45703.2	17q21.31	2009-09-08			ENSG00000180336	ENSG00000180336			26670	protein-coding gene	gene with protein product							Standard	NM_001145080		Approved	FLJ35848	uc002iha.3	A2RUB1	OTTHUMG00000153039	ENST00000409122.2:c.1901A>G	17.37:g.42745180A>G	ENSP00000386452:p.Tyr634Cys	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	72	40	0.555556	NM_001145080	B4DXJ2|B5MD93|B9EGQ6|C4AM97|Q4G0Y1|Q8IVZ7|Q8NA45	Missense_Mutation	SNP	ENST00000409122.2	37	CCDS45703.2	27	0.012362637362637362	0	0.0	1	0.0027624309392265192	0	0.0	26	0.03430079155672823	A	14.07	2.426989	0.43122	0.00227	0.012907	ENSG00000180336	ENST00000359945;ENST00000409122;ENST00000409464	T;T;T	0.39056	1.11;1.1;1.13	5.66	5.66	0.87406	.	0.228426	0.37955	N	0.001878	T	0.31575	0.0801	L	0.39898	1.24	0.45541	D	0.998496	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	T	0.48592	-0.9022	10	0.66056	D	0.02	-12.9591	14.4518	0.67389	1.0:0.0:0.0:0.0	.	634;634;468	A2RUB1-5;A2RUB1;A2RUB1-1	.;CQ104_HUMAN;.	C	634;634;468	ENSP00000353028:Y634C;ENSP00000386452:Y634C;ENSP00000386586:Y468C	ENSP00000353028:Y634C	Y	+	2	0	C17orf104	40100706	1.000000	0.71417	0.898000	0.35279	0.888000	0.51559	6.500000	0.73687	2.151000	0.67156	0.533000	0.62120	TAC	A|0.990;G|0.010	0.010	strong		0.413	C17orf104-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329171.2	NM_001145080	
MTFR1	9650	hgsc.bcm.edu	37	8	66620359	66620359	+	Intron	SNP	G	G	A	rs13274205	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:66620359G>A	ENST00000262146.4	+	7	1059				MTFR1_ENST00000458689.2_Intron	NM_014637.3	NP_055452.3	Q15390	MTFR1_HUMAN	mitochondrial fission regulator 1						aerobic respiration (GO:0009060)|mitochondrial fission (GO:0000266)|mitochondrion organization (GO:0007005)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)				cervix(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(1)|pancreas(1)|urinary_tract(1)	11			Epithelial(68;0.0526)|BRCA - Breast invasive adenocarcinoma(89;0.156)|all cancers(69;0.171)|OV - Ovarian serous cystadenocarcinoma(28;0.194)			AAAGGGAGGTGATACAGGATT	0.413													G|||	1389	0.277356	0.3215	0.3156	5008	,	,		19512	0.0		0.5348	False		,,,				2504	0.2117				p.X349X		Atlas-SNP	.											.	MTFR1	26	.	0			c.G1046A						PASS	.	G	,,	472,912		83,306,303	46.0	38.0	41.0		,1046,	-0.1	0.0	8	dbSNP_121	41	1761,1421		480,801,310	no	intron,coding-synonymous,intron	MTFR1	NM_001145838.1,NM_001145839.1,NM_014637.3	,,	563,1107,613	AA,AG,GG		44.6574,34.104,48.9049	,,	,349/349,	66620359	2233,2333	692	1591	2283	SO:0001627	intron_variant	9650	exon7			GGAGGTGATACAG		CCDS6182.1, CCDS55240.1	8q13.1	2012-11-30							29510	protein-coding gene	gene with protein product	"""likely ortholog of chicken chondrocyte protein with a poly proline region"""					7584026, 7584028, 15389597	Standard	NM_014637		Approved	CHPPR, KIAA0009, FAM54A2	uc003xvn.2	Q15390		ENST00000262146.4:c.933+113G>A	8.37:g.66620359G>A		Somatic	17	0	0		WXS	Illumina HiSeq	Phase_I	19	19	1	NM_001145839	E7EP84|Q6IB94|Q7Z669|Q86XH5|Q8IVD7	Silent	SNP	ENST00000262146.4	37	CCDS6182.1																																																																																			G|0.693;A|0.307	0.307	strong		0.413	MTFR1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378894.1	NM_014637	
MYH2	4620	hgsc.bcm.edu	37	17	10447057	10447057	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:10447057T>C	ENST00000245503.5	-	8	1096	c.712A>G	c.(712-714)Acc>Gcc	p.T238A	MYH2_ENST00000532183.2_Missense_Mutation_p.T238A|CTC-297N7.11_ENST00000587182.2_RNA|MYH2_ENST00000397183.2_Missense_Mutation_p.T238A	NM_017534.5	NP_060004.3	Q9UKX2	MYH2_HUMAN	myosin, heavy chain 2, skeletal muscle, adult	238	Myosin motor.				Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|membrane organization (GO:0061024)|metabolic process (GO:0008152)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|plasma membrane repair (GO:0001778)|response to activity (GO:0014823)	A band (GO:0031672)|actomyosin contractile ring (GO:0005826)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin filament (GO:0032982)|protein complex (GO:0043234)|sarcomere (GO:0030017)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)			NS(1)|biliary_tract(1)|breast(9)|central_nervous_system(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|lung(99)|ovary(6)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(4)	176						TTCCTCACGGTCTTGGCGTTG	0.478																																					p.T238A		Atlas-SNP	.											MYH2,NS,carcinoma,+2,1	MYH2	390	1	0			c.A712G						scavenged	.						88.0	87.0	88.0					17																	10447057		2203	4298	6501	SO:0001583	missense	4620	exon8			TCACGGTCTTGGC		CCDS11156.1	17p13.1	2014-02-04	2006-09-29		ENSG00000125414	ENSG00000125414		"""Myosins / Myosin superfamily : Class II"""	7572	protein-coding gene	gene with protein product		160740	"""myosin, heavy polypeptide 2, skeletal muscle, adult"", ""inclusion body myopathy 3, autosomal dominant"""	IBM3		7545970, 11889243	Standard	NM_001100112		Approved	MYH2A, MYHSA2, MyHC-IIa, MYHas8, MyHC-2A	uc010coi.3	Q9UKX2	OTTHUMG00000130363	ENST00000245503.5:c.712A>G	17.37:g.10447057T>C	ENSP00000245503:p.Thr238Ala	Somatic	344	2	0.00581395		WXS	Illumina HiSeq	Phase_I	307	6	0.019544	NM_017534	A0AVL4|Q14322|Q16229|Q567P6|Q86T56	Missense_Mutation	SNP	ENST00000245503.5	37	CCDS11156.1	.	.	.	.	.	.	.	.	.	.	T	28.5	4.925149	0.92319	.	.	ENSG00000125414	ENST00000532183;ENST00000245503;ENST00000397183	D;D;D	0.85088	-1.94;-1.94;-1.94	5.01	5.01	0.66863	Myosin head, motor domain (3);	0.000000	0.40385	U	0.001103	D	0.96125	0.8737	H	0.99834	4.825	0.58432	D	0.999991	D;P	0.54047	0.964;0.547	D;P	0.75020	0.985;0.751	D	0.97707	1.0188	10	0.87932	D	0	.	14.0597	0.64793	0.0:0.0:0.0:1.0	.	238;238	Q567P6;Q9UKX2	.;MYH2_HUMAN	A	238	ENSP00000433944:T238A;ENSP00000245503:T238A;ENSP00000380367:T238A	ENSP00000245503:T238A	T	-	1	0	MYH2	10387782	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.868000	0.87116	2.109000	0.64355	0.533000	0.62120	ACC	.	.	none		0.478	MYH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252726.3	NM_017534	
CHRNA3	1136	hgsc.bcm.edu	37	15	78894339	78894339	+	Silent	SNP	G	G	A	rs1051730	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:78894339G>A	ENST00000326828.5	-	5	1029	c.645C>T	c.(643-645)taC>taT	p.Y215Y	CHRNA3_ENST00000348639.3_Silent_p.Y215Y	NM_000743.4	NP_000734.2	P32297	ACHA3_HUMAN	cholinergic receptor, nicotinic, alpha 3 (neuronal)	215					activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|behavioral response to nicotine (GO:0035095)|cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|locomotory behavior (GO:0007626)|nervous system development (GO:0007399)|regulation of acetylcholine secretion, neurotransmission (GO:0014056)|regulation of dendrite morphogenesis (GO:0048814)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of membrane potential (GO:0042391)|regulation of smooth muscle contraction (GO:0006940)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission involved in micturition (GO:0060084)|synaptic transmission, cholinergic (GO:0007271)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|ligand-gated ion channel activity (GO:0015276)			central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18					Bupropion(DB01156)|Dextromethorphan(DB00514)|Galantamine(DB00674)|Levomethadyl Acetate(DB01227)|Nicotine(DB00184)|Pentolinium(DB01090)|Varenicline(DB01273)	TGTCGTGTTTGTAGCCTGGGG	0.532													G|||	842	0.168131	0.087	0.2161	5008	,	,		17692	0.0268		0.3688	False		,,,				2504	0.183				p.Y215Y		Atlas-SNP	.											.	CHRNA3	56	.	0			c.C645T	GRCh37	CM078027	CHRNA3	M	rs1051730	PASS	.	G	,	529,3863	240.6+/-251.3	28,473,1695	163.0	139.0	147.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	645,645	5.3	1.0	15	dbSNP_86	147	3000,5586	463.5+/-366.0	555,1890,1848	no	coding-synonymous,coding-synonymous	CHRNA3	NM_000743.4,NM_001166694.1	,	583,2363,3543	AA,AG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	34.9406,12.0446,27.1922	,	215/506,215/490	78894339	3529,9449	2196	4293	6489	SO:0001819	synonymous_variant	1136	exon5			GTGTTTGTAGCCT		CCDS10305.1, CCDS53964.1	15q24	2012-02-11	2012-02-07		ENSG00000080644	ENSG00000080644		"""Cholinergic receptors"", ""Ligand-gated ion channels / Acetylcholine receptors, nicotinic"""	1957	protein-coding gene	gene with protein product	"""acetylcholine receptor, nicotinic, alpha 3 (neuronal)"""	118503	"""cholinergic receptor, nicotinic, alpha polypeptide 3"""			2004777	Standard	NM_000743		Approved		uc002bec.3	P32297	OTTHUMG00000143863	ENST00000326828.5:c.645C>T	15.37:g.78894339G>A		Somatic	288	0	0		WXS	Illumina HiSeq	Phase_I	338	338	1	NM_000743	Q15823|Q4KMN8|Q86U77|Q96RH3|Q99553|Q9BQ93|Q9BRR4	Silent	SNP	ENST00000326828.5	37	CCDS10305.1																																																																																			G|0.754;A|0.246	0.246	strong		0.532	CHRNA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000290111.3		
KIAA1549	57670	hgsc.bcm.edu	37	7	138601826	138601826	+	Missense_Mutation	SNP	G	G	A	rs2251220	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:138601826G>A	ENST00000422774.1	-	2	2594	c.2546C>T	c.(2545-2547)tCg>tTg	p.S849L	KIAA1549_ENST00000440172.1_Missense_Mutation_p.S849L|KIAA1549_ENST00000242365.4_Missense_Mutation_p.S799L			Q9HCM3	K1549_HUMAN	KIAA1549	849				S -> L (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						AGAAACAAACGAGGATCCTGA	0.572			O	BRAF	pilocytic astrocytoma								G|||	2056	0.410543	0.7821	0.2536	5008	,	,		20783	0.2024		0.3519	False		,,,				2504	0.2945				p.S849L	NSCLC(119;1534 1718 44213 46230 50068)	Atlas-SNP	.		Dom	yes		7	7q34	57670	KIAA1549		O	.	KIAA1549	314	.	0			c.C2546T						PASS	.	G	LEU/SER,LEU/SER	2782,1362		940,902,230	54.0	56.0	55.0		2546,2546	3.5	0.2	7	dbSNP_100	55	2720,5702		472,1776,1963	yes	missense,missense	KIAA1549	NM_001164665.1,NM_020910.2	145,145	1412,2678,2193	AA,AG,GG		32.2964,32.8668,43.7848	benign,benign	849/1951,849/1935	138601826	5502,7064	2072	4211	6283	SO:0001583	missense	57670	exon2			ACAAACGAGGATC		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.2546C>T	7.37:g.138601826G>A	ENSP00000416040:p.Ser849Leu	Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	41	21	0.512195	NM_020910	B6HY55|B6HY56|B6HY58|B6HY60|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q5BJD6|Q8IY15|Q9H0M3	Missense_Mutation	SNP	ENST00000422774.1	37	CCDS56513.1	857	0.3923992673992674	381	0.774390243902439	93	0.2569060773480663	124	0.21678321678321677	259	0.341688654353562	G	11.89	1.775135	0.31411	0.671332	0.322964	ENSG00000122778	ENST00000440172;ENST00000242365;ENST00000422774	T;T;T	0.25749	1.78;1.79;1.78	4.39	3.51	0.40186	.	0.675167	0.13091	N	0.414515	T	0.00012	0.0000	N	0.20986	0.625	0.58432	P	6.999999999979245E-6	B;B	0.20459	0.027;0.045	B;B	0.13407	0.004;0.009	T	0.18053	-1.0349	9	0.45353	T	0.12	.	9.9369	0.41556	0.0947:0.0:0.9053:0.0	rs2251220;rs3813698;rs10358772;rs17605836;rs52805605;rs57668245;rs2251220	849;849	Q9HCM3;Q9HCM3-2	K1549_HUMAN;.	L	849;799;849	ENSP00000406661:S849L;ENSP00000242365:S799L;ENSP00000416040:S849L	ENSP00000242365:S799L	S	-	2	0	KIAA1549	138252366	0.995000	0.38212	0.157000	0.22605	0.020000	0.10135	3.409000	0.52657	1.081000	0.41110	-0.300000	0.09419	TCG	G|0.579;A|0.421	0.421	strong		0.572	KIAA1549-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348092.1		
C4orf17	84103	hgsc.bcm.edu	37	4	100443784	100443784	+	Silent	SNP	C	C	G	rs200176388|rs36110345|rs386677740|rs61732380	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:100443784C>G	ENST00000326581.4	+	3	617	c.255C>G	c.(253-255)tcC>tcG	p.S85S	C4orf17_ENST00000514652.1_Silent_p.S85S|C4orf17_ENST00000503257.1_3'UTR	NM_032149.2	NP_115525.2	Q53FE4	CD017_HUMAN	chromosome 4 open reading frame 17	85			S -> P (in dbSNP:rs13119384). {ECO:0000269|PubMed:11230166, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.2}.							central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(9)|prostate(1)|urinary_tract(3)	18				OV - Ovarian serous cystadenocarcinoma(123;2.08e-08)		GTTACCCCTCCAGCACTGCAG	0.498													C|||	1057	0.211062	0.202	0.1888	5008	,	,		16686	0.1161		0.2744	False		,,,				2504	0.272				p.S85S		Atlas-SNP	.											.	C4orf17	42	.	0			c.C255G						PASS	.	C		90,4316		28,34,2141	112.0	104.0	107.0		255	1.6	0.1	4	dbSNP_129	107	186,8414		49,88,4163	no	coding-synonymous	C4orf17	NM_032149.2		77,122,6304	GG,GC,CC		2.1628,2.0427,2.1221		85/360	100443784	276,12730	2203	4300	6503	SO:0001819	synonymous_variant	84103	exon3			CCCCTCCAGCACT	AL136838	CCDS3649.1	4q23	2008-02-05			ENSG00000138813	ENSG00000138813			25274	protein-coding gene	gene with protein product						11230166	Standard	NM_032149		Approved	DKFZP434G072	uc003huw.3	Q53FE4	OTTHUMG00000131027	ENST00000326581.4:c.255C>G	4.37:g.100443784C>G		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	91	41	0.450549	NM_032149	Q6FI84|Q6IS77|Q8NA78|Q9H0D9	Silent	SNP	ENST00000326581.4	37	CCDS3649.1																																																																																			C|0.769;G|0.231	0.231	strong		0.498	C4orf17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253670.2	NM_032149	
RP1L1	94137	hgsc.bcm.edu	37	8	10467124	10467124	+	Missense_Mutation	SNP	G	G	C	rs4841399	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	45	0	0		WXS	Illumina HiSeq	Phase_I	45	37	0.822222	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		
GATA2	2624	hgsc.bcm.edu	37	3	128204951	128204951	+	Missense_Mutation	SNP	C	C	T	rs2335052	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	scavenged	.	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	118	1	0.00847458		WXS	Illumina HiSeq	Phase_I	104	60	0.576923	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	
OR4K14	122740	hgsc.bcm.edu	37	14	20482919	20482919	+	Missense_Mutation	SNP	A	A	C	rs17308108	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:20482919A>C	ENST00000305045.2	-	1	433	c.434T>G	c.(433-435)cTg>cGg	p.L145R		NM_001004712.1	NP_001004712.1	Q8NGD5	OR4KE_HUMAN	olfactory receptor, family 4, subfamily K, member 14	145			L -> R (in dbSNP:rs17308108).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(3)|endometrium(3)|kidney(1)|large_intestine(4)|lung(20)|skin(6)	37	all_cancers(95;0.00108)		Epithelial(56;4.65e-07)|all cancers(55;2e-06)	GBM - Glioblastoma multiforme(265;0.00124)		AGCCAGCACCAGCCTGATGCA	0.488													A|||	465	0.0928514	0.0461	0.0836	5008	,	,		22273	0.1647		0.0686	False		,,,				2504	0.1135				p.L145R		Atlas-SNP	.											.	OR4K14	86	.	0			c.T434G						PASS	.	A	ARG/LEU	242,4164		4,234,1965	74.0	73.0	73.0		434	4.0	0.2	14	dbSNP_123	73	652,7948		28,596,3676	yes	missense	OR4K14	NM_001004712.1	102	32,830,5641	CC,CA,AA		7.5814,5.4925,6.8738	probably-damaging	145/311	20482919	894,12112	2203	4300	6503	SO:0001583	missense	122740	exon1			AGCACCAGCCTGA		CCDS32027.1	14q11.2	2013-09-23			ENSG00000169484	ENSG00000169484		"""GPCR / Class A : Olfactory receptors"""	15352	protein-coding gene	gene with protein product							Standard	NM_001004712		Approved		uc010tky.2	Q8NGD5	OTTHUMG00000170780	ENST00000305045.2:c.434T>G	14.37:g.20482919A>C	ENSP00000305011:p.Leu145Arg	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	63	32	0.507937	NM_001004712	Q6IEU1|Q96R71	Missense_Mutation	SNP	ENST00000305045.2	37	CCDS32027.1	199	0.09111721611721611	26	0.052845528455284556	32	0.08839779005524862	85	0.1486013986013986	56	0.07387862796833773	.	12.44	1.937602	0.34189	0.054925	0.075814	ENSG00000169484	ENST00000305045	T	0.44881	0.91	4.04	4.04	0.47022	GPCR, rhodopsin-like superfamily (1);	0.270951	0.20350	N	0.094073	T	0.00998	0.0033	H	0.97186	3.955	0.45762	P	0.0013480000000000159	D	0.64830	0.994	D	0.71414	0.973	T	0.55798	-0.8084	9	0.87932	D	0	.	12.097	0.53761	1.0:0.0:0.0:0.0	rs17308108;rs52813083;rs17308108	145	Q8NGD5	OR4KE_HUMAN	R	145	ENSP00000305011:L145R	ENSP00000305011:L145R	L	-	2	0	OR4K14	19552759	0.783000	0.28701	0.198000	0.23420	0.111000	0.19643	5.417000	0.66423	1.695000	0.51148	0.413000	0.27773	CTG	A|0.922;C|0.078	0.078	strong		0.488	OR4K14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410343.1		
TMEM140	55281	hgsc.bcm.edu	37	7	134849577	134849577	+	Silent	SNP	A	A	C	rs2288237	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:134849577A>C	ENST00000275767.3	+	2	607	c.384A>C	c.(382-384)gcA>gcC	p.A128A	C7orf49_ENST00000459937.1_Intron	NM_018295.3	NP_060765.4	Q9NV12	TM140_HUMAN	transmembrane protein 140	128						integral component of membrane (GO:0016021)				kidney(1)|large_intestine(2)|lung(2)	5						TGCTGCTGGCAGGCGGCCTGG	0.647													c|||	2283	0.455871	0.4009	0.4798	5008	,	,		16747	0.2589		0.4821	False		,,,				2504	0.6892				p.A128A		Atlas-SNP	.											TMEM140,NS,carcinoma,+1,1	TMEM140	18	1	0			c.A384C						PASS	.	T		1931,2475	618.7+/-393.2	434,1063,706	38.0	37.0	37.0		384	2.5	0.2	7	dbSNP_100	37	4363,4237	568.8+/-389.1	1120,2123,1057	no	coding-synonymous	TMEM140	NM_018295.3		1554,3186,1763	CC,CA,AA		49.2674,43.8266,48.393		128/186	134849577	6294,6712	2203	4300	6503	SO:0001819	synonymous_variant	55281	exon2			GCTGGCAGGCGGC	AK001862	CCDS5837.1	7q33	2006-03-17			ENSG00000146859	ENSG00000146859			21870	protein-coding gene	gene with protein product							Standard	NM_018295		Approved	FLJ11000	uc003vsi.3	Q9NV12	OTTHUMG00000155413	ENST00000275767.3:c.384A>C	7.37:g.134849577A>C		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	123	123	1	NM_018295	A4D1P9|Q8WUC3	Silent	SNP	ENST00000275767.3	37	CCDS5837.1																																																																																			A|0.538;C|0.462	0.462	strong		0.647	TMEM140-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340017.2	NM_018295	
C10orf71	118461	hgsc.bcm.edu	37	10	50531606	50531606	+	Missense_Mutation	SNP	C	C	A	rs386743566|rs55780106	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	45	0	0		WXS	Illumina HiSeq	Phase_I	42	16	0.380952	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	
C17orf102	400591	hgsc.bcm.edu	37	17	32906038	32906038	+	Missense_Mutation	SNP	G	G	C	rs117721431	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:32906038G>C	ENST00000357754.1	-	1	350	c.262C>G	c.(262-264)Cgc>Ggc	p.R88G	TMEM132E_ENST00000321639.5_5'Flank	NM_207454.2	NP_997337.2	A2RUQ5	CQ102_HUMAN	chromosome 17 open reading frame 102	88										central_nervous_system(1)|cervix(1)|large_intestine(3)|lung(3)|ovary(1)	9						GCACAGCAGCGAGGCTGATTC	0.677													G|||	87	0.0173722	0.0023	0.0375	5008	,	,		13250	0.0		0.0507	False		,,,				2504	0.0072				p.R88G		Atlas-SNP	.											C17orf102,NS,carcinoma,0,2	C17orf102	24	2	0			c.C262G						PASS	.	G	GLY/ARG	41,3609		0,41,1784	32.0	38.0	36.0		262	-4.7	0.0	17	dbSNP_132	36	475,7669		18,439,3615	yes	missense	C17orf102	NM_207454.2	125	18,480,5399	CC,CG,GG		5.8325,1.1233,4.3751	benign	88/168	32906038	516,11278	1825	4072	5897	SO:0001583	missense	400591	exon1			AGCAGCGAGGCTG		CCDS42297.1	17q12	2009-02-11			ENSG00000197322	ENSG00000197322			34412	protein-coding gene	gene with protein product							Standard	NM_207454		Approved	FLJ44815	uc002hie.1	A2RUQ5	OTTHUMG00000156883	ENST00000357754.1:c.262C>G	17.37:g.32906038G>C	ENSP00000350392:p.Arg88Gly	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	45	27	0.6	NM_207454	A5PKX0|Q6ZTB3	Missense_Mutation	SNP	ENST00000357754.1	37	CCDS42297.1	57	0.0260989010989011	2	0.0040650406504065045	17	0.04696132596685083	0	0.0	38	0.05013192612137203	G	11.53	1.664770	0.29604	0.011233	0.058325	ENSG00000197322	ENST00000357754	T	0.39592	1.07	3.76	-4.74	0.03249	.	1.940260	0.02759	N	0.118335	T	0.02533	0.0077	N	0.19112	0.55	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.07673	-1.0760	10	0.87932	D	0	.	0.3973	0.00420	0.2813:0.2885:0.1565:0.2736	.	88	A2RUQ5	CQ102_HUMAN	G	88	ENSP00000350392:R88G	ENSP00000350392:R88G	R	-	1	0	C17orf102	29930151	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.564000	0.02152	-1.286000	0.02384	-1.104000	0.02111	CGC	G|0.965;C|0.035	0.035	strong		0.677	C17orf102-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346435.1	NM_207454	
ALDH1A3	220	hgsc.bcm.edu	37	15	101445815	101445815	+	Missense_Mutation	SNP	A	A	G	rs3803430	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:101445815A>G	ENST00000329841.5	+	10	1688	c.1156A>G	c.(1156-1158)Atg>Gtg	p.M386V	RP11-66B24.4_ENST00000560351.1_RNA|ALDH1A3_ENST00000346623.6_Missense_Mutation_p.M279V	NM_000693.2	NP_000684.2	P47895	AL1A3_HUMAN	aldehyde dehydrogenase 1 family, member A3	386			M -> V (in dbSNP:rs3803430).		embryonic eye morphogenesis (GO:0048048)|face development (GO:0060324)|inner ear morphogenesis (GO:0042472)|locomotory behavior (GO:0007626)|neuromuscular process controlling balance (GO:0050885)|nucleus accumbens development (GO:0021768)|olfactory pit development (GO:0060166)|optic cup morphogenesis involved in camera-type eye development (GO:0002072)|positive regulation of apoptotic process (GO:0043065)|retinal metabolic process (GO:0042574)|retinoic acid biosynthetic process (GO:0002138)|retinoic acid metabolic process (GO:0042573)|retinol metabolic process (GO:0042572)|righting reflex (GO:0060013)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	aldehyde dehydrogenase (NAD) activity (GO:0004029)|aldehyde dehydrogenase [NAD(P)+] activity (GO:0004030)|NAD+ binding (GO:0070403)|protein homodimerization activity (GO:0042803)|thyroid hormone binding (GO:0070324)			NS(1)|central_nervous_system(2)|endometrium(3)|large_intestine(7)|lung(9)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(1)	27	Lung NSC(78;0.00144)|all_lung(78;0.0018)|Melanoma(26;0.00852)		OV - Ovarian serous cystadenocarcinoma(32;0.000932)|LUSC - Lung squamous cell carcinoma(107;0.0766)|Lung(145;0.103)		Vitamin A(DB00162)	GGGCTCAGCCATGGAAGACAA	0.517													A|||	638	0.127396	0.348	0.0432	5008	,	,		20403	0.0615		0.0288	False		,,,				2504	0.0583				p.M386V		Atlas-SNP	.											.	ALDH1A3	61	.	0			c.A1156G						PASS	.	A	VAL/MET	1212,3194	420.8+/-339.2	171,870,1162	67.0	68.0	68.0		1156	-1.3	0.7	15	dbSNP_107	68	262,8338	101.9+/-163.1	3,256,4041	yes	missense	ALDH1A3	NM_000693.2	21	174,1126,5203	GG,GA,AA		3.0465,27.5079,11.3332	benign	386/513	101445815	1474,11532	2203	4300	6503	SO:0001583	missense	220	exon10			TCAGCCATGGAAG	U07919	CCDS10389.1	15q26	2010-05-07			ENSG00000184254	ENSG00000184254	1.2.1.5	"""Aldehyde dehydrogenases"""	409	protein-coding gene	gene with protein product	"""retinaldehyde dehydrogenase 3"""	600463		ALDH6		7698756	Standard	XR_111558		Approved	RALDH3	uc002bwn.4	P47895	OTTHUMG00000149870	ENST00000329841.5:c.1156A>G	15.37:g.101445815A>G	ENSP00000332256:p.Met386Val	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	71	52	0.732394	NM_000693	Q6NT64	Missense_Mutation	SNP	ENST00000329841.5	37	CCDS10389.1	243	0.11126373626373626	171	0.3475609756097561	19	0.052486187845303865	33	0.057692307692307696	20	0.026385224274406333	A	2.863	-0.235771	0.05944	0.275079	0.030465	ENSG00000184254	ENST00000329841;ENST00000346623	T	0.75477	-0.94	5.59	-1.34	0.09143	Aldehyde dehydrogenase domain (1);Aldehyde dehydrogenase, C-terminal (1);Aldehyde/histidinol dehydrogenase (1);	0.350509	0.36482	N	0.002565	T	0.00012	0.0000	N	0.00226	-1.805	0.40389	P	0.020480000000000054	B;B	0.09022	0.002;0.0	B;B	0.11329	0.006;0.0	T	0.36138	-0.9760	9	0.17369	T	0.5	.	6.1467	0.20289	0.4493:0.3591:0.1915:0.0	rs3803430;rs52799393;rs60562267;rs3803430	290;386	Q7Z3A2;P47895	.;AL1A3_HUMAN	V	386;290	ENSP00000332256:M386V	ENSP00000332256:M386V	M	+	1	0	ALDH1A3	99263338	0.069000	0.21087	0.701000	0.30321	0.769000	0.43574	-0.201000	0.09464	-0.522000	0.06417	-1.260000	0.01463	ATG	A|0.882;G|0.118	0.118	strong		0.517	ALDH1A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313620.2		
HLA-A	3105	hgsc.bcm.edu	37	6	29911086	29911086	+	Missense_Mutation	SNP	T	T	C	rs1136700	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:29911086T>C	ENST00000396634.1	+	5	726	c.385T>C	c.(385-387)Tcg>Ccg	p.S129P	HLA-A_ENST00000376802.2_Missense_Mutation_p.S129P|HLA-A_ENST00000376809.5_Missense_Mutation_p.S129P|HLA-A_ENST00000376806.5_Missense_Mutation_p.S129P			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	129	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						CGACGTGGGGTCGGACGGGCG	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)			t|||	1516	0.302716	0.289	0.1599	5008	,	,		11361	0.3264		0.2803	False		,,,				2504	0.4213				p.S129P		Atlas-SNP	.											HLA-A,NS,carcinoma,-1,1	HLA-A	89	1	0			c.T385C						scavenged	.	T	PRO/SER	803,2195		163,477,859	27.0	21.0	23.0		385	-0.5	0.3	6	dbSNP_86	23	1878,3516		404,1070,1223	no	missense	HLA-A	NM_002116.7	74	567,1547,2082	CC,CT,TT		34.8165,26.7845,31.9471	benign	129/366	29911086	2681,5711	1499	2697	4196	SO:0001583	missense	3105	exon3	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	GTGGGGTCGGACG	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.385T>C	6.37:g.29911086T>C	ENSP00000379873:p.Ser129Pro	Somatic	216	3	0.0138889		WXS	Illumina HiSeq	Phase_I	136	134	0.985294	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Missense_Mutation	SNP	ENST00000396634.1	37	CCDS34373.1	585	0.26785714285714285	142	0.2886178861788618	58	0.16022099447513813	164	0.2867132867132867	221	0.29155672823219	.	6.812	0.518971	0.13005	0.267845	0.348165	ENSG00000206503	ENST00000396634;ENST00000376806;ENST00000376809;ENST00000355767;ENST00000376802	T;T;T;T	0.00009	9.47;9.47;9.47;9.47	3.78	-0.459	0.12179	MHC class I, alpha chain, alpha1/alpha2 (4);MHC classes I/II-like antigen recognition protein (2);MHC class I-like antigen recognition (2);	3.406660	0.02719	N	0.113799	T	0.00012	0.0000	N	0.00808	-1.17	0.80722	P	0.0	B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0	B;B;B;B;B	0.04013	0.001;0.0;0.0;0.0;0.0	T	0.08680	-1.0710	9	0.02654	T	1	.	5.9403	0.19189	0.0:0.3406:0.4626:0.1968	rs1136700;rs3179190;rs3200177;rs9260153;rs17423992;rs41563619	8;129;129;129;129	B4DVB9;Q5SRN7;P16188;Q5SRN5;P04439	.;.;1A30_HUMAN;.;1A03_HUMAN	P	129	ENSP00000379873:S129P;ENSP00000366002:S129P;ENSP00000366005:S129P;ENSP00000365998:S129P	ENSP00000348012:S129P	S	+	1	0	HLA-A	30019065	0.000000	0.05858	0.258000	0.24420	0.545000	0.35147	-0.115000	0.10741	-0.232000	0.09811	-0.388000	0.06559	TCG	C|0.299;T|0.701	0.299	strong		0.687	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
IZUMO1	284359	hgsc.bcm.edu	37	19	49244220	49244220	+	Missense_Mutation	SNP	G	G	A	rs66877153|rs2307019|rs386810061	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:49244220G>A	ENST00000332955.2	-	10	1545	c.998C>T	c.(997-999)gCg>gTg	p.A333V	RASIP1_ENST00000222145.4_5'Flank|RASIP1_ENST00000594232.1_5'Flank	NM_182575.2	NP_872381.2	Q8IYV9	IZUM1_HUMAN	izumo sperm-egg fusion 1	333			A -> V (in dbSNP:rs2307019). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:15759005, ECO:0000269|PubMed:18082733}.		cell adhesion (GO:0007155)|fusion of sperm to egg plasma membrane (GO:0007342)|multicellular organism reproduction (GO:0032504)|single fertilization (GO:0007338)|sperm-egg recognition (GO:0035036)	acrosomal membrane (GO:0002080)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)			endometrium(4)|kidney(3)|large_intestine(4)|lung(2)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	17		all_lung(116;0.000156)|Lung NSC(112;0.000251)|all_epithelial(76;0.000761)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000134)|all cancers(93;0.000348)|Epithelial(262;0.019)|GBM - Glioblastoma multiforme(486;0.022)		TTGCTCGGCCGCTCCACTGCC	0.512													G|||	2573	0.513778	0.3162	0.5461	5008	,	,		18313	0.8323		0.4473	False		,,,				2504	0.498				p.A333V		Atlas-SNP	.											.	IZUMO1	30	.	0			c.C998T						PASS	.	G	VAL/ALA	1423,2983	463.2+/-353.5	246,931,1026	113.0	98.0	103.0		998	-0.8	0.0	19	dbSNP_100	103	3753,4847	529.8+/-381.7	794,2165,1341	yes	missense	IZUMO1	NM_182575.2	64	1040,3096,2367	AA,AG,GG		43.6395,32.2969,39.797	benign	333/351	49244220	5176,7830	2203	4300	6503	SO:0001583	missense	284359	exon10			TCGGCCGCTCCAC	BC034769	CCDS12732.1	19q13.33	2014-07-23			ENSG00000182264	ENSG00000182264		"""-"""	28539	protein-coding gene	gene with protein product	"""oocyte binding/fusion factor"""	609278				15759005, 18952059, 19658160, 22957301	Standard	NM_182575		Approved	IZUMO, MGC34799, OBF	uc002pkj.3	Q8IYV9	OTTHUMG00000183324	ENST00000332955.2:c.998C>T	19.37:g.49244220G>A	ENSP00000327786:p.Ala333Val	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	104	51	0.490385	NM_182575	Q6Q8P6|Q6Q8P7	Missense_Mutation	SNP	ENST00000332955.2	37	CCDS12732.1	1004	0.4597069597069597	121	0.2459349593495935	178	0.49171270718232046	422	0.7377622377622378	283	0.3733509234828496	G	9.027	0.986244	0.18889	0.322969	0.436395	ENSG00000182264	ENST00000332955	T	0.25912	1.77	4.09	-0.804	0.10882	.	2.476250	0.02608	N	0.101765	T	0.00012	0.0000	L	0.29908	0.895	0.80722	P	0.0	B	0.06786	0.001	B	0.04013	0.001	T	0.40776	-0.9545	9	0.19147	T	0.46	0.0138	5.0059	0.14288	0.1805:0.0:0.5356:0.2839	rs2307019;rs58096827;rs2307019	333	Q8IYV9	IZUM1_HUMAN	V	333	ENSP00000327786:A333V	ENSP00000327786:A333V	A	-	2	0	IZUMO1	53936032	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.272000	0.08560	-0.225000	0.09913	-2.067000	0.00394	GCG	AA|0.500;CG|0.500	.	alt		0.512	IZUMO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466189.1	NM_182575	
SLC12A5	57468	hgsc.bcm.edu	37	20	44664493	44664493	+	Silent	SNP	G	G	T	rs77659338	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:44664493G>T	ENST00000454036.2	+	4	475	c.426G>T	c.(424-426)cgG>cgT	p.R142R	SLC12A5_ENST00000608944.1_Silent_p.R68R|SLC12A5_ENST00000372315.1_Silent_p.R119R|SLC12A5_ENST00000243964.3_Silent_p.R119R	NM_001134771.1	NP_001128243.1	Q9H2X9	S12A5_HUMAN	solute carrier family 12 (potassium/chloride transporter), member 5	142					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)	TCTTCCTGCGGCTCACCTGGG	0.617													G|||	214	0.0427316	0.0514	0.0605	5008	,	,		17654	0.0		0.0875	False		,,,				2504	0.0164				p.R142R		Atlas-SNP	.											.	SLC12A5	181	.	0			c.G426T						PASS	.	G	,	257,4149	148.8+/-183.1	4,249,1950	181.0	128.0	145.0		426,357	-0.1	1.0	20	dbSNP_131	145	651,7949	165.1+/-217.3	22,607,3671	yes	coding-synonymous,coding-synonymous	SLC12A5	NM_001134771.1,NM_020708.4	,	26,856,5621	TT,TG,GG		7.5698,5.833,6.9814	,	142/1140,119/1117	44664493	908,12098	2203	4300	6503	SO:0001819	synonymous_variant	57468	exon4			CCTGCGGCTCACC	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.426G>T	20.37:g.44664493G>T		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	167	90	0.538922	NM_001134771	A2RTX2|Q5VZ41|Q9H4Z0|Q9ULP4	Silent	SNP	ENST00000454036.2	37	CCDS46610.1																																																																																			G|0.935;T|0.065	0.065	strong		0.617	SLC12A5-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000471538.1		
CEP164	22897	hgsc.bcm.edu	37	11	117214881	117214881	+	Splice_Site	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:117214881G>A	ENST00000278935.3	+	4	229		c.e4-1			NM_001271933.1|NM_014956.4	NP_001258862.1|NP_055771.4	Q9UPV0	CE164_HUMAN	centrosomal protein 164kDa						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)		TCTCCTTGCAGAAATTCTTGA	0.453																																					.		Atlas-SNP	.											CEP164,colon,carcinoma,-2,1	CEP164	121	1	0			c.83-1G>A						PASS	.						33.0	30.0	31.0					11																	117214881		2201	4296	6497	SO:0001630	splice_region_variant	22897	exon3			CTTGCAGAAATTC	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.83-1G>A	11.37:g.117214881G>A		Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	157	28	0.178344	NM_001271933	Q6PKH9|Q7Z2X9|Q9NVS0|Q9UFJ6	Splice_Site	SNP	ENST00000278935.3	37	CCDS31683.1	.	.	.	.	.	.	.	.	.	.	G	15.58	2.874286	0.51695	.	.	ENSG00000110274	ENST00000525734;ENST00000278935;ENST00000527609;ENST00000533570;ENST00000529538	.	.	.	4.62	4.62	0.57501	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.4489	0.87586	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	CEP164	116720091	1.000000	0.71417	1.000000	0.80357	0.398000	0.30690	9.156000	0.94705	2.274000	0.75844	0.563000	0.77884	.	.	.	none		0.453	CEP164-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392893.1	NM_014956	Intron
KDM3B	51780	hgsc.bcm.edu	37	5	137717213	137717213	+	Silent	SNP	G	G	A	rs10073922	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:137717213G>A	ENST00000314358.5	+	6	914	c.714G>A	c.(712-714)gaG>gaA	p.E238E		NM_016604.3	NP_057688	Q7LBC6	KDM3B_HUMAN	lysine (K)-specific demethylase 3B	238					chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|metal ion binding (GO:0046872)	p.E238E(1)		breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(15)|liver(2)|lung(18)|ovary(4)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	65						AGAGTGGTGAGATCAAGTCGG	0.383													G|||	1456	0.290735	0.1067	0.4179	5008	,	,		17869	0.2708		0.337	False		,,,				2504	0.4223				p.E238E		Atlas-SNP	.											KDM3B,NS,carcinoma,+2,2	KDM3B	177	2	1	Substitution - coding silent(1)	stomach(1)	c.G714A						PASS	.	G		715,3691	299.6+/-285.9	63,589,1551	142.0	122.0	129.0		714	2.0	1.0	5	dbSNP_119	129	3132,5468	478.0+/-369.8	591,1950,1759	no	coding-synonymous	KDM3B	NM_016604.3		654,2539,3310	AA,AG,GG		36.4186,16.2279,29.5787		238/1762	137717213	3847,9159	2203	4300	6503	SO:0001819	synonymous_variant	51780	exon6			TGGTGAGATCAAG	AF251039	CCDS34242.1	5q31	2011-07-01	2009-04-06	2009-04-06	ENSG00000120733	ENSG00000120733		"""Chromatin-modifying enzymes / K-demethylases"""	1337	protein-coding gene	gene with protein product		609373	"""chromosome 5 open reading frame 7"", ""jumonji domain containing 1B"""	C5orf7, JMJD1B		15138608	Standard	NM_016604		Approved	KIAA1082, NET22	uc003lcy.1	Q7LBC6	OTTHUMG00000163469	ENST00000314358.5:c.714G>A	5.37:g.137717213G>A		Somatic	100	1	0.01		WXS	Illumina HiSeq	Phase_I	75	75	1	NM_016604	A6H8X7|Q9BVH6|Q9BW93|Q9BZ52|Q9NYF4|Q9UPS0	Silent	SNP	ENST00000314358.5	37	CCDS34242.1																																																																																			G|0.716;A|0.284	0.284	strong		0.383	KDM3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373597.1	NM_016604	
ADAMTSL3	57188	hgsc.bcm.edu	37	15	84582124	84582124	+	Missense_Mutation	SNP	G	G	T	rs4842838	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:84582124G>T	ENST00000286744.5	+	16	2205	c.1981G>T	c.(1981-1983)Gtg>Ttg	p.V661L	ADAMTSL3_ENST00000567476.1_Missense_Mutation_p.V661L	NM_207517.2	NP_997400.2	P82987	ATL3_HUMAN	ADAMTS-like 3	661			V -> L (in dbSNP:rs4842838). {ECO:0000269|PubMed:14667842}.			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)			AGCAACATGCGTGGGAGGTAT	0.498													T|||	3434	0.685703	0.8306	0.7248	5008	,	,		18879	0.7202		0.5318	False		,,,				2504	0.5849				p.V661L		Atlas-SNP	.											.	ADAMTSL3	290	.	0			c.G1981T						PASS	.	T	LEU/VAL	3420,986	364.6+/-317.1	1332,756,115	36.0	40.0	38.0	http://www.ncbi.nlm.nih.gov/pubmed?term	1981	-1.8	0.0	15	dbSNP_111	38	4620,3980	547.3+/-385.1	1250,2120,930	yes	missense	ADAMTSL3	NM_207517.2	32	2582,2876,1045	TT,TG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	46.2791,22.3786,38.1824	benign	661/1692	84582124	8040,4966	2203	4300	6503	SO:0001583	missense	57188	exon16			ACATGCGTGGGAG	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.1981G>T	15.37:g.84582124G>T	ENSP00000286744:p.Val661Leu	Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	36	36	1	NM_207517	A1A566|A1A567|Q9ULI7	Missense_Mutation	SNP	ENST00000286744.5	37	CCDS10326.1	1469	0.6726190476190477	404	0.8211382113821138	248	0.6850828729281768	413	0.722027972027972	404	0.5329815303430079	T	9.774	1.173578	0.21704	0.776214	0.537209	ENSG00000156218	ENST00000286744	T	0.60424	0.19	5.05	-1.79	0.07932	.	1.774700	0.02812	N	0.124530	T	0.00012	0.0000	N	0.00174	-1.93	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.37291	-0.9712	9	0.09590	T	0.72	.	2.979	0.05947	0.1094:0.3784:0.224:0.2883	rs4842838;rs61613424;rs4842838	661;661	P82987-2;P82987	.;ATL3_HUMAN	L	661	ENSP00000286744:V661L	ENSP00000286744:V661L	V	+	1	0	ADAMTSL3	82373128	0.387000	0.25188	0.038000	0.18304	0.967000	0.64934	0.155000	0.16362	-0.598000	0.05806	-0.362000	0.07510	GTG	G|0.348;T|0.652	0.652	strong		0.498	ADAMTSL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304007.2	NM_207517	
WDR93	56964	hgsc.bcm.edu	37	15	90245174	90245174	+	Missense_Mutation	SNP	T	T	A	rs4287542	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:90245174T>A	ENST00000268130.7	+	2	298	c.197T>A	c.(196-198)cTt>cAt	p.L66H	WDR93_ENST00000560294.1_Missense_Mutation_p.L66H|RP11-300G22.2_ENST00000557964.1_RNA|WDR93_ENST00000558000.1_Missense_Mutation_p.L66H	NM_020212.1	NP_064597.1	Q6P2C0	WDR93_HUMAN	WD repeat domain 93	66			L -> H (in dbSNP:rs4287542).		electron transport chain (GO:0022900)		oxidoreductase activity, acting on NAD(P)H (GO:0016651)			NS(1)|breast(3)|endometrium(2)|kidney(4)|large_intestine(5)|liver(2)|lung(8)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	33	Lung NSC(78;0.0237)|all_lung(78;0.0478)		KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|BRCA - Breast invasive adenocarcinoma(143;0.128)			CTGGTGAACCTTCTGTTTGAC	0.502													T|||	1963	0.391973	0.5061	0.3617	5008	,	,		20048	0.2063		0.4026	False		,,,				2504	0.4397				p.L66H		Atlas-SNP	.											.	WDR93	63	.	0			c.T197A						PASS	.	T	HIS/LEU	2141,2259	581.7+/-385.4	529,1083,588	88.0	78.0	82.0		197	0.1	0.0	15	dbSNP_111	82	3848,4750	541.6+/-384.0	846,2156,1297	yes	missense	WDR93	NM_020212.1	99	1375,3239,1885	AA,AT,TT		44.7546,48.6591,46.0763	benign	66/687	90245174	5989,7009	2200	4299	6499	SO:0001583	missense	56964	exon2			TGAACCTTCTGTT		CCDS32326.1, CCDS66862.1, CCDS73779.1	15q26.1	2012-11-02						"""WD repeat domain containing"""	26924	protein-coding gene	gene with protein product							Standard	NM_020212		Approved		uc002boj.3	Q6P2C0		ENST00000268130.7:c.197T>A	15.37:g.90245174T>A	ENSP00000268130:p.Leu66His	Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	159	61	0.383648	NM_020212	Q8N7Y8|Q9NP89	Missense_Mutation	SNP	ENST00000268130.7	37	CCDS32326.1	787	0.36034798534798534	218	0.44308943089430897	141	0.38950276243093923	124	0.21678321678321677	304	0.40105540897097625	T	1.654	-0.513158	0.04200	0.486591	0.447546	ENSG00000140527	ENST00000268130	T	0.22134	1.97	5.59	0.0743	0.14394	.	0.586451	0.15989	N	0.234922	T	0.00012	0.0000	N	0.12746	0.255	0.58432	P	4.000000000004E-6	B;B;B	0.20261	0.01;0.043;0.01	B;B;B	0.18561	0.01;0.022;0.01	T	0.45352	-0.9267	9	0.13470	T	0.59	-1.9233	1.6993	0.02869	0.4348:0.0838:0.1407:0.3407	rs4287542;rs57513749;rs4287542	66;66;66	Q6P2C0-2;B4E3E2;Q6P2C0	.;.;WDR93_HUMAN	H	66	ENSP00000268130:L66H	ENSP00000268130:L66H	L	+	2	0	WDR93	88046178	0.011000	0.17503	0.008000	0.14137	0.289000	0.27227	-0.054000	0.11826	0.039000	0.15632	0.528000	0.53228	CTT	T|0.574;A|0.426	0.426	strong		0.502	WDR93-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000416369.1	NM_020212	
EXOC3L2	90332	hgsc.bcm.edu	37	19	45728123	45728123	+	Silent	SNP	C	C	T	rs10410003	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:45728123C>T	ENST00000252482.3	-	5	480	c.453G>A	c.(451-453)ccG>ccA	p.P151P	EXOC3L2_ENST00000413988.1_Silent_p.P151P			Q2M3D2	EX3L2_HUMAN	exocyst complex component 3-like 2	151					exocytosis (GO:0006887)	exocyst (GO:0000145)				endometrium(1)|large_intestine(5)|lung(3)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	12		all_neural(266;0.224)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.00883)		CTTCCCGGGCCGGCTCGCTTT	0.652													C|||	502	0.10024	0.174	0.036	5008	,	,		12994	0.123		0.0447	False		,,,				2504	0.0798				p.P151P		Atlas-SNP	.											.	EXOC3L2	30	.	0			c.G453A						PASS	.	C		690,3714		51,588,1563	25.0	23.0	24.0		453	-9.4	0.6	19	dbSNP_119	24	385,8205		7,371,3917	no	coding-synonymous	EXOC3L2	NM_138568.3		58,959,5480	TT,TC,CC		4.482,15.6676,8.273		151/410	45728123	1075,11919	2202	4295	6497	SO:0001819	synonymous_variant	90332	exon6			CCGGGCCGGCTCG	AK093466	CCDS12657.1	19q13.32	2011-07-07			ENSG00000130201	ENSG00000130201			30162	protein-coding gene	gene with protein product						21566143	Standard	NM_138568		Approved	FLJ36147, XTP7	uc002pay.1	Q2M3D2	OTTHUMG00000155018	ENST00000252482.3:c.453G>A	19.37:g.45728123C>T		Somatic	292	0	0		WXS	Illumina HiSeq	Phase_I	290	137	0.472414	NM_138568	Q8N9W2|Q96GV2	Silent	SNP	ENST00000252482.3	37	CCDS12657.1																																																																																			C|0.898;T|0.102	0.102	strong		0.652	EXOC3L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338073.1	NM_138568	
GTPBP10	85865	hgsc.bcm.edu	37	7	90014408	90014408	+	Missense_Mutation	SNP	G	G	A	rs17863999	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:90014408G>A	ENST00000222511.6	+	10	1170	c.1104G>A	c.(1102-1104)atG>atA	p.M368I	GTPBP10_ENST00000257659.8_Missense_Mutation_p.M289I	NM_033107.3	NP_149098.2	A4D1E9	GTPBA_HUMAN	GTP-binding protein 10 (putative)	368			M -> I (in dbSNP:rs17863999). {ECO:0000269|Ref.1}.		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						CTGATACAATGTCTTCTACTG	0.323													A|||	938	0.1873	0.2216	0.2017	5008	,	,		18948	0.1101		0.1859	False		,,,				2504	0.2117				p.M368I		Atlas-SNP	.											.	GTPBP10	31	.	0			c.G1104A						PASS	.	A	ILE/MET,ILE/MET	1001,3405	730.0+/-410.1	129,743,1331	121.0	125.0	123.0		867,1104	-3.8	0.0	7	dbSNP_123	123	1766,6834	734.6+/-406.9	177,1412,2711	yes	missense,missense	GTPBP10	NM_001042717.2,NM_033107.3	10,10	306,2155,4042	AA,AG,GG		20.5349,22.719,21.2748	benign,benign	289/309,368/388	90014408	2767,10239	2203	4300	6503	SO:0001583	missense	85865	exon10			TACAATGTCTTCT		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.1104G>A	7.37:g.90014408G>A	ENSP00000222511:p.Met368Ile	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	38	20	0.526316	NM_033107	B4DFY6|Q3B7A6|Q5H9V2|Q8IXG8|Q8N982|Q8WU16|Q9BSP1|Q9Y6T6	Missense_Mutation	SNP	ENST00000222511.6	37	CCDS5617.1	372	0.17032967032967034	89	0.18089430894308944	74	0.20441988950276244	70	0.12237762237762238	139	0.18337730870712401	A	0.806	-0.753690	0.03041	0.22719	0.205349	ENSG00000105793	ENST00000257659;ENST00000222511	T;T	0.20598	2.06;2.87	5.1	-3.82	0.04281	.	2.083720	0.01391	N	0.013241	T	0.00012	0.0000	N	0.01705	-0.755	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.33189	-0.9878	8	.	.	.	-5.7237	7.1101	0.25386	0.4438:0.2115:0.3447:0.0	rs17863999;rs56513992;rs17863999	289;368	A4D1E9-2;A4D1E9	.;GTPBA_HUMAN	I	289;368	ENSP00000257659:M289I;ENSP00000222511:M368I	.	M	+	3	0	GTPBP10	89852344	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.043000	0.12043	-1.363000	0.02164	-3.067000	0.00067	ATG	G|0.805;A|0.195	0.195	strong		0.323	GTPBP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059976.3	NM_033107	
MAGEA4	4103	hgsc.bcm.edu	37	X	151092653	151092653	+	Missense_Mutation	SNP	G	G	A	rs1047251	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:151092653G>A	ENST00000360243.2	+	3	784	c.517G>A	c.(517-519)Gcc>Acc	p.A173T	MAGEA4_ENST00000370335.1_Missense_Mutation_p.A173T|MAGEA4_ENST00000370340.3_Missense_Mutation_p.A173T|MAGEA4_ENST00000393921.1_Missense_Mutation_p.A173T|MAGEA4_ENST00000276344.2_Missense_Mutation_p.A173T|MAGEA4_ENST00000370337.4_Missense_Mutation_p.A173T|MAGEA4_ENST00000393920.1_Missense_Mutation_p.A173T	NM_001011550.1	NP_001011550.1	P43358	MAGA4_HUMAN	melanoma antigen family A, 4	173	MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.		A -> T (in dbSNP:rs1047251). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:7642112, ECO:0000269|PubMed:7927540, ECO:0000269|PubMed:8037761}.							breast(2)|central_nervous_system(4)|endometrium(1)|kidney(1)|large_intestine(3)|lung(14)|ovary(2)	27	Acute lymphoblastic leukemia(192;6.56e-05)					AGTGGACCCCGCCAGCAACAC	0.502													A|||	2019	0.534834	0.4773	0.2925	3775	,	,		14730	0.4504		0.3976	False		,,,				2504	0.3384				p.A173T		Atlas-SNP	.											.	MAGEA4	68	.	0			c.G517A						PASS	.	A	THR/ALA,THR/ALA,THR/ALA,THR/ALA	2351,1484		612,781,346,239,225	107.0	106.0	107.0		517,517,517,517	-0.4	0.0	X	dbSNP_86	107	3653,3075		713,1184,1043,531,829	yes	missense,missense,missense,missense	MAGEA4	NM_001011548.1,NM_001011549.1,NM_001011550.1,NM_002362.4	58,58,58,58	1325,1965,1389,770,1054	AA,AG,A,GG,G		45.7045,38.6962,43.1601	benign,benign,benign,benign	173/318,173/318,173/318,173/318	151092653	6004,4559	2203	4300	6503	SO:0001583	missense	4103	exon3			GACCCCGCCAGCA		CCDS14702.1	Xq28	2009-03-13			ENSG00000147381	ENSG00000147381			6802	protein-coding gene	gene with protein product	"""melanoma-associated antigen 4"", ""cancer/testis antigen family 1, member 4"""	300175		MAGE4		8575766	Standard	XM_005274677		Approved	MAGE4A, MAGE4B, MAGE-41, MAGE-X2, MGC21336, CT1.4	uc004ffa.3	P43358	OTTHUMG00000024174	ENST00000360243.2:c.517G>A	X.37:g.151092653G>A	ENSP00000353379:p.Ala173Thr	Somatic	278	0	0		WXS	Illumina HiSeq	Phase_I	188	182	0.968085	NM_001011548	Q14798	Missense_Mutation	SNP	ENST00000360243.2	37	CCDS14702.1	877	0.5286317058468957	148	0.43529411764705883	79	0.2668918918918919	159	0.3878048780487805	221	0.3797250859106529	A	0.018	-1.467449	0.01053	0.613038	0.542955	ENSG00000147381	ENST00000276344;ENST00000448295;ENST00000393921;ENST00000430273;ENST00000370337;ENST00000441865;ENST00000393920;ENST00000370340;ENST00000416020;ENST00000425182;ENST00000457310;ENST00000370335;ENST00000360243;ENST00000431971	T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.04502	3.61;3.61;3.61;3.61;3.61;3.61;3.61;3.61;3.61;3.61;3.61;3.61;3.61;3.61	2.37	-0.42	0.12336	.	1.277240	0.05684	N	0.591025	T	0.00012	0.0000	N	0.01219	-0.95	0.80722	P	0.0	B	0.06786	0.001	B	0.08055	0.003	T	0.33752	-0.9856	8	.	.	.	.	0.041	0.00008	0.3237:0.1809:0.1837:0.3117	rs1047251;rs3187282;rs17220978;rs17845555;rs17858453;rs52807844;rs57643014	173	P43358	MAGA4_HUMAN	T	173	ENSP00000276344:A173T;ENSP00000391904:A173T;ENSP00000377498:A173T;ENSP00000394149:A173T;ENSP00000359362:A173T;ENSP00000402624:A173T;ENSP00000377497:A173T;ENSP00000359365:A173T;ENSP00000394073:A173T;ENSP00000400900:A173T;ENSP00000402186:A173T;ENSP00000359360:A173T;ENSP00000353379:A173T;ENSP00000390096:A173T	.	A	+	1	0	MAGEA4	150843309	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-1.022000	0.03611	-0.660000	0.05352	-0.885000	0.02943	GCC	0|0.004;A|0.556	0.556	strong		0.502	MAGEA4-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060898.1	NM_002362	
ZFYVE16	9765	hgsc.bcm.edu	37	5	79735832	79735832	+	Silent	SNP	C	C	T	rs114761271	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:79735832C>T	ENST00000338008.5	+	4	2580	c.2400C>T	c.(2398-2400)tgC>tgT	p.C800C	ZFYVE16_ENST00000510158.1_Silent_p.C800C|ZFYVE16_ENST00000505560.1_Silent_p.C800C	NM_001284236.1|NM_014733.3	NP_001271165.1|NP_055548	Q7Z3T8	ZFY16_HUMAN	zinc finger, FYVE domain containing 16	800					BMP signaling pathway (GO:0030509)|endosomal transport (GO:0016197)|protein targeting to lysosome (GO:0006622)|regulation of endocytosis (GO:0030100)|signal transduction (GO:0007165)|vesicle organization (GO:0016050)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|early endosome membrane (GO:0031901)|intracellular membrane-bounded organelle (GO:0043231)	1-phosphatidylinositol binding (GO:0005545)|metal ion binding (GO:0046872)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|protein transporter activity (GO:0008565)			breast(4)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(14)|liver(1)|lung(6)|ovary(2)|prostate(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	51		Lung NSC(167;0.00428)|all_lung(232;0.00455)|Ovarian(174;0.0261)		OV - Ovarian serous cystadenocarcinoma(54;1.6e-46)|Epithelial(54;2.02e-41)|all cancers(79;5.05e-36)		GTGTAGTCTGCTATGAAACTA	0.274													C|||	20	0.00399361	0.0	0.0043	5008	,	,		18426	0.0		0.0159	False		,,,				2504	0.001				p.C800C	Melanoma(150;1452 1854 16018 17851 37292)	Atlas-SNP	.											.	ZFYVE16	100	.	0			c.C2400T						PASS	.	C	,	15,4391	23.3+/-48.9	0,15,2188	149.0	167.0	161.0		2400,2400	5.5	1.0	5	dbSNP_132	161	160,8440	75.7+/-138.4	1,158,4141	no	coding-synonymous,coding-synonymous	ZFYVE16	NM_001105251.1,NM_014733.3	,	1,173,6329	TT,TC,CC		1.8605,0.3404,1.3455	,	800/1540,800/1540	79735832	175,12831	2203	4300	6503	SO:0001819	synonymous_variant	9765	exon5			AGTCTGCTATGAA	AB002303	CCDS4050.1	5q14.1	2012-09-20			ENSG00000039319	ENSG00000039319		"""Zinc fingers, FYVE domain containing"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	20756	protein-coding gene	gene with protein product	"""endofin"", ""protein phosphatase 1, regulatory subunit 69"""	608880				11546807	Standard	NM_014733		Approved	KIAA0305, PPP1R69	uc003kgq.4	Q7Z3T8	OTTHUMG00000108178	ENST00000338008.5:c.2400C>T	5.37:g.79735832C>T		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	67	23	0.343284	NM_001105251	O15023|Q5H9U2|Q7LAU7|Q86T69|Q8N5L3|Q8NEK3	Silent	SNP	ENST00000338008.5	37	CCDS4050.1																																																																																			C|0.986;T|0.014	0.014	strong		0.274	ZFYVE16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226982.2	NM_014733	
KIAA1107	23285	hgsc.bcm.edu	37	1	92649498	92649498	+	Missense_Mutation	SNP	T	T	A	rs75212872		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:92649498T>A	ENST00000370378.4	+	9	3774	c.3676T>A	c.(3676-3678)Tat>Aat	p.Y1226N	KIAA1107_ENST00000409154.4_Missense_Mutation_p.Y1281N	NM_015237.2	NP_056052.2	Q9UPP5	K1107_HUMAN	KIAA1107	1281										breast(4)|central_nervous_system(1)|endometrium(3)|kidney(2)|prostate(1)|skin(3)	14						GTCTCCAATATATGAGATGGA	0.373													T|||	1	0.000199681	0.0	0.0	5008	,	,		19930	0.0		0.001	False		,,,				2504	0.0				p.Y1226N		Atlas-SNP	.											.	KIAA1107	60	.	0			c.T3676A						PASS	.						96.0	79.0	84.0					1																	92649498		692	1591	2283	SO:0001583	missense	23285	exon9			CCAATATATGAGA	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.3676T>A	1.37:g.92649498T>A	ENSP00000359404:p.Tyr1226Asn	Somatic	251	0	0		WXS	Illumina HiSeq	Phase_I	206	84	0.407767	NM_015237	O14767|Q8N3X7	Missense_Mutation	SNP	ENST00000370378.4	37	CCDS44172.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	T	15.18	2.757464	0.49468	.	.	ENSG00000069712	ENST00000409154;ENST00000370378	T;T	0.15952	2.38;2.38	5.44	4.28	0.50868	.	0.000000	0.85682	D	0.000000	T	0.26919	0.0659	M	0.71581	2.175	0.54753	D	0.999983	D	0.76494	0.999	D	0.69479	0.964	T	0.04781	-1.0927	10	0.87932	D	0	.	11.4864	0.50356	0.0:0.0717:0.0:0.9283	.	1226	E9PEZ5	.	N	1281;1226	ENSP00000386957:Y1281N;ENSP00000359404:Y1226N	ENSP00000359404:Y1226N	Y	+	1	0	KIAA1107	92422086	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	3.797000	0.55514	0.853000	0.35312	0.460000	0.39030	TAT	T|0.999;A|0.001	0.001	strong		0.373	KIAA1107-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028375.3	XM_034086	
PALLD	23022	hgsc.bcm.edu	37	4	169432841	169432841	+	Silent	SNP	G	G	A	rs1806729	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:169432841G>A	ENST00000505667.1	+	2	359	c.186G>A	c.(184-186)aaG>aaA	p.K62K	PALLD_ENST00000261509.6_Silent_p.K62K|PALLD_ENST00000335742.7_5'UTR|PALLD_ENST00000333488.4_5'UTR			Q8WX93	PALLD_HUMAN	palladin, cytoskeletal associated protein	62					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)		ACTCGGAAAAGGAGATCTCGC	0.507									Pancreatic Cancer, Familial Clustering of				G|||	1182	0.236022	0.2231	0.1844	5008	,	,		18749	0.1925		0.329	False		,,,				2504	0.2393				p.K62K	Esophageal Squamous(109;1482 1532 18347 40239 51172)	Atlas-SNP	.											.	PALLD	179	.	0			c.G186A						PASS	.	G	,	1040,3366	361.4+/-315.7	139,762,1302	39.0	40.0	40.0		186,186	3.7	1.0	4	dbSNP_92	40	2789,5811	426.7+/-355.4	460,1869,1971	no	coding-synonymous,coding-synonymous	PALLD	NM_001166108.1,NM_016081.3	,	599,2631,3273	AA,AG,GG		32.4302,23.6042,29.4403	,	62/1124,62/1107	169432841	3829,9177	2203	4300	6503	SO:0001819	synonymous_variant	23022	exon2	Familial Cancer Database	incl.: Hereditary Pancreatic Adenocarcinoma, Insulin-Dependent Diabetes Mellitus - Exocrine Insufficiency - Familial Pancreatic Cancer, PNCA1	GGAAAAGGAGATC	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.186G>A	4.37:g.169432841G>A		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	100	98	0.98	NM_001166108	B3KTG2|B5MD56|B7ZMM5|Q7L3E0|Q7Z3W0|Q86WE8|Q8N1M2|Q9UGA0|Q9UQF5|Q9Y2J6|Q9Y3E9	Silent	SNP	ENST00000505667.1	37	CCDS54818.1																																																																																			G|0.728;A|0.272	0.272	strong		0.507	PALLD-002	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000363762.1	NM_016081	
TAF4B	6875	hgsc.bcm.edu	37	18	23865851	23865851	+	Silent	SNP	C	C	T	rs12456749	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:23865851C>T	ENST00000269142.5	+	7	1976	c.978C>T	c.(976-978)agC>agT	p.S326S	TAF4B_ENST00000578121.1_Silent_p.S326S|TAF4B_ENST00000400466.2_Silent_p.S326S	NM_005640.1	NP_005631.1	Q92750	TAF4B_HUMAN	TAF4b RNA polymerase II, TATA box binding protein (TBP)-associated factor, 105kDa	326	TAFH. {ECO:0000255|PROSITE- ProRule:PRU00440}.				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)			TCCAGAAAAGCGTGGTTGCCT	0.403													c|||	599	0.119609	0.0439	0.1354	5008	,	,		22634	0.0546		0.2913	False		,,,				2504	0.1012				p.S326S		Atlas-SNP	.											.	TAF4B	71	.	0			c.C978T						PASS	.			294,3536		9,276,1630	107.0	95.0	99.0		978	3.1	1.0	18	dbSNP_120	99	2349,5931		320,1709,2111	no	coding-synonymous	TAF4B	NM_005640.1		329,1985,3741	TT,TC,CC		28.3696,7.6762,21.8249		326/863	23865851	2643,9467	1915	4140	6055	SO:0001819	synonymous_variant	6875	exon7			GAAAAGCGTGGTT	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.978C>T	18.37:g.23865851C>T		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	81	46	0.567901	NM_005640	Q29YA4|Q29YA5	Silent	SNP	ENST00000269142.5	37	CCDS42421.1																																																																																			C|0.797;T|0.203	0.203	strong		0.403	TAF4B-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000446260.3	NM_005640	
ITGB6	3694	hgsc.bcm.edu	37	2	160968628	160968628	+	Silent	SNP	A	A	G	rs16844790	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:160968628A>G	ENST00000283249.2	-	13	2301	c.2064T>C	c.(2062-2064)aaT>aaC	p.N688N	ITGB6_ENST00000409872.1_Silent_p.N688N|ITGB6_ENST00000428609.2_Silent_p.N646N|ITGB6_ENST00000409967.2_Silent_p.N581N	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	232	0	0		WXS	Illumina HiSeq	Phase_I	213	118	0.553991	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	
FAM160A1	729830	hgsc.bcm.edu	37	4	152498625	152498625	+	Silent	SNP	C	C	T	rs17275536	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:152498625C>T	ENST00000505231.1	+	3	288	c.129C>T	c.(127-129)caC>caT	p.H43H	FAM160A1_ENST00000435205.1_Silent_p.H43H|RN7SKP35_ENST00000517210.1_RNA			Q05DH4	F16A1_HUMAN	family with sequence similarity 160, member A1	43										endometrium(2)|kidney(1)	3						TGGAGAAGCACGACCCCTTGA	0.418													T|||	1433	0.286142	0.2935	0.3184	5008	,	,		21202	0.1935		0.341	False		,,,				2504	0.2924				p.H43H		Atlas-SNP	.											.	FAM160A1	60	.	0			c.C129T						PASS	.	T		443,941		65,313,314	73.0	63.0	66.0		129	-7.7	0.5	4	dbSNP_123	66	1061,2121		159,743,689	no	coding-synonymous	FAM160A1	NM_001109977.1		224,1056,1003	TT,TC,CC		33.3438,32.0087,32.9391		43/1041	152498625	1504,3062	692	1591	2283	SO:0001819	synonymous_variant	729830	exon5			GAAGCACGACCCC		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.129C>T	4.37:g.152498625C>T		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	125	62	0.496	NM_001109977	Q6ZUS2	Silent	SNP	ENST00000505231.1	37	CCDS47146.1																																																																																			C|0.718;T|0.282	0.282	strong		0.418	FAM160A1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365691.1	NM_001109977	
EPS8L2	64787	hgsc.bcm.edu	37	11	721931	721931	+	Silent	SNP	C	C	T	rs7949926	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:721931C>T	ENST00000533256.1	+	12	1299	c.924C>T	c.(922-924)ccC>ccT	p.P308P	EPS8L2_ENST00000530636.1_Silent_p.P308P|EPS8L2_ENST00000526198.1_Silent_p.P324P|EPS8L2_ENST00000318562.8_Silent_p.P308P|AP006621.9_ENST00000527021.2_RNA			Q9H6S3	ES8L2_HUMAN	EPS8-like 2	308					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)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|ruffle membrane (GO:0032587)|vesicle (GO:0031982)	actin binding (GO:0003779)	p.P308P(1)		NS(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(2)|pancreas(1)|prostate(2)|soft_tissue(1)|urinary_tract(1)	13		all_cancers(49;1.24e-08)|all_epithelial(84;1.87e-05)|Breast(177;0.000286)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.106)|all_lung(207;0.136)		all cancers(45;4.37e-27)|Epithelial(43;2.81e-26)|OV - Ovarian serous cystadenocarcinoma(40;1.33e-20)|BRCA - Breast invasive adenocarcinoma(625;4.29e-05)|Lung(200;0.0582)|LUSC - Lung squamous cell carcinoma(625;0.0703)		GGGCACGGCCCCCCTCTGAGG	0.667													c|||	538	0.107428	0.2474	0.0692	5008	,	,		12327	0.0357		0.0815	False		,,,				2504	0.046				p.P308P		Atlas-SNP	.											EPS8L2,NS,carcinoma,0,1	EPS8L2	42	1	1	Substitution - coding silent(1)	prostate(1)	c.C924T						PASS	.			950,3438		98,754,1342	30.0	28.0	29.0		924	2.5	1.0	11	dbSNP_116	29	767,7823		44,679,3572	no	coding-synonymous	EPS8L2	NM_022772.3		142,1433,4914	TT,TC,CC		8.929,21.65,13.2301		308/716	721931	1717,11261	2194	4295	6489	SO:0001819	synonymous_variant	64787	exon11			ACGGCCCCCCTCT	AF318331	CCDS31328.1	11p15.5	2008-02-05				ENSG00000177106			21296	protein-coding gene	gene with protein product		614988				12620401	Standard	NM_022772		Approved	FLJ21935, FLJ22171, MGC3088	uc001lqt.3	Q9H6S3		ENST00000533256.1:c.924C>T	11.37:g.721931C>T		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	121	103	0.85124	NM_022772	B3KSX1|B7ZKL3|Q53GM8|Q8WYW7|Q96K06|Q9H6K9	Silent	SNP	ENST00000533256.1	37	CCDS31328.1																																																																																			C|0.874;T|0.126	0.126	strong		0.667	EPS8L2-003	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382344.1	NM_022772	
HLA-A	3105	hgsc.bcm.edu	37	6	29912108	29912108	+	Missense_Mutation	SNP	G	G	C	rs2231095	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:29912108G>C	ENST00000396634.1	+	6	1170	c.829G>C	c.(829-831)Gag>Cag	p.E277Q	HLA-A_ENST00000376802.2_Missense_Mutation_p.E277Q|HLA-A_ENST00000376809.5_Missense_Mutation_p.E277Q|HLA-A_ENST00000376806.5_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	147	0	0		WXS	Illumina HiSeq	Phase_I	118	47	0.398305	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	
MUC4	4585	hgsc.bcm.edu	37	3	195505835	195505835	+	Missense_Mutation	SNP	C	C	T	rs58500707		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195505835C>T	ENST00000463781.3	-	2	13075	c.12616G>A	c.(12616-12618)Gcc>Acc	p.A4206T	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.A4206T	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.A4206T(3)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		AGAGGGGTGGCGTGACCTGTG	0.597																																					p.A4206T		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,6	MUC4	1505	6	3	Substitution - Missense(3)	prostate(2)|stomach(1)	c.G12616A						scavenged	.						16.0	14.0	15.0					3																	195505835		687	1575	2262	SO:0001583	missense	4585	exon2			GGGTGGCGTGACC	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.12616G>A	3.37:g.195505835C>T	ENSP00000417498:p.Ala4206Thr	Somatic	70	3	0.0428571		WXS	Illumina HiSeq	Phase_I	113	11	0.0973451	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	c	3.919	-0.018446	0.07681	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.31510	1.55;1.49	.	.	.	.	.	.	.	.	T	0.17323	0.0416	N	0.19112	0.55	0.19300	N	0.999971	P	0.52316	0.952	B	0.41510	0.359	T	0.11251	-1.0595	6	.	.	.	.	.	.	.	rs58500707	4078	E7ESK3	.	T	4206	ENSP00000417498:A4206T;ENSP00000420243:A4206T	.	A	-	1	0	MUC4	196990614	.	.	0.020000	0.16555	0.044000	0.14063	.	.	0.452000	0.26830	0.074000	0.15403	GCC	.	.	weak		0.597	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
ITGA4	3676	hgsc.bcm.edu	37	2	182392096	182392096	+	Silent	SNP	A	A	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:182392096A>G	ENST00000397033.2	+	22	2842	c.2412A>G	c.(2410-2412)aaA>aaG	p.K804K		NM_000885.4	NP_000876.3	P13612	ITA4_HUMAN	integrin, alpha 4 (antigen CD49D, alpha 4 subunit of VLA-4 receptor)	804					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)	TGGTGGAGAAAATGAACTTAA	0.333																																					p.K804K		Atlas-SNP	.											.	ITGA4	142	.	0			c.A2412G						PASS	.						91.0	87.0	88.0					2																	182392096		1891	4125	6016	SO:0001819	synonymous_variant	3676	exon22			GGAGAAAATGAAC		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.2412A>G	2.37:g.182392096A>G		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	58	32	0.551724	NM_000885	D3DPG4|Q7Z4L6	Silent	SNP	ENST00000397033.2	37	CCDS42788.1																																																																																			.	.	none		0.333	ITGA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334427.1		
ZNF578	147660	hgsc.bcm.edu	37	19	53014346	53014346	+	Missense_Mutation	SNP	G	G	A	rs161931	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:53014346G>A	ENST00000421239.2	+	6	956	c.712G>A	c.(712-714)Gaa>Aaa	p.E238K	CTD-3099C6.5_ENST00000599143.1_RNA	NM_001099694.1	NP_001093164.1	Q96N58	ZN578_HUMAN	zinc finger protein 578	238			E -> K (in dbSNP:rs161931). {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)								GBM - Glioblastoma multiforme(134;0.00819)|OV - Ovarian serous cystadenocarcinoma(262;0.01)		TGAGACTGGCGAAGCCTTTAA	0.308													A|||	3832	0.765176	0.9781	0.7997	5008	,	,		22783	0.6647		0.6412	False		,,,				2504	0.684				p.E238K		Atlas-SNP	.											.	.	.	.	0			c.G712A						PASS	.	A	LYS/GLU	4095,311		1905,285,13	69.0	72.0	71.0		712	1.5	0.0	19	dbSNP_79	71	5316,3282		1637,2042,620	yes	missense	ZNF578	NM_001099694.1	56	3542,2327,633	AA,AG,GG		38.1717,7.0586,27.63	probably-damaging	238/591	53014346	9411,3593	2203	4299	6502	SO:0001583	missense	147660	exon6			ACTGGCGAAGCCT	AK095562	CCDS54310.1	19q13.41	2013-09-20			ENSG00000258405	ENSG00000258405		"""Zinc fingers, C2H2-type"", ""-"""	26449	protein-coding gene	gene with protein product							Standard	NM_001099694		Approved	FLJ31384	uc002pzp.4	Q96N58	OTTHUMG00000156468	ENST00000421239.2:c.712G>A	19.37:g.53014346G>A	ENSP00000459216:p.Glu238Lys	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	76	38	0.5	NM_001099694	B4DR51|I3L1Y6	Missense_Mutation	SNP	ENST00000421239.2	37	CCDS54310.1	1598	0.7316849816849816	475	0.9654471544715447	272	0.7513812154696132	365	0.6381118881118881	486	0.6411609498680739	-	0.015	-1.559240	0.00910	0.929414	0.618283	ENSG00000258405	ENST00000553364	.	.	.	1.48	1.48	0.22813	.	.	.	.	.	T	0.00012	0.0000	N	0.00119	-2.075	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.20438	-1.0275	6	.	.	.	.	5.5843	0.17266	0.8379:0.0:0.1621:0.0	rs161931;rs563619;rs1300562;rs58169326;rs161931	238	G3V4F6	.	K	238	.	.	E	+	1	0	ZNF578	57706158	0.000000	0.05858	0.001000	0.08648	0.079000	0.17450	0.238000	0.18004	-0.092000	0.12417	-1.047000	0.02352	GAA	.	.	weak		0.308	ZNF578-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344298.3	NM_152472	
PIGG	54872	hgsc.bcm.edu	37	4	533001	533001	+	Missense_Mutation	SNP	T	T	C	rs1127410	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:533001T>C	ENST00000453061.2	+	13	2901	c.2795T>C	c.(2794-2796)tTc>tCc	p.F932S	PIGG_ENST00000383028.4_Missense_Mutation_p.F799S|PIGG_ENST00000296306.7_3'UTR|PIGG_ENST00000504346.1_Missense_Mutation_p.F843S|PIGG_ENST00000310340.5_Missense_Mutation_p.F924S	NM_001127178.1	NP_001120650.1	Q5H8A4	PIGG_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class G	932			F -> S (in dbSNP:rs1127410).		C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|GPI anchor biosynthetic process (GO:0006506)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	CP2 mannose-ethanolamine phosphotransferase activity (GO:0051267)|phosphotransferase activity, for other substituted phosphate groups (GO:0016780)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(5)|lung(16)|ovary(3)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	39						ATTCCAGTTTTCACGTACATC	0.388													C|||	1045	0.208666	0.3593	0.0994	5008	,	,		22096	0.2222		0.1282	False		,,,				2504	0.1513				p.F932S		Atlas-SNP	.											.	PIGG	86	.	0			c.T2795C						PASS	.	C	SER/PHE,SER/PHE	1425,2981	684.6+/-404.4	229,967,1007	191.0	167.0	175.0		2795,2771	5.9	0.0	4	dbSNP_86	175	1087,7513	768.9+/-407.6	74,939,3287	yes	missense,missense	PIGG	NM_001127178.1,NM_017733.3	155,155	303,1906,4294	CC,CT,TT		12.6395,32.3423,19.3142	benign,benign	932/984,924/976	533001	2512,10494	2203	4300	6503	SO:0001583	missense	54872	exon13			CAGTTTTCACGTA		CCDS3336.1, CCDS46992.1, CCDS75080.1, CCDS75081.1, CCDS75082.1, CCDS75083.1	4p16.3	2013-02-26	2006-06-28		ENSG00000174227	ENSG00000174227		"""Phosphatidylinositol glycan anchor biosynthesis"""	25985	protein-coding gene	gene with protein product			"""phosphatidylinositol glycan, class G"""			15632136	Standard	XM_005272287		Approved	FLJ20265, GPI7, LAS21	uc003gak.4	Q5H8A4	OTTHUMG00000112457	ENST00000453061.2:c.2795T>C	4.37:g.533001T>C	ENSP00000415203:p.Phe932Ser	Somatic	258	0	0		WXS	Illumina HiSeq	Phase_I	249	115	0.461847	NM_001127178	B4DKC7|Q2TAK5|Q6UX31|Q7L5Y4|Q8N866|Q8NCC9|Q96SY9|Q9BVT7|Q9NXG5	Missense_Mutation	SNP	ENST00000453061.2	37	CCDS46992.1	453	0.20741758241758243	181	0.3678861788617886	40	0.11049723756906077	139	0.243006993006993	93	0.12269129287598944	C	2.913	-0.224932	0.06022	0.323423	0.126395	ENSG00000174227	ENST00000310340;ENST00000453061;ENST00000504346;ENST00000383028;ENST00000453065	T;T;T;T	0.39229	1.09;1.09;1.09;1.09	5.91	5.91	0.95273	.	0.318324	0.33959	N	0.004399	T	0.00012	0.0000	N	0.00368	-1.59	0.09310	P	0.9999999999996261	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.36114	-0.9761	9	0.13853	T	0.58	-11.9767	13.132	0.59389	0.0:0.923:0.0:0.077	rs1127410;rs3183343;rs60748766;rs1127410	799;932;924	Q5H8A4-3;Q5H8A4;Q5H8A4-2	.;PIGG_HUMAN;.	S	924;932;843;799;88	ENSP00000311750:F924S;ENSP00000415203:F932S;ENSP00000424800:F843S;ENSP00000372494:F799S	ENSP00000311750:F924S	F	+	2	0	PIGG	523001	0.839000	0.29477	0.008000	0.14137	0.251000	0.25915	3.208000	0.51114	1.534000	0.49203	-0.119000	0.15052	TTC	T|0.790;C|0.210	0.210	strong		0.388	PIGG-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000357494.1	NM_017733	
TCP10L	140290	hgsc.bcm.edu	37	21	33951068	33951068	+	Missense_Mutation	SNP	T	T	C	rs9622	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:33951068T>C	ENST00000300258.3	-	4	547	c.434A>G	c.(433-435)cAc>cGc	p.H145R	TCP10L_ENST00000472557.1_Missense_Mutation_p.H59R|LINC00846_ENST00000334165.4_lincRNA	NM_144659.5	NP_653260.1	Q8TDR4	TCP1L_HUMAN	t-complex 10-like	145			H -> R (in dbSNP:rs9622). {ECO:0000269|PubMed:10830953, ECO:0000269|Ref.3}.		negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	nucleus (GO:0005634)	protein self-association (GO:0043621)|repressing transcription factor binding (GO:0070491)|RNA polymerase II transcription corepressor activity (GO:0001106)			breast(1)|central_nervous_system(1)|liver(1)|skin(1)	4						CTGATTCTTGTGGCCAGCGTA	0.433													C|||	1093	0.218251	0.2012	0.2133	5008	,	,		18820	0.2599		0.1928	False		,,,				2504	0.228				p.H145R		Atlas-SNP	.											.	TCP10L	24	.	0			c.A434G						PASS	.	C	ARG/HIS	886,3520	741.7+/-411.3	79,728,1396	179.0	154.0	163.0		434	0.5	0.0	21	dbSNP_52	163	1564,7036	745.3+/-407.3	142,1280,2878	yes	missense	TCP10L	NM_144659.5	29	221,2008,4274	CC,CT,TT		18.186,20.1089,18.8375		145/216	33951068	2450,10556	2203	4300	6503	SO:0001583	missense	140290	exon4			TTCTTGTGGCCAG	AF115967	CCDS13616.1	21p22.11	2012-09-20	2012-09-20		ENSG00000242220	ENSG00000242220			11657	protein-coding gene	gene with protein product		608365	"""t-complex 10 (a murine tcp homolog)-like"", ""t-complex 10 (mouse)-like"""			10830953	Standard	NM_144659		Approved	PRED77		Q8TDR4	OTTHUMG00000064901	ENST00000300258.3:c.434A>G	21.37:g.33951068T>C	ENSP00000300258:p.His145Arg	Somatic	364	1	0.00274725		WXS	Illumina HiSeq	Phase_I	374	138	0.368984	NM_144659	Q53EW0|Q96LN5	Missense_Mutation	SNP	ENST00000300258.3	37	CCDS13616.1	484	0.2216117216117216	97	0.19715447154471544	76	0.20994475138121546	159	0.27797202797202797	152	0.20052770448548812	C	1.066	-0.671530	0.03403	0.201089	0.18186	ENSG00000242220	ENST00000300258	T	0.22743	1.94	0.459	0.459	0.16678	.	.	.	.	.	T	0.00012	0.0000	N	0.01188	-0.97	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.41980	-0.9478	7	0.02654	T	1	.	.	.	.	rs9622;rs2246107;rs6517105;rs17353914;rs9622	145	Q8TDR4	TCP1L_HUMAN	R	145	ENSP00000300258:H145R	ENSP00000300258:H145R	H	-	2	0	TCP10L	32872939	0.037000	0.19845	0.010000	0.14722	0.046000	0.14306	-0.931000	0.03967	-0.405000	0.07599	-1.063000	0.02288	CAC	T|0.791;C|0.209	0.209	strong		0.433	TCP10L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139350.1	NM_144659	
KLF17	128209	hgsc.bcm.edu	37	1	44595113	44595113	+	Missense_Mutation	SNP	G	G	C	rs2429051	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:44595113G>C	ENST00000372299.3	+	2	228	c.170G>C	c.(169-171)aGc>aCc	p.S57T	KLF17_ENST00000476802.1_3'UTR	NM_173484.3	NP_775755.3	Q5JT82	KLF17_HUMAN	Kruppel-like factor 17	57			S -> T (in dbSNP:rs2429051). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		gamete generation (GO:0007276)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(2)|central_nervous_system(1)|large_intestine(1)|lung(6)|ovary(3)|prostate(1)|skin(2)|stomach(1)	18	Acute lymphoblastic leukemia(166;0.155)					GGCCTACCAAGCATTCAGCAC	0.537													G|||	2486	0.496406	0.2231	0.5159	5008	,	,		18838	0.628		0.6928	False		,,,				2504	0.5143				p.S57T		Atlas-SNP	.											.	KLF17	92	.	0			c.G170C						PASS	.	G	THR/SER	1311,3095	442.7+/-346.8	204,903,1096	96.0	84.0	88.0		170	-3.9	0.0	1	dbSNP_100	88	5710,2890	671.8+/-402.9	1918,1874,508	yes	missense	KLF17	NM_173484.3	58	2122,2777,1604	CC,CG,GG		33.6047,29.7549,46.0172	benign	57/390	44595113	7021,5985	2203	4300	6503	SO:0001583	missense	128209	exon2			TACCAAGCATTCA	BC049844	CCDS508.1	1p34.1	2011-11-15	2006-02-17	2006-02-17	ENSG00000171872	ENSG00000171872		"""Zinc fingers, C2H2-type"", ""Kruppel-like transcription factors"""	18830	protein-coding gene	gene with protein product		609602	"""zinc finger protein 393"""	ZNF393		16460907	Standard	NM_173484		Approved	Zfp393, FLJ40160	uc001clp.3	Q5JT82	OTTHUMG00000009664	ENST00000372299.3:c.170G>C	1.37:g.44595113G>C	ENSP00000361373:p.Ser57Thr	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	106	41	0.386792	NM_173484	Q86VQ7|Q8N805	Missense_Mutation	SNP	ENST00000372299.3	37	CCDS508.1	1199	0.548992673992674	111	0.22560975609756098	197	0.5441988950276243	377	0.6590909090909091	514	0.6781002638522428	G	10.97	1.500537	0.26861	0.297549	0.663953	ENSG00000171872	ENST00000372299	T	0.09723	2.95	4.58	-3.88	0.04205	.	1.187530	0.06029	N	0.652786	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B	0.27625	0.183	B	0.24394	0.053	T	0.32640	-0.9899	9	0.22109	T	0.4	.	1.6635	0.02797	0.4229:0.1764:0.276:0.1246	rs2429051;rs12734854;rs17854588;rs2429051	57	Q5JT82	KLF17_HUMAN	T	57	ENSP00000361373:S57T	ENSP00000361373:S57T	S	+	2	0	KLF17	44367700	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.374000	0.07484	-0.722000	0.04922	-0.806000	0.03193	AGC	G|0.456;C|0.544	0.544	strong		0.537	KLF17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026646.1	NM_173484	
IL4R	3566	hgsc.bcm.edu	37	16	27374696	27374696	+	Missense_Mutation	SNP	C	C	T	rs3024678	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:27374696C>T	ENST00000395762.2	+	11	2282	c.2023C>T	c.(2023-2025)Cca>Tca	p.P675S	IL4R_ENST00000380922.3_Missense_Mutation_p.P660S|IL4R_ENST00000170630.2_Missense_Mutation_p.P675S|IL4R_ENST00000543915.2_Missense_Mutation_p.P675S	NM_000418.3	NP_000409.1	P24394	IL4RA_HUMAN	interleukin 4 receptor	675			P -> S (in dbSNP:rs3024678). {ECO:0000269|Ref.5}.		defense response to protozoan (GO:0042832)|immune response (GO:0006955)|interleukin-4-mediated signaling pathway (GO:0035771)|intracellular signal transduction (GO:0035556)|negative regulation of T-helper 1 cell differentiation (GO:0045626)|ovulation (GO:0030728)|positive regulation of chemokine secretion (GO:0090197)|positive regulation of macrophage activation (GO:0043032)|positive regulation of T-helper 2 cell differentiation (GO:0045630)|production of molecular mediator involved in inflammatory response (GO:0002532)|regulation of cell proliferation (GO:0042127)|response to estrogen (GO:0043627)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	interleukin-4 receptor activity (GO:0004913)|receptor signaling protein activity (GO:0005057)			breast(3)|endometrium(2)|kidney(2)|large_intestine(2)|lung(15)|ovary(2)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)	33						AAGCAGCTCCCCAGAGCACCT	0.652													C|||	26	0.00519169	0.0015	0.0086	5008	,	,		16559	0.0		0.0149	False		,,,				2504	0.0031				p.P675S		Atlas-SNP	.											.	IL4R	70	.	0			c.C2023T						PASS	.	C	SER/PRO	21,4373	28.1+/-56.4	0,21,2176	44.0	46.0	45.0		2023	3.4	0.9	16	dbSNP_102	45	173,8427	78.9+/-141.6	2,169,4129	yes	missense	IL4R	NM_000418.2	74	2,190,6305	TT,TC,CC		2.0116,0.4779,1.493	possibly-damaging	675/826	27374696	194,12800	2197	4300	6497	SO:0001583	missense	3566	exon11			AGCTCCCCAGAGC	X52425	CCDS10629.1, CCDS58441.1	16p12.1-p11.2	2008-05-14			ENSG00000077238	ENSG00000077238		"""Interleukins and interleukin receptors"", ""CD molecules"""	6015	protein-coding gene	gene with protein product		147781				1679753	Standard	NM_000418		Approved	CD124	uc010bxy.4	P24394	OTTHUMG00000097015	ENST00000395762.2:c.2023C>T	16.37:g.27374696C>T	ENSP00000379111:p.Pro675Ser	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	72	34	0.472222	NM_000418	B4E076|B9EKU8|H3BSY5|Q96P01|Q9H181|Q9H182|Q9H183|Q9H184|Q9H185|Q9H186|Q9H187|Q9H188	Missense_Mutation	SNP	ENST00000395762.2	37	CCDS10629.1	15	0.006868131868131868	2	0.0040650406504065045	4	0.011049723756906077	0	0.0	9	0.011873350923482849	C	12.04	1.819561	0.32145	0.004779	0.020116	ENSG00000077238	ENST00000395762;ENST00000543915;ENST00000380922;ENST00000170630	T;T;T;T	0.08807	3.05;3.05;3.05;3.05	4.52	3.44	0.39384	.	1.460220	0.03972	N	0.291822	T	0.04861	0.0131	L	0.50333	1.59	0.31833	N	0.624544	P;P;P	0.44241	0.829;0.829;0.829	B;B;B	0.41571	0.36;0.36;0.36	T	0.22661	-1.0210	10	0.30854	T	0.27	-24.5793	4.7857	0.13223	0.0:0.7952:0.0:0.2048	rs3024678;rs16976720;rs3024678	660;675;675	B4E076;B9EGC0;P24394	.;.;IL4RA_HUMAN	S	675;675;660;675	ENSP00000379111:P675S;ENSP00000441667:P675S;ENSP00000370309:P660S;ENSP00000170630:P675S	ENSP00000170630:P675S	P	+	1	0	IL4R	27282197	0.000000	0.05858	0.888000	0.34837	0.036000	0.12997	-0.582000	0.05814	2.072000	0.62099	0.561000	0.74099	CCA	C|0.989;T|0.011	0.011	strong		0.652	IL4R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214104.4		
GATA5	140628	hgsc.bcm.edu	37	20	61048549	61048549	+	Silent	SNP	G	G	A	rs41305803	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:61048549G>A	ENST00000252997.2	-	3	670	c.609C>T	c.(607-609)gaC>gaT	p.D203D		NM_080473.4	NP_536721.1	Q9BWX5	GATA5_HUMAN	GATA binding protein 5	203					blood coagulation (GO:0007596)|cellular response to BMP stimulus (GO:0071773)|intestinal epithelial cell differentiation (GO:0060575)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	enhancer sequence-specific DNA binding (GO:0001158)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			kidney(1)|lung(3)|ovary(1)|stomach(1)	6	Breast(26;2.05e-08)		BRCA - Breast invasive adenocarcinoma(19;3.08e-06)			GGCCGGTGCCGTCTCGGCGCC	0.647													G|||	1944	0.388179	0.4501	0.438	5008	,	,		12093	0.3403		0.4404	False		,,,				2504	0.2648				p.D203D		Atlas-SNP	.											.	GATA5	22	.	0			c.C609T						PASS	.	G		1860,2530		391,1078,726	44.0	37.0	39.0		609	-3.5	0.2	20	dbSNP_127	39	3733,4861		818,2097,1382	no	coding-synonymous	GATA5	NM_080473.4		1209,3175,2108	AA,AG,GG		43.4373,42.369,43.0761		203/398	61048549	5593,7391	2195	4297	6492	SO:0001819	synonymous_variant	140628	exon3			GGTGCCGTCTCGG	BC047790, BC117356	CCDS13499.1	20q13.33	2013-07-17	2001-11-28		ENSG00000130700	ENSG00000130700		"""GATA zinc finger domain containing"""	15802	protein-coding gene	gene with protein product		611496	"""GATA-binding protein 5"""			9566909	Standard	NM_080473		Approved	bB379O24.1, GATAS	uc002ycx.1	Q9BWX5	OTTHUMG00000032919	ENST00000252997.2:c.609C>T	20.37:g.61048549G>A		Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	128	49	0.382812	NM_080473	D9ZGF7|Q17RE2|Q86VU4	Silent	SNP	ENST00000252997.2	37	CCDS13499.1																																																																																			G|0.568;A|0.432	0.432	strong		0.647	GATA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080038.2	NM_080473	
MAGEA4	4103	hgsc.bcm.edu	37	X	151092220	151092220	+	Silent	SNP	A	A	G	rs1047248	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:151092220A>G	ENST00000360243.2	+	3	351	c.84A>G	c.(82-84)gcA>gcG	p.A28A	MAGEA4_ENST00000370335.1_Silent_p.A28A|MAGEA4_ENST00000370340.3_Silent_p.A28A|MAGEA4_ENST00000393921.1_Silent_p.A28A|MAGEA4_ENST00000276344.2_Silent_p.A28A|MAGEA4_ENST00000370337.4_Silent_p.A28A|MAGEA4_ENST00000393920.1_Silent_p.A28A	NM_001011550.1	NP_001011550.1	P43358	MAGA4_HUMAN	melanoma antigen family A, 4	28										breast(2)|central_nervous_system(4)|endometrium(1)|kidney(1)|large_intestine(3)|lung(14)|ovary(2)	27	Acute lymphoblastic leukemia(192;6.56e-05)					TGGTGGGTGCACAGGCTCCTA	0.612													G|||	2014	0.53351	0.4902	0.2738	3775	,	,		14322	0.4514		0.3698	False		,,,				2504	0.3569				p.A28A		Atlas-SNP	.											.	MAGEA4	68	.	0			c.A84G						PASS	.	G	,,,	2388,1447		641,748,358,243,213	46.0	44.0	45.0		84,84,84,84	-3.5	0.0	X	dbSNP_86	45	3362,3366		604,1203,951,621,921	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	MAGEA4	NM_001011548.1,NM_001011549.1,NM_001011550.1,NM_002362.4	,,,	1245,1951,1309,864,1134	GG,GA,G,AA,A		49.9703,37.7314,45.5647	,,,	28/318,28/318,28/318,28/318	151092220	5750,4813	2203	4300	6503	SO:0001819	synonymous_variant	4103	exon3			GGGTGCACAGGCT		CCDS14702.1	Xq28	2009-03-13			ENSG00000147381	ENSG00000147381			6802	protein-coding gene	gene with protein product	"""melanoma-associated antigen 4"", ""cancer/testis antigen family 1, member 4"""	300175		MAGE4		8575766	Standard	XM_005274677		Approved	MAGE4A, MAGE4B, MAGE-41, MAGE-X2, MGC21336, CT1.4	uc004ffa.3	P43358	OTTHUMG00000024174	ENST00000360243.2:c.84A>G	X.37:g.151092220A>G		Somatic	231	1	0.004329		WXS	Illumina HiSeq	Phase_I	149	147	0.986577	NM_001011548	Q14798	Silent	SNP	ENST00000360243.2	37	CCDS14702.1																																																																																			A|0.460;G|0.540	0.540	strong		0.612	MAGEA4-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060898.1	NM_002362	
GABRA2	2555	hgsc.bcm.edu	37	4	46314593	46314593	+	Silent	SNP	T	T	C	rs279858	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:46314593T>C	ENST00000510861.1	-	5	569	c.396A>G	c.(394-396)aaA>aaG	p.K132K	GABRA2_ENST00000515082.1_Silent_p.K132K|GABRA2_ENST00000381620.4_Silent_p.K132K|GABRA2_ENST00000514090.1_Silent_p.K132K|GABRA2_ENST00000507069.1_Silent_p.K132K|GABRA2_ENST00000540012.1_Silent_p.K77K|GABRA2_ENST00000356504.1_Silent_p.K132K			P47869	GBRA2_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha 2	132					gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|neurotransmitter transport (GO:0006836)|regulation of neurotransmitter levels (GO:0001505)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	axon (GO:0030424)|cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of synaptic vesicle membrane (GO:0030285)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	benzodiazepine receptor activity (GO:0008503)|chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			NS(1)|breast(1)|cervix(1)|endometrium(2)|large_intestine(9)|lung(33)|ovary(2)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	56					Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amobarbital(DB01351)|Amoxapine(DB00543)|Aprobarbital(DB01352)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Quinidine barbiturate(DB01346)|Secobarbital(DB00418)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Thiopental(DB00599)|Topiramate(DB00273)|Triazolam(DB00897)|Zolpidem(DB00425)|Zopiclone(DB01198)	CTACTGATTTTTTCCCATTGT	0.348													T|||	1818	0.363019	0.2262	0.4683	5008	,	,		14178	0.5327		0.4284	False		,,,				2504	0.2311				p.K132K		Atlas-SNP	.											GABRA2,NS,carcinoma,0,2	GABRA2	134	2	0			c.A396G						PASS	.	T	,	1158,3248	407.8+/-334.4	154,850,1199	115.0	117.0	116.0		396,396	-6.0	0.9	4	dbSNP_79	116	3752,4846	533.3+/-382.4	827,2098,1374	no	coding-synonymous,coding-synonymous	GABRA2	NM_000807.2,NM_001114175.1	,	981,2948,2573	CC,CT,TT		43.6381,26.2823,37.7576	,	132/452,132/452	46314593	4910,8094	2203	4299	6502	SO:0001819	synonymous_variant	2555	exon5			TGATTTTTTCCCA		CCDS3471.1	4p12	2012-06-22			ENSG00000151834	ENSG00000151834		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	4076	protein-coding gene	gene with protein product	"""GABA(A) receptor, alpha 2"""	137140					Standard	NM_000807		Approved		uc010igc.2	P47869	OTTHUMG00000044266	ENST00000510861.1:c.396A>G	4.37:g.46314593T>C		Somatic	194	0	0		WXS	Illumina HiSeq	Phase_I	173	100	0.578035	NM_000807	A8K0U7|B7Z1H8|Q59G14	Silent	SNP	ENST00000510861.1	37	CCDS3471.1																																																																																			T|0.616;C|0.384	0.384	strong		0.348	GABRA2-005	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360848.2		
TECPR1	25851	hgsc.bcm.edu	37	7	97861156	97861156	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:97861156C>A	ENST00000447648.2	-	13	2233	c.1934G>T	c.(1933-1935)aGc>aTc	p.S645I	TECPR1_ENST00000542604.1_Missense_Mutation_p.S575I|TECPR1_ENST00000379795.3_Missense_Mutation_p.S646I			Q7Z6L1	TCPR1_HUMAN	tectonin beta-propeller repeat containing 1	645	PH.				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						GAAGAGGATGCTGTCCCGGAC	0.657																																					p.S645I		Atlas-SNP	.											.	TECPR1	77	.	0			c.G1934T						PASS	.						88.0	98.0	94.0					7																	97861156		2088	4208	6296	SO:0001583	missense	25851	exon13			AGGATGCTGTCCC		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.1934G>T	7.37:g.97861156C>A	ENSP00000404923:p.Ser645Ile	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	61	14	0.229508	NM_015395	A8KAD1|B3KPZ1|C9J024|F5GX57|Q96EB0|Q9P2I9|Q9UFR6	Missense_Mutation	SNP	ENST00000447648.2	37	CCDS47648.1	.	.	.	.	.	.	.	.	.	.	C	24.2	4.500612	0.85176	.	.	ENSG00000205356	ENST00000447648;ENST00000379795;ENST00000542604	T;T;T	0.38722	1.14;1.12;1.15	5.25	5.25	0.73442	Pleckstrin homology domain (1);	0.043912	0.85682	D	0.000000	T	0.62146	0.2404	L	0.60455	1.87	0.46749	D	0.999184	D;D	0.89917	1.0;0.999	D;D	0.72338	0.977;0.949	T	0.64976	-0.6280	10	0.87932	D	0	-32.2674	17.8224	0.88654	0.0:1.0:0.0:0.0	.	575;645	F5GX57;Q7Z6L1	.;TCPR1_HUMAN	I	645;646;575	ENSP00000404923:S645I;ENSP00000369121:S646I;ENSP00000441121:S575I	ENSP00000369121:S646I	S	-	2	0	TECPR1	97699092	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	4.805000	0.62561	2.459000	0.83118	0.655000	0.94253	AGC	.	.	none		0.657	TECPR1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000334661.1	NM_015395	
ARMC8	25852	hgsc.bcm.edu	37	3	137928677	137928677	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:137928677C>T	ENST00000469044.1	+	2	335	c.64C>T	c.(64-66)Cgc>Tgc	p.R22C	ARMC8_ENST00000485396.1_Intron|ARMC8_ENST00000461822.1_Missense_Mutation_p.R22C|ARMC8_ENST00000538260.1_Missense_Mutation_p.R22C|ARMC8_ENST00000491704.1_Intron|ARMC8_ENST00000393058.3_Missense_Mutation_p.R12C|ARMC8_ENST00000489213.1_Intron|ARMC8_ENST00000481646.1_Missense_Mutation_p.R8C|ARMC8_ENST00000471453.1_Missense_Mutation_p.R8C|ARMC8_ENST00000358441.2_Missense_Mutation_p.R8C|ARMC8_ENST00000470821.1_Missense_Mutation_p.R22C	NM_001267041.1|NM_001267042.1	NP_001253970.1|NP_001253971.1	Q8IUR7	ARMC8_HUMAN	armadillo repeat containing 8	22										endometrium(2)|kidney(1)|large_intestine(7)|lung(5)|upper_aerodigestive_tract(1)	16						AGCTAGCAGTCGCCACTATGT	0.398																																					p.R22C		Atlas-SNP	.											ARMC8_ENST00000481646,colon,carcinoma,-1,4	ARMC8	79	4	0			c.C64T						scavenged	.						84.0	84.0	84.0					3																	137928677		2203	4300	6503	SO:0001583	missense	25852	exon2			AGCAGTCGCCACT		CCDS3098.1, CCDS54646.1, CCDS58853.1, CCDS58854.1, CCDS75020.1	3q22	2013-02-14			ENSG00000114098	ENSG00000114098		"""Armadillo repeat containing"""	24999	protein-coding gene	gene with protein product	"""GID complex subunit 5, VID28 homolog (S. cerevisiae)"""					11042152	Standard	NM_014154		Approved	HSPC056, DKFZP434A043, GID5, VID28	uc003esa.2	Q8IUR7	OTTHUMG00000159821	ENST00000469044.1:c.64C>T	3.37:g.137928677C>T	ENSP00000419413:p.Arg22Cys	Somatic	191	0	0		WXS	Illumina HiSeq	Phase_I	160	4	0.025	NM_001267041	A8K0L2|B7Z441|B7Z453|D3DNE6|F5GWK4|Q6PIL2|Q96D19|Q96HZ5|Q9NV02|Q9NV94|Q9Y4R9	Missense_Mutation	SNP	ENST00000469044.1	37		.	.	.	.	.	.	.	.	.	.	C	26.9	4.778100	0.90195	.	.	ENSG00000114098	ENST00000481646;ENST00000469044;ENST00000461600;ENST00000358441;ENST00000461822;ENST00000471453;ENST00000470821;ENST00000471709;ENST00000538260;ENST00000393058;ENST00000468560	T;T;T;T;T;T;T;T;T;T	0.66995	-0.22;-0.24;1.8;1.67;1.28;1.67;1.61;1.65;1.28;-0.18	5.79	5.79	0.91817	.	0.000000	0.85682	D	0.000000	T	0.76863	0.4047	L	0.43923	1.385	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	P;D;D;D	0.69824	0.828;0.95;0.966;0.953	T	0.78026	-0.2365	10	0.87932	D	0	-8.1574	17.534	0.87822	0.0:1.0:0.0:0.0	.	22;22;8;8	B7Z441;F5GWK4;Q8IUR7-2;Q8IUR7-6	.;.;.;.	C	8;22;22;8;22;8;22;22;22;12;8	ENSP00000420333:R8C;ENSP00000419413:R22C;ENSP00000418074:R22C;ENSP00000351221:R8C;ENSP00000420706:R22C;ENSP00000420440:R8C;ENSP00000418405:R22C;ENSP00000420719:R22C;ENSP00000441592:R22C;ENSP00000376778:R12C	ENSP00000351221:R8C	R	+	1	0	ARMC8	139411367	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.223000	0.65283	2.750000	0.94351	0.563000	0.77884	CGC	.	.	none		0.398	ARMC8-003	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000357560.1	NM_015396	
PLCG1	5335	hgsc.bcm.edu	37	20	39802374	39802374	+	Silent	SNP	C	C	T	rs150104210		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:39802374C>T	ENST00000373271.1	+	29	3882	c.3477C>T	c.(3475-3477)ttC>ttT	p.F1159F	PLCG1_ENST00000244007.3_Silent_p.F1159F|PLCG1_ENST00000608689.1_3'UTR|PLCG1_ENST00000373272.2_Silent_p.F1159F	NM_182811.1	NP_877963.1	P19174	PLCG1_HUMAN	phospholipase C, gamma 1	1159	C2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				activation of MAPKK activity (GO:0000186)|activation of phospholipase C activity (GO:0007202)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|calcium-mediated signaling (GO:0019722)|cell migration (GO:0016477)|cellular response to epidermal growth factor stimulus (GO:0071364)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|inositol phosphate metabolic process (GO:0043647)|leukocyte migration (GO:0050900)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phospholipid catabolic process (GO:0009395)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|T cell receptor signaling pathway (GO:0050852)|viral process (GO:0016032)	cell projection (GO:0042995)|cell-cell junction (GO:0005911)|COP9 signalosome (GO:0008180)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	calcium ion binding (GO:0005509)|neurotrophin TRKA receptor binding (GO:0005168)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|protein kinase binding (GO:0019901)|receptor signaling protein activity (GO:0005057)			breast(5)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(16)|skin(6)|urinary_tract(2)	46		Myeloproliferative disorder(115;0.00878)				TTCTGCGCTTCGTGGTGTATG	0.507											OREG0025953	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.F1159F		Atlas-SNP	.											.	PLCG1	111	.	0			c.C3477T						PASS	.	C	,	0,4406		0,0,2203	137.0	116.0	123.0		3477,3477	-1.6	1.0	20	dbSNP_134	123	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous,coding-synonymous	PLCG1	NM_002660.2,NM_182811.1	,	0,3,6500	TT,TC,CC		0.0349,0.0,0.0231	,	1159/1292,1159/1291	39802374	3,13003	2203	4300	6503	SO:0001819	synonymous_variant	5335	exon29			GCGCTTCGTGGTG	M34667	CCDS13313.1, CCDS13314.1	20q12-q13.1	2013-02-14	2004-01-29		ENSG00000124181	ENSG00000124181	3.1.4.11	"""Pleckstrin homology (PH) domain containing"", ""EF-hand domain containing"", ""SH2 domain containing"""	9065	protein-coding gene	gene with protein product		172420	"""phospholipase C, gamma 1 (formerly subtype 148)"""	PLC1		2167438, 3254788	Standard	NM_182811		Approved	PLC148, PLC-II, PLCgamma1, NCKAP3	uc002xjo.1	P19174	OTTHUMG00000033082	ENST00000373271.1:c.3477C>T	20.37:g.39802374C>T		Somatic	239	0	0	888	WXS	Illumina HiSeq	Phase_I	226	135	0.597345	NM_182811	B7ZLY7|B9EGH4|E1P5W4|Q2V575	Silent	SNP	ENST00000373271.1	37	CCDS13314.1																																																																																			C|1.000;T|0.000	0.000	weak		0.507	PLCG1-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000080514.3	NM_182811	
PRIMPOL	201973	hgsc.bcm.edu	37	4	185615764	185615764	+	Missense_Mutation	SNP	C	C	A	rs14969	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:185615764C>A	ENST00000314970.6	+	14	1947	c.1514C>A	c.(1513-1515)aCa>aAa	p.T505K	PRIMPOL_ENST00000512834.1_Missense_Mutation_p.T504K|PRIMPOL_ENST00000515774.1_Missense_Mutation_p.T376K|PRIMPOL_ENST00000503752.1_Missense_Mutation_p.T505K|PRIMPOL_ENST00000510864.1_3'UTR	NM_152683.2	NP_689896	Q96LW4	PRIPO_HUMAN	primase and polymerase (DNA-directed)	505	Interaction with RPA1.		T -> K (in dbSNP:rs14969).		mitochondrial DNA replication (GO:0006264)|replication fork processing (GO:0031297)|response to UV (GO:0009411)|translesion synthesis (GO:0019985)	mitochondrial matrix (GO:0005759)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA primase activity (GO:0003896)|DNA-directed DNA polymerase activity (GO:0003887)|manganese ion binding (GO:0030145)										AGGCTGTCAACAGGTGCATCT	0.413													C|||	733	0.146366	0.3011	0.1369	5008	,	,		20112	0.001		0.1481	False		,,,				2504	0.092				p.T505K		Atlas-SNP	.											.	CCDC111	43	.	0			c.C1514A						PASS	.	C	,LYS/THR	1220,3186	421.3+/-339.3	165,890,1148	97.0	100.0	99.0		,1514	0.0	0.0	4	dbSNP_52	99	1407,7193	271.1+/-289.3	117,1173,3010	yes	utr-3,missense	MLF1IP,CCDC111	NM_024629.3,NM_152683.2	,78	282,2063,4158	AA,AC,CC		16.3605,27.6895,20.1984	,benign	,505/561	185615764	2627,10379	2203	4300	6503	SO:0001583	missense	201973	exon14			TGTCAACAGGTGC	AK057729	CCDS3837.1, CCDS75211.1, CCDS75212.1	4q35.1	2013-09-27	2013-09-27	2013-09-27	ENSG00000164306	ENSG00000164306			26575	protein-coding gene	gene with protein product		615421	"""coiled-coil domain containing 111"""	CCDC111		12477932	Standard	XM_005262814		Approved	FLJ33167	uc003iwk.2	Q96LW4	OTTHUMG00000160495	ENST00000314970.6:c.1514C>A	4.37:g.185615764C>A	ENSP00000313816:p.Thr505Lys	Somatic	285	0	0		WXS	Illumina HiSeq	Phase_I	240	114	0.475	NM_152683	D3DP55|D6RDM1|Q5HYJ9	Missense_Mutation	SNP	ENST00000314970.6	37	CCDS3837.1	313	0.1433150183150183	151	0.30691056910569103	57	0.1574585635359116	0	0.0	105	0.13852242744063326	C	0.026	-1.374732	0.01214	0.276895	0.163605	ENSG00000164306	ENST00000314970;ENST00000515774;ENST00000503752;ENST00000512834	T;T;T;T	0.28069	1.63;1.63;1.63;1.63	4.37	-0.00219	0.14031	.	2.209650	0.01988	N	0.045328	T	0.00012	0.0000	N	0.00538	-1.39	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.35943	-0.9768	9	0.12430	T	0.62	-9.0119	4.1821	0.10380	0.1577:0.4244:0.3259:0.092	rs14969;rs3184981;rs58650800;rs14969	376;505;504	D3DP56;Q96LW4;D6RDM1	.;CC111_HUMAN;.	K	505;376;505;504	ENSP00000313816:T505K;ENSP00000421913:T376K;ENSP00000420860:T505K;ENSP00000425316:T504K	ENSP00000313816:T505K	T	+	2	0	CCDC111	185852758	0.000000	0.05858	0.005000	0.12908	0.003000	0.03518	-0.366000	0.07563	0.055000	0.16094	-0.226000	0.12346	ACA	C|0.824;A|0.176	0.176	strong		0.413	PRIMPOL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000360827.1	NM_152683	
FAM19A4	151647	hgsc.bcm.edu	37	3	68782299	68782299	+	Silent	SNP	C	C	T	rs146641270	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:68782299C>T	ENST00000295569.7	-	6	909	c.417G>A	c.(415-417)acG>acA	p.T139T		NM_001005527.2|NM_182522.4	NP_001005527.1|NP_872328.1	Q96LR4	F19A4_HUMAN	family with sequence similarity 19 (chemokine (C-C motif)-like), member A4	139						extracellular region (GO:0005576)				haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(5)|skin(2)	10		Lung NSC(201;0.0198)		BRCA - Breast invasive adenocarcinoma(55;1.38e-05)|Epithelial(33;0.000124)|LUSC - Lung squamous cell carcinoma(21;0.0248)|KIRC - Kidney renal clear cell carcinoma(39;0.0729)|Kidney(39;0.0904)		TTCGCTACCGCGTTACCTAAA	0.483													C|||	5	0.000998403	0.0	0.0	5008	,	,		18682	0.0		0.001	False		,,,				2504	0.0041				p.T139T		Atlas-SNP	.											.	FAM19A4	23	.	0			c.G417A						PASS	.	C	,	1,4405	2.1+/-5.4	0,1,2202	128.0	119.0	122.0		417,417	-6.3	1.0	3	dbSNP_134	122	16,8584	11.9+/-42.8	0,16,4284	no	coding-synonymous,coding-synonymous	FAM19A4	NM_001005527.1,NM_182522.3	,	0,17,6486	TT,TC,CC		0.186,0.0227,0.1307	,	139/141,139/141	68782299	17,12989	2203	4300	6503	SO:0001819	synonymous_variant	151647	exon6			CTACCGCGTTACC	AY325117	CCDS2907.1	3p14.1	2014-08-14			ENSG00000163377	ENSG00000163377			21591	protein-coding gene	gene with protein product						15028294, 25109685	Standard	NM_182522		Approved	TAFA-4	uc021xah.1	Q96LR4	OTTHUMG00000158744	ENST00000295569.7:c.417G>A	3.37:g.68782299C>T		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	62	29	0.467742	NM_182522	A8MVT2	Silent	SNP	ENST00000295569.7	37	CCDS2907.1																																																																																			C|0.999;T|0.001	0.001	strong		0.483	FAM19A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352002.1	NM_182522	
GPR162	27239	hgsc.bcm.edu	37	12	6935977	6935977	+	Missense_Mutation	SNP	A	A	G	rs11612427	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:6935977A>G	ENST00000311268.3	+	5	2162	c.1375A>G	c.(1375-1377)Aga>Gga	p.R459G	LEPREL2_ENST00000396725.2_RNA|LEPREL2_ENST00000606935.1_RNA|LEPREL2_ENST00000251761.8_RNA|GPR162_ENST00000428545.2_Missense_Mutation_p.R175G|GPR162_ENST00000382315.3_Missense_Mutation_p.R155G	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	74	0	0		WXS	Illumina HiSeq	Phase_I	70	38	0.542857	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	
KIAA0368	23392	hgsc.bcm.edu	37	9	114174415	114174415	+	Missense_Mutation	SNP	T	T	C	rs2418163	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:114174415T>C	ENST00000338205.5	-	20	2312	c.2093A>G	c.(2092-2094)aAc>aGc	p.N698S	RNA5SP294_ENST00000411306.1_RNA|KIAA0368_ENST00000259335.4_Missense_Mutation_p.N876S			Q5VYK3	ECM29_HUMAN	KIAA0368	704					ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)	centrosome (GO:0005813)|cytoplasmic membrane-bounded vesicle (GO:0016023)|early endosome (GO:0005769)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle (GO:0030134)|late endosome (GO:0005770)|membrane (GO:0016020)|multivesicular body (GO:0005771)|nucleus (GO:0005634)|proteasome complex (GO:0000502)				NS(2)|breast(3)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(23)|prostate(3)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	65						TTCTTTACTGTTATTCATCAG	0.353													C|||	2035	0.40635	0.4281	0.3256	5008	,	,		17727	0.3492		0.493	False		,,,				2504	0.4039				p.N876S		Atlas-SNP	.											.	KIAA0368	144	.	0			c.A2627G						PASS	.	C	SER/ASN	1518,2126		313,892,617	68.0	62.0	64.0		2627	4.7	1.0	9	dbSNP_100	64	3880,4322		950,1980,1171	yes	missense	KIAA0368	NM_001080398.1	46	1263,2872,1788	CC,CT,TT		47.3055,41.6575,45.5681	benign	876/2018	114174415	5398,6448	1822	4101	5923	SO:0001583	missense	23392	exon22			TTACTGTTATTCA	AK025689	CCDS48006.1	9q32	2012-11-29	2006-11-23	2006-11-23	ENSG00000136813	ENSG00000136813			29020	protein-coding gene	gene with protein product	"""ECM29 homolog (S. cerevisiae)"""					9205841, 15496406, 20682791	Standard	NM_001080398		Approved	FLJ22036, ECM29	uc004bfe.1	Q5VYK3	OTTHUMG00000020489	ENST00000338205.5:c.2093A>G	9.37:g.114174415T>C	ENSP00000339889:p.Asn698Ser	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	52	50	0.961538	NM_001080398	O15074|Q8WU82	Missense_Mutation	SNP	ENST00000338205.5	37		914	0.4184981684981685	228	0.4634146341463415	136	0.3756906077348066	185	0.32342657342657344	365	0.4815303430079156	C	8.495	0.862983	0.17178	0.416575	0.473055	ENSG00000136813	ENST00000338205;ENST00000259335;ENST00000543827	T	0.63580	-0.05	5.6	4.65	0.58169	.	0.162323	0.56097	N	0.000026	T	0.00012	0.0000	N	0.00841	-1.15	0.09310	P	1.0	B	0.02656	0.0	B	0.01281	0.0	T	0.38156	-0.9674	9	0.02654	T	1	.	8.847	0.35177	0.0:0.5734:0.3373:0.0893	rs2418163;rs17795384;rs52791111;rs2418163	173	B3KXF2	.	S	698;876;173	ENSP00000259335:N876S	ENSP00000259335:N876S	N	-	2	0	KIAA0368	113214236	1.000000	0.71417	0.999000	0.59377	0.991000	0.79684	5.606000	0.67641	1.533000	0.49186	-0.222000	0.12452	AAC	C|0.419;N|0.002	0.419	strong		0.353	KIAA0368-001	NOVEL	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000053637.2	NM_014686	
VRK1	7443	hgsc.bcm.edu	37	14	97321689	97321689	+	Silent	SNP	C	C	T	rs2230532	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	98	0	0		WXS	Illumina HiSeq	Phase_I	86	36	0.418605	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	
IPO11	51194	hgsc.bcm.edu	37	5	61772535	61772535	+	Silent	SNP	G	G	T	rs26635	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:61772535G>T	ENST00000325324.6	+	9	952	c.783G>T	c.(781-783)gtG>gtT	p.V261V	IPO11_ENST00000409296.3_Silent_p.V301V|KIF2A_ENST00000509663.2_Intron	NM_016338.4	NP_057422.3	Q9UI26	IPO11_HUMAN	importin 11	261					ribosomal protein import into nucleus (GO:0006610)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein transporter activity (GO:0008565)	p.V261V(1)		endometrium(2)|kidney(3)|large_intestine(5)|lung(14)|skin(4)|stomach(2)	30		Lung NSC(810;8.99e-06)|Prostate(74;0.0235)|Ovarian(174;0.0511)|Breast(144;0.077)		Lung(70;0.0613)		CAGATAATGTGTGTAGAGATA	0.254													G|||	2216	0.442492	0.413	0.4942	5008	,	,		14958	0.3155		0.4881	False		,,,				2504	0.5297				p.V301V		Atlas-SNP	.											IPO11,NS,carcinoma,0,1	IPO11	76	1	1	Substitution - coding silent(1)	stomach(1)	c.G903T						PASS	.	G	,	1804,2576	497.6+/-363.9	361,1082,747	68.0	76.0	73.0		903,783	-2.3	1.0	5	dbSNP_76	73	4158,4386	554.4+/-386.5	1034,2090,1148	no	coding-synonymous,coding-synonymous	IPO11	NM_001134779.1,NM_016338.4	,	1395,3172,1895	TT,TG,GG		48.6657,41.1872,46.1312	,	301/1016,261/976	61772535	5962,6962	2190	4272	6462	SO:0001819	synonymous_variant	51194	exon9			TAATGTGTGTAGA	AF111109	CCDS34167.1, CCDS47217.1	5q12.1	2008-09-19			ENSG00000086200	ENSG00000086200		"""Importins"""	20628	protein-coding gene	gene with protein product		610889					Standard	NM_016338		Approved	RanBP11	uc011cqr.2	Q9UI26	OTTHUMG00000154400	ENST00000325324.6:c.783G>T	5.37:g.61772535G>T		Somatic	371	0	0		WXS	Illumina HiSeq	Phase_I	422	145	0.343602	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	
MFGE8	4240	hgsc.bcm.edu	37	15	89450546	89450546	+	Silent	SNP	C	C	T	rs1878327	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:89450546C>T	ENST00000566497.1	-	3	328	c.267G>A	c.(265-267)tcG>tcA	p.S89S	MFGE8_ENST00000559997.1_5'UTR|MFGE8_ENST00000268150.8_Silent_p.S89S|MFGE8_ENST00000539437.1_Silent_p.S81S|MFGE8_ENST00000542878.1_Silent_p.S45S|MFGE8_ENST00000268151.7_Silent_p.S89S			Q08431	MFGM_HUMAN	milk fat globule-EGF factor 8 protein	89	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.S89S(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)					CACGCACAGACGAGGCGGCGA	0.617													T|||	3150	0.628994	0.8011	0.6138	5008	,	,		18641	0.4623		0.6322	False		,,,				2504	0.5757				p.S89S		Atlas-SNP	.											MFGE8,NS,carcinoma,0,1	MFGE8	60	1	1	Substitution - coding silent(1)	stomach(1)	c.G267A						PASS	.	T	,	3450,950	360.4+/-315.2	1349,752,99	131.0	91.0	105.0		267,267	-10.6	0.0	15	dbSNP_92	105	5584,3014	465.8+/-366.6	1796,1992,511	no	coding-synonymous,coding-synonymous	MFGE8	NM_001114614.1,NM_005928.2	,	3145,2744,610	TT,TC,CC		35.0547,21.5909,30.497	,	89/336,89/388	89450546	9034,3964	2200	4299	6499	SO:0001819	synonymous_variant	4240	exon3			CACAGACGAGGCG	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.267G>A	15.37:g.89450546C>T		Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	201	200	0.995025	NM_001114614	B2R6M7|Q53FU9|Q7Z3D2|Q9BTL9	Silent	SNP	ENST00000566497.1	37	CCDS10347.1																																																																																			C|0.333;T|0.667	0.667	strong		0.617	MFGE8-015	NOVEL	alternative_3_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000432804.1	NM_005928	
GXYLT1	283464	hgsc.bcm.edu	37	12	42503467	42503467	+	Silent	SNP	T	T	C	rs7312933	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	75	0	0		WXS	Illumina HiSeq	Phase_I	90	47	0.522222	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	
AMPD3	272	hgsc.bcm.edu	37	11	10503736	10503736	+	Missense_Mutation	SNP	C	C	T	rs11042836	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:10503736C>T	ENST00000396554.3	+	4	921	c.580C>T	c.(580-582)Cgg>Tgg	p.R194W	AMPD3_ENST00000444303.2_Missense_Mutation_p.R26W	NM_000480.2	NP_000471.1	Q01432	AMPD3_HUMAN	adenosine monophosphate deaminase 3	185					ADP metabolic process (GO:0046031)|AMP catabolic process (GO:0006196)|ATP metabolic process (GO:0046034)|energy homeostasis (GO:0097009)|IMP salvage (GO:0032264)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase metabolic process (GO:0006144)|purine-containing compound salvage (GO:0043101)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	AMP deaminase activity (GO:0003876)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(12)|ovary(1)|prostate(3)|skin(1)	25				all cancers(16;1.14e-08)|Epithelial(150;2.83e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0291)		GGGTCATCCGCGGGCGGATAC	0.622													C|||	115	0.0229633	0.003	0.0346	5008	,	,		16919	0.0		0.0755	False		,,,				2504	0.0112				p.R194W		Atlas-SNP	.											.	AMPD3	68	.	0			c.C580T						PASS	.	C	TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG	72,4330	63.5+/-100.7	1,70,2130	49.0	56.0	54.0		580,553,574,553,76	-1.5	0.0	11	dbSNP_120	54	729,7859	173.2+/-223.7	37,655,3602	yes	missense,missense,missense,missense,missense	AMPD3	NM_000480.2,NM_001025389.1,NM_001025390.1,NM_001172430.1,NM_001172431.1	101,101,101,101,101	38,725,5732	TT,TC,CC		8.4886,1.6356,6.1663	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	194/777,185/768,192/775,185/768,26/609	10503736	801,12189	2201	4294	6495	SO:0001583	missense	272	exon4			CATCCGCGGGCGG	M84722	CCDS7802.1, CCDS41617.1, CCDS44537.1, CCDS53601.1	11p15	2010-02-10	2010-02-10			ENSG00000133805	3.5.4.6		470	protein-coding gene	gene with protein product	"""erythrocyte-specific AMP deaminase"""	102772	"""adenosine monophosphate deaminase (isoform E)"""			1400401	Standard	NM_001172430		Approved		uc001min.1	Q01432		ENST00000396554.3:c.580C>T	11.37:g.10503736C>T	ENSP00000379802:p.Arg194Trp	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	86	72	0.837209	NM_000480	A0AUX0|B7Z2S2|B7Z763|B7Z877	Missense_Mutation	SNP	ENST00000396554.3	37	CCDS7802.1	76	0.0347985347985348	4	0.008130081300813009	16	0.04419889502762431	0	0.0	56	0.07387862796833773	C	15.69	2.909453	0.52439	0.016356	0.084886	ENSG00000133805	ENST00000444303;ENST00000396554;ENST00000524866;ENST00000396553;ENST00000528723;ENST00000529507	T;T;T;T;T;T	0.36157	1.27;1.27;1.27;1.27;1.27;1.27	5.88	-1.45	0.08828	.	0.829016	0.11383	N	0.569647	T	0.01189	0.0039	L	0.29908	0.895	0.09310	N	1	P;P;D	0.56746	0.921;0.592;0.977	B;B;P	0.44860	0.339;0.058;0.462	T	0.05053	-1.0909	10	0.66056	D	0.02	-0.3438	3.2802	0.06912	0.2074:0.5028:0.097:0.1928	rs11042836;rs52815732;rs11042836	192;185;194	B7Z763;Q01432;A0AUX0	.;AMPD3_HUMAN;.	W	26;194;185;185;192;185	ENSP00000396000:R26W;ENSP00000379802:R194W;ENSP00000433284:R185W;ENSP00000379801:R185W;ENSP00000436987:R192W;ENSP00000431648:R185W	ENSP00000379801:R185W	R	+	1	2	AMPD3	10460312	0.000000	0.05858	0.000000	0.03702	0.018000	0.09664	-0.216000	0.09266	-0.101000	0.12219	-0.140000	0.14226	CGG	C|0.954;T|0.046	0.046	strong		0.622	AMPD3-001	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000385783.2	NM_000480	
ZNF880	400713	hgsc.bcm.edu	37	19	52888210	52888210	+	Silent	SNP	T	T	C	rs56151179	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:52888210T>C	ENST00000422689.2	+	4	1392	c.1377T>C	c.(1375-1377)acT>acC	p.T459T		NM_001145434.1	NP_001138906.1	Q6PDB4	ZN880_HUMAN	zinc finger protein 880	459					regulation of transcription, DNA-templated (GO:0006355)	intracellular (GO:0005622)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(2)|skin(1)	10						GATTTCATACTGGAGAGAAAC	0.388																																					p.T459T		Atlas-SNP	.											.	ZNF880	45	.	0			c.T1377C						PASS	.	T		529,855		102,325,265	74.0	70.0	71.0		1377	2.0	0.9	19	dbSNP_129	71	1217,1965		222,773,596	no	coding-synonymous	ZNF880	NM_001145434.1		324,1098,861	CC,CT,TT		38.2464,38.2225,38.2392		459/578	52888210	1746,2820	692	1591	2283	SO:0001819	synonymous_variant	400713	exon4			TCATACTGGAGAG	BC058819	CCDS46164.1	19q13.41	2013-01-08			ENSG00000221923	ENSG00000221923		"""Zinc fingers, C2H2-type"", ""-"""	37249	protein-coding gene	gene with protein product							Standard	NM_001145434		Approved		uc002pzc.3	Q6PDB4	OTTHUMG00000167972	ENST00000422689.2:c.1377T>C	19.37:g.52888210T>C		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	25	25	1	NM_001145434	B4DNA6	Silent	SNP	ENST00000422689.2	37	CCDS46164.1																																																																																			T|0.633;C|0.367	0.367	strong		0.388	ZNF880-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397374.1	NM_001145434	
MUC4	4585	hgsc.bcm.edu	37	3	195506037	195506037	+	Silent	SNP	G	G	T	rs2432527		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195506037G>T	ENST00000463781.3	-	2	12873	c.12414C>A	c.(12412-12414)tcC>tcA	p.S4138S	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Silent_p.S4138S	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)		TGTCACCTGTGGATACTGAGG	0.577																																					p.S4138S		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	0			c.C12414A						PASS	.						18.0	12.0	13.0					3																	195506037		645	1545	2190	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.12414C>A	3.37:g.195506037G>T		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	95	53	0.557895	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|0.534;T|0.466	0.466	strong		0.577	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
ATOH7	220202	hgsc.bcm.edu	37	10	69991266	69991266	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:69991266T>C	ENST00000373673.3	-	1	605	c.169A>G	c.(169-171)Aac>Gac	p.N57D	RP11-153K11.3_ENST00000444086.1_lincRNA	NM_145178.3	NP_660161.1	Q8N100	ATOH7_HUMAN	atonal homolog 7 (Drosophila)	57	bHLH. {ECO:0000255|PROSITE- ProRule:PRU00981}.				cell differentiation (GO:0030154)|circadian rhythm (GO:0007623)|entrainment of circadian clock (GO:0009649)|neural retina development (GO:0003407)|optic nerve development (GO:0021554)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)										AAGGCAGTGTTGAGCCCCTGC	0.701																																					p.N57D		Atlas-SNP	.											.	ATOH7	4	.	0			c.A169G						PASS	.						38.0	37.0	38.0					10																	69991266		2203	4299	6502	SO:0001583	missense	220202	exon1			CAGTGTTGAGCCC	AF418922	CCDS7276.1	10q22.2	2013-05-21			ENSG00000179774	ENSG00000179774		"""Basic helix-loop-helix proteins"""	13907	protein-coding gene	gene with protein product		609875				11889557	Standard	NM_145178		Approved	Math5, bHLHa13	uc001jnq.3	Q8N100	OTTHUMG00000018346	ENST00000373673.3:c.169A>G	10.37:g.69991266T>C	ENSP00000362777:p.Asn57Asp	Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	55	32	0.581818	NM_145178		Missense_Mutation	SNP	ENST00000373673.3	37	CCDS7276.1	.	.	.	.	.	.	.	.	.	.	T	19.30	3.800203	0.70567	.	.	ENSG00000179774	ENST00000373673	D	0.99394	-5.82	5.01	2.52	0.30459	Helix-loop-helix DNA-binding (5);	0.043911	0.85682	D	0.000000	D	0.99612	0.9859	H	0.98407	4.225	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.98476	1.0603	9	.	.	.	-34.2974	11.5762	0.50862	0.0:0.0:0.2838:0.7162	.	57	Q8N100	ATOH7_HUMAN	D	57	ENSP00000362777:N57D	.	N	-	1	0	ATOH7	69661272	1.000000	0.71417	0.992000	0.48379	0.079000	0.17450	6.216000	0.72212	0.207000	0.20607	0.459000	0.35465	AAC	.	.	none		0.701	ATOH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048312.1		
TDRD6	221400	hgsc.bcm.edu	37	6	46657057	46657057	+	Missense_Mutation	SNP	A	A	G	rs3799277	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:46657057A>G	ENST00000316081.6	+	1	1192	c.1192A>G	c.(1192-1194)Aca>Gca	p.T398A	TDRD6_ENST00000544460.1_Missense_Mutation_p.T398A|RP11-446F17.3_ENST00000434329.2_RNA|RP11-446F17.3_ENST00000571590.1_RNA|RP11-446F17.3_ENST00000422284.2_RNA	NM_001010870.2	NP_001010870.1	O60522	TDRD6_HUMAN	tudor domain containing 6	398			T -> A (in dbSNP:rs3799277).		germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|P granule (GO:0043186)				NS(1)|breast(9)|central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(25)|ovary(2)|pancreas(1)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	80			Lung(136;0.192)			TGACCTGAAGACACTGATACT	0.468													G|||	4448	0.888179	0.9796	0.8631	5008	,	,		20635	0.9097		0.7624	False		,,,				2504	0.8896				p.T398A		Atlas-SNP	.											.	TDRD6	205	.	0			c.A1192G						PASS	.	G	ALA/THR,ALA/THR	4209,197	123.3+/-160.7	2012,185,6	113.0	103.0	106.0		1192,1192	3.8	0.9	6	dbSNP_107	106	6963,1637	303.3+/-306.4	2822,1319,159	yes	missense,missense	TDRD6	NM_001010870.2,NM_001168359.1	58,58	4834,1504,165	GG,GA,AA		19.0349,4.4712,14.1012	benign,benign	398/2097,398/2067	46657057	11172,1834	2203	4300	6503	SO:0001583	missense	221400	exon1			CTGAAGACACTGA	AF039442	CCDS34470.1, CCDS55017.1	6p12.3	2013-01-23			ENSG00000180113	ENSG00000180113		"""Tudor domain containing"""	21339	protein-coding gene	gene with protein product	"""cancer/testis antigen 41.2"", ""spermatogenesis associated 36"""	611200				9610721	Standard	NM_001010870		Approved	NY-CO-45, bA446F17.4, CT41.2, SPATA36	uc003oyj.3	O60522	OTTHUMG00000014788	ENST00000316081.6:c.1192A>G	6.37:g.46657057A>G	ENSP00000346065:p.Thr398Ala	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	97	97	1	NM_001168359	B3KWU2|F5H5M3|Q5HYB1|Q5VTS4|Q6ZMX5	Missense_Mutation	SNP	ENST00000316081.6	37	CCDS34470.1	1888	0.8644688644688645	483	0.9817073170731707	311	0.8591160220994475	515	0.9003496503496503	579	0.7638522427440633	G	0.001	-2.894098	0.00059	0.955288	0.809651	ENSG00000180113	ENST00000544460;ENST00000316081	T;T	0.13538	2.58;2.58	5.55	3.79	0.43588	.	0.855010	0.10567	N	0.659565	T	0.00784	0.0026	N	0.00289	-1.7	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.48043	-0.9069	9	0.07990	T	0.79	-9.3702	8.3551	0.32324	0.3664:0.0:0.6336:0.0	rs3799277;rs60915012;rs3799277	398;398	F5H5M3;O60522	.;TDRD6_HUMAN	A	398	ENSP00000443299:T398A;ENSP00000346065:T398A	ENSP00000346065:T398A	T	+	1	0	TDRD6	46765016	0.999000	0.42202	0.926000	0.36857	0.234000	0.25298	1.285000	0.33261	0.480000	0.27534	-0.726000	0.03593	ACA	A|0.137;G|0.863	0.863	strong		0.468	TDRD6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040800.1	XM_166443	
MEGF6	1953	hgsc.bcm.edu	37	1	3428160	3428160	+	Silent	SNP	T	T	G	rs2820999	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:3428160T>G	ENST00000356575.4	-	9	1294	c.1068A>C	c.(1066-1068)acA>acC	p.T356T	MEGF6_ENST00000294599.4_Silent_p.T251T	NM_001409.3	NP_001400.3	O75095	MEGF6_HUMAN	multiple EGF-like-domains 6	356	EGF-like 6. {ECO:0000255|PROSITE- ProRule:PRU00076}.					extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			cervix(2)|endometrium(3)|large_intestine(3)|lung(8)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19	all_cancers(77;0.00681)|all_epithelial(69;0.00301)|Ovarian(185;0.0634)|Lung NSC(156;0.0969)|all_lung(157;0.105)	all_epithelial(116;7.41e-22)|all_lung(118;8.3e-09)|Lung NSC(185;3.55e-06)|Breast(487;0.000659)|Renal(390;0.00121)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Lung SC(97;0.0262)|Ovarian(437;0.0308)|Medulloblastoma(700;0.211)		Epithelial(90;3.78e-37)|OV - Ovarian serous cystadenocarcinoma(86;6.86e-22)|GBM - Glioblastoma multiforme(42;1.96e-12)|Colorectal(212;6.15e-05)|COAD - Colon adenocarcinoma(227;0.000241)|Kidney(185;0.000448)|BRCA - Breast invasive adenocarcinoma(365;0.000779)|KIRC - Kidney renal clear cell carcinoma(229;0.00645)|STAD - Stomach adenocarcinoma(132;0.00669)|Lung(427;0.213)		CGCGGGGACATGTGCACAGGG	0.642													G|||	2504	0.5	0.7511	0.4049	5008	,	,		17510	0.6409		0.2863	False		,,,				2504	0.3027				p.T356T	Ovarian(73;978 3658)	Atlas-SNP	.											.	MEGF6	91	.	0			c.A1068C						PASS	.	G		2799,1351		950,899,226	46.0	62.0	57.0		1068	3.9	1.0	1	dbSNP_100	57	2487,5913		395,1697,2108	no	coding-synonymous	MEGF6	NM_001409.3		1345,2596,2334	GG,GT,TT		29.6071,32.5542,42.1195		356/1542	3428160	5286,7264	2075	4200	6275	SO:0001819	synonymous_variant	1953	exon9			GGGACATGTGCAC	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.1068A>C	1.37:g.3428160T>G		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	68	48	0.705882	NM_001409	Q4AC86|Q5VV39	Silent	SNP	ENST00000356575.4	37	CCDS41237.1																																																																																			T|0.574;G|0.426	0.426	strong		0.642	MEGF6-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354866.1	NM_001409	
CCDC27	148870	hgsc.bcm.edu	37	1	3669201	3669201	+	Silent	SNP	A	A	G	rs10797410	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:3669201A>G	ENST00000294600.2	+	1	240	c.156A>G	c.(154-156)ccA>ccG	p.P52P		NM_152492.2	NP_689705.2	Q2M243	CCD27_HUMAN	coiled-coil domain containing 27	52										breast(1)|endometrium(2)|kidney(1)|large_intestine(8)|liver(2)|lung(17)|prostate(1)|skin(2)|urinary_tract(2)	36	all_cancers(77;0.0385)|Ovarian(185;0.0634)|Lung NSC(156;0.21)|all_lung(157;0.218)	all_epithelial(116;5.52e-17)|all_lung(118;1.04e-06)|Lung NSC(185;0.000214)|Renal(390;0.00357)|Breast(487;0.00446)|Hepatocellular(190;0.0218)|Lung SC(97;0.0367)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.127)		Epithelial(90;1.11e-38)|OV - Ovarian serous cystadenocarcinoma(86;1.35e-22)|GBM - Glioblastoma multiforme(42;3.46e-16)|Colorectal(212;1.17e-05)|COAD - Colon adenocarcinoma(227;5.76e-05)|Kidney(185;0.00036)|BRCA - Breast invasive adenocarcinoma(365;0.000696)|KIRC - Kidney renal clear cell carcinoma(229;0.00558)|STAD - Stomach adenocarcinoma(132;0.00645)|Lung(427;0.203)		AGGCCAGCCCATCTCAGAGGC	0.607													a|||	2549	0.508986	0.8389	0.4452	5008	,	,		17754	0.2897		0.3996	False		,,,				2504	0.4468				p.P52P		Atlas-SNP	.											.	CCDC27	79	.	0			c.A156G						PASS	.	A		3279,1127	717.7+/-408.7	1241,797,165	134.0	115.0	121.0		156	-6.7	0.0	1	dbSNP_120	121	3194,5406	484.1+/-371.3	596,2002,1702	no	coding-synonymous	CCDC27	NM_152492.2		1837,2799,1867	GG,GA,AA		37.1395,25.5788,49.7693		52/657	3669201	6473,6533	2203	4300	6503	SO:0001819	synonymous_variant	148870	exon1			CAGCCCATCTCAG		CCDS50.1	1p36.32	2008-02-05			ENSG00000162592	ENSG00000162592			26546	protein-coding gene	gene with protein product							Standard	NM_152492		Approved	FLJ32825	uc001akv.2	Q2M243	OTTHUMG00000003504	ENST00000294600.2:c.156A>G	1.37:g.3669201A>G		Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	94	68	0.723404	NM_152492	Q5TBV3|Q96M50	Silent	SNP	ENST00000294600.2	37	CCDS50.1																																																																																			A|0.502;G|0.498	0.498	strong		0.607	CCDC27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009740.1	NM_152492	
CCDC64B	146439	hgsc.bcm.edu	37	16	3078165	3078165	+	Missense_Mutation	SNP	A	A	G	rs12448103	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:3078165A>G	ENST00000572449.1	-	10	1531	c.1469T>C	c.(1468-1470)cTg>cCg	p.L490P	CCDC64B_ENST00000573514.1_Missense_Mutation_p.L283P|CCDC64B_ENST00000389347.4_Missense_Mutation_p.L490P			A1A5D9	BICR2_HUMAN	coiled-coil domain containing 64B	490										breast(1)|endometrium(2)|large_intestine(1)	4						GCCCAGGCGCAGCGAGAAGCG	0.716													A|||	909	0.18151	0.0492	0.2925	5008	,	,		10148	0.128		0.2356	False		,,,				2504	0.2812				p.L490P		Atlas-SNP	.											CCDC64B,NS,carcinoma,0,1	CCDC64B	19	1	0			c.T1469C						scavenged	.	A	PRO/LEU	205,3283		5,195,1544	4.0	5.0	5.0		1469	5.2	0.8	16	dbSNP_120	5	1331,6363		97,1137,2613	yes	missense	CCDC64B	NM_001103175.1	98	102,1332,4157	GG,GA,AA		17.2992,5.8773,13.7364	probably-damaging	490/509	3078165	1536,9646	1744	3847	5591	SO:0001583	missense	146439	exon9			AGGCGCAGCGAGA	BC128602	CCDS45393.1	16p13.3	2008-07-04				ENSG00000162069			33584	protein-coding gene	gene with protein product							Standard	NM_001103175		Approved		uc002ctf.4	A1A5D9		ENST00000572449.1:c.1469T>C	16.37:g.3078165A>G	ENSP00000459043:p.Leu490Pro	Somatic	8	0	0		WXS	Illumina HiSeq	Phase_I	8	4	0.5	NM_001103175	Q658L9	Missense_Mutation	SNP	ENST00000572449.1	37	CCDS45393.1	382	0.1749084249084249	26	0.052845528455284556	112	0.30939226519337015	64	0.11188811188811189	180	0.23746701846965698	a	17.73	3.462111	0.63513	0.058773	0.172992	ENSG00000162069	ENST00000389347	T	0.36157	1.27	5.15	5.15	0.70609	.	0.119688	0.34879	N	0.003617	T	0.00012	0.0000	M	0.68952	2.095	0.23473	P	0.99760263	D	0.89917	1.0	D	0.91635	0.999	T	0.26018	-1.0115	9	0.30854	T	0.27	-7.2384	11.3817	0.49761	1.0:0.0:0.0:0.0	rs12448103	490	A1A5D9	BICR2_HUMAN	P	490	ENSP00000373998:L490P	ENSP00000373998:L490P	L	-	2	0	CCDC64B	3018166	0.249000	0.23941	0.820000	0.32676	0.129000	0.20672	0.546000	0.23284	1.957000	0.56846	0.454000	0.30748	CTG	A|0.823;G|0.177	0.177	strong		0.716	CCDC64B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436991.1		
AAK1	22848	hgsc.bcm.edu	37	2	69746296	69746296	+	Silent	SNP	C	C	T	rs7603932	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:69746296C>T	ENST00000409085.4	-	12	1663	c.1287G>A	c.(1285-1287)ccG>ccA	p.P429P	AAK1_ENST00000406297.3_Silent_p.P429P|AAK1_ENST00000409068.1_Silent_p.P429P|SNORA36C_ENST00000384289.1_RNA|RN7SL604P_ENST00000492589.2_RNA	NM_014911.3	NP_055726	Q2M2I8	AAK1_HUMAN	AP2 associated kinase 1	429	Gln-rich.				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						CCTGAGTTTGCGGCAGAGGCT	0.612													T|||	511	0.102037	0.1483	0.0504	5008	,	,		16655	0.0536		0.1143	False		,,,				2504	0.1135				p.P429P		Atlas-SNP	.											.	AAK1	121	.	0			c.G1287A						PASS	.	T		505,3609		36,433,1588	28.0	36.0	34.0		1287	-4.1	0.0	2	dbSNP_116	34	728,7698		27,674,3512	no	coding-synonymous	AAK1	NM_014911.3		63,1107,5100	TT,TC,CC		8.6399,12.2752,9.8325		429/962	69746296	1233,11307	2057	4213	6270	SO:0001819	synonymous_variant	22848	exon12			AGTTTGCGGCAGA	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.1287G>A	2.37:g.69746296C>T		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	118	58	0.491525	NM_014911	Q4ZFZ3|Q53RX6|Q9UPV4	Silent	SNP	ENST00000409085.4	37	CCDS1893.2																																																																																			C|0.894;T|0.106	0.106	strong		0.612	AAK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251847.4	NM_014911	
KCNN1	3780	hgsc.bcm.edu	37	19	18100552	18100552	+	Silent	SNP	A	A	C	rs41278194	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:18100552A>C	ENST00000222249.9	+	8	1517	c.1198A>C	c.(1198-1200)Agg>Cgg	p.R400R		NM_002248.3	NP_002239.2	Q92952	KCNN1_HUMAN	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 1	400	Calmodulin-binding. {ECO:0000250}.				potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	calcium-activated potassium channel activity (GO:0015269)|calmodulin binding (GO:0005516)|small conductance calcium-activated potassium channel activity (GO:0016286)			endometrium(1)|kidney(1)|lung(5)|urinary_tract(1)	8					Miconazole(DB01110)|Procaine(DB00721)	TAACGTTCTCAGGGAGACGTG	0.507													A|||	10	0.00199681	0.0	0.0	5008	,	,		19008	0.0		0.007	False		,,,				2504	0.0031				p.R400R		Atlas-SNP	.											.	KCNN1	74	.	0			c.A1198C						PASS	.	A		3,3901		0,3,1949	130.0	133.0	132.0		1198	4.6	1.0	19	dbSNP_127	132	73,8277		0,73,4102	no	coding-synonymous	KCNN1	NM_002248.3		0,76,6051	CC,CA,AA		0.8743,0.0768,0.6202		400/544	18100552	76,12178	1952	4175	6127	SO:0001819	synonymous_variant	3780	exon8			GTTCTCAGGGAGA	U69883	CCDS67611.1	19p13.1	2012-07-05				ENSG00000105642		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, calcium-activated"""	6290	protein-coding gene	gene with protein product		602982				8781233, 10516439, 16382103	Standard	NM_002248		Approved	KCa2.1, hSK1	uc002nht.3	Q92952		ENST00000222249.9:c.1198A>C	19.37:g.18100552A>C		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	47	23	0.489362	NM_002248	Q5KR10|Q6DJU4	Silent	SNP	ENST00000222249.9	37																																																																																				A|0.997;C|0.003	0.003	strong		0.507	KCNN1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000471896.2	NM_002248	
PCSK5	5125	hgsc.bcm.edu	37	9	78936492	78936492	+	Missense_Mutation	SNP	A	A	G	rs1110223	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:78936492A>G	ENST00000545128.1	+	30	4496	c.3958A>G	c.(3958-3960)Aag>Gag	p.K1320E		NM_001190482.1	NP_001177411.1	Q92824	PCSK5_HUMAN	proprotein convertase subtilisin/kexin type 5	1320	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						CGTGGCTGTGAAGGGGGTATG	0.557													G|||	1597	0.31889	0.4592	0.2378	5008	,	,		19341	0.1369		0.341	False		,,,				2504	0.3517				p.K1320E		Atlas-SNP	.											.	PCSK5	329	.	0			c.A3958G						PASS	.	G	GLU/LYS	773,979		180,413,283	107.0	87.0	93.0		3958	4.8	0.9	9	dbSNP_86	93	1314,2668		221,872,898	yes	missense	PCSK5	NM_001190482.1	56	401,1285,1181	GG,GA,AA		32.9985,44.121,36.3969	benign	1320/1861	78936492	2087,3647	876	1991	2867	SO:0001583	missense	5125	exon30			GCTGTGAAGGGGG		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.3958A>G	9.37:g.78936492A>G	ENSP00000446280:p.Lys1320Glu	Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	35	18	0.514286	NM_001190482	F5H2G7|Q13527|Q96EP4	Missense_Mutation	SNP	ENST00000545128.1	37	CCDS55320.1	670	0.3067765567765568	234	0.47560975609756095	99	0.27348066298342544	76	0.13286713286713286	261	0.34432717678100266	G	1.456	-0.563675	0.03939	0.44121	0.329985	ENSG00000099139	ENST00000545128;ENST00000376754;ENST00000424854	T;T	0.49432	0.78;1.64	5.68	4.78	0.61160	.	0.398150	0.27397	N	0.019557	T	0.00012	0.0000	N	0.02736	-0.51	0.58432	P	1.999999999946489E-6	.	.	.	.	.	.	T	0.42949	-0.9421	7	0.02654	T	1	-9.562	9.362	0.38201	0.0773:0.1438:0.7788:0.0	rs1110223;rs2803426;rs60945756	.	.	.	E	1320;1050;1020	ENSP00000446280:K1320E;ENSP00000411654:K1020E	ENSP00000365945:K1050E	K	+	1	0	PCSK5	78126312	1.000000	0.71417	0.887000	0.34795	0.398000	0.30690	2.286000	0.43496	0.753000	0.32945	-0.802000	0.03209	AAG	A|0.687;G|0.313	0.313	strong		0.557	PCSK5-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
ONECUT2	9480	hgsc.bcm.edu	37	18	55104016	55104016	+	Silent	SNP	T	T	C	rs61735644	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:55104016T>C	ENST00000491143.2	+	1	1100	c.1068T>C	c.(1066-1068)ttT>ttC	p.F356F	AC090340.1_ENST00000581316.1_RNA	NM_004852.2	NP_004843.2	O95948	ONEC2_HUMAN	one cut homeobox 2	356					cell fate commitment (GO:0045165)|cilium assembly (GO:0042384)|endocrine pancreas development (GO:0031018)|epithelial cell development (GO:0002064)|liver development (GO:0001889)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|organ morphogenesis (GO:0009887)|peripheral nervous system neuron development (GO:0048935)|positive regulation of cell migration (GO:0030335)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell-matrix adhesion (GO:0001952)	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)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|lung(4)|ovary(2)|skin(1)	15		Colorectal(73;0.234)		READ - Rectum adenocarcinoma(59;0.227)|Colorectal(16;0.245)		AGGCGATCTTTGCGCAGAGGG	0.597													C|||	793	0.158347	0.2224	0.147	5008	,	,		17603	0.1448		0.0646	False		,,,				2504	0.1902				p.F356F		Atlas-SNP	.											ONECUT2,brain,glioma,0,2	ONECUT2	42	2	0			c.T1068C						PASS	.	C		764,3514		60,644,1435	35.0	41.0	39.0		1068	3.9	1.0	18	dbSNP_129	39	511,8043		18,475,3784	no	coding-synonymous	ONECUT2	NM_004852.2		78,1119,5219	CC,CT,TT		5.9738,17.8588,9.9361		356/505	55104016	1275,11557	2139	4277	6416	SO:0001819	synonymous_variant	9480	exon1			GATCTTTGCGCAG	Y18198	CCDS42440.1	18q21.31	2012-03-09	2007-07-16		ENSG00000119547	ENSG00000119547		"""Homeoboxes / CUT class"""	8139	protein-coding gene	gene with protein product		604894	"""one cut domain, family member 2"""			9915796	Standard	NM_004852		Approved	OC-2	uc002lgo.3	O95948	OTTHUMG00000159776	ENST00000491143.2:c.1068T>C	18.37:g.55104016T>C		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	98	51	0.520408	NM_004852		Silent	SNP	ENST00000491143.2	37	CCDS42440.1																																																																																			T|0.902;C|0.098	0.098	strong		0.597	ONECUT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357264.3		
CAMK2B	816	hgsc.bcm.edu	37	7	44282868	44282868	+	Silent	SNP	A	A	G	rs11542228	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:44282868A>G	ENST00000395749.2	-	8	658	c.582T>C	c.(580-582)ccT>ccC	p.P194P	CAMK2B_ENST00000347193.4_Silent_p.P194P|CAMK2B_ENST00000258682.6_Silent_p.P194P|CAMK2B_ENST00000440254.2_Silent_p.P194P|CAMK2B_ENST00000457475.1_Silent_p.P194P|CAMK2B_ENST00000358707.3_Silent_p.P194P|CAMK2B_ENST00000346990.4_Silent_p.P194P|CAMK2B_ENST00000502837.2_Silent_p.P65P|CAMK2B_ENST00000395747.2_Silent_p.P194P|CAMK2B_ENST00000350811.3_Silent_p.P194P|CAMK2B_ENST00000353625.4_Silent_p.P194P	NM_001220.4	NP_001211.3	Q13554	KCC2B_HUMAN	calcium/calmodulin-dependent protein kinase II beta	194	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						AGATGTCCACAGGCTTGCCAT	0.617													.|||	1681	0.335663	0.2852	0.317	5008	,	,		20349	0.2222		0.4245	False		,,,				2504	0.4427				p.P194P		Atlas-SNP	.											.	CAMK2B	56	.	0			c.T582C						PASS	.	G	,,,,,,,	1367,3039	687.5+/-404.9	203,961,1039	82.0	72.0	76.0		582,582,582,582,582,582,582,582	-7.1	0.8	7	dbSNP_120	76	3823,4777	611.0+/-395.8	827,2169,1304	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	,,,,,,,	1030,3130,2343	GG,GA,AA		44.4535,31.0259,39.9047	,,,,,,,	194/667,194/543,194/519,194/518,194/504,194/493,194/480,194/450	44282868	5190,7816	2203	4300	6503	SO:0001819	synonymous_variant	816	exon8			GTCCACAGGCTTG	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.582T>C	7.37:g.44282868A>G		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	118	82	0.694915	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|0.378;N|0.001	0.378	strong		0.617	CAMK2B-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251138.2	NM_172084	
GALNT14	79623	hgsc.bcm.edu	37	2	31135184	31135184	+	Missense_Mutation	SNP	G	G	T	rs2288101	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:31135184G>T	ENST00000349752.5	-	14	2044	c.1405C>A	c.(1405-1407)Cag>Aag	p.Q469K	GALNT14_ENST00000324589.5_Missense_Mutation_p.Q474K|GALNT14_ENST00000420311.2_Missense_Mutation_p.Q434K|GALNT14_ENST00000356174.3_Missense_Mutation_p.Q436K|GALNT14_ENST00000486564.1_5'UTR|GALNT14_ENST00000406653.1_Missense_Mutation_p.Q449K	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	87	0	0		WXS	Illumina HiSeq	Phase_I	54	54	1	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	
PCDHB3	56132	hgsc.bcm.edu	37	5	140481475	140481475	+	Missense_Mutation	SNP	A	A	T	rs3733699	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:140481475A>T	ENST00000231130.2	+	1	1242	c.1242A>T	c.(1240-1242)agA>agT	p.R414S	AC005754.7_ENST00000607216.1_RNA	NM_018937.2	NP_061760.1	Q9Y5E6	PCDB3_HUMAN	protocadherin beta 3	414	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.		R -> S (in dbSNP:rs3733699).		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(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(19)|lung(24)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	72			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			GAGAGACCAGATCCGAGTACA	0.483													A|||	746	0.148962	0.1672	0.1974	5008	,	,		20230	0.122		0.159	False		,,,				2504	0.1074				p.R414S		Atlas-SNP	.											.	PCDHB3	208	.	0			c.A1242T						PASS	.	A	SER/ARG	893,3513	343.6+/-307.7	78,737,1388	85.0	81.0	82.0		1242	-1.2	0.0	5	dbSNP_107	82	1525,7075	287.1+/-298.1	143,1239,2918	yes	missense	PCDHB3	NM_018937.2	110	221,1976,4306	TT,TA,AA		17.7326,20.2678,18.5914	benign	414/797	140481475	2418,10588	2203	4300	6503	SO:0001583	missense	56132	exon1			GACCAGATCCGAG	AF152496	CCDS4245.1	5q31	2010-01-26			ENSG00000113205	ENSG00000113205		"""Cadherins / Protocadherins : Clustered"""	8688	other	protocadherin		606329				10380929	Standard	NM_018937		Approved	PCDH-BETA3	uc003lio.3	Q9Y5E6	OTTHUMG00000129622	ENST00000231130.2:c.1242A>T	5.37:g.140481475A>T	ENSP00000231130:p.Arg414Ser	Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	115	56	0.486957	NM_018937	B2R8P2	Missense_Mutation	SNP	ENST00000231130.2	37	CCDS4245.1	344	0.1575091575091575	93	0.18902439024390244	67	0.1850828729281768	64	0.11188811188811189	120	0.158311345646438	A	2.673	-0.277157	0.05679	0.202678	0.177326	ENSG00000113205	ENST00000231130	T	0.01838	4.61	4.39	-1.2	0.09554	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.00012	0.0000	M	0.86740	2.835	0.80722	P	0.0	B	0.23128	0.08	B	0.24006	0.05	T	0.28332	-1.0047	8	0.23302	T	0.38	.	5.51	0.16876	0.3737:0.0:0.4756:0.1508	rs3733699;rs52802898;rs3733699	414	Q9Y5E6	PCDB3_HUMAN	S	414	ENSP00000231130:R414S	ENSP00000231130:R414S	R	+	3	2	PCDHB3	140461659	0.000000	0.05858	0.000000	0.03702	0.097000	0.18754	-3.877000	0.00344	-0.060000	0.13132	0.533000	0.62120	AGA	A|0.825;T|0.175	0.175	strong		0.483	PCDHB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251817.2	NM_018937	
VPS37A	137492	hgsc.bcm.edu	37	8	17123477	17123477	+	Missense_Mutation	SNP	A	A	G	rs372276569		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:17123477A>G	ENST00000324849.4	+	2	861	c.187A>G	c.(187-189)Att>Gtt	p.I63V	VPS37A_ENST00000521829.1_Intron|VPS37A_ENST00000324815.3_Missense_Mutation_p.I63V	NM_001145152.1|NM_152415.2	NP_001138624.1|NP_689628.2	Q8NEZ2	VP37A_HUMAN	vacuolar protein sorting 37 homolog A (S. cerevisiae)	63					cell death (GO:0008219)|endosomal transport (GO:0016197)|intracellular transport of virus (GO:0075733)|membrane organization (GO:0061024)|protein transport (GO:0015031)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral protein processing (GO:0019082)|virion assembly (GO:0019068)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|endosome membrane (GO:0010008)|ESCRT I complex (GO:0000813)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)				autonomic_ganglia(1)|breast(1)|kidney(2)|large_intestine(1)|lung(4)|skin(1)	10				Colorectal(111;0.0553)|COAD - Colon adenocarcinoma(73;0.212)		CAACCTGACAATTAACATTAA	0.284																																					p.I63V		Atlas-SNP	.											.	VPS37A	22	.	0			c.A187G						PASS	.	A	,VAL/ILE	1,4405	2.1+/-5.4	0,1,2202	94.0	96.0	96.0		,187	4.8	1.0	8		96	0,8588		0,0,4294	no	intron,missense	VPS37A	NM_001145152.1,NM_152415.2	,29	0,1,6496	GG,GA,AA		0.0,0.0227,0.0077	,possibly-damaging	,63/398	17123477	1,12993	2203	4294	6497	SO:0001583	missense	137492	exon2			CTGACAATTAACA		CCDS6001.1, CCDS47811.1	8p22	2012-06-29	2006-04-04		ENSG00000155975	ENSG00000155975			24928	protein-coding gene	gene with protein product	"""hepatocellular carcinoma related protein 1"""	609927	"""vacuolar protein sorting 37A (yeast)"", ""polyglutamine binding protein 2"""	PQBP2		15240819, 15218037, 22717650	Standard	NM_152415		Approved	FLJ32642, HCRP1, SPG53	uc003wxj.3	Q8NEZ2	OTTHUMG00000130785	ENST00000324849.4:c.187A>G	8.37:g.17123477A>G	ENSP00000318629:p.Ile63Val	Somatic	230	0	0		WXS	Illumina HiSeq	Phase_I	183	42	0.229508	NM_152415	Q336D5|Q6NW27|Q8N3D7|Q8TBL7|Q96DL9	Missense_Mutation	SNP	ENST00000324849.4	37	CCDS6001.1	.	.	.	.	.	.	.	.	.	.	A	13.81	2.348643	0.41599	2.27E-4	0.0	ENSG00000155975	ENST00000324849;ENST00000324815	T	0.56776	0.44	4.77	4.77	0.60923	Ubiquitin-conjugating enzyme/RWD-like (2);	0.000000	0.85682	D	0.000000	T	0.52141	0.1716	M	0.64997	1.995	0.53005	D	0.999963	B	0.33212	0.402	B	0.36186	0.219	T	0.51284	-0.8725	10	0.27785	T	0.31	-20.1891	14.9938	0.71415	1.0:0.0:0.0:0.0	.	63	Q8NEZ2	VP37A_HUMAN	V	63	ENSP00000318629:I63V	ENSP00000318173:I63V	I	+	1	0	VPS37A	17167848	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.108000	0.89559	2.084000	0.62774	0.528000	0.53228	ATT	.	.	weak		0.284	VPS37A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253301.2	NM_152415	
TMEM79	84283	hgsc.bcm.edu	37	1	156255456	156255456	+	Missense_Mutation	SNP	G	G	A	rs6684514	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:156255456G>A	ENST00000405535.2	+	2	610	c.439G>A	c.(439-441)Gtg>Atg	p.V147M	TMEM79_ENST00000495881.1_3'UTR|SMG5_ENST00000361813.5_5'Flank|TMEM79_ENST00000295694.5_Missense_Mutation_p.V147M|SMG5_ENST00000368267.5_5'Flank|TMEM79_ENST00000357501.2_Intron	NM_032323.2	NP_115699.1	Q9BSE2	TMM79_HUMAN	transmembrane protein 79	147			V -> M (polymorphism that may be associated with atopic dermatitis; dbSNP:rs6684514). {ECO:0000269|PubMed:24084074}.		cornification (GO:0070268)|cuticle development (GO:0042335)|epithelial cell maturation (GO:0002070)|establishment of skin barrier (GO:0061436)|hair follicle morphogenesis (GO:0031069)|positive regulation of epidermis development (GO:0045684)|regulated secretory pathway (GO:0045055)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|trans-Golgi network membrane (GO:0032588)				breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(9)|urinary_tract(1)	21	Hepatocellular(266;0.158)					AGACCTTATCGTGCGCTGTGA	0.647													G|||	1016	0.202875	0.0794	0.2781	5008	,	,		14706	0.2272		0.2694	False		,,,				2504	0.2229				p.V147M		Atlas-SNP	.											.	TMEM79	43	.	0			c.G439A						PASS	.	G	MET/VAL	522,3884	239.6+/-250.7	29,464,1710	61.0	61.0	61.0	http://www.ncbi.nlm.nih.gov/pubmed?term	439	0.2	0.0	1	dbSNP_116	61	2522,6078	410.9+/-350.3	385,1752,2163	yes	missense	TMEM79	NM_032323.2	21	414,2216,3873	AA,AG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	29.3256,11.8475,23.4046	benign	147/395	156255456	3044,9962	2203	4300	6503	SO:0001583	missense	84283	exon2			CTTATCGTGCGCT	BC005094	CCDS1138.1	1q22	2014-04-22			ENSG00000163472	ENSG00000163472			28196	protein-coding gene	gene with protein product	"""mattrin"""	615531					Standard	NM_032323		Approved	MGC13102, FLJ16057, FLJ32254, MATT	uc009wrw.3	Q9BSE2	OTTHUMG00000019788	ENST00000405535.2:c.439G>A	1.37:g.156255456G>A	ENSP00000384748:p.Val147Met	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	74	41	0.554054	NM_032323	B2RE22|D3DVB8	Missense_Mutation	SNP	ENST00000405535.2	37	CCDS1138.1	462	0.21153846153846154	40	0.08130081300813008	82	0.2265193370165746	135	0.23601398601398602	205	0.2704485488126649	G	5.517	0.280376	0.10458	0.118475	0.293256	ENSG00000163472	ENST00000295694;ENST00000405535	T;T	0.50813	0.73;0.73	5.45	0.157	0.14915	.	0.870941	0.10161	N	0.708272	T	0.13543	0.0328	L	0.34521	1.04	0.80722	P	0.0	B	0.25719	0.132	B	0.24974	0.057	T	0.17623	-1.0363	9	0.44086	T	0.13	-0.5773	3.24	0.06777	0.2261:0.1186:0.5339:0.1215	rs6684514;rs59950097;rs6684514	147	Q9BSE2	TMM79_HUMAN	M	147	ENSP00000295694:V147M;ENSP00000384748:V147M	ENSP00000295694:V147M	V	+	1	0	TMEM79	154522080	0.001000	0.12720	0.000000	0.03702	0.167000	0.22549	0.585000	0.23879	-0.510000	0.06523	-1.134000	0.01955	GTG	G|0.784;A|0.216	0.216	strong		0.647	TMEM79-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052101.1	NM_032323	
TNN	63923	hgsc.bcm.edu	37	1	175092674	175092674	+	Missense_Mutation	SNP	C	C	T	rs2285215	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:175092674C>T	ENST00000239462.4	+	12	2902	c.2789C>T	c.(2788-2790)cCg>cTg	p.P930L		NM_022093.1	NP_071376.1	Q9UQP3	TENN_HUMAN	tenascin N	930	Fibronectin type-III 8. {ECO:0000255|PROSITE-ProRule:PRU00316}.		P -> L (in dbSNP:rs2285215).		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)		p.P930L(1)		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)		AGGGAGGTTCCGGTGGGGAAG	0.617													C|||	2996	0.598243	0.6203	0.6671	5008	,	,		17437	0.4921		0.6421	False		,,,				2504	0.5838				p.P930L		Atlas-SNP	.											TNN,colon,carcinoma,0,3	TNN	297	3	1	Substitution - Missense(1)	stomach(1)	c.C2789T						scavenged	.	C	LEU/PRO	2669,1737	647.4+/-398.5	798,1073,332	96.0	81.0	86.0		2789	3.1	0.0	1	dbSNP_100	86	5434,3166	655.1+/-401.2	1732,1970,598	no	missense	TNN	NM_022093.1	98	2530,3043,930	TT,TC,CC		36.814,39.4235,37.698	possibly-damaging	930/1300	175092674	8103,4903	2203	4300	6503	SO:0001583	missense	63923	exon12			AGGTTCCGGTGGG	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.2789C>T	1.37:g.175092674C>T	ENSP00000239462:p.Pro930Leu	Somatic	139	2	0.0143885		WXS	Illumina HiSeq	Phase_I	122	55	0.45082	NM_022093	B9EGP3|Q5R360	Missense_Mutation	SNP	ENST00000239462.4	37	CCDS30943.1	1334	0.6108058608058609	315	0.6402439024390244	243	0.6712707182320442	282	0.493006993006993	494	0.6517150395778364	C	14.27	2.485302	0.44147	0.605765	0.63186	ENSG00000120332	ENST00000239462;ENST00000539081	T	0.56444	0.46	4.98	3.1	0.35709	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.350805	0.30028	N	0.010594	T	0.00012	0.0000	M	0.75150	2.29	0.80722	P	0.0	D	0.55800	0.973	P	0.52598	0.703	T	0.47535	-0.9110	9	0.21540	T	0.41	.	5.8964	0.18941	0.1521:0.6823:0.0:0.1655	rs2285215;rs2285215	930	Q9UQP3	TENN_HUMAN	L	930;753	ENSP00000239462:P930L	ENSP00000239462:P930L	P	+	2	0	TNN	173359297	0.002000	0.14202	0.001000	0.08648	0.668000	0.39293	1.703000	0.37846	0.605000	0.29947	0.462000	0.41574	CCG	C|0.379;T|0.621	0.621	strong		0.617	TNN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084422.1	XM_040527	
MRC2	9902	hgsc.bcm.edu	37	17	60769803	60769803	+	Silent	SNP	A	A	G	rs3826537	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:60769803A>G	ENST00000303375.5	+	30	4833	c.4431A>G	c.(4429-4431)caA>caG	p.Q1477Q	MRC2_ENST00000446119.2_Silent_p.Q343Q	NM_006039.4	NP_006030.2	Q9UBG0	MRC2_HUMAN	mannose receptor, C type 2	1477					collagen catabolic process (GO:0030574)|endocytosis (GO:0006897)|osteoblast differentiation (GO:0001649)	focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)|collagen binding (GO:0005518)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(11)|lung(28)|ovary(2)|prostate(1)|skin(3)	53						TGAATGAGCAACAAGAATAGA	0.657													G|||	1675	0.334465	0.1944	0.4193	5008	,	,		16751	0.3135		0.4085	False		,,,				2504	0.409				p.Q1477Q		Atlas-SNP	.											.	MRC2	126	.	0			c.A4431G						PASS	.	G		941,3379		128,685,1347	16.0	19.0	18.0		4431	4.2	1.0	17	dbSNP_107	18	3396,5086		759,1878,1604	no	coding-synonymous	MRC2	NM_006039.3		887,2563,2951	GG,GA,AA		40.0377,21.7824,33.8775		1477/1480	60769803	4337,8465	2160	4241	6401	SO:0001819	synonymous_variant	9902	exon30			TGAGCAACAAGAA	AB014609	CCDS11634.1	17q23	2011-08-30				ENSG00000011028		"""CD molecules"", ""C-type lectin domain containing"""	16875	protein-coding gene	gene with protein product		612264				9734811, 8702911	Standard	NM_006039		Approved	KIAA0709, ENDO180, CLEC13E, CD280	uc002jad.4	Q9UBG0		ENST00000303375.5:c.4431A>G	17.37:g.60769803A>G		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	76	76	1	NM_006039	A6H8K4|D3DU08|Q7LGE7|Q9Y5P9	Silent	SNP	ENST00000303375.5	37	CCDS11634.1																																																																																			A|0.680;G|0.320	0.320	strong		0.657	MRC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445152.1		
BTN3A2	11118	hgsc.bcm.edu	37	6	26368938	26368938	+	Silent	SNP	C	C	T	rs76764747		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:26368938C>T	ENST00000356386.2	+	4	419	c.231C>T	c.(229-231)aaC>aaT	p.N77N	BTN3A2_ENST00000396948.1_Silent_p.N77N|BTN3A2_ENST00000396934.3_Silent_p.N54N|BTN3A2_ENST00000532994.1_Intron|BTN3A2_ENST00000527422.1_Silent_p.N77N|BTN3A2_ENST00000508906.2_Silent_p.N35N|BTN3A2_ENST00000377708.2_Silent_p.N77N	NM_001197246.2|NM_001197247.1|NM_007047.3	NP_001184175.1|NP_001184176.1|NP_008978.2	P78410	BT3A2_HUMAN	butyrophilin, subfamily 3, member A2	77	Ig-like V-type.				interferon-gamma secretion (GO:0072643)|T cell mediated immunity (GO:0002456)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(5)	10						AGGTGGTGAACGTGTATGCAG	0.557																																					p.N77N		Atlas-SNP	.											.	BTN3A2	44	.	0			c.C231T						PASS	.						309.0	219.0	250.0					6																	26368938		2202	4297	6499	SO:0001819	synonymous_variant	11118	exon2			GGTGAACGTGTAT	U90546	CCDS4605.1, CCDS56399.1, CCDS56400.1	6p22.1	2014-01-14			ENSG00000186470	ENSG00000186470		"""Immunoglobulin superfamily / V-set domain containing"", ""Butyrophilins"""	1139	protein-coding gene	gene with protein product		613594				9149941	Standard	NM_007047		Approved	BTN3.2	uc010jqi.2	P78410	OTTHUMG00000014450	ENST00000356386.2:c.231C>T	6.37:g.26368938C>T		Somatic	373	0	0		WXS	Illumina HiSeq	Phase_I	410	268	0.653659	NM_001197246	B4DRT7|B4E103|F5H791|F8W6E0|O00477|O15338|O75658|Q76PA0|Q9BU81|Q9NR44	Silent	SNP	ENST00000356386.2	37	CCDS4605.1																																																																																			C|0.500;T|0.500	0.500	weak		0.557	BTN3A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040113.2		
OR10T2	128360	hgsc.bcm.edu	37	1	158368392	158368392	+	Missense_Mutation	SNP	C	C	T	rs61818748	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:158368392C>T	ENST00000334438.1	-	1	864	c.865G>A	c.(865-867)Gtc>Atc	p.V289I		NM_001004475.1	NP_001004475.1	Q8NGX3	O10T2_HUMAN	olfactory receptor, family 10, subfamily T, member 2	289						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)|kidney(1)|large_intestine(4)|lung(17)|ovary(2)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	34	all_hematologic(112;0.0378)					AGACTGTAGACAAGAGGATTA	0.418													C|||	112	0.0223642	0.0015	0.0447	5008	,	,		19821	0.0		0.0716	False		,,,				2504	0.0072				p.V289I		Atlas-SNP	.											.	OR10T2	76	.	0			c.G865A						PASS	.	C	ILE/VAL	58,4348	56.2+/-92.4	0,58,2145	56.0	50.0	52.0		865	4.6	1.0	1	dbSNP_129	52	741,7859	178.5+/-227.8	43,655,3602	yes	missense	OR10T2	NM_001004475.1	29	43,713,5747	TT,TC,CC		8.6163,1.3164,6.1433	probably-damaging	289/315	158368392	799,12207	2203	4300	6503	SO:0001583	missense	128360	exon1			TGTAGACAAGAGG	AB065643	CCDS30895.1	1q23.1	2012-08-09			ENSG00000186306	ENSG00000186306		"""GPCR / Class A : Olfactory receptors"""	14816	protein-coding gene	gene with protein product							Standard	NM_001004475		Approved		uc010pih.2	Q8NGX3	OTTHUMG00000017521	ENST00000334438.1:c.865G>A	1.37:g.158368392C>T	ENSP00000334115:p.Val289Ile	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	84	42	0.5	NM_001004475	Q6IF98	Missense_Mutation	SNP	ENST00000334438.1	37	CCDS30895.1	62	0.028388278388278388	1	0.0020325203252032522	18	0.049723756906077346	0	0.0	43	0.05672823218997362	C	13.64	2.297652	0.40694	0.013164	0.086163	ENSG00000186306	ENST00000334438	T	0.25749	1.78	4.57	4.57	0.56435	GPCR, rhodopsin-like superfamily (1);	0.000000	0.37906	N	0.001881	T	0.01835	0.0058	N	0.00263	-1.745	0.25061	N	0.991061	P	0.41041	0.736	P	0.45037	0.467	T	0.31364	-0.9946	10	0.02654	T	1	.	6.8023	0.23758	0.0:0.8083:0.0:0.1916	rs61818748	289	Q8NGX3	O10T2_HUMAN	I	289	ENSP00000334115:V289I	ENSP00000334115:V289I	V	-	1	0	OR10T2	156635016	0.506000	0.26139	0.996000	0.52242	0.923000	0.55619	0.877000	0.28106	2.359000	0.80004	0.655000	0.94253	GTC	C|0.948;T|0.052	0.052	strong		0.418	OR10T2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046371.1	NM_001004475	
KIAA1549L	25758	hgsc.bcm.edu	37	11	33628193	33628193	+	Missense_Mutation	SNP	C	C	T	rs202027343	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:33628193C>T	ENST00000321505.4	+	13	4175	c.3995C>T	c.(3994-3996)gCg>gTg	p.A1332V	KIAA1549L_ENST00000389726.3_Missense_Mutation_p.A1338V			Q6ZVL6	K154L_HUMAN	KIAA1549-like	1332						integral component of membrane (GO:0016021)		p.A1332V(1)									TCAGTGCCAGCGAGTGACGAA	0.483													C|||	2	0.000399361	0.0015	0.0	5008	,	,		19588	0.0		0.0	False		,,,				2504	0.0				p.A1332V		Atlas-SNP	.											C11orf41_ENST00000321505,NS,carcinoma,0,1	.	.	1	1	Substitution - Missense(1)	lung(1)	c.C3995T						scavenged	.						66.0	70.0	68.0					11																	33628193		2014	4179	6193	SO:0001583	missense	25758	exon13			TGCCAGCGAGTGA	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.3995C>T	11.37:g.33628193C>T	ENSP00000315295:p.Ala1332Val	Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	149	3	0.0201342	NM_012194	B0QYU0	Missense_Mutation	SNP	ENST00000321505.4	37	CCDS44565.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	9.041|9.041	0.989675|0.989675	0.18966|0.18966	.|.	.|.	ENSG00000110427|ENSG00000110427	ENST00000321505;ENST00000389726;ENST00000536568|ENST00000526400	.|.	.|.	.|.	5.43|5.43	2.0|2.0	0.26442|0.26442	.|.	0.342654|.	0.30235|.	N|.	0.010091|.	T|.	0.07188|.	0.0182|.	N|N	0.00538|0.00538	-1.39|-1.39	0.09310|0.09310	N|N	1|1	B|.	0.31290|.	0.318|.	B|.	0.20955|.	0.032|.	T|.	0.36016|.	-0.9765|.	9|.	0.30078|.	T|.	0.28|.	-4.9595|-4.9595	3.8169|3.8169	0.08819|0.08819	0.0:0.2812:0.5001:0.2187|0.0:0.2812:0.5001:0.2187	.|.	1338|.	E9PAT2|.	.|.	V|X	1332;1338;1171|730	.|.	ENSP00000315295:A1332V|.	A|R	+|+	2|1	0|2	C11orf41|C11orf41	33584769|33584769	0.000000|0.000000	0.05858|0.05858	0.018000|0.018000	0.16275|0.16275	0.546000|0.546000	0.35178|0.35178	0.804000|0.804000	0.27098|0.27098	0.615000|0.615000	0.30124|0.30124	0.561000|0.561000	0.74099|0.74099	GCG|CGA	.	.	weak		0.483	KIAA1549L-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317998.1	NM_012194	
CD82	3732	hgsc.bcm.edu	37	11	44640640	44640640	+	Silent	SNP	C	C	G	rs7107335	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:44640640C>G	ENST00000227155.4	+	10	1016	c.768C>G	c.(766-768)gtC>gtG	p.V256V	CD82_ENST00000342935.3_Silent_p.V231V|CD82_ENST00000530931.1_3'UTR	NM_002231.3	NP_002222.1	P27701	CD82_HUMAN	CD82 molecule	256						extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				large_intestine(1)|ovary(1)	2						GCCGGCACGTCCATTCCGAAG	0.657													C|||	850	0.169728	0.0825	0.1081	5008	,	,		17542	0.3899		0.1978	False		,,,				2504	0.0757				p.V256V		Atlas-SNP	.											.	CD82	27	.	0			c.C768G						PASS	.	C	,	447,3959	213.8+/-233.3	31,385,1787	151.0	128.0	136.0		693,768	1.1	0.9	11	dbSNP_116	136	1605,6993	299.7+/-304.6	169,1267,2863	no	coding-synonymous,coding-synonymous	CD82	NM_001024844.1,NM_002231.3	,	200,1652,4650	GG,GC,CC		18.6671,10.1453,15.7798	,	231/243,256/268	44640640	2052,10952	2203	4299	6502	SO:0001819	synonymous_variant	3732	exon10			GCACGTCCATTCC	U20770	CCDS7909.1, CCDS31469.1	11p11.2	2013-02-14	2006-03-28	2005-03-03		ENSG00000085117		"""CD molecules"", ""Tetraspanins"""	6210	protein-coding gene	gene with protein product	"""suppression of tumorigenicity 6"", ""R2 leukocyte antigen"""	600623	"""kangai 1 (suppression of tumorigenicity 6, prostate; CD82 antigen (R2 leukocyte antigen, antigen detected by monoclonal and antibody IA4))"", ""CD82 antigen"""	ST6, KAI1			Standard	XM_006718222		Approved	R2, IA4, TSPAN27	uc001myc.3	P27701		ENST00000227155.4:c.768C>G	11.37:g.44640640C>G		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	78	15	0.192308	NM_002231	D3DQN6|E9PC70|Q7Z2D4|Q7Z5N2	Silent	SNP	ENST00000227155.4	37	CCDS7909.1																																																																																			C|0.834;G|0.165	0.165	strong		0.657	CD82-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389886.1		
DDX55	57696	hgsc.bcm.edu	37	12	124104049	124104049	+	Silent	SNP	A	A	G	rs15587	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:124104049A>G	ENST00000238146.4	+	13	1454	c.1404A>G	c.(1402-1404)ggA>ggG	p.G468G	DDX55_ENST00000538744.1_Silent_p.G437G|DDX55_ENST00000421670.3_Silent_p.G75G|DDX55_ENST00000541259.1_3'UTR|SNORA9_ENST00000384170.1_RNA	NM_020936.1	NP_065987.1	Q8NHQ9	DDX55_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 55	468						membrane (GO:0016020)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)			autonomic_ganglia(1)|breast(1)|endometrium(1)|large_intestine(3)|liver(1)|lung(4)|ovary(1)|prostate(1)|skin(1)	14	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000142)|Epithelial(86;0.000637)|all cancers(50;0.00772)		AATTGAGAGGAAAGCAGTTTC	0.458													A|||	1266	0.252796	0.4486	0.2205	5008	,	,		15634	0.0159		0.2654	False		,,,				2504	0.2423				p.G468G		Atlas-SNP	.											.	DDX55	51	.	0			c.A1404G						PASS	.	A		1835,2571	536.7+/-374.5	386,1063,754	124.0	122.0	123.0		1404	-0.9	1.0	12	dbSNP_52	123	2376,6224	394.7+/-344.8	341,1694,2265	no	coding-synonymous	DDX55	NM_020936.1		727,2757,3019	GG,GA,AA		27.6279,41.6478,32.3774		468/601	124104049	4211,8795	2203	4300	6503	SO:0001819	synonymous_variant	57696	exon13			GAGAGGAAAGCAG	AB046815	CCDS9251.1	12q24.31	2003-06-13			ENSG00000111364	ENSG00000111364		"""DEAD-boxes"""	20085	protein-coding gene	gene with protein product						10997877	Standard	NM_020936		Approved	KIAA1595	uc001ufi.3	Q8NHQ9	OTTHUMG00000168695	ENST00000238146.4:c.1404A>G	12.37:g.124104049A>G		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	69	69	1	NM_020936	Q658L6|Q8IYH0|Q9HCH7	Silent	SNP	ENST00000238146.4	37	CCDS9251.1																																																																																			A|0.701;G|0.299	0.299	strong		0.458	DDX55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400616.2		
KRTAP12-2	353323	hgsc.bcm.edu	37	21	46086377	46086377	+	Missense_Mutation	SNP	A	A	G	rs2838622	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:46086377A>G	ENST00000360770.3	-	1	467	c.427T>C	c.(427-429)Tct>Cct	p.S143P	TSPEAR_ENST00000323084.4_Intron	NM_181684.2	NP_859012.1	P59991	KR122_HUMAN	keratin associated protein 12-2	143			S -> P (in dbSNP:rs2838622).			keratin filament (GO:0045095)				central_nervous_system(1)|endometrium(1)|lung(3)	5						CAGCAGGAAGAGATACTGTAG	0.602													G|||	2918	0.582668	0.6967	0.5403	5008	,	,		19253	0.5655		0.492	False		,,,				2504	0.5695				p.S143P		Atlas-SNP	.											.	KRTAP12-2	10	.	0			c.T427C						PASS	.	G	,PRO/SER	2893,1387		1004,885,251	54.0	59.0	57.0		,427	1.8	0.0	21	dbSNP_100	57	3867,4609		924,2019,1295	yes	intron,missense	TSPEAR,KRTAP12-2	NM_144991.2,NM_181684.2	,74	1928,2904,1546	GG,GA,AA		45.6229,32.4065,47.0053	,benign	,143/147	46086377	6760,5996	2140	4238	6378	SO:0001583	missense	353323	exon1			AGGAAGAGATACT	AJ566389	CCDS42965.1	21q22.3	2006-03-13			ENSG00000221864	ENSG00000221864		"""Keratin associated proteins"""	20530	protein-coding gene	gene with protein product							Standard	NM_181684		Approved	KRTAP12.2, KAP12.2	uc002zfu.3	P59991	OTTHUMG00000057636	ENST00000360770.3:c.427T>C	21.37:g.46086377A>G	ENSP00000354001:p.Ser143Pro	Somatic	276	1	0.00362319		WXS	Illumina HiSeq	Phase_I	342	182	0.532164	NM_181684	A6NIS1|A6NMS9|Q0VAS4	Missense_Mutation	SNP	ENST00000360770.3	37	CCDS42965.1	1234	0.565018315018315	353	0.717479674796748	203	0.5607734806629834	303	0.5297202797202797	375	0.4947229551451187	g	0.003	-2.494097	0.00159	0.675935	0.456229	ENSG00000221864	ENST00000360770;ENST00000539483	T	0.02067	4.47	3.62	1.78	0.24846	.	.	.	.	.	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	0.15780	-1.0425	8	0.02654	T	1	.	5.8109	0.18465	0.3543:0.0:0.6457:0.0	rs2838622;rs61048872;rs2838622	143	P59991	KR122_HUMAN	P	143;93	ENSP00000354001:S143P	ENSP00000354001:S143P	S	-	1	0	KRTAP12-2	44910805	0.003000	0.15002	0.002000	0.10522	0.008000	0.06430	-0.301000	0.08232	-0.049000	0.13379	-0.355000	0.07637	TCT	A|0.429;G|0.571	0.571	strong		0.602	KRTAP12-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128039.1	NM_181684	
BTN2A1	11120	hgsc.bcm.edu	37	6	26463574	26463574	+	Missense_Mutation	SNP	G	G	T	rs34505465|rs13195401	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:26463574G>T	ENST00000312541.5	+	4	781	c.533G>T	c.(532-534)tGg>tTg	p.W178L	BTN2A1_ENST00000469185.1_Missense_Mutation_p.W178L|BTN2A1_ENST00000541522.1_Missense_Mutation_p.W117L|BTN2A1_ENST00000429381.1_Missense_Mutation_p.W178L	NM_007049.3|NM_078476.2	NP_008980.1|NP_510961.1	Q7KYR7	BT2A1_HUMAN	butyrophilin, subfamily 2, member A1	178			W -> C (in dbSNP:rs13195402).|W -> L (in dbSNP:rs13195401).		lipid metabolic process (GO:0006629)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)				breast(3)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(2)|lung(9)|ovary(2)|prostate(1)|skin(3)|urinary_tract(3)	27						CTCACAGTGTGGAGGGACCCC	0.592													G|||	120	0.0239617	0.0227	0.0303	5008	,	,		17970	0.0		0.0686	False		,,,				2504	0.0				p.W178L		Atlas-SNP	.											.	BTN2A1	118	.	0			c.G533T						PASS	.	G	LEU/TRP,LEU/TRP,LEU/TRP,LEU/TRP	137,4269	87.8+/-126.4	3,131,2069	82.0	77.0	79.0		350,533,533,533	2.0	0.4	6	dbSNP_121	79	689,7911	159.7+/-212.9	29,631,3640	no	missense,missense,missense,missense	BTN2A1	NM_001197233.1,NM_001197234.1,NM_007049.3,NM_078476.2	61,61,61,61	32,762,5709	TT,TG,GG		8.0116,3.1094,6.3509	probably-damaging,probably-damaging,probably-damaging,probably-damaging	117/467,178/331,178/528,178/335	26463574	826,12180	2203	4300	6503	SO:0001583	missense	11120	exon4			CAGTGTGGAGGGA	U90543	CCDS4613.1, CCDS47390.1, CCDS56404.1, CCDS56405.1	6p22.1	2014-01-14			ENSG00000112763	ENSG00000112763		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Butyrophilins"""	1136	protein-coding gene	gene with protein product		613590				9382921, 9149941	Standard	NM_007049		Approved	BT2.1, BTF1, BTN2.1	uc003nib.2	Q7KYR7	OTTHUMG00000014457	ENST00000312541.5:c.533G>T	6.37:g.26463574G>T	ENSP00000312158:p.Trp178Leu	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	65	32	0.492308	NM_001197234	B4DLP9|E9PGR4|O00475|P78408|Q59EN4|Q7KYQ7|Q7Z386|Q96AV7|Q9NU62	Missense_Mutation	SNP	ENST00000312541.5	37	CCDS4613.1	61	0.027930402930402932	8	0.016260162601626018	10	0.027624309392265192	0	0.0	43	0.05672823218997362	G	12.77	2.038076	0.35989	0.031094	0.080116	ENSG00000112763	ENST00000312541;ENST00000541522;ENST00000429381;ENST00000265424;ENST00000469185	T;T;T;T	0.66638	-0.22;-0.22;-0.22;-0.22	2.88	2.0	0.26442	CD80-like, immunoglobulin C2-set (1);	0.000000	0.50627	D	0.000118	T	0.80248	0.4588	H	0.95950	3.745	0.32048	N	0.59732	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.78086	-0.2341	10	0.87932	D	0	.	8.118	0.30955	0.1282:0.0:0.8718:0.0	rs13195401	178;178	Q96AV7;Q7KYR7	.;BT2A1_HUMAN	L	178;117;178;178;178	ENSP00000312158:W178L;ENSP00000443909:W117L;ENSP00000416945:W178L;ENSP00000419043:W178L	ENSP00000265424:W178L	W	+	2	0	BTN2A1	26571553	1.000000	0.71417	0.362000	0.25862	0.137000	0.21094	3.741000	0.55090	0.764000	0.33197	0.561000	0.74099	TGG	.	.	alt		0.592	BTN2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040122.2	NM_007049	
CD8A	925	hgsc.bcm.edu	37	2	87016506	87016506	+	Silent	SNP	A	A	G	rs3020726	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:87016506A>G	ENST00000409511.2	-	7	1595	c.565T>C	c.(565-567)Ttg>Ctg	p.L189L	CD8A_ENST00000538832.1_Silent_p.L230L|CD8A_ENST00000409781.1_Silent_p.L152L|CD8A_ENST00000283635.3_Silent_p.L189L|CD8A_ENST00000456996.2_Intron|CD8A_ENST00000352580.3_Intron	NM_001145873.1	NP_001139345.1	P01732	CD8A_HUMAN	CD8a molecule	189					antigen processing and presentation (GO:0019882)|cytotoxic T cell differentiation (GO:0045065)|defense response to virus (GO:0051607)|immune response (GO:0006955)|positive regulation of calcium-mediated signaling (GO:0050850)|regulation of immune response (GO:0050776)|T cell activation (GO:0042110)|T cell mediated immunity (GO:0002456)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|T cell receptor complex (GO:0042101)	coreceptor activity (GO:0015026)|MHC class I protein binding (GO:0042288)			lung(4)|ovary(1)|prostate(2)|urinary_tract(1)	8						GTCCCGGCCAAGGGCGCCCAG	0.612													A|||	411	0.0820687	0.0893	0.062	5008	,	,		13566	0.0744		0.1412	False		,,,				2504	0.0337				p.L189L		Atlas-SNP	.											.	CD8A	28	.	0			c.T565C						PASS	.	A	,,	351,4055	175.9+/-205.1	11,329,1863	84.0	87.0	86.0		565,565,	-3.2	0.0	2	dbSNP_101	86	1414,7186	269.0+/-288.2	122,1170,3008	no	coding-synonymous,coding-synonymous,intron	CD8A	NM_001145873.1,NM_001768.6,NM_171827.3	,,	133,1499,4871	GG,GA,AA		16.4419,7.9664,13.5707	,,	189/236,189/236,	87016506	1765,11241	2203	4300	6503	SO:0001819	synonymous_variant	925	exon7			CGGCCAAGGGCGC		CCDS1992.1, CCDS1993.1	2p12	2014-09-17	2006-03-28		ENSG00000153563	ENSG00000153563		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"""	1706	protein-coding gene	gene with protein product		186910	"""CD8 antigen, alpha polypeptide (p32)"", ""T-cell surface glycoprotein CD8 alpha chain"""	CD8		1541829	Standard	NM_171827		Approved		uc002sru.3	P01732	OTTHUMG00000130265	ENST00000409511.2:c.565T>C	2.37:g.87016506A>G		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	134	70	0.522388	NM_001145873	B4DT80|D6W5M8|Q13970|Q4ZG17	Silent	SNP	ENST00000409511.2	37	CCDS1992.1																																																																																			A|0.873;G|0.127	0.127	strong		0.612	CD8A-006	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000330784.3	NM_001768	
MUC4	4585	hgsc.bcm.edu	37	3	195511403	195511403	+	Missense_Mutation	SNP	C	C	T	rs78846267|rs71627021		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195511403C>T	ENST00000463781.3	-	2	7507	c.7048G>A	c.(7048-7050)Gcc>Acc	p.A2350T	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.A2350T	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		AGAGGGGTGGCGTGACCTGTG	0.587																																					p.A2350T		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	0			c.G7048A						scavenged	.						11.0	12.0	12.0					3																	195511403		651	1555	2206	SO:0001583	missense	4585	exon2			GGGTGGCGTGACC	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.7048G>A	3.37:g.195511403C>T	ENSP00000417498:p.Ala2350Thr	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	51	24	0.470588	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	C	5.465	0.270947	0.10349	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.32272	1.46;1.47	.	.	.	.	.	.	.	.	T	0.11665	0.0284	N	0.19112	0.55	0.09310	N	1	P	0.52463	0.953	B	0.34536	0.185	T	0.16512	-1.0400	7	.	.	.	.	2.1665	0.03838	0.3282:0.3412:0.3306:0.0	.	2350	E7ESK3	.	T	2350	ENSP00000417498:A2350T;ENSP00000420243:A2350T	.	A	-	1	0	MUC4	196995798	0.000000	0.05858	0.017000	0.16124	0.071000	0.16799	-2.347000	0.01095	-0.833000	0.04245	0.064000	0.15345	GCC	C|0.995;T|0.005	0.005	weak		0.587	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
AZU1	566	hgsc.bcm.edu	37	19	830854	830854	+	Silent	SNP	T	T	C	rs595844	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:830854T>C	ENST00000233997.2	+	4	528	c.507T>C	c.(505-507)ttT>ttC	p.F169F		NM_001700.3	NP_001691.1	P20160	CAP7_HUMAN	azurocidin 1	169	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				cellular extravasation (GO:0045123)|defense response to Gram-negative bacterium (GO:0050829)|glial cell migration (GO:0008347)|induction of positive chemotaxis (GO:0050930)|inflammatory response (GO:0006954)|macrophage chemotaxis (GO:0048246)|microglial cell activation (GO:0001774)|monocyte activation (GO:0042117)|negative regulation of apoptotic process (GO:0043066)|positive regulation of cell adhesion (GO:0045785)|positive regulation of fractalkine biosynthetic process (GO:0050754)|positive regulation of interleukin-1 beta biosynthetic process (GO:0050725)|positive regulation of MHC class II biosynthetic process (GO:0045348)|positive regulation of phagocytosis (GO:0050766)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of vascular permeability (GO:0043114)	azurophil granule (GO:0042582)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	heparin binding (GO:0008201)|serine-type endopeptidase activity (GO:0004252)|toxic substance binding (GO:0015643)			NS(1)|endometrium(1)|kidney(1)|lung(4)|pancreas(1)|upper_aerodigestive_tract(2)	10		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;6.59e-06)|all_lung(49;9.97e-06)|Breast(49;0.000172)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		TTCCCAGGTTTGTCAACGTGA	0.662													t|||	3340	0.666933	0.941	0.6398	5008	,	,		14888	0.495		0.5497	False		,,,				2504	0.6135				p.F169F		Atlas-SNP	.											AZU1,NS,carcinoma,0,1	AZU1	31	1	0			c.T507C						PASS	.	T		3866,540	769.9+/-413.7	1698,470,35	41.0	40.0	40.0		507	-3.0	0.0	19	dbSNP_83	40	4598,4002	595.3+/-393.4	1242,2114,944	no	coding-synonymous	AZU1	NM_001700.3		2940,2584,979	CC,CT,TT		46.5349,12.256,34.9223		169/252	830854	8464,4542	2203	4300	6503	SO:0001819	synonymous_variant	566	exon4			CAGGTTTGTCAAC	X58794	CCDS12044.1	19p13.3	2012-03-30	2008-08-01		ENSG00000172232	ENSG00000172232			913	protein-coding gene	gene with protein product	"""cationic antimicrobial protein 37"", ""heparin-binding protein"", ""neutrophil azurocidin"""	162815				1919011	Standard	NM_001700		Approved	AZU, CAP37, AZAMP, HBP, NAZC, HUMAZUR	uc002lpz.1	P20160		ENST00000233997.2:c.507T>C	19.37:g.830854T>C		Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	44	44	1	NM_001700	P80014|Q52LG4|Q9UCM1|Q9UCT5	Silent	SNP	ENST00000233997.2	37	CCDS12044.1																																																																																			T|0.360;C|0.640	0.640	strong		0.662	AZU1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457472.2	NM_001700	
HDAC4	9759	hgsc.bcm.edu	37	2	240003870	240003870	+	Silent	SNP	G	G	A	rs1063639	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:240003870G>A	ENST00000345617.3	-	21	3356	c.2565C>T	c.(2563-2565)ccC>ccT	p.P855P	HDAC4_ENST00000543185.1_Silent_p.P439P	NM_006037.3	NP_006028.2	P56524	HDAC4_HUMAN	histone deacetylase 4	855	Histone deacetylase.				B cell activation (GO:0042113)|B cell differentiation (GO:0030183)|cardiac muscle hypertrophy in response to stress (GO:0014898)|chromatin remodeling (GO:0006338)|histone deacetylation (GO:0016575)|histone H3 deacetylation (GO:0070932)|histone H4 deacetylation (GO:0070933)|inflammatory response (GO:0006954)|negative regulation of cell proliferation (GO:0008285)|negative regulation of glycolytic process (GO:0045820)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|osteoblast development (GO:0002076)|peptidyl-lysine deacetylation (GO:0034983)|positive regulation of cell proliferation (GO:0008284)|positive regulation of protein sumoylation (GO:0033235)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of gene expression, epigenetic (GO:0040029)|regulation of protein binding (GO:0043393)|regulation of skeletal muscle fiber development (GO:0048742)|response to denervation involved in regulation of muscle adaptation (GO:0014894)|response to drug (GO:0042493)|response to interleukin-1 (GO:0070555)|skeletal system development (GO:0001501)|transcription, DNA-templated (GO:0006351)	A band (GO:0031672)|actomyosin (GO:0042641)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|histone deacetylase complex (GO:0000118)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)|Z disc (GO:0030018)	activating transcription factor binding (GO:0033613)|core promoter binding (GO:0001047)|histone deacetylase activity (GO:0004407)|histone deacetylase binding (GO:0042826)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|potassium ion binding (GO:0030955)|protein deacetylase activity (GO:0033558)|repressing transcription factor binding (GO:0070491)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(1)|biliary_tract(1)|breast(4)|endometrium(5)|kidney(2)|large_intestine(7)|lung(27)|ovary(3)|pancreas(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(5)	62		all_epithelial(40;1.45e-17)|Breast(86;1.53e-05)|Renal(207;0.000355)|all_lung(227;0.0121)|Ovarian(221;0.0183)|Lung NSC(271;0.0413)|Melanoma(123;0.0749)|all_hematologic(139;0.159)		Epithelial(121;6.38e-25)|OV - Ovarian serous cystadenocarcinoma(60;2.48e-12)|Kidney(56;6.04e-08)|KIRC - Kidney renal clear cell carcinoma(57;1.18e-06)|BRCA - Breast invasive adenocarcinoma(100;3.99e-05)|Lung(119;0.00942)|LUSC - Lung squamous cell carcinoma(224;0.04)		ACAGGACGCTGGGGTCGCTGT	0.592													G|||	2981	0.595248	0.59	0.6499	5008	,	,		15729	0.6885		0.4414	False		,,,				2504	0.6258				p.P855P		Atlas-SNP	.											.	HDAC4	127	.	0			c.C2565T						PASS	.	G		2499,1907	626.5+/-394.7	713,1073,417	171.0	155.0	160.0		2565	-3.0	0.0	2	dbSNP_86	160	4083,4517	561.0+/-387.7	958,2167,1175	no	coding-synonymous	HDAC4	NM_006037.3		1671,3240,1592	AA,AG,GG		47.4767,43.2819,49.3926		855/1085	240003870	6582,6424	2203	4300	6503	SO:0001819	synonymous_variant	9759	exon21			GACGCTGGGGTCG	AB006626	CCDS2529.1	2q37.3	2014-02-12			ENSG00000068024	ENSG00000068024			14063	protein-coding gene	gene with protein product		605314	"""brachydactyly-mental retardation syndrome"""	BDMR		10206986, 10220385, 20691407	Standard	NM_006037		Approved	KIAA0288, HDAC-A, HDACA, HD4, HA6116, HDAC-4	uc002vyk.4	P56524	OTTHUMG00000133344	ENST00000345617.3:c.2565C>T	2.37:g.240003870G>A		Somatic	261	0	0		WXS	Illumina HiSeq	Phase_I	262	118	0.450382	NM_006037	Q9UND6	Silent	SNP	ENST00000345617.3	37	CCDS2529.1																																																																																			G|0.456;A|0.544	0.544	strong		0.592	HDAC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257174.2	NM_006037	
HLA-A	3105	hgsc.bcm.edu	37	6	29911190	29911190	+	Silent	SNP	G	G	A	rs1059514	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:29911190G>A	ENST00000396634.1	+	5	830	c.489G>A	c.(487-489)gcG>gcA	p.A163A	HLA-A_ENST00000376802.2_Silent_p.A163A|HLA-A_ENST00000376809.5_Silent_p.A163A|HLA-A_ENST00000376806.5_Silent_p.A163A			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	163	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						CGGACATGGCGGCTCAGATCA	0.662									Osteosarcoma, Familial Clustering of;Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of;Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of	Multiple Myeloma(9;0.094)			g|||	2420	0.483227	0.3525	0.4885	5008	,	,		12936	0.5675		0.5209	False		,,,				2504	0.5307				p.A163A		Atlas-SNP	.											.	HLA-A	89	.	0			c.G489A						PASS	.						40.0	29.0	33.0					6																	29911190		1504	2704	4208	SO:0001819	synonymous_variant	3105	exon3	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	CATGGCGGCTCAG	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.489G>A	6.37:g.29911190G>A		Somatic	285	0	0		WXS	Illumina HiSeq	Phase_I	137	59	0.430657	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Silent	SNP	ENST00000396634.1	37	CCDS34373.1	1039	0.4757326007326007	187	0.3800813008130081	149	0.4116022099447514	292	0.5104895104895105	411	0.5422163588390502	g	1.866	-0.461526	0.04508	.	.	ENSG00000206503	ENST00000355767	.	.	.	3.78	-0.398	0.12418	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	0.9999999277067	.	.	.	.	.	.	.	.	.	.	.	.	.	.	5.5023	0.16834	0.2922:0.1627:0.5452:0.0	rs1059514;rs3173415;rs16896006;rs17849717;rs17851719;rs41548919	.	.	.	.	-1	.	.	.	+	.	.	HLA-A	30019169	0.000000	0.05858	0.090000	0.20809	0.046000	0.14306	-1.205000	0.03014	0.021000	0.15133	-0.330000	0.08379	.	G|0.519;A|0.481	0.481	strong		0.662	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
OR51G1	79324	hgsc.bcm.edu	37	11	4945199	4945199	+	Missense_Mutation	SNP	C	C	T	rs34742470	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:4945199C>T	ENST00000321961.2	-	1	438	c.371G>A	c.(370-372)cGc>cAc	p.R124H	MMP26_ENST00000477339.1_Intron|MMP26_ENST00000380390.1_Intron	NM_001005237.1	NP_001005237.1	Q8NGK1	O51G1_HUMAN	olfactory receptor, family 51, subfamily G, member 1	124			R -> H (in dbSNP:rs34742470).			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)|large_intestine(2)|lung(11)|ovary(2)|prostate(3)|skin(4)|soft_tissue(1)	25		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;2.58e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0284)|LUSC - Lung squamous cell carcinoma(625;0.19)		GGCCACGTAGCGGTCAATGGA	0.512													C|||	245	0.0489217	0.0144	0.0937	5008	,	,		22850	0.0		0.1441	False		,,,				2504	0.0164				p.R124H		Atlas-SNP	.											.	OR51G1	74	.	0			c.G371A	GRCh37	CM035851	OR51G1	M	rs34742470	PASS	.	C	HIS/ARG	162,4240	108.6+/-147.0	3,156,2042	110.0	98.0	102.0		371	3.3	1.0	11	dbSNP_126	102	1137,7459	234.9+/-267.6	97,943,3258	yes	missense	OR51G1	NM_001005237.1	29	100,1099,5300	TT,TC,CC		13.2271,3.6801,9.9938	probably-damaging	124/322	4945199	1299,11699	2201	4298	6499	SO:0001583	missense	79324	exon1			ACGTAGCGGTCAA	AB065793	CCDS31366.1	11p15.4	2012-08-09			ENSG00000176879	ENSG00000176879		"""GPCR / Class A : Olfactory receptors"""	14738	protein-coding gene	gene with protein product				OR51G3P			Standard	NM_001005237		Approved		uc010qyr.2	Q8NGK1	OTTHUMG00000066532	ENST00000321961.2:c.371G>A	11.37:g.4945199C>T	ENSP00000322546:p.Arg124His	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	69	18	0.26087	NM_001005237	B9EGW8|Q6IFH6	Missense_Mutation	SNP	ENST00000321961.2	37	CCDS31366.1	164	0.07509157509157509	10	0.02032520325203252	47	0.1298342541436464	0	0.0	107	0.14116094986807387	C	14.86	2.662190	0.47572	0.036801	0.132271	ENSG00000176879	ENST00000321961	T	0.77489	-1.1	4.2	3.3	0.37823	GPCR, rhodopsin-like superfamily (1);	0.000000	0.39985	U	0.001205	T	0.06325	0.0163	M	0.92649	3.33	0.29644	P	0.844511	D	0.89917	1.0	D	0.83275	0.996	T	0.62369	-0.6869	9	0.72032	D	0.01	.	11.0449	0.47852	0.0:0.9068:0.0:0.0932	rs34742470;rs61737944	124	Q8NGK1	O51G1_HUMAN	H	124	ENSP00000322546:R124H	ENSP00000322546:R124H	R	-	2	0	OR51G1	4901775	0.992000	0.36948	1.000000	0.80357	0.119000	0.20118	2.992000	0.49417	0.988000	0.38734	-0.232000	0.12228	CGC	C|0.911;T|0.089	0.089	strong		0.512	OR51G1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142345.1	NM_001005237	
OR10V1	390201	hgsc.bcm.edu	37	11	59481214	59481214	+	Silent	SNP	A	A	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:59481214A>G	ENST00000307552.2	-	1	123	c.105T>C	c.(103-105)taT>taC	p.Y35Y	STX3_ENST00000300150.7_5'UTR	NM_001005324.1	NP_001005324.1	Q8NGI7	O10V1_HUMAN	olfactory receptor, family 10, subfamily V, 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)			endometrium(1)|large_intestine(3)|liver(1)|lung(10)|skin(1)	16						GGCTGGTCAGATACATCATCA	0.438																																					p.Y35Y		Atlas-SNP	.											.	OR10V1	40	.	0			c.T105C						PASS	.						70.0	66.0	67.0					11																	59481214		2201	4295	6496	SO:0001819	synonymous_variant	390201	exon1			GGTCAGATACATC	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.105T>C	11.37:g.59481214A>G		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	76	24	0.315789	NM_001005324	Q6IFD9|Q96R50	Silent	SNP	ENST00000307552.2	37	CCDS31565.1																																																																																			.	.	none		0.438	OR10V1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394517.1	NM_001005324	
NSD1	64324	hgsc.bcm.edu	37	5	176636882	176636882	+	Silent	SNP	C	C	T	rs1363405	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:176636882C>T	ENST00000439151.2	+	5	1527	c.1482C>T	c.(1480-1482)tgC>tgT	p.C494C	NSD1_ENST00000361032.4_Silent_p.C391C|NSD1_ENST00000347982.4_Silent_p.C225C|NSD1_ENST00000354179.4_Silent_p.C225C	NM_022455.4	NP_071900.2	Q96L73	NSD1_HUMAN	nuclear receptor binding SET domain protein 1	494					gastrulation with mouth forming second (GO:0001702)|histone H3-K36 methylation (GO:0010452)|histone H4-K20 methylation (GO:0034770)|histone methylation (GO:0016571)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|estrogen receptor binding (GO:0030331)|histone methyltransferase activity (H3-K36 specific) (GO:0046975)|histone methyltransferase activity (H4-K20 specific) (GO:0042799)|retinoic acid receptor binding (GO:0042974)|retinoid X receptor binding (GO:0046965)|thyroid hormone receptor binding (GO:0046966)|transcription cofactor activity (GO:0003712)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(18)|lung(24)|ovary(2)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(3)	96	all_cancers(89;1.57e-05)|Renal(175;0.000269)|Lung NSC(126;0.00111)|all_lung(126;0.002)	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)|Epithelial(233;0.198)	Kidney(146;0.235)		AAAAGCCTTGCGCTAAATCTC	0.418			T	NUP98	AML		Sotos Syndrome		Weaver syndrome;Sotos syndrome;Beckwith-Wiedemann syndrome	HNSCC(47;0.14)			T|||	2344	0.468051	0.7693	0.3343	5008	,	,		17503	0.5298		0.1988	False		,,,				2504	0.3691				p.C494C		Atlas-SNP	.		Dom	yes		5	5q35	64324	nuclear receptor binding SET domain protein 1	yes	L	.	NSD1	416	.	0			c.C1482T						PASS	.	T	,	2971,1435	464.3+/-353.8	1012,947,244	76.0	77.0	77.0		1482,675	4.3	1.0	5	dbSNP_88	77	1635,6965	741.5+/-407.2	157,1321,2822	no	coding-synonymous,coding-synonymous	NSD1	NM_022455.4,NM_172349.2	,	1169,2268,3066	TT,TC,CC		19.0116,32.5692,35.4144	,	494/2697,225/2428	176636882	4606,8400	2203	4300	6503	SO:0001819	synonymous_variant	64324	exon5	Familial Cancer Database	Weaver-Smith syndrome;Cerebral Gigantism;BWS, Exomphalos-Macroglossia-Gigantism (EMG) syndrome, Wiedemann-Beckwith syndrome, WBS	GCCTTGCGCTAAA	AK026066	CCDS4412.1, CCDS4413.1	5q35	2014-09-17	2003-03-12		ENSG00000165671	ENSG00000165671		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	14234	protein-coding gene	gene with protein product		606681	"""Sotos syndrome"""	STO		9628876, 11896389	Standard	NM_022455		Approved	ARA267, FLJ22263, KMT3B	uc003mfr.4	Q96L73	OTTHUMG00000130846	ENST00000439151.2:c.1482C>T	5.37:g.176636882C>T		Somatic	190	0	0		WXS	Illumina HiSeq	Phase_I	160	68	0.425	NM_022455	Q96PD8|Q96RN7	Silent	SNP	ENST00000439151.2	37	CCDS4412.1																																																																																			C|0.607;T|0.393	0.393	strong		0.418	NSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253412.2	NM_172349	
PDIA2	64714	hgsc.bcm.edu	37	16	336916	336916	+	Missense_Mutation	SNP	C	C	T	rs1048786	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:336916C>T	ENST00000219406.6	+	10	1522	c.1504C>T	c.(1504-1506)Ccc>Tcc	p.P502S	PDIA2_ENST00000404312.1_Missense_Mutation_p.P499S	NM_006849.2	NP_006840.2	Q13087	PDIA2_HUMAN	protein disulfide isomerase family A, member 2	502			P -> S (in dbSNP:rs1048786). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:8561901, ECO:0000269|Ref.1}.		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)				CACGGAGGAGCCCCCGGAGGA	0.637													C|||	615	0.122804	0.0552	0.0908	5008	,	,		15364	0.0992		0.1571	False		,,,				2504	0.226				p.P502S		Atlas-SNP	.											PDIA2,NS,carcinoma,0,1	PDIA2	51	1	0			c.C1504T						PASS	.	C	SER/PRO	252,3390		8,236,1577	10.0	13.0	12.0		1504	2.3	0.5	16	dbSNP_86	12	1286,6838		95,1096,2871	yes	missense	PDIA2	NM_006849.2	74	103,1332,4448	TT,TC,CC		15.8296,6.9193,13.0716	benign	502/526	336916	1538,10228	1821	4062	5883	SO:0001583	missense	64714	exon10			GAGGAGCCCCCGG	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.1504C>T	16.37:g.336916C>T	ENSP00000219406:p.Pro502Ser	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	77	56	0.727273	NM_006849	A6ZJ64|B4DI27|Q2WGM4|Q4TT67|Q6B010|Q96KJ6|Q9BW95	Missense_Mutation	SNP	ENST00000219406.6	37	CCDS42089.1	230	0.10531135531135531	27	0.054878048780487805	34	0.09392265193370165	58	0.10139860139860139	111	0.14643799472295516	C	10.80	1.453672	0.26161	0.069193	0.158296	ENSG00000185615	ENST00000219406;ENST00000455994;ENST00000404312;ENST00000435833	T;T;T	0.03496	4.18;4.25;3.91	3.28	2.29	0.28610	.	0.391053	0.25416	N	0.030840	T	0.00012	0.0000	N	0.19112	0.55	0.39817	P	0.027212000000000014	B	0.09022	0.002	B	0.08055	0.003	T	0.47156	-0.9139	9	0.18276	T	0.48	.	7.9835	0.30198	0.0:0.8764:0.0:0.1236	rs1048786;rs1048786	502	Q13087	PDIA2_HUMAN	S	502;471;499;131	ENSP00000219406:P502S;ENSP00000384410:P499S;ENSP00000405081:P131S	ENSP00000219406:P502S	P	+	1	0	PDIA2	276917	0.564000	0.26602	0.546000	0.28166	0.009000	0.06853	0.351000	0.20096	0.568000	0.29311	0.549000	0.68633	CCC	C|0.891;T|0.109	0.109	strong		0.637	PDIA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139315.3	NM_006849	
SLC6A2	6530	hgsc.bcm.edu	37	16	55731835	55731835	+	Silent	SNP	G	G	A	rs5569	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:55731835G>A	ENST00000379906.2	+	9	1542	c.1287G>A	c.(1285-1287)acG>acA	p.T429T	SLC6A2_ENST00000414754.3_Silent_p.T429T|SLC6A2_ENST00000567238.1_Silent_p.T324T|SLC6A2_ENST00000568943.1_Silent_p.T429T|SLC6A2_ENST00000566163.1_Silent_p.T384T|SLC6A2_ENST00000219833.8_Silent_p.T429T|SLC6A2_ENST00000561820.1_Silent_p.T429T	NM_001043.3	NP_001034.1	P23975	SC6A2_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 2	429					monoamine transport (GO:0015844)|norepinephrine transport (GO:0015874)|response to drug (GO:0042493)|response to pain (GO:0048265)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	monoamine transmembrane transporter activity (GO:0008504)|norepinephrine:sodium symporter activity (GO:0005334)			breast(1)|endometrium(3)|kidney(1)|large_intestine(8)|lung(20)|ovary(3)|pancreas(2)|prostate(2)|upper_aerodigestive_tract(1)	41				BRCA - Breast invasive adenocarcinoma(181;0.01)|Kidney(780;0.0267)	Amitriptyline(DB00321)|Amoxapine(DB00543)|Amphetamine(DB00182)|Atomoxetine(DB00289)|Bupropion(DB01156)|Chlorphenamine(DB01114)|Citalopram(DB00215)|Clomipramine(DB01242)|Cocaine(DB00907)|Debrisoquin(DB04840)|Desipramine(DB01151)|Desvenlafaxine(DB06700)|Dexmethylphenidate(DB06701)|Dextroamphetamine(DB01576)|Dextromethorphan(DB00514)|Diethylpropion(DB00937)|Dopamine(DB00988)|Doxepin(DB01142)|Droxidopa(DB06262)|Duloxetine(DB00476)|Ephedra(DB01363)|Ephedrine(DB01364)|Ergotamine(DB00696)|Escitalopram(DB01175)|Ginkgo biloba(DB01381)|Guanadrel(DB00226)|Guanethidine(DB01170)|Imipramine(DB00458)|Iobenguane(DB06704)|Ketamine(DB01221)|Levomilnacipran(DB08918)|Levonordefrin(DB06707)|Loxapine(DB00408)|Maprotiline(DB00934)|Mazindol(DB00579)|Methamphetamine(DB01577)|Methylphenidate(DB00422)|Mianserin(DB06148)|Milnacipran(DB04896)|Mirtazapine(DB00370)|Nefazodone(DB01149)|Norepinephrine(DB00368)|Nortriptyline(DB00540)|Orphenadrine(DB01173)|Paroxetine(DB00715)|Pethidine(DB00454)|Phendimetrazine(DB01579)|Phenmetrazine(DB00830)|Phentermine(DB00191)|Protriptyline(DB00344)|Pseudoephedrine(DB00852)|Reboxetine(DB00234)|Sibutramine(DB01105)|Tapentadol(DB06204)|Tramadol(DB00193)|Trimipramine(DB00726)|Venlafaxine(DB00285)	CTGTCATCACGGGCCTGGCAG	0.587													G|||	1169	0.233427	0.0832	0.3617	5008	,	,		20523	0.2599		0.3598	False		,,,				2504	0.1881				p.T429T		Atlas-SNP	.											.	SLC6A2	189	.	0			c.G1287A						PASS	.	G	,,,	515,3881	236.1+/-248.4	33,449,1716	83.0	73.0	76.0		1287,1287,972,1287	-10.7	0.1	16	dbSNP_52	76	2839,5761	446.8+/-361.4	451,1937,1912	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SLC6A2	NM_001043.3,NM_001172501.1,NM_001172502.1,NM_001172504.1	,,,	484,2386,3628	AA,AG,GG		33.0116,11.7152,25.8079	,,,	429/618,429/618,324/513,429/629	55731835	3354,9642	2198	4300	6498	SO:0001819	synonymous_variant	6530	exon10			CATCACGGGCCTG		CCDS10754.1, CCDS54011.1, CCDS58463.1	16q12.2	2013-07-19	2013-07-19		ENSG00000103546	ENSG00000103546		"""Solute carriers"""	11048	protein-coding gene	gene with protein product	"""norepinephrine transporter"""	163970	"""solute carrier family 6 (neurotransmitter transporter, noradrenalin), member 2"""	NET1, NAT1, SLC6A5		2008212	Standard	NM_001043		Approved	NET	uc021tio.1	P23975	OTTHUMG00000133208	ENST00000379906.2:c.1287G>A	16.37:g.55731835G>A		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	89	89	1	NM_001172501	B2R707|B4DX48|Q96KH8	Silent	SNP	ENST00000379906.2	37	CCDS10754.1																																																																																			G|0.744;N|0.001	.	strong		0.587	SLC6A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256922.2		
TRIM65	201292	hgsc.bcm.edu	37	17	73888354	73888354	+	Silent	SNP	G	G	A	rs34974290	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:73888354G>A	ENST00000269383.3	-	3	803	c.738C>T	c.(736-738)ttC>ttT	p.F246F		NM_001256124.1|NM_173547.3	NP_001243053.1|NP_775818.2	Q6PJ69	TRI65_HUMAN	tripartite motif containing 65	246						intracellular (GO:0005622)	zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|lung(5)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	12			Epithelial(20;7.53e-06)|all cancers(21;9.11e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00092)|LUSC - Lung squamous cell carcinoma(166;0.154)			GCACCTGCAGGAAGGTCTGCT	0.652													G|||	1025	0.204673	0.3094	0.1715	5008	,	,		17118	0.129		0.1938	False		,,,				2504	0.1759				p.F246F		Atlas-SNP	.											.	TRIM65	23	.	0			c.C738T						PASS	.	G		1339,3067	406.2+/-333.8	215,909,1079	23.0	25.0	25.0		738	3.2	1.0	17	dbSNP_126	25	1643,6957	273.1+/-290.5	147,1349,2804	no	coding-synonymous	TRIM65	NM_173547.2		362,2258,3883	AA,AG,GG		19.1047,30.3904,22.9279		246/518	73888354	2982,10024	2203	4300	6503	SO:0001819	synonymous_variant	201292	exon3			CTGCAGGAAGGTC	BC006138	CCDS11732.1	17q25.1	2013-01-09	2011-01-25		ENSG00000141569	ENSG00000141569		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	27316	protein-coding gene	gene with protein product			"""tripartite motif-containing 65"""			12477932	Standard	NM_173547		Approved		uc002jpx.4	Q6PJ69	OTTHUMG00000132127	ENST00000269383.3:c.738C>T	17.37:g.73888354G>A		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	32	18	0.5625	NM_001256124	Q4G0F0|Q6DKJ6|Q9BRP6	Silent	SNP	ENST00000269383.3	37	CCDS11732.1	432|432	0.1978021978021978|0.1978021978021978	147|147	0.29878048780487804|0.29878048780487804	65|65	0.17955801104972377|0.17955801104972377	81|81	0.14160839160839161|0.14160839160839161	139|139	0.18337730870712401|0.18337730870712401	G|G	1.367|1.367	-0.587037|-0.587037	0.03827|0.03827	0.303904|0.303904	0.191047|0.191047	ENSG00000141569|ENSG00000141569	ENST00000540128|ENST00000543309	.|.	.|.	.|.	4.16|4.16	3.19|3.19	0.36642|0.36642	.|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.09310|0.09310	P|P	0.9999999999999842|0.9999999999999842	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.21999|0.21999	-1.0229|-1.0229	3|3	.|.	.|.	.|.	.|.	9.2634|9.2634	0.37625|0.37625	0.1794:0.0:0.8206:0.0|0.1794:0.0:0.8206:0.0	rs34974290|rs34974290	.|.	.|.	.|.	S|F	238|120	.|.	.|.	P|S	-|-	1|2	0|0	TRIM65|TRIM65	71399949|71399949	0.899000|0.899000	0.30636|0.30636	0.967000|0.967000	0.41034|0.41034	0.226000|0.226000	0.24999|0.24999	0.320000|0.320000	0.19540|0.19540	0.979000|0.979000	0.38497|0.38497	0.407000|0.407000	0.27541|0.27541	CCT|TCC	G|0.787;A|0.213	0.213	strong		0.652	TRIM65-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255170.2	NM_173547	
APBA3	9546	hgsc.bcm.edu	37	19	3753769	3753769	+	Silent	SNP	C	C	T	rs3746120	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:3753769C>T	ENST00000316757.3	-	6	1205	c.1005G>A	c.(1003-1005)gcG>gcA	p.A335A	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	335	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)		TCACGTCCTCCGCGTAGAATA	0.692													C|||	1703	0.340056	0.2405	0.4179	5008	,	,		13758	0.4474		0.3797	False		,,,				2504	0.2679				p.A335A		Atlas-SNP	.											APBA3,NS,carcinoma,0,1	APBA3	28	1	0			c.G1005A						PASS	.	C		1070,3286		139,792,1247	9.0	9.0	9.0		1005	-7.9	0.2	19	dbSNP_107	9	3082,5446		560,1962,1742	no	coding-synonymous	APBA3	NM_004886.3		699,2754,2989	TT,TC,CC		36.1398,24.5638,32.226		335/576	3753769	4152,8732	2178	4264	6442	SO:0001819	synonymous_variant	9546	exon6			GTCCTCCGCGTAG	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.1005G>A	19.37:g.3753769C>T		Somatic	15	0	0		WXS	Illumina HiSeq	Phase_I	16	16	1	NM_004886	O60483|Q9UPZ2	Silent	SNP	ENST00000316757.3	37	CCDS12110.1																																																																																			C|0.654;T|0.346	0.346	strong		0.692	APBA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453634.2		
GEMIN5	25929	hgsc.bcm.edu	37	5	154282235	154282235	+	Splice_Site	SNP	T	T	C	rs1421813	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:154282235T>C	ENST00000285873.7	-	20	2805	c.2730A>G	c.(2728-2730)ggA>ggG	p.G910G		NM_001252156.1|NM_015465.4	NP_001239085.1|NP_056280.2	Q8TEQ6	GEMI5_HUMAN	gem (nuclear organelle) associated protein 5	910					gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|ncRNA metabolic process (GO:0034660)|protein complex assembly (GO:0006461)|RNA metabolic process (GO:0016070)|spliceosomal snRNP assembly (GO:0000387)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMN complex (GO:0032797)|SMN-Sm protein complex (GO:0034719)	poly(A) RNA binding (GO:0044822)|snRNA binding (GO:0017069)			breast(1)|central_nervous_system(2)|endometrium(5)|kidney(3)|large_intestine(10)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	38	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)			AGTGACCTTTTCCTGTTTGAA	0.418													T|||	634	0.126597	0.2012	0.1988	5008	,	,		22243	0.0536		0.0895	False		,,,				2504	0.0879				p.G910G		Atlas-SNP	.											.	GEMIN5	120	.	0			c.A2730G						PASS	.	T		810,3596	306.0+/-289.3	82,646,1475	150.0	146.0	147.0		2730	-3.4	1.0	5	dbSNP_88	147	627,7973	153.9+/-208.2	18,591,3691	yes	coding-synonymous-near-splice	GEMIN5	NM_015465.3		100,1237,5166	CC,CT,TT		7.2907,18.384,11.0487		910/1509	154282235	1437,11569	2203	4300	6503	SO:0001630	splice_region_variant	25929	exon20			ACCTTTTCCTGTT	AK022748	CCDS4330.1	5q34	2013-01-10			ENSG00000082516	ENSG00000082516		"""WD repeat domain containing"""	20043	protein-coding gene	gene with protein product		607005				11714716	Standard	NM_015465		Approved		uc003lvx.3	Q8TEQ6	OTTHUMG00000130189	ENST00000285873.7:c.2729-1A>G	5.37:g.154282235T>C		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	104	53	0.509615	NM_015465	Q14CV0|Q8WWV4|Q969W4|Q9H9K3|Q9UFI5	Silent	SNP	ENST00000285873.7	37	CCDS4330.1																																																																																			T|0.893;C|0.107	0.107	strong		0.418	GEMIN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252507.1		Silent
MUC4	4585	hgsc.bcm.edu	37	3	195508986	195508986	+	Silent	SNP	G	G	A	rs370883367|rs71291870		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195508986G>A	ENST00000463781.3	-	2	9924	c.9465C>T	c.(9463-9465)gtC>gtT	p.V3155V	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Silent_p.V3155V	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.V3155V(2)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		AAGTGTCGGTGACAGGAAGAG	0.582																																					p.V3155V		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	2	Substitution - coding silent(2)	stomach(2)	c.C9465T						PASS	.						5.0	4.0	4.0					3																	195508986		555	1304	1859	SO:0001819	synonymous_variant	4585	exon2			GTCGGTGACAGGA	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.9465C>T	3.37:g.195508986G>A		Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	49	23	0.469388	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Silent	SNP	ENST00000463781.3	37	CCDS54700.1																																																																																			AACAG|0.500;GACAT|0.500	.	alt		0.582	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
B4GALNT1	2583	hgsc.bcm.edu	37	12	58023981	58023981	+	Silent	SNP	C	C	A	rs715930	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:58023981C>A	ENST00000341156.4	-	6	1250	c.666G>T	c.(664-666)ctG>ctT	p.L222L	B4GALNT1_ENST00000550943.1_5'Flank|B4GALNT1_ENST00000449184.3_Silent_p.L222L|B4GALNT1_ENST00000418555.2_Silent_p.L167L|B4GALNT1_ENST00000552350.1_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						PASS	.	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	235	0	0		WXS	Illumina HiSeq	Phase_I	227	101	0.444934	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	
KIAA1324	57535	hgsc.bcm.edu	37	1	109656946	109656946	+	Silent	SNP	T	T	C	rs667524	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:109656946T>C	ENST00000369939.3	+	1	324	c.141T>C	c.(139-141)caT>caC	p.H47H	C1orf194_ENST00000369949.4_5'Flank|KIAA1324_ENST00000529753.1_Silent_p.H47H|C1orf194_ENST00000369948.3_5'Flank|C1orf194_ENST00000369945.3_5'Flank	NM_020775.4	NP_065826	Q6UXG2	K1324_HUMAN	KIAA1324	47					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)		CGGAGCTTCATGCCTGCAAAG	0.637													C|||	2690	0.537141	0.7511	0.4841	5008	,	,		15146	0.4812		0.3718	False		,,,				2504	0.5133				p.H47H		Atlas-SNP	.											.	KIAA1324	77	.	0			c.T141C						PASS	.	C		2967,1439		986,995,222	20.0	22.0	22.0		141	4.4	1.0	1	dbSNP_83	22	3079,5515		586,1907,1804	no	coding-synonymous	KIAA1324	NM_020775.3		1572,2902,2026	CC,CT,TT		35.8273,32.66,46.5077		47/1014	109656946	6046,6954	2203	4297	6500	SO:0001819	synonymous_variant	57535	exon1			GCTTCATGCCTGC	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.141T>C	1.37:g.109656946T>C		Somatic	199	0	0		WXS	Illumina HiSeq	Phase_I	180	83	0.461111	NM_020775	Q08AE6|Q5T5C9|Q5T5D0|Q5T5D1|Q9P2M2	Silent	SNP	ENST00000369939.3	37	CCDS794.1																																																																																			T|0.512;C|0.488	0.488	strong		0.637	KIAA1324-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032389.2	NM_020775	
ESYT2	57488	hgsc.bcm.edu	37	7	158528269	158528269	+	Silent	SNP	C	C	G	rs35914882	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:158528269C>G	ENST00000251527.5	-	20	2576	c.2511G>C	c.(2509-2511)gtG>gtC	p.V837V	ESYT2_ENST00000435514.2_Silent_p.V272V	NM_020728.2	NP_065779.1	A0FGR8	ESYT2_HUMAN	extended synaptotagmin-like protein 2	865	C2 3. {ECO:0000255|PROSITE- ProRule:PRU00041}.|Required for phosphatidylinositol 4,5- bisphosphate-dependent location at the cell membrane.				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)	p.V837V(1)		breast(1)|central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(16)|prostate(2)	32						TTCTCCTCTGCACTTCTGGTA	0.443													C|||	449	0.0896565	0.1256	0.0591	5008	,	,		19516	0.0427		0.1252	False		,,,				2504	0.0746				p.V837V		Atlas-SNP	.											ESYT2,medulla,primitive_neuroectodermal_tumour-medulloblastoma,0,1	ESYT2	70	1	1	Substitution - coding silent(1)	central_nervous_system(1)	c.G2511C						scavenged	.			511,3895	233.6+/-246.7	24,463,1716	139.0	143.0	141.0		2511	1.7	1.0	7	dbSNP_126	141	1086,7514	226.4+/-262.1	63,960,3277	no	coding-synonymous	ESYT2	NM_020728.2		87,1423,4993	GG,GC,CC		12.6279,11.5978,12.2789		837/894	158528269	1597,11409	2203	4300	6503	SO:0001819	synonymous_variant	57488	exon20			CCTCTGCACTTCT	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.2511G>C	7.37:g.158528269C>G		Somatic	79	1	0.0126582		WXS	Illumina HiSeq	Phase_I	62	24	0.387097	NM_020728	A4D229|Q69YJ2|Q6UKI4|Q6ZTU0|Q6ZVU1|Q9BQS0|Q9NW47|Q9ULJ2	Silent	SNP	ENST00000251527.5	37	CCDS34791.1																																																																																			C|0.876;G|0.124	0.124	strong		0.443	ESYT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322647.1	NM_020728	
LBP	3929	hgsc.bcm.edu	37	20	36997655	36997655	+	Missense_Mutation	SNP	C	C	T	rs2232613	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:36997655C>T	ENST00000217407.2	+	10	1159	c.998C>T	c.(997-999)cCc>cTc	p.P333L		NM_004139.3	NP_004130.2	P18428	LBP_HUMAN	lipopolysaccharide binding protein	333			P -> L (abolishes lipopolysaccharide binding and causes increased proteolytic degradation of the protein; dbSNP:rs2232613). {ECO:0000269|PubMed:24120359}.		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)				AGGCTCTACCCCAACATGAAC	0.507													C|||	276	0.0551118	0.0983	0.0418	5008	,	,		19010	0.001		0.0726	False		,,,				2504	0.044				p.P333L		Atlas-SNP	.											.	LBP	60	.	0			c.C998T						PASS	.	C	LEU/PRO	423,3983	205.8+/-227.6	28,367,1808	95.0	93.0	94.0		998	4.6	1.0	20	dbSNP_98	94	689,7911	171.7+/-222.6	34,621,3645	yes	missense	LBP	NM_004139.2	98	62,988,5453	TT,TC,CC		8.0116,9.6005,8.5499	probably-damaging	333/482	36997655	1112,11894	2203	4300	6503	SO:0001583	missense	3929	exon10			TCTACCCCAACAT		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.998C>T	20.37:g.36997655C>T	ENSP00000217407:p.Pro333Leu	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	86	49	0.569767	NM_004139	B2R938|O43438|Q92672|Q9H403|Q9UD66	Missense_Mutation	SNP	ENST00000217407.2	37	CCDS13304.1	125	0.05723443223443223	53	0.10772357723577236	17	0.04696132596685083	1	0.0017482517482517483	54	0.0712401055408971	C	20.2	3.950249	0.73787	0.096005	0.080116	ENSG00000129988	ENST00000217407;ENST00000538599	T	0.27890	1.64	5.54	4.58	0.56647	Lipid-binding serum glycoprotein, C-terminal (2);Bactericidal permeability-increasing protein, alpha/beta domain (1);	0.000000	0.64402	D	0.000001	T	0.02047	0.0064	M	0.87097	2.86	0.09310	P	0.99999750602	D	0.89917	1.0	D	0.97110	1.0	T	0.37619	-0.9698	9	0.40728	T	0.16	-36.9081	14.0635	0.64815	0.0:0.8481:0.1518:0.0	rs2232613;rs60019947;rs2232613	333	P18428	LBP_HUMAN	L	333	ENSP00000217407:P333L	ENSP00000217407:P333L	P	+	2	0	LBP	36431069	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	4.338000	0.59316	1.537000	0.49254	0.655000	0.94253	CCC	C|0.926;T|0.074	0.074	strong		0.507	LBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079174.2	NM_004139	
PLEKHG5	57449	hgsc.bcm.edu	37	1	6531589	6531589	+	Missense_Mutation	SNP	C	C	T	rs74809741	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:6531589C>T	ENST00000400915.3	-	13	1474	c.1408G>A	c.(1408-1410)Gcg>Acg	p.A470T	PLEKHG5_ENST00000377728.3_Missense_Mutation_p.A414T|PLEKHG5_ENST00000535355.1_Missense_Mutation_p.A483T|PLEKHG5_ENST00000544978.1_Missense_Mutation_p.A414T|PLEKHG5_ENST00000400913.1_Missense_Mutation_p.A414T|PLEKHG5_ENST00000537245.1_Missense_Mutation_p.A493T|PLEKHG5_ENST00000377725.1_Missense_Mutation_p.A414T|PLEKHG5_ENST00000340850.5_Missense_Mutation_p.A414T|PLEKHG5_ENST00000377740.3_Missense_Mutation_p.A491T|PLEKHG5_ENST00000377732.1_Missense_Mutation_p.A451T|PLEKHG5_ENST00000377748.1_Missense_Mutation_p.A491T|PLEKHG5_ENST00000377737.2_Missense_Mutation_p.A414T	NM_001042663.1	NP_001036128.1	O94827	PKHG5_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 5	470	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				apoptotic signaling pathway (GO:0097190)|endothelial cell chemotaxis (GO:0035767)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)|signal transducer activity (GO:0004871)			liver(1)	1	Ovarian(185;0.02)|all_lung(157;0.154)	all_cancers(23;1.7e-35)|all_epithelial(116;2.78e-22)|all_lung(118;7.57e-07)|Lung NSC(185;4.26e-06)|Colorectal(325;4.47e-05)|all_hematologic(16;0.00014)|Breast(487;0.000688)|Renal(390;0.0007)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0448)		Epithelial(90;5.51e-35)|GBM - Glioblastoma multiforme(13;3.57e-27)|Colorectal(212;6.23e-08)|COAD - Colon adenocarcinoma(227;1.33e-05)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000894)|BRCA - Breast invasive adenocarcinoma(365;0.00107)|STAD - Stomach adenocarcinoma(132;0.00159)|READ - Rectum adenocarcinoma(331;0.0419)		TGTAGCAGCGCTCGCGTGCGC	0.706													c|||	277	0.0553115	0.0946	0.0504	5008	,	,		12520	0.0		0.0557	False		,,,				2504	0.0624				p.A493T		Atlas-SNP	.											.	PLEKHG5	66	.	0			c.G1477A						PASS	.	C	THR/ALA,THR/ALA,THR/ALA,THR/ALA,THR/ALA	386,4010		11,364,1823	13.0	17.0	16.0		1408,1240,1240,1240,1471	3.2	1.0	1	dbSNP_131	16	492,8072		15,462,3805	yes	missense,missense,missense,missense,missense	PLEKHG5	NM_001042663.1,NM_001042664.1,NM_001042665.1,NM_020631.3,NM_198681.2	58,58,58,58,58	26,826,5628	TT,TC,CC		5.745,8.7807,6.7747	benign,benign,benign,benign,benign	470/1063,414/1007,414/1007,414/1007,491/1084	6531589	878,12082	2198	4282	6480	SO:0001583	missense	57449	exon13			GCAGCGCTCGCGT	AK024676	CCDS79.1, CCDS41240.1, CCDS41241.1, CCDS57967.1, CCDS57968.1, CCDS57969.1	1p36.31	2014-09-17		2005-08-09	ENSG00000171680	ENSG00000171680		"""Pleckstrin homology (PH) domain containing"""	29105	protein-coding gene	gene with protein product	"""synectin-binding guanine exchange factor"""	611101				17564964	Standard	NM_001042663		Approved	KIAA0720, Syx, GEF720, Tech	uc010nzr.1	O94827	OTTHUMG00000000905	ENST00000400915.3:c.1408G>A	1.37:g.6531589C>T	ENSP00000383706:p.Ala470Thr	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	76	34	0.447368	NM_001265592	B3KU07|B7Z2M3|B7Z5X2|F5GZ21|F5H1I0|Q5SY17|Q5T8W5|Q5T8W9|Q6ZNM0|Q7Z436|Q86YD8|Q96BS1	Missense_Mutation	SNP	ENST00000400915.3	37	CCDS41241.1	100	0.045787545787545784	40	0.08130081300813008	26	0.0718232044198895	0	0.0	34	0.044854881266490766	C	5.936	0.356710	0.11239	0.087807	0.05745	ENSG00000171680	ENST00000377748;ENST00000340850;ENST00000400913;ENST00000400915;ENST00000377740;ENST00000377732;ENST00000377728;ENST00000377725;ENST00000535355;ENST00000377737;ENST00000535966;ENST00000537245;ENST00000544978	T;T;T;T;T;T;T;T;T;T;T;T	0.68025	-0.3;-0.3;-0.3;-0.3;-0.3;-0.3;-0.3;-0.3;-0.3;-0.3;-0.3;-0.3	5.1	3.21	0.36854	Dbl homology (DH) domain (5);	0.482808	0.24456	N	0.038380	T	0.01353	0.0044	N	0.01729	-0.75	0.36208	D	0.851209	B;B;B;B;B	0.11235	0.0;0.001;0.001;0.004;0.002	B;B;B;B;B	0.13407	0.005;0.004;0.004;0.005;0.009	T	0.03981	-1.0987	10	0.14252	T	0.57	-13.6505	8.2076	0.31465	0.0:0.7448:0.0:0.2552	.	483;414;491;491;470	F5GZ21;O94827-4;Q5SY18;O94827-2;O94827	.;.;.;.;PKHG5_HUMAN	T	491;414;414;470;491;451;414;414;483;414;320;493;414	ENSP00000366977:A491T;ENSP00000344570:A414T;ENSP00000383704:A414T;ENSP00000383706:A470T;ENSP00000366969:A491T;ENSP00000366961:A451T;ENSP00000366957:A414T;ENSP00000366954:A414T;ENSP00000441445:A483T;ENSP00000366966:A414T;ENSP00000439625:A493T;ENSP00000437710:A414T	ENSP00000344570:A414T	A	-	1	0	PLEKHG5	6454176	0.974000	0.33945	0.998000	0.56505	0.113000	0.19764	0.641000	0.24720	1.153000	0.42468	0.313000	0.20887	GCG	C|0.938;T|0.062	0.062	strong		0.706	PLEKHG5-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000002631.1	NM_020631	
GNS	2799	hgsc.bcm.edu	37	12	65141588	65141588	+	Silent	SNP	C	C	T	rs2230291	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:65141588C>T	ENST00000258145.3	-	3	533	c.363G>A	c.(361-363)aaG>aaA	p.K121K	GNS_ENST00000542058.1_Silent_p.K101K|GNS_ENST00000543646.1_Silent_p.K153K|GNS_ENST00000418919.2_Silent_p.K65K	NM_002076.3	NP_002067.1	P15586	GNS_HUMAN	glucosamine (N-acetyl)-6-sulfatase	121					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)	metal ion binding (GO:0046872)|N-acetylglucosamine-6-sulfatase activity (GO:0008449)|sulfuric ester hydrolase activity (GO:0008484)			central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(4)	15	Lung NSC(1;7.25e-14)|all_lung(1;1.25e-12)		LUAD - Lung adenocarcinoma(6;0.115)	GBM - Glioblastoma multiforme(28;0.0435)		TCTGCCAGGACTTACTACTGC	0.448													C|||	195	0.0389377	0.0091	0.0634	5008	,	,		17354	0.0		0.1223	False		,,,				2504	0.0164				p.K121K		Atlas-SNP	.											.	GNS	41	.	0			c.G363A						PASS	.	C		110,4296	85.3+/-124.0	1,108,2094	207.0	193.0	198.0		363	-6.1	0.0	12	dbSNP_132	198	1165,7435	239.3+/-270.5	88,989,3223	no	coding-synonymous	GNS	NM_002076.3		89,1097,5317	TT,TC,CC		13.5465,2.4966,9.8032		121/553	65141588	1275,11731	2203	4300	6503	SO:0001819	synonymous_variant	2799	exon3			CCAGGACTTACTA		CCDS8970.1	12q14	2010-05-04	2008-08-01		ENSG00000135677	ENSG00000135677	3.1.6.14		4422	protein-coding gene	gene with protein product	"""Sanfilippo disease IIID"", ""N-acetylglucosamine-6-sulfatase"""	607664					Standard	NM_002076		Approved		uc001ssg.4	P15586	OTTHUMG00000168819	ENST00000258145.3:c.363G>A	12.37:g.65141588C>T		Somatic	266	0	0		WXS	Illumina HiSeq	Phase_I	254	121	0.476378	NM_002076	B4DYH8|Q53F05	Silent	SNP	ENST00000258145.3	37	CCDS8970.1																																																																																			T|0.080;G|0.000;C|0.920	0.080	strong		0.448	GNS-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000401195.2		
C12orf65	91574	hgsc.bcm.edu	37	12	123738265	123738265	+	Missense_Mutation	SNP	G	G	A	rs78651634	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:123738265G>A	ENST00000253233.1	+	2	688	c.44G>A	c.(43-45)cGa>cAa	p.R15Q	C12orf65_ENST00000366329.2_Missense_Mutation_p.R15Q|RP11-282O18.3_ENST00000543217.2_RNA|RP11-282O18.3_ENST00000541002.3_RNA|C12orf65_ENST00000429587.2_Missense_Mutation_p.R15Q	NM_152269.4	NP_689482.1	Q9H3J6	CL065_HUMAN	chromosome 12 open reading frame 65	15					cell death (GO:0008219)	mitochondrion (GO:0005739)	translation release factor activity (GO:0003747)			endometrium(1)|large_intestine(1)|lung(1)|prostate(1)	4	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000595)|Epithelial(86;0.00199)		CCACTGACCCGAATATGCCCG	0.537													G|||	39	0.00778754	0.0	0.0144	5008	,	,		17860	0.0		0.0258	False		,,,				2504	0.0031				p.R15Q		Atlas-SNP	.											.	C12orf65	15	.	0			c.G44A						PASS	.	G	GLN/ARG,GLN/ARG,GLN/ARG	19,4387	26.2+/-53.5	0,19,2184	87.0	84.0	85.0		44,44,44	4.7	0.2	12	dbSNP_131	85	231,8369	94.2+/-156.2	4,223,4073	yes	missense,missense,missense	C12orf65	NM_001143905.2,NM_001194995.1,NM_152269.4	43,43,43	4,242,6257	AA,AG,GG		2.686,0.4312,1.9222	probably-damaging,probably-damaging,probably-damaging	15/167,15/167,15/167	123738265	250,12756	2203	4300	6503	SO:0001583	missense	91574	exon2			TGACCCGAATATG	AK095982	CCDS9244.1	12q24.31	2013-01-07			ENSG00000130921	ENSG00000130921			26784	protein-coding gene	gene with protein product		613541				20598281, 22688947, 23188110	Standard	NM_152269		Approved	FLJ38663, SPG55	uc001uen.3	Q9H3J6	OTTHUMG00000168852	ENST00000253233.1:c.44G>A	12.37:g.123738265G>A	ENSP00000253233:p.Arg15Gln	Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	167	90	0.538922	NM_001194995	Q8WUC6	Missense_Mutation	SNP	ENST00000253233.1	37	CCDS9244.1	21	0.009615384615384616	0	0.0	4	0.011049723756906077	0	0.0	17	0.022427440633245383	G	21.0	4.084967	0.76642	0.004312	0.02686	ENSG00000130921	ENST00000253233;ENST00000536130;ENST00000546132;ENST00000366329;ENST00000543139;ENST00000429587	T;T;T;T	0.35048	1.33;1.33;1.34;1.33	5.55	4.65	0.58169	.	0.256239	0.37530	N	0.002059	T	0.07234	0.0183	L	0.34521	1.04	0.09310	N	1	P	0.48998	0.918	B	0.34180	0.177	T	0.29941	-0.9995	10	0.87932	D	0	-14.3509	6.1264	0.20182	0.1484:0.0:0.6949:0.1566	.	15	Q9H3J6	CL065_HUMAN	Q	15	ENSP00000253233:R15Q;ENSP00000390647:R15Q;ENSP00000444843:R15Q;ENSP00000391513:R15Q	ENSP00000253233:R15Q	R	+	2	0	C12orf65	122304218	0.002000	0.14202	0.190000	0.23270	0.059000	0.15707	0.590000	0.23954	2.607000	0.88179	0.561000	0.74099	CGA	G|0.984;A|0.016	0.016	strong		0.537	C12orf65-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401375.1	NM_152269	
RBBP6	5930	hgsc.bcm.edu	37	16	24582299	24582299	+	Silent	SNP	C	C	G	rs7196736	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:24582299C>G	ENST00000319715.4	+	18	4344	c.3912C>G	c.(3910-3912)acC>acG	p.T1304T	RBBP6_ENST00000381039.3_Silent_p.T464T|RBBP6_ENST00000348022.2_Silent_p.T1270T	NM_006910.4	NP_008841.2	Q7Z6E9	RBBP6_HUMAN	retinoblastoma binding protein 6	1304					embryonic organ development (GO:0048568)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|somite development (GO:0061053)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(17)|ovary(4)|pancreas(1)|prostate(2)|urinary_tract(1)	46				GBM - Glioblastoma multiforme(48;0.0518)		ATGACAATACCGCGCCAGCTG	0.393													G|||	641	0.127995	0.149	0.1585	5008	,	,		16201	0.0149		0.1402	False		,,,				2504	0.182				p.T1304T		Atlas-SNP	.											RBBP6,NS,adenocarcinoma,+2,1	RBBP6	158	1	0			c.C3912G						PASS	.	G	,	712,3682	755.0+/-412.5	57,598,1542	55.0	53.0	54.0		3912,3810	-3.1	0.5	16	dbSNP_116	54	1472,7128	747.2+/-407.3	128,1216,2956	no	coding-synonymous,coding-synonymous	RBBP6	NM_006910.4,NM_018703.3	,	185,1814,4498	GG,GC,CC		17.1163,16.2039,16.8078	,	1304/1793,1270/1759	24582299	2184,10810	2197	4300	6497	SO:0001819	synonymous_variant	5930	exon18			CAATACCGCGCCA		CCDS10621.1, CCDS10622.1, CCDS45444.1	16p12.2	2008-08-04	2001-11-28		ENSG00000122257	ENSG00000122257			9889	protein-coding gene	gene with protein product	"""proliferation potential-related protein"""	600938	"""retinoblastoma-binding protein 6"""			8595913, 16396680	Standard	NM_006910		Approved	P2P-R, PACT, SNAMA	uc002dmh.3	Q7Z6E9	OTTHUMG00000096991	ENST00000319715.4:c.3912C>G	16.37:g.24582299C>G		Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	195	64	0.328205	NM_006910	Q147T5|Q15290|Q6DKH4|Q6P4C2|Q6YNC9|Q7Z6E8|Q8N0V2|Q96PH3|Q9H3I8|Q9H5M5|Q9NPX4	Silent	SNP	ENST00000319715.4	37	CCDS10621.1																																																																																			C|0.848;G|0.152	0.152	strong		0.393	RBBP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214067.2	NM_006910	
ABCC11	85320	hgsc.bcm.edu	37	16	48258198	48258198	+	Missense_Mutation	SNP	C	C	T	rs17822931	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:48258198C>T	ENST00000394747.1	-	4	887	c.538G>A	c.(538-540)Ggg>Agg	p.G180R	ABCC11_ENST00000356608.2_Missense_Mutation_p.G180R|ABCC11_ENST00000353782.5_Missense_Mutation_p.G180R|ABCC11_ENST00000394748.1_Missense_Mutation_p.G180R|ABCC11_ENST00000537808.1_Missense_Mutation_p.G180R	NM_033151.3	NP_149163.2	Q96J66	ABCCB_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 11	180	ABC transmembrane type-1 1. {ECO:0000255|PROSITE-ProRule:PRU00441}.		G -> R (in dry earwax phenotype; reduced transport activity; dbSNP:rs17822931). {ECO:0000269|PubMed:16444273}.		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)	CTTACTGGCCCGAGTACACTG	0.507													C|||	1507	0.300919	0.0121	0.1398	5008	,	,		22437	0.7798		0.1362	False		,,,				2504	0.4816				p.G180R		Atlas-SNP	.											.	ABCC11	177	.	0			c.G538A	GRCh37	CM062373	ABCC11	M	rs17822931	PASS	.	C	ARG/GLY,ARG/GLY,ARG/GLY	138,4262	98.5+/-137.1	1,136,2063	94.0	83.0	87.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	538,538,538	4.4	0.9	16	dbSNP_123	87	1136,7464	234.0+/-267.1	76,984,3240	yes	missense,missense,missense	ABCC11	NM_032583.3,NM_033151.3,NM_145186.2	125,125,125	77,1120,5303	TT,TC,CC		13.2093,3.1364,9.8	probably-damaging,probably-damaging,probably-damaging	180/1383,180/1383,180/1345	48258198	1274,11726	2200	4300	6500	SO:0001583	missense	85320	exon4			CTGGCCCGAGTAC	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.538G>A	16.37:g.48258198C>T	ENSP00000378230:p.Gly180Arg	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	96	28	0.291667	NM_033151	Q8TDJ0|Q96JA6|Q9BX80	Missense_Mutation	SNP	ENST00000394747.1	37	CCDS10732.1	673	0.30815018315018317	6	0.012195121951219513	43	0.11878453038674033	515	0.9003496503496503	109	0.1437994722955145	C	21.2	4.116723	0.77323	0.031364	0.132093	ENSG00000121270	ENST00000353782;ENST00000356608;ENST00000394748;ENST00000394747;ENST00000537808	D;D;D;D;D	0.91686	-2.89;-2.89;-2.89;-2.89;-2.89	4.45	4.45	0.53987	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1);	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	M	0.79926	2.475	0.21064	P	0.999796107	D;D	0.89917	1.0;0.994	D;D	0.97110	1.0;0.923	T	0.46911	-0.9157	9	0.72032	D	0.01	-18.9594	12.9103	0.58177	0.0:1.0:0.0:0.0	rs17822931;rs52813591;rs58140753;rs17822931	180;180	Q96J66-2;Q96J66	.;ABCCB_HUMAN	R	180	ENSP00000311326:G180R;ENSP00000349017:G180R;ENSP00000378231:G180R;ENSP00000378230:G180R;ENSP00000438530:G180R	ENSP00000311326:G180R	G	-	1	0	ABCC11	46815699	0.990000	0.36364	0.888000	0.34837	0.150000	0.21749	4.118000	0.57884	2.161000	0.67846	0.460000	0.39030	GGG	C|0.792;T|0.208	0.208	strong		0.507	ABCC11-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000429984.1	NM_032583	
OGDH	4967	hgsc.bcm.edu	37	7	44747514	44747514	+	Silent	SNP	C	C	T	rs61756583	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:44747514C>T	ENST00000222673.5	+	23	3030	c.2988C>T	c.(2986-2988)acC>acT	p.T996T	OGDH_ENST00000444676.1_Silent_p.T1011T|OGDH_ENST00000449767.1_Silent_p.T992T|OGDH_ENST00000439616.2_Silent_p.T846T|OGDH_ENST00000543843.1_Silent_p.T947T|OGDH_ENST00000447398.1_Silent_p.T1007T	NM_002541.3	NP_002532.2	Q02218	ODO1_HUMAN	oxoglutarate (alpha-ketoglutarate) dehydrogenase (lipoamide)	996					2-oxoglutarate metabolic process (GO:0006103)|cellular metabolic process (GO:0044237)|cellular nitrogen compound metabolic process (GO:0034641)|cerebellar cortex development (GO:0021695)|generation of precursor metabolites and energy (GO:0006091)|glycolytic process (GO:0006096)|hippocampus development (GO:0021766)|lysine catabolic process (GO:0006554)|NADH metabolic process (GO:0006734)|olfactory bulb mitral cell layer development (GO:0061034)|pyramidal neuron development (GO:0021860)|small molecule metabolic process (GO:0044281)|striatum development (GO:0021756)|succinyl-CoA metabolic process (GO:0006104)|tangential migration from the subventricular zone to the olfactory bulb (GO:0022028)|thalamus development (GO:0021794)|tricarboxylic acid cycle (GO:0006099)	mitochondrial matrix (GO:0005759)|mitochondrial membrane (GO:0031966)|mitochondrion (GO:0005739)|oxoglutarate dehydrogenase complex (GO:0045252)	metal ion binding (GO:0046872)|oxoglutarate dehydrogenase (NAD+) activity (GO:0034602)|oxoglutarate dehydrogenase (succinyl-transferring) activity (GO:0004591)|thiamine pyrophosphate binding (GO:0030976)			breast(2)|endometrium(5)|kidney(2)|large_intestine(6)|lung(13)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(4)	36					Valproic Acid(DB00313)	CTCCAGCCACCGGCAACAAGA	0.642													C|||	234	0.0467252	0.0038	0.0504	5008	,	,		17701	0.0823		0.0417	False		,,,				2504	0.0706				p.T996T		Atlas-SNP	.											.	OGDH	145	.	0			c.C2988T						PASS	.	C	,	51,4355	49.6+/-84.7	1,49,2153	58.0	54.0	55.0		2976,2988	-7.0	0.9	7	dbSNP_129	55	471,8129	137.3+/-194.3	10,451,3839	no	coding-synonymous,coding-synonymous	OGDH	NM_001165036.1,NM_002541.3	,	11,500,5992	TT,TC,CC		5.4767,1.1575,4.0135	,	992/1020,996/1024	44747514	522,12484	2203	4300	6503	SO:0001819	synonymous_variant	4967	exon23			AGCCACCGGCAAC	D10523	CCDS34627.1, CCDS47580.1, CCDS55107.1	7p13-p11.2	2010-11-23			ENSG00000105953	ENSG00000105953	1.2.4.2		8124	protein-coding gene	gene with protein product		613022				8020988, 1542694	Standard	NM_002541		Approved	E1k	uc003tln.3	Q02218	OTTHUMG00000155304	ENST00000222673.5:c.2988C>T	7.37:g.44747514C>T		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	93	62	0.666667	NM_002541	B4E2U9|D3DVL0|E9PBM1|Q96DD3|Q9UDX0	Silent	SNP	ENST00000222673.5	37	CCDS34627.1																																																																																			C|0.956;T|0.044	0.044	strong		0.642	OGDH-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000339391.1		
LRRIQ1	84125	hgsc.bcm.edu	37	12	85459100	85459100	+	Missense_Mutation	SNP	A	A	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:85459100A>C	ENST00000393217.2	+	9	2513	c.2452A>C	c.(2452-2454)Aca>Cca	p.T818P		NM_001079910.1	NP_001073379.1	Q96JM4	LRIQ1_HUMAN	leucine-rich repeats and IQ motif containing 1	818										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)		GGCAGAGTGTACAAATCTTCA	0.398																																					p.T818P		Atlas-SNP	.											.	LRRIQ1	512	.	0			c.A2452C						PASS	.						146.0	138.0	141.0					12																	85459100		2203	4300	6503	SO:0001583	missense	84125	exon9			GAGTGTACAAATC	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.2452A>C	12.37:g.85459100A>C	ENSP00000376910:p.Thr818Pro	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	82	16	0.195122	NM_001079910	Q567P4|Q9BS17|Q9HA36	Missense_Mutation	SNP	ENST00000393217.2	37	CCDS41816.1	.	.	.	.	.	.	.	.	.	.	A	8.766	0.924819	0.18056	.	.	ENSG00000133640	ENST00000256007;ENST00000378580;ENST00000393217	T	0.09817	2.94	5.6	-8.78	0.00824	.	1.013500	0.07926	N	0.976669	T	0.04272	0.0118	N	0.16833	0.445	0.09310	N	0.999996	B;B	0.12630	0.003;0.006	B;B	0.14578	0.002;0.011	T	0.39165	-0.9627	10	0.38643	T	0.18	.	1.7967	0.03062	0.1469:0.2665:0.1369:0.4496	.	818;793	Q96JM4;C9JI57	LRIQ1_HUMAN;.	P	818;793;818	ENSP00000376910:T818P	ENSP00000256007:T818P	T	+	1	0	LRRIQ1	83983231	0.002000	0.14202	0.150000	0.22450	0.780000	0.44128	-1.292000	0.02772	-1.451000	0.01933	0.477000	0.44152	ACA	.	.	none		0.398	LRRIQ1-004	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388249.2	NM_032165	
NRAP	4892	hgsc.bcm.edu	37	10	115389356	115389356	+	Silent	SNP	G	G	A	rs2286736	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:115389356G>A	ENST00000359988.3	-	19	2275	c.2031C>T	c.(2029-2031)ctC>ctT	p.L677L	NRAP_ENST00000360478.3_Silent_p.L642L|NRAP_ENST00000369358.4_Silent_p.L685L|NRAP_ENST00000369360.3_Silent_p.L650L	NM_001261463.1|NM_198060.3	NP_001248392.1|NP_932326.2			nebulin-related anchoring protein											autonomic_ganglia(1)|breast(2)|central_nervous_system(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(18)|lung(39)|ovary(6)|prostate(3)|skin(1)|stomach(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	95		Colorectal(252;0.0233)|Breast(234;0.188)		Epithelial(162;0.00392)|all cancers(201;0.00569)		CCTCGCTCTGGAGCCCATAGG	0.483													G|||	1376	0.27476	0.1823	0.3948	5008	,	,		20478	0.2817		0.2962	False		,,,				2504	0.2853				p.L677L		Atlas-SNP	.											.	NRAP	208	.	0			c.C2031T						PASS	.	G	,	940,3466	354.4+/-312.6	96,748,1359	110.0	92.0	98.0		1926,2031	-0.3	1.0	10	dbSNP_100	98	2620,5980	424.4+/-354.6	371,1878,2051	no	coding-synonymous,coding-synonymous	NRAP	NM_006175.3,NM_198060.2	,	467,2626,3410	AA,AG,GG		30.4651,21.3345,27.372	,	642/1696,677/1731	115389356	3560,9446	2203	4300	6503	SO:0001819	synonymous_variant	4892	exon19			GCTCTGGAGCCCA		CCDS7578.1, CCDS7579.1, CCDS73199.1	10q24-q26	2008-08-01			ENSG00000197893	ENSG00000197893			7988	protein-coding gene	gene with protein product		602873				12789664, 10320340	Standard	NM_006175		Approved		uc001lal.4	Q86VF7	OTTHUMG00000019072	ENST00000359988.3:c.2031C>T	10.37:g.115389356G>A		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	92	45	0.48913	NM_001261463		Silent	SNP	ENST00000359988.3	37	CCDS7579.1																																																																																			G|0.727;A|0.273	0.273	strong		0.483	NRAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050425.2	NM_006175	
ALPK2	115701	hgsc.bcm.edu	37	18	56202683	56202683	+	Missense_Mutation	SNP	T	T	C	rs33910491	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:56202683T>C	ENST00000361673.3	-	5	4949	c.4736A>G	c.(4735-4737)cAg>cGg	p.Q1579R	RP11-1151B14.4_ENST00000591360.1_RNA	NM_052947.3	NP_443179.3	Q86TB3	ALPK2_HUMAN	alpha-kinase 2	1579			Q -> R (in dbSNP:rs33910491).			nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(33)|ovary(7)|prostate(1)|skin(10)|upper_aerodigestive_tract(2)	84						AAACACATACTGACGCTTTCT	0.468													T|||	313	0.0625	0.0061	0.0692	5008	,	,		20991	0.0119		0.1282	False		,,,				2504	0.1186				p.Q1579R		Atlas-SNP	.											.	ALPK2	487	.	0			c.A4736G						PASS	.	T	ARG/GLN	135,4271	96.2+/-134.9	4,127,2072	133.0	125.0	128.0		4736	0.8	0.0	18	dbSNP_126	128	1172,7428	239.9+/-270.8	79,1014,3207	yes	missense	ALPK2	NM_052947.3	43	83,1141,5279	CC,CT,TT		13.6279,3.064,10.0492	benign	1579/2171	56202683	1307,11699	2203	4300	6503	SO:0001583	missense	115701	exon5			ACATACTGACGCT	AY044450	CCDS11966.2	18q21.31	2013-01-11			ENSG00000198796	ENSG00000198796		"""Immunoglobulin superfamily / I-set domain containing"""	20565	protein-coding gene	gene with protein product	"""heart alpha-kinase"""					10021370	Standard	NM_052947		Approved	HAK	uc002lhj.4	Q86TB3	OTTHUMG00000132755	ENST00000361673.3:c.4736A>G	18.37:g.56202683T>C	ENSP00000354991:p.Gln1579Arg	Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	185	85	0.459459	NM_052947	Q6ZUX0|Q8NAT5|Q96L95	Missense_Mutation	SNP	ENST00000361673.3	37	CCDS11966.2	133	0.060897435897435896	8	0.016260162601626018	32	0.08839779005524862	8	0.013986013986013986	85	0.11213720316622691	T	11.81	1.750238	0.30955	0.03064	0.136279	ENSG00000198796	ENST00000361673	T	0.46819	0.86	5.91	0.844	0.18943	.	6.994860	0.00166	N	0.000000	T	0.00300	0.0009	L	0.38838	1.175	0.80722	P	0.0	P;B	0.41102	0.738;0.081	B;B	0.36808	0.233;0.029	T	0.02852	-1.1102	9	0.27785	T	0.31	-1.7837	4.9318	0.13921	0.0:0.1628:0.3373:0.4999	rs33910491	1574;1579	Q86TB3-2;Q86TB3	.;ALPK2_HUMAN	R	1579	ENSP00000354991:Q1579R	ENSP00000354991:Q1579R	Q	-	2	0	ALPK2	54353663	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.317000	0.08060	0.122000	0.18314	-0.331000	0.08364	CAG	T|0.911;C|0.089	0.089	strong		0.468	ALPK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256126.1	NM_052947	
PKHD1L1	93035	hgsc.bcm.edu	37	8	110455321	110455321	+	Missense_Mutation	SNP	C	C	A	rs1673408	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:110455321C>A	ENST00000378402.5	+	36	4644	c.4540C>A	c.(4540-4542)Cgc>Agc	p.R1514S		NM_177531.4	NP_803875.2	Q86WI1	PKHL1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1	1514			R -> S (in dbSNP:rs1673408).		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)			GTTTGTGGGTCGCTCTGAAGC	0.463										HNSCC(38;0.096)			A|||	2809	0.560903	0.5499	0.6556	5008	,	,		18820	0.4048		0.5119	False		,,,				2504	0.7198				p.R1514S		Atlas-SNP	.											.	PKHD1L1	522	.	0			c.C4540A						PASS	.	A	SER/ARG	2143,1641		611,921,360	184.0	172.0	176.0		4540	-5.5	0.0	8	dbSNP_89	176	4423,3825		1203,2017,904	yes	missense	PKHD1L1	NM_177531.4	110	1814,2938,1264	AA,AC,CC		46.3749,43.3668,45.4289	benign	1514/4244	110455321	6566,5466	1892	4124	6016	SO:0001583	missense	93035	exon36			GTGGGTCGCTCTG	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.4540C>A	8.37:g.110455321C>A	ENSP00000367655:p.Arg1514Ser	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	98	76	0.77551	NM_177531	Q567P2|Q9UF27	Missense_Mutation	SNP	ENST00000378402.5	37	CCDS47911.1	1125	0.5151098901098901	266	0.540650406504065	230	0.6353591160220995	245	0.42832167832167833	384	0.5065963060686016	A	9.207	1.030005	0.19512	0.566332	0.536251	ENSG00000205038	ENST00000378402	D	0.84873	-1.91	6.16	-5.52	0.02560	.	0.310744	0.34725	N	0.003731	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	0.42749	-0.9433	9	0.20519	T	0.43	.	10.8392	0.46704	0.1493:0.3299:0.5208:0.0	rs1673408;rs13248709;rs16879579;rs1673408	1514	Q86WI1	PKHL1_HUMAN	S	1514	ENSP00000367655:R1514S	ENSP00000367655:R1514S	R	+	1	0	PKHD1L1	110524497	0.134000	0.22483	0.001000	0.08648	0.890000	0.51754	0.031000	0.13710	-1.364000	0.02161	-0.264000	0.10439	CGC	C|0.475;A|0.525	0.525	strong		0.463	PKHD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381017.1	NM_177531	
FHL5	9457	hgsc.bcm.edu	37	6	97052754	97052754	+	Silent	SNP	C	C	T	rs2064947	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:97052754C>T	ENST00000326771.2	+	4	668	c.288C>T	c.(286-288)aaC>aaT	p.N96N	FHL5_ENST00000541107.1_Silent_p.N96N	NM_020482.4	NP_065228.4	Q5TD97	FHL5_HUMAN	four and a half LIM domains 5	96	LIM zinc-binding 1. {ECO:0000255|PROSITE- ProRule:PRU00125}.				positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(4)|lung(17)|ovary(2)|urinary_tract(1)	27		all_cancers(76;1.57e-07)|Acute lymphoblastic leukemia(125;4.93e-10)|all_hematologic(75;3.55e-07)|all_epithelial(107;0.00266)|Colorectal(196;0.0341)|Lung NSC(302;0.204)		BRCA - Breast invasive adenocarcinoma(108;0.0948)		GCTATTCTAACGAGTGCTCCT	0.502													C|||	682	0.136182	0.1135	0.1801	5008	,	,		17088	0.0357		0.2117	False		,,,				2504	0.1616				p.N96N		Atlas-SNP	.											.	FHL5	73	.	0			c.C288T						PASS	.	C	,	483,3923	225.2+/-241.2	23,437,1743	118.0	107.0	111.0		288,288	-10.7	0.2	6	dbSNP_94	111	1671,6929	306.8+/-308.1	174,1323,2803	no	coding-synonymous,coding-synonymous	FHL5	NM_001170807.1,NM_020482.4	,	197,1760,4546	TT,TC,CC		19.4302,10.9623,16.5616	,	96/285,96/285	97052754	2154,10852	2203	4300	6503	SO:0001819	synonymous_variant	9457	exon4			TTCTAACGAGTGC	AF278541	CCDS5035.1	6q16.1-q16.3	2008-02-05			ENSG00000112214	ENSG00000112214			17371	protein-coding gene	gene with protein product		605126					Standard	NM_020482		Approved	FLJ33049, ACT, dJ393D12.2	uc003pot.2	Q5TD97	OTTHUMG00000015239	ENST00000326771.2:c.288C>T	6.37:g.97052754C>T		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	58	26	0.448276	NM_020482	B2RBD1|E1P526|Q5TD98|Q8WW21|Q9NQU2	Silent	SNP	ENST00000326771.2	37	CCDS5035.1																																																																																			C|0.849;T|0.151	0.151	strong		0.502	FHL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041559.1	NM_020482	
PKD1L2	114780	hgsc.bcm.edu	37	16	81249927	81249927	+	RNA	SNP	C	C	T	rs7185774	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:81249927C>T	ENST00000525539.1	-	0	385				PKD1L2_ENST00000337114.4_RNA	NM_052892.3	NP_443124.3	Q7Z442	PK1L2_HUMAN	polycystic kidney disease 1-like 2						ion transport (GO:0006811)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(20)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44						CCCGATGTGGCCGCAGGTGTC	0.657													C|||	748	0.149361	0.0598	0.2219	5008	,	,		17980	0.0089		0.3598	False		,,,				2504	0.1472				p.G129D		Atlas-SNP	.											.	PKD1L2	361	.	0			c.G386A						PASS	.	C	ASP/GLY,ASP/GLY	481,3669		32,417,1626	59.0	74.0	69.0		386,386	5.1	0.9	16	dbSNP_116	69	2910,5512		479,1952,1780	yes	missense,missense	PKD1L2	NM_001076780.1,NM_052892.3	94,94	511,2369,3406	TT,TC,CC		34.5524,11.5904,26.9726	probably-damaging,probably-damaging	129/992,129/2460	81249927	3391,9181	2075	4211	6286			114780	exon2			ATGTGGCCGCAGG	AY164483	CCDS61998.1, CCDS61999.1	16q23.2	2014-09-11			ENSG00000166473	ENSG00000166473			21715	protein-coding gene	gene with protein product		607894				12782129	Standard	NM_052892		Approved	KIAA1879	uc002fgf.1	Q7Z442	OTTHUMG00000166126		16.37:g.81249927C>T		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	87	85	0.977012	NM_001076780	Q6UEE1|Q6ZN46|Q6ZSP2|Q8N1H9|Q96CL2|Q96Q08	Missense_Mutation	SNP	ENST00000525539.1	37		395	0.18086080586080586	28	0.056910569105691054	105	0.2900552486187845	2	0.0034965034965034965	260	0.34300791556728233	C	17.15	3.316419	0.60524	0.115904	0.345524	ENSG00000166473	ENST00000337114	T	0.18657	2.2	5.09	5.09	0.68999	C-type lectin fold (1);C-type lectin (3);	0.903145	0.09494	N	0.794543	T	0.00012	0.0000	.	.	.	0.29850	P	0.828541	D;D	0.71674	0.998;0.997	D;D	0.66847	0.939;0.947	T	0.28839	-1.0031	8	0.49607	T	0.09	-6.5644	18.5832	0.91180	0.0:1.0:0.0:0.0	rs7185774;rs7185774	129;129	Q7Z442-3;Q7Z442	.;PK1L2_HUMAN	D	129	ENSP00000337397:G129D	ENSP00000337397:G129D	G	-	2	0	PKD1L2	79807428	1.000000	0.71417	0.902000	0.35471	0.035000	0.12851	3.983000	0.56916	2.391000	0.81399	0.650000	0.86243	GGC	C|0.772;T|0.228	0.228	strong		0.657	PKD1L2-001	KNOWN	non_canonical_polymorphism|basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000387972.2		
PRDM9	56979	hgsc.bcm.edu	37	5	23527273	23527273	+	Silent	SNP	T	T	C			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:23527273T>C	ENST00000296682.3	+	11	2258	c.2076T>C	c.(2074-2076)taT>taC	p.Y692Y		NM_020227.2	NP_064612.2	Q9NQV7	PRDM9_HUMAN	PR domain containing 9	692					meiotic gene conversion (GO:0006311)|positive regulation of meiosis I (GO:0060903)|positive regulation of reciprocal meiotic recombination (GO:0010845)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)	histone methyltransferase activity (H3-K4 specific) (GO:0042800)|metal ion binding (GO:0046872)|recombination hotspot binding (GO:0010844)|sequence-specific DNA binding (GO:0043565)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(15)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(27)|lung(87)|ovary(6)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(11)	172						AGAAGCCCTATGTCTGCAGGG	0.607										HNSCC(3;0.000094)																											p.Y692Y		Atlas-SNP	.											PRDM9,NS,carcinoma,+1,1	PRDM9	344	1	0			c.T2076C						PASS	.						11.0	8.0	9.0					5																	23527273		1606	3274	4880	SO:0001819	synonymous_variant	56979	exon11			GCCCTATGTCTGC	AF275816	CCDS43307.1	5p14.2	2014-06-03			ENSG00000164256	ENSG00000164256		"""-"", ""Zinc fingers, C2H2-type"""	13994	protein-coding gene	gene with protein product	"""PR-domain containing protein 9"""	609760	"""minisatellite binding protein 3, 115kDa"", ""minisatellite binding protein 3 (115kD)"""	MSBP3		10668202, 2062643, 24634223	Standard	NM_020227		Approved	PFM6, ZNF899	uc003jgo.3	Q9NQV7	OTTHUMG00000161918	ENST00000296682.3:c.2076T>C	5.37:g.23527273T>C		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	98	26	0.265306	NM_020227	B4DX22|Q27Q50	Silent	SNP	ENST00000296682.3	37	CCDS43307.1																																																																																			.	.	none		0.607	PRDM9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366375.1	NM_020227	
CDH6	1004	hgsc.bcm.edu	37	5	31317529	31317529	+	Silent	SNP	A	A	G	rs2302903	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:31317529A>G	ENST00000265071.2	+	10	1825	c.1560A>G	c.(1558-1560)ggA>ggG	p.G520G	CDH6_ENST00000514738.1_Silent_p.G465G	NM_004932.3	NP_004923.1	P55285	CADH6_HUMAN	cadherin 6, type 2, K-cadherin (fetal kidney)	520	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(3)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(42)|ovary(4)|prostate(6)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(1)	77						CTTATAGTGGACACCAATTTT	0.398													G|||	2523	0.503794	0.4191	0.5317	5008	,	,		15730	0.5268		0.5616	False		,,,				2504	0.5153				p.G520G		Atlas-SNP	.											.	CDH6	175	.	0			c.A1560G						PASS	.	G		1996,2410	617.0+/-392.9	439,1118,646	100.0	94.0	96.0		1560	-0.9	1.0	5	dbSNP_100	96	4618,3982	552.5+/-386.1	1274,2070,956	no	coding-synonymous	CDH6	NM_004932.3		1713,3188,1602	GG,GA,AA		46.3023,45.3019,49.1465		520/791	31317529	6614,6392	2203	4300	6503	SO:0001819	synonymous_variant	1004	exon10			TAGTGGACACCAA	D31784	CCDS3894.1	5p13.3	2010-01-26			ENSG00000113361	ENSG00000113361		"""Cadherins / Major cadherins"""	1765	protein-coding gene	gene with protein product	"""K-Cadherin"""	603007				7743525, 10191097	Standard	NM_004932		Approved		uc003jhe.2	P55285	OTTHUMG00000090673	ENST00000265071.2:c.1560A>G	5.37:g.31317529A>G		Somatic	180	1	0.00555556		WXS	Illumina HiSeq	Phase_I	127	127	1	NM_004932	A8K5H5|Q9BWS0	Silent	SNP	ENST00000265071.2	37	CCDS3894.1																																																																																			A|0.482;G|0.518	0.518	strong		0.398	CDH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207355.2	NM_004932	
ALDH16A1	126133	hgsc.bcm.edu	37	19	49965173	49965173	+	Silent	SNP	A	A	T	rs7259560	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:49965173A>T	ENST00000293350.4	+	7	955	c.792A>T	c.(790-792)ggA>ggT	p.G264G	ALDH16A1_ENST00000540132.1_Silent_p.G101G|CTD-3148I10.9_ENST00000599536.1_5'Flank|ALDH16A1_ENST00000433981.2_Silent_p.G99G|ALDH16A1_ENST00000455361.2_Intron	NM_153329.3	NP_699160.2	Q8IZ83	A16A1_HUMAN	aldehyde dehydrogenase 16 family, member A1	264						extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor (GO:0016620)			cervix(2)|endometrium(3)|kidney(2)|large_intestine(3)|lung(5)|skin(2)|urinary_tract(3)	20		all_lung(116;5.39e-06)|Lung NSC(112;1.97e-05)|all_neural(266;0.0966)|Ovarian(192;0.15)		OV - Ovarian serous cystadenocarcinoma(262;0.00156)|GBM - Glioblastoma multiforme(486;0.0251)		GCCTGGCGGGAGAGTGTGCGG	0.731													c|||	1507	0.300919	0.1422	0.2061	5008	,	,		10303	0.2817		0.4165	False		,,,				2504	0.4836				p.G264G		Atlas-SNP	.											.	ALDH16A1	54	.	0			c.A792T						PASS	.	T	,	796,3562		89,618,1472	19.0	19.0	19.0		,792	-5.6	0.0	19	dbSNP_116	19	3356,5190		682,1992,1599	no	intron,coding-synonymous	ALDH16A1	NM_001145396.1,NM_153329.3	,	771,2610,3071	TT,TA,AA		39.2698,18.2653,32.1761	,	,264/803	49965173	4152,8752	2179	4273	6452	SO:0001819	synonymous_variant	126133	exon7			GGCGGGAGAGTGT	AY007096	CCDS12766.1, CCDS46141.1	19q13.33	2014-08-12			ENSG00000161618	ENSG00000161618		"""Aldehyde dehydrogenases"""	28114	protein-coding gene	gene with protein product		613358					Standard	NM_153329		Approved	MGC10204	uc002pnt.3	Q8IZ83	OTTHUMG00000183163	ENST00000293350.4:c.792A>T	19.37:g.49965173A>T		Somatic	20	0	0		WXS	Illumina HiSeq	Phase_I	39	19	0.487179	NM_153329	B4DLQ1|C9JBH6|Q86YF0|Q8IYL4|Q8TEI8	Silent	SNP	ENST00000293350.4	37	CCDS12766.1																																																																																			A|0.718;T|0.282	0.282	strong		0.731	ALDH16A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465358.1	NM_153329	
ACER3	55331	hgsc.bcm.edu	37	11	76637651	76637651	+	Missense_Mutation	SNP	G	G	A	rs4379869	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:76637651G>A	ENST00000532485.1	+	2	258	c.154G>A	c.(154-156)Gtt>Att	p.V52I	ACER3_ENST00000530182.1_3'UTR|ACER3_ENST00000526597.1_5'UTR|ACER3_ENST00000538157.1_Missense_Mutation_p.V10I|ACER3_ENST00000533873.1_Intron	NM_018367.5	NP_060837.3	Q9NUN7	ACER3_HUMAN	alkaline ceramidase 3	52				V -> I (in Ref. 1; AAK71923, 2; AAL56013, 3; BAG37496, 5; EAW75010 and 6; AAH73853). {ECO:0000305}.	ceramide metabolic process (GO:0006672)|phytosphingosine biosynthetic process (GO:0071602)|positive regulation of cell proliferation (GO:0008284)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|sphingosine biosynthetic process (GO:0046512)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of Golgi membrane (GO:0030173)	phytoceramidase activity (GO:0070774)			endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|prostate(1)	9						GTTCGGTGCAGTTCAGAGTGT	0.353													A|||	3153	0.629593	0.6437	0.5058	5008	,	,		16311	0.5903		0.7167	False		,,,				2504	0.6493				p.V52I		Atlas-SNP	.											ACER3,NS,carcinoma,0,1	ACER3	19	1	0			c.G154A						PASS	.	A	ILE/VAL	2835,1565	490.4+/-361.8	938,959,303	164.0	140.0	148.0		154	2.2	1.0	11	dbSNP_111	148	6318,2266	382.3+/-340.3	2332,1654,306	yes	missense	ACER3	NM_018367.5	29	3270,2613,609	AA,AG,GG		26.3979,35.5682,29.5055	benign	52/268	76637651	9153,3831	2200	4292	6492	SO:0001583	missense	55331	exon2			GGTGCAGTTCAGA	AF214454	CCDS8247.1, CCDS73352.1	11q13.5	2013-01-25	2008-12-19	2008-12-19	ENSG00000078124	ENSG00000078124	3.5.1.23	"""Alkaline ceramidase"""	16066	protein-coding gene	gene with protein product	"""alkaline phytoceramidase"""		"""phytoceramidase, alkaline"""	PHCA		11356846, 18619555	Standard	XM_005274090		Approved	FLJ11238, APHC	uc009yum.1	Q9NUN7	OTTHUMG00000165225	ENST00000532485.1:c.154G>A	11.37:g.76637651G>A	ENSP00000434480:p.Val52Ile	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	106	15	0.141509	NM_018367	B2RC99	Missense_Mutation	SNP	ENST00000532485.1	37	CCDS8247.1	1394	0.6382783882783882	316	0.6422764227642277	184	0.5082872928176796	349	0.6101398601398601	545	0.7189973614775725	A	4.399	0.073629	0.08485	0.644318	0.736021	ENSG00000078124	ENST00000534206;ENST00000532485;ENST00000538157;ENST00000530243	T;T;T	0.41065	1.01;1.01;1.01	5.76	2.15	0.27550	.	0.307034	0.34986	N	0.003539	T	0.00012	0.0000	N	0.00960	-1.095	0.09310	P	0.9999999999994427	B	0.02656	0.0	B	0.01281	0.0	T	0.30679	-0.9970	9	0.18276	T	0.48	-1.6041	5.1628	0.15070	0.6227:0.144:0.2333:0.0	rs4379869;rs57071617;rs4379869	52	Q9NUN7	ACER3_HUMAN	I	10;52;10;10	ENSP00000435733:V10I;ENSP00000434480:V52I;ENSP00000440916:V10I	ENSP00000278544:V52I	V	+	1	0	ACER3	76315299	1.000000	0.71417	0.998000	0.56505	0.951000	0.60555	1.020000	0.30027	0.103000	0.17682	-0.254000	0.11334	GTT	G|0.314;A|0.686	0.686	strong		0.353	ACER3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382770.2	NM_018367	
DPP6	1804	hgsc.bcm.edu	37	7	154667628	154667628	+	Silent	SNP	A	A	G	rs2293353	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:154667628A>G	ENST00000377770.3	+	20	2037	c.1896A>G	c.(1894-1896)ccA>ccG	p.P632P	DPP6_ENST00000332007.3_Silent_p.P570P|DPP6_ENST00000427557.1_Silent_p.P525P|DPP6_ENST00000404039.1_Silent_p.P568P			P42658	DPP6_HUMAN	dipeptidyl-peptidase 6	632					cell death (GO:0008219)|neuronal action potential (GO:0019228)|positive regulation of potassium ion transmembrane transport (GO:1901381)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	dipeptidyl-peptidase activity (GO:0008239)|serine-type peptidase activity (GO:0008236)			NS(3)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(4)|lung(35)|pancreas(4)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	71	all_neural(206;0.181)	all_hematologic(28;0.0044)|all_lung(21;0.0176)|Lung NSC(21;0.0204)	OV - Ovarian serous cystadenocarcinoma(82;0.0562)			ATGGCACCCCAGGCAGCCAGA	0.652													G|||	2941	0.58726	0.7685	0.5937	5008	,	,		16280	0.5625		0.5219	False		,,,				2504	0.4305				p.P632P	NSCLC(125;1384 1783 2490 7422 34254)	Atlas-SNP	.											.	DPP6	383	.	0			c.A1896G						PASS	.	G	,,	3019,1113		1107,805,154	24.0	29.0	27.0		1350,1269,1269	-9.8	0.4	7	dbSNP_100	27	4329,4039		1118,2093,973	no	coding-synonymous,coding-synonymous,coding-synonymous	DPP6	NM_001039350.1,NM_001936.3,NM_130797.2	,,	2225,2898,1127	GG,GA,AA		48.2672,26.9361,41.216	,,	450/684,423/657,423/657	154667628	7348,5152	2066	4184	6250	SO:0001819	synonymous_variant	1804	exon20			CACCCCAGGCAGC	M96859	CCDS75682.1, CCDS75683.1, CCDS75684.1	7q36.2	2006-08-07	2006-01-12		ENSG00000130226	ENSG00000130226			3010	protein-coding gene	gene with protein product		126141	"""dipeptidylpeptidase VI"", ""dipeptidylpeptidase 6"""			1729689	Standard	XM_006715871		Approved	DPPX	uc003wlk.3	P42658	OTTHUMG00000151511	ENST00000377770.3:c.1896A>G	7.37:g.154667628A>G		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	73	28	0.383562	NM_130797		Silent	SNP	ENST00000377770.3	37																																																																																				G|0.584;N|0.001	0.584	strong		0.652	DPP6-003	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000322932.1	NM_130797	
EIF4G1	1981	hgsc.bcm.edu	37	3	184049143	184049143	+	Silent	SNP	C	C	T	rs76779558	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:184049143C>T	ENST00000346169.2	+	29	4522	c.4251C>T	c.(4249-4251)gtC>gtT	p.V1417V	EIF4G1_ENST00000414031.1_Silent_p.V1377V|EIF4G1_ENST00000411531.1_Silent_p.V1378V|EIF4G1_ENST00000350481.5_Silent_p.V1253V|EIF4G1_ENST00000434061.2_Silent_p.V1222V|EIF2B5_ENST00000444495.1_Intron|EIF4G1_ENST00000435046.2_Silent_p.V1221V|EIF4G1_ENST00000441154.1_Silent_p.V1254V|EIF4G1_ENST00000424196.1_Silent_p.V1424V|EIF4G1_ENST00000392537.2_Silent_p.V1330V|EIF4G1_ENST00000427845.1_Silent_p.V1331V|EIF4G1_ENST00000352767.3_Silent_p.V1424V|EIF4G1_ENST00000382330.3_Silent_p.V1424V|EIF4G1_ENST00000342981.4_Silent_p.V1418V|EIF4G1_ENST00000319274.6_Silent_p.V1417V	NM_198241.2	NP_937884	Q04637	IF4G1_HUMAN	eukaryotic translation initiation factor 4 gamma, 1	1417					cell death (GO:0008219)|cellular protein metabolic process (GO:0044267)|cytokine-mediated signaling pathway (GO:0019221)|gene expression (GO:0010467)|insulin receptor signaling pathway (GO:0008286)|lung development (GO:0030324)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|regulation of translational initiation (GO:0006446)|response to ethanol (GO:0045471)|RNA metabolic process (GO:0016070)|translation (GO:0006412)|translational initiation (GO:0006413)|viral process (GO:0016032)	cytosol (GO:0005829)|eukaryotic translation initiation factor 4F complex (GO:0016281)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|translation factor activity, nucleic acid binding (GO:0008135)|translation initiation factor activity (GO:0003743)			central_nervous_system(1)|cervix(2)|endometrium(3)|kidney(5)|large_intestine(14)|lung(41)|ovary(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	75	all_cancers(143;1.06e-10)|Ovarian(172;0.0339)		Epithelial(37;1.53e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			GTGCATTCGTCGCTGAACAGG	0.517													C|||	71	0.0141773	0.0008	0.0086	5008	,	,		19913	0.0179		0.0159	False		,,,				2504	0.0307				p.V1424V		Atlas-SNP	.											.	EIF4G1	151	.	0			c.C4272T						PASS	.	C	,,,,,,	22,4384	29.9+/-59.1	0,22,2181	150.0	160.0	157.0		4272,4272,3666,4254,4251,3759,3990	-1.0	0.0	3	dbSNP_131	157	216,8384	92.1+/-154.2	1,214,4085	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	EIF4G1	NM_001194946.1,NM_001194947.1,NM_004953.4,NM_182917.4,NM_198241.2,NM_198242.2,NM_198244.2	,,,,,,	1,236,6266	TT,TC,CC		2.5116,0.4993,1.8299	,,,,,,	1424/1607,1424/1607,1222/1405,1418/1601,1417/1600,1253/1436,1330/1513	184049143	238,12768	2203	4300	6503	SO:0001819	synonymous_variant	1981	exon30			ATTCGTCGCTGAA	D12686	CCDS3259.1, CCDS3260.1, CCDS3261.1, CCDS46970.1, CCDS46970.2, CCDS54687.1, CCDS54688.1	3q27.1	2013-09-19			ENSG00000114867	ENSG00000114867		"""Parkinson disease"""	3296	protein-coding gene	gene with protein product		600495		EIF4G, EIF4F		1429670, 9372926, 21907011	Standard	NM_182917		Approved	p220, PARK18	uc010hxy.3	Q04637	OTTHUMG00000156784	ENST00000346169.2:c.4251C>T	3.37:g.184049143C>T		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	97	52	0.536082	NM_001194946	D3DNT2|D3DNT4|D3DNT5|E9PFM1|G5E9S1|O43177|O95066|Q5HYG0|Q6ZN21|Q8N102	Silent	SNP	ENST00000346169.2	37	CCDS3259.1																																																																																			C|0.983;T|0.017	0.017	strong		0.517	EIF4G1-007	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000345733.1	NM_182917	
TM6SF2	53345	hgsc.bcm.edu	37	19	19379549	19379549	+	Missense_Mutation	SNP	C	C	T	rs58542926	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:19379549C>T	ENST00000389363.4	-	6	571	c.499G>A	c.(499-501)Gag>Aag	p.E167K	AC138430.4_ENST00000586064.2_RNA|TM6SF2_ENST00000586107.1_5'UTR	NM_001001524.2	NP_001001524.2	Q9BZW4	TM6S2_HUMAN	transmembrane 6 superfamily member 2	167			E -> K (in dbSNP:rs58542926).			integral component of membrane (GO:0016021)				breast(2)|kidney(1)|large_intestine(1)|lung(8)|skin(1)|upper_aerodigestive_tract(1)	14			Epithelial(12;0.0151)			GGCCTGATCTCGGAGCTGTAT	0.577													C|||	334	0.0666933	0.0227	0.0634	5008	,	,		19607	0.0863		0.0676	False		,,,				2504	0.1074				p.E167K		Atlas-SNP	.											.	TM6SF2	39	.	0			c.G499A						PASS	.	C	LYS/GLU	126,3970		3,120,1925	76.0	79.0	78.0		499	5.0	1.0	19	dbSNP_129	78	599,7793		20,559,3617	yes	missense	TM6SF2	NM_001001524.2	56	23,679,5542	TT,TC,CC		7.1378,3.0762,5.8056	probably-damaging	167/378	19379549	725,11763	2048	4196	6244	SO:0001583	missense	53345	exon6			TGATCTCGGAGCT	AF255923	CCDS42528.1	19p13.3-p12	2008-02-05							11861	protein-coding gene	gene with protein product		606563				11124529	Standard	NM_001001524		Approved	Lpr4	uc002nmd.1	Q9BZW4		ENST00000389363.4:c.499G>A	19.37:g.19379549C>T	ENSP00000374014:p.Glu167Lys	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	76	29	0.381579	NM_001001524	Q0IJ64	Missense_Mutation	SNP	ENST00000389363.4	37	CCDS42528.1	139	0.06364468864468864	18	0.036585365853658534	26	0.0718232044198895	42	0.07342657342657342	53	0.06992084432717678	C	17.03	3.283643	0.59867	0.030762	0.071378	ENSG00000213996	ENST00000389363;ENST00000269990	T	0.41065	1.01	5.01	5.01	0.66863	.	0.000000	0.47093	U	0.000242	T	0.05364	0.0142	L	0.61036	1.89	0.24096	P	0.99589286	D	0.67145	0.996	P	0.47402	0.546	T	0.24621	-1.0155	9	0.18276	T	0.48	-13.7739	15.8064	0.78517	0.0:1.0:0.0:0.0	rs58542926	167	Q9BZW4	TM6S2_HUMAN	K	167	ENSP00000374014:E167K	ENSP00000269990:E167K	E	-	1	0	TM6SF2	19240549	0.981000	0.34729	0.999000	0.59377	0.657000	0.38888	2.542000	0.45744	2.340000	0.79590	0.650000	0.86243	GAG	C|0.939;T|0.061	0.061	strong		0.577	TM6SF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460122.2	NM_203510	
IQCA1	79781	hgsc.bcm.edu	37	2	237374309	237374309	+	Silent	SNP	C	C	T	rs35432941	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:237374309C>T	ENST00000409907.3	-	6	1039	c.765G>A	c.(763-765)caG>caA	p.Q255Q	IQCA1_ENST00000431676.2_Silent_p.Q255Q|IQCA1_ENST00000309507.5_Silent_p.Q251Q	NM_024726.4	NP_079002.3	Q86XH1	IQCA1_HUMAN	IQ motif containing with AAA domain 1	255							ATP binding (GO:0005524)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(12)|ovary(1)	26						CCTTTTCAGCCTGGATTACTG	0.428													C|||	372	0.0742812	0.0076	0.0764	5008	,	,		19184	0.001		0.1849	False		,,,				2504	0.1247				p.Q262Q		Atlas-SNP	.											.	IQCA1	170	.	0			c.G786A						PASS	.	C		140,3670		5,130,1770	105.0	93.0	97.0		765	-0.5	0.1	2	dbSNP_126	97	1735,6525		174,1387,2569	no	coding-synonymous	IQCA1	NM_024726.3		179,1517,4339	TT,TC,CC		21.0048,3.6745,15.5344		255/823	237374309	1875,10195	1905	4130	6035	SO:0001819	synonymous_variant	79781	exon6			TTCAGCCTGGATT	AK026180	CCDS46549.1, CCDS59441.1, CCDS74677.1	2q37.3	2014-07-18	2008-07-02	2008-07-02	ENSG00000132321	ENSG00000132321		"""ATPases / AAA-type"""	26195	protein-coding gene	gene with protein product	"""dynein regulatory complex subunit 11"""		"""IQ motif containing with AAA domain"""	IQCA		23427265	Standard	NM_024726		Approved	FLJ22527, DRC11	uc002vwb.3	Q86XH1	OTTHUMG00000153058	ENST00000409907.3:c.765G>A	2.37:g.237374309C>T		Somatic	200	0	0		WXS	Illumina HiSeq	Phase_I	141	65	0.460993	NM_001270585	B4DFH9|E7EWQ0|Q4G164|Q53R37|Q53RV3|Q96NS7|Q9H680	Silent	SNP	ENST00000409907.3	37	CCDS46549.1	177	0.08104395604395605	6	0.012195121951219513	26	0.0718232044198895	0	0.0	145	0.19129287598944592	C	0.806	-0.753650	0.03041	0.036745	0.210048	ENSG00000132321	ENST00000418802	.	.	.	5.37	-0.467	0.12150	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.50313	P	1.32000000000021E-4	.	.	.	.	.	.	T	0.29181	-1.0020	3	.	.	.	.	0.1116	0.00057	0.2791:0.2582:0.2037:0.259	rs35432941;rs62189792	.	.	.	S	274	.	.	G	-	1	0	IQCA1	237039048	0.928000	0.31464	0.108000	0.21378	0.302000	0.27658	0.225000	0.17757	-0.011000	0.14247	0.563000	0.77884	GGC	C|0.896;T|0.104	0.104	strong		0.428	IQCA1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000329266.1	NM_024726	
CERK	64781	hgsc.bcm.edu	37	22	47087670	47087670	+	Silent	SNP	G	G	A	rs36211083	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:47087670G>A	ENST00000216264.8	-	11	1243	c.1131C>T	c.(1129-1131)gaC>gaT	p.D377D	CERK_ENST00000541677.1_Silent_p.D179D|CERK_ENST00000471929.1_5'UTR	NM_022766.5	NP_073603.2	Q8TCT0	CERK1_HUMAN	ceramide kinase	377					ceramide metabolic process (GO:0006672)|glycosphingolipid metabolic process (GO:0006687)|lipid phosphorylation (GO:0046834)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ceramide kinase activity (GO:0001729)|diacylglycerol kinase activity (GO:0004143)|magnesium ion binding (GO:0000287)|NAD+ kinase activity (GO:0003951)			cervix(1)|endometrium(1)|large_intestine(2)|lung(11)|ovary(1)|prostate(2)|skin(2)	20		Breast(42;0.00571)|Ovarian(80;0.00965)|all_neural(38;0.0416)|Lung SC(80;0.164)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0182)|BRCA - Breast invasive adenocarcinoma(115;0.171)		ACTCCTCCACGTCCTCTGAAG	0.622													G|||	502	0.10024	0.1263	0.2003	5008	,	,		10930	0.001		0.1123	False		,,,				2504	0.0838				p.D377D		Atlas-SNP	.											.	CERK	40	.	0			c.C1131T						PASS	.	G		549,3857	244.0+/-253.5	36,477,1690	64.0	50.0	55.0		1131	-4.5	0.9	22	dbSNP_126	55	1033,7567	219.2+/-257.4	61,911,3328	no	coding-synonymous	CERK	NM_022766.5		97,1388,5018	AA,AG,GG		12.0116,12.4603,12.1636		377/538	47087670	1582,11424	2203	4300	6503	SO:0001819	synonymous_variant	64781	exon11			CTCCACGTCCTCT	AB079066	CCDS14077.1	22q13.31	2008-06-10			ENSG00000100422	ENSG00000100422			19256	protein-coding gene	gene with protein product		610307				11956206, 11258795	Standard	NM_022766		Approved	hCERK, FLJ23239, dA59H18.3, DKFZp434E0211, FLJ21430, KIAA1646, LK4, dA59H18.2	uc003bia.3	Q8TCT0	OTTHUMG00000150395	ENST00000216264.8:c.1131C>T	22.37:g.47087670G>A		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	106	45	0.424528	NM_022766	A0JNT4|A8K611|Q6NX59|Q9BYB3|Q9UGE5	Silent	SNP	ENST00000216264.8	37	CCDS14077.1																																																																																			G|0.888;A|0.112	0.112	strong		0.622	CERK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317924.2	NM_022766	
VIT	5212	hgsc.bcm.edu	37	2	36970364	36970364	+	Silent	SNP	A	A	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:36970364A>G	ENST00000389975.3	+	4	542	c.240A>G	c.(238-240)gcA>gcG	p.A80A	VIT_ENST00000457137.2_Silent_p.A80A|VIT_ENST00000401530.1_Silent_p.A80A|VIT_ENST00000404084.1_Silent_p.A58A|VIT_ENST00000497382.1_5'UTR|VIT_ENST00000379241.3_Silent_p.A80A|VIT_ENST00000379242.3_Silent_p.A80A	NM_001177969.1|NM_001177970.1	NP_001171440.1|NP_001171441.1	Q6UXI7	VITRN_HUMAN	vitrin	80	LCCL. {ECO:0000255|PROSITE- ProRule:PRU00123}.			A -> T (in Ref. 1; AAL18263). {ECO:0000305}.	extracellular matrix organization (GO:0030198)|positive regulation of cell-substrate adhesion (GO:0010811)	interstitial matrix (GO:0005614)	glycosaminoglycan binding (GO:0005539)			autonomic_ganglia(1)|breast(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	57		all_hematologic(82;0.248)				ACGTGTATGCATCCTACTCCA	0.493																																					p.A80A		Atlas-SNP	.											.	VIT	138	.	0			c.A240G						PASS	.						142.0	117.0	125.0					2																	36970364		2203	4300	6503	SO:0001819	synonymous_variant	5212	exon4			GTATGCATCCTAC	AF063833	CCDS33180.1, CCDS54347.1, CCDS54348.1, CCDS54349.1, CCDS54350.1	2p22.2	2008-05-15			ENSG00000205221	ENSG00000205221			12697	protein-coding gene	gene with protein product							Standard	NM_001177969		Approved		uc002rpl.3	Q6UXI7	OTTHUMG00000152149	ENST00000389975.3:c.240A>G	2.37:g.36970364A>G		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	98	45	0.459184	NM_001177969	A1A526|A6NKI9|A8K7Y4|E9PF47|Q6P7T3|Q96DM8|Q96DT1|Q9UDN0	Silent	SNP	ENST00000389975.3	37	CCDS54347.1																																																																																			.	.	none		0.493	VIT-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding			
USP31	57478	hgsc.bcm.edu	37	16	23080634	23080634	+	Missense_Mutation	SNP	C	C	A	rs10083789	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:23080634C>A	ENST00000219689.7	-	16	2791	c.2792G>T	c.(2791-2793)cGc>cTc	p.R931L	USP31_ENST00000567975.1_Missense_Mutation_p.R224L	NM_020718.3	NP_065769.3	Q86UV5	UBP48_HUMAN	ubiquitin specific peptidase 31	0	Ubiquitin-like. {ECO:0000255|PROSITE- ProRule:PRU00214}.				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)		GTGCTCACGGCGACTATGACT	0.547													C|||	729	0.145567	0.1157	0.1873	5008	,	,		18828	0.0546		0.3042	False		,,,				2504	0.0869				p.R931L		Atlas-SNP	.											.	USP31	122	.	0			c.G2792T						PASS	.	C	LEU/ARG	674,3720	286.3+/-278.7	54,566,1577	74.0	75.0	75.0		2792	5.1	0.2	16	dbSNP_119	75	2656,5944	427.5+/-355.6	416,1824,2060	yes	missense	USP31	NM_020718.3	102	470,2390,3637	AA,AC,CC		30.8837,15.3391,25.6272	probably-damaging	931/1353	23080634	3330,9664	2197	4300	6497	SO:0001583	missense	57478	exon16			TCACGGCGACTAT	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.2792G>T	16.37:g.23080634C>A	ENSP00000219689:p.Arg931Leu	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	83	29	0.349398	NM_020718	B7ZKS7|Q2M3I4|Q5SZI4|Q5T3T5|Q6NX53|Q8N3F6|Q96F64|Q96IQ3|Q9H5N3|Q9H5T7|Q9NUJ6|Q9NXR0	Missense_Mutation	SNP	ENST00000219689.7	37	CCDS10607.1	399	0.18269230769230768	61	0.12398373983739837	78	0.2154696132596685	32	0.055944055944055944	228	0.3007915567282322	C	15.34	2.805061	0.50315	0.153391	0.308837	ENSG00000103404	ENST00000219689;ENST00000381162	T	0.09723	2.95	6.02	5.07	0.68467	.	0.425160	0.19991	N	0.101577	T	0.00012	0.0000	L	0.50333	1.59	0.51233	P	8.799999999997699E-5	D;D	0.58268	0.977;0.982	P;P	0.52159	0.691;0.518	T	0.54443	-0.8293	9	0.22706	T	0.39	-6.8887	14.4891	0.67639	0.0:0.93:0.0:0.07	rs10083789;rs17345123;rs17796446;rs61275052;rs10083789	234;931	Q70CQ4-2;Q70CQ4	.;UBP31_HUMAN	L	931;234	ENSP00000219689:R931L	ENSP00000219689:R931L	R	-	2	0	USP31	22988135	0.918000	0.31147	0.173000	0.22940	0.975000	0.68041	1.836000	0.39191	1.557000	0.49525	0.650000	0.86243	CGC	C|0.785;A|0.215	0.215	strong		0.547	USP31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211607.1	NM_020718	
TMC4	147798	hgsc.bcm.edu	37	19	54665970	54665970	+	Silent	SNP	C	C	T	rs36655	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:54665970C>T	ENST00000376591.4	-	11	1703	c.1572G>A	c.(1570-1572)caG>caA	p.Q524Q	TMC4_ENST00000416963.1_Silent_p.Q106Q|LENG1_ENST00000222224.3_5'Flank|TMC4_ENST00000301187.4_Silent_p.Q518Q|TMC4_ENST00000476013.2_5'Flank	NM_001145303.1|NM_144686.2	NP_001138775|NP_653287.2	Q7Z404	TMC4_HUMAN	transmembrane channel-like 4	524					ion transport (GO:0006811)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				breast(2)|endometrium(7)|large_intestine(4)|lung(6)|pancreas(1)|skin(1)|urinary_tract(1)	22	all_cancers(19;0.0065)|all_epithelial(19;0.00348)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)					CCTGGAACTCCTGGGTCCCCG	0.687													C|||	1237	0.247005	0.1808	0.2464	5008	,	,		9717	0.1558		0.328	False		,,,				2504	0.3476				p.Q524Q		Atlas-SNP	.											.	TMC4	89	.	0			c.G1572A						PASS	.	C	,	898,3500		88,722,1389	28.0	30.0	29.0		1572,1554	4.7	1.0	19	dbSNP_76	29	2769,5831		434,1901,1965	no	coding-synonymous,coding-synonymous	TMC4	NM_001145303.1,NM_144686.2	,	522,2623,3354	TT,TC,CC		32.1977,20.4184,28.212	,	524/713,518/707	54665970	3667,9331	2199	4300	6499	SO:0001819	synonymous_variant	147798	exon11			GAACTCCTGGGTC	AY236492	CCDS12882.1, CCDS46174.1	19q13.42	2008-02-05			ENSG00000167608	ENSG00000167608			22998	protein-coding gene	gene with protein product						12812529, 12906855	Standard	XM_005277069		Approved		uc010erf.3	Q7Z404	OTTHUMG00000066485	ENST00000376591.4:c.1572G>A	19.37:g.54665970C>T		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	28	14	0.5	NM_001145303	Q7Z5M3|Q8N5E4|Q8TBS7	Silent	SNP	ENST00000376591.4	37	CCDS46174.1																																																																																			C|0.743;T|0.257	0.257	strong		0.687	TMC4-011	NOVEL	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000156164.2		
BIRC6	57448	hgsc.bcm.edu	37	2	32713706	32713706	+	Missense_Mutation	SNP	A	A	T	rs2366894	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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						PASS	.	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	309	1	0.00323625		WXS	Illumina HiSeq	Phase_I	208	208	1	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	
BCL11A	53335	hgsc.bcm.edu	37	2	60689522	60689522	+	Silent	SNP	G	G	A	rs61748090	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:60689522G>A	ENST00000335712.6	-	4	752	c.525C>T	c.(523-525)tgC>tgT	p.C175C	BCL11A_ENST00000359629.5_Silent_p.C175C|BCL11A_ENST00000477659.1_5'UTR|BCL11A_ENST00000358510.4_Silent_p.C141C|BCL11A_ENST00000538214.1_Silent_p.C141C|BCL11A_ENST00000537768.1_Silent_p.C23C|BCL11A_ENST00000356842.4_Silent_p.C175C	NM_022893.3	NP_075044.2	Q9H165	BC11A_HUMAN	B-cell CLL/lymphoma 11A (zinc finger protein)	175	Required for nuclear body formation and for SUMO1 recruitment. {ECO:0000250}.				B cell differentiation (GO:0030183)|negative regulation of axon extension (GO:0030517)|negative regulation of collateral sprouting (GO:0048671)|negative regulation of dendrite development (GO:2000171)|negative regulation of neuron projection development (GO:0010977)|negative regulation of protein homooligomerization (GO:0032463)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of collateral sprouting (GO:0048672)|positive regulation of neuron projection development (GO:0010976)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein sumoylation (GO:0016925)|regulation of dendrite development (GO:0050773)|T cell differentiation (GO:0030217)	cytoplasm (GO:0005737)|nuclear body (GO:0016604)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|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 negative regulation of transcription (GO:0001078)|transcription corepressor activity (GO:0003714)			NS(1)|breast(6)|central_nervous_system(6)|endometrium(4)|kidney(1)|large_intestine(8)|lung(25)|ovary(2)|pancreas(1)|prostate(2)|skin(3)	59			LUSC - Lung squamous cell carcinoma(5;9.29e-08)|Lung(5;1.34e-06)|Epithelial(17;0.0562)|all cancers(80;0.199)			ATGGCTGTTTGCAAGTTGTAC	0.448			T	IGH@	B-CLL								G|||	39	0.00778754	0.0015	0.0014	5008	,	,		19192	0.0		0.0348	False		,,,				2504	0.001				p.C175C		Atlas-SNP	.		Dom	yes		2	2p13	53335	B-cell CLL/lymphoma 11A		L	.	BCL11A	298	.	0			c.C525T						PASS	.	G	,,	31,4375	36.0+/-67.5	0,31,2172	83.0	84.0	84.0		525,525,525	5.0	1.0	2	dbSNP_129	84	219,8381	92.3+/-154.4	5,209,4086	no	coding-synonymous,coding-synonymous,coding-synonymous	BCL11A	NM_018014.3,NM_022893.3,NM_138559.1	,,	5,240,6258	AA,AG,GG		2.5465,0.7036,1.9222	,,	175/774,175/836,175/244	60689522	250,12756	2203	4300	6503	SO:0001819	synonymous_variant	53335	exon4			CTGTTTGCAAGTT	AJ404611	CCDS1861.1, CCDS1862.1, CCDS46295.1	2p16.1	2013-01-08	2002-05-08		ENSG00000119866	ENSG00000119866		"""Zinc fingers, C2H2-type"""	13221	protein-coding gene	gene with protein product		606557	"""ecotropic viral integration site 9"""	EVI9		11719382, 18245381	Standard	NM_018014		Approved	BCL11A-XL, BCL11A-L, BCL11A-S, CTIP1, HBFQTL5, ZNF856	uc002sae.1	Q9H165	OTTHUMG00000129420	ENST00000335712.6:c.525C>T	2.37:g.60689522G>A		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	208	165	0.793269	NM_018014	D6W5D7|Q86W14|Q8WU92|Q96JL6|Q9H163|Q9H164|Q9H3G9|Q9NWA7	Silent	SNP	ENST00000335712.6	37	CCDS1862.1																																																																																			G|0.982;A|0.018	0.018	strong		0.448	BCL11A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251579.2	NM_022893	
ADAMTS7	11173	hgsc.bcm.edu	37	15	79057989	79057989	+	Missense_Mutation	SNP	C	C	T	rs200769684		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	167	0	0		WXS	Illumina HiSeq	Phase_I	173	14	0.0809249	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	
SCAI	286205	hgsc.bcm.edu	37	9	127818276	127818276	+	Missense_Mutation	SNP	C	C	T	rs589292	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:127818276C>T	ENST00000336505.6	-	3	167	c.109G>A	c.(109-111)Gct>Act	p.A37T	SCAI_ENST00000373549.4_Missense_Mutation_p.A60T	NM_001144877.2	NP_001138349.1	Q8N9R8	SCAI_HUMAN	suppressor of cancer cell invasion	37	Necessary to inhibit MKL1-induced SRF transcriptional activity. {ECO:0000250}.		A -> T (in dbSNP:rs589292).		negative regulation of cell migration (GO:0030336)|negative regulation of Rho protein signal transduction (GO:0035024)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	transcription corepressor activity (GO:0003714)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(7)|large_intestine(4)|lung(8)|ovary(2)|pancreas(1)|prostate(5)|stomach(1)|urinary_tract(1)	35						TCTTTAAGAGCAAATTCAGTC	0.323													C|||	1160	0.231629	0.1339	0.2133	5008	,	,		16982	0.3065		0.3101	False		,,,				2504	0.2188				p.A60T		Atlas-SNP	.											.	SCAI	84	.	0			c.G178A						PASS	.	C	THR/ALA,THR/ALA	561,3071		47,467,1302	67.0	60.0	62.0		109,178	3.4	1.0	9	dbSNP_83	62	2493,5657		402,1689,1984	yes	missense,missense	SCAI	NM_001144877.2,NM_173690.4	58,58	449,2156,3286	TT,TC,CC		30.589,15.446,25.9209	possibly-damaging,possibly-damaging	37/607,60/630	127818276	3054,8728	1816	4075	5891	SO:0001583	missense	286205	exon4			TAAGAGCAAATTC	AK093983	CCDS43877.1, CCDS48017.1	9q34.11	2009-11-06	2009-07-09	2009-07-09	ENSG00000173611	ENSG00000173611			26709	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 126"""	C9orf126			Standard	NM_173690		Approved	FLJ36664, NET40	uc004bpd.3	Q8N9R8	OTTHUMG00000020667	ENST00000336505.6:c.109G>A	9.37:g.127818276C>T	ENSP00000336756:p.Ala37Thr	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	79	36	0.455696	NM_173690	Q3SXZ1|Q3SXZ2|Q5T163|Q8N1I4	Missense_Mutation	SNP	ENST00000336505.6	37	CCDS48017.1	545	0.24954212454212454	70	0.14227642276422764	84	0.23204419889502761	176	0.3076923076923077	215	0.2836411609498681	C	15.91	2.971661	0.53614	0.15446	0.30589	ENSG00000173611	ENST00000336505;ENST00000373549	T;T	0.47177	0.86;0.85	5.33	3.38	0.38709	.	0.147846	0.31784	N	0.007061	T	0.00012	0.0000	N	0.08118	0	0.43351	P	0.004585999999999979	B;B	0.27732	0.067;0.187	B;B	0.27715	0.025;0.082	T	0.31558	-0.9939	9	0.09084	T	0.74	-7.1051	9.353	0.38149	0.0:0.7741:0.1451:0.0808	rs589292;rs52797510;rs58484754;rs589292	37;60	Q8N9R8;Q8N9R8-2	SCAI_HUMAN;.	T	37;60	ENSP00000336756:A37T;ENSP00000362650:A60T	ENSP00000336756:A37T	A	-	1	0	SCAI	126858097	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	1.092000	0.30927	1.219000	0.43474	0.655000	0.94253	GCT	C|0.748;T|0.252	0.252	strong		0.323	SCAI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054055.3	NM_173690	
ALMS1	7840	hgsc.bcm.edu	37	2	73679866	73679866	+	Missense_Mutation	SNP	T	T	C	rs10496192	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:73679866T>C	ENST00000264448.6	+	8	6320	c.6209T>C	c.(6208-6210)aTt>aCt	p.I2070T	ALMS1_ENST00000377715.1_Missense_Mutation_p.I2070T|ALMS1_ENST00000409009.1_Missense_Mutation_p.I2028T	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	2070	34 X 47 AA approximate tandem repeat.				endosomal transport (GO:0016197)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of stress fiber assembly (GO:0051492)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)				breast(4)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(31)|lung(68)|ovary(4)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	147						AGTAAAGGTATTCTAAAGATT	0.358													T|||	519	0.103634	0.0787	0.1772	5008	,	,		21501	0.004		0.161	False		,,,				2504	0.1288				p.I2070T		Atlas-SNP	.											.	ALMS1	384	.	0			c.T6209C						PASS	.	T	THR/ILE	292,3342		13,266,1538	49.0	49.0	49.0		6209	-5.1	0.0	2	dbSNP_119	49	1356,6750		100,1156,2797	yes	missense	ALMS1	NM_015120.4	89	113,1422,4335	CC,CT,TT		16.7283,8.0352,14.0375	benign	2070/4168	73679866	1648,10092	1817	4053	5870	SO:0001583	missense	7840	exon8			AAGGTATTCTAAA	AB002326	CCDS42697.1	2p13.1	2014-09-17			ENSG00000116127	ENSG00000116127			428	protein-coding gene	gene with protein product		606844				9063741	Standard	NM_015120		Approved	KIAA0328	uc002sje.1	Q8TCU4	OTTHUMG00000152812	ENST00000264448.6:c.6209T>C	2.37:g.73679866T>C	ENSP00000264448:p.Ile2070Thr	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	108	108	1	NM_015120	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Missense_Mutation	SNP	ENST00000264448.6	37	CCDS42697.1	227	0.10393772893772894	40	0.08130081300813008	59	0.16298342541436464	4	0.006993006993006993	124	0.16358839050131926	T	0.001	-3.029968	0.00041	0.080352	0.167283	ENSG00000116127	ENST00000409009;ENST00000264448;ENST00000377715	T;T;T	0.19532	2.99;2.99;2.14	4.38	-5.09	0.02920	.	0.621363	0.14407	N	0.321532	T	0.00039	0.0001	L	0.39898	1.24	0.80722	P	0.0	B;B;B	0.20261	0.019;0.043;0.034	B;B;B	0.20184	0.013;0.028;0.013	T	0.28554	-1.0040	9	0.34782	T	0.22	.	2.7425	0.05257	0.145:0.4915:0.1234:0.2402	rs10496192;rs17349559;rs52826651;rs10496192	2070;2028;2070	Q8TCU4-3;B8ZZJ3;Q8TCU4	.;.;ALMS1_HUMAN	T	2028;2070;2070	ENSP00000386627:I2028T;ENSP00000264448:I2070T;ENSP00000366944:I2070T	ENSP00000264448:I2070T	I	+	2	0	ALMS1	73533374	0.324000	0.24652	0.000000	0.03702	0.023000	0.10783	-0.190000	0.09615	-0.965000	0.03591	-0.299000	0.09455	ATT	T|0.882;C|0.118	0.118	strong		0.358	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120	
WDR88	126248	hgsc.bcm.edu	37	19	33655144	33655144	+	Silent	SNP	C	C	T	rs1981827	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:33655144C>T	ENST00000355868.3	+	9	1198	c.1122C>T	c.(1120-1122)aaC>aaT	p.N374N	WDR88_ENST00000361680.2_Silent_p.N374N	NM_173479.3	NP_775750.3	Q6ZMY6	WDR88_HUMAN	WD repeat domain 88	374										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)					TTAGCAACAACAAGAAATGGA	0.383													C|||	882	0.176118	0.115	0.1239	5008	,	,		21226	0.1607		0.1282	False		,,,				2504	0.3609				p.N374N		Atlas-SNP	.											.	WDR88	50	.	0			c.C1122T						PASS	.	C		505,3901	234.2+/-247.1	31,443,1729	158.0	147.0	151.0		1122	4.1	0.9	19	dbSNP_92	151	961,7639	210.0+/-251.0	39,883,3378	no	coding-synonymous	WDR88	NM_173479.3		70,1326,5107	TT,TC,CC		11.1744,11.4616,11.2717		374/473	33655144	1466,11540	2203	4300	6503	SO:0001819	synonymous_variant	126248	exon9			CAACAACAAGAAA	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.1122C>T	19.37:g.33655144C>T		Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	122	51	0.418033	NM_173479	Q8NEF8	Silent	SNP	ENST00000355868.3	37	CCDS12429.1																																																																																			C|0.874;T|0.126	0.126	strong		0.383	WDR88-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450840.1	NM_173479	
PRDM9	56979	hgsc.bcm.edu	37	5	23527472	23527472	+	Missense_Mutation	SNP	G	G	A	rs112666693		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:23527472G>A	ENST00000296682.3	+	11	2457	c.2275G>A	c.(2275-2277)Gat>Aat	p.D759N		NM_020227.2	NP_064612.2	Q9NQV7	PRDM9_HUMAN	PR domain containing 9	759					meiotic gene conversion (GO:0006311)|positive regulation of meiosis I (GO:0060903)|positive regulation of reciprocal meiotic recombination (GO:0010845)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)	histone methyltransferase activity (H3-K4 specific) (GO:0042800)|metal ion binding (GO:0046872)|recombination hotspot binding (GO:0010844)|sequence-specific DNA binding (GO:0043565)	p.D759N(1)		NS(1)|breast(1)|central_nervous_system(3)|endometrium(15)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(27)|lung(87)|ovary(6)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(11)	172						GGGCTTTCGCGATAAGTCACA	0.572										HNSCC(3;0.000094)																											p.D759N		Atlas-SNP	.											PRDM9,NS,carcinoma,0,2	PRDM9	344	2	1	Substitution - Missense(1)	kidney(1)	c.G2275A						scavenged	.						63.0	89.0	81.0					5																	23527472		2132	4296	6428	SO:0001583	missense	56979	exon11			TTTCGCGATAAGT	AF275816	CCDS43307.1	5p14.2	2014-06-03			ENSG00000164256	ENSG00000164256		"""-"", ""Zinc fingers, C2H2-type"""	13994	protein-coding gene	gene with protein product	"""PR-domain containing protein 9"""	609760	"""minisatellite binding protein 3, 115kDa"", ""minisatellite binding protein 3 (115kD)"""	MSBP3		10668202, 2062643, 24634223	Standard	NM_020227		Approved	PFM6, ZNF899	uc003jgo.3	Q9NQV7	OTTHUMG00000161918	ENST00000296682.3:c.2275G>A	5.37:g.23527472G>A	ENSP00000296682:p.Asp759Asn	Somatic	86	1	0.0116279		WXS	Illumina HiSeq	Phase_I	69	11	0.15942	NM_020227	B4DX22|Q27Q50	Missense_Mutation	SNP	ENST00000296682.3	37	CCDS43307.1	.	.	.	.	.	.	.	.	.	.	G	0.007	-1.937166	0.00484	.	.	ENSG00000164256	ENST00000296682	T	0.35605	1.3	2.65	-1.92	0.07618	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.11324	0.0276	N	0.02275	-0.615	0.09310	N	1	P	0.35155	0.487	B	0.13407	0.009	T	0.13764	-1.0497	9	0.37606	T	0.19	.	9.3631	0.38208	0.0:0.3794:0.5202:0.1004	.	759	Q9NQV7	PRDM9_HUMAN	N	759	ENSP00000296682:D759N	ENSP00000296682:D759N	D	+	1	0	PRDM9	23563229	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-14.321000	0.00000	-0.886000	0.03966	-4.161000	0.00010	GAT	G|0.500;A|0.500	0.500	weak		0.572	PRDM9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366375.1	NM_020227	
NAT2	10	hgsc.bcm.edu	37	8	18258316	18258316	+	Missense_Mutation	SNP	G	G	A	rs1208	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	50	0	0		WXS	Illumina HiSeq	Phase_I	43	9	0.209302	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	
MYO3B	140469	hgsc.bcm.edu	37	2	171225841	171225841	+	Missense_Mutation	SNP	A	A	G	rs4668246	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:171225841A>G	ENST00000408978.4	+	9	1068	c.925A>G	c.(925-927)Aag>Gag	p.K309E	MYO3B_ENST00000602629.1_3'UTR|MYO3B_ENST00000409044.3_Missense_Mutation_p.K309E|MYO3B_ENST00000334231.6_Missense_Mutation_p.K318E	NM_138995.4	NP_620482.3	Q8WXR4	MYO3B_HUMAN	myosin IIIB	309			K -> E (in dbSNP:rs4668246). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:17344846}.		peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of filopodium assembly (GO:0051491)|protein autophosphorylation (GO:0046777)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|stereocilium bundle tip (GO:0032426)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(25)|ovary(6)|pancreas(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	59						ACAGCTGGCCAAGGTTCTCCA	0.408													A|||	1515	0.302516	0.0756	0.4164	5008	,	,		17794	0.4216		0.4056	False		,,,				2504	0.2996				p.K309E		Atlas-SNP	.											.	MYO3B	320	.	0			c.A925G						PASS	.	A	GLU/LYS,GLU/LYS,GLU/LYS	407,3271		18,371,1450	122.0	106.0	111.0		925,925,925	3.7	1.0	2	dbSNP_111	111	3244,4966		621,2002,1482	yes	missense,missense,missense	MYO3B	NM_001083615.2,NM_001171642.1,NM_138995.3	56,56,56	639,2373,2932	GG,GA,AA		39.5128,11.0658,30.7116	benign,benign,benign	309/1315,309/1276,309/1342	171225841	3651,8237	1839	4105	5944	SO:0001583	missense	140469	exon9			CTGGCCAAGGTTC		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.925A>G	2.37:g.171225841A>G	ENSP00000386213:p.Lys309Glu	Somatic	219	0	0		WXS	Illumina HiSeq	Phase_I	194	75	0.386598	NM_001083615	B8ZZR2|Q53QE1|Q53T08|Q8IX64|Q8IX65|Q8IX66|Q8IX67|Q8IX68|Q96N94	Missense_Mutation	SNP	ENST00000408978.4	37	CCDS42773.1	703|703	0.3218864468864469|0.3218864468864469	49|49	0.09959349593495935|0.09959349593495935	127|127	0.35082872928176795|0.35082872928176795	221|221	0.38636363636363635|0.38636363636363635	306|306	0.40369393139841686|0.40369393139841686	A|A	4.671|4.671	0.124723|0.124723	0.08931|0.08931	0.110658|0.110658	0.395128|0.395128	ENSG00000071909|ENSG00000071909	ENST00000409044;ENST00000408978;ENST00000317915;ENST00000484338;ENST00000334231|ENST00000442690	T;T;T;T|.	0.77489|.	-1.09;-1.1;-1.09;-1.1|.	6.06|6.06	3.72|3.72	0.42706|0.42706	Protein kinase-like domain (1);|.	0.514386|.	0.24072|.	N|.	0.041812|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.12569|0.12569	0.235|0.235	0.38797|0.38797	P|P	0.04488800000000004|0.04488800000000004	B;B;B;B|.	0.06786|.	0.001;0.0;0.001;0.0|.	B;B;B;B|.	0.08055|.	0.003;0.001;0.002;0.001|.	T|T	0.47649|0.47649	-0.9101|-0.9101	9|4	0.02654|.	T|.	1|.	.|.	7.3084|7.3084	0.26461|0.26461	0.7512:0.0:0.2488:0.0|0.7512:0.0:0.2488:0.0	rs4668246;rs17497378;rs52830177;rs57795564;rs4668246|rs4668246;rs17497378;rs52830177;rs57795564;rs4668246	309;309;309;309|.	Q8WXR4-5;B7ZM71;Q8WXR4-4;Q8WXR4|.	.;.;.;MYO3B_HUMAN|.	E|R	309;309;308;318;318|308	ENSP00000386497:K309E;ENSP00000386213:K309E;ENSP00000446237:K318E;ENSP00000335100:K318E|.	ENSP00000314213:K308E|.	K|Q	+|+	1|2	0|0	MYO3B|MYO3B	170934087|170934087	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.989000|0.989000	0.77384|0.77384	2.472000|2.472000	0.45136|0.45136	1.104000|1.104000	0.41587|0.41587	0.528000|0.528000	0.53228|0.53228	AAG|CAA	A|0.686;G|0.314	0.314	strong		0.408	MYO3B-004	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333410.1		
TH	7054	hgsc.bcm.edu	37	11	2190982	2190982	+	Silent	SNP	A	A	G	rs7950050	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:2190982A>G	ENST00000381178.1	-	3	321	c.303T>C	c.(301-303)gcT>gcC	p.A101A	TH_ENST00000352909.3_Silent_p.A70A|TH_ENST00000333684.5_Silent_p.A74A|TH_ENST00000381175.1_Silent_p.A97A	NM_199292.2	NP_954986.2	P07101	TY3H_HUMAN	tyrosine hydroxylase	101					anatomical structure morphogenesis (GO:0009653)|catecholamine biosynthetic process (GO:0042423)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to drug (GO:0035690)|cellular response to glucose stimulus (GO:0071333)|cellular response to growth factor stimulus (GO:0071363)|cellular response to manganese ion (GO:0071287)|cellular response to nicotine (GO:0071316)|cerebral cortex development (GO:0021987)|circadian sleep/wake cycle (GO:0042745)|dopamine biosynthetic process (GO:0042416)|dopamine biosynthetic process from tyrosine (GO:0006585)|eating behavior (GO:0042755)|embryonic camera-type eye morphogenesis (GO:0048596)|epinephrine biosynthetic process (GO:0042418)|eye photoreceptor cell development (GO:0042462)|fatty acid metabolic process (GO:0006631)|glycoside metabolic process (GO:0016137)|heart development (GO:0007507)|heart morphogenesis (GO:0003007)|isoquinoline alkaloid metabolic process (GO:0033076)|learning (GO:0007612)|locomotory behavior (GO:0007626)|mating behavior (GO:0007617)|memory (GO:0007613)|multicellular organismal aging (GO:0010259)|neurotransmitter biosynthetic process (GO:0042136)|norepinephrine biosynthetic process (GO:0042421)|organ morphogenesis (GO:0009887)|phthalate metabolic process (GO:0018963)|phytoalexin metabolic process (GO:0052314)|pigmentation (GO:0043473)|regulation of heart contraction (GO:0008016)|response to activity (GO:0014823)|response to amphetamine (GO:0001975)|response to corticosterone (GO:0051412)|response to electrical stimulus (GO:0051602)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to ether (GO:0045472)|response to herbicide (GO:0009635)|response to hypoxia (GO:0001666)|response to light stimulus (GO:0009416)|response to lipopolysaccharide (GO:0032496)|response to nutrient levels (GO:0031667)|response to peptide hormone (GO:0043434)|response to pyrethroid (GO:0046684)|response to salt stress (GO:0009651)|response to water deprivation (GO:0009414)|response to zinc ion (GO:0010043)|sensory perception of sound (GO:0007605)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|sphingolipid metabolic process (GO:0006665)|synaptic transmission, dopaminergic (GO:0001963)|synaptic vesicle amine transport (GO:0015842)|terpene metabolic process (GO:0042214)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendrite (GO:0030425)|melanosome membrane (GO:0033162)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|nucleus (GO:0005634)|perikaryon (GO:0043204)|smooth endoplasmic reticulum (GO:0005790)|synaptic vesicle (GO:0008021)|terminal bouton (GO:0043195)	amino acid binding (GO:0016597)|dopamine binding (GO:0035240)|enzyme binding (GO:0019899)|ferric iron binding (GO:0008199)|ferrous iron binding (GO:0008198)|oxygen binding (GO:0019825)|tetrahydrobiopterin binding (GO:0034617)|tyrosine 3-monooxygenase activity (GO:0004511)			NS(1)|endometrium(1)|large_intestine(1)|lung(7)|skin(1)	11		all_epithelial(84;1.46e-23)|Lung NSC(207;4.44e-11)|all_lung(207;1.11e-09)|Ovarian(85;1.78e-06)|Breast(177;1.78e-05)|Medulloblastoma(188;0.0208)|all_neural(188;0.0416)	Colorectal(5;0.00245)|COAD - Colon adenocarcinoma(6;0.0239)	BRCA - Breast invasive adenocarcinoma(625;8.45e-09)|Lung(200;0.000152)|LUSC - Lung squamous cell carcinoma(625;0.00154)	L-Phenylalanine(DB00120)|L-Tyrosine(DB00135)|Metyrosine(DB00765)|Tetrahydrobiopterin(DB00360)	CAAAGGCCACAGCCTCCAGGG	0.697													G|||	168	0.0335463	0.1233	0.0058	5008	,	,		14629	0.0		0.001	False		,,,				2504	0.0				p.A101A		Atlas-SNP	.											.	TH	43	.	0			c.T303C						PASS	.	G	,,	522,3882	744.0+/-411.5	23,476,1703	32.0	34.0	34.0		210,303,291	-1.3	0.1	11	dbSNP_116	34	13,8583	796.2+/-407.5	0,13,4285	no	coding-synonymous,coding-synonymous,coding-synonymous	TH	NM_000360.3,NM_199292.2,NM_199293.2	,,	23,489,5988	GG,GA,AA		0.1512,11.8529,4.1154	,,	70/498,101/529,97/525	2190982	535,12465	2202	4298	6500	SO:0001819	synonymous_variant	7054	exon3			GGCCACAGCCTCC	X05290	CCDS7730.1, CCDS7731.1, CCDS31338.1	11p15.5	2013-06-03			ENSG00000180176	ENSG00000180176	1.14.16.2		11782	protein-coding gene	gene with protein product	"""tyrosine 3-monooxygenase"""	191290					Standard	NM_199292		Approved	DYT5b	uc001lvq.3	P07101	OTTHUMG00000009559	ENST00000381178.1:c.303T>C	11.37:g.2190982A>G		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	143	116	0.811189	NM_199292	B7ZL70|B7ZL73|Q0PWM2|Q0PWM3|Q15585|Q15588|Q15589|Q2M3B4	Silent	SNP	ENST00000381178.1	37	CCDS7731.1																																																																																			A|0.952;G|0.048	0.048	strong		0.697	TH-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000026597.1	NM_000360	
TRPA1	8989	hgsc.bcm.edu	37	8	72966002	72966002	+	Silent	SNP	G	G	A	rs3735943	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:72966002G>A	ENST00000262209.4	-	13	1837	c.1630C>T	c.(1630-1632)Ctg>Ttg	p.L544L	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	544					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)	TCTTCATCCAGGCGATCTGTG	0.468													G|||	2907	0.580471	0.5091	0.6671	5008	,	,		18636	0.6905		0.4791	False		,,,				2504	0.6063				p.L544L		Atlas-SNP	.											.	TRPA1	256	.	0			c.C1630T						PASS	.	G		2248,2158	591.8+/-387.6	588,1072,543	82.0	68.0	73.0		1630	3.2	0.2	8	dbSNP_107	73	4234,4366	569.4+/-389.2	1053,2128,1119	no	coding-synonymous	TRPA1	NM_007332.2		1641,3200,1662	AA,AG,GG		49.2326,48.9787,49.8385		544/1120	72966002	6482,6524	2203	4300	6503	SO:0001819	synonymous_variant	8989	exon13			CATCCAGGCGATC	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.1630C>T	8.37:g.72966002G>A		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	96	70	0.729167	NM_007332	A6NIN6	Silent	SNP	ENST00000262209.4	37	CCDS34908.1																																																																																			G|0.483;A|0.517	0.517	strong		0.468	TRPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379079.2	NM_007332	
OR10H3	26532	hgsc.bcm.edu	37	19	15852363	15852363	+	Missense_Mutation	SNP	G	G	A	rs11670007	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:15852363G>A	ENST00000305892.1	+	1	161	c.161G>A	c.(160-162)cGc>cAc	p.R54H		NM_013938.1	NP_039226.1	O60404	O10H3_HUMAN	olfactory receptor, family 10, subfamily H, member 3	54			R -> H (in dbSNP:rs11670007).			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)|kidney(2)|large_intestine(1)|liver(1)|lung(6)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	17						TGGATTGAACGCAGACTCCAC	0.527													g|||	1308	0.261182	0.4319	0.2752	5008	,	,		23202	0.0119		0.3131	False		,,,				2504	0.2239				p.R54H		Atlas-SNP	.											OR10H3,caecum,carcinoma,+1,2	OR10H3	53	2	0			c.G161A						scavenged	.	G	HIS/ARG	1796,2610		372,1052,779	413.0	362.0	379.0		161	-4.7	0.2	19	dbSNP_120	379	2472,6128		379,1714,2207	yes	missense	OR10H3	NM_013938.1	29	751,2766,2986	AA,AG,GG		28.7442,40.7626,32.8156	benign	54/317	15852363	4268,8738	2203	4300	6503	SO:0001583	missense	26532	exon1			TTGAACGCAGACT		CCDS12334.1	19p13.1	2012-08-09				ENSG00000171936		"""GPCR / Class A : Olfactory receptors"""	8174	protein-coding gene	gene with protein product							Standard	NM_013938		Approved		uc010xoq.2	O60404		ENST00000305892.1:c.161G>A	19.37:g.15852363G>A	ENSP00000307130:p.Arg54His	Somatic	208	1	0.00480769		WXS	Illumina HiSeq	Phase_I	156	67	0.429487	NM_013938	Q2HIZ3|Q6IFQ0	Missense_Mutation	SNP	ENST00000305892.1	37	CCDS12334.1	563	0.25778388278388276	198	0.4024390243902439	115	0.31767955801104975	11	0.019230769230769232	239	0.3153034300791557	.	0.009	-1.816832	0.00595	0.407626	0.287442	ENSG00000171936	ENST00000305892	T	0.01084	5.36	2.35	-4.7	0.03288	GPCR, rhodopsin-like superfamily (1);	0.910830	0.09011	N	0.861532	T	0.00012	0.0000	N	0.04820	-0.15	0.80722	P	0.0	B	0.06786	0.001	B	0.06405	0.002	T	0.27468	-1.0073	9	0.10636	T	0.68	.	6.0643	0.19854	0.213:0.265:0.522:0.0	rs11670007;rs52827169;rs61232867;rs11670007	54	O60404	O10H3_HUMAN	H	54	ENSP00000307130:R54H	ENSP00000307130:R54H	R	+	2	0	OR10H3	15713363	0.000000	0.05858	0.225000	0.23894	0.114000	0.19823	-2.725000	0.00808	-0.961000	0.03609	-1.125000	0.01998	CGC	G|0.700;A|0.300	0.300	strong		0.527	OR10H3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460918.1		
ITGAM	3684	hgsc.bcm.edu	37	16	31276811	31276811	+	Missense_Mutation	SNP	G	G	A	rs1143679	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:31276811G>A	ENST00000287497.8	+	3	305	c.230G>A	c.(229-231)cGc>cAc	p.R77H	RNU7-199P_ENST00000517067.1_RNA|ITGAM_ENST00000544665.3_Missense_Mutation_p.R77H			P11215	ITAM_HUMAN	integrin, alpha M (complement component 3 receptor 3 subunit)	77			R -> H (influences susceptibility to SLE; dbSNP:rs1143679). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:18204448}.		activated T cell proliferation (GO:0050798)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cellular extravasation (GO:0045123)|ectodermal cell differentiation (GO:0010668)|extracellular matrix organization (GO:0030198)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|leukocyte migration involved in inflammatory response (GO:0002523)|microglia development (GO:0014005)|neutrophil chemotaxis (GO:0030593)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integrin complex (GO:0008305)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	glycoprotein binding (GO:0001948)|heparin binding (GO:0008201)|metal ion binding (GO:0046872)			endometrium(7)|kidney(1)|large_intestine(10)|lung(32)|ovary(1)|prostate(4)|skin(1)	56						GAGCCCATCCGCCTGCAGGGT	0.632													G|||	426	0.0850639	0.1203	0.0893	5008	,	,		15680	0.0149		0.1312	False		,,,				2504	0.0593				p.R77H		Atlas-SNP	.											.	ITGAM	137	.	0			c.G230A	GRCh37	CM080418	ITGAM	M	rs1143679	PASS	.	G	HIS/ARG,HIS/ARG	375,3739		20,335,1702	12.0	14.0	13.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	230,230	-9.3	0.0	16	dbSNP_86	13	958,7490		66,826,3332	yes	missense,missense	ITGAM	NM_000632.3,NM_001145808.1	29,29	86,1161,5034	AA,AG,GG		11.34,9.1152,10.6114	possibly-damaging,possibly-damaging	77/1153,77/1154	31276811	1333,11229	2057	4224	6281	SO:0001583	missense	3684	exon3			CCATCCGCCTGCA	J03925	CCDS45470.1, CCDS54004.1	16p11.2	2010-03-23	2006-02-10			ENSG00000169896		"""CD molecules"", ""Complement system"", ""Integrins"""	6149	protein-coding gene	gene with protein product		120980	"""integrin, alpha M (complement component receptor 3, alpha; also known as CD11b (p170), macrophage antigen alpha polypeptide)"""	CR3A, CD11B			Standard	NM_001145808		Approved	MAC-1, CD11b	uc002ebr.3	P11215		ENST00000287497.8:c.230G>A	16.37:g.31276811G>A	ENSP00000287497:p.Arg77His	Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	178	99	0.55618	NM_000632	Q4VAK0|Q4VAK1|Q4VAK2	Missense_Mutation	SNP	ENST00000287497.8	37	CCDS45470.1	192	0.08791208791208792	59	0.11991869918699187	31	0.0856353591160221	1	0.0017482517482517483	101	0.13324538258575197	G	11.69	1.714788	0.30413	0.091152	0.1134	ENSG00000169896	ENST00000544665;ENST00000287497	T;T	0.72615	-0.67;-0.67	5.03	-9.33	0.00639	.	.	.	.	.	T	0.00580	0.0019	N	0.24115	0.695	0.09310	N	1	B	0.09022	0.002	B	0.06405	0.002	T	0.06162	-1.0842	9	0.41790	T	0.15	.	6.0249	0.19650	0.2214:0.5921:0.1048:0.0817	rs1143679;rs17362505	77	P11215	ITAM_HUMAN	H	77	ENSP00000441691:R77H;ENSP00000287497:R77H	ENSP00000287497:R77H	R	+	2	0	ITGAM	31184312	0.000000	0.05858	0.018000	0.16275	0.894000	0.52154	-1.319000	0.02702	-2.349000	0.00618	-0.140000	0.14226	CGC	G|0.914;A|0.086	0.086	strong		0.632	ITGAM-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000432816.1	NM_000632	
CD163L1	283316	hgsc.bcm.edu	37	12	7528471	7528471	+	Silent	SNP	G	G	A	rs7306824	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:7528471G>A	ENST00000313599.3	-	10	2568	c.2511C>T	c.(2509-2511)aaC>aaT	p.N837N	CD163L1_ENST00000416109.2_Silent_p.N847N|CD163L1_ENST00000544331.1_5'UTR|CD163L1_ENST00000396630.1_Silent_p.N837N			Q9NR16	C163B_HUMAN	CD163 molecule-like 1	837	SRCR 8. {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						CATCTCCACAGTTTAATTCTC	0.468													A|||	2323	0.463858	0.6331	0.4841	5008	,	,		-128	0.4752		0.2714	False		,,,				2504	0.407				p.N837N		Atlas-SNP	.											CD163L1,colon,carcinoma,0,2	CD163L1	238	2	0			c.C2511T						PASS	.	A		2474,1932	549.1+/-377.7	698,1078,427	99.0	99.0	99.0		2511	-5.5	0.0	12	dbSNP_116	99	2144,6456	714.9+/-406.0	281,1582,2437	no	coding-synonymous	CD163L1	NM_174941.4		979,2660,2864	AA,AG,GG		24.9302,43.8493,35.5067		837/1454	7528471	4618,8388	2203	4300	6503	SO:0001819	synonymous_variant	283316	exon10			TCCACAGTTTAAT	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.2511C>T	12.37:g.7528471G>A		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	75	37	0.493333	NM_174941	B4E0G7|C9JHR7|E7EVK4|Q2M3B7|Q6UWC2	Silent	SNP	ENST00000313599.3	37	CCDS8577.1																																																																																			G|0.601;A|0.399	0.399	strong		0.468	CD163L1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399329.1	NM_174941	
MUC5B	727897	hgsc.bcm.edu	37	11	1266599	1266599	+	Missense_Mutation	SNP	C	C	T	rs139960671	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:1266599C>T	ENST00000529681.1	+	31	8547	c.8489C>T	c.(8488-8490)cCg>cTg	p.P2830L	MUC5B_ENST00000447027.1_Missense_Mutation_p.P2833L|RP11-532E4.2_ENST00000532061.2_RNA	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	2830	7 X Cys-rich subdomain repeats.|Thr-rich.			Missing (in Ref. 6; AAB61398). {ECO:0000305}.	cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to retinoic acid (GO:0071300)|epithelial cell differentiation (GO:0030855)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|response to lipopolysaccharide (GO:0032496)|response to ozone (GO:0010193)|response to sulfur dioxide (GO:0010477)|response to vitamin A (GO:0033189)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)				cervix(2)|endometrium(36)|kidney(9)|lung(89)|urinary_tract(1)	137		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)		ACGACCACCCCGGGCCACACC	0.692													-|||	415	0.0828674	0.0083	0.0793	5008	,	,		13344	0.006		0.2137	False		,,,				2504	0.1309				p.P2830L		Atlas-SNP	.											.	MUC5B	473	.	0			c.C8489T						PASS	.	C	LEU/PRO	162,3882		23,116,1883	69.0	93.0	85.0		8489	-0.9	0.0	11	dbSNP_134	85	1706,6460		354,998,2731	no	missense	MUC5B	NM_002458.2	98	377,1114,4614	TT,TC,CC		20.8915,4.0059,15.2989	benign	2830/5763	1266599	1868,10342	2022	4083	6105	SO:0001583	missense	727897	exon31			CCACCCCGGGCCA	U95031, AF086604	CCDS44515.1, CCDS44515.2	11p15.5	2007-01-19	2006-03-14			ENSG00000117983		"""Mucins"""	7516	protein-coding gene	gene with protein product		600770	"""mucin 5, subtype B, tracheobronchial"""	MUC5		9804771	Standard	NM_002458		Approved	MG1	uc001lta.3	Q9HC84		ENST00000529681.1:c.8489C>T	11.37:g.1266599C>T	ENSP00000436812:p.Pro2830Leu	Somatic	305	1	0.00327869		WXS	Illumina HiSeq	Phase_I	353	342	0.968839	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Missense_Mutation	SNP	ENST00000529681.1	37	CCDS44515.2	198	0.09065934065934066	6	0.012195121951219513	32	0.08839779005524862	2	0.0034965034965034965	158	0.20844327176781002	-	7.110	0.575801	0.13623	0.040059	0.208915	ENSG00000117983	ENST00000529681;ENST00000447027;ENST00000349637;ENST00000406844	T;T	0.22336	1.96;1.96	2.84	-0.897	0.10553	.	.	.	.	.	T	0.00012	0.0000	N	0.24115	0.695	0.80722	P	0.0	B;B	0.30211	0.273;0.168	B;B	0.17722	0.019;0.013	T	0.36407	-0.9749	8	0.87932	D	0	.	5.1841	0.15174	0.3485:0.5427:0.0:0.1089	.	3413;2833	A7Y9J9;E9PBJ0	.;.	L	2830;2833;2802;2790	ENSP00000436812:P2830L;ENSP00000415793:P2833L	ENSP00000343037:P2802L	P	+	2	0	MUC5B	1223175	0.000000	0.05858	0.001000	0.08648	0.017000	0.09413	-0.797000	0.04570	0.038000	0.15604	-0.490000	0.04691	CCG	C|0.895;T|0.105	0.105	strong		0.692	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
CCHCR1	54535	hgsc.bcm.edu	37	6	31116245	31116245	+	Missense_Mutation	SNP	C	C	T	rs130069	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:31116245C>T	ENST00000376266.5	-	10	1372	c.1250G>A	c.(1249-1251)cGg>cAg	p.R417Q	CCHCR1_ENST00000480060.1_5'Flank|CCHCR1_ENST00000396268.3_Missense_Mutation_p.R506Q|CCHCR1_ENST00000396263.2_Missense_Mutation_p.R417Q|CCHCR1_ENST00000451521.2_Missense_Mutation_p.R470Q	NM_019052.3	NP_061925.2	Q8TD31	CCHCR_HUMAN	coiled-coil alpha-helical rod protein 1	417			R -> Q (in dbSNP:rs130069). {ECO:0000269|PubMed:11348465, ECO:0000269|PubMed:14702039}.|R -> W (in dbSNP:rs130068). {ECO:0000269|PubMed:10545595, ECO:0000269|PubMed:10888604, ECO:0000269|PubMed:11348465, ECO:0000269|PubMed:11875053, ECO:0000269|PubMed:14574404, ECO:0000269|PubMed:15489334}.		cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|protein export from nucleus (GO:0006611)	centriole (GO:0005814)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(13)|skin(1)	23						CTGCTGCCACCGACGCCTGGC	0.637													C|||	181	0.0361422	0.0136	0.0403	5008	,	,		17158	0.0119		0.0467	False		,,,				2504	0.0777				p.R506Q		Atlas-SNP	.											.	CCHCR1	68	.	0			c.G1517A						PASS	.		GLN/ARG,GLN/ARG,GLN/ARG	49,2973		0,49,1462	97.0	96.0	96.0		1409,1517,1250	3.3	0.0	6	dbSNP_78	96	262,5156		12,238,2459	yes	missense,missense,missense	CCHCR1	NM_001105563.1,NM_001105564.1,NM_019052.3	43,43,43	12,287,3921	TT,TC,CC		4.8357,1.6214,3.6848	benign,benign,benign	470/836,506/872,417/783	31116245	311,8129	1511	2709	4220	SO:0001583	missense	54535	exon10			TGCCACCGACGCC	AF216493	CCDS4695.1, CCDS43445.1, CCDS47397.1	6p21.3	2007-08-01	2005-02-15	2005-02-16	ENSG00000204536	ENSG00000204536			13930	protein-coding gene	gene with protein product		605310	"""chromosome 6 open reading frame 18"""	C6orf18		10888604, 10545595	Standard	NM_019052		Approved	HCR	uc003nsp.4	Q8TD31	OTTHUMG00000031112	ENST00000376266.5:c.1250G>A	6.37:g.31116245C>T	ENSP00000365442:p.Arg417Gln	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	121	52	0.429752	NM_001105564	A2ABH6|E9PE84|Q2TB67|Q5SQ82|Q5STE9|Q9NRK8|Q9NWY9|Q9NXJ4|Q9NXK3|Q9Y6W1|Q9Y6W2	Missense_Mutation	SNP	ENST00000376266.5	37	CCDS4695.1	76	0.0347985347985348	10	0.02032520325203252	18	0.049723756906077346	9	0.015734265734265736	39	0.051451187335092345	c	3.877	-0.026717	0.07589	0.016214	0.048357	ENSG00000204536	ENST00000396268;ENST00000376266;ENST00000396263;ENST00000440185;ENST00000451521	T;T;T;T	0.03717	3.83;3.83;3.83;3.83	5.13	3.32	0.38043	.	0.626287	0.15688	N	0.249594	T	0.01222	0.0040	L	0.50919	1.6	0.09310	N	1	B;B;B;B	0.18968	0.002;0.004;0.03;0.032	B;B;B;B	0.16722	0.005;0.003;0.016;0.008	T	0.46428	-0.9192	10	0.15952	T	0.53	-24.6082	7.5229	0.27639	0.0:0.8041:0.0:0.1959	rs130069;rs3173364;rs17190701;rs17410369	417;417;470;506	B4DIA2;Q8TD31;E9PE84;Q8TD31-2	.;CCHCR_HUMAN;.;.	Q	506;417;417;417;470	ENSP00000379566:R506Q;ENSP00000365442:R417Q;ENSP00000379561:R417Q;ENSP00000401039:R470Q	ENSP00000365442:R417Q	R	-	2	0	CCHCR1	31224224	0.003000	0.15002	0.019000	0.16419	0.104000	0.19210	0.699000	0.25586	1.281000	0.44480	0.543000	0.68304	CGG	C|0.955;T|0.045	0.045	strong		0.637	CCHCR1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076190.5	NM_019052	
FRG2B	441581	hgsc.bcm.edu	37	10	135438933	135438933	+	Silent	SNP	C	C	T	rs200793608		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:135438933C>T	ENST00000425520.1	-	4	559	c.507G>A	c.(505-507)ccG>ccA	p.P169P	FRG2B_ENST00000443774.1_Silent_p.P170P	NM_001080998.1	NP_001074467.1	Q96QU4	FRG2B_HUMAN	FSHD region gene 2 family, member B	169						nucleus (GO:0005634)				endometrium(2)|kidney(2)|lung(14)|ovary(1)|prostate(1)	20		all_cancers(35;7.01e-07)|all_epithelial(44;1.45e-05)|Lung NSC(174;0.027)|all_lung(145;0.0384)|all_neural(114;0.0726)|Glioma(114;0.172)|Melanoma(40;0.175)		OV - Ovarian serous cystadenocarcinoma(35;1.12e-06)|all cancers(32;1.43e-06)|Epithelial(32;1.71e-06)		TTCGAATTGACGGTGTTTGGA	0.552																																					p.P169P		Atlas-SNP	.											FRG2B,colon,carcinoma,-1,1	FRG2B	47	1	0			c.G507A						scavenged	.						126.0	151.0	143.0					10																	135438933		2193	4291	6484	SO:0001819	synonymous_variant	441581	exon4			AATTGACGGTGTT	AY744466	CCDS44502.1	10q26.3	2012-10-02			ENSG00000225899	ENSG00000225899			33518	protein-coding gene	gene with protein product						15520407	Standard	NM_001080998		Approved		uc010qvg.2	Q96QU4	OTTHUMG00000019328	ENST00000425520.1:c.507G>A	10.37:g.135438933C>T		Somatic	316	2	0.00632911		WXS	Illumina HiSeq	Phase_I	314	4	0.0127389	NM_001080998	Q5VSQ1	Silent	SNP	ENST00000425520.1	37	CCDS44502.1																																																																																			C|0.996;T|0.004	0.004	weak		0.552	FRG2B-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000467780.1	NM_001080998	
CCDC146	57639	hgsc.bcm.edu	37	7	76922490	76922490	+	Silent	SNP	C	C	T	rs17151219	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:76922490C>T	ENST00000285871.4	+	18	2764	c.2637C>T	c.(2635-2637)caC>caT	p.H879H	CCDC146_ENST00000415740.2_3'UTR|CCDC146_ENST00000431197.1_Silent_p.H593H	NM_020879.2	NP_065930.2	Q8IYE0	CC146_HUMAN	coiled-coil domain containing 146	879										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)				AAGAAATGCACGCCTTGGCCA	0.453													T|||	1104	0.220447	0.3835	0.1196	5008	,	,		21433	0.0923		0.173	False		,,,				2504	0.2526				p.H879H		Atlas-SNP	.											.	CCDC146	87	.	0			c.C2637T						PASS	.	T		1533,2873	672.4+/-402.6	273,987,943	109.0	114.0	112.0		2637	-0.6	0.0	7	dbSNP_123	112	1578,7022	745.2+/-407.3	142,1294,2864	no	coding-synonymous	CCDC146	NM_020879.2		415,2281,3807	TT,TC,CC		18.3488,34.7935,23.9197		879/956	76922490	3111,9895	2203	4300	6503	SO:0001819	synonymous_variant	57639	exon18			AATGCACGCCTTG	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.2637C>T	7.37:g.76922490C>T		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	52	51	0.980769	NM_020879	A8K8X6|Q9P223	Silent	SNP	ENST00000285871.4	37	CCDS34671.1																																																																																			C|0.779;T|0.221	0.221	strong		0.453	CCDC146-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341449.1	NM_020879	
HLA-DPB1	3115	hgsc.bcm.edu	37	6	33048538	33048538	+	Missense_Mutation	SNP	T	T	C	rs9277348	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:33048538T>C	ENST00000418931.2	+	2	306	c.190T>C	c.(190-192)Ttc>Ctc	p.F64L	HLA-DPA1_ENST00000419277.1_5'Flank|HLA-DPB1_ENST00000471184.1_3'UTR|HLA-DPB1_ENST00000535465.1_Missense_Mutation_p.F64L	NM_002121.5	NP_002112.3	P04440	DPB1_HUMAN	major histocompatibility complex, class II, DP beta 1	64	Beta-1.		F -> L (in allele DPB1*02:02, allele DPB1*02:03, allele DPB1*05:01, allele DPB1*15:02, allele DPB1*17:02, allele DPB1*19:02, allele DPB1*21:01, allele DPB1*21:01, allele DPB1*22:01, allele DPB1*34:01, allele DPB1*36:01, allele DPB1*38:01, allele DPB1*44:01, allele DPB1*48:01, allele DPB1*58:01, allele DPB1*62:01, allele DPB1*63:01, allele DPB1*95:01 and allele DPB1*97:01; dbSNP:rs9277348).|F -> Y (in allele DPB1*01:01, allele DPB1*01:02, allele DPB1*09:02, allele DPB1*11:01, allele DPB1*13:01, allele DPB1*15:01, allele DPB1*20:02, allele DPB1*21:02, allele DPB1*25:02, allele DPB1*26:01, allele DPB1*27:01, allele DPB1*39:01, allele DPB1*40:01, allele DPB1*49:01, allele DPB1*53:01, allele DPB1*65:01, allele DPB1*74:01, allele DPB1*85:01, allele DPB1*89:01 and allele DPB1*96:01; dbSNP:rs1042117).		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell proliferation (GO:0042102)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	peptide antigen binding (GO:0042605)			cervix(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(3)|ovary(1)|skin(1)	11						CCGGGAGGAGTTCGCGCGCTT	0.612													.|||	573	0.114417	0.0068	0.0331	5008	,	,		14808	0.4901		0.0338	False		,,,				2504	0.0133				p.F64L		Atlas-SNP	.											HLA-DPB1,rectum,carcinoma,-2,1	HLA-DPB1	28	1	0			c.T190C						PASS	.	T	,,LEU/PHE	25,2997		0,25,1486	70.0	70.0	70.0		,,190	-0.2	0.0	6	dbSNP_118	70	142,5276		1,140,2568	yes	utr-5,utr-5,missense	HLA-DPA1,HLA-DPB1	NM_001242524.1,NM_001242525.1,NM_002121.5	,,22	1,165,4054	CC,CT,TT		2.6209,0.8273,1.9787	,,benign	,,64/259	33048538	167,8273	1511	2709	4220	SO:0001583	missense	3115	exon2			GAGGAGTTCGCGC		CCDS4765.1	6p21.3	2013-01-11			ENSG00000223865	ENSG00000223865		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4940	protein-coding gene	gene with protein product		142858		HLA-DP1B			Standard	NM_002121		Approved		uc003ocu.2	P04440	OTTHUMG00000031076	ENST00000418931.2:c.190T>C	6.37:g.33048538T>C	ENSP00000408146:p.Phe64Leu	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	42	19	0.452381	NM_002121	A0PFJ7|A5I886|A8YPB3|B5U8B4|B7VF80|B7VF87|B8ZX68|B8ZYT0|B9W5S8|B9W6F7|B9W6F9|C0MPP5|C0MPQ2|C0MPQ3|C0MPQ5|C0MPQ6|C0MPQ7|C4R9J5|C5IZL1|O00259|O19698|O19700|O19702|O19749|O46884|O77952|O98215|O98216|O98217|O98218|O98219|O98222|O98223|P01916|P04232|P13763|P79493|P79608|Q0P0L4|Q0ZFN3|Q14279|Q27S71|Q29682|Q29684|Q29698|Q29714|Q29775|Q29776|Q29778|Q29779|Q29781|Q29827|Q29828|Q29879|Q29880|Q29898|Q29977|Q2MGW3|Q30015|Q30031|Q30032|Q30033|Q30034|Q30050|Q30051|Q30052|Q30053|Q30054|Q30055|Q30174|Q4GY31|Q4JHD8|Q5ENE0|Q5ENE1|Q5ENW3|Q5EP46|Q5EP47|Q5EP49|Q5EP51|Q5EP52|Q5EP53|Q5EP56|Q5I4H8|Q5I4H9|Q5ISH4|Q5ISH5|Q5SQ73|Q5STP2|Q5YLA6|Q6IVX1|Q6LBX2|Q6LBX3|Q6LBX4|Q6LBX5|Q6LBX6|Q6LBX7|Q6PWX6|Q6TAS4|Q714U1|Q714U2|Q7YQ10|Q860Z7|Q8HWL7|Q8HWT5|Q8SNC4|Q95HC1|Q95IT7|Q95IT8|Q9BD13|Q9GIM2|Q9GIM4|Q9GIX6|Q9GJ41|Q9MY67|Q9TNT7|Q9TQE2|Q9XS11|Q9XS12	Missense_Mutation	SNP	ENST00000418931.2	37	CCDS4765.1	290	0.13278388278388278	5	0.01016260162601626	15	0.04143646408839779	247	0.4318181818181818	23	0.030343007915567283	T	8.115	0.779704	0.16120	0.008273	0.026209	ENSG00000223865	ENST00000418931;ENST00000535465;ENST00000411942;ENST00000428835	T;T;T	0.00285	8.3;8.3;8.3	3.94	-0.233	0.13078	MHC class II, alpha/beta chain, N-terminal (1);MHC class II, beta chain, N-terminal (2);MHC classes I/II-like antigen recognition protein (1);	1.117700	0.06944	N	0.813382	T	0.00073	0.0002	L	0.49126	1.545	0.80722	P	0.0	B;B	0.10296	0.003;0.001	B;B	0.15052	0.012;0.007	T	0.16305	-1.0407	9	0.40728	T	0.16	.	3.7648	0.08619	0.3298:0.099:0.0:0.5712	rs9277348	74;64	Q59GY1;P04440	.;DPB1_HUMAN	L	64;64;64;41	ENSP00000408146:F64L;ENSP00000439674:F64L;ENSP00000412654:F41L	ENSP00000389210:F64L	F	+	1	0	HLA-DPB1	33156516	0.001000	0.12720	0.000000	0.03702	0.003000	0.03518	-0.747000	0.04823	-0.113000	0.11958	0.523000	0.50628	TTC	T|0.945;C|0.055	0.055	strong		0.612	HLA-DPB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076106.2	NM_002121	
PTPRH	5794	hgsc.bcm.edu	37	19	55716800	55716800	+	Silent	SNP	A	A	G	rs2288516	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:55716800A>G	ENST00000376350.3	-	4	535	c.513T>C	c.(511-513)acT>acC	p.T171T	PTPRH_ENST00000588559.1_5'UTR|PTPRH_ENST00000263434.5_Intron	NM_002842.3	NP_002833.3	Q9HD43	PTPRH_HUMAN	protein tyrosine phosphatase, receptor type, H	171	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				apoptotic process (GO:0006915)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(2)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(8)|lung(27)|ovary(2)|prostate(5)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(2)	67		Renal(1328;0.245)	BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0479)		CGGTGATGTTAGTGTGTGCTG	0.567													G|||	2095	0.418331	0.6172	0.3213	5008	,	,		19783	0.1964		0.4145	False		,,,				2504	0.4509				p.T171T		Atlas-SNP	.											.	PTPRH	139	.	0			c.T513C						PASS	.	G	,	2597,1809	530.3+/-372.9	761,1075,367	162.0	145.0	151.0		,513	0.1	0.0	19	dbSNP_100	151	3697,4903	620.3+/-397.0	794,2109,1397	no	intron,coding-synonymous	PTPRH	NM_001161440.1,NM_002842.3	,	1555,3184,1764	GG,GA,AA		42.9884,41.0576,48.393	,	,171/1116	55716800	6294,6712	2203	4300	6503	SO:0001819	synonymous_variant	5794	exon4			GATGTTAGTGTGT		CCDS33110.1, CCDS54321.1	19q13.4	2013-02-11				ENSG00000080031		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9672	protein-coding gene	gene with protein product		602510				8294459	Standard	XM_006723312		Approved	SAP-1	uc002qjq.3	Q9HD43		ENST00000376350.3:c.513T>C	19.37:g.55716800A>G		Somatic	232	1	0.00431034		WXS	Illumina HiSeq	Phase_I	238	104	0.436975	NM_002842	C9JCH2|Q15426|Q2NKN9|Q2NKP0	Silent	SNP	ENST00000376350.3	37	CCDS33110.1																																																																																			A|0.556;G|0.444	0.444	strong		0.567	PTPRH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452649.1		
KIAA1804	84451	hgsc.bcm.edu	37	1	233515413	233515413	+	Silent	SNP	G	G	A	rs1402815	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:233515413G>A	ENST00000366624.3	+	9	2922	c.2661G>A	c.(2659-2661)ccG>ccA	p.P887P	MLK4_ENST00000366622.1_Silent_p.P333P	NM_032435.2	NP_115811.2																					AACATAGACCGTCACATCACA	0.423													G|||	1095	0.21865	0.0144	0.1599	5008	,	,		21358	0.3294		0.3469	False		,,,				2504	0.2904				p.P887P		Atlas-SNP	.											.	KIAA1804	129	.	0			c.G2661A						PASS	.	G		295,4111	162.2+/-194.2	8,279,1916	80.0	71.0	74.0		2661	-4.4	0.0	1	dbSNP_88	74	2908,5692	454.1+/-363.4	472,1964,1864	no	coding-synonymous	KIAA1804	NM_032435.2		480,2243,3780	AA,AG,GG		33.814,6.6954,24.6271		887/1037	233515413	3203,9803	2203	4300	6503	SO:0001819	synonymous_variant	0	exon9			TAGACCGTCACAT																												ENST00000366624.3:c.2661G>A	1.37:g.233515413G>A		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	66	29	0.439394	NM_032435		Silent	SNP	ENST00000366624.3	37	CCDS1598.1																																																																																			G|0.748;A|0.252	0.252	strong		0.423	MLK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092495.1		
MYLIP	29116	hgsc.bcm.edu	37	6	16145325	16145325	+	Missense_Mutation	SNP	A	A	G	rs9370867	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:16145325A>G	ENST00000356840.3	+	6	1223	c.1025A>G	c.(1024-1026)aAc>aGc	p.N342S	MYLIP_ENST00000349606.4_Missense_Mutation_p.N161S	NM_013262.3	NP_037394.2	Q8WY64	MYLIP_HUMAN	myosin regulatory light chain interacting protein	342			N -> S (in dbSNP:rs9370867). {ECO:0000269|PubMed:10593918, ECO:0000269|PubMed:11042152, ECO:0000269|PubMed:15498874, ECO:0000269|Ref.2}.		cellular component movement (GO:0006928)|cholesterol homeostasis (GO:0042632)|negative regulation of low-density lipoprotein particle clearance (GO:0010989)|nervous system development (GO:0007399)|positive regulation of protein catabolic process (GO:0045732)|protein destabilization (GO:0031648)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of low-density lipoprotein particle receptor catabolic process (GO:0032803)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extrinsic component of membrane (GO:0019898)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	cytoskeletal protein binding (GO:0008092)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	28	Breast(50;0.0799)|Ovarian(93;0.103)	all_hematologic(90;0.0895)	Epithelial(50;0.241)			GTTTCAAGAAACAACCAGAGC	0.517													G|||	3856	0.769968	0.9652	0.6945	5008	,	,		22511	0.9435		0.4861	False		,,,				2504	0.6728				p.N342S		Atlas-SNP	.											.	MYLIP	44	.	0			c.A1025G						PASS	.	G	SER/ASN	3906,500	231.7+/-245.5	1738,430,35	100.0	103.0	102.0		1025	3.8	0.0	6	dbSNP_119	102	4094,4506	593.3+/-393.1	967,2160,1173	yes	missense	MYLIP	NM_013262.3	46	2705,2590,1208	GG,GA,AA		47.6047,11.3482,38.4899	benign	342/446	16145325	8000,5006	2203	4300	6503	SO:0001583	missense	29116	exon6			CAAGAAACAACCA	AF187016	CCDS4536.1	6p23-p22.3	2011-11-17			ENSG00000007944	ENSG00000007944			21155	protein-coding gene	gene with protein product	"""E3 ubiquitin ligase-inducible degrader of the low density lipoprotein receptor"""	610082				10593918, 11162443, 19688294	Standard	NM_013262		Approved	MIR, IDOL	uc003nbq.3	Q8WY64	OTTHUMG00000016405	ENST00000356840.3:c.1025A>G	6.37:g.16145325A>G	ENSP00000349298:p.Asn342Ser	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	107	54	0.504673	NM_013262	Q5TIA4|Q9BU73|Q9NRL9|Q9UHE7	Missense_Mutation	SNP	ENST00000356840.3	37	CCDS4536.1	1620	0.7417582417582418	469	0.9532520325203252	239	0.6602209944751382	541	0.9458041958041958	371	0.4894459102902375	G	0.035	-1.312768	0.01331	0.886518	0.476047	ENSG00000007944	ENST00000356840;ENST00000349606	D;T	0.81908	-1.55;1.16	5.65	3.85	0.44370	.	0.514420	0.25666	N	0.029102	T	0.39200	0.1069	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.08868	-1.0701	9	0.02654	T	1	.	9.9368	0.41556	0.1268:0.1148:0.7584:0.0	rs9370867;rs59084742;rs9370867	342	Q8WY64	MYLIP_HUMAN	S	342;161	ENSP00000349298:N342S;ENSP00000008686:N161S	ENSP00000008686:N161S	N	+	2	0	MYLIP	16253304	0.018000	0.18449	0.000000	0.03702	0.446000	0.32137	1.572000	0.36461	0.415000	0.25817	-0.119000	0.15052	AAC	A|0.313;G|0.687	0.687	strong		0.517	MYLIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043864.1	NM_013262	
NEK4	6787	hgsc.bcm.edu	37	3	52802402	52802402	+	Silent	SNP	A	A	C	rs2230534	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:52802402A>C	ENST00000233027.5	-	2	514	c.312T>G	c.(310-312)ccT>ccG	p.P104P	NEK4_ENST00000383721.4_Silent_p.P104P|NEK4_ENST00000535191.1_Intron	NM_001193533.1|NM_003157.4	NP_001180462.1|NP_003148.2	P51957	NEK4_HUMAN	NIMA-related kinase 4	104	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				mitotic nuclear division (GO:0007067)|protein phosphorylation (GO:0006468)	nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(9)|lung(10)	26				BRCA - Breast invasive adenocarcinoma(193;7.44e-05)|Kidney(197;0.000711)|KIRC - Kidney renal clear cell carcinoma(197;0.00086)|OV - Ovarian serous cystadenocarcinoma(275;0.0513)		CCTGATTCTCAGGCAGAAGCT	0.493													a|||	1660	0.33147	0.1475	0.4597	5008	,	,		18867	0.4266		0.4195	False		,,,				2504	0.3006				p.P104P		Atlas-SNP	.											.	NEK4	51	.	0			c.T312G						PASS	.	G	,	781,3625	317.2+/-295.0	69,643,1491	210.0	196.0	201.0		,312	-7.8	0.8	3	dbSNP_98	201	3519,5081	512.8+/-378.0	739,2041,1520	no	intron,coding-synonymous	NEK4	NM_001193533.1,NM_003157.4	,	808,2684,3011	CC,CA,AA		40.9186,17.7258,33.0617	,	,104/842	52802402	4300,8706	2203	4300	6503	SO:0001819	synonymous_variant	6787	exon2			ATTCTCAGGCAGA	L20321	CCDS2863.1, CCDS54593.1	3p21.1	2012-11-15	2012-11-15	2002-05-10	ENSG00000114904	ENSG00000114904	2.7.11.1		11399	protein-coding gene	gene with protein product	"""serine/threonine protein kinase-2"""	601959	"""serine/threonine kinase 2"", ""NIMA (never in mitosis gene a)-related kinase 4"""	STK2		8208544	Standard	NM_001193533		Approved	NRK2, pp12301	uc003dfq.4	P51957	OTTHUMG00000158836	ENST00000233027.5:c.312T>G	3.37:g.52802402A>C		Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	122	120	0.983607	NM_003157	A5YM70|B2R633|B7Z200|Q6P576	Silent	SNP	ENST00000233027.5	37	CCDS2863.1																																																																																			A|0.653;C|0.347	0.347	strong		0.493	NEK4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000352386.2	NM_003157	
MUC4	4585	hgsc.bcm.edu	37	3	195512302	195512302	+	Missense_Mutation	SNP	G	G	A	rs201164821	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195512302G>A	ENST00000463781.3	-	2	6608	c.6149C>T	c.(6148-6150)cCt>cTt	p.P2050L	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_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						PASS	.						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	62	0	0		WXS	Illumina HiSeq	Phase_I	80	18	0.225	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	
SLFN12	55106	hgsc.bcm.edu	37	17	33749546	33749546	+	Missense_Mutation	SNP	A	A	G	rs2586514	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:33749546A>G	ENST00000394562.1	-	4	1025	c.502T>C	c.(502-504)Tgt>Cgt	p.C168R	SLFN12_ENST00000304905.5_Missense_Mutation_p.C168R|SLFN12_ENST00000460530.1_5'Flank|SLFN12_ENST00000452764.3_Missense_Mutation_p.C168R			Q8IYM2	SLN12_HUMAN	schlafen family member 12	168			C -> R (in dbSNP:rs2586514). {ECO:0000269|PubMed:15489334}.				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)		ATATCAACACAGGGCCTCTTT	0.398													G|||	2954	0.589856	0.6278	0.6354	5008	,	,		17852	0.4504		0.5905	False		,,,				2504	0.6493				p.C168R		Atlas-SNP	.											.	SLFN12	56	.	0			c.T502C						PASS	.	G	ARG/CYS	2769,1625		875,1019,303	75.0	78.0	77.0		502	-6.5	0.0	17	dbSNP_100	77	5123,3463		1532,2059,702	yes	missense	SLFN12	NM_018042.3	180	2407,3078,1005	GG,GA,AA		40.3331,36.9822,39.1988	possibly-damaging	168/579	33749546	7892,5088	2197	4293	6490	SO:0001583	missense	55106	exon2			CAACACAGGGCCT	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.502T>C	17.37:g.33749546A>G	ENSP00000378063:p.Cys168Arg	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	88	86	0.977273	NM_018042	A8K711|Q9NP47	Missense_Mutation	SNP	ENST00000394562.1	37	CCDS11295.1	1267	0.5801282051282052	327	0.6646341463414634	223	0.6160220994475138	249	0.4353146853146853	468	0.6174142480211082	g	3.337	-0.135420	0.06711	0.630178	0.596669	ENSG00000172123	ENST00000394562;ENST00000304905;ENST00000452764	T;T;T	0.03468	3.92;3.92;3.92	3.23	-6.47	0.01902	.	.	.	.	.	T	0.00012	0.0000	L	0.58101	1.795	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.36114	-0.9761	8	0.23891	T	0.37	.	1.5985	0.02669	0.3055:0.3582:0.2094:0.1269	rs2586514;rs3744368;rs16970955;rs17846142;rs17859150;rs52828558;rs58226663;rs2586514	168	Q8IYM2	SLN12_HUMAN	R	168	ENSP00000378063:C168R;ENSP00000302077:C168R;ENSP00000394903:C168R	ENSP00000302077:C168R	C	-	1	0	SLFN12	30773659	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.790000	0.04604	-2.103000	0.00844	-1.786000	0.00637	TGT	A|0.416;G|0.584	0.584	strong		0.398	SLFN12-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256491.1	NM_018042	
ANXA11	311	hgsc.bcm.edu	37	10	81926718	81926718	+	Silent	SNP	A	A	G	rs2228427	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:81926718A>G	ENST00000438331.1	-	8	1154	c.672T>C	c.(670-672)atT>atC	p.I224I	ANXA11_ENST00000535999.1_Silent_p.I224I|ANXA11_ENST00000422982.3_Silent_p.I224I|ANXA11_ENST00000265447.4_Silent_p.I224I|ANXA11_ENST00000372231.3_Silent_p.I224I|ANXA11_ENST00000537102.1_Silent_p.I191I|ANXA11_ENST00000360615.4_Silent_p.I224I	NM_145869.1	NP_665876.1	P50995	ANX11_HUMAN	annexin A11	224					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)			CCAGGCAGTCAATGATGGCCT	0.642													.|||	543	0.108427	0.0257	0.1787	5008	,	,		15213	0.0188		0.1302	False		,,,				2504	0.2403				p.I224I		Atlas-SNP	.											.	ANXA11	32	.	0			c.T672C						PASS	.	G	,,	204,4202		6,192,2005	52.0	44.0	46.0		672,672,672	-0.1	0.3	10	dbSNP_98	46	1195,7405		66,1063,3171	no	coding-synonymous,coding-synonymous,coding-synonymous	ANXA11	NM_001157.2,NM_145868.1,NM_145869.1	,,	72,1255,5176	GG,GA,AA		13.8953,4.63,10.7566	,,	224/506,224/506,224/506	81926718	1399,11607	2203	4300	6503	SO:0001819	synonymous_variant	311	exon7			GCAGTCAATGATG	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.672T>C	10.37:g.81926718A>G		Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	44	26	0.590909	NM_145868	B4DVE7	Silent	SNP	ENST00000438331.1	37	CCDS7364.1																																																																																			T|0.009;G|0.096	0.096	strong		0.642	ANXA11-003	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049044.1	NM_145869	
OR13D1	286365	hgsc.bcm.edu	37	9	107457275	107457275	+	Missense_Mutation	SNP	A	A	C	rs10820709	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:107457275A>C	ENST00000318763.5	+	1	616	c.573A>C	c.(571-573)caA>caC	p.Q191H		NM_001004484.1	NP_001004484.1	Q8NGV5	O13D1_HUMAN	olfactory receptor, family 13, subfamily D, member 1	191			Q -> H (in dbSNP:rs10820709). {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)			large_intestine(4)|lung(10)|ovary(1)|prostate(2)|skin(2)	19						CCCTATTGCAAACAGTTCTGA	0.428													A|||	2439	0.487021	0.6778	0.4827	5008	,	,		22591	0.505		0.3151	False		,,,				2504	0.3906				p.Q191H		Atlas-SNP	.											.	OR13D1	42	.	0			c.A573C						PASS	.	A	HIS/GLN	2788,1618	664.0+/-401.3	887,1014,302	164.0	147.0	153.0		573	-0.5	0.2	9	dbSNP_120	153	2602,5998	420.9+/-353.5	407,1788,2105	no	missense	OR13D1	NM_001004484.1	24	1294,2802,2407	CC,CA,AA		30.2558,36.7227,41.4424	probably-damaging	191/347	107457275	5390,7616	2203	4300	6503	SO:0001583	missense	286365	exon1			ATTGCAAACAGTT		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.573A>C	9.37:g.107457275A>C	ENSP00000317357:p.Gln191His	Somatic	299	0	0		WXS	Illumina HiSeq	Phase_I	253	129	0.509881	NM_001004484	B9EIS1|Q6IFL1	Missense_Mutation	SNP	ENST00000318763.5	37	CCDS35094.1	1006	0.4606227106227106	313	0.6361788617886179	155	0.4281767955801105	289	0.5052447552447552	249	0.32849604221635886	A	2.797	-0.249970	0.05867	0.632773	0.302558	ENSG00000179055	ENST00000318763	T	0.00019	9.06	3.87	-0.483	0.12075	GPCR, rhodopsin-like superfamily (1);	0.000000	0.49305	D	0.000142	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.21147	0.052	B	0.27887	0.084	T	0.40346	-0.9568	9	0.35671	T	0.21	.	4.6636	0.12655	0.6395:0.162:0.1985:0.0	rs10820709;rs10820709	191	Q8NGV5	O13D1_HUMAN	H	191	ENSP00000317357:Q191H	ENSP00000317357:Q191H	Q	+	3	2	OR13D1	106497096	0.000000	0.05858	0.150000	0.22450	0.078000	0.17371	-0.772000	0.04694	0.074000	0.16767	0.418000	0.28097	CAA	A|0.560;C|0.440	0.440	strong		0.428	OR13D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053483.1		
DRD5	1816	hgsc.bcm.edu	37	4	9784550	9784550	+	Silent	SNP	G	G	A	rs2227844	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:9784550G>A	ENST00000304374.2	+	1	1293	c.897G>A	c.(895-897)tcG>tcA	p.S299S		NM_000798.4	NP_000789.1	P21918	DRD5_HUMAN	dopamine receptor D5	299					activation of adenylate cyclase activity (GO:0007190)|adenylate cyclase-activating dopamine receptor signaling pathway (GO:0007191)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|associative learning (GO:0008306)|cellular calcium ion homeostasis (GO:0006874)|cellular response to catecholamine stimulus (GO:0071870)|long term synaptic depression (GO:0060292)|negative regulation of blood pressure (GO:0045776)|negative regulation of NAD(P)H oxidase activity (GO:0033861)|norepinephrine-epinephrine vasoconstriction involved in regulation of systemic arterial blood pressure (GO:0001994)|phospholipase C-activating dopamine receptor signaling pathway (GO:0060158)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of adenylate cyclase activity involved in G-protein coupled receptor signaling pathway (GO:0010579)|reactive oxygen species metabolic process (GO:0072593)|regulation of female receptivity (GO:0045924)|regulation of systemic arterial blood pressure by vasopressin (GO:0001992)|response to amphetamine (GO:0001975)|response to cocaine (GO:0042220)|sensitization (GO:0046960)|synaptic transmission (GO:0007268)|synaptic transmission, dopaminergic (GO:0001963)|transmission of nerve impulse (GO:0019226)|wound healing (GO:0042060)	brush border membrane (GO:0031526)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	dopamine binding (GO:0035240)|dopamine neurotransmitter receptor activity (GO:0004952)|dopamine neurotransmitter receptor activity, coupled via Gs (GO:0001588)			NS(2)|endometrium(8)|kidney(4)|large_intestine(8)|lung(22)|prostate(7)|skin(3)|stomach(2)|urinary_tract(1)	57					Apomorphine(DB00714)|Aripiprazole(DB01238)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Chlorpromazine(DB00477)|Cinnarizine(DB00568)|Dopamine(DB00988)|Ergotamine(DB00696)|Fenoldopam(DB00800)|Imipramine(DB00458)|L-DOPA(DB01235)|Lisuride(DB00589)|Loxapine(DB00408)|Methotrimeprazine(DB01403)|Mianserin(DB06148)|Mirtazapine(DB00370)|Olanzapine(DB00334)|Pergolide(DB01186)|Pramipexole(DB00413)|Quetiapine(DB01224)|Ropinirole(DB00268)|Rotigotine(DB05271)|Trimipramine(DB00726)|Ziprasidone(DB00246)	AGACCCTGTCGGTGATCATGG	0.632																																					p.S299S		Atlas-SNP	.											DRD5,colon,carcinoma,0,2	DRD5	119	2	0			c.G897A						scavenged	.						55.0	52.0	53.0					4																	9784550		2203	4297	6500	SO:0001819	synonymous_variant	1816	exon1			CCTGTCGGTGATC	X58454	CCDS3405.1	4p16.1	2012-08-08			ENSG00000169676	ENSG00000169676		"""GPCR / Class A : Dopamine receptors"""	3026	protein-coding gene	gene with protein product		126453		DRD1L2		1774076	Standard	NM_000798		Approved	DRD1B	uc003gmb.4	P21918	OTTHUMG00000128489	ENST00000304374.2:c.897G>A	4.37:g.9784550G>A		Somatic	35	2	0.0571429		WXS	Illumina HiSeq	Phase_I	33	2	0.0606061	NM_000798	B2R9S3|Q8NEQ8	Silent	SNP	ENST00000304374.2	37	CCDS3405.1																																																																																			G|0.885;A|0.115	0.115	strong		0.632	DRD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250293.1		
ADAMTS14	140766	hgsc.bcm.edu	37	10	72513635	72513635	+	Missense_Mutation	SNP	C	C	A	rs12774070	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	53	0	0		WXS	Illumina HiSeq	Phase_I	39	26	0.666667	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	
FAM53A	152877	hgsc.bcm.edu	37	4	1657281	1657281	+	Silent	SNP	G	G	A	rs79735962	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:1657281G>A	ENST00000308132.6	-	4	498	c.306C>T	c.(304-306)acC>acT	p.T102T	FAM53A_ENST00000472884.2_Silent_p.T102T|FAM53A_ENST00000461064.1_Silent_p.T102T|FAM53A_ENST00000489363.1_Silent_p.T102T	NM_001174070.1	NP_001167541.1	Q6NSI3	FA53A_HUMAN	family with sequence similarity 53, member A	102						nucleus (GO:0005634)				breast(2)|central_nervous_system(2)|large_intestine(1)|lung(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	10		all_epithelial(65;0.206)|Breast(71;0.212)	OV - Ovarian serous cystadenocarcinoma(23;0.0145)			TGGGGTCCACGGTGCTGGCTG	0.687													G|||	1123	0.224241	0.0991	0.2291	5008	,	,		13181	0.0595		0.3678	False		,,,				2504	0.4121				p.T102T		Atlas-SNP	.											.	FAM53A	25	.	0			c.C306T						PASS	.	G	,	492,3574		43,406,1584	7.0	8.0	8.0		306,306	-3.3	0.0	4	dbSNP_131	8	2517,5567		409,1699,1934	no	coding-synonymous,coding-synonymous	FAM53A	NM_001013622.3,NM_001174070.1	,	452,2105,3518	AA,AG,GG		31.1356,12.1003,24.7654	,	102/399,102/399	1657281	3009,9141	2033	4042	6075	SO:0001819	synonymous_variant	152877	exon4			GTCCACGGTGCTG	BC070112	CCDS33939.1, CCDS75091.1	4p16.3	2005-08-09			ENSG00000174137	ENSG00000174137			31860	protein-coding gene	gene with protein product							Standard	NM_001013622		Approved	DNTNP	uc021xkl.1	Q6NSI3	OTTHUMG00000159855	ENST00000308132.6:c.306C>T	4.37:g.1657281G>A		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	124	65	0.524194	NM_001013622	Q6ZUL5	Silent	SNP	ENST00000308132.6	37	CCDS33939.1																																																																																			G|0.787;A|0.213	0.213	strong		0.687	FAM53A-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359224.1	NM_001013622	
GFM2	84340	hgsc.bcm.edu	37	5	74017499	74017499	+	Missense_Mutation	SNP	C	C	T	rs1048167	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:74017499C>T	ENST00000296805.3	-	21	2778	c.2321G>A	c.(2320-2322)cGg>cAg	p.R774Q	GFM2_ENST00000345239.2_Missense_Mutation_p.R727Q|GFM2_ENST00000515125.1_5'UTR|GFM2_ENST00000509430.1_Missense_Mutation_p.R774Q	NM_032380.3	NP_115756.2			G elongation factor, mitochondrial 2											breast(2)|endometrium(2)|large_intestine(4)|lung(5)|prostate(1)	14		all_lung(232;0.00101)|Lung NSC(167;0.00278)|Ovarian(174;0.0129)|Breast(144;0.231)		OV - Ovarian serous cystadenocarcinoma(47;1.86e-56)		ACCACTTCTCCGGTTGAGCAG	0.368													C|||	619	0.123602	0.2284	0.1095	5008	,	,		17618	0.0218		0.1382	False		,,,				2504	0.0818				p.R774Q		Atlas-SNP	.											.	GFM2	38	.	0			c.G2321A						PASS	.	C	GLN/ARG,GLN/ARG	991,3415	371.5+/-320.0	112,767,1324	96.0	99.0	98.0		2321,2180	-3.3	0.4	5	dbSNP_86	98	1066,7534	225.4+/-261.5	64,938,3298	yes	missense,missense	GFM2	NM_032380.3,NM_170691.1	43,43	176,1705,4622	TT,TC,CC		12.3953,22.4921,15.8158	benign,benign	774/780,727/733	74017499	2057,10949	2203	4300	6503	SO:0001583	missense	84340	exon21			CTTCTCCGGTTGA	AF111808	CCDS4023.1, CCDS4024.1, CCDS47232.1	5q13	2008-02-05			ENSG00000164347	ENSG00000164347			29682	protein-coding gene	gene with protein product		606544				11735030	Standard	NM_001281302		Approved	EFG2, FLJ21661	uc003kdh.1	Q969S9	OTTHUMG00000102058	ENST00000296805.3:c.2321G>A	5.37:g.74017499C>T	ENSP00000296805:p.Arg774Gln	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	115	54	0.469565	NM_032380		Missense_Mutation	SNP	ENST00000296805.3	37	CCDS4023.1	271	0.12408424908424909	122	0.24796747967479674	47	0.1298342541436464	15	0.026223776223776224	87	0.11477572559366754	C	11.05	1.525283	0.27299	0.224921	0.123953	ENSG00000164347	ENST00000296805;ENST00000345239;ENST00000546082;ENST00000509430	T;T;T	0.54279	0.58;0.58;0.58	5.98	-3.33	0.04958	Elongation factor G/III/V (1);	0.433895	0.26836	N	0.022253	T	0.00012	0.0000	N	0.08118	0	0.50467	P	1.24000000000013E-4	B;B;B	0.18741	0.03;0.003;0.017	B;B;B	0.25987	0.065;0.01;0.048	T	0.22103	-1.0226	9	0.44086	T	0.13	0.0332	13.1975	0.59746	0.0:0.3691:0.0:0.6309	rs1048167;rs3188149;rs1048167	772;727;774	Q969S9-3;Q969S9-2;Q969S9	.;.;RRF2M_HUMAN	Q	774;727;596;774	ENSP00000296805:R774Q;ENSP00000296804:R727Q;ENSP00000427004:R774Q	ENSP00000296805:R774Q	R	-	2	0	GFM2	74053255	0.779000	0.28652	0.446000	0.26920	0.257000	0.26127	-0.165000	0.09968	-0.678000	0.05224	0.650000	0.86243	CGG	C|0.856;T|0.144	0.144	strong		0.368	GFM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219860.2	NM_032380	
MUC4	4585	hgsc.bcm.edu	37	3	195513285	195513285	+	Silent	SNP	G	G	T	rs200293322	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195513285G>T	ENST00000463781.3	-	2	5625	c.5166C>A	c.(5164-5166)tcC>tcA	p.S1722S	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_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	132	0	0		WXS	Illumina HiSeq	Phase_I	122	4	0.0327869	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	
DNAH14	127602	hgsc.bcm.edu	37	1	225555602	225555602	+	Intron	SNP	T	T	G	rs12737248	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:225555602T>G	ENST00000445597.2	+	53	9205				DNAH14_ENST00000439375.2_Missense_Mutation_p.N3969K|DNAH14_ENST00000430092.1_Missense_Mutation_p.N3969K			Q0VDD8	DYH14_HUMAN	dynein, axonemal, heavy chain 14						microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			NS(2)|breast(3)|central_nervous_system(3)|endometrium(8)|kidney(4)|large_intestine(2)|lung(2)|skin(2)|stomach(1)	27						TATTTGAAAATCCTGACTGTG	0.368													T|||	1650	0.329473	0.1914	0.4366	5008	,	,		19879	0.2321		0.5716	False		,,,				2504	0.2914				p.N3969K		Atlas-SNP	.											.	DNAH14	300	.	0			c.T11907G						PASS	.	T	LYS/ASN	358,1026		51,256,385	173.0	148.0	156.0		11907	-10.1	0.0	1	dbSNP_121	156	1781,1401		478,825,288	yes	missense	DNAH14	NM_001373.1	94	529,1081,673	GG,GT,TT		44.0289,25.8671,46.8463	benign	3969/4516	225555602	2139,2427	692	1591	2283	SO:0001627	intron_variant	127602	exon75			TGAAAATCCTGAC	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.9205+9248T>G	1.37:g.225555602T>G		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	41	27	0.658537	NM_001373	A6NG62|A6NNL2|Q0VDD9|Q4VXC7|Q4VXG4|Q4VXG5|Q5VU33|Q5VU34	Missense_Mutation	SNP	ENST00000445597.2	37		847	0.38782051282051283	106	0.21544715447154472	166	0.4585635359116022	141	0.2465034965034965	434	0.5725593667546174	T	3.270	-0.149327	0.06585	0.258671	0.559711	ENSG00000185842	ENST00000430092;ENST00000439375	T;T	0.07800	3.16;3.16	5.03	-10.1	0.00402	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.58432	P	2.9999999999752447E-6	B	0.06786	0.001	B	0.04013	0.001	T	0.45160	-0.9280	7	0.06099	T	0.92	.	1.9825	0.03429	0.2645:0.1249:0.3745:0.2361	rs12737248;rs52802546;rs56554736;rs60613437;rs12737248	3969	Q0VDD8-4	.	K	3969	ENSP00000414402:N3969K;ENSP00000392061:N3969K	ENSP00000414402:N3969K	N	+	3	2	DNAH14	223622225	0.000000	0.05858	0.001000	0.08648	0.797000	0.45037	-1.557000	0.02166	-2.605000	0.00448	-0.628000	0.03992	AAT	T|0.631;G|0.369	0.369	strong		0.368	DNAH14-007	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000331217.3	XM_059166	
ARHGEF10	9639	hgsc.bcm.edu	37	8	1905132	1905132	+	Silent	SNP	G	G	A	rs3735876	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:1905132G>A	ENST00000398564.1	+	29	3813	c.3813G>A	c.(3811-3813)tcG>tcA	p.S1271S	ARHGEF10_ENST00000518288.1_Silent_p.S1270S|ARHGEF10_ENST00000349830.3_Silent_p.S1246S|ARHGEF10_ENST00000521927.1_3'UTR|ARHGEF10_ENST00000520359.1_Silent_p.S1208S|ARHGEF10_ENST00000262112.6_Silent_p.S1242S			O15013	ARHGA_HUMAN	Rho guanine nucleotide exchange factor (GEF) 10	1271	Ser-rich.				centrosome duplication (GO:0051298)|myelination in peripheral nervous system (GO:0022011)|positive regulation of GTP catabolic process (GO:0033126)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of stress fiber assembly (GO:0051496)|spindle assembly involved in mitosis (GO:0090307)	centrosome (GO:0005813)|cytosol (GO:0005829)	kinesin binding (GO:0019894)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			endometrium(3)|large_intestine(11)|lung(11)|prostate(3)|skin(3)|stomach(3)|urinary_tract(1)	35		Colorectal(14;3.46e-05)|Renal(68;0.000518)|Ovarian(12;0.00409)|Myeloproliferative disorder(644;0.0255)|Hepatocellular(245;0.0834)		COAD - Colon adenocarcinoma(149;1.62e-05)|BRCA - Breast invasive adenocarcinoma(11;1.68e-05)|KIRC - Kidney renal clear cell carcinoma(542;0.00361)|READ - Rectum adenocarcinoma(644;0.0718)		TGGGAGATTCGCTGGGATCGA	0.577													G|||	1843	0.368011	0.2133	0.2349	5008	,	,		18564	0.5714		0.4016	False		,,,				2504	0.4274				p.S1246S		Atlas-SNP	.											.	ARHGEF10	255	.	0			c.G3738A						PASS	.	G		1172,3234	413.7+/-336.6	160,852,1191	134.0	127.0	129.0		3738	-11.2	0.0	8	dbSNP_107	129	3323,5277	495.2+/-374.0	630,2063,1607	no	coding-synonymous	ARHGEF10	NM_014629.2		790,2915,2798	AA,AG,GG		38.6395,26.6001,34.561		1246/1345	1905132	4495,8511	2203	4300	6503	SO:0001819	synonymous_variant	9639	exon29			AGATTCGCTGGGA	AF009205	CCDS34794.1	8p23	2014-09-17			ENSG00000104728	ENSG00000104728		"""Rho guanine nucleotide exchange factors"""	14103	protein-coding gene	gene with protein product		608136				9205841, 16896804	Standard	XM_005266039		Approved	KIAA0294, Gef10	uc003wpr.3	O15013	OTTHUMG00000163626	ENST00000398564.1:c.3813G>A	8.37:g.1905132G>A		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	104	84	0.807692	NM_014629	O14665|Q2KHR8|Q68D55|Q8IWD9|Q8IY77	Silent	SNP	ENST00000398564.1	37																																																																																				G|0.648;A|0.352	0.352	strong		0.577	ARHGEF10-203	KNOWN	basic	protein_coding	protein_coding			
ATAD5	79915	hgsc.bcm.edu	37	17	29161503	29161503	+	Missense_Mutation	SNP	A	A	G	rs11080134	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	35	0	0		WXS	Illumina HiSeq	Phase_I	25	15	0.6	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	
PPP2R5A	5525	hgsc.bcm.edu	37	1	212515613	212515613	+	Silent	SNP	C	C	T	rs1774249	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:212515613C>T	ENST00000261461.2	+	4	1138	c.564C>T	c.(562-564)ttC>ttT	p.F188F	PPP2R5A_ENST00000537030.3_Silent_p.F131F|PPP2R5A_ENST00000498129.2_3'UTR	NM_006243.3	NP_006234.1	Q15172	2A5A_HUMAN	protein phosphatase 2, regulatory subunit B', alpha	188					negative regulation of establishment of protein localization to plasma membrane (GO:0090005)|negative regulation of lipid kinase activity (GO:0090219)|positive regulation of protein dephosphorylation (GO:0035307)|signal transduction (GO:0007165)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|M band (GO:0031430)|nucleus (GO:0005634)|protein phosphatase type 2A complex (GO:0000159)|Z disc (GO:0030018)	kinase binding (GO:0019900)|protein phosphatase type 2A regulator activity (GO:0008601)			NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)	16				OV - Ovarian serous cystadenocarcinoma(81;0.0125)|all cancers(67;0.029)|Epithelial(68;0.154)|GBM - Glioblastoma multiforme(131;0.155)		ATCAGAAATTCGTACAACAGG	0.313													C|||	1410	0.28155	0.1853	0.33	5008	,	,		15520	0.2837		0.34	False		,,,				2504	0.3149				p.F188F		Atlas-SNP	.											.	PPP2R5A	48	.	0			c.C564T						PASS	.	C	,	936,3470	354.1+/-312.5	99,738,1366	108.0	103.0	105.0		393,564	4.7	1.0	1	dbSNP_89	105	3045,5555	468.4+/-367.3	542,1961,1797	no	coding-synonymous,coding-synonymous	PPP2R5A	NM_001199756.1,NM_006243.3	,	641,2699,3163	TT,TC,CC		35.407,21.2438,30.6089	,	131/430,188/487	212515613	3981,9025	2203	4300	6503	SO:0001819	synonymous_variant	5525	exon4			GAAATTCGTACAA	BC022474	CCDS1503.1, CCDS55686.1	1q32.2-q32.3	2010-06-18	2010-04-14		ENSG00000066027	ENSG00000066027		"""Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"""	9309	protein-coding gene	gene with protein product		601643	"""protein phosphatase 2, regulatory subunit B (B56), alpha isoform"", ""protein phosphatase 2, regulatory subunit B', alpha isoform"""			7592815	Standard	NM_006243		Approved	PR61A, B56A	uc001hjb.3	Q15172	OTTHUMG00000036750	ENST00000261461.2:c.564C>T	1.37:g.212515613C>T		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	97	38	0.391753	NM_006243	B2R6D2|B7Z7L2|D3DT99|Q2NL72|Q5VVB2|Q8TBI9	Silent	SNP	ENST00000261461.2	37	CCDS1503.1																																																																																			C|0.701;T|0.299	0.299	strong		0.313	PPP2R5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089302.1	NM_006243	
CAPRIN1	4076	hgsc.bcm.edu	37	11	34093289	34093289	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:34093289A>G	ENST00000341394.4	+	3	422	c.233A>G	c.(232-234)tAc>tGc	p.Y78C	CAPRIN1_ENST00000532820.1_Missense_Mutation_p.Y78C|CAPRIN1_ENST00000530820.1_Missense_Mutation_p.Y78C|CAPRIN1_ENST00000529307.1_5'UTR|CAPRIN1_ENST00000389645.3_Missense_Mutation_p.Y78C	NM_005898.4	NP_005889.3	Q14444	CAPR1_HUMAN	cell cycle associated protein 1	78					negative regulation of translation (GO:0017148)|positive regulation of dendrite morphogenesis (GO:0050775)|positive regulation of dendritic spine morphogenesis (GO:0061003)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytoplasmic stress granule (GO:0010494)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.Y78C(2)		breast(2)|endometrium(2)|kidney(1)|large_intestine(6)|lung(5)|ovary(1)|prostate(1)	18		Acute lymphoblastic leukemia(5;0.00045)|all_hematologic(20;0.0016)				CTTGATGATTACCAGGAACGA	0.333																																					p.Y78C		Atlas-SNP	.											CAPRIN1_ENST00000389645,NS,carcinoma,0,2	CAPRIN1	110	2	2	Substitution - Missense(2)	breast(2)	c.A233G						scavenged	.						98.0	106.0	103.0					11																	34093289		2202	4298	6500	SO:0001583	missense	4076	exon3			ATGATTACCAGGA	BC001731	CCDS31453.1, CCDS31454.1	11p13	2010-08-03	2007-03-27	2007-03-27	ENSG00000135387	ENSG00000135387			6743	protein-coding gene	gene with protein product	"""cytoplasmic activation/proliferation-associated protein-1"""	601178	"""membrane component, chromosome 11, surface marker 1"", ""GPI-anchored membrane protein 1"""	M11S1, GPIAP1		7657653, 16177067, 17210633, 14764709, 15471883	Standard	NM_005898		Approved	caprin-1, RNG105	uc001mvh.1	Q14444	OTTHUMG00000166248	ENST00000341394.4:c.233A>G	11.37:g.34093289A>G	ENSP00000340329:p.Tyr78Cys	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	106	2	0.0188679	NM_203364	A6NMY7|D3DR06|Q15074|Q6IMN4|Q6IMN7|Q9BV09	Missense_Mutation	SNP	ENST00000341394.4	37	CCDS31453.1	.	.	.	.	.	.	.	.	.	.	A	16.55	3.155176	0.57259	.	.	ENSG00000135387	ENST00000341394;ENST00000389645;ENST00000534825;ENST00000532820;ENST00000530820	T;T;T;T;T	0.30448	1.53;1.53;1.53;1.53;1.53	5.75	5.75	0.90469	.	0.054394	0.85682	D	0.000000	T	0.40886	0.1135	M	0.81942	2.565	0.80722	D	1	B;B	0.18610	0.017;0.029	B;B	0.18871	0.014;0.023	T	0.35624	-0.9781	10	0.87932	D	0	.	16.0478	0.80731	1.0:0.0:0.0:0.0	.	78;78	Q14444;Q14444-2	CAPR1_HUMAN;.	C	78	ENSP00000340329:Y78C;ENSP00000374296:Y78C;ENSP00000431373:Y78C;ENSP00000434150:Y78C;ENSP00000434204:Y78C	ENSP00000340329:Y78C	Y	+	2	0	CAPRIN1	34049865	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.867000	0.92314	2.192000	0.70111	0.460000	0.39030	TAC	.	.	none		0.333	CAPRIN1-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000388680.2	NM_005898	
KANSL1	284058	hgsc.bcm.edu	37	17	44248848	44248848	+	Missense_Mutation	SNP	G	G	A	rs17662853	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:44248848G>A	ENST00000262419.6	-	2	1132	c.662C>T	c.(661-663)aCt>aTt	p.T221I	KANSL1_ENST00000574590.1_Missense_Mutation_p.T221I|KANSL1_ENST00000575318.1_Missense_Mutation_p.T221I|KANSL1_ENST00000576248.1_5'Flank|KANSL1_ENST00000572904.1_Missense_Mutation_p.T221I|KANSL1_ENST00000432791.1_Missense_Mutation_p.T221I|KANSL1_ENST00000393476.3_5'UTR	NM_001193466.1	NP_001180395	Q7Z3B3	KANL1_HUMAN	KAT8 regulatory NSL complex subunit 1	221			T -> I (in dbSNP:rs17662853).		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)											GCTATACAAAGTTGTGTGTTC	0.458													g|||	303	0.0605032	0.003	0.0548	5008	,	,		24355	0.002		0.1779	False		,,,				2504	0.0818				p.T221I		Atlas-SNP	.											.	.	.	.	0			c.C662T						PASS	.	C	ILE/THR,ILE/THR,ILE/THR	142,4264	99.4+/-138.0	5,132,2066	137.0	172.0	160.0		662,662,662	3.3	0.9	17	dbSNP_123	160	1314,7286	252.9+/-278.8	119,1076,3105	yes	missense,missense,missense	KIAA1267	NM_001193465.1,NM_001193466.1,NM_015443.3	89,89,89	124,1208,5171	AA,AG,GG		15.2791,3.2229,11.1948	possibly-damaging,possibly-damaging,possibly-damaging	221/1105,221/1106,221/1106	44248848	1456,11550	2203	4300	6503	SO:0001583	missense	284058	exon2			TACAAAGTTGTGT	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.662C>T	17.37:g.44248848G>A	ENSP00000262419:p.Thr221Ile	Somatic	374	0	0		WXS	Illumina HiSeq	Phase_I	209	98	0.4689	NM_001193466	A8K5E4|Q6AW85|Q8IYH1|Q9BRH0|Q9NTE7|Q9UFT0|Q9ULF3	Missense_Mutation	SNP	ENST00000262419.6	37	CCDS11503.1	170	0.07783882783882784	1	0.0020325203252032522	25	0.06906077348066299	0	0.0	144	0.18997361477572558	g	10.87	1.472307	0.26423	0.032229	0.152791	ENSG00000120071	ENST00000262419;ENST00000432791	T;T	0.12672	2.66;2.66	5.31	3.32	0.38043	.	0.320980	0.34178	N	0.004186	T	0.00012	0.0000	N	0.19112	0.55	0.09310	P	0.999999999899201	P;P	0.51351	0.944;0.557	P;B	0.44477	0.451;0.277	T	0.42413	-0.9453	9	0.41790	T	0.15	-3.0559	10.5955	0.45336	0.0:0.1441:0.7058:0.1501	rs17662853;rs56532017;rs17662853	221;221	C9JHY2;Q7Z3B3	.;K1267_HUMAN	I	221	ENSP00000262419:T221I;ENSP00000387393:T221I	ENSP00000262419:T221I	T	-	2	0	KIAA1267	41604625	1.000000	0.71417	0.935000	0.37517	0.873000	0.50193	3.991000	0.56973	0.898000	0.36418	-1.177000	0.01723	ACT	G|0.900;A|0.100	0.100	strong		0.458	KANSL1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440274.1	NM_015443	
TTC28	23331	hgsc.bcm.edu	37	22	28504258	28504258	+	Silent	SNP	A	A	G	rs9625409	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:28504258A>G	ENST00000397906.2	-	7	1716	c.1575T>C	c.(1573-1575)aaT>aaC	p.N525N		NM_001145418.1	NP_001138890.1	Q96AY4	TTC28_HUMAN	tetratricopeptide repeat domain 28	525					mitotic nuclear division (GO:0007067)|regulation of mitotic cell cycle (GO:0007346)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|midbody (GO:0030496)				endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)	12						TGCCCAGGGCATTGTAGGCAT	0.572													A|||	297	0.0593051	0.0598	0.0677	5008	,	,		18711	0.002		0.0755	False		,,,				2504	0.0951				p.N525N		Atlas-SNP	.											.	TTC28	84	.	0			c.T1575C						PASS	.	A		96,1288		1,94,597	82.0	75.0	77.0		1575	-10.4	0.3	22	dbSNP_119	77	264,2918		15,234,1342	no	coding-synonymous	TTC28	NM_001145418.1		16,328,1939	GG,GA,AA		8.2967,6.9364,7.8844		525/2482	28504258	360,4206	692	1591	2283	SO:0001819	synonymous_variant	23331	exon7			CAGGGCATTGTAG	AB028966	CCDS46678.1	22q12.1	2013-01-10			ENSG00000100154	ENSG00000100154		"""Tetratricopeptide (TTC) repeat domain containing"""	29179	protein-coding gene	gene with protein product		615098				10470851	Standard	NM_001145418		Approved	KIAA1043	uc003adp.4	Q96AY4	OTTHUMG00000151006	ENST00000397906.2:c.1575T>C	22.37:g.28504258A>G		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	97	54	0.556701	NM_001145418	K7ZRV2|O95928|O95929|Q5W189|Q9NTE4|Q9UG31|Q9UGG5|Q9UPV8|Q9Y3S5	Silent	SNP	ENST00000397906.2	37	CCDS46678.1																																																																																			A|0.942;G|0.058	0.058	strong		0.572	TTC28-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000320930.2	XM_929318	
SREBF2	6721	hgsc.bcm.edu	37	22	42300948	42300948	+	Silent	SNP	C	C	A	rs17848337	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:42300948C>A	ENST00000361204.4	+	18	3341	c.3175C>A	c.(3175-3177)Cgg>Agg	p.R1059R	SREBF2_ENST00000491541.1_3'UTR	NM_004599.2	NP_004590.2	Q12772	SRBP2_HUMAN	sterol regulatory element binding transcription factor 2	1059					cellular lipid metabolic process (GO:0044255)|cellular response to laminar fluid shear stress (GO:0071499)|cholesterol metabolic process (GO:0008203)|lipid metabolic process (GO:0006629)|negative regulation of cholesterol efflux (GO:0090370)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cholesterol homeostasis (GO:2000188)|regulation of lipid transport by negative regulation of transcription from RNA polymerase II promoter (GO:0072368)|response to low-density lipoprotein particle (GO:0055098)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi membrane (GO:0000139)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SREBP-SCAP-Insig complex (GO:0032937)	E-box binding (GO:0070888)|protein C-terminus binding (GO:0008022)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(2)|breast(6)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(9)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	38						ACACAGCCTGCGGCGGCGCAC	0.697													C|||	257	0.0513179	0.0068	0.0548	5008	,	,		16694	0.0565		0.0795	False		,,,				2504	0.0746				p.R1059R		Atlas-SNP	.											.	SREBF2	99	.	0			c.C3175A						PASS	.	C		88,4300		1,86,2107	24.0	29.0	27.0		3175	3.2	1.0	22	dbSNP_123	27	627,7961		28,571,3695	no	coding-synonymous	SREBF2	NM_004599.2		29,657,5802	AA,AC,CC		7.3009,2.0055,5.5102		1059/1142	42300948	715,12261	2194	4294	6488	SO:0001819	synonymous_variant	6721	exon18			AGCCTGCGGCGGC	U02031	CCDS14023.1	22q13.2	2013-05-21			ENSG00000198911	ENSG00000198911		"""Basic helix-loop-helix proteins"""	11290	protein-coding gene	gene with protein product		600481				7903453	Standard	NM_004599		Approved	SREBP2, bHLHd2	uc003bbi.3	Q12772	OTTHUMG00000151261	ENST00000361204.4:c.3175C>A	22.37:g.42300948C>A		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	59	21	0.355932	NM_004599	Q05BD5|Q6GTH7|Q86V36|Q9UH04	Silent	SNP	ENST00000361204.4	37	CCDS14023.1	127	0.05815018315018315	5	0.01016260162601626	18	0.049723756906077346	42	0.07342657342657342	62	0.08179419525065963	C	8.985	0.976199	0.18736	0.020055	0.073009	ENSG00000198911	ENST00000435061	.	.	.	5.48	3.18	0.36537	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	.	.	.	.	.	.	.	-31.2823	14.7204	0.69302	0.2233:0.7767:0.0:0.0	rs17848337	.	.	.	X	247	.	.	C	+	3	2	SREBF2	40630894	0.922000	0.31269	0.997000	0.53966	0.821000	0.46438	1.580000	0.36547	2.572000	0.86782	0.491000	0.48974	TGC	C|0.945;A|0.055	0.055	strong		0.697	SREBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321956.1	NM_004599	
PHIP	55023	hgsc.bcm.edu	37	6	79675701	79675701	+	Missense_Mutation	SNP	A	A	G	rs9350797	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:79675701A>G	ENST00000275034.4	-	28	3445	c.3278T>C	c.(3277-3279)cTt>cCt	p.L1093P	PHIP_ENST00000479165.1_5'UTR	NM_017934.5	NP_060404	Q8WWQ0	PHIP_HUMAN	pleckstrin homology domain interacting protein	1093	Mediates interaction with IRS1. {ECO:0000250}.		L -> P (in dbSNP:rs9350797). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005}.		cytoskeleton organization (GO:0007010)|insulin receptor signaling pathway (GO:0008286)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of mitosis (GO:0045840)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein import into nucleus (GO:0006606)|regulation of cell morphogenesis (GO:0022604)|regulation of growth (GO:0040008)|regulation of protein phosphorylation (GO:0001932)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	insulin receptor binding (GO:0005158)|lysine-acetylated histone binding (GO:0070577)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(10)|kidney(4)|large_intestine(20)|lung(20)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	68		all_cancers(76;0.00125)|Acute lymphoblastic leukemia(125;1.1e-05)|all_hematologic(105;0.00117)|all_epithelial(107;0.219)		BRCA - Breast invasive adenocarcinoma(397;0.231)		AGGGTACTCAAGTTGAAGAGG	0.398													A|||	1086	0.216853	0.1672	0.2824	5008	,	,		16263	0.1855		0.3211	False		,,,				2504	0.1626				p.L1093P		Atlas-SNP	.											.	PHIP	177	.	0			c.T3278C						PASS	.	A	PRO/LEU	869,3537	337.0+/-304.7	96,677,1430	146.0	153.0	151.0		3278	2.8	1.0	6	dbSNP_119	151	2594,6006	421.5+/-353.7	413,1768,2119	yes	missense	PHIP	NM_017934.5	98	509,2445,3549	GG,GA,AA		30.1628,19.7231,26.6262	benign	1093/1822	79675701	3463,9543	2203	4300	6503	SO:0001583	missense	55023	exon28			TACTCAAGTTGAA	AF310250	CCDS4987.1	6q14	2013-01-09			ENSG00000146247	ENSG00000146247		"""WD repeat domain containing"", ""DDB1 and CUL4 associated factors"""	15673	protein-coding gene	gene with protein product	"""DDB1 and CUL4 associated factor 14"""	612870		WDR11		11018022	Standard	NM_017934		Approved	ndrp, FLJ20705, DCAF14, BRWD2	uc003pir.3	Q8WWQ0	OTTHUMG00000015071	ENST00000275034.4:c.3278T>C	6.37:g.79675701A>G	ENSP00000275034:p.Leu1093Pro	Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	119	119	1	NM_017934	A7J992|B2RPK4|Q05CQ9|Q5VVH4|Q66I29|Q69YV1|Q8NBZ5|Q96H52|Q96ME2|Q9H261	Missense_Mutation	SNP	ENST00000275034.4	37	CCDS4987.1	576	0.26373626373626374	90	0.18292682926829268	108	0.2983425414364641	126	0.2202797202797203	252	0.3324538258575198	A	3.253	-0.152753	0.06585	0.197231	0.301628	ENSG00000146247	ENST00000275034	T	0.41758	0.99	5.64	2.76	0.32466	.	0.314442	0.32503	N	0.006007	T	0.04137	0.0115	N	0.01242	-0.935	0.21933	P	0.999465749	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.39078	-0.9631	8	.	.	.	-1.3565	6.8281	0.23895	0.1584:0.0:0.7019:0.1397	rs9350797;rs52802348;rs60889537;rs9350797	1093;1093	A7J992;Q8WWQ0	.;PHIP_HUMAN	P	1093	ENSP00000275034:L1093P	.	L	-	2	0	PHIP	79732420	0.998000	0.40836	0.996000	0.52242	0.985000	0.73830	2.470000	0.45119	0.347000	0.23924	-0.248000	0.11899	CTT	A|0.746;G|0.254	0.254	strong		0.398	PHIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041297.2		
OR8S1	341568	hgsc.bcm.edu	37	12	48919793	48919793	+	Missense_Mutation	SNP	T	T	C	rs2705143	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:48919793T>C	ENST00000310194.1	+	1	379	c.379T>C	c.(379-381)Tgc>Cgc	p.C127R	OR8S1_ENST00000551654.1_Intron	NM_001005203.2	NP_001005203.2	Q8NH09	OR8S1_HUMAN	olfactory receptor, family 8, subfamily S, member 1	127				C -> R (in Ref. 1; BAC05832). {ECO:0000305}.		integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(11)|skin(4)	22						TGCTGCCATCTGCCGCCCACT	0.542													T|||	1277	0.254992	0.3419	0.1585	5008	,	,		20153	0.248		0.168	False		,,,				2504	0.3027				p.C127R		Atlas-SNP	.											.	OR8S1	47	.	0			c.T379C						PASS	.	T	ARG/CYS	1214,3192	422.1+/-339.6	163,888,1152	132.0	120.0	124.0		379	3.9	1.0	12	dbSNP_100	124	1529,7071	288.1+/-298.6	130,1269,2901	no	missense	OR8S1	NM_001005203.2	180	293,2157,4053	CC,CT,TT		17.7791,27.5533,21.0903	possibly-damaging	127/360	48919793	2743,10263	2203	4300	6503	SO:0001583	missense	341568	exon1			GCCATCTGCCGCC		CCDS31789.1	12q13.2	2012-08-09				ENSG00000197376		"""GPCR / Class A : Olfactory receptors"""	19628	protein-coding gene	gene with protein product							Standard	NM_001005203		Approved		uc010slu.2	Q8NH09		ENST00000310194.1:c.379T>C	12.37:g.48919793T>C	ENSP00000310632:p.Cys127Arg	Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	128	65	0.507812	NM_001005203		Missense_Mutation	SNP	ENST00000310194.1	37	CCDS31789.1	486	0.22252747252747251	173	0.3516260162601626	64	0.17679558011049723	127	0.22202797202797203	122	0.16094986807387862	T	13.17	2.156350	0.38021	0.275533	0.177791	ENSG00000197376	ENST00000310194	T	0.06218	3.33	5.03	3.89	0.44902	GPCR, rhodopsin-like superfamily (1);	0.000000	0.44902	D	0.000415	T	0.00012	0.0000	H	0.94542	3.55	0.19300	P	0.9999782305	B	0.22080	0.064	B	0.27262	0.078	T	0.16217	-1.0410	9	0.66056	D	0.02	-51.5792	8.8554	0.35225	0.0:0.0888:0.0:0.9112	rs2705143	127	Q8NH09	OR8S1_HUMAN	R	127	ENSP00000310632:C127R	ENSP00000310632:C127R	C	+	1	0	OR8S1	47206060	1.000000	0.71417	1.000000	0.80357	0.857000	0.48899	1.736000	0.38187	0.939000	0.37446	0.533000	0.62120	TGC	T|0.781;C|0.219	0.219	strong		0.542	OR8S1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406881.1		
SLC26A2	1836	hgsc.bcm.edu	37	5	149361221	149361221	+	Missense_Mutation	SNP	A	A	T	rs3776070	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	65	0	0		WXS	Illumina HiSeq	Phase_I	41	15	0.365854	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	
DST	667	hgsc.bcm.edu	37	6	56507489	56507489	+	Missense_Mutation	SNP	A	A	G	rs1024196	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:56507489A>G	ENST00000244364.6	-	1	305	c.98T>C	c.(97-99)tTg>tCg	p.L33S	DST_ENST00000370769.4_Intron|DST_ENST00000361203.3_Intron|DST_ENST00000518935.1_Missense_Mutation_p.L33S|DST_ENST00000370765.6_Missense_Mutation_p.L33S|DST_ENST00000312431.6_Intron|DST_ENST00000446842.2_Missense_Mutation_p.L33S|DST_ENST00000370754.5_Intron|DST_ENST00000370788.2_Intron|DST_ENST00000421834.2_Intron	NM_001144769.2|NM_001144770.1|NM_015548.4|NM_183380.3	NP_001138241.1|NP_001138242.1|NP_056363.2|NP_899236.1	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)			ACAATGAACCAAGAGAAGATT	0.398													G|||	660	0.131789	0.4281	0.0418	5008	,	,		21129	0.0179		0.0288	False		,,,				2504	0.0184				p.L33S		Atlas-SNP	.											.	DST	1427	.	0			c.T98C						PASS	.	G	SER/LEU,SER/LEU	1704,2702	652.5+/-399.4	335,1034,834	127.0	116.0	120.0		98,98	5.9	0.9	6	dbSNP_86	120	379,8221	802.5+/-407.3	9,361,3930	yes	missense,missense	DST	NM_001723.5,NM_015548.4	145,145	344,1395,4764	GG,GA,AA		4.407,38.6745,16.0157	,	33/2650,33/5172	56507489	2083,10923	2203	4300	6503	SO:0001583	missense	667	exon1			TGAACCAAGAGAA	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	ENST00000244364.6:c.98T>C	6.37:g.56507489A>G	ENSP00000244364:p.Leu33Ser	Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	183	93	0.508197	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	ENST00000244364.6	37	CCDS47443.1	258	0.11813186813186813	214	0.4349593495934959	17	0.04696132596685083	9	0.015734265734265736	18	0.023746701846965697	G	5.858	0.342578	0.11069	0.386745	0.04407	ENSG00000151914	ENST00000244364;ENST00000446842;ENST00000439203;ENST00000370765;ENST00000518935	T;T;T;T;T	0.75154	1.07;0.87;-0.39;-0.91;-0.38	5.86	5.86	0.93980	.	.	.	.	.	T	0.29850	0.0746	N	0.02011	-0.69	0.20307	P	0.999917	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	0.14952	-1.0454	8	0.12430	T	0.62	.	15.6237	0.76833	0.0658:0.0:0.9342:0.0	rs1024196;rs58963769;rs1024196	33;33;33;33	Q6P0N6;Q03001-3;Q03001-9;Q03001-8	.;.;.;.	S	33	ENSP00000244364:L33S;ENSP00000393645:L33S;ENSP00000404924:L33S;ENSP00000359801:L33S;ENSP00000431003:L33S	ENSP00000244364:L33S	L	-	2	0	DST	56615448	1.000000	0.71417	0.901000	0.35422	0.306000	0.27790	5.320000	0.65841	1.638000	0.50547	-0.128000	0.14901	TTG	A|0.848;G|0.152	0.152	strong		0.398	DST-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000041022.4	NM_001723	
CANX	821	hgsc.bcm.edu	37	5	179135309	179135309	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:179135309G>A	ENST00000247461.4	+	5	574	c.374G>A	c.(373-375)cGg>cAg	p.R125Q	CANX_ENST00000504734.1_Missense_Mutation_p.R125Q|CANX_ENST00000415618.2_Missense_Mutation_p.R160Q|CANX_ENST00000452673.2_Missense_Mutation_p.R125Q|CANX_ENST00000512607.2_Missense_Mutation_p.R17Q|CANX_ENST00000503126.1_3'UTR	NM_001746.3	NP_001737.1	P27824	CALX_HUMAN	calnexin	125					aging (GO:0007568)|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)|chaperone-mediated protein folding (GO:0061077)|clathrin-mediated endocytosis (GO:0072583)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)|protein secretion (GO:0009306)|synaptic vesicle endocytosis (GO:0048488)	axon (GO:0030424)|dendrite cytoplasm (GO:0032839)|dendritic spine (GO:0043197)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|ER-mitochondrion membrane contact site (GO:0044233)|extracellular vesicular exosome (GO:0070062)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|protein complex (GO:0043234)|ribosome (GO:0005840)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|poly(A) RNA binding (GO:0044822)	p.R125L(1)		breast(1)|endometrium(3)|kidney(4)|large_intestine(2)|lung(7)|prostate(2)|urinary_tract(3)	22	all_cancers(89;0.000129)|all_epithelial(37;5.59e-05)|Renal(175;0.000159)|Lung NSC(126;0.00121)|all_lung(126;0.00218)	all_cancers(40;0.0413)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)		Antihemophilic Factor(DB00025)|Tenecteplase(DB00031)	TTGATGTCTCGGGCCAAGCAT	0.443																																					p.R125Q		Atlas-SNP	.											.	CANX	47	.	1	Substitution - Missense(1)	lung(1)	c.G374A						PASS	.						227.0	212.0	217.0					5																	179135309		2203	4300	6503	SO:0001583	missense	821	exon5			TGTCTCGGGCCAA	L18887	CCDS4447.1	5q35	2008-07-18			ENSG00000127022	ENSG00000127022			1473	protein-coding gene	gene with protein product	"""major histocompatibility complex class I antigen-binding protein p88"""	114217				1326756, 8136357	Standard	NM_001746		Approved	CNX, IP90, P90	uc003mkl.3	P27824	OTTHUMG00000130910	ENST00000247461.4:c.374G>A	5.37:g.179135309G>A	ENSP00000247461:p.Arg125Gln	Somatic	202	0	0		WXS	Illumina HiSeq	Phase_I	246	78	0.317073	NM_001746	B2R5V8|B4DGP8|B4E2T8|D3DWQ3|D6R9K3	Missense_Mutation	SNP	ENST00000247461.4	37	CCDS4447.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	19.66|19.66	3.869769|3.869769	0.72065|0.72065	.|.	.|.	ENSG00000127022|ENSG00000127022	ENST00000510810;ENST00000508787|ENST00000514383;ENST00000502296;ENST00000504734;ENST00000415618;ENST00000452673;ENST00000247461;ENST00000502498;ENST00000502673;ENST00000506654;ENST00000512607;ENST00000354394;ENST00000376953	.|T;T;T;T;T;T;T;T;T;T	.|0.52295	.|0.67;0.67;0.67;0.67;0.67;0.67;0.67;0.67;0.67;0.67	5.81|5.81	5.81|5.81	0.92471|0.92471	.|Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);	.|0.060915	.|0.64402	.|D	.|0.000003	T|T	0.39358|0.39358	0.1075|0.1075	L|L	0.35542|0.35542	1.07|1.07	0.52099|0.52099	D|D	0.999942|0.999942	.|B;B;B	.|0.32245	.|0.361;0.292;0.247	.|B;B;B	.|0.21151	.|0.033;0.018;0.03	T|T	0.19712|0.19712	-1.0297|-1.0297	5|10	.|0.46703	.|T	.|0.11	-17.6381|-17.6381	20.071|20.071	0.97724|0.97724	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|160;61;125	.|B4DGP8;Q6ZP56;P27824	.|.;.;CALX_HUMAN	R|Q	94;8|125;125;125;160;125;125;125;61;17;17;117;61	.|ENSP00000424341:R125Q;ENSP00000424745:R125Q;ENSP00000424063:R125Q;ENSP00000394817:R160Q;ENSP00000391646:R125Q;ENSP00000247461:R125Q;ENSP00000425246:R125Q;ENSP00000421107:R61Q;ENSP00000426555:R17Q;ENSP00000423588:R17Q	.|ENSP00000247461:R125Q	G|R	+|+	1|2	0|0	CANX|CANX	179067915|179067915	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	6.727000|6.727000	0.74764|0.74764	2.754000|2.754000	0.94517|0.94517	0.561000|0.561000	0.74099|0.74099	GGG|CGG	.	.	none		0.443	CANX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253500.2	NM_001024649	
DHRS13	147015	hgsc.bcm.edu	37	17	27228198	27228198	+	Silent	SNP	G	G	A	rs4795474	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:27228198G>A	ENST00000378895.4	-	4	618	c.492C>T	c.(490-492)cgC>cgT	p.R164R	DHRS13_ENST00000426464.2_Silent_p.R83R|DHRS13_ENST00000581974.1_5'Flank|RP11-20B24.4_ENST00000579187.1_RNA|RP11-20B24.4_ENST00000580603.1_RNA|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	232	1	0.00431034		WXS	Illumina HiSeq	Phase_I	177	176	0.99435	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	
RNF26	79102	hgsc.bcm.edu	37	11	119206427	119206427	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:119206427G>A	ENST00000311413.4	+	1	1191	c.595G>A	c.(595-597)Gcc>Acc	p.A199T	RP11-334E6.10_ENST00000501918.2_RNA	NM_032015.4	NP_114404.1	Q9BY78	RNF26_HUMAN	ring finger protein 26	199						integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)			cervix(1)|endometrium(1)|kidney(1)|lung(7)|ovary(1)|prostate(1)	12		Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;3.8e-05)		TGTGGCCATGGCCATCCTCCT	0.622																																					p.A199T		Atlas-SNP	.											RNF26,NS,carcinoma,-1,1	RNF26	23	1	0			c.G595A						PASS	.						122.0	102.0	109.0					11																	119206427		2199	4295	6494	SO:0001583	missense	79102	exon1			GCCATGGCCATCC	AB055622	CCDS8419.1	11q23	2008-07-21				ENSG00000173456		"""RING-type (C3HC4) zinc fingers"""	14646	protein-coding gene	gene with protein product	"""ring finger protein with leucine zipper"""	606130				11352657	Standard	NM_032015		Approved	MGC2642	uc001pwh.3	Q9BY78		ENST00000311413.4:c.595G>A	11.37:g.119206427G>A	ENSP00000312439:p.Ala199Thr	Somatic	197	0	0		WXS	Illumina HiSeq	Phase_I	179	46	0.256983	NM_032015	Q542Y8	Missense_Mutation	SNP	ENST00000311413.4	37	CCDS8419.1	.	.	.	.	.	.	.	.	.	.	G	15.99	2.996878	0.54147	.	.	ENSG00000173456	ENST00000311413	T	0.78816	-1.21	5.12	3.22	0.36961	.	0.171581	0.38663	N	0.001619	T	0.67618	0.2912	L	0.43152	1.355	0.37508	D	0.917046	B	0.10296	0.003	B	0.08055	0.003	T	0.64584	-0.6373	10	0.72032	D	0.01	-5.96	7.4994	0.27509	0.0812:0.0:0.593:0.3257	.	199	Q9BY78	RNF26_HUMAN	T	199	ENSP00000312439:A199T	ENSP00000312439:A199T	A	+	1	0	RNF26	118711637	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	2.146000	0.42216	0.543000	0.28864	0.561000	0.74099	GCC	.	.	none		0.622	RNF26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388220.1	NM_032015	
ELTD1	64123	hgsc.bcm.edu	37	1	79357360	79357360	+	Missense_Mutation	SNP	G	G	C	rs2275902	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:79357360G>C	ENST00000370742.3	-	14	1922	c.1859C>G	c.(1858-1860)gCc>gGc	p.A620G		NM_022159.3	NP_071442.2	Q9HBW9	ELTD1_HUMAN	EGF, latrophilin and seven transmembrane domain containing 1	620			A -> G (in dbSNP:rs2275902). {ECO:0000269|Ref.1}.		G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(1)|breast(1)|endometrium(3)|kidney(2)|large_intestine(10)|lung(45)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	69				COAD - Colon adenocarcinoma(225;0.0905)|Colorectal(170;0.103)|all cancers(265;0.105)|Epithelial(280;0.148)		AAGAGCGAGGGCTCCTCTTGC	0.463													G|||	1266	0.252796	0.2905	0.2046	5008	,	,		18525	0.2312		0.3091	False		,,,				2504	0.2004				p.A620G		Atlas-SNP	.											.	ELTD1	143	.	0			c.C1859G						PASS	.	G	GLY/ALA	1026,2914		138,750,1082	59.0	60.0	60.0		1859	5.6	1.0	1	dbSNP_100	60	2437,5847		343,1751,2048	yes	missense	ELTD1	NM_022159.3	60	481,2501,3130	CC,CG,GG		29.4182,26.0406,28.3295	probably-damaging	620/691	79357360	3463,8761	1970	4142	6112	SO:0001583	missense	64123	exon14			GCGAGGGCTCCTC	AF192403	CCDS41352.1	1p33-p32	2014-08-08			ENSG00000162618	ENSG00000162618		"""-"", ""GPCR / Class B : Orphans"""	20822	protein-coding gene	gene with protein product						11050079	Standard	NM_022159		Approved	ETL	uc001diq.4	Q9HBW9	OTTHUMG00000009738	ENST00000370742.3:c.1859C>G	1.37:g.79357360G>C	ENSP00000359778:p.Ala620Gly	Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	38	18	0.473684	NM_022159	B1AR71|Q5KU34	Missense_Mutation	SNP	ENST00000370742.3	37	CCDS41352.1	573	0.2623626373626374	138	0.2804878048780488	82	0.2265193370165746	120	0.2097902097902098	233	0.3073878627968338	G	27.6	4.843199	0.91197	0.260406	0.294182	ENSG00000162618	ENST00000370742;ENST00000401034	T;T	0.49432	0.78;0.78	5.59	5.59	0.84812	GPCR, family 2-like (1);	0.000000	0.85682	D	0.000000	T	0.69886	0.3161	M	0.86805	2.84	0.09310	P	0.999999999491564	D	0.76494	0.999	D	0.79108	0.992	T	0.73097	-0.4090	8	.	.	.	.	19.5833	0.95478	0.0:0.0:1.0:0.0	rs2275902;rs17403304;rs52818952;rs2275902	620	Q9HBW9	ELTD1_HUMAN	G	620;78	ENSP00000359778:A620G;ENSP00000383813:A78G	.	A	-	2	0	ELTD1	79129948	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	9.835000	0.99442	2.612000	0.88384	0.655000	0.94253	GCC	G|0.733;C|0.266	0.266	strong		0.463	ELTD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026859.1	NM_022159	
TCF19	6941	hgsc.bcm.edu	37	6	31129310	31129310	+	Missense_Mutation	SNP	C	C	T	rs7750641	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:31129310C>T	ENST00000376257.3	+	3	1079	c.325C>T	c.(325-327)Ccc>Tcc	p.P109S	TCF19_ENST00000376255.4_Missense_Mutation_p.P109S|TCF19_ENST00000496421.1_3'UTR	NM_007109.2	NP_009040.2	Q9Y242	TCF19_HUMAN	transcription factor 19	109			P -> S (in dbSNP:rs7750641). {ECO:0000269|PubMed:14574404}.		cell proliferation (GO:0008283)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			kidney(1)|large_intestine(1)|lung(5)|prostate(1)|skin(1)	9						CCCTGAAGGGCCCCCAGGAAC	0.542													C|||	119	0.023762	0.0091	0.0303	5008	,	,		16616	0.0		0.0855	False		,,,				2504	0.0				p.P109S		Atlas-SNP	.											TCF19,colon,carcinoma,0,1	TCF19	16	1	0			c.C325T						PASS	.	C	SER/PRO,SER/PRO	67,2239		1,65,1087	87.0	93.0	91.0		325,325	-1.2	0.4	6	dbSNP_116	91	592,4420		37,518,1951	yes	missense,missense	TCF19	NM_001077511.1,NM_007109.2	74,74	38,583,3038	TT,TC,CC		11.8117,2.9055,9.0052	benign,benign	109/346,109/346	31129310	659,6659	1153	2506	3659	SO:0001583	missense	6941	exon3			GAAGGGCCCCCAG	U25826	CCDS43446.1	6p21.3	2013-01-28	2009-02-05		ENSG00000137310	ENSG00000137310		"""Zinc fingers, PHD-type"""	11629	protein-coding gene	gene with protein product		600912				1868030, 8595903	Standard	NM_001077511		Approved	SC1	uc003nss.3	Q9Y242	OTTHUMG00000031274	ENST00000376257.3:c.325C>T	6.37:g.31129310C>T	ENSP00000365433:p.Pro109Ser	Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	116	49	0.422414	NM_001077511	A6NCT8|B0UY11|Q0EFA8|Q13176|Q15967|Q5SQ89|Q5STD6|Q5STF5|Q9BUM2|Q9UBH7	Missense_Mutation	SNP	ENST00000376257.3	37	CCDS43446.1	84	0.038461538461538464	7	0.014227642276422764	10	0.027624309392265192	0	0.0	67	0.08839050131926121	C	11.15	1.554187	0.27739	0.029055	0.118117	ENSG00000137310	ENST00000376257;ENST00000376255;ENST00000542218	T;T;T	0.22134	2.05;2.05;1.97	5.71	-1.19	0.09585	Forkhead-associated (FHA) domain (1);SMAD/FHA domain (1);	0.729507	0.13820	N	0.360476	T	0.05914	0.0154	L	0.56769	1.78	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.35475	-0.9787	10	0.33940	T	0.23	-23.8533	4.3142	0.10984	0.21:0.3167:0.3941:0.0793	rs7750641;rs9263793;rs57999952;rs7750641	109	Q9Y242	TCF19_HUMAN	S	109;109;29	ENSP00000365433:P109S;ENSP00000365431:P109S;ENSP00000439397:P29S	ENSP00000365431:P109S	P	+	1	0	TCF19	31237289	0.018000	0.18449	0.445000	0.26908	0.921000	0.55340	-0.156000	0.10100	-0.211000	0.10124	0.549000	0.68633	CCC	C|0.947;T|0.053	0.053	strong		0.542	TCF19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076595.2	NM_007109	
PCDHB8	56128	hgsc.bcm.edu	37	5	140558628	140558628	+	Missense_Mutation	SNP	T	T	C	rs62378901	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:140558628T>C	ENST00000239444.2	+	1	1258	c.1013T>C	c.(1012-1014)gTg>gCg	p.V338A	PCDHB16_ENST00000361016.2_5'Flank	NM_019120.3	NP_061993.2	Q9UN66	PCDB8_HUMAN	protocadherin beta 8	338	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(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)			CTGATTCAAGTGATAGATGTG	0.433													T|||	78	0.0155751	0.0015	0.0231	5008	,	,		28542	0.001		0.0547	False		,,,				2504	0.0041				p.V338A		Atlas-SNP	.											.	PCDHB8	199	.	0			c.T1013C						PASS	.	T	ALA/VAL	34,4372	39.2+/-71.8	0,34,2169	205.0	278.0	253.0		1013	4.2	0.5	5	dbSNP_129	253	311,8289	110.2+/-170.6	0,311,3989	no	missense	PCDHB8	NM_019120.3	64	0,345,6158	CC,CT,TT		3.6163,0.7717,2.6526	probably-damaging	338/802	140558628	345,12661	2203	4300	6503	SO:0001583	missense	56128	exon1			TTCAAGTGATAGA	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.1013T>C	5.37:g.140558628T>C	ENSP00000239444:p.Val338Ala	Somatic	317	0	0		WXS	Illumina HiSeq	Phase_I	402	215	0.534826	NM_019120	B9EGV1	Missense_Mutation	SNP	ENST00000239444.2	37	CCDS4250.1	56	0.02564102564102564	1	0.0020325203252032522	11	0.03038674033149171	1	0.0017482517482517483	43	0.05672823218997362	T	18.76	3.693585	0.68386	0.007717	0.036163	ENSG00000120322	ENST00000239444	T	0.68181	-0.31	4.25	4.25	0.50352	Cadherin (5);Cadherin conserved site (1);Cadherin-like (1);	.	.	.	.	T	0.54549	0.1865	H	0.98965	4.385	0.35908	D	0.830913	D	0.89917	1.0	D	0.75484	0.986	D	0.85483	0.1180	9	0.87932	D	0	.	13.0458	0.58925	0.0:0.0:0.0:1.0	rs62378901	338	Q9UN66	PCDB8_HUMAN	A	338	ENSP00000239444:V338A	ENSP00000239444:V338A	V	+	2	0	PCDHB8	140538812	0.991000	0.36638	0.499000	0.27577	0.851000	0.48451	6.261000	0.72509	1.558000	0.49541	0.477000	0.44152	GTG	T|0.976;C|0.024	0.024	strong		0.433	PCDHB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251816.2	NM_019120	
OVCH1	341350	hgsc.bcm.edu	37	12	29642573	29642573	+	Missense_Mutation	SNP	A	A	C	rs967181	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:29642573A>C	ENST00000318184.5	-	6	681	c.682T>G	c.(682-684)Tgg>Ggg	p.W228G		NM_183378.2	NP_899234.2	Q7RTY7	OVCH1_HUMAN	ovochymase 1	228	Peptidase S1 1. {ECO:0000255|PROSITE- ProRule:PRU00274}.		W -> G (in dbSNP:rs967181).			extracellular region (GO:0005576)	metal ion binding (GO:0046872)|serine-type endopeptidase activity (GO:0004252)			NS(2)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(15)|lung(43)|ovary(5)|pancreas(3)|prostate(2)|skin(1)|soft_tissue(1)|stomach(3)	92	Lung NSC(12;1.84e-09)|Acute lymphoblastic leukemia(23;0.00885)|all_hematologic(23;0.0155)					TCCATTCCCCAATCAGGGAAG	0.507													C|||	2116	0.422524	0.3585	0.3012	5008	,	,		19465	0.5685		0.4692	False		,,,				2504	0.3967				p.W228G		Atlas-SNP	.											OVCH1,colon,carcinoma,0,1	OVCH1	195	1	0			c.T682G						PASS	.	C	GLY/TRP	1361,2521		229,903,809	80.0	77.0	78.0		682	0.1	0.0	12	dbSNP_86	78	3578,4670		802,1974,1348	yes	missense	OVCH1	NM_183378.2	184	1031,2877,2157	CC,CA,AA		43.3802,35.0592,40.7172	benign	228/1135	29642573	4939,7191	1941	4124	6065	SO:0001583	missense	341350	exon6			TTCCCCAATCAGG	BN000128		12p11.23	2012-11-08			ENSG00000187950	ENSG00000187950			23080	protein-coding gene	gene with protein product						12838346	Standard	NM_183378		Approved	OVCH	uc001rix.1	Q7RTY7	OTTHUMG00000167741	ENST00000318184.5:c.682T>G	12.37:g.29642573A>C	ENSP00000326708:p.Trp228Gly	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	74	37	0.5	NM_183378		Missense_Mutation	SNP	ENST00000318184.5	37		946	0.43315018315018317	170	0.34552845528455284	101	0.27900552486187846	323	0.5646853146853147	352	0.46437994722955145	C	0	-2.714028	0.00093	0.350592	0.433802	ENSG00000187950	ENST00000318184	D	0.86230	-2.09	2.07	0.0831	0.14432	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	.	.	.	.	T	0.00012	0.0000	N	0.00014	-2.905	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.39251	-0.9623	8	0.02654	T	1	.	1.0202	0.01516	0.2314:0.3908:0.2268:0.151	rs967181;rs57245294;rs967181	228	Q7RTY7	OVCH1_HUMAN	G	228	ENSP00000326708:W228G	ENSP00000326708:W228G	W	-	1	0	OVCH1	29533840	0.004000	0.15560	0.000000	0.03702	0.000000	0.00434	0.817000	0.27281	-0.301000	0.08882	-0.987000	0.02553	TGG	A|0.579;C|0.421	0.421	strong		0.507	OVCH1-001	KNOWN	non_canonical_TEC|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000395997.2	NM_183378	
TAAR6	319100	hgsc.bcm.edu	37	6	132891538	132891538	+	Silent	SNP	C	C	T	rs8192622	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:132891538C>T	ENST00000275198.1	+	1	78	c.78C>T	c.(76-78)ccC>ccT	p.P26P		NM_175067.1	NP_778237.1	Q96RI8	TAAR6_HUMAN	trace amine associated receptor 6	26					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)|trace-amine receptor activity (GO:0001594)	p.P26P(1)		cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(2)|lung(19)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	41	Breast(56;0.112)			OV - Ovarian serous cystadenocarcinoma(155;0.006)|GBM - Glioblastoma multiforme(226;0.00792)		TGAAAATCCCCTTCTCGCCGG	0.507													C|||	128	0.0255591	0.0045	0.0303	5008	,	,		17329	0.0119		0.0477	False		,,,				2504	0.0419				p.P26P		Atlas-SNP	.											.	TAAR6	68	.	1	Substitution - coding silent(1)	lung(1)	c.C78T						PASS	.	C		40,4366	43.8+/-77.6	1,38,2164	143.0	133.0	136.0		78	3.2	1.0	6	dbSNP_117	136	425,8175	130.5+/-188.4	10,405,3885	no	coding-synonymous	TAAR6	NM_175067.1		11,443,6049	TT,TC,CC		4.9419,0.9079,3.5753		26/346	132891538	465,12541	2203	4300	6503	SO:0001819	synonymous_variant	319100	exon1			AATCCCCTTCTCG	AF380192	CCDS5155.1	6q23.1	2012-08-08	2005-02-23	2005-02-24	ENSG00000146383	ENSG00000146383		"""GPCR / Class A : Trace amine associated receptors"""	20978	protein-coding gene	gene with protein product		608923	"""trace amine receptor 4"""	TRAR4		11459929, 15718104	Standard	NM_175067		Approved	TA4	uc011eck.2	Q96RI8	OTTHUMG00000015579	ENST00000275198.1:c.78C>T	6.37:g.132891538C>T		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	88	87	0.988636	NM_175067	Q5VUQ4	Silent	SNP	ENST00000275198.1	37	CCDS5155.1																																																																																			C|0.966;T|0.034	0.034	strong		0.507	TAAR6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042255.1	NM_175067	
C5	727	hgsc.bcm.edu	37	9	123782299	123782299	+	Silent	SNP	G	G	A	rs2230214	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:123782299G>A	ENST00000223642.1	-	12	1490	c.1461C>T	c.(1459-1461)acC>acT	p.T487T		NM_001735.2	NP_001726.2	P01031	CO5_HUMAN	complement component 5	487					activation of MAPK activity (GO:0000187)|cell chemotaxis (GO:0060326)|cell surface receptor signaling pathway (GO:0007166)|cellular calcium ion homeostasis (GO:0006874)|chemotaxis (GO:0006935)|complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|complement activation, classical pathway (GO:0006958)|cytolysis (GO:0019835)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|in utero embryonic development (GO:0001701)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|leukocyte migration involved in inflammatory response (GO:0002523)|negative regulation of dopamine secretion (GO:0033602)|negative regulation of macrophage chemotaxis (GO:0010760)|negative regulation of norepinephrine secretion (GO:0010700)|positive regulation of angiogenesis (GO:0045766)|positive regulation of chemokine secretion (GO:0090197)|positive regulation of chemotaxis (GO:0050921)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of complement activation (GO:0030449)|response to stress (GO:0006950)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane attack complex (GO:0005579)	chemokine activity (GO:0008009)|endopeptidase inhibitor activity (GO:0004866)|receptor binding (GO:0005102)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(14)|lung(5)|ovary(2)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	46				OV - Ovarian serous cystadenocarcinoma(323;4.98e-53)|GBM - Glioblastoma multiforme(294;0.0242)	Eculizumab(DB01257)|Intravenous Immunoglobulin(DB00028)	GGCTTTTGGGGGTAACAATAA	0.353													G|||	445	0.0888578	0.1278	0.0533	5008	,	,		18437	0.0367		0.0984	False		,,,				2504	0.1053				p.T487T		Atlas-SNP	.											.	C5	124	.	0			c.C1461T						PASS	.	G		631,3775	269.8+/-269.2	40,551,1612	107.0	109.0	108.0		1461	-3.9	1.0	9	dbSNP_98	108	910,7690	202.7+/-245.9	52,806,3442	no	coding-synonymous	C5	NM_001735.2		92,1357,5054	AA,AG,GG		10.5814,14.3214,11.8484		487/1677	123782299	1541,11465	2203	4300	6503	SO:0001819	synonymous_variant	727	exon12			TTTGGGGGTAACA	M57729	CCDS6826.1	9q33-q34	2014-09-17			ENSG00000106804	ENSG00000106804		"""Complement system"", ""Endogenous ligands"""	1331	protein-coding gene	gene with protein product	"""prepro-C5"", ""C5a anaphylatoxin"""	120900					Standard	NM_001735		Approved	CPAMD4, C5a, C5b	uc004bkv.3	P01031	OTTHUMG00000020579	ENST00000223642.1:c.1461C>T	9.37:g.123782299G>A		Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	143	66	0.461538	NM_001735	Q14CJ0|Q27I61	Silent	SNP	ENST00000223642.1	37	CCDS6826.1																																																																																			G|0.895;A|0.105	0.105	strong		0.353	C5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053844.1	NM_001735	
LRP2	4036	hgsc.bcm.edu	37	2	170115588	170115588	+	Silent	SNP	T	T	C	rs2241190	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:170115588T>C	ENST00000263816.3	-	17	2745	c.2460A>G	c.(2458-2460)acA>acG	p.T820T	LRP2_ENST00000443831.1_Silent_p.T683T	NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	820					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)"""	ACTGAACTACTGTGCGTCTCG	0.393													T|||	3117	0.622404	0.7141	0.6383	5008	,	,		16091	0.4841		0.4791	False		,,,				2504	0.7771				p.T820T		Atlas-SNP	.											.	LRP2	751	.	0			c.A2460G						PASS	.	T		3037,1369	690.0+/-405.2	1052,933,218	152.0	149.0	150.0		2460	-0.8	0.0	2	dbSNP_98	150	4022,4578	555.8+/-386.7	941,2140,1219	no	coding-synonymous	LRP2	NM_004525.2		1993,3073,1437	CC,CT,TT		46.7674,31.0713,45.725		820/4656	170115588	7059,5947	2203	4300	6503	SO:0001819	synonymous_variant	4036	exon17			AACTACTGTGCGT		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.2460A>G	2.37:g.170115588T>C		Somatic	179	0	0		WXS	Illumina HiSeq	Phase_I	133	70	0.526316	NM_004525	O00711|Q16215	Silent	SNP	ENST00000263816.3	37	CCDS2232.1																																																																																			T|0.449;C|0.551	0.551	strong		0.393	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525	
CEP290	80184	hgsc.bcm.edu	37	12	88520192	88520192	+	Missense_Mutation	SNP	A	A	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:88520192A>T	ENST00000552810.1	-	12	1309	c.966T>A	c.(964-966)gaT>gaA	p.D322E	CEP290_ENST00000397838.3_5'UTR|CEP290_ENST00000309041.7_Missense_Mutation_p.D322E	NM_025114.3	NP_079390.3	O15078	CE290_HUMAN	centrosomal protein 290kDa	322					cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|establishment or maintenance of cell polarity (GO:0007163)|eye photoreceptor cell development (GO:0042462)|G2/M transition of mitotic cell cycle (GO:0000086)|hindbrain development (GO:0030902)|mitotic cell cycle (GO:0000278)|otic vesicle formation (GO:0030916)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of transcription, DNA-templated (GO:0045893)|pronephros development (GO:0048793)|protein transport (GO:0015031)|regulation of cAMP metabolic process (GO:0030814)|regulation of establishment of protein localization (GO:0070201)|retina development in camera-type eye (GO:0060041)	centriolar satellite (GO:0034451)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|photoreceptor connecting cilium (GO:0032391)|protein complex (GO:0043234)|TCTN-B9D complex (GO:0036038)				breast(4)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(20)|liver(1)|lung(18)|ovary(5)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	73						CAATAATTTCATCATCTTTAG	0.294																																					p.D322E		Atlas-SNP	.											.	CEP290	195	.	0			c.T966A						PASS	.						68.0	62.0	64.0					12																	88520192		1794	4063	5857	SO:0001583	missense	80184	exon12			AATTTCATCATCT	AB002371	CCDS55858.1	12q21.33	2014-09-17				ENSG00000198707			29021	protein-coding gene	gene with protein product	"""Joubert syndrome 5"", ""nephrocystin-6"", ""cancer/testis antigen 87"", ""POC3 centriolar protein homolog (Chlamydomonas)"", ""Meckel syndrome, type 4"""	610142				15474516, 16682973, 16632484	Standard	NM_025114		Approved	KIAA0373, FLJ13615, 3H11Ag, rd16, NPHP6, JBTS5, SLSN6, LCA10, MKS4, BBS14, CT87, POC3	uc001tar.3	O15078		ENST00000552810.1:c.966T>A	12.37:g.88520192A>T	ENSP00000448012:p.Asp322Glu	Somatic	234	0	0		WXS	Illumina HiSeq	Phase_I	197	56	0.284264	NM_025114	Q1PSK5|Q66GS8|Q9H2G6|Q9H6Q7|Q9H8I0	Missense_Mutation	SNP	ENST00000552810.1	37	CCDS55858.1	.	.	.	.	.	.	.	.	.	.	A	3.324	-0.138216	0.06669	.	.	ENSG00000198707	ENST00000552810;ENST00000309041;ENST00000536998;ENST00000545139	T;T	0.50813	0.73;0.73	5.26	4.12	0.48240	.	0.239053	0.38897	N	0.001528	T	0.23289	0.0563	N	0.19112	0.55	0.80722	D	1	B;B	0.14805	0.004;0.011	B;B	0.18561	0.009;0.022	T	0.15723	-1.0427	10	0.02654	T	1	.	3.2543	0.06826	0.5547:0.0:0.1648:0.2805	.	322;322	Q05BJ6;O15078	.;CE290_HUMAN	E	322;322;322;224	ENSP00000448012:D322E;ENSP00000308021:D322E	ENSP00000308021:D322E	D	-	3	2	CEP290	87044323	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.545000	0.36169	0.838000	0.34948	0.455000	0.32223	GAT	.	.	none		0.294	CEP290-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000406344.1	NM_025114	
FAM170A	340069	hgsc.bcm.edu	37	5	118969960	118969960	+	Missense_Mutation	SNP	C	C	T	rs328694	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	128	0	0		WXS	Illumina HiSeq	Phase_I	103	44	0.427184	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	
SACS	26278	hgsc.bcm.edu	37	13	23910850	23910850	+	Missense_Mutation	SNP	C	C	T	rs142869943		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:23910850C>T	ENST00000382292.3	-	9	7438	c.7165G>A	c.(7165-7167)Gtg>Atg	p.V2389M	SACS_ENST00000382298.3_Missense_Mutation_p.V2389M|SACS_ENST00000402364.1_Missense_Mutation_p.V1639M			Q9NZJ4	SACS_HUMAN	sacsin molecular chaperone	2389					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)		CTCACACCCACGGTTTCAAAA	0.353													C|||	1	0.000199681	0.0	0.0	5008	,	,		18298	0.0		0.001	False		,,,				2504	0.0				p.V2389M		Atlas-SNP	.											.	SACS	871	.	0			c.G7165A						PASS	.	C	MET/VAL	0,4406		0,0,2203	35.0	36.0	35.0		7165	4.9	1.0	13	dbSNP_134	35	2,8596	2.2+/-6.3	0,2,4297	yes	missense	SACS	NM_014363.4	21	0,2,6500	TT,TC,CC		0.0233,0.0,0.0154	benign	2389/4580	23910850	2,13002	2203	4299	6502	SO:0001583	missense	26278	exon10			CACCCACGGTTTC	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.7165G>A	13.37:g.23910850C>T	ENSP00000371729:p.Val2389Met	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	81	44	0.54321	NM_014363	O94835|Q5T9J5|Q5T9J7|Q5T9J8|Q68DF5|Q6MZR4|Q8NBF9	Missense_Mutation	SNP	ENST00000382292.3	37	CCDS9300.2	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	6.390	0.440092	0.12104	0.0	2.33E-4	ENSG00000151835	ENST00000382292;ENST00000402364;ENST00000382298	D;D;D	0.94000	-3.33;-3.33;-3.33	5.84	4.88	0.63580	.	0.248470	0.41500	D	0.000871	D	0.87541	0.6203	L	0.27053	0.805	0.34084	D	0.659888	B	0.23185	0.081	B	0.18871	0.023	D	0.86770	0.1972	10	0.33940	T	0.23	.	12.7477	0.57289	0.0:0.8603:0.0:0.1397	.	2389	Q9NZJ4	SACS_HUMAN	M	2389;1639;2389	ENSP00000371729:V2389M;ENSP00000385844:V1639M;ENSP00000371735:V2389M	ENSP00000371729:V2389M	V	-	1	0	SACS	22808850	1.000000	0.71417	1.000000	0.80357	0.078000	0.17371	3.105000	0.50314	2.779000	0.95612	0.655000	0.94253	GTG	C|1.000;T|0.000	0.000	strong		0.353	SACS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044148.3	NM_014363	
TTLL4	9654	hgsc.bcm.edu	37	2	219610433	219610433	+	Silent	SNP	A	A	G	rs586194	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:219610433A>G	ENST00000392102.1	+	7	2146	c.1806A>G	c.(1804-1806)gaA>gaG	p.E602E	TTLL4_ENST00000258398.4_Silent_p.E602E|TTLL4_ENST00000442769.1_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	101	0	0		WXS	Illumina HiSeq	Phase_I	106	106	1	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	
SRGAP1	57522	hgsc.bcm.edu	37	12	64519806	64519806	+	Silent	SNP	T	T	C	rs789722	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:64519806T>C	ENST00000355086.3	+	19	2798	c.2274T>C	c.(2272-2274)tcT>tcC	p.S758S	SRGAP1_ENST00000543397.1_Silent_p.S695S|SRGAP1_ENST00000357825.3_Silent_p.S735S	NM_020762.2	NP_065813.1	Q7Z6B7	SRGP1_HUMAN	SLIT-ROBO Rho GTPase activating protein 1	758	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				axon guidance (GO:0007411)|cell migration (GO:0016477)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho GTPase activator activity (GO:0005100)			breast(4)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(26)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	65			GBM - Glioblastoma multiforme(3;0.000139)|BRCA - Breast invasive adenocarcinoma(9;0.225)	GBM - Glioblastoma multiforme(28;0.0608)		TTGGGCGGTCTGCCAGAGAAC	0.522													t|||	2949	0.588858	0.6936	0.4683	5008	,	,		19833	0.6319		0.5398	False		,,,				2504	0.5389				p.S758S		Atlas-SNP	.											.	SRGAP1	146	.	0			c.T2274C						PASS	.	C		3054,1352	693.2+/-405.6	1050,954,199	146.0	123.0	131.0		2274	-9.5	0.7	12	dbSNP_86	131	4344,4256	580.3+/-391.0	1097,2150,1053	no	coding-synonymous	SRGAP1	NM_020762.2		2147,3104,1252	CC,CT,TT		49.4884,30.6854,43.1186		758/1086	64519806	7398,5608	2203	4300	6503	SO:0001819	synonymous_variant	57522	exon19			GCGGTCTGCCAGA	AB037725	CCDS8967.1	12q13.13	2011-07-04			ENSG00000196935	ENSG00000196935		"""Rho GTPase activating proteins"""	17382	protein-coding gene	gene with protein product		606523				11672528	Standard	NM_020762		Approved	KIAA1304, ARHGAP13	uc010ssp.1	Q7Z6B7	OTTHUMG00000168750	ENST00000355086.3:c.2274T>C	12.37:g.64519806T>C		Somatic	233	0	0		WXS	Illumina HiSeq	Phase_I	217	92	0.423963	NM_020762	Q9H8A3|Q9P2P2	Silent	SNP	ENST00000355086.3	37	CCDS8967.1																																																																																			T|0.405;C|0.595	0.595	strong		0.522	SRGAP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000400896.1		
LZTS2	84445	hgsc.bcm.edu	37	10	102766574	102766574	+	Silent	SNP	A	A	G	rs807024|rs386747052	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:102766574A>G	ENST00000370220.1	+	4	4722	c.1659A>G	c.(1657-1659)gcA>gcG	p.A553A	LZTS2_ENST00000370223.3_Silent_p.A553A					leucine zipper, putative tumor suppressor 2											breast(1)|large_intestine(6)|lung(7)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	22				Epithelial(162;7.3e-09)|all cancers(201;3.72e-07)		TCCTCCTGGCAGAGAGTGATG	0.697													A|||	1840	0.367412	0.385	0.3271	5008	,	,		14091	0.5387		0.2346	False		,,,				2504	0.3323				p.A553A	Esophageal Squamous(8;38 437 13604 19902 37640)	Atlas-SNP	.											LZTS2,colon,carcinoma,+1,1	LZTS2	57	1	0			c.A1659G						PASS	.	A		1461,2925		264,933,996	10.0	12.0	12.0		1659	-10.8	0.2	10	dbSNP_86	12	2083,6487		279,1525,2481	no	coding-synonymous	LZTS2	NM_032429.2		543,2458,3477	GG,GA,AA		24.3057,33.3105,27.3541		553/670	102766574	3544,9412	2193	4285	6478	SO:0001819	synonymous_variant	84445	exon5			CCTGGCAGAGAGT	AB058716	CCDS7507.1	10q24	2004-03-18			ENSG00000107816	ENSG00000107816			29381	protein-coding gene	gene with protein product		610454				11347906, 11709705	Standard	NM_032429		Approved	KIAA1813, LAPSER1	uc001ksj.3	Q9BRK4	OTTHUMG00000018914	ENST00000370220.1:c.1659A>G	10.37:g.102766574A>G		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	62	32	0.516129	NM_032429		Silent	SNP	ENST00000370220.1	37	CCDS7507.1																																																																																			A|0.651;G|0.349	0.349	strong		0.697	LZTS2-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049872.1	XM_046743	
OR5T1	390155	hgsc.bcm.edu	37	11	56043604	56043604	+	Missense_Mutation	SNP	A	A	G	rs12360890	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:56043604A>G	ENST00000313033.2	+	1	576	c.490A>G	c.(490-492)Agc>Ggc	p.S164G		NM_001004745.1	NP_001004745.1	Q8NG75	OR5T1_HUMAN	olfactory receptor, family 5, subfamily T, member 1	164			S -> G (in dbSNP:rs12360890).			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(5)|kidney(1)|large_intestine(2)|lung(27)|ovary(2)|pancreas(1)|prostate(2)|skin(1)	43	Esophageal squamous(21;0.00448)					CTATGTTGCTAGCATTTTACA	0.438													N|||	2210	0.441294	0.1649	0.5821	5008	,	,		22277	0.6478		0.3708	False		,,,				2504	0.5746				p.S164G		Atlas-SNP	.											.	OR5T1	95	.	0			c.A490G						PASS	.	G	GLY/SER	887,3515	740.4+/-411.2	94,699,1408	270.0	230.0	243.0		490	0.4	0.0	11	dbSNP_120	243	3190,5402	651.3+/-400.8	610,1970,1716	no	missense	OR5T1	NM_001004745.1	56	704,2669,3124	GG,GA,AA		37.1276,20.1499,31.376	benign	164/327	56043604	4077,8917	2201	4296	6497	SO:0001583	missense	390155	exon1			GTTGCTAGCATTT	AB065962	CCDS31525.1	11q11	2012-08-09		2004-03-10	ENSG00000181698	ENSG00000181698		"""GPCR / Class A : Olfactory receptors"""	14821	protein-coding gene	gene with protein product				OR5T1P			Standard	NM_001004745		Approved		uc001nio.1	Q8NG75	OTTHUMG00000166853	ENST00000313033.2:c.490A>G	11.37:g.56043604A>G	ENSP00000323612:p.Ser164Gly	Somatic	330	0	0		WXS	Illumina HiSeq	Phase_I	258	56	0.217054	NM_001004745	B2RNM9	Missense_Mutation	SNP	ENST00000313033.2	37	CCDS31525.1	873	0.39972527472527475	62	0.12601626016260162	201	0.5552486187845304	350	0.6118881118881119	260	0.34300791556728233	G	0.011	-1.717357	0.00706	0.201499	0.371276	ENSG00000181698	ENST00000313033	T	0.40476	1.03	3.44	0.435	0.16544	GPCR, rhodopsin-like superfamily (1);	0.000000	0.51477	N	0.000089	T	0.00012	0.0000	N	0.00178	-1.915	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.40850	-0.9541	9	0.02654	T	1	.	3.9789	0.09486	0.3848:0.0:0.4522:0.163	rs12360890;rs52827403;rs58144141;rs12360890	164	Q8NG75	OR5T1_HUMAN	G	164	ENSP00000323612:S164G	ENSP00000323612:S164G	S	+	1	0	OR5T1	55800180	0.064000	0.20934	0.001000	0.08648	0.019000	0.09904	1.817000	0.39002	-0.007000	0.14345	-0.405000	0.06341	AGC	A|0.653;G|0.347	0.347	strong		0.438	OR5T1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391600.1	NM_001004745	
AR	367	hgsc.bcm.edu	37	X	66765158	66765158	+	Missense_Mutation	SNP	T	T	A	rs78686797|rs3032358|rs4045402		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:66765158T>A	ENST00000374690.3	+	1	694	c.170T>A	c.(169-171)cTg>cAg	p.L57Q	AR_ENST00000396044.3_Missense_Mutation_p.L57Q|AR_ENST00000504326.1_Missense_Mutation_p.L57Q|AR_ENST00000513847.1_3'UTR	NM_000044.3	NP_000035.2	P10275	ANDR_HUMAN	androgen receptor	57	Modulating.|Poly-Leu.		L -> Q (in prostate cancer).		androgen receptor signaling pathway (GO:0030521)|cell death (GO:0008219)|cell growth (GO:0016049)|cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of integrin biosynthetic process (GO:0045720)|positive regulation of cell proliferation (GO:0008284)|positive regulation of integrin biosynthetic process (GO:0045726)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of phosphorylation (GO:0042327)|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)|prostate gland development (GO:0030850)|protein oligomerization (GO:0051259)|regulation of establishment of protein localization to plasma membrane (GO:0090003)|sex differentiation (GO:0007548)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transport (GO:0006810)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	androgen binding (GO:0005497)|androgen receptor activity (GO:0004882)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein dimerization activity (GO:0046983)|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)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)	p.L57Q(3)		breast(4)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(12)|lung(20)|ovary(3)|prostate(11)|stomach(2)|upper_aerodigestive_tract(3)	67	all_cancers(1;0.173)|Prostate(1;2.27e-16)|all_epithelial(1;0.102)	all_lung(315;1.3e-11)			Bicalutamide(DB01128)|Cyproterone acetate(DB04839)|Danazol(DB01406)|Drospirenone(DB01395)|Drostanolone(DB00858)|Enzalutamide(DB08899)|Fludrocortisone(DB00687)|Fluoxymesterone(DB01185)|Flutamide(DB00499)|Ketoconazole(DB01026)|Levonorgestrel(DB00367)|Methyltestosterone(DB06710)|Nandrolone decanoate(DB08804)|Nandrolone phenpropionate(DB00984)|Nilutamide(DB00665)|Oxandrolone(DB00621)|Spironolactone(DB00421)|Testosterone Propionate(DB01420)|Testosterone(DB00624)	TTGCTGCTGCTgcagcagcag	0.667									Androgen Insensitivity Syndrome																												p.L57Q		Atlas-SNP	.											.	AR	249	.	3	Substitution - Missense(3)	lung(1)|endometrium(1)|central_nervous_system(1)	c.T170A						PASS	.						9.0	12.0	11.0					X																	66765158		2134	4208	6342	SO:0001583	missense	367	exon1	Familial Cancer Database	CAIS, Testicular Feminisation, AIS, Morris syndrome; incl. Reifenstein Syndrome	TGCTGCTGCAGCA	M20132	CCDS14387.1, CCDS43965.1	Xq12	2013-01-16	2008-08-07		ENSG00000169083	ENSG00000169083		"""Nuclear hormone receptors"""	644	protein-coding gene	gene with protein product	"""testicular feminization"", ""Kennedy disease"""	313700	"""dihydrotestosterone receptor"", ""spinal and bulbar muscular atrophy"""	DHTR, SBMA		3353726, 3377788	Standard	NM_000044		Approved	AIS, NR3C4, SMAX1, HUMARA	uc004dwu.2	P10275	OTTHUMG00000021740	ENST00000374690.3:c.170T>A	X.37:g.66765158T>A	ENSP00000363822:p.Leu57Gln	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	47	6	0.12766	NM_000044	A2RUN2|B1AKD7|Q9UD95	Missense_Mutation	SNP	ENST00000374690.3	37	CCDS14387.1	.	.	.	.	.	.	.	.	.	.	N	0.020	-1.439011	0.01098	.	.	ENSG00000169083	ENST00000374690;ENST00000504326;ENST00000396044;ENST00000538891	D;D;D	0.83992	-1.79;-1.79;-1.79	.	.	.	.	0.157526	0.30101	N	0.010412	T	0.56441	0.1985	N	0.03608	-0.345	0.09310	N	0.999999	.	.	.	.	.	.	T	0.48927	-0.8991	6	0.20519	T	0.43	.	.	.	.	.	57;57;55	E7EVX6;D3YPQ2;P10275	.;.;ANDR_HUMAN	Q	57	ENSP00000363822:L57Q;ENSP00000421155:L57Q;ENSP00000379359:L57Q	ENSP00000363822:L57Q	L	+	2	0	AR	66681883	0.999000	0.42202	0.884000	0.34674	0.488000	0.33401	0.326000	0.19646	0.000000	0.14550	0.000000	0.15137	CTG	.	.	weak		0.667	AR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057007.1	NM_000044	
CDHR2	54825	hgsc.bcm.edu	37	5	176017455	176017455	+	Missense_Mutation	SNP	C	C	T	rs2291442	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:176017455C>T	ENST00000510636.1	+	27	3657	c.3383C>T	c.(3382-3384)aCg>aTg	p.T1128M	CDHR2_ENST00000506348.1_Missense_Mutation_p.T1128M|CDHR2_ENST00000261944.5_Missense_Mutation_p.T1128M	NM_001171976.1	NP_001165447.1	Q9BYE9	CDHR2_HUMAN	cadherin-related family member 2	1128			T -> M (in dbSNP:rs2291442). {ECO:0000269|PubMed:12117771, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		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						GACTCGCTGACGCAGCTGCTG	0.637													c|||	1413	0.282149	0.3033	0.2334	5008	,	,		16317	0.3194		0.2445	False		,,,				2504	0.2883				p.T1128M		Atlas-SNP	.											CDHR2,colon,carcinoma,0,1	CDHR2	152	1	0			c.C3383T						PASS	.		MET/THR,MET/THR	1332,3074	446.3+/-348.0	180,972,1051	65.0	67.0	66.0		3383,3383	0.3	0.0	5	dbSNP_100	66	2337,6263	389.7+/-343.0	298,1741,2261	yes	missense,missense	CDHR2	NM_001171976.1,NM_017675.4	81,81	478,2713,3312	TT,TC,CC		27.1744,30.2315,28.2101	benign,benign	1128/1311,1128/1311	176017455	3669,9337	2203	4300	6503	SO:0001583	missense	54825	exon27			CGCTGACGCAGCT	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.3383C>T	5.37:g.176017455C>T	ENSP00000424565:p.Thr1128Met	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	156	95	0.608974	NM_017675	A1L3U4|A6NC80|Q9NXP8	Missense_Mutation	SNP	ENST00000510636.1	37	CCDS34297.1	616	0.28205128205128205	138	0.2804878048780488	104	0.287292817679558	181	0.31643356643356646	193	0.2546174142480211	c	3.170	-0.170179	0.06461	0.302315	0.271744	ENSG00000074276	ENST00000510636;ENST00000261944;ENST00000506348	T;T;T	0.55760	0.5;0.5;0.5	4.61	0.292	0.15737	.	.	.	.	.	T	0.00012	0.0000	N	0.17674	0.51	0.80722	P	0.0	B	0.13145	0.007	B	0.06405	0.002	T	0.30149	-0.9988	8	0.45353	T	0.12	-2.7345	3.7294	0.08487	0.1833:0.5449:0.112:0.1598	rs2291442;rs59204096;rs2291442	1128	Q9BYE9	CDHR2_HUMAN	M	1128	ENSP00000424565:T1128M;ENSP00000261944:T1128M;ENSP00000421078:T1128M	ENSP00000261944:T1128M	T	+	2	0	CDHR2	175950061	0.000000	0.05858	0.030000	0.17652	0.184000	0.23303	-1.990000	0.01479	-0.169000	0.10834	-1.263000	0.01449	ACG	C|0.719;T|0.281	0.281	strong		0.637	CDHR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372201.1	NM_017675	
HLA-A	3105	hgsc.bcm.edu	37	6	29910558	29910558	+	Missense_Mutation	SNP	T	T	A	rs386698549|rs2075684	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:29910558T>A	ENST00000396634.1	+	4	439	c.98T>A	c.(97-99)tTc>tAc	p.F33Y	HLA-A_ENST00000376802.2_Missense_Mutation_p.F33Y|HLA-A_ENST00000376809.5_Missense_Mutation_p.F33Y|HLA-A_ENST00000376806.5_Missense_Mutation_p.F33Y			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	33	Alpha-1.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	beta-2-microglobulin binding (GO:0030881)|peptide antigen binding (GO:0042605)|TAP binding (GO:0046977)	p.F33S(1)		central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	30						AGGTATTTCTTCACATCCGTG	0.726									Osteosarcoma, Familial Clustering of;Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of;Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of	Multiple Myeloma(9;0.094)			N|||	1103	0.220248	0.1641	0.1556	5008	,	,		13512	0.3333		0.1471	False		,,,				2504	0.3006				p.F33Y		Atlas-SNP	.											HLA-A,NS,lymphoid_neoplasm,0,1	HLA-A	89	1	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.T98A						scavenged	.						16.0	15.0	15.0					6																	29910558		2180	4265	6445	SO:0001583	missense	3105	exon2	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	ATTTCTTCACATC	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.98T>A	6.37:g.29910558T>A	ENSP00000379873:p.Phe33Tyr	Somatic	26	1	0.0384615		WXS	Illumina HiSeq	Phase_I	38	15	0.394737	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Missense_Mutation	SNP	ENST00000396634.1	37	CCDS34373.1	.	.	.	.	.	.	.	.	.	.	.	3.323	-0.138290	0.06669	.	.	ENSG00000206503	ENST00000396634;ENST00000376806;ENST00000376809;ENST00000355767;ENST00000376802	T;T;T;T	0.00008	9.61;9.61;9.61;9.61	3.72	-2.31	0.06765	MHC class I, alpha chain, alpha1/alpha2 (1);MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);	20.031000	0.00447	N	0.000090	T	0.00012	0.0000	.	.	.	0.09310	N	1	B;B;B	0.24092	0.097;0.0;0.0	B;B;B	0.42062	0.374;0.002;0.002	T	0.28902	-1.0029	9	0.02654	T	1	.	5.7818	0.18310	0.2651:0.4571:0.0:0.2778	rs2075684;rs3179175;rs17423951;rs41542415	33;33;33	Q5SRN7;Q5SRN5;P04439	.;.;1A03_HUMAN	Y	33	ENSP00000379873:F33Y;ENSP00000366002:F33Y;ENSP00000366005:F33Y;ENSP00000365998:F33Y	ENSP00000348012:F33Y	F	+	2	0	HLA-A	30018537	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-6.129000	0.00079	-0.931000	0.03746	-4.308000	0.00007	TTC	T|0.574;C|0.414;A|0.012	0.012	strong		0.726	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
LRP3	4037	hgsc.bcm.edu	37	19	33698448	33698448	+	Silent	SNP	G	G	A	rs3745973	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	62	0	0		WXS	Illumina HiSeq	Phase_I	48	28	0.583333	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		
NFE2L3	9603	hgsc.bcm.edu	37	7	26224323	26224323	+	Silent	SNP	T	T	C	rs113074870		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:26224323T>C	ENST00000056233.3	+	4	1264	c.1005T>C	c.(1003-1005)acT>acC	p.T335T		NM_004289.6	NP_004280.5	Q9Y4A8	NF2L3_HUMAN	nuclear factor, erythroid 2-like 3	335					transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			breast(2)|endometrium(1)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|prostate(2)|skin(5)|urinary_tract(7)	29						CAGCAAGGACTTCACAGTCAC	0.418																																					p.T335T		Atlas-SNP	.											.	NFE2L3	77	.	0			c.T1005C						PASS	.						108.0	96.0	100.0					7																	26224323		2203	4300	6503	SO:0001819	synonymous_variant	9603	exon4			AAGGACTTCACAG	AB010812	CCDS5396.1	7p15.2	2013-08-23	2013-08-23		ENSG00000050344	ENSG00000050344		"""basic leucine zipper proteins"""	7783	protein-coding gene	gene with protein product		604135	"""nuclear factor (erythroid-derived 2)-like 3"""			10037736	Standard	NM_004289		Approved	Nrf3	uc003sxq.3	Q9Y4A8	OTTHUMG00000023882	ENST00000056233.3:c.1005T>C	7.37:g.26224323T>C		Somatic	382	0	0		WXS	Illumina HiSeq	Phase_I	465	71	0.152688	NM_004289	Q6NUS0|Q7Z498|Q86UJ4|Q86VR5|Q9UQA4	Silent	SNP	ENST00000056233.3	37	CCDS5396.1																																																																																			T|0.500;C|0.500	0.500	weak		0.418	NFE2L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214088.1		
MUC4	4585	hgsc.bcm.edu	37	3	195508969	195508969	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195508969G>A	ENST00000463781.3	-	2	9941	c.9482C>T	c.(9481-9483)gCa>gTa	p.A3161V	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.A3161V	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		ACCTGTGGATGCTGAGGAAGT	0.587																																					p.A3161V		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,-1,1	MUC4	1505	1	0			c.C9482T						scavenged	.						5.0	3.0	4.0					3																	195508969		555	1269	1824	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.9482C>T	3.37:g.195508969G>A	ENSP00000417498:p.Ala3161Val	Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	52	9	0.173077	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	5.833	0.337875	0.11013	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.37058	1.22;1.32	.	.	.	.	.	.	.	.	T	0.15998	0.0385	N	0.19112	0.55	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.18903	-1.0322	7	.	.	.	.	2.115	0.03712	0.498:0.0:0.2477:0.2543	.	3033	E7ESK3	.	V	3161	ENSP00000417498:A3161V;ENSP00000420243:A3161V	.	A	-	2	0	MUC4	196993748	0.000000	0.05858	0.016000	0.15963	0.016000	0.09150	-4.416000	0.00237	-2.005000	0.00959	-1.973000	0.00462	GCA	.	.	none		0.587	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
NRP1	8829	hgsc.bcm.edu	37	10	33510663	33510663	+	Silent	SNP	G	G	A	rs2229935	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:33510663G>A	ENST00000265371.4	-	9	1791	c.1266C>T	c.(1264-1266)taC>taT	p.Y422Y	NRP1_ENST00000374821.5_Silent_p.Y422Y|NRP1_ENST00000374823.5_Silent_p.Y422Y|NRP1_ENST00000395995.1_Silent_p.Y422Y|NRP1_ENST00000374867.2_Silent_p.Y422Y|NRP1_ENST00000432372.2_Silent_p.Y422Y|NRP1_ENST00000374816.3_Silent_p.Y422Y|NRP1_ENST00000374875.1_Silent_p.Y241Y|NRP1_ENST00000374822.4_Silent_p.Y422Y			O14786	NRP1_HUMAN	neuropilin 1	422	F5/8 type C 1. {ECO:0000255|PROSITE- ProRule:PRU00081}.				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)	TCTTGCAACCGTATACTTCAA	0.393													A|||	1798	0.359026	0.1793	0.4337	5008	,	,		18709	0.623		0.2485	False		,,,				2504	0.3906				p.Y422Y	Melanoma(104;886 1489 44640 45944 51153)	Atlas-SNP	.											.	NRP1	126	.	0			c.C1266T						PASS	.	A	,,	917,3489	738.2+/-411.0	99,719,1385	150.0	145.0	146.0		1266,1266,1266	-0.6	0.8	10	dbSNP_111	146	2285,6315	706.9+/-405.6	302,1681,2317	no	coding-synonymous,coding-synonymous,coding-synonymous	NRP1	NM_001024628.2,NM_001024629.2,NM_003873.5	,,	401,2400,3702	AA,AG,GG		26.5698,20.8125,24.6194	,,	422/645,422/610,422/924	33510663	3202,9804	2203	4300	6503	SO:0001819	synonymous_variant	8829	exon8			GCAACCGTATACT	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.1266C>T	10.37:g.33510663G>A		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	126	50	0.396825	NM_001244973	B0LPG9|O60461|Q5T7F1|Q5T7F2|Q5T7F3|Q86T59|Q96I90|Q96IH5	Silent	SNP	ENST00000265371.4	37	CCDS7177.1																																																																																			G|0.708;A|0.292	0.292	strong		0.393	NRP1-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051203.2		
KIAA1549	57670	hgsc.bcm.edu	37	7	138602523	138602523	+	Missense_Mutation	SNP	T	T	C	rs2774962	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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						PASS	.	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	89	0	0		WXS	Illumina HiSeq	Phase_I	78	39	0.5	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		
TMCO3	55002	hgsc.bcm.edu	37	13	114157846	114157846	+	Silent	SNP	G	G	A	rs9805588	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:114157846G>A	ENST00000434316.2	+	6	1340	c.981G>A	c.(979-981)ggG>ggA	p.G327G	TMCO3_ENST00000375391.1_Silent_p.G327G|TMCO3_ENST00000474393.1_3'UTR	NM_017905.4	NP_060375.4	Q6UWJ1	TMCO3_HUMAN	transmembrane and coiled-coil domains 3	327						integral component of membrane (GO:0016021)	solute:proton antiporter activity (GO:0015299)			NS(1)|endometrium(4)|large_intestine(9)|liver(1)|lung(8)|prostate(1)|stomach(1)	25	Lung NSC(43;0.0161)|all_neural(89;0.0337)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0145)|all_epithelial(44;0.00286)|all_lung(25;0.0273)|Breast(118;0.0411)|Lung NSC(25;0.0983)	all cancers(43;0.0317)			GAGAATTTGGGGTGTTTTTTA	0.343													G|||	376	0.0750799	0.0802	0.0706	5008	,	,		18099	0.001		0.1461	False		,,,				2504	0.0746				p.G327G		Atlas-SNP	.											.	TMCO3	77	.	0			c.G981A						PASS	.	G		298,4108	161.8+/-193.9	12,274,1917	257.0	244.0	248.0		981	-10.8	0.2	13	dbSNP_119	248	1002,7598	215.6+/-254.9	66,870,3364	no	coding-synonymous	TMCO3	NM_017905.4		78,1144,5281	AA,AG,GG		11.6512,6.7635,9.9954		327/678	114157846	1300,11706	2203	4300	6503	SO:0001819	synonymous_variant	55002	exon6			ATTTGGGGTGTTT	BC012564	CCDS9537.1	13q34	2008-02-05	2005-07-22	2005-07-22	ENSG00000150403	ENSG00000150403			20329	protein-coding gene	gene with protein product			"""chromosome 13 open reading frame 11"""	C13orf11			Standard	NM_017905		Approved	FLJ20623	uc001vtu.4	Q6UWJ1	OTTHUMG00000017389	ENST00000434316.2:c.981G>A	13.37:g.114157846G>A		Somatic	245	0	0		WXS	Illumina HiSeq	Phase_I	192	96	0.5	NM_017905	Q5JSB1|Q6NUN1|Q8NG29|Q8TCI6|Q96EA6|Q9NWT2	Silent	SNP	ENST00000434316.2	37	CCDS9537.1																																																																																			G|0.905;A|0.095	0.095	strong		0.343	TMCO3-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045931.3	NM_017905	
PLEKHH2	130271	hgsc.bcm.edu	37	2	43926943	43926943	+	Silent	SNP	T	T	A	rs7606783	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	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	231	0	0		WXS	Illumina HiSeq	Phase_I	300	298	0.993333	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	
CLEC4M	10332	hgsc.bcm.edu	37	19	7831047	7831047	+	Silent	SNP	G	G	A	rs868878	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:7831047G>A	ENST00000327325.5	+	4	856	c.738G>A	c.(736-738)aaG>aaA	p.K246K	CLEC4M_ENST00000334806.5_Silent_p.K195K|CLEC4M_ENST00000595496.1_Intron|CLEC4M_ENST00000596707.1_Intron|CLEC4M_ENST00000394122.2_Silent_p.K234K|CLEC4M_ENST00000357361.2_Silent_p.K246K|CLEC4M_ENST00000597522.1_Intron|CLEC4M_ENST00000596363.1_Silent_p.K218K|CLEC4M_ENST00000359059.5_Intron|CLEC4M_ENST00000248228.4_Silent_p.K224K	NM_001144909.1|NM_014257.4	NP_001138381.1|NP_055072.3	Q9H2X3	CLC4M_HUMAN	C-type lectin domain family 4, member M	246	7 X approximate tandem repeats.				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						ACCAGTCCAAGCAGCAGCAAA	0.527													G|||	309	0.0617013	0.0076	0.0807	5008	,	,		21992	0.0506		0.1551	False		,,,				2504	0.0368				p.K246K		Atlas-SNP	.											.	CLEC4M	58	.	0			c.G738A						PASS	.	G	,,,,,,,,	130,4276	94.8+/-133.5	3,124,2076	147.0	150.0	149.0		585,666,,,,600,669,654,738	0.5	0.1	19	dbSNP_86	149	1130,7470	233.3+/-266.6	72,986,3242	no	coding-synonymous,coding-synonymous,intron,intron,intron,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	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	,,,,,,,,	75,1110,5318	AA,AG,GG		13.1395,2.9505,9.6878	,,,,,,,,	195/349,222/376,,,,200/354,223/377,218/297,246/400	7831047	1260,11746	2203	4300	6503	SO:0001819	synonymous_variant	10332	exon4			GTCCAAGCAGCAG	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.738G>A	19.37:g.7831047G>A		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	47	17	0.361702	NM_014257	A6NKI4|A8K8B3|Q69F40|Q969M4|Q96QP3|Q96QP4|Q96QP5|Q96QP6|Q9BXS3|Q9H2Q9|Q9H8F0|Q9Y2A8	Silent	SNP	ENST00000327325.5	37	CCDS12187.1																																																																																			A|0.087;C|0.000;G|0.913	0.087	strong		0.527	CLEC4M-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000461161.1	NM_014257	
SEMA4B	10509	hgsc.bcm.edu	37	15	90768271	90768271	+	Silent	SNP	C	C	T	rs11547966	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:90768271C>T	ENST00000411539.2	+	10	1526	c.1266C>T	c.(1264-1266)ttC>ttT	p.F422F	SEMA4B_ENST00000332496.6_Silent_p.F422F|SEMA4B_ENST00000379122.3_Silent_p.F417F	NM_198925.2	NP_945119.1	Q9NPR2	SEM4B_HUMAN	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4B	417	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				cell differentiation (GO:0030154)|nervous system development (GO:0007399)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synapse (GO:0045202)	receptor activity (GO:0004872)			NS(1)|breast(2)|endometrium(1)|kidney(2)|large_intestine(2)|lung(2)|ovary(1)|stomach(1)	12	Melanoma(11;0.00551)|Lung NSC(78;0.0125)|all_lung(78;0.0272)		BRCA - Breast invasive adenocarcinoma(143;0.0107)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.217)			TGCTGAACTTCCTCAAGGACC	0.622													C|||	706	0.140974	0.0787	0.1571	5008	,	,		20691	0.0556		0.2575	False		,,,				2504	0.182				p.F422F		Atlas-SNP	.											.	SEMA4B	51	.	0			c.C1266T						PASS	.	C	,	403,3897		12,379,1759	84.0	95.0	91.0		1266,1266	5.2	1.0	15	dbSNP_120	91	2005,6499		224,1557,2471	no	coding-synonymous,coding-synonymous	SEMA4B	NM_020210.3,NM_198925.2	,	236,1936,4230	TT,TC,CC		23.5771,9.3721,18.8066	,	422/838,422/838	90768271	2408,10396	2150	4252	6402	SO:0001819	synonymous_variant	10509	exon11			GAACTTCCTCAAG	AB051532	CCDS45347.1	15q25	2008-07-18						"""Semaphorins"""	10730	protein-coding gene	gene with protein product				SEMAC		7748561	Standard	NM_020210		Approved	SemC, KIAA1745, MGC131831	uc002boz.3	Q9NPR2		ENST00000411539.2:c.1266C>T	15.37:g.90768271C>T		Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	187	111	0.593583	NM_020210	Q6UXE3|Q8WVP9|Q96FK5|Q9C0B8|Q9H691|Q9NPM8|Q9NPN0	Silent	SNP	ENST00000411539.2	37	CCDS45347.1																																																																																			C|0.835;T|0.165	0.165	strong		0.622	SEMA4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416810.1	NM_198925	
FURIN	5045	hgsc.bcm.edu	37	15	91424574	91424574	+	Silent	SNP	G	G	C	rs6226	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:91424574G>C	ENST00000268171.3	+	16	2130	c.1851G>C	c.(1849-1851)ggG>ggC	p.G617G		NM_002569.2	NP_002560.1	P09958	FURIN_HUMAN	furin (paired basic amino acid cleaving enzyme)	617					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)			GCCCTCCAGGGTTCGCCCCCC	0.622													C|||	3615	0.721845	0.9735	0.6556	5008	,	,		18766	0.5357		0.6958	False		,,,				2504	0.6472				p.G617G		Atlas-SNP	.											FURIN,NS,carcinoma,+2,1	FURIN	85	1	0			c.G1851C						PASS	.	C		4070,326	165.8+/-197.2	1884,302,12	66.0	62.0	63.0		1851	1.6	0.3	15	dbSNP_52	63	5855,2739	412.6+/-350.9	1988,1879,430	no	coding-synonymous	FURIN	NM_002569.2		3872,2181,442	CC,CG,GG		31.8711,7.4158,23.5951		617/795	91424574	9925,3065	2198	4297	6495	SO:0001819	synonymous_variant	5045	exon16			TCCAGGGTTCGCC	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.1851G>C	15.37:g.91424574G>C		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	118	36	0.305085	NM_002569	Q14336|Q6LBS3|Q9UCZ5	Silent	SNP	ENST00000268171.3	37	CCDS10364.1																																																																																			C|0.737;G|0.263	0.737	strong		0.622	FURIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313492.1	NM_002569	
NOS1	4842	hgsc.bcm.edu	37	12	117693817	117693817	+	Missense_Mutation	SNP	G	G	A	rs11068428	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:117693817G>A	ENST00000338101.4	-	16	2561	c.2557C>T	c.(2557-2559)Ccc>Tcc	p.P853S	NOS1_ENST00000317775.6_Intron|NOS1_ENST00000344089.3_Intron			Q8WY41	NANO1_HUMAN	nitric oxide synthase 1 (neuronal)	0					cell migration (GO:0016477)|epithelial cell migration (GO:0010631)|negative regulation of translation (GO:0017148)	cytoplasm (GO:0005737)|perinuclear region of cytoplasm (GO:0048471)	RNA binding (GO:0003723)|translation repressor activity (GO:0030371)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(17)|large_intestine(21)|lung(43)|ovary(3)|pancreas(1)|prostate(6)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	117	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.0561)		CCTTTACGGGGAAAGAAACGC	0.592													G|||	1740	0.347444	0.2012	0.5231	5008	,	,		18489	0.502		0.3161	False		,,,				2504	0.2935				p.P853S	Esophageal Squamous(162;1748 2599 51982 52956)	Atlas-SNP	.											.	NOS1	240	.	0			c.C2557T						PASS	.	G	,,,SER/PRO	332,1420		40,252,584	152.0	137.0	142.0		,,,2557	5.1	1.0	12	dbSNP_120	142	1251,2731		204,843,944	yes	intron,intron,intron,missense	NOS1	NM_000620.4,NM_001204213.1,NM_001204214.1,NM_001204218.1	,,,74	244,1095,1528	AA,AG,GG		31.4164,18.9498,27.6073	,,,	,,,853/1469	117693817	1583,4151	876	1991	2867	SO:0001583	missense	4842	exon17			TACGGGGAAAGAA		CCDS41842.1, CCDS55890.1	12q24.22	2013-09-19			ENSG00000089250	ENSG00000089250	1.14.13.39		7872	protein-coding gene	gene with protein product		163731		NOS		1385308, 7682706	Standard	NM_001204213		Approved	nNOS	uc001twn.2	P29475	OTTHUMG00000137376	ENST00000338101.4:c.2557C>T	12.37:g.117693817G>A	ENSP00000337459:p.Pro853Ser	Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	56	32	0.571429	NM_001204218		Missense_Mutation	SNP	ENST00000338101.4	37	CCDS55890.1	790	0.3617216117216117	95	0.19308943089430894	181	0.5	265	0.4632867132867133	249	0.32849604221635886	G	10.24	1.296247	0.23650	0.189498	0.314164	ENSG00000089250	ENST00000338101;ENST00000544320	T	0.01265	5.08	5.93	5.05	0.67936	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.09310	P	1.0	.	.	.	.	.	.	T	0.05750	-1.0866	6	0.27082	T	0.32	-22.5766	11.0829	0.48070	0.0844:0.0:0.9156:0.0	rs11068428;rs11068428	.	.	.	S	853;19	ENSP00000337459:P853S	ENSP00000337459:P853S	P	-	1	0	NOS1	116178200	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.955000	0.49121	1.529000	0.49120	0.655000	0.94253	CCC	G|0.651;A|0.349	0.349	strong		0.592	NOS1-002	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000268053.1		
MUC2	4583	hgsc.bcm.edu	37	11	1092890	1092890	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:1092890C>T	ENST00000441003.2	+	30	4736	c.4709C>T	c.(4708-4710)aCc>aTc	p.T1570I	MUC2_ENST00000359061.5_Missense_Mutation_p.T1571I|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)				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)	ACCACGGTGaccccaacccca	0.637																																					p.T1570I		Atlas-SNP	.											MUC2_ENST00000441003,NS,carcinoma,-1,2	MUC2	614	2	0			c.C4709T						scavenged	.						119.0	156.0	143.0					11																	1092890		1961	3652	5613	SO:0001583	missense	4583	exon30			CGGTGACCCCAAC	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.4709C>T	11.37:g.1092890C>T	ENSP00000415183:p.Thr1570Ile	Somatic	45	2	0.0444444		WXS	Illumina HiSeq	Phase_I	75	9	0.12	NM_002457	Q14878	Missense_Mutation	SNP	ENST00000441003.2	37		.	.	.	.	.	.	.	.	.	.	C	1.561	-0.536608	0.04082	.	.	ENSG00000198788	ENST00000441003;ENST00000359061	T;T	0.15487	2.42;3.24	1.3	-2.33	0.06724	.	0.589600	0.12692	U	0.447130	T	0.07548	0.0190	.	.	.	0.09310	N	1	P	0.34699	0.464	B	0.21546	0.035	T	0.24799	-1.0150	9	0.38643	T	0.18	.	4.395	0.11358	0.3284:0.4793:0.1923:0.0	.	1570	E7EUV1	.	I	1570;1571	ENSP00000415183:T1570I;ENSP00000351956:T1571I	ENSP00000351956:T1571I	T	+	2	0	MUC2	1082890	0.002000	0.14202	0.000000	0.03702	0.033000	0.12548	0.404000	0.20999	-0.107000	0.12088	0.064000	0.15345	ACC	.	.	none		0.637	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
KCNJ12	3768	hgsc.bcm.edu	37	17	21318770	21318770	+	Missense_Mutation	SNP	G	G	A	rs3752033	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:21318770G>A	ENST00000583088.1	+	3	1011	c.116G>A	c.(115-117)cGg>cAg	p.R39Q	KCNJ12_ENST00000331718.5_Missense_Mutation_p.R39Q	NM_021012.4	NP_066292.2	Q14500	KCJ12_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 12	39					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)	GTGCACACGCGGCGCAGGTGC	0.617										Prostate(3;0.18)			.|||	1734	0.346246	0.1505	0.366	5008	,	,		36674	0.4812		0.3559	False		,,,				2504	0.4479				p.R39Q		Atlas-SNP	.											.	.	.	.	0			c.G116A						PASS	.	G	GLN/ARG	526,3880		0,526,1677	114.0	87.0	96.0		116	5.3	1.0	17	dbSNP_107	96	2294,6306		0,2294,2006	yes	missense	KCNJ12	NM_021012.4	43	0,2820,3683	AA,AG,GG		26.6744,11.9383,21.6823	possibly-damaging	39/434	21318770	2820,10186	2203	4300	6503	SO:0001583	missense	100134444	exon3			ACACGCGGCGCAG	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.116G>A	17.37:g.21318770G>A	ENSP00000463778:p.Arg39Gln	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	118	29	0.245763	NM_001194958	O43401|Q15756|Q8NG63	Missense_Mutation	SNP	ENST00000583088.1	37	CCDS11219.1	714	0.3269230769230769	78	0.15853658536585366	121	0.3342541436464088	267	0.46678321678321677	248	0.32717678100263853	G	22.8	4.332021	0.81801	0.119383	0.266744	ENSG00000184185	ENST00000331718	T	0.61980	0.06	5.33	5.33	0.75918	Potassium channel, inwardly rectifying, Kir, N-terminal (1);	0.193728	0.40385	U	0.001108	T	0.00012	0.0000	L	0.52759	1.655	0.58432	D	0.999999	P	0.37276	0.589	B	0.36766	0.232	T	0.43909	-0.9362	10	0.42905	T	0.14	.	19.026	0.92932	0.0:0.0:1.0:0.0	rs3752033;rs3752033	39	Q14500	IRK12_HUMAN	Q	39	ENSP00000328150:R39Q	ENSP00000328150:R39Q	R	+	2	0	KCNJ12	21259363	1.000000	0.71417	0.985000	0.45067	0.979000	0.70002	9.690000	0.98676	2.506000	0.84524	0.591000	0.81541	CGG	G|0.743;A|0.257	0.257	strong		0.617	KCNJ12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255060.2	NM_021012	
ZNF592	9640	hgsc.bcm.edu	37	15	85326939	85326939	+	Missense_Mutation	SNP	C	C	A	rs138966830		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:85326939C>A	ENST00000560079.2	+	4	1321	c.1033C>A	c.(1033-1035)Cca>Aca	p.P345T	ZNF592_ENST00000299927.3_Missense_Mutation_p.P345T	NM_014630.2	NP_055445.2	Q92610	ZN592_HUMAN	zinc finger protein 592	345					cell death (GO:0008219)|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.P345S(1)		breast(2)|endometrium(2)|kidney(1)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(2)|urinary_tract(1)	40			BRCA - Breast invasive adenocarcinoma(143;0.0587)			AAGTATCAAGCCATCGGACAG	0.547																																					p.P345T		Atlas-SNP	.											ZNF592,arm,malignant_melanoma,0,1	ZNF592	95	1	1	Substitution - Missense(1)	skin(1)	c.C1033A						PASS	.						72.0	82.0	78.0					15																	85326939		2203	4299	6502	SO:0001583	missense	9640	exon4			ATCAAGCCATCGG	D86966	CCDS32317.1	15q25.2	2011-03-15				ENSG00000166716		"""Zinc fingers, C2H2-type"""	28986	protein-coding gene	gene with protein product		613624	"""spinocerebellar ataxia, autosomal recessive 5"""	SCAR5		9039502, 12030328, 20531441	Standard	NM_014630		Approved	KIAA0211, CAMOS	uc002bld.3	Q92610		ENST00000560079.2:c.1033C>A	15.37:g.85326939C>A	ENSP00000452877:p.Pro345Thr	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	121	42	0.347107	NM_014630	Q2M1T2|Q504Y9	Missense_Mutation	SNP	ENST00000560079.2	37	CCDS32317.1	.	.	.	.	.	.	.	.	.	.	C	16.61	3.171393	0.57584	.	.	ENSG00000166716	ENST00000299927	T	0.00620	6.17	5.59	5.59	0.84812	.	0.158983	0.56097	D	0.000026	T	0.02494	0.0076	M	0.61703	1.905	0.43771	D	0.996292	D	0.67145	0.996	P	0.59948	0.866	T	0.65467	-0.6161	10	0.40728	T	0.16	-5.8358	17.0815	0.86600	0.0:1.0:0.0:0.0	.	345	Q92610	ZN592_HUMAN	T	345	ENSP00000299927:P345T	ENSP00000299927:P345T	P	+	1	0	ZNF592	83127943	1.000000	0.71417	1.000000	0.80357	0.818000	0.46254	5.786000	0.69006	2.628000	0.89032	0.655000	0.94253	CCA	A|0.001;C|0.999	0.001	weak		0.547	ZNF592-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418779.2	NM_014630	
KRTAP4-6	81871	hgsc.bcm.edu	37	17	39296254	39296254	+	Silent	SNP	C	C	T	rs72483263		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:39296254C>T	ENST00000345847.4	-	1	485	c.486G>A	c.(484-486)ccG>ccA	p.P162P		NM_030976.1	NP_112238.1	Q9BYQ5	KRA46_HUMAN	keratin associated protein 4-6	162	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						ggcagcagcacgggcggcagc	0.662																																					p.P162P		Atlas-SNP	.											.	KRTAP4-6	46	.	0			c.G486A						PASS	.																																			SO:0001819	synonymous_variant	81871	exon1			GCAGCACGGGCGG	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.486G>A	17.37:g.39296254C>T		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	90	26	0.288889	NM_030976	Q9BYR1	Silent	SNP	ENST00000345847.4	37	CCDS54125.1																																																																																			C|0.500;T|0.500	0.500	weak		0.662	KRTAP4-6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257779.1		
DYNC2H1	79659	hgsc.bcm.edu	37	11	103058126	103058126	+	Silent	SNP	C	C	T	rs586592	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:103058126C>T	ENST00000375735.2	+	43	7095	c.6951C>T	c.(6949-6951)caC>caT	p.H2317H	DYNC2H1_ENST00000398093.3_Silent_p.H2317H|DYNC2H1_ENST00000334267.7_Intron	NM_001080463.1|NM_001377.2	NP_001073932.1|NP_001368.2	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1	2317	AAA 3. {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)		CTACAGTTCACTGTAGTGCAC	0.433													T|||	3090	0.617013	0.6596	0.6873	5008	,	,		17977	0.5526		0.6243	False		,,,				2504	0.5685				p.H2317H		Atlas-SNP	.											.	DYNC2H1	246	.	0			c.C6951T						PASS	.	T	,	2728,1320		930,868,226	123.0	121.0	122.0		6951,6951	2.1	1.0	11	dbSNP_83	122	5274,3108		1664,1946,581	no	coding-synonymous,coding-synonymous	DYNC2H1	NM_001080463.1,NM_001377.2	,	2594,2814,807	TT,TC,CC		37.0795,32.6087,35.6235	,	2317/4315,2317/4308	103058126	8002,4428	2024	4191	6215	SO:0001819	synonymous_variant	79659	exon43			AGTTCACTGTAGT	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.6951C>T	11.37:g.103058126C>T		Somatic	152	1	0.00657895		WXS	Illumina HiSeq	Phase_I	119	118	0.991597	NM_001377	O00432|Q16693|Q3C1U8|Q4AC93|Q6ZMX7|Q6ZUM6|Q7Z363|Q8N977|Q92815|Q9HAE4	Silent	SNP	ENST00000375735.2	37	CCDS53701.1																																																																																			C|0.378;T|0.622	0.622	strong		0.433	DYNC2H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387196.1	XM_370652	
GPR98	84059	hgsc.bcm.edu	37	5	90086955	90086955	+	Missense_Mutation	SNP	G	G	A	rs41304892	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:90086955G>A	ENST00000405460.2	+	70	14405	c.14309G>A	c.(14308-14310)cGc>cAc	p.R4770H	GPR98_ENST00000425867.2_Missense_Mutation_p.R431H	NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	4770					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)		TATTCGGATCGCCAGTCAATA	0.453													G|||	7	0.00139776	0.0	0.0029	5008	,	,		19442	0.0		0.005	False		,,,				2504	0.0				p.R4770H		Atlas-SNP	.											.	GPR98	605	.	0			c.G14309A						PASS	.	G	HIS/ARG	1,3827		0,1,1913	105.0	95.0	98.0		14309	-7.1	0.0	5	dbSNP_127	98	50,8186		0,50,4068	yes	missense	GPR98	NM_032119.3	29	0,51,5981	AA,AG,GG		0.6071,0.0261,0.4227	benign	4770/6307	90086955	51,12013	1914	4118	6032	SO:0001583	missense	84059	exon70			CGGATCGCCAGTC	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.14309G>A	5.37:g.90086955G>A	ENSP00000384582:p.Arg4770His	Somatic	255	1	0.00392157		WXS	Illumina HiSeq	Phase_I	269	115	0.427509	NM_032119	O75171|Q8TF58|Q9H0X5|Q9UL61	Missense_Mutation	SNP	ENST00000405460.2	37	CCDS47246.1	6	0.0027472527472527475	0	0.0	1	0.0027624309392265192	0	0.0	5	0.006596306068601583	G	6.244	0.413073	0.11812	2.61E-4	0.006071	ENSG00000164199	ENST00000405460;ENST00000296619;ENST00000425867	T;T	0.35236	1.32;1.32	5.77	-7.1	0.01547	.	1.043920	0.07336	N	0.879923	T	0.10423	0.0255	N	0.02539	-0.55	0.09310	N	1	B;B;B	0.10296	0.001;0.003;0.002	B;B;B	0.01281	0.0;0.0;0.0	T	0.36890	-0.9729	10	0.19147	T	0.46	.	16.6102	0.84881	0.6714:0.0:0.3286:0.0	rs41304892;rs61999354	431;4770;431	E7EML1;Q8WXG9;Q8WXG9-2	.;GPR98_HUMAN;.	H	4770;4770;431	ENSP00000384582:R4770H;ENSP00000392618:R431H	ENSP00000296619:R4770H	R	+	2	0	GPR98	90122711	0.000000	0.05858	0.000000	0.03702	0.846000	0.48090	-0.098000	0.11024	-1.543000	0.01723	0.561000	0.74099	CGC	G|0.997;A|0.003	0.003	strong		0.453	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119	
ZNF423	23090	hgsc.bcm.edu	37	16	49671177	49671177	+	Missense_Mutation	SNP	T	T	C	rs34214571	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:49671177T>C	ENST00000561648.1	-	4	1939	c.1886A>G	c.(1885-1887)aAt>aGt	p.N629S	ZNF423_ENST00000262383.2_Missense_Mutation_p.N629S|ZNF423_ENST00000535559.1_Missense_Mutation_p.N512S|ZNF423_ENST00000563137.2_Missense_Mutation_p.N569S|ZNF423_ENST00000562520.1_Missense_Mutation_p.N569S|ZNF423_ENST00000562871.1_Missense_Mutation_p.N569S|ZNF423_ENST00000567169.1_Missense_Mutation_p.N512S	NM_001271620.1	NP_001258549.1	Q2M1K9	ZN423_HUMAN	zinc finger protein 423	629			N -> S (in dbSNP:rs34214571).		cell differentiation (GO:0030154)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|Notch signaling pathway (GO:0007219)|positive regulation of BMP signaling pathway (GO:0030513)|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)			breast(1)|central_nervous_system(1)|endometrium(8)|kidney(6)|large_intestine(16)|lung(47)|ovary(1)|pancreas(2)|prostate(4)|skin(1)|urinary_tract(2)	89		all_cancers(37;0.0155)				ATACTCCCCATTGGAGATGGA	0.577													T|||	111	0.0221645	0.0129	0.0144	5008	,	,		21834	0.0149		0.0398	False		,,,				2504	0.0297				p.N629S		Atlas-SNP	.											.	ZNF423	463	.	0			c.A1886G						PASS	.	T	SER/ASN	82,4314	70.3+/-108.2	0,82,2116	76.0	71.0	73.0		1886	4.8	1.0	16	dbSNP_126	73	275,8325	104.8+/-165.8	4,267,4029	yes	missense	ZNF423	NM_015069.2	46	4,349,6145	CC,CT,TT		3.1977,1.8653,2.747	benign	629/1285	49671177	357,12639	2198	4300	6498	SO:0001583	missense	23090	exon4			TCCCCATTGGAGA	AB018303	CCDS32445.1, CCDS61930.1	16q12	2014-01-28				ENSG00000102935		"""Zinc fingers, C2H2-type"""	16762	protein-coding gene	gene with protein product	"""OLF-1/EBF associated zinc finger gene"", "" Smad- and Olf-interacting zinc finger protein"", ""early B-cell factor associated zinc finger protein"""	604557				9872452, 10660046	Standard	NM_001271620		Approved	KIAA0760, OAZ, Roaz, Ebfaz, Zfp104, NPHP14, JBTS19	uc031qwd.1	Q2M1K9		ENST00000561648.1:c.1886A>G	16.37:g.49671177T>C	ENSP00000455426:p.Asn629Ser	Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	183	75	0.409836	NM_015069	O94860|Q76N04|Q9NZ13	Missense_Mutation	SNP	ENST00000561648.1	37	CCDS32445.1	48	0.02197802197802198	7	0.014227642276422764	5	0.013812154696132596	5	0.008741258741258742	31	0.040897097625329816	T	5.315	0.243536	0.10077	0.018653	0.031977	ENSG00000102935	ENST00000262383;ENST00000535559	T;T	0.08720	3.06;3.11	4.78	4.78	0.61160	.	0.044527	0.85682	D	0.000000	T	0.01287	0.0042	N	0.19112	0.55	0.45403	D	0.998388	B	0.09022	0.002	B	0.09377	0.004	T	0.43458	-0.9390	9	.	.	.	.	14.3363	0.66592	0.0:0.0:0.0:1.0	rs34214571	629	Q2M1K9	ZN423_HUMAN	S	629;512	ENSP00000262383:N629S;ENSP00000442321:N512S	.	N	-	2	0	ZNF423	48228678	1.000000	0.71417	0.987000	0.45799	0.959000	0.62525	5.940000	0.70187	1.793000	0.52555	0.459000	0.35465	AAT	T|0.972;C|0.028	0.028	strong		0.577	ZNF423-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000423258.1	NM_015069	
RERG	85004	hgsc.bcm.edu	37	12	15262179	15262179	+	Silent	SNP	G	G	A	rs1055151	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:15262179G>A	ENST00000256953.2	-	5	801	c.465C>T	c.(463-465)aaC>aaT	p.N155N	RERG_ENST00000546331.1_Silent_p.N136N|RERG_ENST00000538313.1_Silent_p.N155N|RERG_ENST00000536465.1_Silent_p.N155N	NM_032918.2	NP_116307.1	Q96A58	RERG_HUMAN	RAS-like, estrogen-regulated, growth inhibitor	155					negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|response to hormone (GO:0009725)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	estrogen receptor binding (GO:0030331)|GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)			NS(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	16						TCTCTGTGATGTTCCCTTCTC	0.547													G|||	1229	0.245407	0.115	0.2478	5008	,	,		18500	0.3016		0.3012	False		,,,				2504	0.3047				p.N155N		Atlas-SNP	.											.	RERG	30	.	0			c.C465T						PASS	.	G	,	644,3762	278.7+/-274.4	42,560,1601	154.0	134.0	140.0		408,465	-2.0	0.9	12	dbSNP_86	140	2617,5983	424.1+/-354.6	400,1817,2083	no	coding-synonymous,coding-synonymous	RERG	NM_001190726.1,NM_032918.2	,	442,2377,3684	AA,AG,GG		30.4302,14.6164,25.073	,	136/181,155/200	15262179	3261,9745	2203	4300	6503	SO:0001819	synonymous_variant	85004	exon5			TGTGATGTTCCCT	AF339750	CCDS8673.1, CCDS53753.1	12p13.1	2014-05-09			ENSG00000134533	ENSG00000134533			15980	protein-coding gene	gene with protein product		612664				11533059	Standard	NM_032918		Approved	MGC15754	uc001rct.3	Q96A58	OTTHUMG00000168745	ENST00000256953.2:c.465C>T	12.37:g.15262179G>A		Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	158	70	0.443038	NM_032918	B2R9R0|B4DI02	Silent	SNP	ENST00000256953.2	37	CCDS8673.1																																																																																			G|0.741;A|0.259	0.259	strong		0.547	RERG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400882.1	NM_032918	
PTH1R	5745	hgsc.bcm.edu	37	3	46944274	46944274	+	Silent	SNP	T	T	C	rs1138518	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:46944274T>C	ENST00000313049.5	+	13	1592	c.1389T>C	c.(1387-1389)aaT>aaC	p.N463N	PTH1R_ENST00000430002.2_Silent_p.N463N|PTH1R_ENST00000449590.1_Silent_p.N463N|PTH1R_ENST00000418619.1_Silent_p.N463N			Q03431	PTH1R_HUMAN	parathyroid hormone 1 receptor	463					adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|aging (GO:0007568)|bone mineralization (GO:0030282)|bone resorption (GO:0045453)|cell maturation (GO:0048469)|chondrocyte differentiation (GO:0002062)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|negative regulation of cell proliferation (GO:0008285)|osteoblast development (GO:0002076)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of inositol phosphate biosynthetic process (GO:0060732)|skeletal system development (GO:0001501)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|brush border membrane (GO:0031526)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	parathyroid hormone receptor activity (GO:0004991)|peptide hormone binding (GO:0017046)|protein self-association (GO:0043621)	p.N463N(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|liver(1)|lung(5)|skin(2)|stomach(1)|urinary_tract(2)	19					Preotact(DB05829)|Teriparatide(DB06285)	GTTTCTGCAATGGCGAGGTAA	0.557													C|||	3222	0.643371	0.8215	0.6513	5008	,	,		17106	0.4425		0.6431	False		,,,				2504	0.6043				p.N463N		Atlas-SNP	.											PTH1R,NS,carcinoma,0,1	PTH1R	49	1	1	Substitution - coding silent(1)	stomach(1)	c.T1389C						PASS	.	C	,	3520,886	344.6+/-308.2	1407,706,90	102.0	112.0	109.0		1389,1389	-8.4	0.6	3	dbSNP_86	109	5320,3280	491.4+/-373.1	1652,2016,632	no	coding-synonymous,coding-synonymous	PTH1R	NM_000316.2,NM_001184744.1	,	3059,2722,722	CC,CT,TT		38.1395,20.1089,32.0314	,	463/594,463/594	46944274	8840,4166	2203	4300	6503	SO:0001819	synonymous_variant	5745	exon14			CTGCAATGGCGAG		CCDS2747.1	3p22-p21.1	2012-08-10	2008-11-18	2008-11-18	ENSG00000160801	ENSG00000160801		"""GPCR / Class B : Parathyroid hormone receptors"""	9608	protein-coding gene	gene with protein product		168468	"""parathyroid hormone receptor 1"""	PTHR, PTHR1		8020952	Standard	NM_001184744		Approved		uc021wxg.1	Q03431	OTTHUMG00000133515	ENST00000313049.5:c.1389T>C	3.37:g.46944274T>C		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	93	35	0.376344	NM_001184744	Q2M1U3	Silent	SNP	ENST00000313049.5	37	CCDS2747.1																																																																																			T|0.343;C|0.657	0.657	strong		0.557	PTH1R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257481.1	NM_000316	
CDHR5	53841	hgsc.bcm.edu	37	11	618013	618013	+	Missense_Mutation	SNP	C	C	T	rs7108757	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:618013C>T	ENST00000358353.3	-	15	2381	c.2059G>A	c.(2059-2061)Gcc>Acc	p.A687T	IRF7_ENST00000397562.3_5'Flank|IRF7_ENST00000397574.2_5'Flank|CDHR5_ENST00000397542.2_Missense_Mutation_p.A687T|IRF7_ENST00000348655.6_5'Flank|IRF7_ENST00000397566.1_5'Flank|IRF7_ENST00000525445.1_5'Flank|IRF7_ENST00000397570.1_5'Flank|CDHR5_ENST00000349570.7_Missense_Mutation_p.A493T|IRF7_ENST00000330243.5_5'Flank			Q9HBB8	CDHR5_HUMAN	cadherin-related family member 5	687					cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(7)|ovary(1)|skin(2)	23						ACAAGGACGGCGAGGCCAAGG	0.682													C|||	853	0.170327	0.2708	0.2464	5008	,	,		12071	0.0198		0.2137	False		,,,				2504	0.091				p.A687T		Atlas-SNP	.											.	CDHR5	77	.	0			c.G2059A						PASS	.	C	THR/ALA,THR/ALA,THR/ALA	1212,3188	402.4+/-332.3	172,868,1160	51.0	48.0	49.0		2041,2059,1477	-3.3	0.0	11	dbSNP_116	49	2084,6514	348.1+/-326.9	227,1630,2442	yes	missense,missense,missense	CDHR5	NM_001171968.1,NM_021924.4,NM_031264.3	58,58,58	399,2498,3602	TT,TC,CC		24.2382,27.5455,25.3577	benign,benign,benign	681/840,687/846,493/652	618013	3296,9702	2200	4299	6499	SO:0001583	missense	53841	exon14			GGACGGCGAGGCC	AF258675	CCDS7707.1, CCDS7708.1	11p15.5	2011-07-01	2010-01-25	2010-01-25	ENSG00000099834	ENSG00000099834		"""Cadherins / Cadherin-related"""	7521	protein-coding gene	gene with protein product		606839	"""mucin and cadherin-like"", ""mucin-like protocadherin"""	MUCDHL, MUPCDH		11031102, 10801787	Standard	NM_021924		Approved	FLJ20219, MU-PCDH	uc001lqj.3	Q9HBB8	OTTHUMG00000132018	ENST00000358353.3:c.2059G>A	11.37:g.618013C>T	ENSP00000351118:p.Ala687Thr	Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	161	132	0.819876	NM_021924	C9J7X1|Q9H746|Q9HAU3|Q9HBB5|Q9HBB6|Q9HBB7|Q9NX86|Q9NXI9	Missense_Mutation	SNP	ENST00000358353.3	37	CCDS7707.1	402	0.18406593406593408	140	0.2845528455284553	97	0.26795580110497236	8	0.013986013986013986	157	0.20712401055408972	C	2.676	-0.276429	0.05679	0.275455	0.242382	ENSG00000099834	ENST00000397542;ENST00000358353;ENST00000349570	T;T;T	0.44881	1.01;1.01;0.91	3.05	-3.27	0.05048	.	.	.	.	.	T	0.00012	0.0000	N	0.04880	-0.145	0.80722	P	0.0	B;B;B	0.12013	0.0;0.003;0.005	B;B;B	0.08055	0.001;0.002;0.003	T	0.35992	-0.9766	8	0.35671	T	0.21	0.0039	9.5846	0.39508	0.0:0.5125:0.0:0.4875	rs7108757	681;493;687	Q9HBB8-4;Q9HBB8-2;Q9HBB8	.;.;CDHR5_HUMAN	T	687;687;493	ENSP00000380676:A687T;ENSP00000351118:A687T;ENSP00000345726:A493T	ENSP00000345726:A493T	A	-	1	0	CDHR5	608013	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.278000	0.08490	-1.468000	0.01892	-1.134000	0.01955	GCC	C|0.770;T|0.230	0.230	strong		0.682	CDHR5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255023.2	NM_021924	
DHRS7C	201140	hgsc.bcm.edu	37	17	9676148	9676148	+	Silent	SNP	C	C	T	rs2280489	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:9676148C>T	ENST00000330255.5	-	5	678	c.666G>A	c.(664-666)ccG>ccA	p.P222P	DHRS7C_ENST00000571134.1_Silent_p.P221P	NM_001105571.2|NM_001220493.1	NP_001099041.1|NP_001207422.1	A6NNS2	DRS7C_HUMAN	dehydrogenase/reductase (SDR family) member 7C	222					regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)	extracellular region (GO:0005576)|longitudinal sarcoplasmic reticulum (GO:0014801)|sarcoplasmic reticulum membrane (GO:0033017)	retinol dehydrogenase activity (GO:0004745)			NS(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(9)	15						GGATGAAAGTCGGGCTCACGG	0.582													C|||	502	0.10024	0.112	0.0692	5008	,	,		19224	0.0992		0.1054	False		,,,				2504	0.1022				p.P222P		Atlas-SNP	.											.	DHRS7C	34	.	0			c.G666A						PASS	.	C	,	512,3890	208.5+/-229.5	40,432,1729	75.0	82.0	80.0		663,666	-9.1	0.0	17	dbSNP_100	80	912,7686	198.0+/-242.5	48,816,3435	no	coding-synonymous,coding-synonymous	DHRS7C	NM_001105571.2,NM_001220493.1	,	88,1248,5164	TT,TC,CC		10.6071,11.6311,10.9538	,	221/312,222/313	9676148	1424,11576	2201	4299	6500	SO:0001819	synonymous_variant	201140	exon5			GAAAGTCGGGCTC		CCDS56020.1, CCDS58517.1	17p13.1	2011-09-20				ENSG00000184544		"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 3"""	32423	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 32C, member 2"""					19027726	Standard	NM_001105571		Approved	SDR32C2	uc010vvb.2	A6NNS2		ENST00000330255.5:c.666G>A	17.37:g.9676148C>T		Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	40	16	0.4	NM_001220493	B7ZW74|B9EJH3	Silent	SNP	ENST00000330255.5	37	CCDS56020.1																																																																																			T|0.103;C|0.897	0.103	strong		0.582	DHRS7C-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439863.1	XM_113912	
CDRT1	374286	hgsc.bcm.edu	37	17	15510988	15510988	+	Missense_Mutation	SNP	T	T	C	rs62070402	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:15510988T>C	ENST00000395906.3	-	6	1131	c.1132A>G	c.(1132-1134)Aac>Gac	p.N378D	RP11-385D13.1_ENST00000455584.2_Missense_Mutation_p.N688D	NM_006382.3	NP_006373.2	O95170	CDRT1_HUMAN	CMT1A duplicated region transcript 1	378										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)		GTCCACAGGTTGTACTCATTC	0.483													T|||	1466	0.292732	0.264	0.2767	5008	,	,		20919	0.4514		0.1511	False		,,,				2504	0.3252				p.N378D		Atlas-SNP	.											.	CDRT1	83	.	0			c.A1132G						PASS	.	T	ASP/ASN	1076,3330	382.5+/-324.5	143,790,1270	80.0	76.0	78.0		1132	2.7	1.0	17	dbSNP_129	78	1443,7153	270.4+/-288.9	125,1193,2980	no	missense	CDRT1	NM_006382.3	23	268,1983,4250	CC,CT,TT		16.7869,24.4212,19.3739	possibly-damaging	378/753	15510988	2519,10483	2203	4298	6501	SO:0001583	missense	374286	exon6			ACAGGTTGTACTC	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.1132A>G	17.37:g.15510988T>C	ENSP00000379242:p.Asn378Asp	Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	179	170	0.949721	NM_006382	O43848|O95611	Missense_Mutation	SNP	ENST00000395906.3	37	CCDS45619.1	.	.	.	.	.	.	.	.	.	.	T	13.75	2.328938	0.41197	0.244212	0.167869	ENSG00000251537	ENST00000261644;ENST00000395906	T	0.21734	1.99	4.99	2.69	0.31865	F-box domain, Skp2-like (1);	0.557353	0.14804	U	0.297455	T	0.00012	0.0000	M	0.69823	2.125	0.09310	P	0.9999999699041	P;B	0.42827	0.791;0.421	B;B	0.32677	0.15;0.107	T	0.30297	-0.9983	9	0.35671	T	0.21	.	5.8404	0.18630	0.0:0.0906:0.1708:0.7386	rs62070402	378;702	O95170;Q59EB2	CDRT1_HUMAN;.	D	408;378	ENSP00000379242:N378D	ENSP00000261644:N408D	N	-	1	0	RP11-385D13.1	15451713	0.998000	0.40836	0.993000	0.49108	0.814000	0.46013	1.550000	0.36223	0.824000	0.34613	0.459000	0.35465	AAC	T|0.810;C|0.190	0.190	strong		0.483	CDRT1-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448127.1	NM_006382	
BAGE2	85319	hgsc.bcm.edu	37	21	11058316	11058316	+	RNA	SNP	G	G	T	rs3877860		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:11058316G>T	ENST00000470054.1	-	0	331							Q86Y30	BAGE2_HUMAN	B melanoma antigen family, member 2							extracellular region (GO:0005576)								Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		CTTACAAAATGCACATCGCTG	0.388																																					p.H42N		Atlas-SNP	.											.	.	.	.	0			c.C124A						PASS	.																																					85318	exon3			CAAAATGCACATC	AF218570		21p	2009-03-13			ENSG00000187172	ENSG00000187172			15723	protein-coding gene	gene with protein product	"""cancer/testis antigen family 2, member 2"""					12461691	Standard	NM_182482		Approved	CT2.2		Q86Y30	OTTHUMG00000074128		21.37:g.11058316G>T		Somatic	198	0	0		WXS	Illumina HiSeq	Phase_I	238	13	0.0546218	NM_182481	A8K925|Q08ER0	Missense_Mutation	SNP	ENST00000470054.1	37																																																																																				.	.	weak		0.388	BAGE2-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000157417.3	NM_182482	
